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_dbSNPPopFreq	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
CDK11A	728642	hgsc.bcm.edu	37	chr1	1634967	1634967	+	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	cagagccccgaagcgcttgcGgaggttgttgtaggggtgct	6	9	17	9	3	0	1	0	0	0	1	0	3	0	2	2	4	4	5	2	4	2	4			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr1:1634967G>C	ENST00000378633.1	-	18	2096	c.2017C>G	c.(2017-2019)Cgc>Ggc	p.R673G	CDK11A_ENST00000358779.5_Missense_Mutation_p.R660G|CDK11A_ENST00000404249.3_Missense_Mutation_p.R670G|CDK11A_ENST00000357760.2_Missense_Mutation_p.R669G|CDK11A_ENST00000495016.1_5'Flank|CDK11A_ENST00000356200.3_Missense_Mutation_p.R636G|RP1-283E3.8_ENST00000598846.1_RNA|CDK11A_ENST00000378638.2_Missense_Mutation_p.R636G			Q9UQ88	CD11A_HUMAN	cyclin-dependent kinase 11A	673					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						AAGCGCTTGCGGAGGTTGTTG	0.612																																					p.R670G	Pancreas(186;965 2119 30274 40311 50569)	Atlas-SNP	.											.	CDK11A	38	.	0			c.C2008G						PASS	.						17	31	27					1																	1634967		1542	4054	5596	SO:0001583	missense	728642	exon18			GCTTGCGGAGGTT	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.2017C>G	chr1.hg19:g.1634967G>C	ENSP00000367900:p.Arg673Gly	61.0	0.0	.		81.0	13.0	.	NM_024011	O95227|O95228|O96012|Q12821|Q12853|Q12854|Q2TAJ0|Q5QPR0|Q5QPR1|Q5QPR2|Q9UBC4|Q9UBI3|Q9UEI1|Q9UEI2|Q9UP53|Q9UP54|Q9UP55|Q9UP56|Q9UQ86|Q9UQ87|Q9UQ89	Missense_Mutation	SNP	ENST00000378633.1	hg19		.	.	.	.	.	.	.	.	.	.	-	10.92	1.486914	0.26686	.	.	ENSG00000008128	ENST00000356200;ENST00000404249;ENST00000357760;ENST00000358779;ENST00000378633;ENST00000378638;ENST00000378630;ENST00000341028	T;T;T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94;0.94;2.82	2.51	1.55	0.23275	.	0.000000	0.85682	D	0.000000	T	0.53012	0.1770	L	0.53617	1.68	0.80722	D	1	D;D;D	0.63880	0.979;0.979;0.993	P;P;D	0.66979	0.688;0.688;0.948	T	0.52290	-0.8595	10	0.87932	D	0	.	9.3145	0.37926	0.0:0.0:0.7833:0.2167	.	670;660;287	Q9UQ88-2;Q9UQ88-4;Q9UQ88-5	.;.;.	G	636;670;669;660;673;636;636;57	ENSP00000348529:R636G;ENSP00000384442:R670G;ENSP00000350403:R669G;ENSP00000351629:R660G;ENSP00000367900:R673G;ENSP00000367905:R636G;ENSP00000344418:R57G	ENSP00000344418:R57G	R	-	1	0	CDK11A	1624827	1.000000	0.71417	0.998000	0.56505	0.238000	0.25445	5.403000	0.66338	0.381000	0.24851	0.184000	0.17185	CGC	.	.	.	none		0.612	CDK11A-005	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000001735.1	NM_024011		C	1634967	G	C	1634967	3	2	1	1	0	0	0	0	1	0	0	0	3128	1116	39	4	346	4	CDK11A	1	1634967	Missense_Mutation	SNP	G	TCGA-2K-A9WE-01A-11D-A382-10		1634967	247615654	1	1											
AJAP1	55966	hgsc.bcm.edu	37	chr1	4772481	4772481	+	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	gactgagttcatcgcctgggGgcccacgggggacgaggagg	7	5	19	10	3	1	1	1	1	0	0	2	5	1	3	2	6	0	1	2	6	0	1			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr1:4772481G>T	ENST00000378191.4	+	2	932	c.551G>T	c.(550-552)gGg>gTg	p.G184V	AJAP1_ENST00000378190.3_Missense_Mutation_p.G184V	NM_018836.3	NP_061324.1	Q9UKB5	AJAP1_HUMAN	adherens junctions associated protein 1	184	Thr-rich.				cell adhesion (GO:0007155)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1)	24	all_cancers(77;0.071)|Ovarian(185;0.0721)	all_cancers(23;1.77e-36)|all_epithelial(116;1.26e-21)|all_lung(118;3.51e-08)|Lung NSC(185;3.47e-06)|all_neural(13;8.84e-06)|all_hematologic(16;7.61e-05)|Breast(487;0.000507)|Renal(390;0.0007)|Colorectal(325;0.00117)|Hepatocellular(190;0.0071)|Glioma(11;0.0155)|Myeloproliferative disorder(586;0.0258)|Ovarian(437;0.0409)|Lung SC(97;0.133)|Medulloblastoma(700;0.215)		Epithelial(90;3.89e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.97e-19)|GBM - Glioblastoma multiforme(42;3.71e-19)|Colorectal(212;4.57e-06)|COAD - Colon adenocarcinoma(227;0.00019)|Kidney(185;0.000969)|BRCA - Breast invasive adenocarcinoma(365;0.00122)|STAD - Stomach adenocarcinoma(132;0.00578)|KIRC - Kidney renal clear cell carcinoma(229;0.0126)|READ - Rectum adenocarcinoma(331;0.0689)		ATCGCCTGGGGGCCCACGGGG	0.647																																					p.G184V		Atlas-SNP	.											.	AJAP1	68	.	0			c.G551T						PASS	.						18	18	18					1																	4772481		2200	4298	6498	SO:0001583	missense	55966	exon2			CCTGGGGGCCCAC	AF175409	CCDS54.1	1p36.32	2008-02-05	2008-01-08		ENSG00000196581	ENSG00000196581			30801	protein-coding gene	gene with protein product	"transmembrane protein SHREW1"	610972				14595118	Standard	NM_001042478		Approved	SHREW1, SHREW-1, MOT8	uc001aln.3	Q9UKB5	OTTHUMG00000000645	ENST00000378191.4:c.551G>T	chr1.hg19:g.4772481G>T	ENSP00000367433:p.Gly184Val	94.0	0.0	.		112.0	10.0	.	NM_018836	Q9Y229	Missense_Mutation	SNP	ENST00000378191.4	hg19	CCDS54.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.305939	0.60305	.	.	ENSG00000196581	ENST00000378190;ENST00000378191	T;T	0.74947	-0.89;-0.89	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.79811	0.4510	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81705	-0.0811	10	0.72032	D	0.01	-25.2912	14.3171	0.66460	0.0:0.0:1.0:0.0	.	184	Q9UKB5	AJAP1_HUMAN	V	184	ENSP00000367432:G184V;ENSP00000367433:G184V	ENSP00000367432:G184V	G	+	2	0	AJAP1	4672341	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	7.294000	0.78760	2.432000	0.82394	0.467000	0.42956	GGG	.	.	.	none		0.647	AJAP1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001542.3	NM_018836		T	4772481	G	T	4772481	3	4	1	1	0	0	0	0	1	0	0	0	438	1232	43	4	557	4	AJAP1	1	4772481	Missense_Mutation	SNP	G	TCGA-2K-A9WE-01A-11D-A382-10	3137514	4772481	244478140	2	2											
PHC2	1912	hgsc.bcm.edu	37	chr1	33841054	33841054	+	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	ccaccactgctgctgttgttGcagccactgctgctactggc	5	11	10	15	0	0	0	0	0	0	0	0	0	0	0	3	1	7	7	3	1	1	3			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr1:33841054G>T	ENST00000257118.5	-	1	140	c.87C>A	c.(85-87)tgC>tgA	p.C29*	PHC2_ENST00000373416.1_5'UTR|PHC2_ENST00000419414.2_Nonsense_Mutation_p.C29*|PHC2_ENST00000431992.1_Nonsense_Mutation_p.C29*	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)	29	Ser-rich.				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)				tgctgttgttgcagccactgc	0.592																																					p.C29X		Atlas-SNP	.											.	PHC2	78	.	0			c.C87A						PASS	.						46	43	44					1																	33841054		2203	4300	6503	SO:0001587	stop_gained	1912	exon1			GTTGTTGCAGCCA	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.87C>A	chr1.hg19:g.33841054G>T	ENSP00000257118:p.Cys29*	51.0	0.0	.		72.0	8.0	.	NM_198040	A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	Nonsense_Mutation	SNP	ENST00000257118.5	hg19	CCDS378.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.241461	0.79912	.	.	ENSG00000134686	ENST00000431992;ENST00000257118;ENST00000419414	.	.	.	4.02	2.05	0.26809	.	0.643093	0.14507	N	0.315356	.	.	.	.	.	.	0.29812	N	0.831564	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	-0.2524	6.676	0.23093	0.1055:0.1822:0.7123:0.0	.	.	.	.	X	29	.	ENSP00000257118:C29X	C	-	3	2	PHC2	33613641	0.993000	0.37304	0.115000	0.21578	0.963000	0.63663	2.257000	0.43240	0.295000	0.22570	0.407000	0.27541	TGC	.	.	.	none		0.592	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000011895.1	NM_198040		T	33841054	G	T	33841054	4	4	1	1	0	0	0	0	0	1	0	0	11824	1311	46	4	2545	4	PHC2	1	33841054	Nonsense_Mutation	SNP	G	TCGA-2K-A9WE-01A-11D-A382-10	29068573	33841054	215409567	3	3											
IPO13	9670	hgsc.bcm.edu	37	chr1	44423158	44423158	+	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	atgtggtgcctgggctcattGgcctcatcccacggatcagc	6	10	12	13	1	3	0	3	0	0	0	4	1	4	1	3	4	2	1	3	4	0	1			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr1:44423158G>T	ENST00000372343.3	+	7	2139	c.1477G>T	c.(1477-1479)Ggc>Tgc	p.G493C	IPO13_ENST00000492152.1_3'UTR	NM_014652.3	NP_055467.3	O94829	IPO13_HUMAN	importin 13	493					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)				TGGGCTCATTGGCCTCATCCC	0.552																																					p.G493C		Atlas-SNP	.											.	IPO13	86	.	0			c.G1477T						PASS	.						168	136	147					1																	44423158		2203	4300	6503	SO:0001583	missense	9670	exon7			CTCATTGGCCTCA	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.1477G>T	chr1.hg19:g.44423158G>T	ENSP00000361418:p.Gly493Cys	67.0	0.0	.		107.0	5.0	.	NM_014652	D3DPY4|Q5T4X3|Q7LC04|Q96HS3|Q9H8N3|Q9UFR1	Missense_Mutation	SNP	ENST00000372343.3	hg19	CCDS503.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.354289	0.82243	.	.	ENSG00000117408	ENST00000372343	T	0.67698	-0.28	5.59	5.59	0.84812	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.74068	0.3668	L	0.44542	1.39	0.80722	D	1	D	0.69078	0.997	P	0.56865	0.808	T	0.75747	-0.3209	10	0.66056	D	0.02	1.0371	19.5982	0.95549	0.0:0.0:1.0:0.0	.	493	O94829	IPO13_HUMAN	C	493	ENSP00000361418:G493C	ENSP00000361418:G493C	G	+	1	0	IPO13	44195745	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.735000	0.98825	2.644000	0.89710	0.561000	0.74099	GGC	.	.	.	none		0.552	IPO13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022846.1	NM_014652		T	44423158	G	T	44423158	3	4	1	1	0	0	0	0	1	0	0	0	7801	1348	47	4	1503	4	IPO13	1	44423158	Missense_Mutation	SNP	G	TCGA-2K-A9WE-01A-11D-A382-10	10582104	44423158	204827463	4	4											
MOV10	4343	hgsc.bcm.edu	37	chr1	113232693	113232693	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaaccctgtggtgaccaatcGgatagaggaaggagagagac	15	5	14	7	1	0	4	0	1	0	3	1	8	0	6	2	4	1	0	2	4	4	1			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr1:113232693G>A	ENST00000413052.2	+	5	1199	c.809G>A	c.(808-810)cGg>cAg	p.R270Q	MOV10_ENST00000468624.1_3'UTR|MOV10_ENST00000369644.1_Missense_Mutation_p.R214Q|MOV10_ENST00000357443.2_Missense_Mutation_p.R270Q|MOV10_ENST00000369645.1_Missense_Mutation_p.R270Q	NM_001130079.1|NM_020963.3	NP_001123551.1|NP_066014.1	Q9HCE1	MOV10_HUMAN	Mov10 RISC complex RNA helicase	270					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(3)	38	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)		GTGACCAATCGGATAGAGGAA	0.612																																					p.R270Q		Atlas-SNP	.											.	MOV10	74	.	0			c.G809A						PASS	.						56	58	58					1																	113232693		2203	4300	6503	SO:0001583	missense	4343	exon5			CCAATCGGATAGA	AL833353	CCDS853.1, CCDS65615.1	1p13.2	2014-07-02	2014-07-02		ENSG00000155363	ENSG00000155363			7200	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 113"	610742	"Mov10 (Moloney leukemia virus 10, mouse) homolog", "Mov10, Moloney leukemia virus 10, homolog (mouse)"			12226669	Standard	NM_001286072		Approved	gb110, MGC2948, fSAP113	uc001eck.3	Q9HCE1	OTTHUMG00000011906	ENST00000413052.2:c.809G>A	chr1.hg19:g.113232693G>A	ENSP00000399797:p.Arg270Gln	104.0	0.0	.		104.0	11.0	.	NM_020963	Q5JR03|Q8TEF0|Q9BSY3|Q9BUJ9	Missense_Mutation	SNP	ENST00000413052.2	hg19	CCDS853.1	.	.	.	.	.	.	.	.	.	.	G	17.18	3.325084	0.60634	.	.	ENSG00000155363	ENST00000413052;ENST00000369645;ENST00000285733;ENST00000369644;ENST00000357443;ENST00000369648	D;D;D;D	0.91577	-2.87;-2.87;-2.86;-2.87	5.77	3.91	0.45181	.	0.509312	0.21069	N	0.080688	T	0.74359	0.3706	L	0.36672	1.1	0.80722	D	1	B;B;B	0.21905	0.012;0.062;0.002	B;B;B	0.13407	0.002;0.009;0.001	T	0.70753	-0.4786	10	0.25751	T	0.34	-17.3516	7.7467	0.28873	0.1826:0.0:0.8174:0.0	.	214;270;270	Q5JR04;Q9H8T8;Q9HCE1	.;.;MOV10_HUMAN	Q	270;270;270;214;270;208	ENSP00000399797:R270Q;ENSP00000358659:R270Q;ENSP00000358658:R214Q;ENSP00000350028:R270Q	ENSP00000285733:R270Q	R	+	2	0	MOV10	113034216	0.976000	0.34144	0.985000	0.45067	0.860000	0.49131	2.114000	0.41911	1.462000	0.47948	0.561000	0.74099	CGG	.	.	.	none		0.612	MOV10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032906.1	NM_020963		A	113232693	G	A	113232693	3	1	1	1	0	0	0	0	1	0	0	0	9725	1116	39	1	823	1	MOV10	1	113232693	Missense_Mutation	SNP	G	TCGA-2K-A9WE-01A-11D-A382-10	68809535	113232693	136017928	5	5											
C1orf54	79630	hgsc.bcm.edu	37	chr1	150246488	150246488	+	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	cctctagtccttgtccccatAggacaagaatatgaggatga	12	10	9	10	0	1	3	0	2	1	1	3	5	3	5	4	2	0	0	4	2	5	4			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr1:150246488A>G	ENST00000369102.1	+	4	816		c.e4-1		C1orf54_ENST00000369098.3_Splice_Site|C1orf54_ENST00000369099.3_Splice_Site			Q8WWF1	CA054_HUMAN	chromosome 1 open reading frame 54							extracellular region (GO:0005576)				breast(1)|endometrium(1)|large_intestine(2)|lung(2)|urinary_tract(1)	7	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)			TTGTCCCCATAGGACAAGAAT	0.448																																					.		Atlas-SNP	.											.	C1orf54	20	.	0			c.47-2A>G						PASS	.						156	161	159					1																	150246488		2203	4300	6503	SO:0001630	splice_region_variant	79630	exon2			CCCCATAGGACAA	BC017761	CCDS948.1, CCDS72905.1	1q21.2	2012-06-25			ENSG00000118292	ENSG00000118292			26258	protein-coding gene	gene with protein product						12477932	Standard	NM_024579		Approved	FLJ23221	uc001eud.3	Q8WWF1	OTTHUMG00000012546	ENST00000369102.1:c.47-1A>G	chr1.hg19:g.150246488A>G		107.0	0.0	.		111.0	12.0	.	NM_024579	Q9H5P3	Splice_Site	SNP	ENST00000369102.1	hg19	CCDS948.1	.	.	.	.	.	.	.	.	.	.	A	16.54	3.151255	0.57151	.	.	ENSG00000118292	ENST00000369102;ENST00000369099;ENST00000369098	.	.	.	4.88	3.75	0.43078	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.3061	0.26449	0.901:0.0:0.099:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C1orf54	148513112	0.973000	0.33851	0.962000	0.40283	0.976000	0.68499	2.557000	0.45871	0.991000	0.38814	0.523000	0.50628	.	.	.	.	none		0.448	C1orf54-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035055.1	NM_024579	Intron	G	150246488	A	G	150246488	5	3	1	1	0	0	0	0	0	0	1	0	2048	434	15	3	51	3	C1orf54	1	150246488	Splice_Site	SNP	A	TCGA-2K-A9WE-01A-11D-A382-10	37013795	150246488	99004133	6	6											
DUSP27	92235	hgsc.bcm.edu	37	chr1	167097288	167097288	+	Missense_Mutation	SNP	A	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	tgctcagggagacagagtctAaatcctccagttacaagttt	12	11	9	9	0	2	2	1	0	1	2	4	3	4	2	2	1	2	3	2	1	4	3			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr1:167097288A>C	ENST00000361200.2	+	6	3086	c.2920A>C	c.(2920-2922)Aaa>Caa	p.K974Q	DUSP27_ENST00000443333.1_Missense_Mutation_p.K974Q|DUSP27_ENST00000271385.5_Missense_Mutation_p.K974Q|DUSP27_ENST00000485151.1_Intron			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	974	Ser-rich.				protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						GACAGAGTCTAAATCCTCCAG	0.507																																					p.K974Q		Atlas-SNP	.											.	DUSP27	235	.	0			c.A2920C						PASS	.						70	64	66					1																	167097288		2203	4300	6503	SO:0001583	missense	92235	exon5			GAGTCTAAATCCT	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.2920A>C	chr1.hg19:g.167097288A>C	ENSP00000354483:p.Lys974Gln	128.0	0.0	.		146.0	10.0	.	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	hg19	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	A	10.28	1.307265	0.23821	.	.	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.03386	3.95;3.95;3.95	4.9	3.75	0.43078	.	0.112170	0.40469	N	0.001100	T	0.01592	0.0051	L	0.57536	1.79	0.30368	N	0.783178	P	0.35077	0.483	B	0.33392	0.163	T	0.38845	-0.9642	10	0.66056	D	0.02	-29.7498	3.4315	0.07430	0.6859:0.0:0.3141:0.0	.	974	Q5VZP5	DUS27_HUMAN	Q	974	ENSP00000354483:K974Q;ENSP00000271385:K974Q;ENSP00000404874:K974Q	ENSP00000271385:K974Q	K	+	1	0	DUSP27	165363912	1.000000	0.71417	0.024000	0.17045	0.360000	0.29518	3.431000	0.52814	2.047000	0.60756	0.523000	0.50628	AAA	.	.	.	none		0.507	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		C	167097288	A	C	167097288	3	2	1	1	0	0	0	0	1	0	0	0	4826	363	13	5	2938	5	DUSP27	1	167097288	Missense_Mutation	SNP	A	TCGA-2K-A9WE-01A-11D-A382-10	16850800	167097288	82153333	7	7											
NRBP1	29959	hgsc.bcm.edu	37	chr2	27663700	27663700	+	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	tctatcctctgacagcctttGggctgcctcggccccagcag	5	10	10	16	1	2	1	0	1	2	0	4	1	3	1	5	2	3	2	5	2	1	2			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr2:27663700G>C	ENST00000233557.3	+	15	2054	c.1222G>C	c.(1222-1224)Ggg>Cgg	p.G408R	KRTCAP3_ENST00000288873.3_5'Flank|KRTCAP3_ENST00000543753.1_5'Flank|NRBP1_ENST00000379863.3_Missense_Mutation_p.G416R|KRTCAP3_ENST00000407293.1_5'Flank|NRBP1_ENST00000379852.3_Missense_Mutation_p.G408R			Q9UHY1	NRBP_HUMAN	nuclear receptor binding protein 1	408					ER to Golgi vesicle-mediated transport (GO:0006888)|gene expression (GO:0010467)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell projection (GO:0042995)|endomembrane system (GO:0012505)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19	Acute lymphoblastic leukemia(172;0.155)					GACAGCCTTTGGGCTGCCTCG	0.602																																					p.G408R		Atlas-SNP	.											.	NRBP1	40	.	0			c.G1222C						PASS	.						61	66	64					2																	27663700		2203	4300	6503	SO:0001583	missense	29959	exon14			GCCTTTGGGCTGC	AF113249	CCDS1753.1	2p23	2008-02-05	2005-12-22	2005-12-22	ENSG00000115216	ENSG00000115216			7993	protein-coding gene	gene with protein product		606010	"nuclear receptor binding protein"	NRBP		10843813, 11956649	Standard	NM_013392		Approved	BCON3, MUDPNP, MADM	uc002rkp.3	Q9UHY1	OTTHUMG00000097789	ENST00000233557.3:c.1222G>C	chr2.hg19:g.27663700G>C	ENSP00000233557:p.Gly408Arg	60.0	0.0	.		56.0	9.0	.	NM_013392	B3KV40|D6W558|Q53FZ5|Q96SU3	Missense_Mutation	SNP	ENST00000233557.3	hg19	CCDS1753.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.781434	0.90282	.	.	ENSG00000115216	ENST00000233557;ENST00000421823;ENST00000379852;ENST00000379863	T;T;T	0.28255	1.62;1.62;1.62	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.48370	0.1496	L	0.47716	1.5	0.80722	D	1	D;D;P	0.63046	0.992;0.964;0.901	P;P;P	0.61800	0.894;0.683;0.484	T	0.25984	-1.0116	10	0.51188	T	0.08	-20.4213	18.9284	0.92554	0.0:0.0:1.0:0.0	.	388;416;408	B4DW31;F8W6G1;Q9UHY1	.;.;NRBP_HUMAN	R	408;388;408;416	ENSP00000233557:G408R;ENSP00000369181:G408R;ENSP00000369192:G416R	ENSP00000233557:G408R	G	+	1	0	NRBP1	27517204	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.631000	0.98424	2.821000	0.97095	0.561000	0.74099	GGG	.	.	.	none		0.602	NRBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215033.1	NM_013392		C	27663700	G	C	27663700	3	2	1	1	0	0	0	0	1	0	0	0	10649	1348	47	4	1272	4	NRBP1	2	27663700	Missense_Mutation	SNP	G	TCGA-2K-A9WE-01A-11D-A382-10		27663700	215535673	8	8											
RANBP2	5903	hgsc.bcm.edu	37	chr2	109381490	109381490	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgaggggagctctacaaaaTgtgctgcttgtcagaatccg	11	10	12	8	1	2	2	1	1	1	1	3	3	3	3	1	2	4	3	1	2	4	2			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr2:109381490T>C	ENST00000283195.6	+	20	4621	c.4495T>C	c.(4495-4497)Tgt>Cgt	p.C1499R		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	1499					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						CTCTACAAAATGTGCTGCTTG	0.398																																					p.C1499R		Atlas-SNP	.											.	RANBP2	488	.	0			c.T4495C						PASS	.						76	75	76					2																	109381490		2203	4299	6502	SO:0001583	missense	5903	exon20			ACAAAATGTGCTG	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.4495T>C	chr2.hg19:g.109381490T>C	ENSP00000283195:p.Cys1499Arg	84.0	0.0	.		84.0	12.0	.	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	hg19	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	T	14.03	2.413745	0.42817	.	.	ENSG00000153201	ENST00000283195	D	0.99797	-6.79	5.24	5.24	0.73138	Zinc finger, RanBP2-type (4);	.	.	.	.	D	0.99843	0.9928	H	0.95780	3.72	0.52501	D	0.999951	D	0.76494	0.999	D	0.79108	0.992	D	0.96582	0.9431	9	0.87932	D	0	-15.2685	15.1468	0.72662	0.0:0.0:0.0:1.0	.	1499	P49792	RBP2_HUMAN	R	1499	ENSP00000283195:C1499R	ENSP00000283195:C1499R	C	+	1	0	RANBP2	108747922	1.000000	0.71417	0.980000	0.43619	0.686000	0.39977	5.855000	0.69510	1.975000	0.57531	0.533000	0.62120	TGT	.	.	.	none		0.398	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		C	109381490	T	C	109381490	3	2	1	1	0	0	0	0	1	0	0	0	13041	1464	51	3	4573	3	RANBP2	2	109381490	Missense_Mutation	SNP	T	TCGA-2K-A9WE-01A-11D-A382-10	81717790	109381490	133817883	9	9											
WDR33	55339	hgsc.bcm.edu	37	chr2	128528415	128528415	+	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	cggttcacagcttttctcatTcgttttccatcaaaagtaag	10	15	6	10	2	3	0	3	0	1	0	6	0	4	0	1	1	1	4	1	1	3	7			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr2:128528415T>A	ENST00000322313.4	-	2	299	c.141A>T	c.(139-141)cgA>cgT	p.R47R	WDR33_ENST00000393006.1_Silent_p.R47R|WDR33_ENST00000409658.3_Silent_p.R47R	NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	47					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)		CTTTTCTCATTCGTTTTCCAT	0.413																																					p.R47R		Atlas-SNP	.											.	WDR33	136	.	0			c.A141T						PASS	.						129	119	122					2																	128528415		2203	4300	6503	SO:0001819	synonymous_variant	55339	exon2			TCTCATTCGTTTT		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.141A>T	chr2.hg19:g.128528415T>A		141.0	0.0	.		135.0	14.0	.	NM_001006623	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Silent	SNP	ENST00000322313.4	hg19	CCDS2150.1																																																																																			.	.	.	none		0.413	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383		A	128528415	T	A	128528415	2	1	1	1	0	0	0	0	0	0	0	1	17299	1770	62	5		5	WDR33	2	128528415	Silent	SNP	T	TCGA-2K-A9WE-01A-11D-A382-10	19146925	128528415	114670958	10	10											
TRAK2	66008	hgsc.bcm.edu	37	chr2	202265791	202265791	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcattgtaagttttggtcaTctgctccaccctgtctgtgc	5	16	9	11	0	4	0	2	0	2	0	5	0	5	0	2	1	2	3	2	1	1	4			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr2:202265791T>C	ENST00000332624.3	-	4	741	c.313A>G	c.(313-315)Atg>Gtg	p.M105V	TRAK2_ENST00000430254.1_Missense_Mutation_p.M105V	NM_015049.2	NP_055864.2	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2	105	HAP1 N-terminal.				protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GABA receptor binding (GO:0050811)|receptor binding (GO:0005102)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	23						GTTTTGGTCATCTGCTCCACC	0.333																																					p.M105V		Atlas-SNP	.											.	TRAK2	62	.	0			c.A313G						PASS	.						163	145	151					2																	202265791		2203	4300	6503	SO:0001583	missense	66008	exon4			TGGTCATCTGCTC	AB038951	CCDS2347.1	2q33.1	2012-03-05	2005-12-13	2005-12-13	ENSG00000115993	ENSG00000115993			13206	protein-coding gene	gene with protein product	"gamma-aminobutyric acid(A) receptor-interacting factor", "milton homolog 2 (Drosophila)", "O-linked N-acetylglucosamine transferase interacting protein 98"	607334	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 3"	ALS2CR3		11161814, 16380713, 20230862	Standard	NM_015049		Approved	CALS-C, KIAA0549, GRIF-1, OIP98, MILT2	uc002uyb.4	O60296	OTTHUMG00000132822	ENST00000332624.3:c.313A>G	chr2.hg19:g.202265791T>C	ENSP00000328875:p.Met105Val	95.0	0.0	.		95.0	7.0	.	NM_015049	E7EV21|Q8WVH7|Q96NS2|Q9C0K5|Q9C0K6	Missense_Mutation	SNP	ENST00000332624.3	hg19	CCDS2347.1	.	.	.	.	.	.	.	.	.	.	T	13.26	2.184998	0.38609	.	.	ENSG00000115993	ENST00000332624;ENST00000542292;ENST00000430254	T;T	0.18338	2.22;2.22	5.86	5.86	0.93980	.	0.045004	0.85682	D	0.000000	T	0.12860	0.0312	L	0.38838	1.175	0.80722	D	1	B;B	0.17465	0.01;0.022	B;B	0.12837	0.008;0.008	T	0.12041	-1.0563	10	0.45353	T	0.12	.	5.759	0.18188	0.1499:0.0778:0.0:0.7723	.	105;105	E7EV21;O60296	.;TRAK2_HUMAN	V	105;11;105	ENSP00000328875:M105V;ENSP00000409333:M105V	ENSP00000328875:M105V	M	-	1	0	TRAK2	201974036	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.566000	0.53805	2.367000	0.80283	0.528000	0.53228	ATG	.	.	.	none		0.333	TRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256284.3	NM_015049		C	202265791	T	C	202265791	3	2	1	1	0	0	0	0	1	0	0	0	16462	1435	50	3	2483	3	TRAK2	2	202265791	Missense_Mutation	SNP	T	TCGA-2K-A9WE-01A-11D-A382-10	73737376	202265791	40933582	11	11											
HTR2B	3357	hgsc.bcm.edu	37	chr2	231973805	231973805	+	Frame_Shift_Del	DEL	T	T	-																															cacctgagttgggcagagccTtgtcctttcgagaaccatcc																										TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr2:231973805delT	ENST00000258400.3	-	4	1384	c.872delA	c.(871-873)aagfs	p.K291fs	PSMD1_ENST00000488354.1_3'UTR|PSMD1_ENST00000409643.1_Intron|PSMD1_ENST00000373635.4_Intron|PSMD1_ENST00000308696.6_Intron	NM_000867.4	NP_000858.3	P41595	5HT2B_HUMAN	5-hydroxytryptamine (serotonin) receptor 2B, G protein-coupled	291					activation of phospholipase C activity (GO:0007202)|behavior (GO:0007610)|calcium-mediated signaling (GO:0019722)|cardiac muscle hypertrophy (GO:0003300)|cellular calcium ion homeostasis (GO:0006874)|cellular response to temperature stimulus (GO:0071502)|cGMP biosynthetic process (GO:0006182)|embryonic morphogenesis (GO:0048598)|ERK1 and ERK2 cascade (GO:0070371)|G-protein coupled receptor internalization (GO:0002031)|G-protein coupled receptor signaling pathway (GO:0007186)|heart morphogenesis (GO:0003007)|intestine smooth muscle contraction (GO:0014827)|negative regulation of apoptotic process (GO:0043066)|negative regulation of autophagy (GO:0010507)|negative regulation of cell death (GO:0060548)|neural crest cell differentiation (GO:0014033)|neural crest cell migration (GO:0001755)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphorylation (GO:0016310)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|protein kinase C signaling (GO:0070528)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of behavior (GO:0050795)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|serotonin receptor signaling pathway (GO:0007210)|vasoconstriction (GO:0042310)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	drug binding (GO:0008144)|G-protein alpha-subunit binding (GO:0001965)|Ras GTPase activator activity (GO:0005099)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|urinary_tract(1)	11		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)|Medulloblastoma(418;0.232)		Epithelial(121;4.48e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0141)	Amoxapine(DB00543)|Apomorphine(DB00714)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Clomipramine(DB01242)|Dihydroergotamine(DB00320)|Doxepin(DB01142)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ketamine(DB01221)|Lisuride(DB00589)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Ropinirole(DB00268)|Triflupromazine(DB00508)|Yohimbine(DB01392)	GGGCAGAGCCTTGTCCTTTCG	0.478																																					p.K291fs	Ovarian(155;1331 1891 12853 14038 34991)	Atlas-Indel,Pindel	.											.	HTR2B	33	.	0			c.873delG						PASS	.						195	182	186					2																	231973805		2203	4300	6503	SO:0001589	frameshift_variant	3357	exon4			.		CCDS2483.1	2q36.3-q37.1	2012-08-08	2012-02-03		ENSG00000135914	ENSG00000135914		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5294	protein-coding gene	gene with protein product		601122	"5-hydroxytryptamine (serotonin) receptor 2B"			8143856	Standard	NM_000867		Approved	5-HT(2B), 5-HT2B	uc002vro.3	P41595	OTTHUMG00000133222	ENST00000258400.3:c.872delA	chr2.hg19:g.231973805delT	ENSP00000258400:p.Lys291fs	156.0	0.0	0		172.0	12.0	0.0697674	NM_000867	B2R9D5|Q53TI1|Q62221|Q6P523	Frame_Shift_Del	DEL	ENST00000258400.3	hg19	CCDS2483.1																																																																																			.	.	.	none		0.478	HTR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256957.2	NM_000867		-	231973805	T	-	231973805	7	5	1	1	0	1	0	1	0	0	0	0	7449	1609	56	0	577	0	HTR2B	2	231973805	Frame_Shift_Del	DEL	T	TCGA-2K-A9WE-01A-11D-A382-10	29708014	231973805	11225568	12	12											
DUSP7	1849	hgsc.bcm.edu	37	chr3	52088120	52088120	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catacttgccgagcacgtccAggttggtggagtccttggcg	6	10	14	11	3	0	0	0	0	0	0	2	2	2	1	3	4	3	2	3	4	1	4			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr3:52088120A>G	ENST00000495880.1	-	2	971	c.788T>C	c.(787-789)cTg>cCg	p.L263P	DUSP7_ENST00000296483.6_Missense_Mutation_p.L212P			Q16829	DUS7_HUMAN	dual specificity phosphatase 7	263					inactivation of MAPK activity (GO:0000188)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of MAP kinase activity (GO:0043407)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	17				BRCA - Breast invasive adenocarcinoma(193;5.14e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GAGCACGTCCAGGTTGGTGGA	0.592																																					p.L263P		Atlas-SNP	.											.	DUSP7	34	.	0			c.T788C						PASS	.						281	251	261					3																	52088120		2203	4300	6503	SO:0001583	missense	1849	exon2			ACGTCCAGGTTGG	X93921	CCDS33766.1, CCDS33766.2	3p21	2011-06-09			ENSG00000164086	ENSG00000164086		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3073	protein-coding gene	gene with protein product		602749				8626780, 9205128	Standard	NM_001947		Approved	MKP-X, PYST2	uc003dct.3	Q16829	OTTHUMG00000157819	ENST00000495880.1:c.788T>C	chr3.hg19:g.52088120A>G	ENSP00000417183:p.Leu263Pro	122.0	0.0	.		163.0	18.0	.	NM_001947	Q2M3J7|Q8NFJ0	Missense_Mutation	SNP	ENST00000495880.1	hg19	CCDS33766.2	.	.	.	.	.	.	.	.	.	.	A	25.8	4.671947	0.88348	.	.	ENSG00000164086	ENST00000495880;ENST00000296483;ENST00000469623	T;T;T	0.61742	0.08;0.08;0.08	5.42	5.42	0.78866	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.000000	0.64402	D	0.000001	T	0.70762	0.3261	L	0.49126	1.545	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.79784	0.978;0.993	T	0.72887	-0.4156	10	0.59425	D	0.04	.	15.1265	0.72486	1.0:0.0:0.0:0.0	.	212;263	Q16829-2;Q16829	.;DUS7_HUMAN	P	263;212;196	ENSP00000417183:L263P;ENSP00000296483:L212P;ENSP00000418566:L196P	ENSP00000296483:L212P	L	-	2	0	DUSP7	52063160	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.260000	0.95568	2.044000	0.60594	0.448000	0.29417	CTG	.	.	.	none		0.592	DUSP7-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000349697.1	NM_001947		G	52088120	A	G	52088120	3	3	1	1	0	0	0	0	1	0	0	0	4832	188	7	3	479	3	DUSP7	3	52088120	Missense_Mutation	SNP	A	TCGA-2K-A9WE-01A-11D-A382-10		52088120	145934310	13	13											
TMEM14E	645843	hgsc.bcm.edu	37	chr3	152058400	152058400	+	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	cttccaagtttggaaactatCagcaggcacctgcaactaaa	14	9	7	11	0	1	0	1	0	0	0	2	1	2	1	2	2	4	4	2	2	6	4			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr3:152058400C>T	ENST00000408960.3	-	1	379	c.294G>A	c.(292-294)ctG>ctA	p.L98L	MBNL1_ENST00000282486.6_Intron|MBNL1_ENST00000498502.1_Intron|MBNL1_ENST00000485910.1_Intron|MBNL1_ENST00000485509.1_Intron|MBNL1_ENST00000324196.5_Intron|MBNL1_ENST00000492948.1_Intron|MBNL1_ENST00000355460.2_Intron|MBNL1_ENST00000463374.1_Intron|MBNL1_ENST00000357472.3_Intron|MBNL1_ENST00000324210.5_Intron|MBNL1_ENST00000545754.1_Intron|MBNL1_ENST00000282488.7_Intron|MBNL1_ENST00000493459.1_Intron	NM_001123228.1	NP_001116700.1	Q6UXP3	TM14E_HUMAN	transmembrane protein 14E	98						integral component of membrane (GO:0016021)				lung(1)	1						TGGAAACTATCAGCAGGCACC	0.418																																					p.L98L		Atlas-SNP	.											.	TMEM14E	6	.	0			c.G294A						PASS	.						91	85	87					3																	152058400		1568	3582	5150	SO:0001819	synonymous_variant	645843	exon1			AACTATCAGCAGG		CCDS43161.1	3q25.1	2011-09-15			ENSG00000221962	ENSG00000221962			34386	protein-coding gene	gene with protein product							Standard	NM_001123228		Approved		uc010hvo.3	Q6UXP3	OTTHUMG00000159652	ENST00000408960.3:c.294G>A	chr3.hg19:g.152058400C>T		286.0	0.0	.		302.0	25.0	.	NM_001123228		Silent	SNP	ENST00000408960.3	hg19	CCDS43161.1																																																																																			.	.	.	none		0.418	TMEM14E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356703.1	NM_001123228		T	152058400	C	T	152058400	2	4	1	1	0	0	0	0	0	0	0	1	16078	813	29	2		2	TMEM14E	3	152058400	Silent	SNP	C	TCGA-2K-A9WE-01A-11D-A382-10	99970280	152058400	45964030	14	14											
DNAH5	1767	hgsc.bcm.edu	37	chr5	13917315	13917315	+	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	tacaagtatttcacattgtcCtttgcttcattagttgcatc	9	18	5	9	0	2	0	2	0	0	0	4	0	3	0	1	0	3	4	1	0	4	8			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr5:13917315C>A	ENST00000265104.4	-	8	1130	c.1026G>T	c.(1024-1026)aaG>aaT	p.K342N		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	342	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)					TCACATTGTCCTTTGCTTCAT	0.358									Kartagener syndrome																												p.K342N		Atlas-SNP	.											.	DNAH5	868	.	0			c.G1026T						PASS	.						161	136	144					5																	13917315		2203	4300	6503	SO:0001583	missense	1767	exon8	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	ATTGTCCTTTGCT	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.1026G>T	chr5.hg19:g.13917315C>A	ENSP00000265104:p.Lys342Asn	68.0	0.0	.		66.0	5.0	.	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	hg19	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	18.66	3.671367	0.67814	.	.	ENSG00000039139	ENST00000265104	T	0.56444	0.46	5.63	2.86	0.33363	Dynein heavy chain, domain-1 (1);	0.049678	0.85682	D	0.000000	T	0.73048	0.3537	M	0.91406	3.205	0.54753	D	0.999983	D	0.76494	0.999	D	0.83275	0.996	T	0.72673	-0.4222	10	0.62326	D	0.03	.	6.2795	0.20999	0.0:0.5504:0.0:0.4495	.	342	Q8TE73	DYH5_HUMAN	N	342	ENSP00000265104:K342N	ENSP00000265104:K342N	K	-	3	2	DNAH5	13970315	1.000000	0.71417	0.991000	0.47740	0.744000	0.42396	2.092000	0.41700	0.716000	0.32124	0.561000	0.74099	AAG	.	.	.	none		0.358	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13917315	C	A	13917315	3	1	1	1	0	0	0	0	1	0	0	0	4606	680	24	4	13136	4	DNAH5	5	13917315	Missense_Mutation	SNP	C	TCGA-2K-A9WE-01A-11D-A382-10		13917315	166997945	15	15											
EGFLAM	133584	hgsc.bcm.edu	37	chr5	38370553	38370553	+	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	cagctggcccagtgacatcaTccggaccctctgtgagtacc	8	8	10	15	1	2	2	1	2	1	0	3	3	3	3	4	2	2	2	4	2	1	1			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr5:38370553T>A	ENST00000354891.3	+	6	1047	c.701T>A	c.(700-702)aTc>aAc	p.I234N	EGFLAM_ENST00000322350.5_Missense_Mutation_p.I234N	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	234	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					AGTGACATCATCCGGACCCTC	0.572																																					p.I234N	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.T701A						PASS	.						37	37	37					5																	38370553		2203	4300	6503	SO:0001583	missense	133584	exon6			ACATCATCCGGAC	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.701T>A	chr5.hg19:g.38370553T>A	ENSP00000346964:p.Ile234Asn	36.0	0.0	.		39.0	7.0	.	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Missense_Mutation	SNP	ENST00000354891.3	hg19	CCDS56363.1	.	.	.	.	.	.	.	.	.	.	T	16.60	3.167665	0.57476	.	.	ENSG00000164318	ENST00000354891;ENST00000322350	T;T	0.57273	0.57;0.41	5.82	3.44	0.39384	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.647983	0.16664	N	0.204679	T	0.67040	0.2851	M	0.85197	2.74	0.80722	D	1	P;P	0.48640	0.859;0.913	P;P	0.53722	0.545;0.733	T	0.67914	-0.5547	10	0.87932	D	0	-27.5021	9.7299	0.40355	0.0:0.1404:0.0:0.8596	.	234;234	Q63HQ2;Q63HQ2-2	EGFLA_HUMAN;.	N	234	ENSP00000346964:I234N;ENSP00000313084:I234N	ENSP00000313084:I234N	I	+	2	0	EGFLAM	38406310	0.999000	0.42202	0.002000	0.10522	0.634000	0.38068	7.066000	0.76734	0.481000	0.27557	0.459000	0.35465	ATC	.	.	.	none		0.572	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403		A	38370553	T	A	38370553	3	1	1	1	0	0	0	0	1	0	0	0	4968	1435	50	5	723	5	EGFLAM	5	38370553	Missense_Mutation	SNP	T	TCGA-2K-A9WE-01A-11D-A382-10	24453238	38370553	142544707	16	16											
CCDC90A	63933	hgsc.bcm.edu	37	chr6	13814461	13814461	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaggaggaggagcagcggTgaggcacgtgacacgccgcc	10	2	18	11	4	0	2	0	2	0	0	0	5	0	5	2	5	3	3	2	5	0	0	rs371767736	byFrequency	TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr6:13814461T>C	ENST00000379170.4	-	1	339	c.201A>G	c.(199-201)tcA>tcG	p.S67S	MCUR1_ENST00000359495.2_Silent_p.S67S	NM_001031713.3	NP_001026883.1	Q96AQ8	MCUR1_HUMAN	mitochondrial calcium uniporter regulator 1	67					calcium ion import (GO:0070509)|mitochondrial calcium ion transport (GO:0006851)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)	integral component of mitochondrial inner membrane (GO:0031305)											GGAGCAGCGGTGAGGCACGTG	0.776													T|||	104	0.0207668	0	0.062	5008	,	,		7906	0.001		0.0308	False		,,,				2504	0.0297				p.S67S		Atlas-SNP	.											.	CCDC90A	15	.	0			c.A201G						PASS	.	T		3,2137		0,3,1067	2	3	2		201	-4.7	0	6		2	86,4212		0,86,2063	no	coding-synonymous	CCDC90A	NM_001031713.3		0,89,3130	CC,CT,TT		2.0009,0.1402,1.3824		67/360	13814461	89,6349	1070	2149	3219	SO:0001819	synonymous_variant	63933	exon1			CAGCGGTGAGGCA	BC016850	CCDS35495.1	6p23	2013-03-13	2013-03-13	2013-03-13	ENSG00000050393	ENSG00000050393			21097	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 79", "coiled-coil domain containing 90A"	C6orf79, CCDC90A		23178883	Standard	NM_001031713		Approved	FLJ20958	uc003nbc.2	Q96AQ8	OTTHUMG00000014279	ENST00000379170.4:c.201A>G	chr6.hg19:g.13814461T>C		3.0	0.0	.		9.0	5.0	.	NM_001031713	Q96JS7|Q9H7F8	Silent	SNP	ENST00000379170.4	hg19	CCDS35495.1																																																																																			.	.	.	weak		0.776	MCUR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039909.3	NM_022102		C	13814461	T	C	13814461	2	2	1	1	0	0	0	0	0	0	0	1	2870	1683	59	3		3	CCDC90A	6	13814461	Silent	SNP	T	TCGA-2K-A9WE-01A-11D-A382-10		13814461	157300606	17	17											
SLC39A7	7922	hgsc.bcm.edu	37	chr6	33170059	33170059	+	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	ggccagggccccattctgtcTgtgggactgtgggttctcag	4	11	15	11	0	3	0	1	0	3	0	4	1	3	1	3	4	0	1	3	4	0	2			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr6:33170059T>A	ENST00000374677.3	+	4	1027	c.654T>A	c.(652-654)tcT>tcA	p.S218S	SLC39A7_ENST00000463972.1_3'UTR|HSD17B8_ENST00000374662.3_5'Flank|RNY4P10_ENST00000365571.1_RNA|SLC39A7_ENST00000374675.3_Silent_p.S218S|RXRB_ENST00000374685.4_5'Flank|RXRB_ENST00000544186.1_5'Flank|RXRB_ENST00000413614.2_5'Flank|RXRB_ENST00000374680.3_5'Flank	NM_006979.2	NP_008910.2	Q92504	S39A7_HUMAN	solute carrier family 39 (zinc transporter), member 7	218					transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion transmembrane transporter activity (GO:0046873)			NS(1)|breast(3)|endometrium(2)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						CCATTCTGTCTGTGGGACTGT	0.517																																					p.S218S		Atlas-SNP	.											.	SLC39A7	32	.	0			c.T654A						PASS	.						114	120	118					6																	33170059		1270	2569	3839	SO:0001819	synonymous_variant	7922	exon4			TCTGTCTGTGGGA	AF117221	CCDS43453.1	6p21.3	2014-01-28		2003-10-27	ENSG00000112473	ENSG00000112473		"Solute carriers"	4927	protein-coding gene	gene with protein product		601416	"HLA class II region expressed gene KE4"	HKE4		8812499, 1855816, 19246244, 15705588	Standard	NM_006979		Approved	H2-KE4, D6S2244E, KE4, RING5, ZIP7	uc003odf.3	Q92504	OTTHUMG00000031238	ENST00000374677.3:c.654T>A	chr6.hg19:g.33170059T>A		132.0	0.0	.		143.0	8.0	.	NM_006979	B0UXF6|Q5STP8|Q9UIQ0	Silent	SNP	ENST00000374677.3	hg19	CCDS43453.1																																																																																			.	.	.	none		0.517	SLC39A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076499.2	NM_006979		A	33170059	T	A	33170059	2	1	1	1	0	0	0	0	0	0	0	1	14636	1567	55	5		5	SLC39A7	6	33170059	Silent	SNP	T	TCGA-2K-A9WE-01A-11D-A382-10	19355598	33170059	137945008	18	18											
GTPBP2	54676	hgsc.bcm.edu	37	chr6	43593600	43593600	+	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	aacggttatgtctgccccaaCcctgtcacagcaaggccaca	11	7	8	15	1	2	0	1	0	1	0	2	0	2	0	4	2	4	2	4	2	4	1			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr6:43593600C>A	ENST00000307126.5	-	4	399	c.400G>T	c.(400-402)Gtt>Ttt	p.V134F	GTPBP2_ENST00000307114.7_Splice_Site_p.V46F|GTPBP2_ENST00000476510.1_5'UTR	NM_019096.3	NP_061969.3			GTP binding protein 2											breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(3)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(18;9.36e-06)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000501)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)			TCTGCCCCAACCCTGTCACAG	0.552																																					p.V134F	GBM(116;405 1620 28302 32150 44768)	Atlas-SNP	.											.	GTPBP2	39	.	0			c.G400T						PASS	.						136	113	121					6																	43593600		2203	4300	6503	SO:0001630	splice_region_variant	54676	exon4			CCCCAACCCTGTC	AB024574	CCDS4903.1, CCDS69124.1	6p21	2008-07-28			ENSG00000172432	ENSG00000172432			4670	protein-coding gene	gene with protein product		607434				10833435, 11054535	Standard	NM_019096		Approved		uc003ovs.3	Q9BX10	OTTHUMG00000014744	ENST00000307126.5:c.399-1G>T	chr6.hg19:g.43593600C>A		53.0	0.0	.		69.0	8.0	.	NM_019096		Missense_Mutation	SNP	ENST00000307126.5	hg19	CCDS4903.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.2|21.2	4.109076|4.109076	0.77096|0.77096	.|.	.|.	ENSG00000172432|ENSG00000172432	ENST00000442748|ENST00000307126;ENST00000307114;ENST00000452781	.|T;T;T	.|0.48836	.|1.39;1.42;0.8	4.78|4.78	4.78|4.78	0.61160|0.61160	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.43875|0.43875	0.1267|0.1267	M|M	0.73217|0.73217	2.22|2.22	0.58432|0.58432	D|D	0.999997|0.999997	.|P;P	.|0.49090	.|0.919;0.675	.|B;B	.|0.43623	.|0.425;0.176	T|T	0.55952|0.55952	-0.8059|-0.8059	5|10	.|0.72032	.|D	.|0.01	-12.0424|-12.0424	17.9977|17.9977	0.89189|0.89189	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|126;134	.|Q9BX10-4;Q9BX10	.|.;GTPB2_HUMAN	S|F	99|134;46;126	.|ENSP00000303997:V134F;ENSP00000304893:V46F;ENSP00000410676:V126F	.|ENSP00000304893:V46F	R|V	-|-	3|1	2|0	GTPBP2|GTPBP2	43701578|43701578	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.893000|0.893000	0.52053|0.52053	4.463000|4.463000	0.60128|0.60128	2.480000|2.480000	0.83734|0.83734	0.561000|0.561000	0.74099|0.74099	AGG|GTT	.	.	.	none		0.552	GTPBP2-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040679.1		Missense_Mutation	A	43593600	C	A	43593600	5	1	1	1	0	0	0	0	0	0	1	0	6887	521	18	4	1444	4	GTPBP2	6	43593600	Splice_Site	SNP	C	TCGA-2K-A9WE-01A-11D-A382-10	10423541	43593600	127521467	19	19											
MEP1A	4224	hgsc.bcm.edu	37	chr6	46766863	46766863	+	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	aaatccagaaatggcctgagAgacccaaacaccaggtggac	16	4	10	11	0	0	3	0	1	0	2	1	5	1	4	4	3	1	0	4	3	3	0			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr6:46766863A>T	ENST00000230588.4	+	5	216	c.207A>T	c.(205-207)agA>agT	p.R69S		NM_005588.2	NP_005579.2	Q16819	MEP1A_HUMAN	meprin A, alpha (PABA peptide hydrolase)	69	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)			ATGGCCTGAGAGACCCAAACA	0.423																																					p.R69S		Atlas-SNP	.											.	MEP1A	93	.	0			c.A207T						PASS	.						156	147	150					6																	46766863		2203	4300	6503	SO:0001583	missense	4224	exon5			CCTGAGAGACCCA		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.207A>T	chr6.hg19:g.46766863A>T	ENSP00000230588:p.Arg69Ser	136.0	0.0	.		159.0	20.0	.	NM_005588	A2RRM4|B0AZP9|B2RCS2|Q8TDC9|Q9H1R1	Missense_Mutation	SNP	ENST00000230588.4	hg19	CCDS4918.1	.	.	.	.	.	.	.	.	.	.	A	17.66	3.443835	0.63067	.	.	ENSG00000112818	ENST00000230588	T	0.25579	1.79	5.77	4.62	0.57501	Metallopeptidase, catalytic domain (1);	0.103697	0.64402	D	0.000003	T	0.24353	0.0590	L	0.61218	1.895	0.38384	D	0.945216	D;D	0.69078	0.995;0.997	P;P	0.58721	0.844;0.824	T	0.06899	-1.0801	10	0.27082	T	0.32	-20.7669	8.3767	0.32447	0.9122:0.0:0.0878:0.0	.	97;69	B7ZL91;Q16819	.;MEP1A_HUMAN	S	69	ENSP00000230588:R69S	ENSP00000230588:R69S	R	+	3	2	MEP1A	46874822	1.000000	0.71417	1.000000	0.80357	0.337000	0.28794	1.001000	0.29783	1.039000	0.40074	0.528000	0.53228	AGA	.	.	.	none		0.423	MEP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040803.1	NM_005588		T	46766863	A	T	46766863	3	4	1	1	0	0	0	0	1	0	0	0	9482	301	11	5	225	5	MEP1A	6	46766863	Missense_Mutation	SNP	A	TCGA-2K-A9WE-01A-11D-A382-10	3173263	46766863	124348204	20	20											
HEATR2	54919	hgsc.bcm.edu	37	chr7	780577	780577	+	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	caacgacgaggtgcctgaggTcaggtacgtgggcaggcggc	8	5	18	10	4	1	1	1	1	0	0	1	3	1	1	1	6	3	2	1	6	2	1			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr7:780577T>A	ENST00000297440.6	+	3	922	c.902T>A	c.(901-903)gTc>gAc	p.V301D	HEATR2_ENST00000438961.1_3'UTR|HEATR2_ENST00000313147.5_Missense_Mutation_p.V301D	NM_017802.3	NP_060272.3	Q86Y56	HEAT2_HUMAN	HEAT repeat containing 2	301						cytoplasm (GO:0005737)				breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|prostate(4)|skin(1)	22		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0182)|Epithelial(4;5.48e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.95e-16)|all cancers(6;2.98e-14)		GTGCCTGAGGTCAGGTACGTG	0.592																																					p.V301D		Atlas-SNP	.											.	HEATR2	62	.	0			c.T902A						PASS	.						117	99	105					7																	780577		2203	4300	6503	SO:0001583	missense	54919	exon3			CTGAGGTCAGGTA	AL832914, AK000404, NM_017802, AK056233	CCDS34580.1	7p22.3	2014-05-06	2006-05-19		ENSG00000164818	ENSG00000164818			26013	protein-coding gene	gene with protein product		614864				23040496	Standard	NM_017802		Approved	FLJ20397, FLJ31671, FLJ39381, FLJ25564, CILD18	uc010krz.1	Q86Y56	OTTHUMG00000151416	ENST00000297440.6:c.902T>A	chr7.hg19:g.780577T>A	ENSP00000297440:p.Val301Asp	29.0	0.0	.		47.0	8.0	.	NM_017802	Q69YL1|Q96FI9|Q9NX75	Missense_Mutation	SNP	ENST00000297440.6	hg19	CCDS34580.1	.	.	.	.	.	.	.	.	.	.	T	13.42	2.230973	0.39399	.	.	ENSG00000164818	ENST00000297440;ENST00000313147;ENST00000537862	T;T	0.68025	-0.3;-0.3	4.66	2.28	0.28536	Armadillo-like helical (1);Armadillo-type fold (1);	0.866751	0.09639	N	0.775197	T	0.62073	0.2398	M	0.61703	1.905	0.19945	N	0.999944	P;P	0.39920	0.695;0.478	B;B	0.40199	0.322;0.154	T	0.55186	-0.8180	10	0.87932	D	0	-13.8309	4.2822	0.10838	0.1838:0.1694:0.0:0.6468	.	301;47	Q86Y56;F5H8D4	HEAT2_HUMAN;.	D	301;301;47	ENSP00000297440:V301D;ENSP00000321451:V301D	ENSP00000297440:V301D	V	+	2	0	HEATR2	747103	0.981000	0.34729	0.003000	0.11579	0.034000	0.12701	4.207000	0.58480	0.261000	0.21753	0.528000	0.53228	GTC	.	.	.	none		0.592	HEATR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322542.1	NM_017802		A	780577	T	A	780577	3	1	1	1	0	0	0	0	1	0	0	0	7035	1667	58	5	912	5	HEATR2	7	780577	Missense_Mutation	SNP	T	TCGA-2K-A9WE-01A-11D-A382-10		780577	158358086	21	21											
PDE1C	5137	hgsc.bcm.edu	37	chr7	31862810	31862810	+	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	cggggcacttccctctgaacCagaggtcttgacacctgatc	8	9	10	14	1	2	4	0	3	2	1	4	4	3	4	3	3	1	1	3	3	1	2	rs372917246		TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr7:31862810C>A	ENST00000396191.1	-	14	1914	c.1459G>T	c.(1459-1461)Ggt>Tgt	p.G487C	PDE1C_ENST00000396182.2_Missense_Mutation_p.G487C|PDE1C_ENST00000321453.7_Missense_Mutation_p.G487C|PDE1C_ENST00000396193.1_Missense_Mutation_p.G547C|PDE1C_ENST00000396184.3_Missense_Mutation_p.G487C|PDE1C_ENST00000479980.1_5'Flank	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	487	Catalytic. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	CCCTCTGAACCAGAGGTCTTG	0.443																																					p.G547C		Atlas-SNP	.											.	PDE1C	465	.	0			c.G1639T						PASS	.						106	96	99					7																	31862810		2203	4300	6503	SO:0001583	missense	5137	exon15			CTGAACCAGAGGT	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.1459G>T	chr7.hg19:g.31862810C>A	ENSP00000379494:p.Gly487Cys	108.0	0.0	.		121.0	28.0	.	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Missense_Mutation	SNP	ENST00000396191.1	hg19	CCDS55099.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.809335	0.90707	.	.	ENSG00000154678	ENST00000396193;ENST00000396191;ENST00000321453;ENST00000396184;ENST00000396182	T;T;T;T;T	0.73047	-0.71;-0.71;-0.71;-0.68;-0.68	5.91	5.91	0.95273	.	0.634852	0.16753	N	0.200964	T	0.78910	0.4358	L	0.29908	0.895	0.80722	D	1	D;D;D	0.89917	0.998;0.998;1.0	D;D;D	0.73380	0.927;0.912;0.98	T	0.79507	-0.1775	10	0.72032	D	0.01	.	19.9003	0.96983	0.0:1.0:0.0:0.0	.	487;547;487	Q14123-2;E9PE92;Q14123	.;.;PDE1C_HUMAN	C	547;487;487;487;487	ENSP00000379496:G547C;ENSP00000379494:G487C;ENSP00000318105:G487C;ENSP00000379487:G487C;ENSP00000379485:G487C	ENSP00000318105:G487C	G	-	1	0	PDE1C	31829335	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.060000	0.76692	2.808000	0.96608	0.655000	0.94253	GGT	.	.	.	alt		0.443	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1			A	31862810	C	A	31862810	3	1	1	1	0	0	0	0	1	0	0	0	11642	594	21	4	461	4	PDE1C	7	31862810	Missense_Mutation	SNP	C	TCGA-2K-A9WE-01A-11D-A382-10	31082233	31862810	127275853	22	22											
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121682687	121682687	+	Missense_Mutation	SNP	T	T	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	gagttggaagaacaggcacaTatattgtgctagacagtatg	14	10	12	5	0	0	2	0	0	0	2	0	4	0	3	0	2	2	4	0	2	6	6			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr7:121682687T>G	ENST00000393386.2	+	22	6238	c.5827T>G	c.(5827-5829)Tat>Gat	p.Y1943D	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.Y1076D	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1943	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						AACAGGCACATATATTGTGCT	0.338																																					p.Y1943D		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.T5827G						PASS	.						121	99	107					7																	121682687		2203	4300	6503	SO:0001583	missense	5803	exon22			GGCACATATATTG	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.5827T>G	chr7.hg19:g.121682687T>G	ENSP00000377047:p.Tyr1943Asp	166.0	0.0	.		183.0	26.0	.	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	hg19	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.068493	0.76301	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	T;T	0.14516	2.5;2.5	5.86	5.86	0.93980	Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.64402	D	0.000006	T	0.50599	0.1625	H	0.95004	3.61	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	0.65240	-0.6216	10	0.87932	D	0	.	16.2644	0.82568	0.0:0.0:0.0:1.0	.	1082;1076;1943	P23471-2;C9JFM0;P23471	.;.;PTPRZ_HUMAN	D	1943;1076	ENSP00000377047:Y1943D;ENSP00000410000:Y1076D	ENSP00000377047:Y1943D	Y	+	1	0	PTPRZ1	121469923	1.000000	0.71417	0.179000	0.23059	0.735000	0.41995	8.040000	0.89188	2.244000	0.73946	0.528000	0.53228	TAT	.	.	.	none		0.338	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		G	121682687	T	G	121682687	3	3	1	1	0	0	0	0	1	0	0	0	12827	1406	49	5	5913	5	PTPRZ1	7	121682687	Missense_Mutation	SNP	T	TCGA-2K-A9WE-01A-11D-A382-10	89819877	121682687	37455976	23	23											
ADAM7	8756	hgsc.bcm.edu	37	chr8	24350057	24350058	+	Frame_Shift_Ins	INS	-	-	A																															agatgaatacaaaaggaaatINSaaatttggatactgcaaaaa																										TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr8:24350057_24350058insA	ENST00000175238.6	+	15	1685_1686	c.1602_1603insA	c.(1603-1605)aaafs	p.K535fs	RP11-561E1.1_ENST00000519364.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|ADAM7_ENST00000520720.1_Frame_Shift_Ins_p.K307fs|ADAM7_ENST00000380789.1_Frame_Shift_Ins_p.K535fs	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	535	Cys-rich.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(24)|ovary(1)|skin(15)	64		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		CAAAAGGAAATAAATTTGGATA	0.347																																					p.N534fs		Atlas-Indel,Pindel	.											.	ADAM7	165	.	0			c.1602_1603insA						PASS	.																																			SO:0001589	frameshift_variant	8756	exon15			.	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.1605dupA	chr8.hg19:g.24350060_24350060dupA	ENSP00000175238:p.Lys535fs	386.0	0.0	0		472.0	40.0	0.0847458	NM_003817	A8K8X7|O75959|Q6PEJ6	Frame_Shift_Ins	INS	ENST00000175238.6	hg19	CCDS6045.1																																																																																			.	.	.	none		0.347	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817		A	24350058	-	A	24350057	7	5	1	1	0	1	1	0	0	0	0	0	251	1403	49	0	1660	0	ADAM7	8	24350057	Frame_Shift_Ins	INS	-	TCGA-2K-A9WE-01A-11D-A382-10		24350057	122013965	24	24											
MYST3	7994	hgsc.bcm.edu	37	chr8	41790172	41790172	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcagacttggagcggatggAaatgtgccccttcactggca	9	8	13	11	2	1	1	1	0	0	1	1	4	1	4	2	4	2	2	2	4	1	2			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr8:41790172A>G	ENST00000396930.3	-	18	6109	c.5566T>C	c.(5566-5568)Tcc>Ccc	p.S1856P	KAT6A_ENST00000406337.1_Missense_Mutation_p.S1856P|KAT6A_ENST00000265713.2_Missense_Mutation_p.S1856P	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1856					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)										GAGCGGATGGAAATGTGCCCC	0.592																																					p.S1856P		Atlas-SNP	.											.	.	.	.	0			c.T5566C						PASS	.						118	80	93					8																	41790172		2203	4300	6503	SO:0001583	missense	7994	exon18			GGATGGAAATGTG	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.5566T>C	chr8.hg19:g.41790172A>G	ENSP00000380136:p.Ser1856Pro	75.0	0.0	.		85.0	10.0	.	NM_001099412	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	hg19	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	A	8.585	0.883157	0.17467	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930	T;T;T	0.67865	-0.29;-0.29;-0.29	5.67	5.67	0.87782	.	0.000000	0.64402	D	0.000001	T	0.69459	0.3113	L	0.27053	0.805	0.43994	D	0.996696	D	0.69078	0.997	P	0.60789	0.879	T	0.69731	-0.5066	10	0.38643	T	0.18	-11.9288	15.9132	0.79488	1.0:0.0:0.0:0.0	.	1856	Q92794	KAT6A_HUMAN	P	1856	ENSP00000265713:S1856P;ENSP00000385888:S1856P;ENSP00000380136:S1856P	ENSP00000265713:S1856P	S	-	1	0	KAT6A	41909329	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.712000	0.54875	2.148000	0.66965	0.533000	0.62120	TCC	.	.	.	none		0.592	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		G	41790172	A	G	41790172	3	3	1	1	0	0	0	0	1	0	0	0	10111	246	9	3	452	3	MYST3	8	41790172	Missense_Mutation	SNP	A	TCGA-2K-A9WE-01A-11D-A382-10	17440115	41790172	104573850	25	25											
SLC30A8	169026	hgsc.bcm.edu	37	chr8	118169968	118169968	+	Missense_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	tctccatcctgtgcatctggGtggtgactggcgtgctagtg	4	13	14	10	1	2	1	0	1	2	0	4	1	3	1	2	3	2	2	2	3	1	1			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr8:118169968G>A	ENST00000456015.2	+	4	457	c.457G>A	c.(457-459)Gtg>Atg	p.V153M	SLC30A8_ENST00000519688.1_Missense_Mutation_p.V104M|SLC30A8_ENST00000521243.1_Missense_Mutation_p.V104M|SLC30A8_ENST00000427715.2_Missense_Mutation_p.V104M	NM_173851.2	NP_776250.2	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 (zinc transporter), member 8	153					cellular zinc ion homeostasis (GO:0006882)|insulin secretion (GO:0030073)|positive regulation of insulin secretion (GO:0032024)|regulation of sequestering of zinc ion (GO:0061088)|regulation of vesicle-mediated transport (GO:0060627)|response to glucose (GO:0009749)|response to interferon-gamma (GO:0034341)|response to interleukin-1 (GO:0070555)|sequestering of zinc ion (GO:0032119)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(18)|ovary(2)|pancreas(2)|skin(5)	41	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			GTGCATCTGGGTGGTGACTGG	0.527																																					p.V153M	Ovarian(162;1202 1922 6011 16223 52092)	Atlas-SNP	.											.	SLC30A8	102	.	0			c.G457A						PASS	.						321	285	298					8																	118169968		2203	4300	6503	SO:0001583	missense	169026	exon4			ATCTGGGTGGTGA		CCDS6322.1, CCDS55272.1	8q24.11	2014-08-12			ENSG00000164756			"Solute carriers"	20303	protein-coding gene	gene with protein product		611145					Standard	NM_001172811		Approved		uc003yoh.3	Q8IWU4	OTTHUMG00000164962	ENST00000456015.2:c.457G>A	chr8.hg19:g.118169968G>A	ENSP00000415011:p.Val153Met	144.0	0.0	.		112.0	14.0	.	NM_173851	A0AVP9|A5YM39|B4DPE0|Q8TCL3	Missense_Mutation	SNP	ENST00000456015.2	hg19	CCDS6322.1	.	.	.	.	.	.	.	.	.	.	G	12.84	2.059889	0.36373	.	.	ENSG00000164756	ENST00000521243;ENST00000427715;ENST00000519688;ENST00000456015	T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08	5.77	1.77	0.24775	.	0.454505	0.23945	N	0.043018	T	0.61248	0.2332	M	0.66439	2.03	0.43756	D	0.996263	B	0.26845	0.161	B	0.37731	0.257	T	0.52939	-0.8508	10	0.35671	T	0.21	-0.9189	8.5281	0.33317	0.1502:0.5085:0.3413:0.0	.	153	Q8IWU4	ZNT8_HUMAN	M	104;104;104;153	ENSP00000428545:V104M;ENSP00000407505:V104M;ENSP00000431069:V104M;ENSP00000415011:V153M	ENSP00000407505:V104M	V	+	1	0	SLC30A8	118239149	0.999000	0.42202	0.988000	0.46212	0.836000	0.47400	0.543000	0.23237	0.034000	0.15491	0.655000	0.94253	GTG	.	.	.	none		0.527	SLC30A8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381205.1	NM_173851		A	118169968	G	A	118169968	3	1	1	1	0	0	0	0	1	0	0	0	14574	1261	44	2	471	2	SLC30A8	8	118169968	Missense_Mutation	SNP	G	TCGA-2K-A9WE-01A-11D-A382-10	76379796	118169968	28194054	26	26											
ALDOB	229	hgsc.bcm.edu	37	chr9	104187287	104187287	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcattgaggttgagagtggcAtcctcttcactcatgccacc	8	11	10	12	0	3	2	2	2	1	1	4	3	4	2	3	2	1	3	3	2	0	3			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr9:104187287A>G	ENST00000374855.4	-	8	961	c.837T>C	c.(835-837)gaT>gaC	p.D279D	ALDOB_ENST00000468981.3_5'Flank	NM_000035.3	NP_000026.2	P05062	ALDOB_HUMAN	aldolase B, fructose-bisphosphate	279					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)				TGAGAGTGGCATCCTCTTCAC	0.498																																					p.D279D		Atlas-SNP	.											.	ALDOB	69	.	0			c.T837C						PASS	.						88	82	84					9																	104187287		2203	4300	6503	SO:0001819	synonymous_variant	229	exon8			AGTGGCATCCTCT	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.837T>C	chr9.hg19:g.104187287A>G		130.0	0.0	.		136.0	10.0	.	NM_000035	Q13741|Q13742|Q5T7D6	Silent	SNP	ENST00000374855.4	hg19	CCDS6756.1																																																																																			.	.	.	none		0.498	ALDOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053434.2			G	104187287	A	G	104187287	2	3	1	1	0	0	0	0	0	0	0	1	508	214	8	3		3	ALDOB	9	104187287	Silent	SNP	A	TCGA-2K-A9WE-01A-11D-A382-10		104187287	37026144	27	27											
NUP188	23511	hgsc.bcm.edu	37	chr9	131761490	131761490	+	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	gaaatccttggacccttgacGgagatcctggagggagtgct	9	9	14	9	1	0	2	0	1	0	1	2	7	2	5	3	4	1	1	3	4	1	2			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr9:131761490G>T	ENST00000372577.2	+	33	3576	c.3555G>T	c.(3553-3555)acG>acT	p.T1185T		NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	1185					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						GACCCTTGACGGAGATCCTGG	0.522											OREG0003925	type=REGULATORY REGION|Gene=AK025292|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.T1185T		Atlas-SNP	.											.	NUP188	140	.	0			c.G3555T						PASS	.						90	81	84					9																	131761490		2203	4300	6503	SO:0001819	synonymous_variant	23511	exon33			CTTGACGGAGATC	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.3555G>T	chr9.hg19:g.131761490G>T		75.0	0.0	.	1590	82.0	4.0	.	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Silent	SNP	ENST00000372577.2	hg19	CCDS35156.1																																																																																			.	.	.	none		0.522	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2			T	131761490	G	T	131761490	2	4	1	1	0	0	0	0	0	0	0	1	10765	1103	39	4		4	NUP188	9	131761490	Silent	SNP	G	TCGA-2K-A9WE-01A-11D-A382-10	27574203	131761490	9451941	28	28											
RXRA	6256	hgsc.bcm.edu	37	chr9	137313579	137313579	+	Missense_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	acaaacagcttttcaccctgGtggagtgggccaagcggatc	10	8	12	11	1	1	0	1	0	0	0	2	2	1	2	2	4	3	1	2	4	2	2			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr9:137313579G>A	ENST00000481739.1	+	6	890	c.838G>A	c.(838-840)Gtg>Atg	p.V280M	RXRA_ENST00000540193.1_Missense_Mutation_p.V183M|RXRA_ENST00000356384.4_3'UTR	NM_002957.4	NP_002948.1	P19793	RXRA_HUMAN	retinoid X receptor, alpha	280	Ligand-binding.				camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|cellular lipid metabolic process (GO:0044255)|cholesterol metabolic process (GO:0008203)|embryo implantation (GO:0007566)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|response to retinoic acid (GO:0032526)|retinoic acid receptor signaling pathway (GO:0048384)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|vitamin metabolic process (GO:0006766)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein heterodimerization activity (GO:0046982)|retinoic acid receptor activity (GO:0003708)|retinoic acid-responsive element binding (GO:0044323)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|vitamin D receptor binding (GO:0042809)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19				OV - Ovarian serous cystadenocarcinoma(145;4.66e-08)|Epithelial(140;6.72e-08)|all cancers(34;2.22e-07)	Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Etodolac(DB00749)	TTTCACCCTGGTGGAGTGGGC	0.607																																					p.V280M		Atlas-SNP	.											.	RXRA	52	.	0			c.G838A						PASS	.						168	141	150					9																	137313579		2203	4300	6503	SO:0001583	missense	6256	exon6			ACCCTGGTGGAGT	X52773	CCDS35172.1	9q34	2013-01-16			ENSG00000186350	ENSG00000186350		"Nuclear hormone receptors"	10477	protein-coding gene	gene with protein product	"nuclear receptor subfamily 2 group B member 1"	180245				2159111	Standard	XM_005263409		Approved	NR2B1	uc004cfa.1	P19793	OTTHUMG00000020887	ENST00000481739.1:c.838G>A	chr9.hg19:g.137313579G>A	ENSP00000419692:p.Val280Met	80.0	0.0	.		70.0	7.0	.	NM_002957	B3KY83|Q2NL52|Q2V504	Missense_Mutation	SNP	ENST00000481739.1	hg19	CCDS35172.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.543798	0.86022	.	.	ENSG00000186350	ENST00000481739;ENST00000540193	D;D	0.97455	-4.39;-4.39	4.51	4.51	0.55191	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.060613	0.64402	D	0.000004	D	0.98324	0.9444	M	0.91510	3.215	0.80722	D	1	P;D	0.54964	0.872;0.969	P;P	0.54965	0.541;0.765	D	0.99744	1.1016	10	0.87932	D	0	.	17.2581	0.87063	0.0:0.0:1.0:0.0	.	183;280	B3KY83;P19793	.;RXRA_HUMAN	M	280;183	ENSP00000419692:V280M;ENSP00000442123:V183M	ENSP00000419692:V280M	V	+	1	0	RXRA	136453400	1.000000	0.71417	0.973000	0.42090	0.868000	0.49771	9.335000	0.96500	2.055000	0.61198	0.485000	0.47835	GTG	.	.	.	none		0.607	RXRA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054949.1	NM_002957		A	137313579	G	A	137313579	3	1	1	1	0	0	0	0	1	0	0	0	13776	1261	44	2	860	2	RXRA	9	137313579	Missense_Mutation	SNP	G	TCGA-2K-A9WE-01A-11D-A382-10	5552089	137313579	3899852	29	29											
ANUBL1	93550	hgsc.bcm.edu	37	chr10	46113699	46113699	+	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	caggtgggaggtgatgagtaGtacattctcctgtttagaga	10	12	14	5	0	1	3	0	2	1	1	2	5	1	4	1	3	1	3	1	3	3	5			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr10:46113699G>C	ENST00000344646.5	-	9	2152	c.1937C>G	c.(1936-1938)aCt>aGt	p.T646S	ZFAND4_ENST00000374371.2_Nonsense_Mutation_p.Y193*|ZFAND4_ENST00000374366.3_Missense_Mutation_p.T572S|ZFAND4_ENST00000374370.1_5'UTR	NM_001128324.2|NM_174890.2	NP_001121796.1|NP_777550.2	Q86XD8	ZFAN4_HUMAN	zinc finger, AN1-type domain 4	646							zinc ion binding (GO:0008270)										GTGATGAGTAGTACATTCTCC	0.368																																					p.T646S		Atlas-SNP	.											.	.	.	.	0			c.C1937G						PASS	.						89	89	89					10																	46113699		2203	4300	6503	SO:0001583	missense	93550	exon9			TGAGTAGTACATT	AF311324	CCDS7214.1, CCDS60520.1	10q11.22	2013-01-09	2011-11-10	2011-11-10	ENSG00000172671	ENSG00000172671		"Zinc fingers, AN1-type domain containing"	23504	protein-coding gene	gene with protein product			"AN1, ubiquitin-like, homolog (Xenopus laevis)"	ANUBL1			Standard	XM_005271837		Approved	FLJ40185	uc001jcp.4	Q86XD8	OTTHUMG00000018085	ENST00000344646.5:c.1937C>G	chr10.hg19:g.46113699G>C	ENSP00000339484:p.Thr646Ser	81.0	0.0	.		78.0	12.0	.	NM_001128324	A8K8V4|B2RAX2|Q5VVY5	Missense_Mutation	SNP	ENST00000344646.5	hg19	CCDS7214.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	38|38	6.673531|6.673531	0.97751|0.97751	.|.	.|.	ENSG00000172671|ENSG00000172671	ENST00000344646;ENST00000374366;ENST00000374370|ENST00000374371;ENST00000374376	T;T|.	0.23950|.	1.88;1.88|.	5.99|5.99	1.9|1.9	0.25705|0.25705	Zinc finger, AN1-type (1);|.	0.810801|.	0.10951|.	N|.	0.616052|.	T|.	0.20700|.	0.0498|.	N|N	0.16656|0.16656	0.425|0.425	0.09310|0.09310	N|N	1|1	B|.	0.15473|.	0.013|.	B|.	0.10450|.	0.005|.	T|.	0.24977|.	-1.0145|.	10|.	0.21014|0.25751	T|T	0.42|0.34	.|.	5.5692|5.5692	0.17187|0.17187	0.0692:0.1228:0.5544:0.2537|0.0692:0.1228:0.5544:0.2537	.|.	646|.	Q86XD8|.	ANUB1_HUMAN|.	S|X	646;572;528|193	ENSP00000339484:T646S;ENSP00000363486:T572S|.	ENSP00000339484:T646S|ENSP00000363491:Y193X	T|Y	-|-	2|3	0|2	ANUBL1|ANUBL1	45433705|45433705	0.848000|0.848000	0.29623|0.29623	0.018000|0.018000	0.16275|0.16275	0.998000|0.998000	0.95712|0.95712	0.364000|0.364000	0.20325|0.20325	0.091000|0.091000	0.17302|0.17302	0.655000|0.655000	0.94253|0.94253	ACT|TAC	.	.	.	none		0.368	ZFAND4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047790.1	NM_174890		C	46113699	G	C	46113699	3	2	1	1	0	0	0	0	1	0	0	0	713	1029	36	4	254	4	ANUBL1	10	46113699	Missense_Mutation	SNP	G	TCGA-2K-A9WE-01A-11D-A382-10		46113699	89421048	30	30											
ARHGAP22	58504	hgsc.bcm.edu	37	chr10	49663122	49663122	+	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	gaaggggaccacgggctcggGgagctcccgcaggtacagct	8	4	17	12	3	0	0	0	0	0	0	2	3	1	2	2	6	3	5	2	6	2	1			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr10:49663122G>A	ENST00000249601.4	-	6	1011	c.715C>T	c.(715-717)Ccc>Tcc	p.P239S	ARHGAP22_ENST00000374172.1_Missense_Mutation_p.P130S|ARHGAP22_ENST00000435790.2_Missense_Mutation_p.P245S|ARHGAP22_ENST00000374170.1_Intron|ARHGAP22_ENST00000417912.2_Missense_Mutation_p.P255S|ARHGAP22_ENST00000417247.2_Missense_Mutation_p.P149S	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	239	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						ACGGGCTCGGGGAGCTCCCGC	0.662																																					p.P255S		Atlas-SNP	.											ARHGAP22_ENST00000417912,NS,malignant_melanoma,0,2	ARHGAP22	94	.	0			c.C763T						PASS	.						40	34	36					10																	49663122		2202	4300	6502	SO:0001583	missense	58504	exon6			GCTCGGGGAGCTC	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.715C>T	chr10.hg19:g.49663122G>A	ENSP00000249601:p.Pro239Ser	47.0	0.0	.		70.0	8.0	.	NM_001256024	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Missense_Mutation	SNP	ENST00000249601.4	hg19	CCDS7227.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.938685	0.92526	.	.	ENSG00000128805	ENST00000249601;ENST00000374172;ENST00000417247;ENST00000435790;ENST00000417912	T;T;T;T;T	0.58358	2.26;0.34;2.26;2.26;0.34	4.85	4.85	0.62838	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.75838	0.3904	M	0.85099	2.735	0.80722	D	1	D;D;D;D;D	0.89917	0.995;0.988;1.0;0.988;0.994	D;D;D;D;D	0.87578	0.98;0.954;0.998;0.954;0.966	T	0.80837	-0.1204	10	0.72032	D	0.01	.	16.9763	0.86314	0.0:0.0:1.0:0.0	.	245;239;255;239;149	B4DED8;A6NDI7;Q7Z5H3-2;Q7Z5H3;Q7Z5H3-3	.;.;.;RHG22_HUMAN;.	S	239;130;149;245;255	ENSP00000249601:P239S;ENSP00000363287:P130S;ENSP00000410054:P149S;ENSP00000416701:P245S;ENSP00000412461:P255S	ENSP00000249601:P239S	P	-	1	0	ARHGAP22	49333128	1.000000	0.71417	0.827000	0.32855	0.943000	0.58893	9.747000	0.98863	2.246000	0.74042	0.561000	0.74099	CCC	.	.	.	none		0.662	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226		A	49663122	G	A	49663122	3	1	1	1	0	0	0	0	1	0	0	0	872	1232	43	2	1401	2	ARHGAP22	10	49663122	Missense_Mutation	SNP	G	TCGA-2K-A9WE-01A-11D-A382-10	3549423	49663122	85871625	31	31											
LRDD	55367	hgsc.bcm.edu	37	chr11	801990	801990	+	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	gtgcctcttcctccaggtagGtctccaggtcaccccagctg	5	10	10	16	0	3	0	1	0	2	0	6	0	5	0	6	3	2	2	6	3	1	2			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr11:801990G>C	ENST00000347755.5	-	7	1418	c.1277C>G	c.(1276-1278)aCc>aGc	p.T426S	PIDD_ENST00000534649.1_5'Flank|PIDD_ENST00000411829.2_Missense_Mutation_p.T426S	NM_145886.3|NM_145887.3	NP_665893.2|NP_665894.2																					CTCCAGGTAGGTCTCCAGGTC	0.682																																					p.T426S		Atlas-SNP	.											PIDD_ENST00000347755,NS,carcinoma,0,1	PIDD	76	.	0			c.C1277G						PASS	.						30	28	28					11																	801990		2197	4293	6490	SO:0001583	missense	55367	exon7			AGGTAGGTCTCCA																												ENST00000347755.5:c.1277C>G	chr11.hg19:g.801990G>C	ENSP00000337797:p.Thr426Ser	63.0	0.0	.		79.0	6.0	.	NM_145887		Missense_Mutation	SNP	ENST00000347755.5	hg19	CCDS7716.1	.	.	.	.	.	.	.	.	.	.	G	14.73	2.622155	0.46840	.	.	ENSG00000177595	ENST00000411829;ENST00000347755	T;T	0.47869	0.94;0.83	4.03	3.06	0.35304	.	0.079208	0.49305	U	0.000151	T	0.50854	0.1640	L	0.29908	0.895	0.31516	N	0.662958	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.91635	0.999;0.994;0.997	T	0.47086	-0.9144	10	0.12766	T	0.61	.	12.7861	0.57507	0.0:0.1651:0.8349:0.0	.	426;280;426	Q9HB75;Q9HB75-3;Q9HB75-2	PIDD_HUMAN;.;.	S	426	ENSP00000416801:T426S;ENSP00000337797:T426S	ENSP00000337797:T426S	T	-	2	0	PIDD	791990	0.997000	0.39634	0.994000	0.49952	0.123000	0.20343	3.663000	0.54518	2.084000	0.62774	0.462000	0.41574	ACC	.	.	.	none		0.682	PIDD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257103.1			C	801990	G	C	801990	3	2	1	1	0	0	0	0	1	0	0	0	8943	1261	44	4	1495	4	LRDD	11	801990	Missense_Mutation	SNP	G	TCGA-2K-A9WE-01A-11D-A382-10		801990	134204526	32	32											
OR56A4	120793	hgsc.bcm.edu	37	chr11	6023641	6023641	+	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	tagagctgattgaaagtgatGtcatcacaagagagtttgga	14	11	12	4	0	2	5	2	3	0	2	2	7	2	6	0	1	1	2	0	1	3	3			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr11:6023641G>A	ENST00000330728.4	-	1	783	c.738C>T	c.(736-738)gaC>gaT	p.D246D		NM_001005179.2	NP_001005179.2	Q8NGH8	O56A4_HUMAN	olfactory receptor, family 56, subfamily A, member 4	194						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)		TGAAAGTGATGTCATCACAAG	0.428																																					p.D246D		Atlas-SNP	.											.	OR56A4	66	.	0			c.C738T						PASS	.						51	50	51					11																	6023641		2201	4296	6497	SO:0001819	synonymous_variant	120793	exon1			AGTGATGTCATCA	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.738C>T	chr11.hg19:g.6023641G>A		136.0	0.0	.		114.0	11.0	.	NM_001005179	B9EH17	Silent	SNP	ENST00000330728.4	hg19	CCDS31404.1																																																																																			.	.	.	none		0.428	OR56A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383756.2	NM_001005179		A	6023641	G	A	6023641	2	1	1	1	0	0	0	0	0	0	0	1	11142	1368	48	2		2	OR56A4	11	6023641	Silent	SNP	G	TCGA-2K-A9WE-01A-11D-A382-10	5221651	6023641	128982875	33	33											
TTC17	55761	hgsc.bcm.edu	37	chr11	43465612	43465612	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttctgtttcccagattacaTtccaggtcaaacgtgtaaag	11	14	7	9	1	2	1	1	0	1	1	4	1	4	1	2	1	2	2	2	1	4	5			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr11:43465612T>C	ENST00000039989.4	+	18	2532	c.2518T>C	c.(2518-2520)Ttc>Ctc	p.F840L	TTC17_ENST00000526774.1_3'UTR|TTC17_ENST00000299240.6_Missense_Mutation_p.F897L	NM_018259.5	NP_060729.2	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17	840					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						CCAGATTACATTCCAGGTCAA	0.373																																					p.F840L		Atlas-SNP	.											.	TTC17	112	.	0			c.T2518C						PASS	.						79	78	78					11																	43465612		2203	4300	6503	SO:0001583	missense	55761	exon18			ATTACATTCCAGG	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.2518T>C	chr11.hg19:g.43465612T>C	ENSP00000039989:p.Phe840Leu	234.0	0.0	.		262.0	31.0	.	NM_018259	G3XAB3|Q8NEC0	Missense_Mutation	SNP	ENST00000039989.4	hg19	CCDS31466.1	.	.	.	.	.	.	.	.	.	.	T	29.8	5.032954	0.93575	.	.	ENSG00000052841	ENST00000299240;ENST00000039989	T;T	0.46819	0.86;1.13	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.55401	0.1918	L	0.32530	0.975	0.58432	D	0.999996	D;D;D	0.71674	0.996;0.997;0.998	P;D;D	0.70716	0.817;0.97;0.911	T	0.48692	-0.9013	10	0.19147	T	0.46	-17.1985	14.9183	0.70815	0.0:0.0:0.0:1.0	.	897;840;897	Q8NEC0;Q96AE7;G3XAB3	.;TTC17_HUMAN;.	L	897;840	ENSP00000299240:F897L;ENSP00000039989:F840L	ENSP00000039989:F840L	F	+	1	0	TTC17	43422188	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.394000	0.73223	2.266000	0.75297	0.454000	0.30748	TTC	.	.	.	none		0.373	TTC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389577.2	NM_018259		C	43465612	T	C	43465612	3	2	1	1	0	0	0	0	1	0	0	0	16696	1493	52	3	2588	3	TTC17	11	43465612	Missense_Mutation	SNP	T	TCGA-2K-A9WE-01A-11D-A382-10	37441971	43465612	91540904	34	34											
PRCP	5547	hgsc.bcm.edu	37	chr11	82535970	82535970	+	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	agtgctgctttcccgcactgTcatagaaatctctgatccaa	10	12	7	12	1	2	2	1	1	1	1	5	2	4	2	2	0	2	3	2	0	3	2			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr11:82535970T>A	ENST00000313010.3	-	9	1663	c.1469A>T	c.(1468-1470)gAc>gTc	p.D490V	PRCP_ENST00000535099.1_Missense_Mutation_p.D385V|PRCP_ENST00000393399.2_Missense_Mutation_p.D511V|PRCP_ENST00000525772.1_5'Flank	NM_005040.2	NP_005031.1	P42785	PCP_HUMAN	prolylcarboxypeptidase (angiotensinase C)	490					angiogenesis involved in wound healing (GO:0060055)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|energy homeostasis (GO:0097009)|glucose homeostasis (GO:0042593)|negative regulation of systemic arterial blood pressure (GO:0003085)|plasma kallikrein-kinin cascade (GO:0002353)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of thyroid hormone mediated signaling pathway (GO:0002155)	basal part of cell (GO:0045178)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	serine-type carboxypeptidase activity (GO:0004185)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	17						TCCCGCACTGTCATAGAAATC	0.403																																					p.D511V		Atlas-SNP	.											.	PRCP	69	.	0			c.A1532T						PASS	.						65	63	64					11																	82535970		2203	4300	6503	SO:0001583	missense	5547	exon10			GCACTGTCATAGA	BC001500, BI827978, L13977	CCDS8262.1, CCDS41695.1	11q14	2005-10-04				ENSG00000137509			9344	protein-coding gene	gene with protein product		176785				8344943	Standard	NM_199418		Approved	PCP, HUMPCP	uc001ozr.3	P42785		ENST00000313010.3:c.1469A>T	chr11.hg19:g.82535970T>A	ENSP00000317362:p.Asp490Val	94.0	0.0	.		88.0	6.0	.	NM_199418	A8MU24|B2R7B7|B3KRK5|B5BU34	Missense_Mutation	SNP	ENST00000313010.3	hg19	CCDS8262.1	.	.	.	.	.	.	.	.	.	.	T	8.923	0.961442	0.18583	.	.	ENSG00000137509	ENST00000313010;ENST00000393399;ENST00000535099	T;T;T	0.23552	2.48;2.47;1.9	5.25	-5.04	0.02964	.	2.033150	0.01986	N	0.045194	T	0.08088	0.0202	N	0.02539	-0.55	0.09310	N	1	B;B	0.23249	0.082;0.045	B;B	0.19148	0.017;0.024	T	0.14559	-1.0468	9	.	.	.	5.135	2.3732	0.04336	0.1764:0.4213:0.1508:0.2516	.	490;511	P42785;A8MU24	PCP_HUMAN;.	V	490;511;385	ENSP00000317362:D490V;ENSP00000377055:D511V;ENSP00000442077:D385V	.	D	-	2	0	PRCP	82213618	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	-1.032000	0.03574	-0.462000	0.06984	0.383000	0.25322	GAC	.	.	.	none		0.403	PRCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391792.1	NM_005040		A	82535970	T	A	82535970	3	1	1	1	0	0	0	0	1	0	0	0	12459	1667	58	5	25	5	PRCP	11	82535970	Missense_Mutation	SNP	T	TCGA-2K-A9WE-01A-11D-A382-10	39070358	82535970	52470546	35	35											
FAT3	120114	hgsc.bcm.edu	37	chr11	92615968	92615968	+	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	acggaggctcctgcgtgaacGtgttcggctccttcctctgc	4	11	12	14	4	1	1	0	1	1	0	5	2	4	2	3	3	3	3	3	3	1	2			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr11:92615968G>T	ENST00000298047.6	+	23	12363	c.12346G>T	c.(12346-12348)Gtg>Ttg	p.V4116L	FAT3_ENST00000409404.2_Missense_Mutation_p.V4116L|FAT3_ENST00000533797.1_Missense_Mutation_p.V451L|FAT3_ENST00000525166.1_Missense_Mutation_p.V3966L			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	4116	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)				CTGCGTGAACGTGTTCGGCTC	0.632										TCGA Ovarian(4;0.039)																											p.V4116L		Atlas-SNP	.											.	FAT3	1822	.	0			c.G12346T						PASS	.						68	91	83					11																	92615968		2153	4240	6393	SO:0001583	missense	120114	exon23			GTGAACGTGTTCG	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.12346G>T	chr11.hg19:g.92615968G>T	ENSP00000298047:p.Val4116Leu	89.0	0.0	.		96.0	4.0	.	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	G	15.96	2.986927	0.53934	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166;ENST00000533797	T;T;T;D	0.91631	-1.36;-1.36;-1.36;-2.88	5.37	-3.0	0.05480	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.78400	0.4277	N	0.05608	-0.01	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.09377	0.003;0.004	T	0.56631	-0.7947	9	0.26408	T	0.33	.	6.8066	0.23780	0.3084:0.3052:0.3864:0.0	.	4116;4116	Q8TDW7-3;Q8TDW7	.;FAT3_HUMAN	L	4116;4116;3966;451	ENSP00000298047:V4116L;ENSP00000387040:V4116L;ENSP00000432586:V3966L;ENSP00000436399:V451L	ENSP00000298047:V4116L	V	+	1	0	FAT3	92255616	0.989000	0.36119	0.862000	0.33874	0.992000	0.81027	0.389000	0.20751	-0.491000	0.06697	0.655000	0.94253	GTG	.	.	.	none		0.632	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92615968	G	T	92615968	3	4	1	1	0	0	0	0	1	0	0	0	5698	1145	40	4	12436	4	FAT3	11	92615968	Missense_Mutation	SNP	G	TCGA-2K-A9WE-01A-11D-A382-10	10079998	92615968	42390548	36	36											
AMOTL1	154810	hgsc.bcm.edu	37	chr11	94583286	94583286	+	Missense_Mutation	SNP	A	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	gtttcccttctagacaaagaAttcttgaaggaaaaggagaa	16	10	9	6	0	2	4	0	1	2	3	3	6	3	5	1	2	0	1	1	2	7	5			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr11:94583286A>C	ENST00000433060.2	+	7	1797	c.1656A>C	c.(1654-1656)gaA>gaC	p.E552D	AMOTL1_ENST00000317829.8_Missense_Mutation_p.E502D|AMOTL1_ENST00000317837.9_Intron	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	552					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)				TAGACAAAGAATTCTTGAAGG	0.458																																					p.E552D		Atlas-SNP	.											.	AMOTL1	95	.	0			c.A1656C						PASS	.						26	29	28					11																	94583286		1946	4149	6095	SO:0001583	missense	154810	exon7			CAAAGAATTCTTG	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.1656A>C	chr11.hg19:g.94583286A>C	ENSP00000387739:p.Glu552Asp	99.0	0.0	.		105.0	5.0	.	NM_130847	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Missense_Mutation	SNP	ENST00000433060.2	hg19	CCDS44712.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.044077	0.75732	.	.	ENSG00000166025	ENST00000317829;ENST00000542840;ENST00000433060	T;T	0.24723	1.84;1.84	5.82	0.784	0.18578	.	0.000000	0.85682	D	0.000000	T	0.42585	0.1209	M	0.67625	2.065	0.80722	D	1	P;P	0.50710	0.938;0.887	D;P	0.66716	0.946;0.748	T	0.17961	-1.0352	10	0.52906	T	0.07	-23.6644	9.5207	0.39133	0.4586:0.0:0.5414:0.0	.	502;552	Q8IY63-2;Q8IY63	.;AMOL1_HUMAN	D	502;558;552	ENSP00000320968:E502D;ENSP00000387739:E552D	ENSP00000320968:E502D	E	+	3	2	AMOTL1	94222934	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	1.082000	0.30803	0.127000	0.18452	0.533000	0.62120	GAA	.	.	.	none		0.458	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847		C	94583286	A	C	94583286	3	2	1	1	0	0	0	0	1	0	0	0	583	98	4	5	1682	5	AMOTL1	11	94583286	Missense_Mutation	SNP	A	TCGA-2K-A9WE-01A-11D-A382-10	1967318	94583286	40423230	37	37											
VSIG2	23584	hgsc.bcm.edu	37	chr11	124620639	124620639	+	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	taaggttgattagccccaacCcattggtgtagaaatctggt	11	12	10	8	0	1	2	0	1	1	1	1	2	1	2	3	3	2	2	3	3	5	5			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr11:124620639C>T	ENST00000326621.5	-	3	498	c.398G>A	c.(397-399)gGg>gAg	p.G133E	VSIG2_ENST00000403470.1_Missense_Mutation_p.G133E	NM_014312.3	NP_055127.2	Q96IQ7	VSIG2_HUMAN	V-set and immunoglobulin domain containing 2	133	Ig-like V-type.					integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(5)	19	all_hematologic(175;0.215)	Breast(109;0.00663)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0215)		TAGCCCCAACCCATTGGTGTA	0.527																																					p.G133E		Atlas-SNP	.											.	VSIG2	38	.	0			c.G398A						PASS	.						118	101	107					11																	124620639		2201	4299	6500	SO:0001583	missense	23584	exon3			CCCAACCCATTGG	AF061022	CCDS8452.1	11q24	2013-01-11			ENSG00000019102	ENSG00000019102		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing"	17149	protein-coding gene	gene with protein product		606011				9862345	Standard	NM_014312		Approved	CTXL, CTH	uc001qas.3	Q96IQ7	OTTHUMG00000150357	ENST00000326621.5:c.398G>A	chr11.hg19:g.124620639C>T	ENSP00000318684:p.Gly133Glu	81.0	0.0	.		97.0	10.0	.	NM_014312	O95791|Q9NX42	Missense_Mutation	SNP	ENST00000326621.5	hg19	CCDS8452.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.270140	0.80469	.	.	ENSG00000019102	ENST00000326621;ENST00000403470	T;T	0.69435	-0.4;-0.4	5.08	5.08	0.68730	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000006	T	0.72763	0.3501	L	0.31578	0.945	0.42787	D	0.993885	D	0.89917	1.0	D	0.97110	1.0	T	0.73487	-0.3967	10	0.46703	T	0.11	.	15.5135	0.75802	0.0:1.0:0.0:0.0	.	133	Q96IQ7	VSIG2_HUMAN	E	133	ENSP00000318684:G133E;ENSP00000385013:G133E	ENSP00000318684:G133E	G	-	2	0	VSIG2	124125849	0.993000	0.37304	0.991000	0.47740	0.996000	0.88848	4.302000	0.59092	2.640000	0.89533	0.655000	0.94253	GGG	.	.	.	none		0.527	VSIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317785.1	NM_014312		T	124620639	C	T	124620639	3	4	1	1	0	0	0	0	1	0	0	0	17236	623	22	2	605	2	VSIG2	11	124620639	Missense_Mutation	SNP	C	TCGA-2K-A9WE-01A-11D-A382-10	30037353	124620639	10385877	38	38											
GPR162	27239	hgsc.bcm.edu	37	chr12	6933876	6933876	+	Missense_Mutation	SNP	A	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	gacatccctgcaggtcaccaActtggtcagcgccatcgtct	8	9	9	15	2	3	0	2	0	1	0	5	1	4	0	3	2	3	1	3	2	1	1			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr12:6933876A>C	ENST00000311268.3	+	2	1599	c.812A>C	c.(811-813)aAc>aCc	p.N271T	GPR162_ENST00000382315.3_Intron|GPR162_ENST00000428545.2_Intron	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162	271						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						CAGGTCACCAACTTGGTCAGC	0.597																																					p.N271T		Atlas-SNP	.											.	GPR162	55	.	0			c.A812C						PASS	.						66	65	65					12																	6933876		2203	4300	6503	SO:0001583	missense	27239	exon2			TCACCAACTTGGT	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.812A>C	chr12.hg19:g.6933876A>C	ENSP00000311528:p.Asn271Thr	49.0	0.0	.		64.0	8.0	.	NM_019858	Q16664|Q59EH5|Q66K56	Missense_Mutation	SNP	ENST00000311268.3	hg19	CCDS8563.1	.	.	.	.	.	.	.	.	.	.	A	17.64	3.439584	0.63067	.	.	ENSG00000250510	ENST00000311268	T	0.36340	1.26	4.63	4.63	0.57726	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.34658	0.0905	N	0.19112	0.55	0.80722	D	1	D;D	0.63880	0.993;0.982	P;P	0.57846	0.828;0.762	T	0.05852	-1.0860	9	0.29301	T	0.29	.	8.8275	0.35063	0.9156:0.0:0.0844:0.0	.	271;271	B7Z3U3;Q16538	.;GP162_HUMAN	T	271	ENSP00000311528:N271T	ENSP00000311528:N271T	N	+	2	0	GPR162	6804137	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.379000	0.79691	1.946000	0.56461	0.402000	0.26972	AAC	.	.	.	none		0.597	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	NM_019858		C	6933876	A	C	6933876	3	2	1	1	0	0	0	0	1	0	0	0	6673	43	2	5	833	5	GPR162	12	6933876	Missense_Mutation	SNP	A	TCGA-2K-A9WE-01A-11D-A382-10		6933876	126918019	39	39											
PCNX	22990	hgsc.bcm.edu	37	chr14	71493571	71493571	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtaatgtacctttgtgaacaAttggatattcatatttttgg	11	18	8	4	0	1	1	1	1	0	0	1	2	1	2	1	2	2	2	1	2	6	9			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr14:71493571A>G	ENST00000304743.2	+	15	3884	c.3438A>G	c.(3436-3438)caA>caG	p.Q1146Q	PCNX_ENST00000238570.5_Silent_p.Q1146Q|PCNX_ENST00000439984.3_Silent_p.Q1035Q	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1146						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)		TTTGTGAACAATTGGATATTC	0.299																																					p.Q1146Q		Atlas-SNP	.											.	PCNX	198	.	0			c.A3438G						PASS	.						123	119	121					14																	71493571		2203	4298	6501	SO:0001819	synonymous_variant	22990	exon15			TGAACAATTGGAT	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.3438A>G	chr14.hg19:g.71493571A>G		72.0	0.0	.		77.0	6.0	.	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Silent	SNP	ENST00000304743.2	hg19	CCDS9806.1	.	.	.	.	.	.	.	.	.	.	A	7.910	0.736201	0.15574	.	.	ENSG00000100731	ENST00000554691	.	.	.	5.36	1.6	0.23607	.	.	.	.	.	T	0.57504	0.2058	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48736	-0.9009	4	.	.	.	.	9.0245	0.36220	0.6395:0.0:0.3605:0.0	.	.	.	.	S	205	.	.	N	+	2	0	PCNX	70563324	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	2.208000	0.42797	0.024000	0.15214	-1.054000	0.02325	AAT	.	.	.	none		0.299	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		G	71493571	A	G	71493571	2	3	1	1	0	0	0	0	0	0	0	1	11598	98	4	3		3	PCNX	14	71493571	Silent	SNP	A	TCGA-2K-A9WE-01A-11D-A382-10		71493571	35855969	40	40											
CA12	771	hgsc.bcm.edu	37	chr15	63673897	63673897	+	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	ccagcaggagcacggccgccGcgtgcaggctgcgccggggc	5	2	18	16	6	0	0	0	0	0	0	0	1	0	1	4	5	4	4	4	5	0	0			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr15:63673897G>C	ENST00000178638.3	-	1	463	c.23C>G	c.(22-24)gCg>gGg	p.A8G	CA12_ENST00000344366.3_Missense_Mutation_p.A8G|CA12_ENST00000422263.2_Missense_Mutation_p.A8G	NM_001218.3	NP_001209.1	O43570	CAH12_HUMAN	carbonic anhydrase XII	8					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	16					Benzthiazide(DB00562)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Zonisamide(DB00909)	CACGGCCGCCGCGTGCAGGCT	0.692																																					p.A8G		Atlas-SNP	.											.	CA12	33	.	0			c.C23G						PASS	.																																			SO:0001583	missense	771	exon1			GCCGCCGCGTGCA	AF051882	CCDS10185.1, CCDS10186.1	15q22	2004-01-19			ENSG00000074410	ENSG00000074410		"Carbonic anhydrases"	1371	protein-coding gene	gene with protein product		603263				9636197	Standard	NM_001218		Approved	HsT18816	uc002amc.3	O43570	OTTHUMG00000132881	ENST00000178638.3:c.23C>G	chr15.hg19:g.63673897G>C	ENSP00000178638:p.Ala8Gly	110.0	0.0	.		99.0	13.0	.	NM_206925	B2RE24|Q53YE5|Q9BWG2	Missense_Mutation	SNP	ENST00000178638.3	hg19	CCDS10185.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.289415	0.80914	.	.	ENSG00000074410	ENST00000178638;ENST00000344366;ENST00000422263	T;T;D	0.82344	-0.5;-0.54;-1.6	4.49	3.56	0.40772	.	0.347063	0.26187	N	0.025829	T	0.73249	0.3563	L	0.29908	0.895	0.09310	N	1	B;B;B	0.19583	0.022;0.037;0.022	B;B;B	0.17979	0.009;0.02;0.009	T	0.67035	-0.5772	10	0.87932	D	0	.	10.5982	0.45352	0.0:0.1953:0.8047:0.0	.	8;8;8	B3KUB4;O43570-2;O43570	.;.;CAH12_HUMAN	G	8	ENSP00000178638:A8G;ENSP00000343088:A8G;ENSP00000403028:A8G	ENSP00000178638:A8G	A	-	2	0	CA12	61460950	0.004000	0.15560	0.030000	0.17652	0.720000	0.41350	0.577000	0.23758	1.207000	0.43291	-0.315000	0.08773	GCG	.	.	.	none		0.692	CA12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256370.1	NM_001218		C	63673897	G	C	63673897	3	2	1	1	0	0	0	0	1	0	0	0	2515	1087	38	4	1085	4	CA12	15	63673897	Missense_Mutation	SNP	G	TCGA-2K-A9WE-01A-11D-A382-10		63673897	38857495	41	41											
HS3ST6	64711	hgsc.bcm.edu	37	chr16	1961626	1961626	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtcctggcccgtcatctggtAgaacctgcggttgaagggcc	6	9	14	12	2	2	2	1	1	1	1	3	2	3	2	4	4	2	2	4	4	3	2			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr16:1961626A>G	ENST00000293937.3	-	2	993	c.994T>C	c.(994-996)Tac>Cac	p.Y332H	HS3ST6_ENST00000454677.2_Missense_Mutation_p.Y349H|HS3ST6_ENST00000443547.1_Missense_Mutation_p.Y301H			Q96QI5	HS3S6_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 6	332					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			endometrium(2)|lung(2)	4						GTCATCTGGTAGAACCTGCGG	0.697																																					p.Y301H		Atlas-SNP	.											.	HS3ST6	26	.	0			c.T901C						PASS	.						11	13	12					16																	1961626		2029	4191	6220	SO:0001583	missense	64711	exon2			TCTGGTAGAACCT			16p13.3	2008-10-30	2003-06-11	2003-06-13	ENSG00000162040	ENSG00000162040		"Sulfotransferases, membrane-bound"	14178	protein-coding gene	gene with protein product			"heparan sulfate (glucosamine) 3-O-sulfotransferase 5"	HS3ST5		11157797	Standard	NM_001009606		Approved		uc002cnf.3	Q96QI5	OTTHUMG00000047860	ENST00000293937.3:c.994T>C	chr16.hg19:g.1961626A>G	ENSP00000293937:p.Tyr332His	62.0	0.0	.		76.0	15.0	.	NM_001009606	Q96RX7	Missense_Mutation	SNP	ENST00000293937.3	hg19		.	.	.	.	.	.	.	.	.	.	A	23.7	4.450374	0.84101	.	.	ENSG00000162040	ENST00000293937;ENST00000443547;ENST00000454677	T;T	0.55760	0.5;0.5	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.76126	0.3944	M	0.88842	2.985	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81562	-0.0876	10	0.87932	D	0	.	13.9056	0.63834	1.0:0.0:0.0:0.0	.	332	Q96QI5	HS3S6_HUMAN	H	332;301;371	ENSP00000293937:Y332H;ENSP00000390354:Y301H	ENSP00000293937:Y332H	Y	-	1	0	HS3ST6	1901627	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.233000	0.78125	1.890000	0.54733	0.414000	0.27820	TAC	.	.	.	none		0.697	HS3ST6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001009606		G	1961626	A	G	1961626	3	3	1	1	0	0	0	0	1	0	0	0	7376	420	15	3	38	3	HS3ST6	16	1961626	Missense_Mutation	SNP	A	TCGA-2K-A9WE-01A-11D-A382-10		1961626	88393127	42	42											
PRSS21	10942	hgsc.bcm.edu	37	chr16	2868817	2868817	+	Frame_Shift_Del	DEL	A	A	-																															tgagccctcgctacctggggAattcaccctatgacattgcc																										TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr16:2868817delA	ENST00000005995.3	+	4	439	c.397delA	c.(397-399)aatfs	p.N133fs	PRSS21_ENST00000450020.3_Frame_Shift_Del_p.N133fs|PRSS21_ENST00000455114.1_Frame_Shift_Del_p.N131fs			Q9Y6M0	TEST_HUMAN	protease, serine, 21 (testisin)	133	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				spermatogenesis (GO:0007283)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	15						CTACCTGGGGAATTCACCCTA	0.517																																					p.G132fs		Atlas-INDEL	.											PRSS21,rectum,carcinoma,0,1	PRSS21	32	.	0			c.396delG						PASS	.						211	171	185					16																	2868817		2198	4300	6498	SO:0001589	frameshift_variant	10942	exon4			.	AF058300	CCDS10478.1, CCDS45388.1	16p13.3	2010-05-07			ENSG00000007038	ENSG00000007038		"Serine peptidases / Serine peptidases"	9485	protein-coding gene	gene with protein product		608159				10397266, 9826525	Standard	NM_006799		Approved	ESP-1, TEST1, TESTISIN	uc002crt.4	Q9Y6M0	OTTHUMG00000128931	ENST00000005995.3:c.397delA	chr16.hg19:g.2868817delA	ENSP00000005995:p.Asn133fs	67.0	0.0	0		86.0	10.0	0.116279	NM_144957	Q9NS34|Q9P2V6	Frame_Shift_Del	DEL	ENST00000005995.3	hg19	CCDS10478.1																																																																																			.	.	.	none		0.517	PRSS21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250910.1	NM_006799		-	2868817	A	-	2868817	7	5	1	1	0	1	0	1	0	0	0	0	12628	246	9	0	411	0	PRSS21	16	2868817	Frame_Shift_Del	DEL	A	TCGA-2K-A9WE-01A-11D-A382-10	907191	2868817	87485936	43	43											
CHD9	80205	hgsc.bcm.edu	37	chr16	53326887	53326887	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caaccgactttctcggtgccTaccagtgtaatgcagcctat	9	11	8	13	2	1	0	0	0	1	0	2	1	1	0	4	1	5	2	4	1	4	4			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr16:53326887T>C	ENST00000398510.3	+	28	5520	c.5433T>C	c.(5431-5433)ccT>ccC	p.P1811P	CHD9_ENST00000566029.1_Silent_p.P1811P|CHD9_ENST00000564845.1_Silent_p.P1811P|CHD9_ENST00000447540.1_Silent_p.P1811P			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	1811					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)				TCTCGGTGCCTACCAGTGTAA	0.403																																					p.P1811P		Atlas-SNP	.											.	CHD9	203	.	0			c.T5433C						PASS	.						69	66	67					16																	53326887		1883	4114	5997	SO:0001819	synonymous_variant	80205	exon29			GGTGCCTACCAGT	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.5433T>C	chr16.hg19:g.53326887T>C		189.0	0.0	.		212.0	18.0	.	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Silent	SNP	ENST00000398510.3	hg19																																																																																				.	.	.	none		0.403	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		C	53326887	T	C	53326887	2	2	1	1	0	0	0	0	0	0	0	1	3334	1509	53	3		3	CHD9	16	53326887	Silent	SNP	T	TCGA-2K-A9WE-01A-11D-A382-10	50458070	53326887	37027866	44	44											
USP10	9100	hgsc.bcm.edu	37	chr16	84796615	84796615	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtcgacaagaagatgctgaGgaatacttaggcttcattct	12	11	11	7	1	2	3	1	1	1	2	3	5	2	4	0	3	2	2	0	3	5	4			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr16:84796615G>A	ENST00000219473.7	+	9	1688	c.1575G>A	c.(1573-1575)gaG>gaA	p.E525E	USP10_ENST00000570191.1_Silent_p.E529E	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	525	USP.				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						AAGATGCTGAGGAATACTTAG	0.418																																					p.E529E		Atlas-SNP	.											.	USP10	51	.	0			c.G1587A						PASS	.						161	147	151					16																	84796615		1903	4126	6029	SO:0001819	synonymous_variant	9100	exon10			TGCTGAGGAATAC	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.1575G>A	chr16.hg19:g.84796615G>A		47.0	0.0	.		49.0	7.0	.	NM_001272075	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Silent	SNP	ENST00000219473.7	hg19	CCDS45537.1																																																																																			.	.	.	none		0.418	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1			A	84796615	G	A	84796615	2	1	1	1	0	0	0	0	0	0	0	1	17053	991	35	2		2	USP10	16	84796615	Silent	SNP	G	TCGA-2K-A9WE-01A-11D-A382-10	31469728	84796615	5558138	45	45											
CTNS	1497	hgsc.bcm.edu	37	chr17	3563995	3563995	+	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	ccgaaggccttgccccaaacTaccagcgtttctgcaagcag	10	7	9	15	2	1	0	0	0	1	0	1	1	1	0	5	1	6	3	5	1	4	3			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr17:3563995T>C	ENST00000046640.3	+	0	2029				CTNS_ENST00000441220.2_Silent_p.T282T|CTNS_ENST00000381870.3_Silent_p.T390T|RP11-235E17.6_ENST00000575741.1_RNA	NM_004937.2	NP_004928.2	O60931	CTNS_HUMAN	cystinosin, lysosomal cystine transporter						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)	TGCCCCAAACTACCAGCGTTT	0.602																																					p.T390T		Atlas-SNP	.											.	CTNS	42	.	0			c.T1170C						PASS	.						64	58	60					17																	3563995		2203	4300	6503	SO:0001624	3_prime_UTR_variant	1497	exon13			CCAAACTACCAGC	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.*332T>C	chr17.hg19:g.3563995T>C		169.0	0.0	.		175.0	18.0	.	NM_001031681	D3DTJ5|Q8IZ01|Q9UNK6	Silent	SNP	ENST00000046640.3	hg19	CCDS11031.1																																																																																			.	.	.	none		0.602	CTNS-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317696.1	NM_004937		C	3563995	T	C	3563995	1	2	1	0	1	0	0	0	0	0	0	0	4023	1509	53	3		3	CTNS	17	3563995	3'UTR	SNP	T	TCGA-2K-A9WE-01A-11D-A382-10		3563995	77631215	46	46											
NCOR1	9611	hgsc.bcm.edu	37	chr17	15961807	15961807	+	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	tccgcttgatttgccttaacAacctctggctgataggtctg	7	14	9	11	1	2	2	0	2	2	0	3	2	3	2	3	2	3	2	3	2	3	4			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr17:15961807A>C	ENST00000268712.3	-	38	6245	c.5988T>G	c.(5986-5988)gtT>gtG	p.V1996V	NCOR1_ENST00000395857.3_Silent_p.V580V|NCOR1_ENST00000395851.1_Silent_p.V1893V	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1996	Interaction with C1D. {ECO:0000250}.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		TTGCCTTAACAACCTCTGGCT	0.428																																					p.V1996V		Atlas-SNP	.											.	NCOR1	240	.	0			c.T5988G						PASS	.						180	179	179					17																	15961807		2203	4300	6503	SO:0001819	synonymous_variant	9611	exon38			CTTAACAACCTCT	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.5988T>G	chr17.hg19:g.15961807A>C		78.0	0.0	.		92.0	8.0	.	NM_006311	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Silent	SNP	ENST00000268712.3	hg19	CCDS11175.1																																																																																			.	.	.	none		0.428	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		C	15961807	A	C	15961807	2	2	1	1	0	0	0	0	0	0	0	1	10242	117	5	5		5	NCOR1	17	15961807	Silent	SNP	A	TCGA-2K-A9WE-01A-11D-A382-10	12397812	15961807	65233403	47	47											
IKZF3	22806	hgsc.bcm.edu	37	chr17	37985676	37985676	+	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	ttcattggctgggccttctcCactgtccacattttccattt	5	17	6	13	0	2	0	1	0	1	0	5	0	4	0	4	2	0	1	4	2	0	6			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr17:37985676C>A	ENST00000346872.3	-	3	188	c.127G>T	c.(127-129)Gga>Tga	p.G43*	IKZF3_ENST00000377958.2_Nonsense_Mutation_p.G43*|IKZF3_ENST00000439167.2_Intron|IKZF3_ENST00000377952.2_Nonsense_Mutation_p.G43*|IKZF3_ENST00000394189.2_Nonsense_Mutation_p.G43*|IKZF3_ENST00000535189.1_Intron|IKZF3_ENST00000351680.3_Nonsense_Mutation_p.G43*|IKZF3_ENST00000350532.3_Nonsense_Mutation_p.G43*|IKZF3_ENST00000346243.3_Nonsense_Mutation_p.G43*|IKZF3_ENST00000467757.1_Nonsense_Mutation_p.G43*|IKZF3_ENST00000439016.2_Nonsense_Mutation_p.G43*|IKZF3_ENST00000377945.3_Nonsense_Mutation_p.G43*|IKZF3_ENST00000377944.3_Nonsense_Mutation_p.G43*	NM_012481.4	NP_036613.2	Q9UKT9	IKZF3_HUMAN	IKAROS family zinc finger 3 (Aiolos)	43					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)			GGGCCTTCTCCACTGTCCACA	0.403																																					p.G43X		Atlas-SNP	.											.	IKZF3	79	.	0			c.G127T						PASS	.						182	147	159					17																	37985676		2203	4300	6503	SO:0001587	stop_gained	22806	exon3			CTTCTCCACTGTC	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.127G>T	chr17.hg19:g.37985676C>A	ENSP00000344544:p.Gly43*	72.0	0.0	.		90.0	9.0	.	NM_012481	B4DVV5|Q69BL6|Q69BL7|Q69BL8|Q69BL9|Q69BM0|Q69BM1|Q69BM2|Q69BM3|Q69BM5|Q8N574|Q8WWQ9|Q8WWR0|Q8WWR1|Q8WWR2|Q8WWR3	Nonsense_Mutation	SNP	ENST00000346872.3	hg19	CCDS11346.1	.	.	.	.	.	.	.	.	.	.	C	19.56	3.850524	0.71719	.	.	ENSG00000161405	ENST00000488188;ENST00000346872;ENST00000377945;ENST00000394189;ENST00000377944;ENST00000377958;ENST00000377952;ENST00000351680;ENST00000346243;ENST00000350532;ENST00000467757	.	.	.	5.41	1.04	0.20106	.	1.232630	0.05900	N	0.629846	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	1.0311	7.3734	0.26815	0.0:0.611:0.0:0.389	.	.	.	.	X	43	.	ENSP00000341977:G43X	G	-	1	0	IKZF3	35239202	0.884000	0.30299	0.951000	0.38953	0.945000	0.59286	0.300000	0.19156	-0.019000	0.14055	-0.252000	0.11476	GGA	.	.	.	none		0.403	IKZF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257004.2	NM_012481		A	37985676	C	A	37985676	4	1	1	1	0	0	0	0	0	1	0	0	7623	603	21	4	1426	4	IKZF3	17	37985676	Nonsense_Mutation	SNP	C	TCGA-2K-A9WE-01A-11D-A382-10	22023869	37985676	43209534	48	48											
KRTAP4-5	85289	hgsc.bcm.edu	37	chr17	39305776	39305777	+	In_Frame_Ins	INS	-	-	GCAGCAGCTGGGGCG																															gtcctgcagcaggtggtctgINSgcagcagcaggggcggcagc																								rs146438235		TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr17:39305776_39305777insGCAGCAGCTGGGGCG	ENST00000343246.4	-	1	277_278	c.243_244insCGCCCCAGCTGCTGC	c.(241-246)tgccag>tgcCGCCCCAGCTGCTGCcag	p.80_81insCRPSC		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	80	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)			caggtggtctggcagcagcagg	0.653																																					p.Q82delinsRPSCCQ		Atlas-INDEL	.											.	KRTAP4-5	34	.	0			c.244_245insCGCCCCAGCTGCTGC						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.243_244insCGCCCCAGCTGCTGC	chr17.hg19:g.39305776_39305777insGCAGCAGCTGGGGCG	ENSP00000340546:p.Cys80_Cys81insCysArgProSerCys	45.0	0.0	0		52.0	31.0	0.596154	NM_033188		In_Frame_Ins	INS	ENST00000343246.4	hg19	CCDS32650.1																																																																																			.	.	.	alt		0.653	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1			GCAGCAGCTGGGGCG	39305777	-	GCAGCAGCTGGGGCG	39305776	7	5	1	1	0	1	1	0	0	0	0	0	8561	1357	47	0	305	0	KRTAP4-5	17	39305776	In_Frame_Ins	INS	-	TCGA-2K-A9WE-01A-11D-A382-10	1320100	39305776	41889434	49	49											
NGFR	4804	hgsc.bcm.edu	37	chr17	47590364	47590364	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagtccactgccacatcccCggtgtgagcccaaccgggga	8	6	12	15	2	0	2	0	2	0	0	2	3	2	3	6	3	3	0	6	3	1	0	rs574245308	byFrequency	TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr17:47590364C>T	ENST00000172229.3	+	6	1402	c.1277C>T	c.(1276-1278)cCg>cTg	p.P426L	NGFR_ENST00000504201.1_Missense_Mutation_p.P332L|RP5-1029K10.2_ENST00000514506.1_RNA	NM_002507.3	NP_002498.1	P08138	TNR16_HUMAN	nerve growth factor receptor	426					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)					GCCACATCCCCGGTGTGAGCC	0.711													C|||	2	0.000399361	0	0	5008	,	,		11944	0.001		0	False		,,,				2504	0.001				p.P426L		Atlas-SNP	.											.	NGFR	46	.	0			c.C1277T						PASS	.						8	9	8					17																	47590364		2175	4262	6437	SO:0001583	missense	4804	exon6			CATCCCCGGTGTG	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.1277C>T	chr17.hg19:g.47590364C>T	ENSP00000172229:p.Pro426Leu	45.0	0.0	.		64.0	6.0	.	NM_002507	B2R961|B4E096	Missense_Mutation	SNP	ENST00000172229.3	hg19	CCDS11549.1	.	.	.	.	.	.	.	.	.	.	C	17.55	3.417274	0.62622	.	.	ENSG00000064300	ENST00000172229;ENST00000504201	D;D	0.90844	-2.67;-2.74	4.32	4.32	0.51571	.	0.567072	0.17745	N	0.163402	D	0.92384	0.7583	L	0.51422	1.61	0.53688	D	0.999973	D	0.76494	0.999	P	0.58970	0.849	D	0.91837	0.5480	10	0.42905	T	0.14	-22.1632	15.7498	0.77976	0.0:1.0:0.0:0.0	.	426	P08138	TNR16_HUMAN	L	426;332	ENSP00000172229:P426L;ENSP00000421731:P332L	ENSP00000172229:P426L	P	+	2	0	NGFR	44945363	1.000000	0.71417	0.911000	0.35937	0.910000	0.53928	4.158000	0.58150	2.233000	0.73108	0.561000	0.74099	CCG	.	.	.	none		0.711	NGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365150.1			T	47590364	C	T	47590364	3	4	1	1	0	0	0	0	1	0	0	0	10403	652	23	1	1299	1	NGFR	17	47590364	Missense_Mutation	SNP	C	TCGA-2K-A9WE-01A-11D-A382-10	8284588	47590364	33604846	50	50											
CLTC	1213	hgsc.bcm.edu	37	chr17	57754324	57754324	+	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	0	0	0	0	0	0	0	0	0	ttttttcctagattgaaactGcttctgccttggctagaggc	7	16	9	9	0	1	3	0	1	1	2	2	3	2	3	2	2	3	2	2	2	3	8			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr17:57754324G>C	ENST00000269122.3	+	17	2845	c.2571G>C	c.(2569-2571)ctG>ctC	p.L857L	CLTC_ENST00000579456.1_Intron|CLTC_ENST00000393043.1_Silent_p.L857L|CLTC_ENST00000579815.1_3'UTR	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	857	Heavy chain arm.|Proximal segment.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					GATTGAAACTGCTTCTGCCTT	0.403			T	"ALK, TFE3"	"ALCL, renal "																																p.L857L		Atlas-SNP	.		Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	.	CLTC	124	.	0			c.G2571C						PASS	.						42	45	44					17																	57754324		2203	4300	6503	SO:0001819	synonymous_variant	1213	exon17			GAAACTGCTTCTG	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.2571G>C	chr17.hg19:g.57754324G>C		108.0	0.0	.		107.0	24.0	.	NM_004859	D3DU00|Q6N0A0|Q86TF2	Silent	SNP	ENST00000269122.3	hg19	CCDS32696.1																																																																																			.	.	.	none		0.403	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859		C	57754324	G	C	57754324	2	2	1	1	0	0	0	0	0	0	0	1	3568	1306	46	4		4	CLTC	17	57754324	Silent	SNP	G	TCGA-2K-A9WE-01A-11D-A382-10	10163960	57754324	23440886	51	51											
HELZ	9931	hgsc.bcm.edu	37	chr17	65147177	65147177	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cataccaggttcaaggtccaActgacagaggtactgggaag	13	7	12	9	0	1	2	1	1	0	1	2	3	2	3	2	4	3	2	2	4	5	3			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr17:65147177A>G	ENST00000358691.5	-	18	2507	c.2341T>C	c.(2341-2343)Ttg>Ctg	p.L781L	HELZ_ENST00000580168.1_Silent_p.L782L	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	781						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)					TCAAGGTCCAACTGACAGAGG	0.453																																					p.L781L		Atlas-SNP	.											.	HELZ	160	.	0			c.T2341C						PASS	.						152	153	152					17																	65147177		1998	4160	6158	SO:0001819	synonymous_variant	9931	exon18			GGTCCAACTGACA	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.2341T>C	chr17.hg19:g.65147177A>G		191.0	0.0	.		186.0	30.0	.	NM_014877	I6L9H4	Silent	SNP	ENST00000358691.5	hg19	CCDS42374.1																																																																																			.	.	.	none		0.453	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		G	65147177	A	G	65147177	2	3	1	1	0	0	0	0	0	0	0	1	7056	40	2	3		3	HELZ	17	65147177	Silent	SNP	A	TCGA-2K-A9WE-01A-11D-A382-10	7392853	65147177	16048033	52	52											
CEP192	55125	hgsc.bcm.edu	37	chr18	13068196	13068196	+	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	cactcggctagcaggcccttCtgtggtcaaccacatgatgc	8	9	10	14	1	2	1	1	1	1	0	3	1	2	1	2	3	3	2	2	3	2	2			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr18:13068196C>T	ENST00000325971.8	+	21	4523	c.2930C>T	c.(2929-2931)tCt>tTt	p.S977F	CEP192_ENST00000506447.1_Missense_Mutation_p.S1573F|CEP192_ENST00000430049.2_Missense_Mutation_p.S1098F			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	977					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						GCAGGCCCTTCTGTGGTCAAC	0.498																																					p.S1573F		Atlas-SNP	.											.	CEP192	340	.	0			c.C4718T						PASS	.						71	72	72					18																	13068196		2203	4300	6503	SO:0001583	missense	55125	exon23			GCCCTTCTGTGGT	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.2930C>T	chr18.hg19:g.13068196C>T	ENSP00000317156:p.Ser977Phe	86.0	0.0	.		90.0	8.0	.	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	hg19		.	.	.	.	.	.	.	.	.	.	C	19.48	3.834805	0.71373	.	.	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	T;T;T	0.35421	1.31;1.31;1.31	5.37	5.37	0.77165	.	0.077917	0.53938	D	0.000059	T	0.62986	0.2473	M	0.73962	2.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.994	T	0.64170	-0.6470	10	0.56958	D	0.05	-22.4154	19.4881	0.95039	0.0:1.0:0.0:0.0	.	1098;1573	C9JT09;E9PF99	.;.	F	1573;977;977;1098	ENSP00000427550:S1573F;ENSP00000317156:S977F;ENSP00000389190:S1098F	ENSP00000317156:S977F	S	+	2	0	CEP192	13058196	1.000000	0.71417	0.739000	0.30968	0.125000	0.20455	7.163000	0.77524	2.673000	0.90976	0.655000	0.94253	TCT	.	.	.	none		0.498	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142		T	13068196	C	T	13068196	3	4	1	1	0	0	0	0	1	0	0	0	3253	913	32	2	4804	2	CEP192	18	13068196	Missense_Mutation	SNP	C	TCGA-2K-A9WE-01A-11D-A382-10		13068196	65009052	53	53											
LPPR3	79948	hgsc.bcm.edu	37	chr19	815758	815758	+	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	gtagggcatggagagagtgcGgtcatagcactggaagccca	11	6	16	8	1	1	1	1	0	0	1	1	4	1	3	1	4	3	3	1	4	3	2			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr19:815758G>T	ENST00000520876.3	-	3	247	c.169C>A	c.(169-171)Cgc>Agc	p.R57S	MIR3187_ENST00000583431.1_RNA|LPPR3_ENST00000359894.2_Missense_Mutation_p.R57S	NM_001270366.1	NP_001257295.1	Q6T4P5	LPPR3_HUMAN		57						integral component of membrane (GO:0016021)	phosphatidate phosphatase activity (GO:0008195)										GAGAGAGTGCGGTCATAGCAC	0.617																																					p.R57S		Atlas-SNP	.											.	.	.	.	0			c.C169A						PASS	.						76	53	61					19																	815758		2201	4299	6500	SO:0001583	missense	0	exon3			GAGTGCGGTCATA																												ENST00000520876.3:c.169C>A	chr19.hg19:g.815758G>T	ENSP00000430297:p.Arg57Ser	94.0	0.0	.		119.0	5.0	.	NM_001270366	Q86XQ4|Q96EH1|Q9BQF9|Q9HAJ4	Missense_Mutation	SNP	ENST00000520876.3	hg19	CCDS58636.1	.	.	.	.	.	.	.	.	.	.	G	16.82	3.229444	0.58777	.	.	ENSG00000129951	ENST00000300947;ENST00000359894;ENST00000520876;ENST00000521445	T;T	0.49432	0.78;0.78	3.96	3.96	0.45880	.	0.000000	0.85682	U	0.000000	T	0.56702	0.2003	L	0.38692	1.165	0.44309	D	0.997188	D;D	0.89917	1.0;1.0	D;D	0.91635	0.984;0.999	T	0.55003	-0.8208	10	0.36615	T	0.2	-37.6464	13.5102	0.61508	0.0:0.0:1.0:0.0	.	57;57	Q6T4P5;Q6T4P5-3	LPPR3_HUMAN;.	S	57	ENSP00000352962:R57S;ENSP00000430297:R57S	ENSP00000300947:R57S	R	-	1	0	AC006273.1	766758	1.000000	0.71417	0.996000	0.52242	0.647000	0.38526	3.510000	0.53393	1.765000	0.52091	0.313000	0.20887	CGC	.	.	.	none		0.617	LPPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379096.3			T	815758	G	T	815758	3	4	1	1	0	0	0	0	1	0	0	0	8933	1116	39	4	2091	4	LPPR3	19	815758	Missense_Mutation	SNP	G	TCGA-2K-A9WE-01A-11D-A382-10		815758	58313225	54	54											
FCGBP	8857	hgsc.bcm.edu	37	chr19	40366139	40366139	+	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	aggatggccctgaacttggcAggcgtccagcaagcagccct	9	6	13	13	1	0	1	0	1	0	0	1	2	1	2	3	4	4	3	3	4	2	1			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr19:40366139A>T	ENST00000221347.6	-	30	14102	c.14095T>A	c.(14095-14097)Tgc>Agc	p.C4699S		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4699						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)			TGAACTTGGCAGGCGTCCAGC	0.716																																					p.C4699S		Atlas-SNP	.											.	FCGBP	416	.	0			c.T14095A						PASS	.						18	25	23					19																	40366139		2184	4262	6446	SO:0001583	missense	8857	exon30			CTTGGCAGGCGTC	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.14095T>A	chr19.hg19:g.40366139A>T	ENSP00000221347:p.Cys4699Ser	195.0	0.0	.		195.0	15.0	.	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	hg19	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	A	17.80	3.478498	0.63849	.	.	ENSG00000090920	ENST00000221347	D	0.83837	-1.77	4.32	4.32	0.51571	Uncharacterised domain, cysteine-rich (2);	0.000000	0.85682	U	0.000000	D	0.93848	0.8032	H	0.97540	4.025	0.45239	D	0.998249	D	0.89917	1.0	D	0.91635	0.999	D	0.95437	0.8522	10	0.87932	D	0	.	12.8687	0.57953	1.0:0.0:0.0:0.0	.	4699	Q9Y6R7	FCGBP_HUMAN	S	4699	ENSP00000221347:C4699S	ENSP00000221347:C4699S	C	-	1	0	FCGBP	45057979	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	6.590000	0.74085	1.940000	0.56252	0.254000	0.18369	TGC	.	.	.	none		0.716	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		T	40366139	A	T	40366139	3	4	1	1	0	0	0	0	1	0	0	0	5785	188	7	5	2150	5	FCGBP	19	40366139	Missense_Mutation	SNP	A	TCGA-2K-A9WE-01A-11D-A382-10	39550381	40366139	18762844	55	55											
MEGF8	1954	hgsc.bcm.edu	37	chr19	42848184	42848184	+	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	aatgcagttggtgccaaggaGcctgccaagctgcaccccct	9	7	11	14	0	0	0	0	0	0	0	0	1	0	1	5	2	6	4	5	2	3	1			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr19:42848184G>C	ENST00000251268.6	+	10	1747	c.1747G>C	c.(1747-1749)Gcc>Ccc	p.A583P	MEGF8_ENST00000334370.4_Missense_Mutation_p.A583P	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	583	PSI 1.				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)				GTGCCAAGGAGCCTGCCAAGC	0.622																																					p.A583P		Atlas-SNP	.											.	MEGF8	358	.	0			c.G1747C						PASS	.						57	55	56					19																	42848184		2203	4300	6503	SO:0001583	missense	1954	exon10			CAAGGAGCCTGCC	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.1747G>C	chr19.hg19:g.42848184G>C	ENSP00000251268:p.Ala583Pro	51.0	0.0	.		57.0	7.0	.	NM_001271938	A8KAY0|O75097	Missense_Mutation	SNP	ENST00000251268.6	hg19		.	.	.	.	.	.	.	.	.	.	G	18.31	3.595569	0.66219	.	.	ENSG00000105429	ENST00000334370;ENST00000251268	T;T	0.22134	1.97;1.97	4.84	2.57	0.30868	.	0.720289	0.12870	N	0.432362	T	0.15696	0.0378	N	0.14661	0.345	0.80722	D	1	P;D	0.56968	0.828;0.978	B;P	0.50049	0.374;0.629	T	0.07635	-1.0762	10	0.39692	T	0.17	-12.3962	5.5022	0.16834	0.0943:0.0:0.5465:0.3592	.	583;583	Q7Z7M0;Q7Z7M0-2	MEGF8_HUMAN;.	P	583	ENSP00000334219:A583P;ENSP00000251268:A583P	ENSP00000251268:A583P	A	+	1	0	MEGF8	47540024	0.993000	0.37304	0.949000	0.38748	0.988000	0.76386	2.498000	0.45363	0.388000	0.25054	0.486000	0.48141	GCC	.	.	.	none		0.622	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		C	42848184	G	C	42848184	3	2	1	1	0	0	0	0	1	0	0	0	9470	971	34	4	1785	4	MEGF8	19	42848184	Missense_Mutation	SNP	G	TCGA-2K-A9WE-01A-11D-A382-10	2482045	42848184	16280799	56	56											
ZNF235	9310	hgsc.bcm.edu	37	chr19	44792736	44792737	+	Frame_Shift_Ins	INS	-	-	G																															gagacttctttcccaagtgtINSacctgtttatgaagttcaag																										TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr19:44792736_44792737insG	ENST00000291182.4	-	5	953_954	c.851_852insC	c.(850-852)gtafs	p.V284fs	ZNF235_ENST00000589799.1_Intron|ZNF235_ENST00000589248.1_Intron	NM_004234.4	NP_004225.3	Q14590	ZN235_HUMAN	zinc finger protein 235	284					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(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)				TTCCCAAGTGTACCTGTTTATG	0.431																																					p.V284fs		Atlas-Indel,Pindel	.											.	ZNF235	60	.	0			c.852_853insC						PASS	.																																			SO:0001589	frameshift_variant	9310	exon5			.	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.851_852insC	chr19.hg19:g.44792736_44792737insG	ENSP00000291182:p.Val284fs	176.0	0.0	0		178.0	20.0	0.11236	NM_004234	B4DTQ7|O14898|O14899|Q17RR8	Frame_Shift_Ins	INS	ENST00000291182.4	hg19	CCDS33048.1																																																																																			.	.	.	none		0.431	ZNF235-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460732.1			G	44792737	-	G	44792736	7	5	1	1	0	1	1	0	0	0	0	0	17800	1625	57	0	1368	0	ZNF235	19	44792736	Frame_Shift_Ins	INS	-	TCGA-2K-A9WE-01A-11D-A382-10	1944552	44792736	14336247	57	57											
LMTK3	114783	hgsc.bcm.edu	37	chr19	49002400	49002400	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagctgccctcctcctcctcCtcttcttcttccacccacgg	3	12	5	21	1	3	0	0	0	3	0	8	1	8	0	7	1	2	1	7	1	0	3			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr19:49002400C>T	ENST00000600059.1	-	11	2153	c.1926G>A	c.(1924-1926)gaG>gaA	p.E642E	LMTK3_ENST00000270238.3_Silent_p.E671E			Q96Q04	LMTK3_HUMAN	lemur tyrosine kinase 3	642	Pro-rich.				negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(9)|prostate(1)	16		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)		CCTCCTCCTCCTCTTCTTCTT	0.741																																					p.E671E		Atlas-SNP	.											.	LMTK3	125	.	0			c.G2013A						PASS	.						4	4	4					19																	49002400		1578	3534	5112	SO:0001819	synonymous_variant	114783	exon12			CTCCTCCTCTTCT	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.1926G>A	chr19.hg19:g.49002400C>T		82.0	0.0	.		75.0	5.0	.	NM_001080434	Q4G0U1	Silent	SNP	ENST00000600059.1	hg19																																																																																				.	.	.	none		0.741	LMTK3-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000466137.1	NM_052895		T	49002400	C	T	49002400	2	4	1	1	0	0	0	0	0	0	0	1	8867	680	24	2		2	LMTK3	19	49002400	Silent	SNP	C	TCGA-2K-A9WE-01A-11D-A382-10	4209664	49002400	10126583	58	58											
ZNF606	80095	hgsc.bcm.edu	37	chr19	58490071	58490071	+	Missense_Mutation	SNP	T	T	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	tgacagctctgactgaaggaTtttccacatttattgcattc	10	15	7	9	0	1	3	0	3	1	0	3	4	2	4	1	1	2	2	1	1	2	6			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr19:58490071T>G	ENST00000341164.4	-	7	2597	c.1977A>C	c.(1975-1977)aaA>aaC	p.K659N	ZNF606_ENST00000536132.1_Missense_Mutation_p.K569N	NM_025027.3	NP_079303.2	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	659					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)		GACTGAAGGATTTTCCACATT	0.393																																					p.K659N		Atlas-SNP	.											.	ZNF606	155	.	0			c.A1977C						PASS	.						96	89	91					19																	58490071		2203	4300	6503	SO:0001583	missense	80095	exon7			GAAGGATTTTCCA	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.1977A>C	chr19.hg19:g.58490071T>G	ENSP00000343617:p.Lys659Asn	98.0	0.0	.		103.0	7.0	.	NM_025027	A8KAN2|Q8NE04|Q96JH5	Missense_Mutation	SNP	ENST00000341164.4	hg19	CCDS12968.1	.	.	.	.	.	.	.	.	.	.	T	14.84	2.654627	0.47467	.	.	ENSG00000166704	ENST00000341164;ENST00000536132	T;T	0.27890	1.64;1.64	4.69	0.374	0.16183	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.128450	0.35903	N	0.002912	T	0.50360	0.1611	M	0.78456	2.415	0.39034	D	0.959998	D	0.89917	1.0	D	0.91635	0.999	T	0.52586	-0.8556	10	0.87932	D	0	.	8.7437	0.34573	0.0:0.4376:0.0:0.5624	.	659	Q8WXB4	ZN606_HUMAN	N	659;569	ENSP00000343617:K659N;ENSP00000445624:K569N	ENSP00000343617:K659N	K	-	3	2	ZNF606	63181883	0.000000	0.05858	0.996000	0.52242	0.995000	0.86356	-0.162000	0.10012	0.089000	0.17243	0.459000	0.35465	AAA	.	.	.	none		0.393	ZNF606-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405961.1	NM_025027		G	58490071	T	G	58490071	3	3	1	1	0	0	0	0	1	0	0	0	18044	1490	52	5	405	5	ZNF606	19	58490071	Missense_Mutation	SNP	T	TCGA-2K-A9WE-01A-11D-A382-10	9487671	58490071	638912	59	59											
ZNF831	128611	hgsc.bcm.edu	37	chr20	57767752	57767752	+	Missense_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	ttcccagtgggcatccccggGccctggtcagacaggccgcg	5	6	14	16	3	1	1	1	0	0	1	3	1	3	1	5	4	0	1	5	4	0	1			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr20:57767752G>A	ENST00000371030.2	+	1	1678	c.1678G>A	c.(1678-1680)Gcc>Acc	p.A560T		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	560							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)					GCATCCCCGGGCCCTGGTCAG	0.701																																					p.A560T		Atlas-SNP	.											.	ZNF831	287	.	0			c.G1678A						PASS	.						6	8	7					20																	57767752		1848	3995	5843	SO:0001583	missense	128611	exon1			CCCCGGGCCCTGG	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.1678G>A	chr20.hg19:g.57767752G>A	ENSP00000360069:p.Ala560Thr	84.0	0.0	.		125.0	9.0	.	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	hg19	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	G	17.53	3.411578	0.62399	.	.	ENSG00000124203	ENST00000371030	T	0.10005	2.92	5.21	4.25	0.50352	.	.	.	.	.	T	0.10508	0.0257	N	0.20401	0.57	0.28290	N	0.923571	P	0.52463	0.953	P	0.46543	0.52	T	0.06935	-1.0799	9	0.54805	T	0.06	-18.7895	12.2646	0.54670	0.0817:0.0:0.9183:0.0	.	560	Q5JPB2	ZN831_HUMAN	T	560	ENSP00000360069:A560T	ENSP00000360069:A560T	A	+	1	0	ZNF831	57201147	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	2.682000	0.46934	2.423000	0.82170	0.655000	0.94253	GCC	.	.	.	none		0.701	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		A	57767752	G	A	57767752	3	1	1	1	0	0	0	0	1	0	0	0	18197	1203	42	2	1680	2	ZNF831	20	57767752	Missense_Mutation	SNP	G	TCGA-2K-A9WE-01A-11D-A382-10		57767752	5257768	60	60											
TUBGCP6	85378	hgsc.bcm.edu	37	chr22	50659180	50659180	+	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	gccgggtgggagccatgtctGacacagactcccccaagctg	8	6	13	14	1	1	2	0	1	1	1	2	3	2	3	4	2	2	1	4	2	1	0			TCGA-2K-A9WE-01A-11D-A382-10	TCGA-2K-A9WE-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	85477ef3-5aed-4159-ab85-169a86151ec5	1b9c4eb6-95e2-490d-9d51-2d9ffc29a8ad	g.chr22:50659180G>A	ENST00000248846.5	-	16	3712	c.3608C>T	c.(3607-3609)tCa>tTa	p.S1203L	TUBGCP6_ENST00000439308.2_Missense_Mutation_p.S1203L|TUBGCP6_ENST00000491449.1_5'UTR			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	1203	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)		AGCCATGTCTGACACAGACTC	0.627																																					p.S1203L		Atlas-SNP	.											.	TUBGCP6	132	.	0			c.C3608T						PASS	.						70	64	66					22																	50659180		2203	4300	6503	SO:0001583	missense	85378	exon16			ATGTCTGACACAG	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.3608C>T	chr22.hg19:g.50659180G>A	ENSP00000248846:p.Ser1203Leu	50.0	0.0	.		58.0	6.0	.	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Missense_Mutation	SNP	ENST00000248846.5	hg19	CCDS14087.1	.	.	.	.	.	.	.	.	.	.	N	8.442	0.850991	0.17034	.	.	ENSG00000128159	ENST00000248846;ENST00000439308	T;T	0.21361	2.58;2.01	4.54	-0.414	0.12359	.	0.636742	0.12976	N	0.423723	T	0.16385	0.0394	L	0.43923	1.385	0.32013	N	0.601856	B;B;B	0.32382	0.0;0.368;0.005	B;B;B	0.39339	0.003;0.297;0.004	T	0.36890	-0.9729	10	0.10111	T	0.7	.	6.3147	0.21184	0.2362:0.2907:0.4731:0.0	.	1195;1203;1203	B2RWN4;Q96RT7;Q96RT7-3	.;GCP6_HUMAN;.	L	1203	ENSP00000248846:S1203L;ENSP00000397387:S1203L	ENSP00000248846:S1203L	S	-	2	0	TUBGCP6	49001307	0.389000	0.25205	0.055000	0.19348	0.002000	0.02628	1.791000	0.38744	0.048000	0.15891	-0.290000	0.09829	TCA	.	.	.	none		0.627	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461		A	50659180	G	A	50659180	3	1	1	1	0	0	0	0	1	0	0	0	16782	1294	45	2	1891	2	TUBGCP6	22	50659180	Missense_Mutation	SNP	G	TCGA-2K-A9WE-01A-11D-A382-10		50659180	645386	61	61											
CROCC	9696	hgsc.bcm.edu	37	chr1	17275371	17275371	+	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	gcttgaggcccgccgggagcAgctggaagccgaggggcagg	7	3	20	11	3	0	1	0	1	0	0	0	4	0	3	3	6	3	4	3	6	1	1			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr1:17275371A>T	ENST00000375541.5	+	19	2855	c.2786A>T	c.(2785-2787)cAg>cTg	p.Q929L	CROCC_ENST00000467938.1_Intron	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		CGCCGGGAGCAGCTGGAAGCC	0.662																																					p.Q929L		Atlas-SNP	.											.	CROCC	185	.	0			c.A2786T						PASS	.						22	27	26					1																	17275371		2184	4253	6437	SO:0001583	missense	9696	exon19			GGGAGCAGCTGGA	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"rootletin, ciliary rootlet protein"	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.2786A>T	chr1.hg19:g.17275371A>T	ENSP00000364691:p.Gln929Leu	314.0	0.0	.		194.0	40.0	.	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	hg19	CCDS30616.1	.	.	.	.	.	.	.	.	.	.	A	18.59	3.656362	0.67586	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.26518	1.73	4.38	4.38	0.52667	.	.	.	.	.	T	0.34077	0.0885	M	0.82193	2.58	0.51233	D	0.99991	P;B	0.39250	0.665;0.354	B;B	0.39805	0.31;0.31	T	0.23048	-1.0199	9	0.36615	T	0.2	.	12.1806	0.54210	1.0:0.0:0.0:0.0	.	232;929	Q5TZA2-2;Q5TZA2	.;CROCC_HUMAN	L	929;810	ENSP00000364691:Q929L	ENSP00000364691:Q929L	Q	+	2	0	CROCC	17147958	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	5.396000	0.66297	1.923000	0.55706	0.455000	0.32223	CAG	.	.	.	none		0.662	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675		T	17275371	A	T	17275371	3	4	2	1	0	0	0	0	1	0	0	0	3895	188	7	5	2860	5	CROCC	1	17275371	Missense_Mutation	SNP	A	TCGA-2Z-A9J1-01A-11D-A382-10		17275371	231975250	1	62											
SF3A3	10946	hgsc.bcm.edu	37	chr1	38435391	38435391	+	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	tgcgctgtacattttcatgaGtgagatgtcgctgttcctaa	8	15	10	8	2	1	2	1	2	0	1	3	3	2	2	1	0	2	4	1	0	2	5			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr1:38435391G>C	ENST00000373019.4	-	13	1977	c.1022C>G	c.(1021-1023)aCt>aGt	p.T341S	SF3A3_ENST00000448721.2_Missense_Mutation_p.T288S	NM_006802.2	NP_006793.1	Q12874	SF3A3_HUMAN	splicing factor 3a, subunit 3, 60kDa	341					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)				ATTTTCATGAGTGAGATGTCG	0.423																																					p.T341S		Atlas-SNP	.											.	SF3A3	37	.	0			c.C1022G						PASS	.						123	111	115					1																	38435391		2203	4300	6503	SO:0001583	missense	10946	exon13			TCATGAGTGAGAT	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.1022C>G	chr1.hg19:g.38435391G>C	ENSP00000362110:p.Thr341Ser	46.0	0.0	.		74.0	32.0	.	NM_006802	D3DPT5|Q15460|Q5VT87	Missense_Mutation	SNP	ENST00000373019.4	hg19	CCDS428.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.990064	0.93106	.	.	ENSG00000183431	ENST00000373019;ENST00000448721	.	.	.	5.5	5.5	0.81552	Domain of unknown function DUF3449 (1);	0.044218	0.85682	D	0.000000	D	0.86360	0.5914	M	0.90425	3.115	0.80722	D	1	P;B	0.38048	0.616;0.003	P;B	0.53954	0.738;0.009	D	0.87158	0.2213	9	0.66056	D	0.02	-19.5305	19.7862	0.96440	0.0:0.0:1.0:0.0	.	288;341	E7EUT8;Q12874	.;SF3A3_HUMAN	S	341;288	.	ENSP00000362110:T341S	T	-	2	0	SF3A3	38207978	1.000000	0.71417	0.995000	0.50966	0.964000	0.63967	7.397000	0.79903	2.769000	0.95229	0.655000	0.94253	ACT	.	.	.	none		0.423	SF3A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012976.1	NM_006802		C	38435391	G	C	38435391	3	2	2	1	0	0	0	0	1	0	0	0	14161	1029	36	4	503	4	SF3A3	1	38435391	Missense_Mutation	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	21160020	38435391	210815230	2	63											
GUCA2A	2980	hgsc.bcm.edu	37	chr1	42628612	42628612	+	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	ggcagcgtaggcacagatttCacatgtgcccgggtcctcag	8	8	13	12	2	2	1	2	0	0	1	3	1	3	1	2	3	2	3	2	3	1	2			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr1:42628612C>A	ENST00000357001.2	-	3	318	c.313G>T	c.(313-315)Gaa>Taa	p.E105*		NM_033553.2	NP_291031.2	Q02747	GUC2A_HUMAN	guanylate cyclase activator 2A (guanylin)	105						extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	guanylate cyclase activator activity (GO:0030250)|hormone activity (GO:0005179)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|pancreas(1)|skin(1)	5	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GCACAGATTTCACATGTGCCC	0.622																																					p.E105X		Atlas-SNP	.											.	GUCA2A	9	.	0			c.G313T						PASS	.						88	80	83					1																	42628612		2203	4300	6503	SO:0001587	stop_gained	2980	exon3			AGATTTCACATGT	X74322	CCDS465.1	1p35-p34	2014-01-30			ENSG00000197273	ENSG00000197273		"Endogenous ligands"	4682	protein-coding gene	gene with protein product	"prepro-guanylin"	139392		GUCA2		1327879, 7892222	Standard	NM_033553		Approved	STARA	uc001chd.1	Q02747	OTTHUMG00000007023	ENST00000357001.2:c.313G>T	chr1.hg19:g.42628612C>A	ENSP00000349493:p.Glu105*	61.0	0.0	.		51.0	21.0	.	NM_033553		Nonsense_Mutation	SNP	ENST00000357001.2	hg19	CCDS465.1	.	.	.	.	.	.	.	.	.	.	C	15.98	2.993331	0.54041	.	.	ENSG00000197273	ENST00000357001	.	.	.	4.68	4.68	0.58851	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.47245	D	0.999365	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-20.087	12.9568	0.58432	0.0:1.0:0.0:0.0	.	.	.	.	X	105	.	ENSP00000349493:E105X	E	-	1	0	GUCA2A	42401199	1.000000	0.71417	1.000000	0.80357	0.532000	0.34746	3.575000	0.53870	2.440000	0.82611	0.561000	0.74099	GAA	.	.	.	none		0.622	GUCA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000018306.1	NM_033553		A	42628612	C	A	42628612	4	1	2	1	0	0	0	0	0	1	0	0	6898	835	29	4	38	4	GUCA2A	1	42628612	Nonsense_Mutation	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10	4193221	42628612	206622009	3	64											
RAVER2	55225	hgsc.bcm.edu	37	chr1	65272954	65272954	+	Missense_Mutation	SNP	A	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	gcatgttaccattctttccaAatcagcacattgctggacag	11	12	7	11	0	2	0	1	0	1	0	3	1	3	1	2	1	3	4	2	1	2	4			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr1:65272954A>C	ENST00000294428.3	+	9	1555	c.1477A>C	c.(1477-1479)Aat>Cat	p.N493H	RAVER2_ENST00000371072.4_Missense_Mutation_p.N480H|RAVER2_ENST00000430964.2_Intron			Q9HCJ3	RAVR2_HUMAN	ribonucleoprotein, PTB-binding 2	493						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						ATTCTTTCCAAATCAGCACAT	0.468																																					p.N480H		Atlas-SNP	.											.	RAVER2	56	.	0			c.A1438C						PASS	.						47	45	45					1																	65272954		1934	4152	6086	SO:0001583	missense	55225	exon9			TTTCCAAATCAGC	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.1477A>C	chr1.hg19:g.65272954A>C	ENSP00000294428:p.Asn493His	89.0	0.0	.		104.0	37.0	.	NM_018211	Q6P141|Q9NPV7	Missense_Mutation	SNP	ENST00000294428.3	hg19		.	.	.	.	.	.	.	.	.	.	A	6.507	0.461776	0.12342	.	.	ENSG00000162437	ENST00000371072;ENST00000294428	T;T	0.34072	1.38;1.39	5.21	4.06	0.47325	.	0.485339	0.23981	N	0.042670	T	0.17408	0.0418	L	0.55481	1.735	0.80722	D	1	B	0.17667	0.023	B	0.18871	0.023	T	0.03268	-1.1054	10	0.33141	T	0.24	.	10.8402	0.46710	0.8422:0.1578:0.0:0.0	.	480	Q9HCJ3-2	.	H	480;493	ENSP00000360112:N480H;ENSP00000294428:N493H	ENSP00000294428:N493H	N	+	1	0	RAVER2	65045542	0.925000	0.31364	0.987000	0.45799	0.223000	0.24884	1.663000	0.37429	0.786000	0.33708	0.519000	0.50382	AAT	.	.	.	none		0.468	RAVER2-201	KNOWN	basic	protein_coding	protein_coding		NM_018211		C	65272954	A	C	65272954	3	2	2	1	0	0	0	0	1	0	0	0	13108	14	1	5	1472	5	RAVER2	1	65272954	Missense_Mutation	SNP	A	TCGA-2Z-A9J1-01A-11D-A382-10	22644342	65272954	183977667	4	65											
ACADM	34	hgsc.bcm.edu	37	chr1	76200537	76200537	+	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	gaagtatttggggagaatgaCtgaggagccattgatgtgtg	11	11	16	3	0	0	4	0	3	0	1	0	7	0	5	1	3	1	1	1	3	3	3			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr1:76200537C>A	ENST00000370841.4	+	6	886	c.449C>A	c.(448-450)aCt>aAt	p.T150N	ACADM_ENST00000370834.5_Missense_Mutation_p.T183N|ACADM_ENST00000541113.1_Missense_Mutation_p.T114N|ACADM_ENST00000420607.2_Missense_Mutation_p.T154N|ACADM_ENST00000543667.1_Intron	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	150					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)	GGGAGAATGACTGAGGAGCCA	0.348																																					p.T154N		Atlas-SNP	.											.	ACADM	50	.	0			c.C461A	GRCh37	CD054289	ACADM	D		PASS	.						106	99	101					1																	76200537		2203	4300	6503	SO:0001583	missense	34	exon6			GAATGACTGAGGA	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.449C>A	chr1.hg19:g.76200537C>A	ENSP00000359878:p.Thr150Asn	159.0	0.0	.		127.0	46.0	.	NM_001127328	Q5T4U4|Q9NYF1	Missense_Mutation	SNP	ENST00000370841.4	hg19	CCDS668.1	.	.	.	.	.	.	.	.	.	.	C	16.36	3.100368	0.56183	.	.	ENSG00000117054	ENST00000370841;ENST00000370834;ENST00000541113;ENST00000420607	D;D;D;D	0.99722	-6.53;-6.53;-6.53;-6.53	5.63	2.44	0.29823	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, N-terminal (1);Acyl-CoA dehydrogenase/oxidase, N-terminal (1);	0.368444	0.31772	N	0.007086	D	0.99348	0.9771	M	0.79343	2.45	0.80722	D	1	P;B;P;P;B	0.45212	0.523;0.368;0.853;0.453;0.368	B;P;P;B;P	0.57620	0.401;0.545;0.824;0.409;0.545	D	0.99709	1.1006	10	0.72032	D	0.01	.	9.3592	0.38186	0.0:0.697:0.0:0.303	.	114;64;183;154;150	B7Z9I1;B4DVE0;Q5T4U5;P11310-2;P11310	.;.;.;.;ACADM_HUMAN	N	150;183;114;154	ENSP00000359878:T150N;ENSP00000359871:T183N;ENSP00000442324:T114N;ENSP00000409612:T154N	ENSP00000359871:T183N	T	+	2	0	ACADM	75973125	0.395000	0.25254	0.998000	0.56505	0.837000	0.47467	0.937000	0.28951	0.609000	0.30018	0.655000	0.94253	ACT	.	.	.	none		0.348	ACADM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026967.1			A	76200537	C	A	76200537	3	1	2	1	0	0	0	0	1	0	0	0	113	565	20	4	483	4	ACADM	1	76200537	Missense_Mutation	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10	10927583	76200537	173050084	5	66											
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144917856	144917856	+	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	tatcatgtattcgctggcgaAgtttctcaagcaacatttca	11	14	7	9	2	3	0	3	0	1	0	5	1	3	0	0	1	2	4	0	1	5	5			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr1:144917856A>T	ENST00000369354.3	-	11	1619	c.1430T>A	c.(1429-1431)cTt>cAt	p.L477H	PDE4DIP_ENST00000369349.3_Missense_Mutation_p.L477H|PDE4DIP_ENST00000479408.2_Missense_Mutation_p.L264H|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.L477H|PDE4DIP_ENST00000529945.1_Missense_Mutation_p.L640H|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.L543H|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.L614H|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.L614H|PDE4DIP_ENST00000313431.9_Missense_Mutation_p.L640H|PDE4DIP_ENST00000369351.3_Missense_Mutation_p.L477H			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	477					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)		TCGCTGGCGAAGTTTCTCAAG	0.378			T	PDGFRB	MPD																																p.L640H		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.T1919A						PASS	.						250	262	258					1																	144917856		2203	4296	6499	SO:0001583	missense	9659	exon7			TGGCGAAGTTTCT	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.1430T>A	chr1.hg19:g.144917856A>T	ENSP00000358360:p.Leu477His	289.0	0.0	.		361.0	67.0	.	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	hg19	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	A	16.58	3.163110	0.57476	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000369353;ENST00000530740;ENST00000369359;ENST00000369351;ENST00000369349;ENST00000313431;ENST00000529945;ENST00000479408	T;T;T;T;T;T;T;T;T;T	0.76186	3.76;3.81;4.05;4.11;3.86;3.16;3.17;2.04;1.8;-1.0	5.78	5.78	0.91487	.	.	.	.	.	T	0.82006	0.4943	M	0.72894	2.215	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0;1.0	D;D;D;D;D;D	0.91635	0.999;0.98;0.958;0.996;0.986;0.94	D	0.84469	0.0598	9	0.66056	D	0.02	.	14.0619	0.64804	1.0:0.0:0.0:0.0	.	640;264;477;640;543;477	E9PL24;E9PQG4;Q5VU43-7;Q5VU43-2;Q5VU43-3;Q5VU43	.;.;.;.;.;MYOME_HUMAN	H	543;477;477;640;614;614;477;477;640;640;264	ENSP00000327209:L543H;ENSP00000358360:L477H;ENSP00000358363:L477H;ENSP00000435654:L614H;ENSP00000358366:L614H;ENSP00000358357:L477H;ENSP00000358355:L477H;ENSP00000316434:L640H;ENSP00000433392:L640H;ENSP00000436791:L264H	ENSP00000327209:L543H	L	-	2	0	PDE4DIP	143629213	1.000000	0.71417	1.000000	0.80357	0.104000	0.19210	7.379000	0.79691	2.215000	0.71742	0.460000	0.39030	CTT	.	.	.	none		0.378	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		T	144917856	A	T	144917856	3	4	2	1	0	0	0	0	1	0	0	0	11650	72	3	5	5756	5	PDE4DIP	1	144917856	Missense_Mutation	SNP	A	TCGA-2Z-A9J1-01A-11D-A382-10	68717319	144917856	104332765	6	67											
GPR89A	653519	hgsc.bcm.edu	37	chr1	145816732	145816732	+	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	aagatcacctgtacaacataCtgacgtatctgttaaaagcc	15	10	6	10	1	2	2	1	1	1	1	2	2	2	2	2	0	4	3	2	0	7	4			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr1:145816732C>T	ENST00000313835.9	-	3	254	c.111G>A	c.(109-111)caG>caA	p.Q37Q	GPR89A_ENST00000462900.2_Silent_p.Q12Q|GPR89A_ENST00000454423.3_5'UTR|GPR89A_ENST00000534502.1_Silent_p.Q12Q			B7ZAQ6	GPHRA_HUMAN	G protein-coupled receptor 89A	37					intracellular pH reduction (GO:0051452)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein transport (GO:0015031)|regulation of anion transport (GO:0044070)|signal transduction (GO:0007165)	Golgi cisterna membrane (GO:0032580)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)	signal transducer activity (GO:0004871)|voltage-gated anion channel activity (GO:0008308)			breast(1)|large_intestine(3)|lung(1)|skin(1)	6	all_hematologic(18;0.00473)|Acute lymphoblastic leukemia(18;0.0786)		KIRC - Kidney renal clear cell carcinoma(6;0.0764)|Kidney(552;0.118)|Colorectal(543;0.229)			GTACAACATACTGACGTATCT	0.368																																					p.Q37Q		Atlas-SNP	.											.	GPR89A	14	.	0			c.G111A						PASS	.						14	15	15					1																	145816732		2081	4199	6280	SO:0001819	synonymous_variant	653519	exon3			AACATACTGACGT	AB097024	CCDS72857.1, CCDS72858.1	1q21.1	2008-12-17	2007-06-06	2007-06-06	ENSG00000117262	ENSG00000117262			31984	protein-coding gene	gene with protein product		612821					Standard	NM_001097612		Approved	UNQ192	uc001eot.2	B7ZAQ6	OTTHUMG00000013738	ENST00000313835.9:c.111G>A	chr1.hg19:g.145816732C>T		877.0	1.0	.		939.0	222.0	.	NM_001097612	A6NN37|B2RUV3|B3KMN3|B4DLT3|B4DXE7|Q53FQ9|Q5T2V8|Q5T5P5|Q659E2|Q6NVY5|Q9P0S4|Q9Y302	Silent	SNP	ENST00000313835.9	hg19	CCDS41377.1																																																																																			.	.	.	none		0.368	GPR89A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038507.2	NM_001097612		T	145816732	C	T	145816732	2	4	2	1	0	0	0	0	0	0	0	1	6725	564	20	2		2	GPR89A	1	145816732	Silent	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10	898876	145816732	103433889	7	68											
NUP210L	91181	hgsc.bcm.edu	37	chr1	154067632	154067632	+	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	cacttccacaggatttaaagCctgatgatatttaaagaaat	16	12	6	7	0	0	3	0	2	0	1	1	4	1	4	2	1	1	0	2	1	6	6			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr1:154067632C>G	ENST00000368559.3	-	15	2037	c.1966G>C	c.(1966-1968)Gct>Cct	p.A656P	NUP210L_ENST00000271854.3_Splice_Site_p.A656P	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	656					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)			GGATTTAAAGCCTGATGATAT	0.393																																					p.A656P		Atlas-SNP	.											.	NUP210L	181	.	0			c.G1966C						PASS	.						54	53	53					1																	154067632		1840	4079	5919	SO:0001630	splice_region_variant	91181	exon15			TTAAAGCCTGATG	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.1966-1G>C	chr1.hg19:g.154067632C>G		83.0	0.0	.		113.0	41.0	.	NM_001159484	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Missense_Mutation	SNP	ENST00000368559.3	hg19	CCDS41399.1	.	.	.	.	.	.	.	.	.	.	C	15.71	2.913031	0.52439	.	.	ENSG00000143552	ENST00000368559;ENST00000271854	T;T	0.25579	1.79;1.79	5.49	5.49	0.81192	.	0.202371	0.34603	N	0.003823	T	0.32793	0.0841	L	0.40543	1.245	0.44652	D	0.997636	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.01476	-1.1345	10	0.32370	T	0.25	-33.2323	17.1608	0.86803	0.0:1.0:0.0:0.0	.	656;656	E7EP56;Q5VU65	.;P210L_HUMAN	P	656	ENSP00000357547:A656P;ENSP00000271854:A656P	ENSP00000271854:A656P	A	-	1	0	NUP210L	152334256	1.000000	0.71417	0.999000	0.59377	0.209000	0.24338	3.005000	0.49521	2.569000	0.86673	0.555000	0.69702	GCT	.	.	.	none		0.393	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308	Missense_Mutation	G	154067632	C	G	154067632	5	3	2	1	0	0	0	0	0	0	1	0	10768	753	26	4	3804	4	NUP210L	1	154067632	Splice_Site	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10	8250900	154067632	95182989	8	69											
NCF2	4688	hgsc.bcm.edu	37	chr1	183543737	183543737	+	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	cctccttcttggcatacatgAaagcaatgttatataacacc	13	12	5	11	0	1	1	0	1	1	0	2	1	2	1	3	1	3	3	3	1	6	6			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr1:183543737A>T	ENST00000367535.3	-	4	637	c.386T>A	c.(385-387)tTc>tAc	p.F129Y	NCF2_ENST00000418089.1_Intron|NCF2_ENST00000367536.1_Missense_Mutation_p.F129Y|NCF2_ENST00000413720.1_Intron	NM_000433.3	NP_000424.2	P19878	NCF2_HUMAN	neutrophil cytosolic factor 2	129					aging (GO:0007568)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cellular response to hormone stimulus (GO:0032870)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of blood pressure (GO:0045777)|positive regulation of neuron apoptotic process (GO:0043525)|respiratory burst (GO:0045730)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucose (GO:0009749)|response to hyperoxia (GO:0055093)|response to laminar fluid shear stress (GO:0034616)|response to lipopolysaccharide (GO:0032496)|response to progesterone (GO:0032570)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|NADPH oxidase complex (GO:0043020)|nucleolus (GO:0005730)|phagolysosome (GO:0032010)	electron carrier activity (GO:0009055)|protein C-terminus binding (GO:0008022)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30					Dextromethorphan(DB00514)	GGCATACATGAAAGCAATGTT	0.438																																					p.F129Y		Atlas-SNP	.											.	NCF2	69	.	0			c.T386A						PASS	.						188	171	177					1																	183543737		2203	4300	6503	SO:0001583	missense	4688	exon5			TACATGAAAGCAA	BC001606	CCDS1356.1, CCDS53446.1, CCDS53447.1	1q25	2014-09-17	2008-07-31		ENSG00000116701	ENSG00000116701		"Tetratricopeptide (TTC) repeat domain containing"	7661	protein-coding gene	gene with protein product	"NADPH oxidase activator 2", "chronic granulomatous disease, autosomal 2"	608515	"neutrophil cytosolic factor 2 (65kD, chronic granulomatous disease, autosomal 2)"				Standard	NM_000433		Approved	p67phox, NOXA2	uc001gqk.4	P19878	OTTHUMG00000035329	ENST00000367535.3:c.386T>A	chr1.hg19:g.183543737A>T	ENSP00000356505:p.Phe129Tyr	65.0	0.0	.		113.0	37.0	.	NM_001127651	B2R6Q1|B4DKQ7|B4DQA7|E9PHJ2|E9PHX3|Q2PP06|Q8NFC7|Q9BV51	Missense_Mutation	SNP	ENST00000367535.3	hg19	CCDS1356.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.348077	0.82132	.	.	ENSG00000116701	ENST00000367536;ENST00000392014;ENST00000367535	T;T	0.65549	-0.16;-0.16	5.32	4.19	0.49359	Tetratricopeptide-like helical (1);	0.309294	0.36893	N	0.002350	T	0.58090	0.2098	L	0.36672	1.1	0.80722	D	1	P	0.41131	0.739	P	0.46076	0.503	T	0.60697	-0.7212	10	0.87932	D	0	-10.1463	11.0383	0.47816	0.9268:0.0:0.0732:0.0	.	129	P19878	NCF2_HUMAN	Y	129;157;129	ENSP00000356506:F129Y;ENSP00000356505:F129Y	ENSP00000356505:F129Y	F	-	2	0	NCF2	181810360	0.990000	0.36364	0.986000	0.45419	0.961000	0.63080	7.871000	0.87180	0.969000	0.38237	0.533000	0.62120	TTC	.	.	.	none		0.438	NCF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085483.1	NM_000433		T	183543737	A	T	183543737	3	4	2	1	0	0	0	0	1	0	0	0	10224	246	9	5	1242	5	NCF2	1	183543737	Missense_Mutation	SNP	A	TCGA-2Z-A9J1-01A-11D-A382-10	29476105	183543737	65706884	9	70											
PRELP	5549	hgsc.bcm.edu	37	chr1	203452750	203452750	+	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	aagatagaccagagggtgctGgagaaactgcccggcctggt	11	6	15	9	1	0	4	0	0	0	4	0	5	0	4	3	4	3	1	3	4	3	1			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr1:203452750G>T	ENST00000343110.2	+	2	565	c.438G>T	c.(436-438)ctG>ctT	p.L146L		NM_002725.3|NM_201348.1	NP_002716.1|NP_958505.1	P51888	PRELP_HUMAN	proline/arginine-rich end leucine-rich repeat protein	146					carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			BRCA - Breast invasive adenocarcinoma(75;0.109)			AGAGGGTGCTGGAGAAACTGC	0.592																																					p.L146L		Atlas-SNP	.											.	PRELP	63	.	0			c.G438T						PASS	.						87	87	87					1																	203452750		2203	4300	6503	SO:0001819	synonymous_variant	5549	exon2			GGTGCTGGAGAAA	BC032498	CCDS1438.1	1q32	2008-02-05	2005-07-24		ENSG00000188783	ENSG00000188783		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	9357	protein-coding gene	gene with protein product	"prolargin proteoglycan"	601914	"proline arginine-rich end leucine-rich repeat protein"				Standard	NM_002725		Approved	SLRR2A, prolargin	uc001gzt.3	P51888	OTTHUMG00000035911	ENST00000343110.2:c.438G>T	chr1.hg19:g.203452750G>T		224.0	0.0	.		166.0	61.0	.	NM_201348	Q6FG38	Silent	SNP	ENST00000343110.2	hg19	CCDS1438.1																																																																																			.	.	.	none		0.592	PRELP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087474.1	NM_002725		T	203452750	G	T	203452750	2	4	2	1	0	0	0	0	0	0	0	1	12483	1335	47	4		4	PRELP	1	203452750	Silent	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	19909013	203452750	45797871	10	71											
PUM2	23369	hgsc.bcm.edu	37	chr2	20463043	20463043	+	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	aagcggttgtttctgaaatcTtccaataatctactgcggcc	10	13	8	10	2	3	1	0	1	3	0	4	1	4	1	2	2	3	2	2	2	5	5			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr2:20463043T>A	ENST00000361078.2	-	13	2158	c.2136A>T	c.(2134-2136)gaA>gaT	p.E712D	PUM2_ENST00000536417.1_Missense_Mutation_p.E656D|PUM2_ENST00000403432.1_Missense_Mutation_p.E712D|PUM2_ENST00000319801.5_Missense_Mutation_p.E633D|PUM2_ENST00000338086.5_Missense_Mutation_p.E712D			Q8TB72	PUM2_HUMAN	pumilio RNA-binding family member 2	712	PUM-HD. {ECO:0000255|PROSITE- ProRule:PRU00318}.				regulation of translation (GO:0006417)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear membrane (GO:0031965)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(7)|lung(13)|ovary(2)|prostate(4)|urinary_tract(3)	42	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTCTGAAATCTTCCAATAATC	0.443																																					p.E712D		Atlas-SNP	.											.	PUM2	91	.	0			c.A2136T						PASS	.						68	69	68					2																	20463043		2203	4300	6503	SO:0001583	missense	23369	exon13			GAAATCTTCCAAT	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.2136A>T	chr2.hg19:g.20463043T>A	ENSP00000354370:p.Glu712Asp	109.0	0.0	.		115.0	74.0	.	NM_015317	B3KSL0|B4E2B6|D6W527|O00234|Q53TV7|Q8WY43|Q9HAN2	Missense_Mutation	SNP	ENST00000361078.2	hg19		.	.	.	.	.	.	.	.	.	.	T	14.84	2.655861	0.47467	.	.	ENSG00000055917	ENST00000338086;ENST00000361078;ENST00000319801;ENST00000440577;ENST00000403432;ENST00000536417	T;T;T;T;T;T	0.13420	2.59;2.59;2.59;2.59;2.59;2.59	5.71	5.71	0.89125	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.24044	0.0582	L	0.50993	1.605	0.58432	D	0.999992	B;B;B;P	0.45594	0.001;0.04;0.068;0.862	B;B;B;P	0.56788	0.005;0.042;0.091;0.806	T	0.01290	-1.1394	10	0.39692	T	0.17	-15.117	8.3961	0.32557	0.0:0.146:0.0:0.854	.	656;633;712;712	B4E2B6;B7ZL34;Q8TB72-3;Q8TB72	.;.;.;PUM2_HUMAN	D	712;712;633;524;712;656	ENSP00000338173:E712D;ENSP00000354370:E712D;ENSP00000326746:E633D;ENSP00000409905:E524D;ENSP00000385992:E712D;ENSP00000440093:E656D	ENSP00000326746:E633D	E	-	3	2	PUM2	20326524	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.113000	0.41902	2.171000	0.68590	0.533000	0.62120	GAA	.	.	.	none		0.443	PUM2-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015317		A	20463043	T	A	20463043	3	1	2	1	0	0	0	0	1	0	0	0	12839	1606	56	5	1090	5	PUM2	2	20463043	Missense_Mutation	SNP	T	TCGA-2Z-A9J1-01A-11D-A382-10		20463043	222736330	11	72											
DNMT3A	1788	hgsc.bcm.edu	37	chr2	25467157	25467158	+	Frame_Shift_Ins	INS	-	-	G																															gtcttccttaatggctgcctINSgggcagcccccggccccacc																										TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr2:25467157_25467158insG	ENST00000264709.3	-	15	2054_2055	c.1717_1718insC	c.(1717-1719)cagfs	p.Q573fs	DNMT3A_ENST00000474887.1_5'UTR|DNMT3A_ENST00000321117.5_Frame_Shift_Ins_p.Q573fs|DNMT3A_ENST00000380746.4_Frame_Shift_Ins_p.Q384fs|DNMT3A_ENST00000402667.1_Frame_Shift_Ins_p.Q350fs	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	573	ADD. {ECO:0000255|PROSITE- ProRule:PRU00865}.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)	p.A572_A574del(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AATGGCTGCCTGGGCAGCCCCC	0.658			"Mis, F, N, S"		AML																																p.Q573fs		Atlas-Indel,Pindel	.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	.	DNMT3A	1807	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.1718_1719insC						PASS	.																																			SO:0001589	frameshift_variant	1788	exon15			.		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.1718dupC	chr2.hg19:g.25467160_25467160dupG	ENSP00000264709:p.Gln573fs	119.0	0.0	0		86.0	55.0	0.639535	NM_175629	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Frame_Shift_Ins	INS	ENST00000264709.3	hg19	CCDS33157.1																																																																																			.	.	.	none		0.658	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552		G	25467158	-	G	25467157	7	5	2	1	0	1	1	0	0	0	0	0	4678	1580	55	0	1056	0	DNMT3A	2	25467157	Frame_Shift_Ins	INS	-	TCGA-2Z-A9J1-01A-11D-A382-10	5004114	25467157	217732216	12	73											
SLC8A1	6546	hgsc.bcm.edu	37	chr2	40387976	40387976	+	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	caaccacaagggccaggtttGtcttcttaatgagtttgtcc	9	13	9	10	0	2	1	0	1	2	0	3	1	3	1	3	2	1	2	3	2	3	4			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr2:40387976G>T	ENST00000403092.1	-	9	2231	c.2198C>A	c.(2197-2199)aCa>aAa	p.T733K	SLC8A1-AS1_ENST00000599740.1_RNA|SLC8A1-AS1_ENST00000601679.1_RNA|SLC8A1_ENST00000332839.4_Missense_Mutation_p.T733K|SLC8A1_ENST00000406391.2_Missense_Mutation_p.T697K|SLC8A1-AS1_ENST00000444629.1_RNA|SLC8A1-AS1_ENST00000593848.1_RNA|SLC8A1-AS1_ENST00000599268.1_RNA|SLC8A1_ENST00000542756.1_Missense_Mutation_p.T728K|SLC8A1_ENST00000405901.3_Missense_Mutation_p.T728K|SLC8A1-AS1_ENST00000597170.1_RNA|SLC8A1-AS1_ENST00000593878.1_RNA|SLC8A1_ENST00000402441.1_Missense_Mutation_p.T697K|SLC8A1_ENST00000542024.1_Missense_Mutation_p.T697K|SLC8A1-AS1_ENST00000598247.1_RNA|SLC8A1-AS1_ENST00000596532.1_RNA|SLC8A1-AS1_ENST00000435515.1_RNA|SLC8A1_ENST00000405269.1_Missense_Mutation_p.T697K|SLC8A1_ENST00000406785.2_Missense_Mutation_p.T697K|SLC8A1-AS1_ENST00000599956.1_RNA|SLC8A1_ENST00000408028.2_Missense_Mutation_p.T725K|SLC8A1-AS1_ENST00000597385.1_RNA			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1	733					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)	GGCCAGGTTTGTCTTCTTAAT	0.413																																					p.T733K		Atlas-SNP	.											.	SLC8A1	221	.	0			c.C2198A						PASS	.						133	128	130					2																	40387976		2203	4300	6503	SO:0001583	missense	6546	exon8			AGGTTTGTCTTCT		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.2198C>A	chr2.hg19:g.40387976G>T	ENSP00000384763:p.Thr733Lys	49.0	0.0	.		104.0	83.0	.	NM_021097	A8K6N1|D6W595|O95849|Q4QQG6|Q587I6|Q59GN4|Q9UBL8|Q9UD55|Q9UDN1|Q9UDN2|Q9UKX6	Missense_Mutation	SNP	ENST00000403092.1	hg19	CCDS1806.1	.	.	.	.	.	.	.	.	.	.	G	19.10	3.762222	0.69763	.	.	ENSG00000183023	ENST00000406785;ENST00000378715;ENST00000542756;ENST00000403092;ENST00000405901;ENST00000402441;ENST00000405269;ENST00000332839;ENST00000408028;ENST00000535962;ENST00000406391;ENST00000542024	T;T;T;T;T;T;T;T;T;T	0.30448	1.56;1.57;1.58;1.57;1.56;1.56;1.58;1.53;1.56;1.56	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.53367	0.1792	M	0.72479	2.2	0.80722	D	1	D;D;P;P	0.57899	0.96;0.981;0.57;0.893	P;P;B;B	0.61397	0.888;0.604;0.274;0.344	T	0.51957	-0.8639	10	0.56958	D	0.05	.	17.4714	0.87647	0.0:0.0:1.0:0.0	.	697;720;728;733	P32418-2;P32418-3;F6VPY9;P32418	.;.;.;NAC1_HUMAN	K	697;733;728;733;728;697;697;733;725;720;697;697	ENSP00000383886:T697K;ENSP00000440727:T728K;ENSP00000384763:T733K;ENSP00000385678:T728K;ENSP00000385188:T697K;ENSP00000385535:T697K;ENSP00000332931:T733K;ENSP00000384908:T725K;ENSP00000385811:T697K;ENSP00000443515:T697K	ENSP00000332931:T733K	T	-	2	0	SLC8A1	40241480	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.498000	0.97972	2.788000	0.95919	0.650000	0.86243	ACA	.	.	.	none		0.413	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	NM_021097		T	40387976	G	T	40387976	3	4	2	1	0	0	0	0	1	0	0	0	14719	1377	48	4	735	4	SLC8A1	2	40387976	Missense_Mutation	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	14920819	40387976	202811397	13	74											
ZFP36L2	678	hgsc.bcm.edu	37	chr2	43451900	43451925	+	Frame_Shift_Del	DEL	GCCCCCGGCGCCAGCAGGTCCTCGGC	GCCCCCGGCGCCAGCAGGTCCTCGGC	-																															acgagcaggccgcgcacgggGcccccggcgccagcaggtcc																								rs1050381		TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	GCCCCCGGCGCCAGCAGGTCCTCGGC	GCCCCCGGCGCCAGCAGGTCCTCGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr2:43451900_43451925delGCCCCCGGCGCCAGCAGGTCCTCGGC	ENST00000282388.3	-	2	1311_1336	c.1018_1043delGCCGAGGACCTGCTGGCGCCGGGGGC	c.(1018-1044)gccgaggacctgctggcgccgggggccfs	p.AEDLLAPGA340fs	THADA_ENST00000330266.7_Intron	NM_006887.4	NP_008818.3	P47974	TISD_HUMAN	ZFP36 ring finger protein-like 2	340					cell proliferation (GO:0008283)|definitive hemopoiesis (GO:0060216)|hemopoiesis (GO:0030097)|mRNA catabolic process (GO:0006402)|negative regulation of stem cell differentiation (GO:2000737)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	15		Acute lymphoblastic leukemia(82;0.00323)|all_hematologic(82;0.00824)				CGCGCACGGGGCCCCCGGCGCCAGCAGGTCCTCGGCGCCCCCGGTG	0.77																																					p.340_348del		Atlas-Indel,Pindel	.											.	ZFP36L2	56	.	0			c.1019_1044del						PASS	.																																			SO:0001589	frameshift_variant	678	exon2			.	X78992	CCDS1811.1	2p22.3-p21	2012-11-27	2012-11-27	2001-11-23	ENSG00000152518	ENSG00000152518		"RING-type (C3HC4) zinc fingers"	1108	protein-coding gene	gene with protein product		612053	"zinc finger protein 36, C3H type-like 1", "zinc finger protein 36, C3H type-like 2"	BRF2		7835719, 8545129, 14981510, 17172869	Standard	NM_006887		Approved	ERF2, RNF162C, TIS11D	uc002rsv.4	P47974	OTTHUMG00000128642	ENST00000282388.3:c.1018_1043delGCCGAGGACCTGCTGGCGCCGGGGGC	chr2.hg19:g.43451900_43451925delGCCCCCGGCGCCAGCAGGTCCTCGGC	ENSP00000282388:p.Ala340fs	47.0	0.0	0		29.0	17.0	0.586207	NM_006887	Q53TB4|Q9BSJ3	Frame_Shift_Del	DEL	ENST00000282388.3	hg19	CCDS1811.1																																																																																			.	.	.	none		0.77	ZFP36L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250513.2	NM_006887		-	43451925	GCCCCCGGCGCCAGCAGGTCCTCGGC	-	43451900	7	5	2	1	0	1	0	1	0	0	0	0	17659	1203	42	0	445	0	ZFP36L2	2	43451900	Frame_Shift_Del	DEL	GCCCCCGGCGCCAGCAGGTCCTCGGC	TCGA-2Z-A9J1-01A-11D-A382-10	3063924	43451900	199747473	14	75											
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54839382	54839392	+	Frame_Shift_Del	DEL	CATCTTGAGAA	CATCTTGAGAA	-																															tcctgaaggagcagagagtcCatcttgagaacatggggtcc																										TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	CATCTTGAGAA	CATCTTGAGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr2:54839382_54839392delCATCTTGAGAA	ENST00000356805.4	+	4	666_676	c.385_395delCATCTTGAGAA	c.(385-396)catcttgagaacfs	p.HLEN129fs	SPTBN1_ENST00000333896.5_Frame_Shift_Del_p.HLEN116fs	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	129	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				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)			GCAGAGAGTCCATCTTGAGAACATGGGGTCC	0.555																																					p.128_132del		Atlas-Indel,Pindel	.											.	SPTBN1	378	.	0			c.384_394del						PASS	.																																			SO:0001589	frameshift_variant	6711	exon4			.		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.385_395delCATCTTGAGAA	chr2.hg19:g.54839382_54839392delCATCTTGAGAA	ENSP00000349259:p.His129fs	98.0	0.0	0		122.0	67.0	0.54918	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Frame_Shift_Del	DEL	ENST00000356805.4	hg19	CCDS33198.1																																																																																			.	.	.	none		0.555	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			-	54839392	CATCTTGAGAA	-	54839382	7	5	2	1	0	1	0	1	0	0	0	0	15131	594	21	0	508	0	SPTBN1	2	54839382	Frame_Shift_Del	DEL	CATCTTGAGAA	TCGA-2Z-A9J1-01A-11D-A382-10	11387482	54839382	188359991	15	76											
GFPT1	2673	hgsc.bcm.edu	37	chr2	69575353	69575353	+	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	gtgtttgcacagctcgtccgGggtgatctcctgcagttcgt	4	13	13	11	3	1	1	0	1	1	0	5	1	2	1	2	2	3	5	2	2	0	2			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr2:69575353G>T	ENST00000357308.4	-	11	1137	c.959C>A	c.(958-960)cCc>cAc	p.P320H	GFPT1_ENST00000361060.5_Missense_Mutation_p.P302H	NM_001244710.1	NP_001231639.1	Q06210	GFPT1_HUMAN	glutamine--fructose-6-phosphate transaminase 1	320	Isomerase.				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						AGCTCGTCCGGGGTGATCTCC	0.453																																					p.P320H		Atlas-SNP	.											.	GFPT1	38	.	0			c.C959A						PASS	.						170	155	160					2																	69575353		2203	4300	6503	SO:0001583	missense	2673	exon11			CGTCCGGGGTGAT		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.959C>A	chr2.hg19:g.69575353G>T	ENSP00000349860:p.Pro320His	66.0	0.0	.		113.0	5.0	.	NM_001244710	Q53QE6|Q9BXF8	Missense_Mutation	SNP	ENST00000357308.4	hg19	CCDS58713.1	.	.	.	.	.	.	.	.	.	.	G	14.97	2.693268	0.48202	.	.	ENSG00000198380	ENST00000357308;ENST00000361060	T;T	0.44083	0.95;0.93	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.36026	0.0952	N	0.01446	-0.86	0.80722	D	1	P	0.48162	0.906	P	0.61592	0.891	T	0.52457	-0.8573	10	0.27082	T	0.32	-14.1203	18.5685	0.91126	0.0:0.0:1.0:0.0	.	302	Q06210-2	.	H	320;302	ENSP00000349860:P320H;ENSP00000354347:P302H	ENSP00000349860:P320H	P	-	2	0	GFPT1	69428857	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.613000	0.98350	2.861000	0.98227	0.655000	0.94253	CCC	.	.	.	none		0.453	GFPT1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				T	69575353	G	T	69575353	3	4	2	1	0	0	0	0	1	0	0	0	6352	1232	43	4	1180	4	GFPT1	2	69575353	Missense_Mutation	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	14735971	69575353	173624020	16	77											
TMEM87B	84910	hgsc.bcm.edu	37	chr2	112858240	112858240	+	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	agatgattctgatgatgaaaTtgaggaattcatggtaactt	14	14	10	3	0	2	6	1	5	1	1	2	7	2	7	0	2	1	1	0	2	3	5			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr2:112858240T>A	ENST00000283206.4	+	15	1787	c.1418T>A	c.(1417-1419)aTt>aAt	p.I473N	TMEM87B_ENST00000463427.1_3'UTR	NM_032824.2	NP_116213.1	Q96K49	TM87B_HUMAN	transmembrane protein 87B	473						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)	19						GATGATGAAATTGAGGAATTC	0.294																																					p.I473N		Atlas-SNP	.											.	TMEM87B	52	.	0			c.T1418A						PASS	.						92	94	93					2																	112858240		2202	4290	6492	SO:0001583	missense	84910	exon15			ATGAAATTGAGGA	AC092645	CCDS33275.1	2q13	2008-02-05			ENSG00000153214	ENSG00000153214			25913	protein-coding gene	gene with protein product							Standard	NM_032824		Approved	FLJ14681	uc002thm.2	Q96K49	OTTHUMG00000153266	ENST00000283206.4:c.1418T>A	chr2.hg19:g.112858240T>A	ENSP00000283206:p.Ile473Asn	152.0	0.0	.		215.0	154.0	.	NM_032824	A8K2M9|Q1RLN2|Q53R54	Missense_Mutation	SNP	ENST00000283206.4	hg19	CCDS33275.1	.	.	.	.	.	.	.	.	.	.	T	15.93	2.977833	0.53720	.	.	ENSG00000153214	ENST00000283206	.	.	.	5.85	4.68	0.58851	.	0.677566	0.15093	N	0.280964	T	0.41766	0.1173	N	0.19112	0.55	0.40147	D	0.976904	B	0.02656	0.0	B	0.06405	0.002	T	0.18777	-1.0326	9	0.32370	T	0.25	-5.7707	10.6417	0.45596	0.1437:0.0:0.0:0.8563	.	473	Q96K49	TM87B_HUMAN	N	473	.	ENSP00000283206:I473N	I	+	2	0	TMEM87B	112574711	1.000000	0.71417	0.920000	0.36463	0.996000	0.88848	2.567000	0.45956	1.013000	0.39391	0.528000	0.53228	ATT	.	.	.	none		0.294	TMEM87B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330500.1	NM_032824		A	112858240	T	A	112858240	3	1	2	1	0	0	0	0	1	0	0	0	16223	1493	52	5	1476	5	TMEM87B	2	112858240	Missense_Mutation	SNP	T	TCGA-2Z-A9J1-01A-11D-A382-10	43282887	112858240	130341133	17	78											
PDCD6IP	10015	hgsc.bcm.edu	37	chr3	33894165	33894165	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaactagatcgagtctatggAggtcttacaactaaagtcca	14	10	9	8	1	2	1	0	0	2	1	4	4	3	2	1	2	3	0	1	2	7	4			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr3:33894165A>G	ENST00000307296.3	+	13	2204	c.1827A>G	c.(1825-1827)ggA>ggG	p.G609G	PDCD6IP_ENST00000457054.2_Silent_p.G614G			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	609	Interaction with EIAV p9.|Self-association.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						GAGTCTATGGAGGTCTTACAA	0.338																																					p.G614G		Atlas-SNP	.											.	PDCD6IP	62	.	0			c.A1842G						PASS	.						14	15	14					3																	33894165		1895	4059	5954	SO:0001819	synonymous_variant	10015	exon13			CTATGGAGGTCTT	BC020066	CCDS2660.1, CCDS54561.1	3p22.3	2012-08-30	2001-11-29		ENSG00000170248	ENSG00000170248			8766	protein-coding gene	gene with protein product	"ALG-2 interacting protein X"	608074	"programmed cell death 6-interacting protein"			9880530	Standard	NM_001162429		Approved	Alix, AIP1, Hp95	uc003cfy.4	Q8WUM4	OTTHUMG00000130751	ENST00000307296.3:c.1827A>G	chr3.hg19:g.33894165A>G		570.0	1.0	.		476.0	137.0	.	NM_001162429	C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Silent	SNP	ENST00000307296.3	hg19	CCDS2660.1																																																																																			.	.	.	none		0.338	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2			G	33894165	A	G	33894165	2	3	2	1	0	0	0	0	0	0	0	1	11631	291	11	3		3	PDCD6IP	3	33894165	Silent	SNP	A	TCGA-2Z-A9J1-01A-11D-A382-10		33894165	164128265	18	79											
SCAP	22937	hgsc.bcm.edu	37	chr3	47476560	47476560	+	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	gtccacaggtgggggcgagtAatccttcacaggggtggtga	8	8	17	8	1	1	1	1	1	0	0	3	2	3	1	2	6	0	1	2	6	1	2			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr3:47476560A>T	ENST00000265565.5	-	3	602	c.190T>A	c.(190-192)Tac>Aac	p.Y64N	SCAP_ENST00000545718.1_5'UTR|SCAP_ENST00000441517.2_5'UTR	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone	64					aging (GO:0007568)|cholesterol metabolic process (GO:0008203)|negative regulation of cholesterol biosynthetic process (GO:0045541)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of fatty acid biosynthetic process (GO:0042304)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	26				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		GGGGGCGAGTAATCCTTCACA	0.547																																					p.Y64N	Pancreas(149;978 1908 29304 37806 46700)	Atlas-SNP	.											.	SCAP	88	.	0			c.T190A						PASS	.						103	99	100					3																	47476560		2203	4300	6503	SO:0001583	missense	22937	exon3			GCGAGTAATCCTT	BC020987	CCDS2755.2	3p21.31	2013-01-10			ENSG00000114650	ENSG00000114650		"WD repeat domain containing"	30634	protein-coding gene	gene with protein product	"SREBP cleavage activating protein"	601510				8898195, 8724849, 10570913	Standard	XM_005264967		Approved	KIAA0199	uc003crh.1	Q12770	OTTHUMG00000125539	ENST00000265565.5:c.190T>A	chr3.hg19:g.47476560A>T	ENSP00000265565:p.Tyr64Asn	77.0	0.0	.		93.0	30.0	.	NM_012235	Q8N2E0|Q8WUA1	Missense_Mutation	SNP	ENST00000265565.5	hg19	CCDS2755.2	.	.	.	.	.	.	.	.	.	.	A	18.56	3.649395	0.67358	.	.	ENSG00000114650	ENST00000339815;ENST00000265565;ENST00000416847;ENST00000495603;ENST00000448217	D	0.82167	-1.58	5.13	3.97	0.46021	.	0.000000	0.64402	D	0.000001	T	0.82024	0.4947	M	0.64997	1.995	0.80722	D	1	D	0.57257	0.979	P	0.46275	0.51	T	0.82692	-0.0331	10	0.87932	D	0	-23.869	10.7326	0.46107	0.9242:0.0:0.0758:0.0	.	64	Q12770	SCAP_HUMAN	N	64	ENSP00000265565:Y64N	ENSP00000265565:Y64N	Y	-	1	0	SCAP	47451564	1.000000	0.71417	0.976000	0.42696	0.491000	0.33493	8.686000	0.91250	0.968000	0.38212	0.379000	0.24179	TAC	.	.	.	none		0.547	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246872.2	NM_012235		T	47476560	A	T	47476560	3	4	2	1	0	0	0	0	1	0	0	0	13890	362	13	5	3733	5	SCAP	3	47476560	Missense_Mutation	SNP	A	TCGA-2Z-A9J1-01A-11D-A382-10	13582395	47476560	150545870	19	80											
APOD	347	hgsc.bcm.edu	37	chr3	195295856	195295856	+	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	aagtcaggatattttttagaGagtccactgtttctggaggg	10	14	12	5	0	2	1	1	0	1	1	3	4	3	3	1	3	0	1	1	3	3	5			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr3:195295856G>A	ENST00000343267.3	-	5	846	c.485C>T	c.(484-486)tCt>tTt	p.S162F		NM_001647.3	NP_001638.1	P05090	APOD_HUMAN	apolipoprotein D	162					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)		ATTTTTTAGAGAGTCCACTGT	0.453																																					p.S162F		Atlas-SNP	.											.	APOD	28	.	0			c.C485T						PASS	.						159	162	161					3																	195295856		2203	4300	6503	SO:0001583	missense	347	exon5			TTTAGAGAGTCCA		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.485C>T	chr3.hg19:g.195295856G>A	ENSP00000345179:p.Ser162Phe	166.0	0.0	.		172.0	65.0	.	NM_001647	B2R579|D3DNW6|Q6IBG6	Missense_Mutation	SNP	ENST00000343267.3	hg19	CCDS33925.1	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.646465	0.00792	.	.	ENSG00000189058	ENST00000343267;ENST00000421243	T;T	0.31247	1.5;1.5	6.06	3.67	0.42095	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.835345	0.11357	N	0.572291	T	0.14442	0.0349	N	0.05534	-0.03	0.09310	N	1	B	0.13145	0.007	B	0.17433	0.018	T	0.36890	-0.9729	10	0.13108	T	0.6	-1.0985	6.7986	0.23738	0.1584:0.0:0.1521:0.6895	.	162	P05090	APOD_HUMAN	F	162;190	ENSP00000345179:S162F;ENSP00000415235:S190F	ENSP00000345179:S162F	S	-	2	0	APOD	196777145	0.001000	0.12720	0.022000	0.16811	0.040000	0.13550	1.156000	0.31712	0.513000	0.28278	-1.551000	0.00897	TCT	.	.	.	none		0.453	APOD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342004.1	NM_001647		A	195295856	G	A	195295856	3	1	2	1	0	0	0	0	1	0	0	0	801	942	33	2	88	2	APOD	3	195295856	Missense_Mutation	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	147819296	195295856	2726574	20	81											
SEL1L3	23231	hgsc.bcm.edu	37	chr4	25785855	25785855	+	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	atatgcatgtgttaccttggAagctgctttcttcatcagct	8	16	8	9	0	3	0	2	0	1	0	3	1	3	1	1	1	5	5	1	1	3	5			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr4:25785855A>T	ENST00000399878.3	-	14	2397	c.2275T>A	c.(2275-2277)Tcc>Acc	p.S759T	SEL1L3_ENST00000264868.5_Missense_Mutation_p.S724T|SEL1L3_ENST00000502949.1_Missense_Mutation_p.S606T	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	759						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						GTTACCTTGGAAGCTGCTTTC	0.448																																					p.S759T		Atlas-SNP	.											.	SEL1L3	62	.	0			c.T2275A						PASS	.						219	220	220					4																	25785855		2029	4181	6210	SO:0001583	missense	23231	exon14			CCTTGGAAGCTGC	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.2275T>A	chr4.hg19:g.25785855A>T	ENSP00000382767:p.Ser759Thr	56.0	0.0	.		108.0	35.0	.	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Missense_Mutation	SNP	ENST00000399878.3	hg19	CCDS47037.1	.	.	.	.	.	.	.	.	.	.	A	12.90	2.077669	0.36662	.	.	ENSG00000091490	ENST00000399878;ENST00000264868;ENST00000502949	T;T;T	0.51574	0.7;0.7;0.7	5.58	4.35	0.52113	Tetratricopeptide-like helical (1);	0.265568	0.36303	N	0.002662	T	0.28167	0.0695	N	0.08118	0	0.29071	N	0.883281	B;P	0.39424	0.08;0.673	B;B	0.37550	0.098;0.253	T	0.21008	-1.0258	10	0.44086	T	0.13	-8.4038	13.1165	0.59303	0.7915:0.2085:0.0:0.0	.	166;759	B4DTH5;Q68CR1	.;SE1L3_HUMAN	T	759;724;606	ENSP00000382767:S759T;ENSP00000264868:S724T;ENSP00000425438:S606T	ENSP00000264868:S724T	S	-	1	0	SEL1L3	25394953	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	1.145000	0.31577	2.136000	0.66102	0.454000	0.30748	TCC	.	.	.	none		0.448	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187		T	25785855	A	T	25785855	3	4	2	1	0	0	0	0	1	0	0	0	14025	246	9	5	1167	5	SEL1L3	4	25785855	Missense_Mutation	SNP	A	TCGA-2Z-A9J1-01A-11D-A382-10		25785855	165368421	21	82											
ANKRD50	57182	hgsc.bcm.edu	37	chr4	125591071	125591071	+	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	ttttgaagacaatgactgtaGaggtttttgctccattgtgt	9	17	10	5	0	0	4	0	2	0	2	1	4	1	4	1	1	1	3	1	1	3	6	rs143672935		TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr4:125591071G>T	ENST00000504087.1	-	4	4398	c.3361C>A	c.(3361-3363)Cta>Ata	p.L1121I	ANKRD50_ENST00000515641.1_Missense_Mutation_p.L942I	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	1121										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						AATGACTGTAGAGGTTTTTGC	0.383																																					p.L1121I		Atlas-SNP	.											.	ANKRD50	136	.	0			c.C3361A						PASS	.						117	114	115					4																	125591071		2203	4300	6503	SO:0001583	missense	57182	exon4			ACTGTAGAGGTTT	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.3361C>A	chr4.hg19:g.125591071G>T	ENSP00000425658:p.Leu1121Ile	68.0	0.0	.		131.0	41.0	.	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Missense_Mutation	SNP	ENST00000504087.1	hg19	CCDS34060.1	.	.	.	.	.	.	.	.	.	.	G	11.19	1.565272	0.27915	.	.	ENSG00000151458	ENST00000504087;ENST00000515641	T;T	0.69040	-0.37;-0.34	5.19	4.26	0.50523	.	0.159771	0.42420	D	0.000714	T	0.41994	0.1183	N	0.14661	0.345	0.27106	N	0.962509	B	0.23058	0.079	B	0.20384	0.029	T	0.09314	-1.0680	10	0.25751	T	0.34	.	4.2251	0.10577	0.2905:0.0:0.7095:0.0	.	1121	Q9ULJ7	ANR50_HUMAN	I	1121;942	ENSP00000425658:L1121I;ENSP00000425355:L942I	ENSP00000425658:L1121I	L	-	1	2	ANKRD50	125810521	1.000000	0.71417	0.983000	0.44433	0.981000	0.71138	5.349000	0.66010	2.698000	0.92095	0.561000	0.74099	CTA	.	G|1.000;A|0.000	.	alt		0.383	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337		T	125591071	G	T	125591071	3	4	2	1	0	0	0	0	1	0	0	0	677	933	33	4	932	4	ANKRD50	4	125591071	Missense_Mutation	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	99805216	125591071	65563205	22	83											
CLCN3	1182	hgsc.bcm.edu	37	chr4	170613433	170613433	+	Frame_Shift_Del	DEL	T	T	-																															gaaatatcttttcctacctcTttccaaagtatagcacaaac																										TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr4:170613433delT	ENST00000513761.1	+	7	1457	c.898delT	c.(898-900)tttfs	p.F300fs	CLCN3_ENST00000504131.2_Frame_Shift_Del_p.F283fs|CLCN3_ENST00000360642.3_Frame_Shift_Del_p.F300fs|CLCN3_ENST00000347613.4_Frame_Shift_Del_p.F300fs	NM_001829.3	NP_001820.2	P51790	CLCN3_HUMAN	chloride channel, voltage-sensitive 3	300					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)		TTCCTACCTCTTTCCAAAGTA	0.358																																					p.L299fs		Atlas-Indel,Pindel	.											CLCN3,NS,carcinoma,0,1	CLCN3	85	.	0			c.897delC						PASS	.						140	138	139					4																	170613433		2203	4300	6503	SO:0001589	frameshift_variant	1182	exon7			.	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.898delT	chr4.hg19:g.170613433delT	ENSP00000424603:p.Phe300fs	159.0	0.0	0		208.0	66.0	0.317308	NM_001243372	B7Z932|B9EGJ9|D3DP34|E9PB97|O14918|Q86Z21	Frame_Shift_Del	DEL	ENST00000513761.1	hg19	CCDS34101.1																																																																																			.	.	.	none		0.358	CLCN3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363210.2			-	170613433	T	-	170613433	7	5	2	1	0	1	0	1	0	0	0	0	3466	1609	56	0	920	0	CLCN3	4	170613433	Frame_Shift_Del	DEL	T	TCGA-2Z-A9J1-01A-11D-A382-10	45022362	170613433	20540843	23	84											
C6	729	hgsc.bcm.edu	37	chr5	41199944	41199944	+	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	tagatggaatgcatggttgaAaggctaccagaggcgcagtg	12	8	15	6	1	0	3	0	1	0	2	0	4	0	4	1	4	2	4	1	4	4	3			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr5:41199944A>T	ENST00000263413.3	-	4	635	c.371T>A	c.(370-372)tTt>tAt	p.F124Y	C6_ENST00000337836.5_Missense_Mutation_p.F124Y	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	124	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)				GCATGGTTGAAAGGCTACCAG	0.428																																					p.F124Y		Atlas-SNP	.											.	C6	197	.	0			c.T371A						PASS	.						107	103	104					5																	41199944		2203	4300	6503	SO:0001583	missense	729	exon4			GGTTGAAAGGCTA	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.371T>A	chr5.hg19:g.41199944A>T	ENSP00000263413:p.Phe124Tyr	97.0	0.0	.		166.0	54.0	.	NM_001115131		Missense_Mutation	SNP	ENST00000263413.3	hg19	CCDS3936.1	.	.	.	.	.	.	.	.	.	.	A	11.63	1.696782	0.30142	.	.	ENSG00000039537	ENST00000337836;ENST00000263413;ENST00000417809	T;T;T	0.54866	0.55;0.55;0.55	6.02	-2.3	0.06785	.	0.396912	0.30620	N	0.009226	T	0.39253	0.1071	L	0.50333	1.59	0.20926	N	0.999822	B	0.12013	0.005	B	0.13407	0.009	T	0.29518	-1.0009	10	0.49607	T	0.09	-9.092	7.3592	0.26737	0.265:0.0:0.5786:0.1564	.	124	P13671	CO6_HUMAN	Y	124	ENSP00000338861:F124Y;ENSP00000263413:F124Y;ENSP00000396565:F124Y	ENSP00000263413:F124Y	F	-	2	0	C6	41235701	0.990000	0.36364	0.821000	0.32701	0.114000	0.19823	0.769000	0.26604	-0.309000	0.08779	-0.924000	0.02725	TTT	.	.	.	none		0.428	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1			T	41199944	A	T	41199944	3	4	2	1	0	0	0	0	1	0	0	0	2317	14	1	5	2493	5	C6	5	41199944	Missense_Mutation	SNP	A	TCGA-2Z-A9J1-01A-11D-A382-10		41199944	139715316	24	85											
SGTB	54557	hgsc.bcm.edu	37	chr5	65000107	65000107	+	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	cacaatagtgctagtttaccTgttgcaatagtaaactgcat	13	13	7	8	0	0	0	0	0	0	0	0	0	0	0	1	0	5	6	1	0	8	7			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr5:65000107T>A	ENST00000381007.4	-	5	608	c.373A>T	c.(373-375)Agg>Tgg	p.R125W		NM_019072.2	NP_061945.1	Q96EQ0	SGTB_HUMAN	small glutamine-rich tetratricopeptide repeat (TPR)-containing, beta	125										large_intestine(3)|lung(3)|skin(3)	9		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Ovarian(174;0.0545)|Breast(144;0.174)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0657)|Lung(70;0.00487)		CTAGTTTACCTGTTGCAATAG	0.328																																					p.R125W		Atlas-SNP	.											.	SGTB	22	.	0			c.A373T						PASS	.						123	114	117					5																	65000107		2202	4300	6502	SO:0001630	splice_region_variant	54557	exon5			TTTACCTGTTGCA	AK096321	CCDS3988.1	5q12.3	2013-01-10			ENSG00000197860	ENSG00000197860		"Tetratricopeptide (TTC) repeat domain containing"	23567	protein-coding gene	gene with protein product						12477932	Standard	XM_005248548		Approved	Sgt2, FLJ39002	uc003jud.3	Q96EQ0	OTTHUMG00000097801	ENST00000381007.4:c.374+1A>T	chr5.hg19:g.65000107T>A		78.0	0.0	.		76.0	29.0	.	NM_019072		Missense_Mutation	SNP	ENST00000381007.4	hg19	CCDS3988.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.563251	0.86335	.	.	ENSG00000197860	ENST00000381007;ENST00000506816	T;T	0.65178	-0.14;-0.14	5.56	4.33	0.51752	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	D	0.86293	0.5898	H	0.99042	4.41	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90322	0.4345	10	0.87932	D	0	-13.1767	11.4293	0.50029	0.0:0.0:0.1509:0.8491	.	125	Q96EQ0	SGTB_HUMAN	W	125	ENSP00000370395:R125W;ENSP00000421447:R125W	ENSP00000370395:R125W	R	-	1	2	SGTB	65035863	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	5.100000	0.64560	2.110000	0.64415	0.533000	0.62120	AGG	.	.	.	none		0.328	SGTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215057.2	NM_019072	Missense_Mutation	A	65000107	T	A	65000107	5	1	2	1	0	0	0	0	0	0	1	0	14239	1594	55	5	569	5	SGTB	5	65000107	Splice_Site	SNP	T	TCGA-2Z-A9J1-01A-11D-A382-10	23800163	65000107	115915153	25	86											
MAP1B	4131	hgsc.bcm.edu	37	chr5	71490573	71490573	+	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	agaagtagatctcccgatttCctacttaacttcagtctcat	11	14	5	11	1	3	2	2	0	2	2	6	3	4	2	2	0	2	1	2	0	4	5			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr5:71490573C>G	ENST00000296755.7	+	5	1689	c.1391C>G	c.(1390-1392)tCc>tGc	p.S464C		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	464					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)		CTCCCGATTTCCTACTTAACT	0.453																																					p.S464C	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.C1391G						PASS	.						93	94	94					5																	71490573		2203	4300	6503	SO:0001583	missense	4131	exon5			CGATTTCCTACTT	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.1391C>G	chr5.hg19:g.71490573C>G	ENSP00000296755:p.Ser464Cys	105.0	0.0	.		103.0	30.0	.	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	hg19	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	C	15.60	2.882436	0.51908	.	.	ENSG00000131711	ENST00000296755;ENST00000511641;ENST00000504492	T;T;T	0.04194	3.68;3.68;3.68	5.63	5.63	0.86233	.	0.103851	0.43416	D	0.000571	T	0.09202	0.0227	L	0.43152	1.355	0.53688	D	0.999972	D;P	0.56287	0.975;0.948	P;P	0.48901	0.594;0.514	T	0.01096	-1.1453	10	0.87932	D	0	-6.3887	14.5221	0.67856	0.1465:0.8535:0.0:0.0	.	338;464	A2BDK6;P46821	.;MAP1B_HUMAN	C	464;481;338	ENSP00000296755:S464C;ENSP00000423444:S481C;ENSP00000423416:S338C	ENSP00000296755:S464C	S	+	2	0	MAP1B	71526329	1.000000	0.71417	0.998000	0.56505	0.678000	0.39670	4.720000	0.61944	2.644000	0.89710	0.563000	0.77884	TCC	.	.	.	none		0.453	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		G	71490573	C	G	71490573	3	3	2	1	0	0	0	0	1	0	0	0	9235	855	30	4	1409	4	MAP1B	5	71490573	Missense_Mutation	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10	6490466	71490573	109424687	26	87											
IQGAP2	10788	hgsc.bcm.edu	37	chr5	75960919	75960919	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atggaaatactgaataacacCgacaaccaaggaataaaaag	22	5	7	7	1	0	1	0	1	0	0	0	4	0	3	2	2	3	0	2	2	10	3			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr5:75960919C>T	ENST00000274364.6	+	22	2895	c.2598C>T	c.(2596-2598)acC>acT	p.T866T	IQGAP2_ENST00000502745.1_Silent_p.T362T|IQGAP2_ENST00000379730.3_Silent_p.T368T|IQGAP2_ENST00000396234.3_Silent_p.T362T	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	866					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		TGAATAACACCGACAACCAAG	0.323																																					p.T866T		Atlas-SNP	.											.	IQGAP2	186	.	0			c.C2598T						PASS	.						121	116	118					5																	75960919		2203	4300	6503	SO:0001819	synonymous_variant	10788	exon22			TAACACCGACAAC	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.2598C>T	chr5.hg19:g.75960919C>T		257.0	0.0	.		327.0	21.0	.	NM_006633	A8K4V1|B7Z8A4|J3KR91	Silent	SNP	ENST00000274364.6	hg19	CCDS34188.1																																																																																			.	.	.	none		0.323	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		T	75960919	C	T	75960919	2	4	2	1	0	0	0	0	0	0	0	1	7822	639	23	1		1	IQGAP2	5	75960919	Silent	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10	4470346	75960919	104954341	27	88											
ARSB	411	hgsc.bcm.edu	37	chr5	78135234	78135234	+	Silent	SNP	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	tgcagcagctcaattctgggGgatgggcttccttcactgga	7	11	13	10	0	3	0	2	0	1	0	4	2	4	2	1	4	3	4	1	4	1	3			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr5:78135234G>A	ENST00000264914.4	-	6	1694	c.1158C>T	c.(1156-1158)tcC>tcT	p.S386S	ARSB_ENST00000565165.1_Silent_p.S386S|ARSB_ENST00000396151.3_Silent_p.S386S	NM_000046.3	NP_000037.2	P15848	ARSB_HUMAN	arylsulfatase B	386					autophagy (GO:0006914)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|lysosomal transport (GO:0007041)|lysosome organization (GO:0007040)|post-translational protein modification (GO:0043687)|response to estrogen (GO:0043627)|response to methylmercury (GO:0051597)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|rough endoplasmic reticulum (GO:0005791)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)|N-acetylgalactosamine-4-sulfatase activity (GO:0003943)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		all_lung(232;0.000637)|Lung NSC(167;0.00173)|Ovarian(174;0.0105)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;4.24e-44)|Epithelial(54;3.12e-39)|all cancers(79;3.02e-34)		CAATTCTGGGGGATGGGCTTC	0.403																																					p.S386S	Melanoma(169;563 1968 25780 26156 52266)	Atlas-SNP	.											.	ARSB	47	.	0			c.C1158T						PASS	.						121	122	122					5																	78135234		2203	4300	6503	SO:0001819	synonymous_variant	411	exon7			TCTGGGGGATGGG	M32373	CCDS4043.1, CCDS43334.1	5q14.1	2013-02-14			ENSG00000113273	ENSG00000113273	3.1.6.1	"Arylsulfatase family"	714	protein-coding gene	gene with protein product		611542				2303452	Standard	NM_000046		Approved		uc003kfq.3	P15848	OTTHUMG00000108129	ENST00000264914.4:c.1158C>T	chr5.hg19:g.78135234G>A		81.0	0.0	.		97.0	26.0	.	NM_198709	B2RC20|Q8N322|Q9UDI9	Silent	SNP	ENST00000264914.4	hg19	CCDS4043.1																																																																																			.	.	.	none		0.403	ARSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226932.2	NM_000046		A	78135234	G	A	78135234	2	1	2	1	0	0	0	0	0	0	0	1	988	1219	43	2		2	ARSB	5	78135234	Silent	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	2174315	78135234	102780026	28	89											
ARRDC3	57561	hgsc.bcm.edu	37	chr5	90669556	90669556	+	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	cctggatatatgcaaacagtGgtccttgaagggctctctca	10	11	10	10	0	2	1	1	1	1	0	4	2	3	2	2	3	2	2	2	3	4	3			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr5:90669556G>T	ENST00000265138.3	-	7	1399	c.1133C>A	c.(1132-1134)cCa>cAa	p.P378Q	ARRDC3_ENST00000503192.1_5'Flank	NM_020801.2	NP_065852.1	Q96B67	ARRD3_HUMAN	arrestin domain containing 3	378					fat pad development (GO:0060613)|negative regulation of heat generation (GO:0031651)|negative regulation of locomotion involved in locomotory behavior (GO:0090327)|negative regulation of multicellular organismal metabolic process (GO:0044252)|positive regulation of adrenergic receptor signaling pathway (GO:0071879)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|skin development (GO:0043588)|temperature homeostasis (GO:0001659)	endosome (GO:0005768)|plasma membrane (GO:0005886)	beta-3 adrenergic receptor binding (GO:0031699)			breast(2)|endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	18		all_cancers(142;2.22e-05)|all_epithelial(76;1.58e-07)|all_lung(232;0.000521)|Lung NSC(167;0.000548)|Ovarian(174;0.0798)|Colorectal(57;0.207)		OV - Ovarian serous cystadenocarcinoma(54;4.56e-30)|Epithelial(54;7.55e-26)|all cancers(79;3.63e-22)		TGCAAACAGTGGTCCTTGAAG	0.463																																					p.P378Q		Atlas-SNP	.											.	ARRDC3	56	.	0			c.C1133A						PASS	.						180	157	165					5																	90669556		2203	4300	6503	SO:0001583	missense	57561	exon7			AACAGTGGTCCTT	AB037797	CCDS34202.1	5q14.3	2013-10-11			ENSG00000113369	ENSG00000113369			29263	protein-coding gene	gene with protein product	"alpha-arrestin 3"	612464				10718198, 19605364	Standard	NM_020801		Approved	KIAA1376	uc003kjz.2	Q96B67	OTTHUMG00000162616	ENST00000265138.3:c.1133C>A	chr5.hg19:g.90669556G>T	ENSP00000265138:p.Pro378Gln	180.0	0.0	.		239.0	65.0	.	NM_020801	A8K6T8|Q9P2H1	Missense_Mutation	SNP	ENST00000265138.3	hg19	CCDS34202.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.835200	0.91117	.	.	ENSG00000113369	ENST00000265138	T	0.10668	2.85	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.17959	0.0431	M	0.73962	2.25	0.80722	D	1	P	0.48911	0.917	B	0.38655	0.278	T	0.02173	-1.1201	10	0.49607	T	0.09	-11.4537	20.1986	0.98248	0.0:0.0:1.0:0.0	.	378	Q96B67	ARRD3_HUMAN	Q	378	ENSP00000265138:P378Q	ENSP00000265138:P378Q	P	-	2	0	ARRDC3	90705312	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.881000	0.87252	2.781000	0.95711	0.650000	0.86243	CCA	.	.	.	none		0.463	ARRDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369763.2	NM_020801		T	90669556	G	T	90669556	3	4	2	1	0	0	0	0	1	0	0	0	984	1348	47	4	119	4	ARRDC3	5	90669556	Missense_Mutation	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	12534322	90669556	90245704	29	90											
GRIA1	2890	hgsc.bcm.edu	37	chr5	153144063	153144063	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcatcatctcctcatatacAgccaatctggccgccttcct	9	12	4	16	1	5	0	3	0	2	0	7	0	6	0	5	1	2	0	5	1	3	3			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr5:153144063A>G	ENST00000285900.5	+	12	2236	c.1893A>G	c.(1891-1893)acA>acG	p.T631T	GRIA1_ENST00000448073.4_Silent_p.T641T|GRIA1_ENST00000518142.1_Silent_p.T551T|GRIA1_ENST00000521843.2_Silent_p.T562T|GRIA1_ENST00000340592.5_Silent_p.T631T|GRIA1_ENST00000518783.1_Silent_p.T641T	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	631					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)	CCTCATATACAGCCAATCTGG	0.562																																					p.T641T		Atlas-SNP	.											.	GRIA1	321	.	0			c.A1923G						PASS	.						130	110	117					5																	153144063		2203	4300	6503	SO:0001819	synonymous_variant	2890	exon12			ATATACAGCCAAT		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.1893A>G	chr5.hg19:g.153144063A>G		98.0	0.0	.		127.0	43.0	.	NM_001258021	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Silent	SNP	ENST00000285900.5	hg19	CCDS4322.1																																																																																			.	.	.	none		0.562	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3			G	153144063	A	G	153144063	2	3	2	1	0	0	0	0	0	0	0	1	6774	175	7	3		3	GRIA1	5	153144063	Silent	SNP	A	TCGA-2Z-A9J1-01A-11D-A382-10	62474507	153144063	27771197	30	91											
ADAM19	8728	hgsc.bcm.edu	37	chr5	156915305	156915305	+	Missense_Mutation	SNP	T	T	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	gcaatttggtgcggggggaaTtggccggcttggaggaggcc	6	8	20	7	2	0	0	0	0	0	0	0	3	0	3	2	9	1	2	2	9	2	3			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr5:156915305T>G	ENST00000517905.1	-	21	2562	c.2518A>C	c.(2518-2520)Att>Ctt	p.I840L	ADAM19_ENST00000394020.1_Missense_Mutation_p.I842L|ADAM19_ENST00000257527.4_Missense_Mutation_p.I840L|ADAM19_ENST00000430702.2_Missense_Mutation_p.I573L			Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19	840					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)			GCGGGGGGAATTGGCCGGCTT	0.567																																					p.I840L		Atlas-SNP	.											.	ADAM19	216	.	0			c.A2518C						PASS	.						94	100	98					5																	156915305		2203	4300	6503	SO:0001583	missense	8728	exon21			GGGGAATTGGCCG	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.2518A>C	chr5.hg19:g.156915305T>G	ENSP00000428654:p.Ile840Leu	139.0	0.0	.		127.0	38.0	.	NM_033274	Q9BZL5|Q9UHP2	Missense_Mutation	SNP	ENST00000517905.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.470|0.470	-0.884725|-0.884725	0.02530|0.02530	.|.	.|.	ENSG00000135074|ENSG00000135074	ENST00000430702;ENST00000257527;ENST00000394020;ENST00000517905|ENST00000517374	T;T;T;T|.	0.01430|.	4.9;5.05;5.07;5.04|.	5.69|5.69	2.82|2.82	0.32997|0.32997	.|.	0.572734|.	0.16805|.	N|.	0.198802|.	T|T	0.15565|0.15565	0.0375|0.0375	N|N	0.03608|0.03608	-0.345|-0.345	0.20489|0.20489	N|N	0.999891|0.999891	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.06405|.	0.001;0.0;0.002|.	T|T	0.27400|0.27400	-1.0075|-1.0075	10|5	0.02654|.	T|.	1|.	.|.	8.9891|8.9891	0.36012|0.36012	0.0:0.7653:0.0:0.2347|0.0:0.7653:0.0:0.2347	.|.	840;840;573|.	Q9H013-2;Q9H013;E9PD32|.	.;ADA19_HUMAN;.|.	L|H	573;840;842;840|410	ENSP00000414088:I573L;ENSP00000257527:I840L;ENSP00000377588:I842L;ENSP00000428654:I840L|.	ENSP00000257527:I840L|.	I|Q	-|-	1|3	0|2	ADAM19|ADAM19	156847883|156847883	0.245000|0.245000	0.23899|0.23899	0.340000|0.340000	0.25575|0.25575	0.278000|0.278000	0.26855|0.26855	0.407000|0.407000	0.21049|0.21049	0.321000|0.321000	0.23259|0.23259	-0.608000|-0.608000	0.04076|0.04076	ATT|CAA	.	.	.	none		0.567	ADAM19-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000373918.1	NM_033274		G	156915305	T	G	156915305	3	3	2	1	0	0	0	0	1	0	0	0	240	1493	52	5	250	5	ADAM19	5	156915305	Missense_Mutation	SNP	T	TCGA-2Z-A9J1-01A-11D-A382-10	3771242	156915305	23999955	31	92											
CLINT1	9685	hgsc.bcm.edu	37	chr5	157285937	157285937	+	Splice_Site	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	caactgccccccgatactcaCgctttgtccaccagctcgcg	7	8	7	19	4	1	0	1	0	0	0	3	1	2	0	5	0	4	2	5	0	2	2			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr5:157285937C>G	ENST00000411809.2	-	1	246		c.e1+1		CLINT1_ENST00000523908.1_Splice_Site|CLINT1_ENST00000523094.1_Intron|CLINT1_ENST00000530742.1_Intron|CLINT1_ENST00000296951.5_Splice_Site	NM_014666.3	NP_055481.1	Q14677	EPN4_HUMAN	clathrin interactor 1						clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)	clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|lipid binding (GO:0008289)			breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|urinary_tract(1)	21	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)			CCGATACTCACGCTTTGTCCA	0.701																																					.	Colon(22;427 587 2170 6147 14291)	Atlas-SNP	.											.	CLINT1	86	.	0			c.41+1G>C						PASS	.						37	42	40					5																	157285937		1998	4152	6150	SO:0001630	splice_region_variant	9685	exon2			TACTCACGCTTTG	AF434813	CCDS47330.1, CCDS56388.1, CCDS56389.1	5q33.3	2006-06-13			ENSG00000113282	ENSG00000113282			23186	protein-coding gene	gene with protein product		607265				12213833, 12429846	Standard	NM_014666		Approved	ENTH, KIAA0171, EPNR, CLINT	uc011ddv.2	Q14677	OTTHUMG00000163527	ENST00000411809.2:c.41+1G>C	chr5.hg19:g.157285937C>G		178.0	0.0	.		117.0	41.0	.	NM_014666	B7Z6F8|D3DQJ6|Q8NAF1|Q96E05	Splice_Site	SNP	ENST00000411809.2	hg19	CCDS47330.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.275080	0.80580	.	.	ENSG00000113282	ENST00000411809;ENST00000523908	.	.	.	4.92	4.92	0.64577	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.049	0.71850	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CLINT1	157218515	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.146000	0.64845	2.249000	0.74217	0.655000	0.94253	.	.	.	.	none		0.701	CLINT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374001.1	NM_014666	Intron	G	157285937	C	G	157285937	5	3	2	1	0	0	0	0	0	0	1	0	3533	550	19	4	1883	4	CLINT1	5	157285937	Splice_Site	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10	370632	157285937	23629323	32	93											
FOXI1	2299	hgsc.bcm.edu	37	chr5	169532985	169532985	+	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	agctccttcgacctgccggcGccctccccacctcgctgcag	4	7	9	21	4	0	0	0	0	0	0	4	1	2	0	7	1	3	3	7	1	0	1			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr5:169532985G>T	ENST00000306268.6	+	1	85	c.24G>T	c.(22-24)gcG>gcT	p.A8A	FOXI1_ENST00000449804.2_Silent_p.A8A			Q12951	FOXI1_HUMAN	forkhead box I1	8	Pro-rich.				embryo development (GO:0009790)|inner ear morphogenesis (GO:0042472)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACCTGCCGGCGCCCTCCCCAC	0.692									Pendred syndrome																												p.A8A		Atlas-SNP	.											FOXI1,caecum,carcinoma,0,1	FOXI1	70	.	0			c.G24T						PASS	.						17	20	19					5																	169532985		2201	4295	6496	SO:0001819	synonymous_variant	2299	exon1	Familial Cancer Database	Goiter-Deafness syndrome	GCCGGCGCCCTCC	BC029778	CCDS4372.1, CCDS47337.1	5q34	2008-02-05			ENSG00000168269	ENSG00000168269		"Forkhead boxes"	3815	protein-coding gene	gene with protein product		601093		FKHL10		7957066, 8825632	Standard	NM_144769		Approved	FREAC6	uc003mai.4	Q12951	OTTHUMG00000130436	ENST00000306268.6:c.24G>T	chr5.hg19:g.169532985G>T		269.0	0.0	.		221.0	67.0	.	NM_012188	Q14518|Q66SR7|Q8N6L8	Silent	SNP	ENST00000306268.6	hg19	CCDS4372.1																																																																																			.	.	.	none		0.692	FOXI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252827.2	NM_144769, NM_012188		T	169532985	G	T	169532985	2	4	2	1	0	0	0	0	0	0	0	1	6016	1074	38	4		4	FOXI1	5	169532985	Silent	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	12247048	169532985	11382275	33	94											
CANX	821	hgsc.bcm.edu	37	chr5	179150705	179150705	+	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	gaggcagctgaagagcgcccGtggctgtgggtagtctatat	8	9	16	8	2	1	2	0	1	1	1	1	3	1	2	1	3	2	4	1	3	4	3			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr5:179150705G>A	ENST00000247461.4	+	12	1643	c.1443G>A	c.(1441-1443)ccG>ccA	p.P481P	CANX_ENST00000415618.2_Silent_p.P516P|CANX_ENST00000504734.1_Silent_p.P481P|CANX_ENST00000512607.2_Silent_p.P373P|CANX_ENST00000452673.2_Silent_p.P481P	NM_001746.3	NP_001737.1	P27824	CALX_HUMAN	calnexin	481					aging (GO:0007568)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein folding (GO:0061077)|clathrin-mediated endocytosis (GO:0072583)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|protein secretion (GO:0009306)|synaptic vesicle endocytosis (GO:0048488)	axon (GO:0030424)|dendrite cytoplasm (GO:0032839)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|ER-mitochondrion membrane contact site (GO:0044233)|extracellular vesicular exosome (GO:0070062)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ribosome (GO:0005840)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|kidney(4)|large_intestine(2)|lung(7)|prostate(2)|urinary_tract(3)	22	all_cancers(89;0.000129)|all_epithelial(37;5.59e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0413)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Antihemophilic Factor(DB00025)|Tenecteplase(DB00031)	AAGAGCGCCCGTGGCTGTGGG	0.473																																					p.P481P		Atlas-SNP	.											.	CANX	47	.	0			c.G1443A						PASS	.						142	141	141					5																	179150705		2203	4300	6503	SO:0001819	synonymous_variant	821	exon12			GCGCCCGTGGCTG	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.1443G>A	chr5.hg19:g.179150705G>A		97.0	0.0	.		91.0	29.0	.	NM_001746	B2R5V8|B4DGP8|B4E2T8|D3DWQ3|D6R9K3	Silent	SNP	ENST00000247461.4	hg19	CCDS4447.1																																																																																			.	.	.	none		0.473	CANX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253500.2	NM_001024649		A	179150705	G	A	179150705	2	1	2	1	0	0	0	0	0	0	0	1	2620	1132	40	1		1	CANX	5	179150705	Silent	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	9617720	179150705	1764555	34	95											
RIPK1	8737	hgsc.bcm.edu	37	chr6	3104478	3104478	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaaagagtattcaaacgaaaAtgcagttgtgaagagaatgc	18	8	11	4	1	1	3	1	1	0	2	1	6	1	3	0	0	3	3	0	0	7	3			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr6:3104478A>G	ENST00000259808.4	+	8	1233	c.935A>G	c.(934-936)aAt>aGt	p.N312S	RIPK1_ENST00000479389.1_3'UTR|RIPK1_ENST00000541791.1_Missense_Mutation_p.N266S|RIPK1_ENST00000380409.2_Missense_Mutation_p.N312S			Q13546	RIPK1_HUMAN	receptor (TNFRSF)-interacting serine-threonine kinase 1	312	Interaction with SQSTM1.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|amyloid fibril formation (GO:1990000)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular protein catabolic process (GO:0044257)|cellular response to growth factor stimulus (GO:0071363)|cellular response to tumor necrosis factor (GO:0071356)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|necroptotic signaling pathway (GO:0097527)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|peptidyl-serine autophosphorylation (GO:0036289)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of ATP:ADP antiporter activity (GO:0070926)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to tumor necrosis factor (GO:0034612)|ripoptosome assembly (GO:0097343)|ripoptosome assembly involved in necroptotic process (GO:1901026)|T cell apoptotic process (GO:0070231)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|death domain binding (GO:0070513)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	23	Ovarian(93;0.0386)	all_hematologic(90;0.0895)				TCAAACGAAAATGCAGTTGTG	0.348																																					p.N312S		Atlas-SNP	.											.	RIPK1	56	.	0			c.A935G						PASS	.						99	97	97					6																	3104478		2203	4300	6503	SO:0001583	missense	8737	exon7			ACGAAAATGCAGT	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.935A>G	chr6.hg19:g.3104478A>G	ENSP00000259808:p.Asn312Ser	103.0	0.0	.		76.0	25.0	.	NM_003804	A0AV89|B2RAG1|B4E3F9|Q13180|Q59H33	Missense_Mutation	SNP	ENST00000259808.4	hg19	CCDS4482.1	.	.	.	.	.	.	.	.	.	.	A	10.63	1.402975	0.25291	.	.	ENSG00000137275	ENST00000259808;ENST00000541791;ENST00000380409	T;T;T	0.76968	-1.06;-0.52;-1.06	5.07	1.4	0.22301	Protein kinase-like domain (1);	0.441952	0.29624	N	0.011622	T	0.31796	0.0808	N	0.20401	0.57	0.23254	N	0.998037	B;B	0.18310	0.027;0.008	B;B	0.17722	0.019;0.004	T	0.28902	-1.0029	10	0.12103	T	0.63	-19.08	4.2271	0.10585	0.6064:0.0:0.2524:0.1412	.	266;312	Q13546-2;Q13546	.;RIPK1_HUMAN	S	312;266;312	ENSP00000259808:N312S;ENSP00000442294:N266S;ENSP00000369773:N312S	ENSP00000259808:N312S	N	+	2	0	RIPK1	3049477	0.001000	0.12720	0.004000	0.12327	0.470000	0.32858	0.552000	0.23376	0.062000	0.16340	0.528000	0.53228	AAT	.	.	.	none		0.348	RIPK1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039659.2	NM_003804		G	3104478	A	G	3104478	3	3	2	1	0	0	0	0	1	0	0	0	13393	101	4	3	961	3	RIPK1	6	3104478	Missense_Mutation	SNP	A	TCGA-2Z-A9J1-01A-11D-A382-10		3104478	168010589	35	96											
CPNE5	57699	hgsc.bcm.edu	37	chr6	36746667	36746667	+	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	ttctgtagaataccaagaagGggtcagatttcccaaagaaa	16	9	9	7	0	2	4	1	0	1	4	3	4	3	4	2	2	1	1	2	2	7	4			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr6:36746667G>T	ENST00000244751.2	-	9	1220	c.596C>A	c.(595-597)cCc>cAc	p.P199H		NM_020939.1	NP_065990.1	Q9HCH3	CPNE5_HUMAN	copine V	199	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.					extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(4)|liver(1)|lung(9)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						TACCAAGAAGGGGTCAGATTT	0.542																																					p.P199H		Atlas-SNP	.											.	CPNE5	56	.	0			c.C596A						PASS	.						231	212	218					6																	36746667		2203	4300	6503	SO:0001583	missense	57699	exon9			AAGAAGGGGTCAG	H09181	CCDS4825.1	6p21.2	2010-05-28			ENSG00000124772	ENSG00000124772			2318	protein-coding gene	gene with protein product		604209				9430674	Standard	NM_020939		Approved	CPN5, COPN5, KIAA1599	uc003omr.1	Q9HCH3	OTTHUMG00000014602	ENST00000244751.2:c.596C>A	chr6.hg19:g.36746667G>T	ENSP00000244751:p.Pro199His	160.0	0.0	.		124.0	45.0	.	NM_020939	Q7Z6C8	Missense_Mutation	SNP	ENST00000244751.2	hg19	CCDS4825.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.697643	0.88830	.	.	ENSG00000124772	ENST00000244751	T	0.78003	-1.14	5.22	5.22	0.72569	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.93164	0.7823	H	0.99379	4.54	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95764	0.8803	10	0.87932	D	0	.	16.6249	0.84967	0.0:0.0:1.0:0.0	.	199	Q9HCH3	CPNE5_HUMAN	H	199	ENSP00000244751:P199H	ENSP00000244751:P199H	P	-	2	0	CPNE5	36854645	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.349000	0.97066	2.613000	0.88420	0.579000	0.79373	CCC	.	.	.	none		0.542	CPNE5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040351.1	NM_020939		T	36746667	G	T	36746667	3	4	2	1	0	0	0	0	1	0	0	0	3817	1232	43	4	1237	4	CPNE5	6	36746667	Missense_Mutation	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	33642189	36746667	134368400	36	97											
MRPS10	55173	hgsc.bcm.edu	37	chr6	42179572	42179572	+	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	agcacagcaaaatattcataActgtccaatacagccttatc	16	10	4	11	0	1	0	1	0	0	0	3	0	2	0	2	0	5	2	2	0	7	5			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr6:42179572A>T	ENST00000053468.3	-	4	285	c.270T>A	c.(268-270)agT>agA	p.S90R		NM_018141.3	NP_060611.2	P82664	RT10_HUMAN	mitochondrial ribosomal protein S10	90						mitochondrion (GO:0005739)|ribosome (GO:0005840)				endometrium(1)|lung(1)	2	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00528)			AATATTCATAACTGTCCAATA	0.398																																					p.S90R		Atlas-SNP	.											.	MRPS10	9	.	0			c.T270A						PASS	.						123	117	119					6																	42179572		2203	4300	6503	SO:0001583	missense	55173	exon4			TTCATAACTGTCC		CCDS4866.1	6p21.1	2012-09-13			ENSG00000048544	ENSG00000048544		"Mitochondrial ribosomal proteins / small subunits"	14502	protein-coding gene	gene with protein product		611976				11279123	Standard	NM_018141		Approved	FLJ10567	uc003osa.4	P82664	OTTHUMG00000014694	ENST00000053468.3:c.270T>A	chr6.hg19:g.42179572A>T	ENSP00000053468:p.Ser90Arg	92.0	0.0	.		92.0	32.0	.	NM_018141	B2RE89|Q9H3E5|Q9NVR3	Missense_Mutation	SNP	ENST00000053468.3	hg19	CCDS4866.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.106048	0.77096	.	.	ENSG00000048544	ENST00000053468	.	.	.	5.78	-1.1	0.09872	.	0.000000	0.85682	D	0.000000	T	0.59445	0.2194	M	0.67953	2.075	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.63462	-0.6632	9	0.66056	D	0.02	-14.4952	10.3265	0.43796	0.6463:0.0:0.3537:0.0	.	90	P82664	RT10_HUMAN	R	90	.	ENSP00000053468:S90R	S	-	3	2	MRPS10	42287550	1.000000	0.71417	0.809000	0.32408	0.994000	0.84299	1.312000	0.33574	-0.415000	0.07484	-0.274000	0.10170	AGT	.	.	.	none		0.398	MRPS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040547.1			T	42179572	A	T	42179572	3	4	2	1	0	0	0	0	1	0	0	0	9828	40	2	5	351	5	MRPS10	6	42179572	Missense_Mutation	SNP	A	TCGA-2Z-A9J1-01A-11D-A382-10	5432905	42179572	128935495	37	98											
C6orf170	221322	hgsc.bcm.edu	37	chr6	121447579	121447579	+	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	gggctttcagtgagatgaagCacaaatttttcaagtaattc	13	13	9	6	0	2	2	2	2	0	1	3	3	2	2	0	1	1	3	0	1	4	5			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr6:121447579C>A	ENST00000398212.2	-	26	2977	c.2928G>T	c.(2926-2928)gtG>gtT	p.V976V	TBC1D32_ENST00000398197.2_5'UTR|TBC1D32_ENST00000275159.6_Silent_p.V1017V	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	976					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)										TGAGATGAAGCACAAATTTTT	0.318																																					p.V976V		Atlas-SNP	.											.	C6orf170	146	.	0			c.G2928T						PASS	.						107	102	103					6																	121447579		1821	4080	5901	SO:0001819	synonymous_variant	221322	exon26			ATGAAGCACAAAT	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.2928G>T	chr6.hg19:g.121447579C>A		61.0	0.0	.		106.0	25.0	.	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Silent	SNP	ENST00000398212.2	hg19	CCDS43501.1																																																																																			.	.	.	none		0.318	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		A	121447579	C	A	121447579	2	1	2	1	0	0	0	0	0	0	0	1	2346	697	25	4		4	C6orf170	6	121447579	Silent	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10	79268007	121447579	49667488	38	99											
PCMT1	5110	hgsc.bcm.edu	37	chr6	150070960	150070960	+	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	0	0	1	0	0	0	0	0	0	0	0	cggtgacggtgtgggaggtgGtctcactcttgggaaaactg	7	10	17	7	2	2	1	1	1	2	0	3	3	2	3	0	6	1	0	0	6	2	1			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr6:150070960G>A	ENST00000367380.5	+	0	130				NUP43_ENST00000463048.3_5'Flank|PCMT1_ENST00000544496.1_5'UTR|PCMT1_ENST00000367378.1_Missense_Mutation_p.V33I|PCMT1_ENST00000464889.1_Missense_Mutation_p.V33I|PCMT1_ENST00000367384.2_Missense_Mutation_p.V33I	NM_001252049.1|NM_001252050.1|NM_001252051.1|NM_001252052.1|NM_005389.2	NP_001238978.1|NP_001238979.1|NP_001238980.1|NP_001238981.1|NP_005380.2	P22061	PIMT_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase						protein methylation (GO:0006479)|protein repair (GO:0030091)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			kidney(1)|large_intestine(2)|lung(4)|ovary(1)	8		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.221)	OV - Ovarian serous cystadenocarcinoma(155;5.63e-13)|GBM - Glioblastoma multiforme(68;0.207)		gtgggaggtggTCTCACTCTT	0.687																																					p.V33I		Atlas-SNP	.											.	PCMT1	27	.	0			c.G97A						PASS	.						90	115	107					6																	150070960		692	1591	2283	SO:0001623	5_prime_UTR_variant	5110	exon1			GAGGTGGTCTCAC		CCDS5219.1, CCDS5219.2, CCDS59041.1, CCDS75533.1, CCDS75534.1	6q22.3-q24	2008-02-05			ENSG00000120265	ENSG00000120265	2.1.1.77		8728	protein-coding gene	gene with protein product		176851				1478665, 10343128	Standard	NM_005389		Approved		uc003qne.3	P22061	OTTHUMG00000015794	ENST00000367380.5:c.-78G>A	chr6.hg19:g.150070960G>A		73.0	0.0	.		55.0	17.0	.	NM_005389	A8K109|J3KP72|Q14661|Q16556|Q5VYC1|Q5VYC2|Q93061|Q96II9|Q99625|Q9BQV7|Q9BQV8|Q9NP03	Missense_Mutation	SNP	ENST00000367380.5	hg19		.	.	.	.	.	.	.	.	.	.	G	18.50	3.638391	0.67130	.	.	ENSG00000120265	ENST00000367384;ENST00000367378;ENST00000464889	T;T;T	0.45668	0.89;0.89;0.89	5.14	2.15	0.27550	.	.	.	.	.	T	0.17152	0.0412	L	0.44542	1.39	0.80722	D	1	B;B;B	0.28971	0.229;0.229;0.229	B;B;B	0.24006	0.05;0.05;0.05	T	0.05599	-1.0875	9	0.51188	T	0.08	.	9.3336	0.38036	0.0:0.2582:0.4735:0.2683	.	33;33;33	F8WAX2;F8WAV5;F8WDT3	.;.;.	I	33	ENSP00000356354:V33I;ENSP00000356348:V33I;ENSP00000420813:V33I	ENSP00000356348:V33I	V	+	1	0	PCMT1	150112653	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.803000	0.38863	0.532000	0.28657	0.591000	0.81541	GTC	.	.	.	none		0.687	PCMT1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				A	150070960	G	A	150070960	1	1	2	0	1	0	0	0	0	0	0	0	11592	1261	44	2		2	PCMT1	6	150070960	5'UTR	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	28623381	150070960	21044107	39	100											
TULP4	56995	hgsc.bcm.edu	37	chr6	158915829	158915829	+	Missense_Mutation	SNP	A	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	tctaatatctggggaaccaaAtttaagattgtgggcttggc	11	13	11	6	0	2	1	0	0	2	1	2	2	2	2	1	4	1	1	1	4	5	6			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr6:158915829A>C	ENST00000367097.3	+	11	3178	c.1821A>C	c.(1819-1821)aaA>aaC	p.K607N	TULP4_ENST00000367094.2_Missense_Mutation_p.K607N	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	607					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)		GGGGAACCAAATTTAAGATTG	0.418																																					p.K607N		Atlas-SNP	.											.	TULP4	137	.	0			c.A1821C						PASS	.						139	125	129					6																	158915829		2203	4300	6503	SO:0001583	missense	56995	exon11			AACCAAATTTAAG		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.1821A>C	chr6.hg19:g.158915829A>C	ENSP00000356064:p.Lys607Asn	112.0	0.0	.		89.0	8.0	.	NM_020245	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Missense_Mutation	SNP	ENST00000367097.3	hg19	CCDS34561.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.588248	0.86851	.	.	ENSG00000130338	ENST00000367097;ENST00000367094	D;D	0.87887	-2.31;-2.31	5.56	1.87	0.25490	Tubby, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.87716	0.6247	M	0.64404	1.975	0.80722	D	1	D;D	0.76494	0.996;0.999	D;D	0.83275	0.99;0.996	D	0.86643	0.1893	10	0.72032	D	0.01	-18.8341	8.5636	0.33525	0.7684:0.0:0.2316:0.0	.	607;607	Q9NRJ4-2;Q9NRJ4	.;TULP4_HUMAN	N	607	ENSP00000356064:K607N;ENSP00000356061:K607N	ENSP00000356061:K607N	K	+	3	2	TULP4	158835817	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.229000	0.42990	0.084000	0.17077	0.533000	0.62120	AAA	.	.	.	none		0.418	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245		C	158915829	A	C	158915829	3	2	2	1	0	0	0	0	1	0	0	0	16788	98	4	5	1863	5	TULP4	6	158915829	Missense_Mutation	SNP	A	TCGA-2Z-A9J1-01A-11D-A382-10	8844869	158915829	12199238	40	101											
IGF2R	3482	hgsc.bcm.edu	37	chr6	160453699	160453699	+	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	acttgttctctgagcggcgaGcagcaggatgtctccataga	9	10	12	10	2	2	2	0	1	2	1	4	4	2	3	1	2	3	3	1	2	1	3			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr6:160453699G>T	ENST00000356956.1	+	8	1147	c.999G>T	c.(997-999)gaG>gaT	p.E333D		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	333					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)	TGAGCGGCGAGCAGCAGGATG	0.517																																					p.E333D		Atlas-SNP	.											.	IGF2R	251	.	0			c.G999T						PASS	.						93	89	90					6																	160453699		2203	4300	6503	SO:0001583	missense	3482	exon8			CGGCGAGCAGCAG	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.999G>T	chr6.hg19:g.160453699G>T	ENSP00000349437:p.Glu333Asp	60.0	0.0	.		63.0	26.0	.	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	hg19	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	G	5.387	0.256638	0.10185	.	.	ENSG00000197081	ENST00000356956	T	0.04119	3.7	5.09	2.12	0.27331	Mannose-6-phosphate receptor, binding (1);	1.300900	0.04701	N	0.415851	T	0.02156	0.0067	L	0.56199	1.76	0.41272	D	0.986859	B	0.09022	0.002	B	0.10450	0.005	T	0.41945	-0.9480	10	0.21014	T	0.42	-9.1428	7.3787	0.26843	0.1477:0.3885:0.4638:0.0	.	333	P11717	MPRI_HUMAN	D	333	ENSP00000349437:E333D	ENSP00000349437:E333D	E	+	3	2	IGF2R	160373689	0.106000	0.21978	0.943000	0.38184	0.088000	0.18126	0.006000	0.13152	0.658000	0.30925	0.655000	0.94253	GAG	.	.	.	none		0.517	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		T	160453699	G	T	160453699	3	4	2	1	0	0	0	0	1	0	0	0	7583	962	34	4	1029	4	IGF2R	6	160453699	Missense_Mutation	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	1537870	160453699	10661368	41	102											
NUPL2	11097	hgsc.bcm.edu	37	chr7	23221710	23221710	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcgacgccgtcgcaatggcCatttgtcaattcttccttca	8	12	8	13	4	3	0	2	0	1	0	5	1	4	0	3	1	1	1	3	1	2	4			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr7:23221710C>T	ENST00000258742.5	+	1	265	c.6C>T	c.(4-6)gcC>gcT	p.A2A	NUPL2_ENST00000410002.3_Silent_p.A2A|NUPL2_ENST00000487595.1_3'UTR|AC005082.1_ENST00000366347.4_Intron	NM_007342.2	NP_031368.1	O15504	NUPL2_HUMAN	nucleoporin like 2	2					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 export from nucleus (GO:0006611)|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)	metal ion binding (GO:0046872)|nuclear export signal receptor activity (GO:0005049)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TCGCAATGGCCATTTGTCAAT	0.632																																					p.A2A		Atlas-SNP	.											.	NUPL2	51	.	0			c.C6T						PASS	.						80	67	72					7																	23221710		2203	4300	6503	SO:0001819	synonymous_variant	11097	exon1			AATGGCCATTTGT	U97198	CCDS5379.1	7p15	2003-08-07			ENSG00000136243	ENSG00000136243			17010	protein-coding gene	gene with protein product	"nucleoporin-like protein 1"					10358091, 9450185	Standard	NM_007342		Approved	NLP_1, CG1, hCG1, H_RG271G13.9	uc003svu.3	O15504	OTTHUMG00000096955	ENST00000258742.5:c.6C>T	chr7.hg19:g.23221710C>T		47.0	0.0	.		54.0	12.0	.	NM_007342	A4D143|B4DP42|Q49AE7|Q9BS49	Silent	SNP	ENST00000258742.5	hg19	CCDS5379.1																																																																																			.	.	.	none		0.632	NUPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214017.2	NM_007342		T	23221710	C	T	23221710	2	4	2	1	0	0	0	0	0	0	0	1	10782	581	21	2		2	NUPL2	7	23221710	Silent	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10		23221710	135916953	42	103											
TXNDC3	51314	hgsc.bcm.edu	37	chr7	37923905	37923905	+	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	atgtaactgtttttatttagAtgatgttttgcgtattatta	10	22	7	2	1	0	2	0	1	0	1	0	2	0	2	0	0	2	4	0	0	6	11			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr7:37923905A>T	ENST00000199447.4	+	13	1367	c.995A>T	c.(994-996)gAt>gTt	p.D332V	NME8_ENST00000440017.1_Splice_Site_p.D332V|EPDR1_ENST00000476620.1_Intron	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	332	NDK 2.				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)										TTTTATTTAGATGATGTTTTG	0.303																																					p.D332V		Atlas-SNP	.											.	.	.	.	0			c.A995T						PASS	.						80	77	78					7																	37923905		2202	4292	6494	SO:0001630	splice_region_variant	51314	exon13			ATTTAGATGATGT	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.995-1A>T	chr7.hg19:g.37923905A>T		134.0	0.0	.		318.0	67.0	.	NM_016616	Q9NZH1	Missense_Mutation	SNP	ENST00000199447.4	hg19	CCDS5452.1	.	.	.	.	.	.	.	.	.	.	A	12.79	2.043787	0.36085	.	.	ENSG00000086288	ENST00000199447;ENST00000440017	T;T	0.56275	0.47;0.47	3.85	3.85	0.44370	.	0.717261	0.12527	N	0.461140	T	0.65626	0.2709	M	0.70595	2.14	0.58432	D	0.999998	D	0.53885	0.963	P	0.58130	0.833	T	0.64364	-0.6425	9	.	.	.	.	10.9803	0.47490	1.0:0.0:0.0:0.0	.	332	Q8N427	TXND3_HUMAN	V	332	ENSP00000199447:D332V;ENSP00000397063:D332V	.	D	+	2	0	TXNDC3	37890430	0.994000	0.37717	0.997000	0.53966	0.087000	0.18053	2.623000	0.46435	1.966000	0.57179	0.477000	0.44152	GAT	.	.	.	none		0.303	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219946.1	NM_016616	Missense_Mutation	T	37923905	A	T	37923905	5	4	2	1	0	0	0	0	0	0	1	0	16810	347	12	5	1037	5	TXNDC3	7	37923905	Splice_Site	SNP	A	TCGA-2Z-A9J1-01A-11D-A382-10	14702195	37923905	121214758	43	104											
SAMD9	54809	hgsc.bcm.edu	37	chr7	92732597	92732597	+	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	ccaattcctaagaatttttcAcactgtgatagtgaaatggt	13	14	7	7	0	1	3	1	2	0	1	2	3	2	3	2	1	0	0	2	1	5	5			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr7:92732597A>T	ENST00000379958.2	-	3	3083	c.2814T>A	c.(2812-2814)tgT>tgA	p.C938*		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	938						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)			AGAATTTTTCACACTGTGATA	0.383																																					p.C938X		Atlas-SNP	.											.	SAMD9	239	.	0			c.T2814A						PASS	.						61	61	61					7																	92732597		2181	4289	6470	SO:0001587	stop_gained	54809	exon2			TTTTTCACACTGT	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.2814T>A	chr7.hg19:g.92732597A>T	ENSP00000369292:p.Cys938*	78.0	0.0	.		125.0	64.0	.	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Nonsense_Mutation	SNP	ENST00000379958.2	hg19	CCDS34680.1	.	.	.	.	.	.	.	.	.	.	A	36	5.805384	0.96967	.	.	ENSG00000205413	ENST00000379958;ENST00000446617	.	.	.	4.79	4.79	0.61399	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.3085	13.2668	0.60139	1.0:0.0:0.0:0.0	.	.	.	.	X	938	.	ENSP00000369292:C938X	C	-	3	2	SAMD9	92570533	1.000000	0.71417	0.970000	0.41538	0.280000	0.26924	3.958000	0.56737	2.022000	0.59522	0.496000	0.49642	TGT	.	.	.	none		0.383	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		T	92732597	A	T	92732597	4	4	2	1	0	0	0	0	0	1	0	0	13839	157	6	5	1959	5	SAMD9	7	92732597	Nonsense_Mutation	SNP	A	TCGA-2Z-A9J1-01A-11D-A382-10	54808692	92732597	66406066	44	105											
LRWD1	222229	hgsc.bcm.edu	37	chr7	102108717	102108717	+	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	tctccccccacagcctgctgTgaagctggagcccctgcact	6	8	9	18	0	1	1	0	1	1	0	2	2	1	2	6	1	5	3	6	1	1	0			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr7:102108717T>A	ENST00000292616.5	+	7	964	c.812T>A	c.(811-813)gTg>gAg	p.V271E	MIR5090_ENST00000582533.1_RNA	NM_152892.1	NP_690852.1	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain containing 1	271					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						CAGCCTGCTGTGAAGCTGGAG	0.662																																					p.V271E		Atlas-SNP	.											.	LRWD1	41	.	0			c.T812A						PASS	.						50	53	52					7																	102108717		2202	4298	6500	SO:0001583	missense	222229	exon7			CTGCTGTGAAGCT	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.812T>A	chr7.hg19:g.102108717T>A	ENSP00000292616:p.Val271Glu	112.0	0.0	.		114.0	21.0	.	NM_152892	A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2	Missense_Mutation	SNP	ENST00000292616.5	hg19	CCDS34715.1	.	.	.	.	.	.	.	.	.	.	T	16.01	3.002082	0.54254	.	.	ENSG00000161036	ENST00000292616	T	0.64085	-0.08	4.94	2.59	0.31030	WD40 repeat-like-containing domain (1);	0.950099	0.08884	N	0.879606	T	0.45597	0.1350	N	0.19112	0.55	0.09310	N	1	B	0.23735	0.09	B	0.21360	0.034	T	0.38564	-0.9655	10	0.62326	D	0.03	-3.8122	6.2922	0.21067	0.0:0.1964:0.0:0.8036	.	271	Q9UFC0	LRWD1_HUMAN	E	271	ENSP00000292616:V271E	ENSP00000292616:V271E	V	+	2	0	LRWD1	101895722	0.864000	0.29904	0.021000	0.16686	0.754000	0.42855	1.484000	0.35508	0.383000	0.24910	0.459000	0.35465	GTG	.	.	.	none		0.662	LRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349493.1	NM_152892		A	102108717	T	A	102108717	3	1	2	1	0	0	0	0	1	0	0	0	9054	1696	59	5	838	5	LRWD1	7	102108717	Missense_Mutation	SNP	T	TCGA-2Z-A9J1-01A-11D-A382-10	9376120	102108717	57029946	45	106											
KCND2	3751	hgsc.bcm.edu	37	chr7	119915439	119915439	+	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	ttgcttcgcctggctgcagcGcctagtcgttaccgttttgt	3	15	11	12	4	0	0	0	0	0	0	2	0	0	0	3	1	4	5	3	1	2	6			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr7:119915439G>T	ENST00000331113.4	+	1	1718	c.753G>T	c.(751-753)gcG>gcT	p.A251A		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)	TGGCTGCAGCGCCTAGTCGTT	0.532																																					p.A251A		Atlas-SNP	.											.	KCND2	194	.	0			c.G753T						PASS	.						184	152	163					7																	119915439		2203	4300	6503	SO:0001819	synonymous_variant	3751	exon1			TGCAGCGCCTAGT	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.753G>T	chr7.hg19:g.119915439G>T		69.0	0.0	.		82.0	25.0	.	NM_012281	O95012|O95021|Q2TBD3|Q9UBY7|Q9UN98|Q9UNH9	Silent	SNP	ENST00000331113.4	hg19	CCDS5776.1																																																																																			.	.	.	none		0.532	KCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346996.1	NM_012281		T	119915439	G	T	119915439	2	4	2	1	0	0	0	0	0	0	0	1	8026	1074	38	4		4	KCND2	7	119915439	Silent	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	17806722	119915439	39223224	46	107											
CALU	813	hgsc.bcm.edu	37	chr7	128399077	128399077	+	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	aggagtatgactacatgaaaGatatagtagtacaggtgggt	15	10	13	3	0	0	3	0	2	0	1	0	4	0	4	0	3	2	3	0	3	7	6			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr7:128399077G>C	ENST00000249364.4	+	4	670	c.568G>C	c.(568-570)Gat>Cat	p.D190H	CALU_ENST00000535011.2_Missense_Mutation_p.D190H|CALU_ENST00000538546.1_Missense_Mutation_p.D39H|CALU_ENST00000542996.2_Missense_Mutation_p.D198H|CALU_ENST00000449187.2_Missense_Mutation_p.D190H|RN7SL81P_ENST00000493781.2_RNA|CALU_ENST00000535623.1_3'UTR|CALU_ENST00000479257.1_Missense_Mutation_p.D198H	NM_001219.4	NP_001210.1	O43852	CALU_HUMAN	calumenin	190	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|sarcoplasmic reticulum (GO:0016529)	calcium ion binding (GO:0005509)			kidney(2)|large_intestine(3)|lung(5)	10						CTACATGAAAGATATAGTAGT	0.448																																					p.D198H		Atlas-SNP	.											.	CALU	42	.	0			c.G592C						PASS	.						182	188	186					7																	128399077		2203	4300	6503	SO:0001583	missense	813	exon5			ATGAAAGATATAG	AF013759	CCDS5805.1, CCDS47703.1, CCDS56506.1, CCDS56507.1, CCDS56508.1	7q32	2013-01-10			ENSG00000128595	ENSG00000128595		"EF-hand domain containing"	1458	protein-coding gene	gene with protein product		603420				9598325	Standard	NM_001219		Approved		uc003vnq.3	O43852	OTTHUMG00000158274	ENST00000249364.4:c.568G>C	chr7.hg19:g.128399077G>C	ENSP00000249364:p.Asp190His	160.0	0.0	.		267.0	86.0	.	NM_001199671	B3KPG9|D6QS48|D6QS49|D6QS50|D6QS51|D6QS52|D6QS53|D6QS54|D6QS55|D6QS56|D6QS57|D6QS58|D6QS59|F5H1Q9|F5H879|O60456|Q6FHB9|Q96RL3|Q9NR43	Missense_Mutation	SNP	ENST00000249364.4	hg19	CCDS5805.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.6|27.6	4.848469|4.848469	0.91277|0.91277	.|.	.|.	ENSG00000128595|ENSG00000128595	ENST00000542996;ENST00000538394;ENST00000535011;ENST00000538546;ENST00000249364;ENST00000449187;ENST00000479257|ENST00000493278	T;T;T;T;T;T|.	0.72615|.	-0.67;-0.67;-0.67;-0.67;-0.67;-0.67|.	6.08|6.08	6.08|6.08	0.98989|0.98989	EF-hand-like domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.78923|0.78923	0.4360|0.4360	M|M	0.80847|0.80847	2.515|2.515	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.85130|.	0.997;0.982|.	T|T	0.78188|0.78188	-0.2301|-0.2301	10|5	0.52906|.	T|.	0.07|.	-11.1092|-11.1092	18.1659|18.1659	0.89727|0.89727	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	198;190|.	D6QS48;O43852|.	.;CALU_HUMAN|.	H|T	198;190;190;39;190;190;198|21	ENSP00000438248:D198H;ENSP00000442110:D190H;ENSP00000438994:D39H;ENSP00000249364:D190H;ENSP00000408838:D190H;ENSP00000420381:D198H|.	ENSP00000249364:D190H|.	D|R	+|+	1|2	0|0	CALU|CALU	128186313|128186313	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.924000|0.924000	0.55760|0.55760	5.650000|5.650000	0.67944|0.67944	2.894000|2.894000	0.99253|0.99253	0.591000|0.591000	0.81541|0.81541	GAT|AGA	.	.	.	none		0.448	CALU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350533.1	NM_001219		C	128399077	G	C	128399077	3	2	2	1	0	0	0	0	1	0	0	0	2596	942	33	4	776	4	CALU	7	128399077	Missense_Mutation	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	8483638	128399077	30739586	47	108											
PODXL	5420	hgsc.bcm.edu	37	chr7	131241029	131241029	+	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	ggccactcaccattctgggaGggcgacggcgacggcgacgg	7	4	17	13	6	2	0	1	0	1	0	2	4	2	1	2	6	0	0	2	6	0	1	rs11277659|rs547816245|rs532078953|rs79759078|rs571821675	byFrequency	TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr7:131241029G>C	ENST00000378555.3	-	1	337	c.90C>G	c.(88-90)ccC>ccG	p.P30P	PODXL_ENST00000465001.1_Intron|PODXL_ENST00000537928.1_Silent_p.P30P|PODXL_ENST00000541194.1_Silent_p.P30P|PODXL_ENST00000322985.9_Silent_p.P30P			O00592	PODXL_HUMAN	podocalyxin-like	30					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					CATTCTGGGAGggcgacggcg	0.751																																					p.P30P		Atlas-SNP	.											.	PODXL	53	.	0			c.C90G						PASS	.						5	7	6					7																	131241029		1981	3946	5927	SO:0001819	synonymous_variant	5420	exon1			CTGGGAGGGCGAC		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.90C>G	chr7.hg19:g.131241029G>C		134.0	0.0	.		119.0	5.0	.	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Silent	SNP	ENST00000378555.3	hg19	CCDS34755.1																																																																																			.	.	.	none		0.751	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111		C	131241029	G	C	131241029	2	2	2	1	0	0	0	0	0	0	0	1	12187	987	35	4		4	PODXL	7	131241029	Silent	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	2841952	131241029	27897634	48	109											
NUP205	23165	hgsc.bcm.edu	37	chr7	135304279	135304279	+	Missense_Mutation	SNP	T	T	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	tcactgaacagaaggaaacaTcagtcttgggaccagcagag	15	6	11	9	0	3	3	2	1	1	2	3	5	3	5	1	2	3	1	1	2	3	1	rs368979726		TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr7:135304279T>G	ENST00000285968.6	+	29	4098	c.4072T>G	c.(4072-4074)Tca>Gca	p.S1358A		NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	1358					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						GAAGGAAACATCAGTCTTGGG	0.512																																					p.S1358A		Atlas-SNP	.											.	NUP205	198	.	0			c.T4072G						PASS	.						105	97	100					7																	135304279		2203	4300	6503	SO:0001583	missense	23165	exon29			GAAACATCAGTCT	D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"chromosome 7 open reading frame 14"	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.4072T>G	chr7.hg19:g.135304279T>G	ENSP00000285968:p.Ser1358Ala	80.0	0.0	.		124.0	66.0	.	NM_015135	A6H8X3|Q86YC1	Missense_Mutation	SNP	ENST00000285968.6	hg19	CCDS34759.1	.	.	.	.	.	.	.	.	.	.	T	0.014	-1.590307	0.00864	.	.	ENSG00000155561	ENST00000285968	T	0.32515	1.45	5.67	-5.37	0.02681	.	0.440675	0.20449	N	0.092139	T	0.09379	0.0231	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31752	-0.9932	10	0.07644	T	0.81	-14.6623	3.48	0.07598	0.1026:0.2499:0.415:0.2326	.	1358	Q92621	NU205_HUMAN	A	1358	ENSP00000285968:S1358A	ENSP00000285968:S1358A	S	+	1	0	NUP205	134954819	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	-0.303000	0.08210	-0.845000	0.04179	0.397000	0.26171	TCA	.	.	.	alt		0.512	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1			G	135304279	T	G	135304279	3	3	2	1	0	0	0	0	1	0	0	0	10766	1435	50	5	4186	5	NUP205	7	135304279	Missense_Mutation	SNP	T	TCGA-2Z-A9J1-01A-11D-A382-10	4063250	135304279	23834384	49	110											
SHH	6469	hgsc.bcm.edu	37	chr7	155595950	155595950	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgggccgtgagcggcgcgtAggcgcccgcggcctcctcgc	2	5	17	17	8	0	1	0	1	0	0	2	1	1	1	4	4	1	1	4	4	1	1			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr7:155595950A>G	ENST00000297261.2	-	3	1183	c.1033T>C	c.(1033-1035)Tac>Cac	p.Y345H		NM_000193.2	NP_000184.1	Q15465	SHH_HUMAN	sonic hedgehog	345					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)		AGCGGCGCGTAGGCGCCCGCG	0.731																																					p.Y345H		Atlas-SNP	.											.	SHH	34	.	0			c.T1033C						PASS	.						5	4	5					7																	155595950		1760	3591	5351	SO:0001583	missense	6469	exon3			GCGCGTAGGCGCC		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.1033T>C	chr7.hg19:g.155595950A>G	ENSP00000297261:p.Tyr345His	1212.0	0.0	.		963.0	232.0	.	NM_000193	A4D247|Q75MC9	Missense_Mutation	SNP	ENST00000297261.2	hg19	CCDS5942.1	.	.	.	.	.	.	.	.	.	.	a	16.31	3.085965	0.55861	.	.	ENSG00000164690	ENST00000297261	D	0.99727	-6.55	3.6	3.6	0.41247	Hedgehog/intein hint domain, C-terminal (1);Peptidase C46, hedgehog protein, hint region (1);	0.326281	0.29080	N	0.013202	D	0.99701	0.9886	M	0.91972	3.26	0.46542	D	0.999093	D;D	0.76494	0.997;0.999	D;D	0.77557	0.959;0.99	D	0.97578	1.0109	10	0.87932	D	0	.	12.3657	0.55226	1.0:0.0:0.0:0.0	.	345;348	Q15465;D9ZGF9	SHH_HUMAN;.	H	345	ENSP00000297261:Y345H	ENSP00000297261:Y345H	Y	-	1	0	SHH	155288711	1.000000	0.71417	0.995000	0.50966	0.917000	0.54804	8.289000	0.89923	1.502000	0.48669	0.398000	0.26397	TAC	.	.	.	none		0.731	SHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322327.1	NM_000193		G	155595950	A	G	155595950	3	3	2	1	0	0	0	0	1	0	0	0	14292	420	15	3	359	3	SHH	7	155595950	Missense_Mutation	SNP	A	TCGA-2Z-A9J1-01A-11D-A382-10	20291671	155595950	3542713	50	111											
DLC1	10395	hgsc.bcm.edu	37	chr8	13251117	13251117	+	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	gagtggaagatgggaggtccGtggactcagtgtcagaagac	11	7	17	6	1	2	3	2	0	0	3	3	7	3	6	1	4	0	0	1	4	2	0	rs528243762		TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr8:13251117G>C	ENST00000276297.4	-	4	1668	c.1259C>G	c.(1258-1260)aCg>aGg	p.T420R	DLC1_ENST00000511869.1_Missense_Mutation_p.T420R|DLC1_ENST00000316609.5_Missense_Mutation_p.T420R	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	420					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						TGGGAGGTCCGTGGACTCAGT	0.408																																					p.T420R		Atlas-SNP	.											.	DLC1	411	.	0			c.C1259G						PASS	.						152	146	148					8																	13251117		2203	4300	6503	SO:0001583	missense	10395	exon4			AGGTCCGTGGACT	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.1259C>G	chr8.hg19:g.13251117G>C	ENSP00000276297:p.Thr420Arg	84.0	0.0	.		91.0	31.0	.	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Missense_Mutation	SNP	ENST00000276297.4	hg19	CCDS5989.1	.	.	.	.	.	.	.	.	.	.	G	10.23	1.291766	0.23564	.	.	ENSG00000164741	ENST00000276297;ENST00000316609;ENST00000511869	T;T;T	0.14022	3.59;2.54;2.58	4.78	-2.55	0.06288	.	1.511200	0.04057	N	0.305696	T	0.11836	0.0288	L	0.29908	0.895	0.09310	N	1	P;P;P	0.37781	0.603;0.485;0.608	B;B;B	0.43360	0.417;0.299;0.144	T	0.20672	-1.0268	10	0.41790	T	0.15	.	2.5185	0.04674	0.418:0.1155:0.3487:0.1178	.	420;420;420	E9PF76;Q96QB1-3;Q96QB1	.;.;RHG07_HUMAN	R	420	ENSP00000276297:T420R;ENSP00000321034:T420R;ENSP00000425878:T420R	ENSP00000276297:T420R	T	-	2	0	DLC1	13295488	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.428000	0.21395	-0.405000	0.07599	-0.133000	0.14855	ACG	.	.	.	none		0.408	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		C	13251117	G	C	13251117	3	2	2	1	0	0	0	0	1	0	0	0	4552	1145	40	4	3472	4	DLC1	8	13251117	Missense_Mutation	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10		13251117	133112905	51	112											
EPHX2	2053	hgsc.bcm.edu	37	chr8	27398077	27398077	+	Frame_Shift_Del	DEL	T	T	-																															ggctttttttgcaggaggacTttttgtaaatagcccagaag																										TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr8:27398077delT	ENST00000521400.1	+	15	1713	c.1283delT	c.(1282-1284)cttfs	p.L428fs	EPHX2_ENST00000521780.1_Frame_Shift_Del_p.L362fs|EPHX2_ENST00000517536.1_Frame_Shift_Del_p.L245fs|EPHX2_ENST00000518379.1_Frame_Shift_Del_p.L396fs|EPHX2_ENST00000380476.3_Frame_Shift_Del_p.L375fs	NM_001979.5	NP_001970.2	P34913	HYES_HUMAN	epoxide hydrolase 2, cytoplasmic	428	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)		GCAGGAGGACTTTTTGTAAAT	0.498																																					p.L428fs		Atlas-Indel,Pindel	.											.	EPHX2	57	.	0			c.1282delC						PASS	.						73	78	76					8																	27398077		2203	4300	6503	SO:0001589	frameshift_variant	2053	exon15			.	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.1283delT	chr8.hg19:g.27398077delT	ENSP00000430269:p.Leu428fs	141.0	0.0	0		142.0	47.0	0.330986	NM_001979	B2Z3B1|B3KTU8|B3KUA0|G3V134|J3KPH7|Q16764|Q9HBJ1|Q9HBJ2	Frame_Shift_Del	DEL	ENST00000521400.1	hg19	CCDS6060.1																																																																																			.	.	.	none		0.498	EPHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219954.4			-	27398077	T	-	27398077	7	5	2	1	0	1	0	1	0	0	0	0	5182	1609	56	0	1341	0	EPHX2	8	27398077	Frame_Shift_Del	DEL	T	TCGA-2Z-A9J1-01A-11D-A382-10	14146960	27398077	118965945	52	113											
VDAC3	7419	hgsc.bcm.edu	37	chr8	42262963	42262963	+	Frame_Shift_Del	DEL	T	T	-																															gtcacaaggttggcttgggaTttgaactggaagcttaatgt																										TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr8:42262963delT	ENST00000022615.4	+	10	903	c.835delT	c.(835-837)tttfs	p.F279fs	VDAC3_ENST00000392935.3_Frame_Shift_Del_p.F280fs|VDAC3_ENST00000521158.1_Frame_Shift_Del_p.F280fs|VDAC3_ENST00000522572.1_Frame_Shift_Del_p.F130fs			Q9Y277	VDAC3_HUMAN	voltage-dependent anion channel 3	279					adenine transport (GO:0015853)	extracellular vesicular exosome (GO:0070062)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|pore complex (GO:0046930)	nucleotide binding (GO:0000166)|porin activity (GO:0015288)|voltage-gated anion channel activity (GO:0008308)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	7	all_cancers(6;3.86e-23)|all_lung(13;6.47e-12)|Lung NSC(13;1.08e-10)|Ovarian(28;0.00769)|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;3.48e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00266)|Lung(22;0.00849)|LUSC - Lung squamous cell carcinoma(45;0.024)		Dihydroxyaluminium(DB01375)	TGGCTTGGGATTTGAACTGGA	0.408																																					p.G279fs		Atlas-Indel,Pindel	.											.	VDAC3	17	.	0			c.837delA						PASS	.						166	161	163					8																	42262963		2203	4300	6503	SO:0001589	frameshift_variant	7419	exon10			.	AF038962	CCDS6131.1, CCDS47850.1	8p11.21	2011-11-15			ENSG00000078668	ENSG00000078668		"Voltage-dependent anion channels"	12674	protein-coding gene	gene with protein product		610029				9653160, 9781040	Standard	NM_001135694		Approved	HD-VDAC3	uc003xpc.3	Q9Y277	OTTHUMG00000164168	ENST00000022615.4:c.835delT	chr8.hg19:g.42262963delT	ENSP00000022615:p.Phe279fs	146.0	0.0	0		145.0	43.0	0.296552	NM_001135694	Q9UIS0	Frame_Shift_Del	DEL	ENST00000022615.4	hg19	CCDS6131.1																																																																																			.	.	.	none		0.408	VDAC3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000377574.1			-	42262963	T	-	42262963	7	5	2	1	0	1	0	1	0	0	0	0	17160	1493	52	0	868	0	VDAC3	8	42262963	Frame_Shift_Del	DEL	T	TCGA-2Z-A9J1-01A-11D-A382-10	14864886	42262963	104101059	53	114											
CEP110	11064	hgsc.bcm.edu	37	chr9	123898196	123898196	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgagctagaggctcggctaaAcctaagggatgctgaagcca	12	7	13	9	1	0	3	0	2	0	1	1	4	0	4	2	3	4	4	2	3	5	3			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr9:123898196A>G	ENST00000373855.1	+	15	2398	c.2138A>G	c.(2137-2139)aAc>aGc	p.N713S	CNTRL_ENST00000238341.5_Missense_Mutation_p.N713S|CNTRL_ENST00000373850.1_Missense_Mutation_p.N161S|CNTRL_ENST00000373847.1_Missense_Mutation_p.N161S			Q7Z7A1	CNTRL_HUMAN	centriolin	713					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						GCTCGGCTAAACCTAAGGGAT	0.493																																					p.N713S		Atlas-SNP	.											.	CNTRL	161	.	0			c.A2138G						PASS	.						71	61	64					9																	123898196		2203	4300	6503	SO:0001583	missense	11064	exon13			GGCTAAACCTAAG	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.2138A>G	chr9.hg19:g.123898196A>G	ENSP00000362962:p.Asn713Ser	129.0	0.0	.		147.0	58.0	.	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	hg19	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	A	2.901	-0.227527	0.06022	.	.	ENSG00000119397	ENST00000373855;ENST00000238341;ENST00000454238;ENST00000373851;ENST00000373850;ENST00000373847	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	5.78	0.0413	0.14213	.	.	.	.	.	T	0.21186	0.0510	N	0.08118	0	0.09310	N	1	B;B;B	0.14012	0.0;0.009;0.0	B;B;B	0.13407	0.0;0.009;0.0	T	0.23619	-1.0183	9	0.24483	T	0.36	.	9.828	0.40923	0.4762:0.0:0.5238:0.0	.	713;713;713	B2RP65;F5GZN0;Q7Z7A1	.;.;CNTRL_HUMAN	S	713;713;713;195;161;161	ENSP00000362962:N713S;ENSP00000238341:N713S;ENSP00000362956:N161S;ENSP00000362953:N161S	ENSP00000238341:N713S	N	+	2	0	CNTRL	122938017	0.122000	0.22280	0.002000	0.10522	0.009000	0.06853	0.478000	0.22212	-0.052000	0.13311	-0.250000	0.11733	AAC	.	.	.	none		0.493	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018		G	123898196	A	G	123898196	3	3	2	1	0	0	0	0	1	0	0	0	3247	43	2	3	2188	3	CEP110	9	123898196	Missense_Mutation	SNP	A	TCGA-2Z-A9J1-01A-11D-A382-10		123898196	17315235	54	115											
GPSM1	26086	hgsc.bcm.edu	37	chr9	139235387	139235387	+	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	tggcgcagctgcagctggtgCtcggccgcctgaccagcccg	4	6	15	16	4	0	1	0	1	0	0	1	1	0	1	4	3	5	5	4	3	0	0			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr9:139235387C>A	ENST00000440944.1	+	9	1364	c.1144C>A	c.(1144-1146)Ctc>Atc	p.L382I	GPSM1_ENST00000392945.3_Missense_Mutation_p.L382I	NM_001145638.1	NP_001139110	Q86YR5	GPSM1_HUMAN	G-protein signaling modulator 1	382	Interaction with STK11/LKB1. {ECO:0000250}.|Mediates association with membranes. {ECO:0000250}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GDP-dissociation inhibitor activity (GO:0005092)			biliary_tract(1)|endometrium(1)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)		GCAGCTGGTGCTCGGCCGCCT	0.711																																					p.L382I		Atlas-SNP	.											.	GPSM1	50	.	0			c.C1144A						PASS	.						10	12	11					9																	139235387		2122	4195	6317	SO:0001583	missense	26086	exon9			CTGGTGCTCGGCC	AI272212	CCDS6996.2, CCDS48055.1, CCDS48056.1	9q34.3	2013-01-10	2010-06-24		ENSG00000160360	ENSG00000160360		"Tetratricopeptide (TTC) repeat domain containing"	17858	protein-coding gene	gene with protein product	"AGS3 homolog (C. elegans)"	609491	"G-protein signalling modulator 1 (AGS3-like, C. elegans)"			11278352, 10969064	Standard	NM_001145639		Approved	AGS3, DKFZP727I051	uc004chd.2	Q86YR5	OTTHUMG00000020930	ENST00000440944.1:c.1144C>A	chr9.hg19:g.139235387C>A	ENSP00000392828:p.Leu382Ile	126.0	0.0	.		83.0	30.0	.	NM_015597	A9Z1X4|B1B0W3|Q86SR5|Q969T1|Q9UFS8	Missense_Mutation	SNP	ENST00000440944.1	hg19	CCDS48055.1	.	.	.	.	.	.	.	.	.	.	C	16.27	3.074785	0.55646	.	.	ENSG00000160360	ENST00000392945;ENST00000440944;ENST00000354753	T;T;T	0.79554	-1.28;-1.28;-1.28	3.91	3.91	0.45181	Tetratricopeptide-like helical (1);	0.098698	0.42420	D	0.000720	D	0.89114	0.6623	M	0.77103	2.36	0.80722	D	1	P;P	0.47545	0.897;0.797	D;P	0.74674	0.984;0.88	D	0.89811	0.3982	10	0.51188	T	0.08	-11.6845	15.0757	0.72074	0.0:1.0:0.0:0.0	.	382;382	Q86YR5;Q86YR5-3	GPSM1_HUMAN;.	I	382;382;359	ENSP00000376674:L382I;ENSP00000392828:L382I;ENSP00000346797:L359I	ENSP00000346797:L359I	L	+	1	0	GPSM1	138355208	0.995000	0.38212	0.895000	0.35142	0.190000	0.23558	3.345000	0.52182	2.028000	0.59812	0.462000	0.41574	CTC	.	.	.	none		0.711	GPSM1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015597		A	139235387	C	A	139235387	3	1	2	1	0	0	0	0	1	0	0	0	6741	797	28	4	1178	4	GPSM1	9	139235387	Missense_Mutation	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10	15337191	139235387	1978044	55	116											
ITIH2	3698	hgsc.bcm.edu	37	chr10	7773959	7773959	+	Splice_Site	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	agcgttatcacggcgacttcGgtacttccacttatccattt	8	14	7	12	4	1	0	1	0	0	0	4	1	3	0	2	2	2	2	2	2	3	6			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr10:7773959G>T	ENST00000358415.4	+	13	1813	c.1647G>T	c.(1645-1647)tcG>tcT	p.S549S	ITIH2_ENST00000379587.4_Splice_Site_p.S538S	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	549					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						CGGCGACTTCGGTACTTCCAC	0.443																																					p.S549S		Atlas-SNP	.											.	ITIH2	144	.	0			c.G1647T						PASS	.						110	103	106					10																	7773959		2203	4300	6503	SO:0001630	splice_region_variant	3698	exon13			GACTTCGGTACTT	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.1647+1G>T	chr10.hg19:g.7773959G>T		88.0	0.0	.		83.0	28.0	.	NM_002216	Q14659|Q15484|Q5T986	Silent	SNP	ENST00000358415.4	hg19	CCDS31141.1																																																																																			.	.	.	none		0.443	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216	Silent	T	7773959	G	T	7773959	5	4	2	1	0	0	0	0	0	0	1	0	7911	1130	39	4	1697	4	ITIH2	10	7773959	Splice_Site	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10		7773959	127760788	56	117											
TNKS2	80351	hgsc.bcm.edu	37	chr10	93593660	93593660	+	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	tctctacacagagctgcataTtgtggtcatctacaaacctg	11	12	7	11	0	3	1	1	0	2	1	4	1	3	1	1	1	5	2	1	1	4	4			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr10:93593660T>A	ENST00000371627.4	+	12	1705	c.1326T>A	c.(1324-1326)taT>taA	p.Y442*		NM_025235.3	NP_079511.1	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2	442					multicellular organism growth (GO:0035264)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein polyubiquitination (GO:0000209)|regulation of multicellular organism growth (GO:0040014)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			biliary_tract(1)|breast(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	48		Colorectal(252;0.162)				GAGCTGCATATTGTGGTCATC	0.398																																					p.Y442X		Atlas-SNP	.											.	TNKS2	103	.	0			c.T1326A						PASS	.						143	128	133					10																	93593660		2203	4300	6503	SO:0001587	stop_gained	80351	exon12			TGCATATTGTGGT	AF342982	CCDS7417.1	10q23.3	2013-01-10			ENSG00000107854	ENSG00000107854		"Poly (ADP-ribose) polymerases", "Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15677	protein-coding gene	gene with protein product		607128					Standard	NM_025235		Approved	TNKL, TANK2, PARP-5b, PARP-5c, PARP5B, PARP5C, pART6	uc001khp.3	Q9H2K2	OTTHUMG00000018747	ENST00000371627.4:c.1326T>A	chr10.hg19:g.93593660T>A	ENSP00000360689:p.Tyr442*	72.0	0.0	.		111.0	43.0	.	NM_025235	B2RBD3|Q9H8F2|Q9HAS4	Nonsense_Mutation	SNP	ENST00000371627.4	hg19	CCDS7417.1	.	.	.	.	.	.	.	.	.	.	T	40	7.973135	0.98588	.	.	ENSG00000107854	ENST00000371627	.	.	.	5.83	-0.787	0.10943	.	0.091772	0.47093	D	0.000248	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.2073	0.54358	0.0:0.6102:0.0:0.3898	.	.	.	.	X	442	.	ENSP00000360689:Y442X	Y	+	3	2	TNKS2	93583640	0.632000	0.27172	0.995000	0.50966	0.860000	0.49131	-0.277000	0.08502	-0.088000	0.12506	0.533000	0.62120	TAT	.	.	.	none		0.398	TNKS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049374.1	NM_025235		A	93593660	T	A	93593660	4	1	2	1	0	0	0	0	0	1	0	0	16333	1500	52	5	1372	5	TNKS2	10	93593660	Nonsense_Mutation	SNP	T	TCGA-2Z-A9J1-01A-11D-A382-10	85819701	93593660	41941087	57	118											
KRTAP5-5	439915	hgsc.bcm.edu	37	chr11	1651643	1651645	+	In_Frame_Del	DEL	CTA	CTA	-																															cagtccagctgctgtaagccCtactgctgccagtccagctg																								rs576867883|rs4752771|rs71025765|rs77039648		TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	CTA	CTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr11:1651643_1651645delCTA	ENST00000399676.2	+	1	611_613	c.573_575delCTA	c.(571-576)ccctac>ccc	p.Y192del		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	192	8 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)		p.Y182_P191delYCCQSSCCKP(1)		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)		GCTGTAAGCCCTACTGCTGCCAG	0.606																																					p.191_192del		Atlas-INDEL	.											.	KRTAP5-5	86	.	1	Deletion - In frame(1)	urinary_tract(1)	c.572_574del						PASS	.																																			SO:0001651	inframe_deletion	439915	exon1			.	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.573_575delCTA	chr11.hg19:g.1651643_1651645delCTA	ENSP00000382584:p.Tyr192del	70.0	0.0	0		56.0	14.0	0.25	NM_001001480	A8MWN2	In_Frame_Del	DEL	ENST00000399676.2	hg19	CCDS41592.1																																																																																			.	.	.	none		0.606	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1			-	1651645	CTA	-	1651643	7	5	2	1	0	1	0	1	0	0	0	0	8571	668	24	0	575	0	KRTAP5-5	11	1651643	In_Frame_Del	DEL	CTA	TCGA-2Z-A9J1-01A-11D-A382-10		1651643	133354873	58	119											
KRTAP5-8	57830	hgsc.bcm.edu	37	chr11	71249121	71249121	+	Missense_Mutation	SNP	C	C	G																															catgggctgctgtggctgctCtggaggctgtggctccggct																								rs200585722		TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr11:71249121C>G	ENST00000398534.3	+	1	51	c.20C>G	c.(19-21)tCt>tGt	p.S7C		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	7						keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						TGTGGCTGCTCTGGAGGCTGT	0.657																																					p.S7C		Atlas-SNP	.											.	KRTAP5-8	28	.	0			c.C20G						PASS	.						47	66	60					11																	71249121		2189	4282	6471	SO:0001583	missense	57830	exon1			GCTGCTCTGGAGG	AB126077	CCDS41683.1	11q13.4	2008-02-05			ENSG00000241233	ENSG00000241233		"Keratin associated proteins"	23603	protein-coding gene	gene with protein product						15144888	Standard	NM_021046		Approved	KRTAP5.8, UHSKerB, KRTAP5-2	uc001oqr.1	O75690	OTTHUMG00000057571	ENST00000398534.3:c.20C>G	chr11.hg19:g.71249121C>G	ENSP00000420723:p.Ser7Cys	110.0	0.0	.		92.0	16.0	.	NM_021046	Q6L8G7|Q6UTX6	Missense_Mutation	SNP	ENST00000398534.3	hg19	CCDS41683.1	.	.	.	.	.	.	.	.	.	.	c	3.358	-0.131059	0.06753	.	.	ENSG00000241233	ENST00000398534	T	0.01527	4.8	1.57	1.57	0.23409	.	.	.	.	.	T	0.03564	0.0102	M	0.74389	2.26	0.09310	N	1	P	0.39094	0.659	B	0.43225	0.412	T	0.34204	-0.9838	9	0.62326	D	0.03	.	3.9595	0.09404	0.0:0.775:0.0:0.225	.	7	O75690	KRA58_HUMAN	C	7	ENSP00000420723:S7C	ENSP00000420723:S7C	S	+	2	0	KRTAP5-8	70926769	0.030000	0.19436	0.804000	0.32291	0.223000	0.24884	-0.589000	0.05767	1.182000	0.42928	0.514000	0.50259	TCT	.	.	.	weak		0.657	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046		G	71249121	C	G	71249121	3	3	2	1	0	0	0	0	1	0	0	0	8574	913	32	4	22	4	KRTAP5-8	11	71249121	Missense_Mutation	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10	69597478	71249121	63757395	59	120	1	2									
KRTAP5-8	57830	hgsc.bcm.edu	37	chr11	71249125	71249125	+	Silent	SNP	A	A	G																															ggctgctgtggctgctctggAggctgtggctccggctgtgg																								rs537752041|rs113379698|rs55848980	byFrequency	TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr11:71249125A>G	ENST00000398534.3	+	1	55	c.24A>G	c.(22-24)ggA>ggG	p.G8G		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	8						keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						GCTGCTCTGGAGGCTGTGGCT	0.652																																					p.G8G		Atlas-SNP	.											KRTAP5-8,rectum,carcinoma,0,1	KRTAP5-8	28	.	0			c.A24G						PASS	.						47	66	60					11																	71249125		2189	4280	6469	SO:0001819	synonymous_variant	57830	exon1			CTCTGGAGGCTGT	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.24A>G	chr11.hg19:g.71249125A>G		104.0	1.0	.		91.0	18.0	.	NM_021046	Q6L8G7|Q6UTX6	Silent	SNP	ENST00000398534.3	hg19	CCDS41683.1																																																																																			.	A|0.500;G|0.500	0.500	weak		0.652	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046		G	71249125	A	G	71249125	2	3	2	1	0	0	0	0	0	0	0	1	8574	291	11	3		3	KRTAP5-8	11	71249125	Silent	SNP	A	TCGA-2Z-A9J1-01A-11D-A382-10	4	71249125	63757391	60	121	1	2									
P4HA3	283208	hgsc.bcm.edu	37	chr11	74009326	74009327	+	Frame_Shift_Ins	INS	-	-	C																															catcctctgtcttccactctINSccgtaagatcctcggaagag																										TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr11:74009326_74009327insC	ENST00000331597.4	-	4	692_693	c.647_648insG	c.(646-648)ggafs	p.G216fs	P4HA3_ENST00000427714.2_Frame_Shift_Ins_p.G216fs	NM_182904.3	NP_878907.1	Q7Z4N8	P4HA3_HUMAN	prolyl 4-hydroxylase, alpha polypeptide III	216						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)					TCTTCCACTCTCCGTAAGATCC	0.49																																					p.G216fs		Atlas-Indel,Pindel	.											.	P4HA3	43	.	0			c.648_649insG						PASS	.																																			SO:0001589	frameshift_variant	283208	exon4			.	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.648dupG	chr11.hg19:g.74009328_74009328dupC	ENSP00000332170:p.Gly216fs	28.0	0.0	0		74.0	27.0	0.364865	NM_182904	A0AV13|B4DUD3|Q5EBL3|Q5JPA9	Frame_Shift_Ins	INS	ENST00000331597.4	hg19	CCDS8230.1																																																																																			.	.	.	none		0.49	P4HA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382988.1	NM_182904		C	74009327	-	C	74009326	7	5	2	1	0	1	1	0	0	0	0	0	11365	1538	54	0	1026	0	P4HA3	11	74009326	Frame_Shift_Ins	INS	-	TCGA-2Z-A9J1-01A-11D-A382-10	2760201	74009326	60997190	61	122											
ATM	472	hgsc.bcm.edu	37	chr11	108192079	108192079	+	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	agccttgagtctgtgtattcGctctatcccacacttagcag	8	13	8	12	1	2	1	0	1	2	0	4	1	3	1	2	0	2	3	2	0	3	5			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr11:108192079G>T	ENST00000452508.2	+	46	6693	c.6504G>T	c.(6502-6504)tcG>tcT	p.S2168S	ATM_ENST00000278616.4_Silent_p.S2168S|C11orf65_ENST00000525729.1_Intron			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2168	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				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)	CTGTGTATTCGCTCTATCCCA	0.408			"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.S2168S		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	.	ATM	1657	.	0			c.G6504T						PASS	.						169	157	161					11																	108192079		2201	4298	6499	SO:0001819	synonymous_variant	472	exon45	Familial Cancer Database	AT, Louis-Bar syndrome	GTATTCGCTCTAT	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.6504G>T	chr11.hg19:g.108192079G>T		86.0	0.0	.		86.0	4.0	.	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Silent	SNP	ENST00000452508.2	hg19	CCDS31669.1																																																																																			.	.	.	none		0.408	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		T	108192079	G	T	108192079	2	4	2	1	0	0	0	0	0	0	0	1	1109	1074	38	4		4	ATM	11	108192079	Silent	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	34182753	108192079	26814437	62	123											
PHLDB1	23187	hgsc.bcm.edu	37	chr11	118498946	118498946	+	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	tctctgtcccggcgagctctCtccccgctgcccacccggac	3	8	9	21	4	2	0	0	0	2	0	6	2	4	1	5	2	2	2	5	2	0	0			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr11:118498946C>T	ENST00000361417.2	+	7	1818	c.1407C>T	c.(1405-1407)ctC>ctT	p.L469L	PHLDB1_ENST00000356063.5_Silent_p.L469L	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	469										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)		GGCGAGCTCTCTCCCCGCTGC	0.677																																					p.L469L		Atlas-SNP	.											.	PHLDB1	103	.	0			c.C1407T						PASS	.						55	68	64					11																	118498946		2200	4295	6495	SO:0001819	synonymous_variant	23187	exon6			AGCTCTCTCCCCG		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.1407C>T	chr11.hg19:g.118498946C>T		151.0	0.0	.		127.0	12.0	.	NM_001144758	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Silent	SNP	ENST00000361417.2	hg19	CCDS8401.1																																																																																			.	.	.	none		0.677	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157		T	118498946	C	T	118498946	2	4	2	1	0	0	0	0	0	0	0	1	11858	900	32	2		2	PHLDB1	11	118498946	Silent	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10	10306867	118498946	16507570	63	124											
CDON	50937	hgsc.bcm.edu	37	chr11	125891166	125891166	+	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	ccacagatactgtcgcagggCcactcacaatggcaccgatg	11	6	10	14	2	1	1	1	0	0	1	2	2	1	1	3	2	1	2	3	2	2	1	rs374113801		TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr11:125891166C>T	ENST00000392693.3	-	3	453	c.326G>A	c.(325-327)gGc>gAc	p.G109D	CDON_ENST00000263577.7_Missense_Mutation_p.G109D	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	109	Ig-like C2-type 1.				anterior/posterior pattern specification (GO:0009952)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cerebral cortex development (GO:0021987)|embryonic body morphogenesis (GO:0010172)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|lens development in camera-type eye (GO:0002088)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein heterodimerization activity (GO:0043497)|skeletal muscle satellite cell differentiation (GO:0014816)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(9)|ovary(3)|prostate(2)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	61	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		TGTCGCAGGGCCACTCACAAT	0.438																																					p.G109D		Atlas-SNP	.											.	CDON	137	.	0			c.G326A						PASS	.						50	50	50					11																	125891166		2201	4299	6500	SO:0001583	missense	50937	exon3			GCAGGGCCACTCA	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.326G>A	chr11.hg19:g.125891166C>T	ENSP00000376458:p.Gly109Asp	45.0	0.0	.		55.0	22.0	.	NM_016952	O14631	Missense_Mutation	SNP	ENST00000392693.3	hg19	CCDS58192.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.459|7.459	0.644339|0.644339	0.14451|0.14451	.|.	.|.	ENSG00000064309|ENSG00000064309	ENST00000392693;ENST00000263577;ENST00000531586;ENST00000527967;ENST00000534818|ENST00000534661	T;T;T;T;T|.	0.76060|.	2.79;2.79;2.79;2.79;-0.99|.	5.78|5.78	2.38|2.38	0.29361|0.29361	Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	1.028080|.	0.07726|.	N|.	0.944420|.	T|.	0.19525|.	0.0469|.	N|N	0.10645|0.10645	0.015|0.015	0.09310|0.09310	N|N	1|1	B;P;B|.	0.34615|.	0.001;0.459;0.404|.	B;B;B|.	0.43575|.	0.003;0.424;0.299|.	T|.	0.24225|.	-1.0166|.	10|.	0.18710|.	T|.	0.47|.	-3.2722|-3.2722	10.1949|10.1949	0.43049|0.43049	0.0:0.7427:0.1165:0.1408|0.0:0.7427:0.1165:0.1408	.|.	109;109;109|.	E9PRD8;Q4KMG0;Q4KMG0-2|.	.;CDON_HUMAN;.|.	D|X	109|84	ENSP00000376458:G109D;ENSP00000263577:G109D;ENSP00000434212:G109D;ENSP00000436940:G109D;ENSP00000437176:G109D|.	ENSP00000263577:G109D|.	G|W	-|-	2|3	0|0	CDON|CDON	125396376|125396376	0.000000|0.000000	0.05858|0.05858	0.350000|0.350000	0.25708|0.25708	0.421000|0.421000	0.31385|0.31385	0.293000|0.293000	0.19029|0.19029	0.760000|0.760000	0.33108|0.33108	0.563000|0.563000	0.77884|0.77884	GGC|TGG	.	.	.	alt		0.438	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952		T	125891166	C	T	125891166	3	4	2	1	0	0	0	0	1	0	0	0	3172	739	26	2	3540	2	CDON	11	125891166	Missense_Mutation	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10	7392220	125891166	9115350	64	125											
CLEC1A	51267	hgsc.bcm.edu	37	chr12	10223995	10223995	+	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	tctggcttcaccattcctgcCcttctctcacagacacaacg	8	11	5	17	1	4	1	2	0	2	1	6	1	5	1	3	1	2	1	3	1	1	3			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr12:10223995C>G	ENST00000315330.4	-	6	842	c.780G>C	c.(778-780)agG>agC	p.R260S	CLEC1A_ENST00000457018.2_Missense_Mutation_p.R227S|CLEC1A_ENST00000420265.2_Missense_Mutation_p.R168S	NM_016511.2	NP_057595.2	Q8NC01	CLC1A_HUMAN	C-type lectin domain family 1, member A	260					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	23						CCATTCCTGCCCTTCTCTCAC	0.507																																					p.R260S		Atlas-SNP	.											.	CLEC1A	48	.	0			c.G780C						PASS	.						195	172	179					12																	10223995		2203	4300	6503	SO:0001583	missense	51267	exon6			TCCTGCCCTTCTC	AY358587	CCDS8612.1, CCDS73443.1	12p13.31	2005-02-09				ENSG00000150048		"C-type lectin domain containing"	24355	protein-coding gene	gene with protein product		606782				10671229, 11745369	Standard	XM_005253383		Approved	CLEC1, MGC34328	uc001qxb.3	Q8NC01		ENST00000315330.4:c.780G>C	chr12.hg19:g.10223995C>G	ENSP00000326407:p.Arg260Ser	60.0	0.0	.		138.0	65.0	.	NM_016511	Q8IUW7|Q9NZH3	Missense_Mutation	SNP	ENST00000315330.4	hg19	CCDS8612.1	.	.	.	.	.	.	.	.	.	.	C	7.988	0.752743	0.15778	.	.	ENSG00000150048	ENST00000315330;ENST00000457018;ENST00000420265	T;T;T	0.16897	2.31;2.31;2.31	5.33	-3.61	0.04556	C-type lectin fold (1);C-type lectin-like (1);	2.595010	0.01388	N	0.013141	T	0.13372	0.0324	L	0.29908	0.895	0.09310	N	1	B;B;B	0.17465	0.022;0.017;0.005	B;B;B	0.14023	0.005;0.01;0.004	T	0.34625	-0.9821	10	0.54805	T	0.06	.	7.4304	0.27124	0.1095:0.449:0.0:0.4415	.	168;227;260	E7ESV9;E9PFB4;Q8NC01	.;.;CLC1A_HUMAN	S	260;227;168	ENSP00000326407:R260S;ENSP00000415048:R227S;ENSP00000417010:R168S	ENSP00000326407:R260S	R	-	3	2	CLEC1A	10115262	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-2.449000	0.01008	-0.797000	0.04450	-1.119000	0.02030	AGG	.	.	.	none		0.507	CLEC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399924.1	NM_016511		G	10223995	C	G	10223995	3	3	2	1	0	0	0	0	1	0	0	0	3507	622	22	4	66	4	CLEC1A	12	10223995	Missense_Mutation	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10		10223995	123627900	65	126											
KIAA0528	9847	hgsc.bcm.edu	37	chr12	22622701	22622701	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaacacagttccagtggaaaTtgtaaaagttcttcattatc	14	13	7	7	0	2	0	1	0	1	0	4	2	3	1	1	1	1	3	1	1	5	6			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr12:22622701T>C	ENST00000333957.4	-	22	2730	c.2475A>G	c.(2473-2475)caA>caG	p.Q825Q	C2CD5_ENST00000446597.1_Silent_p.Q825Q|C2CD5_ENST00000396028.2_Silent_p.Q816Q|C2CD5_ENST00000542676.1_Silent_p.Q825Q|C2CD5_ENST00000544930.1_Silent_p.Q640Q|C2CD5_ENST00000545552.1_Silent_p.Q838Q|C2CD5_ENST00000536386.1_Silent_p.Q827Q	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	825					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)										CCAGTGGAAATTGTAAAAGTT	0.328																																					p.Q825Q		Atlas-SNP	.											.	.	.	.	0			c.A2475G						PASS	.						94	97	96					12																	22622701		2203	4300	6503	SO:0001819	synonymous_variant	9847	exon22			TGGAAATTGTAAA	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.2475A>G	chr12.hg19:g.22622701T>C		67.0	0.0	.		163.0	36.0	.	NM_014802	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Silent	SNP	ENST00000333957.4	hg19	CCDS31758.1	.	.	.	.	.	.	.	.	.	.	T	7.147	0.583074	0.13749	.	.	ENSG00000111731	ENST00000539615	.	.	.	5.11	1.78	0.24846	.	.	.	.	.	T	0.51839	0.1698	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42068	-0.9473	4	.	.	.	-8.9389	5.1412	0.14959	0.0:0.5095:0.0:0.4905	.	.	.	.	S	109	.	.	N	-	2	0	KIAA0528	22513968	0.997000	0.39634	1.000000	0.80357	0.880000	0.50808	0.254000	0.18314	0.677000	0.31305	-0.777000	0.03380	AAT	.	.	.	none		0.328	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802		C	22622701	T	C	22622701	2	2	2	1	0	0	0	0	0	0	0	1	8189	1490	52	3		3	KIAA0528	12	22622701	Silent	SNP	T	TCGA-2Z-A9J1-01A-11D-A382-10	12398706	22622701	111229194	66	127											
DDX11	1663	hgsc.bcm.edu	37	chr12	31242339	31242339	+	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	ctttctcctttgctgcagaaCctttgtgtaaatgaagacgt	9	15	8	9	1	1	3	0	1	1	2	2	3	1	3	2	0	3	3	2	0	4	4			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr12:31242339C>T	ENST00000407793.2	+	8	1046	c.795C>T	c.(793-795)aaC>aaT	p.N265N	DDX11_ENST00000545668.1_Silent_p.N265N|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000350437.4_Silent_p.N265N|DDX11_ENST00000542838.1_Silent_p.N265N|DDX11_ENST00000228264.6_Silent_p.N239N	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	265	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					TGCTGCAGAACCTTTGTGTAA	0.517										Multiple Myeloma(12;0.14)																											p.N265N		Atlas-SNP	.											.	DDX11	188	.	0			c.C795T						PASS	.						79	77	78					12																	31242339		2203	4300	6503	SO:0001819	synonymous_variant	1663	exon8			GCAGAACCTTTGT	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"DEAD-boxes"	2736	protein-coding gene	gene with protein product	"CHL1-like helicase homolog (S. cerevisiae)"	601150	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)", "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.795C>T	chr12.hg19:g.31242339C>T		440.0	0.0	.		384.0	21.0	.	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Silent	SNP	ENST00000407793.2	hg19	CCDS44856.1																																																																																			.	.	.	none		0.517	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653		T	31242339	C	T	31242339	2	4	2	1	0	0	0	0	0	0	0	1	4345	506	18	2		2	DDX11	12	31242339	Silent	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10	8619638	31242339	102609556	67	128											
DDX11	1663	hgsc.bcm.edu	37	chr12	31256511	31256511	+	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	cagcctctgttcctatgcagGcagggccatcaggcaccaga	9	7	11	14	0	2	1	1	0	1	1	3	1	3	1	4	3	2	4	4	3	1	2			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr12:31256511G>C	ENST00000407793.2	+	26	2783	c.2532G>C	c.(2530-2532)agG>agC	p.R844S	DDX11_ENST00000545668.1_Splice_Site_p.R844S|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000350437.4_Splice_Site_p.G796A|DDX11_ENST00000542838.1_Splice_Site_p.G846A|DDX11_ENST00000228264.6_Splice_Site_p.G820A	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	844					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					TCCTATGCAGGCAGGGCCATC	0.627										Multiple Myeloma(12;0.14)																											p.G846A		Atlas-SNP	.											.	DDX11	188	.	0			c.G2537C						PASS	.						17	24	22					12																	31256511		2190	4291	6481	SO:0001630	splice_region_variant	1663	exon26			ATGCAGGCAGGGC	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"DEAD-boxes"	2736	protein-coding gene	gene with protein product	"CHL1-like helicase homolog (S. cerevisiae)"	601150	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)", "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.2532-1G>C	chr12.hg19:g.31256511G>C		127.0	0.0	.		149.0	78.0	.	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000407793.2	hg19	CCDS44856.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	2.472|2.472|2.472	-0.321689|-0.321689|-0.321689	0.05386|0.05386|0.05386	.|.|.	.|.|.	ENSG00000013573|ENSG00000013573|ENSG00000013573	ENST00000404673;ENST00000539702|ENST00000542838;ENST00000228264;ENST00000350437|ENST00000407793;ENST00000545668	.|D;D;D|T;T	.|0.97831|0.73152	.|-3.51;-3.51;-4.56|-0.72;-0.72	3.14|3.14|3.14	3.14|3.14|3.14	0.36123|0.36123|0.36123	.|.|Helicase, ATP-dependent, c2 type (1);	.|0.593501|.	.|0.17209|.	.|N|.	.|0.182822|.	D|D|D	0.86957|0.86957|0.86957	0.6058|0.6058|0.6058	H|H|H	0.98446|0.98446|0.98446	4.235|4.235|4.235	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|D;D;D|D	.|0.76494|0.63046	.|0.999;0.999;0.999|0.992	.|D;D;D|P	.|0.70716|0.56434	.|0.957;0.968;0.97|0.798	D|D|D	0.90935|0.90935|0.90935	0.4793|0.4793|0.4793	5|9|8	.|.|.	.|.|.	.|.|.	.|.|.	11.816|11.816|11.816	0.52211|0.52211|0.52211	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	.|820;796;846|844	.|Q96FC9-3;Q96FC9-4;Q96FC9-2|Q96FC9	.|.;.;.|DDX11_HUMAN	P|A|S	545;112|846;820;796|844	.|ENSP00000443426:G846A;ENSP00000228264:G820A;ENSP00000309965:G796A|ENSP00000384703:R844S;ENSP00000440402:R844S	.|.|.	A|G|R	+|+|+	1|2|3	0|0|2	DDX11|DDX11|DDX11	31147778|31147778|31147778	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.640000|0.640000|0.640000	0.38277|0.38277|0.38277	8.292000|8.292000|8.292000	0.89930|0.89930|0.89930	1.582000|1.582000|1.582000	0.49881|0.49881|0.49881	0.430000|0.430000|0.430000	0.28490|0.28490|0.28490	GCA|GGC|AGG	.	.	.	none		0.627	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	Missense_Mutation	C	31256511	G	C	31256511	5	2	2	1	0	0	0	0	0	0	1	0	4345	1217	42	4	2635	4	DDX11	12	31256511	Splice_Site	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	14172	31256511	102595384	68	129											
AAAS	8086	hgsc.bcm.edu	37	chr12	53701653	53701655	+	In_Frame_Del	DEL	GAA	GAA	-																															ctgagcagggcccctttgttGaaggaaggatggaaagtgat																										TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr12:53701653_53701655delGAA	ENST00000209873.4	-	15	1555_1557	c.1390_1392delTTC	c.(1390-1392)ttcdel	p.F464del	AAAS_ENST00000394384.3_In_Frame_Del_p.F431del|AAAS_ENST00000549983.1_5'Flank|AAAS_ENST00000550286.1_In_Frame_Del_p.F340del	NM_015665.5	NP_056480.1	Q9NRG9	AAAS_HUMAN	achalasia, adrenocortical insufficiency, alacrimia	464					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nucleocytoplasmic transport (GO:0006913)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|regulation of nucleocytoplasmic transport (GO:0046822)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2)	20						CCCCTTTGTTGAAGGAAGGATGG	0.596																																					p.464_465del		Atlas-Indel,Pindel	.											.	AAAS	46	.	0			c.1391_1393del						PASS	.																																			SO:0001651	inframe_deletion	8086	exon15			.	AJ289841	CCDS8856.1, CCDS53797.1	12q13	2013-06-27	2010-06-24		ENSG00000094914	ENSG00000094914		"WD repeat domain containing"	13666	protein-coding gene	gene with protein product	"aladin", "Allgrove, triple-A"	605378	"achalasia, adrenocortical insufficiency, alacrimia (Allgrove, triple-A)"			11062474	Standard	NM_015665		Approved		uc001scr.4	Q9NRG9	OTTHUMG00000169729	ENST00000209873.4:c.1390_1392delTTC	chr12.hg19:g.53701653_53701655delGAA	ENSP00000209873:p.Phe464del	110.0	0.0	0		132.0	64.0	0.484848	NM_015665	Q5JB47|Q9NWI6|Q9UG19	In_Frame_Del	DEL	ENST00000209873.4	hg19	CCDS8856.1																																																																																			.	.	.	none		0.596	AAAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405632.1			-	53701655	GAA	-	53701653	7	5	2	1	0	1	0	1	0	0	0	0	8	1281	45	0	256	0	AAAS	12	53701653	In_Frame_Del	DEL	GAA	TCGA-2Z-A9J1-01A-11D-A382-10	22445142	53701653	80150242	69	130											
OR6C1	390321	hgsc.bcm.edu	37	chr12	55714634	55714634	+	Frame_Shift_Del	DEL	T	T	-																															caagtttctgggtaacattaTttcaggagataaaaccattt																										TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr12:55714634delT	ENST00000379668.2	+	1	289	c.251delT	c.(250-252)attfs	p.I84fs		NM_001005182.1	NP_001005182.1	Q96RD1	OR6C1_HUMAN	olfactory receptor, family 6, subfamily C, member 1	84						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(5)|liver(2)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)	25						GGTAACATTATTTCAGGAGAT	0.388																																					p.I84fs		Atlas-Indel,Pindel	.											.	OR6C1	58	.	0			c.250delA						PASS	.						60	63	62					12																	55714634		2202	4299	6501	SO:0001589	frameshift_variant	390321	exon1			.	AF399506	CCDS31818.1	12q13.13	2012-08-09			ENSG00000205330	ENSG00000205330		"GPCR / Class A : Olfactory receptors"	8355	protein-coding gene	gene with protein product							Standard	NM_001005182		Approved	OST267	uc010spi.2	Q96RD1	OTTHUMG00000168102	ENST00000379668.2:c.251delT	chr12.hg19:g.55714634delT	ENSP00000368990:p.Ile84fs	30.0	0.0	0		83.0	47.0	0.566265	NM_001005182	B2RNM0	Frame_Shift_Del	DEL	ENST00000379668.2	hg19	CCDS31818.1																																																																																			.	.	.	none		0.388	OR6C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398152.1	NM_001005182		-	55714634	T	-	55714634	7	5	2	1	0	1	0	1	0	0	0	0	11197	1493	52	0	253	0	OR6C1	12	55714634	Frame_Shift_Del	DEL	T	TCGA-2Z-A9J1-01A-11D-A382-10	2012981	55714634	78137261	70	131											
PAWR	5074	hgsc.bcm.edu	37	chr12	79988144	79988144	+	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	aatttcttctttgagttttcCaatcatttcctctttatctt	7	23	2	9	0	5	1	1	1	4	0	7	1	7	1	2	0	0	1	2	0	3	9			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr12:79988144C>G	ENST00000328827.4	-	6	1273	c.901G>C	c.(901-903)Gga>Cga	p.G301R		NM_002583.2	NP_002574.2	Q96IZ0	PAWR_HUMAN	PRKC, apoptosis, WT1, regulator	301	Leucine-zipper.				actin filament bundle assembly (GO:0051017)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|interleukin-2 biosynthetic process (GO:0042094)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of amyloid precursor protein biosynthetic process (GO:0042986)|positive regulation of apoptotic process (GO:0043065)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|enzyme binding (GO:0019899)|leucine zipper domain binding (GO:0043522)|transcription corepressor activity (GO:0003714)			NS(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						TTGAGTTTTCCAATCATTTCC	0.303																																					p.G301R		Atlas-SNP	.											.	PAWR	14	.	0			c.G901C						PASS	.						119	113	115					12																	79988144		2200	4296	6496	SO:0001583	missense	5074	exon6			GTTTTCCAATCAT	U63809	CCDS31863.1	12q21.2	2013-03-07			ENSG00000177425	ENSG00000177425			8614	protein-coding gene	gene with protein product	"prostate apoptosis response-4"	601936				8943350, 9790775	Standard	NM_002583		Approved	par-4, PAR4	uc001syx.3	Q96IZ0	OTTHUMG00000170080	ENST00000328827.4:c.901G>C	chr12.hg19:g.79988144C>G	ENSP00000328088:p.Gly301Arg	77.0	0.0	.		126.0	70.0	.	NM_002583	O75796|Q6FHY9|Q8N700	Missense_Mutation	SNP	ENST00000328827.4	hg19	CCDS31863.1	.	.	.	.	.	.	.	.	.	.	C	16.05	3.013680	0.54468	.	.	ENSG00000177425	ENST00000328827;ENST00000550603	T;T	0.81415	2.46;-1.49	5.8	3.99	0.46301	.	0.639303	0.16466	N	0.213178	T	0.72614	0.3482	L	0.29908	0.895	0.44728	D	0.997724	P	0.41929	0.765	P	0.45406	0.479	T	0.65311	-0.6199	9	.	.	.	-5.6848	7.9645	0.30091	0.0:0.7279:0.1308:0.1413	.	301	Q96IZ0	PAWR_HUMAN	R	301;32	ENSP00000328088:G301R;ENSP00000447507:G32R	.	G	-	1	0	PAWR	78512275	0.989000	0.36119	1.000000	0.80357	0.997000	0.91878	2.388000	0.44398	0.802000	0.34089	0.563000	0.77884	GGA	.	.	.	none		0.303	PAWR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407175.1	NM_002583		G	79988144	C	G	79988144	3	3	2	1	0	0	0	0	1	0	0	0	11484	603	21	4	129	4	PAWR	12	79988144	Missense_Mutation	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10	24273510	79988144	53863751	71	132											
MYO1H	283446	hgsc.bcm.edu	37	chr12	109843836	109843836	+	Missense_Mutation	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	ccatgagatcaagtggatagCcaaggtgatgctcctctttt	10	12	10	9	0	2	2	1	2	1	1	3	4	3	3	3	2	2	1	3	2	3	3			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr12:109843836C>T	ENST00000431443.2	+	7	911	c.911C>T	c.(910-912)gCc>gTc	p.A304V	MYO1H_ENST00000310903.5_Missense_Mutation_p.A304V|MYO1H_ENST00000542883.1_3'UTR	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	304	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						AAGTGGATAGCCAAGGTGATG	0.522																																					p.A304V		Atlas-SNP	.											.	MYO1H	98	.	0			c.C911T						PASS	.						65	61	62					12																	109843836		1955	4143	6098	SO:0001583	missense	283446	exon7			GGATAGCCAAGGT		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.911C>T	chr12.hg19:g.109843836C>T	ENSP00000444076:p.Ala304Val	72.0	0.0	.		85.0	42.0	.	NM_001101421	F5H3C6	Missense_Mutation	SNP	ENST00000431443.2	hg19		.	.	.	.	.	.	.	.	.	.	C	33	5.232509	0.95207	.	.	ENSG00000174527	ENST00000310903;ENST00000431443	D;D	0.90955	-2.76;-2.76	4.88	4.88	0.63580	.	.	.	.	.	D	0.92928	0.7750	M	0.91249	3.19	0.41761	D	0.989713	P	0.39903	0.694	B	0.39094	0.29	D	0.94791	0.7962	9	0.87932	D	0	.	17.4368	0.87554	0.0:1.0:0.0:0.0	.	304	F5H3C6	.	V	304	ENSP00000439182:A304V;ENSP00000444076:A304V	ENSP00000439182:A304V	A	+	2	0	MYO1H	108328219	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.046000	0.76592	2.439000	0.82584	0.650000	0.86243	GCC	.	.	.	none		0.522	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597		T	109843836	C	T	109843836	3	4	2	1	0	0	0	0	1	0	0	0	10082	739	26	2	937	2	MYO1H	12	109843836	Missense_Mutation	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10	29855692	109843836	24008059	72	133											
RIMBP2	23504	hgsc.bcm.edu	37	chr12	130921587	130921587	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggcctcatccatcctggCgtggggacccaggtgctcgt	5	8	13	15	2	1	0	1	0	0	0	4	1	3	1	5	5	1	1	5	5	0	0			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr12:130921587C>T	ENST00000261655.4	-	10	2018	c.1855G>A	c.(1855-1857)Gcc>Acc	p.A619T	RIMBP2_ENST00000535703.1_Missense_Mutation_p.A527T|RIMBP2_ENST00000536002.1_Missense_Mutation_p.A527T	NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	619	Pro-rich.				negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.A619S(1)		NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		TCCATCCTGGCGTGGGGACCC	0.667																																					p.A619T		Atlas-SNP	.											RIMBP2,NS,carcinoma,0,1	RIMBP2	220	.	1	Substitution - Missense(1)	lung(1)	c.G1855A						PASS	.						66	57	60					12																	130921587		2203	4300	6503	SO:0001583	missense	23504	exon10			TCCTGGCGTGGGG	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.1855G>A	chr12.hg19:g.130921587C>T	ENSP00000261655:p.Ala619Thr	130.0	0.0	.		130.0	33.0	.	NM_015347	Q96ID2	Missense_Mutation	SNP	ENST00000261655.4	hg19	CCDS31925.1	.	.	.	.	.	.	.	.	.	.	C	1.099	-0.661600	0.03454	.	.	ENSG00000060709	ENST00000261655;ENST00000392375;ENST00000535703;ENST00000536002	T;T;T	0.19669	2.13;2.98;2.98	4.23	-2.05	0.07321	.	2.528880	0.01158	N	0.006570	T	0.12220	0.0297	N	0.22421	0.69	0.09310	N	1	B;B;B	0.28128	0.103;0.201;0.007	B;B;B	0.24269	0.017;0.052;0.001	T	0.13388	-1.0511	10	0.14252	T	0.57	.	4.7566	0.13086	0.2207:0.3515:0.0:0.4278	.	527;527;619	C9JWN3;O15034-2;O15034	.;.;RIMB2_HUMAN	T	619;527;527;527	ENSP00000261655:A619T;ENSP00000440347:A527T;ENSP00000439159:A527T	ENSP00000261655:A619T	A	-	1	0	RIMBP2	129487540	0.000000	0.05858	0.009000	0.14445	0.258000	0.26162	-0.349000	0.07731	-0.046000	0.13446	0.561000	0.74099	GCC	.	.	.	none		0.667	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347		T	130921587	C	T	130921587	3	4	2	1	0	0	0	0	1	0	0	0	13376	768	27	1	1343	1	RIMBP2	12	130921587	Missense_Mutation	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10	21077751	130921587	2930308	73	134											
NBEA	26960	hgsc.bcm.edu	37	chr13	36229093	36229093	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taacagcagataatcgctatAttcttatctgtggattctgg	11	15	8	7	1	3	1	0	0	3	1	4	2	3	2	0	2	2	2	0	2	5	7			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr13:36229093A>G	ENST00000400445.3	+	53	8608	c.8074A>G	c.(8074-8076)Att>Gtt	p.I2692V	NBEA_ENST00000310336.4_Missense_Mutation_p.I2692V|NBEA_ENST00000379939.2_Missense_Mutation_p.I2689V|NBEA_ENST00000537702.1_Missense_Mutation_p.I485V|NBEA_ENST00000540320.1_Missense_Mutation_p.I2692V|NBEA_ENST00000379922.3_Missense_Mutation_p.I270V	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	2692					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)		TAATCGCTATATTCTTATCTG	0.363																																					p.I2692V		Atlas-SNP	.											NBEA,NS,carcinoma,0,1	NBEA	340	.	0			c.A8074G						PASS	.						90	87	88					13																	36229093		1855	4090	5945	SO:0001583	missense	26960	exon53			CGCTATATTCTTA	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.8074A>G	chr13.hg19:g.36229093A>G	ENSP00000383295:p.Ile2692Val	84.0	1.0	.		114.0	25.0	.	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	A	13.66	2.304230	0.40795	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518;ENST00000402346;ENST00000537702;ENST00000379922	T;T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52;1.52	5.65	4.49	0.54785	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.048458	0.85682	N	0.000000	T	0.26521	0.0648	L	0.37800	1.135	0.58432	D	0.999999	B;P;B	0.39748	0.034;0.686;0.112	B;B;B	0.42738	0.035;0.396;0.168	T	0.02437	-1.1159	10	0.24483	T	0.36	.	9.9577	0.41678	0.9158:0.0:0.0842:0.0	.	2692;270;2689	Q8NFP9;Q8NFP9-2;Q5T321	NBEA_HUMAN;.;.	V	2692;2692;2689;2692;1319;270;485;270	ENSP00000440951:I2692V;ENSP00000383295:I2692V;ENSP00000369271:I2689V;ENSP00000308534:I2692V;ENSP00000440233:I485V;ENSP00000369254:I270V	ENSP00000308534:I2692V	I	+	1	0	NBEA	35127093	1.000000	0.71417	0.995000	0.50966	0.781000	0.44180	6.181000	0.71988	0.961000	0.38030	0.533000	0.62120	ATT	.	.	.	none		0.363	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		G	36229093	A	G	36229093	3	3	2	1	0	0	0	0	1	0	0	0	10194	449	16	3	8284	3	NBEA	13	36229093	Missense_Mutation	SNP	A	TCGA-2Z-A9J1-01A-11D-A382-10		36229093	78940785	74	135											
LMO7	4008	hgsc.bcm.edu	37	chr13	76381810	76381810	+	Missense_Mutation	SNP	T	T	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	cttagagaatgatgatttctTtgtcagaaagactggggctt	11	14	11	5	0	2	5	1	2	1	3	2	6	2	5	0	2	0	1	0	2	3	4			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr13:76381810T>G	ENST00000321797.8	+	8	1413	c.692T>G	c.(691-693)tTt>tGt	p.F231C	LMO7_ENST00000465261.2_Missense_Mutation_p.F231C|RP11-29G8.3_ENST00000563635.1_RNA|LMO7_ENST00000357063.3_Missense_Mutation_p.F516C|LMO7_ENST00000526202.1_Intron|LMO7_ENST00000377534.3_Missense_Mutation_p.F516C|LMO7_ENST00000341547.4_Intron			Q8WWI1	LMO7_HUMAN	LIM domain 7	516					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)		GATGATTTCTTTGTCAGAAAG	0.443																																					p.F231C		Atlas-SNP	.											.	LMO7	334	.	0			c.T692G						PASS	.						86	81	83					13																	76381810		1568	3582	5150	SO:0001583	missense	4008	exon7			ATTTCTTTGTCAG	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.692T>G	chr13.hg19:g.76381810T>G	ENSP00000317802:p.Phe231Cys	77.0	0.0	.		142.0	38.0	.	NM_015842	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	hg19		.	.	.	.	.	.	.	.	.	.	T	22.4	4.281530	0.80692	.	.	ENSG00000136153	ENST00000357063;ENST00000377534;ENST00000321797;ENST00000465261;ENST00000526528	T;T;T;T	0.58506	0.33;0.33;0.33;0.33	5.83	5.83	0.93111	.	0.053706	0.85682	D	0.000000	T	0.73590	0.3606	M	0.68952	2.095	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.65573	0.936;0.936	T	0.76599	-0.2900	10	0.87932	D	0	-19.7539	16.1968	0.82036	0.0:0.0:0.0:1.0	.	516;231	Q8WWI1;E9PLH4	LMO7_HUMAN;.	C	516;516;231;231;137	ENSP00000349571:F516C;ENSP00000366757:F516C;ENSP00000317802:F231C;ENSP00000433352:F231C	ENSP00000317802:F231C	F	+	2	0	LMO7	75279811	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.503000	0.81632	2.225000	0.72522	0.533000	0.62120	TTT	.	.	.	none		0.443	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358		G	76381810	T	G	76381810	3	3	2	1	0	0	0	0	1	0	0	0	8862	1841	64	5	1589	5	LMO7	13	76381810	Missense_Mutation	SNP	T	TCGA-2Z-A9J1-01A-11D-A382-10	40152717	76381810	38788068	75	136											
RNF219	79596	hgsc.bcm.edu	37	chr13	79219122	79219122	+	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	ggttgttgatgcatatgacaGgctgacgtacctttgaaaaa	12	12	11	6	1	0	4	0	4	0	0	0	4	0	4	1	2	2	5	1	2	4	5			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr13:79219122G>T	ENST00000282003.6	-	2	141	c.83C>A	c.(82-84)cCt>cAt	p.P28H		NM_024546.3	NP_078822.3	Q5W0B1	RN219_HUMAN	ring finger protein 219	28							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)		GCATATGACAGGCTGACGTAC	0.378																																					p.P28H		Atlas-SNP	.											.	RNF219	94	.	0			c.C83A						PASS	.						133	117	123					13																	79219122		2203	4300	6503	SO:0001583	missense	79596	exon2			ATGACAGGCTGAC	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.83C>A	chr13.hg19:g.79219122G>T	ENSP00000282003:p.Pro28His	80.0	0.0	.		111.0	7.0	.	NM_024546	B2RN99|Q8TBY2|Q9H0T2|Q9H8M0	Missense_Mutation	SNP	ENST00000282003.6	hg19	CCDS31997.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.719656	0.89205	.	.	ENSG00000152193	ENST00000282003	T	0.30714	1.52	5.66	5.66	0.87406	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	0.64125	0.2570	M	0.86502	2.82	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.69569	-0.5110	10	0.87932	D	0	-11.4156	19.7324	0.96188	0.0:0.0:1.0:0.0	.	28	Q5W0B1	RN219_HUMAN	H	28	ENSP00000282003:P28H	ENSP00000282003:P28H	P	-	2	0	RNF219	78117123	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.230000	0.95299	2.663000	0.90544	0.655000	0.94253	CCT	.	.	.	none		0.378	RNF219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045363.1	NM_024546		T	79219122	G	T	79219122	3	4	2	1	0	0	0	0	1	0	0	0	13495	1000	35	4	2117	4	RNF219	13	79219122	Missense_Mutation	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	2837312	79219122	35950756	76	137											
ESR2	2100	hgsc.bcm.edu	37	chr14	64699969	64699969	+	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	agcacgtgggcattcagcatCtccagcagcaggtcatacac	11	7	10	13	1	3	0	2	0	1	0	4	0	3	0	1	2	5	5	1	2	1	2			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr14:64699969C>A	ENST00000341099.4	-	9	1896	c.1479G>T	c.(1477-1479)gaG>gaT	p.E493D	ESR2_ENST00000553796.1_Intron|ESR2_ENST00000357782.2_Intron|ESR2_ENST00000353772.3_Intron|ESR2_ENST00000554572.1_Intron|ESR2_ENST00000555278.1_Intron|ESR2_ENST00000542956.1_Intron|ESR2_ENST00000557772.1_3'UTR|ESR2_ENST00000267525.6_Missense_Mutation_p.E402D|ESR2_ENST00000555483.1_5'UTR|ESR2_ENST00000358599.5_Intron	NM_001437.2	NP_001428.1	Q92731	ESR2_HUMAN	estrogen receptor 2 (ER beta)	493	Steroid-binding.				brain development (GO:0007420)|cell-cell signaling (GO:0007267)|epithelial cell maturation involved in prostate gland development (GO:0060743)|extracellular negative regulation of signal transduction (GO:1900116)|gene expression (GO:0010467)|hormone-mediated apoptotic signaling pathway (GO:0008628)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|ovarian follicle development (GO:0001541)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|uterus development (GO:0060065)|vagina development (GO:0060068)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor antagonist activity (GO:0048019)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	23				all cancers(60;0.00916)|OV - Ovarian serous cystadenocarcinoma(108;0.0111)|BRCA - Breast invasive adenocarcinoma(234;0.0437)	Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estropipate(DB04574)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Trilostane(DB01108)	CATTCAGCATCTCCAGCAGCA	0.542																																					p.E493D		Atlas-SNP	.											.	ESR2	82	.	0			c.G1479T						PASS	.						183	151	162					14																	64699969		2203	4300	6503	SO:0001583	missense	2100	exon9			CAGCATCTCCAGC	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.1479G>T	chr14.hg19:g.64699969C>A	ENSP00000343925:p.Glu493Asp	62.0	0.0	.		68.0	19.0	.	NM_001437	A8K8K5|G3V5M5|O60608|O60685|O60702|O60703|O75583|O75584|Q0MWT5|Q0MWT6|Q86Z31|Q9UEV6|Q9UHD3|Q9UQK9	Missense_Mutation	SNP	ENST00000341099.4	hg19	CCDS9762.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.218986	0.79464	.	.	ENSG00000140009	ENST00000341099;ENST00000267525	D;T	0.92149	-2.98;0.13	5.68	5.68	0.88126	Nuclear hormone receptor, ligand-binding (2);	0.000000	0.85682	D	0.000000	D	0.96300	0.8793	M	0.87758	2.905	0.32928	D	0.51671	D;D	0.89917	1.0;0.978	D;D	0.83275	0.996;0.913	D	0.98321	1.0528	10	0.87932	D	0	.	14.0109	0.64495	0.0:0.928:0.0:0.072	.	402;493	Q92731-7;Q92731	.;ESR2_HUMAN	D	493;402	ENSP00000343925:E493D;ENSP00000267525:E402D	ENSP00000267525:E402D	E	-	3	2	ESR2	63769722	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	2.875000	0.48491	2.683000	0.91414	0.561000	0.74099	GAG	.	.	.	none		0.542	ESR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280621.1			A	64699969	C	A	64699969	3	1	2	1	0	0	0	0	1	0	0	0	5259	912	32	4	203	4	ESR2	14	64699969	Missense_Mutation	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10		64699969	42649571	77	138											
MGA	23269	hgsc.bcm.edu	37	chr15	41988958	41988958	+	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	tttcaggaaaagaggacttgGgcagaaagagaacaactatg	17	7	12	5	0	1	3	1	0	0	3	1	6	1	5	0	3	2	1	0	3	6	3			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr15:41988958G>C	ENST00000570161.1	+	2	1750	c.1750G>C	c.(1750-1752)Ggc>Cgc	p.G584R	MGA_ENST00000389936.4_Missense_Mutation_p.G584R|MGA_ENST00000545763.1_Missense_Mutation_p.G584R|MGA_ENST00000566586.1_Missense_Mutation_p.G584R|MGA_ENST00000219905.7_Missense_Mutation_p.G584R			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)	AGAGGACTTGGGCAGAAAGAG	0.428																																					p.G584R		Atlas-SNP	.											.	MGA	264	.	0			c.G1750C						PASS	.						40	36	37					15																	41988958		1893	4128	6021	SO:0001583	missense	23269	exon3			GACTTGGGCAGAA	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.1750G>C	chr15.hg19:g.41988958G>C	ENSP00000457035:p.Gly584Arg	173.0	0.0	.		157.0	52.0	.	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	hg19	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	G	17.54	3.414212	0.62511	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	D;D;D	0.87809	-2.26;-2.3;-2.18	5.23	4.3	0.51218	.	2.318350	0.01436	N	0.014901	D	0.90854	0.7127	L	0.34521	1.04	0.29365	N	0.864383	D;D	0.76494	0.999;0.964	D;P	0.71656	0.974;0.691	T	0.77133	-0.2700	10	0.87932	D	0	.	10.1653	0.42877	0.0744:0.1383:0.7873:0.0	.	584;584	F5H7K2;E7ENI0	.;.	R	584	ENSP00000219905:G584R;ENSP00000374586:G584R;ENSP00000442467:G584R	ENSP00000219905:G584R	G	+	1	0	MGA	39776250	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.246000	0.51414	1.178000	0.42870	0.462000	0.41574	GGC	.	.	.	none		0.428	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		C	41988958	G	C	41988958	3	2	2	1	0	0	0	0	1	0	0	0	9547	1232	43	4	1756	4	MGA	15	41988958	Missense_Mutation	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10		41988958	60542434	78	139											
FLYWCH1	84256	hgsc.bcm.edu	37	chr16	2980631	2980631	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccgatgagcaaggcctggaGgcccggcgccagagggagaa	10	2	17	12	3	0	3	0	1	0	2	0	6	0	4	4	5	1	1	4	5	2	0			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr16:2980631G>A	ENST00000253928.9	+	4	951	c.546G>A	c.(544-546)gaG>gaA	p.E182E	FLYWCH1_ENST00000399667.2_Silent_p.E182E|FLYWCH1_ENST00000416288.2_Silent_p.E181E			Q4VC44	FWCH1_HUMAN	FLYWCH-type zinc finger 1	182						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(1)|lung(3)	4						AAGGCCTGGAGGCCCGGCGCC	0.731																																					p.E181E		Atlas-SNP	.											.	FLYWCH1	27	.	0			c.G543A						PASS	.						4	4	4					16																	2980631		1763	3796	5559	SO:0001819	synonymous_variant	84256	exon4			CCTGGAGGCCCGG	AL136585	CCDS45390.1	16p13.3	2013-01-10	2007-06-21	2007-06-21	ENSG00000059122	ENSG00000059122		"Zinc fingers"	25404	protein-coding gene	gene with protein product						11230166, 10997877	Standard	XM_006720959		Approved	DKFZp761A132	uc002csc.3	Q4VC44		ENST00000253928.9:c.546G>A	chr16.hg19:g.2980631G>A		86.0	0.0	.		90.0	29.0	.	NM_020912	D3DUA1|Q6ZSQ1|Q8WV62|Q9BQG6|Q9BUS5|Q9HCM0	Silent	SNP	ENST00000253928.9	hg19																																																																																				.	.	.	none		0.731	FLYWCH1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000436479.1	NM_032296		A	2980631	G	A	2980631	2	1	2	1	0	0	0	0	0	0	0	1	5954	991	35	2		2	FLYWCH1	16	2980631	Silent	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10		2980631	87374122	79	140											
PLLP	51090	hgsc.bcm.edu	37	chr16	57292497	57292497	+	Splice_Site	DEL	C	C	-																															ctgatgttaaagatcattaaCtgcaggacatgggggtaggg																										TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr16:57292497delC	ENST00000219207.5	-	3	456		c.e3-1		PLLP_ENST00000569059.1_Splice_Site	NM_015993.2	NP_057077.1	Q9Y342	PLLP_HUMAN	plasmolipin						ion transport (GO:0006811)|myelination (GO:0042552)|response to wounding (GO:0009611)	compact myelin (GO:0043218)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)				endometrium(1)|prostate(1)	2						AGATCATTAACTGCAGGACAT	0.562																																					p.L104X		Atlas-Indel,Pindel	.											.	PLLP	11	.	0			c.310delT						PASS	.						79	77	78					16																	57292497		2198	4300	6498	SO:0001630	splice_region_variant	51090	exon3			.	AF137386	CCDS10777.1	16q13	2010-06-24	2010-06-24	2005-03-21	ENSG00000102934	ENSG00000102934			18553	protein-coding gene	gene with protein product	"plasma membrane proteolipid"	600340	"transmembrane 4 superfamily member 11 (plasmolipin)", "plasma membrane proteolipid (plasmolipin)"	TM4SF11		11707781	Standard	NM_015993		Approved	PMLP	uc002elg.2	Q9Y342	OTTHUMG00000133465	ENST00000219207.5:c.310-1G>-	chr16.hg19:g.57292497delC		104.0	0.0	0		96.0	19.0	0.197917	NM_015993	B2R9T6	Frame_Shift_Del	DEL	ENST00000219207.5	hg19	CCDS10777.1																																																																																			.	.	.	none		0.562	PLLP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257341.2		Intron	-	57292497	C	-	57292497	8	5	2	1	0	1	0	1	0	0	1	0	12106	579	20	0	247	0	PLLP	16	57292497	Splice_Site	DEL	C	TCGA-2Z-A9J1-01A-11D-A382-10	54311866	57292497	33062256	80	141											
HYDIN	54768	hgsc.bcm.edu	37	chr16	71163576	71163576	+	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	gtgaaaacgttattgaagaaCagcttgctgtctccctgcac	11	11	9	10	1	1	3	0	2	1	1	2	3	1	3	1	0	5	4	1	0	5	3			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr16:71163576C>G	ENST00000393567.2	-	9	1344	c.1194G>C	c.(1192-1194)ctG>ctC	p.L398L	HYDIN_ENST00000393550.2_Silent_p.L398L|HYDIN_ENST00000541601.1_Silent_p.L415L|HYDIN_ENST00000448691.1_Silent_p.L398L|HYDIN_ENST00000288168.10_Silent_p.L415L|HYDIN_ENST00000321489.5_Silent_p.L398L|HYDIN_ENST00000448089.2_Silent_p.L398L|HYDIN_ENST00000538248.1_Silent_p.L425L	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	398					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)				TATTGAAGAACAGCTTGCTGT	0.458																																					p.L425L		Atlas-SNP	.											.	HYDIN	788	.	0			c.G1275C						PASS	.						59	58	58					16																	71163576		2198	4300	6498	SO:0001819	synonymous_variant	54768	exon9			GAAGAACAGCTTG	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.1194G>C	chr16.hg19:g.71163576C>G		65.0	0.0	.		93.0	45.0	.	NM_001198542	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	hg19	CCDS59269.1																																																																																			.	.	.	none		0.458	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			G	71163576	C	G	71163576	2	3	2	1	0	0	0	0	0	0	0	1	7474	465	17	4		4	HYDIN	16	71163576	Silent	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10	13871079	71163576	19191177	81	142											
DNAH2	146754	hgsc.bcm.edu	37	chr17	7663108	7663108	+	Splice_Site	DEL	G	G	-																															tctccactgggttcctcacaGgtggaattctcacccactct																										TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr17:7663108delG	ENST00000572933.1	+	17	4097		c.e17-1		DNAH2_ENST00000389173.2_Splice_Site			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2						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)				GTTCCTCACAGGTGGAATTCT	0.517																																					.		Atlas-Indel,Pindel	.											.	DNAH2	498	.	0			c.2638-2G>-						PASS	.						200	181	188					17																	7663108		2203	4300	6503	SO:0001630	splice_region_variant	146754	exon16			.	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.2638-1G>-	chr17.hg19:g.7663108delG		93.0	0.0	0		113.0	23.0	0.20354	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Splice_Site	DEL	ENST00000572933.1	hg19	CCDS32551.1																																																																																			.	.	.	none		0.517	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	Intron	-	7663108	G	-	7663108	8	5	2	1	0	1	0	1	0	0	1	0	4604	1014	35	0	2699	0	DNAH2	17	7663108	Splice_Site	DEL	G	TCGA-2Z-A9J1-01A-11D-A382-10		7663108	73532102	82	143											
GJD3	125111	hgsc.bcm.edu	37	chr17	38519536	38519536	+	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	gggccggctcacgaagcagtCgaccgtgtgcgggcagggcg	6	4	19	12	6	1	0	1	0	0	0	2	2	1	0	2	4	2	3	2	4	1	0			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr17:38519536C>T	ENST00000578689.1	-	1	531	c.532G>A	c.(532-534)Gac>Aac	p.D178N	CTD-2267D19.3_ENST00000578774.1_Silent_p.V116V|GJD3_ENST00000337376.4_Missense_Mutation_p.D178N	NM_152219.3	NP_689343.3	Q8N144	CXD3_HUMAN	gap junction protein, delta 3, 31.9kDa	178					cell communication (GO:0007154)|gap junction assembly (GO:0016264)	cell surface (GO:0009986)|connexon complex (GO:0005922)|integral component of plasma membrane (GO:0005887)	ion channel activity (GO:0005216)						Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00143)			ACGAAGCAGTCGACCGTGTGC	0.706																																					p.D178N		Atlas-SNP	.											.	GJD3	2	.	0			c.G532A						PASS	.						2	3	2					17																	38519536		1475	3103	4578	SO:0001583	missense	125111	exon1			AGCAGTCGACCGT	AF514298	CCDS58547.1	17q21.1	2012-04-19	2007-11-06	2007-11-06	ENSG00000183153	ENSG00000183153		"Ion channels / Gap junction proteins (connexins)"	19147	protein-coding gene	gene with protein product	"connexin 31.9"	607425	"gap junction protein, chi 1, 31.9kDa"	GJC1		12176752	Standard	NM_152219		Approved	CX31.9, GJA11, Cx30.2	uc010cwz.3	Q8N144		ENST00000578689.1:c.532G>A	chr17.hg19:g.38519536C>T	ENSP00000463752:p.Asp178Asn	30.0	0.0	.		36.0	20.0	.	NM_152219	Q6ZUW6	Missense_Mutation	SNP	ENST00000578689.1	hg19	CCDS58547.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.595832	0.86953	.	.	ENSG00000183153	ENST00000337376	D	0.96265	-3.96	3.43	3.43	0.39272	Gap junction protein, cysteine-rich domain (1);Connexin, conserved site (1);	0.000000	0.64402	U	0.000001	D	0.97117	0.9058	L	0.59912	1.85	0.48185	D	0.9996	D	0.89917	1.0	D	0.80764	0.994	D	0.96558	0.9413	10	0.39692	T	0.17	.	14.649	0.68784	0.0:1.0:0.0:0.0	.	178	Q8N144	CXD3_HUMAN	N	178	ENSP00000336832:D178N	ENSP00000336832:D178N	D	-	1	0	GJD3	35773062	1.000000	0.71417	0.997000	0.53966	0.878000	0.50629	3.330000	0.52068	1.760000	0.52011	0.313000	0.20887	GAC	.	.	.	none		0.706	GJD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447449.1	NM_152219		T	38519536	C	T	38519536	3	4	2	1	0	0	0	0	1	0	0	0	6425	884	31	1	356	1	GJD3	17	38519536	Missense_Mutation	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10	30856428	38519536	42675674	83	144											
KRT13	3860	hgsc.bcm.edu	37	chr17	39657556	39657556	+	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	cgaccagaggcattagaggtGgtggtaacagaggcactaga	13	6	15	7	1	0	4	0	0	0	4	0	5	0	4	1	5	1	3	1	5	3	3			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr17:39657556G>T	ENST00000246635.3	-	8	1375	c.1329C>A	c.(1327-1329)acC>acA	p.T443T	AC019349.5_ENST00000411759.1_RNA|KRT13_ENST00000587118.1_5'Flank|KRT13_ENST00000336861.3_3'UTR	NM_153490.2	NP_705694	P13646	K1C13_HUMAN	keratin 13	443	Tail.				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)				CATTAGAGGTGGTGGTAACAG	0.572																																					p.T443T		Atlas-SNP	.											.	KRT13	72	.	0			c.C1329A						PASS	.						66	50	56					17																	39657556		2199	4292	6491	SO:0001819	synonymous_variant	3860	exon8			AGAGGTGGTGGTA		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.1329C>A	chr17.hg19:g.39657556G>T		149.0	0.0	.		195.0	26.0	.	NM_153490	Q53G54|Q6AZK5|Q8N240	Silent	SNP	ENST00000246635.3	hg19	CCDS11396.1																																																																																			.	.	.	none		0.572	KRT13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257297.1	NM_153490		T	39657556	G	T	39657556	2	4	2	1	0	0	0	0	0	0	0	1	8457	1335	47	4		4	KRT13	17	39657556	Silent	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	1138020	39657556	41537654	84	145											
PCYT2	5833	hgsc.bcm.edu	37	chr17	79865660	79865660	+	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	ccgactcacctggctgctgtGatgggctttggttaccagca	6	11	12	12	1	1	1	1	1	0	0	1	2	1	1	3	3	3	5	3	3	1	2			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr17:79865660G>T	ENST00000538936.2	-	5	589	c.481C>A	c.(481-483)Cac>Aac	p.H161N	PCYT2_ENST00000331285.3_Missense_Mutation_p.H83N|PCYT2_ENST00000538721.2_Missense_Mutation_p.H161N|PCYT2_ENST00000570388.1_Missense_Mutation_p.H83N|PCYT2_ENST00000571105.1_Missense_Mutation_p.H161N|PCYT2_ENST00000570391.1_Missense_Mutation_p.H129N	NM_001256435.1|NM_002861.3	NP_001243364.1|NP_002852.1	Q99447	PCY2_HUMAN	phosphate cytidylyltransferase 2, ethanolamine	161					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)	ethanolamine-phosphate cytidylyltransferase activity (GO:0004306)			breast(2)|endometrium(1)|lung(4)|ovary(1)	8	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)		Lamivudine(DB00709)	TGGCTGCTGTGATGGGCTTTG	0.662																																					p.H161N		Atlas-SNP	.											.	PCYT2	23	.	0			c.C481A						PASS	.						65	52	56					17																	79865660		2203	4300	6503	SO:0001583	missense	5833	exon5			TGCTGTGATGGGC	D84307	CCDS11791.1, CCDS54178.1, CCDS58610.1, CCDS62364.1	17q25.3	2008-07-18				ENSG00000185813			8756	protein-coding gene	gene with protein product		602679				9083101	Standard	XM_005256386		Approved	ET	uc002kch.2	Q99447		ENST00000538936.2:c.481C>A	chr17.hg19:g.79865660G>T	ENSP00000439245:p.His161Asn	56.0	0.0	.		54.0	33.0	.	NM_002861	B7Z7A5|B7ZAS0|F5H8B1|Q6IBM3|Q96G08	Missense_Mutation	SNP	ENST00000538936.2	hg19	CCDS11791.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.332723	0.81801	.	.	ENSG00000185813	ENST00000538721;ENST00000538936;ENST00000331285	.	.	.	4.34	4.34	0.51931	.	0.052098	0.85682	D	0.000000	T	0.71660	0.3366	M	0.78456	2.415	0.80722	D	1	P;B;P;D;D	0.54772	0.791;0.129;0.541;0.968;0.968	P;B;B;P;P	0.51453	0.449;0.029;0.157;0.67;0.67	T	0.73375	-0.4002	9	0.32370	T	0.25	-36.5261	17.0425	0.86493	0.0:0.0:1.0:0.0	.	129;129;161;83;161	B7Z4W6;B7ZAS0;F5H8B1;B7Z7A5;Q99447	.;.;.;.;PCY2_HUMAN	N	161;161;83	.	ENSP00000331719:H83N	H	-	1	0	PCYT2	77458952	1.000000	0.71417	0.926000	0.36857	0.658000	0.38924	7.146000	0.77373	2.233000	0.73108	0.561000	0.74099	CAC	.	.	.	none		0.662	PCYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439939.1	NM_002861		T	79865660	G	T	79865660	3	4	2	1	0	0	0	0	1	0	0	0	11619	1290	45	4	782	4	PCYT2	17	79865660	Missense_Mutation	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	40208104	79865660	1329550	85	146											
FOXK2	3607	hgsc.bcm.edu	37	chr17	80477826	80477826	+	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	acccgcgggcggcggggccgGgggcggcggggccgggggcg	1	0	27	13	9	0	0	0	0	0	0	0	0	0	0	3	11	0	0	3	11	0	0			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr17:80477826G>C	ENST00000335255.5	+	1	236	c.62G>C	c.(61-63)gGg>gCg	p.G21A		NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	21	Gly-rich.			AAAAALSGAGTPPAGGGAGGGGAGGGGSPPGGWAVARLEGR EFEYLMKKRSVTIGRNSSQGSVDVSMGHSSFISRRHLEIFT PPGGGGHGGAAPELPPAQPRPDAGGDFYLRCLGKNG -> Q (in Ref. 1; CAA43200). {ECO:0000305}.	positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	17	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			ggcggggccgggggcggcggg	0.846																																					p.G21A		Atlas-SNP	.											FOXK2,NS,carcinoma,0,1	FOXK2	46	.	0			c.G62C						PASS	.						1	1	1					17																	80477826		122	223	345	SO:0001583	missense	3607	exon1			GGGCCGGGGGCGG	U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"Forkhead boxes"	6036	protein-coding gene	gene with protein product		147685	"interleukin enhancer binding factor 1"	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.62G>C	chr17.hg19:g.80477826G>C	ENSP00000335677:p.Gly21Ala	3.0	0.0	.		4.0	3.0	.	NM_004514	A6NEP5|Q13622|Q13623|Q13624	Missense_Mutation	SNP	ENST00000335255.5	hg19	CCDS11813.1	.	.	.	.	.	.	.	.	.	.	.	2.177	-0.388435	0.04932	.	.	ENSG00000141568	ENST00000335255;ENST00000335241	D	0.93076	-3.16	1.8	1.8	0.24995	.	.	.	.	.	D	0.89375	0.6697	N	0.08118	0	0.25222	N	0.98989	D;D;D	0.71674	0.998;0.996;0.998	D;D;D	0.68621	0.959;0.91;0.959	T	0.80350	-0.1419	9	0.14252	T	0.57	.	6.724	0.23346	0.0:0.0:1.0:0.0	.	21;21;21	Q01167-3;Q01167;Q01167-2	.;FOXK2_HUMAN;.	A	21	ENSP00000335677:G21A	ENSP00000334321:G21A	G	+	2	0	FOXK2	78071115	0.917000	0.31117	0.403000	0.26384	0.773000	0.43773	0.923000	0.28757	0.820000	0.34516	0.486000	0.48141	GGG	.	.	.	none		0.846	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430		C	80477826	G	C	80477826	3	2	2	1	0	0	0	0	1	0	0	0	6022	1232	43	4	64	4	FOXK2	17	80477826	Missense_Mutation	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	612166	80477826	717384	86	147											
MUM1	84939	hgsc.bcm.edu	37	chr19	1371012	1371012	+	Missense_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	gcgtctaccaggaggtggggGccaaggtgctccagcgcacc	7	5	16	13	2	1	0	0	0	1	0	2	1	2	1	4	5	3	2	4	5	2	1			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr19:1371012G>A	ENST00000415183.3	+	11	1950	c.1924G>A	c.(1924-1926)Gcc>Acc	p.A642T	MUM1_ENST00000591806.1_Missense_Mutation_p.A642T|MUM1_ENST00000344663.3_Missense_Mutation_p.A642T|MUM1_ENST00000311401.5_Missense_Mutation_p.A573T			Q2TAK8	MUM1_HUMAN	melanoma associated antigen (mutated) 1	641					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)		GGAGGTGGGGGCCAAGGTGCT	0.657																																					p.A642T		Atlas-SNP	.											.	MUM1	54	.	0			c.G1924A						PASS	.						57	41	46					19																	1371012		2185	4281	6466	SO:0001583	missense	84939	exon12			GTGGGGGCCAAGG	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.1924G>A	chr19.hg19:g.1371012G>A	ENSP00000394925:p.Ala642Thr	87.0	0.0	.		66.0	20.0	.	NM_032853	A1L489|B5ME02|B7ZLY8|J3KQD6|Q13109|Q5XKB9|Q8N2I4|Q96A67	Missense_Mutation	SNP	ENST00000415183.3	hg19		.	.	.	.	.	.	.	.	.	.	G	11.35	1.612141	0.28712	.	.	ENSG00000160953	ENST00000344663;ENST00000311401;ENST00000415183	T;T;T	0.41400	1.0;1.0;1.0	4.82	-3.93	0.04143	.	1.208560	0.05866	N	0.623862	T	0.18841	0.0452	N	0.14661	0.345	0.09310	N	1	B;B;B;B	0.31077	0.022;0.085;0.307;0.048	B;B;B;B	0.23275	0.01;0.01;0.045;0.02	T	0.11397	-1.0589	10	0.17369	T	0.5	.	4.9552	0.14035	0.3899:0.0:0.3792:0.2309	.	642;642;573;641	B7ZLY8;D6W5Y8;Q2TAK8-2;Q2TAK8	.;.;.;MUM1_HUMAN	T	642;573;642	ENSP00000345789:A642T;ENSP00000309135:A573T;ENSP00000394925:A642T	ENSP00000309135:A573T	A	+	1	0	MUM1	1322012	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.289000	0.08365	-1.136000	0.02892	-0.379000	0.06801	GCC	.	.	.	none		0.657	MUM1-016	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000449510.1	NM_032853		A	1371012	G	A	1371012	3	1	2	1	0	0	0	0	1	0	0	0	9992	1203	42	2	1966	2	MUM1	19	1371012	Missense_Mutation	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10		1371012	57757971	87	148											
NFIC	4782	hgsc.bcm.edu	37	chr19	3449135	3449135	+	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	gcccgtcatcgccgtgcacaGcggtaagcgccacgggcccc	6	4	13	18	6	1	0	1	0	0	0	2	0	1	0	5	2	3	2	5	2	1	1			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr19:3449135G>T	ENST00000443272.2	+	7	1133	c.1082G>T	c.(1081-1083)aGc>aTc	p.S361I	NFIC_ENST00000395111.3_Missense_Mutation_p.S352I|NFIC_ENST00000590282.1_Missense_Mutation_p.S361I|NFIC_ENST00000341919.3_Missense_Mutation_p.S361I|NFIC_ENST00000589123.1_Missense_Mutation_p.S352I|NFIC_ENST00000346156.5_Missense_Mutation_p.S328I|NFIC_ENST00000586919.1_Missense_Mutation_p.S328I	NM_001245002.1	NP_001231931.1	P08651	NFIC_HUMAN	nuclear factor I/C (CCAAT-binding transcription factor)	361					DNA replication (GO:0006260)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)|nucleus (GO:0005634)	core promoter proximal region DNA binding (GO:0001159)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.8e-05)|Epithelial(107;2.94e-108)|BRCA - Breast invasive adenocarcinoma(158;0.00154)|STAD - Stomach adenocarcinoma(1328;0.191)		GCCGTGCACAGCGGTAAGCGC	0.672																																					p.S361I		Atlas-SNP	.											.	NFIC	36	.	0			c.G1082T						PASS	.						61	45	50					19																	3449135		2203	4299	6502	SO:0001583	missense	4782	exon7			TGCACAGCGGTAA	X12492	CCDS12107.1, CCDS45914.1, CCDS58640.1, CCDS59330.1, CCDS59331.1	19p13.3	2008-02-05				ENSG00000141905			7786	protein-coding gene	gene with protein product		600729		NFI		3398920, 7590749	Standard	NM_205843		Approved	CTF, NF-I, CTF5	uc010xhi.2	P08651		ENST00000443272.2:c.1082G>T	chr19.hg19:g.3449135G>T	ENSP00000396843:p.Ser361Ile	79.0	0.0	.		65.0	20.0	.	NM_001245004	A8K1H0|B7Z4U5|B7Z9C3|K7EMU1|P08652|Q14932|Q9UPJ3|Q9UPJ9|Q9UPK0|Q9UPK1	Missense_Mutation	SNP	ENST00000443272.2	hg19	CCDS59330.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.600339	0.87055	.	.	ENSG00000141905	ENST00000443272;ENST00000395111;ENST00000346156;ENST00000341919;ENST00000343825;ENST00000269778	T;T;T	0.52526	0.66;0.66;0.66	3.96	3.96	0.45880	.	0.099564	0.64402	D	0.000002	T	0.63307	0.2500	L	0.55481	1.735	0.52099	D	0.999941	D;D;B;D;P	0.76494	0.968;0.999;0.386;0.997;0.822	P;D;B;D;B	0.87578	0.81;0.998;0.085;0.994;0.359	T	0.67401	-0.5680	10	0.66056	D	0.02	.	14.6163	0.68552	0.0:0.0:1.0:0.0	.	361;361;352;361;352	B7Z4U5;P08651;P08651-3;P08651-5;P08651-2	.;NFIC_HUMAN;.;.;.	I	352;352;328;361;361;361	ENSP00000378543:S352I;ENSP00000301935:S328I;ENSP00000342194:S361I	ENSP00000269778:S361I	S	+	2	0	NFIC	3400135	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	8.952000	0.93031	1.764000	0.52075	0.561000	0.74099	AGC	.	.	.	none		0.672	NFIC-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452834.1	NM_005597		T	3449135	G	T	3449135	3	4	2	1	0	0	0	0	1	0	0	0	10379	971	34	4	1115	4	NFIC	19	3449135	Missense_Mutation	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	2078123	3449135	55679848	88	149											
PLIN4	729359	hgsc.bcm.edu	37	chr19	4511775	4511775	+	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	accggtcaccccactgcagaCggtgtccttggtaccagtta	8	9	10	14	2	1	1	1	0	0	1	2	1	2	1	5	3	2	3	5	3	2	3	rs368515268		TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr19:4511775C>G	ENST00000301286.3	-	3	2154	c.2155G>C	c.(2155-2157)Gtc>Ctc	p.V719L		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	719	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						CCACTGCAGACGGTGTCCTTG	0.572																																					p.V719L		Atlas-SNP	.											PLIN4_ENST00000301286,colon,carcinoma,0,2	PLIN4	191	.	0			c.G2155C						PASS	.						215	218	217					19																	4511775		2100	4210	6310	SO:0001583	missense	729359	exon3			TGCAGACGGTGTC	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.2155G>C	chr19.hg19:g.4511775C>G	ENSP00000301286:p.Val719Leu	153.0	0.0	.		123.0	5.0	.	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	hg19	CCDS45927.1	.	.	.	.	.	.	.	.	.	.	C	11.52	1.662091	0.29515	.	.	ENSG00000167676	ENST00000301286	T	0.08102	3.13	4.59	2.38	0.29361	.	0.438854	0.16196	N	0.225159	T	0.11367	0.0277	M	0.83692	2.655	0.09310	N	0.999998	B	0.12630	0.006	B	0.13407	0.009	T	0.41858	-0.9485	10	0.12766	T	0.61	-8.0371	8.0958	0.30826	0.0:0.7475:0.1587:0.0938	.	719	Q96Q06	PLIN4_HUMAN	L	719	ENSP00000301286:V719L	ENSP00000301286:V719L	V	-	1	0	PLIN4	4462775	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-2.421000	0.01031	0.336000	0.23639	0.205000	0.17691	GTC	.	.	.	alt		0.572	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901		G	4511775	C	G	4511775	3	3	2	1	0	0	0	0	1	0	0	0	12099	536	19	4	1934	4	PLIN4	19	4511775	Missense_Mutation	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10	1062640	4511775	54617208	89	150											
ZNF709	163051	hgsc.bcm.edu	37	chr19	12575506	12575506	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctccagtgtgagttctttcAtgcattcgaaaggaactgga	10	13	10	8	1	3	1	1	1	2	0	5	4	3	3	1	2	2	2	1	2	2	3			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr19:12575506A>G	ENST00000397732.3	-	4	1401	c.1230T>C	c.(1228-1230)caT>caC	p.H410H	ZNF709_ENST00000428311.1_Silent_p.H410H|CTD-3105H18.18_ENST00000598753.1_Intron	NM_152601.3	NP_689814.1	Q8N972	ZN709_HUMAN	zinc finger protein 709	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)			large_intestine(3)|upper_aerodigestive_tract(3)	6						GAGTTCTTTCATGCATTCGAA	0.413																																					p.H410H	GBM(33;565 669 12371 29134 51667)	Atlas-SNP	.											.	ZNF709	80	.	0			c.T1230C						PASS	.						104	108	106					19																	12575506		2201	4299	6500	SO:0001819	synonymous_variant	163051	exon4			TCTTTCATGCATT	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.1230T>C	chr19.hg19:g.12575506A>G		110.0	0.0	.		92.0	33.0	.	NM_152601	A8K4E6	Silent	SNP	ENST00000397732.3	hg19	CCDS42504.1																																																																																			.	.	.	none		0.413	ZNF709-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344088.1	NM_152601		G	12575506	A	G	12575506	2	3	2	1	0	0	0	0	0	0	0	1	18125	214	8	3		3	ZNF709	19	12575506	Silent	SNP	A	TCGA-2Z-A9J1-01A-11D-A382-10	8063731	12575506	46553477	90	151											
SIN3B	23309	hgsc.bcm.edu	37	chr19	16974595	16974595	+	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	cagcttcaccgctgtgaggaCgagcgcttcgaggtgtgtgt	6	10	15	10	4	1	1	1	1	0	0	2	4	1	2	1	2	2	3	1	2	0	2			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr19:16974595C>T	ENST00000248054.5	+	10	1392	c.1371C>T	c.(1369-1371)gaC>gaT	p.D457D	SIN3B_ENST00000595541.1_Silent_p.D47D|SIN3B_ENST00000379803.1_Silent_p.D489D					SIN3 transcription regulator family member B									p.D489D(1)		endometrium(4)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26						GCTGTGAGGACGAGCGCTTCG	0.617																																					p.D489D		Atlas-SNP	.											SIN3B,NS,carcinoma,0,2	SIN3B	90	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1467T						PASS	.						114	83	93					19																	16974595		2203	4300	6503	SO:0001819	synonymous_variant	23309	exon11			TGAGGACGAGCGC	AB014600	CCDS32946.1, CCDS74308.1	19p13.12	2013-08-21	2013-08-21						19354	protein-coding gene	gene with protein product		607777	"SIN3 homolog B, transcription regulator (yeast)", "SIN3 transcription regulator homolog B (yeast)"			9734811	Standard	XM_005259832		Approved	KIAA0700	uc002ney.2	O75182		ENST00000248054.5:c.1371C>T	chr19.hg19:g.16974595C>T		73.0	0.0	.		75.0	29.0	.	NM_015260		Silent	SNP	ENST00000248054.5	hg19																																																																																				.	.	.	none		0.617	SIN3B-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000462846.1	NM_015260		T	16974595	C	T	16974595	2	4	2	1	0	0	0	0	0	0	0	1	14339	535	19	1		1	SIN3B	19	16974595	Silent	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10	4399089	16974595	42154388	91	152											
PLVAP	83483	hgsc.bcm.edu	37	chr19	17471595	17471595	+	Frame_Shift_Del	DEL	T	T	-																															actcaccgatgggctgggggTtggggacagggcccatgggc																										TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr19:17471595delT	ENST00000252590.4	-	4	1287	c.1226delA	c.(1225-1227)aacfs	p.N409fs	CTD-2278I10.1_ENST00000597592.1_RNA	NM_031310.1	NP_112600.1	Q9BX97	PLVAP_HUMAN	plasmalemma vesicle associated protein	409					MAPK cascade (GO:0000165)|positive regulation of cellular extravasation (GO:0002693)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GGGCTGGGGGTTGGGGACAGG	0.627																																					p.N409fs		Atlas-Indel,Pindel	.											.	PLVAP	64	.	0			c.1227delC						PASS	.						52	54	53					19																	17471595		2203	4300	6503	SO:0001589	frameshift_variant	83483	exon4			.	AF326591	CCDS32952.1	19p13.2	2008-07-17				ENSG00000130300			13635	protein-coding gene	gene with protein product	"fenestrated-endothelial linked structure protein; PV-1 protein"	607647				11401446	Standard	NM_031310		Approved	gp68, PV-1, PV1, FELS	uc002ngk.1	Q9BX97		ENST00000252590.4:c.1226delA	chr19.hg19:g.17471595delT	ENSP00000252590:p.Asn409fs	151.0	0.0	0		119.0	35.0	0.294118	NM_031310	Q86VP0|Q8N8Y0|Q8ND68|Q8TER8|Q9BZD5	Frame_Shift_Del	DEL	ENST00000252590.4	hg19	CCDS32952.1																																																																																			.	.	.	none		0.627	PLVAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463655.1	NM_031310		-	17471595	T	-	17471595	7	5	2	1	0	1	0	1	0	0	0	0	12123	1725	60	0	114	0	PLVAP	19	17471595	Frame_Shift_Del	DEL	T	TCGA-2Z-A9J1-01A-11D-A382-10	497000	17471595	41657388	92	153											
FKBP8	23770	hgsc.bcm.edu	37	chr19	18652713	18652713	+	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	ccccatccagtacctcgaagTcctcgagcggtgggaccccg	7	6	11	17	4	0	0	0	0	0	0	4	3	2	1	7	2	2	1	7	2	2	1			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr19:18652713T>A	ENST00000596558.2	-	2	177	c.68A>T	c.(67-69)gAc>gTc	p.D23V	FKBP8_ENST00000222308.4_Missense_Mutation_p.D23V|FKBP8_ENST00000610101.1_Missense_Mutation_p.D23V|FKBP8_ENST00000597960.3_Missense_Mutation_p.D23V|FKBP8_ENST00000608443.1_Missense_Mutation_p.D23V|FKBP8_ENST00000453489.2_Missense_Mutation_p.D52V			Q14318	FKBP8_HUMAN	FK506 binding protein 8, 38kDa	23	Glu-rich.				apoptotic process (GO:0006915)|camera-type eye development (GO:0043010)|cell fate specification (GO:0001708)|chaperone-mediated protein folding (GO:0061077)|dorsal/ventral neural tube patterning (GO:0021904)|intracellular signal transduction (GO:0035556)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|positive regulation of BMP signaling pathway (GO:0030513)|protein peptidyl-prolyl isomerization (GO:0000413)|regulation of gene expression (GO:0010468)|smoothened signaling pathway (GO:0007224)|viral process (GO:0016032)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	FK506 binding (GO:0005528)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	15						TACCTCGAAGTCCTCGAGCGG	0.632																																					p.D23V		Atlas-SNP	.											.	FKBP8	69	.	0			c.A68T						PASS	.						37	31	33					19																	18652713		2203	4300	6503	SO:0001583	missense	23770	exon2			TCGAAGTCCTCGA	L37033	CCDS32961.1	19p12	2013-01-10	2002-08-29		ENSG00000105701	ENSG00000105701		"Tetratricopeptide (TTC) repeat domain containing"	3724	protein-coding gene	gene with protein product	"FK506-binding protein 8 (38kD)"	604840	"FK506-binding protein 8 (38kD)"			7543869	Standard	NM_012181		Approved	FKBP38, FKBPr38	uc002njj.1	Q14318		ENST00000596558.2:c.68A>T	chr19.hg19:g.18652713T>A	ENSP00000472302:p.Asp23Val	119.0	0.0	.		80.0	25.0	.	NM_012181	C8C9T5|Q53GU3|Q7Z349|Q86YK6	Missense_Mutation	SNP	ENST00000596558.2	hg19		.	.	.	.	.	.	.	.	.	.	T	8.207	0.799502	0.16397	.	.	ENSG00000105701	ENST00000222308;ENST00000544835;ENST00000453489	T;T;T	0.44083	0.93;1.28;1.1	3.13	2.1	0.27182	.	0.058219	0.64402	D	0.000003	T	0.26738	0.0654	L	0.29908	0.895	0.35397	D	0.791268	P;B;B	0.35982	0.531;0.308;0.434	B;B;B	0.36030	0.216;0.051;0.11	T	0.23226	-1.0194	10	0.41790	T	0.15	-23.4139	5.7686	0.18241	0.0:0.1377:0.0:0.8623	.	52;23;23	B7Z6M0;Q14318;Q14318-2	.;FKBP8_HUMAN;.	V	23;23;52	ENSP00000222308:D23V;ENSP00000441267:D23V;ENSP00000388891:D52V	ENSP00000222308:D23V	D	-	2	0	FKBP8	18513713	1.000000	0.71417	0.999000	0.59377	0.075000	0.17131	1.562000	0.36353	0.621000	0.30232	0.402000	0.26972	GAC	.	.	.	none		0.632	FKBP8-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000466374.3	NM_012181		A	18652713	T	A	18652713	3	1	2	1	0	0	0	0	1	0	0	0	5921	1667	58	5	1205	5	FKBP8	19	18652713	Missense_Mutation	SNP	T	TCGA-2Z-A9J1-01A-11D-A382-10	1181118	18652713	40476270	93	154											
SFRS14	10147	hgsc.bcm.edu	37	chr19	19106049	19106049	+	Frame_Shift_Del	DEL	T	T	-																															tctggaagcccaggttcttaTcggtcagcttctgctgggcg																										TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr19:19106049delT	ENST00000601879.1	-	9	3329	c.3032delA	c.(3031-3033)gatfs	p.D1011fs	SUGP2_ENST00000600377.1_Frame_Shift_Del_p.D1025fs|SUGP2_ENST00000452918.2_Frame_Shift_Del_p.D1011fs|SUGP2_ENST00000337018.6_Frame_Shift_Del_p.D1011fs|AC004447.2_ENST00000594142.1_RNA|SUGP2_ENST00000456085.2_Frame_Shift_Del_p.D780fs			Q8IX01	SUGP2_HUMAN	SURP and G patch domain containing 2	1011	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						CAGGTTCTTATCGGTCAGCTT	0.602																																					p.D1011fs		Atlas-Indel,Pindel	.											.	SUGP2	107	.	0			c.3033delT						PASS	.						66	53	58					19																	19106049		2203	4300	6503	SO:0001589	frameshift_variant	10147	exon9			.	AB002363	CCDS12392.1	19p13	2013-01-28	2010-08-10	2010-08-10	ENSG00000064607	ENSG00000064607		"G patch domain containing"	18641	protein-coding gene	gene with protein product		607993	"splicing factor, arginine/serine-rich 14"	SFRS14		12594045	Standard	NM_014884		Approved	KIAA0365	uc002nkx.2	Q8IX01		ENST00000601879.1:c.3032delA	chr19.hg19:g.19106049delT	ENSP00000472286:p.Asp1011fs	71.0	0.0	0		58.0	19.0	0.327586	NM_001017392	C9JI71|O15071|O60369|Q5JPH7|Q8WUF7	Frame_Shift_Del	DEL	ENST00000601879.1	hg19	CCDS12392.1																																																																																			.	.	.	none		0.602	SUGP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464627.1	NM_001017392		-	19106049	T	-	19106049	7	5	2	1	0	1	0	1	0	0	0	0	14183	1435	50	0	224	0	SFRS14	19	19106049	Frame_Shift_Del	DEL	T	TCGA-2Z-A9J1-01A-11D-A382-10	453336	19106049	40022934	94	155											
GPATCH1	55094	hgsc.bcm.edu	37	chr19	33600735	33600735	+	Silent	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	ctcaaggccaggagtctggcCcagaacgctcagagcagcag	11	4	13	13	1	3	2	2	0	1	2	3	3	3	3	2	3	3	3	2	3	2	0			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr19:33600735C>T	ENST00000170564.2	+	11	1712	c.1398C>T	c.(1396-1398)gcC>gcT	p.A466A		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	466					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)					GGAGTCTGGCCCAGAACGCTC	0.537																																					p.A466A	Pancreas(67;88 1713 4567 18227)	Atlas-SNP	.											.	GPATCH1	79	.	0			c.C1398T						PASS	.						45	47	46					19																	33600735		2203	4300	6503	SO:0001819	synonymous_variant	55094	exon11			TCTGGCCCAGAAC	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.1398C>T	chr19.hg19:g.33600735C>T		228.0	0.0	.		218.0	78.0	.	NM_018025	Q8IZV6|Q8N3B7|Q9NW94	Silent	SNP	ENST00000170564.2	hg19	CCDS12428.1																																																																																			.	.	.	none		0.537	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025		T	33600735	C	T	33600735	2	4	2	1	0	0	0	0	0	0	0	1	6597	610	22	2		2	GPATCH1	19	33600735	Silent	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10	14494686	33600735	25528248	95	156											
STRN4	29888	hgsc.bcm.edu	37	chr19	47226540	47226540	+	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	acgtggctcagcacgcttggGtctgcacccaccgcagggag	7	6	14	14	3	2	0	1	0	1	0	2	1	2	1	2	3	2	5	2	3	0	1			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr19:47226540G>A	ENST00000263280.6	-	13	1645	c.1596C>T	c.(1594-1596)gaC>gaT	p.D532D	STRN4_ENST00000539396.1_Splice_Site_p.D413D|STRN4_ENST00000594357.2_5'UTR|STRN4_ENST00000391910.3_Splice_Site_p.D539D	NM_001039877.1|NM_013403.2	NP_001034966.1|NP_037535.2	Q9NRL3	STRN4_HUMAN	striatin, calmodulin binding protein 4	532						cell projection (GO:0042995)|cytoplasm (GO:0005737)|membrane (GO:0016020)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000563)|all cancers(93;0.00138)|Epithelial(262;0.0217)|GBM - Glioblastoma multiforme(486;0.035)		GCACGCTTGGGTCTGCACCCA	0.697																																					p.D539D		Atlas-SNP	.											.	STRN4	33	.	0			c.C1617T						PASS	.						18	17	17					19																	47226540		2111	4136	6247	SO:0001630	splice_region_variant	29888	exon13			GCTTGGGTCTGCA	AF212940	CCDS12690.1, CCDS42581.1	19q13.32	2013-01-10			ENSG00000090372	ENSG00000090372		"WD repeat domain containing"	15721	protein-coding gene	gene with protein product		614767				10748158	Standard	XM_006723171		Approved	zinedin, ZIN	uc002pfm.3	Q9NRL3		ENST00000263280.6:c.1595-1C>T	chr19.hg19:g.47226540G>A		83.0	0.0	.		55.0	14.0	.	NM_001039877	A0A024R0V2|B4DQH7|F8VYA6|Q8NE53	Silent	SNP	ENST00000263280.6	hg19	CCDS12690.1																																																																																			.	.	.	none		0.697	STRN4-001	KNOWN	NMD_exception|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466607.2		Silent	A	47226540	G	A	47226540	5	1	2	1	0	0	0	0	0	0	1	0	15343	1275	44	2	685	2	STRN4	19	47226540	Splice_Site	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	13625805	47226540	11902443	96	157											
ZNF543	125919	hgsc.bcm.edu	37	chr19	57839668	57839668	+	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	accagcggattcacagtggaGagaagccttataagtgcagt	13	8	12	8	1	1	1	1	0	0	1	1	4	1	3	2	2	3	1	2	2	3	3			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr19:57839668G>A	ENST00000321545.4	+	4	1183	c.838G>A	c.(838-840)Gag>Aag	p.E280K		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	280					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)		TCACAGTGGAGAGAAGCCTTA	0.522																																					p.E280K		Atlas-SNP	.											.	ZNF543	61	.	0			c.G838A						PASS	.						54	53	53					19																	57839668		2203	4300	6503	SO:0001583	missense	125919	exon4			AGTGGAGAGAAGC	AL834534	CCDS33130.1	19q13.43	2013-01-08				ENSG00000178229		"Zinc fingers, C2H2-type", "-"	25281	protein-coding gene	gene with protein product							Standard	NM_213598		Approved	DKFZp434H055	uc002qoi.2	Q08ER8		ENST00000321545.4:c.838G>A	chr19.hg19:g.57839668G>A	ENSP00000322545:p.Glu280Lys	100.0	0.0	.		96.0	4.0	.	NM_213598	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	Missense_Mutation	SNP	ENST00000321545.4	hg19	CCDS33130.1	.	.	.	.	.	.	.	.	.	.	G	15.89	2.967976	0.53507	.	.	ENSG00000178229	ENST00000321545	T	0.24350	1.86	2.58	1.54	0.23209	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.33147	0.0853	N	0.25245	0.725	0.27992	N	0.935614	D	0.89917	1.0	D	0.91635	0.999	T	0.13683	-1.0500	9	0.87932	D	0	.	8.9097	0.35546	0.1221:0.0:0.8779:0.0	.	280	Q08ER8	ZN543_HUMAN	K	280	ENSP00000322545:E280K	ENSP00000322545:E280K	E	+	1	0	ZNF543	62531480	1.000000	0.71417	0.436000	0.26797	0.434000	0.31775	4.493000	0.60341	0.650000	0.30769	0.561000	0.74099	GAG	.	.	.	none		0.522	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865		A	57839668	G	A	57839668	3	1	2	1	0	0	0	0	1	0	0	0	17988	943	33	2	852	2	ZNF543	19	57839668	Missense_Mutation	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	10613128	57839668	1289315	97	158											
KCNB1	3745	hgsc.bcm.edu	37	chr20	47991224	47991224	+	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	atctggaccacgcggcggacAttctggaattgcagcacgct	9	8	12	12	4	2	0	0	0	2	0	2	3	2	3	1	4	2	3	1	4	1	2			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr20:47991224A>T	ENST00000371741.4	-	2	1039	c.873T>A	c.(871-873)aaT>aaA	p.N291K		NM_004975.2	NP_004966.1	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 1	291					energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|dendrite membrane (GO:0032590)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(22)|pancreas(2)|prostate(7)|skin(4)|stomach(1)|urinary_tract(1)	53			BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Dalfampridine(DB06637)	CGCGGCGGACATTCTGGAATT	0.532																																					p.N291K		Atlas-SNP	.											KCNB1,caecum,carcinoma,0,1	KCNB1	142	.	0			c.T873A						PASS	.						89	84	86					20																	47991224		2203	4300	6503	SO:0001583	missense	3745	exon2			GCGGACATTCTGG	AF026005	CCDS13418.1	20q13.2	2012-07-05			ENSG00000158445	ENSG00000158445		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6231	protein-coding gene	gene with protein product		600397				7774931, 16382104	Standard	NM_004975		Approved	Kv2.1	uc002xur.1	Q14721	OTTHUMG00000033051	ENST00000371741.4:c.873T>A	chr20.hg19:g.47991224A>T	ENSP00000360806:p.Asn291Lys	153.0	0.0	.		168.0	47.0	.	NM_004975	Q14193	Missense_Mutation	SNP	ENST00000371741.4	hg19	CCDS13418.1	.	.	.	.	.	.	.	.	.	.	A	15.59	2.877204	0.51801	.	.	ENSG00000158445	ENST00000371741;ENST00000538812	D	0.97553	-4.43	6.02	-12.0	0.00017	Ion transport (1);	0.099189	0.64402	D	0.000003	D	0.96494	0.8856	L	0.39397	1.21	0.36927	D	0.891708	D	0.89917	1.0	D	0.79108	0.992	D	0.96575	0.9426	10	0.72032	D	0.01	.	22.2779	0.99969	0.8078:0.0:0.1922:0.0	.	291	Q14721	KCNB1_HUMAN	K	291;246	ENSP00000360806:N291K	ENSP00000360806:N291K	N	-	3	2	KCNB1	47424631	0.000000	0.05858	0.114000	0.21550	0.973000	0.67179	-1.491000	0.02302	-2.492000	0.00516	-0.912000	0.02778	AAT	.	.	.	none		0.532	KCNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080374.3	NM_004975		T	47991224	A	T	47991224	3	4	2	1	0	0	0	0	1	0	0	0	8019	214	8	5	1707	5	KCNB1	20	47991224	Missense_Mutation	SNP	A	TCGA-2Z-A9J1-01A-11D-A382-10		47991224	15034296	98	159											
ZNF831	128611	hgsc.bcm.edu	37	chr20	57829325	57829325	+	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	gagaccacagccagactgcaGggaggactctgacatcaagc	13	4	12	12	0	2	3	1	1	1	2	2	6	2	5	2	2	3	1	2	2	1	0			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr20:57829325G>C	ENST00000371030.2	+	5	4561	c.4561G>C	c.(4561-4563)Ggg>Cgg	p.G1521R		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1521							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)					CCAGACTGCAGGGAGGACTCT	0.517																																					p.G1521R		Atlas-SNP	.											.	ZNF831	287	.	0			c.G4561C						PASS	.						40	44	42					20																	57829325		2112	4245	6357	SO:0001583	missense	128611	exon5			ACTGCAGGGAGGA	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.4561G>C	chr20.hg19:g.57829325G>C	ENSP00000360069:p.Gly1521Arg	81.0	0.0	.		141.0	69.0	.	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	hg19	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	G	14.63	2.591315	0.46214	.	.	ENSG00000124203	ENST00000371030	T	0.04654	3.58	5.46	1.13	0.20643	.	0.926151	0.09118	N	0.846118	T	0.05914	0.0154	L	0.57536	1.79	0.09310	N	1	B	0.19583	0.037	B	0.12837	0.008	T	0.39292	-0.9621	10	0.54805	T	0.06	-4.3833	3.834	0.08886	0.2676:0.0:0.5651:0.1673	.	1521	Q5JPB2	ZN831_HUMAN	R	1521	ENSP00000360069:G1521R	ENSP00000360069:G1521R	G	+	1	0	ZNF831	57262720	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.188000	0.09642	0.291000	0.22468	0.650000	0.86243	GGG	.	.	.	none		0.517	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		C	57829325	G	C	57829325	3	2	2	1	0	0	0	0	1	0	0	0	18197	1000	35	4	4579	4	ZNF831	20	57829325	Missense_Mutation	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10	9838101	57829325	5196195	99	160											
RWDD2B	10069	hgsc.bcm.edu	37	chr21	30378846	30378846	+	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	tggtttcccctggctccattAacactgaacactttttcttc	7	16	5	13	0	1	1	0	1	1	0	4	1	3	1	3	2	2	2	3	2	2	5			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr21:30378846A>T	ENST00000493196.1	-	5	952	c.852T>A	c.(850-852)gtT>gtA	p.V284V	RWDD2B_ENST00000486719.1_5'UTR	NM_016940.2	NP_058636.1	P57060	RWD2B_HUMAN	RWD domain containing 2B	284										endometrium(1)|kidney(1)|large_intestine(8)|lung(2)	12						TGGCTCCATTAACACTGAACA	0.388																																					p.V284V		Atlas-SNP	.											.	RWDD2B	24	.	0			c.T852A						PASS	.						124	112	116					21																	30378846		2203	4300	6503	SO:0001819	synonymous_variant	10069	exon5			TCCATTAACACTG	AF212232	CCDS13582.1	21q22.11	2012-12-07	2007-07-17	2007-07-17	ENSG00000156253	ENSG00000156253			1302	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 6"	C21orf6		10729227	Standard	NM_016940		Approved	GL011	uc002yms.3	P57060	OTTHUMG00000078805	ENST00000493196.1:c.852T>A	chr21.hg19:g.30378846A>T		128.0	0.0	.		115.0	50.0	.	NM_016940		Silent	SNP	ENST00000493196.1	hg19	CCDS13582.1																																																																																			.	.	.	none		0.388	RWDD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171858.1			T	30378846	A	T	30378846	2	4	2	1	0	0	0	0	0	0	0	1	13769	349	13	5		5	RWDD2B	21	30378846	Silent	SNP	A	TCGA-2Z-A9J1-01A-11D-A382-10		30378846	17751049	100	161											
TMEM50B	757	hgsc.bcm.edu	37	chr21	34841130	34841131	+	Frame_Shift_Del	DEL	TC	TC	-																															acagatgccacagcatttctTctctcactccagtcaataca																										TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr21:34841130_34841131delTC	ENST00000542230.2	-	2	276_277	c.62_63delGA	c.(61-63)agafs	p.R22fs		NM_006134.6	NP_006125.2	P56557	TM50B_HUMAN	transmembrane protein 50B	22						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(1)|ovary(1)|skin(1)	4						CAGCATTTCTTCTCTCACTCCA	0.396																																					p.21_22del		Atlas-Indel,Pindel	.											.	TMEM50B	25	.	0			c.63_64del						PASS	.																																			SO:0001589	frameshift_variant	757	exon2			.	AF045606	CCDS13625.1	21q22.1	2008-07-29	2005-06-02	2005-06-02	ENSG00000142188	ENSG00000142188			1280	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 4"	C21orf4			Standard	NR_040016		Approved		uc002yrs.2	P56557	OTTHUMG00000065286	ENST00000542230.2:c.62_63delGA	chr21.hg19:g.34841134_34841135delTC	ENSP00000439768:p.Arg22fs	76.0	0.0	0		102.0	28.0	0.27451	NM_006134	B2R4L4|D3DSF1|O60537|Q5PY47	Frame_Shift_Del	DEL	ENST00000542230.2	hg19	CCDS13625.1																																																																																			.	.	.	none		0.396	TMEM50B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140080.5			-	34841131	TC	-	34841130	7	5	2	1	0	1	0	1	0	0	0	0	16188	1780	62	0	437	0	TMEM50B	21	34841130	Frame_Shift_Del	DEL	TC	TCGA-2Z-A9J1-01A-11D-A382-10	4462284	34841130	13288765	101	162											
CSNK1E	1454	hgsc.bcm.edu	37	chr22	38694925	38694925	+	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	ggagcggcagaagttgaggtAtgttgagaattcggctggag	10	9	18	4	2	0	3	0	2	0	2	1	6	0	5	0	5	1	5	0	5	3	4			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chr22:38694925A>T	ENST00000396832.1	-	7	1011	c.751T>A	c.(751-753)Tac>Aac	p.Y251N	CSNK1E_ENST00000405675.3_Missense_Mutation_p.Y251N|CSNK1E_ENST00000359867.3_Missense_Mutation_p.Y251N|CSNK1E_ENST00000403904.1_Missense_Mutation_p.Y251N|CSNK1E_ENST00000498529.1_5'UTR|CSNK1E_ENST00000400206.2_Missense_Mutation_p.Y251N|CSNK1E_ENST00000413574.2_Missense_Mutation_p.Y251N	NM_152221.2	NP_689407.1	P49674	KC1E_HUMAN	casein kinase 1, epsilon	251	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular protein localization (GO:0034613)|circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22	Melanoma(58;0.045)					AAGTTGAGGTATGTTGAGAAT	0.592																																					p.Y251N	Esophageal Squamous(119;108 755 9651 12170 13692 17603 24932 28315 37982 41601)	Atlas-SNP	.											.	CSNK1E	143	.	0			c.T751A						PASS	.						167	155	159					22																	38694925		2203	4300	6503	SO:0001583	missense	1454	exon7			TGAGGTATGTTGA		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.751T>A	chr22.hg19:g.38694925A>T	ENSP00000380044:p.Tyr251Asn	134.0	0.0	.		100.0	28.0	.	NM_001894		Missense_Mutation	SNP	ENST00000396832.1	hg19	CCDS13970.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.15|15.15	2.748201|2.748201	0.49257|0.49257	.|.	.|.	ENSG00000213923|ENSG00000213923	ENST00000451964|ENST00000359867;ENST00000396832;ENST00000402865;ENST00000400206;ENST00000403904;ENST00000413574;ENST00000405675	.|T;T;T;T;T;T	.|0.12255	.|2.7;2.7;2.7;2.7;2.7;2.7	4.95|4.95	4.95|4.95	0.65309|0.65309	.|Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|0.060906	.|0.64402	.|D	.|0.000002	T|T	0.58104|0.58104	0.2099|0.2099	H|H	0.99555|0.99555	4.625|4.625	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	0.78142|0.78142	-0.2319|-0.2319	5|10	.|0.87932	.|D	.|0	.|.	14.6566|14.6566	0.68838|0.68838	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|251;251;251	.|B0QY35;B0QY34;P49674	.|.;.;KC1E_HUMAN	Q|N	188|251	.|ENSP00000352929:Y251N;ENSP00000380044:Y251N;ENSP00000383067:Y251N;ENSP00000384074:Y251N;ENSP00000407235:Y251N;ENSP00000384426:Y251N	.|ENSP00000352929:Y251N	H|Y	-|-	3|1	2|0	CSNK1E|CSNK1E	37024871|37024871	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.964000|0.964000	0.63967|0.63967	9.325000|9.325000	0.96381|0.96381	1.862000|1.862000	0.54008|0.54008	0.533000|0.533000	0.62120|0.62120	CAT|TAC	.	.	.	none		0.592	CSNK1E-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321462.1	NM_001894		T	38694925	A	T	38694925	3	4	2	1	0	0	0	0	1	0	0	0	3955	449	16	5	515	5	CSNK1E	22	38694925	Missense_Mutation	SNP	A	TCGA-2Z-A9J1-01A-11D-A382-10		38694925	12609641	102	163											
P2RY8	286530	hgsc.bcm.edu	37	chrX	1584748	1584748	+	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	ccaccgcggccaggcccaccGcgcgcctccgctgctcccgg	3	3	12	23	7	0	0	0	0	0	0	2	0	2	0	8	3	1	2	8	3	0	0			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chrX:1584748G>C	ENST00000381297.4	-	2	914	c.704C>G	c.(703-705)gCg>gGg	p.A235G	P2RY8_ENST00000460672.1_5'Flank	NM_178129.4	NP_835230.1	Q86VZ1	P2RY8_HUMAN	purinergic receptor P2Y, G-protein coupled, 8	235						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)				CAGGCCCACCGCGCGCCTCCG	0.662			T	CRLF2	"B-ALL, Downs associated ALL"																																p.A235G		Atlas-SNP	.		Dom	yes		"X,Y"	Xp22.3; Yp11.3	286530	"purinergic receptor P2Y, G-protein coupled, 8"		L	.	P2RY8	53	.	0			c.C704G						PASS	.						45	38	40					X																	1584748		2201	4294	6495	SO:0001583	missense	286530	exon2			CCCACCGCGCGCC	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.704C>G	chrX.hg19:g.1584748G>C	ENSP00000370697:p.Ala235Gly	172.0	0.0	.		94.0	38.0	.	NM_178129		Missense_Mutation	SNP	ENST00000381297.4	hg19	CCDS14115.1	.	.	.	.	.	.	.	.	.	.	g	14.43	2.532899	0.45073	.	.	ENSG00000182162	ENST00000381297	T	0.40756	1.02	2.73	2.73	0.32206	GPCR, rhodopsin-like superfamily (1);	0.338053	0.26738	U	0.022749	T	0.56124	0.1964	M	0.85630	2.765	0.09310	N	1	P	0.52170	0.951	P	0.50537	0.643	T	0.56111	-0.8033	10	0.56958	D	0.05	.	13.5149	0.61535	0.0:0.0:1.0:0.0	.	235	Q86VZ1	P2RY8_HUMAN	G	235	ENSP00000370697:A235G	ENSP00000370697:A235G	A	-	2	0	P2RY8	1544748	1.000000	0.71417	0.236000	0.24074	0.670000	0.39368	5.742000	0.68646	1.007000	0.39238	0.279000	0.19357	GCG	.	.	.	none		0.662	P2RY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055602.1	NM_178129		C	1584748	G	C	1584748	3	2	2	1	0	0	0	0	1	0	0	0	11362	1087	38	4	379	4	P2RY8	23	1584748	Missense_Mutation	SNP	G	TCGA-2Z-A9J1-01A-11D-A382-10		1584748	153685812	103	164											
XKRX	402415	hgsc.bcm.edu	37	chrX	100183149	100183149	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaccatgtacaaagcagatgCagcctccccacagtacaaaa	17	5	6	13	0	0	1	0	0	0	1	1	1	1	1	4	0	6	4	4	0	6	2			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chrX:100183149C>T	ENST00000372956.2	-	1	749	c.145G>A	c.(145-147)Gca>Aca	p.A49T	XKRX_ENST00000328526.5_Missense_Mutation_p.A62T|XKRX_ENST00000468904.1_Missense_Mutation_p.A49T			Q6PP77	XKR2_HUMAN	XK, Kell blood group complex subunit-related, X-linked	49						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(3)	22						AAAGCAGATGCAGCCTCCCCA	0.413																																					p.A49T		Atlas-SNP	.											.	XKRX	53	.	0			c.G145A						PASS	.						135	127	130					X																	100183149		2203	4300	6503	SO:0001583	missense	402415	exon1			CAGATGCAGCCTC	AY589511	CCDS14476.1, CCDS14476.2	Xq22	2008-02-05	2006-01-12		ENSG00000182489	ENSG00000182489			29845	protein-coding gene	gene with protein product		300684	"X Kell blood group precursor-related, X-linked"				Standard	NM_212559		Approved	XPLAC, XKR2	uc004egn.2	Q6PP77	OTTHUMG00000022010	ENST00000372956.2:c.145G>A	chrX.hg19:g.100183149C>T	ENSP00000362047:p.Ala49Thr	210.0	0.0	.		192.0	150.0	.	NM_212559	B2RNN6|B4DKU2|Q5H9J6	Missense_Mutation	SNP	ENST00000372956.2	hg19	CCDS14476.2	.	.	.	.	.	.	.	.	.	.	C	12.68	2.009363	0.35415	.	.	ENSG00000182489	ENST00000328526;ENST00000372956;ENST00000468904	T;T;T	0.64085	-0.08;-0.08;-0.08	5.17	2.09	0.27110	.	0.428985	0.25369	N	0.031170	T	0.42630	0.1211	L	0.28115	0.83	0.34225	D	0.675849	B	0.25441	0.126	B	0.28916	0.096	T	0.41179	-0.9523	10	0.15066	T	0.55	-0.4089	6.8026	0.23760	0.2543:0.6499:0.0:0.0958	.	49	Q6PP77	XKR2_HUMAN	T	62;49;49	ENSP00000327570:A62T;ENSP00000362047:A49T;ENSP00000419884:A49T	ENSP00000327570:A62T	A	-	1	0	XKRX	100069805	0.589000	0.26807	0.995000	0.50966	0.958000	0.62258	0.851000	0.27751	0.963000	0.38082	0.429000	0.28392	GCA	.	.	.	none		0.413	XKRX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057501.3	NM_212559		T	100183149	C	T	100183149	3	4	2	1	0	0	0	0	1	0	0	0	17451	710	25	2	1216	2	XKRX	23	100183149	Missense_Mutation	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10	98598401	100183149	55087411	104	165											
ATP2B3	492	hgsc.bcm.edu	37	chrX	152826188	152826188	+	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	tgcgcccctgcactcgccacCctcagagcactacaccatca	9	6	6	20	2	2	1	2	0	0	1	3	1	2	1	5	0	4	2	5	0	1	1			TCGA-2Z-A9J1-01A-11D-A382-10	TCGA-2Z-A9J1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	facc4ec7-af1e-4980-ae56-1f0cd0c7ae54	a57e8ad5-ef7e-47cc-8cc1-0bee5ece05fa	g.chrX:152826188C>A	ENST00000349466.2	+	18	3220	c.2894C>A	c.(2893-2895)cCc>cAc	p.P965H	ATP2B3_ENST00000393842.1_Missense_Mutation_p.P951H|ATP2B3_ENST00000359149.3_Missense_Mutation_p.P965H|ATP2B3_ENST00000263519.4_Missense_Mutation_p.P965H|ATP2B3_ENST00000370186.1_Missense_Mutation_p.P951H|ATP2B3_ENST00000460549.1_3'UTR|ATP2B3_ENST00000370181.2_Missense_Mutation_p.P951H			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	965					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)					CACTCGCCACCCTCAGAGCAC	0.562																																					p.P965H		Atlas-SNP	.											.	ATP2B3	552	.	0			c.C2894A						PASS	.						230	170	190					X																	152826188		2203	4300	6503	SO:0001583	missense	492	exon17			CGCCACCCTCAGA	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.2894C>A	chrX.hg19:g.152826188C>A	ENSP00000343886:p.Pro965His	102.0	0.0	.		66.0	41.0	.	NM_001001344	B7WNR8|B7WNY5|Q12995|Q16858	Missense_Mutation	SNP	ENST00000349466.2	hg19	CCDS35440.1	.	.	.	.	.	.	.	.	.	.	C	18.27	3.587407	0.66105	.	.	ENSG00000067842	ENST00000370186;ENST00000349466;ENST00000393842;ENST00000359149;ENST00000263519;ENST00000370181	D;D;D;D;D;D	0.95656	-3.77;-3.77;-3.77;-3.77;-3.77;-3.77	4.99	4.99	0.66335	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.97711	0.9249	M	0.82433	2.59	0.80722	D	1	D;D	0.89917	1.0;0.993	D;P	0.85130	0.997;0.889	D	0.98698	1.0699	10	0.87932	D	0	-26.3635	16.126	0.81395	0.0:1.0:0.0:0.0	.	965;965	Q16720;Q16720-2	AT2B3_HUMAN;.	H	951;965;951;965;965;951	ENSP00000359205:P951H;ENSP00000343886:P965H;ENSP00000377425:P951H;ENSP00000352062:P965H;ENSP00000263519:P965H;ENSP00000359200:P951H	ENSP00000263519:P965H	P	+	2	0	ATP2B3	152479382	1.000000	0.71417	0.082000	0.20525	0.421000	0.31385	7.728000	0.84847	2.057000	0.61298	0.519000	0.50382	CCC	.	.	.	none		0.562	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060957.1	NM_021949		A	152826188	C	A	152826188	3	1	2	1	0	0	0	0	1	0	0	0	1141	623	22	4	2960	4	ATP2B3	23	152826188	Missense_Mutation	SNP	C	TCGA-2Z-A9J1-01A-11D-A382-10	52643039	152826188	2444372	105	166											
AGRN	375790	hgsc.bcm.edu	37	chr1	984390	984390	+	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	tgtacaatggcaacgcccggGgcaaggacttcctggcattg	9	8	13	11	2	0	0	0	0	0	0	1	1	1	1	2	5	2	4	2	5	4	3			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr1:984390G>T	ENST00000379370.2	+	24	4299	c.4249G>T	c.(4249-4251)Ggc>Tgc	p.G1417C		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	1417	Laminin G-like 1. {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)		CAACGCCCGGGGCAAGGACTT	0.711																																					p.G1417C		Atlas-SNP	.											.	AGRN	110	.	0			c.G4249T						PASS	.						7	8	8					1																	984390		2166	4270	6436	SO:0001583	missense	375790	exon24			GCCCGGGGCAAGG	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.4249G>T	chr1.hg19:g.984390G>T	ENSP00000368678:p.Gly1417Cys	194.0	0.0	.		100.0	27.0	.	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Missense_Mutation	SNP	ENST00000379370.2	hg19	CCDS30551.1	.	.	.	.	.	.	.	.	.	.	g	14.88	2.666084	0.47677	.	.	ENSG00000188157	ENST00000379370	T	0.76448	-1.02	4.62	4.62	0.57501	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	0.177734	0.37178	U	0.002213	D	0.90212	0.6940	M	0.91612	3.225	0.49130	D	0.999757	D	0.89917	1.0	D	0.79784	0.993	D	0.92456	0.5974	10	0.66056	D	0.02	-30.8549	16.6039	0.84823	0.0:0.0:1.0:0.0	.	1417	O00468	AGRIN_HUMAN	C	1417	ENSP00000368678:G1417C	ENSP00000368678:G1417C	G	+	1	0	AGRN	974253	1.000000	0.71417	0.932000	0.37286	0.031000	0.12232	5.858000	0.69532	2.284000	0.76573	0.555000	0.69702	GGC	.	.	.	none		0.711	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576		T	984390	G	T	984390	3	4	3	1	0	0	0	0	1	0	0	0	397	1232	43	4	4343	4	AGRN	1	984390	Missense_Mutation	SNP	G	TCGA-2Z-A9J2-01A-11D-A382-10		984390	248266231	1	167											
KIF1B	23095	hgsc.bcm.edu	37	chr1	10394605	10394605	+	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	gtttacctgagcaatctgctGtatcccgtgcccctgatcca	7	12	8	14	1	1	2	0	2	1	0	3	2	3	2	5	0	4	4	5	0	3	3			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr1:10394605G>A	ENST00000377086.1	+	28	3154	c.2952G>A	c.(2950-2952)ctG>ctA	p.L984L	KIF1B_ENST00000263934.6_Silent_p.L938L|KIF1B_ENST00000377081.1_Silent_p.L984L			O60333	KIF1B_HUMAN	kinesin family member 1B	984					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)		GCAATCTGCTGTATCCCGTGC	0.507																																					p.L938L		Atlas-SNP	.											.	KIF1B	242	.	0			c.G2814A						PASS	.						292	261	271					1																	10394605		2203	4300	6503	SO:0001819	synonymous_variant	23095	exon26			TCTGCTGTATCCC	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.2952G>A	chr1.hg19:g.10394605G>A		90.0	0.0	.		81.0	33.0	.	NM_015074	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Silent	SNP	ENST00000377086.1	hg19																																																																																				.	.	.	none		0.507	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1			A	10394605	G	A	10394605	2	1	3	1	0	0	0	0	0	0	0	1	8291	1364	48	2		2	KIF1B	1	10394605	Silent	SNP	G	TCGA-2Z-A9J2-01A-11D-A382-10	9410215	10394605	238856016	2	168											
PEX14	5195	hgsc.bcm.edu	37	chr1	10596271	10596271	+	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	attttctctctctcaccagaTtgccacggcagtgaagtttc	8	14	7	12	1	3	2	1	1	2	1	6	2	3	2	2	1	1	2	2	1	1	4			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr1:10596271T>G	ENST00000356607.4	+	3	166	c.86T>G	c.(85-87)aTt>aGt	p.I29S	PEX14_ENST00000538836.1_Intron|PEX14_ENST00000492696.1_3'UTR	NM_004565.2	NP_004556.1	O75381	PEX14_HUMAN	peroxisomal biogenesis factor 14	29					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)		TCTCACCAGATTGCCACGGCA	0.458																																					p.I29S		Atlas-SNP	.											.	PEX14	40	.	0			c.T86G						PASS	.						54	55	55					1																	10596271		2203	4300	6503	SO:0001630	splice_region_variant	5195	exon3			ACCAGATTGCCAC	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.85-1T>G	chr1.hg19:g.10596271T>G		336.0	1.0	.		226.0	87.0	.	NM_004565	B2R7N1|B3KML6|B7Z1N2|Q8WX51	Missense_Mutation	SNP	ENST00000356607.4	hg19	CCDS30582.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.524443	0.85600	.	.	ENSG00000142655	ENST00000356607	T	0.52526	0.66	5.82	5.82	0.92795	Peroxisome membrane anchor protein Pex14p, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.73799	0.3633	M	0.89214	3.015	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.72338	0.943;0.977	T	0.79619	-0.1728	10	0.87932	D	0	.	16.1986	0.82053	0.0:0.0:0.0:1.0	.	29;29	O75381-2;O75381	.;PEX14_HUMAN	S	29	ENSP00000349016:I29S	ENSP00000349016:I29S	I	+	2	0	PEX14	10518858	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	7.082000	0.76851	2.227000	0.72691	0.455000	0.32223	ATT	.	.	.	none		0.458	PEX14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005414.1		Missense_Mutation	G	10596271	T	G	10596271	5	3	3	1	0	0	0	0	0	0	1	0	11749	1507	52	5	96	5	PEX14	1	10596271	Splice_Site	SNP	T	TCGA-2Z-A9J2-01A-11D-A382-10	201666	10596271	238654350	3	169											
ARHGEF19	128272	hgsc.bcm.edu	37	chr1	16529006	16529007	+	Frame_Shift_Ins	INS	-	-	CTCAGGTCCCGCACCTGCAGCTCAGCCAT																															ggatgccctgcagcttcaggINSctcaggtcccgcacctgcag																										TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr1:16529006_16529007insCTCAGGTCCCGCACCTGCAGCTCAGCCAT	ENST00000270747.3	-	13	2106_2107	c.1970_1971insATGGCTGAGCTGCAGGTGCGGGACCTGAG	c.(1969-1971)agcfs	p.S657fs	ARHGEF19_ENST00000478117.1_De_novo_Start_OutOfFrame	NM_153213.3	NP_694945.2	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19	657	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)		GCAGCTTCAGGCTCAGGTCCCG	0.663																																					p.S657_L658delinsRWLSCRCGTX		Pindel	.											.	ARHGEF19	49	.	0			c.1971_1972insATGGCTGAGCTGCAGGTGCGGGACCTGAG						PASS	.																																			SO:0001589	frameshift_variant	128272	exon13			.	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.1942_1970dupATGGCTGAGCTGCAGGTGCGGGACCTGAG	chr1.hg19:g.16529006_16529007insCTCAGGTCCCGCACCTGCAGCTCAGCCAT	ENSP00000270747:p.Ser657fs	256.0	0.0	.		163.0	21.0	0.129	NM_153213	A6NJ04|Q5TEV2|Q6PJQ4|Q8N244	Frame_Shift_Ins	INS	ENST00000270747.3	hg19	CCDS170.1																																																																																			.	.	.	none		0.663	ARHGEF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006289.1	NM_153213		CTCAGGTCCCGCACCTGCAGCTCAGCCAT	16529007	-	CTCAGGTCCCGCACCTGCAGCTCAGCCAT	16529006	7	5	3	1	0	1	1	0	0	0	0	0	902	1194	42	0	453	0	ARHGEF19	1	16529006	Frame_Shift_Ins	INS	-	TCGA-2Z-A9J2-01A-11D-A382-10	5932735	16529006	232721615	4	170											
GJA4	2701	hgsc.bcm.edu	37	chr1	35260710	35260710	+	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	caacctgaccacagaggagaGgctggcgtcttccaggcccc	9	5	12	15	1	1	3	0	1	1	2	2	4	2	3	5	4	1	1	5	4	1	1			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr1:35260710G>C	ENST00000342280.4	+	2	984	c.896G>C	c.(895-897)aGg>aCg	p.R299T		NM_002060.2	NP_002051.2	P35212	CXA4_HUMAN	gap junction protein, alpha 4, 37kDa	299					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)				ACAGAGGAGAGGCTGGCGTCT	0.612																																					p.R299T		Atlas-SNP	.											.	GJA4	25	.	0			c.G896C						PASS	.						50	46	48					1																	35260710		2203	4300	6503	SO:0001583	missense	2701	exon2			AGGAGAGGCTGGC	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.896G>C	chr1.hg19:g.35260710G>C	ENSP00000343676:p.Arg299Thr	47.0	0.0	.		40.0	15.0	.	NM_002060	A8K698|D3DPR4|Q9P106|Q9UBL1|Q9UNA9|Q9UNB0|Q9UNB1|Q9Y5N7	Missense_Mutation	SNP	ENST00000342280.4	hg19	CCDS30669.1	.	.	.	.	.	.	.	.	.	.	G	6.072	0.381657	0.11524	.	.	ENSG00000187513	ENST00000342280	T	0.81247	-1.47	5.25	5.25	0.73442	.	0.525534	0.20845	N	0.084627	T	0.67961	0.2949	L	0.36672	1.1	0.28591	N	0.90966	B	0.02656	0.0	B	0.01281	0.0	T	0.53961	-0.8364	10	0.17832	T	0.49	.	7.1313	0.25502	0.1489:0.1466:0.7045:0.0	.	299	P35212	CXA4_HUMAN	T	299	ENSP00000343676:R299T	ENSP00000343676:R299T	R	+	2	0	GJA4	35033297	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	2.161000	0.42358	2.438000	0.82558	0.561000	0.74099	AGG	.	.	.	none		0.612	GJA4-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011556.1	NM_002060		C	35260710	G	C	35260710	3	2	3	1	0	0	0	0	1	0	0	0	6410	1000	35	4	898	4	GJA4	1	35260710	Missense_Mutation	SNP	G	TCGA-2Z-A9J2-01A-11D-A382-10	18731704	35260710	213989911	5	171											
SLFNL1	200172	hgsc.bcm.edu	37	chr1	41486067	41486067	+	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	ccagtgcataggccttccgcGgccgcctcaccacttcaatg	7	8	9	17	3	2	0	2	0	0	0	3	0	3	0	6	2	1	1	6	2	2	3	rs189387361		TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr1:41486067G>T	ENST00000359345.1	-	1	2842	c.266C>A	c.(265-267)cCg>cAg	p.P89Q	SLFNL1_ENST00000439569.2_Missense_Mutation_p.P89Q|SLFNL1_ENST00000372611.1_Missense_Mutation_p.P89Q|SLFNL1_ENST00000302946.8_Missense_Mutation_p.P89Q|SLFNL1_ENST00000397197.2_Missense_Mutation_p.P89Q|SLFNL1_ENST00000372613.2_Missense_Mutation_p.P89Q	NM_144990.3	NP_659427.3	Q499Z3	SLNL1_HUMAN	schlafen-like 1	89							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)				GGCCTTCCGCGGCCGCCTCAC	0.677																																					p.P89Q		Atlas-SNP	.											.	SLFNL1	37	.	0			c.C266A						PASS	.						50	55	53					1																	41486067		2203	4299	6502	SO:0001583	missense	200172	exon3			TTCCGCGGCCGCC	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.266C>A	chr1.hg19:g.41486067G>T	ENSP00000352299:p.Pro89Gln	50.0	0.0	.		33.0	9.0	.	NM_001168247	A8K8D1|Q49AG8|Q5VW72|Q5VW74|Q8N7V7|Q8TCH6|Q8WVZ8	Missense_Mutation	SNP	ENST00000359345.1	hg19	CCDS460.1	.	.	.	.	.	.	.	.	.	.	G	18.11	3.551154	0.65311	.	.	ENSG00000171790	ENST00000302946;ENST00000372613;ENST00000372611;ENST00000359345;ENST00000439569;ENST00000397197	T;T;T;T;T;T	0.59772	0.24;0.24;0.24;0.24;0.24;0.24	5.8	4.81	0.61882	.	0.328529	0.26390	N	0.024655	T	0.69070	0.3070	L	0.55481	1.735	0.24286	N	0.995182	D;D;D	0.76494	0.998;0.997;0.999	D;D;D	0.70487	0.969;0.923;0.953	T	0.60480	-0.7255	10	0.49607	T	0.09	-30.5925	12.8379	0.57784	0.0:0.0:0.8264:0.1736	.	89;89;89	Q499Z3-3;Q499Z3-2;Q499Z3	.;.;SLNL1_HUMAN	Q	89	ENSP00000304401:P89Q;ENSP00000361696:P89Q;ENSP00000361694:P89Q;ENSP00000352299:P89Q;ENSP00000398938:P89Q;ENSP00000380381:P89Q	ENSP00000304401:P89Q	P	-	2	0	SLFNL1	41258654	0.916000	0.31088	0.960000	0.40013	0.865000	0.49528	2.555000	0.45854	2.739000	0.93911	0.561000	0.74099	CCG	.	G|0.999;A|0.001	.	alt		0.677	SLFNL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015650.1	NM_144990		T	41486067	G	T	41486067	3	4	3	1	0	0	0	0	1	0	0	0	14751	1116	39	4	973	4	SLFNL1	1	41486067	Missense_Mutation	SNP	G	TCGA-2Z-A9J2-01A-11D-A382-10	6225357	41486067	207764554	6	172											
KIAA0467	23334	hgsc.bcm.edu	37	chr1	43896443	43896443	+	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	cagctcagtacctgtgtgcaGcctgcctacctgcctgggtg	5	10	12	14	0	1	0	1	0	0	0	1	0	1	0	5	1	7	3	5	1	2	2			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr1:43896443G>C	ENST00000562955.1	+	31	4586	c.4586G>C	c.(4585-4587)aGc>aCc	p.S1529T	SZT2_ENST00000372442.1_Missense_Mutation_p.S687T	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	1586					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						CCTGTGTGCAGCCTGCCTACC	0.617																																					p.S1529T		Atlas-SNP	.											.	SZT2	383	.	0			c.G4586C						PASS	.						80	84	83					1																	43896443		2203	4299	6502	SO:0001583	missense	23334	exon31			TGTGCAGCCTGCC	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.4586G>C	chr1.hg19:g.43896443G>C	ENSP00000457168:p.Ser1529Thr	29.0	0.0	.		39.0	14.0	.	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Missense_Mutation	SNP	ENST00000562955.1	hg19	CCDS30694.2	.	.	.	.	.	.	.	.	.	.	G	8.339	0.828333	0.16749	.	.	ENSG00000198198	ENST00000372442	.	.	.	5.79	4.86	0.63082	.	0.161368	0.56097	D	0.000037	T	0.19765	0.0475	N	0.04880	-0.145	0.25888	N	0.983513	B	0.15473	0.013	B	0.14023	0.01	T	0.08576	-1.0715	9	0.06365	T	0.9	.	13.1417	0.59438	0.0:0.3852:0.6148:0.0	.	1529	Q5T011-5	.	T	687	.	ENSP00000361519:S687T	S	+	2	0	SZT2	43669030	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.200000	0.65158	2.733000	0.93635	0.655000	0.94253	AGC	.	.	.	none		0.617	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		C	43896443	G	C	43896443	3	2	3	1	0	0	0	0	1	0	0	0	8185	971	34	4	2118	4	KIAA0467	1	43896443	Missense_Mutation	SNP	G	TCGA-2Z-A9J2-01A-11D-A382-10	2410376	43896443	205354178	7	173											
ZCCHC11	23318	hgsc.bcm.edu	37	chr1	52941009	52941009	+	Missense_Mutation	SNP	A	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	gaatacaaccattggttgccAtattgttcgacttgactggt	10	14	9	8	1	0	1	0	1	0	0	1	3	0	1	2	2	3	2	2	2	4	7			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr1:52941009A>C	ENST00000371544.3	-	13	2484	c.2222T>G	c.(2221-2223)aTg>aGg	p.M741R	ZCCHC11_ENST00000371541.1_5'UTR|ZCCHC11_ENST00000257177.4_Missense_Mutation_p.M741R	NM_001009881.2|NM_015269.2	NP_001009881.1|NP_056084.1	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11	741					cytokine production (GO:0001816)|miRNA catabolic process (GO:0010587)|miRNA metabolic process (GO:0010586)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|pre-miRNA processing (GO:0031054)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|RNA 3'-end processing (GO:0031123)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(17)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	58						ATTGGTTGCCATATTGTTCGA	0.408																																					p.M741R		Atlas-SNP	.											.	ZCCHC11	151	.	0			c.T2222G						PASS	.						171	170	170					1																	52941009		2203	4300	6503	SO:0001583	missense	23318	exon13			GTTGCCATATTGT	D83776	CCDS30715.1, CCDS30716.1	1p32.3	2014-03-05			ENSG00000134744	ENSG00000134744		"Zinc fingers, CCHC domain containing"	28981	protein-coding gene	gene with protein product	"TUTase4"	613692				8724849, 12239557	Standard	NM_015269		Approved	KIAA0191, PAPD3, TUT4	uc001cty.2	Q5TAX3	OTTHUMG00000008200	ENST00000371544.3:c.2222T>G	chr1.hg19:g.52941009A>C	ENSP00000360599:p.Met741Arg	90.0	0.0	.		63.0	10.0	.	NM_001009881	A2RRP0|B7Z8J5|D3DQ35|Q12764|Q5TAX2|Q5TAX4|Q86XZ3	Missense_Mutation	SNP	ENST00000371544.3	hg19	CCDS30716.1	.	.	.	.	.	.	.	.	.	.	A	0.008	-1.888457	0.00527	.	.	ENSG00000134744	ENST00000257177;ENST00000371544;ENST00000528642;ENST00000484723	T;T;T;T	0.39997	1.05;1.05;1.06;1.06	5.49	0.239	0.15484	.	1.086240	0.06799	N	0.788393	T	0.20414	0.0491	N	0.14661	0.345	0.09310	N	1	B;B	0.13145	0.007;0.007	B;B	0.12837	0.005;0.008	T	0.22034	-1.0228	10	0.15066	T	0.55	.	1.1744	0.01832	0.2833:0.2912:0.2819:0.1435	.	500;741	E9PKX1;Q5TAX3	.;TUT4_HUMAN	R	741;741;670;500	ENSP00000257177:M741R;ENSP00000360599:M741R;ENSP00000433486:M670R;ENSP00000435256:M500R	ENSP00000257177:M741R	M	-	2	0	ZCCHC11	52713597	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.599000	0.24089	0.061000	0.16311	0.455000	0.32223	ATG	.	.	.	none		0.408	ZCCHC11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022462.1	XM_038288		C	52941009	A	C	52941009	3	2	3	1	0	0	0	0	1	0	0	0	17592	217	8	5	2787	5	ZCCHC11	1	52941009	Missense_Mutation	SNP	A	TCGA-2Z-A9J2-01A-11D-A382-10	9044566	52941009	196309612	8	174											
ARHGAP29	9411	hgsc.bcm.edu	37	chr1	94650461	94650461	+	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	gctctattttcaatctctgaGgcacatattttgagtataaa	12	16	6	7	0	3	2	1	2	2	0	4	2	3	2	0	1	0	3	0	1	6	8			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr1:94650461G>T	ENST00000260526.6	-	18	2258	c.2076C>A	c.(2074-2076)gcC>gcA	p.A692A	ARHGAP29_ENST00000482481.1_5'UTR	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	692	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				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)		CAATCTCTGAGGCACATATTT	0.328																																					p.A692A		Atlas-SNP	.											.	ARHGAP29	132	.	0			c.C2076A						PASS	.						74	76	75					1																	94650461		2201	4299	6500	SO:0001819	synonymous_variant	9411	exon18			CTCTGAGGCACAT		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.2076C>A	chr1.hg19:g.94650461G>T		69.0	0.0	.		90.0	11.0	.	NM_004815	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Silent	SNP	ENST00000260526.6	hg19	CCDS748.1																																																																																			.	.	.	none		0.328	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815		T	94650461	G	T	94650461	2	4	3	1	0	0	0	0	0	0	0	1	878	987	35	4		4	ARHGAP29	1	94650461	Silent	SNP	G	TCGA-2Z-A9J2-01A-11D-A382-10	41709452	94650461	154600160	9	175											
SASS6	163786	hgsc.bcm.edu	37	chr1	100573433	100573433	+	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	gctggtccttatccttgattTcctgttctaaaactgccact	7	16	6	12	0	1	1	0	1	1	0	4	1	4	1	4	1	2	2	4	1	3	5			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr1:100573433T>A	ENST00000287482.5	-	9	1129	c.989A>T	c.(988-990)gAa>gTa	p.E330V	SASS6_ENST00000535161.1_Missense_Mutation_p.E163V|SASS6_ENST00000462159.1_5'UTR	NM_194292.1	NP_919268.1	Q6UVJ0	SAS6_HUMAN	spindle assembly 6 homolog (C. elegans)	330					centriole replication (GO:0007099)|centrosome duplication (GO:0051298)	centriole (GO:0005814)|centrosome (GO:0005813)|deuterosome (GO:0098536)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	19		all_epithelial(167;4.58e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.085)|all cancers(265;0.139)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.197)		ATCCTTGATTTCCTGTTCTAA	0.353																																					p.E330V		Atlas-SNP	.											.	SASS6	61	.	0			c.A989T						PASS	.						109	108	108					1																	100573433		2203	4300	6503	SO:0001583	missense	163786	exon9			TTGATTTCCTGTT	AL834265	CCDS764.1	1p21.3	2008-02-05			ENSG00000156876	ENSG00000156876			25403	protein-coding gene	gene with protein product		609321				15665853, 14654843	Standard	NM_194292		Approved	DKFZp761A078, SAS-6, FLJ22097, SAS6	uc001dsu.3	Q6UVJ0	OTTHUMG00000010754	ENST00000287482.5:c.989A>T	chr1.hg19:g.100573433T>A	ENSP00000287482:p.Glu330Val	84.0	0.0	.		64.0	23.0	.	NM_194292	D3DT55|Q8N3K0	Missense_Mutation	SNP	ENST00000287482.5	hg19	CCDS764.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.649344	0.87958	.	.	ENSG00000156876	ENST00000287482;ENST00000539329;ENST00000535161	T;T	0.81163	-1.46;-1.46	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	D	0.88085	0.6342	M	0.77820	2.39	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.89635	0.3858	10	0.72032	D	0.01	-25.3753	16.2466	0.82448	0.0:0.0:0.0:1.0	.	330	Q6UVJ0	SAS6_HUMAN	V	330;303;163	ENSP00000287482:E330V;ENSP00000440169:E163V	ENSP00000287482:E330V	E	-	2	0	SASS6	100346021	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.495000	0.81514	2.229000	0.72834	0.477000	0.44152	GAA	.	.	.	none		0.353	SASS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029656.2	NM_194292		A	100573433	T	A	100573433	3	1	3	1	0	0	0	0	1	0	0	0	13863	1783	62	5	1020	5	SASS6	1	100573433	Missense_Mutation	SNP	T	TCGA-2Z-A9J2-01A-11D-A382-10	5922972	100573433	148677188	10	176											
IGSF9	57549	hgsc.bcm.edu	37	chr1	159912854	159912854	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgatgacatgcagggggggcCggccggccgggggcagcagg	6	2	22	11	4	0	1	0	1	0	0	0	2	0	1	3	8	2	3	3	8	0	0			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr1:159912854C>T	ENST00000368094.1	-	3	343	c.146G>A	c.(145-147)cGg>cAg	p.R49Q	IGSF9_ENST00000361509.3_Missense_Mutation_p.R49Q	NM_001135050.1	NP_001128522.1	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9	49	Ig-like 1.				dendrite development (GO:0016358)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				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)			CAgggggggccggccggccgg	0.637																																					p.R49Q		Atlas-SNP	.											.	IGSF9	123	.	0			c.G146A						PASS	.						23	29	27					1																	159912854		2203	4300	6503	SO:0001583	missense	57549	exon3			GGGGGCCGGCCGG	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.146G>A	chr1.hg19:g.159912854C>T	ENSP00000357073:p.Arg49Gln	200.0	0.0	.		188.0	12.0	.	NM_001135050		Missense_Mutation	SNP	ENST00000368094.1	hg19	CCDS44254.1	.	.	.	.	.	.	.	.	.	.	C	11.24	1.579962	0.28180	.	.	ENSG00000085552	ENST00000361509;ENST00000368094;ENST00000198587	T;T	0.27557	1.66;1.66	4.84	1.88	0.25563	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.204861	0.23402	N	0.048567	T	0.03608	0.0103	N	0.04508	-0.205	0.24333	N	0.994993	B;B	0.27853	0.007;0.191	B;B	0.20955	0.001;0.032	T	0.44360	-0.9333	9	.	.	.	-6.5247	8.9188	0.35599	0.0:0.7473:0.0:0.2527	.	49;49	Q9P2J2;C9JI81	TUTLA_HUMAN;.	Q	49	ENSP00000355049:R49Q;ENSP00000357073:R49Q	.	R	-	2	0	IGSF9	158179478	0.003000	0.15002	0.965000	0.40720	0.867000	0.49689	0.098000	0.15189	0.179000	0.19938	0.557000	0.71058	CGG	.	.	.	none		0.637	IGSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059115.1	NM_020789		T	159912854	C	T	159912854	3	4	3	1	0	0	0	0	1	0	0	0	7612	652	23	1	3469	1	IGSF9	1	159912854	Missense_Mutation	SNP	C	TCGA-2Z-A9J2-01A-11D-A382-10	59339421	159912854	89337767	11	177											
SLC9A11	284525	hgsc.bcm.edu	37	chr1	173503688	173503688	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tattgatatcagtgctgataCatttaaacctcttgccattg	11	16	6	8	0	2	2	1	2	1	0	2	2	2	2	2	0	4	1	2	0	5	8			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr1:173503688C>T	ENST00000367714.3	-	16	2331	c.1909G>A	c.(1909-1911)Gta>Ata	p.V637I	SLC9C2_ENST00000466087.1_5'UTR|SLC9C2_ENST00000536496.1_Intron	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	637					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										AGTGCTGATACATTTAAACCT	0.249																																					p.V637I		Atlas-SNP	.											.	.	.	.	0			c.G1909A						PASS	.						37	44	42					1																	173503688		2162	4205	6367	SO:0001583	missense	284525	exon16			CTGATACATTTAA	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.1909G>A	chr1.hg19:g.173503688C>T	ENSP00000356687:p.Val637Ile	320.0	1.0	.		457.0	218.0	.	NM_178527	Q86UF3	Missense_Mutation	SNP	ENST00000367714.3	hg19	CCDS1308.1	.	.	.	.	.	.	.	.	.	.	C	5.777	0.327746	0.10956	.	.	ENSG00000162753	ENST00000367714	D	0.97328	-4.34	5.76	5.76	0.90799	.	0.407412	0.20491	N	0.091286	D	0.95341	0.8488	L	0.57536	1.79	0.80722	D	1	D	0.56968	0.978	P	0.48738	0.588	D	0.93530	0.6869	10	0.22706	T	0.39	-2.8591	15.4679	0.75416	0.0:1.0:0.0:0.0	.	637	Q5TAH2	S9A11_HUMAN	I	637	ENSP00000356687:V637I	ENSP00000356687:V637I	V	-	1	0	SLC9A11	171770311	0.824000	0.29247	0.416000	0.26546	0.130000	0.20726	1.138000	0.31491	2.721000	0.93114	0.609000	0.83330	GTA	.	.	.	none		0.249	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527		T	173503688	C	T	173503688	3	4	3	1	0	0	0	0	1	0	0	0	14724	478	17	2	1517	2	SLC9A11	1	173503688	Missense_Mutation	SNP	C	TCGA-2Z-A9J2-01A-11D-A382-10	13590834	173503688	75746933	12	178											
KIAA1614	57710	hgsc.bcm.edu	37	chr1	180882414	180882414	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcggcggcggccaaacccgCgggcggcagcccccagtgag	6	1	18	16	6	0	1	0	1	0	0	0	1	0	1	4	6	2	1	4	6	1	0			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr1:180882414C>T	ENST00000367588.4	+	1	90	c.35C>T	c.(34-36)gCg>gTg	p.A12V		NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	12										NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						GCCAAACCCGCGGGCGGCAGC	0.776																																					p.A12V		Atlas-SNP	.											.	KIAA1614	75	.	0			c.C35T						PASS	.						2	2	2					1																	180882414		932	2251	3183	SO:0001583	missense	57710	exon1			AACCCGCGGGCGG	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.35C>T	chr1.hg19:g.180882414C>T	ENSP00000356560:p.Ala12Val	236.0	0.0	.		181.0	50.0	.	NM_020950	Q5VZ45|Q9HCF8	Missense_Mutation	SNP	ENST00000367588.4	hg19	CCDS41442.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.440830	0.83993	.	.	ENSG00000135835	ENST00000367588	T	0.18174	2.23	3.93	2.91	0.33838	.	.	.	.	.	T	0.23688	0.0573	L	0.27053	0.805	0.20638	N	0.999872	D	0.89917	1.0	D	0.71870	0.975	T	0.08953	-1.0697	9	0.30078	T	0.28	-12.4368	8.5894	0.33677	0.0:0.6809:0.3191:0.0	.	12	Q5VZ46	K1614_HUMAN	V	12	ENSP00000356560:A12V	ENSP00000356560:A12V	A	+	2	0	KIAA1614	179149037	0.003000	0.15002	0.646000	0.29493	0.784000	0.44337	0.640000	0.24705	1.924000	0.55735	0.555000	0.69702	GCG	.	.	.	none		0.776	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531		T	180882414	C	T	180882414	3	4	3	1	0	0	0	0	1	0	0	0	8255	768	27	1	37	1	KIAA1614	1	180882414	Missense_Mutation	SNP	C	TCGA-2Z-A9J2-01A-11D-A382-10	7378726	180882414	68368207	13	179											
NFASC	23114	hgsc.bcm.edu	37	chr1	204955212	204955212	+	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	gaggtgatgggcctcgcagtGagaccaaggagttcaccacc	10	6	14	11	1	1	2	1	2	0	1	2	5	1	3	4	3	0	2	4	3	1	1			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr1:204955212G>A	ENST00000404076.1	+	21	3120	c.2698G>A	c.(2698-2700)Gag>Aag	p.E900K	NFASC_ENST00000367171.4_Missense_Mutation_p.E906K|NFASC_ENST00000367169.4_Intron|NFASC_ENST00000338586.6_Missense_Mutation_p.E921K|NFASC_ENST00000539706.1_Missense_Mutation_p.E917K|NFASC_ENST00000404907.1_Missense_Mutation_p.E917K|NFASC_ENST00000339876.6_Intron|NFASC_ENST00000338515.6_Missense_Mutation_p.E921K|NFASC_ENST00000360049.4_Missense_Mutation_p.E917K|NFASC_ENST00000367172.4_Missense_Mutation_p.E921K|NFASC_ENST00000513543.1_Missense_Mutation_p.E917K|NFASC_ENST00000401399.1_Intron|NFASC_ENST00000367170.4_Missense_Mutation_p.E921K			O94856	NFASC_HUMAN	neurofascin	921	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			GCCTCGCAGTGAGACCAAGGA	0.612																																					p.E932K		Atlas-SNP	.											.	NFASC	396	.	0			c.G2794A						PASS	.						75	65	68					1																	204955212		2203	4300	6503	SO:0001583	missense	23114	exon21			CGCAGTGAGACCA	AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	29866	protein-coding gene	gene with protein product		609145	"neurofascin homolog (chicken)"			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000404076.1:c.2698G>A	chr1.hg19:g.204955212G>A	ENSP00000385676:p.Glu900Lys	136.0	0.0	.		108.0	15.0	.	NM_001160331	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Missense_Mutation	SNP	ENST00000404076.1	hg19		.	.	.	.	.	.	.	.	.	.	G	13.96	2.393311	0.42410	.	.	ENSG00000163531	ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000404076;ENST00000404907;ENST00000513543;ENST00000430393	T;T;T;T;T;T;T;T;T;T;T	0.55760	0.5;0.5;0.5;0.5;0.5;0.5;0.5;0.5;0.5;0.5;0.5	5.66	5.66	0.87406	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.52532	D	0.000079	T	0.54175	0.1842	L	0.54965	1.715	0.80722	D	1	B;B;B;P;B	0.38078	0.146;0.106;0.248;0.617;0.125	B;B;B;B;B	0.41412	0.053;0.089;0.115;0.356;0.115	T	0.46317	-0.9200	10	0.19590	T	0.45	.	19.3505	0.94381	0.0:0.0:1.0:0.0	.	921;932;917;906;917	O94856;O94856-11;O94856-8;F8W791;O94856-3	NFASC_HUMAN;.;.;.;.	K	921;906;921;921;921;932;917;917;900;917;917;908	ENSP00000356140:E921K;ENSP00000356139:E906K;ENSP00000356138:E921K;ENSP00000342128:E921K;ENSP00000343509:E921K;ENSP00000438614:E917K;ENSP00000353154:E917K;ENSP00000385676:E900K;ENSP00000384061:E917K;ENSP00000425908:E917K;ENSP00000415031:E908K	ENSP00000295776:E932K	E	+	1	0	NFASC	203221835	1.000000	0.71417	0.993000	0.49108	0.993000	0.82548	7.613000	0.82986	2.665000	0.90641	0.563000	0.77884	GAG	.	.	.	none		0.612	NFASC-012	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000131243.1	NM_001005388		A	204955212	G	A	204955212	3	1	3	1	0	0	0	0	1	0	0	0	10366	1291	45	2	2927	2	NFASC	1	204955212	Missense_Mutation	SNP	G	TCGA-2Z-A9J2-01A-11D-A382-10	24072798	204955212	44295409	14	180											
ARID4B	51742	hgsc.bcm.edu	37	chr1	235416071	235416072	+	Frame_Shift_Ins	INS	-	-	T																															tcagcaaaatgcctctctccINStttcaggcacagtgaagatc																										TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr1:235416071_235416072insT	ENST00000264183.3	-	6	824_825	c.327_328insA	c.(325-330)aaaggafs	p.G110fs	ARID4B_ENST00000349213.3_Frame_Shift_Ins_p.G110fs|ARID4B_ENST00000366603.2_Frame_Shift_Ins_p.G110fs	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	110					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)			TGCCTCTCTCCTTTCAGGCACA	0.356																																					p.G110fs		Atlas-Indel,Pindel	.											.	ARID4B	142	.	0			c.328_329insA						PASS	.																																			SO:0001589	frameshift_variant	51742	exon6			.	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.328dupA	chr1.hg19:g.235416074_235416074dupT	ENSP00000264183:p.Gly110fs	210.0	0.0	0		177.0	51.0	0.288136	NM_016374	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	Frame_Shift_Ins	INS	ENST00000264183.3	hg19	CCDS31061.1																																																																																			.	.	.	none		0.356	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374		T	235416072	-	T	235416071	7	5	3	1	0	1	1	0	0	0	0	0	920	690	24	0	3686	0	ARID4B	1	235416071	Frame_Shift_Ins	INS	-	TCGA-2Z-A9J2-01A-11D-A382-10	30460859	235416071	13834550	15	181											
LCLAT1	253558	hgsc.bcm.edu	37	chr2	30863435	30863435	+	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	agatcatagaacttgcatgtTaccgacttttacacaaacag	15	11	6	9	1	1	2	1	0	0	2	1	3	1	2	1	0	5	2	1	0	5	5			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr2:30863435T>A	ENST00000309052.4	+	7	1404	c.1195T>A	c.(1195-1197)Tac>Aac	p.Y399N	LCLAT1_ENST00000379509.3_Missense_Mutation_p.Y361N|LCLAT1_ENST00000540623.1_Missense_Mutation_p.Y361N|LCLAT1_ENST00000491680.2_3'UTR	NM_182551.3	NP_872357.2	Q6UWP7	LCLT1_HUMAN	lysocardiolipin acyltransferase 1	399					cardiolipin acyl-chain remodeling (GO:0035965)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|multicellular organismal development (GO:0007275)|phosphatidic acid biosynthetic process (GO:0006654)|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)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)	19						ACTTGCATGTTACCGACTTTT	0.333																																					p.Y399N		Atlas-SNP	.											.	LCLAT1	51	.	0			c.T1195A						PASS	.						94	94	94					2																	30863435		2203	4300	6503	SO:0001583	missense	253558	exon7			GCATGTTACCGAC	AK095284	CCDS1772.1, CCDS42670.1	2p23.1	2008-12-15	2008-12-15	2008-12-15	ENSG00000172954	ENSG00000172954			26756	protein-coding gene	gene with protein product		614241	"lysocardiolipin acyltransferase"	LYCAT		18931347, 15152008, 16620771, 17675553	Standard	NM_001002257		Approved	FLJ37965, ALCAT1, AGPAT8	uc002rnl.3	Q6UWP7	OTTHUMG00000099349	ENST00000309052.4:c.1195T>A	chr2.hg19:g.30863435T>A	ENSP00000310551:p.Tyr399Asn	92.0	0.0	.		97.0	10.0	.	NM_182551	A6H8Z7|Q8N1Q7	Missense_Mutation	SNP	ENST00000309052.4	hg19	CCDS1772.1	.	.	.	.	.	.	.	.	.	.	T	12.53	1.965768	0.34659	.	.	ENSG00000172954	ENST00000379509;ENST00000309052;ENST00000540623	T;T;T	0.34275	1.46;1.37;1.46	6.03	4.89	0.63831	.	0.047907	0.85682	D	0.000000	T	0.26666	0.0652	L	0.27053	0.805	0.44221	D	0.997051	P	0.50272	0.933	B	0.44108	0.441	T	0.06075	-1.0847	10	0.72032	D	0.01	-20.2528	6.5263	0.22303	0.0:0.2756:0.0:0.7244	.	399	Q6UWP7	LCLT1_HUMAN	N	361;399;361	ENSP00000368823:Y361N;ENSP00000310551:Y399N;ENSP00000442857:Y361N	ENSP00000310551:Y399N	Y	+	1	0	LCLAT1	30716939	1.000000	0.71417	1.000000	0.80357	0.012000	0.07955	4.148000	0.58085	1.114000	0.41781	-0.379000	0.06801	TAC	.	.	.	none		0.333	LCLAT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000216780.1	NM_182551		A	30863435	T	A	30863435	3	1	3	1	0	0	0	0	1	0	0	0	8684	1754	61	5	1217	5	LCLAT1	2	30863435	Missense_Mutation	SNP	T	TCGA-2Z-A9J2-01A-11D-A382-10		30863435	212335938	16	182											
TMEM17	200728	hgsc.bcm.edu	37	chr2	62729639	62729639	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caattaaggttattaggatgAtaacagtgatcacaatgaat	17	12	8	4	0	1	3	1	3	0	0	1	4	1	4	0	2	1	1	0	2	7	4			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr2:62729639A>G	ENST00000335390.5	-	3	462	c.251T>C	c.(250-252)aTc>aCc	p.I84T		NM_198276.2	NP_938017.2	Q86X19	TMM17_HUMAN	transmembrane protein 17	84					cilium assembly (GO:0042384)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	Lung NSC(7;0.0274)|all_lung(7;0.0568)		LUSC - Lung squamous cell carcinoma(7;1.31e-05)|Epithelial(17;0.169)			TATTAGGATGATAACAGTGAT	0.353																																					p.I84T		Atlas-SNP	.											.	TMEM17	19	.	0			c.T251C						PASS	.						102	100	100					2																	62729639		2203	4300	6503	SO:0001583	missense	200728	exon3			AGGATGATAACAG		CCDS1871.1	2p15	2008-02-05			ENSG00000186889	ENSG00000186889			26623	protein-coding gene	gene with protein product		614950				12477932	Standard	NM_198276		Approved	FLJ34583	uc002sbt.2	Q86X19	OTTHUMG00000129455	ENST00000335390.5:c.251T>C	chr2.hg19:g.62729639A>G	ENSP00000335094:p.Ile84Thr	162.0	0.0	.		137.0	9.0	.	NM_198276	Q53QP7|Q53R98	Missense_Mutation	SNP	ENST00000335390.5	hg19	CCDS1871.1	.	.	.	.	.	.	.	.	.	.	A	15.40	2.822568	0.50739	.	.	ENSG00000186889	ENST00000335390	D	0.88431	-2.38	5.96	5.96	0.96718	.	0.341351	0.33631	N	0.004712	T	0.80358	0.4608	N	0.19112	0.55	0.31954	N	0.609326	P	0.35226	0.491	B	0.31946	0.138	D	0.83619	0.0138	10	0.51188	T	0.08	-14.8168	11.4636	0.50225	0.9304:0.0:0.0696:0.0	.	84	Q86X19	TMM17_HUMAN	T	84	ENSP00000335094:I84T	ENSP00000335094:I84T	I	-	2	0	TMEM17	62583143	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	5.869000	0.69613	2.279000	0.76181	0.533000	0.62120	ATC	.	.	.	none		0.353	TMEM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251618.3	NM_198276		G	62729639	A	G	62729639	3	3	3	1	0	0	0	0	1	0	0	0	16097	333	12	3	353	3	TMEM17	2	62729639	Missense_Mutation	SNP	A	TCGA-2Z-A9J2-01A-11D-A382-10	31866204	62729639	180469734	17	183											
KDM3A	55818	hgsc.bcm.edu	37	chr2	86669203	86669203	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcggagaaagttggccggtAttggtggggaggaggtttct	7	11	18	5	2	1	1	0	0	1	1	2	4	1	3	1	8	0	3	1	8	2	4			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr2:86669203A>G	ENST00000409556.1	+	3	398	c.33A>G	c.(31-33)gtA>gtG	p.V11V	KDM3A_ENST00000542128.1_Silent_p.V11V|KDM3A_ENST00000409064.1_Silent_p.V11V|KDM3A_ENST00000312912.5_Silent_p.V11V			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	11					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						GTTGGCCGGTATTGGTGGGGA	0.627																																					p.V11V	NSCLC(96;1150 1523 6936 46253 49736)	Atlas-SNP	.											.	KDM3A	179	.	0			c.A33G						PASS	.						96	97	97					2																	86669203		2203	4300	6503	SO:0001819	synonymous_variant	55818	exon2			GCCGGTATTGGTG	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.33A>G	chr2.hg19:g.86669203A>G		71.0	0.0	.		51.0	10.0	.	NM_001146688	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Silent	SNP	ENST00000409556.1	hg19	CCDS1990.1																																																																																			.	.	.	none		0.627	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433		G	86669203	A	G	86669203	2	3	3	1	0	0	0	0	0	0	0	1	8133	436	16	3		3	KDM3A	2	86669203	Silent	SNP	A	TCGA-2Z-A9J2-01A-11D-A382-10	23939564	86669203	156530170	18	184											
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125405359	125405359	+	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	caagatctggacatcagtgcAgcacaacaatacagagctga	16	6	9	10	0	2	3	1	1	1	2	2	4	2	4	0	1	5	3	0	1	4	1			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr2:125405359A>T	ENST00000431078.1	+	13	2262	c.1898A>T	c.(1897-1899)cAg>cTg	p.Q633L		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	633	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		ACATCAGTGCAGCACAACAAT	0.542																																					p.Q633L		Atlas-SNP	.											.	CNTNAP5	405	.	0			c.A1898T						PASS	.						41	42	42					2																	125405359		2106	4236	6342	SO:0001583	missense	129684	exon13			CAGTGCAGCACAA	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.1898A>T	chr2.hg19:g.125405359A>T	ENSP00000399013:p.Gln633Leu	196.0	0.0	.		187.0	14.0	.	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	hg19	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	A	13.11	2.138971	0.37728	.	.	ENSG00000155052	ENST00000431078	T	0.28895	1.59	5.5	5.5	0.81552	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (2);	0.000000	0.48286	D	0.000181	T	0.28995	0.0720	L	0.56124	1.755	0.43183	D	0.995009	B	0.28713	0.22	B	0.26416	0.069	T	0.07139	-1.0788	10	0.42905	T	0.14	.	10.8862	0.46968	0.8426:0.1573:0.0:0.0	.	633	Q8WYK1	CNTP5_HUMAN	L	633	ENSP00000399013:Q633L	ENSP00000399013:Q633L	Q	+	2	0	CNTNAP5	125121829	1.000000	0.71417	1.000000	0.80357	0.466000	0.32739	2.831000	0.48144	2.093000	0.63338	0.459000	0.35465	CAG	.	.	.	none		0.542	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			T	125405359	A	T	125405359	3	4	3	1	0	0	0	0	1	0	0	0	3652	188	7	5	1948	5	CNTNAP5	2	125405359	Missense_Mutation	SNP	A	TCGA-2Z-A9J2-01A-11D-A382-10	38736156	125405359	117794014	19	185											
YSK4	80122	hgsc.bcm.edu	37	chr2	135738784	135738784	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccacacagttctcatggagaTaagcaacaccttgaagtatt	14	10	7	10	0	1	2	1	1	1	1	2	3	1	2	2	1	2	3	2	1	4	5			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr2:135738784T>C	ENST00000375845.3	-	9	3557	c.3527A>G	c.(3526-3528)tAt>tGt	p.Y1176C	MAP3K19_ENST00000392917.3_Missense_Mutation_p.Y308C|MAP3K19_ENST00000358371.4_Missense_Mutation_p.Y1063C|MAP3K19_ENST00000375844.3_Missense_Mutation_p.Y358C|MAP3K19_ENST00000315513.3_Missense_Mutation_p.Y37C|MAP3K19_ENST00000392918.3_Missense_Mutation_p.Y310C|MAP3K19_ENST00000392915.1_3'UTR	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	1176	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)										CTCATGGAGATAAGCAACACC	0.408																																					p.Y1176C		Atlas-SNP	.											.	.	.	.	0			c.A3527G						PASS	.						146	143	144					2																	135738784		2203	4300	6503	SO:0001583	missense	80122	exon9			TGGAGATAAGCAA	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.3527A>G	chr2.hg19:g.135738784T>C	ENSP00000365005:p.Tyr1176Cys	55.0	0.0	.		70.0	26.0	.	NM_025052	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	hg19	CCDS2176.2	.	.	.	.	.	.	.	.	.	.	T	20.4	3.984760	0.74474	.	.	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000375844;ENST00000392918;ENST00000392917;ENST00000437365;ENST00000315513	T;T;T;T;T;T;T	0.75260	-0.92;-0.92;-0.92;-0.92;-0.92;-0.92;-0.92	5.75	5.75	0.90469	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.42053	D	0.000766	D	0.88592	0.6478	M	0.90595	3.13	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	0.97110	1.0;0.968;1.0;1.0;1.0	D	0.90863	0.4740	10	0.87932	D	0	.	15.2483	0.73523	0.0:0.0:0.0:1.0	.	308;1063;310;358;1176	B7ZMH9;Q56UN5-3;Q56UN5-4;Q56UN5-5;Q56UN5	.;.;.;.;YSK4_HUMAN	C	1176;1063;358;310;308;566;37	ENSP00000365005:Y1176C;ENSP00000351140:Y1063C;ENSP00000365004:Y358C;ENSP00000376650:Y310C;ENSP00000376649:Y308C;ENSP00000392827:Y566C;ENSP00000321160:Y37C	ENSP00000321160:Y37C	Y	-	2	0	YSK4	135455254	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.921000	0.63397	2.192000	0.70111	0.460000	0.39030	TAT	.	.	.	none		0.408	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052		C	135738784	T	C	135738784	3	2	3	1	0	0	0	0	1	0	0	0	17507	1406	49	3	467	3	YSK4	2	135738784	Missense_Mutation	SNP	T	TCGA-2Z-A9J2-01A-11D-A382-10	10333425	135738784	107460589	20	186											
TTN	7273	hgsc.bcm.edu	37	chr2	179396967	179396967	+	Missense_Mutation	SNP	A	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	acttttcctcctttgacatgAagtcaagttcgcttttgtat	8	18	6	9	1	1	2	1	2	0	0	4	2	3	2	2	0	0	3	2	0	3	7			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr2:179396967A>C	ENST00000591111.1	-	308	99676	c.99452T>G	c.(99451-99453)tTc>tGc	p.F33151C	TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.F25919C|TTN_ENST00000342992.6_Missense_Mutation_p.F32224C|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.F25852C|TTN-AS1_ENST00000592182.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.F25727C|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.F34792C			Q8WZ42	TITIN_HUMAN	titin	33151					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)			CTTTGACATGAAGTCAAGTTC	0.423																																					p.F34792C		Atlas-SNP	.											.	TTN	18412	.	0			c.T104375G						PASS	.						151	137	142					2																	179396967		1938	4141	6079	SO:0001583	missense	7273	exon358			GACATGAAGTCAA	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.99452T>G	chr2.hg19:g.179396967A>C	ENSP00000465570:p.Phe33151Cys	31.0	0.0	.		32.0	9.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	9.296	1.051828	0.19827	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.64618	-0.11;0.12;0.1;0.09	5.55	4.39	0.52855	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.42944	0.1225	N	0.08118	0	0.25146	N	0.990465	B;B;B;B	0.20368	0.044;0.044;0.044;0.044	B;B;B;B	0.09377	0.002;0.002;0.004;0.004	T	0.39563	-0.9608	9	0.87932	D	0	.	11.6729	0.51413	0.1339:0.0:0.0:0.8661	.	25727;25852;25919;33151	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	C	32224;25727;25919;25852;25724	ENSP00000343764:F32224C;ENSP00000434586:F25727C;ENSP00000340554:F25919C;ENSP00000352154:F25852C	ENSP00000340554:F25919C	F	-	2	0	TTN	179105213	1.000000	0.71417	1.000000	0.80357	0.817000	0.46193	1.227000	0.32576	0.935000	0.37341	-0.282000	0.10007	TTC	.	.	.	none		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179396967	A	C	179396967	3	2	3	1	0	0	0	0	1	0	0	0	16747	246	9	5	3624	5	TTN	2	179396967	Missense_Mutation	SNP	A	TCGA-2Z-A9J2-01A-11D-A382-10	43658183	179396967	63802406	21	187											
XRCC5	7520	hgsc.bcm.edu	37	chr2	216982471	216982471	+	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	tatccttaactagctgagtcCtggatgcactaatcgtgagc	10	12	9	10	1	0	2	0	2	0	0	3	3	2	3	2	1	4	2	2	1	4	4			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr2:216982471C>A	ENST00000392133.3	+	6	783	c.322C>A	c.(322-324)Ctg>Atg	p.L108M	XRCC5_ENST00000392132.2_Missense_Mutation_p.L108M			P13010	XRCC5_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)	108					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)		TAGCTGAGTCCTGGATGCACT	0.418								Non-homologous end-joining																													p.L108M		Atlas-SNP	.											.	XRCC5	64	.	0			c.C322A						PASS	.						158	133	141					2																	216982471		2203	4300	6503	SO:0001583	missense	7520	exon4			TGAGTCCTGGATG	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.322C>A	chr2.hg19:g.216982471C>A	ENSP00000375978:p.Leu108Met	55.0	0.0	.		71.0	20.0	.	NM_021141	A8K3X5|Q0Z7V0|Q4VBQ5|Q53HH7|Q7M4N0|Q9UCQ0|Q9UCQ1	Missense_Mutation	SNP	ENST00000392133.3	hg19	CCDS2402.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.948208	0.73787	.	.	ENSG00000079246	ENST00000392133;ENST00000392132;ENST00000417391	T;T	0.35789	1.29;1.29	5.74	3.87	0.44632	Ku70/Ku80, N-terminal alpha/beta (1);von Willebrand factor, type A (1);	0.154656	0.44097	D	0.000500	T	0.44244	0.1284	M	0.65975	2.015	0.54753	D	0.999988	P	0.45396	0.857	P	0.50791	0.65	T	0.32428	-0.9907	10	0.38643	T	0.18	.	8.8825	0.35382	0.0:0.7152:0.1506:0.1342	.	108	P13010	XRCC5_HUMAN	M	108;108;95	ENSP00000375978:L108M;ENSP00000375977:L108M	ENSP00000375977:L108M	L	+	1	2	XRCC5	216690716	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.453000	0.44970	1.319000	0.45190	0.650000	0.86243	CTG	.	.	.	none		0.418	XRCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256675.3	NM_021141		A	216982471	C	A	216982471	3	1	3	1	0	0	0	0	1	0	0	0	17468	680	24	4	336	4	XRCC5	2	216982471	Missense_Mutation	SNP	C	TCGA-2Z-A9J2-01A-11D-A382-10	37585504	216982471	26216902	22	188											
SH3BP4	23677	hgsc.bcm.edu	37	chr2	235950616	235950616	+	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	atgaaagtgtcagccgagatAaaaaatgacctttttagcaa	17	10	8	6	1	1	3	1	2	0	1	1	4	1	3	2	0	2	1	2	0	6	4			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr2:235950616A>T	ENST00000409212.1	+	4	1710	c.1203A>T	c.(1201-1203)atA>atT	p.I401I	SH3BP4_ENST00000392011.2_Silent_p.I401I|SH3BP4_ENST00000344528.4_Silent_p.I401I			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	401					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)		CAGCCGAGATAAAAAATGACC	0.532																																					p.I401I		Atlas-SNP	.											.	SH3BP4	109	.	0			c.A1203T						PASS	.						43	45	44					2																	235950616		2203	4300	6503	SO:0001819	synonymous_variant	23677	exon4			CGAGATAAAAAAT	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.1203A>T	chr2.hg19:g.235950616A>T		78.0	0.0	.		68.0	19.0	.	NM_014521	O95082|Q309A3|Q53QD0|Q53TD1	Silent	SNP	ENST00000409212.1	hg19	CCDS2513.1																																																																																			.	.	.	none		0.532	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1			T	235950616	A	T	235950616	2	4	3	1	0	0	0	0	0	0	0	1	14259	352	13	5		5	SH3BP4	2	235950616	Silent	SNP	A	TCGA-2Z-A9J2-01A-11D-A382-10	18968145	235950616	7248757	23	189											
DLEC1	9940	hgsc.bcm.edu	37	chr3	38158502	38158502	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcagtaccatctacatcTccttcacccctatggtgctc	8	11	6	16	0	3	0	1	0	2	0	5	0	3	0	4	1	4	4	4	1	3	4			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr3:38158502T>C	ENST00000308059.6	+	30	4237	c.4216T>C	c.(4216-4218)Tcc>Ccc	p.S1406P	DLEC1_ENST00000452631.2_Missense_Mutation_p.S1409P|DLEC1_ENST00000346219.3_Missense_Mutation_p.S1406P					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)		CATCTACATCTCCTTCACCCC	0.587																																					p.S1406P		Atlas-SNP	.											.	DLEC1	278	.	0			c.T4216C						PASS	.						95	97	97					3																	38158502		2099	4231	6330	SO:0001583	missense	9940	exon30			TACATCTCCTTCA	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.4216T>C	chr3.hg19:g.38158502T>C	ENSP00000308597:p.Ser1406Pro	59.0	0.0	.		32.0	10.0	.	NM_007337		Missense_Mutation	SNP	ENST00000308059.6	hg19	CCDS2672.2	.	.	.	.	.	.	.	.	.	.	T	14.83	2.652603	0.47362	.	.	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.08458	3.12;3.09;3.35	4.39	4.39	0.52855	.	0.000000	0.64402	U	0.000001	T	0.27697	0.0681	M	0.75264	2.295	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.98;0.998;0.98;0.98	T	0.02026	-1.1227	10	0.72032	D	0.01	-25.6014	12.5811	0.56391	0.0:0.0:0.0:1.0	.	1409;1406;1406;1406	F8W6T4;B7ZW06;Q9Y238-3;Q9Y238	.;.;.;DLEC1_HUMAN	P	1406;1406;1409	ENSP00000308597:S1406P;ENSP00000315914:S1406P;ENSP00000410427:S1409P	ENSP00000308597:S1406P	S	+	1	0	DLEC1	38133506	1.000000	0.71417	0.978000	0.43139	0.097000	0.18754	3.903000	0.56318	1.610000	0.50200	0.379000	0.24179	TCC	.	.	.	none		0.587	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		C	38158502	T	C	38158502	3	2	3	1	0	0	0	0	1	0	0	0	4554	1551	54	3	4334	3	DLEC1	3	38158502	Missense_Mutation	SNP	T	TCGA-2Z-A9J2-01A-11D-A382-10		38158502	159863928	24	190											
BAP1	51533	hgsc.bcm.edu	37	chr3	52443600	52443600	+	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	tgctctgaaggtcgtagatcTcctccacttgcacccccttg	6	12	8	15	1	2	2	0	1	2	1	5	2	3	2	4	1	2	3	4	1	2	3			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr3:52443600T>C	ENST00000327906.3	+	0	0				PHF7_ENST00000347025.2_5'Flank|BAP1_ENST00000460680.1_Missense_Mutation_p.E31G|BAP1_ENST00000296288.5_Missense_Mutation_p.E31G	NM_016483.4	NP_057567.3	Q9BWX1	PHF7_HUMAN	PHD finger protein 7							Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)	p.E31A(1)		breast(2)|large_intestine(4)|lung(3)	9				BRCA - Breast invasive adenocarcinoma(193;1.71e-05)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)|OV - Ovarian serous cystadenocarcinoma(275;0.0275)		GTCGTAGATCTCCTCCACTTG	0.617																																					p.E31G		Atlas-SNP	.											BAP1,NS,carcinoma,0,2	BAP1	371	.	1	Substitution - Missense(1)	kidney(1)	c.A92G						PASS	.						218	227	224					3																	52443600		2203	4300	6503	SO:0001631	upstream_gene_variant	8314	exon3			TAGATCTCCTCCA	AY014283	CCDS2854.1, CCDS2855.1	3p21.31	2013-01-28			ENSG00000010318	ENSG00000010318		"Zinc fingers, PHD-type"	18458	protein-coding gene	gene with protein product						11042152, 11829468	Standard	NM_016483		Approved	NYD-SP6, HSPC226	uc003ddy.3	Q9BWX1	OTTHUMG00000158495		chr3.hg19:g.52443600T>C	Exception_encountered	142.0	0.0	.		53.0	21.0	.	NM_004656	K4DI82	Missense_Mutation	SNP	ENST00000327906.3	hg19	CCDS2854.1	.	.	.	.	.	.	.	.	.	.	T	33	5.244578	0.95272	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	T;T	0.61274	0.12;0.12	4.97	4.97	0.65823	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (3);	0.000000	0.85682	D	0.000000	T	0.82144	0.4973	H	0.94264	3.515	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87513	0.2441	10	0.87932	D	0	-3.7767	14.6644	0.68896	0.0:0.0:0.0:1.0	.	31	Q92560	BAP1_HUMAN	G	31	ENSP00000417132:E31G;ENSP00000296288:E31G	ENSP00000296288:E31G	E	-	2	0	BAP1	52418640	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.825000	0.86693	1.875000	0.54330	0.533000	0.62120	GAG	.	.	.	none		0.617	PHF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351155.1	NM_016483		C	52443600	T	C	52443600	1	2	3	0	1	0	0	0	0	0	0	0	1311	1551	54	3		3	BAP1	3	52443600	5'Flank	SNP	T	TCGA-2Z-A9J2-01A-11D-A382-10	14285098	52443600	145578830	25	191											
ITIH1	3697	hgsc.bcm.edu	37	chr3	52813055	52813055	+	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	tctcaggagagaatgccggcCttgtcaggtgagttctgggc	7	10	15	9	1	3	2	2	1	2	1	4	4	3	3	2	4	1	1	2	4	1	2			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr3:52813055C>A	ENST00000273283.2	+	4	427	c.403C>A	c.(403-405)Ctt>Att	p.L135I	ITIH1_ENST00000540715.1_De_novo_Start_OutOfFrame|ITIH1_ENST00000537050.1_5'Flank|ITIH1_ENST00000542827.1_Missense_Mutation_p.L135I	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	135	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				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)		GAATGCCGGCCTTGTCAGGTG	0.547																																					p.L135I		Atlas-SNP	.											.	ITIH1	108	.	0			c.C403A						PASS	.						113	94	100					3																	52813055		2203	4300	6503	SO:0001583	missense	3697	exon4			GCCGGCCTTGTCA		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.403C>A	chr3.hg19:g.52813055C>A	ENSP00000273283:p.Leu135Ile	54.0	0.0	.		24.0	6.0	.	NM_002215	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Missense_Mutation	SNP	ENST00000273283.2	hg19	CCDS2864.1	.	.	.	.	.	.	.	.	.	.	C	17.94	3.512092	0.64522	.	.	ENSG00000055957	ENST00000542827;ENST00000273283	T;T	0.26373	1.74;1.74	5.05	3.2	0.36748	Vault protein inter-alpha-trypsin (2);Vault protein inter-alpha-trypsin, metazoa (1);	0.000000	0.85682	D	0.000000	T	0.43211	0.1237	L	0.57536	1.79	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.27571	-1.0070	10	0.48119	T	0.1	-15.2366	10.4182	0.44335	0.0:0.8434:0.0:0.1566	.	135	P19827	ITIH1_HUMAN	I	135	ENSP00000442584:L135I;ENSP00000273283:L135I	ENSP00000273283:L135I	L	+	1	0	ITIH1	52788095	0.901000	0.30685	0.994000	0.49952	0.897000	0.52465	0.730000	0.26043	1.345000	0.45676	0.561000	0.74099	CTT	.	.	.	none		0.547	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215		A	52813055	C	A	52813055	3	1	3	1	0	0	0	0	1	0	0	0	7910	681	24	4	417	4	ITIH1	3	52813055	Missense_Mutation	SNP	C	TCGA-2Z-A9J2-01A-11D-A382-10	369455	52813055	145209375	26	192											
ERC2	26059	hgsc.bcm.edu	37	chr3	55768866	55768866	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccatgacttcttcctgcgtcTttttctttttggaggcagac	5	17	8	11	1	3	2	0	1	3	1	4	3	4	3	2	2	1	1	2	2	0	6			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr3:55768866T>C	ENST00000288221.6	-	15	2900	c.2645A>G	c.(2644-2646)aAg>aGg	p.K882R		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	882	Poly-Lys.					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)		TTCCTGCGTCTTTTTCTTTTT	0.443																																					p.K880R		Atlas-SNP	.											.	ERC2	221	.	0			c.A2639G						PASS	.						91	83	86					3																	55768866		1846	4120	5966	SO:0001583	missense	26059	exon14			TGCGTCTTTTTCT	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.2645A>G	chr3.hg19:g.55768866T>C	ENSP00000288221:p.Lys882Arg	49.0	0.0	.		46.0	4.0	.	NM_015576	Q2T9F6|Q86TK4	Missense_Mutation	SNP	ENST00000288221.6	hg19	CCDS46851.1	.	.	.	.	.	.	.	.	.	.	T	29.3	4.998014	0.93227	.	.	ENSG00000187672	ENST00000288221	T	0.47177	0.85	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.57475	0.2056	L	0.37750	1.13	0.46222	D	0.998937	D	0.57257	0.979	D	0.71414	0.973	T	0.52087	-0.8622	10	0.24483	T	0.36	-20.7165	15.6587	0.77165	0.0:0.0:0.0:1.0	.	882	O15083	ERC2_HUMAN	R	882	ENSP00000288221:K882R	ENSP00000288221:K882R	K	-	2	0	ERC2	55743906	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.109000	0.64355	0.533000	0.62120	AAG	.	.	.	none		0.443	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576		C	55768866	T	C	55768866	3	2	3	1	0	0	0	0	1	0	0	0	5213	1609	56	3	240	3	ERC2	3	55768866	Missense_Mutation	SNP	T	TCGA-2Z-A9J2-01A-11D-A382-10	2955811	55768866	142253564	27	193											
WDR52	55779	hgsc.bcm.edu	37	chr3	113125861	113125861	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatccctgcagcttgagaccGgtgaacgtaaaagccatttc	11	9	10	11	2	0	2	0	2	0	1	2	4	1	2	3	1	4	3	3	1	3	3	rs543988684		TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr3:113125861G>A	ENST00000295868.2	-	8	1080	c.918C>T	c.(916-918)acC>acT	p.T306T	WDR52_ENST00000393845.2_Silent_p.T306T|WDR52-AS1_ENST00000473329.1_RNA|WDR52-AS1_ENST00000498480.1_RNA	NM_018338.3	NP_060808.2														breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						GCTTGAGACCGGTGAACGTAA	0.398													T|||	1	0.000199681	0	0	5008	,	,		16680	0		0	False		,,,				2504	0.001				p.T306T		Atlas-SNP	.											.	WDR52	151	.	0			c.C918T						PASS	.						140	127	131					3																	113125861		2203	4300	6503	SO:0001819	synonymous_variant	55779	exon8			GAGACCGGTGAAC																												ENST00000295868.2:c.918C>T	chr3.hg19:g.113125861G>A		101.0	0.0	.		150.0	28.0	.	NM_001164496		Silent	SNP	ENST00000295868.2	hg19	CCDS2972.1																																																																																			.	.	.	none		0.398	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3			A	113125861	G	A	113125861	2	1	3	1	0	0	0	0	0	0	0	1	17316	1103	39	1		1	WDR52	3	113125861	Silent	SNP	G	TCGA-2Z-A9J2-01A-11D-A382-10	57356995	113125861	84896569	28	194											
OTOL1	131149	hgsc.bcm.edu	37	chr3	161220933	161220933	+	Missense_Mutation	SNP	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	gagaaaaaggagaccaagggGctatgggctcacctggcctg	12	5	15	9	0	1	2	1	0	0	2	1	4	1	2	3	5	0	2	3	5	4	1			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr3:161220933G>A	ENST00000327928.4	+	4	637	c.637G>A	c.(637-639)Gct>Act	p.A213T		NM_001080440.1	NP_001073909.1	A6NHN0	OTOL1_HUMAN	otolin 1	213	Collagen-like 2.					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						AGACCAAGGGGCTATGGGCTC	0.557																																					p.A213T		Atlas-SNP	.											.	OTOL1	63	.	0			c.G637A						PASS	.						5	6	6					3																	161220933		1825	3981	5806	SO:0001583	missense	131149	exon4			CAAGGGGCTATGG		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.637G>A	chr3.hg19:g.161220933G>A	ENSP00000330808:p.Ala213Thr	135.0	0.0	.		280.0	68.0	.	NM_001080440		Missense_Mutation	SNP	ENST00000327928.4	hg19	CCDS46948.1	.	.	.	.	.	.	.	.	.	.	G	6.893	0.534174	0.13188	.	.	ENSG00000182447	ENST00000327928	D	0.94232	-3.38	5.12	2.14	0.27477	.	0.710572	0.13922	N	0.353481	D	0.85911	0.5807	L	0.35542	1.07	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.69785	-0.5051	10	0.18276	T	0.48	.	4.7642	0.13123	0.0881:0.1479:0.611:0.153	.	213	A6NHN0	OTOL1_HUMAN	T	213	ENSP00000330808:A213T	ENSP00000330808:A213T	A	+	1	0	OTOL1	162703627	0.071000	0.21146	0.002000	0.10522	0.050000	0.14768	0.782000	0.26788	0.111000	0.17947	0.557000	0.71058	GCT	.	.	.	none		0.557	OTOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353184.1	NM_001080440		A	161220933	G	A	161220933	3	1	3	1	0	0	0	0	1	0	0	0	11311	1203	42	2	651	2	OTOL1	3	161220933	Missense_Mutation	SNP	G	TCGA-2Z-A9J2-01A-11D-A382-10	48095072	161220933	36801497	29	195											
BCL6	604	hgsc.bcm.edu	37	chr3	187446278	187446278	+	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	gacgtgcacttcggggggtgCatgtagagtggtgagtggct	6	10	19	6	2	0	2	0	1	0	1	1	3	0	2	0	5	2	4	0	5	1	2			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr3:187446278C>A	ENST00000406870.2	-	6	1776	c.1410G>T	c.(1408-1410)atG>atT	p.M470I	BCL6_ENST00000232014.4_Missense_Mutation_p.M470I|RP11-211G3.3_ENST00000437407.1_Intron|BCL6_ENST00000450123.2_Missense_Mutation_p.M470I|RP11-211G3.3_ENST00000449623.1_Intron	NM_001706.4	NP_001697.2	P41182	BCL6_HUMAN	B-cell CLL/lymphoma 6	470					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)		TCGGGGGGTGCATGTAGAGTG	0.632			"T, Mis"	"IG loci, ZNFN1A1, LCP1, PIM1, TFRC, CIITA, NACA, HSPCB, HSPCA, HIST1H4I, IL21R,  POU2AF1, ARHH, EIF4A2, SFRS3"	"NHL, CLL"																																p.M470I		Atlas-SNP	.		Dom	yes		3	3q27	604	B-cell CLL/lymphoma 6		L	.	BCL6	107	.	0			c.G1410T						PASS	.						65	58	60					3																	187446278		2203	4300	6503	SO:0001583	missense	604	exon5			GGGGTGCATGTAG		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.1410G>T	chr3.hg19:g.187446278C>A	ENSP00000384371:p.Met470Ile	53.0	0.0	.		71.0	35.0	.	NM_001134738	A7E241|B8PSA7|D3DNV5	Missense_Mutation	SNP	ENST00000406870.2	hg19	CCDS3289.1	.	.	.	.	.	.	.	.	.	.	C	11.24	1.581183	0.28180	.	.	ENSG00000113916	ENST00000406870;ENST00000232014;ENST00000450123	T;T;T	0.07567	3.19;3.19;3.18	5.09	3.14	0.36123	.	0.499500	0.22842	N	0.054964	T	0.05823	0.0152	N	0.25647	0.755	0.41396	D	0.987646	B;B	0.09022	0.0;0.002	B;B	0.04013	0.001;0.001	T	0.30357	-0.9981	10	0.33940	T	0.23	.	7.6733	0.28471	0.2589:0.6611:0.0:0.08	.	470;470	B8PSA7;P41182	.;BCL6_HUMAN	I	470	ENSP00000384371:M470I;ENSP00000232014:M470I;ENSP00000413122:M470I	ENSP00000232014:M470I	M	-	3	0	BCL6	188928972	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	1.641000	0.37197	1.468000	0.48064	0.561000	0.74099	ATG	.	.	.	none		0.632	BCL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344202.1	NM_138931		A	187446278	C	A	187446278	3	1	3	1	0	0	0	0	1	0	0	0	1376	710	25	4	730	4	BCL6	3	187446278	Missense_Mutation	SNP	C	TCGA-2Z-A9J2-01A-11D-A382-10	26225345	187446278	10576152	30	196											
MUC4	4585	hgsc.bcm.edu	37	chr3	195492266	195492266	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccactgcaggcactcgagaCggtagttgggcctttcttcc	6	10	12	13	2	1	1	0	0	1	1	3	2	2	1	3	3	1	4	3	3	1	4			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr3:195492266C>T	ENST00000346145.4	-	8	1004	c.965G>A	c.(964-966)cGt>cAt	p.R322H	MUC4_ENST00000475231.1_Missense_Mutation_p.R4506H|MUC4_ENST00000463781.3_Missense_Mutation_p.R4558H|MUC4_ENST00000349607.4_Missense_Mutation_p.R271H	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1315					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)		GCACTCGAGACGGTAGTTGGG	0.652																																					p.R4558H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	.	0			c.G13673A						PASS	.						45	42	43					3																	195492266		2203	4300	6503	SO:0001583	missense	4585	exon9			TCGAGACGGTAGT	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.965G>A	chr3.hg19:g.195492266C>T	ENSP00000304207:p.Arg322His	110.0	0.0	.		77.0	4.0	.	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000346145.4	hg19	CCDS3310.1	.	.	.	.	.	.	.	.	.	.	.	12.67	2.008048	0.35415	.	.	ENSG00000145113	ENST00000349607;ENST00000346145;ENST00000463781;ENST00000475231;ENST00000392409	T;T;T;T	0.41065	1.01;1.36;1.3;1.3	4.15	3.26	0.37387	AMOP (2);	0.208574	0.21556	U	0.072656	T	0.61476	0.2350	M	0.73598	2.24	0.30861	N	0.73352	D;D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.75484	0.986;0.971;0.955;0.955;0.938;0.938;0.981	T	0.64947	-0.6287	10	0.59425	D	0.04	-0.2742	11.3015	0.49309	0.0:0.9096:0.0:0.0904	.	4430;1315;271;322;4558;4506;1263	E7ESK3;Q99102;Q99102-12;Q99102-13;E9PDY6;E7ENC5;Q99102-10	.;MUC4_HUMAN;.;.;.;.;.	H	271;322;4558;4506;1284	ENSP00000338109:R271H;ENSP00000304207:R322H;ENSP00000417498:R4558H;ENSP00000420243:R4506H	ENSP00000304207:R322H	R	-	2	0	MUC4	196977937	0.955000	0.32602	0.992000	0.48379	0.138000	0.21146	2.284000	0.43478	0.942000	0.37525	0.461000	0.40582	CGT	.	.	.	none		0.652	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406		T	195492266	C	T	195492266	3	4	3	1	0	0	0	0	1	0	0	0	9985	536	19	1	2633	1	MUC4	3	195492266	Missense_Mutation	SNP	C	TCGA-2Z-A9J2-01A-11D-A382-10	8045988	195492266	2530164	31	197											
NUP54	53371	hgsc.bcm.edu	37	chr4	77053755	77053755	+	Frame_Shift_Del	DEL	T	T	-																															atagaaagggttacaccaagTtgctgcaattgtgtttttat																										TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr4:77053755delT	ENST00000264883.3	-	6	968	c.828delA	c.(826-828)caafs	p.Q276fs	NUP54_ENST00000458189.2_Frame_Shift_Del_p.Q96fs|NUP54_ENST00000342467.6_Frame_Shift_Del_p.Q96fs|NUP54_ENST00000514987.1_Frame_Shift_Del_p.Q228fs|NUP54_ENST00000515460.1_5'Flank	NM_017426.2	NP_059122.2	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	276	9 X 2 AA repeats of F-G.			FEQANIKTQLQQL -> LNKPYKNTIAAT (in Ref. 1; AAF67488). {ECO:0000305}.	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						TTACACCAAGTTGCTGCAATT	0.403																																					p.L277fs		Atlas-Indel,Pindel	.											.	NUP54	48	.	0			c.829delC						PASS	.						216	209	211					4																	77053755		2203	4300	6503	SO:0001589	frameshift_variant	53371	exon6			.	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.828delA	chr4.hg19:g.77053755delT	ENSP00000264883:p.Gln276fs	199.0	0.0	0		140.0	33.0	0.235714	NM_017426	B2RCK7|B4DT35|Q96EA7|Q9NVL5|Q9P0I1	Frame_Shift_Del	DEL	ENST00000264883.3	hg19	CCDS3576.1																																																																																			.	.	.	none		0.403	NUP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252402.3			-	77053755	T	-	77053755	7	5	3	1	0	1	0	1	0	0	0	0	10774	1722	60	0	723	0	NUP54	4	77053755	Frame_Shift_Del	DEL	T	TCGA-2Z-A9J2-01A-11D-A382-10		77053755	114100521	32	198											
PTPN13	5783	hgsc.bcm.edu	37	chr4	87724921	87724947	+	In_Frame_Del	DEL	TCTGGTAAATACACGGGTGCCAACTTA	TCTGGTAAATACACGGGTGCCAACTTA	-																															ctgtcgtcaaagtgcttcccTctggtaaatacacgggtgcc																								rs114813002	byFrequency	TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	TCTGGTAAATACACGGGTGCCAACTTA	TCTGGTAAATACACGGGTGCCAACTTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr4:87724921_87724947delTCTGGTAAATACACGGGTGCCAACTTA	ENST00000411767.2	+	43	6628_6654	c.6565_6591delTCTGGTAAATACACGGGTGCCAACTTA	c.(6565-6591)tctggtaaatacacgggtgccaacttadel	p.SGKYTGANL2189del	PTPN13_ENST00000427191.2_In_Frame_Del_p.SGKYTGANL2170del|PTPN13_ENST00000316707.6_In_Frame_Del_p.SGKYTGANL1998del|PTPN13_ENST00000511467.1_In_Frame_Del_p.SGKYTGANL2194del|PTPN13_ENST00000436978.1_In_Frame_Del_p.SGKYTGANL2194del			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	2189					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)	p.T2198T(1)		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)		AGTGCTTCCCTCTGGTAAATACACGGGTGCCAACTTAAAATCAGTCA	0.454																																					p.2193_2202del		Atlas-Indel,Pindel	.											.	PTPN13	203	.	1	Substitution - coding silent(1)	lung(1)	c.6579_6605del						PASS	.																																			SO:0001651	inframe_deletion	5783	exon43			.		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.6565_6591delTCTGGTAAATACACGGGTGCCAACTTA	chr4.hg19:g.87724921_87724947delTCTGGTAAATACACGGGTGCCAACTTA	ENSP00000407249:p.Ser2189_Leu2197del	76.0	0.0	0		73.0	12.0	0.164384	NM_080685	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	In_Frame_Del	DEL	ENST00000411767.2	hg19	CCDS47094.1																																																																																			.	.	.	none		0.454	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			-	87724947	TCTGGTAAATACACGGGTGCCAACTTA	-	87724921	7	5	3	1	0	1	0	1	0	0	0	0	12793	1551	54	0	6746	0	PTPN13	4	87724921	In_Frame_Del	DEL	TCTGGTAAATACACGGGTGCCAACTTA	TCGA-2Z-A9J2-01A-11D-A382-10	10671166	87724921	103429355	33	199											
GPR98	84059	hgsc.bcm.edu	37	chr5	90012405	90012405	+	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	gagagtgttgcagtattgtaCattgttcgggaacctgcaca	10	12	12	7	1	0	1	0	0	0	1	1	3	0	2	1	1	4	6	1	1	3	6			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr5:90012405C>A	ENST00000405460.2	+	43	9402	c.9306C>A	c.(9304-9306)taC>taA	p.Y3102*		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	3102	Calx-beta 22. {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)		CAGTATTGTACATTGTTCGGG	0.428																																					p.Y3102X		Atlas-SNP	.											.	GPR98	605	.	0			c.C9306A						PASS	.						93	86	88					5																	90012405		1869	4102	5971	SO:0001587	stop_gained	84059	exon43			ATTGTACATTGTT	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.9306C>A	chr5.hg19:g.90012405C>A	ENSP00000384582:p.Tyr3102*	136.0	0.0	.		138.0	16.0	.	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Nonsense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	49|49	15.942102|15.942102	0.99849|0.99849	.|.	.|.	ENSG00000164199|ENSG00000164199	ENST00000509621|ENST00000405460;ENST00000296619	.|.	.|.	.|.	6.01|6.01	1.91|1.91	0.25777|0.25777	.|.	.|0.473406	.|0.26016	.|N	.|0.026847	T|.	0.13798|.	0.0334|.	.|.	.|.	.|.	0.09310|0.09310	N|N	0.999999|0.999999	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.34279|.	-0.9835|.	4|.	.|0.02654	.|T	.|1	.|.	9.5215|9.5215	0.39138|0.39138	0.0:0.513:0.0:0.487|0.0:0.513:0.0:0.487	.|.	.|.	.|.	.|.	K|X	668|3102	.|.	.|ENSP00000296619:Y3102X	T|Y	+|+	2|3	0|2	GPR98|GPR98	90048161|90048161	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.398000|0.398000	0.30690|0.30690	-0.367000|-0.367000	0.07553|0.07553	0.049000|0.049000	0.15920|0.15920	0.650000|0.650000	0.86243|0.86243	ACA|TAC	.	.	.	none		0.428	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		A	90012405	C	A	90012405	4	1	3	1	0	0	0	0	0	1	0	0	6728	489	17	4	9476	4	GPR98	5	90012405	Nonsense_Mutation	SNP	C	TCGA-2Z-A9J2-01A-11D-A382-10		90012405	90902855	34	200											
MCC	4163	hgsc.bcm.edu	37	chr5	112420999	112420999	+	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	ctctgtagtcgagtttgaagCtctctgacctgaaatcataa	11	13	8	9	1	3	3	1	3	2	0	5	4	3	3	1	0	1	3	1	0	4	3	rs560764461		TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr5:112420999C>A	ENST00000302475.4	-	7	1400	c.837G>T	c.(835-837)gaG>gaT	p.E279D	MCC_ENST00000514701.3_5'UTR|MCC_ENST00000515367.2_Missense_Mutation_p.E216D|MCC_ENST00000408903.3_Missense_Mutation_p.E469D	NM_002387.2	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers	279					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)		GAGTTTGAAGCTCTCTGACCT	0.537													C|||	1	0.000199681	8e-04	0	5008	,	,		18161	0		0	False		,,,				2504	0				p.E469D		Atlas-SNP	.											.	MCC	234	.	0			c.G1407T						PASS	.						134	134	134					5																	112420999		2202	4300	6502	SO:0001583	missense	4163	exon9			TTGAAGCTCTCTG		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.837G>T	chr5.hg19:g.112420999C>A	ENSP00000305617:p.Glu279Asp	46.0	0.0	.		62.0	25.0	.	NM_001085377	D3DT05|Q6ZR04	Missense_Mutation	SNP	ENST00000302475.4	hg19	CCDS4111.1	.	.	.	.	.	.	.	.	.	.	C	19.80	3.894175	0.72639	.	.	ENSG00000171444	ENST00000302475;ENST00000515367;ENST00000408903	T;T;T	0.55930	0.49;0.49;0.49	5.73	2.6	0.31112	Usher syndrome type-1C protein-binding protein 1, PDZ domain (1);	0.000000	0.85682	D	0.000000	T	0.53514	0.1801	L	0.27053	0.805	0.47407	D	0.99941	D;D;D;D	0.57257	0.979;0.979;0.974;0.979	D;D;D;D	0.71414	0.973;0.973;0.969;0.973	T	0.50039	-0.8874	10	0.44086	T	0.13	-27.2275	7.6576	0.28383	0.0:0.5691:0.0:0.4309	.	279;241;469;279	B7Z6G0;B3KTX0;P23508-2;P23508	.;.;.;CRCM_HUMAN	D	279;216;469	ENSP00000305617:E279D;ENSP00000421615:E216D;ENSP00000386227:E469D	ENSP00000305617:E279D	E	-	3	2	MCC	112448898	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	0.795000	0.26972	0.781000	0.33589	0.655000	0.94253	GAG	.	.	.	none		0.537	MCC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250736.3	NM_001085377		A	112420999	C	A	112420999	3	1	3	1	0	0	0	0	1	0	0	0	9380	796	28	4	1696	4	MCC	5	112420999	Missense_Mutation	SNP	C	TCGA-2Z-A9J2-01A-11D-A382-10	22408594	112420999	68494261	35	201											
PCDHGB7	56099	hgsc.bcm.edu	37	chr5	140797588	140797588	+	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	gggaacctcgctaaggatctAgggcttagtgtcctggatgt	8	11	14	8	1	1	0	0	0	1	0	3	3	2	3	2	4	1	2	2	4	4	3			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr5:140797588A>C	ENST00000398594.2	+	1	162	c.162A>C	c.(160-162)ctA>ctC	p.L54L	PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_018927.3	NP_061750.1	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7	54	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(13)|lung(15)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(3)	56			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTAAGGATCTAGGGCTTAGTG	0.612											OREG0016863	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L54L		Atlas-SNP	.											.	PCDHGB7	117	.	0			c.A162C						PASS	.						62	68	66					5																	140797588		1962	4150	6112	SO:0001819	synonymous_variant	56099	exon1			GGATCTAGGGCTT	AF152523	CCDS47293.1, CCDS75344.1	5q31	2010-01-26			ENSG00000254122	ENSG00000254122		"Cadherins / Protocadherins : Clustered"	8714	other	protocadherin	"cadherin ME6"	606304				10380929	Standard	NM_032101		Approved	ME6, PCDH-GAMMA-B7		Q9Y5F8	OTTHUMG00000164054	ENST00000398594.2:c.162A>C	chr5.hg19:g.140797588A>C		132.0	0.0	.	1659	59.0	21.0	.	NM_018927	Q9UN63	Silent	SNP	ENST00000398594.2	hg19	CCDS47293.1																																																																																			.	.	.	none		0.612	PCDHGB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376973.1	NM_018927		C	140797588	A	C	140797588	2	2	3	1	0	0	0	0	0	0	0	1	11575	407	15	5		5	PCDHGB7	5	140797588	Silent	SNP	A	TCGA-2Z-A9J2-01A-11D-A382-10	28376589	140797588	40117672	36	202											
SH3TC2	79628	hgsc.bcm.edu	37	chr5	148386485	148386485	+	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	tctgcccaggcgataatacaCcttggcatagtacagggcct	10	9	10	12	1	1	0	0	0	1	0	1	1	1	0	3	3	3	2	3	3	4	5			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr5:148386485C>G	ENST00000515425.1	-	16	3735	c.3634G>C	c.(3634-3636)Gtg>Ctg	p.V1212L	SH3TC2_ENST00000538184.1_3'UTR|SH3TC2_ENST00000502274.1_Missense_Mutation_p.V74L|SH3TC2_ENST00000512049.1_Missense_Mutation_p.V1205L	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	1212					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)			CGATAATACACCTTGGCATAG	0.552																																					p.V1212L		Atlas-SNP	.											.	SH3TC2	178	.	0			c.G3634C						PASS	.						114	117	116					5																	148386485		2203	4300	6503	SO:0001583	missense	79628	exon16			AATACACCTTGGC	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.3634G>C	chr5.hg19:g.148386485C>G	ENSP00000423660:p.Val1212Leu	126.0	0.0	.		112.0	26.0	.	NM_024577	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Missense_Mutation	SNP	ENST00000515425.1	hg19	CCDS4293.1	.	.	.	.	.	.	.	.	.	.	C	19.75	3.885931	0.72410	.	.	ENSG00000169247	ENST00000502274;ENST00000515425;ENST00000512049	T;D;T	0.81499	0.55;-1.5;-0.91	6.17	6.17	0.99709	Tetratricopeptide-like helical (1);	0.133551	0.49916	D	0.000137	T	0.79003	0.4373	M	0.62723	1.935	0.80722	D	1	B;B;B	0.24043	0.096;0.096;0.096	B;B;B	0.24848	0.051;0.056;0.051	T	0.74583	-0.3617	10	0.51188	T	0.08	-10.8348	13.9957	0.64397	0.0:0.9315:0.0:0.0685	.	1205;1212;1212	Q14CC0;E9PDF1;Q8TF17	.;.;S3TC2_HUMAN	L	74;1212;1205	ENSP00000421092:V74L;ENSP00000423660:V1212L;ENSP00000421860:V1205L	ENSP00000421092:V74L	V	-	1	0	SH3TC2	148366678	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	3.051000	0.49885	2.941000	0.99782	0.655000	0.94253	GTG	.	.	.	none		0.552	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577		G	148386485	C	G	148386485	3	3	3	1	0	0	0	0	1	0	0	0	14275	507	18	4	240	4	SH3TC2	5	148386485	Missense_Mutation	SNP	C	TCGA-2Z-A9J2-01A-11D-A382-10	7588897	148386485	32528775	37	203											
C2	717	hgsc.bcm.edu	37	chr6	31905164	31905164	+	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	tctatctcatgatgaacaacCaaatgcgactcctcggcatg	12	10	7	12	2	2	2	1	2	2	0	5	3	3	2	2	1	3	1	2	1	4	1			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr6:31905164C>A	ENST00000299367.5	+	8	1333	c.1057C>A	c.(1057-1059)Caa>Aaa	p.Q353K	C2_ENST00000469372.1_Missense_Mutation_p.Q107K|CFB_ENST00000477310.1_Missense_Mutation_p.Q171K|CFB_ENST00000456570.1_Missense_Mutation_p.Q200K|C2_ENST00000452323.2_Missense_Mutation_p.Q139K|C2_ENST00000442278.2_Missense_Mutation_p.Q221K|CFB_ENST00000556679.1_Missense_Mutation_p.Q200K	NM_000063.4	NP_000054.2	P06681	CO2_HUMAN	complement component 2	353	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)|skin(2)|urinary_tract(2)	27		Ovarian(999;0.00965)		LUAD - Lung adenocarcinoma(999;0.247)		GATGAACAACCAAATGCGACT	0.473																																					p.Q353K		Atlas-SNP	.											.	C2	50	.	0			c.C1057A						PASS	.						212	207	209					6																	31905164		1511	2709	4220	SO:0001583	missense	717	exon8			AACAACCAAATGC		CCDS4728.1, CCDS54991.1, CCDS56416.1, CCDS75427.1, CCDS75428.1	6p21.3	2014-09-17			ENSG00000166278	ENSG00000166278		"Complement system"	1248	protein-coding gene	gene with protein product		613927					Standard	NM_001145903		Approved		uc011hbs.1	P06681	OTTHUMG00000031190	ENST00000299367.5:c.1057C>A	chr6.hg19:g.31905164C>A	ENSP00000299367:p.Gln353Lys	113.0	0.0	.		83.0	24.0	.	NM_000063	B4DPF3|B4DV20|E9PFN7|O19694|Q13904	Missense_Mutation	SNP	ENST00000299367.5	hg19	CCDS4728.1	.	.	.	.	.	.	.	.	.	.	C	13.08	2.131136	0.37630	.	.	ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000166278;ENSG00000243649;ENSG00000244255;ENSG00000244255	ENST00000469372;ENST00000497706;ENST00000432397;ENST00000452323;ENST00000299367;ENST00000375493;ENST00000442278;ENST00000556679;ENST00000456570;ENST00000477310	D;D;D;D;D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66;-1.66;-1.66;-1.66;-1.66	4.97	4.06	0.47325	von Willebrand factor, type A (3);	0.000000	0.36972	N	0.002318	T	0.74068	0.3668	L	0.49350	1.555	0.26005	N	0.98206	P;P;P;P;P;P;P;B;P	0.45672	0.791;0.84;0.49;0.84;0.673;0.807;0.814;0.048;0.864	P;P;B;B;B;P;P;P;B	0.48488	0.463;0.498;0.299;0.413;0.395;0.486;0.579;0.45;0.407	T	0.65689	-0.6107	10	0.25106	T	0.35	-13.0037	13.1289	0.59369	0.0:0.8253:0.1747:0.0	.	200;324;139;107;221;38;221;353;140	B4E1Z4;B4DV48;B4DPF3;B4DQI1;E9PFN7;F8VNY6;B4DV20;P06681;E9PDZ0	.;.;.;.;.;.;.;CO2_HUMAN;.	K	107;140;140;139;353;38;221;200;200;171	ENSP00000418923:Q107K;ENSP00000417482:Q140K;ENSP00000392322:Q139K;ENSP00000299367:Q353K;ENSP00000395683:Q221K;ENSP00000451848:Q200K;ENSP00000410815:Q200K;ENSP00000418996:Q171K	ENSP00000299367:Q353K	Q	+	1	0	CFB;C2;XXbac-BPG116M5.17	32013143	0.995000	0.38212	0.955000	0.39395	0.047000	0.14425	1.563000	0.36364	2.596000	0.87737	0.544000	0.68410	CAA	.	.	.	none		0.473	C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076379.9			A	31905164	C	A	31905164	3	1	3	1	0	0	0	0	1	0	0	0	2076	595	21	4	1164	4	C2	6	31905164	Missense_Mutation	SNP	C	TCGA-2Z-A9J2-01A-11D-A382-10		31905164	139209903	38	204											
WDR27	253769	hgsc.bcm.edu	37	chr6	170038673	170038674	+	Frame_Shift_Del	DEL	TT	TT	-																															tgccccacgagccgaccacaTtcgcagggtcccgtcccggg																								rs115828649	byFrequency	TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr6:170038673_170038674delTT	ENST00000448612.1	-	18	1939_1940	c.1830_1831delAA	c.(1828-1833)cgaatgfs	p.M611fs	WDR27_ENST00000546525.1_5'UTR|WDR27_ENST00000423258.1_Frame_Shift_Del_p.M484fs|WDR27_ENST00000333572.6_Frame_Shift_Del_p.M611fs	NM_182552.4	NP_872358.4	A2RRH5	WDR27_HUMAN	WD repeat domain 27	581						nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|skin(1)	12		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)		GCCGACCACATTCGCAGGGTCC	0.599																																					p.611_611del		Atlas-INDEL	.											.	WDR27	129	.	0			c.1831_1832del						PASS	.																																			SO:0001589	frameshift_variant	253769	exon18			.	AK131435	CCDS47520.1, CCDS47520.2, CCDS56459.1	6q27	2013-01-09	2003-06-18		ENSG00000184465	ENSG00000184465		"WD repeat domain containing"	21248	protein-coding gene	gene with protein product							Standard	NM_182552		Approved	MGC43690	uc003qwx.3	A2RRH5	OTTHUMG00000016061	ENST00000448612.1:c.1830_1831delAA	chr6.hg19:g.170038673_170038674delTT	ENSP00000416289:p.Met611fs	213.0	0.0	0		101.0	21.0	0.207921	NM_182552	A5PLM8|C9JGV0|Q5T066	Frame_Shift_Del	DEL	ENST00000448612.1	hg19	CCDS47520.2																																																																																			.	.	.	none		0.599	WDR27-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000407334.1	NM_182552		-	170038674	TT	-	170038673	7	5	3	1	0	1	0	1	0	0	0	0	17296	1493	52	0	774	0	WDR27	6	170038673	Frame_Shift_Del	DEL	TT	TCGA-2Z-A9J2-01A-11D-A382-10	138133509	170038673	1076394	39	205	2	2									
WDR27	253769	hgsc.bcm.edu	37	chr6	170038676	170038680	+	Frame_Shift_Del	DEL	GCAGG	GCAGG	-																															cccacgagccgaccacattcGcagggtcccgtcccgggccg																								rs201534381		TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	GCAGG	GCAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr6:170038676_170038680delGCAGG	ENST00000448612.1	-	18	1933_1937	c.1824_1828delCCTGC	c.(1822-1830)accctgcgafs	p.LR609fs	WDR27_ENST00000546525.1_5'UTR|WDR27_ENST00000423258.1_Frame_Shift_Del_p.LR482fs|WDR27_ENST00000333572.6_Frame_Shift_Del_p.LR609fs	NM_182552.4	NP_872358.4	A2RRH5	WDR27_HUMAN	WD repeat domain 27	579						nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|skin(1)	12		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)		GACCACATTCGCAGGGTCCCGTCCC	0.605																																					p.609_610del		Atlas-INDEL	.											.	WDR27	129	.	0			c.1825_1829del						PASS	.																																			SO:0001589	frameshift_variant	253769	exon18			.	AK131435	CCDS47520.1, CCDS47520.2, CCDS56459.1	6q27	2013-01-09	2003-06-18		ENSG00000184465	ENSG00000184465		"WD repeat domain containing"	21248	protein-coding gene	gene with protein product							Standard	NM_182552		Approved	MGC43690	uc003qwx.3	A2RRH5	OTTHUMG00000016061	ENST00000448612.1:c.1824_1828delCCTGC	chr6.hg19:g.170038676_170038680delGCAGG	ENSP00000416289:p.Leu609fs	214.0	0.0	0		104.0	21.0	0.201923	NM_182552	A5PLM8|C9JGV0|Q5T066	Frame_Shift_Del	DEL	ENST00000448612.1	hg19	CCDS47520.2																																																																																			.	.	.	none		0.605	WDR27-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000407334.1	NM_182552		-	170038680	GCAGG	-	170038676	7	5	3	1	0	1	0	1	0	0	0	0	17296	1095	38	0	777	0	WDR27	6	170038676	Frame_Shift_Del	DEL	GCAGG	TCGA-2Z-A9J2-01A-11D-A382-10	3	170038676	1076391	40	206	2	2									
AZGP1	563	hgsc.bcm.edu	37	chr7	99565822	99565822	+	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	tgtatttcaggtatttccgcAgagtcgcagggcactcctcc	7	12	10	12	2	1	1	1	0	0	1	5	1	4	1	3	2	0	5	3	2	2	4			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr7:99565822A>T	ENST00000292401.4	-	3	705	c.569T>A	c.(568-570)cTg>cAg	p.L190Q	AZGP1_ENST00000411734.1_Missense_Mutation_p.L187Q|AZGP1_ENST00000483612.1_5'Flank	NM_001185.3	NP_001176.1	P25311	ZA2G_HUMAN	alpha-2-glycoprotein 1, zinc-binding	190					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell adhesion (GO:0007155)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein transmembrane transport (GO:0071806)|retina homeostasis (GO:0001895)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|MHC class I protein complex (GO:0042612)|nucleus (GO:0005634)	glycoprotein binding (GO:0001948)|peptide antigen binding (GO:0042605)|protein transmembrane transporter activity (GO:0008320)|ribonuclease activity (GO:0004540)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|stomach(1)	16	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					GTATTTCCGCAGAGTCGCAGG	0.547																																					p.L190Q		Atlas-SNP	.											.	AZGP1	41	.	0			c.T569A						PASS	.						99	96	97					7																	99565822		2203	4300	6503	SO:0001583	missense	563	exon3			TTCCGCAGAGTCG	BC005306	CCDS5680.1	7q22.1	2013-01-11	2006-11-07		ENSG00000160862	ENSG00000160862		"Immunoglobulin superfamily / C1-set domain containing"	910	protein-coding gene	gene with protein product		194460	"alpha-2-glycoprotein 1, zinc"			2049092	Standard	NM_001185		Approved	ZA2G, ZAG	uc003ush.3	P25311	OTTHUMG00000023066	ENST00000292401.4:c.569T>A	chr7.hg19:g.99565822A>T	ENSP00000292401:p.Leu190Gln	59.0	0.0	.		33.0	10.0	.	NM_001185	D6W5T8|O60386|Q5XKQ4|Q8N4N0	Missense_Mutation	SNP	ENST00000292401.4	hg19	CCDS5680.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.240853	0.79912	.	.	ENSG00000160862	ENST00000292401;ENST00000411734	D;D	0.96554	-4.05;-4.05	2.76	2.76	0.32466	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.000000	0.26522	U	0.023916	D	0.98560	0.9519	H	0.97918	4.105	0.45762	D	0.99865	D	0.76494	0.999	D	0.75020	0.985	D	0.98106	1.0417	10	0.87932	D	0	.	9.2502	0.37551	1.0:0.0:0.0:0.0	.	190	P25311	ZA2G_HUMAN	Q	190;187	ENSP00000292401:L190Q;ENSP00000396093:L187Q	ENSP00000292401:L190Q	L	-	2	0	AZGP1	99403758	1.000000	0.71417	0.063000	0.19743	0.661000	0.39034	7.145000	0.77365	1.200000	0.43188	0.260000	0.18958	CTG	.	.	.	none		0.547	AZGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059387.4	NM_001185		T	99565822	A	T	99565822	3	4	3	1	0	0	0	0	1	0	0	0	1239	188	7	5	335	5	AZGP1	7	99565822	Missense_Mutation	SNP	A	TCGA-2Z-A9J2-01A-11D-A382-10		99565822	59572841	41	207											
GPR37	2861	hgsc.bcm.edu	37	chr7	124387366	124387366	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtctatgcacagagcacatAaggtgaaagtggtgactccc	12	8	12	9	0	1	3	0	2	1	1	2	3	2	3	1	3	2	2	1	3	3	2			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr7:124387366A>G	ENST00000303921.2	-	2	1705	c.1055T>C	c.(1054-1056)tTa>tCa	p.L352S		NM_005302.3	NP_005293.1	O15354	GPR37_HUMAN	G protein-coupled receptor 37 (endothelin receptor type B-like)	352					dopamine biosynthetic process (GO:0042416)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotion involved in locomotory behavior (GO:0031987)|positive regulation of dopamine metabolic process (GO:0045964)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ubiquitin ligase complex (GO:0000151)	G-protein coupled receptor activity (GO:0004930)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						CAGAGCACATAAGGTGAAAGT	0.473																																					p.L352S		Atlas-SNP	.											.	GPR37	89	.	0			c.T1055C						PASS	.						60	62	61					7																	124387366		2203	4300	6503	SO:0001583	missense	2861	exon2			GCACATAAGGTGA		CCDS5792.1	7q31	2012-08-21			ENSG00000170775	ENSG00000170775		"GPCR / Class A : Orphans"	4494	protein-coding gene	gene with protein product		602583				9339362	Standard	NM_005302		Approved	EDNRBL, hET(B)R-LP, PAELR	uc003vli.4	O15354	OTTHUMG00000157197	ENST00000303921.2:c.1055T>C	chr7.hg19:g.124387366A>G	ENSP00000306449:p.Leu352Ser	43.0	0.0	.		58.0	6.0	.	NM_005302	A4D0Y6|O00348|O14768|Q8TD39	Missense_Mutation	SNP	ENST00000303921.2	hg19	CCDS5792.1	.	.	.	.	.	.	.	.	.	.	A	16.35	3.098540	0.56183	.	.	ENSG00000170775	ENST00000303921	T	0.81415	-1.49	5.77	5.77	0.91146	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46442	D	0.000298	D	0.89259	0.6664	M	0.76002	2.32	0.51233	D	0.999911	D	0.89917	1.0	D	0.97110	1.0	D	0.90432	0.4425	10	0.87932	D	0	-7.7845	15.2683	0.73681	1.0:0.0:0.0:0.0	.	352	O15354	GPR37_HUMAN	S	352	ENSP00000306449:L352S	ENSP00000306449:L352S	L	-	2	0	GPR37	124174602	0.998000	0.40836	0.949000	0.38748	0.352000	0.29268	9.339000	0.96797	2.202000	0.70862	0.533000	0.62120	TTA	.	.	.	none		0.473	GPR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347873.1	NM_005302		G	124387366	A	G	124387366	3	3	3	1	0	0	0	0	1	0	0	0	6698	372	13	3	790	3	GPR37	7	124387366	Missense_Mutation	SNP	A	TCGA-2Z-A9J2-01A-11D-A382-10	24821544	124387366	34751297	42	208											
TMEM139	135932	hgsc.bcm.edu	37	chr7	142983223	142983223	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgcctatctcctggtccggtTtctggaatgggggcttcggt	3	14	14	10	2	2	0	0	0	2	0	5	1	3	1	3	6	1	2	3	6	2	3			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr7:142983223T>C	ENST00000359333.3	+	2	686	c.173T>C	c.(172-174)tTt>tCt	p.F58S	TMEM139_ENST00000409541.1_Missense_Mutation_p.F58S|TMEM139_ENST00000409102.1_Missense_Mutation_p.F58S|TMEM139_ENST00000410004.1_Missense_Mutation_p.F58S|CASP2_ENST00000392925.2_5'Flank|CASP2_ENST00000310447.5_5'Flank|TMEM139_ENST00000409244.1_Missense_Mutation_p.F58S|TMEM139_ENST00000471161.1_Intron|AC073342.12_ENST00000427392.1_RNA|AC073342.12_ENST00000446192.1_RNA	NM_001242775.2|NM_001282876.1|NM_001282877.1	NP_001229704.1|NP_001269805.1|NP_001269806.1	Q8IV31	TM139_HUMAN	transmembrane protein 139	58						integral component of membrane (GO:0016021)				endometrium(1)|lung(4)|ovary(1)|prostate(1)	7	Melanoma(164;0.059)					CTGGTCCGGTTTCTGGAATGG	0.552																																					p.F58S		Atlas-SNP	.											.	TMEM139	18	.	0			c.T173C						PASS	.						156	150	152					7																	142983223		2203	4300	6503	SO:0001583	missense	135932	exon3			TCCGGTTTCTGGA	AK075067	CCDS5878.1	7q34	2006-03-17			ENSG00000178826	ENSG00000178826			22058	protein-coding gene	gene with protein product							Standard	NM_153345		Approved	FLJ90586	uc003wck.4	Q8IV31	OTTHUMG00000152652	ENST00000359333.3:c.173T>C	chr7.hg19:g.142983223T>C	ENSP00000352284:p.Phe58Ser	64.0	0.0	.		42.0	15.0	.	NM_001242773	B2RCL5|D3DXD4|Q6ZME2|Q8NC22|Q96AU8	Missense_Mutation	SNP	ENST00000359333.3	hg19	CCDS5878.1	.	.	.	.	.	.	.	.	.	.	T	9.451	1.090601	0.20471	.	.	ENSG00000178826	ENST00000409102;ENST00000359333;ENST00000409244;ENST00000409541;ENST00000410004	.	.	.	5.0	0.855	0.19013	.	0.643829	0.15236	N	0.273162	T	0.17023	0.0409	N	0.19112	0.55	0.09310	N	1	B	0.19583	0.037	B	0.17433	0.018	T	0.15407	-1.0438	9	0.22706	T	0.39	0.0033	1.6402	0.02750	0.1701:0.0953:0.1765:0.5581	.	58	Q8IV31	TM139_HUMAN	S	58	.	ENSP00000352284:F58S	F	+	2	0	TMEM139	142693345	0.000000	0.05858	0.374000	0.26016	0.030000	0.12068	0.273000	0.18662	0.315000	0.23110	0.456000	0.33151	TTT	.	.	.	none		0.552	TMEM139-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327145.1	NM_153345		C	142983223	T	C	142983223	3	2	3	1	0	0	0	0	1	0	0	0	16066	1841	64	3	175	3	TMEM139	7	142983223	Missense_Mutation	SNP	T	TCGA-2Z-A9J2-01A-11D-A382-10	18595857	142983223	16155440	43	209											
PDIA4	9601	hgsc.bcm.edu	37	chr7	148712027	148712027	+	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	aaactccaccagaatgatatCtgcatcattcacaacttcat	15	11	3	12	0	4	2	3	1	1	1	5	2	5	2	2	0	3	1	2	0	4	3	rs565062386		TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr7:148712027C>A	ENST00000286091.4	-	4	815	c.583G>T	c.(583-585)Gat>Tat	p.D195Y		NM_004911.4	NP_004902.1	P13667	PDIA4_HUMAN	protein disulfide isomerase family A, member 4	195	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)			AGAATGATATCTGCATCATTC	0.537																																					p.D195Y		Atlas-SNP	.											.	PDIA4	57	.	0			c.G583T						PASS	.						138	103	115					7																	148712027		2203	4300	6503	SO:0001583	missense	9601	exon4			TGATATCTGCATC	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.583G>T	chr7.hg19:g.148712027C>A	ENSP00000286091:p.Asp195Tyr	93.0	0.0	.		80.0	16.0	.	NM_004911	A8K4K6|Q549T6	Missense_Mutation	SNP	ENST00000286091.4	hg19	CCDS5893.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.081506	0.76528	.	.	ENSG00000155660	ENST00000286091	T	0.43688	0.94	4.7	4.7	0.59300	Thioredoxin domain (1);Thioredoxin-like fold (3);Disulphide isomerase (1);	0.000000	0.85682	D	0.000000	T	0.58424	0.2121	L	0.53780	1.695	0.80722	D	1	D	0.69078	0.997	P	0.62298	0.9	T	0.63633	-0.6593	10	0.87932	D	0	.	17.6525	0.88169	0.0:1.0:0.0:0.0	.	195	P13667	PDIA4_HUMAN	Y	195	ENSP00000286091:D195Y	ENSP00000286091:D195Y	D	-	1	0	PDIA4	148342960	1.000000	0.71417	0.824000	0.32777	0.694000	0.40290	7.561000	0.82288	2.153000	0.67306	0.404000	0.27445	GAT	.	.	.	none		0.537	PDIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317077.1	NM_004911		A	148712027	C	A	148712027	3	1	3	1	0	0	0	0	1	0	0	0	11677	913	32	4	1382	4	PDIA4	7	148712027	Missense_Mutation	SNP	C	TCGA-2Z-A9J2-01A-11D-A382-10	5728804	148712027	10426636	44	210											
TMEM176A	55365	hgsc.bcm.edu	37	chr7	150500886	150500886	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tccagaagaagtcagaaggcTacacctatgtacctccttca	13	9	7	12	0	2	3	2	0	0	3	4	3	4	3	4	1	2	2	4	1	6	4			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr7:150500886T>C	ENST00000484928.1	+	5	1102	c.521T>C	c.(520-522)cTa>cCa	p.L174P	TMEM176A_ENST00000461345.1_Missense_Mutation_p.L115P|TMEM176B_ENST00000447204.2_5'Flank|TMEM176A_ENST00000004103.3_Missense_Mutation_p.L174P			Q96HP8	T176A_HUMAN	transmembrane protein 176A	174					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)		GTCAGAAGGCTACACCTATGT	0.582																																					p.L174P		Atlas-SNP	.											.	TMEM176A	35	.	0			c.T521C						PASS	.						53	51	52					7																	150500886		2203	4300	6503	SO:0001583	missense	55365	exon5			GAAGGCTACACCT	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.521T>C	chr7.hg19:g.150500886T>C	ENSP00000417626:p.Leu174Pro	66.0	0.0	.		58.0	25.0	.	NM_018487	D3DX00|Q9NYC7	Missense_Mutation	SNP	ENST00000484928.1	hg19	CCDS5909.1	.	.	.	.	.	.	.	.	.	.	T	11.79	1.743811	0.30865	.	.	ENSG00000002933	ENST00000484928;ENST00000004103;ENST00000461345;ENST00000475536;ENST00000468689	T;T;T;T;T	0.24908	4.37;4.37;4.37;4.37;1.83	3.33	-6.65	0.01795	.	2.443990	0.01405	N	0.013769	T	0.38268	0.1034	L	0.47716	1.5	0.21020	N	0.999808	D	0.65815	0.995	P	0.61658	0.892	T	0.53732	-0.8397	10	0.37606	T	0.19	-16.8622	11.8227	0.52247	0.8007:0.0:0.0:0.1993	.	174	Q96HP8	T176A_HUMAN	P	174;174;115;126;115	ENSP00000417626:L174P;ENSP00000004103:L174P;ENSP00000420818:L115P;ENSP00000417834:L126P;ENSP00000420081:L115P	ENSP00000004103:L174P	L	+	2	0	TMEM176A	150131819	0.000000	0.05858	0.001000	0.08648	0.230000	0.25150	-0.970000	0.03810	-1.688000	0.01435	0.374000	0.22700	CTA	.	.	.	none		0.582	TMEM176A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350222.1	NM_018487		C	150500886	T	C	150500886	3	2	3	1	0	0	0	0	1	0	0	0	16104	1522	53	3	535	3	TMEM176A	7	150500886	Missense_Mutation	SNP	T	TCGA-2Z-A9J2-01A-11D-A382-10	1788859	150500886	8637777	45	211											
NUDT18	79873	hgsc.bcm.edu	37	chr8	21966703	21966708	+	Splice_Site	DEL	CGCACG	CGCACG	-																															gcacacgttcttccgcagccCgcacggggcgccggcggctc																								rs58343576		TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	CGCACG	CGCACG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr8:21966703_21966708delCGCACG	ENST00000309188.6	-	2	223_228	c.105_110delCGTGCG	c.(103-111)cccgtgcgg>ccg	p.VR36del	NUDT18_ENST00000522405.1_5'UTR|NUDT18_ENST00000521807.2_In_Frame_Del_p.RA36del	NM_024815.3	NP_079091.3	Q6ZVK8	NUD18_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 18	36					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)		TTCCGCAGCCCGCAcggggcgccggc	0.782																																					p.36_37del		Pindel	.											.	NUDT18	13	.	0			c.106_110del						PASS	.																																			SO:0001630	splice_region_variant	79873	exon2			.		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.102+3CGTGCG>-	chr8.hg19:g.21966703_21966708delCGCACG		5.0	0.0	.		13.0	10.0	0.769	NM_024815	Q8IZ75|Q9H687	Frame_Shift_Del	DEL	ENST00000309188.6	hg19																																																																																				.	.	.	none		0.782	NUDT18-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_024815	In_Frame_Del	-	21966708	CGCACG	-	21966703	8	5	3	1	0	1	0	1	0	0	1	0	10742	639	23	0	874	0	NUDT18	8	21966703	Splice_Site	DEL	CGCACG	TCGA-2Z-A9J2-01A-11D-A382-10		21966703	124397319	46	212											
KIF13B	23303	hgsc.bcm.edu	37	chr8	29024953	29024953	+	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	cggagatcccggataattcgGgcattagggtcctcattcac	9	10	11	11	3	2	1	2	0	0	1	5	3	4	2	2	4	0	1	2	4	2	4			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr8:29024953G>T	ENST00000524189.1	-	11	1133	c.1095C>A	c.(1093-1095)gcC>gcA	p.A365A	KIF13B_ENST00000521515.1_Silent_p.A365A	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	365					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)		GGATAATTCGGGCATTAGGGT	0.547																																					p.A365A		Atlas-SNP	.											.	KIF13B	192	.	0			c.C1095A						PASS	.						62	60	61					8																	29024953		1950	4157	6107	SO:0001819	synonymous_variant	23303	exon11			AATTCGGGCATTA	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.1095C>A	chr8.hg19:g.29024953G>T		62.0	0.0	.		97.0	14.0	.	NM_015254	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Silent	SNP	ENST00000524189.1	hg19	CCDS55217.1																																																																																			.	.	.	none		0.547	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1			T	29024953	G	T	29024953	2	4	3	1	0	0	0	0	0	0	0	1	8282	1219	43	4		4	KIF13B	8	29024953	Silent	SNP	G	TCGA-2Z-A9J2-01A-11D-A382-10	7058250	29024953	117339069	47	213											
MYST3	7994	hgsc.bcm.edu	37	chr8	41906305	41906305	+	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	aggaattgagtcctttatttGagacttttaaaattgttcca	12	17	7	5	0	0	2	0	2	0	1	2	4	2	3	2	1	0	1	2	1	4	8			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr8:41906305G>T	ENST00000396930.3	-	3	734	c.191C>A	c.(190-192)tCa>tAa	p.S64*	KAT6A_ENST00000265713.2_Nonsense_Mutation_p.S64*|KAT6A_ENST00000485568.1_Nonsense_Mutation_p.S64*|KAT6A_ENST00000406337.1_Nonsense_Mutation_p.S64*	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	64	Required for activation of RUNX1-1.|Required for nuclear localization.				aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										TCCTTTATTTGAGACTTTTAA	0.368																																					p.S64X		Atlas-SNP	.											.	.	.	.	0			c.C191A						PASS	.						171	168	169					8																	41906305		2203	4300	6503	SO:0001587	stop_gained	7994	exon3			TTATTTGAGACTT	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.191C>A	chr8.hg19:g.41906305G>T	ENSP00000380136:p.Ser64*	105.0	0.0	.		116.0	27.0	.	NM_001099412	Q76L81	Nonsense_Mutation	SNP	ENST00000396930.3	hg19	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	G	40	8.032524	0.98619	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930;ENST00000485568	.	.	.	5.66	5.66	0.87406	.	0.106722	0.42172	D	0.000758	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	-13.388	19.7395	0.96220	0.0:0.0:1.0:0.0	.	.	.	.	X	64	.	ENSP00000265713:S64X	S	-	2	0	KAT6A	42025462	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.335000	0.96500	2.669000	0.90835	0.655000	0.94253	TCA	.	.	.	none		0.368	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		T	41906305	G	T	41906305	4	4	3	1	0	0	0	0	0	1	0	0	10111	1294	45	4	5887	4	MYST3	8	41906305	Nonsense_Mutation	SNP	G	TCGA-2Z-A9J2-01A-11D-A382-10	12881352	41906305	104457717	48	214											
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77776082	77776082	+	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	gtactgctacagaaagcacaAaagaagaaccccagttagaa	19	5	8	9	0	0	4	0	0	0	4	0	4	0	4	2	0	5	4	2	0	9	3			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr8:77776082A>T	ENST00000521891.2	+	11	10580	c.10132A>T	c.(10132-10134)Aaa>Taa	p.K3378*	ZFHX4_ENST00000455469.2_Nonsense_Mutation_p.K3333*|ZFHX4_ENST00000050961.6_Nonsense_Mutation_p.K3329*|ZFHX4_ENST00000518282.1_Nonsense_Mutation_p.K3352*	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	3329					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)			AGAAAGCACAAAAGAAGAACC	0.408										HNSCC(33;0.089)																											p.K3378X		Atlas-SNP	.											.	ZFHX4	878	.	0			c.A10132T						PASS	.						31	29	30					8																	77776082		1849	4085	5934	SO:0001587	stop_gained	79776	exon11			AGCACAAAAGAAG		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.10132A>T	chr8.hg19:g.77776082A>T	ENSP00000430497:p.Lys3378*	37.0	0.0	.		63.0	11.0	.	NM_024721	G3V138|Q18PS0|Q6ZN20	Nonsense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	A	52	18.637453	0.99908	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	.	.	.	4.5	4.5	0.54988	.	0.000000	0.47455	U	0.000231	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.9762	0.64275	1.0:0.0:0.0:0.0	.	.	.	.	X	3378;3362;3333;3329;3352	.	ENSP00000050961:K3329X	K	+	1	0	ZFHX4	77938637	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.177000	0.77650	1.907000	0.55213	0.496000	0.49642	AAA	.	.	.	none		0.408	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77776082	A	T	77776082	4	4	3	1	0	0	0	0	0	1	0	0	17647	15	1	5	10170	5	ZFHX4	8	77776082	Nonsense_Mutation	SNP	A	TCGA-2Z-A9J2-01A-11D-A382-10	35869777	77776082	68587940	49	215											
RIMS2	9699	hgsc.bcm.edu	37	chr8	105257207	105257207	+	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	agaaacaggcctggccgtggAaatgaggaactggatgactc	13	6	14	8	1	0	3	0	2	0	1	1	6	0	6	2	5	2	0	2	5	3	0			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr8:105257207A>T	ENST00000436393.2	+	24	3693	c.3452A>T	c.(3451-3453)gAa>gTa	p.E1151V	RIMS2_ENST00000262231.10_Missense_Mutation_p.E972V|RIMS2_ENST00000507740.1_Missense_Mutation_p.E947V|RIMS2_ENST00000339750.2_Missense_Mutation_p.E69V|RIMS2_ENST00000406091.3_Missense_Mutation_p.E1133V			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	1195					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)			CTGGCCGTGGAAATGAGGAAC	0.468										HNSCC(12;0.0054)																											p.E1133V		Atlas-SNP	.											.	RIMS2	1357	.	0			c.A3398T						PASS	.						130	136	134					8																	105257207		2024	4187	6211	SO:0001583	missense	9699	exon20			CCGTGGAAATGAG	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.3452A>T	chr8.hg19:g.105257207A>T	ENSP00000390665:p.Glu1151Val	166.0	0.0	.		281.0	24.0	.	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	ENST00000436393.2	hg19		.	.	.	.	.	.	.	.	.	.	A	21.4	4.140378	0.77775	.	.	ENSG00000176406	ENST00000329869;ENST00000406091;ENST00000402998;ENST00000262231;ENST00000507740;ENST00000408894;ENST00000436393;ENST00000523362;ENST00000339750	T;T;T;T;T;T;T	0.25250	2.39;2.1;2.13;2.01;2.49;1.83;1.81	5.05	5.05	0.67936	.	.	.	.	.	T	0.47002	0.1422	L	0.58510	1.815	0.80722	D	1	D;D;D;P;P	0.63880	0.993;0.993;0.984;0.939;0.939	D;D;D;P;P	0.72338	0.977;0.977;0.946;0.58;0.58	T	0.44390	-0.9331	9	0.59425	D	0.04	.	14.9548	0.71104	1.0:0.0:0.0:0.0	.	1195;1151;972;947;1133	Q9UQ26;D6RA03;Q9UQ26-1;Q9UQ26-3;F8WD47	RIMS2_HUMAN;.;.;.;.	V	1170;1133;1195;972;947;1140;1151;69;69	ENSP00000384892:E1133V;ENSP00000262231:E972V;ENSP00000423559:E947V;ENSP00000386228:E1140V;ENSP00000390665:E1151V;ENSP00000428478:E69V;ENSP00000342051:E69V	ENSP00000262231:E972V	E	+	2	0	RIMS2	105326383	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.116000	0.77119	2.119000	0.64992	0.528000	0.53228	GAA	.	.	.	none		0.468	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117		T	105257207	A	T	105257207	3	4	3	1	0	0	0	0	1	0	0	0	13381	246	9	5	3672	5	RIMS2	8	105257207	Missense_Mutation	SNP	A	TCGA-2Z-A9J2-01A-11D-A382-10	27481125	105257207	41106815	50	216											
C9orf72	203228	hgsc.bcm.edu	37	chr9	27566893	27566893	+	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	tacatctatagcaccactctCtgcatttcgaaggatttctc	10	14	5	12	1	3	0	0	0	3	0	6	2	3	1	1	1	3	2	1	1	4	5			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr9:27566893C>T	ENST00000380003.3	-	2	289	c.226G>A	c.(226-228)Gag>Aag	p.E76K	C9orf72_ENST00000379997.3_Missense_Mutation_p.E76K|C9orf72_ENST00000488117.1_5'UTR	NM_001256054.1|NM_018325.3	NP_001242983.1|NP_060795.1	Q96LT7	CI072_HUMAN	chromosome 9 open reading frame 72	76					autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|extracellular space (GO:0005615)|lysosome (GO:0005764)|nucleus (GO:0005634)	Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|ovary(4)|pancreas(1)	23		all_neural(11;7.57e-10)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.00016)		GCACCACTCTCTGCATTTCGA	0.403																																					p.E76K		Atlas-SNP	.											.	C9orf72	48	.	0			c.G226A						PASS	.						101	96	98					9																	27566893		2203	4300	6503	SO:0001583	missense	203228	exon2			CACTCTCTGCATT	AL832467	CCDS6522.1, CCDS6523.1	9p21.1	2014-09-17			ENSG00000147894	ENSG00000147894			28337	protein-coding gene	gene with protein product		614260				21944778, 24549040	Standard	NM_145005		Approved	MGC23980	uc003zqq.3	Q96LT7	OTTHUMG00000019716	ENST00000380003.3:c.226G>A	chr9.hg19:g.27566893C>T	ENSP00000369339:p.Glu76Lys	97.0	0.0	.		114.0	37.0	.	NM_018325	A8K5W0|D3DRK6|G8I0B6|Q6NUS9	Missense_Mutation	SNP	ENST00000380003.3	hg19	CCDS6522.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.026734	0.93518	.	.	ENSG00000147894	ENST00000380003;ENST00000379997;ENST00000379995	T;T;T	0.44083	0.93;0.93;0.93	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	T	0.52645	0.1747	N	0.24115	0.695	0.80722	D	1	D;P	0.67145	0.996;0.952	D;P	0.73708	0.981;0.641	T	0.42816	-0.9429	9	.	.	.	.	20.4777	0.99188	0.0:1.0:0.0:0.0	.	76;76	Q96LT7-2;Q96LT7	.;CI072_HUMAN	K	76	ENSP00000369339:E76K;ENSP00000369333:E76K;ENSP00000369331:E76K	.	E	-	1	0	C9orf72	27556893	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.487000	0.81328	2.840000	0.97914	0.655000	0.94253	GAG	.	.	.	none		0.403	C9orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051969.1	NM_018325		T	27566893	C	T	27566893	3	4	3	1	0	0	0	0	1	0	0	0	2497	922	32	2	1263	2	C9orf72	9	27566893	Missense_Mutation	SNP	C	TCGA-2Z-A9J2-01A-11D-A382-10		27566893	113646538	51	217											
TMEM2	23670	hgsc.bcm.edu	37	chr9	74345097	74345097	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcccagattgtggaacaaagTattcctctgttcaataccat	12	13	6	10	0	2	1	1	0	1	1	4	2	4	2	3	1	2	2	3	1	5	5			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr9:74345097T>C	ENST00000377044.4	-	9	2385	c.1846A>G	c.(1846-1848)Act>Gct	p.T616A	TMEM2_ENST00000377066.5_Missense_Mutation_p.T553A	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	616					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)		TGGAACAAAGTATTCCTCTGT	0.423																																					p.T616A		Atlas-SNP	.											.	TMEM2	112	.	0			c.A1846G						PASS	.						124	117	119					9																	74345097		2203	4300	6503	SO:0001583	missense	23670	exon9			ACAAAGTATTCCT		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.1846A>G	chr9.hg19:g.74345097T>C	ENSP00000366243:p.Thr616Ala	140.0	0.0	.		129.0	28.0	.	NM_013390	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Missense_Mutation	SNP	ENST00000377044.4	hg19	CCDS6638.1	.	.	.	.	.	.	.	.	.	.	T	17.81	3.481878	0.63849	.	.	ENSG00000135048	ENST00000377044;ENST00000377066	T;T	0.58652	0.32;0.32	5.63	5.63	0.86233	Pectin lyase fold/virulence factor (1);	0.295695	0.41294	D	0.000910	T	0.60287	0.2257	M	0.78456	2.415	0.80722	D	1	B;B	0.28178	0.061;0.202	B;B	0.28232	0.04;0.087	T	0.58763	-0.7579	10	0.29301	T	0.29	.	15.8301	0.78743	0.0:0.0:0.0:1.0	.	616;553	Q9UHN6;Q9UHN6-2	TMEM2_HUMAN;.	A	616;553	ENSP00000366243:T616A;ENSP00000366266:T553A	ENSP00000366243:T616A	T	-	1	0	TMEM2	73534917	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.579000	0.82511	2.140000	0.66376	0.477000	0.44152	ACT	.	.	.	none		0.423	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390		C	74345097	T	C	74345097	3	2	3	1	0	0	0	0	1	0	0	0	16133	1638	57	3	2369	3	TMEM2	9	74345097	Missense_Mutation	SNP	T	TCGA-2Z-A9J2-01A-11D-A382-10	46778204	74345097	66868334	52	218											
PHF2	5253	hgsc.bcm.edu	37	chr9	96421819	96421819	+	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	gcagagcatgaggacgagctCccggagcacttcaaaccttc	11	6	11	13	2	1	2	1	1	0	1	3	5	2	4	2	2	4	4	2	2	1	2			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr9:96421819C>T	ENST00000359246.4	+	11	1633	c.1266C>T	c.(1264-1266)ctC>ctT	p.L422L	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	422					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)		AGGACGAGCTCCCGGAGCACT	0.612																																					p.L422L		Atlas-SNP	.											.	PHF2	113	.	0			c.C1266T						PASS	.						61	56	58					9																	96421819		2203	4300	6503	SO:0001819	synonymous_variant	5253	exon11			CGAGCTCCCGGAG	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.1266C>T	chr9.hg19:g.96421819C>T		248.0	0.0	.		159.0	47.0	.	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Silent	SNP	ENST00000359246.4	hg19	CCDS35069.1																																																																																			.	.	.	none		0.612	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392		T	96421819	C	T	96421819	2	4	3	1	0	0	0	0	0	0	0	1	11837	842	30	2		2	PHF2	9	96421819	Silent	SNP	C	TCGA-2Z-A9J2-01A-11D-A382-10	22076722	96421819	44791612	53	219											
CUBN	8029	hgsc.bcm.edu	37	chr10	17110184	17110184	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caggtgattaggttggactaAtatatgccaagtacagttga	13	12	11	5	0	0	2	0	2	0	0	0	3	0	3	1	3	2	3	1	3	6	7			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr10:17110184A>G	ENST00000377833.4	-	21	2952	c.2887T>C	c.(2887-2889)Tta>Cta	p.L963L		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	963	CUB 5. {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)	GGTTGGACTAATATATGCCAA	0.398																																					p.L963L		Atlas-SNP	.											.	CUBN	515	.	0			c.T2887C						PASS	.						165	157	160					10																	17110184		2203	4300	6503	SO:0001819	synonymous_variant	8029	exon21			GGACTAATATATG	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.2887T>C	chr10.hg19:g.17110184A>G		100.0	0.0	.		138.0	52.0	.	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	hg19	CCDS7113.1																																																																																			.	.	.	none		0.398	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		G	17110184	A	G	17110184	2	3	3	1	0	0	0	0	0	0	0	1	4053	98	4	3		3	CUBN	10	17110184	Silent	SNP	A	TCGA-2Z-A9J2-01A-11D-A382-10		17110184	118424563	54	220											
PTPLA	9200	hgsc.bcm.edu	37	chr10	17659300	17659301	+	Frame_Shift_Ins	INS	-	-	CCGCTGC																															cccagcctgcagcccgagagINSccgctgcccgctgccgccgc																										TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr10:17659300_17659301insCCGCTGC	ENST00000361271.3	-	1	75_76	c.38_39insGCAGCGG	c.(37-39)ggcfs	p.-13fs	PTPLA_ENST00000326961.6_Frame_Shift_Ins_p.-13fs	NM_014241.3	NP_055056.3	B0YJ81	HACD1_HUMAN	protein tyrosine phosphatase-like (proline instead of catalytic arginine), member A						fatty acid biosynthetic process (GO:0006633)|multicellular organismal development (GO:0007275)|myotube differentiation (GO:0014902)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|skin(1)	13						CAGCCCGAGAGCCGCTGCCCGC	0.762																																					p.G13fs		Pindel	.											.	PTPLA	34	.	0			c.39_40insGCAGCGG						PASS	.																																			SO:0001589	frameshift_variant	9200	exon1			.	AF114494	CCDS7121.1	10p14-p13	2008-08-01	2005-11-11		ENSG00000165996	ENSG00000165996			9639	protein-coding gene	gene with protein product	"cementum attachment protein"	610467	"protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a"			10644438	Standard	XM_005252641		Approved	CAP	uc001ipg.3	B0YJ81	OTTHUMG00000017750	ENST00000361271.3:c.32_38dupGCAGCGG	chr10.hg19:g.17659301_17659307dupCCGCTGC	ENSP00000355308:p.Gly13fs	50.0	0.0	.		38.0	10.0	0.263	NM_014241	B0YJ80|Q6JIC5|Q96FW7|Q9HB93|Q9UHX2	Frame_Shift_Ins	INS	ENST00000361271.3	hg19	CCDS7121.1																																																																																			.	.	.	none		0.762	PTPLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047046.1	NM_014241		CCGCTGC	17659301	-	CCGCTGC	17659300	7	5	3	1	0	1	1	0	0	0	0	0	12785	958	34	0	855	0	PTPLA	10	17659300	Frame_Shift_Ins	INS	-	TCGA-2Z-A9J2-01A-11D-A382-10	549116	17659300	117875447	55	221											
C10orf137	26098	hgsc.bcm.edu	37	chr10	127411636	127411636	+	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	gtccttttttctctttggtaGctttggcatggcatatgact	5	19	9	8	0	1	1	0	1	1	0	3	1	2	1	1	3	1	4	1	3	2	7			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr10:127411636G>T	ENST00000356792.4	+	3	549		c.e3-1		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)				CTCTTTGGTAGCTTTGGCATG	0.373																																					.		Atlas-SNP	.											.	C10orf137	153	.	0			c.318-1G>T						PASS	.						359	325	337					10																	127411636		2203	4300	6503	SO:0001630	splice_region_variant	26098	exon3			TTGGTAGCTTTGG																												ENST00000356792.4:c.318-1G>T	chr10.hg19:g.127411636G>T		107.0	0.0	.		93.0	6.0	.	NM_001202438	B2RC65|Q3KR40|Q4G190|Q5VZQ4|Q8IZ74|Q9Y3W4	Splice_Site	SNP	ENST00000356792.4	hg19	CCDS55733.1	.	.	.	.	.	.	.	.	.	.	G	18.57	3.652557	0.67472	.	.	ENSG00000107938	ENST00000356792;ENST00000392732;ENST00000337623	.	.	.	5.7	5.7	0.88788	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8405	0.96681	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C10orf137	127401626	1.000000	0.71417	0.681000	0.30009	0.712000	0.41017	9.094000	0.94168	2.692000	0.91855	0.655000	0.94253	.	.	.	.	none		0.373	C10orf137-007	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388539.1		Intron	T	127411636	G	T	127411636	5	4	3	1	0	0	0	0	0	0	1	0	1596	985	34	4	327	4	C10orf137	10	127411636	Splice_Site	SNP	G	TCGA-2Z-A9J2-01A-11D-A382-10	109752336	127411636	8123111	56	222											
OR51Q1	390061	hgsc.bcm.edu	37	chr11	5443619	5443619	+	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	gtccaccagcgcatgtatctGtttctctccatgctggccct	5	13	8	15	1	2	0	0	0	2	0	5	0	4	0	4	1	2	4	4	1	1	2			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr11:5443619G>T	ENST00000300778.4	+	1	279	c.189G>T	c.(187-189)ctG>ctT	p.L63L	AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron	NM_001004757.2	NP_001004757.1	Q8NH59	O51Q1_HUMAN	olfactory receptor, family 51, subfamily Q, member 1 (gene/pseudogene)	63						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(3)|liver(2)|lung(21)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	37		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.18e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GCATGTATCTGTTTCTCTCCA	0.552																																					p.L63L		Atlas-SNP	.											.	OR51Q1	79	.	0			c.G189T						PASS	.						268	231	243					11																	5443619		2201	4297	6498	SO:0001819	synonymous_variant	390061	exon1			GTATCTGTTTCTC	AB065531	CCDS31381.1	11p15.4	2013-10-10	2013-10-10		ENSG00000167360	ENSG00000167360		"GPCR / Class A : Olfactory receptors"	14851	protein-coding gene	gene with protein product			"olfactory receptor, family 51, subfamily Q, member 1"				Standard	NM_001004757		Approved		uc010qzd.2	Q8NH59	OTTHUMG00000066896	ENST00000300778.4:c.189G>T	chr11.hg19:g.5443619G>T		60.0	0.0	.		77.0	8.0	.	NM_001004757	B2RNN1	Silent	SNP	ENST00000300778.4	hg19	CCDS31381.1																																																																																			.	.	.	none		0.552	OR51Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143373.1	NM_001004757		T	5443619	G	T	5443619	2	4	3	1	0	0	0	0	0	0	0	1	11111	1364	48	4		4	OR51Q1	11	5443619	Silent	SNP	G	TCGA-2Z-A9J2-01A-11D-A382-10		5443619	129562897	57	223											
NLRP10	338322	hgsc.bcm.edu	37	chr11	7982378	7982378	+	Missense_Mutation	SNP	T	T	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	caaacccctcttcttcaactTttcttcaaagggcctctgca	9	13	4	15	0	6	0	2	0	4	0	6	0	6	0	3	1	3	1	3	1	3	5			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr11:7982378T>G	ENST00000328600.2	-	2	942	c.781A>C	c.(781-783)Aag>Cag	p.K261Q		NM_176821.3	NP_789791.1	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	261	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)		TTCTTCAACTTTTCTTCAAAG	0.552																																					p.K261Q		Atlas-SNP	.											.	NLRP10	146	.	0			c.A781C						PASS	.						65	66	66					11																	7982378		2201	4296	6497	SO:0001583	missense	338322	exon2			TCAACTTTTCTTC	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.781A>C	chr11.hg19:g.7982378T>G	ENSP00000327763:p.Lys261Gln	73.0	0.0	.		66.0	23.0	.	NM_176821	Q2M3C4|Q6JGT0	Missense_Mutation	SNP	ENST00000328600.2	hg19	CCDS7784.1	.	.	.	.	.	.	.	.	.	.	T	2.103	-0.405652	0.04832	.	.	ENSG00000182261	ENST00000328600	T	0.79247	-1.25	4.68	-9.36	0.00629	NACHT nucleoside triphosphatase (1);	1.973700	0.03508	N	0.219126	T	0.43366	0.1244	N	0.02315	-0.6	0.09310	N	1	B	0.11235	0.004	B	0.18263	0.021	T	0.42120	-0.9470	10	0.12430	T	0.62	.	2.4824	0.04590	0.0922:0.362:0.2663:0.2796	.	261	Q86W26	NAL10_HUMAN	Q	261	ENSP00000327763:K261Q	ENSP00000327763:K261Q	K	-	1	0	NLRP10	7938954	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.595000	0.05727	-1.919000	0.01071	-1.137000	0.01932	AAG	.	.	.	none		0.552	NLRP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385705.1	NM_176821		G	7982378	T	G	7982378	3	3	3	1	0	0	0	0	1	0	0	0	10479	1850	64	5	1190	5	NLRP10	11	7982378	Missense_Mutation	SNP	T	TCGA-2Z-A9J2-01A-11D-A382-10	2538759	7982378	127024138	58	224											
OR4C11	219429	hgsc.bcm.edu	37	chr11	55371658	55371658	+	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	aagcaagaatctgcaaaggaCaaataaaatagaaagaagta	24	5	8	4	0	1	3	0	0	1	3	1	4	1	4	0	1	2	3	0	1	11	3			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr11:55371658C>T	ENST00000302231.4	-	1	216	c.192G>A	c.(190-192)ttG>ttA	p.L64L		NM_001004700.2	NP_001004700.2	Q6IEV9	OR4CB_HUMAN	olfactory receptor, family 4, subfamily C, member 11	64						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|prostate(1)|skin(1)	33						CTGCAAAGGACAAATAAAATA	0.403																																					p.L64L		Atlas-SNP	.											.	OR4C11	73	.	0			c.G192A						PASS	.						78	75	76					11																	55371658		2178	3997	6175	SO:0001819	synonymous_variant	219429	exon1			AAAGGACAAATAA	AB065774	CCDS31503.1	11q11	2012-08-09		2004-03-10	ENSG00000172188	ENSG00000172188		"GPCR / Class A : Olfactory receptors"	15167	protein-coding gene	gene with protein product				OR4C11P			Standard	NM_001004700		Approved		uc010rii.2	Q6IEV9	OTTHUMG00000165290	ENST00000302231.4:c.192G>A	chr11.hg19:g.55371658C>T		30.0	0.0	.		43.0	28.0	.	NM_001004700	B9EIL4|Q8NGL8	Silent	SNP	ENST00000302231.4	hg19	CCDS31503.1																																																																																			.	.	.	none		0.403	OR4C11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383268.1	NM_001004700		T	55371658	C	T	55371658	2	4	3	1	0	0	0	0	0	0	0	1	11052	477	17	2		2	OR4C11	11	55371658	Silent	SNP	C	TCGA-2Z-A9J2-01A-11D-A382-10	47389280	55371658	79634858	59	225											
CD5	921	hgsc.bcm.edu	37	chr11	60891376	60891376	+	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	tccgccagaagaagcagcgcCagtggattggcccaacggga	11	4	14	12	3	0	2	0	0	0	2	1	4	1	4	4	3	3	1	4	3	3	1			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr11:60891376C>T	ENST00000347785.3	+	8	1412	c.1246C>T	c.(1246-1248)Cag>Tag	p.Q416*		NM_014207.3	NP_055022.2	P06127	CD5_HUMAN	CD5 molecule	416					apoptotic signaling pathway (GO:0097190)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|T cell costimulation (GO:0031295)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_lung(304;5.94e-05)|Lung NSC(402;7.26e-05)		BRCA - Breast invasive adenocarcinoma(625;0.000946)|Lung(977;0.0086)|LUSC - Lung squamous cell carcinoma(625;0.0528)		GAAGCAGCGCCAGTGGATTGG	0.632																																					p.Q416X		Atlas-SNP	.											.	CD5	52	.	0			c.C1246T						PASS	.						77	68	71					11																	60891376		2203	4299	6502	SO:0001587	stop_gained	921	exon8			CAGCGCCAGTGGA	X04391	CCDS8000.1	11q13	2008-07-18	2006-03-28		ENSG00000110448	ENSG00000110448		"CD molecules"	1685	protein-coding gene	gene with protein product		153340	"CD5 antigen (p56-62)"	LEU1		1711157	Standard	NM_014207		Approved	T1	uc009ynk.3	P06127	OTTHUMG00000167825	ENST00000347785.3:c.1246C>T	chr11.hg19:g.60891376C>T	ENSP00000342681:p.Gln416*	42.0	0.0	.		30.0	12.0	.	NM_014207	A0N0P4|A8K9I3	Nonsense_Mutation	SNP	ENST00000347785.3	hg19	CCDS8000.1	.	.	.	.	.	.	.	.	.	.	C	36	5.948840	0.97134	.	.	ENSG00000110448	ENST00000347785	.	.	.	4.32	4.32	0.51571	.	0.000000	0.44902	D	0.000408	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	-22.0462	15.0108	0.71547	0.0:1.0:0.0:0.0	.	.	.	.	X	416	.	ENSP00000342681:Q416X	Q	+	1	0	CD5	60647952	1.000000	0.71417	1.000000	0.80357	0.807000	0.45602	4.549000	0.60726	1.951000	0.56629	0.313000	0.20887	CAG	.	.	.	none		0.632	CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396465.2	NM_014207		T	60891376	C	T	60891376	4	4	3	1	0	0	0	0	0	1	0	0	3023	595	21	2	1276	2	CD5	11	60891376	Nonsense_Mutation	SNP	C	TCGA-2Z-A9J2-01A-11D-A382-10	5519718	60891376	74115140	60	226											
MED17	9440	hgsc.bcm.edu	37	chr11	93535078	93535078	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcattggtcaaatatcaatgAtgtttatgaatctagtgtga	13	16	8	4	0	4	3	3	3	1	0	4	3	4	3	0	1	0	1	0	1	6	5			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr11:93535078A>G	ENST00000251871.3	+	9	1693	c.1406A>G	c.(1405-1407)gAt>gGt	p.D469G	RN7SL195P_ENST00000582088.1_RNA|MED17_ENST00000533367.1_3'UTR	NM_004268.4	NP_004259.3	Q9NVC6	MED17_HUMAN	mediator complex subunit 17	469					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)				AATATCAATGATGTTTATGAA	0.328																																					p.D469G		Atlas-SNP	.											.	MED17	37	.	0			c.A1406G						PASS	.						77	69	71					11																	93535078		2201	4298	6499	SO:0001583	missense	9440	exon9			TCAATGATGTTTA	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.1406A>G	chr11.hg19:g.93535078A>G	ENSP00000251871:p.Asp469Gly	190.0	0.0	.		207.0	18.0	.	NM_004268	B3KN07|Q9HA81|Q9UNP7|Q9Y2W0|Q9Y660	Missense_Mutation	SNP	ENST00000251871.3	hg19	CCDS8295.1	.	.	.	.	.	.	.	.	.	.	A	18.21	3.573152	0.65765	.	.	ENSG00000042429	ENST00000251871;ENST00000427225	T	0.55588	0.51	5.68	5.68	0.88126	.	0.044636	0.85682	D	0.000000	T	0.46073	0.1374	L	0.44542	1.39	0.80722	D	1	P	0.47762	0.9	B	0.38500	0.275	T	0.50074	-0.8870	10	0.49607	T	0.09	-26.9024	16.2164	0.82224	1.0:0.0:0.0:0.0	.	469	Q9NVC6	MED17_HUMAN	G	469;439	ENSP00000251871:D469G	ENSP00000251871:D469G	D	+	2	0	MED17	93174726	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.916000	0.92745	2.289000	0.77006	0.533000	0.62120	GAT	.	.	.	none		0.328	MED17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394800.2	NM_004268		G	93535078	A	G	93535078	3	3	3	1	0	0	0	0	1	0	0	0	9442	333	12	3	1440	3	MED17	11	93535078	Missense_Mutation	SNP	A	TCGA-2Z-A9J2-01A-11D-A382-10	32643702	93535078	41471438	61	227											
FOXM1	2305	hgsc.bcm.edu	37	chr12	2967807	2967812	+	In_Frame_Del	DEL	CTGTAG	CTGTAG	-																															ggggcaagggcagggctctaCtgtagctcaggaataaactg																										TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	CTGTAG	CTGTAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr12:2967807_2967812delCTGTAG	ENST00000359843.3	-	9	2352_2357	c.2284_2289delCTACAG	c.(2284-2289)ctacagdel	p.LQ762del	Y_RNA_ENST00000410561.1_RNA|AC005841.1_ENST00000382678.3_5'Flank|ITFG2_ENST00000545509.1_Intron|FOXM1_ENST00000342628.2_In_Frame_Del_p.LQ800del|FOXM1_ENST00000361953.3_In_Frame_Del_p.LQ747del	NM_021953.3	NP_068772.2	Q08050	FOXM1_HUMAN	forkhead box M1	762					cell cycle (GO:0007049)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|liver development (GO:0001889)|mitotic cell cycle (GO:0000278)|negative regulation of cell aging (GO:0090344)|negative regulation of stress-activated MAPK cascade (GO:0032873)|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 double-strand break repair (GO:2000781)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle (GO:0051726)|regulation of cell cycle arrest (GO:0071156)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of Ras protein signal transduction (GO:0046578)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein kinase binding (GO:0019901)|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)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|skin(1)|urinary_tract(3)	24			OV - Ovarian serous cystadenocarcinoma(31;0.000622)			CAGGGCTCTACTGTAGCTCAGGAATA	0.597																																					p.800_802del		Atlas-Indel,Pindel	.											.	FOXM1	62	.	0			c.2399_2404del						PASS	.																																			SO:0001651	inframe_deletion	2305	exon10			.	Y12773	CCDS8515.1, CCDS8516.1, CCDS8517.1	12p13	2007-09-18			ENSG00000111206	ENSG00000111206		"Forkhead boxes"	3818	protein-coding gene	gene with protein product	"M-phase phosphoprotein 2"	602341		FKHL16		9032290, 9441747	Standard	NM_202002		Approved	HFH-11, trident, HNF-3, INS-1, MPP2, MPHOSPH2, TGT3	uc001qlf.3	Q08050	OTTHUMG00000168118	ENST00000359843.3:c.2284_2289delCTACAG	chr12.hg19:g.2967807_2967812delCTGTAG	ENSP00000352901:p.Leu762_Gln763del	39.0	0.0	0		44.0	17.0	0.386364	NM_202002	O43258|O43259|O43260|Q4ZGG7|Q9BRL2	In_Frame_Del	DEL	ENST00000359843.3	hg19	CCDS8515.1																																																																																			.	.	.	none		0.597	FOXM1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398272.1	NM_021953		-	2967812	CTGTAG	-	2967807	7	5	3	1	0	1	0	1	0	0	0	0	6025	564	20	0	6	0	FOXM1	12	2967807	In_Frame_Del	DEL	CTGTAG	TCGA-2Z-A9J2-01A-11D-A382-10		2967807	130884088	62	228											
KCNA5	3741	hgsc.bcm.edu	37	chr12	5154784	5154784	+	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	gggacatgaggcccatcactGttgggggcaagatcgtgggc	8	7	17	9	1	1	2	1	1	0	1	2	3	1	3	1	5	0	2	1	5	1	1			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr12:5154784G>T	ENST00000252321.3	+	1	1700	c.1471G>T	c.(1471-1473)Gtt>Ttt	p.V491F		NM_002234.3	NP_002225.2	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 5	491					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)	GCCCATCACTGTTGGGGGCAA	0.592																																					p.V491F		Atlas-SNP	.											.	KCNA5	138	.	0			c.G1471T						PASS	.						120	110	114					12																	5154784		2203	4300	6503	SO:0001583	missense	3741	exon1			ATCACTGTTGGGG	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.1471G>T	chr12.hg19:g.5154784G>T	ENSP00000252321:p.Val491Phe	112.0	0.0	.		90.0	18.0	.	NM_002234	Q4KKT8|Q4VAJ1|Q4VAJ2|Q9UDA4	Missense_Mutation	SNP	ENST00000252321.3	hg19	CCDS8536.1	.	.	.	.	.	.	.	.	.	.	G	11.06	1.527624	0.27299	.	.	ENSG00000130037	ENST00000252321	D	0.97553	-4.43	4.87	3.99	0.46301	Ion transport (1);	0.000000	0.64402	D	0.000002	D	0.95749	0.8617	L	0.54323	1.7	0.38272	D	0.942173	B	0.27997	0.197	B	0.36464	0.225	D	0.95565	0.8633	10	0.62326	D	0.03	.	12.4131	0.55478	0.0804:0.0:0.9196:0.0	.	491	P22460	KCNA5_HUMAN	F	491	ENSP00000252321:V491F	ENSP00000252321:V491F	V	+	1	0	KCNA5	5025045	0.998000	0.40836	0.069000	0.20011	0.781000	0.44180	2.520000	0.45554	1.292000	0.44672	0.561000	0.74099	GTT	.	.	.	none		0.592	KCNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398925.2	NM_002234		T	5154784	G	T	5154784	3	4	3	1	0	0	0	0	1	0	0	0	8013	1377	48	4	1473	4	KCNA5	12	5154784	Missense_Mutation	SNP	G	TCGA-2Z-A9J2-01A-11D-A382-10	2186977	5154784	128697111	63	229											
KCNH3	23416	hgsc.bcm.edu	37	chr12	49942732	49942732	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccctactacctggtgggccGgaggccagctggagggaaca	8	6	15	12	1	0	0	0	0	0	0	1	3	1	3	4	6	4	1	4	6	3	2	rs574111580	byFrequency	TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr12:49942732G>A	ENST00000257981.6	+	8	1504	c.1244G>A	c.(1243-1245)cGg>cAg	p.R415Q		NM_012284.1	NP_036416.1	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 3	415					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36						CTGGTGGGCCGGAGGCCAGCT	0.701													G|||	2	0.000399361	0	0	5008	,	,		15321	0.002		0	False		,,,				2504	0				p.R415Q		Atlas-SNP	.											.	KCNH3	88	.	0			c.G1244A						PASS	.						12	15	14					12																	49942732		2194	4291	6485	SO:0001583	missense	23416	exon8			TGGGCCGGAGGCC	AB022696	CCDS8786.1	12q13	2012-07-05				ENSG00000135519		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6252	protein-coding gene	gene with protein product		604527				10455180, 16382104	Standard	NM_012284		Approved	Kv12.2, BEC1, elk2	uc001ruh.1	Q9ULD8	OTTHUMG00000169517	ENST00000257981.6:c.1244G>A	chr12.hg19:g.49942732G>A	ENSP00000257981:p.Arg415Gln	99.0	0.0	.		87.0	22.0	.	NM_012284	Q9UQ06	Missense_Mutation	SNP	ENST00000257981.6	hg19	CCDS8786.1	.	.	.	.	.	.	.	.	.	.	G	12.92	2.082658	0.36758	.	.	ENSG00000135519	ENST00000257981	D	0.98633	-5.04	4.53	0.652	0.17823	Ion transport (1);	0.609308	0.13925	N	0.353267	D	0.95014	0.8386	L	0.32530	0.975	0.21147	N	0.999771	B	0.02656	0.0	B	0.04013	0.001	D	0.87894	0.2686	10	0.18276	T	0.48	.	6.7337	0.23397	0.3979:0.0:0.6021:0.0	.	415	Q9ULD8	KCNH3_HUMAN	Q	415	ENSP00000257981:R415Q	ENSP00000257981:R415Q	R	+	2	0	KCNH3	48228999	0.005000	0.15991	0.164000	0.22755	0.642000	0.38348	-0.270000	0.08584	0.025000	0.15241	-0.140000	0.14226	CGG	.	.	.	none		0.701	KCNH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404571.2	NM_012284		A	49942732	G	A	49942732	3	1	3	1	0	0	0	0	1	0	0	0	8040	1116	39	1	1274	1	KCNH3	12	49942732	Missense_Mutation	SNP	G	TCGA-2Z-A9J2-01A-11D-A382-10	44787948	49942732	83909163	64	230											
ANKRD52	283373	hgsc.bcm.edu	37	chr12	56646601	56646601	+	Frame_Shift_Del	DEL	G	G	-																															atgaagacaggtacggccaaGgttgtcaggtgtattgatgt																										TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr12:56646601delG	ENST00000267116.7	-	12	1385	c.1264delC	c.(1264-1266)cttfs	p.L422fs		NM_173595.3	NP_775866.2	Q8NB46	ANR52_HUMAN	ankyrin repeat domain 52	422										endometrium(9)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)|skin(1)	29						GTACGGCCAAGGTTGTCAGGT	0.532																																					p.L422fs		Atlas-Indel,Pindel	.											.	ANKRD52	81	.	0			c.1265delT						PASS	.						60	62	62					12																	56646601		2092	4249	6341	SO:0001589	frameshift_variant	283373	exon12			.	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.1264delC	chr12.hg19:g.56646601delG	ENSP00000267116:p.Leu422fs	80.0	0.0	0		74.0	20.0	0.27027	NM_173595	A6NE79|B1Q2K2	Frame_Shift_Del	DEL	ENST00000267116.7	hg19	CCDS44920.1																																																																																			.	.	.	none		0.532	ANKRD52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408539.1	NM_173595		-	56646601	G	-	56646601	7	5	3	1	0	1	0	1	0	0	0	0	678	1000	35	0	2034	0	ANKRD52	12	56646601	Frame_Shift_Del	DEL	G	TCGA-2Z-A9J2-01A-11D-A382-10	6703869	56646601	77205294	65	231											
KIAA1033	23325	hgsc.bcm.edu	37	chr12	105538550	105538550	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caatctaacaactgtagcccTtcatgactgggccacttata	12	11	6	12	0	2	1	1	1	1	0	2	1	2	1	2	1	3	1	2	1	6	5			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr12:105538550T>C	ENST00000332180.5	+	22	2321	c.2234T>C	c.(2233-2235)cTt>cCt	p.L745P		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						ACTGTAGCCCTTCATGACTGG	0.398																																					p.L745P		Atlas-SNP	.											.	KIAA1033	83	.	0			c.T2234C						PASS	.						113	106	108					12																	105538550		1901	4120	6021	SO:0001583	missense	23325	exon22			TAGCCCTTCATGA	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.2234T>C	chr12.hg19:g.105538550T>C	ENSP00000328062:p.Leu745Pro	75.0	0.0	.		91.0	48.0	.	NM_015275		Missense_Mutation	SNP	ENST00000332180.5	hg19	CCDS41826.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.549404	0.86127	.	.	ENSG00000136051	ENST00000332180	T	0.48201	0.82	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.62085	0.2399	L	0.54323	1.7	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.64042	0.921;0.921	T	0.60510	-0.7249	10	0.39692	T	0.17	.	15.9674	0.79985	0.0:0.0:0.0:1.0	.	746;745	B7ZKT9;Q2M389	.;WASH7_HUMAN	P	745	ENSP00000328062:L745P	ENSP00000328062:L745P	L	+	2	0	KIAA1033	104062680	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.994000	0.88315	2.170000	0.68504	0.477000	0.44152	CTT	.	.	.	none		0.398	KIAA1033-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406138.4	NM_015275		C	105538550	T	C	105538550	3	2	3	1	0	0	0	0	1	0	0	0	8213	1609	56	3	2320	3	KIAA1033	12	105538550	Missense_Mutation	SNP	T	TCGA-2Z-A9J2-01A-11D-A382-10	48891949	105538550	28313345	66	232											
SPATA13	221178	hgsc.bcm.edu	37	chr13	24797769	24797769	+	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	actggccaggtgcccgccgtGtgtgagattctcgtgaggga	6	9	16	10	3	1	2	0	2	1	1	2	4	1	3	3	3	1	0	3	3	0	1			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr13:24797769G>A	ENST00000382095.4	+	2	185				SPATA13_ENST00000424834.2_Silent_p.V234V|SPATA13_ENST00000382108.3_Silent_p.V234V|RP11-307N16.6_ENST00000382141.4_Silent_p.V234V	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)		TGCCCGCCGTGTGTGAGATTC	0.602																																					p.V234V		Atlas-SNP	.											.	SPATA13	92	.	0			c.G702A						PASS	.						52	52	52					13																	24797769		692	1591	2283	SO:0001627	intron_variant	221178	exon2			CGCCGTGTGTGAG	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.-222-25846G>A	chr13.hg19:g.24797769G>A		70.0	0.0	.		42.0	13.0	.	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Silent	SNP	ENST00000382095.4	hg19	CCDS9305.1	.	.	.	.	.	.	.	.	.	.	G	5.253	0.232192	0.09969	.	.	ENSG00000182957	ENST00000424834	.	.	.	4.5	-1.53	0.08611	.	1.228160	0.06596	N	0.752934	T	0.26919	0.0659	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.32079	-0.9920	6	0.54805	T	0.06	.	1.1339	0.01751	0.2807:0.3551:0.1824:0.1817	.	.	.	.	M	272	.	ENSP00000371576:V272M	V	+	1	0	SPATA13	23695769	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.066000	0.03454	-0.522000	0.06417	-0.702000	0.03669	GTG	.	.	.	none		0.602	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023		A	24797769	G	A	24797769	1	1	3	0	1	0	0	0	0	0	0	0	15012	1364	48	2		2	SPATA13	13	24797769	Intron	SNP	G	TCGA-2Z-A9J2-01A-11D-A382-10		24797769	90372109	67	233											
RTL1	388015	hgsc.bcm.edu	37	chr14	101347376	101347376	+	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	tgcgaggtgtcttgcaggccGtcatgcaggccacactgacg	7	8	14	12	3	2	1	1	1	1	0	2	2	2	1	2	3	3	2	2	3	0	1			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr14:101347376G>A	ENST00000534062.1	-	1	3808	c.3750C>T	c.(3748-3750)gaC>gaT	p.D1250D	MIR433_ENST00000384837.1_RNA|MIR127_ENST00000384876.1_RNA|MIR431_ENST00000385266.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	1250					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						CTTGCAGGCCGTCATGCAGGC	0.637																																					p.D1250D		Atlas-SNP	.											.	RTL1	120	.	0			c.C3750T						PASS	.						18	18	18					14																	101347376		1567	3579	5146	SO:0001819	synonymous_variant	388015	exon1			CAGGCCGTCATGC		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.3750C>T	chr14.hg19:g.101347376G>A		116.0	0.0	.		79.0	9.0	.	NM_001134888	E9PKS8	Silent	SNP	ENST00000534062.1	hg19	CCDS53910.1																																																																																			.	.	.	none		0.637	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888		A	101347376	G	A	101347376	2	1	3	1	0	0	0	0	0	0	0	1	13737	1136	40	1		1	RTL1	14	101347376	Silent	SNP	G	TCGA-2Z-A9J2-01A-11D-A382-10		101347376	6002164	68	234											
MTA1	9112	hgsc.bcm.edu	37	chr14	105927224	105927224	+	Frame_Shift_Del	DEL	G	G	-																															gaggagtggtctgcatcagaGgccaaccttttcgaggaagc																										TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr14:105927224delG	ENST00000331320.7	+	10	1090	c.876delG	c.(874-876)gagfs	p.E292fs	MTA1_ENST00000435036.2_5'Flank|MTA1_ENST00000406191.1_Frame_Shift_Del_p.E292fs|MTA1_ENST00000405646.1_Frame_Shift_Del_p.E275fs	NM_001203258.1|NM_004689.3	NP_001190187.1|NP_004680.2	Q13330	MTA1_HUMAN	metastasis associated 1	292	SANT. {ECO:0000255|PROSITE- ProRule:PRU00624}.				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)		CTGCATCAGAGGCCAACCTTT	0.572																																					p.E292fs		Atlas-Indel,Pindel	.											.	MTA1	61	.	0			c.875delA						PASS	.						104	104	104					14																	105927224		2203	4298	6501	SO:0001589	frameshift_variant	9112	exon10			.	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.876delG	chr14.hg19:g.105927224delG	ENSP00000333633:p.Glu292fs	166.0	0.0	0		96.0	38.0	0.395833	NM_004689	A5PLK4|Q86SW2|Q8NFI8|Q96GI8	Frame_Shift_Del	DEL	ENST00000331320.7	hg19	CCDS32169.1																																																																																			.	.	.	none		0.572	MTA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317849.15			-	105927224	G	-	105927224	7	5	3	1	0	1	0	1	0	0	0	0	9915	991	35	0	914	0	MTA1	14	105927224	Frame_Shift_Del	DEL	G	TCGA-2Z-A9J2-01A-11D-A382-10	4579848	105927224	1422316	69	235											
DMXL2	23312	hgsc.bcm.edu	37	chr15	51799330	51799330	+	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	tataaaactataattacttaCctaaacatgcttgtacagat	17	14	3	7	0	0	1	0	0	0	1	0	1	0	1	1	0	6	2	1	0	10	9			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr15:51799330C>T	ENST00000251076.5	-	16	3052		c.e16+1		DMXL2_ENST00000449909.3_Splice_Site|DMXL2_ENST00000543779.2_Splice_Site	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2							cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		TAATTACTTACCTAAACATGC	0.279																																					.		Atlas-SNP	.											.	DMXL2	262	.	0			c.2764+1G>A						PASS	.						63	60	61					15																	51799330		2195	4290	6485	SO:0001630	splice_region_variant	23312	exon17			TACTTACCTAAAC	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.2764+1G>A	chr15.hg19:g.51799330C>T		55.0	0.0	.		37.0	11.0	.	NM_015263	B2RTR3|B7ZMH3|F5GWF1|O94938	Splice_Site	SNP	ENST00000251076.5	hg19	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.497642	0.85069	.	.	ENSG00000104093	ENST00000251076;ENST00000543779;ENST00000449909	.	.	.	4.83	4.83	0.62350	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.5259	0.87800	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DMXL2	49586622	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.440000	0.80464	2.210000	0.71456	0.484000	0.47621	.	.	.	.	none		0.279	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263	Intron	T	51799330	C	T	51799330	5	4	3	1	0	0	0	0	0	0	1	0	4597	521	18	2	6460	2	DMXL2	15	51799330	Splice_Site	SNP	C	TCGA-2Z-A9J2-01A-11D-A382-10		51799330	50732062	70	236											
CNOT1	23019	hgsc.bcm.edu	37	chr16	58583738	58583738	+	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	gctcaatactgactctcttcAtaaccagatactgtgaaacc	13	11	5	12	0	3	3	2	2	1	1	4	3	3	3	2	0	4	1	2	0	5	4			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr16:58583738A>T	ENST00000317147.5	-	25	3739	c.3407T>A	c.(3406-3408)aTg>aAg	p.M1136K	SNORA46_ENST00000384762.1_RNA|CNOT1_ENST00000569732.1_5'Flank|CNOT1_ENST00000441024.2_Missense_Mutation_p.M1136K|CNOT1_ENST00000569240.1_Missense_Mutation_p.M1131K|CNOT1_ENST00000245138.4_Missense_Mutation_p.M26K	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1136	Interaction with CNOT6, CNOT6L, CNOT7 and CNOT8.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		GACTCTCTTCATAACCAGATA	0.408																																					p.M1136K		Atlas-SNP	.											.	CNOT1	359	.	0			c.T3407A						PASS	.						166	155	159					16																	58583738		2198	4300	6498	SO:0001583	missense	23019	exon25			CTCTTCATAACCA	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.3407T>A	chr16.hg19:g.58583738A>T	ENSP00000320949:p.Met1136Lys	66.0	0.0	.		106.0	27.0	.	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	hg19	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.638031	0.87760	.	.	ENSG00000125107	ENST00000317147;ENST00000422872;ENST00000245138;ENST00000394200;ENST00000441024	T;T	0.18016	2.24;2.24	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.22898	0.0553	L	0.31845	0.965	0.80722	D	1	D;P;P;P	0.56746	0.977;0.814;0.666;0.95	P;P;B;P	0.58391	0.696;0.838;0.212;0.687	T	0.01914	-1.1248	10	0.06236	T	0.91	.	15.4197	0.75000	1.0:0.0:0.0:0.0	.	26;1136;1136;1131	B5MDN3;A5YKK6-4;A5YKK6;A5YKK6-2	.;.;CNOT1_HUMAN;.	K	1136;565;26;1131;1136	ENSP00000320949:M1136K;ENSP00000413113:M1136K	ENSP00000245138:M26K	M	-	2	0	CNOT1	57141239	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.050000	0.60909	0.402000	0.26972	ATG	.	.	.	none		0.408	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		T	58583738	A	T	58583738	3	4	3	1	0	0	0	0	1	0	0	0	3619	217	8	5	4045	5	CNOT1	16	58583738	Missense_Mutation	SNP	A	TCGA-2Z-A9J2-01A-11D-A382-10		58583738	31771015	71	237											
CNOT1	23019	hgsc.bcm.edu	37	chr16	58615281	58615281	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtttccaaggtctatataTgaggtctactgggaacactt	11	14	9	7	0	2	1	0	1	2	0	3	2	3	2	1	3	2	1	1	3	6	6			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr16:58615281T>C	ENST00000317147.5	-	11	1515	c.1183A>G	c.(1183-1185)Ata>Gta	p.I395V	CNOT1_ENST00000441024.2_Missense_Mutation_p.I395V|CNOT1_ENST00000569240.1_Missense_Mutation_p.I395V	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	395					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)		GGTCTATATATGAGGTCTACT	0.413																																					p.I395V		Atlas-SNP	.											.	CNOT1	359	.	0			c.A1183G						PASS	.						116	106	109					16																	58615281		2198	4300	6498	SO:0001583	missense	23019	exon11			TATATATGAGGTC	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.1183A>G	chr16.hg19:g.58615281T>C	ENSP00000320949:p.Ile395Val	115.0	0.0	.		123.0	46.0	.	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	hg19	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	T	13.10	2.136887	0.37728	.	.	ENSG00000125107	ENST00000317147;ENST00000394200;ENST00000441024	T;T	0.44482	0.94;0.92	5.67	5.67	0.87782	.	0.042158	0.85682	D	0.000000	T	0.23451	0.0567	N	0.12182	0.205	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.0;0.001	T	0.12604	-1.0541	9	.	.	.	0.0017	10.2862	0.43568	0.0:0.0733:0.0:0.9267	.	395;395;395	A5YKK6-4;A5YKK6;A5YKK6-2	.;CNOT1_HUMAN;.	V	395	ENSP00000320949:I395V;ENSP00000413113:I395V	.	I	-	1	0	CNOT1	57172782	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.097000	0.64542	2.158000	0.67659	0.533000	0.62120	ATA	.	.	.	none		0.413	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		C	58615281	T	C	58615281	3	2	3	1	0	0	0	0	1	0	0	0	3619	1464	51	3	6325	3	CNOT1	16	58615281	Missense_Mutation	SNP	T	TCGA-2Z-A9J2-01A-11D-A382-10	31543	58615281	31739472	72	238											
ABR	29	hgsc.bcm.edu	37	chr17	1082993	1082993	+	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	tgtcgatccaggacaggcgcGgcaggccccggtggctgagc	6	5	17	13	4	0	1	0	1	0	0	2	3	1	2	3	6	1	2	3	6	0	0			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr17:1082993G>C	ENST00000302538.5	-	1	175	c.29C>G	c.(28-30)cCg>cGg	p.P10R	AC016292.1_ENST00000438344.1_RNA|ABR_ENST00000544583.2_Intron	NM_001282149.1|NM_021962.3	NP_001269078.1|NP_068781.2	Q12979	ABR_HUMAN	active BCR-related	10					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)		GGACAGGCGCGGCAGGCCCCG	0.711																																					p.P10R	Esophageal Squamous(197;2016 2115 4129 29033 46447)	Atlas-SNP	.											.	ABR	119	.	0			c.C29G						PASS	.						9	12	11					17																	1082993		2175	4265	6440	SO:0001583	missense	29	exon1			AGGCGCGGCAGGC	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.29C>G	chr17.hg19:g.1082993G>C	ENSP00000303909:p.Pro10Arg	226.0	0.0	.		169.0	38.0	.	NM_021962	B3KW89|B7Z6H7|D3DTH3|D3DTH4|F5H3S2|F5H8B3|Q13693|Q13694	Missense_Mutation	SNP	ENST00000302538.5	hg19	CCDS10999.1	.	.	.	.	.	.	.	.	.	.	g	16.44	3.124012	0.56613	.	.	ENSG00000159842	ENST00000302538	T	0.21734	1.99	3.83	3.83	0.44106	.	2.609730	0.02144	N	0.057429	T	0.15565	0.0375	N	0.19112	0.55	0.80722	D	1	P	0.36183	0.542	B	0.22601	0.04	T	0.20273	-1.0280	10	0.87932	D	0	.	11.091	0.48115	0.0:0.0:1.0:0.0	.	10	Q12979	ABR_HUMAN	R	10	ENSP00000303909:P10R	ENSP00000303909:P10R	P	-	2	0	ABR	1029743	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.945000	0.63568	1.972000	0.57404	0.511000	0.50034	CCG	.	.	.	none		0.711	ABR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206675.4			C	1082993	G	C	1082993	3	2	3	1	0	0	0	0	1	0	0	0	99	1116	39	4	2781	4	ABR	17	1082993	Missense_Mutation	SNP	G	TCGA-2Z-A9J2-01A-11D-A382-10		1082993	80112217	73	239											
DNAH2	146754	hgsc.bcm.edu	37	chr17	7689641	7689641	+	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	tctgtgccgcgccggagaccCtaacttcaacattgttagag	9	10	10	12	3	2	2	1	0	1	2	2	3	2	2	3	1	3	1	3	1	3	4			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr17:7689641C>G	ENST00000572933.1	+	40	7789	c.6329C>G	c.(6328-6330)cCt>cGt	p.P2110R	DNAH2_ENST00000389173.2_Missense_Mutation_p.P2110R			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	2110	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(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)				GCCGGAGACCCTAACTTCAAC	0.607																																					p.P2110R		Atlas-SNP	.											.	DNAH2	498	.	0			c.C6329G						PASS	.						39	39	39					17																	7689641		2203	4300	6503	SO:0001583	missense	146754	exon39			GAGACCCTAACTT	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.6329C>G	chr17.hg19:g.7689641C>G	ENSP00000458355:p.Pro2110Arg	47.0	0.0	.		36.0	23.0	.	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	C	19.08	3.757144	0.69648	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.25912	1.77	5.43	5.43	0.79202	ATPase, dynein-related, AAA domain (1);	0.129591	0.52532	D	0.000068	T	0.37679	0.1012	M	0.62723	1.935	0.80722	D	1	D	0.54397	0.966	P	0.54431	0.752	T	0.02596	-1.1136	10	0.17369	T	0.5	.	13.8398	0.63432	0.0:0.8467:0.1533:0.0	.	2110	Q9P225	DYH2_HUMAN	R	2110	ENSP00000373825:P2110R	ENSP00000353818:P2110R	P	+	2	0	DNAH2	7630366	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	4.930000	0.63462	2.827000	0.97445	0.650000	0.86243	CCT	.	.	.	none		0.607	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		G	7689641	C	G	7689641	3	3	3	1	0	0	0	0	1	0	0	0	4604	681	24	4	6483	4	DNAH2	17	7689641	Missense_Mutation	SNP	C	TCGA-2Z-A9J2-01A-11D-A382-10	6606648	7689641	73505569	74	240											
NCOR1	9611	hgsc.bcm.edu	37	chr17	15961343	15961343	+	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	ttcctgctgtggtcgatagtGatgtaatggtccttcatatt	7	17	10	7	1	1	1	1	1	0	0	4	2	3	1	2	2	1	2	2	2	3	6	rs376750361		TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr17:15961343G>A	ENST00000268712.3	-	39	6303	c.6046C>T	c.(6046-6048)Cac>Tac	p.H2016Y	NCOR1_ENST00000395857.3_Missense_Mutation_p.H600Y|NCOR1_ENST00000395851.1_Missense_Mutation_p.H1913Y	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	2016	Interaction with C1D. {ECO:0000250}.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		GGTCGATAGTGATGTAATGGT	0.483																																					p.H2016Y		Atlas-SNP	.											.	NCOR1	240	.	0			c.C6046T						PASS	.						93	74	81					17																	15961343		2203	4300	6503	SO:0001583	missense	9611	exon39			GATAGTGATGTAA	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.6046C>T	chr17.hg19:g.15961343G>A	ENSP00000268712:p.His2016Tyr	84.0	0.0	.		78.0	11.0	.	NM_006311	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	hg19	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	G	0.872	-0.731627	0.03135	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849;ENST00000395857	T;T;T	0.42513	0.97;1.52;0.98	5.87	5.87	0.94306	.	0.160125	0.56097	D	0.000034	T	0.48943	0.1528	L	0.46157	1.445	0.40181	D	0.977297	P;P;B;D;P;P	0.55172	0.572;0.893;0.378;0.97;0.71;0.773	B;B;B;P;B;B	0.48901	0.116;0.242;0.04;0.594;0.169;0.34	T	0.50600	-0.8809	10	0.72032	D	0.01	-10.6861	19.1839	0.93635	0.0:0.0:1.0:0.0	.	826;1920;2016;1913;536;30	B4DZ48;E7EVK1;O75376;O75376-2;Q86YY1;Q86YY2	.;.;NCOR1_HUMAN;.;.;.	Y	2016;1913;1920;600	ENSP00000268712:H2016Y;ENSP00000379192:H1913Y;ENSP00000379198:H600Y	ENSP00000268712:H2016Y	H	-	1	0	NCOR1	15902068	1.000000	0.71417	0.993000	0.49108	0.083000	0.17756	6.790000	0.75115	2.780000	0.95670	0.655000	0.94253	CAC	.	.	.	alt		0.483	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		A	15961343	G	A	15961343	3	1	3	1	0	0	0	0	1	0	0	0	10242	1290	45	2	1308	2	NCOR1	17	15961343	Missense_Mutation	SNP	G	TCGA-2Z-A9J2-01A-11D-A382-10	8271702	15961343	65233867	75	241											
CCDC103	388389	hgsc.bcm.edu	37	chr17	42979927	42979927	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctggctgatcacgtggggccGgctgaccgggcagcggtgct	4	7	18	12	4	1	2	1	2	0	0	1	2	1	2	2	6	2	4	2	6	0	0			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr17:42979927G>A	ENST00000417826.2	+	4	566	c.471G>A	c.(469-471)ccG>ccA	p.P157P	AC015936.3_ENST00000441312.1_RNA|FAM187A_ENST00000412523.2_Intron|CCDC103_ENST00000410006.2_Silent_p.P157P|EFTUD2_ENST00000426333.2_5'Flank|FAM187A_ENST00000331733.4_5'UTR	NM_001258399.1|NM_213607.2	NP_001245328.1|NP_998772.1	Q8IW40	CC103_HUMAN	coiled-coil domain containing 103	157					axonemal dynein complex assembly (GO:0070286)|cell projection organization (GO:0030030)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|outer dynein arm assembly (GO:0036158)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|motile cilium (GO:0031514)	protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|large_intestine(3)|prostate(1)|skin(1)	7		Prostate(33;0.109)				ACGTGGGGCCGGCTGACCGGG	0.642																																					p.P157P		Atlas-SNP	.											.	CCDC103	15	.	0			c.G471A						PASS	.						56	63	61					17																	42979927		2203	4300	6503	SO:0001819	synonymous_variant	388389	exon4			GGGGCCGGCTGAC	AK023156	CCDS11490.1, CCDS58554.1	17q21.31	2013-02-22			ENSG00000167131	ENSG00000167131			32700	protein-coding gene	gene with protein product		614677				22581229	Standard	NM_213607		Approved	FLJ13094, FLJ34211, PR46b, CILD17	uc031ray.1	Q8IW40	OTTHUMG00000154264	ENST00000417826.2:c.471G>A	chr17.hg19:g.42979927G>A		102.0	0.0	.		99.0	20.0	.	NM_001258395	A8K145|B8ZZU0	Silent	SNP	ENST00000417826.2	hg19	CCDS11490.1																																																																																			.	.	.	none		0.642	CCDC103-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334578.1	NM_213607		A	42979927	G	A	42979927	2	1	3	1	0	0	0	0	0	0	0	1	2740	1103	39	1		1	CCDC103	17	42979927	Silent	SNP	G	TCGA-2Z-A9J2-01A-11D-A382-10	27018584	42979927	38215283	76	242											
HELZ	9931	hgsc.bcm.edu	37	chr17	65144699	65144700	+	Frame_Shift_Ins	INS	-	-	T																															cctacttgatgatagcttcaINStgggagcggtagttctcaca																										TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr17:65144699_65144700insT	ENST00000358691.5	-	20	2772_2773	c.2606_2607insA	c.(2605-2607)catfs	p.H869fs	HELZ_ENST00000580168.1_Frame_Shift_Ins_p.H870fs	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	869						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)					TGATAGCTTCATGGGAGCGGTA	0.49																																					p.H869fs		Atlas-Indel,Pindel	.											.	HELZ	160	.	0			c.2607_2608insA						PASS	.																																			SO:0001589	frameshift_variant	9931	exon20			.	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.2607dupA	chr17.hg19:g.65144700_65144700dupT	ENSP00000351524:p.His869fs	78.0	0.0	0		134.0	60.0	0.447761	NM_014877	I6L9H4	Frame_Shift_Ins	INS	ENST00000358691.5	hg19	CCDS42374.1																																																																																			.	.	.	none		0.49	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		T	65144700	-	T	65144699	7	5	3	1	0	1	1	0	0	0	0	0	7056	214	8	0	3277	0	HELZ	17	65144699	Frame_Shift_Ins	INS	-	TCGA-2Z-A9J2-01A-11D-A382-10	22164772	65144699	16050511	77	243											
MIDN	90007	hgsc.bcm.edu	37	chr19	1255611	1255611	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cccgacctggcccccagaacTacctcctgcgagaagctcac	9	5	8	19	2	1	2	1	0	0	2	2	4	2	2	6	1	4	1	6	1	3	1			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr19:1255611T>C	ENST00000591446.2	+	6	1456	c.1047T>C	c.(1045-1047)acT>acC	p.T349T	MIDN_ENST00000300952.2_Silent_p.T349T			Q504T8	MIDN_HUMAN	midnolin	349						cytosol (GO:0005829)|nucleolus (GO:0005730)				NS(1)|endometrium(3)|kidney(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCCCAGAACTACCTCCTGCG	0.726																																					p.T349T		Atlas-SNP	.											.	MIDN	34	.	0			c.T1047C						PASS	.						19	26	24					19																	1255611		2194	4287	6481	SO:0001819	synonymous_variant	90007	exon7			CAGAACTACCTCC	AC004221	CCDS32864.1	19p13.3	2013-09-20			ENSG00000167470	ENSG00000167470			16298	protein-coding gene	gene with protein product		606700				10974535	Standard	XM_005259671		Approved		uc002lrp.3	Q504T8	OTTHUMG00000180144	ENST00000591446.2:c.1047T>C	chr19.hg19:g.1255611T>C		136.0	0.0	.		67.0	25.0	.	NM_177401	Q96BW8	Silent	SNP	ENST00000591446.2	hg19	CCDS32864.1																																																																																			.	.	.	none		0.726	MIDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449965.2			C	1255611	T	C	1255611	2	2	3	1	0	0	0	0	0	0	0	1	9586	1509	53	3		3	MIDN	19	1255611	Silent	SNP	T	TCGA-2Z-A9J2-01A-11D-A382-10		1255611	57873372	78	244											
ZSCAN5B	342933	hgsc.bcm.edu	37	chr19	56701355	56701355	+	Frame_Shift_Del	DEL	G	G	-																															tggctgaaaactttgctgcaGtatttacatttaaacggcct																										TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr19:56701355delG	ENST00000586855.2	-	5	1642	c.1329delC	c.(1327-1329)tacfs	p.Y443fs	ZSCAN5B_ENST00000358992.3_Frame_Shift_Del_p.Y443fs			A6NJL1	ZSA5B_HUMAN	zinc finger and SCAN domain containing 5B	443					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						CTTTGCTGCAGTATTTACATT	0.547																																					p.C444fs		Atlas-Indel,Pindel	.											.	ZSCAN5B	160	.	0			c.1330delT						PASS	.						89	90	90					19																	56701355		2075	4230	6305	SO:0001589	frameshift_variant	342933	exon4			.		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.1329delC	chr19.hg19:g.56701355delG	ENSP00000466072:p.Tyr443fs	156.0	0.0	0		127.0	45.0	0.354331	NM_001080456		Frame_Shift_Del	DEL	ENST00000586855.2	hg19	CCDS46203.1																																																																																			.	.	.	none		0.547	ZSCAN5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457834.2	NM_001080456		-	56701355	G	-	56701355	7	5	3	1	0	1	0	1	0	0	0	0	18251	1024	36	0	162	0	ZSCAN5B	19	56701355	Frame_Shift_Del	DEL	G	TCGA-2Z-A9J2-01A-11D-A382-10	55445744	56701355	2427628	79	245											
SIRPA	140885	hgsc.bcm.edu	37	chr20	1903069	1903069	+	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	gactacagctgacctggttgGagaatggaaacgtgtcccgg	10	8	14	9	2	0	2	0	1	0	1	1	5	1	3	2	4	3	2	2	4	3	2			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr20:1903069G>C	ENST00000358771.4	+	4	1017	c.865G>C	c.(865-867)Gag>Cag	p.E289Q	SIRPA_ENST00000356025.3_Missense_Mutation_p.E289Q|SIRPA_ENST00000400068.3_Missense_Mutation_p.E289Q	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	289	Ig-like C1-type 2.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		GACCTGGTTGGAGAATGGAAA	0.537																																					p.E289Q	GBM(155;1668 1920 5945 42733 48121)	Atlas-SNP	.											.	SIRPA	83	.	0			c.G865C						PASS	.						147	127	134					20																	1903069		2203	4300	6503	SO:0001583	missense	140885	exon5			TGGTTGGAGAATG	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"Signal-regulatory proteins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	9662	protein-coding gene	gene with protein product		602461	"protein tyrosine phosphatase, non-receptor type substrate 1"	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.865G>C	chr20.hg19:g.1903069G>C	ENSP00000351621:p.Glu289Gln	394.0	0.0	.		278.0	18.0	.	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	hg19	CCDS13022.1	.	.	.	.	.	.	.	.	.	.	G	19.36	3.812345	0.70912	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.00608	6.25;6.25;6.25	5.35	5.35	0.76521	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000013	T	0.02119	0.0066	L	0.59967	1.855	0.46798	D	0.999207	P;D;P	0.76494	0.926;0.999;0.912	P;D;P	0.72982	0.596;0.979;0.691	T	0.62282	-0.6887	10	0.59425	D	0.04	.	14.7506	0.69522	0.0:0.0:1.0:0.0	.	269;289;289	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	Q	289	ENSP00000382941:E289Q;ENSP00000348307:E289Q;ENSP00000351621:E289Q	ENSP00000348307:E289Q	E	+	1	0	SIRPA	1851069	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	5.119000	0.64679	2.941000	0.99782	0.655000	0.94253	GAG	.	.	.	none		0.537	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792		C	1903069	G	C	1903069	3	2	3	1	0	0	0	0	1	0	0	0	14345	1175	41	4	879	4	SIRPA	20	1903069	Missense_Mutation	SNP	G	TCGA-2Z-A9J2-01A-11D-A382-10		1903069	61122451	80	246											
RBM12	10137	hgsc.bcm.edu	37	chr20	34240509	34240509	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatttaagtcaatgacagcAgctgtggcttcatcccgaga	11	11	9	10	1	3	2	3	1	0	1	4	3	4	2	1	1	2	3	1	1	2	3			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr20:34240509A>G	ENST00000374114.3	-	3	2999	c.2736T>C	c.(2734-2736)gcT>gcC	p.A912A	CPNE1_ENST00000352393.4_Intron|CPNE1_ENST00000317677.5_Intron|CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000397446.1_Intron|RP1-309K20.6_ENST00000541176.2_Intron|CPNE1_ENST00000397443.1_Intron|CPNE1_ENST00000317619.3_Intron|RBM12_ENST00000359646.1_Silent_p.A912A|RBM12_ENST00000374104.3_Silent_p.A912A|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	912	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.					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)			CAATGACAGCAGCTGTGGCTT	0.403																																					p.A912A		Atlas-SNP	.											.	RBM12	93	.	0			c.T2736C						PASS	.						87	85	86					20																	34240509		2203	4300	6503	SO:0001819	synonymous_variant	10137	exon2			GACAGCAGCTGTG	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.2736T>C	chr20.hg19:g.34240509A>G		97.0	0.0	.		71.0	10.0	.	NM_001198840	B3KRU2|E1P5R6|O94865|Q8N3B1|Q9H196	Silent	SNP	ENST00000374114.3	hg19	CCDS13261.1																																																																																			.	.	.	none		0.403	RBM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078894.1	NM_006047		G	34240509	A	G	34240509	2	3	3	1	0	0	0	0	0	0	0	1	13126	175	7	3		3	RBM12	20	34240509	Silent	SNP	A	TCGA-2Z-A9J2-01A-11D-A382-10	32337440	34240509	28785011	81	247											
BCR	613	hgsc.bcm.edu	37	chr22	23524065	23524065	+	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	cagagcacctctgagcaggaGaagcgccttacctggccccg	9	5	12	15	2	1	3	0	1	1	2	1	4	1	3	5	2	4	2	5	2	2	1			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr22:23524065G>T	ENST00000305877.8	+	1	1669	c.918G>T	c.(916-918)gaG>gaT	p.E306D	BCR_ENST00000359540.3_Missense_Mutation_p.E306D|BCR_ENST00000398512.5_Missense_Mutation_p.E306D	NM_004327.3	NP_004318.3	P11274	BCR_HUMAN	breakpoint cluster region	306	Binding to ABL SH2-domain.|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)	CTGAGCAGGAGAAGCGCCTTA	0.642			T	"ABL1,  FGFR1, JAK2 "	"CML, ALL, AML"																																p.E306D		Atlas-SNP	.		Dom	yes		22	22q11.21	613	breakpoint cluster region		L	.	BCR	74	.	0			c.G918T						PASS	.						26	29	28					22																	23524065		2203	4300	6503	SO:0001583	missense	613	exon1			GCAGGAGAAGCGC		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.918G>T	chr22.hg19:g.23524065G>T	ENSP00000303507:p.Glu306Asp	25.0	0.0	.		19.0	11.0	.	NM_021574	P78501|Q12842|Q4LE80|Q6NZI3	Missense_Mutation	SNP	ENST00000305877.8	hg19	CCDS13806.1	.	.	.	.	.	.	.	.	.	.	G	12.24	1.878350	0.33162	.	.	ENSG00000186716	ENST00000305877;ENST00000359540;ENST00000398512;ENST00000290956;ENST00000292697;ENST00000420248	T;T;T	0.39787	1.88;1.89;1.06	4.67	3.59	0.41128	.	0.062995	0.64402	D	0.000007	T	0.26882	0.0658	N	0.25647	0.755	0.40319	D	0.978809	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.09164	-1.0687	10	0.33141	T	0.24	.	8.5781	0.33612	0.0903:0.1551:0.7547:0.0	.	306;306	P11274-2;P11274	.;BCR_HUMAN	D	306	ENSP00000303507:E306D;ENSP00000352535:E306D;ENSP00000381524:E306D	ENSP00000290956:E306D	E	+	3	2	BCR	21854065	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	1.473000	0.35387	2.315000	0.78130	0.557000	0.71058	GAG	.	.	.	none		0.642	BCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075819.1	NM_004327		T	23524065	G	T	23524065	3	4	3	1	0	0	0	0	1	0	0	0	1388	933	33	4	920	4	BCR	22	23524065	Missense_Mutation	SNP	G	TCGA-2Z-A9J2-01A-11D-A382-10		23524065	27780501	82	248											
UPB1	51733	hgsc.bcm.edu	37	chr22	24896185	24896185	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgagacgaccccgcattgTgcacgtggggctggttcaga	7	8	15	11	3	1	2	1	1	0	2	1	4	1	2	2	3	1	5	2	3	0	2			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr22:24896185T>C	ENST00000326010.5	+	2	559	c.215T>C	c.(214-216)gTg>gCg	p.V72A	UPB1_ENST00000382760.2_Missense_Mutation_p.V72A|UPB1_ENST00000413389.2_Intron	NM_016327.2	NP_057411.1	Q9UBR1	BUP1_HUMAN	ureidopropionase, beta	72	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	beta-ureidopropionase activity (GO:0003837)|metal ion binding (GO:0046872)			endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	22	Colorectal(2;0.0339)					CCCCGCATTGTGCACGTGGGG	0.547																																					p.V72A		Atlas-SNP	.											.	UPB1	60	.	0			c.T215C						PASS	.						79	82	81					22																	24896185		2203	4300	6503	SO:0001583	missense	51733	exon2			GCATTGTGCACGT	AB013885	CCDS13827.1	22q11.2	2008-04-11			ENSG00000100024	ENSG00000100024			16297	protein-coding gene	gene with protein product		606673				10542323	Standard	XR_244378		Approved	BUP1	uc003aaf.3	Q9UBR1	OTTHUMG00000150749	ENST00000326010.5:c.215T>C	chr22.hg19:g.24896185T>C	ENSP00000324343:p.Val72Ala	59.0	0.0	.		59.0	14.0	.	NM_016327	A3KMF8|Q9UIR3	Missense_Mutation	SNP	ENST00000326010.5	hg19	CCDS13827.1	.	.	.	.	.	.	.	.	.	.	T	13.18	2.159972	0.38119	.	.	ENSG00000100024	ENST00000326010;ENST00000382760;ENST00000426507	D;T	0.86769	-2.17;-0.97	4.66	3.62	0.41486	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (3);	0.509443	0.20750	N	0.086361	D	0.94450	0.8214	H	0.97587	4.035	0.80722	D	1	P	0.52316	0.952	P	0.59357	0.856	D	0.93657	0.6978	10	0.87932	D	0	-16.6106	8.6137	0.33817	0.0:0.0941:0.0:0.9059	.	72	Q9UBR1	BUP1_HUMAN	A	72	ENSP00000324343:V72A;ENSP00000372208:V72A	ENSP00000324343:V72A	V	+	2	0	UPB1	23226185	1.000000	0.71417	0.100000	0.21137	0.023000	0.10783	3.159000	0.50731	0.738000	0.32606	-0.473000	0.04963	GTG	.	.	.	none		0.547	UPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319869.1			C	24896185	T	C	24896185	3	2	3	1	0	0	0	0	1	0	0	0	17014	1696	59	3	221	3	UPB1	22	24896185	Missense_Mutation	SNP	T	TCGA-2Z-A9J2-01A-11D-A382-10	1372120	24896185	26408381	83	249											
RRP7A	27341	hgsc.bcm.edu	37	chr22	42912116	42912116	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acagactggacgaggccacaGgtggacaggaggcgggacag	12	2	18	9	2	0	1	0	0	0	1	0	6	0	5	1	7	0	0	1	7	0	0			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr22:42912116G>A	ENST00000323013.6	-	3	258	c.243C>T	c.(241-243)acC>acT	p.T81T		NM_015703.4	NP_056518.2	Q9Y3A4	RRP7A_HUMAN	ribosomal RNA processing 7 homolog A (S. cerevisiae)	81	RRM.						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						CGAGGCCACAGGTGGACAGGA	0.617																																					p.T81T		Atlas-SNP	.											.	RRP7A	25	.	0			c.C243T						PASS	.						46	44	45					22																	42912116		2203	4300	6503	SO:0001819	synonymous_variant	27341	exon3			GCCACAGGTGGAC	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.243C>T	chr22.hg19:g.42912116G>A		126.0	0.0	.		68.0	14.0	.	NM_015703	A4FTX2|B2RBG4|Q0VAD0|Q5JZ94|Q6P4B5|Q8IVR9|Q8IVY0|Q8N5Q3|Q8NEY6|Q9Y3H5	Silent	SNP	ENST00000323013.6	hg19	CCDS14036.1																																																																																			.	.	.	none		0.617	RRP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320451.1	NM_015703		A	42912116	G	A	42912116	2	1	3	1	0	0	0	0	0	0	0	1	13702	987	35	2		2	RRP7A	22	42912116	Silent	SNP	G	TCGA-2Z-A9J2-01A-11D-A382-10	18015931	42912116	8392450	84	250											
PANX2	56666	hgsc.bcm.edu	37	chr22	50617455	50617455	+	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	cgttccacgtccgctcacctCccgccgcccctgctgtggcc	2	8	9	22	5	1	0	1	0	0	0	4	0	4	0	8	1	1	3	8	1	0	1			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chr22:50617455C>A	ENST00000395842.2	+	3	1783	c.1783C>A	c.(1783-1785)Ccc>Acc	p.P595T	PANX2_ENST00000159647.5_Missense_Mutation_p.P595T	NM_052839.3	NP_443071.2	Q96RD6	PANX2_HUMAN	pannexin 2	595					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)		CCGCTCACCTCCCGCCGCCCC	0.692																																					p.P595T		Atlas-SNP	.											.	PANX2	69	.	0			c.C1783A						PASS	.						24	23	23					22																	50617455		2186	4299	6485	SO:0001583	missense	56666	exon3			TCACCTCCCGCCG		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.1783C>A	chr22.hg19:g.50617455C>A	ENSP00000379183:p.Pro595Thr	142.0	0.0	.		88.0	30.0	.	NM_052839	B7Z684|Q96RD5|Q9UGX8	Missense_Mutation	SNP	ENST00000395842.2	hg19	CCDS14085.2	.	.	.	.	.	.	.	.	.	.	C	7.891	0.732382	0.15507	.	.	ENSG00000073150	ENST00000159647;ENST00000395842;ENST00000401643	T;T	0.21932	1.98;2.0	3.71	1.26	0.21427	.	0.243973	0.25450	N	0.030597	T	0.08758	0.0217	N	0.14661	0.345	0.26828	N	0.968647	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.22103	-1.0226	10	0.21014	T	0.42	-2.0275	3.3091	0.07010	0.2806:0.4825:0.1443:0.0926	.	595;595	Q96RD6-1;Q96RD6	.;PANX2_HUMAN	T	595;595;272	ENSP00000159647:P595T;ENSP00000379183:P595T	ENSP00000159647:P595T	P	+	1	0	PANX2	48959582	0.000000	0.05858	0.968000	0.41197	0.590000	0.36582	0.686000	0.25392	0.860000	0.35481	0.305000	0.20034	CCC	.	.	.	none		0.692	PANX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075010.3	NM_052839		A	50617455	C	A	50617455	3	1	3	1	0	0	0	0	1	0	0	0	11428	855	30	4	1793	4	PANX2	22	50617455	Missense_Mutation	SNP	C	TCGA-2Z-A9J2-01A-11D-A382-10	7705339	50617455	687111	85	251											
FAAH2	158584	hgsc.bcm.edu	37	chrX	57475117	57475117	+	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	gtggcacctaagcatcatgtCcctctaacacggcctttcaa	10	10	7	14	1	3	0	2	0	1	0	4	0	4	0	3	2	2	2	3	2	3	3			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chrX:57475117C>G	ENST00000374900.4	+	10	1509	c.1389C>G	c.(1387-1389)gtC>gtG	p.V463V	FAAH2_ENST00000491179.1_3'UTR	NM_174912.3	NP_777572.2	Q6GMR7	FAAH2_HUMAN	fatty acid amide hydrolase 2	463						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						AGCATCATGTCCCTCTAACAC	0.423										HNSCC(52;0.14)																											p.V463V		Atlas-SNP	.											.	FAAH2	66	.	0			c.C1389G						PASS	.						228	164	185					X																	57475117		2203	4300	6503	SO:0001819	synonymous_variant	158584	exon10			TCATGTCCCTCTA	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.1389C>G	chrX.hg19:g.57475117C>G		96.0	0.0	.		69.0	35.0	.	NM_174912	Q86VT2|Q96N98	Silent	SNP	ENST00000374900.4	hg19	CCDS14375.1																																																																																			.	.	.	none		0.423	FAAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056919.1	NM_174912		G	57475117	C	G	57475117	2	3	3	1	0	0	0	0	0	0	0	1	5358	842	30	4		4	FAAH2	23	57475117	Silent	SNP	C	TCGA-2Z-A9J2-01A-11D-A382-10		57475117	97795443	86	252											
ZCCHC5	203430	hgsc.bcm.edu	37	chrX	77913324	77913324	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgagagttctaggaattcCtgggcatttgaaggctccag	9	11	13	8	0	1	2	0	2	1	1	3	4	3	3	2	3	0	4	2	3	3	4			TCGA-2Z-A9J2-01A-11D-A382-10	TCGA-2Z-A9J2-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b136f8d-949c-4f48-9ca6-f9bb90a10bb3	2d763603-a0f5-4dbe-a146-ef518556d752	g.chrX:77913324C>T	ENST00000321110.1	-	2	889	c.594G>A	c.(592-594)caG>caA	p.Q198Q		NM_152694.2	NP_689907.1	Q8N8U3	ZCHC5_HUMAN	zinc finger, CCHC domain containing 5	198							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)|prostate(1)|skin(1)	37						CTAGGAATTCCTGGGCATTTG	0.547																																					p.Q198Q		Atlas-SNP	.											.	ZCCHC5	101	.	0			c.G594A						PASS	.						38	38	38					X																	77913324		2203	4300	6503	SO:0001819	synonymous_variant	203430	exon2			GAATTCCTGGGCA	AK096184	CCDS14440.1	Xq13.3	2008-02-05			ENSG00000179300	ENSG00000179300		"Zinc fingers, CCHC domain containing"	22997	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_152694		Approved	FLJ38865, Mar3, Mart3, ZHC5	uc004edc.1	Q8N8U3	OTTHUMG00000021892	ENST00000321110.1:c.594G>A	chrX.hg19:g.77913324C>T		67.0	0.0	.		71.0	5.0	.	NM_152694	B2RMZ0|Q5JQE9	Silent	SNP	ENST00000321110.1	hg19	CCDS14440.1																																																																																			.	.	.	none		0.547	ZCCHC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057319.1	NM_152694		T	77913324	C	T	77913324	2	4	3	1	0	0	0	0	0	0	0	1	17603	680	24	2		2	ZCCHC5	23	77913324	Silent	SNP	C	TCGA-2Z-A9J2-01A-11D-A382-10	20438207	77913324	77357236	87	253											
KIF1B	23095	hgsc.bcm.edu	37	chr1	10338126	10338126	+	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	aactggttcgtgaattaaagGaggaggtgacacggctgaag	13	8	15	5	2	0	3	0	3	0	0	1	5	0	5	0	5	1	2	0	5	5	2			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:10338126G>T	ENST00000377086.1	+	13	1322	c.1120G>T	c.(1120-1122)Gag>Tag	p.E374*	KIF1B_ENST00000377081.1_Nonsense_Mutation_p.E374*|KIF1B_ENST00000263934.6_Nonsense_Mutation_p.E368*|KIF1B_ENST00000377083.1_Nonsense_Mutation_p.E368*|KIF1B_ENST00000377093.4_Nonsense_Mutation_p.E368*			O60333	KIF1B_HUMAN	kinesin family member 1B	374					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)		TGAATTAAAGGAGGAGGTGAC	0.398																																					p.E368X		Atlas-SNP	.											.	KIF1B	242	.	0			c.G1102T						PASS	.						109	96	100					1																	10338126		2203	4300	6503	SO:0001587	stop_gained	23095	exon12			TTAAAGGAGGAGG	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.1120G>T	chr1.hg19:g.10338126G>T	ENSP00000366290:p.Glu374*	104.0	0.0	.		76.0	28.0	.	NM_183416	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Nonsense_Mutation	SNP	ENST00000377086.1	hg19		.	.	.	.	.	.	.	.	.	.	G	39	7.518828	0.98332	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377093;ENST00000377086;ENST00000377083;ENST00000377081	.	.	.	5.25	5.25	0.73442	.	0.050900	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.2117	0.93758	0.0:0.0:1.0:0.0	.	.	.	.	X	374;368;368;374;368;374	.	ENSP00000263934:E368X	E	+	1	0	KIF1B	10260713	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.813000	0.99286	2.611000	0.88343	0.591000	0.81541	GAG	.	.	.	none		0.398	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1			T	10338126	G	T	10338126	4	4	4	1	0	0	0	0	0	1	0	0	8291	1175	41	4	1144	4	KIF1B	1	10338126	Nonsense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10		10338126	238912495	1	254											
LDLRAP1	26119	hgsc.bcm.edu	37	chr1	25889207	25889207	+	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	tttggcaggtgtccaaggaaGgtgagactttgcatctacat	10	12	12	7	0	1	1	0	1	1	1	2	3	2	2	1	4	2	2	1	4	3	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:25889207G>A	ENST00000374338.4	+	5	651	c.532G>A	c.(532-534)Gag>Aag	p.E178K	LDLRAP1_ENST00000488127.1_3'UTR	NM_015627.2	NP_056442.2	Q5SW96	ARH_HUMAN	low density lipoprotein receptor adaptor protein 1	178	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				amyloid precursor protein metabolic process (GO:0042982)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|positive regulation of cholesterol metabolic process (GO:0090205)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of signal transduction (GO:0009967)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of protein binding (GO:0043393)|transport (GO:0006810)	axon (GO:0030424)|basal plasma membrane (GO:0009925)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|early endosome (GO:0005769)|neurofilament (GO:0005883)|recycling endosome (GO:0055037)	AP-2 adaptor complex binding (GO:0035612)|beta-amyloid binding (GO:0001540)|clathrin adaptor activity (GO:0035615)|clathrin binding (GO:0030276)|low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphotyrosine binding (GO:0001784)|receptor signaling complex scaffold activity (GO:0030159)|signaling adaptor activity (GO:0035591)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)|urinary_tract(1)	9		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;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.63e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000728)|STAD - Stomach adenocarcinoma(196;0.000766)|BRCA - Breast invasive adenocarcinoma(304;0.000969)|GBM - Glioblastoma multiforme(114;0.00914)|READ - Rectum adenocarcinoma(331;0.0649)		GTCCAAGGAAGGTGAGACTTT	0.572																																					p.E178K		Atlas-SNP	.											.	LDLRAP1	28	.	0			c.G532A						PASS	.						133	119	124					1																	25889207		2203	4300	6503	SO:0001630	splice_region_variant	26119	exon5			AAGGAAGGTGAGA	BC029770	CCDS30639.1	1p36-p35	2014-09-17			ENSG00000157978	ENSG00000157978			18640	protein-coding gene	gene with protein product		605747					Standard	NM_015627		Approved	ARH, ARH2, FHCB1, FHCB2, MGC34705, DKFZp586D0624	uc001bkl.4	Q5SW96	OTTHUMG00000007386	ENST00000374338.4:c.532+1G>A	chr1.hg19:g.25889207G>A		107.0	0.0	.		84.0	28.0	.	NM_015627	A2BHI5|Q6TQS9|Q8N2Y0|Q9UFI9	Missense_Mutation	SNP	ENST00000374338.4	hg19	CCDS30639.1	.	.	.	.	.	.	.	.	.	.	G	16.81	3.226311	0.58668	.	.	ENSG00000157978	ENST00000374338	T	0.64991	-0.13	5.56	5.56	0.83823	Phosphotyrosine interaction domain (1);Pleckstrin homology-type (1);	0.265161	0.43579	D	0.000547	T	0.57460	0.2055	M	0.67953	2.075	0.80722	D	1	B	0.10296	0.003	B	0.14578	0.011	T	0.51926	-0.8643	10	0.15499	T	0.54	-18.0094	11.9152	0.52761	0.0794:0.0:0.9206:0.0	.	178	Q5SW96	ARH_HUMAN	K	178	ENSP00000363458:E178K	ENSP00000363458:E178K	E	+	1	0	LDLRAP1	25761794	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.534000	0.82004	2.620000	0.88729	0.555000	0.69702	GAG	.	.	.	none		0.572	LDLRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019350.3	NM_015627	Missense_Mutation	A	25889207	G	A	25889207	5	1	4	1	0	0	0	0	0	0	1	0	8715	1014	35	2	550	2	LDLRAP1	1	25889207	Splice_Site	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	15551081	25889207	223361414	2	255											
RNF19B	127544	hgsc.bcm.edu	37	chr1	33402549	33402549	+	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	cagtatgggagcggggggagCcacactcatctgaggtgatg	9	7	17	8	1	2	2	1	2	1	0	2	4	2	4	1	5	2	1	1	5	1	1			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:33402549C>G	ENST00000373456.7	-	9	2056	c.2057G>C	c.(2056-2058)gGc>gCc	p.G686A	RNF19B_ENST00000235150.4_Missense_Mutation_p.G685A|RNF19B_ENST00000356990.5_3'UTR	NM_153341.2	NP_699172.2	Q6ZMZ0	RN19B_HUMAN	ring finger protein 19B	686					interferon-gamma secretion (GO:0072643)|natural killer cell mediated cytotoxicity (GO:0042267)|protein ubiquitination (GO:0016567)	cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(2)|large_intestine(3)|lung(4)	13		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				GCGGGGGGAGCCACACTCATC	0.612																																					p.G686A		Atlas-SNP	.											.	RNF19B	43	.	0			c.G2057C						PASS	.						91	91	91					1																	33402549		2203	4300	6503	SO:0001583	missense	127544	exon9			GGGGAGCCACACT	AK074486	CCDS372.2, CCDS44107.1, CCDS72754.1	1p35.1	2010-05-11	2007-08-20	2007-08-20	ENSG00000116514	ENSG00000116514		"RING-type (C3HC4) zinc fingers"	26886	protein-coding gene	gene with protein product		610872	"IBR domain containing 3"	IBRDC3		12477932	Standard	XM_006710356		Approved	FLJ90005	uc010oho.2	Q6ZMZ0	OTTHUMG00000004013	ENST00000373456.7:c.2057G>C	chr1.hg19:g.33402549C>G	ENSP00000362555:p.Gly686Ala	60.0	0.0	.		42.0	19.0	.	NM_153341	B7ZLB2|E9PAW6|G3XA82|Q0VG77|Q5TH44|Q5TH45|Q6P6A4|Q8N2S8|Q8WUF3	Missense_Mutation	SNP	ENST00000373456.7	hg19	CCDS372.2	.	.	.	.	.	.	.	.	.	.	C	12.90	2.077464	0.36662	.	.	ENSG00000116514	ENST00000373456;ENST00000235150	T;T	0.30448	1.53;1.54	5.12	5.12	0.69794	.	0.160327	0.56097	D	0.000036	T	0.19127	0.0459	N	0.19112	0.55	0.35754	D	0.819621	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.002	T	0.12426	-1.0548	10	0.36615	T	0.2	.	9.4831	0.38913	0.0:0.7744:0.1461:0.0795	.	685;686	G3XA82;Q6ZMZ0	.;RN19B_HUMAN	A	686;685	ENSP00000362555:G686A;ENSP00000235150:G685A	ENSP00000235150:G685A	G	-	2	0	RNF19B	33175136	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.052000	0.49893	2.565000	0.86533	0.585000	0.79938	GGC	.	.	.	none		0.612	RNF19B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011465.3	NM_153341		G	33402549	C	G	33402549	3	3	4	1	0	0	0	0	1	0	0	0	13484	739	26	4	145	4	RNF19B	1	33402549	Missense_Mutation	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10	7513342	33402549	215848072	3	256											
EPHA10	284656	hgsc.bcm.edu	37	chr1	38192854	38192854	+	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	actacggtgacgacaatggcGgggctctggtccctggaccc	7	7	14	13	3	1	1	0	1	1	0	2	3	2	2	2	6	1	1	2	6	2	1	rs544755981		TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:38192854G>C	ENST00000373048.4	-	8	1691	c.1692C>G	c.(1690-1692)ccC>ccG	p.P564P	EPHA10_ENST00000427468.2_Silent_p.P564P|EPHA10_ENST00000446149.2_5'UTR|EPHA10_ENST00000330210.7_Silent_p.P59P|EPHA10_ENST00000540011.1_Silent_p.P59P	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	564					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)				CGACAATGGCGGGGCTCTGGT	0.647																																					p.P564P		Atlas-SNP	.											.	EPHA10	120	.	0			c.C1692G						PASS	.						48	63	58					1																	38192854		2041	4187	6228	SO:0001819	synonymous_variant	284656	exon8			AATGGCGGGGCTC	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.1692C>G	chr1.hg19:g.38192854G>C		124.0	0.0	.		113.0	39.0	.	NM_001099439	A4FU89|J3KPB5|Q6NW42	Silent	SNP	ENST00000373048.4	hg19	CCDS41305.1																																																																																			.	.	.	none		0.647	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641		C	38192854	G	C	38192854	2	2	4	1	0	0	0	0	0	0	0	1	5168	1103	39	4		4	EPHA10	1	38192854	Silent	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	4790305	38192854	211057767	4	257											
PDE4B	5142	hgsc.bcm.edu	37	chr1	66798100	66798100	+	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	agcacgggggcaccttcagtAgcaccggaatcagcggtggt	9	6	15	11	3	2	0	2	0	0	0	2	1	2	1	2	5	3	4	2	5	2	2			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:66798100A>C	ENST00000329654.4	+	8	821				PDE4B_ENST00000423207.2_Intron|PDE4B_ENST00000371049.3_Intron|PDE4B_ENST00000371045.5_Missense_Mutation_p.S10R	NM_001037341.1	NP_001032418.1	Q07343	PDE4B_HUMAN	phosphodiesterase 4B, cAMP-specific						cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|leukocyte migration (GO:0050900)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|neutrophil homeostasis (GO:0001780)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of high voltage-gated calcium channel activity (GO:1901841)|T cell receptor signaling pathway (GO:0050852)	cell periphery (GO:0071944)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	37					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theobromine(DB01412)|Theophylline(DB00277)	CACCTTCAGTAGCACCGGAAT	0.547																																					p.S10R		Atlas-SNP	.											.	PDE4B	231	.	0			c.A28C						PASS	.						83	83	83					1																	66798100		2203	4300	6503	SO:0001627	intron_variant	5142	exon1			TTCAGTAGCACCG	L20971	CCDS632.1, CCDS30742.1, CCDS30743.1, CCDS72802.1	1p31	2010-06-24	2010-06-24		ENSG00000184588	ENSG00000184588		"Phosphodiesterases"	8781	protein-coding gene	gene with protein product	"phosphodiesterase E4 dunce homolog (Drosophila)"	600127	"phosphodiesterase 4B, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E4)", "phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 dunce homolog, Drosophila)"	DPDE4			Standard	XM_005270925		Approved		uc001dco.3	Q07343	OTTHUMG00000009088	ENST00000329654.4:c.635-91A>C	chr1.hg19:g.66798100A>C		81.0	0.0	.		88.0	44.0	.	NM_001037339	A5YW33|O15443|Q13945|Q5TEK4|Q5TEK5|Q5TEK6	Missense_Mutation	SNP	ENST00000329654.4	hg19	CCDS632.1	.	.	.	.	.	.	.	.	.	.	A	13.91	2.377873	0.42105	.	.	ENSG00000184588	ENST00000371045	T	0.65178	-0.14	5.27	4.15	0.48705	.	.	.	.	.	T	0.17365	0.0417	N	0.03608	-0.345	0.80722	D	1	B	0.23058	0.079	B	0.18871	0.023	T	0.08046	-1.0741	9	0.20519	T	0.43	.	9.4851	0.38924	0.9147:0.0:0.0853:0.0	.	52	Q13945	.	R	10	ENSP00000360084:S10R	ENSP00000360084:S10R	S	+	1	0	PDE4B	66570688	0.424000	0.25490	0.978000	0.43139	0.741000	0.42261	1.394000	0.34509	1.049000	0.40321	0.459000	0.35465	AGC	.	.	.	none		0.547	PDE4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025188.3	NM_002600		C	66798100	A	C	66798100	1	2	4	0	1	0	0	0	0	0	0	0	11647	420	15	5		5	PDE4B	1	66798100	Intron	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10	28605246	66798100	182452521	5	258											
BCL10	8915	hgsc.bcm.edu	37	chr1	85741991	85741991	+	Missense_Mutation	SNP	T	T	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	ttactcacgtccttcttcacTtcagtgaggtcctcctcggt	5	15	7	14	2	4	1	3	1	1	0	8	1	7	1	3	2	1	0	3	2	1	4			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:85741991T>G	ENST00000370580.1	-	1	782	c.45A>C	c.(43-45)gaA>gaC	p.E15D	RP11-131L23.1_ENST00000427819.1_RNA|RP11-131L23.1_ENST00000426125.1_RNA	NM_003921.4	NP_003912.1	O95999	BCL10_HUMAN	B-cell CLL/lymphoma 10	15	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)		CCTTCTTCACTTCAGTGAGGT	0.697			T	IGH@	MALT																																p.E15D	NSCLC(34;993 1034 12176 32621 50182)	Atlas-SNP	.		Dom	yes		1	1p22	8915	B-cell CLL/lymphoma 10		L	.	BCL10	39	.	0			c.A45C						PASS	.						71	65	67					1																	85741991		2203	4300	6503	SO:0001583	missense	8915	exon1			CTTCACTTCAGTG	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.45A>C	chr1.hg19:g.85741991T>G	ENSP00000359612:p.Glu15Asp	76.0	0.0	.		59.0	34.0	.	NM_003921	Q5VUF1	Missense_Mutation	SNP	ENST00000370580.1	hg19	CCDS704.1	.	.	.	.	.	.	.	.	.	.	T	15.60	2.882269	0.51908	.	.	ENSG00000142867	ENST00000370580;ENST00000271015;ENST00000394761	T	0.51071	0.72	5.23	4.11	0.48088	DEATH-like (2);Caspase Recruitment (1);	0.324282	0.35291	N	0.003301	T	0.08670	0.0215	N	0.04508	-0.205	0.36773	D	0.883901	B	0.02656	0.0	B	0.04013	0.001	T	0.12268	-1.0554	10	0.22706	T	0.39	-20.4797	5.3938	0.16259	0.0:0.1576:0.1505:0.6919	.	15	O95999	BCL10_HUMAN	D	15	ENSP00000359612:E15D	ENSP00000271015:E15D	E	-	3	2	BCL10	85514579	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	0.650000	0.24858	1.027000	0.39758	0.379000	0.24179	GAA	.	.	.	none		0.697	BCL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027612.1	NM_003921		G	85741991	T	G	85741991	3	3	4	1	0	0	0	0	1	0	0	0	1362	1606	56	5	668	5	BCL10	1	85741991	Missense_Mutation	SNP	T	TCGA-2Z-A9J3-01A-12D-A382-10	18943891	85741991	163508630	6	259											
GBP3	2635	hgsc.bcm.edu	37	chr1	89473418	89473418	+	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	ctctgttgtttagatctttaGcttatgcgacatatatctct	8	19	6	8	1	3	1	0	0	3	1	4	2	3	1	0	0	2	3	0	0	5	8			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:89473418G>A	ENST00000370481.4	-	11	1997	c.1777C>T	c.(1777-1779)Cta>Tta	p.L593L		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)		TAGATCTTTAGCTTATGCGAC	0.338																																					p.L593L		Atlas-SNP	.											.	GBP3	53	.	0			c.C1777T						PASS	.						261	254	256					1																	89473418		2203	4300	6503	SO:0001819	synonymous_variant	2635	exon11			TCTTTAGCTTATG	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.1777C>T	chr1.hg19:g.89473418G>A		51.0	0.0	.		68.0	25.0	.	NM_018284	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Silent	SNP	ENST00000370481.4	hg19	CCDS717.2																																																																																			.	.	.	none		0.338	GBP3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313541.3	NM_018284		A	89473418	G	A	89473418	2	1	4	1	0	0	0	0	0	0	0	1	6282	962	34	2		2	GBP3	1	89473418	Silent	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	3731427	89473418	159777203	7	260											
ZNF644	84146	hgsc.bcm.edu	37	chr1	91404516	91404516	+	Missense_Mutation	SNP	T	T	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	acgtctgtgatctttgaagcTttcaggccttttggcgtcag	6	15	11	9	2	4	2	2	2	2	0	4	2	4	2	1	2	1	1	1	2	1	4			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:91404516T>G	ENST00000370440.1	-	3	2612	c.2395A>C	c.(2395-2397)Agc>Cgc	p.S799R	ZNF644_ENST00000337393.5_Missense_Mutation_p.S799R|ZNF644_ENST00000467231.1_Intron|ZNF644_ENST00000361321.5_Intron|ZNF644_ENST00000347275.5_Intron			Q9H582	ZN644_HUMAN	zinc finger protein 644	799					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)		TCTTTGAAGCTTTCAGGCCTT	0.378																																					p.S799R		Atlas-SNP	.											.	ZNF644	120	.	0			c.A2395C						PASS	.						68	71	70					1																	91404516		2203	4300	6503	SO:0001583	missense	84146	exon3			TGAAGCTTTCAGG	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.2395A>C	chr1.hg19:g.91404516T>G	ENSP00000359469:p.Ser799Arg	42.0	0.0	.		71.0	32.0	.	NM_201269	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Missense_Mutation	SNP	ENST00000370440.1	hg19	CCDS731.1	.	.	.	.	.	.	.	.	.	.	T	7.752	0.703462	0.15172	.	.	ENSG00000122482	ENST00000370440;ENST00000337393;ENST00000536941	T;T	0.47528	0.84;0.84	5.94	0.94	0.19513	.	1.368040	0.03945	N	0.287532	T	0.10594	0.0259	N	0.08118	0	0.26551	N	0.973916	B	0.02656	0.0	B	0.01281	0.0	T	0.13308	-1.0514	10	0.24483	T	0.36	2.2487	8.3928	0.32540	0.0:0.6073:0.0:0.3927	.	799	Q9H582	ZN644_HUMAN	R	799;799;371	ENSP00000359469:S799R;ENSP00000337008:S799R	ENSP00000337008:S799R	S	-	1	0	ZNF644	91177104	0.847000	0.29606	0.982000	0.44146	0.624000	0.37722	1.199000	0.32235	0.154000	0.19237	0.482000	0.46254	AGC	.	.	.	none		0.378	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186		G	91404516	T	G	91404516	3	3	4	1	0	0	0	0	1	0	0	0	18072	1609	56	5	1604	5	ZNF644	1	91404516	Missense_Mutation	SNP	T	TCGA-2Z-A9J3-01A-12D-A382-10	1931098	91404516	157846105	8	261											
DCLRE1B	64858	hgsc.bcm.edu	37	chr1	114450642	114450643	+	Frame_Shift_Ins	INS	-	-	A																															tcctccaggtgattttcgatINSacacaccatccatgctaaag																										TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:114450642_114450643insA	ENST00000369563.3	+	3	813_814	c.367_368insA	c.(367-369)tacfs	p.Y123fs	AP4B1_ENST00000256658.4_5'Flank|DCLRE1B_ENST00000466480.1_3'UTR	NM_022836.3	NP_073747.1	Q9H816	DCR1B_HUMAN	DNA cross-link repair 1B	123					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|protection from non-homologous end joining at telomere (GO:0031848)|telomere maintenance (GO:0000723)|telomeric 3' overhang formation (GO:0031860)|telomeric loop formation (GO:0031627)	centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)			breast(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(6)|stomach(1)	18	Lung SC(450;0.184)	all_cancers(81;1.46e-05)|all_epithelial(167;2.42e-05)|all_lung(203;0.000353)|Lung NSC(69;0.000518)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGATTTTCGATACACACCATCC	0.47								Other identified genes with known or suspected DNA repair function																													p.Y123_T124delinsX		Atlas-Indel,Pindel	.											.	DCLRE1B	36	.	0			c.367_368insA						PASS	.																																			SO:0001589	frameshift_variant	64858	exon3			.	BC029687	CCDS866.1	1p11.1	2010-06-24	2010-06-24		ENSG00000118655	ENSG00000118655			17641	protein-coding gene	gene with protein product	"APOLLO", "PSO2 homolog (S. cerevisiae)"	609683	"DNA cross-link repair 1B (PSO2 homolog, S. cerevisiae)"				Standard	NM_022836		Approved	SNM1B, FLJ12810, FLJ13998	uc001eeg.3	Q9H816	OTTHUMG00000011937	ENST00000369563.3:c.368dupA	chr1.hg19:g.114450643_114450643dupA	ENSP00000358576:p.Tyr123fs	68.0	0.0	0		57.0	26.0	0.45614	NM_022836	Q9H9E5	Frame_Shift_Ins	INS	ENST00000369563.3	hg19	CCDS866.1																																																																																			.	.	.	none		0.47	DCLRE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033020.2	NM_022836		A	114450643	-	A	114450642	7	5	4	1	0	1	1	0	0	0	0	0	4297	1406	49	0	377	0	DCLRE1B	1	114450642	Frame_Shift_Ins	INS	-	TCGA-2Z-A9J3-01A-12D-A382-10	23046126	114450642	134799979	9	262											
SPTA1	6708	hgsc.bcm.edu	37	chr1	158622405	158622405	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tataacgttgcaatagacgaCgtctgcgttcttctgcccga	9	12	9	11	5	3	1	0	0	3	1	3	3	3	1	1	0	4	3	1	0	4	6			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:158622405C>T	ENST00000368147.4	-	23	3407	c.3227G>A	c.(3226-3228)cGt>cAt	p.R1076H		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1076					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CAATAGACGACGTCTGCGTTC	0.438																																					p.R1076H		Atlas-SNP	.											.	SPTA1	720	.	0			c.G3227A						PASS	.						110	102	104					1																	158622405		1890	4110	6000	SO:0001583	missense	6708	exon23			AGACGACGTCTGC	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.3227G>A	chr1.hg19:g.158622405C>T	ENSP00000357129:p.Arg1076His	61.0	0.0	.		84.0	33.0	.	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	12.22	1.872785	0.33069	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.67523	-0.27;-0.27	5.3	4.39	0.52855	.	0.000000	0.32703	N	0.005759	T	0.41949	0.1181	L	0.54323	1.7	0.37353	D	0.910892	P	0.43542	0.81	B	0.34722	0.188	T	0.51764	-0.8664	10	0.52906	T	0.07	.	9.127	0.36821	0.0:0.8351:0.0:0.1649	.	1076	P02549	SPTA1_HUMAN	H	1076	ENSP00000357130:R1076H;ENSP00000357129:R1076H	ENSP00000357129:R1076H	R	-	2	0	SPTA1	156889029	1.000000	0.71417	0.236000	0.24074	0.013000	0.08279	3.123000	0.50453	1.488000	0.48433	-0.136000	0.14681	CGT	.	.	.	none		0.438	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		T	158622405	C	T	158622405	3	4	4	1	0	0	0	0	1	0	0	0	15128	536	19	1	4152	1	SPTA1	1	158622405	Missense_Mutation	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10	44171763	158622405	90628216	10	263											
NCSTN	23385	hgsc.bcm.edu	37	chr1	160326855	160326855	+	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	atgagtactcatgggtccagGgccctttgcattctaatgag	9	12	11	9	0	2	2	1	2	1	0	3	2	3	2	2	2	2	2	2	2	2	4			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:160326855G>C	ENST00000294785.5	+	16	1944	c.1819G>C	c.(1819-1821)Ggc>Cgc	p.G607R	NCSTN_ENST00000368063.1_Missense_Mutation_p.G587R|NCSTN_ENST00000368065.4_Missense_Mutation_p.G349R|NCSTN_ENST00000535857.1_Missense_Mutation_p.G469R|NCSTN_ENST00000392212.4_Missense_Mutation_p.G587R	NM_015331.2	NP_056146.1	Q92542	NICA_HUMAN	nicastrin	607					amyloid precursor protein catabolic process (GO:0042987)|apoptotic signaling pathway (GO:0097190)|beta-amyloid metabolic process (GO:0050435)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|myeloid cell homeostasis (GO:0002262)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|protein processing (GO:0016485)|proteolysis (GO:0006508)|T cell proliferation (GO:0042098)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase activity (GO:0004175)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(2)	34	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			ATGGGTCCAGGGCCCTTTGCA	0.552																																					p.G607R		Atlas-SNP	.											.	NCSTN	64	.	0			c.G1819C						PASS	.						200	168	179					1																	160326855		2203	4300	6503	SO:0001583	missense	23385	exon16			GTCCAGGGCCCTT	AF240468	CCDS1203.1	1q22-q23	2014-09-17			ENSG00000162736	ENSG00000162736			17091	protein-coding gene	gene with protein product		605254				9039502, 10993067	Standard	XM_005245053		Approved	KIAA0253, APH2	uc001fvx.3	Q92542	OTTHUMG00000033110	ENST00000294785.5:c.1819G>C	chr1.hg19:g.160326855G>C	ENSP00000294785:p.Gly607Arg	93.0	0.0	.		98.0	43.0	.	NM_015331	Q5T207|Q5T208|Q86VV5	Missense_Mutation	SNP	ENST00000294785.5	hg19	CCDS1203.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.946235	0.92593	.	.	ENSG00000162736	ENST00000294785;ENST00000368063;ENST00000535857;ENST00000392212;ENST00000368065	T;T;T;T	0.81163	-1.46;-1.45;-0.53;-1.45	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.87585	0.6214	M	0.71206	2.165	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	D	0.87185	0.2230	10	0.51188	T	0.08	-23.4934	18.0578	0.89368	0.0:0.0:1.0:0.0	.	469;587;607	F6Y097;Q92542-2;Q92542	.;.;NICA_HUMAN	R	607;587;469;587;349	ENSP00000294785:G607R;ENSP00000357042:G587R;ENSP00000442605:G469R;ENSP00000376047:G587R	ENSP00000294785:G607R	G	+	1	0	NCSTN	158593479	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	8.756000	0.91651	2.606000	0.88127	0.650000	0.86243	GGC	.	.	.	none		0.552	NCSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080622.1	NM_015331		C	160326855	G	C	160326855	3	2	4	1	0	0	0	0	1	0	0	0	10248	1232	43	4	1881	4	NCSTN	1	160326855	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	1704450	160326855	88923766	11	264											
IGFN1	91156	hgsc.bcm.edu	37	chr1	201174369	201174369	+	Frame_Shift_Del	DEL	C	C	-																															caaatatgaagtgtatgtgtCccctgacgggctgacccacc																										TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:201174369delC	ENST00000335211.4	+	11	1206	c.1076delC	c.(1075-1077)tccfs	p.S359fs	IGFN1_ENST00000295591.8_5'UTR|IGFN1_ENST00000451870.2_Frame_Shift_Del_p.S359fs	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	359	Ig-like 2.					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						GTGTATGTGTCCCCTGACGGG	0.617																																					p.S359fs		Atlas-Indel,Pindel	.											.	IGFN1	220	.	0			c.1075delT						PASS	.						33	32	32					1																	201174369		692	1591	2283	SO:0001589	frameshift_variant	91156	exon11			.	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.1076delC	chr1.hg19:g.201174369delC	ENSP00000334714:p.Ser359fs	122.0	0.0	0		122.0	46.0	0.377049	NM_001164586	F8WAI1|Q9NT72	Frame_Shift_Del	DEL	ENST00000335211.4	hg19	CCDS53455.1																																																																																			.	.	.	none		0.617	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275		-	201174369	C	-	201174369	7	5	4	1	0	1	0	1	0	0	0	0	7597	855	30	0	1114	0	IGFN1	1	201174369	Frame_Shift_Del	DEL	C	TCGA-2Z-A9J3-01A-12D-A382-10	40847514	201174369	48076252	12	265											
RPS6KC1	26750	hgsc.bcm.edu	37	chr1	213302993	213302993	+	Frame_Shift_Del	DEL	C	C	-																															ttttggtctcaatctttcttCggattcttcagcactagggg																										TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:213302993delC	ENST00000366960.3	+	6	746	c.596delC	c.(595-597)tcgfs	p.S199fs	RPS6KC1_ENST00000366959.3_Frame_Shift_Del_p.S187fs|RPS6KC1_ENST00000490299.1_3'UTR|RPS6KC1_ENST00000543470.1_Frame_Shift_Del_p.S18fs|RPS6KC1_ENST00000543354.1_Intron	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	199					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)		AATCTTTCTTCGGATTCTTCA	0.433																																					p.S199fs		Atlas-Indel,Pindel	.											.	RPS6KC1	114	.	0			c.595delT						PASS	.						96	95	96					1																	213302993		2203	4300	6503	SO:0001589	frameshift_variant	26750	exon6			.	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.596delC	chr1.hg19:g.213302993delC	ENSP00000355927:p.Ser199fs	42.0	0.0	0		71.0	23.0	0.323944	NM_012424	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Frame_Shift_Del	DEL	ENST00000366960.3	hg19	CCDS1513.1																																																																																			.	.	.	none		0.433	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3	NM_012424		-	213302993	C	-	213302993	7	5	4	1	0	1	0	1	0	0	0	0	13671	893	31	0	618	0	RPS6KC1	1	213302993	Frame_Shift_Del	DEL	C	TCGA-2Z-A9J3-01A-12D-A382-10	12128624	213302993	35947628	13	266											
AGT	183	hgsc.bcm.edu	37	chr1	230846200	230846200	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacagccgttggggagaggaCggtggccccatggaccacgc	8	4	17	12	3	0	1	0	0	0	1	0	5	0	3	4	6	1	1	4	6	0	1	rs559327874		TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:230846200C>T	ENST00000366667.4	-	2	611	c.397G>A	c.(397-399)Gtc>Atc	p.V133I	RP11-99J16__A.2_ENST00000412344.1_RNA	NM_000029.3	NP_000020.1	P01019	ANGT_HUMAN	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	133					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)		GGGGAGAGGACGGTGGCCCCA	0.592													C|||	1	0.000199681	0	0	5008	,	,		20155	0		0	False		,,,				2504	0.001				p.V133I		Atlas-SNP	.											.	AGT	62	.	0			c.G397A						PASS	.						99	99	99					1																	230846200		2203	4300	6503	SO:0001583	missense	183	exon2			AGAGGACGGTGGC	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.397G>A	chr1.hg19:g.230846200C>T	ENSP00000355627:p.Val133Ile	94.0	0.0	.		74.0	25.0	.	NM_000029	Q16358|Q16359|Q96F91	Missense_Mutation	SNP	ENST00000366667.4	hg19	CCDS1585.1	.	.	.	.	.	.	.	.	.	.	C	0.057	-1.234253	0.01505	.	.	ENSG00000135744	ENST00000366667;ENST00000430091	D	0.84370	-1.84	5.09	-7.39	0.01402	Serpin domain (3);	0.452988	0.23554	N	0.046932	T	0.56232	0.1971	N	0.08118	0	0.09310	N	1	B;B;B	0.12630	0.002;0.006;0.002	B;B;B	0.11329	0.001;0.006;0.001	T	0.59915	-0.7364	10	0.07813	T	0.8	.	5.113	0.14819	0.0807:0.2591:0.1175:0.5427	.	133;133;133	B0ZBE2;B2R5S1;P01019	.;.;ANGT_HUMAN	I	133	ENSP00000355627:V133I	ENSP00000355627:V133I	V	-	1	0	AGT	228912823	0.013000	0.17824	0.000000	0.03702	0.003000	0.03518	-0.338000	0.07842	-0.993000	0.03467	-1.247000	0.01520	GTC	.	.	.	none		0.592	AGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092102.1	NM_000029		T	230846200	C	T	230846200	3	4	4	1	0	0	0	0	1	0	0	0	399	536	19	1	1076	1	AGT	1	230846200	Missense_Mutation	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10	17543207	230846200	18404421	14	267											
KIF26B	55083	hgsc.bcm.edu	37	chr1	245319611	245319611	+	Missense_Mutation	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	aagtctgctcgcccaccaagCccgcagcgcccttctccccg	6	6	8	21	4	2	0	0	0	2	0	4	0	2	0	6	0	3	2	6	0	2	1			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:245319611C>T	ENST00000407071.2	+	2	531	c.91C>T	c.(91-93)Ccc>Tcc	p.P31S		NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	31					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)			GCCCACCAAGCCCGCAGCGCC	0.701																																					p.P31S		Atlas-SNP	.											.	KIF26B	343	.	0			c.C91T						PASS	.						5	7	7					1																	245319611		1523	3110	4633	SO:0001583	missense	55083	exon2			ACCAAGCCCGCAG	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.91C>T	chr1.hg19:g.245319611C>T	ENSP00000385545:p.Pro31Ser	117.0	0.0	.		95.0	50.0	.	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	hg19	CCDS44342.1	.	.	.	.	.	.	.	.	.	.	C	10.02	1.236563	0.22711	.	.	ENSG00000162849	ENST00000407071	T	0.74315	-0.83	4.77	3.77	0.43336	.	.	.	.	.	T	0.47911	0.1471	N	0.04508	-0.205	0.80722	D	1	B	0.12630	0.006	B	0.10450	0.005	T	0.42068	-0.9473	9	0.15499	T	0.54	.	8.2256	0.31566	0.193:0.715:0.0:0.0919	.	31	Q2KJY2	KI26B_HUMAN	S	31	ENSP00000385545:P31S	ENSP00000385545:P31S	P	+	1	0	KIF26B	243386234	0.999000	0.42202	0.998000	0.56505	0.966000	0.64601	0.589000	0.23939	2.177000	0.69029	0.561000	0.74099	CCC	.	.	.	none		0.701	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		T	245319611	C	T	245319611	3	4	4	1	0	0	0	0	1	0	0	0	8302	739	26	2	97	2	KIF26B	1	245319611	Missense_Mutation	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10	14473411	245319611	3931010	15	268											
LPIN1	23175	hgsc.bcm.edu	37	chr2	11924034	11924034	+	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	gatcctgaagtggcggccctGtattttcccaaaaagtaaaa	13	10	9	9	1	0	1	0	1	0	0	2	2	2	1	3	2	0	2	3	2	6	4			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:11924034G>A	ENST00000256720.2	+	8	1329	c.1236G>A	c.(1234-1236)ctG>ctA	p.L412L	LPIN1_ENST00000396098.1_Silent_p.L454L|LPIN1_ENST00000396099.1_Silent_p.L454L|LPIN1_ENST00000449576.2_Silent_p.L497L|LPIN1_ENST00000425416.2_Silent_p.L418L|LPIN1_ENST00000396097.1_Silent_p.L142L	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	412					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)		TGGCGGCCCTGTATTTTCCCA	0.423																																					p.L497L		Atlas-SNP	.											.	LPIN1	99	.	0			c.G1491A						PASS	.						169	173	172					2																	11924034		2203	4300	6503	SO:0001819	synonymous_variant	23175	exon10			GGCCCTGTATTTT	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.1236G>A	chr2.hg19:g.11924034G>A		98.0	0.0	.		82.0	35.0	.	NM_001261428	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Silent	SNP	ENST00000256720.2	hg19	CCDS1682.1																																																																																			.	.	.	none		0.423	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693		A	11924034	G	A	11924034	2	1	4	1	0	0	0	0	0	0	0	1	8925	1364	48	2		2	LPIN1	2	11924034	Silent	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10		11924034	231275339	16	269											
NRXN1	9378	hgsc.bcm.edu	37	chr2	51255154	51255154	+	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	aagctgagctgcaggcggccGccgcgcgtcagaatcagctc	8	5	14	14	5	2	2	2	1	0	1	3	2	2	2	2	2	4	4	2	2	2	0			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:51255154G>A	ENST00000406316.2	-	2	1734	c.258C>T	c.(256-258)ggC>ggT	p.G86G	NRXN1_ENST00000406859.3_Silent_p.G86G|NRXN1_ENST00000405472.3_Silent_p.G86G|NRXN1_ENST00000401669.2_Silent_p.G86G|NRXN1_ENST00000402717.3_Silent_p.G86G|NRXN1_ENST00000405581.1_Silent_p.G86G|NRXN1_ENST00000404971.1_Silent_p.G86G	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	86	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)			GCAGGCGGCCGCCGCGCGTCA	0.662																																					p.G86G		Atlas-SNP	.											.	NRXN1	1118	.	0			c.C258T						PASS	.						13	17	16					2																	51255154		1982	4144	6126	SO:0001819	synonymous_variant	9378	exon2			GCGGCCGCCGCGC	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.258C>T	chr2.hg19:g.51255154G>A		39.0	0.0	.		48.0	19.0	.	NM_004801	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	hg19	CCDS54360.1																																																																																			.	.	.	none		0.662	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			A	51255154	G	A	51255154	2	1	4	1	0	0	0	0	0	0	0	1	10672	1074	38	1		1	NRXN1	2	51255154	Silent	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	39331120	51255154	191944219	17	270											
C2orf86	51057	hgsc.bcm.edu	37	chr2	63380691	63380691	+	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	atgtctttttcaagttcattCcttctgtcaattatttgtct	7	22	4	8	0	6	0	3	0	3	0	7	0	7	0	1	0	0	1	1	0	3	7			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:63380691C>G	ENST00000272321.7	-	16	2624	c.2097G>C	c.(2095-2097)agG>agC	p.R699S	WDPCP_ENST00000398544.3_Missense_Mutation_p.R540S|WDPCP_ENST00000409199.1_Missense_Mutation_p.R507S|WDPCP_ENST00000409120.1_Missense_Mutation_p.R507S	NM_015910.5	NP_056994.3	O95876	FRITZ_HUMAN	WD repeat containing planar cell polarity effector	699					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)		p.R699S(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(19)|ovary(1)|skin(1)	35						CAAGTTCATTCCTTCTGTCAA	0.294																																					p.R699S		Atlas-SNP	.											WDPCP,NS,carcinoma,0,1	WDPCP	79	.	1	Substitution - Missense(1)	lung(1)	c.G2097C						PASS	.						86	80	82					2																	63380691		1798	4058	5856	SO:0001583	missense	51057	exon16			TTCATTCCTTCTG		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.2097G>C	chr2.hg19:g.63380691C>G	ENSP00000272321:p.Arg699Ser	50.0	0.0	.		59.0	19.0	.	NM_015910	Q53RW4|Q7Z2Z3	Missense_Mutation	SNP	ENST00000272321.7	hg19	CCDS42688.1	.	.	.	.	.	.	.	.	.	.	C	0.015	-1.562941	0.00903	.	.	ENSG00000143951	ENST00000272321;ENST00000409199;ENST00000409120;ENST00000398544	T;T;T;T	0.72505	-0.66;-0.08;-0.08;-0.08	4.57	-3.39	0.04868	.	.	.	.	.	T	0.49115	0.1538	N	0.14661	0.345	0.09310	N	1	B;B	0.30281	0.18;0.275	B;B	0.25405	0.017;0.06	T	0.26744	-1.0094	9	0.62326	D	0.03	-0.5444	10.4749	0.44659	0.0:0.3924:0.0:0.6076	.	699;540	O95876;O95876-3	FRITZ_HUMAN;.	S	699;507;507;540	ENSP00000272321:R699S;ENSP00000386592:R507S;ENSP00000386769:R507S;ENSP00000381552:R540S	ENSP00000272321:R699S	R	-	3	2	WDPCP	63234195	0.007000	0.16637	0.001000	0.08648	0.161000	0.22273	-0.042000	0.12063	-1.185000	0.02716	-1.124000	0.02001	AGG	.	.	.	none		0.294	WDPCP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326820.1	NM_015910		G	63380691	C	G	63380691	3	3	4	1	0	0	0	0	1	0	0	0	2203	854	30	4	155	4	C2orf86	2	63380691	Missense_Mutation	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10	12125537	63380691	179818682	18	271											
DYSF	8291	hgsc.bcm.edu	37	chr2	71740432	71740437	+	Intron	DEL	TACTCT	TACTCT	-																															acagcaccatggacacgagaTactctggaaagaagtggccg																										TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	TACTCT	TACTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:71740432_71740437delTACTCT	ENST00000258104.3	+	6	734				DYSF_ENST00000409366.1_Intron|DYSF_ENST00000394120.2_Intron|DYSF_ENST00000409762.1_In_Frame_Del_p.YS174del|DYSF_ENST00000409651.1_In_Frame_Del_p.YS175del|DYSF_ENST00000410020.3_In_Frame_Del_p.YS175del|DYSF_ENST00000410041.1_In_Frame_Del_p.YS175del|DYSF_ENST00000413539.2_In_Frame_Del_p.YS174del|DYSF_ENST00000409744.1_Intron|DYSF_ENST00000409582.3_In_Frame_Del_p.YS174del|DYSF_ENST00000429174.2_Intron	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin						plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						GGACACGAGATACTCTGGAAAGAAGT	0.636																																					p.174_176del		Atlas-Indel,Pindel	.											.	DYSF	536	.	0			c.522_527del						PASS	.																																			SO:0001627	intron_variant	8291	exon6			.	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"fer-1-like family member 1"	603009	"limb girdle muscular dystrophy 2B (autosomal recessive)"	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.458-409TACTCT>-	chr2.hg19:g.71740432_71740437delTACTCT		206.0	0.0	0		156.0	38.0	0.24359	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	hg19	CCDS1918.1																																																																																			.	.	.	none		0.636	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		-	71740437	TACTCT	-	71740432	6	5	4	0	1	1	0	1	0	0	0	0	4861	1406	49	0		0	DYSF	2	71740432	Intron	DEL	TACTCT	TCGA-2Z-A9J3-01A-12D-A382-10	8359741	71740432	171458941	19	272											
ACTR1B	10120	hgsc.bcm.edu	37	chr2	98275931	98275931	+	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	gtagcggatggtcagcagccCccggtgctcctggtggggtg	4	8	18	11	2	1	0	1	0	0	0	2	1	2	1	3	6	4	3	3	6	1	1			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:98275931C>T	ENST00000289228.5	-	4	415	c.199G>A	c.(199-201)Ggg>Agg	p.G67R		NM_005735.3	NP_005726.1	P42025	ACTY_HUMAN	ARP1 actin-related protein 1 homolog B, centractin beta (yeast)	67					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)			endometrium(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	15						GTCAGCAGCCCCCGGTGCTCC	0.652																																					p.G67R		Atlas-SNP	.											ACTR1B,colon,carcinoma,0,1	ACTR1B	34	.	0			c.G199A						PASS	.						152	150	151					2																	98275931		2203	4300	6503	SO:0001583	missense	10120	exon4			GCAGCCCCCGGTG	X82207	CCDS2033.1	2q11.1-q11.2	2008-05-20	2001-11-28		ENSG00000115073	ENSG00000115073			168	protein-coding gene	gene with protein product		605144	"ARP1 (actin-related protein 1, yeast) homolog B (centractin beta)"	CTRN2		7696711, 10343100	Standard	NM_005735		Approved		uc002syb.2	P42025	OTTHUMG00000130549	ENST00000289228.5:c.199G>A	chr2.hg19:g.98275931C>T	ENSP00000289228:p.Gly67Arg	45.0	0.0	.		34.0	12.0	.	NM_005735	D3DVH2|Q53SK5|Q9BRB7	Missense_Mutation	SNP	ENST00000289228.5	hg19	CCDS2033.1	.	.	.	.	.	.	.	.	.	.	.	33	5.207637	0.95033	.	.	ENSG00000115073	ENST00000289228	D	0.94650	-3.48	5.18	5.18	0.71444	.	0.062472	0.64402	D	0.000005	D	0.97763	0.9266	M	0.92026	3.265	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98725	1.0710	10	0.87932	D	0	.	16.1821	0.81915	0.0:1.0:0.0:0.0	.	67	P42025	ACTY_HUMAN	R	67	ENSP00000289228:G67R	ENSP00000289228:G67R	G	-	1	0	ACTR1B	97642363	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.795000	0.85887	2.427000	0.82271	0.555000	0.69702	GGG	.	.	.	none		0.652	ACTR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252973.1	NM_005735		T	98275931	C	T	98275931	3	4	4	1	0	0	0	0	1	0	0	0	210	623	22	2	963	2	ACTR1B	2	98275931	Missense_Mutation	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10	26535499	98275931	144923442	20	273											
MERTK	10461	hgsc.bcm.edu	37	chr2	112705128	112705128	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcctgaaaaatccccctcCgtgctaactgttccaggtaa	11	9	7	14	1	0	1	0	1	0	0	3	1	3	1	5	1	3	3	5	1	4	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:112705128C>T	ENST00000295408.4	+	4	998	c.741C>T	c.(739-741)tcC>tcT	p.S247S	MERTK_ENST00000409780.1_Silent_p.S71S|MERTK_ENST00000421804.2_Silent_p.S247S			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	247	Ig-like C2-type 2.			S -> G (in Ref. 1; AAB60430). {ECO:0000305}.	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						AATCCCCCTCCGTGCTAACTG	0.507																																					p.S247S		Atlas-SNP	.											.	MERTK	112	.	0			c.C741T						PASS	.						51	54	53					2																	112705128		2203	4300	6503	SO:0001819	synonymous_variant	10461	exon4			CCCCTCCGTGCTA	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.741C>T	chr2.hg19:g.112705128C>T		112.0	0.0	.		131.0	50.0	.	NM_006343	Q9HBB4	Silent	SNP	ENST00000295408.4	hg19	CCDS2094.1																																																																																			.	.	.	none		0.507	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2			T	112705128	C	T	112705128	2	4	4	1	0	0	0	0	0	0	0	1	9486	639	23	1		1	MERTK	2	112705128	Silent	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10	14429197	112705128	130494245	21	274											
STAM2	10254	hgsc.bcm.edu	37	chr2	152980339	152980339	+	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	gaattcacatttggaggcagAgatctcagtggaccaatttg	12	11	11	7	0	2	1	2	0	1	1	3	5	2	3	1	3	0	1	1	3	2	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:152980339A>C	ENST00000263904.4	-	13	1639	c.1290T>G	c.(1288-1290)tcT>tcG	p.S430S		NM_005843.4	NP_005834.4	O75886	STAM2_HUMAN	signal transducing adaptor molecule (SH3 domain and ITAM motif) 2	430					endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(3)|large_intestine(4)|lung(8)|ovary(1)	16				BRCA - Breast invasive adenocarcinoma(221;0.22)		TTGGAGGCAGAGATCTCAGTG	0.408																																					p.S430S		Atlas-SNP	.											.	STAM2	44	.	0			c.T1290G						PASS	.						125	110	115					2																	152980339		2203	4300	6503	SO:0001819	synonymous_variant	10254	exon13			AGGCAGAGATCTC	AF042274	CCDS2196.1	2q23.3	2009-04-29			ENSG00000115145	ENSG00000115145			11358	protein-coding gene	gene with protein product	"HSE1 homolog (S. cerevisiae)"	606244				10899310, 10993906	Standard	NM_005843		Approved	Hbp	uc002tyc.4	O75886	OTTHUMG00000131885	ENST00000263904.4:c.1290T>G	chr2.hg19:g.152980339A>C		68.0	0.0	.		91.0	39.0	.	NM_005843	A8K8A0|D3DPA1|Q7LDQ0|Q9UF58	Silent	SNP	ENST00000263904.4	hg19	CCDS2196.1																																																																																			.	.	.	none		0.408	STAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254835.2	NM_005843		C	152980339	A	C	152980339	2	2	4	1	0	0	0	0	0	0	0	1	15261	291	11	5		5	STAM2	2	152980339	Silent	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10	40275211	152980339	90219034	22	275											
UPP2	151531	hgsc.bcm.edu	37	chr2	158978032	158978032	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacccgaagtactgaactggAcaaagaactgtctgaagaac	16	6	9	10	1	1	4	0	2	1	2	1	6	1	5	1	1	4	1	1	1	7	1			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:158978032A>G	ENST00000005756.4	+	5	760	c.566A>G	c.(565-567)gAc>gGc	p.D189G	UPP2_ENST00000460456.1_Intron|UPP2_ENST00000409859.4_Missense_Mutation_p.D246G|UPP2_ENST00000605860.1_Missense_Mutation_p.D246G	NM_173355.3	NP_775491.1	O95045	UPP2_HUMAN	uridine phosphorylase 2	189					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)	ACTGAACTGGACAAAGAACTG	0.423																																					p.D246G		Atlas-SNP	.											.	UPP2	60	.	0			c.A737G						PASS	.						183	178	180					2																	158978032		2203	4299	6502	SO:0001583	missense	151531	exon7			AACTGGACAAAGA	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.566A>G	chr2.hg19:g.158978032A>G	ENSP00000005756:p.Asp189Gly	288.0	0.0	.		349.0	67.0	.	NM_001135098	B3KV87	Missense_Mutation	SNP	ENST00000005756.4	hg19	CCDS2207.1	.	.	.	.	.	.	.	.	.	.	A	14.27	2.486167	0.44147	.	.	ENSG00000007001	ENST00000409859;ENST00000005756	D;D	0.90732	-2.72;-2.72	5.75	4.53	0.55603	Nucleoside phosphorylase domain (1);	0.047805	0.85682	D	0.000000	D	0.95085	0.8408	M	0.88704	2.975	0.58432	D	0.999998	D	0.65815	0.995	D	0.66847	0.947	D	0.95272	0.8378	10	0.66056	D	0.02	.	10.8108	0.46547	0.8584:0.0:0.0:0.1416	.	189	O95045	UPP2_HUMAN	G	246;189	ENSP00000387230:D246G;ENSP00000005756:D189G	ENSP00000005756:D189G	D	+	2	0	UPP2	158686278	1.000000	0.71417	1.000000	0.80357	0.034000	0.12701	6.094000	0.71431	2.195000	0.70347	0.533000	0.62120	GAC	.	.	.	none		0.423	UPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254929.2	NM_173355		G	158978032	A	G	158978032	3	3	4	1	0	0	0	0	1	0	0	0	17025	275	10	3	763	3	UPP2	2	158978032	Missense_Mutation	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10	5997693	158978032	84221341	23	276											
LY75	4065	hgsc.bcm.edu	37	chr2	160743016	160743016	+	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	agctgatttaaaccaatccaGaaaatcttagcaatgccttc	15	11	5	10	0	1	2	0	1	1	1	3	2	2	2	3	0	4	2	3	0	7	4			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:160743016G>C	ENST00000263636.4	-	5	855	c.828C>G	c.(826-828)ttC>ttG	p.F276L	LY75_ENST00000553424.1_Missense_Mutation_p.F276L|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.F276L|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.F276L|LY75_ENST00000554112.1_Missense_Mutation_p.F276L	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	276	C-type lectin 1. {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)		AACCAATCCAGAAAATCTTAG	0.338																																					p.F276L		Atlas-SNP	.											.	LY75	151	.	0			c.C828G						PASS	.						103	104	103					2																	160743016		2203	4300	6503	SO:0001583	missense	4065	exon5			AATCCAGAAAATC	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.828C>G	chr2.hg19:g.160743016G>C	ENSP00000263636:p.Phe276Leu	21.0	0.0	.		30.0	16.0	.	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	hg19	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	G	10.68	1.418920	0.25552	.	.	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.20069	2.1;2.1;2.1;2.1;2.1	5.77	3.95	0.45737	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.223549	0.22745	N	0.056144	T	0.12689	0.0308	L	0.33753	1.03	0.32662	N	0.517909	B;P;P	0.44309	0.259;0.832;0.763	B;B;B	0.42495	0.082;0.389;0.309	T	0.11616	-1.0580	10	0.02654	T	1	-9.0045	5.7022	0.17889	0.2339:0.1426:0.6235:0.0	.	276;276;276	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	L	276	ENSP00000451511:F276L;ENSP00000451446:F276L;ENSP00000263636:F276L;ENSP00000423463:F276L;ENSP00000421035:F276L	ENSP00000423463:F276L	F	-	3	2	LY75;LY75-CD302	160451262	1.000000	0.71417	0.993000	0.49108	0.856000	0.48823	0.890000	0.28295	0.755000	0.32990	0.557000	0.71058	TTC	.	.	.	none		0.338	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1			C	160743016	G	C	160743016	3	2	4	1	0	0	0	0	1	0	0	0	9106	933	33	4	4464	4	LY75	2	160743016	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	1764984	160743016	82456357	24	277											
SCN9A	6335	hgsc.bcm.edu	37	chr2	167142945	167142945	+	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	ctgtcctctgattctgatttCgacaatttctcagcatctcc	7	16	5	13	1	4	2	1	2	4	0	8	3	5	2	2	0	1	1	2	0	1	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:167142945C>T	ENST00000409435.1	-	10	1502	c.1503G>A	c.(1501-1503)tcG>tcA	p.S501S	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Silent_p.S502S|SCN9A_ENST00000409672.1_Silent_p.S501S|SCN9A_ENST00000375387.4_Silent_p.S502S			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	501				S -> P (in Ref. 4; AAT85835). {ECO:0000305}.	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.S501S(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)	ATTCTGATTTCGACAATTTCT	0.428																																					p.S501S		Atlas-SNP	.											SCN9A,NS,carcinoma,0,1	SCN9A	296	.	1	Substitution - coding silent(1)	prostate(1)	c.G1503A						PASS	.						170	161	164					2																	167142945		1910	4120	6030	SO:0001819	synonymous_variant	6335	exon11			TGATTTCGACAAT	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.1503G>A	chr2.hg19:g.167142945C>T		51.0	0.0	.		53.0	13.0	.	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Silent	SNP	ENST00000409435.1	hg19	CCDS46441.1																																																																																			.	.	.	none		0.428	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		T	167142945	C	T	167142945	2	4	4	1	0	0	0	0	0	0	0	1	13938	871	31	1		1	SCN9A	2	167142945	Silent	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10	6399929	167142945	76056428	25	278											
PARD3B	117583	hgsc.bcm.edu	37	chr2	205550903	205550903	+	Splice_Site	DEL	G	G	-																															cttgtgtttgttctactataGggtcctggttactgggtgaa																										TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:205550903delG	ENST00000406610.2	+	2	327		c.e2-1		PARD3B_ENST00000358768.2_Splice_Site|PARD3B_ENST00000351153.1_Splice_Site|PARD3B_ENST00000462231.1_Splice_Site|PARD3B_ENST00000349953.3_Splice_Site	NM_057177.6|NM_152526.5|NM_205863.3	NP_476518.4|NP_689739.4|NP_995585.2	Q8TEW8	PAR3L_HUMAN	par-3 family cell polarity regulator beta						cell cycle (GO:0007049)|cell division (GO:0051301)	membrane (GO:0016020)|tight junction (GO:0005923)				breast(1)|endometrium(9)|kidney(2)|large_intestine(6)|liver(4)|lung(33)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	65		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		TTCTACTATAGGGTCCTGGTT	0.328																																					.		Atlas-Indel,Pindel	.											.	PARD3B	314	.	0			c.121-2G>-						PASS	.						127	114	118					2																	205550903		1830	4085	5915	SO:0001630	splice_region_variant	117583	exon2			.	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.121-1G>-	chr2.hg19:g.205550903delG		58.0	0.0	0		103.0	25.0	0.242718	NM_057177	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	Splice_Site	DEL	ENST00000406610.2	hg19																																																																																				.	.	.	none		0.328	PARD3B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000335992.1	NM_057177	Intron	-	205550903	G	-	205550903	8	5	4	1	0	1	0	1	0	0	1	0	11451	1014	35	0	126	0	PARD3B	2	205550903	Splice_Site	DEL	G	TCGA-2Z-A9J3-01A-12D-A382-10	38407958	205550903	37648470	26	279											
KIAA1486	57624	hgsc.bcm.edu	37	chr2	226378138	226378138	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaagttacgtgggcaaacaTttccgcatgggattcatgac	11	10	12	8	2	1	1	1	1	0	0	2	3	2	3	1	3	2	3	1	3	3	3	rs373061629		TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:226378138T>C	ENST00000272907.6	+	3	686	c.273T>C	c.(271-273)caT>caC	p.H91H	NYAP2_ENST00000409269.2_Intron	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	91					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												TGGGCAAACATTTCCGCATGG	0.507																																					p.H91H		Atlas-SNP	.											.	.	.	.	0			c.T273C						PASS	.	T		0,4116		0,0,2058	79	83	82		273	-5.2	0.9	2		82	1,8379		0,1,4189	no	coding-synonymous	KIAA1486	NM_020864.1		0,1,6247	CC,CT,TT		0.0119,0.0,0.0080		91/654	226378138	1,12495	2058	4190	6248	SO:0001819	synonymous_variant	57624	exon3			CAAACATTTCCGC	AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"KIAA1486"	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.273T>C	chr2.hg19:g.226378138T>C		116.0	0.0	.		117.0	52.0	.	NM_020864	A2RRN4|Q96NL2	Silent	SNP	ENST00000272907.6	hg19	CCDS46529.1																																																																																			.	.	.	weak		0.507	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864		C	226378138	T	C	226378138	2	2	4	1	0	0	0	0	0	0	0	1	8244	1490	52	3		3	KIAA1486	2	226378138	Silent	SNP	T	TCGA-2Z-A9J3-01A-12D-A382-10	20827235	226378138	16821235	27	280											
KCNJ13	3769	hgsc.bcm.edu	37	chr2	233633084	233633084	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaacctcgggtcaacagagaTgcaaaacagtgatgtaacat	16	7	10	8	1	1	2	1	1	0	1	2	4	1	2	1	1	5	2	1	1	5	1			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:233633084T>C	ENST00000233826.3	-	3	1039	c.900A>G	c.(898-900)gcA>gcG	p.A300A	GIGYF2_ENST00000409480.1_Intron|GIGYF2_ENST00000452341.2_Intron|KCNJ13_ENST00000409779.1_3'UTR|GIGYF2_ENST00000409196.3_Intron|GIGYF2_ENST00000409451.3_Intron|GIGYF2_ENST00000373566.3_Intron|AC064852.4_ENST00000427571.1_RNA|GIGYF2_ENST00000373563.4_Intron|GIGYF2_ENST00000409547.1_Intron|KCNJ13_ENST00000410029.1_Silent_p.A300A	NM_002242.4	NP_002233.2	O60928	KCJ13_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 13	300					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	inward rectifier potassium channel activity (GO:0005242)			endometrium(3)|large_intestine(2)|lung(2)|stomach(1)|urinary_tract(1)	9		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0306)|Lung NSC(271;0.0908)		Epithelial(121;5.9e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0617)		TCAACAGAGATGCAAAACAGT	0.428																																					p.A300A		Atlas-SNP	.											.	KCNJ13	18	.	0			c.A900G						PASS	.						167	160	163					2																	233633084		2203	4300	6503	SO:0001819	synonymous_variant	3769	exon3			CAGAGATGCAAAA	AJ006128	CCDS2498.1, CCDS54437.1	2q37	2014-01-28			ENSG00000115474	ENSG00000115474		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6259	protein-coding gene	gene with protein product		603208				9878260, 9620703, 16382105	Standard	NM_002242		Approved	Kir7.1, Kir1.4, LCA16	uc002vtp.3	O60928	OTTHUMG00000153292	ENST00000233826.3:c.900A>G	chr2.hg19:g.233633084T>C		131.0	0.0	.		145.0	65.0	.	NM_002242	A0PGH1|O76023|Q53SA1|Q8N3Y4	Silent	SNP	ENST00000233826.3	hg19	CCDS2498.1																																																																																			.	.	.	none		0.428	KCNJ13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257036.1	NM_002242		C	233633084	T	C	233633084	2	2	4	1	0	0	0	0	0	0	0	1	8054	1451	51	3		3	KCNJ13	2	233633084	Silent	SNP	T	TCGA-2Z-A9J3-01A-12D-A382-10	7254946	233633084	9566289	28	281											
TTC21A	199223	hgsc.bcm.edu	37	chr3	39175774	39175775	+	Frame_Shift_Ins	INS	-	-	TCCA																															acctgtgtgagcagcactgtINSgccatcctcctgcagactga																										TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr3:39175774_39175775insTCCA	ENST00000431162.2	+	21	2972_2973	c.2838_2839insTCCA	c.(2839-2841)gccfs	p.A947fs	TTC21A_ENST00000301819.6_Frame_Shift_Ins_p.A948fs|TTC21A_ENST00000493856.1_3'UTR|TTC21A_ENST00000440121.1_Frame_Shift_Ins_p.A899fs			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	947										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)		AGCAGCACTGTGCCATCCTCCT	0.599																																					p.C946fs		Atlas-INDEL	.											.	TTC21A	96	.	0			c.2838_2839insTCCA						PASS	.																																			SO:0001589	frameshift_variant	199223	exon21			.	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	Exception_encountered	chr3.hg19:g.39175774_39175775insTCCA	ENSP00000398211:p.Ala947fs	84.0	0.0	0		82.0	36.0	0.439024	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Frame_Shift_Ins	INS	ENST00000431162.2	hg19	CCDS46800.1																																																																																			.	.	.	none		0.599	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755		TCCA	39175775	-	TCCA	39175774	7	5	4	1	0	1	1	0	0	0	0	0	16699	1702	59	0	2923	0	TTC21A	3	39175774	Frame_Shift_Ins	INS	-	TCGA-2Z-A9J3-01A-12D-A382-10		39175774	158846656	29	282	3	2									
TTC21A	199223	hgsc.bcm.edu	37	chr3	39175775	39175775	+	Missense_Mutation	SNP	G	G	T																															acctgtgtgagcagcactgtGccatcctcctgcagactgag																										TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr3:39175775G>T	ENST00000431162.2	+	21	2973	c.2839G>T	c.(2839-2841)Gcc>Tcc	p.A947S	TTC21A_ENST00000301819.6_Missense_Mutation_p.A948S|TTC21A_ENST00000493856.1_3'UTR|TTC21A_ENST00000440121.1_Missense_Mutation_p.A899S			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	947										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)		GCAGCACTGTGCCATCCTCCT	0.602																																					p.A947S		Atlas-SNP	.											.	TTC21A	96	.	0			c.G2839T						PASS	.						147	155	152					3																	39175775		2086	4219	6305	SO:0001583	missense	199223	exon21			CACTGTGCCATCC	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.2839G>T	chr3.hg19:g.39175775G>T	ENSP00000398211:p.Ala947Ser	83.0	0.0	.		81.0	36.0	.	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	hg19	CCDS46800.1	.	.	.	.	.	.	.	.	.	.	G	7.855	0.724787	0.15439	.	.	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.36699	1.24;1.24;1.24	4.65	0.648	0.17801	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.519636	0.18015	N	0.154438	T	0.17408	0.0418	N	0.25992	0.78	0.09310	N	1	B;B;B;B	0.26775	0.159;0.003;0.002;0.001	B;B;B;B	0.24848	0.056;0.003;0.007;0.003	T	0.22977	-1.0201	10	0.08599	T	0.76	-4.3657	3.9914	0.09538	0.4069:0.0:0.4332:0.1599	.	68;899;948;947	B4DSJ5;Q8NDW8-6;Q8NDW8-7;Q8NDW8	.;.;.;TT21A_HUMAN	S	948;930;947;899	ENSP00000301819:A948S;ENSP00000398211:A947S;ENSP00000410882:A899S	ENSP00000301819:A948S	A	+	1	0	TTC21A	39150779	0.000000	0.05858	0.076000	0.20297	0.790000	0.44656	0.000000	0.12993	0.182000	0.20032	0.561000	0.74099	GCC	.	.	.	none		0.602	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755		T	39175775	G	T	39175775	3	4	4	1	0	0	0	0	1	0	0	0	16699	1319	46	4	2924	4	TTC21A	3	39175775	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	1	39175775	158846655	30	283	3	2									
TGM4	7047	hgsc.bcm.edu	37	chr3	44943387	44943387	+	Missense_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	cacctatgtgaatgagaatgGcgagaaaatcaccagtatga	16	8	10	7	1	1	4	1	3	0	2	1	6	1	4	2	1	0	1	2	1	6	2			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr3:44943387G>A	ENST00000296125.4	+	8	1003	c.935G>A	c.(934-936)gGc>gAc	p.G312D	RP11-272D20.2_ENST00000427258.1_RNA	NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	312					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)	AATGAGAATGGCGAGAAAATC	0.502																																					p.G312D		Atlas-SNP	.											.	TGM4	82	.	0			c.G935A						PASS	.						129	124	125					3																	44943387		2203	4300	6503	SO:0001583	missense	7047	exon8			AGAATGGCGAGAA	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.935G>A	chr3.hg19:g.44943387G>A	ENSP00000296125:p.Gly312Asp	70.0	0.0	.		74.0	28.0	.	NM_003241	Q16707|Q96QN4	Missense_Mutation	SNP	ENST00000296125.4	hg19	CCDS2723.1	.	.	.	.	.	.	.	.	.	.	G	10.68	1.418147	0.25552	.	.	ENSG00000163810	ENST00000296125	T	0.58652	0.32	2.99	2.09	0.27110	Transglutaminase-like (2);	0.000000	0.44902	U	0.000419	T	0.70219	0.3199	M	0.73217	2.22	0.09310	N	0.999999	D	0.69078	0.997	D	0.70016	0.967	T	0.61163	-0.7118	10	0.72032	D	0.01	.	10.0566	0.42248	0.1074:0.0:0.8926:0.0	.	312	P49221	TGM4_HUMAN	D	312	ENSP00000296125:G312D	ENSP00000296125:G312D	G	+	2	0	TGM4	44918391	0.008000	0.16893	0.002000	0.10522	0.018000	0.09664	0.567000	0.23608	0.541000	0.28827	0.563000	0.77884	GGC	.	.	.	none		0.502	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241		A	44943387	G	A	44943387	3	1	4	1	0	0	0	0	1	0	0	0	15844	1203	42	2	965	2	TGM4	3	44943387	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	5767612	44943387	153079043	31	284											
EPHA6	285220	hgsc.bcm.edu	37	chr3	96706660	96706660	+	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	gtaacttggccatgtttcctGataccattccaagggttgat	9	14	9	9	0	0	2	0	2	0	0	2	2	2	2	4	2	2	3	4	2	3	6			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr3:96706660G>T	ENST00000389672.5	+	3	975	c.937G>T	c.(937-939)Gat>Tat	p.D313Y	EPHA6_ENST00000470610.2_Missense_Mutation_p.D313Y|EPHA6_ENST00000542517.1_Missense_Mutation_p.D219Y	NM_001080448.2	NP_001073917.2	Q9UF33	EPHA6_HUMAN	EPH receptor A6	219						integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)	p.D219Y(2)|p.D219H(1)|p.D313Y(1)		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						CATGTTTCCTGATACCATTCC	0.478																																					p.D313Y		Atlas-SNP	.											EPHA6_ENST00000389672,rectum,carcinoma,-2,4	EPHA6	439	.	4	Substitution - Missense(4)	lung(3)|breast(1)	c.G937T						PASS	.						214	217	216					3																	96706660		1981	4178	6159	SO:0001583	missense	285220	exon3			TTTCCTGATACCA	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.937G>T	chr3.hg19:g.96706660G>T	ENSP00000374323:p.Asp313Tyr	75.0	0.0	.		74.0	32.0	.	NM_001080448	D6RAL5	Missense_Mutation	SNP	ENST00000389672.5	hg19	CCDS46876.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.4|22.4	4.282417|4.282417	0.80692|0.80692	.|.	.|.	ENSG00000080224|ENSG00000080224	ENST00000470610;ENST00000389672;ENST00000542517|ENST00000506569	T;T;T|.	0.75938|.	4.94;-0.98;4.4|.	5.47|5.47	5.47|5.47	0.80525|0.80525	.|.	0.150900|.	0.41097|.	U|.	0.000948|.	D|.	0.83524|.	0.5273|.	M|M	0.87456|0.87456	2.885|2.885	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.76071|.	0.987;0.982|.	D|.	0.85544|.	0.1217|.	10|.	0.87932|.	D|.	0|.	.|.	18.3228|18.3228	0.90244|0.90244	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	313;313|.	B3KS12;E7EU71|.	.;.|.	Y|L	313;313;219|257	ENSP00000420598:D313Y;ENSP00000374323:D313Y;ENSP00000439758:D219Y|.	ENSP00000374323:D313Y|.	D|X	+|+	1|2	0|2	EPHA6|EPHA6	98189350|98189350	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	9.869000|9.869000	0.99810|0.99810	2.549000|2.549000	0.85964|0.85964	0.650000|0.650000	0.86243|0.86243	GAT|TGA	.	.	.	none		0.478	EPHA6-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353845.3	NM_001080448		T	96706660	G	T	96706660	3	4	4	1	0	0	0	0	1	0	0	0	5173	1290	45	4	947	4	EPHA6	3	96706660	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	51763273	96706660	101315770	32	285											
MBD4	8930	hgsc.bcm.edu	37	chr3	129156116	129156116	+	Missense_Mutation	SNP	A	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	ttttgtgaagataattagcaAgtgaacttttggatctgaac	13	15	9	4	0	1	4	0	3	1	1	1	5	1	5	0	1	3	1	0	1	6	6			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr3:129156116A>C	ENST00000249910.1	-	3	546	c.371T>G	c.(370-372)cTt>cGt	p.L124R	MBD4_ENST00000507208.1_Missense_Mutation_p.L124R|MBD4_ENST00000429544.2_Missense_Mutation_p.L124R|IFT122_ENST00000504021.1_5'Flank|IFT122_ENST00000507564.1_5'Flank|MBD4_ENST00000503197.1_Missense_Mutation_p.L124R|MBD4_ENST00000509587.1_Intron|IFT122_ENST00000347300.2_5'Flank|IFT122_ENST00000348417.2_5'Flank|IFT122_ENST00000431818.2_5'Flank|MBD4_ENST00000393278.2_Intron|IFT122_ENST00000349441.2_5'Flank|IFT122_ENST00000296266.3_5'Flank	NM_003925.1	NP_003916.1	O95243	MBD4_HUMAN	methyl-CpG binding domain protein 4	124	MBD. {ECO:0000255|PROSITE- ProRule:PRU00338}.				base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)	22						ATAATTAGCAAGTGAACTTTT	0.338								Base excision repair (BER), DNA glycosylases																													p.L124R		Atlas-SNP	.											.	MBD4	53	.	0			c.T371G						PASS	.						45	47	46					3																	129156116		2202	4298	6500	SO:0001583	missense	8930	exon3			TTAGCAAGTGAAC	AF072250	CCDS3058.1, CCDS63766.1, CCDS63767.1, CCDS63768.1, CCDS63769.1	3q21.3	2004-03-02			ENSG00000129071	ENSG00000129071			6919	protein-coding gene	gene with protein product		603574				9774669, 10097147	Standard	NM_003925		Approved	MED1	uc003emh.2	O95243	OTTHUMG00000159463	ENST00000249910.1:c.371T>G	chr3.hg19:g.129156116A>C	ENSP00000249910:p.Leu124Arg	21.0	0.0	.		33.0	24.0	.	NM_003925	B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Missense_Mutation	SNP	ENST00000249910.1	hg19	CCDS3058.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.946829	0.73672	.	.	ENSG00000129071	ENST00000429544;ENST00000249910;ENST00000503197;ENST00000507208	D;D;D;D	0.97772	-4.53;-4.53;-4.53;-4.53	5.44	5.44	0.79542	Methyl-CpG DNA binding (4);DNA-binding, integrase-type (1);	0.141330	0.48286	D	0.000200	D	0.98880	0.9621	M	0.90198	3.095	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.999;0.999	D;D;D;D	0.87578	0.964;0.983;0.998;0.964	D	0.99780	1.1027	10	0.87932	D	0	-7.3728	15.2347	0.73419	1.0:0.0:0.0:0.0	.	124;124;124;124	E9PEE4;O95243-2;O95243-3;O95243	.;.;.;MBD4_HUMAN	R	124	ENSP00000394080:L124R;ENSP00000249910:L124R;ENSP00000424873:L124R;ENSP00000422327:L124R	ENSP00000249910:L124R	L	-	2	0	MBD4	130638806	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.294000	0.78760	2.090000	0.63153	0.529000	0.55759	CTT	.	.	.	none		0.338	MBD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355529.1	NM_003925		C	129156116	A	C	129156116	3	2	4	1	0	0	0	0	1	0	0	0	9353	72	3	5	1395	5	MBD4	3	129156116	Missense_Mutation	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10	32449456	129156116	68866314	33	286											
XRN1	54464	hgsc.bcm.edu	37	chr3	142141761	142141764	+	Splice_Site	DEL	TACC	TACC	-																															gtagtttcttctggagcacaTaccctggaattagtcagatg																								rs183730909|rs370828065|rs146086047	byFrequency	TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	TACC	TACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr3:142141761_142141764delTACC	ENST00000264951.4	-	7	828_831	c.711_714delGGTA	c.(709-714)cgggta>cg	p.RV237fs	XRN1_ENST00000392981.2_Splice_Site_p.RV237fs|RNU1-100P_ENST00000365255.1_RNA|XRN1_ENST00000544157.1_Splice_Site_p.RV27fs|XRN1_ENST00000463916.1_Splice_Site_p.RV237fs	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	237					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						CTGGAGCACATACCCTGGAATTAG	0.304																																					p.238_239del		Atlas-Indel,Pindel	.											.	XRN1	138	.	0			c.712_715del						PASS	.																																			SO:0001630	splice_region_variant	54464	exon7			.	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.711-1GGTA>-	chr3.hg19:g.142141761_142141764delTACC		156.0	0.0	0		361.0	59.0	0.163435	NM_001042604	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Frame_Shift_Del	DEL	ENST00000264951.4	hg19	CCDS3123.1																																																																																			.	.	.	none		0.304	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001	Frame_Shift_Del	-	142141764	TACC	-	142141761	8	5	4	1	0	1	0	1	0	0	1	0	17471	1393	49	0	4550	0	XRN1	3	142141761	Splice_Site	DEL	TACC	TCGA-2Z-A9J3-01A-12D-A382-10	12985645	142141761	55880669	34	287											
B3GALNT1	8706	hgsc.bcm.edu	37	chr3	160803876	160803876	+	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	atactcctggtaagaaatatGggttttttggtaaaatcctc	12	15	8	6	0	0	1	0	0	0	1	3	1	2	1	2	3	1	3	2	3	6	7			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr3:160803876G>T	ENST00000392781.2	-	8	1414	c.667C>A	c.(667-669)Cat>Aat	p.H223N	B3GALNT1_ENST00000417187.1_Intron|B3GALNT1_ENST00000320474.4_Missense_Mutation_p.H223N|B3GALNT1_ENST00000392780.1_Missense_Mutation_p.H223N|B3GALNT1_ENST00000392779.2_Missense_Mutation_p.H223N|B3GALNT1_ENST00000473285.1_Missense_Mutation_p.H223N|B3GALNT1_ENST00000488170.1_Missense_Mutation_p.H223N	NM_001038628.1	NP_001033717.1	O75752	B3GL1_HUMAN	beta-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group)	223					oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	galactosylgalactosylglucosylceramide beta-D-acetylgalactosaminyltransferase activity (GO:0047273)|UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			breast(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13			LUSC - Lung squamous cell carcinoma(72;4.41e-05)|Lung(72;4.61e-05)			TAAGAAATATGGGTTTTTTGG	0.358																																					p.H223N		Atlas-SNP	.											.	B3GALNT1	34	.	0			c.C667A						PASS	.						36	38	37					3																	160803876		2201	4295	6496	SO:0001583	missense	8706	exon8			AAATATGGGTTTT	Y15062	CCDS3193.1	3q25	2014-07-18	2006-06-14	2006-05-09	ENSG00000169255	ENSG00000169255	2.4.1.79	"Blood group antigens", "Beta 3-glycosyltransferases"	918	protein-coding gene	gene with protein product	"globoside synthase", "P antigen synthase"	603094	"UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 3 (Globoside blood group)", "UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 1 (Globoside blood group)"	B3GALT3		9582303, 10993897	Standard	XM_005247861		Approved	beta3Gal-T3, galT3, P1, GLOB	uc003fdv.3	O75752	OTTHUMG00000159064	ENST00000392781.2:c.667C>A	chr3.hg19:g.160803876G>T	ENSP00000376532:p.His223Asn	42.0	0.0	.		104.0	65.0	.	NM_001038628	D3DNM4|Q3Y531|Q6IAI5|Q8NFM8|Q8NFM9|Q9HA06	Missense_Mutation	SNP	ENST00000392781.2	hg19	CCDS3193.1	.	.	.	.	.	.	.	.	.	.	G	11.78	1.740650	0.30865	.	.	ENSG00000169255	ENST00000320474;ENST00000392779;ENST00000392780;ENST00000392781;ENST00000473285;ENST00000488170	T;T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99;0.99	5.94	3.93	0.45458	.	0.169504	0.42420	D	0.000710	T	0.23572	0.0570	N	0.17474	0.49	0.42318	D	0.992247	P	0.48162	0.906	B	0.39562	0.303	T	0.04621	-1.0938	10	0.54805	T	0.06	.	7.1051	0.25358	0.2735:0.0:0.7265:0.0	.	223	O75752	B3GL1_HUMAN	N	223	ENSP00000323479:H223N;ENSP00000376530:H223N;ENSP00000376531:H223N;ENSP00000376532:H223N;ENSP00000418226:H223N;ENSP00000420163:H223N	ENSP00000323479:H223N	H	-	1	0	B3GALNT1	162286570	1.000000	0.71417	0.924000	0.36721	0.783000	0.44284	4.406000	0.59748	1.525000	0.49052	0.561000	0.74099	CAT	.	.	.	none		0.358	B3GALNT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353125.1	NM_033167		T	160803876	G	T	160803876	3	4	4	1	0	0	0	0	1	0	0	0	1245	1348	47	4	332	4	B3GALNT1	3	160803876	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	18662115	160803876	37218554	35	288											
STX18	53407	hgsc.bcm.edu	37	chr4	4459185	4459185	+	Missense_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	caatgaaatccaaaacagcgGtcctgtgctccttcacttgc	11	10	7	13	1	1	1	1	1	0	0	4	1	4	1	3	1	4	1	3	1	4	2			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr4:4459185G>A	ENST00000306200.2	-	4	458	c.395C>T	c.(394-396)aCc>aTc	p.T132I	STX18_ENST00000505286.1_Missense_Mutation_p.T132I	NM_016930.2	NP_058626.1	Q9P2W9	STX18_HUMAN	syntaxin 18	132					ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.0534)		CAAAACAGCGGTCCTGTGCTC	0.363																																					p.T132I		Atlas-SNP	.											.	STX18	16	.	0			c.C395T						PASS	.						78	78	78					4																	4459185		2203	4300	6503	SO:0001583	missense	53407	exon4			ACAGCGGTCCTGT	AB028741	CCDS3377.1	4p16.3-p16.2	2013-09-23			ENSG00000168818	ENSG00000168818			15942	protein-coding gene	gene with protein product		606046				10788491	Standard	NM_016930		Approved	Ufe1	uc003gic.3	Q9P2W9	OTTHUMG00000090331	ENST00000306200.2:c.395C>T	chr4.hg19:g.4459185G>A	ENSP00000305810:p.Thr132Ile	182.0	0.0	.		219.0	85.0	.	NM_016930	Q596L3|Q5TZP5	Missense_Mutation	SNP	ENST00000306200.2	hg19	CCDS3377.1	.	.	.	.	.	.	.	.	.	.	G	10.34	1.323926	0.24080	.	.	ENSG00000168818	ENST00000505286;ENST00000306200;ENST00000512195;ENST00000507908	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	4.97	0.964	0.19655	.	0.463921	0.24001	N	0.042479	T	0.44953	0.1318	M	0.61703	1.905	0.09310	N	1	B	0.17268	0.021	B	0.23018	0.043	T	0.46048	-0.9219	10	0.45353	T	0.12	-9.8899	13.7013	0.62611	0.0:0.1307:0.7212:0.1481	.	132	Q9P2W9	STX18_HUMAN	I	132;132;51;51	ENSP00000426648:T132I;ENSP00000305810:T132I;ENSP00000425483:T51I;ENSP00000422376:T51I	ENSP00000305810:T132I	T	-	2	0	STX18	4510086	0.117000	0.22190	0.182000	0.23118	0.960000	0.62799	0.441000	0.21611	0.225000	0.20959	0.655000	0.94253	ACC	.	.	.	none		0.363	STX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206696.1			A	4459185	G	A	4459185	3	1	4	1	0	0	0	0	1	0	0	0	15353	1261	44	2	644	2	STX18	4	4459185	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10		4459185	186695091	36	289											
EVC	2121	hgsc.bcm.edu	37	chr4	5755635	5755635	+	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	cctggctgaggcccagccgaCtgctgacccggaaaagtttc	8	7	12	14	2	0	2	0	2	0	0	1	4	0	3	4	3	2	3	4	3	2	1	rs372893834		TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr4:5755635C>T	ENST00000264956.6	+	10	1623	c.1439C>T	c.(1438-1440)aCt>aTt	p.T480I	EVC_ENST00000509451.1_Missense_Mutation_p.T480I|EVC_ENST00000382674.2_Missense_Mutation_p.T480I	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	480					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)				GCCCAGCCGACTGCTGACCCG	0.607																																					p.T480I		Atlas-SNP	.											.	EVC	90	.	0			c.C1439T						PASS	.						69	65	66					4																	5755635		2203	4300	6503	SO:0001583	missense	2121	exon10			AGCCGACTGCTGA	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.1439C>T	chr4.hg19:g.5755635C>T	ENSP00000264956:p.Thr480Ile	140.0	0.0	.		108.0	59.0	.	NM_153717		Missense_Mutation	SNP	ENST00000264956.6	hg19	CCDS3383.1	.	.	.	.	.	.	.	.	.	.	C	6.430	0.447423	0.12223	.	.	ENSG00000072840	ENST00000264956;ENST00000382674;ENST00000509451	T;T;T	0.52295	0.67;0.67;0.74	5.04	1.76	0.24704	.	1.042050	0.07485	N	0.904571	T	0.37320	0.0999	L	0.48362	1.52	0.09310	N	0.999999	B	0.20780	0.048	B	0.18561	0.022	T	0.28073	-1.0055	10	0.20046	T	0.44	.	5.4056	0.16320	0.1469:0.6168:0.1437:0.0925	.	480	P57679	EVC_HUMAN	I	480	ENSP00000264956:T480I;ENSP00000372120:T480I;ENSP00000426774:T480I	ENSP00000264956:T480I	T	+	2	0	EVC	5806536	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-0.097000	0.11042	0.494000	0.27859	0.561000	0.74099	ACT	.	.	.	alt		0.607	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1			T	5755635	C	T	5755635	3	4	4	1	0	0	0	0	1	0	0	0	5287	565	20	2	1477	2	EVC	4	5755635	Missense_Mutation	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10	1296450	5755635	185398641	37	290											
SLIT2	9353	hgsc.bcm.edu	37	chr4	20493404	20493404	+	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	gtcaccagtcatttatggctCcttcttgtagtgttttgcac	6	17	8	10	0	3	0	2	0	1	0	4	0	4	0	2	1	1	4	2	1	2	7			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr4:20493404C>A	ENST00000504154.1	+	9	1048	c.796C>A	c.(796-798)Cct>Act	p.P266T	SLIT2_ENST00000503837.1_Missense_Mutation_p.P270T|SLIT2_ENST00000503823.1_Missense_Mutation_p.P266T|SLIT2_ENST00000273739.5_Missense_Mutation_p.P270T	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	266	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						ATTTATGGCTCCTTCTTGTAG	0.408																																					p.P266T		Atlas-SNP	.											.,1	SLIT2	290	.	0			c.C796A						PASS	.						137	137	137					4																	20493404		2203	4300	6503	SO:0001583	missense	9353	exon9			ATGGCTCCTTCTT	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.796C>A	chr4.hg19:g.20493404C>A	ENSP00000422591:p.Pro266Thr	53.0	0.0	.		65.0	32.0	.	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	hg19	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	C	16.48	3.134469	0.56828	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	T;T;T;T	0.81415	-1.48;-1.49;-1.36;-1.41	5.63	5.63	0.86233	.	0.149034	0.64402	D	0.000006	T	0.77618	0.4157	L	0.54323	1.7	0.45108	D	0.998129	B;B	0.11235	0.004;0.002	B;B	0.06405	0.002;0.002	T	0.71220	-0.4657	10	0.15066	T	0.55	.	20.0572	0.97657	0.0:1.0:0.0:0.0	.	266;266	O94813-3;O94813	.;SLIT2_HUMAN	T	266;266;270;270;270	ENSP00000427548:P266T;ENSP00000422591:P266T;ENSP00000273739:P270T;ENSP00000422261:P270T	ENSP00000273739:P270T	P	+	1	0	SLIT2	20102502	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.200000	0.51051	2.826000	0.97356	0.655000	0.94253	CCT	.	.	.	none		0.408	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			A	20493404	C	A	20493404	3	1	4	1	0	0	0	0	1	0	0	0	14753	855	30	4	830	4	SLIT2	4	20493404	Missense_Mutation	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10	14737769	20493404	170660872	38	291											
APBB2	323	hgsc.bcm.edu	37	chr4	41015837	41015837	+	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	caaatcgccattcccaatgaTggtggaggcctggccctgga	9	8	12	12	1	0	1	0	1	0	0	2	3	1	3	4	5	0	0	4	5	2	1			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr4:41015837T>A	ENST00000295974.8	-	6	1227	c.598A>T	c.(598-600)Atc>Ttc	p.I200F	APBB2_ENST00000508593.1_Missense_Mutation_p.I200F|APBB2_ENST00000506352.1_Missense_Mutation_p.I200F|APBB2_ENST00000513140.1_Missense_Mutation_p.I200F	NM_001166050.1|NM_004307.1	NP_001159522.1|NP_004298.1	Q92870	APBB2_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 2	200					axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|extracellular matrix organization (GO:0030198)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|transcription factor binding (GO:0008134)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|skin(2)|urinary_tract(1)	34						TTCCCAATGATGGTGGAGGCC	0.557																																					p.I200F	Ovarian(3;20 75 16686 49997)	Atlas-SNP	.											.	APBB2	61	.	0			c.A598T						PASS	.						265	252	256					4																	41015837		1987	4158	6145	SO:0001583	missense	323	exon6			CAATGATGGTGGA	U62325	CCDS43224.1, CCDS54760.1, CCDS54761.1, CCDS54762.1	4p13	2011-10-10	2008-07-31		ENSG00000163697	ENSG00000163697			582	protein-coding gene	gene with protein product	"Fe65-like"	602710				8955346, 9585438	Standard	NM_173075		Approved	FE65L, FE65L1, MGC35575	uc003gvn.3	Q92870	OTTHUMG00000160416	ENST00000295974.8:c.598A>T	chr4.hg19:g.41015837T>A	ENSP00000295974:p.Ile200Phe	66.0	0.0	.		60.0	23.0	.	NM_173075	B4DSL4|E9PG87|Q8IUI6	Missense_Mutation	SNP	ENST00000295974.8	hg19	CCDS54761.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	4.898|4.898	0.166940|0.166940	0.09339|0.09339	.|.	.|.	ENSG00000163697|ENSG00000163697	ENST00000513611|ENST00000295974;ENST00000316212;ENST00000513140;ENST00000508593;ENST00000506352	.|T;T;T;T	.|0.25749	.|1.78;1.78;1.78;1.78	5.8|5.8	-2.84|-2.84	0.05751|0.05751	.|.	.|1.102730	.|0.06664	.|N	.|0.765002	T|T	0.17959|0.17959	0.0431|0.0431	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.21821	.|0.017;0.037;0.061;0.037	.|B;B;B;B	.|0.24006	.|0.046;0.023;0.05;0.023	T|T	0.33420|0.33420	-0.9869|-0.9869	5|10	.|0.56958	.|D	.|0.05	-3.9618|-3.9618	14.6774|14.6774	0.68989|0.68989	0.0:0.2997:0.0:0.7003|0.0:0.2997:0.0:0.7003	.|.	.|183;200;200;200	.|B4DJ88;E9PG87;Q92870-2;Q92870	.|.;.;.;APBB2_HUMAN	L|F	189|200;199;200;200;200	.|ENSP00000295974:I200F;ENSP00000426018:I200F;ENSP00000427211:I200F;ENSP00000421539:I200F	.|ENSP00000295974:I200F	H|I	-|-	2|1	0|0	APBB2|APBB2	40710594|40710594	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.057000|0.057000	0.15508|0.15508	-4.051000|-4.051000	0.00305|0.00305	-1.047000|-1.047000	0.03242|0.03242	-0.464000|-0.464000	0.05259|0.05259	CAT|ATC	.	.	.	none		0.557	APBB2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360523.3	NM_173075		A	41015837	T	A	41015837	3	1	4	1	0	0	0	0	1	0	0	0	761	1464	51	5	1733	5	APBB2	4	41015837	Missense_Mutation	SNP	T	TCGA-2Z-A9J3-01A-12D-A382-10	20522433	41015837	150138439	39	292											
RUFY3	22902	hgsc.bcm.edu	37	chr4	71639251	71639251	+	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	ggagttatagatttttcaatGtatctcaaggacgggaacag	13	12	11	5	1	2	1	2	0	1	1	3	4	2	4	0	3	1	2	0	3	6	5			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr4:71639251G>T	ENST00000226328.4	+	6	1283	c.720G>T	c.(718-720)atG>atT	p.M240I	RUFY3_ENST00000502653.1_Missense_Mutation_p.M187I|RUFY3_ENST00000536664.1_Missense_Mutation_p.M224I|RUFY3_ENST00000417478.2_Missense_Mutation_p.M300I|RUFY3_ENST00000381006.3_Missense_Mutation_p.M240I	NM_014961.3	NP_055776.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3	240					negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)				endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			ATTTTTCAATGTATCTCAAGG	0.343																																					p.M300I		Atlas-SNP	.											.	RUFY3	61	.	0			c.G900T						PASS	.						74	77	76					4																	71639251		2203	4299	6502	SO:0001583	missense	22902	exon6			TTCAATGTATCTC	AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189		"Zinc fingers, FYVE domain containing"	30285	protein-coding gene	gene with protein product	"single axon-related 1"	611194				17439943	Standard	NM_001130709		Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910	ENST00000226328.4:c.720G>T	chr4.hg19:g.71639251G>T	ENSP00000226328:p.Met240Ile	204.0	0.0	.		176.0	69.0	.	NM_001130709	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	Missense_Mutation	SNP	ENST00000226328.4	hg19	CCDS3547.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.971077	0.74246	.	.	ENSG00000018189	ENST00000417478;ENST00000381006;ENST00000226328;ENST00000536664;ENST00000513597;ENST00000502653	T;T;T;T;T;T	0.21361	2.71;3.1;2.74;2.74;2.01;3.1	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.41373	0.1156	L	0.55834	1.745	0.80722	D	1	B;B;P;B	0.45126	0.123;0.335;0.851;0.057	B;B;P;B	0.58391	0.041;0.19;0.838;0.032	T	0.01920	-1.1247	10	0.40728	T	0.16	-25.3268	19.6602	0.95864	0.0:0.0:1.0:0.0	.	224;240;240;300	B4DKC2;Q7L099-3;Q7L099;Q7L099-2	.;.;RUFY3_HUMAN;.	I	300;240;240;224;176;187	ENSP00000399771:M300I;ENSP00000370394:M240I;ENSP00000226328:M240I;ENSP00000443652:M224I;ENSP00000425574:M176I;ENSP00000425400:M187I	ENSP00000226328:M240I	M	+	3	0	RUFY3	71858115	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.390000	0.97246	2.638000	0.89438	0.460000	0.39030	ATG	.	.	.	none		0.343	RUFY3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252161.2	NM_014961		T	71639251	G	T	71639251	3	4	4	1	0	0	0	0	1	0	0	0	13753	1377	48	4	1104	4	RUFY3	4	71639251	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	30623414	71639251	119515025	40	293											
SLC4A4	8671	hgsc.bcm.edu	37	chr4	72222802	72222802	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtgacctatactttgctcCggaagcaccggcatcaaacc	11	8	9	13	2	1	1	1	1	0	0	2	2	2	2	4	3	4	3	4	3	4	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr4:72222802C>T	ENST00000264485.5	+	6	745	c.628C>T	c.(628-630)Cgg>Tgg	p.R210W	SLC4A4_ENST00000514331.1_3'UTR|SLC4A4_ENST00000340595.3_Missense_Mutation_p.R166W|SLC4A4_ENST00000425175.1_Missense_Mutation_p.R210W|SLC4A4_ENST00000351898.6_Missense_Mutation_p.R210W|SLC4A4_ENST00000512686.1_Missense_Mutation_p.R166W	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	210					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)	TACTTTGCTCCGGAAGCACCG	0.443																																					p.R210W		Atlas-SNP	.											.	SLC4A4	269	.	0			c.C628T						PASS	.						134	135	134					4																	72222802		2203	4300	6503	SO:0001583	missense	8671	exon6			TTGCTCCGGAAGC	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.628C>T	chr4.hg19:g.72222802C>T	ENSP00000264485:p.Arg210Trp	58.0	0.0	.		76.0	23.0	.	NM_001098484	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	hg19	CCDS43236.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.185700	0.78789	.	.	ENSG00000080493	ENST00000264485;ENST00000425175;ENST00000351898;ENST00000512686;ENST00000340595	T;T;T;T;T	0.68765	-0.35;-0.35;-0.35;-0.35;-0.35	5.84	5.84	0.93424	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.000000	0.85682	D	0.000000	D	0.84220	0.5424	M	0.89534	3.04	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	0.97110	1.0;0.997;1.0;1.0;0.995;1.0	D	0.86729	0.1947	10	0.87932	D	0	.	13.0889	0.59156	0.2651:0.7349:0.0:0.0	.	210;210;166;166;190;210	A5JJ20;Q9Y6R1-4;Q9Y6R1-2;Q9Y6R1-3;Q9Y6R3;Q9Y6R1	.;.;.;.;.;S4A4_HUMAN	W	210;210;210;166;166	ENSP00000264485:R210W;ENSP00000393557:R210W;ENSP00000307349:R210W;ENSP00000422400:R166W;ENSP00000344272:R166W	ENSP00000264485:R210W	R	+	1	2	SLC4A4	72441666	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.075000	0.41538	2.751000	0.94390	0.655000	0.94253	CGG	.	.	.	none		0.443	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		T	72222802	C	T	72222802	3	4	4	1	0	0	0	0	1	0	0	0	14669	643	23	1	767	1	SLC4A4	4	72222802	Missense_Mutation	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10	583551	72222802	118931474	41	294											
ARHGAP10	79658	hgsc.bcm.edu	37	chr4	148800473	148800473	+	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	catgatcccatttgagcacaGatctggagggaaacttgtaa	13	10	10	8	0	1	3	0	2	1	1	2	5	2	5	1	2	2	2	1	2	2	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr4:148800473G>C	ENST00000336498.3	+	9	1162	c.923G>C	c.(922-924)aGa>aCa	p.R308T	ARHGAP10_ENST00000414545.2_5'Flank	NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10	0					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		TTTGAGCACAGATCTGGAGGG	0.373																																					p.R308T		Atlas-SNP	.											.	ARHGAP10	92	.	0			c.G923C						PASS	.						134	125	128					4																	148800473		2203	4300	6503	SO:0001583	missense	79658	exon9			AGCACAGATCTGG	BC047914	CCDS34075.1	4q31.23	2013-09-20			ENSG00000071205	ENSG00000071205		"Rho GTPase activating proteins"	26099	protein-coding gene	gene with protein product		609746				8288572	Standard	NM_024605		Approved	FLJ20896, FLJ41791, GRAF2	uc003ilf.3	A1A4S6	OTTHUMG00000161460	ENST00000336498.3:c.923G>C	chr4.hg19:g.148800473G>C	ENSP00000336923:p.Arg308Thr	68.0	0.0	.		82.0	26.0	.	NM_024605	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000336498.3	hg19	CCDS34075.1	.	.	.	.	.	.	.	.	.	.	G	17.19	3.327682	0.60743	.	.	ENSG00000071205	ENST00000336498	T	0.42513	0.97	5.1	5.1	0.69264	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	T	0.44705	0.1306	L	0.27053	0.805	0.80722	D	1	D	0.63880	0.993	P	0.52957	0.714	T	0.39272	-0.9622	10	0.45353	T	0.12	.	18.1426	0.89644	0.0:0.0:1.0:0.0	.	308	A1A4S6	RHG10_HUMAN	T	308	ENSP00000336923:R308T	ENSP00000336923:R308T	R	+	2	0	ARHGAP10	149019923	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.116000	0.57871	2.378000	0.81104	0.561000	0.74099	AGA	.	.	.	none		0.373	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1	NM_024605		C	148800473	G	C	148800473	3	2	4	1	0	0	0	0	1	0	0	0	862	942	33	4	957	4	ARHGAP10	4	148800473	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	76577671	148800473	42353803	42	295											
ETFDH	2110	hgsc.bcm.edu	37	chr4	159629584	159629584	+	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	agataaatgctcagaactgtGtacattgtaaaacatgtgat	16	12	8	5	0	1	3	1	1	0	2	1	3	1	3	0	0	4	3	0	0	6	4			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr4:159629584G>T	ENST00000511912.1	+	13	2091	c.1759G>T	c.(1759-1761)Gta>Tta	p.V587L	ETFDH_ENST00000307738.5_Missense_Mutation_p.V540L	NM_001281738.1|NM_004453.2	NP_001268667.1|NP_004444.2	Q16134	ETFD_HUMAN	electron-transferring-flavoprotein dehydrogenase	587	4Fe-4S ferredoxin-type. {ECO:0000255|PROSITE-ProRule:PRU00711}.				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)		TCAGAACTGTGTACATTGTAA	0.363																																					p.V587L		Atlas-SNP	.											.	ETFDH	57	.	0			c.G1759T						PASS	.						115	112	113					4																	159629584		2203	4300	6503	SO:0001583	missense	2110	exon13			AACTGTGTACATT	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.1759G>T	chr4.hg19:g.159629584G>T	ENSP00000426638:p.Val587Leu	90.0	0.0	.		81.0	34.0	.	NM_004453	B4E3R9|J3KND9|Q7Z347	Missense_Mutation	SNP	ENST00000511912.1	hg19	CCDS3800.1	.	.	.	.	.	.	.	.	.	.	G	19.84	3.902545	0.72754	.	.	ENSG00000171503	ENST00000511912;ENST00000307738	D;D	0.93763	-3.28;-3.28	6.05	5.21	0.72293	4Fe-4S ferredoxin, iron-sulpur binding domain (1);	0.000000	0.85682	D	0.000000	D	0.89143	0.6631	L	0.31804	0.96	0.58432	D	0.999998	B;B;B	0.34264	0.064;0.111;0.446	B;B;B	0.33890	0.122;0.122;0.172	D	0.88267	0.2927	10	0.49607	T	0.09	-21.6302	15.2075	0.73190	0.067:0.0:0.933:0.0	.	540;526;587	B4E3R9;B4DEQ0;Q16134	.;.;ETFD_HUMAN	L	587;540	ENSP00000426638:V587L;ENSP00000303552:V540L	ENSP00000303552:V540L	V	+	1	0	ETFDH	159849034	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.864000	0.99589	1.568000	0.49683	0.650000	0.86243	GTA	.	.	.	none		0.363	ETFDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365718.2			T	159629584	G	T	159629584	3	4	4	1	0	0	0	0	1	0	0	0	5273	1377	48	4	1809	4	ETFDH	4	159629584	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	10829111	159629584	31524692	43	296											
PCDHA9	9752	hgsc.bcm.edu	37	chr5	140230427	140230427	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttctccttgtgctggatctAcagagcgaacgggagaaccc	9	10	11	11	2	2	2	0	0	2	2	3	5	2	3	2	2	5	1	2	2	3	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr5:140230427A>G	ENST00000532602.1	+	1	3380	c.2347A>G	c.(2347-2349)Aca>Gca	p.T783A	PCDHA7_ENST00000525929.1_Intron|PCDHA9_ENST00000378122.3_Missense_Mutation_p.T783A|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	783	5 X 4 AA repeats of P-X-X-P.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCTGGATCTACAGAGCGAAC	0.483																																					p.T783A	Melanoma(55;1800 1972 14909)	Atlas-SNP	.											.	PCDHA9	373	.	0			c.A2347G						PASS	.						70	74	72					5																	140230427		2197	4272	6469	SO:0001583	missense	9752	exon1			GGATCTACAGAGC	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.2347A>G	chr5.hg19:g.140230427A>G	ENSP00000436042:p.Thr783Ala	208.0	0.0	.		182.0	149.0	.	NM_031857	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	hg19	CCDS54920.1	.	.	.	.	.	.	.	.	.	.	A	1.760	-0.487128	0.04352	.	.	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.10860	2.83;2.83	4.24	0.115	0.14643	.	4.198160	0.02428	U	0.083234	T	0.04137	0.0115	N	0.03000	-0.44	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.33137	-0.9880	10	0.07482	T	0.82	.	4.5943	0.12322	0.3795:0.1576:0.4629:0.0	.	783;783	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	A	783	ENSP00000436042:T783A;ENSP00000367362:T783A	ENSP00000367362:T783A	T	+	1	0	PCDHA9	140210611	0.000000	0.05858	0.003000	0.11579	0.269000	0.26545	-0.159000	0.10056	0.004000	0.14682	-0.415000	0.06103	ACA	.	.	.	none		0.483	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		G	140230427	A	G	140230427	3	3	4	1	0	0	0	0	1	0	0	0	11538	391	14	3	2349	3	PCDHA9	5	140230427	Missense_Mutation	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10		140230427	40684833	44	297											
PCDHGC4	56098	hgsc.bcm.edu	37	chr5	140865167	140865167	+	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	agcagctggacttggaaattGgggaggcagctcctccagga	10	7	15	9	0	0	0	0	0	0	0	2	4	2	4	2	6	3	4	2	6	1	2			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr5:140865167G>A	ENST00000306593.1	+	1	427	c.427G>A	c.(427-429)Ggg>Agg	p.G143R	PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018928.2|NM_032406.1	NP_061751.1|NP_115782.1	Q9Y5F7	PCDGL_HUMAN	protocadherin gamma subfamily C, 4	143	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(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(13)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	42			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTGGAAATTGGGGAGGCAGC	0.542																																					p.G143R		Atlas-SNP	.											.	PCDHGC4	91	.	0			c.G427A						PASS	.						62	66	65					5																	140865167		2203	4300	6503	SO:0001583	missense	56098	exon1			GAAATTGGGGAGG	AF152525	CCDS4262.1, CCDS75349.1	5q31	2010-01-26			ENSG00000242419	ENSG00000242419		"Cadherins / Protocadherins : Clustered"	8717	other	protocadherin		606305				10380929	Standard	NM_018928		Approved	PCDH-GAMMA-C4		Q9Y5F7	OTTHUMG00000129625	ENST00000306593.1:c.427G>A	chr5.hg19:g.140865167G>A	ENSP00000306918:p.Gly143Arg	49.0	0.0	.		43.0	16.0	.	NM_018928	Q495T2|Q9Y5C3	Missense_Mutation	SNP	ENST00000306593.1	hg19	CCDS4262.1	.	.	.	.	.	.	.	.	.	.	G	15.02	2.710368	0.48517	.	.	ENSG00000242419	ENST00000306593	T	0.49432	0.78	5.0	4.12	0.48240	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.35711	0.0941	N	0.11341	0.13	0.09310	N	1	D;P	0.54207	0.965;0.951	P;P	0.50659	0.514;0.647	T	0.08066	-1.0740	9	0.27082	T	0.32	.	9.464	0.38802	0.2253:0.0:0.7747:0.0	.	143;143	Q9Y5F7-2;Q9Y5F7	.;PCDGL_HUMAN	R	143	ENSP00000306918:G143R	ENSP00000306918:G143R	G	+	1	0	PCDHGC4	140845351	0.000000	0.05858	1.000000	0.80357	0.991000	0.79684	0.335000	0.19806	1.305000	0.44909	0.561000	0.74099	GGG	.	.	.	none		0.542	PCDHGC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251820.1	NM_018928		A	140865167	G	A	140865167	3	1	4	1	0	0	0	0	1	0	0	0	11577	1348	47	2	429	2	PCDHGC4	5	140865167	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	634740	140865167	40050093	45	298											
RARS	5917	hgsc.bcm.edu	37	chr5	167944991	167944992	+	Frame_Shift_Ins	INS	-	-	TA																															ttctccacactctctgtgatINStatatatatgagctggcaac																										TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr5:167944991_167944992insTA	ENST00000231572.3	+	14	1851_1852	c.1797_1798insTA	c.(1798-1800)tatfs	p.Y600fs	RARS_ENST00000538719.1_Frame_Shift_Ins_p.Y394fs	NM_002887.3	NP_002878.2	P54136	SYRC_HUMAN	arginyl-tRNA synthetase	600					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	arginine binding (GO:0034618)|arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|tRNA binding (GO:0000049)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|stomach(1)	22	Renal(175;0.000159)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0208)|all_neural(177;0.0227)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0693)|Epithelial(171;0.131)|OV - Ovarian serous cystadenocarcinoma(192;0.156)		CTCTCTGTGATTATATATATGA	0.386																																					p.D599fs		Atlas-Indel,Pindel	.											.	RARS	58	.	0			c.1797_1798insTA						PASS	.																																			SO:0001589	frameshift_variant	5917	exon14			.	BC000528	CCDS4367.1	5q35.1	2011-07-01			ENSG00000113643	ENSG00000113643	6.1.1.19	"Aminoacyl tRNA synthetases / Class I"	9870	protein-coding gene	gene with protein product	"arginine tRNA ligase 1, cytoplasmic"	107820				7590355	Standard	NM_002887		Approved	DALRD1	uc003lzx.3	P54136	OTTHUMG00000130411	ENST00000231572.3:c.1804_1805dupTA	chr5.hg19:g.167944998_167944999dupTA	ENSP00000231572:p.Tyr600fs	63.0	0.0	0		77.0	30.0	0.38961	NM_002887	B2RBS9|Q53GY4|Q9BWA1	Frame_Shift_Ins	INS	ENST00000231572.3	hg19	CCDS4367.1																																																																																			.	.	.	none		0.386	RARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252794.2	NM_002887		TA	167944992	-	TA	167944991	7	5	4	1	0	1	1	0	0	0	0	0	13071	1490	52	0	1851	0	RARS	5	167944991	Frame_Shift_Ins	INS	-	TCGA-2Z-A9J3-01A-12D-A382-10	27079824	167944991	12970269	46	299											
GABRP	2568	hgsc.bcm.edu	37	chr5	170235705	170235705	+	Missense_Mutation	SNP	T	T	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	ctttcctggtggtgttgtccTgggtttcattttggatctct	2	20	11	8	0	2	0	1	0	1	0	5	1	4	1	2	4	0	2	2	4	0	5			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr5:170235705T>G	ENST00000518525.1	+	9	1245	c.781T>G	c.(781-783)Tgg>Ggg	p.W261G	GABRP_ENST00000519598.1_Missense_Mutation_p.W261G|GABRP_ENST00000519385.1_Missense_Mutation_p.W261G|GABRP_ENST00000265294.4_Missense_Mutation_p.W261G			O00591	GBRP_HUMAN	gamma-aminobutyric acid (GABA) A receptor, pi	261					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)	GGTGTTGTCCTGGGTTTCATT	0.428																																					p.W261G		Atlas-SNP	.											.	GABRP	65	.	0			c.T781G						PASS	.						236	212	220					5																	170235705		2203	4300	6503	SO:0001583	missense	2568	exon8			TTGTCCTGGGTTT	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.781T>G	chr5.hg19:g.170235705T>G	ENSP00000430100:p.Trp261Gly	44.0	0.0	.		49.0	23.0	.	NM_014211	A8KA36|D3DQL2|Q32MJ1	Missense_Mutation	SNP	ENST00000518525.1	hg19	CCDS4375.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.193383	0.78902	.	.	ENSG00000094755	ENST00000518525;ENST00000539175;ENST00000265294;ENST00000519385;ENST00000519598	D;D;D;D	0.83755	-1.76;-1.76;-1.76;-1.76	4.94	4.94	0.65067	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.217481	0.51477	D	0.000081	D	0.92325	0.7565	M	0.90082	3.085	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.93898	0.7186	10	0.87932	D	0	.	14.5722	0.68218	0.0:0.0:0.0:1.0	.	261;261	E7EWG0;O00591	.;GBRP_HUMAN	G	261;159;261;261;261	ENSP00000430100:W261G;ENSP00000265294:W261G;ENSP00000430727:W261G;ENSP00000430772:W261G	ENSP00000265294:W261G	W	+	1	0	GABRP	170168283	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.924000	0.87555	1.970000	0.57323	0.533000	0.62120	TGG	.	.	.	none		0.428	GABRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252834.3	NM_014211		G	170235705	T	G	170235705	3	3	4	1	0	0	0	0	1	0	0	0	6181	1580	55	5	807	5	GABRP	5	170235705	Missense_Mutation	SNP	T	TCGA-2Z-A9J3-01A-12D-A382-10	2290714	170235705	10679555	47	300											
PFN3	345456	hgsc.bcm.edu	37	chr5	176827428	176827428	+	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	tgcctgtccggccccgtgagCacgcccacctcctgcggcga	4	6	12	19	5	0	1	0	1	0	0	2	2	2	1	7	2	3	1	7	2	0	0			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr5:176827428C>T	ENST00000358571.2	-	1	209	c.150G>A	c.(148-150)gtG>gtA	p.V50V	F12_ENST00000514943.1_5'Flank	NM_001029886.2	NP_001025057.1	P60673	PROF3_HUMAN	profilin 3	50					actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	lipid binding (GO:0008289)			lung(1)	1	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCCCCGTGAGCACGCCCACCT	0.741																																					p.V50V		Atlas-SNP	.											.	PFN3	4	.	0			c.G150A						PASS	.						4	5	5					5																	176827428		1993	3872	5865	SO:0001819	synonymous_variant	345456	exon1			CGTGAGCACGCCC	AC090063	CCDS34301.1	5q35.2	2008-08-26			ENSG00000196570	ENSG00000196570			18627	protein-coding gene	gene with protein product		612812				11867228	Standard	NM_001029886		Approved		uc003mgl.2	P60673	OTTHUMG00000163408	ENST00000358571.2:c.150G>A	chr5.hg19:g.176827428C>T		23.0	0.0	.		17.0	6.0	.	NM_001029886	A2RUL3	Silent	SNP	ENST00000358571.2	hg19	CCDS34301.1																																																																																			.	.	.	none		0.741	PFN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373234.1	NM_001029886		T	176827428	C	T	176827428	2	4	4	1	0	0	0	0	0	0	0	1	11776	697	25	2		2	PFN3	5	176827428	Silent	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10	6591723	176827428	4087832	48	301											
DSP	1832	hgsc.bcm.edu	37	chr6	7542208	7542208	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggccgcatgatccgcgcCgagtctggcccggacctgcg	4	6	15	16	6	1	1	0	1	1	0	2	3	2	2	5	3	1	1	5	3	0	0			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr6:7542208C>T	ENST00000379802.3	+	1	401	c.60C>T	c.(58-60)gcC>gcT	p.A20A	DSP_ENST00000418664.2_Silent_p.A20A|RP3-512B11.3_ENST00000561592.1_RNA	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	20	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)		TGATCCGCGCCGAGTCTGGCC	0.682																																					p.A20A		Atlas-SNP	.											.	DSP	306	.	0			c.C60T						PASS	.						11	13	12					6																	7542208		2191	4284	6475	SO:0001819	synonymous_variant	1832	exon1			CCGCGCCGAGTCT	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.60C>T	chr6.hg19:g.7542208C>T		170.0	0.0	.		148.0	71.0	.	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	hg19	CCDS4501.1																																																																																			.	.	.	none		0.682	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		T	7542208	C	T	7542208	2	4	4	1	0	0	0	0	0	0	0	1	4783	639	23	1		1	DSP	6	7542208	Silent	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10		7542208	163572859	49	302											
DSP	1832	hgsc.bcm.edu	37	chr6	7584626	7584627	+	Frame_Shift_Ins	INS	-	-	T																															agatcgcaaccggggggatcINSattgacccaaaggagagcca																										TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr6:7584626_7584627insT	ENST00000379802.3	+	24	7472_7473	c.7131_7132insT	c.(7132-7134)attfs	p.I2378fs	DSP_ENST00000418664.2_Frame_Shift_Ins_p.I1779fs	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2378	4.5 X 38 AA tandem repeats (Domain B).|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)		CCGGGGGGATCATTGACCCAAA	0.45																																					p.I2377fs		Atlas-INDEL	.											.	DSP	306	.	0			c.7131_7132insT						PASS	.																																			SO:0001589	frameshift_variant	1832	exon24			.	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	Exception_encountered	chr6.hg19:g.7584626_7584627insT	ENSP00000369129:p.Ile2378fs	75.0	0.0	0		74.0	32.0	0.432432	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Frame_Shift_Ins	INS	ENST00000379802.3	hg19	CCDS4501.1																																																																																			.	.	.	none		0.45	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		T	7584627	-	T	7584626	7	5	4	1	0	1	1	0	0	0	0	0	4783	816	29	0	7225	0	DSP	6	7584626	Frame_Shift_Ins	INS	-	TCGA-2Z-A9J3-01A-12D-A382-10	42418	7584626	163530441	50	303	4	2									
DSP	1832	hgsc.bcm.edu	37	chr6	7584627	7584627	+	Missense_Mutation	SNP	A	A	T																															agatcgcaaccggggggatcAttgacccaaaggagagccat																										TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr6:7584627A>T	ENST00000379802.3	+	24	7473	c.7132A>T	c.(7132-7134)Att>Ttt	p.I2378F	DSP_ENST00000418664.2_Missense_Mutation_p.I1779F	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2378	4.5 X 38 AA tandem repeats (Domain B).|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)		CGGGGGGATCATTGACCCAAA	0.448																																					p.I2378F		Atlas-SNP	.											.	DSP	306	.	0			c.A7132T						PASS	.						76	75	75					6																	7584627		2203	4300	6503	SO:0001583	missense	1832	exon24			GGGATCATTGACC	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.7132A>T	chr6.hg19:g.7584627A>T	ENSP00000369129:p.Ile2378Phe	73.0	0.0	.		77.0	34.0	.	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	hg19	CCDS4501.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.991459	0.74703	.	.	ENSG00000096696	ENST00000379802;ENST00000418664	T;T	0.79749	-1.3;-1.3	5.6	5.6	0.85130	.	0.000000	0.64402	D	0.000005	D	0.89030	0.6599	M	0.87328	2.875	0.41548	D	0.988558	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.89707	0.3909	10	0.45353	T	0.12	.	15.7802	0.78255	1.0:0.0:0.0:0.0	.	1826;2378	Q4LE79;P15924	.;DESP_HUMAN	F	2378;1779	ENSP00000369129:I2378F;ENSP00000396591:I1779F	ENSP00000369129:I2378F	I	+	1	0	DSP	7529626	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	9.301000	0.96167	2.127000	0.65507	0.533000	0.62120	ATT	.	.	.	none		0.448	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		T	7584627	A	T	7584627	3	4	4	1	0	0	0	0	1	0	0	0	4783	217	8	5	7226	5	DSP	6	7584627	Missense_Mutation	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10	1	7584627	163530440	51	304	4	2									
GCNT2	2651	hgsc.bcm.edu	37	chr6	10529857	10529857	+	Missense_Mutation	SNP	A	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	cgtccaccaagaactgttaaAccacaaaaattcctacgtga	16	8	5	12	2	0	2	0	1	0	1	2	2	2	2	4	0	3	1	4	0	7	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr6:10529857A>C	ENST00000379597.3	+	1	1269	c.713A>C	c.(712-714)aAc>aCc	p.N238T	GCNT2_ENST00000397423.2_Intron|GCNT2_ENST00000495262.1_Missense_Mutation_p.N238T|GCNT2_ENST00000410107.1_Intron			Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)	238					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)		GAACTGTTAAACCACAAAAAT	0.448																																					p.N238T		Atlas-SNP	.											.	GCNT2	123	.	0			c.A713C						PASS	.						75	78	77					6																	10529857		2202	4300	6502	SO:0001583	missense	2651	exon3			TGTTAAACCACAA	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.713A>C	chr6.hg19:g.10529857A>C	ENSP00000368917:p.Asn238Thr	70.0	0.0	.		53.0	17.0	.	NM_145649		Missense_Mutation	SNP	ENST00000379597.3	hg19	CCDS34338.1	.	.	.	.	.	.	.	.	.	.	A	1.996	-0.430677	0.04669	.	.	ENSG00000111846	ENST00000495262;ENST00000379597	T;T	0.09723	2.95;2.95	5.6	-5.91	0.02269	.	1.868580	0.02099	N	0.053783	T	0.00875	0.0029	N	0.02765	-0.5	0.09310	N	0.999996	B;B	0.06786	0.001;0.001	B;B	0.12156	0.007;0.007	T	0.40961	-0.9535	10	0.10636	T	0.68	-17.1412	3.8801	0.09074	0.5225:0.0949:0.2781:0.1045	.	238;237	Q8N0V5;Q08M29	GNT2A_HUMAN;.	T	238	ENSP00000419411:N238T;ENSP00000368917:N238T	ENSP00000368917:N238T	N	+	2	0	GCNT2	10637843	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	0.109000	0.15417	-0.665000	0.05317	0.519000	0.50382	AAC	.	.	.	none		0.448	GCNT2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327912.3	NM_145649		C	10529857	A	C	10529857	3	2	4	1	0	0	0	0	1	0	0	0	6308	43	2	5	715	5	GCNT2	6	10529857	Missense_Mutation	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10	2945230	10529857	160585210	52	305											
OR2J3	442186	hgsc.bcm.edu	37	chr6	29080095	29080095	+	Missense_Mutation	SNP	T	T	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	tgtcctcatgcaccctcgttTctgccacctgctggctgtgg	3	13	10	15	1	2	0	1	0	1	0	4	0	3	0	4	2	3	4	4	2	0	1			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr6:29080095T>G	ENST00000377169.1	+	1	428	c.428T>G	c.(427-429)tTc>tGc	p.F143C		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	143						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						CACCCTCGTTTCTGCCACCTG	0.522																																					p.F143C		Atlas-SNP	.											.	OR2J3	53	.	0			c.T428G						PASS	.						370	396	387					6																	29080095		1387	2633	4020	SO:0001583	missense	442186	exon1			CTCGTTTCTGCCA		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.428T>G	chr6.hg19:g.29080095T>G	ENSP00000366374:p.Phe143Cys	75.0	0.0	.		114.0	45.0	.	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Missense_Mutation	SNP	ENST00000377169.1	hg19	CCDS43433.1	.	.	.	.	.	.	.	.	.	.	T	13.69	2.313785	0.40996	.	.	ENSG00000204701	ENST00000377169	T	0.00036	8.86	2.78	2.78	0.32641	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00073	0.0002	L	0.37850	1.14	0.21782	N	0.999544	P	0.51933	0.949	P	0.56343	0.796	T	0.04855	-1.0922	9	0.87932	D	0	.	6.8216	0.23861	0.2081:0.0:0.0:0.7919	.	143	O76001	OR2J3_HUMAN	C	143	ENSP00000366374:F143C	ENSP00000366374:F143C	F	+	2	0	OR2J3	29188074	0.000000	0.05858	0.855000	0.33649	0.771000	0.43674	0.608000	0.24223	1.268000	0.44264	0.358000	0.22013	TTC	.	.	.	none		0.522	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2			G	29080095	T	G	29080095	3	3	4	1	0	0	0	0	1	0	0	0	11011	1783	62	5	430	5	OR2J3	6	29080095	Missense_Mutation	SNP	T	TCGA-2Z-A9J3-01A-12D-A382-10	18550238	29080095	142034972	53	306											
MDC1	9656	hgsc.bcm.edu	37	chr6	30680834	30680834	+	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	tctgtgtcactgtcctctccAggaggttggctcctctccag	4	13	10	14	0	4	0	1	0	3	0	8	1	6	1	4	3	0	2	4	3	0	1			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr6:30680834A>C	ENST00000376406.3	-	5	1532	c.885T>G	c.(883-885)ccT>ccG	p.P295P	MDC1-AS1_ENST00000442150.1_RNA|MDC1_ENST00000494654.1_5'Flank|MDC1_ENST00000376405.2_Silent_p.P295P	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	295	Required for nuclear localization (NLS1).				DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						TGTCCTCTCCAGGAGGTTGGC	0.542								Other conserved DNA damage response genes																													p.P295P		Atlas-SNP	.											.	MDC1	218	.	0			c.T885G						PASS	.						146	124	132					6																	30680834		1511	2709	4220	SO:0001819	synonymous_variant	9656	exon5			CTCTCCAGGAGGT	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.885T>G	chr6.hg19:g.30680834A>C		71.0	0.0	.		87.0	38.0	.	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Silent	SNP	ENST00000376406.3	hg19	CCDS34384.1																																																																																			.	.	.	none		0.542	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641		C	30680834	A	C	30680834	2	2	4	1	0	0	0	0	0	0	0	1	9410	175	7	5		5	MDC1	6	30680834	Silent	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10	1600739	30680834	140434233	54	307											
C6orf153	88745	hgsc.bcm.edu	37	chr6	42989441	42989441	+	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	ccggggccggggccggggccCgacgtccccgcggggcccgg	1	1	21	18	8	0	0	0	0	0	0	1	1	1	0	7	9	0	0	7	9	0	0	rs202053592	byFrequency	TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr6:42989441C>T	ENST00000244496.5	+	1	59	c.49C>T	c.(49-51)Cga>Tga	p.R17*		NM_033112.2	NP_149103.1	Q96EU6	RRP36_HUMAN	ribosomal RNA processing 36 homolog (S. cerevisiae)	17					ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(5)|lung(1)|ovary(1)|prostate(1)	11						ggccggggcccgacgtccccg	0.776																																					p.R17X		Atlas-SNP	.											.	RRP36	20	.	0			c.C49T						PASS	.						2	2	2					6																	42989441		866	1798	2664	SO:0001587	stop_gained	88745	exon1			GGGGCCCGACGTC	BC011933	CCDS34453.1	6p21.1	2010-07-06	2010-07-06	2010-07-06	ENSG00000124541	ENSG00000124541			21374	protein-coding gene	gene with protein product		613475	"chromosome 6 open reading frame 153"	C6orf153		20038530	Standard	NM_033112		Approved	dJ20C7.4	uc003otp.1	Q96EU6	OTTHUMG00000014715	ENST00000244496.5:c.49C>T	chr6.hg19:g.42989441C>T	ENSP00000244496:p.Arg17*	27.0	0.0	.		23.0	10.0	.	NM_033112	Q9BRF6|Q9P0C8	Nonsense_Mutation	SNP	ENST00000244496.5	hg19	CCDS34453.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.442813	0.43326	.	.	ENSG00000124541	ENST00000244496	.	.	.	3.24	-0.816	0.10839	.	0.576146	0.10077	U	0.718890	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	.	2.3532	0.04289	0.1591:0.2847:0.4261:0.13	.	.	.	.	X	17	.	ENSP00000244496:R17X	R	+	1	2	RRP36	43097419	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.257000	0.08745	-0.199000	0.10317	-0.339000	0.08088	CGA	.	.	.	none		0.776	RRP36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040572.1	NM_033112		T	42989441	C	T	42989441	4	4	4	1	0	0	0	0	0	1	0	0	2340	644	23	1	51	1	C6orf153	6	42989441	Nonsense_Mutation	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10	12308607	42989441	128125626	55	308											
DLK2	65989	hgsc.bcm.edu	37	chr6	43418926	43418926	+	Frame_Shift_Del	DEL	C	C	-																															catttacctcacagcgggcaCccacaaagcccaccaagcag																										TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr6:43418926delC	ENST00000357338.3	-	6	1203	c.503delG	c.(502-504)ggtfs	p.G168fs	DLK2_ENST00000372488.3_Frame_Shift_Del_p.G168fs|DLK2_ENST00000372485.1_Frame_Shift_Del_p.G162fs|DLK2_ENST00000414245.1_Frame_Shift_Del_p.G162fs	NM_206539.1	NP_996262.1	Q6UY11	DLK2_HUMAN	delta-like 2 homolog (Drosophila)	168	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				negative regulation of Notch signaling pathway (GO:0045746)|regulation of fat cell differentiation (GO:0045598)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.G168D(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	7	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			ACAGCGGGCACCCACAAAGCC	0.612																																					p.G168fs		Atlas-Indel,Pindel	.											.	DLK2	22	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.504delT						PASS	.						80	57	65					6																	43418926		2203	4300	6503	SO:0001589	frameshift_variant	65989	exon6			.	AK055380	CCDS4897.1, CCDS75461.1	6p21.1	2008-02-05	2007-07-05	2007-07-05	ENSG00000171462	ENSG00000171462			21113	protein-coding gene	gene with protein product			"EGF-like-domain, multiple 9"	EGFL9			Standard	NM_001286656		Approved	MGC2487	uc003ovb.3	Q6UY11	OTTHUMG00000014735	ENST00000357338.3:c.503delG	chr6.hg19:g.43418926delC	ENSP00000349893:p.Gly168fs	137.0	0.0	0		110.0	51.0	0.463636	NM_206539	B3KNZ7|Q5T3T8|Q9BQ54	Frame_Shift_Del	DEL	ENST00000357338.3	hg19	CCDS4897.1																																																																																			.	.	.	none		0.612	DLK2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040618.1	NM_023932		-	43418926	C	-	43418926	7	5	4	1	0	1	0	1	0	0	0	0	4567	507	18	0	652	0	DLK2	6	43418926	Frame_Shift_Del	DEL	C	TCGA-2Z-A9J3-01A-12D-A382-10	429485	43418926	127696141	56	309											
HIVEP2	3097	hgsc.bcm.edu	37	chr6	143094459	143094459	+	Frame_Shift_Del	DEL	C	C	-																															gatcagctgtgaaacaggatCttcaaacatcttgacatcta																										TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr6:143094459delC	ENST00000367604.1	-	4	2056	c.1417delG	c.(1417-1419)gatfs	p.D473fs	HIVEP2_ENST00000012134.2_Frame_Shift_Del_p.D473fs|HIVEP2_ENST00000367603.2_Frame_Shift_Del_p.D473fs			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	473					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		GAAACAGGATCTTCAAACATC	0.483																																					p.D473fs	Esophageal Squamous(107;843 1510 13293 16805 42198)	Atlas-INDEL	.											.	HIVEP2	225	.	0			c.1418delA						PASS	.						138	135	136					6																	143094459		2033	4190	6223	SO:0001589	frameshift_variant	3097	exon5			.	M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"Zinc fingers, C2H2-type"	4921	protein-coding gene	gene with protein product	"c-myc intron binding protein 1"	143054	"human immunodeficiency virus type I enhancer-binding protein 2"			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.1417delG	chr6.hg19:g.143094459delC	ENSP00000356576:p.Asp473fs	75.0	0.0	0		61.0	24.0	0.393443	NM_006734	Q02646|Q5THT5|Q9NS05	Frame_Shift_Del	DEL	ENST00000367604.1	hg19	CCDS43510.1																																																																																			.	.	.	none		0.483	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1			-	143094459	C	-	143094459	7	5	4	1	0	1	0	1	0	0	0	0	7194	913	32	0	5947	0	HIVEP2	6	143094459	Frame_Shift_Del	DEL	C	TCGA-2Z-A9J3-01A-12D-A382-10	99675533	143094459	28020608	57	310											
PHKG1	5260	hgsc.bcm.edu	37	chr7	56155338	56155338	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaggatgtccacctccttcAgcgtggcttctcgcagctcc	5	10	10	16	2	2	0	1	0	1	0	6	1	5	1	4	2	2	4	4	2	0	2			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr7:56155338A>G	ENST00000297373.2	-	3	409	c.215T>C	c.(214-216)cTg>cCg	p.L72P	PHKG1_ENST00000537360.1_Silent_p.A36A|PHKG1_ENST00000452681.2_Missense_Mutation_p.L72P|PHKG1_ENST00000489604.1_5'UTR	NM_001258460.1|NM_006213.4	NP_001245389.1|NP_006204.1	Q16816	PHKG1_HUMAN	phosphorylase kinase, gamma 1 (muscle)	72	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)|phosphorylase kinase complex (GO:0005964)	ATP binding (GO:0005524)|phosphorylase kinase activity (GO:0004689)|tau-protein kinase activity (GO:0050321)			endometrium(1)|large_intestine(1)|lung(5)	7	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			CACCTCCTTCAGCGTGGCTTC	0.647																																					p.L72P	Melanoma(184;580 2064 5329 24177 35303)	Atlas-SNP	.											.	PHKG1	38	.	0			c.T215C						PASS	.						76	51	60					7																	56155338		2203	4300	6503	SO:0001583	missense	5260	exon3			TCCTTCAGCGTGG	X80590	CCDS5525.1, CCDS59057.1	7p11.2	2009-07-10			ENSG00000164776	ENSG00000164776	2.7.11.19		8930	protein-coding gene	gene with protein product		172470		PHKG		8530014	Standard	NM_001258459		Approved		uc011kdb.2	Q16816	OTTHUMG00000023869	ENST00000297373.2:c.215T>C	chr7.hg19:g.56155338A>G	ENSP00000297373:p.Leu72Pro	45.0	0.0	.		83.0	65.0	.	NM_001258459	B7Z1D0|F5H2S1|Q75LP5	Missense_Mutation	SNP	ENST00000297373.2	hg19	CCDS5525.1	.	.	.	.	.	.	.	.	.	.	A	12.96	2.095532	0.36952	.	.	ENSG00000164776	ENST00000452681;ENST00000297373	T;T	0.46063	3.1;0.88	5.42	4.25	0.50352	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.606658	0.14620	N	0.308456	T	0.44307	0.1287	L	0.60957	1.885	0.80722	D	1	B;B;P	0.45827	0.082;0.451;0.867	B;B;P	0.48901	0.287;0.273;0.594	T	0.26360	-1.0105	10	0.36615	T	0.2	-17.4861	5.7614	0.18203	0.7557:0.0:0.086:0.1583	.	72;72;72	B7Z6U2;F5H2S1;Q16816	.;.;PHKG1_HUMAN	P	72	ENSP00000445440:L72P;ENSP00000297373:L72P	ENSP00000297373:L72P	L	-	2	0	PHKG1	56122832	0.997000	0.39634	0.998000	0.56505	0.790000	0.44656	3.544000	0.53640	0.981000	0.38548	0.460000	0.39030	CTG	.	.	.	none		0.647	PHKG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251587.1	NM_006213		G	56155338	A	G	56155338	3	3	4	1	0	0	0	0	1	0	0	0	11853	188	7	3	980	3	PHKG1	7	56155338	Missense_Mutation	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10		56155338	102983325	58	311											
BAZ1B	9031	hgsc.bcm.edu	37	chr7	72856678	72856678	+	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	caacagagccactagacactGttctgtcttcaccatgcagc	11	9	7	14	0	3	2	1	0	2	2	3	2	3	2	2	0	4	2	2	0	2	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr7:72856678G>C	ENST00000339594.4	-	19	4638	c.4300C>G	c.(4300-4302)Cag>Gag	p.Q1434E	BAZ1B_ENST00000404251.1_Missense_Mutation_p.Q1434E	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	1434					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)				ACTAGACACTGTTCTGTCTTC	0.493																																					p.Q1434E	Esophageal Squamous(112;1167 1561 21085 43672 48228)	Atlas-SNP	.											.	BAZ1B	147	.	0			c.C4300G						PASS	.						139	124	129					7																	72856678		2203	4300	6503	SO:0001583	missense	9031	exon19			GACACTGTTCTGT	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.4300C>G	chr7.hg19:g.72856678G>C	ENSP00000342434:p.Gln1434Glu	78.0	0.0	.		158.0	118.0	.	NM_032408	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Missense_Mutation	SNP	ENST00000339594.4	hg19	CCDS5549.1	.	.	.	.	.	.	.	.	.	.	G	12.75	2.030593	0.35797	.	.	ENSG00000009954	ENST00000339594;ENST00000404251	T;T	0.17213	2.29;2.29	5.54	4.63	0.57726	Bromodomain (3);	0.184208	0.49305	N	0.000149	T	0.14485	0.0350	L	0.29908	0.895	0.41806	D	0.989949	B	0.02656	0.0	B	0.04013	0.001	T	0.03139	-1.1068	10	0.35671	T	0.21	-23.1276	15.2408	0.73468	0.0:0.1411:0.8589:0.0	.	1434	Q9UIG0	BAZ1B_HUMAN	E	1434	ENSP00000342434:Q1434E;ENSP00000385442:Q1434E	ENSP00000342434:Q1434E	Q	-	1	0	BAZ1B	72494614	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.883000	0.69721	1.266000	0.44231	0.643000	0.83706	CAG	.	.	.	none		0.493	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408		C	72856678	G	C	72856678	3	2	4	1	0	0	0	0	1	0	0	0	1330	1386	48	4	155	4	BAZ1B	7	72856678	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	16701340	72856678	86281985	59	312											
CLIP2	7461	hgsc.bcm.edu	37	chr7	73752959	73752959	+	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	gtgcagtatctgggagagacGcagttcgcaccgggccagtg	8	7	16	10	3	1	1	0	0	1	1	2	3	1	2	2	2	1	5	2	2	1	2			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr7:73752959G>A	ENST00000395060.1	+	2	303	c.303G>A	c.(301-303)acG>acA	p.T101T	CLIP2_ENST00000223398.6_Silent_p.T101T|CLIP2_ENST00000361545.5_Silent_p.T101T			Q9UDT6	CLIP2_HUMAN	CAP-GLY domain containing linker protein 2	101	CAP-Gly 1. {ECO:0000255|PROSITE- ProRule:PRU00045}.					cytoplasmic microtubule (GO:0005881)|microtubule associated complex (GO:0005875)|microtubule plus-end (GO:0035371)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|pancreas(1)|prostate(2)|skin(3)	30						TGGGAGAGACGCAGTTCGCAC	0.687																																					p.T101T		Atlas-SNP	.											.	CLIP2	134	.	0			c.G303A						PASS	.						60	47	51					7																	73752959		2177	4269	6446	SO:0001819	synonymous_variant	7461	exon3			AGAGACGCAGTTC	AB006629	CCDS5569.1, CCDS5570.1	7q11.23	2008-06-12	2007-01-04	2007-01-04	ENSG00000106665	ENSG00000106665			2586	protein-coding gene	gene with protein product		603432	"cytoplasmic linker 2", "Williams-Beuren syndrome chromosome region 3"	WBSCR4, CYLN2, WBSCR3		8812460, 9799601	Standard	NM_003388		Approved	CLIP-115, KIAA0291, WSCR4, CLIP, WSCR3	uc003uam.3	Q9UDT6	OTTHUMG00000022980	ENST00000395060.1:c.303G>A	chr7.hg19:g.73752959G>A		54.0	0.0	.		102.0	17.0	.	NM_032421	O14527|O43611	Silent	SNP	ENST00000395060.1	hg19	CCDS5569.1																																																																																			.	.	.	none		0.687	CLIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252556.1	NM_003388		A	73752959	G	A	73752959	2	1	4	1	0	0	0	0	0	0	0	1	3535	1074	38	1		1	CLIP2	7	73752959	Silent	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	896281	73752959	85385704	60	313											
AKAP9	10142	hgsc.bcm.edu	37	chr7	91624968	91624968	+	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	ctcatagtagcacagctgcaGacttactacaagccaaacaa	16	7	6	12	0	1	1	1	0	0	1	1	1	1	1	1	0	7	4	1	0	7	4			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr7:91624968G>A	ENST00000359028.2	+	8	1045	c.820G>A	c.(820-822)Gac>Aac	p.D274N	AKAP9_ENST00000356239.3_Missense_Mutation_p.D262N|AKAP9_ENST00000358100.2_Missense_Mutation_p.D274N|AKAP9_ENST00000394564.1_Missense_Mutation_p.D262N			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	274	Gln-rich.				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)			CACAGCTGCAGACTTACTACA	0.378			T	BRAF	papillary thyroid																																p.D262N		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.G784A						PASS	.						96	86	89					7																	91624968		2203	4300	6503	SO:0001583	missense	10142	exon7			GCTGCAGACTTAC	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.820G>A	chr7.hg19:g.91624968G>A	ENSP00000351922:p.Asp274Asn	189.0	0.0	.		430.0	95.0	.	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	hg19		.	.	.	.	.	.	.	.	.	.	G	24.2	4.506910	0.85282	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394565;ENST00000394564;ENST00000438114	T;T;T;T;T	0.34072	1.38;1.38;1.38;1.38;1.38	5.1	5.1	0.69264	.	0.000000	0.43110	D	0.000602	T	0.49525	0.1562	L	0.27053	0.805	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;0.997	D;D;D;D	0.80764	0.994;0.986;0.993;0.942	T	0.53697	-0.8402	10	0.72032	D	0.01	.	18.8833	0.92365	0.0:0.0:1.0:0.0	.	262;262;274;262	Q99996-2;Q99996-3;A4D1E4;Q6PJH3	.;.;.;.	N	262;274;274;274;274;262;213	ENSP00000348573:D262N;ENSP00000351922:D274N;ENSP00000350813:D274N;ENSP00000378065:D262N;ENSP00000391704:D213N	ENSP00000348573:D262N	D	+	1	0	AKAP9	91462904	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.602000	0.90868	2.535000	0.85469	0.655000	0.94253	GAC	.	.	.	none		0.378	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		A	91624968	G	A	91624968	3	1	4	1	0	0	0	0	1	0	0	0	459	942	33	2	810	2	AKAP9	7	91624968	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	17872009	91624968	67513695	61	314											
PEX1	5189	hgsc.bcm.edu	37	chr7	92147296	92147296	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggctcggcgtgtctttggcTgaataaggagtttggtgtca	6	14	15	6	2	2	1	1	1	1	0	3	2	2	2	0	5	0	3	0	5	2	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr7:92147296T>C	ENST00000248633.4	-	5	628	c.533A>G	c.(532-534)cAg>cGg	p.Q178R	PEX1_ENST00000438045.1_Intron|PEX1_ENST00000428214.1_Missense_Mutation_p.Q178R|PEX1_ENST00000541751.1_5'Flank	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	178					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)			TGTCTTTGGCTGAATAAGGAG	0.383																																					p.Q178R		Atlas-SNP	.											.	PEX1	102	.	0			c.A533G						PASS	.						53	57	55					7																	92147296		2158	4289	6447	SO:0001583	missense	5189	exon5			TTTGGCTGAATAA	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.533A>G	chr7.hg19:g.92147296T>C	ENSP00000248633:p.Gln178Arg	60.0	0.0	.		198.0	152.0	.	NM_000466	A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Missense_Mutation	SNP	ENST00000248633.4	hg19	CCDS5627.1	.	.	.	.	.	.	.	.	.	.	T	10.98	1.505840	0.26949	.	.	ENSG00000127980	ENST00000248633;ENST00000428214;ENST00000545192	D;D	0.94417	-3.37;-3.42	5.84	0.871	0.19107	Peroxisome biogenesis factor 1, N-terminal (1);	0.673780	0.16046	N	0.232189	D	0.86209	0.5878	L	0.29908	0.895	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.72972	-0.4129	10	0.25751	T	0.34	-2.6037	1.138	0.01759	0.1586:0.3287:0.1645:0.3482	.	178	O43933	PEX1_HUMAN	R	178	ENSP00000248633:Q178R;ENSP00000394413:Q178R	ENSP00000248633:Q178R	Q	-	2	0	PEX1	91985232	1.000000	0.71417	0.999000	0.59377	0.841000	0.47740	1.064000	0.30579	0.122000	0.18314	0.528000	0.53228	CAG	.	.	.	none		0.383	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466		C	92147296	T	C	92147296	3	2	4	1	0	0	0	0	1	0	0	0	11742	1580	55	3	3398	3	PEX1	7	92147296	Missense_Mutation	SNP	T	TCGA-2Z-A9J3-01A-12D-A382-10	522328	92147296	66991367	62	315											
MTFR1	9650	hgsc.bcm.edu	37	chr8	66617006	66617006	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cccaagcagacagatttcctTaccagacttgtctcaagaag	13	9	7	12	0	1	4	1	0	1	4	3	4	2	4	3	0	2	1	3	0	4	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr8:66617006T>C	ENST00000262146.4	+	5	485	c.359T>C	c.(358-360)tTa>tCa	p.L120S	MTFR1_ENST00000458689.2_Missense_Mutation_p.L87S|MTFR1_ENST00000517944.1_3'UTR	NM_014637.3	NP_055452.3	Q15390	MTFR1_HUMAN	mitochondrial fission regulator 1	120					aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(1)|pancreas(1)|urinary_tract(1)	11			Epithelial(68;0.0526)|BRCA - Breast invasive adenocarcinoma(89;0.156)|all cancers(69;0.171)|OV - Ovarian serous cystadenocarcinoma(28;0.194)			CAGATTTCCTTACCAGACTTG	0.507																																					p.L120S		Atlas-SNP	.											.	MTFR1	26	.	0			c.T359C						PASS	.						74	74	74					8																	66617006		2203	4300	6503	SO:0001583	missense	9650	exon5			TTTCCTTACCAGA		CCDS6182.1, CCDS55240.1	8q13.1	2012-11-30							29510	protein-coding gene	gene with protein product	"likely ortholog of chicken chondrocyte protein with a poly proline region"					7584026, 7584028, 15389597	Standard	NM_014637		Approved	CHPPR, KIAA0009, FAM54A2	uc003xvn.2	Q15390		ENST00000262146.4:c.359T>C	chr8.hg19:g.66617006T>C	ENSP00000262146:p.Leu120Ser	137.0	0.0	.		197.0	67.0	.	NM_014637	E7EP84|Q6IB94|Q7Z669|Q86XH5|Q8IVD7	Missense_Mutation	SNP	ENST00000262146.4	hg19	CCDS6182.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.66|14.66	2.602219|2.602219	0.46423|0.46423	.|.	.|.	ENSG00000066855|ENSG00000066855	ENST00000518609;ENST00000262146;ENST00000458689|ENST00000518800	T;T|.	0.46063|.	0.88;0.88|.	5.39|5.39	1.66|1.66	0.24008|0.24008	.|.	0.233115|.	0.35838|.	N|.	0.002944|.	T|T	0.61924|0.61924	0.2386|0.2386	M|M	0.66439|0.66439	2.03|2.03	0.37434|0.37434	D|D	0.914169|0.914169	B;B;P;B|.	0.34977|.	0.097;0.345;0.478;0.095|.	B;B;B;B|.	0.41813|.	0.063;0.367;0.305;0.094|.	T|T	0.60855|0.60855	-0.7180|-0.7180	10|5	0.28530|.	T|.	0.3|.	-0.7048|-0.7048	9.3755|9.3755	0.38281|0.38281	0.0:0.1972:0.0:0.8028|0.0:0.1972:0.0:0.8028	.|.	120;104;87;120|.	B4E3G8;E5RJS5;E7EP84;Q15390|.	.;.;.;MTFR1_HUMAN|.	S|H	104;120;87|78	ENSP00000262146:L120S;ENSP00000391502:L87S|.	ENSP00000262146:L120S|.	L|Y	+|+	2|1	0|0	MTFR1|MTFR1	66779560|66779560	1.000000|1.000000	0.71417|0.71417	0.979000|0.979000	0.43373|0.43373	0.943000|0.943000	0.58893|0.58893	3.364000|3.364000	0.52328|0.52328	0.042000|0.042000	0.15717|0.15717	0.460000|0.460000	0.39030|0.39030	TTA|TAC	.	.	.	none		0.507	MTFR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378894.1	NM_014637		C	66617006	T	C	66617006	3	2	4	1	0	0	0	0	1	0	0	0	9932	1764	61	3	373	3	MTFR1	8	66617006	Missense_Mutation	SNP	T	TCGA-2Z-A9J3-01A-12D-A382-10		66617006	79747016	63	316											
MMP16	4325	hgsc.bcm.edu	37	chr8	89068476	89068476	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagggtaaccaggttgaagaGttgtatccttgaacacccaa	13	9	11	8	0	0	3	0	2	0	1	1	4	1	3	3	2	2	4	3	2	5	5			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr8:89068476G>A	ENST00000286614.6	-	8	1534	c.1253C>T	c.(1252-1254)aCt>aTt	p.T418I		NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	418					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)	AGGTTGAAGAGTTGTATCCTT	0.368																																					p.T418I		Atlas-SNP	.											.	MMP16	176	.	0			c.C1253T						PASS	.						92	88	90					8																	89068476		2203	4300	6503	SO:0001583	missense	4325	exon8			TGAAGAGTTGTAT	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.1253C>T	chr8.hg19:g.89068476G>A	ENSP00000286614:p.Thr418Ile	109.0	0.0	.		175.0	101.0	.	NM_005941	B2RAN7|Q14824|Q52H48	Missense_Mutation	SNP	ENST00000286614.6	hg19	CCDS6246.1	.	.	.	.	.	.	.	.	.	.	G	13.92	2.381730	0.42207	.	.	ENSG00000156103	ENST00000286614	T	0.02863	4.13	5.91	5.91	0.95273	Hemopexin/matrixin (2);	0.310233	0.39274	N	0.001410	T	0.04724	0.0128	L	0.33189	0.99	0.58432	D	0.99999	B	0.20052	0.041	B	0.29077	0.098	T	0.53913	-0.8371	10	0.33141	T	0.24	.	20.2985	0.98592	0.0:0.0:1.0:0.0	.	418	P51512	MMP16_HUMAN	I	418	ENSP00000286614:T418I	ENSP00000286614:T418I	T	-	2	0	MMP16	89137592	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	4.781000	0.62389	2.793000	0.96121	0.655000	0.94253	ACT	.	.	.	none		0.368	MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375304.2	NM_005941		A	89068476	G	A	89068476	3	1	4	1	0	0	0	0	1	0	0	0	9662	1029	36	2	582	2	MMP16	8	89068476	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	22451470	89068476	57295546	64	317											
ZNF517	340385	hgsc.bcm.edu	37	chr8	146033121	146033121	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaaggccttcagccgcagcTcccggctgctgcagcaccag	7	5	12	17	2	1	0	1	0	0	0	2	0	2	0	4	2	5	7	4	2	1	1			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr8:146033121T>C	ENST00000531720.1	+	4	865	c.820T>C	c.(820-822)Tcc>Ccc	p.S274P	ZNF517_ENST00000525105.1_Intron|ZNF517_ENST00000526178.1_Intron|ZNF517_ENST00000359971.3_Missense_Mutation_p.S274P			Q6ZMY9	ZN517_HUMAN	zinc finger protein 517	274					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(2)|lung(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;5.47e-39)|OV - Ovarian serous cystadenocarcinoma(54;6.38e-39)|all cancers(56;5.47e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)			CAGCCGCAGCTCCCGGCTGCT	0.692																																					p.S274P		Atlas-SNP	.											.	ZNF517	30	.	0			c.T820C						PASS	.						21	23	23					8																	146033121		2201	4297	6498	SO:0001583	missense	340385	exon5			CGCAGCTCCCGGC	AK096527	CCDS6434.1	8q24.3	2013-01-08				ENSG00000197363		"Zinc fingers, C2H2-type", "-"	27984	protein-coding gene	gene with protein product							Standard	NM_213605		Approved		uc003zed.1	Q6ZMY9		ENST00000531720.1:c.820T>C	chr8.hg19:g.146033121T>C	ENSP00000436103:p.Ser274Pro	49.0	0.0	.		67.0	37.0	.	NM_213605		Missense_Mutation	SNP	ENST00000531720.1	hg19	CCDS6434.1	.	.	.	.	.	.	.	.	.	.	T	15.77	2.930921	0.52866	.	.	ENSG00000197363	ENST00000359971;ENST00000531720	T;T	0.08102	3.13;3.13	2.08	2.08	0.27032	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.14141	0.0342	M	0.65975	2.015	0.20196	N	0.999927	D	0.61080	0.989	P	0.50590	0.645	T	0.13818	-1.0495	9	0.66056	D	0.02	.	4.8554	0.13557	0.4587:0.0:0.0:0.5413	.	274	Q6ZMY9	ZN517_HUMAN	P	274	ENSP00000353058:S274P;ENSP00000436103:S274P	ENSP00000353058:S274P	S	+	1	0	ZNF517	146003925	0.000000	0.05858	0.981000	0.43875	0.745000	0.42441	-2.135000	0.01306	0.947000	0.37659	0.379000	0.24179	TCC	.	.	.	none		0.692	ZNF517-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382642.1	XM_291261		C	146033121	T	C	146033121	3	2	4	1	0	0	0	0	1	0	0	0	17973	1551	54	3	834	3	ZNF517	8	146033121	Missense_Mutation	SNP	T	TCGA-2Z-A9J3-01A-12D-A382-10	56964645	146033121	330901	65	318											
DDX58	23586	hgsc.bcm.edu	37	chr9	32466289	32466289	+	Splice_Site	DEL	T	T	-																															aagaataacgtagacttaccTtttccctaaatactgcttcg																										TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr9:32466289delT	ENST00000379883.2	-	16	2493	c.2336delA	c.(2335-2337)aag>ag	p.K779fs	DDX58_ENST00000379882.1_Splice_Site_p.K734fs|DDX58_ENST00000379868.1_Splice_Site_p.K576fs|DDX58_ENST00000542096.1_Splice_Site_p.K708fs	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	779	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)		TAGACTTACCTTTTCCCTAAA	0.348																																					p.K779fs		Atlas-Indel,Pindel	.											.	DDX58	82	.	0			c.2337delG						PASS	.						194	182	186					9																	32466289		2203	4300	6503	SO:0001630	splice_region_variant	23586	exon16			.	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.2337+1A>-	chr9.hg19:g.32466289delT		39.0	0.0	0		32.0	13.0	0.40625	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Frame_Shift_Del	DEL	ENST00000379883.2	hg19	CCDS6526.1																																																																																			.	.	.	none		0.348	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314	Frame_Shift_Del	-	32466289	T	-	32466289	8	5	4	1	0	1	0	1	0	0	1	0	4377	1623	56	0	453	0	DDX58	9	32466289	Splice_Site	DEL	T	TCGA-2Z-A9J3-01A-12D-A382-10		32466289	108747142	66	319											
PTPN3	5774	hgsc.bcm.edu	37	chr9	112145801	112145801	+	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	gccgtggttcatgacgtcggGgggatctggccagtactggt	5	10	17	9	3	2	1	1	1	1	0	3	2	2	2	2	6	1	2	2	6	1	2			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr9:112145801G>T	ENST00000374541.2	-	23	2388	c.2284C>A	c.(2284-2286)Ccc>Acc	p.P762T	PTPN3_ENST00000262539.3_Missense_Mutation_p.P608T|PTPN3_ENST00000394827.3_Missense_Mutation_p.P230T|PTPN3_ENST00000412145.1_Missense_Mutation_p.P631T|PTPN3_ENST00000446349.1_Missense_Mutation_p.P586T	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						ATGACGTCGGGGGGATCTGGC	0.557																																					p.P762T		Atlas-SNP	.											.	PTPN3	106	.	0			c.C2284A						PASS	.						126	118	121					9																	112145801		2203	4300	6503	SO:0001583	missense	5774	exon23			CGTCGGGGGGATC		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.2284C>A	chr9.hg19:g.112145801G>T	ENSP00000363667:p.Pro762Thr	112.0	0.0	.		85.0	34.0	.	NM_002829	A0AUW9|E7EN99|E9PGU7	Missense_Mutation	SNP	ENST00000374541.2	hg19	CCDS6776.1	.	.	.	.	.	.	.	.	.	.	G	8.494	0.862742	0.17178	.	.	ENSG00000070159	ENST00000394831;ENST00000412145;ENST00000446349;ENST00000374541;ENST00000394827;ENST00000262539	D;D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68;-1.68	4.75	3.82	0.43975	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.053687	0.85682	N	0.000000	D	0.82949	0.5148	N	0.21194	0.64	0.58432	D	0.999999	D;B;B	0.89917	1.0;0.057;0.034	D;B;B	0.91635	0.999;0.083;0.032	T	0.77879	-0.2423	10	0.12103	T	0.63	.	14.3098	0.66407	0.0:0.0:0.8503:0.1497	.	608;717;762	B7Z3H5;B7Z9V1;P26045	.;.;PTN3_HUMAN	T	762;631;586;762;230;608	ENSP00000416654:P631T;ENSP00000395384:P586T;ENSP00000363667:P762T;ENSP00000378304:P230T;ENSP00000262539:P608T	ENSP00000262539:P608T	P	-	1	0	PTPN3	111185622	1.000000	0.71417	0.840000	0.33206	0.135000	0.20990	7.828000	0.86729	1.080000	0.41073	0.462000	0.41574	CCC	.	.	.	none		0.557	PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4			T	112145801	G	T	112145801	3	4	4	1	0	0	0	0	1	0	0	0	12802	1232	43	4	473	4	PTPN3	9	112145801	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	79679512	112145801	29067630	67	320											
NUP188	23511	hgsc.bcm.edu	37	chr9	131731688	131731688	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctttctagctacttcagTgccctcatcctggtggaggg	5	15	10	11	0	4	0	2	0	2	0	5	1	5	1	2	3	3	1	2	3	2	5			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr9:131731688T>C	ENST00000372577.2	+	10	828	c.807T>C	c.(805-807)agT>agC	p.S269S		NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	269					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						GCTACTTCAGTGCCCTCATCC	0.423																																					p.S269S		Atlas-SNP	.											.	NUP188	140	.	0			c.T807C						PASS	.						138	115	123					9																	131731688		2203	4300	6503	SO:0001819	synonymous_variant	23511	exon10			CTTCAGTGCCCTC	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.807T>C	chr9.hg19:g.131731688T>C		73.0	0.0	.		82.0	33.0	.	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Silent	SNP	ENST00000372577.2	hg19	CCDS35156.1																																																																																			.	.	.	none		0.423	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2			C	131731688	T	C	131731688	2	2	4	1	0	0	0	0	0	0	0	1	10765	1693	59	3		3	NUP188	9	131731688	Silent	SNP	T	TCGA-2Z-A9J3-01A-12D-A382-10	19585887	131731688	9481743	68	321											
NUP214	8021	hgsc.bcm.edu	37	chr9	134073449	134073453	+	Frame_Shift_Del	DEL	CAGCC	CAGCC	-																															acttctagaggagcaacagtCagcccagcttccccaggctc																								rs368154028		TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	CAGCC	CAGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr9:134073449_134073453delCAGCC	ENST00000359428.5	+	29	4712_4716	c.4568_4572delCAGCC	c.(4567-4572)tcagccfs	p.SA1523fs	NUP214_ENST00000451030.1_Frame_Shift_Del_p.SA1524fs|NUP214_ENST00000411637.2_Frame_Shift_Del_p.SA1513fs|NUP214_ENST00000483497.2_Frame_Shift_Del_p.SA349fs			P35658	NU214_HUMAN	nucleoporin 214kDa	1523	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)		GAGCAACAGTCAGCCCAGCTTCCCC	0.537			T	"DEK, SET, ABL1"	"AML, T-ALL"																																p.1523_1524del	Pancreas(4;24 48 25510 30394 32571)	Atlas-Indel,Pindel	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.4567_4571del						PASS	.																																			SO:0001589	frameshift_variant	8021	exon29			.	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.4568_4572delCAGCC	chr9.hg19:g.134073449_134073453delCAGCC	ENSP00000352400:p.Ser1523fs	88.0	0.0	0		76.0	34.0	0.447368	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Frame_Shift_Del	DEL	ENST00000359428.5	hg19	CCDS6940.1																																																																																			.	.	.	none		0.537	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		-	134073453	CAGCC	-	134073449	7	5	4	1	0	1	0	1	0	0	0	0	10769	838	29	0	4682	0	NUP214	9	134073449	Frame_Shift_Del	DEL	CAGCC	TCGA-2Z-A9J3-01A-12D-A382-10	2341761	134073449	7139982	69	322											
PTPLA	9200	hgsc.bcm.edu	37	chr10	17645619	17645619	+	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	cttgaactcacttggaccccAgtcacaatcacagaagtagg	13	8	8	12	0	3	2	3	1	0	1	3	3	3	3	2	2	1	1	2	2	4	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr10:17645619A>T	ENST00000361271.3	-	4	460	c.423T>A	c.(421-423)acT>acA	p.T141T		NM_014241.3	NP_055056.3	B0YJ81	HACD1_HUMAN	protein tyrosine phosphatase-like (proline instead of catalytic arginine), member A	141					fatty acid biosynthetic process (GO:0006633)|multicellular organismal development (GO:0007275)|myotube differentiation (GO:0014902)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|skin(1)	13						CTTGGACCCCAGTCACAATCA	0.353																																					p.T141T		Atlas-SNP	.											.	PTPLA	34	.	0			c.T423A						PASS	.						90	84	86					10																	17645619		2203	4300	6503	SO:0001819	synonymous_variant	9200	exon4			GACCCCAGTCACA	AF114494	CCDS7121.1	10p14-p13	2008-08-01	2005-11-11		ENSG00000165996	ENSG00000165996			9639	protein-coding gene	gene with protein product	"cementum attachment protein"	610467	"protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a"			10644438	Standard	XM_005252641		Approved	CAP	uc001ipg.3	B0YJ81	OTTHUMG00000017750	ENST00000361271.3:c.423T>A	chr10.hg19:g.17645619A>T		210.0	0.0	.		169.0	11.0	.	NM_014241	B0YJ80|Q6JIC5|Q96FW7|Q9HB93|Q9UHX2	Silent	SNP	ENST00000361271.3	hg19	CCDS7121.1																																																																																			.	.	.	none		0.353	PTPLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047046.1	NM_014241		T	17645619	A	T	17645619	2	4	4	1	0	0	0	0	0	0	0	1	12785	175	7	5		5	PTPLA	10	17645619	Silent	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10		17645619	117889128	70	323											
OGDHL	55753	hgsc.bcm.edu	37	chr10	50944091	50944100	+	Frame_Shift_Del	DEL	GGATGGTCAT	GGATGGTCAT	-																															tatgggccgtgcgcgcctcaGgatggtcatgaagcgtgggc																										TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	GGATGGTCAT	GGATGGTCAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr10:50944091_50944100delGGATGGTCAT	ENST00000374103.4	-	22	2963_2972	c.2878_2887delATGACCATCC	c.(2878-2889)atgaccatcctgfs	p.MTIL960fs	OGDHL_ENST00000419399.1_Frame_Shift_Del_p.MTIL903fs|OGDHL_ENST00000432695.1_Frame_Shift_Del_p.MTIL751fs|OGDHL_ENST00000490844.1_5'UTR	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	960					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						GCGCGCCTCAGGATGGTCATGAAGCGTGGG	0.605																																					p.960_963del		Atlas-Indel,Pindel	.											.	OGDHL	149	.	0			c.2879_2888del						PASS	.																																			SO:0001589	frameshift_variant	55753	exon22			.	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.2878_2887delATGACCATCC	chr10.hg19:g.50944091_50944100delGGATGGTCAT	ENSP00000363216:p.Met960fs	28.0	0.0	0		32.0	13.0	0.40625	NM_018245	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Frame_Shift_Del	DEL	ENST00000374103.4	hg19	CCDS7234.1																																																																																			.	.	.	none		0.605	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245		-	50944100	GGATGGTCAT	-	50944091	7	5	4	1	0	1	0	1	0	0	0	0	10847	991	35	0	153	0	OGDHL	10	50944091	Frame_Shift_Del	DEL	GGATGGTCAT	TCGA-2Z-A9J3-01A-12D-A382-10	33298472	50944091	84590656	71	324											
PYROXD2	84795	hgsc.bcm.edu	37	chr10	100147000	100147001	+	Frame_Shift_Del	DEL	GA	GA	-																															ctctccaaatctggtggtgtGaggatgtctctgccaaccac																								rs376868556		TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr10:100147000_100147001delGA	ENST00000370575.4	-	14	1559_1560	c.1511_1512delTC	c.(1510-1512)ctcfs	p.L504fs	PYROXD2_ENST00000483923.1_5'UTR	NM_032709.2	NP_116098.2	Q8N2H3	PYRD2_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 2	504							oxidoreductase activity (GO:0016491)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	12						CTGGTGGTGTGAGGATGTCTCT	0.52																																					p.504_505del		Atlas-Indel,Pindel	.											.	PYROXD2	43	.	0			c.1512_1513del						PASS	.																																			SO:0001589	frameshift_variant	84795	exon14			.	AK074429	CCDS7474.1	10q24.2	2009-04-22	2009-04-22	2009-04-22	ENSG00000119943	ENSG00000119943			23517	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 33"	C10orf33			Standard	NM_032709		Approved	FLJ23849	uc001kpc.3	Q8N2H3	OTTHUMG00000018877	ENST00000370575.4:c.1511_1512delTC	chr10.hg19:g.100147000_100147001delGA	ENSP00000359607:p.Leu504fs	120.0	0.0	0		96.0	46.0	0.479167	NM_032709	D3DR61|Q5TAA9|Q9BRQ1	Frame_Shift_Del	DEL	ENST00000370575.4	hg19	CCDS7474.1																																																																																			.	.	.	none		0.52	PYROXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049782.2	NM_032709		-	100147001	GA	-	100147000	7	5	4	1	0	1	0	1	0	0	0	0	12880	1277	45	0	245	0	PYROXD2	10	100147000	Frame_Shift_Del	DEL	GA	TCGA-2Z-A9J3-01A-12D-A382-10	49202909	100147000	35387747	72	325											
GBF1	8729	hgsc.bcm.edu	37	chr10	104018748	104018748	+	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	ggagattaacattgtggttgGggccatcaaacgaaatgccc	12	9	12	8	1	1	1	1	0	0	1	1	3	1	1	2	4	3	1	2	4	3	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr10:104018748G>T	ENST00000369983.3	+	2	313	c.53G>T	c.(52-54)gGg>gTg	p.G18V	AL160011.1_ENST00000516180.2_RNA	NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	18					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		ATTGTGGTTGGGGCCATCAAA	0.403																																					p.G18V		Atlas-SNP	.											.	GBF1	142	.	0			c.G53T						PASS	.						138	147	144					10																	104018748		2203	4300	6503	SO:0001583	missense	8729	exon2			TGGTTGGGGCCAT	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.53G>T	chr10.hg19:g.104018748G>T	ENSP00000359000:p.Gly18Val	101.0	0.0	.		83.0	39.0	.	NM_001199378	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	hg19	CCDS7533.1	.	.	.	.	.	.	.	.	.	.	G	17.66	3.445710	0.63178	.	.	ENSG00000107862	ENST00000369983	T	0.09163	3.01	5.95	5.95	0.96441	.	0.061547	0.64402	D	0.000005	T	0.10078	0.0247	N	0.12182	0.205	0.80722	D	1	P;P;P;P	0.44195	0.756;0.756;0.828;0.617	B;B;B;B	0.42062	0.374;0.283;0.217;0.173	T	0.09640	-1.0665	10	0.66056	D	0.02	-16.8934	20.3931	0.98965	0.0:0.0:1.0:0.0	.	18;18;18;18	Q149P1;Q149P0;Q92538;Q504U7	.;.;GBF1_HUMAN;.	V	18	ENSP00000359000:G18V	ENSP00000359000:G18V	G	+	2	0	GBF1	104008738	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.804000	0.75186	2.824000	0.97209	0.655000	0.94253	GGG	.	.	.	none		0.403	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			T	104018748	G	T	104018748	3	4	4	1	0	0	0	0	1	0	0	0	6278	1232	43	4	55	4	GBF1	10	104018748	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	3871748	104018748	31515999	73	326											
SORCS3	22986	hgsc.bcm.edu	37	chr10	107016678	107016678	+	Frame_Shift_Del	DEL	A	A	-																															tgtttttgatctacaagtttAaaaggtatgtcctattatca																										TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr10:107016678delA	ENST00000369701.3	+	25	3666	c.3439delA	c.(3439-3441)aaafs	p.K1147fs		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	1147					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)		CTACAAGTTTAAAAGGTATGT	0.413																																					p.F1146fs	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-Indel,Pindel	.											.	SORCS3	282	.	0			c.3438delT						PASS	.						145	124	131					10																	107016678		2203	4300	6503	SO:0001589	frameshift_variant	22986	exon25			.	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.3439delA	chr10.hg19:g.107016678delA	ENSP00000358715:p.Lys1147fs	51.0	0.0	0		38.0	15.0	0.394737	NM_014978	Q5VXF9|Q9NQJ2	Frame_Shift_Del	DEL	ENST00000369701.3	hg19	CCDS7558.1																																																																																			.	.	.	none		0.413	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		-	107016678	A	-	107016678	7	5	4	1	0	1	0	1	0	0	0	0	14945	363	13	0	3537	0	SORCS3	10	107016678	Frame_Shift_Del	DEL	A	TCGA-2Z-A9J3-01A-12D-A382-10	2997930	107016678	28518069	74	327											
PTPRE	5791	hgsc.bcm.edu	37	chr10	129846027	129846027	+	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	aacgcatcctgtgtctctaaGgttcaggaagcagaggaaag	13	8	12	8	1	2	1	1	0	1	1	4	3	3	3	1	3	2	3	1	3	4	2			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr10:129846027G>C	ENST00000254667.3	+	5	488		c.e5-1		PTPRE_ENST00000419012.2_Splice_Site|PTPRE_ENST00000306042.5_Splice_Site|PTPRE_ENST00000430713.2_Splice_Site|PTPRE_ENST00000471218.1_Splice_Site	NM_006504.4	NP_006495.1	P23469	PTPRE_HUMAN	protein tyrosine phosphatase, receptor type, E						negative regulation of insulin receptor signaling pathway (GO:0046627)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of mast cell activation (GO:0033003)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	22		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)			Alendronate(DB00630)	GTGTCTCTAAGGTTCAGGAAG	0.557																																					.	Colon(52;977 1184 20575 41685)	Atlas-SNP	.											.	PTPRE	132	.	0			c.210-1G>C						PASS	.						102	98	100					10																	129846027		2203	4300	6503	SO:0001630	splice_region_variant	5791	exon5			CTCTAAGGTTCAG	AF406557	CCDS7657.1, CCDS7658.1	10q26	2011-06-09			ENSG00000132334	ENSG00000132334		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9669	protein-coding gene	gene with protein product		600926				8595895	Standard	NM_130435		Approved	PTPE	uc001lkb.3	P23469	OTTHUMG00000019254	ENST00000254667.3:c.210-1G>C	chr10.hg19:g.129846027G>C		86.0	0.0	.		94.0	45.0	.	NM_006504	Q13345|Q5VWH3|Q5VWH4|Q96KQ6	Splice_Site	SNP	ENST00000254667.3	hg19	CCDS7657.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.337182	0.81911	.	.	ENSG00000132334	ENST00000254667;ENST00000442830;ENST00000419012;ENST00000430713;ENST00000455661;ENST00000306042	.	.	.	5.05	5.05	0.67936	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4659	0.90755	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PTPRE	129736017	1.000000	0.71417	0.997000	0.53966	0.947000	0.59692	8.680000	0.91225	2.519000	0.84933	0.650000	0.86243	.	.	.	.	none		0.557	PTPRE-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050990.1		Intron	C	129846027	G	C	129846027	5	2	4	1	0	0	0	0	0	0	1	0	12813	1014	35	4	258	4	PTPRE	10	129846027	Splice_Site	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	22829349	129846027	5688720	75	328											
DNHD1	144132	hgsc.bcm.edu	37	chr11	6579352	6579352	+	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	tgttaagccagccagtggctCtgttggtacccagtggtgtg	6	12	14	9	0	1	0	0	0	1	0	1	0	1	0	3	3	3	4	3	3	2	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr11:6579352C>A	ENST00000527990.2	+	23	8827	c.8827C>A	c.(8827-8829)Ctg>Atg	p.L2943M	DNHD1_ENST00000254579.6_Missense_Mutation_p.L2943M			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	2943					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)		GCCAGTGGCTCTGTTGGTACC	0.547																																					p.L2943M		Atlas-SNP	.											.	DNHD1	198	.	0			c.C8827A						PASS	.						74	65	68					11																	6579352		692	1591	2283	SO:0001583	missense	144132	exon25			GTGGCTCTGTTGG	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.8827C>A	chr11.hg19:g.6579352C>A	ENSP00000436180:p.Leu2943Met	80.0	0.0	.		76.0	30.0	.	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	hg19	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	C	1.131	-0.652479	0.03480	.	.	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000534210;ENST00000524401	T;T	0.32988	1.43;1.43	5.49	3.61	0.41365	.	.	.	.	.	T	0.35537	0.0935	N	0.14661	0.345	0.27084	N	0.963003	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.22173	-1.0224	9	0.29301	T	0.29	.	11.372	0.49704	0.0:0.851:0.0:0.149	.	2943;690	Q96M86;E9PHZ7	DNHD1_HUMAN;.	M	2943;2943;690;8	ENSP00000254579:L2943M;ENSP00000436180:L2943M	ENSP00000254579:L2943M	L	+	1	2	DNHD1	6535928	0.729000	0.28090	0.197000	0.23402	0.007000	0.05969	0.773000	0.26661	0.670000	0.31165	0.650000	0.86243	CTG	.	.	.	none		0.547	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		A	6579352	C	A	6579352	3	1	4	1	0	0	0	0	1	0	0	0	4670	912	32	4	8926	4	DNHD1	11	6579352	Missense_Mutation	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10		6579352	128427164	76	329											
PPFIBP2	8495	hgsc.bcm.edu	37	chr11	7672127	7672127	+	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	aaccacagggtgatggagtgGttacgatctgtggacctggc	9	9	15	8	1	1	1	0	1	1	0	1	4	1	3	2	5	2	1	2	5	2	1			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr11:7672127G>T	ENST00000299492.4	+	22	2566	c.2178G>T	c.(2176-2178)tgG>tgT	p.W726C	PPFIBP2_ENST00000533792.1_Missense_Mutation_p.W568C|PPFIBP2_ENST00000530181.1_Missense_Mutation_p.W583C|PPFIBP2_ENST00000528883.1_Missense_Mutation_p.W614C|PPFIBP2_ENST00000530582.1_3'UTR	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	726	SAM 3. {ECO:0000255|PROSITE- ProRule:PRU00184}.				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)		TGATGGAGTGGTTACGATCTG	0.532																																					p.W726C		Atlas-SNP	.											.	PPFIBP2	87	.	0			c.G2178T						PASS	.						207	179	188					11																	7672127		2201	4296	6497	SO:0001583	missense	8495	exon22			GGAGTGGTTACGA	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.2178G>T	chr11.hg19:g.7672127G>T	ENSP00000299492:p.Trp726Cys	101.0	0.0	.		65.0	29.0	.	NM_003621	B7Z433|E9PK77|O75337|Q8WW26	Missense_Mutation	SNP	ENST00000299492.4	hg19	CCDS31419.1	.	.	.	.	.	.	.	.	.	.	G	13.74	2.326893	0.41197	.	.	ENSG00000166387	ENST00000299492;ENST00000537211;ENST00000533792;ENST00000541115;ENST00000528883;ENST00000530181	D;D;D;D	0.92911	-3.13;-3.13;-3.13;-3.13	5.35	4.43	0.53597	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.000000	0.64402	D	0.000003	D	0.96836	0.8967	M	0.93898	3.47	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;1.0;0.999;0.999;0.998;0.999	D	0.97670	1.0166	10	0.87932	D	0	-9.916	13.4534	0.61184	0.0:0.0:0.842:0.158	.	614;614;649;568;583;726	E9PK77;B7Z433;F5GWB0;E9PP16;E9PMU1;Q8ND30	.;.;.;.;.;LIPB2_HUMAN	C	726;67;568;649;614;583	ENSP00000299492:W726C;ENSP00000436498:W568C;ENSP00000435469:W614C;ENSP00000437321:W583C	ENSP00000299492:W726C	W	+	3	0	PPFIBP2	7628703	1.000000	0.71417	0.998000	0.56505	0.017000	0.09413	9.601000	0.98297	1.607000	0.50170	-0.181000	0.13052	TGG	.	.	.	none		0.532	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621		T	7672127	G	T	7672127	3	4	4	1	0	0	0	0	1	0	0	0	12321	1270	44	4	2260	4	PPFIBP2	11	7672127	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	1092775	7672127	127334389	77	330											
OR5P2	120065	hgsc.bcm.edu	37	chr11	7818479	7818479	+	Missense_Mutation	SNP	A	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	cggtgtgattcccgtccttcAgggaattcatgagacgaagt	9	11	12	9	3	2	2	2	2	0	1	4	5	4	3	2	2	0	0	2	2	2	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr11:7818479A>C	ENST00000329434.2	-	1	41	c.11T>G	c.(10-12)cTg>cGg	p.L4R	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	4						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|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)		CCCGTCCTTCAGGGAATTCAT	0.408																																					p.L4R		Atlas-SNP	.											.	OR5P2	68	.	0			c.T11G						PASS	.						47	55	53					11																	7818479		2095	4291	6386	SO:0001583	missense	120065	exon1			TCCTTCAGGGAAT	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.11T>G	chr11.hg19:g.7818479A>C	ENSP00000331823:p.Leu4Arg	31.0	0.0	.		41.0	21.0	.	NM_153444	Q3MIS8	Missense_Mutation	SNP	ENST00000329434.2	hg19	CCDS7782.1	.	.	.	.	.	.	.	.	.	.	A	15.97	2.989773	0.54041	.	.	ENSG00000183303	ENST00000329434	T	0.00145	8.67	5.2	-5.77	0.02369	.	0.363029	0.22658	N	0.057223	T	0.00144	0.0004	L	0.39898	1.24	0.19300	N	0.999978	P	0.44776	0.843	P	0.50970	0.655	T	0.52697	-0.8541	10	0.87932	D	0	5.2615	0.7576	0.01001	0.2152:0.2208:0.1453:0.4188	.	4	Q8WZ92	OR5P2_HUMAN	R	4	ENSP00000331823:L4R	ENSP00000331823:L4R	L	-	2	0	OR5P2	7775055	0.001000	0.12720	0.014000	0.15608	0.001000	0.01503	0.470000	0.22084	-0.713000	0.04981	-0.531000	0.04308	CTG	.	.	.	none		0.408	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444		C	7818479	A	C	7818479	3	2	4	1	0	0	0	0	1	0	0	0	11185	188	7	5	961	5	OR5P2	11	7818479	Missense_Mutation	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10	146352	7818479	127188037	78	331											
CAT	847	hgsc.bcm.edu	37	chr11	34475367	34475367	+	Missense_Mutation	SNP	A	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	ggtttctttcttgttcagtgAtcgggggattccagatggac	6	15	13	7	1	3	2	1	1	2	1	5	4	4	4	1	4	0	2	1	4	0	5			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr11:34475367A>C	ENST00000241052.4	+	6	694	c.605A>C	c.(604-606)gAt>gCt	p.D202A		NM_001752.3	NP_001743.1	P04040	CATA_HUMAN	catalase	202					aerobic respiration (GO:0009060)|cellular response to growth factor stimulus (GO:0071363)|cholesterol metabolic process (GO:0008203)|hemoglobin metabolic process (GO:0020027)|hydrogen peroxide catabolic process (GO:0042744)|menopause (GO:0042697)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleobase-containing small molecule metabolic process (GO:0055086)|osteoblast differentiation (GO:0001649)|positive regulation of cell division (GO:0051781)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein homotetramerization (GO:0051289)|protein tetramerization (GO:0051262)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to reactive oxygen species (GO:0000302)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)|ureteric bud development (GO:0001657)|UV protection (GO:0009650)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial intermembrane space (GO:0005758)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	aminoacylase activity (GO:0004046)|antioxidant activity (GO:0016209)|catalase activity (GO:0004096)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|oxidoreductase activity, acting on peroxide as acceptor (GO:0016684)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			breast(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|stomach(1)|urinary_tract(3)	26		Lung NSC(402;2.76e-08)|Acute lymphoblastic leukemia(5;0.00143)|all_hematologic(20;0.0116)|Melanoma(852;0.027)		BRCA - Breast invasive adenocarcinoma(625;0.000995)	Fomepizole(DB01213)	TTGTTCAGTGATCGGGGGATT	0.353																																					p.D202A		Atlas-SNP	.											.	CAT	42	.	0			c.A605C						PASS	.						111	105	107					11																	34475367		2202	4298	6500	SO:0001583	missense	847	exon6			TCAGTGATCGGGG	AY028632	CCDS7891.1	11p13	2012-10-02			ENSG00000121691	ENSG00000121691	1.11.1.6		1516	protein-coding gene	gene with protein product		115500					Standard	NM_001752		Approved		uc001mvm.3	P04040	OTTHUMG00000044353	ENST00000241052.4:c.605A>C	chr11.hg19:g.34475367A>C	ENSP00000241052:p.Asp202Ala	67.0	0.0	.		77.0	34.0	.	NM_001752	A8K6C0|B2RCZ9|D3DR07|Q2M1U4|Q4VXX5|Q9BWT9|Q9UC85	Missense_Mutation	SNP	ENST00000241052.4	hg19	CCDS7891.1	.	.	.	.	.	.	.	.	.	.	A	17.56	3.420175	0.62622	.	.	ENSG00000121691	ENST00000241052	D	0.93426	-3.22	5.84	5.84	0.93424	Catalase domain (1);Catalase, N-terminal (2);	0.046947	0.85682	D	0.000000	D	0.98143	0.9387	H	0.99404	4.55	0.80722	D	1	D	0.63880	0.993	D	0.66351	0.943	D	0.99081	1.0837	10	0.87932	D	0	-36.6195	13.2555	0.60076	0.8681:0.1319:0.0:0.0	.	202	P04040	CATA_HUMAN	A	202	ENSP00000241052:D202A	ENSP00000241052:D202A	D	+	2	0	CAT	34431943	1.000000	0.71417	0.940000	0.37924	0.519000	0.34347	9.339000	0.96797	2.232000	0.73038	0.533000	0.62120	GAT	.	.	.	none		0.353	CAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103197.2	NM_001752		C	34475367	A	C	34475367	3	2	4	1	0	0	0	0	1	0	0	0	2688	333	12	5	627	5	CAT	11	34475367	Missense_Mutation	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10	26656888	34475367	100531149	79	332											
EXT2	2132	hgsc.bcm.edu	37	chr11	44129381	44129381	+	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	cctcctgggcctcattgccaCtggcatgtttcagttttggc	4	14	10	13	0	2	0	2	0	0	0	3	0	3	0	4	3	1	3	4	3	0	4			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr11:44129381C>T	ENST00000343631.3	+	2	248	c.119C>T	c.(118-120)aCt>aTt	p.T40I	EXT2_ENST00000533608.1_Missense_Mutation_p.T40I|EXT2_ENST00000358681.4_Missense_Mutation_p.T40I|EXT2_ENST00000395673.3_Missense_Mutation_p.T73I			Q93063	EXT2_HUMAN	exostosin glycosyltransferase 2	40					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						CTCATTGCCACTGGCATGTTT	0.512			"Mis, N, F, S"			"exostoses, osteosarcoma"			Hereditary Multiple Exostoses																												p.T73I		Atlas-SNP	.	yes	Rec		Multiple Exostoses Type 2	11	11p12-p11	2132	multiple exostoses type 2 gene		M	.	EXT2	129	.	0			c.C218T						PASS	.						160	166	164					11																	44129381		2203	4300	6503	SO:0001583	missense	2132	exon2	Familial Cancer Database	HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	TTGCCACTGGCAT		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.119C>T	chr11.hg19:g.44129381C>T	ENSP00000342656:p.Thr40Ile	101.0	0.0	.		84.0	32.0	.	NM_000401	B2R5Z6|C9JU51|J3KPT2|O15288	Missense_Mutation	SNP	ENST00000343631.3	hg19	CCDS7908.1	.	.	.	.	.	.	.	.	.	.	C	16.25	3.071234	0.55646	.	.	ENSG00000151348	ENST00000533608;ENST00000532479;ENST00000527014;ENST00000358681;ENST00000395673;ENST00000343631	T;T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69;0.69	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.45155	0.1328	L	0.27053	0.805	0.80722	D	1	P;P;D;P;P	0.53885	0.954;0.938;0.963;0.873;0.873	P;B;P;B;B	0.48921	0.541;0.391;0.595;0.293;0.293	T	0.19778	-1.0295	10	0.22706	T	0.39	-1.6238	19.302	0.94148	0.0:1.0:0.0:0.0	.	40;40;40;40;53	Q6NUL1;C9JU51;Q93063-2;Q93063;D3DR24	.;.;.;EXT2_HUMAN;.	I	40;40;40;40;73;40	ENSP00000431173:T40I;ENSP00000433827:T40I;ENSP00000434716:T40I;ENSP00000351509:T40I;ENSP00000379032:T73I;ENSP00000342656:T40I	ENSP00000342656:T40I	T	+	2	0	EXT2	44085957	1.000000	0.71417	0.988000	0.46212	0.988000	0.76386	7.380000	0.79704	2.568000	0.86640	0.650000	0.86243	ACT	.	.	.	none		0.512	EXT2-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390074.1	NM_000401		T	44129381	C	T	44129381	3	4	4	1	0	0	0	0	1	0	0	0	5326	565	20	2	224	2	EXT2	11	44129381	Missense_Mutation	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10	9654014	44129381	90877135	80	333											
KIAA0652	9776	hgsc.bcm.edu	37	chr11	46690086	46690086	+	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	ggatataccctttgccatgtTtgctcccaagaatttggagc	9	13	9	10	0	0	1	0	0	0	1	1	3	1	3	3	2	4	2	3	2	4	5			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr11:46690086T>A	ENST00000434074.1	+	14	1879	c.1190T>A	c.(1189-1191)tTt>tAt	p.F397Y	ATG13_ENST00000524625.1_Missense_Mutation_p.F360Y|ATG13_ENST00000312040.4_Missense_Mutation_p.F397Y|ATG13_ENST00000528494.1_Missense_Mutation_p.F430Y|ATG13_ENST00000359513.4_Missense_Mutation_p.F397Y|ATG13_ENST00000529655.1_Missense_Mutation_p.F360Y|ATG13_ENST00000526508.1_Missense_Mutation_p.F397Y|ATG13_ENST00000530500.1_Missense_Mutation_p.F281Y|ATG13_ENST00000451945.1_Missense_Mutation_p.F360Y	NM_001205120.1	NP_001192049.1	O75143	ATG13_HUMAN	autophagy related 13	397					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						TTTGCCATGTTTGCTCCCAAG	0.512																																					p.F430Y		Atlas-SNP	.											.	ATG13	60	.	0			c.T1289A						PASS	.						166	147	153					11																	46690086		2201	4299	6500	SO:0001583	missense	9776	exon15			CCATGTTTGCTCC	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.1190T>A	chr11.hg19:g.46690086T>A	ENSP00000400642:p.Phe397Tyr	77.0	0.0	.		61.0	33.0	.	NM_001205119	B4DFI4|D3DQQ1|D3DQQ2|E9PQZ8|Q53EN6|Q9BRL3|Q9H8B0	Missense_Mutation	SNP	ENST00000434074.1	hg19	CCDS44582.1	.	.	.	.	.	.	.	.	.	.	T	18.65	3.669804	0.67814	.	.	ENSG00000175224	ENST00000395549;ENST00000434074;ENST00000312040;ENST00000451945;ENST00000529655;ENST00000530500;ENST00000526508;ENST00000524625;ENST00000359513;ENST00000528494;ENST00000525009	.	.	.	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.73009	0.3532	L	0.53249	1.67	0.58432	D	0.999997	D;D;D;D	0.71674	0.995;0.997;0.998;0.997	P;D;D;D	0.78314	0.829;0.977;0.991;0.984	T	0.67573	-0.5636	9	0.11182	T	0.66	-15.6578	16.422	0.83766	0.0:0.0:0.0:1.0	.	281;397;430;360	B4DFI4;O75143;E9PQZ8;O75143-2	.;ATG13_HUMAN;.;.	Y	360;397;397;360;360;281;397;360;397;430;129	.	ENSP00000310321:F397Y	F	+	2	0	ATG13	46646662	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.307000	0.78920	2.270000	0.75569	0.533000	0.62120	TTT	.	.	.	none		0.512	ATG13-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390300.2	NM_014741		A	46690086	T	A	46690086	3	1	4	1	0	0	0	0	1	0	0	0	8195	1841	64	5	1240	5	KIAA0652	11	46690086	Missense_Mutation	SNP	T	TCGA-2Z-A9J3-01A-12D-A382-10	2560705	46690086	88316430	81	334											
OR5W2	390148	hgsc.bcm.edu	37	chr11	55682005	55682005	+	Frame_Shift_Del	DEL	G	G	-																															actttcatctctgggttattGgtaattcccaagagaaaaaa																										TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr11:55682005delG	ENST00000344514.1	-	1	53	c.54delC	c.(52-54)accfs	p.T18fs		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	18						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			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						CTGGGTTATTGGTAATTCCCA	0.343																																					p.N19fs	Melanoma(48;171 1190 15239 43886 49348)	Atlas-Indel,Pindel	.											.	OR5W2	112	.	0			c.55delA						PASS	.						49	52	51					11																	55682005		2201	4296	6497	SO:0001589	frameshift_variant	390148	exon1			.	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.54delC	chr11.hg19:g.55682005delG	ENSP00000342448:p.Thr18fs	82.0	0.0	0		81.0	33.0	0.407407	NM_001001960		Frame_Shift_Del	DEL	ENST00000344514.1	hg19	CCDS31513.1																																																																																			.	.	.	none		0.343	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960		-	55682005	G	-	55682005	7	5	4	1	0	1	0	1	0	0	0	0	11192	1335	47	0	880	0	OR5W2	11	55682005	Frame_Shift_Del	DEL	G	TCGA-2Z-A9J3-01A-12D-A382-10	8991919	55682005	79324511	82	335											
SYTL2	54843	hgsc.bcm.edu	37	chr11	85445743	85445743	+	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	tctctaacttttggattgaaGtatctgcgacagttgacttt	9	17	8	7	1	2	2	0	2	2	0	3	4	2	3	0	1	2	2	0	1	3	7			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr11:85445743G>T	ENST00000528231.1	-	6	903	c.626C>A	c.(625-627)aCt>aAt	p.T209N	SYTL2_ENST00000527523.1_Missense_Mutation_p.T161N|SYTL2_ENST00000316356.4_Missense_Mutation_p.T210N|SYTL2_ENST00000389960.4_Missense_Mutation_p.T209N|SYTL2_ENST00000524452.1_Missense_Mutation_p.T209N	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	209					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)		TTGGATTGAAGTATCTGCGAC	0.358																																					p.T210N		Atlas-SNP	.											.	SYTL2	231	.	0			c.C629A						PASS	.						94	93	94					11																	85445743		2203	4299	6502	SO:0001583	missense	54843	exon6			ATTGAAGTATCTG	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.626C>A	chr11.hg19:g.85445743G>T	ENSP00000431701:p.Thr209Asn	79.0	0.0	.		77.0	32.0	.	NM_001162953	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	hg19	CCDS53688.1	.	.	.	.	.	.	.	.	.	.	G	3.458	-0.110581	0.06924	.	.	ENSG00000137501	ENST00000389960;ENST00000316356;ENST00000528231;ENST00000527523;ENST00000524452	T;T;T;T;T	0.26660	1.8;1.82;1.82;1.72;1.8	5.54	-0.768	0.11013	.	.	.	.	.	T	0.08758	0.0217	N	0.08118	0	0.09310	N	0.999999	B;B;B;B;B	0.33477	0.413;0.413;0.138;0.217;0.396	B;B;B;B;B	0.28139	0.071;0.071;0.032;0.071;0.086	T	0.25012	-1.0144	8	.	.	.	.	1.8756	0.03217	0.4894:0.1246:0.2655:0.1205	.	161;209;209;210;67	Q9HCH5-14;Q9HCH5-6;Q9HCH5;Q9HCH5-13;Q9HCH5-15	.;.;SYTL2_HUMAN;.;.	N	209;210;209;161;209	ENSP00000374610:T209N;ENSP00000318803:T210N;ENSP00000431701:T209N;ENSP00000434010:T161N;ENSP00000435238:T209N	.	T	-	2	0	SYTL2	85123391	0.000000	0.05858	0.287000	0.24848	0.027000	0.11550	-0.258000	0.08733	-0.286000	0.09076	-0.806000	0.03193	ACT	.	.	.	none		0.358	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927		T	85445743	G	T	85445743	3	4	4	1	0	0	0	0	1	0	0	0	15495	1029	36	4	4711	4	SYTL2	11	85445743	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	29763738	85445743	49560773	83	336											
HTR3A	3359	hgsc.bcm.edu	37	chr11	113853914	113853914	+	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	ggcgaagttcagaactacaaGccccttcaggtggtgactgc	10	8	12	11	1	2	2	2	1	0	1	2	3	2	2	2	3	4	1	2	3	4	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr11:113853914G>T	ENST00000504030.2	+	5	892	c.447G>T	c.(445-447)aaG>aaT	p.K149N	HTR3A_ENST00000355556.2_Missense_Mutation_p.K155N|HTR3A_ENST00000506841.2_Missense_Mutation_p.K149N|HTR3A_ENST00000375498.2_Missense_Mutation_p.K155N|HTR3A_ENST00000535865.1_5'UTR|HTR3A_ENST00000299961.5_Missense_Mutation_p.K134N			P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A, ionotropic	149					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)	AGAACTACAAGCCCCTTCAGG	0.542																																					p.K155N		Atlas-SNP	.											.	HTR3A	93	.	0			c.G465T						PASS	.						201	180	187					11																	113853914		2201	4296	6497	SO:0001583	missense	3359	exon5			CTACAAGCCCCTT	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.447G>T	chr11.hg19:g.113853914G>T	ENSP00000424189:p.Lys149Asn	97.0	0.0	.		89.0	26.0	.	NM_000869	B4DSY6|G5E986|O60854|Q7KZM7|Q99918|Q9BSZ9	Missense_Mutation	SNP	ENST00000504030.2	hg19		.	.	.	.	.	.	.	.	.	.	G	19.87	3.907299	0.72868	.	.	ENSG00000166736	ENST00000504030;ENST00000355556;ENST00000375498;ENST00000506841;ENST00000299961	T;T;T;T;T	0.79033	-1.23;-1.23;-1.23;-1.23;-1.23	5.39	3.5	0.40072	.	0.000000	0.85682	D	0.000000	D	0.84777	0.5547	M	0.63428	1.95	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.996;1.0	D	0.85804	0.1375	10	0.87932	D	0	-36.4163	11.5276	0.50588	0.2021:0.0:0.7979:0.0	.	134;155;155	B4DSY6;G5E986;Q7KZM7	.;.;.	N	149;155;155;149;134	ENSP00000424189:K149N;ENSP00000347754:K155N;ENSP00000364648:K155N;ENSP00000424776:K149N;ENSP00000299961:K134N	ENSP00000299961:K134N	K	+	3	2	HTR3A	113359124	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.295000	0.51794	1.278000	0.44430	0.555000	0.69702	AAG	.	.	.	none		0.542	HTR3A-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000360822.2	NM_000869		T	113853914	G	T	113853914	3	4	4	1	0	0	0	0	1	0	0	0	7451	962	34	4	509	4	HTR3A	11	113853914	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	28408171	113853914	21152602	84	337											
ABCG4	64137	hgsc.bcm.edu	37	chr11	119025032	119025032	+	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	acgggagctgaggaccttccGcaagatgtcctgctacatca	10	8	11	12	2	1	2	1	1	0	1	3	4	3	4	3	2	3	3	3	2	2	2			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr11:119025032G>T	ENST00000449422.2	+	4	607	c.419G>T	c.(418-420)cGc>cTc	p.R140L	ABCG4_ENST00000531739.1_Missense_Mutation_p.R140L|ABCG4_ENST00000307417.3_Missense_Mutation_p.R140L	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	140	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)	p.R140H(1)		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)		AGGACCTTCCGCAAGATGTCC	0.577																																					p.R140L		Atlas-SNP	.											ABCG4,NS,carcinoma,0,1	ABCG4	77	.	1	Substitution - Missense(1)	endometrium(1)	c.G419T						PASS	.						107	89	95					11																	119025032		2200	4295	6495	SO:0001583	missense	64137	exon4			CCTTCCGCAAGAT	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.419G>T	chr11.hg19:g.119025032G>T	ENSP00000406874:p.Arg140Leu	73.0	0.0	.		50.0	22.0	.	NM_022169	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Missense_Mutation	SNP	ENST00000449422.2	hg19	CCDS8415.1	.	.	.	.	.	.	.	.	.	.	G	32	5.170473	0.94768	.	.	ENSG00000172350	ENST00000307417;ENST00000524604;ENST00000449422;ENST00000531739	D;D;D;D	0.94793	-3.52;-3.52;-3.52;-3.52	4.89	4.89	0.63831	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.103879	0.64402	D	0.000012	D	0.94631	0.8269	M	0.78049	2.395	0.58432	D	0.999999	P	0.42296	0.775	B	0.42087	0.375	D	0.95566	0.8634	10	0.87932	D	0	-22.3413	16.9713	0.86301	0.0:0.0:1.0:0.0	.	140	Q9H172	ABCG4_HUMAN	L	140	ENSP00000304111:R140L;ENSP00000431915:R140L;ENSP00000406874:R140L;ENSP00000434318:R140L	ENSP00000304111:R140L	R	+	2	0	ABCG4	118530242	1.000000	0.71417	0.992000	0.48379	0.937000	0.57800	9.246000	0.95438	2.539000	0.85634	0.491000	0.48974	CGC	.	.	.	none		0.577	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169		T	119025032	G	T	119025032	3	4	4	1	0	0	0	0	1	0	0	0	70	1087	38	4	429	4	ABCG4	11	119025032	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	5171118	119025032	15981484	85	338											
CD163L1	283316	hgsc.bcm.edu	37	chr12	7528025	7528025	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttctccaatatattttccTcctgtggttgagagagcagt	8	16	8	9	0	1	2	0	1	1	1	4	3	3	2	3	1	1	2	3	1	3	6	rs368493737		TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr12:7528025T>C	ENST00000313599.3	-	11	2910	c.2853A>G	c.(2851-2853)ggA>ggG	p.G951G	CD163L1_ENST00000396630.1_Silent_p.G951G|CD163L1_ENST00000544331.1_5'Flank|CD163L1_ENST00000416109.2_Silent_p.G961G			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	951	SRCR 9. {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						TATATTTTCCTCCTGTGGTTG	0.493																																					p.G951G		Atlas-SNP	.											.	CD163L1	238	.	0			c.A2853G						PASS	.	T		1,4405	2.1+/-5.4	0,1,2202	88	76	80		2853	0	0	12		80	0,8600		0,0,4300	no	coding-synonymous	CD163L1	NM_174941.4		0,1,6502	CC,CT,TT		0.0,0.0227,0.0077		951/1454	7528025	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	283316	exon11			TTTTCCTCCTGTG	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.2853A>G	chr12.hg19:g.7528025T>C		45.0	0.0	.		59.0	23.0	.	NM_174941	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Silent	SNP	ENST00000313599.3	hg19	CCDS8577.1																																																																																			.	.	.	weak		0.493	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941		C	7528025	T	C	7528025	2	2	4	1	0	0	0	0	0	0	0	1	2970	1538	54	3		3	CD163L1	12	7528025	Silent	SNP	T	TCGA-2Z-A9J3-01A-12D-A382-10		7528025	126323870	86	339											
C12orf69	440087	hgsc.bcm.edu	37	chr12	14959531	14959531	+	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	acatcgaagctgtcagataaGcaatcaagaagctgctggtg	14	8	11	8	1	2	2	2	0	0	2	3	3	2	2	0	1	4	4	0	1	5	1			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr12:14959531G>A	ENST00000316048.2	-	2	156	c.84C>T	c.(82-84)tgC>tgT	p.C28C	C12orf60_ENST00000527783.1_Intron|C12orf60_ENST00000330828.2_Intron	NM_001013698.2	NP_001013720.2	A2RU48	SMCO3_HUMAN	single-pass membrane protein with coiled-coil domains 3	28						integral component of membrane (GO:0016021)											TGTCAGATAAGCAATCAAGAA	0.463																																					p.C28C		Atlas-SNP	.											.	.	.	.	0			c.C84T						PASS	.						88	85	86					12																	14959531		1875	4127	6002	SO:0001819	synonymous_variant	0	exon2			AGATAAGCAATCA		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.84C>T	chr12.hg19:g.14959531G>A		54.0	0.0	.		56.0	29.0	.	NM_001013698	Q8NAI5	Silent	SNP	ENST00000316048.2	hg19	CCDS41759.1																																																																																			.	.	.	none		0.463	SMCO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394738.1	NM_001013698		A	14959531	G	A	14959531	2	1	4	1	0	0	0	0	0	0	0	1	1713	963	34	2		2	C12orf69	12	14959531	Silent	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	7431506	14959531	118892364	87	340											
EIF4B	1975	hgsc.bcm.edu	37	chr12	53432173	53432173	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagctccagctcaaccatcTgaggaaggaccaggaaggaa	14	5	12	10	0	2	1	1	1	1	0	3	5	3	5	3	4	3	3	3	4	5	1			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr12:53432173T>C	ENST00000262056.9	+	12	1880	c.1554T>C	c.(1552-1554)tcT>tcC	p.S518S	EIF4B_ENST00000416762.3_Silent_p.S479S|RP11-983P16.4_ENST00000552905.1_RNA|RP11-983P16.4_ENST00000550601.1_RNA|EIF4B_ENST00000420463.3_Silent_p.S523S|RP11-983P16.4_ENST00000546566.1_RNA	NM_001417.4	NP_001408.2	P23588	IF4B_HUMAN	eukaryotic translation initiation factor 4B	518					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation initiation factor activity (GO:0003743)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)	22						CTCAACCATCTGAGGAAGGAC	0.408																																					p.S518S		Atlas-SNP	.											.	EIF4B	38	.	0			c.T1554C						PASS	.						141	138	139					12																	53432173		1865	4111	5976	SO:0001819	synonymous_variant	1975	exon12			ACCATCTGAGGAA	X55733	CCDS41788.1, CCDS73474.1	12q13.13	2013-02-12			ENSG00000063046	ENSG00000063046		"RNA binding motif (RRM) containing"	3285	protein-coding gene	gene with protein product		603928					Standard	XM_005268709		Approved		uc001sbh.4	P23588	OTTHUMG00000169570	ENST00000262056.9:c.1554T>C	chr12.hg19:g.53432173T>C		81.0	0.0	.		82.0	43.0	.	NM_001417	Q4G0E3|Q53HQ2|Q6GPH5|Q6IB46|Q8WYK5	Silent	SNP	ENST00000262056.9	hg19	CCDS41788.1																																																																																			.	.	.	none		0.408	EIF4B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404852.2	NM_001417		C	53432173	T	C	53432173	2	2	4	1	0	0	0	0	0	0	0	1	5029	1567	55	3		3	EIF4B	12	53432173	Silent	SNP	T	TCGA-2Z-A9J3-01A-12D-A382-10	38472642	53432173	80419722	88	341											
AVIL	10677	hgsc.bcm.edu	37	chr12	58201151	58201151	+	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	tccctttgaagatggccatgAagtggcgtggctccgttccc	6	11	12	12	2	0	3	0	2	0	1	3	3	3	3	4	3	0	2	4	3	2	2			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr12:58201151A>T	ENST00000257861.3	-	12	1884	c.1454T>A	c.(1453-1455)tTc>tAc	p.F485Y	AVIL_ENST00000550083.1_5'Flank|TSFM_ENST00000548851.1_Intron|AVIL_ENST00000537081.1_Missense_Mutation_p.F478Y|RNU6-1083P_ENST00000384022.1_RNA|RP11-571M6.17_ENST00000602802.1_lincRNA	NM_006576.3	NP_006567.3	O75366	AVIL_HUMAN	advillin	485	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)					GATGGCCATGAAGTGGCGTGG	0.522																																					p.F485Y		Atlas-SNP	.											.	AVIL	60	.	0			c.T1454A						PASS	.						162	143	149					12																	58201151		2203	4300	6503	SO:0001583	missense	10677	exon12			GCCATGAAGTGGC	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.1454T>A	chr12.hg19:g.58201151A>T	ENSP00000257861:p.Phe485Tyr	79.0	0.0	.		60.0	29.0	.	NM_006576	B2RAU7|Q2NKM9	Missense_Mutation	SNP	ENST00000257861.3	hg19	CCDS8959.1	.	.	.	.	.	.	.	.	.	.	A	28.4	4.914701	0.92178	.	.	ENSG00000135407	ENST00000537081;ENST00000257861	T;T	0.59083	0.29;0.29	4.77	4.77	0.60923	Gelsolin domain (1);	0.000000	0.85682	D	0.000000	D	0.83487	0.5265	H	0.97682	4.055	0.58432	D	0.999999	D;D	0.76494	0.999;0.991	D;D	0.77004	0.989;0.938	D	0.89012	0.3429	10	0.72032	D	0.01	-23.5203	13.6731	0.62438	1.0:0.0:0.0:0.0	.	478;485	O75366-2;O75366	.;AVIL_HUMAN	Y	478;485	ENSP00000443207:F478Y;ENSP00000257861:F485Y	ENSP00000257861:F485Y	F	-	2	0	AVIL	56487418	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.010000	0.93611	2.122000	0.65172	0.459000	0.35465	TTC	.	.	.	none		0.522	AVIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409276.1	NM_006576		T	58201151	A	T	58201151	3	4	4	1	0	0	0	0	1	0	0	0	1227	246	9	5	1037	5	AVIL	12	58201151	Missense_Mutation	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10	4768978	58201151	75650744	89	342											
FAM71C	196472	hgsc.bcm.edu	37	chr12	100042118	100042118	+	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	actttatccagatcagcaaaAgaggagaagtgattgacgtg	15	9	11	6	1	1	5	1	2	0	3	2	6	2	5	1	1	1	1	1	1	4	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr12:100042118A>C	ENST00000324341.1	+	1	588	c.166A>C	c.(166-168)Aga>Cga	p.R56R	ANKS1B_ENST00000547776.2_Intron|ANKS1B_ENST00000329257.7_Intron|ANKS1B_ENST00000547010.1_Intron	NM_153364.3	NP_699195.1	Q8NEG0	FA71C_HUMAN	family with sequence similarity 71, member C	56										breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(2;0.00733)|Epithelial(2;0.0385)|all cancers(2;0.19)		GATCAGCAAAAGAGGAGAAGT	0.522																																					p.R56R		Atlas-SNP	.											.	FAM71C	48	.	0			c.A166C						PASS	.						147	130	136					12																	100042118		2203	4300	6503	SO:0001819	synonymous_variant	196472	exon1			AGCAAAAGAGGAG		CCDS9072.1	12q23.1	2006-02-03				ENSG00000180219			28594	protein-coding gene	gene with protein product						12477932	Standard	NM_153364		Approved	MGC39520	uc001tgn.3	Q8NEG0		ENST00000324341.1:c.166A>C	chr12.hg19:g.100042118A>C		77.0	0.0	.		65.0	32.0	.	NM_153364	B2R6Y6	Silent	SNP	ENST00000324341.1	hg19	CCDS9072.1																																																																																			.	.	.	none		0.522	FAM71C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408458.1	NM_153364		C	100042118	A	C	100042118	2	2	4	1	0	0	0	0	0	0	0	1	5616	64	3	5		5	FAM71C	12	100042118	Silent	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10	41840967	100042118	33809777	90	343											
DRAM1	55332	hgsc.bcm.edu	37	chr12	102271585	102271585	+	Silent	SNP	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	gcgatgctgtgcttcctgagGggaatggctttcgtcccctt	4	13	13	11	2	0	1	0	1	0	0	3	3	2	2	3	3	2	3	3	3	1	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr12:102271585G>A	ENST00000258534.8	+	1	457	c.18G>A	c.(16-18)agG>agA	p.R6R	DRAM1_ENST00000544152.1_Silent_p.R6R	NM_018370.2	NP_060840.2	Q8N682	DRAM1_HUMAN	DNA-damage regulated autophagy modulator 1	6					apoptotic process (GO:0006915)|autophagy (GO:0006914)|regulation of autophagy (GO:0010506)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)				central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)	12						GCTTCCTGAGGGGAATGGCTT	0.711																																					p.R6R		Atlas-SNP	.											.	DRAM1	46	.	0			c.G18A						PASS	.						52	54	53					12																	102271585		1844	3904	5748	SO:0001819	synonymous_variant	55332	exon1			CCTGAGGGGAATG	BC018435, DA721965	CCDS41823.1	12q23.2	2014-02-12	2009-06-12		ENSG00000136048	ENSG00000136048			25645	protein-coding gene	gene with protein product	"damage-regulated autophagy modulator"	610776				16839881	Standard	NM_018370		Approved	FLJ11259, DRAM	uc001tix.3	Q8N682		ENST00000258534.8:c.18G>A	chr12.hg19:g.102271585G>A		18.0	0.0	.		25.0	8.0	.	NM_018370	B7Z4T0|Q7L3E3|Q9NUN1	Silent	SNP	ENST00000258534.8	hg19	CCDS41823.1																																																																																			.	.	.	none		0.711	DRAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409195.1	NM_018370		A	102271585	G	A	102271585	2	1	4	1	0	0	0	0	0	0	0	1	4755	1223	43	2		2	DRAM1	12	102271585	Silent	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	2229467	102271585	31580310	91	344											
STAB2	55576	hgsc.bcm.edu	37	chr12	104031881	104031881	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacagttgtacatgccaagAaggctaccgtggggatggcc	10	7	14	10	1	0	1	0	0	0	1	0	2	0	2	3	4	3	4	3	4	4	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr12:104031881A>G	ENST00000388887.2	+	8	1001	c.797A>G	c.(796-798)gAa>gGa	p.E266G		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						ACATGCCAAGAAGGCTACCGT	0.493																																					p.E266G		Atlas-SNP	.											.	STAB2	370	.	0			c.A797G						PASS	.						196	165	176					12																	104031881		2203	4300	6503	SO:0001583	missense	55576	exon8			GCCAAGAAGGCTA	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.797A>G	chr12.hg19:g.104031881A>G	ENSP00000373539:p.Glu266Gly	77.0	0.0	.		89.0	34.0	.	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	hg19	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	A	18.87	3.715138	0.68844	.	.	ENSG00000136011	ENST00000388887	T	0.06142	3.34	5.34	5.34	0.76211	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);	0.719585	0.13832	N	0.359654	T	0.12475	0.0303	M	0.70842	2.15	0.28806	N	0.898514	P	0.42161	0.772	B	0.44315	0.446	T	0.06409	-1.0828	10	0.37606	T	0.19	.	10.2614	0.43430	0.8523:0.0:0.0:0.1477	.	266	Q8WWQ8	STAB2_HUMAN	G	266	ENSP00000373539:E266G	ENSP00000373539:E266G	E	+	2	0	STAB2	102556011	0.801000	0.28930	0.907000	0.35723	0.972000	0.66771	3.463000	0.53050	2.022000	0.59522	0.459000	0.35465	GAA	.	.	.	none		0.493	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			G	104031881	A	G	104031881	3	3	4	1	0	0	0	0	1	0	0	0	15250	246	9	3	827	3	STAB2	12	104031881	Missense_Mutation	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10	1760296	104031881	29820014	92	345											
LRRC43	254050	hgsc.bcm.edu	37	chr12	122674790	122674790	+	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	cctggtgctgcagggaaaccCactggccttggtgccctact	6	9	12	14	0	0	0	0	0	0	0	0	1	0	1	4	4	5	2	4	4	2	2			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr12:122674790C>T	ENST00000339777.4	+	5	804	c.776C>T	c.(775-777)cCa>cTa	p.P259L	LRRC43_ENST00000425921.1_Missense_Mutation_p.P74L	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	259	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)		CAGGGAAACCCACTGGCCTTG	0.632																																					p.P259L		Atlas-SNP	.											.	LRRC43	105	.	0			c.C776T						PASS	.						91	102	98					12																	122674790		2161	4261	6422	SO:0001583	missense	254050	exon5			GAAACCCACTGGC	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.776C>T	chr12.hg19:g.122674790C>T	ENSP00000344233:p.Pro259Leu	82.0	0.0	.		66.0	35.0	.	NM_001098519	Q6ZVT9	Missense_Mutation	SNP	ENST00000339777.4	hg19	CCDS45001.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.938331	0.92526	.	.	ENSG00000158113	ENST00000537729;ENST00000339777;ENST00000289014;ENST00000425921	T;T;T	0.38560	1.13;1.13;1.13	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.65739	0.2720	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.69335	-0.5172	10	0.87932	D	0	-43.7481	18.3879	0.90472	0.0:1.0:0.0:0.0	.	259	Q8N309	LRC43_HUMAN	L	74;259;130;74	ENSP00000438751:P74L;ENSP00000344233:P259L;ENSP00000416628:P74L	ENSP00000289014:P130L	P	+	2	0	LRRC43	121240743	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.184000	0.72008	2.460000	0.83146	0.561000	0.74099	CCA	.	.	.	none		0.632	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759		T	122674790	C	T	122674790	3	4	4	1	0	0	0	0	1	0	0	0	9008	594	21	2	794	2	LRRC43	12	122674790	Missense_Mutation	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10	18642909	122674790	11177105	93	346											
PARP4	143	hgsc.bcm.edu	37	chr13	25026604	25026604	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttcacgagctgtaatgtcAggctctcatcctggaggtgc	7	12	11	11	1	4	0	3	0	2	0	6	2	5	1	1	3	2	3	1	3	1	2			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr13:25026604A>G	ENST00000381989.3	-	24	3059	c.2954T>C	c.(2953-2955)cTg>cCg	p.L985P		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	985	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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)		CTGTAATGTCAGGCTCTCATC	0.557																																					p.L985P		Atlas-SNP	.											.	PARP4	142	.	0			c.T2954C						PASS	.						139	133	135					13																	25026604		2203	4300	6503	SO:0001583	missense	143	exon24			AATGTCAGGCTCT	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.2954T>C	chr13.hg19:g.25026604A>G	ENSP00000371419:p.Leu985Pro	81.0	0.0	.		73.0	39.0	.	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	hg19	CCDS9307.1	.	.	.	.	.	.	.	.	.	.	A	15.66	2.898475	0.52227	.	.	ENSG00000102699	ENST00000381989	T	0.08193	3.12	5.29	5.29	0.74685	von Willebrand factor, type A (3);	0.158962	0.43110	D	0.000618	T	0.28532	0.0706	M	0.78916	2.43	0.58432	D	0.999999	D	0.89917	1.0	D	0.83275	0.996	T	0.01133	-1.1441	10	0.39692	T	0.17	-12.1098	13.2758	0.60186	1.0:0.0:0.0:0.0	.	985	Q9UKK3	PARP4_HUMAN	P	985	ENSP00000371419:L985P	ENSP00000371419:L985P	L	-	2	0	PARP4	23924604	1.000000	0.71417	0.985000	0.45067	0.099000	0.18886	3.961000	0.56759	2.242000	0.73789	0.519000	0.50382	CTG	.	.	.	none		0.557	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437		G	25026604	A	G	25026604	3	3	4	1	0	0	0	0	1	0	0	0	11470	188	7	3	2264	3	PARP4	13	25026604	Missense_Mutation	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10		25026604	90143274	94	347											
PDS5B	23047	hgsc.bcm.edu	37	chr13	33332296	33332298	+	In_Frame_Del	DEL	TGG	TGG	-																															tcacgcttttatcagaaagaTggtagaaaatattaaacaaa																										TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	TGG	TGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr13:33332296_33332298delTGG	ENST00000315596.10	+	27	3314_3316	c.3128_3130delTGG	c.(3127-3132)atggta>ata	p.1043_1044MV>I		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	1043					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)		ATCAGAAAGATGGTAGAAAATAT	0.266																																					p.1043_1043del		Atlas-Indel,Pindel	.											.	PDS5B	141	.	0			c.3127_3129del						PASS	.																																			SO:0001651	inframe_deletion	23047	exon27			.	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.3128_3130delTGG	chr13.hg19:g.33332296_33332298delTGG	ENSP00000313851:p.Met1043_Val1044delinsIle	335.0	0.0	0		351.0	137.0	0.390313	NM_015032	Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	In_Frame_Del	DEL	ENST00000315596.10	hg19	CCDS41878.1																																																																																			.	.	.	none		0.266	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3	NM_015032		-	33332298	TGG	-	33332296	7	5	4	1	0	1	0	1	0	0	0	0	11699	1464	51	0	3230	0	PDS5B	13	33332296	In_Frame_Del	DEL	TGG	TCGA-2Z-A9J3-01A-12D-A382-10	8305692	33332296	81837582	95	348											
LECT1	11061	hgsc.bcm.edu	37	chr13	53298215	53298215	+	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	cgctttaatgtagcacttctCtcctccagcaaaacgaattc	11	12	5	13	2	1	0	0	0	1	0	5	1	3	0	2	0	3	4	2	0	5	5			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr13:53298215C>T	ENST00000377962.3	-	4	463	c.385G>A	c.(385-387)Gag>Aag	p.E129K	LECT1_ENST00000448904.2_Missense_Mutation_p.E129K			O75829	LECT1_HUMAN	leukocyte cell derived chemotaxin 1	129	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.				cartilage development (GO:0051216)|endothelial cell morphogenesis (GO:0001886)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|proteoglycan metabolic process (GO:0006029)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|urinary_tract(1)	15		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.38e-08)		TAGCACTTCTCTCCTCCAGCA	0.448																																					p.E129K		Atlas-SNP	.											.	LECT1	44	.	0			c.G385A						PASS	.						148	115	126					13																	53298215		2203	4300	6503	SO:0001583	missense	11061	exon4			ACTTCTCTCCTCC	AB006000	CCDS9437.1, CCDS45051.1	13q14.3	2012-10-10			ENSG00000136110	ENSG00000136110		"BRICHOS domain containing"	17005	protein-coding gene	gene with protein product	"BRICHOS domain containing 3"	605147	"multiple myeloma tumor suppressor 1"	MYETS1		9731231, 10103018	Standard	XM_006719760		Approved	CHM-I, CHM1, chondromodulin, BRICD3	uc001vhf.2	O75829	OTTHUMG00000016980	ENST00000377962.3:c.385G>A	chr13.hg19:g.53298215C>T	ENSP00000367198:p.Glu129Lys	44.0	0.0	.		51.0	27.0	.	NM_007015	Q5TAM4|Q8TAY6|Q9UM18	Missense_Mutation	SNP	ENST00000377962.3	hg19	CCDS9437.1	.	.	.	.	.	.	.	.	.	.	C	32	5.173276	0.94807	.	.	ENSG00000136110	ENST00000448904;ENST00000377962;ENST00000431550	T;T;T	0.78816	-1.21;-1.21;-1.21	5.9	5.06	0.68205	BRICHOS (2);	0.136600	0.64402	N	0.000003	D	0.83538	0.5276	M	0.69823	2.125	0.58432	D	0.999999	D;D	0.56746	0.971;0.977	P;P	0.53988	0.621;0.739	D	0.85425	0.1145	10	0.62326	D	0.03	.	14.9399	0.70986	0.0:0.9316:0.0:0.0684	.	129;129	O75829-2;O75829	.;LECT1_HUMAN	K	129;129;51	ENSP00000388576:E129K;ENSP00000367198:E129K;ENSP00000396035:E51K	ENSP00000367198:E129K	E	-	1	0	LECT1	52196216	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.253000	0.58791	1.495000	0.48549	0.655000	0.94253	GAG	.	.	.	none		0.448	LECT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045110.3			T	53298215	C	T	53298215	3	4	4	1	0	0	0	0	1	0	0	0	8719	922	32	2	635	2	LECT1	13	53298215	Missense_Mutation	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10	19965919	53298215	61871663	96	349											
LMO7	4008	hgsc.bcm.edu	37	chr13	76195877	76195877	+	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	ttcacgttttacagttggatGtcctatgatgttctcttcca	7	18	7	9	1	2	1	1	1	1	0	5	2	4	2	2	1	1	3	2	1	2	7			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr13:76195877G>T	ENST00000341547.4	+	1	1308	c.48G>T	c.(46-48)atG>atT	p.M16I	RP11-173B14.5_ENST00000568302.1_RNA|RP11-173B14.5_ENST00000568735.1_RNA|LMO7_ENST00000377534.3_Missense_Mutation_p.M16I|RP11-29G8.3_ENST00000563635.1_RNA|LMO7_ENST00000357063.3_Missense_Mutation_p.M16I	NM_005358.5	NP_005349.3	Q8WWI1	LMO7_HUMAN	LIM domain 7	16					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)		ACAGTTGGATGTCCTATGATG	0.383																																					p.M16I		Atlas-SNP	.											.	LMO7	334	.	0			c.G48T						PASS	.						72	70	71					13																	76195877		2203	4300	6503	SO:0001583	missense	4008	exon1			TTGGATGTCCTAT	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.48G>T	chr13.hg19:g.76195877G>T	ENSP00000342112:p.Met16Ile	41.0	0.0	.		59.0	14.0	.	NM_005358	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000341547.4	hg19	CCDS9454.1	.	.	.	.	.	.	.	.	.	.	G	9.697	1.153520	0.21371	.	.	ENSG00000136153	ENST00000341547;ENST00000357063;ENST00000377534	T;T;T	0.52983	0.64;0.64;0.64	3.82	1.3	0.21679	.	.	.	.	.	T	0.32763	0.0840	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.29882	-0.9997	8	0.87932	D	0	.	4.1462	0.10217	0.1966:0.0:0.2294:0.574	.	16	Q8WWI1-3	.	I	16	ENSP00000342112:M16I;ENSP00000349571:M16I;ENSP00000366757:M16I	ENSP00000342112:M16I	M	+	3	0	LMO7	75093878	0.001000	0.12720	0.000000	0.03702	0.011000	0.07611	0.376000	0.20535	0.096000	0.17463	-0.518000	0.04402	ATG	.	.	.	none		0.383	LMO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045297.1	NM_005358		T	76195877	G	T	76195877	3	4	4	1	0	0	0	0	1	0	0	0	8862	1377	48	4	50	4	LMO7	13	76195877	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	22897662	76195877	38974001	97	350											
LMO7	4008	hgsc.bcm.edu	37	chr13	76378589	76378589	+	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	catcctatgtaccagcacctCtgagaaagaaaaagccagac	16	6	7	12	0	1	3	0	1	1	3	2	4	2	3	4	0	3	2	4	0	5	2			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr13:76378589C>A	ENST00000321797.8	+	6	848	c.127C>A	c.(127-129)Ctg>Atg	p.L43M	LMO7_ENST00000526202.1_Missense_Mutation_p.L237M|LMO7_ENST00000341547.4_Missense_Mutation_p.L328M|LMO7_ENST00000465261.2_Missense_Mutation_p.L43M|LMO7_ENST00000377534.3_Missense_Mutation_p.L328M|RP11-29G8.3_ENST00000563635.1_RNA|LMO7_ENST00000357063.3_Missense_Mutation_p.L328M			Q8WWI1	LMO7_HUMAN	LIM domain 7	328					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)		ACCAGCACCTCTGAGAAAGAA	0.443																																					p.L328M		Atlas-SNP	.											.	LMO7	334	.	0			c.C982A						PASS	.						119	128	125					13																	76378589		2203	4300	6503	SO:0001583	missense	4008	exon9			GCACCTCTGAGAA	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.127C>A	chr13.hg19:g.76378589C>A	ENSP00000317802:p.Leu43Met	64.0	0.0	.		77.0	30.0	.	NM_005358	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.42|14.42	2.530501|2.530501	0.45073|0.45073	.|.	.|.	ENSG00000136153|ENSG00000136153	ENST00000341547;ENST00000357063;ENST00000377534;ENST00000377499;ENST00000321797;ENST00000526202;ENST00000465261;ENST00000497947;ENST00000526371;ENST00000526528;ENST00000489941;ENST00000525373|ENST00000447038	T;T;T;T;T;T;T;T;T;T;T;T|.	0.35789|.	1.29;1.29;1.29;1.29;1.29;1.29;1.29;1.29;1.29;1.29;1.29;1.29|.	5.98|5.98	1.59|1.59	0.23543|0.23543	.|.	0.077397|.	0.52532|.	D|.	0.000064|.	T|T	0.57829|0.57829	0.2080|0.2080	M|M	0.77820|0.77820	2.39|2.39	0.28496|0.28496	N|N	0.914238|0.914238	D;D;D;D;D|.	0.89917|.	0.997;0.997;0.998;1.0;0.998|.	D;D;D;D;D|.	0.87578|.	0.988;0.974;0.994;0.998;0.984|.	T|T	0.54689|0.54689	-0.8256|-0.8256	10|5	0.87932|.	D|.	0|.	-10.7237|-10.7237	11.4846|11.4846	0.50346|0.50346	0.0:0.2787:0.0:0.7213|0.0:0.2787:0.0:0.7213	.|.	237;328;328;43;276|.	E9PMS6;Q8WWI1-3;Q8WWI1;E9PLH4;F8J2B5|.	.;.;LMO7_HUMAN;.;.|.	M|Y	328;328;328;276;43;237;43;43;43;43;43;43|45	ENSP00000342112:L328M;ENSP00000349571:L328M;ENSP00000366757:L328M;ENSP00000366719:L276M;ENSP00000317802:L43M;ENSP00000431129:L237M;ENSP00000433352:L43M;ENSP00000431271:L43M;ENSP00000432269:L43M;ENSP00000434201:L43M;ENSP00000431636:L43M;ENSP00000431896:L43M|.	ENSP00000317802:L43M|.	L|S	+|+	1|2	2|0	LMO7|LMO7	75276590|75276590	0.022000|0.022000	0.18835|0.18835	0.976000|0.976000	0.42696|0.42696	0.782000|0.782000	0.44232|0.44232	0.202000|0.202000	0.17295|0.17295	0.426000|0.426000	0.26116|0.26116	-0.918000|-0.918000	0.02743|0.02743	CTG|TCT	.	.	.	none		0.443	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358		A	76378589	C	A	76378589	3	1	4	1	0	0	0	0	1	0	0	0	8862	912	32	4	1016	4	LMO7	13	76378589	Missense_Mutation	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10	182712	76378589	38791289	98	351											
TEP1	7011	hgsc.bcm.edu	37	chr14	20846278	20846278	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagggaaggcagccagccGtgccccttctcgccaggccc	6	4	14	17	2	1	0	0	0	1	0	2	1	1	1	6	4	3	2	6	4	1	1			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr14:20846278G>A	ENST00000262715.5	-	39	5666	c.5626C>T	c.(5626-5628)Cgg>Tgg	p.R1876W	TEP1_ENST00000545983.1_Missense_Mutation_p.R214W|TEP1_ENST00000556935.1_Missense_Mutation_p.R1768W	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1876					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)		GCAGCCAGCCGTGCCCCTTCT	0.627																																					p.R1876W		Atlas-SNP	.											.	TEP1	224	.	0			c.C5626T						PASS	.						84	82	83					14																	20846278		2203	4300	6503	SO:0001583	missense	7011	exon39			CCAGCCGTGCCCC		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.5626C>T	chr14.hg19:g.20846278G>A	ENSP00000262715:p.Arg1876Trp	79.0	0.0	.		68.0	40.0	.	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	hg19	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.195644	0.38806	.	.	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935;ENST00000545983	T;T;T	0.51817	0.69;1.55;1.55	5.48	3.57	0.40892	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.353602	0.31897	N	0.006884	T	0.54663	0.1872	L	0.51422	1.61	0.09310	N	1	D;D;D;D	0.76494	0.998;0.997;0.999;0.997	P;P;P;P	0.56916	0.761;0.653;0.809;0.765	T	0.48779	-0.9005	10	0.59425	D	0.04	-11.432	11.9525	0.52962	0.0:0.0:0.5654:0.4346	.	214;1768;1219;1876	B4E0B6;G3V5X7;G3V2A4;Q99973	.;.;.;TEP1_HUMAN	W	1876;1876;1768;214	ENSP00000262715:R1876W;ENSP00000452574:R1768W;ENSP00000438849:R214W	ENSP00000262715:R1876W	R	-	1	2	TEP1	19916118	0.002000	0.14202	0.040000	0.18447	0.215000	0.24574	1.163000	0.31798	1.306000	0.44926	0.557000	0.71058	CGG	.	.	.	none		0.627	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		A	20846278	G	A	20846278	3	1	4	1	0	0	0	0	1	0	0	0	15771	1144	40	1	2325	1	TEP1	14	20846278	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10		20846278	86503262	99	352											
PRMT5	10419	hgsc.bcm.edu	37	chr14	23393872	23393872	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagagtatttgatggggtccTtttcaaacacttcatatgtc	10	15	9	7	0	2	2	2	1	0	1	4	3	3	2	1	2	1	1	1	2	3	6			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr14:23393872T>C	ENST00000324366.8	-	9	1209	c.986A>G	c.(985-987)aAg>aGg	p.K329R	PRMT5-AS1_ENST00000599580.2_RNA|PRMT5_ENST00000553897.1_Missense_Mutation_p.K285R|PRMT5-AS1_ENST00000424245.2_RNA|PRMT5_ENST00000216350.8_Missense_Mutation_p.K268R|PRMT5-AS1_ENST00000590290.1_RNA|PRMT5_ENST00000397441.2_Missense_Mutation_p.K312R|PRMT5_ENST00000553641.1_5'Flank|PRMT5-AS1_ENST00000587245.2_RNA|PRMT5-AS1_ENST00000595662.1_RNA|PRMT5_ENST00000538452.1_Missense_Mutation_p.K223R|PRMT5-AS1_ENST00000609885.1_RNA|PRMT5_ENST00000397440.4_Missense_Mutation_p.K158R|PRMT5-AS1_ENST00000457443.2_RNA	NM_006109.3	NP_006100.2	O14744	ANM5_HUMAN	protein arginine methyltransferase 5	329	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|endothelial cell activation (GO:0042118)|gene expression (GO:0010467)|histone H4-R3 methylation (GO:0043985)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|peptidyl-arginine N-methylation (GO:0035246)|regulation of mitosis (GO:0007088)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|methylosome (GO:0034709)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|histone-arginine N-methyltransferase activity (GO:0008469)|methyltransferase activity (GO:0008168)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|transcription corepressor activity (GO:0003714)			endometrium(4)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	25	all_cancers(95;2.76e-05)			GBM - Glioblastoma multiforme(265;0.0126)		GATGGGGTCCTTTTCAAACAC	0.488																																					p.K329R		Atlas-SNP	.											.	PRMT5	101	.	0			c.A986G						PASS	.						107	96	100					14																	23393872		2203	4300	6503	SO:0001583	missense	10419	exon9			GGGTCCTTTTCAA	AF015913	CCDS9579.1, CCDS41922.1, CCDS61394.1, CCDS61395.1, CCDS61396.1	14q11.2	2014-06-12	2006-02-16	2006-02-16	ENSG00000100462	ENSG00000100462	2.1.1.125	"Protein arginine methyltransferases"	10894	protein-coding gene	gene with protein product		604045	"skb1 (S. pombe) homolog", "SKB1 homolog (S. pombe)"	HRMT1L5, SKB1		9843966	Standard	NM_001282955		Approved	SKB1Hs	uc001whm.1	O14744	OTTHUMG00000028709	ENST00000324366.8:c.986A>G	chr14.hg19:g.23393872T>C	ENSP00000319169:p.Lys329Arg	77.0	0.0	.		67.0	4.0	.	NM_006109	A8MTP3|A8MZ91|B4DX49|B4DY30|B5BU10|D3DS33|E2QRE7|Q6IBR1|Q9UKH1	Missense_Mutation	SNP	ENST00000324366.8	hg19	CCDS9579.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.435772	0.83885	.	.	ENSG00000100462	ENST00000324366;ENST00000397441;ENST00000397440;ENST00000216350;ENST00000538452;ENST00000553897;ENST00000553502;ENST00000555530;ENST00000556043;ENST00000553550	T;T;T;T;T;T	0.21932	1.98;1.98;1.98;1.98;1.98;1.98	5.92	5.92	0.95590	.	0.088928	0.85682	D	0.000000	T	0.30885	0.0779	L	0.43701	1.375	0.80722	D	1	P;B;B;P;P	0.52692	0.778;0.363;0.333;0.955;0.516	B;B;B;P;B	0.54060	0.398;0.38;0.208;0.741;0.313	T	0.01143	-1.1438	10	0.28530	T	0.3	-21.0851	15.346	0.74337	0.0:0.0:0.0:1.0	.	285;268;158;329;312	G3V5W5;B4DX49;A8MTP3;O14744;A8MZ91	.;.;.;ANM5_HUMAN;.	R	329;312;158;268;223;285;72;224;81;175	ENSP00000319169:K329R;ENSP00000380583:K312R;ENSP00000380582:K158R;ENSP00000216350:K268R;ENSP00000444915:K223R;ENSP00000452555:K285R	ENSP00000216350:K268R	K	-	2	0	PRMT5	22463712	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.970000	0.76099	2.270000	0.75569	0.459000	0.35465	AAG	.	.	.	none		0.488	PRMT5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071674.3			C	23393872	T	C	23393872	3	2	4	1	0	0	0	0	1	0	0	0	12549	1609	56	3	963	3	PRMT5	14	23393872	Missense_Mutation	SNP	T	TCGA-2Z-A9J3-01A-12D-A382-10	2547594	23393872	83955668	100	353											
RALGAPA1	253959	hgsc.bcm.edu	37	chr14	36103901	36103901	+	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	acagatgccaaatcagagagGctcatgggaaaataccttgg	15	7	11	8	0	2	2	2	0	0	2	2	4	2	3	2	3	2	1	2	3	4	2			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr14:36103901G>C	ENST00000389698.3	-	32	4746	c.4356C>G	c.(4354-4356)agC>agG	p.S1452R	RALGAPA1_ENST00000382366.3_Missense_Mutation_p.S1465R|RALGAPA1_ENST00000307138.6_Missense_Mutation_p.S1452R|RALGAPA1_ENST00000258840.6_Missense_Mutation_p.S1499R	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	1452	Minimal domain that binds to TCF3/E12. {ECO:0000250}.				activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						AATCAGAGAGGCTCATGGGAA	0.413																																					p.S1452R		Atlas-SNP	.											.	RALGAPA1	289	.	0			c.C4356G						PASS	.						48	45	46					14																	36103901		2203	4297	6500	SO:0001583	missense	253959	exon32			AGAGAGGCTCATG	AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"tuberin-like protein 1", "GAP-related interacting protein to E12"	608884	"GTPase activating RANGAP domain-like 1", "GTPase activating Rap/RanGAP domain-like 1"	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.4356C>G	chr14.hg19:g.36103901G>C	ENSP00000374348:p.Ser1452Arg	125.0	0.0	.		124.0	52.0	.	NM_194301	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Missense_Mutation	SNP	ENST00000389698.3	hg19	CCDS32065.1	.	.	.	.	.	.	.	.	.	.	G	14.17	2.455222	0.43634	.	.	ENSG00000174373	ENST00000389698;ENST00000307138;ENST00000335518;ENST00000258840;ENST00000554259;ENST00000382366;ENST00000553892	T;T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56;1.56	5.38	-0.0408	0.13870	.	0.096424	0.85682	D	0.000000	T	0.27278	0.0669	L	0.59436	1.845	0.32562	N	0.531019	P;B;P;B	0.43826	0.818;0.399;0.666;0.399	B;B;B;B	0.39840	0.311;0.266;0.23;0.147	T	0.38802	-0.9644	10	0.48119	T	0.1	-9.7139	10.9048	0.47073	0.4098:0.0:0.5902:0.0	.	1499;1465;1452;1452	Q6GYQ0-6;B9EK38;Q6GYQ0-2;Q6GYQ0	.;.;.;RGPA1_HUMAN	R	1452;1452;1452;1499;90;1465;1499	ENSP00000374348:S1452R;ENSP00000302647:S1452R;ENSP00000258840:S1499R;ENSP00000451133:S90R;ENSP00000371803:S1465R;ENSP00000451877:S1499R	ENSP00000258840:S1499R	S	-	3	2	RALGAPA1	35173652	1.000000	0.71417	0.982000	0.44146	0.971000	0.66376	0.968000	0.29357	-0.201000	0.10284	-0.142000	0.14014	AGC	.	.	.	none		0.413	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022		C	36103901	G	C	36103901	3	2	4	1	0	0	0	0	1	0	0	0	13026	1194	42	4	1943	4	RALGAPA1	14	36103901	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	12710029	36103901	71245639	101	354											
BMP4	652	hgsc.bcm.edu	37	chr14	54417256	54417256	+	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	gtgggtccgagtctgatggaGgtgagtcacctcaatggcta	8	10	15	8	1	3	2	2	2	1	0	4	4	4	3	2	4	0	1	2	4	2	1			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr14:54417256G>T	ENST00000245451.4	-	4	1114	c.721C>A	c.(721-723)Ctc>Atc	p.L241I	BMP4_ENST00000417573.1_Missense_Mutation_p.L241I|MIR5580_ENST00000580850.1_RNA|BMP4_ENST00000558984.1_Missense_Mutation_p.L241I|BMP4_ENST00000559087.1_Missense_Mutation_p.L241I	NM_001202.3	NP_001193.2	P12644	BMP4_HUMAN	bone morphogenetic protein 4	241					activation of MAPKK activity (GO:0000186)|anterior/posterior axis specification (GO:0009948)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|BMP signaling pathway (GO:0030509)|BMP signaling pathway involved in heart induction (GO:0003130)|BMP signaling pathway involved in nephric duct formation (GO:0071893)|BMP signaling pathway involved in renal system segmentation (GO:0061151)|BMP signaling pathway involved in ureter morphogenesis (GO:0061149)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|branching morphogenesis of an epithelial tube (GO:0048754)|bronchus development (GO:0060433)|bud dilation involved in lung branching (GO:0060503)|bud elongation involved in lung branching (GO:0060449)|cardiac septum development (GO:0003279)|cellular response to growth factor stimulus (GO:0071363)|chondrocyte differentiation (GO:0002062)|cloacal septation (GO:0060197)|common-partner SMAD protein phosphorylation (GO:0007182)|cranial suture morphogenesis (GO:0060363)|deltoid tuberosity development (GO:0035993)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal joint morphogenesis (GO:0060272)|endocardial cushion development (GO:0003197)|endochondral ossification (GO:0001958)|epithelial cell proliferation involved in lung morphogenesis (GO:0060502)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|epithelial-mesenchymal cell signaling (GO:0060684)|erythrocyte differentiation (GO:0030218)|extracellular matrix organization (GO:0030198)|germ cell development (GO:0007281)|glomerular capillary formation (GO:0072104)|glomerular visceral epithelial cell development (GO:0072015)|hematopoietic progenitor cell differentiation (GO:0002244)|inner ear receptor cell differentiation (GO:0060113)|intermediate mesodermal cell differentiation (GO:0048392)|kidney development (GO:0001822)|lens induction in camera-type eye (GO:0060235)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|lymphoid progenitor cell differentiation (GO:0002320)|macrophage differentiation (GO:0030225)|mammary gland formation (GO:0060592)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|mesenchymal cell proliferation involved in ureter development (GO:0072198)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesodermal cell fate determination (GO:0007500)|mesonephros development (GO:0001823)|metanephric collecting duct development (GO:0072205)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of branch elongation involved in ureteric bud branching by BMP signaling pathway (GO:0072097)|negative regulation of branching involved in ureteric bud morphogenesis (GO:0090191)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell proliferation involved in heart morphogenesis (GO:2000137)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of glomerular mesangial cell proliferation (GO:0072125)|negative regulation of glomerulus development (GO:0090194)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mesenchymal cell proliferation involved in ureter development (GO:0072200)|negative regulation of metanephric comma-shaped body morphogenesis (GO:2000007)|negative regulation of metanephric S-shaped body morphogenesis (GO:2000005)|negative regulation of mitosis (GO:0045839)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostatic bud formation (GO:0060686)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of T cell differentiation in thymus (GO:0033085)|negative regulation of thymocyte apoptotic process (GO:0070244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|odontogenesis (GO:0042476)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of cardiac muscle fiber development (GO:0055020)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell death (GO:0010942)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epidermal cell differentiation (GO:0045606)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of kidney development (GO:0090184)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of ossification (GO:0045778)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|protein localization to nucleus (GO:0034504)|pulmonary artery endothelial tube morphogenesis (GO:0061155)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|regulation of smooth muscle cell differentiation (GO:0051150)|renal system development (GO:0072001)|renal system process (GO:0003014)|secondary heart field specification (GO:0003139)|SMAD protein signal transduction (GO:0060395)|smooth muscle tissue development (GO:0048745)|smoothened signaling pathway (GO:0007224)|specification of organ position (GO:0010159)|specification of ureteric bud anterior/posterior symmetry by BMP signaling pathway (GO:0072101)|steroid hormone mediated signaling pathway (GO:0043401)|telencephalon development (GO:0021537)|telencephalon regionalization (GO:0021978)|tendon cell differentiation (GO:0035990)|trachea development (GO:0060438)|trachea formation (GO:0060440)|type B pancreatic cell development (GO:0003323)|ureter epithelial cell differentiation (GO:0072192)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	BMP receptor binding (GO:0070700)|chemoattractant activity (GO:0042056)|cytokine activity (GO:0005125)|heparin binding (GO:0008201)			breast(1)|endometrium(3)|large_intestine(2)|lung(9)|prostate(3)|urinary_tract(1)	19						GTCTGATGGAGGTGAGTCACC	0.592																																					p.L241I		Atlas-SNP	.											.	BMP4	45	.	0			c.C721A						PASS	.						103	84	90					14																	54417256		2203	4300	6503	SO:0001583	missense	652	exon4			GATGGAGGTGAGT	AF035427	CCDS9715.1	14q22-q23	2014-01-30			ENSG00000125378	ENSG00000125378		"Bone morphogenetic proteins", "Endogenous ligands"	1071	protein-coding gene	gene with protein product		112262		BMP2B		7558046, 7579580	Standard	NM_001202		Approved		uc010aoh.3	P12644	OTTHUMG00000140303	ENST00000245451.4:c.721C>A	chr14.hg19:g.54417256G>T	ENSP00000245451:p.Leu241Ile	141.0	0.0	.		107.0	44.0	.	NM_130851	Q9UM80	Missense_Mutation	SNP	ENST00000245451.4	hg19	CCDS9715.1	.	.	.	.	.	.	.	.	.	.	G	13.02	2.113400	0.37339	.	.	ENSG00000125378	ENST00000245451;ENST00000417573	T;T	0.66638	-0.22;-0.22	5.09	5.09	0.68999	Transforming growth factor-beta, N-terminal (1);	0.131959	0.52532	D	0.000066	T	0.71239	0.3316	M	0.72118	2.19	0.54753	D	0.999984	B	0.24092	0.097	B	0.36030	0.216	T	0.67377	-0.5686	10	0.30078	T	0.28	.	17.6566	0.88179	0.0:0.0:1.0:0.0	.	241	P12644	BMP4_HUMAN	I	241	ENSP00000245451:L241I;ENSP00000394165:L241I	ENSP00000245451:L241I	L	-	1	0	BMP4	53487006	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.385000	0.73182	2.647000	0.89833	0.655000	0.94253	CTC	.	.	.	none		0.592	BMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276894.2	NM_001202		T	54417256	G	T	54417256	3	4	4	1	0	0	0	0	1	0	0	0	1462	1000	35	4	509	4	BMP4	14	54417256	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	18313355	54417256	52932284	102	355											
SYT16	83851	hgsc.bcm.edu	37	chr14	62536436	62536436	+	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	agtttccgttcagtgacatcTgagaaaggaaagcagacagg	14	8	12	7	1	2	3	1	2	1	2	3	5	3	4	1	2	1	3	1	2	2	2			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr14:62536436T>G	ENST00000430451.2	+	2	836	c.639T>G	c.(637-639)tcT>tcG	p.S213S	SYT16_ENST00000446982.2_Silent_p.S213S|RP11-355I22.5_ENST00000553990.1_lincRNA	NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	213					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)		CAGTGACATCTGAGAAAGGAA	0.483																																					p.S213S		Atlas-SNP	.											.	SYT16	144	.	0			c.T639G						PASS	.						142	137	139					14																	62536436		1933	4132	6065	SO:0001819	synonymous_variant	83851	exon2			GACATCTGAGAAA	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.639T>G	chr14.hg19:g.62536436T>G		115.0	0.0	.		102.0	43.0	.	NM_031914	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Silent	SNP	ENST00000430451.2	hg19	CCDS45121.1																																																																																			.	.	.	none		0.483	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914		G	62536436	T	G	62536436	2	3	4	1	0	0	0	0	0	0	0	1	15484	1567	55	5		5	SYT16	14	62536436	Silent	SNP	T	TCGA-2Z-A9J3-01A-12D-A382-10	8119180	62536436	44813104	103	356											
SYNE2	23224	hgsc.bcm.edu	37	chr14	64548159	64548159	+	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	tggtcctgcatctctttcccAggccacagttaagatggagg	8	11	11	11	0	1	1	0	0	1	1	4	2	3	2	3	4	1	2	3	4	1	2			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr14:64548159A>G	ENST00000344113.4	+	57	11558		c.e57-1		SYNE2_ENST00000555002.1_Splice_Site|SYNE2_ENST00000357395.3_Splice_Site|SYNE2_ENST00000358025.3_Splice_Site|SYNE2_ENST00000394768.2_Splice_Site|SYNE2_ENST00000554584.1_Splice_Site	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2						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)		TCTCTTTCCCAGGCCACAGTT	0.463																																					.		Atlas-SNP	.											.	SYNE2	577	.	0			c.11347-2A>G						PASS	.						86	84	85					14																	64548159		2203	4300	6503	SO:0001630	splice_region_variant	23224	exon57			TTTCCCAGGCCAC	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.11347-1A>G	chr14.hg19:g.64548159A>G		76.0	0.0	.		67.0	28.0	.	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Splice_Site	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	A	12.28	1.889919	0.33348	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.653	0.68811	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SYNE2	63617912	1.000000	0.71417	0.993000	0.49108	0.227000	0.25037	5.959000	0.70339	2.257000	0.74773	0.533000	0.62120	.	.	.	.	none		0.463	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	Intron	G	64548159	A	G	64548159	5	3	4	1	0	0	0	0	0	0	1	0	15458	202	7	3	11567	3	SYNE2	14	64548159	Splice_Site	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10	2011723	64548159	42801381	104	357											
RDH12	145226	hgsc.bcm.edu	37	chr14	68195931	68195931	+	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	ccggggtcaccacctacgcaGtgcacccaggcgtcgtccgc	6	5	12	18	5	1	0	1	0	0	0	3	0	2	0	5	3	2	2	5	3	1	1			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr14:68195931G>T	ENST00000551171.1	+	8	1006	c.682G>T	c.(682-684)Gtg>Ttg	p.V228L	RDH12_ENST00000267502.3_Missense_Mutation_p.V228L|RDH12_ENST00000539142.1_Missense_Mutation_p.V228L	NM_152443.2	NP_689656.2	Q96NR8	RDH12_HUMAN	retinol dehydrogenase 12 (all-trans/9-cis/11-cis)	228					photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	intracellular (GO:0005622)|photoreceptor inner segment membrane (GO:0060342)	retinol dehydrogenase activity (GO:0004745)			large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(4)	12				all cancers(60;0.000704)|OV - Ovarian serous cystadenocarcinoma(108;0.00161)|BRCA - Breast invasive adenocarcinoma(234;0.00953)	Vitamin A(DB00162)	CACCTACGCAGTGCACCCAGG	0.607																																					p.V228L		Atlas-SNP	.											.	RDH12	43	.	0			c.G682T						PASS	.						105	105	105					14																	68195931		2203	4300	6503	SO:0001583	missense	145226	exon8			TACGCAGTGCACC	AK054835	CCDS9787.1	14q24.1	2013-02-14	2006-05-09		ENSG00000139988	ENSG00000139988	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	19977	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 7C, member 2"	608830	"retinol dehydrogenase 12 (all-trans and 9-cis)"			12226107, 19027726	Standard	NM_152443		Approved	FLJ30273, SDR7C2, LCA13, RP53	uc001xjz.4	Q96NR8		ENST00000551171.1:c.682G>T	chr14.hg19:g.68195931G>T	ENSP00000449079:p.Val228Leu	774.0	1.0	.		594.0	249.0	.	NM_152443	B2RDA2|Q8TAW6	Missense_Mutation	SNP	ENST00000551171.1	hg19	CCDS9787.1	.	.	.	.	.	.	.	.	.	.	G	8.284	0.816291	0.16607	.	.	ENSG00000139988	ENST00000551171;ENST00000267502;ENST00000539142	D;D;D	0.85629	-2.01;-2.01;-2.01	5.74	4.8	0.61643	NAD(P)-binding domain (1);	0.124014	0.53938	D	0.000046	T	0.65176	0.2666	N	0.04994	-0.135	0.80722	D	1	B	0.20988	0.05	B	0.23574	0.047	T	0.61446	-0.7061	10	0.02654	T	1	.	9.6167	0.39696	0.0:0.3024:0.5731:0.1245	.	228	Q96NR8	RDH12_HUMAN	L	228	ENSP00000449079:V228L;ENSP00000267502:V228L;ENSP00000438715:V228L	ENSP00000267502:V228L	V	+	1	0	RDH12	67265684	0.998000	0.40836	0.958000	0.39756	0.104000	0.19210	2.905000	0.48727	2.703000	0.92315	0.655000	0.94253	GTG	.	.	.	none		0.607	RDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406918.1			T	68195931	G	T	68195931	3	4	4	1	0	0	0	0	1	0	0	0	13204	1029	36	4	704	4	RDH12	14	68195931	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	3647772	68195931	39153609	105	358											
TTLL5	23093	hgsc.bcm.edu	37	chr14	76173407	76173407	+	Missense_Mutation	SNP	T	T	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	cattttggtctcccgttacaTtaacaaccccctgctcatag	9	13	5	14	1	2	0	1	0	1	0	3	0	2	0	3	1	4	2	3	1	4	5			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr14:76173407T>G	ENST00000298832.9	+	8	837	c.632T>G	c.(631-633)aTt>aGt	p.I211S	TTLL5_ENST00000286650.5_Missense_Mutation_p.I211S|TTLL5_ENST00000557636.1_Missense_Mutation_p.I211S|TTLL5_ENST00000555422.1_3'UTR	NM_015072.4	NP_055887.3	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	211	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				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)		TCCCGTTACATTAACAACCCC	0.393																																					p.I211S		Atlas-SNP	.											.	TTLL5	102	.	0			c.T632G						PASS	.						131	126	128					14																	76173407		2203	4300	6503	SO:0001583	missense	23093	exon8			GTTACATTAACAA	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.632T>G	chr14.hg19:g.76173407T>G	ENSP00000298832:p.Ile211Ser	91.0	0.0	.		81.0	26.0	.	NM_015072	B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4	Missense_Mutation	SNP	ENST00000298832.9	hg19	CCDS32124.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.515506	0.85389	.	.	ENSG00000119685	ENST00000557636;ENST00000286650;ENST00000298832	T;T;T	0.12984	2.63;2.63;2.63	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.53417	0.1795	H	0.97465	4.01	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.999	D;D;D	0.79108	0.976;0.992;0.992	T	0.71606	-0.4542	10	0.87932	D	0	.	15.3992	0.74823	0.0:0.0:0.0:1.0	.	211;211;211	G3V2J9;Q6EMB2;Q6EMB2-3	.;TTLL5_HUMAN;.	S	211	ENSP00000450713:I211S;ENSP00000286650:I211S;ENSP00000298832:I211S	ENSP00000286650:I211S	I	+	2	0	TTLL5	75243160	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.303000	0.78871	2.178000	0.69098	0.533000	0.62120	ATT	.	.	.	none		0.393	TTLL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414453.1	NM_015072		G	76173407	T	G	76173407	3	3	4	1	0	0	0	0	1	0	0	0	16742	1493	52	5	658	5	TTLL5	14	76173407	Missense_Mutation	SNP	T	TCGA-2Z-A9J3-01A-12D-A382-10	7977476	76173407	31176133	106	359											
ITPK1	3705	hgsc.bcm.edu	37	chr14	93429129	93429129	+	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	caagccgttcttctccagcaGccgcatggtgtcatccccgc	6	9	9	17	3	3	0	1	0	2	0	5	0	4	0	5	1	3	3	5	1	1	2			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr14:93429129G>T	ENST00000267615.6	-	6	603	c.430C>A	c.(430-432)Ctg>Atg	p.L144M	ITPK1_ENST00000555495.1_Missense_Mutation_p.L25M|ITPK1_ENST00000556603.2_Missense_Mutation_p.L144M|ITPK1_ENST00000354313.3_Missense_Mutation_p.L144M|ITPK1_ENST00000556954.1_5'UTR			Q13572	ITPK1_HUMAN	inositol-tetrakisphosphate 1-kinase	144	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.				blood coagulation (GO:0007596)|dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|inositol trisphosphate metabolic process (GO:0032957)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|inositol tetrakisphosphate 1-kinase activity (GO:0047325)|inositol-1,3,4,5,6-pentakisphosphate 1-phosphatase activity (GO:0052825)|inositol-1,3,4,6-tetrakisphosphate 1-phosphatase activity (GO:0052831)|inositol-1,3,4,6-tetrakisphosphate 6-phosphatase activity (GO:0052830)|inositol-1,3,4-trisphosphate 5-kinase activity (GO:0052726)|inositol-1,3,4-trisphosphate 6-kinase activity (GO:0052725)|inositol-3,4,6-trisphosphate 1-kinase activity (GO:0052835)|isomerase activity (GO:0016853)|magnesium ion binding (GO:0000287)			endometrium(1)|large_intestine(3)|lung(6)|ovary(1)	11		all_cancers(154;0.077)|all_epithelial(191;0.247)		Epithelial(152;0.124)|all cancers(159;0.169)		TTCTCCAGCAGCCGCATGGTG	0.632																																					p.L144M		Atlas-SNP	.											.	ITPK1	53	.	0			c.C430A						PASS	.						139	101	114					14																	93429129		2203	4300	6503	SO:0001583	missense	3705	exon6			CCAGCAGCCGCAT	U51336	CCDS9907.1, CCDS45157.1	14q32.12	2012-08-16	2011-04-28		ENSG00000100605	ENSG00000100605	2.7.1.134		6177	protein-coding gene	gene with protein product		601838	"inositol 1,3,4-triphosphate 5/6 kinase"			8662638, 11042108	Standard	NM_014216		Approved		uc001ybh.3	Q13572	OTTHUMG00000171226	ENST00000267615.6:c.430C>A	chr14.hg19:g.93429129G>T	ENSP00000267615:p.Leu144Met	57.0	0.0	.		40.0	11.0	.	NM_001142593	Q9BTL6|Q9H2E7	Missense_Mutation	SNP	ENST00000267615.6	hg19	CCDS9907.1	.	.	.	.	.	.	.	.	.	.	G	15.85	2.954724	0.53293	.	.	ENSG00000100605	ENST00000354313;ENST00000405174;ENST00000556603;ENST00000555495;ENST00000267615;ENST00000311458;ENST00000554999;ENST00000556185;ENST00000555553;ENST00000553452;ENST00000557309	T	0.08720	3.06	5.51	5.51	0.81932	ATP-grasp fold (1);	0.311884	0.33959	N	0.004388	T	0.15003	0.0362	L	0.52011	1.625	0.38708	D	0.953155	B;B	0.31256	0.316;0.084	B;B	0.42555	0.391;0.139	T	0.04128	-1.0975	10	0.45353	T	0.12	-9.5343	14.2724	0.66159	0.0:0.0:0.8512:0.1488	.	144;144	Q13572;Q13572-2	ITPK1_HUMAN;.	M	144;174;144;25;144;144;102;162;150;144;144	ENSP00000346272:L144M	ENSP00000267615:L144M	L	-	1	2	ITPK1	92498882	1.000000	0.71417	0.990000	0.47175	0.917000	0.54804	3.936000	0.56568	2.570000	0.86706	0.549000	0.68633	CTG	.	.	.	none		0.632	ITPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412421.2	NM_014216		T	93429129	G	T	93429129	3	4	4	1	0	0	0	0	1	0	0	0	7923	962	34	4	886	4	ITPK1	14	93429129	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	17255722	93429129	13920411	107	360											
FAM98B	283742	hgsc.bcm.edu	37	chr15	38776684	38776685	+	IGR	INS	-	-	GGG																															tgggggagggggaggagggtINSgggggggaggaggaggaggt																										TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr15:38776684_38776685insGGG	ENST00000491535.1	+	0	3111				FAM98B_ENST00000397609.2_In_Frame_Ins_p.383_384insG	NM_001042429.1	NP_001035894.1	Q52LJ0	FA98B_HUMAN	family with sequence similarity 98, member B							cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-splicing ligase complex (GO:0072669)	poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|skin(1)	8		all_cancers(109;3.11e-17)|all_epithelial(112;2.64e-15)|Lung NSC(122;2.11e-11)|all_lung(180;5.61e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;9e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0209)		gggaggagggtgggggGGAGGA	0.658																																					p.W376delinsWG		Atlas-INDEL	.											.	FAM98B	53	.	0			c.1126_1127insGGG						PASS	.																																			SO:0001628	intergenic_variant	283742	exon8			.		CCDS10047.2	15q14	2006-11-29		2005-11-20	ENSG00000171262	ENSG00000171262			26773	protein-coding gene	gene with protein product						12477932	Standard	NM_173611		Approved	FLJ38426	uc001zkc.3	Q52LJ0	OTTHUMG00000129831		chr15.hg19:g.38776688_38776690dupGGG		47.0	0.0	0		41.0	14.0	0.341463	NM_173611	A8MUW5|Q8N935	In_Frame_Ins	INS	ENST00000491535.1	hg19	CCDS42015.1																																																																																			.	.	.	none		0.658	FAM98B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252071.2	NM_173611		GGG	38776685	-	GGG	38776684	6	5	4	0	1	1	1	0	0	0	0	0	5664	1696	59	0		0	FAM98B	15	38776684	IGR	INS	-	TCGA-2Z-A9J3-01A-12D-A382-10		38776684	63754708	108	361											
SPTBN5	51332	hgsc.bcm.edu	37	chr15	42163671	42163671	+	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	caggcggccacccgctggctGcccatctccacttggtgctg	4	8	12	17	2	1	0	0	0	1	0	2	0	1	0	4	4	2	3	4	4	0	1			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr15:42163671G>C	ENST00000320955.6	-	29	5576	c.5349C>G	c.(5347-5349)ggC>ggG	p.G1783G		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1783					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)		CCCGCTGGCTGCCCATCTCCA	0.637																																					p.G1748G		Atlas-SNP	.											.	SPTBN5	171	.	0			c.C5244G						PASS	.						21	25	24					15																	42163671		1840	3839	5679	SO:0001819	synonymous_variant	51332	exon29			CTGGCTGCCCATC	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.5349C>G	chr15.hg19:g.42163671G>C		166.0	0.0	.		127.0	51.0	.	NM_016642		Silent	SNP	ENST00000320955.6	hg19																																																																																				.	.	.	none		0.637	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		C	42163671	G	C	42163671	2	2	4	1	0	0	0	0	0	0	0	1	15134	1306	46	4		4	SPTBN5	15	42163671	Silent	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	3386987	42163671	60367721	109	362											
MAP1A	4130	hgsc.bcm.edu	37	chr15	43815125	43815125	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaggtccctggaagagtcaAaatagacaggagccgtgcta	14	6	12	9	1	1	2	1	0	0	2	2	4	2	4	2	3	2	1	2	3	6	2			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr15:43815125A>G	ENST00000300231.5	+	4	1904	c.1454A>G	c.(1453-1455)aAa>aGa	p.K485R	MAP1A_ENST00000399453.1_Missense_Mutation_p.K485R|MAP1A_ENST00000382031.1_Missense_Mutation_p.K723R			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	485	9 X 3 AA repeats of K-K-[DE].|Lys-rich (basic).		K -> Q (in dbSNP:rs2584715).		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)	GGAAGAGTCAAAATAGACAGG	0.527																																					p.K485R		Atlas-SNP	.											.	MAP1A	189	.	0			c.A1454G						PASS	.						31	31	31					15																	43815125		1903	4110	6013	SO:0001583	missense	4130	exon4			GAGTCAAAATAGA	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.1454A>G	chr15.hg19:g.43815125A>G	ENSP00000300231:p.Lys485Arg	134.0	0.0	.		115.0	57.0	.	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	hg19	CCDS42031.1	.	.	.	.	.	.	.	.	.	.	A	12.79	2.044131	0.36085	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231;ENST00000442025	T;T;T	0.50813	0.73;0.73;0.73	5.39	5.39	0.77823	.	0.000000	0.33670	N	0.004672	T	0.56819	0.2011	M	0.78637	2.42	0.47441	D	0.999427	P	0.50528	0.936	P	0.46320	0.512	T	0.64943	-0.6288	10	0.66056	D	0.02	-21.4983	15.5825	0.76455	1.0:0.0:0.0:0.0	.	485	P78559	MAP1A_HUMAN	R	723;485;485;485	ENSP00000371462:K723R;ENSP00000382380:K485R;ENSP00000300231:K485R	ENSP00000300231:K485R	K	+	2	0	MAP1A	41602417	1.000000	0.71417	0.982000	0.44146	0.961000	0.63080	5.234000	0.65343	2.263000	0.75096	0.533000	0.62120	AAA	.	.	.	none		0.527	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373		G	43815125	A	G	43815125	3	3	4	1	0	0	0	0	1	0	0	0	9234	14	1	3	1456	3	MAP1A	15	43815125	Missense_Mutation	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10	1651454	43815125	58716267	110	363											
DMXL2	23312	hgsc.bcm.edu	37	chr15	51749533	51749533	+	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	taaataacataccacactagCtccagtgctagtctgtccag	13	10	6	12	0	1	0	0	0	1	0	3	0	3	0	3	0	4	2	3	0	6	5			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr15:51749533C>A	ENST00000251076.5	-	36	8550	c.8263G>T	c.(8263-8265)Gct>Tct	p.A2755S	RP11-707P17.2_ENST00000559977.1_RNA|DMXL2_ENST00000543779.2_Missense_Mutation_p.A2756S|DMXL2_ENST00000449909.3_Missense_Mutation_p.A2119S|RP11-707P17.2_ENST00000559173.1_RNA|RP11-707P17.1_ENST00000561007.1_RNA|RP11-707P17.2_ENST00000560727.1_RNA	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	2755						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		ACCACACTAGCTCCAGTGCTA	0.418																																					p.A2756S		Atlas-SNP	.											.	DMXL2	262	.	0			c.G8266T						PASS	.						105	93	97					15																	51749533		2196	4293	6489	SO:0001583	missense	23312	exon36			CACTAGCTCCAGT	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.8263G>T	chr15.hg19:g.51749533C>A	ENSP00000251076:p.Ala2755Ser	48.0	0.0	.		60.0	28.0	.	NM_001174116	B2RTR3|B7ZMH3|F5GWF1|O94938	Missense_Mutation	SNP	ENST00000251076.5	hg19	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	C	31	5.092771	0.94149	.	.	ENSG00000104093	ENST00000251076;ENST00000543779;ENST00000449909;ENST00000436119	T;T;T	0.25912	1.91;1.91;1.77	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.28532	0.0706	L	0.47716	1.5	0.80722	D	1	B;D;B;B	0.53151	0.019;0.958;0.376;0.135	B;B;B;B	0.41202	0.014;0.35;0.062;0.061	T	0.01894	-1.1252	10	0.46703	T	0.11	.	20.3754	0.98918	0.0:1.0:0.0:0.0	.	2756;2119;2755;2756	F5GWF1;B2RTR3;Q8TDJ6;B7ZMH3	.;.;DMXL2_HUMAN;.	S	2755;2756;2119;321	ENSP00000251076:A2755S;ENSP00000441858:A2756S;ENSP00000400855:A2119S	ENSP00000251076:A2755S	A	-	1	0	DMXL2	49536825	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.944000	0.75940	2.894000	0.99253	0.591000	0.81541	GCT	.	.	.	none		0.418	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		A	51749533	C	A	51749533	3	1	4	1	0	0	0	0	1	0	0	0	4597	797	28	4	879	4	DMXL2	15	51749533	Missense_Mutation	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10	7934408	51749533	50781859	111	364											
KIAA1024	23251	hgsc.bcm.edu	37	chr15	79760702	79760702	+	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	gtcatcctcgttattgtcgtGcccatctgcacaatgaaatc	9	13	7	12	2	2	1	1	1	1	0	6	1	3	1	2	0	2	2	2	0	3	2			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr15:79760702G>T	ENST00000305428.3	+	4	2802	c.2727G>T	c.(2725-2727)gtG>gtT	p.V909V		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	909						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						TTATTGTCGTGCCCATCTGCA	0.468																																					p.V909V		Atlas-SNP	.											.	KIAA1024	146	.	0			c.G2727T						PASS	.						79	68	72					15																	79760702		2196	4293	6489	SO:0001819	synonymous_variant	23251	exon4			TGTCGTGCCCATC	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.2727G>T	chr15.hg19:g.79760702G>T		31.0	0.0	.		57.0	5.0	.	NM_015206	A7MD43	Silent	SNP	ENST00000305428.3	hg19	CCDS32306.1																																																																																			.	.	.	none		0.468	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206		T	79760702	G	T	79760702	2	4	4	1	0	0	0	0	0	0	0	1	8212	1306	46	4		4	KIAA1024	15	79760702	Silent	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	28011169	79760702	22770690	112	365											
NR2F2	7026	hgsc.bcm.edu	37	chr15	96875731	96875731	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accatcgcaaccagtgccagTactgccgcctcaaaaagtgc	12	6	8	15	2	1	0	1	0	0	0	2	0	1	0	5	0	5	2	5	0	4	1			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr15:96875731T>C	ENST00000394166.3	+	1	1786	c.397T>C	c.(397-399)Tac>Cac	p.Y133H	NR2F2_ENST00000394171.2_5'Flank|NR2F2_ENST00000421109.2_Intron|NR2F2_ENST00000453270.2_5'Flank|MIR1469_ENST00000410719.1_RNA	NM_021005.3	NP_066285.1	P24468	COT2_HUMAN	nuclear receptor subfamily 2, group F, member 2	133	Interaction with ZFPM2. {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)			CCAGTGCCAGTACTGCCGCCT	0.607																																					p.Y133H		Atlas-SNP	.											.	NR2F2	35	.	0			c.T397C						PASS	.						78	71	74					15																	96875731		2197	4298	6495	SO:0001583	missense	7026	exon1			TGCCAGTACTGCC	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.397T>C	chr15.hg19:g.96875731T>C	ENSP00000377721:p.Tyr133His	111.0	0.0	.		76.0	35.0	.	NM_021005	B4DQJ2|B6ZGU1|Q03754|Q3KQR7	Missense_Mutation	SNP	ENST00000394166.3	hg19	CCDS10375.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.179895	0.78564	.	.	ENSG00000185551	ENST00000394166	D	0.97303	-4.33	4.92	4.92	0.64577	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (4);	0.000000	0.64402	D	0.000005	D	0.97754	0.9263	L	0.61387	1.9	0.80722	D	1	D	0.76494	0.999	D	0.72338	0.977	D	0.98274	1.0505	10	0.62326	D	0.03	.	13.4089	0.60931	0.0:0.0:0.0:1.0	.	133	P24468	COT2_HUMAN	H	133	ENSP00000377721:Y133H	ENSP00000377721:Y133H	Y	+	1	0	NR2F2	94676735	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.990000	0.88215	1.843000	0.53566	0.459000	0.35465	TAC	.	.	.	none		0.607	NR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313534.1			C	96875731	T	C	96875731	3	2	4	1	0	0	0	0	1	0	0	0	10635	1638	57	3	446	3	NR2F2	15	96875731	Missense_Mutation	SNP	T	TCGA-2Z-A9J3-01A-12D-A382-10	17115029	96875731	5655661	113	366											
IL32	9235	hgsc.bcm.edu	37	chr16	3119208	3119208	+	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	ggtggtggccctggtccatgCagtgcaggccctctggaaac	6	8	15	12	0	1	0	0	0	1	0	2	1	2	1	3	6	3	2	3	6	1	0			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr16:3119208C>A	ENST00000534507.1	+	6	768	c.557C>A	c.(556-558)gCa>gAa	p.A186E	RNU1-125P_ENST00000516752.1_RNA|IL32_ENST00000548652.1_Missense_Mutation_p.A131E|IL32_ENST00000530538.2_Missense_Mutation_p.A140E|IL32_ENST00000552356.1_Missense_Mutation_p.A120E|IL32_ENST00000525643.2_Missense_Mutation_p.A140E|IL32_ENST00000548476.1_Missense_Mutation_p.A186E|IL32_ENST00000533097.2_Missense_Mutation_p.A140E|IL32_ENST00000528163.2_Missense_Mutation_p.A140E|IL32_ENST00000529699.1_Missense_Mutation_p.A120E|IL32_ENST00000551122.1_Intron|IL32_ENST00000444393.3_Missense_Mutation_p.A140E|IL32_ENST00000530890.1_Missense_Mutation_p.A120E|IL32_ENST00000440815.3_Missense_Mutation_p.A140E|IL32_ENST00000552936.1_Missense_Mutation_p.A164E|IL32_ENST00000008180.9_Missense_Mutation_p.A120E|IL32_ENST00000396887.3_Intron|IL32_ENST00000549213.1_Intron|IL32_ENST00000529550.1_Missense_Mutation_p.A140E|IL32_ENST00000551513.1_Missense_Mutation_p.A177E|IL32_ENST00000531965.1_Missense_Mutation_p.A130E|IL32_ENST00000526464.2_Missense_Mutation_p.A140E|IL32_ENST00000548246.1_Missense_Mutation_p.A100E|IL32_ENST00000382213.3_Missense_Mutation_p.A131E|IL32_ENST00000325568.5_Missense_Mutation_p.A140E|IL32_ENST00000552664.1_Missense_Mutation_p.A140E|IL32_ENST00000396890.2_Missense_Mutation_p.A186E			P24001	IL32_HUMAN	interleukin 32	186					cell adhesion (GO:0007155)|defense response (GO:0006952)|immune response (GO:0006955)	extracellular space (GO:0005615)|membrane (GO:0016020)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	15						CTGGTCCATGCAGTGCAGGCC	0.602																																					p.A140E		Atlas-SNP	.											.	IL32	32	.	0			c.C419A						PASS	.						49	57	54					16																	3119208		2197	4298	6495	SO:0001583	missense	9235	exon7			TCCATGCAGTGCA	M59807	CCDS32377.1, CCDS32378.1, CCDS32379.1, CCDS45394.1	16p13.3	2011-07-21			ENSG00000008517	ENSG00000008517		"Interleukins and interleukin receptors"	16830	protein-coding gene	gene with protein product	"natural killer cell transcript 4"	606001				1729377, 9653642	Standard	XM_005255686		Approved	NK4, TAIF, TAIFb, TAIFd	uc002ctn.3	P24001	OTTHUMG00000167498	ENST00000534507.1:c.557C>A	chr16.hg19:g.3119208C>A	ENSP00000431775:p.Ala186Glu	220.0	0.0	.		210.0	41.0	.	NM_004221	A6NNM0|A8MPX0|B4DJM1|B8Q191|D3DUB0|D3DUB2|Q5VFH7|Q5VFH8|Q8WV38|Q96GK9	Missense_Mutation	SNP	ENST00000534507.1	hg19		.	.	.	.	.	.	.	.	.	.	c	7.440	0.640466	0.14386	.	.	ENSG00000008517	ENST00000325568;ENST00000534507;ENST00000531965;ENST00000529699;ENST00000526464;ENST00000440815;ENST00000529550;ENST00000525643;ENST00000548807;ENST00000528163;ENST00000530890;ENST00000444393;ENST00000533097;ENST00000008180;ENST00000396890;ENST00000525228;ENST00000548652;ENST00000530538;ENST00000552936;ENST00000548476;ENST00000552664;ENST00000552356;ENST00000551513;ENST00000382213;ENST00000548246	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	0.57752	0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38	1.89	-0.329	0.12686	.	.	.	.	.	T	0.33789	0.0875	N	0.19112	0.55	0.09310	N	1	B;B;B;B;B;B	0.18166	0.007;0.026;0.026;0.026;0.007;0.026	B;B;B;B;B;B	0.10450	0.003;0.005;0.005;0.005;0.003;0.005	T	0.17018	-1.0383	9	0.38643	T	0.18	.	8.4032	0.32599	0.3619:0.6381:0.0:0.0	.	100;120;131;120;186;140	B8Q191;C6GKH1;A6NNM0;A8MPX0;P24001;P24001-2	.;.;.;.;IL32_HUMAN;.	E	140;186;130;120;140;140;140;140;186;140;120;140;140;120;186;111;131;140;164;186;140;120;177;131;100	ENSP00000324742:A140E;ENSP00000431775:A186E;ENSP00000433177:A130E;ENSP00000436937:A120E;ENSP00000450364:A140E;ENSP00000405063:A140E;ENSP00000437020:A140E;ENSP00000432218:A140E;ENSP00000448354:A186E;ENSP00000432850:A140E;ENSP00000433747:A120E;ENSP00000411958:A140E;ENSP00000432917:A140E;ENSP00000008180:A120E;ENSP00000380099:A186E;ENSP00000431740:A111E;ENSP00000446624:A131E;ENSP00000436929:A140E;ENSP00000447033:A164E;ENSP00000449483:A186E;ENSP00000448683:A140E;ENSP00000446978:A120E;ENSP00000449147:A177E;ENSP00000371648:A131E;ENSP00000447979:A100E	ENSP00000008180:A120E	A	+	2	0	IL32	3059209	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.401000	0.02502	-0.380000	0.07894	-2.641000	0.00151	GCA	.	.	.	none		0.602	IL32-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000394812.2	NM_004221		A	3119208	C	A	3119208	3	1	4	1	0	0	0	0	1	0	0	0	7699	710	25	4	441	4	IL32	16	3119208	Missense_Mutation	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10		3119208	87235545	114	367											
UQCRC2	7385	hgsc.bcm.edu	37	chr16	21974207	21974208	+	Splice_Site	INS	-	-	T																															tttcagaatccgcagactcgINStaagtacatttccagatcac																										TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr16:21974207_21974208insT	ENST00000268379.4	+	6	1278		c.e6+1		UQCRC2_ENST00000561553.1_Splice_Site	NM_003366.2	NP_003357.2	P22695	QCR2_HUMAN	ubiquinol-cytochrome c reductase core protein II						aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(4)|prostate(1)|skin(1)	15				GBM - Glioblastoma multiforme(48;0.0264)		CCGCAGACTCGTAAGTACATTT	0.361																																					.	Colon(123;450 1645 12841 25393 45623)	Atlas-Indel,Pindel	.											.	UQCRC2	46	.	0			c.514+1->T						PASS	.																																			SO:0001630	splice_region_variant	7385	exon6			.	J04973	CCDS10601.1	16p12	2011-07-04			ENSG00000140740	ENSG00000140740	1.10.2.2	"Mitochondrial respiratory chain complex / Complex III"	12586	protein-coding gene	gene with protein product		191329				8288258, 2547763	Standard	NM_003366		Approved	QCR2, UQCR2	uc002djx.3	P22695	OTTHUMG00000131585	ENST00000268379.4:c.514+1->T	chr16.hg19:g.21974208_21974208dupT		53.0	0.0	0		62.0	34.0	0.548387	NM_003366	B3KSN4|Q9BQ05	Splice_Site	INS	ENST00000268379.4	hg19	CCDS10601.1																																																																																			.	.	.	none		0.361	UQCRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254466.1	NM_003366	Intron	T	21974208	-	T	21974207	8	5	4	1	0	1	1	0	0	0	1	0	17032	1159	40	0	537	0	UQCRC2	16	21974207	Splice_Site	INS	-	TCGA-2Z-A9J3-01A-12D-A382-10	18854999	21974207	68380546	115	368											
SALL1	6299	hgsc.bcm.edu	37	chr16	51171131	51171131	+	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	ccggccaggggagcattgggCtctgagttctggagcctctc	5	9	15	12	1	3	1	0	1	3	0	4	3	3	3	3	5	2	3	3	5	0	2			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr16:51171131C>T	ENST00000251020.4	-	3	3900	c.3867G>A	c.(3865-3867)gaG>gaA	p.E1289E	SALL1_ENST00000440970.1_Silent_p.E1192E|SALL1_ENST00000566102.1_3'UTR|SALL1_ENST00000541611.1_Silent_p.E112E	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	1289					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)			GAGCATTGGGCTCTGAGTTCT	0.587																																					p.E1289E	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.G3867A						PASS	.						72	68	69					16																	51171131		2198	4300	6498	SO:0001819	synonymous_variant	6299	exon3			ATTGGGCTCTGAG	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.3867G>A	chr16.hg19:g.51171131C>T		98.0	0.0	.		132.0	38.0	.	NM_002968	Q99881|Q9NSC3|Q9P1R0	Silent	SNP	ENST00000251020.4	hg19	CCDS10747.1																																																																																			.	.	.	none		0.587	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		T	51171131	C	T	51171131	2	4	4	1	0	0	0	0	0	0	0	1	13823	796	28	2		2	SALL1	16	51171131	Silent	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10	29196924	51171131	39183622	116	369											
PDPR	55066	hgsc.bcm.edu	37	chr16	70170204	70170204	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccagacatgaggtgcatcAtgggcgagtctcctgcagtg	9	8	13	11	1	2	2	1	1	1	1	3	3	2	2	2	2	2	2	2	2	0	0	rs541394087		TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr16:70170204A>G	ENST00000288050.4	+	10	2062	c.1105A>G	c.(1105-1107)Atg>Gtg	p.M369V	PDPR_ENST00000398122.3_Missense_Mutation_p.M269V|PDPR_ENST00000562100.1_3'UTR|PDPR_ENST00000568530.1_Missense_Mutation_p.M369V	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	369					cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		GAGGTGCATCATGGGCGAGTC	0.517													.|||	1	0.000199681	0	0	5008	,	,		26659	0.001		0	False		,,,				2504	0				p.M369V		Atlas-SNP	.											.	PDPR	66	.	0			c.A1105G						PASS	.						78	81	80					16																	70170204		1977	4175	6152	SO:0001583	missense	55066	exon10			TGCATCATGGGCG		CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857			30264	protein-coding gene	gene with protein product						9395502	Standard	NM_017990		Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.1105A>G	chr16.hg19:g.70170204A>G	ENSP00000288050:p.Met369Val	73.0	0.0	.		99.0	15.0	.	NM_017990	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Missense_Mutation	SNP	ENST00000288050.4	hg19	CCDS45520.1	.	.	.	.	.	.	.	.	.	.	A	12.62	1.993038	0.35131	.	.	ENSG00000090857	ENST00000288050;ENST00000398122;ENST00000205055	T;T	0.79749	-1.3;-1.3	4.42	3.31	0.37934	FAD dependent oxidoreductase (1);	0.040270	0.85682	D	0.000000	T	0.62036	0.2395	N	0.04387	-0.21	0.80722	D	1	B;B	0.33448	0.412;0.002	B;B	0.40982	0.345;0.007	T	0.52472	-0.8571	10	0.09843	T	0.71	.	10.3359	0.43850	0.8344:0.1656:0.0:0.0	.	97;369	Q9NWE6;Q8NCN5	.;PDPR_HUMAN	V	369;269;97	ENSP00000288050:M369V;ENSP00000381190:M269V	ENSP00000205055:M97V	M	+	1	0	PDPR	68727705	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.221000	0.65272	0.526000	0.28541	0.374000	0.22700	ATG	.	.	.	none		0.517	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1	NM_017990		G	70170204	A	G	70170204	3	3	4	1	0	0	0	0	1	0	0	0	11696	217	8	3	1135	3	PDPR	16	70170204	Missense_Mutation	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10	18999073	70170204	20184549	117	370											
SLC43A2	124935	hgsc.bcm.edu	37	chr17	1486541	1486541	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaggtcaccccaaagcccAcgagcagcaggttggtgaag	11	4	14	12	1	1	1	1	1	0	0	1	2	1	1	3	4	3	4	3	4	2	1			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr17:1486541A>G	ENST00000301335.5	-	11	1395	c.1307T>C	c.(1306-1308)gTg>gCg	p.V436A	SLC43A2_ENST00000571650.1_Missense_Mutation_p.V440A|SLC43A2_ENST00000382147.4_Missense_Mutation_p.V440A|SLC43A2_ENST00000412517.3_Missense_Mutation_p.V299A	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	436					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)		CCCAAAGCCCACGAGCAGCAG	0.597																																					p.V436A		Atlas-SNP	.											.	SLC43A2	37	.	0			c.T1307C						PASS	.						101	101	101					17																	1486541		2203	4300	6503	SO:0001583	missense	124935	exon11			AAGCCCACGAGCA	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.1307T>C	chr17.hg19:g.1486541A>G	ENSP00000301335:p.Val436Ala	68.0	0.0	.		113.0	25.0	.	NM_152346	B7Z6X9|C9JNU8|D3DTH9|Q5CD75|Q6IPM1|Q8NBX1|Q8NC21|Q8WZ00	Missense_Mutation	SNP	ENST00000301335.5	hg19	CCDS11006.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.176893	0.78564	.	.	ENSG00000167703	ENST00000301335;ENST00000382147;ENST00000412517	D;D;D	0.81579	-1.51;-1.51;-1.51	5.67	5.67	0.87782	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.86443	0.5934	M	0.85373	2.75	0.58432	D	0.999998	B;P	0.45283	0.257;0.855	B;P	0.49561	0.083;0.615	D	0.85660	0.1288	10	0.28530	T	0.3	-17.3303	16.2045	0.82114	1.0:0.0:0.0:0.0	.	436;440	Q8N370;Q8N370-3	LAT4_HUMAN;.	A	436;440;299	ENSP00000301335:V436A;ENSP00000371582:V440A;ENSP00000408284:V299A	ENSP00000301335:V436A	V	-	2	0	SLC43A2	1433291	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	9.287000	0.95975	2.288000	0.76882	0.533000	0.62120	GTG	.	.	.	none		0.597	SLC43A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206717.4	NM_152346		G	1486541	A	G	1486541	3	3	4	1	0	0	0	0	1	0	0	0	14646	159	6	3	418	3	SLC43A2	17	1486541	Missense_Mutation	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10		1486541	79708669	118	371											
NCOR1	9611	hgsc.bcm.edu	37	chr17	16004686	16004686	+	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	gctaccaccaaatcttcatcTctaggttccaccttctcact	9	13	3	16	0	4	0	2	0	3	0	7	0	5	0	4	1	1	2	4	1	3	5	rs201420293		TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr17:16004686T>A	ENST00000268712.3	-	20	2825	c.2568A>T	c.(2566-2568)agA>agT	p.R856S	NCOR1_ENST00000395851.1_Missense_Mutation_p.R872S|NCOR1_ENST00000395848.1_Missense_Mutation_p.R763S|RNU6-314P_ENST00000516574.1_RNA|NCOR1_ENST00000583226.1_5'Flank	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	856					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)		AATCTTCATCTCTAGGTTCCA	0.483																																					p.R872S		Atlas-SNP	.											.	NCOR1	240	.	0			c.A2616T						PASS	.						190	177	181					17																	16004686		2203	4300	6503	SO:0001583	missense	9611	exon19			TTCATCTCTAGGT	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.2568A>T	chr17.hg19:g.16004686T>A	ENSP00000268712:p.Arg856Ser	46.0	0.0	.		80.0	47.0	.	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	hg19	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	T	2.512	-0.312814	0.05422	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849;ENST00000395848	T;T;T;T	0.45668	3.41;1.54;0.89;1.54	5.76	-0.452	0.12205	.	0.776473	0.13041	N	0.418546	T	0.22126	0.0533	L	0.29908	0.895	0.46774	D	0.999197	B;B;B	0.21309	0.054;0.0;0.0	B;B;B	0.21360	0.034;0.0;0.0	T	0.15178	-1.0446	10	0.18710	T	0.47	-1.0053	0.985	0.01444	0.2157:0.2558:0.1112:0.4173	.	763;856;872	E9PGV6;O75376;O75376-2	.;NCOR1_HUMAN;.	S	856;872;763;763	ENSP00000268712:R856S;ENSP00000379192:R872S;ENSP00000379190:R763S;ENSP00000379189:R763S	ENSP00000268712:R856S	R	-	3	2	NCOR1	15945411	0.001000	0.12720	0.350000	0.25708	0.105000	0.19272	-0.318000	0.08050	-0.108000	0.12066	-1.109000	0.02080	AGA	.	T|0.999;C|0.001	.	alt		0.483	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		A	16004686	T	A	16004686	3	1	4	1	0	0	0	0	1	0	0	0	10242	1548	54	5	4862	5	NCOR1	17	16004686	Missense_Mutation	SNP	T	TCGA-2Z-A9J3-01A-12D-A382-10	14518145	16004686	65190524	119	372											
FAM20A	54757	hgsc.bcm.edu	37	chr17	66538847	66538847	+	Missense_Mutation	SNP	A	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	tactctacctggagagacaaAgaaaacactctgcaggattt	15	9	8	9	0	2	2	0	0	2	2	2	5	2	4	1	2	4	1	1	2	5	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr17:66538847A>C	ENST00000592554.1	-	6	1638	c.916T>G	c.(916-918)Ttt>Gtt	p.F306V	AC079210.1_ENST00000600820.1_5'Flank|FAM20A_ENST00000226094.5_5'UTR|PRKAR1A_ENST00000588188.2_Intron	NM_001243746.1|NM_017565.3	NP_001230675.1|NP_060035.2	Q96MK3	FA20A_HUMAN	family with sequence similarity 20, member A	306					calcium ion homeostasis (GO:0055074)|enamel mineralization (GO:0070166)|tooth eruption (GO:0044691)	cell (GO:0005623)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)				cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(1)	9	Breast(10;1.64e-13)					GGAGAGACAAAGAAAACACTC	0.522																																					p.F306V		Atlas-SNP	.											.	FAM20A	35	.	0			c.T916G						PASS	.						107	107	107					17																	66538847		2203	4300	6503	SO:0001583	missense	54757	exon6			AGACAAAGAAAAC	AK056789	CCDS11679.1	17q24.2	2014-02-07			ENSG00000108950	ENSG00000108950			23015	protein-coding gene	gene with protein product		611062					Standard	NM_017565		Approved	DKFZp434F2322	uc002jho.3	Q96MK3	OTTHUMG00000180152	ENST00000592554.1:c.916T>G	chr17.hg19:g.66538847A>C	ENSP00000468308:p.Phe306Val	57.0	0.0	.		85.0	21.0	.	NM_017565	B2RN47|B2RN49|Q9UF95	Missense_Mutation	SNP	ENST00000592554.1	hg19	CCDS11679.1	.	.	.	.	.	.	.	.	.	.	A	32	5.105452	0.94245	.	.	ENSG00000108950	ENST00000226094	.	.	.	6.04	6.04	0.98038	.	0.087086	0.85682	D	0.000000	T	0.77398	0.4124	M	0.89414	3.03	0.80722	D	1	P	0.47034	0.889	P	0.50825	0.651	T	0.81820	-0.0757	9	0.66056	D	0.02	-17.9903	16.5763	0.84648	1.0:0.0:0.0:0.0	.	306	Q96MK3	FA20A_HUMAN	V	306	.	ENSP00000226094:F306V	F	-	1	0	FAM20A	64050442	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	8.962000	0.93254	2.317000	0.78254	0.459000	0.35465	TTT	.	.	.	none		0.522	FAM20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450029.2	NM_017565		C	66538847	A	C	66538847	3	2	4	1	0	0	0	0	1	0	0	0	5541	72	3	5	733	5	FAM20A	17	66538847	Missense_Mutation	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10	50534161	66538847	14656363	120	373											
UBE2O	63893	hgsc.bcm.edu	37	chr17	74391896	74391896	+	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	cgcactgtgctgaagaacttCttggcttctggaggctggaa	8	11	13	9	1	2	2	0	1	2	1	2	4	2	4	0	4	2	4	0	4	3	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr17:74391896C>T	ENST00000319380.7	-	15	2920	c.2856G>A	c.(2854-2856)aaG>aaA	p.K952K	UBE2O_ENST00000587581.1_5'Flank	NM_022066.3	NP_071349.3	Q9C0C9	UBE2O_HUMAN	ubiquitin-conjugating enzyme E2O	952					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						TGAAGAACTTCTTGGCTTCTG	0.502																																					p.K952K		Atlas-SNP	.											.	UBE2O	207	.	0			c.G2856A						PASS	.						124	116	119					17																	74391896		2203	4300	6503	SO:0001819	synonymous_variant	63893	exon15			GAACTTCTTGGCT	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.2856G>A	chr17.hg19:g.74391896C>T		41.0	0.0	.		51.0	17.0	.	NM_022066	A6NDU5|Q69YP4|Q6PIZ2|Q86UA4|Q8N425|Q8TBN1|Q9BSW1|Q9H6E6|Q9H7E4|Q9H9B2	Silent	SNP	ENST00000319380.7	hg19	CCDS32742.1																																																																																			.	.	.	none		0.502	UBE2O-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450123.1	NM_022066		T	74391896	C	T	74391896	2	4	4	1	0	0	0	0	0	0	0	1	16880	912	32	2		2	UBE2O	17	74391896	Silent	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10	7853049	74391896	6803314	121	374											
FOXK2	3607	hgsc.bcm.edu	37	chr17	80477826	80477826	+	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	acccgcgggcggcggggccgGgggcggcggggccgggggcg	1	0	27	13	9	0	0	0	0	0	0	0	0	0	0	3	11	0	0	3	11	0	0			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr17:80477826G>C	ENST00000335255.5	+	1	236	c.62G>C	c.(61-63)gGg>gCg	p.G21A		NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	21	Gly-rich.			AAAAALSGAGTPPAGGGAGGGGAGGGGSPPGGWAVARLEGR EFEYLMKKRSVTIGRNSSQGSVDVSMGHSSFISRRHLEIFT PPGGGGHGGAAPELPPAQPRPDAGGDFYLRCLGKNG -> Q (in Ref. 1; CAA43200). {ECO:0000305}.	positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	17	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			ggcggggccgggggcggcggg	0.846																																					p.G21A		Atlas-SNP	.											FOXK2,NS,carcinoma,0,1	FOXK2	46	.	0			c.G62C						PASS	.						1	1	1					17																	80477826		122	223	345	SO:0001583	missense	3607	exon1			GGGCCGGGGGCGG	U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"Forkhead boxes"	6036	protein-coding gene	gene with protein product		147685	"interleukin enhancer binding factor 1"	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.62G>C	chr17.hg19:g.80477826G>C	ENSP00000335677:p.Gly21Ala	0.0	0.0	.		4.0	2.0	.	NM_004514	A6NEP5|Q13622|Q13623|Q13624	Missense_Mutation	SNP	ENST00000335255.5	hg19	CCDS11813.1	.	.	.	.	.	.	.	.	.	.	.	2.177	-0.388435	0.04932	.	.	ENSG00000141568	ENST00000335255;ENST00000335241	D	0.93076	-3.16	1.8	1.8	0.24995	.	.	.	.	.	D	0.89375	0.6697	N	0.08118	0	0.25222	N	0.98989	D;D;D	0.71674	0.998;0.996;0.998	D;D;D	0.68621	0.959;0.91;0.959	T	0.80350	-0.1419	9	0.14252	T	0.57	.	6.724	0.23346	0.0:0.0:1.0:0.0	.	21;21;21	Q01167-3;Q01167;Q01167-2	.;FOXK2_HUMAN;.	A	21	ENSP00000335677:G21A	ENSP00000334321:G21A	G	+	2	0	FOXK2	78071115	0.917000	0.31117	0.403000	0.26384	0.773000	0.43773	0.923000	0.28757	0.820000	0.34516	0.486000	0.48141	GGG	.	.	.	none		0.846	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430		C	80477826	G	C	80477826	3	2	4	1	0	0	0	0	1	0	0	0	6022	1232	43	4	64	4	FOXK2	17	80477826	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	6085930	80477826	717384	122	375											
ENOSF1	55556	hgsc.bcm.edu	37	chr18	677380	677380	+	Frame_Shift_Del	DEL	A	A	-																															gcagaaactgatatgtagtcAaatataatcaggtgctgcac																										TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr18:677380delA	ENST00000251101.7	-	14	1201	c.1113delT	c.(1111-1113)tttfs	p.F371fs	ENOSF1_ENST00000583973.1_5'UTR|ENOSF1_ENST00000319815.6_Frame_Shift_Del_p.F141fs|ENOSF1_ENST00000340116.7_Frame_Shift_Del_p.F378fs|ENOSF1_ENST00000383578.3_Frame_Shift_Del_p.F289fs|ENOSF1_ENST00000580982.1_Frame_Shift_Del_p.F295fs	NM_017512.5	NP_059982.2	Q7L5Y1	ENOF1_HUMAN	enolase superfamily member 1	371					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						ATATGTAGTCAAATATAATCA	0.423																																					p.D379fs		Atlas-Indel,Pindel	.											ENOSF1,NS,lymphoid_neoplasm,0,1	ENOSF1	44	.	0			c.1135delG						PASS	.						84	86	85					18																	677380		2203	4300	6503	SO:0001589	frameshift_variant	55556	exon13			.	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.1113delT	chr18.hg19:g.677380delA	ENSP00000251101:p.Phe371fs	132.0	0.0	0		123.0	56.0	0.455285	NM_202758	A6NMP3|A8K9R5|B3KSL6|B3KXE4|D3DUH0|Q15407|Q15594|Q15595|Q6ZS08|Q9HAS5|Q9HAS6	Frame_Shift_Del	DEL	ENST00000251101.7	hg19	CCDS11822.1																																																																																			.	.	.	none		0.423	ENOSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254312.2	NM_017512		-	677380	A	-	677380	7	5	4	1	0	1	0	1	0	0	0	0	5127	127	5	0	230	0	ENOSF1	18	677380	Frame_Shift_Del	DEL	A	TCGA-2Z-A9J3-01A-12D-A382-10		677380	77399868	123	376											
APCDD1	147495	hgsc.bcm.edu	37	chr18	10487720	10487720	+	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	gtgacccacaccaatggctgCgtggccctgggcatcaaact	9	7	11	14	1	1	1	1	1	0	0	1	1	1	1	3	3	2	2	3	3	2	0	rs139112764		TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr18:10487720C>A	ENST00000355285.5	+	5	1584	c.1230C>A	c.(1228-1230)tgC>tgA	p.C410*		NM_153000.4	NP_694545.1			adenomatosis polyposis coli down-regulated 1											NS(1)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				READ - Rectum adenocarcinoma(15;0.08)		CCAATGGCTGCGTGGCCCTGG	0.602																																					p.C410X		Atlas-SNP	.											APCDD1,caecum,carcinoma,0,1	APCDD1	57	.	0			c.C1230A						PASS	.						77	68	71					18																	10487720		2203	4300	6503	SO:0001587	stop_gained	147495	exon5			TGGCTGCGTGGCC	AB056722	CCDS11849.1	18p11.21	2006-07-07			ENSG00000154856	ENSG00000154856			15718	protein-coding gene	gene with protein product		607479				12384519	Standard	NM_153000		Approved	B7323	uc002kom.4	Q8J025	OTTHUMG00000131635	ENST00000355285.5:c.1230C>A	chr18.hg19:g.10487720C>A	ENSP00000347433:p.Cys410*	67.0	0.0	.		101.0	46.0	.	NM_153000		Nonsense_Mutation	SNP	ENST00000355285.5	hg19	CCDS11849.1	.	.	.	.	.	.	.	.	.	.	C	38	6.674971	0.97755	.	.	ENSG00000154856	ENST00000355285;ENST00000423585	.	.	.	5.07	-4.6	0.03390	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-34.3709	13.6645	0.62387	0.0:0.3885:0.0:0.6115	.	.	.	.	X	410;461	.	ENSP00000347433:C410X	C	+	3	2	APCDD1	10477720	0.361000	0.24972	0.907000	0.35723	0.991000	0.79684	-0.250000	0.08830	-1.024000	0.03338	-0.251000	0.11542	TGC	.	C|1.000;T|0.000	.	alt		0.602	APCDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254529.2	NM_153000		A	10487720	C	A	10487720	4	1	4	1	0	0	0	0	0	1	0	0	765	776	27	4	1248	4	APCDD1	18	10487720	Nonsense_Mutation	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10	9810340	10487720	67589528	124	377											
TCF4	6925	hgsc.bcm.edu	37	chr18	53018225	53018225	+	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	catatccatgtcacctccaaGgagactctgctaaaaggtta	13	10	7	11	0	2	1	1	0	1	1	4	2	4	1	3	2	1	2	3	2	5	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr18:53018225G>A	ENST00000356073.4	-	7	990	c.379C>T	c.(379-381)Ctt>Ttt	p.L127F	TCF4_ENST00000567880.1_Intron|TCF4_ENST00000564403.2_Missense_Mutation_p.L127F|TCF4_ENST00000537578.1_Missense_Mutation_p.L103F|TCF4_ENST00000564228.1_Missense_Mutation_p.L56F|TCF4_ENST00000570177.2_5'UTR|TCF4_ENST00000561992.1_5'UTR|TCF4_ENST00000568673.1_Missense_Mutation_p.L103F|TCF4_ENST00000566279.1_Intron|TCF4_ENST00000566286.1_Missense_Mutation_p.L125F|TCF4_ENST00000354452.3_Missense_Mutation_p.L127F|TCF4_ENST00000543082.1_Missense_Mutation_p.L85F|TCF4_ENST00000544241.2_Missense_Mutation_p.L56F|TCF4_ENST00000537856.3_5'UTR|TCF4_ENST00000398339.1_Missense_Mutation_p.L229F|TCF4_ENST00000564999.1_Missense_Mutation_p.L127F|TCF4_ENST00000568740.1_Missense_Mutation_p.L102F|TCF4_ENST00000540999.1_Missense_Mutation_p.L103F|TCF4_ENST00000565018.2_Missense_Mutation_p.L127F	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4	127					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)		TCACCTCCAAGGAGACTCTGC	0.428																																					p.L229F		Atlas-SNP	.											.	TCF4	178	.	0			c.C685T						PASS	.						91	88	89					18																	53018225		2203	4300	6503	SO:0001583	missense	6925	exon8			CTCCAAGGAGACT	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.379C>T	chr18.hg19:g.53018225G>A	ENSP00000348374:p.Leu127Phe	66.0	0.0	.		107.0	47.0	.	NM_001243226	B3KT62|B3KUC0|B4DT37|B4DUG3|B7Z5M6|B7Z6Y1|G0LNT9|G0LNU0|G0LNU1|G0LNU2|G0LNU4|G0LNU5|G0LNU8|G0LNU9|G0LNV0|G0LNV1|G0LNV2|H3BPQ1|Q08AP2|Q08AP3|Q15439|Q15440|Q15441	Missense_Mutation	SNP	ENST00000356073.4	hg19	CCDS11960.1	.	.	.	.	.	.	.	.	.	.	G	15.75	2.926592	0.52759	.	.	ENSG00000196628	ENST00000354452;ENST00000356073;ENST00000543082;ENST00000540999;ENST00000537578;ENST00000544241;ENST00000398339	T;T;T;T;T;T;T	0.73897	-0.79;-0.79;-0.79;-0.79;-0.79;-0.79;-0.79	5.57	5.57	0.84162	.	0.162083	0.42682	D	0.000670	T	0.82038	0.4950	L	0.59436	1.845	0.58432	D	0.999994	D;B;D;D;P;P;D	0.69078	0.957;0.418;0.975;0.997;0.947;0.913;0.957	P;B;P;P;P;P;P	0.59221	0.729;0.267;0.835;0.854;0.568;0.66;0.729	D	0.83433	0.0039	10	0.87932	D	0	-25.4497	16.8254	0.85929	0.0:0.0:1.0:0.0	.	103;127;103;229;127;85;56	B7Z5M6;G0LNT9;B7Z6Y1;E9PH57;P15884;B3KUC0;B3KT62	.;.;.;.;ITF2_HUMAN;.;.	F	127;127;85;103;103;56;229	ENSP00000346440:L127F;ENSP00000348374:L127F;ENSP00000439656:L85F;ENSP00000445202:L103F;ENSP00000440731:L103F;ENSP00000441562:L56F;ENSP00000381382:L229F	ENSP00000346440:L127F	L	-	1	0	TCF4	51169223	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.547000	0.60712	2.781000	0.95711	0.655000	0.94253	CTT	.	.	.	none		0.428	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	NM_003199		A	53018225	G	A	53018225	3	1	4	1	0	0	0	0	1	0	0	0	15707	1000	35	2	1688	2	TCF4	18	53018225	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	42530505	53018225	25059023	125	378											
PNPLA6	10908	hgsc.bcm.edu	37	chr19	7619899	7619899	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaatatgcgcagctggtgcTcggggcacctgcacctgcgc	7	8	13	13	3	0	0	0	0	0	0	1	0	0	0	2	3	5	5	2	3	3	2			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr19:7619899T>C	ENST00000221249.6	+	25	3072	c.2641T>C	c.(2641-2643)Tcg>Ccg	p.S881P	PNPLA6_ENST00000600737.1_Missense_Mutation_p.S919P|PNPLA6_ENST00000545201.2_Missense_Mutation_p.S854P|PNPLA6_ENST00000450331.3_Missense_Mutation_p.S881P|PNPLA6_ENST00000414982.3_Missense_Mutation_p.S929P	NM_006702.4	NP_006693.3	Q8IY17	PLPL6_HUMAN	patatin-like phospholipase domain containing 6	920					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						CAGCTGGTGCTCGGGGCACCT	0.711																																					p.S929P		Atlas-SNP	.											.	PNPLA6	163	.	0			c.T2785C						PASS	.						12	13	12					19																	7619899		2199	4290	6489	SO:0001583	missense	10908	exon24			TGGTGCTCGGGGC	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.2641T>C	chr19.hg19:g.7619899T>C	ENSP00000221249:p.Ser881Pro	12.0	0.0	.		35.0	13.0	.	NM_001166111	A6NGQ0|B4DFB9|B7Z7T2|F5H5K9|J3KQS3|O60859|Q86W58|Q9UG58	Missense_Mutation	SNP	ENST00000221249.6	hg19	CCDS32891.1	.	.	.	.	.	.	.	.	.	.	t	28.6	4.930713	0.92389	.	.	ENSG00000032444	ENST00000221249;ENST00000545201;ENST00000414982;ENST00000450331	T;T;T;T	0.26957	1.7;1.7;1.7;1.7	5.35	5.35	0.76521	.	0.140180	0.50627	D	0.000120	T	0.56746	0.2006	M	0.90082	3.085	0.58432	D	0.999999	D;B;D;D	0.65815	0.992;0.149;0.995;0.987	D;B;D;D	0.68765	0.912;0.162;0.96;0.937	T	0.66101	-0.6007	10	0.72032	D	0.01	.	13.3305	0.60483	0.0:0.0:0.0:1.0	.	920;854;919;881	Q8IY17;F5H5K9;Q8IY17-3;Q8IY17-2	PLPL6_HUMAN;.;.;.	P	881;854;929;881	ENSP00000221249:S881P;ENSP00000443323:S854P;ENSP00000407509:S929P;ENSP00000394348:S881P	ENSP00000221249:S881P	S	+	1	0	PNPLA6	7525899	1.000000	0.71417	0.996000	0.52242	0.748000	0.42578	7.996000	0.88334	2.040000	0.60383	0.454000	0.30748	TCG	.	.	.	none		0.711	PNPLA6-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459275.1	NM_006702		C	7619899	T	C	7619899	3	2	4	1	0	0	0	0	1	0	0	0	12176	1551	54	3	2875	3	PNPLA6	19	7619899	Missense_Mutation	SNP	T	TCGA-2Z-A9J3-01A-12D-A382-10		7619899	51509084	126	379											
ZNF627	199692	hgsc.bcm.edu	37	chr19	11727866	11727866	+	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	tatttctcttgtaagcattcGaagacacatgttaacgcata	13	14	6	8	2	1	1	0	0	1	1	3	2	1	1	0	0	2	4	0	0	5	7	rs200860012		TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr19:11727866G>A	ENST00000361113.5	+	4	756	c.548G>A	c.(547-549)cGa>cAa	p.R183Q	ZNF627_ENST00000588174.1_3'UTR	NM_145295.3	NP_660338.1	Q7L945	ZN627_HUMAN	zinc finger protein 627	183					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.R183Q(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14						GTAAGCATTCGAAGACACATG	0.403													G|||	1	0.000199681	0	0	5008	,	,		24586	0		0	False		,,,				2504	0.001				p.R183Q	Melanoma(112;173 1614 10731 17751 23322)	Atlas-SNP	.											ZNF627,caecum,carcinoma,0,2	ZNF627	43	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.G548A						PASS	.	G	GLN/ARG	0,4336		0,0,2168	84	85	85		548	-2.7	0	19		85	1,8559		0,1,4279	yes	missense	ZNF627	NM_145295.3	43	0,1,6447	AA,AG,GG		0.0117,0.0,0.0078	possibly-damaging	183/462	11727866	1,12895	2168	4280	6448	SO:0001583	missense	199692	exon4			GCATTCGAAGACA	AK074846	CCDS42502.1	19p13.2	2013-01-08				ENSG00000198551		"Zinc fingers, C2H2-type", "-"	30570	protein-coding gene	gene with protein product		612248				12477932	Standard	NM_145295		Approved	FLJ90365	uc002msk.2	Q7L945		ENST00000361113.5:c.548G>A	chr19.hg19:g.11727866G>A	ENSP00000354414:p.Arg183Gln	69.0	0.0	.		99.0	48.0	.	NM_145295	O14846|Q4KMP9|Q6NT81|Q9BRG4	Missense_Mutation	SNP	ENST00000361113.5	hg19	CCDS42502.1	.	.	.	.	.	.	.	.	.	.	g	7.616	0.675785	0.14841	0.0	1.17E-4	ENSG00000198551	ENST00000361113	T	0.36520	1.25	1.36	-2.73	0.05950	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.19046	0.0457	L	0.33189	0.99	0.18873	N	0.999989	P	0.42584	0.784	B	0.38616	0.277	T	0.22173	-1.0224	9	0.07030	T	0.85	.	6.5443	0.22397	0.6527:0.0:0.3473:0.0	.	183	Q7L945	ZN627_HUMAN	Q	183	ENSP00000354414:R183Q	ENSP00000354414:R183Q	R	+	2	0	ZNF627	11588866	0.000000	0.05858	0.001000	0.08648	0.966000	0.64601	-1.336000	0.02660	-0.762000	0.04664	0.313000	0.20887	CGA	.	.	.	weak		0.403	ZNF627-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458875.1	NM_145295		A	11727866	G	A	11727866	3	1	4	1	0	0	0	0	1	0	0	0	18063	1058	37	1	562	1	ZNF627	19	11727866	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	4107967	11727866	47401117	127	380											
FBXW9	84261	hgsc.bcm.edu	37	chr19	12805491	12805491	+	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	cagctgccgcaggtcccacaAgttgacgttgcgatctcggg	7	8	13	13	4	1	1	0	1	1	0	3	2	2	1	2	2	3	4	2	2	1	2	rs201026853	byFrequency	TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr19:12805491A>T	ENST00000380339.3	-	3	631	c.595T>A	c.(595-597)Ttg>Atg	p.L199M	FBXW9_ENST00000544494.1_De_novo_Start_OutOfFrame|FBXW9_ENST00000393261.3_Missense_Mutation_p.L199M|FBXW9_ENST00000587955.1_Missense_Mutation_p.L189M			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	199					SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						AGGTCCCACAAGTTGACGTTG	0.602																																					p.L199M		Atlas-SNP	.											.	FBXW9	30	.	0			c.T595A						PASS	.						60	67	65					19																	12805491		2043	4197	6240	SO:0001583	missense	84261	exon3			CCCACAAGTTGAC	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.595T>A	chr19.hg19:g.12805491A>T	ENSP00000369696:p.Leu199Met	87.0	0.0	.		92.0	36.0	.	NM_032301	B3KVP7|Q9BT89	Missense_Mutation	SNP	ENST00000380339.3	hg19		.	.	.	.	.	.	.	.	.	.	A	17.06	3.292183	0.59976	.	.	ENSG00000132004	ENST00000393261;ENST00000380339	T;T	0.66638	-0.22;-0.22	4.24	-0.503	0.12000	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.64402	D	0.000003	T	0.77745	0.4176	M	0.82132	2.575	0.80722	D	1	D;P;D	0.89917	0.992;0.955;1.0	P;D;D	0.91635	0.899;0.93;0.999	T	0.75825	-0.3181	10	0.56958	D	0.05	-18.2074	8.7017	0.34329	0.4517:0.0:0.5483:0.0	.	189;199;199	Q5XUX1-2;Q5XUX1;Q5XUX1-3	.;FBXW9_HUMAN;.	M	199	ENSP00000376945:L199M;ENSP00000369696:L199M	ENSP00000369696:L199M	L	-	1	2	FBXW9	12666491	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	0.885000	0.28227	0.106000	0.17784	-0.486000	0.04755	TTG	.	A|0.999;G|0.001	.	alt		0.602	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301		T	12805491	A	T	12805491	3	4	4	1	0	0	0	0	1	0	0	0	5778	69	3	5	813	5	FBXW9	19	12805491	Missense_Mutation	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10	1077625	12805491	46323492	128	381											
UNC13A	23025	hgsc.bcm.edu	37	chr19	17751432	17751432	+	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	tgctcatgacggcaggcaccCctgggcacatatacttggag	9	8	12	12	1	1	1	1	1	0	0	1	2	1	2	2	4	2	4	2	4	2	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr19:17751432C>T	ENST00000519716.2	-	22	2674	c.2675G>A	c.(2674-2676)gGg>gAg	p.G892E	UNC13A_ENST00000550896.1_Missense_Mutation_p.G890E|UNC13A_ENST00000551649.1_Missense_Mutation_p.G892E|UNC13A_ENST00000428389.2_Missense_Mutation_p.G980E|UNC13A_ENST00000252773.7_Missense_Mutation_p.G892E|UNC13A_ENST00000552293.1_Missense_Mutation_p.G892E	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	892					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						GGCAGGCACCCCTGGGCACAT	0.637																																					p.G892E		Atlas-SNP	.											.	UNC13A	299	.	0			c.G2675A						PASS	.						59	69	65					19																	17751432		2187	4272	6459	SO:0001583	missense	23025	exon21			GGCACCCCTGGGC	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.2675G>A	chr19.hg19:g.17751432C>T	ENSP00000429562:p.Gly892Glu	85.0	0.0	.		66.0	29.0	.	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	hg19	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	C	17.10	3.303018	0.60195	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	D;D;D;D;D;D	0.83837	-1.75;-1.69;-1.75;-1.61;-1.63;-1.77	3.28	3.28	0.37604	.	0.149281	0.45867	U	0.000325	D	0.90092	0.6905	M	0.80746	2.51	0.58432	D	0.999999	D	0.89917	1.0	D	0.79108	0.992	D	0.91311	0.5074	10	0.87932	D	0	-25.1003	12.4632	0.55743	0.0:1.0:0.0:0.0	.	892	Q9UPW8	UN13A_HUMAN	E	892;980;892;892;892;890	ENSP00000429562:G892E;ENSP00000400409:G980E;ENSP00000252773:G892E;ENSP00000447236:G892E;ENSP00000447572:G892E;ENSP00000446831:G890E	ENSP00000252773:G892E	G	-	2	0	UNC13A	17612432	1.000000	0.71417	0.985000	0.45067	0.602000	0.36980	7.340000	0.79292	1.842000	0.53543	0.186000	0.17326	GGG	.	.	.	none		0.637	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		T	17751432	C	T	17751432	3	4	4	1	0	0	0	0	1	0	0	0	16996	623	22	2	2524	2	UNC13A	19	17751432	Missense_Mutation	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10	4945941	17751432	41377551	129	382											
ZNF229	7772	hgsc.bcm.edu	37	chr19	44932512	44932512	+	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	tctcgcctaaatgcactcttTggtggttccgcagacctgag	7	12	10	12	2	2	2	0	1	2	1	4	2	3	2	3	2	1	3	3	2	2	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr19:44932512T>A	ENST00000588931.1	-	6	2877	c.2444A>T	c.(2443-2445)cAa>cTa	p.Q815L	ZNF229_ENST00000291187.4_Missense_Mutation_p.Q809L|ZNF229_ENST00000591289.1_Intron|CTC-512J12.4_ENST00000588655.1_RNA	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	815					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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)				ATGCACTCTTTGGTGGTTCCG	0.473																																					p.Q815L		Atlas-SNP	.											.	ZNF229	123	.	0			c.A2444T						PASS	.						89	96	94					19																	44932512		2150	4282	6432	SO:0001583	missense	7772	exon6			ACTCTTTGGTGGT	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.2444A>T	chr19.hg19:g.44932512T>A	ENSP00000466519:p.Gln815Leu	66.0	0.0	.		92.0	45.0	.	NM_014518	B2RWN3|Q59FV2|Q86WL9	Missense_Mutation	SNP	ENST00000588931.1	hg19	CCDS42574.1	.	.	.	.	.	.	.	.	.	.	T	15.55	2.866557	0.51588	.	.	ENSG00000167383	ENST00000291187	.	.	.	3.62	3.62	0.41486	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.25457	0.0619	L	0.35793	1.09	0.27093	N	0.962818	P	0.37997	0.614	B	0.26202	0.067	T	0.13495	-1.0507	8	0.62326	D	0.03	.	11.3701	0.49694	0.0:0.0:0.0:1.0	.	815	Q9UJW7	ZN229_HUMAN	L	815	.	ENSP00000291187:Q815L	Q	-	2	0	ZNF229	49624352	0.430000	0.25538	0.055000	0.19348	0.371000	0.29859	0.889000	0.28282	1.509000	0.48786	0.491000	0.48974	CAA	.	.	.	none		0.473	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518		A	44932512	T	A	44932512	3	1	4	1	0	0	0	0	1	0	0	0	17794	1812	63	5	37	5	ZNF229	19	44932512	Missense_Mutation	SNP	T	TCGA-2Z-A9J3-01A-12D-A382-10	27181080	44932512	14196471	130	383											
GRIN2D	2906	hgsc.bcm.edu	37	chr19	48918125	48918125	+	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	tggtcactgcccgcagccctCcaccggatgccccccgcccg	4	5	10	22	4	1	0	1	0	0	0	2	1	2	1	8	2	3	1	8	2	0	0			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr19:48918125C>A	ENST00000263269.3	+	6	1505	c.1417C>A	c.(1417-1419)Cca>Aca	p.P473T		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	473					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)	CCGCAGCCCTCCACCGGATGC	0.597																																					p.P473T		Atlas-SNP	.											.	GRIN2D	76	.	0			c.C1417A						PASS	.						42	49	46					19																	48918125		2203	4300	6503	SO:0001583	missense	2906	exon6			AGCCCTCCACCGG	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.1417C>A	chr19.hg19:g.48918125C>A	ENSP00000263269:p.Pro473Thr	103.0	0.0	.		88.0	39.0	.	NM_000836		Missense_Mutation	SNP	ENST00000263269.3	hg19	CCDS12719.1	.	.	.	.	.	.	.	.	.	.	C	12.48	1.952119	0.34471	.	.	ENSG00000105464	ENST00000263269	T	0.11277	2.79	4.36	4.36	0.52297	Ionotropic glutamate receptor (1);	0.596252	0.16331	N	0.219129	T	0.08179	0.0204	N	0.14661	0.345	0.28778	N	0.900003	P	0.42757	0.789	P	0.46110	0.504	T	0.12656	-1.0539	10	0.14656	T	0.56	.	9.899	0.41335	0.0:0.9037:0.0:0.0963	.	473	O15399	NMDE4_HUMAN	T	473	ENSP00000263269:P473T	ENSP00000263269:P473T	P	+	1	0	GRIN2D	53609937	0.913000	0.31002	0.994000	0.49952	0.917000	0.54804	1.202000	0.32271	2.445000	0.82738	0.655000	0.94253	CCA	.	.	.	none		0.597	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1			A	48918125	C	A	48918125	3	1	4	1	0	0	0	0	1	0	0	0	6789	855	30	4	1435	4	GRIN2D	19	48918125	Missense_Mutation	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10	3985613	48918125	10210858	131	384											
HSD17B14	51171	hgsc.bcm.edu	37	chr19	49316501	49316502	+	Frame_Shift_Ins	INS	-	-	C																															acccgtaccccagctctgcaINSccccccgtcacgagcagttc																										TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr19:49316501_49316502insC	ENST00000263278.4	-	9	1009_1010	c.743_744insG	c.(742-744)ggtfs	p.G248fs	HSD17B14_ENST00000599157.1_Frame_Shift_Ins_p.G224fs|BCAT2_ENST00000316273.6_5'Flank|BCAT2_ENST00000599246.1_5'Flank|BCAT2_ENST00000598162.1_5'Flank|BCAT2_ENST00000597011.1_5'Flank|BCAT2_ENST00000545387.2_5'Flank|BCAT2_ENST00000601496.1_5'Flank|BCAT2_ENST00000402551.1_5'Flank	NM_016246.2	NP_057330.2	Q9BPX1	DHB14_HUMAN	hydroxysteroid (17-beta) dehydrogenase 14	248					steroid catabolic process (GO:0006706)	cytosol (GO:0005829)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			large_intestine(3)|lung(1)|skin(1)	5		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;0.000341)|all cancers(93;0.000764)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.0346)		CCAGCTCTGCACCCCCCGTCAC	0.658																																					p.G248fs		Atlas-Indel,Pindel	.											.	HSD17B14	25	.	0			c.744_745insG						PASS	.			2,4256		0,2,2127						-5.4	0.5			23	5,8237		0,5,4116	no	frameshift	HSD17B14	NM_016246.2		0,7,6243	A1A1,A1R,RR		0.0607,0.047,0.056				7,12493				SO:0001589	frameshift_variant	51171	exon9			.	AF126781	CCDS12736.1	19q13.33	2011-09-14	2006-11-22	2006-11-22		ENSG00000087076		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	23238	protein-coding gene	gene with protein product	"retinal short-chain dehydrogenase/reductase 3", "short chain dehydrogenase/reductase family 47C, member 1"	612832	"dehydrogenase/reductase (SDR family) member 10"	DHRS10		10800688, 17067289, 19027726	Standard	XM_005258969		Approved	retSDR3, SDR47C1	uc002pkv.1	Q9BPX1		ENST00000263278.4:c.744dupG	chr19.hg19:g.49316507_49316507dupC	ENSP00000263278:p.Gly248fs	140.0	0.0	0		126.0	51.0	0.404762	NM_016246	Q9UKU3	Frame_Shift_Ins	INS	ENST00000263278.4	hg19	CCDS12736.1																																																																																			.	.	.	none		0.658	HSD17B14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466212.1	NM_016246		C	49316502	-	C	49316501	7	5	4	1	0	1	1	0	0	0	0	0	7390	146	6	0	72	0	HSD17B14	19	49316501	Frame_Shift_Ins	INS	-	TCGA-2Z-A9J3-01A-12D-A382-10	398376	49316501	9812482	132	385											
PLEKHA4	57664	hgsc.bcm.edu	37	chr19	49341323	49341323	+	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	tcagtagccagggcttgggaGaggctgagaacccgctcccg	8	6	15	12	2	1	2	1	1	0	2	2	4	2	2	3	3	2	4	3	3	2	2			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr19:49341323G>T	ENST00000263265.6	-	19	2583	c.2028C>A	c.(2026-2028)ctC>ctA	p.L676L	HSD17B14_ENST00000599157.1_5'Flank|PLEKHA4_ENST00000355496.5_Missense_Mutation_p.L578I|HSD17B14_ENST00000263278.4_5'Flank	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	676						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)		GGGCTTGGGAGAGGCTGAGAA	0.562																																					p.L578I		Atlas-SNP	.											.	PLEKHA4	70	.	0			c.C1732A						PASS	.						78	82	81					19																	49341323		2203	4300	6503	SO:0001819	synonymous_variant	57664	exon16			TTGGGAGAGGCTG	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.2028C>A	chr19.hg19:g.49341323G>T		184.0	0.0	.		142.0	69.0	.	NM_001161354	Q8N4M8|Q8N658	Missense_Mutation	SNP	ENST00000263265.6	hg19	CCDS12737.1	.	.	.	.	.	.	.	.	.	.	g	18.76	3.692992	0.68271	.	.	ENSG00000105559	ENST00000355496	T	0.19105	2.17	3.97	0.263	0.15602	.	1.342660	0.05462	N	0.551512	T	0.13286	0.0322	.	.	.	0.22266	N	0.999243	B	0.21309	0.054	B	0.22152	0.038	T	0.34030	-0.9845	9	0.29301	T	0.29	.	5.5324	0.16993	0.1144:0.4003:0.4854:0.0	.	578	Q9H4M7-2	.	I	578	ENSP00000347683:L578I	ENSP00000347683:L578I	L	-	1	0	PLEKHA4	54033135	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	1.127000	0.31357	0.452000	0.26830	0.546000	0.68486	CTC	.	.	.	none		0.562	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466216.1			T	49341323	G	T	49341323	2	4	4	1	0	0	0	0	0	0	0	1	12065	942	33	4		4	PLEKHA4	19	49341323	Silent	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10	24822	49341323	9787660	133	386											
ZNF471	57573	hgsc.bcm.edu	37	chr19	57035735	57035735	+	Missense_Mutation	SNP	A	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	acaggaattacctctgaagcAgttcatgtatgatgatgcat	13	12	9	7	0	2	3	1	3	1	0	2	4	2	4	1	1	3	4	1	1	4	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr19:57035735A>C	ENST00000308031.5	+	5	432	c.299A>C	c.(298-300)cAg>cCg	p.Q100P	ZNF471_ENST00000593197.1_Intron|ZNF471_ENST00000591537.1_Intron	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	100					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			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)		CCTCTGAAGCAGTTCATGTAT	0.368																																					p.Q100P	Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)	Atlas-SNP	.											.	ZNF471	99	.	0			c.A299C						PASS	.						87	84	85					19																	57035735		2203	4300	6503	SO:0001583	missense	57573	exon5			TGAAGCAGTTCAT	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.299A>C	chr19.hg19:g.57035735A>C	ENSP00000309161:p.Gln100Pro	76.0	0.0	.		66.0	32.0	.	NM_020813	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Missense_Mutation	SNP	ENST00000308031.5	hg19	CCDS12945.1	.	.	.	.	.	.	.	.	.	.	A	6.621	0.483070	0.12581	.	.	ENSG00000196263	ENST00000308031	T	0.05649	3.41	3.56	1.43	0.22495	.	.	.	.	.	T	0.06371	0.0164	L	0.31476	0.935	0.09310	N	0.999998	D	0.57257	0.979	P	0.49012	0.598	T	0.34254	-0.9836	9	0.36615	T	0.2	.	3.613	0.08067	0.6493:0.2294:0.1213:0.0	.	100	Q9BX82	ZN471_HUMAN	P	100	ENSP00000309161:Q100P	ENSP00000309161:Q100P	Q	+	2	0	ZNF471	61727547	0.000000	0.05858	0.004000	0.12327	0.558000	0.35554	0.340000	0.19892	0.234000	0.21139	0.460000	0.39030	CAG	.	.	.	none		0.368	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813		C	57035735	A	C	57035735	3	2	4	1	0	0	0	0	1	0	0	0	17942	188	7	5	313	5	ZNF471	19	57035735	Missense_Mutation	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10	7694412	57035735	2093248	134	387											
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385869	58385869	+	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	tttcccacattctccacattCatgttttttttcagtgtgaa	8	19	4	10	0	3	1	2	1	1	0	5	1	4	1	2	0	0	1	2	0	1	7	rs199684163|rs10687775|rs55789144|rs66767659	byFrequency	TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr19:58385869C>A	ENST00000435989.2	-	3	1123	c.889G>T	c.(889-891)Gaa>Taa	p.E297*	ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597342.1_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						TCTCCACATTCATGTTTTTTT	0.363																																					p.E297X		Atlas-SNP	.											ZNF814,NS,carcinoma,0,6	ZNF814	93	.	0			c.G889T						PASS	.						5	4	5					19																	58385869		591	1308	1899	SO:0001587	stop_gained	730051	exon3			CACATTCATGTTT		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.889G>T	chr19.hg19:g.58385869C>A	ENSP00000410545:p.Glu297*	19.0	1.0	.		15.0	6.0	.	NM_001144989	A6NF35	Nonsense_Mutation	SNP	ENST00000435989.2	hg19	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	27.5	4.839119	0.91117	.	.	ENSG00000204514	ENST00000435989	.	.	.	1.93	-3.87	0.04218	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	0.6944	0.00896	0.1754:0.2303:0.1739:0.4204	.	.	.	.	X	297	.	ENSP00000410545:E297X	E	-	1	0	ZNF814	63077681	0.000000	0.05858	0.000000	0.03702	0.378000	0.30076	-0.792000	0.04594	-0.856000	0.04120	0.121000	0.15741	GAA	.	.	.	weak		0.363	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		A	58385869	C	A	58385869	4	1	4	1	0	0	0	0	0	1	0	0	18188	835	29	4	1682	4	ZNF814	19	58385869	Nonsense_Mutation	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10	1350134	58385869	743114	135	388											
CST2	1470	hgsc.bcm.edu	37	chr20	23805942	23805942	+	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	cacctctatgtcgaagaagtAattcaccccgcccacgatct	11	9	6	15	3	3	1	1	0	2	1	4	3	3	1	4	0	0	1	4	0	4	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr20:23805942A>T	ENST00000304725.2	-	2	317	c.247T>A	c.(247-249)Tac>Aac	p.Y83N		NM_001322.2	NP_001313.1	P09228	CYTT_HUMAN	cystatin SA	83					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)	extracellular space (GO:0005615)	cysteine-type endopeptidase inhibitor activity (GO:0004869)	p.Y83D(1)		breast(1)|cervix(1)|large_intestine(1)|liver(1)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	10						TCGAAGAAGTAATTCACCCCG	0.537																																					p.Y83N	Pancreas(193;496 3017 22514 29918)	Atlas-SNP	.											CST2,face,carcinoma,0,1	CST2	39	.	1	Substitution - Missense(1)	skin(1)	c.T247A						PASS	.						274	212	233					20																	23805942		2203	4300	6503	SO:0001583	missense	1470	exon2			AGAAGTAATTCAC	M19671	CCDS13161.1	20p11.2	2007-11-29			ENSG00000170369	ENSG00000170369			2474	protein-coding gene	gene with protein product	"cystatin 2"	123856					Standard	NM_001322		Approved		uc002wtq.1	P09228	OTTHUMG00000032086	ENST00000304725.2:c.247T>A	chr20.hg19:g.23805942A>T	ENSP00000307540:p.Tyr83Asn	58.0	0.0	.		58.0	24.0	.	NM_001322	Q9UCQ7	Missense_Mutation	SNP	ENST00000304725.2	hg19	CCDS13161.1	.	.	.	.	.	.	.	.	.	.	A	12.88	2.069071	0.36470	.	.	ENSG00000170369	ENST00000304725	T	0.43688	0.94	2.36	2.36	0.29203	Proteinase inhibitor I25, cystatin, conserved site (1);Proteinase inhibitor I25, cystatin (2);	0.075028	0.56097	U	0.000033	T	0.69744	0.3145	H	0.95982	3.75	0.09310	N	0.999996	D	0.89917	1.0	D	0.91635	0.999	T	0.60591	-0.7233	10	0.87932	D	0	.	6.5923	0.22654	1.0:0.0:0.0:0.0	.	83	P09228	CYTT_HUMAN	N	83	ENSP00000307540:Y83N	ENSP00000307540:Y83N	Y	-	1	0	CST2	23753942	0.227000	0.23707	0.027000	0.17364	0.002000	0.02628	2.917000	0.48821	1.087000	0.41251	0.254000	0.18369	TAC	.	.	.	none		0.537	CST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078352.2			T	23805942	A	T	23805942	3	4	4	1	0	0	0	0	1	0	0	0	3974	362	13	5	186	5	CST2	20	23805942	Missense_Mutation	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10		23805942	39219578	136	389											
RNF114	55905	hgsc.bcm.edu	37	chr20	48562762	48562762	+	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	tgtggaacactgcaaattatTccatagcacggataccaaat	15	10	7	9	1	0	0	0	0	0	0	1	2	1	2	2	2	4	2	2	2	6	4			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr20:48562762T>A	ENST00000244061.2	+	4	490	c.488T>A	c.(487-489)tTc>tAc	p.F163Y		NM_018683.3	NP_061153.1	Q9Y508	RN114_HUMAN	ring finger protein 114	163					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(1)|ovary(1)	5						TGCAAATTATTCCATAGCACG	0.393																																					p.F163Y		Atlas-SNP	.											.	RNF114	9	.	0			c.T488A						PASS	.						96	81	86					20																	48562762		2203	4300	6503	SO:0001583	missense	55905	exon4			AATTATTCCATAG	AF265215	CCDS33482.1	20q13	2013-01-09	2008-06-16	2008-06-16	ENSG00000124226	ENSG00000124226		"RING-type (C3HC4) zinc fingers"	13094	protein-coding gene	gene with protein product		612451	"zinc finger protein 313"	ZNF313		18364390	Standard	NM_018683		Approved	PSORS12	uc002xux.3	Q9Y508	OTTHUMG00000032709	ENST00000244061.2:c.488T>A	chr20.hg19:g.48562762T>A	ENSP00000244061:p.Phe163Tyr	98.0	0.0	.		110.0	29.0	.	NM_018683	B2RDQ9|B4DWY5|E1P627|Q6N0B0	Missense_Mutation	SNP	ENST00000244061.2	hg19	CCDS33482.1	.	.	.	.	.	.	.	.	.	.	T	2.824	-0.244101	0.05906	.	.	ENSG00000124226	ENST00000449816;ENST00000244061	T	0.79352	-1.26	5.97	-0.203	0.13204	Zinc finger, C2H2-like (1);Drought induced 19/ RING finger protein 114 (1);	1.127120	0.06197	N	0.682425	T	0.50888	0.1642	N	0.11789	0.175	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42498	-0.9448	10	0.02654	T	1	4.9286	0.9014	0.01275	0.2089:0.2819:0.1149:0.3943	.	163;163	Q9Y508-2;Q9Y508	.;RN114_HUMAN	Y	163	ENSP00000244061:F163Y	ENSP00000244061:F163Y	F	+	2	0	RNF114	47996169	0.000000	0.05858	0.011000	0.14972	0.973000	0.67179	0.164000	0.16542	0.061000	0.16311	-0.242000	0.12053	TTC	.	.	.	none		0.393	RNF114-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079663.1	NM_018683		A	48562762	T	A	48562762	3	1	4	1	0	0	0	0	1	0	0	0	13442	1783	62	5	502	5	RNF114	20	48562762	Missense_Mutation	SNP	T	TCGA-2Z-A9J3-01A-12D-A382-10	24756820	48562762	14462758	137	390											
IFNAR1	3454	hgsc.bcm.edu	37	chr21	34707892	34707892	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatagatgacaactttatcCtgaggtggaacaggagcgat	13	10	11	7	1	1	3	1	2	0	1	2	6	2	5	1	3	3	0	1	3	4	3			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr21:34707892C>T	ENST00000270139.3	+	2	291	c.139C>T	c.(139-141)Ctg>Ttg	p.L47L	IFNAR1_ENST00000442357.2_Silent_p.L47L|IFNAR1_ENST00000493503.1_3'UTR|IFNAR1_ENST00000416947.2_5'UTR	NM_000629.2	NP_000620.2	P17181	INAR1_HUMAN	interferon (alpha, beta and omega) receptor 1	47	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)"	CAACTTTATCCTGAGGTGGAA	0.353																																					p.L47L	Esophageal Squamous(73;817 1211 32990 35667 42746)	Atlas-SNP	.											.	IFNAR1	44	.	0			c.C139T						PASS	.						135	122	126					21																	34707892		2203	4300	6503	SO:0001819	synonymous_variant	3454	exon2			TTTATCCTGAGGT		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.139C>T	chr21.hg19:g.34707892C>T		111.0	0.0	.		112.0	45.0	.	NM_000629	B2R6L9|B4DNT3|D3DSF0|Q53GW9|Q53H11|Q6PKD7|Q7M4L2|Q8WTZ2	Silent	SNP	ENST00000270139.3	hg19	CCDS13624.1																																																																																			.	.	.	none		0.353	IFNAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139823.4			T	34707892	C	T	34707892	2	4	4	1	0	0	0	0	0	0	0	1	7551	680	24	2		2	IFNAR1	21	34707892	Silent	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10		34707892	13422003	138	391											
DYRK1A	1859	hgsc.bcm.edu	37	chr21	38865374	38865374	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagaggtgctactgggaaTgccttatgaccttgccattg	8	12	11	10	0	0	2	0	1	0	1	1	3	1	3	4	2	4	1	4	2	3	4			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr21:38865374T>C	ENST00000398960.2	+	7	1082	c.1007T>C	c.(1006-1008)aTg>aCg	p.M336T	DYRK1A_ENST00000338785.3_Missense_Mutation_p.M336T|DYRK1A_ENST00000321219.8_Missense_Mutation_p.M336T|DYRK1A_ENST00000339659.4_Missense_Mutation_p.M327T|DYRK1A_ENST00000455387.2_Missense_Mutation_p.M108T|DYRK1A_ENST00000451934.1_Missense_Mutation_p.M336T|DYRK1A_ENST00000398956.2_Missense_Mutation_p.M336T	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	336	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						CTACTGGGAATGCCTTATGAC	0.398																																					p.M336T	Melanoma(114;464 1602 31203 43785 45765)	Atlas-SNP	.											.	DYRK1A	85	.	0			c.T1007C						PASS	.						171	157	161					21																	38865374		2203	4300	6503	SO:0001583	missense	1859	exon7			TGGGAATGCCTTA	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.1007T>C	chr21.hg19:g.38865374T>C	ENSP00000381932:p.Met336Thr	65.0	0.0	.		83.0	34.0	.	NM_001396	O60769|Q92582|Q92810|Q9UNM5	Missense_Mutation	SNP	ENST00000398960.2	hg19	CCDS42925.1	.	.	.	.	.	.	.	.	.	.	T	15.65	2.895956	0.52121	.	.	ENSG00000157540	ENST00000338785;ENST00000339659;ENST00000321219;ENST00000451934;ENST00000398960;ENST00000398956;ENST00000455387	T;T;T;T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05	5.76	5.76	0.90799	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	0.48892	0.1525	N	0.20766	0.605	0.80722	D	1	B;B;B;B;B	0.18166	0.026;0.026;0.0;0.0;0.026	B;B;B;B;B	0.21360	0.034;0.034;0.003;0.002;0.034	T	0.40156	-0.9578	10	0.24483	T	0.36	.	16.3786	0.83431	0.0:0.0:0.0:1.0	.	336;336;336;327;336	Q13627-3;Q13627-4;Q13627;Q13627-2;Q13627-5	.;.;DYR1A_HUMAN;.;.	T	336;327;336;336;336;336;108	ENSP00000342690:M336T;ENSP00000340373:M327T;ENSP00000319032:M336T;ENSP00000416089:M336T;ENSP00000381932:M336T;ENSP00000381929:M336T;ENSP00000407854:M108T	ENSP00000319032:M336T	M	+	2	0	DYRK1A	37787244	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.997000	0.88414	2.323000	0.78572	0.528000	0.53228	ATG	.	.	.	none		0.398	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1	NM_001396		C	38865374	T	C	38865374	3	2	4	1	0	0	0	0	1	0	0	0	4856	1464	51	3	1033	3	DYRK1A	21	38865374	Missense_Mutation	SNP	T	TCGA-2Z-A9J3-01A-12D-A382-10	4157482	38865374	9264521	139	392											
MORC2	22880	hgsc.bcm.edu	37	chr22	31331124	31331124	+	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	aggtaaagggggcgaccgagGacgctgaggtctacgcacag	11	4	17	9	4	1	1	0	1	1	0	1	4	1	2	1	5	1	3	1	5	3	2			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr22:31331124G>A	ENST00000397641.3	-	19	2245	c.1837C>T	c.(1837-1839)Cct>Tct	p.P613S	MORC2-AS1_ENST00000441558.1_RNA|MORC2_ENST00000469915.1_5'Flank|MORC2_ENST00000215862.4_Missense_Mutation_p.P551S			Q9Y6X9	MORC2_HUMAN	MORC family CW-type zinc finger 2	613						cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	21						GGCGACCGAGGACGCTGAGGT	0.587																																					p.P551S		Atlas-SNP	.											.	MORC2	78	.	0			c.C1651T						PASS	.						33	35	34					22																	31331124		2203	4300	6503	SO:0001583	missense	22880	exon20			ACCGAGGACGCTG	AB020659	CCDS33636.1	22q12.2	2005-06-15	2005-06-15	2005-06-15	ENSG00000133422	ENSG00000133422			23573	protein-coding gene	gene with protein product			"zinc finger, CW-type with coiled-coil domain 1", "zinc finger, CW type with coiled-coil domain 1"	ZCWCC1		14607086	Standard	XM_005261391		Approved	ZCW3, KIAA0852, AC004542.C22.1	uc003aje.1	Q9Y6X9	OTTHUMG00000151193	ENST00000397641.3:c.1837C>T	chr22.hg19:g.31331124G>A	ENSP00000380763:p.Pro613Ser	98.0	0.0	.		90.0	43.0	.	NM_014941	B2RNB1|Q9UF28|Q9Y6V2	Missense_Mutation	SNP	ENST00000397641.3	hg19		.	.	.	.	.	.	.	.	.	.	G	22.1	4.246432	0.80024	.	.	ENSG00000133422	ENST00000397641;ENST00000215862	T;T	0.13657	2.58;2.57	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.36963	0.0986	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.00870	-1.1533	10	0.32370	T	0.25	.	18.1401	0.89637	0.0:0.0:1.0:0.0	.	613	Q9Y6X9	MORC2_HUMAN	S	613;551	ENSP00000380763:P613S;ENSP00000215862:P551S	ENSP00000215862:P551S	P	-	1	0	MORC2	29661124	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.984000	0.88150	2.726000	0.93360	0.655000	0.94253	CCT	.	.	.	none		0.587	MORC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321710.2	NM_014941		A	31331124	G	A	31331124	3	1	4	1	0	0	0	0	1	0	0	0	9709	1174	41	2	1293	2	MORC2	22	31331124	Missense_Mutation	SNP	G	TCGA-2Z-A9J3-01A-12D-A382-10		31331124	19973442	140	393											
MYH9	4627	hgsc.bcm.edu	37	chr22	36702564	36702570	+	Frame_Shift_Del	DEL	TGCGGAA	TGCGGAA	-																															cttgtaaagctgccccacagTgcggaacatgcccttccgcg																										TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	TGCGGAA	TGCGGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr22:36702564_36702570delTGCGGAA	ENST00000216181.5	-	16	2157_2163	c.1927_1933delTTCCGCA	c.(1927-1935)ttccgcactfs	p.FRT643fs		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	643	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						TGCCCCACAGTGCGGAACATGCCCTTC	0.618			T	ALK	ALCL		"Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"		Hereditary Macrothrombocytopenia, MYH9-associated																												p.643_645del		Atlas-Indel,Pindel	.		Dom	yes		22	22q13.1	4627	"myosin, heavy polypeptide 9, non-muscle"	yes	L	.	MYH9	225	.	0			c.1928_1934del						PASS	.																																			SO:0001589	frameshift_variant	4627	exon16	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	.		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.1927_1933delTTCCGCA	chr22.hg19:g.36702564_36702570delTGCGGAA	ENSP00000216181:p.Phe643fs	89.0	0.0	0		57.0	17.0	0.298246	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Frame_Shift_Del	DEL	ENST00000216181.5	hg19	CCDS13927.1																																																																																			.	.	.	none		0.618	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473		-	36702570	TGCGGAA	-	36702564	7	5	4	1	0	1	0	1	0	0	0	0	10049	1696	59	0	4053	0	MYH9	22	36702564	Frame_Shift_Del	DEL	TGCGGAA	TCGA-2Z-A9J3-01A-12D-A382-10	5371440	36702564	14602002	141	394											
OFD1	8481	hgsc.bcm.edu	37	chrX	13779314	13779314	+	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	tccctcctgtctccagccctCcggagcagaaagtggggtaa	8	8	11	14	1	1	1	0	0	1	1	5	2	4	2	5	3	2	2	5	3	2	1			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chrX:13779314C>A	ENST00000340096.6	+	17	2698	c.2371C>A	c.(2371-2373)Ccg>Acg	p.P791T	OFD1_ENST00000380567.1_Missense_Mutation_p.P651T|OFD1_ENST00000490265.1_3'UTR|OFD1_ENST00000380550.3_Missense_Mutation_p.P751T	NM_003611.2	NP_003602.1	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1	791	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						CTCCAGCCCTCCGGAGCAGAA	0.488																																					p.P791T		Atlas-SNP	.											.	OFD1	109	.	0			c.C2371A						PASS	.						105	81	89					X																	13779314		2203	4300	6503	SO:0001583	missense	8481	exon17			AGCCCTCCGGAGC	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.2371C>A	chrX.hg19:g.13779314C>A	ENSP00000344314:p.Pro791Thr	29.0	0.0	.		44.0	40.0	.	NM_003611	B9ZVU5|O75666|Q4VAK4	Missense_Mutation	SNP	ENST00000340096.6	hg19	CCDS14157.1	.	.	.	.	.	.	.	.	.	.	C	0.006	-2.112891	0.00353	.	.	ENSG00000046651	ENST00000380550;ENST00000340096;ENST00000380567	D;D;D	0.95622	-3.76;-3.76;-1.63	5.03	-1.66	0.08265	.	0.918676	0.09274	N	0.824684	D	0.90463	0.7013	L	0.56769	1.78	0.09310	N	1	B;P;B;B;B	0.38370	0.004;0.628;0.021;0.007;0.004	B;B;B;B;B	0.34489	0.005;0.184;0.009;0.009;0.005	T	0.79300	-0.1860	10	0.13853	T	0.58	4.1682	4.147	0.10220	0.3081:0.4058:0.2115:0.0746	.	791;751;459;651;791	A8K2T9;O75665-3;B4DLQ3;A6NF31;O75665	.;.;.;.;OFD1_HUMAN	T	751;791;651	ENSP00000369923:P751T;ENSP00000344314:P791T;ENSP00000369941:P651T	ENSP00000344314:P791T	P	+	1	0	OFD1	13689235	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.462000	0.06704	-1.265000	0.02449	-2.646000	0.00150	CCG	.	.	.	none		0.488	OFD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055808.1	NM_003611		A	13779314	C	A	13779314	3	1	4	1	0	0	0	0	1	0	0	0	10845	855	30	4	2437	4	OFD1	23	13779314	Missense_Mutation	SNP	C	TCGA-2Z-A9J3-01A-12D-A382-10		13779314	141491246	142	395											
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-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	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	chrX.hg19:g.66765164A>T	ENSP00000363822:p.Gln59Leu	73.0	0.0	.		69.0	8.0	.	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	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	4	1	0	0	0	0	1	0	0	0	836	188	7	5	178	5	AR	23	66765164	Missense_Mutation	SNP	A	TCGA-2Z-A9J3-01A-12D-A382-10	52985850	66765164	88505396	143	396											
PRAMEF1	65121	hgsc.bcm.edu	37	chr1	12854459	12854459	+	Missense_Mutation	SNP	T	T	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	aagaaagcttcgttgttaccTgaaggagatgaagaatcttc	14	11	10	6	1	1	5	0	2	1	3	3	6	1	5	1	1	2	3	1	1	6	4			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr1:12854459T>G	ENST00000332296.7	+	3	786	c.683T>G	c.(682-684)cTg>cGg	p.L228R	PRAMEF1_ENST00000400814.3_5'Flank	NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	228					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)					cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35	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;0.00812)|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)		CGTTGTTACCTGAAGGAGATG	0.413																																					p.L228R		Atlas-SNP	.											.	PRAMEF1	78	.	0			c.T683G						PASS	.						199	196	197					1																	12854459		2202	4293	6495	SO:0001583	missense	65121	exon3			GTTACCTGAAGGA	AL049686	CCDS148.1	1p36.21	2013-01-17			ENSG00000116721	ENSG00000116721		"-"	28840	protein-coding gene	gene with protein product							Standard	NM_023013		Approved		uc001auj.2	O95521	OTTHUMG00000001928	ENST00000332296.7:c.683T>G	chr1.hg19:g.12854459T>G	ENSP00000332134:p.Leu228Arg	211.0	0.0	.		209.0	51.0	.	NM_023013	Q9UQP2	Missense_Mutation	SNP	ENST00000332296.7	hg19	CCDS148.1	.	.	.	.	.	.	.	.	.	.	.	11.91	1.778239	0.31502	.	.	ENSG00000116721	ENST00000332296	T	0.01279	5.06	1.61	1.61	0.23674	.	0.000000	0.64402	D	0.000019	T	0.07098	0.0180	M	0.86953	2.85	0.18873	N	0.999984	D	0.89917	1.0	D	0.97110	1.0	T	0.04811	-1.0925	10	0.87932	D	0	.	5.2932	0.15739	0.0:0.0:0.0:1.0	.	228	O95521	PRAM1_HUMAN	R	228	ENSP00000332134:L228R	ENSP00000332134:L228R	L	+	2	0	PRAMEF1	12777046	0.002000	0.14202	0.009000	0.14445	0.014000	0.08584	1.259000	0.32956	0.987000	0.38709	0.358000	0.22013	CTG	.	.	.	none		0.413	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005458.1	NM_023013		G	12854459	T	G	12854459	3	3	5	1	0	0	0	0	1	0	0	0	12435	1580	55	5	689	5	PRAMEF1	1	12854459	Missense_Mutation	SNP	T	TCGA-2Z-A9J5-01A-21D-A382-10		12854459	236396162	1	397											
RHCE	6006	hgsc.bcm.edu	37	chr1	25718532	25718532	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgctctctgatcattatccTccgttcccttgggtagaggc	5	15	9	12	1	2	2	1	1	1	1	6	2	5	2	3	2	1	3	3	2	2	5			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr1:25718532T>C	ENST00000294413.7	-	4	645	c.587A>G	c.(586-588)gAg>gGg	p.E196G	RHCE_ENST00000346452.4_Intron|RHCE_ENST00000455194.1_Intron|RHCE_ENST00000374352.2_Missense_Mutation_p.E180G|RHCE_ENST00000413854.1_Missense_Mutation_p.E196G|RHCE_ENST00000243186.6_Missense_Mutation_p.E196G|RHCE_ENST00000349438.4_Missense_Mutation_p.E196G|RHCE_ENST00000425135.1_Missense_Mutation_p.E196G|RHCE_ENST00000349320.3_Missense_Mutation_p.E180G|RHCE_ENST00000340849.4_Intron	NM_020485.4	NP_065231	P18577	RHCE_HUMAN	Rh blood group, CcEe antigens	196						integral component of plasma membrane (GO:0005887)	ammonium transmembrane transporter activity (GO:0008519)			endometrium(8)|large_intestine(6)|lung(3)	17		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0426)|OV - Ovarian serous cystadenocarcinoma(117;2.12e-27)|Colorectal(126;3.16e-08)|COAD - Colon adenocarcinoma(152;1.72e-06)|STAD - Stomach adenocarcinoma(196;0.00035)|KIRC - Kidney renal clear cell carcinoma(1967;0.000769)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|GBM - Glioblastoma multiforme(114;0.00458)|READ - Rectum adenocarcinoma(331;0.0649)		ATCATTATCCTCCGTTCCCTT	0.537																																					p.E196G		Atlas-SNP	.											.	RHCE	36	.	0			c.A587G						PASS	.						285	226	246					1																	25718532		2203	4300	6503	SO:0001583	missense	6006	exon4			TTATCCTCCGTTC	BC075081	CCDS30634.1, CCDS30635.1, CCDS30636.1, CCDS30637.1	1p36.11	2014-09-17	2006-02-23		ENSG00000188672	ENSG00000188672		"CD molecules", "Blood group antigens"	10008	protein-coding gene	gene with protein product		111700	"Rhesus blood group, CcEe antigens"	RH		8220426	Standard	NM_138618		Approved	CD240CE	uc001bkf.3	P18577	OTTHUMG00000007650	ENST00000294413.7:c.587A>G	chr1.hg19:g.25718532T>C	ENSP00000294413:p.Glu196Gly	160.0	0.0	.		196.0	68.0	.	NM_138618	A7DW68|B7UDF3|B7UDF4|B7UDF5|B7UDF6|B7UDF7|B7UDF8|B7UDF9|B7UDG0|B7UDG1|B7UDG2|B7UDG3|Q02163|Q02164|Q02165|Q16160|Q2MJW0|Q2VC86|Q3LTM6|Q6AZX5|Q6J2U3|Q7RU06|Q8IZT2|Q8IZT3|Q8IZT4|Q8IZT5|Q9UD13|Q9UD14|Q9UD15|Q9UD16|Q9UD73|Q9UD74|Q9UEC2|Q9UEC3|Q9UPN0	Missense_Mutation	SNP	ENST00000294413.7	hg19	CCDS30635.1	.	.	.	.	.	.	.	.	.	.	t	10.89	1.478742	0.26511	.	.	ENSG00000188672	ENST00000413854;ENST00000374352;ENST00000243186;ENST00000425135;ENST00000349320;ENST00000294413;ENST00000447203;ENST00000349438	T;T;T;T;T;T;T	0.22134	1.97;1.97;1.97;1.97;1.97;1.97;1.97	3.99	1.46	0.22682	Ammonium transporter AmtB-like (3);	1.495710	0.03510	N	0.219354	T	0.31670	0.0804	L	0.49699	1.58	0.09310	N	1	B;B;P	0.39809	0.004;0.004;0.689	B;B;P	0.51657	0.033;0.02;0.676	T	0.13019	-1.0525	10	0.40728	T	0.16	-0.1541	3.4811	0.07602	0.2098:0.1119:0.0:0.6784	.	180;196;196	Q5VSJ9;Q5VSJ8;P18577	.;.;RHCE_HUMAN	G	196;180;196;196;180;196;196;196	ENSP00000415417:E196G;ENSP00000363472:E180G;ENSP00000243186:E196G;ENSP00000392809:E196G;ENSP00000311185:E180G;ENSP00000294413:E196G;ENSP00000334570:E196G	ENSP00000243186:E196G	E	-	2	0	RHCE	25591119	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-0.027000	0.12371	0.150000	0.19136	0.459000	0.35465	GAG	.	.	.	none		0.537	RHCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020312.2	NM_020485		C	25718532	T	C	25718532	3	2	5	1	0	0	0	0	1	0	0	0	13338	1551	54	3	694	3	RHCE	1	25718532	Missense_Mutation	SNP	T	TCGA-2Z-A9J5-01A-21D-A382-10	12864073	25718532	223532089	2	398											
AIM1L	55057	hgsc.bcm.edu	37	chr1	26665868	26665868	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctctgttagcttcacttgcTcccccttgaggccctcctca	4	13	6	18	0	3	1	2	1	1	0	5	1	5	1	5	1	2	3	5	1	1	4			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr1:26665868T>C	ENST00000308182.5	-	5	551	c.122A>G	c.(121-123)gAg>gGg	p.E41G	AIM1L_ENST00000522993.1_5'Flank|AIM1L_ENST00000527815.1_Missense_Mutation_p.E212G			Q8N1P7	AIM1L_HUMAN	absent in melanoma 1-like	41	Beta/gamma crystallin 'Greek key' 1. {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)		CTTCACTTGCTCCCCCTTGAG	0.552																																					p.E1086G		Atlas-SNP	.											.	AIM1L	98	.	0			c.A3257G						PASS	.						68	74	72					1																	26665868		2203	4300	6503	SO:0001583	missense	55057	exon6			ACTTGCTCCCCCT			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.122A>G	chr1.hg19:g.26665868T>C	ENSP00000310435:p.Glu41Gly	80.0	0.0	.		93.0	4.0	.	NM_001039775	B2RNG3|Q5T137|Q5T150	Missense_Mutation	SNP	ENST00000308182.5	hg19		.	.	.	.	.	.	.	.	.	.	T	6.765	0.510112	0.12883	.	.	ENSG00000176092	ENST00000527815;ENST00000308182	T;T	0.76839	-1.05;-1.05	5.26	1.53	0.23141	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.358794	0.28940	N	0.013650	T	0.69780	0.3149	M	0.64997	1.995	0.54753	D	0.999987	B	0.34103	0.437	B	0.33846	0.171	T	0.61811	-0.6986	10	0.31617	T	0.26	.	7.8916	0.29682	0.1101:0.0:0.3649:0.525	.	41	Q8N1P7	AIM1L_HUMAN	G	212;41	ENSP00000433931:E212G;ENSP00000310435:E41G	ENSP00000310435:E41G	E	-	2	0	AIM1L	26538455	1.000000	0.71417	0.883000	0.34634	0.302000	0.27658	2.050000	0.41297	0.390000	0.25115	-2.293000	0.00265	GAG	.	.	.	none		0.552	AIM1L-201	KNOWN	basic	protein_coding	protein_coding		NM_001039775.2		C	26665868	T	C	26665868	3	2	5	1	0	0	0	0	1	0	0	0	431	1551	54	3	1788	3	AIM1L	1	26665868	Missense_Mutation	SNP	T	TCGA-2Z-A9J5-01A-21D-A382-10	947336	26665868	222584753	3	399											
ARID1A	8289	hgsc.bcm.edu	37	chr1	27056349	27056349	+	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	tgggcggcctctcttatacaCagcaggtagatggtgattgt	8	12	13	8	1	1	2	0	1	1	1	2	2	1	2	1	4	2	2	1	4	3	4			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr1:27056349C>T	ENST00000324856.7	+	2	1716	c.1345C>T	c.(1345-1347)Cag>Tag	p.Q449*	ARID1A_ENST00000374152.2_Nonsense_Mutation_p.Q66*|ARID1A_ENST00000457599.2_Nonsense_Mutation_p.Q449*	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	449					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)		CTCTTATACACAGCAGGTAGA	0.557			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.Q449X		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.C1345T						PASS	.						33	36	35					1																	27056349		2203	4300	6503	SO:0001587	stop_gained	8289	exon2			TATACACAGCAGG	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.1345C>T	chr1.hg19:g.27056349C>T	ENSP00000320485:p.Gln449*	216.0	0.0	.		241.0	66.0	.	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Nonsense_Mutation	SNP	ENST00000324856.7	hg19	CCDS285.1	.	.	.	.	.	.	.	.	.	.	C	37	6.225161	0.97390	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000524572;ENST00000374152	.	.	.	5.94	5.94	0.96194	.	0.056021	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	-6.9651	20.3771	0.98923	0.0:1.0:0.0:0.0	.	.	.	.	X	449;449;66;66	.	ENSP00000320485:Q449X	Q	+	1	0	ARID1A	26928936	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.217000	0.77982	2.824000	0.97209	0.650000	0.86243	CAG	.	.	.	none		0.557	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		T	27056349	C	T	27056349	4	4	5	1	0	0	0	0	0	1	0	0	913	479	17	2	1351	2	ARID1A	1	27056349	Nonsense_Mutation	SNP	C	TCGA-2Z-A9J5-01A-21D-A382-10	390481	27056349	222194272	4	400											
AGL	178	hgsc.bcm.edu	37	chr1	100340327	100340327	+	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	cagacggtttggctgtactgTagatatgaacattgcactaa	12	12	10	7	1	0	3	0	1	0	2	0	3	0	3	0	2	3	5	0	2	5	6			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr1:100340327T>A	ENST00000294724.4	+	8	1521	c.1043T>A	c.(1042-1044)gTa>gAa	p.V348E	AGL_ENST00000361522.4_Missense_Mutation_p.V331E|AGL_ENST00000370161.2_Missense_Mutation_p.V332E|AGL_ENST00000477753.1_3'UTR|AGL_ENST00000361302.3_Missense_Mutation_p.V332E|AGL_ENST00000370165.3_Missense_Mutation_p.V348E|AGL_ENST00000370163.3_Missense_Mutation_p.V348E|AGL_ENST00000361915.3_Missense_Mutation_p.V348E	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	348					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)		GGCTGTACTGTAGATATGAAC	0.338																																					p.V348E		Atlas-SNP	.											.	AGL	137	.	0			c.T1043A						PASS	.						141	124	130					1																	100340327		2203	4300	6503	SO:0001583	missense	178	exon8			GTACTGTAGATAT	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.1043T>A	chr1.hg19:g.100340327T>A	ENSP00000294724:p.Val348Glu	100.0	0.0	.		106.0	19.0	.	NM_000644	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Missense_Mutation	SNP	ENST00000294724.4	hg19	CCDS759.1	.	.	.	.	.	.	.	.	.	.	T	18.30	3.594592	0.66219	.	.	ENSG00000162688	ENST00000361915;ENST00000370165;ENST00000370163;ENST00000294724;ENST00000361302;ENST00000370161;ENST00000361522	D;D;D;D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04;-2.04;-2.04;-2.04	4.84	4.84	0.62591	Glycoside hydrolase, superfamily (1);	0.137739	0.48767	D	0.000175	D	0.90280	0.6960	M	0.83012	2.62	0.80722	D	1	D;D;P	0.53619	0.961;0.961;0.796	P;P;P	0.61940	0.896;0.896;0.701	D	0.92046	0.5644	10	0.87932	D	0	.	14.6928	0.69098	0.0:0.0:0.0:1.0	.	331;332;348	P35573-2;P35573-3;P35573	.;.;GDE_HUMAN	E	348;348;348;348;332;332;331	ENSP00000355106:V348E;ENSP00000359184:V348E;ENSP00000359182:V348E;ENSP00000294724:V348E;ENSP00000354971:V332E;ENSP00000359180:V332E;ENSP00000354635:V331E	ENSP00000294724:V348E	V	+	2	0	AGL	100112915	1.000000	0.71417	0.612000	0.29024	0.342000	0.28953	6.856000	0.75450	1.933000	0.56026	0.477000	0.44152	GTA	.	.	.	none		0.338	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028		A	100340327	T	A	100340327	3	1	5	1	0	0	0	0	1	0	0	0	384	1638	57	5	1138	5	AGL	1	100340327	Missense_Mutation	SNP	T	TCGA-2Z-A9J5-01A-21D-A382-10	73283978	100340327	148910294	5	401											
RPTN	126638	hgsc.bcm.edu	37	chr1	152128604	152128604	+	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	agtgggaactctggccttgtCtgtccgtctgactgtagtgg	5	13	14	9	1	3	1	0	1	3	0	4	2	4	2	2	3	1	1	2	3	2	2			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr1:152128604C>T	ENST00000316073.3	-	3	1035	c.971G>A	c.(970-972)aGa>aAa	p.R324K		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	324	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						CTGGCCTTGTCTGTCCGTCTG	0.493																																					p.R324K		Atlas-SNP	.											.	RPTN	123	.	0			c.G971A						PASS	.						742	647	676					1																	152128604		1568	3582	5150	SO:0001583	missense	126638	exon3			CCTTGTCTGTCCG	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.971G>A	chr1.hg19:g.152128604C>T	ENSP00000317895:p.Arg324Lys	109.0	0.0	.		152.0	41.0	.	NM_001122965	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	hg19	CCDS41397.1	.	.	.	.	.	.	.	.	.	.	c	10.67	1.414408	0.25465	.	.	ENSG00000215853	ENST00000316073	T	0.12879	2.64	4.56	-1.55	0.08558	.	.	.	.	.	T	0.07683	0.0193	L	0.58428	1.81	0.09310	N	1	D	0.76494	0.999	D	0.77557	0.99	T	0.17228	-1.0376	9	0.06099	T	0.92	.	1.7411	0.02952	0.1409:0.4549:0.1381:0.2662	.	324	Q6XPR3	RPTN_HUMAN	K	324	ENSP00000317895:R324K	ENSP00000317895:R324K	R	-	2	0	RPTN	150395228	0.176000	0.23096	0.007000	0.13788	0.295000	0.27426	0.448000	0.21726	-0.262000	0.09392	0.393000	0.25936	AGA	.	.	.	none		0.493	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312		T	152128604	C	T	152128604	3	4	5	1	0	0	0	0	1	0	0	0	13677	913	32	2	1387	2	RPTN	1	152128604	Missense_Mutation	SNP	C	TCGA-2Z-A9J5-01A-21D-A382-10	51788277	152128604	97122017	6	402											
DHX9	1660	hgsc.bcm.edu	37	chr1	182828229	182828229	+	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	atgaattgatgtaccagttgGaacaggatcatgatttgcaa	14	12	10	5	0	1	3	1	3	0	0	1	5	1	5	1	2	3	3	1	2	4	4			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr1:182828229G>A	ENST00000367549.3	+	11	1227	c.1117G>A	c.(1117-1119)Gaa>Aaa	p.E373K		NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	373	MTAD.				ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						GTACCAGTTGGAACAGGATCA	0.378																																					p.E373K	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.G1117A						PASS	.						116	104	108					1																	182828229		1867	4116	5983	SO:0001583	missense	1660	exon11			CAGTTGGAACAGG	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.1117G>A	chr1.hg19:g.182828229G>A	ENSP00000356520:p.Glu373Lys	94.0	0.0	.		93.0	33.0	.	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Missense_Mutation	SNP	ENST00000367549.3	hg19	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	G	16.45	3.125740	0.56721	.	.	ENSG00000135829	ENST00000399175;ENST00000367549	T	0.03580	3.88	5.9	5.9	0.94986	.	0.066463	0.64402	D	0.000009	T	0.03871	0.0109	N	0.19112	0.55	0.58432	D	0.999999	B	0.15719	0.014	B	0.09377	0.004	T	0.55147	-0.8186	10	0.29301	T	0.29	.	18.0703	0.89404	0.0:0.0:1.0:0.0	.	373	Q08211	DHX9_HUMAN	K	373	ENSP00000356520:E373K	ENSP00000356520:E373K	E	+	1	0	DHX9	181094852	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.439000	0.73430	2.786000	0.95864	0.563000	0.77884	GAA	.	.	.	none		0.378	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		A	182828229	G	A	182828229	3	1	5	1	0	0	0	0	1	0	0	0	4518	1175	41	2	1155	2	DHX9	1	182828229	Missense_Mutation	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10	30699625	182828229	66422392	7	403											
CR1	1378	hgsc.bcm.edu	37	chr1	207782641	207782641	+	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	cttccttctctcagtcatatCttgtgagccacctccaacca	8	13	4	16	0	4	1	2	1	2	0	7	1	6	1	5	0	2	0	5	0	2	4			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr1:207782641C>T	ENST00000367049.4	+	37	5903	c.5903C>T	c.(5902-5904)tCt>tTt	p.S1968F	CR1_ENST00000367051.1_Missense_Mutation_p.S1518F|CR1_ENST00000400960.2_Missense_Mutation_p.S1518F|RP11-78B10.2_ENST00000596003.1_RNA|CR1_ENST00000367052.1_Missense_Mutation_p.S1518F|CR1_ENST00000367053.1_Missense_Mutation_p.S1518F|RP11-78B10.2_ENST00000597497.1_RNA	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1518					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						TCAGTCATATCTTGTGAGCCA	0.348																																					p.S1968F		Atlas-SNP	.											.	CR1	354	.	0			c.C5903T						PASS	.						87	84	85					1																	207782641		1871	4106	5977	SO:0001583	missense	1378	exon37			TCATATCTTGTGA	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.5903C>T	chr1.hg19:g.207782641C>T	ENSP00000356016:p.Ser1968Phe	65.0	0.0	.		71.0	20.0	.	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	hg19	CCDS44308.1	.	.	.	.	.	.	.	.	.	.	C	9.427	1.084621	0.20309	.	.	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000534202;ENST00000367049	T;T;T;T;T;T	0.23552	1.9;1.9;1.9;1.9;1.9;1.9	2.66	0.685	0.18009	Complement control module (2);Sushi/SCR/CCP (1);	.	.	.	.	T	0.33847	0.0877	L	0.41492	1.28	0.09310	N	1	P;D;D	0.71674	0.848;0.998;0.995	B;D;P	0.77004	0.247;0.989;0.844	T	0.12863	-1.0531	9	0.59425	D	0.04	.	3.1826	0.06589	0.2595:0.5917:0.0:0.1488	.	1518;1518;1968	Q5SR44;P17927;E9PDY4	.;CR1_HUMAN;.	F	1518;1518;1518;1518;1068;1968	ENSP00000356019:S1518F;ENSP00000356018:S1518F;ENSP00000356020:S1518F;ENSP00000383744:S1518F;ENSP00000436139:S1068F;ENSP00000356016:S1968F	ENSP00000356016:S1968F	S	+	2	0	CR1	205849264	0.075000	0.21258	0.002000	0.10522	0.048000	0.14542	0.375000	0.20518	0.176000	0.19873	0.555000	0.69702	TCT	.	.	.	none		0.348	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573		T	207782641	C	T	207782641	3	4	5	1	0	0	0	0	1	0	0	0	3842	913	32	2	6049	2	CR1	1	207782641	Missense_Mutation	SNP	C	TCGA-2Z-A9J5-01A-21D-A382-10	24954412	207782641	41467980	8	404											
HSD11B1	3290	hgsc.bcm.edu	37	chr1	209907854	209907854	+	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	agctataatatggacagattCataaacaagtaggaactccc	17	9	7	8	0	1	1	1	0	0	1	2	3	2	3	1	2	3	2	1	2	8	6			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr1:209907854C>T	ENST00000367028.2	+	7	1036	c.867C>T	c.(865-867)ttC>ttT	p.F289F	HSD11B1_ENST00000367027.3_Silent_p.F289F|HSD11B1_ENST00000261465.1_Silent_p.F289F	NM_001206741.1	NP_001193670.1	P28845	DHI1_HUMAN	hydroxysteroid (11-beta) dehydrogenase 1	289					glucocorticoid biosynthetic process (GO:0006704)|lung development (GO:0030324)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	11-beta-hydroxysteroid dehydrogenase (NADP+) activity (GO:0070524)|11-beta-hydroxysteroid dehydrogenase [NAD(P)] activity (GO:0003845)			breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(9)	16				OV - Ovarian serous cystadenocarcinoma(81;1.04e-55)|Epithelial(68;1.57e-52)|all cancers(67;1.83e-46)|Colorectal(1306;0.115)	Prednisone(DB00635)	TGGACAGATTCATAAACAAGT	0.433																																					p.F289F		Atlas-SNP	.											.	HSD11B1	35	.	0			c.C867T						PASS	.						88	86	87					1																	209907854		2203	4300	6503	SO:0001819	synonymous_variant	3290	exon7			CAGATTCATAAAC	BC012593	CCDS1489.1	1q32-q41	2011-09-20			ENSG00000117594	ENSG00000117594	1.1.1.146	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	5208	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 26C, member 1"	600713		HSD11B, HSD11		1885595, 19027726	Standard	NM_005525		Approved	SDR26C1	uc001hhk.3	P28845	OTTHUMG00000036481	ENST00000367028.2:c.867C>T	chr1.hg19:g.209907854C>T		52.0	0.0	.		49.0	19.0	.	NM_001206741	B2R9Z1|D3DT89	Silent	SNP	ENST00000367028.2	hg19	CCDS1489.1																																																																																			.	.	.	none		0.433	HSD11B1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088743.2	NM_005525		T	209907854	C	T	209907854	2	4	5	1	0	0	0	0	0	0	0	1	7382	825	29	2		2	HSD11B1	1	209907854	Silent	SNP	C	TCGA-2Z-A9J5-01A-21D-A382-10	2125213	209907854	39342767	9	405											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228506775	228506775	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcgcagcgcctgccacaggaGgcagaggaggtggcacctga	9	4	16	12	2	0	2	0	1	0	1	1	4	0	4	3	5	2	3	3	5	0	0			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr1:228506775G>A	ENST00000422127.1	+	54	14366	c.14322G>A	c.(14320-14322)gaG>gaA	p.E4774E	OBSCN_ENST00000284548.11_Silent_p.E4774E|OBSCN_ENST00000570156.2_Silent_p.E5731E|OBSCN_ENST00000366709.4_Silent_p.E1893E|OBSCN_ENST00000366707.4_Silent_p.E2408E	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4774					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)				TGCCACAGGAGGCAGAGGAGG	0.642																																					p.E5731E		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G17193A						PASS	.						26	31	29					1																	228506775		2199	4289	6488	SO:0001819	synonymous_variant	84033	exon65			ACAGGAGGCAGAG	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.14322G>A	chr1.hg19:g.228506775G>A		135.0	0.0	.		139.0	47.0	.	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	hg19	CCDS58065.1																																																																																			.	.	.	none		0.642	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228506775	G	A	228506775	2	1	5	1	0	0	0	0	0	0	0	1	10819	991	35	2		2	OBSCN	1	228506775	Silent	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10	18598921	228506775	20743846	10	406											
RYR2	6262	hgsc.bcm.edu	37	chr1	237791158	237791159	+	Frame_Shift_Ins	INS	-	-	T																															gtccgatgggctcaggagtcINStgtcattgaagaccccgagc																										TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr1:237791158_237791159insT	ENST00000366574.2	+	41	6535_6536	c.6218_6219insT	c.(6217-6222)tctgtcfs	p.V2074fs	RYR2_ENST00000360064.6_Frame_Shift_Ins_p.V2072fs|RYR2_ENST00000542537.1_Frame_Shift_Ins_p.V2058fs	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2074	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)			GCTCAGGAGTCTGTCATTGAAG	0.49																																					p.S2073fs		Atlas-Indel,Pindel	.											.	RYR2	1273	.	0			c.6218_6219insT						PASS	.																																			SO:0001589	frameshift_variant	6262	exon41			.	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.6219dupT	chr1.hg19:g.237791159_237791159dupT	ENSP00000355533:p.Val2074fs	60.0	0.0	0		87.0	28.0	0.321839	NM_001035	Q15411|Q546N8|Q5T3P2	Frame_Shift_Ins	INS	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.	.	none		0.49	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237791159	-	T	237791158	7	5	5	1	0	1	1	0	0	0	0	0	13782	913	32	0	6380	0	RYR2	1	237791158	Frame_Shift_Ins	INS	-	TCGA-2Z-A9J5-01A-21D-A382-10	9284383	237791158	11459463	11	407											
PLD5	200150	hgsc.bcm.edu	37	chr1	242383316	242383316	+	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	cagggattgccagtccaaacCggcactgccgatatacacgt	11	7	10	13	3	0	0	0	0	0	0	1	2	1	1	4	2	4	1	4	2	3	3	rs552058954	byFrequency	TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr1:242383316C>A	ENST00000536534.2	-	5	950	c.709G>T	c.(709-711)Ggt>Tgt	p.G237C	PLD5_ENST00000427495.1_Missense_Mutation_p.G175C|PLD5_ENST00000442594.2_Missense_Mutation_p.G145C			Q8N7P1	PLD5_HUMAN	phospholipase D family, member 5	237	PLD phosphodiesterase 1.					integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(22)|ovary(6)|skin(3)|urinary_tract(1)	55	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)			CAGTCCAAACCGGCACTGCCG	0.517																																					p.G237C		Atlas-SNP	.											PLD5_ENST00000536534,bladder,carcinoma,0,2	PLD5	216	.	0			c.G709T						PASS	.						114	98	103					1																	242383316		2203	4300	6503	SO:0001583	missense	200150	exon6			CCAAACCGGCACT	AK098092	CCDS1621.1, CCDS1621.2, CCDS55692.1	1q43	2008-02-05			ENSG00000180287	ENSG00000180287			26879	protein-coding gene	gene with protein product							Standard	NM_001195811		Approved	FLJ40773	uc001hzn.2	Q8N7P1	OTTHUMG00000039867	ENST00000536534.2:c.709G>T	chr1.hg19:g.242383316C>A	ENSP00000440896:p.Gly237Cys	103.0	0.0	.		138.0	24.0	.	NM_152666	A1KXV0|B7Z324|Q494U9|Q8NB22	Missense_Mutation	SNP	ENST00000536534.2	hg19	CCDS1621.2	.	.	.	.	.	.	.	.	.	.	C	16.30	3.084149	0.55861	.	.	ENSG00000180287	ENST00000427495;ENST00000442594;ENST00000536534	T;T;T	0.13778	2.56;2.56;2.56	5.58	-1.11	0.09840	Phospholipase D/Transphosphatidylase (1);	0.233267	0.48286	D	0.000186	T	0.15739	0.0379	N	0.22421	0.69	0.26533	N	0.974214	D;D;D	0.65815	0.995;0.975;0.995	P;P;P	0.60949	0.881;0.571;0.667	T	0.08827	-1.0703	10	0.87932	D	0	-2.9252	8.6192	0.33851	0.0:0.348:0.0:0.652	.	145;237;175	Q8N7P1-2;Q8N7P1;Q8N7P1-4	.;PLD5_HUMAN;.	C	175;145;237	ENSP00000401285:G175C;ENSP00000414188:G145C;ENSP00000440896:G237C	ENSP00000401285:G175C	G	-	1	0	PLD5	240449939	0.119000	0.22226	0.141000	0.22245	0.912000	0.54170	0.959000	0.29240	-0.136000	0.11475	-0.136000	0.14681	GGT	.	.	.	none		0.517	PLD5-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397213.2	NM_152666		A	242383316	C	A	242383316	3	1	5	1	0	0	0	0	1	0	0	0	12056	652	23	4	925	4	PLD5	1	242383316	Missense_Mutation	SNP	C	TCGA-2Z-A9J5-01A-21D-A382-10	4592158	242383316	6867305	12	408											
BIRC6	57448	hgsc.bcm.edu	37	chr2	32631577	32631577	+	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	ttgatttaagtgatgatttaCtggaggattcagacagtgaa	13	14	11	3	0	1	5	1	4	0	1	1	7	1	7	0	2	1	0	0	2	3	6			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr2:32631577C>A	ENST00000421745.2	+	9	1563	c.1429C>A	c.(1429-1431)Ctg>Atg	p.L477M		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	477					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)					TGATGATTTACTGGAGGATTC	0.284																																					p.L477M	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.C1429A						PASS	.						69	76	74					2																	32631577		2203	4299	6502	SO:0001583	missense	57448	exon9			GATTTACTGGAGG	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.1429C>A	chr2.hg19:g.32631577C>A	ENSP00000393596:p.Leu477Met	185.0	0.0	.		278.0	121.0	.	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	C	11.51	1.659685	0.29515	.	.	ENSG00000115760	ENST00000421745	T	0.79653	-1.29	5.54	4.66	0.58398	.	0.000000	0.64402	D	0.000014	T	0.73071	0.3540	N	0.22421	0.69	0.38105	D	0.937395	P	0.48162	0.906	P	0.46758	0.526	T	0.75847	-0.3173	10	0.40728	T	0.16	.	12.9011	0.58125	0.0:0.867:0.0:0.133	.	477	Q9NR09	BIRC6_HUMAN	M	477	ENSP00000393596:L477M	ENSP00000393596:L477M	L	+	1	2	BIRC6	32485081	0.991000	0.36638	1.000000	0.80357	0.994000	0.84299	0.299000	0.19138	2.607000	0.88179	0.585000	0.79938	CTG	.	.	.	none		0.284	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		A	32631577	C	A	32631577	3	1	5	1	0	0	0	0	1	0	0	0	1438	564	20	4	1463	4	BIRC6	2	32631577	Missense_Mutation	SNP	C	TCGA-2Z-A9J5-01A-21D-A382-10		32631577	210567796	13	409											
ELMOD3	84173	hgsc.bcm.edu	37	chr2	85617285	85617285	+	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	tgtaatcggcagcagaaggtCatccccgtggtgaacagctt	10	9	12	10	2	1	2	1	1	0	1	3	2	2	2	2	3	3	4	2	3	3	2			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr2:85617285C>A	ENST00000409890.2	+	13	1507	c.840C>A	c.(838-840)gtC>gtA	p.V280V	ELMOD3_ENST00000490508.1_3'UTR|ELMOD3_ENST00000409344.3_Silent_p.V280V|ELMOD3_ENST00000393852.4_Silent_p.V280V|ELMOD3_ENST00000409013.3_Silent_p.V280V|ELMOD3_ENST00000315658.7_Silent_p.V280V			Q96FG2	ELMD3_HUMAN	ELMO/CED-12 domain containing 3	280	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				phagocytosis (GO:0006909)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	12						AGCAGAAGGTCATCCCCGTGG	0.572																																					p.V280V		Atlas-SNP	.											.	ELMOD3	53	.	0			c.C840A						PASS	.						103	84	90					2																	85617285		2203	4300	6503	SO:0001819	synonymous_variant	84173	exon13			GAAGGTCATCCCC	AF258573	CCDS1973.1, CCDS46352.1	2p11.2	2014-01-28	2008-08-14	2008-08-14	ENSG00000115459	ENSG00000115459		"RNA binding motif (RRM) containing"	26158	protein-coding gene	gene with protein product		615427	"RNA binding motif protein 29", "RNA binding motif and ELMO/CED-12 domain 1", "deafness, autosomal recessive 88"	RBM29, RBED1, DFNB88		24039609	Standard	NM_032213		Approved	FLJ21977	uc010ysn.2	Q96FG2	OTTHUMG00000130170	ENST00000409890.2:c.840C>A	chr2.hg19:g.85617285C>A		90.0	0.0	.		175.0	28.0	.	NM_001135022	B8ZZD6|D6W5K4|Q2M1K3|Q2XSU3|Q2XSU4|Q8NAC1|Q8TCK4|Q8WV70|Q8WY75|Q9H6Q8	Silent	SNP	ENST00000409890.2	hg19	CCDS46352.1																																																																																			.	.	.	none		0.572	ELMOD3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329124.1	NM_032213		A	85617285	C	A	85617285	2	1	5	1	0	0	0	0	0	0	0	1	5072	813	29	4		4	ELMOD3	2	85617285	Silent	SNP	C	TCGA-2Z-A9J5-01A-21D-A382-10	52985708	85617285	157582088	14	410											
FOXD4L1	200350	hgsc.bcm.edu	37	chr2	114257882	114257882	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tttgtccccgaccgcgtggaGctactgccccctgctccagc	4	9	10	18	3	0	0	0	0	0	0	2	2	2	1	6	1	5	2	6	1	1	2			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr2:114257882G>A	ENST00000306507.5	+	1	1222	c.1049G>A	c.(1048-1050)aGc>aAc	p.S350N		NM_012184.4	NP_036316.1	Q9NU39	FX4L1_HUMAN	forkhead box D4-like 1	350					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						ACCGCGTGGAGCTACTGCCCC	0.627																																					p.S350N		Atlas-SNP	.											.	FOXD4L1	48	.	0			c.G1049A						PASS	.						18	24	22					2																	114257882		2081	4032	6113	SO:0001583	missense	200350	exon1			CGTGGAGCTACTG	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.1049G>A	chr2.hg19:g.114257882G>A	ENSP00000302756:p.Ser350Asn	165.0	0.0	.		197.0	75.0	.	NM_012184	B3KWN1|B9EGF3	Missense_Mutation	SNP	ENST00000306507.5	hg19	CCDS2117.1	.	.	.	.	.	.	.	.	.	.	.	8.149	0.786951	0.16189	.	.	ENSG00000184492	ENST00000306507	D	0.94650	-3.48	2.37	2.37	0.29283	.	0.222365	0.21869	U	0.067914	D	0.86648	0.5983	N	0.24115	0.695	0.23841	N	0.996697	B	0.29432	0.244	B	0.26864	0.074	T	0.75013	-0.3467	10	0.19590	T	0.45	.	8.2663	0.31815	0.0:0.0:1.0:0.0	.	350	Q9NU39	FX4L1_HUMAN	N	350	ENSP00000302756:S350N	ENSP00000302756:S350N	S	+	2	0	FOXD4L1	113974352	0.973000	0.33851	0.872000	0.34217	0.242000	0.25591	3.399000	0.52586	1.337000	0.45525	0.184000	0.17185	AGC	.	.	.	none		0.627	FOXD4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254148.1	NM_012184		A	114257882	G	A	114257882	3	1	5	1	0	0	0	0	1	0	0	0	6007	971	34	2	1051	2	FOXD4L1	2	114257882	Missense_Mutation	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10	28640597	114257882	128941491	15	411											
TUBA3D	113457	hgsc.bcm.edu	37	chr2	132240242	132240242	+	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	cggaggcctgggcccgcctgGaccataagttcgatctcatg	7	8	13	13	3	1	0	1	0	1	0	3	3	1	2	4	4	0	1	4	4	1	2			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr2:132240242G>A	ENST00000321253.6	+	5	1281	c.1174G>A	c.(1174-1176)Gac>Aac	p.D392N	MZT2A_ENST00000410036.2_5'Flank	NM_080386.3	NP_525125.2	Q13748	TBA3C_HUMAN	tubulin, alpha 3d	392			D -> V (in dbSNP:rs17076703).		'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)		GGCCCGCCTGGACCATAAGTT	0.652																																					p.D392N	Ovarian(137;2059 2432 35543 39401)	Atlas-SNP	.											.	TUBA3D	60	.	0			c.G1174A						PASS	.						106	105	106					2																	132240242		2203	4300	6503	SO:0001583	missense	113457	exon5			CGCCTGGACCATA	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.1174G>A	chr2.hg19:g.132240242G>A	ENSP00000326042:p.Asp392Asn	127.0	0.0	.		161.0	58.0	.	NM_080386	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Missense_Mutation	SNP	ENST00000321253.6	hg19	CCDS33290.1	.	.	.	.	.	.	.	.	.	.	g	12.98	2.099992	0.37048	.	.	ENSG00000075886	ENST00000321253;ENST00000341158	D	0.84070	-1.8	2.41	2.41	0.29592	Tubulin/FtsZ, 2-layer sandwich domain (2);Tubulin, C-terminal (1);Tubulin/FtsZ, C-terminal (1);	0.000000	0.47852	U	0.000215	T	0.75591	0.3870	N	0.21097	0.63	0.46874	D	0.999238	B	0.09022	0.002	B	0.35931	0.214	T	0.73883	-0.3842	10	0.66056	D	0.02	.	10.5186	0.44905	0.0:0.0:1.0:0.0	.	392	Q13748	TBA3C_HUMAN	N	392	ENSP00000326042:D392N	ENSP00000326042:D392N	D	+	1	0	TUBA3D	131956712	1.000000	0.71417	1.000000	0.80357	0.790000	0.44656	7.072000	0.76777	1.334000	0.45468	0.194000	0.17425	GAC	.	.	.	none		0.652	TUBA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331800.2	NM_080386		A	132240242	G	A	132240242	3	1	5	1	0	0	0	0	1	0	0	0	16759	1174	41	2	1192	2	TUBA3D	2	132240242	Missense_Mutation	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10	17982360	132240242	110959131	16	412											
CDK15	65061	hgsc.bcm.edu	37	chr2	202698681	202698681	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtcacctgggagagctcaaActggctgattttggtaagtc	10	11	12	8	0	2	2	2	1	0	1	3	3	2	2	1	3	2	3	1	3	2	3			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr2:202698681A>G	ENST00000374598.4	+	7	717	c.717A>G	c.(715-717)aaA>aaG	p.K239K	CDK15_ENST00000410091.3_Silent_p.K188K|CDK15_ENST00000450471.2_Silent_p.K239K|CDK15_ENST00000488419.1_3'UTR|CDK15_ENST00000434439.1_Silent_p.K239K|CDK15_ENST00000260967.2_Silent_p.K188K			Q96Q40	CDK15_HUMAN	cyclin-dependent kinase 15	239	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|metal ion binding (GO:0046872)			breast(3)|endometrium(2)|kidney(5)|large_intestine(1)|lung(14)|ovary(1)	26					Adenosine triphosphate(DB00171)	GAGAGCTCAAACTGGCTGATT	0.512																																					p.K239K		Atlas-SNP	.											.	CDK15	66	.	0			c.A717G						PASS	.						116	102	107					2																	202698681		2203	4300	6503	SO:0001819	synonymous_variant	65061	exon7			GCTCAAACTGGCT	AB053308	CCDS2350.1, CCDS58746.1, CCDS58747.1	2q33.2	2011-11-08	2009-12-16	2009-12-16	ENSG00000138395	ENSG00000138395		"Cyclin-dependent kinases"	14434	protein-coding gene	gene with protein product			"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 7", "PFTAIRE protein kinase 2"	ALS2CR7, PFTK2		11586298, 16236519, 19884882	Standard	NM_139158		Approved	PFTAIRE2	uc002uyt.3	Q96Q40	OTTHUMG00000132838	ENST00000374598.4:c.717A>G	chr2.hg19:g.202698681A>G		76.0	0.0	.		111.0	19.0	.	NM_001261435	A8K8R9|B8ZZX0|C9J1N8|C9K003|F8W6H8|Q4ZG86|Q53TV1|Q6ZMR9|Q8IUP1	Silent	SNP	ENST00000374598.4	hg19																																																																																				.	.	.	none		0.512	CDK15-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000336053.2			G	202698681	A	G	202698681	2	3	5	1	0	0	0	0	0	0	0	1	3133	40	2	3		3	CDK15	2	202698681	Silent	SNP	A	TCGA-2Z-A9J5-01A-21D-A382-10	70458439	202698681	40500692	17	413											
SCN10A	6336	hgsc.bcm.edu	37	chr3	38739055	38739055	+	Frame_Shift_Del	DEL	C	C	-																															ttcatctgggagtgatgcagCctcctcctcagctctgggca																								rs148979438	byFrequency	TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr3:38739055delC	ENST00000449082.2	-	27	5655	c.5656delG	c.(5656-5658)gctfs	p.A1887fs		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1887					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)	AGTGATGCAGCCTCCTCCTCA	0.498																																					p.A1886fs		Atlas-Indel,Pindel	.											.	SCN10A	359	.	0			c.5657delC						PASS	.						144	131	135					3																	38739055		2203	4300	6503	SO:0001589	frameshift_variant	6336	exon27			.	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.5656delG	chr3.hg19:g.38739055delC	ENSP00000390600:p.Ala1887fs	97.0	0.0	0		148.0	72.0	0.486486	NM_006514	A6NDQ1	Frame_Shift_Del	DEL	ENST00000449082.2	hg19	CCDS33736.1																																																																																			.	.	.	none		0.498	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		-	38739055	C	-	38739055	7	5	5	1	0	1	0	1	0	0	0	0	13925	739	26	0	218	0	SCN10A	3	38739055	Frame_Shift_Del	DEL	C	TCGA-2Z-A9J5-01A-21D-A382-10		38739055	159283375	18	414											
PLXNB1	5364	hgsc.bcm.edu	37	chr3	48464321	48464321	+	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	ctggccatggggctgggcgtGtggtctgagccacagggata	6	8	18	9	1	1	1	0	1	1	0	1	2	1	2	2	6	1	1	2	6	1	1			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr3:48464321G>A	ENST00000358536.4	-	4	1412	c.1143C>T	c.(1141-1143)caC>caT	p.H381H	PLXNB1_ENST00000448774.2_Intron|PLXNB1_ENST00000358459.4_Silent_p.H381H|PLXNB1_ENST00000456774.1_Silent_p.H381H|PLXNB1_ENST00000296440.6_Silent_p.H381H	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	381	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GGCTGGGCGTGTGGTCTGAGC	0.607																																					p.H381H		Atlas-SNP	.											.	PLXNB1	150	.	0			c.C1143T						PASS	.						52	51	51					3																	48464321		2203	4300	6503	SO:0001819	synonymous_variant	5364	exon4			GGGCGTGTGGTCT	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"Plexins"	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.1143C>T	chr3.hg19:g.48464321G>A		124.0	0.0	.		188.0	54.0	.	NM_001130082	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Silent	SNP	ENST00000358536.4	hg19	CCDS2765.1																																																																																			.	.	.	none		0.607	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673		A	48464321	G	A	48464321	2	1	5	1	0	0	0	0	0	0	0	1	12130	1368	48	2		2	PLXNB1	3	48464321	Silent	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10	9725266	48464321	149558109	19	415											
DOCK3	1795	hgsc.bcm.edu	37	chr3	51350329	51350329	+	Frame_Shift_Del	DEL	T	T	-																															ctgttcagcatgtggcagaaTttgggtaggttttttctccc																										TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr3:51350329delT	ENST00000266037.9	+	31	3272	c.3249delT	c.(3247-3249)aatfs	p.N1083fs		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	1083					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)		TGTGGCAGAATTTGGGTAGGT	0.408																																					p.N1083fs		Atlas-Indel,Pindel	.											.	DOCK3	397	.	0			c.3248delA						PASS	.						296	274	281					3																	51350329		1904	4122	6026	SO:0001589	frameshift_variant	1795	exon31			.	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.3249delT	chr3.hg19:g.51350329delT	ENSP00000266037:p.Asn1083fs	82.0	0.0	0		111.0	56.0	0.504505	NM_004947	O15017	Frame_Shift_Del	DEL	ENST00000266037.9	hg19	CCDS46835.1																																																																																			.	.	.	none		0.408	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		-	51350329	T	-	51350329	7	5	5	1	0	1	0	1	0	0	0	0	4690	1490	52	0	3371	0	DOCK3	3	51350329	Frame_Shift_Del	DEL	T	TCGA-2Z-A9J5-01A-21D-A382-10	2886008	51350329	146672101	20	416											
ROBO2	6092	hgsc.bcm.edu	37	chr3	77617480	77617480	+	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	gcagatatcagcccaccagcAcaaggagtggaccacaggca	14	3	11	13	0	1	1	1	0	0	1	1	3	1	3	3	3	2	3	3	3	2	1			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr3:77617480A>T	ENST00000461745.1	+	13	2766	c.1866A>T	c.(1864-1866)gcA>gcT	p.A622A	ROBO2_ENST00000332191.8_Silent_p.A622A|ROBO2_ENST00000487694.3_Silent_p.A638A	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	622					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)		GCCCACCAGCACAAGGAGTGG	0.418																																					p.A622A		Atlas-SNP	.											.	ROBO2	527	.	0			c.A1866T						PASS	.						108	106	106					3																	77617480		2035	4193	6228	SO:0001819	synonymous_variant	6092	exon13			ACCAGCACAAGGA	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.1866A>T	chr3.hg19:g.77617480A>T		79.0	0.0	.		106.0	19.0	.	NM_002942	O43608|Q19AB4|Q19AB5	Silent	SNP	ENST00000461745.1	hg19	CCDS43109.1																																																																																			.	.	.	none		0.418	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		T	77617480	A	T	77617480	2	4	5	1	0	0	0	0	0	0	0	1	13527	146	6	5		5	ROBO2	3	77617480	Silent	SNP	A	TCGA-2Z-A9J5-01A-21D-A382-10	26267151	77617480	120404950	21	417											
CHMP2B	25978	hgsc.bcm.edu	37	chr3	87299049	87299049	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcaggcagttaacaagaagAtggatccacaaaagacatta	18	7	9	7	0	0	3	0	0	0	3	1	4	1	4	1	2	2	3	1	2	6	2			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr3:87299049A>G	ENST00000263780.4	+	4	584	c.346A>G	c.(346-348)Atg>Gtg	p.M116V	CHMP2B_ENST00000471660.1_Missense_Mutation_p.M75V|CHMP2B_ENST00000472024.1_3'UTR|CHMP2B_ENST00000494980.1_Missense_Mutation_p.M86V	NM_014043.3	NP_054762.2	Q9UQN3	CHM2B_HUMAN	charged multivesicular body protein 2B	116					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)		TAACAAGAAGATGGATCCACA	0.284																																					p.M116V		Atlas-SNP	.											.	CHMP2B	28	.	0			c.A346G						PASS	.						71	71	71					3																	87299049		2203	4295	6498	SO:0001583	missense	25978	exon4			AAGAAGATGGATC	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.346A>G	chr3.hg19:g.87299049A>G	ENSP00000263780:p.Met116Val	445.0	0.0	.		679.0	141.0	.	NM_014043	B4DJG8|Q53HC7|Q9Y4U6	Missense_Mutation	SNP	ENST00000263780.4	hg19	CCDS2918.1	.	.	.	.	.	.	.	.	.	.	A	15.37	2.813168	0.50527	.	.	ENSG00000083937	ENST00000471660;ENST00000263780;ENST00000494980	T;T;T	0.72282	-0.64;-0.64;-0.64	5.95	3.58	0.41010	.	0.068172	0.85682	N	0.000000	T	0.63943	0.2554	M	0.64170	1.965	0.80722	D	1	P;B	0.37573	0.6;0.0	B;B	0.35931	0.214;0.001	T	0.57230	-0.7847	10	0.26408	T	0.33	-13.8833	10.4077	0.44274	0.8709:0.0:0.1291:0.0	.	75;116	B4DJG8;Q9UQN3	.;CHM2B_HUMAN	V	75;116;86	ENSP00000419998:M75V;ENSP00000263780:M116V;ENSP00000418920:M86V	ENSP00000263780:M116V	M	+	1	0	CHMP2B	87381739	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.727000	0.68523	0.505000	0.28104	0.460000	0.39030	ATG	.	.	.	none		0.284	CHMP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352779.2	NM_014043		G	87299049	A	G	87299049	3	3	5	1	0	0	0	0	1	0	0	0	3357	333	12	3	360	3	CHMP2B	3	87299049	Missense_Mutation	SNP	A	TCGA-2Z-A9J5-01A-21D-A382-10	9681569	87299049	110723381	22	418											
EPHA3	2042	hgsc.bcm.edu	37	chr3	89259542	89259542	+	Frame_Shift_Del	DEL	C	C	-																															cctggtggaggttagagggtCttgtgtcaacaattctaagg																										TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr3:89259542delC	ENST00000336596.2	+	3	911	c.686delC	c.(685-687)tctfs	p.S229fs	EPHA3_ENST00000452448.2_Frame_Shift_Del_p.S229fs|EPHA3_ENST00000494014.1_Frame_Shift_Del_p.S229fs	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	229	Cys-rich.		S -> Y (in a lung large cell carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.S229Y(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)		GTTAGAGGGTCTTGTGTCAAC	0.483										TSP Lung(6;0.00050)																											p.S229fs		Atlas-Indel,Pindel	.											EPHA3_ENST00000452448,colon,carcinoma,-2,6	EPHA3	501	.	1	Substitution - Missense(1)	lung(1)	c.685delT						PASS	.						156	150	152					3																	89259542		2203	4300	6503	SO:0001589	frameshift_variant	2042	exon3			.	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3387	protein-coding gene	gene with protein product		179611	"EphA3"	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.686delC	chr3.hg19:g.89259542delC	ENSP00000337451:p.Ser229fs	86.0	0.0	0		123.0	55.0	0.447154	NM_005233	Q9H2V3|Q9H2V4	Frame_Shift_Del	DEL	ENST00000336596.2	hg19	CCDS2922.1																																																																																			.	.	.	none		0.483	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		-	89259542	C	-	89259542	7	5	5	1	0	1	0	1	0	0	0	0	5170	913	32	0	696	0	EPHA3	3	89259542	Frame_Shift_Del	DEL	C	TCGA-2Z-A9J5-01A-21D-A382-10	1960493	89259542	108762888	23	419											
SEMA5B	54437	hgsc.bcm.edu	37	chr3	122647427	122647427	+	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	atgaacaccttccggccggcGacgatcaggactcgcacgta	10	6	11	14	6	1	1	1	1	0	0	3	4	2	2	3	3	1	2	3	3	2	2			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr3:122647427G>A	ENST00000357599.3	-	7	959	c.573C>T	c.(571-573)gtC>gtT	p.V191V	AC078794.1_ENST00000408284.1_RNA|SEMA5B_ENST00000451055.2_Silent_p.V245V|SEMA5B_ENST00000195173.4_Silent_p.V191V	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	191	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		TCCGGCCGGCGACGATCAGGA	0.592																																					p.V245V		Atlas-SNP	.											.	SEMA5B	303	.	0			c.C735T						PASS	.						65	49	54					3																	122647427		2199	4288	6487	SO:0001819	synonymous_variant	54437	exon7			GCCGGCGACGATC	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.573C>T	chr3.hg19:g.122647427G>A		149.0	0.0	.		208.0	92.0	.	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Silent	SNP	ENST00000357599.3	hg19	CCDS35491.1																																																																																			.	.	.	none		0.592	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702		A	122647427	G	A	122647427	2	1	5	1	0	0	0	0	0	0	0	1	14051	1045	37	1		1	SEMA5B	3	122647427	Silent	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10	33387885	122647427	75375003	24	420											
SLC7A14	57709	hgsc.bcm.edu	37	chr3	170244552	170244552	+	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	ctgccaacgccaagagagatGaggtccactgtggtgagtac	11	7	13	10	1	0	4	0	2	0	2	1	5	1	4	3	2	3	1	3	2	3	1			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr3:170244552G>A	ENST00000231706.5	-	2	489	c.174C>T	c.(172-174)ctC>ctT	p.L58L	CLDN11_ENST00000451576.1_Intron|CLDN11_ENST00000486975.1_Intron	NM_020949.2	NP_066000.2	Q8TBB6	S7A14_HUMAN	solute carrier family 7, member 14	58					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)			CAAGAGAGATGAGGTCCACTG	0.567																																					p.L58L		Atlas-SNP	.											.	SLC7A14	110	.	0			c.C174T						PASS	.						260	195	217					3																	170244552		2203	4300	6503	SO:0001819	synonymous_variant	57709	exon2			AGAGATGAGGTCC	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.174C>T	chr3.hg19:g.170244552G>A		84.0	0.0	.		147.0	57.0	.	NM_020949	B3KV33|Q9HCF9	Silent	SNP	ENST00000231706.5	hg19	CCDS33892.1																																																																																			.	.	.	none		0.567	SLC7A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352598.2	NM_020949		A	170244552	G	A	170244552	2	1	5	1	0	0	0	0	0	0	0	1	14709	1277	45	2		2	SLC7A14	3	170244552	Silent	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10	47597125	170244552	27777878	25	421											
CC2D2A	57545	hgsc.bcm.edu	37	chr4	15482437	15482437	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctcctgagtatgacagtccGgagaggcccacggagtaagt	10	7	13	11	2	0	3	0	2	0	1	2	5	2	4	4	3	0	2	4	3	2	2			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr4:15482437G>A	ENST00000503292.1	+	5	413	c.233G>A	c.(232-234)cGg>cAg	p.R78Q	CC2D2A_ENST00000515124.1_Missense_Mutation_p.R78Q|CC2D2A_ENST00000438599.2_Silent_p.P113P|CC2D2A_ENST00000413206.1_Missense_Mutation_p.R78Q|CC2D2A_ENST00000424120.1_Missense_Mutation_p.R78Q|CC2D2A_ENST00000389652.5_Missense_Mutation_p.R29Q|CC2D2A_ENST00000513811.1_3'UTR|CC2D2A_ENST00000511544.1_Silent_p.P113P|CC2D2A_ENST00000507954.1_Missense_Mutation_p.R78Q|CC2D2A_ENST00000503658.1_Silent_p.P113P	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	78					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|urinary_tract(2)	32						ATGACAGTCCGGAGAGGCCCA	0.552																																					p.R78Q		Atlas-SNP	.											.	CC2D2A	158	.	0			c.G233A						PASS	.						31	32	32					4																	15482437		1898	4119	6017	SO:0001583	missense	57545	exon5			CAGTCCGGAGAGG	AB037766, EU450799	CCDS47026.1, CCDS47027.1, CCDS47027.2, CCDS54744.1	4p15.33	2014-09-17	2007-10-19		ENSG00000048342	ENSG00000048342			29253	protein-coding gene	gene with protein product	"Meckel syndrome, type 6"	612013				10718198, 18513680	Standard	NM_001080522		Approved	KIAA1345, MKS6, JBTS9	uc010idv.2	Q9P2K1	OTTHUMG00000160255	ENST00000503292.1:c.233G>A	chr4.hg19:g.15482437G>A	ENSP00000421809:p.Arg78Gln	247.0	0.0	.		285.0	78.0	.	NM_001080522	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	Missense_Mutation	SNP	ENST00000503292.1	hg19	CCDS47026.1	.	.	.	.	.	.	.	.	.	.	G	12.43	1.934877	0.34189	.	.	ENSG00000048342	ENST00000424120;ENST00000413206;ENST00000426932;ENST00000510333;ENST00000512702;ENST00000507954;ENST00000515124;ENST00000503292;ENST00000389652	T;T;T;T;T;T;T	0.26810	1.71;1.71;1.71;1.71;1.71;1.71;1.71	4.96	2.33	0.28932	.	0.862507	0.09564	N	0.785128	T	0.21962	0.0529	L	0.54323	1.7	0.09310	N	1	B;B;B;B	0.31125	0.048;0.048;0.09;0.309	B;B;B;B	0.23852	0.008;0.008;0.021;0.049	T	0.18524	-1.0334	10	0.36615	T	0.2	.	6.9029	0.24293	0.2849:0.0:0.7151:0.0	.	78;29;78;78	Q9P2K1;Q9P2K1-2;C9JKY6;D6RB72	C2D2A_HUMAN;.;.;.	Q	78;78;29;29;78;78;78;78;29	ENSP00000403465:R78Q;ENSP00000398391:R78Q;ENSP00000422875:R78Q;ENSP00000427221:R78Q;ENSP00000424368:R78Q;ENSP00000421809:R78Q;ENSP00000374303:R29Q	ENSP00000374303:R29Q	R	+	2	0	CC2D2A	15091535	0.123000	0.22298	0.014000	0.15608	0.115000	0.19883	1.888000	0.39708	0.291000	0.22468	-0.241000	0.12123	CGG	.	.	.	none		0.552	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2	NM_001080522		A	15482437	G	A	15482437	3	1	5	1	0	0	0	0	1	0	0	0	2730	1116	39	1	353	1	CC2D2A	4	15482437	Missense_Mutation	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10		15482437	175671839	26	422											
FAM105B	90268	hgsc.bcm.edu	37	chr5	14687708	14687708	+	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	aatttgatgggaagaatgagGacctggttgataaaattaaa	17	11	11	2	0	0	4	0	3	0	1	0	6	0	6	1	3	0	1	1	3	7	4			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr5:14687708G>A	ENST00000284274.4	+	5	625	c.547G>A	c.(547-549)Gac>Aac	p.D183N		NM_138348.4	NP_612357.4	Q96BN8	OTUL_HUMAN		183	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)					GAAGAATGAGGACCTGGTTGA	0.403																																					p.D183N		Atlas-SNP	.											.	FAM105B	36	.	0			c.G547A						PASS	.						142	146	144					5																	14687708		1838	4091	5929	SO:0001583	missense	90268	exon5			AATGAGGACCTGG																												ENST00000284274.4:c.547G>A	chr5.hg19:g.14687708G>A	ENSP00000284274:p.Asp183Asn	82.0	0.0	.		95.0	28.0	.	NM_138348	D3DTD3|Q8NAS0|Q96IA3	Missense_Mutation	SNP	ENST00000284274.4	hg19	CCDS43302.1	.	.	.	.	.	.	.	.	.	.	G	14.78	2.638791	0.47153	.	.	ENSG00000154124	ENST00000284274	T	0.18657	2.2	6.17	4.42	0.53409	.	0.137100	0.64402	N	0.000005	T	0.11879	0.0289	N	0.14661	0.345	0.33190	D	0.550715	B	0.06786	0.001	B	0.10450	0.005	T	0.17501	-1.0367	10	0.18276	T	0.48	-18.6943	10.8094	0.46538	0.1439:0.0:0.8561:0.0	.	183	Q96BN8	F105B_HUMAN	N	183	ENSP00000284274:D183N	ENSP00000284274:D183N	D	+	1	0	FAM105B	14740708	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	2.288000	0.43514	0.960000	0.38005	0.655000	0.94253	GAC	.	.	.	none		0.403	FAM105B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366012.1			A	14687708	G	A	14687708	3	1	5	1	0	0	0	0	1	0	0	0	5392	1174	41	2	565	2	FAM105B	5	14687708	Missense_Mutation	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10		14687708	166227552	27	423											
C5orf42	65250	hgsc.bcm.edu	37	chr5	37184927	37184927	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctacttttttcttcaaccgAcaaagcttcagagaacgtat	12	13	5	11	2	3	1	2	0	1	1	3	3	3	1	2	0	4	2	2	0	5	7			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr5:37184927A>G	ENST00000508244.1	-	24	4537	c.4444T>C	c.(4444-4446)Tcg>Ccg	p.S1482P	C5orf42_ENST00000274258.7_Missense_Mutation_p.S363P|C5orf42_ENST00000425232.2_Missense_Mutation_p.S1482P			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	1482						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)			TCTTCAACCGACAAAGCTTCA	0.393																																					p.S1482P		Atlas-SNP	.											.	C5orf42	422	.	0			c.T4444C						PASS	.						128	120	123					5																	37184927		2203	4300	6503	SO:0001583	missense	65250	exon25			CAACCGACAAAGC		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.4444T>C	chr5.hg19:g.37184927A>G	ENSP00000421690:p.Ser1482Pro	63.0	0.0	.		93.0	20.0	.	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	hg19	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	A	17.26	3.343649	0.61073	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39	5.86	0.619	0.17630	.	0.554792	0.15252	N	0.272275	T	0.44519	0.1297	N	0.19112	0.55	0.18873	N	0.999988	B;B	0.14438	0.005;0.01	B;B	0.11329	0.004;0.006	T	0.26224	-1.0109	10	0.41790	T	0.15	.	4.2899	0.10872	0.517:0.0:0.2653:0.2177	.	1482;363	E9PH94;Q9H799	.;CE042_HUMAN	P	1482;1482;363;530;363	ENSP00000421690:S1482P;ENSP00000389014:S1482P;ENSP00000274258:S363P;ENSP00000424223:S530P	ENSP00000274258:S363P	S	-	1	0	C5orf42	37220684	0.001000	0.12720	0.113000	0.21522	0.112000	0.19704	0.064000	0.14437	0.509000	0.28195	0.482000	0.46254	TCG	.	.	.	none		0.393	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		G	37184927	A	G	37184927	3	3	5	1	0	0	0	0	1	0	0	0	2303	275	10	3	5261	3	C5orf42	5	37184927	Missense_Mutation	SNP	A	TCGA-2Z-A9J5-01A-21D-A382-10	22497219	37184927	143730333	28	424											
APC	324	hgsc.bcm.edu	37	chr5	112174167	112174167	+	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	caaattagaatacaagagatCttcaaatgatagtttaaata	20	12	5	4	0	2	3	1	1	1	2	2	4	2	3	0	0	1	1	0	0	10	7			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr5:112174167C>A	ENST00000457016.1	+	16	3256	c.2876C>A	c.(2875-2877)tCt>tAt	p.S959Y	APC_ENST00000508376.2_Missense_Mutation_p.S959Y|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.S959Y			P25054	APC_HUMAN	adenomatous polyposis coli	959	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)		TACAAGAGATCTTCAAATGAT	0.343		12	"D, Mis, N, F, S"		"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"	"colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.S959Y	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.C2876A						PASS	.						69	69	69					5																	112174167		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,	AGAGATCTTCAAA	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.2876C>A	chr5.hg19:g.112174167C>A	ENSP00000413133:p.Ser959Tyr	127.0	0.0	.		147.0	43.0	.	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	hg19	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	15.35	2.808071	0.50421	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D;D	0.93763	-2.55;-3.28;-2.55;-2.55;-2.73	5.9	5.9	0.94986	.	0.049171	0.85682	D	0.000000	D	0.85762	0.5772	N	0.08118	0	0.52099	D	0.999941	P;P	0.44877	0.845;0.845	B;B	0.34536	0.185;0.185	D	0.87864	0.2666	10	0.59425	D	0.04	-14.3819	20.2787	0.98501	0.0:1.0:0.0:0.0	.	961;959	Q4LE70;P25054	.;APC_HUMAN	Y	959;941;959;959;959	ENSP00000413133:S959Y;ENSP00000423224:S941Y;ENSP00000257430:S959Y;ENSP00000427089:S959Y;ENSP00000423828:S959Y	ENSP00000257430:S959Y	S	+	2	0	APC	112202066	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.668000	0.61568	2.798000	0.96311	0.650000	0.86243	TCT	.	.	.	none		0.343	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112174167	C	A	112174167	3	1	5	1	0	0	0	0	1	0	0	0	763	913	32	4	2934	4	APC	5	112174167	Missense_Mutation	SNP	C	TCGA-2Z-A9J5-01A-21D-A382-10	74989240	112174167	68741093	29	425											
PCDHAC1	56135	hgsc.bcm.edu	37	chr5	140306623	140306623	+	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	cttgaggctgccagcggccgCtatgtcctcgcggaactttc	5	10	12	14	4	0	1	0	1	0	0	3	2	1	2	3	3	3	2	3	3	2	3			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr5:140306623C>A	ENST00000253807.2	+	1	146	c.146C>A	c.(145-147)gCt>gAt	p.A49D	PCDHA1_ENST00000394633.3_Intron|PCDHAC1_ENST00000409700.3_Missense_Mutation_p.A49D|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA7_ENST00000525929.1_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	49	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|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)			CCAGCGGCCGCTATGTCCTCG	0.652																																					p.A49D		Atlas-SNP	.											.	PCDHAC1	141	.	0			c.C146A						PASS	.						52	62	58					5																	140306623		2203	4300	6503	SO:0001583	missense	56135	exon1			CGGCCGCTATGTC	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.146C>A	chr5.hg19:g.140306623C>A	ENSP00000253807:p.Ala49Asp	41.0	0.0	.		45.0	18.0	.	NM_031882	Q9Y5F5|Q9Y5I5	Missense_Mutation	SNP	ENST00000253807.2	hg19	CCDS4241.1	.	.	.	.	.	.	.	.	.	.	C	6.060	0.379337	0.11466	.	.	ENSG00000248383	ENST00000409700;ENST00000253807	T;T	0.26810	1.71;1.71	5.29	1.17	0.20885	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.11196	0.0273	N	0.05124	-0.11	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.16289	0.006;0.015	T	0.28964	-1.0027	9	0.36615	T	0.2	.	5.5223	0.16939	0.0:0.4802:0.231:0.2888	.	49;49	Q9H158;Q9H158-2	PCDC1_HUMAN;.	D	49	ENSP00000386356:A49D;ENSP00000253807:A49D	ENSP00000253807:A49D	A	+	2	0	PCDHAC1	140286807	0.000000	0.05858	0.008000	0.14137	0.148000	0.21650	-0.208000	0.09371	0.196000	0.20367	0.561000	0.74099	GCT	.	.	.	none		0.652	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898		A	140306623	C	A	140306623	3	1	5	1	0	0	0	0	1	0	0	0	11539	797	28	4	148	4	PCDHAC1	5	140306623	Missense_Mutation	SNP	C	TCGA-2Z-A9J5-01A-21D-A382-10	28132456	140306623	40608637	30	426											
BAI3	577	hgsc.bcm.edu	37	chr6	69646517	69646517	+	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	gtatcaccttacgggacacaCtgcagcggcccattaagaga	12	7	10	12	2	1	1	1	0	0	1	1	3	1	2	2	2	3	2	2	2	3	3			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr6:69646517C>G	ENST00000370598.1	+	5	1796	c.975C>G	c.(973-975)caC>caG	p.H325Q		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	325	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				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)				ACGGGACACACTGCAGCGGCC	0.498																																					p.H325Q		Atlas-SNP	.											.	BAI3	451	.	0			c.C975G						PASS	.						123	95	105					6																	69646517		2203	4300	6503	SO:0001583	missense	577	exon5			GACACACTGCAGC	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.975C>G	chr6.hg19:g.69646517C>G	ENSP00000359630:p.His325Gln	91.0	0.0	.		130.0	27.0	.	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	hg19	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	C	15.46	2.841299	0.51057	.	.	ENSG00000135298	ENST00000370598	T	0.49720	0.77	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.18551	0.0445	N	0.04018	-0.295	0.80722	D	1	P	0.51933	0.949	P	0.46208	0.507	T	0.08638	-1.0712	10	0.10377	T	0.69	.	19.2236	0.93808	0.0:1.0:0.0:0.0	.	325	O60242	BAI3_HUMAN	Q	325	ENSP00000359630:H325Q	ENSP00000359630:H325Q	H	+	3	2	BAI3	69703238	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.807000	0.86032	2.545000	0.85829	0.585000	0.79938	CAC	.	.	.	none		0.498	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			G	69646517	C	G	69646517	3	3	5	1	0	0	0	0	1	0	0	0	1300	564	20	4	985	4	BAI3	6	69646517	Missense_Mutation	SNP	C	TCGA-2Z-A9J5-01A-21D-A382-10		69646517	101468550	31	427											
C6orf182	285753	hgsc.bcm.edu	37	chr6	109480588	109480588	+	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	aaagctattcctcctgactcAgaaaagtccatttccatttg	12	13	5	11	0	1	2	1	1	0	1	5	2	5	2	4	0	1	1	4	0	4	4			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr6:109480588A>T	ENST00000517392.1	+	9	1365	c.939A>T	c.(937-939)tcA>tcT	p.S313S	CEP57L1_ENST00000520883.1_Silent_p.S213S|CEP57L1_ENST00000336977.4_Silent_p.S213S|CEP57L1_ENST00000407272.1_Silent_p.S313S|CEP57L1_ENST00000359793.3_Silent_p.S313S|CEP57L1_ENST00000523787.1_Silent_p.S316S|CEP57L1_ENST00000368968.2_Silent_p.S313S|CEP57L1_ENST00000521522.1_Silent_p.S260S|CEP57L1_ENST00000368970.2_Silent_p.S330S	NM_001271852.1|NM_001271853.1	NP_001258781.1|NP_001258782.1	Q8IYX8	CE57L_HUMAN	centrosomal protein 57kDa-like 1	313					microtubule anchoring (GO:0034453)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)	11						CTCCTGACTCAGAAAAGTCCA	0.383																																					p.S313S		Atlas-SNP	.											.	CEP57L1	24	.	0			c.A939T						PASS	.						82	84	83					6																	109480588		2203	4300	6503	SO:0001819	synonymous_variant	285753	exon9			TGACTCAGAAAAG	AK092723	CCDS5071.1, CCDS64491.1	6q21	2014-01-28	2010-09-30	2010-09-30	ENSG00000183137	ENSG00000183137			21561	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 182"	C6orf182			Standard	NM_001083535		Approved	bA487F23.2, MGC21731	uc003psy.4	Q8IYX8	OTTHUMG00000015336	ENST00000517392.1:c.939A>T	chr6.hg19:g.109480588A>T		197.0	0.0	.		243.0	58.0	.	NM_001271853	G5E992	Silent	SNP	ENST00000517392.1	hg19	CCDS5071.1																																																																																			.	.	.	none		0.383	CEP57L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041734.4	NM_173830		T	109480588	A	T	109480588	2	4	5	1	0	0	0	0	0	0	0	1	2348	175	7	5		5	C6orf182	6	109480588	Silent	SNP	A	TCGA-2Z-A9J5-01A-21D-A382-10	39834071	109480588	61634479	32	428											
CTAGE9	643854	hgsc.bcm.edu	37	chr6	132030533	132030533	+	Frame_Shift_Del	DEL	A	A	-																															gtctgagtggatcctccaacAaagtttgaggagagggaaaa																										TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr6:132030533delA	ENST00000314099.8	-	1	1673	c.1625delT	c.(1624-1626)ttgfs	p.L543fs	ENPP3_ENST00000358229.5_Intron|ENPP3_ENST00000357639.3_Intron|ENPP3_ENST00000414305.1_Intron	NM_001145659.1|NM_001278507.1	NP_001139131.1|NP_001265436.1	A4FU28	CTGE9_HUMAN	CTAGE family, member 9	543						integral component of membrane (GO:0016021)				endometrium(1)|lung(1)	2						ATCCTCCAACAAAGTTTGAGG	0.522																																					p.L542fs		Atlas-Indel,Pindel	.											.	CTAGE9	56	.	0			c.1626delG						PASS	.						1	1	1					6																	132030533		17	57	74	SO:0001589	frameshift_variant	643854	exon1			.		CCDS47475.1	6q23.2	2010-06-23			ENSG00000236761	ENSG00000236761			37275	protein-coding gene	gene with protein product							Standard	NM_001145659		Approved		uc011ece.2	A4FU28	OTTHUMG00000047966	ENST00000314099.8:c.1625delT	chr6.hg19:g.132030533delA	ENSP00000395587:p.Leu543fs	268.0	0.0	0		393.0	36.0	0.0916031	NM_001145659		Frame_Shift_Del	DEL	ENST00000314099.8	hg19	CCDS47475.1																																																																																			.	.	.	none		0.522	CTAGE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109220.1	NM_001145659		-	132030533	A	-	132030533	7	5	5	1	0	1	0	1	0	0	0	0	3998	131	5	0	712	0	CTAGE9	6	132030533	Frame_Shift_Del	DEL	A	TCGA-2Z-A9J5-01A-21D-A382-10	22549945	132030533	39084534	33	429											
CARD11	84433	hgsc.bcm.edu	37	chr7	2976750	2976750	+	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	tgcaggcctcccgccgcaccAtctcgatcctcatctcgtcg	5	9	8	19	5	3	0	1	0	2	0	8	1	5	0	5	1	1	2	5	1	0	0	rs372864426	byFrequency	TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr7:2976750A>T	ENST00000396946.4	-	9	1665	c.1262T>A	c.(1261-1263)aTg>aAg	p.M421K		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	421					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)		CCGCCGCACCATCTCGATCCT	0.597			Mis		DLBCL																																p.M421K		Atlas-SNP	.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	.	CARD11	339	.	0			c.T1262A						PASS	.						159	128	139					7																	2976750		2203	4300	6503	SO:0001583	missense	84433	exon9			CGCACCATCTCGA	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.1262T>A	chr7.hg19:g.2976750A>T	ENSP00000380150:p.Met421Lys	70.0	0.0	.		80.0	46.0	.	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	hg19	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	A	16.17	3.047193	0.55110	.	.	ENSG00000198286	ENST00000396946	T	0.35236	1.32	5.22	5.22	0.72569	.	0.182330	0.56097	D	0.000021	T	0.27594	0.0678	N	0.22421	0.69	0.45390	D	0.998376	B	0.26363	0.147	B	0.25759	0.063	T	0.08126	-1.0737	10	0.59425	D	0.04	-37.5613	14.2746	0.66173	1.0:0.0:0.0:0.0	.	421	Q9BXL7	CAR11_HUMAN	K	421	ENSP00000380150:M421K	ENSP00000380150:M421K	M	-	2	0	CARD11	2943276	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.387000	0.52501	1.981000	0.57761	0.459000	0.35465	ATG	.	.	.	alt		0.597	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		T	2976750	A	T	2976750	3	4	5	1	0	0	0	0	1	0	0	0	2647	217	8	5	2270	5	CARD11	7	2976750	Missense_Mutation	SNP	A	TCGA-2Z-A9J5-01A-21D-A382-10		2976750	156161913	34	430											
CLIP2	7461	hgsc.bcm.edu	37	chr7	73790571	73790571	+	Frame_Shift_Del	DEL	A	A	-																															tggggctaatggacaactggAaatccaagctggactcgctg																										TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr7:73790571delA	ENST00000395060.1	+	9	1840	c.1840delA	c.(1840-1842)aaafs	p.K614fs	CLIP2_ENST00000223398.6_Frame_Shift_Del_p.K614fs|CLIP2_ENST00000361545.5_Frame_Shift_Del_p.K579fs			Q9UDT6	CLIP2_HUMAN	CAP-GLY domain containing linker protein 2	614						cytoplasmic microtubule (GO:0005881)|microtubule associated complex (GO:0005875)|microtubule plus-end (GO:0035371)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|pancreas(1)|prostate(2)|skin(3)	30						GGACAACTGGAAATCCAAGCT	0.632																																					p.W613X		Atlas-Indel,Pindel	.											.	CLIP2	134	.	0			c.1839delG						PASS	.						63	56	58					7																	73790571		2203	4300	6503	SO:0001589	frameshift_variant	7461	exon10			.	AB006629	CCDS5569.1, CCDS5570.1	7q11.23	2008-06-12	2007-01-04	2007-01-04	ENSG00000106665	ENSG00000106665			2586	protein-coding gene	gene with protein product		603432	"cytoplasmic linker 2", "Williams-Beuren syndrome chromosome region 3"	WBSCR4, CYLN2, WBSCR3		8812460, 9799601	Standard	NM_003388		Approved	CLIP-115, KIAA0291, WSCR4, CLIP, WSCR3	uc003uam.3	Q9UDT6	OTTHUMG00000022980	ENST00000395060.1:c.1840delA	chr7.hg19:g.73790571delA	ENSP00000378500:p.Lys614fs	207.0	0.0	0		263.0	116.0	0.441065	NM_003388	O14527|O43611	Frame_Shift_Del	DEL	ENST00000395060.1	hg19	CCDS5569.1																																																																																			.	.	.	none		0.632	CLIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252556.1	NM_003388		-	73790571	A	-	73790571	7	5	5	1	0	1	0	1	0	0	0	0	3535	247	9	0	1874	0	CLIP2	7	73790571	Frame_Shift_Del	DEL	A	TCGA-2Z-A9J5-01A-21D-A382-10	70813821	73790571	85348092	35	431											
ADAM22	53616	hgsc.bcm.edu	37	chr7	87785232	87785232	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtggttaccttttgtgtacCaatattggcaatatcccaag	10	15	8	8	0	0	0	0	0	0	0	1	0	1	0	3	2	2	3	3	2	7	7			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr7:87785232C>T	ENST00000265727.7	+	22	1897	c.1818C>T	c.(1816-1818)acC>acT	p.T606T	ADAM22_ENST00000398209.3_Silent_p.T606T|ADAM22_ENST00000398204.4_Silent_p.T606T|ADAM22_ENST00000398201.4_Silent_p.T606T|ADAM22_ENST00000315984.7_Silent_p.T606T			Q9P0K1	ADA22_HUMAN	ADAM metallopeptidase domain 22	606	Cys-rich.				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)			TTTTGTGTACCAATATTGGCA	0.358																																					p.T606T		Atlas-SNP	.											.	ADAM22	280	.	0			c.C1818T						PASS	.						227	211	216					7																	87785232		1870	4106	5976	SO:0001819	synonymous_variant	53616	exon22			GTGTACCAATATT	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.1818C>T	chr7.hg19:g.87785232C>T		152.0	0.0	.		232.0	53.0	.	NM_021722	O75075|O75076|Q9P0K2|Q9UIA1|Q9UKK2	Silent	SNP	ENST00000265727.7	hg19	CCDS47637.1																																																																																			.	.	.	none		0.358	ADAM22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268370.2	NM_021723		T	87785232	C	T	87785232	2	4	5	1	0	0	0	0	0	0	0	1	244	581	21	2		2	ADAM22	7	87785232	Silent	SNP	C	TCGA-2Z-A9J5-01A-21D-A382-10	13994661	87785232	71353431	36	432											
PSMC2	5701	hgsc.bcm.edu	37	chr7	103008257	103008257	+	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	actgtgtccaaatagcactgGtaagtagaaagttcttgctt	12	13	9	7	0	1	1	0	0	1	1	2	1	2	1	1	1	2	5	1	1	5	6			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr7:103008257G>T	ENST00000435765.1	+	12	1555		c.e12+1		SLC26A5_ENST00000339444.6_Intron|PSMC2_ENST00000544811.1_Splice_Site|SLC26A5_ENST00000393735.2_Intron|SLC26A5_ENST00000356767.4_Intron|PSMC2_ENST00000292644.3_Splice_Site	NM_002803.3	NP_002794.1	P35998	PRS7_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 2						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|osteoblast differentiation (GO:0001649)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	21						AATAGCACTGGTAAGTAGAAA	0.393																																					.		Atlas-SNP	.											.	PSMC2	38	.	0			c.1144+1G>T						PASS	.						108	111	110					7																	103008257		2203	4300	6503	SO:0001630	splice_region_variant	5701	exon11			GCACTGGTAAGTA	D11094	CCDS5731.1	7q22.1-q22.3	2010-04-21			ENSG00000161057	ENSG00000161057		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9548	protein-coding gene	gene with protein product	"proteasome 26S subunit, ATPase, 2", "mammalian suppressor of sgv-1 of yeast", "protease 26S subunit 7", "putative protein product of Nbla10058"	154365				9473509, 1377363	Standard	NM_002803		Approved	MSS1, S7, Nbla10058	uc003vbs.3	P35998	OTTHUMG00000157206	ENST00000435765.1:c.1144+1G>T	chr7.hg19:g.103008257G>T		45.0	0.0	.		95.0	41.0	.	NM_002803	A4D0Q1|B7Z5E2|Q3LIA5|Q9UDI3	Splice_Site	SNP	ENST00000435765.1	hg19	CCDS5731.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.553104	0.86127	.	.	ENSG00000161057	ENST00000435765;ENST00000292644;ENST00000544811	.	.	.	5.1	5.1	0.69264	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.5674	0.91121	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PSMC2	102795493	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.483000	0.97937	2.367000	0.80283	0.644000	0.83932	.	.	.	.	none		0.393	PSMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347922.1	NM_002803	Intron	T	103008257	G	T	103008257	5	4	5	1	0	0	0	0	0	0	1	0	12696	1275	44	4	1187	4	PSMC2	7	103008257	Splice_Site	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10	15223025	103008257	56130406	37	433											
TNPO3	23534	hgsc.bcm.edu	37	chr7	128632137	128632137	+	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	ggttgccttctttcagagtaGaatataactagagaagaaga	15	11	10	5	0	2	5	1	0	1	5	2	6	2	5	1	1	2	2	1	1	7	7			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr7:128632137G>C	ENST00000265388.5	-	10	1417	c.1274C>G	c.(1273-1275)tCt>tGt	p.S425C	TNPO3_ENST00000393245.1_Missense_Mutation_p.S425C|TNPO3_ENST00000482320.1_Missense_Mutation_p.S359C|TNPO3_ENST00000471234.1_Missense_Mutation_p.S425C|TNPO3_ENST00000471166.1_Missense_Mutation_p.S425C			Q9Y5L0	TNPO3_HUMAN	transportin 3	425					splicing factor protein import into nucleus (GO:0035048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(3)	22						TTTCAGAGTAGAATATAACTA	0.398																																					p.S425C	Pancreas(147;583 2585 39696 52331)	Atlas-SNP	.											.	TNPO3	148	.	0			c.C1274G						PASS	.						97	101	100					7																	128632137		2203	4300	6503	SO:0001583	missense	23534	exon10			AGAGTAGAATATA	AF145029	CCDS5809.1, CCDS55162.1	7q32.2	2014-02-03			ENSG00000064419	ENSG00000064419		"Importins"	17103	protein-coding gene	gene with protein product	"importin 12"	610032	"limb girdle muscular dystrophy 1F (autosomal dominant)"	LGMD1F		10366588, 10713112, 23543484, 23667635	Standard	NM_012470		Approved	TRN-SR, MTR10A, TRN-SR2, IPO12	uc003vol.2	Q9Y5L0	OTTHUMG00000158409	ENST00000265388.5:c.1274C>G	chr7.hg19:g.128632137G>C	ENSP00000265388:p.Ser425Cys	42.0	0.0	.		63.0	22.0	.	NM_012470	A4D1K9|C9IZM0|Q6NUM1|Q96G71|Q96GU9|Q9Y3R2	Missense_Mutation	SNP	ENST00000265388.5	hg19	CCDS5809.1	.	.	.	.	.	.	.	.	.	.	G	19.58	3.854304	0.71719	.	.	ENSG00000064419	ENST00000393245;ENST00000265388;ENST00000482320;ENST00000471234;ENST00000471166	T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3	5.49	5.49	0.81192	Armadillo-like helical (1);Armadillo-type fold (1);	0.159224	0.56097	D	0.000021	T	0.59609	0.2206	N	0.19112	0.55	0.58432	D	0.999998	P;P;P	0.51933	0.949;0.943;0.911	B;B;P	0.46685	0.405;0.405;0.524	T	0.64499	-0.6393	10	0.56958	D	0.05	.	17.2251	0.86967	0.0:0.0:1.0:0.0	.	425;425;425	C9IZM0;C9J7E5;Q9Y5L0	.;.;TNPO3_HUMAN	C	425;425;359;425;425	ENSP00000376936:S425C;ENSP00000265388:S425C;ENSP00000420089:S359C;ENSP00000418646:S425C;ENSP00000418267:S425C	ENSP00000265388:S425C	S	-	2	0	TNPO3	128419373	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.358000	0.97109	2.732000	0.93576	0.557000	0.71058	TCT	.	.	.	none		0.398	TNPO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350929.1	NM_012470		C	128632137	G	C	128632137	3	2	5	1	0	0	0	0	1	0	0	0	16349	942	33	4	1549	4	TNPO3	7	128632137	Missense_Mutation	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10	25623880	128632137	30506526	38	434											
PLXNA4	91584	hgsc.bcm.edu	37	chr7	131815331	131815331	+	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	tcgtggtccagaggtccaagGatctgcggaagggccaagaa	11	6	15	9	2	1	2	0	0	1	2	4	4	3	4	3	5	1	0	3	5	4	0			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr7:131815331G>T	ENST00000359827.3	-	32	6554	c.5592C>A	c.(5590-5592)atC>atA	p.I1864I	PLXNA4_ENST00000321063.4_Silent_p.I1864I			Q9HCM2	PLXA4_HUMAN	plexin A4	1864					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						GAGGTCCAAGGATCTGCGGAA	0.512																																					p.I1864I		Atlas-SNP	.											.	PLXNA4	873	.	0			c.C5592A						PASS	.						143	142	142					7																	131815331		2021	4169	6190	SO:0001819	synonymous_variant	91584	exon32			TCCAAGGATCTGC	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.5592C>A	chr7.hg19:g.131815331G>T		93.0	0.0	.		111.0	36.0	.	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	hg19	CCDS43646.1																																																																																			.	.	.	none		0.512	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		T	131815331	G	T	131815331	2	4	5	1	0	0	0	0	0	0	0	1	12129	1164	41	4		4	PLXNA4	7	131815331	Silent	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10	3183194	131815331	27323332	39	435											
CNOT4	4850	hgsc.bcm.edu	37	chr7	135078775	135078775	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgtggttcaagtgcatgaTgctattgcgtggaaaggcca	9	12	14	6	1	1	1	1	1	0	0	1	2	1	2	1	3	3	3	1	3	3	3			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr7:135078775T>C	ENST00000315544.5	-	10	1801	c.1522A>G	c.(1522-1524)Atc>Gtc	p.I508V	CNOT4_ENST00000428680.2_Missense_Mutation_p.I505V|CNOT4_ENST00000451834.1_Missense_Mutation_p.I505V|CNOT4_ENST00000541284.1_Missense_Mutation_p.I508V|CNOT4_ENST00000423368.2_Missense_Mutation_p.I508V|CNOT4_ENST00000414802.1_Intron|CNOT4_ENST00000356162.4_Intron|CNOT4_ENST00000361528.4_Missense_Mutation_p.I505V	NM_001190848.1	NP_001177777.1	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	508					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						AAGTGCATGATGCTATTGCGT	0.507																																					p.I508V	Ovarian(51;766 1130 5502 35047 50875)	Atlas-SNP	.											.	CNOT4	146	.	0			c.A1522G						PASS	.						64	70	68					7																	135078775		1977	4179	6156	SO:0001583	missense	4850	exon10			GCATGATGCTATT	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.1522A>G	chr7.hg19:g.135078775T>C	ENSP00000326731:p.Ile508Val	141.0	0.0	.		213.0	103.0	.	NM_001190850	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Missense_Mutation	SNP	ENST00000315544.5	hg19	CCDS55166.1	.	.	.	.	.	.	.	.	.	.	T	13.29	2.192948	0.38707	.	.	ENSG00000080802	ENST00000541284;ENST00000451834;ENST00000423368;ENST00000262563;ENST00000361528;ENST00000428680;ENST00000315544	T;T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89;0.89	5.96	3.49	0.39957	.	0.196794	0.53938	N	0.000045	T	0.25044	0.0608	N	0.19112	0.55	0.42892	D	0.994204	B;B;B;B;B;B	0.20671	0.028;0.047;0.003;0.006;0.047;0.047	B;B;B;B;B;B	0.21917	0.016;0.025;0.005;0.01;0.037;0.037	T	0.05852	-1.0860	10	0.26408	T	0.33	-7.2682	7.7871	0.29097	0.0:0.0716:0.1392:0.7891	.	505;508;508;505;508;505	E7ET38;F8VQP3;O95628;O95628-2;O95628-4;O95628-8	.;.;CNOT4_HUMAN;.;.;.	V	508;505;508;508;505;505;508	ENSP00000445508:I508V;ENSP00000388491:I505V;ENSP00000406777:I508V;ENSP00000354673:I505V;ENSP00000399108:I505V;ENSP00000326731:I508V	ENSP00000262563:I508V	I	-	1	0	CNOT4	134729315	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.181000	0.42547	1.092000	0.41356	0.533000	0.62120	ATC	.	.	.	none		0.507	CNOT4-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_013316		C	135078775	T	C	135078775	3	2	5	1	0	0	0	0	1	0	0	0	3623	1464	51	3	519	3	CNOT4	7	135078775	Missense_Mutation	SNP	T	TCGA-2Z-A9J5-01A-21D-A382-10	3263444	135078775	24059888	40	436											
ABCF2	10061	hgsc.bcm.edu	37	chr7	150915213	150915213	+	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	ttgacttccctgctccattgGgccctaccagagccactcgt	6	11	8	16	1	0	2	0	1	0	1	3	2	2	2	5	1	3	1	5	1	1	4			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr7:150915213G>C	ENST00000287844.2	-	11	1401	c.1292C>G	c.(1291-1293)cCc>cGc	p.P431R	ABCF2_ENST00000473874.1_5'Flank|ABCF2_ENST00000222388.2_Missense_Mutation_p.P431R	NM_007189.1	NP_009120.1	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 2	431	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|large_intestine(4)|lung(15)|ovary(1)|skin(2)	24			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGCTCCATTGGGCCCTACCAG	0.507																																					p.P431R		Atlas-SNP	.											.	ABCF2	54	.	0			c.C1292G						PASS	.						143	121	128					7																	150915213		2203	4300	6503	SO:0001583	missense	10061	exon11			CCATTGGGCCCTA	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.1292C>G	chr7.hg19:g.150915213G>C	ENSP00000287844:p.Pro431Arg	75.0	0.0	.		112.0	55.0	.	NM_005692	O60864|Q75MJ0|Q75MJ1|Q96TE8	Missense_Mutation	SNP	ENST00000287844.2	hg19	CCDS5923.1	.	.	.	.	.	.	.	.	.	.	G	32	5.113188	0.94339	.	.	ENSG00000033050	ENST00000222388;ENST00000287844	D;D	0.94537	-3.45;-3.45	5.49	5.49	0.81192	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.85682	D	0.000000	D	0.96153	0.8746	L	0.45581	1.43	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.74348	0.983;0.983	D	0.96634	0.9469	10	0.87932	D	0	-34.616	18.3531	0.90345	0.0:0.0:1.0:0.0	.	431;431	Q9UG63;Q75MJ1	ABCF2_HUMAN;.	R	431	ENSP00000222388:P431R;ENSP00000287844:P431R	ENSP00000222388:P431R	P	-	2	0	ABCF2	150546146	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.139000	0.94554	2.571000	0.86741	0.591000	0.81541	CCC	.	.	.	none		0.507	ABCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336086.1	NM_005692		C	150915213	G	C	150915213	3	2	5	1	0	0	0	0	1	0	0	0	66	1232	43	4	640	4	ABCF2	7	150915213	Missense_Mutation	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10	15836438	150915213	8223450	41	437											
C8orf41	80185	hgsc.bcm.edu	37	chr8	33361326	33361326	+	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	gtaaaagaaggcggtgctctGgctccatgtgggtcaggatc	9	9	15	8	1	2	1	1	0	1	1	4	2	3	2	1	5	1	3	1	5	3	1			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr8:33361326G>C	ENST00000431156.2	-	5	1673	c.1055C>G	c.(1054-1056)cCa>cGa	p.P352R	TTI2_ENST00000520636.1_Missense_Mutation_p.P321R|TTI2_ENST00000519356.1_5'UTR|TTI2_ENST00000360742.5_Missense_Mutation_p.P352R	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	352																	GCGGTGCTCTGGCTCCATGTG	0.522																																					p.P352R		Atlas-SNP	.											.	.	.	.	0			c.C1055G						PASS	.						62	53	56					8																	33361326		2203	4300	6503	SO:0001583	missense	80185	exon5			TGCTCTGGCTCCA	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.1055C>G	chr8.hg19:g.33361326G>C	ENSP00000411169:p.Pro352Arg	74.0	0.0	.		80.0	28.0	.	NM_001265581	D3DSV7|Q96IM2|Q9H5N4	Missense_Mutation	SNP	ENST00000431156.2	hg19	CCDS6090.1	.	.	.	.	.	.	.	.	.	.	G	16.03	3.006383	0.54361	.	.	ENSG00000129696	ENST00000360742;ENST00000431156;ENST00000522668;ENST00000520636	T;T;T	0.77229	-1.08;-1.08;-1.08	5.5	5.5	0.81552	.	0.137293	0.49916	D	0.000134	T	0.79452	0.4448	M	0.63428	1.95	0.80722	D	1	P;P	0.45634	0.863;0.863	P;P	0.49637	0.617;0.617	T	0.75277	-0.3374	10	0.25106	T	0.35	-6.1452	12.4975	0.55937	0.0763:0.0:0.9237:0.0	.	352;321	Q6NXR4;E5RIH5	TTI2_HUMAN;.	R	352;352;352;321	ENSP00000353971:P352R;ENSP00000411169:P352R;ENSP00000428401:P321R	ENSP00000353971:P352R	P	-	2	0	C8orf41	33480868	0.981000	0.34729	1.000000	0.80357	0.990000	0.78478	4.372000	0.59530	2.850000	0.98022	0.650000	0.86243	CCA	.	.	.	none		0.522	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115		C	33361326	G	C	33361326	3	2	5	1	0	0	0	0	1	0	0	0	2429	1348	47	4	487	4	C8orf41	8	33361326	Missense_Mutation	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10		33361326	113002696	42	438											
RNF19A	25897	hgsc.bcm.edu	37	chr8	101273971	101273971	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggttgtgtcttgcttctgctActgatgttgtgtctaaatgc	5	18	11	7	0	3	1	0	1	3	0	3	1	3	1	0	1	4	4	0	1	3	6			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr8:101273971A>G	ENST00000519449.1	-	9	1797	c.1481T>C	c.(1480-1482)gTa>gCa	p.V494A	RNF19A_ENST00000523255.1_5'UTR|RNF19A_ENST00000341084.2_Missense_Mutation_p.V494A	NM_001280539.1|NM_015435.3	NP_001267468.1|NP_056250.3	Q9NV58	RN19A_HUMAN	ring finger protein 19A, RBR E3 ubiquitin protein ligase	494					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)			TGCTTCTGCTACTGATGTTGT	0.423																																					p.V494A		Atlas-SNP	.											.	RNF19A	67	.	0			c.T1481C						PASS	.						174	143	153					8																	101273971		2203	4300	6503	SO:0001583	missense	25897	exon9			TCTGCTACTGATG	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.1481T>C	chr8.hg19:g.101273971A>G	ENSP00000428968:p.Val494Ala	135.0	0.0	.		144.0	24.0	.	NM_015435	A3KCU9|Q52LG1|Q9H5H9|Q9H8M8|Q9UFG0|Q9UFX6|Q9Y4Y1	Missense_Mutation	SNP	ENST00000519449.1	hg19	CCDS6286.1	.	.	.	.	.	.	.	.	.	.	A	18.32	3.598075	0.66332	.	.	ENSG00000034677	ENST00000519449;ENST00000341084	D;D	0.85955	-2.05;-2.05	5.34	5.34	0.76211	.	0.116360	0.64402	D	0.000017	T	0.78761	0.4334	L	0.51422	1.61	0.80722	D	1	P	0.40083	0.702	B	0.36092	0.217	T	0.76971	-0.2761	10	0.07175	T	0.84	.	14.9917	0.71393	1.0:0.0:0.0:0.0	.	494	Q9NV58	RN19A_HUMAN	A	494	ENSP00000428968:V494A;ENSP00000342667:V494A	ENSP00000342667:V494A	V	-	2	0	RNF19A	101343147	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.033000	0.60031	0.482000	0.46254	GTA	.	.	.	none		0.423	RNF19A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380004.1	NM_015435		G	101273971	A	G	101273971	3	3	5	1	0	0	0	0	1	0	0	0	13483	391	14	3	1047	3	RNF19A	8	101273971	Missense_Mutation	SNP	A	TCGA-2Z-A9J5-01A-21D-A382-10	67912645	101273971	45090051	43	439											
COL22A1	169044	hgsc.bcm.edu	37	chr8	139809070	139809071	+	Missense_Mutation	DNP	CC	CC	TA																															gaagatgcttaccttttcacCcttttccccttggccaaaag																										TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr8:139809070_139809071CC>TA	ENST00000303045.6	-	12	2033_2034	c.1587_1588GG>TA	c.(1585-1590)aaGGgt>aaTAgt	p.529_530KG>NS	COL22A1_ENST00000435777.1_Missense_Mutation_p.529_530KG>NS	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	529	Collagen-like 2.|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)			ACCTTTTCACCCTTTTCCCCTT	0.46										HNSCC(7;0.00092)																											p.G530S|p.K529N		Atlas-SNP	.											.	COL22A1	390	.	0			c.G1588A|c.G1587T						PASS	.																																			SO:0001583	missense	169044	exon12			TTTCACCCTTTTC|TTCACCCTTTTCC	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.1587_1588delinsTA	chr8.hg19:g.139809070_139809071delinsTA	ENSP00000303153:p.K529_G530delinsNS	91.0	0.0	.		90.0	24.0	.	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	hg19	CCDS6376.1																																																																																			.	.	.	none		0.46	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		TA	139809071	CC	TA	139809070	3	4	5	1	0	0	0	0	1	0	0	0	3683	623	22	2	3508	2	COL22A1	8	139809070	Missense_Mutation	DNP	CC	TCGA-2Z-A9J5-01A-21D-A382-10	38535099	139809070	6554952	44	440											
ASTN2	23245	hgsc.bcm.edu	37	chr9	119976776	119976776	+	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	tcatcctcctcacagtcataGtcatccaggatgggagtctc	9	11	8	13	0	5	0	4	0	1	0	9	2	8	2	3	2	0	0	3	2	1	1			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr9:119976776G>T	ENST00000313400.4	-	3	976	c.876C>A	c.(874-876)gaC>gaA	p.D292E	ASTN2_ENST00000361477.3_5'UTR|ASTN2_ENST00000373996.3_Missense_Mutation_p.D292E|ASTN2_ENST00000361209.2_Missense_Mutation_p.D292E			O75129	ASTN2_HUMAN	astrotactin 2	292					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						CACAGTCATAGTCATCCAGGA	0.622																																					p.D292E		Atlas-SNP	.											.	ASTN2	307	.	0			c.C876A						PASS	.						79	76	77					9																	119976776		2203	4300	6503	SO:0001583	missense	23245	exon3			GTCATAGTCATCC	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.876C>A	chr9.hg19:g.119976776G>T	ENSP00000314038:p.Asp292Glu	85.0	0.0	.		90.0	4.0	.	NM_014010	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	hg19		.	.	.	.	.	.	.	.	.	.	G	14.86	2.662602	0.47572	.	.	ENSG00000148219	ENST00000313400;ENST00000373996;ENST00000373986;ENST00000361209	T;T;T;T	0.13538	2.69;2.68;2.63;2.58	5.16	4.26	0.50523	.	0.073163	0.52532	D	0.000066	T	0.16854	0.0405	N	0.08118	0	0.40900	D	0.984144	D;D;D	0.67145	0.99;0.994;0.996	P;D;D	0.72625	0.789;0.978;0.94	T	0.22417	-1.0217	9	.	.	.	-25.8287	13.3233	0.60444	0.0775:0.0:0.9225:0.0	.	292;292;292	O75129-2;O75129;O75129-3	.;ASTN2_HUMAN;.	E	292;292;19;292	ENSP00000314038:D292E;ENSP00000363108:D292E;ENSP00000363098:D19E;ENSP00000354504:D292E	.	D	-	3	2	ASTN2	119016597	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	4.188000	0.58351	1.159000	0.42565	0.655000	0.94253	GAC	.	.	.	none		0.622	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010		T	119976776	G	T	119976776	3	4	5	1	0	0	0	0	1	0	0	0	1065	1020	36	4	3302	4	ASTN2	9	119976776	Missense_Mutation	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10		119976776	21236655	45	441											
SETX	23064	hgsc.bcm.edu	37	chr9	135204944	135204944	+	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	tgacccagctaagagatggtCctctagtttcacatccttta	10	13	7	11	0	2	2	1	1	1	1	4	3	4	2	3	1	1	2	3	1	3	5			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr9:135204944C>T	ENST00000224140.5	-	10	2223	c.2041G>A	c.(2041-2043)Gac>Aac	p.D681N	SETX_ENST00000372169.2_Missense_Mutation_p.D681N|SETX_ENST00000393220.1_Missense_Mutation_p.D681N	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	681					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)		AAGAGATGGTCCTCTAGTTTC	0.343																																					p.D681N		Atlas-SNP	.											.	SETX	234	.	0			c.G2041A						PASS	.						82	82	82					9																	135204944		2203	4300	6503	SO:0001583	missense	23064	exon10			GATGGTCCTCTAG	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.2041G>A	chr9.hg19:g.135204944C>T	ENSP00000224140:p.Asp681Asn	34.0	0.0	.		37.0	19.0	.	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	hg19	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	C	15.56	2.868576	0.51588	.	.	ENSG00000107290	ENST00000224140;ENST00000372169;ENST00000393220	D;D;D	0.87966	-2.24;-2.32;-1.94	5.37	5.37	0.77165	.	5.735300	0.00357	N	0.000020	D	0.89157	0.6635	L	0.32530	0.975	0.09310	N	1	P;P;P	0.51351	0.944;0.906;0.944	P;P;P	0.52957	0.714;0.521;0.714	T	0.78214	-0.2291	10	0.24483	T	0.36	.	15.85	0.78924	0.0:1.0:0.0:0.0	.	681;681;681	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	N	681	ENSP00000224140:D681N;ENSP00000361242:D681N;ENSP00000376913:D681N	ENSP00000224140:D681N	D	-	1	0	SETX	134194765	0.003000	0.15002	0.023000	0.16930	0.177000	0.22998	1.467000	0.35321	2.523000	0.85059	0.555000	0.69702	GAC	.	.	.	none		0.343	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		T	135204944	C	T	135204944	3	4	5	1	0	0	0	0	1	0	0	0	14154	855	30	2	6060	2	SETX	9	135204944	Missense_Mutation	SNP	C	TCGA-2Z-A9J5-01A-21D-A382-10	15228168	135204944	6008487	46	442											
CEL	1056	hgsc.bcm.edu	37	chr9	135946849	135946849	+	Missense_Mutation	SNP	T	T	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	ccgtgccgcccacgggtgacTccggggccccccccgtgccg	2	4	14	21	6	0	1	0	1	0	0	1	1	1	1	9	3	2	0	9	3	0	0	rs587780308		TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr9:135946849T>G	ENST00000372080.4	+	11	1985	c.1969T>G	c.(1969-1971)Tcc>Gcc	p.S657A	CEL_ENST00000351304.7_Missense_Mutation_p.S588A	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	654	17 X 11 AA tandem repeats, glycodomain, O-linked (mucin type).				cholesterol catabolic process (GO:0006707)|fatty acid catabolic process (GO:0009062)|intestinal cholesterol absorption (GO:0030299)|intestinal lipid catabolic process (GO:0044258)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|pancreatic juice secretion (GO:0030157)|protein esterification (GO:0018350)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	acylglycerol lipase activity (GO:0047372)|catalytic activity (GO:0003824)|heparin binding (GO:0008201)|hydrolase activity (GO:0016787)|sterol esterase activity (GO:0004771)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		CACGGGTGACTCCGGGGCCCC	0.851																																					p.S657A		Atlas-SNP	.											.	CEL	71	.	0			c.T1969G						PASS	.						1	1	1					9																	135946849		65	235	300	SO:0001583	missense	1056	exon11			GGTGACTCCGGGG	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.1969T>G	chr9.hg19:g.135946849T>G	ENSP00000361151:p.Ser657Ala	10.0	0.0	.		42.0	11.0	.	NM_001807	Q16398|Q5T7U7|Q9UCH1|Q9UP41	Missense_Mutation	SNP	ENST00000372080.4	hg19	CCDS43896.1	.	.	.	.	.	.	.	.	.	.	t	9.616	1.132507	0.21041	.	.	ENSG00000170835	ENST00000372080;ENST00000351304;ENST00000303626	T;T	0.70749	-0.33;-0.51	1.65	-3.25	0.05079	.	.	.	.	.	T	0.49150	0.1540	L	0.28115	0.83	0.09310	N	1	B	0.25007	0.116	B	0.19148	0.024	T	0.27971	-1.0058	9	0.48119	T	0.1	.	3.5479	0.07835	0.2212:0.4916:0.0:0.2872	.	654	P19835	CEL_HUMAN	A	657;588;623	ENSP00000361151:S657A;ENSP00000342217:S588A	ENSP00000304021:S623A	S	+	1	0	CEL	134936670	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	-0.474000	0.06607	-0.858000	0.04110	0.352000	0.21897	TCC	.	.	.	none		0.851	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1			G	135946849	T	G	135946849	3	3	5	1	0	0	0	0	1	0	0	0	3211	1551	54	5	2011	5	CEL	9	135946849	Missense_Mutation	SNP	T	TCGA-2Z-A9J5-01A-21D-A382-10	741905	135946849	5266582	47	443											
KIAA1984	84960	hgsc.bcm.edu	37	chr9	139700623	139700623	+	Missense_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	agtggcgggtgcagctgaagGccctggtgaagcagctggag	8	6	19	8	1	0	2	0	2	0	0	0	3	0	3	1	5	4	4	1	5	2	0			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr9:139700623G>A	ENST00000338005.6	+	10	1077	c.1042G>A	c.(1042-1044)Gcc>Acc	p.A348T	KIAA1984_ENST00000371682.3_3'UTR|RP11-216L13.19_ENST00000415992.1_RNA|RP11-216L13.18_ENST00000471502.1_RNA|RABL6_ENST00000311502.7_5'Flank|RABL6_ENST00000371671.4_5'Flank|KIAA1984-AS1_ENST00000414656.1_RNA|RABL6_ENST00000371663.4_5'Flank|RABL6_ENST00000357466.2_5'Flank	NM_001039374.4	NP_001034463.4	Q5T5S1	CC183_HUMAN		348										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)		GCAGCTGAAGGCCCTGGTGAA	0.657																																					p.A348T		Atlas-SNP	.											.	KIAA1984	39	.	0			c.G1042A						PASS	.						27	38	34					9																	139700623		2068	4195	6263	SO:0001583	missense	84960	exon10			CTGAAGGCCCTGG																												ENST00000338005.6:c.1042G>A	chr9.hg19:g.139700623G>A	ENSP00000338013:p.Ala348Thr	55.0	0.0	.		78.0	40.0	.	NM_001039374	B2RP89|C9JD38|Q6P2D9|Q8NAI4|Q8TF18	Missense_Mutation	SNP	ENST00000338005.6	hg19	CCDS43906.1	.	.	.	.	.	.	.	.	.	.	G	14.65	2.598637	0.46318	.	.	ENSG00000213213	ENST00000423962;ENST00000338005	T	0.14144	2.53	5.07	2.03	0.26663	.	0.168502	0.27366	U	0.019683	T	0.25044	0.0608	M	0.63843	1.955	0.21473	N	0.999672	D	0.76494	0.999	D	0.72075	0.976	T	0.09314	-1.0680	10	0.30078	T	0.28	-14.64	4.0722	0.09887	0.1981:0.0:0.6209:0.181	.	348	Q5T5S1	K1984_HUMAN	T	348	ENSP00000338013:A348T	ENSP00000338013:A348T	A	+	1	0	KIAA1984	138820444	0.407000	0.25352	0.029000	0.17559	0.440000	0.31957	0.595000	0.24029	0.107000	0.17824	0.561000	0.74099	GCC	.	.	.	none		0.657	KIAA1984-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354899.1			A	139700623	G	A	139700623	3	1	5	1	0	0	0	0	1	0	0	0	8273	1203	42	2	1080	2	KIAA1984	9	139700623	Missense_Mutation	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10	3753774	139700623	1512808	48	444											
ATP5C1	509	hgsc.bcm.edu	37	chr10	7841871	7841871	+	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	aaggctccatcatctttaatAaattcaggcaagacagattt	15	12	6	8	0	3	2	2	0	1	2	4	2	4	2	1	2	0	2	1	2	5	5			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr10:7841871A>T	ENST00000356708.7	+	5	644	c.565A>T	c.(565-567)Aaa>Taa	p.K189*	ATP5C1_ENST00000493053.1_3'UTR|ATP5C1_ENST00000541227.1_Nonsense_Mutation_p.K142*|ATP5C1_ENST00000335698.4_Nonsense_Mutation_p.K189*	NM_001001973.1	NP_001001973.1	P36542	ATPG_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1	189					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, catalytic core F(1) (GO:0000275)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)			breast(2)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	16						CATCTTTAATAAATTCAGGCA	0.318																																					p.K189X	Melanoma(143;1012 1820 16249 30920 33158)	Atlas-SNP	.											.	ATP5C1	32	.	0			c.A565T						PASS	.						45	48	47					10																	7841871		2200	4300	6500	SO:0001587	stop_gained	509	exon5			TTTAATAAATTCA	D16561	CCDS7081.1, CCDS31142.1	10p14	2012-10-12			ENSG00000165629	ENSG00000165629		"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	833	protein-coding gene	gene with protein product		108729		ATP5CL1, ATP5C		8168843, 8227057	Standard	NM_005174		Approved		uc001iju.3	P36542	OTTHUMG00000017639	ENST00000356708.7:c.565A>T	chr10.hg19:g.7841871A>T	ENSP00000349142:p.Lys189*	38.0	0.0	.		39.0	12.0	.	NM_001001973	A8KA31|Q5VYP3|Q6I9V2|Q96AS8	Nonsense_Mutation	SNP	ENST00000356708.7	hg19	CCDS31142.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.058482	0.76074	.	.	ENSG00000165629	ENST00000356708;ENST00000335698;ENST00000541227	.	.	.	5.6	3.74	0.42951	.	0.116219	0.64402	D	0.000020	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.0	13.9922	0.64374	0.4013:0.5987:0.0:0.0	.	.	.	.	X	189;189;142	.	ENSP00000338568:K189X	K	+	1	0	ATP5C1	7881877	1.000000	0.71417	0.883000	0.34634	0.442000	0.32017	1.528000	0.35985	0.827000	0.34685	-0.148000	0.13756	AAA	.	.	.	none		0.318	ATP5C1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046708.1	NM_005174		T	7841871	A	T	7841871	4	4	5	1	0	0	0	0	0	1	0	0	1149	363	13	5	583	5	ATP5C1	10	7841871	Nonsense_Mutation	SNP	A	TCGA-2Z-A9J5-01A-21D-A382-10		7841871	127692876	49	445											
CCDC7	79741	hgsc.bcm.edu	37	chr10	32760011	32760011	+	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	gataagtaaagatcaaactcTtttacaagcagagcctccaa	17	9	6	9	0	2	2	1	0	1	2	3	3	3	2	2	0	4	2	2	0	7	4			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr10:32760011T>A	ENST00000362006.5	+	7	1073	c.530T>A	c.(529-531)cTt>cAt	p.L177H	CCDC7_ENST00000537047.1_Intron|CCDC7_ENST00000277657.6_Missense_Mutation_p.L177H|CCDC7_ENST00000535327.1_Intron|CCDC7_ENST00000539197.1_Intron|CCDC7_ENST00000545067.1_Intron	NM_145023.4	NP_659460.3	Q96M83	CCDC7_HUMAN	coiled-coil domain containing 7	177										NS(1)|breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(2)	14		Breast(68;0.000207)|Prostate(175;0.0107)				GATCAAACTCTTTTACAAGCA	0.294																																					p.L177H		Atlas-SNP	.											.	CCDC7	47	.	0			c.T530A						PASS	.						33	35	34					10																	32760011		2200	4294	6494	SO:0001583	missense	221016	exon7			AAACTCTTTTACA	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.530T>A	chr10.hg19:g.32760011T>A	ENSP00000355078:p.Leu177His	147.0	0.0	.		202.0	59.0	.	NM_145023	Q5VW55|Q8IVQ0|Q8NEQ0	Missense_Mutation	SNP	ENST00000362006.5	hg19	CCDS7173.1	.	.	.	.	.	.	.	.	.	.	T	8.249	0.808496	0.16467	.	.	ENSG00000216937	ENST00000324147;ENST00000277657;ENST00000362006	T;T	0.34072	1.38;1.38	5.06	-2.02	0.07388	.	.	.	.	.	T	0.20414	0.0491	N	0.14661	0.345	0.09310	N	0.999999	P	0.39157	0.662	B	0.42386	0.386	T	0.16748	-1.0392	9	0.49607	T	0.09	-20.8565	3.2857	0.06931	0.3191:0.2688:0.0:0.412	.	177	Q96M83	CCDC7_HUMAN	H	182;177;177	ENSP00000277657:L177H;ENSP00000355078:L177H	ENSP00000277657:L177H	L	+	2	0	CCDC7	32800017	0.021000	0.18746	0.000000	0.03702	0.073000	0.16967	0.379000	0.20585	-0.261000	0.09405	0.482000	0.46254	CTT	.	.	.	none		0.294	CCDC7-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047490.1	NM_145023		A	32760011	T	A	32760011	3	1	5	1	0	0	0	0	1	0	0	0	2844	1609	56	5	552	5	CCDC7	10	32760011	Missense_Mutation	SNP	T	TCGA-2Z-A9J5-01A-21D-A382-10	24918140	32760011	102774736	50	446											
ANKRD30A	91074	hgsc.bcm.edu	37	chr10	37508184	37508184	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acacaatgctcacttctaaaTtgaaggaaaaacaagacaaa	21	7	5	8	0	2	2	1	1	1	1	2	3	2	3	0	1	2	1	0	1	8	3			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr10:37508184T>C	ENST00000602533.1	+	34	3475	c.3376T>C	c.(3376-3378)Ttg>Ctg	p.L1126L	ANKRD30A_ENST00000361713.1_Silent_p.L1126L|ANKRD30A_ENST00000374660.1_Silent_p.L1245L			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1182					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						CACTTCTAAATTGAAGGAAAA	0.383																																					p.L1126L		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.T3376C						PASS	.						91	91	91					10																	37508184		1852	4084	5936	SO:0001819	synonymous_variant	91074	exon34			TCTAAATTGAAGG	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.3376T>C	chr10.hg19:g.37508184T>C		165.0	0.0	.		260.0	82.0	.	NM_052997	Q5W025	Silent	SNP	ENST00000602533.1	hg19																																																																																				.	.	.	none		0.383	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		C	37508184	T	C	37508184	2	2	5	1	0	0	0	0	0	0	0	1	658	1490	52	3		3	ANKRD30A	10	37508184	Silent	SNP	T	TCGA-2Z-A9J5-01A-21D-A382-10	4748173	37508184	98026563	51	447											
RHOBTB1	9886	hgsc.bcm.edu	37	chr10	62670721	62670721	+	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	gagagaaacactcacttcatCaacaacatcccgagaacgct	16	6	6	13	2	3	2	3	0	0	2	4	5	4	2	1	0	4	1	1	0	4	1			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr10:62670721C>T	ENST00000337910.5	-	4	557	c.220G>A	c.(220-222)Gat>Aat	p.D74N	RHOBTB1_ENST00000357917.4_Missense_Mutation_p.D74N|RNU2-72P_ENST00000411175.1_RNA	NM_001242359.1|NM_014836.4	NP_001229288.1|NP_055651.1	O94844	RHBT1_HUMAN	Rho-related BTB domain containing 1	74	Rho-like.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	Prostate(12;0.0112)					CTCACTTCATCAACAACATCC	0.493																																					p.D74N		Atlas-SNP	.											.	RHOBTB1	61	.	0			c.G220A						PASS	.						151	117	128					10																	62670721		2203	4300	6503	SO:0001583	missense	9886	exon4			CTTCATCAACAAC	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.220G>A	chr10.hg19:g.62670721C>T	ENSP00000338671:p.Asp74Asn	80.0	0.0	.		84.0	21.0	.	NM_014836		Missense_Mutation	SNP	ENST00000337910.5	hg19	CCDS7261.1	.	.	.	.	.	.	.	.	.	.	C	36	5.770273	0.96914	.	.	ENSG00000072422	ENST00000357917;ENST00000337910;ENST00000536302	T;T	0.24151	1.87;1.87	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.51109	0.1655	M	0.63428	1.95	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	T	0.49234	-0.8961	10	0.62326	D	0.03	.	19.4554	0.94886	0.0:1.0:0.0:0.0	.	74	O94844	RHBT1_HUMAN	N	74	ENSP00000350595:D74N;ENSP00000338671:D74N	ENSP00000338671:D74N	D	-	1	0	RHOBTB1	62340727	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.724000	0.84798	2.591000	0.87537	0.555000	0.69702	GAT	.	.	.	none		0.493	RHOBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048220.1			T	62670721	C	T	62670721	3	4	5	1	0	0	0	0	1	0	0	0	13346	826	29	2	1902	2	RHOBTB1	10	62670721	Missense_Mutation	SNP	C	TCGA-2Z-A9J5-01A-21D-A382-10	25162537	62670721	72864026	52	448											
JMJD1C	221037	hgsc.bcm.edu	37	chr10	64968945	64968945	+	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	tgactaagtaatccaataccAtctgctgaggtcacaggggt	12	10	10	9	0	2	2	1	2	1	0	3	2	3	2	2	3	2	2	2	3	4	3			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr10:64968945A>T	ENST00000399262.2	-	9	2963	c.2745T>A	c.(2743-2745)gaT>gaA	p.D915E	JMJD1C_ENST00000399251.1_Missense_Mutation_p.D696E|JMJD1C_ENST00000542921.1_Missense_Mutation_p.D733E|JMJD1C_ENST00000402544.1_Missense_Mutation_p.D696E	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	915					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)					ATCCAATACCATCTGCTGAGG	0.423																																					p.D915E		Atlas-SNP	.											.	JMJD1C	347	.	0			c.T2745A						PASS	.						90	83	85					10																	64968945		1898	4113	6011	SO:0001583	missense	221037	exon9			AATACCATCTGCT	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.2745T>A	chr10.hg19:g.64968945A>T	ENSP00000382204:p.Asp915Glu	99.0	0.0	.		114.0	36.0	.	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	hg19	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.016377	0.75161	.	.	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000399251;ENST00000542921	T;T;T;T	0.55234	0.53;0.53;0.53;0.53	6.03	4.88	0.63580	.	0.096988	0.64402	N	0.000002	T	0.37999	0.1024	L	0.35723	1.085	0.39613	D	0.969902	B;B	0.27625	0.183;0.183	B;B	0.29942	0.109;0.109	T	0.40136	-0.9579	10	0.49607	T	0.09	-16.6076	1.8984	0.03262	0.5723:0.1677:0.0997:0.1604	.	915;733	Q15652;A0T124	JHD2C_HUMAN;.	E	915;696;696;733	ENSP00000382204:D915E;ENSP00000384990:D696E;ENSP00000382195:D696E;ENSP00000444682:D733E	ENSP00000382195:D696E	D	-	3	2	JMJD1C	64638951	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.732000	0.38146	1.062000	0.40625	0.533000	0.62120	GAT	.	.	.	none		0.423	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		T	64968945	A	T	64968945	3	4	5	1	0	0	0	0	1	0	0	0	7957	214	8	5	4949	5	JMJD1C	10	64968945	Missense_Mutation	SNP	A	TCGA-2Z-A9J5-01A-21D-A382-10	2298224	64968945	70565802	53	449											
ZFYVE27	118813	hgsc.bcm.edu	37	chr10	99498260	99498260	+	Missense_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	gacatcagaacgtgaggggaGtgggccggagctgagcccca	10	4	17	10	2	1	3	1	2	0	1	1	6	1	5	3	4	3	1	3	4	1	0			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr10:99498260G>A	ENST00000393677.4	+	2	230	c.26G>A	c.(25-27)aGt>aAt	p.S9N	ZFYVE27_ENST00000337540.7_Missense_Mutation_p.S9N|ZFYVE27_ENST00000370613.3_Missense_Mutation_p.S9N|ZFYVE27_ENST00000370610.3_Intron|ZFYVE27_ENST00000453958.2_Missense_Mutation_p.S9N|ZFYVE27_ENST00000359980.3_Missense_Mutation_p.S9N|ZFYVE27_ENST00000357540.4_Missense_Mutation_p.S9N|ZFYVE27_ENST00000356257.4_Missense_Mutation_p.S9N	NM_144588.6	NP_653189.3	Q5T4F4	ZFY27_HUMAN	zinc finger, FYVE domain containing 27	9					cell death (GO:0008219)|neuron projection development (GO:0031175)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein localization to plasma membrane (GO:0072659)	axon (GO:0030424)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|recycling endosome membrane (GO:0055038)	metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	8		Colorectal(252;0.0846)		Epithelial(162;7.08e-10)|all cancers(201;5.18e-08)		CGTGAGGGGAGTGGGCCGGAG	0.517																																					p.S9N		Atlas-SNP	.											.	ZFYVE27	31	.	0			c.G26A						PASS	.						138	134	135					10																	99498260		2203	4300	6503	SO:0001583	missense	118813	exon1			AGGGGAGTGGGCC	BC030621	CCDS31263.1, CCDS31264.1, CCDS53562.1, CCDS53563.1, CCDS53564.1, CCDS53565.1	10q24.2	2013-09-11			ENSG00000155256	ENSG00000155256		"Zinc fingers, FYVE domain containing"	26559	protein-coding gene	gene with protein product	"protrudin"	610243				14702039	Standard	NM_144588		Approved	FLJ32919, SPG33	uc001kol.2	Q5T4F4	OTTHUMG00000018867	ENST00000393677.4:c.26G>A	chr10.hg19:g.99498260G>A	ENSP00000377282:p.Ser9Asn	78.0	0.0	.		62.0	15.0	.	NM_001002261	B7Z3S0|B7Z404|B7Z626|G8JLC3|G8JLF0|J3KP98|Q5T4F1|Q5T4F2|Q5T4F3|Q8N1K0|Q8N6D6|Q8NCA0|Q8NDE4|Q96M08	Missense_Mutation	SNP	ENST00000393677.4	hg19	CCDS31263.1	.	.	.	.	.	.	.	.	.	.	G	8.596	0.885766	0.17540	.	.	ENSG00000155256	ENST00000337540;ENST00000357540;ENST00000370613;ENST00000393677;ENST00000453958;ENST00000359980;ENST00000356257	T;T;T;T;T	0.45668	0.89;1.46;1.45;1.46;1.46	5.04	2.0	0.26442	.	0.853122	0.10772	N	0.635877	T	0.25975	0.0633	N	0.19112	0.55	0.26977	N	0.965458	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.06405	0.0;0.0;0.001;0.001;0.002;0.0	T	0.19778	-1.0295	10	0.48119	T	0.1	0.0993	5.8759	0.18828	0.2398:0.2259:0.5343:0.0	.	9;9;9;9;9;9	B7Z404;B7Z626;Q5T4F4-5;Q5T4F4-3;Q5T4F4-2;Q5T4F4	.;.;.;.;.;ZFY27_HUMAN	N	9	ENSP00000337993:S9N;ENSP00000377282:S9N;ENSP00000401580:S9N;ENSP00000353069:S9N;ENSP00000348593:S9N	ENSP00000337993:S9N	S	+	2	0	ZFYVE27	99488250	0.979000	0.34478	0.883000	0.34634	0.179000	0.23085	0.667000	0.25112	0.535000	0.28714	-0.258000	0.10820	AGT	.	.	.	none		0.517	ZFYVE27-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049745.2	NM_144588		A	99498260	G	A	99498260	3	1	5	1	0	0	0	0	1	0	0	0	17681	1029	36	2	28	2	ZFYVE27	10	99498260	Missense_Mutation	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10	34529315	99498260	36036487	54	450											
SEC23IP	11196	hgsc.bcm.edu	37	chr10	121663721	121663721	+	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	ccgaagtgagacgctgtactTggttttacaagggggacaca	11	9	13	8	2	0	1	0	1	0	1	0	4	0	2	1	3	2	3	1	3	4	4			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr10:121663721T>A	ENST00000369075.3	+	4	1105	c.1033T>A	c.(1033-1035)Tgg>Agg	p.W345R	SEC23IP_ENST00000543134.1_Missense_Mutation_p.W134R	NM_007190.3	NP_009121.1	Q9Y6Y8	S23IP_HUMAN	SEC23 interacting protein	345	Interaction with SEC23A.				acrosome assembly (GO:0001675)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|single fertilization (GO:0007338)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear endoplasmic reticulum (GO:0097038)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	36		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		ACGCTGTACTTGGTTTTACAA	0.468																																					p.W345R		Atlas-SNP	.											.	SEC23IP	100	.	0			c.T1033A						PASS	.						87	90	89					10																	121663721		2203	4300	6503	SO:0001583	missense	11196	exon4			TGTACTTGGTTTT	AB019435	CCDS7618.1	10q26.11-q26.12	2013-01-10			ENSG00000107651	ENSG00000107651		"Sterile alpha motif (SAM) domain containing"	17018	protein-coding gene	gene with protein product						10400679	Standard	NM_007190		Approved	p125	uc001leu.2	Q9Y6Y8	OTTHUMG00000019161	ENST00000369075.3:c.1033T>A	chr10.hg19:g.121663721T>A	ENSP00000358071:p.Trp345Arg	125.0	0.0	.		164.0	38.0	.	NM_007190	D3DRD2|Q8IXH5|Q9BUK5	Missense_Mutation	SNP	ENST00000369075.3	hg19	CCDS7618.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.9|25.9	4.683414|4.683414	0.88542|0.88542	.|.	.|.	ENSG00000107651|ENSG00000107651	ENST00000442952|ENST00000369075;ENST00000543134;ENST00000446561	.|D;D;T	.|0.91237	.|-2.81;-2.81;1.33	5.33|5.33	5.33|5.33	0.75918|0.75918	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|D	.|0.96231	.|0.8771	M|M	0.91768|0.91768	3.24|3.24	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.999;0.996	.|D	.|0.97154	.|0.9833	.|10	.|0.87932	.|D	.|0	-7.97|-7.97	15.6047|15.6047	0.76658|0.76658	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|134;345	.|F5H0L8;Q9Y6Y8	.|.;S23IP_HUMAN	X|R	110|345;134;79	.|ENSP00000358071:W345R;ENSP00000438773:W134R;ENSP00000396906:W79R	.|ENSP00000358071:W345R	L|W	+|+	2|1	0|0	SEC23IP|SEC23IP	121653711|121653711	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.991000|0.991000	0.79684|0.79684	7.544000|7.544000	0.82117|0.82117	2.137000|2.137000	0.66172|0.66172	0.460000|0.460000	0.39030|0.39030	TTG|TGG	.	.	.	none		0.468	SEC23IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050688.1			A	121663721	T	A	121663721	3	1	5	1	0	0	0	0	1	0	0	0	14006	1812	63	5	1047	5	SEC23IP	10	121663721	Missense_Mutation	SNP	T	TCGA-2Z-A9J5-01A-21D-A382-10	22165461	121663721	13871026	55	451											
ANO3	63982	hgsc.bcm.edu	37	chr11	26663544	26663544	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaatctgcagcccatgaaccTtcatggactgatggatgagt	11	10	11	9	0	2	3	1	3	1	0	2	6	2	5	2	2	3	1	2	2	2	1			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr11:26663544T>C	ENST00000256737.3	+	22	3095	c.2243T>C	c.(2242-2244)cTt>cCt	p.L748P	ANO3_ENST00000537978.1_Missense_Mutation_p.L732P|ANO3_ENST00000531568.1_Missense_Mutation_p.L602P|ANO3_ENST00000525139.1_Missense_Mutation_p.L732P	NM_031418.2	NP_113606.2	Q9BYT9	ANO3_HUMAN	anoctamin 3	748					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						CCCATGAACCTTCATGGACTG	0.408																																					p.L748P		Atlas-SNP	.											.	ANO3	145	.	0			c.T2243C						PASS	.						119	110	113					11																	26663544		2203	4299	6502	SO:0001583	missense	63982	exon22			TGAACCTTCATGG	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.2243T>C	chr11.hg19:g.26663544T>C	ENSP00000256737:p.Leu748Pro	82.0	0.0	.		79.0	17.0	.	NM_031418	B7Z3F5	Missense_Mutation	SNP	ENST00000256737.3	hg19	CCDS31447.1	.	.	.	.	.	.	.	.	.	.	T	12.63	1.995368	0.35226	.	.	ENSG00000134343	ENST00000537978;ENST00000525139;ENST00000256737;ENST00000538001;ENST00000531568	T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07	6.07	6.07	0.98685	.	0.232790	0.43747	D	0.000531	T	0.37404	0.1002	N	0.03608	-0.345	0.58432	D	0.999996	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.003	T	0.30592	-0.9973	10	0.28530	T	0.3	.	10.8996	0.47043	0.0:0.0695:0.0:0.9305	.	650;748	B7Z7Y6;Q9BYT9	.;ANO3_HUMAN	P	732;732;748;650;602	ENSP00000440737:L732P;ENSP00000432576:L732P;ENSP00000256737:L748P;ENSP00000432394:L602P	ENSP00000256737:L748P	L	+	2	0	ANO3	26620120	1.000000	0.71417	0.963000	0.40424	0.930000	0.56654	5.868000	0.69605	2.326000	0.78906	0.533000	0.62120	CTT	.	.	.	none		0.408	ANO3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387806.1	NM_031418		C	26663544	T	C	26663544	3	2	5	1	0	0	0	0	1	0	0	0	698	1609	56	3	2329	3	ANO3	11	26663544	Missense_Mutation	SNP	T	TCGA-2Z-A9J5-01A-21D-A382-10		26663544	108342972	56	452											
PAMR1	25891	hgsc.bcm.edu	37	chr11	35457562	35457562	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcactcatactggagctgggTatgcagatgttggtatccca	9	11	12	9	0	1	1	1	0	0	1	2	2	2	2	1	3	3	6	1	3	3	4	rs147274037		TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr11:35457562T>C	ENST00000378880.2	-	9	1667	c.1222A>G	c.(1222-1224)Acc>Gcc	p.T408A	PAMR1_ENST00000278360.3_Missense_Mutation_p.T425A|PAMR1_ENST00000378878.3_Missense_Mutation_p.T297A|PAMR1_ENST00000532848.1_Missense_Mutation_p.T368A	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN	peptidase domain containing associated with muscle regeneration 1	408	Sushi 2. {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						TGGAGCTGGGTATGCAGATGT	0.582																																					p.T425A		Atlas-SNP	.											.	PAMR1	85	.	0			c.A1273G						PASS	.	T	ALA/THR,ALA/THR	2,4402	4.2+/-10.8	0,2,2200	195	176	183		1222,1273	5.5	1	11	dbSNP_134	183	0,8596		0,0,4298	no	missense,missense	PAMR1	NM_001001991.1,NM_015430.2	58,58	0,2,6498	CC,CT,TT		0.0,0.0454,0.0154	probably-damaging,probably-damaging	408/721,425/738	35457562	2,12998	2202	4298	6500	SO:0001583	missense	25891	exon10			GCTGGGTATGCAG		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.1222A>G	chr11.hg19:g.35457562T>C	ENSP00000368158:p.Thr408Ala	153.0	0.0	.		206.0	57.0	.	NM_015430	A8MQ58|B7ZA73|Q5EBL7|Q5JPI4|Q6N062|Q71RE9|Q96JW2|Q9Y432	Missense_Mutation	SNP	ENST00000378880.2	hg19	CCDS31460.1	.	.	.	.	.	.	.	.	.	.	T	19.93	3.918376	0.73098	4.54E-4	0.0	ENSG00000149090	ENST00000278360;ENST00000378880;ENST00000378878;ENST00000532848;ENST00000527605	T;T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01;-0.01	5.54	5.54	0.83059	Complement control module (2);Sushi/SCR/CCP (3);	0.095778	0.64402	D	0.000001	T	0.70290	0.3207	L	0.29908	0.895	0.58432	D	0.999999	D;D;B	0.76494	0.996;0.999;0.433	D;D;B	0.83275	0.973;0.996;0.134	T	0.74250	-0.3726	10	0.87932	D	0	.	15.6714	0.77279	0.0:0.0:0.0:1.0	.	297;408;425	A8MQ58;Q6UXH9;Q6UXH9-2	.;PAMR1_HUMAN;.	A	425;408;297;368;385	ENSP00000278360:T425A;ENSP00000368158:T408A;ENSP00000368156:T297A;ENSP00000433868:T368A;ENSP00000432591:T385A	ENSP00000278360:T425A	T	-	1	0	PAMR1	35414138	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	2.230000	0.42999	2.107000	0.64212	0.459000	0.35465	ACC	.	T|1.000;C|0.000	0.000	weak		0.582	PAMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389177.1	NM_015430		C	35457562	T	C	35457562	3	2	5	1	0	0	0	0	1	0	0	0	11420	1638	57	3	952	3	PAMR1	11	35457562	Missense_Mutation	SNP	T	TCGA-2Z-A9J5-01A-21D-A382-10	8794018	35457562	99548954	57	453											
GANAB	23193	hgsc.bcm.edu	37	chr11	62394377	62394377	+	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	agggtctggggaccatgatgCttctggtagctttgaatgtc	7	13	14	7	0	2	2	0	2	2	0	3	3	2	3	1	4	2	3	1	4	2	3			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr11:62394377C>T	ENST00000356638.3	-	20	2368	c.2352G>A	c.(2350-2352)aaG>aaA	p.K784K	GANAB_ENST00000540933.1_Silent_p.K687K|GANAB_ENST00000534779.1_Silent_p.K692K|GANAB_ENST00000346178.4_Silent_p.K806K	NM_198334.1	NP_938148.1	Q14697	GANAB_HUMAN	glucosidase, alpha; neutral AB	784					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)	GACCATGATGCTTCTGGTAGC	0.517																																					p.K806K	Melanoma(23;1005 1074 15747 18937)	Atlas-SNP	.											.	GANAB	110	.	0			c.G2418A						PASS	.						84	79	80					11																	62394377		2202	4299	6501	SO:0001819	synonymous_variant	23193	exon21			ATGATGCTTCTGG	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.2352G>A	chr11.hg19:g.62394377C>T		104.0	0.0	.		100.0	29.0	.	NM_198335	A6NC20|Q8WTS9|Q9P0X0	Silent	SNP	ENST00000356638.3	hg19	CCDS8026.1																																																																																			.	.	.	none		0.517	GANAB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395689.1	NM_198334		T	62394377	C	T	62394377	2	4	5	1	0	0	0	0	0	0	0	1	6240	796	28	2		2	GANAB	11	62394377	Silent	SNP	C	TCGA-2Z-A9J5-01A-21D-A382-10	26936815	62394377	72612139	58	454											
NAALADL1	10004	hgsc.bcm.edu	37	chr11	64815657	64815657	+	Frame_Shift_Del	DEL	C	C	-																															gtccacgttgatgtaggccaCcgtgcgctcctgcagcttgt																										TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr11:64815657delC	ENST00000358658.3	-	10	1342	c.1315delG	c.(1315-1317)gtgfs	p.V439fs	NAALADL1_ENST00000339885.2_Frame_Shift_Del_p.V439fs|NAALADL1_ENST00000355369.2_Frame_Shift_Del_p.V439fs|NAALADL1_ENST00000526799.1_5'UTR|NAALADL1_ENST00000528884.1_5'UTR|NAALADL1_ENST00000356632.3_Frame_Shift_Del_p.V404fs|RN7SL114P_ENST00000582042.1_RNA|NAALADL1_ENST00000340252.4_Frame_Shift_Del_p.V490fs|NAALADL1_ENST00000355721.3_Frame_Shift_Del_p.V398fs	NM_005468.2	NP_005459.2	Q9UQQ1	NALDL_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 1	439	NAALADase.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	29						ATGTAGGCCACCGTGCGCTCC	0.632																																					p.V439fs		Atlas-Indel,Pindel	.											.	NAALADL1	58	.	0			c.1316delT						PASS	.						119	119	119					11																	64815657		2201	4297	6498	SO:0001589	frameshift_variant	10004	exon10			.	AF010141	CCDS31604.1	11q12	2011-08-16			ENSG00000168060	ENSG00000168060			23536	protein-coding gene	gene with protein product	"ileal peptidase I100"	602640				10085079	Standard	NM_005468		Approved		uc001ocn.3	Q9UQQ1	OTTHUMG00000165595	ENST00000358658.3:c.1315delG	chr11.hg19:g.64815657delC	ENSP00000351484:p.Val439fs	85.0	0.0	0		83.0	28.0	0.337349	NM_005468	C9J8A1|C9J964|C9JL35|C9JSN0|O43176	Frame_Shift_Del	DEL	ENST00000358658.3	hg19	CCDS31604.1																																																																																			.	.	.	none		0.632	NAALADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385162.1	NM_005468		-	64815657	C	-	64815657	7	5	5	1	0	1	0	1	0	0	0	0	10136	507	18	0	943	0	NAALADL1	11	64815657	Frame_Shift_Del	DEL	C	TCGA-2Z-A9J5-01A-21D-A382-10	2421280	64815657	70190859	59	455											
MUS81	80198	hgsc.bcm.edu	37	chr11	65628851	65628851	+	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	cccggactcaccatctggagAgaacagtccagccccgcagg	10	4	11	16	2	2	1	1	0	1	1	3	4	3	3	5	3	2	1	5	3	1	0			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr11:65628851A>T	ENST00000308110.4	+	3	645	c.296A>T	c.(295-297)gAg>gTg	p.E99V	MUS81_ENST00000533035.1_Missense_Mutation_p.E24V|CFL1_ENST00000525451.2_5'Flank|CFL1_ENST00000534769.1_5'UTR|CFL1_ENST00000531413.1_5'Flank	NM_025128.4	NP_079404.3	Q96NY9	MUS81_HUMAN	MUS81 structure-specific endonuclease subunit	99					DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	intercellular bridge (GO:0045171)|nucleus (GO:0005634)	3'-flap endonuclease activity (GO:0048257)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	13				READ - Rectum adenocarcinoma(159;0.166)		CCATCTGGAGAGAACAGTCCA	0.607								Homologous recombination																													p.E99V		Atlas-SNP	.											.	MUS81	68	.	0			c.A296T						PASS	.						33	32	32					11																	65628851		2191	4295	6486	SO:0001583	missense	80198	exon3			CTGGAGAGAACAG		CCDS8115.1	11q13	2013-07-03	2013-07-03			ENSG00000172732			29814	protein-coding gene	gene with protein product	"SLX3 structure-specific endonuclease subunit homolog (S. cerevisiae)"	606591	"MUS81 endonuclease homolog (yeast)", "MUS81 endonuclease homolog (S. cerevisiae)"			11741546, 12374758	Standard	NM_025128		Approved	FLJ44872, SLX3	uc001ofv.4	Q96NY9		ENST00000308110.4:c.296A>T	chr11.hg19:g.65628851A>T	ENSP00000307853:p.Glu99Val	44.0	0.0	.		48.0	17.0	.	NM_025128	Q9H7D9	Missense_Mutation	SNP	ENST00000308110.4	hg19	CCDS8115.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.77|10.77	1.444355|1.444355	0.25987|0.25987	.|.	.|.	ENSG00000172732|ENSG00000172732	ENST00000529857;ENST00000533035;ENST00000308110;ENST00000437855;ENST00000525768|ENST00000529374	T;T;T;T|.	0.49139|.	0.79;2.41;0.79;1.77|.	3.66|3.66	-0.0927|-0.0927	0.13655|0.13655	.|.	2.043970|.	0.01586|.	N|.	0.021309|.	T|T	0.20536|0.20536	0.0494|0.0494	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	B|.	0.15473|.	0.013|.	B|.	0.10450|.	0.005|.	T|T	0.26950|0.26950	-1.0088|-1.0088	10|5	0.28530|.	T|.	0.3|.	0.0131|0.0131	5.0512|5.0512	0.14508|0.14508	0.4401:0.4472:0.1127:0.0|0.4401:0.4472:0.1127:0.0	.|.	99|.	Q96NY9|.	MUS81_HUMAN|.	V|S	164;24;99;99;24|23	ENSP00000431979:E164V;ENSP00000432287:E24V;ENSP00000307853:E99V;ENSP00000431478:E24V|.	ENSP00000307853:E99V|.	E|R	+|+	2|3	0|2	MUS81|MUS81	65385427|65385427	0.009000|0.009000	0.17119|0.17119	0.004000|0.004000	0.12327|0.12327	0.013000|0.013000	0.08279|0.08279	0.123000|0.123000	0.15708|0.15708	-0.026000|-0.026000	0.13895|0.13895	0.448000|0.448000	0.29417|0.29417	GAG|AGA	.	.	.	none		0.607	MUS81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390941.3	NM_025128		T	65628851	A	T	65628851	3	4	5	1	0	0	0	0	1	0	0	0	9995	304	11	5	306	5	MUS81	11	65628851	Missense_Mutation	SNP	A	TCGA-2Z-A9J5-01A-21D-A382-10	813194	65628851	69377665	60	456											
C11orf82	220042	hgsc.bcm.edu	37	chr11	82643420	82643420	+	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	ctctttggaaatgcgagagcCccttgagtcaagtaatacaa	13	10	9	9	1	2	2	1	1	1	1	2	4	2	3	2	1	3	1	2	1	5	4			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr11:82643420C>T	ENST00000533655.1	+	6	1252	c.1040C>T	c.(1039-1041)cCc>cTc	p.P347L	C11orf82_ENST00000329143.3_Missense_Mutation_p.P46L|C11orf82_ENST00000525361.1_Intron|C11orf82_ENST00000528759.1_3'UTR|C11orf82_ENST00000430323.2_Missense_Mutation_p.P347L	NM_145018.3	NP_659455.3	Q8IXT1	DDIAS_HUMAN		347					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						ATGCGAGAGCCCCTTGAGTCA	0.408																																					p.P347L		Atlas-SNP	.											.	C11orf82	71	.	0			c.C1040T						PASS	.						98	108	105					11																	82643420		2203	4300	6503	SO:0001583	missense	220042	exon6			GAGAGCCCCTTGA																												ENST00000533655.1:c.1040C>T	chr11.hg19:g.82643420C>T	ENSP00000435421:p.Pro347Leu	94.0	0.0	.		71.0	19.0	.	NM_145018	Q96LK6|Q9H856	Missense_Mutation	SNP	ENST00000533655.1	hg19	CCDS8263.1	.	.	.	.	.	.	.	.	.	.	C	6.484	0.457558	0.12342	.	.	ENSG00000165490	ENST00000430323;ENST00000533655;ENST00000329143	T;T;T	0.21932	2.22;2.22;1.98	5.58	-2.57	0.06248	.	1.219580	0.05461	N	0.551274	T	0.18383	0.0441	L	0.55481	1.735	0.09310	N	1	B	0.12630	0.006	B	0.11329	0.006	T	0.30238	-0.9985	9	.	.	.	7.3012	5.3775	0.16174	0.0:0.4007:0.2401:0.3592	.	347	Q8IXT1	NOXIN_HUMAN	L	347;347;46	ENSP00000414687:P347L;ENSP00000435421:P347L;ENSP00000329930:P46L	.	P	+	2	0	C11orf82	82321068	0.000000	0.05858	0.000000	0.03702	0.100000	0.18952	0.291000	0.18994	-0.836000	0.04229	-0.259000	0.10710	CCC	.	.	.	none		0.408	C11orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391936.1			T	82643420	C	T	82643420	3	4	5	1	0	0	0	0	1	0	0	0	1667	623	22	2	1054	2	C11orf82	11	82643420	Missense_Mutation	SNP	C	TCGA-2Z-A9J5-01A-21D-A382-10	17014569	82643420	52363096	61	457											
ARHGAP20	57569	hgsc.bcm.edu	37	chr11	110451689	110451689	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttgtgtacactaaaatgtTcaccggcttggattcaagag	11	13	9	8	1	2	1	2	0	0	1	2	2	2	2	1	2	1	3	1	2	4	6			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr11:110451689T>C	ENST00000260283.4	-	16	2265	c.1981A>G	c.(1981-1983)Aac>Gac	p.N661D	ARHGAP20_ENST00000529591.1_Missense_Mutation_p.N204D|ARHGAP20_ENST00000528829.1_Missense_Mutation_p.N625D|ARHGAP20_ENST00000357139.3_Missense_Mutation_p.N635D|ARHGAP20_ENST00000533353.1_Missense_Mutation_p.N635D|ARHGAP20_ENST00000524756.1_Missense_Mutation_p.N638D|ARHGAP20_ENST00000527598.1_Missense_Mutation_p.N625D	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	661					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)		ACTAAAATGTTCACCGGCTTG	0.517																																					p.N661D		Atlas-SNP	.											.	ARHGAP20	150	.	0			c.A1981G						PASS	.						83	82	82					11																	110451689		2201	4298	6499	SO:0001583	missense	57569	exon16			AAATGTTCACCGG	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.1981A>G	chr11.hg19:g.110451689T>C	ENSP00000260283:p.Asn661Asp	93.0	0.0	.		86.0	17.0	.	NM_020809	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Missense_Mutation	SNP	ENST00000260283.4	hg19	CCDS31673.1	.	.	.	.	.	.	.	.	.	.	T	3.414	-0.119605	0.06838	.	.	ENSG00000137727	ENST00000260283;ENST00000357139;ENST00000529591;ENST00000524756;ENST00000528829;ENST00000533353;ENST00000527598	T;T;T;T;T;T;T	0.09073	3.02;3.02;3.06;3.02;3.02;3.02;3.02	5.37	1.55	0.23275	.	1.230650	0.05450	N	0.549242	T	0.05593	0.0147	N	0.16478	0.41	0.09310	N	0.999999	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.06405	0.002;0.001;0.002	T	0.40813	-0.9543	10	0.41790	T	0.15	.	3.1674	0.06540	0.243:0.2555:0.0:0.5016	.	635;661;638	Q9P2F6-2;Q9P2F6;Q9P2F6-3	.;RHG20_HUMAN;.	D	661;635;204;638;625;635;625	ENSP00000260283:N661D;ENSP00000349660:N635D;ENSP00000437905:N204D;ENSP00000432076:N638D;ENSP00000436319:N625D;ENSP00000436522:N635D;ENSP00000431399:N625D	ENSP00000260283:N661D	N	-	1	0	ARHGAP20	109956899	0.000000	0.05858	0.099000	0.21106	0.006000	0.05464	-0.012000	0.12699	0.357000	0.24183	0.383000	0.25322	AAC	.	.	.	none		0.517	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809		C	110451689	T	C	110451689	3	2	5	1	0	0	0	0	1	0	0	0	870	1783	62	3	1598	3	ARHGAP20	11	110451689	Missense_Mutation	SNP	T	TCGA-2Z-A9J5-01A-21D-A382-10	27808269	110451689	24554827	62	458											
CLEC7A	64581	hgsc.bcm.edu	37	chr12	10279210	10279211	+	Frame_Shift_Ins	INS	-	-	A																															taggagtcacactgtcttctINSaaagatgattgtgtgggttg																										TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr12:10279210_10279211insA	ENST00000304084.8	-	3	453_454	c.299_300insT	c.(298-300)ttafs	p.L100fs	CLEC7A_ENST00000533022.1_Frame_Shift_Ins_p.L100fs|CLEC7A_ENST00000353231.5_Intron|CLEC7A_ENST00000396484.2_Intron|CLEC7A_ENST00000298523.5_Intron	NM_197947.2	NP_922938.1	Q9BXN2	CLC7A_HUMAN	C-type lectin domain family 7, member A	100					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						CACTGTCTTCTAAAGATGATTG	0.421																																					p.L100fs		Pindel	.											.	CLEC7A	55	.	0			c.300_301insT						PASS	.																																			SO:0001589	frameshift_variant	64581	exon3			.	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.300dupT	chr12.hg19:g.10279213_10279213dupA	ENSP00000302569:p.Leu100fs	76.0	0.0	.		111.0	15.0	0.135	NM_197947	B2R861|B7Z494|B7Z5A9|B7Z5B9|Q6IPS7|Q96D32|Q96DR9|Q96LD3|Q96PA4|Q96PA5|Q96PA6|Q96PA7|Q96PA8|Q9H1K3	Frame_Shift_Ins	INS	ENST00000304084.8	hg19	CCDS41753.1																																																																																			.	.	.	none		0.421	CLEC7A-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390772.1	NM_197954		A	10279211	-	A	10279210	7	5	5	1	0	1	1	0	0	0	0	0	3523	1519	53	0	459	0	CLEC7A	12	10279210	Frame_Shift_Ins	INS	-	TCGA-2Z-A9J5-01A-21D-A382-10		10279210	123572685	63	459											
FRS2	10818	hgsc.bcm.edu	37	chr12	69962872	69962872	+	Missense_Mutation	SNP	T	T	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	agataaccatcggaacaagtTtaaggtcagtaaaactggtt	16	10	9	6	1	1	1	1	0	0	1	2	2	1	2	1	3	3	3	1	3	6	5			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr12:69962872T>G	ENST00000550389.1	+	3	308	c.62T>G	c.(61-63)tTt>tGt	p.F21C	FRS2_ENST00000397997.2_Missense_Mutation_p.F21C|FRS2_ENST00000299293.2_Missense_Mutation_p.F21C|FRS2_ENST00000549921.1_Missense_Mutation_p.F21C	NM_001278353.1|NM_001278357.1	NP_001265282.1|NP_001265286.1	Q8WU20	FRS2_HUMAN	fibroblast growth factor receptor substrate 2	21	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|anterior/posterior axis specification, embryo (GO:0008595)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|gastrulation with mouth forming second (GO:0001702)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|lens fiber cell development (GO:0070307)|neuroblast proliferation (GO:0007405)|neurotrophin TRK receptor signaling pathway (GO:0048011)|optic placode formation involved in camera-type eye formation (GO:0046619)|organ induction (GO:0001759)|phosphatidylinositol-mediated signaling (GO:0048015)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|regulation of apoptotic process (GO:0042981)|regulation of epithelial cell proliferation (GO:0050678)|regulation of ERK1 and ERK2 cascade (GO:0070372)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	fibroblast growth factor receptor binding (GO:0005104)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatase activator activity (GO:0019211)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22	Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.94e-18)|Lung(24;9.68e-05)|OV - Ovarian serous cystadenocarcinoma(12;0.000984)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)			CGGAACAAGTTTAAGGTCAGT	0.378																																					p.F21C		Atlas-SNP	.											.	FRS2	88	.	0			c.T62G						PASS	.						88	86	86					12																	69962872		1849	4090	5939	SO:0001583	missense	10818	exon6			ACAAGTTTAAGGT	AF036717	CCDS41809.1	12q15	2008-02-05				ENSG00000166225			16971	protein-coding gene	gene with protein product		607743				8761293, 9660748	Standard	NM_001278351		Approved	SNT-1, FRS2alpha, SNT1, FRS2A	uc001suz.3	Q8WU20		ENST00000550389.1:c.62T>G	chr12.hg19:g.69962872T>G	ENSP00000447241:p.Phe21Cys	85.0	0.0	.		125.0	59.0	.	NM_001042555	B0LPF2|B2R684|O43558|Q7LDQ6	Missense_Mutation	SNP	ENST00000550389.1	hg19	CCDS41809.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.633974	0.87660	.	.	ENSG00000166225	ENST00000547219;ENST00000299293;ENST00000549921;ENST00000548154;ENST00000550389;ENST00000550937;ENST00000549092;ENST00000397997;ENST00000551325	D;D;D;D;D;D	0.91011	-2.77;-2.77;-2.77;-2.77;-2.77;-2.77	5.22	5.22	0.72569	Pleckstrin homology-type (1);Insulin receptor substrate-1, PTB (3);	0.000000	0.85682	D	0.000000	D	0.95367	0.8496	M	0.83953	2.67	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95594	0.8657	9	.	.	.	-20.3769	15.4105	0.74914	0.0:0.0:0.0:1.0	.	21	Q8WU20	FRS2_HUMAN	C	21	ENSP00000299293:F21C;ENSP00000450048:F21C;ENSP00000447241:F21C;ENSP00000447804:F21C;ENSP00000381083:F21C;ENSP00000449432:F21C	.	F	+	2	0	FRS2	68249139	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.997000	0.88414	2.100000	0.63781	0.533000	0.62120	TTT	.	.	.	none		0.378	FRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403760.1	NM_006654		G	69962872	T	G	69962872	3	3	5	1	0	0	0	0	1	0	0	0	6068	1841	64	5	64	5	FRS2	12	69962872	Missense_Mutation	SNP	T	TCGA-2Z-A9J5-01A-21D-A382-10	59683662	69962872	63889023	64	460											
MYO1H	283446	hgsc.bcm.edu	37	chr12	109858829	109858829	+	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	cttctttacagacatctgaaAgaagtaagtctgacacttaa	15	12	6	8	0	3	4	0	2	3	2	3	4	3	4	0	0	1	1	0	0	5	5			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr12:109858829A>T	ENST00000431443.2	+	15	1623	c.1623A>T	c.(1621-1623)aaA>aaT	p.K541N	MYO1H_ENST00000310903.5_Missense_Mutation_p.K531N	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	541	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						GACATCTGAAAGAAGTAAGTC	0.284																																					p.K531N		Atlas-SNP	.											.	MYO1H	98	.	0			c.A1593T						PASS	.						69	66	67					12																	109858829		1795	4064	5859	SO:0001583	missense	283446	exon15			TCTGAAAGAAGTA		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.1623A>T	chr12.hg19:g.109858829A>T	ENSP00000444076:p.Lys541Asn	86.0	0.0	.		118.0	7.0	.	NM_001101421	F5H3C6	Missense_Mutation	SNP	ENST00000431443.2	hg19		.	.	.	.	.	.	.	.	.	.	A	20.4	3.990003	0.74589	.	.	ENSG00000174527	ENST00000310903;ENST00000431443	D;D	0.87179	-2.22;-2.22	5.0	2.64	0.31445	.	.	.	.	.	D	0.90584	0.7048	M	0.87038	2.855	0.40543	D	0.981045	D	0.59357	0.985	P	0.53722	0.733	D	0.89020	0.3434	9	0.54805	T	0.06	.	8.3992	0.32574	0.8368:0.0:0.1632:0.0	.	531	F5H3C6	.	N	531;541	ENSP00000439182:K531N;ENSP00000444076:K541N	ENSP00000439182:K531N	K	+	3	2	MYO1H	108343212	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	2.758000	0.47565	0.379000	0.24794	0.533000	0.62120	AAA	.	.	.	none		0.284	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597		T	109858829	A	T	109858829	3	4	5	1	0	0	0	0	1	0	0	0	10082	69	3	5	1651	5	MYO1H	12	109858829	Missense_Mutation	SNP	A	TCGA-2Z-A9J5-01A-21D-A382-10	39895957	109858829	23993066	65	461											
TSC22D1	8848	hgsc.bcm.edu	37	chr13	45008845	45008845	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggtggtggcagggggggAgccagtctgcagctgggcct	4	7	21	9	0	1	0	0	0	1	0	1	1	1	1	2	7	3	3	2	7	0	0			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr13:45008845A>G	ENST00000458659.2	-	3	3629	c.3139T>C	c.(3139-3141)Tcc>Ccc	p.S1047P	TSC22D1_ENST00000501704.2_Intron|RP11-71C5.2_ENST00000426579.2_RNA|TSC22D1_ENST00000261489.2_Missense_Mutation_p.S118P	NM_183422.3	NP_904358.2	Q15714	T22D1_HUMAN	TSC22 domain family, member 1	1047					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)		GCAGGGGGGGAGCCAGTCTGC	0.627																																					p.S1047P		Atlas-SNP	.											.	TSC22D1	88	.	0			c.T3139C						PASS	.						26	31	29					13																	45008845		2201	4298	6499	SO:0001583	missense	8848	exon3			GGGGGGAGCCAGT	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.3139T>C	chr13.hg19:g.45008845A>G	ENSP00000397435:p.Ser1047Pro	33.0	0.0	.		51.0	23.0	.	NM_183422	B3KRL7|B9EGI0|O00666|Q6AHX5|Q6IBU1|Q8NCN1|Q96JS5	Missense_Mutation	SNP	ENST00000458659.2	hg19	CCDS31966.1	.	.	.	.	.	.	.	.	.	.	A	11.59	1.682552	0.29872	.	.	ENSG00000102804	ENST00000458659;ENST00000261489	T	0.36878	1.23	5.91	5.91	0.95273	.	0.267097	0.27088	N	0.020995	T	0.51210	0.1661	L	0.40543	1.245	0.80722	D	1	D;D	0.76494	0.999;0.965	D;P	0.77557	0.99;0.469	T	0.46020	-0.9221	10	0.42905	T	0.14	.	15.1833	0.72978	1.0:0.0:0.0:0.0	.	1047;118	Q15714;Q15714-2	T22D1_HUMAN;.	P	1047;118	ENSP00000397435:S1047P	ENSP00000261489:S118P	S	-	1	0	TSC22D1	43906845	1.000000	0.71417	1.000000	0.80357	0.109000	0.19521	1.907000	0.39897	2.254000	0.74563	0.533000	0.62120	TCC	.	.	.	none		0.627	TSC22D1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044743.2	NM_006022		G	45008845	A	G	45008845	3	3	5	1	0	0	0	0	1	0	0	0	16619	304	11	3	86	3	TSC22D1	13	45008845	Missense_Mutation	SNP	A	TCGA-2Z-A9J5-01A-21D-A382-10		45008845	70161033	66	462											
GPR183	1880	hgsc.bcm.edu	37	chr13	99947502	99947502	+	Missense_Mutation	SNP	T	T	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	aaaagggtccatgcagcaatTgaagttcatcaggcatactg	14	9	10	8	0	2	1	2	1	0	0	3	1	3	1	1	2	3	4	1	2	5	3			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr13:99947502T>G	ENST00000376414.4	-	2	981	c.898A>C	c.(898-900)Aat>Cat	p.N300H	UBAC2_ENST00000376440.2_Intron|UBAC2_ENST00000403766.3_Intron	NM_004951.4	NP_004942.1	P32249	GP183_HUMAN	G protein-coupled receptor 183	300					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						ATGCAGCAATTGAAGTTCATC	0.388																																					p.N300H		Atlas-SNP	.											.	GPR183	38	.	0			c.A898C						PASS	.						101	93	96					13																	99947502		2203	4300	6503	SO:0001583	missense	1880	exon2			AGCAATTGAAGTT	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.898A>C	chr13.hg19:g.99947502T>G	ENSP00000365596:p.Asn300His	129.0	0.0	.		139.0	42.0	.	NM_004951	B2R8N5|Q53F99|Q5JUH7	Missense_Mutation	SNP	ENST00000376414.4	hg19	CCDS9492.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.177974	0.78564	.	.	ENSG00000169508	ENST00000376414	T	0.52526	0.66	5.91	5.91	0.95273	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.69205	0.3085	M	0.75615	2.305	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.70364	-0.4892	9	.	.	.	.	16.3483	0.83171	0.0:0.0:0.0:1.0	.	300	P32249	GP183_HUMAN	H	300	ENSP00000365596:N300H	.	N	-	1	0	GPR183	98745503	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.254000	0.74563	0.533000	0.62120	AAT	.	.	.	none		0.388	GPR183-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045582.2	NM_004951		G	99947502	T	G	99947502	3	3	5	1	0	0	0	0	1	0	0	0	6685	1812	63	5	191	5	GPR183	13	99947502	Missense_Mutation	SNP	T	TCGA-2Z-A9J5-01A-21D-A382-10	54938657	99947502	15222376	67	463											
SYNE2	23224	hgsc.bcm.edu	37	chr14	64593109	64593109	+	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	gtttgaactattcctgacccTcagtcagtgcctcagcagtg	8	12	9	12	0	3	2	3	2	0	0	4	2	4	2	3	0	3	2	3	0	2	3			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr14:64593109T>A	ENST00000344113.4	+	72	13831	c.13619T>A	c.(13618-13620)cTc>cAc	p.L4540H	ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000358025.3_Missense_Mutation_p.L4540H|SYNE2_ENST00000357395.3_Missense_Mutation_p.L925H|SYNE2_ENST00000394768.2_Missense_Mutation_p.L925H|SYNE2_ENST00000554584.1_Missense_Mutation_p.L4491H|SYNE2_ENST00000555002.1_Missense_Mutation_p.L1174H	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	4540					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)		TTCCTGACCCTCAGTCAGTGC	0.428																																					p.L4540H		Atlas-SNP	.											.	SYNE2	577	.	0			c.T13619A						PASS	.						82	81	81					14																	64593109		2203	4300	6503	SO:0001583	missense	23224	exon72			TGACCCTCAGTCA	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.13619T>A	chr14.hg19:g.64593109T>A	ENSP00000341781:p.Leu4540His	223.0	0.0	.		273.0	78.0	.	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	T	13.43	2.234296	0.39498	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	T;T;T;T;T;T	0.62105	0.69;3.99;0.68;0.05;4.04;3.99	5.81	5.81	0.92471	.	0.145716	0.31542	N	0.007462	T	0.69424	0.3109	L	0.29908	0.895	0.80722	D	1	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.72338	0.917;0.95;0.977	T	0.72868	-0.4162	10	0.72032	D	0.01	.	14.7401	0.69448	0.0:0.0:0.0:1.0	.	925;4540;4540	Q8WXH0-7;Q8WXH0;Q8WXH0-2	.;SYNE2_HUMAN;.	H	4540;925;4540;4491;4491;1174;925	ENSP00000350719:L4540H;ENSP00000349969:L925H;ENSP00000341781:L4540H;ENSP00000452570:L4491H;ENSP00000450831:L1174H;ENSP00000378249:L925H	ENSP00000261678:L4491H	L	+	2	0	SYNE2	63662862	0.997000	0.39634	0.973000	0.42090	0.936000	0.57629	4.859000	0.62954	2.213000	0.71641	0.533000	0.62120	CTC	.	.	.	none		0.428	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		A	64593109	T	A	64593109	3	1	5	1	0	0	0	0	1	0	0	0	15458	1551	54	5	13901	5	SYNE2	14	64593109	Missense_Mutation	SNP	T	TCGA-2Z-A9J5-01A-21D-A382-10		64593109	42756431	68	464											
YLPM1	56252	hgsc.bcm.edu	37	chr14	75276225	75276225	+	Missense_Mutation	SNP	T	T	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	acctccacctcctccacctcTacctcctcctcctccagtga	6	10	2	23	0	1	1	0	1	1	0	8	1	8	1	11	0	1	0	11	0	1	1			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr14:75276225T>G	ENST00000552421.1	+	6	2670	c.2546T>G	c.(2545-2547)cTa>cGa	p.L849R	YLPM1_ENST00000325680.7_Missense_Mutation_p.L1555R|YLPM1_ENST00000238571.3_Missense_Mutation_p.L1360R			P49750	YLPM1_HUMAN	YLP motif containing 1	1360	Arg-rich.				regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		cctccacctctacctcctcct	0.502																																					p.L1555R		Atlas-SNP	.											.	YLPM1	298	.	0			c.T4664G						PASS	.						82	80	81					14																	75276225		2002	4190	6192	SO:0001583	missense	56252	exon7			CACCTCTACCTCC	AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 169"		"chromosome 14 open reading frame 170"	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000552421.1:c.2546T>G	chr14.hg19:g.75276225T>G	ENSP00000447921:p.Leu849Arg	82.0	0.0	.		77.0	17.0	.	NM_019589	P49752|Q96I64|Q9P1V7	Missense_Mutation	SNP	ENST00000552421.1	hg19		.	.	.	.	.	.	.	.	.	.	T	6.984	0.551642	0.13374	.	.	ENSG00000119596	ENST00000552421;ENST00000325680;ENST00000238571;ENST00000423680	.	.	.	5.09	4.19	0.49359	.	0.475155	0.19470	N	0.113468	T	0.27663	0.0680	N	0.14661	0.345	0.25321	N	0.989116	B;B	0.16603	0.018;0.018	B;B	0.20955	0.026;0.032	T	0.23762	-1.0179	9	0.62326	D	0.03	-0.0056	11.0988	0.48161	0.0:0.9121:0.0:0.0879	.	1360;1555	P49750-3;P49750-4	.;.	R	849;1555;1360;1268	.	ENSP00000238571:L1360R	L	+	2	0	YLPM1	74345978	0.171000	0.23029	0.575000	0.28536	0.367000	0.29736	2.720000	0.47252	1.109000	0.41680	-0.462000	0.05337	CTA	.	.	.	none		0.502	YLPM1-008	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404450.1	NM_019589		G	75276225	T	G	75276225	3	3	5	1	0	0	0	0	1	0	0	0	17498	1522	53	5	4690	5	YLPM1	14	75276225	Missense_Mutation	SNP	T	TCGA-2Z-A9J5-01A-21D-A382-10	10683116	75276225	32073315	69	465											
C14orf118	55668	hgsc.bcm.edu	37	chr14	76662242	76662242	+	Frame_Shift_Del	DEL	A	A	-																															caggcaaatgtacactggggAccaccatgttcacgtgacat																										TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr14:76662242delA	ENST00000261530.7	+	9	1281	c.1215delA	c.(1213-1215)ggafs	p.G405fs	GPATCH2L_ENST00000553588.1_Frame_Shift_Del_p.D26fs|GPATCH2L_ENST00000312858.5_Frame_Shift_Del_p.G400fs|GPATCH2L_ENST00000556675.1_3'UTR	NM_017926.2	NP_060396.2	Q9NWQ4	GPT2L_HUMAN	G patch domain containing 2-like	405																	TACACTGGGGACCACCATGTT	0.408																																					p.G405fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.1214delG						PASS	.						197	187	190					14																	76662242		2203	4300	6503	SO:0001589	frameshift_variant	55668	exon9			.	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.1215delA	chr14.hg19:g.76662242delA	ENSP00000261530:p.Gly405fs	74.0	0.0	0		75.0	12.0	0.16	NM_017926	B3KN42|Q6PEJ7|Q9H3M3|Q9NWH0|Q9ULR8	Frame_Shift_Del	DEL	ENST00000261530.7	hg19	CCDS9848.1																																																																																			.	.	.	none		0.408	GPATCH2L-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000413698.2	NM_017926		-	76662242	A	-	76662242	7	5	5	1	0	1	0	1	0	0	0	0	1743	262	10	0	1289	0	C14orf118	14	76662242	Frame_Shift_Del	DEL	A	TCGA-2Z-A9J5-01A-21D-A382-10	1386017	76662242	30687298	70	466											
SPPL2A	84888	hgsc.bcm.edu	37	chr15	51028376	51028376	+	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	gaaaaataagtctcacttccAtgtttttgccacgacatgca	13	12	6	10	1	1	0	1	0	1	0	3	2	2	0	2	0	2	2	2	0	3	4			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr15:51028376A>T	ENST00000261854.5	-	8	1128	c.854T>A	c.(853-855)aTg>aAg	p.M285K		NM_032802.3	NP_116191.2	Q8TCT8	SPP2A_HUMAN	signal peptide peptidase like 2A	285					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)		TCTCACTTCCATGTTTTTGCC	0.348																																					p.M285K	Melanoma(50;790 1209 4069 22965 33125)	Atlas-SNP	.											.	SPPL2A	26	.	0			c.T854A						PASS	.						133	112	119					15																	51028376		2196	4294	6490	SO:0001583	missense	84888	exon8			ACTTCCATGTTTT		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.854T>A	chr15.hg19:g.51028376A>T	ENSP00000261854:p.Met285Lys	65.0	0.0	.		56.0	13.0	.	NM_032802	B2RDS0|Q8TAW1|Q96SZ8	Missense_Mutation	SNP	ENST00000261854.5	hg19	CCDS10138.1	.	.	.	.	.	.	.	.	.	.	A	12.31	1.898643	0.33535	.	.	ENSG00000138600	ENST00000261854	T	0.17054	2.3	5.07	2.72	0.32119	.	0.534882	0.21346	N	0.076048	T	0.09512	0.0234	N	0.19112	0.55	0.22378	N	0.999157	B	0.22414	0.069	B	0.11329	0.006	T	0.31024	-0.9958	10	0.27785	T	0.31	-4.6682	7.4553	0.27264	0.7429:0.0:0.2571:0.0	.	285	Q8TCT8	PSL2_HUMAN	K	285	ENSP00000261854:M285K	ENSP00000261854:M285K	M	-	2	0	AC012100.1	48815668	0.996000	0.38824	1.000000	0.80357	0.815000	0.46073	4.339000	0.59322	0.350000	0.24002	-0.371000	0.07208	ATG	.	.	.	none		0.348	SPPL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254543.3	NM_032802		T	51028376	A	T	51028376	3	4	5	1	0	0	0	0	1	0	0	0	15100	217	8	5	740	5	SPPL2A	15	51028376	Missense_Mutation	SNP	A	TCGA-2Z-A9J5-01A-21D-A382-10		51028376	51503016	71	467											
KIAA1370	56204	hgsc.bcm.edu	37	chr15	52901851	52901851	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atggagaaagcttctttaccTtttcccacgttctcattttc	8	17	5	11	1	2	1	1	0	2	1	5	2	3	1	2	1	2	2	2	1	2	8			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr15:52901851T>C	ENST00000261844.7	-	6	1412	c.1260A>G	c.(1258-1260)aaA>aaG	p.K420K	FAM214A_ENST00000546305.2_Silent_p.K427K	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	420																	CTTCTTTACCTTTTCCCACGT	0.413																																					p.K420K		Atlas-SNP	.											.	.	.	.	0			c.A1260G						PASS	.						67	60	62					15																	52901851		1821	4073	5894	SO:0001819	synonymous_variant	56204	exon6			TTTACCTTTTCCC	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.1260A>G	chr15.hg19:g.52901851T>C		61.0	0.0	.		57.0	14.0	.	NM_019600	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Silent	SNP	ENST00000261844.7	hg19	CCDS45263.1																																																																																			.	.	.	none		0.413	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600		C	52901851	T	C	52901851	2	2	5	1	0	0	0	0	0	0	0	1	8233	1606	56	3		3	KIAA1370	15	52901851	Silent	SNP	T	TCGA-2Z-A9J5-01A-21D-A382-10	1873475	52901851	49629541	72	468											
POLG	5428	hgsc.bcm.edu	37	chr15	89870191	89870191	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccagccccctcgatgggcaActtgctggctgtggctggtt	4	10	13	14	1	0	0	0	0	0	0	1	1	0	0	3	4	3	5	3	4	1	2			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr15:89870191A>G	ENST00000268124.5	-	8	1870	c.1537T>C	c.(1537-1539)Ttg>Ctg	p.L513L	POLG_ENST00000442287.2_Silent_p.L513L	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	513					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)			TCGATGGGCAACTTGCTGGCT	0.582								DNA polymerases (catalytic subunits)																													p.L513L	Colon(73;648 1203 11348 18386 27782)	Atlas-SNP	.											.	POLG	75	.	0			c.T1537C						PASS	.						139	129	132					15																	89870191		2200	4299	6499	SO:0001819	synonymous_variant	5428	exon8			TGGGCAACTTGCT	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.1537T>C	chr15.hg19:g.89870191A>G		67.0	0.0	.		70.0	23.0	.	NM_002693	Q8NFM2|Q92515	Silent	SNP	ENST00000268124.5	hg19	CCDS10350.1																																																																																			.	.	.	none		0.582	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000312854.2	NM_002693		G	89870191	A	G	89870191	2	3	5	1	0	0	0	0	0	0	0	1	12207	40	2	3		3	POLG	15	89870191	Silent	SNP	A	TCGA-2Z-A9J5-01A-21D-A382-10	36968340	89870191	12661201	73	469											
WFIKKN1	117166	hgsc.bcm.edu	37	chr16	682600	682600	+	Frame_Shift_Del	DEL	A	A	-																															aggactgtgcggctgctgagAagtgctgcatcaacgtgtgt																										TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr16:682600delA	ENST00000319070.2	+	2	512	c.190delA	c.(190-192)aagfs	p.K64fs		NM_053284.2	NP_444514.1	Q96NZ8	WFKN1_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 1	64	WAP. {ECO:0000255|PROSITE- ProRule:PRU00722}.				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)				GGCTGCTGAGAAGTGCTGCAT	0.697																																					p.E63fs		Atlas-Indel,Pindel	.											WFIKKN1,larynx,carcinoma,0,1	WFIKKN1	30	.	0			c.189delG						PASS	.						22	24	24					16																	682600		2175	4293	6468	SO:0001589	frameshift_variant	117166	exon2			.	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.190delA	chr16.hg19:g.682600delA	ENSP00000324763:p.Lys64fs	133.0	0.0	0		187.0	35.0	0.187166	NM_053284	Q7LDW0|Q8NBQ1|Q96S20	Frame_Shift_Del	DEL	ENST00000319070.2	hg19	CCDS10414.1																																																																																			.	.	.	none		0.697	WFIKKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206731.2	NM_053284		-	682600	A	-	682600	7	5	5	1	0	1	0	1	0	0	0	0	17370	247	9	0	196	0	WFIKKN1	16	682600	Frame_Shift_Del	DEL	A	TCGA-2Z-A9J5-01A-21D-A382-10		682600	89672153	74	470											
TFAP4	7023	hgsc.bcm.edu	37	chr16	4311843	4311843	+	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	tgctgccgcagctcaatcatCtcccgccgcaggtcctccgc	5	8	9	19	4	3	0	2	0	1	0	6	0	5	0	5	1	3	4	5	1	1	0			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr16:4311843C>G	ENST00000204517.6	-	4	790	c.462G>C	c.(460-462)gaG>gaC	p.E154D		NM_003223.2	NP_003214.1	Q01664	TFAP4_HUMAN	transcription factor AP-4 (activating enhancer binding protein 4)	154	Leucine-zipper 2.				cellular response to dexamethasone stimulus (GO:0071549)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001269)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|histone deacetylase binding (GO:0042826)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|endometrium(2)|lung(8)|ovary(1)|prostate(1)|skin(1)	14						GCTCAATCATCTCCCGCCGCA	0.692											OREG0023575	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E154D		Atlas-SNP	.											.	TFAP4	31	.	0			c.G462C						PASS	.						38	36	37					16																	4311843		2196	4300	6496	SO:0001583	missense	7023	exon4			AATCATCTCCCGC	X57435	CCDS10510.1	16p13	2013-05-21	2001-11-28		ENSG00000090447	ENSG00000090447		"Basic helix-loop-helix proteins"	11745	protein-coding gene	gene with protein product		600743	"transcription factor AP-4 (activating enhancer-binding protein 4)"			2123466	Standard	NM_003223		Approved	AP-4, bHLHc41	uc010uxg.2	Q01664	OTTHUMG00000129435	ENST00000204517.6:c.462G>C	chr16.hg19:g.4311843C>G	ENSP00000204517:p.Glu154Asp	57.0	0.0	.	617	78.0	43.0	.	NM_003223	O60409	Missense_Mutation	SNP	ENST00000204517.6	hg19	CCDS10510.1	.	.	.	.	.	.	.	.	.	.	C	12.55	1.972243	0.34754	.	.	ENSG00000090447	ENST00000204517	D	0.99023	-5.34	5.03	5.03	0.67393	.	0.060936	0.64402	D	0.000005	D	0.97077	0.9045	L	0.46157	1.445	0.46078	D	0.998852	B	0.09022	0.002	B	0.08055	0.003	D	0.95121	0.8246	10	0.35671	T	0.21	.	11.4972	0.50415	0.0:0.9161:0.0:0.0839	.	154	Q01664	TFAP4_HUMAN	D	154	ENSP00000204517:E154D	ENSP00000204517:E154D	E	-	3	2	TFAP4	4251844	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	0.767000	0.26575	2.330000	0.79161	0.462000	0.41574	GAG	.	.	.	none		0.692	TFAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251595.2	NM_003223		G	4311843	C	G	4311843	3	3	5	1	0	0	0	0	1	0	0	0	15804	912	32	4	570	4	TFAP4	16	4311843	Missense_Mutation	SNP	C	TCGA-2Z-A9J5-01A-21D-A382-10	3629243	4311843	86042910	75	471											
SOCS1	8651	hgsc.bcm.edu	37	chr16	11348785	11348785	+	Missense_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	ggttctcgcggcccacggtgGccacgatgcgctggcggcac	4	6	16	15	6	1	0	0	0	1	0	2	1	1	0	2	6	1	3	2	6	0	1			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr16:11348785G>A	ENST00000332029.2	-	2	701	c.551C>T	c.(550-552)gCc>gTc	p.A184V	RMI2_ENST00000572173.1_Intron	NM_003745.1	NP_003736.1	O15524	SOCS1_HUMAN	suppressor of cytokine signaling 1	184	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.R127_*212del(1)|p.0?(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(66)|lung(3)	71						GCCCACGGTGGCCACGATGCG	0.741			"F, O"		"Hodgkin Lymphoma, PMBL"																																p.A184V	Colon(177;456 3548 27231)	Atlas-SNP	.		Rec	yes		16	16p13.13	8651	suppressor of cytokine signaling 1		L	.	SOCS1	84	.	2	Whole gene deletion(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(2)	c.C551T						PASS	.						9	9	9					16																	11348785		2159	4260	6419	SO:0001583	missense	8651	exon2			ACGGTGGCCACGA	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.551C>T	chr16.hg19:g.11348785G>A	ENSP00000329418:p.Ala184Val	99.0	0.0	.		188.0	47.0	.	NM_003745	O15097|Q9NSA7	Missense_Mutation	SNP	ENST00000332029.2	hg19	CCDS10546.1	.	.	.	.	.	.	.	.	.	.	G	15.83	2.948453	0.53186	.	.	ENSG00000185338	ENST00000332029	T	0.44083	0.93	4.25	4.25	0.50352	SOCS protein, C-terminal (4);	0.656455	0.15111	N	0.279946	T	0.45776	0.1359	L	0.54323	1.7	0.29000	N	0.887502	P	0.43662	0.814	P	0.47346	0.544	T	0.39683	-0.9602	10	0.41790	T	0.15	-20.1611	11.6312	0.51175	0.0:0.0:0.8094:0.1906	.	184	O15524	SOCS1_HUMAN	V	184	ENSP00000329418:A184V	ENSP00000329418:A184V	A	-	2	0	SOCS1	11256286	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.340000	0.43974	2.211000	0.71520	0.561000	0.74099	GCC	.	.	.	none		0.741	SOCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252018.1			A	11348785	G	A	11348785	3	1	5	1	0	0	0	0	1	0	0	0	14926	1203	42	2	88	2	SOCS1	16	11348785	Missense_Mutation	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10	7036942	11348785	79005968	76	472											
SNX29	92017	hgsc.bcm.edu	37	chr16	12371799	12371799	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttctctaaagtgccaaatcTttggagtgttgatggagaag	11	14	11	5	0	2	2	0	1	2	1	3	4	2	3	1	2	1	1	1	2	4	4			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr16:12371799T>C	ENST00000566228.1	+	15	1757	c.1688T>C	c.(1687-1689)cTt>cCt	p.L563P	SNX29_ENST00000323433.4_Missense_Mutation_p.L178P|SNX29_ENST00000306030.3_Missense_Mutation_p.L178P	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	563						extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						GTGCCAAATCTTTGGAGTGTT	0.378																																					p.L563P		Atlas-SNP	.											.	SNX29	60	.	0			c.T1688C						PASS	.						59	58	58					16																	12371799		1852	4102	5954	SO:0001583	missense	92017	exon15			CAAATCTTTGGAG	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.1688T>C	chr16.hg19:g.12371799T>C	ENSP00000456480:p.Leu563Pro	95.0	0.0	.		134.0	31.0	.	NM_032167	B5MDW2|Q8N2X2|Q9HA26	Missense_Mutation	SNP	ENST00000566228.1	hg19	CCDS10553.2	.	.	.	.	.	.	.	.	.	.	T	15.89	2.965775	0.53507	.	.	ENSG00000048471	ENST00000306030;ENST00000323433	.	.	.	5.46	4.37	0.52481	.	0.155686	0.42682	N	0.000679	T	0.60534	0.2276	L	0.54323	1.7	0.45733	D	0.998639	.	.	.	.	.	.	T	0.61382	-0.7074	7	0.72032	D	0.01	-5.764	7.971	0.30127	0.0:0.0924:0.0:0.9076	.	.	.	.	P	178	.	ENSP00000306940:L178P	L	+	2	0	SNX29	12279300	1.000000	0.71417	0.986000	0.45419	0.996000	0.88848	1.877000	0.39598	0.920000	0.36970	0.533000	0.62120	CTT	.	.	.	none		0.378	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422622.1			C	12371799	T	C	12371799	3	2	5	1	0	0	0	0	1	0	0	0	14911	1609	56	3	559	3	SNX29	16	12371799	Missense_Mutation	SNP	T	TCGA-2Z-A9J5-01A-21D-A382-10	1023014	12371799	77982954	77	473											
NFATC3	4775	hgsc.bcm.edu	37	chr16	68156669	68156669	+	Frame_Shift_Del	DEL	C	C	-																															caccccatcactcacctgttCcttcacctggtcactccccc																										TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr16:68156669delC	ENST00000346183.3	+	2	907	c.883delC	c.(883-885)cctfs	p.P295fs	RP11-67A1.2_ENST00000548144.1_RNA|NFATC3_ENST00000329524.4_Frame_Shift_Del_p.P295fs|NFATC3_ENST00000349223.5_Frame_Shift_Del_p.P295fs|NFATC3_ENST00000535127.2_3'UTR|NFATC3_ENST00000575270.1_Frame_Shift_Del_p.P295fs	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	295	3 X SP repeats.				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)		CTCACCTGTTCCTTCACCTGG	0.557																																					p.V294fs		Atlas-Indel,Pindel	.											.	NFATC3	190	.	0			c.882delT						PASS	.						112	100	104					16																	68156669		2198	4300	6498	SO:0001589	frameshift_variant	4775	exon2			.	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.883delC	chr16.hg19:g.68156669delC	ENSP00000300659:p.Pro295fs	58.0	0.0	0		97.0	43.0	0.443299	NM_173163	O75211|Q14516|Q99840|Q99841|Q99842	Frame_Shift_Del	DEL	ENST00000346183.3	hg19	CCDS10860.1																																																																																			.	.	.	none		0.557	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555		-	68156669	C	-	68156669	7	5	5	1	0	1	0	1	0	0	0	0	10371	855	30	0	889	0	NFATC3	16	68156669	Frame_Shift_Del	DEL	C	TCGA-2Z-A9J5-01A-21D-A382-10	55784870	68156669	22198084	78	474											
CHRNE	1145	hgsc.bcm.edu	37	chr17	4802092	4802092	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttgaagtaggccccgaggAagatgaggctggagcccacg	10	5	17	9	2	0	3	0	2	0	1	0	6	0	5	3	5	1	3	3	5	3	2			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr17:4802092A>G	ENST00000293780.4	-	12	1431	c.1421T>C	c.(1420-1422)tTc>tCc	p.F474S	C17orf107_ENST00000521575.1_5'Flank|CHRNE_ENST00000575637.1_5'Flank|C17orf107_ENST00000381365.3_5'Flank	NM_000080.3	NP_000071.1	Q04844	ACHE_HUMAN	cholinergic receptor, nicotinic, epsilon (muscle)	474					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|cation transmembrane transporter activity (GO:0008324)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|lung(3)|prostate(1)	12					Galantamine(DB00674)	GGCCCCGAGGAAGATGAGGCT	0.602																																					p.F474S		Atlas-SNP	.											.	CHRNE	25	.	0			c.T1421C						PASS	.						57	41	46					17																	4802092		2202	4300	6502	SO:0001583	missense	1145	exon12			CCGAGGAAGATGA	X66403	CCDS11058.1	17p13.2	2012-02-11	2012-02-07		ENSG00000108556	ENSG00000108556		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1966	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, epsilon (muscle)"	100725	"cholinergic receptor, nicotinic, epsilon"			7688301	Standard	NM_000080		Approved	ACHRE	uc002fzk.1	Q04844	OTTHUMG00000090778	ENST00000293780.4:c.1421T>C	chr17.hg19:g.4802092A>G	ENSP00000293780:p.Phe474Ser	82.0	0.0	.		83.0	7.0	.	NM_000080	D3DTK6	Missense_Mutation	SNP	ENST00000293780.4	hg19	CCDS11058.1	.	.	.	.	.	.	.	.	.	.	A	27.4	4.829048	0.90955	.	.	ENSG00000108556	ENST00000293780	D	0.88741	-2.42	4.76	4.76	0.60689	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.95472	0.8529	M	0.93420	3.415	0.53688	D	0.999973	D	0.89917	1.0	D	0.91635	0.999	D	0.96218	0.9158	10	0.87932	D	0	.	12.2686	0.54693	1.0:0.0:0.0:0.0	.	474	Q04844	ACHE_HUMAN	S	474	ENSP00000293780:F474S	ENSP00000293780:F474S	F	-	2	0	CHRNE	4742871	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	9.047000	0.93823	2.001000	0.58596	0.533000	0.62120	TTC	.	.	.	none		0.602	CHRNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207560.3			G	4802092	A	G	4802092	3	3	5	1	0	0	0	0	1	0	0	0	3397	246	9	3	64	3	CHRNE	17	4802092	Missense_Mutation	SNP	A	TCGA-2Z-A9J5-01A-21D-A382-10		4802092	76393118	79	475											
ALKBH5	54890	hgsc.bcm.edu	37	chr17	18088203	18088203	+	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	acatcttcgagcgccccatcGtgtccgtgtccttctttagc	5	13	8	15	4	2	0	0	0	2	0	6	1	4	0	4	0	2	0	4	0	1	4			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr17:18088203G>C	ENST00000399138.4	+	1	651	c.646G>C	c.(646-648)Gtg>Ctg	p.V216L	ALKBH5_ENST00000541285.1_Intron|RP11-258F1.1_ENST00000583062.1_RNA|RP11-258F1.1_ENST00000577847.1_RNA	NM_017758.3	NP_060228.3	Q6P6C2	ALKB5_HUMAN	AlkB family member 5, RNA demethylase	216					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|oxidative single-stranded RNA demethylation (GO:0035553)|response to hypoxia (GO:0001666)|spermatogenesis (GO:0007283)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|oxidative RNA demethylase activity (GO:0035515)|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)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|skin(1)	10	all_neural(463;0.228)					GCGCCCCATCGTGTCCGTGTC	0.617																																					p.V216L	Ovarian(166;154 1953 40235 46283 46309)	Atlas-SNP	.											.	ALKBH5	24	.	0			c.G646C						PASS	.						63	70	68					17																	18088203		2164	4257	6421	SO:0001583	missense	54890	exon1			CCCATCGTGTCCG	AK000315	CCDS42272.1	17p11.2	2014-07-23	2014-07-23	2006-02-09	ENSG00000091542	ENSG00000091542	1.14.11.-	"Alkylation repair homologs"	25996	protein-coding gene	gene with protein product		613303	"oxoglutarate and iron-dependent oxygenase domain containing", "alkB, alkylation repair homolog 5 (E. coli)"	OFOXD1		11997338, 24778178	Standard	NM_017758		Approved	FLJ20308	uc010cpw.3	Q6P6C2	OTTHUMG00000059397	ENST00000399138.4:c.646G>C	chr17.hg19:g.18088203G>C	ENSP00000382091:p.Val216Leu	52.0	0.0	.		78.0	22.0	.	NM_017758	B4DVJ4|D3DXC6|Q9NXD6	Missense_Mutation	SNP	ENST00000399138.4	hg19	CCDS42272.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.590056	0.86851	.	.	ENSG00000091542	ENST00000261650;ENST00000500385;ENST00000399138	T	0.13307	2.6	5.31	4.28	0.50868	.	0.000000	0.85682	D	0.000000	T	0.21145	0.0509	L	0.58669	1.825	0.80722	D	1	P	0.47106	0.89	P	0.47346	0.544	T	0.01146	-1.1437	10	0.40728	T	0.16	0.4929	15.4042	0.74866	0.0:0.1394:0.8606:0.0	.	216	Q6P6C2-2	.	L	216;205;216	ENSP00000382091:V216L	ENSP00000261650:V216L	V	+	1	0	ALKBH5	18028928	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.861000	0.87004	2.484000	0.83849	0.655000	0.94253	GTG	.	.	.	none		0.617	ALKBH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132069.3	NM_017758		C	18088203	G	C	18088203	3	2	5	1	0	0	0	0	1	0	0	0	530	1145	40	4	648	4	ALKBH5	17	18088203	Missense_Mutation	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10	13286111	18088203	63107007	80	476											
SLC47A1	55244	hgsc.bcm.edu	37	chr17	19459000	19459000	+	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	1	0	0	0	0	0	0	0	0	aactgcatcaagctacatggGgaggtaatgactgccctttt	11	11	10	9	0	1	1	1	1	0	0	1	2	1	2	1	3	5	3	1	3	4	4			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr17:19459000G>T	ENST00000270570.4	+	8	822	c.736G>T	c.(736-738)Gga>Tga	p.G246*	SLC47A1_ENST00000542886.1_Missense_Mutation_p.G213V|SNORA59B_ENST00000458926.1_RNA|SLC47A1_ENST00000395585.1_Nonsense_Mutation_p.G246*|SLC47A1_ENST00000571335.1_Intron|SLC47A1_ENST00000436810.2_Nonsense_Mutation_p.G223*|SLC47A1_ENST00000575023.1_Intron|SLC47A1_ENST00000457293.1_Nonsense_Mutation_p.G246*	NM_018242.2	NP_060712.2	Q96FL8	S47A1_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 1	246					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)	AGCTACATGGGGAGGTAATGA	0.507																																					p.G246X		Atlas-SNP	.											.	SLC47A1	55	.	0			c.G736T						PASS	.						122	112	116					17																	19459000		2203	4300	6503	SO:0001587	stop_gained	55244	exon8			ACATGGGGAGGTA		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.736G>T	chr17.hg19:g.19459000G>T	ENSP00000270570:p.Gly246*	50.0	0.0	.		74.0	15.0	.	NM_018242	Q53HF5|Q6PD77|Q86VL4|Q9NVA3	Nonsense_Mutation	SNP	ENST00000270570.4	hg19	CCDS11209.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	38|38	7.249755|7.249755	0.98164|0.98164	.|.	.|.	ENSG00000142494|ENSG00000142494	ENST00000542886|ENST00000436810;ENST00000270570;ENST00000457293;ENST00000395585	.|.	.|.	.|.	5.34|5.34	5.34|5.34	0.76211|0.76211	.|.	0.325890|0.325890	0.36338|0.36338	N|N	0.002649|0.002649	T|.	0.74030|.	0.3663|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.72714|.	-0.4210|.	6|.	0.87932|0.39692	D|T	0|0.17	-5.9107|-5.9107	18.0822|18.0822	0.89444|0.89444	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	V|X	213|223;246;246;246	.|.	ENSP00000440435:G213V|ENSP00000270570:G246X	G|G	+|+	2|1	0|0	SLC47A1|SLC47A1	19399592|19399592	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.968000|0.968000	0.65278|0.65278	7.096000|7.096000	0.76960|0.76960	2.517000|2.517000	0.84864|0.84864	0.650000|0.650000	0.86243|0.86243	GGG|GGA	.	.	.	none		0.507	SLC47A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132250.1	NM_018242		T	19459000	G	T	19459000	4	4	5	1	0	0	0	0	0	1	0	0	14660	1233	43	4	766	4	SLC47A1	17	19459000	Nonsense_Mutation	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10	1370797	19459000	61736210	81	477											
MYO18A	399687	hgsc.bcm.edu	37	chr17	27438845	27438845	+	Frame_Shift_Del	DEL	G	G	-																															ctcttccaatagccagagcaGgcccctcgcctcgtctgtgc																										TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr17:27438845delG	ENST00000527372.1	-	16	2815	c.2635delC	c.(2635-2637)ctgfs	p.L880fs	MYO18A_ENST00000531253.1_Frame_Shift_Del_p.L880fs|MYO18A_ENST00000533112.1_Frame_Shift_Del_p.L880fs|MYO18A_ENST00000354329.4_Frame_Shift_Del_p.L880fs	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	880	Myosin motor.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			AGCCAGAGCAGGCCCCTCGCC	0.612											OREG0024287	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L879fs	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-Indel,Pindel	.											.	MYO18A	217	.	0			c.2636delT						PASS	.						43	49	47					17																	27438845		1884	4105	5989	SO:0001589	frameshift_variant	399687	exon16			.	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.2635delC	chr17.hg19:g.27438845delG	ENSP00000437073:p.Leu880fs	64.0	0.0	0	794	95.0	46.0	0.484211	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Frame_Shift_Del	DEL	ENST00000527372.1	hg19	CCDS45642.1																																																																																			.	.	.	none		0.612	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		-	27438845	G	-	27438845	7	5	5	1	0	1	0	1	0	0	0	0	10072	991	35	0	3637	0	MYO18A	17	27438845	Frame_Shift_Del	DEL	G	TCGA-2Z-A9J5-01A-21D-A382-10	7979845	27438845	53756365	82	478											
EZH1	2145	hgsc.bcm.edu	37	chr17	40870014	40870014	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcaaaaggaagcagtctgTgccacatggttctggttcaa	12	9	11	9	0	3	0	1	0	2	0	3	1	3	1	1	3	3	4	1	3	4	2			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr17:40870014T>C	ENST00000428826.2	-	10	1124	c.1003A>G	c.(1003-1005)Aca>Gca	p.T335A	EZH1_ENST00000590078.1_Missense_Mutation_p.T265A|EZH1_ENST00000592743.1_Missense_Mutation_p.T335A|EZH1_ENST00000415827.2_Missense_Mutation_p.T326A|EZH1_ENST00000435174.1_Missense_Mutation_p.T196A|EZH1_ENST00000585893.1_Missense_Mutation_p.T295A			Q92800	EZH1_HUMAN	enhancer of zeste 1 polycomb repressive complex 2 subunit	335					anatomical structure morphogenesis (GO:0009653)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)	p.T335A(1)		breast(1)|endometrium(4)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	27		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0784)		AAGCAGTCTGTGCCACATGGT	0.428																																					p.T335A		Atlas-SNP	.											EZH1,bladder,carcinoma,0,1	EZH1	62	.	1	Substitution - Missense(1)	urinary_tract(1)	c.A1003G						PASS	.						161	146	151					17																	40870014		2203	4300	6503	SO:0001583	missense	2145	exon10			AGTCTGTGCCACA		CCDS32659.1	17q21.1-q21.3	2014-05-28	2014-05-28			ENSG00000108799		"Chromatin-modifying enzymes / K-methyltransferases"	3526	protein-coding gene	gene with protein product		601674	"enhancer of zeste (Drosophila) homolog 1", "enhancer of zeste homolog 1 (Drosophila)"			8921387	Standard	NM_001991		Approved	KIAA0388, KMT6B	uc002iaz.3	Q92800		ENST00000428826.2:c.1003A>G	chr17.hg19:g.40870014T>C	ENSP00000404658:p.Thr335Ala	84.0	1.0	.		114.0	44.0	.	NM_001991	A6NCH6|B4DIJ1|B4DIZ7|B4DSS2|B4E3R7|O43287|Q14459|Q53XP3	Missense_Mutation	SNP	ENST00000428826.2	hg19	CCDS32659.1	.	.	.	.	.	.	.	.	.	.	T	9.108	1.005805	0.19199	.	.	ENSG00000108799	ENST00000264646;ENST00000428826;ENST00000415827;ENST00000435174	T;T	0.77358	-1.09;-1.09	4.51	-2.48	0.06423	.	0.844588	0.11228	N	0.585983	T	0.46014	0.1371	N	0.04880	-0.145	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.001;0.0	T	0.31586	-0.9938	10	0.12430	T	0.62	.	1.1979	0.01878	0.2247:0.3103:0.1147:0.3503	.	196;295;341;335	Q92800-5;Q92800-3;Q92800-2;Q92800	.;.;.;EZH1_HUMAN	A	338;335;295;196	ENSP00000404658:T335A;ENSP00000404071:T196A	ENSP00000264646:T338A	T	-	1	0	EZH1	38123540	0.006000	0.16342	0.989000	0.46669	0.998000	0.95712	-0.035000	0.12205	-0.242000	0.09667	0.460000	0.39030	ACA	.	.	.	none		0.428	EZH1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452347.1	NM_001991		C	40870014	T	C	40870014	3	2	5	1	0	0	0	0	1	0	0	0	5335	1696	59	3	1288	3	EZH1	17	40870014	Missense_Mutation	SNP	T	TCGA-2Z-A9J5-01A-21D-A382-10	13431169	40870014	40325196	83	479											
IGF2BP1	10642	hgsc.bcm.edu	37	chr17	47075185	47075185	+	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	aaagtgtttgcggagcacaaGatctcctacagcggccagtt	11	9	11	10	2	1	1	0	0	1	1	2	2	1	2	2	2	4	3	2	2	3	3			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr17:47075185G>A	ENST00000290341.3	+	1	412	c.78G>A	c.(76-78)aaG>aaA	p.K26K	RP11-501C14.5_ENST00000505903.1_RNA|IGF2BP1_ENST00000515586.1_3'UTR|IGF2BP1_ENST00000431824.2_Silent_p.K26K	NM_006546.3	NP_006537.3	Q9NZI8	IF2B1_HUMAN	insulin-like growth factor 2 mRNA binding protein 1	26	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of mRNA stability involved in response to stress (GO:0010610)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|translation regulator activity (GO:0045182)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						CGGAGCACAAGATCTCCTACA	0.587																																					p.K26K	Esophageal Squamous(198;1041 2123 8248 37119 38268)	Atlas-SNP	.											.	IGF2BP1	80	.	0			c.G78A						PASS	.						115	111	113					17																	47075185		2203	4300	6503	SO:0001819	synonymous_variant	10642	exon1			GCACAAGATCTCC	AF198254	CCDS11543.1, CCDS54138.1	17q21.32	2013-02-12			ENSG00000159217	ENSG00000159217		"RNA binding motif (RRM) containing"	28866	protein-coding gene	gene with protein product	"IGF II mRNA binding protein 1"	608288				9891060, 11992722	Standard	NM_001160423		Approved	IMP-1	uc002iom.3	Q9NZI8	OTTHUMG00000161173	ENST00000290341.3:c.78G>A	chr17.hg19:g.47075185G>A		77.0	0.0	.		119.0	26.0	.	NM_001160423	C9JT33	Silent	SNP	ENST00000290341.3	hg19	CCDS11543.1																																																																																			.	.	.	none		0.587	IGF2BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364046.1	NM_006546		A	47075185	G	A	47075185	2	1	5	1	0	0	0	0	0	0	0	1	7580	933	33	2		2	IGF2BP1	17	47075185	Silent	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10	6205171	47075185	34120025	84	480											
AFG3L2	10939	hgsc.bcm.edu	37	chr18	12340242	12340242	+	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	acttttctcaagtcatcttgAgcaccagttgtaattcttcc	9	16	5	11	0	4	1	2	1	3	0	6	1	5	1	2	0	1	3	2	0	2	7			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr18:12340242A>C	ENST00000269143.3	-	15	2169	c.1938T>G	c.(1936-1938)gcT>gcG	p.A646A		NM_006796.2	NP_006787.2	Q9Y4W6	AFG32_HUMAN	AFG3-like AAA ATPase 2	646					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)	AGTCATCTTGAGCACCAGTTG	0.393																																					p.A646A		Atlas-SNP	.											.	AFG3L2	60	.	0			c.T1938G						PASS	.						146	140	142					18																	12340242		2203	4300	6503	SO:0001819	synonymous_variant	10939	exon15			ATCTTGAGCACCA	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.1938T>G	chr18.hg19:g.12340242A>C		50.0	0.0	.		65.0	14.0	.	NM_006796	Q6P1L0	Silent	SNP	ENST00000269143.3	hg19	CCDS11859.1																																																																																			.	.	.	none		0.393	AFG3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254603.2	NM_006796		C	12340242	A	C	12340242	2	2	5	1	0	0	0	0	0	0	0	1	360	291	11	5		5	AFG3L2	18	12340242	Silent	SNP	A	TCGA-2Z-A9J5-01A-21D-A382-10		12340242	65737006	85	481											
DAZAP1	26528	hgsc.bcm.edu	37	chr19	1434904	1434904	+	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	gcaagggttccacccctaccGacgctagcccgcggcgccgc	6	4	12	19	6	0	0	0	0	0	0	1	1	1	0	6	2	2	3	6	2	3	3			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr19:1434904G>C	ENST00000233078.4	+	12	1378	c.1217G>C	c.(1216-1218)cGa>cCa	p.R406P	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)		CACCCCTACCGACGCTAGCCC	0.672																																					p.R406P		Atlas-SNP	.											.	DAZAP1	52	.	0			c.G1217C						PASS	.						9	10	10					19																	1434904		2136	4184	6320	SO:0001583	missense	26528	exon12			CCTACCGACGCTA		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.1217G>C	chr19.hg19:g.1434904G>C	ENSP00000233078:p.Arg406Pro	60.0	0.0	.		80.0	26.0	.	NM_018959	Q96MJ3|Q9NRR9	Missense_Mutation	SNP	ENST00000233078.4	hg19	CCDS12065.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.091413	0.76756	.	.	ENSG00000071626	ENST00000233078	T	0.34275	1.37	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.48169	0.1485	N	0.24115	0.695	0.80722	D	1	D;D;D	0.76494	0.998;0.998;0.999	D;D;D	0.81914	0.989;0.989;0.995	T	0.53215	-0.8470	10	0.87932	D	0	.	17.8389	0.88709	0.0:0.0:1.0:0.0	.	473;406;172	Q5IRN4;Q96EP5;B3KS63	.;DAZP1_HUMAN;.	P	406	ENSP00000233078:R406P	ENSP00000233078:R406P	R	+	2	0	DAZAP1	1385904	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.449000	0.97603	2.454000	0.82982	0.561000	0.74099	CGA	.	.	.	none		0.672	DAZAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449522.3	NM_170711		C	1434904	G	C	1434904	3	2	5	1	0	0	0	0	1	0	0	0	4246	1058	37	4	1356	4	DAZAP1	19	1434904	Missense_Mutation	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10		1434904	57694079	86	482											
NOTCH3	4854	hgsc.bcm.edu	37	chr19	15292387	15292387	+	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	caagcagaggccccgcccacCtggggctgcagtcgggcagg	7	3	16	15	2	0	1	0	0	0	1	1	1	0	1	4	5	2	4	4	5	1	0			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr19:15292387C>T	ENST00000263388.2	-	17	2867	c.2792G>A	c.(2791-2793)aGc>aAc	p.S931N		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	931	EGF-like 24. {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)			CCCCGCCCACCTGGGGCTGCA	0.682																																					p.S931N		Atlas-SNP	.											.	NOTCH3	340	.	0			c.G2792A						PASS	.						7	6	7					19																	15292387		1946	3760	5706	SO:0001630	splice_region_variant	4854	exon17			GCCCACCTGGGGC	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.2792+1G>A	chr19.hg19:g.15292387C>T		161.0	0.0	.		182.0	48.0	.	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	hg19	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	C	31	5.091511	0.94149	.	.	ENSG00000074181	ENST00000263388;ENST00000539383	D	0.91686	-2.89	5.45	5.45	0.79879	EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.37857	N	0.001920	D	0.90745	0.7095	N	0.04820	-0.15	0.80722	D	1	D;D	0.89917	1.0;0.996	D;D	0.81914	0.995;0.968	D	0.90376	0.4384	9	.	.	.	.	18.0459	0.89332	0.0:1.0:0.0:0.0	.	882;931	Q59FL3;Q9UM47	.;NOTC3_HUMAN	N	931;881	ENSP00000263388:S931N	.	S	-	2	0	NOTCH3	15153387	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	2.739000	0.47409	2.569000	0.86673	0.561000	0.74099	AGC	.	.	.	none		0.682	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435	Missense_Mutation	T	15292387	C	T	15292387	5	4	5	1	0	0	0	0	0	0	1	0	10557	695	24	2	4241	2	NOTCH3	19	15292387	Splice_Site	SNP	C	TCGA-2Z-A9J5-01A-21D-A382-10	13857483	15292387	43836596	87	483											
IFI30	10437	hgsc.bcm.edu	37	chr19	18286479	18286479	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cattgtctgcatggaagagtTtgaggacatggagagaagtc	12	10	14	5	0	1	3	0	1	1	2	2	7	1	6	0	3	1	2	0	3	2	2			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr19:18286479T>C	ENST00000407280.3	+	4	630	c.455T>C	c.(454-456)tTt>tCt	p.F152S	PIK3R2_ENST00000593731.1_3'UTR	NM_006332.3	NP_006323.2	P13284	GILT_HUMAN	interferon, gamma-inducible protein 30	152					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						ATGGAAGAGTTTGAGGACATG	0.577																																					p.F152S		Atlas-SNP	.											.	IFI30	12	.	0			c.T455C						PASS	.						42	43	43					19																	18286479		2019	4194	6213	SO:0001583	missense	10437	exon4			AAGAGTTTGAGGA	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.455T>C	chr19.hg19:g.18286479T>C	ENSP00000384886:p.Phe152Ser	46.0	0.0	.		67.0	22.0	.	NM_006332	Q76MF9|Q8NEI4|Q8WU77|Q9UL08	Missense_Mutation	SNP	ENST00000407280.3	hg19	CCDS46015.1	.	.	.	.	.	.	.	.	.	.	T	1.463	-0.561981	0.03939	.	.	ENSG00000216490	ENST00000407280	.	.	.	4.4	3.38	0.38709	.	.	.	.	.	T	0.11367	0.0277	N	0.01284	-0.91	0.09310	N	1	B	0.16166	0.016	B	0.17433	0.018	T	0.27054	-1.0085	8	0.07175	T	0.84	-23.2549	7.7231	0.28744	0.0:0.1025:0.0:0.8975	.	152	P13284	GILT_HUMAN	S	152	.	ENSP00000384886:F152S	F	+	2	0	IFI30	18147479	0.047000	0.20315	0.668000	0.29813	0.003000	0.03518	1.938000	0.40203	1.983000	0.57843	0.459000	0.35465	TTT	.	.	.	none		0.577	IFI30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466396.3	NM_006332		C	18286479	T	C	18286479	3	2	5	1	0	0	0	0	1	0	0	0	7522	1841	64	3	469	3	IFI30	19	18286479	Missense_Mutation	SNP	T	TCGA-2Z-A9J5-01A-21D-A382-10	2994092	18286479	40842504	88	484											
SIGLEC10	89790	hgsc.bcm.edu	37	chr19	51920173	51920173	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcccgggctccagggtctcGgggatgtagacatcaggctt	6	9	15	11	2	2	1	1	0	1	1	4	2	3	2	2	5	1	3	2	5	1	2	rs139091162		TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr19:51920173G>A	ENST00000339313.5	-	3	569	c.453C>T	c.(451-453)ccC>ccT	p.P151P	SIGLEC10_ENST00000439889.2_Intron|SIGLEC10_ENST00000436984.2_Intron|SIGLEC10_ENST00000353836.5_Silent_p.P151P|SIGLEC10_ENST00000525998.1_Silent_p.P151P|CTD-2616J11.2_ENST00000532688.1_RNA|CTD-2616J11.3_ENST00000532473.1_RNA|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000356298.5_Silent_p.P151P|SIGLEC10_ENST00000442846.3_Intron|SIGLEC10_ENST00000441969.3_Intron|SIGLEC10_ENST00000432469.2_Intron			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	151	Ig-like C2-type 1.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		CCAGGGTCTCGGGGATGTAGA	0.622																																					p.P151P		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.C453T						PASS	.	G	,,,,,,	2,4404		0,2,2201	67	78	75		,453,,,,,453	-9.4	0	19	dbSNP_134	75	0,8600		0,0,4300	no	intron,coding-synonymous,intron,intron,intron,intron,coding-synonymous	SIGLEC10	NM_001171156.1,NM_001171157.1,NM_001171158.1,NM_001171159.1,NM_001171160.1,NM_001171161.1,NM_033130.4	,,,,,,	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	,,,,,,	,151/603,,,,,151/698	51920173	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	89790	exon3			GGTCTCGGGGATG	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.453C>T	chr19.hg19:g.51920173G>A		176.0	0.0	.		171.0	37.0	.	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Silent	SNP	ENST00000339313.5	hg19	CCDS12832.1																																																																																			.	G|1.000;A|0.000	0.000	weak		0.622	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130		A	51920173	G	A	51920173	2	1	5	1	0	0	0	0	0	0	0	1	14319	1103	39	1		1	SIGLEC10	19	51920173	Silent	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10	33633694	51920173	7208810	89	485											
ZNF350	59348	hgsc.bcm.edu	37	chr19	52468148	52468148	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaataagacataattgatcaCggaaggcacaaccacattca	19	7	6	9	1	2	2	2	1	0	1	2	3	2	3	1	2	1	1	1	2	5	4	rs148220969		TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr19:52468148C>T	ENST00000243644.4	-	5	1785	c.1558G>A	c.(1558-1560)Gtg>Atg	p.V520M	HCCAT3_ENST00000595010.1_RNA|HCCAT3_ENST00000600253.1_RNA|ZNF350_ENST00000600703.1_5'Flank	NM_021632.3	NP_067645.3	Q9GZX5	ZN350_HUMAN	zinc finger protein 350	520					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V520M(1)		breast(4)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0179)		TAATTGATCACGGAAGGCACA	0.413																																					p.V520M		Atlas-SNP	.											ZNF350,NS,carcinoma,0,1	ZNF350	48	.	1	Substitution - Missense(1)	endometrium(1)	c.G1558A						PASS	.	C	MET/VAL	0,4406		0,0,2203	103	90	95		1558	1.4	0	19	dbSNP_134	95	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZNF350	NM_021632.3	21	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	520/533	52468148	1,13005	2203	4300	6503	SO:0001583	missense	59348	exon5			TGATCACGGAAGG	AF295096	CCDS12845.1	19q13.41	2013-05-23			ENSG00000256683	ENSG00000256683		"Zinc fingers, C2H2-type", "-"	16656	protein-coding gene	gene with protein product		605422				11090615, 11161714	Standard	NM_021632		Approved	ZBRK1, ZFQR	uc002pyd.3	Q9GZX5	OTTHUMG00000182538	ENST00000243644.4:c.1558G>A	chr19.hg19:g.52468148C>T	ENSP00000243644:p.Val520Met	55.0	0.0	.		67.0	19.0	.	NM_021632	Q96G73|Q9HAQ4	Missense_Mutation	SNP	ENST00000243644.4	hg19	CCDS12845.1	.	.	.	.	.	.	.	.	.	.	C	10.50	1.367472	0.24771	0.0	1.16E-4	ENSG00000256683	ENST00000243644	T	0.05855	3.38	3.64	1.41	0.22369	.	0.275159	0.19550	N	0.111587	T	0.03915	0.0110	L	0.34521	1.04	0.09310	N	1	P	0.34587	0.458	B	0.19391	0.025	T	0.39761	-0.9598	10	0.48119	T	0.1	.	6.2576	0.20881	0.0:0.7534:0.0:0.2466	.	520	Q9GZX5	ZN350_HUMAN	M	520	ENSP00000243644:V520M	ENSP00000243644:V520M	V	-	1	0	ZNF350	57159960	0.000000	0.05858	0.031000	0.17742	0.243000	0.25628	-0.184000	0.09698	0.763000	0.33175	-0.186000	0.12905	GTG	.	C|1.000;T|0.000	0.000	weak		0.413	ZNF350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462278.1	NM_021632		T	52468148	C	T	52468148	3	4	5	1	0	0	0	0	1	0	0	0	17875	536	19	1	44	1	ZNF350	19	52468148	Missense_Mutation	SNP	C	TCGA-2Z-A9J5-01A-21D-A382-10	547975	52468148	6660835	90	486											
ZNF549	256051	hgsc.bcm.edu	37	chr19	58049579	58049583	+	Frame_Shift_Del	DEL	TCACT	TCACT	-																															aatccttcatatacaaacagTcacttcttgatcaccataga																										TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	TCACT	TCACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr19:58049579_58049583delTCACT	ENST00000376233.3	+	4	1388_1392	c.1207_1211delTCACT	c.(1207-1212)tcacttfs	p.SL403fs	ZNF549_ENST00000240719.3_Frame_Shift_Del_p.SL390fs|ZNF549_ENST00000594943.1_Intron|ZNF549_ENST00000602149.1_Intron|ZNF550_ENST00000601415.1_Intron	NM_001199295.1	NP_001186224	Q6P9A3	ZN549_HUMAN	zinc finger protein 549	403					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	21		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		ATACAAACAGTCACTTCTTGATCAC	0.434																																					p.402_404del		Atlas-Indel,Pindel	.											.	ZNF549	118	.	0			c.1206_1210del						PASS	.																																			SO:0001589	frameshift_variant	256051	exon4			.	AK092236	CCDS12952.1, CCDS56106.1	19q13.43	2013-01-08				ENSG00000121406		"Zinc fingers, C2H2-type", "-"	26632	protein-coding gene	gene with protein product						12477932	Standard	NM_153263		Approved	FLJ34917	uc002qpb.2	Q6P9A3		ENST00000376233.3:c.1207_1211delTCACT	chr19.hg19:g.58049579_58049583delTCACT	ENSP00000365407:p.Ser403fs	92.0	0.0	0		98.0	19.0	0.193878	NM_001199295	B3KV91|O43336|Q8NAR4	Frame_Shift_Del	DEL	ENST00000376233.3	hg19	CCDS56106.1																																																																																			.	.	.	none		0.434	ZNF549-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466780.1	NM_153263		-	58049583	TCACT	-	58049579	7	5	5	1	0	1	0	1	0	0	0	0	17993	1667	58	0	1178	0	ZNF549	19	58049579	Frame_Shift_Del	DEL	TCACT	TCGA-2Z-A9J5-01A-21D-A382-10	5581431	58049579	1079404	91	487											
ZSCAN22	342945	hgsc.bcm.edu	37	chr19	58849868	58849868	+	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	acaaggatgtccccacagacCagcgtggccgtgaatctggt	10	7	12	12	2	1	2	0	1	1	1	2	3	2	3	4	3	1	0	4	3	2	0			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr19:58849868C>T	ENST00000329665.4	+	3	799	c.652C>T	c.(652-654)Cag>Tag	p.Q218*		NM_181846.2	NP_862829.1	P10073	ZSC22_HUMAN	zinc finger and SCAN domain containing 22	218					transcription, DNA-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)		CCCCACAGACCAGCGTGGCCG	0.517																																					p.Q218X		Atlas-SNP	.											.	ZSCAN22	47	.	0			c.C652T						PASS	.						149	152	151					19																	58849868		2203	4300	6503	SO:0001587	stop_gained	342945	exon3			ACAGACCAGCGTG	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.652C>T	chr19.hg19:g.58849868C>T	ENSP00000332433:p.Gln218*	115.0	0.0	.		118.0	33.0	.	NM_181846	Q15922|Q7Z3L8	Nonsense_Mutation	SNP	ENST00000329665.4	hg19	CCDS12975.1	.	.	.	.	.	.	.	.	.	.	C	20.0	3.930821	0.73327	.	.	ENSG00000182318	ENST00000329665	.	.	.	4.02	0.338	0.15974	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	.	7.3595	0.26737	0.0:0.5848:0.3188:0.0964	.	.	.	.	X	218	.	ENSP00000332433:Q218X	Q	+	1	0	ZSCAN22	63541680	0.000000	0.05858	0.001000	0.08648	0.120000	0.20174	-0.156000	0.10100	0.350000	0.24002	0.313000	0.20887	CAG	.	.	.	none		0.517	ZSCAN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466765.1	NM_181846		T	58849868	C	T	58849868	4	4	5	1	0	0	0	0	0	1	0	0	18246	595	21	2	658	2	ZSCAN22	19	58849868	Nonsense_Mutation	SNP	C	TCGA-2Z-A9J5-01A-21D-A382-10	800289	58849868	279115	92	488											
SDCBP2	27111	hgsc.bcm.edu	37	chr20	1294040	1294040	+	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	gcgctcgtccttgcacaggtGgatctcgcgcaccccgggct	4	8	13	16	5	1	0	0	0	1	0	4	1	2	1	3	3	1	4	3	3	0	1			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr20:1294040G>A	ENST00000360779.3	-	5	501	c.328C>T	c.(328-330)Cac>Tac	p.H110Y	SDCBP2_ENST00000381812.1_Missense_Mutation_p.H110Y|SDCBP2_ENST00000339987.3_Missense_Mutation_p.H110Y|SDCBP2_ENST00000467129.1_5'Flank|SDCBP2_ENST00000381808.3_Missense_Mutation_p.H25Y	NM_080489.4	NP_536737.3	Q9H190	SDCB2_HUMAN	syndecan binding protein (syntenin) 2	110	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(3)|lung(1)|skin(1)|stomach(1)	7						TTGCACAGGTGGATCTCGCGC	0.716																																					p.H110Y		Atlas-SNP	.											.	SDCBP2	78	.	0			c.C328T						PASS	.						27	27	27					20																	1294040		2202	4298	6500	SO:0001583	missense	27111	exon5			ACAGGTGGATCTC	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.328C>T	chr20.hg19:g.1294040G>A	ENSP00000354013:p.His110Tyr	124.0	0.0	.		123.0	24.0	.	NM_080489	O95892|Q5W0X1|Q9BZ42|Q9H567|Q9NRY8	Missense_Mutation	SNP	ENST00000360779.3	hg19	CCDS42848.1	.	.	.	.	.	.	.	.	.	.	G	12.18	1.859249	0.32884	.	.	ENSG00000125775	ENST00000381812;ENST00000381808;ENST00000360779;ENST00000339987	T;T;T;T	0.27557	1.66;1.66;1.66;1.66	5.01	3.08	0.35506	PDZ/DHR/GLGF (3);	0.270706	0.36555	N	0.002529	T	0.19485	0.0468	L	0.46157	1.445	0.32669	N	0.517107	B;B	0.22003	0.063;0.003	B;B	0.17433	0.018;0.012	T	0.21690	-1.0238	10	0.08179	T	0.78	-6.8767	4.5438	0.12071	0.1812:0.0:0.6438:0.175	.	110;110	B4DKI5;Q9H190	.;SDCB2_HUMAN	Y	110;25;110;110	ENSP00000371233:H110Y;ENSP00000371229:H25Y;ENSP00000354013:H110Y;ENSP00000342935:H110Y	ENSP00000342935:H110Y	H	-	1	0	SDCBP2	1242040	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.052000	0.49893	0.708000	0.31955	0.462000	0.41574	CAC	.	.	.	none		0.716	SDCBP2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077513.2	NM_080489		A	1294040	G	A	1294040	3	1	5	1	0	0	0	0	1	0	0	0	13969	1348	47	2	570	2	SDCBP2	20	1294040	Missense_Mutation	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10		1294040	61731480	93	489											
LRRN4	164312	hgsc.bcm.edu	37	chr20	6031523	6031523	+	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	tgacagtccagctgctgcagGttgggggtcatcttgaaaat	9	11	13	8	0	2	2	1	2	1	0	3	2	3	2	1	3	3	4	1	3	2	2			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr20:6031523G>A	ENST00000378858.4	-	3	986	c.762C>T	c.(760-762)aaC>aaT	p.N254N		NM_152611.4	NP_689824.2	Q8WUT4	LRRN4_HUMAN	leucine rich repeat neuronal 4	254					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						GCTGCTGCAGGTTGGGGGTCA	0.552																																					p.N254N		Atlas-SNP	.											.	LRRN4	54	.	0			c.C762T						PASS	.						133	123	127					20																	6031523		2203	4300	6503	SO:0001819	synonymous_variant	164312	exon3			CTGCAGGTTGGGG	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.762C>T	chr20.hg19:g.6031523G>A		116.0	0.0	.		138.0	36.0	.	NM_152611	A8K258|Q5JWV6|Q9H419	Silent	SNP	ENST00000378858.4	hg19	CCDS13097.1																																																																																			.	.	.	none		0.552	LRRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077907.2	NM_152611		A	6031523	G	A	6031523	2	1	5	1	0	0	0	0	0	0	0	1	9044	1252	44	2		2	LRRN4	20	6031523	Silent	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10	4737483	6031523	56993997	94	490											
C20orf112	140688	hgsc.bcm.edu	37	chr20	31044026	31044026	+	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	agtgccgtggccggcgggagCttgtcacacaggttgatggg	6	8	18	9	3	1	1	1	1	0	0	1	2	1	2	2	5	2	2	2	5	0	2			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr20:31044026C>G	ENST00000359676.5	-	3	424	c.282G>C	c.(280-282)aaG>aaC	p.K94N	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		94						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|kidney(2)|large_intestine(5)|lung(5)	15						CCGGCGGGAGCTTGTCACACA	0.682																																					p.K338N		Atlas-SNP	.											.	C20orf112	39	.	0			c.G1014C						PASS	.						51	49	50					20																	31044026		2202	4298	6500	SO:0001583	missense	140688	exon6			CGGGAGCTTGTCA																												ENST00000359676.5:c.282G>C	chr20.hg19:g.31044026C>G	ENSP00000352704:p.Lys94Asn	72.0	0.0	.		87.0	27.0	.	NM_001256798	Q5JYB7|Q6P0Y4|Q9BR34|Q9NQF6	Missense_Mutation	SNP	ENST00000359676.5	hg19	CCDS13202.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.957547	0.73902	.	.	ENSG00000197183	ENST00000359676;ENST00000397984	.	.	.	5.1	5.1	0.69264	.	0.203164	0.43110	D	0.000607	T	0.55194	0.1905	L	0.50333	1.59	0.80722	D	1	P	0.44429	0.835	P	0.44477	0.451	T	0.60831	-0.7185	9	0.87932	D	0	-7.3123	11.0544	0.47909	0.0:0.9154:0.0:0.0846	.	94	Q96MY1	CT112_HUMAN	N	94	.	ENSP00000352704:K94N	K	-	3	2	C20orf112	30507687	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	1.181000	0.32017	2.378000	0.81104	0.561000	0.74099	AAG	.	.	.	none		0.682	C20orf112-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078628.2			G	31044026	C	G	31044026	3	3	5	1	0	0	0	0	1	0	0	0	2083	796	28	4	1052	4	C20orf112	20	31044026	Missense_Mutation	SNP	C	TCGA-2Z-A9J5-01A-21D-A382-10	25012503	31044026	31981494	95	491											
ZNF512B	57473	hgsc.bcm.edu	37	chr20	62595216	62595216	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacgttgcaggtggggcagaCggcttccccgcgctcatgga	6	7	15	13	4	1	1	1	0	0	1	2	2	2	2	2	5	1	5	2	5	0	2	rs370483162		TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr20:62595216C>T	ENST00000450537.1	-	9	1591	c.1531G>A	c.(1531-1533)Gtc>Atc	p.V511I	ZNF512B_ENST00000217130.3_Missense_Mutation_p.V511I|ZNF512B_ENST00000369888.1_Missense_Mutation_p.V511I			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	511					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)					GTGGGGCAGACGGCTTCCCCG	0.652													C|||	1	0.000199681	0	0	5008	,	,		17133	0		0	False		,,,				2504	0.001				p.V511I		Atlas-SNP	.											.	ZNF512B	72	.	0			c.G1531A						PASS	.	C	ILE/VAL	0,4406		0,0,2203	68	68	68		1531	2.7	1	20		68	1,8597	1.2+/-3.3	0,1,4298	no	missense	ZNF512B	NM_020713.1	29	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	511/893	62595216	1,13003	2203	4299	6502	SO:0001583	missense	57473	exon9			GGCAGACGGCTTC	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.1531G>A	chr20.hg19:g.62595216C>T	ENSP00000393795:p.Val511Ile	34.0	0.0	.		42.0	10.0	.	NM_020713	Q08AK9|Q9ULM4	Missense_Mutation	SNP	ENST00000450537.1	hg19	CCDS13548.1	.	.	.	.	.	.	.	.	.	.	C	10.59	1.392201	0.25118	0.0	1.16E-4	ENSG00000196700	ENST00000369888;ENST00000450537;ENST00000217130	T;T;T	0.26067	1.76;1.76;1.76	4.62	2.68	0.31781	.	0.224107	0.37261	N	0.002172	T	0.20659	0.0497	L	0.50333	1.59	0.29642	N	0.844651	B	0.12630	0.006	B	0.08055	0.003	T	0.16041	-1.0416	10	0.24483	T	0.36	-14.6217	8.8556	0.35225	0.0:0.8211:0.0:0.1789	.	511	Q96KM6	Z512B_HUMAN	I	511	ENSP00000358904:V511I;ENSP00000393795:V511I;ENSP00000217130:V511I	ENSP00000217130:V511I	V	-	1	0	ZNF512B	62065660	0.039000	0.19947	0.980000	0.43619	0.635000	0.38103	0.410000	0.21098	0.384000	0.24942	-0.444000	0.05651	GTC	.	.	.	weak		0.652	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713		T	62595216	C	T	62595216	3	4	5	1	0	0	0	0	1	0	0	0	17969	536	19	1	1183	1	ZNF512B	20	62595216	Missense_Mutation	SNP	C	TCGA-2Z-A9J5-01A-21D-A382-10	31551190	62595216	430304	96	492											
MN1	4330	hgsc.bcm.edu	37	chr22	28194900	28194900	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgctgctgctgctgctgctgTtgctgttgctgttgctgctg	0	16	14	11	1	0	0	0	0	0	0	0	0	0	0	0	0	9	13	0	0	0	3	rs202212250|rs530519178	byFrequency	TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr22:28194900T>C	ENST00000302326.4	-	1	2586	c.1632A>G	c.(1630-1632)caA>caG	p.Q544Q		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	544	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						gctgctgctgttgctgttgct	0.647			T	ETV6	"AML, meningioma"								C|||	5	0.000998403	0.0023	0	5008	,	,		12597	0		0	False		,,,				2504	0.002				p.Q544Q		Atlas-SNP	.		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"L, O"	.	MN1	122	.	0			c.A1632G						PASS	.																																			SO:0001819	synonymous_variant	4330	exon1			CTGCTGTTGCTGT	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.1632A>G	chr22.hg19:g.28194900T>C		26.0	0.0	.		57.0	7.0	.	NM_002430	A9Z1V9	Silent	SNP	ENST00000302326.4	hg19	CCDS42998.1																																																																																			.	.	.	none		0.647	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430		C	28194900	T	C	28194900	2	2	5	1	0	0	0	0	0	0	0	1	9680	1722	60	3		3	MN1	22	28194900	Silent	SNP	T	TCGA-2Z-A9J5-01A-21D-A382-10		28194900	23109666	97	493											
CPT1B	1375	hgsc.bcm.edu	37	chr22	51009666	51009666	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacagtctcagtccgtcccTcccggaacattctggtcatt	7	11	8	15	2	3	0	2	0	2	0	7	1	6	1	3	2	1	1	3	2	1	2			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chr22:51009666T>C	ENST00000360719.2	-	15	1933	c.1796A>G	c.(1795-1797)gAg>gGg	p.E599G	CPT1B_ENST00000434492.2_Missense_Mutation_p.E394G|CPT1B_ENST00000440709.1_Missense_Mutation_p.E518G|CHKB-CPT1B_ENST00000453634.1_3'UTR|CPT1B_ENST00000312108.7_Missense_Mutation_p.E599G|CPT1B_ENST00000395650.2_Missense_Mutation_p.E599G|CPT1B_ENST00000457250.1_Missense_Mutation_p.E565G|CPT1B_ENST00000405237.3_Missense_Mutation_p.E599G	NM_001145135.1|NM_152245.2	NP_001138607.1|NP_689451.1	Q92523	CPT1B_HUMAN	carnitine palmitoyltransferase 1B (muscle)	599					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)		AGTCCGTCCCTCCCGGAACAT	0.572																																					p.E599G	Esophageal Squamous(170;988 1933 25577 30295 48163)	Atlas-SNP	.											.	CPT1B	61	.	0			c.A1796G						PASS	.						126	105	112					22																	51009666		2203	4300	6503	SO:0001583	missense	1375	exon15			CGTCCCTCCCGGA	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.1796A>G	chr22.hg19:g.51009666T>C	ENSP00000353945:p.Glu599Gly	35.0	0.0	.		50.0	17.0	.	NM_001145135	B7Z4U4|B7Z5T8|E9PCP2|Q13389|Q99655|Q9BY90	Missense_Mutation	SNP	ENST00000360719.2	hg19	CCDS14098.1	.	.	.	.	.	.	.	.	.	.	T	31	5.076517	0.94000	.	.	ENSG00000205560	ENST00000405237;ENST00000312108;ENST00000360719;ENST00000457250;ENST00000440709;ENST00000434492;ENST00000395650	D;D;D;D;D;D;D	0.89939	-2.59;-2.59;-2.59;-2.59;-2.59;-2.59;-2.59	5.82	5.82	0.92795	.	0.102840	0.64402	D	0.000004	D	0.94175	0.8131	M	0.83312	2.635	0.80722	D	1	P;D;D;D	0.63046	0.822;0.984;0.986;0.992	B;D;D;D	0.65874	0.341;0.939;0.911;0.911	D	0.94829	0.7994	10	0.87932	D	0	-34.8941	14.122	0.65195	0.0:0.0:0.0:1.0	.	518;565;394;599	E9PCP2;B7Z4U4;A2RRE8;Q92523	.;.;.;CPT1B_HUMAN	G	599;599;599;565;518;394;599	ENSP00000385486:E599G;ENSP00000312189:E599G;ENSP00000353945:E599G;ENSP00000409342:E565G;ENSP00000414713:E518G;ENSP00000410966:E394G;ENSP00000379011:E599G	ENSP00000312189:E599G	E	-	2	0	CPT1B	49356532	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.611000	0.82962	2.224000	0.72417	0.459000	0.35465	GAG	.	.	.	none		0.572	CPT1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317264.5	NM_152246		C	51009666	T	C	51009666	3	2	5	1	0	0	0	0	1	0	0	0	3834	1551	54	3	542	3	CPT1B	22	51009666	Missense_Mutation	SNP	T	TCGA-2Z-A9J5-01A-21D-A382-10	22814766	51009666	294900	98	494											
HUWE1	10075	hgsc.bcm.edu	37	chrX	53565805	53565805	+	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	gttccctgtacctgcaaagcGaaggaacttctgtgtgtcag	9	11	11	10	1	2	0	1	0	1	0	3	2	3	1	2	1	4	3	2	1	4	3			TCGA-2Z-A9J5-01A-21D-A382-10	TCGA-2Z-A9J5-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	237ddfd6-6bf8-4d4b-aa08-0da80f631160	b35fa663-4ad4-4c0b-9d5a-c6490a0c9009	g.chrX:53565805G>T	ENST00000342160.3	-	75	12326	c.11869C>A	c.(11869-11871)Cgc>Agc	p.R3957S	HUWE1_ENST00000262854.6_Missense_Mutation_p.R3957S			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	3957					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						CCTGCAAAGCGAAGGAACTTC	0.498																																					p.R3957S		Atlas-SNP	.											.	HUWE1	724	.	0			c.C11869A						PASS	.						34	27	29					X																	53565805		2203	4300	6503	SO:0001583	missense	10075	exon76			CAAAGCGAAGGAA	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.11869C>A	chrX.hg19:g.53565805G>T	ENSP00000340648:p.Arg3957Ser	25.0	0.0	.		37.0	21.0	.	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	hg19	CCDS35301.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.00|14.00	2.406129|2.406129	0.42715|0.42715	.|.	.|.	ENSG00000086758|ENSG00000086758	ENST00000342160;ENST00000262854|ENST00000427052;ENST00000426907	T;T|.	0.36520|.	1.25;1.25|.	5.17|5.17	5.17|5.17	0.71159|0.71159	.|.	0.061518|.	0.64402|.	D|.	0.000003|.	T|.	0.42291|.	0.1196|.	N|N	0.17379|0.17379	0.485|0.485	0.58432|0.58432	D|D	0.999999|0.999999	B;D;D|.	0.63046|.	0.245;0.987;0.992|.	B;D;D|.	0.70487|.	0.044;0.931;0.969|.	T|.	0.30297|.	-0.9983|.	10|.	0.26408|.	T|.	0.33|.	.|.	11.8503|11.8503	0.52407|0.52407	0.0:0.0:0.825:0.175|0.0:0.0:0.825:0.175	.|.	779;3957;3941|.	Q5H935;Q7Z6Z7;Q7Z6Z7-2|.	.;HUWE1_HUMAN;.|.	S|X	3957|2990;779	ENSP00000340648:R3957S;ENSP00000262854:R3957S|.	ENSP00000262854:R3957S|.	R|S	-|-	1|2	0|0	HUWE1|HUWE1	53582530|53582530	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	6.789000|6.789000	0.75110|0.75110	2.276000|2.276000	0.75962|0.75962	0.600000|0.600000	0.82982|0.82982	CGC|TCG	.	.	.	none		0.498	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		T	53565805	G	T	53565805	3	4	5	1	0	0	0	0	1	0	0	0	7468	1058	37	4	1291	4	HUWE1	23	53565805	Missense_Mutation	SNP	G	TCGA-2Z-A9J5-01A-21D-A382-10		53565805	101704755	99	495											
HSPG2	3339	hgsc.bcm.edu	37	chr1	22176680	22176680	+	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	ccggaccgtgggggtgacccCaagtgctggggacagagggc	7	4	19	11	2	0	2	0	1	0	1	0	4	0	4	4	6	1	1	4	6	1	0	rs372361312		TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr1:22176680C>T	ENST00000374695.3	-	57	7379	c.7300G>A	c.(7300-7302)Ggg>Agg	p.G2434R	HSPG2_ENST00000430507.1_3'UTR	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2434	Ig-like C2-type 9.				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)	GGGGTGACCCCAAGTGCTGGG	0.637																																					p.G2434R		Atlas-SNP	.											.	HSPG2	311	.	0			c.G7300A						PASS	.						37	42	40					1																	22176680		2203	4300	6503	SO:0001583	missense	3339	exon57			TGACCCCAAGTGC	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.7300G>A	chr1.hg19:g.22176680C>T	ENSP00000363827:p.Gly2434Arg	146.0	0.0	.		89.0	11.0	.	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	C	12.90	2.075228	0.36662	.	.	ENSG00000142798	ENST00000374695	T	0.75938	-0.98	5.29	3.33	0.38152	.	0.000000	0.39083	N	0.001469	T	0.67268	0.2875	M	0.63843	1.955	0.22330	N	0.999195	B;B	0.16802	0.01;0.019	B;B	0.20577	0.03;0.025	T	0.54918	-0.8221	10	0.29301	T	0.29	.	7.5389	0.27727	0.0:0.7341:0.1656:0.1003	.	374;2434	Q59EG0;P98160	.;PGBM_HUMAN	R	2434	ENSP00000363827:G2434R	ENSP00000363827:G2434R	G	-	1	0	HSPG2	22049267	0.006000	0.16342	0.483000	0.27378	0.979000	0.70002	0.634000	0.24614	0.522000	0.28464	0.561000	0.74099	GGG	.	.	.	none		0.637	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		T	22176680	C	T	22176680	3	4	6	1	0	0	0	0	1	0	0	0	7437	594	21	2	6039	2	HSPG2	1	22176680	Missense_Mutation	SNP	C	TCGA-2Z-A9J6-01A-11D-A382-10		22176680	227073941	1	496											
TAF12	6883	hgsc.bcm.edu	37	chr1	28948461	28948461	+	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	gctaagacgacctcctgcccCaggagtgcctggtatcttta	8	10	10	13	1	1	1	0	0	1	1	2	3	2	2	5	2	2	2	5	2	3	4			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr1:28948461C>T	ENST00000263974.4	-	2	567	c.133G>A	c.(133-135)Ggg>Agg	p.G45R	TAF12_ENST00000373824.4_Missense_Mutation_p.G45R	NM_001135218.1	NP_001128690.1	Q16514	TAF12_HUMAN	TAF12 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 20kDa	45					chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of RNA biosynthetic process (GO:2001141)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			ovary(1)|upper_aerodigestive_tract(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;0.000451)|all_lung(284;0.00063)|Renal(390;0.00121)|Breast(348;0.00502)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)		Colorectal(126;3.21e-08)|COAD - Colon adenocarcinoma(152;1.74e-06)|STAD - Stomach adenocarcinoma(196;0.00303)|KIRC - Kidney renal clear cell carcinoma(1967;0.0109)|BRCA - Breast invasive adenocarcinoma(304;0.0228)|READ - Rectum adenocarcinoma(331;0.0649)		CCTCCTGCCCCAGGAGTGCCT	0.468																																					p.G45R		Atlas-SNP	.											.	TAF12	17	.	0			c.G133A						PASS	.						157	149	151					1																	28948461		2203	4300	6503	SO:0001583	missense	6883	exon2			CTGCCCCAGGAGT	BC011986	CCDS326.1	1p35	2008-02-05	2002-08-29	2001-12-07	ENSG00000120656	ENSG00000120656			11545	protein-coding gene	gene with protein product		600773	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, J, 20kD"	TAF2J		7729427	Standard	NM_005644		Approved	TAFII20	uc001bqy.3	Q16514	OTTHUMG00000003655	ENST00000263974.4:c.133G>A	chr1.hg19:g.28948461C>T	ENSP00000263974:p.Gly45Arg	132.0	0.0	.		112.0	5.0	.	NM_001135218	D3DPM5|Q15775|Q5T077	Missense_Mutation	SNP	ENST00000263974.4	hg19	CCDS326.1	.	.	.	.	.	.	.	.	.	.	C	9.352	1.065712	0.20067	.	.	ENSG00000120656	ENST00000373824;ENST00000263974	.	.	.	5.17	5.17	0.71159	.	0.101675	0.64402	D	0.000002	T	0.45955	0.1368	L	0.32530	0.975	0.43724	D	0.996205	B;B	0.26512	0.126;0.151	B;B	0.32533	0.147;0.095	T	0.32666	-0.9898	9	0.13470	T	0.59	-5.9182	11.6763	0.51432	0.0:0.913:0.0:0.087	.	15;45	Q16514-2;Q16514	.;TAF12_HUMAN	R	45	.	ENSP00000263974:G45R	G	-	1	0	TAF12	28821048	1.000000	0.71417	1.000000	0.80357	0.011000	0.07611	3.514000	0.53422	2.405000	0.81733	0.591000	0.81541	GGG	.	.	.	none		0.468	TAF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010367.1	NM_005644		T	28948461	C	T	28948461	3	4	6	1	0	0	0	0	1	0	0	0	15528	594	21	2	372	2	TAF12	1	28948461	Missense_Mutation	SNP	C	TCGA-2Z-A9J6-01A-11D-A382-10	6771781	28948461	220302160	2	497											
FPGT	8790	hgsc.bcm.edu	37	chr1	74671342	74671342	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttcttctttgagtgactcAgttataacatccctaaagat	11	16	6	8	0	3	3	1	2	2	1	4	3	4	3	1	0	1	2	1	0	4	6			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr1:74671342A>G	ENST00000609362.1	+	4	1648	c.1611A>G	c.(1609-1611)tcA>tcG	p.S537S	FPGT_ENST00000370894.5_3'UTR|FPGT_ENST00000524915.1_Intron|FPGT_ENST00000534056.1_Silent_p.S283S|FPGT-TNNI3K_ENST00000533006.1_Intron|FPGT_ENST00000370898.3_Silent_p.S550S|FPGT-TNNI3K_ENST00000557284.2_Intron|FPGT-TNNI3K_ENST00000370893.1_Intron|TNNI3K_ENST00000370891.2_Intron|FPGT-TNNI3K_ENST00000370899.3_Intron|FPGT-TNNI3K_ENST00000370895.1_Intron	NM_003838.4	NP_003829.3	O14772	FPGT_HUMAN	fucose-1-phosphate guanylyltransferase	537					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						TGAGTGACTCAGTTATAACAT	0.383																																					p.S537S		Atlas-SNP	.											.	FPGT	77	.	0			c.A1611G						PASS	.						136	124	128					1																	74671342		2203	4300	6503	SO:0001819	synonymous_variant	8790	exon4			TGACTCAGTTATA	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.1611A>G	chr1.hg19:g.74671342A>G		74.0	0.0	.		90.0	31.0	.	NM_003838	A6NMH3|B4DRX2|B4E2Y7|E9PNQ2|Q8N5J7	Silent	SNP	ENST00000609362.1	hg19	CCDS663.1																																																																																			.	.	.	none		0.383	FPGT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	74671342	A	G	74671342	2	3	6	1	0	0	0	0	0	0	0	1	6044	175	7	3		3	FPGT	1	74671342	Silent	SNP	A	TCGA-2Z-A9J6-01A-11D-A382-10	45722881	74671342	174579279	3	498											
CA14	23632	hgsc.bcm.edu	37	chr1	150235713	150235713	+	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	ctcagctggaaaagcttcagGggacattgttctccacagaa	12	9	10	10	0	3	1	2	0	1	1	4	3	3	3	1	3	2	3	1	3	3	3			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr1:150235713G>C	ENST00000369111.4	+	8	1706	c.736G>C	c.(736-738)Ggg>Cgg	p.G246R	snoU13_ENST00000458929.1_RNA	NM_012113.1	NP_036245.1	Q9ULX7	CAH14_HUMAN	carbonic anhydrase XIV	246					bicarbonate transport (GO:0015701)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|metal ion binding (GO:0046872)			central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)	18	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)		Acetazolamide(DB00819)|Zonisamide(DB00909)	AAAGCTTCAGGGGACATTGTT	0.517																																					p.G246R		Atlas-SNP	.											.	CA14	37	.	0			c.G736C						PASS	.						92	97	95					1																	150235713		2203	4300	6503	SO:0001583	missense	23632	exon8			CTTCAGGGGACAT	AB025904	CCDS947.1	1q21	2008-02-05			ENSG00000118298	ENSG00000118298		"Carbonic anhydrases"	1372	protein-coding gene	gene with protein product		604832				10512682	Standard	XM_005245059		Approved		uc001etx.3	Q9ULX7	OTTHUMG00000012549	ENST00000369111.4:c.736G>C	chr1.hg19:g.150235713G>C	ENSP00000358107:p.Gly246Arg	149.0	0.0	.		178.0	77.0	.	NM_012113	Q5TB24|Q8NCF4	Missense_Mutation	SNP	ENST00000369111.4	hg19	CCDS947.1	.	.	.	.	.	.	.	.	.	.	G	13.89	2.372423	0.42003	.	.	ENSG00000118298	ENST00000369111	T	0.65549	-0.16	5.46	3.56	0.40772	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.341654	0.31279	N	0.007932	T	0.13970	0.0338	N	0.01817	-0.705	0.24121	N	0.995806	B	0.18610	0.029	B	0.24701	0.055	T	0.22208	-1.0223	10	0.29301	T	0.29	.	7.2635	0.26217	0.089:0.1705:0.7405:0.0	.	246	Q9ULX7	CAH14_HUMAN	R	246	ENSP00000358107:G246R	ENSP00000358107:G246R	G	+	1	0	CA14	148502337	0.976000	0.34144	0.954000	0.39281	0.918000	0.54935	1.973000	0.40550	0.834000	0.34852	0.655000	0.94253	GGG	.	.	.	none		0.517	CA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035064.2	NM_012113		C	150235713	G	C	150235713	3	2	6	1	0	0	0	0	1	0	0	0	2517	1232	43	4	766	4	CA14	1	150235713	Missense_Mutation	SNP	G	TCGA-2Z-A9J6-01A-11D-A382-10	75564371	150235713	99014908	4	499											
RPRD2	23248	hgsc.bcm.edu	37	chr1	150437078	150437078	+	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	caccagtggcctgaaaacacCtgcacctgccacgacaacat	13	5	7	16	1	0	1	0	1	0	0	0	2	0	1	5	1	4	1	5	1	3	0			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr1:150437078C>A	ENST00000369068.4	+	10	1491	c.1487C>A	c.(1486-1488)cCt>cAt	p.P496H	RPRD2_ENST00000492220.1_3'UTR|RPRD2_ENST00000401000.4_Missense_Mutation_p.P470H|RPRD2_ENST00000539519.1_Missense_Mutation_p.P470H	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	496	Ser-rich.					DNA-directed RNA polymerase II, holoenzyme (GO:0016591)				central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						CTGAAAACACCTGCACCTGCC	0.547											OREG0013786	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P496H		Atlas-SNP	.											.	RPRD2	189	.	0			c.C1487A						PASS	.						73	92	86					1																	150437078		2064	4183	6247	SO:0001583	missense	23248	exon10			AAACACCTGCACC	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.1487C>A	chr1.hg19:g.150437078C>A	ENSP00000358064:p.Pro496His	72.0	0.0	.	1732	92.0	39.0	.	NM_015203	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Missense_Mutation	SNP	ENST00000369068.4	hg19	CCDS44216.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.080155	0.76528	.	.	ENSG00000163125	ENST00000401000;ENST00000539519;ENST00000369068	T;T;T	0.68479	-0.33;0.06;-0.24	5.34	4.42	0.53409	.	0.188129	0.45361	N	0.000370	T	0.53142	0.1778	M	0.61703	1.905	0.52099	D	0.999945	B;B;B	0.24368	0.005;0.062;0.102	B;B;B	0.24155	0.003;0.023;0.051	T	0.61535	-0.7043	10	0.87932	D	0	-12.2819	15.5276	0.75923	0.1392:0.8608:0.0:0.0	.	470;496;470	B4E2Q6;Q5VT52;Q5VT52-3	.;RPRD2_HUMAN;.	H	470;470;496	ENSP00000383785:P470H;ENSP00000445482:P470H;ENSP00000358064:P496H	ENSP00000358064:P496H	P	+	2	0	RPRD2	148703702	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.060000	0.76692	1.472000	0.48140	-0.182000	0.12963	CCT	.	.	.	none		0.547	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203		A	150437078	C	A	150437078	3	1	6	1	0	0	0	0	1	0	0	0	13630	681	24	4	1525	4	RPRD2	1	150437078	Missense_Mutation	SNP	C	TCGA-2Z-A9J6-01A-11D-A382-10	201365	150437078	98813543	5	500											
KDM5B	10765	hgsc.bcm.edu	37	chr1	202724423	202724423	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcaagtagttaattgaatagCtccagtggtcttcaatgtgc	11	13	10	7	0	2	1	1	1	1	0	3	1	3	1	1	1	2	4	1	1	6	5			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr1:202724423C>T	ENST00000367265.3	-	11	2678	c.1514G>A	c.(1513-1515)aGc>aAc	p.S505N	KDM5B_ENST00000367264.2_Missense_Mutation_p.S541N|KDM5B_ENST00000456180.1_5'UTR	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	505	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				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						AATTGAATAGCTCCAGTGGTC	0.403																																					p.S505N		Atlas-SNP	.											.	KDM5B	166	.	0			c.G1514A						PASS	.						113	113	113					1																	202724423		2203	4300	6503	SO:0001583	missense	10765	exon11			GAATAGCTCCAGT	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.1514G>A	chr1.hg19:g.202724423C>T	ENSP00000356234:p.Ser505Asn	78.0	0.0	.		77.0	25.0	.	NM_006618	O95811|Q15752|Q9Y3Q5	Missense_Mutation	SNP	ENST00000367265.3	hg19	CCDS30974.1	.	.	.	.	.	.	.	.	.	.	C	36	5.653576	0.96724	.	.	ENSG00000117139	ENST00000367265;ENST00000538292;ENST00000367264;ENST00000235790	T;T;T	0.73152	-0.72;-0.72;-0.72	5.73	5.73	0.89815	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.000000	0.85682	D	0.000000	D	0.83367	0.5239	M	0.69358	2.11	0.80722	D	1	D;D	0.63046	0.992;0.989	P;D	0.68039	0.798;0.955	D	0.84199	0.0449	10	0.87932	D	0	-17.7337	19.9036	0.96999	0.0:1.0:0.0:0.0	.	541;505	Q9UGL1-2;Q9UGL1	.;KDM5B_HUMAN	N	505;347;541;347	ENSP00000356234:S505N;ENSP00000356233:S541N;ENSP00000235790:S347N	ENSP00000235790:S347N	S	-	2	0	KDM5B	200991046	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.814000	0.86154	2.706000	0.92434	0.655000	0.94253	AGC	.	.	.	none		0.403	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618		T	202724423	C	T	202724423	3	4	6	1	0	0	0	0	1	0	0	0	8141	797	28	2	3188	2	KDM5B	1	202724423	Missense_Mutation	SNP	C	TCGA-2Z-A9J6-01A-11D-A382-10	52287345	202724423	46526198	6	501											
CGREF1	10669	hgsc.bcm.edu	37	chr2	27324436	27324436	+	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	tggccctcagcttcccctctGggccctggaacatctccatc	5	10	8	18	0	3	0	1	0	2	0	6	1	4	1	5	3	2	1	5	3	1	1			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr2:27324436G>T	ENST00000260595.5	-	6	955	c.663C>A	c.(661-663)ccC>ccA	p.P221P	CGREF1_ENST00000452318.2_Intron|CGREF1_ENST00000402550.1_Intron|CGREF1_ENST00000402394.1_Silent_p.P221P|CGREF1_ENST00000312734.4_Silent_p.P221P|CGREF1_ENST00000405600.1_Silent_p.P221P|CGREF1_ENST00000404694.3_Silent_p.P343P			Q99674	CGRE1_HUMAN	cell growth regulator with EF-hand domain 1	221					cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			kidney(1)|lung(4)|ovary(1)|prostate(2)|skin(1)|soft_tissue(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTCCCCTCTGGGCCCTGGAA	0.652																																					p.P221P		Atlas-SNP	.											.	CGREF1	31	.	0			c.C663A						PASS	.						113	133	126					2																	27324436		2203	4300	6503	SO:0001819	synonymous_variant	10669	exon6			CCCTCTGGGCCCT	BC034764	CCDS33162.1, CCDS33162.2, CCDS54339.1	2p23.3	2013-01-10			ENSG00000138028	ENSG00000138028		"EF-hand domain containing"	16962	protein-coding gene	gene with protein product		606137				8968090	Standard	NM_006569		Approved	CGR11	uc002riq.3	Q99674	OTTHUMG00000152009	ENST00000260595.5:c.663C>A	chr2.hg19:g.27324436G>T		47.0	0.0	.		50.0	15.0	.	NM_001166239	A6NHV7|B4DXY8|B5MCB7|B5MCC9|B5MCP5|E7EU99|Q8N4B7	Silent	SNP	ENST00000260595.5	hg19																																																																																				.	.	.	none		0.652	CGREF1-201	KNOWN	basic	protein_coding	protein_coding		NM_006569		T	27324436	G	T	27324436	2	4	6	1	0	0	0	0	0	0	0	1	3307	1335	47	4		4	CGREF1	2	27324436	Silent	SNP	G	TCGA-2Z-A9J6-01A-11D-A382-10		27324436	215874937	7	502											
C2orf78	388960	hgsc.bcm.edu	37	chr2	74043789	74043789	+	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	tctgctgcttctaggccatcAgcctacaaaacatcatcttg	10	12	6	13	0	5	0	2	0	3	0	5	0	5	0	2	1	5	2	2	1	4	4			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr2:74043789A>T	ENST00000409561.1	+	3	2560	c.2439A>T	c.(2437-2439)tcA>tcT	p.S813S		NM_001080474.1	NP_001073943.1	A6NCI8	CB078_HUMAN	chromosome 2 open reading frame 78	813										cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|soft_tissue(1)|urinary_tract(1)	34						CTAGGCCATCAGCCTACAAAA	0.522																																					p.S813S		Atlas-SNP	.											.	C2orf78	150	.	0			c.A2439T						PASS	.						71	69	70					2																	74043789		2020	4178	6198	SO:0001819	synonymous_variant	388960	exon3			GCCATCAGCCTAC	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.2439A>T	chr2.hg19:g.74043789A>T		70.0	0.0	.		83.0	34.0	.	NM_001080474		Silent	SNP	ENST00000409561.1	hg19	CCDS46338.1																																																																																			.	.	.	none		0.522	C2orf78-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000328083.1	NM_001080474		T	74043789	A	T	74043789	2	4	6	1	0	0	0	0	0	0	0	1	2197	175	7	5		5	C2orf78	2	74043789	Silent	SNP	A	TCGA-2Z-A9J6-01A-11D-A382-10	46719353	74043789	169155584	8	503											
TGOLN2	10618	hgsc.bcm.edu	37	chr2	85553951	85553951	+	Frame_Shift_Del	DEL	T	T	-																															cgggggagaaatgaggtcagTttcctccccagattcggttt																										TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr2:85553951delT	ENST00000409232.3	-	2	965	c.904delA	c.(904-906)actfs	p.T302fs	TGOLN2_ENST00000409015.1_Frame_Shift_Del_p.T302fs|TGOLN2_ENST00000282120.2_Intron|TGOLN2_ENST00000398263.2_Intron|TGOLN2_ENST00000377386.3_Frame_Shift_Del_p.T302fs|TGOLN2_ENST00000444342.2_Frame_Shift_Del_p.T302fs			O43493	TGON2_HUMAN	trans-golgi network protein 2	302						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)											ATGAGGTCAGTTTCCTCCCCA	0.512																																					p.T302fs		Atlas-Indel,Pindel	.											.	TGOLN2	32	.	0			c.905delC						PASS	.						56	52	53					2																	85553951		1901	4128	6029	SO:0001589	frameshift_variant	10618	exon2			.	AF027515	CCDS46351.1, CCDS56126.1, CCDS56127.1	2p11.2	2012-06-25			ENSG00000152291	ENSG00000152291			15450	protein-coding gene	gene with protein product	"trans-Golgi network protein (46, 48, 51kD isoforms)"	603062				9422759, 21994457	Standard	NM_001206840		Approved	TGN51, TGN46, TGN48, TGN38, TTGN2	uc021vjw.1	O43493	OTTHUMG00000153017	ENST00000409232.3:c.904delA	chr2.hg19:g.85553951delT	ENSP00000386443:p.Thr302fs	117.0	0.0	0		130.0	41.0	0.315385	NM_001206841	B2R686|B8ZZ88|D6W5K3|F8WBK2|O15282|O43492|O43499|O43500|O43501|Q53G68|Q53GV2|Q6MZV1|Q6ZTM7|Q8N6T8|Q92760|Q96QL2	Frame_Shift_Del	DEL	ENST00000409232.3	hg19	CCDS56126.1																																																																																			.	.	.	none		0.512	TGOLN2-006	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000329045.2	NM_006464		-	85553951	T	-	85553951	7	5	6	1	0	1	0	1	0	0	0	0	15848	1725	60	0	421	0	TGOLN2	2	85553951	Frame_Shift_Del	DEL	T	TCGA-2Z-A9J6-01A-11D-A382-10	11510162	85553951	157645422	9	504											
PKP4	8502	hgsc.bcm.edu	37	chr2	159477605	159477605	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaggaaccctctattcaccAgaacagacatctctccatga	14	8	5	14	0	3	3	1	1	2	2	5	4	4	4	3	1	2	0	3	1	4	2			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr2:159477605A>G	ENST00000389759.3	+	5	496	c.384A>G	c.(382-384)ccA>ccG	p.P128P	PKP4_ENST00000389757.3_Silent_p.P128P	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	128					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						TCTATTCACCAGAACAGACAT	0.423										HNSCC(62;0.18)																											p.P128P		Atlas-SNP	.											.	PKP4	133	.	0			c.A384G						PASS	.						110	98	102					2																	159477605		2203	4300	6503	SO:0001819	synonymous_variant	8502	exon5			TTCACCAGAACAG	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.384A>G	chr2.hg19:g.159477605A>G		241.0	0.0	.		253.0	83.0	.	NM_001005476	Q86W91	Silent	SNP	ENST00000389759.3	hg19	CCDS33305.1																																																																																			.	.	.	none		0.423	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1			G	159477605	A	G	159477605	2	3	6	1	0	0	0	0	0	0	0	1	11994	175	7	3		3	PKP4	2	159477605	Silent	SNP	A	TCGA-2Z-A9J6-01A-11D-A382-10	73923654	159477605	83721768	10	505											
HSPE1	3336	hgsc.bcm.edu	37	chr2	198367837	198367837	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaatatggaggcaccaaagtAgttctagatgacaaggtgtg	14	9	13	5	0	1	2	0	1	1	1	1	4	1	3	1	3	0	3	1	3	6	4			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr2:198367837A>G	ENST00000233893.5	+	3	686	c.243A>G	c.(241-243)gtA>gtG	p.V81V	HSPE1_ENST00000465573.1_3'UTR|HSPE1-MOB4_ENST00000604458.1_Intron|HSPE1_ENST00000409468.1_Silent_p.V81V|HSPE1_ENST00000409729.1_Silent_p.V26V|HSPD1_ENST00000345042.2_5'Flank	NM_002157.2	NP_002148.1	P61604	CH10_HUMAN	heat shock 10kDa protein 1	81					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|osteoblast differentiation (GO:0001649)|protein folding (GO:0006457)|response to unfolded protein (GO:0006986)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			lung(1)	1			Epithelial(96;0.225)			GCACCAAAGTAGTTCTAGATG	0.343																																					p.V81V		Atlas-SNP	.											.	HSPE1	2	.	0			c.A243G						PASS	.						148	159	155					2																	198367837		2203	4300	6503	SO:0001819	synonymous_variant	3336	exon3			CAAAGTAGTTCTA	AF109872	CCDS2320.1	2q33.1	2013-10-17	2013-10-17		ENSG00000115541	ENSG00000115541		"Heat Shock Proteins / Chaperonins"	5269	protein-coding gene	gene with protein product	"chaperonin 10"	600141	"heat shock 10kD protein 1 (chaperonin 10)"			7914093, 7698325	Standard	NM_002157		Approved	CPN10, GROES		P61604	OTTHUMG00000132749	ENST00000233893.5:c.243A>G	chr2.hg19:g.198367837A>G		69.0	0.0	.		31.0	13.0	.	NM_002157	O95421|Q04984|Q53X54|Q9UDH0	Silent	SNP	ENST00000233893.5	hg19	CCDS2320.1																																																																																			.	.	.	none		0.343	HSPE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256112.1	NM_002157		G	198367837	A	G	198367837	2	3	6	1	0	0	0	0	0	0	0	1	7436	407	15	3		3	HSPE1	2	198367837	Silent	SNP	A	TCGA-2Z-A9J6-01A-11D-A382-10	38890232	198367837	44831536	11	506											
CD200R1	131450	hgsc.bcm.edu	37	chr3	112648333	112648333	+	Missense_Mutation	SNP	T	T	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	gcacagcatttgtagccatcTttacaggccatgaagtgtta	11	12	9	9	0	1	1	0	1	1	0	1	1	1	1	2	1	3	4	2	1	4	5			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr3:112648333T>G	ENST00000471858.1	-	3	387	c.155A>C	c.(154-156)aAg>aCg	p.K52T	CD200R1_ENST00000440122.2_Missense_Mutation_p.K75T|CD200R1_ENST00000490004.1_Missense_Mutation_p.K52T|CD200R1_ENST00000295863.4_Missense_Mutation_p.K30T|CD200R1_ENST00000308611.3_Missense_Mutation_p.K75T	NM_170780.2	NP_740750.1	Q8TD46	MO2R1_HUMAN	CD200 receptor 1	52					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						TGTAGCCATCTTTACAGGCCA	0.373																																					p.K75T		Atlas-SNP	.											.	CD200R1	91	.	0			c.A224C						PASS	.						76	73	74					3																	112648333		2203	4300	6503	SO:0001583	missense	131450	exon4			GCCATCTTTACAG	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.155A>C	chr3.hg19:g.112648333T>G	ENSP00000418928:p.Lys52Thr	30.0	0.0	.		50.0	14.0	.	NM_138806	B3KWZ9|E9PCM9|Q52LJ7|Q6IS95|Q6UW94|Q6WHB8|Q8TD44|Q8TD45|Q8TD52	Missense_Mutation	SNP	ENST00000471858.1	hg19	CCDS2970.1	.	.	.	.	.	.	.	.	.	.	T	6.153	0.396370	0.11638	.	.	ENSG00000163606	ENST00000471858;ENST00000308611;ENST00000295863;ENST00000440122;ENST00000490004	T;T;T;T;T	0.09255	3.0;3.0;3.0;3.0;3.0	5.5	-11.0	0.00169	Immunoglobulin subtype (1);	2.986180	0.00757	N	0.001111	T	0.04318	0.0119	N	0.08118	0	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;0.0;0.0;0.0	T	0.21484	-1.0244	10	0.25751	T	0.34	.	6.6183	0.22788	0.2992:0.0:0.3016:0.3992	.	30;52;75;52;75	B4E2U2;Q8TD46-3;Q8TD46-2;Q8TD46;Q8TD46-4	.;.;.;MO2R1_HUMAN;.	T	52;75;30;75;52	ENSP00000418928:K52T;ENSP00000311035:K75T;ENSP00000295863:K30T;ENSP00000405733:K75T;ENSP00000418801:K52T	ENSP00000295863:K30T	K	-	2	0	CD200R1	114131023	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.518000	0.02246	-2.599000	0.00452	-2.119000	0.00349	AAG	.	.	.	none		0.373	CD200R1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354467.1	NM_138806		G	112648333	T	G	112648333	3	3	6	1	0	0	0	0	1	0	0	0	2983	1609	56	5	889	5	CD200R1	3	112648333	Missense_Mutation	SNP	T	TCGA-2Z-A9J6-01A-11D-A382-10		112648333	85374097	12	507											
IGSF10	285313	hgsc.bcm.edu	37	chr3	151155418	151155418	+	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	atttcgggccacacagataaAgtcggctgaatctgaaagcc	13	8	10	10	2	1	3	0	2	1	1	3	3	1	3	2	2	1	1	2	2	4	2			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr3:151155418A>T	ENST00000282466.3	-	6	6930	c.6931T>A	c.(6931-6933)Ttt>Att	p.F2311I	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	2311	Ig-like C2-type 9.				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)			ACACAGATAAAGTCGGCTGAA	0.418																																					p.F2311I		Atlas-SNP	.											.	IGSF10	279	.	0			c.T6931A						PASS	.						138	133	135					3																	151155418		2203	4300	6503	SO:0001583	missense	285313	exon6			AGATAAAGTCGGC	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.6931T>A	chr3.hg19:g.151155418A>T	ENSP00000282466:p.Phe2311Ile	104.0	0.0	.		139.0	22.0	.	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	hg19	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.468341	0.84533	.	.	ENSG00000152580	ENST00000282466	T	0.28454	1.61	5.77	5.77	0.91146	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.48767	D	0.000161	T	0.53061	0.1773	M	0.64676	1.99	0.80722	D	1	D;D	0.69078	0.997;0.964	D;P	0.69654	0.965;0.841	T	0.55604	-0.8115	10	0.87932	D	0	.	16.084	0.81025	1.0:0.0:0.0:0.0	.	2311;338	Q6WRI0;Q6WRI0-2	IGS10_HUMAN;.	I	2311	ENSP00000282466:F2311I	ENSP00000282466:F2311I	F	-	1	0	IGSF10	152638108	1.000000	0.71417	0.040000	0.18447	0.970000	0.65996	8.904000	0.92590	2.202000	0.70862	0.482000	0.46254	TTT	.	.	.	none		0.418	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		T	151155418	A	T	151155418	3	4	6	1	0	0	0	0	1	0	0	0	7604	72	3	5	944	5	IGSF10	3	151155418	Missense_Mutation	SNP	A	TCGA-2Z-A9J6-01A-11D-A382-10	38507085	151155418	46867012	13	508											
PHC3	80012	hgsc.bcm.edu	37	chr3	169896600	169896600	+	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	gaaccactgtagacagagatCtgtggctgctgcattcgaga	11	9	12	9	1	1	3	0	0	1	3	2	6	1	3	1	1	3	4	1	1	2	2	rs375674359		TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr3:169896600C>A	ENST00000494943.1	-	2	173	c.105G>T	c.(103-105)caG>caT	p.Q35H	PHC3_ENST00000467570.1_Missense_Mutation_p.Q47H|PHC3_ENST00000474275.1_Missense_Mutation_p.Q35H|PHC3_ENST00000495893.2_Missense_Mutation_p.Q47H|PHC3_ENST00000481639.1_Missense_Mutation_p.Q47H|PHC3_ENST00000497658.1_Missense_Mutation_p.Q47H			Q8NDX5	PHC3_HUMAN	polyhomeotic homolog 3 (Drosophila)	35					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)			AGACAGAGATCTGTGGCTGCT	0.458																																					p.Q47H		Atlas-SNP	.											.	PHC3	113	.	0			c.G141T						PASS	.	C	HIS/GLN	1,4131		0,1,2065	247	248	248		141	5.2	1	3		248	0,8456		0,0,4228	no	missense	PHC3	NM_024947.3	24	0,1,6293	AA,AC,CC		0.0,0.0242,0.0079	benign	47/996	169896600	1,12587	2066	4228	6294	SO:0001583	missense	80012	exon2			AGAGATCTGTGGC		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.105G>T	chr3.hg19:g.169896600C>A	ENSP00000420271:p.Gln35His	84.0	0.0	.		72.0	14.0	.	NM_024947	A2RRP9|Q5HYF0|Q6NSG2|Q8NFT7|Q8NFZ1|Q8TBM2|Q9H971|Q9H9I4	Missense_Mutation	SNP	ENST00000494943.1	hg19		.	.	.	.	.	.	.	.	.	.	C	23.0	4.364917	0.82463	2.42E-4	0.0	ENSG00000173889	ENST00000494943;ENST00000495893;ENST00000467570;ENST00000484931;ENST00000466189;ENST00000475729;ENST00000474275;ENST00000465896;ENST00000497658;ENST00000481639	T;T	0.39592	1.07;1.08	6.03	5.15	0.70609	.	0.098560	0.46145	D	0.000311	T	0.58032	0.2094	L	0.54323	1.7	0.40012	D	0.975309	D;D;D;D;D;D;D;D	0.64830	0.994;0.994;0.98;0.994;0.994;0.994;0.994;0.988	D;D;D;D;D;P;D;D	0.78314	0.986;0.991;0.965;0.986;0.991;0.805;0.986;0.984	T	0.54200	-0.8329	9	.	.	.	-6.4983	13.908	0.63848	0.0:0.9291:0.0:0.0709	.	47;47;35;47;47;35;47;47	B4E2T1;E7EX82;Q8NDX5;Q8NDX5-5;G5E9U7;Q8NDX5-4;Q8NDX5-3;Q8NDX5-7	.;.;PHC3_HUMAN;.;.;.;.;.	H	35;47;47;47;47;47;35;47;47;47	ENSP00000420271:Q35H;ENSP00000420294:Q47H	.	Q	-	3	2	PHC3	171379294	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.462000	0.35266	2.861000	0.98227	0.655000	0.94253	CAG	.	.	.	weak		0.458	PHC3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000352182.3	NM_024947		A	169896600	C	A	169896600	3	1	6	1	0	0	0	0	1	0	0	0	11825	912	32	4	2902	4	PHC3	3	169896600	Missense_Mutation	SNP	C	TCGA-2Z-A9J6-01A-11D-A382-10	18741182	169896600	28125830	14	509											
SLC6A19	340024	hgsc.bcm.edu	37	chr5	1221280	1221280	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcaggttcaataaggacaTcgagttcatgatcggccaca	12	9	11	9	2	2	1	2	1	0	0	4	3	2	2	1	4	0	3	1	4	2	3			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr5:1221280T>C	ENST00000304460.10	+	11	1609	c.1553T>C	c.(1552-1554)aTc>aCc	p.I518T		NM_001003841.2	NP_001003841.1	Q695T7	S6A19_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 19	518					amino acid transport (GO:0006865)|ion transport (GO:0006811)|response to nutrient (GO:0007584)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|neutral amino acid transmembrane transporter activity (GO:0015175)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(25)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			AATAAGGACATCGAGTTCATG	0.542																																					p.I518T		Atlas-SNP	.											.	SLC6A19	99	.	0			c.T1553C						PASS	.						124	92	103					5																	1221280		2203	4300	6503	SO:0001583	missense	340024	exon11			AGGACATCGAGTT	AK096054	CCDS34130.1	5p15	2013-07-19			ENSG00000174358	ENSG00000174358		"Solute carriers"	27960	protein-coding gene	gene with protein product	"Hartnup disease"	608893					Standard	NM_001003841		Approved		uc003jbw.4	Q695T7	OTTHUMG00000161636	ENST00000304460.10:c.1553T>C	chr5.hg19:g.1221280T>C	ENSP00000305302:p.Ile518Thr	89.0	0.0	.		60.0	28.0	.	NM_001003841	A8K446	Missense_Mutation	SNP	ENST00000304460.10	hg19	CCDS34130.1	.	.	.	.	.	.	.	.	.	.	T	18.98	3.737729	0.69304	.	.	ENSG00000174358	ENST00000304460	T	0.79033	-1.23	4.81	4.81	0.61882	.	0.107611	0.64402	D	0.000006	D	0.87916	0.6298	M	0.92367	3.3	0.51012	D	0.9999	P	0.50528	0.936	P	0.54174	0.744	D	0.90994	0.4837	10	0.87932	D	0	.	14.3786	0.66897	0.0:0.0:0.0:1.0	.	518	Q695T7	S6A19_HUMAN	T	518	ENSP00000305302:I518T	ENSP00000305302:I518T	I	+	2	0	SLC6A19	1274280	1.000000	0.71417	0.978000	0.43139	0.517000	0.34286	7.825000	0.86693	1.808000	0.52836	0.402000	0.26972	ATC	.	.	.	none		0.542	SLC6A19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365557.1	XM_291120		C	1221280	T	C	1221280	3	2	6	1	0	0	0	0	1	0	0	0	14695	1435	50	3	1595	3	SLC6A19	5	1221280	Missense_Mutation	SNP	T	TCGA-2Z-A9J6-01A-11D-A382-10		1221280	179693980	15	510											
ADAMTS6	11174	hgsc.bcm.edu	37	chr5	64755996	64755996	+	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	aaaagctgcacactcactcaCccgaaaccccacaatgagag	16	4	6	15	1	2	1	2	1	0	1	2	3	2	1	3	0	3	2	3	0	4	0			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr5:64755996C>T	ENST00000536360.1	-	4	1445		c.e4+1					Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 6							proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|pancreas(1)|prostate(1)|skin(3)	18		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)		CACTCACTCACCCGAAACCCC	0.398																																					.		Atlas-SNP	.											.	ADAMTS6	174	.	0			c.631+1G>A						PASS	.						136	131	132					5																	64755996		2203	4300	6503	SO:0001630	splice_region_variant	11174	exon5			CACTCACCCGAAA	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.631+1G>A	chr5.hg19:g.64755996C>T		49.0	0.0	.		59.0	4.0	.	NM_197941	Q59EX6|Q5IR87|Q5IR88|Q5IR89|Q68DL1	Splice_Site	SNP	ENST00000536360.1	hg19		.	.	.	.	.	.	.	.	.	.	C	17.65	3.442004	0.63067	.	.	ENSG00000049192	ENST00000381055;ENST00000261306;ENST00000464680;ENST00000536360	.	.	.	6.06	6.06	0.98353	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.6397	0.99537	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ADAMTS6	64791752	1.000000	0.71417	1.000000	0.80357	0.424000	0.31475	7.353000	0.79414	2.880000	0.98712	0.650000	0.86243	.	.	.	.	none		0.398	ADAMTS6-201	KNOWN	basic	protein_coding	protein_coding		NM_197941	Intron	T	64755996	C	T	64755996	5	4	6	1	0	0	0	0	0	0	1	0	270	521	18	2	2809	2	ADAMTS6	5	64755996	Splice_Site	SNP	C	TCGA-2Z-A9J6-01A-11D-A382-10	63534716	64755996	116159264	16	511											
ST7	7982	hgsc.bcm.edu	37	chr7	116770588	116770588	+	Frame_Shift_Del	DEL	A	A	-																															agcctcttacttactatgacAtgaatctctctgcccaagac																										TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr7:116770588delA	ENST00000393446.2	+	5	796	c.493delA	c.(493-495)atgfs	p.M165fs	ST7_ENST00000393451.3_Frame_Shift_Del_p.M165fs|ST7_ENST00000487459.1_3'UTR|ST7_ENST00000393449.1_Frame_Shift_Del_p.M165fs|ST7-AS2_ENST00000432541.1_RNA|ST7_ENST00000323984.3_Frame_Shift_Del_p.M165fs|ST7_ENST00000465133.1_Frame_Shift_Del_p.M122fs|ST7_ENST00000393444.3_Frame_Shift_Del_p.M122fs|ST7-AS2_ENST00000442719.1_RNA|ST7-AS2_ENST00000434993.1_RNA|ST7_ENST00000432298.1_Frame_Shift_Del_p.M119fs|ST7_ENST00000265437.5_Frame_Shift_Del_p.M165fs|ST7_ENST00000393443.1_Frame_Shift_Del_p.M115fs|ST7_ENST00000422922.1_Frame_Shift_Del_p.M119fs|ST7_ENST00000393447.4_Frame_Shift_Del_p.M122fs			Q9Y561	LRP12_HUMAN	suppression of tumorigenicity 7	0	LDL-receptor class A 1. {ECO:0000255|PROSITE-ProRule:PRU00124}.				endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(1)	21	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		TTACTATGACATGAATCTCTC	0.428																																					p.D164fs		Atlas-Indel,Pindel	.											.	ST7	64	.	0			c.492delC						PASS	.						171	168	169					7																	116770588		2203	4299	6502	SO:0001589	frameshift_variant	7982	exon5			.	AJ277291	CCDS5769.1, CCDS5770.1	7q31.2	2008-06-06			ENSG00000004866	ENSG00000004866			11351	protein-coding gene	gene with protein product		600833		FAM4A1		8105370, 8938430	Standard	NM_021908		Approved	TSG7, SEN4, ETS7q, HELG, RAY1, FAM4A	uc003vin.3	Q9NRC1	OTTHUMG00000023888	ENST00000393446.2:c.493delA	chr7.hg19:g.116770588delA	ENSP00000377092:p.Met165fs	39.0	0.0	0		116.0	33.0	0.284483	NM_018412	A8K137|B4DRQ2	Frame_Shift_Del	DEL	ENST00000393446.2	hg19																																																																																				.	.	.	none		0.428	ST7-013	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000319687.1	NM_021908		-	116770588	A	-	116770588	7	5	6	1	0	1	0	1	0	0	0	0	15241	217	8	0	511	0	ST7	7	116770588	Frame_Shift_Del	DEL	A	TCGA-2Z-A9J6-01A-11D-A382-10		116770588	42368075	17	512											
PIP	5304	hgsc.bcm.edu	37	chr7	142832288	142832288	+	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	tctctcttcccacaatcagtCggaagatcataataaagaat	15	11	5	10	1	4	2	2	0	2	2	7	3	5	3	1	1	0	0	1	1	6	3	rs376369577		TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr7:142832288C>T	ENST00000291009.3	+	2	137	c.97C>T	c.(97-99)Cgg>Tgg	p.R33W		NM_002652.2	NP_002643.1	P12273	PIP_HUMAN	prolactin-induced protein	33					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of T cell apoptotic process (GO:0070233)|positive regulation of gene expression (GO:0010628)|proteolysis (GO:0006508)|regulation of immune system process (GO:0002682)|retina homeostasis (GO:0001895)	apical plasma membrane (GO:0016324)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	actin binding (GO:0003779)|aspartic-type endopeptidase activity (GO:0004190)|glycoprotein binding (GO:0001948)|IgG binding (GO:0019864)|protein dimerization activity (GO:0046983)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	18	Melanoma(164;0.059)	Ovarian(593;2.82e-05)|Breast(660;0.012)		BRCA - Breast invasive adenocarcinoma(188;0.0026)|LUSC - Lung squamous cell carcinoma(290;0.0733)|Lung(243;0.08)		CACAATCAGTCGGAAGATCAT	0.463																																					p.R33W		Atlas-SNP	.											.	PIP	34	.	0			c.C97T						PASS	.	C	TRP/ARG	0,4406		0,0,2203	52	47	49		97	0	0	7		49	1,8597	1.2+/-3.3	0,1,4298	no	missense-near-splice	PIP	NM_002652.2	101	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	benign	33/147	142832288	1,13003	2203	4299	6502	SO:0001630	splice_region_variant	5304	exon2			ATCAGTCGGAAGA		CCDS34768.1	7q34	2013-09-19			ENSG00000159763	ENSG00000159763			8993	protein-coding gene	gene with protein product	"prolactin-inducible protein"	176720				2727805, 1955075	Standard	NM_002652		Approved	GCDFP-15, GCDFP15, GPIP4	uc003wcf.1	P12273	OTTHUMG00000152635	ENST00000291009.3:c.96-1C>T	chr7.hg19:g.142832288C>T		68.0	0.0	.		103.0	63.0	.	NM_002652	A0A963|A0A9C3|A0A9F3|A4D2I1	Missense_Mutation	SNP	ENST00000291009.3	hg19	CCDS34768.1	.	.	.	.	.	.	.	.	.	.	C	8.675	0.903680	0.17760	0.0	1.16E-4	ENSG00000159763	ENST00000291009	T	0.14640	2.49	4.2	0.0331	0.14178	.	0.625933	0.12805	N	0.437679	T	0.08980	0.0222	L	0.39397	1.21	0.09310	N	1	B	0.21452	0.056	B	0.15052	0.012	T	0.32877	-0.9890	10	0.51188	T	0.08	.	1.421	0.02312	0.172:0.4618:0.1673:0.1989	.	33	P12273	PIP_HUMAN	W	33	ENSP00000291009:R33W	ENSP00000291009:R33W	R	+	1	2	PIP	142542410	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.057000	0.14279	-0.096000	0.12329	-0.535000	0.04281	CGG	.	.	.	weak		0.463	PIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327089.1	NM_002652	Missense_Mutation	T	142832288	C	T	142832288	5	4	6	1	0	0	0	0	0	0	1	0	11942	898	31	1	103	1	PIP	7	142832288	Splice_Site	SNP	C	TCGA-2Z-A9J6-01A-11D-A382-10	26061700	142832288	16306375	18	513											
GSTK1	373156	hgsc.bcm.edu	37	chr7	142961758	142961758	+	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	caaggatttcttgtctgtgaTgcttgaaaaaggtgaagaga	13	12	12	4	0	2	4	0	3	2	1	2	6	2	5	0	2	1	1	0	2	4	3			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr7:142961758T>A	ENST00000358406.5	+	3	343	c.272T>A	c.(271-273)aTg>aAg	p.M91K	GSTK1_ENST00000443571.2_Intron|AC073342.12_ENST00000427392.1_RNA|GSTK1_ENST00000494735.1_3'UTR|GSTK1_ENST00000479303.1_Missense_Mutation_p.M91K|GSTK1_ENST00000409500.3_Missense_Mutation_p.M91K	NM_015917.2	NP_057001.1	Q9Y2Q3	GSTK1_HUMAN	glutathione S-transferase kappa 1	91					epithelial cell differentiation (GO:0030855)|glutathione metabolic process (GO:0006749)|oxidation-reduction process (GO:0055114)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|peroxisome (GO:0005777)	glutathione peroxidase activity (GO:0004602)|glutathione transferase activity (GO:0004364)|protein disulfide oxidoreductase activity (GO:0015035)|receptor binding (GO:0005102)			lung(4)	4	Melanoma(164;0.059)				Glutathione(DB00143)	TTGTCTGTGATGCTTGAAAAA	0.488																																					p.M91K		Atlas-SNP	.											.	GSTK1	36	.	0			c.T272A						PASS	.						171	176	175					7																	142961758		2203	4300	6503	SO:0001583	missense	373156	exon3			CTGTGATGCTTGA		CCDS5877.1, CCDS47730.1, CCDS47731.1, CCDS47732.1	7q34	2012-06-21			ENSG00000197448	ENSG00000197448	2.5.1.18	"Glutathione S-transferases / Mitochondrial (kappa)"	16906	protein-coding gene	gene with protein product		602321				12720545, 14742434	Standard	NM_015917		Approved	GST13	uc003wcj.3	Q9Y2Q3	OTTHUMG00000152637	ENST00000358406.5:c.272T>A	chr7.hg19:g.142961758T>A	ENSP00000351181:p.Met91Lys	49.0	0.0	.		65.0	30.0	.	NM_015917	B4DIH1|B4DSY2|Q6P4H0|Q7Z520|Q9P1S4	Missense_Mutation	SNP	ENST00000358406.5	hg19	CCDS5877.1	.	.	.	.	.	.	.	.	.	.	T	13.43	2.234674	0.39498	.	.	ENSG00000197448	ENST00000436038;ENST00000409500;ENST00000358406;ENST00000479303	.	.	.	5.76	3.38	0.38709	DSBA-like thioredoxin domain (1);Thioredoxin-like fold (1);	0.436900	0.29383	N	0.012301	T	0.31295	0.0792	L	0.42245	1.32	0.09310	N	1	B;B;B	0.33583	0.003;0.418;0.151	B;B;B	0.40134	0.014;0.32;0.155	T	0.27673	-1.0067	9	0.05833	T	0.94	-6.0991	6.2182	0.20667	0.1428:0.0781:0.0:0.7791	.	91;91;91	Q9Y2Q3-3;Q9Y2Q3-2;Q9Y2Q3	.;.;GSTK1_HUMAN	K	81;91;91;91	.	ENSP00000351181:M91K	M	+	2	0	GSTK1	142671880	0.012000	0.17670	0.000000	0.03702	0.043000	0.13939	2.071000	0.41500	0.449000	0.26747	0.529000	0.55759	ATG	.	.	.	none		0.488	GSTK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327091.1	NM_015917		A	142961758	T	A	142961758	3	1	6	1	0	0	0	0	1	0	0	0	6843	1464	51	5	282	5	GSTK1	7	142961758	Missense_Mutation	SNP	T	TCGA-2Z-A9J6-01A-11D-A382-10	129470	142961758	16176905	19	514											
CHD7	55636	hgsc.bcm.edu	37	chr8	61707584	61707584	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaagcaagtgctttgaagaaAaaggtcaacaagggaaaaac	20	5	11	5	0	1	2	1	1	0	1	1	4	1	3	0	2	4	2	0	2	9	1			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr8:61707584A>G	ENST00000423902.2	+	4	2615	c.2136A>G	c.(2134-2136)aaA>aaG	p.K712K	CHD7_ENST00000524602.1_Intron|CHD7_ENST00000525508.1_Silent_p.K712K	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	712	Lys-rich.				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)			CTTTGAAGAAAAAGGTCAACA	0.403																																					p.K712K		Atlas-SNP	.											.	CHD7	534	.	1	Insertion - In frame(1)	lung(1)	c.A2136G						PASS	.						78	79	78					8																	61707584		1823	4071	5894	SO:0001819	synonymous_variant	55636	exon4			GAAGAAAAAGGTC	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.2136A>G	chr8.hg19:g.61707584A>G		104.0	0.0	.		100.0	7.0	.	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Silent	SNP	ENST00000423902.2	hg19	CCDS47865.1																																																																																			.	.	.	none		0.403	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		G	61707584	A	G	61707584	2	3	6	1	0	0	0	0	0	0	0	1	3332	11	1	3		3	CHD7	8	61707584	Silent	SNP	A	TCGA-2Z-A9J6-01A-11D-A382-10		61707584	84656438	20	515											
VCPIP1	80124	hgsc.bcm.edu	37	chr8	67576667	67576667	+	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	ttctattgtaattctgtcgcCatgctgtaaaggaactggtt	9	16	9	7	1	2	0	0	0	2	0	3	1	2	1	1	2	2	4	1	2	5	7			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr8:67576667C>A	ENST00000310421.4	-	1	2785	c.2527G>T	c.(2527-2529)Ggc>Tgc	p.G843C		NM_025054.4	NP_079330.2	Q96JH7	VCIP1_HUMAN	valosin containing protein (p97)/p47 complex interacting protein 1	843					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)			ATTCTGTCGCCATGCTGTAAA	0.428																																					p.G843C	NSCLC(179;265 2915 6144 43644)	Atlas-SNP	.											.	VCPIP1	110	.	0			c.G2527T						PASS	.						108	111	110					8																	67576667		2203	4300	6503	SO:0001583	missense	80124	exon1			TGTCGCCATGCTG	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.2527G>T	chr8.hg19:g.67576667C>A	ENSP00000309031:p.Gly843Cys	108.0	0.0	.		143.0	46.0	.	NM_025054	Q504T4|Q86T93|Q86W01|Q8N3A9|Q9H5R8	Missense_Mutation	SNP	ENST00000310421.4	hg19	CCDS6192.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.576700	0.86645	.	.	ENSG00000175073	ENST00000310421	T	0.69806	-0.43	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.83142	0.5190	M	0.78637	2.42	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84857	0.0817	10	0.87932	D	0	-12.7363	19.4386	0.94807	0.0:1.0:0.0:0.0	.	843	Q96JH7	VCIP1_HUMAN	C	843	ENSP00000309031:G843C	ENSP00000309031:G843C	G	-	1	0	VCPIP1	67739221	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.456000	0.80751	2.578000	0.87016	0.655000	0.94253	GGC	.	.	.	none		0.428	VCPIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379227.1			A	67576667	C	A	67576667	3	1	6	1	0	0	0	0	1	0	0	0	17153	594	21	4	1153	4	VCPIP1	8	67576667	Missense_Mutation	SNP	C	TCGA-2Z-A9J6-01A-11D-A382-10	5869083	67576667	78787355	21	516											
USP20	10868	hgsc.bcm.edu	37	chr9	132625464	132625464	+	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	ctctctctcccctgcacccaGcccgccgctgactcagttct	4	10	6	21	2	4	1	1	1	3	0	6	1	4	1	5	0	2	3	5	0	0	1			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr9:132625464G>T	ENST00000315480.4	+	9	655		c.e9-1		USP20_ENST00000358355.1_Splice_Site|USP20_ENST00000372429.3_Splice_Site			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20						endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				CCTGCACCCAGCCCGCCGCTG	0.607																																					.		Atlas-SNP	.											.	USP20	186	.	0			c.498-1G>T						PASS	.						13	15	15					9																	132625464		1952	3941	5893	SO:0001630	splice_region_variant	10868	exon9			CACCCAGCCCGCC	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"Ubiquitin-specific peptidases"	12619	protein-coding gene	gene with protein product		615143	"ubiquitin specific protease 20"			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.498-1G>T	chr9.hg19:g.132625464G>T		91.0	0.0	.		125.0	41.0	.	NM_001110303	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Splice_Site	SNP	ENST00000315480.4	hg19	CCDS43892.1	.	.	.	.	.	.	.	.	.	.	G	14.01	2.408788	0.42715	.	.	ENSG00000136878	ENST00000372429;ENST00000315480;ENST00000358355	.	.	.	5.65	5.65	0.86999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.7287	0.91726	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	USP20	131665285	1.000000	0.71417	1.000000	0.80357	0.044000	0.14063	9.781000	0.99029	2.655000	0.90218	0.655000	0.94253	.	.	.	.	none		0.607	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2		Intron	T	132625464	G	T	132625464	5	4	6	1	0	0	0	0	0	0	1	0	17064	985	34	4	523	4	USP20	9	132625464	Splice_Site	SNP	G	TCGA-2Z-A9J6-01A-11D-A382-10		132625464	8587967	22	517											
CUBN	8029	hgsc.bcm.edu	37	chr10	17164868	17164868	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gttcctgagtaaatctcacaTtcgttaacatcagctgagca	12	12	7	10	1	2	2	2	2	1	0	5	2	3	2	1	0	3	5	1	0	3	4			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr10:17164868T>C	ENST00000377833.4	-	6	584	c.519A>G	c.(517-519)gaA>gaG	p.E173E		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	173	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AAATCTCACATTCGTTAACAT	0.413																																					p.E173E		Atlas-SNP	.											.	CUBN	515	.	0			c.A519G						PASS	.						85	73	77					10																	17164868		2203	4300	6503	SO:0001819	synonymous_variant	8029	exon6			CTCACATTCGTTA	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.519A>G	chr10.hg19:g.17164868T>C		146.0	0.0	.		153.0	62.0	.	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	hg19	CCDS7113.1																																																																																			.	.	.	none		0.413	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		C	17164868	T	C	17164868	2	2	6	1	0	0	0	0	0	0	0	1	4053	1490	52	3		3	CUBN	10	17164868	Silent	SNP	T	TCGA-2Z-A9J6-01A-11D-A382-10		17164868	118369879	23	518											
CTBP2	1488	hgsc.bcm.edu	37	chr10	126715159	126715159	+	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	ggggatgctgtctgcagaggAgccgcagcgcccagagaagc	9	4	17	11	2	1	2	0	0	1	2	1	5	1	4	2	3	5	3	2	3	1	0	rs529129641|rs372118432	byFrequency	TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr10:126715159A>G	ENST00000337195.5	-	3	458				CTBP2_ENST00000411419.2_Intron|CTBP2_ENST00000309035.6_Silent_p.A390A|CTBP2_ENST00000494626.2_Intron|CTBP2_ENST00000531469.1_Intron	NM_001329.2	NP_001320.1	P56545	CTBP2_HUMAN	C-terminal binding protein 2						negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)|white fat cell differentiation (GO:0050872)	cell junction (GO:0030054)|nucleus (GO:0005634)|synapse (GO:0045202)|transcriptional repressor complex (GO:0017053)	NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		TCTGCAGAGGAGCCGCAGCGC	0.701																																					p.A390A		Atlas-SNP	.											.,1	CTBP2	100	.	0			c.T1170C						PASS	.						9	7	8					10																	126715159		2126	4169	6295	SO:0001627	intron_variant	1488	exon1			CAGAGGAGCCGCA	AF016507	CCDS7643.1, CCDS7644.1	10q26.13	2008-08-01			ENSG00000175029	ENSG00000175029			2495	protein-coding gene	gene with protein product		602619				9479502, 11864595	Standard	NM_022802		Approved	ribeye	uc001lie.4	P56545	OTTHUMG00000019224	ENST00000337195.5:c.58+12406T>C	chr10.hg19:g.126715159A>G		80.0	0.0	.		49.0	5.0	.	NM_022802	A8K2X5|D3DRF5|O43449|Q5SQP7|Q69YI3|Q86SV0|Q9H2T8	Silent	SNP	ENST00000337195.5	hg19	CCDS7643.1																																																																																			.	.	.	none		0.701	CTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050900.3	NM_001083914		G	126715159	A	G	126715159	1	3	6	0	1	0	0	0	0	0	0	0	4000	291	11	3		3	CTBP2	10	126715159	Intron	SNP	A	TCGA-2Z-A9J6-01A-11D-A382-10	109550291	126715159	8819588	24	519											
METT5D1	196074	hgsc.bcm.edu	37	chr11	28311807	28311807	+	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	caggcagaagccttattaatGaaagctggagtgcagccagg	13	7	13	8	0	0	2	0	1	0	1	0	3	0	3	2	3	4	3	2	3	4	2			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr11:28311807G>T	ENST00000407364.3	+	5	814	c.462G>T	c.(460-462)atG>atT	p.M154I	METTL15_ENST00000342303.5_Missense_Mutation_p.M154I|METTL15_ENST00000303459.6_Missense_Mutation_p.M154I|METTL15_ENST00000406787.3_Missense_Mutation_p.M154I			A6NJ78	MET15_HUMAN	methyltransferase like 15	154							methyltransferase activity (GO:0008168)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	14						CCTTATTAATGAAAGCTGGAG	0.448																																					p.M154I		Atlas-SNP	.											.	METTL15	63	.	0			c.G462T						PASS	.						49	50	49					11																	28311807		2202	4296	6498	SO:0001583	missense	196074	exon5			ATTAATGAAAGCT	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.462G>T	chr11.hg19:g.28311807G>T	ENSP00000384369:p.Met154Ile	42.0	0.0	.		73.0	23.0	.	NM_152636	A8MRS5|B7WNU2|Q3MHD3|Q8N601|Q8NBA7	Missense_Mutation	SNP	ENST00000407364.3	hg19	CCDS44559.1	.	.	.	.	.	.	.	.	.	.	G	6.896	0.534856	0.13188	.	.	ENSG00000169519	ENST00000406787;ENST00000342303;ENST00000407364;ENST00000303459	T;T;T;T	0.28255	1.62;1.62;1.62;1.62	5.88	1.95	0.26073	.	0.738697	0.14439	N	0.319525	T	0.19046	0.0457	L	0.31926	0.97	0.09310	N	0.999999	B;B;B	0.19331	0.0;0.001;0.035	B;B;B	0.15484	0.0;0.001;0.013	T	0.24404	-1.0161	9	.	.	.	.	5.2287	0.15410	0.2941:0.279:0.4269:0.0	.	154;154;154	A6NJ78;A6NJ78-2;A6NJ78-4	MET15_HUMAN;.;.	I	154	ENSP00000385507:M154I;ENSP00000342259:M154I;ENSP00000384369:M154I;ENSP00000307251:M154I	.	M	+	3	0	METTL15	28268383	0.001000	0.12720	0.988000	0.46212	0.444000	0.32077	-0.076000	0.11412	0.115000	0.18071	0.655000	0.94253	ATG	.	.	.	none		0.448	METTL15-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318135.2	NM_152636		T	28311807	G	T	28311807	3	4	6	1	0	0	0	0	1	0	0	0	9499	1290	45	4	472	4	METT5D1	11	28311807	Missense_Mutation	SNP	G	TCGA-2Z-A9J6-01A-11D-A382-10		28311807	106694709	25	520											
CDC42BPG	55561	hgsc.bcm.edu	37	chr11	64594522	64594522	+	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	attggctccagaggactaacCggggacttgtccctggcgcc	7	8	13	13	2	0	1	0	0	0	1	2	3	2	3	4	5	1	1	4	5	1	3			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr11:64594522C>T	ENST00000342711.5	-	34	4388	c.4389G>A	c.(4387-4389)ccG>ccA	p.P1463P		NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						GAGGACTAACCGGGGACTTGT	0.597																																					p.P1463P		Atlas-SNP	.											.	CDC42BPG	101	.	0			c.G4389A						PASS	.						43	46	45					11																	64594522		2201	4297	6498	SO:0001630	splice_region_variant	55561	exon34			ACTAACCGGGGAC	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.4389+1G>A	chr11.hg19:g.64594522C>T		93.0	0.0	.		92.0	39.0	.	NM_017525		Silent	SNP	ENST00000342711.5	hg19	CCDS31601.1																																																																																			.	.	.	none		0.597	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516	Silent	T	64594522	C	T	64594522	5	4	6	1	0	0	0	0	0	0	1	0	3076	666	23	1	282	1	CDC42BPG	11	64594522	Splice_Site	SNP	C	TCGA-2Z-A9J6-01A-11D-A382-10	36282715	64594522	70411994	26	521											
TM7SF2	7108	hgsc.bcm.edu	37	chr11	64882278	64882278	+	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	tcaatggcttccagttgctcTacgtgggtgatgccctctgg	5	13	12	11	1	3	1	1	1	2	0	4	1	4	1	2	3	3	3	2	3	2	3			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr11:64882278T>A	ENST00000279263.7	+	6	859	c.697T>A	c.(697-699)Tac>Aac	p.Y233N	AP003068.12_ENST00000527789.1_RNA|TM7SF2_ENST00000540748.1_Missense_Mutation_p.Y117N|TM7SF2_ENST00000531029.1_3'UTR|TM7SF2_ENST00000345348.5_Missense_Mutation_p.Y233N	NM_003273.2	NP_003264.2	O76062	ERG24_HUMAN	transmembrane 7 superfamily member 2	233					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						CCAGTTGCTCTACGTGGGTGA	0.607																																					p.Y233N		Atlas-SNP	.											.	TM7SF2	30	.	0			c.T697A						PASS	.						96	113	108					11																	64882278		2162	4249	6411	SO:0001583	missense	7108	exon6			TTGCTCTACGTGG	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.697T>A	chr11.hg19:g.64882278T>A	ENSP00000279263:p.Tyr233Asn	112.0	0.0	.		98.0	34.0	.	NM_003273	A8K4H0|O95982|Q8IY06|Q96E64|Q96GZ1	Missense_Mutation	SNP	ENST00000279263.7	hg19	CCDS41669.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.647237	0.87958	.	.	ENSG00000149809	ENST00000526809;ENST00000279263;ENST00000524986;ENST00000534371;ENST00000540748;ENST00000525385;ENST00000345348;ENST00000531321;ENST00000526085;ENST00000527968	D;D;D;D;D;D;D;D;D;D	0.99270	-5.66;-5.66;-5.66;-5.66;-5.66;-5.66;-5.66;-5.66;-5.66;-5.66	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	D	0.99638	0.9867	H	0.98155	4.16	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.998;0.999	D	0.97633	1.0143	10	0.87932	D	0	-4.6127	13.1215	0.59329	0.0:0.0:0.0:1.0	.	117;233;233	F5GYV3;O76062-2;O76062	.;.;ERG24_HUMAN	N	115;233;204;165;117;204;233;139;84;65	ENSP00000432171:Y115N;ENSP00000279263:Y233N;ENSP00000435972:Y204N;ENSP00000432187:Y165N;ENSP00000441215:Y117N;ENSP00000433325:Y204N;ENSP00000329520:Y233N;ENSP00000431300:Y139N;ENSP00000434447:Y84N;ENSP00000431685:Y65N	ENSP00000279263:Y233N	Y	+	1	0	TM7SF2	64638854	1.000000	0.71417	0.982000	0.44146	0.983000	0.72400	7.466000	0.80914	2.200000	0.70718	0.459000	0.35465	TAC	.	.	.	none		0.607	TM7SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385234.1	NM_003273		A	64882278	T	A	64882278	3	1	6	1	0	0	0	0	1	0	0	0	15986	1522	53	5	719	5	TM7SF2	11	64882278	Missense_Mutation	SNP	T	TCGA-2Z-A9J6-01A-11D-A382-10	287756	64882278	70124238	27	522											
C11orf30	56946	hgsc.bcm.edu	37	chr11	76255546	76255546	+	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	agaccatccacctgcaggcaGaccagctccagcacaaactc	13	4	7	17	0	0	2	0	0	0	2	3	2	2	2	5	1	4	4	5	1	1	0			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr11:76255546G>A	ENST00000529032.1	+	18	2953	c.2953G>A	c.(2953-2955)Gac>Aac	p.D985N	C11orf30_ENST00000334736.3_Missense_Mutation_p.D985N|C11orf30_ENST00000343878.3_Missense_Mutation_p.D985N|C11orf30_ENST00000524490.1_Missense_Mutation_p.D887N|C11orf30_ENST00000533248.1_Missense_Mutation_p.D894N|C11orf30_ENST00000524767.1_Missense_Mutation_p.D1000N|C11orf30_ENST00000525919.1_Missense_Mutation_p.D986N|C11orf30_ENST00000525038.1_Missense_Mutation_p.D986N			Q7Z589	EMSY_HUMAN	chromosome 11 open reading frame 30	985	Gln-rich.				chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(10)|liver(1)|lung(23)|ovary(5)|prostate(2)|skin(4)|stomach(1)|urinary_tract(2)	60						CCTGCAGGCAGACCAGCTCCA	0.542																																					p.D985N		Atlas-SNP	.											.	C11orf30	123	.	0			c.G2953A						PASS	.						106	107	107					11																	76255546		2200	4292	6492	SO:0001583	missense	56946	exon19			CAGGCAGACCAGC	AF226047	CCDS8244.1, CCDS73349.1, CCDS73350.1, CCDS73351.1	11q13.5	2010-07-01			ENSG00000158636	ENSG00000158636			18071	protein-coding gene	gene with protein product		608574					Standard	XM_005274106		Approved	EMSY	uc001oxl.3	Q7Z589	OTTHUMG00000165282	ENST00000529032.1:c.2953G>A	chr11.hg19:g.76255546G>A	ENSP00000432327:p.Asp985Asn	42.0	0.0	.		77.0	22.0	.	NM_020193	B7ZKT8|B7ZKU0|B7ZKU2|Q17RM7|Q4G109|Q8NBU6|Q8TE50|Q9H8I9|Q9NRH0	Missense_Mutation	SNP	ENST00000529032.1	hg19	CCDS8244.1	.	.	.	.	.	.	.	.	.	.	G	15.43	2.829846	0.50845	.	.	ENSG00000158636	ENST00000524490;ENST00000334736;ENST00000343878;ENST00000393457;ENST00000524767;ENST00000533248;ENST00000525919;ENST00000525038;ENST00000529032;ENST00000532719	.	.	.	5.92	5.92	0.95590	.	0.269805	0.41938	D	0.000786	T	0.58163	0.2103	N	0.19112	0.55	0.38630	D	0.951348	D;B;B;B;B;B;B	0.59357	0.985;0.148;0.148;0.144;0.023;0.148;0.023	P;B;B;B;B;B;B	0.55508	0.777;0.056;0.056;0.056;0.01;0.056;0.01	T	0.53781	-0.8390	9	0.20519	T	0.43	-1.593	20.3081	0.98638	0.0:0.0:1.0:0.0	.	894;986;1000;339;986;887;985	B7ZKT8;B7ZKU2;B7ZKU0;B3KWW8;Q17RM7;E9PMC9;Q7Z589	.;.;.;.;.;.;EMSY_HUMAN	N	887;985;985;667;1000;894;986;986;985;125	.	ENSP00000334130:D985N	D	+	1	0	C11orf30	75933194	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.155000	0.71833	2.795000	0.96236	0.655000	0.94253	GAC	.	.	.	none		0.542	C11orf30-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383288.2	NM_020193		A	76255546	G	A	76255546	3	1	6	1	0	0	0	0	1	0	0	0	1638	942	33	2	3023	2	C11orf30	11	76255546	Missense_Mutation	SNP	G	TCGA-2Z-A9J6-01A-11D-A382-10	11373268	76255546	58750970	28	523											
HDAC7	51564	hgsc.bcm.edu	37	chr12	48179627	48179627	+	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	caaggccagcaccactgcgcCtcctgccaggttcatcagtt	8	8	9	16	1	2	0	2	0	0	0	3	0	3	0	5	2	3	3	5	2	1	2			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr12:48179627C>T	ENST00000427332.2	-	23	2653	c.2497G>A	c.(2497-2499)Ggc>Agc	p.G833S	AC004466.1_ENST00000599515.1_3'UTR|HDAC7_ENST00000354334.3_Missense_Mutation_p.G835S|HDAC7_ENST00000080059.7_Missense_Mutation_p.G872S|HDAC7_ENST00000488927.1_5'Flank|HDAC7_ENST00000552960.1_Missense_Mutation_p.G855S|HDAC7_ENST00000380610.4_Missense_Mutation_p.G889S			Q8WUI4	HDAC7_HUMAN	histone deacetylase 7	833	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)		ACCACTGCGCCTCCTGCCAGG	0.602																																					p.G872S		Atlas-SNP	.											.	HDAC7	71	.	0			c.G2614A						PASS	.						49	40	43					12																	48179627		2203	4300	6503	SO:0001583	missense	51564	exon23			CTGCGCCTCCTGC	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.2497G>A	chr12.hg19:g.48179627C>T	ENSP00000404394:p.Gly833Ser	176.0	0.0	.		203.0	62.0	.	NM_015401	B3KY08|B4DWI0|B4E0Q5|Q6P1W9|Q6W9G7|Q7Z4K2|Q7Z5I1|Q96K01|Q9BR73|Q9H7L0|Q9NW41|Q9NWA9|Q9NYK9|Q9UFU7	Missense_Mutation	SNP	ENST00000427332.2	hg19		.	.	.	.	.	.	.	.	.	.	C	32	5.175569	0.94807	.	.	ENSG00000061273	ENST00000080059;ENST00000354334;ENST00000552960;ENST00000380610;ENST00000427332	T;T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.46;-0.46	4.78	4.78	0.61160	Histone deacetylase domain (2);	0.000000	0.85682	D	0.000000	T	0.81356	0.4805	M	0.78916	2.43	0.80722	D	1	P;P;B;D	0.71674	0.489;0.784;0.433;0.998	B;P;B;D	0.67900	0.368;0.84;0.353;0.954	D	0.84350	0.0532	10	0.87932	D	0	.	16.8244	0.85927	0.0:1.0:0.0:0.0	.	833;872;855;835	Q8WUI4;Q8WUI4-5;Q8WUI4-6;Q8WUI4-7	HDAC7_HUMAN;.;.;.	S	872;835;855;889;833	ENSP00000080059:G872S;ENSP00000351326:G835S;ENSP00000448532:G855S;ENSP00000369984:G889S;ENSP00000404394:G833S	ENSP00000080059:G872S	G	-	1	0	HDAC7	46465894	1.000000	0.71417	0.995000	0.50966	0.971000	0.66376	7.742000	0.85008	2.407000	0.81776	0.543000	0.68304	GGC	.	.	.	none		0.602	HDAC7-013	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000328804.2			T	48179627	C	T	48179627	3	4	6	1	0	0	0	0	1	0	0	0	7019	681	24	2	377	2	HDAC7	12	48179627	Missense_Mutation	SNP	C	TCGA-2Z-A9J6-01A-11D-A382-10		48179627	85672268	29	524											
CCDC64	92558	hgsc.bcm.edu	37	chr12	120427989	120427991	+	In_Frame_Del	DEL	AGG	AGG	-																															gctgtcggtgatccgacagaAggagaaggatctggtgttgg																								rs560592174		TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr12:120427989_120427991delAGG	ENST00000397558.2	+	1	317_319	c.317_319delAGG	c.(316-321)aaggag>aag	p.E107del		NM_207311.2	NP_997194.2	Q6ZP65	BICR1_HUMAN	coiled-coil domain containing 64	107					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)					ATCCGACAGAAGGAGAAGGATCT	0.67																																					p.106_106del		Atlas-Indel,Pindel	.											.	CCDC64	40	.	0			c.316_318del						PASS	.																																			SO:0001651	inframe_deletion	92558	exon1			.	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.317_319delAGG	chr12.hg19:g.120427989_120427991delAGG	ENSP00000380690:p.Glu107del	157.0	0.0	0		168.0	42.0	0.25	NM_207311	A8MUC8|B4DWL0|B5MDJ0|O95000	In_Frame_Del	DEL	ENST00000397558.2	hg19	CCDS41845.1																																																																																			.	.	.	none		0.67	CCDC64-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403390.2	NM_207311		-	120427991	AGG	-	120427989	7	5	6	1	0	1	0	1	0	0	0	0	2837	72	3	0	319	0	CCDC64	12	120427989	In_Frame_Del	DEL	AGG	TCGA-2Z-A9J6-01A-11D-A382-10	72248362	120427989	13423906	30	525											
ZNF219	51222	hgsc.bcm.edu	37	chr14	21560330	21560330	+	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	caggtagcccaagaggctcgGgggctcacggcgctcggccg	6	4	17	14	5	1	1	1	0	0	1	3	1	1	1	2	6	1	4	2	6	2	1			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr14:21560330G>A	ENST00000360947.3	-	3	1537	c.1126C>T	c.(1126-1128)Ccg>Tcg	p.P376S	RP11-998D10.7_ENST00000554733.2_lincRNA|ZNF219_ENST00000451119.2_Missense_Mutation_p.P376S|ZNF219_ENST00000421093.2_Missense_Mutation_p.P376S|ZNF219_ENST00000556101.1_5'Flank	NM_016423.2	NP_057507.2	Q9P2Y4	ZN219_HUMAN	zinc finger protein 219	376					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of neurotransmitter levels (GO:0001505)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histamine receptor activity (GO:0004969)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(2)	8	all_cancers(95;0.00185)		OV - Ovarian serous cystadenocarcinoma(11;9.86e-11)|Epithelial(56;1.27e-08)|all cancers(55;6.06e-08)	GBM - Glioblastoma multiforme(265;0.0191)		AAGAGGCTCGGGGGCTCACGG	0.761																																					p.P376S		Atlas-SNP	.											.	ZNF219	28	.	0			c.C1126T						PASS	.						1	1	1					14																	21560330		1016	2266	3282	SO:0001583	missense	51222	exon3			GGCTCGGGGGCTC	AB015427	CCDS9568.1	14q11	2013-01-08			ENSG00000165804	ENSG00000165804		"Zinc fingers, C2H2-type"	13011	protein-coding gene	gene with protein product		605036				10819330	Standard	NM_016423		Approved		uc001vzs.2	Q9P2Y4	OTTHUMG00000029647	ENST00000360947.3:c.1126C>T	chr14.hg19:g.21560330G>A	ENSP00000354206:p.Pro376Ser	99.0	0.0	.		34.0	14.0	.	NM_001102454	D3DS16|Q53Y57|Q8IYC1|Q9BW28	Missense_Mutation	SNP	ENST00000360947.3	hg19	CCDS9568.1	.	.	.	.	.	.	.	.	.	.	G	10.77	1.445264	0.25987	.	.	ENSG00000165804	ENST00000360947;ENST00000451119;ENST00000421093	T;T;T	0.06294	3.32;3.32;3.32	4.67	3.77	0.43336	.	0.153084	0.43110	D	0.000614	T	0.04543	0.0124	N	0.24115	0.695	0.35849	D	0.826595	B	0.24186	0.099	B	0.19391	0.025	T	0.40572	-0.9556	10	0.20046	T	0.44	-14.7276	10.523	0.44931	0.0:0.2258:0.7742:0.0	.	376	Q9P2Y4	ZN219_HUMAN	S	376	ENSP00000354206:P376S;ENSP00000388558:P376S;ENSP00000392401:P376S	ENSP00000354206:P376S	P	-	1	0	ZNF219	20630170	.	.	0.977000	0.42913	0.987000	0.75469	.	.	1.152000	0.42452	0.563000	0.77884	CCG	.	.	.	none		0.761	ZNF219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073931.2			A	21560330	G	A	21560330	3	1	6	1	0	0	0	0	1	0	0	0	17785	1232	43	2	1054	2	ZNF219	14	21560330	Missense_Mutation	SNP	G	TCGA-2Z-A9J6-01A-11D-A382-10		21560330	85789210	31	526											
UBE3A	7337	hgsc.bcm.edu	37	chr15	25616263	25616263	+	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	tcactagatttcgactgttaAattcattgcttatgacttta	11	18	5	7	1	2	2	2	1	0	1	3	3	2	2	0	0	1	2	0	0	5	8			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr15:25616263A>T	ENST00000397954.2	-	4	1066	c.1067T>A	c.(1066-1068)tTt>tAt	p.F356Y	UBE3A_ENST00000566215.1_Missense_Mutation_p.F333Y|SNHG14_ENST00000554726.1_RNA|UBE3A_ENST00000232165.3_Missense_Mutation_p.F353Y|UBE3A_ENST00000428984.2_Missense_Mutation_p.F333Y|UBE3A_ENST00000438097.1_Missense_Mutation_p.F333Y			Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A	356					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)		TCGACTGTTAAATTCATTGCT	0.383																																					p.F356Y		Atlas-SNP	.											UBE3A,colon,carcinoma,0,1	UBE3A	109	.	0			c.T1067A						PASS	.						108	104	105					15																	25616263		2203	4300	6503	SO:0001583	missense	7337	exon7			CTGTTAAATTCAT	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.1067T>A	chr15.hg19:g.25616263A>T	ENSP00000381045:p.Phe356Tyr	60.0	0.0	.		59.0	23.0	.	NM_000462	A8K8Z9|P78355|Q93066|Q9UEP4|Q9UEP5|Q9UEP6|Q9UEP7|Q9UEP8|Q9UEP9	Missense_Mutation	SNP	ENST00000397954.2	hg19	CCDS45192.1	.	.	.	.	.	.	.	.	.	.	A	9.469	1.095036	0.20471	.	.	ENSG00000114062	ENST00000232165;ENST00000356465;ENST00000397954;ENST00000438097;ENST00000428984	T;T;T;T	0.17854	2.25;2.25;2.25;2.25	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.09202	0.0227	N	0.11560	0.145	0.58432	D	0.999999	B;B	0.15141	0.012;0.004	B;B	0.15484	0.013;0.009	T	0.08911	-1.0699	10	0.02654	T	1	.	16.0417	0.80687	1.0:0.0:0.0:0.0	.	353;356	Q05086-3;Q05086	.;UBE3A_HUMAN	Y	353;353;356;333;333	ENSP00000232165:F353Y;ENSP00000381045:F356Y;ENSP00000411258:F333Y;ENSP00000401265:F333Y	ENSP00000232165:F353Y	F	-	2	0	UBE3A	23167356	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.135000	0.77276	2.198000	0.70561	0.482000	0.46254	TTT	.	.	.	none		0.383	UBE3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000434203.1	NM_000462		T	25616263	A	T	25616263	3	4	6	1	0	0	0	0	1	0	0	0	16891	14	1	5	1592	5	UBE3A	15	25616263	Missense_Mutation	SNP	A	TCGA-2Z-A9J6-01A-11D-A382-10		25616263	76915129	32	527											
LTK	4058	hgsc.bcm.edu	37	chr15	41797613	41797613	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcaccaggtgtggccgacTgtgcctcaggaaactcttca	8	10	10	13	1	4	0	3	0	2	0	5	2	4	1	3	3	2	0	3	3	1	1			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr15:41797613T>C	ENST00000263800.6	-	14	1909	c.1813A>G	c.(1813-1815)Agt>Ggt	p.S605G	LTK_ENST00000355166.5_Missense_Mutation_p.S544G|LTK_ENST00000561619.1_Missense_Mutation_p.S303G|LTK_ENST00000453182.2_Missense_Mutation_p.S475G	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	605	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		TGTGGCCGACTGTGCCTCAGG	0.597										TSP Lung(18;0.14)																											p.S605G		Atlas-SNP	.											.	LTK	117	.	0			c.A1813G						PASS	.						56	62	60					15																	41797613		2203	4300	6503	SO:0001583	missense	4058	exon14			GCCGACTGTGCCT	D16105	CCDS10077.1, CCDS10078.1, CCDS45237.1	15q15.1-q21.1	2009-07-10	2008-01-23		ENSG00000062524	ENSG00000062524	2.7.10.1		6721	protein-coding gene	gene with protein product		151520	"leukocyte tyrosine kinase"			2320375	Standard	NM_206961		Approved	TYK1	uc001zoa.3	P29376	OTTHUMG00000130339	ENST00000263800.6:c.1813A>G	chr15.hg19:g.41797613T>C	ENSP00000263800:p.Ser605Gly	240.0	0.0	.		172.0	60.0	.	NM_002344	A6NNJ8|B4DL89|E9PFX4	Missense_Mutation	SNP	ENST00000263800.6	hg19	CCDS10077.1	.	.	.	.	.	.	.	.	.	.	T	12.70	2.017279	0.35606	.	.	ENSG00000062524	ENST00000355166;ENST00000263800;ENST00000453182	D;D;D	0.83075	-1.68;-1.68;-1.68	4.2	4.2	0.49525	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.84320	0.5446	L	0.45422	1.42	0.09310	N	0.999995	P;B;P;P	0.50272	0.933;0.012;0.846;0.872	P;B;P;P	0.56343	0.796;0.011;0.467;0.674	T	0.74231	-0.3732	9	0.30078	T	0.28	.	12.4104	0.55464	0.0:0.0:0.0:1.0	.	475;475;544;605	E9PFX4;B4DL89;P29376-4;P29376	.;.;.;LTK_HUMAN	G	544;605;475	ENSP00000347293:S544G;ENSP00000263800:S605G;ENSP00000392196:S475G	ENSP00000263800:S605G	S	-	1	0	LTK	39584905	0.590000	0.26815	0.008000	0.14137	0.354000	0.29330	2.992000	0.49417	1.768000	0.52137	0.402000	0.26972	AGT	.	.	.	none		0.597	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2			C	41797613	T	C	41797613	3	2	6	1	0	0	0	0	1	0	0	0	9087	1580	55	3	809	3	LTK	15	41797613	Missense_Mutation	SNP	T	TCGA-2Z-A9J6-01A-11D-A382-10	16181350	41797613	60733779	33	528											
CREBBP	1387	hgsc.bcm.edu	37	chr16	3779274	3779274	+	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	tggtggggggctgagtccggGccacgctggggaagccagct	5	6	20	10	2	0	1	0	1	0	0	1	2	1	2	3	7	2	3	3	7	1	0			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr16:3779274G>C	ENST00000262367.5	-	31	6583	c.5774C>G	c.(5773-5775)gCc>gGc	p.A1925G	CREBBP_ENST00000382070.3_Missense_Mutation_p.A1887G	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1925					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)		CTGAGTCCGGGCCACGCTGGG	0.736			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.A1925G		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.C5774G						PASS	.						7	8	8					16																	3779274		2041	4026	6067	SO:0001583	missense	1387	exon31			GTCCGGGCCACGC	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.5774C>G	chr16.hg19:g.3779274G>C	ENSP00000262367:p.Ala1925Gly	54.0	0.0	.		57.0	12.0	.	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	hg19	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	g	8.148	0.786786	0.16189	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.83591	-1.74;-1.68	5.16	4.2	0.49525	.	0.484348	0.20989	N	0.082069	T	0.70334	0.3212	L	0.29908	0.895	0.33812	D	0.628027	B;B	0.17038	0.02;0.02	B;B	0.14578	0.011;0.011	T	0.67341	-0.5695	10	0.19147	T	0.46	-4.3631	7.9121	0.29798	0.0813:0.0:0.76:0.1587	.	1955;1925	Q4LE28;Q92793	.;CBP_HUMAN	G	1925;1955;1887;460	ENSP00000262367:A1925G;ENSP00000371502:A1887G	ENSP00000262367:A1925G	A	-	2	0	CREBBP	3719275	0.952000	0.32445	1.000000	0.80357	0.997000	0.91878	3.424000	0.52764	1.184000	0.42957	0.655000	0.94253	GCC	.	.	.	none		0.736	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		C	3779274	G	C	3779274	3	2	6	1	0	0	0	0	1	0	0	0	3863	1203	42	4	1558	4	CREBBP	16	3779274	Missense_Mutation	SNP	G	TCGA-2Z-A9J6-01A-11D-A382-10		3779274	86575479	34	529											
GRIN2A	2903	hgsc.bcm.edu	37	chr16	10032281	10032281	+	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	tgacgaagctgatgaattccCtgtagccagggaagatagtg	12	9	13	7	1	0	4	0	3	0	1	1	6	1	5	2	1	2	2	2	1	5	3			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr16:10032281C>A	ENST00000396573.2	-	4	851	c.542G>T	c.(541-543)aGg>aTg	p.R181M	GRIN2A_ENST00000330684.3_Missense_Mutation_p.R181M|GRIN2A_ENST00000562109.1_Missense_Mutation_p.R181M|GRIN2A_ENST00000566670.1_5'UTR|GRIN2A_ENST00000404927.2_Missense_Mutation_p.R181M|GRIN2A_ENST00000535259.1_Missense_Mutation_p.R24M|GRIN2A_ENST00000396575.2_Missense_Mutation_p.R181M	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	181					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)	GATGAATTCCCTGTAGCCAGG	0.517																																					p.R181M		Atlas-SNP	.											.	GRIN2A	366	.	0			c.G542T						PASS	.						108	96	100					16																	10032281		2197	4300	6497	SO:0001583	missense	2903	exon4			AATTCCCTGTAGC		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.542G>T	chr16.hg19:g.10032281C>A	ENSP00000379818:p.Arg181Met	29.0	0.0	.		104.0	28.0	.	NM_000833	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	hg19	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	c	22.6	4.306611	0.81247	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000535259;ENST00000330684;ENST00000396575	D;D;D;D;D	0.92752	-3.1;-3.1;-3.1;-3.1;-3.1	5.47	5.47	0.80525	Extracellular ligand-binding receptor (1);	0.051432	0.85682	D	0.000000	D	0.94879	0.8345	M	0.61703	1.905	0.41884	D	0.990333	D;D;D	0.61697	0.964;0.99;0.989	P;D;P	0.63033	0.844;0.91;0.87	D	0.94078	0.7341	9	.	.	.	.	18.6894	0.91577	0.0:1.0:0.0:0.0	.	24;181;181	F5GZ52;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	M	181;181;24;181;181	ENSP00000379818:R181M;ENSP00000385872:R181M;ENSP00000441572:R24M;ENSP00000332549:R181M;ENSP00000379820:R181M	.	R	-	2	0	GRIN2A	9939782	1.000000	0.71417	0.997000	0.53966	0.954000	0.61252	4.792000	0.62467	2.724000	0.93272	0.561000	0.74099	AGG	.	.	.	none		0.517	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			A	10032281	C	A	10032281	3	1	6	1	0	0	0	0	1	0	0	0	6786	681	24	4	3896	4	GRIN2A	16	10032281	Missense_Mutation	SNP	C	TCGA-2Z-A9J6-01A-11D-A382-10	6253007	10032281	80322472	35	530											
ABCC6	368	hgsc.bcm.edu	37	chr16	16244436	16244436	+	Splice_Site	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	gccggggcgggagccttaccGggcacagtccatcacggagc	7	4	16	14	4	1	0	1	0	0	0	2	2	2	2	4	5	3	1	4	5	1	1			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr16:16244436G>C	ENST00000205557.7	-	30	4431	c.4402C>G	c.(4402-4404)Cgg>Ggg	p.R1468G		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1468	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)	GAGCCTTACCGGGCACAGTCC	0.672																																					p.R1468G		Atlas-SNP	.											.	ABCC6	110	.	0			c.C4402G						PASS	.						32	27	29					16																	16244436		2197	4298	6495	SO:0001630	splice_region_variant	368	exon30			CTTACCGGGCACA	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+1C>G	chr16.hg19:g.16244436G>C		121.0	0.0	.		141.0	71.0	.	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	hg19	CCDS10568.1	.	.	.	.	.	.	.	.	.	.	G	13.40	2.225530	0.39300	.	.	ENSG00000091262	ENST00000205557;ENST00000205558	T	0.76316	-1.01	4.38	3.3	0.37823	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.45361	U	0.000380	D	0.89508	0.6735	M	0.93328	3.405	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.75020	0.985;0.985	D	0.90091	0.4177	10	0.87932	D	0	.	10.7299	0.46089	0.0:0.0:0.3466:0.6534	.	1468;1468	O95255;A8Y988	MRP6_HUMAN;.	G	1468;406	ENSP00000205557:R1468G	ENSP00000205557:R1468G	R	-	1	2	ABCC6	16151937	1.000000	0.71417	0.987000	0.45799	0.152000	0.21847	2.582000	0.46085	0.699000	0.31761	0.561000	0.74099	CGG	.	.	.	none		0.672	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		Missense_Mutation	C	16244436	G	C	16244436	5	2	6	1	0	0	0	0	0	0	1	0	57	1130	39	4	117	4	ABCC6	16	16244436	Splice_Site	SNP	G	TCGA-2Z-A9J6-01A-11D-A382-10	6212155	16244436	74110317	36	531											
MYH4	4622	hgsc.bcm.edu	37	chr17	10352186	10352187	+	Frame_Shift_Ins	INS	-	-	A																															gtactgtggaccaccttgtcINSaaagtttctttgcttcttat																										TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr17:10352186_10352187insA	ENST00000255381.2	-	31	4469_4470	c.4359_4360insT	c.(4357-4362)tttgacfs	p.D1454fs	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1454					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						ACCACCTTGTCAAAGTTTCTTT	0.446																																					p.D1454_K1455delinsX		Atlas-Indel,Pindel	.											.	MYH4	349	.	0			c.4360_4361insT						PASS	.																																			SO:0001589	frameshift_variant	4622	exon31			.		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.4360dupT	chr17.hg19:g.10352189_10352189dupA	ENSP00000255381:p.Asp1454fs	76.0	0.0	0		138.0	38.0	0.275362	NM_017533		Frame_Shift_Ins	INS	ENST00000255381.2	hg19	CCDS11154.1																																																																																			.	.	.	none		0.446	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		A	10352187	-	A	10352186	7	5	6	1	0	1	1	0	0	0	0	0	10044	826	29	0	1499	0	MYH4	17	10352186	Frame_Shift_Ins	INS	-	TCGA-2Z-A9J6-01A-11D-A382-10		10352186	70843024	37	532											
RAI1	10743	hgsc.bcm.edu	37	chr17	17698698	17698698	+	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	ttgcccggggacttcaagcaGgaggaggtgggtggggtgaa	8	7	20	6	1	1	1	1	1	0	0	1	4	1	4	1	8	2	1	1	8	2	2			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr17:17698698G>T	ENST00000353383.1	+	3	2905	c.2436G>T	c.(2434-2436)caG>caT	p.Q812H	RAI1_ENST00000261641.6_Missense_Mutation_p.Q812H	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	812					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)		ACTTCAAGCAGGAGGAGGTGG	0.677																																					p.Q812H		Atlas-SNP	.											.	RAI1	121	.	0			c.G2436T						PASS	.						29	37	34					17																	17698698		2203	4300	6503	SO:0001583	missense	10743	exon3			CAAGCAGGAGGAG	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.2436G>T	chr17.hg19:g.17698698G>T	ENSP00000323074:p.Gln812His	109.0	0.0	.		111.0	30.0	.	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Missense_Mutation	SNP	ENST00000353383.1	hg19	CCDS11188.1	.	.	.	.	.	.	.	.	.	.	G	13.33	2.204428	0.38905	.	.	ENSG00000108557	ENST00000353383;ENST00000395774;ENST00000395776;ENST00000355970;ENST00000261641;ENST00000315321	T;T;T	0.69806	-0.43;2.31;0.17	5.37	4.39	0.52855	.	0.247497	0.35495	N	0.003161	T	0.61211	0.2329	L	0.60455	1.87	0.30237	N	0.795346	B	0.25441	0.126	B	0.22753	0.041	T	0.62987	-0.6737	10	0.54805	T	0.06	.	11.0862	0.48089	0.1501:0.0:0.8499:0.0	.	812	Q7Z5J4	RAI1_HUMAN	H	812;812;812;812;812;764	ENSP00000323074:Q812H;ENSP00000379120:Q812H;ENSP00000261641:Q812H	ENSP00000261641:Q812H	Q	+	3	2	RAI1	17639423	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	2.004000	0.40854	1.256000	0.44068	0.561000	0.74099	CAG	.	.	.	none		0.677	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665		T	17698698	G	T	17698698	3	4	6	1	0	0	0	0	1	0	0	0	13020	991	35	4	2438	4	RAI1	17	17698698	Missense_Mutation	SNP	G	TCGA-2Z-A9J6-01A-11D-A382-10	7346512	17698698	63496512	38	533			1	1		2	2	15	G		2.396864e-05
RAI1	10743	hgsc.bcm.edu	37	chr17	17698712	17698712	+	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	caagcaggaggaggtgggtgGggtgaaggaggaggcaggtg	10	4	24	3	0	0	1	0	1	0	0	0	5	0	5	0	10	1	2	0	10	2	0			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr17:17698712G>T	ENST00000353383.1	+	3	2919	c.2450G>T	c.(2449-2451)gGg>gTg	p.G817V	RAI1_ENST00000261641.6_Missense_Mutation_p.G817V	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	817					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)		GAGGTGGGTGGGGTGAAGGAG	0.687																																					p.G817V		Atlas-SNP	.											.	RAI1	121	.	0			c.G2450T						PASS	.						27	35	32					17																	17698712		2201	4299	6500	SO:0001583	missense	10743	exon3			TGGGTGGGGTGAA	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.2450G>T	chr17.hg19:g.17698712G>T	ENSP00000323074:p.Gly817Val	100.0	0.0	.		115.0	30.0	.	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Missense_Mutation	SNP	ENST00000353383.1	hg19	CCDS11188.1	.	.	.	.	.	.	.	.	.	.	G	18.45	3.625786	0.66901	.	.	ENSG00000108557	ENST00000353383;ENST00000395774;ENST00000395776;ENST00000355970;ENST00000261641;ENST00000315321	T;T;T	0.66460	-0.21;2.51;0.39	5.37	4.31	0.51392	.	0.157090	0.43260	D	0.000600	T	0.56352	0.1979	L	0.44542	1.39	0.80722	D	1	D	0.54397	0.966	P	0.47299	0.543	T	0.55835	-0.8078	10	0.31617	T	0.26	.	3.5178	0.07731	0.3696:0.0:0.6304:0.0	.	817	Q7Z5J4	RAI1_HUMAN	V	817;817;817;817;817;769	ENSP00000323074:G817V;ENSP00000379120:G817V;ENSP00000261641:G817V	ENSP00000261641:G817V	G	+	2	0	RAI1	17639437	1.000000	0.71417	0.992000	0.48379	0.764000	0.43329	2.141000	0.42168	2.519000	0.84933	0.561000	0.74099	GGG	.	.	.	none		0.687	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665		T	17698712	G	T	17698712	3	4	6	1	0	0	0	0	1	0	0	0	13020	1232	43	4	2452	4	RAI1	17	17698712	Missense_Mutation	SNP	G	TCGA-2Z-A9J6-01A-11D-A382-10	14	17698712	63496498	39	534			1	1		2	2	15	G		2.396864e-05
SLC5A10	125206	hgsc.bcm.edu	37	chr17	18922878	18922878	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcagtctttgtcctgggcGtcttctggcgacgtgccaac	4	12	12	13	3	3	0	0	0	3	0	4	1	4	0	2	2	3	1	2	2	1	2			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr17:18922878G>A	ENST00000395645.3	+	12	1402	c.1384G>A	c.(1384-1386)Gtc>Atc	p.V462I	SLC5A10_ENST00000395647.2_Missense_Mutation_p.V478I|SLC5A10_ENST00000417251.2_Missense_Mutation_p.V426I|SLC5A10_ENST00000395643.2_Missense_Mutation_p.V435I|SLC5A10_ENST00000395642.1_Missense_Mutation_p.V432I|SLC5A10_ENST00000317977.6_Missense_Mutation_p.V432I	NM_001042450.2	NP_001035915.1	A0PJK1	SC5AA_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 10	462					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)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(3)|ovary(3)|prostate(3)|skin(3)	24						TGTCCTGGGCGTCTTCTGGCG	0.637																																					p.V478I		Atlas-SNP	.											.	SLC5A10	55	.	0			c.G1432A						PASS	.						69	61	64					17																	18922878		2203	4300	6503	SO:0001583	missense	125206	exon12			CTGGGCGTCTTCT		CCDS11201.2, CCDS42275.1, CCDS59277.1, CCDS59278.1, CCDS74008.1	17p11.2	2013-07-19	2013-07-19		ENSG00000154025	ENSG00000154025		"Solute carriers"	23155	protein-coding gene	gene with protein product			"solute carrier family 5 (sodium/glucose cotransporter), member 10"				Standard	NM_152351		Approved	SGLT5	uc002gut.2	A0PJK1	OTTHUMG00000178143	ENST00000395645.3:c.1384G>A	chr17.hg19:g.18922878G>A	ENSP00000379007:p.Val462Ile	37.0	0.0	.		68.0	18.0	.	NM_152351	A8MUC9|B4DPI0|B7WPR4|Q6P5X0|Q8IXM4|Q96LQ1	Missense_Mutation	SNP	ENST00000395645.3	hg19	CCDS42275.1	.	.	.	.	.	.	.	.	.	.	G	0.941	-0.709631	0.03230	.	.	ENSG00000154025	ENST00000317977;ENST00000395647;ENST00000395642;ENST00000417251;ENST00000395645;ENST00000395643	D;D;D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.09;-2.19;-2.19	4.49	0.944	0.19537	Sodium/solute symporter, conserved site (1);	0.231384	0.43579	N	0.000551	T	0.59905	0.2228	N	0.01454	-0.855	0.31052	N	0.715133	B;B;B;B;B	0.09022	0.001;0.0;0.001;0.001;0.002	B;B;B;B;B	0.12156	0.007;0.003;0.007;0.002;0.005	T	0.57493	-0.7802	10	0.02654	T	1	.	7.4201	0.27067	0.6057:0.0:0.3942:0.0	.	426;435;462;478;432	B4DPI0;A0PJK1-2;A0PJK1;A0PJK1-4;A0PJK1-3	.;.;SC5AA_HUMAN;.;.	I	432;478;432;426;462;435	ENSP00000324346:V432I;ENSP00000379008:V478I;ENSP00000379004:V432I;ENSP00000401875:V426I;ENSP00000379007:V462I;ENSP00000379005:V435I	ENSP00000324346:V432I	V	+	1	0	SLC5A10	18863603	0.322000	0.24634	1.000000	0.80357	0.531000	0.34715	0.814000	0.27239	0.213000	0.20722	-0.340000	0.08031	GTC	.	.	.	none		0.637	SLC5A10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132129.2	NM_152351		A	18922878	G	A	18922878	3	1	6	1	0	0	0	0	1	0	0	0	14675	1145	40	1	1478	1	SLC5A10	17	18922878	Missense_Mutation	SNP	G	TCGA-2Z-A9J6-01A-11D-A382-10	1224166	18922878	62272332	40	535											
SPAG9	9043	hgsc.bcm.edu	37	chr17	49157055	49157055	+	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	gttcttgagagtcttcaaatTcaatgaatttctaataaaga	15	15	6	5	0	5	3	2	2	3	2	5	4	5	3	0	0	0	1	0	0	6	7			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr17:49157055T>A	ENST00000262013.7	-	2	522	c.314A>T	c.(313-315)gAa>gTa	p.E105V	SPAG9_ENST00000357122.4_Missense_Mutation_p.E105V|SPAG9_ENST00000505279.1_Missense_Mutation_p.E105V|RP11-481C4.1_ENST00000509833.1_RNA	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	105					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)			GTCTTCAAATTCAATGAATTT	0.294																																					p.E105V		Atlas-SNP	.											.	SPAG9	151	.	0			c.A314T						PASS	.						82	83	83					17																	49157055		2203	4300	6503	SO:0001583	missense	9043	exon2			TCAAATTCAATGA	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.314A>T	chr17.hg19:g.49157055T>A	ENSP00000262013:p.Glu105Val	49.0	0.0	.		94.0	22.0	.	NM_001130528	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Missense_Mutation	SNP	ENST00000262013.7	hg19	CCDS45740.1	.	.	.	.	.	.	.	.	.	.	T	15.09	2.731306	0.48939	.	.	ENSG00000008294	ENST00000262013;ENST00000505279;ENST00000357122;ENST00000546269	T;T;T	0.48201	0.82;0.82;0.82	5.19	5.19	0.71726	JNK/Rab-associated protein-1, N-terminal (1);	0.317983	0.29752	N	0.011294	T	0.67674	0.2918	M	0.81341	2.54	0.50632	D	0.999886	P;P;B	0.50369	0.523;0.934;0.348	P;P;B	0.59643	0.543;0.861;0.22	T	0.73110	-0.4086	10	0.87932	D	0	-16.6007	15.3432	0.74314	0.0:0.0:0.0:1.0	.	105;105;105	O60271-2;O60271;O60271-4	.;JIP4_HUMAN;.	V	105	ENSP00000262013:E105V;ENSP00000426900:E105V;ENSP00000349636:E105V	ENSP00000262013:E105V	E	-	2	0	SPAG9	46512054	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.896000	0.56266	2.088000	0.63022	0.528000	0.53228	GAA	.	.	.	none		0.294	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971		A	49157055	T	A	49157055	3	1	6	1	0	0	0	0	1	0	0	0	14998	1783	62	5	3767	5	SPAG9	17	49157055	Missense_Mutation	SNP	T	TCGA-2Z-A9J6-01A-11D-A382-10	30234177	49157055	32038155	41	536											
BAIAP2	10458	hgsc.bcm.edu	37	chr17	79031740	79031740	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagatgggggagctggccAgcgagagccagggctccaaa	11	4	17	9	1	0	3	0	1	0	2	1	5	1	4	3	4	3	2	3	4	2	0			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr17:79031740A>G	ENST00000321300.6	+	3	283	c.190A>G	c.(190-192)Agc>Ggc	p.S64G	BAIAP2_ENST00000435091.3_Missense_Mutation_p.S64G|BAIAP2_ENST00000575712.1_Missense_Mutation_p.S64G|BAIAP2_ENST00000573894.1_3'UTR|BAIAP2_ENST00000428708.2_Missense_Mutation_p.S64G|BAIAP2_ENST00000392411.3_Intron|BAIAP2_ENST00000575245.1_Missense_Mutation_p.S97G|BAIAP2_ENST00000321280.7_Missense_Mutation_p.S64G	NM_001144888.1|NM_017451.2	NP_001138360.1|NP_059345.1	Q9UQB8	BAIP2_HUMAN	BAI1-associated protein 2	64	IMD. {ECO:0000255|PROSITE- ProRule:PRU00668}.				actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|filopodium assembly (GO:0046847)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of synaptic plasticity (GO:0048167)|response to bacterium (GO:0009617)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	cytoskeletal adaptor activity (GO:0008093)|identical protein binding (GO:0042802)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)	18	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			GGAGCTGGCCAGCGAGAGCCA	0.622																																					p.S64G		Atlas-SNP	.											.	BAIAP2	74	.	0			c.A190G						PASS	.						41	39	40					17																	79031740		2203	4300	6503	SO:0001583	missense	10458	exon3			CTGGCCAGCGAGA	AB015019	CCDS11775.1, CCDS11776.1, CCDS11777.1, CCDS45806.1	17q25.3	2014-09-11			ENSG00000175866				947	protein-coding gene	gene with protein product		605475				10343108	Standard	NM_017451		Approved	BAP2	uc002jzg.2	Q9UQB8	OTTHUMG00000177698	ENST00000321300.6:c.190A>G	chr17.hg19:g.79031740A>G	ENSP00000316338:p.Ser64Gly	40.0	0.0	.		56.0	25.0	.	NM_001144888	O43858|Q53HB1|Q86WC1|Q8N5C0|Q96CR7|Q9UBR3|Q9UQ43	Missense_Mutation	SNP	ENST00000321300.6	hg19	CCDS11775.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.264088	0.80358	.	.	ENSG00000175866	ENST00000321300;ENST00000428708;ENST00000435091;ENST00000321280	T;T;T;T	0.38077	1.16;1.16;1.16;1.16	4.99	3.83	0.44106	IRSp53/MIM homology domain (IMD) (3);	0.043292	0.85682	D	0.000000	T	0.53222	0.1783	M	0.67953	2.075	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.85130	0.997;0.969;0.952;0.995;0.995;0.977	T	0.49744	-0.8907	10	0.30078	T	0.28	-13.536	10.5453	0.45056	0.8379:0.1621:0.0:0.0	.	64;64;64;64;64;64	Q9UQB8;Q9UQB8-2;Q9UQB8-3;Q9UQB8-5;Q9UQB8-6;Q9UQB8-4	BAIP2_HUMAN;.;.;.;.;.	G	64	ENSP00000316338:S64G;ENSP00000401022:S64G;ENSP00000413069:S64G;ENSP00000315685:S64G	ENSP00000315685:S64G	S	+	1	0	BAIAP2	76646335	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.338000	0.72963	1.875000	0.54330	0.459000	0.35465	AGC	.	.	.	none		0.622	BAIAP2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438553.1			G	79031740	A	G	79031740	3	3	6	1	0	0	0	0	1	0	0	0	1301	188	7	3	200	3	BAIAP2	17	79031740	Missense_Mutation	SNP	A	TCGA-2Z-A9J6-01A-11D-A382-10	29874685	79031740	2163470	42	537											
LAMA3	3909	hgsc.bcm.edu	37	chr18	21418824	21418824	+	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	ccactgcattgccagttatgGgcgatttgtcaatcaaaggt	10	12	10	9	1	2	0	2	0	0	0	2	1	2	0	2	2	2	2	2	2	3	3	rs546055094		TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr18:21418824G>T	ENST00000313654.9	+	26	3414	c.3173G>T	c.(3172-3174)gGg>gTg	p.G1058V	LAMA3_ENST00000399516.3_Missense_Mutation_p.G1058V	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	1058	Domain IV 1 (domain IV B).				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					GCCAGTTATGGGCGATTTGTC	0.418																																					p.G1058V		Atlas-SNP	.											.	LAMA3	397	.	0			c.G3173T						PASS	.						188	186	187					18																	21418824		1957	4143	6100	SO:0001583	missense	3909	exon26			GTTATGGGCGATT	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.3173G>T	chr18.hg19:g.21418824G>T	ENSP00000324532:p.Gly1058Val	64.0	0.0	.		79.0	24.0	.	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	hg19	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	G	15.43	2.831649	0.50845	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000416669	T;T	0.26373	1.76;1.74	5.52	4.65	0.58169	.	.	.	.	.	T	0.47600	0.1454	M	0.67953	2.075	0.80722	D	1	D;D	0.76494	0.999;0.993	D;P	0.66602	0.945;0.843	T	0.50988	-0.8762	9	0.66056	D	0.02	.	14.7529	0.69540	0.0697:0.0:0.9303:0.0	.	1058;1058	Q6VU67;Q16787	.;LAMA3_HUMAN	V	1058;1058;1056	ENSP00000324532:G1058V;ENSP00000382432:G1058V	ENSP00000324532:G1058V	G	+	2	0	LAMA3	19672822	0.990000	0.36364	0.012000	0.15200	0.220000	0.24768	4.035000	0.57297	1.476000	0.48215	0.655000	0.94253	GGG	.	.	.	none		0.418	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		T	21418824	G	T	21418824	3	4	6	1	0	0	0	0	1	0	0	0	8614	1232	43	4	3275	4	LAMA3	18	21418824	Missense_Mutation	SNP	G	TCGA-2Z-A9J6-01A-11D-A382-10		21418824	56658424	43	538											
SMAD2	4087	hgsc.bcm.edu	37	chr18	45395677	45395677	+	Missense_Mutation	SNP	A	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	ttcatcctttttaagattaaAagcatattcgcagttttcaa	13	17	4	7	1	2	1	2	0	0	1	4	1	3	1	1	0	1	3	1	0	5	9			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr18:45395677A>C	ENST00000402690.2	-	4	851	c.457T>G	c.(457-459)Ttt>Gtt	p.F153V	SMAD2_ENST00000587353.1_5'UTR|SMAD2_ENST00000591214.1_Missense_Mutation_p.F123V|SMAD2_ENST00000586040.1_Missense_Mutation_p.F123V|SMAD2_ENST00000356825.4_Missense_Mutation_p.F123V|SMAD2_ENST00000262160.6_Missense_Mutation_p.F153V	NM_001003652.3	NP_001003652.1	Q15796	SMAD2_HUMAN	SMAD family member 2	153	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|cell fate commitment (GO:0045165)|common-partner SMAD protein phosphorylation (GO:0007182)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|endoderm formation (GO:0001706)|gastrulation (GO:0007369)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|insulin secretion (GO:0030073)|intracellular signal transduction (GO:0035556)|lung development (GO:0030324)|mesoderm formation (GO:0001707)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|nodal signaling pathway (GO:0038092)|organ growth (GO:0035265)|palate development (GO:0060021)|pancreas development (GO:0031016)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900224)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|primary miRNA processing (GO:0031053)|regulation of binding (GO:0051098)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to cholesterol (GO:0070723)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|zygotic specification of dorsal/ventral axis (GO:0007352)	activin responsive factor complex (GO:0032444)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|phosphatase binding (GO:0019902)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|type I transforming growth factor beta receptor binding (GO:0034713)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(21)|liver(1)|lung(8)|prostate(2)|urinary_tract(1)	43						TTAAGATTAAAAGCATATTCG	0.373																																					p.F153V		Atlas-SNP	.											.	SMAD2	85	.	0			c.T457G						PASS	.						106	106	106					18																	45395677		2203	4300	6503	SO:0001583	missense	4087	exon4			GATTAAAAGCATA	U65019	CCDS11934.1	18q21	2006-11-06	2006-11-06	2004-05-26	ENSG00000175387	ENSG00000175387		"SMADs"	6768	protein-coding gene	gene with protein product		601366	"MAD, mothers against decapentaplegic homolog 2 (Drosophila)", "SMAD, mothers against DPP homolog 2 (Drosophila)"	MADH2		8752209, 8673135	Standard	NM_001003652		Approved	MADR2, JV18-1	uc002lcz.4	Q15796	OTTHUMG00000132652	ENST00000402690.2:c.457T>G	chr18.hg19:g.45395677A>C	ENSP00000384449:p.Phe153Val	90.0	0.0	.		124.0	9.0	.	NM_005901		Missense_Mutation	SNP	ENST00000402690.2	hg19	CCDS11934.1	.	.	.	.	.	.	.	.	.	.	A	19.89	3.911800	0.72983	.	.	ENSG00000175387	ENST00000262160;ENST00000356825;ENST00000402690	T;T;T	0.77358	-1.09;-1.09;-1.09	5.17	5.17	0.71159	MAD homology, MH1 (3);MAD homology 1, Dwarfin-type (2);	0.000000	0.85682	D	0.000000	D	0.85999	0.5828	M	0.70595	2.14	0.80722	D	1	D;D;D	0.63046	0.992;0.989;0.992	D;P;D	0.62955	0.909;0.897;0.909	D	0.87886	0.2681	10	0.87932	D	0	.	15.2967	0.73913	1.0:0.0:0.0:0.0	.	123;123;153	B7Z5N5;Q15796-2;Q15796	.;.;SMAD2_HUMAN	V	153;123;153	ENSP00000262160:F153V;ENSP00000349282:F123V;ENSP00000384449:F153V	ENSP00000262160:F153V	F	-	1	0	SMAD2	43649675	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.287000	0.95975	2.074000	0.62210	0.482000	0.46254	TTT	.	.	.	none		0.373	SMAD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450571.1	NM_005901		C	45395677	A	C	45395677	3	2	6	1	0	0	0	0	1	0	0	0	14771	14	1	5	978	5	SMAD2	18	45395677	Missense_Mutation	SNP	A	TCGA-2Z-A9J6-01A-11D-A382-10	23976853	45395677	32681571	44	539											
OR7G1	125962	hgsc.bcm.edu	37	chr19	9226308	9226308	+	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	gagatgacagccaggagaatGagcaggttccccaggatggt	12	6	15	8	0	0	4	0	2	0	2	1	7	1	5	3	4	2	2	3	4	1	1			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr19:9226308G>A	ENST00000541538.1	-	1	131	c.132C>T	c.(130-132)ctC>ctT	p.L44L	OR7G1_ENST00000293614.1_Silent_p.L44L	NM_001005192.2	NP_001005192.2	Q8NGA0	OR7G1_HUMAN	olfactory receptor, family 7, subfamily G, member 1	44						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	20						CCAGGAGAATGAGCAGGTTCC	0.478																																					p.L44L		Atlas-SNP	.											.	OR7G1	53	.	0			c.C132T						PASS	.						147	138	141					19																	9226308		2203	4300	6503	SO:0001819	synonymous_variant	125962	exon1			GAGAATGAGCAGG		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.132C>T	chr19.hg19:g.9226308G>A		82.0	0.0	.		63.0	20.0	.	NM_001005192	Q6IFJ5|Q96RA1	Silent	SNP	ENST00000541538.1	hg19	CCDS32898.2																																																																																			.	.	.	none		0.478	OR7G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397912.1			A	9226308	G	A	9226308	2	1	6	1	0	0	0	0	0	0	0	1	11229	1277	45	2		2	OR7G1	19	9226308	Silent	SNP	G	TCGA-2Z-A9J6-01A-11D-A382-10		9226308	49902675	45	540											
QTRT1	81890	hgsc.bcm.edu	37	chr19	10823829	10823829	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccgtccgcaccagcatcgtGgagaagcgcttcccggactt	7	7	12	15	5	0	1	0	0	0	1	3	3	2	2	4	2	2	3	4	2	1	2			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr19:10823829G>A	ENST00000250237.5	+	10	1105	c.1095G>A	c.(1093-1095)gtG>gtA	p.V365V		NM_031209.2	NP_112486.1	Q9BXR0	TGT_HUMAN	queuine tRNA-ribosyltransferase 1	365					queuosine biosynthetic process (GO:0008616)|tRNA modification (GO:0006400)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|queuine tRNA-ribosyltransferase activity (GO:0008479)			large_intestine(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	12			Epithelial(33;1.55e-05)|all cancers(31;3.42e-05)			CCAGCATCGTGGAGAAGCGCT	0.687																																					p.V365V		Atlas-SNP	.											.	QTRT1	25	.	0			c.G1095A						PASS	.						62	60	60					19																	10823829		2203	4300	6503	SO:0001819	synonymous_variant	81890	exon10			CATCGTGGAGAAG	AF302783	CCDS12248.1	19p13.3	2014-06-11	2008-07-31		ENSG00000213339	ENSG00000213339	2.4.2.29		23797	protein-coding gene	gene with protein product	"tRNA-guanine transglycosylase"	609615				20354154	Standard	NM_031209		Approved	TGT	uc002mpr.3	Q9BXR0		ENST00000250237.5:c.1095G>A	chr19.hg19:g.10823829G>A		57.0	0.0	.		41.0	13.0	.	NM_031209	B4DFM7|Q96BQ4|Q9BXQ9	Silent	SNP	ENST00000250237.5	hg19	CCDS12248.1																																																																																			.	.	.	none		0.687	QTRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452086.1	NM_031209		A	10823829	G	A	10823829	2	1	6	1	0	0	0	0	0	0	0	1	12898	1335	47	2		2	QTRT1	19	10823829	Silent	SNP	G	TCGA-2Z-A9J6-01A-11D-A382-10	1597521	10823829	48305154	46	541											
ETHE1	23474	hgsc.bcm.edu	37	chr19	44012185	44012185	+	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	gccgagggttcagagtcctcTcctcctccacggtggacact	6	9	11	15	2	2	1	1	0	1	1	6	3	5	2	5	3	0	1	5	3	0	1			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr19:44012185T>A	ENST00000292147.2	-	6	689	c.623A>T	c.(622-624)gAg>gTg	p.E208V	ETHE1_ENST00000600651.1_Missense_Mutation_p.E208V	NM_014297.3	NP_055112.2	O95571	ETHE1_HUMAN	ethylmalonic encephalopathy 1	208					cellular nitrogen compound metabolic process (GO:0034641)|glutathione metabolic process (GO:0006749)|hydrogen sulfide metabolic process (GO:0070813)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	iron ion binding (GO:0005506)|sulfur dioxygenase activity (GO:0050313)			central_nervous_system(1)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	5		Prostate(69;0.0153)				CAGAGTCCTCTCCTCCTCCAC	0.557																																					p.E208V		Atlas-SNP	.											.	ETHE1	7	.	0			c.A623T						PASS	.						74	59	64					19																	44012185		2203	4300	6503	SO:0001583	missense	23474	exon6			GTCCTCTCCTCCT		CCDS12622.1	19q13.32	2014-06-20				ENSG00000105755	1.13.11.18		23287	protein-coding gene	gene with protein product		608451				19136963	Standard	NM_014297		Approved	YF13H12, HSCO	uc002owp.3	O95571		ENST00000292147.2:c.623A>T	chr19.hg19:g.44012185T>A	ENSP00000292147:p.Glu208Val	49.0	0.0	.		52.0	24.0	.	NM_014297	Q96HR0|Q9H001	Missense_Mutation	SNP	ENST00000292147.2	hg19	CCDS12622.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.543602	0.86022	.	.	ENSG00000105755	ENST00000292147	D	0.96856	-4.15	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	D	0.98557	0.9518	H	0.95365	3.66	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.979;0.995	D	0.99433	1.0936	10	0.87932	D	0	-8.9073	13.0221	0.58794	0.0:0.0:0.0:1.0	.	181;208	B2RCZ7;O95571	.;ETHE1_HUMAN	V	208	ENSP00000292147:E208V	ENSP00000292147:E208V	E	-	2	0	ETHE1	48704025	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.780000	0.68956	2.232000	0.73038	0.524000	0.50904	GAG	.	.	.	none		0.557	ETHE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463184.1	NM_014297		A	44012185	T	A	44012185	3	1	6	1	0	0	0	0	1	0	0	0	5274	1551	54	5	149	5	ETHE1	19	44012185	Missense_Mutation	SNP	T	TCGA-2Z-A9J6-01A-11D-A382-10	33188356	44012185	15116798	47	542											
ZNF180	7733	hgsc.bcm.edu	37	chr19	44980632	44980632	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttacaaactagttacattcaTagagtttctcttcagtatga	13	16	5	7	0	3	2	2	1	1	1	4	2	3	2	0	0	3	3	0	0	6	8	rs141416252		TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr19:44980632T>C	ENST00000221327.4	-	5	2347	c.2066A>G	c.(2065-2067)tAt>tGt	p.Y689C	ZNF180_ENST00000585514.1_5'Flank|ZNF180_ENST00000391956.4_Missense_Mutation_p.Y664C|AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000592529.1_Missense_Mutation_p.Y662C	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	689					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)				GTTACATTCATAGAGTTTCTC	0.313																																					p.Y689C	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											.	ZNF180	103	.	0			c.A2066G						PASS	.	T	CYS/TYR	2,4402	4.2+/-10.8	0,2,2200	70	76	74		2066	2.1	0	19	dbSNP_134	74	0,8598		0,0,4299	no	missense	ZNF180	NM_013256.3	194	0,2,6499	CC,CT,TT		0.0,0.0454,0.0154	probably-damaging	689/693	44980632	2,13000	2202	4299	6501	SO:0001583	missense	7733	exon5			CATTCATAGAGTT	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.2066A>G	chr19.hg19:g.44980632T>C	ENSP00000221327:p.Tyr689Cys	75.0	0.0	.		77.0	25.0	.	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	hg19	CCDS12639.1	.	.	.	.	.	.	.	.	.	.	T	11.70	1.716111	0.30413	4.54E-4	0.0	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.03065	4.06;4.06	5.39	2.09	0.27110	.	0.920664	0.08851	N	0.884394	T	0.07458	0.0188	M	0.83953	2.67	0.19300	N	0.999979	B;B;B	0.22746	0.074;0.044;0.044	B;B;B	0.18561	0.022;0.01;0.01	T	0.32877	-0.9890	10	0.87932	D	0	-3.506	5.3213	0.15883	0.0:0.1527:0.2806:0.5667	.	664;688;689	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	C	689;664	ENSP00000221327:Y689C;ENSP00000375818:Y664C	ENSP00000221327:Y689C	Y	-	2	0	ZNF180	49672472	0.001000	0.12720	0.000000	0.03702	0.939000	0.58152	0.680000	0.25306	0.088000	0.17205	0.482000	0.46254	TAT	.	T|1.000;C|0.000	0.000	weak		0.313	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256		C	44980632	T	C	44980632	3	2	6	1	0	0	0	0	1	0	0	0	17760	1406	49	3	16	3	ZNF180	19	44980632	Missense_Mutation	SNP	T	TCGA-2Z-A9J6-01A-11D-A382-10	968447	44980632	14148351	48	543											
PROKR2	128674	hgsc.bcm.edu	37	chr20	5294901	5294901	+	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	cttggtcatgtcctcatcctCatccatagggaggtcataat	9	13	8	11	0	4	0	4	0	0	0	7	1	7	1	3	3	0	0	3	3	2	3			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr20:5294901C>T	ENST00000217270.3	-	1	114	c.115G>A	c.(115-117)Gag>Aag	p.E39K	PROKR2_ENST00000546004.1_Missense_Mutation_p.E39K	NM_144773.2	NP_658986.1	Q8NFJ6	PKR2_HUMAN	prokineticin receptor 2	39					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						TCCTCATCCTCATCCATAGGG	0.507										HNSCC(71;0.22)																											p.E39K		Atlas-SNP	.											.	PROKR2	90	.	0			c.G115A						PASS	.						139	121	127					20																	5294901		2203	4300	6503	SO:0001583	missense	128674	exon1			CATCCTCATCCAT	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.115G>A	chr20.hg19:g.5294901C>T	ENSP00000217270:p.Glu39Lys	111.0	0.0	.		114.0	33.0	.	NM_144773	A5JUU1|Q2M3C0|Q5TDY1|Q9NTT0	Missense_Mutation	SNP	ENST00000217270.3	hg19	CCDS13089.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.007135	0.75046	.	.	ENSG00000101292	ENST00000546004;ENST00000217270	T;T	0.71103	-0.54;-0.54	4.6	4.6	0.57074	.	0.259050	0.40640	N	0.001056	T	0.67552	0.2905	M	0.68593	2.085	0.58432	D	0.999999	B	0.30146	0.27	B	0.32724	0.151	T	0.63902	-0.6532	10	0.11485	T	0.65	.	15.2898	0.73857	0.0:1.0:0.0:0.0	.	39	Q8NFJ6	PKR2_HUMAN	K	39	ENSP00000440790:E39K;ENSP00000217270:E39K	ENSP00000217270:E39K	E	-	1	0	PROKR2	5242901	0.998000	0.40836	0.996000	0.52242	0.934000	0.57294	3.102000	0.50291	2.269000	0.75478	0.655000	0.94253	GAG	.	.	.	none		0.507	PROKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077854.1	NM_144773		T	5294901	C	T	5294901	3	4	6	1	0	0	0	0	1	0	0	0	12563	835	29	2	1046	2	PROKR2	20	5294901	Missense_Mutation	SNP	C	TCGA-2Z-A9J6-01A-11D-A382-10		5294901	57730619	49	544											
SLC13A3	64849	hgsc.bcm.edu	37	chr20	45239165	45239165	+	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	ttttcaggatggcattggcaAtgggaagcatcatggcagtg	10	11	14	6	0	2	0	2	0	0	0	2	2	2	2	0	5	1	4	0	5	2	3			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr20:45239165A>T	ENST00000279027.4	-	3	479	c.461T>A	c.(460-462)aTt>aAt	p.I154N	SLC13A3_ENST00000413164.2_Missense_Mutation_p.I154N|SLC13A3_ENST00000396360.1_Missense_Mutation_p.I107N|SLC13A3_ENST00000417157.2_Missense_Mutation_p.I107N|SLC13A3_ENST00000372121.1_Missense_Mutation_p.I154N|SLC13A3_ENST00000472148.1_Missense_Mutation_p.I107N|SLC13A3_ENST00000495082.1_Missense_Mutation_p.I107N|SLC13A3_ENST00000339636.3_Missense_Mutation_p.I154N|SLC13A3_ENST00000435032.1_De_novo_Start_InFrame|SLC13A3_ENST00000290317.5_Missense_Mutation_p.I107N	NM_001193342.1|NM_022829.5	NP_001180271.1|NP_073740.2	Q8WWT9	S13A3_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	154					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-affinity sodium:dicarboxylate symporter activity (GO:0015362)			breast(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	GGCATTGGCAATGGGAAGCAT	0.552																																					p.I154N		Atlas-SNP	.											.	SLC13A3	88	.	0			c.T461A						PASS	.						210	192	198					20																	45239165		2203	4300	6503	SO:0001583	missense	64849	exon3			TTGGCAATGGGAA	AF154121	CCDS13400.1, CCDS42886.1, CCDS54469.1, CCDS54470.1	20q13.12	2013-05-22			ENSG00000158296	ENSG00000158296		"Solute carriers"	14430	protein-coding gene	gene with protein product		606411				10794676, 10992006	Standard	NM_001011554		Approved	NADC3, SDCT2	uc002xsf.2	Q8WWT9	OTTHUMG00000033042	ENST00000279027.4:c.461T>A	chr20.hg19:g.45239165A>T	ENSP00000279027:p.Ile154Asn	56.0	0.0	.		53.0	19.0	.	NM_022829	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Missense_Mutation	SNP	ENST00000279027.4	hg19	CCDS13400.1	.	.	.	.	.	.	.	.	.	.	A	20.5	3.993818	0.74703	.	.	ENSG00000158296	ENST00000290317;ENST00000396360;ENST00000279027;ENST00000472148;ENST00000413164;ENST00000495082;ENST00000468915;ENST00000420568;ENST00000372121;ENST00000417157;ENST00000339636	T;T;T;T;T;T;T;T;T;T;T	0.05925	3.37;3.37;3.37;3.37;3.37;3.37;3.37;3.37;3.37;3.37;3.37	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.31918	0.0812	M	0.89163	3.01	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;0.999;1.0	T	0.19224	-1.0312	10	0.87932	D	0	-25.0823	16.1297	0.81418	1.0:0.0:0.0:0.0	.	154;107;107;107;154	B4DIR8;Q8WWT9-3;F6WI18;C9J4A3;Q8WWT9	.;.;.;.;S13A3_HUMAN	N	107;107;154;107;154;107;107;117;154;107;154	ENSP00000290317:I107N;ENSP00000379648:I107N;ENSP00000279027:I154N;ENSP00000420177:I107N;ENSP00000415852:I154N;ENSP00000419621:I107N;ENSP00000417784:I107N;ENSP00000395095:I117N;ENSP00000361193:I154N;ENSP00000397955:I107N;ENSP00000344912:I154N	ENSP00000279027:I154N	I	-	2	0	SLC13A3	44672572	1.000000	0.71417	0.974000	0.42286	0.386000	0.30323	9.287000	0.95975	2.270000	0.75569	0.460000	0.39030	ATT	.	.	.	none		0.552	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2			T	45239165	A	T	45239165	3	4	6	1	0	0	0	0	1	0	0	0	14406	101	4	5	1391	5	SLC13A3	20	45239165	Missense_Mutation	SNP	A	TCGA-2Z-A9J6-01A-11D-A382-10	39944264	45239165	17786355	50	545											
TTC3	7267	hgsc.bcm.edu	37	chr21	38494164	38494164	+	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	tctatgctgggggaatatgaCtgggccctgcaagcaaacat	11	9	12	9	0	1	1	0	1	1	0	1	2	1	2	1	3	4	3	1	3	5	2			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr21:38494164C>G	ENST00000399017.2	+	12	3695	c.948C>G	c.(946-948)gaC>gaG	p.D316E	TTC3_ENST00000354749.2_Missense_Mutation_p.D316E|TTC3_ENST00000355666.1_Missense_Mutation_p.D316E|TTC3_ENST00000540756.1_Missense_Mutation_p.D6E|TTC3_ENST00000479930.1_3'UTR	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	316					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)				GGGAATATGACTGGGCCCTGC	0.343																																					p.D316E	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.C948G						PASS	.						62	63	63					21																	38494164		2203	4300	6503	SO:0001583	missense	7267	exon12			ATATGACTGGGCC	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.948C>G	chr21.hg19:g.38494164C>G	ENSP00000381981:p.Asp316Glu	217.0	0.0	.		181.0	24.0	.	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	hg19	CCDS13651.1	.	.	.	.	.	.	.	.	.	.	C	5.051	0.195106	0.09599	.	.	ENSG00000182670	ENST00000418766;ENST00000450533;ENST00000438055;ENST00000355666;ENST00000540756;ENST00000399017;ENST00000354749	T;T;T;T;T;T;T	0.39406	1.34;1.34;1.34;3.27;1.08;3.27;3.27	5.55	2.52	0.30459	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.196102	0.35525	N	0.003151	T	0.15782	0.0380	N	0.02539	-0.55	0.24581	N	0.993876	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.21042	-1.0257	10	0.20046	T	0.44	-8.2624	8.1826	0.31319	0.4198:0.4365:0.1436:0.0	.	6;316	B4DSZ9;P53804	.;TTC3_HUMAN	E	316;316;298;316;6;316;316	ENSP00000403943:D316E;ENSP00000408456:D316E;ENSP00000391891:D298E;ENSP00000347889:D316E;ENSP00000442875:D6E;ENSP00000381981:D316E;ENSP00000346791:D316E	ENSP00000346791:D316E	D	+	3	2	TTC3	37416034	0.996000	0.38824	1.000000	0.80357	0.999000	0.98932	0.383000	0.20651	0.679000	0.31345	0.650000	0.86243	GAC	.	.	.	none		0.343	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			G	38494164	C	G	38494164	3	3	6	1	0	0	0	0	1	0	0	0	16709	564	20	4	990	4	TTC3	21	38494164	Missense_Mutation	SNP	C	TCGA-2Z-A9J6-01A-11D-A382-10		38494164	9635731	51	546											
MYO18B	84700	hgsc.bcm.edu	37	chr22	26164198	26164198	+	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	cctgggagctcagacattctGggcaaggagagcgaggggtc	9	6	17	9	1	2	2	1	0	1	2	3	5	2	3	1	5	2	2	1	5	1	1			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr22:26164198G>C	ENST00000407587.2	+	4	484	c.315G>C	c.(313-315)ctG>ctC	p.L105L	MYO18B_ENST00000536101.1_Silent_p.L105L|MYO18B_ENST00000335473.7_Silent_p.L105L			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	105	Ser-rich.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						CAGACATTCTGGGCAAGGAGA	0.602																																					p.L105L		Atlas-SNP	.											.	MYO18B	322	.	0			c.G315C						PASS	.						76	82	80					22																	26164198		1969	4152	6121	SO:0001819	synonymous_variant	84700	exon4			CATTCTGGGCAAG	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.315G>C	chr22.hg19:g.26164198G>C		157.0	0.0	.		186.0	10.0	.	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	hg19																																																																																				.	.	.	none		0.602	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		C	26164198	G	C	26164198	2	2	6	1	0	0	0	0	0	0	0	1	10073	1335	47	4		4	MYO18B	22	26164198	Silent	SNP	G	TCGA-2Z-A9J6-01A-11D-A382-10		26164198	25140368	52	547											
ITIH5L	347365	hgsc.bcm.edu	37	chrX	54777684	54777684	+	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	ctcgcaaagatatagaactgCggctgatggtgatagtatag	13	10	12	6	2	0	4	0	2	0	2	1	4	0	4	0	2	2	3	0	2	7	5			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chrX:54777684C>T	ENST00000218436.6	-	12	3511	c.3482G>A	c.(3481-3483)cGc>cAc	p.R1161H		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	1161					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										TATAGAACTGCGGCTGATGGT	0.587													C|||	1	0.000264901	8e-04	0	3775	,	,		14301	0		0	False		,,,				2504	0				p.R1161H		Atlas-SNP	.											.	.	.	.	0			c.G3482A						PASS	.						80	66	71					X																	54777684		2203	4300	6503	SO:0001583	missense	347365	exon12			GAACTGCGGCTGA	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.3482G>A	chrX.hg19:g.54777684C>T	ENSP00000218436:p.Arg1161His	123.0	0.0	.		153.0	106.0	.	NM_198510	A6NN03	Missense_Mutation	SNP	ENST00000218436.6	hg19	CCDS14361.1	.	.	.	.	.	.	.	.	.	.	C	2.230	-0.376357	0.05000	.	.	ENSG00000102313	ENST00000218436	T	0.11495	2.77	3.58	-4.03	0.04021	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	2.392490	0.02752	N	0.117600	T	0.06690	0.0171	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.32613	-0.9900	10	0.38643	T	0.18	.	2.5439	0.04732	0.1157:0.3461:0.1136:0.4246	.	1161	Q6UXX5	ITH5L_HUMAN	H	1161	ENSP00000218436:R1161H	ENSP00000218436:R1161H	R	-	2	0	ITIH5L	54794409	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-1.458000	0.02372	-0.749000	0.04747	-0.742000	0.03525	CGC	.	.	.	none		0.587	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510		T	54777684	C	T	54777684	3	4	6	1	0	0	0	0	1	0	0	0	7915	768	27	1	467	1	ITIH5L	23	54777684	Missense_Mutation	SNP	C	TCGA-2Z-A9J6-01A-11D-A382-10		54777684	100492876	53	548											
S100PBP	64766	hgsc.bcm.edu	37	chr1	33292095	33292095	+	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	tggaccagctcatactaaacCattaaacagacgctctgtac	14	9	6	12	1	2	1	1	0	1	1	2	2	2	2	2	1	5	3	2	1	6	4			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr1:33292095C>T	ENST00000373475.5	+	3	649	c.395C>T	c.(394-396)cCa>cTa	p.P132L	S100PBP_ENST00000373476.1_Missense_Mutation_p.P132L|S100PBP_ENST00000356689.3_3'UTR|S100PBP_ENST00000398243.3_Missense_Mutation_p.P132L	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)				CATACTAAACCATTAAACAGA	0.418																																					p.P132L		Atlas-SNP	.											.	S100PBP	31	.	0			c.C395T						PASS	.						57	57	57					1																	33292095		2203	4300	6503	SO:0001583	missense	64766	exon3			CTAAACCATTAAA	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.395C>T	chr1.hg19:g.33292095C>T	ENSP00000362574:p.Pro132Leu	169.0	0.0	.		191.0	32.0	.	NM_001256121		Missense_Mutation	SNP	ENST00000373475.5	hg19	CCDS30666.1	.	.	.	.	.	.	.	.	.	.	C	11.87	1.768157	0.31320	.	.	ENSG00000116497	ENST00000373476;ENST00000373475;ENST00000531123;ENST00000398243;ENST00000356689;ENST00000531256;ENST00000482212	.	.	.	5.85	5.85	0.93711	.	0.276721	0.35040	N	0.003497	T	0.60753	0.2293	N	0.19112	0.55	0.39844	D	0.973141	D;D	0.63046	0.992;0.992	D;P	0.64410	0.925;0.856	T	0.58200	-0.7678	8	.	.	.	-1.5056	16.0378	0.80642	0.0:1.0:0.0:0.0	.	132;132	A8MTZ6;Q96BU1	.;S1PBP_HUMAN	L	132	.	.	P	+	2	0	S100PBP	33064682	1.000000	0.71417	0.999000	0.59377	0.905000	0.53344	3.345000	0.52182	2.941000	0.99782	0.655000	0.94253	CCA	.	.	.	none		0.418	S100PBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011266.1	NM_022753		T	33292095	C	T	33292095	3	4	7	1	0	0	0	0	1	0	0	0	13804	594	21	2	397	2	S100PBP	1	33292095	Missense_Mutation	SNP	C	TCGA-2Z-A9J7-01A-11D-A382-10		33292095	215958526	1	549											
CDC20	991	hgsc.bcm.edu	37	chr1	43825898	43825898	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gattggagttctgggaatgtActggccgtggcactggacaa	9	10	15	7	1	1	0	0	0	1	0	1	4	1	3	1	5	1	3	1	5	3	3			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr1:43825898A>G	ENST00000372462.1	+	5	794	c.591A>G	c.(589-591)gtA>gtG	p.V197V	RP1-92O14.3_ENST00000424948.1_RNA|CDC20_ENST00000478882.1_3'UTR|CDC20_ENST00000310955.6_Silent_p.V197V			Q12834	CDC20_HUMAN	cell division cycle 20	197					activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell cycle (GO:0007049)|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 cell proliferation (GO:0008284)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein ubiquitination (GO:0016567)|regulation of dendrite development (GO:0050773)|regulation of meiosis (GO:0040020)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|spindle (GO:0005819)	enzyme binding (GO:0019899)|protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	15	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				CTGGGAATGTACTGGCCGTGG	0.517																																					p.V197V	Esophageal Squamous(137;1154 1759 10362 10401 46925)	Atlas-SNP	.											.	CDC20	34	.	0			c.A591G						PASS	.						155	146	149					1																	43825898		2203	4300	6503	SO:0001819	synonymous_variant	991	exon6			GAATGTACTGGCC	U05340	CCDS484.1	1p34.1	2013-01-17	2013-01-17		ENSG00000117399	ENSG00000117399		"WD repeat domain containing"	1723	protein-coding gene	gene with protein product		603618	"CDC20 (cell division cycle 20, S. cerevisiae, homolog)", "CDC20 cell division cycle 20 homolog (S. cerevisiae)", "cell division cycle 20 homolog (S. cerevisiae)"			7513050, 9353311	Standard	NM_001255		Approved	p55CDC, CDC20A	uc001cix.3	Q12834	OTTHUMG00000007420	ENST00000372462.1:c.591A>G	chr1.hg19:g.43825898A>G		80.0	0.0	.		100.0	50.0	.	NM_001255	B2R6Z6|D3DPJ1|Q5JUY4|Q9BW56|Q9UQI9	Silent	SNP	ENST00000372462.1	hg19	CCDS484.1																																																																																			.	.	.	none		0.517	CDC20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019488.1	NM_001255		G	43825898	A	G	43825898	2	3	7	1	0	0	0	0	0	0	0	1	3061	378	14	3		3	CDC20	1	43825898	Silent	SNP	A	TCGA-2Z-A9J7-01A-11D-A382-10	10533803	43825898	205424723	2	550											
PLK3	1263	hgsc.bcm.edu	37	chr1	45266511	45266511	+	Splice_Site	DEL	G	G	-																															cctgatgccccctcttcacaGgggggcttcgcccgctgcta																										TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr1:45266511delG	ENST00000372201.4	+	2	449		c.e2-1		PLK3_ENST00000465443.1_Splice_Site	NM_004073.2	NP_004064.2	Q9H4B4	PLK3_HUMAN	polo-like kinase 3						apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cytoplasmic microtubule organization (GO:0031122)|endomitotic cell cycle (GO:0007113)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|Golgi disassembly (GO:0090166)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G1/S transition checkpoint (GO:0044819)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process involved in cellular response to hypoxia (GO:2000777)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of cell division (GO:0051302)|regulation of cytokinesis (GO:0032465)|response to osmotic stress (GO:0006970)|response to radiation (GO:0009314)|response to reactive oxygen species (GO:0000302)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|Golgi stack (GO:0005795)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|large_intestine(2)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					CCTCTTCACAGGGGGGCTTCG	0.701																																					.		Atlas-Indel,Pindel	.											.	PLK3	41	.	0			c.211-2G>-						PASS	.						10	13	12					1																	45266511		2175	4262	6437	SO:0001630	splice_region_variant	1263	exon2			.	AJ293866	CCDS515.1	1p34.1	2013-01-18	2010-06-24	2004-01-28	ENSG00000173846	ENSG00000173846			2154	protein-coding gene	gene with protein product		602913	"cytokine-inducible kinase", "polo-like kinase 3 (Drosophila)"	CNK		8702627	Standard	NM_004073		Approved	FNK, PRK	uc001cmn.3	Q9H4B4	OTTHUMG00000008491	ENST00000372201.4:c.211-1G>-	chr1.hg19:g.45266511delG		90.0	0.0	0		69.0	34.0	0.492754	NM_004073	Q15767|Q5JR99|Q96CV1	Splice_Site	DEL	ENST00000372201.4	hg19	CCDS515.1																																																																																			.	.	.	none		0.701	PLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023429.1	NM_004073	Intron	-	45266511	G	-	45266511	8	5	7	1	0	1	0	1	0	0	1	0	12104	1014	35	0	216	0	PLK3	1	45266511	Splice_Site	DEL	G	TCGA-2Z-A9J7-01A-11D-A382-10	1440613	45266511	203984110	3	551											
PTGER3	5733	hgsc.bcm.edu	37	chr1	71512615	71512615	+	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	cgaagagctagtcccgttgcCccctcgcccggtgctgatga	6	8	12	15	4	0	3	0	2	0	1	2	4	1	3	4	1	3	3	4	1	2	2			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr1:71512615C>T	ENST00000306666.5	-	1	856	c.646G>A	c.(646-648)Ggc>Agc	p.G216S	PTGER3_ENST00000370932.2_Missense_Mutation_p.G216S|PTGER3_ENST00000370931.3_Missense_Mutation_p.G216S|ZRANB2-AS1_ENST00000450461.1_RNA|PTGER3_ENST00000356595.4_Missense_Mutation_p.G216S|PTGER3_ENST00000354608.5_Missense_Mutation_p.G216S|PTGER3_ENST00000414819.1_Missense_Mutation_p.G216S|PTGER3_ENST00000351052.5_Missense_Mutation_p.G216S|PTGER3_ENST00000370924.4_Missense_Mutation_p.G216S|PTGER3_ENST00000460330.1_Missense_Mutation_p.G216S	NM_198719.1	NP_942012.1	P43115	PE2R3_HUMAN	prostaglandin E receptor 3 (subtype EP3)	216					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)	GTCCCGTTGCCCCCTCGCCCG	0.647																																					p.G216S		Atlas-SNP	.											.	PTGER3	246	.	0			c.G646A						PASS	.						84	82	83					1																	71512615		2203	4300	6503	SO:0001583	missense	5733	exon1			CGTTGCCCCCTCG	X83863	CCDS652.1, CCDS655.1, CCDS656.1, CCDS657.1, CCDS658.1	1p31.2	2012-08-08			ENSG00000050628	ENSG00000050628		"GPCR / Class A : Prostanoid receptors"	9595	protein-coding gene	gene with protein product		176806				7759114, 9073510	Standard	NM_001126044		Approved	EP3	uc001dfo.3	P43115	OTTHUMG00000009399	ENST00000306666.5:c.646G>A	chr1.hg19:g.71512615C>T	ENSP00000302313:p.Gly216Ser	90.0	0.0	.		137.0	42.0	.	NM_001126044	B0AZN4|B1AK19|B5BUP5|O00326|Q12943|Q12944|Q12945|Q16546|Q5CZ59|Q5CZ61|Q5CZ62|Q5CZ63|Q5CZ64	Missense_Mutation	SNP	ENST00000306666.5	hg19	CCDS657.1	.	.	.	.	.	.	.	.	.	.	C	15.96	2.986926	0.53934	.	.	ENSG00000050628	ENST00000370931;ENST00000370932;ENST00000351052;ENST00000460330;ENST00000370934;ENST00000354608;ENST00000356595;ENST00000414819;ENST00000306666;ENST00000370924	T;T;T;T;T;T;T;T;T	0.70749	-0.51;-0.51;-0.51;-0.51;-0.51;-0.51;-0.51;-0.51;-0.51	5.1	3.19	0.36642	GPCR, rhodopsin-like superfamily (1);	0.214089	0.44902	D	0.000416	T	0.37210	0.0995	N	0.08118	0	0.30485	N	0.772003	P;B;P;P;P;B;B;B	0.52061	0.805;0.201;0.95;0.698;0.885;0.101;0.29;0.338	P;B;P;B;P;B;B;B	0.50440	0.492;0.26;0.641;0.393;0.492;0.12;0.185;0.282	T	0.28364	-1.0046	10	0.16420	T	0.52	-16.9936	9.9405	0.41578	0.0:0.7752:0.0:0.2248	.	216;216;216;216;216;216;216;216	Q147U0;Q6TTN3;F5H821;B1AK19;Q147X8;P43115-3;P43115-4;P43115	.;.;.;.;.;.;.;PE2R3_HUMAN	S	216	ENSP00000359969:G216S;ENSP00000359970:G216S;ENSP00000280208:G216S;ENSP00000418073:G216S;ENSP00000346624:G216S;ENSP00000349003:G216S;ENSP00000401423:G216S;ENSP00000302313:G216S;ENSP00000359962:G216S	ENSP00000302313:G216S	G	-	1	0	PTGER3	71285203	0.866000	0.29940	0.964000	0.40570	0.935000	0.57460	2.370000	0.44240	1.372000	0.46190	0.462000	0.41574	GGC	.	.	.	none		0.647	PTGER3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026076.1	NM_000957		T	71512615	C	T	71512615	3	4	7	1	0	0	0	0	1	0	0	0	12755	623	22	2	845	2	PTGER3	1	71512615	Missense_Mutation	SNP	C	TCGA-2Z-A9J7-01A-11D-A382-10	26246104	71512615	177738006	4	552											
FUBP1	8880	hgsc.bcm.edu	37	chr1	78432739	78432739	+	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	atcaagttacttactgaatcCaaccattccatctggaactt	13	13	4	11	0	2	1	1	1	1	0	4	2	4	2	3	1	4	1	3	1	6	4			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr1:78432739C>A	ENST00000370768.2	-	5	418	c.337G>T	c.(337-339)Gga>Tga	p.G113*	FUBP1_ENST00000436586.2_Nonsense_Mutation_p.G134*|FUBP1_ENST00000370767.1_Nonsense_Mutation_p.G113*	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1	113	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						TTACTGAATCCAACCATTCCA	0.274			"F, N"		oligodendroglioma																																p.G113X		Atlas-SNP	.		Rec	yes		1	1p13.1	8880	far upstream element (FUSE) binding protein 1		O	.	FUBP1	112	.	0			c.G337T						PASS	.						45	47	46					1																	78432739		2200	4293	6493	SO:0001587	stop_gained	8880	exon5			TGAATCCAACCAT	U05040	CCDS683.1	1p31.1	2008-02-05			ENSG00000162613	ENSG00000162613			4004	protein-coding gene	gene with protein product		603444		FUBP		8125259	Standard	XM_005271309		Approved	FBP	uc001dii.3	Q96AE4	OTTHUMG00000040799	ENST00000370768.2:c.337G>T	chr1.hg19:g.78432739C>A	ENSP00000359804:p.Gly113*	179.0	0.0	.		175.0	81.0	.	NM_003902	Q12828	Nonsense_Mutation	SNP	ENST00000370768.2	hg19	CCDS683.1	.	.	.	.	.	.	.	.	.	.	C	35	5.472734	0.96274	.	.	ENSG00000162613	ENST00000370773;ENST00000370767;ENST00000370768;ENST00000394922;ENST00000436586;ENST00000421641	.	.	.	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-15.1391	19.4544	0.94882	0.0:1.0:0.0:0.0	.	.	.	.	X	112;113;113;112;134;133	.	ENSP00000294623:G112X	G	-	1	0	FUBP1	78205327	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.776000	0.85560	2.669000	0.90835	0.591000	0.81541	GGA	.	.	.	none		0.274	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902		A	78432739	C	A	78432739	4	1	7	1	0	0	0	0	0	1	0	0	6099	603	21	4	1661	4	FUBP1	1	78432739	Nonsense_Mutation	SNP	C	TCGA-2Z-A9J7-01A-11D-A382-10	6920124	78432739	170817882	5	553											
CDC42BPA	8476	hgsc.bcm.edu	37	chr1	227268711	227268711	+	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	tacttaagttctcatacaaaGtagtaagctgaaagatagtt	16	13	7	5	0	1	2	1	1	1	1	2	2	1	2	0	0	3	5	0	0	8	8			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr1:227268711G>C	ENST00000366769.3	-	17	3654	c.2363C>G	c.(2362-2364)aCt>aGt	p.T788S	CDC42BPA_ENST00000535525.1_Missense_Mutation_p.T788S|CDC42BPA_ENST00000366767.3_Missense_Mutation_p.T707S|CDC42BPA_ENST00000488131.1_5'UTR|CDC42BPA_ENST00000366766.2_Missense_Mutation_p.T788S|CDC42BPA_ENST00000366764.2_Missense_Mutation_p.T788S|CDC42BPA_ENST00000366765.3_Missense_Mutation_p.T788S|CDC42BPA_ENST00000334218.5_Missense_Mutation_p.T788S	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)				CTCATACAAAGTAGTAAGCTG	0.368																																					p.T788S		Atlas-SNP	.											.	CDC42BPA	528	.	0			c.C2363G						PASS	.						141	128	132					1																	227268711		2203	4300	6503	SO:0001583	missense	8476	exon17			TACAAAGTAGTAA	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.2363C>G	chr1.hg19:g.227268711G>C	ENSP00000355731:p.Thr788Ser	78.0	0.0	.		82.0	40.0	.	NM_003607		Missense_Mutation	SNP	ENST00000366769.3	hg19	CCDS1558.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.006|0.006	-2.071546|-2.071546	0.00379|0.00379	.|.	.|.	ENSG00000143776|ENSG00000143776	ENST00000366769;ENST00000366767;ENST00000334218;ENST00000366766;ENST00000366764;ENST00000366762;ENST00000535525;ENST00000366765|ENST00000442054	T;T;T;T;T;T;T|.	0.64085|.	0.0;-0.01;-0.01;0.01;-0.08;-0.04;0.01|.	5.49|5.49	2.62|2.62	0.31277|0.31277	.|.	0.580520|.	0.20021|.	N|.	0.100917|.	T|.	0.16428|.	0.0395|.	N|N	0.03154|0.03154	-0.405|-0.405	0.09310|0.09310	N|N	1|1	B;B;B;B;B|.	0.10296|.	0.003;0.001;0.0;0.0;0.0|.	B;B;B;B;B|.	0.09377|.	0.004;0.002;0.001;0.001;0.0|.	T|.	0.25813|.	-1.0121|.	10|.	0.02654|.	T|.	1|.	.|.	10.8933|10.8933	0.47008|0.47008	0.2036:0.0:0.7964:0.0|0.2036:0.0:0.7964:0.0	.|.	788;788;707;788;788|.	F5H5N0;Q5VT25-4;Q5VT25-3;Q5VT25-5;Q5VT25-2|.	.;.;.;.;.|.	S|X	788;707;788;788;788;52;788;788|81	ENSP00000355731:T788S;ENSP00000355729:T707S;ENSP00000335341:T788S;ENSP00000355728:T788S;ENSP00000355726:T788S;ENSP00000443275:T788S;ENSP00000355727:T788S|.	ENSP00000335341:T788S|.	T|Y	-|-	2|3	0|2	CDC42BPA|CDC42BPA	225335334|225335334	0.950000|0.950000	0.32346|0.32346	0.001000|0.001000	0.08648|0.08648	0.197000|0.197000	0.23852|0.23852	2.806000|2.806000	0.47947|0.47947	0.288000|0.288000	0.22398|0.22398	-0.216000|-0.216000	0.12614|0.12614	ACT|TAC	.	.	.	none		0.368	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826		C	227268711	G	C	227268711	3	2	7	1	0	0	0	0	1	0	0	0	3074	1029	36	4	2876	4	CDC42BPA	1	227268711	Missense_Mutation	SNP	G	TCGA-2Z-A9J7-01A-11D-A382-10	148835972	227268711	21981910	6	554											
TTC15	51112	hgsc.bcm.edu	37	chr2	3392180	3392180	+	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	accgaggggcgccccgaaccCgtggccatgcgagggcccca	7	2	15	17	5	0	0	0	0	0	0	0	3	0	0	7	4	2	0	7	4	1	0			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr2:3392180C>G	ENST00000324266.5	+	2	981	c.786C>G	c.(784-786)ccC>ccG	p.P262P	TRAPPC12_ENST00000382110.2_Silent_p.P262P	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	262					vesicle-mediated transport (GO:0016192)												GCCCCGAACCCGTGGCCATGC	0.736																																					p.P262P		Atlas-SNP	.											.	.	.	.	0			c.C786G						PASS	.						8	10	9					2																	3392180		2160	4207	6367	SO:0001819	synonymous_variant	51112	exon2			CGAACCCGTGGCC	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.786C>G	chr2.hg19:g.3392180C>G		111.0	0.0	.		127.0	55.0	.	NM_016030	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Silent	SNP	ENST00000324266.5	hg19	CCDS1652.1																																																																																			.	.	.	none		0.736	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030		G	3392180	C	G	3392180	2	3	7	1	0	0	0	0	0	0	0	1	16694	639	23	4		4	TTC15	2	3392180	Silent	SNP	C	TCGA-2Z-A9J7-01A-11D-A382-10		3392180	239807193	7	555											
EGR4	1961	hgsc.bcm.edu	37	chr2	73519561	73519561	+	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	agggggcacccgcgcaaggcGaggcctcccagaacgcctct	8	3	14	16	4	1	1	0	0	1	1	2	2	2	1	4	4	1	2	4	4	2	0			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr2:73519561G>C	ENST00000545030.1	-	2	868	c.794C>G	c.(793-795)tCg>tGg	p.S265W	EGR4_ENST00000436467.2_Missense_Mutation_p.S162W	NM_001965.3	NP_001956.3	Q05215	EGR4_HUMAN	early growth response 4	265	Pro-rich.				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						CGCGCAAGGCGAGGCCTCCCA	0.721																																					p.S265W		Atlas-SNP	.											.	EGR4	52	.	0			c.C794G						PASS	.						8	11	10					2																	73519561		2169	4251	6420	SO:0001583	missense	1961	exon2			CAAGGCGAGGCCT		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.794C>G	chr2.hg19:g.73519561G>C	ENSP00000445626:p.Ser265Trp	105.0	0.0	.		106.0	50.0	.	NM_001965	B2RAE3|G3V1T5|Q2Z1P5	Missense_Mutation	SNP	ENST00000545030.1	hg19	CCDS1925.2	.	.	.	.	.	.	.	.	.	.	G	11.04	1.521481	0.27211	.	.	ENSG00000135625	ENST00000545030;ENST00000436467	T;T	0.15603	2.41;2.75	4.39	4.39	0.52855	.	0.663371	0.14050	N	0.344855	T	0.24236	0.0587	N	0.24115	0.695	0.43122	D	0.994847	D;D	0.63880	0.988;0.993	P;D	0.63703	0.828;0.917	T	0.02263	-1.1186	10	0.87932	D	0	-8.1456	9.4657	0.38811	0.0984:0.0:0.9016:0.0	.	162;265	Q05215;G3V1T5	EGR4_HUMAN;.	W	265;162	ENSP00000445626:S265W;ENSP00000419687:S162W	ENSP00000419687:S162W	S	-	2	0	EGR4	73373069	0.112000	0.22096	0.985000	0.45067	0.221000	0.24807	1.161000	0.31773	2.267000	0.75376	0.555000	0.69702	TCG	.	.	.	none		0.721	EGR4-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001965		C	73519561	G	C	73519561	3	2	7	1	0	0	0	0	1	0	0	0	4976	1059	37	4	979	4	EGR4	2	73519561	Missense_Mutation	SNP	G	TCGA-2Z-A9J7-01A-11D-A382-10	70127381	73519561	169679812	8	556											
SPEG	10290	hgsc.bcm.edu	37	chr2	220299815	220299815	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcggggctcctgtggccgTggccggggcgccagtcttcc	1	7	18	15	5	1	0	0	0	1	0	3	0	3	0	5	7	0	1	5	7	0	1	rs565137573	byFrequency	TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr2:220299815T>C	ENST00000312358.7	+	1	248	c.116T>C	c.(115-117)gTg>gCg	p.V39A		NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	39					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)		CCTGTGGCCGTGGCCGGGGCG	0.781													T|||	43	0.00858626	0.0287	0.0072	5008	,	,		10028	0		0	False		,,,				2504	0				p.V39A		Atlas-SNP	.											SPEG,brain,glioma,0,1	SPEG	272	.	0			c.T116C						PASS	.						1	2	2					2																	220299815		898	2387	3285	SO:0001583	missense	10290	exon1			TGGCCGTGGCCGG	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.116T>C	chr2.hg19:g.220299815T>C	ENSP00000311684:p.Val39Ala	4.0	2.0	.		9.0	4.0	.	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	hg19	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	T	3.599	-0.081974	0.07141	.	.	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.63913	-0.07	3.19	-3.42	0.04825	Immunoglobulin-like fold (1);	0.959955	0.08421	N	0.948317	T	0.30070	0.0753	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25847	-1.0120	10	0.05436	T	0.98	.	4.6272	0.12484	0.0:0.2917:0.4213:0.2871	.	39	Q15772	SPEG_HUMAN	A	39	ENSP00000311684:V39A	ENSP00000265327:V39A	V	+	2	0	SPEG	220008059	0.000000	0.05858	0.071000	0.20095	0.324000	0.28378	-2.176000	0.01262	-1.212000	0.02620	0.460000	0.39030	GTG	.	.	.	none		0.781	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		C	220299815	T	C	220299815	3	2	7	1	0	0	0	0	1	0	0	0	15048	1696	59	3	118	3	SPEG	2	220299815	Missense_Mutation	SNP	T	TCGA-2Z-A9J7-01A-11D-A382-10	146780254	220299815	22899558	9	557											
PET112L	5188	hgsc.bcm.edu	37	chr4	152622569	152622569	+	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	ggagctccgggagtgtctccCgaatctggtcaatattgatc	8	11	12	10	2	3	1	1	1	2	0	6	4	4	3	2	3	1	1	2	3	3	2	rs199827552		TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr4:152622569C>A	ENST00000515812.1	-	8	1002	c.986G>T	c.(985-987)cGg>cTg	p.R329L	PET112_ENST00000263985.6_Missense_Mutation_p.R370L																breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	23						GAGTGTCTCCCGAATCTGGTC	0.557																																					p.R370L		Atlas-SNP	.											.	PET112	43	.	0			c.G1109T						PASS	.						72	68	69					4																	152622569		2203	4300	6503	SO:0001583	missense	5188	exon9			GTCTCCCGAATCT																												ENST00000515812.1:c.986G>T	chr4.hg19:g.152622569C>A	ENSP00000426859:p.Arg329Leu	86.0	0.0	.		122.0	58.0	.	NM_004564		Missense_Mutation	SNP	ENST00000515812.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.72	2.321005	0.41096	.	.	ENSG00000059691	ENST00000263985;ENST00000515812	T;T	0.50548	0.76;0.74	5.7	5.7	0.88788	.	0.226336	0.38720	N	0.001597	T	0.49712	0.1573	M	0.80982	2.52	0.80722	D	1	B	0.30914	0.3	B	0.22601	0.04	T	0.54774	-0.8243	10	0.66056	D	0.02	-18.6049	13.5076	0.61493	0.0:0.9194:0.0:0.0805	.	370	O75879	GATB_HUMAN	L	370;329	ENSP00000263985:R370L;ENSP00000426859:R329L	ENSP00000263985:R370L	R	-	2	0	PET112	152842019	0.876000	0.30132	0.835000	0.33067	0.365000	0.29674	1.675000	0.37555	2.679000	0.91253	0.650000	0.86243	CGG	.	C|0.999;T|0.001	.	alt		0.557	PET112-002	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365672.1			A	152622569	C	A	152622569	3	1	7	1	0	0	0	0	1	0	0	0	11741	652	23	4	584	4	PET112L	4	152622569	Missense_Mutation	SNP	C	TCGA-2Z-A9J7-01A-11D-A382-10		152622569	38531707	10	558											
ZNF622	90441	hgsc.bcm.edu	37	chr5	16465654	16465654	+	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	gaagccctcggcggtcactgGggccatgctggccaccttcc	5	7	13	16	2	1	0	1	0	0	0	3	1	2	0	5	5	2	1	5	5	1	1			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr5:16465654G>A	ENST00000308683.2	-	1	247	c.121C>T	c.(121-123)Cca>Tca	p.P41S		NM_033414.2	NP_219482.1	Q969S3	ZN622_HUMAN	zinc finger protein 622	41					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						GCGGTCACTGGGGCCATGCTG	0.682																																					p.P41S		Atlas-SNP	.											.	ZNF622	49	.	0			c.C121T						PASS	.						33	34	34					5																	16465654		2203	4298	6501	SO:0001583	missense	90441	exon1			TCACTGGGGCCAT	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.121C>T	chr5.hg19:g.16465654G>A	ENSP00000310042:p.Pro41Ser	137.0	0.0	.		128.0	54.0	.	NM_033414		Missense_Mutation	SNP	ENST00000308683.2	hg19	CCDS3886.1	.	.	.	.	.	.	.	.	.	.	G	33	5.267658	0.95399	.	.	ENSG00000173545	ENST00000308683	.	.	.	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.79992	0.4542	M	0.76838	2.35	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.80448	-0.1378	9	0.46703	T	0.11	-4.253	18.4546	0.90715	0.0:0.0:1.0:0.0	.	41	Q969S3	ZN622_HUMAN	S	41	.	ENSP00000310042:P41S	P	-	1	0	ZNF622	16518654	1.000000	0.71417	0.995000	0.50966	0.872000	0.50106	9.482000	0.97935	2.576000	0.86940	0.650000	0.86243	CCA	.	.	.	none		0.682	ZNF622-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207105.1	NM_033414		A	16465654	G	A	16465654	3	1	7	1	0	0	0	0	1	0	0	0	18058	1232	43	2	1336	2	ZNF622	5	16465654	Missense_Mutation	SNP	G	TCGA-2Z-A9J7-01A-11D-A382-10		16465654	164449606	11	559											
PPAP2A	8611	hgsc.bcm.edu	37	chr5	54771139	54771139	+	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	taacttacaacgataatactGaatggaatgattattccacc	16	12	5	8	1	0	2	0	2	0	0	1	4	1	3	2	1	4	0	2	1	8	6			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr5:54771139G>A	ENST00000307259.8	-	2	618	c.198C>T	c.(196-198)ttC>ttT	p.F66F	PPAP2A_ENST00000515132.1_Intron|PPAP2A_ENST00000264775.5_Intron	NM_003711.2	NP_003702.2	O14494	LPP1_HUMAN	phosphatidic acid phosphatase type 2A	66					androgen receptor signaling pathway (GO:0030521)|germ cell migration (GO:0008354)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|lipid metabolic process (GO:0006629)|negative regulation of cell proliferation (GO:0008285)|phospholipid dephosphorylation (GO:0046839)|protein dephosphorylation (GO:0006470)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of lipid metabolic process (GO:0019216)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidate phosphatase activity (GO:0008195)			breast(2)|endometrium(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	9		Lung NSC(810;4.08e-05)|Prostate(74;0.0181)|Breast(144;0.0544)				CGATAATACTGAATGGAATGA	0.348																																					p.F66F		Atlas-SNP	.											.	PPAP2A	42	.	0			c.C198T						PASS	.						119	111	114					5																	54771139		2203	4300	6503	SO:0001819	synonymous_variant	8611	exon2			AATACTGAATGGA	AB000888	CCDS34159.1, CCDS34160.1	5q11	2009-05-27			ENSG00000067113	ENSG00000067113	3.1.3.4		9228	protein-coding gene	gene with protein product		607124				9305923	Standard	NM_003711		Approved	PAP-2a, LPP1	uc003jpz.4	O14494	OTTHUMG00000162240	ENST00000307259.8:c.198C>T	chr5.hg19:g.54771139G>A		134.0	0.0	.		113.0	50.0	.	NM_003711	B7ZKN8|G3XA95|O60457|O60463|Q17RZ4	Silent	SNP	ENST00000307259.8	hg19	CCDS34159.1																																																																																			.	.	.	none		0.348	PPAP2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368073.1			A	54771139	G	A	54771139	2	1	7	1	0	0	0	0	0	0	0	1	12297	1281	45	2		2	PPAP2A	5	54771139	Silent	SNP	G	TCGA-2Z-A9J7-01A-11D-A382-10	38305485	54771139	126144121	12	560											
CMYA5	202333	hgsc.bcm.edu	37	chr5	79033639	79033639	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaaaaagttaccccattgaaAgaaaataaacaaaaggaaac	24	5	6	6	0	0	2	0	1	0	1	0	4	0	3	2	1	3	1	2	1	11	3			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr5:79033639A>G	ENST00000446378.2	+	2	9082	c.9051A>G	c.(9049-9051)aaA>aaG	p.K3017K		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	3017					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)		CCCCATTGAAAGAAAATAAAC	0.348																																					p.K3017K		Atlas-SNP	.											.	CMYA5	643	.	0			c.A9051G						PASS	.						44	43	44					5																	79033639		1804	4068	5872	SO:0001819	synonymous_variant	202333	exon2			ATTGAAAGAAAAT	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.9051A>G	chr5.hg19:g.79033639A>G		318.0	0.0	.		396.0	189.0	.	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Silent	SNP	ENST00000446378.2	hg19	CCDS47238.1																																																																																			.	.	.	none		0.348	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		G	79033639	A	G	79033639	2	3	7	1	0	0	0	0	0	0	0	1	3592	69	3	3		3	CMYA5	5	79033639	Silent	SNP	A	TCGA-2Z-A9J7-01A-11D-A382-10	24262500	79033639	101881621	13	561											
PCDHGC4	56098	hgsc.bcm.edu	37	chr5	140865299	140865299	+	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	tggatgtgaagaagcgcagcGacggcagcctggtcccagag	10	5	16	10	3	0	3	0	1	0	2	1	5	1	4	2	3	3	2	2	3	2	0			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr5:140865299G>A	ENST00000306593.1	+	1	559	c.559G>A	c.(559-561)Gac>Aac	p.D187N	PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA7_ENST00000518325.1_Intron	NM_018928.2|NM_032406.1	NP_061751.1|NP_115782.1	Q9Y5F7	PCDGL_HUMAN	protocadherin gamma subfamily C, 4	187	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(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(13)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	42			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAAGCGCAGCGACGGCAGCCT	0.557																																					p.D187N		Atlas-SNP	.											.	PCDHGC4	91	.	0			c.G559A						PASS	.						39	43	42					5																	140865299		2203	4300	6503	SO:0001583	missense	56098	exon1			CGCAGCGACGGCA	AF152525	CCDS4262.1, CCDS75349.1	5q31	2010-01-26			ENSG00000242419	ENSG00000242419		"Cadherins / Protocadherins : Clustered"	8717	other	protocadherin		606305				10380929	Standard	NM_018928		Approved	PCDH-GAMMA-C4		Q9Y5F7	OTTHUMG00000129625	ENST00000306593.1:c.559G>A	chr5.hg19:g.140865299G>A	ENSP00000306918:p.Asp187Asn	67.0	0.0	.		76.0	44.0	.	NM_018928	Q495T2|Q9Y5C3	Missense_Mutation	SNP	ENST00000306593.1	hg19	CCDS4262.1	.	.	.	.	.	.	.	.	.	.	G	17.19	3.325972	0.60743	.	.	ENSG00000242419	ENST00000306593	T	0.19938	2.11	5.0	5.0	0.66597	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.44603	0.1301	M	0.70275	2.135	0.30765	N	0.7436	D;D	0.89917	1.0;0.985	D;P	0.81914	0.995;0.804	T	0.42783	-0.9431	9	0.48119	T	0.1	.	12.8602	0.57910	0.0779:0.0:0.9221:0.0	.	187;187	Q9Y5F7-2;Q9Y5F7	.;PCDGL_HUMAN	N	187	ENSP00000306918:D187N	ENSP00000306918:D187N	D	+	1	0	PCDHGC4	140845483	0.986000	0.35501	1.000000	0.80357	0.998000	0.95712	3.383000	0.52471	2.596000	0.87737	0.561000	0.74099	GAC	.	.	.	none		0.557	PCDHGC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251820.1	NM_018928		A	140865299	G	A	140865299	3	1	7	1	0	0	0	0	1	0	0	0	11577	1058	37	1	561	1	PCDHGC4	5	140865299	Missense_Mutation	SNP	G	TCGA-2Z-A9J7-01A-11D-A382-10	61831660	140865299	40049961	14	562											
JAKMIP2	9832	hgsc.bcm.edu	37	chr5	147028036	147028036	+	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	tcttttgatttcttcgcaaaTcctacaaagaaaaattaaaa	17	14	3	7	1	2	2	0	1	2	1	4	2	3	2	1	0	1	1	1	0	7	6			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr5:147028036T>A	ENST00000265272.5	-	5	1306	c.839A>T	c.(838-840)gAt>gTt	p.D280V	JAKMIP2_ENST00000333010.6_Splice_Site_p.D238V|JAKMIP2_ENST00000507386.1_Splice_Site_p.D280V	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2	280						Golgi apparatus (GO:0005794)				NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTTCGCAAATCCTACAAAGA	0.323																																					p.D280V		Atlas-SNP	.											.	JAKMIP2	154	.	0			c.A839T						PASS	.						127	122	124					5																	147028036		2202	4294	6496	SO:0001630	splice_region_variant	9832	exon5			CGCAAATCCTACA	AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049			29067	protein-coding gene	gene with protein product		611197				9628581	Standard	NM_001270941		Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.838-1A>T	chr5.hg19:g.147028036T>A		89.0	0.0	.		71.0	30.0	.	NM_001270941	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Missense_Mutation	SNP	ENST00000265272.5	hg19	CCDS4285.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.352623	0.82132	.	.	ENSG00000176049	ENST00000507386;ENST00000265272;ENST00000333010;ENST00000539401	T;T;T	0.34072	1.38;1.38;1.38	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.60792	0.2296	M	0.75615	2.305	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.80764	0.994;0.994;0.994;0.994	T	0.65730	-0.6097	10	0.87932	D	0	.	15.5322	0.75974	0.0:0.0:0.0:1.0	.	238;280;280;280	B4DSG0;Q96AA8-3;G5E9Y0;Q96AA8	.;.;.;JKIP2_HUMAN	V	280;280;238;280	ENSP00000421398:D280V;ENSP00000265272:D280V;ENSP00000328989:D238V	ENSP00000265272:D280V	D	-	2	0	JAKMIP2	147008229	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	5.481000	0.66826	2.127000	0.65507	0.482000	0.46254	GAT	.	.	.	none		0.323	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790	Missense_Mutation	A	147028036	T	A	147028036	5	1	7	1	0	0	0	0	0	0	1	0	7948	1449	50	5	1661	5	JAKMIP2	5	147028036	Splice_Site	SNP	T	TCGA-2Z-A9J7-01A-11D-A382-10	6162737	147028036	33887224	15	563											
PEX6	5190	hgsc.bcm.edu	37	chr6	42946507	42946507	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcactgggagggtctctcCgcgcctcaccagcagcggcc	5	5	15	16	3	2	0	1	0	1	0	4	1	3	1	4	4	2	2	4	4	0	0			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr6:42946507C>T	ENST00000304611.8	-	1	451	c.382G>A	c.(382-384)Gga>Aga	p.G128R	PEX6_ENST00000244546.4_Missense_Mutation_p.G128R	NM_000287.3	NP_000278.3	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	128					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)			AGGGTCTCTCCGCGCCTCACC	0.761																																					p.G128R		Atlas-SNP	.											.	PEX6	44	.	0			c.G382A						PASS	.						2	3	3					6																	42946507		1580	3280	4860	SO:0001583	missense	5190	exon1			TCTCTCCGCGCCT	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.382G>A	chr6.hg19:g.42946507C>T	ENSP00000303511:p.Gly128Arg	16.0	0.0	.		25.0	14.0	.	NM_000287	Q5T8W1|Q8WYQ0|Q8WYQ1|Q8WYQ2|Q99476	Missense_Mutation	SNP	ENST00000304611.8	hg19	CCDS4877.1	.	.	.	.	.	.	.	.	.	.	C	17.37	3.372469	0.61624	.	.	ENSG00000124587	ENST00000304611;ENST00000244546	D;D	0.98090	-4.15;-4.71	4.89	4.89	0.63831	.	0.000000	0.44902	D	0.000405	D	0.96012	0.8701	N	0.19112	0.55	0.42599	D	0.993279	D	0.71674	0.998	P	0.58077	0.832	D	0.96930	0.9680	10	0.87932	D	0	-9.8384	15.434	0.75129	0.0:1.0:0.0:0.0	.	128	Q13608	PEX6_HUMAN	R	128	ENSP00000303511:G128R;ENSP00000244546:G128R	ENSP00000244546:G128R	G	-	1	0	PEX6	43054485	1.000000	0.71417	0.998000	0.56505	0.027000	0.11550	2.230000	0.42999	2.709000	0.92574	0.650000	0.86243	GGA	.	.	.	none		0.761	PEX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040569.1	NM_000287		T	42946507	C	T	42946507	3	4	7	1	0	0	0	0	1	0	0	0	11757	661	23	1	2628	1	PEX6	6	42946507	Missense_Mutation	SNP	C	TCGA-2Z-A9J7-01A-11D-A382-10		42946507	128168560	16	564											
MICAL1	64780	hgsc.bcm.edu	37	chr6	109771667	109771667	+	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	tagtttcccgagcttgccatGggtggcaaagtcagcagctg	8	10	13	10	1	1	0	1	0	0	0	2	1	2	0	2	2	4	5	2	2	2	3			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr6:109771667G>T	ENST00000358807.3	-	8	1338	c.1027C>A	c.(1027-1029)Cat>Aat	p.H343N	MICAL1_ENST00000358577.3_Intron|MICAL1_ENST00000368952.4_Missense_Mutation_p.H362N|MICAL1_ENST00000483856.1_5'Flank	NM_022765.3	NP_073602.3	Q8TDZ2	MICA1_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 1	343	Monooxygenase domain. {ECO:0000250}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of protein phosphorylation (GO:0001933)|oxidation-reduction process (GO:0055114)|signal transduction (GO:0007165)|sulfur oxidation (GO:0019417)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|liver(1)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0142)|all cancers(137;0.0197)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)|BRCA - Breast invasive adenocarcinoma(108;0.0574)		AGCTTGCCATGGGTGGCAAAG	0.597																																					p.H343N		Atlas-SNP	.											.	MICAL1	79	.	0			c.C1027A						PASS	.						41	41	41					6																	109771667		2203	4300	6503	SO:0001583	missense	64780	exon8			TGCCATGGGTGGC	AB048948	CCDS5076.1, CCDS55047.1	6q21	2013-03-26	2013-03-26	2005-02-16	ENSG00000135596	ENSG00000135596			20619	protein-coding gene	gene with protein product		607129	"NEDD9 interacting protein with calponin homology and LIM domains"	NICAL		11827972	Standard	NM_022765		Approved	MICAL, FLJ11937, DKFZp434B1517, FLJ21739	uc003ptk.3	Q8TDZ2	OTTHUMG00000015350	ENST00000358807.3:c.1027C>A	chr6.hg19:g.109771667G>T	ENSP00000351664:p.His343Asn	130.0	0.0	.		114.0	5.0	.	NM_022765	B7Z3R5|E1P5F0|Q7Z633|Q8IVS9|Q96G47|Q9H6X6|Q9H7I0|Q9HAA1|Q9UFF7	Missense_Mutation	SNP	ENST00000358807.3	hg19	CCDS5076.1	.	.	.	.	.	.	.	.	.	.	G	0.321	-0.961904	0.02249	.	.	ENSG00000135596	ENST00000358807;ENST00000368952	T;T	0.11495	2.77;2.77	4.5	1.46	0.22682	.	0.762737	0.12285	N	0.482545	T	0.00815	0.0027	N	0.00793	-1.18	0.50813	D	0.999894	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.50276	-0.8847	10	0.02654	T	1	.	11.6301	0.51168	0.0:0.0:0.3423:0.6577	.	362;343	B7Z3R5;Q8TDZ2	.;MICA1_HUMAN	N	343;362	ENSP00000351664:H343N;ENSP00000357948:H362N	ENSP00000351664:H343N	H	-	1	0	MICAL1	109878360	1.000000	0.71417	0.292000	0.24919	0.914000	0.54420	1.139000	0.31504	0.159000	0.19401	0.563000	0.77884	CAT	.	.	.	none		0.597	MICAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041759.2	NM_022765		T	109771667	G	T	109771667	3	4	7	1	0	0	0	0	1	0	0	0	9576	1348	47	4	2248	4	MICAL1	6	109771667	Missense_Mutation	SNP	G	TCGA-2Z-A9J7-01A-11D-A382-10	66825160	109771667	61343400	17	565											
ITGB8	3696	hgsc.bcm.edu	37	chr7	20403321	20403321	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtgccttgcgctgggtccAgaatgtggatggtgtgttca	6	12	16	7	1	1	1	1	0	0	1	2	2	2	2	2	4	2	2	2	4	1	2			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr7:20403321A>G	ENST00000222573.4	+	2	873	c.189A>G	c.(187-189)ccA>ccG	p.P63P	ITGB8_ENST00000537992.1_5'UTR	NM_002214.2	NP_002205.1	P26012	ITB8_HUMAN	integrin, beta 8	63					cartilage development (GO:0051216)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|ganglioside metabolic process (GO:0001573)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of gene expression (GO:0010629)|placenta blood vessel development (GO:0060674)|positive regulation of gene expression (GO:0010628)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	extracellular matrix protein binding (GO:1990430)|receptor activity (GO:0004872)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(4)|stomach(2)|urinary_tract(1)	37						CGCTGGGTCCAGAATGTGGAT	0.398																																					p.P63P		Atlas-SNP	.											.	ITGB8	159	.	0			c.A189G						PASS	.						70	62	65					7																	20403321		2203	4299	6502	SO:0001819	synonymous_variant	3696	exon2			GGGTCCAGAATGT		CCDS5370.1	7p15.3	2010-03-23			ENSG00000105855	ENSG00000105855		"Integrins"	6163	protein-coding gene	gene with protein product		604160					Standard	XM_005249751		Approved		uc003suu.3	P26012	OTTHUMG00000023594	ENST00000222573.4:c.189A>G	chr7.hg19:g.20403321A>G		64.0	0.0	.		136.0	36.0	.	NM_002214	A4D133|B4DHD4	Silent	SNP	ENST00000222573.4	hg19	CCDS5370.1																																																																																			.	.	.	none		0.398	ITGB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059915.3	NM_002214		G	20403321	A	G	20403321	2	3	7	1	0	0	0	0	0	0	0	1	7908	175	7	3		3	ITGB8	7	20403321	Silent	SNP	A	TCGA-2Z-A9J7-01A-11D-A382-10		20403321	138735342	18	566											
KLHL7	55975	hgsc.bcm.edu	37	chr7	23145688	23145688	+	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	agagcagcaagaagaagaccGagaagaaacttgctgctcgg	16	4	13	8	2	0	6	0	0	0	6	1	7	0	6	1	1	5	4	1	1	5	1			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr7:23145688G>A	ENST00000339077.5	+	1	286	c.43G>A	c.(43-45)Gag>Aag	p.E15K	KLHL7_ENST00000322275.5_Missense_Mutation_p.E15K|KLHL7_ENST00000539124.1_5'UTR|KLHL7_ENST00000410047.1_5'Flank|KLHL7_ENST00000479288.1_3'UTR|KLHL7_ENST00000542558.1_5'UTR|KLHL7_ENST00000409689.1_5'Flank|KLHL7_ENST00000545771.1_5'Flank|KLHL7_ENST00000322231.7_5'UTR|KLHL7-AS1_ENST00000419813.1_lincRNA	NM_001031710.2	NP_001026880.2	Q8IXQ5	KLHL7_HUMAN	kelch-like family member 7	15					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						GAAGAAGACCGAGAAGAAACT	0.602																																					p.E15K		Atlas-SNP	.											.	KLHL7	102	.	0			c.G43A						PASS	.						60	49	53					7																	23145688		2202	4300	6502	SO:0001583	missense	55975	exon1			AAGACCGAGAAGA		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.43G>A	chr7.hg19:g.23145688G>A	ENSP00000343273:p.Glu15Lys	82.0	0.0	.		160.0	41.0	.	NM_001172428	A4D144|B7Z5I9|G5E9G3|Q7Z765|Q96MV2|Q9BQF8|Q9UDQ9	Missense_Mutation	SNP	ENST00000339077.5	hg19	CCDS34609.1	.	.	.	.	.	.	.	.	.	.	G	19.60	3.858661	0.71834	.	.	ENSG00000122550	ENST00000538858;ENST00000536369;ENST00000339077;ENST00000322275	T;T	0.73363	-0.52;-0.74	4.87	3.99	0.46301	.	0.059372	0.64402	D	0.000003	T	0.62073	0.2398	N	0.08118	0	0.80722	D	1	D;D	0.56521	0.976;0.964	P;P	0.50825	0.651;0.458	T	0.61332	-0.7084	10	0.23302	T	0.38	.	13.4923	0.61402	0.0757:0.0:0.9243:0.0	.	15;15	Q8IXQ5;Q8IXQ5-3	KLHL7_HUMAN;.	K	15	ENSP00000343273:E15K;ENSP00000323270:E15K	ENSP00000323270:E15K	E	+	1	0	KLHL7	23112213	1.000000	0.71417	0.956000	0.39512	0.600000	0.36913	5.114000	0.64648	1.409000	0.46915	0.591000	0.81541	GAG	.	.	.	none		0.602	KLHL7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326860.3	NM_018846		A	23145688	G	A	23145688	3	1	7	1	0	0	0	0	1	0	0	0	8401	1059	37	1	45	1	KLHL7	7	23145688	Missense_Mutation	SNP	G	TCGA-2Z-A9J7-01A-11D-A382-10	2742367	23145688	135992975	19	567											
GRM3	2913	hgsc.bcm.edu	37	chr7	86469144	86469144	+	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	tcaacgaagctaagttcataGgttttaccatgtacaccacg	13	11	7	10	2	2	0	2	0	0	0	2	1	2	0	2	1	4	4	2	1	6	6			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr7:86469144G>A	ENST00000361669.2	+	4	3413	c.2314G>A	c.(2314-2316)Ggt>Agt	p.G772S	GRM3_ENST00000394720.2_Intron|GRM3_ENST00000546348.1_Missense_Mutation_p.G364S|GRM3_ENST00000439827.1_Intron|GRM3_ENST00000536043.1_Missense_Mutation_p.G644S	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3	772					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)					TAAGTTCATAGGTTTTACCAT	0.418																																					p.G772S	GBM(52;969 1098 3139 52280)	Atlas-SNP	.											.	GRM3	237	.	0			c.G2314A						PASS	.						124	113	117					7																	86469144		2203	4300	6503	SO:0001583	missense	2913	exon4			TTCATAGGTTTTA		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.2314G>A	chr7.hg19:g.86469144G>A	ENSP00000355316:p.Gly772Ser	74.0	0.0	.		183.0	35.0	.	NM_000840	Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Missense_Mutation	SNP	ENST00000361669.2	hg19	CCDS5600.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.573564	0.86542	.	.	ENSG00000198822	ENST00000361669;ENST00000546348;ENST00000536043	D;D;D	0.89050	-2.46;-2.46;-2.46	5.54	5.54	0.83059	GPCR, family 3, conserved site (1);GPCR, family 3, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.94512	0.8233	M	0.78916	2.43	0.80722	D	1	D;D;D	0.76494	0.999;0.994;0.995	D;D;D	0.75484	0.986;0.965;0.979	D	0.94683	0.7867	10	0.66056	D	0.02	.	18.4662	0.90755	0.0:0.0:1.0:0.0	.	364;644;772	B7Z204;F5GYZ2;Q14832	.;.;GRM3_HUMAN	S	772;364;644	ENSP00000355316:G772S;ENSP00000444064:G364S;ENSP00000441407:G644S	ENSP00000355316:G772S	G	+	1	0	GRM3	86307080	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.869000	0.99810	2.603000	0.88011	0.563000	0.77884	GGT	.	.	.	none		0.418	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253362.2			A	86469144	G	A	86469144	3	1	7	1	0	0	0	0	1	0	0	0	6805	1000	35	2	2324	2	GRM3	7	86469144	Missense_Mutation	SNP	G	TCGA-2Z-A9J7-01A-11D-A382-10	63323456	86469144	72669519	20	568											
MUC17	140453	hgsc.bcm.edu	37	chr7	100681533	100681533	+	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	aactcttagtgaaggaacgaCtccattaacaagtatacctg	15	10	7	9	1	1	1	0	1	1	0	2	3	2	2	2	1	4	1	2	1	8	4			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr7:100681533C>A	ENST00000306151.4	+	3	6900	c.6836C>A	c.(6835-6837)aCt>aAt	p.T2279N		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2279	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					GAAGGAACGACTCCATTAACA	0.478																																					p.T2279N		Atlas-SNP	.											.	MUC17	804	.	0			c.C6836A						PASS	.																																			SO:0001583	missense	140453	exon3			GAACGACTCCATT	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.6836C>A	chr7.hg19:g.100681533C>A	ENSP00000302716:p.Thr2279Asn	94.0	0.0	.		217.0	10.0	.	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	2.491	-0.317530	0.05386	.	.	ENSG00000169876	ENST00000306151	T	0.02472	4.28	0.762	0.762	0.18454	.	.	.	.	.	T	0.03390	0.0098	N	0.19112	0.55	0.09310	N	1	P	0.51933	0.949	P	0.51297	0.665	T	0.49679	-0.8914	9	0.35671	T	0.21	.	6.9517	0.24548	0.0:0.9999:0.0:1.0E-4	.	2279	Q685J3	MUC17_HUMAN	N	2279	ENSP00000302716:T2279N	ENSP00000302716:T2279N	T	+	2	0	MUC17	100468253	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	0.068000	0.14531	0.132000	0.18615	0.134000	0.15878	ACT	.	.	.	none		0.478	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100681533	C	A	100681533	3	1	7	1	0	0	0	0	1	0	0	0	9981	565	20	4	6846	4	MUC17	7	100681533	Missense_Mutation	SNP	C	TCGA-2Z-A9J7-01A-11D-A382-10	14212389	100681533	58457130	21	569											
CUL1	8454	hgsc.bcm.edu	37	chr7	148484199	148484199	+	Missense_Mutation	SNP	T	T	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	cgatgccgaagccagcatgaTctccaagttaaaggtgagtt	12	9	11	9	2	1	2	0	2	1	0	2	4	1	2	3	1	3	3	3	1	4	2			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr7:148484199T>G	ENST00000325222.4	+	13	1745	c.1466T>G	c.(1465-1467)aTc>aGc	p.I489S	CUL1_ENST00000409469.1_Missense_Mutation_p.I489S|CUL1_ENST00000602748.1_Missense_Mutation_p.I489S	NM_003592.2	NP_003583.2	Q13616	CUL1_HUMAN	cullin 1	489					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)			GCCAGCATGATCTCCAAGTTA	0.468																																					p.I489S		Atlas-SNP	.											.	CUL1	80	.	0			c.T1466G						PASS	.						75	70	72					7																	148484199		2203	4300	6503	SO:0001583	missense	8454	exon13			GCATGATCTCCAA	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.1466T>G	chr7.hg19:g.148484199T>G	ENSP00000326804:p.Ile489Ser	58.0	0.0	.		155.0	53.0	.	NM_003592	D3DWG3|O60719|Q08AL6|Q8IYW1	Missense_Mutation	SNP	ENST00000325222.4	hg19	CCDS34772.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.349001	0.82132	.	.	ENSG00000055130	ENST00000409469;ENST00000325222;ENST00000543583;ENST00000433865	T;T	0.79749	-1.3;-1.3	5.5	5.5	0.81552	Cullin, N-terminal (1);Cullin homology (3);	0.046639	0.85682	D	0.000000	D	0.92883	0.7736	H	0.96430	3.82	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77557	0.988;0.99	D	0.95044	0.8181	10	0.87932	D	0	0.0152	15.6219	0.76813	0.0:0.0:0.0:1.0	.	416;489	E7EWR0;Q13616	.;CUL1_HUMAN	S	489;489;447;416	ENSP00000387160:I489S;ENSP00000326804:I489S	ENSP00000326804:I489S	I	+	2	0	CUL1	148115132	1.000000	0.71417	1.000000	0.80357	0.718000	0.41266	7.746000	0.85057	2.098000	0.63641	0.533000	0.62120	ATC	.	.	.	none		0.468	CUL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467785.1	NM_003592		G	148484199	T	G	148484199	3	3	7	1	0	0	0	0	1	0	0	0	4056	1435	50	5	1512	5	CUL1	7	148484199	Missense_Mutation	SNP	T	TCGA-2Z-A9J7-01A-11D-A382-10	47802666	148484199	10654464	22	570											
OPLAH	26873	hgsc.bcm.edu	37	chr8	145112996	145112996	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agggtgacgccagctgtgctGgcctcgaagacgtgctcgaa	8	7	15	11	4	0	2	0	1	0	1	2	4	0	2	2	2	3	3	2	2	2	0			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr8:145112996G>A	ENST00000426825.1	-	8	1086	c.1005C>T	c.(1003-1005)gcC>gcT	p.A335A	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	335					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)			CAGCTGTGCTGGCCTCGAAGA	0.657																																					p.A335A		Atlas-SNP	.											.	OPLAH	78	.	0			c.C1005T						PASS	.						43	51	48					8																	145112996		2054	4182	6236	SO:0001819	synonymous_variant	26873	exon8			TGTGCTGGCCTCG	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.1005C>T	chr8.hg19:g.145112996G>A		156.0	0.0	.		169.0	80.0	.	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Silent	SNP	ENST00000426825.1	hg19																																																																																				.	.	.	none		0.657	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570		A	145112996	G	A	145112996	2	1	7	1	0	0	0	0	0	0	0	1	10883	1335	47	2		2	OPLAH	8	145112996	Silent	SNP	G	TCGA-2Z-A9J7-01A-11D-A382-10		145112996	1251026	23	571											
PTPRD	5789	hgsc.bcm.edu	37	chr9	8486309	8486309	+	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	cactgaataagagcagtattCatctgagtgtggttaatcac	13	12	9	7	0	3	3	2	2	1	1	3	3	3	3	0	1	1	3	0	1	4	4			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr9:8486309C>T	ENST00000381196.4	-	25	3051	c.2508G>A	c.(2506-2508)atG>atA	p.M836I	PTPRD_ENST00000397617.3_Intron|PTPRD_ENST00000540109.1_Missense_Mutation_p.M836I|PTPRD_ENST00000356435.5_Missense_Mutation_p.M836I|PTPRD_ENST00000397606.3_Intron|PTPRD_ENST00000397611.3_Intron|PTPRD_ENST00000537002.1_Intron|PTPRD_ENST00000360074.4_Missense_Mutation_p.M823I|PTPRD_ENST00000358503.5_Missense_Mutation_p.M814I|PTPRD_ENST00000486161.1_Intron|PTPRD_ENST00000355233.5_Intron|PTPRD_ENST00000471274.1_5'UTR	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	836	Fibronectin type-III 6. {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)	p.M836I(1)		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)		GAGCAGTATTCATCTGAGTGT	0.483										TSP Lung(15;0.13)																											p.M836I		Atlas-SNP	.											PTPRD,leg,malignant_melanoma,0,1	PTPRD	1348	.	1	Substitution - Missense(1)	skin(1)	c.G2508A						PASS	.						73	71	72					9																	8486309		2203	4300	6503	SO:0001583	missense	5789	exon28			AGTATTCATCTGA	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.2508G>A	chr9.hg19:g.8486309C>T	ENSP00000370593:p.Met836Ile	98.0	1.0	.		75.0	36.0	.	NM_002839	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	hg19	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	C	16.21	3.059631	0.55325	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000540109	T;T;T;T;T	0.56776	0.44;0.44;0.44;0.44;0.44	5.93	5.93	0.95920	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.49218	0.1544	L	0.36672	1.1	0.80722	D	1	B;P;B	0.37573	0.397;0.6;0.137	B;B;B	0.39299	0.138;0.296;0.216	T	0.32508	-0.9904	9	.	.	.	.	20.3539	0.98825	0.0:1.0:0.0:0.0	.	823;836;836	G3XAE2;Q2HXI4;P23468	.;.;PTPRD_HUMAN	I	836;836;823;814;836	ENSP00000370593:M836I;ENSP00000348812:M836I;ENSP00000353187:M823I;ENSP00000351293:M814I;ENSP00000438164:M836I	.	M	-	3	0	PTPRD	8476309	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.487000	0.81328	2.826000	0.97356	0.655000	0.94253	ATG	.	.	.	none		0.483	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			T	8486309	C	T	8486309	3	4	7	1	0	0	0	0	1	0	0	0	12812	826	29	2	3374	2	PTPRD	9	8486309	Missense_Mutation	SNP	C	TCGA-2Z-A9J7-01A-11D-A382-10		8486309	132727122	24	572											
CACNA1B	774	hgsc.bcm.edu	37	chr9	140904505	140904505	+	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	gccatcgctgtggacaacctGgccaacgcccaagagctgac	10	5	11	15	2	0	2	0	1	0	1	1	3	0	3	4	2	3	2	4	2	3	0			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr9:140904505G>C	ENST00000371372.1	+	17	2281	c.2136G>C	c.(2134-2136)ctG>ctC	p.L712L	CACNA1B_ENST00000277551.2_Silent_p.L712L|CACNA1B_ENST00000371363.1_Silent_p.L712L|CACNA1B_ENST00000277550.3_Silent_p.L3L|CACNA1B_ENST00000371355.4_Silent_p.L713L|CACNA1B_ENST00000371357.1_Silent_p.L713L|CACNA1B_ENST00000277549.5_5'UTR	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	712					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	TGGACAACCTGGCCAACGCCC	0.607																																					p.L712L		Atlas-SNP	.											.	CACNA1B	266	.	0			c.G2136C						PASS	.						71	75	74					9																	140904505		2160	4269	6429	SO:0001819	synonymous_variant	774	exon17			CAACCTGGCCAAC	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.2136G>C	chr9.hg19:g.140904505G>C		108.0	0.0	.		100.0	43.0	.	NM_001243812	B1AQK5	Silent	SNP	ENST00000371372.1	hg19	CCDS59522.1																																																																																			.	.	.	none		0.607	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		C	140904505	G	C	140904505	2	2	7	1	0	0	0	0	0	0	0	1	2541	1335	47	4		4	CACNA1B	9	140904505	Silent	SNP	G	TCGA-2Z-A9J7-01A-11D-A382-10	132418196	140904505	308926	25	573											
CACNA1B	774	hgsc.bcm.edu	37	chr9	140918184	140918185	+	Missense_Mutation	DNP	AC	AC	GT																															aggctgtggagaaggagaccAcggagaaggaggccacggag																								rs145816559|rs370787788	byFrequency	TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr9:140918184_140918185AC>GT	ENST00000371372.1	+	19	3134_3135	c.2989_2990AC>GT	c.(2989-2991)ACg>GTg	p.T997V	CACNA1B_ENST00000277551.2_Missense_Mutation_p.T997V|CACNA1B_ENST00000371367.5_5'UTR|CACNA1B_ENST00000545473.1_5'Flank|CACNA1B_ENST00000371363.1_Missense_Mutation_p.T997V|CACNA1B_ENST00000371355.4_Missense_Mutation_p.T998V|CACNA1B_ENST00000371357.1_Missense_Mutation_p.T998V|CACNA1B_ENST00000277549.5_Missense_Mutation_p.T189V	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	997					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)	p.T996_E1000delTTEKE(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	GAAGGAGACCACGGAGAAGGAG	0.718																																					p.T997A|p.T997M		Atlas-SNP	.											.	CACNA1B	266	.	1	Deletion - In frame(1)	breast(1)	c.A2989G|c.C2990T						PASS	.																																			SO:0001583	missense	774	exon19			GAGACCACGGAGA|AGACCACGGAGAA	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	Exception_encountered	chr9.hg19:g.140918184_140918185delinsGT	ENSP00000360423:p.Thr997Val	0.0	0.0	.		191.0|189.0	24.0|30.0	.	NM_001243812	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	hg19	CCDS59522.1																																																																																			.	.	.	none		0.718	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		GT	140918185	AC	GT	140918184	3	3	7	1	0	0	0	0	1	0	0	0	2541	159	6	3	3063	3	CACNA1B	9	140918184	Missense_Mutation	DNP	AC	TCGA-2Z-A9J7-01A-11D-A382-10	13679	140918184	295247	26	574											
CUBN	8029	hgsc.bcm.edu	37	chr10	16967343	16967343	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgaggtgaacagagttgaTgaagcatgactgccacaaaa	15	7	11	8	1	0	5	0	4	0	1	1	6	1	5	2	1	3	2	2	1	4	1			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr10:16967343T>C	ENST00000377833.4	-	43	6608	c.6543A>G	c.(6541-6543)tcA>tcG	p.S2181S		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2181	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)	ACAGAGTTGATGAAGCATGAC	0.388																																					p.S2181S		Atlas-SNP	.											.	CUBN	515	.	0			c.A6543G						PASS	.						69	69	69					10																	16967343		2203	4300	6503	SO:0001819	synonymous_variant	8029	exon43			AGTTGATGAAGCA	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.6543A>G	chr10.hg19:g.16967343T>C		319.0	1.0	.		350.0	165.0	.	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	hg19	CCDS7113.1																																																																																			.	.	.	none		0.388	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		C	16967343	T	C	16967343	2	2	7	1	0	0	0	0	0	0	0	1	4053	1451	51	3		3	CUBN	10	16967343	Silent	SNP	T	TCGA-2Z-A9J7-01A-11D-A382-10		16967343	118567404	27	575											
ADD3	120	hgsc.bcm.edu	37	chr10	111884029	111884029	+	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	accagtccccgaaccaaaatCacggtatgccagtattttat	13	10	6	12	2	1	0	1	0	0	0	2	1	2	0	5	1	2	2	5	1	6	4			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr10:111884029C>T	ENST00000356080.4	+	10	1765	c.1398C>T	c.(1396-1398)atC>atT	p.I466I	ADD3_ENST00000277900.8_Silent_p.I466I|ADD3_ENST00000360162.3_Silent_p.I466I	NM_016824.3	NP_058432.1	Q9UEY8	ADDG_HUMAN	adducin 3 (gamma)	466						cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	29		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)		GAACCAAAATCACGGTATGCC	0.363																																					p.I466I		Atlas-SNP	.											.	ADD3	89	.	0			c.C1398T						PASS	.						81	80	80					10																	111884029		2203	4300	6503	SO:0001819	synonymous_variant	120	exon10			CAAAATCACGGTA	U37122	CCDS7561.1, CCDS7562.1	10q25.2	2005-11-08			ENSG00000148700	ENSG00000148700			245	protein-coding gene	gene with protein product		601568		ADDL		8893809	Standard	XM_005269529		Approved		uc001kyv.3	Q9UEY8	OTTHUMG00000019032	ENST00000356080.4:c.1398C>T	chr10.hg19:g.111884029C>T		155.0	0.0	.		193.0	96.0	.	NM_001121	D3DRA8|O43243|Q5VU09|Q92773|Q9UEY7	Silent	SNP	ENST00000356080.4	hg19	CCDS7561.1																																																																																			.	.	.	none		0.363	ADD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050289.1	NM_019903		T	111884029	C	T	111884029	2	4	7	1	0	0	0	0	0	0	0	1	306	816	29	2		2	ADD3	10	111884029	Silent	SNP	C	TCGA-2Z-A9J7-01A-11D-A382-10	94916686	111884029	23650718	28	576											
SAA4	6291	hgsc.bcm.edu	37	chr11	18254055	18254055	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttggatatcattatgtcccaAtaggctctgcccatgtcccc	8	13	7	13	0	2	0	1	0	1	0	4	1	4	1	4	2	1	1	4	2	4	4			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr11:18254055A>G	ENST00000278222.4	-	3	297	c.117T>C	c.(115-117)taT>taC	p.Y39Y	SAA2-SAA4_ENST00000524555.1_RNA	NM_006512.3	NP_006503.2	P35542	SAA4_HUMAN	serum amyloid A4, constitutive	39					acute-phase response (GO:0006953)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|skin(1)|stomach(1)	13						TTATGTCCCAATAGGCTCTGC	0.438																																					p.Y117Y		Atlas-SNP	.											.	.	.	.	0			c.T351C						PASS	.						143	142	142					11																	18254055		2199	4293	6492	SO:0001819	synonymous_variant	100528017	exon5			GTCCCAATAGGCT	M81349	CCDS7832.1	11p15.1-p14	2008-07-21			ENSG00000148965	ENSG00000148965			10516	protein-coding gene	gene with protein product		104752				8325654	Standard	NM_006512		Approved	C-SAA, CSAA		P35542	OTTHUMG00000166483	ENST00000278222.4:c.117T>C	chr11.hg19:g.18254055A>G		101.0	0.0	.		108.0	48.0	.	NM_001199744	Q6FHJ4	Silent	SNP	ENST00000278222.4	hg19	CCDS7832.1																																																																																			.	.	.	none		0.438	SAA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389988.1	NM_006512		G	18254055	A	G	18254055	2	3	7	1	0	0	0	0	0	0	0	1	13813	108	4	3		3	SAA4	11	18254055	Silent	SNP	A	TCGA-2Z-A9J7-01A-11D-A382-10		18254055	116752461	29	577											
KRTAP5-9	3846	hgsc.bcm.edu	37	chr11	71259971	71260114	+	In_Frame_Del	DEL	TCAGGCTGTGGGTCATCCTGCTGCCAGTGCAGCTGCTGCAAGCCCTACTGCTCCCAGTGCAGCTGCTGTAAGCCCTGTTGCTCCTCCTCGGGTCGTGGGTCATCCTGCTGCCAATCCAGCTGCTGCAAGCCCTGCTGCTCATCC	TCAGGCTGTGGGTCATCCTGCTGCCAGTGCAGCTGCTGCAAGCCCTACTGCTCCCAGTGCAGCTGCTGTAAGCCCTGTTGCTCCTCCTCGGGTCGTGGGTCATCCTGCTGCCAATCCAGCTGCTGCAAGCCCTGCTGCTCATCC	-																															gcaagccctgctgttgctctTcaggctgtgggtcatcctgc																								rs200171268|rs202087444|rs569788113|rs543172155|rs371997244|rs535053140|rs200091258|rs114705722|rs201275630|rs35547146|rs202236982|rs372250247|rs564532132|rs369827874|rs546472579|rs117137984|rs531897567|rs200956303|rs267603173|rs572772724|rs61746411|rs367545102|rs557667941	byFrequency	TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	TCAGGCTGTGGGTCATCCTGCTGCCAGTGCAGCTGCTGCAAGCCCTACTGCTCCCAGTGCAGCTGCTGTAAGCCCTGTTGCTCCTCCTCGGGTCGTGGGTCATCCTGCTGCCAATCCAGCTGCTGCAAGCCCTGCTGCTCATCC	TCAGGCTGTGGGTCATCCTGCTGCCAGTGCAGCTGCTGCAAGCCCTACTGCTCCCAGTGCAGCTGCTGTAAGCCCTGTTGCTCCTCCTCGGGTCGTGGGTCATCCTGCTGCCAATCCAGCTGCTGCAAGCCCTGCTGCTCATCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr11:71259971_71260114delTCAGGCTGTGGGTCATCCTGCTGCCAGTGCAGCTGCTGCAAGCCCTACTGCTCCCAGTGCAGCTGCTGTAAGCCCTGTTGCTCCTCCTCGGGTCGTGGGTCATCCTGCTGCCAATCCAGCTGCTGCAAGCCCTGCTGCTCATCC	ENST00000528743.2	+	1	506_649	c.268_411delTCAGGCTGTGGGTCATCCTGCTGCCAGTGCAGCTGCTGCAAGCCCTACTGCTCCCAGTGCAGCTGCTGTAAGCCCTGTTGCTCCTCCTCGGGTCGTGGGTCATCCTGCTGCCAATCCAGCTGCTGCAAGCCCTGCTGCTCATCC	c.(268-411)tcaggctgtgggtcatcctgctgccagtgcagctgctgcaagccctactgctcccagtgcagctgctgtaagccctgttgctcctcctcgggtcgtgggtcatcctgctgccaatccagctgctgcaagccctgctgctcatccdel	p.SGCGSSCCQCSCCKPYCSQCSCCKPCCSSSGRGSSCCQSSCCKPCCSS90del		NM_005553.3	NP_005544.4	P26371	KRA59_HUMAN	keratin associated protein 5-9	90	8 X 4 AA repeats of C-C-X-P.				epidermis development (GO:0008544)	keratin filament (GO:0045095)		p.S119S(1)|p.K103M(1)|p.C97F(1)|p.C130Y(1)		kidney(1)|large_intestine(1)|lung(6)|prostate(3)	11						CTGTTGCTCTTCAGGCTGTGGGTCATCCTGCTGCCAGTGCAGCTGCTGCAAGCCCTACTGCTCCCAGTGCAGCTGCTGTAAGCCCTGTTGCTCCTCCTCGGGTCGTGGGTCATCCTGCTGCCAATCCAGCTGCTGCAAGCCCTGCTGCTCATCCTCAGGCTGTG	0.622																																					p.89_137del		Pindel	.											.	KRTAP5-9	19	.	4	Substitution - Missense(3)|Substitution - coding silent(1)	lung(3)|prostate(1)	c.267_410del						PASS	.																																			SO:0001651	inframe_deletion	3846	exon1			.	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.268_411delTCAGGCTGTGGGTCATCCTGCTGCCAGTGCAGCTGCTGCAAGCCCTACTGCTCCCAGTGCAGCTGCTGTAAGCCCTGTTGCTCCTCCTCGGGTCGTGGGTCATCCTGCTGCCAATCCAGCTGCTGCAAGCCCTGCTGCTCATCC	chr11.hg19:g.71259971_71260114delTCAGGCTGTGGGTCATCCTGCTGCCAGTGCAGCTGCTGCAAGCCCTACTGCTCCCAGTGCAGCTGCTGTAAGCCCTGTTGCTCCTCCTCGGGTCGTGGGTCATCCTGCTGCCAATCCAGCTGCTGCAAGCCCTGCTGCTCATCC	ENSP00000431443:p.Ser90_Ser137del	91.0	0.0	.		85.0	16.0	0.188	NM_005553	Q14564|Q3MIP8	In_Frame_Del	DEL	ENST00000528743.2	hg19	CCDS53677.1																																																																																			.	.	.	none		0.622	KRTAP5-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393901.2			-	71260114	TCAGGCTGTGGGTCATCCTGCTGCCAGTGCAGCTGCTGCAAGCCCTACTGCTCCCAGTGCAGCTGCTGTAAGCCCTGTTGCTCCTCCTCGGGTCGTGGGTCATCCTGCTGCCAATCCAGCTGCTGCAAGCCCTGCTGCTCATCC	-	71259971	7	5	7	1	0	1	0	1	0	0	0	0	8575	1783	62	0	270	0	KRTAP5-9	11	71259971	In_Frame_Del	DEL	TCAGGCTGTGGGTCATCCTGCTGCCAGTGCAGCTGCTGCAAGCCCTACTGCTCCCAGTGCAGCTGCTGTAAGCCCTGTTGCTCCTCCTCGGGTCGTGGGTCATCCTGCTGCCAATCCAGCTGCTGCAAGCCCTGCTGCTCATCC	TCGA-2Z-A9J7-01A-11D-A382-10	53005916	71259971	63746545	30	578											
BRCA2	675	hgsc.bcm.edu	37	chr13	32910939	32910939	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaccaaaaatattcccatggAaaagaatcaagatgtatgtg	19	9	7	6	0	1	2	1	0	0	2	2	3	2	3	2	1	1	1	2	1	9	3	rs80359331		TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr13:32910939A>G	ENST00000380152.3	+	11	2680	c.2447A>G	c.(2446-2448)gAa>gGa	p.E816G	BRCA2_ENST00000544455.1_Missense_Mutation_p.E816G			P51587	BRCA2_HUMAN	breast cancer 2, early onset	816	Interaction with NPM1.				brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			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)		ATTCCCATGGAAAAGAATCAA	0.328			"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.E816G	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.A2447G						PASS	.						52	56	55					13																	32910939		2203	4296	6499	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)	CCATGGAAAAGAA	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.2447A>G	chr13.hg19:g.32910939A>G	ENSP00000369497:p.Glu816Gly	271.0	0.0	.		306.0	146.0	.	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	hg19	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	A	5.922	0.354207	0.11182	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.72051	-0.62;-0.62	5.43	1.47	0.22746	.	1.104510	0.06758	N	0.781238	T	0.55689	0.1936	L	0.29908	0.895	0.09310	N	1	B	0.22276	0.067	B	0.17433	0.018	T	0.36114	-0.9761	10	0.27785	T	0.31	.	5.4273	0.16433	0.5898:0.1389:0.2713:0.0	.	816	P51587	BRCA2_HUMAN	G	816	ENSP00000369497:E816G;ENSP00000439902:E816G	ENSP00000369497:E816G	E	+	2	0	BRCA2	31808939	0.000000	0.05858	0.003000	0.11579	0.089000	0.18198	0.028000	0.13644	0.020000	0.15106	0.482000	0.46254	GAA	.	.	.	none		0.328	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		G	32910939	A	G	32910939	3	3	7	1	0	0	0	0	1	0	0	0	1501	246	9	3	2485	3	BRCA2	13	32910939	Missense_Mutation	SNP	A	TCGA-2Z-A9J7-01A-11D-A382-10		32910939	82258939	31	579											
HOMEZ	57594	hgsc.bcm.edu	37	chr14	23744832	23744832	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatcatcatcatcttcctcCtcctcctcctcctcttcctc	4	16	0	21	0	6	0	4	0	2	0	14	0	13	0	7	0	0	0	7	0	0	2			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr14:23744832C>T	ENST00000357460.5	-	2	1769	c.1605G>A	c.(1603-1605)gaG>gaA	p.E535E	HOMEZ_ENST00000431326.2_Silent_p.E537E|HOMEZ_ENST00000561013.1_Silent_p.E537E	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	535	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)		catcttcctcctcctcctcct	0.483																																					p.E535E		Atlas-SNP	.											.	HOMEZ	80	.	0			c.G1605A						PASS	.						38	38	38					14																	23744832		2192	4269	6461	SO:0001819	synonymous_variant	57594	exon2			TTCCTCCTCCTCC	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.1605G>A	chr14.hg19:g.23744832C>T		29.0	0.0	.		68.0	9.0	.	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Silent	SNP	ENST00000357460.5	hg19	CCDS45085.1																																																																																			.	.	.	none		0.483	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834		T	23744832	C	T	23744832	2	4	7	1	0	0	0	0	0	0	0	1	7288	680	24	2		2	HOMEZ	14	23744832	Silent	SNP	C	TCGA-2Z-A9J7-01A-11D-A382-10		23744832	83604708	32	580											
MFAP1	4236	hgsc.bcm.edu	37	chr15	44106734	44106734	+	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	ggcttaaggcgaggctccatCtcatcttcactgtctgtgta	7	13	10	11	1	4	0	2	0	3	0	6	1	5	0	1	3	0	3	1	3	2	3			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr15:44106734C>T	ENST00000267812.3	-	4	814	c.582G>A	c.(580-582)gaG>gaA	p.E194E		NM_005926.2	NP_005917.2	P55081	MFAP1_HUMAN	microfibrillar-associated protein 1	194					extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|microfibril (GO:0001527)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|lung(6)|skin(2)|upper_aerodigestive_tract(3)	15		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.33e-07)		GAGGCTCCATCTCATCTTCAC	0.453																																					p.E194E		Atlas-SNP	.											.	MFAP1	36	.	0			c.G582A						PASS	.						229	214	219					15																	44106734		2198	4298	6496	SO:0001819	synonymous_variant	4236	exon4			CTCCATCTCATCT		CCDS10105.1	15q15-q21	2014-05-20			ENSG00000140259	ENSG00000140259			7032	protein-coding gene	gene with protein product		600215				7835894	Standard	NM_005926		Approved		uc001zth.1	P55081	OTTHUMG00000060145	ENST00000267812.3:c.582G>A	chr15.hg19:g.44106734C>T		80.0	0.0	.		81.0	33.0	.	NM_005926	Q86TG6	Silent	SNP	ENST00000267812.3	hg19	CCDS10105.1																																																																																			.	.	.	none		0.453	MFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133491.2	NM_005926		T	44106734	C	T	44106734	2	4	7	1	0	0	0	0	0	0	0	1	9520	912	32	2		2	MFAP1	15	44106734	Silent	SNP	C	TCGA-2Z-A9J7-01A-11D-A382-10		44106734	58424658	33	581											
LCTL	197021	hgsc.bcm.edu	37	chr15	66856303	66856303	+	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	cagggagaatcggtagtggtTgacgtgcagttccctcagca	9	9	14	9	2	1	2	1	1	0	1	3	3	2	2	1	3	2	5	1	3	2	3			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr15:66856303T>A	ENST00000341509.5	-	3	447	c.316A>T	c.(316-318)Aac>Tac	p.N106Y	LCTL_ENST00000537670.1_5'UTR|LCTL_ENST00000563438.1_5'UTR	NM_207338.2	NP_997221.2	Q6UWM7	LCTL_HUMAN	lactase-like	106					carbohydrate metabolic process (GO:0005975)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						CGGTAGTGGTTGACGTGCAGT	0.632																																					p.N106Y		Atlas-SNP	.											.	LCTL	73	.	0			c.A316T						PASS	.						146	126	133					15																	66856303		2201	4299	6500	SO:0001583	missense	197021	exon3			AGTGGTTGACGTG	AY358729	CCDS10220.1, CCDS61678.1	15q21.3	2008-02-05			ENSG00000188501	ENSG00000188501			15583	protein-coding gene	gene with protein product	"klotho gamma", "KL lactase phlorizin hydrolase"					12084582	Standard	NM_207338		Approved	KLPH, FLJ33279, KLG	uc002aqc.3	Q6UWM7	OTTHUMG00000133207	ENST00000341509.5:c.316A>T	chr15.hg19:g.66856303T>A	ENSP00000343490:p.Asn106Tyr	89.0	0.0	.		78.0	40.0	.	NM_207338	B3KQY0	Missense_Mutation	SNP	ENST00000341509.5	hg19	CCDS10220.1	.	.	.	.	.	.	.	.	.	.	T	15.20	2.762455	0.49574	.	.	ENSG00000188501	ENST00000341509	T	0.34472	1.36	5.21	4.06	0.47325	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.375249	0.35207	N	0.003378	T	0.40956	0.1138	M	0.83692	2.655	0.80722	D	1	B	0.33826	0.427	B	0.33799	0.17	T	0.40534	-0.9558	10	0.87932	D	0	-12.579	8.7922	0.34857	0.3018:0.0:0.0:0.6982	.	106	Q6UWM7	LCTL_HUMAN	Y	106	ENSP00000343490:N106Y	ENSP00000343490:N106Y	N	-	1	0	LCTL	64643357	0.884000	0.30299	0.353000	0.25747	0.919000	0.55068	3.436000	0.52856	0.900000	0.36469	0.379000	0.24179	AAC	.	.	.	none		0.632	LCTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256921.2	NM_207338		A	66856303	T	A	66856303	3	1	7	1	0	0	0	0	1	0	0	0	8701	1812	63	5	1431	5	LCTL	15	66856303	Missense_Mutation	SNP	T	TCGA-2Z-A9J7-01A-11D-A382-10	22749569	66856303	35675089	34	582											
CFDP1	10428	hgsc.bcm.edu	37	chr16	75327931	75327951	+	Splice_Site	DEL	TTCAATGTACCTAGAAGATGA	TTCAATGTACCTAGAAGATGA	-																															cggtcaaggaaggctttccgTtcaatgtacctagaagatga																								rs375111551		TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	TTCAATGTACCTAGAAGATGA	TTCAATGTACCTAGAAGATGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr16:75327931_75327951delTTCAATGTACCTAGAAGATGA	ENST00000283882.3	-	7	942_951	c.810_819delTCATCTTCTAGGTACATTGAA	c.(808-819)ggtcatcttcta>gg	p.GHLL270del		NM_006324.2	NP_006315.1	Q9UEE9	CFDP1_HUMAN	craniofacial development protein 1	270	BCNT-C. {ECO:0000255|PROSITE- ProRule:PRU00610}.				cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|negative regulation of fibroblast apoptotic process (GO:2000270)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)					endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5						AGGCTTTCCGTTCAATGTACCTAGAAGATGAAAACAGTGTT	0.457																																					p.270_274del		Atlas-Indel,Pindel	.											.	CFDP1	17	.	0			c.810_820del						PASS	.																																			SO:0001630	splice_region_variant	10428	exon7			.	AB009285	CCDS10916.1	16q22.2-q22.3	2011-08-12			ENSG00000153774	ENSG00000153774			1873	protein-coding gene	gene with protein product	"Bucentaur", "centromere protein 29"	608108				9602175, 9006920, 11992732	Standard	NM_006324		Approved	BCNT, p97, CP27, SWC5, Yeti, CENP-29	uc002fdy.3	Q9UEE9	OTTHUMG00000137615	ENST00000283882.3:c.810-1TCATCTTCTAGGTACATTGAA>-	chr16.hg19:g.75327931_75327951delTTCAATGTACCTAGAAGATGA		66.0	0.0	0		52.0	11.0	0.211538	NM_006324	O00393|O00404|Q9UEF0|Q9UEF1|Q9UEF8	Frame_Shift_Del	DEL	ENST00000283882.3	hg19	CCDS10916.1																																																																																			.	.	.	none		0.457	CFDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269031.2	NM_006324	In_Frame_Del	-	75327951	TTCAATGTACCTAGAAGATGA	-	75327931	8	5	7	1	0	1	0	1	0	0	1	0	3284	1722	60	0	84	0	CFDP1	16	75327931	Splice_Site	DEL	TTCAATGTACCTAGAAGATGA	TCGA-2Z-A9J7-01A-11D-A382-10		75327931	15026822	35	583											
CDH13	1012	hgsc.bcm.edu	37	chr16	83378492	83378492	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtggagaccactgatgtcaAtggcaaaactctcgaggggc	11	8	13	9	1	2	2	1	1	1	1	3	4	2	2	1	4	1	1	1	4	3	0	rs374048975		TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr16:83378492A>G	ENST00000566620.1	+	6	952	c.662A>G	c.(661-663)aAt>aGt	p.N221S	CDH13_ENST00000428848.3_Missense_Mutation_p.N182S|CDH13_ENST00000268613.10_Missense_Mutation_p.N268S|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	221	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)		ACTGATGTCAATGGCAAAACT	0.448																																					p.N268S		Atlas-SNP	.											.	CDH13	97	.	0			c.A803G						PASS	.						79	81	81					16																	83378492		1855	4088	5943	SO:0001583	missense	1012	exon7			ATGTCAATGGCAA	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.662A>G	chr16.hg19:g.83378492A>G	ENSP00000454435:p.Asn221Ser	71.0	0.0	.		81.0	33.0	.	NM_001220488	A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	Missense_Mutation	SNP	ENST00000566620.1	hg19	CCDS58486.1	.	.	.	.	.	.	.	.	.	.	A	13.03	2.115445	0.37339	.	.	ENSG00000140945	ENST00000268613;ENST00000428848;ENST00000536143	T	0.60548	0.18	5.76	0.716	0.18191	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.35508	0.0934	N	0.05510	-0.035	0.58432	D	0.999997	B;B;B	0.23185	0.081;0.0;0.001	B;B;B	0.30251	0.113;0.008;0.004	T	0.08554	-1.0716	9	0.41790	T	0.15	.	8.7915	0.34854	0.483:0.0:0.517:0.0	.	182;268;221	B7Z590;B7Z9B1;P55290	.;.;CAD13_HUMAN	S	268;221;182	ENSP00000268613:N268S	ENSP00000268613:N268S	N	+	2	0	CDH13	81935993	0.228000	0.23718	0.573000	0.28510	0.906000	0.53458	0.515000	0.22801	0.193000	0.20303	0.533000	0.62120	AAT	.	.	.	weak		0.448	CDH13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432917.1	NM_001257		G	83378492	A	G	83378492	3	3	7	1	0	0	0	0	1	0	0	0	3101	101	4	3	684	3	CDH13	16	83378492	Missense_Mutation	SNP	A	TCGA-2Z-A9J7-01A-11D-A382-10	8050561	83378492	6976261	36	584											
ACSF3	197322	hgsc.bcm.edu	37	chr16	89167635	89167635	+	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	actggagcagtagaggaaccGgcagaggtcccggtcccaga	11	4	15	11	2	0	3	0	0	0	3	2	5	2	5	3	5	2	3	3	5	2	1			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr16:89167635G>T	ENST00000317447.4	+	3	923	c.546G>T	c.(544-546)ccG>ccT	p.P182P	ACSF3_ENST00000378345.4_Intron|ACSF3_ENST00000406948.3_Silent_p.P182P	NM_001127214.2|NM_001243279.1|NM_001284316.1|NM_174917.3	NP_001120686.1|NP_001230208.1|NP_001271245.1|NP_777577.2	Q4G176	ACSF3_HUMAN	acyl-CoA synthetase family member 3	182					fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|malonate catabolic process (GO:0090410)	mitochondrion (GO:0005739)	acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)|malonyl-CoA synthetase activity (GO:0090409)			central_nervous_system(1)|endometrium(1)|kidney(2)|lung(9)|prostate(1)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(80;0.0281)		TAGAGGAACCGGCAGAGGTCC	0.657																																					p.P182P		Atlas-SNP	.											.	ACSF3	40	.	0			c.G546T						PASS	.						16	13	14					16																	89167635		2196	4299	6495	SO:0001819	synonymous_variant	197322	exon3			GGAACCGGCAGAG	AK075499	CCDS10974.1, CCDS73926.1	16q24.3	2013-01-15			ENSG00000176715	ENSG00000176715		"Acyl-CoA synthetase family"	27288	protein-coding gene	gene with protein product	"malonyl-CoA synthetase"	614245				17762044, 21846720	Standard	XM_005256293		Approved		uc010cig.2	Q4G176	OTTHUMG00000138044	ENST00000317447.4:c.546G>T	chr16.hg19:g.89167635G>T		102.0	0.0	.		76.0	40.0	.	NM_174917	A8K4J8|C9JQL6|Q6INA0|Q8N2F7	Silent	SNP	ENST00000317447.4	hg19	CCDS10974.1																																																																																			.	.	.	none		0.657	ACSF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269919.1	NM_174917		T	89167635	G	T	89167635	2	4	7	1	0	0	0	0	0	0	0	1	176	1103	39	4		4	ACSF3	16	89167635	Silent	SNP	G	TCGA-2Z-A9J7-01A-11D-A382-10	5789143	89167635	1187118	37	585											
MPRIP	23164	hgsc.bcm.edu	37	chr17	17039564	17039564	+	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	tgccaaggtggctgttaccaGcagcagcagcagcagcagca	11	5	13	12	0	0	0	0	0	0	0	0	0	0	0	2	2	9	9	2	2	2	1	rs3833098|rs113250356|rs35599326|rs202138172	byFrequency	TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr17:17039564G>C	ENST00000341712.4	+	6	536	c.536G>C	c.(535-537)aGc>aCc	p.S179T	MPRIP_ENST00000395804.3_Missense_Mutation_p.S179T|MPRIP_ENST00000395811.5_Missense_Mutation_p.S179T|MPRIP_ENST00000444976.1_Missense_Mutation_p.S179T			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	179	Interaction with F-actin. {ECO:0000250}.|Ser-rich.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)		p.S189delS(1)		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						GCTGTTACcagcagcagcagc	0.597																																					p.S179T		Atlas-SNP	.											.	MPRIP	87	.	1	Deletion - In frame(1)	kidney(1)	c.G536C						PASS	.						22	22	22					17																	17039564		2203	4295	6498	SO:0001583	missense	23164	exon6			TTACCAGCAGCAG	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.536G>C	chr17.hg19:g.17039564G>C	ENSP00000342379:p.Ser179Thr	64.0	0.0	.		102.0	9.0	.	NM_015134	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Missense_Mutation	SNP	ENST00000341712.4	hg19	CCDS32578.1	.	.	.	.	.	.	.	.	.	.	G	11.03	1.519798	0.27211	.	.	ENSG00000133030	ENST00000444976;ENST00000395811;ENST00000395804;ENST00000341712	D;D;D;D	0.94046	-3.34;-3.34;-3.34;-3.34	2.12	2.12	0.27331	.	.	.	.	.	D	0.90566	0.7043	L	0.34521	1.04	0.29751	N	0.836355	P;P	0.51933	0.949;0.61	P;B	0.50659	0.647;0.135	D	0.85374	0.1115	9	0.52906	T	0.07	.	7.7647	0.28972	0.0:0.0:1.0:0.0	.	179;179	Q6WCQ1-2;Q6WCQ1	.;MPRIP_HUMAN	T	179	ENSP00000400189:S179T;ENSP00000379156:S179T;ENSP00000379149:S179T;ENSP00000342379:S179T	ENSP00000342379:S179T	S	+	2	0	MPRIP	16980289	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.655000	0.46707	1.509000	0.48786	0.591000	0.81541	AGC	.	.	.	none		0.597	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134		C	17039564	G	C	17039564	3	2	7	1	0	0	0	0	1	0	0	0	9750	971	34	4	558	4	MPRIP	17	17039564	Missense_Mutation	SNP	G	TCGA-2Z-A9J7-01A-11D-A382-10		17039564	64155646	38	586											
ATP5G1	516	hgsc.bcm.edu	37	chr17	46973049	46973049	+	Missense_Mutation	SNP	A	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	caagcagcagctcttctcctAtgccattcttggctttgccc	6	13	7	15	0	3	0	0	0	3	0	4	0	3	0	3	1	5	4	3	1	2	5			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr17:46973049A>C	ENST00000393366.2	+	5	432	c.329A>C	c.(328-330)tAt>tCt	p.Y110S	RP11-463M16.4_ENST00000508743.1_RNA|ATP5G1_ENST00000355938.5_Missense_Mutation_p.Y110S|ATP5G1_ENST00000503641.1_Missense_Mutation_p.Y101S|ATP5G1_ENST00000506855.1_Missense_Mutation_p.Y84S|ATP5G1_ENST00000513781.1_3'UTR	NM_005175.2	NP_005166.1	P05496	AT5G1_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C1 (subunit 9)	110					ATP hydrolysis coupled proton transport (GO:0015991)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrion (GO:0005739)|proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045263)	hydrogen ion transmembrane transporter activity (GO:0015078)|lipid binding (GO:0008289)|transporter activity (GO:0005215)			liver(1)|lung(1)	2						CTCTTCTCCTATGCCATTCTT	0.582																																					p.Y110S		Atlas-SNP	.											.	ATP5G1	7	.	0			c.A329C						PASS	.						205	184	191					17																	46973049		2203	4300	6503	SO:0001583	missense	516	exon5			TCTCCTATGCCAT	D13118	CCDS11539.1	17q21.32	2012-10-12	2010-06-11		ENSG00000159199	ENSG00000159199		"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	841	protein-coding gene	gene with protein product		603192	"ATP synthase, H+ transporting, mitochondrial F0 complex, subunit c (subunit 9), isoform 1", "ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C1 (subunit 9)"	ATP5G		8328972	Standard	NM_005175		Approved		uc002ioh.3	P05496	OTTHUMG00000160520	ENST00000393366.2:c.329A>C	chr17.hg19:g.46973049A>C	ENSP00000377033:p.Tyr110Ser	37.0	0.0	.		76.0	22.0	.	NM_005175		Missense_Mutation	SNP	ENST00000393366.2	hg19	CCDS11539.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.469812	0.84533	.	.	ENSG00000159199	ENST00000355938;ENST00000503641;ENST00000393366;ENST00000506855	T;T;T;T	0.40756	1.02;1.02;1.02;1.02	4.64	4.64	0.57946	ATPase, F0/V0 complex, subunit C (3);	0.000000	0.85682	D	0.000000	T	0.47040	0.1424	L	0.61036	1.89	0.80722	D	1	B	0.29136	0.234	B	0.37047	0.24	T	0.53251	-0.8465	10	0.87932	D	0	-6.5187	13.8811	0.63682	1.0:0.0:0.0:0.0	.	110	P05496	AT5G1_HUMAN	S	110;101;110;84	ENSP00000348205:Y110S;ENSP00000426094:Y101S;ENSP00000377033:Y110S;ENSP00000422950:Y84S	ENSP00000348205:Y110S	Y	+	2	0	ATP5G1	44328048	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	9.139000	0.94554	1.951000	0.56629	0.454000	0.30748	TAT	.	.	.	none		0.582	ATP5G1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360948.2	NM_005175		C	46973049	A	C	46973049	3	2	7	1	0	0	0	0	1	0	0	0	1153	449	16	5	343	5	ATP5G1	17	46973049	Missense_Mutation	SNP	A	TCGA-2Z-A9J7-01A-11D-A382-10	29933485	46973049	34222161	39	587											
CLTC	1213	hgsc.bcm.edu	37	chr17	57742269	57742269	+	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	gcctcttgctgacatcacacAggtaatgtgattaaaatata	14	12	7	8	0	2	2	1	2	1	0	2	2	2	2	1	1	1	2	1	1	5	5			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr17:57742269A>G	ENST00000269122.3	+	10	1917	c.1643A>G	c.(1642-1644)cAg>cGg	p.Q548R	CLTC_ENST00000579456.1_Intron|CLTC_ENST00000393043.1_Splice_Site_p.Q548R	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	548	Distal segment.|Heavy chain arm.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					GACATCACACAGGTAATGTGA	0.433			T	"ALK, TFE3"	"ALCL, renal "																																p.Q548R		Atlas-SNP	.		Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	.	CLTC	124	.	0			c.A1643G						PASS	.						88	84	85					17																	57742269		2203	4300	6503	SO:0001630	splice_region_variant	1213	exon10			TCACACAGGTAAT	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.1644+1A>G	chr17.hg19:g.57742269A>G		66.0	0.0	.		98.0	26.0	.	NM_004859	D3DU00|Q6N0A0|Q86TF2	Missense_Mutation	SNP	ENST00000269122.3	hg19	CCDS32696.1	.	.	.	.	.	.	.	.	.	.	A	16.96	3.265813	0.59540	.	.	ENSG00000141367	ENST00000269122;ENST00000393043	T;T	0.17528	2.27;2.27	5.45	5.45	0.79879	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.31857	0.0810	L	0.42686	1.345	0.80722	D	1	P;B	0.49185	0.92;0.0	D;B	0.71870	0.975;0.01	T	0.02933	-1.1092	10	0.13108	T	0.6	.	15.8028	0.78468	1.0:0.0:0.0:0.0	.	548;548	Q00610;Q00610-2	CLH1_HUMAN;.	R	548	ENSP00000269122:Q548R;ENSP00000376763:Q548R	ENSP00000269122:Q548R	Q	+	2	0	CLTC	55097051	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	9.287000	0.95975	2.196000	0.70406	0.460000	0.39030	CAG	.	.	.	none		0.433	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859	Missense_Mutation	G	57742269	A	G	57742269	5	3	7	1	0	0	0	0	0	0	1	0	3568	202	7	3	1681	3	CLTC	17	57742269	Splice_Site	SNP	A	TCGA-2Z-A9J7-01A-11D-A382-10	10769220	57742269	23452941	40	588											
USP36	57602	hgsc.bcm.edu	37	chr17	76803450	76803450	+	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	tcccagatctgctgctattcGagttgctggtcccaggcagc	6	11	11	13	1	1	1	0	0	1	1	4	2	3	1	2	2	4	5	2	2	1	3	rs532327037		TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr17:76803450G>A	ENST00000542802.3	-	14	2119	c.1676C>T	c.(1675-1677)tCg>tTg	p.S559L	USP36_ENST00000312010.6_Missense_Mutation_p.S559L|USP36_ENST00000449938.2_Missense_Mutation_p.S259L|USP36_ENST00000588467.1_5'Flank			Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	559					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)			GCTGCTATTCGAGTTGCTGGT	0.582													G|||	1	0.000199681	0	0	5008	,	,		17767	0.001		0	False		,,,				2504	0				p.S559L		Atlas-SNP	.											.	USP36	243	.	0			c.C1676T						PASS	.						51	52	52					17																	76803450		2203	4300	6503	SO:0001583	missense	57602	exon14			CTATTCGAGTTGC	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.1676C>T	chr17.hg19:g.76803450G>A	ENSP00000441214:p.Ser559Leu	99.0	0.0	.		186.0	54.0	.	NM_025090	Q05C98|Q05DD0|Q6IQ38|Q8NDM8|Q9NVC8	Missense_Mutation	SNP	ENST00000542802.3	hg19	CCDS32755.1	.	.	.	.	.	.	.	.	.	.	G	10.85	1.466850	0.26335	.	.	ENSG00000055483	ENST00000312010;ENST00000449938;ENST00000542802	T;T;T	0.18810	3.24;2.19;3.24	4.16	-6.85	0.01681	.	2.812930	0.01095	N	0.005268	T	0.12433	0.0302	N	0.25647	0.755	0.09310	N	1	B;B	0.11235	0.002;0.004	B;B	0.04013	0.001;0.001	T	0.15983	-1.0418	10	0.22706	T	0.39	4.049	6.0048	0.19541	0.4716:0.2424:0.2859:0.0	.	559;559	Q9P275;Q9P275-2	UBP36_HUMAN;.	L	559;259;559	ENSP00000310590:S559L;ENSP00000401119:S259L;ENSP00000441214:S559L	ENSP00000310590:S559L	S	-	2	0	USP36	74315045	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.389000	0.02530	-1.303000	0.02332	-0.258000	0.10820	TCG	.	.	.	none		0.582	USP36-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437472.3	NM_025090		A	76803450	G	A	76803450	3	1	7	1	0	0	0	0	1	0	0	0	17079	1059	37	1	1723	1	USP36	17	76803450	Missense_Mutation	SNP	G	TCGA-2Z-A9J7-01A-11D-A382-10	19061181	76803450	4391760	41	589											
ZNF180	7733	hgsc.bcm.edu	37	chr19	44988631	44988631	+	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	gactttgatgataatctcttGaggaaggaaagaatcctgaa	15	11	10	5	0	1	5	0	4	1	1	3	8	2	7	1	2	0	0	1	2	5	3			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr19:44988631G>C	ENST00000221327.4	-	3	429	c.148C>G	c.(148-150)Caa>Gaa	p.Q50E	ZNF180_ENST00000586637.1_Nonsense_Mutation_p.S59*|ZNF180_ENST00000592529.1_Missense_Mutation_p.Q23E|ZNF180_ENST00000587047.1_Silent_p.L51L|ZNF180_ENST00000585514.1_5'UTR|ZNF180_ENST00000391956.4_Intron	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	50					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q50E(1)		NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				ATAATCTCTTGAGGAAGGAAA	0.463																																					p.Q50E	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											ZNF180,NS,carcinoma,0,1	ZNF180	103	.	1	Substitution - Missense(1)	endometrium(1)	c.C148G						PASS	.						81	75	77					19																	44988631		2203	4300	6503	SO:0001583	missense	7733	exon3			TCTCTTGAGGAAG	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.148C>G	chr19.hg19:g.44988631G>C	ENSP00000221327:p.Gln50Glu	75.0	0.0	.		68.0	27.0	.	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	hg19	CCDS12639.1	.	.	.	.	.	.	.	.	.	.	G	11.94	1.787995	0.31593	.	.	ENSG00000167384	ENST00000221327	T	0.07567	3.18	3.62	2.56	0.30785	.	0.229752	0.22273	N	0.062227	T	0.04998	0.0134	N	0.19112	0.55	0.80722	D	1	B;B	0.15930	0.015;0.015	B;B	0.11329	0.006;0.006	T	0.36890	-0.9729	10	0.15066	T	0.55	-9.8046	9.1823	0.37149	0.0:0.2219:0.7781:0.0	.	49;50	Q58F03;Q9UJW8	.;ZN180_HUMAN	E	50	ENSP00000221327:Q50E	ENSP00000221327:Q50E	Q	-	1	0	ZNF180	49680471	1.000000	0.71417	0.933000	0.37362	0.963000	0.63663	3.520000	0.53465	1.084000	0.41184	0.650000	0.86243	CAA	.	.	.	none		0.463	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256		C	44988631	G	C	44988631	3	2	7	1	0	0	0	0	1	0	0	0	17760	1299	45	4	1942	4	ZNF180	19	44988631	Missense_Mutation	SNP	G	TCGA-2Z-A9J7-01A-11D-A382-10		44988631	14140352	42	590											
LILRB1	10859	hgsc.bcm.edu	37	chr19	55148104	55148105	+	Splice_Site	DEL	GT	GT	-																															acaggcagatggacactgagGtgagtcctttcctctccagg																								rs201250339	byFrequency	TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr19:55148104_55148105delGT	ENST00000396331.1	+	15	2163		c.e15+1		LILRB1_ENST00000462628.1_Splice_Site|LILRB1_ENST00000396332.4_Splice_Site|AC009892.10_ENST00000456337.1_Intron|LILRB1_ENST00000324602.7_Splice_Site|LILRB1_ENST00000396327.3_Splice_Site|LILRB1_ENST00000434867.2_Splice_Site|LILRB1_ENST00000396315.1_Splice_Site|LILRB1_ENST00000418536.2_Splice_Site|LILRB1_ENST00000396321.2_Splice_Site|LILRB1_ENST00000396317.1_Splice_Site|LILRB1_ENST00000448689.1_Splice_Site|LILRB1_ENST00000427581.2_Splice_Site	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1						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)		GGACACTGAGGTGAGTCCTTTC	0.619										HNSCC(37;0.09)																											p.604_604del		Pindel	.											.	LILRB1	140	.	0			c.1812_1812del						PASS	.																																			SO:0001630	splice_region_variant	10859	exon14			.	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.1806+1GT>-	chr19.hg19:g.55148104_55148105delGT		104.0	0.0	.		103.0	12.0	0.117	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Frame_Shift_Del	DEL	ENST00000396331.1	hg19	CCDS42617.1																																																																																			.	.	.	none		0.619	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		Intron	-	55148105	GT	-	55148104	8	5	7	1	0	1	0	1	0	0	1	0	8797	1275	44	0	1863	0	LILRB1	19	55148104	Splice_Site	DEL	GT	TCGA-2Z-A9J7-01A-11D-A382-10	10159473	55148104	3980879	43	591											
UQCR10	29796	hgsc.bcm.edu	37	chr22	30163499	30163499	+	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	tcttcgagcgcgccttcgatCaaggcgcggacgctatctac	7	9	11	14	7	3	0	1	0	2	0	5	3	3	1	1	2	2	1	1	2	3	4	rs377432442		TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chr22:30163499C>T	ENST00000330029.6	+	1	142	c.112C>T	c.(112-114)Caa>Taa	p.Q38*	UQCR10_ENST00000401406.3_Nonsense_Mutation_p.Q38*|ZMAT5_ENST00000344318.3_5'Flank|ZMAT5_ENST00000397781.3_5'Flank	NM_001003684.1|NM_013387.3	NP_001003684.1|NP_037519.2	Q9UDW1	QCR9_HUMAN	ubiquinol-cytochrome c reductase, complex III subunit X	38					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)	ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)	5						CGCCTTCGATCAAGGCGCGGA	0.602																																					p.Q38X		Atlas-SNP	.											UQCR10,NS,carcinoma,0,1	UQCR10	10	.	0			c.C112T						PASS	.						41	47	45					22																	30163499		2010	4167	6177	SO:0001587	stop_gained	29796	exon1			TTCGATCAAGGCG	AB028598	CCDS46680.1, CCDS46681.1	22q12.2	2011-07-04			ENSG00000184076	ENSG00000184076		"Mitochondrial respiratory chain complex / Complex III"	30863	protein-coding gene	gene with protein product	"ubiquinol-cytochrome c reductase, complex III subunit X, 7.2kDa", "complex III subunit 9"	610843				11042152	Standard	NM_013387		Approved	HSPC051, UCRC, QCR9, UCCR7.2	uc003agq.1	Q9UDW1	OTTHUMG00000151283	ENST00000330029.6:c.112C>T	chr22.hg19:g.30163499C>T	ENSP00000332887:p.Gln38*	63.0	0.0	.		75.0	35.0	.	NM_001003684	B5MCM5|Q9T2V6	Nonsense_Mutation	SNP	ENST00000330029.6	hg19	CCDS46680.1	.	.	.	.	.	.	.	.	.	.	C	36	5.758193	0.96898	.	.	ENSG00000184076	ENST00000330029;ENST00000401406;ENST00000406782	.	.	.	5.73	5.73	0.89815	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	1.1857	15.4576	0.75327	0.0:1.0:0.0:0.0	.	.	.	.	X	38	.	ENSP00000332887:Q38X	Q	+	1	0	UQCR10	28493499	1.000000	0.71417	0.991000	0.47740	0.874000	0.50279	6.063000	0.71162	2.720000	0.93068	0.558000	0.71614	CAA	.	.	.	alt		0.602	UQCR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322081.1	NM_013387		T	30163499	C	T	30163499	4	4	7	1	0	0	0	0	0	1	0	0	17028	827	29	2	114	2	UQCR10	22	30163499	Nonsense_Mutation	SNP	C	TCGA-2Z-A9J7-01A-11D-A382-10		30163499	21141067	44	592											
PLCXD1	55344	hgsc.bcm.edu	37	chrX	205414	205414	+	Missense_Mutation	SNP	A	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	tctcagggagccacgacacgAtgacgtactgcctgaacaag	12	6	11	12	3	1	2	1	2	1	0	2	5	1	3	2	1	4	1	2	1	3	1			TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chrX:205414A>C	ENST00000381657.2	+	3	656	c.142A>C	c.(142-144)Atg>Ctg	p.M48L	PLCXD1_ENST00000399012.1_Missense_Mutation_p.M48L|PLCXD1_ENST00000484611.2_3'UTR|PLCXD1_ENST00000381663.3_Missense_Mutation_p.M48L	NM_018390.3	NP_060860.1	Q9NUJ7	PLCX1_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 1	48	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				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)				CCACGACACGATGACGTACTG	0.627																																					p.M48L		Atlas-SNP	.											.	PLCXD1	18	.	0			c.A142C						PASS	.						348	270	296					X																	205414		2203	4296	6499	SO:0001583	missense	55344	exon3			GACACGATGACGT	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.142A>C	chrX.hg19:g.205414A>C	ENSP00000371073:p.Met48Leu	281.0	0.0	.		176.0	163.0	.	NM_018390	A2BH51|A2BH52	Missense_Mutation	SNP	ENST00000381657.2	hg19	CCDS14103.1	.	.	.	.	.	.	.	.	.	.	.	11.38	1.622626	0.28889	.	.	ENSG00000182378	ENST00000399012;ENST00000430923;ENST00000445062;ENST00000381657;ENST00000429181;ENST00000381663;ENST00000443019;ENST00000415337;ENST00000447472;ENST00000448477	.	.	.	1.79	1.79	0.24919	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (1);	0.132030	0.64402	D	0.000002	T	0.36331	0.0963	.	.	.	0.09310	N	1	D	0.59357	0.985	P	0.61070	0.883	T	0.20240	-1.0281	8	0.11182	T	0.66	-50.3823	5.6988	0.17871	1.0:0.0:0.0:0.0	.	48	Q9NUJ7	PLCX1_HUMAN	L	48	.	ENSP00000371073:M48L	M	+	1	0	PLCXD1	145414	0.996000	0.38824	0.416000	0.26546	0.619000	0.37552	3.400000	0.52594	0.552000	0.29026	0.320000	0.21374	ATG	.	.	.	none		0.627	PLCXD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058879.2	NM_018390		C	205414	A	C	205414	3	2	7	1	0	0	0	0	1	0	0	0	12048	333	12	5	148	5	PLCXD1	23	205414	Missense_Mutation	SNP	A	TCGA-2Z-A9J7-01A-11D-A382-10		205414	155065146	45	593											
NRK	203447	hgsc.bcm.edu	37	chrX	105179166	105179166	+	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	ccttacatctttgcagtataCgctggattcgtagaagtacc	10	13	8	10	2	1	1	0	0	1	1	2	2	1	2	2	1	4	5	2	1	6	7	rs56273831		TCGA-2Z-A9J7-01A-11D-A382-10	TCGA-2Z-A9J7-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f706942e-5a4c-4299-bbb2-7da02d8f774d	29721c4c-1077-4ae3-9583-4d7cd96257fe	g.chrX:105179166C>A	ENST00000243300.9	+	21	3807	c.3504C>A	c.(3502-3504)taC>taA	p.Y1168*	NRK_ENST00000428173.2_Nonsense_Mutation_p.Y1169*	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	1168					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						TTGCAGTATACGCTGGATTCG	0.383										HNSCC(51;0.14)																											p.Y1168X		Atlas-SNP	.											.	NRK	321	.	0			c.C3504A						PASS	.						165	146	152					X																	105179166		1880	4096	5976	SO:0001587	stop_gained	203447	exon21			AGTATACGCTGGA	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.3504C>A	chrX.hg19:g.105179166C>A	ENSP00000434830:p.Tyr1168*	64.0	0.0	.		58.0	56.0	.	NM_198465	Q32ND6|Q5H9K2|Q6ZMP2	Nonsense_Mutation	SNP	ENST00000243300.9	hg19		.	.	.	.	.	.	.	.	.	.	C	39	7.642014	0.98406	.	.	ENSG00000123572	ENST00000243300;ENST00000428173	.	.	.	4.78	2.21	0.28008	.	0.336622	0.21892	N	0.067570	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	2.9928	0.05988	0.2156:0.1161:0.0:0.6683	.	.	.	.	X	1168;1169	.	ENSP00000434830:Y1168X	Y	+	3	2	NRK	105065822	0.992000	0.36948	0.557000	0.28306	0.083000	0.17756	1.051000	0.30417	0.764000	0.33197	-0.296000	0.09543	TAC	.	.	.	alt		0.383	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465		A	105179166	C	A	105179166	4	1	7	1	0	0	0	0	0	1	0	0	10662	547	19	4	3586	4	NRK	23	105179166	Nonsense_Mutation	SNP	C	TCGA-2Z-A9J7-01A-11D-A382-10	104973752	105179166	50091394	46	594											
ZFYVE9	9372	hgsc.bcm.edu	37	chr1	52769546	52769547	+	Frame_Shift_Ins	INS	-	-	A																															ttcaaggtttggtggttgatINSatggaagttcggaaaactag																										TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr1:52769546_52769547insA	ENST00000371591.1	+	12	3518_3519	c.3387_3388insA	c.(3388-3390)atgfs	p.M1130fs	ZFYVE9_ENST00000357206.2_Frame_Shift_Ins_p.M1071fs|ZFYVE9_ENST00000469134.1_3'UTR|ZFYVE9_ENST00000287727.3_Frame_Shift_Ins_p.M1130fs	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	1130					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						TGGTGGTTGATATGGAAGTTCG	0.371																																					p.D1129fs		Atlas-Indel,Pindel	.											.	ZFYVE9	131	.	0			c.3387_3388insA						PASS	.																																			SO:0001589	frameshift_variant	9372	exon13			.	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.3388dupA	chr1.hg19:g.52769547_52769547dupA	ENSP00000360647:p.Met1130fs	173.0	0.0	0		109.0	48.0	0.440367	NM_004799	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Frame_Shift_Ins	INS	ENST00000371591.1	hg19	CCDS563.1																																																																																			.	.	.	none		0.371	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324		A	52769547	-	A	52769546	7	5	8	1	0	1	1	0	0	0	0	0	17683	1403	49	0	3440	0	ZFYVE9	1	52769546	Frame_Shift_Ins	INS	-	TCGA-2Z-A9J8-01A-11D-A42J-10		52769546	196481075	1	595											
CAMSAP1L1	23271	hgsc.bcm.edu	37	chr1	200818453	200818453	+	Frame_Shift_Del	DEL	A	A	-																															gccaaatggctaaagtctccAactacacctattgatcctga																										TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr1:200818453delA	ENST00000236925.4	+	12	2638	c.2589delA	c.(2587-2589)ccafs	p.P863fs	CAMSAP2_ENST00000358823.2_Frame_Shift_Del_p.P852fs|CAMSAP2_ENST00000413307.2_Frame_Shift_Del_p.P836fs			Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein family, member 2	863					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)										TAAAGTCTCCAACTACACCTA	0.398																																					p.P852fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.2555delC						PASS	.						103	110	108					1																	200818453		2199	4300	6499	SO:0001589	frameshift_variant	23271	exon11			.	AB029001	CCDS1404.1, CCDS72998.1, CCDS72999.1	1q32	2011-08-18	2011-08-18	2011-08-18	ENSG00000118200	ENSG00000118200			29188	protein-coding gene	gene with protein product		613775	"calmodulin regulated spectrin-associated protein 1-like 1"	CAMSAP1L1		15897902, 19508979	Standard	XM_005245040		Approved	KIAA1078	uc001gvk.3	Q08AD1	OTTHUMG00000035740	ENST00000236925.4:c.2589delA	chr1.hg19:g.200818453delA	ENSP00000236925:p.Pro863fs	361.0	0.0	0		294.0	124.0	0.421769	NM_203459	B1APG6|Q08AD2|Q6PGN8|Q96FB3|Q9UG20|Q9UPS4	Frame_Shift_Del	DEL	ENST00000236925.4	hg19																																																																																				.	.	.	none		0.398	CAMSAP2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086956.2	NM_203459		-	200818453	A	-	200818453	7	5	8	1	0	1	0	1	0	0	0	0	2614	117	5	0	2598	0	CAMSAP1L1	1	200818453	Frame_Shift_Del	DEL	A	TCGA-2Z-A9J8-01A-11D-A42J-10	148048907	200818453	48432168	2	596											
C1orf101	257044	hgsc.bcm.edu	37	chr1	244662360	244662360	+	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	gatcctgatgagttgctgggGaatgcagaagaaccttcaat	12	10	12	7	0	1	4	1	2	0	2	2	6	2	5	2	2	3	3	2	2	4	2			TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr1:244662360G>A	ENST00000366534.4	+	7	462	c.408G>A	c.(406-408)ggG>ggA	p.G136G	C1orf101_ENST00000366533.4_Silent_p.G136G|C1orf101_ENST00000366531.3_Intron|C1orf101_ENST00000473875.1_Intron	NM_001130957.1	NP_001124429.1	Q5SY80	CA101_HUMAN	chromosome 1 open reading frame 101	136						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)			AGTTGCTGGGGAATGCAGAAG	0.353																																					p.G136G		Atlas-SNP	.											.	C1orf101	158	.	0			c.G408A						PASS	.						107	104	105					1																	244662360		2203	4300	6503	SO:0001819	synonymous_variant	257044	exon7			GCTGGGGAATGCA	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.408G>A	chr1.hg19:g.244662360G>A		372.0	0.0	.		316.0	133.0	.	NM_173807	B4DZR4|B7Z7X5|E9PEA3|Q8IYZ6	Silent	SNP	ENST00000366534.4	hg19	CCDS44340.1																																																																																			.	.	.	none		0.353	C1orf101-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096701.1	NM_173807		A	244662360	G	A	244662360	2	1	8	1	0	0	0	0	0	0	0	1	1978	1161	41	2		2	C1orf101	1	244662360	Silent	SNP	G	TCGA-2Z-A9J8-01A-11D-A42J-10	43843907	244662360	4588261	3	597											
FAM110C	642273	hgsc.bcm.edu	37	chr2	46002	46003	+	Frame_Shift_Ins	INS	-	-	T																															ccttgtccttacccggccccINStggaagagcttcttcaccag																										TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr2:46002_46003insT	ENST00000327669.4	-	1	382_383	c.383_384insA	c.(382-384)cagfs	p.Q128fs		NM_001077710.2	NP_001071178.2	Q1W6H9	F110C_HUMAN	family with sequence similarity 110, member C	128					positive regulation of cell migration (GO:0030335)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell projection assembly (GO:0060491)	cell cortex (GO:0005938)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)			central_nervous_system(1)|kidney(1)|lung(2)	4	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.00221)		all cancers(51;0.000815)|Epithelial(75;0.00379)|OV - Ovarian serous cystadenocarcinoma(76;0.0127)|GBM - Glioblastoma multiforme(21;0.232)		TACCCGGCCCCTGGAAGAGCTT	0.688																																					p.Q128fs		Atlas-Indel,Pindel	.											.	FAM110C	11	.	0			c.384_385insA						PASS	.																																			SO:0001589	frameshift_variant	642273	exon1			.	DQ431183	CCDS42645.1	2p25.3	2011-12-01			ENSG00000184731	ENSG00000184731			33340	protein-coding gene	gene with protein product		611395				17499476, 19698782	Standard	NM_001077710		Approved		uc010yim.2	Q1W6H9	OTTHUMG00000151321	ENST00000327669.4:c.384dupA	chr2.hg19:g.46003_46003dupT	ENSP00000328347:p.Gln128fs	66.0	0.0	0		47.0	19.0	0.404255	NM_001077710		Frame_Shift_Ins	INS	ENST00000327669.4	hg19	CCDS42645.1																																																																																			.	.	.	none		0.688	FAM110C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322220.1	NM_001077710		T	46003	-	T	46002	7	5	8	1	0	1	1	0	0	0	0	0	5402	680	24	0	589	0	FAM110C	2	46002	Frame_Shift_Ins	INS	-	TCGA-2Z-A9J8-01A-11D-A42J-10		46002	243153371	4	598											
ERBB4	2066	hgsc.bcm.edu	37	chr2	212578365	212578365	+	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	acaagaactggaatctaccaCaaagttatctgattaaaaaa	20	9	5	7	0	2	2	0	1	2	1	2	3	2	3	1	1	2	1	1	1	9	3			TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr2:212578365C>T	ENST00000342788.4	-	8	1202	c.892G>A	c.(892-894)Gtg>Atg	p.V298M	ERBB4_ENST00000436443.1_Missense_Mutation_p.V298M|ERBB4_ENST00000402597.1_Missense_Mutation_p.V298M	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	298	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)	GAATCTACCACAAAGTTATCT	0.333										TSP Lung(8;0.080)																											p.V298M		Atlas-SNP	.											.	ERBB4	480	.	0			c.G892A						PASS	.						74	72	73					2																	212578365		2203	4300	6503	SO:0001583	missense	2066	exon8			CTACCACAAAGTT	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.892G>A	chr2.hg19:g.212578365C>T	ENSP00000342235:p.Val298Met	73.0	0.0	.		56.0	20.0	.	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	hg19	CCDS2394.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.742600	0.89573	.	.	ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597	T;T;T	0.32023	1.47;1.47;1.47	5.61	5.61	0.85477	Growth factor, receptor (1);Furin-like cysteine-rich domain (1);	0.000000	0.85682	D	0.000000	T	0.63105	0.2483	M	0.85630	2.765	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;0.997;0.999;1.0;1.0	T	0.68104	-0.5497	10	0.87932	D	0	.	19.6299	0.95698	0.0:1.0:0.0:0.0	.	298;298;157;298;298	Q15303-4;Q15303-2;Q53QS8;Q15303-3;Q15303	.;.;.;.;ERBB4_HUMAN	M	298	ENSP00000342235:V298M;ENSP00000403204:V298M;ENSP00000385565:V298M	ENSP00000342235:V298M	V	-	1	0	ERBB4	212286610	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.818000	0.86416	2.639000	0.89480	0.655000	0.94253	GTG	.	.	.	none		0.333	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		T	212578365	C	T	212578365	3	4	8	1	0	0	0	0	1	0	0	0	5211	478	17	2	3118	2	ERBB4	2	212578365	Missense_Mutation	SNP	C	TCGA-2Z-A9J8-01A-11D-A42J-10	212532363	212578365	30621008	5	599											
CUL3	8452	hgsc.bcm.edu	37	chr2	225378264	225378264	+	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	aaaaaattctgcagacatttCcaaaaaaggagcctcaaaat	20	8	5	8	0	2	1	1	0	1	1	3	2	3	2	2	1	2	1	2	1	8	2			TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr2:225378264C>A	ENST00000264414.4	-	5	969	c.631G>T	c.(631-633)Gaa>Taa	p.E211*	CUL3_ENST00000432260.2_5'Flank|CUL3_ENST00000409777.1_Nonsense_Mutation_p.E187*|CUL3_ENST00000344951.4_Nonsense_Mutation_p.E145*|CUL3_ENST00000409096.1_Nonsense_Mutation_p.E187*	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	211					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)		GCAGACATTTCCAAAAAAGGA	0.303																																					p.E217X		Atlas-SNP	.											.	CUL3	96	.	0			c.G649T						PASS	.						57	60	59					2																	225378264		2202	4300	6502	SO:0001587	stop_gained	8452	exon5			ACATTTCCAAAAA	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.631G>T	chr2.hg19:g.225378264C>A	ENSP00000264414:p.Glu211*	240.0	0.0	.		251.0	107.0	.	NM_001257198	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Nonsense_Mutation	SNP	ENST00000264414.4	hg19	CCDS2462.1	.	.	.	.	.	.	.	.	.	.	C	38	6.790642	0.97841	.	.	ENSG00000036257	ENST00000264414;ENST00000344951;ENST00000409096;ENST00000409777	.	.	.	5.77	5.77	0.91146	.	0.095159	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	.	20.0562	0.97651	0.0:1.0:0.0:0.0	.	.	.	.	X	211;145;187;187	.	ENSP00000264414:E211X	E	-	1	0	CUL3	225086508	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	5.738000	0.68613	2.758000	0.94735	0.644000	0.83932	GAA	.	.	.	none		0.303	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2			A	225378264	C	A	225378264	4	1	8	1	0	0	0	0	0	1	0	0	4058	864	30	4	1723	4	CUL3	2	225378264	Nonsense_Mutation	SNP	C	TCGA-2Z-A9J8-01A-11D-A42J-10	12799899	225378264	17821109	6	600											
CUL3	8452	hgsc.bcm.edu	37	chr2	225449664	225449664	+	Frame_Shift_Del	DEL	A	A	-																															gccgaggagagactcaccggAaaggcccggatccgcatctt																										TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr2:225449664delA	ENST00000264414.4	-	1	401	c.63delT	c.(61-63)tttfs	p.F21fs	CUL3_ENST00000344951.4_Frame_Shift_Del_p.F21fs	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	21					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)		GACTCACCGGAAAGGCCCGGA	0.731																																					p.P22fs		Atlas-Indel,Pindel	.											.	CUL3	96	.	0			c.64delC						PASS	.						31	30	30					2																	225449664		2195	4298	6493	SO:0001589	frameshift_variant	8452	exon1			.	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.63delT	chr2.hg19:g.225449664delA	ENSP00000264414:p.Phe21fs	138.0	0.0	0		107.0	37.0	0.345794	NM_001257197	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Frame_Shift_Del	DEL	ENST00000264414.4	hg19	CCDS2462.1																																																																																			.	.	.	none		0.731	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2			-	225449664	A	-	225449664	7	5	8	1	0	1	0	1	0	0	0	0	4058	243	9	0	2307	0	CUL3	2	225449664	Frame_Shift_Del	DEL	A	TCGA-2Z-A9J8-01A-11D-A42J-10	71400	225449664	17749709	7	601											
NCBP2	22916	hgsc.bcm.edu	37	chr3	196666228	196666228	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcatagatttgttcttcagTtgtgtaaaaagaaagatttc	13	17	7	4	0	3	3	2	0	1	3	4	3	3	3	0	0	0	3	0	0	5	8			TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr3:196666228T>C	ENST00000321256.5	-	2	247	c.154A>G	c.(154-156)Act>Gct	p.T52A	NCBP2-AS1_ENST00000447775.1_RNA|NCBP2_ENST00000447325.1_5'UTR|NCBP2_ENST00000422610.1_5'UTR|NCBP2_ENST00000467803.1_5'Flank|NCBP2_ENST00000427641.2_Intron|NCBP2_ENST00000452404.2_Missense_Mutation_p.T34A	NM_007362.3	NP_031388.2	P52298	NCBP2_HUMAN	nuclear cap binding protein subunit 2, 20kDa	52	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of RNA export from nucleus (GO:0046833)|positive regulation of viral transcription (GO:0050434)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|snRNA export from nucleus (GO:0006408)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mRNA cap binding complex (GO:0005845)|nuclear cap binding complex (GO:0005846)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA 7-methylguanosine cap binding (GO:0000340)|RNA cap binding (GO:0000339)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.42e-24)|all cancers(36;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(49;4.13e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00551)		TGTTCTTCAGTTGTGTAAAAA	0.318																																					p.T52A		Atlas-SNP	.											.	NCBP2	12	.	0			c.A154G						PASS	.						100	98	99					3																	196666228		2203	4300	6503	SO:0001583	missense	22916	exon2			CTTCAGTTGTGTA	D59253	CCDS3323.1, CCDS46986.1	3q29	2013-02-12	2002-08-29		ENSG00000114503	ENSG00000114503		"RNA binding motif (RRM) containing"	7659	protein-coding gene	gene with protein product		605133	"nuclear cap binding protein subunit 2, 20kD"			7478990, 7651522, 8682299	Standard	NM_001042540		Approved	NIP1, CBP20, Cbc2	uc003fxd.1	P52298	OTTHUMG00000155520	ENST00000321256.5:c.154A>G	chr3.hg19:g.196666228T>C	ENSP00000326806:p.Thr52Ala	100.0	0.0	.		81.0	28.0	.	NM_007362	B2RE91|B4DMK7|E9PAR5|Q14924|Q2TS50	Missense_Mutation	SNP	ENST00000321256.5	hg19	CCDS3323.1	.	.	.	.	.	.	.	.	.	.	T	16.80	3.223483	0.58668	.	.	ENSG00000114503	ENST00000321256;ENST00000452404	T;T	0.80123	-1.34;-1.34	5.6	5.6	0.85130	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	D	0.88592	0.6478	M	0.83483	2.645	0.80722	D	1	B;D;B	0.60575	0.032;0.988;0.063	B;P;B	0.58391	0.052;0.838;0.141	D	0.90237	0.4283	10	0.72032	D	0.01	.	15.2696	0.73689	0.0:0.0:0.0:1.0	.	34;71;52	P52298-2;Q7Z3W9;P52298	.;.;NCBP2_HUMAN	A	52;34	ENSP00000326806:T52A;ENSP00000412785:T34A	ENSP00000326806:T52A	T	-	1	0	NCBP2	198150625	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.808000	0.62583	2.270000	0.75569	0.459000	0.35465	ACT	.	.	.	none		0.318	NCBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340470.2	NM_007362		C	196666228	T	C	196666228	3	2	8	1	0	0	0	0	1	0	0	0	10219	1725	60	3	328	3	NCBP2	3	196666228	Missense_Mutation	SNP	T	TCGA-2Z-A9J8-01A-11D-A42J-10		196666228	1356202	8	602											
STAP1	26228	hgsc.bcm.edu	37	chr4	68424597	68424597	+	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	aaaggttaaagattactgctCtacctttgtactttgaaggt	12	15	8	6	0	1	2	0	1	1	1	1	2	1	2	1	2	4	3	1	2	7	6			TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr4:68424597C>A	ENST00000265404.2	+	1	152	c.70C>A	c.(70-72)Cta>Ata	p.L24I	STAP1_ENST00000396225.1_Missense_Mutation_p.L24I	NM_012108.2	NP_036240.1	Q9ULZ2	STAP1_HUMAN	signal transducing adaptor family member 1	24					intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)				NS(1)|large_intestine(1)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	12						GATTACTGCTCTACCTTTGTA	0.408																																					p.L24I		Atlas-SNP	.											.	STAP1	46	.	0			c.C70A						PASS	.						110	116	114					4																	68424597		2203	4300	6503	SO:0001583	missense	26228	exon1			ACTGCTCTACCTT	AB023483	CCDS3515.1	4q13.2	2013-02-14	2007-08-09		ENSG00000035720	ENSG00000035720		"SH2 domain containing"	24133	protein-coding gene	gene with protein product	"BCR downstream signaling 1"	604298				10518561, 10679268	Standard	NM_012108		Approved	STAP-1, BRDG1	uc003hde.4	Q9ULZ2	OTTHUMG00000129304	ENST00000265404.2:c.70C>A	chr4.hg19:g.68424597C>A	ENSP00000265404:p.Leu24Ile	127.0	0.0	.		93.0	31.0	.	NM_012108	B2R980	Missense_Mutation	SNP	ENST00000265404.2	hg19	CCDS3515.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.102975	0.76983	.	.	ENSG00000035720	ENST00000265404;ENST00000396225	T;T	0.29917	1.55;1.55	5.36	5.36	0.76844	.	0.000000	0.64402	D	0.000015	T	0.53706	0.1813	M	0.71581	2.175	0.38906	D	0.957426	P	0.46457	0.878	D	0.74674	0.984	T	0.49679	-0.8914	10	0.26408	T	0.33	-11.5578	14.6071	0.68486	0.0:1.0:0.0:0.0	.	24	Q9ULZ2	STAP1_HUMAN	I	24	ENSP00000265404:L24I;ENSP00000379527:L24I	ENSP00000265404:L24I	L	+	1	2	STAP1	68107192	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.623000	0.46435	2.507000	0.84556	0.655000	0.94253	CTA	.	.	.	none		0.408	STAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251434.1	NM_012108		A	68424597	C	A	68424597	3	1	8	1	0	0	0	0	1	0	0	0	15264	912	32	4	72	4	STAP1	4	68424597	Missense_Mutation	SNP	C	TCGA-2Z-A9J8-01A-11D-A42J-10		68424597	122729679	9	603											
NAAA	27163	hgsc.bcm.edu	37	chr4	76841890	76841890	+	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	agaaagcacgtagcagcctaCctccggtcatcttccttggg	9	9	10	13	2	2	1	1	0	1	1	4	1	4	1	4	2	4	3	4	2	3	4			TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr4:76841890C>G	ENST00000286733.4	-	7	1004		c.e7+1		NAAA_ENST00000399497.3_Splice_Site|NAAA_ENST00000507956.1_Splice_Site|NAAA_ENST00000511606.1_Splice_Site|NAAA_ENST00000505594.1_Splice_Site	NM_014435.3	NP_055250.2	Q02083	NAAA_HUMAN	N-acylethanolamine acid amidase						lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	11						TAGCAGCCTACCTCCGGTCAT	0.493																																					.		Atlas-SNP	.											.	NAAA	26	.	0			c.902+1G>C						PASS	.						137	143	141					4																	76841890		2005	4193	6198	SO:0001630	splice_region_variant	27163	exon8			AGCCTACCTCCGG	M92449	CCDS43239.1	4q21.1	2011-09-23	2008-04-24	2008-04-24	ENSG00000138744	ENSG00000138744	3.5.1.-		736	protein-coding gene	gene with protein product		607469	"N-acylsphingosine amidohydrolase (acid ceramidase)-like"	ASAHL		10610717, 1446826	Standard	NM_001042402		Approved		uc003hjb.3	Q02083	OTTHUMG00000160855	ENST00000286733.4:c.902+1G>C	chr4.hg19:g.76841890C>G		220.0	0.0	.		150.0	67.0	.	NM_001042402	Q5KTF2|Q96EY2|Q9BRA8	Splice_Site	SNP	ENST00000286733.4	hg19	CCDS43239.1	.	.	.	.	.	.	.	.	.	.	C	12.32	1.902094	0.33628	.	.	ENSG00000138744	ENST00000399497;ENST00000286733;ENST00000513045;ENST00000507956;ENST00000505594	.	.	.	5.86	5.86	0.93980	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.6924	0.88272	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NAAA	77060914	1.000000	0.71417	1.000000	0.80357	0.081000	0.17604	6.194000	0.72082	2.781000	0.95711	0.650000	0.86243	.	.	.	.	none		0.493	NAAA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362843.4		Intron	G	76841890	C	G	76841890	5	3	8	1	0	0	0	0	0	0	1	0	10134	521	18	4	199	4	NAAA	4	76841890	Splice_Site	SNP	C	TCGA-2Z-A9J8-01A-11D-A42J-10	8417293	76841890	114312386	10	604											
NIPBL	25836	hgsc.bcm.edu	37	chr5	36995727	36995743	+	Frame_Shift_Del	DEL	GTATAGATCAATCAGTG	GTATAGATCAATCAGTG	-																															ttacctttcattaataggtaGtatagatcaatcagtgttaa																								rs368762999		TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	GTATAGATCAATCAGTG	GTATAGATCAATCAGTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr5:36995727_36995743delGTATAGATCAATCAGTG	ENST00000282516.8	+	11	3624_3640	c.3125_3141delGTATAGATCAATCAGTG	c.(3124-3141)agtatagatcaatcagtgfs	p.SIDQSV1042fs	NIPBL_ENST00000504430.1_3'UTR|NIPBL_ENST00000448238.2_Frame_Shift_Del_p.SIDQSV1042fs	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	1042					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)	p.Q1045E(2)		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)			TTAATAGGTAGTATAGATCAATCAGTGTTAAAAGAAT	0.304																																					p.1042_1047del		Atlas-Indel,Pindel	.											.	NIPBL	513	.	2	Substitution - Missense(2)	lung(2)	c.3124_3140del						PASS	.																																			SO:0001589	frameshift_variant	25836	exon11			.	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.3125_3141delGTATAGATCAATCAGTG	chr5.hg19:g.36995727_36995743delGTATAGATCAATCAGTG	ENSP00000282516:p.Ser1042fs	160.0	0.0	0		128.0	54.0	0.421875	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Frame_Shift_Del	DEL	ENST00000282516.8	hg19	CCDS3920.1																																																																																			.	.	.	none		0.304	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		-	36995743	GTATAGATCAATCAGTG	-	36995727	7	5	8	1	0	1	0	1	0	0	0	0	10435	1029	36	0	3163	0	NIPBL	5	36995727	Frame_Shift_Del	DEL	GTATAGATCAATCAGTG	TCGA-2Z-A9J8-01A-11D-A42J-10		36995727	143919533	11	605											
CLK4	57396	hgsc.bcm.edu	37	chr5	178043950	178043950	+	Splice_Site	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	caaagtgtccacgatttcatCtagagtgaggagggaaaaag	15	8	12	6	1	2	2	1	1	1	1	3	5	3	4	1	2	0	0	1	2	4	2			TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr5:178043950C>G	ENST00000316308.4	-	5	644		c.e5-1		CLK4_ENST00000522749.1_Splice_Site|RN7SKP70_ENST00000516655.1_RNA	NM_020666.2	NP_065717.1	Q9HAZ1	CLK4_HUMAN	CDC-like kinase 4						protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(2)	21	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.235)		ACGATTTCATCTAGAGTGAGG	0.378																																					.		Atlas-SNP	.											.	CLK4	103	.	0			c.476-1G>C						PASS	.						99	91	94					5																	178043950		2203	4300	6503	SO:0001630	splice_region_variant	57396	exon6			TTTCATCTAGAGT	AF294429	CCDS4437.1	5q35	2008-05-02			ENSG00000113240	ENSG00000113240		"CDC-like kinases"	13659	protein-coding gene	gene with protein product		607969				11170754	Standard	NM_020666		Approved		uc003mjf.1	Q9HAZ1	OTTHUMG00000130893	ENST00000316308.4:c.476-1G>C	chr5.hg19:g.178043950C>G		276.0	0.0	.		232.0	73.0	.	NM_020666		Splice_Site	SNP	ENST00000316308.4	hg19	CCDS4437.1	.	.	.	.	.	.	.	.	.	.	C	15.91	2.972257	0.53614	.	.	ENSG00000113240	ENST00000316308;ENST00000536763	.	.	.	5.38	5.38	0.77491	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.6461	0.85177	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CLK4	177976556	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.669000	0.83911	2.529000	0.85273	0.650000	0.86243	.	.	.	.	none		0.378	CLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253479.2		Intron	G	178043950	C	G	178043950	5	3	8	1	0	0	0	0	0	0	1	0	3541	927	32	4	1006	4	CLK4	5	178043950	Splice_Site	SNP	C	TCGA-2Z-A9J8-01A-11D-A42J-10	141048223	178043950	2871310	12	606											
RXRB	6257	hgsc.bcm.edu	37	chr6	33168099	33168099	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgttctccgcctgccaccGccgccgccgccgccgctgcg	1	7	12	21	8	1	0	0	0	1	0	2	0	1	0	9	0	2	3	9	0	0	2			TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr6:33168099G>A	ENST00000374680.3	-	1	366	c.155C>T	c.(154-156)gCg>gTg	p.A52V	SLC39A7_ENST00000374677.3_5'Flank|RNY4P10_ENST00000365571.1_RNA|RXRB_ENST00000544186.1_Intron|RXRB_ENST00000374685.4_Missense_Mutation_p.A52V|SLC39A7_ENST00000374675.3_5'Flank|RXRB_ENST00000413614.2_Missense_Mutation_p.R39W	NM_001270401.1|NM_021976.4	NP_001257330.1|NP_068811.1	P28702	RXRB_HUMAN	retinoid X receptor, beta	52	Modulating. {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)	gcctgccaccgccgccgccgc	0.736																																					p.A52V		Atlas-SNP	.											.	RXRB	34	.	0			c.C155T						PASS	.						4	5	5					6																	33168099		1328	2374	3702	SO:0001583	missense	6257	exon1			GCCACCGCCGCCG	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.155C>T	chr6.hg19:g.33168099G>A	ENSP00000363812:p.Ala52Val	120.0	0.0	.		83.0	4.0	.	NM_021976	P28703|Q59G65|Q5JP92|Q5STQ1	Missense_Mutation	SNP	ENST00000374680.3	hg19	CCDS4768.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.61|17.61	3.433234|3.433234	0.62844|0.62844	.|.	.|.	ENSG00000204231|ENSG00000204231	ENST00000374685;ENST00000374680|ENST00000413614	D;D|D	0.92805|0.94092	-3.11;-3.11|-3.35	4.89|4.89	3.94|3.94	0.45596|0.45596	.|.	1.429120|.	0.04277|.	N|.	0.343109|.	T|T	0.75517|0.75517	0.3860|0.3860	N|N	0.08118|0.08118	0|0	0.25642|0.25642	N|N	0.9862|0.9862	B;B;B;B|B	0.18310|0.06786	0.027;0.001;0.001;0.001|0.001	B;B;B;B|B	0.08055|0.01281	0.003;0.0;0.0;0.0|0.0	T|T	0.67856|0.67856	-0.5562|-0.5562	10|9	0.31617|0.87932	T|D	0.26|0	.|.	7.295|7.295	0.26387|0.26387	0.1227:0.0:0.8773:0.0|0.1227:0.0:0.8773:0.0	.|.	52;52;92;52|39	B7Z6J2;B7Z6X3;Q59G65;P28702|B7Z3E4	.;.;.;RXRB_HUMAN|.	V|W	52|39	ENSP00000363817:A52V;ENSP00000363812:A52V|ENSP00000415561:R39W	ENSP00000363812:A52V|ENSP00000415561:R39W	A|R	-|-	2|1	0|2	RXRB|RXRB	33276077|33276077	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.847000|0.847000	0.48162|0.48162	1.319000|1.319000	0.33655|0.33655	2.535000|2.535000	0.85469|0.85469	0.549000|0.549000	0.68633|0.68633	GCG|CGG	.	.	.	none		0.736	RXRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076642.2	NM_021976		A	33168099	G	A	33168099	3	1	8	1	0	0	0	0	1	0	0	0	13777	1087	38	1	1486	1	RXRB	6	33168099	Missense_Mutation	SNP	G	TCGA-2Z-A9J8-01A-11D-A42J-10		33168099	137946968	13	607											
TTYH3	80727	hgsc.bcm.edu	37	chr7	2696131	2696132	+	Frame_Shift_Ins	INS	-	-	TCGT																															agccctcatgttcagctccaINStcgtctgcagcgtcccgcac																										TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr7:2696131_2696132insTCGT	ENST00000258796.7	+	11	1418_1419	c.1213_1214insTCGT	c.(1213-1215)atcfs	p.-406fs	TTYH3_ENST00000407643.1_Frame_Shift_Ins_p.-374fs|TTYH3_ENST00000403167.1_Frame_Shift_Ins_p.-235fs	NM_025250.2	NP_079526.1	Q9C0H2	TTYH3_HUMAN	tweety family member 3						chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|intracellular calcium activated chloride channel activity (GO:0005229)			kidney(1)|large_intestine(3)|lung(9)|prostate(2)|upper_aerodigestive_tract(2)	17		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.04e-14)		GTTCAGCTCCATCGTCTGCAGC	0.639																																					p.I405fs		Atlas-Indel,Pindel	.											.	TTYH3	36	.	0			c.1213_1214insTCGT						PASS	.																																			SO:0001589	frameshift_variant	80727	exon11			.		CCDS34588.1	7p22	2013-09-02	2013-09-02		ENSG00000136295	ENSG00000136295			22222	protein-coding gene	gene with protein product		608919	"tweety homolog 3 (Drosophila)"				Standard	NM_025250		Approved	KIAA1691	uc003smp.3	Q9C0H2	OTTHUMG00000152050	ENST00000258796.7:c.1214_1217dupTCGT	chr7.hg19:g.2696132_2696135dupTCGT	ENSP00000258796:p.Val406fs	38.0	0.0	0		30.0	11.0	0.366667	NM_025250	A4D201|B7WP98|Q6L749|Q6ZVG3|Q8TEG6	Frame_Shift_Ins	INS	ENST00000258796.7	hg19	CCDS34588.1																																																																																			.	.	.	none		0.639	TTYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325082.2	XM_166523		TCGT	2696132	-	TCGT	2696131	7	5	8	1	0	1	1	0	0	0	0	0	16753	217	8	0	1255	0	TTYH3	7	2696131	Frame_Shift_Ins	INS	-	TCGA-2Z-A9J8-01A-11D-A42J-10		2696131	156442532	14	608											
AP1S1	1174	hgsc.bcm.edu	37	chr7	100802478	100802478	+	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	aggctgacctactgcaagagGtacgggccagggacagtgag	11	5	16	9	1	0	3	0	2	0	1	0	4	0	4	2	4	3	3	2	4	3	2			TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr7:100802478G>T	ENST00000337619.5	+	4	547		c.e4+1		MIR4653_ENST00000585107.1_RNA	NM_001283.3	NP_001274.1	P61966	AP1S1_HUMAN	adaptor-related protein complex 1, sigma 1 subunit						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)|receptor-mediated endocytosis (GO:0006898)|regulation of defense response to virus by virus (GO:0050690)|response to virus (GO:0009615)|viral process (GO:0016032)	AP-1 adaptor complex (GO:0030121)|coated pit (GO:0005905)|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)	protein transporter activity (GO:0008565)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)	8	Lung NSC(181;0.168)|all_lung(186;0.215)					ACTGCAAGAGGTACGGGCCAG	0.622																																					.		Atlas-SNP	.											.	AP1S1	22	.	0			c.429+1G>T						PASS	.						32	34	33					7																	100802478		2157	4257	6414	SO:0001630	splice_region_variant	1174	exon4			CAAGAGGTACGGG	AB015319	CCDS47669.1	7q22.1	2014-02-04			ENSG00000106367	ENSG00000106367			559	protein-coding gene	gene with protein product	"clathrin-associated/assembly/adaptor protein, small 1 (19kD)", "clathrin coat assembly protein AP19", "sigma1A subunit of AP-1 clathrin adaptor complex", "AP-1 complex subunit sigma-1A", "sigma1A-adaptin", "golgi adaptor HA1/AP1 adaptin sigma-1A subunit", "clathrin assembly protein complex 1 sigma-1A small chain", "HA1 19 kDa subunit"	603531	"erythrokeratodermia variabilis 3 (Kamouraska type)"	CLAPS1, EKV3		9653655, 9733768, 19057675	Standard	NM_001283		Approved	AP19, SIGMA1A, WUGSC:H_DJ0747G18.2	uc003uxv.4	P61966	OTTHUMG00000157103	ENST00000337619.5:c.429+1G>T	chr7.hg19:g.100802478G>T		51.0	0.0	.		27.0	7.0	.	NM_001283	B2R5D8|P82267|Q00382|Q53YA7|Q9BTN4|Q9UDW9	Splice_Site	SNP	ENST00000337619.5	hg19	CCDS47669.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.977593	0.74360	.	.	ENSG00000106367	ENST00000337619;ENST00000429457	.	.	.	4.46	4.46	0.54185	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9897	0.71377	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AP1S1	100589198	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	9.269000	0.95684	2.474000	0.83562	0.555000	0.69702	.	.	.	.	none		0.622	AP1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347439.1	NM_001283	Intron	T	100802478	G	T	100802478	5	4	8	1	0	0	0	0	0	0	1	0	736	1275	44	4	444	4	AP1S1	7	100802478	Splice_Site	SNP	G	TCGA-2Z-A9J8-01A-11D-A42J-10	98106347	100802478	58336185	15	609											
OC90	729330	hgsc.bcm.edu	37	chr8	133044287	133044287	+	Frame_Shift_Del	DEL	A	A	-																															ttcccaggtgcaggaaggtgAatctgtcacaggctgaaagg																										TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr8:133044287delA	ENST00000443356.2	-	13	1006	c.920delT	c.(919-921)ttcfs	p.F307fs	OC90_ENST00000254627.3_Frame_Shift_Del_p.F291fs|OC90_ENST00000603859.1_Frame_Shift_Del_p.F291fs|OC90_ENST00000262283.5_Frame_Shift_Del_p.F503fs			Q02509	OC90_HUMAN	otoconin 90	307					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)			CAGGAAGGTGAATCTGTCACA	0.547																																					p.F291fs		Atlas-Indel,Pindel	.											OC90_ENST00000262283,NS,carcinoma,0,2	OC90	163	.	0			c.873delC						PASS	.						114	111	112					8																	133044287		2066	4223	6289	SO:0001589	frameshift_variant	729330	exon12			.	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.920delT	chr8.hg19:g.133044287delA	ENSP00000390050:p.Phe307fs	96.0	0.0	0		85.0	45.0	0.529412	NM_001080399	B4DNG8	Frame_Shift_Del	DEL	ENST00000443356.2	hg19																																																																																				.	.	.	none		0.547	OC90-201	KNOWN	basic	protein_coding	protein_coding		NM_001080399		-	133044287	A	-	133044287	7	5	8	1	0	1	0	1	0	0	0	0	10821	246	9	0	573	0	OC90	8	133044287	Frame_Shift_Del	DEL	A	TCGA-2Z-A9J8-01A-11D-A42J-10		133044287	13319735	16	610											
MAPK15	225689	hgsc.bcm.edu	37	chr8	144803996	144803996	+	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	caggtggccaaccaggccctGatccggggtgactggaaccg	8	5	15	13	2	0	2	0	2	0	0	1	3	1	3	5	6	2	0	5	6	2	0			TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr8:144803996G>T	ENST00000338033.4	+	13	1523	c.1404G>T	c.(1402-1404)ctG>ctT	p.L468L	RP11-429J17.5_ENST00000527908.1_RNA	NM_139021.2	NP_620590.2	Q8TD08	MK15_HUMAN	mitogen-activated protein kinase 15	468					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)			ACCAGGCCCTGATCCGGGGTG	0.692																																					p.L468L		Atlas-SNP	.											.	MAPK15	32	.	0			c.G1404T						PASS	.						31	40	37					8																	144803996		1969	4120	6089	SO:0001819	synonymous_variant	225689	exon13			GGCCCTGATCCGG	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.1404G>T	chr8.hg19:g.144803996G>T		93.0	0.0	.		56.0	33.0	.	NM_139021	Q2TCF9|Q8N362	Silent	SNP	ENST00000338033.4	hg19	CCDS6409.2																																																																																			.	.	.	none		0.692	MAPK15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000300348.1	NM_139021		T	144803996	G	T	144803996	2	4	8	1	0	0	0	0	0	0	0	1	9284	1277	45	4		4	MAPK15	8	144803996	Silent	SNP	G	TCGA-2Z-A9J8-01A-11D-A42J-10	11759709	144803996	1560026	17	611											
RRAGA	10670	hgsc.bcm.edu	37	chr9	19049688	19049688	+	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	cagccatgaagaaaaaggtgCtgctgatggggaagagcggg	13	5	17	6	1	0	4	0	2	0	2	0	5	0	5	1	4	4	2	1	4	4	0			TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr9:19049688C>A	ENST00000380527.1	+	1	317	c.31C>A	c.(31-33)Ctg>Atg	p.L11M		NM_006570.4	NP_006561.1			Ras-related GTP binding A											endometrium(1)|large_intestine(1)|lung(1)	3						GAAAAAGGTGCTGCTGATGGG	0.647																																					p.L11M		Atlas-SNP	.											.	RRAGA	17	.	0			c.C31A						PASS	.						43	43	43					9																	19049688		2203	4300	6503	SO:0001583	missense	10670	exon1			AAGGTGCTGCTGA	BC006433	CCDS6488.1	9p21.3	2008-02-05			ENSG00000155876	ENSG00000155876			16963	protein-coding gene	gene with protein product		612194				7499430, 8995684	Standard	NM_006570		Approved	RAGA, FIP-1	uc003znj.3	Q7L523	OTTHUMG00000019621	ENST00000380527.1:c.31C>A	chr9.hg19:g.19049688C>A	ENSP00000369899:p.Leu11Met	164.0	0.0	.		127.0	50.0	.	NM_006570		Missense_Mutation	SNP	ENST00000380527.1	hg19	CCDS6488.1	.	.	.	.	.	.	.	.	.	.	C	17.95	3.513952	0.64522	.	.	ENSG00000155876	ENST00000380527	T	0.74737	-0.87	4.81	4.81	0.61882	.	0.000000	0.64402	D	0.000019	D	0.90027	0.6886	H	0.95504	3.68	0.50813	D	0.999899	D	0.89917	1.0	D	0.97110	1.0	D	0.92530	0.6032	10	0.72032	D	0.01	-0.4855	15.8	0.78447	0.0:1.0:0.0:0.0	.	11	Q7L523	RRAGA_HUMAN	M	11	ENSP00000369899:L11M	ENSP00000369899:L11M	L	+	1	2	RRAGA	19039688	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	2.590000	0.46154	2.677000	0.91161	0.655000	0.94253	CTG	.	.	.	none		0.647	RRAGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051824.1	NM_006570		A	19049688	C	A	19049688	3	1	8	1	0	0	0	0	1	0	0	0	13685	796	28	4	33	4	RRAGA	9	19049688	Missense_Mutation	SNP	C	TCGA-2Z-A9J8-01A-11D-A42J-10		19049688	122163743	18	612											
ZNF195	7748	hgsc.bcm.edu	37	chr11	3380633	3380633	+	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	ctcttatgtacaataaggttGgaggactgggtaaagttttt	11	15	11	4	0	1	0	0	0	1	0	1	2	1	2	0	4	1	4	0	4	6	7			TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr11:3380633G>T	ENST00000399602.4	-	6	1731	c.1605C>A	c.(1603-1605)tcC>tcA	p.S535S	ZNF195_ENST00000354599.6_Silent_p.S463S|ZNF195_ENST00000005082.9_Silent_p.S512S|ZNF195_ENST00000343338.7_Silent_p.S467S|ZNF195_ENST00000526601.1_Silent_p.S516S|ZNF195_ENST00000528796.1_Intron|ZNF195_ENST00000429541.2_Silent_p.S467S	NM_001130520.2	NP_001123992.1	O14628	ZN195_HUMAN	zinc finger protein 195	535					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)		CAATAAGGTTGGAGGACTGGG	0.398																																					p.S535S		Atlas-SNP	.											ZNF195,NS,carcinoma,0,1	ZNF195	77	.	0			c.C1605A						PASS	.						138	140	139					11																	3380633		2042	4219	6261	SO:0001819	synonymous_variant	7748	exon6			AAGGTTGGAGGAC		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.1605C>A	chr11.hg19:g.3380633G>T		99.0	0.0	.		90.0	4.0	.	NM_001130520	A8K234|B3KTK2|B4DEL0|C9JLY9|L7MNK2|Q0VAJ6|Q658N8|Q6ZNA9	Silent	SNP	ENST00000399602.4	hg19	CCDS44522.1																																																																																			.	.	.	none		0.398	ZNF195-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032321.2			T	3380633	G	T	3380633	2	4	8	1	0	0	0	0	0	0	0	1	17770	1335	47	4		4	ZNF195	11	3380633	Silent	SNP	G	TCGA-2Z-A9J8-01A-11D-A42J-10		3380633	131625883	19	613											
MS4A7	58475	hgsc.bcm.edu	37	chr11	60156941	60156941	+	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	tcctccttgctgacagcatgGtagccctgaggactgcctct	6	11	10	14	0	1	2	0	2	1	0	3	3	3	3	4	2	4	3	4	2	1	2			TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr11:60156941G>T	ENST00000300184.3	+	5	614	c.418G>T	c.(418-420)Gta>Tta	p.V140L	MS4A7_ENST00000358246.1_Missense_Mutation_p.V95L|MS4A7_ENST00000534016.1_Missense_Mutation_p.V95L|MS4A7_ENST00000530234.2_Intron|MS4A14_ENST00000531787.1_Intron	NM_021201.4|NM_206939.1	NP_067024.1|NP_996822.1	Q9GZW8	MS4A7_HUMAN	membrane-spanning 4-domains, subfamily A, member 7	140						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						TGACAGCATGGTAGCCCTGAG	0.458																																					p.V140L		Atlas-SNP	.											.	MS4A7	38	.	0			c.G418T						PASS	.						123	106	111					11																	60156941		2203	4300	6503	SO:0001583	missense	58475	exon5			AGCATGGTAGCCC	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.418G>T	chr11.hg19:g.60156941G>T	ENSP00000300184:p.Val140Leu	104.0	0.0	.		87.0	36.0	.	NM_021201	A6NP53|Q6IAG8	Missense_Mutation	SNP	ENST00000300184.3	hg19	CCDS7985.1	.	.	.	.	.	.	.	.	.	.	G	12.80	2.047263	0.36085	.	.	ENSG00000166927	ENST00000300184;ENST00000358246;ENST00000534016;ENST00000530614;ENST00000530027	T;T;T;T;T	0.02121	4.44;4.44;4.44;4.44;4.44	3.69	0.755	0.18415	.	1.192500	0.06080	N	0.661653	T	0.05227	0.0139	M	0.66939	2.045	0.09310	N	0.999995	P;P;P	0.48503	0.911;0.891;0.835	P;P;B	0.51516	0.672;0.487;0.394	T	0.41052	-0.9530	10	0.10902	T	0.67	-14.9503	5.1754	0.15131	0.4047:0.0:0.5953:0.0	.	95;95;140	E9PIV6;Q9GZW8-2;Q9GZW8	.;.;MS4A7_HUMAN	L	140;95;95;95;76	ENSP00000300184:V140L;ENSP00000350983:V95L;ENSP00000434637:V95L;ENSP00000433861:V95L;ENSP00000434819:V76L	ENSP00000300184:V140L	V	+	1	0	MS4A7	59913517	0.030000	0.19436	0.014000	0.15608	0.010000	0.07245	0.052000	0.14163	0.173000	0.19788	0.563000	0.77884	GTA	.	.	.	none		0.458	MS4A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394299.1			T	60156941	G	T	60156941	3	4	8	1	0	0	0	0	1	0	0	0	9873	1261	44	4	432	4	MS4A7	11	60156941	Missense_Mutation	SNP	G	TCGA-2Z-A9J8-01A-11D-A42J-10	56776308	60156941	74849575	20	614											
DPF2	5977	hgsc.bcm.edu	37	chr11	65108472	65108472	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgtactcctaccctgccCggcgctggcggaaaaagcgg	8	6	13	14	4	0	0	0	0	0	0	1	1	1	1	3	4	5	3	3	4	4	2			TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr11:65108472C>T	ENST00000528416.1	+	3	362	c.229C>T	c.(229-231)Cgg>Tgg	p.R77W	DPF2_ENST00000415073.2_Missense_Mutation_p.R77W|DPF2_ENST00000252268.4_Missense_Mutation_p.R77W|DPF2_ENST00000532264.1_3'UTR	NM_006268.4	NP_006259.1	Q92785	REQU_HUMAN	D4, zinc and double PHD fingers family 2	77					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						CTACCCTGCCCGGCGCTGGCG	0.537																																					p.R77W		Atlas-SNP	.											.	DPF2	54	.	0			c.C229T						PASS	.						61	56	58					11																	65108472		2201	4297	6498	SO:0001583	missense	5977	exon3			CCTGCCCGGCGCT	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.229C>T	chr11.hg19:g.65108472C>T	ENSP00000436901:p.Arg77Trp	76.0	0.0	.		69.0	32.0	.	NM_006268	A8K7C9|B4DT58	Missense_Mutation	SNP	ENST00000528416.1	hg19	CCDS8100.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.376421	0.82682	.	.	ENSG00000133884	ENST00000528416;ENST00000415073;ENST00000252268	D;D;D	0.91407	-2.75;-2.84;-2.76	5.4	3.49	0.39957	.	0.000000	0.34025	N	0.004326	D	0.94604	0.8261	M	0.77103	2.36	0.52501	D	0.999951	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;1.0;0.998	D	0.94286	0.7524	10	0.87932	D	0	-16.7802	12.6765	0.56897	0.2988:0.7012:0.0:0.0	.	77;77;77	B4DT58;E9PN04;Q92785	.;.;REQU_HUMAN	W	77	ENSP00000436901:R77W;ENSP00000399714:R77W;ENSP00000252268:R77W	ENSP00000252268:R77W	R	+	1	2	DPF2	64865048	0.929000	0.31497	1.000000	0.80357	0.994000	0.84299	1.997000	0.40786	0.631000	0.30412	0.460000	0.39030	CGG	.	.	.	none		0.537	DPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387293.3	NM_006268		T	65108472	C	T	65108472	3	4	8	1	0	0	0	0	1	0	0	0	4719	643	23	1	239	1	DPF2	11	65108472	Missense_Mutation	SNP	C	TCGA-2Z-A9J8-01A-11D-A42J-10	4951531	65108472	69898044	21	615											
ANKRD33	341405	hgsc.bcm.edu	37	chr12	52282036	52282036	+	5'UTR	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	atagtccacctggaggcattCggagacccagtgattgtgct	9	10	12	10	1	0	2	0	1	0	1	2	4	1	3	3	3	1	2	3	3	1	3			TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr12:52282036C>A	ENST00000340970.4	+	0	36				ANKRD33_ENST00000538991.1_5'UTR|ANKRD33_ENST00000301190.6_Missense_Mutation_p.F22L			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)		TGGAGGCATTCGGAGACCCAG	0.577																																					p.F22L		Atlas-SNP	.											ANKRD33,colon,carcinoma,0,1	ANKRD33	33	.	0			c.C66A						PASS	.						113	104	107					12																	52282036		2203	4300	6503	SO:0001623	5_prime_UTR_variant	341405	exon1			GGCATTCGGAGAC		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.-336C>A	chr12.hg19:g.52282036C>A		124.0	0.0	.		100.0	47.0	.	NM_182608	Q0VAA7|Q5K619|Q5K621|Q5K622|Q5K623|Q5K624|Q6ZUN0	Missense_Mutation	SNP	ENST00000340970.4	hg19	CCDS44892.1	.	.	.	.	.	.	.	.	.	.	C	3.679	-0.065896	0.07273	.	.	ENSG00000167612	ENST00000301190	T	0.18338	2.22	3.17	1.2	0.21068	.	.	.	.	.	T	0.06554	0.0168	N	0.03608	-0.345	0.19775	N	0.999956	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42799	-0.9430	9	0.11485	T	0.65	.	9.0053	0.36109	0.0:0.5521:0.4479:0.0	.	22;22	F8VTQ6;Q7Z3H0-2	.;.	L	22	ENSP00000301190:F22L	ENSP00000301190:F22L	F	+	3	2	ANKRD33	50568303	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.466000	0.22019	0.317000	0.23160	-0.467000	0.05162	TTC	.	.	.	none		0.577	ANKRD33-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404515.1	NM_182608		A	52282036	C	A	52282036	1	1	8	0	1	0	0	0	0	0	0	0	661	883	31	4		4	ANKRD33	12	52282036	5'UTR	SNP	C	TCGA-2Z-A9J8-01A-11D-A42J-10		52282036	81569859	22	616											
PSMB5	5693	hgsc.bcm.edu	37	chr14	23502654	23502654	+	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	tgtactgatacaccatgttgGcaagcagtttggaggcagct	10	11	12	8	0	0	1	0	1	0	0	0	2	0	2	1	3	4	7	1	3	3	4			TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr14:23502654G>C	ENST00000361611.6	-	2	691	c.428C>G	c.(427-429)gCc>gGc	p.A143G	PSMB5_ENST00000460922.2_Intron|AL132780.1_ENST00000385031.1_RNA|PSMB5_ENST00000425762.2_Missense_Mutation_p.A40G|PSMB5_ENST00000493471.2_Missense_Mutation_p.A143G	NM_002797.3	NP_002788.1	P28074	PSB5_HUMAN	proteasome (prosome, macropain) subunit, beta type, 5	143					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to oxidative stress (GO:0006979)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	7	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0121)	Bortezomib(DB00188)|Carfilzomib(DB08889)	CACCATGTTGGCAAGCAGTTT	0.522																																					p.A143G		Atlas-SNP	.											.	PSMB5	31	.	0			c.C428G						PASS	.						141	122	128					14																	23502654		2203	4300	6503	SO:0001583	missense	5693	exon2			ATGTTGGCAAGCA	D29011	CCDS9584.1, CCDS45083.1, CCDS45084.1	14q11.2	2008-08-29			ENSG00000100804	ENSG00000100804		"Proteasome (prosome, macropain) subunits"	9542	protein-coding gene	gene with protein product		600306				8066462, 8811196	Standard	NM_001130725		Approved	X, MB1	uc001wii.3	P28074	OTTHUMG00000028713	ENST00000361611.6:c.428C>G	chr14.hg19:g.23502654G>C	ENSP00000355325:p.Ala143Gly	69.0	0.0	.		57.0	31.0	.	NM_001144932	B2R4N9|B4DUM9|D3DS43|E9PAV2|Q16242|Q6PEW2|Q7Z3B5|Q86T01|Q9TNN9	Missense_Mutation	SNP	ENST00000361611.6	hg19	CCDS9584.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.26|17.26	3.344679|3.344679	0.61073|0.61073	.|.	.|.	ENSG00000100804|ENSG00000100804	ENST00000361611;ENST00000493471;ENST00000425762|ENST00000555895	T;T;T|.	0.37752|.	1.18;1.18;1.18|.	4.88|4.88	4.88|4.88	0.63580|0.63580	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.77370|0.77370	0.4120|0.4120	M|M	0.80028|0.80028	2.48|2.48	0.80722|0.80722	D|D	1|1	D;P|.	0.58620|.	0.983;0.906|.	P;P|.	0.54026|.	0.682;0.74|.	T|T	0.79310|0.79310	-0.1856|-0.1856	10|5	0.66056|.	D|.	0.02|.	-10.7057|-10.7057	16.8115|16.8115	0.85722|0.85722	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	143;143|.	P28074-2;P28074|.	.;PSB5_HUMAN|.	G|A	143;143;40|92	ENSP00000355325:A143G;ENSP00000452424:A143G;ENSP00000395206:A40G|.	ENSP00000334973:A143G|.	A|P	-|-	2|1	0|0	PSMB5|PSMB5	22572494|22572494	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.993000|0.993000	0.82548|0.82548	7.146000|7.146000	0.77373|0.77373	2.237000|2.237000	0.73441|0.73441	0.561000|0.561000	0.74099|0.74099	GCC|CCA	.	.	.	none		0.522	PSMB5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071695.4	NM_002797		C	23502654	G	C	23502654	3	2	8	1	0	0	0	0	1	0	0	0	12690	1203	42	4	460	4	PSMB5	14	23502654	Missense_Mutation	SNP	G	TCGA-2Z-A9J8-01A-11D-A42J-10		23502654	83846886	23	617											
WDR90	197335	hgsc.bcm.edu	37	chr16	703789	703789	+	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	tctgcggggttggcaaggacCaccacgggaggacggtaaca	10	5	16	10	3	1	0	0	0	1	0	1	3	1	3	2	7	2	3	2	7	2	2			TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr16:703789C>G	ENST00000293879.4	+	13	1423	c.1423C>G	c.(1423-1425)Cac>Gac	p.H475D	WDR90_ENST00000549091.1_Missense_Mutation_p.H475D|LA16c-349E10.1_ENST00000573609.1_RNA			Q96KV7	WDR90_HUMAN	WD repeat domain 90	475										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				TGGCAAGGACCACCACGGGAG	0.637																																					p.H475D		Atlas-SNP	.											.	WDR90	107	.	0			c.C1423G						PASS	.						37	44	42					16																	703789		1983	4152	6135	SO:0001583	missense	197335	exon13			AAGGACCACCACG	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.1423C>G	chr16.hg19:g.703789C>G	ENSP00000293879:p.His475Asp	237.0	1.0	.		189.0	81.0	.	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	hg19	CCDS42092.1	.	.	.	.	.	.	.	.	.	.	C	0.096	-1.158985	0.01686	.	.	ENSG00000161996	ENST00000549091;ENST00000293879	T;T	0.25749	1.81;1.78	4.74	-1.93	0.07594	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	0.781704	0.10327	U	0.687997	T	0.09642	0.0237	N	0.11560	0.145	0.09310	N	0.999998	B;B;B	0.20052	0.008;0.005;0.041	B;B;B	0.20384	0.025;0.012;0.029	T	0.38845	-0.9642	10	0.10902	T	0.67	.	4.0027	0.09587	0.2474:0.1843:0.4737:0.0946	.	475;476;475	Q96KV7;C9JMK1;Q96KV7-3	WDR90_HUMAN;.;.	D	475	ENSP00000448122:H475D;ENSP00000293879:H475D	ENSP00000293879:H475D	H	+	1	0	WDR90	643790	0.000000	0.05858	0.343000	0.25615	0.626000	0.37791	-0.720000	0.04969	0.041000	0.15688	0.561000	0.74099	CAC	.	.	.	none		0.637	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294		G	703789	C	G	703789	3	3	8	1	0	0	0	0	1	0	0	0	17349	594	21	4	1473	4	WDR90	16	703789	Missense_Mutation	SNP	C	TCGA-2Z-A9J8-01A-11D-A42J-10		703789	89650964	24	618											
BTBD12	84464	hgsc.bcm.edu	37	chr16	3656681	3656681	+	Missense_Mutation	SNP	T	T	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	aggaaggaggaggctgggagTcgctgttgggcacattctct	8	9	17	7	1	1	0	0	0	1	0	3	4	1	4	0	6	0	4	0	6	1	2			TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr16:3656681T>G	ENST00000294008.3	-	3	1194	c.554A>C	c.(553-555)gAc>gCc	p.D185A		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	185	Interaction with SLX4IP, ERCC4 and MSH2.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						AGGCTGGGAGTCGCTGTTGGG	0.488								Direct reversal of damage																													p.D185A		Atlas-SNP	.											.	SLX4	173	.	0			c.A554C						PASS	.						132	127	129					16																	3656681		2197	4300	6497	SO:0001583	missense	84464	exon3			TGGGAGTCGCTGT	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.554A>C	chr16.hg19:g.3656681T>G	ENSP00000294008:p.Asp185Ala	129.0	0.0	.		83.0	35.0	.	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	hg19	CCDS10506.2	.	.	.	.	.	.	.	.	.	.	T	11.65	1.700644	0.30142	.	.	ENSG00000188827	ENST00000294008	T	0.01228	5.14	5.03	-0.379	0.12493	.	1.301390	0.05020	N	0.472509	T	0.01029	0.0034	L	0.29908	0.895	0.09310	N	1	B	0.30068	0.267	B	0.22386	0.039	T	0.45175	-0.9279	10	0.07325	T	0.83	.	2.0194	0.03505	0.2658:0.0792:0.1375:0.5175	.	185	Q8IY92	SLX4_HUMAN	A	185	ENSP00000294008:D185A	ENSP00000294008:D185A	D	-	2	0	SLX4	3596682	0.000000	0.05858	0.000000	0.03702	0.110000	0.19582	-1.151000	0.03175	0.022000	0.15160	0.459000	0.35465	GAC	.	.	.	none		0.488	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444		G	3656681	T	G	3656681	3	3	8	1	0	0	0	0	1	0	0	0	1542	1667	58	5	5002	5	BTBD12	16	3656681	Missense_Mutation	SNP	T	TCGA-2Z-A9J8-01A-11D-A42J-10	2952892	3656681	86698072	25	619											
SLC14A2	8170	hgsc.bcm.edu	37	chr18	43252937	43252937	+	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	cctggactggaggcatcttcCtcatagctctgttcatatcc	7	13	8	13	0	4	0	2	0	2	0	6	2	6	2	3	3	1	3	3	3	2	4			TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr18:43252937C>T	ENST00000255226.6	+	17	3118	c.2302C>T	c.(2302-2304)Ctc>Ttc	p.L768F	RP11-116O18.3_ENST00000589510.1_RNA|SLC14A2_ENST00000589658.1_Missense_Mutation_p.L245F|SLC14A2_ENST00000586448.1_Missense_Mutation_p.L768F	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	768					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						AGGCATCTTCCTCATAGCTCT	0.512																																					p.L768F		Atlas-SNP	.											.	SLC14A2	121	.	0			c.C2302T						PASS	.						270	210	230					18																	43252937		2203	4300	6503	SO:0001583	missense	8170	exon18			ATCTTCCTCATAG	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.2302C>T	chr18.hg19:g.43252937C>T	ENSP00000255226:p.Leu768Phe	73.0	0.0	.		74.0	22.0	.	NM_001242692	A8K8Q7|Q2TBD6|Q96PH5	Missense_Mutation	SNP	ENST00000255226.6	hg19	CCDS11924.1	.	.	.	.	.	.	.	.	.	.	C	15.94	2.981375	0.53827	.	.	ENSG00000132874	ENST00000255226	T	0.58506	0.33	5.79	5.79	0.91817	.	0.000000	0.53938	D	0.000059	T	0.68504	0.3008	M	0.75447	2.3	0.80722	D	1	P	0.46706	0.883	P	0.51101	0.659	T	0.68965	-0.5270	10	0.45353	T	0.12	-34.2809	15.6071	0.76682	0.1381:0.8619:0.0:0.0	.	768	Q15849	UT2_HUMAN	F	768	ENSP00000255226:L768F	ENSP00000255226:L768F	L	+	1	0	SLC14A2	41506935	1.000000	0.71417	0.997000	0.53966	0.216000	0.24613	3.665000	0.54532	2.735000	0.93741	0.561000	0.74099	CTC	.	.	.	none		0.512	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1			T	43252937	C	T	43252937	3	4	8	1	0	0	0	0	1	0	0	0	14410	681	24	2	2364	2	SLC14A2	18	43252937	Missense_Mutation	SNP	C	TCGA-2Z-A9J8-01A-11D-A42J-10		43252937	34824311	26	620											
ZNF236	7776	hgsc.bcm.edu	37	chr18	74637348	74637348	+	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	aggccagaaagcctatgactCgaagctcatcggaaggactg	13	6	12	10	2	1	2	1	1	0	1	3	5	1	4	2	3	2	1	2	3	4	1			TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr18:74637348C>G	ENST00000253159.8	+	22	4057	c.3859C>G	c.(3859-3861)Cga>Gga	p.R1287G	ZNF236_ENST00000320610.9_Missense_Mutation_p.R1289G	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	1287					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)		GCCTATGACTCGAAGCTCATC	0.483																																					p.R1287G		Atlas-SNP	.											.	ZNF236	325	.	0			c.C3859G						PASS	.						72	73	73					18																	74637348		2014	4162	6176	SO:0001583	missense	7776	exon22			ATGACTCGAAGCT	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.3859C>G	chr18.hg19:g.74637348C>G	ENSP00000253159:p.Arg1287Gly	104.0	0.0	.		93.0	42.0	.	NM_007345	B2RTX9|Q9UL37	Missense_Mutation	SNP	ENST00000253159.8	hg19	CCDS42447.1	.	.	.	.	.	.	.	.	.	.	C	11.36	1.614965	0.28712	.	.	ENSG00000130856	ENST00000253159;ENST00000543926;ENST00000320610	T;T	0.11495	2.77;2.95	4.85	3.98	0.46160	.	0.483231	0.20519	N	0.090734	T	0.09512	0.0234	L	0.27053	0.805	0.09310	N	0.99999	B	0.11235	0.004	B	0.08055	0.003	T	0.20009	-1.0288	10	0.44086	T	0.13	.	14.8772	0.70504	0.1444:0.8556:0.0:0.0	.	1287	Q9UL36	ZN236_HUMAN	G	1287	ENSP00000253159:R1287G;ENSP00000444524:R1287G	ENSP00000253159:R1287G	R	+	1	2	ZNF236	72766336	0.998000	0.40836	0.002000	0.10522	0.144000	0.21451	4.056000	0.57448	1.154000	0.42482	0.650000	0.86243	CGA	.	.	.	none		0.483	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1			G	74637348	C	G	74637348	3	3	8	1	0	0	0	0	1	0	0	0	17801	876	31	4	3945	4	ZNF236	18	74637348	Missense_Mutation	SNP	C	TCGA-2Z-A9J8-01A-11D-A42J-10	31384411	74637348	3439900	27	621											
DOT1L	84444	hgsc.bcm.edu	37	chr19	2223434	2223434	+	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	caatggggcacactactcccCactcacctcagacgaggagc	11	5	9	16	1	2	1	2	0	0	1	3	3	3	2	3	3	2	1	3	3	2	1			TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr19:2223434C>T	ENST00000398665.3	+	25	3581	c.3545C>T	c.(3544-3546)cCa>cTa	p.P1182L		NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	1182					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)		CACTACTCCCCACTCACCTCA	0.692																																					p.P1182L		Atlas-SNP	.											.	DOT1L	205	.	0			c.C3545T						PASS	.						41	47	45					19																	2223434		1953	4141	6094	SO:0001583	missense	84444	exon25			ACTCCCCACTCAC	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.3545C>T	chr19.hg19:g.2223434C>T	ENSP00000381657:p.Pro1182Leu	76.0	0.0	.		42.0	20.0	.	NM_032482	O60379|Q96JL1	Missense_Mutation	SNP	ENST00000398665.3	hg19	CCDS42460.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.6|23.6	4.435602|4.435602	0.83885|0.83885	.|.	.|.	ENSG00000104885|ENSG00000104885	ENST00000440640|ENST00000398665;ENST00000221482;ENST00000457590	.|T;T	.|0.42513	.|1.28;0.97	4.91|4.91	4.91|4.91	0.64330|0.64330	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.63977|0.63977	0.2557|0.2557	M|M	0.66939|0.66939	2.045|2.045	0.54753|0.54753	D|D	0.999988|0.999988	.|D;D	.|0.89917	.|0.998;1.0	.|D;D	.|0.91635	.|0.914;0.999	T|T	0.68250|0.68250	-0.5458|-0.5458	5|10	.|0.87932	.|D	.|0	-14.6797|-14.6797	17.0688|17.0688	0.86567|0.86567	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1182;1182	.|Q8TEK3;Q8TEK3-2	.|DOT1L_HUMAN;.	Y|L	969|1182;1182;62	.|ENSP00000381657:P1182L;ENSP00000407411:P62L	.|ENSP00000221482:P1182L	H|P	+|+	1|2	0|0	DOT1L|DOT1L	2174434|2174434	0.999000|0.999000	0.42202|0.42202	0.892000|0.892000	0.35008|0.35008	0.462000|0.462000	0.32619|0.32619	7.226000|7.226000	0.78060|0.78060	2.284000|2.284000	0.76573|0.76573	0.561000|0.561000	0.74099|0.74099	CAC|CCA	.	.	.	none		0.692	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482		T	2223434	C	T	2223434	3	4	8	1	0	0	0	0	1	0	0	0	4711	594	21	2	3643	2	DOT1L	19	2223434	Missense_Mutation	SNP	C	TCGA-2Z-A9J8-01A-11D-A42J-10		2223434	56905549	28	622											
RASGRP4	115727	hgsc.bcm.edu	37	chr19	38905689	38905689	+	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	acaggcagccggaaacccgcGcagccagcccaggtgcggcg	9	1	15	16	5	0	0	0	0	0	0	0	1	0	1	4	4	5	2	4	4	1	0			TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chr19:38905689G>A	ENST00000587738.1	-	9	1099	c.1029C>T	c.(1027-1029)tgC>tgT	p.C343C	RASGRP4_ENST00000586305.1_Silent_p.C329C|RASGRP4_ENST00000587753.1_Intron|RASGRP4_ENST00000293062.9_Silent_p.C246C|RASGRP4_ENST00000454404.2_Silent_p.C309C|RASGRP4_ENST00000426920.2_Intron|RASGRP4_ENST00000433821.2_Intron			Q8TDF6	GRP4_HUMAN	RAS guanyl releasing protein 4	343	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				activation of phospholipase C activity (GO:0007202)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|myeloid cell differentiation (GO:0030099)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|response to extracellular stimulus (GO:0009991)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|GTP-dependent protein binding (GO:0030742)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			cervix(1)|kidney(1)|large_intestine(4)|lung(12)|pancreas(1)|prostate(3)|skin(1)	23	all_cancers(60;4.21e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			GGAAACCCGCGCAGCCAGCCC	0.672																																					p.C343C		Atlas-SNP	.											.	RASGRP4	54	.	0			c.C1029T						PASS	.						10	16	14					19																	38905689		1966	4151	6117	SO:0001819	synonymous_variant	115727	exon9			ACCCGCGCAGCCA	AY048119	CCDS46068.1, CCDS54262.1, CCDS54263.1, CCDS54264.1	19q13.1	2013-01-10						"EF-hand domain containing"	18958	protein-coding gene	gene with protein product		607320				11956218	Standard	NM_170604		Approved		uc021uub.1	Q8TDF6		ENST00000587738.1:c.1029C>T	chr19.hg19:g.38905689G>A		170.0	0.0	.		149.0	70.0	.	NM_170604	A6H8M4|C0LTP2|C0LTP3|C0LTP4|C0LTP5|C0LTP7|C9J416|C9JHZ1|Q8N858|Q96QN5|Q96QN6|Q96QN7	Silent	SNP	ENST00000587738.1	hg19	CCDS46068.1																																																																																			.	.	.	none		0.672	RASGRP4-013	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460540.1	NM_170604		A	38905689	G	A	38905689	2	1	8	1	0	0	0	0	0	0	0	1	13090	1079	38	1		1	RASGRP4	19	38905689	Silent	SNP	G	TCGA-2Z-A9J8-01A-11D-A42J-10	36682255	38905689	20223294	29	623											
DIAPH2	1730	hgsc.bcm.edu	37	chrX	96171470	96171470	+	Missense_Mutation	SNP	A	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	ggattctaggagatgaaagaAgtcttttactattggcaaga	14	12	11	4	0	2	4	0	1	2	3	2	6	2	5	0	3	1	1	0	3	6	6			TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chrX:96171470A>C	ENST00000324765.8	+	8	1113	c.766A>C	c.(766-768)Agt>Cgt	p.S256R	DIAPH2_ENST00000373054.4_Missense_Mutation_p.S252R|DIAPH2_ENST00000355827.4_Missense_Mutation_p.S256R|DIAPH2_ENST00000373049.4_Missense_Mutation_p.S256R|DIAPH2_ENST00000373061.3_Missense_Mutation_p.S256R			O60879	DIAP2_HUMAN	diaphanous-related formin 2	256	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin filament polymerization (GO:0030041)|cytokinesis (GO:0000910)|female gamete generation (GO:0007292)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)	endosome (GO:0005768)	receptor binding (GO:0005102)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51						AGATGAAAGAAGTCTTTTACT	0.299																																					p.S256R		Atlas-SNP	.											.	DIAPH2	148	.	0			c.A766C						PASS	.						62	57	58					X																	96171470		2203	4297	6500	SO:0001583	missense	1730	exon8			GAAAGAAGTCTTT	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.766A>C	chrX.hg19:g.96171470A>C	ENSP00000321348:p.Ser256Arg	310.0	1.0	.		310.0	241.0	.	NM_007309	A6NG19|O60878|Q8WX06|Q8WX48|Q9UJL2	Missense_Mutation	SNP	ENST00000324765.8	hg19	CCDS14467.1	.	.	.	.	.	.	.	.	.	.	A	17.92	3.506176	0.64410	.	.	ENSG00000147202	ENST00000373061;ENST00000373054;ENST00000355827;ENST00000373049;ENST00000324765;ENST00000537885	D;D;D;D;D	0.87179	-2.22;-2.22;-2.22;-2.22;-2.22	5.52	5.52	0.82312	GTPase-binding/formin homology 3 (1);Armadillo-type fold (1);Diaphanous GTPase-binding (1);	0.000000	0.85682	D	0.000000	D	0.92645	0.7663	M	0.69823	2.125	0.58432	D	0.999997	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.91635	0.999;0.992;0.995	D	0.93186	0.6579	10	0.62326	D	0.03	.	14.6448	0.68754	1.0:0.0:0.0:0.0	.	256;256;263	O60879;O60879-2;B7ZLJ0	DIAP2_HUMAN;.;.	R	256;252;256;256;256;263	ENSP00000362152:S256R;ENSP00000362145:S252R;ENSP00000348082:S256R;ENSP00000362140:S256R;ENSP00000321348:S256R	ENSP00000321348:S256R	S	+	1	0	DIAPH2	96058126	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.073000	0.76784	1.840000	0.53500	0.441000	0.28932	AGT	.	.	.	none		0.299	DIAPH2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058871.2	NM_006729, NM_007309		C	96171470	A	C	96171470	3	2	8	1	0	0	0	0	1	0	0	0	4521	72	3	5	796	5	DIAPH2	23	96171470	Missense_Mutation	SNP	A	TCGA-2Z-A9J8-01A-11D-A42J-10		96171470	59099090	30	624											
GPRASP1	9737	hgsc.bcm.edu	37	chrX	101910027	101910027	+	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	cccgagccagggccaagcaaGaagccaggtcagaggaggaa	14	1	15	11	1	1	2	1	0	0	2	1	5	1	4	4	4	3	1	4	4	4	0			TCGA-2Z-A9J8-01A-11D-A42J-10	TCGA-2Z-A9J8-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cb146a7-7274-4738-9b83-05c82018a495	a106d5a1-9938-4c4f-aec9-6163033a57bd	g.chrX:101910027G>C	ENST00000361600.5	+	5	1987	c.1186G>C	c.(1186-1188)Gaa>Caa	p.E396Q	GPRASP1_ENST00000444152.1_Missense_Mutation_p.E396Q|RP4-769N13.7_ENST00000602441.1_RNA|GPRASP1_ENST00000537097.1_Missense_Mutation_p.E396Q|GPRASP1_ENST00000415986.1_Missense_Mutation_p.E396Q	NM_014710.4	NP_055525.3	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting protein 1	396					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						GGCCAAGCAAGAAGCCAGGTC	0.542																																					p.E396Q		Atlas-SNP	.											.	GPRASP1	140	.	0			c.G1186C						PASS	.						51	59	56					X																	101910027		2203	4300	6503	SO:0001583	missense	9737	exon3			AAGCAAGAAGCCA	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.1186G>C	chrX.hg19:g.101910027G>C	ENSP00000355146:p.Glu396Gln	64.0	0.0	.		66.0	57.0	.	NM_001099411	O43168|Q96LA1	Missense_Mutation	SNP	ENST00000361600.5	hg19	CCDS35352.1	.	.	.	.	.	.	.	.	.	.	G	11.02	1.517068	0.27123	.	.	ENSG00000198932	ENST00000415986;ENST00000444152;ENST00000361600;ENST00000537097	T;T;T;T	0.22945	1.93;1.93;1.93;1.93	2.32	1.44	0.22558	.	.	.	.	.	T	0.43678	0.1258	M	0.71036	2.16	0.22127	N	0.999348	D	0.89917	1.0	D	0.91635	0.999	T	0.16276	-1.0408	9	0.35671	T	0.21	-5.7701	6.5511	0.22433	0.1669:0.0:0.8331:0.0	.	396	Q5JY77	GASP1_HUMAN	Q	396	ENSP00000393691:E396Q;ENSP00000409420:E396Q;ENSP00000355146:E396Q;ENSP00000445683:E396Q	ENSP00000355146:E396Q	E	+	1	0	GPRASP1	101796683	0.458000	0.25760	0.007000	0.13788	0.025000	0.11179	2.670000	0.46833	0.414000	0.25790	-0.393000	0.06486	GAA	.	.	.	none		0.542	GPRASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057634.2	NM_014710		C	101910027	G	C	101910027	3	2	8	1	0	0	0	0	1	0	0	0	6729	943	33	4	1188	4	GPRASP1	23	101910027	Missense_Mutation	SNP	G	TCGA-2Z-A9J8-01A-11D-A42J-10	5738557	101910027	53360533	31	625											
RERE	473	hgsc.bcm.edu	37	chr1	8425963	8425975	+	Frame_Shift_Del	DEL	CCTACGATGGGCT	CCTACGATGGGCT	-																															aacacggcctgcctgcggtgCctacgatgggctcgggagct																								rs527863652		TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	CCTACGATGGGCT	CCTACGATGGGCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr1:8425963_8425975delCCTACGATGGGCT	ENST00000337907.3	-	14	1978_1990	c.1344_1356delAGCCCATCGTAGG	c.(1342-1356)cgagcccatcgtaggfs	p.RAHRR448fs	RERE_ENST00000460659.1_5'UTR|RERE_ENST00000400907.2_Frame_Shift_Del_p.RAHRR448fs|RERE_ENST00000400908.2_Frame_Shift_Del_p.RAHRR448fs|RERE_ENST00000476556.1_5'UTR|RERE_ENST00000377464.1_Frame_Shift_Del_p.RAHRR180fs	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	448					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)		GCCTGCGGTGCCTACGATGGGCTCGGGAGCTGG	0.61																																					p.449_453del		Atlas-Indel,Pindel	.											.	RERE	129	.	0			c.1345_1357del						PASS	.																																			SO:0001589	frameshift_variant	473	exon14			.	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.1344_1356delAGCCCATCGTAGG	chr1.hg19:g.8425963_8425975delCCTACGATGGGCT	ENSP00000338629:p.Arg448fs	70.0	0.0	0		54.0	14.0	0.259259	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Frame_Shift_Del	DEL	ENST00000337907.3	hg19	CCDS95.1																																																																																			.	.	.	none		0.61	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1			-	8425975	CCTACGATGGGCT	-	8425963	7	5	9	1	0	1	0	1	0	0	0	0	13244	738	26	0	3388	0	RERE	1	8425963	Frame_Shift_Del	DEL	CCTACGATGGGCT	TCGA-2Z-A9JD-01A-11D-A42J-10		8425963	240824658	1	626											
ZMYM6	9204	hgsc.bcm.edu	37	chr1	35453206	35453206	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aacatgtcataatcattctcTtgtgtgcgcttcaaccacat	11	14	5	11	1	4	0	3	0	1	0	5	0	4	0	1	0	3	1	1	0	3	4			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr1:35453206T>C	ENST00000357182.4	-	16	3704	c.3477A>G	c.(3475-3477)caA>caG	p.Q1159Q	ZMYM6_ENST00000493328.1_5'UTR|ZMYM6_ENST00000373340.2_Intron|ZMYM6NB_ENST00000373337.3_5'Flank|RP11-244H3.1_ENST00000417456.1_RNA|ZMYM6_ENST00000487874.1_Intron	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6	1159					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)				aatcattctcttgtgtgcgct	0.318																																					p.Q1159Q		Atlas-SNP	.											.	ZMYM6	110	.	0			c.A3477G						PASS	.						39	38	39					1																	35453206		1856	4087	5943	SO:0001819	synonymous_variant	9204	exon16			ATTCTCTTGTGTG	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.3477A>G	chr1.hg19:g.35453206T>C		325.0	0.0	.		266.0	91.0	.	NM_007167	B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	Silent	SNP	ENST00000357182.4	hg19	CCDS387.2																																																																																			.	.	.	none		0.318	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011999.1	NM_007167		C	35453206	T	C	35453206	2	2	9	1	0	0	0	0	0	0	0	1	17716	1606	56	3		3	ZMYM6	1	35453206	Silent	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10	27027243	35453206	213797415	2	627											
KIAA0467	23334	hgsc.bcm.edu	37	chr1	43907699	43907699	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccagagatcttcggccctTgttcccctgggcaactgggc	6	9	12	14	1	1	1	0	0	1	1	3	2	2	1	4	3	2	2	4	3	1	3			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr1:43907699T>C	ENST00000562955.1	+	55	7600	c.7600T>C	c.(7600-7602)Tgt>Cgt	p.C2534R	SZT2_ENST00000372442.1_Missense_Mutation_p.C1692R	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	2591					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						CTTCGGCCCTTGTTCCCCTGG	0.602																																					p.C2534R		Atlas-SNP	.											.	SZT2	383	.	0			c.T7600C						PASS	.						50	48	49					1																	43907699		2203	4300	6503	SO:0001583	missense	23334	exon55			GGCCCTTGTTCCC	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.7600T>C	chr1.hg19:g.43907699T>C	ENSP00000457168:p.Cys2534Arg	96.0	0.0	.		100.0	39.0	.	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Missense_Mutation	SNP	ENST00000562955.1	hg19	CCDS30694.2	.	.	.	.	.	.	.	.	.	.	T	8.595	0.885587	0.17540	.	.	ENSG00000198198	ENST00000372442	.	.	.	5.21	4.07	0.47477	.	0.294570	0.39759	N	0.001273	T	0.42177	0.1191	L	0.29908	0.895	0.39585	D	0.969494	B	0.02656	0.0	B	0.04013	0.001	T	0.23190	-1.0195	9	0.25751	T	0.34	.	9.7297	0.40352	0.0:0.0868:0.0:0.9132	.	2534	Q5T011-5	.	R	1692	.	ENSP00000361519:C1692R	C	+	1	0	SZT2	43680286	0.999000	0.42202	0.901000	0.35422	0.818000	0.46254	3.426000	0.52778	0.805000	0.34159	0.533000	0.62120	TGT	.	.	.	none		0.602	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		C	43907699	T	C	43907699	3	2	9	1	0	0	0	0	1	0	0	0	8185	1812	63	3	5228	3	KIAA0467	1	43907699	Missense_Mutation	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10	8454493	43907699	205342922	3	628											
AGBL4	84871	hgsc.bcm.edu	37	chr1	49100226	49100226	+	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	gcagggtaggatggacccatGgagagggatccagccagtga	11	5	17	8	0	0	2	0	1	0	1	1	6	1	5	3	5	1	2	3	5	1	1			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr1:49100226G>A	ENST00000371839.1	-	9	1006	c.890C>T	c.(889-891)cCa>cTa	p.P297L	AGBL4_ENST00000334103.7_Missense_Mutation_p.P30L|AGBL4_ENST00000371838.1_Missense_Mutation_p.P297L	NM_032785.3	NP_116174.3	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4	297					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)		ATGGACCCATGGAGAGGGATC	0.483																																					p.P297L		Atlas-SNP	.											.	AGBL4	54	.	0			c.C890T						PASS	.						86	89	88					1																	49100226		1970	4152	6122	SO:0001583	missense	84871	exon9			ACCCATGGAGAGG	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.890C>T	chr1.hg19:g.49100226G>A	ENSP00000360905:p.Pro297Leu	34.0	0.0	.		103.0	5.0	.	NM_032785	B3KT26|B4DG37	Missense_Mutation	SNP	ENST00000371839.1	hg19	CCDS44137.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.8|20.8	4.056437|4.056437	0.76074|0.76074	.|.	.|.	ENSG00000186094|ENSG00000186094	ENST00000416121|ENST00000371839;ENST00000411952;ENST00000334103;ENST00000371838	.|T;T;T	.|0.17691	.|2.64;2.64;2.26	5.6|5.6	5.6|5.6	0.85130|0.85130	.|Peptidase M14, carboxypeptidase A (1);	.|0.046068	.|0.85682	.|D	.|0.000000	T|T	0.34019|0.34019	0.0883|0.0883	L|L	0.43598|0.43598	1.365|1.365	0.80722|0.80722	D|D	1|1	.|P;D;P;B;B	.|0.76494	.|0.677;0.999;0.948;0.256;0.182	.|B;D;P;B;B	.|0.71414	.|0.299;0.973;0.754;0.173;0.102	T|T	0.00655|0.00655	-1.1624|-1.1624	5|9	.|.	.|.	.|.	-17.6024|-17.6024	17.0797|17.0797	0.86595|0.86595	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|112;309;30;142;297	.|A0AVJ2;Q5VU57-2;B4DGK1;B1AMW2;Q5VU57	.|.;.;.;.;CBPC6_HUMAN	Y|L	143|297;291;30;297	.|ENSP00000360905:P297L;ENSP00000335516:P30L;ENSP00000360904:P297L	.|.	H|P	-|-	1|2	0|0	AGBL4|AGBL4	48872813|48872813	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	8.608000|8.608000	0.90895|0.90895	2.636000|2.636000	0.89361|0.89361	0.462000|0.462000	0.41574|0.41574	CAT|CCA	.	.	.	none		0.483	AGBL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021346.4	NM_032785		A	49100226	G	A	49100226	3	1	9	1	0	0	0	0	1	0	0	0	377	1348	47	2	645	2	AGBL4	1	49100226	Missense_Mutation	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10	5192527	49100226	200150395	4	629											
ALG14	199857	hgsc.bcm.edu	37	chr1	95448663	95448663	+	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	gcccaaggtacaccgatttgGgatacttttctttcagagcc	9	12	9	11	1	2	1	1	0	1	1	2	3	2	2	3	2	3	1	3	2	3	6			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr1:95448663G>T	ENST00000370205.5	-	4	666	c.620C>A	c.(619-621)cCc>cAc	p.P207H		NM_144988.3	NP_659425.1	Q96F25	ALG14_HUMAN	ALG14, UDP-N-acetylglucosaminyltransferase subunit	207					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)		CACCGATTTGGGATACTTTTC	0.408																																					p.P207H		Atlas-SNP	.											.	ALG14	13	.	0			c.C620A						PASS	.						92	87	89					1																	95448663		2203	4300	6503	SO:0001583	missense	199857	exon4			GATTTGGGATACT		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.620C>A	chr1.hg19:g.95448663G>T	ENSP00000359224:p.Pro207His	62.0	0.0	.		97.0	36.0	.	NM_144988	A8K030	Missense_Mutation	SNP	ENST00000370205.5	hg19	CCDS752.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.958451	0.92726	.	.	ENSG00000172339	ENST00000370205	T	0.50548	0.74	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.72036	0.3411	M	0.88704	2.975	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.76468	-0.2948	10	0.87932	D	0	-29.758	20.1766	0.98178	0.0:0.0:1.0:0.0	.	207	Q96F25	ALG14_HUMAN	H	207	ENSP00000359224:P207H	ENSP00000359224:P207H	P	-	2	0	ALG14	95221251	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.232000	0.95325	2.772000	0.95346	0.655000	0.94253	CCC	.	.	.	none		0.408	ALG14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029699.2	NM_144988		T	95448663	G	T	95448663	3	4	9	1	0	0	0	0	1	0	0	0	516	1232	43	4	34	4	ALG14	1	95448663	Missense_Mutation	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10	46348437	95448663	153801958	5	630											
COL11A1	1301	hgsc.bcm.edu	37	chr1	103461460	103461460	+	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	tgagacctctgacaccatctGctccctgtggaataaattag	11	11	8	11	0	2	2	0	2	2	1	3	4	3	3	3	1	1	1	3	1	4	2	rs372933541		TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr1:103461460G>C	ENST00000370096.3	-	28	2612	c.2300C>G	c.(2299-2301)gCa>gGa	p.A767G	COL11A1_ENST00000512756.1_Missense_Mutation_p.A651G|COL11A1_ENST00000353414.4_Missense_Mutation_p.A728G|COL11A1_ENST00000358392.2_Missense_Mutation_p.A779G	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	767	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.A779E(1)|p.A767E(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)		GACACCATCTGCTCCCTGTGG	0.308																																					p.A779G		Atlas-SNP	.											COL11A1_ENST00000370096,NS,carcinoma,0,2	COL11A1	972	.	2	Substitution - Missense(2)	endometrium(2)	c.C2336G						PASS	.						79	88	85					1																	103461460		2203	4297	6500	SO:0001583	missense	1301	exon28			CCATCTGCTCCCT	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.2300C>G	chr1.hg19:g.103461460G>C	ENSP00000359114:p.Ala767Gly	115.0	0.0	.		184.0	10.0	.	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	G	19.66	3.868258	0.72065	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000512756	D;D;D;D	0.93426	-3.22;-3.22;-3.22;-3.22	5.62	5.62	0.85841	.	0.055500	0.64402	D	0.000001	D	0.89026	0.6598	N	0.25789	0.76	0.80722	D	1	B;P;P;P	0.49961	0.347;0.93;0.93;0.886	P;P;P;B	0.49085	0.479;0.6;0.6;0.396	D	0.90656	0.4586	10	0.59425	D	0.04	.	14.8656	0.70412	0.0706:0.0:0.9294:0.0	.	651;728;779;767	E9PCU0;P12107-3;P12107-2;P12107	.;.;.;COBA1_HUMAN	G	767;779;728;651	ENSP00000359114:A767G;ENSP00000351163:A779G;ENSP00000302551:A728G;ENSP00000426533:A651G	ENSP00000302551:A728G	A	-	2	0	COL11A1	103234048	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.158000	0.94723	2.640000	0.89533	0.591000	0.81541	GCA	.	.	.	none		0.308	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		C	103461460	G	C	103461460	3	2	9	1	0	0	0	0	1	0	0	0	3669	1319	46	4	3280	4	COL11A1	1	103461460	Missense_Mutation	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10	8012797	103461460	145789161	6	631											
LRIG2	9860	hgsc.bcm.edu	37	chr1	113661942	113661942	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaatactgtccatacacctAtattgctgaggaggacgttc	12	11	9	9	1	0	2	0	1	0	1	2	4	1	4	2	2	3	2	2	2	5	6			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr1:113661942A>G	ENST00000361127.5	+	17	2966	c.2768A>G	c.(2767-2769)tAt>tGt	p.Y923C	LRIG2_ENST00000492207.1_3'UTR	NM_014813.1	NP_055628.1	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like domains 2	923					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)		CCATACACCTATATTGCTGAG	0.463																																					p.Y923C		Atlas-SNP	.											.	LRIG2	67	.	0			c.A2768G						PASS	.						151	140	143					1																	113661942		2203	4300	6503	SO:0001583	missense	9860	exon17			ACACCTATATTGC	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.2768A>G	chr1.hg19:g.113661942A>G	ENSP00000355396:p.Tyr923Cys	103.0	0.0	.		118.0	8.0	.	NM_014813	Q9NSN2	Missense_Mutation	SNP	ENST00000361127.5	hg19	CCDS30808.1	.	.	.	.	.	.	.	.	.	.	A	15.39	2.820350	0.50633	.	.	ENSG00000198799	ENST00000361127	T	0.70045	-0.45	5.12	2.63	0.31362	.	0.209042	0.42682	D	0.000676	T	0.65439	0.2691	M	0.62723	1.935	0.44500	D	0.997441	D	0.61080	0.989	D	0.63192	0.912	T	0.64896	-0.6299	10	0.41790	T	0.15	.	10.232	0.43260	0.6218:0.0:0.0:0.3782	.	923	O94898	LRIG2_HUMAN	C	923	ENSP00000355396:Y923C	ENSP00000355396:Y923C	Y	+	2	0	LRIG2	113463465	1.000000	0.71417	0.126000	0.21872	0.817000	0.46193	5.801000	0.69115	0.291000	0.22468	0.482000	0.46254	TAT	.	.	.	none		0.463	LRIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033549.2	NM_014813		G	113661942	A	G	113661942	3	3	9	1	0	0	0	0	1	0	0	0	8952	449	16	3	2834	3	LRIG2	1	113661942	Missense_Mutation	SNP	A	TCGA-2Z-A9JD-01A-11D-A42J-10	10200482	113661942	135588679	7	632											
PDZK1	5174	hgsc.bcm.edu	37	chr1	145756430	145756430	+	Frame_Shift_Del	DEL	G	G	-																															agggtaggtcaaatcatcaaGgacatagattctggaagtcc																										TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr1:145756430delG	ENST00000344770.2	+	6	880	c.807delG	c.(805-807)aagfs	p.K269fs	PDZK1_ENST00000451928.2_Frame_Shift_Del_p.K158fs|PDZK1_ENST00000417171.1_Frame_Shift_Del_p.K269fs	NM_002614.4	NP_002605.2	Q5T2W1	NHRF3_HUMAN	PDZ domain containing 1	269	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				carnitine transport (GO:0015879)|cell proliferation (GO:0008283)|drug transport (GO:0015893)|establishment of protein localization to plasma membrane (GO:0090002)|positive regulation of ion transmembrane transport (GO:0034767)|positive regulation of protein targeting to membrane (GO:0090314)|regulation of anion transport (GO:0044070)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|transporter activity (GO:0005215)			NS(1)|endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)	7	all_hematologic(18;0.00473)|Acute lymphoblastic leukemia(18;0.0786)		KIRC - Kidney renal clear cell carcinoma(6;0.0764)|Kidney(552;0.118)|Colorectal(543;0.229)			AAATCATCAAGGACATAGATT	0.453																																					p.K269fs		Atlas-Indel,Pindel	.											.	PDZK1	15	.	0			c.806delA						PASS	.																																			SO:0001589	frameshift_variant	5174	exon7			.	AF012281	CCDS72859.1, CCDS72860.1	1q21	2009-08-21			ENSG00000174827	ENSG00000174827			8821	protein-coding gene	gene with protein product		603831				9461128	Standard	NM_002614		Approved	PDZD1, NHERF3	uc001eoo.2	Q5T2W1	OTTHUMG00000013735	ENST00000344770.2:c.807delG	chr1.hg19:g.145756430delG	ENSP00000342143:p.Lys269fs	167.0	0.0	0		286.0	31.0	0.108392	NM_002614	B4DPB9|E7EU02|O60450|Q5T5P6|Q9BQ41	Frame_Shift_Del	DEL	ENST00000344770.2	hg19	CCDS924.1																																																																																			.	.	.	none		0.453	PDZK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038502.2	NM_002614		-	145756430	G	-	145756430	7	5	9	1	0	1	0	1	0	0	0	0	11714	991	35	0	825	0	PDZK1	1	145756430	Frame_Shift_Del	DEL	G	TCGA-2Z-A9JD-01A-11D-A42J-10	32094488	145756430	103494191	8	633											
FLG2	388698	hgsc.bcm.edu	37	chr1	152324407	152324407	+	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	tgtactcactgtggccagatCcccttcttccagttgtcctg	5	14	8	14	0	2	1	1	0	1	1	5	1	5	1	5	1	1	2	5	1	1	4			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr1:152324407C>T	ENST00000388718.5	-	3	5927	c.5855G>A	c.(5854-5856)gGa>gAa	p.G1952E	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1952					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)			GTGGCCAGATCCCCTTCTTCC	0.527																																					p.G1952E		Atlas-SNP	.											.	FLG2	431	.	0			c.G5855A						PASS	.						326	307	313					1																	152324407		2203	4300	6503	SO:0001583	missense	388698	exon3			CCAGATCCCCTTC	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.5855G>A	chr1.hg19:g.152324407C>T	ENSP00000373370:p.Gly1952Glu	31.0	0.0	.		69.0	31.0	.	NM_001014342	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	hg19	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	c	0.563	-0.844454	0.02671	.	.	ENSG00000143520	ENST00000388718	T	0.04119	3.7	3.91	-3.47	0.04753	.	.	.	.	.	T	0.00784	0.0026	L	0.38531	1.155	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.48969	-0.8987	9	0.02654	T	1	0.2959	6.2752	0.20977	0.0:0.2193:0.4883:0.2924	.	1952	Q5D862	FILA2_HUMAN	E	1952	ENSP00000373370:G1952E	ENSP00000373370:G1952E	G	-	2	0	FLG2	150591031	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-1.819000	0.01716	-0.486000	0.06744	-0.371000	0.07208	GGA	.	.	.	none		0.527	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		T	152324407	C	T	152324407	3	4	9	1	0	0	0	0	1	0	0	0	5930	855	30	2	1324	2	FLG2	1	152324407	Missense_Mutation	SNP	C	TCGA-2Z-A9JD-01A-11D-A42J-10	6567977	152324407	96926214	9	634											
ADAM15	8751	hgsc.bcm.edu	37	chr1	155028274	155028274	+	Missense_Mutation	SNP	T	T	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	tgtccatagtagaggcgggaTgtggtaacagagaccaagac	13	7	14	7	1	0	3	0	0	0	3	1	5	1	4	2	3	1	2	2	3	4	3			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr1:155028274T>G	ENST00000356955.2	+	7	722	c.621T>G	c.(619-621)gaT>gaG	p.D207E	ADAM15_ENST00000368413.1_Intron|ADAM15_ENST00000449910.2_Missense_Mutation_p.D207E|ADAM15_ENST00000271836.6_Missense_Mutation_p.D207E|ADAM15_ENST00000472434.1_3'UTR|ADAM15_ENST00000368410.2_Intron|ADAM15_ENST00000360674.4_Missense_Mutation_p.D207E|ADAM15_ENST00000355956.2_Missense_Mutation_p.D207E|ADAM15_ENST00000531455.1_Missense_Mutation_p.D217E|ADAM15_ENST00000447332.3_Missense_Mutation_p.D191E|ADAM15_ENST00000359280.4_Missense_Mutation_p.D207E|ADAM15_ENST00000368412.3_Missense_Mutation_p.D207E	NM_207197.2	NP_997080.1	Q13444	ADA15_HUMAN	ADAM metallopeptidase domain 15	207					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)			AGAGGCGGGATGTGGTAACAG	0.587																																					p.D217E		Atlas-SNP	.											.	ADAM15	92	.	0			c.T651G						PASS	.						163	148	153					1																	155028274		2203	4300	6503	SO:0001583	missense	8751	exon7			GCGGGATGTGGTA	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.621T>G	chr1.hg19:g.155028274T>G	ENSP00000349436:p.Asp207Glu	96.0	0.0	.		86.0	32.0	.	NM_001261464	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	hg19	CCDS1087.1	.	.	.	.	.	.	.	.	.	.	T	17.22	3.333297	0.60853	.	.	ENSG00000143537	ENST00000356955;ENST00000449910;ENST00000359280;ENST00000360674;ENST00000368412;ENST00000355956;ENST00000271836;ENST00000531455	T;T;T;T;T;T;T;T	0.00832	5.81;5.81;5.81;5.73;5.64;5.8;5.78;5.81	5.06	-8.02	0.01118	.	0.000000	0.43579	D	0.000558	T	0.00695	0.0023	N	0.24115	0.695	0.58432	D	0.999998	D;D;D;D;P;D;D;D;P;D	0.89917	0.999;0.999;1.0;1.0;0.867;0.999;0.999;0.999;0.933;0.999	D;D;D;D;P;D;D;D;P;D	0.91635	0.978;0.978;0.986;0.999;0.832;0.99;0.99;0.99;0.886;0.997	T	0.28839	-1.0031	10	0.18710	T	0.47	.	15.9225	0.79586	0.0:0.2266:0.0:0.7734	.	217;224;191;207;207;207;207;207;207;207	E9PN65;B7Z390;B4DMH8;Q13444-10;Q13444-2;Q13444-4;Q13444-5;Q13444-3;Q13444-9;Q13444	.;.;.;.;.;.;.;.;.;ADA15_HUMAN	E	207;207;207;207;207;207;207;217	ENSP00000349436:D207E;ENSP00000403843:D207E;ENSP00000352226:D207E;ENSP00000353892:D207E;ENSP00000357397:D207E;ENSP00000348227:D207E;ENSP00000271836:D207E;ENSP00000432927:D217E	ENSP00000271836:D207E	D	+	3	2	ADAM15	153294898	0.001000	0.12720	0.505000	0.27651	0.980000	0.70556	-2.038000	0.01419	-1.727000	0.01368	0.379000	0.24179	GAT	.	.	.	none		0.587	ADAM15-019	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387168.1	NM_003815		G	155028274	T	G	155028274	3	3	9	1	0	0	0	0	1	0	0	0	237	1461	51	5	647	5	ADAM15	1	155028274	Missense_Mutation	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10	2703867	155028274	94222347	10	635											
EFNA1	1942	hgsc.bcm.edu	37	chr1	155106478	155106478	+	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	gcatcggtcacagtgctgccCcacgcctcttcccacttgcc	5	9	8	19	2	2	0	1	0	1	0	4	0	3	0	5	1	3	2	5	1	0	2			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr1:155106478C>A	ENST00000368407.3	+	5	1071	c.553C>A	c.(553-555)Cca>Aca	p.P185T	EFNA1_ENST00000368406.2_Missense_Mutation_p.P163T|SLC50A1_ENST00000368401.5_5'Flank|EFNA1_ENST00000469878.1_3'UTR|SLC50A1_ENST00000303343.8_5'Flank|SLC50A1_ENST00000484157.1_5'Flank|SLC50A1_ENST00000368404.4_5'Flank	NM_004428.2	NP_004419.2	P20827	EFNA1_HUMAN	ephrin-A1	185					activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|aortic valve morphogenesis (GO:0003180)|axon guidance (GO:0007411)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|endocardial cushion to mesenchymal transition involved in heart valve formation (GO:0003199)|ephrin receptor signaling pathway (GO:0048013)|mitral valve morphogenesis (GO:0003183)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|notochord formation (GO:0014028)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of angiogenesis (GO:0045765)|regulation of axonogenesis (GO:0050770)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|substrate adhesion-dependent cell spreading (GO:0034446)	anchored component of plasma membrane (GO:0046658)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ephrin receptor binding (GO:0046875)|receptor binding (GO:0005102)			breast(1)|endometrium(1)|kidney(1)|lung(1)|skin(1)	5	all_epithelial(22;4.71e-30)|all_lung(78;3.15e-27)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;2.28e-10)|all cancers(21;6.16e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000395)|LUSC - Lung squamous cell carcinoma(543;0.193)			CAGTGCTGCCCCACGCCTCTT	0.572																																					p.P185T		Atlas-SNP	.											.	EFNA1	10	.	0			c.C553A						PASS	.						122	97	105					1																	155106478		2203	4300	6503	SO:0001583	missense	1942	exon5			GCTGCCCCACGCC		CCDS1091.1, CCDS1092.1	1q21-q22	2011-03-09			ENSG00000169242	ENSG00000169242		"Ephrins"	3221	protein-coding gene	gene with protein product		191164		TNFAIP4, EPLG1		2233719, 8660976	Standard	NM_182685		Approved	LERK1, ECKLG	uc001fhh.3	P20827	OTTHUMG00000035312	ENST00000368407.3:c.553C>A	chr1.hg19:g.155106478C>A	ENSP00000357392:p.Pro185Thr	64.0	0.0	.		47.0	14.0	.	NM_004428	D3DV86|Q5SR60|Q5SR61|Q6I9T9|Q8N578	Missense_Mutation	SNP	ENST00000368407.3	hg19	CCDS1091.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.965044	0.74131	.	.	ENSG00000169242	ENST00000368407;ENST00000368406	D;D	0.97256	-3.16;-4.31	5.64	5.64	0.86602	.	0.168948	0.53938	D	0.000052	D	0.95535	0.8549	L	0.27053	0.805	0.37000	D	0.8952	D;P	0.60575	0.988;0.915	P;B	0.58721	0.844;0.313	D	0.95458	0.8540	10	0.44086	T	0.13	3.0189	15.557	0.76203	0.0:1.0:0.0:0.0	.	163;185	P20827-2;P20827	.;EFNA1_HUMAN	T	185;163	ENSP00000357392:P185T;ENSP00000357391:P163T	ENSP00000357391:P163T	P	+	1	0	EFNA1	153373102	0.598000	0.26882	1.000000	0.80357	0.983000	0.72400	2.090000	0.41682	2.826000	0.97356	0.561000	0.74099	CCA	.	.	.	none		0.572	EFNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085428.1	NM_004428		A	155106478	C	A	155106478	3	1	9	1	0	0	0	0	1	0	0	0	4952	623	22	4	571	4	EFNA1	1	155106478	Missense_Mutation	SNP	C	TCGA-2Z-A9JD-01A-11D-A42J-10	78204	155106478	94144143	11	636											
FDPS	2224	hgsc.bcm.edu	37	chr1	155279709	155279709	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacgggtacccagtcctggcCtggcacagtgcccgctgctg	5	7	13	16	2	0	0	0	0	0	0	1	0	1	0	4	3	3	4	4	3	1	1			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr1:155279709C>T	ENST00000356657.6	+	2	291	c.129C>T	c.(127-129)gcC>gcT	p.A43A	FDPS_ENST00000368356.4_Silent_p.A43A|FDPS_ENST00000447866.1_Intron|FDPS_ENST00000487002.1_3'UTR	NM_001135821.1	NP_001129293.1	P14324	FPPS_HUMAN	farnesyl diphosphate synthase	43					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)	CAGTCCTGGCCTGGCACAGTG	0.682																																					p.A43A		Atlas-SNP	.											.	FDPS	41	.	0			c.C129T						PASS	.						16	18	17					1																	155279709		2202	4300	6502	SO:0001819	synonymous_variant	2224	exon2			CCTGGCCTGGCAC	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.129C>T	chr1.hg19:g.155279709C>T		87.0	0.0	.		75.0	33.0	.	NM_001135821	D3DV91|E9PCI9|Q96G29	Silent	SNP	ENST00000356657.6	hg19	CCDS1110.1																																																																																			.	.	.	none		0.682	FDPS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039053.1	NM_002004		T	155279709	C	T	155279709	2	4	9	1	0	0	0	0	0	0	0	1	5810	668	24	2		2	FDPS	1	155279709	Silent	SNP	C	TCGA-2Z-A9JD-01A-11D-A42J-10	173231	155279709	93970912	12	637											
OR10K2	391107	hgsc.bcm.edu	37	chr1	158390085	158390085	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caatctgactaaagtggttaTggtgagatgccagcttgagg	11	11	13	6	0	1	3	0	3	1	1	1	4	1	3	1	3	2	2	1	3	4	3			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr1:158390085T>C	ENST00000314902.2	-	1	571	c.572A>G	c.(571-573)cAt>cGt	p.H191R		NM_001004476.1	NP_001004476.1	Q6IF99	O10K2_HUMAN	olfactory receptor, family 10, subfamily K, member 2	191						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)					AAAGTGGTTATGGTGAGATGC	0.438																																					p.H191R		Atlas-SNP	.											.	OR10K2	69	.	0			c.A572G						PASS	.						155	136	142					1																	158390085		2203	4300	6503	SO:0001583	missense	391107	exon1			TGGTTATGGTGAG	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.572A>G	chr1.hg19:g.158390085T>C	ENSP00000324251:p.His191Arg	57.0	0.0	.		127.0	8.0	.	NM_001004476		Missense_Mutation	SNP	ENST00000314902.2	hg19	CCDS30896.1	.	.	.	.	.	.	.	.	.	.	t	3.646	-0.072430	0.07228	.	.	ENSG00000180708	ENST00000314902	T	0.00044	8.83	4.13	2.97	0.34412	GPCR, rhodopsin-like superfamily (1);	0.136917	0.33477	N	0.004876	T	0.00039	0.0001	N	0.14661	0.345	0.09310	N	1	B	0.33883	0.43	B	0.37833	0.259	T	0.00346	-1.1800	10	0.87932	D	0	.	10.0033	0.41942	0.0:0.0:0.1708:0.8292	.	191	Q6IF99	O10K2_HUMAN	R	191	ENSP00000324251:H191R	ENSP00000324251:H191R	H	-	2	0	OR10K2	156656709	0.001000	0.12720	0.006000	0.13384	0.007000	0.05969	1.152000	0.31663	0.710000	0.31997	-0.658000	0.03865	CAT	.	.	.	none		0.438	OR10K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051854.1	NM_001004476		C	158390085	T	C	158390085	3	2	9	1	0	0	0	0	1	0	0	0	10921	1464	51	3	368	3	OR10K2	1	158390085	Missense_Mutation	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10	3110376	158390085	90860536	13	638											
SPTA1	6708	hgsc.bcm.edu	37	chr1	158592846	158592846	+	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	cttccagcaactgttcccagCgcttcagcagagcggcataa	10	8	9	14	2	1	1	1	0	0	1	3	1	3	1	2	1	5	5	2	1	2	4	rs199993378		TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr1:158592846C>T	ENST00000368147.4	-	43	6227	c.6047G>A	c.(6046-6048)cGc>cAc	p.R2016H		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)	p.R2016H(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)					CTGTTCCCAGCGCTTCAGCAG	0.478																																					p.R2016H		Atlas-SNP	.											SPTA1,colon,carcinoma,0,2	SPTA1	720	.	1	Substitution - Missense(1)	lung(1)	c.G6047A						PASS	.	C	HIS/ARG	3,3867		0,3,1932	231	230	231		6047	-1.5	0.6	1		231	1,8273		0,1,4136	yes	missense	SPTA1	NM_003126.2	29	0,4,6068	TT,TC,CC		0.0121,0.0775,0.0329	benign	2016/2420	158592846	4,12140	1935	4137	6072	SO:0001583	missense	6708	exon43			TCCCAGCGCTTCA	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.6047G>A	chr1.hg19:g.158592846C>T	ENSP00000357129:p.Arg2016His	74.0	0.0	.		124.0	40.0	.	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	10.22	1.288856	0.23478	7.75E-4	1.21E-4	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.40476	1.03;1.03	4.78	-1.49	0.08718	.	.	.	.	.	T	0.17619	0.0423	L	0.56340	1.77	0.38903	D	0.957367	P	0.47106	0.89	B	0.41723	0.365	T	0.10132	-1.0643	9	0.40728	T	0.16	.	5.6431	0.17575	0.1234:0.5367:0.0:0.3399	.	2016	P02549	SPTA1_HUMAN	H	2016;2013	ENSP00000357130:R2016H;ENSP00000357129:R2013H	ENSP00000357129:R2013H	R	-	2	0	SPTA1	156859470	0.999000	0.42202	0.633000	0.29310	0.020000	0.10135	0.741000	0.26202	-0.360000	0.08138	-0.136000	0.14681	CGC	.	.	.	weak		0.478	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		T	158592846	C	T	158592846	3	4	9	1	0	0	0	0	1	0	0	0	15128	768	27	1	1252	1	SPTA1	1	158592846	Missense_Mutation	SNP	C	TCGA-2Z-A9JD-01A-11D-A42J-10	202761	158592846	90657775	14	639											
MAPKAPK2	9261	hgsc.bcm.edu	37	chr1	206905963	206905963	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacaatgcgcgttgactacgAgcagatcaagataaaaaaga	18	6	9	8	3	1	4	1	1	0	3	1	5	1	4	0	0	3	2	0	0	6	3			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr1:206905963A>G	ENST00000367103.3	+	10	1296	c.1103A>G	c.(1102-1104)gAg>gGg	p.E368G	MAPKAPK2_ENST00000294981.4_3'UTR	NM_004759.4|NM_032960.3	NP_004750.1|NP_116584.2	P49137	MAPK2_HUMAN	mitogen-activated protein kinase-activated protein kinase 2	368	p38 MAPK-binding site.				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)			GTTGACTACGAGCAGATCAAG	0.572																																					p.E368G		Atlas-SNP	.											.	MAPKAPK2	45	.	0			c.A1103G						PASS	.						93	92	93					1																	206905963		2203	4300	6503	SO:0001583	missense	9261	exon10			ACTACGAGCAGAT	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.1103A>G	chr1.hg19:g.206905963A>G	ENSP00000356070:p.Glu368Gly	232.0	0.0	.		199.0	64.0	.	NM_032960	Q5SY30|Q5SY41|Q8IYD6	Missense_Mutation	SNP	ENST00000367103.3	hg19	CCDS31001.1	.	.	.	.	.	.	.	.	.	.	A	18.95	3.732623	0.69189	.	.	ENSG00000162889	ENST00000367103	T	0.49139	0.79	5.33	5.33	0.75918	Protein kinase-like domain (1);	.	.	.	.	T	0.46852	0.1414	M	0.65498	2.005	0.80722	D	1	B	0.32010	0.351	B	0.27887	0.084	T	0.50668	-0.8801	9	0.56958	D	0.05	-27.7491	14.4797	0.67573	1.0:0.0:0.0:0.0	.	368	P49137	MAPK2_HUMAN	G	368	ENSP00000356070:E368G	ENSP00000356070:E368G	E	+	2	0	MAPKAPK2	204972586	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	9.231000	0.95317	2.024000	0.59613	0.533000	0.62120	GAG	.	.	.	none		0.572	MAPKAPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088465.1	NM_004759		G	206905963	A	G	206905963	3	3	9	1	0	0	0	0	1	0	0	0	9296	304	11	3	1199	3	MAPKAPK2	1	206905963	Missense_Mutation	SNP	A	TCGA-2Z-A9JD-01A-11D-A42J-10	48313117	206905963	42344658	15	640											
OR2T34	127068	hgsc.bcm.edu	37	chr1	248737994	248737995	+	Missense_Mutation	DNP	AG	AG	GT																															catgcttgctctcagcaaagAgtcccgtgagggtgaaatca																										TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr1:248737994_248737995AG>GT	ENST00000328782.2	-	1	85_86	c.64_65CT>AC	c.(64-66)CTc>ACc	p.L22T		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	22						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)			CTCAGCAAAGAGTCCCGTGAGG	0.515																																					p.L22P|p.L22I		Atlas-SNP	.											.	OR2T34	72	.	0			c.T65C|c.C64A						PASS	.																																			SO:0001583	missense	127068	exon1			GCAAAGAGTCCCG|CAAAGAGTCCCGT	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.64_65delinsGT	chr1.hg19:g.248737994_248737995delinsGT	ENSP00000330904:p.Leu22Thr	223.0|219.0	0.0	.		429.0	111.0|110.0	.	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	hg19	CCDS31120.1																																																																																			.	.	.	none		0.515	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821		GT	248737995	AG	GT	248737994	3	3	9	1	0	0	0	0	1	0	0	0	11032	304	11	3	895	3	OR2T34	1	248737994	Missense_Mutation	DNP	AG	TCGA-2Z-A9JD-01A-11D-A42J-10	41832031	248737994	512627	16	641											
OR2T34	127068	hgsc.bcm.edu	37	chr1	248738035	248738035	+	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	gtgcttgctgtttgattctgAgaagtctgattccctgagca	7	15	11	8	0	2	4	0	4	2	1	3	5	3	4	1	0	3	4	1	0	1	4			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr1:248738035A>C	ENST00000328782.2	-	1	45	c.24T>G	c.(22-24)tcT>tcG	p.S8S		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	8						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)			TTTGATTCTGAGAAGTCTGAT	0.448																																					p.S8S		Atlas-SNP	.											.	OR2T34	72	.	0			c.T24G						PASS	.						46	64	58					1																	248738035		2069	4274	6343	SO:0001819	synonymous_variant	127068	exon1			ATTCTGAGAAGTC	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.24T>G	chr1.hg19:g.248738035A>C		204.0	0.0	.		391.0	118.0	.	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Silent	SNP	ENST00000328782.2	hg19	CCDS31120.1																																																																																			.	.	.	none		0.448	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821		C	248738035	A	C	248738035	2	2	9	1	0	0	0	0	0	0	0	1	11032	291	11	5		5	OR2T34	1	248738035	Silent	SNP	A	TCGA-2Z-A9JD-01A-11D-A42J-10	41	248738035	512586	17	642											
GREB1	9687	hgsc.bcm.edu	37	chr2	11758487	11758487	+	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	gagcatgccaggtcgccccaGccccgtggccccgcagagga	7	3	14	17	3	0	1	0	0	0	1	1	3	0	2	7	3	3	2	7	3	0	0			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr2:11758487G>A	ENST00000381486.2	+	22	3786	c.3486G>A	c.(3484-3486)caG>caA	p.Q1162Q	GREB1_ENST00000396123.1_Silent_p.Q160Q|GREB1_ENST00000234142.5_Silent_p.Q1162Q	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1162	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)		GGTCGCCCCAGCCCCGTGGCC	0.697																																					p.Q1162Q	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.G3486A						PASS	.						17	20	19					2																	11758487		1961	4056	6017	SO:0001819	synonymous_variant	9687	exon22			GCCCCAGCCCCGT		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.3486G>A	chr2.hg19:g.11758487G>A		224.0	0.0	.		113.0	38.0	.	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Silent	SNP	ENST00000381486.2	hg19	CCDS42655.1																																																																																			.	.	.	none		0.697	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		A	11758487	G	A	11758487	2	1	9	1	0	0	0	0	0	0	0	1	6767	962	34	2		2	GREB1	2	11758487	Silent	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10		11758487	231440886	18	643											
DNAJC5G	285126	hgsc.bcm.edu	37	chr2	27500849	27500849	+	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	ctttggtgaagaaggcgtcaGatactattttattctgaata	12	15	9	5	1	2	4	1	2	1	2	2	4	2	4	0	2	1	0	0	2	7	7			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr2:27500849G>C	ENST00000296097.3	+	4	759	c.341G>C	c.(340-342)aGa>aCa	p.R114T	SLC30A3_ENST00000447008.2_5'Flank|DNAJC5G_ENST00000404433.1_Missense_Mutation_p.R98T|DNAJC5G_ENST00000406962.1_Intron|DNAJC5G_ENST00000402462.1_Missense_Mutation_p.R114T	NM_173650.1	NP_775921.1	Q8N7S2	DNJ5G_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 5 gamma	114						membrane (GO:0016020)				cervix(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAAGGCGTCAGATACTATTTT	0.403																																					p.R114T		Atlas-SNP	.											.	DNAJC5G	19	.	0			c.G341C						PASS	.						77	76	77					2																	27500849		2203	4300	6503	SO:0001583	missense	285126	exon4			GCGTCAGATACTA	AF368277	CCDS1744.1	2p23	2011-09-02			ENSG00000163793	ENSG00000163793		"Heat shock proteins / DNAJ (HSP40)"	24844	protein-coding gene	gene with protein product		613946					Standard	NM_173650		Approved	FLJ40417, CSP-gamma	uc002rjl.1	Q8N7S2	OTTHUMG00000097079	ENST00000296097.3:c.341G>C	chr2.hg19:g.27500849G>C	ENSP00000296097:p.Arg114Thr	120.0	0.0	.		149.0	53.0	.	NM_173650	B4DY29|Q53SY5|Q8IYQ4|Q96RJ8	Missense_Mutation	SNP	ENST00000296097.3	hg19	CCDS1744.1	.	.	.	.	.	.	.	.	.	.	G	10.98	1.504325	0.26949	.	.	ENSG00000163793	ENST00000296097;ENST00000402462;ENST00000404433	T;T;T	0.72282	-0.64;-0.64;-0.64	4.96	0.26	0.15588	.	0.389286	0.21364	N	0.075745	T	0.48187	0.1486	N	0.19112	0.55	0.80722	D	1	B	0.12013	0.005	B	0.10450	0.005	T	0.13415	-1.0510	10	0.25106	T	0.35	.	6.3686	0.21469	0.1661:0.6106:0.2233:0.0	.	114	Q8N7S2	DNJ5G_HUMAN	T	114;114;98	ENSP00000296097:R114T;ENSP00000384305:R114T;ENSP00000385829:R98T	ENSP00000296097:R114T	R	+	2	0	DNAJC5G	27354353	0.612000	0.27000	0.938000	0.37757	0.835000	0.47333	1.289000	0.33307	0.116000	0.18110	0.563000	0.77884	AGA	.	.	.	none		0.403	DNAJC5G-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214200.1	NM_173650		C	27500849	G	C	27500849	3	2	9	1	0	0	0	0	1	0	0	0	4654	942	33	4	347	4	DNAJC5G	2	27500849	Missense_Mutation	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10	15742362	27500849	215698524	19	644											
MSH2	4436	hgsc.bcm.edu	37	chr2	47637500	47637500	+	Frame_Shift_Del	DEL	A	A	-																															agactgctggagacatggggAaactgagacaggtaagcaaa																										TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr2:47637500delA	ENST00000233146.2	+	3	857	c.634delA	c.(634-636)aaafs	p.K212fs	MSH2_ENST00000543555.1_Frame_Shift_Del_p.K146fs|MSH2_ENST00000406134.1_Frame_Shift_Del_p.K212fs	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	212					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)			AGACATGGGGAAACTGAGACA	0.433			"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.G211fs		Atlas-Indel,Pindel	.	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.633delG						PASS	.						92	93	93					2																	47637500		2203	4300	6503	SO:0001589	frameshift_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	.	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.634delA	chr2.hg19:g.47637500delA	ENSP00000233146:p.Lys212fs	80.0	0.0	0		105.0	42.0	0.4	NM_000251	B4E2Z2|O75488	Frame_Shift_Del	DEL	ENST00000233146.2	hg19	CCDS1834.1																																																																																			.	.	.	none		0.433	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3			-	47637500	A	-	47637500	7	5	9	1	0	1	0	1	0	0	0	0	9877	247	9	0	644	0	MSH2	2	47637500	Frame_Shift_Del	DEL	A	TCGA-2Z-A9JD-01A-11D-A42J-10	20136651	47637500	195561873	20	645											
AQP12B	653437	hgsc.bcm.edu	37	chr2	241622206	241622206	+	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	ccgcctggctgcctcacagaGggtgaaggtggcaaagaaga	11	5	15	10	1	1	4	1	1	0	3	1	4	1	4	3	4	1	2	3	4	3	0			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr2:241622206G>T	ENST00000407834.3	-	1	111	c.49C>A	c.(49-51)Ctc>Atc	p.L17I		NM_001102467.1	NP_001095937.1	A6NM10	AQ12B_HUMAN	aquaporin 12B	17						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)		GCCTCACAGAGGGTGAAGGTG	0.677																																					p.L17I		Atlas-SNP	.											.	AQP12B	33	.	0			c.C49A						PASS	.						49	55	53					2																	241622206		2168	4270	6438	SO:0001583	missense	653437	exon1			CACAGAGGGTGAA	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.49C>A	chr2.hg19:g.241622206G>T	ENSP00000384894:p.Leu17Ile	109.0	0.0	.		64.0	44.0	.	NM_001102467	A4QPB9	Missense_Mutation	SNP	ENST00000407834.3	hg19	CCDS46560.1	.	.	.	.	.	.	.	.	.	.	.	9.399	1.077458	0.20227	.	.	ENSG00000185176	ENST00000407834	T	0.10477	2.87	3.19	2.24	0.28232	.	0.462193	0.22773	N	0.055816	T	0.08313	0.0207	L	0.38175	1.15	0.30214	N	0.797416	B	0.27351	0.176	B	0.26202	0.067	T	0.17806	-1.0357	9	.	.	.	-14.734	9.3887	0.38359	0.0:0.0:0.7749:0.2251	.	17	A6NM10-2	.	I	17	ENSP00000384894:L17I	.	L	-	1	0	AQP12B	241270879	0.017000	0.18338	0.381000	0.26106	0.247000	0.25773	0.485000	0.22324	0.549000	0.28973	0.479000	0.44913	CTC	.	.	.	none		0.677	AQP12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325625.1			T	241622206	G	T	241622206	3	4	9	1	0	0	0	0	1	0	0	0	825	1000	35	4	886	4	AQP12B	2	241622206	Missense_Mutation	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10	193984706	241622206	1577167	21	646											
BAP1	8314	hgsc.bcm.edu	37	chr3	52437652	52437652	+	Frame_Shift_Del	DEL	G	G	-																															ggcgagcgcagtggcgagttGaaagcactgccgatctcaga																										TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr3:52437652delG	ENST00000460680.1	-	13	1980	c.1509delC	c.(1507-1509)ttcfs	p.F503fs	BAP1_ENST00000296288.5_Frame_Shift_Del_p.F485fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		GTGGCGAGTTGAAAGCACTGC	0.632			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.N504fs	GBM(101;493 1458 7992 21037 25532)	Atlas-Indel,Pindel	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	0			c.1510delA						PASS	.						49	51	50					3																	52437652		2203	4300	6503	SO:0001589	frameshift_variant	8314	exon13			.	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1509delC	chr3.hg19:g.52437652delG	ENSP00000417132:p.Phe503fs	112.0	0.0	0		50.0	39.0	0.78	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Frame_Shift_Del	DEL	ENST00000460680.1	hg19	CCDS2853.1																																																																																			.	.	.	none		0.632	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			-	52437652	G	-	52437652	7	5	9	1	0	1	0	1	0	0	0	0	1311	1281	45	0	700	0	BAP1	3	52437652	Frame_Shift_Del	DEL	G	TCGA-2Z-A9JD-01A-11D-A42J-10		52437652	145584778	22	647	5	2									
BAP1	8314	hgsc.bcm.edu	37	chr3	52437657	52437657	+	Missense_Mutation	SNP	C	C	G																															gcgcagtggcgagttgaaagCactgccgatctcagaggccg																										TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr3:52437657C>G	ENST00000460680.1	-	13	1975	c.1504G>C	c.(1504-1506)Gct>Cct	p.A502P	BAP1_ENST00000296288.5_Missense_Mutation_p.A484P	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		GAGTTGAAAGCACTGCCGATC	0.642			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.A502P	GBM(101;493 1458 7992 21037 25532)	Atlas-SNP	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	0			c.G1504C						PASS	.						48	51	50					3																	52437657		2203	4300	6503	SO:0001583	missense	8314	exon13			TGAAAGCACTGCC	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1504G>C	chr3.hg19:g.52437657C>G	ENSP00000417132:p.Ala502Pro	108.0	0.0	.		50.0	41.0	.	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Missense_Mutation	SNP	ENST00000460680.1	hg19	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	C	30	5.055937	0.93793	.	.	ENSG00000163930	ENST00000460680;ENST00000296288;ENST00000478368	T;T;T	0.64438	-0.07;-0.1;-0.03	6.05	6.05	0.98169	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (1);	0.000000	0.85682	D	0.000000	T	0.73552	0.3601	L	0.34521	1.04	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.74375	-0.3686	10	0.87932	D	0	.	20.6086	0.99469	0.0:1.0:0.0:0.0	.	502	Q92560	BAP1_HUMAN	P	502;484;3	ENSP00000417132:A502P;ENSP00000296288:A484P;ENSP00000420647:A3P	ENSP00000296288:A484P	A	-	1	0	BAP1	52412697	1.000000	0.71417	0.994000	0.49952	0.964000	0.63967	7.313000	0.78978	2.880000	0.98712	0.655000	0.94253	GCT	.	.	.	none		0.642	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			G	52437657	C	G	52437657	3	3	9	1	0	0	0	0	1	0	0	0	1311	710	25	4	705	4	BAP1	3	52437657	Missense_Mutation	SNP	C	TCGA-2Z-A9JD-01A-11D-A42J-10	5	52437657	145584773	23	648	5	2									
CACNA1D	776	hgsc.bcm.edu	37	chr3	53684852	53684852	+	Missense_Mutation	SNP	T	T	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	tatttttacagtcgagacatTtttgaagattatagcgtatg	12	17	8	4	2	0	3	0	1	0	2	1	4	0	3	0	0	2	1	0	0	6	9			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr3:53684852T>G	ENST00000350061.5	+	4	1041	c.530T>G	c.(529-531)tTt>tGt	p.F177C	CACNA1D_ENST00000288139.4_Missense_Mutation_p.F177C|CACNA1D_ENST00000422281.2_Missense_Mutation_p.F177C	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	177					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)			breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GTCGAGACATTTTTGAAGATT	0.353																																					p.F177C		Atlas-SNP	.											.	CACNA1D	324	.	0			c.T530G						PASS	.						151	151	151					3																	53684852		2203	4300	6503	SO:0001583	missense	776	exon4			AGACATTTTTGAA	AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.530T>G	chr3.hg19:g.53684852T>G	ENSP00000288133:p.Phe177Cys	44.0	0.0	.		66.0	57.0	.	NM_001128840	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Missense_Mutation	SNP	ENST00000350061.5	hg19	CCDS46848.1	.	.	.	.	.	.	.	.	.	.	t	20.2	3.958340	0.73902	.	.	ENSG00000157388	ENST00000350061;ENST00000288139;ENST00000422281	D;D;D	0.98419	-4.92;-4.92;-4.92	5.06	5.06	0.68205	Ion transport (1);	0.000000	0.64402	D	0.000001	D	0.97723	0.9253	L	0.60012	1.86	0.80722	D	1	B;P;B	0.47962	0.118;0.903;0.096	B;P;B	0.50136	0.22;0.632;0.072	D	0.98463	1.0597	10	0.87932	D	0	.	15.0208	0.71630	0.0:0.0:0.0:1.0	.	177;177;177	B0FYA3;Q01668;Q01668-2	.;CAC1D_HUMAN;.	C	177	ENSP00000288133:F177C;ENSP00000288139:F177C;ENSP00000409174:F177C	ENSP00000288139:F177C	F	+	2	0	CACNA1D	53659892	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.860000	0.86993	2.139000	0.66308	0.358000	0.22013	TTT	.	.	.	none		0.353	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720		G	53684852	T	G	53684852	3	3	9	1	0	0	0	0	1	0	0	0	2543	1841	64	5	544	5	CACNA1D	3	53684852	Missense_Mutation	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10	1247195	53684852	144337578	24	649											
CCDC39	339829	hgsc.bcm.edu	37	chr3	180334122	180334122	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagctctgacgactgcctttTgtgctagctgtaggtagttc	6	14	12	9	1	1	1	0	1	1	0	2	3	1	1	1	1	4	6	1	1	3	6			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr3:180334122T>C	ENST00000442201.2	-	19	2735	c.2616A>G	c.(2614-2616)acA>acG	p.T872T	TTC14_ENST00000382584.4_Intron|CCDC39_ENST00000273654.4_3'UTR	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	872	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)			GACTGCCTTTTGTGCTAGCTG	0.378																																					p.T872T		Atlas-SNP	.											.	CCDC39	242	.	0			c.A2616G						PASS	.						112	106	108					3																	180334122		1869	4110	5979	SO:0001819	synonymous_variant	339829	exon19			GCCTTTTGTGCTA	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.2616A>G	chr3.hg19:g.180334122T>C		45.0	0.0	.		102.0	70.0	.	NM_181426	B4E2H1	Silent	SNP	ENST00000442201.2	hg19	CCDS46964.1	.	.	.	.	.	.	.	.	.	.	T	4.423	0.078286	0.08485	.	.	ENSG00000145075	ENST00000473854	.	.	.	4.62	-6.0	0.02206	.	.	.	.	.	T	0.15869	0.0382	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24799	-1.0150	4	.	.	.	.	1.1368	0.01757	0.2271:0.1119:0.2181:0.4429	.	.	.	.	R	56	.	.	Q	-	2	0	CCDC39	181816816	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-0.781000	0.04648	-1.154000	0.02825	-0.585000	0.04130	CAA	.	.	.	none		0.378	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028		C	180334122	T	C	180334122	2	2	9	1	0	0	0	0	0	0	0	1	2813	1799	63	3		3	CCDC39	3	180334122	Silent	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10	126649270	180334122	17688308	25	650											
ZNF141	7700	hgsc.bcm.edu	37	chr4	366865	366865	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcctttaaatggtctttaatAtttaatgaacataagagaat	16	15	6	4	0	1	2	0	1	1	1	1	3	1	2	1	1	1	0	1	1	8	8			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr4:366865A>G	ENST00000240499.7	+	4	788	c.639A>G	c.(637-639)atA>atG	p.I213M	ZNF141_ENST00000505939.1_Intron|ZNF141_ENST00000512994.1_Intron	NM_003441.2	NP_003432.1	Q15928	ZN141_HUMAN	zinc finger protein 141	213					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						GGTCTTTAATATTTAATGAAC	0.358																																					p.I213M		Atlas-SNP	.											.	ZNF141	48	.	0			c.A639G						PASS	.						53	60	57					4																	366865		2178	4293	6471	SO:0001583	missense	7700	exon4			TTTAATATTTAAT	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.639A>G	chr4.hg19:g.366865A>G	ENSP00000240499:p.Ile213Met	59.0	0.0	.		77.0	33.0	.	NM_003441	Q6DK07	Missense_Mutation	SNP	ENST00000240499.7	hg19	CCDS33931.1	.	.	.	.	.	.	.	.	.	.	A	10.31	1.315890	0.23908	.	.	ENSG00000131127	ENST00000240499	T	0.15256	2.44	1.23	-1.64	0.08318	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08179	0.0204	N	0.20986	0.625	0.09310	N	1	P	0.40681	0.727	B	0.35688	0.208	T	0.25606	-1.0127	8	.	.	.	.	4.0674	0.09866	0.6895:0.0:0.0:0.3105	.	213	Q15928	ZN141_HUMAN	M	213	ENSP00000240499:I213M	.	I	+	3	3	ZNF141	356865	0.000000	0.05858	0.006000	0.13384	0.958000	0.62258	-2.175000	0.01263	-0.521000	0.06426	0.254000	0.18369	ATA	.	.	.	none		0.358	ZNF141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357710.1	NM_003441		G	366865	A	G	366865	3	3	9	1	0	0	0	0	1	0	0	0	17742	439	16	3	653	3	ZNF141	4	366865	Missense_Mutation	SNP	A	TCGA-2Z-A9JD-01A-11D-A42J-10		366865	190787411	26	651											
N4BP2	55728	hgsc.bcm.edu	37	chr4	40121601	40121601	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaaagaagaaaatattttaTctttatctttgaagcatcta	18	15	4	4	0	3	3	0	1	3	2	3	3	3	3	0	0	1	1	0	0	10	7			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr4:40121601T>C	ENST00000261435.6	+	9	2286	c.1870T>C	c.(1870-1872)Tct>Cct	p.S624P		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	624					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						AAATATTTTATCTTTATCTTT	0.323																																					p.S624P		Atlas-SNP	.											.	N4BP2	166	.	0			c.T1870C						PASS	.						42	49	47					4																	40121601		2181	4262	6443	SO:0001583	missense	55728	exon9			ATTTTATCTTTAT	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.1870T>C	chr4.hg19:g.40121601T>C	ENSP00000261435:p.Ser624Pro	182.0	0.0	.		257.0	92.0	.	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	hg19	CCDS3457.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	6.926|6.926	0.540553|0.540553	0.13250|0.13250	.|.	.|.	ENSG00000078177|ENSG00000078177	ENST00000513269|ENST00000261435;ENST00000381804	.|T	.|0.19669	.|2.13	4.54|4.54	4.54|4.54	0.55810|0.55810	.|.	.|0.364797	.|0.28815	.|N	.|0.014051	T|T	0.19644|0.19644	0.0472|0.0472	L|L	0.56769|0.56769	1.78|1.78	0.25803|0.25803	N|N	0.984481|0.984481	.|B;B	.|0.14438	.|0.01;0.003	.|B;B	.|0.16722	.|0.016;0.003	T|T	0.11891|0.11891	-1.0569|-1.0569	5|10	.|0.52906	.|T	.|0.07	-9.1621|-9.1621	5.7056|5.7056	0.17907|0.17907	0.1577:0.0:0.1896:0.6527|0.1577:0.0:0.1896:0.6527	.|.	.|624;624	.|Q86UW6-2;Q86UW6	.|.;N4BP2_HUMAN	T|P	270|624;544	.|ENSP00000261435:S624P	.|ENSP00000261435:S624P	I|S	+|+	2|1	0|0	N4BP2|N4BP2	39797996|39797996	0.317000|0.317000	0.24589|0.24589	0.949000|0.949000	0.38748|0.38748	0.075000|0.075000	0.17131|0.17131	2.005000|2.005000	0.40864|0.40864	2.269000|2.269000	0.75478|0.75478	0.454000|0.454000	0.30748|0.30748	ATC|TCT	.	.	.	none		0.323	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177		C	40121601	T	C	40121601	3	2	9	1	0	0	0	0	1	0	0	0	10117	1435	50	3	1896	3	N4BP2	4	40121601	Missense_Mutation	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10	39754736	40121601	151032675	27	652											
SHROOM3	57619	hgsc.bcm.edu	37	chr4	77660481	77660481	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggtgggtgcacccctgccTccagctcggagtgacagtta	8	8	13	12	1	0	1	0	1	0	0	2	2	1	2	4	3	3	3	4	3	2	1			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr4:77660481T>C	ENST00000296043.6	+	5	2108	c.1155T>C	c.(1153-1155)ccT>ccC	p.P385P		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	385					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)			CACCCCTGCCTCCAGCTCGGA	0.632																																					p.P385P		Atlas-SNP	.											.	SHROOM3	134	.	0			c.T1155C						PASS	.						43	42	42					4																	77660481		2203	4300	6503	SO:0001819	synonymous_variant	57619	exon5			CCTGCCTCCAGCT	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.1155T>C	chr4.hg19:g.77660481T>C		113.0	0.0	.		91.0	33.0	.	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Silent	SNP	ENST00000296043.6	hg19	CCDS3579.2																																																																																			.	.	.	none		0.632	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859		C	77660481	T	C	77660481	2	2	9	1	0	0	0	0	0	0	0	1	14308	1538	54	3		3	SHROOM3	4	77660481	Silent	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10	37538880	77660481	113493795	28	653											
IL6ST	3572	hgsc.bcm.edu	37	chr5	55247359	55247359	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatctgtgtatgctgccatTcgtaccatgtacaatgtgtc	8	15	8	10	1	2	0	1	0	1	0	4	0	2	0	2	0	4	4	2	0	4	4			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr5:55247359T>C	ENST00000381298.2	-	14	2085	c.1773A>G	c.(1771-1773)cgA>cgG	p.R591R	IL6ST_ENST00000522633.2_3'UTR|IL6ST_ENST00000381294.3_Silent_p.R530R|IL6ST_ENST00000381287.4_3'UTR|IL6ST_ENST00000381293.2_Intron|IL6ST_ENST00000336909.5_Silent_p.R591R|IL6ST_ENST00000381286.3_Intron|IL6ST_ENST00000536319.1_3'UTR|IL6ST_ENST00000502326.3_Silent_p.R591R	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	591	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				ATGCTGCCATTCGTACCATGT	0.383			O		hepatocellular ca																																p.R591R		Atlas-SNP	.		Dom	yes		5	5q11	3572	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"		E	.	IL6ST	75	.	0			c.A1773G						PASS	.						142	129	133					5																	55247359		2203	4300	6503	SO:0001819	synonymous_variant	3572	exon14			TGCCATTCGTACC	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.1773A>G	chr5.hg19:g.55247359T>C		36.0	0.0	.		51.0	17.0	.	NM_002184	A0N0L4|Q5FC04|Q9UQ41	Silent	SNP	ENST00000381298.2	hg19	CCDS3971.1																																																																																			.	.	.	none		0.383	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		C	55247359	T	C	55247359	2	2	9	1	0	0	0	0	0	0	0	1	7710	1770	62	3		3	IL6ST	5	55247359	Silent	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10		55247359	125667901	29	654											
GFM2	84340	hgsc.bcm.edu	37	chr5	74017604	74017604	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcgttcgaagcacagttgaaTaaccctaatcaaaataattt	16	11	6	8	2	1	1	1	1	0	0	2	2	1	1	1	0	2	3	1	0	7	6			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr5:74017604T>C	ENST00000296805.3	-	21	2673	c.2216A>G	c.(2215-2217)tAt>tGt	p.Y739C	GFM2_ENST00000515125.1_5'UTR|GFM2_ENST00000345239.2_Missense_Mutation_p.Y692C|GFM2_ENST00000509430.1_Missense_Mutation_p.Y739C	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)		CACAGTTGAATAACCCTAATC	0.343																																					p.Y739C		Atlas-SNP	.											.	GFM2	38	.	0			c.A2216G						PASS	.						61	58	59					5																	74017604		2203	4300	6503	SO:0001583	missense	84340	exon21			GTTGAATAACCCT	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.2216A>G	chr5.hg19:g.74017604T>C	ENSP00000296805:p.Tyr739Cys	36.0	0.0	.		65.0	32.0	.	NM_032380		Missense_Mutation	SNP	ENST00000296805.3	hg19	CCDS4023.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.965843	0.74131	.	.	ENSG00000164347	ENST00000296805;ENST00000345239;ENST00000546082;ENST00000509430	T;T;T	0.62105	0.05;0.05;0.05	5.85	5.85	0.93711	Elongation factor G/III/V (1);Translation elongation factor EFG/EF2, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.87581	0.6213	H	0.98577	4.27	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	0.92382	0.5914	10	0.87932	D	0	-16.682	16.2444	0.82434	0.0:0.0:0.0:1.0	.	737;692;739	Q969S9-3;Q969S9-2;Q969S9	.;.;RRF2M_HUMAN	C	739;692;561;739	ENSP00000296805:Y739C;ENSP00000296804:Y692C;ENSP00000427004:Y739C	ENSP00000296805:Y739C	Y	-	2	0	GFM2	74053360	1.000000	0.71417	1.000000	0.80357	0.675000	0.39556	7.524000	0.81866	2.233000	0.73108	0.455000	0.32223	TAT	.	.	.	none		0.343	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380		C	74017604	T	C	74017604	3	2	9	1	0	0	0	0	1	0	0	0	6349	1406	49	3	127	3	GFM2	5	74017604	Missense_Mutation	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10	18770245	74017604	106897656	30	655											
PCDHGB2	56103	hgsc.bcm.edu	37	chr5	140741837	140741837	+	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	cgcggtgattctggcaatctCcctgcgcctgcgactctctt	4	12	10	15	4	3	1	0	1	3	0	5	2	3	1	2	2	2	1	2	2	1	2			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr5:140741837C>T	ENST00000522605.1	+	1	2135	c.2135C>T	c.(2134-2136)tCc>tTc	p.S712F	PCDHGB1_ENST00000523390.1_Intron|PCDHGA5_ENST00000518069.1_5'Flank|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018923.2|NM_032096.1	NP_061746.1|NP_115267.1	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2	712					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)			CTGGCAATCTCCCTGCGCCTG	0.572																																					p.S712F		Atlas-SNP	.											.	PCDHGB2	196	.	0			c.C2135T						PASS	.						94	98	97					5																	140741837		2036	4193	6229	SO:0001583	missense	56103	exon1			CAATCTCCCTGCG	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.2135C>T	chr5.hg19:g.140741837C>T	ENSP00000429018:p.Ser712Phe	163.0	0.0	.		92.0	10.0	.	NM_018923	Q3MIJ3|Q9UN65	Missense_Mutation	SNP	ENST00000522605.1	hg19	CCDS54924.1	.	.	.	.	.	.	.	.	.	.	.	9.528	1.110098	0.20714	.	.	ENSG00000253910	ENST00000522605	T	0.13778	2.56	4.96	3.01	0.34805	.	.	.	.	.	T	0.09291	0.0229	L	0.38175	1.15	0.09310	N	1	B;P	0.48016	0.288;0.904	B;B	0.37198	0.162;0.243	T	0.25916	-1.0118	9	0.87932	D	0	.	4.844	0.13505	0.0:0.4413:0.3815:0.1772	.	712;712	Q9Y5G2-2;Q9Y5G2	.;PCDGE_HUMAN	F	712	ENSP00000429018:S712F	ENSP00000429018:S712F	S	+	2	0	PCDHGB2	140722021	0.577000	0.26708	0.243000	0.24186	0.540000	0.34992	1.496000	0.35638	1.193000	0.43086	0.461000	0.40582	TCC	.	.	.	none		0.572	PCDHGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374741.1	NM_018923		T	140741837	C	T	140741837	3	4	9	1	0	0	0	0	1	0	0	0	11570	855	30	2	2137	2	PCDHGB2	5	140741837	Missense_Mutation	SNP	C	TCGA-2Z-A9JD-01A-11D-A42J-10	66724233	140741837	40173423	31	656											
PCDHGB6	56100	hgsc.bcm.edu	37	chr5	140788766	140788766	+	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	gtctctctacccagtgtaaaGtaatcatagaaatccttgat	13	13	6	9	0	3	2	1	1	2	1	5	2	4	2	2	0	1	2	2	0	6	5			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr5:140788766G>T	ENST00000520790.1	+	1	997	c.997G>T	c.(997-999)Gta>Tta	p.V333L	PCDHGB3_ENST00000576222.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA9_ENST00000573521.1_Intron	NM_018926.2|NM_032100.1	NP_061749.1|NP_115271.1	Q9Y5F9	PCDGI_HUMAN	protocadherin gamma subfamily B, 6	333	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)|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)			CCAGTGTAAAGTAATCATAGA	0.398																																					p.V333L		Atlas-SNP	.											.	PCDHGB6	120	.	0			c.G997T						PASS	.						100	101	101					5																	140788766		1895	4117	6012	SO:0001583	missense	56100	exon1			TGTAAAGTAATCA	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.997G>T	chr5.hg19:g.140788766G>T	ENSP00000428603:p.Val333Leu	263.0	0.0	.		131.0	54.0	.	NM_032100	Q9Y5C5	Missense_Mutation	SNP	ENST00000520790.1	hg19	CCDS54929.1	.	.	.	.	.	.	.	.	.	.	-	14.96	2.692194	0.48202	.	.	ENSG00000253305	ENST00000520790	T	0.57107	0.42	5.33	3.52	0.40303	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.58438	0.2122	M	0.67700	2.07	0.24431	N	0.994579	P;D	0.54047	0.863;0.964	P;P	0.52554	0.702;0.499	T	0.49615	-0.8921	9	0.49607	T	0.09	.	7.0434	0.25033	0.1481:0.0:0.7137:0.1381	.	333;333	Q9Y5F9;Q9Y5F9-2	PCDGI_HUMAN;.	L	333	ENSP00000428603:V333L	ENSP00000428603:V333L	V	+	1	0	PCDHGB6	140768950	0.819000	0.29175	0.770000	0.31555	0.968000	0.65278	0.600000	0.24104	0.604000	0.29930	0.460000	0.39030	GTA	.	.	.	none		0.398	PCDHGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374746.1	NM_018926		T	140788766	G	T	140788766	3	4	9	1	0	0	0	0	1	0	0	0	11574	1029	36	4	999	4	PCDHGB6	5	140788766	Missense_Mutation	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10	46929	140788766	40126494	32	657											
ARHGAP26	23092	hgsc.bcm.edu	37	chr5	142281604	142281604	+	Splice_Site	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	ttaaccattagcatacagaaCgtgagtgggcatagggacag	14	8	12	7	1	0	2	0	1	0	1	0	3	0	3	1	2	4	2	1	2	5	4	rs142837036		TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr5:142281604C>A	ENST00000274498.4	+	7	1080	c.702C>A	c.(700-702)aaC>aaA	p.N234K	ARHGAP26_ENST00000378004.3_Splice_Site_p.N234K	NM_015071.4	NP_055886.1	Q9UNA1	RHG26_HUMAN	Rho GTPase activating protein 26	234					actin cytoskeleton organization (GO:0030036)|filopodium assembly (GO:0046847)|nervous system development (GO:0007399)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)	p.N234N(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(7)|ovary(1)	25		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCATACAGAACGTGAGTGGGC	0.463																																					p.N234K		Atlas-SNP	.											ARHGAP26,colon,carcinoma,+1,1	ARHGAP26	57	.	1	Substitution - coding silent(1)	ovary(1)	c.C702A						PASS	.						126	111	116					5																	142281604		2203	4300	6503	SO:0001630	splice_region_variant	23092	exon7			ACAGAACGTGAGT	AB014521	CCDS4277.1, CCDS47297.1	5q31	2011-06-29			ENSG00000145819	ENSG00000145819		"Rho GTPase activating proteins"	17073	protein-coding gene	gene with protein product	"GTPase regulator associated with the focal adhesion kinase pp125"	605370				9858476, 8649427	Standard	NM_001135608		Approved	GRAF, KIAA0621, OPHN1L, OPHN1L1	uc011dbj.2	Q9UNA1	OTTHUMG00000059705	ENST00000274498.4:c.702+1C>A	chr5.hg19:g.142281604C>A		47.0	0.0	.		119.0	40.0	.	NM_015071	O75117|Q5D035|Q9BYS6|Q9BYS7|Q9UJ00	Missense_Mutation	SNP	ENST00000274498.4	hg19	CCDS4277.1	.	.	.	.	.	.	.	.	.	.	C	16.74	3.206681	0.58343	.	.	ENSG00000145819	ENST00000274498;ENST00000378004	T;T	0.04015	3.73;3.73	5.49	-7.51	0.01346	.	0.000000	0.85682	D	0.000000	T	0.04543	0.0124	L	0.48218	1.51	0.58432	D	0.999991	P;B	0.42620	0.785;0.18	B;B	0.42827	0.399;0.188	T	0.13845	-1.0494	10	0.19590	T	0.45	.	13.6099	0.62071	0.0:0.2143:0.0:0.7857	.	234;234	Q9UNA1;Q9UNA1-2	RHG26_HUMAN;.	K	234	ENSP00000274498:N234K;ENSP00000367243:N234K	ENSP00000274498:N234K	N	+	3	2	ARHGAP26	142261788	0.998000	0.40836	0.887000	0.34795	0.680000	0.39746	0.442000	0.21628	-1.491000	0.01840	-2.010000	0.00438	AAC	.	C|1.000;T|0.000	.	alt		0.463	ARHGAP26-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132744.3	NM_015071	Missense_Mutation	A	142281604	C	A	142281604	5	1	9	1	0	0	0	0	0	0	1	0	875	550	19	4	728	4	ARHGAP26	5	142281604	Splice_Site	SNP	C	TCGA-2Z-A9JD-01A-11D-A42J-10	1492838	142281604	38633656	33	658											
C5orf4	10826	hgsc.bcm.edu	37	chr5	154200926	154200926	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaggaaaaccacatggtgaTggaggacaagtgggagccca	15	4	14	8	0	0	1	0	1	0	0	0	5	0	5	2	5	2	0	2	5	4	0			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr5:154200926T>C	ENST00000326080.5	-	8	1162	c.739A>G	c.(739-741)Atc>Gtc	p.I247V	FAXDC2_ENST00000517938.1_Missense_Mutation_p.I224V|FAXDC2_ENST00000523997.1_5'Flank	NM_032385.3	NP_115761.2	Q96IV6	FXDC2_HUMAN	fatty acid hydroxylase domain containing 2	247					fatty acid biosynthetic process (GO:0006633)	integral component of membrane (GO:0016021)	iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)										CACATGGTGATGGAGGACAAG	0.552																																					p.I247V		Atlas-SNP	.											.	.	.	.	0			c.A739G						PASS	.						187	195	192					5																	154200926		2118	4218	6336	SO:0001583	missense	10826	exon8			TGGTGATGGAGGA	AF159165	CCDS43390.1	5q31-q32	2013-03-04	2013-03-04	2013-03-04	ENSG00000170271	ENSG00000170271		"Fatty acid hydroxylase domain containing"	1334	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 4"	C5orf4		10843801	Standard	NM_032385		Approved	FLJ13758	uc003lvs.4	Q96IV6	OTTHUMG00000164141	ENST00000326080.5:c.739A>G	chr5.hg19:g.154200926T>C	ENSP00000320604:p.Ile247Val	61.0	0.0	.		139.0	52.0	.	NM_032385	B4DIE1|Q9BSX6|Q9H8C7	Missense_Mutation	SNP	ENST00000326080.5	hg19	CCDS43390.1	.	.	.	.	.	.	.	.	.	.	T	2.017	-0.425684	0.04701	.	.	ENSG00000170271	ENST00000326080;ENST00000517938	D;D	0.84660	-1.88;-1.88	5.24	5.24	0.73138	Fatty acid hydroxylase (1);	0.050639	0.85682	D	0.000000	T	0.69223	0.3087	N	0.05487	-0.04	0.80722	D	1	B	0.12013	0.005	B	0.14023	0.01	T	0.64334	-0.6432	10	0.17832	T	0.49	.	11.1394	0.48394	0.0:0.0739:0.0:0.9261	.	247	Q96IV6	CE004_HUMAN	V	247;224	ENSP00000320604:I247V;ENSP00000430286:I224V	ENSP00000320604:I247V	I	-	1	0	C5orf4	154181119	1.000000	0.71417	0.995000	0.50966	0.569000	0.35902	4.848000	0.62874	1.977000	0.57605	0.533000	0.62120	ATC	.	.	.	none		0.552	FAXDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377429.1	NM_032385		C	154200926	T	C	154200926	3	2	9	1	0	0	0	0	1	0	0	0	2300	1464	51	3	270	3	C5orf4	5	154200926	Missense_Mutation	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10	11919322	154200926	26714334	34	659											
DOCK2	1794	hgsc.bcm.edu	37	chr5	169127100	169127100	+	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	cacctggtggacaggaccacCgtggtggccaggaagctggg	8	5	17	11	1	0	0	0	0	0	0	0	3	0	3	4	7	1	1	4	7	1	0	rs141406325	byFrequency	TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr5:169127100C>A	ENST00000256935.8	+	13	1295	c.1215C>A	c.(1213-1215)acC>acA	p.T405T		NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	405					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)			ACAGGACCACCGTGGTGGCCA	0.562																																					p.T405T		Atlas-SNP	.											.	DOCK2	389	.	0			c.C1215A						PASS	.						156	143	148					5																	169127100		2203	4300	6503	SO:0001819	synonymous_variant	1794	exon13			GACCACCGTGGTG	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.1215C>A	chr5.hg19:g.169127100C>A		20.0	0.0	.		74.0	25.0	.	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	hg19	CCDS4371.1																																																																																			.	C|0.999;T|0.001	.	alt		0.562	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		A	169127100	C	A	169127100	2	1	9	1	0	0	0	0	0	0	0	1	4689	639	23	4		4	DOCK2	5	169127100	Silent	SNP	C	TCGA-2Z-A9JD-01A-11D-A42J-10	14926174	169127100	11788160	35	660											
PGC	5225	hgsc.bcm.edu	37	chr6	41712458	41712458	+	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	aaagcggtacttccaagcagGatcatacttgtgggtcctca	11	10	10	10	1	2	0	2	0	0	0	4	1	4	1	2	3	4	2	2	3	4	4			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr6:41712458G>C	ENST00000373025.3	-	2	210	c.148C>G	c.(148-150)Cct>Gct	p.P50A	PGC_ENST00000425343.2_Missense_Mutation_p.P50A	NM_002630.3	NP_002621.1	P20142	PEPC_HUMAN	progastricsin (pepsinogen C)	50					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)			TTCCAAGCAGGATCATACTTG	0.532																																					p.P50A		Atlas-SNP	.											.	PGC	56	.	0			c.C148G						PASS	.						90	76	81					6																	41712458		2203	4300	6503	SO:0001583	missense	5225	exon2			AAGCAGGATCATA		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.148C>G	chr6.hg19:g.41712458G>C	ENSP00000362116:p.Pro50Ala	62.0	0.0	.		79.0	33.0	.	NM_002630	B4DVZ3|Q5T3D7|Q5T3D8	Missense_Mutation	SNP	ENST00000373025.3	hg19	CCDS4859.1	.	.	.	.	.	.	.	.	.	.	G	12.24	1.878022	0.33162	.	.	ENSG00000096088	ENST00000373025;ENST00000424183;ENST00000394278;ENST00000356667;ENST00000425343;ENST00000415707	T;T;T;T	0.65364	1.59;-0.15;0.44;0.44	5.15	4.22	0.49857	Peptidase aspartic (1);	0.459575	0.22142	N	0.064040	T	0.62744	0.2453	M	0.66939	2.045	0.18873	N	0.999988	D	0.71674	0.998	D	0.64687	0.928	T	0.53315	-0.8456	10	0.23302	T	0.38	.	12.4904	0.55897	0.0:0.0:0.8332:0.1668	.	50	P20142	PEPC_HUMAN	A	50;50;50;50;50;54	ENSP00000362116:P50A;ENSP00000349094:P50A;ENSP00000405094:P50A;ENSP00000399429:P54A	ENSP00000349094:P50A	P	-	1	0	PGC	41820436	1.000000	0.71417	0.086000	0.20670	0.005000	0.04900	3.402000	0.52608	2.426000	0.82243	0.555000	0.69702	CCT	.	.	.	none		0.532	PGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040521.2			C	41712458	G	C	41712458	3	2	9	1	0	0	0	0	1	0	0	0	11792	1174	41	4	1359	4	PGC	6	41712458	Missense_Mutation	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10		41712458	129402609	36	661											
CUL7	9820	hgsc.bcm.edu	37	chr6	43020188	43020188	+	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	ctctgaatgagggacttcacGtcggtttccatctcctccag	7	12	9	13	2	3	2	1	2	2	0	7	3	5	3	3	2	0	1	3	2	1	2	rs4711738	byFrequency	TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr6:43020188G>C	ENST00000265348.3	-	2	424	c.339C>G	c.(337-339)gaC>gaG	p.D113E	CUL7_ENST00000535468.1_Missense_Mutation_p.D165E			Q14999	CUL7_HUMAN	cullin 7	113					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)			GGGACTTCACGTCGGTTTCCA	0.612																																					p.D165E		Atlas-SNP	.											.	CUL7	133	.	0			c.C495G						PASS	.						91	78	83					6																	43020188		2203	4300	6503	SO:0001583	missense	9820	exon2			CTTCACGTCGGTT	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.339C>G	chr6.hg19:g.43020188G>C	ENSP00000265348:p.Asp113Glu	74.0	0.0	.		51.0	19.0	.	NM_001168370	B4DYZ0|F5H0L1|Q5T654	Missense_Mutation	SNP	ENST00000265348.3	hg19	CCDS4881.1	.	.	.	.	.	.	.	.	.	.	A	15.26	2.780558	0.49891	.	.	ENSG00000044090	ENST00000265348;ENST00000535468	D;T	0.91180	-2.8;-0.03	5.51	-9.29	0.00653	.	0.176300	0.49916	D	0.000124	D	0.89791	0.6817	L	0.36672	1.1	0.09310	P	0.9999999999999996	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	D	0.88870	0.3332	9	0.87932	D	0	-20.9624	25.0489	0.99993	0.2693:0.0:0.7307:0.0	.	165;113	F5H0L1;Q14999	.;CUL7_HUMAN	E	113;165	ENSP00000265348:D113E;ENSP00000438788:D165E	ENSP00000265348:D113E	D	-	3	2	CUL7	43128166	0.000000	0.05858	0.045000	0.18777	0.499000	0.33736	-2.094000	0.01351	-2.277000	0.00677	-1.214000	0.01621	GAC	.	G|0.755;A|0.245	.	alt		0.612	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040575.1	NM_014780		C	43020188	G	C	43020188	3	2	9	1	0	0	0	0	1	0	0	0	4062	1136	40	4	4953	4	CUL7	6	43020188	Missense_Mutation	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10	1307730	43020188	128094879	37	662											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51523921	51523921	+	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	tgctccttactgttggcgaaTcaccaatttcaatgacaatc	11	13	6	11	1	2	1	2	1	0	0	4	2	3	1	2	1	2	2	2	1	5	3			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr6:51523921T>A	ENST00000371117.3	-	61	11278	c.11003A>T	c.(11002-11004)gAt>gTt	p.D3668V		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3668					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)					TGTTGGCGAATCACCAATTTC	0.428																																					p.D3668V		Atlas-SNP	.											.	PKHD1	927	.	0			c.A11003T						PASS	.						175	161	166					6																	51523921		2203	4300	6503	SO:0001583	missense	5314	exon61			GGCGAATCACCAA	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.11003A>T	chr6.hg19:g.51523921T>A	ENSP00000360158:p.Asp3668Val	21.0	0.0	.		69.0	25.0	.	NM_138694	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	T	19.58	3.854844	0.71719	.	.	ENSG00000170927	ENST00000371117	D	0.88896	-2.44	6.03	6.03	0.97812	.	0.148294	0.46758	D	0.000263	D	0.92541	0.7631	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	D	0.93498	0.6842	10	0.87932	D	0	.	15.7393	0.77876	0.0:0.0:0.0:1.0	.	3668	P08F94	PKHD1_HUMAN	V	3668	ENSP00000360158:D3668V	ENSP00000360158:D3668V	D	-	2	0	PKHD1	51631880	1.000000	0.71417	0.989000	0.46669	0.860000	0.49131	5.307000	0.65762	2.308000	0.77769	0.533000	0.62120	GAT	.	.	.	none		0.428	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51523921	T	A	51523921	3	1	9	1	0	0	0	0	1	0	0	0	11978	1435	50	5	1249	5	PKHD1	6	51523921	Missense_Mutation	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10	8503733	51523921	119591146	38	663											
COL19A1	1310	hgsc.bcm.edu	37	chr6	70850849	70850849	+	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	ctaccccttctccttagggaGagccttttacaaaaggagaa	12	10	8	11	0	1	2	0	0	1	2	2	4	1	2	4	2	3	0	4	2	6	5			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr6:70850849G>C	ENST00000322773.4	+	20	1552	c.1450G>C	c.(1450-1452)Gag>Cag	p.E484Q	COL19A1_ENST00000393344.1_Missense_Mutation_p.E106Q	NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	484	Collagen-like 4.|Triple-helical region 3 (COL3).				cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						TCCTTAGGGAGAGCCTTTTAC	0.383																																					p.E484Q		Atlas-SNP	.											.	COL19A1	232	.	0			c.G1450C						PASS	.						174	188	183					6																	70850849		2203	4300	6503	SO:0001583	missense	1310	exon20			TAGGGAGAGCCTT		CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"Collagens"	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.1450G>C	chr6.hg19:g.70850849G>C	ENSP00000316030:p.Glu484Gln	32.0	0.0	.		91.0	28.0	.	NM_001858	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Missense_Mutation	SNP	ENST00000322773.4	hg19	CCDS4970.1	.	.	.	.	.	.	.	.	.	.	G	12.40	1.925830	0.34002	.	.	ENSG00000082293	ENST00000322773;ENST00000393344	D;D	0.93906	-3.31;-3.31	4.27	4.27	0.50696	.	0.657664	0.14822	N	0.296417	D	0.92136	0.7507	L	0.52206	1.635	0.80722	D	1	D	0.56746	0.977	P	0.57057	0.812	D	0.88677	0.3199	10	0.16420	T	0.52	.	15.7248	0.77747	0.0:0.0:1.0:0.0	.	484	Q14993	COJA1_HUMAN	Q	484;106	ENSP00000316030:E484Q;ENSP00000377013:E106Q	ENSP00000316030:E484Q	E	+	1	0	COL19A1	70907570	1.000000	0.71417	0.987000	0.45799	0.383000	0.30230	3.488000	0.53229	2.649000	0.89929	0.650000	0.86243	GAG	.	.	.	none		0.383	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1			C	70850849	G	C	70850849	3	2	9	1	0	0	0	0	1	0	0	0	3678	943	33	4	1524	4	COL19A1	6	70850849	Missense_Mutation	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10	19326928	70850849	100264218	39	664											
EEF1A1	1915	hgsc.bcm.edu	37	chr6	74227637	74227637	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caccgcaactgtctgtctcaTatcacgaacagcaaagcgac	13	7	7	14	3	3	0	2	0	2	0	4	2	3	0	1	0	4	2	1	0	4	1			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr6:74227637T>C	ENST00000316292.9	-	7	2276	c.1285A>G	c.(1285-1287)Atg>Gtg	p.M429V	EEF1A1_ENST00000491404.1_Intron|EEF1A1_ENST00000331523.2_Missense_Mutation_p.M429V|EEF1A1_ENST00000309268.6_Missense_Mutation_p.M429V	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1	429					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation elongation factor activity (GO:0003746)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						GTCTGTCTCATATCACGAACA	0.403											OREG0003893	type=REGULATORY REGION|Gene=BC038897|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.M429V		Atlas-SNP	.											.	EEF1A1	56	.	0			c.A1285G						PASS	.						46	49	48					6																	74227637		2203	4300	6503	SO:0001583	missense	1915	exon8			GTCTCATATCACG	BC019669	CCDS4980.1	6q14.1	2010-06-30	2004-11-19		ENSG00000156508	ENSG00000156508			3189	protein-coding gene	gene with protein product		130590	"leukocyte receptor cluster (LRC) member 7"	EF1A, EEF1A, LENG7		8812466, 10941842	Standard	NM_001402		Approved	EE1A1	uc003phj.3	P68104	OTTHUMG00000015031	ENST00000316292.9:c.1285A>G	chr6.hg19:g.74227637T>C	ENSP00000339063:p.Met429Val	335.0	0.0	.	1151	339.0	134.0	.	NM_001402	P04719|P04720|Q6IQ15	Missense_Mutation	SNP	ENST00000316292.9	hg19	CCDS4980.1	.	.	.	.	.	.	.	.	.	.	T	12.31	1.898780	0.33535	.	.	ENSG00000156508	ENST00000316292;ENST00000309268;ENST00000331523;ENST00000391977	T;T;T	0.44482	0.92;0.92;0.92	4.81	4.81	0.61882	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal (2);Translation elongation factor EFTu/EF1A, C-terminal (2);	0.000000	0.85682	U	0.000000	T	0.55321	0.1913	H	0.99919	4.95	0.80722	D	1	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.06405	0.001;0.001;0.002	T	0.70208	-0.4935	10	0.87932	D	0	.	10.7978	0.46470	0.0:0.0775:0.0:0.9225	.	429;429;429	P68104;Q6IPS9;Q5VTE0	EF1A1_HUMAN;.;EF1A3_HUMAN	V	429;429;429;408	ENSP00000339063:M429V;ENSP00000339053:M429V;ENSP00000330054:M429V	ENSP00000339053:M429V	M	-	1	0	EEF1A1	74284358	1.000000	0.71417	0.999000	0.59377	0.952000	0.60782	5.900000	0.69853	1.929000	0.55896	0.454000	0.30748	ATG	.	.	.	weak		0.403	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041210.2	NM_001402		C	74227637	T	C	74227637	3	2	9	1	0	0	0	0	1	0	0	0	4925	1406	49	3	107	3	EEF1A1	6	74227637	Missense_Mutation	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10	3376788	74227637	96887430	40	665											
SGK1	6446	hgsc.bcm.edu	37	chr6	134494465	134494467	+	In_Frame_Del	DEL	CTT	CTT	-																															aactttgactgcatagaacaCttcttctgccttgtgtcttg																										TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr6:134494465_134494467delCTT	ENST00000237305.7	-	5	450_452	c.362_364delAAG	c.(361-366)gaagtg>gtg	p.E121del	SGK1_ENST00000367857.5_In_Frame_Del_p.E111del|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000413996.3_In_Frame_Del_p.E135del|SGK1_ENST00000475719.2_In_Frame_Del_p.E121del|SGK1_ENST00000528577.1_In_Frame_Del_p.E149del|SGK1_ENST00000367858.5_In_Frame_Del_p.E216del	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	121	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)		GCATAGAACACTTCTTCTGCCTT	0.389																																					p.216_217del		Atlas-Indel,Pindel	.											.	SGK1	387	.	0			c.648_650del						PASS	.		,,,	0,4264		0,0,2132					,,,	-3.9	0			112	7,8247		3,1,4123	no	coding,coding,coding,coding	SGK1	NM_005627.3,NM_001143678.1,NM_001143677.1,NM_001143676.1	,,,	3,1,6255	A1A1,A1R,RR		0.0848,0.0,0.0559	,,,	,,,		7,12511				SO:0001651	inframe_deletion	6446	exon7			.	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.362_364delAAG	chr6.hg19:g.134494468_134494470delCTT	ENSP00000237305:p.Glu121del	141.0	0.0	0		119.0	38.0	0.319328	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	In_Frame_Del	DEL	ENST00000237305.7	hg19	CCDS5170.1																																																																																			.	.	.	none		0.389	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			-	134494467	CTT	-	134494465	7	5	9	1	0	1	0	1	0	0	0	0	14220	565	20	0	963	0	SGK1	6	134494465	In_Frame_Del	DEL	CTT	TCGA-2Z-A9JD-01A-11D-A42J-10	60266828	134494465	36620602	41	666											
LATS1	9113	hgsc.bcm.edu	37	chr6	150004253	150004253	+	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	taattgttttttacgatgtaGacgctgctgatgagatttga	10	17	10	4	2	0	4	0	3	0	2	0	6	0	4	0	0	2	4	0	0	3	7			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr6:150004253G>C	ENST00000543571.1	-	4	2519	c.1972C>G	c.(1972-1974)Cta>Gta	p.L658V	LATS1_ENST00000392273.3_Missense_Mutation_p.L658V|LATS1_ENST00000542747.1_5'UTR|LATS1_ENST00000253339.5_Missense_Mutation_p.L658V	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1											central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		TTACGATGTAGACGCTGCTGA	0.323																																					p.L658V		Atlas-SNP	.											.	LATS1	241	.	0			c.C1972G						PASS	.						71	64	66					6																	150004253		2203	4300	6503	SO:0001583	missense	9113	exon4			GATGTAGACGCTG	AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"LATS (large tumor suppressor, Drosophila) homolog 1", "LATS, large tumor suppressor, homolog 1 (Drosophila)"			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000543571.1:c.1972C>G	chr6.hg19:g.150004253G>C	ENSP00000437550:p.Leu658Val	58.0	0.0	.		80.0	24.0	.	NM_001270519		Missense_Mutation	SNP	ENST00000543571.1	hg19	CCDS34551.1	.	.	.	.	.	.	.	.	.	.	G	3.874	-0.027265	0.07589	.	.	ENSG00000131023	ENST00000543571;ENST00000253339;ENST00000392273	T;T;T	0.41758	0.99;0.99;0.99	5.63	5.63	0.86233	.	0.000000	0.45606	D	0.000360	T	0.21718	0.0523	N	0.16790	0.44	0.37536	D	0.91811	B;P;B	0.47191	0.059;0.891;0.012	B;P;B	0.47299	0.008;0.543;0.008	T	0.02220	-1.1193	9	.	.	.	.	13.7301	0.62783	0.08:0.0:0.92:0.0	.	510;658;658	Q59FN4;O95835-2;O95835	.;.;LATS1_HUMAN	V	658	ENSP00000437550:L658V;ENSP00000253339:L658V;ENSP00000444678:L658V	.	L	-	1	2	LATS1	150045946	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.749000	0.55150	2.814000	0.96858	0.655000	0.94253	CTA	.	.	.	none		0.323	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043923.4	NM_004690		C	150004253	G	C	150004253	3	2	9	1	0	0	0	0	1	0	0	0	8653	933	33	4	1440	4	LATS1	6	150004253	Missense_Mutation	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10	15509788	150004253	21110814	42	667											
KIAA1324L	222223	hgsc.bcm.edu	37	chr7	86568242	86568242	+	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	ttgttgctgaatgtgcctggCttgcaaggaaaacattctga	10	13	11	7	0	1	2	0	2	1	0	1	3	1	3	1	2	4	4	1	2	4	4			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr7:86568242C>A	ENST00000450689.2	-	7	1067	c.882G>T	c.(880-882)aaG>aaT	p.K294N	KIAA1324L_ENST00000416314.1_Missense_Mutation_p.K127N|KIAA1324L_ENST00000297222.6_Missense_Mutation_p.K54N|KIAA1324L_ENST00000444627.1_Missense_Mutation_p.K294N	NM_001142749.2	NP_001136221.1	A8MWY0	K132L_HUMAN	KIAA1324-like	294						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(14)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44	Esophageal squamous(14;0.0058)					ATGTGCCTGGCTTGCAAGGAA	0.463																																					p.K294N		Atlas-SNP	.											.	KIAA1324L	225	.	0			c.G882T						PASS	.						131	122	125					7																	86568242		2203	4300	6503	SO:0001583	missense	222223	exon7			GCCTGGCTTGCAA	AK055902	CCDS34677.1, CCDS47632.1, CCDS34677.2	7q21.12	2008-09-18			ENSG00000164659	ENSG00000164659			21945	protein-coding gene	gene with protein product	"EIG121-like"	614048					Standard	NM_001142749		Approved	FLJ31340, EIG121L	uc011kha.2	A8MWY0	OTTHUMG00000153995	ENST00000450689.2:c.882G>T	chr7.hg19:g.86568242C>A	ENSP00000413445:p.Lys294Asn	28.0	0.0	.		78.0	40.0	.	NM_001142749	A4D1C9|B4DJV3|Q17RI6|Q96DP2	Missense_Mutation	SNP	ENST00000450689.2	hg19	CCDS47632.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.96|17.96	3.515588|3.515588	0.64634|0.64634	.|.	.|.	ENSG00000164659|ENSG00000164659	ENST00000423294|ENST00000450689;ENST00000297222;ENST00000444627;ENST00000416314	.|T;T;T;T	.|0.49432	.|0.99;0.78;0.99;0.78	5.47|5.47	1.68|1.68	0.24146|0.24146	.|Growth factor, receptor (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.60521|0.60521	0.2275|0.2275	M|M	0.66939|0.66939	2.045|2.045	0.54753|0.54753	D|D	0.999985|0.999985	.|D;D;D	.|0.69078	.|0.997;0.958;0.958	.|D;P;P	.|0.69654	.|0.965;0.663;0.663	T|T	0.59257|0.59257	-0.7488|-0.7488	5|10	.|0.62326	.|D	.|0.03	.|.	9.0638|9.0638	0.36451|0.36451	0.0:0.7011:0.0:0.2989|0.0:0.7011:0.0:0.2989	.|.	.|294;54;127	.|A8MWY0;A8MWY0-2;B4DJV3	.|K132L_HUMAN;.;.	S|N	255|294;54;294;127	.|ENSP00000413445:K294N;ENSP00000297222:K54N;ENSP00000397377:K294N;ENSP00000402390:K127N	.|ENSP00000297222:K54N	A|K	-|-	1|3	0|2	KIAA1324L|KIAA1324L	86406178|86406178	0.998000|0.998000	0.40836|0.40836	1.000000|1.000000	0.80357|0.80357	0.898000|0.898000	0.52572|0.52572	0.565000|0.565000	0.23578|0.23578	0.287000|0.287000	0.22375|0.22375	-0.251000|-0.251000	0.11542|0.11542	GCC|AAG	.	.	.	none		0.463	KIAA1324L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333372.3	NM_152748		A	86568242	C	A	86568242	3	1	9	1	0	0	0	0	1	0	0	0	8231	796	28	4	2271	4	KIAA1324L	7	86568242	Missense_Mutation	SNP	C	TCGA-2Z-A9JD-01A-11D-A42J-10		86568242	72570421	43	668											
PON1	5444	hgsc.bcm.edu	37	chr7	94931604	94931604	+	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	caaaggtctcctgtctcaggAtccacagatatgttatccac	11	11	7	12	0	2	1	1	0	2	1	6	2	4	2	3	2	0	1	3	2	3	2			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr7:94931604A>T	ENST00000222381.3	-	8	1053	c.822T>A	c.(820-822)gaT>gaA	p.D274E	PON1_ENST00000542556.1_Missense_Mutation_p.D274E	NM_000446.5	NP_000437.3	P27169	PON1_HUMAN	paraoxonase 1	274					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)	CTGTCTCAGGATCCACAGATA	0.378																																					p.D274E	GBM(119;715 1622 17358 22490 33240)	Atlas-SNP	.											.	PON1	55	.	0			c.T822A						PASS	.						80	79	80					7																	94931604		2203	4300	6503	SO:0001583	missense	5444	exon8			CTCAGGATCCACA	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.822T>A	chr7.hg19:g.94931604A>T	ENSP00000222381:p.Asp274Glu	45.0	0.0	.		86.0	15.0	.	NM_000446	B2RA40|Q16052|Q6B0J6|Q9UCB1	Missense_Mutation	SNP	ENST00000222381.3	hg19	CCDS5638.1	.	.	.	.	.	.	.	.	.	.	A	16.48	3.135537	0.56828	.	.	ENSG00000005421	ENST00000222381;ENST00000542556	T;T	0.58797	0.31;0.31	4.67	-0.246	0.13022	Six-bladed beta-propeller, TolB-like (1);	0.044644	0.85682	D	0.000000	T	0.67767	0.2928	M	0.92367	3.3	0.53005	D	0.999967	D;D	0.57899	0.981;0.968	P;B	0.47941	0.562;0.359	T	0.74937	-0.3494	10	0.87932	D	0	-32.2036	11.0367	0.47804	0.5075:0.0:0.4925:0.0	.	274;274	F5H4W9;P27169	.;PON1_HUMAN	E	274	ENSP00000222381:D274E;ENSP00000444854:D274E	ENSP00000222381:D274E	D	-	3	2	PON1	94769540	0.658000	0.27402	0.985000	0.45067	0.630000	0.37929	-0.167000	0.09940	-0.036000	0.13669	-0.256000	0.11100	GAT	.	.	.	none		0.378	PON1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000332865.2	NM_000446		T	94931604	A	T	94931604	3	4	9	1	0	0	0	0	1	0	0	0	12255	330	12	5	253	5	PON1	7	94931604	Missense_Mutation	SNP	A	TCGA-2Z-A9JD-01A-11D-A42J-10	8363362	94931604	64207059	44	669											
TMEM139	135932	hgsc.bcm.edu	37	chr7	142983809	142983809	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgctcctgatctgcagagcTtggcggcagtccccacatta	7	10	10	14	1	1	2	0	1	1	1	3	2	3	2	3	2	3	4	3	2	1	2			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr7:142983809T>C	ENST00000359333.3	+	3	1051	c.538T>C	c.(538-540)Ttg>Ctg	p.L180L	TMEM139_ENST00000409541.1_Silent_p.L180L|AC073342.12_ENST00000446192.1_RNA|TMEM139_ENST00000409102.1_Silent_p.L180L|TMEM139_ENST00000471161.1_3'UTR|AC073342.12_ENST00000427392.1_RNA|TMEM139_ENST00000410004.1_Silent_p.L180L|CASP2_ENST00000392925.2_5'Flank|CASP2_ENST00000310447.5_5'Flank|TMEM139_ENST00000409244.1_Silent_p.L180L	NM_001242775.2|NM_001282876.1|NM_001282877.1	NP_001229704.1|NP_001269805.1|NP_001269806.1	Q8IV31	TM139_HUMAN	transmembrane protein 139	180						integral component of membrane (GO:0016021)				endometrium(1)|lung(4)|ovary(1)|prostate(1)	7	Melanoma(164;0.059)					TCTGCAGAGCTTGGCGGCAGT	0.562																																					p.L180L		Atlas-SNP	.											.	TMEM139	18	.	0			c.T538C						PASS	.						110	99	103					7																	142983809		2203	4300	6503	SO:0001819	synonymous_variant	135932	exon4			CAGAGCTTGGCGG	AK075067	CCDS5878.1	7q34	2006-03-17			ENSG00000178826	ENSG00000178826			22058	protein-coding gene	gene with protein product							Standard	NM_153345		Approved	FLJ90586	uc003wck.4	Q8IV31	OTTHUMG00000152652	ENST00000359333.3:c.538T>C	chr7.hg19:g.142983809T>C		102.0	0.0	.		128.0	39.0	.	NM_001242773	B2RCL5|D3DXD4|Q6ZME2|Q8NC22|Q96AU8	Silent	SNP	ENST00000359333.3	hg19	CCDS5878.1																																																																																			.	.	.	none		0.562	TMEM139-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327145.1	NM_153345		C	142983809	T	C	142983809	2	2	9	1	0	0	0	0	0	0	0	1	16066	1606	56	3		3	TMEM139	7	142983809	Silent	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10	48052205	142983809	16154854	45	670											
CLCN1	1180	hgsc.bcm.edu	37	chr7	143047464	143047464	+	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	ctttcctcctctggctgacaGattgaggcctgggagcagga	7	10	13	11	0	1	3	0	2	1	1	3	5	3	5	3	4	1	2	3	4	0	2			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr7:143047464G>T	ENST00000343257.2	+	21	2490		c.e21-1			NM_000083.2	NP_000074	P35523	CLCN1_HUMAN	chloride channel, voltage-sensitive 1						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)					CTGGCTGACAGATTGAGGCCT	0.557																																					.		Atlas-SNP	.											.	CLCN1	141	.	0			c.2404-1G>T						PASS	.						66	58	61					7																	143047464		2203	4300	6503	SO:0001630	splice_region_variant	1180	exon21			CTGACAGATTGAG	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.2404-1G>T	chr7.hg19:g.143047464G>T		59.0	0.0	.		77.0	46.0	.	NM_000083	A4D2H5|Q2M202	Splice_Site	SNP	ENST00000343257.2	hg19	CCDS5881.1	.	.	.	.	.	.	.	.	.	.	G	17.76	3.469487	0.63625	.	.	ENSG00000188037	ENST00000343257	.	.	.	4.4	4.4	0.53042	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.1768	0.86844	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CLCN1	142757586	1.000000	0.71417	1.000000	0.80357	0.730000	0.41778	8.823000	0.92018	2.302000	0.77476	0.462000	0.41574	.	.	.	.	none		0.557	CLCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327420.1	NM_000083	Intron	T	143047464	G	T	143047464	5	4	9	1	0	0	0	0	0	0	1	0	3464	956	33	4	2485	4	CLCN1	7	143047464	Splice_Site	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10	63655	143047464	16091199	46	671											
MTUS1	57509	hgsc.bcm.edu	37	chr8	17613134	17613134	+	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	tcaccagtaactacagcaggGtcagtttcataatcaaccac	14	9	6	12	0	4	0	4	0	0	0	4	0	4	0	2	1	4	3	2	1	4	4			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr8:17613134G>C	ENST00000262102.6	-	2	407	c.183C>G	c.(181-183)gaC>gaG	p.D61E	MTUS1_ENST00000381862.3_Missense_Mutation_p.D61E|MTUS1_ENST00000519263.1_Missense_Mutation_p.D61E|MTUS1_ENST00000381869.3_Missense_Mutation_p.D61E	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	61					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)		CTACAGCAGGGTCAGTTTCAT	0.413																																					p.D61E		Atlas-SNP	.											.	MTUS1	144	.	0			c.C183G						PASS	.						159	148	152					8																	17613134		1882	4117	5999	SO:0001583	missense	57509	exon2			AGCAGGGTCAGTT	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.183C>G	chr8.hg19:g.17613134G>C	ENSP00000262102:p.Asp61Glu	100.0	0.0	.		105.0	13.0	.	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	hg19	CCDS43717.1	.	.	.	.	.	.	.	.	.	.	g	13.81	2.347152	0.41599	.	.	ENSG00000129422	ENST00000381869;ENST00000262102;ENST00000519263;ENST00000381862	T;T;T;T	0.21361	2.99;2.99;2.99;2.01	3.82	2.92	0.33932	.	1.076460	0.07367	N	0.885099	T	0.13200	0.0320	N	0.24115	0.695	0.09310	N	1	P;B;B	0.36535	0.557;0.341;0.341	B;B;B	0.30495	0.116;0.059;0.059	T	0.21724	-1.0237	10	0.72032	D	0.01	0.0574	5.5626	0.17152	0.2502:0.0:0.7498:0.0	.	61;61;61	Q9ULD2-5;Q9ULD2-2;Q9ULD2	.;.;MTUS1_HUMAN	E	61	ENSP00000371293:D61E;ENSP00000262102:D61E;ENSP00000430167:D61E;ENSP00000371286:D61E	ENSP00000262102:D61E	D	-	3	2	MTUS1	17657414	0.000000	0.05858	0.131000	0.22000	0.459000	0.32528	0.483000	0.22292	1.149000	0.42402	0.558000	0.71614	GAC	.	.	.	none		0.413	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		C	17613134	G	C	17613134	3	2	9	1	0	0	0	0	1	0	0	0	9972	1252	44	4	4004	4	MTUS1	8	17613134	Missense_Mutation	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10		17613134	128750888	47	672											
C8orf80	389643	hgsc.bcm.edu	37	chr8	27931921	27931923	+	In_Frame_Del	DEL	CTG	CTG	-																															gccaaaaacatccttcgtttCtgccattccttgttacgtga																										TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr8:27931921_27931923delCTG	ENST00000413272.2	-	2	147_149	c.5_7delCAG	c.(4-9)gcagaa>gaa	p.A2del	NUGGC_ENST00000341513.6_In_Frame_Del_p.A2del	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	2					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)										TCCTTCGTTTCTGCCATTCCTTG	0.438																																					p.2_3del		Atlas-Indel,Pindel	.											.	.	.	.	0			c.6_8del						PASS	.																																			SO:0001651	inframe_deletion	389643	exon2			.	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.5_7delCAG	chr8.hg19:g.27931921_27931923delCTG	ENSP00000408697:p.Ala2del	32.0	0.0	0		59.0	12.0	0.20339	NM_001010906	Q6ZP73	In_Frame_Del	DEL	ENST00000413272.2	hg19	CCDS47833.1																																																																																			.	.	.	none		0.438	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906		-	27931923	CTG	-	27931921	7	5	9	1	0	1	0	1	0	0	0	0	2441	922	32	0	2455	0	C8orf80	8	27931921	In_Frame_Del	DEL	CTG	TCGA-2Z-A9JD-01A-11D-A42J-10	10318787	27931921	118432101	48	673											
SNAI2	6591	hgsc.bcm.edu	37	chr8	49831524	49831524	+	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	tgcaaatgctctgttgcagtGagggcaagaaaaaggcttct	12	10	12	7	0	2	2	0	1	2	1	2	2	2	2	0	2	3	6	0	2	4	2			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr8:49831524G>T	ENST00000396822.1	-	4	1006	c.649C>A	c.(649-651)Cac>Aac	p.H217N	SNAI2_ENST00000020945.1_Missense_Mutation_p.H217N			O43623	SNAI2_HUMAN	snail family zinc finger 2	217					canonical Wnt signaling pathway (GO:0060070)|cartilage morphogenesis (GO:0060536)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to ionizing radiation (GO:0071479)|desmosome disassembly (GO:0035921)|embryo development (GO:0009790)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|epithelium development (GO:0060429)|negative regulation of anoikis (GO:2000811)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell-cell adhesion by negative regulation of transcription from RNA polymerase II promoter (GO:1900387)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of stem cell proliferation (GO:2000647)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|negative regulation of vitamin D receptor signaling pathway (GO:0070563)|neural crest cell development (GO:0014032)|Notch signaling pathway (GO:0007219)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone acetylation (GO:0035066)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of chemokine production (GO:0032642)|regulation of osteoblast differentiation (GO:0045667)|regulation of tight junction assembly (GO:2000810)|sensory perception of sound (GO:0007605)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|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 distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)	18		all_cancers(86;0.0368)|all_epithelial(80;0.000624)|Lung NSC(129;0.0019)|all_lung(136;0.00502)				CTGTTGCAGTGAGGGCAAGAA	0.423																																					p.H217N		Atlas-SNP	.											.	SNAI2	53	.	0			c.C649A						PASS	.						80	80	80					8																	49831524		2203	4300	6503	SO:0001583	missense	6591	exon3			TGCAGTGAGGGCA	U97060	CCDS6146.1	8q11.21	2013-05-23	2013-05-23	2002-02-28	ENSG00000019549	ENSG00000019549		"Snail homologs", "Zinc fingers, C2H2-type"	11094	protein-coding gene	gene with protein product		602150	"slug homolog, zinc finger protein (chicken)", "snail homolog 2 (Drosophila)"	SLUG		9337409, 9721220	Standard	NM_003068		Approved	SLUGH1, SNAIL2	uc003xqp.3	O43623	OTTHUMG00000149912	ENST00000396822.1:c.649C>A	chr8.hg19:g.49831524G>T	ENSP00000380034:p.His217Asn	33.0	0.0	.		38.0	10.0	.	NM_003068	B2R6P6|Q53FC1	Missense_Mutation	SNP	ENST00000396822.1	hg19	CCDS6146.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.443898	0.83993	.	.	ENSG00000019549	ENST00000020945;ENST00000396822	T;T	0.07327	3.2;3.2	5.22	5.22	0.72569	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	0.13200	0.0320	L	0.45051	1.395	0.80722	D	1	P	0.37370	0.592	B	0.41135	0.348	T	0.01814	-1.1268	10	0.72032	D	0.01	-12.9153	18.7761	0.91912	0.0:0.0:1.0:0.0	.	217	O43623	SNAI2_HUMAN	N	217	ENSP00000020945:H217N;ENSP00000380034:H217N	ENSP00000020945:H217N	H	-	1	0	SNAI2	49994077	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.476000	0.97823	2.430000	0.82344	0.650000	0.86243	CAC	.	.	.	none		0.423	SNAI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313873.2	NM_003068		T	49831524	G	T	49831524	3	4	9	1	0	0	0	0	1	0	0	0	14840	1290	45	4	161	4	SNAI2	8	49831524	Missense_Mutation	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10	21899603	49831524	96532498	49	674											
CRH	1392	hgsc.bcm.edu	37	chr8	67089639	67089639	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaccggcccgcggctcaggAgcgccctgcatggcgggcag	5	3	18	15	5	1	0	1	0	0	0	1	2	1	2	3	6	2	3	3	6	0	0			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr8:67089639A>G	ENST00000276571.3	-	2	520	c.74T>C	c.(73-75)cTc>cCc	p.L25P		NM_000756.2	NP_000747.1	P06850	CRF_HUMAN	corticotropin releasing hormone	25					adrenal gland development (GO:0030325)|associative learning (GO:0008306)|cellular response to cocaine (GO:0071314)|cellular response to dexamethasone stimulus (GO:0071549)|diterpenoid metabolic process (GO:0016101)|feeding behavior (GO:0007631)|female pregnancy (GO:0007565)|ferulate metabolic process (GO:0033494)|glucocorticoid biosynthetic process (GO:0006704)|hormone-mediated apoptotic signaling pathway (GO:0008628)|hypothalamus development (GO:0021854)|inflammatory response (GO:0006954)|ion homeostasis (GO:0050801)|learning or memory (GO:0007611)|locomotory exploration behavior (GO:0035641)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|lung development (GO:0030324)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell death (GO:0060548)|negative regulation of circadian sleep/wake cycle, REM sleep (GO:0042322)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of gene expression (GO:0010629)|negative regulation of glucagon secretion (GO:0070093)|negative regulation of luteinizing hormone secretion (GO:0033685)|negative regulation of norepinephrine secretion (GO:0010700)|parturition (GO:0007567)|positive regulation of behavioral fear response (GO:2000987)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of circadian sleep/wake cycle, wakefulness (GO:0010841)|positive regulation of corticosterone secretion (GO:2000854)|positive regulation of corticotropin secretion (GO:0051461)|positive regulation of cortisol secretion (GO:0051464)|positive regulation of digestive system process (GO:0060456)|positive regulation of gene expression (GO:0010628)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of protein phosphorylation (GO:0001934)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of serotonin secretion (GO:0014062)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to ether (GO:0045472)|response to immobilization stress (GO:0035902)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|perikaryon (GO:0043204)|varicosity (GO:0043196)	hormone activity (GO:0005179)|neuropeptide hormone activity (GO:0005184)|receptor binding (GO:0005102)			breast(1)|endometrium(1)|lung(2)|urinary_tract(1)	5		all_cancers(86;2.58e-06)|all_epithelial(80;6.27e-09)|all_lung(136;0.000414)|Lung NSC(129;0.0011)	Epithelial(68;0.0136)|all cancers(69;0.0507)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)		Corticotropin(DB01285)	GCGGCTCAGGAGCGCCCTGCA	0.726											OREG0018805	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L25P		Atlas-SNP	.											.	CRH	8	.	0			c.T74C						PASS	.						2	2	2					8																	67089639		1380	3141	4521	SO:0001583	missense	1392	exon2			CTCAGGAGCGCCC		CCDS6188.1	8q13	2013-02-25				ENSG00000147571		"Endogenous ligands"	2355	protein-coding gene	gene with protein product	"corticotropin-releasing factor", "corticoliberin"	122560					Standard	NM_000756		Approved	CRF	uc003xvy.2	P06850		ENST00000276571.3:c.74T>C	chr8.hg19:g.67089639A>G	ENSP00000276571:p.Leu25Pro	100.0	0.0	.	1096	50.0	19.0	.	NM_000756	B3KQS4	Missense_Mutation	SNP	ENST00000276571.3	hg19	CCDS6188.1	.	.	.	.	.	.	.	.	.	.	A	10.74	1.434760	0.25813	.	.	ENSG00000147571	ENST00000276571	.	.	.	5.59	4.43	0.53597	.	0.209947	0.40908	D	0.000995	T	0.65668	0.2713	M	0.67953	2.075	0.58432	D	0.999999	D	0.53885	0.963	P	0.54401	0.751	T	0.67722	-0.5597	9	0.87932	D	0	.	9.8159	0.40851	0.8272:0.1728:0.0:0.0	.	25	P06850	CRF_HUMAN	P	25	.	ENSP00000276571:L25P	L	-	2	0	CRH	67252193	1.000000	0.71417	0.880000	0.34516	0.177000	0.22998	3.898000	0.56281	0.937000	0.37394	-0.418000	0.06021	CTC	.	.	.	none		0.726	CRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378926.1	NM_000756		G	67089639	A	G	67089639	3	3	9	1	0	0	0	0	1	0	0	0	3871	304	11	3	520	3	CRH	8	67089639	Missense_Mutation	SNP	A	TCGA-2Z-A9JD-01A-11D-A42J-10	17258115	67089639	79274383	50	675											
ESRP1	54845	hgsc.bcm.edu	37	chr8	95653652	95653652	+	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	agttgatcctgctgttctggAaagtcgtggatctggccaac	8	12	12	9	1	2	1	0	1	2	0	4	3	3	3	2	3	2	3	2	3	2	2	rs548563810		TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr8:95653652A>T	ENST00000433389.2	+	1	296	c.106A>T	c.(106-108)Aaa>Taa	p.K36*	ESRP1_ENST00000423620.2_Nonsense_Mutation_p.K36*|RP11-22C11.2_ENST00000562760.1_RNA|ESRP1_ENST00000454170.2_Nonsense_Mutation_p.K36*|ESRP1_ENST00000358397.5_Nonsense_Mutation_p.K36*	NM_001034915.2|NM_017697.3	NP_001030087.2|NP_060167.2	Q6NXG1	ESRP1_HUMAN	epithelial splicing regulatory protein 1	36					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						GCTGTTCTGGAAAGTCGTGGA	0.537																																					p.K36X		Atlas-SNP	.											.	ESRP1	148	.	0			c.A106T						PASS	.						92	93	93					8																	95653652		1921	4129	6050	SO:0001587	stop_gained	54845	exon1			TTCTGGAAAGTCG	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.106A>T	chr8.hg19:g.95653652A>T	ENSP00000405738:p.Lys36*	88.0	0.0	.		57.0	28.0	.	NM_001122827	A6NHA8|A8MPX1|E9PB47|Q2M2B0|Q499G3|Q6PJ86|Q9NXL8	Nonsense_Mutation	SNP	ENST00000433389.2	hg19	CCDS47897.1	.	.	.	.	.	.	.	.	.	.	A	38	7.048454	0.98029	.	.	ENSG00000104413	ENST00000423620;ENST00000433389;ENST00000358397;ENST00000454170	.	.	.	4.95	2.37	0.29283	.	0.269234	0.36444	N	0.002599	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.5406	7.2173	0.25967	0.7766:0.145:0.0784:0.0	.	.	.	.	X	36	.	ENSP00000351168:K36X	K	+	1	0	ESRP1	95722828	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	2.272000	0.43373	0.710000	0.31997	0.533000	0.62120	AAA	.	.	.	none		0.537	ESRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379326.1	NM_017697		T	95653652	A	T	95653652	4	4	9	1	0	0	0	0	0	1	0	0	5260	247	9	5	108	5	ESRP1	8	95653652	Nonsense_Mutation	SNP	A	TCGA-2Z-A9JD-01A-11D-A42J-10	28564013	95653652	50710370	51	676											
OXR1	55074	hgsc.bcm.edu	37	chr8	107670240	107670240	+	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	ctacctgacgacgttcaccgAgaagagtgggcgccttctgc	8	8	12	13	4	2	3	1	1	1	2	2	5	2	3	3	1	2	1	3	1	2	3			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr8:107670240A>G	ENST00000442977.2	+	3	322				OXR1_ENST00000531443.1_Intron|OXR1_ENST00000312046.6_Missense_Mutation_p.E9G|OXR1_ENST00000452423.2_Intron|OXR1_ENST00000445937.1_Intron|OXR1_ENST00000497705.1_Intron|OXR1_ENST00000517566.2_Intron|RP11-649G15.2_ENST00000518591.1_RNA	NM_001198532.1	NP_001185461.1	Q8N573	OXR1_HUMAN	oxidation resistance 1						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)			ACGTTCACCGAGAAGAGTGGG	0.701																																					p.E9G		Atlas-SNP	.											.	OXR1	190	.	0			c.A26G						PASS	.						6	10	9					8																	107670240		662	1568	2230	SO:0001627	intron_variant	55074	exon1			TCACCGAGAAGAG	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.224-21198A>G	chr8.hg19:g.107670240A>G		413.0	0.0	.		217.0	89.0	.	NM_181354	A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7	Missense_Mutation	SNP	ENST00000442977.2	hg19	CCDS56548.1	.	.	.	.	.	.	.	.	.	.	A	0.018	-1.470777	0.01044	.	.	ENSG00000164830	ENST00000312046	T	0.10005	2.92	4.0	1.95	0.26073	.	.	.	.	.	T	0.03695	0.0105	.	.	.	0.24866	N	0.992312	B	0.02656	0.0	B	0.01281	0.0	T	0.43442	-0.9391	8	0.02654	T	1	.	6.6439	0.22925	0.1057:0.1789:0.7154:0.0	.	9	Q8N573-2	.	G	9	ENSP00000311026:E9G	ENSP00000311026:E9G	E	+	2	0	OXR1	107739416	0.992000	0.36948	0.738000	0.30950	0.020000	0.10135	2.097000	0.41748	0.877000	0.35895	-0.313000	0.08912	GAG	.	.	.	none		0.701	OXR1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_181354		G	107670240	A	G	107670240	1	3	9	0	1	0	0	0	0	0	0	0	11341	304	11	3		3	OXR1	8	107670240	Intron	SNP	A	TCGA-2Z-A9JD-01A-11D-A42J-10	12016588	107670240	38693782	52	677											
EBAG9	9166	hgsc.bcm.edu	37	chr8	110567083	110567083	+	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	ctggaacctgactattttaaGgacatgacaccaactattag	14	11	7	9	0	0	2	0	2	0	0	0	4	0	4	2	2	2	0	2	2	6	5	rs370306388		TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr8:110567083G>T	ENST00000337573.5	+	4	588	c.288G>T	c.(286-288)aaG>aaT	p.K96N	EBAG9_ENST00000529502.1_3'UTR|EBAG9_ENST00000531677.1_Missense_Mutation_p.K96N|EBAG9_ENST00000395785.2_Missense_Mutation_p.K96N	NM_001278938.1|NM_004215.3	NP_001265867.1|NP_004206.1	O00559	RCAS1_HUMAN	estrogen receptor binding site associated, antigen, 9	96					regulation of cell growth (GO:0001558)	focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	peptidase activator activity involved in apoptotic process (GO:0016505)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(2)	10			OV - Ovarian serous cystadenocarcinoma(57;1.39e-14)			ACTATTTTAAGGACATGACAC	0.363																																					p.K96N		Atlas-SNP	.											.	EBAG9	23	.	0			c.G288T						PASS	.						126	116	119					8																	110567083		2203	4300	6503	SO:0001583	missense	9166	exon4			TTTTAAGGACATG	AB007619	CCDS6313.1	8q23	2013-03-07			ENSG00000147654	ENSG00000147654			3123	protein-coding gene	gene with protein product		605772					Standard	NM_004215		Approved	EB9, RCAS1	uc003ynf.3	O00559	OTTHUMG00000165346	ENST00000337573.5:c.288G>T	chr8.hg19:g.110567083G>T	ENSP00000337675:p.Lys96Asn	36.0	0.0	.		114.0	5.0	.	NM_004215	A8K3N6|Q5Y8C7|Q6IB20|Q9BS76	Missense_Mutation	SNP	ENST00000337573.5	hg19	CCDS6313.1	.	.	.	.	.	.	.	.	.	.	G	17.81	3.480071	0.63849	.	.	ENSG00000147654	ENST00000395785;ENST00000337573;ENST00000530629;ENST00000531677	.	.	.	5.53	2.09	0.27110	.	0.000000	0.85682	D	0.000000	T	0.64538	0.2607	L	0.52266	1.64	0.58432	D	0.999994	D	0.89917	1.0	D	0.83275	0.996	T	0.62932	-0.6749	9	0.62326	D	0.03	9.6559	5.8258	0.18552	0.261:0.0:0.5919:0.1471	.	96	O00559	RCAS1_HUMAN	N	96	.	ENSP00000337675:K96N	K	+	3	2	EBAG9	110636259	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.315000	0.33608	0.739000	0.32628	-0.181000	0.13052	AAG	.	.	.	alt		0.363	EBAG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383536.1	NM_004215		T	110567083	G	T	110567083	3	4	9	1	0	0	0	0	1	0	0	0	4881	991	35	4	298	4	EBAG9	8	110567083	Missense_Mutation	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10	2896843	110567083	35796939	53	678											
ZFAT	57623	hgsc.bcm.edu	37	chr8	135521962	135521962	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcaatgatctgctgcaggAtgttcacggccgtggggtcc	6	10	14	11	2	3	1	2	1	1	0	4	2	4	2	2	4	2	4	2	4	1	1			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr8:135521962A>G	ENST00000377838.3	-	15	3566	c.3392T>C	c.(3391-3393)aTc>aCc	p.I1131T	ZFAT_ENST00000429442.2_Missense_Mutation_p.I1119T|ZFAT_ENST00000520214.1_Missense_Mutation_p.I1119T|ZFAT_ENST00000517307.1_5'Flank|ZFAT_ENST00000523399.1_Missense_Mutation_p.I1069T|ZFAT_ENST00000520727.1_Missense_Mutation_p.I1119T|ZFAT_ENST00000520356.1_Intron	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	1131					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)			CTGCTGCAGGATGTTCACGGC	0.587																																					p.I1131T		Atlas-SNP	.											.	ZFAT	265	.	0			c.T3392C						PASS	.						118	122	121					8																	135521962		2085	4214	6299	SO:0001583	missense	57623	exon15			TGCAGGATGTTCA	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.3392T>C	chr8.hg19:g.135521962A>G	ENSP00000367069:p.Ile1131Thr	53.0	0.0	.		40.0	15.0	.	NM_020863	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Missense_Mutation	SNP	ENST00000377838.3	hg19	CCDS47924.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.471547	0.84533	.	.	ENSG00000066827	ENST00000520727;ENST00000429442;ENST00000377838;ENST00000520214;ENST00000521673;ENST00000318135;ENST00000523399	T;T;T;T;T	0.16457	2.84;2.34;2.75;2.84;2.78	5.81	5.81	0.92471	.	0.112528	0.64402	D	0.000017	T	0.29126	0.0724	L	0.29908	0.895	0.51767	D	0.999935	D;D;D	0.76494	0.993;0.999;0.999	D;D;D	0.78314	0.977;0.991;0.991	T	0.02821	-1.1106	10	0.24483	T	0.36	-26.8601	15.3472	0.74346	1.0:0.0:0.0:0.0	.	250;1069;1131	B7Z741;E9PER3;Q9P243	.;.;ZFAT_HUMAN	T	1119;1119;1131;1119;51;1018;1069	ENSP00000427831:I1119T;ENSP00000394501:I1119T;ENSP00000367069:I1131T;ENSP00000428483:I1119T;ENSP00000429091:I1069T	ENSP00000326997:I1018T	I	-	2	0	ZFAT	135591144	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	6.820000	0.75267	2.221000	0.72209	0.455000	0.32223	ATC	.	.	.	none		0.587	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939		G	135521962	A	G	135521962	3	3	9	1	0	0	0	0	1	0	0	0	17644	333	12	3	347	3	ZFAT	8	135521962	Missense_Mutation	SNP	A	TCGA-2Z-A9JD-01A-11D-A42J-10	24954879	135521962	10842060	54	679											
PTK2	5747	hgsc.bcm.edu	37	chr8	141685559	141685559	+	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	ccaattcttttcttctttacCtggtttacccacaggctgat	7	17	5	12	0	3	1	0	1	3	0	3	1	3	1	3	2	2	2	3	2	3	8			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr8:141685559C>T	ENST00000522684.1	-	28	2831	c.2602G>A	c.(2602-2604)Gat>Aat	p.D868N	PTK2_ENST00000395218.2_Missense_Mutation_p.G868S|PTK2_ENST00000430260.2_Splice_Site_p.D178N|PTK2_ENST00000538769.1_Splice_Site_p.D536N|PTK2_ENST00000521059.1_Splice_Site_p.D868N|PTK2_ENST00000340930.3_Missense_Mutation_p.G868S|PTK2_ENST00000519465.1_Splice_Site_p.D496N|PTK2_ENST00000519419.1_Splice_Site_p.D912N|PTK2_ENST00000517887.1_Splice_Site_p.D912N|PTK2_ENST00000535192.1_Splice_Site_p.D822N	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	868	Interaction with TGFB1I1.|Pro-rich.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell motility (GO:0048870)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|central nervous system neuron axonogenesis (GO:0021955)|embryo development (GO:0009790)|endothelial cell migration (GO:0043542)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|establishment of nucleus localization (GO:0040023)|extracellular matrix organization (GO:0030198)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|growth hormone receptor signaling pathway (GO:0060396)|heart morphogenesis (GO:0003007)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of organ growth (GO:0046621)|negative regulation of synapse assembly (GO:0051964)|netrin-activated signaling pathway (GO:0038007)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|placenta development (GO:0001890)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|regulation of endothelial cell migration (GO:0010594)|regulation of focal adhesion assembly (GO:0051893)|regulation of osteoblast differentiation (GO:0045667)|regulation of Rho GTPase activity (GO:0032319)|signal complex assembly (GO:0007172)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	apical plasma membrane (GO:0016324)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|stress fiber (GO:0001725)	actin binding (GO:0003779)|ATP binding (GO:0005524)|JUN kinase binding (GO:0008432)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(6)|lung(23)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	48	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			TCTTCTTTACCTGGTTTACCC	0.383																																					p.D890N		Atlas-SNP	.											.	PTK2	311	.	0			c.G2668A						PASS	.						169	146	153					8																	141685559		2203	4300	6503	SO:0001630	splice_region_variant	5747	exon28			CTTTACCTGGTTT	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.2602+1G>A	chr8.hg19:g.141685559C>T		85.0	0.0	.		86.0	32.0	.	NM_005607	B4E2N6|F5H4S4|Q14291|Q9UD85	Missense_Mutation	SNP	ENST00000522684.1	hg19	CCDS6381.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	33|33|33	5.217585|5.217585|5.217585	0.95104|0.95104|0.95104	.|.|.	.|.|.	ENSG00000169398|ENSG00000169398|ENSG00000169398	ENST00000522684;ENST00000535192;ENST00000519465;ENST00000517887;ENST00000521059;ENST00000395214;ENST00000354438;ENST00000395221;ENST00000523539;ENST00000538769;ENST00000519419;ENST00000430260;ENST00000521986|ENST00000395218;ENST00000340930|ENST00000519654	T;T;T;T;T;T;T;T;T;T|T;T|.	0.75821|0.74209|.	-0.93;-0.97;-0.93;-0.93;-0.93;-0.91;-0.91;-0.93;1.48;-0.92|-0.82;-0.81|.	5.73|5.73|5.73	5.73|5.73|5.73	0.89815|0.89815|0.89815	.|.|.	0.045906|.|.	0.85682|.|.	D|.|.	0.000000|.|.	T|T|T	0.66416|0.66416|0.66416	0.2787|0.2787|0.2787	L|L|L	0.36672|0.36672|0.36672	1.1|1.1|1.1	0.80722|0.80722|0.80722	D|D|D	1|1|1	B;P;P;P;B;B;B;B;B|D|.	0.38788|0.89917|.	0.0;0.647;0.561;0.611;0.418;0.0;0.0;0.112;0.177|1.0|.	B;B;B;B;B;B;B;B;B|D|.	0.41440|0.78314|.	0.003;0.357;0.169;0.159;0.157;0.003;0.003;0.048;0.159|0.991|.	T|T|T	0.60296|0.60296|0.60296	-0.7291|-0.7291|-0.7291	10|9|5	0.41790|0.08381|.	T|T|.	0.15|0.77|.	.|.|.	19.8869|19.8869|19.8869	0.96915|0.96915|0.96915	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	563;788;868;890;822;820;695;536;496|868|.	B4DH13;Q59GN8;Q05397;Q658W2;Q8IYN9;Q59GM6;Q05397-2;Q8N9D7;E9PEI4|B4E2N6|.	.;.;FAK1_HUMAN;.;.;.;.;.;.|.|.	N|S|K	868;822;496;912;868;820;789;563;540;536;912;178;566|868|832	ENSP00000429911:D868N;ENSP00000438009:D822N;ENSP00000429170:D496N;ENSP00000429082:D912N;ENSP00000429474:D868N;ENSP00000428492:D540N;ENSP00000445742:D536N;ENSP00000429129:D912N;ENSP00000403416:D178N;ENSP00000430603:D566N|ENSP00000378644:G868S;ENSP00000341189:G868S|.	ENSP00000346424:D789N|ENSP00000341189:G868S|.	D|G|R	-|-|-	1|1|2	0|0|0	PTK2|PTK2|PTK2	141754741|141754741|141754741	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.993000|0.993000|0.993000	0.82548|0.82548|0.82548	7.332000|7.332000|7.332000	0.79203|0.79203|0.79203	2.693000|2.693000|2.693000	0.91896|0.91896|0.91896	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GAT|GGT|AGA	.	.	.	none		0.383	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607	Missense_Mutation	T	141685559	C	T	141685559	5	4	9	1	0	0	0	0	0	0	1	0	12773	695	24	2	576	2	PTK2	8	141685559	Splice_Site	SNP	C	TCGA-2Z-A9JD-01A-11D-A42J-10	6163597	141685559	4678463	55	680											
GPT	2875	hgsc.bcm.edu	37	chr8	145732381	145732381	+	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	agttcaccctcgagtactccTgagcaccccagctggggcca	8	7	10	16	1	1	1	1	1	0	0	3	2	2	1	5	2	3	4	5	2	1	2			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr8:145732381T>C	ENST00000528431.1	+	12	1646	c.1489T>C	c.(1489-1491)Tga>Cga	p.*497R	MFSD3_ENST00000301327.4_5'Flank|GPT_ENST00000394955.2_Nonstop_Mutation_p.*497R			P24298	ALAT1_HUMAN	glutamic-pyruvate transaminase (alanine aminotransferase)	0					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-alanine catabolic process (GO:0042853)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	L-alanine:2-oxoglutarate aminotransferase activity (GO:0004021)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(1)|lung(2)|ovary(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)		L-Alanine(DB00160)|Phenelzine(DB00780)	CGAGTACTCCTGAGCACCCCA	0.617																																					p.X497R		Atlas-SNP	.											.	GPT	31	.	0			c.T1489C						PASS	.						44	45	45					8																	145732381		2201	4300	6501	SO:0001578	stop_lost	2875	exon11			TACTCCTGAGCAC		CCDS6430.1	8q24.3	2013-09-19			ENSG00000167701	ENSG00000167701	2.6.1.2		4552	protein-coding gene	gene with protein product		138200					Standard	NM_005309		Approved	ALT1, GPT1	uc003zdh.4	P24298	OTTHUMG00000165176	ENST00000528431.1:c.1489T>C	chr8.hg19:g.145732381T>C	ENSP00000433586:p.*497Argext*?	135.0	0.0	.		86.0	32.0	.	NM_005309	B0YJ18|D3DWM7|P78398|Q93076	Missense_Mutation	SNP	ENST00000528431.1	hg19	CCDS6430.1	.	.	.	.	.	.	.	.	.	.	T	12.04	1.819054	0.32145	.	.	ENSG00000167701	ENST00000528431;ENST00000394955	.	.	.	4.68	4.68	0.58851	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.0974	0.53763	0.0:0.0:0.0:1.0	.	.	.	.	R	497	.	.	X	+	1	0	GPT	145703189	1.000000	0.71417	0.992000	0.48379	0.454000	0.32378	2.085000	0.41634	1.736000	0.51660	0.459000	0.35465	TGA	.	.	.	none		0.617	GPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382471.1			C	145732381	T	C	145732381	4	2	9	1	0	0	0	0	0	0	0	0	6744	1593	55	3	1531	3	GPT	8	145732381	Nonstop_Mutation	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10	4046822	145732381	631641	56	681											
SMARCA2	6595	hgsc.bcm.edu	37	chr9	2115822	2115822	+	Splice_Site	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	catattgaccccccaaacagGatctgcaggcccaagaccga	13	5	8	15	1	1	2	0	1	1	1	1	4	1	3	5	2	2	1	5	2	3	2			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr9:2115822G>C	ENST00000382203.1	+	25	3666	c.3457G>C	c.(3457-3459)Gat>Cat	p.D1153H	SMARCA2_ENST00000357248.2_Splice_Site_p.D1153H|SMARCA2_ENST00000349721.2_Splice_Site_p.D1153H|SMARCA2_ENST00000382194.1_Splice_Site_p.D1153H			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	1153	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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)		CCCCAAACAGGATCTGCAGGC	0.562																																					p.D1153H		Atlas-SNP	.											.	SMARCA2	313	.	0			c.G3457C						PASS	.						24	23	23					9																	2115822		2203	4300	6503	SO:0001630	splice_region_variant	6595	exon25			AAACAGGATCTGC	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.3457-1G>C	chr9.hg19:g.2115822G>C		130.0	0.0	.		236.0	84.0	.	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Missense_Mutation	SNP	ENST00000382203.1	hg19	CCDS34977.1	.	.	.	.	.	.	.	.	.	.	G	19.66	3.868893	0.72065	.	.	ENSG00000080503	ENST00000349721;ENST00000357248;ENST00000382203;ENST00000382194	T;T;T;T	0.75477	-0.94;-0.94;-0.94;-0.94	5.67	5.67	0.87782	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.91838	0.7417	H	0.97611	4.04	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;0.999	D	0.94201	0.7450	9	.	.	.	-30.3516	19.7699	0.96359	0.0:0.0:1.0:0.0	.	754;1153;1153	B4DK35;P51531-2;P51531	.;.;SMCA2_HUMAN	H	1153	ENSP00000265773:D1153H;ENSP00000349788:D1153H;ENSP00000371638:D1153H;ENSP00000371629:D1153H	.	D	+	1	0	SMARCA2	2105822	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	9.869000	0.99810	2.680000	0.91292	0.563000	0.77884	GAT	.	.	.	none		0.562	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070	Missense_Mutation	C	2115822	G	C	2115822	5	2	9	1	0	0	0	0	0	0	1	0	14782	1188	41	4	3551	4	SMARCA2	9	2115822	Splice_Site	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10		2115822	139097609	57	682											
TLN1	7094	hgsc.bcm.edu	37	chr9	35706215	35706215	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgggttaccaccagcctccTtggcagtgtatagcaactgc	8	11	10	12	0	0	0	0	0	0	0	1	0	1	0	4	2	5	4	4	2	4	5			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr9:35706215T>C	ENST00000314888.9	-	40	5692	c.5339A>G	c.(5338-5340)aAg>aGg	p.K1780R	TLN1_ENST00000540444.1_Missense_Mutation_p.K1764R|TLN1_ENST00000464379.1_Intron	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1780	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)			ACCAGCCTCCTTGGCAGTGTA	0.567																																					p.K1780R		Atlas-SNP	.											.	TLN1	185	.	0			c.A5339G						PASS	.						141	142	141					9																	35706215		2203	4300	6503	SO:0001583	missense	7094	exon40			GCCTCCTTGGCAG	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.5339A>G	chr9.hg19:g.35706215T>C	ENSP00000316029:p.Lys1780Arg	29.0	0.0	.		32.0	7.0	.	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	hg19	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	T	19.31	3.802610	0.70682	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.17213	2.29;2.29	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.30696	0.0773	L	0.56769	1.78	0.80722	D	1	D	0.60575	0.988	P	0.54401	0.751	T	0.01684	-1.1296	10	0.41790	T	0.15	-22.297	15.0599	0.71944	0.0:0.0:0.0:1.0	.	1780	Q9Y490	TLN1_HUMAN	R	1780;1764	ENSP00000316029:K1780R;ENSP00000442981:K1764R	ENSP00000316029:K1780R	K	-	2	0	TLN1	35696215	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.036000	0.88901	2.033000	0.60031	0.454000	0.30748	AAG	.	.	.	none		0.567	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		C	35706215	T	C	35706215	3	2	9	1	0	0	0	0	1	0	0	0	15959	1609	56	3	2358	3	TLN1	9	35706215	Missense_Mutation	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10	33590393	35706215	105507216	58	683											
TJP2	9414	hgsc.bcm.edu	37	chr9	71855017	71855017	+	Missense_Mutation	SNP	T	T	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	aaaagttctcgaaagttattTgatcaagccaacaagcttaa	17	11	6	7	1	2	1	1	1	1	0	3	2	2	1	1	0	3	3	1	0	8	4			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr9:71855017T>G	ENST00000377245.4	+	17	2728	c.2520T>G	c.(2518-2520)ttT>ttG	p.F840L	TJP2_ENST00000535702.1_Missense_Mutation_p.F844L|TJP2_ENST00000453658.2_Missense_Mutation_p.F817L|TJP2_ENST00000265384.7_Missense_Mutation_p.F840L|TJP2_ENST00000348208.4_Missense_Mutation_p.F840L|TJP2_ENST00000539225.1_Missense_Mutation_p.F871L	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	840	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						GAAAGTTATTTGATCAAGCCA	0.353																																					p.F871L		Atlas-SNP	.											.	TJP2	120	.	0			c.T2613G						PASS	.						67	66	66					9																	71855017		2203	4300	6503	SO:0001583	missense	9414	exon17			GTTATTTGATCAA	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.2520T>G	chr9.hg19:g.71855017T>G	ENSP00000366453:p.Phe840Leu	50.0	0.0	.		74.0	14.0	.	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Missense_Mutation	SNP	ENST00000377245.4	hg19	CCDS6627.1	.	.	.	.	.	.	.	.	.	.	T	16.92	3.254434	0.59212	.	.	ENSG00000119139	ENST00000453658;ENST00000377245;ENST00000348208;ENST00000265384;ENST00000535702;ENST00000539225	T;T;T;T;T;T	0.16324	2.35;2.35;2.35;2.35;2.35;2.35	5.93	0.821	0.18799	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (2);	0.263501	0.38837	N	0.001554	T	0.13030	0.0316	L	0.29908	0.895	0.36065	D	0.841715	B;B;B;B;B	0.32188	0.073;0.026;0.073;0.066;0.359	B;B;B;B;B	0.36092	0.053;0.138;0.053;0.217;0.157	T	0.16305	-1.0407	10	0.45353	T	0.12	.	10.2592	0.43416	0.0:0.2837:0.0:0.7163	.	871;844;840;840;840	F5H301;F5H886;Q9UDY2-2;Q9UDY2;Q9UDY2-5	.;.;.;ZO2_HUMAN;.	L	817;840;840;840;844;871	ENSP00000392178:F817L;ENSP00000366453:F840L;ENSP00000345893:F840L;ENSP00000265384:F840L;ENSP00000442090:F844L;ENSP00000438262:F871L	ENSP00000265384:F840L	F	+	3	2	TJP2	71044837	0.944000	0.32072	0.950000	0.38849	0.987000	0.75469	0.031000	0.13710	-0.088000	0.12506	0.533000	0.62120	TTT	.	.	.	none		0.353	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629		G	71855017	T	G	71855017	3	3	9	1	0	0	0	0	1	0	0	0	15942	1809	63	5	2743	5	TJP2	9	71855017	Missense_Mutation	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10	36148802	71855017	69358414	59	684											
C9orf5	23731	hgsc.bcm.edu	37	chr9	111849612	111849612	+	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	aagtgaatgacaagctttttGagtatccagactaaaaaaag	18	10	8	5	0	0	4	0	3	0	1	1	4	1	4	1	0	1	2	1	0	8	4			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr9:111849612G>A	ENST00000374586.3	-	6	1192	c.1161C>T	c.(1159-1161)ctC>ctT	p.L387L		NM_032012.3	NP_114401.2	Q9H330	TM245_HUMAN	transmembrane protein 245	387						integral component of membrane (GO:0016021)											CAAGCTTTTTGAGTATCCAGA	0.358																																					p.L387L		Atlas-SNP	.											.	.	.	.	0			c.C1161T						PASS	.						72	65	67					9																	111849612		1808	4078	5886	SO:0001819	synonymous_variant	23731	exon6			CTTTTTGAGTATC	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.1161C>T	chr9.hg19:g.111849612G>A		35.0	0.0	.		64.0	23.0	.	NM_032012	B4DSW7|Q5JTQ5|Q5SS43|Q6ZME3|Q8NDJ5|Q96CG6	Silent	SNP	ENST00000374586.3	hg19	CCDS43858.1																																																																																			.	.	.	none		0.358	TMEM245-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053587.2	NM_032012		A	111849612	G	A	111849612	2	1	9	1	0	0	0	0	0	0	0	1	2488	1277	45	2		2	C9orf5	9	111849612	Silent	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10	39994595	111849612	29363819	60	685											
DENND1A	57706	hgsc.bcm.edu	37	chr9	126143930	126143930	+	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	ggcctcagggccagcccctgCttggtctcagcagccctggc	4	7	13	17	0	2	0	2	0	1	0	3	0	2	0	5	4	4	2	5	4	0	1			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr9:126143930C>T	ENST00000373624.2	-	22	3012	c.2811G>A	c.(2809-2811)aaG>aaA	p.K937K	DENND1A_ENST00000542603.1_Silent_p.K722K|DENND1A_ENST00000394219.3_Silent_p.K948K|DENND1A_ENST00000473039.1_5'UTR	NM_020946.1	NP_065997.1	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A	937	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						CCAGCCCCTGCTTGGTCTCAG	0.692																																					p.K937K		Atlas-SNP	.											.	DENND1A	112	.	0			c.G2811A						PASS	.						10	13	12					9																	126143930		2174	4283	6457	SO:0001819	synonymous_variant	57706	exon22			CCCCTGCTTGGTC	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.2811G>A	chr9.hg19:g.126143930C>T		176.0	0.0	.		91.0	24.0	.	NM_020946	A8MZA3|B1AM80|B7Z3C8|B7Z669|D3PFD3|Q05C88|Q5VWF0|Q6PJZ5|Q8IVD6|Q9H796	Silent	SNP	ENST00000373624.2	hg19	CCDS35133.1																																																																																			.	.	.	none		0.692	DENND1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053997.1	NM_024820		T	126143930	C	T	126143930	2	4	9	1	0	0	0	0	0	0	0	1	4428	796	28	2		2	DENND1A	9	126143930	Silent	SNP	C	TCGA-2Z-A9JD-01A-11D-A42J-10	14294318	126143930	15069501	61	686											
C9orf119	375757	hgsc.bcm.edu	37	chr9	131038966	131038966	+	Frame_Shift_Del	DEL	C	C	-																															tgtgggtccaatcagactttCccctcggattcctctctagg																								rs191475291	byFrequency	TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr9:131038966delC	ENST00000320188.5	+	2	358	c.358delC	c.(358-360)cccfs	p.P120fs	SWI5_ENST00000419867.2_Frame_Shift_Del_p.P55fs|GOLGA2_ENST00000490628.1_5'Flank|GOLGA2_ENST00000421699.2_5'Flank|SWI5_ENST00000608796.1_Frame_Shift_Del_p.P55fs|SWI5_ENST00000418976.1_Intron|SWI5_ENST00000495313.1_Intron|GOLGA2_ENST00000609374.1_5'Flank	NM_001040011.1	NP_001035100.1	Q1ZZU3	SWI5_HUMAN	SWI5 recombination repair homolog (yeast)	120					cellular response to ionizing radiation (GO:0071479)|double-strand break repair via homologous recombination (GO:0000724)	nucleus (GO:0005634)|Swi5-Sfr1 complex (GO:0032798)											ATCAGACTTTCCCCTCGGATT	0.602																																					p.F119fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.357delT						PASS	.						120	127	125					9																	131038966		1912	4128	6040	SO:0001589	frameshift_variant	375757	exon2			.	BC029911	CCDS43883.1	9q34.13	2011-07-29	2011-07-29	2011-07-29	ENSG00000175854	ENSG00000175854			31412	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 119"	C9orf119		21252223, 20976249	Standard	NM_001040011		Approved	bA395P17.9	uc004bup.3	Q1ZZU3	OTTHUMG00000020729	ENST00000320188.5:c.358delC	chr9.hg19:g.131038966delC	ENSP00000316609:p.Pro120fs	60.0	0.0	0		52.0	15.0	0.288462	NM_001040011	Q5SYX7|Q5SYX8|Q8N2W6	Frame_Shift_Del	DEL	ENST00000320188.5	hg19	CCDS43883.1																																																																																			.	.	.	none		0.602	SWI5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001040011		-	131038966	C	-	131038966	7	5	9	1	0	1	0	1	0	0	0	0	2454	855	30	0	364	0	C9orf119	9	131038966	Frame_Shift_Del	DEL	C	TCGA-2Z-A9JD-01A-11D-A42J-10	4895036	131038966	10174465	62	687											
ABL1	25	hgsc.bcm.edu	37	chr9	133748374	133748374	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctgctgtacatggccacTcagatctcgtcagccatgga	8	10	11	12	1	3	1	2	0	1	1	4	2	3	2	2	2	4	3	2	2	1	1			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr9:133748374T>C	ENST00000318560.5	+	6	1416	c.1035T>C	c.(1033-1035)acT>acC	p.T345T		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	345	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	ACATGGCCACTCAGATCTCGT	0.582			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"																																p.T364T		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.T1092C						PASS	.						72	58	63					9																	133748374		2203	4300	6503	SO:0001819	synonymous_variant	25	exon6			GGCCACTCAGATC	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.1035T>C	chr9.hg19:g.133748374T>C		71.0	0.0	.		105.0	34.0	.	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	hg19	CCDS35166.1																																																																																			.	.	.	none		0.582	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		C	133748374	T	C	133748374	2	2	9	1	0	0	0	0	0	0	0	1	92	1538	54	3		3	ABL1	9	133748374	Silent	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10	2709408	133748374	7465057	63	688											
KIAA0649	9858	hgsc.bcm.edu	37	chr9	138379517	138379517	+	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	agatgcagtgtggaggggggGcgtcgggagcgagagagaca	10	4	22	5	3	0	3	0	0	0	3	1	7	0	5	0	5	2	1	0	5	0	0			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr9:138379517G>C	ENST00000356818.2	+	4	3710	c.3161G>C	c.(3160-3162)gGc>gCc	p.G1054A	PPP1R26_ENST00000605660.1_Missense_Mutation_p.G1054A|PPP1R26_ENST00000605286.1_Missense_Mutation_p.G1054A|PPP1R26_ENST00000401470.3_Missense_Mutation_p.G1054A|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000604351.1_Missense_Mutation_p.G1054A	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	1054					negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										TGGAGGGGGGGCGTCGGGAGC	0.731																																					p.G1054A		Atlas-SNP	.											.	.	.	.	0			c.G3161C						PASS	.						3	4	3					9																	138379517		1868	3764	5632	SO:0001583	missense	9858	exon4			GGGGGGGCGTCGG	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.3161G>C	chr9.hg19:g.138379517G>C	ENSP00000349274:p.Gly1054Ala	101.0	0.0	.		49.0	18.0	.	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Missense_Mutation	SNP	ENST00000356818.2	hg19	CCDS6988.1	.	.	.	.	.	.	.	.	.	.	G	1.308	-0.602936	0.03744	.	.	ENSG00000196422	ENST00000356818	T	0.09538	2.97	4.83	-2.28	0.06826	.	0.939982	0.08989	N	0.864613	T	0.04861	0.0131	L	0.29908	0.895	0.09310	N	1	B	0.31459	0.324	B	0.31686	0.134	T	0.36841	-0.9731	10	0.02654	T	1	-13.12	0.8556	0.01182	0.2412:0.1264:0.3609:0.2714	.	1054	Q5T8A7	PPR26_HUMAN	A	1054	ENSP00000349274:G1054A	ENSP00000349274:G1054A	G	+	2	0	KIAA0649	137519338	0.153000	0.22777	0.000000	0.03702	0.003000	0.03518	0.409000	0.21082	-0.377000	0.07930	0.555000	0.69702	GGC	.	.	.	none		0.731	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811		C	138379517	G	C	138379517	3	2	9	1	0	0	0	0	1	0	0	0	8194	1203	42	4	3163	4	KIAA0649	9	138379517	Missense_Mutation	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10	4631143	138379517	2833914	64	689											
SEC16A	9919	hgsc.bcm.edu	37	chr9	139369535	139369535	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttcgataaggacacagaaaAgttaatgggctgagccagat	15	8	12	6	1	0	3	0	1	0	2	1	5	0	4	1	2	1	3	1	2	4	3			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr9:139369535A>G	ENST00000371706.3	-	1	2032	c.1999T>C	c.(1999-2001)Ttt>Ctt	p.F667L	SEC16A_ENST00000431893.2_Missense_Mutation_p.F667L|SEC16A_ENST00000313050.7_Missense_Mutation_p.F845L|SEC16A_ENST00000290037.6_Missense_Mutation_p.F667L			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	667					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)		GACACAGAAAAGTTAATGGGC	0.498																																					p.F845L		Atlas-SNP	.											.	SEC16A	249	.	0			c.T2533C						PASS	.						43	43	43					9																	139369535		1941	4138	6079	SO:0001583	missense	9919	exon3			CAGAAAAGTTAAT	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.1999T>C	chr9.hg19:g.139369535A>G	ENSP00000360771:p.Phe667Leu	101.0	0.0	.		57.0	18.0	.	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Missense_Mutation	SNP	ENST00000371706.3	hg19		.	.	.	.	.	.	.	.	.	.	A	13.94	2.387911	0.42308	.	.	ENSG00000148396	ENST00000313050;ENST00000371706;ENST00000290037;ENST00000431893	T;T;T;T	0.22539	1.95;1.96;1.95;1.96	5.64	-3.27	0.05048	.	0.400968	0.28042	N	0.016839	T	0.13372	0.0324	M	0.64997	1.995	0.09310	N	0.999999	B;B;B	0.14438	0.006;0.01;0.01	B;B;B	0.13407	0.004;0.009;0.009	T	0.20075	-1.0286	10	0.23891	T	0.37	-5.91	0.7546	0.00996	0.4548:0.1181:0.199:0.2281	.	845;667;667	F1T0I1;O15027-5;O15027-4	.;.;.	L	845;667;667;667	ENSP00000325827:F845L;ENSP00000360771:F667L;ENSP00000290037:F667L;ENSP00000387583:F667L	ENSP00000290037:F667L	F	-	1	0	SEC16A	138489356	0.012000	0.17670	0.000000	0.03702	0.039000	0.13416	0.012000	0.13287	-0.356000	0.08187	0.528000	0.53228	TTT	.	.	.	none		0.498	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459		G	139369535	A	G	139369535	3	3	9	1	0	0	0	0	1	0	0	0	13999	72	3	3	4660	3	SEC16A	9	139369535	Missense_Mutation	SNP	A	TCGA-2Z-A9JD-01A-11D-A42J-10	990018	139369535	1843896	65	690											
ATP5C1	509	hgsc.bcm.edu	37	chr10	7842038	7842038	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagcccatcttttcccttaaTaccgttgcaagtgctggtaa	10	13	7	11	1	1	0	0	0	1	0	2	0	2	0	3	1	4	4	3	1	5	6			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr10:7842038T>C	ENST00000356708.7	+	6	700	c.621T>C	c.(619-621)aaT>aaC	p.N207N	ATP5C1_ENST00000493053.1_3'UTR|ATP5C1_ENST00000541227.1_Silent_p.N160N|ATP5C1_ENST00000335698.4_Silent_p.N207N	NM_001001973.1	NP_001001973.1	P36542	ATPG_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1	207					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, catalytic core F(1) (GO:0000275)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)			breast(2)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	16						TTTCCCTTAATACCGTTGCAA	0.323																																					p.N207N	Melanoma(143;1012 1820 16249 30920 33158)	Atlas-SNP	.											.	ATP5C1	32	.	0			c.T621C						PASS	.						114	122	119					10																	7842038		2203	4300	6503	SO:0001819	synonymous_variant	509	exon6			CCTTAATACCGTT	D16561	CCDS7081.1, CCDS31142.1	10p14	2012-10-12			ENSG00000165629	ENSG00000165629		"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	833	protein-coding gene	gene with protein product		108729		ATP5CL1, ATP5C		8168843, 8227057	Standard	NM_005174		Approved		uc001iju.3	P36542	OTTHUMG00000017639	ENST00000356708.7:c.621T>C	chr10.hg19:g.7842038T>C		67.0	0.0	.		67.0	18.0	.	NM_001001973	A8KA31|Q5VYP3|Q6I9V2|Q96AS8	Silent	SNP	ENST00000356708.7	hg19	CCDS31142.1																																																																																			.	.	.	none		0.323	ATP5C1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046708.1	NM_005174		C	7842038	T	C	7842038	2	2	9	1	0	0	0	0	0	0	0	1	1149	1403	49	3		3	ATP5C1	10	7842038	Silent	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10		7842038	127692709	66	691											
ARID5B	84159	hgsc.bcm.edu	37	chr10	63851119	63851119	+	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	gcaccgtgaaggtggaccagCtgggcagtgacgacatccac	10	5	14	12	2	0	2	0	2	0	0	1	4	1	3	3	3	1	3	3	3	1	0			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr10:63851119C>T	ENST00000279873.7	+	10	2307	c.1897C>T	c.(1897-1899)Ctg>Ttg	p.L633L	ARID5B_ENST00000309334.5_Silent_p.L390L	NM_032199.2	NP_115575.1	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	633					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)					GGTGGACCAGCTGGGCAGTGA	0.552																																					p.L633L		Atlas-SNP	.											.	ARID5B	125	.	0			c.C1897T						PASS	.						65	58	60					10																	63851119		2203	4300	6503	SO:0001819	synonymous_variant	84159	exon10			GACCAGCTGGGCA	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.1897C>T	chr10.hg19:g.63851119C>T		53.0	0.0	.		140.0	53.0	.	NM_032199	B4DLB3|Q05DG6|Q32Q59|Q5VST4|Q6NZ42|Q7Z3M4|Q8N421|Q9H786	Silent	SNP	ENST00000279873.7	hg19	CCDS31208.1																																																																																			.	.	.	none		0.552	ARID5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048233.1	XM_084482		T	63851119	C	T	63851119	2	4	9	1	0	0	0	0	0	0	0	1	922	796	28	2		2	ARID5B	10	63851119	Silent	SNP	C	TCGA-2Z-A9JD-01A-11D-A42J-10	56009081	63851119	71683628	67	692											
LDB3	11155	hgsc.bcm.edu	37	chr10	88441289	88441290	+	Frame_Shift_Del	DEL	CC	CC	-																															caggcaccccggagctcaggCccacctttagccctgccttc																										TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr10:88441289_88441290delCC	ENST00000361373.4	+	4	439_440	c.418_419delCC	c.(418-420)cccfs	p.P140fs	LDB3_ENST00000372056.4_Frame_Shift_Del_p.P140fs|LDB3_ENST00000372066.3_Intron|LDB3_ENST00000310944.6_Frame_Shift_Del_p.P140fs|LDB3_ENST00000542786.1_Frame_Shift_Del_p.P140fs|LDB3_ENST00000458213.2_Intron|LDB3_ENST00000352360.5_Intron|LDB3_ENST00000429277.2_Frame_Shift_Del_p.P140fs|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						GGAGCTCAGGCCCACCTTTAGC	0.733																																					p.139_140del		Atlas-Indel,Pindel	.											LDB3_ENST00000429277,NS,carcinoma,0,3	LDB3	164	.	0			c.417_418del						PASS	.																																			SO:0001589	frameshift_variant	11155	exon4			.	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.418_419delCC	chr10.hg19:g.88441289_88441290delCC	ENSP00000355296:p.Pro140fs	176.0	0.0	0		79.0	27.0	0.341772	NM_001171611		Frame_Shift_Del	DEL	ENST00000361373.4	hg19	CCDS7377.1																																																																																			.	.	.	none		0.733	LDB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049160.2			-	88441290	CC	-	88441289	7	5	9	1	0	1	0	1	0	0	0	0	8704	739	26	0	432	0	LDB3	10	88441289	Frame_Shift_Del	DEL	CC	TCGA-2Z-A9JD-01A-11D-A42J-10	24590170	88441289	47093458	68	693											
PDZD8	118987	hgsc.bcm.edu	37	chr10	119044910	119044910	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctggccaacaggcctttcaTagtacaccaggactcggtca	10	9	9	13	1	3	0	2	0	1	0	4	1	3	1	3	4	2	1	3	4	3	3			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr10:119044910T>C	ENST00000334464.5	-	5	1573	c.1334A>G	c.(1333-1335)tAt>tGt	p.Y445C	PDZD8_ENST00000482496.1_5'UTR	NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	445	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)		AGGCCTTTCATAGTACACCAG	0.433																																					p.Y445C		Atlas-SNP	.											.	PDZD8	85	.	0			c.A1334G						PASS	.						62	61	61					10																	119044910		2203	4300	6503	SO:0001583	missense	118987	exon5			CTTTCATAGTACA	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.1334A>G	chr10.hg19:g.119044910T>C	ENSP00000334642:p.Tyr445Cys	62.0	0.0	.		82.0	34.0	.	NM_173791	Q86WE0|Q86WE5|Q9UFF1	Missense_Mutation	SNP	ENST00000334464.5	hg19	CCDS7600.1	.	.	.	.	.	.	.	.	.	.	T	19.19	3.779065	0.70107	.	.	ENSG00000165650	ENST00000334464	T	0.73575	-0.76	5.82	5.82	0.92795	PDZ/DHR/GLGF (3);	0.000000	0.85682	D	0.000000	D	0.86062	0.5843	M	0.74546	2.27	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	D	0.87636	0.2519	10	0.87932	D	0	-11.1467	16.1776	0.81862	0.0:0.0:0.0:1.0	.	445	Q8NEN9	PDZD8_HUMAN	C	445	ENSP00000334642:Y445C	ENSP00000334642:Y445C	Y	-	2	0	PDZD8	119034900	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.139000	0.71728	2.222000	0.72286	0.477000	0.44152	TAT	.	.	.	none		0.433	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791		C	119044910	T	C	119044910	3	2	9	1	0	0	0	0	1	0	0	0	11712	1406	49	3	2134	3	PDZD8	10	119044910	Missense_Mutation	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10	30603621	119044910	16489837	69	694											
SFXN4	119559	hgsc.bcm.edu	37	chr10	120919242	120919242	+	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	aaatgtctgcttgctcaccgTgggtgccatgaaaggcagga	10	9	13	9	1	2	1	1	1	1	0	2	2	2	2	2	3	3	3	2	3	2	1			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr10:120919242T>A	ENST00000355697.2	-	6	377	c.358A>T	c.(358-360)Acg>Tcg	p.T120S	SFXN4_ENST00000461438.1_5'UTR|SFXN4_ENST00000330036.6_Missense_Mutation_p.T111S	NM_213649.1	NP_998814.1	Q6P4A7	SFXN4_HUMAN	sideroflexin 4	120					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	11		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0261)		TTGCTCACCGTGGGTGCCATG	0.602																																					p.T120S		Atlas-SNP	.											.	SFXN4	24	.	0			c.A358T						PASS	.						116	89	98					10																	120919242		2203	4300	6503	SO:0001583	missense	119559	exon6			TCACCGTGGGTGC		CCDS7610.1	10q26.11	2006-03-13			ENSG00000183605	ENSG00000183605		"Sideroflexins"	16088	protein-coding gene	gene with protein product		615564				14756423	Standard	NM_213649		Approved		uc001leb.3	Q6P4A7	OTTHUMG00000019147	ENST00000355697.2:c.358A>T	chr10.hg19:g.120919242T>A	ENSP00000347924:p.Thr120Ser	61.0	0.0	.		89.0	50.0	.	NM_213649	Q6WSU4|Q86TD9	Missense_Mutation	SNP	ENST00000355697.2	hg19	CCDS7610.1	.	.	.	.	.	.	.	.	.	.	T	0.212	-1.035964	0.02029	.	.	ENSG00000183605	ENST00000355697;ENST00000330036;ENST00000369131;ENST00000419372	T;T	0.30714	1.52;1.52	3.76	-5.8	0.02347	.	1.090950	0.07109	N	0.841756	T	0.19765	0.0475	L	0.36672	1.1	0.09310	N	1	B	0.21225	0.053	B	0.27076	0.076	T	0.40924	-0.9537	10	0.87932	D	0	-9.8843	2.055	0.03579	0.5105:0.0894:0.134:0.266	.	120	Q6P4A7	SFXN4_HUMAN	S	120;111;4;4	ENSP00000347924:T120S;ENSP00000333200:T111S	ENSP00000333200:T111S	T	-	1	0	SFXN4	120909232	0.530000	0.26330	0.224000	0.23877	0.001000	0.01503	-0.849000	0.04322	-1.211000	0.02624	-2.509000	0.00188	ACG	.	.	.	none		0.602	SFXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050642.3	XM_058406		A	120919242	T	A	120919242	3	1	9	1	0	0	0	0	1	0	0	0	14210	1696	59	5	691	5	SFXN4	10	120919242	Missense_Mutation	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10	1874332	120919242	14615505	70	695											
ACADSB	36	hgsc.bcm.edu	37	chr10	124793964	124793964	+	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	gaagctctactcaatataacAaataatggaatacactttgc	17	11	5	8	0	2	0	1	0	1	0	2	2	2	1	0	1	5	1	0	1	9	6			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr10:124793964A>C	ENST00000358776.4	+	2	149	c.135A>C	c.(133-135)acA>acC	p.T45T	ACADSB_ENST00000368869.4_5'UTR|ACADSB_ENST00000496730.2_3'UTR	NM_001609.3	NP_001600.1	P45954	ACDSB_HUMAN	acyl-CoA dehydrogenase, short/branched chain	45					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)	TCAATATAACAAATAATGGAA	0.373																																					p.T45T		Atlas-SNP	.											.	ACADSB	45	.	0			c.A135C						PASS	.						99	98	98					10																	124793964		2203	4300	6503	SO:0001819	synonymous_variant	36	exon2			TATAACAAATAAT	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.135A>C	chr10.hg19:g.124793964A>C		29.0	0.0	.		26.0	10.0	.	NM_001609	B4DQ51|Q5SQN6|Q96CX7	Silent	SNP	ENST00000358776.4	hg19	CCDS7634.1	.	.	.	.	.	.	.	.	.	.	A	3.942	-0.014024	0.07681	.	.	ENSG00000196177	ENST00000411816	.	.	.	4.92	-2.44	0.06502	.	.	.	.	.	T	0.29223	0.0727	.	.	.	0.20196	N	0.999925	.	.	.	.	.	.	T	0.32613	-0.9900	4	.	.	.	.	7.4231	0.27083	0.349:0.5011:0.1499:0.0	.	.	.	.	P	51	.	.	Q	+	2	0	ACADSB	124783954	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	0.032000	0.13732	-0.640000	0.05495	0.482000	0.46254	CAA	.	.	.	none		0.373	ACADSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050843.1	NM_001609		C	124793964	A	C	124793964	2	2	9	1	0	0	0	0	0	0	0	1	115	117	5	5		5	ACADSB	10	124793964	Silent	SNP	A	TCGA-2Z-A9JD-01A-11D-A42J-10	3874722	124793964	10740783	71	696											
RRP8	23378	hgsc.bcm.edu	37	chr11	6624661	6624661	+	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	tgcgaggaggccgcaggcggAggtcgtgagattacgggccc	7	5	19	10	5	0	1	0	1	0	1	1	5	0	3	2	6	2	1	2	6	1	1			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr11:6624661A>T	ENST00000254605.6	-	1	189	c.72T>A	c.(70-72)ccT>ccA	p.P24P	ILK_ENST00000396751.2_5'Flank|RRP8_ENST00000534343.1_Silent_p.P24P|RP11-732A19.8_ENST00000527191.1_RNA|ILK_ENST00000537806.1_5'Flank|ILK_ENST00000420936.2_5'Flank|ILK_ENST00000299421.4_5'Flank|ILK_ENST00000528995.1_5'Flank	NM_015324.3	NP_056139.1	O43159	RRP8_HUMAN	ribosomal RNA processing 8, methyltransferase, homolog (yeast)	24					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						CCGCAGGCGGAGGTCGTGAGA	0.662																																					p.P24P		Atlas-SNP	.											.	RRP8	40	.	0			c.T72A						PASS	.						18	19	19					11																	6624661		2195	4290	6485	SO:0001819	synonymous_variant	23378	exon1			AGGCGGAGGTCGT	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.72T>A	chr11.hg19:g.6624661A>T		154.0	0.0	.		76.0	27.0	.	NM_015324	Q7KZ78|Q9BVM6	Silent	SNP	ENST00000254605.6	hg19	CCDS31411.1																																																																																			.	.	.	none		0.662	RRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384505.1	NM_015324		T	6624661	A	T	6624661	2	4	9	1	0	0	0	0	0	0	0	1	13703	291	11	5		5	RRP8	11	6624661	Silent	SNP	A	TCGA-2Z-A9JD-01A-11D-A42J-10		6624661	128381855	72	697											
GLYAT	10249	hgsc.bcm.edu	37	chr11	58482795	58482795	+	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	acatggaaacttacctgctcCtgagggcagacaaccactgt	12	8	9	12	0	0	2	0	1	0	1	1	3	1	3	3	2	4	2	3	2	3	1			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr11:58482795C>A	ENST00000344743.3	-	3	324	c.183G>T	c.(181-183)caG>caT	p.Q61H	GLYAT_ENST00000278400.3_Missense_Mutation_p.Q61H|GLYAT_ENST00000529732.1_Missense_Mutation_p.Q61H	NM_201648.2	NP_964011.2	Q6IB77	GLYAT_HUMAN	glycine-N-acyltransferase	61					acyl-CoA metabolic process (GO:0006637)|glycine metabolic process (GO:0006544)|monocarboxylic acid metabolic process (GO:0032787)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)|glycine N-benzoyltransferase activity (GO:0047962)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|autonomic_ganglia(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16		Breast(21;0.0044)|all_epithelial(135;0.0157)			Glycine(DB00145)	TTACCTGCTCCTGAGGGCAGA	0.403																																					p.Q61H		Atlas-SNP	.											.	GLYAT	53	.	0			c.G183T						PASS	.						95	83	87					11																	58482795		2201	4295	6496	SO:0001583	missense	10249	exon3			CTGCTCCTGAGGG	AF023466	CCDS7970.1, CCDS7971.1	11q12.1	2008-03-11					2.3.1.13		13734	protein-coding gene	gene with protein product		607424					Standard	NM_201648		Approved	GAT, ACGNAT	uc001nnb.3	Q6IB77		ENST00000344743.3:c.183G>T	chr11.hg19:g.58482795C>A	ENSP00000340200:p.Gln61His	5.0	0.0	.		29.0	8.0	.	NM_005838	O14833|Q96QK7	Missense_Mutation	SNP	ENST00000344743.3	hg19	CCDS7970.1	.	.	.	.	.	.	.	.	.	.	C	14.01	2.407287	0.42715	.	.	ENSG00000149124	ENST00000344743;ENST00000529732;ENST00000278400	T;T;T	0.19105	2.17;2.17;2.17	5.45	-0.0385	0.13880	Acyl-CoA N-acyltransferase (1);Glycine N-acyltransferase, N-terminal (1);	0.572184	0.17708	N	0.164699	T	0.28665	0.0710	M	0.92077	3.27	0.28386	N	0.919319	B;B	0.26041	0.043;0.14	B;B	0.28709	0.033;0.093	T	0.35226	-0.9797	10	0.72032	D	0.01	-7.5927	3.2923	0.06953	0.1842:0.3996:0.0:0.4162	.	61;61	Q6IB77-2;Q6IB77	.;GLYAT_HUMAN	H	61	ENSP00000340200:Q61H;ENSP00000431688:Q61H;ENSP00000278400:Q61H	ENSP00000278400:Q61H	Q	-	3	2	GLYAT	58239371	0.343000	0.24818	0.996000	0.52242	0.948000	0.59901	0.352000	0.20113	0.105000	0.17753	0.650000	0.86243	CAG	.	.	.	none		0.403	GLYAT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394593.1			A	58482795	C	A	58482795	3	1	9	1	0	0	0	0	1	0	0	0	6486	680	24	4	727	4	GLYAT	11	58482795	Missense_Mutation	SNP	C	TCGA-2Z-A9JD-01A-11D-A42J-10	51858134	58482795	76523721	73	698											
PLA2G16	11145	hgsc.bcm.edu	37	chr11	63342507	63342507	+	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	gcaacgcttgcagcgatgatGacatctctgacctgcaacaa	12	8	9	12	2	1	3	0	3	1	0	2	4	1	3	1	0	5	4	1	0	3	1			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr11:63342507G>A	ENST00000323646.5	-	4	753	c.399C>T	c.(397-399)gtC>gtT	p.V133V	PLA2G16_ENST00000394613.3_5'UTR|PLA2G16_ENST00000415826.1_Silent_p.V133V	NM_007069.3	NP_009000.2	P53816	HRSL3_HUMAN	phospholipase A2, group XVI	133					glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|negative regulation of cell cycle (GO:0045786)|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 metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	1-acyl-2-lysophosphatidylserine acylhydrolase activity (GO:0052740)|phosphatidylcholine 1-acylhydrolase activity (GO:0008970)|phosphatidylserine 1-acylhydrolase activity (GO:0052739)|phospholipase A2 activity (GO:0004623)			kidney(2)|lung(1)|ovary(1)|skin(1)	5						CAGCGATGATGACATCTCTGA	0.483																																					p.V133V		Atlas-SNP	.											.	PLA2G16	12	.	0			c.C399T						PASS	.						90	79	83					11																	63342507		2201	4298	6499	SO:0001819	synonymous_variant	11145	exon5			GATGATGACATCT	X92814	CCDS8047.1	11q12.3	2014-03-14	2008-09-19	2008-09-19	ENSG00000176485	ENSG00000176485	3.1.1.4		17825	protein-coding gene	gene with protein product	"adipose-specific PLA2"	613867	"HRAS-like suppressor 3"	HRASLS3		9771974, 18614531	Standard	NM_007069		Approved	HREV107, H-REV107-1, HREV107-3, MGC118754., AdPLA	uc009you.1	P53816	OTTHUMG00000167852	ENST00000323646.5:c.399C>T	chr11.hg19:g.63342507G>A		23.0	0.0	.		41.0	16.0	.	NM_001128203	B2R7Q4|B7XAK5|Q3SYI3|Q9HDD1	Silent	SNP	ENST00000323646.5	hg19	CCDS8047.1																																																																																			.	.	.	none		0.483	PLA2G16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396632.1	NM_001128203		A	63342507	G	A	63342507	2	1	9	1	0	0	0	0	0	0	0	1	12000	1277	45	2		2	PLA2G16	11	63342507	Silent	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10	4859712	63342507	71664009	74	699											
RTN3	10313	hgsc.bcm.edu	37	chr11	63487846	63487846	+	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	aatgtttttaatgagacagaAttctcattaaatgtgacaac	16	14	6	5	0	1	3	1	2	1	2	2	4	1	3	0	0	1	1	0	0	6	5			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr11:63487846A>T	ENST00000377819.5	+	3	2026	c.1872A>T	c.(1870-1872)gaA>gaT	p.E624D	RTN3_ENST00000540798.1_Missense_Mutation_p.E512D|RTN3_ENST00000354497.4_Intron|RTN3_ENST00000339997.4_Missense_Mutation_p.E605D|RTN3_ENST00000356000.3_Intron|RTN3_ENST00000341307.2_Intron|RTN3_ENST00000537981.1_Intron	NM_001265589.1	NP_001252518.1	O95197	RTN3_HUMAN	reticulon 3	624					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						ATGAGACAGAATTCTCATTAA	0.393																																					p.E624D		Atlas-SNP	.											.	RTN3	104	.	0			c.A1872T						PASS	.						69	74	72					11																	63487846		2201	4298	6499	SO:0001583	missense	10313	exon3			GACAGAATTCTCA	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.1872A>T	chr11.hg19:g.63487846A>T	ENSP00000367050:p.Glu624Asp	58.0	0.0	.		75.0	31.0	.	NM_001265589	B3KQS2|B7Z308|B7Z4M0|F5H774|Q147U9|Q496K2|Q53GN3|Q59EP0|Q5UEP2|Q6T930|Q7RTM7|Q7RTM8|Q7RTN3	Missense_Mutation	SNP	ENST00000377819.5	hg19	CCDS58141.1	.	.	.	.	.	.	.	.	.	.	A	11.66	1.704085	0.30232	.	.	ENSG00000133318	ENST00000377819;ENST00000339997;ENST00000540798	T;T;T	0.25749	1.78;1.78;1.78	4.6	2.0	0.26442	.	0.000000	0.33040	N	0.005359	T	0.13030	0.0316	N	0.14661	0.345	0.09310	N	0.999999	P;P;P	0.46512	0.879;0.808;0.879	B;B;B	0.39590	0.304;0.16;0.304	T	0.11991	-1.0565	10	0.54805	T	0.06	0.0791	8.2702	0.31840	0.5995:0.4005:0.0:0.0	.	512;624;605	F5H774;O95197;O95197-2	.;RTN3_HUMAN;.	D	624;605;512	ENSP00000367050:E624D;ENSP00000344106:E605D;ENSP00000442733:E512D	ENSP00000344106:E605D	E	+	3	2	RTN3	63244422	0.150000	0.22732	0.061000	0.19648	0.633000	0.38033	1.087000	0.30865	0.853000	0.35312	0.459000	0.35465	GAA	.	.	.	none		0.393	RTN3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000397846.1	NM_006054		T	63487846	A	T	63487846	3	4	9	1	0	0	0	0	1	0	0	0	13740	98	4	5	1882	5	RTN3	11	63487846	Missense_Mutation	SNP	A	TCGA-2Z-A9JD-01A-11D-A42J-10	145339	63487846	71518670	75	700											
SAC3D1	10004	hgsc.bcm.edu	37	chr11	64811959	64811959	+	IGR	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	ttgcctctgggcttcatggtCaacctcttggccctggatgg	4	13	12	12	0	4	0	2	0	2	0	4	1	4	1	3	5	2	1	3	5	1	3			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr11:64811959C>T	ENST00000358658.3	-	0	2699				SAC3D1_ENST00000398846.1_Silent_p.V279V|SAC3D1_ENST00000530213.1_3'UTR|SAC3D1_ENST00000531072.1_Silent_p.V279V	NM_005468.2	NP_005459.2	Q9UQQ1	NALDL_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 1							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	29						GCTTCATGGTCAACCTCTTGG	0.657																																					p.V279V		Atlas-SNP	.											.	SAC3D1	13	.	0			c.C837T						PASS	.						44	48	47					11																	64811959		1994	4161	6155	SO:0001628	intergenic_variant	29901	exon2			CATGGTCAACCTC	AF010141	CCDS31604.1	11q12	2011-08-16			ENSG00000168060	ENSG00000168060			23536	protein-coding gene	gene with protein product	"ileal peptidase I100"	602640				10085079	Standard	NM_005468		Approved		uc001ocn.3	Q9UQQ1	OTTHUMG00000165595		chr11.hg19:g.64811959C>T		79.0	0.0	.		53.0	26.0	.	NM_013299	C9J8A1|C9J964|C9JL35|C9JSN0|O43176	Silent	SNP	ENST00000358658.3	hg19	CCDS31604.1																																																																																			.	.	.	none		0.657	NAALADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385162.1	NM_005468		T	64811959	C	T	64811959	1	4	9	0	1	0	0	0	0	0	0	0	13815	813	29	2		2	SAC3D1	11	64811959	IGR	SNP	C	TCGA-2Z-A9JD-01A-11D-A42J-10	1324113	64811959	70194557	76	701											
PPFIA1	8500	hgsc.bcm.edu	37	chr11	70179622	70179622	+	Missense_Mutation	SNP	A	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	agaaaggttacgacagatggAagcacagttggaggagaaga	17	5	15	4	1	0	4	0	0	0	4	0	8	0	6	0	4	2	3	0	4	4	2			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr11:70179622A>C	ENST00000253925.7	+	10	1474	c.1259A>C	c.(1258-1260)gAa>gCa	p.E420A	AP000487.6_ENST00000528607.1_RNA|PPFIA1_ENST00000389547.3_Missense_Mutation_p.E420A	NM_003626.3	NP_003617.1	Q13136	LIPA1_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	420					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)			CGACAGATGGAAGCACAGTTG	0.532																																					p.E420A		Atlas-SNP	.											.	PPFIA1	114	.	0			c.A1259C						PASS	.						145	118	128					11																	70179622		2200	4294	6494	SO:0001583	missense	8500	exon10			AGATGGAAGCACA	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.1259A>C	chr11.hg19:g.70179622A>C	ENSP00000253925:p.Glu420Ala	213.0	0.0	.		200.0	83.0	.	NM_177423	A6NLE3|Q13135|Q14567|Q8N4I2	Missense_Mutation	SNP	ENST00000253925.7	hg19	CCDS31627.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.904811	0.92035	.	.	ENSG00000131626	ENST00000253925;ENST00000389547	D;D	0.83837	-1.77;-1.77	5.48	5.48	0.80851	.	0.000000	0.64402	U	0.000001	D	0.88804	0.6536	M	0.80616	2.505	0.58432	D	0.999999	P;D	0.54964	0.762;0.969	P;P	0.53593	0.542;0.73	D	0.90559	0.4514	10	0.87932	D	0	.	15.6079	0.76689	1.0:0.0:0.0:0.0	.	420;420	Q13136;Q13136-2	LIPA1_HUMAN;.	A	420	ENSP00000253925:E420A;ENSP00000374198:E420A	ENSP00000253925:E420A	E	+	2	0	PPFIA1	69857270	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.070000	0.93974	2.087000	0.62958	0.454000	0.30748	GAA	.	.	.	none		0.532	PPFIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393905.1	NM_003626		C	70179622	A	C	70179622	3	2	9	1	0	0	0	0	1	0	0	0	12316	246	9	5	1293	5	PPFIA1	11	70179622	Missense_Mutation	SNP	A	TCGA-2Z-A9JD-01A-11D-A42J-10	5367663	70179622	64826894	77	702											
C12orf35	55196	hgsc.bcm.edu	37	chr12	32134899	32134899	+	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	tgtcagcacaattggaaattTcactaacttgaaagtaaata	17	12	6	6	0	2	1	2	1	0	0	2	2	2	2	0	1	2	2	0	1	7	6			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr12:32134899T>A	ENST00000312561.4	+	4	1424	c.1010T>A	c.(1009-1011)tTc>tAc	p.F337Y	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	337																	ATTGGAAATTTCACTAACTTG	0.398																																					p.F337Y		Atlas-SNP	.											.	.	.	.	0			c.T1010A						PASS	.						87	84	85					12																	32134899		2203	4300	6503	SO:0001583	missense	55196	exon4			GAAATTTCACTAA	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.1010T>A	chr12.hg19:g.32134899T>A	ENSP00000310338:p.Phe337Tyr	104.0	0.0	.		174.0	62.0	.	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	hg19	CCDS8725.2	.	.	.	.	.	.	.	.	.	.	T	16.32	3.090401	0.55968	.	.	ENSG00000174718	ENST00000312561;ENST00000381054	T;T	0.07908	3.77;3.15	5.45	-2.32	0.06745	.	0.655283	0.14267	N	0.330452	T	0.04407	0.0121	N	0.24115	0.695	0.09310	N	1	B	0.18013	0.025	B	0.17433	0.018	T	0.42207	-0.9465	9	.	.	.	.	5.6415	0.17567	0.1296:0.3781:0.0:0.4923	.	337	Q9HCM1	CL035_HUMAN	Y	337	ENSP00000310338:F337Y;ENSP00000370442:F337Y	.	F	+	2	0	C12orf35	32026166	0.000000	0.05858	0.001000	0.08648	0.163000	0.22366	-0.100000	0.10990	-0.329000	0.08527	0.454000	0.30748	TTC	.	.	.	none		0.398	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169		A	32134899	T	A	32134899	3	1	9	1	0	0	0	0	1	0	0	0	1684	1783	62	5	1012	5	C12orf35	12	32134899	Missense_Mutation	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10		32134899	101716996	78	703											
GXYLT1	283464	hgsc.bcm.edu	37	chr12	42481670	42481671	+	Missense_Mutation	DNP	CA	CA	TG																															atattttgtaaatttttccaCagtatgtatgcactgttttt																								rs202200134|rs200973030		TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr12:42481670_42481671CA>TG	ENST00000398675.3	-	8	1472_1473	c.1240_1241TG>CA	c.(1240-1242)TGt>CAt	p.C414H	GXYLT1_ENST00000280876.6_Missense_Mutation_p.C383H	NM_001099650.1|NM_173601.1	NP_001093120.1|NP_775872.1	Q4G148	GXLT1_HUMAN	glucoside xylosyltransferase 1	414					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|O-glycan processing (GO:0016266)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	UDP-xylosyltransferase activity (GO:0035252)			kidney(2)|large_intestine(4)|liver(3)|lung(8)	17						AATTTTTCCACAGTATGTATGC	0.312																																					p.C414Y|p.C414R		Atlas-SNP	.											Q8IXV1_HUMAN,NS,carcinoma,-1,2|Q8IXV1_HUMAN,NS,carcinoma,0,2	GXYLT1	47	.	0			c.G1241A|c.T1240C						PASS	.																																			SO:0001583	missense	283464	exon8			TTTCCACAGTATG|TTCCACAGTATGT	BC015597	CCDS41771.1, CCDS41772.1	12q12	2013-10-11	2009-11-17	2009-11-17	ENSG00000151233	ENSG00000151233		"Glycosyltransferase family 8 domain containing"	27482	protein-coding gene	gene with protein product		613321	"glycosyltransferase 8 domain containing 3"	GLT8D3		19940119	Standard	NM_001099650		Approved	FLJ43151	uc001rms.4	Q4G148	OTTHUMG00000169379	ENST00000398675.3:c.1240_1241delinsTG	chr12.hg19:g.42481670_42481671delinsTG	ENSP00000381666:p.Cys414His	30.0|31.0	0.0	.		42.0	5.0	.	NM_173601	B3KWJ2|Q8IXV1|Q96BH4	Missense_Mutation	SNP	ENST00000398675.3	hg19	CCDS41772.1																																																																																			.	.	.	weak		0.312	GXYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403778.1	XM_290597		TG	42481671	CA	TG	42481670	3	4	9	1	0	0	0	0	1	0	0	0	6910	478	17	2	85	2	GXYLT1	12	42481670	Missense_Mutation	DNP	CA	TCGA-2Z-A9JD-01A-11D-A42J-10	10346771	42481670	91370225	79	704											
KRT2	3849	hgsc.bcm.edu	37	chr12	53040651	53040651	+	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	ctccttggcctgctgcagggCctcctccaggtcattcaact	5	11	9	16	0	2	0	2	0	0	0	5	0	5	0	5	3	3	2	5	3	1	2			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr12:53040651C>A	ENST00000309680.3	-	7	1363	c.1342G>T	c.(1342-1344)Gcc>Tcc	p.A448S		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	448	Coil 2.|Rod.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		TGCTGCAGGGCCTCCTCCAGG	0.587																																					p.A448S		Atlas-SNP	.											KRT2,NS,carcinoma,0,1	KRT2	94	.	0			c.G1342T						PASS	.						104	92	96					12																	53040651		2203	4300	6503	SO:0001583	missense	3849	exon7			GCAGGGCCTCCTC		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"-", "Intermediate filaments type II, keratins (basic)"	6439	protein-coding gene	gene with protein product	"epidermal ichthyosis bullosa of Siemens"	600194	"keratin 2A (epidermal ichthyosis bullosa of Siemens)"	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.1342G>T	chr12.hg19:g.53040651C>A	ENSP00000310861:p.Ala448Ser	30.0	1.0	.		38.0	13.0	.	NM_000423	Q4VAQ2	Missense_Mutation	SNP	ENST00000309680.3	hg19	CCDS8835.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.707130	0.89018	.	.	ENSG00000172867	ENST00000309680	D	0.88818	-2.43	4.48	3.59	0.41128	Filament (1);	.	.	.	.	D	0.94905	0.8353	M	0.89601	3.045	0.40673	D	0.98223	D	0.89917	1.0	D	0.87578	0.998	D	0.95802	0.8834	9	0.87932	D	0	.	12.9841	0.58581	0.0:0.9208:0.0:0.0792	.	448	P35908	K22E_HUMAN	S	448	ENSP00000310861:A448S	ENSP00000310861:A448S	A	-	1	0	KRT2	51326918	1.000000	0.71417	0.991000	0.47740	0.969000	0.65631	4.827000	0.62723	1.257000	0.44085	0.563000	0.77884	GCC	.	.	.	none		0.587	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423		A	53040651	C	A	53040651	3	1	9	1	0	0	0	0	1	0	0	0	8464	739	26	4	589	4	KRT2	12	53040651	Missense_Mutation	SNP	C	TCGA-2Z-A9JD-01A-11D-A42J-10	10558981	53040651	80811244	80	705											
MTERFD3	80298	hgsc.bcm.edu	37	chr12	107372223	107372223	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atactggctacagcagtctcAtcggcacctagttcttgtaa	10	12	8	11	1	2	0	1	0	2	0	4	0	2	0	1	2	3	5	1	2	4	6			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr12:107372223A>G	ENST00000552029.1	-	2	2338	c.270T>C	c.(268-270)gaT>gaC	p.D90D	C12orf23_ENST00000551237.1_3'UTR|MTERFD3_ENST00000240050.4_Silent_p.D90D|MTERFD3_ENST00000392830.2_Silent_p.D90D			Q49AM1	MTEF2_HUMAN		90					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)	transcription regulatory region DNA binding (GO:0044212)			breast(1)|kidney(1)|large_intestine(2)|lung(3)	7						CAGCAGTCTCATCGGCACCTA	0.423																																					p.D90D		Atlas-SNP	.											.	MTERFD3	32	.	0			c.T270C						PASS	.						128	134	132					12																	107372223		2203	4300	6503	SO:0001819	synonymous_variant	80298	exon3			AGTCTCATCGGCA																												ENST00000552029.1:c.270T>C	chr12.hg19:g.107372223A>G		59.0	0.0	.		48.0	18.0	.	NM_001033050	Q53HM2|Q9H4L6|Q9H7Y9	Silent	SNP	ENST00000552029.1	hg19	CCDS9111.1																																																																																			.	.	.	none		0.423	MTERFD3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406835.1			G	107372223	A	G	107372223	2	3	9	1	0	0	0	0	0	0	0	1	9928	214	8	3		3	MTERFD3	12	107372223	Silent	SNP	A	TCGA-2Z-A9JD-01A-11D-A42J-10	54331572	107372223	26479672	81	706											
EP400	57634	hgsc.bcm.edu	37	chr12	132505838	132505838	+	Frame_Shift_Del	DEL	C	C	-																															ctgcctcagaggctggtgctCccctcgcaggcccaggcccg																										TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr12:132505838delC	ENST00000333577.4	+	24	4879	c.4770delC	c.(4768-4770)ctcfs	p.L1590fs	EP400_ENST00000389562.2_Frame_Shift_Del_p.L1553fs|EP400_ENST00000332482.4_Frame_Shift_Del_p.L1517fs|EP400_ENST00000389561.2_Frame_Shift_Del_p.L1554fs|EP400_ENST00000330386.6_Intron			Q96L91	EP400_HUMAN	E1A binding protein p400	1590					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)		GGCTGGTGCTCCCCTCGCAGG	0.682																																					p.L1554fs		Atlas-Indel,Pindel	.											.	EP400	370	.	0			c.4661delT						PASS	.						5	4	4					12																	132505838		1830	3662	5492	SO:0001589	frameshift_variant	57634	exon23			.	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.4770delC	chr12.hg19:g.132505838delC	ENSP00000333602:p.Leu1590fs	111.0	0.0	0		56.0	20.0	0.357143	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Frame_Shift_Del	DEL	ENST00000333577.4	hg19																																																																																				.	.	.	none		0.682	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		-	132505838	C	-	132505838	7	5	9	1	0	1	0	1	0	0	0	0	5151	842	30	0	4745	0	EP400	12	132505838	Frame_Shift_Del	DEL	C	TCGA-2Z-A9JD-01A-11D-A42J-10	25133615	132505838	1346057	82	707											
CDADC1	81602	hgsc.bcm.edu	37	chr13	49852539	49852539	+	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	gtaggatgtggttacaatgcTtttcctgttggatctgagta	8	16	12	5	0	1	1	0	1	1	0	2	3	2	3	1	3	2	5	1	3	4	6			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr13:49852539T>A	ENST00000251108.6	+	7	1217	c.1104T>A	c.(1102-1104)gcT>gcA	p.A368A	CDADC1_ENST00000444959.1_Silent_p.A170A	NM_001193478.1|NM_030911.3	NP_001180407.1|NP_112173.1	Q9BWV3	CDAC1_HUMAN	cytidine and dCMP deaminase domain containing 1	368							hydrolase activity (GO:0016787)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	16		Lung NSC(96;0.000705)|Breast(56;0.0011)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;1.06e-08)|COAD - Colon adenocarcinoma(199;0.216)		GTTACAATGCTTTTCCTGTTG	0.408																																					p.A368A		Atlas-SNP	.											.	CDADC1	40	.	0			c.T1104A						PASS	.						411	350	370					13																	49852539		2203	4300	6503	SO:0001819	synonymous_variant	81602	exon7			CAATGCTTTTCCT	AY027525	CCDS9415.1	13q14.11	2008-02-05			ENSG00000102543	ENSG00000102543			20299	protein-coding gene	gene with protein product							Standard	NM_001193478		Approved	NYD-SP15	uc001vcu.3	Q9BWV3	OTTHUMG00000016913	ENST00000251108.6:c.1104T>A	chr13.hg19:g.49852539T>A		53.0	0.0	.		79.0	31.0	.	NM_030911	Q49A08|Q4G119|Q5TAW9|Q7Z764|Q9NT36	Silent	SNP	ENST00000251108.6	hg19	CCDS9415.1																																																																																			.	.	.	none		0.408	CDADC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044902.2	NM_030911		A	49852539	T	A	49852539	2	1	9	1	0	0	0	0	0	0	0	1	3055	1596	56	5		5	CDADC1	13	49852539	Silent	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10		49852539	65317339	83	708											
MYH6	4624	hgsc.bcm.edu	37	chr14	23862152	23862152	+	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	ttcttccagctgcagtttatCattttccaggtccatgatgc	7	16	7	11	0	2	1	1	1	1	0	5	1	5	1	3	1	3	3	3	1	1	6	rs375169402		TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr14:23862152C>T	ENST00000356287.3	-	23	3249	c.3220G>A	c.(3220-3222)Gat>Aat	p.D1074N	MYH6_ENST00000405093.3_Missense_Mutation_p.D1074N			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	1074					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)		TGCAGTTTATCATTTTCCAGG	0.542																																					p.D1074N		Atlas-SNP	.											MYH6,neck,malignant_melanoma,0,1	MYH6	274	.	0			c.G3220A						PASS	.	C	ASN/ASP	0,4406		0,0,2203	131	116	121		3220	4.8	1	14		121	1,8599	1.2+/-3.3	0,1,4299	no	missense	MYH6	NM_002471.3	23	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	1074/1940	23862152	1,13005	2203	4300	6503	SO:0001583	missense	4624	exon24			GTTTATCATTTTC	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.3220G>A	chr14.hg19:g.23862152C>T	ENSP00000348634:p.Asp1074Asn	40.0	1.0	.		42.0	17.0	.	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	hg19	CCDS9600.1	.	.	.	.	.	.	.	.	.	.	c	35	5.538945	0.96474	0.0	1.16E-4	ENSG00000197616	ENST00000405093;ENST00000356287	T;T	0.77750	-1.12;-1.12	4.82	4.82	0.62117	Myosin tail (1);	.	.	.	.	D	0.87398	0.6167	M	0.82323	2.585	0.80722	D	1	D	0.58620	0.983	P	0.60682	0.878	D	0.86950	0.2085	9	0.34782	T	0.22	.	18.2902	0.90127	0.0:1.0:0.0:0.0	.	1074	P13533	MYH6_HUMAN	N	1074	ENSP00000386041:D1074N;ENSP00000348634:D1074N	ENSP00000348634:D1074N	D	-	1	0	MYH6	22931992	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.591000	0.82666	2.391000	0.81399	0.557000	0.71058	GAT	.	.	.	weak		0.542	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			T	23862152	C	T	23862152	3	4	9	1	0	0	0	0	1	0	0	0	10045	826	29	2	2663	2	MYH6	14	23862152	Missense_Mutation	SNP	C	TCGA-2Z-A9JD-01A-11D-A42J-10		23862152	83487388	84	709											
SIPA1L1	26037	hgsc.bcm.edu	37	chr14	72200389	72200389	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcccttcccgcaggagagtTctcagcctcggacagctccc	6	8	9	18	2	1	1	1	0	1	1	6	3	4	2	4	2	2	3	4	2	0	2			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr14:72200389T>C	ENST00000555818.1	+	19	5279	c.4931T>C	c.(4930-4932)tTc>tCc	p.F1644S	SIPA1L1_ENST00000358550.2_Missense_Mutation_p.F1623S|SIPA1L1_ENST00000537413.1_Missense_Mutation_p.F1098S|SIPA1L1_ENST00000554874.1_3'UTR|SIPA1L1_ENST00000381232.3_Missense_Mutation_p.F1623S	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	1644					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)		GCAGGAGAGTTCTCAGCCTCG	0.562																																					p.F1644S		Atlas-SNP	.											.	SIPA1L1	219	.	0			c.T4931C						PASS	.						86	87	87					14																	72200389		2203	4300	6503	SO:0001583	missense	26037	exon19			GAGAGTTCTCAGC	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.4931T>C	chr14.hg19:g.72200389T>C	ENSP00000450832:p.Phe1644Ser	28.0	0.0	.		28.0	12.0	.	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	hg19	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	T	16.87	3.241374	0.58995	.	.	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550;ENST00000537413	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	5.09	5.09	0.68999	.	0.048982	0.85682	D	0.000000	T	0.50548	0.1622	L	0.55990	1.75	0.58432	D	0.999995	D;D;D;D;D	0.71674	0.998;0.982;0.995;0.981;0.994	P;P;D;P;D	0.75020	0.898;0.677;0.962;0.642;0.985	T	0.52434	-0.8576	10	0.66056	D	0.02	-24.1525	15.1848	0.72993	0.0:0.0:0.0:1.0	.	1098;1644;1098;1623;1644	F5GYF8;A6H8W6;B4DYX7;O43166-2;O43166	.;.;.;.;SI1L1_HUMAN	S	1623;1644;1623;1098	ENSP00000370630:F1623S;ENSP00000450832:F1644S;ENSP00000351352:F1623S;ENSP00000440682:F1098S	ENSP00000351352:F1644S	F	+	2	0	SIPA1L1	71270142	1.000000	0.71417	1.000000	0.80357	0.151000	0.21798	7.655000	0.83696	2.044000	0.60594	0.459000	0.35465	TTC	.	.	.	none		0.562	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		C	72200389	T	C	72200389	3	2	9	1	0	0	0	0	1	0	0	0	14342	1783	62	3	5001	3	SIPA1L1	14	72200389	Missense_Mutation	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10	48338237	72200389	35149151	85	710											
COQ6	51004	hgsc.bcm.edu	37	chr14	74422588	74422588	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctatatcgtggagaatgaTgtcatcatgcatgctctcac	10	12	10	9	1	3	2	3	1	1	1	5	3	3	2	0	2	2	3	0	2	3	2			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr14:74422588T>C	ENST00000334571.2	+	4	478	c.438T>C	c.(436-438)gaT>gaC	p.D146D	COQ6_ENST00000394026.4_Silent_p.D121D|COQ6_ENST00000555552.1_3'UTR|COQ6_ENST00000554920.1_Silent_p.D146D|COQ6_ENST00000238709.4_Silent_p.D71D	NM_182476.2	NP_872282.1	Q9Y2Z9	COQ6_HUMAN	coenzyme Q6 monooxygenase	146					small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(234;0.00337)		TGGAGAATGATGTCATCATGC	0.473																																					p.D146D		Atlas-SNP	.											.	COQ6	27	.	0			c.T438C						PASS	.						178	167	171					14																	74422588		2203	4300	6503	SO:0001819	synonymous_variant	51004	exon4			GAATGATGTCATC	AF132944	CCDS9823.1, CCDS9824.1, CCDS9824.2	14q24.1	2013-05-01	2013-05-01		ENSG00000119723	ENSG00000119723			20233	protein-coding gene	gene with protein product		614647	"coenzyme Q6 homolog (yeast)", "coenzyme Q6 homolog, monooxygenase (yeast)", "coenzyme Q6 homolog, monooxygenase (S. cerevisiae)"			21540551	Standard	NM_182476		Approved	CGI-10	uc001xph.3	Q9Y2Z9	OTTHUMG00000171260	ENST00000334571.2:c.438T>C	chr14.hg19:g.74422588T>C		38.0	0.0	.		29.0	12.0	.	NM_182476	B7Z3K8|Q53GG6|Q86U30|Q96CA1|Q96CK2	Silent	SNP	ENST00000334571.2	hg19	CCDS9823.1																																																																																			.	.	.	none		0.473	COQ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412616.1			C	74422588	T	C	74422588	2	2	9	1	0	0	0	0	0	0	0	1	3751	1461	51	3		3	COQ6	14	74422588	Silent	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10	2222199	74422588	32926952	86	711											
FBLN5	10516	hgsc.bcm.edu	37	chr14	92336630	92336630	+	Frame_Shift_Del	DEL	T	T	-																															ggagctgcctctgaagttgaTgacagtgttgacagtgatca																										TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr14:92336630delT	ENST00000342058.4	-	11	1878	c.1285delA	c.(1285-1287)atcfs	p.I429fs	TC2N_ENST00000555302.1_5'Flank|TC2N_ENST00000435962.2_5'Flank|FBLN5_ENST00000267620.10_Frame_Shift_Del_p.I470fs|FBLN5_ENST00000556154.1_Frame_Shift_Del_p.I434fs|FBLN5_ENST00000556961.1_5'UTR	NM_006329.3	NP_006320.2	Q9UBX5	FBLN5_HUMAN	fibulin 5	429					cell-matrix adhesion (GO:0007160)|elastic fiber assembly (GO:0048251)|extracellular matrix organization (GO:0030198)|protein localization to cell surface (GO:0034394)|regulation of cell growth (GO:0001558)|regulation of removal of superoxide radicals (GO:2000121)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	28		all_cancers(154;0.0722)				CTGAAGTTGATGACAGTGTTG	0.582																																					p.I429fs		Atlas-Indel,Pindel	.											.	FBLN5	60	.	0			c.1286delT						PASS	.						113	115	115					14																	92336630		2203	4300	6503	SO:0001589	frameshift_variant	10516	exon11			.	AJ133490	CCDS9898.1	14q31	2014-09-17				ENSG00000140092		"Fibulins"	3602	protein-coding gene	gene with protein product		604580				10640802	Standard	NM_006329		Approved	EVEC, UP50, DANCE, ARMD3	uc001xzx.4	Q9UBX5		ENST00000342058.4:c.1285delA	chr14.hg19:g.92336630delT	ENSP00000345008:p.Ile429fs	61.0	0.0	0		97.0	33.0	0.340206	NM_006329	O75966|Q6IAL4|Q6UWA3	Frame_Shift_Del	DEL	ENST00000342058.4	hg19	CCDS9898.1																																																																																			.	.	.	none		0.582	FBLN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411787.1			-	92336630	T	-	92336630	7	5	9	1	0	1	0	1	0	0	0	0	5707	1464	51	0	65	0	FBLN5	14	92336630	Frame_Shift_Del	DEL	T	TCGA-2Z-A9JD-01A-11D-A42J-10	17914042	92336630	15012910	87	712											
CASC5	57082	hgsc.bcm.edu	37	chr15	40915982	40915983	+	Frame_Shift_Ins	INS	-	-	T																															cgattcccatactgttttcaINSttgactgtcaagccacagag																										TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr15:40915982_40915983insT	ENST00000346991.5	+	11	3988_3989	c.3598_3599insT	c.(3598-3600)attfs	p.I1200fs	CASC5_ENST00000399668.2_Frame_Shift_Ins_p.I1174fs			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	1200	2 X 104 AA approximate repeats.				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)		TACTGTTTTCATTGACTGTCAA	0.381																																					p.I1200fs		Atlas-Indel,Pindel	.											.	CASC5	269	.	0			c.3598_3599insT						PASS	.																																			SO:0001589	frameshift_variant	57082	exon11			.	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.3600dupT	chr15.hg19:g.40915984_40915984dupT	ENSP00000335463:p.Ile1200fs	82.0	0.0	0		99.0	33.0	0.333333	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Frame_Shift_Ins	INS	ENST00000346991.5	hg19	CCDS42023.1																																																																																			.	.	.	none		0.381	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		T	40915983	-	T	40915982	7	5	9	1	0	1	1	0	0	0	0	0	2665	217	8	0	3636	0	CASC5	15	40915982	Frame_Shift_Ins	INS	-	TCGA-2Z-A9JD-01A-11D-A42J-10		40915982	61615410	88	713											
INO80	54617	hgsc.bcm.edu	37	chr15	41313309	41313309	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcattgcagtaagaatccaaTggcactgcggtaacctgcag	12	9	10	10	1	1	1	1	0	0	1	2	1	2	1	2	2	4	5	2	2	4	3			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr15:41313309T>C	ENST00000361937.3	-	26	3487	c.3063A>G	c.(3061-3063)ccA>ccG	p.P1021P	RP11-540O11.4_ENST00000558967.1_RNA|INO80_ENST00000401393.3_Silent_p.P1021P			Q9ULG1	INO80_HUMAN	INO80 complex subunit	1021	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						AAGAATCCAATGGCACTGCGG	0.473																																					p.P1021P		Atlas-SNP	.											.	INO80	122	.	0			c.A3063G						PASS	.						72	66	68					15																	41313309		2203	4300	6503	SO:0001819	synonymous_variant	54617	exon26			ATCCAATGGCACT	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.3063A>G	chr15.hg19:g.41313309T>C		35.0	0.0	.		45.0	20.0	.	NM_017553	A6H8X4|Q9NTG6	Silent	SNP	ENST00000361937.3	hg19	CCDS10071.1																																																																																			.	.	.	none		0.473	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252527.2	NM_017553		C	41313309	T	C	41313309	2	2	9	1	0	0	0	0	0	0	0	1	7753	1451	51	3		3	INO80	15	41313309	Silent	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10	397327	41313309	61218083	89	714											
GANC	2595	hgsc.bcm.edu	37	chr15	42640335	42640335	+	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	gcgaggtggaagtgtgatacCaataaagacaactgtaggaa	16	7	13	5	1	0	2	0	1	0	1	0	5	0	4	1	3	2	1	1	3	8	3			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr15:42640335C>A	ENST00000318010.8	+	21	2579	c.2339C>A	c.(2338-2340)cCa>cAa	p.P780Q	RP11-164J13.1_ENST00000495723.1_RNA|CAPN3_ENST00000356316.3_5'UTR	NM_198141.2	NP_937784.2	Q8TET4	GANC_HUMAN	glucosidase, alpha; neutral C	780					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)	AGTGTGATACCAATAAAGACA	0.413																																					p.P780Q		Atlas-SNP	.											.	GANC	57	.	0			c.C2339A						PASS	.						89	85	86					15																	42640335		2203	4299	6502	SO:0001583	missense	2595	exon21			TGATACCAATAAA	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.2339C>A	chr15.hg19:g.42640335C>A	ENSP00000326227:p.Pro780Gln	52.0	0.0	.		64.0	29.0	.	NM_198141	Q52LQ4|Q8IWZ0|Q8IZM4|Q8IZM5	Missense_Mutation	SNP	ENST00000318010.8	hg19	CCDS10084.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.428560	0.83667	.	.	ENSG00000214013	ENST00000318010	D	0.91945	-2.94	6.02	6.02	0.97574	.	0.105339	0.64402	D	0.000002	D	0.96818	0.8961	M	0.87097	2.86	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	D	0.96665	0.9492	10	0.87932	D	0	-7.3534	20.547	0.99278	0.0:1.0:0.0:0.0	.	780	Q8TET4	GANC_HUMAN	Q	780	ENSP00000326227:P780Q	ENSP00000447925:P12Q	P	+	2	0	GANC	40427627	0.685000	0.27652	0.792000	0.32020	0.547000	0.35210	2.956000	0.49129	2.850000	0.98022	0.650000	0.86243	CCA	.	.	.	none		0.413	GANC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252887.2	NM_198141		A	42640335	C	A	42640335	3	1	9	1	0	0	0	0	1	0	0	0	6241	594	21	4	2421	4	GANC	15	42640335	Missense_Mutation	SNP	C	TCGA-2Z-A9JD-01A-11D-A42J-10	1327026	42640335	59891057	90	715											
SLC28A1	9154	hgsc.bcm.edu	37	chr15	85438656	85438656	+	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	cccgaatcagtacctccctcAgatcacctggacagtgtgag	10	8	9	14	1	3	2	3	1	0	1	4	4	4	3	4	1	1	1	4	1	2	1			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr15:85438656A>G	ENST00000286749.3	+	5	551				SLC28A1_ENST00000338602.2_Missense_Mutation_p.Q170R|SLC28A1_ENST00000538177.1_Intron|SLC28A1_ENST00000394573.1_Intron|SLC28A1_ENST00000537703.1_Intron|SLC28A1_ENST00000537216.1_Intron|SLC28A1_ENST00000537624.1_Intron			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1						nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	TACCTCCCtcagatcacctgg	0.562																																					p.Q170R		Atlas-SNP	.											.	SLC28A1	118	.	0			c.A509G						PASS	.						66	54	58					15																	85438656		2203	4299	6502	SO:0001627	intron_variant	9154	exon7			TCCCTCAGATCAC	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.461+302A>G	chr15.hg19:g.85438656A>G		104.0	0.0	.		123.0	55.0	.	NM_201651	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Missense_Mutation	SNP	ENST00000286749.3	hg19	CCDS10334.1	.	.	.	.	.	.	.	.	.	.	A	10.09	1.255659	0.22965	.	.	ENSG00000156222	ENST00000338602	T	0.12672	2.66	3.41	2.29	0.28610	.	.	.	.	.	T	0.10337	0.0253	.	.	.	0.09310	N	0.999999	B	0.12013	0.005	B	0.10450	0.005	T	0.27331	-1.0077	8	0.72032	D	0.01	.	5.4062	0.16323	0.8714:0.0:0.1286:0.0	.	170	O00337-2	.	R	170	ENSP00000341629:Q170R	ENSP00000341629:Q170R	Q	+	2	0	SLC28A1	83239660	0.000000	0.05858	0.006000	0.13384	0.008000	0.06430	0.098000	0.15189	0.691000	0.31592	0.460000	0.39030	CAG	.	.	.	none		0.562	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2			G	85438656	A	G	85438656	1	3	9	0	1	0	0	0	0	0	0	0	14544	188	7	3		3	SLC28A1	15	85438656	Intron	SNP	A	TCGA-2Z-A9JD-01A-11D-A42J-10	42798321	85438656	17092736	91	716											
TMEM8A	58986	hgsc.bcm.edu	37	chr16	426371	426371	+	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	cctggtggtcggggctcgggGacagcagaccagaggaggca	8	4	19	10	2	0	2	0	0	0	2	2	4	0	4	2	8	1	3	2	8	0	0			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr16:426371G>A	ENST00000431232.2	-	6	1149	c.989C>T	c.(988-990)tCc>tTc	p.S330F	TMEM8A_ENST00000250930.3_Missense_Mutation_p.S137F|TMEM8A_ENST00000476735.1_5'Flank	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	330					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						GGGGCTCGGGGACAGCAGACC	0.642																																					p.S330F		Atlas-SNP	.											.	TMEM8A	49	.	0			c.C989T						PASS	.						42	40	41					16																	426371		2202	4298	6500	SO:0001583	missense	58986	exon6			CTCGGGGACAGCA	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.989C>T	chr16.hg19:g.426371G>A	ENSP00000401338:p.Ser330Phe	110.0	0.0	.		57.0	27.0	.	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Missense_Mutation	SNP	ENST00000431232.2	hg19	CCDS10407.1	.	.	.	.	.	.	.	.	.	.	G	15.42	2.827992	0.50845	.	.	ENSG00000129925	ENST00000431232;ENST00000250930	T;T	0.33216	1.83;1.42	4.71	3.76	0.43208	.	1.026870	0.07737	N	0.946183	T	0.37100	0.0991	L	0.47716	1.5	0.09310	N	1	D	0.57899	0.981	P	0.50231	0.635	T	0.17077	-1.0381	10	0.56958	D	0.05	.	8.027	0.30442	0.2011:0.0:0.7989:0.0	.	330	Q9HCN3	TMM8A_HUMAN	F	330;137	ENSP00000401338:S330F;ENSP00000250930:S137F	ENSP00000250930:S137F	S	-	2	0	TMEM8A	366372	0.001000	0.12720	0.005000	0.12908	0.002000	0.02628	0.149000	0.16243	1.202000	0.43218	0.655000	0.94253	TCC	.	.	.	none		0.642	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259		A	426371	G	A	426371	3	1	9	1	0	0	0	0	1	0	0	0	16226	1174	41	2	1358	2	TMEM8A	16	426371	Missense_Mutation	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10		426371	89928382	92	717											
RHOT2	89941	hgsc.bcm.edu	37	chr16	720472	720472	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagtgttcggccaagaaccTgaggaacatctcagagctgt	11	8	11	11	1	1	3	1	1	1	2	3	4	1	4	3	2	3	2	3	2	3	1			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr16:720472T>C	ENST00000315082.4	+	8	569	c.455T>C	c.(454-456)cTg>cCg	p.L152P	RHOT2_ENST00000569943.2_3'UTR	NM_138769.2	NP_620124.1	Q8IXI1	MIRO2_HUMAN	ras homolog family member T2	152					cellular homeostasis (GO:0019725)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrion transport along microtubule (GO:0047497)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|pancreas(2)|prostate(1)	13		Hepatocellular(780;0.0218)				GCCAAGAACCTGAGGAACATC	0.612																																					p.L152P		Atlas-SNP	.											.	RHOT2	35	.	0			c.T455C						PASS	.						102	103	103					16																	720472		2200	4300	6500	SO:0001583	missense	89941	exon8			AGAACCTGAGGAA	BC014942	CCDS10417.1	16p13.3	2013-01-10	2012-02-27	2004-03-24	ENSG00000140983	ENSG00000140983		"EF-hand domain containing"	21169	protein-coding gene	gene with protein product	"mitochondrial Rho (MIRO) GTPase 2"	613889	"chromosome 16 open reading frame 39", "ras homolog gene family, member T2"	C16orf39, ARHT2		12482879	Standard	NM_138769		Approved	MIRO-2	uc002cip.3	Q8IXI1	OTTHUMG00000121139	ENST00000315082.4:c.455T>C	chr16.hg19:g.720472T>C	ENSP00000321971:p.Leu152Pro	117.0	0.0	.		56.0	16.0	.	NM_138769	A2IDC2|Q8NF53|Q96C13|Q96S17|Q9BT60|Q9H7M8	Missense_Mutation	SNP	ENST00000315082.4	hg19	CCDS10417.1	.	.	.	.	.	.	.	.	.	.	T	11.67	1.708096	0.30322	.	.	ENSG00000140983	ENST00000315082	T	0.69561	-0.41	5.11	4.0	0.46444	.	0.141279	0.48767	D	0.000179	T	0.77745	0.4176	M	0.68728	2.09	0.80722	D	1	P;D	0.89917	0.503;1.0	B;D	0.87578	0.384;0.998	T	0.76547	-0.2919	10	0.51188	T	0.08	-1.6952	10.2105	0.43138	0.149:0.0:0.0:0.851	.	25;152	Q8IXI1-2;Q8IXI1	.;MIRO2_HUMAN	P	152	ENSP00000321971:L152P	ENSP00000321971:L152P	L	+	2	0	RHOT2	660473	1.000000	0.71417	0.586000	0.28679	0.001000	0.01503	5.906000	0.69900	0.760000	0.33108	-0.496000	0.04628	CTG	.	.	.	none		0.612	RHOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241617.1	NM_138769		C	720472	T	C	720472	3	2	9	1	0	0	0	0	1	0	0	0	13357	1580	55	3	485	3	RHOT2	16	720472	Missense_Mutation	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10	294101	720472	89634281	93	718											
DNAH3	55567	hgsc.bcm.edu	37	chr16	21147803	21147803	+	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	caggggcaatcatgtctttgCgaattccattggtcagatag	10	12	11	8	1	3	1	2	0	1	1	4	2	4	1	1	3	1	1	1	3	3	4	rs200178510		TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr16:21147803C>T	ENST00000261383.3	-	6	727	c.728G>A	c.(727-729)cGc>cAc	p.R243H	DNAH3_ENST00000415178.1_Missense_Mutation_p.R243H	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	243	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		CATGTCTTTGCGAATTCCATT	0.473																																					p.R243H		Atlas-SNP	.											.	DNAH3	1142	.	0			c.G728A						PASS	.						179	167	171					16																	21147803		2201	4300	6501	SO:0001583	missense	55567	exon6			TCTTTGCGAATTC	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.728G>A	chr16.hg19:g.21147803C>T	ENSP00000261383:p.Arg243His	59.0	0.0	.		106.0	39.0	.	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	hg19	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	C	13.93	2.383171	0.42207	.	.	ENSG00000158486	ENST00000261383;ENST00000415178;ENST00000396036	T;T	0.22945	1.93;2.08	5.53	-3.06	0.05379	.	1.226080	0.05829	N	0.617229	T	0.19208	0.0461	L	0.53249	1.67	0.09310	N	1	B;P	0.34662	0.002;0.462	B;B	0.23018	0.0;0.043	T	0.24012	-1.0172	10	0.48119	T	0.1	.	6.1464	0.20289	0.0:0.3114:0.2689:0.4197	.	243;214	Q8TD57;Q8TD57-2	DYH3_HUMAN;.	H	243;243;214	ENSP00000261383:R243H;ENSP00000394245:R243H	ENSP00000261383:R243H	R	-	2	0	DNAH3	21055304	0.000000	0.05858	0.101000	0.21167	0.871000	0.50021	-0.672000	0.05244	-0.547000	0.06207	0.655000	0.94253	CGC	.	C|0.999;T|0.001	0.001	weak		0.473	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		T	21147803	C	T	21147803	3	4	9	1	0	0	0	0	1	0	0	0	4605	768	27	1	11849	1	DNAH3	16	21147803	Missense_Mutation	SNP	C	TCGA-2Z-A9JD-01A-11D-A42J-10	20427331	21147803	69206950	94	719											
E2F4	1874	hgsc.bcm.edu	37	chr16	67226969	67226969	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gacaaactgattgagctcaaGgcagagatcgaggagctgca	14	6	13	8	1	1	3	1	2	0	1	2	7	1	4	0	2	4	4	0	2	2	1			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr16:67226969G>A	ENST00000379378.3	+	3	362	c.303G>A	c.(301-303)aaG>aaA	p.K101K	E2F4_ENST00000564718.1_3'UTR|EXOC3L1_ENST00000562887.1_5'Flank|EXOC3L1_ENST00000314586.6_5'Flank	NM_001950.3	NP_001941.2	Q16254	E2F4_HUMAN	E2F transcription factor 4, p107/p130-binding	101	Dimerization. {ECO:0000255}.				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)		TTGAGCTCAAGGCAGAGATCG	0.592																																					p.K101K		Atlas-SNP	.											.	E2F4	25	.	0			c.G303A						PASS	.						38	32	34					16																	67226969		2190	4288	6478	SO:0001819	synonymous_variant	1874	exon3			GCTCAAGGCAGAG	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.303G>A	chr16.hg19:g.67226969G>A		64.0	0.0	.		40.0	17.0	.	NM_001950	A6NGR8|B5BU56|Q12991|Q15328	Silent	SNP	ENST00000379378.3	hg19	CCDS32464.1																																																																																			.	.	.	none		0.592	E2F4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421565.1	NM_001950		A	67226969	G	A	67226969	2	1	9	1	0	0	0	0	0	0	0	1	4871	991	35	2		2	E2F4	16	67226969	Silent	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10	46079166	67226969	23127784	95	720											
ZFHX3	463	hgsc.bcm.edu	37	chr16	72845510	72845510	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctccacgcagtcaggtgccAcgctgtggaggtgggtgagg	6	8	17	10	2	2	1	1	1	1	0	3	2	2	2	2	5	1	2	2	5	0	0			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr16:72845510A>G	ENST00000268489.5	-	7	4502	c.3830T>C	c.(3829-3831)gTg>gCg	p.V1277A	RP5-991G20.2_ENST00000558618.1_RNA|ZFHX3_ENST00000397992.5_Missense_Mutation_p.V363A	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	1277					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)				GTCAGGTGCCACGCTGTGGAG	0.587																																					p.V1277A		Atlas-SNP	.											.	ZFHX3	404	.	0			c.T3830C						PASS	.						65	58	60					16																	72845510		2198	4300	6498	SO:0001583	missense	463	exon7			GGTGCCACGCTGT	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.3830T>C	chr16.hg19:g.72845510A>G	ENSP00000268489:p.Val1277Ala	36.0	0.0	.		43.0	22.0	.	NM_006885	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	hg19	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	A	19.34	3.809308	0.70797	.	.	ENSG00000140836	ENST00000268489;ENST00000397992	T;T	0.78707	-1.2;-1.19	5.4	5.4	0.78164	.	0.000000	0.45126	D	0.000397	D	0.85344	0.5675	L	0.53617	1.68	0.80722	D	1	D	0.71674	0.998	D	0.79784	0.993	D	0.86875	0.2038	10	0.87932	D	0	.	15.3888	0.74726	1.0:0.0:0.0:0.0	.	1277	Q15911	ZFHX3_HUMAN	A	1277;363	ENSP00000268489:V1277A;ENSP00000438926:V363A	ENSP00000268489:V1277A	V	-	2	0	ZFHX3	71403011	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.287000	0.95975	2.164000	0.68074	0.533000	0.62120	GTG	.	.	.	none		0.587	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		G	72845510	A	G	72845510	3	3	9	1	0	0	0	0	1	0	0	0	17646	159	6	3	7297	3	ZFHX3	16	72845510	Missense_Mutation	SNP	A	TCGA-2Z-A9JD-01A-11D-A42J-10	5618541	72845510	17509243	96	721											
DEF8	54849	hgsc.bcm.edu	37	chr16	90021581	90021581	+	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	ccccgtcttcctccagaggcCctgcctgagctgccccctgg	3	8	10	20	1	1	2	0	1	1	1	3	2	3	2	8	2	3	1	8	2	0	1			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr16:90021581C>A	ENST00000268676.7	+	4	401	c.312C>A	c.(310-312)gcC>gcA	p.A104A	DEF8_ENST00000563594.1_Silent_p.A43A|DEF8_ENST00000418391.2_Silent_p.A43A|DEF8_ENST00000567874.1_De_novo_Start_InFrame|DEF8_ENST00000570182.1_Silent_p.A43A|DEF8_ENST00000569453.1_Silent_p.A43A|DEF8_ENST00000563795.1_Silent_p.A43A	NM_207514.2	NP_997397.1	Q6ZN54	DEFI8_HUMAN	differentially expressed in FDCP 8 homolog (mouse)	104					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)		CTCCAGAGGCCCTGCCTGAGC	0.642																																					p.A104A		Atlas-SNP	.											.	DEF8	28	.	0			c.C312A						PASS	.						67	67	67					16																	90021581		2198	4300	6498	SO:0001819	synonymous_variant	54849	exon4			AGAGGCCCTGCCT	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.312C>A	chr16.hg19:g.90021581C>A		37.0	0.0	.		34.0	9.0	.	NM_207514	B3KT65|B4DK62|B4E0S9|B7Z3H6|H3BUG7|Q8N8N3|Q9NXL0	Silent	SNP	ENST00000268676.7	hg19	CCDS10989.1																																																																																			.	.	.	none		0.642	DEF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000272878.1	NM_207514		A	90021581	C	A	90021581	2	1	9	1	0	0	0	0	0	0	0	1	4389	610	22	4		4	DEF8	16	90021581	Silent	SNP	C	TCGA-2Z-A9JD-01A-11D-A42J-10	17176071	90021581	333172	97	722											
WDR81	124997	hgsc.bcm.edu	37	chr17	1634093	1634093	+	Frame_Shift_Del	DEL	C	C	-																															tgagcagtggcgagagcccaCcgctgagcgccggcaacatc																										TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr17:1634093delC	ENST00000409644.1	+	3	3820	c.3820delC	c.(3820-3822)ccgfs	p.P1274fs	WDR81_ENST00000545662.1_5'UTR|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000437219.2_Frame_Shift_Del_p.P71fs|WDR81_ENST00000419248.1_Frame_Shift_Del_p.P47fs|WDR81_ENST00000446363.1_5'UTR|WDR81_ENST00000309182.5_Frame_Shift_Del_p.P223fs	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1274					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)		CGAGAGCCCACCGCTGAGCGC	0.677																																					p.P1273fs		Atlas-Indel,Pindel	.											.	WDR81	180	.	0			c.3819delA						PASS	.						32	35	34					17																	1634093		2202	4296	6498	SO:0001589	frameshift_variant	124997	exon3			.	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.3820delC	chr17.hg19:g.1634093delC	ENSP00000386609:p.Pro1274fs	88.0	0.0	0		81.0	29.0	0.358025	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Frame_Shift_Del	DEL	ENST00000409644.1	hg19	CCDS54062.1																																																																																			.	.	.	none		0.677	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348		-	1634093	C	-	1634093	7	5	9	1	0	1	0	1	0	0	0	0	17342	507	18	0	3892	0	WDR81	17	1634093	Frame_Shift_Del	DEL	C	TCGA-2Z-A9JD-01A-11D-A42J-10		1634093	79561117	98	723											
SPAG7	9552	hgsc.bcm.edu	37	chr17	4863151	4863151	+	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	cttgtccttgtagtcgctggCagggctcaccaccacaggcc	6	9	11	15	1	1	0	1	0	0	0	3	0	2	0	4	3	0	4	4	3	1	3			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr17:4863151C>A	ENST00000206020.3	-	6	545	c.478G>T	c.(478-480)Gcc>Tcc	p.A160S	SPAG7_ENST00000575142.1_Missense_Mutation_p.A149S|SPAG7_ENST00000573366.1_Missense_Mutation_p.A109S	NM_004890.2	NP_004881.2	O75391	SPAG7_HUMAN	sperm associated antigen 7	160						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			central_nervous_system(1)|endometrium(1)|kidney(2)|lung(3)|ovary(2)|urinary_tract(1)	10						TAGTCGCTGGCAGGGCTCACC	0.632																																					p.A160S		Atlas-SNP	.											.	SPAG7	22	.	0			c.G478T						PASS	.						72	77	75					17																	4863151		2152	4249	6401	SO:0001583	missense	9552	exon6			CGCTGGCAGGGCT	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.478G>T	chr17.hg19:g.4863151C>A	ENSP00000206020:p.Ala160Ser	31.0	0.0	.		54.0	12.0	.	NM_004890	Q96EU5	Missense_Mutation	SNP	ENST00000206020.3	hg19	CCDS42240.1	.	.	.	.	.	.	.	.	.	.	C	9.879	1.201019	0.22121	.	.	ENSG00000091640	ENST00000206020	.	.	.	5.1	2.0	0.26442	.	0.275517	0.41194	D	0.000922	T	0.14657	0.0354	N	0.04508	-0.205	0.24039	N	0.996084	B	0.10296	0.003	B	0.06405	0.002	T	0.26608	-1.0098	9	0.16420	T	0.52	0.0294	8.9143	0.35572	0.0:0.7497:0.0:0.2503	.	160	O75391	SPAG7_HUMAN	S	160	.	ENSP00000206020:A160S	A	-	1	0	SPAG7	4803874	0.998000	0.40836	0.178000	0.23040	0.860000	0.49131	1.596000	0.36718	0.315000	0.23110	0.561000	0.74099	GCC	.	.	.	none		0.632	SPAG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438747.1	NM_004890		A	4863151	C	A	4863151	3	1	9	1	0	0	0	0	1	0	0	0	14996	710	25	4	213	4	SPAG7	17	4863151	Missense_Mutation	SNP	C	TCGA-2Z-A9JD-01A-11D-A42J-10	3229058	4863151	76332059	99	724											
CLDN7	1366	hgsc.bcm.edu	37	chr17	7164034	7164034	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ataccaggagcaagctaccaAggcggcaagacctggagaca	15	3	12	11	1	0	2	0	0	0	2	0	4	0	3	3	4	4	3	3	4	5	2			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr17:7164034A>G	ENST00000360325.7	-	3	834	c.400T>C	c.(400-402)Ttg>Ctg	p.L134L	CLDN7_ENST00000397317.4_Silent_p.L134L|CLDN7_ENST00000573745.1_5'Flank|CLDN7_ENST00000538261.3_Intron|RP1-4G17.5_ENST00000577138.1_Intron|CLDN7_ENST00000571881.2_Missense_Mutation_p.L125P	NM_001307.5	NP_001298.3	O95471	CLD7_HUMAN	claudin 7	134					calcium-independent cell-cell adhesion (GO:0016338)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	6						CAAGCTACCAAGGCGGCAAGA	0.537																																					p.L134L		Atlas-SNP	.											.	CLDN7	11	.	0			c.T400C						PASS	.						82	91	88					17																	7164034		2203	4300	6503	SO:0001819	synonymous_variant	1366	exon3			CTACCAAGGCGGC	AJ011497	CCDS11096.1, CCDS54081.1	17p13.1	2013-09-20			ENSG00000181885	ENSG00000181885		"Claudins"	2049	protein-coding gene	gene with protein product		609131		CEPTRL2, CPETRL2		9892664	Standard	NM_001307		Approved	Hs.84359	uc002gfm.4	O95471	OTTHUMG00000178005	ENST00000360325.7:c.400T>C	chr17.hg19:g.7164034A>G		124.0	0.0	.		123.0	29.0	.	NM_001307	B2R9X7|D3DTP0|Q6IPN3|Q7Z4Y7|Q9BVN0	Silent	SNP	ENST00000360325.7	hg19	CCDS11096.1																																																																																			.	.	.	none		0.537	CLDN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440204.2	NM_001307		G	7164034	A	G	7164034	2	3	9	1	0	0	0	0	0	0	0	1	3492	69	3	3		3	CLDN7	17	7164034	Silent	SNP	A	TCGA-2Z-A9JD-01A-11D-A42J-10	2300883	7164034	74031176	100	725											
MPRIP	23164	hgsc.bcm.edu	37	chr17	17049353	17049353	+	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	ttttctccctttctcagcccGacctgctgaatttcaagaaa	9	14	5	13	1	3	2	2	1	2	1	5	3	3	2	3	0	2	1	3	0	3	4			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr17:17049353G>A	ENST00000341712.4	+	10	1153	c.1153G>A	c.(1153-1155)Gac>Aac	p.D385N	MPRIP_ENST00000395804.3_Missense_Mutation_p.D385N|MPRIP_ENST00000395811.5_Missense_Mutation_p.D385N|MPRIP_ENST00000444976.1_Missense_Mutation_p.D347N			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	385						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)		p.D385N(1)		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						TTCTCAGCCCGACCTGCTGAA	0.547																																					p.D385N		Atlas-SNP	.											MPRIP,NS,carcinoma,0,1	MPRIP	87	.	1	Substitution - Missense(1)	endometrium(1)	c.G1153A						PASS	.						76	66	69					17																	17049353		2203	4300	6503	SO:0001583	missense	23164	exon10			CAGCCCGACCTGC	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.1153G>A	chr17.hg19:g.17049353G>A	ENSP00000342379:p.Asp385Asn	80.0	0.0	.		114.0	35.0	.	NM_015134	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Missense_Mutation	SNP	ENST00000341712.4	hg19	CCDS32578.1	.	.	.	.	.	.	.	.	.	.	G	36	5.698781	0.96802	.	.	ENSG00000133030	ENST00000444976;ENST00000395811;ENST00000395804;ENST00000341712	T;T;T;T	0.26957	1.7;1.98;1.98;1.98	5.97	5.97	0.96955	Pleckstrin homology-type (1);	.	.	.	.	T	0.44623	0.1302	L	0.34521	1.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.28713	-1.0035	9	0.87932	D	0	.	20.428	0.99075	0.0:0.0:1.0:0.0	.	385;385	Q6WCQ1-2;Q6WCQ1	.;MPRIP_HUMAN	N	347;385;385;385	ENSP00000400189:D347N;ENSP00000379156:D385N;ENSP00000379149:D385N;ENSP00000342379:D385N	ENSP00000342379:D385N	D	+	1	0	MPRIP	16990078	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	9.184000	0.94893	2.837000	0.97791	0.655000	0.94253	GAC	.	.	.	none		0.547	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134		A	17049353	G	A	17049353	3	1	9	1	0	0	0	0	1	0	0	0	9750	1058	37	1	1191	1	MPRIP	17	17049353	Missense_Mutation	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10	9885319	17049353	64145857	101	726											
TSHZ1	10194	hgsc.bcm.edu	37	chr18	72999615	72999615	+	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	ccgctgagcgctttgcagtcCatcatgaacacccacctggg	8	8	10	15	2	1	2	1	2	0	0	2	2	2	2	4	1	3	3	4	1	1	1			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr18:72999615C>A	ENST00000580243.1	+	2	2601	c.2253C>A	c.(2251-2253)tcC>tcA	p.S751S	TSHZ1_ENST00000322038.5_Silent_p.S706S			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	751					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)		CTTTGCAGTCCATCATGAACA	0.572																																					p.S706S		Atlas-SNP	.											.	TSHZ1	104	.	0			c.C2118A						PASS	.						83	78	79					18																	72999615		2203	4300	6503	SO:0001819	synonymous_variant	10194	exon2			GCAGTCCATCATG	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.2253C>A	chr18.hg19:g.72999615C>A		91.0	0.0	.		63.0	24.0	.	NM_005786	O60534|Q4LE29|Q53EU4	Silent	SNP	ENST00000580243.1	hg19																																																																																				.	.	.	none		0.572	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786		A	72999615	C	A	72999615	2	1	9	1	0	0	0	0	0	0	0	1	16635	581	21	4		4	TSHZ1	18	72999615	Silent	SNP	C	TCGA-2Z-A9JD-01A-11D-A42J-10		72999615	5077633	102	727											
PODNL1	90379	hgsc.bcm.edu	37	chr19	14063934	14063934	+	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	1	0	0	0	0	0	0	0	0	gctgggagttccagtacctgGgtgggcctccccattgaaag	7	9	14	11	0	0	1	0	1	0	0	2	2	2	2	5	3	1	3	5	3	2	3			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr19:14063934G>T	ENST00000254337.6	+	1	153				PODNL1_ENST00000538517.2_Silent_p.T5T|PODNL1_ENST00000588317.1_5'UTR|PODNL1_ENST00000538371.2_Silent_p.T5T	NM_138353.2	NP_612362.2	Q66K64	DCA15_HUMAN	DDB1 and CUL4 associated factor 15						protein ubiquitination (GO:0016567)					breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)	11						CCAGTACCTGGGTGGGCCTCC	0.612																																					p.T5T		Atlas-SNP	.											.	PODNL1	27	.	0			c.C15A						PASS	.						49	47	47					19																	14063934		692	1591	2283	SO:0001627	intron_variant	79883	exon1			TACCTGGGTGGGC	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.132+478G>T	chr19.hg19:g.14063934G>T		84.0	0.0	.		58.0	17.0	.	NM_001146255	B3KS86|Q96DW0|Q9BU31	Silent	SNP	ENST00000254337.6	hg19	CCDS32926.1																																																																																			.	.	.	none		0.612	DCAF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458099.1	NM_138353		T	14063934	G	T	14063934	1	4	9	0	1	0	0	0	0	0	0	0	12186	1219	43	4		4	PODNL1	19	14063934	Intron	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10		14063934	45065049	103	728											
LPHN1	22859	hgsc.bcm.edu	37	chr19	14281546	14281546	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tacttgtaggtcccaggacaGgggtcaggaaaggcatccga	11	7	14	9	1	1	0	1	0	0	0	3	3	3	2	2	6	1	2	2	6	3	3	rs149098258		TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr19:14281546G>A	ENST00000340736.6	-	4	639	c.342C>T	c.(340-342)ccC>ccT	p.P114P	LPHN1_ENST00000361434.3_Silent_p.P114P|CTB-55O6.12_ENST00000592086.1_RNA|LPHN1_ENST00000591528.1_5'UTR|CTB-55O6.12_ENST00000588387.1_RNA	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	114	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						TCCCAGGACAGGGGTCAGGAA	0.567													G|||	1	0.000199681	8e-04	0	5008	,	,		19572	0		0	False		,,,				2504	0				p.P114P		Atlas-SNP	.											.	LPHN1	107	.	0			c.C342T						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	89	61	71		342,342	3.3	1	19	dbSNP_134	71	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	LPHN1	NM_001008701.2,NM_014921.4	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	114/1475,114/1470	14281546	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	22859	exon4			AGGACAGGGGTCA	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.342C>T	chr19.hg19:g.14281546G>A		104.0	0.0	.		91.0	43.0	.	NM_001008701	Q96IE7|Q9BU07|Q9HAR3	Silent	SNP	ENST00000340736.6	hg19	CCDS32928.1																																																																																			.	G|1.000;A|0.000	0.000	weak		0.567	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921		A	14281546	G	A	14281546	2	1	9	1	0	0	0	0	0	0	0	1	8922	987	35	2		2	LPHN1	19	14281546	Silent	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10	217612	14281546	44847437	104	729											
ZBTB32	27033	hgsc.bcm.edu	37	chr19	36205878	36205878	+	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	gagggctcgaggggacagggCtaaaaagccagatccaggcc	12	3	16	10	1	0	1	0	0	0	1	2	4	1	2	3	5	1	2	3	5	3	1			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr19:36205878C>T	ENST00000392197.2	+	3	668	c.350C>T	c.(349-351)gCt>gTt	p.A117V	ZBTB32_ENST00000262630.3_Missense_Mutation_p.A117V			Q9Y2Y4	ZBT32_HUMAN	zinc finger and BTB domain containing 32	117					DNA repair (GO:0006281)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cytokine production (GO:0001817)|T cell proliferation (GO:0042098)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(1)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	14	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GGGGACAGGGCTAAAAAGCCA	0.597																																					p.A117V		Atlas-SNP	.											.	ZBTB32	33	.	0			c.C350T						PASS	.						46	49	48					19																	36205878		2203	4300	6503	SO:0001583	missense	27033	exon2			ACAGGGCTAAAAA	AF130255	CCDS12471.1	19q13.1	2013-01-08			ENSG00000011590	ENSG00000011590		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16763	protein-coding gene	gene with protein product	"repressor of GATA"	605859				10572087	Standard	XM_005258739		Approved	TZFP, FAZF, FAXF, Rog, ZNF538	uc002oay.3	Q9Y2Y4	OTTHUMG00000048118	ENST00000392197.2:c.350C>T	chr19.hg19:g.36205878C>T	ENSP00000376035:p.Ala117Val	92.0	0.0	.		99.0	42.0	.	NM_014383	Q8WVP2	Missense_Mutation	SNP	ENST00000392197.2	hg19	CCDS12471.1	.	.	.	.	.	.	.	.	.	.	C	10.10	1.256716	0.22965	.	.	ENSG00000011590	ENST00000262630;ENST00000392197	T;T	0.09723	2.95;2.95	5.43	1.98	0.26296	BTB/POZ-like (1);	1.171210	0.06374	N	0.714002	T	0.08891	0.0220	L	0.27053	0.805	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.37957	-0.9683	10	0.52906	T	0.07	1.7382	6.4857	0.22087	0.317:0.5964:0.0:0.0867	.	117	Q9Y2Y4	ZBT32_HUMAN	V	117	ENSP00000262630:A117V;ENSP00000376035:A117V	ENSP00000262630:A117V	A	+	2	0	ZBTB32	40897718	0.000000	0.05858	0.001000	0.08648	0.081000	0.17604	0.161000	0.16481	0.292000	0.22492	0.655000	0.94253	GCT	.	.	.	none		0.597	ZBTB32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109491.3	NM_014383		T	36205878	C	T	36205878	3	4	9	1	0	0	0	0	1	0	0	0	17547	797	28	2	352	2	ZBTB32	19	36205878	Missense_Mutation	SNP	C	TCGA-2Z-A9JD-01A-11D-A42J-10	21924332	36205878	22923105	105	730											
SIPA1L3	23094	hgsc.bcm.edu	37	chr19	38684203	38684203	+	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	ccgcagaagggcctgcagcgGacgctgtcggacgagagcct	8	4	16	13	5	0	2	0	0	0	2	1	5	0	4	3	3	3	3	3	3	1	0			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr19:38684203G>C	ENST00000222345.6	+	18	5132	c.4623G>C	c.(4621-4623)cgG>cgC	p.R1541R		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	1541					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)			GCCTGCAGCGGACGCTGTCGG	0.687																																					p.R1541R		Atlas-SNP	.											.	SIPA1L3	150	.	0			c.G4623C						PASS	.						12	14	13					19																	38684203		2191	4288	6479	SO:0001819	synonymous_variant	23094	exon18			GCAGCGGACGCTG	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.4623G>C	chr19.hg19:g.38684203G>C		100.0	0.0	.		35.0	12.0	.	NM_015073	Q2TV87	Silent	SNP	ENST00000222345.6	hg19	CCDS33007.1																																																																																			.	.	.	none		0.687	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278		C	38684203	G	C	38684203	2	2	9	1	0	0	0	0	0	0	0	1	14344	1161	41	4		4	SIPA1L3	19	38684203	Silent	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10	2478325	38684203	20444780	106	731											
ATP1A3	478	hgsc.bcm.edu	37	chr19	42492528	42492528	+	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	0	0	0	0	0	0	0	0	0	ccactgacatcttgtgctctGtctgaggaacaggagtttgg	8	12	12	9	0	3	2	0	2	3	0	3	4	3	4	1	3	2	2	1	3	1	2			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr19:42492528G>C	ENST00000302102.5	-	3	245	c.95C>G	c.(94-96)aCa>aGa	p.T32R	ATP1A3_ENST00000543770.1_Splice_Site_p.T43R|ATP1A3_ENST00000545399.1_Splice_Site_p.T45R|ATP1A3_ENST00000468774.2_5'UTR|ATP1A3_ENST00000602133.1_Splice_Site_p.T2R	NM_152296.4	NP_689509.1	P13637	AT1A3_HUMAN	ATPase, Na+/K+ transporting, alpha 3 polypeptide	32					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						CTTGTGCTCTGTCTGAGGAAC	0.607																																					p.T45R		Atlas-SNP	.											.	ATP1A3	117	.	0			c.C134G						PASS	.						176	172	173					19																	42492528		2203	4300	6503	SO:0001630	splice_region_variant	478	exon3			TGCTCTGTCTGAG		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.94-1C>G	chr19.hg19:g.42492528G>C		73.0	0.0	.		42.0	15.0	.	NM_001256214	B7Z2T0|B7Z401|F5H6J6|Q16732|Q16735|Q969K5	Missense_Mutation	SNP	ENST00000302102.5	hg19	CCDS12594.1	.	.	.	.	.	.	.	.	.	.	G	19.23	3.787354	0.70337	.	.	ENSG00000105409	ENST00000302102;ENST00000441343;ENST00000545399;ENST00000368080;ENST00000543770;ENST00000448429	D;D;D;D	0.88046	-2.33;-2.33;-2.33;-2.33	4.62	4.62	0.57501	ATPase, P-type cation-transporter, N-terminal (1);	0.328937	0.27811	N	0.017754	T	0.77525	0.4143	N	0.08118	0	0.80722	D	1	B;B;B;B	0.32893	0.187;0.249;0.389;0.161	B;B;B;B	0.35114	0.091;0.091;0.196;0.042	T	0.80743	-0.1246	10	0.87932	D	0	.	15.4001	0.74834	0.0:0.0:1.0:0.0	.	45;43;32;32	B7Z2T0;F5H6J6;E9PC51;P13637	.;.;.;AT1A3_HUMAN	R	32;32;45;2;43;45	ENSP00000302397:T32R;ENSP00000411503:T32R;ENSP00000444688:T45R;ENSP00000437577:T43R	ENSP00000302397:T32R	T	-	2	0	ATP1A3	47184368	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.752000	0.68728	2.328000	0.79073	0.485000	0.47835	ACA	.	.	.	none		0.607	ATP1A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268107.1	NM_152296	Missense_Mutation	C	42492528	G	C	42492528	5	2	9	1	0	0	0	0	0	0	1	0	1130	1391	48	4	3030	4	ATP1A3	19	42492528	Splice_Site	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10	3808325	42492528	16636455	107	732											
RTN2	6253	hgsc.bcm.edu	37	chr19	45991773	45991773	+	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	gatggtgaatagaccaatcaCtcctgtgggtacagagatgg	12	9	13	7	0	1	3	1	1	0	2	2	5	2	3	2	3	1	1	2	3	4	2			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr19:45991773C>T	ENST00000245923.4	-	9	1688	c.1453G>A	c.(1453-1455)Gtg>Atg	p.V485M	RTN2_ENST00000590526.1_Missense_Mutation_p.V211M|PPM1N_ENST00000401705.1_5'Flank|RTN2_ENST00000430715.2_Missense_Mutation_p.V145M|RTN2_ENST00000344680.4_Missense_Mutation_p.V412M	NM_005619.4	NP_005610.1	O75298	RTN2_HUMAN	reticulon 2	485	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)		AGACCAATCACTCCTGTGGGT	0.577																																					p.V485M		Atlas-SNP	.											.	RTN2	45	.	0			c.G1453A						PASS	.						97	93	94					19																	45991773		2203	4300	6503	SO:0001583	missense	6253	exon9			CAATCACTCCTGT	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.1453G>A	chr19.hg19:g.45991773C>T	ENSP00000245923:p.Val485Met	83.0	0.0	.		85.0	7.0	.	NM_005619	O60509|Q7RTM6|Q7RTN1|Q7RTN2	Missense_Mutation	SNP	ENST00000245923.4	hg19	CCDS12665.1	.	.	.	.	.	.	.	.	.	.	C	18.63	3.665718	0.67700	.	.	ENSG00000125744	ENST00000344680;ENST00000245923;ENST00000430715	T;T;T	0.53857	0.6;0.6;0.6	5.45	5.45	0.79879	.	0.061059	0.64402	D	0.000004	T	0.72614	0.3482	M	0.77103	2.36	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.87578	0.982;0.998	T	0.74575	-0.3620	10	0.54805	T	0.06	-8.7254	14.8394	0.70212	0.0:1.0:0.0:0.0	.	412;485	O75298-2;O75298	.;RTN2_HUMAN	M	412;485;145	ENSP00000345127:V412M;ENSP00000245923:V485M;ENSP00000398178:V145M	ENSP00000245923:V485M	V	-	1	0	RTN2	50683613	1.000000	0.71417	1.000000	0.80357	0.487000	0.33371	3.022000	0.49659	2.580000	0.87095	0.555000	0.69702	GTG	.	.	.	none		0.577	RTN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459574.1	NM_005619		T	45991773	C	T	45991773	3	4	9	1	0	0	0	0	1	0	0	0	13739	565	20	2	196	2	RTN2	19	45991773	Missense_Mutation	SNP	C	TCGA-2Z-A9JD-01A-11D-A42J-10	3499245	45991773	13137210	108	733											
GRIN2D	2906	hgsc.bcm.edu	37	chr19	48945411	48945411	+	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	gaccgcccctccctagatgaGatcgagatgctggagcggct	8	7	13	13	3	0	3	0	1	0	3	2	7	1	4	4	2	2	2	4	2	1	1			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr19:48945411G>C	ENST00000263269.3	+	12	2533	c.2445G>C	c.(2443-2445)gaG>gaC	p.E815D		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	815					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)	CCCTAGATGAGATCGAGATGC	0.562																																					p.E815D		Atlas-SNP	.											.	GRIN2D	76	.	0			c.G2445C						PASS	.						105	103	104					19																	48945411		2203	4300	6503	SO:0001583	missense	2906	exon12			AGATGAGATCGAG	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.2445G>C	chr19.hg19:g.48945411G>C	ENSP00000263269:p.Glu815Asp	77.0	0.0	.		45.0	14.0	.	NM_000836		Missense_Mutation	SNP	ENST00000263269.3	hg19	CCDS12719.1	.	.	.	.	.	.	.	.	.	.	G	11.42	1.633555	0.29068	.	.	ENSG00000105464	ENST00000263269	T	0.32023	1.47	4.5	0.644	0.17776	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.000000	0.85682	D	0.000000	T	0.17492	0.0420	N	0.25825	0.765	0.40143	D	0.976859	B	0.16166	0.016	B	0.15052	0.012	T	0.06552	-1.0820	10	0.33940	T	0.23	.	6.9597	0.24590	0.1793:0.1404:0.6803:0.0	.	815	O15399	NMDE4_HUMAN	D	815	ENSP00000263269:E815D	ENSP00000263269:E815D	E	+	3	2	GRIN2D	53637223	1.000000	0.71417	1.000000	0.80357	0.771000	0.43674	0.723000	0.25939	0.146000	0.19002	0.456000	0.33151	GAG	.	.	.	none		0.562	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1			C	48945411	G	C	48945411	3	2	9	1	0	0	0	0	1	0	0	0	6789	933	33	4	2487	4	GRIN2D	19	48945411	Missense_Mutation	SNP	G	TCGA-2Z-A9JD-01A-11D-A42J-10	2953638	48945411	10183572	109	734											
RIPK4	54101	hgsc.bcm.edu	37	chr21	43164161	43164161	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggacgatggcagcttggacTcagaggagctgcggctgagc	8	6	17	10	3	1	2	1	1	0	1	1	6	1	5	0	5	4	4	0	5	0	1			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chr21:43164161T>C	ENST00000352483.2	-	8	1284	c.1220A>G	c.(1219-1221)gAg>gGg	p.E407G	RIPK4_ENST00000542057.1_Missense_Mutation_p.E296G|AP001615.9_ENST00000423276.1_RNA|RIPK4_ENST00000332512.3_Missense_Mutation_p.E359G|RIPK4_ENST00000544709.1_Missense_Mutation_p.E296G			P57078	RIPK4_HUMAN	receptor-interacting serine-threonine kinase 4	407					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						CAGCTTGGACTCAGAGGAGCT	0.617																																					p.E359G		Atlas-SNP	.											.	RIPK4	151	.	0			c.A1076G						PASS	.						38	40	40					21																	43164161		2203	4300	6503	SO:0001583	missense	54101	exon7			TTGGACTCAGAGG	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.1220A>G	chr21.hg19:g.43164161T>C	ENSP00000330161:p.Glu407Gly	98.0	0.0	.		70.0	28.0	.	NM_020639	Q96KH0	Missense_Mutation	SNP	ENST00000352483.2	hg19		.	.	.	.	.	.	.	.	.	.	T	19.83	3.899939	0.72754	.	.	ENSG00000183421	ENST00000332512;ENST00000352483;ENST00000544709;ENST00000542057;ENST00000330470	T;T;T;T	0.78707	-0.96;-1.03;-1.2;-1.2	5.12	3.96	0.45880	.	0.000000	0.64402	D	0.000007	T	0.75019	0.3793	N	0.08118	0	0.46061	D	0.998849	D	0.89917	1.0	D	0.80764	0.994	T	0.78056	-0.2353	10	0.66056	D	0.02	-32.5994	11.4902	0.50377	0.0:0.0:0.1505:0.8495	.	359	P57078-2	.	G	359;407;296;296;98	ENSP00000332454:E359G;ENSP00000330161:E407G;ENSP00000441754:E296G;ENSP00000442901:E296G	ENSP00000330975:E98G	E	-	2	0	RIPK4	42037230	1.000000	0.71417	0.455000	0.27031	0.995000	0.86356	3.720000	0.54933	0.777000	0.33496	0.533000	0.62120	GAG	.	.	.	none		0.617	RIPK4-201	KNOWN	basic	protein_coding	protein_coding		NM_020639		C	43164161	T	C	43164161	3	2	9	1	0	0	0	0	1	0	0	0	13396	1551	54	3	1286	3	RIPK4	21	43164161	Missense_Mutation	SNP	T	TCGA-2Z-A9JD-01A-11D-A42J-10		43164161	4965734	110	735											
SLITRK4	139065	hgsc.bcm.edu	37	chrX	142718226	142718226	+	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	gcttctcctatgtaaatgttAtatggcatgttctccagcca	9	15	7	10	0	2	0	0	0	2	0	4	0	2	0	3	1	1	5	3	1	5	6			TCGA-2Z-A9JD-01A-11D-A42J-10	TCGA-2Z-A9JD-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d0c6a1f3-cb7d-4abc-b7be-b60b373335bb	edf87796-76e3-4a71-8bb0-cb01677c6e77	g.chrX:142718226A>C	ENST00000381779.4	-	2	924	c.699T>G	c.(697-699)taT>taG	p.Y233*	SLITRK4_ENST00000356928.1_Nonsense_Mutation_p.Y233*|SLITRK4_ENST00000338017.4_Nonsense_Mutation_p.Y233*	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	233	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)					TGTAAATGTTATATGGCATGT	0.423																																					p.Y233X		Atlas-SNP	.											.	SLITRK4	162	.	0			c.T699G						PASS	.						82	76	78					X																	142718226		2203	4300	6503	SO:0001587	stop_gained	139065	exon2			AATGTTATATGGC	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.699T>G	chrX.hg19:g.142718226A>C	ENSP00000371198:p.Tyr233*	107.0	0.0	.		101.0	78.0	.	NM_001184750	Q5JXG3|Q8TCM8|Q96DL3	Nonsense_Mutation	SNP	ENST00000381779.4	hg19	CCDS14679.1	.	.	.	.	.	.	.	.	.	.	A	36	5.612265	0.96637	.	.	ENSG00000179542	ENST00000381779;ENST00000356928;ENST00000338017	.	.	.	5.73	4.57	0.56435	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.24483	T	0.36	-9.3393	9.7669	0.40565	0.918:0.0:0.082:0.0	.	.	.	.	X	233	.	ENSP00000336627:Y233X	Y	-	3	2	SLITRK4	142545892	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	2.982000	0.49337	0.803000	0.34113	-0.323000	0.08544	TAT	.	.	.	none		0.423	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078		C	142718226	A	C	142718226	4	2	9	1	0	0	0	0	0	1	0	0	14758	456	16	5	1818	5	SLITRK4	23	142718226	Nonsense_Mutation	SNP	A	TCGA-2Z-A9JD-01A-11D-A42J-10		142718226	12552334	111	736											
CAMTA1	23261	hgsc.bcm.edu	37	chr1	7811258	7811258	+	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	ttgttcttgtttcccctgcaGtacgcactttataaaaagat	10	16	6	9	1	1	1	0	0	1	1	2	1	2	1	2	0	2	5	2	0	5	8			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr1:7811258G>T	ENST00000303635.7	+	20	4896		c.e20-1		CAMTA1_ENST00000439411.2_Splice_Site|CAMTA1_ENST00000476864.1_Splice_Site	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1						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)		TTCCCCTGCAGTACGCACTTT	0.483			T	WWTR1	epitheliod hemangioendothelioma																																.		Atlas-SNP	.		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	.	CAMTA1	226	.	0			c.4690-1G>T						PASS	.						191	204	200					1																	7811258		2203	4300	6503	SO:0001630	splice_region_variant	23261	exon20			CCTGCAGTACGCA	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.4690-1G>T	chr1.hg19:g.7811258G>T		99.0	0.0	.		92.0	6.0	.	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Splice_Site	SNP	ENST00000303635.7	hg19	CCDS30576.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.759921	0.89932	.	.	ENSG00000171735	ENST00000303635;ENST00000439411;ENST00000414738;ENST00000303646;ENST00000495233;ENST00000490905;ENST00000476864	.	.	.	5.65	5.65	0.86999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.7272	0.96168	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CAMTA1	7733845	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.869000	0.99810	2.646000	0.89796	0.655000	0.94253	.	.	.	.	none		0.483	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215	Intron	T	7811258	G	T	7811258	5	4	10	1	0	0	0	0	0	0	1	0	2615	1043	36	4	4767	4	CAMTA1	1	7811258	Splice_Site	SNP	G	TCGA-2Z-A9JE-01A-11D-A42J-10		7811258	241439363	1	737											
MFN2	9927	hgsc.bcm.edu	37	chr1	12067259	12067260	+	Frame_Shift_Del	DEL	GC	GC	-																															catgccagcgagaagctgcaGcttgtcatcagctacactgg																								rs531748892		TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr1:12067259_12067260delGC	ENST00000235329.5	+	17	2344_2345	c.2022_2023delGC	c.(2020-2025)cagcttfs	p.QL674fs	MFN2_ENST00000444836.1_Frame_Shift_Del_p.QL674fs	NM_014874.3	NP_055689.1	O95140	MFN2_HUMAN	mitofusin 2	674					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)		AGAAGCTGCAGCTTGTCATCAG	0.604																																					p.674_674del		Atlas-INDEL	.											.	MFN2	83	.	0			c.2021_2022del						PASS	.																																			SO:0001589	frameshift_variant	9927	exon17			.	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.2022_2023delGC	chr1.hg19:g.12067259_12067260delGC	ENSP00000235329:p.Gln674fs	171.0	0.0	0		138.0	57.0	0.413043	NM_014874	A8K1B3|O95572|Q5JXC3|Q5JXC4|Q9H131|Q9NSX8	Frame_Shift_Del	DEL	ENST00000235329.5	hg19	CCDS30587.1																																																																																			.	.	.	none		0.604	MFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006859.2	NM_014874		-	12067260	GC	-	12067259	7	5	10	1	0	1	0	1	0	0	0	0	9531	962	34	0	2080	0	MFN2	1	12067259	Frame_Shift_Del	DEL	GC	TCGA-2Z-A9JE-01A-11D-A42J-10	4256001	12067259	237183362	2	738	6	2									
MFN2	9927	hgsc.bcm.edu	37	chr1	12067262	12067262	+	Silent	SNP	T	T	A																															gccagcgagaagctgcagctTgtcatcagctacactggctc																										TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr1:12067262T>A	ENST00000235329.5	+	17	2347	c.2025T>A	c.(2023-2025)ctT>ctA	p.L675L	MFN2_ENST00000444836.1_Silent_p.L675L	NM_014874.3	NP_055689.1	O95140	MFN2_HUMAN	mitofusin 2	675					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)		AGCTGCAGCTTGTCATCAGCT	0.607																																					p.L675L		Atlas-SNP	.											.	MFN2	83	.	0			c.T2025A						PASS	.						54	48	50					1																	12067262		2203	4300	6503	SO:0001819	synonymous_variant	9927	exon17			GCAGCTTGTCATC	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.2025T>A	chr1.hg19:g.12067262T>A		177.0	0.0	.		139.0	57.0	.	NM_014874	A8K1B3|O95572|Q5JXC3|Q5JXC4|Q9H131|Q9NSX8	Silent	SNP	ENST00000235329.5	hg19	CCDS30587.1																																																																																			.	.	.	none		0.607	MFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006859.2	NM_014874		A	12067262	T	A	12067262	2	1	10	1	0	0	0	0	0	0	0	1	9531	1799	63	5		5	MFN2	1	12067262	Silent	SNP	T	TCGA-2Z-A9JE-01A-11D-A42J-10	3	12067262	237183359	3	739	6	2									
TNFRSF1B	7133	hgsc.bcm.edu	37	chr1	12254074	12254074	+	Missense_Mutation	SNP	A	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	gagtggtgaactgtgtcatcAtgacccaggtgaaaagtaag	13	9	13	6	0	2	3	2	3	0	0	2	4	2	3	1	2	1	1	1	2	4	1			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr1:12254074A>C	ENST00000376259.3	+	7	939	c.850A>C	c.(850-852)Atg>Ctg	p.M284L	TNFRSF1B_ENST00000492361.1_3'UTR|MIR4632_ENST00000584158.1_RNA	NM_001066.2	NP_001057.1	P20333	TNR1B_HUMAN	tumor necrosis factor receptor superfamily, member 1B	284					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)	CTGTGTCATCATGACCCAGGT	0.483																																					p.M284L		Atlas-SNP	.											.	TNFRSF1B	28	.	0			c.A850C						PASS	.						204	191	195					1																	12254074		2203	4300	6503	SO:0001583	missense	7133	exon7			GTCATCATGACCC	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.850A>C	chr1.hg19:g.12254074A>C	ENSP00000365435:p.Met284Leu	130.0	0.0	.		92.0	42.0	.	NM_001066	B1AJZ3|Q16042|Q6YI29|Q9UIH1	Missense_Mutation	SNP	ENST00000376259.3	hg19	CCDS145.1	.	.	.	.	.	.	.	.	.	.	A	0.009	-1.854484	0.00558	.	.	ENSG00000028137	ENST00000376259	D	0.84800	-1.9	4.12	-8.25	0.01025	.	3.614700	0.00710	N	0.000824	T	0.72518	0.3470	L	0.36672	1.1	0.20403	N	0.999903	B	0.02656	0.0	B	0.01281	0.0	T	0.62863	-0.6764	10	0.10636	T	0.68	-4.0556	5.32	0.15876	0.1423:0.3801:0.3863:0.0912	.	284	P20333	TNR1B_HUMAN	L	284	ENSP00000365435:M284L	ENSP00000365435:M284L	M	+	1	0	TNFRSF1B	12176661	0.001000	0.12720	0.085000	0.20634	0.704000	0.40688	-2.970000	0.00668	-2.877000	0.00320	-0.290000	0.09829	ATG	.	.	.	none		0.483	TNFRSF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005133.1	NM_001066		C	12254074	A	C	12254074	3	2	10	1	0	0	0	0	1	0	0	0	16306	217	8	5	876	5	TNFRSF1B	1	12254074	Missense_Mutation	SNP	A	TCGA-2Z-A9JE-01A-11D-A42J-10	186812	12254074	236996547	4	740											
UBR4	23352	hgsc.bcm.edu	37	chr1	19430633	19430633	+	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	tcctgcgtctcatcgatcagCttggtcctctgcaccaccag	6	11	8	16	2	3	0	2	0	2	0	7	1	5	0	4	1	3	2	4	1	0	1			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr1:19430633C>A	ENST00000375254.3	-	87	12873	c.12846G>T	c.(12844-12846)aaG>aaT	p.K4282N	UBR4_ENST00000543981.1_5'Flank|UBR4_ENST00000375217.2_Missense_Mutation_p.K4275N|UBR4_ENST00000375267.2_Missense_Mutation_p.K4282N|UBR4_ENST00000375224.1_5'UTR|UBR4_ENST00000375226.2_Missense_Mutation_p.K4258N	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	4282					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)		CATCGATCAGCTTGGTCCTCT	0.537																																					p.K4282N		Atlas-SNP	.											.	UBR4	415	.	0			c.G12846T						PASS	.						149	121	131					1																	19430633		2203	4300	6503	SO:0001583	missense	23352	exon87			GATCAGCTTGGTC	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.12846G>T	chr1.hg19:g.19430633C>A	ENSP00000364403:p.Lys4282Asn	98.0	0.0	.		121.0	68.0	.	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	hg19	CCDS189.1	.	.	.	.	.	.	.	.	.	.	C	18.64	3.668267	0.67814	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226	T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16	5.38	2.51	0.30379	.	0.098404	0.64402	D	0.000002	T	0.66177	0.2763	L	0.41415	1.275	0.80722	D	1	D	0.57899	0.981	D	0.67231	0.95	T	0.62685	-0.6802	10	0.48119	T	0.1	.	8.5074	0.33195	0.0:0.7562:0.0:0.2438	.	4282	Q5T4S7	UBR4_HUMAN	N	4282;4282;4275;4258	ENSP00000364403:K4282N;ENSP00000364416:K4282N;ENSP00000364365:K4275N;ENSP00000364374:K4258N	ENSP00000364365:K4275N	K	-	3	2	UBR4	19303220	0.996000	0.38824	1.000000	0.80357	0.880000	0.50808	0.488000	0.22371	0.405000	0.25532	0.655000	0.94253	AAG	.	.	.	none		0.537	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		A	19430633	C	A	19430633	3	1	10	1	0	0	0	0	1	0	0	0	16916	796	28	4	2785	4	UBR4	1	19430633	Missense_Mutation	SNP	C	TCGA-2Z-A9JE-01A-11D-A42J-10	7176559	19430633	229819988	5	741											
PUM1	9698	hgsc.bcm.edu	37	chr1	31452956	31452956	+	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	ctgtgtaggggtccgtccctGggggagcagcgctgatgatg	5	9	18	9	2	0	2	0	2	0	0	2	3	2	3	2	4	2	3	2	4	1	1			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr1:31452956G>T	ENST00000257075.5	-	9	1400	c.1307C>A	c.(1306-1308)cCa>cAa	p.P436Q	PUM1_ENST00000373741.4_Missense_Mutation_p.P472Q|PUM1_ENST00000440538.2_Missense_Mutation_p.P437Q|PUM1_ENST00000426105.2_Missense_Mutation_p.P436Q|PUM1_ENST00000373742.2_Missense_Mutation_p.P377Q|PUM1_ENST00000373747.3_Missense_Mutation_p.P437Q|PUM1_ENST00000490546.1_5'UTR|PUM1_ENST00000423018.2_Missense_Mutation_p.P340Q|PUM1_ENST00000424085.2_Missense_Mutation_p.P194Q	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	436	Ala-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)		GTCCGTCCCTGGGGGAGCAGC	0.498																																					p.P436Q		Atlas-SNP	.											.	PUM1	107	.	0			c.C1307A						PASS	.						60	55	57					1																	31452956		2203	4300	6503	SO:0001583	missense	9698	exon9			GTCCCTGGGGGAG	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.1307C>A	chr1.hg19:g.31452956G>T	ENSP00000257075:p.Pro436Gln	79.0	0.0	.		71.0	26.0	.	NM_014676	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Missense_Mutation	SNP	ENST00000257075.5	hg19	CCDS338.1	.	.	.	.	.	.	.	.	.	.	G	35	5.426313	0.96131	.	.	ENSG00000134644	ENST00000424085;ENST00000257075;ENST00000373747;ENST00000373749;ENST00000426105;ENST00000440538;ENST00000373741;ENST00000423018;ENST00000373742;ENST00000543952	T;T;T;T;T;T;T;T	0.18810	2.26;2.19;2.47;2.48;2.42;2.46;2.4;2.22	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.47820	0.1466	M	0.66939	2.045	0.80722	D	1	D;D;D;D;D;D;D;D	0.76494	0.998;0.998;0.996;0.999;0.993;0.996;0.993;0.996	D;D;D;D;P;P;P;P	0.83275	0.927;0.991;0.927;0.996;0.878;0.878;0.878;0.878	T	0.28808	-1.0032	10	0.48119	T	0.1	-6.3805	19.8328	0.96642	0.0:0.0:1.0:0.0	.	377;340;472;437;436;436;437;436	B4DG92;E7EWT3;Q5T1Z8;Q14671-2;Q14671;E9PCJ0;Q5T1Z4;Q53HH5	.;.;.;.;PUM1_HUMAN;.;.;.	Q	194;436;437;174;436;437;472;340;377;436	ENSP00000400141:P194Q;ENSP00000257075:P436Q;ENSP00000362852:P437Q;ENSP00000391723:P436Q;ENSP00000401777:P437Q;ENSP00000362846:P472Q;ENSP00000399440:P340Q;ENSP00000362847:P377Q	ENSP00000257075:P436Q	P	-	2	0	PUM1	31225543	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.785000	0.99042	2.758000	0.94735	0.591000	0.81541	CCA	.	.	.	none		0.498	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1			T	31452956	G	T	31452956	3	4	10	1	0	0	0	0	1	0	0	0	12838	1348	47	4	2315	4	PUM1	1	31452956	Missense_Mutation	SNP	G	TCGA-2Z-A9JE-01A-11D-A42J-10	12022323	31452956	217797665	6	742											
NASP	4678	hgsc.bcm.edu	37	chr1	46073205	46073206	+	Frame_Shift_Ins	INS	-	-	A																															gactctagattggttaactgINSaaacctctgaagaggcaaaa																										TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr1:46073205_46073206insA	ENST00000350030.3	+	6	709_710	c.622_623insA	c.(622-624)gaafs	p.E208fs	NASP_ENST00000537798.1_Frame_Shift_Ins_p.E144fs|NASP_ENST00000351223.3_Intron|NASP_ENST00000402363.3_Frame_Shift_Ins_p.E210fs|NASP_ENST00000372052.4_Intron	NM_002482.3	NP_002473.2	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein (histone-binding)	208	Glu-rich (acidic).				blastocyst development (GO:0001824)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone exchange (GO:0043486)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	Hsp90 protein binding (GO:0051879)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	17	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)					TTGGTTAACTGAAACCTCTGAA	0.465																																					p.E208fs		Atlas-Indel,Pindel	.											.	NASP	77	.	0			c.622_623insA						PASS	.																																			SO:0001589	frameshift_variant	4678	exon6			.	M97856	CCDS524.1, CCDS525.1, CCDS55597.1	1p34.1	2013-01-10			ENSG00000132780	ENSG00000132780		"Tetratricopeptide (TTC) repeat domain containing"	7644	protein-coding gene	gene with protein product		603185				1426632	Standard	NM_002482		Approved	FLB7527, FLJ31599, FLJ35510, MGC19722, MGC20372, MGC2297, DKFZp547F162, PRO1999	uc001coi.2	P49321	OTTHUMG00000007826	ENST00000350030.3:c.625dupA	chr1.hg19:g.46073208_46073208dupA	ENSP00000255120:p.Glu208fs	207.0	0.0	0		210.0	104.0	0.495238	NM_002482	A8K6H2|B4DQP3|D3DQ07|F5H3J2|Q53GW5|Q5T622|Q5T625|Q96A69|Q9BTW2	Frame_Shift_Ins	INS	ENST00000350030.3	hg19	CCDS524.1																																																																																			.	.	.	none		0.465	NASP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021533.2	NM_002482		A	46073206	-	A	46073205	7	5	10	1	0	1	1	0	0	0	0	0	10179	1291	45	0	721	0	NASP	1	46073205	Frame_Shift_Ins	INS	-	TCGA-2Z-A9JE-01A-11D-A42J-10	14620249	46073205	203177416	7	743											
TTC4	7268	hgsc.bcm.edu	37	chr1	55197174	55197174	+	Frame_Shift_Del	DEL	C	C	-																															cccaggctaggaatatcaggCtctcagaagctgcctgtgag																										TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr1:55197174delC	ENST00000371281.3	+	7	784	c.697delC	c.(697-699)ctcfs	p.L233fs	MROH7-TTC4_ENST00000414150.2_3'UTR|TTC4_ENST00000371284.5_3'UTR	NM_004623.4	NP_004614.3	O95801	TTC4_HUMAN	tetratricopeptide repeat domain 4	233										breast(2)|endometrium(3)|kidney(1)|lung(2)|stomach(1)	9						GAATATCAGGCTCTCAGAAGC	0.468																																					p.R232fs		Atlas-Indel,Pindel	.											.	TTC4	21	.	0			c.696delG						PASS	.						56	51	53					1																	55197174		2203	4300	6503	SO:0001589	frameshift_variant	7268	exon7			.		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.697delC	chr1.hg19:g.55197174delC	ENSP00000360329:p.Leu233fs	51.0	0.0	0		56.0	23.0	0.410714	NM_004623	Q53Y95|Q5TA96|Q9H3I2	Frame_Shift_Del	DEL	ENST00000371281.3	hg19	CCDS596.1																																																																																			.	.	.	none		0.468	TTC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027432.1	NM_004623		-	55197174	C	-	55197174	7	5	10	1	0	1	0	1	0	0	0	0	16722	797	28	0	723	0	TTC4	1	55197174	Frame_Shift_Del	DEL	C	TCGA-2Z-A9JE-01A-11D-A42J-10	9123969	55197174	194053447	8	744											
C8A	731	hgsc.bcm.edu	37	chr1	57383327	57383327	+	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	ggagaagagagtgtgacaatCcagcacctcagaatggaggg	14	5	15	7	0	1	4	1	1	0	3	2	7	2	5	2	3	1	1	2	3	3	0			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr1:57383327C>T	ENST00000361249.3	+	11	1789	c.1693C>T	c.(1693-1695)Cca>Tca	p.P565S		NM_000562.2	NP_000553.1	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	565	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	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						GTGTGACAATCCAGCACCTCA	0.582																																					p.P565S		Atlas-SNP	.											.	C8A	103	.	0			c.C1693T						PASS	.						68	66	67					1																	57383327		2203	4300	6503	SO:0001583	missense	731	exon11			GACAATCCAGCAC	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.1693C>T	chr1.hg19:g.57383327C>T	ENSP00000354458:p.Pro565Ser	253.0	0.0	.		260.0	125.0	.	NM_000562	A2RUI4|A2RUI5|Q13668|Q9H130	Missense_Mutation	SNP	ENST00000361249.3	hg19	CCDS606.1	.	.	.	.	.	.	.	.	.	.	C	15.72	2.917645	0.52546	.	.	ENSG00000157131	ENST00000361249	T	0.54479	0.57	4.82	4.82	0.62117	.	0.099528	0.64402	D	0.000001	T	0.78941	0.4363	M	0.92649	3.33	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.84585	0.0663	10	0.87932	D	0	-13.7116	16.2551	0.82510	0.0:1.0:0.0:0.0	.	565	P07357	CO8A_HUMAN	S	565	ENSP00000354458:P565S	ENSP00000354458:P565S	P	+	1	0	C8A	57155915	1.000000	0.71417	0.397000	0.26308	0.211000	0.24417	5.614000	0.67695	2.487000	0.83934	0.563000	0.77884	CCA	.	.	.	none		0.582	C8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022890.1	NM_000562		T	57383327	C	T	57383327	3	4	10	1	0	0	0	0	1	0	0	0	2418	855	30	2	1735	2	C8A	1	57383327	Missense_Mutation	SNP	C	TCGA-2Z-A9JE-01A-11D-A42J-10	2186153	57383327	191867294	9	745											
HAPLN2	60484	hgsc.bcm.edu	37	chr1	156594250	156594250	+	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	gcctggccacctactcccagCtctaccagggtgagcggccg	6	6	12	17	2	1	1	0	1	1	0	2	1	2	1	6	3	4	1	6	3	2	2			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr1:156594250C>G	ENST00000255039.1	+	5	954	c.547C>G	c.(547-549)Ctc>Gtc	p.L183V	HAPLN2_ENST00000494218.1_3'UTR	NM_021817.2	NP_068589.1	Q9GZV7	HPLN2_HUMAN	hyaluronan and proteoglycan link protein 2	183	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323}.				cell adhesion (GO:0007155)|establishment of blood-nerve barrier (GO:0008065)|extracellular matrix assembly (GO:0085029)	proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			NS(1)|endometrium(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(1)	7	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CTACTCCCAGCTCTACCAGGG	0.672																																					p.L183V		Atlas-SNP	.											.	HAPLN2	20	.	0			c.C547G						PASS	.						23	23	23					1																	156594250		2202	4300	6502	SO:0001583	missense	60484	exon5			TCCCAGCTCTACC	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.547C>G	chr1.hg19:g.156594250C>G	ENSP00000255039:p.Leu183Val	201.0	0.0	.		145.0	56.0	.	NM_021817	Q5T3J0	Missense_Mutation	SNP	ENST00000255039.1	hg19	CCDS1148.1	.	.	.	.	.	.	.	.	.	.	C	14.28	2.488481	0.44249	.	.	ENSG00000132702	ENST00000255039;ENST00000544775;ENST00000456112	T;T	0.12879	2.64;2.64	4.15	3.23	0.37069	C-type lectin fold (1);Link (4);C-type lectin-like (1);	0.000000	0.85682	D	0.000000	T	0.30603	0.0770	M	0.89414	3.03	0.52501	D	0.99995	D	0.89917	1.0	D	0.91635	0.999	T	0.27262	-1.0079	10	0.87932	D	0	-16.7817	10.9343	0.47237	0.0:0.9065:0.0:0.0935	.	183	Q9GZV7	HPLN2_HUMAN	V	183;156;183	ENSP00000255039:L183V;ENSP00000388835:L183V	ENSP00000255039:L183V	L	+	1	0	HAPLN2	154860874	1.000000	0.71417	1.000000	0.80357	0.028000	0.11728	5.552000	0.67281	1.100000	0.41517	-0.136000	0.14681	CTC	.	.	.	none		0.672	HAPLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081039.1	NM_021817		G	156594250	C	G	156594250	3	3	10	1	0	0	0	0	1	0	0	0	6962	797	28	4	557	4	HAPLN2	1	156594250	Missense_Mutation	SNP	C	TCGA-2Z-A9JE-01A-11D-A42J-10	99210923	156594250	92656371	10	746											
ATP1A2	477	hgsc.bcm.edu	37	chr1	160104412	160104412	+	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	tgagtcaagtcaaccccaggTgaggcctctgcaggaagccc	10	6	12	13	0	3	2	2	2	1	0	3	3	3	3	4	3	3	1	4	3	3	0			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr1:160104412T>G	ENST00000361216.3	+	14	2053		c.e14+2		ATP1A2_ENST00000392233.3_Splice_Site	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide						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)			CAACCCCAGGTGAGGCCTCTG	0.557																																					.		Atlas-SNP	.											.	ATP1A2	167	.	0			c.1964+2T>G						PASS	.						97	81	87					1																	160104412		2203	4300	6503	SO:0001630	splice_region_variant	477	exon14			CCCAGGTGAGGCC	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.1964+2T>G	chr1.hg19:g.160104412T>G		90.0	0.0	.		111.0	53.0	.	NM_000702	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Splice_Site	SNP	ENST00000361216.3	hg19	CCDS1196.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.037149	0.75617	.	.	ENSG00000018625	ENST00000361216;ENST00000392233;ENST00000447527;ENST00000435866	.	.	.	5.0	5.0	0.66597	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.994	0.64386	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ATP1A2	158371036	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	7.802000	0.85969	1.997000	0.58415	0.459000	0.35465	.	.	.	.	none		0.557	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702	Intron	G	160104412	T	G	160104412	5	3	10	1	0	0	0	0	0	0	1	0	1129	1710	59	5	2020	5	ATP1A2	1	160104412	Splice_Site	SNP	T	TCGA-2Z-A9JE-01A-11D-A42J-10	3510162	160104412	89146209	11	747											
NEK2	4751	hgsc.bcm.edu	37	chr1	211846908	211846908	+	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	tctagctagcccaaagtctcCaagcttgacgttttgcttgc	8	13	8	12	1	2	1	0	1	2	0	3	1	2	1	2	0	5	4	2	0	4	6			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr1:211846908C>A	ENST00000366999.4	-	3	610	c.472G>T	c.(472-474)Gga>Tga	p.G158*	NEK2_ENST00000540251.1_Nonsense_Mutation_p.G115*|NEK2_ENST00000366998.3_Nonsense_Mutation_p.G158*|NEK2_ENST00000462283.1_5'Flank|RP11-122M14.1_ENST00000415202.1_RNA	NM_002497.3	NP_002488.1	P51955	NEK2_HUMAN	NIMA-related kinase 2	158	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blastocyst development (GO:0001824)|centrosome separation (GO:0051299)|chromosome segregation (GO:0007059)|G2/M transition of mitotic cell cycle (GO:0000086)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of centriole-centriole cohesion (GO:1903126)|negative regulation of DNA binding (GO:0043392)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of mitosis (GO:0007088)|regulation of mitotic centrosome separation (GO:0046602)|spindle assembly (GO:0051225)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|microtubule (GO:0005874)|midbody (GO:0030496)|nucleus (GO:0005634)|protein complex (GO:0043234)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|stomach(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.00203)|all cancers(67;0.0339)|Epithelial(68;0.0546)		CCAAAGTCTCCAAGCTTGACG	0.423																																					p.G158X		Atlas-SNP	.											.	NEK2	49	.	0			c.G472T						PASS	.						103	101	101					1																	211846908		2203	4300	6503	SO:0001587	stop_gained	4751	exon3			AGTCTCCAAGCTT	U11050	CCDS1500.1, CCDS55682.1, CCDS73024.1	1q32.3	2014-06-12	2012-11-15		ENSG00000117650	ENSG00000117650			7745	protein-coding gene	gene with protein product	"HsPK 21", "protein phosphatase 1, regulatory subunit 111"	604043	"NIMA (never in mitosis gene a)-related kinase 2"			8274451, 24043777	Standard	NM_002497		Approved	NLK1, NEK2A, RP67, PPP1R111	uc001hir.2	P51955	OTTHUMG00000037121	ENST00000366999.4:c.472G>T	chr1.hg19:g.211846908C>A	ENSP00000355966:p.Gly158*	117.0	0.0	.		92.0	33.0	.	NM_002497	Q53FD6|Q5I1Z9|Q5VXZ1|Q6NZX8|Q7Z634|Q86XH2|Q96QN9	Nonsense_Mutation	SNP	ENST00000366999.4	hg19	CCDS1500.1	.	.	.	.	.	.	.	.	.	.	C	39	7.512866	0.98329	.	.	ENSG00000117650	ENST00000366999;ENST00000540251;ENST00000366998	.	.	.	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.1585	0.93522	0.0:1.0:0.0:0.0	.	.	.	.	X	158;115;158	.	ENSP00000355965:G158X	G	-	1	0	NEK2	209913531	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.438000	0.80431	2.591000	0.87537	0.563000	0.77884	GGA	.	.	.	none		0.423	NEK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090154.1	NM_002497		A	211846908	C	A	211846908	4	1	10	1	0	0	0	0	0	1	0	0	10331	603	21	4	889	4	NEK2	1	211846908	Nonsense_Mutation	SNP	C	TCGA-2Z-A9JE-01A-11D-A42J-10	51742496	211846908	37403713	12	748											
TMEM63A	9725	hgsc.bcm.edu	37	chr1	226040425	226040425	+	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	gatgacagtgaagacacacaGcatccatgcatacatggctc	14	7	9	11	0	0	3	0	2	0	1	2	4	1	3	1	1	3	3	1	1	2	1			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr1:226040425G>A	ENST00000366835.3	-	20	2113	c.1843C>T	c.(1843-1845)Ctg>Ttg	p.L615L		NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	615					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)					AAGACACACAGCATCCATGCA	0.552																																					p.L615L		Atlas-SNP	.											.	TMEM63A	75	.	0			c.C1843T						PASS	.						198	123	148					1																	226040425		2203	4300	6503	SO:0001819	synonymous_variant	9725	exon20			CACACAGCATCCA		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.1843C>T	chr1.hg19:g.226040425G>A		67.0	0.0	.		85.0	47.0	.	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Silent	SNP	ENST00000366835.3	hg19	CCDS31042.1																																																																																			.	.	.	none		0.552	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698		A	226040425	G	A	226040425	2	1	10	1	0	0	0	0	0	0	0	1	16202	962	34	2		2	TMEM63A	1	226040425	Silent	SNP	G	TCGA-2Z-A9JE-01A-11D-A42J-10	14193517	226040425	23210196	13	749											
ROCK2	9475	hgsc.bcm.edu	37	chr2	11333932	11333932	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atccttggaatttctttagcAtctgctctatacacatctgt	9	17	5	10	0	4	0	0	0	4	0	5	1	5	1	1	1	3	2	1	1	4	6			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr2:11333932A>G	ENST00000315872.6	-	30	4108	c.3660T>C	c.(3658-3660)gaT>gaC	p.D1220D	ROCK2_ENST00000401753.1_Silent_p.D977D	NM_004850.3	NP_004841.2	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein kinase 2	1220	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)		TTTCTTTAGCATCTGCTCTAT	0.313																																					p.D1220D		Atlas-SNP	.											.	ROCK2	224	.	0			c.T3660C						PASS	.						96	87	90					2																	11333932		1821	4078	5899	SO:0001819	synonymous_variant	9475	exon30			TTTAGCATCTGCT	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.3660T>C	chr2.hg19:g.11333932A>G		51.0	0.0	.		54.0	27.0	.	NM_004850	Q53QZ0|Q53SJ7|Q9UQN5	Silent	SNP	ENST00000315872.6	hg19	CCDS42654.1																																																																																			.	.	.	none		0.313	ROCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313886.3			G	11333932	A	G	11333932	2	3	10	1	0	0	0	0	0	0	0	1	13531	214	8	3		3	ROCK2	2	11333932	Silent	SNP	A	TCGA-2Z-A9JE-01A-11D-A42J-10		11333932	231865441	14	750											
KCNS3	3790	hgsc.bcm.edu	37	chr2	18112835	18112835	+	Frame_Shift_Del	DEL	T	T	-																															ctgcctgtccgctaagcttaTcgctatctcctccttgagcg																										TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr2:18112835delT	ENST00000403915.1	+	3	1011	c.560delT	c.(559-561)atcfs	p.I187fs	KCNS3_ENST00000304101.4_Frame_Shift_Del_p.I187fs|KCNS3_ENST00000465292.1_Intron	NM_001282428.1	NP_001269357.1	Q9BQ31	KCNS3_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3	187					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)			endometrium(5)|kidney(1)|large_intestine(7)|lung(11)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					GCTAAGCTTATCGCTATCTCC	0.517																																					p.I187fs		Atlas-Indel,Pindel	.											KCNS3,NS,carcinoma,0,1	KCNS3	85	.	0			c.559delA						PASS	.						71	71	71					2																	18112835		2203	4300	6503	SO:0001589	frameshift_variant	3790	exon3			.	AF043472	CCDS1692.1	2p24	2011-07-05			ENSG00000170745	ENSG00000170745		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6302	protein-coding gene	gene with protein product		603888				10484328, 16382104	Standard	NM_002252		Approved	Kv9.3	uc002rcw.3	Q9BQ31	OTTHUMG00000044150	ENST00000403915.1:c.560delT	chr2.hg19:g.18112835delT	ENSP00000385968:p.Ile187fs	93.0	0.0	0		117.0	49.0	0.418803	NM_002252	D6W520|O43651|Q4ZFY1|Q96B56	Frame_Shift_Del	DEL	ENST00000403915.1	hg19	CCDS1692.1																																																																																			.	.	.	none		0.517	KCNS3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323808.1	NM_002252		-	18112835	T	-	18112835	7	5	10	1	0	1	0	1	0	0	0	0	8097	1435	50	0	562	0	KCNS3	2	18112835	Frame_Shift_Del	DEL	T	TCGA-2Z-A9JE-01A-11D-A42J-10	6778903	18112835	225086538	15	751											
EPAS1	2034	hgsc.bcm.edu	37	chr2	46583908	46583908	+	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	ttgacttcactcatccctgcGaccatgaggagattcgtgag	9	11	10	11	2	2	4	2	3	0	1	4	6	3	4	2	1	1	0	2	1	0	3			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr2:46583908G>A	ENST00000263734.3	+	4	925	c.415G>A	c.(415-417)Gac>Aac	p.D139N		NM_001430.4	NP_001421.2	Q99814	EPAS1_HUMAN	endothelial PAS domain protein 1	139	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				angiogenesis (GO:0001525)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|erythrocyte differentiation (GO:0030218)|lung development (GO:0030324)|mitochondrion organization (GO:0007005)|myoblast fate commitment (GO:0048625)|norepinephrine metabolic process (GO:0042415)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart rate (GO:0002027)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|surfactant homeostasis (GO:0043129)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|histone acetyltransferase binding (GO:0035035)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	LUSC - Lung squamous cell carcinoma(58;0.151)			TCATCCCTGCGACCATGAGGA	0.438																																					p.D139N		Atlas-SNP	.											EPAS1,caecum,carcinoma,0,1	EPAS1	83	.	0			c.G415A						PASS	.						150	143	145					2																	46583908		2203	4300	6503	SO:0001583	missense	2034	exon4			CCCTGCGACCATG	U81984	CCDS1825.1	2p21-p16	2013-05-21			ENSG00000116016	ENSG00000116016		"Basic helix-loop-helix proteins"	3374	protein-coding gene	gene with protein product	"HIF-1 alpha-like factor"	603349				9000051, 9079689, 18378852	Standard	NM_001430		Approved	MOP2, PASD2, HIF2A, HLF, bHLHe73	uc002ruv.3	Q99814	OTTHUMG00000128818	ENST00000263734.3:c.415G>A	chr2.hg19:g.46583908G>A	ENSP00000263734:p.Asp139Asn	60.0	0.0	.		64.0	27.0	.	NM_001430	Q86VA2|Q99630	Missense_Mutation	SNP	ENST00000263734.3	hg19	CCDS1825.1	.	.	.	.	.	.	.	.	.	.	G	35	5.583690	0.96578	.	.	ENSG00000116016	ENST00000449347;ENST00000263734	T;T	0.28069	1.63;1.63	5.31	5.31	0.75309	PAS (3);PAS fold (1);	0.045322	0.85682	D	0.000000	T	0.73385	0.3580	H	0.98276	4.19	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84327	0.0519	10	0.87932	D	0	.	19.1734	0.93590	0.0:0.0:1.0:0.0	.	139	Q99814	EPAS1_HUMAN	N	139	ENSP00000406137:D139N;ENSP00000263734:D139N	ENSP00000263734:D139N	D	+	1	0	EPAS1	46437412	1.000000	0.71417	0.999000	0.59377	0.894000	0.52154	9.618000	0.98365	2.767000	0.95098	0.561000	0.74099	GAC	.	.	.	none		0.438	EPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250752.2	NM_001430		A	46583908	G	A	46583908	3	1	10	1	0	0	0	0	1	0	0	0	5152	1058	37	1	429	1	EPAS1	2	46583908	Missense_Mutation	SNP	G	TCGA-2Z-A9JE-01A-11D-A42J-10	28471073	46583908	196615465	16	752											
ADD2	119	hgsc.bcm.edu	37	chr2	70931525	70931525	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatctgtcgcagggcccagaTgttggaggagttgttcccct	6	11	14	10	1	1	1	0	0	1	1	3	4	2	3	3	3	0	4	3	3	0	3			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr2:70931525T>C	ENST00000264436.4	-	4	694	c.250A>G	c.(250-252)Atc>Gtc	p.I84V	ADD2_ENST00000355733.3_Missense_Mutation_p.I84V|ADD2_ENST00000413157.2_Missense_Mutation_p.I84V|ADD2_ENST00000407644.2_Missense_Mutation_p.I84V|ADD2_ENST00000473232.1_5'Flank|ADD2_ENST00000430656.1_Missense_Mutation_p.I100V	NM_001617.3	NP_001608.1	P35612	ADDB_HUMAN	adducin 2 (beta)	84					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						AGGGCCCAGATGTTGGAGGAG	0.597																																					p.I100V		Atlas-SNP	.											.	ADD2	261	.	0			c.A298G						PASS	.						157	135	142					2																	70931525		2203	4300	6503	SO:0001583	missense	119	exon3			CCCAGATGTTGGA	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.250A>G	chr2.hg19:g.70931525T>C	ENSP00000264436:p.Ile84Val	65.0	0.0	.		52.0	16.0	.	NM_001185055	A8K4P2|B4DM17|D6W5G7|D6W5G8|Q13482|Q16412|Q59G82|Q5U5P4|Q6P0P2|Q6PGQ4|Q7Z688|Q7Z689|Q7Z690|Q7Z691	Missense_Mutation	SNP	ENST00000264436.4	hg19	CCDS1906.1	.	.	.	.	.	.	.	.	.	.	T	14.25	2.479766	0.44044	.	.	ENSG00000075340	ENST00000264436;ENST00000407644;ENST00000456320;ENST00000355733;ENST00000522886;ENST00000356565;ENST00000517596;ENST00000413157;ENST00000430656;ENST00000415348;ENST00000425976	T;T;T;T;T;T;T;T	0.31247	3.48;3.48;1.5;1.5;1.5;1.5;1.5;1.5	5.14	3.95	0.45737	.	0.140051	0.49305	N	0.000141	T	0.22627	0.0546	L	0.29908	0.895	0.38061	D	0.93606	B;B;B;B;B;B	0.23185	0.0;0.002;0.006;0.007;0.011;0.081	B;B;B;B;B;B	0.24006	0.001;0.009;0.003;0.005;0.007;0.05	T	0.09228	-1.0684	10	0.72032	D	0.01	-26.4503	9.2523	0.37562	0.0:0.0863:0.0:0.9137	.	100;84;84;84;84;84	B4DM17;P35612-4;E9PAN1;Q05DK5;P35612;P35612-3	.;.;.;.;ADDB_HUMAN;.	V	84;84;84;84;84;84;84;84;100;84;84	ENSP00000264436:I84V;ENSP00000384677:I84V;ENSP00000347972:I84V;ENSP00000430243:I84V;ENSP00000388072:I84V;ENSP00000398112:I100V;ENSP00000412357:I84V;ENSP00000412681:I84V	ENSP00000264436:I84V	I	-	1	0	ADD2	70785033	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.225000	0.42954	0.940000	0.37473	0.533000	0.62120	ATC	.	.	.	none		0.597	ADD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251918.4	NM_001617		C	70931525	T	C	70931525	3	2	10	1	0	0	0	0	1	0	0	0	305	1464	51	3	2163	3	ADD2	2	70931525	Missense_Mutation	SNP	T	TCGA-2Z-A9JE-01A-11D-A42J-10	24347617	70931525	172267848	17	753											
ANKRD23	200539	hgsc.bcm.edu	37	chr2	97505808	97505808	+	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	ggggtgccgggtgcgcactgCcacgtgcaggggggtgctcc	3	6	20	12	3	0	0	0	0	0	0	1	0	1	0	3	6	5	3	3	6	0	0			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr2:97505808C>A	ENST00000318357.4	-	7	690	c.649G>T	c.(649-651)Gca>Tca	p.A217S	ANKRD23_ENST00000476975.1_5'UTR|ANKRD23_ENST00000418232.1_Missense_Mutation_p.A217S|ANKRD23_ENST00000331001.2_Missense_Mutation_p.A175S	NM_144994.7	NP_659431.5	Q86SG2	ANR23_HUMAN	ankyrin repeat domain 23	217					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						GTGCGCACTGCCACGTGCAGG	0.632																																					p.A217S		Atlas-SNP	.											.	ANKRD23	28	.	0			c.G649T						PASS	.						20	18	19					2																	97505808		2181	4275	6456	SO:0001583	missense	200539	exon7			GCACTGCCACGTG		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.649G>T	chr2.hg19:g.97505808C>A	ENSP00000321679:p.Ala217Ser	58.0	0.0	.		30.0	16.0	.	NM_144994	Q711K7|Q8NAJ7	Missense_Mutation	SNP	ENST00000318357.4	hg19	CCDS2027.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.152672	0.78001	.	.	ENSG00000163126	ENST00000318357;ENST00000418232;ENST00000331001	T;T;T	0.80824	-1.42;-1.42;-1.42	4.73	4.73	0.59995	Ankyrin repeat-containing domain (4);	0.193284	0.25447	N	0.030603	D	0.89480	0.6727	M	0.85373	2.75	0.80722	D	1	P;D	0.69078	0.692;0.997	P;D	0.69142	0.534;0.962	D	0.90821	0.4709	10	0.87932	D	0	-13.8287	13.0871	0.59146	0.0:1.0:0.0:0.0	.	175;217	Q86SG2-2;Q86SG2	.;ANR23_HUMAN	S	217;217;175	ENSP00000321679:A217S;ENSP00000398987:A217S;ENSP00000333108:A175S	ENSP00000321679:A217S	A	-	1	0	ANKRD23	96869535	1.000000	0.71417	0.994000	0.49952	0.600000	0.36913	4.133000	0.57983	2.450000	0.82876	0.650000	0.86243	GCA	.	.	.	none		0.632	ANKRD23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252956.1	NM_144994		A	97505808	C	A	97505808	3	1	10	1	0	0	0	0	1	0	0	0	652	739	26	4	280	4	ANKRD23	2	97505808	Missense_Mutation	SNP	C	TCGA-2Z-A9JE-01A-11D-A42J-10	26574283	97505808	145693565	18	754											
MYO7B	4648	hgsc.bcm.edu	37	chr2	128341726	128341726	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctctgcatcaacttcgccaAcgagcacctgcagcagttct	9	9	8	15	2	3	0	1	0	2	0	4	1	3	0	2	0	6	6	2	0	2	2			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr2:128341726A>G	ENST00000409816.2	+	12	1405	c.1373A>G	c.(1372-1374)aAc>aGc	p.N458S	MYO7B_ENST00000389524.4_Missense_Mutation_p.N458S|MYO7B_ENST00000428314.1_Missense_Mutation_p.N458S			Q6PIF6	MYO7B_HUMAN	myosin VIIB	458	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)		AACTTCGCCAACGAGCACCTG	0.602																																					p.N458S		Atlas-SNP	.											.	MYO7B	359	.	0			c.A1373G						PASS	.						62	64	64					2																	128341726		2203	4300	6503	SO:0001583	missense	4648	exon13			TCGCCAACGAGCA		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.1373A>G	chr2.hg19:g.128341726A>G	ENSP00000386461:p.Asn458Ser	78.0	0.0	.		94.0	45.0	.	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	hg19	CCDS46405.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.531422	0.85706	.	.	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	D;D;D	0.91351	-2.83;-2.83;-2.83	4.7	4.7	0.59300	Myosin head, motor domain (3);	0.110919	0.64402	D	0.000018	D	0.96327	0.8802	H	0.94385	3.53	0.58432	D	0.999999	D	0.76494	0.999	D	0.68483	0.958	D	0.97450	1.0027	10	0.87932	D	0	.	14.6119	0.68522	1.0:0.0:0.0:0.0	.	458	Q6PIF6	MYO7B_HUMAN	S	458	ENSP00000374175:N458S;ENSP00000415090:N458S;ENSP00000386461:N458S	ENSP00000374175:N458S	N	+	2	0	MYO7B	128058196	1.000000	0.71417	0.869000	0.34112	0.923000	0.55619	9.021000	0.93673	2.104000	0.64026	0.533000	0.62120	AAC	.	.	.	none		0.602	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001		G	128341726	A	G	128341726	3	3	10	1	0	0	0	0	1	0	0	0	10090	43	2	3	1419	3	MYO7B	2	128341726	Missense_Mutation	SNP	A	TCGA-2Z-A9JE-01A-11D-A42J-10	30835918	128341726	114857647	19	755											
GPR155	151556	hgsc.bcm.edu	37	chr2	175346273	175346273	+	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	actttgtgtagcaaaaatagGgaatagtccagctttgctaa	14	12	9	6	0	0	0	0	0	0	0	1	1	1	1	1	1	3	4	1	1	7	6			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr2:175346273G>A	ENST00000392552.2	-	2	650	c.412C>T	c.(412-414)Cct>Tct	p.P138S	GPR155_ENST00000295500.4_Missense_Mutation_p.P138S|GPR155_ENST00000392551.2_Missense_Mutation_p.P138S	NM_001267051.1|NM_152529.6	NP_001253980.1|NP_689742.4	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155	138					cognition (GO:0050890)|intracellular signal transduction (GO:0035556)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	26						GCAAAAATAGGGAATAGTCCA	0.294																																					p.P138S		Atlas-SNP	.											.	GPR155	76	.	0			c.C412T						PASS	.						141	152	148					2																	175346273		2203	4299	6502	SO:0001583	missense	151556	exon2			AAATAGGGAATAG	AY255528	CCDS2259.1, CCDS74605.1	2q31.1	2012-04-10			ENSG00000163328	ENSG00000163328			22951	protein-coding gene	gene with protein product						12679517	Standard	NM_001033045		Approved	DEPDC3, DEP.7, FLJ31819, PGR22	uc002uiu.4	Q7Z3F1	OTTHUMG00000132336	ENST00000392552.2:c.412C>T	chr2.hg19:g.175346273G>A	ENSP00000376335:p.Pro138Ser	115.0	0.0	.		105.0	52.0	.	NM_001267051	B2RCI2|D3DPE2|Q4G0Y6|Q53SJ3|Q53TA8|Q69YG8|Q86SP9|Q8N261|Q8N639|Q8N8K3|Q96MV6	Missense_Mutation	SNP	ENST00000392552.2	hg19	CCDS2259.1	.	.	.	.	.	.	.	.	.	.	G	14.11	2.436500	0.43224	.	.	ENSG00000163328	ENST00000392552;ENST00000392551;ENST00000295500	T;T;T	0.39229	1.09;1.09;1.09	6.03	6.03	0.97812	.	0.047770	0.85682	D	0.000000	T	0.30198	0.0757	N	0.04994	-0.135	0.58432	D	0.999998	P	0.35684	0.515	B	0.38225	0.268	T	0.13361	-1.0512	10	0.36615	T	0.2	-16.4904	20.5568	0.99304	0.0:0.0:1.0:0.0	.	138	Q7Z3F1	GP155_HUMAN	S	138	ENSP00000376335:P138S;ENSP00000376334:P138S;ENSP00000295500:P138S	ENSP00000295500:P138S	P	-	1	0	GPR155	175054519	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.945000	0.63568	2.861000	0.98227	0.655000	0.94253	CCT	.	.	.	none		0.294	GPR155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255455.1	NM_152529		A	175346273	G	A	175346273	3	1	10	1	0	0	0	0	1	0	0	0	6667	1232	43	2	2260	2	GPR155	2	175346273	Missense_Mutation	SNP	G	TCGA-2Z-A9JE-01A-11D-A42J-10	47004547	175346273	67853100	20	756											
USP37	57695	hgsc.bcm.edu	37	chr2	219360546	219360546	+	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	taataacagggcaagtgtatGctctggtagctgaaatatct	13	12	10	6	0	2	1	0	1	2	0	2	1	2	1	0	2	3	5	0	2	7	5			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr2:219360546G>T	ENST00000258399.3	-	14	1821	c.1409C>A	c.(1408-1410)gCa>gAa	p.A470E	USP37_ENST00000454775.1_Missense_Mutation_p.A470E|USP37_ENST00000415516.1_Missense_Mutation_p.A398E|USP37_ENST00000418019.1_Missense_Mutation_p.A470E	NM_020935.2	NP_065986	Q86T82	UBP37_HUMAN	ubiquitin specific peptidase 37	470	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)		GCAAGTGTATGCTCTGGTAGC	0.358																																					p.A470E		Atlas-SNP	.											.	USP37	76	.	0			c.C1409A						PASS	.						106	106	106					2																	219360546		2203	4300	6503	SO:0001583	missense	57695	exon14			GTGTATGCTCTGG	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.1409C>A	chr2.hg19:g.219360546G>T	ENSP00000258399:p.Ala470Glu	73.0	0.0	.		106.0	49.0	.	NM_020935	A2RUQ8|B7ZM38|B7ZM41|E9PHL3|Q2KHT2|Q53S10|Q7Z3A5|Q9HCH8	Missense_Mutation	SNP	ENST00000258399.3	hg19	CCDS2418.1	.	.	.	.	.	.	.	.	.	.	G	15.48	2.846484	0.51164	.	.	ENSG00000135913	ENST00000258399;ENST00000454775;ENST00000415516;ENST00000418019	T;T;T;T	0.28895	1.59;1.59;1.59;1.59	5.49	3.12	0.35913	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.291794	0.36101	N	0.002789	T	0.15089	0.0364	N	0.10733	0.035	0.80722	D	1	B;B	0.10296	0.002;0.003	B;B	0.04013	0.001;0.001	T	0.06075	-1.0847	10	0.33141	T	0.24	-3.8005	9.7959	0.40735	0.8596:0.0:0.1404:0.0	.	398;470	Q86T82-2;Q86T82	.;UBP37_HUMAN	E	470;470;398;470	ENSP00000258399:A470E;ENSP00000393662:A470E;ENSP00000400902:A398E;ENSP00000396585:A470E	ENSP00000258399:A470E	A	-	2	0	USP37	219068790	1.000000	0.71417	0.985000	0.45067	0.983000	0.72400	5.379000	0.66196	0.383000	0.24910	-0.383000	0.06682	GCA	.	.	.	none		0.358	USP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256779.3	NM_020935		T	219360546	G	T	219360546	3	4	10	1	0	0	0	0	1	0	0	0	17080	1319	46	4	1582	4	USP37	2	219360546	Missense_Mutation	SNP	G	TCGA-2Z-A9JE-01A-11D-A42J-10	44014273	219360546	23838827	21	757											
COL4A3	1285	hgsc.bcm.edu	37	chr2	228174025	228174025	+	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	tctctctggaaaggattttcAttcatcatggtgaggagaaa	12	13	10	6	0	5	2	3	1	2	1	6	5	5	4	0	4	0	0	0	4	2	3			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr2:228174025A>T	ENST00000396578.3	+	50	4908	c.4746A>T	c.(4744-4746)tcA>tcT	p.S1582S	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)	1582	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)		AAGGATTTTCATTCATCATGG	0.473																																					p.S1582S		Atlas-SNP	.											.	COL4A3	293	.	0			c.A4746T						PASS	.						55	55	55					2																	228174025		1943	4165	6108	SO:0001819	synonymous_variant	1285	exon50			ATTTTCATTCATC		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.4746A>T	chr2.hg19:g.228174025A>T		61.0	0.0	.		45.0	23.0	.	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Silent	SNP	ENST00000396578.3	hg19	CCDS42829.1																																																																																			.	.	.	none		0.473	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091		T	228174025	A	T	228174025	2	4	10	1	0	0	0	0	0	0	0	1	3693	204	8	5		5	COL4A3	2	228174025	Silent	SNP	A	TCGA-2Z-A9JE-01A-11D-A42J-10	8813479	228174025	15025348	22	758											
ARMC9	80210	hgsc.bcm.edu	37	chr2	232141353	232141353	+	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	ggctctttcttcccaggcgcCcgctgcagacagcgatgatt	6	10	11	14	3	2	2	0	1	2	1	3	3	3	2	2	2	2	3	2	2	0	3			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr2:232141353C>A	ENST00000349938.4	+	15	1533	c.1339C>A	c.(1339-1341)Ccg>Acg	p.P447T	ARMC9_ENST00000483477.1_3'UTR	NM_001271466.1|NM_025139.4	NP_001258395.1|NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9	447						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)		TCCCAGGCGCCCGCTGCAGAC	0.507																																					p.P447T		Atlas-SNP	.											.	ARMC9	129	.	0			c.C1339A						PASS	.						112	108	110					2																	232141353		2203	4300	6503	SO:0001583	missense	80210	exon15			AGGCGCCCGCTGC	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.1339C>A	chr2.hg19:g.232141353C>A	ENSP00000258417:p.Pro447Thr	46.0	0.0	.		46.0	25.0	.	NM_025139	Q53TI3|Q6P162|Q7L594|Q86WG2|Q96JF9|Q9H9R8	Missense_Mutation	SNP	ENST00000349938.4	hg19	CCDS2484.1	.	.	.	.	.	.	.	.	.	.	C	2.253	-0.371083	0.05034	.	.	ENSG00000135931	ENST00000349938;ENST00000359743;ENST00000436339;ENST00000446447	T;T;T	0.52057	0.68;0.68;0.68	5.42	3.56	0.40772	Armadillo-like helical (1);Armadillo-type fold (1);	0.410909	0.25958	N	0.027202	T	0.21427	0.0516	N	0.08118	0	0.09310	N	1	B	0.13145	0.007	B	0.09377	0.004	T	0.20472	-1.0274	10	0.06236	T	0.91	-13.5235	8.8812	0.35376	0.1329:0.4254:0.4417:0.0	.	447	Q7Z3E5	ARMC9_HUMAN	T	447;447;164;89	ENSP00000258417:P447T;ENSP00000392086:P164T;ENSP00000411778:P89T	ENSP00000258417:P447T	P	+	1	0	ARMC9	231849597	0.114000	0.22134	0.675000	0.29917	0.451000	0.32288	1.453000	0.35167	1.281000	0.44480	0.563000	0.77884	CCG	.	.	.	none		0.507	ARMC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256966.3	NM_025139		A	232141353	C	A	232141353	3	1	10	1	0	0	0	0	1	0	0	0	958	623	22	4	1393	4	ARMC9	2	232141353	Missense_Mutation	SNP	C	TCGA-2Z-A9JE-01A-11D-A42J-10	3967328	232141353	11058020	23	759											
UGT1A6	54578	hgsc.bcm.edu	37	chr2	234602011	234602011	+	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	ataacatgattgttattggcCtgtacttcatcaactgccag	11	14	7	9	0	2	1	2	1	0	0	2	1	2	1	2	1	4	2	2	1	4	6			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr2:234602011C>A	ENST00000305139.6	+	1	500	c.361C>A	c.(361-363)Ctg>Atg	p.L121M	UGT1A10_ENST00000373445.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A1_ENST00000373450.4_Intron|AC114812.8_ENST00000439336.1_RNA|UGT1A6_ENST00000406651.1_5'Flank|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000480628.1_Intron	NM_001072.3	NP_001063.2	P19224	UD16_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A6	121					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)	TGTTATTGGCCTGTACTTCAT	0.458																																					p.L121M		Atlas-SNP	.											.	UGT1A6	63	.	0			c.C361A						PASS	.						88	74	79					2																	234602011		2203	4300	6503	SO:0001583	missense	54578	exon1			ATTGGCCTGTACT	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.361C>A	chr2.hg19:g.234602011C>A	ENSP00000303174:p.Leu121Met	56.0	0.0	.		73.0	25.0	.	NM_001072	A6NKK6|B8K289|Q96TE7	Missense_Mutation	SNP	ENST00000305139.6	hg19	CCDS2507.1	.	.	.	.	.	.	.	.	.	.	C	0.098	-1.155968	0.01686	.	.	ENSG00000167165	ENST00000441351;ENST00000305139	T;T	0.60920	0.15;0.15	5.31	-3.87	0.04218	.	.	.	.	.	T	0.21347	0.0514	N	0.02368	-0.58	0.09310	N	0.999996	B;B	0.06786	0.001;0.001	B;B	0.15484	0.01;0.013	T	0.25537	-1.0129	9	0.09084	T	0.74	.	3.2857	0.06931	0.3165:0.3751:0.0657:0.2427	.	121;121	B8K289;P19224	.;UD16_HUMAN	M	121	ENSP00000389637:L121M;ENSP00000303174:L121M	ENSP00000303174:L121M	L	+	1	2	UGT1A6	234266750	0.000000	0.05858	0.007000	0.13788	0.022000	0.10575	-1.635000	0.02018	-0.410000	0.07542	-0.256000	0.11100	CTG	.	.	.	none		0.458	UGT1A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130988.1	NM_205862		A	234602011	C	A	234602011	3	1	10	1	0	0	0	0	1	0	0	0	16961	680	24	4	363	4	UGT1A6	2	234602011	Missense_Mutation	SNP	C	TCGA-2Z-A9JE-01A-11D-A42J-10	2460658	234602011	8597362	24	760											
ANO7	50636	hgsc.bcm.edu	37	chr2	242149796	242149796	+	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	tccaggtcgggcaacaccctTctcgcagcctgggtgagcct	6	8	12	15	2	1	1	0	1	1	0	4	1	2	1	4	3	3	2	4	3	1	1			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr2:242149796T>G	ENST00000274979.8	+	14	1711	c.1608T>G	c.(1606-1608)ctT>ctG	p.L536L	ANO7_ENST00000402430.3_Silent_p.L535L	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	536					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						GCAACACCCTTCTCGCAGCCT	0.677																																					p.L536L		Atlas-SNP	.											.	ANO7	136	.	0			c.T1608G						PASS	.						97	77	84					2																	242149796		2203	4300	6503	SO:0001819	synonymous_variant	50636	exon14			CACCCTTCTCGCA	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.1608T>G	chr2.hg19:g.242149796T>G		64.0	0.0	.		52.0	19.0	.	NM_001001891	Q6IWH6	Silent	SNP	ENST00000274979.8	hg19	CCDS33423.1																																																																																			.	.	.	none		0.677	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891		G	242149796	T	G	242149796	2	3	10	1	0	0	0	0	0	0	0	1	702	1770	62	5		5	ANO7	2	242149796	Silent	SNP	T	TCGA-2Z-A9JE-01A-11D-A42J-10	7547785	242149796	1049577	25	761											
ITPR1	3708	hgsc.bcm.edu	37	chr3	4821261	4821263	+	In_Frame_Del	DEL	ATC	ATC	-																															cctcgaagttgctcctggccAtcatggaaagcaggcacgac																										TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	ATC	ATC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr3:4821261_4821263delATC	ENST00000443694.2	+	46	6274_6276	c.6274_6276delATC	c.(6274-6276)atcdel	p.I2092del	ITPR1_ENST00000354582.6_In_Frame_Del_p.I2092del|ITPR1_ENST00000302640.8_In_Frame_Del_p.I2092del|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000423119.2_In_Frame_Del_p.I2059del|ITPR1_ENST00000357086.4_In_Frame_Del_p.I2059del|ITPR1_ENST00000456211.2_In_Frame_Del_p.I2044del			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	2107					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)	GCTCCTGGCCATCATGGAAAGCA	0.532																																					p.2091_2092del		Pindel	.											.	ITPR1	659	.	0			c.6273_6275del						PASS	.																																			SO:0001651	inframe_deletion	3708	exon48			.	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.6274_6276delATC	chr3.hg19:g.4821261_4821263delATC	ENSP00000401671:p.Ile2092del	160.0	0.0	.		152.0	88.0	0.579	NM_001168272	E7EPX7|E9PDE9|Q14660|Q99897	In_Frame_Del	DEL	ENST00000443694.2	hg19	CCDS54551.1																																																																																			.	.	.	none		0.532	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		-	4821263	ATC	-	4821261	7	5	10	1	0	1	0	1	0	0	0	0	7927	217	8	0	6505	0	ITPR1	3	4821261	In_Frame_Del	DEL	ATC	TCGA-2Z-A9JE-01A-11D-A42J-10		4821261	193201169	26	762											
XYLB	9942	hgsc.bcm.edu	37	chr3	38404498	38404498	+	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	tcaagtcctagccttgtccgGggcgggccaggttcgtttgc	4	11	14	12	3	1	0	1	0	0	0	4	0	3	0	4	4	2	2	4	4	2	4			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr3:38404498G>A	ENST00000207870.3	+	4	371	c.281G>A	c.(280-282)gGg>gAg	p.G94E	XYLB_ENST00000542835.1_Intron	NM_005108.3	NP_005099.2	O75191	XYLB_HUMAN	xylulokinase homolog (H. influenzae)	94					carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|D-xylose metabolic process (GO:0042732)|generation of precursor metabolites and energy (GO:0006091)|xylulose catabolic process (GO:0005998)|xylulose metabolic process (GO:0005997)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|xylulokinase activity (GO:0004856)			endometrium(3)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(1)|prostate(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.00372)|Kidney(284;0.00405)		GCCTTGTCCGGGGCGGGCCAG	0.537																																					p.G94E		Atlas-SNP	.											.	XYLB	50	.	0			c.G281A						PASS	.						85	85	85					3																	38404498		2203	4300	6503	SO:0001583	missense	9942	exon4			TGTCCGGGGCGGG	AB015046	CCDS2678.1	3p22-p21.3	2006-12-18	2001-12-04		ENSG00000093217	ENSG00000093217			12839	protein-coding gene	gene with protein product		604049	"xylulokinase (H. influenzae) homolog"			9763671	Standard	NM_005108		Approved	FLJ10343, FLJ12539	uc003cic.2	O75191	OTTHUMG00000131294	ENST00000207870.3:c.281G>A	chr3.hg19:g.38404498G>A	ENSP00000207870:p.Gly94Glu	50.0	0.0	.		38.0	36.0	.	NM_005108	B2RAW4|B4DDT2|B9EH64	Missense_Mutation	SNP	ENST00000207870.3	hg19	CCDS2678.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.266815	0.80469	.	.	ENSG00000093217	ENST00000207870	T	0.45668	0.89	4.74	4.74	0.60224	Carbohydrate kinase, FGGY, N-terminal (1);	0.098371	0.64402	D	0.000001	T	0.72285	0.3441	M	0.92970	3.365	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.79852	-0.1628	10	0.72032	D	0.01	.	16.0139	0.80422	0.0:0.0:1.0:0.0	.	94	O75191	XYLB_HUMAN	E	94	ENSP00000207870:G94E	ENSP00000207870:G94E	G	+	2	0	XYLB	38379502	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	7.862000	0.87013	2.554000	0.86153	0.455000	0.32223	GGG	.	.	.	none		0.537	XYLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254062.2	NM_005108		A	38404498	G	A	38404498	3	1	10	1	0	0	0	0	1	0	0	0	17474	1232	43	2	295	2	XYLB	3	38404498	Missense_Mutation	SNP	G	TCGA-2Z-A9JE-01A-11D-A42J-10	33583237	38404498	159617932	27	763											
BAP1	8314	hgsc.bcm.edu	37	chr3	52439781	52439781	+	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	ggtcccaaaccccccagtacCtgtgtggttgccctcagagg	7	8	11	15	0	1	1	1	0	0	1	2	1	2	1	6	3	3	2	6	3	2	2			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr3:52439781C>A	ENST00000460680.1	-	10	1402	c.931G>T	c.(931-933)Gat>Tat	p.D311Y	BAP1_ENST00000296288.5_Splice_Site_p.D293Y	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		CCCCCAGTACCTGTGTGGTTG	0.577			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.D311Y	GBM(101;493 1458 7992 21037 25532)	Atlas-SNP	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	0			c.G931T						PASS	.						43	45	44					3																	52439781		2203	4300	6503	SO:0001630	splice_region_variant	8314	exon10			CAGTACCTGTGTG	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.931+1G>T	chr3.hg19:g.52439781C>A		72.0	0.0	.		60.0	53.0	.	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Missense_Mutation	SNP	ENST00000460680.1	hg19	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	C	18.22	3.575175	0.65878	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	T;T	0.57752	0.38;0.39	5.38	5.38	0.77491	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (1);	0.050678	0.85682	D	0.000000	T	0.48132	0.1483	L	0.54323	1.7	0.58432	D	0.999994	B	0.33379	0.41	B	0.25884	0.064	T	0.43540	-0.9385	9	.	.	.	-1.5677	19.0887	0.93217	0.0:1.0:0.0:0.0	.	311	Q92560	BAP1_HUMAN	Y	311;293	ENSP00000417132:D311Y;ENSP00000296288:D293Y	.	D	-	1	0	BAP1	52414821	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	5.016000	0.64041	2.674000	0.91012	0.655000	0.94253	GAT	.	.	.	none		0.577	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1		Missense_Mutation	A	52439781	C	A	52439781	5	1	10	1	0	0	0	0	0	0	1	0	1311	695	24	4	1290	4	BAP1	3	52439781	Splice_Site	SNP	C	TCGA-2Z-A9JE-01A-11D-A42J-10	14035283	52439781	145582649	28	764											
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113392215	113392215	+	Frame_Shift_Del	DEL	T	T	-																															ctgcattgtgtgtctcccggTttttctttctgaaacaaaaa																										TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr3:113392215delT	ENST00000478658.1	-	2	73	c.56delA	c.(55-57)aacfs	p.N19fs	KIAA2018_ENST00000316407.4_Frame_Shift_Del_p.N19fs|KIAA2018_ENST00000491165.1_Frame_Shift_Del_p.N19fs			Q68DE3	K2018_HUMAN	KIAA2018	19	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.					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						TGTCTCCCGGTTTTTCTTTCT	0.259																																					p.N19fs		Pindel	.											.	KIAA2018	180	.	0			c.57delC						PASS	.						56	52	53					3																	113392215		1782	4045	5827	SO:0001589	frameshift_variant	205717	exon4			.	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.56delA	chr3.hg19:g.113392215delT	ENSP00000420721:p.Asn19fs	388.0	0.0	.		393.0	139.0	0.354	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Frame_Shift_Del	DEL	ENST00000478658.1	hg19	CCDS43133.1																																																																																			.	.	.	none		0.259	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		-	113392215	T	-	113392215	7	5	10	1	0	1	0	1	0	0	0	0	8275	1725	60	0	6697	0	KIAA2018	3	113392215	Frame_Shift_Del	DEL	T	TCGA-2Z-A9JE-01A-11D-A42J-10	60952434	113392215	84630215	29	765											
SPON2	10417	hgsc.bcm.edu	37	chr4	1165761	1165761	+	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	agggctctggcggaacagatGgactctcccccaagaggctg	9	6	14	12	1	2	2	0	0	2	2	3	4	2	4	2	5	1	2	2	5	2	0			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr4:1165761G>T	ENST00000290902.5	-	2	431	c.99C>A	c.(97-99)tcC>tcA	p.S33S	SPON2_ENST00000431380.1_Silent_p.S33S	NM_012445.3	NP_036577	Q9BUD6	SPON2_HUMAN	spondin 2, extracellular matrix protein	33	Spondin. {ECO:0000255|PROSITE- ProRule:PRU00364}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|pancreas(1)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(23;0.00805)	UCEC - Uterine corpus endometrioid carcinoma (64;0.139)|Colorectal(103;0.19)		CGGAACAGATGGACTCTCCCC	0.682																																					p.S33S		Atlas-SNP	.											.	SPON2	22	.	0			c.C99A						PASS	.						29	41	37					4																	1165761		2193	4276	6469	SO:0001819	synonymous_variant	10417	exon2			ACAGATGGACTCT	AB027466	CCDS3347.1	4p16.3	2008-07-29			ENSG00000159674	ENSG00000159674			11253	protein-coding gene	gene with protein product	"Mindin", "M-spondin"	605918				10512675, 15094111	Standard	NM_012445		Approved	DIL1	uc003gco.4	Q9BUD6	OTTHUMG00000089002	ENST00000290902.5:c.99C>A	chr4.hg19:g.1165761G>T		235.0	0.0	.		146.0	59.0	.	NM_012445	D3DVN9|Q4W5N4|Q9ULW1	Silent	SNP	ENST00000290902.5	hg19	CCDS3347.1																																																																																			.	.	.	none		0.682	SPON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202080.2			T	1165761	G	T	1165761	2	4	10	1	0	0	0	0	0	0	0	1	15095	1335	47	4		4	SPON2	4	1165761	Silent	SNP	G	TCGA-2Z-A9JE-01A-11D-A42J-10		1165761	189988515	30	766											
UNC5C	8633	hgsc.bcm.edu	37	chr4	96140151	96140151	+	Frame_Shift_Del	DEL	C	C	-																															acaataaggtgacctcccagCgagttgaagctgccaaatgc																								rs61741188	byFrequency	TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr4:96140151delC	ENST00000453304.1	-	9	1962	c.1614delG	c.(1612-1614)tcgfs	p.S538fs	UNC5C_ENST00000506749.1_Frame_Shift_Del_p.S557fs	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																																					p.L539fs		Atlas-Indel,Pindel	.											.	UNC5C	141	.	0			c.1615delC						PASS	.						108	86	94					4																	96140151		2203	4300	6503	SO:0001589	frameshift_variant	8633	exon9			.	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.1614delG	chr4.hg19:g.96140151delC	ENSP00000406022:p.Ser538fs	43.0	0.0	0		54.0	25.0	0.462963	NM_003728	Q8IUT0	Frame_Shift_Del	DEL	ENST00000453304.1	hg19	CCDS3643.1																																																																																			.	.	.	none		0.443	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728		-	96140151	C	-	96140151	7	5	10	1	0	1	0	1	0	0	0	0	17005	755	27	0	1213	0	UNC5C	4	96140151	Frame_Shift_Del	DEL	C	TCGA-2Z-A9JE-01A-11D-A42J-10	94974390	96140151	95014125	31	767											
C4orf21	55345	hgsc.bcm.edu	37	chr4	113539801	113539801	+	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	catactccttttccagtgttCcacatgtatttacctcctga	8	16	4	13	0	0	1	0	1	0	0	4	1	4	1	5	0	2	2	5	0	3	7			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr4:113539801C>A	ENST00000505019.1	-	6	1522	c.1397G>T	c.(1396-1398)gGa>gTa	p.G466V	C4orf21_ENST00000445203.2_Missense_Mutation_p.G435V|C4orf21_ENST00000309071.5_Missense_Mutation_p.G466V	NM_018392.4	NP_060862.3	Q86YA3	ZGRF1_HUMAN		466						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.G466V(2)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(6)|lung(21)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		TTCCAGTGTTCCACATGTATT	0.338																																					p.G466V		Atlas-SNP	.											C4orf21_ENST00000505019,NS,carcinoma,0,1	C4orf21	223	.	2	Substitution - Missense(2)	lung(2)	c.G1397T						PASS	.						104	112	109					4																	113539801		2203	4300	6503	SO:0001583	missense	55345	exon6			AGTGTTCCACATG																												ENST00000505019.1:c.1397G>T	chr4.hg19:g.113539801C>A	ENSP00000424737:p.Gly466Val	66.0	0.0	.		67.0	27.0	.	NM_018392	B3KQX2|B4DSN6|B4DYU8|E9PDE1|G5EA02|Q6ZU11|Q9NSW3|Q9NUJ4	Missense_Mutation	SNP	ENST00000505019.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.56	2.274501	0.40194	.	.	ENSG00000138658	ENST00000505019;ENST00000309071;ENST00000445203	D;T;T	0.82619	-1.63;1.87;1.45	4.86	-3.04	0.05412	.	1.350960	0.04855	N	0.443112	T	0.70894	0.3276	L	0.32530	0.975	0.09310	N	1	B;B	0.32893	0.389;0.1	B;B	0.32211	0.142;0.027	T	0.59075	-0.7522	10	0.66056	D	0.02	-0.8765	2.4375	0.04486	0.0987:0.3354:0.1808:0.3851	.	466;466	Q86YA3;G5EA02	CD021_HUMAN;.	V	466;466;435	ENSP00000424737:G466V;ENSP00000309095:G466V;ENSP00000390505:G435V	ENSP00000309095:G466V	G	-	2	0	C4orf21	113759250	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-1.202000	0.03023	-0.666000	0.05310	-0.262000	0.10625	GGA	.	.	.	none		0.338	C4orf21-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256413.1			A	113539801	C	A	113539801	3	1	10	1	0	0	0	0	1	0	0	0	2256	855	30	4	5009	4	C4orf21	4	113539801	Missense_Mutation	SNP	C	TCGA-2Z-A9JE-01A-11D-A42J-10	17399650	113539801	77614475	32	768											
KIAA0922	23240	hgsc.bcm.edu	37	chr4	154517528	154517528	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggaaaagttacctcactcaTactaatccggtaggtgtgtt	11	13	9	8	1	2	0	2	0	0	0	3	1	3	1	2	3	2	3	2	3	6	5			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr4:154517528T>C	ENST00000409663.3	+	20	2163	c.2111T>C	c.(2110-2112)aTa>aCa	p.I704T	KIAA0922_ENST00000409959.3_Missense_Mutation_p.I705T|KIAA0922_ENST00000440693.1_Missense_Mutation_p.I621T	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	704						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)				ACCTCACTCATACTAATCCGG	0.423																																					p.I705T		Atlas-SNP	.											.	KIAA0922	214	.	0			c.T2114C						PASS	.						140	124	130					4																	154517528		2203	4300	6503	SO:0001583	missense	23240	exon20			CACTCATACTAAT	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.2111T>C	chr4.hg19:g.154517528T>C	ENSP00000386574:p.Ile704Thr	39.0	0.0	.		59.0	24.0	.	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	hg19	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	T	22.2	4.261278	0.80246	.	.	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	T;T;T;T	0.22336	2.24;1.96;2.24;1.96	5.65	5.65	0.86999	.	0.100685	0.64402	D	0.000003	T	0.48624	0.1510	M	0.79475	2.455	0.58432	D	0.999993	D;D;D	0.89917	1.0;1.0;0.996	D;D;D	0.85130	0.997;0.987;0.918	T	0.52593	-0.8555	10	0.87932	D	0	-10.8786	14.8705	0.70453	0.0:0.0:0.0:1.0	.	621;705;704	A2VDJ0-3;A2VDJ0-5;A2VDJ0	.;.;T131L_HUMAN	T	704;621;705;482	ENSP00000386574:I704T;ENSP00000409663:I621T;ENSP00000386787:I705T;ENSP00000240487:I482T	ENSP00000240487:I482T	I	+	2	0	KIAA0922	154736978	1.000000	0.71417	0.903000	0.35520	0.997000	0.91878	6.265000	0.72534	2.163000	0.67991	0.533000	0.62120	ATA	.	.	.	none		0.423	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196		C	154517528	T	C	154517528	3	2	10	1	0	0	0	0	1	0	0	0	8208	1406	49	3	2192	3	KIAA0922	4	154517528	Missense_Mutation	SNP	T	TCGA-2Z-A9JE-01A-11D-A42J-10	40977727	154517528	36636748	33	769											
CMBL	134147	hgsc.bcm.edu	37	chr5	10282333	10282333	+	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	ttgagtggaatcacaacatcAttttcagcaaaaatgaacaa	18	10	6	7	0	3	2	3	2	0	0	3	3	3	3	0	1	3	1	0	1	6	3	rs115129340	byFrequency	TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr5:10282333A>T	ENST00000296658.3	-	5	954	c.534T>A	c.(532-534)aaT>aaA	p.N178K	CMBL_ENST00000510532.1_Intron	NM_138809.3	NP_620164.1	Q96DG6	CMBL_HUMAN	carboxymethylenebutenolidase homolog (Pseudomonas)	178						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(1)|lung(9)|skin(1)|stomach(1)	13						TCACAACATCATTTTCAGCAA	0.403																																					p.N178K		Atlas-SNP	.											.	CMBL	24	.	0			c.T534A						PASS	.						102	104	103					5																	10282333		2203	4300	6503	SO:0001583	missense	134147	exon5			AACATCATTTTCA		CCDS3878.1	5p15.2	2010-06-25	2006-09-12		ENSG00000164237	ENSG00000164237	3.1.-.-		25090	protein-coding gene	gene with protein product		613379	"carboxymethylenebutenolidase-like (Pseudomonas)"			3804974, 20177059	Standard	NM_138809		Approved	FLJ23617	uc003jes.3	Q96DG6	OTTHUMG00000131043	ENST00000296658.3:c.534T>A	chr5.hg19:g.10282333A>T	ENSP00000296658:p.Asn178Lys	253.0	0.0	.		201.0	71.0	.	NM_138809	D3DTC7|Q8TED6	Missense_Mutation	SNP	ENST00000296658.3	hg19	CCDS3878.1	.	.	.	.	.	.	.	.	.	.	A	13.71	2.317951	0.40996	.	.	ENSG00000164237	ENST00000296658	T	0.39592	1.07	5.23	-5.94	0.02247	Dienelactone hydrolase (1);	0.494575	0.21750	N	0.069694	T	0.16642	0.0400	N	0.16201	0.385	0.31061	N	0.714115	B	0.06786	0.001	B	0.12156	0.007	T	0.11867	-1.0570	10	0.20519	T	0.43	-25.4727	5.87	0.18799	0.2378:0.0:0.4348:0.3274	.	178	Q96DG6	CMBL_HUMAN	K	178	ENSP00000296658:N178K	ENSP00000296658:N178K	N	-	3	2	CMBL	10335333	0.000000	0.05858	0.528000	0.27938	0.911000	0.54048	-2.751000	0.00792	-1.004000	0.03421	0.533000	0.62120	AAT	.	A|0.990;G|0.010	.	alt		0.403	CMBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253689.1	NM_138809		T	10282333	A	T	10282333	3	4	10	1	0	0	0	0	1	0	0	0	3578	214	8	5	211	5	CMBL	5	10282333	Missense_Mutation	SNP	A	TCGA-2Z-A9JE-01A-11D-A42J-10		10282333	170632927	34	770											
DDX46	9879	hgsc.bcm.edu	37	chr5	134118720	134118720	+	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	attaaatcctgggtccagtgTggaatttccatgaagatctt	11	14	9	7	0	1	2	0	1	1	1	4	3	4	3	3	2	0	0	3	2	4	3			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr5:134118720T>A	ENST00000354283.4	+	9	1266	c.1131T>A	c.(1129-1131)tgT>tgA	p.C377*	DDX46_ENST00000452510.2_Nonsense_Mutation_p.C377*|DDX46_ENST00000509178.1_3'UTR			Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	377					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GGGTCCAGTGTGGAATTTCCA	0.408																																					p.C377X	Colon(13;391 453 4901 21675 24897)	Atlas-SNP	.											.	DDX46	77	.	0			c.T1131A						PASS	.						181	166	171					5																	134118720		2203	4300	6503	SO:0001587	stop_gained	9879	exon9			CCAGTGTGGAATT		CCDS34240.1, CCDS75306.1	5q31.1	2010-01-25			ENSG00000145833	ENSG00000145833		"DEAD-boxes"	18681	protein-coding gene	gene with protein product							Standard	XM_005272142		Approved	KIAA0801, FLJ25329, PRPF5, Prp5	uc003kzw.3	Q7L014	OTTHUMG00000163072	ENST00000354283.4:c.1131T>A	chr5.hg19:g.134118720T>A	ENSP00000346236:p.Cys377*	145.0	0.0	.		150.0	65.0	.	NM_014829	O94894|Q96EI0|Q9Y658	Nonsense_Mutation	SNP	ENST00000354283.4	hg19	CCDS34240.1	.	.	.	.	.	.	.	.	.	.	T	37	6.395914	0.97533	.	.	ENSG00000145833	ENST00000452510;ENST00000354283	.	.	.	5.16	4.01	0.46588	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.8672	10.2948	0.43618	0.0:0.0776:0.0:0.9224	.	.	.	.	X	377	.	ENSP00000346236:C377X	C	+	3	2	DDX46	134146619	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.230000	0.58632	1.946000	0.56461	0.528000	0.53228	TGT	.	.	.	none		0.408	DDX46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371584.1	NM_014829		A	134118720	T	A	134118720	4	1	10	1	0	0	0	0	0	1	0	0	4366	1702	59	5	1165	5	DDX46	5	134118720	Nonsense_Mutation	SNP	T	TCGA-2Z-A9JE-01A-11D-A42J-10	123836387	134118720	46796540	35	771											
PCDHGA1	56114	hgsc.bcm.edu	37	chr5	140712543	140712543	+	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	tccctcactgcggactcgcgGaagagccacctgattttccc	7	9	9	16	3	1	2	1	1	0	1	4	4	3	4	4	2	2	0	4	2	1	2	rs560568026		TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr5:140712543G>A	ENST00000517417.1	+	1	2292	c.2292G>A	c.(2290-2292)cgG>cgA	p.R764R	PCDHGA1_ENST00000378105.3_Silent_p.R764R	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	764					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)			CGGACTCGCGGAAGAGCCACC	0.577																																					p.R764R		Atlas-SNP	.											.	PCDHGA1	397	.	0			c.G2292A						PASS	.						105	115	112					5																	140712543		2203	4298	6501	SO:0001819	synonymous_variant	56114	exon1			CTCGCGGAAGAGC	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.2292G>A	chr5.hg19:g.140712543G>A		283.0	0.0	.		207.0	59.0	.	NM_018912	Q2M273|Q9Y5D6	Silent	SNP	ENST00000517417.1	hg19	CCDS54922.1																																																																																			.	.	.	none		0.577	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		A	140712543	G	A	140712543	2	1	10	1	0	0	0	0	0	0	0	1	11557	1161	41	2		2	PCDHGA1	5	140712543	Silent	SNP	G	TCGA-2Z-A9JE-01A-11D-A42J-10	6593823	140712543	40202717	36	772											
PCDHGB4	8641	hgsc.bcm.edu	37	chr5	140769788	140769788	+	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	tcaggacaagacatactttgCggtgattcatctggggcctt	9	12	11	9	1	3	2	2	1	1	1	3	3	3	3	1	4	2	0	1	4	2	4			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr5:140769788C>T	ENST00000519479.1	+	1	2337	c.2337C>T	c.(2335-2337)tgC>tgT	p.C779C	PCDHGA5_ENST00000518069.1_Intron|PCDHGA8_ENST00000398604.2_5'Flank|PCDHGA4_ENST00000571252.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_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	779					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)			ACATACTTTGCGGTGATTCAT	0.388																																					p.C779C		Atlas-SNP	.											.	PCDHGB4	125	.	0			c.C2337T						PASS	.						222	223	223					5																	140769788		1904	4126	6030	SO:0001819	synonymous_variant	8641	exon1			ACTTTGCGGTGAT	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.2337C>T	chr5.hg19:g.140769788C>T		177.0	0.0	.		112.0	27.0	.	NM_032098	O15099|Q2M267|Q9UN64	Silent	SNP	ENST00000519479.1	hg19	CCDS54928.1																																																																																			.	.	.	none		0.388	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1	NM_003736		T	140769788	C	T	140769788	2	4	10	1	0	0	0	0	0	0	0	1	11572	776	27	1		1	PCDHGB4	5	140769788	Silent	SNP	C	TCGA-2Z-A9JE-01A-11D-A42J-10	57245	140769788	40145472	37	773											
FAT2	2196	hgsc.bcm.edu	37	chr5	150920245	150920245	+	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	aagtacttggctgtatgctcGcggtccagggtcttccttga	6	13	12	10	2	1	1	0	1	1	0	4	1	3	1	2	3	2	4	2	3	3	5	rs111242057		TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr5:150920245G>A	ENST00000261800.5	-	10	8934	c.8922C>T	c.(8920-8922)cgC>cgT	p.R2974R		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2974	Cadherin 26. {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)			CTGTATGCTCGCGGTCCAGGG	0.532																																					p.R2974R		Atlas-SNP	.											.	FAT2	465	.	0			c.C8922T						PASS	.						107	89	95					5																	150920245		2203	4300	6503	SO:0001819	synonymous_variant	2196	exon10			ATGCTCGCGGTCC	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.8922C>T	chr5.hg19:g.150920245G>A		82.0	0.0	.		74.0	32.0	.	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	hg19	CCDS4317.1																																																																																			.	G|0.500;A|0.500	0.500	weak		0.532	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		A	150920245	G	A	150920245	2	1	10	1	0	0	0	0	0	0	0	1	5697	1074	38	1		1	FAT2	5	150920245	Silent	SNP	G	TCGA-2Z-A9JE-01A-11D-A42J-10	10150457	150920245	29995015	38	774											
DAAM2	23500	hgsc.bcm.edu	37	chr6	39869623	39869623	+	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	ggaacgtgagcggtggcagcGgcagcggaaggtcctggctg	7	5	20	9	4	0	1	0	1	0	0	1	3	1	3	1	7	4	3	1	7	2	0			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr6:39869623G>T	ENST00000398904.2	+	25	3199	c.3017G>T	c.(3016-3018)cGg>cTg	p.R1006L	RP11-61I13.3_ENST00000437947.1_RNA|DAAM2_ENST00000538976.1_Missense_Mutation_p.R1005L|DAAM2_ENST00000274867.4_Missense_Mutation_p.R1006L			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	1006					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)					CGGTGGCAGCGGCAGCGGAAG	0.682																																					p.R1006L		Atlas-SNP	.											.	DAAM2	101	.	0			c.G3017T						PASS	.						21	28	26					6																	39869623		2083	4209	6292	SO:0001583	missense	23500	exon25			GGCAGCGGCAGCG	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.3017G>T	chr6.hg19:g.39869623G>T	ENSP00000381876:p.Arg1006Leu	19.0	0.0	.		37.0	20.0	.	NM_001201427	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	hg19	CCDS56426.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.598634	0.87055	.	.	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	T;T;T	0.80123	-1.34;-1.34;-1.34	5.51	5.51	0.81932	Actin-binding FH2/DRF autoregulatory (1);	0.162307	0.43260	D	0.000587	T	0.75057	0.3798	L	0.50333	1.59	0.80722	D	1	P;P	0.51933	0.949;0.915	P;B	0.44447	0.45;0.263	T	0.79624	-0.1726	10	0.72032	D	0.01	.	18.9986	0.92824	0.0:0.0:1.0:0.0	.	1005;1006	G5EA45;Q86T65	.;DAAM2_HUMAN	L	1006;1006;1005	ENSP00000274867:R1006L;ENSP00000381876:R1006L;ENSP00000437808:R1005L	ENSP00000274867:R1006L	R	+	2	0	DAAM2	39977601	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.632000	0.67819	2.586000	0.87340	0.561000	0.74099	CGG	.	.	.	none		0.682	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1			T	39869623	G	T	39869623	3	4	10	1	0	0	0	0	1	0	0	0	4218	1116	39	4	3108	4	DAAM2	6	39869623	Missense_Mutation	SNP	G	TCGA-2Z-A9JE-01A-11D-A42J-10		39869623	131245444	39	775											
SMPDL3A	10924	hgsc.bcm.edu	37	chr6	123116945	123116945	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccctggcccttttggagatgTtctgtgtgattctccatatc	5	16	9	11	0	2	2	0	1	2	1	4	3	2	2	3	2	0	1	3	2	1	5			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr6:123116945T>C	ENST00000368440.4	+	2	413	c.236T>C	c.(235-237)gTt>gCt	p.V79A	SMPDL3A_ENST00000487215.1_3'UTR|SMPDL3A_ENST00000539041.1_Intron	NM_006714.3	NP_006705.1	Q92484	ASM3A_HUMAN	sphingomyelin phosphodiesterase, acid-like 3A	79					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)		TTTGGAGATGTTCTGTGTGAT	0.388																																					p.V79A		Atlas-SNP	.											.	SMPDL3A	31	.	0			c.T236C						PASS	.						165	150	155					6																	123116945		2203	4300	6503	SO:0001583	missense	10924	exon2			GAGATGTTCTGTG	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.236T>C	chr6.hg19:g.123116945T>C	ENSP00000357425:p.Val79Ala	88.0	0.0	.		65.0	31.0	.	NM_006714	B7Z729|Q8WV13	Missense_Mutation	SNP	ENST00000368440.4	hg19	CCDS5128.1	.	.	.	.	.	.	.	.	.	.	T	18.15	3.560482	0.65538	.	.	ENSG00000172594	ENST00000368440	D	0.94966	-3.57	5.27	5.27	0.74061	Metallophosphoesterase domain (1);	0.160331	0.56097	D	0.000031	D	0.86585	0.5968	L	0.29908	0.895	0.80722	D	1	B	0.31655	0.334	B	0.28385	0.089	D	0.87329	0.2323	10	0.51188	T	0.08	-12.4189	15.4763	0.75481	0.0:0.0:0.0:1.0	.	79	Q92484	ASM3A_HUMAN	A	79	ENSP00000357425:V79A	ENSP00000357425:V79A	V	+	2	0	SMPDL3A	123158644	1.000000	0.71417	0.999000	0.59377	0.979000	0.70002	7.651000	0.83577	2.112000	0.64535	0.528000	0.53228	GTT	.	.	.	none		0.388	SMPDL3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042039.1	NM_006714		C	123116945	T	C	123116945	3	2	10	1	0	0	0	0	1	0	0	0	14821	1725	60	3	242	3	SMPDL3A	6	123116945	Missense_Mutation	SNP	T	TCGA-2Z-A9JE-01A-11D-A42J-10	83247322	123116945	47998122	40	776											
REPS1	85021	hgsc.bcm.edu	37	chr6	139262521	139262521	+	Frame_Shift_Del	DEL	T	T	-																															ggcattaagctttcaggaagTttttctggtaaatcatagcc																										TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr6:139262521delT	ENST00000450536.2	-	8	1660	c.1086delA	c.(1084-1086)aaafs	p.K362fs	REPS1_ENST00000415951.2_Frame_Shift_Del_p.K362fs|REPS1_ENST00000258062.5_Frame_Shift_Del_p.K362fs|REPS1_ENST00000367663.4_Frame_Shift_Del_p.K362fs|REPS1_ENST00000409812.2_Frame_Shift_Del_p.K362fs			Q96D71	REPS1_HUMAN	RALBP1 associated Eps domain containing 1	362	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)		TTTCAGGAAGTTTTTCTGGTA	0.403																																					p.L363fs		Atlas-Indel,Pindel	.											.	REPS1	58	.	0			c.1087delC						PASS	.						175	177	176					6																	139262521		2203	4300	6503	SO:0001589	frameshift_variant	85021	exon8			.		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.1086delA	chr6.hg19:g.139262521delT	ENSP00000392065:p.Lys362fs	99.0	0.0	0		91.0	39.0	0.428571	NM_001128617	B7ZBZ8|B7ZBZ9|B7ZC00|J3KP76|Q5JWJ5|Q5JWJ6|Q5JWJ7|Q8NDR7|Q8WU62|Q9BXY9	Frame_Shift_Del	DEL	ENST00000450536.2	hg19																																																																																				.	.	.	none		0.403	REPS1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000042447.3			-	139262521	T	-	139262521	7	5	10	1	0	1	0	1	0	0	0	0	13241	1722	60	0	1356	0	REPS1	6	139262521	Frame_Shift_Del	DEL	T	TCGA-2Z-A9JE-01A-11D-A42J-10	16145576	139262521	31852546	41	777											
USP42	84132	hgsc.bcm.edu	37	chr7	6180604	6180605	+	Frame_Shift_Ins	INS	-	-	TA																															tccatatcttgatataacatINStggagataaaggtaaatttc																										TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr7:6180604_6180605insTA	ENST00000306177.5	+	7	942_943	c.784_785insTA	c.(784-786)ttgfs	p.L262fs		NM_032172.2	NP_115548.1	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	262	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)		TGATATAACATTGGAGATAAAG	0.248																																					p.L262fs		Atlas-Indel,Pindel	.											.	USP42	138	.	0			c.784_785insTA						PASS	.																																			SO:0001589	frameshift_variant	84132	exon7			.	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	Exception_encountered	chr7.hg19:g.6180604_6180605insTA	ENSP00000301962:p.Leu262fs	634.0	0.0	0		990.0	431.0	0.435354	NM_032172	A2RUE3|B5MDA5|Q0VIN8|Q3C166|Q6P9B4	Frame_Shift_Ins	INS	ENST00000306177.5	hg19	CCDS47535.1																																																																																			.	.	.	none		0.248	USP42-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324262.3	XM_166526		TA	6180605	-	TA	6180604	7	5	10	1	0	1	1	0	0	0	0	0	17085	1490	52	0	806	0	USP42	7	6180604	Frame_Shift_Ins	INS	-	TCGA-2Z-A9JE-01A-11D-A42J-10		6180604	152958059	42	778											
CCDC146	57639	hgsc.bcm.edu	37	chr7	76885742	76885744	+	In_Frame_Del	DEL	AGA	AGA	-																															ttagaaattaaaaatttacgAgaagatttggcatctaaaca																										TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr7:76885742_76885744delAGA	ENST00000285871.4	+	6	727_729	c.600_602delAGA	c.(598-603)cgagaa>cga	p.E201del	AC073635.5_ENST00000476561.2_RNA|CCDC146_ENST00000431197.1_5'UTR	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	201										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)				AAAATTTACGAGAAGATTTGGCA	0.325																																					p.200_201del		Atlas-Indel,Pindel	.											.	CCDC146	87	.	0			c.599_601del						PASS	.																																			SO:0001651	inframe_deletion	57639	exon6			.	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.600_602delAGA	chr7.hg19:g.76885745_76885747delAGA	ENSP00000285871:p.Glu201del	195.0	0.0	0		398.0	83.0	0.208543	NM_020879	A8K8X6|Q9P223	In_Frame_Del	DEL	ENST00000285871.4	hg19	CCDS34671.1																																																																																			.	.	.	none		0.325	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879		-	76885744	AGA	-	76885742	7	5	10	1	0	1	0	1	0	0	0	0	2782	291	11	0	618	0	CCDC146	7	76885742	In_Frame_Del	DEL	AGA	TCGA-2Z-A9JE-01A-11D-A42J-10	70705138	76885742	82252921	43	779											
SEMA3E	9723	hgsc.bcm.edu	37	chr7	82997040	82997040	+	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	ctatctgtgcaccatactttCtcgcagtattcttccactct	7	16	4	14	1	4	0	0	0	4	0	6	0	5	0	2	0	2	3	2	0	3	6			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr7:82997040C>G	ENST00000307792.3	-	17	2657	c.2190G>C	c.(2188-2190)gaG>gaC	p.E730D	SEMA3E_ENST00000427262.1_Missense_Mutation_p.E670D	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	730					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)				ACCATACTTTCTCGCAGTATT	0.463																																					p.E730D		Atlas-SNP	.											.	SEMA3E	125	.	0			c.G2190C						PASS	.						171	168	169					7																	82997040		2203	4300	6503	SO:0001583	missense	9723	exon17			TACTTTCTCGCAG	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.2190G>C	chr7.hg19:g.82997040C>G	ENSP00000303212:p.Glu730Asp	118.0	0.0	.		226.0	111.0	.	NM_012431	B4E1P1|Q75M94|Q75M97	Missense_Mutation	SNP	ENST00000307792.3	hg19	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	C	16.64	3.180104	0.57800	.	.	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514	T;T	0.80123	-1.34;-1.34	5.74	0.768	0.18487	.	0.000000	0.85682	D	0.000000	D	0.82683	0.5090	M	0.80746	2.51	0.51012	D	0.999905	B	0.33612	0.419	B	0.43018	0.405	T	0.79431	-0.1806	10	0.59425	D	0.04	.	10.2558	0.43397	0.0:0.3408:0.0:0.6592	.	730	O15041	SEM3E_HUMAN	D	730;670;730	ENSP00000303212:E730D;ENSP00000405052:E670D	ENSP00000303212:E730D	E	-	3	2	SEMA3E	82834976	0.988000	0.35896	0.971000	0.41717	0.958000	0.62258	0.183000	0.16919	-0.090000	0.12462	-0.482000	0.04802	GAG	.	.	.	none		0.463	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431		G	82997040	C	G	82997040	3	3	10	1	0	0	0	0	1	0	0	0	14041	912	32	4	141	4	SEMA3E	7	82997040	Missense_Mutation	SNP	C	TCGA-2Z-A9JE-01A-11D-A42J-10	6111298	82997040	76141623	44	780											
FLJ36031	168455	hgsc.bcm.edu	37	chr7	106301196	106301196	+	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	agcgccttggtgctgtcagcCagcgacagttgcgaccgcga	7	7	14	13	5	1	0	1	0	0	0	1	3	1	0	3	1	5	2	3	1	0	2			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr7:106301196C>G	ENST00000523505.1	-	1	246	c.147G>C	c.(145-147)ctG>ctC	p.L49L		NM_175884.4	NP_787080.2	Q8N9Z2	CC71L_HUMAN	coiled-coil domain containing 71-like	49										endometrium(1)	1						TGCTGTCAGCCAGCGACAGTT	0.677																																					p.L49L		Atlas-SNP	.											.	CCDC71L	2	.	0			c.G147C						PASS	.						13	16	15					7																	106301196		2068	4201	6269	SO:0001819	synonymous_variant	168455	exon1			GTCAGCCAGCGAC		CCDS55151.1	7q22.3	2011-12-12	2011-12-12	2011-12-12	ENSG00000253276	ENSG00000253276			26685	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 74"	C7orf74		12477932	Standard	NM_175884		Approved	FLJ36031	uc003vdt.3	Q8N9Z2	OTTHUMG00000164150	ENST00000523505.1:c.147G>C	chr7.hg19:g.106301196C>G		103.0	0.0	.		127.0	73.0	.	NM_175884	Q7Z756	Silent	SNP	ENST00000523505.1	hg19	CCDS55151.1																																																																																			.	.	.	none		0.677	CCDC71L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377493.1	NM_175884		G	106301196	C	G	106301196	2	3	10	1	0	0	0	0	0	0	0	1	5935	581	21	4		4	FLJ36031	7	106301196	Silent	SNP	C	TCGA-2Z-A9JE-01A-11D-A42J-10	23304156	106301196	52837467	45	781											
INTS10	55174	hgsc.bcm.edu	37	chr8	19680900	19680901	+	Frame_Shift_Ins	INS	-	-	T																															acttgaacaaagcagctgaaINSttttatatcaattatgtcac																										TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr8:19680900_19680901insT	ENST00000397977.3	+	6	1010_1011	c.612_613insT	c.(613-615)tttfs	p.F205fs		NM_018142.2	NP_060612.2	Q9NVR2	INT10_HUMAN	integrator complex subunit 10	205					snRNA processing (GO:0016180)	integrator complex (GO:0032039)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	20				Colorectal(111;0.057)|COAD - Colon adenocarcinoma(73;0.215)		AAGCAGCTGAATTTTATATCAA	0.327																																					p.E204fs		Atlas-Indel,Pindel	.											.	INTS10	46	.	0			c.612_613insT						PASS	.																																			SO:0001589	frameshift_variant	55174	exon6			.	AK001431	CCDS6011.2	8p21.3	2006-04-26	2006-03-15	2006-03-15	ENSG00000104613	ENSG00000104613			25548	protein-coding gene	gene with protein product		611353	"chromosome 8 open reading frame 35"	C8orf35		16239144	Standard	XM_005273558		Approved	FLJ10569, INT10	uc003wzj.3	Q9NVR2	OTTHUMG00000131065	ENST00000397977.3:c.616dupT	chr8.hg19:g.19680904_19680904dupT	ENSP00000381064:p.Phe205fs	104.0	0.0	0		75.0	27.0	0.36	NM_018142	Q6IA93|Q7L538|Q7L8C8|Q9H3W8	Frame_Shift_Ins	INS	ENST00000397977.3	hg19	CCDS6011.2																																																																																			.	.	.	none		0.327	INTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253724.2	NM_018142		T	19680901	-	T	19680900	7	5	10	1	0	1	1	0	0	0	0	0	7783	98	4	0	634	0	INTS10	8	19680900	Frame_Shift_Ins	INS	-	TCGA-2Z-A9JE-01A-11D-A42J-10		19680900	126683122	46	782											
GRINA	2907	hgsc.bcm.edu	37	chr8	145066228	145066230	+	In_Frame_Del	DEL	CTG	CTG	-																															gacttccggcgaaagcacccCtggaaccttgttgcactggt																										TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr8:145066228_145066230delCTG	ENST00000313269.5	+	4	953_955	c.675_677delCTG	c.(673-678)ccctgg>ccg	p.W226del	GRINA_ENST00000395068.4_In_Frame_Del_p.W226del	NM_000837.1	NP_000828.1	Q7Z429	LFG1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (glutamate binding)	226						integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|stomach(1)	9	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;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GAAAGCACCCCTGGAACCTTGTT	0.581																																					p.225_226del		Atlas-Indel,Pindel	.											.	GRINA	25	.	0			c.674_676del						PASS	.																																			SO:0001651	inframe_deletion	2907	exon4			.	NM_001009184	CCDS34961.1	8q24.3	2010-03-18	2008-04-01						4589	protein-coding gene	gene with protein product	"transmembrane BAX inhibitor motif containing 3"	138251		NMDARA1		1719427, 8406459	Standard	XM_005250899		Approved	HNRGW, TMBIM3, LFG1	uc003zao.1	Q7Z429		ENST00000313269.5:c.675_677delCTG	chr8.hg19:g.145066228_145066230delCTG	ENSP00000314380:p.Trp226del	62.0	0.0	0		66.0	29.0	0.439394	NM_001009184	B3KXM7|O43836|Q8IVW7	In_Frame_Del	DEL	ENST00000313269.5	hg19	CCDS34961.1																																																																																			.	.	.	none		0.581	GRINA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384048.1	NM_001009184		-	145066230	CTG	-	145066228	7	5	10	1	0	1	0	1	0	0	0	0	6792	668	24	0	685	0	GRINA	8	145066228	In_Frame_Del	DEL	CTG	TCGA-2Z-A9JE-01A-11D-A42J-10	125385328	145066228	1297794	47	783											
OMD	4958	hgsc.bcm.edu	37	chr9	95179162	95179162	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaaggcaaaccaggaggcaTtgattctaatctgttactgc	13	10	10	8	0	2	2	0	1	2	1	2	3	2	3	1	3	3	3	1	3	4	4	rs376323161		TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr9:95179162T>C	ENST00000375550.4	-	2	954	c.679A>G	c.(679-681)Atg>Gtg	p.M227V	CENPP_ENST00000375587.3_Intron	NM_005014.2	NP_005005.1	Q99983	OMD_HUMAN	osteomodulin	227					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(3)|skin(2)	16						CCAGGAGGCATTGATTCTAAT	0.333			T	USP6	aneurysmal bone cysts																																p.M227V		Atlas-SNP	.		Dom	yes		9	9q22.31	4958	osteomodulin		M	.	OMD	42	.	0			c.A679G						PASS	.	T	,VAL/MET	0,4406		0,0,2203	106	107	107		,679	5.5	1	9		107	1,8599	1.2+/-3.3	0,1,4299	no	intron,missense	OMD,CENPP	NM_001012267.1,NM_005014.2	,21	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	,possibly-damaging	,227/422	95179162	1,13005	2203	4300	6503	SO:0001583	missense	4958	exon2			GAGGCATTGATTC	AB000114	CCDS6696.1	9q22.31	2008-02-05			ENSG00000127083	ENSG00000127083		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	8134	protein-coding gene	gene with protein product	"osteoadherin proteoglycan"						Standard	NM_005014		Approved	osteoadherin, SLRR2C	uc004asd.4	Q99983	OTTHUMG00000020225	ENST00000375550.4:c.679A>G	chr9.hg19:g.95179162T>C	ENSP00000364700:p.Met227Val	66.0	0.0	.		88.0	37.0	.	NM_005014	Q5TBF4	Missense_Mutation	SNP	ENST00000375550.4	hg19	CCDS6696.1	.	.	.	.	.	.	.	.	.	.	t	13.99	2.403284	0.42613	0.0	1.16E-4	ENSG00000127083	ENST00000375550	T	0.03951	3.75	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.03136	0.0092	N	0.00436	-1.5	0.42460	D	0.992789	D	0.60575	0.988	P	0.52109	0.69	T	0.67833	-0.5568	10	0.52906	T	0.07	-16.0215	15.9136	0.79491	0.0:0.0:0.0:1.0	.	227	Q99983	OMD_HUMAN	V	227	ENSP00000364700:M227V	ENSP00000364700:M227V	M	-	1	0	OMD	94218983	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	3.112000	0.50368	2.216000	0.71823	0.528000	0.53228	ATG	.	.	.	weak		0.333	OMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053090.1	NM_005014		C	95179162	T	C	95179162	3	2	10	1	0	0	0	0	1	0	0	0	10872	1493	52	3	594	3	OMD	9	95179162	Missense_Mutation	SNP	T	TCGA-2Z-A9JE-01A-11D-A42J-10		95179162	46034269	48	784											
GRIN3A	116443	hgsc.bcm.edu	37	chr9	104433388	104433388	+	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	gaaagtggtattggctagaaAcctgggaaagaggagcaaag	16	6	15	4	0	0	2	0	0	0	2	0	5	0	4	1	4	2	3	1	4	6	3			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr9:104433388A>T	ENST00000361820.3	-	3	1906	c.1306T>A	c.(1306-1308)Ttt>Att	p.F436I		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	436					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)	TTGGCTAGAAACCTGGGAAAG	0.408																																					p.F436I		Atlas-SNP	.											.	GRIN3A	186	.	0			c.T1306A						PASS	.						71	74	73					9																	104433388		2203	4300	6503	SO:0001630	splice_region_variant	116443	exon3			CTAGAAACCTGGG		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.1305-1T>A	chr9.hg19:g.104433388A>T		62.0	0.0	.		93.0	43.0	.	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	hg19	CCDS6758.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.198025	0.79015	.	.	ENSG00000198785	ENST00000361820	D	0.86497	-2.13	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.92639	0.7661	M	0.79258	2.445	0.58432	D	0.999994	D	0.59767	0.986	P	0.61533	0.89	D	0.93383	0.6745	10	0.72032	D	0.01	.	16.3634	0.83296	1.0:0.0:0.0:0.0	.	436	Q8TCU5	NMD3A_HUMAN	I	436	ENSP00000355155:F436I	ENSP00000355155:F436I	F	-	1	0	GRIN3A	103473209	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	9.248000	0.95456	2.324000	0.78689	0.533000	0.62120	TTT	.	.	.	none		0.408	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		Missense_Mutation	T	104433388	A	T	104433388	5	4	10	1	0	0	0	0	0	0	1	0	6790	57	2	5	2069	5	GRIN3A	9	104433388	Splice_Site	SNP	A	TCGA-2Z-A9JE-01A-11D-A42J-10	9254226	104433388	36780043	49	785											
FBXW2	26190	hgsc.bcm.edu	37	chr9	123533652	123533652	+	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	atatcataactggcaaagtcCcactggtagagaccaagtgc	14	8	9	10	0	1	1	1	0	0	1	2	2	2	1	2	2	2	2	2	2	5	3			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr9:123533652C>G	ENST00000608872.1	-	7	1237	c.1050G>C	c.(1048-1050)tgG>tgC	p.W350C	FBXW2_ENST00000493559.1_5'UTR|FBXW2_ENST00000340778.5_Missense_Mutation_p.W285C	NM_012164.3	NP_036296.2	Q9UKT8	FBXW2_HUMAN	F-box and WD repeat domain containing 2	350					cellular protein modification process (GO:0006464)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)			ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	4						TGGCAAAGTCCCACTGGTAGA	0.428																																					p.W350C		Atlas-SNP	.											.	FBXW2	34	.	0			c.G1050C						PASS	.						101	90	93					9																	123533652		1905	4133	6038	SO:0001583	missense	26190	exon7			AAAGTCCCACTGG	AF129531	CCDS43872.1	9q34	2013-01-09	2007-02-08		ENSG00000119402	ENSG00000119402		"F-boxes / WD-40 domains", "WD repeat domain containing"	13608	protein-coding gene	gene with protein product		609071	"F-box and WD-40 domain protein 2"			10531035, 10828603	Standard	NM_012164		Approved	FBW2, Md6, Fwd2	uc004bkm.1	Q9UKT8	OTTHUMG00000020576	ENST00000608872.1:c.1050G>C	chr9.hg19:g.123533652C>G	ENSP00000476369:p.Trp350Cys	68.0	0.0	.		82.0	29.0	.	NM_012164	B3KRL8|Q4VXH2|Q7Z4V6|Q8WV51|Q9HA09|Q9UKA3	Missense_Mutation	SNP	ENST00000608872.1	hg19	CCDS43872.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.824693	0.90955	.	.	ENSG00000119402	ENST00000373926;ENST00000340778;ENST00000444833	T;T	0.30981	1.51;1.51	5.77	5.77	0.91146	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.57888	0.2084	M	0.74467	2.265	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.999	P;D;D	0.77557	0.823;0.99;0.99	T	0.58792	-0.7574	10	0.87932	D	0	-4.808	17.8518	0.88748	0.0:1.0:0.0:0.0	.	285;350;350	Q9UKT8-2;B2RAW3;Q9UKT8	.;.;FBXW2_HUMAN	C	350;285;350	ENSP00000363036:W350C;ENSP00000341161:W285C	ENSP00000341161:W285C	W	-	3	0	FBXW2	122573473	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.885000	0.99019	0.655000	0.94253	TGG	.	.	.	none		0.428	FBXW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053834.2			G	123533652	C	G	123533652	3	3	10	1	0	0	0	0	1	0	0	0	5773	624	22	4	322	4	FBXW2	9	123533652	Missense_Mutation	SNP	C	TCGA-2Z-A9JE-01A-11D-A42J-10	19100264	123533652	17679779	50	786											
ZNF79	7633	hgsc.bcm.edu	37	chr9	130197411	130197411	+	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	tgacggtagcttttgcacagGaaaggtggaggtgcctcgtg	8	10	16	7	2	0	1	0	1	0	0	1	3	0	3	1	5	3	3	1	5	2	3			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr9:130197411G>A	ENST00000342483.5	+	3	554	c.148G>A	c.(148-150)Gaa>Aaa	p.E50K	ZNF79_ENST00000543471.1_Missense_Mutation_p.E26K	NM_007135.2	NP_009066.2	Q15937	ZNF79_HUMAN	zinc finger protein 79	50	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|stomach(2)	28						TTTTGCACAGGAAAGGTGGAG	0.507																																					p.E50K		Atlas-SNP	.											.	ZNF79	47	.	0			c.G148A						PASS	.						140	135	137					9																	130197411		2203	4300	6503	SO:0001583	missense	7633	exon3			GCACAGGAAAGGT	X65232	CCDS6871.1, CCDS69664.1, CCDS75904.1	9q34	2013-01-08	2006-05-12		ENSG00000196152	ENSG00000196152		"Zinc fingers, C2H2-type"	13153	protein-coding gene	gene with protein product		194552	"zinc finger protein 79 (pT7)"			8478004	Standard	NM_007135		Approved	pT7	uc004bqw.4	Q15937	OTTHUMG00000020703	ENST00000342483.5:c.148G>A	chr9.hg19:g.130197411G>A	ENSP00000362446:p.Glu50Lys	129.0	0.0	.		141.0	59.0	.	NM_007135	Q5VVW1|Q96NV1	Missense_Mutation	SNP	ENST00000342483.5	hg19	CCDS6871.1	.	.	.	.	.	.	.	.	.	.	G	11.55	1.671323	0.29693	.	.	ENSG00000196152	ENST00000342483;ENST00000543471	T;T	0.01295	5.04;5.04	3.19	0.134	0.14771	Krueppel-associated box (3);	.	.	.	.	T	0.01800	0.0057	L	0.56396	1.775	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43327	-0.9398	9	0.62326	D	0.03	.	3.6122	0.08065	0.2508:0.2087:0.5405:0.0	.	50	Q15937	ZNF79_HUMAN	K	50;26	ENSP00000362446:E50K;ENSP00000438418:E26K	ENSP00000362446:E50K	E	+	1	0	ZNF79	129237232	0.009000	0.17119	0.000000	0.03702	0.032000	0.12392	0.751000	0.26348	-0.088000	0.12506	0.462000	0.41574	GAA	.	.	.	none		0.507	ZNF79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054188.1	NM_007135		A	130197411	G	A	130197411	3	1	10	1	0	0	0	0	1	0	0	0	18173	1175	41	2	158	2	ZNF79	9	130197411	Missense_Mutation	SNP	G	TCGA-2Z-A9JE-01A-11D-A42J-10	6663759	130197411	11016020	51	787											
ADARB2	105	hgsc.bcm.edu	37	chr10	1279742	1279743	+	Frame_Shift_Del	DEL	TT	TT	-																															cgcagccggtagccaccttcTtttaaccgcacgaatatcga																								rs191642114		TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr10:1279742_1279743delTT	ENST00000381312.1	-	6	1731_1732	c.1406_1407delAA	c.(1405-1407)aaafs	p.K469fs	ADARB2_ENST00000469464.1_5'UTR	NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)	469	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)		AGCCACCTTCTTTTAACCGCAC	0.53																																					p.469_470del		Atlas-Indel,Pindel	.											.	ADARB2	95	.	0			c.1407_1408del						PASS	.																																			SO:0001589	frameshift_variant	105	exon6			.	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.1406_1407delAA	chr10.hg19:g.1279744_1279745delTT	ENSP00000370713:p.Lys469fs	104.0	0.0	0		99.0	45.0	0.454545	NM_018702	B2RPJ5|Q5VUT6|Q5VW42	Frame_Shift_Del	DEL	ENST00000381312.1	hg19	CCDS7058.1																																																																																			.	.	.	none		0.53	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702		-	1279743	TT	-	1279742	7	5	10	1	0	1	0	1	0	0	0	0	283	1606	56	0	832	0	ADARB2	10	1279742	Frame_Shift_Del	DEL	TT	TCGA-2Z-A9JE-01A-11D-A42J-10		1279742	134255005	52	788											
KIAA1462	57608	hgsc.bcm.edu	37	chr10	30315194	30315194	+	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	gcctcccgggagcccggcctGgccccttgtggtggccttca	2	8	14	17	2	1	0	1	0	0	0	2	1	2	1	7	5	1	0	7	5	0	2			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr10:30315194G>A	ENST00000375377.1	-	3	3984	c.3883C>T	c.(3883-3885)Cag>Tag	p.Q1295*		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	1295					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						AGCCCGGCCTGGCCCCTTGTG	0.612																																					p.Q1295X		Atlas-SNP	.											.	KIAA1462	162	.	0			c.C3883T						PASS	.						50	50	50					10																	30315194		1881	4108	5989	SO:0001587	stop_gained	57608	exon3			CGGCCTGGCCCCT	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.3883C>T	chr10.hg19:g.30315194G>A	ENSP00000364526:p.Gln1295*	38.0	0.0	.		37.0	17.0	.	NM_020848	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Nonsense_Mutation	SNP	ENST00000375377.1	hg19	CCDS41500.1	.	.	.	.	.	.	.	.	.	.	G	40	8.310626	0.98754	.	.	ENSG00000165757	ENST00000375377	.	.	.	4.92	4.01	0.46588	.	1.055720	0.07447	N	0.898331	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	0.0089	10.5989	0.45354	0.0947:0.0:0.9053:0.0	.	.	.	.	X	1295	.	ENSP00000364526:Q1295X	Q	-	1	0	KIAA1462	30355200	0.000000	0.05858	0.002000	0.10522	0.066000	0.16364	0.115000	0.15540	1.069000	0.40788	0.655000	0.94253	CAG	.	.	.	none		0.612	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848		A	30315194	G	A	30315194	4	1	10	1	0	0	0	0	0	1	0	0	8241	1357	47	2	204	2	KIAA1462	10	30315194	Nonsense_Mutation	SNP	G	TCGA-2Z-A9JE-01A-11D-A42J-10	29035452	30315194	105219553	53	789											
C10orf10	11067	hgsc.bcm.edu	37	chr10	45473410	45473410	+	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	tcctgtccaggacccccaagCagcatctcctccgtggtctc	6	9	8	18	1	2	0	0	0	2	0	7	1	5	1	6	2	2	2	6	2	1	0			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr10:45473410C>A	ENST00000298295.3	-	2	286	c.69G>T	c.(67-69)ctG>ctT	p.L23L	RASSF4_ENST00000334940.6_Intron|RASSF4_ENST00000374417.2_Intron|RASSF4_ENST00000340258.5_Intron|C10orf10_ENST00000496638.1_Intron|RASSF4_ENST00000472561.1_Intron	NM_007021.3	NP_008952.1	Q9NTK1	DEPP_HUMAN	chromosome 10 open reading frame 10	23						mitochondrion (GO:0005739)				lung(1)	1						GACCCCCAAGCAGCATCTCCT	0.617																																					p.L23L		Atlas-SNP	.											.	C10orf10	6	.	0			c.G69T						PASS	.						47	51	50					10																	45473410		2202	4296	6498	SO:0001819	synonymous_variant	11067	exon2			CCCAAGCAGCATC	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.69G>T	chr10.hg19:g.45473410C>A		98.0	0.0	.		88.0	42.0	.	NM_007021	B2R6A1|O94997|Q5T735|Q76MX8	Silent	SNP	ENST00000298295.3	hg19	CCDS7210.1																																																																																			.	.	.	none		0.617	C10orf10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047758.1	NM_007021		A	45473410	C	A	45473410	2	1	10	1	0	0	0	0	0	0	0	1	1582	697	25	4		4	C10orf10	10	45473410	Silent	SNP	C	TCGA-2Z-A9JE-01A-11D-A42J-10	15158216	45473410	90061337	54	790											
PPYR1	5540	hgsc.bcm.edu	37	chr10	47086821	47086842	+	Frame_Shift_Del	DEL	AATCTCCACAAGGTGAAAACAG	AATCTCCACAAGGTGAAAACAG	-																															cctggccttgctgctcccaaAatctccacaaggtgaaaaca																										TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	AATCTCCACAAGGTGAAAACAG	AATCTCCACAAGGTGAAAACAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr10:47086821_47086842delAATCTCCACAAGGTGAAAACAG	ENST00000395716.1	+	2	123_144	c.38_59delAATCTCCACAAGGTGAAAACAG	c.(37-60)aaatctccacaaggtgaaaacagafs	p.KSPQGENR13fs	NPY4R_ENST00000374312.1_Frame_Shift_Del_p.KSPQGENR13fs			P50391	NPY4R_HUMAN	neuropeptide Y receptor Y4	13					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)										CTGCTCCCAAAATCTCCACAAGGTGAAAACAGAAGCAAACCC	0.491																																					p.13_20del		Atlas-Indel,Pindel	.											.	PPYR1	54	.	0			c.37_58del						PASS	.																																			SO:0001589	frameshift_variant	5540	exon3			.		CCDS73100.1	10q11.2	2013-03-26	2013-03-26	2013-03-26	ENSG00000204174	ENSG00000204174		"GPCR / Class A : Neuropeptide receptors : Y"	9329	protein-coding gene	gene with protein product		601790	"pancreatic polypeptide receptor 1"	PPYR1		9417917	Standard	NM_005972		Approved	Y4, PP1	uc001jee.3	P50391	OTTHUMG00000018108	ENST00000395716.1:c.38_59delAATCTCCACAAGGTGAAAACAG	chr10.hg19:g.47086821_47086842delAATCTCCACAAGGTGAAAACAG	ENSP00000379066:p.Lys13fs	225.0	0.0	0		228.0	27.0	0.118421	NM_005972	Q13456|Q5ISU3|Q5T2X9|Q6FH06	Frame_Shift_Del	DEL	ENST00000395716.1	hg19	CCDS31193.1																																																																																			.	.	.	none		0.491	NPY4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047837.1			-	47086842	AATCTCCACAAGGTGAAAACAG	-	47086821	7	5	10	1	0	1	0	1	0	0	0	0	12426	14	1	0	40	0	PPYR1	10	47086821	Frame_Shift_Del	DEL	AATCTCCACAAGGTGAAAACAG	TCGA-2Z-A9JE-01A-11D-A42J-10	1613411	47086821	88447926	55	791											
TIMM23	100287932	hgsc.bcm.edu	37	chr10	51623127	51623127	+	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	acgcgggacgccagccaaatCcgcgtgcgagtaacctgctc	9	5	12	15	6	0	0	0	0	0	0	2	2	1	1	4	1	4	2	4	1	2	1			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr10:51623127C>T	ENST00000260867.4	-	1	211	c.88G>A	c.(88-90)Gat>Aat	p.D30N	TIMM23_ENST00000374065.3_Missense_Mutation_p.D30N|TIMM23_ENST00000374064.3_Missense_Mutation_p.D30N	NM_006327.3	NP_006318.1	O14925	TIM23_HUMAN	translocase of inner mitochondrial membrane 23 homolog (yeast)	30					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial inner membrane (GO:0005743)|mitochondrial inner membrane presequence translocase complex (GO:0005744)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO:0015450)			endometrium(1)|large_intestine(1)|pancreas(1)	3						CCAGCCAAATCCGCGTGCGAG	0.562																																					p.D30N		Atlas-SNP	.											.	TIMM23	4	.	0			c.G88A						PASS	.						14	14	14					10																	51623127		2190	4252	6442	SO:0001583	missense	100287932	exon1			CCAAATCCGCGTG	AF030162	CCDS73091.1	10q11.21-q11.23	2010-03-17			ENSG00000138297				17312	protein-coding gene	gene with protein product		605034				10339406	Standard	NM_006327		Approved	TIM23	uc010qha.2	O14925	OTTHUMG00000018213	ENST00000260867.4:c.88G>A	chr10.hg19:g.51623127C>T	ENSP00000260867:p.Asp30Asn	617.0	1.0	.		656.0	126.0	.	NM_006327	Q53FF8|Q5T1E6|Q6P5S5	Missense_Mutation	SNP	ENST00000260867.4	hg19	CCDS7238.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.10|16.10	3.026269|3.026269	0.54683|0.54683	.|.	.|.	ENSG00000138297|ENSG00000138297	ENST00000260867;ENST00000374064;ENST00000374065|ENST00000444743	.|.	.|.	.|.	4.5|4.5	3.59|3.59	0.41128|0.41128	.|.	0.052211|.	0.85682|.	D|.	0.000000|.	T|T	0.49270|0.49270	0.1547|0.1547	L|L	0.27053|0.27053	0.805|0.805	0.45704|0.45704	D|D	0.998618|0.998618	P;P|.	0.42078|.	0.77;0.608|.	B;B|.	0.42827|.	0.399;0.202|.	T|T	0.39057|0.39057	-0.9632|-0.9632	9|5	0.33940|.	T|.	0.23|.	-6.7486|-6.7486	11.0311|11.0311	0.47774|0.47774	0.0:0.9103:0.0:0.0897|0.0:0.9103:0.0:0.0897	.|.	30;30|.	B1APJ0;O14925|.	.;TIM23_HUMAN|.	N|E	30|26	.|.	ENSP00000260867:D30N|.	D|G	-|-	1|2	0|0	TIMM23|TIMM23	51293133|51293133	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.781000|0.781000	0.44180|0.44180	6.170000|6.170000	0.71920|0.71920	1.237000|1.237000	0.43756|0.43756	-0.216000|-0.216000	0.12614|0.12614	GAT|GGA	.	.	.	none		0.562	TIMM23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048040.1	NM_006327.2		T	51623127	C	T	51623127	3	4	10	1	0	0	0	0	1	0	0	0	15923	855	30	2	569	2	TIMM23	10	51623127	Missense_Mutation	SNP	C	TCGA-2Z-A9JE-01A-11D-A42J-10	4536306	51623127	83911620	56	792											
RAG1	5896	hgsc.bcm.edu	37	chr11	36596889	36596889	+	Missense_Mutation	SNP	A	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	ctgccatcctgagtcctctcAttgctgagagggaggccatg	7	10	12	12	0	1	2	1	2	1	1	4	4	3	3	4	2	2	1	4	2	0	1	rs143227621		TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr11:36596889A>C	ENST00000299440.5	+	2	2147	c.2035A>C	c.(2035-2037)Att>Ctt	p.I679L		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	679					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				GAGTCCTCTCATTGCTGAGAG	0.512									Familial Hemophagocytic Lymphohistiocytosis																												p.I679L	Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)	Atlas-SNP	.											.	RAG1	151	.	0			c.A2035C						PASS	.						56	51	52					11																	36596889		2202	4298	6500	SO:0001583	missense	5896	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	CCTCTCATTGCTG	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"RING-type (C3HC4) zinc fingers"	9831	protein-coding gene	gene with protein product	"recombination activating protein 1", "RING finger protein 74", "V(D)J recombination-activating protein 1"	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.2035A>C	chr11.hg19:g.36596889A>C	ENSP00000299440:p.Ile679Leu	51.0	0.0	.		72.0	32.0	.	NM_000448	E9PPC4|Q8IY72|Q8NER2	Missense_Mutation	SNP	ENST00000299440.5	hg19	CCDS7902.1	.	.	.	.	.	.	.	.	.	.	A	16.37	3.103025	0.56183	.	.	ENSG00000166349	ENST00000534663;ENST00000299440	D;D	0.85702	-2.02;-2.02	5.98	3.67	0.42095	.	0.171732	0.49916	D	0.000132	D	0.83069	0.5174	M	0.69248	2.105	0.44816	D	0.997826	B	0.21520	0.057	B	0.27076	0.076	T	0.78453	-0.2198	10	0.87932	D	0	.	9.4229	0.38561	0.8006:0.0:0.1994:0.0	.	679	P15918	RAG1_HUMAN	L	679	ENSP00000434610:I679L;ENSP00000299440:I679L	ENSP00000299440:I679L	I	+	1	0	RAG1	36553465	1.000000	0.71417	0.939000	0.37840	0.991000	0.79684	3.264000	0.51553	0.519000	0.28406	0.524000	0.50904	ATT	.	A|1.000;G|0.000	.	alt		0.512	RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448		C	36596889	A	C	36596889	3	2	10	1	0	0	0	0	1	0	0	0	13016	217	8	5	2037	5	RAG1	11	36596889	Missense_Mutation	SNP	A	TCGA-2Z-A9JE-01A-11D-A42J-10		36596889	98409627	57	793											
CELF1	10658	hgsc.bcm.edu	37	chr11	47498949	47498950	+	Frame_Shift_Ins	INS	-	-	A																															ctgcagcagctagtgcagccINSaaattctgtaactgcattgc																								rs35704230		TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr11:47498949_47498950insA	ENST00000358597.3	-	8	790_791	c.791_792insT	c.(790-792)ttgfs	p.L264fs	CELF1_ENST00000539455.1_5'Flank|CELF1_ENST00000310513.5_Frame_Shift_Ins_p.L260fs|CELF1_ENST00000361904.3_Frame_Shift_Ins_p.L260fs|CELF1_ENST00000531165.1_Frame_Shift_Ins_p.L291fs|CELF1_ENST00000395292.2_Frame_Shift_Ins_p.L260fs|CELF1_ENST00000395290.2_Frame_Shift_Ins_p.L263fs|CELF1_ENST00000532048.1_Frame_Shift_Ins_p.L290fs			Q92879	CELF1_HUMAN	CUGBP, Elav-like family member 1	264					embryo development (GO:0009790)|germ cell development (GO:0007281)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of translation (GO:0017148)|positive regulation of multicellular organism growth (GO:0040018)|regulation of RNA splicing (GO:0043484)|RNA interference (GO:0016246)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	BRE binding (GO:0042835)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation repressor activity, nucleic acid binding (GO:0000900)			central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|ovary(2)	18						CTAGTGCAGCCAAATTCTGTAA	0.485																																					p.L290fs	Pancreas(163;1949 1966 9906 43218 43785)	Atlas-Indel,Pindel	.											.	CELF1	43	.	0			c.870_871insT						PASS	.																																			SO:0001589	frameshift_variant	10658	exon11			.	U63289	CCDS7938.1, CCDS7939.1, CCDS31482.1, CCDS53622.1, CCDS53623.1	11p11	2013-02-12	2010-02-19	2010-02-19				"RNA binding motif (RRM) containing"	2549	protein-coding gene	gene with protein product	"CUG RNA-binding protein", "nuclear polyadenylated RNA-binding protein, 50-kD", "bruno-like 2", "embryo deadenylation element binding protein"	601074	"CUG triplet repeat, RNA-binding protein 1", "CUG triplet repeat, RNA binding protein 1"	CUGBP1		8948631, 9371827	Standard	NM_006560		Approved	CUG-BP, hNab50, BRUNOL2, NAB50, CUGBP, NAPOR, EDEN-BP	uc001nfl.3	Q92879		ENST00000358597.3:c.792dupT	chr11.hg19:g.47498952_47498952dupA	ENSP00000351409:p.Leu264fs	50.0	0.0	0		46.0	15.0	0.326087	NM_001172639	B4E2U5|D3DQS0|F8W940|Q4LE52|Q9NP83|Q9NR06	Frame_Shift_Ins	INS	ENST00000358597.3	hg19	CCDS31482.1																																																																																			.	.	.	none		0.485	CELF1-024	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398352.1	NM_006560		A	47498950	-	A	47498949	7	5	10	1	0	1	1	0	0	0	0	0	3217	593	21	0	691	0	CELF1	11	47498949	Frame_Shift_Ins	INS	-	TCGA-2Z-A9JE-01A-11D-A42J-10	10902060	47498949	87507567	58	794											
SSRP1	6749	hgsc.bcm.edu	37	chr11	57102553	57102553	+	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	cattctcaccatggaaccttTcacctcctgatagacgtcgt	9	12	6	14	2	2	2	2	1	1	1	5	3	3	3	4	1	1	0	4	1	2	3			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr11:57102553T>A	ENST00000278412.2	-	2	309	c.43A>T	c.(43-45)Aaa>Taa	p.K15*		NM_003146.2	NP_003137.1	Q08945	SSRP1_HUMAN	structure specific recognition protein 1	15					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						ATGGAACCTTTCACCTCCTGA	0.522																																					p.K15X	Colon(89;1000 1340 6884 23013 41819)	Atlas-SNP	.											.	SSRP1	75	.	0			c.A43T						PASS	.						392	378	383					11																	57102553		2201	4296	6497	SO:0001587	stop_gained	6749	exon2			AACCTTTCACCTC	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.43A>T	chr11.hg19:g.57102553T>A	ENSP00000278412:p.Lys15*	87.0	0.0	.		64.0	28.0	.	NM_003146	Q5BJG8	Nonsense_Mutation	SNP	ENST00000278412.2	hg19	CCDS7952.1	.	.	.	.	.	.	.	.	.	.	T	40	8.368646	0.98781	.	.	ENSG00000149136	ENST00000278412	.	.	.	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	-22.8175	16.0566	0.80812	0.0:0.0:0.0:1.0	.	.	.	.	X	15	.	ENSP00000278412:K15X	K	-	1	0	SSRP1	56859129	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.528000	0.81941	2.272000	0.75746	0.460000	0.39030	AAA	.	.	.	none		0.522	SSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392460.1	NM_003146		A	57102553	T	A	57102553	4	1	10	1	0	0	0	0	0	1	0	0	15206	1792	62	5	2150	5	SSRP1	11	57102553	Nonsense_Mutation	SNP	T	TCGA-2Z-A9JE-01A-11D-A42J-10	9603604	57102553	77903963	59	795											
DAK	26007	hgsc.bcm.edu	37	chr11	61111630	61111630	+	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	tcagcctcgaagcggatggcGctggtgctggaacgggtgtg	6	8	18	9	4	1	0	1	0	0	0	2	3	1	2	1	5	4	2	1	5	2	0			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr11:61111630G>A	ENST00000394900.3	+	13	1354	c.1125G>A	c.(1123-1125)gcG>gcA	p.A375A		NM_015533.3	NP_056348.2	Q3LXA3	DHAK_HUMAN	dihydroxyacetone kinase 2 homolog (S. cerevisiae)	375	DhaL. {ECO:0000255|PROSITE- ProRule:PRU00813}.				carbohydrate phosphorylation (GO:0046835)|cellular carbohydrate metabolic process (GO:0044262)|glycerol metabolic process (GO:0006071)|innate immune response (GO:0045087)|regulation of innate immune response (GO:0045088)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|FAD-AMP lyase (cyclizing) activity (GO:0034012)|glycerone kinase activity (GO:0004371)|metal ion binding (GO:0046872)|triokinase activity (GO:0050354)			NS(1)|breast(3)|endometrium(3)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	23						AGCGGATGGCGCTGGTGCTGG	0.627																																					p.A375A		Atlas-SNP	.											.	DAK	52	.	0			c.G1125A						PASS	.						58	52	54					11																	61111630		2203	4299	6502	SO:0001819	synonymous_variant	26007	exon13			GATGGCGCTGGTG		CCDS8003.1	11q12.2	2009-11-06	2006-04-04		ENSG00000149476	ENSG00000149476			24552	protein-coding gene	gene with protein product		615844	"dihydroxyacetone kinase 2 homolog (yeast)"				Standard	XM_005273898		Approved	DKFZP586B1621, NET45	uc001nre.3	Q3LXA3	OTTHUMG00000168076	ENST00000394900.3:c.1125G>A	chr11.hg19:g.61111630G>A		73.0	0.0	.		82.0	37.0	.	NM_015533	Q2L9C1|Q53EQ9|Q9BVA7|Q9H895	Silent	SNP	ENST00000394900.3	hg19	CCDS8003.1																																																																																			.	.	.	none		0.627	DAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394425.4	NM_015533		A	61111630	G	A	61111630	2	1	10	1	0	0	0	0	0	0	0	1	4230	1074	38	1		1	DAK	11	61111630	Silent	SNP	G	TCGA-2Z-A9JE-01A-11D-A42J-10	4009077	61111630	73894886	60	796											
FAM86C	55199	hgsc.bcm.edu	37	chr11	71504494	71504494	+	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	gtggagaccctgatggccaaGgagtccacccagggccaccg	9	4	14	14	1	0	2	0	1	0	1	1	4	1	3	6	4	0	0	6	4	1	0			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr11:71504494G>T	ENST00000359244.4	+	3	251	c.228G>T	c.(226-228)aaG>aaT	p.K76N	FAM86C1_ENST00000346333.6_Intron|FAM86C1_ENST00000426628.2_Intron	NM_018172.2	NP_060642.2	Q9NVL1	FA86C_HUMAN	family with sequence similarity 86, member C1	76										lung(1)	1						TGATGGCCAAGGAGTCCACCC	0.582																																					p.K76N		Atlas-SNP	.											.	FAM86C1	27	.	0			c.G228T						PASS	.						31	29	30					11																	71504494		2146	4258	6404	SO:0001583	missense	55199	exon3			GGCCAAGGAGTCC	AK130709	CCDS8202.1, CCDS41686.1, CCDS44664.1	11q13.4	2011-07-07	2011-07-07	2011-07-07	ENSG00000158483	ENSG00000158483			25561	protein-coding gene	gene with protein product			"family with sequence similarity 86, member C"	FAM86C		12477932	Standard	NM_152563		Approved	FLJ10661, FLJ27199	uc001oqv.4	Q9NVL1	OTTHUMG00000160552	ENST00000359244.4:c.228G>T	chr11.hg19:g.71504494G>T	ENSP00000352182:p.Lys76Asn	164.0	0.0	.		136.0	67.0	.	NM_018172	Q8N5D3	Missense_Mutation	SNP	ENST00000359244.4	hg19	CCDS41686.1	.	.	.	.	.	.	.	.	.	.	.	3.988	-0.005114	0.07773	.	.	ENSG00000158483	ENST00000359244	T	0.03689	3.84	2.05	1.07	0.20283	.	.	.	.	.	T	0.03477	0.0100	L	0.43152	1.355	0.80722	D	1	B	0.24920	0.114	B	0.17098	0.017	T	0.42548	-0.9445	9	0.72032	D	0.01	.	4.3775	0.11277	0.2179:0.0:0.7821:0.0	.	76	Q9NVL1	FA86C_HUMAN	N	76	ENSP00000352182:K76N	ENSP00000352182:K76N	K	+	3	2	FAM86C1	71182142	0.990000	0.36364	0.357000	0.25798	0.051000	0.14879	0.917000	0.28665	0.181000	0.19994	0.184000	0.17185	AAG	.	.	.	none		0.582	FAM86C1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361120.1	NM_152563		T	71504494	G	T	71504494	3	4	10	1	0	0	0	0	1	0	0	0	5653	991	35	4	323	4	FAM86C	11	71504494	Missense_Mutation	SNP	G	TCGA-2Z-A9JE-01A-11D-A42J-10	10392864	71504494	63502022	61	797											
PATE1	160065	hgsc.bcm.edu	37	chr11	125618623	125618623	+	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	atgacctgtgcaatgaagacCtttagaagttaatggttctt	12	14	9	6	0	1	4	0	2	1	2	1	4	1	4	2	1	1	3	2	1	5	5			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr11:125618623C>T	ENST00000305738.5	+	5	388	c.376C>T	c.(376-378)Ctt>Ttt	p.L126F	PATE1_ENST00000437148.2_Missense_Mutation_p.L114F	NM_138294.2	NP_612151.1	Q8WXA2	PATE1_HUMAN	prostate and testis expressed 1	126						extracellular region (GO:0005576)				large_intestine(1)|lung(5)	6						CAATGAAGACCTTTAGAAGTT	0.448																																					p.L126F		Atlas-SNP	.											.	PATE1	21	.	0			c.C376T						PASS	.						159	140	146					11																	125618623		2201	4299	6500	SO:0001583	missense	160065	exon5			GAAGACCTTTAGA	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.376C>T	chr11.hg19:g.125618623C>T	ENSP00000307164:p.Leu126Phe	78.0	0.0	.		71.0	24.0	.	NM_138294	Q3KNX2	Missense_Mutation	SNP	ENST00000305738.5	hg19	CCDS8464.1	.	.	.	.	.	.	.	.	.	.	C	5.470	0.271808	0.10349	.	.	ENSG00000171053	ENST00000305738;ENST00000437148	T;T	0.28255	1.62;1.68	4.07	-4.44	0.03557	.	0.700859	0.11743	N	0.533837	T	0.13415	0.0325	N	0.14661	0.345	0.09310	N	1	B;B	0.15930	0.015;0.015	B;B	0.19946	0.016;0.027	T	0.18493	-1.0335	10	0.35671	T	0.21	-0.2771	4.3005	0.10922	0.5287:0.2:0.0:0.2713	.	114;126	Q8WXA2-2;Q8WXA2	.;PATE1_HUMAN	F	126;114	ENSP00000307164:L126F;ENSP00000396056:L114F	ENSP00000307164:L126F	L	+	1	0	PATE1	125123833	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.846000	0.04336	-0.985000	0.03503	-0.143000	0.13931	CTT	.	.	.	none		0.448	PATE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386726.2	NM_138294		T	125618623	C	T	125618623	3	4	10	1	0	0	0	0	1	0	0	0	11480	681	24	2	394	2	PATE1	11	125618623	Missense_Mutation	SNP	C	TCGA-2Z-A9JE-01A-11D-A42J-10	54114129	125618623	9387893	62	798											
TAS2R19	259294	hgsc.bcm.edu	37	chr12	11174899	11174899	+	Missense_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	gccacatgctgaaatggttcGttacagcccaggcattagaa	12	9	10	10	1	0	2	0	1	0	1	1	2	0	2	2	2	3	4	2	2	4	3	rs550008134		TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr12:11174899G>A	ENST00000390673.2	-	1	320	c.272C>T	c.(271-273)aCg>aTg	p.T91M	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176888.1	NP_795369.1	P59542	T2R19_HUMAN	taste receptor, type 2, member 19	91					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						GAAATGGTTCGTTACAGCCCA	0.393													.|||	1	0.000199681	8e-04	0	5008	,	,		22828	0		0	False		,,,				2504	0				p.T91M		Atlas-SNP	.											.	TAS2R19	30	.	0			c.C272T						PASS	.						84	85	85					12																	11174899		2203	4299	6502	SO:0001583	missense	259294	exon1			TGGTTCGTTACAG	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.272C>T	chr12.hg19:g.11174899G>A	ENSP00000375091:p.Thr91Met	123.0	0.0	.		120.0	44.0	.	NM_176888	Q3MIJ4|Q645X8	Missense_Mutation	SNP	ENST00000390673.2	hg19	CCDS8640.1	.	.	.	.	.	.	.	.	.	.	G	10.69	1.420729	0.25639	.	.	ENSG00000212124	ENST00000390673	T	0.37752	1.18	2.55	-5.1	0.02911	.	2.297980	0.02805	N	0.123574	T	0.55353	0.1915	M	0.87456	2.885	0.09310	N	1	D	0.59767	0.986	D	0.63113	0.911	T	0.61332	-0.7084	10	0.62326	D	0.03	.	1.2085	0.01899	0.2053:0.1607:0.3984:0.2355	.	91	P59542	T2R19_HUMAN	M	91	ENSP00000375091:T91M	ENSP00000375091:T91M	T	-	2	0	TAS2R19	11066166	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-3.414000	0.00479	-2.602000	0.00450	-1.220000	0.01600	ACG	.	.	.	none		0.393	TAS2R19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370080.1	NM_176888		A	11174899	G	A	11174899	3	1	10	1	0	0	0	0	1	0	0	0	15582	1145	40	1	630	1	TAS2R19	12	11174899	Missense_Mutation	SNP	G	TCGA-2Z-A9JE-01A-11D-A42J-10		11174899	122676996	63	799											
KRT2	3849	hgsc.bcm.edu	37	chr12	53045631	53045632	+	In_Frame_Ins	INS	-	-	CGCCTCCAAAGCCGCTGC																															gccacctccaaagctgctgcINScgcctccaaaaccacctcct																										TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr12:53045631_53045632insCGCCTCCAAAGCCGCTGC	ENST00000309680.3	-	1	316_317	c.295_296insGCAGCGGCTTTGGAGGCG	c.(295-297)ggc>gGCAGCGGCTTTGGAGGCGgc	p.99_99G>GSGFGGG		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	99	Head.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		aaagctgctgccgcctccaaaa	0.619																																					p.G99delinsGSGFGGG		Atlas-INDEL	.											.	KRT2	94	.	0			c.296_297insGCAGCGGCTTTGGAGGCG						PASS	.																																			SO:0001652	inframe_insertion	3849	exon1			.		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"-", "Intermediate filaments type II, keratins (basic)"	6439	protein-coding gene	gene with protein product	"epidermal ichthyosis bullosa of Siemens"	600194	"keratin 2A (epidermal ichthyosis bullosa of Siemens)"	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.295_296insGCAGCGGCTTTGGAGGCG	chr12.hg19:g.53045631_53045632insCGCCTCCAAAGCCGCTGC	Exception_encountered	146.0	0.0	0		171.0	32.0	0.187135	NM_000423	Q4VAQ2	In_Frame_Ins	INS	ENST00000309680.3	hg19	CCDS8835.1																																																																																			.	.	.	none		0.619	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423		CGCCTCCAAAGCCGCTGC	53045632	-	CGCCTCCAAAGCCGCTGC	53045631	7	5	10	1	0	1	1	0	0	0	0	0	8464	739	26	0	1659	0	KRT2	12	53045631	In_Frame_Ins	INS	-	TCGA-2Z-A9JE-01A-11D-A42J-10	41870732	53045631	80806264	64	800											
GPR133	283383	hgsc.bcm.edu	37	chr12	131466438	131466438	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actttcctcaggggtcacgtTttcttttttctggaagacac	7	16	8	10	1	4	1	2	0	2	1	5	2	5	2	1	3	0	1	1	3	1	6			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr12:131466438T>C	ENST00000261654.5	+	5	879	c.320T>C	c.(319-321)tTt>tCt	p.F107S	GPR133_ENST00000535015.1_Missense_Mutation_p.F139S	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	107					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)		GGGGTCACGTTTTCTTTTTTC	0.458																																					p.F107S		Atlas-SNP	.											.	GPR133	136	.	0			c.T320C						PASS	.						100	98	99					12																	131466438		2203	4300	6503	SO:0001583	missense	283383	exon5			TCACGTTTTCTTT	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.320T>C	chr12.hg19:g.131466438T>C	ENSP00000261654:p.Phe107Ser	113.0	0.0	.		105.0	44.0	.	NM_198827	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Missense_Mutation	SNP	ENST00000261654.5	hg19	CCDS9272.1	.	.	.	.	.	.	.	.	.	.	T	14.63	2.593261	0.46214	.	.	ENSG00000111452	ENST00000261654;ENST00000535015	T;T	0.75154	-0.91;-0.91	4.28	4.28	0.50868	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.140598	0.47852	D	0.000204	D	0.84705	0.5531	M	0.75447	2.3	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.86671	0.1910	10	0.87932	D	0	.	12.924	0.58249	0.0:0.0:0.0:1.0	.	139;107	B7ZLF7;Q6QNK2	.;GP133_HUMAN	S	107;139	ENSP00000261654:F107S;ENSP00000444425:F139S	ENSP00000261654:F107S	F	+	2	0	GPR133	130032391	1.000000	0.71417	0.019000	0.16419	0.079000	0.17450	6.609000	0.74173	1.703000	0.51240	0.460000	0.39030	TTT	.	.	.	none		0.458	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827		C	131466438	T	C	131466438	3	2	10	1	0	0	0	0	1	0	0	0	6650	1841	64	3	338	3	GPR133	12	131466438	Missense_Mutation	SNP	T	TCGA-2Z-A9JE-01A-11D-A42J-10	78420807	131466438	2385457	65	801											
PROX2	283571	hgsc.bcm.edu	37	chr14	75321933	75321933	+	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	cttccaggaaggatctgagtCtctccctgcggagacagccc	8	8	11	14	1	2	2	0	1	2	1	5	5	4	4	3	3	2	0	3	3	1	1			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr14:75321933C>A	ENST00000445876.1	-	5	1680	c.1681G>T	c.(1681-1683)Gac>Tac	p.D561Y	PROX2_ENST00000556084.2_Missense_Mutation_p.D334Y|RP11-316E14.6_ENST00000553381.1_RNA|PROX2_ENST00000556489.2_Missense_Mutation_p.D561Y			Q3B8N5	PROX2_HUMAN	prospero homeobox 2	561	Prospero-like.				multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(3)	6			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00652)		GGATCTGAGTCTCTCCCTGCG	0.448																																					p.D561Y		Atlas-SNP	.											.	PROX2	44	.	0			c.G1681T						PASS	.						51	49	49					14																	75321933		1854	4093	5947	SO:0001583	missense	283571	exon4			CTGAGTCTCTCCC		CCDS45136.1, CCDS45136.2, CCDS73663.1	14q24.3	2012-10-02			ENSG00000119608	ENSG00000119608		"Homeoboxes / PROS class"	26715	protein-coding gene	gene with protein product		615094					Standard	NM_001080408		Approved	FLJ36749	uc031qpi.1	Q3B8N5	OTTHUMG00000171481	ENST00000445876.1:c.1681G>T	chr14.hg19:g.75321933C>A	ENSP00000405932:p.Asp561Tyr	79.0	0.0	.		62.0	32.0	.	NM_001243007	C9J5W1|Q8N9Q3	Missense_Mutation	SNP	ENST00000445876.1	hg19	CCDS45136.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.9|25.9	4.682820|4.682820	0.88542|0.88542	.|.	.|.	ENSG00000119608|ENSG00000119608	ENST00000556489;ENST00000389664;ENST00000424024;ENST00000445876|ENST00000556084	T;T|.	0.59906|.	0.23;0.23|.	5.22|5.22	5.22|5.22	0.72569|0.72569	.|.	0.157197|.	0.56097|.	D|.	0.000038|.	T|T	0.77870|0.77870	0.4195|0.4195	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|.	0.97110|.	1.0;1.0|.	T|T	0.78417|0.78417	-0.2212|-0.2212	10|5	0.87932|.	D|.	0|.	.|.	18.7863|18.7863	0.91955|0.91955	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	561;334|.	G3V3G0;Q3B8N5-2|.	.;.|.	Y|D	561;561;334;561|333	ENSP00000451223:D561Y;ENSP00000405932:D561Y|.	ENSP00000374315:D561Y|.	D|E	-|-	1|3	0|2	PROX2|PROX2	74391686|74391686	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	7.818000|7.818000	0.86416|0.86416	2.446000|2.446000	0.82766|0.82766	0.462000|0.462000	0.41574|0.41574	GAC|GAG	.	.	.	none		0.448	PROX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	75321933	C	A	75321933	3	1	10	1	0	0	0	0	1	0	0	0	12571	913	32	4	101	4	PROX2	14	75321933	Missense_Mutation	SNP	C	TCGA-2Z-A9JE-01A-11D-A42J-10		75321933	32027607	66	802											
ANGEL1	23357	hgsc.bcm.edu	37	chr14	77275538	77275538	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtcctcttcccactgctcTgtggccagggcacccactgg	4	9	12	16	0	2	0	0	0	2	0	4	0	4	0	4	4	1	2	4	4	0	1			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr14:77275538T>C	ENST00000251089.2	-	2	625	c.513A>G	c.(511-513)acA>acG	p.T171T	ANGEL1_ENST00000554941.1_5'Flank	NM_015305.3	NP_056120.2	Q9UNK9	ANGE1_HUMAN	angel homolog 1 (Drosophila)	171										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	22			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0285)		CCCACTGCTCTGTGGCCAGGG	0.657																																					p.T171T		Atlas-SNP	.											.	ANGEL1	63	.	0			c.A513G						PASS	.						29	28	29					14																	77275538		2203	4300	6503	SO:0001819	synonymous_variant	23357	exon2			CTGCTCTGTGGCC	AF111169	CCDS9852.1	14q24.3	2014-06-17		2005-08-04	ENSG00000013523	ENSG00000013523			19961	protein-coding gene	gene with protein product				KIAA0759		11943475	Standard	NM_015305		Approved	Ccr4e	uc001xsv.3	Q9UNK9	OTTHUMG00000171494	ENST00000251089.2:c.513A>G	chr14.hg19:g.77275538T>C		64.0	0.0	.		72.0	27.0	.	NM_015305	B4DWL7|O94859|Q8NCS9	Silent	SNP	ENST00000251089.2	hg19	CCDS9852.1																																																																																			.	.	.	none		0.657	ANGEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413712.2	NM_015305		C	77275538	T	C	77275538	2	2	10	1	0	0	0	0	0	0	0	1	608	1567	55	3		3	ANGEL1	14	77275538	Silent	SNP	T	TCGA-2Z-A9JE-01A-11D-A42J-10	1953605	77275538	30074002	67	803											
MYO1E	4643	hgsc.bcm.edu	37	chr15	59466345	59466345	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttcttctctcatttgaacgTatttcttccgggccacgaat	7	16	6	12	3	4	1	1	1	3	0	6	2	5	1	2	1	1	1	2	1	3	6			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr15:59466345T>C	ENST00000288235.4	-	20	2543	c.2144A>G	c.(2143-2145)tAc>tGc	p.Y715C	MIR2116_ENST00000517221.1_RNA	NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	715	IQ. {ECO:0000255|PROSITE- ProRule:PRU00116}.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(6)|lung(10)|pancreas(2)|prostate(1)|urinary_tract(1)	33				all cancers(107;0.207)		CATTTGAACGTATTTCTTCCG	0.343																																					p.Y715C		Atlas-SNP	.											.	MYO1E	99	.	0			c.A2144G						PASS	.						130	134	133					15																	59466345		2191	4291	6482	SO:0001583	missense	4643	exon20			TGAACGTATTTCT	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.2144A>G	chr15.hg19:g.59466345T>C	ENSP00000288235:p.Tyr715Cys	62.0	0.0	.		78.0	32.0	.	NM_004998	Q14778	Missense_Mutation	SNP	ENST00000288235.4	hg19	CCDS32254.1	.	.	.	.	.	.	.	.	.	.	T	19.63	3.863662	0.71949	.	.	ENSG00000157483	ENST00000288235	D	0.96073	-3.9	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	D	0.97383	0.9144	M	0.85373	2.75	0.80722	D	1	D	0.67145	0.996	P	0.60886	0.88	D	0.97585	1.0113	10	0.51188	T	0.08	.	15.4114	0.74923	0.0:0.0:0.0:1.0	.	715	Q12965	MYO1E_HUMAN	C	715	ENSP00000288235:Y715C	ENSP00000288235:Y715C	Y	-	2	0	MYO1E	57253637	1.000000	0.71417	0.962000	0.40283	0.856000	0.48823	6.126000	0.71635	2.220000	0.72140	0.533000	0.62120	TAC	.	.	.	none		0.343	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1	NM_004998		C	59466345	T	C	59466345	3	2	10	1	0	0	0	0	1	0	0	0	10079	1638	57	3	1218	3	MYO1E	15	59466345	Missense_Mutation	SNP	T	TCGA-2Z-A9JE-01A-11D-A42J-10		59466345	43065047	68	804											
ATF7IP2	80063	hgsc.bcm.edu	37	chr16	10525251	10525251	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatgagtgtagtagaaccagTatttcaaattgtgaaagtgc	14	12	11	4	0	1	3	1	2	0	1	1	4	1	3	1	0	2	3	1	0	6	5			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr16:10525251T>C	ENST00000396560.2	+	3	1001	c.774T>C	c.(772-774)agT>agC	p.S258S	ATF7IP2_ENST00000324570.5_Silent_p.S258S|ATF7IP2_ENST00000356427.2_Silent_p.S258S|ATF7IP2_ENST00000543967.1_Intron|ATF7IP2_ENST00000396559.1_Silent_p.S258S	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	258					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				large_intestine(3)	3						GTAGAACCAGTATTTCAAATT	0.338																																					p.S258S		Atlas-SNP	.											.	ATF7IP2	40	.	0			c.T774C						PASS	.						62	63	63					16																	10525251		2197	4300	6497	SO:0001819	synonymous_variant	80063	exon3			AACCAGTATTTCA	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.774T>C	chr16.hg19:g.10525251T>C		194.0	0.0	.		181.0	73.0	.	NM_024997	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	Silent	SNP	ENST00000396560.2	hg19	CCDS10540.1																																																																																			.	.	.	none		0.338	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997		C	10525251	T	C	10525251	2	2	10	1	0	0	0	0	0	0	0	1	1088	1635	57	3		3	ATF7IP2	16	10525251	Silent	SNP	T	TCGA-2Z-A9JE-01A-11D-A42J-10		10525251	79829502	69	805											
TXNDC11	51061	hgsc.bcm.edu	37	chr16	11782282	11782282	+	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	aagggactatagagaacgctGaagttttgaataaaagactc	17	9	10	5	1	0	4	0	2	0	2	1	6	0	5	0	1	1	2	0	1	8	5			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr16:11782282G>T	ENST00000356957.3	-	10	2108	c.2001C>A	c.(1999-2001)ttC>ttA	p.F667L	TXNDC11_ENST00000570917.1_5'UTR|TXNDC11_ENST00000283033.5_Missense_Mutation_p.F640L			Q6PKC3	TXD11_HUMAN	thioredoxin domain containing 11	667	Thioredoxin 2. {ECO:0000255|PROSITE- ProRule:PRU00691}.				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						AGAGAACGCTGAAGTTTTGAA	0.378																																					p.F640L		Atlas-SNP	.											.	TXNDC11	75	.	0			c.C1920A						PASS	.						46	48	47					16																	11782282		2197	4300	6497	SO:0001583	missense	51061	exon9			AACGCTGAAGTTT	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.2001C>A	chr16.hg19:g.11782282G>T	ENSP00000349439:p.Phe667Leu	47.0	0.0	.		65.0	26.0	.	NM_015914	O95887|Q6PJA6|Q8N2Q4|Q96K45|Q96K53	Missense_Mutation	SNP	ENST00000356957.3	hg19		.	.	.	.	.	.	.	.	.	.	G	19.95	3.922136	0.73213	.	.	ENSG00000153066	ENST00000356957;ENST00000283033	T;T	0.21543	2.0;2.0	5.97	5.02	0.67125	Thioredoxin-like fold (1);	0.098588	0.64402	D	0.000001	T	0.30293	0.0760	M	0.64170	1.965	0.58432	D	0.999998	P;P	0.41498	0.752;0.649	P;B	0.44732	0.459;0.149	T	0.06716	-1.0811	10	0.72032	D	0.01	-23.2994	14.0652	0.64824	0.0718:0.0:0.9282:0.0	.	667;640	Q6PKC3;Q6PKC3-2	TXD11_HUMAN;.	L	667;640	ENSP00000349439:F667L;ENSP00000283033:F640L	ENSP00000283033:F640L	F	-	3	2	TXNDC11	11689783	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.999000	0.76283	1.535000	0.49220	0.655000	0.94253	TTC	.	.	.	none		0.378	TXNDC11-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000437057.1	NM_015914		T	11782282	G	T	11782282	3	4	10	1	0	0	0	0	1	0	0	0	16804	1281	45	4	972	4	TXNDC11	16	11782282	Missense_Mutation	SNP	G	TCGA-2Z-A9JE-01A-11D-A42J-10	1257031	11782282	78572471	70	806											
MKL2	57496	hgsc.bcm.edu	37	chr16	14355241	14355241	+	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	actcctctcagcaccaccgcGccgagcatgttctctgctga	7	9	8	17	3	2	1	1	1	2	0	5	2	3	1	4	0	3	4	4	0	0	1	rs150140535		TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr16:14355241G>A	ENST00000341243.5	+	15	3207	c.3207G>A	c.(3205-3207)gcG>gcA	p.A1069A	MKL2_ENST00000318282.5_Silent_p.A1030A|MKL2_ENST00000574045.1_Silent_p.A1030A|MKL2_ENST00000571589.1_Silent_p.A1080A			Q9ULH7	MKL2_HUMAN	MKL/myocardin-like 2	1069					blood vessel morphogenesis (GO:0048514)|cardiac muscle tissue development (GO:0048738)|embryonic organ development (GO:0048568)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|muscle organ development (GO:0007517)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(6)|liver(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GCACCACCGCGCCGAGCATGT	0.507																																					p.A1030A		Atlas-SNP	.											.	MKL2	103	.	0			c.G3090A						PASS	.	G		0,4394		0,0,2197	72	69	70		3090	-4.2	0	16	dbSNP_134	70	1,8599		0,1,4299	no	coding-synonymous	MKL2	NM_014048.3		0,1,6496	AA,AG,GG		0.0116,0.0,0.0077		1030/1050	14355241	1,12993	2197	4300	6497	SO:0001819	synonymous_variant	57496	exon17			CACCGCGCCGAGC	AB033069	CCDS32391.1	16p13.12	2012-11-29			ENSG00000186260	ENSG00000186260			29819	protein-coding gene	gene with protein product		609463				10574462	Standard	NM_014048		Approved	MRTF-B, FLJ31823	uc002dcg.3	Q9ULH7	OTTHUMG00000177379	ENST00000341243.5:c.3207G>A	chr16.hg19:g.14355241G>A		79.0	0.0	.		78.0	41.0	.	NM_014048	A6ND53|B4DGT8|Q68CT1|Q6UB16|Q86WW2|Q8N226	Silent	SNP	ENST00000341243.5	hg19																																																																																				.	G|1.000;A|0.000	0.000	weak		0.507	MKL2-202	KNOWN	basic	protein_coding	protein_coding		NM_014048		A	14355241	G	A	14355241	2	1	10	1	0	0	0	0	0	0	0	1	9609	1074	38	1		1	MKL2	16	14355241	Silent	SNP	G	TCGA-2Z-A9JE-01A-11D-A42J-10	2572959	14355241	75999512	71	807											
KIAA0430	9665	hgsc.bcm.edu	37	chr16	15702262	15702262	+	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	tctgtaaggagatctgtcatCataaggcagttatctttttg	10	16	9	6	0	5	1	2	0	3	1	5	2	5	1	0	2	0	3	0	2	3	5			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr16:15702262C>T	ENST00000396368.3	-	21	4274	c.4068G>A	c.(4066-4068)atG>atA	p.M1356I	CTB-193M12.1_ENST00000549756.1_RNA|KIAA0430_ENST00000540441.2_Missense_Mutation_p.M1191I|KIAA0430_ENST00000548025.1_Missense_Mutation_p.M1353I|KIAA0430_ENST00000547936.1_5'Flank|KIAA0430_ENST00000602337.1_Missense_Mutation_p.M1353I|KIAA0430_ENST00000344181.3_Missense_Mutation_p.M958I|KIAA0430_ENST00000551742.1_Missense_Mutation_p.M1356I	NM_001184998.1|NM_001184999.1|NM_014647.3	NP_001171927.1|NP_001171928.1|NP_055462.2	Q9Y4F3	MARF1_HUMAN	KIAA0430	1356	HTH OST-type 6. {ECO:0000255|PROSITE- ProRule:PRU00975}.				double-strand break repair (GO:0006302)|female meiotic division (GO:0007143)|negative regulation of phosphatase activity (GO:0010923)|oogenesis (GO:0048477)|regulation of gene expression (GO:0010468)	membrane (GO:0016020)|peroxisome (GO:0005777)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(4)|endometrium(8)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(5)|skin(1)	40						GATCTGTCATCATAAGGCAGT	0.408																																					p.M1356I		Atlas-SNP	.											.	KIAA0430	154	.	0			c.G4068A						PASS	.						97	94	95					16																	15702262		1863	4103	5966	SO:0001583	missense	9665	exon21			TGTCATCATAAGG	AB007890	CCDS10562.2, CCDS53990.1, CCDS55991.1	16p13.11	2013-01-11			ENSG00000166783	ENSG00000166783		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	29562	protein-coding gene	gene with protein product	"limkain b1", "protein phosphatase 1, regulatory subunit 34", "meiosis arrest female 1"	614593				9455477, 10493829, 15932519, 22442484, 23090997	Standard	NM_014647		Approved	LKAP, PPP1R34, Marf1	uc010uzw.2	Q9Y4F3	OTTHUMG00000129884	ENST00000396368.3:c.4068G>A	chr16.hg19:g.15702262C>T	ENSP00000379654:p.Met1356Ile	130.0	0.0	.		155.0	70.0	.	NM_014647	A8MSK2|B2RNX2|B4DYY9|B7ZMG1|B7ZMG2|F8VV09|Q6P1R6|Q8WYR2|Q9Y4J9	Missense_Mutation	SNP	ENST00000396368.3	hg19	CCDS10562.2	.	.	.	.	.	.	.	.	.	.	C	14.50	2.554977	0.45487	.	.	ENSG00000166783	ENST00000396368;ENST00000540441;ENST00000321370;ENST00000344181;ENST00000548025;ENST00000551742;ENST00000551298	T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99	5.87	4.87	0.63330	.	0.198570	0.56097	D	0.000028	T	0.28433	0.0703	N	0.14661	0.345	0.33689	D	0.613049	B;B;B;B	0.34399	0.274;0.452;0.452;0.32	B;B;B;B	0.35182	0.124;0.117;0.117;0.197	T	0.44003	-0.9356	10	0.48119	T	0.1	.	13.6513	0.62312	0.2707:0.7293:0.0:0.0	.	1355;1353;1352;1355	Q9Y4F3-5;F8VV09;Q9Y4F3-4;Q9Y4F3	.;.;.;LKAP_HUMAN	I	1356;1191;1296;958;1353;1356;1136	ENSP00000379654:M1356I;ENSP00000439819:M1191I;ENSP00000341939:M958I;ENSP00000449376:M1353I;ENSP00000450309:M1356I	ENSP00000315718:M1296I	M	-	3	0	KIAA0430	15609763	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.870000	0.39529	2.781000	0.95711	0.655000	0.94253	ATG	.	.	.	none		0.408	KIAA0430-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252131.2	NM_014647		T	15702262	C	T	15702262	3	4	10	1	0	0	0	0	1	0	0	0	8184	826	29	2	1188	2	KIAA0430	16	15702262	Missense_Mutation	SNP	C	TCGA-2Z-A9JE-01A-11D-A42J-10	1347021	15702262	74652491	72	808											
MAZ	4150	hgsc.bcm.edu	37	chr16	29820995	29820995	+	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	cccagctggccggccacatgCagacccatctggggggggcc	6	4	15	16	1	1	1	0	0	1	1	1	1	1	1	5	6	2	2	5	6	0	0	rs71143751|rs561533545		TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr16:29820995C>T	ENST00000322945.6	+	5	1444				PRRT2_ENST00000300797.6_5'Flank|AC009133.15_ENST00000566537.1_RNA|PRRT2_ENST00000358758.7_5'Flank|MAZ_ENST00000563402.1_Intron|MAZ_ENST00000566906.2_Intron|AC009133.14_ENST00000563806.1_RNA|MAZ_ENST00000219782.6_Nonsense_Mutation_p.Q472*|MAZ_ENST00000568544.1_Intron|AC009133.14_ENST00000569981.1_RNA|AC009133.20_ENST00000569039.1_RNA|MAZ_ENST00000545521.1_Intron|MAZ_ENST00000562337.1_Intron|PRRT2_ENST00000567659.1_5'Flank|MAZ_ENST00000568282.1_Nonsense_Mutation_p.Q73*	NM_002383.2	NP_002374.2	P56270	MAZ_HUMAN	MYC-associated zinc finger protein (purine-binding transcription factor)						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						CGGCCACATGCAGACCCATCT	0.736																																					p.Q472X	Colon(72;875 1167 15364 30899 37091)	Atlas-SNP	.											.	MAZ	48	.	0			c.C1414T						PASS	.						7	9	8					16																	29820995		1899	4077	5976	SO:0001627	intron_variant	4150	exon5			CACATGCAGACCC	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.1280-403C>T	chr16.hg19:g.29820995C>T		102.0	0.0	.		65.0	29.0	.	NM_001042539	A8QJL9|C6G496|G5E927|H3BQD6|Q15703|Q8NFN7|Q99443	Nonsense_Mutation	SNP	ENST00000322945.6	hg19	CCDS42143.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.839048	0.91117	.	.	ENSG00000103495	ENST00000219782	.	.	.	4.64	3.67	0.42095	.	11.966600	0.00496	U	0.000156	.	.	.	.	.	.	0.53688	A	0.999978	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	.	10.112	0.42568	0.0:0.9001:0.0:0.0999	.	.	.	.	X	472	.	ENSP00000219782:Q472X	Q	+	1	0	MAZ	29728496	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.967000	0.56802	2.313000	0.78055	0.561000	0.74099	CAG	.	.	.	none		0.736	MAZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435536.1	NM_002383		T	29820995	C	T	29820995	1	4	10	0	1	0	0	0	0	0	0	0	9347	711	25	2		2	MAZ	16	29820995	Intron	SNP	C	TCGA-2Z-A9JE-01A-11D-A42J-10	14118733	29820995	60533758	73	809											
CMTM3	123920	hgsc.bcm.edu	37	chr16	66643431	66643431	+	Frame_Shift_Del	DEL	G	G	-																															atggggcttccaaagccgctGgggtgagcagccgccccacc																										TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr16:66643431delG	ENST00000424011.2	+	4	923	c.397delG	c.(397-399)gggfs	p.G133fs	CMTM3_ENST00000568477.1_Frame_Shift_Del_p.G47fs|CMTM3_ENST00000562707.1_Frame_Shift_Del_p.G133fs|CMTM3_ENST00000566121.1_Frame_Shift_Del_p.G47fs|CMTM3_ENST00000460097.1_Frame_Shift_Del_p.G47fs|CMTM3_ENST00000564060.1_Intron|CMTM3_ENST00000565666.1_Frame_Shift_Del_p.G48fs|CMTM3_ENST00000565922.1_Intron|CMTM3_ENST00000565003.1_Frame_Shift_Del_p.G47fs|CMTM3_ENST00000360086.4_Intron|CMTM3_ENST00000361909.4_Frame_Shift_Del_p.G133fs|CMTM3_ENST00000567572.1_Frame_Shift_Del_p.G133fs			Q96MX0	CKLF3_HUMAN	CKLF-like MARVEL transmembrane domain containing 3	133	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				chemotaxis (GO:0006935)|positive regulation of B cell receptor signaling pathway (GO:0050861)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)				central_nervous_system(1)|endometrium(1)|lung(2)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0671)|Epithelial(162;0.164)		CAAAGCCGCTGGGGTGAGCAG	0.642																																					p.A132fs		Atlas-INDEL	.											.	CMTM3	13	.	0			c.396delT						PASS	.						26	24	25					16																	66643431		2197	4298	6495	SO:0001589	frameshift_variant	123920	exon3			.	AK056324	CCDS10815.1	16q22.1-q22.3	2008-02-05	2005-11-08	2005-11-08	ENSG00000140931	ENSG00000140931			19174	protein-coding gene	gene with protein product		607886	"chemokine-like factor superfamily 3"	CKLFSF3		15087455	Standard	NM_144601		Approved	FLJ31762, BNAS2	uc002epv.3	Q96MX0	OTTHUMG00000137503	ENST00000424011.2:c.397delG	chr16.hg19:g.66643431delG	ENSP00000400482:p.Gly133fs	54.0	0.0	0		25.0	11.0	0.44	NM_181553	A6NCL9|Q8IUU8|Q8IWQ6|Q8IYE2|Q8IZ39|Q8IZ59	Frame_Shift_Del	DEL	ENST00000424011.2	hg19	CCDS10815.1																																																																																			.	.	.	none		0.642	CMTM3-001	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268814.2	NM_144601		-	66643431	G	-	66643431	7	5	10	1	0	1	0	1	0	0	0	0	3586	1348	47	0	407	0	CMTM3	16	66643431	Frame_Shift_Del	DEL	G	TCGA-2Z-A9JE-01A-11D-A42J-10	36822436	66643431	23711322	74	810											
ITGAE	3682	hgsc.bcm.edu	37	chr17	3638168	3638168	+	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	ttcaaggccatgcttgtcatGtaggaatcttccccggagtt	8	13	10	10	1	3	0	2	0	1	0	4	2	4	2	3	3	1	3	3	3	3	5			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr17:3638168G>T	ENST00000263087.4	-	21	2696	c.2598C>A	c.(2596-2598)taC>taA	p.Y866*	ITGAE_ENST00000571185.1_5'UTR	NM_002208.4	NP_002199.3	P38570	ITAE_HUMAN	integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)	866					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)		TGCTTGTCATGTAGGAATCTT	0.507																																					p.Y866X	NSCLC(182;635 2928 8995 38788)	Atlas-SNP	.											.	ITGAE	96	.	0			c.C2598A						PASS	.						280	262	268					17																	3638168		2203	4300	6503	SO:0001587	stop_gained	3682	exon21			TGTCATGTAGGAA	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.2598C>A	chr17.hg19:g.3638168G>T	ENSP00000263087:p.Tyr866*	103.0	0.0	.		145.0	43.0	.	NM_002208	Q17RS6|Q9NZU9	Nonsense_Mutation	SNP	ENST00000263087.4	hg19	CCDS32531.1	.	.	.	.	.	.	.	.	.	.	G	39	7.651620	0.98412	.	.	ENSG00000083457	ENST00000263087	.	.	.	5.05	1.99	0.26369	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.383	0.26866	0.2781:0.0:0.7219:0.0	.	.	.	.	X	866	.	ENSP00000263087:Y866X	Y	-	3	2	ITGAE	3584917	0.982000	0.34865	0.996000	0.52242	0.761000	0.43186	0.794000	0.26958	0.275000	0.22094	-0.199000	0.12753	TAC	.	.	.	none		0.507	ITGAE-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438169.1	NM_002208		T	3638168	G	T	3638168	4	4	10	1	0	0	0	0	0	1	0	0	7892	1372	48	4	985	4	ITGAE	17	3638168	Nonsense_Mutation	SNP	G	TCGA-2Z-A9JE-01A-11D-A42J-10		3638168	77557042	75	811											
CAMTA2	23125	hgsc.bcm.edu	37	chr17	4883018	4883018	+	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	ggggagaagtctgtgatggtGctaagagcaggagacagctg	11	7	18	5	0	1	4	0	1	1	3	1	6	1	4	0	4	3	3	0	4	2	1			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr17:4883018G>T	ENST00000348066.3	-	9	1722	c.1599C>A	c.(1597-1599)agC>agA	p.S533R	CAMTA2_ENST00000358183.4_Missense_Mutation_p.S533R|CAMTA2_ENST00000571831.1_5'Flank|CAMTA2_ENST00000381311.5_Missense_Mutation_p.S535R|CAMTA2_ENST00000572543.1_Missense_Mutation_p.S538R|CAMTA2_ENST00000414043.3_Missense_Mutation_p.S556R|CAMTA2_ENST00000361571.5_Missense_Mutation_p.S532R	NM_015099.3	NP_055914.2	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	533					cardiac muscle hypertrophy in response to stress (GO:0014898)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|transcription factor binding (GO:0008134)	p.S533S(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						CTGTGATGGTGCTAAGAGCAG	0.542																																					p.S556R		Atlas-SNP	.											CAMTA2,NS,carcinoma,0,1	CAMTA2	93	.	1	Substitution - coding silent(1)	endometrium(1)	c.C1668A						PASS	.						104	107	106					17																	4883018		2203	4300	6503	SO:0001583	missense	23125	exon9			GATGGTGCTAAGA	AB020716	CCDS11063.1, CCDS54071.1, CCDS54072.1, CCDS54073.1	17p13.3	2004-09-01			ENSG00000108509	ENSG00000108509			18807	protein-coding gene	gene with protein product		611508				11925432	Standard	NM_015099		Approved	KIAA0909	uc010cku.2	O94983	OTTHUMG00000099417	ENST00000348066.3:c.1599C>A	chr17.hg19:g.4883018G>T	ENSP00000321813:p.Ser533Arg	61.0	0.0	.		89.0	23.0	.	NM_001171167	B9EGL0|D3DTL5|E7EWU5|Q7Z6M8|Q8N3V0|Q8NDG4|Q96G17	Missense_Mutation	SNP	ENST00000348066.3	hg19	CCDS11063.1	.	.	.	.	.	.	.	.	.	.	G	8.773	0.926378	0.18056	.	.	ENSG00000108509	ENST00000414043;ENST00000381311;ENST00000361571;ENST00000358183;ENST00000348066	T;T;T;T;T	0.31510	2.71;1.72;1.49;1.72;1.5	4.79	0.537	0.17144	Immunoglobulin-like fold (1);	0.266108	0.34777	N	0.003688	T	0.21103	0.0508	L	0.36672	1.1	0.09310	N	1	B;B;B;B;B	0.27380	0.096;0.177;0.096;0.117;0.001	B;B;B;B;B	0.35655	0.094;0.042;0.131;0.207;0.002	T	0.16276	-1.0408	10	0.25106	T	0.35	-7.7034	4.4993	0.11856	0.3542:0.1555:0.4903:0.0	.	509;556;535;533;532	B7ZM30;E7EWU5;O94983-3;O94983;O94983-4	.;.;.;CMTA2_HUMAN;.	R	556;535;532;533;533	ENSP00000412886:S556R;ENSP00000370712:S535R;ENSP00000354828:S532R;ENSP00000350910:S533R;ENSP00000321813:S533R	ENSP00000321813:S533R	S	-	3	2	CAMTA2	4823742	0.526000	0.26298	0.938000	0.37757	0.972000	0.66771	0.949000	0.29109	0.318000	0.23185	-0.126000	0.14955	AGC	.	.	.	none		0.542	CAMTA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216876.1	NM_015099		T	4883018	G	T	4883018	3	4	10	1	0	0	0	0	1	0	0	0	2616	1310	46	4	2119	4	CAMTA2	17	4883018	Missense_Mutation	SNP	G	TCGA-2Z-A9JE-01A-11D-A42J-10	1244850	4883018	76312192	76	812											
PER1	5187	hgsc.bcm.edu	37	chr17	8053954	8053954	+	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	ggggcccaggggatgggacgCccccaggacaaaatgattcc	10	4	15	12	1	0	1	0	1	0	0	1	4	1	4	4	6	0	0	4	6	2	1			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr17:8053954C>A	ENST00000317276.4	-	2	308	c.71G>T	c.(70-72)gGc>gTc	p.G24V	PER1_ENST00000581082.1_Missense_Mutation_p.G24V|PER1_ENST00000354903.5_Intron	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	24	Interaction with BTRC. {ECO:0000269|PubMed:15917222}.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						GGATGGGACGCCCCCAGGACA	0.642			T	ETV6	"AML, CMML"			Other conserved DNA damage response genes																													p.G24V		Atlas-SNP	.		Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	PER1,colon,carcinoma,0,1	PER1	104	.	0			c.G71T						PASS	.						49	53	51					17																	8053954		2203	4299	6502	SO:0001583	missense	5187	exon2			GGGACGCCCCCAG	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.71G>T	chr17.hg19:g.8053954C>A	ENSP00000314420:p.Gly24Val	35.0	0.0	.		39.0	18.0	.	NM_002616	B2RPA8|B4DI49|D3DTR3	Missense_Mutation	SNP	ENST00000317276.4	hg19	CCDS11131.1	.	.	.	.	.	.	.	.	.	.	C	9.788	1.177180	0.21787	.	.	ENSG00000179094	ENST00000317276	T	0.13196	2.61	5.38	1.21	0.21127	.	0.547369	0.18544	N	0.138112	T	0.12646	0.0307	L	0.38175	1.15	0.24187	N	0.995562	B;P	0.41366	0.235;0.747	P;B	0.45913	0.497;0.283	T	0.22173	-1.0224	10	0.20519	T	0.43	-3.3931	8.5305	0.33331	0.0:0.6761:0.0:0.3239	.	24;24	Q6IN51;O15534	.;PER1_HUMAN	V	24	ENSP00000314420:G24V	ENSP00000314420:G24V	G	-	2	0	PER1	7994679	0.283000	0.24277	0.131000	0.22000	0.193000	0.23685	0.608000	0.24223	0.025000	0.15241	0.563000	0.77884	GGC	.	.	.	none		0.642	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2			A	8053954	C	A	8053954	3	1	10	1	0	0	0	0	1	0	0	0	11736	739	26	4	3889	4	PER1	17	8053954	Missense_Mutation	SNP	C	TCGA-2Z-A9JE-01A-11D-A42J-10	3170936	8053954	73141256	77	813											
NCOR1	9611	hgsc.bcm.edu	37	chr17	15952256	15952256	+	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	gggtggggagatgggctcgtAgggctccgaagagacgtgac	8	6	20	7	3	0	3	0	1	0	2	2	6	1	3	1	5	0	3	1	5	2	1			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr17:15952256A>T	ENST00000268712.3	-	41	6696	c.6439T>A	c.(6439-6441)Tac>Aac	p.Y2147N	NCOR1_ENST00000395857.3_Missense_Mutation_p.Y731N|NCOR1_ENST00000395851.1_Missense_Mutation_p.Y2044N	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	2147	Interaction with C1D. {ECO:0000250}.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		ATGGGCTCGTAGGGCTCCGAA	0.517																																					p.Y2147N		Atlas-SNP	.											.	NCOR1	240	.	0			c.T6439A						PASS	.						82	74	77					17																	15952256		2203	4300	6503	SO:0001583	missense	9611	exon41			GCTCGTAGGGCTC	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.6439T>A	chr17.hg19:g.15952256A>T	ENSP00000268712:p.Tyr2147Asn	82.0	0.0	.		137.0	83.0	.	NM_006311	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	hg19	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	A	15.19	2.758738	0.49468	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849;ENST00000395857	T;T;T	0.50001	0.76;1.32;0.77	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.63462	0.2513	L	0.52573	1.65	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;0.999;0.999;0.998;1.0;0.999	D;D;D;D;D;D	0.87578	0.998;0.993;0.994;0.989;0.996;0.974	T	0.66006	-0.6030	10	0.72032	D	0.01	-5.9972	14.5928	0.68383	1.0:0.0:0.0:0.0	.	957;2051;2147;2044;667;161	B4DZ48;E7EVK1;O75376;O75376-2;Q86YY1;Q86YY2	.;.;NCOR1_HUMAN;.;.;.	N	2147;2044;2051;731	ENSP00000268712:Y2147N;ENSP00000379192:Y2044N;ENSP00000379198:Y731N	ENSP00000268712:Y2147N	Y	-	1	0	NCOR1	15892981	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.393000	0.90182	2.117000	0.64856	0.533000	0.62120	TAC	.	.	.	none		0.517	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		T	15952256	A	T	15952256	3	4	10	1	0	0	0	0	1	0	0	0	10242	420	15	5	907	5	NCOR1	17	15952256	Missense_Mutation	SNP	A	TCGA-2Z-A9JE-01A-11D-A42J-10	7898302	15952256	65242954	78	814											
IFI35	3430	hgsc.bcm.edu	37	chr17	41166305	41166305	+	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	gcctagcagtcttcacctctGagtcaggctaggggcctccc	6	9	11	15	0	4	1	2	1	2	0	5	1	5	1	4	3	1	2	4	3	2	3			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr17:41166305G>A	ENST00000415816.2	+	7	1073	c.850G>A	c.(850-852)Gag>Aag	p.E284K	IFI35_ENST00000438323.2_Missense_Mutation_p.E286K	NM_005533.4	NP_005524.2	P80217	IN35_HUMAN	interferon-induced protein 35	284				EVEALTVVPQGQQGLAVFTSESG -> GRGPDSRTPRTAGP SSLHL (in Ref. 1; no nucleotide entry). {ECO:0000305}.	cytokine-mediated signaling pathway (GO:0019221)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)	8		Breast(137;0.00499)		BRCA - Breast invasive adenocarcinoma(366;0.157)		CTTCACCTCTGAGTCAGGCTA	0.637																																					p.E286K		Atlas-SNP	.											.	IFI35	23	.	0			c.G856A						PASS	.						52	45	48					17																	41166305		2203	4300	6503	SO:0001583	missense	3430	exon7			ACCTCTGAGTCAG	BC001356	CCDS11450.1	17q21	2006-04-05			ENSG00000068079	ENSG00000068079			5399	protein-coding gene	gene with protein product		600735					Standard	NM_005533		Approved	IFP35	uc021txx.1	P80217	OTTHUMG00000167720	ENST00000415816.2:c.850G>A	chr17.hg19:g.41166305G>A	ENSP00000394579:p.Glu284Lys	58.0	0.0	.		79.0	17.0	.	NM_005533	C9JGX1|Q92984|Q99537|Q9BV98	Missense_Mutation	SNP	ENST00000415816.2	hg19		.	.	.	.	.	.	.	.	.	.	G	11.04	1.522297	0.27211	.	.	ENSG00000068079	ENST00000415816;ENST00000438323	T;T	0.46063	0.88;0.88	5.8	-0.216	0.13153	.	0.759943	0.12402	N	0.472023	T	0.27134	0.0665	L	0.27053	0.805	0.09310	N	1	B	0.12013	0.005	B	0.10450	0.005	T	0.18241	-1.0343	10	0.38643	T	0.18	.	8.4304	0.32755	0.454:0.0:0.546:0.0	.	284	P80217	IN35_HUMAN	K	284;286	ENSP00000394579:E284K;ENSP00000395590:E286K	ENSP00000394579:E284K	E	+	1	0	IFI35	38419831	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.264000	0.08658	-0.250000	0.09555	-0.379000	0.06801	GAG	.	.	.	none		0.637	IFI35-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000395851.1	NM_005533		A	41166305	G	A	41166305	3	1	10	1	0	0	0	0	1	0	0	0	7523	1291	45	2	882	2	IFI35	17	41166305	Missense_Mutation	SNP	G	TCGA-2Z-A9JE-01A-11D-A42J-10	25214049	41166305	40028905	79	815											
NFKBID	84807	hgsc.bcm.edu	37	chr19	36387912	36387912	+	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	tggtccagggaccacagcggGgaactgtgggggtcctgaag	8	6	18	9	1	0	1	0	1	0	0	2	3	2	3	3	6	2	0	3	6	2	0			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr19:36387912G>A	ENST00000396901.1	-	5	628	c.55C>T	c.(55-57)Ccc>Tcc	p.P19S	NFKBID_ENST00000606253.1_Missense_Mutation_p.P19S|NFKBID_ENST00000352614.2_Missense_Mutation_p.P171S|NFKBID_ENST00000585544.1_5'Flank	NM_139239.1	NP_640332.1	Q8NI38	IKBD_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, delta	19					inflammatory response (GO:0006954)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell differentiation in thymus (GO:0033085)|positive regulation of thymocyte apoptotic process (GO:0070245)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	14						ACCACAGCGGGGAACTGTGGG	0.642																																					p.P19S		Atlas-SNP	.											.	NFKBID	30	.	0			c.C55T						PASS	.						44	47	46					19																	36387912		1902	4111	6013	SO:0001583	missense	84807	exon5			CAGCGGGGAACTG	AF385434	CCDS42552.1	19q13.12	2013-01-10				ENSG00000167604		"Ankyrin repeat domain containing"	15671	protein-coding gene	gene with protein product						12477932	Standard	NM_139239		Approved	TA-NFKBH, IkappaBNS	uc002oci.1	Q8NI38		ENST00000396901.1:c.55C>T	chr19.hg19:g.36387912G>A	ENSP00000380109:p.Pro19Ser	221.0	0.0	.		184.0	80.0	.	NM_139239	Q8NI39|Q9BRG9	Missense_Mutation	SNP	ENST00000396901.1	hg19	CCDS42552.1	.	.	.	.	.	.	.	.	.	.	G	0.991	-0.693860	0.03303	.	.	ENSG00000167604	ENST00000352614;ENST00000396901	T;T	0.55588	0.51;1.21	4.65	1.2	0.21068	.	1.284560	0.04994	N	0.467779	T	0.36138	0.0956	L	0.29908	0.895	0.09310	N	0.999999	P;B	0.36909	0.573;0.001	B;B	0.33690	0.168;0.001	T	0.17684	-1.0361	10	0.21014	T	0.42	.	4.3062	0.10947	0.0894:0.1562:0.5932:0.1613	.	171;19	Q8NI38-2;Q8NI38	.;IKBD_HUMAN	S	171;19	ENSP00000252985:P171S;ENSP00000380109:P19S	ENSP00000252985:P171S	P	-	1	0	NFKBID	41079752	0.117000	0.22190	0.035000	0.18076	0.055000	0.15305	1.330000	0.33781	0.168000	0.19655	0.491000	0.48974	CCC	.	.	.	none		0.642	NFKBID-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452927.3	NM_032721		A	36387912	G	A	36387912	3	1	10	1	0	0	0	0	1	0	0	0	10386	1232	43	2	918	2	NFKBID	19	36387912	Missense_Mutation	SNP	G	TCGA-2Z-A9JE-01A-11D-A42J-10		36387912	22741071	80	816											
ZC3H4	23211	hgsc.bcm.edu	37	chr19	47570155	47570155	+	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	tccaccggccgccagcacgcGggggtcgtagggagcggtgg	5	4	19	13	6	0	0	0	0	0	0	2	1	1	1	4	6	2	2	4	6	1	1			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr19:47570155G>T	ENST00000253048.5	-	15	3407	c.3370C>A	c.(3370-3372)Cgc>Agc	p.R1124S	ZC3H4_ENST00000594019.1_5'UTR	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	1124							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)		GCCAGCACGCGGGGGTCGTAG	0.746																																					p.R1124S		Atlas-SNP	.											ZC3H4,NS,carcinoma,0,1	ZC3H4	96	.	0			c.C3370A						PASS	.						8	11	10					19																	47570155		1843	3992	5835	SO:0001583	missense	23211	exon15			GCACGCGGGGGTC	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.3370C>A	chr19.hg19:g.47570155G>T	ENSP00000253048:p.Arg1124Ser	38.0	0.0	.		34.0	2.0	.	NM_015168	Q9Y420	Missense_Mutation	SNP	ENST00000253048.5	hg19	CCDS42582.1	.	.	.	.	.	.	.	.	.	.	G	13.49	2.251319	0.39797	.	.	ENSG00000130749	ENST00000253048	T	0.20598	2.06	5.54	3.28	0.37604	.	0.000000	0.64402	D	0.000001	T	0.41994	0.1183	M	0.63843	1.955	0.58432	D	0.999996	D	0.89917	1.0	D	0.85130	0.997	T	0.35549	-0.9784	10	0.52906	T	0.07	.	13.642	0.62257	0.0:0.0:0.7192:0.2808	.	1124	Q9UPT8	ZC3H4_HUMAN	S	1124	ENSP00000253048:R1124S	ENSP00000253048:R1124S	R	-	1	0	ZC3H4	52261995	0.921000	0.31238	0.330000	0.25442	0.016000	0.09150	1.525000	0.35953	1.302000	0.44855	0.563000	0.77884	CGC	.	.	.	none		0.746	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1			T	47570155	G	T	47570155	3	4	10	1	0	0	0	0	1	0	0	0	17582	1116	39	4	545	4	ZC3H4	19	47570155	Missense_Mutation	SNP	G	TCGA-2Z-A9JE-01A-11D-A42J-10	11182243	47570155	11558828	81	817											
PEG3	5178	hgsc.bcm.edu	37	chr19	57328814	57328814	+	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	tgtgaccggtcgcttgactcCcttgctcttcccgatttgga	4	14	10	13	3	1	2	0	2	1	0	4	4	3	3	3	2	1	2	3	2	0	4			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr19:57328814C>A	ENST00000326441.9	-	10	1359	c.996G>T	c.(994-996)agG>agT	p.R332S	ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000599935.1_Intron|PEG3_ENST00000593695.1_Missense_Mutation_p.R206S|PEG3_ENST00000598410.1_Missense_Mutation_p.R208S|ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000221722.5_Intron|ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000423103.2_Missense_Mutation_p.R332S	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	332					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)		CGCTTGACTCCCTTGCTCTTC	0.493																																					p.R332S		Atlas-SNP	.											.	PEG3	414	.	0			c.G996T						PASS	.						76	72	74					19																	57328814		2203	4300	6503	SO:0001583	missense	5178	exon9			TGACTCCCTTGCT	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.996G>T	chr19.hg19:g.57328814C>A	ENSP00000326581:p.Arg332Ser	85.0	0.0	.		103.0	47.0	.	NM_001146184	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	hg19	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	C	14.52	2.558552	0.45590	.	.	ENSG00000198300	ENST00000326441;ENST00000423103;ENST00000292074	T;T	0.02525	4.26;4.26	4.27	1.01	0.19927	.	0.000000	0.50627	D	0.000103	T	0.05686	0.0149	L	0.36672	1.1	.	.	.	D;D;D	0.76494	0.999;0.999;0.988	D;D;P	0.71184	0.972;0.972;0.815	T	0.39623	-0.9605	9	0.21014	T	0.42	-34.9522	6.1823	0.20478	0.0:0.6841:0.0:0.3159	.	208;332;267	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	S	332;332;302	ENSP00000326581:R332S;ENSP00000403051:R332S	ENSP00000292074:R302S	R	-	3	2	ZIM2	62020626	0.000000	0.05858	0.145000	0.22337	0.716000	0.41182	-0.873000	0.04214	0.335000	0.23614	0.561000	0.74099	AGG	.	.	.	none		0.493	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			A	57328814	C	A	57328814	3	1	10	1	0	0	0	0	1	0	0	0	11727	622	22	4	3774	4	PEG3	19	57328814	Missense_Mutation	SNP	C	TCGA-2Z-A9JE-01A-11D-A42J-10	9758659	57328814	1800169	82	818											
ZNF776	284309	hgsc.bcm.edu	37	chr19	58265364	58265364	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagagagttcacactggagAaagaccttatgagtgtggag	13	8	13	7	0	1	4	1	1	0	3	1	7	1	5	2	2	0	1	2	2	2	2			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr19:58265364A>G	ENST00000317178.5	+	3	1129	c.866A>G	c.(865-867)gAa>gGa	p.E289G		NM_173632.3	NP_775903.3	Q68DI1	ZN776_HUMAN	zinc finger protein 776	289					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(2)|kidney(13)|large_intestine(3)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	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;0.0256)		CACACTGGAGAAAGACCTTAT	0.423																																					p.E289G		Atlas-SNP	.											.	ZNF776	115	.	0			c.A866G						PASS	.						93	83	86					19																	58265364		2203	4300	6503	SO:0001583	missense	284309	exon3			CTGGAGAAAGACC	AK095607	CCDS12962.2	19q13.43	2013-01-08			ENSG00000152443	ENSG00000152443		"Zinc fingers, C2H2-type", "-"	26765	protein-coding gene	gene with protein product							Standard	NM_173632		Approved	FLJ38288		Q68DI1	OTTHUMG00000156943	ENST00000317178.5:c.866A>G	chr19.hg19:g.58265364A>G	ENSP00000321812:p.Glu289Gly	52.0	0.0	.		47.0	26.0	.	NM_173632	Q6ZS36|Q8N968	Missense_Mutation	SNP	ENST00000317178.5	hg19	CCDS12962.2	.	.	.	.	.	.	.	.	.	.	A	25.7	4.660779	0.88154	.	.	ENSG00000152443	ENST00000317178	T	0.27557	1.66	1.92	0.722	0.18225	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.47525	0.1450	M	0.71581	2.175	0.80722	D	1	B;D	0.89917	0.349;1.0	B;D	0.91635	0.127;0.999	T	0.39396	-0.9616	9	0.87932	D	0	.	5.8253	0.18550	0.7628:0.0:0.0:0.2372	.	289;289	Q68DI1;B4DSC6	ZN776_HUMAN;.	G	289	ENSP00000321812:E289G	ENSP00000321812:E289G	E	+	2	0	ZNF776	62957176	0.110000	0.22057	0.524000	0.27887	0.982000	0.71751	1.099000	0.31013	-0.012000	0.14223	0.254000	0.18369	GAA	.	.	.	none		0.423	ZNF776-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346722.2	NM_173632		G	58265364	A	G	58265364	3	3	10	1	0	0	0	0	1	0	0	0	18161	246	9	3	876	3	ZNF776	19	58265364	Missense_Mutation	SNP	A	TCGA-2Z-A9JE-01A-11D-A42J-10	936550	58265364	863619	83	819											
ZNF217	7764	hgsc.bcm.edu	37	chr20	52194908	52194908	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatgaatattgaggtaataaTttgaacggaaaaactttcca	17	12	8	4	1	0	3	0	3	0	0	1	5	1	4	1	2	2	1	1	2	7	6			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr20:52194908T>C	ENST00000371471.2	-	3	1873	c.1448A>G	c.(1447-1449)aAt>aGt	p.N483S	ZNF217_ENST00000302342.3_Missense_Mutation_p.N483S			O75362	ZN217_HUMAN	zinc finger protein 217	483					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)			GAGGTAATAATTTGAACGGAA	0.259																																					p.N483S		Atlas-SNP	.											.	ZNF217	227	.	0			c.A1448G						PASS	.						79	78	78					20																	52194908		2201	4294	6495	SO:0001583	missense	7764	exon2			TAATAATTTGAAC	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.1448A>G	chr20.hg19:g.52194908T>C	ENSP00000360526:p.Asn483Ser	512.0	0.0	.		407.0	197.0	.	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	hg19	CCDS13443.1	.	.	.	.	.	.	.	.	.	.	T	16.06	3.016204	0.54468	.	.	ENSG00000171940	ENST00000371471;ENST00000302342	T;T	0.07216	3.21;3.21	5.0	3.83	0.44106	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.056391	0.64402	D	0.000002	T	0.18299	0.0439	M	0.66939	2.045	0.42547	D	0.993093	D	0.62365	0.991	P	0.57101	0.813	T	0.02519	-1.1147	10	0.25751	T	0.34	-48.1811	11.2946	0.49272	0.1361:0.0:0.0:0.8639	.	483	O75362	ZN217_HUMAN	S	483	ENSP00000360526:N483S;ENSP00000304308:N483S	ENSP00000304308:N483S	N	-	2	0	ZNF217	51628315	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.445000	0.52921	2.010000	0.58986	0.533000	0.62120	AAT	.	.	.	none		0.259	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		C	52194908	T	C	52194908	3	2	10	1	0	0	0	0	1	0	0	0	17784	1493	52	3	1710	3	ZNF217	20	52194908	Missense_Mutation	SNP	T	TCGA-2Z-A9JE-01A-11D-A42J-10		52194908	10830612	84	820											
USP25	29761	hgsc.bcm.edu	37	chr21	17135271	17135271	+	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	gattaatgacacccagatacTacagcaagccttgaaggtat	15	9	8	9	0	0	3	0	2	0	1	0	4	0	3	2	1	4	2	2	1	6	5			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr21:17135271T>A	ENST00000285679.6	+	2	476	c.107T>A	c.(106-108)cTa>cAa	p.L36Q	USP25_ENST00000351097.5_Missense_Mutation_p.L36Q|USP25_ENST00000400183.2_Missense_Mutation_p.L36Q|USP25_ENST00000285681.2_Missense_Mutation_p.L36Q	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	36	UBA-like.				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)		ACCCAGATACTACAGCAAGCC	0.363																																					p.L36Q		Atlas-SNP	.											.	USP25	156	.	0			c.T107A						PASS	.						139	140	140					21																	17135271		2203	4300	6503	SO:0001583	missense	29761	exon2			AGATACTACAGCA	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.107T>A	chr21.hg19:g.17135271T>A	ENSP00000285679:p.Leu36Gln	46.0	0.0	.		67.0	40.0	.	NM_013396	C0LSZ0|Q6DHZ9|Q9H9W1	Missense_Mutation	SNP	ENST00000285679.6	hg19	CCDS33515.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.460251	0.84317	.	.	ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000351097;ENST00000400183	T;T;T;T	0.56776	0.89;0.93;0.44;0.95	5.33	5.33	0.75918	UBA-like (1);	0.000000	0.85682	D	0.000000	T	0.68430	0.3000	L	0.55990	1.75	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;0.998;1.0;0.999	D;D;D;D	0.97110	0.999;0.995;1.0;0.997	T	0.71768	-0.4493	10	0.87932	D	0	.	15.3004	0.73945	0.0:0.0:0.0:1.0	.	36;36;36;36	Q9UHP3-3;Q96B65;Q9UHP3-1;Q9UHP3	.;.;.;UBP25_HUMAN	Q	36	ENSP00000285681:L36Q;ENSP00000285679:L36Q;ENSP00000299574:L36Q;ENSP00000383044:L36Q	ENSP00000285679:L36Q	L	+	2	0	USP25	16057142	1.000000	0.71417	0.988000	0.46212	0.992000	0.81027	7.673000	0.83973	2.024000	0.59613	0.459000	0.35465	CTA	.	.	.	none		0.363	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			A	17135271	T	A	17135271	3	1	10	1	0	0	0	0	1	0	0	0	17068	1522	53	5	113	5	USP25	21	17135271	Missense_Mutation	SNP	T	TCGA-2Z-A9JE-01A-11D-A42J-10		17135271	30994624	85	821											
BACH1	571	hgsc.bcm.edu	37	chr21	30699093	30699114	+	Frame_Shift_Del	DEL	CCCTCATGGACTTTATTCTTTG	CCCTCATGGACTTTATTCTTTG	-																															ccccacaattcttccatagaCcctcatggactttattcttt																										TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	CCCTCATGGACTTTATTCTTTG	CCCTCATGGACTTTATTCTTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr21:30699093_30699114delCCCTCATGGACTTTATTCTTTG	ENST00000399921.1	+	3	1191_1212	c.948_969delCCCTCATGGACTTTATTCTTTG	c.(946-969)gaccctcatggactttattctttgfs	p.DPHGLYSL316fs	BACH1_ENST00000286800.3_Frame_Shift_Del_p.DPHGLYSL316fs	NM_206866.1	NP_996749.1	Q9BX63	FANCJ_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 1	0	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|urinary_tract(2)	27						CTTCCATAGACCCTCATGGACTTTATTCTTTGTCTCTTTTAC	0.405																																					p.316_323del		Atlas-Indel,Pindel	.											.	BACH1	66	.	0			c.947_968del						PASS	.																																			SO:0001589	frameshift_variant	571	exon3			.	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.948_969delCCCTCATGGACTTTATTCTTTG	chr21.hg19:g.30699093_30699114delCCCTCATGGACTTTATTCTTTG	ENSP00000382805:p.Asp316fs	60.0	0.0	0		49.0	19.0	0.387755	NM_206866	Q3MJE2|Q8NCI5	Frame_Shift_Del	DEL	ENST00000399921.1	hg19	CCDS13585.1																																																																																			.	.	.	none		0.405	BACH1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171974.1	NM_206866		-	30699114	CCCTCATGGACTTTATTCTTTG	-	30699093	7	5	10	1	0	1	0	1	0	0	0	0	1283	506	18	0	954	0	BACH1	21	30699093	Frame_Shift_Del	DEL	CCCTCATGGACTTTATTCTTTG	TCGA-2Z-A9JE-01A-11D-A42J-10	13563822	30699093	17430802	86	822											
CLIC6	54102	hgsc.bcm.edu	37	chr21	36042470	36042470	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccggcgggggacggcgtagaAgcgggggtcccggcggggga	5	2	24	10	7	0	1	0	0	0	1	1	3	1	3	2	9	1	1	2	9	2	1	rs557556798|rs62213790	byFrequency	TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr21:36042470A>G	ENST00000360731.3	+	1	783	c.783A>G	c.(781-783)gaA>gaG	p.E261E	CLIC6_ENST00000349499.2_Silent_p.E261E			Q96NY7	CLIC6_HUMAN	chloride intracellular channel 6	261	13 X 10 AA tandem repeat of G-D-[SNG]- [VIM]-[DEQ]-A-[EAG]-[GDVE]-[PRG]-[LAVP].					chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	voltage-gated chloride channel activity (GO:0005247)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19						ACGGCGTAGAAGCGGGGGTCC	0.761																																					p.E261E		Atlas-SNP	.											CLIC6,NS,carcinoma,0,1	CLIC6	49	.	0			c.A783G						PASS	.						1	2	2					21																	36042470		755	1897	2652	SO:0001819	synonymous_variant	54102	exon1			CGTAGAAGCGGGG	AF426169	CCDS13638.1	21q22.12	2012-09-26			ENSG00000159212	ENSG00000159212		"Ion channels / Chloride channels : Intracellular"	2065	protein-coding gene	gene with protein product		615321		CLIC1L		10830953	Standard	NM_053277		Approved	CLIC5	uc002yuf.1	Q96NY7	OTTHUMG00000086237	ENST00000360731.3:c.783A>G	chr21.hg19:g.36042470A>G		23.0	0.0	.		14.0	4.0	.	NM_053277	A8K0U8|Q8IX31	Silent	SNP	ENST00000360731.3	hg19																																																																																				.	.	.	weak		0.761	CLIC6-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000194156.1			G	36042470	A	G	36042470	2	3	10	1	0	0	0	0	0	0	0	1	3532	69	3	3		3	CLIC6	21	36042470	Silent	SNP	A	TCGA-2Z-A9JE-01A-11D-A42J-10	5343377	36042470	12087425	87	823											
KRTAP10-8	386681	hgsc.bcm.edu	37	chr21	46032738	46032738	+	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	cctgccagcccagctgctgcCacccggcctcctgcctgtcc	3	7	9	22	1	0	0	0	0	0	0	2	0	2	0	9	1	6	2	9	1	0	0			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chr21:46032738C>T	ENST00000334662.2	+	1	743	c.721C>T	c.(721-723)Cac>Tac	p.H241Y	TSPEAR_ENST00000323084.4_Intron	NM_198695.2	NP_941968.2	P60410	KR108_HUMAN	keratin associated protein 10-8	241	19 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	17						cagctgctgccacccggcctc	0.711																																					p.H241Y		Atlas-SNP	.											.	KRTAP10-8	34	.	0			c.C721T						PASS	.						37	45	42					21																	46032738		2203	4298	6501	SO:0001583	missense	386681	exon1			TGCTGCCACCCGG	AB076355	CCDS13713.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000187766	ENSG00000187766		"Keratin associated proteins"	20525	protein-coding gene	gene with protein product			"keratin associated protein 18-8"	KRTAP18-8			Standard	NM_198695		Approved	KRTAP18.8, KAP10.8	uc002zfo.1	P60410	OTTHUMG00000057632	ENST00000334662.2:c.721C>T	chr21.hg19:g.46032738C>T	ENSP00000335565:p.His241Tyr	59.0	0.0	.		37.0	20.0	.	NM_198695	A0JNW4	Missense_Mutation	SNP	ENST00000334662.2	hg19	CCDS13713.1	.	.	.	.	.	.	.	.	.	.	c	3.898	-0.022702	0.07634	.	.	ENSG00000187766	ENST00000334662	T	0.00717	5.79	3.24	-3.04	0.05412	.	.	.	.	.	T	0.00608	0.0020	N	0.14661	0.345	0.09310	N	1	B	0.25521	0.128	B	0.29663	0.105	T	0.45101	-0.9284	9	0.56958	D	0.05	.	5.7146	0.17952	0.0:0.4714:0.1368:0.3918	.	241	P60410	KR108_HUMAN	Y	241	ENSP00000335565:H241Y	ENSP00000335565:H241Y	H	+	1	0	KRTAP10-8	44857166	0.000000	0.05858	0.374000	0.26016	0.007000	0.05969	-3.222000	0.00551	-0.687000	0.05162	-1.250000	0.01514	CAC	.	.	.	none		0.711	KRTAP10-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128035.1	NM_198695		T	46032738	C	T	46032738	3	4	10	1	0	0	0	0	1	0	0	0	8522	594	21	2	723	2	KRTAP10-8	21	46032738	Missense_Mutation	SNP	C	TCGA-2Z-A9JE-01A-11D-A42J-10	9990268	46032738	2097157	88	824											
FANCB	2187	hgsc.bcm.edu	37	chrX	14863248	14863248	+	Missense_Mutation	SNP	T	T	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	cttgctatcaggggtcaacgTgaccctttttgcttccaatc	7	14	8	12	1	2	1	2	1	0	0	4	1	3	1	2	2	3	2	2	2	3	5			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chrX:14863248T>G	ENST00000324138.3	-	7	1810	c.1657A>C	c.(1657-1659)Acg>Ccg	p.T553P	FANCB_ENST00000398334.1_Missense_Mutation_p.T553P	NM_152633.2	NP_689846.1	Q8NB91	FANCB_HUMAN	Fanconi anemia, complementation group B	553					DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24	Hepatocellular(33;0.183)					GGGGTCAACGTGACCCTTTTT	0.403								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.T553P		Atlas-SNP	.											.	FANCB	78	.	0			c.A1657C						PASS	.						101	90	93					X																	14863248		2203	4300	6503	SO:0001583	missense	2187	exon7	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TCAACGTGACCCT	AK091383	CCDS14161.1	Xp22.2	2014-09-17			ENSG00000181544	ENSG00000181544		"Fanconi anemia, complementation groups"	3583	protein-coding gene	gene with protein product		300515				9382107, 15502827	Standard	NM_152633		Approved	FAB, FLJ34064, FAAP95	uc004cwh.1	Q8NB91	OTTHUMG00000021168	ENST00000324138.3:c.1657A>C	chrX.hg19:g.14863248T>G	ENSP00000326819:p.Thr553Pro	130.0	0.0	.		141.0	124.0	.	NM_152633	B2RMZ4|Q7Z2U2|Q86XG1	Missense_Mutation	SNP	ENST00000324138.3	hg19	CCDS14161.1	.	.	.	.	.	.	.	.	.	.	T	7.265	0.606039	0.14002	.	.	ENSG00000181544	ENST00000324138;ENST00000398334;ENST00000452869	.	.	.	5.36	4.17	0.49024	.	0.080592	0.52532	D	0.000066	T	0.24084	0.0583	N	0.08118	0	0.09310	N	0.999997	B	0.10296	0.003	B	0.06405	0.002	T	0.20605	-1.0270	9	0.72032	D	0.01	-5.8518	11.0343	0.47791	0.0:0.0:0.1533:0.8467	.	553	Q8NB91	FANCB_HUMAN	P	553	.	ENSP00000326819:T553P	T	-	1	0	FANCB	14773169	1.000000	0.71417	0.224000	0.23877	0.027000	0.11550	3.643000	0.54374	0.657000	0.30906	0.425000	0.28330	ACG	.	.	.	none		0.403	FANCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055835.1	NM_152633		G	14863248	T	G	14863248	3	3	10	1	0	0	0	0	1	0	0	0	5670	1696	59	5	934	5	FANCB	23	14863248	Missense_Mutation	SNP	T	TCGA-2Z-A9JE-01A-11D-A42J-10		14863248	140407312	89	825											
LPAR4	2846	hgsc.bcm.edu	37	chrX	78010830	78010830	+	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	tattaggactaggaggaattCtgccattgtgtgtgctggtg	8	14	14	5	0	1	0	0	0	1	0	1	3	1	3	1	4	2	1	1	4	4	5			TCGA-2Z-A9JE-01A-11D-A42J-10	TCGA-2Z-A9JE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fa7ded84-a75d-4ee6-b8c4-cb4858ba6c62	0ce30bd0-7241-4ecb-aa30-df5138e4b738	g.chrX:78010830C>G	ENST00000435339.3	+	2	850	c.464C>G	c.(463-465)tCt>tGt	p.S155C		NM_005296.2	NP_005287.1	Q99677	LPAR4_HUMAN	lysophosphatidic acid receptor 4	155					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)|lipid binding (GO:0008289)			breast(3)|endometrium(3)|kidney(4)|large_intestine(4)|lung(16)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	38						AGGAGGAATTCTGCCATTGTG	0.468																																					p.S155C		Atlas-SNP	.											.	LPAR4	83	.	0			c.C464G						PASS	.						191	127	149					X																	78010830		2203	4300	6503	SO:0001583	missense	2846	exon2			GGAATTCTGCCAT	U90322	CCDS14441.1	Xq21.1	2012-08-08	2008-04-11	2008-04-11	ENSG00000147145	ENSG00000147145		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	4478	protein-coding gene	gene with protein product		300086	"G protein-coupled receptor 23"	GPR23			Standard	NM_005296		Approved	P2Y9, P2Y5-LIKE, P2RY9, LPA4	uc010nme.3	Q99677	OTTHUMG00000021895	ENST00000435339.3:c.464C>G	chrX.hg19:g.78010830C>G	ENSP00000408205:p.Ser155Cys	28.0	0.0	.		50.0	47.0	.	NM_005296	B2RAC7|O15132|Q502U9|Q6NSP5	Missense_Mutation	SNP	ENST00000435339.3	hg19	CCDS14441.1	.	.	.	.	.	.	.	.	.	.	C	17.15	3.317040	0.60524	.	.	ENSG00000147145	ENST00000435339;ENST00000373301	T;T	0.35789	1.29;1.29	4.21	4.21	0.49690	GPCR, rhodopsin-like superfamily (1);	0.149396	0.45867	D	0.000329	T	0.48259	0.1490	L	0.38733	1.17	0.52501	D	0.99995	D	0.69078	0.997	D	0.69142	0.962	T	0.50398	-0.8833	10	0.59425	D	0.04	.	14.3969	0.67018	0.0:1.0:0.0:0.0	.	155	Q99677	LPAR4_HUMAN	C	155	ENSP00000408205:S155C;ENSP00000362398:S155C	ENSP00000362398:S155C	S	+	2	0	LPAR4	77897486	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	7.233000	0.78125	1.943000	0.56356	0.422000	0.28245	TCT	.	.	.	none		0.468	LPAR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057322.2	NM_005296		G	78010830	C	G	78010830	3	3	10	1	0	0	0	0	1	0	0	0	8914	913	32	4	466	4	LPAR4	23	78010830	Missense_Mutation	SNP	C	TCGA-2Z-A9JE-01A-11D-A42J-10	63147582	78010830	77259730	90	826											
TAS1R3	83756	hgsc.bcm.edu	37	chr1	1267767	1267767	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccgcccacgccctcttcaacTacagcatcagcagcaggctc	9	6	7	19	2	3	0	2	0	1	0	4	0	3	0	3	1	5	4	3	1	2	2			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr1:1267767T>C	ENST00000339381.5	+	3	888	c.856T>C	c.(856-858)Tac>Cac	p.Y286H		NM_152228.1	NP_689414	Q7RTX0	TS1R3_HUMAN	taste receptor, type 1, member 3	286					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)		CCTCTTCAACTACAGCATCAG	0.672																																					p.Y286H		Atlas-SNP	.											.	TAS1R3	39	.	0			c.T856C						PASS	.						25	21	22					1																	1267767		2187	4285	6472	SO:0001583	missense	83756	exon3			TTCAACTACAGCA	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.856T>C	chr1.hg19:g.1267767T>C	ENSP00000344411:p.Tyr286His	133.0	0.0	.		54.0	19.0	.	NM_152228	Q5TA49|Q8NGW9	Missense_Mutation	SNP	ENST00000339381.5	hg19	CCDS30556.1	.	.	.	.	.	.	.	.	.	.	T	0.130	-1.114776	0.01799	.	.	ENSG00000169962	ENST00000339381	D	0.82619	-1.63	4.6	-1.77	0.07982	Extracellular ligand-binding receptor (1);	0.501897	0.20842	N	0.084691	T	0.64438	0.2598	N	0.13235	0.315	0.09310	N	1	B	0.09022	0.002	B	0.14023	0.01	T	0.53641	-0.8410	10	0.48119	T	0.1	.	7.3836	0.26870	0.1219:0.4662:0.0:0.4119	.	286	Q7RTX0	TS1R3_HUMAN	H	286	ENSP00000344411:Y286H	ENSP00000344411:Y286H	Y	+	1	0	TAS1R3	1257630	0.000000	0.05858	0.018000	0.16275	0.007000	0.05969	-2.021000	0.01440	-0.213000	0.10094	-0.411000	0.06167	TAC	.	.	.	none		0.672	TAS1R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008493.1			C	1267767	T	C	1267767	3	2	11	1	0	0	0	0	1	0	0	0	15576	1522	53	3	866	3	TAS1R3	1	1267767	Missense_Mutation	SNP	T	TCGA-2Z-A9JG-01A-11D-A42J-10		1267767	247982854	1	827											
LEPR	3953	hgsc.bcm.edu	37	chr1	66088612	66088612	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaaaagctattttgggaagAtgttccgaaccccaagaatt	15	10	9	7	1	0	2	0	0	0	2	1	5	1	3	3	1	2	2	3	1	7	5			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr1:66088612A>G	ENST00000349533.6	+	19	2806	c.2621A>G	c.(2620-2622)gAt>gGt	p.D874G	LEPR_ENST00000344610.8_Missense_Mutation_p.D874G|LEPR_ENST00000371060.3_Missense_Mutation_p.D874G|LEPR_ENST00000371059.3_Missense_Mutation_p.D874G|LEPR_ENST00000371058.1_Missense_Mutation_p.D874G|LEPR_ENST00000406510.3_Intron	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)		TTTTGGGAAGATGTTCCGAAC	0.338																																					p.D874G		Atlas-SNP	.											.	LEPR	284	.	0			c.A2621G						PASS	.						96	97	96					1																	66088612		2203	4300	6503	SO:0001583	missense	3953	exon19			GGGAAGATGTTCC	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.2621A>G	chr1.hg19:g.66088612A>G	ENSP00000330393:p.Asp874Gly	59.0	0.0	.		92.0	32.0	.	NM_001003680	Q6FHL5	Missense_Mutation	SNP	ENST00000349533.6	hg19	CCDS631.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.971394	0.74246	.	.	ENSG00000116678	ENST00000344610;ENST00000349533;ENST00000371060;ENST00000371059;ENST00000371058	T;T;T;T;T	0.71817	-0.31;-0.28;-0.29;-0.6;-0.31	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	T	0.79540	0.4463	M	0.72479	2.2	0.80722	D	1	P;P;D	0.89917	0.864;0.917;1.0	B;P;D	0.97110	0.416;0.62;1.0	T	0.82283	-0.0534	10	0.62326	D	0.03	-22.0107	15.1416	0.72615	1.0:0.0:0.0:0.0	.	874;874;874	P48357;P48357-2;P48357-3	LEPR_HUMAN;.;.	G	874	ENSP00000340884:D874G;ENSP00000330393:D874G;ENSP00000360099:D874G;ENSP00000360098:D874G;ENSP00000360097:D874G	ENSP00000340884:D874G	D	+	2	0	LEPR	65861200	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	6.605000	0.74155	2.019000	0.59389	0.528000	0.53228	GAT	.	.	.	none		0.338	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303		G	66088612	A	G	66088612	3	3	11	1	0	0	0	0	1	0	0	0	8735	333	12	3	2687	3	LEPR	1	66088612	Missense_Mutation	SNP	A	TCGA-2Z-A9JG-01A-11D-A42J-10	64820845	66088612	183162009	2	828											
PRCC	5546	hgsc.bcm.edu	37	chr1	156767106	156767106	+	Missense_Mutation	SNP	A	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	acaggccagcagcggcggaaAcaccagatcacatatcttat	14	6	9	12	2	2	1	1	0	1	1	2	2	2	2	2	3	3	1	2	3	3	2			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr1:156767106A>C	ENST00000271526.4	+	6	1634	c.1362A>C	c.(1360-1362)aaA>aaC	p.K454N	PRCC_ENST00000353233.3_Missense_Mutation_p.K422N	NM_005973.4	NP_005964.3	Q92733	PRCC_HUMAN	papillary renal cell carcinoma (translocation-associated)	454					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)					AGCGGCGGAAACACCAGATCA	0.473			T	TFE3	papillary renal						OREG0013886	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K454N		Atlas-SNP	.		Dom	yes		1	1q21.1	5546	papillary renal cell carcinoma (translocation-associated)		E	.	PRCC	39	.	0			c.A1362C						PASS	.						85	92	90					1																	156767106		2203	4300	6503	SO:0001583	missense	5546	exon6			GCGGAAACACCAG	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.1362A>C	chr1.hg19:g.156767106A>C	ENSP00000271526:p.Lys454Asn	77.0	0.0	.	1781	118.0	44.0	.	NM_005973	A8K1F7|O00665|O00724|Q5SZ06	Missense_Mutation	SNP	ENST00000271526.4	hg19	CCDS1157.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.33|18.33	3.599257|3.599257	0.66332|0.66332	.|.	.|.	ENSG00000143294|ENSG00000143294	ENST00000271526;ENST00000353233;ENST00000368201;ENST00000526188|ENST00000454659	T;T|.	0.69306|.	-0.39;-0.27|.	5.43|5.43	3.09|3.09	0.35607|0.35607	Mitotic checkpoint protein PRCC, C-terminal (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.53546|0.53546	0.1803|0.1803	M|M	0.78456|0.78456	2.415|2.415	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.999;0.999|.	T|T	0.54702|0.54702	-0.8254|-0.8254	10|5	0.87932|.	D|.	0|.	-12.1328|-12.1328	7.4238|7.4238	0.27088|0.27088	0.7463:0.0:0.2537:0.0|0.7463:0.0:0.2537:0.0	.|.	422;454|.	A6NG79;Q92733|.	.;PRCC_HUMAN|.	N|T	454;422;430;161|220	ENSP00000271526:K454N;ENSP00000339300:K422N|.	ENSP00000271526:K454N|.	K|N	+|+	3|2	2|0	PRCC|PRCC	155033730|155033730	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	1.177000|1.177000	0.31969|0.31969	0.493000|0.493000	0.27837|0.27837	-0.261000|-0.261000	0.10672|0.10672	AAA|AAC	.	.	.	none		0.473	PRCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098941.2	NM_005973		C	156767106	A	C	156767106	3	2	11	1	0	0	0	0	1	0	0	0	12457	40	2	5	1384	5	PRCC	1	156767106	Missense_Mutation	SNP	A	TCGA-2Z-A9JG-01A-11D-A42J-10	90678494	156767106	92483515	3	829											
SOAT1	6646	hgsc.bcm.edu	37	chr1	179310206	179310206	+	Missense_Mutation	SNP	T	T	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	tgtcttatgcttttggcaaaTttcctaccgttgtttggacc	6	18	8	9	1	1	0	0	0	1	0	2	1	2	1	3	2	2	4	3	2	3	7			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr1:179310206T>G	ENST00000367619.3	+	7	684	c.541T>G	c.(541-543)Ttt>Gtt	p.F181V	SOAT1_ENST00000539888.1_Missense_Mutation_p.F116V|SOAT1_ENST00000540564.1_Missense_Mutation_p.F123V|SOAT1_ENST00000535686.1_De_novo_Start_InFrame	NM_003101.5	NP_003092.4	P35610	SOAT1_HUMAN	sterol O-acyltransferase 1	181					cholesterol efflux (GO:0033344)|cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol storage (GO:0010878)|macrophage derived foam cell differentiation (GO:0010742)|positive regulation of amyloid precursor protein biosynthetic process (GO:0042986)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|cholesterol O-acyltransferase activity (GO:0034736)|fatty-acyl-CoA binding (GO:0000062)|sterol O-acyltransferase activity (GO:0004772)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|stomach(1)	20					Ezetimibe(DB00973)|Hesperetin(DB01094)	TTTTGGCAAATTTCCTACCGT	0.423																																					p.F181V		Atlas-SNP	.											.	SOAT1	53	.	0			c.T541G						PASS	.						144	134	137					1																	179310206		2203	4300	6503	SO:0001583	missense	6646	exon7			GGCAAATTTCCTA	L21934	CCDS1330.1, CCDS58047.1, CCDS58048.1	1q25	2008-08-26	2008-08-26		ENSG00000057252	ENSG00000057252	2.3.1.26		11177	protein-coding gene	gene with protein product	"acyl-Coenzyme A: cholesterol acyltransferase"	102642	"sterol O-acyltransferase (acyl-Coenzyme A: cholesterol acyltransferase) 1"	SOAT, STAT		8407899	Standard	NM_003101		Approved	ACAT	uc001gml.3	P35610	OTTHUMG00000035253	ENST00000367619.3:c.541T>G	chr1.hg19:g.179310206T>G	ENSP00000356591:p.Phe181Val	57.0	0.0	.		85.0	41.0	.	NM_003101	A6NC40|A8K3P4|A9Z1V7|B4DU95|Q5T0X4|Q8N1E4	Missense_Mutation	SNP	ENST00000367619.3	hg19	CCDS1330.1	.	.	.	.	.	.	.	.	.	.	T	14.41	2.527498	0.44969	.	.	ENSG00000057252	ENST00000539888;ENST00000540564;ENST00000367619;ENST00000426956	T;T;T;T	0.17691	2.26;2.26;2.26;2.26	5.96	-2.2	0.06994	.	0.382132	0.35013	N	0.003507	T	0.19846	0.0477	M	0.61703	1.905	0.80722	D	1	B;B	0.25850	0.006;0.136	B;B	0.35312	0.026;0.2	T	0.06826	-1.0805	10	0.52906	T	0.07	-32.5711	11.9488	0.52944	0.0:0.2527:0.0:0.7473	.	123;181	A8K3P4;P35610	.;SOAT1_HUMAN	V	116;123;181;181	ENSP00000441356:F116V;ENSP00000445315:F123V;ENSP00000356591:F181V;ENSP00000411309:F181V	ENSP00000356591:F181V	F	+	1	0	SOAT1	177576829	0.994000	0.37717	0.005000	0.12908	0.977000	0.68977	0.305000	0.19254	-0.663000	0.05331	-0.290000	0.09829	TTT	.	.	.	none		0.423	SOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085286.2	NM_003101		G	179310206	T	G	179310206	3	3	11	1	0	0	0	0	1	0	0	0	14923	1493	52	5	563	5	SOAT1	1	179310206	Missense_Mutation	SNP	T	TCGA-2Z-A9JG-01A-11D-A42J-10	22543100	179310206	69940415	4	830											
SMG7	9887	hgsc.bcm.edu	37	chr1	183495889	183495889	+	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	tgccagcactgcctcgtccaCcttggagacattggtgagcc	7	9	11	14	1	0	2	0	1	0	1	2	3	1	2	5	2	4	1	5	2	0	2			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr1:183495889C>T	ENST00000347615.2	+	5	590	c.471C>T	c.(469-471)caC>caT	p.H157H	SMG7_ENST00000507406.1_3'UTR|SMG7_ENST00000507469.1_Silent_p.H157H|SMG7_ENST00000515829.2_Silent_p.H157H|SMG7_ENST00000367537.3_Silent_p.H186H|SMG7_ENST00000456731.2_Silent_p.H115H|SMG7_ENST00000508461.1_Silent_p.H115H	NM_173156.2	NP_775179.1	Q92540	SMG7_HUMAN	SMG7 nonsense mediated mRNA decay factor	157					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(16)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	46						GCCTCGTCCACCTTGGAGACA	0.443																																					p.H157H		Atlas-SNP	.											.	SMG7	165	.	0			c.C471T						PASS	.						208	179	189					1																	183495889		2203	4300	6503	SO:0001819	synonymous_variant	9887	exon5			CGTCCACCTTGGA	D87437	CCDS1355.1, CCDS41445.1, CCDS41445.2, CCDS53444.1, CCDS53445.1	1q25	2013-07-02	2013-07-02	2006-02-16	ENSG00000116698	ENSG00000116698			16792	protein-coding gene	gene with protein product	"EST1 telomerase component homolog C (S. cerevisiae)"	610964	"chromosome 1 open reading frame 16", "smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C1orf16		14636577, 15721257	Standard	NM_173156		Approved	KIAA0250, EST1C, SGA56M, SMG-7	uc001gqf.3	Q92540	OTTHUMG00000035221	ENST00000347615.2:c.471C>T	chr1.hg19:g.183495889C>T		51.0	0.0	.		59.0	24.0	.	NM_201569	B4DRB2|E9PCI0|E9PEH2|Q5T1Q0|Q6PIE0|Q7Z7H9|Q8IXC1|Q8IXC2	Silent	SNP	ENST00000347615.2	hg19	CCDS1355.1																																																																																			.	.	.	none		0.443	SMG7-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000085432.1	NM_014837		T	183495889	C	T	183495889	2	4	11	1	0	0	0	0	0	0	0	1	14811	506	18	2		2	SMG7	1	183495889	Silent	SNP	C	TCGA-2Z-A9JG-01A-11D-A42J-10	4185683	183495889	65754732	5	831											
TPR	7175	hgsc.bcm.edu	37	chr1	186289494	186289494	+	Frame_Shift_Del	DEL	G	G	-																															agtgactagaacttgtttgtGgcatatcttcaggtggccca																										TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr1:186289494delG	ENST00000367478.4	-	46	6814	c.6518delC	c.(6517-6519)ccafs	p.P2173fs		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	2173					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)		ACTTGTTTGTGGCATATCTTC	0.398			T	NTRK1	papillary thyroid																																p.P2173fs		Atlas-Indel,Pindel	.		Dom	yes		1	1q25	7175	translocated promoter region		E	TPR_ENST00000367478,NS,carcinoma,0,2	TPR	441	.	0			c.6519delA						PASS	.						87	82	84					1																	186289494		1872	4103	5975	SO:0001589	frameshift_variant	7175	exon46			.	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.6518delC	chr1.hg19:g.186289494delG	ENSP00000356448:p.Pro2173fs	53.0	0.0	0		85.0	38.0	0.447059	NM_003292	Q15655|Q5SWY0|Q99968	Frame_Shift_Del	DEL	ENST00000367478.4	hg19	CCDS41446.1																																																																																			.	.	.	none		0.398	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		-	186289494	G	-	186289494	7	5	11	1	0	1	0	1	0	0	0	0	16428	1348	47	0	597	0	TPR	1	186289494	Frame_Shift_Del	DEL	G	TCGA-2Z-A9JG-01A-11D-A42J-10	2793605	186289494	62961127	6	832											
IRF2BP2	359948	hgsc.bcm.edu	37	chr1	234743069	234743069	+	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	caagggaagcagaacttgtgCgaagggacggacgggcactg	12	4	17	8	3	0	1	0	0	0	1	0	5	0	4	0	4	3	2	0	4	4	1			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr1:234743069C>G	ENST00000366609.3	-	2	1608	c.1578G>C	c.(1576-1578)tcG>tcC	p.S526S	RP4-781K5.2_ENST00000436039.1_RNA|IRF2BP2_ENST00000366610.3_Silent_p.S510S|IRF2BP2_ENST00000491430.1_5'UTR	NM_182972.2	NP_892017.2	Q7Z5L9	I2BP2_HUMAN	interferon regulatory factor 2 binding protein 2	526	Cys-rich.				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)			AGAACTTGTGCGAAGGGACGG	0.592																																					p.S526S		Atlas-SNP	.											.	IRF2BP2	37	.	0			c.G1578C						PASS	.						79	84	83					1																	234743069		2203	4300	6503	SO:0001819	synonymous_variant	359948	exon2			CTTGTGCGAAGGG	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.1578G>C	chr1.hg19:g.234743069C>G		115.0	0.0	.		64.0	29.0	.	NM_182972	B1AM35|B1AM36|Q6P083|Q7Z5L8|Q8N351|Q8WUH8	Silent	SNP	ENST00000366609.3	hg19	CCDS1602.1																																																																																			.	.	.	none		0.592	IRF2BP2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000092705.1	NM_182972		G	234743069	C	G	234743069	2	3	11	1	0	0	0	0	0	0	0	1	7837	755	27	4		4	IRF2BP2	1	234743069	Silent	SNP	C	TCGA-2Z-A9JG-01A-11D-A42J-10	48453575	234743069	14507552	7	833											
PPPDE1	51029	hgsc.bcm.edu	37	chr1	244849928	244849928	+	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	aacgaatatacctcatccatTggaattggagtttttcattc	12	15	6	8	1	2	0	2	0	0	0	4	3	3	2	2	2	2	1	2	2	5	7			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr1:244849928T>A	ENST00000302550.11	+	2	451	c.72T>A	c.(70-72)atT>atA	p.I24I	DESI2_ENST00000263831.7_Silent_p.I24I	NM_016076.3	NP_057160.2	Q9BSY9	DESI2_HUMAN	desumoylating isopeptidase 2	24	PPPDE peptidase.					cytoplasm (GO:0005737)	peptidase activity (GO:0008233)										CCTCATCCATTGGAATTGGAG	0.358																																					p.I24I		Atlas-SNP	.											.	.	.	.	0			c.T72A						PASS	.						130	130	130					1																	244849928		2203	4300	6503	SO:0001819	synonymous_variant	51029	exon2			ATCCATTGGAATT	AK025651	CCDS1626.1, CCDS73055.1	1q44	2012-05-16	2012-05-16	2012-05-16	ENSG00000121644	ENSG00000121644			24264	protein-coding gene	gene with protein product		614638	"chromosome 1 open reading frame 121", "family with sequence similarity 152, member A", "PPPDE peptidase domain containing 1"	C1orf121, FAM152A, PPPDE1		10810093, 22370726	Standard	XM_005273154		Approved	CGI-146, FLJ21998	uc001iao.3	Q9BSY9	OTTHUMG00000040398	ENST00000302550.11:c.72T>A	chr1.hg19:g.244849928T>A		46.0	0.0	.		37.0	10.0	.	NM_016076	B1APK6|Q5VVC6|Q9NYS2|Q9Y3E4	Silent	SNP	ENST00000302550.11	hg19	CCDS1626.1																																																																																			.	.	.	none		0.358	DESI2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097168.1	NM_016076		A	244849928	T	A	244849928	2	1	11	1	0	0	0	0	0	0	0	1	12418	1800	63	5		5	PPPDE1	1	244849928	Silent	SNP	T	TCGA-2Z-A9JG-01A-11D-A42J-10	10106859	244849928	4400693	8	834											
AHCTF1	25909	hgsc.bcm.edu	37	chr1	247081550	247081560	+	Splice_Site	DEL	TTATGTTTACC	TTATGTTTACC	-																															tgttcagtgacattatgtttAcctgcagcaaactttccacg																										TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	TTATGTTTACC	TTATGTTTACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr1:247081550_247081560delTTATGTTTACC	ENST00000391829.2	-	2	236_245	c.113_122delGGTAAACATAA	c.(112-123)tggtaaacataa>ta	p.W*T*38fs	AHCTF1_ENST00000366508.1_Splice_Site_p.W*T*73fs|AHCTF1_ENST00000326225.3_Splice_Site_p.W*T*47fs			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	38	Necessary for cytoplasmic localization. {ECO:0000250}.|Seven-bladed beta propeller repeats. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			CATTATGTTTACCTGCAGCAAACTTTCCACG	0.346																																					.	Colon(145;197 1800 4745 15099 26333)	Atlas-Indel,Pindel	.											.	AHCTF1	187	.	0			.						PASS	.																																			SO:0001630	splice_region_variant	25909	.			.		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.121+1GGTAAACATAA>-	chr1.hg19:g.247081550_247081560delTTATGTTTACC		147.0	0.0	0		139.0	25.0	0.179856	.	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Splice_Site	DEL	ENST00000391829.2	hg19																																																																																				.	.	.	none		0.346	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446	Frame_Shift_Del	-	247081560	TTATGTTTACC	-	247081550	8	5	11	1	0	1	0	1	0	0	1	0	408	405	14	0	6817	0	AHCTF1	1	247081550	Splice_Site	DEL	TTATGTTTACC	TCGA-2Z-A9JG-01A-11D-A42J-10	2231622	247081550	2169071	9	835											
CAD	790	hgsc.bcm.edu	37	chr2	27456276	27456276	+	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	tggccatggcgttgcatcggCagcagtgccgggtgctgggc	4	8	18	11	3	0	0	0	0	0	0	1	0	0	0	2	5	4	5	2	5	0	1			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr2:27456276C>A	ENST00000403525.1	+	19	3043	c.2899C>A	c.(2899-2901)Cag>Aag	p.Q967K	CAD_ENST00000264705.4_Missense_Mutation_p.Q1030K			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)					GTTGCATCGGCAGCAGTGCCG	0.572																																					p.Q1030K		Atlas-SNP	.											.	CAD	199	.	0			c.C3088A						PASS	.						56	55	55					2																	27456276		2203	4300	6503	SO:0001583	missense	790	exon20			CATCGGCAGCAGT	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.2899C>A	chr2.hg19:g.27456276C>A	ENSP00000384510:p.Gln967Lys	53.0	0.0	.		88.0	4.0	.	NM_004341	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Missense_Mutation	SNP	ENST00000403525.1	hg19		.	.	.	.	.	.	.	.	.	.	C	29.1	4.976973	0.92982	.	.	ENSG00000084774	ENST00000264705;ENST00000403525	D;D	0.97232	-4.3;-4.3	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	0.97275	0.9109	L	0.41632	1.29	0.80722	D	1	D;D	0.69078	0.968;0.997	P;P	0.62885	0.808;0.908	D	0.97473	1.0042	10	0.54805	T	0.06	-0.5919	18.5877	0.91196	0.0:1.0:0.0:0.0	.	967;1030	F8VPD4;P27708	.;PYR1_HUMAN	K	1030;967	ENSP00000264705:Q1030K;ENSP00000384510:Q967K	ENSP00000264705:Q1030K	Q	+	1	0	CAD	27309780	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.375000	0.59549	2.804000	0.96469	0.655000	0.94253	CAG	.	.	.	none		0.572	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1			A	27456276	C	A	27456276	3	1	11	1	0	0	0	0	1	0	0	0	2567	711	25	4	3166	4	CAD	2	27456276	Missense_Mutation	SNP	C	TCGA-2Z-A9JG-01A-11D-A42J-10		27456276	215743097	10	836											
POLR1A	25885	hgsc.bcm.edu	37	chr2	86272888	86272888	+	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	caatctggcccagcaggcacGagatctggaggacaggaaat	13	5	13	10	1	2	1	0	0	2	1	2	5	2	4	1	5	1	2	1	5	2	0			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr2:86272888G>A	ENST00000263857.6	-	20	3116	c.2738C>T	c.(2737-2739)tCg>tTg	p.S913L	POLR1A_ENST00000409681.1_Missense_Mutation_p.S913L			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	913					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						CAGCAGGCACGAGATCTGGAG	0.522																																					p.S913L		Atlas-SNP	.											.	POLR1A	137	.	0			c.C2738T						PASS	.						44	48	47					2																	86272888		1910	4133	6043	SO:0001583	missense	25885	exon20			AGGCACGAGATCT	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.2738C>T	chr2.hg19:g.86272888G>A	ENSP00000263857:p.Ser913Leu	183.0	0.0	.		337.0	96.0	.	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	hg19	CCDS42706.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.658584	0.88154	.	.	ENSG00000068654	ENST00000263857;ENST00000409681	T;T	0.76709	-1.04;-1.04	5.95	5.95	0.96441	RNA polymerase Rpb1, domain 4 (1);	0.129604	0.53938	D	0.000043	D	0.90383	0.6990	M	0.90705	3.14	0.80722	D	1	D	0.89917	1.0	D	0.70227	0.968	D	0.91550	0.5256	10	0.87932	D	0	-16.9868	18.5659	0.91116	0.0:0.0:1.0:0.0	.	913	O95602	RPA1_HUMAN	L	913	ENSP00000263857:S913L;ENSP00000386300:S913L	ENSP00000263857:S913L	S	-	2	0	POLR1A	86126399	1.000000	0.71417	0.956000	0.39512	0.960000	0.62799	9.038000	0.93771	2.825000	0.97269	0.655000	0.94253	TCG	.	.	.	none		0.522	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425		A	86272888	G	A	86272888	3	1	11	1	0	0	0	0	1	0	0	0	12216	1059	37	1	2484	1	POLR1A	2	86272888	Missense_Mutation	SNP	G	TCGA-2Z-A9JG-01A-11D-A42J-10	58816612	86272888	156926485	11	837											
PAX8	7849	hgsc.bcm.edu	37	chr2	114000281	114000281	+	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	actcactcagcgtgtgtccgGgactcagggacttggtggcc	6	9	14	12	2	3	0	3	0	0	0	4	2	4	2	2	4	1	0	2	4	0	1			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr2:114000281G>T	ENST00000429538.3	-	5	658	c.464C>A	c.(463-465)cCc>cAc	p.P155H	AC016683.6_ENST00000556070.1_RNA|PAX8_ENST00000263334.5_Missense_Mutation_p.P155H|AC016683.6_ENST00000422956.2_RNA|PAX8_ENST00000397647.3_Missense_Mutation_p.P155H|AC016683.6_ENST00000437551.1_RNA|PAX8_ENST00000263335.7_Missense_Mutation_p.P155H|PAX8_ENST00000348715.5_Missense_Mutation_p.P155H|AC016683.6_ENST00000436293.2_RNA|AC016683.6_ENST00000451179.1_RNA|AC016683.6_ENST00000333145.5_RNA|AC016683.6_ENST00000553869.2_RNA|AC016683.6_ENST00000445745.1_RNA|RP11-65I12.1_ENST00000553319.1_RNA	NM_003466.3	NP_003457.1	Q06710	PAX8_HUMAN	paired box 8	155					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						CGTGTGTCCGGGACTCAGGGA	0.537			T	PPARG	follicular thyroid		Thyroid dysgenesis																														p.P155H	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.C464A						PASS	.						156	159	158					2																	114000281		2151	4261	6412	SO:0001583	missense	7849	exon5			TGTCCGGGACTCA	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.464C>A	chr2.hg19:g.114000281G>T	ENSP00000395498:p.Pro155His	126.0	0.0	.		155.0	39.0	.	NM_013952	Q09155|Q16337|Q16338|Q16339|Q4ZG35|Q96J49	Missense_Mutation	SNP	ENST00000429538.3	hg19	CCDS46398.1	.	.	.	.	.	.	.	.	.	.	g	25.0	4.591911	0.86953	.	.	ENSG00000125618	ENST00000263335;ENST00000397647;ENST00000348715;ENST00000429538;ENST00000263334	D;D;D;D;D	0.97959	-4.62;-4.63;-4.41;-3.99;-4.41	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	D	0.98261	0.9424	L	0.60455	1.87	0.80722	D	1	D;D;D;B;D	0.89917	1.0;0.994;1.0;0.01;0.986	D;D;D;B;P	0.85130	0.996;0.927;0.997;0.039;0.808	D	0.99094	1.0841	10	0.59425	D	0.04	.	16.774	0.85546	0.0:0.0:1.0:0.0	.	155;155;155;155;155	Q06710-2;Q06710-3;Q06710;Q06710-5;Q06710-4	.;.;PAX8_HUMAN;.;.	H	155	ENSP00000263335:P155H;ENSP00000380768:P155H;ENSP00000314750:P155H;ENSP00000395498:P155H;ENSP00000263334:P155H	ENSP00000263334:P155H	P	-	2	0	PAX8	113716751	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	8.038000	0.88943	2.550000	0.86006	0.552000	0.68991	CCC	.	.	.	none		0.537	PAX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250353.5			T	114000281	G	T	114000281	3	4	11	1	0	0	0	0	1	0	0	0	11492	1232	43	4	795	4	PAX8	2	114000281	Missense_Mutation	SNP	G	TCGA-2Z-A9JG-01A-11D-A42J-10	27727393	114000281	129199092	12	838											
HOXD1	3231	hgsc.bcm.edu	37	chr2	177054137	177054137	+	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	cggcctccctgccgccttcaGcacgttcgagtggatgaaag	7	8	12	14	4	1	1	1	1	0	0	3	3	2	2	4	2	2	2	4	2	1	2			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr2:177054137G>T	ENST00000331462.4	+	1	831	c.608G>T	c.(607-609)aGc>aTc	p.S203I	HOXD-AS1_ENST00000436126.1_RNA|HOXD-AS1_ENST00000417086.1_RNA|HOXD-AS1_ENST00000413969.1_RNA|HOXD-AS1_ENST00000452365.1_RNA|HOXD-AS1_ENST00000425005.1_RNA	NM_024501.2	NP_078777.1	Q9GZZ0	HXD1_HUMAN	homeobox D1	203					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)		GCCGCCTTCAGCACGTTCGAG	0.662																																					p.S203I		Atlas-SNP	.											.	HOXD1	33	.	0			c.G608T						PASS	.						26	30	28					2																	177054137		2160	4210	6370	SO:0001583	missense	3231	exon1			CCTTCAGCACGTT		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.608G>T	chr2.hg19:g.177054137G>T	ENSP00000328598:p.Ser203Ile	258.0	0.0	.		152.0	91.0	.	NM_024501	B2RAB4	Missense_Mutation	SNP	ENST00000331462.4	hg19	CCDS2271.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.448129	0.84101	.	.	ENSG00000128645	ENST00000331462;ENST00000375170	D	0.90844	-2.74	5.43	5.43	0.79202	.	0.000000	0.53938	D	0.000044	D	0.93628	0.7965	L	0.56769	1.78	0.41132	D	0.985896	D;D;D	0.76494	0.99;0.999;0.993	P;D;P	0.71656	0.802;0.974;0.806	D	0.92749	0.6214	10	0.36615	T	0.2	.	15.5055	0.75735	0.0:0.1387:0.8613:0.0	.	203;142;203	Q96CA4;Q8IZ25;Q9GZZ0	.;.;HXD1_HUMAN	I	203;142	ENSP00000328598:S203I	ENSP00000328598:S203I	S	+	2	0	HOXD1	176762383	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.488000	0.45276	2.532000	0.85374	0.561000	0.74099	AGC	.	.	.	none		0.662	HOXD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255693.2			T	177054137	G	T	177054137	3	4	11	1	0	0	0	0	1	0	0	0	7325	971	34	4	610	4	HOXD1	2	177054137	Missense_Mutation	SNP	G	TCGA-2Z-A9JG-01A-11D-A42J-10	63053856	177054137	66145236	13	839											
CAPN7	23473	hgsc.bcm.edu	37	chr3	15287046	15287046	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgcagctgacccacctccAtacattgatggaattcgaat	11	12	7	11	1	0	2	0	2	0	0	2	4	1	3	3	1	3	2	3	1	3	4			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr3:15287046A>G	ENST00000253693.2	+	17	2131	c.1878A>G	c.(1876-1878)ccA>ccG	p.P626P		NM_014296.2	NP_055111.1	Q9Y6W3	CAN7_HUMAN	calpain 7	626	Domain III.				positive regulation of epithelial cell migration (GO:0010634)|self proteolysis (GO:0097264)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|endopeptidase activity (GO:0004175)|MIT domain binding (GO:0090541)			breast(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|skin(2)	22						ACCCACCTCCATACATTGATG	0.368																																					p.P626P		Atlas-SNP	.											.	CAPN7	63	.	0			c.A1878G						PASS	.						141	140	140					3																	15287046		2203	4300	6503	SO:0001819	synonymous_variant	23473	exon17			ACCTCCATACATT	AB028639	CCDS2624.1	3p24	2008-07-18			ENSG00000131375	ENSG00000131375			1484	protein-coding gene	gene with protein product	"calpain like protease", "homolog of Aspergillus Nidulans PALB"	606400				8163008, 10051333	Standard	NM_014296		Approved	PalBH	uc003bzn.3	Q9Y6W3	OTTHUMG00000129863	ENST00000253693.2:c.1878A>G	chr3.hg19:g.15287046A>G		64.0	0.0	.		86.0	27.0	.	NM_014296		Silent	SNP	ENST00000253693.2	hg19	CCDS2624.1																																																																																			.	.	.	none		0.368	CAPN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252105.2	NM_014296		G	15287046	A	G	15287046	2	3	11	1	0	0	0	0	0	0	0	1	2633	204	8	3		3	CAPN7	3	15287046	Silent	SNP	A	TCGA-2Z-A9JG-01A-11D-A42J-10		15287046	182735384	14	840											
DNAH1	25981	hgsc.bcm.edu	37	chr3	52392687	52392687	+	Frame_Shift_Del	DEL	G	G	-																															gtggaggactggctgcgggaGgtggagcgcagcatgaaggc																										TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr3:52392687delG	ENST00000420323.2	+	25	4461	c.4200delG	c.(4198-4200)gagfs	p.E1400fs		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1400	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)		GGCTGCGGGAGGTGGAGCGCA	0.632																																					p.E1400fs		Atlas-Indel,Pindel	.											.	DNAH1	534	.	0			c.4199delA						PASS	.						50	58	55					3																	52392687		2169	4259	6428	SO:0001589	frameshift_variant	25981	exon25			.	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.4200delG	chr3.hg19:g.52392687delG	ENSP00000401514:p.Glu1400fs	216.0	0.0	0		131.0	62.0	0.473282	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Frame_Shift_Del	DEL	ENST00000420323.2	hg19	CCDS46842.1																																																																																			.	.	.	none		0.632	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		-	52392687	G	-	52392687	7	5	11	1	0	1	0	1	0	0	0	0	4599	991	35	0	4294	0	DNAH1	3	52392687	Frame_Shift_Del	DEL	G	TCGA-2Z-A9JG-01A-11D-A42J-10	37105641	52392687	145629743	15	841											
TMPRSS7	344805	hgsc.bcm.edu	37	chr3	111799843	111799844	+	Frame_Shift_Del	DEL	GA	GA	-																															cattgttagctggggacatgGaagtggacgaccaaactttc																										TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr3:111799843_111799844delGA	ENST00000452346.2	+	18	2447_2448	c.2444_2445delGA	c.(2443-2445)ggafs	p.G815fs	TMPRSS7_ENST00000419127.1_Frame_Shift_Del_p.G689fs			Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7	815	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(2)|endometrium(6)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						TGGGGACATGGAAGTGGACGAC	0.411																																					p.689_689del		Atlas-INDEL	.											.	TMPRSS7	126	.	0			c.2065_2066del						PASS	.																																			SO:0001589	frameshift_variant	344805	exon16			.	BN000125	CCDS43129.2	3q13.2	2010-04-13	2004-03-16		ENSG00000176040	ENSG00000176040		"Serine peptidases / Transmembrane"	30846	protein-coding gene	gene with protein product			"type II transmembrane serine protease 7"			12838346	Standard	NM_001042575		Approved		uc010hqb.2	Q7RTY8	OTTHUMG00000157148	ENST00000452346.2:c.2444_2445delGA	chr3.hg19:g.111799843_111799844delGA	ENSP00000398236:p.Gly815fs	197.0	0.0	0		147.0	43.0	0.292517	NM_001042575	C9J8P7|E9PAS3|Q17RH4	Frame_Shift_Del	DEL	ENST00000452346.2	hg19																																																																																				.	.	.	none		0.411	TMPRSS7-003	NOVEL	NAGNAG_splice_site|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000347592.2	XM_293599		-	111799844	GA	-	111799843	7	5	11	1	0	1	0	1	0	0	0	0	16264	1174	41	0	2124	0	TMPRSS7	3	111799843	Frame_Shift_Del	DEL	GA	TCGA-2Z-A9JG-01A-11D-A42J-10	59407156	111799843	86222587	16	842											
LIAS	11019	hgsc.bcm.edu	37	chr4	39465225	39465225	+	Splice_Site	DEL	G	G	-																															accgccacagccacgatcatGgtagggccagcctcaacctc																										TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr4:39465225delG	ENST00000261434.3	+	4	511	c.393delG	c.(391-393)atg>at	p.M131fs	LIAS_ENST00000381846.1_Splice_Site_p.M131fs|LIAS_ENST00000515061.1_3'UTR|LIAS_ENST00000340169.2_Splice_Site_p.M131fs|LIAS_ENST00000513731.1_Intron	NM_006859.2	NP_006850.2			lipoic acid synthetase											breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(2)|ovary(2)	12						CCACGATCATGGTAGGGCCAG	0.463																																					p.M131fs		Atlas-Indel,Pindel	.											.	LIAS	26	.	0			c.392delT						PASS	.						70	65	67					4																	39465225		2203	4300	6503	SO:0001630	splice_region_variant	11019	exon4			.	AJ224162	CCDS3453.1, CCDS3454.1, CCDS63950.1	4p14	2008-02-05			ENSG00000121897	ENSG00000121897			16429	protein-coding gene	gene with protein product		607031				11124703	Standard	NM_006859		Approved	LAS	uc003guf.3	O43766	OTTHUMG00000099369	ENST00000261434.3:c.393+1G>-	chr4.hg19:g.39465225delG		50.0	0.0	0		53.0	40.0	0.754717	NM_194451		Frame_Shift_Del	DEL	ENST00000261434.3	hg19	CCDS3453.1																																																																																			.	.	.	none		0.463	LIAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216815.1	NM_194451	Frame_Shift_Del	-	39465225	G	-	39465225	8	5	11	1	0	1	0	1	0	0	1	0	8785	1362	47	0	407	0	LIAS	4	39465225	Splice_Site	DEL	G	TCGA-2Z-A9JG-01A-11D-A42J-10		39465225	151689051	17	843											
UBE2K	3093	hgsc.bcm.edu	37	chr4	39779353	39779353	+	Missense_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	cagctcgactttgggcacatGtgtatgctggagcaccagtt	8	11	12	10	1	0	0	0	0	0	0	1	2	0	1	1	2	3	6	1	2	1	3			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr4:39779353G>A	ENST00000261427.5	+	6	735	c.451G>A	c.(451-453)Gtg>Atg	p.V151M	UBE2K_ENST00000295963.6_Missense_Mutation_p.V90M|UBE2K_ENST00000445950.2_Intron|UBE2K_ENST00000503368.1_Missense_Mutation_p.V100M|UBE2K_ENST00000438068.2_3'UTR	NM_001111112.1|NM_005339.4	NP_001104582.1|NP_005330.1	P61086	UBE2K_HUMAN	ubiquitin-conjugating enzyme E2K	151					intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|protein K48-linked ubiquitination (GO:0070936)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)			large_intestine(1)|lung(1)|ovary(2)	4						TTGGGCACATGTGTATGCTGG	0.378																																					p.V151M	NSCLC(101;689 1592 16105 29682 31745)	Atlas-SNP	.											.	UBE2K	16	.	0			c.G451A						PASS	.						106	110	108					4																	39779353		2203	4300	6503	SO:0001583	missense	3093	exon6			GCACATGTGTATG	U58522	CCDS33976.1, CCDS47043.1, CCDS47044.1	4p14	2011-05-19	2011-05-19	2007-12-04	ENSG00000078140	ENSG00000078140		"Ubiquitin-conjugating enzymes E2"	4914	protein-coding gene	gene with protein product		602846	"huntingtin interacting protein 2", "ubiquitin-conjugating enzyme E2K (UBC1 homolog, yeast)"	HIP2		8702625, 17873885	Standard	NM_005339		Approved	HYPG, UBC1	uc003guu.4	P61086	OTTHUMG00000160543	ENST00000261427.5:c.451G>A	chr4.hg19:g.39779353G>A	ENSP00000261427:p.Val151Met	144.0	0.0	.		181.0	52.0	.	NM_005339	A6NJC1|A8K5Y9|B2RDF8|C9JGP1|O54806|P27924|Q16721|Q9CVV9|Q9Y2D3	Missense_Mutation	SNP	ENST00000261427.5	hg19	CCDS33976.1	.	.	.	.	.	.	.	.	.	.	G	16.89	3.246872	0.59103	.	.	ENSG00000078140	ENST00000261427;ENST00000295963;ENST00000510934;ENST00000503368	T;T;T;T	0.72167	-0.63;-0.63;-0.63;-0.63	5.55	5.55	0.83447	Ubiquitin-conjugating enzyme/RWD-like (1);	0.000000	0.85682	D	0.000000	T	0.65575	0.2704	L	0.28274	0.84	0.52501	D	0.999954	B;P;B	0.50156	0.008;0.932;0.24	B;B;P	0.45712	0.003;0.327;0.491	T	0.64262	-0.6449	10	0.33940	T	0.23	-15.8268	19.8764	0.96873	0.0:0.0:1.0:0.0	.	90;151;100	B4DIZ2;P61086;P61086-2	.;UBE2K_HUMAN;.	M	151;90;90;100	ENSP00000261427:V151M;ENSP00000295963:V90M;ENSP00000425301:V90M;ENSP00000421203:V100M	ENSP00000261427:V151M	V	+	1	0	UBE2K	39455748	1.000000	0.71417	0.999000	0.59377	0.973000	0.67179	4.143000	0.58051	2.768000	0.95171	0.655000	0.94253	GTG	.	.	.	none		0.378	UBE2K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361061.1	NM_005339		A	39779353	G	A	39779353	3	1	11	1	0	0	0	0	1	0	0	0	16874	1377	48	2	473	2	UBE2K	4	39779353	Missense_Mutation	SNP	G	TCGA-2Z-A9JG-01A-11D-A42J-10	314128	39779353	151374923	18	844											
EPHA5	2044	hgsc.bcm.edu	37	chr4	66535302	66535302	+	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	tcgttgctggggctggccagGagggtccggagtgcggcgca	4	7	20	10	4	0	0	0	0	0	0	2	2	1	2	2	7	2	4	2	7	0	1			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr4:66535302G>T	ENST00000273854.3	-	1	759	c.159C>A	c.(157-159)ctC>ctA	p.L53L	RP11-807H7.1_ENST00000509473.1_lincRNA|EPHA5_ENST00000511294.1_Silent_p.L53L|EPHA5_ENST00000432638.2_Silent_p.L53L|EPHA5_ENST00000354839.4_Silent_p.L53L	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	53					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						GGCTGGCCAGGAGGGTCCGGA	0.711										TSP Lung(17;0.13)																											p.L53L		Atlas-SNP	.											.	EPHA5	315	.	0			c.C159A						PASS	.						13	16	15					4																	66535302		2176	4272	6448	SO:0001819	synonymous_variant	2044	exon1			GGCCAGGAGGGTC	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.159C>A	chr4.hg19:g.66535302G>T		275.0	0.0	.		183.0	120.0	.	NM_004439	Q7Z3F2	Silent	SNP	ENST00000273854.3	hg19	CCDS3513.1																																																																																			.	.	.	none		0.711	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		T	66535302	G	T	66535302	2	4	11	1	0	0	0	0	0	0	0	1	5172	1161	41	4		4	EPHA5	4	66535302	Silent	SNP	G	TCGA-2Z-A9JG-01A-11D-A42J-10	26755949	66535302	124618974	19	845											
FAT4	79633	hgsc.bcm.edu	37	chr4	126239708	126239708	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcaccactgtgtctgccacTgacccagacttgggtaccaa	10	9	8	14	0	2	2	1	1	1	1	2	2	2	2	4	1	2	1	4	1	2	2			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr4:126239708T>C	ENST00000394329.3	+	1	2155	c.2142T>C	c.(2140-2142)acT>acC	p.T714T		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	714	Cadherin 7. {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						TGTCTGCCACTGACCCAGACT	0.463																																					p.T714T		Atlas-SNP	.											.	FAT4	1752	.	0			c.T2142C						PASS	.						75	78	77					4																	126239708		2014	4191	6205	SO:0001819	synonymous_variant	79633	exon1			TGCCACTGACCCA	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.2142T>C	chr4.hg19:g.126239708T>C		84.0	0.0	.		120.0	30.0	.	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	hg19	CCDS3732.3																																																																																			.	.	.	none		0.463	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		C	126239708	T	C	126239708	2	2	11	1	0	0	0	0	0	0	0	1	5699	1567	55	3		3	FAT4	4	126239708	Silent	SNP	T	TCGA-2Z-A9JG-01A-11D-A42J-10	59704406	126239708	64914568	20	846											
POU5F2	134187	hgsc.bcm.edu	37	chr5	93076747	93076747	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgcagcttccacatgttggCgacgcttagctgctgggcct	5	11	12	13	3	0	0	0	0	0	0	2	1	1	0	2	2	3	6	2	2	1	3			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr5:93076747C>T	ENST00000510627.4	-	1	596	c.523G>A	c.(523-525)Gcc>Acc	p.A175T	FAM172A_ENST00000509739.1_Intron|FAM172A_ENST00000509163.1_Intron|FAM172A_ENST00000395965.3_Intron|FAM172A_ENST00000505869.1_Intron|RP11-185E12.2_ENST00000606528.1_RNA|POU5F2_ENST00000606183.1_5'UTR	NM_153216.1	NP_694948.1	Q8N7G0	PO5F2_HUMAN	POU domain class 5, transcription factor 2	175	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)						all_cancers(142;3.87e-05)|all_epithelial(76;4.59e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0415)|all cancers(79;2.03e-19)		CACATGTTGGCGACGCTTAGC	0.557																																					p.A175T		Atlas-SNP	.											.	POU5F2	10	.	0			c.G523A						PASS	.						85	87	86					5																	93076747		2162	4282	6444	SO:0001583	missense	134187	exon1			TGTTGGCGACGCT		CCDS59489.1	5q15	2011-06-20				ENSG00000248483		"Homeoboxes / POU class"	26367	protein-coding gene	gene with protein product						7908264	Standard	NM_153216		Approved	SPRM-1, FLJ25680	uc003kkl.1	Q8N7G0		ENST00000510627.4:c.523G>A	chr5.hg19:g.93076747C>T	ENSP00000464890:p.Ala175Thr	31.0	0.0	.		44.0	26.0	.	NM_153216	Q15169|Q6MZL7|Q8N748	Missense_Mutation	SNP	ENST00000510627.4	hg19	CCDS59489.1																																																																																			.	.	.	none		0.557	POU5F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369873.5	NM_153216		T	93076747	C	T	93076747	3	4	11	1	0	0	0	0	1	0	0	0	12290	768	27	1	467	1	POU5F2	5	93076747	Missense_Mutation	SNP	C	TCGA-2Z-A9JG-01A-11D-A42J-10		93076747	87838513	21	847											
GLRA1	2741	hgsc.bcm.edu	37	chr5	151231003	151231003	+	Missense_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	gggtggtcatggtgagcacaGtggtgatgcctaggcccaca	8	8	16	9	0	1	2	1	2	0	0	1	2	1	2	2	5	2	1	2	5	1	1			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr5:151231003G>A	ENST00000455880.2	-	7	1146	c.860C>T	c.(859-861)aCt>aTt	p.T287I	GLRA1_ENST00000274576.4_Missense_Mutation_p.T287I|GLRA1_ENST00000545569.1_Missense_Mutation_p.T204I|GLRA1_ENST00000471351.2_5'UTR			P23415	GLRA1_HUMAN	glycine receptor, alpha 1	287					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)	GGTGAGCACAGTGGTGATGCC	0.537																																					p.T287I		Atlas-SNP	.											.	GLRA1	61	.	0			c.C860T						PASS	.						138	120	126					5																	151231003		2203	4300	6503	SO:0001583	missense	2741	exon7			AGCACAGTGGTGA		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.860C>T	chr5.hg19:g.151231003G>A	ENSP00000411593:p.Thr287Ile	83.0	0.0	.		155.0	39.0	.	NM_000171	B2R6T3|Q14C77|Q6DJV9	Missense_Mutation	SNP	ENST00000455880.2	hg19	CCDS54942.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.960480	0.92791	.	.	ENSG00000145888	ENST00000274576;ENST00000455880;ENST00000545569	D;D;D	0.86562	-2.14;-2.14;-2.14	5.2	5.2	0.72013	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.94072	0.8100	M	0.84433	2.695	0.80722	D	1	D;D;D	0.69078	0.974;0.997;0.993	D;D;D	0.69479	0.916;0.964;0.939	D	0.94738	0.7916	10	0.87932	D	0	.	19.1084	0.93307	0.0:0.0:1.0:0.0	.	287;204;287	P23415;Q14C71;P23415-2	GLRA1_HUMAN;.;.	I	287;287;204	ENSP00000274576:T287I;ENSP00000411593:T287I;ENSP00000445913:T204I	ENSP00000274576:T287I	T	-	2	0	GLRA1	151211196	1.000000	0.71417	0.963000	0.40424	0.991000	0.79684	9.640000	0.98453	2.579000	0.87056	0.655000	0.94253	ACT	.	.	.	none		0.537	GLRA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373959.1			A	151231003	G	A	151231003	3	1	11	1	0	0	0	0	1	0	0	0	6461	1029	36	2	525	2	GLRA1	5	151231003	Missense_Mutation	SNP	G	TCGA-2Z-A9JG-01A-11D-A42J-10	58154256	151231003	29684257	22	848											
NEDD9	4739	hgsc.bcm.edu	37	chr6	11185765	11185765	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatgggtctcacattggtcaTagtagaagcacagcaactgc	13	9	10	9	0	2	1	2	0	1	1	3	1	2	1	0	2	4	3	0	2	5	3			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr6:11185765T>C	ENST00000379446.5	-	7	2301	c.2135A>G	c.(2134-2136)tAt>tGt	p.Y712C	NEDD9_ENST00000504387.1_Missense_Mutation_p.Y712C|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	712	Divergent helix-loop-helix motif.				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)			ACATTGGTCATAGTAGAAGCA	0.547																																					p.Y712C		Atlas-SNP	.											.	NEDD9	191	.	0			c.A2135G						PASS	.						163	135	145					6																	11185765		2203	4300	6503	SO:0001583	missense	4739	exon8			TGGTCATAGTAGA	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.2135A>G	chr6.hg19:g.11185765T>C	ENSP00000368759:p.Tyr712Cys	54.0	0.0	.		56.0	25.0	.	NM_001142393	A8K9G7|A8MSJ9|G5E9Y9|Q5T9R4|Q5XKI0	Missense_Mutation	SNP	ENST00000379446.5	hg19	CCDS4520.1	.	.	.	.	.	.	.	.	.	.	T	17.14	3.312654	0.60414	.	.	ENSG00000111859	ENST00000379446;ENST00000504387	T;T	0.21734	1.99;1.99	6.11	4.89	0.63831	CAS family, DUF3513 (1);	0.387436	0.30869	N	0.008715	T	0.11452	0.0279	N	0.08118	0	0.80722	D	1	P;D;D	0.58970	0.933;0.973;0.984	P;P;P	0.62649	0.77;0.852;0.905	T	0.06844	-1.0804	10	0.39692	T	0.17	-19.1901	7.3267	0.26560	0.1154:0.0:0.2691:0.6154	.	712;712;712	G5E9Y9;A8K9G7;Q14511	.;.;CASL_HUMAN	C	712	ENSP00000368759:Y712C;ENSP00000422871:Y712C	ENSP00000368759:Y712C	Y	-	2	0	NEDD9	11293751	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	4.547000	0.60712	2.343000	0.79666	0.533000	0.62120	TAT	.	.	.	none		0.547	NEDD9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039853.2	NM_006403		C	11185765	T	C	11185765	3	2	11	1	0	0	0	0	1	0	0	0	10320	1406	49	3	373	3	NEDD9	6	11185765	Missense_Mutation	SNP	T	TCGA-2Z-A9JG-01A-11D-A42J-10		11185765	159929302	23	849											
PHF3	23469	hgsc.bcm.edu	37	chr6	64421622	64421622	+	Frame_Shift_Del	DEL	A	A	-																															caatagcattgccacctgatAaaaaaagtaaaatagaagtt																										TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr6:64421622delA	ENST00000262043.3	+	16	4478	c.4138delA	c.(4138-4140)aaafs	p.K1381fs	PHF3_ENST00000393387.1_Frame_Shift_Del_p.K1381fs			Q92576	PHF3_HUMAN	PHD finger protein 3	1381					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)			GCCACCTGATAAAAAAAGTAA	0.378																																					p.D1379fs	GBM(135;136 1820 29512 34071 46235)	Atlas-Indel,Pindel	.											.	PHF3	191	.	0			c.4137delT						PASS	.						89	99	96					6																	64421622		2203	4300	6503	SO:0001589	frameshift_variant	23469	exon15			.	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.4138delA	chr6.hg19:g.64421622delA	ENSP00000262043:p.Lys1381fs	86.0	0.0	0		185.0	76.0	0.410811	NM_015153	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Frame_Shift_Del	DEL	ENST00000262043.3	hg19	CCDS4966.1																																																																																			.	.	.	none		0.378	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2			-	64421622	A	-	64421622	7	5	11	1	0	1	0	1	0	0	0	0	11843	363	13	0	4196	0	PHF3	6	64421622	Frame_Shift_Del	DEL	A	TCGA-2Z-A9JG-01A-11D-A42J-10	53235857	64421622	106693445	24	850											
VTA1	51534	hgsc.bcm.edu	37	chr6	142491530	142491530	+	Frame_Shift_Del	DEL	T	T	-																															aagtcttttgatagatgtcaTaacagtatttggagaactca																										TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr6:142491530delT	ENST00000367630.4	+	4	441	c.383delT	c.(382-384)atafs	p.I128fs	VTA1_ENST00000452973.2_Frame_Shift_Del_p.I70fs|VTA1_ENST00000367621.1_Frame_Shift_Del_p.I70fs|VTA1_ENST00000491881.1_3'UTR	NM_016485.3	NP_057569.2	Q9NP79	VTA1_HUMAN	vesicle (multivesicular body) trafficking 1	128	Interaction with IST1.				endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				endometrium(2)|large_intestine(1)|lung(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	Breast(32;0.155)			OV - Ovarian serous cystadenocarcinoma(155;1.34e-05)|GBM - Glioblastoma multiforme(68;0.00182)		ATAGATGTCATAACAGTATTT	0.318																																					p.I128X		Atlas-INDEL	.											.	VTA1	29	.	0			c.382delA						PASS	.						132	144	140					6																	142491530		2203	4294	6497	SO:0001589	frameshift_variant	51534	exon4			.	AF060225	CCDS5197.1, CCDS69214.1, CCDS75531.1	6q24.1	2013-08-05	2013-08-05	2007-04-03	ENSG00000009844	ENSG00000009844			20954	protein-coding gene	gene with protein product		610902	"chromosome 6 open reading frame 55", "Vps20-associated 1 homolog (S. cerevisiae)"	C6orf55		11489251, 15644320	Standard	NM_001286372		Approved	HSPC228, My012	uc003qiw.3	Q9NP79	OTTHUMG00000015707	ENST00000367630.4:c.383delT	chr6.hg19:g.142491530delT	ENSP00000356602:p.Ile128fs	15.0	0.0	0		28.0	10.0	0.357143	NM_016485	B4DW55|E1P594|E7ETQ7|Q5TGM1|Q6IAE8|Q9H0R2|Q9H3K9|Q9P0Q0	Frame_Shift_Del	DEL	ENST00000367630.4	hg19	CCDS5197.1																																																																																			.	.	.	none		0.318	VTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042483.2	NM_016485		-	142491530	T	-	142491530	7	5	11	1	0	1	0	1	0	0	0	0	17245	1406	49	0	397	0	VTA1	6	142491530	Frame_Shift_Del	DEL	T	TCGA-2Z-A9JG-01A-11D-A42J-10	78069908	142491530	28623537	25	851											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152497619	152497619	+	Missense_Mutation	SNP	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	atgctttgctttcatggctgGctttagcaagtcgttctccc	5	16	9	11	1	2	0	1	0	1	0	4	0	2	0	1	2	3	6	1	2	2	5			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr6:152497619G>A	ENST00000367255.5	-	130	24138	c.23537C>T	c.(23536-23538)gCc>gTc	p.A7846V	SYNE1_ENST00000356820.4_Missense_Mutation_p.A2370V|SYNE1_ENST00000341594.5_Missense_Mutation_p.A7458V|SYNE1_ENST00000265368.4_Missense_Mutation_p.A7846V|SYNE1_ENST00000423061.1_Missense_Mutation_p.A7775V|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000448038.1_Missense_Mutation_p.A7775V	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	7846					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)		TTCATGGCTGGCTTTAGCAAG	0.443										HNSCC(10;0.0054)																											p.A7846V		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C23537T						PASS	.						291	276	281					6																	152497619		2203	4300	6503	SO:0001583	missense	23345	exon130			TGGCTGGCTTTAG	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.23537C>T	chr6.hg19:g.152497619G>A	ENSP00000356224:p.Ala7846Val	65.0	0.0	.		82.0	29.0	.	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	35	5.446314	0.96187	.	.	ENSG00000131018	ENST00000367255;ENST00000367257;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000313630;ENST00000367251	T;T;T;T;T;T;T;T	0.52754	0.65;0.65;0.65;0.65;0.65;0.65;0.65;0.65	5.75	5.75	0.90469	.	0.000000	0.56097	D	0.000025	T	0.65344	0.2682	M	0.71036	2.16	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	0.83275	0.996;0.996;0.993;0.996;0.986	T	0.66118	-0.6003	10	0.62326	D	0.03	.	19.9341	0.97130	0.0:0.0:1.0:0.0	.	7846;7846;7775;7775;48	Q8NF91;E7EQI5;Q8NF91-4;E9PEL9;B7Z9Y6	SYNE1_HUMAN;.;.;.;.	V	7846;492;7775;7846;7775;7458;2370;8;768	ENSP00000356224:A7846V;ENSP00000356226:A492V;ENSP00000396024:A7775V;ENSP00000265368:A7846V;ENSP00000390975:A7775V;ENSP00000341887:A7458V;ENSP00000349276:A2370V;ENSP00000356220:A768V	ENSP00000265368:A7846V	A	-	2	0	SYNE1	152539312	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	9.692000	0.98682	2.711000	0.92665	0.563000	0.77884	GCC	.	.	.	none		0.443	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152497619	G	A	152497619	3	1	11	1	0	0	0	0	1	0	0	0	15457	1203	42	2	2997	2	SYNE1	6	152497619	Missense_Mutation	SNP	G	TCGA-2Z-A9JG-01A-11D-A42J-10	10006089	152497619	18617448	26	852											
BUD31	8896	hgsc.bcm.edu	37	chr7	99008752	99008752	+	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	gaagccggaaagcacccccaGatggctgggagttgattgag	11	6	15	9	1	0	3	0	2	0	1	0	6	0	5	3	3	2	3	3	3	2	2			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr7:99008752G>A	ENST00000403633.2	+	3	566	c.37G>A	c.(37-39)Gat>Aat	p.D13N	snoU13_ENST00000458831.1_RNA|PDAP1_ENST00000350498.3_5'Flank|BUD31_ENST00000456893.1_Missense_Mutation_p.D13N|BUD31_ENST00000222969.5_Missense_Mutation_p.D13N			P41223	BUD31_HUMAN	BUD31 homolog (S. cerevisiae)	13					regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)	4	all_cancers(62;1.76e-08)|all_epithelial(64;1.63e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			AGCACCCCCAGATGGCTGGGA	0.473																																					p.D13N		Atlas-SNP	.											.	BUD31	12	.	0			c.G37A						PASS	.						72	75	74					7																	99008752		2203	4300	6503	SO:0001583	missense	8896	exon3			CCCCCAGATGGCT	BC022821	CCDS5663.1	7q22.1	2012-06-07	2007-01-12	2006-03-16	ENSG00000106245	ENSG00000106245			29629	protein-coding gene	gene with protein product	"G10 maternal transcript homolog (Xenopus laevis)", "functional spliceosome-associated protein 17"	603477	"BUD31 homolog (yeast)"			7841202	Standard	NM_003910		Approved	YCR063W, EDG-2, EDG2, G10, fSAP17, Cwc14	uc003uqg.4	P41223	OTTHUMG00000154602	ENST00000403633.2:c.37G>A	chr7.hg19:g.99008752G>A	ENSP00000386023:p.Asp13Asn	136.0	0.0	.		148.0	90.0	.	NM_003910	A4D274|B7Z4S9|D6W5S6|Q6IB53|Q9UDV1	Missense_Mutation	SNP	ENST00000403633.2	hg19	CCDS5663.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.447418	0.84101	.	.	ENSG00000106245	ENST00000403633;ENST00000222969;ENST00000456893	.	.	.	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.57066	0.2028	L	0.35644	1.08	0.80722	D	1	B;B	0.17038	0.02;0.002	B;B	0.18871	0.023;0.008	T	0.53940	-0.8367	9	0.59425	D	0.04	-21.7032	19.2823	0.94057	0.0:0.0:1.0:0.0	.	13;13	B7Z4S9;P41223	.;BUD31_HUMAN	N	13	.	ENSP00000222969:D13N	D	+	1	0	BUD31	98846688	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.128000	0.94424	2.550000	0.86006	0.655000	0.94253	GAT	.	.	.	none		0.473	BUD31-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336275.1	NM_003910		A	99008752	G	A	99008752	3	1	11	1	0	0	0	0	1	0	0	0	1576	942	33	2	39	2	BUD31	7	99008752	Missense_Mutation	SNP	G	TCGA-2Z-A9JG-01A-11D-A42J-10		99008752	60129911	27	853											
MBLAC1	255374	hgsc.bcm.edu	37	chr7	99725163	99725163	+	Missense_Mutation	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	gctccgtgaccctggtcctaCcccagacccggggcccggcc	4	5	12	20	3	0	2	0	1	0	1	2	2	2	2	8	4	1	1	8	4	1	1			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr7:99725163C>T	ENST00000398075.2	+	2	544	c.145C>T	c.(145-147)Ccc>Tcc	p.P49S	RP11-506M12.1_ENST00000494221.1_RNA	NM_203397.1	NP_981942.1	A4D2B0	MBLC1_HUMAN	metallo-beta-lactamase domain containing 1	49							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						CCTGGTCCTACCCCAGACCCG	0.751																																					p.P49S		Atlas-SNP	.											.	MBLAC1	13	.	0			c.C145T						PASS	.						7	8	8					7																	99725163		1845	4050	5895	SO:0001583	missense	255374	exon2			GTCCTACCCCAGA	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.145C>T	chr7.hg19:g.99725163C>T	ENSP00000381150:p.Pro49Ser	169.0	0.0	.		94.0	31.0	.	NM_203397	Q8N5X8	Missense_Mutation	SNP	ENST00000398075.2	hg19	CCDS43620.1	.	.	.	.	.	.	.	.	.	.	C	12.04	1.818874	0.32145	.	.	ENSG00000214309	ENST00000398075;ENST00000421390	T;T	0.50001	1.19;0.76	4.23	4.23	0.50019	.	.	.	.	.	T	0.54481	0.1861	L	0.29908	0.895	0.36843	D	0.88752	D	0.89917	1.0	D	0.80764	0.994	T	0.55768	-0.8089	9	0.27785	T	0.31	.	14.4901	0.67645	0.0:1.0:0.0:0.0	.	49	A4D2B0	MBLC1_HUMAN	S	49	ENSP00000381150:P49S;ENSP00000406055:P49S	ENSP00000381150:P49S	P	+	1	0	MBLAC1	99563099	0.957000	0.32711	0.694000	0.30210	0.029000	0.11900	0.489000	0.22387	2.361000	0.80049	0.561000	0.74099	CCC	.	.	.	none		0.751	MBLAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337353.1	NM_203397		T	99725163	C	T	99725163	3	4	11	1	0	0	0	0	1	0	0	0	9358	507	18	2	147	2	MBLAC1	7	99725163	Missense_Mutation	SNP	C	TCGA-2Z-A9JG-01A-11D-A42J-10	716411	99725163	59413500	28	854											
KLHDC10	23008	hgsc.bcm.edu	37	chr7	129760626	129760626	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aacctgttagtatttggaggTacgggcatcccatttggaga	10	12	12	7	1	0	1	0	0	0	1	1	3	1	2	2	4	2	4	2	4	4	5			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr7:129760626T>C	ENST00000335420.5	+	4	647	c.513T>C	c.(511-513)ggT>ggC	p.G171G		NM_014997.3	NP_055812.1	Q6PID8	KLD10_HUMAN	kelch domain containing 10	171						cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|liver(2)|lung(10)|prostate(1)	17						TATTTGGAGGTACGGGCATCC	0.468																																					p.G171G		Atlas-SNP	.											.	KLHDC10	36	.	0			c.T513C						PASS	.						219	193	202					7																	129760626		2203	4300	6503	SO:0001819	synonymous_variant	23008	exon4			TGGAGGTACGGGC		CCDS5815.1	7q32.2	2008-08-20			ENSG00000128607	ENSG00000128607			22194	protein-coding gene	gene with protein product	"scruin like at the midline homolog (Drosophila)"	615152					Standard	NM_014997		Approved	KIAA0265, slim	uc003vpj.2	Q6PID8	OTTHUMG00000157654	ENST00000335420.5:c.513T>C	chr7.hg19:g.129760626T>C		96.0	0.0	.		164.0	51.0	.	NM_014997	Q86Y99|Q92554	Silent	SNP	ENST00000335420.5	hg19	CCDS5815.1																																																																																			.	.	.	none		0.468	KLHDC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349347.2			C	129760626	T	C	129760626	2	2	11	1	0	0	0	0	0	0	0	1	8362	1625	57	3		3	KLHDC10	7	129760626	Silent	SNP	T	TCGA-2Z-A9JG-01A-11D-A42J-10	30035463	129760626	29378037	29	855											
ESYT2	57488	hgsc.bcm.edu	37	chr7	158528197	158528197	+	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	attcgtttggcacttactttGccaaggagccctttgtcttt	6	17	8	10	1	1	0	0	0	1	0	2	1	1	1	2	2	3	2	2	2	2	6			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr7:158528197G>A	ENST00000251527.5	-	20	2648	c.2583C>T	c.(2581-2583)ggC>ggT	p.G861G	ESYT2_ENST00000435514.2_Silent_p.G296G	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	889	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				endocytosis (GO:0006897)|lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						CACTTACTTTGCCAAGGAGCC	0.468																																					p.G861G		Atlas-SNP	.											.	ESYT2	70	.	0			c.C2583T						PASS	.						153	158	156					7																	158528197		2203	4300	6503	SO:0001819	synonymous_variant	57488	exon20			TACTTTGCCAAGG	AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868		"Synaptotagmins"	22211	protein-coding gene	gene with protein product			"family with sequence similarity 62 (C2 domain containing), member B"	FAM62B		17672888	Standard	NM_020728		Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.2583C>T	chr7.hg19:g.158528197G>A		69.0	0.0	.		50.0	10.0	.	NM_020728	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Silent	SNP	ENST00000251527.5	hg19	CCDS34791.1																																																																																			.	.	.	none		0.468	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728		A	158528197	G	A	158528197	2	1	11	1	0	0	0	0	0	0	0	1	5267	1306	46	2		2	ESYT2	7	158528197	Silent	SNP	G	TCGA-2Z-A9JG-01A-11D-A42J-10	28767571	158528197	610466	30	856											
RB1CC1	9821	hgsc.bcm.edu	37	chr8	53596456	53596456	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaatacctaccgtcccagcActgtaggtacacactcttcg	10	10	7	14	2	1	1	0	1	1	0	3	1	2	1	3	1	4	3	3	1	5	5			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr8:53596456A>G	ENST00000025008.5	-	4	712	c.189T>C	c.(187-189)agT>agC	p.S63S	RB1CC1_ENST00000521611.1_Intron|RB1CC1_ENST00000435644.2_Silent_p.S63S|RB1CC1_ENST00000539297.1_Silent_p.S63S	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	63					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)				CCGTCCCAGCACTGTAGGTAC	0.428																																					p.S63S	GBM(180;1701 2102 13475 42023 52570)	Atlas-SNP	.											.	RB1CC1	163	.	0			c.T189C						PASS	.						124	100	108					8																	53596456		2203	4300	6503	SO:0001819	synonymous_variant	9821	exon4			CCCAGCACTGTAG	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.189T>C	chr8.hg19:g.53596456A>G		47.0	0.0	.		61.0	17.0	.	NM_001083617	Q86YR4|Q8WVU9|Q92601	Silent	SNP	ENST00000025008.5	hg19	CCDS34892.1																																																																																			.	.	.	none		0.428	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781		G	53596456	A	G	53596456	2	3	11	1	0	0	0	0	0	0	0	1	13112	156	6	3		3	RB1CC1	8	53596456	Silent	SNP	A	TCGA-2Z-A9JG-01A-11D-A42J-10		53596456	92767566	31	857											
GGH	8836	hgsc.bcm.edu	37	chr8	63936714	63936714	+	Frame_Shift_Del	DEL	A	A	-																															gacagcaacaactcagtaggAaaattctggaacattctgct																										TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr8:63936714delA	ENST00000260118.6	-	6	933	c.531delT	c.(529-531)tttfs	p.F177fs	GGH_ENST00000518113.1_5'UTR|RP11-659E9.4_ENST00000521556.1_RNA	NM_003878.2	NP_003869.1	Q92820	GGH_HUMAN	gamma-glutamyl hydrolase (conjugase, folylpolygammaglutamyl hydrolase)	177	Gamma-glutamyl hydrolase. {ECO:0000255|PROSITE-ProRule:PRU00607}.				glutamine metabolic process (GO:0006541)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to insulin (GO:0032868)|response to zinc ion (GO:0010043)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	exopeptidase activity (GO:0008238)|gamma-glutamyl-peptidase activity (GO:0034722)|omega peptidase activity (GO:0008242)			breast(1)|kidney(1)|large_intestine(1)|liver(1)|lung(6)|stomach(1)	11	Breast(64;0.0716)	all_cancers(86;0.189)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.131)			Folic Acid(DB00158)|Methotrexate(DB00563)	ACTCAGTAGGAAAATTCTGGA	0.353																																					p.P178fs		Atlas-Indel,Pindel	.											.	GGH	32	.	0			c.532delC						PASS	.						44	43	43					8																	63936714		2203	4300	6503	SO:0001589	frameshift_variant	8836	exon6			.	U55206	CCDS6177.1	8q12.3	2008-02-05			ENSG00000137563	ENSG00000137563	3.4.19.9		4248	protein-coding gene	gene with protein product		601509				8816764, 10570974	Standard	NM_003878		Approved		uc003xuw.3	Q92820	OTTHUMG00000164365	ENST00000260118.6:c.531delT	chr8.hg19:g.63936714delA	ENSP00000260118:p.Phe177fs	111.0	0.0	0		248.0	61.0	0.245968	NM_003878		Frame_Shift_Del	DEL	ENST00000260118.6	hg19	CCDS6177.1																																																																																			.	.	.	none		0.353	GGH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378453.1			-	63936714	A	-	63936714	7	5	11	1	0	1	0	1	0	0	0	0	6364	243	9	0	441	0	GGH	8	63936714	Frame_Shift_Del	DEL	A	TCGA-2Z-A9JG-01A-11D-A42J-10	10340258	63936714	82427308	32	858											
TLN1	7094	hgsc.bcm.edu	37	chr9	35714845	35714845	+	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	ctgcagcgatggtctgtgtgGctgaggctgcagcctgcttg	4	11	16	10	1	1	1	0	1	1	0	1	2	1	1	1	3	5	5	1	3	0	1			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr9:35714845G>T	ENST00000314888.9	-	22	3136	c.2783C>A	c.(2782-2784)gCc>gAc	p.A928D	TLN1_ENST00000540444.1_Missense_Mutation_p.A928D	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	928					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)			GGTCTGTGTGGCTGAGGCTGC	0.627																																					p.A928D		Atlas-SNP	.											.	TLN1	185	.	0			c.C2783A						PASS	.						43	48	47					9																	35714845		2202	4299	6501	SO:0001583	missense	7094	exon22			TGTGTGGCTGAGG	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.2783C>A	chr9.hg19:g.35714845G>T	ENSP00000316029:p.Ala928Asp	29.0	0.0	.		21.0	6.0	.	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	hg19	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	G	31	5.060455	0.93846	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.76186	-1.0;-0.99	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	D	0.87645	0.6229	M	0.83223	2.63	0.80722	D	1	D	0.71674	0.998	D	0.71414	0.973	D	0.88934	0.3375	10	0.87932	D	0	-11.6429	19.5343	0.95242	0.0:0.0:1.0:0.0	.	928	Q9Y490	TLN1_HUMAN	D	928	ENSP00000316029:A928D;ENSP00000442981:A928D	ENSP00000316029:A928D	A	-	2	0	TLN1	35704845	1.000000	0.71417	0.911000	0.35937	0.993000	0.82548	9.753000	0.98904	2.601000	0.87937	0.655000	0.94253	GCC	.	.	.	none		0.627	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		T	35714845	G	T	35714845	3	4	11	1	0	0	0	0	1	0	0	0	15959	1203	42	4	4986	4	TLN1	9	35714845	Missense_Mutation	SNP	G	TCGA-2Z-A9JG-01A-11D-A42J-10		35714845	105498586	33	859											
ASPN	54829	hgsc.bcm.edu	37	chr9	95237024	95237025	+	In_Frame_Ins	INS	-	-	TCCTCA																															ttggaaaaagagagttgtccINStcatcatcatcatcatcatc																								rs113747060|rs71362392|rs111419727|rs3078372|rs397838876|rs376433743|rs557103556	byFrequency	TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr9:95237024_95237025insTCCTCA	ENST00000375544.3	-	2	398_399	c.155_156insTGAGGA	c.(154-156)gag>gaTGAGGAg	p.51_52insDE	ASPN_ENST00000395538.3_In_Frame_Ins_p.51_52insDE|ASPN_ENST00000450139.2_In_Frame_Ins_p.23_24insDE|CENPP_ENST00000375587.3_Intron|ASPN_ENST00000375543.1_In_Frame_Ins_p.51_52insDE	NM_017680.4	NP_060150	Q9BXN1	ASPN_HUMAN	asporin	51	Poly-Asp.				bone mineralization (GO:0030282)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	9						GAGAGTTGTCCtcatcatcatc	0.396																																					p.E52delinsDEE		Atlas-INDEL	.											.,2	ASPN	52	.	0			c.156_157insTGAGGA						PASS	.																																			SO:0001652	inframe_insertion	54829	exon2			.	AF316824		9q22.31	2008-05-14	2007-02-15		ENSG00000106819	ENSG00000106819		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	14872	protein-coding gene	gene with protein product	"asporin proteoglycan"	608135	"asporin (LRR class 1)"				Standard	NM_017680		Approved	FLJ20129, SLRR1C, PLAP1	uc004ase.2	Q9BXN1	OTTHUMG00000020227	ENST00000375544.3:c.155_156insTGAGGA	chr9.hg19:g.95237024_95237025insTCCTCA	ENSP00000364694:p.Asp51_Glu52insAspGlu	49.0	0.0	0		67.0	24.0	0.358209	NM_001193335	Q5TBF3|Q96K79|Q96LD0|Q9NXP3	In_Frame_Ins	INS	ENST00000375544.3	hg19																																																																																				.	-|0.500;TCA|0.500	.	alt		0.396	ASPN-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053094.1	NM_017680		TCCTCA	95237025	-	TCCTCA	95237024	7	5	11	1	0	1	1	0	0	0	0	0	1057	680	24	0	1014	0	ASPN	9	95237024	In_Frame_Ins	INS	-	TCGA-2Z-A9JG-01A-11D-A42J-10	59522179	95237024	45976407	34	860											
ANKS6	203286	hgsc.bcm.edu	37	chr9	101546386	101546386	+	Missense_Mutation	SNP	A	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	cgccccgtccccattgaccaAgttcacgtggctggggtctt	5	10	11	15	3	2	1	1	1	1	0	3	1	3	1	5	3	0	2	5	3	1	3			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr9:101546386A>C	ENST00000353234.4	-	4	1008	c.961T>G	c.(961-963)Ttg>Gtg	p.L321V	ANKS6_ENST00000375018.1_Missense_Mutation_p.L321V|ANKS6_ENST00000540940.1_Missense_Mutation_p.L126V|ANKS6_ENST00000375019.2_Missense_Mutation_p.L20V			Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain containing 6	321						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)				CCATTGACCAAGTTCACGTGG	0.587																																					p.L321V		Atlas-SNP	.											.	ANKS6	59	.	0			c.T961G						PASS	.						68	72	71					9																	101546386		2118	4226	6344	SO:0001583	missense	203286	exon4			TGACCAAGTTCAC	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.961T>G	chr9.hg19:g.101546386A>C	ENSP00000297837:p.Leu321Val	49.0	0.0	.		27.0	6.0	.	NM_173551	A0SE62|Q5VSL0|Q5VSL2|Q5VSL3|Q5VSL4|Q68DB8|Q6P2R2|Q8N9L6|Q96D62	Missense_Mutation	SNP	ENST00000353234.4	hg19	CCDS43856.1	.	.	.	.	.	.	.	.	.	.	A	9.120	1.008825	0.19199	.	.	ENSG00000165138	ENST00000375019;ENST00000375018;ENST00000353234;ENST00000540940	T;T;T;T	0.53423	1.37;1.37;1.37;0.62	5.52	2.4	0.29515	Ankyrin repeat-containing domain (4);	0.526064	0.21137	N	0.079547	T	0.21841	0.0526	N	0.13299	0.325	0.30021	N	0.814303	B	0.13145	0.007	B	0.17433	0.018	T	0.11131	-1.0600	10	0.14252	T	0.57	-2.3181	0.9732	0.01420	0.2075:0.1252:0.3954:0.2718	.	321	Q68DC2	ANKS6_HUMAN	V	20;321;321;126	ENSP00000364159:L20V;ENSP00000364158:L321V;ENSP00000297837:L321V;ENSP00000442189:L126V	ENSP00000297837:L321V	L	-	1	2	ANKS6	100586207	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	1.386000	0.34419	0.281000	0.22233	-0.248000	0.11899	TTG	.	.	.	none		0.587	ANKS6-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277053.1	NM_173551		C	101546386	A	C	101546386	3	2	11	1	0	0	0	0	1	0	0	0	692	69	3	5	1702	5	ANKS6	9	101546386	Missense_Mutation	SNP	A	TCGA-2Z-A9JG-01A-11D-A42J-10	6309362	101546386	39667045	35	861											
FAM102A	399665	hgsc.bcm.edu	37	chr9	130742371	130742371	+	Missense_Mutation	SNP	A	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	agtcagctcctccagggtgaAagtagtttggaatttgaatt	11	13	11	6	0	1	2	1	2	0	0	3	3	3	3	2	2	1	3	2	2	4	4			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr9:130742371A>C	ENST00000373095.1	-	1	421	c.46T>G	c.(46-48)Ttc>Gtc	p.F16V		NM_001035254.2	NP_001030331.1	Q5T9C2	F102A_HUMAN	family with sequence similarity 102, member A	16										breast(1)|cervix(1)|large_intestine(3)|lung(1)|ovary(4)	10						TCCAGGGTGAAAGTAGTTTGG	0.527																																					p.F16V		Atlas-SNP	.											.	FAM102A	32	.	0			c.T46G						PASS	.						118	133	128					9																	130742371		2203	4300	6503	SO:0001583	missense	399665	exon1			GGGTGAAAGTAGT		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.46T>G	chr9.hg19:g.130742371A>C	ENSP00000362187:p.Phe16Val	183.0	0.0	.		93.0	30.0	.	NM_001035254	A2A329|Q8TEL4	Missense_Mutation	SNP	ENST00000373095.1	hg19	CCDS35150.1	.	.	.	.	.	.	.	.	.	.	A	13.06	2.125094	0.37533	.	.	ENSG00000167106	ENST00000373095	T	0.35789	1.29	4.87	4.87	0.63330	.	0.300781	0.36374	N	0.002623	T	0.24509	0.0594	N	0.20807	0.61	0.80722	D	1	B	0.12013	0.005	B	0.12156	0.007	T	0.04870	-1.0921	10	0.25106	T	0.35	-14.1942	13.6554	0.62336	1.0:0.0:0.0:0.0	.	16	Q5T9C2	F102A_HUMAN	V	16	ENSP00000362187:F16V	ENSP00000362187:F16V	F	-	1	0	FAM102A	129782192	1.000000	0.71417	0.978000	0.43139	0.992000	0.81027	3.399000	0.52586	1.821000	0.53095	0.379000	0.24179	TTC	.	.	.	none		0.527	FAM102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054298.2			C	130742371	A	C	130742371	3	2	11	1	0	0	0	0	1	0	0	0	5386	14	1	5	1152	5	FAM102A	9	130742371	Missense_Mutation	SNP	A	TCGA-2Z-A9JG-01A-11D-A42J-10	29195985	130742371	10471060	36	862											
C9orf96	169436	hgsc.bcm.edu	37	chr9	136253234	136253234	+	Missense_Mutation	SNP	T	T	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	gcctcctgtcccagcagatcTcttctctgtacctctgcctg	4	13	7	17	0	3	1	0	0	3	1	7	1	5	1	5	0	3	2	5	0	1	2			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr9:136253234T>G	ENST00000371957.3	+	5	405	c.298T>G	c.(298-300)Tct>Gct	p.S100A	C9orf96_ENST00000426926.2_Missense_Mutation_p.S100A|C9orf96_ENST00000371955.1_5'UTR	NM_153710.3	NP_714921.4	Q8NE28	STKL1_HUMAN		100	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|stomach(2)	25				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		CCAGCAGATCTCTTCTCTGTA	0.562																																					p.S100A		Atlas-SNP	.											.	C9orf96	77	.	0			c.T298G						PASS	.						88	73	78					9																	136253234		2203	4300	6503	SO:0001583	missense	169436	exon5			CAGATCTCTTCTC																												ENST00000371957.3:c.298T>G	chr9.hg19:g.136253234T>G	ENSP00000361025:p.Ser100Ala	109.0	0.0	.		68.0	30.0	.	NM_153710	Q5T8U8|Q6ZMP6|Q6ZMQ5	Missense_Mutation	SNP	ENST00000371957.3	hg19	CCDS35169.1	.	.	.	.	.	.	.	.	.	.	T	10.80	1.451340	0.26074	.	.	ENSG00000198870	ENST00000426926;ENST00000371957	T;T	0.20463	2.07;2.07	4.12	2.93	0.34026	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.113616	0.39341	N	0.001387	T	0.19927	0.0479	L	0.60455	1.87	0.80722	D	1	B	0.18968	0.032	B	0.19391	0.025	T	0.04495	-1.0947	10	0.59425	D	0.04	-19.6937	6.8088	0.23792	0.2081:0.0:0.0:0.7919	.	100	Q8NE28	SGK71_HUMAN	A	100	ENSP00000398807:S100A;ENSP00000361025:S100A	ENSP00000361025:S100A	S	+	1	0	C9orf96	135243055	1.000000	0.71417	0.994000	0.49952	0.495000	0.33615	2.499000	0.45372	0.537000	0.28751	0.459000	0.35465	TCT	.	.	.	none		0.562	C9orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054855.1			G	136253234	T	G	136253234	3	3	11	1	0	0	0	0	1	0	0	0	2510	1551	54	5	316	5	C9orf96	9	136253234	Missense_Mutation	SNP	T	TCGA-2Z-A9JG-01A-11D-A42J-10	5510863	136253234	4960197	37	863											
ARID5B	84159	hgsc.bcm.edu	37	chr10	63829547	63829547	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccacttgtacccgcagacAttatgaaaggtaagaaacca	15	8	8	10	1	0	3	0	1	0	2	0	3	0	3	3	1	3	3	3	1	5	4			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr10:63829547A>G	ENST00000279873.7	+	8	1600	c.1190A>G	c.(1189-1191)cAt>cGt	p.H397R	ARID5B_ENST00000309334.5_Missense_Mutation_p.H154R	NM_032199.2	NP_115575.1	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	397	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				adipose tissue development (GO:0060612)|adrenal gland development (GO:0030325)|cell development (GO:0048468)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|fat pad development (GO:0060613)|female gonad development (GO:0008585)|fibroblast migration (GO:0010761)|kidney development (GO:0001822)|liver development (GO:0001889)|male gonad development (GO:0008584)|multicellular organism growth (GO:0035264)|muscle organ morphogenesis (GO:0048644)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(13)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	Prostate(12;0.016)|all_hematologic(501;0.215)					ACCCGCAGACATTATGAAAGG	0.418																																					p.H397R		Atlas-SNP	.											.	ARID5B	125	.	0			c.A1190G						PASS	.						47	47	47					10																	63829547		2203	4300	6503	SO:0001583	missense	84159	exon8			GCAGACATTATGA	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.1190A>G	chr10.hg19:g.63829547A>G	ENSP00000279873:p.His397Arg	53.0	0.0	.		100.0	53.0	.	NM_032199	B4DLB3|Q05DG6|Q32Q59|Q5VST4|Q6NZ42|Q7Z3M4|Q8N421|Q9H786	Missense_Mutation	SNP	ENST00000279873.7	hg19	CCDS31208.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.710719	0.89112	.	.	ENSG00000150347	ENST00000279873;ENST00000309334	T;T	0.64085	-0.08;-0.08	6.1	6.1	0.99115	ARID/BRIGHT DNA-binding domain (5);	0.000000	0.85682	D	0.000000	T	0.81365	0.4807	M	0.83312	2.635	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	D	0.83956	0.0319	10	0.87932	D	0	-17.5963	16.686	0.85306	1.0:0.0:0.0:0.0	.	154;397	Q14865-2;Q14865	.;ARI5B_HUMAN	R	397;154	ENSP00000279873:H397R;ENSP00000308862:H154R	ENSP00000279873:H397R	H	+	2	0	ARID5B	63499553	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.791000	0.91849	2.340000	0.79590	0.528000	0.53228	CAT	.	.	.	none		0.418	ARID5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048233.1	XM_084482		G	63829547	A	G	63829547	3	3	11	1	0	0	0	0	1	0	0	0	922	217	8	3	1220	3	ARID5B	10	63829547	Missense_Mutation	SNP	A	TCGA-2Z-A9JG-01A-11D-A42J-10		63829547	71705200	38	864											
DPYSL4	10570	hgsc.bcm.edu	37	chr10	134011925	134011925	+	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	gttggtttctttaggagcagAagcggttgctggagctcggc	6	12	16	7	2	1	1	0	0	1	1	2	3	1	3	0	5	4	6	0	5	2	5			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr10:134011925A>T	ENST00000338492.4	+	7	792	c.628A>T	c.(628-630)Aag>Tag	p.K210*	DPYSL4_ENST00000368629.1_Intron|DPYSL4_ENST00000368627.1_Intron	NM_006426.2	NP_006417.2	O14531	DPYL4_HUMAN	dihydropyrimidinase-like 4	210					axon guidance (GO:0007411)|nervous system development (GO:0007399)|pyrimidine nucleobase catabolic process (GO:0006208)	cytosol (GO:0005829)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		all_cancers(35;4.33e-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;7.21e-05)|Epithelial(32;8.01e-05)|all cancers(32;9.29e-05)|BRCA - Breast invasive adenocarcinoma(275;0.206)		TTAGGAGCAGAAGCGGTTGCT	0.632																																					p.K210X		Atlas-SNP	.											.	DPYSL4	91	.	0			c.A628T						PASS	.						54	48	50					10																	134011925		2191	4296	6487	SO:0001587	stop_gained	10570	exon7			GAGCAGAAGCGGT	AB006713	CCDS7665.1	10q25.2-q26	2008-05-14			ENSG00000151640	ENSG00000151640			3016	protein-coding gene	gene with protein product		608407				8973361, 9652388	Standard	NM_006426		Approved	ULIP4, DRP-4	uc009ybb.3	O14531	OTTHUMG00000019283	ENST00000338492.4:c.628A>T	chr10.hg19:g.134011925A>T	ENSP00000339850:p.Lys210*	63.0	0.0	.		41.0	25.0	.	NM_006426	B2RMQ1|D3DRG5|O00240|Q5T0Q7	Nonsense_Mutation	SNP	ENST00000338492.4	hg19	CCDS7665.1	.	.	.	.	.	.	.	.	.	.	A	37	6.019877	0.97205	.	.	ENSG00000151640	ENST00000338492	.	.	.	3.7	3.7	0.42460	.	0.166643	0.51477	D	0.000090	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.4525	12.9144	0.58197	1.0:0.0:0.0:0.0	.	.	.	.	X	210	.	ENSP00000339850:K210X	K	+	1	0	DPYSL4	133861915	0.974000	0.33945	0.998000	0.56505	0.612000	0.37316	2.815000	0.48018	1.704000	0.51252	0.454000	0.30748	AAG	.	.	.	none		0.632	DPYSL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051050.2			T	134011925	A	T	134011925	4	4	11	1	0	0	0	0	0	1	0	0	4751	247	9	5	654	5	DPYSL4	10	134011925	Nonsense_Mutation	SNP	A	TCGA-2Z-A9JG-01A-11D-A42J-10	70182378	134011925	1522822	39	865											
FRG2B	441581	hgsc.bcm.edu	37	chr10	135438923	135438923	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cacagaggtcaccaagctttTtcgaattgacggtgtttgga	10	12	11	8	2	1	2	1	1	0	1	2	4	1	3	1	3	1	2	1	3	2	4			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr10:135438923T>C	ENST00000425520.1	-	4	569	c.517A>G	c.(517-519)Aaa>Gaa	p.K173E	FRG2B_ENST00000443774.1_Missense_Mutation_p.K174E	NM_001080998.1	NP_001074467.1	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B	173						nucleus (GO:0005634)				endometrium(2)|kidney(2)|lung(14)|ovary(1)|prostate(1)	20		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		ACCAAGCTTTTTCGAATTGAC	0.562																																					p.K173E		Atlas-SNP	.											.	FRG2B	47	.	0			c.A517G						PASS	.						123	147	139					10																	135438923		2190	4294	6484	SO:0001583	missense	441581	exon4			AGCTTTTTCGAAT	AY744466	CCDS44502.1	10q26.3	2012-10-02			ENSG00000225899	ENSG00000225899			33518	protein-coding gene	gene with protein product						15520407	Standard	NM_001080998		Approved		uc010qvg.2	Q96QU4	OTTHUMG00000019328	ENST00000425520.1:c.517A>G	chr10.hg19:g.135438923T>C	ENSP00000401310:p.Lys173Glu	303.0	0.0	.		293.0	127.0	.	NM_001080998	Q5VSQ1	Missense_Mutation	SNP	ENST00000425520.1	hg19	CCDS44502.1	.	.	.	.	.	.	.	.	.	.	.	12.42	1.931878	0.34096	.	.	ENSG00000225899	ENST00000443774;ENST00000425520	T;T	0.64260	-0.09;-0.09	.	.	.	.	0.384192	0.19253	N	0.118862	T	0.62998	0.2474	L	0.34521	1.04	0.09310	N	1	D	0.56035	0.974	D	0.67725	0.953	T	0.53436	-0.8439	8	0.87932	D	0	-16.2917	.	.	.	.	173	Q96QU4	FRG2B_HUMAN	E	174;173	ENSP00000408343:K174E;ENSP00000401310:K173E	ENSP00000401310:K173E	K	-	1	0	FRG2B	135288913	0.016000	0.18221	0.226000	0.23910	0.228000	0.25075	0.264000	0.18497	0.103000	0.17682	0.102000	0.15555	AAA	.	.	.	none		0.562	FRG2B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467780.1	NM_001080998		C	135438923	T	C	135438923	3	2	11	1	0	0	0	0	1	0	0	0	6054	1850	64	3	322	3	FRG2B	10	135438923	Missense_Mutation	SNP	T	TCGA-2Z-A9JG-01A-11D-A42J-10	1426998	135438923	95824	40	866											
KCNQ1	3784	hgsc.bcm.edu	37	chr11	2608884	2608884	+	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	aggccccccggagccacactCtgctgtcacccagccccaaa	9	4	8	20	1	2	0	1	0	1	0	2	1	2	1	7	2	3	1	7	2	1	0			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr11:2608884C>G	ENST00000155840.5	+	9	1321	c.1213C>G	c.(1213-1215)Ctg>Gtg	p.L405V	KCNQ1_ENST00000335475.5_Missense_Mutation_p.L278V	NM_000218.2	NP_000209.2	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 1	405					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)	GAGCCACACTCTGCTGTCACC	0.652																																					p.L405V		Atlas-SNP	.											.	KCNQ1	60	.	0			c.C1213G						PASS	.						76	81	79					11																	2608884		2202	4299	6501	SO:0001583	missense	3784	exon9			CACACTCTGCTGT	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.1213C>G	chr11.hg19:g.2608884C>G	ENSP00000155840:p.Leu405Val	122.0	0.0	.		65.0	23.0	.	NM_000218	O00347|O60607|O94787|Q14D14|Q7Z6G9|Q92960|Q9UMN8|Q9UMN9	Missense_Mutation	SNP	ENST00000155840.5	hg19	CCDS7736.1	.	.	.	.	.	.	.	.	.	.	C	0.313	-0.966773	0.02232	.	.	ENSG00000053918	ENST00000155840;ENST00000335475	D;D	0.99239	-5.61;-5.51	4.86	2.9	0.33743	.	0.361282	0.26983	N	0.021502	D	0.96519	0.8864	L	0.35854	1.095	0.24869	N	0.992293	B;B;B	0.18610	0.003;0.002;0.029	B;B;B	0.13407	0.009;0.004;0.009	D	0.91555	0.5260	10	0.30078	T	0.28	-13.9224	4.0468	0.09776	0.1633:0.5886:0.1585:0.0896	.	278;278;405	P51787-2;Q14D14;P51787	.;.;KCNQ1_HUMAN	V	405;278	ENSP00000155840:L405V;ENSP00000334497:L278V	ENSP00000155840:L405V	L	+	1	2	KCNQ1	2565460	0.048000	0.20356	0.242000	0.24170	0.042000	0.13812	0.264000	0.18497	0.519000	0.28406	0.650000	0.86243	CTG	.	.	.	none		0.652	KCNQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027382.2	NM_000218		G	2608884	C	G	2608884	3	3	11	1	0	0	0	0	1	0	0	0	8089	912	32	4	1256	4	KCNQ1	11	2608884	Missense_Mutation	SNP	C	TCGA-2Z-A9JG-01A-11D-A42J-10		2608884	132397632	41	867											
OR4A5	81318	hgsc.bcm.edu	37	chr11	51411524	51411524	+	Missense_Mutation	SNP	A	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	gtttttctatagcatttctcAtctctgaatttctcaacgta	9	19	4	9	1	4	1	2	1	4	0	7	1	4	1	0	0	2	3	0	0	5	7			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr11:51411524A>C	ENST00000319760.6	-	1	924	c.872T>G	c.(871-873)aTg>aGg	p.M291R		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	291						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			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)				AGCATTTCTCATCTCTGAATT	0.353																																					p.M291R		Atlas-SNP	.											.	OR4A5	116	.	0			c.T872G						PASS	.						30	32	31					11																	51411524		2201	4294	6495	SO:0001583	missense	81318	exon1			TTTCTCATCTCTG	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.872T>G	chr11.hg19:g.51411524A>C	ENSP00000367664:p.Met291Arg	39.0	0.0	.		104.0	45.0	.	NM_001005272	Q6IF84	Missense_Mutation	SNP	ENST00000319760.6	hg19	CCDS31497.1	.	.	.	.	.	.	.	.	.	.	.	11.66	1.703620	0.30232	.	.	ENSG00000221840	ENST00000319760	T	0.37584	1.19	2.2	2.2	0.27929	.	0.425474	0.20570	N	0.089751	T	0.40372	0.1114	L	0.38175	1.15	0.26994	N	0.965077	D	0.54964	0.969	P	0.58780	0.845	T	0.11446	-1.0587	10	0.87932	D	0	.	8.3006	0.32012	1.0:0.0:0.0:0.0	.	291	Q8NH83	OR4A5_HUMAN	R	291	ENSP00000367664:M291R	ENSP00000367664:M291R	M	-	2	0	OR4A5	51268100	0.141000	0.22595	0.071000	0.20095	0.246000	0.25737	3.336000	0.52113	1.270000	0.44297	0.136000	0.15936	ATG	.	.	.	none		0.353	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272		C	51411524	A	C	51411524	3	2	11	1	0	0	0	0	1	0	0	0	11050	217	8	5	79	5	OR4A5	11	51411524	Missense_Mutation	SNP	A	TCGA-2Z-A9JG-01A-11D-A42J-10	48802640	51411524	83594992	42	868											
PCNXL3	399909	hgsc.bcm.edu	37	chr11	65395000	65395000	+	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	tccactttgactacccgcgcCtctcccagggctttctgctt	4	13	7	17	2	2	1	0	1	2	0	4	1	3	1	4	1	2	2	4	1	1	4			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr11:65395000C>G	ENST00000355703.3	+	22	4188	c.3649C>G	c.(3649-3651)Ctc>Gtc	p.L1217V		NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	1217						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						CTACCCGCGCCTCTCCCAGGG	0.612																																					p.L1217V		Atlas-SNP	.											.	PCNXL3	140	.	0			c.C3649G						PASS	.						175	174	175					11																	65395000		2052	4183	6235	SO:0001583	missense	399909	exon22			CCGCGCCTCTCCC	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.3649C>G	chr11.hg19:g.65395000C>G	ENSP00000347931:p.Leu1217Val	72.0	0.0	.		25.0	10.0	.	NM_032223	Q6MZN8	Missense_Mutation	SNP	ENST00000355703.3	hg19	CCDS44650.1	.	.	.	.	.	.	.	.	.	.	C	14.61	2.586169	0.46110	.	.	ENSG00000197136	ENST00000355703	T	0.07327	3.2	5.47	5.47	0.80525	.	0.063724	0.64402	D	0.000005	T	0.08223	0.0205	L	0.34521	1.04	0.29366	N	0.86432	B;B	0.31705	0.336;0.3	B;B	0.35550	0.205;0.066	T	0.15694	-1.0428	10	0.25106	T	0.35	.	12.2064	0.54355	0.1703:0.8297:0.0:0.0	.	104;1217	Q9H6A9-3;Q9H6A9	.;PCX3_HUMAN	V	1217	ENSP00000347931:L1217V	ENSP00000347931:L1217V	L	+	1	0	PCNXL3	65151576	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.969000	0.63735	2.735000	0.93741	0.655000	0.94253	CTC	.	.	.	none		0.612	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223		G	65395000	C	G	65395000	3	3	11	1	0	0	0	0	1	0	0	0	11600	681	24	4	3735	4	PCNXL3	11	65395000	Missense_Mutation	SNP	C	TCGA-2Z-A9JG-01A-11D-A42J-10	13983476	65395000	69611516	43	869											
KIAA1377	57562	hgsc.bcm.edu	37	chr11	101829047	101829047	+	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	aaaatgtgttccagcttaaaCtggaggaaactcagaaactc	16	9	8	8	0	1	1	1	0	0	1	3	3	2	3	1	2	4	2	1	2	6	2			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr11:101829047C>G	ENST00000263468.8	+	5	925	c.655C>G	c.(655-657)Ctg>Gtg	p.L219V	KIAA1377_ENST00000537689.1_Missense_Mutation_p.L20V	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	219										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)		CCAGCTTAAACTGGAGGAAAC	0.333																																					p.L219V		Atlas-SNP	.											.	KIAA1377	111	.	0			c.C655G						PASS	.						124	133	130					11																	101829047		2203	4299	6502	SO:0001583	missense	57562	exon5			CTTAAACTGGAGG	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.655C>G	chr11.hg19:g.101829047C>G	ENSP00000263468:p.Leu219Val	68.0	0.0	.		102.0	32.0	.	NM_020802	Q4G0U6	Missense_Mutation	SNP	ENST00000263468.8	hg19	CCDS31658.1	.	.	.	.	.	.	.	.	.	.	C	15.78	2.935593	0.52866	.	.	ENSG00000110318	ENST00000263468;ENST00000537689	T;T	0.18338	2.22;2.22	5.68	3.82	0.43975	.	0.000000	0.47455	D	0.000228	T	0.39517	0.1081	M	0.76002	2.32	0.29116	N	0.880558	D	0.89917	1.0	D	0.91635	0.999	T	0.30621	-0.9972	10	0.56958	D	0.05	-4.4834	11.0161	0.47689	0.0:0.8476:0.0:0.1524	.	219	Q9P2H0	K1377_HUMAN	V	219;20	ENSP00000263468:L219V;ENSP00000443184:L20V	ENSP00000263468:L219V	L	+	1	2	KIAA1377	101334257	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.310000	0.51911	0.753000	0.32945	0.650000	0.86243	CTG	.	.	.	none		0.333	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802		G	101829047	C	G	101829047	3	3	11	1	0	0	0	0	1	0	0	0	8234	564	20	4	673	4	KIAA1377	11	101829047	Missense_Mutation	SNP	C	TCGA-2Z-A9JG-01A-11D-A42J-10	36434047	101829047	33177469	44	870											
VWF	7450	hgsc.bcm.edu	37	chr12	6103203	6103203	+	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	gcaaacagtggtaagaggagGacctggcagtgggagctgtc	11	6	17	7	0	0	1	0	0	0	1	1	4	0	4	1	5	2	4	1	5	2	1			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr12:6103203G>T	ENST00000261405.5	-	37	6677	c.6423C>A	c.(6421-6423)gtC>gtA	p.V2141V		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	2141	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)	GTAAGAGGAGGACCTGGCAGT	0.582																																					p.V2141V		Atlas-SNP	.											.	VWF	338	.	0			c.C6423A						PASS	.						89	78	82					12																	6103203		2203	4300	6503	SO:0001819	synonymous_variant	7450	exon37			GAGGAGGACCTGG		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.6423C>A	chr12.hg19:g.6103203G>T		62.0	0.0	.		141.0	40.0	.	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	hg19	CCDS8539.1																																																																																			.	.	.	none		0.582	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		T	6103203	G	T	6103203	2	4	11	1	0	0	0	0	0	0	0	1	17258	1161	41	4		4	VWF	12	6103203	Silent	SNP	G	TCGA-2Z-A9JG-01A-11D-A42J-10		6103203	127748692	45	871											
KLHDC5	57542	hgsc.bcm.edu	37	chr12	27950834	27950834	+	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	gagcgaggacatgctcaccgTgcagtcctacaacaccgtca	11	6	10	14	3	2	0	2	0	0	0	3	3	3	1	3	1	5	2	3	1	2	1			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr12:27950834T>A	ENST00000381271.2	+	3	1564	c.1253T>A	c.(1252-1254)gTg>gAg	p.V418E	RP11-860B13.3_ENST00000543527.1_RNA	NM_020782.1	NP_065833.1	Q9P2K6	KLH42_HUMAN	kelch-like family member 42	418					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)											ATGCTCACCGTGCAGTCCTAC	0.587																																					p.V418E		Atlas-SNP	.											.	.	.	.	0			c.T1253A						PASS	.						121	84	97					12																	27950834		2203	4300	6503	SO:0001583	missense	57542	exon3			TCACCGTGCAGTC	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.1253T>A	chr12.hg19:g.27950834T>A	ENSP00000370671:p.Val418Glu	91.0	0.0	.		264.0	86.0	.	NM_020782	Q2VPK1|Q8N334	Missense_Mutation	SNP	ENST00000381271.2	hg19	CCDS31763.1	.	.	.	.	.	.	.	.	.	.	T	31	5.074624	0.94000	.	.	ENSG00000087448	ENST00000381271	T	0.70749	-0.51	5.56	5.56	0.83823	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.82001	0.4942	M	0.65975	2.015	0.54753	D	0.999987	D	0.89917	1.0	D	0.69307	0.963	D	0.84164	0.0430	10	0.87932	D	0	.	14.9054	0.70715	0.0:0.0:0.0:1.0	.	418	Q9P2K6	KLDC5_HUMAN	E	418	ENSP00000370671:V418E	ENSP00000370671:V418E	V	+	2	0	KLHDC5	27842101	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.474000	0.81024	2.109000	0.64355	0.533000	0.62120	GTG	.	.	.	none		0.587	KLHL42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402904.1	NM_020782		A	27950834	T	A	27950834	3	1	11	1	0	0	0	0	1	0	0	0	8366	1696	59	5	1263	5	KLHDC5	12	27950834	Missense_Mutation	SNP	T	TCGA-2Z-A9JG-01A-11D-A42J-10	21847631	27950834	105901061	46	872											
SMAGP	57228	hgsc.bcm.edu	37	chr12	51639787	51639787	+	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	actctccatctggacgatggCactgggctcaccttctgtag	7	11	10	13	1	4	0	1	0	3	0	5	2	4	1	2	3	0	3	2	3	1	2			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr12:51639787C>T	ENST00000603798.1	-	4	904	c.232G>A	c.(232-234)Gcc>Acc	p.A78T	DAZAP2_ENST00000425012.2_Intron|DAZAP2_ENST00000604900.1_Intron|SMAGP_ENST00000603864.1_Missense_Mutation_p.A78T|SMAGP_ENST00000398453.3_Missense_Mutation_p.A78T|SMAGP_ENST00000605627.1_Missense_Mutation_p.A64T	NM_001031628.1	NP_001026798.1	Q0VAQ4	SMAGP_HUMAN	small cell adhesion glycoprotein	78						cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)											TGGACGATGGCACTGGGCTCA	0.507																																					p.A78T		Atlas-SNP	.											.	SMAGP	7	.	0			c.G232A						PASS	.						140	133	135					12																	51639787		2012	4176	6188	SO:0001583	missense	57228	exon4			CGATGGCACTGGG		CCDS44889.1	12q13.13	2010-02-17			ENSG00000170545	ENSG00000170545			26918	protein-coding gene	gene with protein product	"small trans-membrane and glycosylated protein"					15021913	Standard	NM_001031628		Approved	MGC149453, MGC149454, hSMAGP	uc001rye.1	Q0VAQ4		ENST00000603798.1:c.232G>A	chr12.hg19:g.51639787C>T	ENSP00000475068:p.Ala78Thr	82.0	0.0	.		198.0	113.0	.	NM_001031628	A6NIL5	Missense_Mutation	SNP	ENST00000603798.1	hg19	CCDS44889.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.937529	0.52972	.	.	ENSG00000170545	ENST00000380103;ENST00000398453	T	0.79033	-1.23	5.28	3.33	0.38152	.	0.384184	0.18291	U	0.145714	T	0.68559	0.3014	.	.	.	0.80722	D	1	B	0.12630	0.006	B	0.15052	0.012	T	0.63686	-0.6581	9	0.66056	D	0.02	2.7494	8.1908	0.31368	0.0:0.7302:0.0:0.2698	.	78	Q0VAQ4	SMAGP_HUMAN	T	78	ENSP00000381471:A78T	ENSP00000369446:A78T	A	-	1	0	SMAGP	49926054	0.000000	0.05858	1.000000	0.80357	0.993000	0.82548	-0.024000	0.12435	0.630000	0.30394	0.655000	0.94253	GCC	.	.	.	none		0.507	SMAGP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469789.1	NM_020467		T	51639787	C	T	51639787	3	4	11	1	0	0	0	0	1	0	0	0	14778	710	25	2	65	2	SMAGP	12	51639787	Missense_Mutation	SNP	C	TCGA-2Z-A9JG-01A-11D-A42J-10	23688953	51639787	82212108	47	873											
CEP290	80184	hgsc.bcm.edu	37	chr12	88523531	88523532	+	Frame_Shift_Ins	INS	-	-	AAAA																															ttacattatctgtctgatgcINSacaatagctttcattctatt																										TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr12:88523531_88523532insAAAA	ENST00000552810.1	-	10	1134_1135	c.791_792insTTTT	c.(790-792)gtgfs	p.-264fs	CEP290_ENST00000309041.7_Frame_Shift_Ins_p.-264fs|CEP290_ENST00000397838.3_5'Flank	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa						cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						CTGTCTGATGCACAATAGCTTT	0.272																																					p.V264fs		Atlas-INDEL	.											.	CEP290	195	.	0			c.792_793insTTTT						PASS	.																																			SO:0001589	frameshift_variant	80184	exon10			.	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.791_792insTTTT	chr12.hg19:g.88523531_88523532insAAAA	ENSP00000448012:p.Val264fs	56.0	0.0	0		145.0	12.0	0.0827586	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Frame_Shift_Ins	INS	ENST00000552810.1	hg19	CCDS55858.1																																																																																			.	.	.	none		0.272	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		AAAA	88523532	-	AAAA	88523531	7	5	11	1	0	1	1	0	0	0	0	0	3255	697	25	0	6827	0	CEP290	12	88523531	Frame_Shift_Ins	INS	-	TCGA-2Z-A9JG-01A-11D-A42J-10	36883744	88523531	45328364	48	874	7	2									
CEP290	80184	hgsc.bcm.edu	37	chr12	88523533	88523534	+	Frame_Shift_Ins	INS	-	-	A																															acattatctgtctgatgcacINSaatagctttcattctattat																										TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr12:88523533_88523534insA	ENST00000552810.1	-	10	1132_1133	c.789_790insT	c.(787-792)attgtgfs	p.V264fs	CEP290_ENST00000309041.7_Frame_Shift_Ins_p.V264fs|CEP290_ENST00000397838.3_5'Flank	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	264					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						GTCTGATGCACAATAGCTTTCA	0.272																																					p.V264fs		Atlas-INDEL	.											.	CEP290	195	.	0			c.790_791insT						PASS	.																																			SO:0001589	frameshift_variant	80184	exon10			.	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.790dupT	chr12.hg19:g.88523535_88523535dupA	ENSP00000448012:p.Val264fs	56.0	0.0	0		144.0	12.0	0.0833333	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Frame_Shift_Ins	INS	ENST00000552810.1	hg19	CCDS55858.1																																																																																			.	.	.	none		0.272	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		A	88523534	-	A	88523533	7	5	11	1	0	1	1	0	0	0	0	0	3255	478	17	0	6829	0	CEP290	12	88523533	Frame_Shift_Ins	INS	-	TCGA-2Z-A9JG-01A-11D-A42J-10	2	88523533	45328362	49	875	7	2									
CUX2	23316	hgsc.bcm.edu	37	chr12	111729279	111729279	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgacagactgcagccccccaGctttgaccccagtgggcagc	8	5	11	17	1	0	2	0	1	0	1	0	3	0	2	5	1	4	3	5	1	0	1			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr12:111729279G>A	ENST00000261726.6	+	5	513	c.359G>A	c.(358-360)aGc>aAc	p.S120N		NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	120					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						CAGCCCCCCAGCTTTGACCCC	0.622																																					p.S120N		Atlas-SNP	.											.	CUX2	145	.	0			c.G359A						PASS	.						48	55	53					12																	111729279		1950	4145	6095	SO:0001583	missense	23316	exon5			CCCCCAGCTTTGA	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.359G>A	chr12.hg19:g.111729279G>A	ENSP00000261726:p.Ser120Asn	100.0	0.0	.		133.0	20.0	.	NM_015267	A7E2Y4	Missense_Mutation	SNP	ENST00000261726.6	hg19	CCDS41837.1	.	.	.	.	.	.	.	.	.	.	g	16.86	3.238901	0.58995	.	.	ENSG00000111249	ENST00000261726;ENST00000397643;ENST00000552889	T	0.47869	0.83	4.7	3.8	0.43715	.	0.460095	0.27143	N	0.020730	T	0.32526	0.0832	L	0.29908	0.895	0.30049	N	0.81191	B;B	0.30281	0.275;0.139	B;B	0.28232	0.087;0.04	T	0.19289	-1.0310	10	0.18276	T	0.48	-16.1008	12.2036	0.54340	0.0831:0.0:0.9169:0.0	.	180;120	F5GWR6;O14529	.;CUX2_HUMAN	N	120;180;58	ENSP00000261726:S120N	ENSP00000261726:S120N	S	+	2	0	CUX2	110213662	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	5.435000	0.66532	2.161000	0.67846	0.556000	0.70494	AGC	.	.	.	none		0.622	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267		A	111729279	G	A	111729279	3	1	11	1	0	0	0	0	1	0	0	0	4067	971	34	2	377	2	CUX2	12	111729279	Missense_Mutation	SNP	G	TCGA-2Z-A9JG-01A-11D-A42J-10	23205746	111729279	22122616	50	876											
MSI1	4440	hgsc.bcm.edu	37	chr12	120795647	120795647	+	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	tgttgatttcatgaaaatgaAtttcacacactttctccacg	12	15	5	9	1	3	3	2	3	1	0	4	3	3	3	1	0	0	1	1	0	3	4			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr12:120795647A>T	ENST00000257552.2	-	8	594	c.506T>A	c.(505-507)aTt>aAt	p.I169N	MSI1_ENST00000546622.1_5'UTR	NM_002442.3	NP_002433.1	O43347	MSI1H_HUMAN	musashi RNA-binding protein 1	169	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				epithelial cell differentiation (GO:0030855)|nervous system development (GO:0007399)|response to hormone (GO:0009725)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|polysome (GO:0005844)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			breast(4)|central_nervous_system(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(5)|skin(2)	19	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ATGAAAATGAATTTCACACAC	0.498																																					p.I169N		Atlas-SNP	.											.	MSI1	40	.	0			c.T506A						PASS	.						132	100	111					12																	120795647		2203	4300	6503	SO:0001583	missense	4440	exon8			AAATGAATTTCAC	AB012851	CCDS9196.1	12q24	2013-07-16	2012-12-13					"RNA binding motif (RRM) containing"	7330	protein-coding gene	gene with protein product		603328	"Musashi (Drosophila) homolog 1", "musashi homolog 1 (Drosophila)"			9790759	Standard	NM_002442		Approved		uc001tye.2	O43347	OTTHUMG00000169344	ENST00000257552.2:c.506T>A	chr12.hg19:g.120795647A>T	ENSP00000257552:p.Ile169Asn	125.0	0.0	.		143.0	29.0	.	NM_002442	Q96PU0|Q96PU1|Q96PU2|Q96PU3	Missense_Mutation	SNP	ENST00000257552.2	hg19	CCDS9196.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.6|21.6	4.172958|4.172958	0.78452|0.78452	.|.	.|.	ENSG00000135097|ENSG00000135097	ENST00000546985|ENST00000257552	.|T	.|0.74526	.|-0.85	4.83|4.83	4.83|4.83	0.62350|0.62350	.|Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	.|0.092070	.|0.45867	.|D	.|0.000324	T|T	0.73992|0.73992	0.3658|0.3658	N|N	0.11023|0.11023	0.085|0.085	0.80722|0.80722	D|D	1|1	.|D	.|0.63046	.|0.992	.|D	.|0.75020	.|0.985	T|T	0.79995|0.79995	-0.1568|-0.1568	5|10	.|0.72032	.|D	.|0.01	.|.	14.7048|14.7048	0.69183|0.69183	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|169	.|O43347	.|MSI1H_HUMAN	I|N	101|169	.|ENSP00000257552:I169N	.|ENSP00000257552:I169N	F|I	-|-	1|2	0|0	MSI1|MSI1	119280030|119280030	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.972000|0.972000	0.66771|0.66771	8.830000|8.830000	0.92063|0.92063	1.942000|1.942000	0.56320|0.56320	0.454000|0.454000	0.30748|0.30748	TTC|ATT	.	.	.	none		0.498	MSI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403629.1	NM_002442		T	120795647	A	T	120795647	3	4	11	1	0	0	0	0	1	0	0	0	9882	101	4	5	610	5	MSI1	12	120795647	Missense_Mutation	SNP	A	TCGA-2Z-A9JG-01A-11D-A42J-10	9066368	120795647	13056248	51	877											
PAN3	255967	hgsc.bcm.edu	37	chr13	28794514	28794514	+	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	gctactgctggattagcgccAggtaagttgagtaactattt	10	13	11	7	1	0	1	0	1	0	0	0	2	0	2	1	2	4	5	1	2	5	7			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr13:28794514A>G	ENST00000380958.3	+	6	1151	c.999A>G	c.(997-999)ccA>ccG	p.P333P	PAN3_ENST00000399613.1_Splice_Site_p.P133P	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)		GATTAGCGCCAGGTAAGTTGA	0.423																																					p.P333P		Atlas-SNP	.											.	PAN3	123	.	0			c.A999G						PASS	.						153	156	155					13																	28794514		2203	4300	6503	SO:0001630	splice_region_variant	255967	exon6			AGCGCCAGGTAAG	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.1000+1A>G	chr13.hg19:g.28794514A>G		38.0	0.0	.		55.0	24.0	.	NM_175854		Silent	SNP	ENST00000380958.3	hg19	CCDS9329.2																																																																																			.	.	.	none		0.423	PAN3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044318.4	NM_175854	Silent	G	28794514	A	G	28794514	5	3	11	1	0	0	0	0	0	0	1	0	11422	202	7	3	1021	3	PAN3	13	28794514	Splice_Site	SNP	A	TCGA-2Z-A9JG-01A-11D-A42J-10		28794514	86375364	52	878											
FRY	10129	hgsc.bcm.edu	37	chr13	32808840	32808840	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acctctgtcagcacatgcctTatctgaccttctctcaagat	9	13	5	14	0	5	2	2	1	3	1	6	2	5	2	3	0	2	1	3	0	2	2			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr13:32808840T>C	ENST00000380250.3	+	42	6153	c.5657T>C	c.(5656-5658)tTa>tCa	p.L1886S		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1886						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)		GCACATGCCTTATCTGACCTT	0.517																																					p.L1886S		Atlas-SNP	.											.	FRY	312	.	0			c.T5657C						PASS	.						100	97	98					13																	32808840		1988	4170	6158	SO:0001583	missense	10129	exon42			ATGCCTTATCTGA	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.5657T>C	chr13.hg19:g.32808840T>C	ENSP00000369600:p.Leu1886Ser	71.0	0.0	.		104.0	14.0	.	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	hg19	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.899503	0.91962	.	.	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.41758	0.99	6.07	6.07	0.98685	.	0.072441	0.56097	D	0.000028	T	0.60170	0.2248	M	0.81112	2.525	0.80722	D	1	P	0.46512	0.879	P	0.51550	0.673	T	0.65500	-0.6153	10	0.87932	D	0	.	16.6277	0.84984	0.0:0.0:0.0:1.0	.	1886	Q5TBA9	FRY_HUMAN	S	1886;723	ENSP00000369600:L1886S	ENSP00000369600:L1886S	L	+	2	0	FRY	31706840	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.841000	0.86834	2.330000	0.79161	0.528000	0.53228	TTA	.	.	.	none		0.517	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		C	32808840	T	C	32808840	3	2	11	1	0	0	0	0	1	0	0	0	6070	1764	61	3	5823	3	FRY	13	32808840	Missense_Mutation	SNP	T	TCGA-2Z-A9JG-01A-11D-A42J-10	4014326	32808840	82361038	53	879											
SAV1	60485	hgsc.bcm.edu	37	chr14	51111608	51111608	+	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	cagtgagttgtatttgtgttAtgatctatataatattttct	10	21	7	3	0	2	2	0	2	2	0	2	2	2	2	0	0	0	3	0	0	6	10			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr14:51111608A>T	ENST00000324679.4	-	3	1023	c.660T>A	c.(658-660)caT>caA	p.H220Q		NM_021818.3	NP_068590.1	Q9H4B6	SAV1_HUMAN	salvador family WW domain containing protein 1	220	WW 1. {ECO:0000255|PROSITE- ProRule:PRU00224}.				hair follicle development (GO:0001942)|hippo signaling (GO:0035329)|intestinal epithelial cell differentiation (GO:0060575)|keratinocyte differentiation (GO:0030216)|lung epithelial cell differentiation (GO:0060487)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of epithelial cell proliferation (GO:0050680)|positive regulation of apoptotic process (GO:0043065)|regulation of stem cell maintenance (GO:2000036)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)				breast(1)|kidney(2)|lung(2)|prostate(1)	6	all_epithelial(31;0.000611)|Breast(41;0.0333)					TATTTGTGTTATGATCTATAT	0.433																																					p.H220Q		Atlas-SNP	.											.	SAV1	18	.	0			c.T660A						PASS	.						119	110	113					14																	51111608		2203	4300	6503	SO:0001583	missense	60485	exon3			TGTGTTATGATCT	AK023071	CCDS9701.1	14q13-q23	2014-04-14	2014-04-14		ENSG00000151748	ENSG00000151748			17795	protein-coding gene	gene with protein product	"WW domain-containing adaptor 45"	607203	"salvador homolog 1 (Drosophila)"			12202036, 11027580	Standard	NM_021818		Approved	WW45, WWP4, salvador	uc001wyh.2	Q9H4B6	OTTHUMG00000140293	ENST00000324679.4:c.660T>A	chr14.hg19:g.51111608A>T	ENSP00000324729:p.His220Gln	46.0	0.0	.		58.0	27.0	.	NM_021818	A8K4B8|D3DSB6|Q6IA58|Q9H949|Q9HAK9	Missense_Mutation	SNP	ENST00000324679.4	hg19	CCDS9701.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.162805	0.78226	.	.	ENSG00000151748	ENST00000555720;ENST00000324679;ENST00000535862	D;D	0.84442	-1.85;-1.85	6.17	2.69	0.31865	WW/Rsp5/WWP (5);	0.000000	0.85682	D	0.000000	D	0.91971	0.7457	M	0.89414	3.03	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90365	0.4376	10	0.87932	D	0	-19.637	8.5304	0.33331	0.5208:0.0:0.4792:0.0	.	220	Q9H4B6	SAV1_HUMAN	Q	152;220;187	ENSP00000451492:H152Q;ENSP00000324729:H220Q	ENSP00000324729:H220Q	H	-	3	2	SAV1	50181358	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	1.498000	0.35660	0.241000	0.21283	0.533000	0.62120	CAT	.	.	.	none		0.433	SAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276879.1			T	51111608	A	T	51111608	3	4	11	1	0	0	0	0	1	0	0	0	13869	446	16	5	503	5	SAV1	14	51111608	Missense_Mutation	SNP	A	TCGA-2Z-A9JG-01A-11D-A42J-10		51111608	56237932	54	880											
ARHGAP11A	9824	hgsc.bcm.edu	37	chr15	32928491	32928491	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagtaagtctgaggaaacctTactaactccagagcgactag	14	8	9	10	1	1	2	0	1	1	1	2	4	2	3	2	1	4	1	2	1	5	4			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr15:32928491T>C	ENST00000361627.3	+	12	2239	c.1517T>C	c.(1516-1518)tTa>tCa	p.L506S	ARHGAP11A_ENST00000543522.1_Missense_Mutation_p.L317S|ARHGAP11A_ENST00000565905.1_Missense_Mutation_p.L317S	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	506					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)		GAGGAAACCTTACTAACTCCA	0.363																																					p.L506S	Colon(45;757 1134 30003 36652)	Atlas-SNP	.											.	ARHGAP11A	84	.	0			c.T1517C						PASS	.						54	56	55					15																	32928491		2201	4300	6501	SO:0001583	missense	9824	exon12			AAACCTTACTAAC	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.1517T>C	chr15.hg19:g.32928491T>C	ENSP00000355090:p.Leu506Ser	88.0	0.0	.		90.0	33.0	.	NM_014783	B4DZN9|Q6PI96|Q9Y3S6	Missense_Mutation	SNP	ENST00000361627.3	hg19	CCDS10028.1	.	.	.	.	.	.	.	.	.	.	.	18.14	3.557614	0.65425	.	.	ENSG00000198826	ENST00000361627;ENST00000543522	T	0.23348	1.91	5.86	4.75	0.60458	.	0.316141	0.22955	N	0.053611	T	0.49098	0.1537	M	0.74881	2.28	0.46028	D	0.998824	D	0.89917	1.0	D	0.81914	0.995	T	0.51655	-0.8678	10	0.87932	D	0	.	11.3555	0.49613	0.0:0.0705:0.0:0.9295	.	506	Q6P4F7	RHGBA_HUMAN	S	506;317	ENSP00000355090:L506S	ENSP00000355090:L506S	L	+	2	0	ARHGAP11A	30715783	1.000000	0.71417	0.956000	0.39512	0.776000	0.43924	5.480000	0.66820	2.226000	0.72624	0.528000	0.53228	TTA	.	.	.	none		0.363	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783		C	32928491	T	C	32928491	3	2	11	1	0	0	0	0	1	0	0	0	863	1764	61	3	1586	3	ARHGAP11A	15	32928491	Missense_Mutation	SNP	T	TCGA-2Z-A9JG-01A-11D-A42J-10		32928491	69602901	55	881											
TP53BP1	7158	hgsc.bcm.edu	37	chr15	43769942	43769942	+	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	acagatgctttggggctaaaAggcatgtcctctgacctagg	10	10	12	9	0	1	2	0	1	1	1	2	2	2	2	2	4	1	3	2	4	3	3			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr15:43769942A>C	ENST00000263801.3	-	8	1041	c.789T>G	c.(787-789)ccT>ccG	p.P263P	TP53BP1_ENST00000382044.4_Silent_p.P268P|TP53BP1_ENST00000450115.2_Silent_p.P268P|TP53BP1_ENST00000382039.3_Silent_p.P268P	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	263					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)		TGGGGCTAAAAGGCATGTCCT	0.393								Other conserved DNA damage response genes																													p.P268P		Atlas-SNP	.											.	TP53BP1	157	.	0			c.T804G						PASS	.						90	90	90					15																	43769942		2201	4298	6499	SO:0001819	synonymous_variant	7158	exon8			GCTAAAAGGCATG	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.789T>G	chr15.hg19:g.43769942A>C		89.0	0.0	.		62.0	21.0	.	NM_001141980	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Silent	SNP	ENST00000263801.3	hg19	CCDS10096.1																																																																																			.	.	.	none		0.393	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			C	43769942	A	C	43769942	2	2	11	1	0	0	0	0	0	0	0	1	16395	59	3	5		5	TP53BP1	15	43769942	Silent	SNP	A	TCGA-2Z-A9JG-01A-11D-A42J-10	10841451	43769942	58761450	56	882											
MEX3B	84206	hgsc.bcm.edu	37	chr15	82336360	82336360	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agctggagctgtcgttgcggTagctagagaaaggcttgcgg	8	9	17	7	3	0	1	0	0	0	1	1	3	0	2	0	4	5	6	0	4	3	4			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr15:82336360T>C	ENST00000329713.4	-	2	1286	c.851A>G	c.(850-852)tAc>tGc	p.Y284C	MEX3B_ENST00000558133.1_3'UTR|AC026956.1_ENST00000410589.1_RNA	NM_032246.4	NP_115622.2	Q6ZN04	MEX3B_HUMAN	mex-3 RNA binding family member B	284					protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|upper_aerodigestive_tract(1)	19						GTCGTTGCGGTAGCTAGAGAA	0.677																																					p.Y284C		Atlas-SNP	.											.	MEX3B	50	.	0			c.A851G						PASS	.						26	33	31					15																	82336360		2197	4294	6491	SO:0001583	missense	84206	exon2			TTGCGGTAGCTAG	AK131424	CCDS10319.1	15q25.1	2013-08-21	2013-08-21	2007-07-18	ENSG00000183496	ENSG00000183496		"RING-type (C3HC4) zinc fingers", "Mex-3 homologs"	25297	protein-coding gene	gene with protein product		611008	"ring finger and KH domain containing 3", "mex-3 homolog B (C. elegans)"	RKHD3		11230166, 17267406	Standard	NM_032246		Approved	DKFZp434J0617, RNF195	uc002bgq.2	Q6ZN04	OTTHUMG00000147356	ENST00000329713.4:c.851A>G	chr15.hg19:g.82336360T>C	ENSP00000329918:p.Tyr284Cys	45.0	0.0	.		25.0	10.0	.	NM_032246	Q4G0W1|Q8IVG2|Q9H0J0	Missense_Mutation	SNP	ENST00000329713.4	hg19	CCDS10319.1	.	.	.	.	.	.	.	.	.	.	T	16.81	3.224775	0.58668	.	.	ENSG00000183496	ENST00000329713	T	0.25414	1.8	4.53	3.38	0.38709	.	0.078776	0.53938	D	0.000055	T	0.41789	0.1174	M	0.65498	2.005	0.80722	D	1	D	0.71674	0.998	P	0.61328	0.887	T	0.25293	-1.0136	10	0.66056	D	0.02	-27.3162	8.9376	0.35708	0.2958:0.0:0.0:0.7042	.	284	Q6ZN04	MEX3B_HUMAN	C	284	ENSP00000329918:Y284C	ENSP00000329918:Y284C	Y	-	2	0	MEX3B	80123415	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.620000	0.61226	0.730000	0.32425	0.460000	0.39030	TAC	.	.	.	none		0.677	MEX3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304000.1	XM_290645		C	82336360	T	C	82336360	3	2	11	1	0	0	0	0	1	0	0	0	9517	1638	57	3	862	3	MEX3B	15	82336360	Missense_Mutation	SNP	T	TCGA-2Z-A9JG-01A-11D-A42J-10	38566418	82336360	20195032	57	883											
GTF3C1	2975	hgsc.bcm.edu	37	chr16	27523094	27523094	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtcgtaggtctgtgtgagcaTatcccgctcgaacacaatgt	9	11	11	10	3	1	1	0	1	1	0	4	2	2	1	1	1	2	3	1	1	4	2			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr16:27523094T>C	ENST00000356183.4	-	7	1117	c.1102A>G	c.(1102-1104)Atg>Gtg	p.M368V	GTF3C1_ENST00000561623.1_Missense_Mutation_p.M368V	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	368					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						TGTGTGAGCATATCCCGCTCG	0.502																																					p.M368V		Atlas-SNP	.											.	GTF3C1	210	.	0			c.A1102G						PASS	.						200	149	166					16																	27523094		2197	4300	6497	SO:0001583	missense	2975	exon7			TGAGCATATCCCG	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.1102A>G	chr16.hg19:g.27523094T>C	ENSP00000348510:p.Met368Val	79.0	0.0	.		103.0	55.0	.	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	hg19	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	T	18.17	3.565410	0.65651	.	.	ENSG00000077235	ENST00000356183;ENST00000388971	T	0.22336	1.96	5.64	5.64	0.86602	.	0.138042	0.64402	D	0.000005	T	0.34454	0.0898	L	0.29908	0.895	0.41036	D	0.985195	P;D	0.63046	0.539;0.992	B;D	0.74674	0.113;0.984	T	0.06041	-1.0849	10	0.41790	T	0.15	-5.9122	15.5262	0.75910	0.0:0.0:0.0:1.0	.	368;368	Q12789;Q12789-3	TF3C1_HUMAN;.	V	368;366	ENSP00000348510:M368V	ENSP00000348510:M368V	M	-	1	0	GTF3C1	27430595	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	4.439000	0.59968	2.146000	0.66826	0.528000	0.53228	ATG	.	.	.	none		0.502	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520		C	27523094	T	C	27523094	3	2	11	1	0	0	0	0	1	0	0	0	6879	1406	49	3	5351	3	GTF3C1	16	27523094	Missense_Mutation	SNP	T	TCGA-2Z-A9JG-01A-11D-A42J-10		27523094	62831659	58	884											
ZNF629	23361	hgsc.bcm.edu	37	chr16	30795034	30795034	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccgcagtcggggcacttgtaGggcttctcgccggtgtgcgt	3	10	16	12	5	1	0	0	0	1	0	3	0	1	0	2	4	1	4	2	4	1	3			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr16:30795034G>A	ENST00000262525.4	-	3	822	c.615C>T	c.(613-615)ccC>ccT	p.P205P		NM_001080417.1	NP_001073886.1	Q9UEG4	ZN629_HUMAN	zinc finger protein 629	205					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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)			GGCACTTGTAGGGCTTCTCGC	0.652																																					p.P205P		Atlas-SNP	.											.	ZNF629	44	.	0			c.C615T						PASS	.						55	58	57					16																	30795034		2197	4300	6497	SO:0001819	synonymous_variant	23361	exon3			CTTGTAGGGCTTC	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.615C>T	chr16.hg19:g.30795034G>A		132.0	0.0	.		60.0	39.0	.	NM_001080417	Q15938	Silent	SNP	ENST00000262525.4	hg19	CCDS45463.1																																																																																			.	.	.	none		0.652	ZNF629-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434291.1	NM_015309		A	30795034	G	A	30795034	2	1	11	1	0	0	0	0	0	0	0	1	18065	987	35	2		2	ZNF629	16	30795034	Silent	SNP	G	TCGA-2Z-A9JG-01A-11D-A42J-10	3271940	30795034	59559719	59	885											
IRX6	79190	hgsc.bcm.edu	37	chr16	55359021	55359021	+	Missense_Mutation	SNP	T	T	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	accatgtccttcccacacttTggacacccgtaccgcggcgc	7	8	8	18	4	0	0	0	0	0	0	2	1	2	1	5	2	1	1	5	2	1	3			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr16:55359021T>G	ENST00000290552.7	+	1	1350	c.18T>G	c.(16-18)ttT>ttG	p.F6L	RP11-26L20.3_ENST00000558730.2_RNA	NM_024335.2	NP_077311.2	P78412	IRX6_HUMAN	iroquois homeobox 6	6					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						TCCCACACTTTGGACACCCGT	0.652																																					p.F6L		Atlas-SNP	.											.	IRX6	66	.	0			c.T18G						PASS	.						57	54	55					16																	55359021		2198	4300	6498	SO:0001583	missense	79190	exon1			ACACTTTGGACAC	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.18T>G	chr16.hg19:g.55359021T>G	ENSP00000290552:p.Phe6Leu	96.0	0.0	.		50.0	25.0	.	NM_024335	B2RN06|Q7Z2K0	Missense_Mutation	SNP	ENST00000290552.7	hg19	CCDS32449.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.232797	0.79688	.	.	ENSG00000159387	ENST00000290552	D	0.92965	-3.14	5.02	-1.06	0.10002	.	0.385027	0.28606	N	0.014743	D	0.92260	0.7545	L	0.48935	1.535	0.45690	D	0.998605	D	0.71674	0.998	D	0.79784	0.993	D	0.88273	0.2931	10	0.45353	T	0.12	-11.0867	8.3205	0.32126	0.0:0.4967:0.1265:0.3768	.	6	P78412	IRX6_HUMAN	L	6	ENSP00000290552:F6L	ENSP00000290552:F6L	F	+	3	2	IRX6	53916522	0.995000	0.38212	0.992000	0.48379	0.986000	0.74619	0.251000	0.18257	-0.377000	0.07930	0.454000	0.30748	TTT	.	.	.	none		0.652	IRX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417445.4	NM_024335		G	55359021	T	G	55359021	3	3	11	1	0	0	0	0	1	0	0	0	7855	1809	63	5	20	5	IRX6	16	55359021	Missense_Mutation	SNP	T	TCGA-2Z-A9JG-01A-11D-A42J-10	24563987	55359021	34995732	60	886											
KARS	3735	hgsc.bcm.edu	37	chr16	75674216	75674216	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccattgaccttcagctgaTgaattgcttgactgcggatt	8	13	9	11	1	1	4	1	4	0	0	1	5	1	5	3	1	3	2	3	1	1	5			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr16:75674216T>C	ENST00000302445.3	-	3	293	c.254A>G	c.(253-255)cAt>cGt	p.H85R	KARS_ENST00000319410.5_Missense_Mutation_p.H113R|KARS_ENST00000568378.1_Intron	NM_005548.2	NP_005539.1	Q15046	SYK_HUMAN	lysyl-tRNA synthetase	85					cell death (GO:0008219)|diadenosine tetraphosphate biosynthetic process (GO:0015966)|gene expression (GO:0010467)|lysyl-tRNA aminoacylation (GO:0006430)|tRNA aminoacylation for protein translation (GO:0006418)|tRNA processing (GO:0008033)|viral process (GO:0016032)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|microtubule cytoskeleton (GO:0015630)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	amino acid binding (GO:0016597)|ATP binding (GO:0005524)|lysine-tRNA ligase activity (GO:0004824)|metal ion binding (GO:0046872)|tRNA binding (GO:0000049)			kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	18					L-Lysine(DB00123)	CTTCAGCTGATGAATTGCTTG	0.448																																					p.H113R		Atlas-SNP	.											.	KARS	77	.	0			c.A338G						PASS	.						228	222	224					16																	75674216		2198	4300	6498	SO:0001583	missense	3735	exon4			AGCTGATGAATTG	AF285758	CCDS10923.1, CCDS45532.1	16q23.1	2014-09-17			ENSG00000065427	ENSG00000065427	6.1.1.6	"Aminoacyl tRNA synthetases / Class II"	6215	protein-coding gene	gene with protein product	"lysine tRNA ligase"	601421	"deafness, autosomal recessive 89"	DFNB89		8812440, 9278442, 23768514	Standard	NM_005548		Approved	KARS2, KARS1	uc002fer.3	Q15046	OTTHUMG00000137609	ENST00000302445.3:c.254A>G	chr16.hg19:g.75674216T>C	ENSP00000303043:p.His85Arg	58.0	0.0	.		76.0	46.0	.	NM_001130089	A8MSK1|D3DUK4|O14946|Q96J25|Q9HB23	Missense_Mutation	SNP	ENST00000302445.3	hg19	CCDS10923.1	.	.	.	.	.	.	.	.	.	.	T	10.46	1.356197	0.24598	.	.	ENSG00000065427	ENST00000319410;ENST00000302445	T;T	0.62232	0.04;0.04	5.72	5.72	0.89469	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);	0.241798	0.49916	D	0.000134	T	0.51363	0.1670	L	0.34521	1.04	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.44528	-0.9322	10	0.25106	T	0.35	-17.2345	14.8506	0.70295	0.0:0.0:0.0:1.0	.	113;85	Q15046-2;Q15046	.;SYK_HUMAN	R	113;85	ENSP00000325448:H113R;ENSP00000303043:H85R	ENSP00000303043:H85R	H	-	2	0	KARS	74231717	1.000000	0.71417	0.996000	0.52242	0.123000	0.20343	4.811000	0.62606	2.189000	0.69895	0.533000	0.62120	CAT	.	.	.	none		0.448	KARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269023.1	NM_005548		C	75674216	T	C	75674216	3	2	11	1	0	0	0	0	1	0	0	0	7987	1464	51	3	1587	3	KARS	16	75674216	Missense_Mutation	SNP	T	TCGA-2Z-A9JG-01A-11D-A42J-10	20315195	75674216	14680537	61	887											
TMEM88	92162	hgsc.bcm.edu	37	chr17	7758984	7758984	+	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	cagccgcggcaaatccgggcCtcaccagggtcccaggccgt	7	4	13	17	4	1	0	1	0	0	0	3	0	3	0	6	4	1	1	6	4	1	0			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr17:7758984C>G	ENST00000301599.6	+	2	442	c.432C>G	c.(430-432)gcC>gcG	p.A144A	CYB5D1_ENST00000571846.1_5'Flank|CYB5D1_ENST00000332439.4_5'Flank|CYB5D1_ENST00000570446.1_5'Flank|TMEM88_ENST00000574668.1_Intron|LSMD1_ENST00000570555.1_5'Flank	NM_203411.1	NP_981956.1	Q6PEY1	TMM88_HUMAN	transmembrane protein 88	144					multicellular organismal development (GO:0007275)|Wnt signaling pathway (GO:0016055)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				lung(1)	1		all_cancers(10;0.00528)|Prostate(122;0.202)				AAATCCGGGCCTCACCAGGGT	0.667																																					p.A144A		Atlas-SNP	.											.	TMEM88	6	.	0			c.C432G						PASS	.						8	9	9					17																	7758984		2138	4187	6325	SO:0001819	synonymous_variant	92162	exon2			CCGGGCCTCACCA	BC057812	CCDS11121.1	17p13.1	2005-12-13				ENSG00000167874			32371	protein-coding gene	gene with protein product							Standard	NM_203411		Approved	MGC71744, FLJ20025	uc002giy.3	Q6PEY1		ENST00000301599.6:c.432C>G	chr17.hg19:g.7758984C>G		87.0	0.0	.		36.0	8.0	.	NM_203411		Silent	SNP	ENST00000301599.6	hg19	CCDS11121.1																																																																																			.	.	.	none		0.667	TMEM88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440252.1	NM_203411		G	7758984	C	G	7758984	2	3	11	1	0	0	0	0	0	0	0	1	16224	668	24	4		4	TMEM88	17	7758984	Silent	SNP	C	TCGA-2Z-A9JG-01A-11D-A42J-10		7758984	73436226	62	888											
AOC2	314	hgsc.bcm.edu	37	chr17	41002294	41002294	+	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	ctgggctctgcagcatcaatCctgtggcctgcctccccgac	5	9	10	17	1	2	0	1	0	1	0	4	1	4	0	5	2	3	3	5	2	1	0			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr17:41002294C>T	ENST00000253799.3	+	4	2227	c.2200C>T	c.(2200-2202)Cct>Tct	p.P734S	AOC3_ENST00000308423.2_5'Flank|AOC2_ENST00000452774.2_Missense_Mutation_p.P707S	NM_009590.2	NP_033720.2	O75106	AOC2_HUMAN	amine oxidase, copper containing 2 (retina-specific)	734					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)		CAGCATCAATCCTGTGGCCTG	0.597																																					p.P734S		Atlas-SNP	.											.	AOC2	61	.	0			c.C2200T						PASS	.						164	172	170					17																	41002294		2203	4300	6503	SO:0001583	missense	314	exon4			ATCAATCCTGTGG	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.2200C>T	chr17.hg19:g.41002294C>T	ENSP00000253799:p.Pro734Ser	84.0	0.0	.		76.0	43.0	.	NM_009590	A5PKW2|O00120|O75105|Q4TTW5|Q9UNY0	Missense_Mutation	SNP	ENST00000253799.3	hg19	CCDS11443.1	.	.	.	.	.	.	.	.	.	.	C	6.560	0.471616	0.12461	.	.	ENSG00000131480	ENST00000253799;ENST00000452774	T;T	0.03468	3.92;3.92	5.19	4.23	0.50019	Copper amine oxidase, C-terminal (1);	0.669731	0.15067	N	0.282419	T	0.03136	0.0092	N	0.19112	0.55	0.38233	D	0.941088	B;B	0.11235	0.002;0.004	B;B	0.18871	0.005;0.023	T	0.35699	-0.9778	10	0.09338	T	0.73	-35.8049	13.9375	0.64034	0.0:0.9263:0.0:0.0737	.	734;707	O75106;O75106-2	AOC2_HUMAN;.	S	734;707	ENSP00000253799:P734S;ENSP00000406134:P707S	ENSP00000253799:P734S	P	+	1	0	AOC2	38255820	0.811000	0.29063	0.992000	0.48379	0.319000	0.28217	2.760000	0.47581	1.195000	0.43115	-0.254000	0.11334	CCT	.	.	.	none		0.597	AOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452442.1	NM_009590, NM_001158		T	41002294	C	T	41002294	3	4	11	1	0	0	0	0	1	0	0	0	727	855	30	2	2214	2	AOC2	17	41002294	Missense_Mutation	SNP	C	TCGA-2Z-A9JG-01A-11D-A42J-10	33243310	41002294	40192916	63	889											
FZD2	2535	hgsc.bcm.edu	37	chr17	42636200	42636200	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcctgggccgtgccggccGtcaagaccatcaccatcctg	6	6	11	18	4	2	1	2	0	0	1	3	1	3	1	8	2	1	0	8	2	1	0			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr17:42636200G>A	ENST00000315323.3	+	1	1276	c.1144G>A	c.(1144-1146)Gtc>Atc	p.V382I		NM_001466.3	NP_001457.1	Q14332	FZD2_HUMAN	frizzled class receptor 2	382					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)		CGTGCCGGCCGTCAAGACCAT	0.672																																					p.V382I		Atlas-SNP	.											.	FZD2	81	.	0			c.G1144A						PASS	.						68	68	68					17																	42636200		2203	4299	6502	SO:0001583	missense	2535	exon1			CCGGCCGTCAAGA	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.1144G>A	chr17.hg19:g.42636200G>A	ENSP00000323901:p.Val382Ile	80.0	0.0	.		48.0	13.0	.	NM_001466	Q0VG82	Missense_Mutation	SNP	ENST00000315323.3	hg19	CCDS11484.1	.	.	.	.	.	.	.	.	.	.	g	10.67	1.416262	0.25552	.	.	ENSG00000180340	ENST00000541149;ENST00000315323	D	0.83755	-1.76	5.0	5.0	0.66597	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.74238	0.3690	N	0.21373	0.66	0.47584	D	0.999468	B	0.24368	0.102	B	0.20955	0.032	T	0.69680	-0.5080	10	0.31617	T	0.26	.	17.9002	0.88901	0.0:0.0:1.0:0.0	.	382	Q14332	FZD2_HUMAN	I	458;382	ENSP00000323901:V382I	ENSP00000323901:V382I	V	+	1	0	FZD2	39991726	0.999000	0.42202	0.998000	0.56505	0.978000	0.69477	2.822000	0.48073	2.291000	0.77112	0.561000	0.74099	GTC	.	.	.	none		0.672	FZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457806.1	NM_001466		A	42636200	G	A	42636200	3	1	11	1	0	0	0	0	1	0	0	0	6137	1145	40	1	1146	1	FZD2	17	42636200	Missense_Mutation	SNP	G	TCGA-2Z-A9JG-01A-11D-A42J-10	1633906	42636200	38559010	64	890											
CCDC45	90799	hgsc.bcm.edu	37	chr17	62518864	62518864	+	Frame_Shift_Del	DEL	G	G	-																															ttccaaatgctaggaagctaGgggagcctatccgagcagct																										TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr17:62518864delG	ENST00000556440.2	+	8	1270	c.760delG	c.(760-762)gggfs	p.G254fs	CEP95_ENST00000553412.1_Frame_Shift_Del_p.G90fs	NM_138363.1	NP_612372.1	Q96GE4	CEP95_HUMAN	centrosomal protein 95kDa	254						centrosome (GO:0005813)|cytoplasm (GO:0005737)|spindle pole (GO:0000922)				endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)	13						TAGGAAGCTAGGGGAGCCTAT	0.443																																					p.L253fs		Atlas-Indel,Pindel	.											.	CEP95	103	.	0			c.759delA						PASS	.						88	87	87					17																	62518864		1892	4115	6007	SO:0001589	frameshift_variant	90799	exon8			.	AL832822	CCDS45763.1	17q24.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000258890	ENSG00000258890			25141	protein-coding gene	gene with protein product			"coiled-coil domain containing 45"	CCDC45		21399614	Standard	NM_138363		Approved	DKFZp667E1824	uc002jem.3	Q96GE4	OTTHUMG00000179174	ENST00000556440.2:c.760delG	chr17.hg19:g.62518864delG	ENSP00000450461:p.Gly254fs	89.0	0.0	0		141.0	75.0	0.531915	NM_138363	B4DMD2|Q96M81	Frame_Shift_Del	DEL	ENST00000556440.2	hg19	CCDS45763.1																																																																																			.	.	.	none		0.443	CEP95-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445100.2	NM_138363		-	62518864	G	-	62518864	7	5	11	1	0	1	0	1	0	0	0	0	2818	1000	35	0	790	0	CCDC45	17	62518864	Frame_Shift_Del	DEL	G	TCGA-2Z-A9JG-01A-11D-A42J-10	19882664	62518864	18676346	65	891											
USH1G	124590	hgsc.bcm.edu	37	chr17	72919094	72919094	+	Frame_Shift_Del	DEL	C	C	-																															ccatcctcgtcgggggcattCagctcctttcgggtggcctc																										TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr17:72919094delC	ENST00000319642.1	-	1	257	c.75delG	c.(73-75)ctgfs	p.L25fs	OTOP2_ENST00000580223.1_5'Flank|OTOP2_ENST00000331427.4_5'Flank	NM_001282489.1|NM_173477.2	NP_001269418.1|NP_775748.2	Q495M9	USH1G_HUMAN	Usher syndrome 1G (autosomal recessive)	25					equilibrioception (GO:0050957)|inner ear morphogenesis (GO:0042472)|inner ear receptor cell differentiation (GO:0060113)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	spectrin binding (GO:0030507)		HN1/USH1G(2)	endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(1)|skin(3)	14	all_lung(278;0.172)|Lung NSC(278;0.207)					CGGGGGCATTCAGCTCCTTTC	0.667																																					p.N26fs		Atlas-INDEL	.											.	USH1G	40	.	0			c.76delA						PASS	.						31	24	27					17																	72919094		2191	4292	6483	SO:0001589	frameshift_variant	124590	exon1			.	AK091243	CCDS32725.1	17q25.1	2013-01-10			ENSG00000182040	ENSG00000182040		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	16356	protein-coding gene	gene with protein product		607696				12588794	Standard	NM_001282489		Approved	Sans, FLJ33924, ANKS4A	uc002jme.1	Q495M9	OTTHUMG00000178864	ENST00000319642.1:c.75delG	chr17.hg19:g.72919094delC	ENSP00000320076:p.Leu25fs	192.0	0.0	0		123.0	41.0	0.333333	NM_173477	Q8N251	Frame_Shift_Del	DEL	ENST00000319642.1	hg19	CCDS32725.1																																																																																			.	.	.	none		0.667	USH1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443676.1	NM_173477		-	72919094	C	-	72919094	7	5	11	1	0	1	0	1	0	0	0	0	17047	813	29	0	1322	0	USH1G	17	72919094	Frame_Shift_Del	DEL	C	TCGA-2Z-A9JG-01A-11D-A42J-10	10400230	72919094	8276116	66	892											
MYL12A	10627	hgsc.bcm.edu	37	chr18	3254019	3254019	+	Missense_Mutation	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	tgaagatgtcatcagaaatgCctttgcttgctttgatgaag	11	14	10	6	0	2	5	2	3	0	2	2	5	2	5	1	0	3	2	1	0	3	3			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr18:3254019C>T	ENST00000217652.3	+	3	709	c.314C>T	c.(313-315)gCc>gTc	p.A105V	MYL12A_ENST00000536605.1_Missense_Mutation_p.A105V|RP13-270P17.1_ENST00000578800.1_RNA|RP13-270P17.1_ENST00000581905.1_RNA|MYL12A_ENST00000580887.1_Missense_Mutation_p.A111V|MYL12A_ENST00000578611.1_Missense_Mutation_p.A105V|MYL12A_ENST00000579226.1_Missense_Mutation_p.A105V	NM_006471.2	NP_006462.1	P19105	ML12A_HUMAN	myosin, light chain 12A, regulatory, non-sarcomeric	105	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				platelet aggregation (GO:0070527)|protein targeting to plasma membrane (GO:0072661)|regulation of cell shape (GO:0008360)	extracellular vesicular exosome (GO:0070062)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)			NS(1)|kidney(2)|large_intestine(2)	5						ATCAGAAATGCCTTTGCTTGC	0.368																																					p.A105V		Atlas-SNP	.											.	MYL12A	12	.	0			c.C314T						PASS	.						91	83	86					18																	3254019		2203	4300	6503	SO:0001583	missense	10627	exon3			GAAATGCCTTTGC	X54304	CCDS11830.1	18p11.31	2013-01-10	2002-08-29		ENSG00000101608	ENSG00000101608		"Myosins / Light chain", "EF-hand domain containing"	16701	protein-coding gene	gene with protein product	"myosin regulatory light chain 3"		"myosin, light polypeptide, regulatory, non-sarcomeric (20kD)"			2216787	Standard	NM_006471		Approved	MLCB, MYL2B, MRLC3, MRCL3	uc002klr.3	P19105	OTTHUMG00000131509	ENST00000217652.3:c.314C>T	chr18.hg19:g.3254019C>T	ENSP00000217652:p.Ala105Val	223.0	0.0	.		199.0	73.0	.	NM_006471	Q53X45	Missense_Mutation	SNP	ENST00000217652.3	hg19	CCDS11830.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.564221	0.86335	.	.	ENSG00000101608	ENST00000217652;ENST00000536605	D;D	0.81996	-1.56;-1.56	5.42	5.42	0.78866	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.88040	0.6330	M	0.90705	3.14	0.80722	D	1	B;B	0.29886	0.26;0.26	B;B	0.33295	0.161;0.161	D	0.87864	0.2666	10	0.72032	D	0.01	.	19.4096	0.94665	0.0:1.0:0.0:0.0	.	105;105	Q53X45;P19105	.;ML12A_HUMAN	V	105	ENSP00000217652:A105V;ENSP00000441231:A105V	ENSP00000217652:A105V	A	+	2	0	MYL12A	3244019	1.000000	0.71417	0.994000	0.49952	0.985000	0.73830	7.651000	0.83577	2.817000	0.96982	0.563000	0.77884	GCC	.	.	.	none		0.368	MYL12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254364.2	NM_006471		T	3254019	C	T	3254019	3	4	11	1	0	0	0	0	1	0	0	0	10052	739	26	2	320	2	MYL12A	18	3254019	Missense_Mutation	SNP	C	TCGA-2Z-A9JG-01A-11D-A42J-10		3254019	74823229	67	893											
LAMA1	284217	hgsc.bcm.edu	37	chr18	7016662	7016662	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggcctgagtccagcccataAtagccatgctgtttcaccaa	10	10	8	13	0	1	1	1	1	0	0	2	1	2	1	5	1	3	2	5	1	3	3			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr18:7016662A>G	ENST00000389658.3	-	21	2910	c.2817T>C	c.(2815-2817)taT>taC	p.Y939Y		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	939	Laminin EGF-like 9. {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)				CCAGCCCATAATAGCCATGCT	0.517																																					p.Y939Y		Atlas-SNP	.											.	LAMA1	458	.	0			c.T2817C						PASS	.						35	28	30					18																	7016662		2203	4300	6503	SO:0001819	synonymous_variant	284217	exon21			CCCATAATAGCCA	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.2817T>C	chr18.hg19:g.7016662A>G		21.0	0.0	.		42.0	14.0	.	NM_005559		Silent	SNP	ENST00000389658.3	hg19	CCDS32787.1																																																																																			.	.	.	none		0.517	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		G	7016662	A	G	7016662	2	3	11	1	0	0	0	0	0	0	0	1	8612	108	4	3		3	LAMA1	18	7016662	Silent	SNP	A	TCGA-2Z-A9JG-01A-11D-A42J-10	3762643	7016662	71060586	68	894											
ROCK1	6093	hgsc.bcm.edu	37	chr18	18600173	18600174	+	Frame_Shift_Del	DEL	TA	TA	-																															atgcagctgttcttccagctTatagattgttttttgcaaac																										TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr18:18600173_18600174delTA	ENST00000399799.2	-	12	2239_2240	c.1299_1300delTA	c.(1297-1302)tataagfs	p.YK433fs		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	433	Interaction with FHOD1.				actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					TCTTCCAGCTTATAGATTGTTT	0.267																																					p.434_434del		Atlas-INDEL	.											.	ROCK1	162	.	0			c.1300_1301del						PASS	.																																			SO:0001589	frameshift_variant	6093	exon12			.		CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.1299_1300delTA	chr18.hg19:g.18600175_18600176delTA	ENSP00000382697:p.Tyr433fs	40.0	0.0	0		20.0	10.0	0.5	NM_005406	B0YJ91|Q2KHM4|Q59GZ4	Frame_Shift_Del	DEL	ENST00000399799.2	hg19	CCDS11870.2																																																																																			.	.	.	none		0.267	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2	NM_005406		-	18600174	TA	-	18600173	7	5	11	1	0	1	0	1	0	0	0	0	13530	1763	61	0	2852	0	ROCK1	18	18600173	Frame_Shift_Del	DEL	TA	TCGA-2Z-A9JG-01A-11D-A42J-10	11583511	18600173	59477075	69	895											
DUS3L	56931	hgsc.bcm.edu	37	chr19	5786483	5786483	+	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	tccctgggcacttaccgggcAatcatgatcccggtgacacc	8	8	10	15	2	1	2	1	2	0	0	3	2	3	2	4	3	1	2	4	3	2	1			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr19:5786483A>T	ENST00000309061.7	-	10	1653	c.1557T>A	c.(1555-1557)atT>atA	p.I519I	PRR22_ENST00000419421.2_5'Flank|CTB-54O9.9_ENST00000586012.1_5'Flank|DUS3L_ENST00000590681.1_5'Flank|DUS3L_ENST00000320699.8_Silent_p.I277I	NM_020175.2	NP_064560.2	Q96G46	DUS3L_HUMAN	dihydrouridine synthase 3-like (S. cerevisiae)	519							flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA dihydrouridine synthase activity (GO:0017150)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|skin(2)	14						CTTACCGGGCAATCATGATCC	0.582																																					p.I519I		Atlas-SNP	.											.	DUS3L	42	.	0			c.T1557A						PASS	.						109	77	88					19																	5786483		2203	4299	6502	SO:0001819	synonymous_variant	56931	exon10			CCGGGCAATCATG		CCDS32880.1, CCDS54202.1	19p13.3	2014-02-12			ENSG00000141994	ENSG00000141994			26920	protein-coding gene	gene with protein product						12477932	Standard	NM_020175		Approved	DUS3, FLJ13896	uc002mdc.3	Q96G46	OTTHUMG00000162311	ENST00000309061.7:c.1557T>A	chr19.hg19:g.5786483A>T		74.0	0.0	.		28.0	12.0	.	NM_020175	Q96HM5|Q9BSU4|Q9H877|Q9NPR1	Silent	SNP	ENST00000309061.7	hg19	CCDS32880.1																																																																																			.	.	.	none		0.582	DUS3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451870.2	NM_020175		T	5786483	A	T	5786483	2	4	11	1	0	0	0	0	0	0	0	1	4809	126	5	5		5	DUS3L	19	5786483	Silent	SNP	A	TCGA-2Z-A9JG-01A-11D-A42J-10		5786483	53342500	70	896											
ZNF565	147929	hgsc.bcm.edu	37	chr19	36674230	36674230	+	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	cacccgtgtgaattctctgaTgctgaacaaggtgtgaggca	10	10	12	9	1	1	4	0	4	1	0	2	4	1	4	1	2	2	2	1	2	3	1			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr19:36674230T>A	ENST00000355114.5	-	5	1484	c.758A>T	c.(757-759)cAt>cTt	p.H253L	ZNF565_ENST00000392173.2_Missense_Mutation_p.H213L|ZNF565_ENST00000304116.5_Missense_Mutation_p.H213L			Q8N9K5	ZN565_HUMAN	zinc finger protein 565	253					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(4)|lung(4)|ovary(1)|skin(2)	11	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.206)			AATTCTCTGATGCTGAACAAG	0.443																																					p.H213L		Atlas-SNP	.											.	ZNF565	46	.	0			c.A638T						PASS	.						74	67	69					19																	36674230		2203	4300	6503	SO:0001583	missense	147929	exon5			CTCTGATGCTGAA	AK094310	CCDS12491.1	19q13.12	2013-09-20			ENSG00000196357	ENSG00000196357		"Zinc fingers, C2H2-type", "-"	26726	protein-coding gene	gene with protein product		614275					Standard	NM_001042474		Approved	FLJ36991	uc002odn.3	Q8N9K5	OTTHUMG00000180508	ENST00000355114.5:c.758A>T	chr19.hg19:g.36674230T>A	ENSP00000347234:p.His253Leu	58.0	0.0	.		56.0	22.0	.	NM_001042474	B3KQ35|Q6NUS2	Missense_Mutation	SNP	ENST00000355114.5	hg19		.	.	.	.	.	.	.	.	.	.	t	19.57	3.852244	0.71719	.	.	ENSG00000196357	ENST00000392173;ENST00000304116;ENST00000355114	D;D;D	0.86865	-2.18;-2.18;-2.18	4.33	3.22	0.36961	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.177862	0.27473	N	0.019217	D	0.94689	0.8287	H	0.97682	4.055	0.34458	D	0.701394	D	0.89917	1.0	D	0.66602	0.945	D	0.96372	0.9274	10	0.87932	D	0	.	9.2445	0.37518	0.0:0.0:0.181:0.819	.	213	Q8N9K5	ZN565_HUMAN	L	213;213;253	ENSP00000376013:H213L;ENSP00000306869:H213L;ENSP00000347234:H253L	ENSP00000306869:H213L	H	-	2	0	ZNF565	41366070	1.000000	0.71417	0.999000	0.59377	0.972000	0.66771	3.769000	0.55303	1.955000	0.56771	0.456000	0.33151	CAT	.	.	.	none		0.443	ZNF565-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000451697.1	NM_152477		A	36674230	T	A	36674230	3	1	11	1	0	0	0	0	1	0	0	0	18008	1464	51	5	865	5	ZNF565	19	36674230	Missense_Mutation	SNP	T	TCGA-2Z-A9JG-01A-11D-A42J-10	30887747	36674230	22454753	71	897											
ZNF540	163255	hgsc.bcm.edu	37	chr19	38102608	38102609	+	Frame_Shift_Del	DEL	AA	AA	-																															aaagatctatcagtcaaaagAaaatcgtctctaaaaaaatg																										TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr19:38102608_38102609delAA	ENST00000592533.1	+	5	759_760	c.427_428delAA	c.(427-429)aaafs	p.K143fs	ZNF540_ENST00000343599.5_Frame_Shift_Del_p.K143fs|ZNF540_ENST00000586792.1_3'UTR|ZNF540_ENST00000316433.4_Frame_Shift_Del_p.K143fs|ZNF540_ENST00000589117.1_Frame_Shift_Del_p.K111fs	NM_152606.4	NP_689819.1	Q8NDQ6	ZN540_HUMAN	zinc finger protein 540	143					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)			CAGTCAAAAGAAAATCGTCTCT	0.366																																					p.142_143del		Atlas-Indel,Pindel	.											.	ZNF540	75	.	0			c.426_427del						PASS	.																																			SO:0001589	frameshift_variant	163255	exon5			.	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.427_428delAA	chr19.hg19:g.38102610_38102611delAA	ENSP00000466274:p.Lys143fs	127.0	0.0	0		137.0	55.0	0.40146	NM_152606	A0AVS5|A8K371|Q05D58|Q3LIC5|Q6ZN36|Q7Z3C8|Q86T31	Frame_Shift_Del	DEL	ENST00000592533.1	hg19	CCDS12506.1																																																																																			.	.	.	none		0.366	ZNF540-009	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459481.1	NM_152606		-	38102609	AA	-	38102608	7	5	11	1	0	1	0	1	0	0	0	0	17987	247	9	0	441	0	ZNF540	19	38102608	Frame_Shift_Del	DEL	AA	TCGA-2Z-A9JG-01A-11D-A42J-10	1428378	38102608	21026375	72	898											
MYH14	79784	hgsc.bcm.edu	37	chr19	50747513	50747513	+	Missense_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	ccccagccatgctgcggatgGtctcagcagttctccagttt	6	11	10	14	1	2	0	1	0	2	0	4	1	2	1	4	2	4	4	4	2	0	2			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr19:50747513G>A	ENST00000596571.1	+	9	1105	c.1105G>A	c.(1105-1107)Gtc>Atc	p.V369I	MYH14_ENST00000376970.2_Missense_Mutation_p.V369I|MYH14_ENST00000440075.2_Missense_Mutation_p.V377I|MYH14_ENST00000262269.8_Missense_Mutation_p.V377I|MYH14_ENST00000601313.1_Missense_Mutation_p.V377I|MYH14_ENST00000425460.1_Missense_Mutation_p.V377I|MYH14_ENST00000598205.1_Missense_Mutation_p.V377I			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	369	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)		GCTGCGGATGGTCTCAGCAGT	0.552																																					p.V377I		Atlas-SNP	.											.	MYH14	261	.	0			c.G1129A						PASS	.						84	89	87					19																	50747513		2125	4242	6367	SO:0001583	missense	79784	exon11			CGGATGGTCTCAG	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.1105G>A	chr19.hg19:g.50747513G>A	ENSP00000472819:p.Val369Ile	125.0	0.0	.		66.0	30.0	.	NM_001077186	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	hg19	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	G	8.469	0.857136	0.17106	.	.	ENSG00000105357	ENST00000301415;ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	D;D;D;D	0.88509	-2.39;-2.39;-2.39;-2.39	3.42	2.37	0.29283	Myosin head, motor domain (2);	.	.	.	.	D	0.82829	0.5122	L	0.42632	1.34	0.49582	D	0.999809	P;B;B	0.37864	0.61;0.198;0.063	B;B;B	0.36666	0.23;0.056;0.028	T	0.79492	-0.1781	9	0.41790	T	0.15	.	9.1808	0.37141	0.1121:0.0:0.8879:0.0	.	377;369;377	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	I	369;377;369;377;369;377	ENSP00000406273:V377I;ENSP00000366169:V369I;ENSP00000407879:V377I;ENSP00000262269:V377I	ENSP00000262269:V377I	V	+	1	0	MYH14	55439325	1.000000	0.71417	0.354000	0.25760	0.137000	0.21094	2.140000	0.42159	1.017000	0.39495	0.462000	0.41574	GTC	.	.	.	none		0.552	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		A	50747513	G	A	50747513	3	1	11	1	0	0	0	0	1	0	0	0	10040	1261	44	2	1167	2	MYH14	19	50747513	Missense_Mutation	SNP	G	TCGA-2Z-A9JG-01A-11D-A42J-10	12644905	50747513	8381470	73	899											
PTPRT	11122	hgsc.bcm.edu	37	chr20	40713469	40713469	+	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	actggaggtgctggactataCgataaccatcctgtggctga	10	10	12	9	1	0	1	0	1	0	0	1	4	1	3	2	4	3	2	2	4	3	3	rs528913627		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr20:40713469C>T	ENST00000373187.1	-	29	3988	c.3989G>A	c.(3988-3990)cGt>cAt	p.R1330H	PTPRT_ENST00000373193.3_Missense_Mutation_p.R1333H|PTPRT_ENST00000373184.1_Missense_Mutation_p.R1340H|PTPRT_ENST00000373190.1_Missense_Mutation_p.R1329H|PTPRT_ENST00000373198.4_Missense_Mutation_p.R1349H|PTPRT_ENST00000356100.2_Missense_Mutation_p.R1339H|PTPRT_ENST00000373201.1_Missense_Mutation_p.R1320H			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	1330	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)				CTGGACTATACGATAACCATC	0.587													C|||	1	0.000199681	0	0	5008	,	,		20626	0		0.001	False		,,,				2504	0				p.R1349H		Atlas-SNP	.											.	PTPRT	372	.	0			c.G4046A						PASS	.						61	66	65					20																	40713469		2077	4194	6271	SO:0001583	missense	11122	exon30			ACTATACGATAAC	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.3989G>A	chr20.hg19:g.40713469C>T	ENSP00000362283:p.Arg1330His	39.0	0.0	.		109.0	43.0	.	NM_133170	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	ENST00000373187.1	hg19	CCDS42874.1	.	.	.	.	.	.	.	.	.	.	C	35	5.441039	0.96168	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	T;T;T;T;T;T;T	0.18174	2.23;2.23;2.23;2.23;2.23;2.23;2.23	5.55	5.55	0.83447	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	T	0.37517	0.1006	L	0.49640	1.575	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.66716	0.944;0.946	T	0.00800	-1.1561	10	0.46703	T	0.11	.	19.6982	0.96039	0.0:1.0:0.0:0.0	.	1352;1330	O14522-1;O14522	.;PTPRT_HUMAN	H	1329;1330;1333;1339;1352;1340;1320	ENSP00000362286:R1329H;ENSP00000362283:R1330H;ENSP00000362289:R1333H;ENSP00000348408:R1339H;ENSP00000362294:R1352H;ENSP00000362280:R1340H;ENSP00000362297:R1320H	ENSP00000348408:R1339H	R	-	2	0	PTPRT	40146883	0.995000	0.38212	0.990000	0.47175	0.981000	0.71138	3.067000	0.50010	2.894000	0.99253	0.655000	0.94253	CGT	.	.	.	none		0.587	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			T	40713469	C	T	40713469	3	4	11	1	0	0	0	0	1	0	0	0	12825	536	19	1	348	1	PTPRT	20	40713469	Missense_Mutation	SNP	C	TCGA-2Z-A9JG-01A-11D-A42J-10		40713469	22312051	74	900											
PARD6B	84612	hgsc.bcm.edu	37	chr20	49354557	49354557	+	Missense_Mutation	SNP	A	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	acctataaataatgatgataAttatcacaaagctgtttcaa	18	13	4	6	0	2	2	2	2	0	0	2	2	2	2	1	0	1	2	1	0	8	6			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr20:49354557A>C	ENST00000371610.2	+	2	473	c.230A>C	c.(229-231)aAt>aCt	p.N77T	PARD6B_ENST00000396039.1_Missense_Mutation_p.N77T	NM_032521.2	NP_115910.1	Q9BYG5	PAR6B_HUMAN	par-6 family cell polarity regulator beta	77	OPR.				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						AATGATGATAATTATCACAAA	0.338																																					p.N77T		Atlas-SNP	.											.	PARD6B	31	.	0			c.A230C						PASS	.						82	79	80					20																	49354557		2203	4300	6503	SO:0001583	missense	84612	exon2			ATGATAATTATCA	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.230A>C	chr20.hg19:g.49354557A>C	ENSP00000360672:p.Asn77Thr	132.0	0.0	.		244.0	87.0	.	NM_032521	A2A2A7|Q9Y510	Missense_Mutation	SNP	ENST00000371610.2	hg19	CCDS33485.1	.	.	.	.	.	.	.	.	.	.	A	19.74	3.883714	0.72410	.	.	ENSG00000124171	ENST00000371610;ENST00000396039	T;T	0.23552	1.9;1.9	6.17	5.08	0.68730	Phox/Bem1p (2);	0.000000	0.85682	D	0.000000	T	0.52757	0.1754	M	0.83603	2.65	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.57849	-0.7740	10	0.87932	D	0	-43.1371	11.3759	0.49728	0.9302:0.0:0.0698:0.0	.	77	Q9BYG5	PAR6B_HUMAN	T	77	ENSP00000360672:N77T;ENSP00000379354:N77T	ENSP00000360672:N77T	N	+	2	0	PARD6B	48787964	1.000000	0.71417	0.830000	0.32933	0.794000	0.44872	8.920000	0.92779	1.160000	0.42584	0.533000	0.62120	AAT	.	.	.	none		0.338	PARD6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079697.2	NM_032521		C	49354557	A	C	49354557	3	2	11	1	0	0	0	0	1	0	0	0	11453	101	4	5	236	5	PARD6B	20	49354557	Missense_Mutation	SNP	A	TCGA-2Z-A9JG-01A-11D-A42J-10	8641088	49354557	13670963	75	901											
KRTAP27-1	643812	hgsc.bcm.edu	37	chr21	31709386	31709386	+	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	cttactaggcaattgagaacCaccagtaacacagcaagttg	15	8	8	10	0	0	1	0	1	0	1	0	2	0	1	2	1	4	4	2	1	6	5			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr21:31709386C>A	ENST00000382835.2	-	1	626	c.601G>T	c.(601-603)Ggt>Tgt	p.G201C		NM_001077711.1	NP_001071179.1	Q3LI81	KR271_HUMAN	keratin associated protein 27-1	201						intermediate filament (GO:0005882)				endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(1)	18						AATTGAGAACCACCAGTAACA	0.408																																					p.G201C		Atlas-SNP	.											.	KRTAP27-1	53	.	0			c.G601T						PASS	.						66	64	65					21																	31709386		2203	4300	6503	SO:0001583	missense	643812	exon1			GAGAACCACCAGT	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.601G>T	chr21.hg19:g.31709386C>A	ENSP00000372286:p.Gly201Cys	59.0	0.0	.		166.0	35.0	.	NM_001077711		Missense_Mutation	SNP	ENST00000382835.2	hg19	CCDS33532.1	.	.	.	.	.	.	.	.	.	.	C	15.08	2.727069	0.48833	.	.	ENSG00000206107	ENST00000382835	T	0.60920	0.15	4.13	4.13	0.48395	.	0.307763	0.20789	U	0.085656	T	0.72195	0.3430	M	0.65975	2.015	0.40737	D	0.982795	D	0.89917	1.0	D	0.97110	1.0	T	0.75172	-0.3411	10	0.87932	D	0	-10.8309	12.1805	0.54210	0.0:1.0:0.0:0.0	.	201	Q3LI81	KR271_HUMAN	C	201	ENSP00000372286:G201C	ENSP00000372286:G201C	G	-	1	0	KRTAP27-1	30631257	1.000000	0.71417	0.999000	0.59377	0.511000	0.34104	2.904000	0.48719	2.586000	0.87340	0.484000	0.47621	GGT	.	.	.	none		0.408	KRTAP27-1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132470.3	NM_001077711		A	31709386	C	A	31709386	3	1	11	1	0	0	0	0	1	0	0	0	8551	594	21	4	26	4	KRTAP27-1	21	31709386	Missense_Mutation	SNP	C	TCGA-2Z-A9JG-01A-11D-A42J-10		31709386	16420509	76	902											
BCL2L13	23786	hgsc.bcm.edu	37	chr22	18138483	18138483	+	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	tcaccagccaattcaatggcGtcctcttctactgtgcctct	7	13	6	15	1	5	0	2	0	3	0	6	0	6	0	4	1	3	0	4	1	3	3	rs144712899	byFrequency	TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr22:18138483G>C	ENST00000317582.5	+	2	353	c.6G>C	c.(4-6)gcG>gcC	p.A2A	BCL2L13_ENST00000355028.3_Silent_p.A2A|BCL2L13_ENST00000493680.1_Silent_p.A2A|BCL2L13_ENST00000543133.1_5'UTR|BCL2L13_ENST00000337612.5_5'UTR|BCL2L13_ENST00000538149.1_5'UTR|BCL2L13_ENST00000399782.1_Silent_p.A2A|BCL2L13_ENST00000418951.2_Silent_p.A2A	NM_015367.3	NP_056182.2	Q9BXK5	B2L13_HUMAN	BCL2-like 13 (apoptosis facilitator)	2					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			breast(2)|central_nervous_system(1)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|skin(3)|urinary_tract(2)	15		all_epithelial(15;0.123)		Lung(27;0.199)		ATTCAATGGCGTCCTCTTCTA	0.393																																					p.A2A		Atlas-SNP	.											BCL2L13,NS,adenocarcinoma,0,2	BCL2L13	27	.	0			c.G6C						PASS	.						131	119	123					22																	18138483		2203	4300	6503	SO:0001819	synonymous_variant	23786	exon2			AATGGCGTCCTCT	AF146568	CCDS13746.1, CCDS59447.1, CCDS59448.1, CCDS74810.1, CCDS74811.1, CCDS74812.1, CCDS74813.1, CCDS74814.1	22q11	2014-03-07			ENSG00000099968	ENSG00000099968			17164	protein-coding gene	gene with protein product						11262395, 11381032	Standard	NM_015367		Approved	MIL1, BCL-RAMBO	uc002zmw.4	Q9BXK5	OTTHUMG00000150088	ENST00000317582.5:c.6G>C	chr22.hg19:g.18138483G>C		69.0	1.0	.		58.0	26.0	.	NM_001270732	B3KPE7|Q96B37|Q96IB7|Q9BY01|Q9HC05|Q9UFE0|Q9UKN3	Silent	SNP	ENST00000317582.5	hg19	CCDS13746.1																																																																																			.	G|1.000;A|0.000	.	alt		0.393	BCL2L13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316184.1	NM_015367		C	18138483	G	C	18138483	2	2	11	1	0	0	0	0	0	0	0	1	1371	1132	40	4		4	BCL2L13	22	18138483	Silent	SNP	G	TCGA-2Z-A9JG-01A-11D-A42J-10		18138483	33166083	77	903											
RANBP1	5902	hgsc.bcm.edu	37	chr22	20109854	20109854	+	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	ggaaggagcgaggcactggtGacgtcaagctcctgaagcac	11	5	15	10	2	1	2	1	2	0	0	2	5	2	4	1	4	3	3	1	4	3	0			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr22:20109854G>T	ENST00000331821.3	+	3	322	c.220G>T	c.(220-222)Gac>Tac	p.D74Y	RANBP1_ENST00000402752.1_Missense_Mutation_p.D74Y|RANBP1_ENST00000430524.1_5'UTR	NM_002882.2	NP_002873.1	P43487	RANG_HUMAN	RAN binding protein 1	74	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)					AGGCACTGGTGACGTCAAGCT	0.552																																					p.D74Y		Atlas-SNP	.											.	RANBP1	19	.	0			c.G220T						PASS	.						77	67	71					22																	20109854		2203	4300	6503	SO:0001583	missense	5902	exon3			ACTGGTGACGTCA	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.220G>T	chr22.hg19:g.20109854G>T	ENSP00000327583:p.Asp74Tyr	132.0	0.0	.		84.0	29.0	.	NM_002882	Q53EY3	Missense_Mutation	SNP	ENST00000331821.3	hg19	CCDS13775.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.848424	0.91277	.	.	ENSG00000099901	ENST00000432879;ENST00000402752;ENST00000447917;ENST00000331821;ENST00000411892;ENST00000416427;ENST00000421656;ENST00000423859;ENST00000418705	T;T;T;T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76	5.53	5.53	0.82687	Pleckstrin homology-type (1);Ran binding protein 1 (3);	0.000000	0.85682	D	0.000000	T	0.74061	0.3667	M	0.87038	2.855	0.80722	D	1	D;D;D	0.76494	0.996;0.999;0.994	D;D;D	0.70935	0.923;0.971;0.954	T	0.78685	-0.2108	10	0.87932	D	0	-53.8354	19.4537	0.94878	0.0:0.0:1.0:0.0	.	74;74;74	B4DE76;Q53EY3;P43487	.;.;RANG_HUMAN	Y	151;74;74;74;74;24;24;24;24	ENSP00000404724:D151Y;ENSP00000384925:D74Y;ENSP00000327583:D74Y;ENSP00000395472:D74Y;ENSP00000404126:D24Y;ENSP00000400940:D24Y;ENSP00000404298:D24Y;ENSP00000413502:D24Y	ENSP00000327583:D74Y	D	+	1	0	RANBP1	18489854	1.000000	0.71417	0.376000	0.26042	0.865000	0.49528	9.618000	0.98365	2.606000	0.88127	0.563000	0.77884	GAC	.	.	.	none		0.552	RANBP1-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343733.1	NM_002882		T	20109854	G	T	20109854	3	4	11	1	0	0	0	0	1	0	0	0	13038	1290	45	4	230	4	RANBP1	22	20109854	Missense_Mutation	SNP	G	TCGA-2Z-A9JG-01A-11D-A42J-10	1971371	20109854	31194712	78	904											
CSNK1E	1454	hgsc.bcm.edu	37	chr22	38690505	38690505	+	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	tcgcgttcgtgttctcgccgCtcccggtccacatcctcggg	2	11	11	17	7	1	0	0	0	1	0	8	0	4	0	4	2	0	3	4	2	0	2			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr22:38690505C>G	ENST00000396832.1	-	8	1181	c.921G>C	c.(919-921)gaG>gaC	p.E307D	CSNK1E_ENST00000359867.3_Missense_Mutation_p.E307D|CSNK1E_ENST00000498529.1_5'Flank|CSNK1E_ENST00000403904.1_Missense_Mutation_p.E307D|CSNK1E_ENST00000400206.2_Missense_Mutation_p.E307D	NM_152221.2	NP_689407.1	P49674	KC1E_HUMAN	casein kinase 1, epsilon	307					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)					GTTCTCGCCGCTCCCGGTCCA	0.706																																					p.E307D	Esophageal Squamous(119;108 755 9651 12170 13692 17603 24932 28315 37982 41601)	Atlas-SNP	.											.	CSNK1E	143	.	0			c.G921C						PASS	.						15	11	12					22																	38690505		2191	4283	6474	SO:0001583	missense	1454	exon8			TCGCCGCTCCCGG		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.921G>C	chr22.hg19:g.38690505C>G	ENSP00000380044:p.Glu307Asp	146.0	0.0	.		52.0	24.0	.	NM_001894		Missense_Mutation	SNP	ENST00000396832.1	hg19	CCDS13970.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	17.10|17.10|17.10	3.303339|3.303339|3.303339	0.60195|0.60195|0.60195	.|.|.	.|.|.	ENSG00000213923|ENSG00000213923|ENSG00000213923	ENST00000431632|ENST00000359867;ENST00000396832;ENST00000402865;ENST00000400206;ENST00000403904|ENST00000366216	.|T;T;T;T|.	.|0.56611|.	.|0.45;0.45;0.45;0.45|.	5.56|5.56|5.56	2.28|2.28|2.28	0.28536|0.28536|0.28536	.|.|.	.|0.045920|.	.|0.85682|.	.|N|.	.|0.000000|.	T|T|T	0.50752|0.50752|0.50752	0.1634|0.1634|0.1634	L|L|L	0.36672|0.36672|0.36672	1.1|1.1|1.1	0.46044|0.46044|0.46044	D|D|D	0.998836|0.998836|0.998836	.|B|.	.|0.02656|.	.|0.0|.	.|B|.	.|0.08055|.	.|0.003|.	T|T|T	0.31392|0.31392|0.31392	-0.9945|-0.9945|-0.9945	5|10|5	.|0.16896|.	.|T|.	.|0.51|.	.|.|.	9.1766|9.1766|9.1766	0.37116|0.37116|0.37116	0.0:0.7182:0.0:0.2818|0.0:0.7182:0.0:0.2818|0.0:0.7182:0.0:0.2818	.|.|.	.|307|.	.|P49674|.	.|KC1E_HUMAN|.	P|D|T	35|307|10	.|ENSP00000352929:E307D;ENSP00000380044:E307D;ENSP00000383067:E307D;ENSP00000384074:E307D|.	.|ENSP00000352929:E307D|.	A|E|S	-|-|-	1|3|2	0|2|0	CSNK1E|CSNK1E|CSNK1E	37020451|37020451|37020451	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.997000|0.997000|0.997000	0.53966|0.53966|0.53966	0.575000|0.575000|0.575000	0.36095|0.36095|0.36095	1.803000|1.803000|1.803000	0.38863|0.38863|0.38863	0.286000|0.286000|0.286000	0.22352|0.22352|0.22352	-0.142000|-0.142000|-0.142000	0.14014|0.14014|0.14014	GCG|GAG|AGC	.	.	.	none		0.706	CSNK1E-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321462.1	NM_001894		G	38690505	C	G	38690505	3	3	11	1	0	0	0	0	1	0	0	0	3955	796	28	4	341	4	CSNK1E	22	38690505	Missense_Mutation	SNP	C	TCGA-2Z-A9JG-01A-11D-A42J-10	18580651	38690505	12614061	79	905											
MOV10L1	54456	hgsc.bcm.edu	37	chr22	50591546	50591546	+	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	cctcacggctgttctaccacAgggaactcgaggtctgtgcg	7	9	12	13	3	3	0	1	0	2	0	4	2	3	1	2	3	3	2	2	3	2	2	rs529208457		TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chr22:50591546A>C	ENST00000262794.5	+	22	3048	c.2965A>C	c.(2965-2967)Agg>Cgg	p.R989R	MOV10L1_ENST00000540615.1_Silent_p.R969R|MOV10L1_ENST00000395843.1_Silent_p.R32R|MOV10L1_ENST00000395852.1_Silent_p.R116R|MOV10L1_ENST00000545383.1_Silent_p.R989R|MOV10L1_ENST00000354853.2_Silent_p.R32R|MOV10L1_ENST00000395858.3_Silent_p.R989R	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	989					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		GTTCTACCACAGGGAACTCGA	0.587																																					p.R989R		Atlas-SNP	.											.	MOV10L1	238	.	0			c.A2965C						PASS	.						178	170	172					22																	50591546		2203	4300	6503	SO:0001819	synonymous_variant	54456	exon22			TACCACAGGGAAC	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"cardiac helicase activated by MEF2C protein"	605794	"Mov10 (mouse)-like 1", "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.2965A>C	chr22.hg19:g.50591546A>C		163.0	0.0	.		79.0	32.0	.	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	hg19	CCDS14084.1																																																																																			.	.	.	none		0.587	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995		C	50591546	A	C	50591546	2	2	11	1	0	0	0	0	0	0	0	1	9726	179	7	5		5	MOV10L1	22	50591546	Silent	SNP	A	TCGA-2Z-A9JG-01A-11D-A42J-10	11901041	50591546	713020	80	906											
DCAF8L2	347442	hgsc.bcm.edu	37	chrX	27765728	27765728	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tactgtacactttaaccagcGtggcacccggctggccagta	9	9	10	13	2	0	0	0	0	0	0	0	0	0	0	3	3	4	4	3	3	4	5			TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chrX:27765728G>A	ENST00000451261.2	+	5	1115	c.716G>A	c.(715-717)cGt>cAt	p.R239H		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	239										central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						TTTAACCAGCGTGGCACCCGG	0.537																																					p.R239H		Atlas-SNP	.											.	DCAF8L2	79	.	0			c.G716A						PASS	.						91	69	76					X																	27765728		692	1591	2283	SO:0001583	missense	347442	exon1			ACCAGCGTGGCAC		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.716G>A	chrX.hg19:g.27765728G>A	ENSP00000462745:p.Arg239His	45.0	0.0	.		83.0	69.0	.	NM_001136533	B2RXH9|J3KT06	Missense_Mutation	SNP	ENST00000451261.2	hg19	CCDS59162.1																																																																																			.	.	.	none		0.537	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354		A	27765728	G	A	27765728	3	1	11	1	0	0	0	0	1	0	0	0	4280	1145	40	1	718	1	DCAF8L2	23	27765728	Missense_Mutation	SNP	G	TCGA-2Z-A9JG-01A-11D-A42J-10		27765728	127504832	81	907											
PHF16	9767	hgsc.bcm.edu	37	chrX	46918210	46918210	+	Frame_Shift_Del	DEL	A	A	-																															aggacctccagtgctatgtgAagccaaccaagaatatgagc																										TCGA-2Z-A9JG-01A-11D-A42J-10	TCGA-2Z-A9JG-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7c8dab16-b1ab-45d2-b73f-239d8a74c8c3	c6173f98-c359-458d-a604-779cc45d612f	g.chrX:46918210delA	ENST00000218343.4	+	11	2501	c.2203delA	c.(2203-2205)aagfs	p.K735fs	PHF16_ENST00000397189.1_Frame_Shift_Del_p.K735fs	NM_014735.3	NP_055550.1														NS(2)|endometrium(8)|kidney(4)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(2)	33						GTGCTATGTGAAGCCAACCAA	0.488																																					p.V734fs		Atlas-INDEL	.											.	PHF16	72	.	0			c.2202delG						PASS	.						56	50	52					X																	46918210		2203	4300	6503	SO:0001589	frameshift_variant	9767	exon11			.																												ENST00000218343.4:c.2203delA	chrX.hg19:g.46918210delA	ENSP00000218343:p.Lys735fs	28.0	0.0	0		45.0	36.0	0.8	NM_014735		Frame_Shift_Del	DEL	ENST00000218343.4	hg19	CCDS14271.1																																																																																			.	.	.	none		0.488	PHF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056376.1			-	46918210	A	-	46918210	7	5	11	1	0	1	0	1	0	0	0	0	11834	247	9	0	2241	0	PHF16	23	46918210	Frame_Shift_Del	DEL	A	TCGA-2Z-A9JG-01A-11D-A42J-10	19152482	46918210	108352350	82	908											
WDR64	128025	hgsc.bcm.edu	37	chr1	241959614	241959614	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gattggcgtagaagcccaaaAggactcttcagatggcatta	13	9	11	8	1	2	2	1	0	1	2	2	4	2	3	1	3	1	2	1	3	5	4			TCGA-2Z-A9JI-01A-11D-A42J-10	TCGA-2Z-A9JI-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bfd6e6f-8fab-42fd-a989-337b66a1d899	df9506ba-fa32-4644-b582-2207bd0595fc	g.chr1:241959614A>G	ENST00000366552.2	+	26	3311	c.3104A>G	c.(3103-3105)aAg>aGg	p.K1035R	WDR64_ENST00000437684.2_Missense_Mutation_p.K868R	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	1035										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)			GAAGCCCAAAAGGACTCTTCA	0.408																																					p.K1035R		Atlas-SNP	.											.	WDR64	234	.	0			c.A3104G						PASS	.						107	99	101					1																	241959614		2203	4300	6503	SO:0001583	missense	128025	exon26			CCCAAAAGGACTC	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.3104A>G	chr1.hg19:g.241959614A>G	ENSP00000355510:p.Lys1035Arg	77.0	0.0	.		87.0	4.0	.	NM_144625	B1ANT0|Q7Z573|Q96LY9	Missense_Mutation	SNP	ENST00000366552.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	4.601|4.601	0.111704|0.111704	0.08831|0.08831	.|.	.|.	ENSG00000162843|ENSG00000162843	ENST00000366552;ENST00000437684;ENST00000414635|ENST00000425826	T;T;T|.	0.39406|.	1.2;1.08;1.08|.	5.22|5.22	-5.72|-5.72	0.02406|0.02406	.|.	0.578909|.	0.16512|.	N|.	0.211202|.	T|T	0.15176|0.15176	0.0366|0.0366	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B;B|.	0.06786|.	0.001;0.0|.	B;B|.	0.08055|.	0.003;0.0|.	T|T	0.33266|0.33266	-0.9875|-0.9875	10|5	0.11794|.	T|.	0.64|.	-0.7601|-0.7601	8.4526|8.4526	0.32880|0.32880	0.6919:0.0:0.1815:0.1266|0.6919:0.0:0.1815:0.1266	.|.	1035;588|.	B1ANS9;D1MPS4|.	WDR64_HUMAN;.|.	R|G	1035;868;639|514	ENSP00000355510:K1035R;ENSP00000402446:K868R;ENSP00000406656:K639R|.	ENSP00000355510:K1035R|.	K|R	+|+	2|1	0|2	WDR64|WDR64	240026237|240026237	0.540000|0.540000	0.26410|0.26410	0.074000|0.074000	0.20217|0.20217	0.023000|0.023000	0.10783|0.10783	-0.383000|-0.383000	0.07398|0.07398	-0.978000|-0.978000	0.03533|0.03533	-0.376000|-0.376000	0.06991|0.06991	AAG|AGG	.	.	.	none		0.408	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625		G	241959614	A	G	241959614	3	3	12	1	0	0	0	0	1	0	0	0	17327	72	3	3	3206	3	WDR64	1	241959614	Missense_Mutation	SNP	A	TCGA-2Z-A9JI-01A-11D-A42J-10		241959614	7291007	1	909											
MARCO	8685	hgsc.bcm.edu	37	chr2	119727691	119727691	+	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	gctgtggggtggggcccagtTctgaatctgcaggcgcggct	4	9	18	10	2	2	1	0	1	2	0	2	1	2	1	1	6	1	4	1	6	1	1			TCGA-2Z-A9JI-01A-11D-A42J-10	TCGA-2Z-A9JI-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bfd6e6f-8fab-42fd-a989-337b66a1d899	df9506ba-fa32-4644-b582-2207bd0595fc	g.chr2:119727691T>A	ENST00000327097.4	+	3	336	c.201T>A	c.(199-201)gtT>gtA	p.V67V	MARCO_ENST00000541757.1_De_novo_Start_InFrame	NM_006770.3	NP_006761.1	Q9UEW3	MARCO_HUMAN	macrophage receptor with collagenous structure	67					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						GGGGCCCAGTTCTGAATCTGC	0.542																																					p.V67V	GBM(8;18 374 7467 11269 32796)	Atlas-SNP	.											.	MARCO	120	.	0			c.T201A						PASS	.						57	67	63					2																	119727691		2201	4300	6501	SO:0001630	splice_region_variant	8685	exon3			CCCAGTTCTGAAT	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.200-1T>A	chr2.hg19:g.119727691T>A		24.0	0.0	.		64.0	12.0	.	NM_006770	B4DW79|Q9Y5S3	Silent	SNP	ENST00000327097.4	hg19	CCDS2124.1																																																																																			.	.	.	none		0.542	MARCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254190.2	NM_006770	Silent	A	119727691	T	A	119727691	5	1	12	1	0	0	0	0	0	0	1	0	9318	1797	62	5	211	5	MARCO	2	119727691	Splice_Site	SNP	T	TCGA-2Z-A9JI-01A-11D-A42J-10		119727691	123471682	2	910											
EIF4G1	1981	hgsc.bcm.edu	37	chr3	184035257	184035257	+	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	ccagatctcctacccagcctCccagggggcctactacatcc	8	7	7	19	0	1	1	0	0	1	1	4	1	3	1	7	2	4	0	7	2	3	3			TCGA-2Z-A9JI-01A-11D-A42J-10	TCGA-2Z-A9JI-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bfd6e6f-8fab-42fd-a989-337b66a1d899	df9506ba-fa32-4644-b582-2207bd0595fc	g.chr3:184035257C>T	ENST00000346169.2	+	5	567	c.296C>T	c.(295-297)tCc>tTc	p.S99F	EIF4G1_ENST00000434061.2_5'Flank|EIF4G1_ENST00000350481.5_Intron|EIF4G1_ENST00000382330.3_Missense_Mutation_p.S106F|EIF4G1_ENST00000411531.1_Missense_Mutation_p.S59F|EIF4G1_ENST00000342981.4_Missense_Mutation_p.S99F|EIF4G1_ENST00000427845.1_Missense_Mutation_p.S12F|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000319274.6_Missense_Mutation_p.S99F|EIF4G1_ENST00000392537.2_Missense_Mutation_p.S12F|EIF4G1_ENST00000424196.1_Missense_Mutation_p.S106F|EIF4G1_ENST00000414031.1_Missense_Mutation_p.S59F|EIF4G1_ENST00000352767.3_Missense_Mutation_p.S106F|EIF4G1_ENST00000441154.1_5'Flank	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	99					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)			TACCCAGCCTCCCAGGGGGCC	0.612																																					p.S106F		Atlas-SNP	.											.	EIF4G1	151	.	0			c.C317T						PASS	.						47	53	51					3																	184035257		2203	4300	6503	SO:0001583	missense	1981	exon6			CAGCCTCCCAGGG	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.296C>T	chr3.hg19:g.184035257C>T	ENSP00000316879:p.Ser99Phe	145.0	0.0	.		98.0	23.0	.	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Missense_Mutation	SNP	ENST00000346169.2	hg19	CCDS3259.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.539596	0.85917	.	.	ENSG00000114867	ENST00000346169;ENST00000414031;ENST00000392537;ENST00000450424;ENST00000421110;ENST00000382330;ENST00000455679;ENST00000440448;ENST00000352767;ENST00000427141;ENST00000427845;ENST00000342981;ENST00000319274;ENST00000424196;ENST00000456033;ENST00000411531	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.37411	1.98;1.98;1.2;1.98;1.98;1.98;1.2;1.2;1.98;1.2;1.2;1.98;1.98;1.98;1.2;1.98	5.08	4.16	0.48862	.	0.514295	0.20823	N	0.085028	T	0.31702	0.0805	L	0.43152	1.355	0.54753	D	0.999989	P;P;P	0.41947	0.766;0.766;0.766	B;B;B	0.37198	0.243;0.243;0.243	T	0.28808	-1.0032	10	0.56958	D	0.05	-13.2414	15.7036	0.77560	0.0:0.8635:0.1365:0.0	.	106;99;99	E9PFM1;D3DNT2;Q04637	.;.;IF4G1_HUMAN	F	99;59;12;99;106;106;59;99;106;66;12;99;99;106;59;59	ENSP00000316879:S99F;ENSP00000391935:S59F;ENSP00000376320:S12F;ENSP00000391412:S99F;ENSP00000413159:S106F;ENSP00000371767:S106F;ENSP00000415842:S59F;ENSP00000407240:S99F;ENSP00000338020:S106F;ENSP00000411214:S66F;ENSP00000407682:S12F;ENSP00000343450:S99F;ENSP00000323737:S99F;ENSP00000416255:S106F;ENSP00000415943:S59F;ENSP00000395974:S59F	ENSP00000323737:S99F	S	+	2	0	EIF4G1	185517951	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.833000	0.55790	2.640000	0.89533	0.655000	0.94253	TCC	.	.	.	none		0.612	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917		T	184035257	C	T	184035257	3	4	12	1	0	0	0	0	1	0	0	0	5038	855	30	2	306	2	EIF4G1	3	184035257	Missense_Mutation	SNP	C	TCGA-2Z-A9JI-01A-11D-A42J-10		184035257	13987173	3	911											
ETV1	2115	hgsc.bcm.edu	37	chr7	13946127	13946127	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatgagaatttgaagggtcAtccagaagagctaccaaaaa	19	7	9	6	0	1	4	1	2	0	3	2	5	2	4	2	1	2	1	2	1	7	2			TCGA-2Z-A9JI-01A-11D-A42J-10	TCGA-2Z-A9JI-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bfd6e6f-8fab-42fd-a989-337b66a1d899	df9506ba-fa32-4644-b582-2207bd0595fc	g.chr7:13946127A>G	ENST00000430479.1	-	12	1705	c.1038T>C	c.(1036-1038)gaT>gaC	p.D346D	ETV1_ENST00000242066.5_Silent_p.D328D|ETV1_ENST00000405358.4_Silent_p.D360D|ETV1_ENST00000405218.2_Silent_p.D346D|ETV1_ENST00000399357.3_Silent_p.D243D|ETV1_ENST00000403685.1_Silent_p.D328D|ETV1_ENST00000403527.1_Silent_p.D306D|ETV1_ENST00000343495.5_Silent_p.D328D|ETV1_ENST00000420159.2_Silent_p.D288D|ETV1_ENST00000405192.2_Silent_p.D323D	NM_004956.4	NP_004947.2	P50549	ETV1_HUMAN	ets variant 1	346					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						TTGAAGGGTCATCCAGAAGAG	0.433			T	"EWSR1, TMPRSS2, SLC45A3, C15orf21, HNRNPA2B1. ACSL3"	"Ewing sarcoma, prostate"																																p.D346D		Atlas-SNP	.		Dom	yes		7	7p22	2115	ets variant gene 1		"M, E"	.	ETV1	138	.	0			c.T1038C						PASS	.						69	70	69					7																	13946127		1894	4131	6025	SO:0001819	synonymous_variant	2115	exon12			AGGGTCATCCAGA		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.1038T>C	chr7.hg19:g.13946127A>G		156.0	0.0	.		217.0	31.0	.	NM_004956	A4D118|B2R768|B7Z2I4|B7Z618|B7Z9P2|C9JT37|E9PHB1|F5GXR2|O75849|Q4KMQ6|Q59GA7|Q6AI30|Q9UQ71|Q9Y636	Silent	SNP	ENST00000430479.1	hg19	CCDS55088.1																																																																																			.	.	.	none		0.433	ETV1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326111.1	NM_004956		G	13946127	A	G	13946127	2	3	12	1	0	0	0	0	0	0	0	1	5279	214	8	3		3	ETV1	7	13946127	Silent	SNP	A	TCGA-2Z-A9JI-01A-11D-A42J-10		13946127	145192536	4	912											
AP3M1	26985	hgsc.bcm.edu	37	chr10	75889698	75889698	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagagatcaggcattccagaTagtttaatgcaagcatcaat	15	10	9	7	0	2	2	2	0	0	2	3	4	3	2	1	1	2	4	1	1	4	4			TCGA-2Z-A9JI-01A-11D-A42J-10	TCGA-2Z-A9JI-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bfd6e6f-8fab-42fd-a989-337b66a1d899	df9506ba-fa32-4644-b582-2207bd0595fc	g.chr10:75889698T>C	ENST00000355264.4	-	5	947	c.636A>G	c.(634-636)ctA>ctG	p.L212L	AP3M1_ENST00000372745.1_Silent_p.L212L	NM_012095.4	NP_036227.1	Q9Y2T2	AP3M1_HUMAN	adaptor-related protein complex 3, mu 1 subunit	212	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				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)					GCATTCCAGATAGTTTAATGC	0.358																																					p.L212L		Atlas-SNP	.											.	AP3M1	28	.	0			c.A636G						PASS	.						133	125	128					10																	75889698		2203	4300	6503	SO:0001819	synonymous_variant	26985	exon6			TCCAGATAGTTTA	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.636A>G	chr10.hg19:g.75889698T>C		64.0	0.0	.		55.0	18.0	.	NM_207012	Q5JQ12|Q9H5L2	Silent	SNP	ENST00000355264.4	hg19	CCDS7342.1																																																																																			.	.	.	none		0.358	AP3M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048747.1			C	75889698	T	C	75889698	2	2	12	1	0	0	0	0	0	0	0	1	747	1393	49	3		3	AP3M1	10	75889698	Silent	SNP	T	TCGA-2Z-A9JI-01A-11D-A42J-10		75889698	59645049	5	913											
IFITM3	10410	hgsc.bcm.edu	37	chr11	320733	320733	+	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	gcccccagcacagccacctcGtgctcctccttgagcatctc	6	8	7	20	1	1	1	0	1	1	0	5	1	3	1	6	0	4	3	6	0	0	1			TCGA-2Z-A9JI-01A-11D-A42J-10	TCGA-2Z-A9JI-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bfd6e6f-8fab-42fd-a989-337b66a1d899	df9506ba-fa32-4644-b582-2207bd0595fc	g.chr11:320733G>C	ENST00000399808.4	-	1	317	c.81C>G	c.(79-81)caC>caG	p.H27Q	RP11-326C3.10_ENST00000534271.1_RNA|RP11-326C3.14_ENST00000602809.1_lincRNA|RP11-326C3.11_ENST00000602756.1_RNA|IFITM3_ENST00000602735.1_Missense_Mutation_p.H6Q|RP11-326C3.11_ENST00000508004.2_RNA|IFITM3_ENST00000526811.1_Missense_Mutation_p.H6Q|RP11-326C3.11_ENST00000602429.1_RNA	NM_021034.2	NP_066362.2	Q01628	IFM3_HUMAN	interferon induced transmembrane protein 3	27					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)		CAGCCACCTCGTGCTCCTCCT	0.617																																					p.H27Q		Atlas-SNP	.											IFITM3,brain,glioma,0,1	IFITM3	132	.	0			c.C81G						PASS	.						92	104	100					11																	320733		1948	4127	6075	SO:0001583	missense	10410	exon1			CACCTCGTGCTCC	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.81C>G	chr11.hg19:g.320733G>C	ENSP00000382707:p.His27Gln	44.0	2.0	.		47.0	3.0	.	NM_021034	Q53Y76|Q96HK8|Q96J15	Missense_Mutation	SNP	ENST00000399808.4	hg19	CCDS41585.1	.	.	.	.	.	.	.	.	.	.	G	12.56	1.973443	0.34848	.	.	ENSG00000142089	ENST00000399808;ENST00000270031;ENST00000526811	T;T	0.77877	-0.81;-1.13	4.61	-4.17	0.03857	.	0.761271	0.10830	U	0.629401	T	0.59985	0.2234	L	0.46885	1.475	0.09310	N	1	B	0.12013	0.005	B	0.12837	0.008	T	0.47315	-0.9127	10	0.09590	T	0.72	-2.442	3.6745	0.08287	0.4606:0.0:0.2595:0.2799	.	27	Q01628	IFM3_HUMAN	Q	27;11;6	ENSP00000382707:H27Q;ENSP00000432108:H6Q	ENSP00000372047:H11Q	H	-	3	2	IFITM3	310733	0.000000	0.05858	0.000000	0.03702	0.337000	0.28794	-3.370000	0.00494	-0.556000	0.06134	0.461000	0.40582	CAC	.	.	.	weak		0.617	IFITM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384765.1	NM_021034		C	320733	G	C	320733	3	2	12	1	0	0	0	0	1	0	0	0	7535	1136	40	4	328	4	IFITM3	11	320733	Missense_Mutation	SNP	G	TCGA-2Z-A9JI-01A-11D-A42J-10		320733	134685783	6	914											
KRTAP5-4	387267	hgsc.bcm.edu	37	chr11	1643084	1643085	+	Frame_Shift_Ins	INS	-	-	C																															aacccccacaagagccatagINSccccccttggagcccccaca																										TCGA-2Z-A9JI-01A-11D-A42J-10	TCGA-2Z-A9JI-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bfd6e6f-8fab-42fd-a989-337b66a1d899	df9506ba-fa32-4644-b582-2207bd0595fc	g.chr11:1643084_1643085insC	ENST00000399682.1	-	1	283_284	c.239_240insG	c.(238-240)ggcfs	p.G80fs		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)		AAGAGCCATAGCCCCCCTTGGA	0.658																																					p.G80fs		Atlas-INDEL	.											KRTAP5-4,right_lower_lobe,carcinoma,0,1	KRTAP5-4	78	.	0			c.240_241insG						PASS	.																																			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.240dupG	chr11.hg19:g.1643090_1643090dupC	ENSP00000382590:p.Gly80fs	228.0	0.0	0		256.0	19.0	0.0742188	NM_001012709		Frame_Shift_Ins	INS	ENST00000399682.1	hg19																																																																																				.	.	.	none		0.658	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709		C	1643085	-	C	1643084	7	5	12	1	0	1	1	0	0	0	0	0	8570	958	34	0	450	0	KRTAP5-4	11	1643084	Frame_Shift_Ins	INS	-	TCGA-2Z-A9JI-01A-11D-A42J-10	1322351	1643084	133363432	7	915											
RNF10	9921	hgsc.bcm.edu	37	chr12	121013657	121013657	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggagagtgataattcagacCgtgttcctgtgcccagtttt	8	13	12	8	1	1	3	1	1	0	2	2	4	2	3	3	1	1	2	3	1	1	5			TCGA-2Z-A9JI-01A-11D-A42J-10	TCGA-2Z-A9JI-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bfd6e6f-8fab-42fd-a989-337b66a1d899	df9506ba-fa32-4644-b582-2207bd0595fc	g.chr12:121013657C>T	ENST00000325954.4	+	16	2724	c.2263C>T	c.(2263-2265)Cgt>Tgt	p.R755C	RNF10_ENST00000413266.2_Missense_Mutation_p.R760C|RNF10_ENST00000542701.1_3'UTR	NM_014868.4	NP_055683.3	Q8N5U6	RNF10_HUMAN	ring finger protein 10	755					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)					TAATTCAGACCGTGTTCCTGT	0.453																																					p.R755C		Atlas-SNP	.											.	RNF10	75	.	0			c.C2263T						PASS	.						183	188	186					12																	121013657		2203	4300	6503	SO:0001583	missense	9921	exon16			TCAGACCGTGTTC	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.2263C>T	chr12.hg19:g.121013657C>T	ENSP00000322242:p.Arg755Cys	53.0	0.0	.		72.0	4.0	.	NM_014868	Q92550|Q9NPP8|Q9ULW4	Missense_Mutation	SNP	ENST00000325954.4	hg19	CCDS9201.1	.	.	.	.	.	.	.	.	.	.	C	18.76	3.691846	0.68271	.	.	ENSG00000022840	ENST00000325954;ENST00000458409;ENST00000413266;ENST00000538254	D;D	0.89810	-2.57;-2.56	5.39	5.39	0.77823	.	0.219513	0.48767	D	0.000176	D	0.91002	0.7170	L	0.55481	1.735	0.80722	D	1	D;D	0.62365	0.991;0.979	P;B	0.52424	0.698;0.42	D	0.91486	0.5208	10	0.59425	D	0.04	.	19.1841	0.93635	0.0:1.0:0.0:0.0	.	760;755	Q8N5U6-2;Q8N5U6	.;RNF10_HUMAN	C	755;755;760;90	ENSP00000322242:R755C;ENSP00000415682:R760C	ENSP00000322242:R755C	R	+	1	0	RNF10	119498040	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.590000	0.67530	2.537000	0.85549	0.655000	0.94253	CGT	.	.	.	none		0.453	RNF10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401898.4			T	121013657	C	T	121013657	3	4	12	1	0	0	0	0	1	0	0	0	13435	652	23	1	2325	1	RNF10	12	121013657	Missense_Mutation	SNP	C	TCGA-2Z-A9JI-01A-11D-A42J-10		121013657	12838238	8	916											
ZNF268	10795	hgsc.bcm.edu	37	chr12	133764464	133764464	+	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	tcttgagtccacaggtcccaCctctccaagaacgaaacagt	12	8	7	14	1	2	2	0	1	2	1	5	3	4	2	4	1	2	0	4	1	3	1	rs200829573		TCGA-2Z-A9JI-01A-11D-A42J-10	TCGA-2Z-A9JI-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bfd6e6f-8fab-42fd-a989-337b66a1d899	df9506ba-fa32-4644-b582-2207bd0595fc	g.chr12:133764464C>T	ENST00000536435.2	+	3	370	c.40C>T	c.(40-42)Cct>Tct	p.P14S	ZNF268_ENST00000228289.5_Missense_Mutation_p.P14S|ZNF268_ENST00000537565.1_Intron|ZNF268_ENST00000539248.2_Missense_Mutation_p.P14S|ZNF268_ENST00000592241.1_Intron|ZNF268_ENST00000541009.2_Missense_Mutation_p.P14S|ZNF268_ENST00000536899.2_Intron|ZNF268_ENST00000541211.2_Missense_Mutation_p.P14S|ZNF268_ENST00000542986.2_Missense_Mutation_p.P14S|ZNF268_ENST00000416488.1_Missense_Mutation_p.P179S|CTD-2140B24.4_ENST00000540096.2_Missense_Mutation_p.P179S|ZNF268_ENST00000542711.2_Intron	NM_001165885.1|NM_003415.2	NP_001159357.1|NP_003406.1	Q14587	ZN268_HUMAN	zinc finger protein 268	14					cell differentiation (GO:0030154)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein homodimerization activity (GO:0090073)|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 during mitosis (GO:0046022)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein heterodimerization activity (GO:0043497)|regulation of transcription, DNA-templated (GO:0006355)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|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(2)|breast(3)|endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(1)	24	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.000215)|all_epithelial(31;0.096)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		ACAGGTCCCACCTCTCCAAGA	0.478																																					p.P14S		Atlas-SNP	.											ZNF268,NS,carcinoma,0,1	ZNF268	71	.	0			c.C40T						PASS	.	C	SER/PRO,,SER/PRO,,SER/PRO,,,SER/PRO,SER/PRO	0,3738		0,0,1869	28	27	27		40,,40,,40,,,40,40	1.3	1	12		27	6,8220		0,6,4107	yes	missense,utr-5,missense,intron,missense,intron,intron,missense,missense	ZNF268	NM_001165881.2,NM_001165882.2,NM_001165883.1,NM_001165884.2,NM_001165885.1,NM_001165886.1,NM_001165887.1,NM_003415.2,NM_152943.2	74,,74,,74,,,74,74	0,6,5976	TT,TC,CC		0.0729,0.0,0.0502	probably-damaging,,probably-damaging,,probably-damaging,,,probably-damaging,probably-damaging	14/948,,14/136,,14/168,,,14/948,14/194	133764464	6,11958	1869	4113	5982	SO:0001583	missense	10795	exon3			GTCCCACCTCTCC	X78926	CCDS45012.1, CCDS53851.1, CCDS53852.1, CCDS53853.1, CCDS53854.1, CCDS59239.1, CCDS59240.1	12q24.33	2013-01-08				ENSG00000090612		"Zinc fingers, C2H2-type", "-"	13061	protein-coding gene	gene with protein product		604753				7865130	Standard	NM_003415		Approved	HZF3	uc010tcf.2	Q14587	OTTHUMG00000167946	ENST00000536435.2:c.40C>T	chr12.hg19:g.133764464C>T	ENSP00000444412:p.Pro14Ser	60.0	0.0	.		105.0	23.0	.	NM_152943	Q8TDG8|Q96RH4|Q9BZJ9	Missense_Mutation	SNP	ENST00000536435.2	hg19	CCDS45012.1	.	.	.	.	.	.	.	.	.	.	C	12.88	2.070813	0.36566	0.0	7.29E-4	ENSG00000090612	ENST00000416488;ENST00000541009;ENST00000536435;ENST00000228289;ENST00000541211;ENST00000541975	T;T;T;T	0.08282	4.89;4.79;3.11;3.11	3.37	1.33	0.21861	.	.	.	.	.	T	0.04318	0.0119	N	0.19112	0.55	0.80722	D	1	B	0.20368	0.044	B	0.13407	0.009	T	0.40289	-0.9571	8	.	.	.	.	4.2438	0.10662	0.0:0.6255:0.2396:0.1349	.	14	Q14587	ZN268_HUMAN	S	179;14;14;14;14;14	ENSP00000409295:P179S;ENSP00000439539:P14S;ENSP00000444412:P14S;ENSP00000228289:P14S	.	P	+	1	0	ZNF268	132274537	0.791000	0.28800	0.974000	0.42286	0.365000	0.29674	0.980000	0.29513	0.779000	0.33543	-0.258000	0.10820	CCT	.	C|0.998;T|0.002	0.002	weak		0.478	ZNF268-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397191.2	NM_152943		T	133764464	C	T	133764464	3	4	12	1	0	0	0	0	1	0	0	0	17819	507	18	2	46	2	ZNF268	12	133764464	Missense_Mutation	SNP	C	TCGA-2Z-A9JI-01A-11D-A42J-10	12750807	133764464	87431	9	917											
KRT24	192666	hgsc.bcm.edu	37	chr17	38855731	38855731	+	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	agcaggcggcggtaggtctcGatctccacctccaggcgtgt	6	8	14	13	4	2	0	0	0	2	0	5	1	3	0	3	5	1	2	3	5	1	1			TCGA-2Z-A9JI-01A-11D-A42J-10	TCGA-2Z-A9JI-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bfd6e6f-8fab-42fd-a989-337b66a1d899	df9506ba-fa32-4644-b582-2207bd0595fc	g.chr17:38855731G>C	ENST00000264651.2	-	6	1382	c.1326C>G	c.(1324-1326)atC>atG	p.I442M		NM_019016.2	NP_061889.2	Q2M2I5	K1C24_HUMAN	keratin 24	442	Coil 2.|Rod.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00526)				GGTAGGTCTCGATCTCCACCT	0.473																																					p.I442M	GBM(61;380 1051 14702 23642 31441)	Atlas-SNP	.											.	KRT24	60	.	0			c.C1326G						PASS	.						156	154	154					17																	38855731		2203	4300	6503	SO:0001583	missense	192666	exon6			GGTCTCGATCTCC		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.1326C>G	chr17.hg19:g.38855731G>C	ENSP00000264651:p.Ile442Met	74.0	0.0	.		78.0	22.0	.	NM_019016	Q9NXG7	Missense_Mutation	SNP	ENST00000264651.2	hg19	CCDS11372.1	.	.	.	.	.	.	.	.	.	.	G	17.94	3.511147	0.64522	.	.	ENSG00000167916	ENST00000264651	D	0.95518	-3.73	5.62	-1.6	0.08426	Filament (1);Intermediate filament protein, conserved site (1);	.	.	.	.	D	0.98178	0.9398	H	0.98295	4.195	0.42436	D	0.992697	D	0.89917	1.0	D	0.97110	1.0	D	0.96395	0.9292	9	0.87932	D	0	.	8.0643	0.30651	0.5304:0.0:0.3664:0.1033	.	442	Q2M2I5	K1C24_HUMAN	M	442	ENSP00000264651:I442M	ENSP00000264651:I442M	I	-	3	3	KRT24	36109257	0.845000	0.29573	0.994000	0.49952	0.971000	0.66376	-0.007000	0.12810	-0.225000	0.09913	0.591000	0.81541	ATC	.	.	.	none		0.473	KRT24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257217.1	NM_019016		C	38855731	G	C	38855731	3	2	12	1	0	0	0	0	1	0	0	0	8468	1048	37	4	263	4	KRT24	17	38855731	Missense_Mutation	SNP	G	TCGA-2Z-A9JI-01A-11D-A42J-10		38855731	42339479	10	918											
RBM10	8241	hgsc.bcm.edu	37	chrX	47030582	47030582	+	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	gaggaggaggaggaggaggaGgatgaggaggaggaggagaa	15	1	25	0	0	0	2	0	1	0	1	0	14	0	12	0	11	0	0	0	11	1	0			TCGA-2Z-A9JI-01A-11D-A42J-10	TCGA-2Z-A9JI-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bfd6e6f-8fab-42fd-a989-337b66a1d899	df9506ba-fa32-4644-b582-2207bd0595fc	g.chrX:47030582G>T	ENST00000377604.3	+	4	1099	c.357G>T	c.(355-357)gaG>gaT	p.E119D	RBM10_ENST00000329236.7_Intron|RBM10_ENST00000345781.6_Intron	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	119	Poly-Glu.				3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						aggaggaggaggatgaggagg	0.662																																					p.E184D	Melanoma(171;120 2705 19495 39241)	Atlas-SNP	.											.	RBM10	117	.	0			c.G552T						PASS	.						20	19	19					X																	47030582		2202	4294	6496	SO:0001583	missense	8241	exon4			GGAGGAGGATGAG	U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"Zinc fingers, RAN-binding domain containing", "G patch domain containing", "RNA binding motif (RRM) containing"	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.357G>T	chrX.hg19:g.47030582G>T	ENSP00000366829:p.Glu119Asp	90.0	0.0	.		65.0	5.0	.	NM_001204468	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Missense_Mutation	SNP	ENST00000377604.3	hg19	CCDS14274.1	.	.	.	.	.	.	.	.	.	.	G	7.514	0.655267	0.14580	.	.	ENSG00000182872	ENST00000377604	T	0.11169	2.8	3.1	1.15	0.20763	Nucleotide-binding, alpha-beta plait (1);	0.859005	0.09469	N	0.797951	T	0.04815	0.0130	N	0.08118	0	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.38628	-0.9652	10	0.11182	T	0.66	-1.7872	6.9396	0.24486	0.0:0.0:0.4873:0.5127	.	184;119;119	Q7Z3D7;P98175-2;P98175	.;.;RBM10_HUMAN	D	119	ENSP00000366829:E119D	ENSP00000366829:E119D	E	+	3	2	RBM10	46915526	1.000000	0.71417	0.776000	0.31678	0.914000	0.54420	0.961000	0.29267	0.165000	0.19558	0.502000	0.49764	GAG	.	.	.	none		0.662	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676		T	47030582	G	T	47030582	3	4	12	1	0	0	0	0	1	0	0	0	13124	991	35	4	367	4	RBM10	23	47030582	Missense_Mutation	SNP	G	TCGA-2Z-A9JI-01A-11D-A42J-10		47030582	108239978	11	919											
CELF3	11189	hgsc.bcm.edu	37	chr1	151679166	151679166	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgtagtgctgcatccccgCgtaggcctgctgcagggggt	4	10	16	11	2	0	0	0	0	0	0	1	0	1	0	3	3	4	6	3	3	2	2			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr1:151679166C>T	ENST00000290583.4	-	9	1760	c.967G>A	c.(967-969)Gcg>Acg	p.A323T	CELF3_ENST00000392706.3_Intron|CELF3_ENST00000470688.1_5'UTR|CELF3_ENST00000290585.4_Missense_Mutation_p.A273T|RP11-98D18.1_ENST00000457548.1_RNA	NM_001172648.1|NM_007185.4	NP_001166119.1|NP_009116.3	Q5SZQ8	CELF3_HUMAN	CUGBP, Elav-like family member 3	323					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	21						TGCATCCCCGCGTAGGCCTGC	0.687																																					p.A323T		Atlas-SNP	.											.	CELF3	49	.	0			c.G967A						PASS	.						9	10	9					1																	151679166		1879	3579	5458	SO:0001583	missense	11189	exon9			TCCCCGCGTAGGC	U80759	CCDS1002.1, CCDS53367.1	1q21	2013-02-12	2010-02-19	2010-02-19	ENSG00000159409	ENSG00000159409		"Trinucleotide (CAG) repeat containing", "RNA binding motif (RRM) containing"	11967	protein-coding gene	gene with protein product	"expanded repeat domain, CAG/CTG 4", "CAG repeat domain", "CUG-BP and ETR-3 like factor 3"	612678	"trinucleotide repeat containing 4"	TNRC4		9225980	Standard	XM_005244859		Approved	CAGH4, BRUNOL1, ERDA4, MGC57297	uc001eys.2	Q5SZQ8	OTTHUMG00000013064	ENST00000290583.4:c.967G>A	chr1.hg19:g.151679166C>T	ENSP00000290583:p.Ala323Thr	170.0	0.0	.		101.0	44.0	.	NM_007185	B7ZKK6|O15414|Q499Y6|Q5SZQ7|Q6NVK0|Q8IZ98|Q9BZC2|Q9HB30	Missense_Mutation	SNP	ENST00000290583.4	hg19	CCDS1002.1	.	.	.	.	.	.	.	.	.	.	.	15.89	2.966802	0.53507	.	.	ENSG00000159409	ENST00000290585;ENST00000290583	T;T	0.16897	2.31;2.32	4.49	4.49	0.54785	.	0.126953	0.53938	D	0.000048	T	0.04272	0.0118	N	0.16567	0.415	0.80722	D	1	B;B;B;B	0.33826	0.006;0.01;0.063;0.427	B;B;B;B	0.23419	0.005;0.013;0.008;0.046	T	0.37009	-0.9724	10	0.22109	T	0.4	-7.7777	15.906	0.79430	0.0:1.0:0.0:0.0	.	273;323;323;322	Q5SZQ7;Q5SZQ8-2;Q5SZQ8;Q5SZQ8-3	.;.;CELF3_HUMAN;.	T	273;323	ENSP00000290585:A273T;ENSP00000290583:A323T	ENSP00000290583:A323T	A	-	1	0	CELF3	149945790	0.182000	0.23173	0.988000	0.46212	0.985000	0.73830	0.640000	0.24705	2.325000	0.78763	0.561000	0.74099	GCG	.	.	.	none		0.687	CELF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036663.2	NM_007185		T	151679166	C	T	151679166	3	4	13	1	0	0	0	0	1	0	0	0	3219	768	27	1	446	1	CELF3	1	151679166	Missense_Mutation	SNP	C	TCGA-2Z-A9JJ-01A-11D-A42J-10		151679166	97571455	1	920											
C1orf74	148304	hgsc.bcm.edu	37	chr1	209956222	209956222	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagaggagatgctgagatcaGcaaagtcattctgagtccta	13	9	11	8	0	3	4	2	2	1	3	4	6	4	4	1	1	2	2	1	1	2	2			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr1:209956222G>A	ENST00000294811.1	-	2	1014	c.758C>T	c.(757-759)gCt>gTt	p.A253V		NM_152485.2	NP_689698.1	Q96LT6	CA074_HUMAN	chromosome 1 open reading frame 74	253										endometrium(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)	15				OV - Ovarian serous cystadenocarcinoma(81;0.0328)		GCTGAGATCAGCAAAGTCATT	0.478																																					p.A253V		Atlas-SNP	.											.	C1orf74	30	.	0			c.C758T						PASS	.						107	113	111					1																	209956222		2203	4300	6503	SO:0001583	missense	148304	exon2			AGATCAGCAAAGT	AK057807	CCDS1491.1	1q32.2	2008-02-05			ENSG00000162757	ENSG00000162757			26319	protein-coding gene	gene with protein product						12477932	Standard	NM_152485		Approved	FLJ25078	uc001hhp.1	Q96LT6	OTTHUMG00000036483	ENST00000294811.1:c.758C>T	chr1.hg19:g.209956222G>A	ENSP00000294811:p.Ala253Val	79.0	0.0	.		80.0	4.0	.	NM_152485		Missense_Mutation	SNP	ENST00000294811.1	hg19	CCDS1491.1	.	.	.	.	.	.	.	.	.	.	G	14.81	2.646718	0.47258	.	.	ENSG00000162757	ENST00000294811	T	0.47869	0.83	5.75	3.87	0.44632	.	0.659417	0.14008	N	0.347653	T	0.36524	0.0970	L	0.36672	1.1	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.27262	-1.0079	10	0.51188	T	0.08	-1.6294	7.8075	0.29211	0.1481:0.0:0.7188:0.1331	.	253	Q96LT6	CA074_HUMAN	V	253	ENSP00000294811:A253V	ENSP00000294811:A253V	A	-	2	0	C1orf74	208022845	0.493000	0.26035	0.984000	0.44739	0.988000	0.76386	2.185000	0.42584	0.763000	0.33175	0.655000	0.94253	GCT	.	.	.	none		0.478	C1orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088745.1	NM_152485		A	209956222	G	A	209956222	3	1	13	1	0	0	0	0	1	0	0	0	2060	971	34	2	55	2	C1orf74	1	209956222	Missense_Mutation	SNP	G	TCGA-2Z-A9JJ-01A-11D-A42J-10	58277056	209956222	39294399	2	921											
CELSR3	1951	hgsc.bcm.edu	37	chr3	48687979	48687979	+	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	tgtctggggccaccacacacCagatctcagggacttagggc	9	7	12	13	0	2	1	1	0	2	1	3	2	2	2	3	4	0	0	3	4	1	1			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr3:48687979C>A	ENST00000164024.4	-	16	6686	c.6406G>T	c.(6406-6408)Ggt>Tgt	p.G2136C	CELSR3_ENST00000544264.1_Missense_Mutation_p.G2136C	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	2136					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)		CACCACACACCAGATCTCAGG	0.607																																					p.G2136C		Atlas-SNP	.											.	CELSR3	237	.	0			c.G6406T						PASS	.						63	56	59					3																	48687979		2202	4300	6502	SO:0001583	missense	1951	exon16			ACACACCAGATCT	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.6406G>T	chr3.hg19:g.48687979C>A	ENSP00000164024:p.Gly2136Cys	295.0	0.0	.		168.0	53.0	.	NM_001407	O75092	Missense_Mutation	SNP	ENST00000164024.4	hg19	CCDS2775.1	.	.	.	.	.	.	.	.	.	.	C	17.68	3.448586	0.63178	.	.	ENSG00000008300	ENST00000164024;ENST00000544264	T;T	0.57273	0.41;0.41	5.42	4.55	0.56014	GPCR, family 2, extracellular hormone receptor domain (3);	.	.	.	.	T	0.75620	0.3874	M	0.91818	3.245	0.80722	D	1	D;D	0.76494	0.995;0.999	D;D	0.69654	0.965;0.947	T	0.80730	-0.1252	9	0.87932	D	0	.	11.6972	0.51551	0.0:0.8515:0.0:0.1485	.	2136;2206	Q9NYQ7;Q5Y190	CELR3_HUMAN;.	C	2136	ENSP00000164024:G2136C;ENSP00000445694:G2136C	ENSP00000164024:G2136C	G	-	1	0	CELSR3	48662983	0.999000	0.42202	1.000000	0.80357	0.999000	0.98932	4.669000	0.61575	1.285000	0.44548	0.643000	0.83706	GGT	.	.	.	none		0.607	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		A	48687979	C	A	48687979	3	1	13	1	0	0	0	0	1	0	0	0	3225	594	21	4	3612	4	CELSR3	3	48687979	Missense_Mutation	SNP	C	TCGA-2Z-A9JJ-01A-11D-A42J-10		48687979	149334451	3	922											
HEG1	57493	hgsc.bcm.edu	37	chr3	124732410	124732410	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaggcaaaggaggccctgaAgaagaagaagaggaggagga	18	1	18	4	0	0	6	0	1	0	5	0	10	0	10	1	6	0	1	1	6	5	0			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr3:124732410A>G	ENST00000311127.4	-	6	2080	c.2013T>C	c.(2011-2013)tcT>tcC	p.S671S	HEG1_ENST00000477536.1_5'UTR	NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	671	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						GAGGCCCTgaagaagaagaag	0.473																																					p.S671S		Atlas-SNP	.											.	HEG1	109	.	0			c.T2013C						PASS	.						46	52	50					3																	124732410		2119	4239	6358	SO:0001819	synonymous_variant	57493	exon6			CCCTGAAGAAGAA	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.2013T>C	chr3.hg19:g.124732410A>G		71.0	0.0	.		84.0	11.0	.	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Silent	SNP	ENST00000311127.4	hg19	CCDS46898.1																																																																																			.	.	.	none		0.473	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386		G	124732410	A	G	124732410	2	3	13	1	0	0	0	0	0	0	0	1	7051	59	3	3		3	HEG1	3	124732410	Silent	SNP	A	TCGA-2Z-A9JJ-01A-11D-A42J-10	76044431	124732410	73290020	4	923											
PCYT1A	5130	hgsc.bcm.edu	37	chr3	195968896	195968896	+	Missense_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	cgcatacacatcataatcccGcacaattcgggtgatgatgt	12	10	8	11	3	1	2	1	2	0	0	3	2	2	2	1	1	1	2	1	1	3	3			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr3:195968896G>A	ENST00000292823.2	-	8	803	c.631C>T	c.(631-633)Cgg>Tgg	p.R211W	PCYT1A_ENST00000431016.1_Missense_Mutation_p.R211W|PCYT1A_ENST00000419333.1_Missense_Mutation_p.R211W	NM_005017.2	NP_005008.2	P49585	PCY1A_HUMAN	phosphate cytidylyltransferase 1, choline, alpha	211					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|glycogen granule (GO:0042587)	choline-phosphate cytidylyltransferase activity (GO:0004105)|lipid binding (GO:0008289)			cervix(1)|endometrium(3)|large_intestine(8)|lung(5)|ovary(1)	18	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.28e-24)|all cancers(36;1.01e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00259)	Choline(DB00122)|Lamivudine(DB00709)	TCATAATCCCGCACAATTCGG	0.488																																					p.R211W		Atlas-SNP	.											.	PCYT1A	34	.	0			c.C631T						PASS	.						147	123	131					3																	195968896		2203	4300	6503	SO:0001583	missense	5130	exon8			AATCCCGCACAAT	L28957	CCDS3315.1	3q29	2010-07-19	2005-09-05		ENSG00000161217	ENSG00000161217	2.7.7.15		8754	protein-coding gene	gene with protein product	"phosphate cytidylyltransferase 1, choline, alpha isoform"	123695	"phosphate cytidylyltransferase 1, choline, alpha isoform"	PCYT1		7918629	Standard	NM_005017		Approved	CT, CTPCT	uc003fwg.3	P49585	OTTHUMG00000155670	ENST00000292823.2:c.631C>T	chr3.hg19:g.195968896G>A	ENSP00000292823:p.Arg211Trp	118.0	0.0	.		91.0	4.0	.	NM_005017	A9LYK9|D3DXB1|Q86Y88	Missense_Mutation	SNP	ENST00000292823.2	hg19	CCDS3315.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.813714	0.90790	.	.	ENSG00000161217	ENST00000419333;ENST00000292823;ENST00000416798;ENST00000431016;ENST00000411591;ENST00000433733;ENST00000430755	.	.	.	5.65	5.65	0.86999	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	T	0.72590	0.3479	M	0.87381	2.88	0.80722	D	1	D	0.71674	0.998	P	0.48654	0.585	T	0.79004	-0.1980	9	0.87932	D	0	-1.6477	13.7119	0.62674	0.0:0.0:0.8461:0.1538	.	211	P49585	PCY1A_HUMAN	W	211;211;172;211;211;84;145	.	ENSP00000292823:R211W	R	-	1	2	PCYT1A	197453293	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.185000	0.72013	2.685000	0.91497	0.650000	0.86243	CGG	.	.	.	none		0.488	PCYT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341147.1	NM_005017		A	195968896	G	A	195968896	3	1	13	1	0	0	0	0	1	0	0	0	11617	1086	38	1	484	1	PCYT1A	3	195968896	Missense_Mutation	SNP	G	TCGA-2Z-A9JJ-01A-11D-A42J-10	71236486	195968896	2053534	5	924											
BMP2K	55589	hgsc.bcm.edu	37	chr4	79792157	79792157	+	Missense_Mutation	SNP	G	G	C																															cagcagcagcagcagcagcaGcagcagcaccaccaccacca																										TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr4:79792157G>C	ENST00000335016.5	+	11	1618	c.1452G>C	c.(1450-1452)caG>caC	p.Q484H	BMP2K_ENST00000502871.1_Missense_Mutation_p.Q484H	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	484	Gln/His-rich.			Missing (in Ref. 2; CAB70863). {ECO:0000305}.	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						agcagcagcagcagcagcacc	0.498																																					p.Q484H		Atlas-SNP	.											.	BMP2K	169	.	0			c.G1452C						PASS	.						19	23	21					4																	79792157		2101	4115	6216	SO:0001583	missense	55589	exon11			GCAGCAGCAGCAG	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.1452G>C	chr4.hg19:g.79792157G>C	ENSP00000334836:p.Gln484His	11.0	0.0	.		10.0	5.0	.	NM_017593	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Missense_Mutation	SNP	ENST00000335016.5	hg19	CCDS47083.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	3.194|3.194	-0.165237|-0.165237	0.06461|0.06461	.|.	.|.	ENSG00000138756|ENSG00000138756	ENST00000502613|ENST00000502871;ENST00000335016;ENST00000264889	.|T;T	.|0.74002	.|0.91;-0.8	0.515|0.515	0.515|0.515	0.17013|0.17013	.|.	.|3.723490	.|0.01123	.|N	.|0.005826	T|T	0.56688|0.56688	0.2002|0.2002	N|N	0.19112|0.19112	0.55|0.55	0.21325|0.21325	N|N	0.999728|0.999728	.|B;B	.|0.23540	.|0.087;0.032	.|B;B	.|0.04013	.|0.001;0.001	T|T	0.41413|0.41413	-0.9510|-0.9510	5|10	.|0.26408	.|T	.|0.33	.|.	2.8589|2.8589	0.05580|0.05580	0.3668:0.0:0.6332:0.0|0.3668:0.0:0.6332:0.0	.|.	.|484;484	.|Q9NSY1;Q4W5H2	.|BMP2K_HUMAN;.	P|H	177|484;484;498	.|ENSP00000421768:Q484H;ENSP00000334836:Q484H	.|ENSP00000264889:Q498H	A|Q	+|+	1|3	0|2	BMP2K|BMP2K	80011181|80011181	0.879000|0.879000	0.30193|0.30193	0.126000|0.126000	0.21872|0.21872	0.036000|0.036000	0.12997|0.12997	1.288000|1.288000	0.33296|0.33296	0.550000|0.550000	0.28991|0.28991	0.163000|0.163000	0.16589|0.16589	GCA|CAG	.	.	.	none		0.498	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593		C	79792157	G	C	79792157	3	2	13	1	0	0	0	0	1	0	0	0	1460	962	34	4	1494	4	BMP2K	4	79792157	Missense_Mutation	SNP	G	TCGA-2Z-A9JJ-01A-11D-A42J-10		79792157	111362119	6	925	8	2									
BMP2K	55589	hgsc.bcm.edu	37	chr4	79792160	79792160	+	Missense_Mutation	SNP	G	G	C																															cagcagcagcagcagcagcaGcagcaccaccaccaccacca																								rs202184856|rs575644040	byFrequency	TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr4:79792160G>C	ENST00000335016.5	+	11	1621	c.1455G>C	c.(1453-1455)caG>caC	p.Q485H	BMP2K_ENST00000502871.1_Missense_Mutation_p.Q485H	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	485	Gln/His-rich.			Missing (in Ref. 2; CAB70863). {ECO:0000305}.	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						agcagcagcagcagcaccacc	0.493													G|||	44	0.00878594	0.0015	0.0043	5008	,	,		11170	0.0159		0.0219	False		,,,				2504	0.001				p.Q485H		Atlas-SNP	.											.	BMP2K	169	.	0			c.G1455C						PASS	.						19	23	22					4																	79792160		2144	4181	6325	SO:0001583	missense	55589	exon11			GCAGCAGCAGCAC	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.1455G>C	chr4.hg19:g.79792160G>C	ENSP00000334836:p.Gln485His	11.0	0.0	.		11.0	5.0	.	NM_017593	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Missense_Mutation	SNP	ENST00000335016.5	hg19	CCDS47083.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.107|0.107	-1.144327|-1.144327	0.01728|0.01728	.|.	.|.	ENSG00000138756|ENSG00000138756	ENST00000502613|ENST00000502871;ENST00000335016;ENST00000264889	.|T;T	.|0.73897	.|0.94;-0.79	.|.	.|.	.|.	.|.	.|2.710950	.|0.01643	.|U	.|0.024172	T|T	0.51941|0.51941	0.1704|0.1704	N|N	0.08118|0.08118	0|0	0.27818|0.27818	N|N	0.94189|0.94189	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.39210|0.39210	-0.9625|-0.9625	4|9	.|0.44086	.|T	.|0.13	.|.	5.0772|5.0772	0.14638|0.14638	0.0:0.6216:0.3784:0.0|0.0:0.6216:0.3784:0.0	.|.	.|485;485	.|Q9NSY1;Q4W5H2	.|BMP2K_HUMAN;.	P|H	178|485;485;499	.|ENSP00000421768:Q485H;ENSP00000334836:Q485H	.|ENSP00000264889:Q499H	A|Q	+|+	1|3	0|2	BMP2K|BMP2K	80011184|80011184	0.113000|0.113000	0.22115|0.22115	0.097000|0.097000	0.21041|0.21041	0.022000|0.022000	0.10575|0.10575	-0.733000|-0.733000	0.04898|0.04898	-1.546000|-1.546000	0.01717|0.01717	-1.555000|-1.555000	0.00892|0.00892	GCA|CAG	.	.	.	none		0.493	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593		C	79792160	G	C	79792160	3	2	13	1	0	0	0	0	1	0	0	0	1460	962	34	4	1497	4	BMP2K	4	79792160	Missense_Mutation	SNP	G	TCGA-2Z-A9JJ-01A-11D-A42J-10	3	79792160	111362116	7	926	8	2									
TUBB	203068	hgsc.bcm.edu	37	chr6	30691726	30691726	+	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	cacccagcaggtcttcgatgCcaagaacatgatggctgcct	10	8	10	13	1	1	2	0	1	1	1	2	3	1	2	3	2	4	2	3	2	2	1			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr6:30691726C>G	ENST00000327892.8	+	4	1193	c.887C>G	c.(886-888)gCc>gGc	p.A296G	TUBB_ENST00000396389.1_Missense_Mutation_p.A278G|TUBB_ENST00000330914.3_Missense_Mutation_p.A224G|TUBB_ENST00000396384.1_Missense_Mutation_p.A224G|TUBB_ENST00000435534.1_Intron|XXbac-BPG252P9.9_ENST00000607476.1_RNA	NM_178014.2	NP_821133.1	P07437	TBB5_HUMAN	tubulin, beta class I	296					cell division (GO:0051301)|cellular component movement (GO:0006928)|cellular process (GO:0009987)|cytoskeleton-dependent intracellular transport (GO:0030705)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|natural killer cell mediated cytotoxicity (GO:0042267)|protein polymerization (GO:0051258)|spindle assembly (GO:0051225)	cell body (GO:0044297)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nuclear envelope lumen (GO:0005641)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|MHC class I protein binding (GO:0042288)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(1)|endometrium(1)|kidney(8)|large_intestine(3)|lung(1)|ovary(1)|urinary_tract(1)	16					Colchicine(DB01394)|Podofilox(DB01179)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)	GTCTTCGATGCCAAGAACATG	0.592																																					p.A296G		Atlas-SNP	.											.	TUBB	30	.	0			c.C887G						PASS	.						63	62	62					6																	30691726		2203	4300	6503	SO:0001583	missense	203068	exon4			TCGATGCCAAGAA	AB062393	CCDS4687.1	6p21.33	2011-10-10	2011-10-10		ENSG00000196230	ENSG00000196230		"Tubulins"	20778	protein-coding gene	gene with protein product	"class I beta-tubulin", "beta1-tubulin"	191130	"tubulin, beta polypeptide", "tubulin, beta"			11504633, 8270253	Standard	NM_001293212		Approved	OK/SW-cl.56, MGC16435, M40, Tubb5	uc003nrl.3	P07437	OTTHUMG00000031059	ENST00000327892.8:c.887C>G	chr6.hg19:g.30691726C>G	ENSP00000339001:p.Ala296Gly	39.0	0.0	.		47.0	16.0	.	NM_178014	P05218|Q8WUC1|Q9CY33	Missense_Mutation	SNP	ENST00000327892.8	hg19	CCDS4687.1	.	.	.	.	.	.	.	.	.	.	C	13.62	2.291594	0.40494	.	.	ENSG00000196230	ENST00000327892;ENST00000422827;ENST00000330914;ENST00000396389;ENST00000396384;ENST00000538863	D;D;D;D	0.81659	-1.52;-1.52;-1.52;-1.52	4.25	4.25	0.50352	Tubulin/FtsZ, 2-layer sandwich domain (3);Tubulin/FtsZ, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.87877	0.6288	H	0.97103	3.94	0.80722	D	1	B;B	0.20550	0.046;0.038	B;B	0.40782	0.34;0.23	D	0.89650	0.3869	10	0.87932	D	0	.	14.1681	0.65490	0.0:1.0:0.0:0.0	.	296;296	P07437;F8VW92	TBB5_HUMAN;.	G	296;205;224;278;224;150	ENSP00000339001:A296G;ENSP00000365578:A224G;ENSP00000379672:A278G;ENSP00000379668:A224G	ENSP00000339001:A296G	A	+	2	0	TUBB	30799705	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.377000	0.79668	2.204000	0.70986	0.591000	0.81541	GCC	.	.	.	none		0.592	TUBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076074.2	NM_178014		G	30691726	C	G	30691726	3	3	13	1	0	0	0	0	1	0	0	0	16764	739	26	4	901	4	TUBB	6	30691726	Missense_Mutation	SNP	C	TCGA-2Z-A9JJ-01A-11D-A42J-10		30691726	140423341	8	927											
SPDEF	25803	hgsc.bcm.edu	37	chr6	34506127	34506127	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatgcccttcttgtaatacTggcggatggagcggctcagc	7	11	13	10	2	2	1	1	1	1	0	2	3	2	3	1	4	4	2	1	4	2	4			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr6:34506127T>C	ENST00000374037.3	-	6	1346	c.932A>G	c.(931-933)cAg>cGg	p.Q311R	SPDEF_ENST00000544425.1_Missense_Mutation_p.Q295R	NM_012391.2	NP_036523.1	O95238	SPDEF_HUMAN	SAM pointed domain containing ETS transcription factor	311					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						CTTGTAATACTGGCGGATGGA	0.597																																					p.Q311R		Atlas-SNP	.											.	SPDEF	34	.	0			c.A932G						PASS	.						194	179	184					6																	34506127		2203	4300	6503	SO:0001583	missense	25803	exon6			TAATACTGGCGGA	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.932A>G	chr6.hg19:g.34506127T>C	ENSP00000363149:p.Gln311Arg	180.0	0.0	.		94.0	11.0	.	NM_012391	B4DWH8|F5H778	Missense_Mutation	SNP	ENST00000374037.3	hg19	CCDS4794.1	.	.	.	.	.	.	.	.	.	.	T	29.9	5.045373	0.93685	.	.	ENSG00000124664	ENST00000374037;ENST00000544425	T;T	0.13307	2.6;2.6	5.55	5.55	0.83447	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (5);	0.000000	0.85682	D	0.000000	T	0.26340	0.0643	M	0.63428	1.95	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.996	T	0.01476	-1.1345	10	0.56958	D	0.05	.	15.6884	0.77430	0.0:0.0:0.0:1.0	.	295;311	F5H778;O95238	.;SPDEF_HUMAN	R	311;295	ENSP00000363149:Q311R;ENSP00000442715:Q295R	ENSP00000363149:Q311R	Q	-	2	0	SPDEF	34614105	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.027000	0.88791	2.108000	0.64289	0.533000	0.62120	CAG	.	.	.	none		0.597	SPDEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040246.1	NM_012391		C	34506127	T	C	34506127	3	2	13	1	0	0	0	0	1	0	0	0	15038	1580	55	3	79	3	SPDEF	6	34506127	Missense_Mutation	SNP	T	TCGA-2Z-A9JJ-01A-11D-A42J-10	3814401	34506127	136608940	9	928											
DNAH8	1769	hgsc.bcm.edu	37	chr6	38835956	38835956	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgagaggactaagagataTgaacctttccaaactggtat	15	10	9	7	0	0	3	0	2	0	2	1	6	1	4	2	2	2	1	2	2	5	4			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr6:38835956T>C	ENST00000359357.3	+	46	6415	c.6161T>C	c.(6160-6162)aTg>aCg	p.M2054T	DNAH8_ENST00000449981.2_Missense_Mutation_p.M2271T|DNAH8_ENST00000441566.1_Missense_Mutation_p.M2018T			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2054					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						CTAAGAGATATGAACCTTTCC	0.358																																					p.M2271T		Atlas-SNP	.											.	DNAH8	1239	.	0			c.T6812C						PASS	.						110	109	109					6																	38835956		2203	4300	6503	SO:0001583	missense	1769	exon48			GAGATATGAACCT	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.6161T>C	chr6.hg19:g.38835956T>C	ENSP00000352312:p.Met2054Thr	44.0	0.0	.		104.0	20.0	.	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.4|21.4	4.149799|4.149799	0.78001|0.78001	.|.	.|.	ENSG00000124721|ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566|ENST00000394393	T;T;T|.	0.18960|.	2.18;2.18;2.18|.	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.69342|.	0.3100|.	M|M	0.76328|0.76328	2.33|2.33	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.87578|.	0.998|.	T|.	0.70753|.	-0.4786|.	10|.	0.87932|.	D|.	0|.	.|.	16.1376|16.1376	0.81497|0.81497	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	2054|.	Q96JB1|.	DYH8_HUMAN|.	T|R	2259;2259;2054;2018|100	ENSP00000333363:M2259T;ENSP00000352312:M2054T;ENSP00000402294:M2018T|.	ENSP00000333363:M2259T|.	M|X	+|+	2|1	0|0	DNAH8|DNAH8	38943934|38943934	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	8.010000|8.010000	0.88615|0.88615	2.212000|2.212000	0.71576|0.71576	0.533000|0.533000	0.62120|0.62120	ATG|TGA	.	.	.	none		0.358	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		C	38835956	T	C	38835956	3	2	13	1	0	0	0	0	1	0	0	0	4609	1464	51	3	6335	3	DNAH8	6	38835956	Missense_Mutation	SNP	T	TCGA-2Z-A9JJ-01A-11D-A42J-10	4329829	38835956	132279111	10	929											
DST	667	hgsc.bcm.edu	37	chr6	56382076	56382076	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggtcatcaataatatcctTgtgtctcaaaatctccatgg	13	13	6	9	0	4	0	3	0	2	0	7	0	5	0	2	2	0	0	2	2	6	3			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr6:56382076T>C	ENST00000361203.3	-	66	17324	c.17317A>G	c.(17317-17319)Aag>Gag	p.K5773E	DST_ENST00000370788.2_Missense_Mutation_p.K3687E|DST_ENST00000312431.6_3'UTR|DST_ENST00000421834.2_Missense_Mutation_p.K3796E|DST_ENST00000370754.5_Missense_Mutation_p.K6062E|DST_ENST00000340834.4_5'UTR|DST_ENST00000446842.2_Missense_Mutation_p.K5558E|DST_ENST00000370769.4_Missense_Mutation_p.K5884E|DST_ENST00000244364.6_Missense_Mutation_p.K3470E			Q03001	DYST_HUMAN	dystonin	5773					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)			ATAATATCCTTGTGTCTCAAA	0.328																																					p.K3470E		Atlas-SNP	.											.	DST	1427	.	0			c.A10408G						PASS	.						190	183	185					6																	56382076		1876	4096	5972	SO:0001583	missense	667	exon52			TATCCTTGTGTCT	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.17317A>G	chr6.hg19:g.56382076T>C	ENSP00000354508:p.Lys5773Glu	14.0	0.0	.		34.0	11.0	.	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	hg19		.	.	.	.	.	.	.	.	.	.	T	19.78	3.891493	0.72524	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8;0.8	5.45	5.45	0.79879	.	0.000000	0.53938	D	0.000044	T	0.59088	0.2168	M	0.71581	2.175	0.30416	N	0.778577	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;0.994	D;D;D;D;D	0.87578	0.998;0.992;0.998;0.998;0.941	T	0.58509	-0.7624	9	0.31617	T	0.26	.	15.8029	0.78471	0.0:0.0:0.0:1.0	.	3796;5884;6062;5882;3470	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	E	3470;6062;5884;3796;5558;3687;5773	ENSP00000244364:K3470E;ENSP00000359790:K6062E;ENSP00000359805:K5884E;ENSP00000400883:K3796E;ENSP00000393645:K5558E;ENSP00000359824:K3687E;ENSP00000354508:K5773E	ENSP00000244364:K3470E	K	-	1	0	DST	56490035	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.997000	0.88414	2.189000	0.69895	0.533000	0.62120	AAG	.	.	.	none		0.328	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		C	56382076	T	C	56382076	3	2	13	1	0	0	0	0	1	0	0	0	4785	1821	63	3	5239	3	DST	6	56382076	Missense_Mutation	SNP	T	TCGA-2Z-A9JJ-01A-11D-A42J-10	17546120	56382076	114732991	11	930											
FAM46A	55603	hgsc.bcm.edu	37	chr6	82461742	82461742	+	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	ccgccaccgccgaagtcgccGccgccgaagtcgccgccgcc	5	2	12	22	10	0	0	0	0	0	0	2	2	0	0	10	0	0	0	10	0	2	0			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr6:82461742G>A	ENST00000320172.6	-	2	431	c.117C>T	c.(115-117)ggC>ggT	p.G39G	FAM46A_ENST00000369756.3_Silent_p.G120G|FAM46A_ENST00000369754.3_Silent_p.G58G	NM_017633.2	NP_060103.2	Q96IP4	FA46A_HUMAN	family with sequence similarity 46, member A	39			Missing. {ECO:0000269|PubMed:12054608, ECO:0000269|PubMed:16545789}.		regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)		poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	12		all_cancers(76;6.74e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000282)|all_epithelial(107;0.0104)		BRCA - Breast invasive adenocarcinoma(397;0.0428)		cgaagtcgccgccgccgaagt	0.667																																					p.G39G		Atlas-SNP	.											.	FAM46A	37	.	0			c.C117T						PASS	.						7	8	8					6																	82461742		1601	3424	5025	SO:0001819	synonymous_variant	55603	exon2			GTCGCCGCCGCCG	AF350451	CCDS34489.1	6q14	2008-07-03	2004-08-19	2004-08-26	ENSG00000112773	ENSG00000112773			18345	protein-coding gene	gene with protein product		611357	"chromosome 6 open reading frame 37"	C6orf37		12054608, 17803723	Standard	NM_017633		Approved	FLJ20037	uc003pjg.3	Q96IP4	OTTHUMG00000015097	ENST00000320172.6:c.117C>T	chr6.hg19:g.82461742G>A		43.0	0.0	.		37.0	5.0	.	NM_017633	A8K7U4|Q5TF86|Q8NFZ9|Q9BW32|Q9NXV5	Silent	SNP	ENST00000320172.6	hg19	CCDS34489.1																																																																																			.	.	.	none		0.667	FAM46A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041331.1			A	82461742	G	A	82461742	2	1	13	1	0	0	0	0	0	0	0	1	5572	1074	38	1		1	FAM46A	6	82461742	Silent	SNP	G	TCGA-2Z-A9JJ-01A-11D-A42J-10	26079666	82461742	88653325	12	931											
ABCB5	340273	hgsc.bcm.edu	37	chr7	20739491	20739492	+	Frame_Shift_Ins	INS	-	-	T																															acattaaagcatgatgcagaINSaatttattccatgatattcg																										TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr7:20739491_20739492insT	ENST00000404938.2	+	18	2850_2851	c.2198_2199insT	c.(2197-2202)gaaattfs	p.EI733fs	ABCB5_ENST00000258738.6_Frame_Shift_Ins_p.EI288fs	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	733	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						CATGATGCAGAAATTTATTCCA	0.307																																					p.E733fs		Atlas-Indel,Pindel	.											.	ABCB5	357	.	0			c.2198_2199insT						PASS	.																																			SO:0001589	frameshift_variant	340273	exon18			.	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	Exception_encountered	chr7.hg19:g.20739491_20739492insT	ENSP00000384881:p.Glu733fs	48.0	0.0	0		78.0	17.0	0.217949	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Frame_Shift_Ins	INS	ENST00000404938.2	hg19	CCDS55090.1																																																																																			.	.	.	none		0.307	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559		T	20739492	-	T	20739491	7	5	13	1	0	1	1	0	0	0	0	0	44	246	9	0	2305	0	ABCB5	7	20739491	Frame_Shift_Ins	INS	-	TCGA-2Z-A9JJ-01A-11D-A42J-10		20739491	138399172	13	932											
GPR124	25960	hgsc.bcm.edu	37	chr8	37690712	37690712	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acgacatcaccagggtgctgTacaccttcgtgctggtgagg	8	9	13	11	2	1	1	1	1	0	0	2	2	1	1	2	3	3	3	2	3	1	2			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr8:37690712T>C	ENST00000412232.2	+	9	1295	c.1282T>C	c.(1282-1284)Tac>Cac	p.Y428H	GPR124_ENST00000315215.7_Missense_Mutation_p.Y428H	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	428					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)			CAGGGTGCTGTACACCTTCGT	0.667																																					p.Y428H		Atlas-SNP	.											.	GPR124	85	.	0			c.T1282C						PASS	.						41	37	38					8																	37690712		2203	4297	6500	SO:0001583	missense	25960	exon9			GTGCTGTACACCT	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.1282T>C	chr8.hg19:g.37690712T>C	ENSP00000406367:p.Tyr428His	51.0	0.0	.		27.0	8.0	.	NM_032777	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Missense_Mutation	SNP	ENST00000412232.2	hg19	CCDS6097.2	.	.	.	.	.	.	.	.	.	.	T	12.84	2.058746	0.36277	.	.	ENSG00000020181	ENST00000416514;ENST00000315215;ENST00000412232	T;T	0.59502	0.26;0.26	5.11	5.11	0.69529	.	0.144593	0.47852	N	0.000209	T	0.41858	0.1177	N	0.16743	0.435	0.47094	D	0.999312	B;B	0.27416	0.178;0.009	B;B	0.29862	0.108;0.009	T	0.29119	-1.0022	10	0.15499	T	0.54	-21.7041	14.9163	0.70801	0.0:0.0:0.0:1.0	.	428;428	Q96PE1-2;Q96PE1	.;GP124_HUMAN	H	421;428;428	ENSP00000323508:Y428H;ENSP00000406367:Y428H	ENSP00000323508:Y428H	Y	+	1	0	GPR124	37809870	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.087000	0.50167	1.924000	0.55735	0.533000	0.62120	TAC	.	.	.	none		0.667	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2			C	37690712	T	C	37690712	3	2	13	1	0	0	0	0	1	0	0	0	6645	1638	57	3	1295	3	GPR124	8	37690712	Missense_Mutation	SNP	T	TCGA-2Z-A9JJ-01A-11D-A42J-10		37690712	108673310	14	933											
VPS13A	23230	hgsc.bcm.edu	37	chr9	79936242	79936242	+	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	aatgttaaacaatttagtcaAggtaagaaaagaaatttgaa	21	11	7	2	0	1	3	1	1	0	2	1	3	1	3	0	1	1	2	0	1	11	5			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr9:79936242A>G	ENST00000360280.3	+	43	5833	c.5573A>G	c.(5572-5574)aAg>aGg	p.K1858R	VPS13A_ENST00000376636.3_Splice_Site_p.K1819R|VPS13A_ENST00000376634.4_Splice_Site_p.K1858R|VPS13A_ENST00000357409.5_Splice_Site_p.K1858R	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	1858					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						AATTTAGTCAAGGTAAGAAAA	0.279																																					p.K1858R		Atlas-SNP	.											.	VPS13A	735	.	0			c.A5573G						PASS	.						26	26	26					9																	79936242		2195	4278	6473	SO:0001630	splice_region_variant	23230	exon43			TAGTCAAGGTAAG	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.5574+1A>G	chr9.hg19:g.79936242A>G		88.0	0.0	.		221.0	75.0	.	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	hg19	CCDS6655.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.69|16.69	3.193752|3.193752	0.58017|0.58017	.|.	.|.	ENSG00000197969|ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409|ENST00000419472	T;T;T;T|.	0.50813|.	0.73;0.73;0.73;0.73|.	5.81|5.81	5.81|5.81	0.92471|0.92471	.|.	0.551714|.	0.20291|.	N|.	0.095247|.	T|T	0.63295|0.63295	0.2499|0.2499	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	D|D	1|1	B;P;B;B;B|.	0.44877|.	0.376;0.845;0.411;0.404;0.404|.	B;P;B;B;B|.	0.48677|.	0.108;0.586;0.055;0.234;0.234|.	T|T	0.61855|0.61855	-0.6977|-0.6977	10|5	0.44086|.	T|.	0.13|.	.|.	12.3993|12.3993	0.55404|0.55404	0.821:0.179:0.0:0.0|0.821:0.179:0.0:0.0	.|.	110;1819;1858;1858;1858|.	B1ALW4;Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4|.	.;.;VP13A_HUMAN;.;.|.	R|G	1858;1819;1858;1858|111	ENSP00000365821:K1858R;ENSP00000365823:K1819R;ENSP00000353422:K1858R;ENSP00000349985:K1858R|.	ENSP00000349985:K1858R|.	K|R	+|+	2|1	0|2	VPS13A|VPS13A	79126062|79126062	0.998000|0.998000	0.40836|0.40836	0.940000|0.940000	0.37924|0.37924	0.835000|0.835000	0.47333|0.47333	1.435000|1.435000	0.34969|0.34969	2.214000|2.214000	0.71695|0.71695	0.477000|0.477000	0.44152|0.44152	AAG|AGG	.	.	.	none		0.279	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	Missense_Mutation	G	79936242	A	G	79936242	5	3	13	1	0	0	0	0	0	0	1	0	17201	86	3	3	5743	3	VPS13A	9	79936242	Splice_Site	SNP	A	TCGA-2Z-A9JJ-01A-11D-A42J-10		79936242	61277189	15	934											
ALKBH8	91801	hgsc.bcm.edu	37	chr11	107427686	107427686	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaccgggagcagctggttcCgactcacaccattacccaaa	13	6	8	14	2	1	0	1	0	0	0	2	2	2	1	4	2	4	3	4	2	3	2			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr11:107427686C>T	ENST00000428149.2	-	3	324	c.173G>A	c.(172-174)cGg>cAg	p.R58Q	ALKBH8_ENST00000389568.3_Missense_Mutation_p.R58Q|ALKBH8_ENST00000429370.1_Missense_Mutation_p.R58Q|ALKBH8_ENST00000417449.2_Missense_Mutation_p.R61Q|ALKBH8_ENST00000530933.1_5'UTR	NM_138775.2	NP_620130.2	Q96BT7	ALKB8_HUMAN	alkB, alkylation repair homolog 8 (E. coli)	58	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)		CAGCTGGTTCCGACTCACACC	0.433																																					p.R58Q		Atlas-SNP	.											.	ALKBH8	88	.	0			c.G173A						PASS	.						96	94	94					11																	107427686		2201	4298	6499	SO:0001583	missense	91801	exon3			TGGTTCCGACTCA	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.173G>A	chr11.hg19:g.107427686C>T	ENSP00000415885:p.Arg58Gln	74.0	0.0	.		139.0	48.0	.	NM_138775	B1Q2M0|B4DEF6|Q8N989	Missense_Mutation	SNP	ENST00000428149.2	hg19	CCDS8337.2	.	.	.	.	.	.	.	.	.	.	C	30	5.054614	0.93793	.	.	ENSG00000137760	ENST00000428149;ENST00000429370;ENST00000389568;ENST00000417449	T;T;T;T	0.45276	0.9;2.44;0.9;0.9	5.67	5.67	0.87782	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	T	0.64193	0.2576	M	0.61703	1.905	0.58432	D	0.999998	D	0.89917	1.0	D	0.85130	0.997	T	0.63919	-0.6528	10	0.59425	D	0.04	-18.0663	18.7588	0.91842	0.0:1.0:0.0:0.0	.	58	Q96BT7	ALKB8_HUMAN	Q	58;58;58;61	ENSP00000415885:R58Q;ENSP00000391225:R58Q;ENSP00000374219:R58Q;ENSP00000397673:R61Q	ENSP00000260318:R58Q	R	-	2	0	ALKBH8	106932896	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	6.676000	0.74498	2.697000	0.92050	0.655000	0.94253	CGG	.	.	.	none		0.433	ALKBH8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347071.2	NM_138775		T	107427686	C	T	107427686	3	4	13	1	0	0	0	0	1	0	0	0	533	652	23	1	1861	1	ALKBH8	11	107427686	Missense_Mutation	SNP	C	TCGA-2Z-A9JJ-01A-11D-A42J-10		107427686	27578830	16	935											
ITPR2	3709	hgsc.bcm.edu	37	chr12	26810812	26810812	+	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	ctccatggggttgtctgcttGcattgagaccacccttcaaa	8	12	9	12	0	2	1	1	1	1	1	3	2	3	1	3	2	2	3	3	2	1	4			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr12:26810812G>A	ENST00000381340.3	-	18	2436	c.2020C>T	c.(2020-2022)Caa>Taa	p.Q674*		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	674					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)	TTGTCTGCTTGCATTGAGACC	0.373																																					p.Q674X		Atlas-SNP	.											.	ITPR2	270	.	0			c.C2020T						PASS	.						100	91	94					12																	26810812		1861	4097	5958	SO:0001587	stop_gained	3709	exon18			CTGCTTGCATTGA	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.2020C>T	chr12.hg19:g.26810812G>A	ENSP00000370744:p.Gln674*	80.0	0.0	.		106.0	30.0	.	NM_002223	O94773	Nonsense_Mutation	SNP	ENST00000381340.3	hg19	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	G	43	10.411246	0.99400	.	.	ENSG00000123104	ENST00000381340	.	.	.	4.4	4.4	0.53042	.	0.380582	0.29908	N	0.010886	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	17.5669	0.87922	0.0:0.0:1.0:0.0	.	.	.	.	X	674	.	ENSP00000370744:Q674X	Q	-	1	0	ITPR2	26702079	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	5.467000	0.66737	2.448000	0.82819	0.655000	0.94253	CAA	.	.	.	none		0.373	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		A	26810812	G	A	26810812	4	1	13	1	0	0	0	0	0	1	0	0	7928	1328	46	2	6245	2	ITPR2	12	26810812	Nonsense_Mutation	SNP	G	TCGA-2Z-A9JJ-01A-11D-A42J-10		26810812	107041083	17	936											
SIRT7	51547	hgsc.bcm.edu	37	chr17	79871988	79871988	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggttcacgatgtaaagcttcGgccgccggctagggggcttg	6	9	16	10	4	1	0	1	0	0	0	2	1	1	0	2	5	1	5	2	5	3	5	rs560137203		TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr17:79871988G>A	ENST00000328666.6	-	8	934	c.872C>T	c.(871-873)cCg>cTg	p.P291L	PCYT2_ENST00000570391.1_5'Flank|PCYT2_ENST00000538936.2_5'Flank|PCYT2_ENST00000571105.1_5'Flank|PCYT2_ENST00000331285.3_5'Flank|PCYT2_ENST00000538721.2_5'Flank|PCYT2_ENST00000570388.1_5'Flank	NM_016538.2	NP_057622.1	Q9NRC8	SIR7_HUMAN	sirtuin 7	291	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)			GTAAAGCTTCGGCCGCCGGCT	0.572													G|||	1	0.000199681	0	0	5008	,	,		19606	0.001		0	False		,,,				2504	0				p.P291L		Atlas-SNP	.											.	SIRT7	37	.	0			c.C872T						PASS	.						58	59	59					17																	79871988		2203	4300	6503	SO:0001583	missense	51547	exon8			AGCTTCGGCCGCC	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.872C>T	chr17.hg19:g.79871988G>A	ENSP00000329466:p.Pro291Leu	145.0	0.0	.		82.0	4.0	.	NM_016538	A8K2K0|B3KSU8|Q3MIK4|Q9NSZ6|Q9NUS6	Missense_Mutation	SNP	ENST00000328666.6	hg19	CCDS11792.1	.	.	.	.	.	.	.	.	.	.	G	19.60	3.857274	0.71834	.	.	ENSG00000187531	ENST00000328666;ENST00000536038	T	0.15834	2.39	4.27	3.3	0.37823	.	0.000000	0.85682	D	0.000000	T	0.31389	0.0795	M	0.75884	2.315	0.80722	D	1	P;D	0.53151	0.953;0.958	B;P	0.52793	0.372;0.709	T	0.12091	-1.0561	10	0.56958	D	0.05	-21.8466	12.1883	0.54252	0.0829:0.0:0.9171:0.0	.	291;291	A8K2K0;Q9NRC8	.;SIRT7_HUMAN	L	291;274	ENSP00000329466:P291L	ENSP00000329466:P291L	P	-	2	0	SIRT7	77465280	1.000000	0.71417	0.992000	0.48379	0.659000	0.38960	9.121000	0.94375	1.034000	0.39945	0.549000	0.68633	CCG	.	.	.	none		0.572	SIRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439961.1	NM_016538		A	79871988	G	A	79871988	3	1	13	1	0	0	0	0	1	0	0	0	14356	1116	39	1	342	1	SIRT7	17	79871988	Missense_Mutation	SNP	G	TCGA-2Z-A9JJ-01A-11D-A42J-10		79871988	1323222	18	937											
MUC16	94025	hgsc.bcm.edu	37	chr19	9062897	9062897	+	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	ctggaggtagggagtctggtGatggtttctgtggaagtctc	6	13	17	5	0	3	1	0	1	3	0	4	4	3	4	0	6	0	2	0	6	2	2			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr19:9062897G>A	ENST00000397910.4	-	3	24752	c.24549C>T	c.(24547-24549)atC>atT	p.I8183I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	8185	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						GGAGTCTGGTGATGGTTTCTG	0.488																																					p.I8183I		Atlas-SNP	.											.	MUC16	4315	.	0			c.C24549T						PASS	.						121	116	118					19																	9062897		2075	4211	6286	SO:0001819	synonymous_variant	94025	exon3			TCTGGTGATGGTT	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.24549C>T	chr19.hg19:g.9062897G>A		43.0	0.0	.		54.0	24.0	.	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.	.	none		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9062897	G	A	9062897	2	1	13	1	0	0	0	0	0	0	0	1	9980	1280	45	2		2	MUC16	19	9062897	Silent	SNP	G	TCGA-2Z-A9JJ-01A-11D-A42J-10		9062897	50066086	19	938											
PRDM15	63977	hgsc.bcm.edu	37	chr21	43230577	43230577	+	Missense_Mutation	SNP	T	T	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	acaccttggtcccgcacagcTggcagctctgcgcctccacc	6	7	9	19	2	1	0	0	0	1	0	3	0	3	0	5	2	3	4	5	2	0	1			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chr21:43230577T>G	ENST00000269844.3	-	28	3793	c.3683A>C	c.(3682-3684)cAg>cCg	p.Q1228P	PRDM15_ENST00000398548.1_Missense_Mutation_p.Q899P|PRDM15_ENST00000422911.1_Missense_Mutation_p.Q919P|PRDM15_ENST00000538201.1_Missense_Mutation_p.Q882P|PRDM15_ENST00000447207.2_Missense_Mutation_p.Q862P|PRDM15_ENST00000470586.1_5'UTR	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	1228					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						CCCGCACAGCTGGCAGCTCTG	0.647																																					p.Q1228P		Atlas-SNP	.											.	PRDM15	110	.	0			c.A3683C						PASS	.						91	60	71					21																	43230577		2203	4299	6502	SO:0001583	missense	63977	exon28			CACAGCTGGCAGC	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.3683A>C	chr21.hg19:g.43230577T>G	ENSP00000269844:p.Gln1228Pro	76.0	0.0	.		38.0	13.0	.	NM_022115	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Missense_Mutation	SNP	ENST00000269844.3	hg19	CCDS13676.1	.	.	.	.	.	.	.	.	.	.	t	21.2	4.114809	0.77210	.	.	ENSG00000141956	ENST00000422911;ENST00000398548;ENST00000538201;ENST00000447207;ENST00000269844	T;T;T;T;T	0.08008	4.82;4.82;4.82;4.82;3.14	4.11	4.11	0.48088	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	.	.	.	.	T	0.11067	0.0270	N	0.14661	0.345	0.43868	D	0.996471	D;D;D	0.62365	0.961;0.989;0.991	P;P;P	0.57468	0.815;0.767;0.821	T	0.16600	-1.0397	9	0.54805	T	0.06	-30.9208	12.2904	0.54815	0.0:0.0:0.0:1.0	.	1228;919;899	P57071;E9PDJ6;E9PF37	PRD15_HUMAN;.;.	P	919;899;882;862;1228	ENSP00000408592:Q919P;ENSP00000381556:Q899P;ENSP00000444044:Q882P;ENSP00000390245:Q862P;ENSP00000269844:Q1228P	ENSP00000269844:Q1228P	Q	-	2	0	PRDM15	42103646	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.744000	0.85034	1.496000	0.48567	0.255000	0.18592	CAG	.	.	.	none		0.647	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115		G	43230577	T	G	43230577	3	3	13	1	0	0	0	0	1	0	0	0	12466	1580	55	5	856	5	PRDM15	21	43230577	Missense_Mutation	SNP	T	TCGA-2Z-A9JJ-01A-11D-A42J-10		43230577	4899318	20	939											
DMD	1756	hgsc.bcm.edu	37	chrX	31462641	31462641	+	Missense_Mutation	SNP	A	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	tcaggtcttccagagtgctgAggttatacggtgagagctga	9	11	14	7	1	2	4	1	3	1	2	3	5	3	4	1	3	3	3	1	3	2	3			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chrX:31462641A>C	ENST00000357033.4	-	60	9247	c.9041T>G	c.(9040-9042)cTc>cGc	p.L3014R	DMD_ENST00000541735.1_Missense_Mutation_p.L554R|DMD_ENST00000378677.2_Missense_Mutation_p.L3010R|DMD_ENST00000343523.2_Missense_Mutation_p.L554R|DMD_ENST00000359836.1_Missense_Mutation_p.L554R|DMD_ENST00000474231.1_Missense_Mutation_p.L554R|DMD_ENST00000378707.3_Missense_Mutation_p.L554R	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	3014					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)				CAGAGTGCTGAGGTTATACGG	0.448																																					p.L3014R		Atlas-SNP	.											.	DMD	2127	.	0			c.T9041G	GRCh37	CD054319	DMD	D		PASS	.						148	119	129					X																	31462641		2202	4300	6502	SO:0001583	missense	1756	exon60			GTGCTGAGGTTAT	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.9041T>G	chrX.hg19:g.31462641A>C	ENSP00000354923:p.Leu3014Arg	37.0	0.0	.		123.0	58.0	.	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	A	18.45	3.625732	0.66901	.	.	ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000358062;ENST00000378677;ENST00000357033;ENST00000359836;ENST00000343523;ENST00000542849;ENST00000535280;ENST00000378707;ENST00000541735;ENST00000474231	T;T;T;T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86	5.56	5.56	0.83823	.	0.000000	0.30911	U	0.008637	T	0.61160	0.2325	M	0.62723	1.935	0.49213	D	0.999766	P;D;D;D;D;B;P;P;D;D;P	0.76494	0.951;0.999;0.986;0.997;0.997;0.185;0.741;0.741;0.999;0.999;0.934	P;D;P;D;D;B;P;B;D;D;P	0.71184	0.699;0.969;0.876;0.952;0.952;0.187;0.67;0.395;0.972;0.952;0.685	T	0.58487	-0.7628	10	0.10902	T	0.67	.	13.5718	0.61851	1.0:0.0:0.0:0.0	.	3006;3014;3010;1673;1670;554;554;554;554;554;2891	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6;F8VX32;E7ESB2;E7EQS5;E7EQR9;F5GZY3;F5GZT3	.;DMD_HUMAN;.;.;.;.;.;.;.;.;.	R	3006;1673;1670;710;3010;3014;554;554;3014;2891;554;554;554	ENSP00000350765:L710R;ENSP00000367948:L3010R;ENSP00000354923:L3014R;ENSP00000352894:L554R;ENSP00000340057:L554R;ENSP00000367979:L554R;ENSP00000444119:L554R;ENSP00000417123:L554R	ENSP00000340057:L554R	L	-	2	0	DMD	31372562	1.000000	0.71417	0.982000	0.44146	0.871000	0.50021	6.407000	0.73280	1.848000	0.53677	0.437000	0.28790	CTC	.	.	.	none		0.448	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		C	31462641	A	C	31462641	3	2	13	1	0	0	0	0	1	0	0	0	4582	304	11	5	2210	5	DMD	23	31462641	Missense_Mutation	SNP	A	TCGA-2Z-A9JJ-01A-11D-A42J-10		31462641	123807919	21	940											
TIMP1	7076	hgsc.bcm.edu	37	chrX	47445924	47445924	+	Missense_Mutation	SNP	T	T	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	ccctcctcccttccaggtgtTtccctgtttatccatcccct	3	15	4	19	0	0	0	0	0	0	0	6	0	6	0	8	1	0	2	8	1	1	4			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chrX:47445924T>G	ENST00000218388.4	+	6	628	c.458T>G	c.(457-459)tTt>tGt	p.F153C	MIR4769_ENST00000584126.1_RNA|SYN1_ENST00000340666.4_Intron|SYN1_ENST00000295987.7_Intron|TIMP1_ENST00000377017.1_Missense_Mutation_p.F89C	NM_003254.2	NP_003245.1	P01033	TIMP1_HUMAN	TIMP metallopeptidase inhibitor 1	153					aging (GO:0007568)|blood coagulation (GO:0007596)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of trophoblast cell migration (GO:1901164)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell proliferation (GO:0008284)|regulation of integrin-mediated signaling pathway (GO:2001044)|response to cytokine (GO:0034097)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	cytokine activity (GO:0005125)|metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)			endometrium(1)|large_intestine(2)	3						TTCCAGGTGTTTCCCTGTTTA	0.577																																					p.F153C		Atlas-SNP	.											.	TIMP1	12	.	0			c.T458G						PASS	.						138	106	117					X																	47445924		2203	4300	6503	SO:0001583	missense	7076	exon6			AGGTGTTTCCCTG		CCDS14281.1	Xp11.3-p11.23	2008-07-29	2005-08-08		ENSG00000102265	ENSG00000102265			11820	protein-coding gene	gene with protein product		305370	"tissue inhibitor of metalloproteinase 1 (erythroid potentiating activity, collagenase inhibitor)"	TIMP, CLGI			Standard	XM_005272645		Approved	EPO	uc004dif.3	P01033	OTTHUMG00000021447	ENST00000218388.4:c.458T>G	chrX.hg19:g.47445924T>G	ENSP00000218388:p.Phe153Cys	79.0	0.0	.		46.0	18.0	.	NM_003254	Q14252|Q9UCU1	Missense_Mutation	SNP	ENST00000218388.4	hg19	CCDS14281.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.76|15.76	2.929866|2.929866	0.52759|0.52759	.|.	.|.	ENSG00000102265|ENSG00000102265	ENST00000218388;ENST00000377017|ENST00000445623	D;D|D	0.93307|0.92858	-3.2;-3.2|-3.12	5.35|5.35	4.05|4.05	0.47172|0.47172	Tissue inhibitor of metalloproteinases-like, OB-fold (1);|.	0.712428|0.712428	0.12937|0.12937	N|N	0.426934|0.426934	D|D	0.91412|0.91412	0.7290|0.7290	M|M	0.68317|0.68317	2.08|2.08	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.64506|.	0.926|.	D|D	0.85916|0.85916	0.1443|0.1443	10|8	0.38643|0.14252	T|T	0.18|0.57	.|.	7.9867|7.9867	0.30216|0.30216	0.1993:0.0:0.0:0.8007|0.1993:0.0:0.0:0.8007	.|.	153|.	P01033|.	TIMP1_HUMAN|.	C|V	153;89|111	ENSP00000218388:F153C;ENSP00000366216:F89C|ENSP00000410983:F111V	ENSP00000218388:F153C|ENSP00000410983:F111V	F|F	+|+	2|1	0|0	TIMP1|TIMP1	47330868|47330868	0.944000|0.944000	0.32072|0.32072	1.000000|1.000000	0.80357|0.80357	0.970000|0.970000	0.65996|0.65996	1.733000|1.733000	0.38156|0.38156	1.793000|1.793000	0.52555|0.52555	0.425000|0.425000	0.28330|0.28330	TTT|TTC	.	.	.	none		0.577	TIMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056423.1	NM_003254		G	47445924	T	G	47445924	3	3	13	1	0	0	0	0	1	0	0	0	15929	1841	64	5	476	5	TIMP1	23	47445924	Missense_Mutation	SNP	T	TCGA-2Z-A9JJ-01A-11D-A42J-10	15983283	47445924	107824636	22	941											
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-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	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	chrX.hg19:g.50350751G>C	ENSP00000289292:p.Gln1131Glu	50.0	0.0	.		125.0	5.0	.	NM_020717	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	hg19	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	13	1	0	0	0	0	1	0	0	0	14309	1386	48	4	1106	4	SHROOM4	23	50350751	Missense_Mutation	SNP	G	TCGA-2Z-A9JJ-01A-11D-A42J-10	2904827	50350751	104919809	23	942											
HUWE1	10075	hgsc.bcm.edu	37	chrX	53627271	53627271	+	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	gctccatcctgttccccatcTacagatgtataagaggggag	10	10	10	11	0	1	2	0	0	1	2	4	3	4	3	4	2	1	3	4	2	3	4			TCGA-2Z-A9JJ-01A-11D-A42J-10	TCGA-2Z-A9JJ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d24232d5-301a-471f-bfc3-a6cc25ff860b	47cbf5dc-dc36-4c04-905c-d43e8c5d986e	g.chrX:53627271T>C	ENST00000342160.3	-	28	3429		c.e28-2		HUWE1_ENST00000218328.8_Splice_Site|HUWE1_ENST00000262854.6_Splice_Site			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase						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						GTTCCCCATCTACAGATGTAT	0.453																																					.		Atlas-SNP	.											.	HUWE1	724	.	0			c.2972-2A>G						PASS	.						60	49	53					X																	53627271		2201	4299	6500	SO:0001630	splice_region_variant	10075	exon30			CCCATCTACAGAT	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.2972-2A>G	chrX.hg19:g.53627271T>C		30.0	0.0	.		98.0	4.0	.	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Splice_Site	SNP	ENST00000342160.3	hg19	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	T	15.18	2.757675	0.49468	.	.	ENSG00000086758	ENST00000342160;ENST00000427052;ENST00000262854;ENST00000218328	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.6011	0.62020	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	HUWE1	53643996	1.000000	0.71417	0.883000	0.34634	0.741000	0.42261	5.399000	0.66314	1.855000	0.53841	0.425000	0.28330	.	.	.	.	none		0.453	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119	Intron	C	53627271	T	C	53627271	5	2	13	1	0	0	0	0	0	0	1	0	7468	1536	53	3	10378	3	HUWE1	23	53627271	Splice_Site	SNP	T	TCGA-2Z-A9JJ-01A-11D-A42J-10	3276520	53627271	101643289	24	943											
PLOD1	5351	hgsc.bcm.edu	37	chr1	12030830	12030830	+	Missense_Mutation	SNP	T	T	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	caaattcctgctggagtacaTtgcgcccatgacggagaagc	11	8	11	11	2	0	2	0	1	0	1	1	4	1	3	2	2	4	2	2	2	3	3			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr1:12030830T>G	ENST00000196061.4	+	17	1886	c.1859T>G	c.(1858-1860)aTt>aGt	p.I620S	PLOD1_ENST00000376369.3_Missense_Mutation_p.I667S	NM_000302.3	NP_000293.2	Q02809	PLOD1_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1	620					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)	CTGGAGTACATTGCGCCCATG	0.592																																					p.I620S		Atlas-SNP	.											.	PLOD1	75	.	0			c.T1859G						PASS	.						100	83	89					1																	12030830		2203	4300	6503	SO:0001583	missense	5351	exon17			AGTACATTGCGCC	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.1859T>G	chr1.hg19:g.12030830T>G	ENSP00000196061:p.Ile620Ser	151.0	0.0	.		70.0	13.0	.	NM_000302	B4DR87|Q96AV9|Q9H132	Missense_Mutation	SNP	ENST00000196061.4	hg19	CCDS142.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.681482	0.88542	.	.	ENSG00000083444	ENST00000414311;ENST00000376369;ENST00000196061	T;T	0.68765	-0.35;-0.35	5.94	5.94	0.96194	Prolyl 4-hydroxylase, alpha subunit (1);	0.150032	0.56097	D	0.000024	T	0.69169	0.3081	M	0.83953	2.67	0.80722	D	1	P;B	0.40431	0.717;0.434	B;B	0.35413	0.202;0.202	T	0.75816	-0.3184	10	0.87932	D	0	.	15.579	0.76418	0.0:0.0:0.0:1.0	.	667;620	B4DR87;Q02809	.;PLOD1_HUMAN	S	284;667;620	ENSP00000365548:I667S;ENSP00000196061:I620S	ENSP00000196061:I620S	I	+	2	0	PLOD1	11953417	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.267000	0.72546	2.279000	0.76181	0.459000	0.35465	ATT	.	.	.	none		0.592	PLOD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006865.1	NM_000302		G	12030830	T	G	12030830	3	3	14	1	0	0	0	0	1	0	0	0	12108	1493	52	5	1925	5	PLOD1	1	12030830	Missense_Mutation	SNP	T	TCGA-2Z-A9JK-01A-11D-A42J-10		12030830	237219791	1	944											
PTPRU	10076	hgsc.bcm.edu	37	chr1	29585229	29585229	+	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	ggaatatgactggatcccacGgccgtcagtggcaccaggct	9	7	13	12	2	1	1	1	1	0	0	2	3	2	3	3	5	0	2	3	5	2	1	rs145487041		TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr1:29585229G>T	ENST00000345512.3	+	3	547	c.418G>T	c.(418-420)Ggc>Tgc	p.G140C	PTPRU_ENST00000428026.2_Missense_Mutation_p.G140C|PTPRU_ENST00000356870.3_Missense_Mutation_p.G140C|PTPRU_ENST00000460170.2_Missense_Mutation_p.G140C|PTPRU_ENST00000323874.8_Missense_Mutation_p.G140C|PTPRU_ENST00000373779.3_Missense_Mutation_p.G140C	NM_005704.4	NP_005695.3	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	140	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				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)		TGGATCCCACGGCCGTCAGTG	0.642																																					p.G140C		Atlas-SNP	.											.	PTPRU	374	.	0			c.G418T						PASS	.						58	58	58					1																	29585229		2203	4300	6503	SO:0001583	missense	10076	exon3			TCCCACGGCCGTC	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.418G>T	chr1.hg19:g.29585229G>T	ENSP00000334941:p.Gly140Cys	130.0	0.0	.		107.0	6.0	.	NM_001195001	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	Missense_Mutation	SNP	ENST00000345512.3	hg19	CCDS334.1	.	.	.	.	.	.	.	.	.	.	G	32	5.152038	0.94645	.	.	ENSG00000060656	ENST00000345512;ENST00000373779;ENST00000356870;ENST00000323874;ENST00000428026;ENST00000460170	T;T;T;T;T;T	0.02974	4.09;4.09;4.09;4.09;4.09;4.09	5.72	5.72	0.89469	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.140445	0.46145	D	0.000315	T	0.20941	0.0504	M	0.89478	3.035	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	0.83275	0.994;0.994;0.994;0.996;0.996	T	0.00446	-1.1734	9	.	.	.	.	18.8634	0.92281	0.0:0.0:1.0:0.0	.	140;140;140;140;140	Q92729-3;Q92729-4;Q92729-2;E9PH42;Q92729	.;.;.;.;PTPRU_HUMAN	C	140	ENSP00000334941:G140C;ENSP00000362884:G140C;ENSP00000349333:G140C;ENSP00000314987:G140C;ENSP00000392332:G140C;ENSP00000432906:G140C	.	G	+	1	0	PTPRU	29457816	1.000000	0.71417	0.961000	0.40146	0.975000	0.68041	9.869000	0.99810	2.699000	0.92147	0.591000	0.81541	GGC	.	G|1.000;A|0.000	.	alt		0.642	PTPRU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010447.1			T	29585229	G	T	29585229	3	4	14	1	0	0	0	0	1	0	0	0	12826	1116	39	4	428	4	PTPRU	1	29585229	Missense_Mutation	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10	17554399	29585229	219665392	2	945											
B4GALT2	8704	hgsc.bcm.edu	37	chr1	44447485	44447485	+	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	accccagcccagacggtggcGgtcatcatcccctttagaca	9	7	9	16	2	2	2	2	0	0	2	3	2	3	2	5	3	1	0	5	3	1	2			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr1:44447485G>T	ENST00000356836.6	+	3	1228	c.438G>T	c.(436-438)gcG>gcT	p.A146A	B4GALT2_ENST00000434555.2_Silent_p.A80A|B4GALT2_ENST00000309519.7_Silent_p.A175A|B4GALT2_ENST00000372324.1_Silent_p.A146A	NM_001005417.2|NM_030587.2	NP_001005417.1|NP_085076.2	O60909	B4GT2_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 2	146					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|galactosyltransferase activity (GO:0008378)|lactose synthase activity (GO:0004461)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)	p.A146A(1)		endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			N-Acetyl-D-glucosamine(DB00141)	AGACGGTGGCGGTCATCATCC	0.657																																					p.A175A		Atlas-SNP	.											B4GALT2,pharynx,carcinoma,0,1	B4GALT2	35	.	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.G525T						PASS	.						73	63	67					1																	44447485		2203	4300	6503	SO:0001819	synonymous_variant	8704	exon3			GGTGGCGGTCATC	AF038660	CCDS506.1, CCDS55596.1	1p34-p33	2013-02-19			ENSG00000117411	ENSG00000117411		"Beta 4-glycosyltransferases"	925	protein-coding gene	gene with protein product		604013				9405390, 9597550	Standard	NM_003780		Approved	beta4Gal-T2	uc010okl.2	O60909	OTTHUMG00000008296	ENST00000356836.6:c.438G>T	chr1.hg19:g.44447485G>T		235.0	0.0	.		139.0	31.0	.	NM_030587	B3KTP0|B4DE14|D3DPY6|D3DPY7|O60511|Q4V9L9|Q5T4X5|Q5T4Y5|Q9BUP6|Q9NSY7	Silent	SNP	ENST00000356836.6	hg19	CCDS506.1																																																																																			.	.	.	none		0.657	B4GALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022840.1	NM_003780		T	44447485	G	T	44447485	2	4	14	1	0	0	0	0	0	0	0	1	1271	1103	39	4		4	B4GALT2	1	44447485	Silent	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10	14862256	44447485	204803136	3	946											
DOCK7	85440	hgsc.bcm.edu	37	chr1	63096983	63096983	+	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	gctaacaatattcattaaatGgattgcagtccaagcaaaag	17	10	7	7	0	1	0	1	0	0	0	2	1	2	1	1	1	3	3	1	1	8	5			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr1:63096983G>T	ENST00000340370.5	-	11	1227	c.1210C>A	c.(1210-1212)Cat>Aat	p.H404N	DOCK7_ENST00000404627.2_Missense_Mutation_p.H404N|DOCK7_ENST00000251157.5_Missense_Mutation_p.H404N	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	404					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						TTCATTAAATGGATTGCAGTC	0.373																																					p.H404N		Atlas-SNP	.											.	DOCK7	184	.	0			c.C1210A						PASS	.						90	86	87					1																	63096983		2202	4300	6502	SO:0001583	missense	85440	exon11			TTAAATGGATTGC		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.1210C>A	chr1.hg19:g.63096983G>T	ENSP00000340742:p.His404Asn	344.0	0.0	.		259.0	66.0	.	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	hg19	CCDS30734.1	.	.	.	.	.	.	.	.	.	.	G	15.07	2.723622	0.48728	.	.	ENSG00000116641	ENST00000371140;ENST00000251157;ENST00000340370;ENST00000404627	T;T;T	0.40756	1.02;1.02;1.02	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.50240	0.1604	L	0.52126	1.63	0.80722	D	1	P;D;B;D;B	0.89917	0.823;1.0;0.383;0.998;0.036	B;D;B;D;B	0.83275	0.414;0.991;0.219;0.996;0.034	T	0.32745	-0.9895	10	0.27785	T	0.31	.	18.2163	0.89886	0.0:0.0:1.0:0.0	.	404;404;404;404;404	Q96NI0;Q96N67-2;Q96N67-5;Q96N67-4;Q96N67-3	.;.;.;.;.	N	404	ENSP00000251157:H404N;ENSP00000340742:H404N;ENSP00000384446:H404N	ENSP00000251157:H404N	H	-	1	0	DOCK7	62869571	1.000000	0.71417	0.999000	0.59377	0.353000	0.29299	9.652000	0.98499	2.519000	0.84933	0.655000	0.94253	CAT	.	.	.	none		0.373	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		T	63096983	G	T	63096983	3	4	14	1	0	0	0	0	1	0	0	0	4694	1348	47	4	5275	4	DOCK7	1	63096983	Missense_Mutation	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10	18649498	63096983	186153638	4	947											
RBM8A	9939	hgsc.bcm.edu	37	chr1	145507671	145507671	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcgatcgaaggcgagatggCggacgtgctagatcttcacg	9	8	14	10	6	2	2	1	0	1	2	4	6	2	3	0	3	1	1	0	3	2	2			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr1:145507671C>T	ENST00000330165.8	+	1	74	c.5C>T	c.(4-6)gCg>gTg	p.A2V	RP11-315I20.1_ENST00000412239.1_RNA|RP11-315I20.1_ENST00000448561.1_RNA|RP11-315I20.1_ENST00000599626.1_RNA|RP11-315I20.1_ENST00000601726.1_RNA|RP11-315I20.1_ENST00000437797.1_RNA|RP11-315I20.1_ENST00000600340.1_RNA|RP11-315I20.1_ENST00000596355.1_RNA|RP11-315I20.1_ENST00000447686.2_RNA|RP11-315I20.1_ENST00000598103.1_RNA|RP11-315I20.1_ENST00000595518.1_RNA|RP11-315I20.1_ENST00000598354.1_RNA|RP11-315I20.1_ENST00000421764.1_RNA|RBM8A_ENST00000369307.3_Missense_Mutation_p.A2V|RP11-315I20.1_ENST00000599469.1_RNA|RP11-315I20.1_ENST00000599147.1_RNA|RP11-315I20.1_ENST00000597144.1_RNA|GNRHR2_ENST00000312753.5_RNA|RP11-315I20.1_ENST00000595494.1_RNA	NM_005105.3	NP_005096.1	Q9Y5S9	RBM8A_HUMAN	RNA binding motif protein 8A	2					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			kidney(2)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	6	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GGCGAGATGGCGGACGTGCTA	0.597											OREG0013748	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A2V		Atlas-SNP	.											.	RBM8A	18	.	0			c.C5T						PASS	.						43	32	36					1																	145507671		2203	4296	6499	SO:0001583	missense	9939	exon1			AGATGGCGGACGT	AF127761	CCDS72872.1	1q21.1	2013-02-12			ENSG00000131795			"RNA binding motif (RRM) containing"	9905	protein-coding gene	gene with protein product		605313		RBM8		11004516, 11013075	Standard	NM_005105		Approved	ZNRP, BOV-1A, BOV-1B, BOV-1C, RBM8B, Y14	uc001ent.2	Q9Y5S9	OTTHUMG00000013736	ENST00000330165.8:c.5C>T	chr1.hg19:g.145507671C>T	ENSP00000333001:p.Ala2Val	140.0	0.0	.	1695	81.0	20.0	.	NM_005105	B3KQI9|Q6FHD1|Q6IQ40|Q9GZX8|Q9NZI4	Missense_Mutation	SNP	ENST00000330165.8	hg19	CCDS916.1	.	.	.	.	.	.	.	.	.	.	C	32	5.170105	0.94768	.	.	ENSG00000131795	ENST00000330165;ENST00000369307	T;T	0.16743	2.37;2.32	4.83	3.9	0.45041	.	0.059004	0.64402	D	0.000003	T	0.29652	0.0740	M	0.80847	2.515	0.58432	D	0.999996	D;D	0.76494	0.999;0.994	P;P	0.61940	0.896;0.575	T	0.21008	-1.0258	10	0.87932	D	0	-0.8918	13.1116	0.59277	0.0:0.8376:0.1624:0.0	.	2;2	Q9Y5S9-2;Q9Y5S9	.;RBM8A_HUMAN	V	2	ENSP00000333001:A2V;ENSP00000358313:A2V	ENSP00000333001:A2V	A	+	2	0	RBM8A	144219028	1.000000	0.71417	0.999000	0.59377	0.907000	0.53573	4.593000	0.61034	1.380000	0.46344	0.650000	0.86243	GCG	.	.	.	none		0.597	RBM8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038503.2	NM_005105		T	145507671	C	T	145507671	3	4	14	1	0	0	0	0	1	0	0	0	13159	768	27	1	7	1	RBM8A	1	145507671	Missense_Mutation	SNP	C	TCGA-2Z-A9JK-01A-11D-A42J-10	82410688	145507671	103742950	5	948											
CACNA1E	777	hgsc.bcm.edu	37	chr1	181727893	181727893	+	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	cttcttttttcttcctggcaGtattattctgctccctgtac	4	20	5	12	0	3	0	0	0	3	0	5	0	5	0	2	1	2	4	2	1	3	9			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr1:181727893G>T	ENST00000367573.2	+	32	4494		c.e32-1		CACNA1E_ENST00000367570.1_Splice_Site|CACNA1E_ENST00000367567.4_Splice_Site|CACNA1E_ENST00000526775.1_Splice_Site|CACNA1E_ENST00000357570.5_Splice_Site|CACNA1E_ENST00000358338.5_Splice_Site|CACNA1E_ENST00000360108.3_Splice_Site	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit						calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						CTTCCTGGCAGTATTATTCTG	0.483																																					.		Atlas-SNP	.											.	CACNA1E	778	.	0			c.4495-1G>T						PASS	.						212	189	196					1																	181727893		1933	4148	6081	SO:0001630	splice_region_variant	777	exon32			CTGGCAGTATTAT	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.4495-1G>T	chr1.hg19:g.181727893G>T		85.0	0.0	.		56.0	4.0	.	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Splice_Site	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.703404	0.88924	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.0045	0.92844	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CACNA1E	179994516	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	9.338000	0.96553	2.583000	0.87209	0.561000	0.74099	.	.	.	.	none		0.483	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	Intron	T	181727893	G	T	181727893	5	4	14	1	0	0	0	0	0	0	1	0	2544	1043	36	4	4620	4	CACNA1E	1	181727893	Splice_Site	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10	36220222	181727893	67522728	6	949											
ZNF648	127665	hgsc.bcm.edu	37	chr1	182027010	182027010	+	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	caccgggtcagcggtgccctCtttttcggcctccccaccat	4	10	9	18	3	2	0	1	0	1	0	4	0	3	0	6	3	2	0	6	3	0	2			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr1:182027010C>G	ENST00000339948.3	-	2	343	c.136G>C	c.(136-138)Gag>Cag	p.E46Q		NM_001009992.1	NP_001009992.1	Q5T619	ZN648_HUMAN	zinc finger protein 648	46					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						GCGGTGCCCTCTTTTTCGGCC	0.572																																					p.E46Q	NSCLC(71;908 1374 5429 20458 35642)	Atlas-SNP	.											.	ZNF648	111	.	0			c.G136C						PASS	.						94	90	92					1																	182027010		2203	4300	6503	SO:0001583	missense	127665	exon2			TGCCCTCTTTTTC	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.136G>C	chr1.hg19:g.182027010C>G	ENSP00000344129:p.Glu46Gln	142.0	0.0	.		85.0	22.0	.	NM_001009992	B2RP16	Missense_Mutation	SNP	ENST00000339948.3	hg19	CCDS30952.1	.	.	.	.	.	.	.	.	.	.	C	4.143	0.024840	0.08054	.	.	ENSG00000179930	ENST00000339948	T	0.08546	3.08	2.36	-0.605	0.11623	.	.	.	.	.	T	0.02342	0.0072	N	0.03608	-0.345	0.09310	N	1	B	0.29432	0.244	B	0.14578	0.011	T	0.44711	-0.9310	9	0.13853	T	0.58	.	2.579	0.04814	0.2206:0.3541:0.0:0.4253	.	46	Q5T619	ZN648_HUMAN	Q	46	ENSP00000344129:E46Q	ENSP00000344129:E46Q	E	-	1	0	ZNF648	180293633	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.574000	0.05868	-0.145000	0.11294	-0.140000	0.14226	GAG	.	.	.	none		0.572	ZNF648-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090794.1	XM_060597		G	182027010	C	G	182027010	3	3	14	1	0	0	0	0	1	0	0	0	18075	922	32	4	1574	4	ZNF648	1	182027010	Missense_Mutation	SNP	C	TCGA-2Z-A9JK-01A-11D-A42J-10	299117	182027010	67223611	7	950											
PRG4	10216	hgsc.bcm.edu	37	chr1	186276990	186276990	+	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	actacccctaaagggactgcTccaactaccctcaaggaacc	13	6	6	16	0	1	0	1	0	0	0	2	2	2	2	5	2	5	1	5	2	7	3			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr1:186276990T>A	ENST00000445192.2	+	7	2184	c.2139T>A	c.(2137-2139)gcT>gcA	p.A713A	PRG4_ENST00000367486.3_Silent_p.A670A|PRG4_ENST00000367483.4_Silent_p.A672A|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367485.4_Silent_p.A620A	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	713	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						AAGGGACTGCTCCAACTACCC	0.587																																					p.A713A		Atlas-SNP	.											.	PRG4	259	.	0			c.T2139A						PASS	.						163	176	172					1																	186276990		2203	4300	6503	SO:0001819	synonymous_variant	10216	exon7			GACTGCTCCAACT	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.2139T>A	chr1.hg19:g.186276990T>A		114.0	0.0	.		96.0	29.0	.	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Silent	SNP	ENST00000445192.2	hg19	CCDS1369.1																																																																																			.	.	.	none		0.587	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		A	186276990	T	A	186276990	2	1	14	1	0	0	0	0	0	0	0	1	12491	1538	54	5		5	PRG4	1	186276990	Silent	SNP	T	TCGA-2Z-A9JK-01A-11D-A42J-10	4249980	186276990	62973631	8	951											
SLC30A10	55532	hgsc.bcm.edu	37	chr1	220101416	220101416	+	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	caccacgttgaccaacagccCcaggacgccgacgatgagca	12	3	10	16	4	0	2	0	2	0	0	0	5	0	3	5	1	3	2	5	1	1	1	rs575895791		TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr1:220101416C>G	ENST00000366926.3	-	1	528	c.367G>C	c.(367-369)Ggg>Cgg	p.G123R	SLC30A10_ENST00000536992.1_Missense_Mutation_p.G123R|SLC30A10_ENST00000536446.1_Intron	NM_018713.2	NP_061183.2	Q6XR72	ZNT10_HUMAN	solute carrier family 30, member 10	123					zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)			NS(1)|endometrium(1)|large_intestine(1)|lung(9)|skin(1)	13				GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.209)		ACCAACAGCCCCAGGACGCCG	0.701																																					p.G123R	Colon(76;360 1614 43677 51136)	Atlas-SNP	.											.	SLC30A10	58	.	0			c.G367C						PASS	.						6	7	7					1																	220101416		2096	4139	6235	SO:0001583	missense	55532	exon1			ACAGCCCCAGGAC	AY212919	CCDS31026.1	1q41	2013-05-22			ENSG00000196660	ENSG00000196660		"Solute carriers"	25355	protein-coding gene	gene with protein product	"zinc transporter 8"	611146				15154973	Standard	NR_046437		Approved	DKFZp547M236, ZnT-10, ZRC1, ZNT8	uc001hlw.3	Q6XR72	OTTHUMG00000037434	ENST00000366926.3:c.367G>C	chr1.hg19:g.220101416C>G	ENSP00000355893:p.Gly123Arg	378.0	0.0	.		207.0	50.0	.	NM_018713	Q49AL9|Q9NPW0	Missense_Mutation	SNP	ENST00000366926.3	hg19	CCDS31026.1	.	.	.	.	.	.	.	.	.	.	C	33	5.218613	0.95104	.	.	ENSG00000196660	ENST00000366926;ENST00000536992	T;T	0.67698	-0.28;-0.28	3.83	3.83	0.44106	.	0.068464	0.56097	D	0.000024	D	0.86401	0.5924	H	0.97540	4.025	0.58432	D	0.999998	D	0.65815	0.995	P	0.60345	0.873	D	0.92052	0.5649	9	.	.	.	-26.9391	16.2635	0.82563	0.0:1.0:0.0:0.0	.	123	Q6XR72	ZNT10_HUMAN	R	123	ENSP00000355893:G123R;ENSP00000440627:G123R	.	G	-	1	0	SLC30A10	218168039	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.241000	0.78201	2.120000	0.65058	0.491000	0.48974	GGG	.	.	.	none		0.701	SLC30A10-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357709.1	NM_018713		G	220101416	C	G	220101416	3	3	14	1	0	0	0	0	1	0	0	0	14567	623	22	4	1106	4	SLC30A10	1	220101416	Missense_Mutation	SNP	C	TCGA-2Z-A9JK-01A-11D-A42J-10	33824426	220101416	29149205	9	952											
CEP170	9859	hgsc.bcm.edu	37	chr1	243329104	243329104	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agcagagctgcctaagtgaaGtagggttttattatctccac	11	12	10	8	0	1	2	0	1	1	1	2	2	1	2	2	1	3	4	2	1	5	5			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr1:243329104G>A	ENST00000366542.1	-	13	2209	c.2158C>T	c.(2158-2160)Ctt>Ttt	p.L720F	RP11-261C10.4_ENST00000422938.1_RNA|CEP170_ENST00000366544.1_Missense_Mutation_p.L622F|CEP170_ENST00000490813.1_5'Flank|RP11-261C10.4_ENST00000437499.1_RNA|CEP170_ENST00000366543.1_Missense_Mutation_p.L622F	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	720						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)			CCTAAGTGAAGTAGGGTTTTA	0.383																																					p.L720F		Atlas-SNP	.											.	CEP170	153	.	0			c.C2158T						PASS	.						147	135	138					1																	243329104		1831	4076	5907	SO:0001583	missense	9859	exon13			AGTGAAGTAGGGT	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.2158C>T	chr1.hg19:g.243329104G>A	ENSP00000355500:p.Leu720Phe	33.0	0.0	.		97.0	18.0	.	NM_014812	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Missense_Mutation	SNP	ENST00000366542.1	hg19	CCDS44339.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.417794	0.00188	.	.	ENSG00000143702	ENST00000366542;ENST00000366544;ENST00000366543	T;T;T	0.46063	0.9;0.89;0.88	5.25	3.19	0.36642	.	0.544947	0.17645	N	0.166872	T	0.18383	0.0441	N	0.08118	0	0.09310	N	0.999998	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.10450	0.005;0.001;0.001;0.002	T	0.27673	-1.0067	10	0.09590	T	0.72	-0.0301	6.3901	0.21581	0.3865:0.0:0.6135:0.0	.	683;622;622;720	B1ARM6;Q5SW79-3;Q5SW79-2;Q5SW79	.;.;.;CE170_HUMAN	F	720;622;622	ENSP00000355500:L720F;ENSP00000355502:L622F;ENSP00000355501:L622F	ENSP00000355500:L720F	L	-	1	0	CEP170	241395727	0.877000	0.30153	0.039000	0.18376	0.213000	0.24496	1.532000	0.36029	0.496000	0.27904	0.484000	0.47621	CTT	.	.	.	none		0.383	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812		A	243329104	G	A	243329104	3	1	14	1	0	0	0	0	1	0	0	0	3252	1029	36	2	2658	2	CEP170	1	243329104	Missense_Mutation	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10	23227688	243329104	5921517	10	953											
CGREF1	10669	hgsc.bcm.edu	37	chr2	27324530	27324530	+	Missense_Mutation	SNP	T	T	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	cctctacctggccctttgctTcttctctgggaccaggggct	3	13	10	15	0	3	0	0	0	3	0	4	1	3	1	4	4	2	2	4	4	1	4			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr2:27324530T>G	ENST00000260595.5	-	6	861	c.569A>C	c.(568-570)gAa>gCa	p.E190A	CGREF1_ENST00000404694.3_Missense_Mutation_p.E312A|CGREF1_ENST00000402550.1_Intron|CGREF1_ENST00000402394.1_Missense_Mutation_p.E190A|CGREF1_ENST00000452318.2_Intron|CGREF1_ENST00000312734.4_Missense_Mutation_p.E190A|CGREF1_ENST00000405600.1_Missense_Mutation_p.E190A			Q99674	CGRE1_HUMAN	cell growth regulator with EF-hand domain 1	190					cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			kidney(1)|lung(4)|ovary(1)|prostate(2)|skin(1)|soft_tissue(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCCCTTTGCTTCTTCTCTGGG	0.572																																					p.E190A		Atlas-SNP	.											.	CGREF1	31	.	0			c.A569C						PASS	.						113	127	122					2																	27324530		2203	4300	6503	SO:0001583	missense	10669	exon6			TTTGCTTCTTCTC	BC034764	CCDS33162.1, CCDS33162.2, CCDS54339.1	2p23.3	2013-01-10			ENSG00000138028	ENSG00000138028		"EF-hand domain containing"	16962	protein-coding gene	gene with protein product		606137				8968090	Standard	NM_006569		Approved	CGR11	uc002riq.3	Q99674	OTTHUMG00000152009	ENST00000260595.5:c.569A>C	chr2.hg19:g.27324530T>G	ENSP00000260595:p.Glu190Ala	76.0	0.0	.		48.0	8.0	.	NM_001166239	A6NHV7|B4DXY8|B5MCB7|B5MCC9|B5MCP5|E7EU99|Q8N4B7	Missense_Mutation	SNP	ENST00000260595.5	hg19		.	.	.	.	.	.	.	.	.	.	T	9.570	1.120780	0.20877	.	.	ENSG00000138028	ENST00000402394;ENST00000405600;ENST00000389521;ENST00000312734;ENST00000404694;ENST00000260595	T;T;T;T;T	0.79141	-1.16;-1.16;-1.16;-1.19;-1.24	5.0	-0.767	0.11016	.	1.119980	0.06665	N	0.765091	T	0.66376	0.2783	.	.	.	0.09310	N	1	B;B;B	0.12013	0.005;0.005;0.005	B;B;B	0.12156	0.007;0.004;0.004	T	0.53641	-0.8410	9	0.48119	T	0.1	-19.8	7.492	0.27466	0.0:0.079:0.4061:0.5149	.	312;190;190	B5MCC9;B5MCP5;Q99674	.;.;CGRE1_HUMAN	A	190;190;190;190;312;190	ENSP00000385452:E190A;ENSP00000386113:E190A;ENSP00000324025:E190A;ENSP00000385574:E312A;ENSP00000260595:E190A	ENSP00000260595:E190A	E	-	2	0	CGREF1	27178034	0.000000	0.05858	0.011000	0.14972	0.004000	0.04260	-0.031000	0.12287	-0.061000	0.13110	-0.817000	0.03123	GAA	.	.	.	none		0.572	CGREF1-201	KNOWN	basic	protein_coding	protein_coding		NM_006569		G	27324530	T	G	27324530	3	3	14	1	0	0	0	0	1	0	0	0	3307	1783	62	5	583	5	CGREF1	2	27324530	Missense_Mutation	SNP	T	TCGA-2Z-A9JK-01A-11D-A42J-10		27324530	215874843	11	954											
EIF2AK3	9451	hgsc.bcm.edu	37	chr2	88926504	88926505	+	Frame_Shift_Ins	INS	-	-	T																															ctgccgcgcggtcgcaactcINStgtctcatcgtctggttccg																								rs13034488		TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr2:88926504_88926505insT	ENST00000303236.3	-	1	589_590	c.288_289insA	c.(286-291)acagagfs	p.E97fs	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	97					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						GGTCGCAACTCTGTCTCATCGT	0.723																																					p.E97fs	GBM(138;671 1851 16235 39058 45249)	Atlas-Indel,Pindel	.											.	EIF2AK3	160	.	0			c.289_290insA						PASS	.																																			SO:0001589	frameshift_variant	9451	exon1			.	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.289dupA	chr2.hg19:g.88926505_88926505dupT	ENSP00000307235:p.Glu97fs	476.0	0.0	0		219.0	50.0	0.22831	NM_004836	A0AVH1|A0AVH2|B2RCU9|O95846|Q53QY0|Q53SB1	Frame_Shift_Ins	INS	ENST00000303236.3	hg19	CCDS33241.1																																																																																			.	.	.	none		0.723	EIF2AK3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000338233.2	NM_004836		T	88926505	-	T	88926504	7	5	14	1	0	1	1	0	0	0	0	0	5000	922	32	0	3129	0	EIF2AK3	2	88926504	Frame_Shift_Ins	INS	-	TCGA-2Z-A9JK-01A-11D-A42J-10	61601974	88926504	154272869	12	955											
SULT1C4	27233	hgsc.bcm.edu	37	chr2	108998295	108998295	+	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	aaagtaaacgggcaccgactCatcaacgatttcctttcctc	12	10	6	13	3	2	0	2	0	0	0	5	2	4	0	3	1	2	2	3	1	4	3			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr2:108998295C>T	ENST00000272452.2	+	2	573	c.247C>T	c.(247-249)Cat>Tat	p.H83Y	SULT1C4_ENST00000409309.3_Missense_Mutation_p.H83Y	NM_006588.2	NP_006579.2	O75897	ST1C4_HUMAN	sulfotransferase family, cytosolic, 1C, member 4	83					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	sulfotransferase activity (GO:0008146)			endometrium(1)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	12						GGCACCGACTCATCAACGATT	0.398																																					p.H83Y		Atlas-SNP	.											.	SULT1C4	41	.	0			c.C247T						PASS	.						141	121	128					2																	108998295		2203	4300	6503	SO:0001583	missense	27233	exon2			CCGACTCATCAAC	AF055584	CCDS2077.1	2q12.3	2008-09-04	2007-03-16	2007-03-16	ENSG00000198075	ENSG00000198075		"Sulfotransferases, cytosolic"	11457	protein-coding gene	gene with protein product		608357	"sulfotransferase family, cytosolic, 1C, member 2"	SULT1C2		10783263, 9852044	Standard	NM_006588		Approved	SULT1C	uc002tea.1	O75897	OTTHUMG00000130958	ENST00000272452.2:c.247C>T	chr2.hg19:g.108998295C>T	ENSP00000272452:p.His83Tyr	192.0	0.0	.		166.0	38.0	.	NM_006588	Q069I8|Q08AS5|Q53S63	Missense_Mutation	SNP	ENST00000272452.2	hg19	CCDS2077.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.590686	0.00126	.	.	ENSG00000198075	ENST00000272452;ENST00000409309	D;D	0.82526	-1.62;-1.62	4.33	2.52	0.30459	Sulfotransferase domain (1);	0.595797	0.15452	N	0.261600	T	0.65616	0.2708	N	0.25957	0.775	0.09310	N	1	B;B;B	0.11235	0.004;0.001;0.001	B;B;B	0.12837	0.008;0.005;0.006	T	0.49624	-0.8920	10	0.02654	T	1	.	5.8095	0.18457	0.0:0.5749:0.0:0.4251	.	83;83;83	Q08AS5;O75897;Q6PD90	.;ST1C4_HUMAN;.	Y	83	ENSP00000272452:H83Y;ENSP00000387225:H83Y	ENSP00000272452:H83Y	H	+	1	0	SULT1C4	108364727	0.000000	0.05858	0.002000	0.10522	0.071000	0.16799	0.010000	0.13242	0.569000	0.29329	0.609000	0.83330	CAT	.	.	.	none		0.398	SULT1C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253561.1	NM_006588		T	108998295	C	T	108998295	3	4	14	1	0	0	0	0	1	0	0	0	15391	826	29	2	253	2	SULT1C4	2	108998295	Missense_Mutation	SNP	C	TCGA-2Z-A9JK-01A-11D-A42J-10	20071791	108998295	134201078	13	956											
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125192134	125192134	+	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	cagaagttgatgagtactctCaaagatgtgatctccctgaa	13	11	9	8	0	2	6	1	4	2	2	4	6	2	6	1	0	1	2	1	0	4	2			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr2:125192134C>G	ENST00000431078.1	+	5	967	c.603C>G	c.(601-603)ctC>ctG	p.L201L		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	201	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		TGAGTACTCTCAAAGATGTGA	0.483																																					p.L201L		Atlas-SNP	.											.	CNTNAP5	405	.	0			c.C603G						PASS	.						123	118	120					2																	125192134		2000	4194	6194	SO:0001819	synonymous_variant	129684	exon5			TACTCTCAAAGAT	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.603C>G	chr2.hg19:g.125192134C>G		121.0	0.0	.		92.0	25.0	.	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Silent	SNP	ENST00000431078.1	hg19	CCDS46401.1																																																																																			.	.	.	none		0.483	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			G	125192134	C	G	125192134	2	3	14	1	0	0	0	0	0	0	0	1	3652	813	29	4		4	CNTNAP5	2	125192134	Silent	SNP	C	TCGA-2Z-A9JK-01A-11D-A42J-10	16193839	125192134	118007239	14	957											
CCDC115	84317	hgsc.bcm.edu	37	chr2	131099478	131099478	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggggccctaccgacttggCgcccatcgcgtagcgagcct	6	6	13	16	5	0	0	0	0	0	0	1	2	0	0	4	3	3	1	4	3	2	3			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr2:131099478C>T	ENST00000259229.2	-	2	374	c.151G>A	c.(151-153)Gcc>Acc	p.A51T	CCDC115_ENST00000409127.1_Missense_Mutation_p.A46T|IMP4_ENST00000409935.1_5'Flank|IMP4_ENST00000259239.3_5'Flank|CCDC115_ENST00000437688.2_Missense_Mutation_p.A46T	NM_032357.2	NP_115733.2	Q96NT0	CC115_HUMAN	coiled-coil domain containing 115	51						endosome (GO:0005768)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(1)	7	Colorectal(110;0.1)					ACCGACTTGGCGCCCATCGCG	0.672																																					p.A51T		Atlas-SNP	.											.	CCDC115	19	.	0			c.G151A						PASS	.						37	40	39					2																	131099478		2203	4300	6503	SO:0001583	missense	84317	exon2			ACTTGGCGCCCAT	AK054693	CCDS2159.1	2q21.1	2010-12-24			ENSG00000136710	ENSG00000136710			28178	protein-coding gene	gene with protein product		613734				21118521	Standard	XM_005263825		Approved	MGC12981, FLJ30131, ccp1	uc002tqy.1	Q96NT0	OTTHUMG00000131631	ENST00000259229.2:c.151G>A	chr2.hg19:g.131099478C>T	ENSP00000259229:p.Ala51Thr	131.0	0.0	.		94.0	4.0	.	NM_032357	B4DJ47|Q9BR88	Missense_Mutation	SNP	ENST00000259229.2	hg19	CCDS2159.1	.	.	.	.	.	.	.	.	.	.	C	0.224	-1.026510	0.02045	.	.	ENSG00000136710	ENST00000259229;ENST00000409127;ENST00000437688	D;D;D	0.93488	-3.23;-3.23;-3.23	4.81	3.93	0.45458	.	0.385448	0.29034	N	0.013355	D	0.90721	0.7088	M	0.72118	2.19	0.23356	N	0.997847	B;B;B;B	0.24132	0.023;0.006;0.098;0.023	B;B;B;B	0.17433	0.018;0.011;0.018;0.018	T	0.76801	-0.2825	10	0.14252	T	0.57	-10.8785	12.2248	0.54453	0.0:0.9104:0.0:0.0896	.	46;51;51;46	B4DJ47;F8WCZ3;Q96NT0;B8ZZ99	.;.;CC115_HUMAN;.	T	51;46;46	ENSP00000259229:A51T;ENSP00000387301:A46T;ENSP00000399756:A46T	ENSP00000259229:A51T	A	-	1	0	CCDC115	130815948	0.527000	0.26306	0.976000	0.42696	0.085000	0.17905	0.339000	0.19875	0.761000	0.33130	-0.797000	0.03246	GCC	.	.	.	none		0.672	CCDC115-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254524.2	NM_032357		T	131099478	C	T	131099478	3	4	14	1	0	0	0	0	1	0	0	0	2754	768	27	1	407	1	CCDC115	2	131099478	Missense_Mutation	SNP	C	TCGA-2Z-A9JK-01A-11D-A42J-10	5907344	131099478	112099895	15	958											
BAP1	8314	hgsc.bcm.edu	37	chr3	52441229	52441230	+	Frame_Shift_Del	DEL	AG	AG	-																															cttcagcccatccagctcaaAgagccggcctgtgataggca																										TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr3:52441229_52441230delAG	ENST00000460680.1	-	7	1011_1012	c.540_541delCT	c.(538-543)ctctttfs	p.F181fs	BAP1_ENST00000296288.5_Frame_Shift_Del_p.F181fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		TCCAGCTCAAAGAGCCGGCCTG	0.599			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.181_181del	GBM(101;493 1458 7992 21037 25532)	Atlas-Indel,Pindel	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	0			c.541_542del						PASS	.																																			SO:0001589	frameshift_variant	8314	exon7			.	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.540_541delCT	chr3.hg19:g.52441231_52441232delAG	ENSP00000417132:p.Phe181fs	172.0	0.0	0		67.0	23.0	0.343284	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Frame_Shift_Del	DEL	ENST00000460680.1	hg19	CCDS2853.1																																																																																			.	.	.	none		0.599	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			-	52441230	AG	-	52441229	7	5	14	1	0	1	0	1	0	0	0	0	1311	72	3	0	1692	0	BAP1	3	52441229	Frame_Shift_Del	DEL	AG	TCGA-2Z-A9JK-01A-11D-A42J-10		52441229	145581201	16	959											
XRN1	54464	hgsc.bcm.edu	37	chr3	142137718	142137718	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccaacacagagaattttcCtggccctgtaaattgtaaat	13	12	7	9	0	0	1	0	0	0	1	2	2	2	1	3	1	1	2	3	1	6	5			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr3:142137718C>T	ENST00000264951.4	-	11	1296	c.1179G>A	c.(1177-1179)caG>caA	p.Q393Q	XRN1_ENST00000544157.1_Silent_p.Q183Q|RNU1-100P_ENST00000365255.1_RNA|XRN1_ENST00000392981.2_Silent_p.Q393Q|XRN1_ENST00000463916.1_Silent_p.Q393Q	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	393					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						GAGAATTTTCCTGGCCCTGTA	0.333																																					p.Q393Q		Atlas-SNP	.											.	XRN1	138	.	0			c.G1179A						PASS	.						83	82	83					3																	142137718		2202	4298	6500	SO:0001819	synonymous_variant	54464	exon11			ATTTTCCTGGCCC	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.1179G>A	chr3.hg19:g.142137718C>T		189.0	0.0	.		155.0	25.0	.	NM_001042604	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Silent	SNP	ENST00000264951.4	hg19	CCDS3123.1																																																																																			.	.	.	none		0.333	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001		T	142137718	C	T	142137718	2	4	14	1	0	0	0	0	0	0	0	1	17471	680	24	2		2	XRN1	3	142137718	Silent	SNP	C	TCGA-2Z-A9JK-01A-11D-A42J-10	89696489	142137718	55884712	17	960											
PPARGC1A	10891	hgsc.bcm.edu	37	chr4	23886468	23886468	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccacccagaaagctgtctgtAtccaagtcgttcacatctag	11	10	7	13	1	3	1	1	0	2	1	5	1	4	1	3	0	1	3	3	0	4	3			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr4:23886468A>G	ENST00000264867.2	-	2	260	c.141T>C	c.(139-141)gaT>gaC	p.D47D	PPARGC1A_ENST00000509702.1_5'Flank|PPARGC1A_ENST00000507380.1_Silent_p.D47D	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	47					androgen metabolic process (GO:0008209)|androgen receptor signaling pathway (GO:0030521)|brown fat cell differentiation (GO:0050873)|cellular glucose homeostasis (GO:0001678)|cellular respiration (GO:0045333)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to nitrite (GO:0071250)|cellular response to oxidative stress (GO:0034599)|cellular response to thyroid hormone stimulus (GO:0097067)|cellular response to tumor necrosis factor (GO:0071356)|circadian regulation of gene expression (GO:0032922)|digestion (GO:0007586)|fatty acid oxidation (GO:0019395)|flavone metabolic process (GO:0051552)|galactose metabolic process (GO:0006012)|gluconeogenesis (GO:0006094)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of receptor activity (GO:2000272)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of cellular respiration (GO:1901857)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of histone acetylation (GO:0035066)|positive regulation of mitochondrial DNA metabolic process (GO:1901860)|positive regulation of mitochondrion organization (GO:0010822)|positive regulation of muscle tissue development (GO:1901863)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|regulation of circadian rhythm (GO:0042752)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|response to cold (GO:0009409)|response to epinephrine (GO:0071871)|response to leucine (GO:0043201)|response to muscle activity (GO:0014850)|response to norepinephrine (GO:0071873)|response to starvation (GO:0042594)|response to statin (GO:0036273)|RNA splicing (GO:0008380)|temperature homeostasis (GO:0001659)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytosol (GO:0005829)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|liver(1)|lung(24)|ovary(3)|skin(5)	51		Breast(46;0.0503)				AGCTGTCTGTATCCAAGTCGT	0.453																																					p.D47D	Esophageal Squamous(29;694 744 13796 34866 44181)	Atlas-SNP	.											.	PPARGC1A	129	.	0			c.T141C						PASS	.						105	96	99					4																	23886468		2203	4300	6503	SO:0001819	synonymous_variant	10891	exon2			GTCTGTATCCAAG	AF106698	CCDS3429.1	4p15.1	2013-02-12	2006-10-17	2004-02-04	ENSG00000109819	ENSG00000109819		"RNA binding motif (RRM) containing"	9237	protein-coding gene	gene with protein product		604517	"peroxisome proliferative activated receptor, gamma, coactivator 1", "peroxisome proliferative activated receptor, gamma, coactivator 1, alpha"	PPARGC1		10585775	Standard	NM_013261		Approved	PGC1, PGC1A	uc003gqs.3	Q9UBK2	OTTHUMG00000097747	ENST00000264867.2:c.141T>C	chr4.hg19:g.23886468A>G		68.0	0.0	.		84.0	19.0	.	NM_013261	B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	Silent	SNP	ENST00000264867.2	hg19	CCDS3429.1																																																																																			.	.	.	none		0.453	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1	NM_013261		G	23886468	A	G	23886468	2	3	14	1	0	0	0	0	0	0	0	1	12307	446	16	3		3	PPARGC1A	4	23886468	Silent	SNP	A	TCGA-2Z-A9JK-01A-11D-A42J-10		23886468	167267808	18	961											
TMPRSS11D	9407	hgsc.bcm.edu	37	chr4	68699085	68699085	+	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	agacaatgttattaggtctgGaccggccccacattctaatg	11	11	9	10	1	2	1	0	0	2	1	2	2	2	2	3	3	0	1	3	3	4	4			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr4:68699085G>C	ENST00000283916.6	-	7	627	c.529C>G	c.(529-531)Cca>Gca	p.P177A	TMPRSS11D_ENST00000509584.1_5'UTR|TMPRSS11D_ENST00000545541.1_Missense_Mutation_p.P60A|UBA6-AS1_ENST00000500538.2_RNA	NM_004262.2	NP_004253.1	O60235	TM11D_HUMAN	transmembrane protease, serine 11D	177					proteolysis (GO:0006508)|respiratory gaseous exchange (GO:0007585)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						ATTAGGTCTGGACCGGCCCCA	0.473																																					p.P177A		Atlas-SNP	.											.	TMPRSS11D	68	.	0			c.C529G						PASS	.						119	112	115					4																	68699085		2203	4300	6503	SO:0001583	missense	9407	exon7			GGTCTGGACCGGC	AB002134	CCDS3518.1	4q13.2	2010-04-13			ENSG00000153802	ENSG00000153802		"Serine peptidases / Transmembrane"	24059	protein-coding gene	gene with protein product	"airway trypsin like protease"	605369				9565616, 9070615	Standard	XM_005265710		Approved		uc003hdq.3	O60235	OTTHUMG00000129300	ENST00000283916.6:c.529C>G	chr4.hg19:g.68699085G>C	ENSP00000283916:p.Pro177Ala	78.0	0.0	.		56.0	10.0	.	NM_004262	Q08AF6	Missense_Mutation	SNP	ENST00000283916.6	hg19	CCDS3518.1	.	.	.	.	.	.	.	.	.	.	G	12.92	2.081750	0.36758	.	.	ENSG00000153802	ENST00000283916;ENST00000545541	D;D	0.88354	-2.37;-2.33	5.6	0.928	0.19443	Peptidase cysteine/serine, trypsin-like (1);	0.225492	0.31612	N	0.007344	T	0.69655	0.3135	N	0.08118	0	0.25528	N	0.987309	B	0.30406	0.278	B	0.30179	0.112	T	0.59616	-0.7421	10	0.10636	T	0.68	.	3.9107	0.09202	0.337:0.0:0.5055:0.1575	.	177	O60235	TM11D_HUMAN	A	177;60	ENSP00000283916:P177A;ENSP00000442045:P60A	ENSP00000283916:P177A	P	-	1	0	TMPRSS11D	68381680	0.020000	0.18652	0.951000	0.38953	0.767000	0.43475	0.094000	0.15107	0.053000	0.16036	-0.142000	0.14014	CCA	.	.	.	none		0.473	TMPRSS11D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251430.3	NM_004262		C	68699085	G	C	68699085	3	2	14	1	0	0	0	0	1	0	0	0	16253	1174	41	4	743	4	TMPRSS11D	4	68699085	Missense_Mutation	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10	44812617	68699085	122455191	19	962											
C4orf3	401152	hgsc.bcm.edu	37	chr4	120221611	120221611	+	Missense_Mutation	SNP	T	T	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	actgaggcctcacatcgaagTtctgcctccctccctcgcta	7	10	7	17	2	2	1	1	1	1	0	6	2	4	1	4	1	1	2	4	1	2	2			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr4:120221611T>G	ENST00000504110.1	-	1	465	c.80A>C	c.(79-81)aAc>aCc	p.N27T	C4orf3_ENST00000399075.4_Missense_Mutation_p.N160T	NM_001001701.3	NP_001001701.2	Q8WVX3	CD003_HUMAN	chromosome 4 open reading frame 3	27						integral component of membrane (GO:0016021)				breast(1)|large_intestine(1)|lung(4)	6						CACATCGAAGTTCTGCCTCCC	0.572																																					p.N160T		Atlas-SNP	.											.	C4orf3	16	.	0			c.A479C						PASS	.						159	168	165					4																	120221611		2000	4164	6164	SO:0001583	missense	401152	exon2			TCGAAGTTCTGCC		CCDS43266.1, CCDS54798.1	4q26	2012-02-24			ENSG00000164096	ENSG00000164096			19225	protein-coding gene	gene with protein product	"HCV F-transactivated protein 1"						Standard	NM_001001701		Approved		uc021xrf.1	Q8WVX3	OTTHUMG00000161333	ENST00000504110.1:c.80A>C	chr4.hg19:g.120221611T>G	ENSP00000427214:p.Asn27Thr	130.0	0.0	.		85.0	19.0	.	NM_001170330	Q6J203	Missense_Mutation	SNP	ENST00000504110.1	hg19	CCDS43266.1	.	.	.	.	.	.	.	.	.	.	T	15.24	2.774317	0.49786	.	.	ENSG00000164096	ENST00000399075;ENST00000504110	T;T	0.36340	1.26;1.29	4.91	-3.88	0.04205	.	1.224740	0.06070	N	0.659986	T	0.25044	0.0608	.	.	.	0.26239	N	0.978893	B	0.24368	0.102	B	0.24701	0.055	T	0.42982	-0.9419	8	0.72032	D	0.01	0.36	5.526	0.16959	0.0:0.3354:0.2671:0.3975	.	27	Q8WVX3	CD003_HUMAN	T	160;27	ENSP00000382026:N160T;ENSP00000427214:N27T	ENSP00000382026:N160T	N	-	2	0	C4orf3	120441059	0.000000	0.05858	0.000000	0.03702	0.152000	0.21847	-0.401000	0.07232	-0.254000	0.09500	0.460000	0.39030	AAC	.	.	.	none		0.572	C4orf3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364576.3	NM_001001701		G	120221611	T	G	120221611	3	3	14	1	0	0	0	0	1	0	0	0	2262	1725	60	5	128	5	C4orf3	4	120221611	Missense_Mutation	SNP	T	TCGA-2Z-A9JK-01A-11D-A42J-10	51522526	120221611	70932665	20	963											
CMYA5	202333	hgsc.bcm.edu	37	chr5	79041105	79041106	+	Frame_Shift_Ins	INS	-	-	T																															tgaggaaatgatgaagaaggINSttttagcacagtatgatgag																										TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr5:79041105_79041106insT	ENST00000446378.2	+	4	10826_10827	c.10795_10796insT	c.(10795-10797)gttfs	p.V3599fs		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	3599	B-box coiled-coil; BBC.				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)		GATGAAGAAGGTTTTAGCACAG	0.401																																					p.V3599fs		Atlas-Indel,Pindel	.											.	CMYA5	643	.	0			c.10795_10796insT						PASS	.																																			SO:0001589	frameshift_variant	202333	exon4			.	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.10799dupT	chr5.hg19:g.79041109_79041109dupT	ENSP00000394770:p.Val3599fs	444.0	0.0	0		348.0	28.0	0.0804598	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Frame_Shift_Ins	INS	ENST00000446378.2	hg19	CCDS47238.1																																																																																			.	.	.	none		0.401	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		T	79041106	-	T	79041105	7	5	14	1	0	1	1	0	0	0	0	0	3592	1261	44	0	10809	0	CMYA5	5	79041105	Frame_Shift_Ins	INS	-	TCGA-2Z-A9JK-01A-11D-A42J-10		79041105	101874155	21	964											
PCSK1	5122	hgsc.bcm.edu	37	chr5	95768715	95768715	+	Missense_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	cgcaaaagaggacgaaagcaGtgcactgcagactccaggct	14	4	12	11	2	0	2	0	0	0	2	1	4	1	3	1	2	3	5	1	2	3	0			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr5:95768715G>A	ENST00000311106.3	-	1	269	c.32C>T	c.(31-33)aCt>aTt	p.T11I	CTD-2337A12.1_ENST00000502645.2_RNA|PCSK1_ENST00000508626.1_5'Flank	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	11					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)"	GACGAAAGCAGTGCACTGCAG	0.522																																					p.T11I		Atlas-SNP	.											.	PCSK1	93	.	0			c.C32T						PASS	.						122	128	126					5																	95768715		2203	4300	6503	SO:0001583	missense	5122	exon1			AAAGCAGTGCACT		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.32C>T	chr5.hg19:g.95768715G>A	ENSP00000308024:p.Thr11Ile	241.0	0.0	.		136.0	39.0	.	NM_000439	B7Z8T7|E9PHA1|P78478|Q92532	Missense_Mutation	SNP	ENST00000311106.3	hg19	CCDS4081.1	.	.	.	.	.	.	.	.	.	.	G	1.548	-0.540118	0.04053	.	.	ENSG00000175426	ENST00000311106;ENST00000509190	T;T	0.62639	0.01;0.58	5.24	3.43	0.39272	.	0.676173	0.16441	N	0.214310	T	0.38134	0.1029	N	0.13003	0.285	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.16012	-1.0417	10	0.12766	T	0.61	-2.7841	6.8983	0.24269	0.3283:0.0:0.6717:0.0	.	11	P29120	NEC1_HUMAN	I	11	ENSP00000308024:T11I;ENSP00000427294:T11I	ENSP00000308024:T11I	T	-	2	0	PCSK1	95794471	0.059000	0.20769	0.005000	0.12908	0.831000	0.47069	1.742000	0.38248	1.439000	0.47511	0.655000	0.94253	ACT	.	.	.	none		0.522	PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1	NM_000439		A	95768715	G	A	95768715	3	1	14	1	0	0	0	0	1	0	0	0	11607	1029	36	2	2328	2	PCSK1	5	95768715	Missense_Mutation	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10	16727610	95768715	85146545	22	965											
SEMA6A	57556	hgsc.bcm.edu	37	chr5	115803312	115803312	+	Frame_Shift_Del	DEL	C	C	-																															gtgattatgggaagacactgCccccaaagggtctgtgctgt																										TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr5:115803312delC	ENST00000343348.6	-	18	2648	c.1861delG	c.(1861-1863)gcafs	p.A621fs	SEMA6A_ENST00000513137.1_Frame_Shift_Del_p.A48fs|SEMA6A_ENST00000257414.8_Frame_Shift_Del_p.A638fs|CTB-118N6.3_ENST00000508640.1_RNA|CTB-118N6.3_ENST00000508424.1_RNA|SEMA6A_ENST00000510263.1_Frame_Shift_Del_p.A621fs|SEMA6A_ENST00000282394.6_Intron|CTB-118N6.3_ENST00000510682.1_RNA|CTB-118N6.3_ENST00000514214.1_RNA	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	621					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)		GAAGACACTGCCCCCAAAGGG	0.542																																					p.A621fs		Atlas-INDEL	.											.	SEMA6A	93	.	0			c.1862delC						PASS	.						81	79	80					5																	115803312		1974	4167	6141	SO:0001589	frameshift_variant	57556	exon18			.	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.1861delG	chr5.hg19:g.115803312delC	ENSP00000345512:p.Ala621fs	84.0	0.0	0		90.0	12.0	0.133333	NM_020796	Q9P2H9	Frame_Shift_Del	DEL	ENST00000343348.6	hg19	CCDS47256.1																																																																																			.	.	.	none		0.542	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371270.1	NM_020796		-	115803312	C	-	115803312	7	5	14	1	0	1	0	1	0	0	0	0	14052	739	26	0	1239	0	SEMA6A	5	115803312	Frame_Shift_Del	DEL	C	TCGA-2Z-A9JK-01A-11D-A42J-10	20034597	115803312	65111948	23	966											
CEP120	153241	hgsc.bcm.edu	37	chr5	122682287	122682287	+	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	acttattattcgatcctcgtGattatacacacccgttctca	10	15	4	12	3	1	1	1	1	1	0	5	2	2	1	2	0	1	1	2	0	4	6			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr5:122682287G>A	ENST00000306467.5	-	20	3191	c.2887C>T	c.(2887-2889)Cac>Tac	p.H963Y	CEP120_ENST00000306481.6_Missense_Mutation_p.H937Y|CEP120_ENST00000328236.5_Missense_Mutation_p.H963Y			Q8N960	CE120_HUMAN	centrosomal protein 120kDa	963					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						CGATCCTCGTGATTATACACA	0.403																																					p.H963Y		Atlas-SNP	.											.	CEP120	72	.	0			c.C2887T						PASS	.						171	170	171					5																	122682287		2203	4300	6503	SO:0001583	missense	153241	exon21			CCTCGTGATTATA	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.2887C>T	chr5.hg19:g.122682287G>A	ENSP00000303058:p.His963Tyr	57.0	0.0	.		95.0	19.0	.	NM_153223	Q6AI52|Q6AW89|Q8IWB5|Q8N9Y0|Q8NDE8	Missense_Mutation	SNP	ENST00000306467.5	hg19	CCDS4134.2	.	.	.	.	.	.	.	.	.	.	G	17.88	3.497201	0.64186	.	.	ENSG00000168944	ENST00000306467;ENST00000328236;ENST00000306481	T;T;T	0.19394	2.15;2.15;2.15	5.27	5.27	0.74061	.	0.000000	0.64402	U	0.000002	T	0.30978	0.0782	L	0.46157	1.445	0.80722	D	1	D	0.62365	0.991	P	0.53518	0.728	T	0.00878	-1.1530	10	0.34782	T	0.22	-10.3632	15.2858	0.73828	0.0:0.0:0.8595:0.1405	.	963	Q8N960	CE120_HUMAN	Y	963;963;937	ENSP00000303058:H963Y;ENSP00000327504:H963Y;ENSP00000307419:H937Y	ENSP00000303058:H963Y	H	-	1	0	CEP120	122710186	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.378000	0.73150	2.476000	0.83614	0.655000	0.94253	CAC	.	.	.	none		0.403	CEP120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250899.2	NM_153223		A	122682287	G	A	122682287	3	1	14	1	0	0	0	0	1	0	0	0	3248	1290	45	2	77	2	CEP120	5	122682287	Missense_Mutation	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10	6878975	122682287	58232973	24	967											
DOCK2	1794	hgsc.bcm.edu	37	chr5	169463521	169463521	+	Frame_Shift_Del	DEL	T	T	-																															ttttcctcccctacctagaaTttctacaaagataacaacag																										TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr5:169463521delT	ENST00000256935.8	+	36	3707	c.3627delT	c.(3625-3627)aatfs	p.N1209fs	DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000520908.1_Frame_Shift_Del_p.N701fs|DOCK2_ENST00000540750.1_Frame_Shift_Del_p.N270fs	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1209	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)			CTACCTAGAATTTCTACAAAG	0.418																																					p.N1209fs		Atlas-INDEL	.											.	DOCK2	389	.	0			c.3626delA						PASS	.						139	136	137					5																	169463521		2203	4300	6503	SO:0001589	frameshift_variant	1794	exon36			.	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.3627delT	chr5.hg19:g.169463521delT	ENSP00000256935:p.Asn1209fs	93.0	0.0	0		70.0	31.0	0.442857	NM_004946	Q2M3I0|Q96AK7	Frame_Shift_Del	DEL	ENST00000256935.8	hg19	CCDS4371.1																																																																																			.	.	.	none		0.418	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		-	169463521	T	-	169463521	7	5	14	1	0	1	0	1	0	0	0	0	4689	1490	52	0	3769	0	DOCK2	5	169463521	Frame_Shift_Del	DEL	T	TCGA-2Z-A9JK-01A-11D-A42J-10	46781234	169463521	11451739	25	968	9	3									
DOCK2	1794	hgsc.bcm.edu	37	chr5	169463522	169463523	+	Frame_Shift_Del	DEL	TT	TT	-																															tttcctcccctacctagaatTtctacaaagataacaacagg																										TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr5:169463522_169463523delTT	ENST00000256935.8	+	36	3708_3709	c.3628_3629delTT	c.(3628-3630)ttcfs	p.F1210fs	DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000520908.1_Frame_Shift_Del_p.F702fs|DOCK2_ENST00000540750.1_Frame_Shift_Del_p.F271fs	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1210	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)			TACCTAGAATTTCTACAAAGAT	0.411																																					p.1209_1210del		Pindel	.											.	DOCK2	389	.	0			c.3627_3628del						PASS	.																																			SO:0001589	frameshift_variant	1794	exon36			.	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.3628_3629delTT	chr5.hg19:g.169463522_169463523delTT	ENSP00000256935:p.Phe1210fs	96.0	0.0	.		72.0	26.0	0.361	NM_004946	Q2M3I0|Q96AK7	Frame_Shift_Del	DEL	ENST00000256935.8	hg19	CCDS4371.1																																																																																			.	.	.	none		0.411	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		-	169463523	TT	-	169463522	7	5	14	1	0	1	0	1	0	0	0	0	4689	1841	64	0	3770	0	DOCK2	5	169463522	Frame_Shift_Del	DEL	TT	TCGA-2Z-A9JK-01A-11D-A42J-10	1	169463522	11451738	26	969	9	3									
DOCK2	1794	hgsc.bcm.edu	37	chr5	169463523	169463523	+	Missense_Mutation	SNP	T	T	A																															ttcctcccctacctagaattTctacaaagataacaacaggg																										TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr5:169463523T>A	ENST00000256935.8	+	36	3709	c.3629T>A	c.(3628-3630)tTc>tAc	p.F1210Y	DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000520908.1_Missense_Mutation_p.F702Y|DOCK2_ENST00000540750.1_Missense_Mutation_p.F271Y	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1210	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)			ACCTAGAATTTCTACAAAGAT	0.413																																					p.F1210Y		Atlas-SNP	.											.	DOCK2	389	.	0			c.T3629A						PASS	.						138	135	136					5																	169463523		2203	4300	6503	SO:0001583	missense	1794	exon36			AGAATTTCTACAA	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.3629T>A	chr5.hg19:g.169463523T>A	ENSP00000256935:p.Phe1210Tyr	97.0	0.0	.		72.0	32.0	.	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.394444	0.83011	.	.	ENSG00000134516	ENST00000256935;ENST00000520908;ENST00000540750	T;T;T	0.56444	0.46;0.46;0.46	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.58221	0.2107	L	0.58925	1.835	0.48185	D	0.999609	D;B	0.52996	0.957;0.053	P;B	0.50617	0.646;0.035	T	0.54906	-0.8223	10	0.22109	T	0.4	.	15.5299	0.75952	0.0:0.0:0.0:1.0	.	702;1210	E7ERW7;Q92608	.;DOCK2_HUMAN	Y	1210;702;271	ENSP00000256935:F1210Y;ENSP00000429283:F702Y;ENSP00000438827:F271Y	ENSP00000256935:F1210Y	F	+	2	0	DOCK2	169396101	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.216000	0.77974	2.147000	0.66899	0.533000	0.62120	TTC	.	.	.	none		0.413	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		A	169463523	T	A	169463523	3	1	14	1	0	0	0	0	1	0	0	0	4689	1783	62	5	3771	5	DOCK2	5	169463523	Missense_Mutation	SNP	T	TCGA-2Z-A9JK-01A-11D-A42J-10	1	169463523	11451737	27	970	9	3									
GPR116	221395	hgsc.bcm.edu	37	chr6	46836697	46836697	+	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	acctcctcgtggtataaaatCtttggtatattttaattcca	11	17	5	8	1	1	0	0	0	1	0	4	0	3	0	3	2	0	2	3	2	6	8			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr6:46836697C>A	ENST00000283296.7	-	12	1832	c.1544G>T	c.(1543-1545)aGa>aTa	p.R515I	GPR116_ENST00000362015.4_Missense_Mutation_p.R515I|GPR116_ENST00000545669.1_5'UTR|GPR116_ENST00000265417.7_Missense_Mutation_p.R515I|GPR116_ENST00000456426.2_Missense_Mutation_p.R373I	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	515	Ig-like 3.				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)			GGTATAAAATCTTTGGTATAT	0.418																																					p.R515I	NSCLC(59;410 1274 8751 36715 50546)	Atlas-SNP	.											GPR116,colon,carcinoma,0,2	GPR116	133	.	0			c.G1544T						PASS	.						99	101	100					6																	46836697		2203	4300	6503	SO:0001583	missense	221395	exon12			TAAAATCTTTGGT	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.1544G>T	chr6.hg19:g.46836697C>A	ENSP00000283296:p.Arg515Ile	76.0	0.0	.		72.0	16.0	.	NM_015234	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Missense_Mutation	SNP	ENST00000283296.7	hg19	CCDS4919.1	.	.	.	.	.	.	.	.	.	.	C	11.42	1.634757	0.29068	.	.	ENSG00000069122	ENST00000452370;ENST00000283296;ENST00000362015;ENST00000456426;ENST00000265417	T;T;T;T	0.21734	1.99;1.99;1.99;1.99	5.47	-3.16	0.05217	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.789290	0.11856	N	0.522870	T	0.05593	0.0147	N	0.24115	0.695	0.58432	D	0.999999	B;P;P;P	0.45126	0.346;0.533;0.851;0.533	B;B;B;B	0.37650	0.052;0.183;0.255;0.183	T	0.32666	-0.9898	10	0.56958	D	0.05	-8.9279	12.8097	0.57634	0.0:0.1961:0.0:0.8039	.	70;515;373;515	B4DTV3;E9PBS6;Q8IZF2-3;Q8IZF2	.;.;.;GP116_HUMAN	I	515;515;515;373;515	ENSP00000283296:R515I;ENSP00000354563:R515I;ENSP00000412866:R373I;ENSP00000265417:R515I	ENSP00000265417:R515I	R	-	2	0	GPR116	46944656	0.851000	0.29673	0.344000	0.25628	0.337000	0.28794	0.065000	0.14466	-0.513000	0.06496	0.591000	0.81541	AGA	.	.	.	none		0.418	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234		A	46836697	C	A	46836697	3	1	14	1	0	0	0	0	1	0	0	0	6640	913	32	4	2536	4	GPR116	6	46836697	Missense_Mutation	SNP	C	TCGA-2Z-A9JK-01A-11D-A42J-10		46836697	124278370	28	971											
KATNA1	11104	hgsc.bcm.edu	37	chr6	149922828	149922828	+	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	gaatgttgtcttgcattctgTagctactgctttagcaagga	9	15	10	7	0	2	0	0	0	2	0	2	2	2	1	0	1	5	6	0	1	5	7			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr6:149922828T>A	ENST00000335647.5	-	6	834	c.790A>T	c.(790-792)Aca>Tca	p.T264S	KATNA1_ENST00000335643.8_Missense_Mutation_p.T188S|KATNA1_ENST00000494504.1_5'UTR|KATNA1_ENST00000367411.2_Missense_Mutation_p.T264S					katanin p60 (ATPase containing) subunit A 1											endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	12		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;2.95e-12)|GBM - Glioblastoma multiforme(68;0.173)		TTGCATTCTGTAGCTACTGCT	0.453																																					p.T264S		Atlas-SNP	.											.	KATNA1	34	.	0			c.A790T						PASS	.						116	105	109					6																	149922828		2203	4300	6503	SO:0001583	missense	11104	exon7			ATTCTGTAGCTAC	AF056022	CCDS5217.1, CCDS56456.1	6q24.3	2011-01-25	2011-01-25		ENSG00000186625	ENSG00000186625		"ATPases / AAA-type"	6216	protein-coding gene	gene with protein product		606696	"katanin p60 (ATPase-containing) subunit A 1"			9658175	Standard	NM_007044		Approved		uc003qms.3	O75449	OTTHUMG00000015787	ENST00000335647.5:c.790A>T	chr6.hg19:g.149922828T>A	ENSP00000335106:p.Thr264Ser	138.0	0.0	.		97.0	25.0	.	NM_007044		Missense_Mutation	SNP	ENST00000335647.5	hg19	CCDS5217.1	.	.	.	.	.	.	.	.	.	.	T	29.5	5.007563	0.93287	.	.	ENSG00000186625	ENST00000335647;ENST00000335643;ENST00000367411;ENST00000444282	D;D;D;D	0.92699	-3.09;-3.09;-3.09;-3.09	5.85	5.85	0.93711	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.87605	0.6219	N	0.04355	-0.22	0.80722	D	1	D;B;D	0.89917	0.991;0.282;1.0	D;B;D	0.97110	0.973;0.317;1.0	D	0.89105	0.3492	9	.	.	.	.	16.2365	0.82377	0.0:0.0:0.0:1.0	.	264;188;264	A8K7S5;O75449-2;O75449	.;.;KTNA1_HUMAN	S	264;188;264;264	ENSP00000335106:T264S;ENSP00000335180:T188S;ENSP00000356381:T264S;ENSP00000390322:T264S	.	T	-	1	0	KATNA1	149964521	1.000000	0.71417	0.997000	0.53966	0.972000	0.66771	8.013000	0.88655	2.238000	0.73509	0.477000	0.44152	ACA	.	.	.	none		0.453	KATNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042641.2	NM_007044		A	149922828	T	A	149922828	3	1	14	1	0	0	0	0	1	0	0	0	7991	1638	57	5	705	5	KATNA1	6	149922828	Missense_Mutation	SNP	T	TCGA-2Z-A9JK-01A-11D-A42J-10	103086131	149922828	21192239	29	972											
TIAM2	26230	hgsc.bcm.edu	37	chr6	155572110	155572110	+	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	tttcctggttgaatccatttCtgtctctaggaaaagctaga	10	15	8	8	0	2	2	0	1	2	1	5	3	4	3	2	2	1	2	2	2	5	5			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr6:155572110C>A	ENST00000461783.3	+	24	5288	c.4015C>A	c.(4015-4017)Ctg>Atg	p.L1339M	TIAM2_ENST00000275246.7_Missense_Mutation_p.L264M|RP11-477D19.2_ENST00000435295.1_RNA|TIAM2_ENST00000360366.4_Missense_Mutation_p.L1363M|TIAM2_ENST00000318981.5_Missense_Mutation_p.L1339M|TIAM2_ENST00000529824.2_Missense_Mutation_p.L1368M|TIAM2_ENST00000456877.2_Missense_Mutation_p.L651M|TIAM2_ENST00000456144.1_Missense_Mutation_p.L1368M|TIAM2_ENST00000528391.2_Missense_Mutation_p.L675M|TIAM2_ENST00000367174.2_Missense_Mutation_p.L715M			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1339					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)	p.L1339L(1)		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)		GAATCCATTTCTGTCTCTAGG	0.428																																					p.L1339M		Atlas-SNP	.											TIAM2,mouth,carcinoma,0,1	TIAM2	161	.	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C4015A						PASS	.						166	158	160					6																	155572110		2203	4300	6503	SO:0001583	missense	26230	exon21			CCATTTCTGTCTC		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.4015C>A	chr6.hg19:g.155572110C>A	ENSP00000437188:p.Leu1339Met	97.0	0.0	.		90.0	29.0	.	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	hg19	CCDS34558.1	.	.	.	.	.	.	.	.	.	.	C	16.66	3.186124	0.57909	.	.	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000367174;ENST00000360366;ENST00000529824;ENST00000456877;ENST00000528391;ENST00000275246	T;T;T;T;T;T;T;T;T;T	0.08458	3.56;3.5;3.56;3.56;3.39;3.56;3.56;3.39;3.39;3.09	5.43	3.65	0.41850	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.152382	0.42964	D	0.000622	T	0.03739	0.0106	N	0.08118	0	0.27056	N	0.963673	P;D;D;D	0.65815	0.944;0.995;0.995;0.991	P;P;P;P	0.62560	0.497;0.904;0.861;0.73	T	0.29941	-0.9995	10	0.46703	T	0.11	.	7.1279	0.25482	0.0:0.709:0.1414:0.1496	.	675;1368;1363;1339	E9PKT1;Q8IVF5-2;Q8IVF5-5;Q8IVF5	.;.;.;TIAM2_HUMAN	M	1339;1585;1339;1368;1339;715;1363;1368;651;675;264	ENSP00000437188:L1339M;ENSP00000434901:L1339M;ENSP00000407746:L1368M;ENSP00000327315:L1339M;ENSP00000356142:L715M;ENSP00000353528:L1363M;ENSP00000433348:L1368M;ENSP00000407183:L651M;ENSP00000435335:L675M;ENSP00000275246:L264M	ENSP00000275246:L264M	L	+	1	2	TIAM2	155613802	0.939000	0.31865	1.000000	0.80357	0.997000	0.91878	0.940000	0.28992	1.312000	0.45043	0.655000	0.94253	CTG	.	.	.	none		0.428	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454		A	155572110	C	A	155572110	3	1	14	1	0	0	0	0	1	0	0	0	15903	912	32	4	4089	4	TIAM2	6	155572110	Missense_Mutation	SNP	C	TCGA-2Z-A9JK-01A-11D-A42J-10	5649282	155572110	15542957	30	973											
TMEM106B	54664	hgsc.bcm.edu	37	chr7	12254528	12254528	+	Missense_Mutation	SNP	T	T	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	aaacatgaggaatggactggTtaatagtgaagtccataatg	16	10	11	4	0	0	2	0	2	0	0	1	4	1	4	1	3	1	1	1	3	6	3			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr7:12254528T>G	ENST00000396667.3	+	3	414	c.92T>G	c.(91-93)gTt>gGt	p.V31G	TMEM106B_ENST00000396668.3_Missense_Mutation_p.V31G|TMEM106B_ENST00000453686.1_3'UTR	NM_018374.3	NP_060844.2	Q9NUM4	T106B_HUMAN	transmembrane protein 106B	31					cell death (GO:0008219)|dendrite morphogenesis (GO:0048813)|lysosome localization (GO:0032418)|transport (GO:0006810)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				NS(1)|endometrium(8)|large_intestine(2)|lung(7)	18				UCEC - Uterine corpus endometrioid carcinoma (126;0.185)		AATGGACTGGTTAATAGTGAA	0.393																																					p.V31G		Atlas-SNP	.											.	TMEM106B	34	.	0			c.T92G						PASS	.						112	103	106					7																	12254528		2203	4300	6503	SO:0001583	missense	54664	exon2			GACTGGTTAATAG	BC033901	CCDS5358.1	7p21.3	2012-06-06			ENSG00000106460	ENSG00000106460			22407	protein-coding gene	gene with protein product		613413				20154673, 22511793	Standard	NM_018374		Approved	MGC33727, FLJ11273	uc003ssh.3	Q9NUM4	OTTHUMG00000125537	ENST00000396667.3:c.92T>G	chr7.hg19:g.12254528T>G	ENSP00000379901:p.Val31Gly	66.0	0.0	.		85.0	16.0	.	NM_001134232	A4D108|Q53FL9|Q8N4L0	Missense_Mutation	SNP	ENST00000396667.3	hg19	CCDS5358.1	.	.	.	.	.	.	.	.	.	.	T	11.35	1.612576	0.28712	.	.	ENSG00000106460	ENST00000396668;ENST00000444443;ENST00000396667	T;T;T	0.21543	2.0;2.0;2.0	5.41	5.41	0.78517	.	0.496686	0.20899	N	0.083673	T	0.16300	0.0392	N	0.22421	0.69	0.58432	D	0.999995	B	0.22909	0.077	B	0.33392	0.163	T	0.13072	-1.0523	10	0.23891	T	0.37	-18.5982	10.1599	0.42844	0.0:0.0745:0.0:0.9255	.	31	Q9NUM4	T106B_HUMAN	G	31	ENSP00000379902:V31G;ENSP00000401302:V31G;ENSP00000379901:V31G	ENSP00000379901:V31G	V	+	2	0	TMEM106B	12221053	0.996000	0.38824	0.980000	0.43619	0.448000	0.32197	3.752000	0.55172	2.197000	0.70478	0.533000	0.62120	GTT	.	.	.	none		0.393	TMEM106B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246870.3	NM_018374		G	12254528	T	G	12254528	3	3	14	1	0	0	0	0	1	0	0	0	16033	1725	60	5	94	5	TMEM106B	7	12254528	Missense_Mutation	SNP	T	TCGA-2Z-A9JK-01A-11D-A42J-10		12254528	146884135	31	974											
VKORC1L1	154807	hgsc.bcm.edu	37	chr7	65413712	65413713	+	Frame_Shift_Del	DEL	AA	AA	-																															tttggaaaggatggtgtattAaaccagccaaacagtgtctt																										TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr7:65413712_65413713delAA	ENST00000360768.3	+	2	354_355	c.249_250delAA	c.(247-252)ttaaacfs	p.N84fs	VKORC1L1_ENST00000434382.2_Intron	NM_001284342.1|NM_173517.4	NP_001271271.1|NP_775788.2	Q8N0U8	VKORL_HUMAN	vitamin K epoxide reductase complex, subunit 1-like 1	84					cellular response to oxidative stress (GO:0034599)|peptidyl-glutamic acid carboxylation (GO:0017187)|vitamin K metabolic process (GO:0042373)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	quinone binding (GO:0048038)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			large_intestine(1)|prostate(1)	2		Lung NSC(55;0.197)			Menadione(DB00170)	ATGGTGTATTAAACCAGCCAAA	0.317																																					p.83_83del		Atlas-INDEL	.											.	VKORC1L1	14	.	0			c.248_249del						PASS	.																																			SO:0001589	frameshift_variant	154807	exon2			.		CCDS5529.1, CCDS64663.1	7q11.21	2013-10-07			ENSG00000196715	ENSG00000196715			21492	protein-coding gene	gene with protein product		608838				23928358	Standard	NM_001284342		Approved		uc003tul.3	Q8N0U8	OTTHUMG00000129449	ENST00000360768.3:c.249_250delAA	chr7.hg19:g.65413712_65413713delAA	ENSP00000353998:p.Asn84fs	894.0	0.0	0		763.0	78.0	0.102228	NM_173517	B4E222|E7ETM5|Q6AHW9|Q6TEK6	Frame_Shift_Del	DEL	ENST00000360768.3	hg19	CCDS5529.1																																																																																			.	.	.	none		0.317	VKORC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251612.3	NM_173517		-	65413713	AA	-	65413712	7	5	14	1	0	1	0	1	0	0	0	0	17185	359	13	0	255	0	VKORC1L1	7	65413712	Frame_Shift_Del	DEL	AA	TCGA-2Z-A9JK-01A-11D-A42J-10	53159184	65413712	93724951	32	975											
MFHAS1	9258	hgsc.bcm.edu	37	chr8	8747815	8747815	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acaggaactttccctctataGgcaaagatctgaaatttacc	14	11	6	10	0	2	2	0	1	2	1	3	3	3	3	2	2	2	1	2	2	6	5			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr8:8747815G>A	ENST00000276282.6	-	1	3340	c.2754C>T	c.(2752-2754)gcC>gcT	p.A918A		NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	918										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)		TCCCTCTATAGGCAAAGATCT	0.483																																					p.A918A	Melanoma(103;1201 2045 17515 28966)	Atlas-SNP	.											.	MFHAS1	58	.	0			c.C2754T						PASS	.						80	82	81					8																	8747815		2203	4300	6503	SO:0001819	synonymous_variant	9258	exon1			TCTATAGGCAAAG	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.2754C>T	chr8.hg19:g.8747815G>A		118.0	0.0	.		120.0	29.0	.	NM_004225	Q96CI0	Silent	SNP	ENST00000276282.6	hg19	CCDS34844.1																																																																																			.	.	.	none		0.483	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225		A	8747815	G	A	8747815	2	1	14	1	0	0	0	0	0	0	0	1	9528	987	35	2		2	MFHAS1	8	8747815	Silent	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10		8747815	137616207	33	976											
PDLIM2	64236	hgsc.bcm.edu	37	chr8	22442384	22442384	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggacagctccttggaagTgctggcgactcgcttccagg	6	9	15	11	2	0	0	0	0	0	0	3	3	2	2	2	5	2	3	2	5	1	2			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr8:22442384T>C	ENST00000397760.4	+	4	696	c.296T>C	c.(295-297)gTg>gCg	p.V99A	PDLIM2_ENST00000448520.1_3'UTR|PDLIM2_ENST00000339162.7_Missense_Mutation_p.V99A|PDLIM2_ENST00000308354.7_Missense_Mutation_p.V349A|PDLIM2_ENST00000265810.4_Missense_Mutation_p.V99A|PDLIM2_ENST00000409141.1_Missense_Mutation_p.V99A|PDLIM2_ENST00000397761.2_Missense_Mutation_p.V99A|PDLIM2_ENST00000409417.1_Missense_Mutation_p.V99A			Q96JY6	PDLI2_HUMAN	PDZ and LIM domain 2 (mystique)	99						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)		TCCTTGGAAGTGCTGGCGACT	0.627																																					p.V349A		Atlas-SNP	.											.	PDLIM2	42	.	0			c.T1046C						PASS	.						133	104	114					8																	22442384		2203	4300	6503	SO:0001583	missense	64236	exon4			TGGAAGTGCTGGC	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.296T>C	chr8.hg19:g.22442384T>C	ENSP00000380867:p.Val99Ala	106.0	0.0	.		67.0	7.0	.	NM_021630	D3DSR5|J3KNH4|Q7Z584|Q86WM8|Q8WZ29|Q9H4L9|Q9H7I2	Missense_Mutation	SNP	ENST00000397760.4	hg19		.	.	.	.	.	.	.	.	.	.	T	10.93	1.490481	0.26686	.	.	ENSG00000120913	ENST00000456545;ENST00000308354;ENST00000452226;ENST00000397760;ENST00000339162;ENST00000381194;ENST00000397761;ENST00000436754;ENST00000426493;ENST00000429812;ENST00000409141;ENST00000265810;ENST00000409417	T;T;T;T;T;T;T;T;T;T;T;T	0.11169	2.8;2.8;2.8;2.8;2.8;2.8;2.8;2.8;2.8;2.8;2.8;2.8	4.64	3.46	0.39613	.	0.669254	0.14051	N	0.344789	T	0.10294	0.0252	M	0.65975	2.015	0.25771	N	0.984832	P;P;B;B	0.36837	0.571;0.571;0.043;0.255	B;B;B;B	0.33392	0.163;0.163;0.027;0.078	T	0.16660	-1.0395	10	0.07030	T	0.85	-10.5924	8.8203	0.35020	0.0:0.0:0.1903:0.8097	.	99;99;99;99	Q96JY6-3;Q96JY6-4;Q96JY6;C9JS55	.;.;PDLI2_HUMAN;.	A	99;349;99;99;99;99;99;99;99;99;99;99;99	ENSP00000401992:V99A;ENSP00000312634:V349A;ENSP00000394376:V99A;ENSP00000380867:V99A;ENSP00000342035:V99A;ENSP00000380868:V99A;ENSP00000397738:V99A;ENSP00000392920:V99A;ENSP00000407643:V99A;ENSP00000386868:V99A;ENSP00000265810:V99A;ENSP00000387084:V99A	ENSP00000265810:V99A	V	+	2	0	PDLIM2	22498329	0.202000	0.23423	0.987000	0.45799	0.658000	0.38924	0.550000	0.23345	0.856000	0.35383	0.482000	0.46254	GTG	.	.	.	none		0.627	PDLIM2-202	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000334167.1			C	22442384	T	C	22442384	3	2	14	1	0	0	0	0	1	0	0	0	11687	1696	59	3	306	3	PDLIM2	8	22442384	Missense_Mutation	SNP	T	TCGA-2Z-A9JK-01A-11D-A42J-10	13694569	22442384	123921638	34	977											
RP1	6101	hgsc.bcm.edu	37	chr8	55538963	55538963	+	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	atgcaccgcaatctcaagcaGaagtggcatctgggtatttg	11	10	11	9	1	2	1	1	0	2	1	3	1	2	1	1	2	2	5	1	2	4	2			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr8:55538963G>A	ENST00000220676.1	+	4	2669	c.2521G>A	c.(2521-2523)Gaa>Aaa	p.E841K		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	841					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)			ATCTCAAGCAGAAGTGGCATC	0.323																																					p.E841K	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.G2521A						PASS	.						43	46	45					8																	55538963		2201	4300	6501	SO:0001583	missense	6101	exon4			CAAGCAGAAGTGG	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.2521G>A	chr8.hg19:g.55538963G>A	ENSP00000220676:p.Glu841Lys	115.0	0.0	.		181.0	60.0	.	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	hg19	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	G	13.18	2.159150	0.38119	.	.	ENSG00000104237	ENST00000220676	T	0.60424	0.19	4.91	4.02	0.46733	.	0.613701	0.15204	N	0.274879	T	0.49406	0.1555	M	0.62723	1.935	0.09310	N	0.999995	P	0.37441	0.595	B	0.31290	0.127	T	0.53464	-0.8435	10	0.72032	D	0.01	-10.8547	8.0414	0.30523	0.227:0.0:0.773:0.0	.	841	P56715	RP1_HUMAN	K	841	ENSP00000220676:E841K	ENSP00000220676:E841K	E	+	1	0	RP1	55701516	0.996000	0.38824	0.220000	0.23810	0.508000	0.34012	2.176000	0.42500	2.642000	0.89623	0.655000	0.94253	GAA	.	.	.	none		0.323	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		A	55538963	G	A	55538963	3	1	14	1	0	0	0	0	1	0	0	0	13545	943	33	2	2531	2	RP1	8	55538963	Missense_Mutation	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10	33096579	55538963	90825059	35	978											
LAPTM4B	55353	hgsc.bcm.edu	37	chr8	98788210	98788210	+	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	acgctcctgaaaacttgcgcGcgcgctcgcgccactgcgcc	6	6	11	18	8	0	1	0	1	0	0	2	1	1	1	3	0	3	2	3	0	2	1			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr8:98788210G>A	ENST00000445593.2	+	1	926	c.246G>A	c.(244-246)gcG>gcA	p.A82A	LAPTM4B_ENST00000521545.2_5'UTR|RNU7-177P_ENST00000517101.1_RNA	NM_018407.4	NP_060877.3	Q86VI4	LAP4B_HUMAN	lysosomal protein transmembrane 4 beta	135					transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	10	Breast(36;1.59e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.149)			AAACTTGCGCGCGCGCTCGCG	0.736																																					p.A82A		Atlas-SNP	.											.	LAPTM4B	26	.	0			c.G246A						PASS	.						8	9	9					8																	98788210		2092	4153	6245	SO:0001819	synonymous_variant	55353	exon1			TTGCGCGCGCGCT	AF317417	CCDS6275.1	8q22.1	2008-08-11	2008-08-11		ENSG00000104341	ENSG00000104341			13646	protein-coding gene	gene with protein product		613296					Standard	NM_018407		Approved	LC27	uc003yia.3	Q86VI4	OTTHUMG00000164740	ENST00000445593.2:c.246G>A	chr8.hg19:g.98788210G>A		63.0	0.0	.		38.0	10.0	.	NM_018407	Q3ZCV5|Q7L909|Q86VH8|Q9H060	Silent	SNP	ENST00000445593.2	hg19	CCDS6275.1	.	.	.	.	.	.	.	.	.	.	G	12.42	1.933237	0.34096	.	.	ENSG00000104341	ENST00000517924	.	.	.	3.43	2.54	0.30619	.	.	.	.	.	T	0.52484	0.1737	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43572	-0.9383	4	.	.	.	-0.9742	5.4195	0.16392	0.1221:0.2784:0.5995:0.0	.	.	.	.	H	45	.	.	R	+	2	0	LAPTM4B	98857386	0.368000	0.25031	0.934000	0.37439	0.097000	0.18754	3.208000	0.51114	0.762000	0.33152	0.643000	0.83706	CGC	.	.	.	none		0.736	LAPTM4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000380014.1			A	98788210	G	A	98788210	2	1	14	1	0	0	0	0	0	0	0	1	8632	1074	38	1		1	LAPTM4B	8	98788210	Silent	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10	43249247	98788210	47575812	36	979											
SMC2	10592	hgsc.bcm.edu	37	chr9	106882315	106882315	+	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	ttgcctctatcaggtgctcgAtcccaggcagcttccatttt	6	14	8	13	1	2	0	1	0	1	0	5	1	4	0	3	2	3	3	3	2	1	5			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr9:106882315A>T	ENST00000286398.7	+	16	2292	c.2004A>T	c.(2002-2004)cgA>cgT	p.R668R	SMC2_ENST00000374787.3_Silent_p.R668R|SMC2_ENST00000374793.3_Silent_p.R668R|SMC2_ENST00000303219.8_Silent_p.R668R	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	668	Flexible hinge.				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						CAGGTGCTCGATCCCAGGCAG	0.393																																					p.R668R		Atlas-SNP	.											.	SMC2	127	.	0			c.A2004T						PASS	.						124	131	129					9																	106882315		2203	4300	6503	SO:0001819	synonymous_variant	10592	exon16			TGCTCGATCCCAG	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.2004A>T	chr9.hg19:g.106882315A>T		75.0	0.0	.		84.0	17.0	.	NM_006444	Q6IEE0|Q9P1P2	Silent	SNP	ENST00000286398.7	hg19	CCDS35086.1																																																																																			.	.	.	none		0.393	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1			T	106882315	A	T	106882315	2	4	14	1	0	0	0	0	0	0	0	1	14796	320	12	5		5	SMC2	9	106882315	Silent	SNP	A	TCGA-2Z-A9JK-01A-11D-A42J-10		106882315	34331116	37	980											
SH2D3C	10044	hgsc.bcm.edu	37	chr9	130511796	130511796	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acaggtactggatgtgtgtgTagctctcgcctgccttcacc	6	12	11	12	1	2	0	1	0	1	0	3	1	2	1	3	2	3	3	3	2	2	3			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr9:130511796T>C	ENST00000314830.8	-	5	946	c.833A>G	c.(832-834)tAc>tGc	p.Y278C	SH2D3C_ENST00000373277.4_Missense_Mutation_p.Y121C|SH2D3C_ENST00000471939.1_Intron|SH2D3C_ENST00000429553.1_5'UTR|SH2D3C_ENST00000373276.3_Missense_Mutation_p.Y210C|SH2D3C_ENST00000420366.1_Missense_Mutation_p.Y120C|SH2D3C_ENST00000373274.3_Missense_Mutation_p.Y118C	NM_170600.2	NP_733745.1	Q8N5H7	SH2D3_HUMAN	SH2 domain containing 3C	278	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						GATGTGTGTGTAGCTCTCGCC	0.592																																					p.Y278C		Atlas-SNP	.											.	SH2D3C	102	.	0			c.A833G						PASS	.						95	81	86					9																	130511796		2203	4300	6503	SO:0001583	missense	10044	exon5			TGTGTGTAGCTCT	AF124251	CCDS6877.1, CCDS6878.1, CCDS48026.1, CCDS48028.1, CCDS59145.1	9q33.1-q33.3	2013-02-14	2002-01-14		ENSG00000095370	ENSG00000095370		"SH2 domain containing"	16884	protein-coding gene	gene with protein product		604722	"SH2 domain-containing 3C"			10187783	Standard	NM_170600		Approved	NSP3	uc004bsc.3	Q8N5H7	OTTHUMG00000020717	ENST00000314830.8:c.833A>G	chr9.hg19:g.130511796T>C	ENSP00000317817:p.Tyr278Cys	89.0	0.0	.		73.0	25.0	.	NM_170600	A8K5S8|E9PG48|Q5HYE5|Q5JU31|Q6UY42|Q8N6X3|Q9Y2X5	Missense_Mutation	SNP	ENST00000314830.8	hg19	CCDS6877.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.88|18.88	3.717121|3.717121	0.68844|0.68844	.|.	.|.	ENSG00000095370|ENSG00000095370	ENST00000440630|ENST00000373277;ENST00000420366;ENST00000373276;ENST00000373274;ENST00000314830;ENST00000414380	.|T;T;T;T;T;T	.|0.43294	.|2.38;2.38;2.13;2.39;2.35;0.95	5.67|5.67	5.67|5.67	0.87782|0.87782	.|SH2 motif (4);	.|0.341438	.|0.31268	.|N	.|0.007942	T|T	0.58524|0.58524	0.2128|0.2128	M|M	0.63169|0.63169	1.94|1.94	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.71674	.|0.996;0.998;0.998;0.992;0.998	.|D;D;P;P;D	.|0.67231	.|0.926;0.95;0.815;0.719;0.917	T|T	0.61903|0.61903	-0.6967|-0.6967	5|10	.|0.72032	.|D	.|0.01	0.3469|0.3469	11.0757|11.0757	0.48030|0.48030	0.0:0.0746:0.0:0.9254|0.0:0.0746:0.0:0.9254	.|.	.|118;278;210;121;120	.|E9PG48;Q8N5H7;E7EUN5;Q8N5H7-2;Q8N5H7-5	.|.;SH2D3_HUMAN;.;.;.	A|C	115|121;120;210;118;278;95	.|ENSP00000362374:Y121C;ENSP00000388536:Y120C;ENSP00000362373:Y210C;ENSP00000362371:Y118C;ENSP00000317817:Y278C;ENSP00000413760:Y95C	.|ENSP00000317817:Y278C	T|Y	-|-	1|2	0|0	SH2D3C|SH2D3C	129551617|129551617	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	1.686000|1.686000	0.37669|0.37669	2.169000|2.169000	0.68431|0.68431	0.459000|0.459000	0.35465|0.35465	ACA|TAC	.	.	.	none		0.592	SH2D3C-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054264.1	NM_005489		C	130511796	T	C	130511796	3	2	14	1	0	0	0	0	1	0	0	0	14247	1638	57	3	1781	3	SH2D3C	9	130511796	Missense_Mutation	SNP	T	TCGA-2Z-A9JK-01A-11D-A42J-10	23629481	130511796	10701635	38	981											
HERC4	26091	hgsc.bcm.edu	37	chr10	69749982	69749982	+	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	tcttaccaagtactttcagtGgtgccttttctaggttcaca	8	16	7	10	0	4	0	2	0	2	0	4	0	4	0	2	2	3	2	2	2	4	7			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr10:69749982G>A	ENST00000395198.3	-	14	1866	c.1619C>T	c.(1618-1620)cCa>cTa	p.P540L	HERC4_ENST00000373700.4_Missense_Mutation_p.P540L|HERC4_ENST00000412272.2_Missense_Mutation_p.P540L|HERC4_ENST00000395187.2_3'UTR|HERC4_ENST00000277817.6_Missense_Mutation_p.P430L	NM_022079.2	NP_071362.1	Q5GLZ8	HERC4_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 4	540					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						TACTTTCAGTGGTGCCTTTTC	0.353																																					p.P540L		Atlas-SNP	.											.	HERC4	78	.	0			c.C1619T						PASS	.						90	88	89					10																	69749982		2203	4300	6503	SO:0001583	missense	26091	exon14			TTCAGTGGTGCCT	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.1619C>T	chr10.hg19:g.69749982G>A	ENSP00000378624:p.Pro540Leu	30.0	0.0	.		47.0	11.0	.	NM_022079	Q5GC98|Q5GC99|Q5GCA0|Q8IXP9|Q9HCH9	Missense_Mutation	SNP	ENST00000395198.3	hg19	CCDS41533.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.711019	0.89112	.	.	ENSG00000148634	ENST00000277817;ENST00000412272;ENST00000395198;ENST00000373700	T;T;T;T	0.46819	1.14;0.86;0.89;0.89	5.53	5.53	0.82687	.	0.050900	0.85682	D	0.000000	T	0.65365	0.2684	M	0.69185	2.1	0.80722	D	1	D;P;B;P;D;P	0.63046	0.992;0.694;0.024;0.952;0.972;0.918	P;B;B;P;P;P	0.58721	0.826;0.379;0.016;0.703;0.844;0.613	T	0.68209	-0.5469	10	0.87932	D	0	.	19.4511	0.94867	0.0:0.0:1.0:0.0	.	540;430;540;390;540;540	Q5GLZ8-3;Q5GLZ8-6;A8K9U4;Q5VXS9;Q5GLZ8-2;Q5GLZ8	.;.;.;.;.;HERC4_HUMAN	L	430;540;540;540	ENSP00000277817:P430L;ENSP00000416504:P540L;ENSP00000378624:P540L;ENSP00000362804:P540L	ENSP00000277817:P430L	P	-	2	0	HERC4	69419988	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.930000	0.92872	2.599000	0.87857	0.591000	0.81541	CCA	.	.	.	none		0.353	HERC4-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359262.1	NM_015601		A	69749982	G	A	69749982	3	1	14	1	0	0	0	0	1	0	0	0	7067	1348	47	2	1606	2	HERC4	10	69749982	Missense_Mutation	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10		69749982	65784765	39	982											
PPA1	5464	hgsc.bcm.edu	37	chr10	71974287	71974287	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcacacacatcaattgggTcattgtcaccacaacagcca	13	10	5	13	0	4	0	4	0	0	0	4	0	4	0	2	1	2	0	2	1	2	3			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr10:71974287T>C	ENST00000373232.3	-	5	452	c.353A>G	c.(352-354)gAc>gGc	p.D118G	PPA1_ENST00000608321.1_Missense_Mutation_p.D118G	NM_021129.3	NP_066952.1	Q15181	IPYR_HUMAN	pyrophosphatase (inorganic) 1	118					diphosphate metabolic process (GO:0071344)|gene expression (GO:0010467)|phosphate-containing compound metabolic process (GO:0006796)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)			breast(2)|endometrium(1)|large_intestine(2)|lung(3)|skin(2)	10						ATCAATTGGGTCATTGTCACC	0.333																																					p.D118G		Atlas-SNP	.											.	PPA1	24	.	0			c.A353G						PASS	.						115	105	108					10																	71974287		2203	4300	6503	SO:0001583	missense	5464	exon5			ATTGGGTCATTGT	AF154065	CCDS7299.1	10q11.1-q24	2012-10-02	2005-10-07	2005-10-07	ENSG00000180817	ENSG00000180817	3.6.1.1		9226	protein-coding gene	gene with protein product	"cytosolic inorganic pyrophosphatase", "inorganic pyrophosphatase 1", "pyrophosphate phospho-hydrolase"	179030	"pyrophosphatase (inorganic)"	PP		10542310, 975879	Standard	NM_021129		Approved	SID6-8061, Ppase, IOPPP, PP1	uc001jqv.1	Q15181	OTTHUMG00000018399	ENST00000373232.3:c.353A>G	chr10.hg19:g.71974287T>C	ENSP00000362329:p.Asp118Gly	65.0	0.0	.		46.0	11.0	.	NM_021129	Q2M348|Q5SQT7|Q6P7P4|Q9UQJ5|Q9Y5B1	Missense_Mutation	SNP	ENST00000373232.3	hg19	CCDS7299.1	.	.	.	.	.	.	.	.	.	.	T	27.8	4.859975	0.91433	.	.	ENSG00000180817	ENST00000373232;ENST00000373230	T;T	0.71103	-0.54;-0.54	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	D	0.88514	0.6457	H	0.96460	3.825	0.80722	D	1	P	0.44776	0.843	P	0.61940	0.896	D	0.91533	0.5244	10	0.87932	D	0	-2.9842	14.5337	0.67944	0.0:0.0:0.0:1.0	.	118	Q15181	IPYR_HUMAN	G	118	ENSP00000362329:D118G;ENSP00000362327:D118G	ENSP00000362327:D118G	D	-	2	0	PPA1	71644293	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.819000	0.86621	2.113000	0.64589	0.482000	0.46254	GAC	.	.	.	none		0.333	PPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048490.2	NM_021129		C	71974287	T	C	71974287	3	2	14	1	0	0	0	0	1	0	0	0	12293	1667	58	3	544	3	PPA1	10	71974287	Missense_Mutation	SNP	T	TCGA-2Z-A9JK-01A-11D-A42J-10	2224305	71974287	63560460	40	983											
CDH23	64072	hgsc.bcm.edu	37	chr10	73572275	73572275	+	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	ggatcccttctgtcggaaccTggagctggccgcccaggcgg	5	7	15	14	3	1	0	0	0	1	0	3	3	2	3	4	6	2	1	4	6	1	1	rs371829335		TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr10:73572275T>A	ENST00000224721.6	+	66	9439	c.9434T>A	c.(9433-9435)cTg>cAg	p.L3145Q	CDH23_ENST00000398788.3_Missense_Mutation_p.L900Q|CDH23_ENST00000475158.1_3'UTR	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	3140					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						TGTCGGAACCTGGAGCTGGCC	0.637											OREG0020259	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L3140Q		Atlas-SNP	.											.	CDH23	365	.	0			c.T9419A						PASS	.	T	GLN/LEU,GLN/LEU,GLN/LEU,GLN/LEU,GLN/LEU	0,3978		0,0,1989	70	77	74		2699,2699,110,110,9419	5.5	1	10		74	1,8311		0,1,4155	no	missense,missense,missense,missense,missense	CDH23	NM_001171933.1,NM_001171934.1,NM_001171935.1,NM_001171936.1,NM_022124.5	113,113,113,113,113	0,1,6144	AA,AT,TT		0.012,0.0,0.0081	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	900/1115,900/1080,37/252,37/217,3140/3355	73572275	1,12289	1989	4156	6145	SO:0001583	missense	64072	exon65			GGAACCTGGAGCT	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.9434T>A	chr10.hg19:g.73572275T>A	ENSP00000224721:p.Leu3145Gln	101.0	0.0	.	1146	57.0	20.0	.	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	hg19		.	.	.	.	.	.	.	.	.	.	T	23.5	4.428786	0.83667	0.0	1.2E-4	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721;ENST00000398788	D	0.82893	-1.66	5.54	5.54	0.83059	.	0.093214	0.45867	D	0.000338	D	0.86916	0.6048	L	0.36672	1.1	0.54753	D	0.999982	D;D;P;P	0.71674	0.996;0.998;0.938;0.938	P;D;P;P	0.71184	0.859;0.972;0.523;0.523	D	0.88372	0.2995	10	0.87932	D	0	.	15.8465	0.78895	0.0:0.0:0.0:1.0	.	37;37;3140;3140	Q5QGS5;Q5QGS6;E9PEX1;Q9H251	.;.;.;CAD23_HUMAN	Q	3145;3140;3143;900	ENSP00000381768:L900Q	ENSP00000224721:L3145Q	L	+	2	0	CDH23	73242281	1.000000	0.71417	1.000000	0.80357	0.628000	0.37860	7.836000	0.86788	2.326000	0.78906	0.533000	0.62120	CTG	.	.	.	none		0.637	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		A	73572275	T	A	73572275	3	1	14	1	0	0	0	0	1	0	0	0	3110	1580	55	5	10101	5	CDH23	10	73572275	Missense_Mutation	SNP	T	TCGA-2Z-A9JK-01A-11D-A42J-10	1597988	73572275	61962472	41	984											
TNKS2	80351	hgsc.bcm.edu	37	chr10	93588096	93588096	+	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	acgagaagctgatgttactcGaatcaaaaaacatctctctc	15	10	6	10	2	3	2	1	1	2	1	6	4	3	2	0	0	3	2	0	0	6	1			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr10:93588096G>A	ENST00000371627.4	+	9	1416	c.1037G>A	c.(1036-1038)cGa>cAa	p.R346Q		NM_025235.3	NP_079511.1	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2	346					multicellular organism growth (GO:0035264)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein polyubiquitination (GO:0000209)|regulation of multicellular organism growth (GO:0040014)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.R346Q(1)		biliary_tract(1)|breast(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	48		Colorectal(252;0.162)				GATGTTACTCGAATCAAAAAA	0.343																																					p.R346Q		Atlas-SNP	.											TNKS2,rectum,carcinoma,0,1	TNKS2	103	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1037A						PASS	.						66	66	66					10																	93588096		2203	4300	6503	SO:0001583	missense	80351	exon9			TTACTCGAATCAA	AF342982	CCDS7417.1	10q23.3	2013-01-10			ENSG00000107854	ENSG00000107854		"Poly (ADP-ribose) polymerases", "Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15677	protein-coding gene	gene with protein product		607128					Standard	NM_025235		Approved	TNKL, TANK2, PARP-5b, PARP-5c, PARP5B, PARP5C, pART6	uc001khp.3	Q9H2K2	OTTHUMG00000018747	ENST00000371627.4:c.1037G>A	chr10.hg19:g.93588096G>A	ENSP00000360689:p.Arg346Gln	132.0	2.0	.		213.0	53.0	.	NM_025235	B2RBD3|Q9H8F2|Q9HAS4	Missense_Mutation	SNP	ENST00000371627.4	hg19	CCDS7417.1	.	.	.	.	.	.	.	.	.	.	G	19.60	3.857368	0.71834	.	.	ENSG00000107854	ENST00000371627	T	0.63913	-0.07	5.5	5.5	0.81552	Ankyrin repeat-containing domain (4);	0.000000	0.50627	D	0.000107	T	0.50411	0.1614	N	0.25245	0.725	0.46096	D	0.998866	B	0.25351	0.124	B	0.23150	0.044	T	0.41574	-0.9501	10	0.22109	T	0.4	.	19.4011	0.94630	0.0:0.0:1.0:0.0	.	346	Q9H2K2	TNKS2_HUMAN	Q	346	ENSP00000360689:R346Q	ENSP00000360689:R346Q	R	+	2	0	TNKS2	93578076	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.480000	0.66820	2.591000	0.87537	0.462000	0.41574	CGA	.	.	.	none		0.343	TNKS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049374.1	NM_025235		A	93588096	G	A	93588096	3	1	14	1	0	0	0	0	1	0	0	0	16333	1058	37	1	1071	1	TNKS2	10	93588096	Missense_Mutation	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10	20015821	93588096	41946651	42	985											
LCOR	84458	hgsc.bcm.edu	37	chr10	98715299	98715299	+	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	gaaaaagcatgttagatgctGgacccgattcttggggctca	11	10	12	8	1	2	1	1	0	1	1	2	4	2	2	1	3	2	4	1	3	3	3			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr10:98715299G>C	ENST00000371097.4	+	8	1468	c.922G>C	c.(922-924)Gga>Cga	p.G308R	LCOR_ENST00000540664.1_Missense_Mutation_p.G308R|LCOR_ENST00000356016.3_Missense_Mutation_p.G308R|LCOR_ENST00000498444.1_Intron|LCOR_ENST00000371103.3_Missense_Mutation_p.G308R			Q96JN0	LCOR_HUMAN	ligand dependent nuclear receptor corepressor	308					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(1)|large_intestine(3)|lung(1)|ovary(3)|prostate(1)|urinary_tract(1)	13		Colorectal(252;0.162)		Epithelial(162;4.43e-09)|all cancers(201;2.96e-07)		GTTAGATGCTGGACCCGATTC	0.478																																					p.G308R		Atlas-SNP	.											.	LCOR	32	.	0			c.G922C						PASS	.						44	46	45					10																	98715299		2203	4300	6503	SO:0001583	missense	84458	exon8			GATGCTGGACCCG		CCDS7451.1, CCDS53561.1	10q24	2006-06-28			ENSG00000196233	ENSG00000196233			29503	protein-coding gene	gene with protein product		607698				12535528, 15193453	Standard	NM_001170765		Approved	MLR2, FLJ38026, KIAA1795		Q96JN0	OTTHUMG00000018841	ENST00000371097.4:c.922G>C	chr10.hg19:g.98715299G>C	ENSP00000360138:p.Gly308Arg	116.0	0.0	.		142.0	33.0	.	NM_001170766	D3DR47|Q5VW16|Q7Z723|Q86T32|Q86T33|Q8N3L6	Missense_Mutation	SNP	ENST00000371097.4	hg19	CCDS7451.1	.	.	.	.	.	.	.	.	.	.	G	13.53	2.265945	0.40095	.	.	ENSG00000196233	ENST00000540664;ENST00000371103;ENST00000371097;ENST00000356016	.	.	.	5.65	5.65	0.86999	.	0.275445	0.42548	D	0.000696	T	0.35480	0.0933	N	0.14661	0.345	0.37180	D	0.903461	B;B	0.29037	0.148;0.231	B;B	0.23716	0.022;0.048	T	0.39035	-0.9633	9	0.48119	T	0.1	-3.1435	13.3313	0.60488	0.0722:0.0:0.9278:0.0	.	308;308	Q96JN0;Q96JN0-2	LCOR_HUMAN;.	R	308	.	ENSP00000348298:G308R	G	+	1	0	LCOR	98705289	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.971000	0.63749	2.827000	0.97445	0.650000	0.86243	GGA	.	.	.	none		0.478	LCOR-009	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049628.2			C	98715299	G	C	98715299	3	2	14	1	0	0	0	0	1	0	0	0	8696	1349	47	4	932	4	LCOR	10	98715299	Missense_Mutation	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10	5127203	98715299	36819448	43	986											
TRIM8	81603	hgsc.bcm.edu	37	chr10	104404444	104404444	+	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	tctgcctgcacgttttcgtgGagccagtgcagctgccgtgc	4	11	13	13	3	1	0	0	0	1	0	2	1	1	1	3	1	7	4	3	1	0	2			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr10:104404444G>A	ENST00000302424.7	+	1	192	c.70G>A	c.(70-72)Gag>Aag	p.E24K	RP11-47A8.5_ENST00000607967.1_lincRNA	NM_030912.2	NP_112174.2	Q9BZR9	TRIM8_HUMAN	tripartite motif containing 8	24					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|PML body (GO:0016605)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		CGTTTTCGTGGAGCCAGTGCA	0.662																																					p.E24K		Atlas-SNP	.											.	TRIM8	35	.	0			c.G70A						PASS	.						33	37	36					10																	104404444		2202	4299	6501	SO:0001583	missense	81603	exon1			TTCGTGGAGCCAG	AF281046	CCDS31274.1	10q24.3	2013-01-09	2011-01-25	2002-06-14	ENSG00000171206	ENSG00000171206		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	15579	protein-coding gene	gene with protein product	"glioblastoma expressed ring finger protein"	606125	"ring finger protein 27", "tripartite motif-containing 8"	RNF27		11118312, 12163497	Standard	NM_030912		Approved	GERP	uc001kvz.2	Q9BZR9	OTTHUMG00000018964	ENST00000302424.7:c.70G>A	chr10.hg19:g.104404444G>A	ENSP00000302120:p.Glu24Lys	231.0	0.0	.		153.0	33.0	.	NM_030912	A6NI31|Q9C028	Missense_Mutation	SNP	ENST00000302424.7	hg19	CCDS31274.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.941410	0.92526	.	.	ENSG00000171206	ENST00000302424;ENST00000369896	T	0.19105	2.17	4.06	4.06	0.47325	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.057637	0.64402	D	0.000002	T	0.32436	0.0829	L	0.35644	1.08	0.58432	D	0.999999	D	0.56968	0.978	P	0.57911	0.829	T	0.13602	-1.0503	10	0.72032	D	0.01	.	16.81	0.85717	0.0:0.0:1.0:0.0	.	24	Q9BZR9	TRIM8_HUMAN	K	24	ENSP00000302120:E24K	ENSP00000302120:E24K	E	+	1	0	TRIM8	104394434	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.463000	0.80869	2.277000	0.76020	0.561000	0.74099	GAG	.	.	.	none		0.662	TRIM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050084.3	NM_030912		A	104404444	G	A	104404444	3	1	14	1	0	0	0	0	1	0	0	0	16560	1175	41	2	72	2	TRIM8	10	104404444	Missense_Mutation	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10	5689145	104404444	31130303	44	987											
OR51E2	81285	hgsc.bcm.edu	37	chr11	4703309	4703309	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaataggacaaggagatgaaCattacgtccacgcccatgac	16	6	9	10	2	0	3	0	2	0	1	1	5	1	4	2	2	2	0	2	2	5	2			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr11:4703309C>T	ENST00000396950.3	-	2	872	c.633G>A	c.(631-633)atG>atA	p.M211I		NM_030774.3	NP_110401.1	Q9H255	O51E2_HUMAN	olfactory receptor, family 51, subfamily E, member 2	211					cellular response to fatty acid (GO:0071398)|detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|positive regulation of blood pressure (GO:0045777)|positive regulation of renin secretion into blood stream (GO:1900135)|steroid hormone mediated signaling pathway (GO:0043401)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|signaling receptor activity (GO:0038023)|steroid hormone receptor activity (GO:0003707)			NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(3)	23		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;3e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00476)|LUSC - Lung squamous cell carcinoma(625;0.2)		AGGAGATGAACATTACGTCCA	0.488																																					p.M211I		Atlas-SNP	.											.	OR51E2	77	.	0			c.G633A						PASS	.						100	89	93					11																	4703309		2201	4298	6499	SO:0001583	missense	81285	exon2			GATGAACATTACG	AY033942	CCDS7751.1	11p15	2012-08-09			ENSG00000167332	ENSG00000167332		"GPCR / Class A : Olfactory receptors"	15195	protein-coding gene	gene with protein product		611268				11118034	Standard	NM_030774		Approved	PSGR	uc001lzk.2	Q9H255	OTTHUMG00000133362	ENST00000396950.3:c.633G>A	chr11.hg19:g.4703309C>T	ENSP00000380153:p.Met211Ile	140.0	0.0	.		88.0	18.0	.	NM_030774	B2RA63|Q6IF94	Missense_Mutation	SNP	ENST00000396950.3	hg19	CCDS7751.1	.	.	.	.	.	.	.	.	.	.	C	3.080	-0.189220	0.06299	.	.	ENSG00000167332	ENST00000396950	T	0.32988	1.43	5.07	2.07	0.26955	GPCR, rhodopsin-like superfamily (1);	0.278770	0.25645	N	0.029258	T	0.08179	0.0204	N	0.02225	-0.63	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.29274	-1.0017	10	0.07030	T	0.85	.	2.2245	0.03980	0.1478:0.4044:0.2869:0.1609	.	211	Q9H255	O51E2_HUMAN	I	211	ENSP00000380153:M211I	ENSP00000380153:M211I	M	-	3	0	OR51E2	4659885	0.000000	0.05858	0.538000	0.28064	0.770000	0.43624	-1.295000	0.02764	0.273000	0.22049	0.655000	0.94253	ATG	.	.	.	none		0.488	OR51E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257198.1	NM_030774		T	4703309	C	T	4703309	3	4	14	1	0	0	0	0	1	0	0	0	11102	478	17	2	333	2	OR51E2	11	4703309	Missense_Mutation	SNP	C	TCGA-2Z-A9JK-01A-11D-A42J-10		4703309	130303207	45	988											
TUT1	64852	hgsc.bcm.edu	37	chr11	62346467	62346467	+	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	agtggggaagccagggccgaGtccagcgatggagattctgg	9	6	18	8	2	1	1	0	0	1	1	2	5	2	2	3	5	2	0	3	5	1	1			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr11:62346467G>T	ENST00000476907.1	-	5	1417	c.726C>A	c.(724-726)gaC>gaA	p.D242E	TUT1_ENST00000308436.7_Missense_Mutation_p.D280E|MIR3654_ENST00000496634.2_Missense_Mutation_p.D242E			Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6 snRNA-specific	242	Pro-rich.				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						CCAGGGCCGAGTCCAGCGATG	0.562																																					p.D280E		Atlas-SNP	.											.	TUT1	122	.	0			c.C840A						PASS	.						32	38	36					11																	62346467		2202	4299	6501	SO:0001583	missense	64852	exon5			GGCCGAGTCCAGC	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.726C>A	chr11.hg19:g.62346467G>T	ENSP00000419607:p.Asp242Glu	135.0	0.0	.		108.0	23.0	.	NM_022830	A1A527|A8K995|Q2NL65|Q7L583|Q9H6H7	Missense_Mutation	SNP	ENST00000476907.1	hg19		.	.	.	.	.	.	.	.	.	.	G	18.86	3.712700	0.68730	.	.	ENSG00000149016	ENST00000308436;ENST00000476907;ENST00000278279	T;T	0.40225	1.04;1.08	5.44	1.53	0.23141	.	0.150712	0.44097	D	0.000493	T	0.48169	0.1485	L	0.44542	1.39	0.21064	N	0.999795	D	0.76494	0.999	D	0.80764	0.994	T	0.27157	-1.0082	10	0.33940	T	0.23	-19.8764	6.6964	0.23201	0.3737:0.0:0.6263:0.0	.	280	F5H0R1	.	E	280;242;103	ENSP00000308000:D280E;ENSP00000419607:D242E	ENSP00000441670:D242E	D	-	3	2	TUT1	62103043	1.000000	0.71417	0.999000	0.59377	0.766000	0.43426	0.664000	0.25068	0.289000	0.22422	0.563000	0.77884	GAC	.	.	.	none		0.562	TUT1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000351319.2	NM_022830		T	62346467	G	T	62346467	3	4	14	1	0	0	0	0	1	0	0	0	16792	1020	36	4	1918	4	TUT1	11	62346467	Missense_Mutation	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10	57643158	62346467	72660049	46	989											
CTSF	8722	hgsc.bcm.edu	37	chr11	66332038	66332038	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcggaactcacggttgccgtAgcccacaagcaacaccgcat	11	5	10	15	4	1	0	1	0	0	0	1	1	1	1	3	2	5	4	3	2	4	2			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr11:66332038A>G	ENST00000310325.5	-	11	1421	c.1312T>C	c.(1312-1314)Tac>Cac	p.Y438H	ACTN3_ENST00000502692.1_RNA|CTSF_ENST00000533168.1_5'Flank|ACTN3_ENST00000513398.1_RNA	NM_003793.3	NP_003784.2	Q9UBX1	CATF_HUMAN	cathepsin F	438					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|vesicle (GO:0031982)	cysteine-type endopeptidase activity (GO:0004197)			endometrium(1)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	19						CGGTTGCCGTAGCCCACAAGC	0.622																																					p.Y438H		Atlas-SNP	.											.	CTSF	42	.	0			c.T1312C						PASS	.						21	21	21					11																	66332038		2180	4276	6456	SO:0001583	missense	8722	exon11			TGCCGTAGCCCAC	AF071749	CCDS8144.1	11q13.2	2012-02-29			ENSG00000174080	ENSG00000174080		"Cathepsins"	2531	protein-coding gene	gene with protein product		603539				9822672, 10318784	Standard	NM_003793		Approved	CATSF, CLN13	uc001oip.3	Q9UBX1	OTTHUMG00000167090	ENST00000310325.5:c.1312T>C	chr11.hg19:g.66332038A>G	ENSP00000310832:p.Tyr438His	148.0	0.0	.		104.0	19.0	.	NM_003793	B2R964|O95240|Q9NSU4|Q9UKQ5	Missense_Mutation	SNP	ENST00000310325.5	hg19	CCDS8144.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.472758	0.84640	.	.	ENSG00000174080	ENST00000310325	T	0.37411	1.2	4.97	4.97	0.65823	Peptidase C1A, papain C-terminal (3);	0.131244	0.53938	D	0.000058	T	0.76709	0.4025	H	0.99726	4.73	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	D	0.86364	0.1719	10	0.87932	D	0	.	12.6418	0.56714	1.0:0.0:0.0:0.0	.	438	Q9UBX1	CATF_HUMAN	H	438	ENSP00000310832:Y438H	ENSP00000310832:Y438H	Y	-	1	0	CTSF	66088614	1.000000	0.71417	0.974000	0.42286	0.886000	0.51366	7.567000	0.82357	1.880000	0.54463	0.459000	0.35465	TAC	.	.	.	none		0.622	CTSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393047.1	NM_003793		G	66332038	A	G	66332038	3	3	14	1	0	0	0	0	1	0	0	0	4036	420	15	3	154	3	CTSF	11	66332038	Missense_Mutation	SNP	A	TCGA-2Z-A9JK-01A-11D-A42J-10	3985571	66332038	68674478	47	990											
ATM	472	hgsc.bcm.edu	37	chr11	108178695	108178695	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcttgctgttgtggactacAtgagaagacaaaagaggtaa	14	10	12	5	0	0	3	0	1	0	3	0	5	0	4	0	2	3	4	0	2	5	4			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr11:108178695A>G	ENST00000452508.2	+	39	5935	c.5746A>G	c.(5746-5748)Atg>Gtg	p.M1916V	ATM_ENST00000278616.4_Missense_Mutation_p.M1916V			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1916			M -> I (in a breast pleomorphic lobular carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			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)	TGTGGACTACATGAGAAGACA	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)																											p.M1916V		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	ATM_ENST00000278616,colon,carcinoma,0,4	ATM	1657	.	0			c.A5746G						PASS	.						157	143	148					11																	108178695		2201	4298	6499	SO:0001583	missense	472	exon38	Familial Cancer Database	AT, Louis-Bar syndrome	GACTACATGAGAA	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.5746A>G	chr11.hg19:g.108178695A>G	ENSP00000388058:p.Met1916Val	70.0	0.0	.		57.0	4.0	.	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	hg19	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	A	13.57	2.275921	0.40294	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.74209	-0.82;-0.82	6.03	2.2	0.27929	Armadillo-type fold (1);	0.154649	0.64402	N	0.000014	T	0.61350	0.2340	L	0.44542	1.39	0.23492	N	0.997568	B	0.16166	0.016	B	0.08055	0.003	T	0.53954	-0.8365	10	0.54805	T	0.06	.	5.5933	0.17313	0.4052:0.2709:0.0:0.3239	.	1916	Q13315	ATM_HUMAN	V	1916	ENSP00000278616:M1916V;ENSP00000388058:M1916V	ENSP00000278616:M1916V	M	+	1	0	ATM	107683905	0.535000	0.26370	0.999000	0.59377	0.996000	0.88848	-0.063000	0.11655	0.490000	0.27771	0.533000	0.62120	ATG	.	.	.	none		0.358	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		G	108178695	A	G	108178695	3	3	14	1	0	0	0	0	1	0	0	0	1109	217	8	3	5892	3	ATM	11	108178695	Missense_Mutation	SNP	A	TCGA-2Z-A9JK-01A-11D-A42J-10	41846657	108178695	26827821	48	991											
ALG9	79796	hgsc.bcm.edu	37	chr11	111707006	111707006	+	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	tgaactctgatggaatgaacTgaagctgccaactgtcagaa	14	9	10	8	0	2	5	1	4	1	1	2	6	2	6	1	1	5	1	1	1	6	0			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr11:111707006T>A	ENST00000531154.1	-	13	1443	c.971A>T	c.(970-972)cAg>cTg	p.Q324L	ALG9_ENST00000524880.1_3'UTR|ALG9_ENST00000398006.2_Missense_Mutation_p.Q317L|ALG9_ENST00000527228.1_5'UTR	NM_024740.2	NP_079016.2	Q9H6U8	ALG9_HUMAN	ALG9, alpha-1,2-mannosyltransferase	488					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)		TGGAATGAACTGAAGCTGCCA	0.418																																					p.Q495L		Atlas-SNP	.											.	ALG9	77	.	0			c.A1484T						PASS	.						71	67	68					11																	111707006		1858	4094	5952	SO:0001583	missense	79796	exon14			ATGAACTGAAGCT		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.971A>T	chr11.hg19:g.111707006T>A	ENSP00000435517:p.Gln324Leu	70.0	0.0	.		51.0	10.0	.	NM_024740	Q6ZMD5|Q7Z4R4|Q96GS7|Q96PB9|Q9H068	Missense_Mutation	SNP	ENST00000531154.1	hg19	CCDS41714.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.88|19.88	3.908962|3.908962	0.72868|0.72868	.|.	.|.	ENSG00000086848|ENSG00000086848	ENST00000531154;ENST00000398006;ENST00000428306|ENST00000532425	T;T|.	0.73575|.	-0.76;-0.76|.	5.2|5.2	5.2|5.2	0.72013|0.72013	.|.	0.049825|.	0.85682|.	D|.	0.000000|.	T|T	0.71221|0.71221	0.3314|0.3314	M|M	0.62723|0.62723	1.935|1.935	0.80722|0.80722	D|D	1|1	B;B;B|.	0.21225|.	0.031;0.053;0.027|.	B;B;B|.	0.20384|.	0.01;0.029;0.017|.	T|T	0.70710|0.70710	-0.4797|-0.4797	10|5	0.54805|.	T|.	0.06|.	-14.0058|-14.0058	15.3545|15.3545	0.74418|0.74418	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	317;495;488|.	B4DQI3;Q9H6U8-3;Q9H6U8|.	.;.;ALG9_HUMAN|.	L|C	324;317;721|73	ENSP00000435517:Q324L;ENSP00000381090:Q317L|.	ENSP00000381090:Q317L|.	Q|S	-|-	2|1	0|0	ALG9|ALG9	111212216|111212216	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.974000|7.974000	0.88039|0.88039	2.090000|2.090000	0.63153|0.63153	0.460000|0.460000	0.39030|0.39030	CAG|AGT	.	.	.	none		0.418	ALG9-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000391485.1	NM_024740		A	111707006	T	A	111707006	3	1	14	1	0	0	0	0	1	0	0	0	524	1580	55	5	384	5	ALG9	11	111707006	Missense_Mutation	SNP	T	TCGA-2Z-A9JK-01A-11D-A42J-10	3528311	111707006	23299510	49	992											
CACNA1C	775	hgsc.bcm.edu	37	chr12	2602503	2602503	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttgccttcgccatgctcaCggtgttccagtgcatcacca	6	12	8	15	2	2	0	2	0	0	0	4	0	3	0	4	1	3	3	4	1	0	3	rs538694667		TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr12:2602503C>T	ENST00000347598.4	+	7	1064	c.1064C>T	c.(1063-1065)aCg>aTg	p.T355M	CACNA1C_ENST00000344100.3_Missense_Mutation_p.T355M|CACNA1C_ENST00000399637.1_Missense_Mutation_p.T355M|CACNA1C_ENST00000399601.1_Missense_Mutation_p.T355M|CACNA1C_ENST00000399655.1_Missense_Mutation_p.T355M|CACNA1C_ENST00000399591.1_Missense_Mutation_p.T355M|CACNA1C_ENST00000399595.1_Missense_Mutation_p.T355M|CACNA1C_ENST00000399641.1_Missense_Mutation_p.T355M|CACNA1C_ENST00000399644.1_Missense_Mutation_p.T355M|CACNA1C_ENST00000399617.1_Missense_Mutation_p.T355M|CACNA1C_ENST00000399629.1_Missense_Mutation_p.T355M|CACNA1C_ENST00000402845.3_Missense_Mutation_p.T355M|CACNA1C_ENST00000480911.1_Missense_Mutation_p.T355M|CACNA1C_ENST00000335762.5_Missense_Mutation_p.T355M|CACNA1C_ENST00000327702.7_Missense_Mutation_p.T355M|CACNA1C_ENST00000399597.1_Missense_Mutation_p.T355M|CACNA1C_ENST00000406454.3_Missense_Mutation_p.T355M|CACNA1C_ENST00000399638.1_Missense_Mutation_p.T355M|CACNA1C_ENST00000399634.1_Missense_Mutation_p.T355M|CACNA1C_ENST00000399603.1_Missense_Mutation_p.T355M|CACNA1C_ENST00000399649.1_Missense_Mutation_p.T355M|CACNA1C_ENST00000399621.1_Missense_Mutation_p.T355M|CACNA1C_ENST00000399606.1_Missense_Mutation_p.T355M	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	355					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)	GCCATGCTCACGGTGTTCCAG	0.622																																					p.T355M		Atlas-SNP	.											.	CACNA1C	1023	.	0			c.C1064T						PASS	.						202	194	197					12																	2602503		2203	4300	6503	SO:0001583	missense	775	exon7			TGCTCACGGTGTT	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.1064C>T	chr12.hg19:g.2602503C>T	ENSP00000266376:p.Thr355Met	137.0	0.0	.		96.0	21.0	.	NM_001129831	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	hg19	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.590362	0.86851	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000480911;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97455	-4.39;-4.39;-4.39;-4.39;-4.39;-4.39;-4.39;-4.39;-4.39;-4.39;-4.39;-4.39;-4.39;-4.39;-4.39;-4.39;-4.39;-4.39;-4.39;-4.39;-4.39;-4.39;-4.39	4.91	4.91	0.64330	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98874	0.9619	M	0.93854	3.465	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.999;0.998;1.0;0.999;0.999;0.997;0.999;1.0;1.0;0.999;0.997;1.0;0.999;0.999;1.0;0.997;1.0;0.999;1.0;0.997;0.999;0.999;0.997;0.997	D	0.99628	1.0985	10	0.87932	D	0	.	18.2978	0.90153	0.0:1.0:0.0:0.0	.	355;352;355;355;355;355;355;355;355;355;355;326;355;355;355;355;355;355;355;355;355;355;355;355	Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	M	355;355;355;355;355;355;355;355;355;355;355;355;355;355;355;355;355;355;355;355;355;355;355;196	ENSP00000336982:T355M;ENSP00000382563:T355M;ENSP00000437936:T355M;ENSP00000382552:T355M;ENSP00000382547:T355M;ENSP00000382506:T355M;ENSP00000382530:T355M;ENSP00000382546:T355M;ENSP00000382500:T355M;ENSP00000382549:T355M;ENSP00000266376:T355M;ENSP00000382515:T355M;ENSP00000382510:T355M;ENSP00000341092:T355M;ENSP00000382537:T355M;ENSP00000329877:T355M;ENSP00000382557:T355M;ENSP00000385724:T355M;ENSP00000382512:T355M;ENSP00000382542:T355M;ENSP00000382526:T355M;ENSP00000385896:T355M;ENSP00000382504:T355M	ENSP00000323129:T196M	T	+	2	0	CACNA1C	2472764	1.000000	0.71417	0.618000	0.29105	0.925000	0.55904	7.609000	0.82925	2.560000	0.86352	0.462000	0.41574	ACG	.	.	.	none		0.622	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		T	2602503	C	T	2602503	3	4	14	1	0	0	0	0	1	0	0	0	2542	536	19	1	1090	1	CACNA1C	12	2602503	Missense_Mutation	SNP	C	TCGA-2Z-A9JK-01A-11D-A42J-10		2602503	131249392	50	993											
TAS2R31	259290	hgsc.bcm.edu	37	chr12	11183487	11183487	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttgtccgtacaatctcttTcatgtttatcacaaaaagtt	11	18	4	8	1	3	0	2	0	1	0	5	0	4	0	1	0	1	3	1	0	5	7			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr12:11183487T>C	ENST00000390675.2	-	1	519	c.448A>G	c.(448-450)Aaa>Gaa	p.K150E	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176885.2	NP_795366.2	P59538	T2R31_HUMAN	taste receptor, type 2, member 31	150					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						ACAATCTCTTTCATGTTTATC	0.388																																					p.K150E		Atlas-SNP	.											.	TAS2R31	24	.	0			c.A448G						PASS	.						80	81	81					12																	11183487		2099	4256	6355	SO:0001583	missense	259290	exon1			TCTCTTTCATGTT	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.448A>G	chr12.hg19:g.11183487T>C	ENSP00000375093:p.Lys150Glu	174.0	0.0	.		173.0	37.0	.	NM_176885	P59547|Q17R84|Q645X5	Missense_Mutation	SNP	ENST00000390675.2	hg19	CCDS53747.1	.	.	.	.	.	.	.	.	.	.	.	5.887	0.347768	0.11126	.	.	ENSG00000256436	ENST00000390675	T	0.00705	5.81	2.45	-4.89	0.03103	.	.	.	.	.	T	0.00440	0.0014	N	0.11756	0.17	0.09310	N	1	B	0.10296	0.003	B	0.11329	0.006	T	0.45026	-0.9289	9	0.26408	T	0.33	.	0.8461	0.01161	0.1672:0.3487:0.1681:0.316	.	150	P59538	T2R31_HUMAN	E	150	ENSP00000375093:K150E	ENSP00000375093:K150E	K	-	1	0	TAS2R31	11074754	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-3.555000	0.00432	-1.724000	0.01373	0.163000	0.16589	AAA	.	.	.	none		0.388	TAS2R31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400233.1	NM_176885		C	11183487	T	C	11183487	3	2	14	1	0	0	0	0	1	0	0	0	15586	1792	62	3	485	3	TAS2R31	12	11183487	Missense_Mutation	SNP	T	TCGA-2Z-A9JK-01A-11D-A42J-10	8580984	11183487	122668408	51	994											
LRRK2	120892	hgsc.bcm.edu	37	chr12	40757356	40757356	+	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	agactgcgtgcactttttaaGgtaaattctgtggtttttaa	10	17	9	5	1	1	1	0	0	1	1	1	1	1	1	0	2	2	3	0	2	4	8			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr12:40757356G>T	ENST00000298910.7	+	48	7239	c.7181G>T	c.(7180-7182)aGg>aTg	p.R2394M		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	2394					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)				CACTTTTTAAGGTAAATTCTG	0.368																																					p.R2394M		Atlas-SNP	.											.	LRRK2	763	.	0			c.G7181T						PASS	.						87	90	89					12																	40757356		2203	4300	6503	SO:0001630	splice_region_variant	120892	exon48			TTTTAAGGTAAAT	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.7181+1G>T	chr12.hg19:g.40757356G>T		38.0	0.0	.		73.0	4.0	.	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	hg19	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	G	11.66	1.706286	0.30232	.	.	ENSG00000188906	ENST00000298910	T	0.73047	-0.71	5.28	4.14	0.48551	WD40 repeat-like-containing domain (1);	0.140743	0.64402	D	0.000006	T	0.54062	0.1835	N	0.14661	0.345	0.80722	D	1	P;P	0.45348	0.856;0.856	B;B	0.41946	0.371;0.371	T	0.58482	-0.7629	10	0.87932	D	0	.	10.141	0.42736	0.9181:0.0:0.0819:0.0	.	2394;2394	Q17RV3;Q5S007	.;LRRK2_HUMAN	M	2394	ENSP00000298910:R2394M	ENSP00000298910:R2394M	R	+	2	0	LRRK2	39043623	1.000000	0.71417	1.000000	0.80357	0.018000	0.09664	4.153000	0.58118	0.853000	0.35312	-0.373000	0.07131	AGG	.	.	.	none		0.368	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513	Missense_Mutation	T	40757356	G	T	40757356	5	4	14	1	0	0	0	0	0	0	1	0	9040	1014	35	4	7371	4	LRRK2	12	40757356	Splice_Site	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10	29573869	40757356	93094539	52	995											
ADCY6	112	hgsc.bcm.edu	37	chr12	49171000	49171000	+	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	tcccccaagatcttgatcctCaggcagtgattctcctgaat	9	12	7	13	0	3	4	1	3	2	1	6	4	5	4	4	1	0	1	4	1	2	2			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr12:49171000C>T	ENST00000307885.4	-	5	1957	c.1263G>A	c.(1261-1263)ctG>ctA	p.L421L	ADCY6_ENST00000550422.1_Silent_p.L421L|ADCY6_ENST00000552090.1_5'Flank|ADCY6_ENST00000357869.3_Silent_p.L421L	NM_015270.3	NP_056085.1	O43306	ADCY6_HUMAN	adenylate cyclase 6	421					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						TCTTGATCCTCAGGCAGTGAT	0.582																																					p.L421L		Atlas-SNP	.											.	ADCY6	81	.	0			c.G1263A						PASS	.						102	103	103					12																	49171000		2203	4300	6503	SO:0001819	synonymous_variant	112	exon6			GATCCTCAGGCAG		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.1263G>A	chr12.hg19:g.49171000C>T		68.0	0.0	.		37.0	6.0	.	NM_020983	Q9NR75|Q9UDB0	Silent	SNP	ENST00000307885.4	hg19	CCDS8767.1																																																																																			.	.	.	none		0.582	ADCY6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408863.1	NM_020983		T	49171000	C	T	49171000	2	4	14	1	0	0	0	0	0	0	0	1	298	813	29	2		2	ADCY6	12	49171000	Silent	SNP	C	TCGA-2Z-A9JK-01A-11D-A42J-10	8413644	49171000	84680895	53	996											
XPOT	11260	hgsc.bcm.edu	37	chr12	64825465	64825465	+	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	agtggagtccgtactttcctTcatcgaatgattatttgcct	8	16	8	9	2	1	1	1	1	0	0	4	3	3	2	3	1	2	1	3	1	3	5			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr12:64825465T>A	ENST00000332707.5	+	18	2653	c.2124T>A	c.(2122-2124)ctT>ctA	p.L708L		NM_007235.4	NP_009166.2	O43592	XPOT_HUMAN	exportin, tRNA	708	Necessary for tRNA-binding, cytoplasmic localization and nuclear export.				intracellular protein transport (GO:0006886)|tRNA export from nucleus (GO:0006409)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(7)|lung(12)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				GBM - Glioblastoma multiforme(28;0.0404)		GTACTTTCCTTCATCGAATGA	0.428																																					p.L708L		Atlas-SNP	.											.	XPOT	105	.	0			c.T2124A						PASS	.						96	85	88					12																	64825465		2203	4300	6503	SO:0001819	synonymous_variant	11260	exon18			TTTCCTTCATCGA	AF039022	CCDS31852.1	12q14.1	2012-10-17	2012-10-17		ENSG00000184575	ENSG00000184575		"Exportins"	12826	protein-coding gene	gene with protein product		603180	"exportin, tRNA (nuclear export receptor for tRNAs)"			9660920, 9512417	Standard	NM_007235		Approved	XPO3	uc001ssb.3	O43592	OTTHUMG00000168794	ENST00000332707.5:c.2124T>A	chr12.hg19:g.64825465T>A		90.0	0.0	.		108.0	27.0	.	NM_007235	A6NLH1|O43784|Q8WUG2|Q9BVS7	Silent	SNP	ENST00000332707.5	hg19	CCDS31852.1																																																																																			.	.	.	none		0.428	XPOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401122.1	NM_007235		A	64825465	T	A	64825465	2	1	14	1	0	0	0	0	0	0	0	1	17462	1770	62	5		5	XPOT	12	64825465	Silent	SNP	T	TCGA-2Z-A9JK-01A-11D-A42J-10	15654465	64825465	69026430	54	997											
CPSF6	11052	hgsc.bcm.edu	37	chr12	69656194	69656194	+	Frame_Shift_Del	DEL	A	A	-																															ggaccatagtagatcacgagAaaagagtcgacgtcataaat																										TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr12:69656194delA	ENST00000435070.2	+	9	1621	c.1511delA	c.(1510-1512)gaafs	p.E504fs	CPSF6_ENST00000456847.3_Frame_Shift_Del_p.E431fs|CPSF6_ENST00000551516.1_Intron|CPSF6_ENST00000266679.8_Frame_Shift_Del_p.E541fs	NM_007007.2	NP_008938.2	Q16630	CPSF6_HUMAN	cleavage and polyadenylation specific factor 6, 68kDa	504	Arg-rich.				mRNA polyadenylation (GO:0006378)|mRNA processing (GO:0006397)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|mRNA cleavage factor complex (GO:0005849)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(7)|lung(8)	16	all_epithelial(5;2.47e-36)|Lung NSC(4;1.1e-32)|all_lung(4;6.26e-31)|Breast(13;1.59e-06)|Esophageal squamous(21;0.187)		Epithelial(6;4.89e-17)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;6.04e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.171)|Kidney(9;0.241)			AGATCACGAGAAAAGAGTCGA	0.428																																					p.E504fs		Atlas-Indel,Pindel	.											.	CPSF6	96	.	0			c.1510delG						PASS	.						139	121	127					12																	69656194		2203	4300	6503	SO:0001589	frameshift_variant	11052	exon9			.	X67336	CCDS8988.1, CCDS73494.1	12q15	2013-06-18	2002-08-29			ENSG00000111605		"RNA binding motif (RRM) containing"	13871	protein-coding gene	gene with protein product	"cleavage factor Im complex 68 kDa subunit"	604979	"cleavage and polyadenylation specific factor 6, 68kD subunit"			9659921, 17267687	Standard	NM_007007		Approved	CFIM, HPBRII-4, HPBRII-7, CFIM68	uc001sut.4	Q16630		ENST00000435070.2:c.1511delA	chr12.hg19:g.69656194delA	ENSP00000391774:p.Glu504fs	145.0	0.0	0		103.0	35.0	0.339806	NM_007007	A8K7K9|Q53ES1|Q9BSJ7|Q9BW18	Frame_Shift_Del	DEL	ENST00000435070.2	hg19	CCDS8988.1																																																																																			.	.	.	none		0.428	CPSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403609.1	NM_007007		-	69656194	A	-	69656194	7	5	14	1	0	1	0	1	0	0	0	0	3831	246	9	0	1545	0	CPSF6	12	69656194	Frame_Shift_Del	DEL	A	TCGA-2Z-A9JK-01A-11D-A42J-10	4830729	69656194	64195701	55	998											
TPH2	121278	hgsc.bcm.edu	37	chr12	72335374	72335374	+	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	attcctgaagctaaataaacCtaactctggcaaaaatgacg	17	9	6	9	1	1	2	0	2	1	0	2	2	2	2	2	1	3	2	2	1	8	4			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr12:72335374C>G	ENST00000333850.3	+	2	257	c.116C>G	c.(115-117)cCt>cGt	p.P39R	TPH2_ENST00000546576.1_3'UTR	NM_173353.3	NP_775489.2	Q8IWU9	TPH2_HUMAN	tryptophan hydroxylase 2	39					aromatic amino acid family metabolic process (GO:0009072)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to lithium ion (GO:0071285)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|response to activity (GO:0014823)|response to calcium ion (GO:0051592)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to nutrient levels (GO:0031667)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|neuron projection (GO:0043005)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|tryptophan 5-monooxygenase activity (GO:0004510)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	41					L-Tryptophan(DB00150)	CTAAATAAACCTAACTCTGGC	0.388																																					p.P39R		Atlas-SNP	.											.	TPH2	81	.	0			c.C116G						PASS	.						67	62	64					12																	72335374		2203	4300	6503	SO:0001583	missense	121278	exon2			ATAAACCTAACTC	AY098914	CCDS31859.1	12q15	2008-02-07				ENSG00000139287	1.14.16.4		20692	protein-coding gene	gene with protein product		607478				12511643	Standard	NM_173353		Approved	NTPH, FLJ37295	uc009zrw.1	Q8IWU9		ENST00000333850.3:c.116C>G	chr12.hg19:g.72335374C>G	ENSP00000329093:p.Pro39Arg	43.0	0.0	.		62.0	16.0	.	NM_173353	A6NGA4|Q14CB0	Missense_Mutation	SNP	ENST00000333850.3	hg19	CCDS31859.1	.	.	.	.	.	.	.	.	.	.	C	14.25	2.480817	0.44044	.	.	ENSG00000139287	ENST00000333850;ENST00000266669	D	0.99422	-5.88	5.91	5.01	0.66863	.	0.525534	0.21326	N	0.076363	D	0.96626	0.8899	N	0.08118	0	0.24376	N	0.994812	B	0.02656	0.0	B	0.01281	0.0	D	0.92945	0.6375	10	0.44086	T	0.13	-2.874	10.3721	0.44060	0.0:0.7946:0.1359:0.0695	.	39	Q8IWU9	TPH2_HUMAN	R	39	ENSP00000329093:P39R	ENSP00000266669:P39R	P	+	2	0	TPH2	70621641	0.321000	0.24625	1.000000	0.80357	0.956000	0.61745	1.432000	0.34936	1.475000	0.48197	0.650000	0.86243	CCT	.	.	.	none		0.388	TPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405234.1	NM_173353		G	72335374	C	G	72335374	3	3	14	1	0	0	0	0	1	0	0	0	16414	681	24	4	122	4	TPH2	12	72335374	Missense_Mutation	SNP	C	TCGA-2Z-A9JK-01A-11D-A42J-10	2679180	72335374	61516521	56	999											
IPO4	79711	hgsc.bcm.edu	37	chr14	24651547	24651547	+	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	gcaaaggagtctcccccagcCgcggctgccagggcagggat	8	4	15	14	2	1	0	0	0	1	0	2	2	1	2	4	4	2	3	4	4	1	0	rs374946858		TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr14:24651547C>A	ENST00000354464.6	-	25	2711	c.2535G>T	c.(2533-2535)gcG>gcT	p.A845A	RP11-468E2.2_ENST00000561419.1_3'UTR	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4	845					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)		CTCCCCCAGCCGCGGCTGCCA	0.617																																					p.A845A		Atlas-SNP	.											.	IPO4	74	.	0			c.G2535T						PASS	.						24	30	28					14																	24651547		2100	4212	6312	SO:0001819	synonymous_variant	79711	exon25			CCCAGCCGCGGCT	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.2535G>T	chr14.hg19:g.24651547C>A		229.0	0.0	.		135.0	35.0	.	NM_024658	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Silent	SNP	ENST00000354464.6	hg19	CCDS9616.1																																																																																			.	.	.	alt		0.617	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658		A	24651547	C	A	24651547	2	1	14	1	0	0	0	0	0	0	0	1	7802	639	23	4		4	IPO4	14	24651547	Silent	SNP	C	TCGA-2Z-A9JK-01A-11D-A42J-10		24651547	82697993	57	1000											
KIAA0831	22863	hgsc.bcm.edu	37	chr14	55836392	55836395	+	Frame_Shift_Del	DEL	GAGA	GAGA	-																															tcaccgaggctgctgcagagGagatcatcccacctgcactg																										TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	GAGA	GAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr14:55836392_55836395delGAGA	ENST00000247178.5	-	10	1456_1459	c.1421_1424delTCTC	c.(1420-1425)atctccfs	p.IS474fs		NM_014924.4	NP_055739.2	Q6ZNE5	BAKOR_HUMAN	autophagy related 14	474	BATS. {ECO:0000250}.				autophagic vacuole assembly (GO:0000045)|endosome to lysosome transport (GO:0008333)|positive regulation of autophagy (GO:0010508)	autophagic vacuole (GO:0005776)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|pre-autophagosomal structure membrane (GO:0034045)				central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(6)|prostate(2)	13						TGCTGCAGAGGAGATCATCCCACC	0.539																																					p.474_475del		Atlas-Indel,Pindel	.											.	ATG14	36	.	0			c.1422_1425del						PASS	.																																			SO:0001589	frameshift_variant	22863	exon10			.	AB020638	CCDS32087.1	14q22.2	2014-02-12	2012-06-06	2010-06-29	ENSG00000126775	ENSG00000126775			19962	protein-coding gene	gene with protein product	"Barkor", "beclin 1-associated autophagy-related key regulator"	613515	"KIAA0831", "ATG14 autophagy related 14 homolog (S. cerevisiae)"	KIAA0831		18843052	Standard	NM_014924		Approved	ATG14L	uc001xbx.2	Q6ZNE5	OTTHUMG00000172129	ENST00000247178.5:c.1421_1424delTCTC	chr14.hg19:g.55836392_55836395delGAGA	ENSP00000247178:p.Ile474fs	182.0	0.0	0		75.0	29.0	0.386667	NM_014924	A6NJE4|A8K9U5|B7ZWP5|O94920|Q32MK7|Q32MK8	Frame_Shift_Del	DEL	ENST00000247178.5	hg19	CCDS32087.1																																																																																			.	.	.	none		0.539	ATG14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416992.1	NM_014924		-	55836395	GAGA	-	55836392	7	5	14	1	0	1	0	1	0	0	0	0	8202	1174	41	0	58	0	KIAA0831	14	55836392	Frame_Shift_Del	DEL	GAGA	TCGA-2Z-A9JK-01A-11D-A42J-10	31184845	55836392	51513148	58	1001											
C15orf39	56905	hgsc.bcm.edu	37	chr15	75499492	75499494	+	In_Frame_Del	DEL	CAT	CAT	-																															gcctctcactccacggtgccCattggactttgccccccaga																										TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	CAT	CAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr15:75499492_75499494delCAT	ENST00000360639.2	+	2	1423_1425	c.1103_1105delCAT	c.(1102-1107)ccattg>ctg	p.P368del	C15orf39_ENST00000394987.4_In_Frame_Del_p.P368del|C15orf39_ENST00000567617.1_In_Frame_Del_p.P368del			Q6ZRI6	CO039_HUMAN	chromosome 15 open reading frame 39	368						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16						CCACGGTGCCCATTGGACTTTGC	0.621																																					p.368_368del		Atlas-Indel,Pindel	.											C15orf39,colon,carcinoma,0,1	C15orf39	64	.	0			c.1102_1104del						PASS	.																																			SO:0001651	inframe_deletion	56905	exon2			.	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.1103_1105delCAT	chr15.hg19:g.75499492_75499494delCAT	ENSP00000353854:p.Pro368del	149.0	0.0	0		104.0	34.0	0.326923	NM_015492	B3KWI3|C9J888|Q71JB1|Q7L3S0|Q8N3F2|Q96FB6|Q9NTU5	In_Frame_Del	DEL	ENST00000360639.2	hg19	CCDS10276.1																																																																																			.	.	.	none		0.621	C15orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286410.1	NM_015492		-	75499494	CAT	-	75499492	7	5	14	1	0	1	0	1	0	0	0	0	1795	594	21	0	1105	0	C15orf39	15	75499492	In_Frame_Del	DEL	CAT	TCGA-2Z-A9JK-01A-11D-A42J-10		75499492	27031900	59	1002											
CREBBP	1387	hgsc.bcm.edu	37	chr16	3778974	3778974	+	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	tgggctgctgctggggaaggGgcgcctgctgccactgcccg	3	7	18	13	2	0	0	0	0	0	0	0	1	0	1	3	5	5	4	3	5	1	0			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr16:3778974G>T	ENST00000262367.5	-	31	6883	c.6074C>A	c.(6073-6075)cCc>cAc	p.P2025H	CREBBP_ENST00000382070.3_Missense_Mutation_p.P1987H	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	2025					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)		CTGGGGAAGGGGCGCCTGCTG	0.716			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.P2025H		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.C6074A						PASS	.						8	10	10					16																	3778974		2177	4282	6459	SO:0001583	missense	1387	exon31			GGAAGGGGCGCCT	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.6074C>A	chr16.hg19:g.3778974G>T	ENSP00000262367:p.Pro2025His	67.0	0.0	.		32.0	8.0	.	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	hg19	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	g	9.873	1.199349	0.22121	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.84589	-1.87;-1.74	5.11	5.11	0.69529	Nuclear receptor coactivator, CREB-bp-like, interlocking (1);	0.174784	0.40908	D	0.000996	T	0.79958	0.4536	L	0.36672	1.1	0.40858	D	0.983818	P;P	0.42123	0.771;0.771	B;B	0.43623	0.425;0.425	T	0.76908	-0.2785	10	0.16420	T	0.52	-5.7528	13.5145	0.61533	0.0:0.0:0.844:0.156	.	2055;2025	Q4LE28;Q92793	.;CBP_HUMAN	H	2025;2055;1987;560	ENSP00000262367:P2025H;ENSP00000371502:P1987H	ENSP00000262367:P2025H	P	-	2	0	CREBBP	3718975	0.990000	0.36364	0.985000	0.45067	0.936000	0.57629	2.389000	0.44407	2.387000	0.81309	0.655000	0.94253	CCC	.	.	.	none		0.716	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		T	3778974	G	T	3778974	3	4	14	1	0	0	0	0	1	0	0	0	3863	1232	43	4	1258	4	CREBBP	16	3778974	Missense_Mutation	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10		3778974	86575779	60	1003											
MARVELD3	91862	hgsc.bcm.edu	37	chr16	71668183	71668183	+	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	ttccacagggggctacacggGcatcaccagcttggggggca	8	6	15	12	1	1	0	1	0	0	0	2	0	2	0	2	6	2	4	2	6	1	3			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr16:71668183G>C	ENST00000268485.3	+	3	727	c.683G>C	c.(682-684)gGc>gCc	p.G228A	MARVELD3_ENST00000565261.1_Intron|MARVELD3_ENST00000567501.1_Silent_p.G41G|MARVELD3_ENST00000299952.4_Intron	NM_052858.4	NP_443090.4	Q96A59	MALD3_HUMAN	MARVEL domain containing 3	228	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|tight junction (GO:0005923)				NS(1)|endometrium(3)|large_intestine(5)|lung(6)|skin(2)	17		Ovarian(137;0.125)				GGCTACACGGGCATCACCAGC	0.557																																					p.G228A		Atlas-SNP	.											MARVELD3_ENST00000268485,lower_third,carcinoma,0,1	MARVELD3	63	.	0			c.G683C						PASS	.						95	98	97					16																	71668183		2198	4300	6498	SO:0001583	missense	91862	exon3			ACACGGGCATCAC	BC013376	CCDS10904.1, CCDS32478.1, CCDS59270.1	16q22.2	2008-02-05	2004-07-12	2004-07-14	ENSG00000140832	ENSG00000140832			30525	protein-coding gene	gene with protein product		614094	"MARVEL (membrane-associating) domain containing 3"	MRVLDC3			Standard	NM_001017967		Approved		uc002fat.4	Q96A59	OTTHUMG00000137591	ENST00000268485.3:c.683G>C	chr16.hg19:g.71668183G>C	ENSP00000268485:p.Gly228Ala	87.0	0.0	.		59.0	16.0	.	NM_052858	A8K820|H3BQM5|Q96MJ4	Missense_Mutation	SNP	ENST00000268485.3	hg19	CCDS10904.1	.	.	.	.	.	.	.	.	.	.	G	12.69	2.014124	0.35511	.	.	ENSG00000140832	ENST00000268485	T	0.40756	1.02	5.91	5.91	0.95273	Marvel (1);	.	.	.	.	T	0.57169	0.2035	L	0.46157	1.445	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.41179	-0.9523	9	0.12766	T	0.61	.	19.2867	0.94077	0.0:0.0:1.0:0.0	.	228	Q96A59	MALD3_HUMAN	A	228	ENSP00000268485:G228A	ENSP00000268485:G228A	G	+	2	0	MARVELD3	70225684	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.076000	0.71267	2.793000	0.96121	0.655000	0.94253	GGC	.	.	.	none		0.557	MARVELD3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268991.2	NM_052858		C	71668183	G	C	71668183	3	2	14	1	0	0	0	0	1	0	0	0	9326	1203	42	4	693	4	MARVELD3	16	71668183	Missense_Mutation	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10	67889209	71668183	18686570	61	1004											
ANKRD11	29123	hgsc.bcm.edu	37	chr16	89341269	89341269	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcggagtccagcagcatcgTgcaggcgctgaatggcactg	8	7	14	12	3	0	1	0	1	0	0	3	2	1	2	1	3	3	5	1	3	1	0			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr16:89341269T>C	ENST00000301030.4	-	11	8126	c.7666A>G	c.(7666-7668)Acg>Gcg	p.T2556A	ANKRD11_ENST00000378330.2_Missense_Mutation_p.T2556A	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	2556					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)		AGCAGCATCGTGCAGGCGCTG	0.632																																					p.T2556A		Atlas-SNP	.											.	ANKRD11	195	.	0			c.A7666G						PASS	.						63	60	61					16																	89341269		2198	4300	6498	SO:0001583	missense	29123	exon11			GCATCGTGCAGGC	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.7666A>G	chr16.hg19:g.89341269T>C	ENSP00000301030:p.Thr2556Ala	94.0	0.0	.		65.0	12.0	.	NM_001256183	Q6NTG1|Q6QMF8	Missense_Mutation	SNP	ENST00000301030.4	hg19	CCDS32513.1	.	.	.	.	.	.	.	.	.	.	T	18.87	3.716462	0.68844	.	.	ENSG00000167522	ENST00000301030;ENST00000378330	T;T	0.45668	0.89;0.89	5.16	5.16	0.70880	.	0.000000	0.64402	D	0.000002	T	0.66781	0.2824	M	0.83953	2.67	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.71163	-0.4673	10	0.52906	T	0.07	.	14.9521	0.71083	0.0:0.0:0.0:1.0	.	2556	Q6UB99	ANR11_HUMAN	A	2556	ENSP00000301030:T2556A;ENSP00000367581:T2556A	ENSP00000301030:T2556A	T	-	1	0	ANKRD11	87868770	1.000000	0.71417	1.000000	0.80357	0.633000	0.38033	7.859000	0.86982	2.077000	0.62373	0.533000	0.62120	ACG	.	.	.	none		0.632	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		C	89341269	T	C	89341269	3	2	14	1	0	0	0	0	1	0	0	0	639	1696	59	3	337	3	ANKRD11	16	89341269	Missense_Mutation	SNP	T	TCGA-2Z-A9JK-01A-11D-A42J-10	17673086	89341269	1013484	62	1005											
SMYD4	114826	hgsc.bcm.edu	37	chr17	1687738	1687738	+	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	gcacaagatctgctgccacaGcgcagcacgtcatctccctg	9	7	9	16	2	3	1	1	0	2	1	4	1	3	1	2	0	4	4	2	0	1	0			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr17:1687738G>C	ENST00000305513.7	-	8	2069	c.1902C>G	c.(1900-1902)cgC>cgG	p.R634R		NM_052928.2	NP_443160.2	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	634							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						TGCTGCCACAGCGCAGCACGT	0.542											OREG0024075	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R634R		Atlas-SNP	.											.	SMYD4	50	.	0			c.C1902G						PASS	.						133	123	126					17																	1687738		2203	4300	6503	SO:0001819	synonymous_variant	114826	exon8			GCCACAGCGCAGC	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.1902C>G	chr17.hg19:g.1687738G>C		88.0	0.0	.	597	62.0	14.0	.	NM_052928	Q8N1P2|Q8NAT0|Q96LV4|Q96PV2	Silent	SNP	ENST00000305513.7	hg19	CCDS11013.1																																																																																			.	.	.	none		0.542	SMYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207108.4	XM_056082		C	1687738	G	C	1687738	2	2	14	1	0	0	0	0	0	0	0	1	14837	958	34	4		4	SMYD4	17	1687738	Silent	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10		1687738	79507472	63	1006											
PAFAH1B1	5048	hgsc.bcm.edu	37	chr17	2577395	2577395	+	Missense_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	aggacacagagaatgggtacGtatggtacggccaaatcaag	15	6	13	7	2	1	1	1	0	0	1	1	3	1	2	1	4	2	3	1	4	6	3			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr17:2577395G>A	ENST00000397195.5	+	8	1164	c.713G>A	c.(712-714)cGt>cAt	p.R238H	PAFAH1B1_ENST00000451360.2_Missense_Mutation_p.R67H|PAFAH1B1_ENST00000572915.2_Intron	NM_000430.3	NP_000421.1			platelet-activating factor acetylhydrolase 1b, regulatory subunit 1 (45kDa)											endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(1)|skin(1)	11						GAATGGGTACGTATGGTACGG	0.448																																					p.R238H		Atlas-SNP	.											.	PAFAH1B1	26	.	0			c.G713A						PASS	.						130	102	112					17																	2577395		2203	4300	6503	SO:0001583	missense	5048	exon8			GGGTACGTATGGT	L25107	CCDS32528.1	17p13.3	2014-04-04	2010-02-10		ENSG00000007168	ENSG00000007168		"WD repeat domain containing"	8574	protein-coding gene	gene with protein product	"lissencephaly-1"	601545	"platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit (45kD)", "Miller-Dieker syndrome chromosome region", "platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit 45kDa", "platelet-activating factor acetylhydrolase, isoform Ib, subunit 1 (45kDa)"	MDCR, MDS		8355785, 9063735	Standard	NM_000430		Approved	LIS1, PAFAH	uc002fuw.4	P43034	OTTHUMG00000177574	ENST00000397195.5:c.713G>A	chr17.hg19:g.2577395G>A	ENSP00000380378:p.Arg238His	373.0	0.0	.		267.0	20.0	.	NM_000430		Missense_Mutation	SNP	ENST00000397195.5	hg19	CCDS32528.1	.	.	.	.	.	.	.	.	.	.	G	34	5.372309	0.95923	.	.	ENSG00000007168	ENST00000397195;ENST00000397193;ENST00000451360	T;T	0.62105	0.05;0.05	5.74	5.74	0.90152	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	0.67599	0.2910	L	0.52011	1.625	0.80722	D	1	P;D	0.59767	0.9;0.986	P;P	0.53035	0.554;0.716	T	0.60969	-0.7157	10	0.18276	T	0.48	.	18.9232	0.92534	0.0:0.0:1.0:0.0	.	67;238	B4DF38;P43034	.;LIS1_HUMAN	H	238;67;67	ENSP00000380378:R238H;ENSP00000395628:R67H	ENSP00000380377:R67H	R	+	2	0	PAFAH1B1	2524145	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.869000	0.99810	2.703000	0.92315	0.655000	0.94253	CGT	.	.	.	none		0.448	PAFAH1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437797.2	NM_000430		A	2577395	G	A	2577395	3	1	14	1	0	0	0	0	1	0	0	0	11391	1145	40	1	739	1	PAFAH1B1	17	2577395	Missense_Mutation	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10	889657	2577395	78617815	64	1007											
GLP2R	9340	hgsc.bcm.edu	37	chr17	9792980	9792980	+	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	agtgagggggatgtcaccatGgccaacaccatggaggagat	12	6	15	8	0	1	2	1	1	0	1	1	5	1	4	3	5	1	0	3	5	1	0			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr17:9792980G>A	ENST00000262441.5	+	13	2133	c.1620G>A	c.(1618-1620)atG>atA	p.M540I	GLP2R_ENST00000574745.1_Missense_Mutation_p.M360I	NM_004246.1	NP_004237.1	O95838	GLP2R_HUMAN	glucagon-like peptide 2 receptor	540					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|positive regulation of cell proliferation (GO:0008284)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|glucagon receptor activity (GO:0004967)			endometrium(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	44					Glucagon recombinant(DB00040)|Teduglutide(DB08900)	ATGTCACCATGGCCAACACCA	0.642																																					p.M540I		Atlas-SNP	.											.	GLP2R	90	.	0			c.G1620A						PASS	.						32	27	29					17																	9792980		2203	4300	6503	SO:0001583	missense	9340	exon13			CACCATGGCCAAC	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.1620G>A	chr17.hg19:g.9792980G>A	ENSP00000262441:p.Met540Ile	96.0	0.0	.		73.0	31.0	.	NM_004246	Q4VAT3	Missense_Mutation	SNP	ENST00000262441.5	hg19	CCDS11150.1	.	.	.	.	.	.	.	.	.	.	G	12.72	2.023235	0.35701	.	.	ENSG00000065325	ENST00000396206;ENST00000262441	T	0.53423	0.62	5.97	2.5	0.30297	.	0.263906	0.20265	N	0.095796	T	0.24624	0.0597	N	0.08118	0	0.21652	N	0.9996	B	0.02656	0.0	B	0.01281	0.0	T	0.14227	-1.0480	10	0.40728	T	0.16	.	8.2404	0.31656	0.0:0.3617:0.3907:0.2476	.	540	O95838	GLP2R_HUMAN	I	540	ENSP00000262441:M540I	ENSP00000262441:M540I	M	+	3	0	GLP2R	9733705	0.146000	0.22672	1.000000	0.80357	0.985000	0.73830	0.185000	0.16958	1.468000	0.48064	0.655000	0.94253	ATG	.	.	.	none		0.642	GLP2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252601.4			A	9792980	G	A	9792980	3	1	14	1	0	0	0	0	1	0	0	0	6460	1348	47	2	1670	2	GLP2R	17	9792980	Missense_Mutation	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10	7215585	9792980	71402230	65	1008											
MYO18A	399687	hgsc.bcm.edu	37	chr17	27437065	27437065	+	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	ccagccctcagctacaggcaGgaagcagtgcacaaaatgca	14	4	10	13	0	1	0	1	0	0	0	1	1	1	1	2	2	6	5	2	2	4	1			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr17:27437065G>C	ENST00000527372.1	-	19	3322	c.3142C>G	c.(3142-3144)Ctg>Gtg	p.L1048V	MYO18A_ENST00000531253.1_Missense_Mutation_p.L1048V|MYO18A_ENST00000354329.4_Missense_Mutation_p.L1048V|MYO18A_ENST00000533112.1_Missense_Mutation_p.L1048V	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	1048	Myosin motor.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			GCTACAGGCAGGAAGCAGTGC	0.637																																					p.L1048V	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.C3142G						PASS	.						39	49	46					17																	27437065		2178	4283	6461	SO:0001583	missense	399687	exon19			CAGGCAGGAAGCA	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.3142C>G	chr17.hg19:g.27437065G>C	ENSP00000437073:p.Leu1048Val	85.0	0.0	.		66.0	19.0	.	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	hg19	CCDS45642.1	.	.	.	.	.	.	.	.	.	.	G	14.51	2.555798	0.45487	.	.	ENSG00000196535	ENST00000354329;ENST00000359450;ENST00000533112;ENST00000531253;ENST00000527372;ENST00000458428	D;D;D;D	0.87103	-2.21;-2.21;-2.21;-2.21	5.06	4.09	0.47781	Myosin head, motor domain (2);	0.000000	0.64402	D	0.000001	D	0.89058	0.6607	L	0.35793	1.09	0.36621	D	0.875739	P;D;D;D;D	0.71674	0.537;0.998;0.998;0.998;0.998	B;D;D;D;D	0.83275	0.219;0.996;0.996;0.996;0.983	D	0.88752	0.3251	10	0.27082	T	0.32	.	13.476	0.61308	0.0772:0.0:0.9228:0.0	.	717;660;1048;1048;1048	Q92614-2;F8W6Y3;Q92614-3;Q92614-4;Q92614	.;.;.;.;MY18A_HUMAN	V	1048;1048;1048;1048;1048;660	ENSP00000346291:L1048V;ENSP00000435932:L1048V;ENSP00000434228:L1048V;ENSP00000437073:L1048V	ENSP00000346291:L1048V	L	-	1	2	MYO18A	24461191	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	3.662000	0.54510	1.268000	0.44264	0.561000	0.74099	CTG	.	.	.	none		0.637	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		C	27437065	G	C	27437065	3	2	14	1	0	0	0	0	1	0	0	0	10072	991	35	4	3118	4	MYO18A	17	27437065	Missense_Mutation	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10	17644085	27437065	53758145	66	1009											
EME1	146956	hgsc.bcm.edu	37	chr17	48452912	48452918	+	Frame_Shift_Del	DEL	TCTAGCT	TCTAGCT	-																															agcaactgagccctgaggacTctagctccccagttaaaagt																										TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	TCTAGCT	TCTAGCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr17:48452912_48452918delTCTAGCT	ENST00000338165.4	+	2	425_431	c.343_349delTCTAGCT	c.(343-351)tctagctccfs	p.SSS115fs	EME1_ENST00000511648.2_Frame_Shift_Del_p.SSS115fs|MRPL27_ENST00000507088.1_5'Flank|MRPL27_ENST00000503633.1_5'Flank|MRPL27_ENST00000225969.4_5'Flank|EME1_ENST00000393271.2_Frame_Shift_Del_p.SSS115fs|MRPL27_ENST00000442592.3_5'Flank	NM_152463.2	NP_689676.2	Q96AY2	EME1_HUMAN	essential meiotic structure-specific endonuclease 1	115					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)			CCCTGAGGACTCTAGCTCCCCAGTTAA	0.43								Direct reversal of damage;Homologous recombination																													p.114_116del		Atlas-Indel,Pindel	.											.	EME1	39	.	0			c.342_348del						PASS	.																																			SO:0001589	frameshift_variant	146956	exon2			.	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.343_349delTCTAGCT	chr17.hg19:g.48452912_48452918delTCTAGCT	ENSP00000339897:p.Ser115fs	162.0	0.0	0		112.0	19.0	0.169643	NM_152463	Q96N62	Frame_Shift_Del	DEL	ENST00000338165.4	hg19	CCDS11565.1																																																																																			.	.	.	none		0.43	EME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367118.3	NM_152463		-	48452918	TCTAGCT	-	48452912	7	5	14	1	0	1	0	1	0	0	0	0	5090	1551	54	0	345	0	EME1	17	48452912	Frame_Shift_Del	DEL	TCTAGCT	TCGA-2Z-A9JK-01A-11D-A42J-10	21015847	48452912	32742298	67	1010											
RNF213	57674	hgsc.bcm.edu	37	chr17	78321044	78321044	+	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	ctttgctgcagcaaaggcttCaaatagaaagccttccccgc	11	9	8	13	1	1	1	1	0	0	1	2	1	2	1	3	1	4	4	3	1	4	4			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr17:78321044C>T	ENST00000582970.1	+	29	9052	c.8909C>T	c.(8908-8910)tCa>tTa	p.S2970L	RNF213_ENST00000336301.6_Missense_Mutation_p.S1043L|RNF213_ENST00000508628.2_Missense_Mutation_p.S3019L	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	2970					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)			GCAAAGGCTTCAAATAGAAAG	0.483																																					p.S2970L		Atlas-SNP	.											.	RNF213	766	.	0			c.C8909T						PASS	.						36	32	34					17																	78321044		2203	4300	6503	SO:0001583	missense	57674	exon29			AGGCTTCAAATAG	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.8909C>T	chr17.hg19:g.78321044C>T	ENSP00000464087:p.Ser2970Leu	86.0	0.0	.		84.0	17.0	.	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	hg19	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	C	5.507	0.278473	0.10403	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.31510	1.49	5.82	5.82	0.92795	.	0.215070	0.40144	N	0.001174	T	0.39253	0.1071	M	0.72576	2.205	0.18873	N	0.999983	B	0.25441	0.126	B	0.21546	0.035	T	0.32079	-0.9920	10	0.59425	D	0.04	.	20.093	0.97828	0.0:1.0:0.0:0.0	.	1043	Q63HN8	RN213_HUMAN	L	2970;3019;1043	ENSP00000338218:S1043L	ENSP00000338218:S1043L	S	+	2	0	RNF213	75935639	0.971000	0.33674	0.008000	0.14137	0.003000	0.03518	4.793000	0.62474	2.751000	0.94390	0.563000	0.77884	TCA	.	.	.	none		0.483	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		T	78321044	C	T	78321044	3	4	14	1	0	0	0	0	1	0	0	0	13490	838	29	2	9338	2	RNF213	17	78321044	Missense_Mutation	SNP	C	TCGA-2Z-A9JK-01A-11D-A42J-10	29868132	78321044	2874166	68	1011											
ZCCHC2	54877	hgsc.bcm.edu	37	chr18	60241523	60241523	+	Missense_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	cccagaagtctgaagttgtcGttcctgcacccaaacccgct	9	9	8	15	2	1	2	0	1	1	1	3	2	2	2	4	0	2	4	4	0	3	2	rs377112503		TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr18:60241523G>A	ENST00000269499.5	+	13	2627	c.2209G>A	c.(2209-2211)Gtt>Att	p.V737I	ZCCHC2_ENST00000586834.1_Missense_Mutation_p.V416I	NM_017742.4	NP_060212.4	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2	737						cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25						TGAAGTTGTCGTTCCTGCACC	0.448																																					p.V737I		Atlas-SNP	.											.	ZCCHC2	64	.	0			c.G2209A						PASS	.	G	ILE/VAL	1,3945		0,1,1972	103	101	102		2209	0.9	0	18		102	0,8358		0,0,4179	no	missense	ZCCHC2	NM_017742.4	29	0,1,6151	AA,AG,GG		0.0,0.0253,0.0081	benign	737/1179	60241523	1,12303	1973	4179	6152	SO:0001583	missense	54877	exon13			GTTGTCGTTCCTG	AB051531	CCDS45880.1	18q21.33	2012-04-19			ENSG00000141664	ENSG00000141664		"Zinc fingers, CCHC domain containing"	22916	protein-coding gene	gene with protein product			"chromosome 18 open reading frame 49"	C18orf49		11214970	Standard	NM_017742		Approved	FLJ20281, KIAA1744, FLJ20222	uc002lip.4	Q9C0B9		ENST00000269499.5:c.2209G>A	chr18.hg19:g.60241523G>A	ENSP00000269499:p.Val737Ile	121.0	0.0	.		117.0	25.0	.	NM_017742	B2RPG6|Q8N3S1|Q9NXF6	Missense_Mutation	SNP	ENST00000269499.5	hg19	CCDS45880.1	.	.	.	.	.	.	.	.	.	.	G	6.618	0.482373	0.12581	2.53E-4	0.0	ENSG00000141664	ENST00000269499	T	0.24723	1.84	5.58	0.954	0.19595	.	0.920531	0.09269	N	0.825430	T	0.11324	0.0276	N	0.12182	0.205	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.37686	-0.9695	10	0.07030	T	0.85	-3.16	6.2352	0.20758	0.1872:0.1457:0.6671:0.0	.	737	Q9C0B9	ZCHC2_HUMAN	I	737	ENSP00000269499:V737I	ENSP00000269499:V737I	V	+	1	0	ZCCHC2	58392503	0.009000	0.17119	0.002000	0.10522	0.823000	0.46562	0.222000	0.17699	-0.134000	0.11516	0.655000	0.94253	GTT	.	.	.	weak		0.448	ZCCHC2-005	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450083.1	NM_017742		A	60241523	G	A	60241523	3	1	14	1	0	0	0	0	1	0	0	0	17599	1145	40	1	2259	1	ZCCHC2	18	60241523	Missense_Mutation	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10		60241523	17835725	69	1012											
CD226	10666	hgsc.bcm.edu	37	chr18	67614032	67614032	+	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	ggtaagtgtaaagagagcagGaatagtagccaacatcatct	16	8	11	6	0	2	1	1	0	1	1	2	3	2	2	1	2	3	4	1	2	7	4			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr18:67614032G>A	ENST00000280200.4	-	3	588	c.320C>T	c.(319-321)tCc>tTc	p.S107F	CD226_ENST00000577287.1_Intron|CD226_ENST00000581982.1_Intron|CD226_ENST00000582621.1_Missense_Mutation_p.S107F	NM_006566.2	NP_006557.2	Q15762	CD226_HUMAN	CD226 molecule	107	Ig-like C2-type 1.				cell adhesion (GO:0007155)|cell recognition (GO:0008037)|cytokine production (GO:0001816)|positive regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060369)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of mast cell activation (GO:0033005)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)			breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(14)|prostate(1)|urinary_tract(1)	24		Esophageal squamous(42;0.129)				AAGAGAGCAGGAATAGTAGCC	0.403																																					p.S107F	NSCLC(184;838 2130 8673 21498 50749)	Atlas-SNP	.											.	CD226	51	.	0			c.C320T						PASS	.						112	104	107					18																	67614032		2203	4300	6503	SO:0001583	missense	10666	exon3			GAGCAGGAATAGT	U56102	CCDS11997.1	18q22.3	2013-01-11	2006-03-28		ENSG00000150637	ENSG00000150637		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	16961	protein-coding gene	gene with protein product		605397	"CD226 antigen"			8673704	Standard	NM_006566		Approved	DNAM-1, DNAM1, PTA1, TLiSA1	uc002lkm.4	Q15762	OTTHUMG00000132809	ENST00000280200.4:c.320C>T	chr18.hg19:g.67614032G>A	ENSP00000280200:p.Ser107Phe	192.0	0.0	.		167.0	39.0	.	NM_006566	B2R818	Missense_Mutation	SNP	ENST00000280200.4	hg19	CCDS11997.1	.	.	.	.	.	.	.	.	.	.	G	1.423	-0.572473	0.03882	.	.	ENSG00000150637	ENST00000280200	T	0.63913	-0.07	5.51	1.31	0.21738	Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.347798	0.34314	N	0.004071	T	0.50446	0.1616	M	0.72479	2.2	0.30526	N	0.767936	P	0.35077	0.483	B	0.28553	0.091	T	0.50659	-0.8802	10	0.09843	T	0.71	.	9.698	0.40169	0.0:0.4401:0.4089:0.151	.	107	Q15762	CD226_HUMAN	F	107	ENSP00000280200:S107F	ENSP00000280200:S107F	S	-	2	0	CD226	65765012	0.975000	0.34042	0.882000	0.34594	0.201000	0.24016	0.136000	0.15974	0.340000	0.23745	-0.176000	0.13171	TCC	.	.	.	none		0.403	CD226-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256226.3	NM_006566		A	67614032	G	A	67614032	3	1	14	1	0	0	0	0	1	0	0	0	2988	1174	41	2	710	2	CD226	18	67614032	Missense_Mutation	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10	7372509	67614032	10463216	70	1013											
SALL3	27164	hgsc.bcm.edu	37	chr18	76753052	76753052	+	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	cccggggtccctgctgggtgCggcgcccggcctgccaagtc	2	6	16	17	4	0	0	0	0	0	0	2	0	1	0	5	5	3	1	5	5	1	0			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr18:76753052C>T	ENST00000537592.2	+	2	1061	c.1061C>T	c.(1060-1062)gCg>gTg	p.A354V	SALL3_ENST00000575389.2_Missense_Mutation_p.A354V|SALL3_ENST00000536229.3_Missense_Mutation_p.A221V	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	354					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)		CTGCTGGGTGCGGCGCCCGGC	0.751																																					p.A354V		Atlas-SNP	.											.	SALL3	162	.	0			c.C1061T						PASS	.						8	10	9					18																	76753052		2140	4216	6356	SO:0001583	missense	27164	exon2			TGGGTGCGGCGCC	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.1061C>T	chr18.hg19:g.76753052C>T	ENSP00000441823:p.Ala354Val	84.0	0.0	.		54.0	11.0	.	NM_171999	Q9UGH1	Missense_Mutation	SNP	ENST00000537592.2	hg19	CCDS12013.1	.	.	.	.	.	.	.	.	.	.	C	15.03	2.712415	0.48517	.	.	ENSG00000256463	ENST00000537592;ENST00000536229	T	0.09163	3.01	4.37	4.37	0.52481	.	0.274240	0.25671	N	0.029076	T	0.04227	0.0117	N	0.02916	-0.46	0.28697	N	0.904262	P	0.37158	0.585	B	0.25140	0.058	T	0.29274	-1.0017	10	0.20519	T	0.43	-6.7884	17.1219	0.86704	0.0:1.0:0.0:0.0	.	354	Q9BXA9	SALL3_HUMAN	V	354	ENSP00000441823:A354V	ENSP00000299466:A354V	A	+	2	0	SALL3	74854040	0.982000	0.34865	0.003000	0.11579	0.005000	0.04900	5.445000	0.66594	2.269000	0.75478	0.460000	0.39030	GCG	.	.	.	none		0.751	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999		T	76753052	C	T	76753052	3	4	14	1	0	0	0	0	1	0	0	0	13825	768	27	1	1067	1	SALL3	18	76753052	Missense_Mutation	SNP	C	TCGA-2Z-A9JK-01A-11D-A42J-10	9139020	76753052	1324196	71	1014											
ZNF823	55552	hgsc.bcm.edu	37	chr19	11833714	11833714	+	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	gtttctctccagtgtgtgttCtttcgtgcaaatgaaataaa	10	16	8	7	1	2	1	0	1	2	0	5	1	3	1	1	0	1	3	1	0	4	4			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr19:11833714C>A	ENST00000341191.6	-	4	788	c.635G>T	c.(634-636)aGa>aTa	p.R212I	ZNF823_ENST00000545749.1_Missense_Mutation_p.R30I	NM_001080493.2	NP_001073962.1	P16415	ZN823_HUMAN	zinc finger protein 823	212					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)	26						AGTGTGTGTTCTTTCGTGCAA	0.433										HNSCC(68;0.2)																											p.R212I		Atlas-SNP	.											.	ZNF823	104	.	0			c.G635T						PASS	.						103	109	107					19																	11833714		2199	4299	6498	SO:0001583	missense	55552	exon4			TGTGTTCTTTCGT	X51760	CCDS45981.1	19p13.2	2013-01-08			ENSG00000197933	ENSG00000197933		"Zinc fingers, C2H2-type", "-"	30936	protein-coding gene	gene with protein product	"ZFP 36 for a zinc finger protein"						Standard	XM_006722789		Approved	HSZFP36	uc002msm.2	P16415	OTTHUMG00000156528	ENST00000341191.6:c.635G>T	chr19.hg19:g.11833714C>A	ENSP00000340683:p.Arg212Ile	80.0	0.0	.		95.0	25.0	.	NM_001080493	A0PJL4|B7Z8D4|Q6P4A9	Missense_Mutation	SNP	ENST00000341191.6	hg19	CCDS45981.1	.	.	.	.	.	.	.	.	.	.	c	16.91	3.253614	0.59212	.	.	ENSG00000197933	ENST00000545749;ENST00000341191;ENST00000431998	T;T;T	0.24908	1.83;1.83;1.83	0.632	0.632	0.17705	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.47432	0.1445	M	0.81179	2.53	0.39861	D	0.973379	D	0.89917	1.0	D	0.91635	0.999	T	0.51325	-0.8720	9	0.59425	D	0.04	.	8.7993	0.34898	0.0:1.0:0.0:0.0	.	212	P16415	ZN823_HUMAN	I	30;212;168	ENSP00000440162:R30I;ENSP00000340683:R212I;ENSP00000410654:R168I	ENSP00000340683:R212I	R	-	2	0	ZNF823	11694714	0.000000	0.05858	0.361000	0.25849	0.489000	0.33432	-1.844000	0.01679	0.618000	0.30179	0.298000	0.19748	AGA	.	.	.	none		0.433	ZNF823-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344516.2	NM_001080493		A	11833714	C	A	11833714	3	1	14	1	0	0	0	0	1	0	0	0	18191	913	32	4	1201	4	ZNF823	19	11833714	Missense_Mutation	SNP	C	TCGA-2Z-A9JK-01A-11D-A42J-10		11833714	47295269	72	1015											
ZNF546	339327	hgsc.bcm.edu	37	chr19	40521590	40521590	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcatactggtgaaaaacccTatcaatgtaaagaatgtgga	16	11	8	6	0	2	2	2	1	0	1	2	3	2	3	1	2	2	1	1	2	8	4	rs371824172		TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr19:40521590T>C	ENST00000347077.4	+	7	2629	c.2413T>C	c.(2413-2415)Tat>Cat	p.Y805H	ZNF546_ENST00000596894.1_Intron|ZNF546_ENST00000600094.1_Missense_Mutation_p.Y779H	NM_178544.3	NP_848639.2	Q86UE3	ZN546_HUMAN	zinc finger protein 546	805					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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)					TGAAAAACCCTATCAATGTAA	0.358																																					p.Y805H		Atlas-SNP	.											.	ZNF546	93	.	0			c.T2413C						PASS	.						55	56	56					19																	40521590		2203	4300	6503	SO:0001583	missense	339327	exon7			AAACCCTATCAAT	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.2413T>C	chr19.hg19:g.40521590T>C	ENSP00000339823:p.Tyr805His	180.0	0.0	.		172.0	43.0	.	NM_178544	A8K913	Missense_Mutation	SNP	ENST00000347077.4	hg19	CCDS12548.1	.	.	.	.	.	.	.	.	.	.	t	16.66	3.184714	0.57909	.	.	ENSG00000187187	ENST00000347077;ENST00000392042	T	0.21734	1.99	3.08	3.08	0.35506	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.26484	0.0647	L	0.34521	1.04	0.22500	N	0.999044	P	0.50710	0.938	P	0.54238	0.746	T	0.05354	-1.0890	9	0.62326	D	0.03	.	9.8957	0.41318	0.0:0.0:0.0:1.0	.	805	Q86UE3	ZN546_HUMAN	H	805;414	ENSP00000339823:Y805H	ENSP00000339823:Y805H	Y	+	1	0	ZNF546	45213430	0.002000	0.14202	0.877000	0.34402	0.988000	0.76386	1.274000	0.33132	1.639000	0.50556	0.533000	0.62120	TAT	.	.	.	alt		0.358	ZNF546-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462495.2	NM_178544		C	40521590	T	C	40521590	3	2	14	1	0	0	0	0	1	0	0	0	17990	1522	53	3	2431	3	ZNF546	19	40521590	Missense_Mutation	SNP	T	TCGA-2Z-A9JK-01A-11D-A42J-10	28687876	40521590	18607393	73	1016											
ZNF534	147658	hgsc.bcm.edu	37	chr19	52941686	52941686	+	Missense_Mutation	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	taatccatactggagagaaaCcttatgattgtaaggaatgt	15	12	9	5	0	0	2	0	1	0	1	1	5	1	4	2	2	2	1	2	2	6	5			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr19:52941686C>T	ENST00000332323.6	+	4	1073	c.1012C>T	c.(1012-1014)Cct>Tct	p.P338S	ZNF534_ENST00000433050.1_Missense_Mutation_p.P325S|ZNF534_ENST00000432303.2_Intron|ZNF534_ENST00000301085.4_Intron	NM_001143939.1	NP_001137411.1	Q76KX8	ZN534_HUMAN	zinc finger protein 534	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|lung(1)|prostate(1)|skin(1)	4						TGGAGAGAAACCTTATGATTG	0.408																																					p.P338S		Atlas-SNP	.											ZNF534_ENST00000332323,NS,carcinoma,0,1	ZNF534	105	.	0			c.C1012T						PASS	.						60	54	56					19																	52941686		1568	3582	5150	SO:0001583	missense	147658	exon4			GAGAAACCTTATG	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.1012C>T	chr19.hg19:g.52941686C>T	ENSP00000327538:p.Pro338Ser	72.0	0.0	.		79.0	28.0	.	NM_001143939	Q76KX9	Missense_Mutation	SNP	ENST00000332323.6	hg19	CCDS46165.1	.	.	.	.	.	.	.	.	.	.	C	16.58	3.162751	0.57368	.	.	ENSG00000198633	ENST00000332323;ENST00000433050;ENST00000391790	T;T	0.16743	2.32;2.32	1.82	1.82	0.25136	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36580	0.0972	M	0.72576	2.205	0.80722	D	1	D;D	0.89917	1.0;0.977	D;P	0.73380	0.98;0.724	T	0.22977	-1.0201	9	0.72032	D	0.01	.	10.6089	0.45410	0.0:1.0:0.0:0.0	.	325;338	Q76KX8-2;Q76KX8	.;ZN534_HUMAN	S	338;325;337	ENSP00000327538:P338S;ENSP00000391358:P325S	ENSP00000327538:P338S	P	+	1	0	ZNF534	57633498	0.017000	0.18338	0.171000	0.22900	0.041000	0.13682	2.724000	0.47285	0.983000	0.38602	0.467000	0.42956	CCT	.	.	.	none		0.408	ZNF534-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460877.1	NM_182512		T	52941686	C	T	52941686	3	4	14	1	0	0	0	0	1	0	0	0	17985	507	18	2	1026	2	ZNF534	19	52941686	Missense_Mutation	SNP	C	TCGA-2Z-A9JK-01A-11D-A42J-10	12420096	52941686	6187297	74	1017											
CEP250	11190	hgsc.bcm.edu	37	chr20	34091233	34091233	+	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	tcagaggacccggcagaccaAgatcctggaggaggacctgg	11	4	15	11	1	1	3	1	0	0	3	2	7	2	7	4	6	0	1	4	6	1	0			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr20:34091233A>T	ENST00000397527.1	+	30	5756	c.5036A>T	c.(5035-5037)aAg>aTg	p.K1679M	CEP250_ENST00000342580.4_Missense_Mutation_p.K1623M	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	1679	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)			CGGCAGACCAAGATCCTGGAG	0.572																																					p.K1679M		Atlas-SNP	.											.	CEP250	141	.	0			c.A5036T						PASS	.						108	116	113					20																	34091233		2203	4300	6503	SO:0001583	missense	11190	exon30			AGACCAAGATCCT	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.5036A>T	chr20.hg19:g.34091233A>T	ENSP00000380661:p.Lys1679Met	171.0	0.0	.		111.0	20.0	.	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	hg19	CCDS13255.1	.	.	.	.	.	.	.	.	.	.	A	13.90	2.374127	0.42105	.	.	ENSG00000126001	ENST00000397527;ENST00000342580;ENST00000422671	T;T;T	0.50813	2.82;2.81;0.73	4.51	3.38	0.38709	.	0.096996	0.45361	D	0.000370	T	0.50905	0.1643	L	0.29908	0.895	0.20307	N	0.999913	D	0.89917	1.0	D	0.75484	0.986	T	0.28332	-1.0047	10	0.72032	D	0.01	.	7.1017	0.25340	0.8007:0.0:0.1993:0.0	.	1679	Q9BV73	CP250_HUMAN	M	1679;1623;167	ENSP00000380661:K1679M;ENSP00000341541:K1623M;ENSP00000395992:K167M	ENSP00000341541:K1623M	K	+	2	0	CEP250	33554647	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	1.847000	0.39299	1.906000	0.55180	0.374000	0.22700	AAG	.	.	.	none		0.572	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		T	34091233	A	T	34091233	3	4	14	1	0	0	0	0	1	0	0	0	3254	72	3	5	5142	5	CEP250	20	34091233	Missense_Mutation	SNP	A	TCGA-2Z-A9JK-01A-11D-A42J-10		34091233	28934287	75	1018											
DIDO1	11083	hgsc.bcm.edu	37	chr20	61528138	61528138	+	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	cactcgatggggtagcggagAgccatggcctcttggggatg	7	8	17	9	2	1	1	0	0	1	1	2	4	1	2	2	6	2	1	2	6	1	2	rs545443252		TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr20:61528138A>T	ENST00000266070.4	-	7	2124	c.1799T>A	c.(1798-1800)cTc>cAc	p.L600H	DIDO1_ENST00000395343.1_Missense_Mutation_p.L600H|DIDO1_ENST00000395340.1_Missense_Mutation_p.L600H|DIDO1_ENST00000395335.2_Missense_Mutation_p.L600H	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	600					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)					GGTAGCGGAGAGCCATGGCCT	0.602																																					p.L600H	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.T1799A						PASS	.						68	70	69					20																	61528138		2203	4300	6503	SO:0001583	missense	11083	exon7			GCGGAGAGCCATG	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.1799T>A	chr20.hg19:g.61528138A>T	ENSP00000266070:p.Leu600His	120.0	0.0	.		82.0	15.0	.	NM_080797	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	hg19	CCDS33506.1	.	.	.	.	.	.	.	.	.	.	A	12.70	2.017626	0.35606	.	.	ENSG00000101191	ENST00000266070;ENST00000395343;ENST00000395340;ENST00000395335	T;T;T;T	0.13307	2.93;2.93;2.6;2.6	5.7	-0.659	0.11424	.	0.514056	0.13468	U	0.385637	T	0.11707	0.0285	M	0.62723	1.935	0.09310	N	1	B;B	0.23854	0.092;0.056	B;B	0.22880	0.042;0.019	T	0.29640	-1.0005	10	0.46703	T	0.11	-5.1348	2.052	0.03573	0.3424:0.145:0.3719:0.1407	.	600;600	Q9BTC0-1;Q9BTC0	.;DIDO1_HUMAN	H	600	ENSP00000266070:L600H;ENSP00000378752:L600H;ENSP00000378749:L600H;ENSP00000378744:L600H	ENSP00000266070:L600H	L	-	2	0	DIDO1	60998583	0.253000	0.23982	0.004000	0.12327	0.017000	0.09413	0.678000	0.25277	-0.398000	0.07679	-0.691000	0.03719	CTC	.	.	.	none		0.602	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		T	61528138	A	T	61528138	3	4	14	1	0	0	0	0	1	0	0	0	4524	304	11	5	4992	5	DIDO1	20	61528138	Missense_Mutation	SNP	A	TCGA-2Z-A9JK-01A-11D-A42J-10	27436905	61528138	1497382	76	1019											
PRIC285	85441	hgsc.bcm.edu	37	chr20	62191860	62191860	+	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	ccacctcctccaggttggccTtggagttctcattcccttcg	4	13	8	16	1	1	0	1	0	1	0	6	1	4	1	6	3	0	2	6	3	0	5			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr20:62191860T>A	ENST00000467148.1	-	16	7541	c.7472A>T	c.(7471-7473)aAg>aTg	p.K2491M	HELZ2_ENST00000427522.2_Missense_Mutation_p.K1922M	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2491	Interaction with THRAP3.				cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										CAGGTTGGCCTTGGAGTTCTC	0.632																																					p.K2491M		Atlas-SNP	.											.	.	.	.	0			c.A7472T						PASS	.						183	172	176					20																	62191860		2203	4300	6503	SO:0001583	missense	85441	exon17			TTGGCCTTGGAGT	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.7472A>T	chr20.hg19:g.62191860T>A	ENSP00000417401:p.Lys2491Met	49.0	0.0	.		28.0	7.0	.	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	hg19	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	T	17.59	3.426968	0.62733	.	.	ENSG00000130589	ENST00000427522;ENST00000467148	D;D	0.92446	-3.04;-3.04	4.12	1.67	0.24075	ATPase, AAA+ type, core (1);	0.371166	0.26804	N	0.022405	D	0.92743	0.7693	M	0.69823	2.125	0.35376	D	0.78947	P;D	0.52996	0.943;0.957	P;P	0.56648	0.803;0.734	D	0.92434	0.5956	10	0.66056	D	0.02	-29.268	6.5428	0.22390	0.0:0.5434:0.0:0.4566	.	2491;1922	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	M	1922;2491	ENSP00000393257:K1922M;ENSP00000417401:K2491M	ENSP00000393257:K1922M	K	-	2	0	RP4-697K14.7	61662304	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	0.575000	0.23729	0.508000	0.28173	0.402000	0.26972	AAG	.	.	.	none		0.632	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		A	62191860	T	A	62191860	3	1	14	1	0	0	0	0	1	0	0	0	12495	1609	56	5	493	5	PRIC285	20	62191860	Missense_Mutation	SNP	T	TCGA-2Z-A9JK-01A-11D-A42J-10	663722	62191860	833660	77	1020											
PRIC285	85441	hgsc.bcm.edu	37	chr20	62202151	62202151	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctccacagcctgcgtgcgccGgacccactcctgcagctcct	5	7	9	20	3	0	0	0	0	0	0	3	1	3	1	6	1	5	2	6	1	0	0			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr20:62202151G>A	ENST00000467148.1	-	2	418	c.349C>T	c.(349-351)Cgg>Tgg	p.R117W	HELZ2_ENST00000427522.2_5'Flank|HELZ2_ENST00000479540.1_5'UTR	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	117					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)										TGCGTGCGCCGGACCCACTCC	0.697																																					p.R117W		Atlas-SNP	.											.	.	.	.	0			c.C349T						PASS	.						20	19	20					20																	62202151		2197	4293	6490	SO:0001583	missense	85441	exon3			TGCGCCGGACCCA	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.349C>T	chr20.hg19:g.62202151G>A	ENSP00000417401:p.Arg117Trp	162.0	0.0	.		101.0	20.0	.	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	hg19	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	G	9.347	1.064605	0.20067	.	.	ENSG00000130589	ENST00000467148	T	0.02682	4.2	4.57	0.183	0.15082	.	0.900092	0.09600	N	0.780350	T	0.02304	0.0071	N	0.22421	0.69	0.09310	N	1	B;B	0.20052	0.041;0.002	B;B	0.10450	0.005;0.001	T	0.45293	-0.9271	10	0.72032	D	0.01	-17.7927	5.2244	0.15385	0.245:0.2695:0.4855:0.0	.	117;117	Q4VXQ0;Q9BYK8	.;PR285_HUMAN	W	117	ENSP00000417401:R117W	ENSP00000417401:R117W	R	-	1	2	RP4-697K14.7	61672595	0.012000	0.17670	0.000000	0.03702	0.001000	0.01503	1.831000	0.39141	0.087000	0.17167	-0.125000	0.14975	CGG	.	.	.	none		0.697	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		A	62202151	G	A	62202151	3	1	14	1	0	0	0	0	1	0	0	0	12495	1115	39	1	7695	1	PRIC285	20	62202151	Missense_Mutation	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10	10291	62202151	823369	78	1021											
YWHAH	7533	hgsc.bcm.edu	37	chr22	32352566	32352566	+	Silent	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	cccatccggctgggcctggcCctcaacttctccgtgttcta	4	11	9	17	2	3	0	1	0	2	0	5	0	4	0	5	3	1	2	5	3	2	3			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr22:32352566C>T	ENST00000248975.5	+	2	801	c.528C>T	c.(526-528)gcC>gcT	p.A176A	YWHAH_ENST00000397492.1_3'UTR|YWHAH_ENST00000471374.1_3'UTR	NM_003405.3	NP_003396.1	Q04917	1433F_HUMAN	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta	176					apoptotic process (GO:0006915)|glucocorticoid catabolic process (GO:0006713)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular protein transport (GO:0006886)|intrinsic apoptotic signaling pathway (GO:0097193)|membrane depolarization during action potential (GO:0086010)|membrane organization (GO:0061024)|negative regulation of dendrite morphogenesis (GO:0050774)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of sodium ion transport (GO:0002028)|regulation of synaptic plasticity (GO:0048167)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|glucocorticoid receptor binding (GO:0035259)|insulin-like growth factor receptor binding (GO:0005159)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|sodium channel regulator activity (GO:0017080)			breast(1)|central_nervous_system(1)|large_intestine(1)|upper_aerodigestive_tract(1)	4						TGGGCCTGGCCCTCAACTTCT	0.522																																					p.A176A	Ovarian(98;460 2060 9263 44007)	Atlas-SNP	.											.	YWHAH	14	.	0			c.C528T						PASS	.						73	63	66					22																	32352566		2203	4300	6503	SO:0001819	synonymous_variant	7533	exon2			CCTGGCCCTCAAC	X78138	CCDS13901.1	22q12.1-q13.1	2013-12-03	2013-12-03		ENSG00000128245	ENSG00000128245			12853	protein-coding gene	gene with protein product	"14-3-3 eta"	113508	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide"	YWHA1			Standard	NM_003405		Approved		uc003alz.3	Q04917	OTTHUMG00000030833	ENST00000248975.5:c.528C>T	chr22.hg19:g.32352566C>T		90.0	0.0	.		61.0	18.0	.	NM_003405		Silent	SNP	ENST00000248975.5	hg19	CCDS13901.1																																																																																			.	.	.	none		0.522	YWHAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075721.2	NM_003405		T	32352566	C	T	32352566	2	4	14	1	0	0	0	0	0	0	0	1	17516	610	22	2		2	YWHAH	22	32352566	Silent	SNP	C	TCGA-2Z-A9JK-01A-11D-A42J-10		32352566	18952000	79	1022											
DDX17	10521	hgsc.bcm.edu	37	chr22	38897263	38897263	+	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	aaatttcttcgggggaaggcCaccaccacctcttgctccaa	10	9	8	14	1	2	0	0	0	2	0	4	1	3	1	5	3	1	1	5	3	3	3			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr22:38897263C>A	ENST00000396821.3	-	2	409	c.310G>T	c.(310-312)Ggc>Tgc	p.G104C	DDX17_ENST00000432525.1_5'UTR|DDX17_ENST00000381633.3_Missense_Mutation_p.G25C	NM_001098504.1|NM_006386.4	NP_001091974|NP_006377.2	Q92841	DDX17_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 17	104	Poly-Gly.				ATP catabolic process (GO:0006200)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of skeletal muscle cell differentiation (GO:2001014)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA helicase activity (GO:0003724)|RNA-dependent ATPase activity (GO:0008186)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(6)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	25	Melanoma(58;0.0286)					GGGGGAAGGCCACCACCACCT	0.388																																					p.G104C	Ovarian(55;1085 1454 6392 21425)	Atlas-SNP	.											.	DDX17	73	.	0			c.G310T						PASS	.						72	73	73					22																	38897263		2203	4300	6503	SO:0001583	missense	10521	exon2			GAAGGCCACCACC	U59321	CCDS33646.1, CCDS46706.1	22q13.1	2012-02-23	2012-02-23		ENSG00000100201	ENSG00000100201		"DEAD-boxes"	2740	protein-coding gene	gene with protein product		608469	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 17 (72kD)", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 17"			8871553, 17226766	Standard	NM_006386		Approved	P72	uc003avy.4	Q92841	OTTHUMG00000151136	ENST00000396821.3:c.310G>T	chr22.hg19:g.38897263C>A	ENSP00000380033:p.Gly104Cys	85.0	0.0	.		108.0	28.0	.	NM_006386	B1AHM0|Q69YT1|Q6ICD6	Missense_Mutation	SNP	ENST00000396821.3	hg19	CCDS46706.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.476078	0.84640	.	.	ENSG00000100201	ENST00000396821;ENST00000381633;ENST00000403230;ENST00000404499	T;T;T	0.31510	1.49;1.49;1.49	5.58	5.58	0.84498	.	0.187005	0.56097	D	0.000023	T	0.37732	0.1014	N	0.19112	0.55	0.80722	D	1	P;D;D	0.65815	0.938;0.992;0.995	B;P;P	0.60473	0.282;0.754;0.875	T	0.18429	-1.0337	10	0.56958	D	0.05	-11.3755	15.4155	0.74962	0.0:0.8215:0.1785:0.0	.	25;106;104	Q92841;Q59F66;Q92841-4	DDX17_HUMAN;.;.	C	104;25;104;106	ENSP00000380033:G104C;ENSP00000371046:G25C;ENSP00000385536:G104C	ENSP00000371046:G25C	G	-	1	0	DDX17	37227209	0.996000	0.38824	1.000000	0.80357	0.985000	0.73830	3.659000	0.54489	2.625000	0.88918	0.591000	0.81541	GGC	.	.	.	none		0.388	DDX17-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321476.2	NM_030881		A	38897263	C	A	38897263	3	1	14	1	0	0	0	0	1	0	0	0	4346	594	21	4	1933	4	DDX17	22	38897263	Missense_Mutation	SNP	C	TCGA-2Z-A9JK-01A-11D-A42J-10	6544697	38897263	12407303	80	1023											
LDOC1L	84247	hgsc.bcm.edu	37	chr22	44892956	44892956	+	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	ctgatagttgttgcgcaaggGgctgtcaggttgcatgtggg	6	12	17	6	1	1	1	1	1	0	0	1	1	1	1	0	4	2	6	0	4	2	4			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chr22:44892956G>C	ENST00000341255.3	-	2	990	c.481C>G	c.(481-483)Ccc>Gcc	p.P161A		NM_032287.2	NP_115663.2	Q6ICC9	LDOCL_HUMAN	leucine zipper, down-regulated in cancer 1-like	161										breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(3)|prostate(2)	11		Ovarian(80;0.024)|all_neural(38;0.0416)		LUAD - Lung adenocarcinoma(64;0.0161)		TTGCGCAAGGGGCTGTCAGGT	0.627																																					p.P161A		Atlas-SNP	.											.	LDOC1L	24	.	0			c.C481G						PASS	.						44	45	44					22																	44892956		2203	4300	6503	SO:0001583	missense	84247	exon2			GCAAGGGGCTGTC	CR456439	CCDS33662.1	22q13.3	2006-09-06			ENSG00000188636	ENSG00000188636			13343	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_032287		Approved	dJ1033E15.2, DKFZp761O17121, Mart6, Mar6	uc003beu.1	Q6ICC9	OTTHUMG00000150465	ENST00000341255.3:c.481C>G	chr22.hg19:g.44892956G>C	ENSP00000340434:p.Pro161Ala	114.0	0.0	.		63.0	17.0	.	NM_032287	Q6ZTR1	Missense_Mutation	SNP	ENST00000341255.3	hg19	CCDS33662.1	.	.	.	.	.	.	.	.	.	.	G	18.49	3.636050	0.67130	.	.	ENSG00000188636	ENST00000341255	T	0.20598	2.06	3.1	3.1	0.35709	.	0.000000	0.46442	D	0.000284	T	0.26629	0.0651	L	0.39898	1.24	0.31559	N	0.657769	D	0.53151	0.958	P	0.54759	0.76	T	0.11690	-1.0577	10	0.54805	T	0.06	-18.0316	9.9334	0.41537	0.0:0.0:1.0:0.0	.	161	Q6ICC9	LDOCL_HUMAN	A	161	ENSP00000340434:P161A	ENSP00000340434:P161A	P	-	1	0	LDOC1L	43271620	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.858000	0.55979	2.054000	0.61138	0.591000	0.81541	CCC	.	.	.	none		0.627	LDOC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318222.1	NM_032287		C	44892956	G	C	44892956	3	2	14	1	0	0	0	0	1	0	0	0	8717	1232	43	4	242	4	LDOC1L	22	44892956	Missense_Mutation	SNP	G	TCGA-2Z-A9JK-01A-11D-A42J-10	5995693	44892956	6411610	81	1024											
KLHL15	80311	hgsc.bcm.edu	37	chrX	24006241	24006241	+	Frame_Shift_Del	DEL	T	T	-																															tatttgtttgtccagcacagTcacaccatggccacttctac																										TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chrX:24006241delT	ENST00000328046.8	-	4	1867	c.1612delA	c.(1612-1614)actfs	p.T538fs		NM_030624.2	NP_085127.2	Q96M94	KLH15_HUMAN	kelch-like family member 15	538					protein ubiquitination (GO:0016567)					autonomic_ganglia(1)|breast(1)|endometrium(8)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	22						TCCAGCACAGTCACACCATGG	0.458																																					p.T538fs		Atlas-Indel,Pindel	.											.	KLHL15	50	.	0			c.1613delC						PASS	.						210	179	190					X																	24006241		2203	4300	6503	SO:0001589	frameshift_variant	80311	exon4			.	AB051464	CCDS35217.1	Xp22.1-p21	2013-01-30	2013-01-30		ENSG00000174010	ENSG00000174010		"Kelch-like", "BTB/POZ domain containing"	29347	protein-coding gene	gene with protein product			"kelch-like 15 (Drosophila)"			11214970, 14702039	Standard	NM_030624		Approved	KIAA1677	uc004dba.4	Q96M94	OTTHUMG00000021261	ENST00000328046.8:c.1612delA	chrX.hg19:g.24006241delT	ENSP00000332791:p.Thr538fs	117.0	0.0	0		137.0	65.0	0.474453	NM_030624	Q32MN3|Q8NDA3|Q96BM6|Q9C0I6	Frame_Shift_Del	DEL	ENST00000328046.8	hg19	CCDS35217.1																																																																																			.	.	.	none		0.458	KLHL15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056078.1	XM_040383		-	24006241	T	-	24006241	7	5	14	1	0	1	0	1	0	0	0	0	8378	1667	58	0	206	0	KLHL15	23	24006241	Frame_Shift_Del	DEL	T	TCGA-2Z-A9JK-01A-11D-A42J-10		24006241	131264319	82	1025											
TAF7L	54457	hgsc.bcm.edu	37	chrX	100533091	100533091	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctctttacttcattttccaCgtctggagattcaatgtact	8	18	5	10	1	4	1	2	0	2	1	6	2	5	1	1	1	2	1	1	1	3	7			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chrX:100533091C>T	ENST00000372907.3	-	8	792	c.781G>A	c.(781-783)Gtg>Atg	p.V261M	TAF7L_ENST00000324762.6_Missense_Mutation_p.V175M|TAF7L_ENST00000372905.2_Missense_Mutation_p.V175M|TAF7L_ENST00000356784.1_Missense_Mutation_p.V175M	NM_024885.3	NP_079161.3	Q5H9L4	TAF7L_HUMAN	TAF7-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 50kDa	261					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						TCATTTTCCACGTCTGGAGAT	0.448																																					p.V261M	Ovarian(104;431 1530 3210 15406 18594)	Atlas-SNP	.											.	TAF7L	64	.	0			c.G781A						PASS	.						108	94	98					X																	100533091		2203	4300	6503	SO:0001583	missense	54457	exon8			TTTCCACGTCTGG	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.781G>A	chrX.hg19:g.100533091C>T	ENSP00000361998:p.Val261Met	32.0	0.0	.		26.0	6.0	.	NM_024885	Q5H9L6|Q86XI4|Q9BXU5|Q9H5R0	Missense_Mutation	SNP	ENST00000372907.3	hg19	CCDS35347.1	.	.	.	.	.	.	.	.	.	.	C	16.01	3.001964	0.54254	.	.	ENSG00000102387	ENST00000372907;ENST00000372905;ENST00000324762;ENST00000356784	T;T;T;T	0.29917	3.63;1.55;1.55;3.03	5.08	4.21	0.49690	TAFII55 protein, conserved region (1);Armadillo-like helical (1);	0.597438	0.13950	N	0.351626	T	0.64305	0.2586	M	0.91249	3.19	0.42809	D	0.993953	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.992	T	0.70536	-0.4845	10	0.87932	D	0	-4.719	14.2598	0.66078	0.1501:0.8499:0.0:0.0	.	261;175	Q5H9L4;Q5H9L4-3	TAF7L_HUMAN;.	M	261;175;175;175	ENSP00000361998:V261M;ENSP00000361996:V175M;ENSP00000320283:V175M;ENSP00000349235:V175M	ENSP00000320283:V175M	V	-	1	0	TAF7L	100419747	1.000000	0.71417	0.971000	0.41717	0.421000	0.31385	5.391000	0.66266	1.000000	0.39049	0.600000	0.82982	GTG	.	.	.	none		0.448	TAF7L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057526.2			T	100533091	C	T	100533091	3	4	14	1	0	0	0	0	1	0	0	0	15545	536	19	1	631	1	TAF7L	23	100533091	Missense_Mutation	SNP	C	TCGA-2Z-A9JK-01A-11D-A42J-10	76526850	100533091	54737469	83	1026											
GLRA4	441509	hgsc.bcm.edu	37	chrX	102979831	102979831	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgaagatttcttacctttaAaattgggccgaatcctggca	12	13	8	8	1	1	2	0	1	1	1	2	3	2	2	3	2	1	1	3	2	5	5			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chrX:102979831A>G	ENST00000372617.4	-	2	617	c.197T>C	c.(196-198)tTt>tCt	p.F66S	GLRA4_ENST00000469567.1_5'Flank	NM_001024452.2	NP_001019623.2	Q5JXX5	GLRA4_HUMAN	glycine receptor, alpha 4	66						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						CTTACCTTTAAAATTGGGCCG	0.498																																					p.F66S		Atlas-SNP	.											.	GLRA4	86	.	0			c.T197C						PASS	.						67	66	66					X																	102979831		1924	4150	6074	SO:0001583	missense	441509	exon2			CCTTTAAAATTGG	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.197T>C	chrX.hg19:g.102979831A>G	ENSP00000361700:p.Phe66Ser	53.0	0.0	.		46.0	23.0	.	NM_001024452		Missense_Mutation	SNP	ENST00000372617.4	hg19	CCDS43980.2	.	.	.	.	.	.	.	.	.	.	A	18.89	3.718769	0.68844	.	.	ENSG00000188828	ENST00000372617	T	0.78246	-1.16	5.79	5.79	0.91817	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	T	0.81612	0.4859	M	0.68952	2.095	0.58432	D	0.999995	B;P	0.36712	0.389;0.566	P;B	0.46208	0.507;0.378	T	0.83188	-0.0085	10	0.87932	D	0	.	12.8792	0.58008	1.0:0.0:0.0:0.0	.	66;25	Q5JXX5;B9WSA6	GLRA4_HUMAN;.	S	66	ENSP00000361700:F66S	ENSP00000361700:F66S	F	-	2	0	GLRA4	102866487	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	9.339000	0.96797	1.949000	0.56562	0.430000	0.28490	TTT	.	.	.	none		0.498	GLRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057742.2	NM_001024452		G	102979831	A	G	102979831	3	3	14	1	0	0	0	0	1	0	0	0	6464	14	1	3	1183	3	GLRA4	23	102979831	Missense_Mutation	SNP	A	TCGA-2Z-A9JK-01A-11D-A42J-10	2446740	102979831	52290729	84	1027											
BCORL1	63035	hgsc.bcm.edu	37	chrX	129189870	129189870	+	Missense_Mutation	SNP	T	T	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	ttccgatgtcttgaagaggcTgaagctttcctcgaggatct	8	13	11	9	2	2	3	0	2	2	1	5	6	4	4	2	2	1	2	2	2	2	3			TCGA-2Z-A9JK-01A-11D-A42J-10	TCGA-2Z-A9JK-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3603eaf-6e76-43f5-b87f-ab5d8e0f825f	8d7349a0-4f31-4374-9461-c37dd99f05ed	g.chrX:129189870T>G	ENST00000218147.7	+	13	5092	c.4895T>G	c.(4894-4896)cTg>cGg	p.L1632R	BCORL1_ENST00000540052.1_Missense_Mutation_p.L1632R|BCORL1_ENST00000359304.2_Missense_Mutation_p.L1502R|BCORL1_ENST00000303743.5_Missense_Mutation_p.L1706R			Q5H9F3	BCORL_HUMAN	BCL6 corepressor-like 1	1632					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|liver(3)|lung(30)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	75						TTGAAGAGGCTGAAGCTTTCC	0.572																																					p.L1632R		Atlas-SNP	.											.	BCORL1	213	.	0			c.T4895G						PASS	.						138	132	134					X																	129189870		2203	4300	6503	SO:0001583	missense	63035	exon12			AGAGGCTGAAGCT	AL136450	CCDS14616.1	Xq25-q26.1	2014-09-17	2010-06-10		ENSG00000085185	ENSG00000085185		"Ankyrin repeat domain containing"	25657	protein-coding gene	gene with protein product		300688	"chromosome X open reading frame 10", "BCL6 co-repressor-like 1"	CXorf10			Standard	NM_021946		Approved	FLJ11362	uc022cdu.1	Q5H9F3	OTTHUMG00000022379	ENST00000218147.7:c.4895T>G	chrX.hg19:g.129189870T>G	ENSP00000218147:p.Leu1632Arg	70.0	0.0	.		52.0	28.0	.	NM_021946	B5MDQ8|Q5H9F2|Q5H9F4|Q6ZVE0|Q8TEN3|Q9Y528	Missense_Mutation	SNP	ENST00000218147.7	hg19	CCDS14616.1	.	.	.	.	.	.	.	.	.	.	T	17.38	3.374672	0.61735	.	.	ENSG00000085185	ENST00000218147;ENST00000303743;ENST00000359304;ENST00000540052;ENST00000456822	T;T;T;T;T	0.55052	0.66;0.54;0.68;0.66;0.59	4.6	4.6	0.57074	.	0.000000	0.28166	N	0.016356	T	0.68686	0.3028	M	0.71036	2.16	0.53688	D	0.999976	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.997	T	0.71738	-0.4502	10	0.87932	D	0	-9.3763	9.9728	0.41765	0.1531:0.0:0.0:0.8469	.	1706;1632	Q5H9F3-3;Q5H9F3	.;BCORL_HUMAN	R	1632;1706;1502;1632;1306	ENSP00000218147:L1632R;ENSP00000307541:L1706R;ENSP00000352253:L1502R;ENSP00000437775:L1632R;ENSP00000399483:L1306R	ENSP00000218147:L1632R	L	+	2	0	BCORL1	129017551	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.720000	0.68470	1.704000	0.51252	0.417000	0.27973	CTG	.	.	.	none		0.572	BCORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058223.1	NM_021946		G	129189870	T	G	129189870	3	3	14	1	0	0	0	0	1	0	0	0	1387	1580	55	5	5167	5	BCORL1	23	129189870	Missense_Mutation	SNP	T	TCGA-2Z-A9JK-01A-11D-A42J-10	26210039	129189870	26080690	85	1028											
ZBTB48	3104	hgsc.bcm.edu	37	chr1	6640799	6640799	+	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	ttaaggcacactggagtgtcCttgcctgctgcagtcacttt	7	13	10	11	0	1	0	1	0	0	0	2	1	2	1	2	2	3	3	2	2	1	3			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr1:6640799C>T	ENST00000377674.4	+	2	288	c.130C>T	c.(130-132)Ctt>Ttt	p.L44F		NM_001278647.1|NM_001278648.1|NM_005341.2	NP_001265576.1|NP_001265577.1|NP_005332.1	P10074	ZBT48_HUMAN	zinc finger and BTB domain containing 48	44	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	11	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.35e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00109)|STAD - Stomach adenocarcinoma(132;0.017)|READ - Rectum adenocarcinoma(331;0.0642)		CTGGAGTGTCCTTGCCTGCTG	0.602																																					p.L44F	Esophageal Squamous(125;1449 1657 4031 29866 49542)	Atlas-SNP	.											.	ZBTB48	33	.	0			c.C130T						PASS	.						110	102	105					1																	6640799		2203	4300	6503	SO:0001583	missense	3104	exon2			AGTGTCCTTGCCT	BC013573	CCDS84.1	1p36.3	2013-01-08	2006-09-20	2006-09-20	ENSG00000204859	ENSG00000204859		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	4930	protein-coding gene	gene with protein product		165270	"GLI-Kruppel family member HKR3"	HKR3		2850480, 8661141	Standard	NM_001278647		Approved	ZNF855	uc001anx.3	P10074	OTTHUMG00000001438	ENST00000377674.4:c.130C>T	chr1.hg19:g.6640799C>T	ENSP00000366902:p.Leu44Phe	143.0	0.0	.		131.0	59.0	.	NM_005341	Q5SY19	Missense_Mutation	SNP	ENST00000377674.4	hg19	CCDS84.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.035982	0.75617	.	.	ENSG00000204859	ENST00000319084;ENST00000435905;ENST00000377674	T;T;T	0.64991	-0.13;-0.13;-0.13	5.72	2.83	0.33086	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.065722	0.64402	D	0.000011	D	0.83613	0.5292	H	0.98466	4.24	0.58432	D	0.999995	D	0.89917	1.0	D	0.71870	0.975	T	0.81543	-0.0885	10	0.87932	D	0	-16.7317	5.8832	0.18866	0.0:0.636:0.1391:0.2249	.	44	P10074	ZBT48_HUMAN	F	44	ENSP00000313416:L44F;ENSP00000416054:L44F;ENSP00000366902:L44F	ENSP00000313416:L44F	L	+	1	0	ZBTB48	6563386	0.985000	0.35326	0.031000	0.17742	0.925000	0.55904	3.095000	0.50235	0.338000	0.23692	-0.176000	0.13171	CTT	.	.	.	none		0.602	ZBTB48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004193.1	NM_005341		T	6640799	C	T	6640799	3	4	15	1	0	0	0	0	1	0	0	0	17561	681	24	2	132	2	ZBTB48	1	6640799	Missense_Mutation	SNP	C	TCGA-2Z-A9JL-01A-11D-A42J-10		6640799	242609822	1	1029											
NIPAL3	57185	hgsc.bcm.edu	37	chr1	24782759	24782759	+	Missense_Mutation	SNP	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	tggcaaccgccgtctatcagGctgcgtgagttacaaatcct	9	10	10	12	3	2	1	1	1	1	0	3	1	3	1	3	2	3	3	3	2	4	2			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr1:24782759G>A	ENST00000374399.4	+	8	1137	c.769G>A	c.(769-771)Gct>Act	p.A257T	NIPAL3_ENST00000339255.2_Missense_Mutation_p.A257T|NIPAL3_ENST00000003912.3_Missense_Mutation_p.A175T	NM_020448.4	NP_065181.1	Q6P499	NPAL3_HUMAN	NIPA-like domain containing 3	257						integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|skin(1)	14						CGTCTATCAGGCTGCGTGAGT	0.552																																					p.A257T		Atlas-SNP	.											.	NIPAL3	36	.	0			c.G769A						PASS	.						400	354	370					1																	24782759		2203	4300	6503	SO:0001583	missense	57185	exon8			TATCAGGCTGCGT	BX640883	CCDS30631.1	1p36.12-p35.1	2009-03-24		2009-03-24	ENSG00000001461	ENSG00000001461			25233	protein-coding gene	gene with protein product				NPAL3		8619474, 9110174	Standard	NM_020448		Approved	DJ462O23.2	uc001bjh.3	Q6P499	OTTHUMG00000003299	ENST00000374399.4:c.769G>A	chr1.hg19:g.24782759G>A	ENSP00000363520:p.Ala257Thr	56.0	0.0	.		45.0	18.0	.	NM_020448	A2A298|Q6MZT9|Q9BVE6	Missense_Mutation	SNP	ENST00000374399.4	hg19	CCDS30631.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.7|23.7	4.445577|4.445577	0.84101|0.84101	.|.	.|.	ENSG00000001461|ENSG00000001461	ENST00000374399;ENST00000003912;ENST00000339255|ENST00000432012	D;D;D|.	0.90004|.	-2.6;-2.6;-2.6|.	5.49|5.49	5.49|5.49	0.81192|0.81192	.|.	0.043600|.	0.85682|.	D|.	0.000000|.	T|T	0.74898|0.74898	0.3777|0.3777	M|M	0.68317|0.68317	2.08|2.08	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	0.999;1.0;1.0|.	D;D;D|.	0.91635|.	0.974;0.999;0.999|.	T|T	0.72669|0.72669	-0.4223|-0.4223	10|5	0.72032|.	D|.	0.01|.	-25.3634|-25.3634	18.717|18.717	0.91679|0.91679	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	35;257;257|.	Q7Z354;Q6P499;A6NN97|.	.;NPAL3_HUMAN;.|.	T|D	257;175;257|35	ENSP00000363520:A257T;ENSP00000003912:A175T;ENSP00000343549:A257T|.	ENSP00000003912:A175T|.	A|G	+|+	1|2	0|0	NIPAL3|NIPAL3	24655346|24655346	1.000000|1.000000	0.71417|0.71417	0.990000|0.990000	0.47175|0.47175	0.538000|0.538000	0.34931|0.34931	7.419000|7.419000	0.80179|0.80179	2.745000|2.745000	0.94114|0.94114	0.561000|0.561000	0.74099|0.74099	GCT|GGC	.	.	.	none		0.552	NIPAL3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276996.1	NM_020448		A	24782759	G	A	24782759	3	1	15	1	0	0	0	0	1	0	0	0	10433	1203	42	2	795	2	NIPAL3	1	24782759	Missense_Mutation	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10	18141960	24782759	224467862	2	1030											
MAN1C1	57134	hgsc.bcm.edu	37	chr1	26107539	26107539	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gccagaggtggtggagagctAcatgtacctgtggcgacaga	10	7	16	8	1	0	3	0	0	0	3	0	5	0	3	2	4	3	2	2	4	2	2			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr1:26107539A>G	ENST00000374332.4	+	10	1916	c.1586A>G	c.(1585-1587)tAc>tGc	p.Y529C	MAN1C1_ENST00000263979.3_Missense_Mutation_p.Y349C|MAN1C1_ENST00000374329.1_Missense_Mutation_p.Y300C	NM_020379.2	NP_065112.1	Q9NR34	MA1C1_HUMAN	mannosidase, alpha, class 1C, member 1	529					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)		GTGGAGAGCTACATGTACCTG	0.632																																					p.Y529C		Atlas-SNP	.											.	MAN1C1	48	.	0			c.A1586G						PASS	.						85	86	86					1																	26107539		2203	4300	6503	SO:0001583	missense	57134	exon10			AGAGCTACATGTA	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.1586A>G	chr1.hg19:g.26107539A>G	ENSP00000363452:p.Tyr529Cys	130.0	0.0	.		117.0	44.0	.	NM_020379	A6NNE2|B2RNP2|Q9Y545	Missense_Mutation	SNP	ENST00000374332.4	hg19	CCDS265.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.609272	0.87258	.	.	ENSG00000117643	ENST00000374332;ENST00000374331;ENST00000263979;ENST00000374329	T;T;T	0.72051	-0.62;-0.62;-0.62	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	D	0.86723	0.6001	M	0.89840	3.065	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.89675	0.3886	10	0.87932	D	0	.	15.1618	0.72791	1.0:0.0:0.0:0.0	.	529	Q9NR34	MA1C1_HUMAN	C	529;349;349;300	ENSP00000363452:Y529C;ENSP00000263979:Y349C;ENSP00000363449:Y300C	ENSP00000263979:Y349C	Y	+	2	0	MAN1C1	25980126	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.257000	0.78362	1.990000	0.58119	0.459000	0.35465	TAC	.	.	.	none		0.632	MAN1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012828.3	NM_020379		G	26107539	A	G	26107539	3	3	15	1	0	0	0	0	1	0	0	0	9220	391	14	3	1624	3	MAN1C1	1	26107539	Missense_Mutation	SNP	A	TCGA-2Z-A9JL-01A-11D-A42J-10	1324780	26107539	223143082	3	1031											
MED18	54797	hgsc.bcm.edu	37	chr1	28661029	28661029	+	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	ttgaccatgagatggtattcCtccttaagggccagcaagcc	10	10	10	11	0	0	2	0	2	0	1	2	3	2	2	5	2	2	2	5	2	3	4			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr1:28661029C>A	ENST00000373842.4	+	3	384	c.175C>A	c.(175-177)Ctc>Atc	p.L59I	MED18_ENST00000398997.2_Missense_Mutation_p.L59I|MED18_ENST00000479574.1_3'UTR	NM_001127350.1|NM_017638.2	NP_001120822.1|NP_060108.2	Q9BUE0	MED18_HUMAN	mediator complex subunit 18	59						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7		Colorectal(325;0.000147)|Lung NSC(340;0.000818)|all_lung(284;0.000996)|Renal(390;0.00357)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|all_neural(195;0.0557)|Ovarian(437;0.113)		OV - Ovarian serous cystadenocarcinoma(117;2.36e-22)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0141)|READ - Rectum adenocarcinoma(331;0.0649)		GATGGTATTCCTCCTTAAGGG	0.542																																					p.L59I		Atlas-SNP	.											.	MED18	30	.	0			c.C175A						PASS	.						201	198	199					1																	28661029		2203	4300	6503	SO:0001583	missense	54797	exon3			GTATTCCTCCTTA	BC002694	CCDS322.1	1p35.3	2007-07-30	2007-07-30		ENSG00000130772	ENSG00000130772			25944	protein-coding gene	gene with protein product		612384	"mediator of RNA polymerase II transcription, subunit 18 homolog (S. cerevisiae)"			15175163	Standard	NM_001127350		Approved	FLJ20045, p28b	uc009vtg.3	Q9BUE0	OTTHUMG00000003537	ENST00000373842.4:c.175C>A	chr1.hg19:g.28661029C>A	ENSP00000362948:p.Leu59Ile	64.0	0.0	.		70.0	22.0	.	NM_017638	D3DPM1|Q9NXU9	Missense_Mutation	SNP	ENST00000373842.4	hg19	CCDS322.1	.	.	.	.	.	.	.	.	.	.	C	14.36	2.511243	0.44660	.	.	ENSG00000130772	ENST00000373842;ENST00000398997	.	.	.	5.75	4.82	0.62117	Mediator complex, subunit Med18, metazoa/fungi (1);	0.122337	0.56097	N	0.000029	T	0.28433	0.0703	N	0.16478	0.41	0.25320	N	0.989127	B	0.11235	0.004	B	0.10450	0.005	T	0.13683	-1.0500	9	0.31617	T	0.26	-17.3861	13.8543	0.63517	0.1541:0.8459:0.0:0.0	.	59	Q9BUE0	MED18_HUMAN	I	59	.	ENSP00000362948:L59I	L	+	1	0	MED18	28533616	1.000000	0.71417	0.999000	0.59377	0.949000	0.60115	5.634000	0.67833	1.418000	0.47098	0.655000	0.94253	CTC	.	.	.	none		0.542	MED18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009856.1	NM_017638		A	28661029	C	A	28661029	3	1	15	1	0	0	0	0	1	0	0	0	9443	681	24	4	181	4	MED18	1	28661029	Missense_Mutation	SNP	C	TCGA-2Z-A9JL-01A-11D-A42J-10	2553490	28661029	220589592	4	1032											
MAGI3	260425	hgsc.bcm.edu	37	chr1	113933805	113933805	+	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	tacctggggcggctccgcgaGgagcccggcgggggcacctg	4	4	19	14	5	0	0	0	0	0	0	1	2	1	1	4	7	2	2	4	7	1	1			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr1:113933805G>C	ENST00000307546.9	+	1	225	c.150G>C	c.(148-150)gaG>gaC	p.E50D	MAGI3_ENST00000369617.4_Missense_Mutation_p.E50D|MAGI3_ENST00000369615.1_Missense_Mutation_p.E50D|MAGI3_ENST00000369611.4_Missense_Mutation_p.E50D|MAGI3_ENST00000486456.1_3'UTR	NM_001142782.1	NP_001136254.1	Q5TCQ9	MAGI3_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 3	50	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)		GGCTCCGCGAGGAGCCCGGCG	0.751																																					p.E50D		Atlas-SNP	.											.	MAGI3	181	.	0			c.G150C						PASS	.						6	8	7					1																	113933805		2042	4028	6070	SO:0001583	missense	260425	exon1			CCGCGAGGAGCCC	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.150G>C	chr1.hg19:g.113933805G>C	ENSP00000304604:p.Glu50Asp	105.0	0.0	.		89.0	33.0	.	NM_152900	Q5TCQ8|Q5TCR0|Q9H2V6|Q9H5Y8|Q9HBC4|Q9HCD8	Missense_Mutation	SNP	ENST00000307546.9	hg19	CCDS44196.1	.	.	.	.	.	.	.	.	.	.	G	13.93	2.383157	0.42207	.	.	ENSG00000081026	ENST00000369617;ENST00000307546;ENST00000369615;ENST00000369611	T;T;T;T	0.15603	2.54;2.41;2.55;2.55	3.94	0.539	0.17156	.	0.435271	0.20391	N	0.093244	T	0.04724	0.0128	L	0.42245	1.32	0.23784	N	0.996855	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.43442	-0.9391	10	0.17369	T	0.5	-0.2476	13.3417	0.60549	0.0:0.4771:0.5229:0.0	.	50;50;50	Q5TCQ9-4;Q5TCQ9-3;Q5TCQ9-2	.;.;.	D	50	ENSP00000358630:E50D;ENSP00000304604:E50D;ENSP00000358628:E50D;ENSP00000358624:E50D	ENSP00000304604:E50D	E	+	3	2	MAGI3	113735328	1.000000	0.71417	0.997000	0.53966	0.982000	0.71751	1.935000	0.40173	0.126000	0.18424	0.456000	0.33151	GAG	.	.	.	none		0.751	MAGI3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000032429.1	NM_152900		C	113933805	G	C	113933805	3	2	15	1	0	0	0	0	1	0	0	0	9199	991	35	4	152	4	MAGI3	1	113933805	Missense_Mutation	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10	85272776	113933805	135316816	5	1033											
VANGL1	81839	hgsc.bcm.edu	37	chr1	116228127	116228127	+	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	cagcacctggccttctgcatCaccaacggcatgacccccaa	10	6	7	18	1	2	1	1	1	1	0	2	1	2	1	5	2	3	3	5	2	2	1			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr1:116228127C>T	ENST00000355485.2	+	7	1564	c.1293C>T	c.(1291-1293)atC>atT	p.I431I	VANGL1_ENST00000369509.1_Silent_p.I431I|VANGL1_ENST00000310260.3_Silent_p.I431I|VANGL1_ENST00000369510.4_Silent_p.I429I	NM_001172411.1|NM_138959.2	NP_001165882.1|NP_620409.1	Q8TAA9	VANG1_HUMAN	VANGL planar cell polarity protein 1	431					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)		CCTTCTGCATCACCAACGGCA	0.607																																					p.I431I		Atlas-SNP	.											.	VANGL1	65	.	0			c.C1293T						PASS	.						54	45	48					1																	116228127		2203	4300	6503	SO:0001819	synonymous_variant	81839	exon7			CTGCATCACCAAC	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.1293C>T	chr1.hg19:g.116228127C>T		126.0	0.0	.		103.0	32.0	.	NM_138959	Q5T1D3|Q5T1D4|Q86WG8|Q8N559	Silent	SNP	ENST00000355485.2	hg19	CCDS883.1																																																																																			.	.	.	none		0.607	VANGL1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033096.1			T	116228127	C	T	116228127	2	4	15	1	0	0	0	0	0	0	0	1	17131	816	29	2		2	VANGL1	1	116228127	Silent	SNP	C	TCGA-2Z-A9JL-01A-11D-A42J-10	2294322	116228127	133022494	6	1034											
LOR	4014	hgsc.bcm.edu	37	chr1	153233991	153233991	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cggcggctctgtctgcggctActctggcggcggctctggct	1	10	16	14	5	4	0	0	0	4	0	4	0	4	0	0	7	2	4	0	7	1	1	rs11272549|rs561634896	byFrequency	TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr1:153233991A>G	ENST00000368742.3	+	2	623	c.566A>G	c.(565-567)tAc>tGc	p.Y189C		NM_000427.2	NP_000418.2	P23490	LORI_HUMAN	loricrin	189			Y -> YSGGG (in dbSNP:rs11275959). {ECO:0000269|PubMed:1355480, ECO:0000269|PubMed:2007607}.		keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein binding, bridging (GO:0030674)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			lung(2)	2	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			gtctgcggctactctggcggc	0.741																																					p.Y189C		Atlas-SNP	.											.	LOR	19	.	0			c.A566G						PASS	.						1	1	1					1																	153233991		409	1072	1481	SO:0001583	missense	4014	exon2			GCGGCTACTCTGG	M61120	CCDS30870.1	1q21	2008-02-05			ENSG00000203782	ENSG00000203782			6663	protein-coding gene	gene with protein product		152445				2007607, 1355480	Standard	NM_000427		Approved		uc001fbm.3	P23490	OTTHUMG00000013938	ENST00000368742.3:c.566A>G	chr1.hg19:g.153233991A>G	ENSP00000357731:p.Tyr189Cys	7.0	0.0	.		9.0	4.0	.	NM_000427	Q5T869|Q5XKF8	Missense_Mutation	SNP	ENST00000368742.3	hg19	CCDS30870.1	.	.	.	.	.	.	.	.	.	.	A	4.164	0.028992	0.08054	.	.	ENSG00000203782	ENST00000368742;ENST00000392652	T	0.38401	1.14	3.99	-7.07	0.01563	.	.	.	.	.	T	0.06462	0.0166	N	0.08118	0	0.09310	N	1	P	0.49447	0.924	B	0.43301	0.415	T	0.21895	-1.0232	9	0.87932	D	0	.	6.6851	0.23140	0.1469:0.4008:0.4523:0.0	.	189	P23490	LORI_HUMAN	C	189	ENSP00000357731:Y189C	ENSP00000357731:Y189C	Y	+	2	0	LOR	151500615	0.010000	0.17322	0.007000	0.13788	0.401000	0.30781	-0.173000	0.09854	-1.412000	0.02030	-0.817000	0.03123	TAC	.	.	.	none		0.741	LOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039107.1	NM_000427		G	153233991	A	G	153233991	3	3	15	1	0	0	0	0	1	0	0	0	8904	391	14	3	568	3	LOR	1	153233991	Missense_Mutation	SNP	A	TCGA-2Z-A9JL-01A-11D-A42J-10	37005864	153233991	96016630	7	1035											
MEF2D	4209	hgsc.bcm.edu	37	chr1	156444934	156444934	+	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	gtgggcatggaagagaagggGaggccctggctgagtaaact	11	6	18	6	0	0	2	0	1	0	1	0	5	0	4	1	6	1	3	1	6	4	1			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr1:156444934G>A	ENST00000348159.4	-	9	1452	c.972C>T	c.(970-972)ctC>ctT	p.L324L	MEF2D_ENST00000360595.3_Silent_p.L317L|MEF2D_ENST00000464356.2_Silent_p.L316L|MEF2D_ENST00000340875.5_Silent_p.L323L|MEF2D_ENST00000353795.3_Silent_p.L278L|MEF2D_ENST00000368240.2_Silent_p.L317L	NM_005920.2	NP_005911.1	Q14814	MEF2D_HUMAN	myocyte enhancer factor 2D	324					adult heart development (GO:0007512)|apoptotic process (GO:0006915)|chondrocyte differentiation (GO:0002062)|endochondral ossification (GO:0001958)|muscle organ development (GO:0007517)|nervous system development (GO:0007399)|osteoblast differentiation (GO:0001649)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|histone deacetylase binding (GO:0042826)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	15	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					AAGAGAAGGGGAGGCCCTGGC	0.562																																					p.L324L		Atlas-SNP	.											.	MEF2D	43	.	0			c.C972T						PASS	.						125	113	117					1																	156444934		2203	4300	6503	SO:0001819	synonymous_variant	4209	exon9			GAAGGGGAGGCCC	BC054520	CCDS1143.1, CCDS60304.1	1q12-q23	2008-02-05	2007-04-24		ENSG00000116604	ENSG00000116604		"Myocyte enhancer factors"	6997	protein-coding gene	gene with protein product		600663				8269842	Standard	NM_005920		Approved		uc001fpb.4	Q14814	OTTHUMG00000033095	ENST00000348159.4:c.972C>T	chr1.hg19:g.156444934G>A		91.0	0.0	.		73.0	30.0	.	NM_005920	D3DVC0|Q14815|Q5T9U5|Q5T9U6	Silent	SNP	ENST00000348159.4	hg19	CCDS1143.1																																																																																			.	.	.	none		0.562	MEF2D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080562.2	NM_005920		A	156444934	G	A	156444934	2	1	15	1	0	0	0	0	0	0	0	1	9465	1161	41	2		2	MEF2D	1	156444934	Silent	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10	3210943	156444934	92805687	8	1036											
IGSF8	93185	hgsc.bcm.edu	37	chr1	160063548	160063548	+	Missense_Mutation	SNP	T	T	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	gacggcccttttctctgcaaTctgggcccagctgccatcag	6	10	10	15	1	3	0	1	0	2	0	4	1	3	0	3	2	3	2	3	2	1	2			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr1:160063548T>G	ENST00000368086.1	-	3	1072	c.856A>C	c.(856-858)Att>Ctt	p.I286L	IGSF8_ENST00000314485.7_Missense_Mutation_p.I286L|IGSF8_ENST00000460351.1_5'Flank			Q969P0	IGSF8_HUMAN	immunoglobulin superfamily, member 8	286	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)			TTCTCTGCAATCTGGGCCCAG	0.607																																					p.I286L		Atlas-SNP	.											.	IGSF8	59	.	0			c.A856C						PASS	.						40	35	36					1																	160063548		2203	4300	6503	SO:0001583	missense	93185	exon3			CTGCAATCTGGGC	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.856A>C	chr1.hg19:g.160063548T>G	ENSP00000357065:p.Ile286Leu	50.0	0.0	.		46.0	16.0	.	NM_052868	Q8NG09|Q96DP4|Q9BTG9	Missense_Mutation	SNP	ENST00000368086.1	hg19	CCDS1195.1	.	.	.	.	.	.	.	.	.	.	T	14.66	2.603020	0.46423	.	.	ENSG00000162729	ENST00000314485;ENST00000368086;ENST00000358475;ENST00000448417	T;T;T	0.09817	3.4;3.4;2.94	3.64	2.5	0.30297	Immunoglobulin subtype (1);	0.369184	0.25747	N	0.028562	T	0.02119	0.0066	L	0.29908	0.895	0.34147	D	0.667062	B	0.28055	0.199	B	0.20577	0.03	T	0.46331	-0.9199	10	0.21540	T	0.41	-5.507	7.4263	0.27100	0.0:0.1134:0.0:0.8866	.	286	Q969P0	IGSF8_HUMAN	L	286	ENSP00000316664:I286L;ENSP00000357065:I286L;ENSP00000397464:I286L	ENSP00000316664:I286L	I	-	1	0	IGSF8	158330172	1.000000	0.71417	0.843000	0.33291	0.928000	0.56348	4.346000	0.59367	0.595000	0.29777	0.402000	0.26972	ATT	.	.	.	none		0.607	IGSF8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060636.1	NM_052868		G	160063548	T	G	160063548	3	3	15	1	0	0	0	0	1	0	0	0	7611	1435	50	5	1001	5	IGSF8	1	160063548	Missense_Mutation	SNP	T	TCGA-2Z-A9JL-01A-11D-A42J-10	3618614	160063548	89187073	9	1037											
UAP1	6675	hgsc.bcm.edu	37	chr1	162551113	162551113	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttatcgggcacttgcagcccAgaatattgtggaggatatgg	10	11	13	7	1	0	1	0	0	0	1	1	3	0	3	1	4	2	2	1	4	4	5			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr1:162551113A>G	ENST00000367925.1	+	4	730	c.698A>G	c.(697-699)cAg>cGg	p.Q233R	UAP1_ENST00000367926.4_Missense_Mutation_p.Q233R|UAP1_ENST00000367924.1_Missense_Mutation_p.Q233R|UAP1_ENST00000271469.3_Missense_Mutation_p.Q233R			Q16222	UAP1_HUMAN	UDP-N-acetylglucosamine pyrophosphorylase 1	233					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)			CTTGCAGCCCAGAATATTGTG	0.408																																					p.Q233R		Atlas-SNP	.											.	UAP1	47	.	0			c.A698G						PASS	.						221	224	223					1																	162551113		2203	4300	6503	SO:0001583	missense	6675	exon5			CAGCCCAGAATAT	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.698A>G	chr1.hg19:g.162551113A>G	ENSP00000356902:p.Gln233Arg	127.0	0.0	.		99.0	37.0	.	NM_003115	B2R6R8|Q5VTA9|Q5VTB0|Q5VTB1|Q96GM2	Missense_Mutation	SNP	ENST00000367925.1	hg19		.	.	.	.	.	.	.	.	.	.	A	11.45	1.642238	0.29157	.	.	ENSG00000117143	ENST00000367926;ENST00000271469;ENST00000367925;ENST00000367924	T;T;T;T	0.17054	2.3;2.3;2.3;2.3	5.14	4.01	0.46588	.	0.337918	0.35838	N	0.002956	T	0.03220	0.0094	N	0.16266	0.395	0.37520	D	0.917514	B	0.02656	0.0	B	0.04013	0.001	T	0.39663	-0.9603	9	0.18710	T	0.47	-3.3684	10.0169	0.42020	0.9193:0.0:0.0807:0.0	.	233	Q16222-2	.	R	233	ENSP00000356903:Q233R;ENSP00000271469:Q233R;ENSP00000356902:Q233R;ENSP00000356901:Q233R	ENSP00000271469:Q233R	Q	+	2	0	UAP1	160817737	0.998000	0.40836	0.995000	0.50966	0.996000	0.88848	5.904000	0.69886	0.902000	0.36520	0.482000	0.46254	CAG	.	.	.	none		0.408	UAP1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000083203.1	NM_003115		G	162551113	A	G	162551113	3	3	15	1	0	0	0	0	1	0	0	0	16837	188	7	3	712	3	UAP1	1	162551113	Missense_Mutation	SNP	A	TCGA-2Z-A9JL-01A-11D-A42J-10	2487565	162551113	86699508	10	1038											
RGL1	23179	hgsc.bcm.edu	37	chr1	183775571	183775571	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtttaccatgtcaccctcaaAagagtccagattcaacaggc	13	9	7	12	0	3	2	3	0	0	2	4	2	4	2	3	1	2	1	3	1	4	3			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr1:183775571A>G	ENST00000360851.3	+	2	268	c.90A>G	c.(88-90)aaA>aaG	p.K30K	RGL1_ENST00000536277.1_Intron|RGL1_ENST00000304685.4_Silent_p.K65K|RGL1_ENST00000539189.1_Silent_p.K30K			Q9NZL6	RGL1_HUMAN	ral guanine nucleotide dissociation stimulator-like 1	30					cellular lipid metabolic process (GO:0044255)|positive regulation of Ral GTPase activity (GO:0032852)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(5)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(17)|ovary(4)|prostate(3)|stomach(1)	51						TCACCCTCAAAAGAGTCCAGA	0.478																																					p.K65K		Atlas-SNP	.											.	RGL1	91	.	0			c.A195G						PASS	.						108	101	103					1																	183775571		2203	4300	6503	SO:0001819	synonymous_variant	23179	exon3			CCTCAAAAGAGTC	AF186780	CCDS1359.1, CCDS72992.1	1q25.2	2008-02-05			ENSG00000143344	ENSG00000143344			30281	protein-coding gene	gene with protein product		605667				10760592, 10231032	Standard	XM_005245010		Approved	RGL	uc001gqm.3	Q9NZL6	OTTHUMG00000035328	ENST00000360851.3:c.90A>G	chr1.hg19:g.183775571A>G		76.0	0.0	.		54.0	20.0	.	NM_015149	Q5SXQ2|Q5SXQ6|Q9HBY3|Q9HBY4|Q9NZL5|Q9UG43|Q9Y2G6	Silent	SNP	ENST00000360851.3	hg19																																																																																				.	.	.	none		0.478	RGL1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000085742.1	NM_015149		G	183775571	A	G	183775571	2	3	15	1	0	0	0	0	0	0	0	1	13289	11	1	3		3	RGL1	1	183775571	Silent	SNP	A	TCGA-2Z-A9JL-01A-11D-A42J-10	21224458	183775571	65475050	11	1039											
TPO	7173	hgsc.bcm.edu	37	chr2	1507790	1507790	+	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	aggtgcagaaacaccaaaggCggcttccagtgtctctgcgc	10	7	12	12	2	1	1	0	0	1	1	3	1	2	1	2	3	3	2	2	3	2	1	rs529772798		TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr2:1507790C>T	ENST00000345913.4	+	14	2548	c.2457C>T	c.(2455-2457)ggC>ggT	p.G819G	TPO_ENST00000497517.2_3'UTR|TPO_ENST00000349624.3_Silent_p.G646G|TPO_ENST00000382201.3_Silent_p.G762G|TPO_ENST00000329066.4_Silent_p.G819G|TPO_ENST00000382198.1_Silent_p.G646G|TPO_ENST00000337415.3_Silent_p.G819G|TPO_ENST00000346956.3_Intron	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	819	EGF-like; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				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)	ACACCAAAGGCGGCTTCCAGT	0.612													C|||	1	0.000199681	0	0	5008	,	,		15689	0		0	False		,,,				2504	0.001				p.G819G		Atlas-SNP	.											.	TPO	224	.	0			c.C2457T						PASS	.						80	77	78					2																	1507790		2203	4300	6503	SO:0001819	synonymous_variant	7173	exon14			CAAAGGCGGCTTC		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.2457C>T	chr2.hg19:g.1507790C>T		56.0	0.0	.		46.0	9.0	.	NM_001206744	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Silent	SNP	ENST00000345913.4	hg19	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	C	1.431	-0.570373	0.03910	.	.	ENSG00000115705	ENST00000446278	.	.	.	4.4	0.28	0.15682	.	.	.	.	.	T	0.51075	0.1653	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34104	-0.9842	4	.	.	.	-25.6411	5.437	0.16486	0.4042:0.4402:0.0:0.1556	.	.	.	.	V	294	.	.	A	+	2	0	TPO	1486797	0.097000	0.21791	0.962000	0.40283	0.072000	0.16883	-0.085000	0.11250	-0.290000	0.09025	-0.898000	0.02899	GCG	.	.	.	none		0.612	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		T	1507790	C	T	1507790	2	4	15	1	0	0	0	0	0	0	0	1	16422	755	27	1		1	TPO	2	1507790	Silent	SNP	C	TCGA-2Z-A9JL-01A-11D-A42J-10		1507790	241691583	12	1040											
ODC1	4953	hgsc.bcm.edu	37	chr2	10584694	10584694	+	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	ctgcataaaagggggtgacaCgagggagagcttttaaccac	13	7	13	8	1	0	2	0	1	0	1	0	4	0	2	1	3	3	2	1	3	3	3			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr2:10584694C>G	ENST00000234111.4	-	4	692	c.182G>C	c.(181-183)cGt>cCt	p.R61P	ODC1_ENST00000446285.1_Intron|ODC1_ENST00000405333.1_Missense_Mutation_p.R61P|SNORA80B_ENST00000383906.1_RNA	NM_002539.1	NP_002530.1	P11926	DCOR_HUMAN	ornithine decarboxylase 1	61					cellular nitrogen compound metabolic process (GO:0034641)|kidney development (GO:0001822)|polyamine metabolic process (GO:0006595)|positive regulation of cell proliferation (GO:0008284)|putrescine biosynthetic process from ornithine (GO:0033387)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|response to virus (GO:0009615)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ornithine decarboxylase activity (GO:0004586)|protein homodimerization activity (GO:0042803)			NS(1)|central_nervous_system(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(3)	19	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.161)	Spermine(DB00127)	GGGGGTGACACGAGGGAGAGC	0.473																																					p.R61P		Atlas-SNP	.											.	ODC1	40	.	0			c.G182C						PASS	.						100	96	98					2																	10584694		2203	4300	6503	SO:0001583	missense	4953	exon4			GTGACACGAGGGA		CCDS1672.1	2p25	2012-10-02			ENSG00000115758	ENSG00000115758	4.1.1.17		8109	protein-coding gene	gene with protein product		165640					Standard	NM_002539		Approved	ODC	uc002rao.1	P11926	OTTHUMG00000090450	ENST00000234111.4:c.182G>C	chr2.hg19:g.10584694C>G	ENSP00000234111:p.Arg61Pro	78.0	0.0	.		78.0	26.0	.	NM_002539	Q53TU3|Q6LDS9	Missense_Mutation	SNP	ENST00000234111.4	hg19	CCDS1672.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.427288	0.83667	.	.	ENSG00000115758	ENST00000234111;ENST00000405333;ENST00000443218	T;T	0.51817	0.69;0.69	5.37	4.46	0.54185	Orn/DAP/Arg decarboxylase 2, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.70378	0.3217	M	0.91920	3.255	0.80722	D	1	P	0.52170	0.951	P	0.56648	0.803	T	0.77988	-0.2380	10	0.56958	D	0.05	.	16.1391	0.81512	0.0:0.8669:0.1331:0.0	.	61	P11926	DCOR_HUMAN	P	61	ENSP00000234111:R61P;ENSP00000385333:R61P	ENSP00000234111:R61P	R	-	2	0	ODC1	10502145	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	4.865000	0.62998	2.508000	0.84585	0.655000	0.94253	CGT	.	.	.	none		0.473	ODC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206896.2			G	10584694	C	G	10584694	3	3	15	1	0	0	0	0	1	0	0	0	10832	536	19	4	1239	4	ODC1	2	10584694	Missense_Mutation	SNP	C	TCGA-2Z-A9JL-01A-11D-A42J-10	9076904	10584694	232614679	13	1041											
APOB	338	hgsc.bcm.edu	37	chr2	21266783	21266783	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcagcgcaggcagcgccAgcagcgccagcagcgcgggc	8	0	17	16	5	0	0	0	0	0	0	0	0	0	0	2	2	7	6	2	2	0	0	rs17240441	byFrequency	TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr2:21266783A>G	ENST00000233242.1	-	1	162	c.35T>C	c.(34-36)cTg>cCg	p.L12P	APOB_ENST00000399256.4_Missense_Mutation_p.L12P	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	12			Missing. {ECO:0000269|PubMed:22095935}.	Missing (in Ref. 5; AAB60718/CAA28420). {ECO:0000305}.	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)					aggcagcgccagcagcgccag	0.806																																					p.L12P		Atlas-SNP	.											.	APOB	761	.	0			c.T35C						PASS	.						1	1	1					2																	21266783		310	673	983	SO:0001583	missense	338	exon1			AGCGCCAGCAGCG	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.35T>C	chr2.hg19:g.21266783A>G	ENSP00000233242:p.Leu12Pro	30.0	0.0	.		19.0	4.0	.	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	A	9.939	1.216839	0.22373	.	.	ENSG00000084674	ENST00000233242;ENST00000535079;ENST00000399256	T;T	0.10763	5.13;2.84	2.53	-2.89	0.05665	.	2.226600	0.02990	N	0.146703	T	0.08714	0.0216	L	0.27053	0.805	0.09310	N	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.41324	-0.9515	10	0.66056	D	0.02	.	7.1381	0.25539	0.5833:0.0:0.4167:0.0	.	12	P04114	APOB_HUMAN	P	12	ENSP00000233242:L12P;ENSP00000382200:L12P	ENSP00000233242:L12P	L	-	2	0	APOB	21120288	0.325000	0.24660	0.003000	0.11579	0.001000	0.01503	-0.176000	0.09811	-0.683000	0.05190	-1.342000	0.01247	CTG	.	.	.	none		0.806	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			G	21266783	A	G	21266783	3	3	15	1	0	0	0	0	1	0	0	0	785	188	7	3	13772	3	APOB	2	21266783	Missense_Mutation	SNP	A	TCGA-2Z-A9JL-01A-11D-A42J-10	10682089	21266783	221932590	14	1042											
FKBP1B	2281	hgsc.bcm.edu	37	chr2	24283781	24283782	+	Frame_Shift_Del	DEL	AG	AG	-																															gaagtcatcaaaggttttgaAgagggtgcagcccaggtagg																								rs146963692		TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr2:24283781_24283782delAG	ENST00000380986.4	+	3	319_320	c.183_184delAG	c.(181-186)gaagagfs	p.EE61fs	FKBP1B_ENST00000380991.4_Frame_Shift_Del_p.EE61fs|FKBP1B_ENST00000452109.1_Frame_Shift_Del_p.EE32fs	NM_004116.3|NM_054033.2	NP_004107.1|NP_473374.1	P68106	FKB1B_HUMAN	FK506 binding protein 1B, 12.6 kDa	61	PPIase FKBP-type. {ECO:0000255|PROSITE- ProRule:PRU00277}.				'de novo' protein folding (GO:0006458)|calcium ion transmembrane transport (GO:0070588)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|chaperone-mediated protein folding (GO:0061077)|cytosolic calcium ion homeostasis (GO:0051480)|insulin secretion (GO:0030073)|negative regulation of heart rate (GO:0010459)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|neuronal action potential propagation (GO:0019227)|positive regulation of axon regeneration (GO:0048680)|positive regulation of sequestering of calcium ion (GO:0051284)|protein maturation by protein folding (GO:0022417)|protein peptidyl-prolyl isomerization (GO:0000413)|protein refolding (GO:0042026)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to glucose (GO:0009749)|response to hydrogen peroxide (GO:0042542)|response to redox state (GO:0051775)|response to vitamin E (GO:0033197)|smooth muscle contraction (GO:0006939)|T cell proliferation (GO:0042098)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	calcium channel inhibitor activity (GO:0019855)|cyclic nucleotide binding (GO:0030551)|FK506 binding (GO:0005528)|ion channel binding (GO:0044325)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|receptor binding (GO:0005102)			lung(2)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AAGGTTTTGAAGAGGGTGCAGC	0.49											OREG0014491	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.61_61del		Atlas-Indel,Pindel	.											.	FKBP1B	11	.	0			c.182_183del						PASS	.																																			SO:0001589	frameshift_variant	2281	exon3			.	D38037	CCDS1706.1, CCDS33153.1	2p23.3	2013-03-20	2002-08-29		ENSG00000119782	ENSG00000119782			3712	protein-coding gene	gene with protein product	"calstabin 2"	600620	"FK506-binding protein 1B (12.6 kD)"	FKBP1L		7513996	Standard	NM_004116		Approved	OTK4, FKBP12.6, PPIase, FKBP9	uc002rer.3	P68106	OTTHUMG00000151889	ENST00000380986.4:c.183_184delAG	chr2.hg19:g.24283783_24283784delAG	ENSP00000370373:p.Glu61fs	106.0	0.0	0	770	73.0	22.0	0.30137	NM_004116	Q13664|Q16645|Q53TM2|Q9BQ40	Frame_Shift_Del	DEL	ENST00000380986.4	hg19	CCDS1706.1																																																																																			.	.	.	none		0.49	FKBP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207622.1	NM_004116		-	24283782	AG	-	24283781	7	5	15	1	0	1	0	1	0	0	0	0	5914	69	3	0	193	0	FKBP1B	2	24283781	Frame_Shift_Del	DEL	AG	TCGA-2Z-A9JL-01A-11D-A42J-10	3016998	24283781	218915592	15	1043											
USP34	9736	hgsc.bcm.edu	37	chr2	61415653	61415653	+	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	gtattctttaacagaactatTttcaggggaaggaagatctt	13	14	9	5	0	3	2	1	0	2	2	3	4	3	4	0	3	2	1	0	3	6	8			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr2:61415653T>A	ENST00000398571.2	-	80	10301	c.10225A>T	c.(10225-10227)Aat>Tat	p.N3409Y	AHSA2_ENST00000394457.3_3'UTR	NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	3409					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)			ACAGAACTATTTTCAGGGGAA	0.443																																					p.N3409Y		Atlas-SNP	.											.	USP34	334	.	0			c.A10225T						PASS	.						103	96	98					2																	61415653		1910	4131	6041	SO:0001583	missense	9736	exon80			AACTATTTTCAGG	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.10225A>T	chr2.hg19:g.61415653T>A	ENSP00000381577:p.Asn3409Tyr	131.0	0.0	.		121.0	39.0	.	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	hg19	CCDS42686.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	15.19|15.19	2.760105|2.760105	0.49468|0.49468	.|.	.|.	ENSG00000115464|ENSG00000115464	ENST00000411912|ENST00000263989;ENST00000398569;ENST00000398571;ENST00000436269	.|T	.|0.03860	.|3.78	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	.|0.196719	.|0.53938	.|D	.|0.000049	T|T	0.05686|0.05686	0.0149|0.0149	N|N	0.24115|0.24115	0.695|0.695	0.40804|0.40804	D|D	0.98336|0.98336	.|P	.|0.42785	.|0.79	.|B	.|0.41723	.|0.365	T|T	0.42275|0.42275	-0.9461|-0.9461	5|10	.|0.59425	.|D	.|0.04	.|.	15.9357|15.9357	0.79704|0.79704	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|3409	.|Q70CQ2	.|UBP34_HUMAN	I|Y	1085|3257;3174;3409;287	.|ENSP00000381577:N3409Y	.|ENSP00000263989:N3257Y	K|N	-|-	2|1	0|0	USP34|USP34	61269157|61269157	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.873000|0.873000	0.50193|0.50193	5.146000|5.146000	0.64845|0.64845	2.218000|2.218000	0.71995|0.71995	0.482000|0.482000	0.46254|0.46254	AAA|AAT	.	.	.	none		0.443	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			A	61415653	T	A	61415653	3	1	15	1	0	0	0	0	1	0	0	0	17077	1841	64	5	419	5	USP34	2	61415653	Missense_Mutation	SNP	T	TCGA-2Z-A9JL-01A-11D-A42J-10	37131872	61415653	181783720	16	1044											
ALS2CR4	65062	hgsc.bcm.edu	37	chr2	202507331	202507331	+	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	1	0	0	0	0	0	0	0	0	0	aagtagctaaggctcgcttaCcacaggattcttccccattc	10	11	7	13	1	1	0	0	0	1	0	4	1	2	1	3	2	2	4	3	2	4	6			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr2:202507331C>G	ENST00000409883.2	-	1	159				TMEM237_ENST00000409444.2_Splice_Site	NM_001044385.2	NP_001037850.1	Q96Q45	TM237_HUMAN	transmembrane protein 237						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						GGCTCGCTTACCACAGGATTC	0.602																																					.		Atlas-SNP	.											.	TMEM237	21	.	0			c.18+1G>C						PASS	.						54	53	54					2																	202507331		1839	4091	5930	SO:0001627	intron_variant	65062	exon2			CGCTTACCACAGG	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.42+750G>C	chr2.hg19:g.202507331C>G		155.0	0.0	.		133.0	43.0	.	NM_152388	B4E1R8|B4E2R8|E9PAR8|E9PBF8|E9PG24|E9PGX0|Q53TS9|Q53TT2|Q7Z3B6|Q8IZ18|Q8NBF8|Q96CY1	Splice_Site	SNP	ENST00000409883.2	hg19	CCDS46489.1	.	.	.	.	.	.	.	.	.	.	C	9.997	1.232443	0.22626	.	.	ENSG00000155755	ENST00000409444;ENST00000426684	.	.	.	4.24	4.24	0.50183	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.3694	0.55246	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TMEM237	202215576	1.000000	0.71417	1.000000	0.80357	0.077000	0.17291	3.211000	0.51137	2.378000	0.81104	0.650000	0.86243	.	.	.	.	none		0.602	TMEM237-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335753.1	NM_152388		G	202507331	C	G	202507331	1	3	15	0	1	0	0	0	0	0	0	0	554	521	18	4		4	ALS2CR4	2	202507331	Intron	SNP	C	TCGA-2Z-A9JL-01A-11D-A42J-10	141091678	202507331	40692042	17	1045											
UGT1A5	54579	hgsc.bcm.edu	37	chr2	234621902	234621902	+	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	tttcatggacccaggacgaaTttgatcgccttttgctgggt	7	14	11	9	2	1	1	1	1	0	0	2	4	1	3	2	3	1	1	2	3	1	4			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr2:234621902T>A	ENST00000373414.3	+	1	265	c.265T>A	c.(265-267)Ttt>Att	p.F89I	UGT1A6_ENST00000406651.1_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A1_ENST00000608381.1_Missense_Mutation_p.F89I|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A10_ENST00000373445.1_Intron			P35504	UD15_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A5	89						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			cervix(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|urinary_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;4.51e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000523)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.00645)		CCAGGACGAATTTGATCGCCT	0.418																																					p.F89I		Atlas-SNP	.											.	UGT1A5	66	.	0			c.T265A						PASS	.						113	107	109					2																	234621902		2203	4300	6503	SO:0001583	missense	54579	exon1			GACGAATTTGATC	M84129	CCDS33404.1	2q37	2010-03-05	2005-07-20		ENSG00000240224	ENSG00000240224		"UDP glucuronosyltransferases"	12537	other	complex locus constituent		606430	"UDP glycosyltransferase 1 family, polypeptide A5"			9295054, 1339448	Standard	NM_019078		Approved	UGT1E		P35504	OTTHUMG00000059120	ENST00000373414.3:c.265T>A	chr2.hg19:g.234621902T>A	ENSP00000362513:p.Phe89Ile	106.0	0.0	.		75.0	35.0	.	NM_019078	B8K294	Missense_Mutation	SNP	ENST00000373414.3	hg19	CCDS33404.1	.	.	.	.	.	.	.	.	.	.	T	11.60	1.687353	0.29962	.	.	ENSG00000240224	ENST00000373414	T	0.64085	-0.08	4.72	3.54	0.40534	.	0.648102	0.15890	N	0.239620	T	0.53045	0.1772	L	0.41710	1.295	0.09310	N	1	B;B	0.32467	0.372;0.372	B;B	0.35727	0.209;0.209	T	0.42327	-0.9458	10	0.37606	T	0.19	.	9.8612	0.41116	0.3562:0.0:0.0:0.6438	.	89;89	Q5DSZ9;P35504	.;UD15_HUMAN	I	89	ENSP00000362513:F89I	ENSP00000362513:F89I	F	+	1	0	UGT1A5	234286641	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-4.003000	0.00316	0.661000	0.30985	-0.522000	0.04353	TTT	.	.	.	none		0.418	UGT1A5-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130985.1	NM_019078		A	234621902	T	A	234621902	3	1	15	1	0	0	0	0	1	0	0	0	16960	1493	52	5	267	5	UGT1A5	2	234621902	Missense_Mutation	SNP	T	TCGA-2Z-A9JL-01A-11D-A42J-10	32114571	234621902	8577471	18	1046											
TRAK1	22906	hgsc.bcm.edu	37	chr3	42240711	42240711	+	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	agggaacgatgcgcaaggagCtgcagttggaagaggccgag	12	4	18	7	3	0	1	0	0	0	1	0	6	0	4	1	4	4	4	1	4	3	1			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr3:42240711C>T	ENST00000327628.5	+	11	1556	c.1156C>T	c.(1156-1158)Ctg>Ttg	p.L386L	TRAK1_ENST00000341421.3_Silent_p.L328L|TRAK1_ENST00000449246.1_Silent_p.L312L|TRAK1_ENST00000396175.1_Silent_p.L328L|TRAK1_ENST00000487159.1_3'UTR	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	386	Interaction with HGS.				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						GCGCAAGGAGCTGCAGTTGGA	0.493																																					p.L386L	GBM(44;195 884 22595 31865 41850)	Atlas-SNP	.											.	TRAK1	188	.	0			c.C1156T						PASS	.						119	103	109					3																	42240711		2203	4300	6503	SO:0001819	synonymous_variant	22906	exon11			AAGGAGCTGCAGT		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.1156C>T	chr3.hg19:g.42240711C>T		124.0	0.0	.		85.0	36.0	.	NM_001265608	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Silent	SNP	ENST00000327628.5	hg19	CCDS43072.1																																																																																			.	.	.	none		0.493	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965		T	42240711	C	T	42240711	2	4	15	1	0	0	0	0	0	0	0	1	16461	796	28	2		2	TRAK1	3	42240711	Silent	SNP	C	TCGA-2Z-A9JL-01A-11D-A42J-10		42240711	155781719	19	1047											
SETD2	29072	hgsc.bcm.edu	37	chr3	47163553	47163553	+	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	taacagaagctgaactagtgCtaccgatgctctgcttatat	12	12	8	9	1	1	2	0	1	1	1	1	3	1	2	1	0	7	4	1	0	7	5			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr3:47163553C>G	ENST00000409792.3	-	3	2615	c.2573G>C	c.(2572-2574)aGc>aCc	p.S858T		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	858					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TGAACTAGTGCTACCGATGCT	0.353			"N, F, S, Mis"		clear cell renal carcinoma																																p.S858T		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.G2573C						PASS	.						61	64	63					3																	47163553		2203	4299	6502	SO:0001583	missense	29072	exon3			CTAGTGCTACCGA	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.2573G>C	chr3.hg19:g.47163553C>G	ENSP00000386759:p.Ser858Thr	63.0	0.0	.		55.0	20.0	.	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	C	11.25	1.583267	0.28268	.	.	ENSG00000181555	ENST00000451092;ENST00000543224;ENST00000409792;ENST00000412450	D;T	0.88664	-2.41;1.46	5.18	5.18	0.71444	.	0.316635	0.28230	N	0.016105	T	0.79690	0.4489	N	0.14661	0.345	0.29982	N	0.81761	B;B	0.31100	0.308;0.149	B;B	0.26969	0.075;0.047	T	0.77988	-0.2380	10	0.51188	T	0.08	.	14.0566	0.64774	0.0:1.0:0.0:0.0	.	858;858	F2Z317;Q9BYW2	.;SETD2_HUMAN	T	858;858;858;814	ENSP00000386759:S858T;ENSP00000416401:S814T	ENSP00000386759:S858T	S	-	2	0	SETD2	47138557	1.000000	0.71417	1.000000	0.80357	0.827000	0.46813	0.895000	0.28363	2.679000	0.91253	0.655000	0.94253	AGC	.	.	.	none		0.353	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		G	47163553	C	G	47163553	3	3	15	1	0	0	0	0	1	0	0	0	14144	797	28	4	5197	4	SETD2	3	47163553	Missense_Mutation	SNP	C	TCGA-2Z-A9JL-01A-11D-A42J-10	4922842	47163553	150858877	20	1048											
WDR52	55779	hgsc.bcm.edu	37	chr3	113115478	113115478	+	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	atccaaaattttcttccgtcCcgcaaaaatcgtgagccctt	11	12	5	13	3	1	1	0	1	1	0	5	1	4	1	4	0	1	1	4	0	4	4			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr3:113115478C>T	ENST00000295868.2	-	14	1828	c.1666G>A	c.(1666-1668)Gga>Aga	p.G556R	WDR52_ENST00000475568.1_5'UTR|WDR52_ENST00000393845.2_Missense_Mutation_p.G556R	NM_018338.3	NP_060808.2														breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						TTCTTCCGTCCCGCAAAAATC	0.393																																					p.G556R		Atlas-SNP	.											.	WDR52	151	.	0			c.G1666A						PASS	.						99	101	100					3																	113115478		2203	4300	6503	SO:0001583	missense	55779	exon14			TCCGTCCCGCAAA																												ENST00000295868.2:c.1666G>A	chr3.hg19:g.113115478C>T	ENSP00000295868:p.Gly556Arg	125.0	0.0	.		79.0	35.0	.	NM_001164496		Missense_Mutation	SNP	ENST00000295868.2	hg19	CCDS2972.1	.	.	.	.	.	.	.	.	.	.	C	15.31	2.796236	0.50208	.	.	ENSG00000206530	ENST00000393845;ENST00000295868	T;T	0.65549	-0.16;0.57	5.39	5.39	0.77823	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	.	.	.	.	T	0.53270	0.1786	L	0.44542	1.39	0.80722	D	1	P	0.47350	0.894	B	0.39935	0.314	T	0.54912	-0.8222	9	0.38643	T	0.18	.	13.4572	0.61206	0.0:0.9237:0.0:0.0763	.	556	Q96MT7	WDR52_HUMAN	R	556	ENSP00000377428:G556R;ENSP00000295868:G556R	ENSP00000295868:G556R	G	-	1	0	WDR52	114598168	1.000000	0.71417	0.981000	0.43875	0.044000	0.14063	4.867000	0.63013	2.690000	0.91761	0.655000	0.94253	GGA	.	.	.	none		0.393	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3			T	113115478	C	T	113115478	3	4	15	1	0	0	0	0	1	0	0	0	17316	632	22	2	4001	2	WDR52	3	113115478	Missense_Mutation	SNP	C	TCGA-2Z-A9JL-01A-11D-A42J-10	65951925	113115478	84906952	21	1049											
ADPRH	141	hgsc.bcm.edu	37	chr3	119305359	119305359	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acctgggggcccttgcgtctGctctttttacagcctatgct	4	14	10	13	1	2	0	0	0	2	0	2	0	2	0	3	2	5	2	3	2	2	5			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr3:119305359G>A	ENST00000478399.1	+	3	1931	c.526G>A	c.(526-528)Gct>Act	p.A176T	ADPRH_ENST00000357003.3_Missense_Mutation_p.A176T|ADPRH_ENST00000471850.1_3'UTR|ADPRH_ENST00000478927.1_Missense_Mutation_p.A176T|ADPRH_ENST00000465513.1_Missense_Mutation_p.A176T			P54922	ADPRH_HUMAN	ADP-ribosylarginine hydrolase	176					cellular protein modification process (GO:0006464)|protein de-ADP-ribosylation (GO:0051725)		ADP-ribosylarginine hydrolase activity (GO:0003875)|magnesium ion binding (GO:0000287)			breast(1)|kidney(1)|lung(10)|ovary(1)	13		Lung NSC(201;0.0977)		GBM - Glioblastoma multiforme(114;0.23)		CCTTGCGTCTGCTCTTTTTAC	0.532																																					p.A176T	GBM(133;579 1804 5989 9967 40052)	Atlas-SNP	.											ADPRH,NS,carcinoma,0,1	ADPRH	33	.	0			c.G526A						PASS	.						117	121	120					3																	119305359		2203	4300	6503	SO:0001583	missense	141	exon4			GCGTCTGCTCTTT	L13291	CCDS2990.1	3q13.31-q13.33	2004-02-27			ENSG00000144843	ENSG00000144843			269	protein-coding gene	gene with protein product		603081				8349667, 12070318	Standard	NM_001125		Approved	ARH1	uc003ecs.3	P54922	OTTHUMG00000159420	ENST00000478399.1:c.526G>A	chr3.hg19:g.119305359G>A	ENSP00000420200:p.Ala176Thr	74.0	0.0	.		65.0	27.0	.	NM_001125	B2R8H1|D3DN83	Missense_Mutation	SNP	ENST00000478399.1	hg19	CCDS2990.1	.	.	.	.	.	.	.	.	.	.	G	18.67	3.673577	0.67928	.	.	ENSG00000144843	ENST00000478399;ENST00000478927;ENST00000357003;ENST00000465513	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	5.54	5.54	0.83059	.	0.054304	0.64402	D	0.000001	T	0.69387	0.3105	M	0.92923	3.36	0.54753	D	0.999986	D	0.89917	1.0	D	0.68039	0.955	T	0.75542	-0.3281	10	0.72032	D	0.01	-25.2229	11.8438	0.52371	0.0:0.0:0.8258:0.1742	.	176	P54922	ADPRH_HUMAN	T	176	ENSP00000420200:A176T;ENSP00000417528:A176T;ENSP00000349496:A176T;ENSP00000417430:A176T	ENSP00000349496:A176T	A	+	1	0	ADPRH	120788049	1.000000	0.71417	0.967000	0.41034	0.139000	0.21198	6.774000	0.75012	2.884000	0.98904	0.655000	0.94253	GCT	.	.	.	none		0.532	ADPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355199.1	NM_001125		A	119305359	G	A	119305359	3	1	15	1	0	0	0	0	1	0	0	0	331	1319	46	2	532	2	ADPRH	3	119305359	Missense_Mutation	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10	6189881	119305359	78717071	22	1050											
MBD4	8930	hgsc.bcm.edu	37	chr3	129152076	129152076	+	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	cagaaacttccaaagcacagGtattgccattttgcctggga	12	10	9	10	0	0	1	0	0	0	1	1	2	1	2	3	2	4	2	3	2	3	5	rs376050040		TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr3:129152076G>T	ENST00000249910.1	-	6	1601	c.1426C>A	c.(1426-1428)Cct>Act	p.P476T	MBD4_ENST00000503197.1_Missense_Mutation_p.P476T|MBD4_ENST00000429544.2_Missense_Mutation_p.P470T|MBD4_ENST00000393278.2_Missense_Mutation_p.P158T|MBD4_ENST00000507208.1_Missense_Mutation_p.P476T|MBD4_ENST00000509587.1_5'Flank	NM_003925.1	NP_003916.1	O95243	MBD4_HUMAN	methyl-CpG binding domain protein 4	476					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)	22						CAAAGCACAGGTATTGCCATT	0.423								Base excision repair (BER), DNA glycosylases																													p.P476T		Atlas-SNP	.											.	MBD4	53	.	0			c.C1426A						PASS	.						85	86	86					3																	129152076		2203	4300	6503	SO:0001583	missense	8930	exon6			GCACAGGTATTGC	AF072250	CCDS3058.1, CCDS63766.1, CCDS63767.1, CCDS63768.1, CCDS63769.1	3q21.3	2004-03-02			ENSG00000129071	ENSG00000129071			6919	protein-coding gene	gene with protein product		603574				9774669, 10097147	Standard	NM_003925		Approved	MED1	uc003emh.2	O95243	OTTHUMG00000159463	ENST00000249910.1:c.1426C>A	chr3.hg19:g.129152076G>T	ENSP00000249910:p.Pro476Thr	82.0	0.0	.		83.0	33.0	.	NM_003925	B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Missense_Mutation	SNP	ENST00000249910.1	hg19	CCDS3058.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.834013	0.91036	.	.	ENSG00000129071	ENST00000429544;ENST00000249910;ENST00000503197;ENST00000393278;ENST00000507208	D;D;D;D;D	0.85484	-1.99;-1.99;-1.99;-1.99;-1.99	6.14	6.14	0.99180	HhH-GPD domain (1);DNA glycosylase (2);	0.000000	0.85682	D	0.000000	D	0.94221	0.8145	M	0.89840	3.065	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;0.99;1.0;0.998	D;D;D;D;D	0.77557	0.983;0.99;0.933;0.987;0.976	D	0.93945	0.7227	10	0.62326	D	0.03	-10.1723	20.4701	0.99162	0.0:0.0:1.0:0.0	.	476;158;470;476;476	E9PEE4;Q2MD36;O95243-2;O95243-3;O95243	.;.;.;.;MBD4_HUMAN	T	470;476;476;158;476	ENSP00000394080:P470T;ENSP00000249910:P476T;ENSP00000424873:P476T;ENSP00000376959:P158T;ENSP00000422327:P476T	ENSP00000249910:P476T	P	-	1	0	MBD4	130634766	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	7.414000	0.80117	2.937000	0.99478	0.650000	0.86243	CCT	.	.	.	alt		0.423	MBD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355529.1	NM_003925		T	129152076	G	T	129152076	3	4	15	1	0	0	0	0	1	0	0	0	9353	1261	44	4	328	4	MBD4	3	129152076	Missense_Mutation	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10	9846717	129152076	68870354	23	1051											
NOP14	8602	hgsc.bcm.edu	37	chr4	2956275	2956275	+	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	caccgcctcctccaaagtggGcagcagtcagctcagctggg	8	6	12	15	1	2	0	2	0	0	0	4	0	4	0	4	2	3	4	4	2	1	0			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr4:2956275G>T	ENST00000314262.6	-	4	536	c.488C>A	c.(487-489)gCc>gAc	p.A163D	NOP14_ENST00000398071.4_Missense_Mutation_p.A163D|NOP14_ENST00000502735.1_Missense_Mutation_p.A163D|NOP14_ENST00000416614.2_Missense_Mutation_p.A163D|NOP14-AS1_ENST00000503709.1_RNA	NM_003703.1	NP_003694.1	P78316	NOP14_HUMAN	NOP14 nucleolar protein	163					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						TCCAAAGTGGGCAGCAGTCAG	0.587																																					p.A163D		Atlas-SNP	.											.	NOP14	69	.	0			c.C488A						PASS	.						56	55	56					4																	2956275		2203	4300	6503	SO:0001583	missense	8602	exon4			AAGTGGGCAGCAG	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.488C>A	chr4.hg19:g.2956275G>T	ENSP00000315674:p.Ala163Asp	32.0	0.0	.		21.0	7.0	.	NM_003703	D3DVR6|Q7LGI5|Q7Z6K0|Q8TBR6	Missense_Mutation	SNP	ENST00000314262.6	hg19	CCDS33945.1	.	.	.	.	.	.	.	.	.	.	G	18.03	3.533447	0.64972	.	.	ENSG00000087269	ENST00000416614;ENST00000314262;ENST00000502735;ENST00000398071;ENST00000546137	T;T;T;T	0.31769	1.48;1.48;1.48;1.48	5.04	5.04	0.67666	.	0.446649	0.26143	N	0.026084	T	0.34395	0.0896	L	0.56769	1.78	0.46149	D	0.998894	P;P	0.41080	0.737;0.601	B;B	0.37833	0.259;0.259	T	0.35450	-0.9788	10	0.87932	D	0	-7.8632	17.9807	0.89140	0.0:0.0:1.0:0.0	.	163;163	E9PFK5;P78316	.;NOP14_HUMAN	D	163;163;163;163;62	ENSP00000405068:A163D;ENSP00000315674:A163D;ENSP00000427415:A163D;ENSP00000381146:A163D	ENSP00000315674:A163D	A	-	2	0	NOP14	2926073	1.000000	0.71417	0.491000	0.27477	0.060000	0.15804	9.636000	0.98440	2.336000	0.79503	0.650000	0.86243	GCC	.	.	.	none		0.587	NOP14-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358135.2	NM_003703		T	2956275	G	T	2956275	3	4	15	1	0	0	0	0	1	0	0	0	10543	1203	42	4	2145	4	NOP14	4	2956275	Missense_Mutation	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10		2956275	188198001	24	1052											
DSPP	1834	hgsc.bcm.edu	37	chr4	88537513	88537513	+	Missense_Mutation	SNP	A	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	gacagcagtgacagcaatgaAagcagcgacagcagtgacag	16	3	13	9	1	0	3	0	3	0	0	0	5	0	3	0	0	5	4	0	0	2	0	rs112275895		TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr4:88537513A>C	ENST00000282478.7	+	4	3732	c.3699A>C	c.(3697-3699)gaA>gaC	p.E1233D	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.E1233D			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1233	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcaatgaaagcagcgaca	0.547																																					p.E1233D		Atlas-SNP	.											.	DSPP	174	.	0			c.A3699C						PASS	.																																			SO:0001583	missense	1834	exon5			CAATGAAAGCAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3699A>C	chr4.hg19:g.88537513A>C	ENSP00000282478:p.Glu1233Asp	334.0	0.0	.		294.0	34.0	.	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	hg19	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.785366	0.00628	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88741	-2.42;-2.42	2.61	-5.21	0.02815	.	.	.	.	.	T	0.57213	0.2038	N	0.01048	-1.04	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.57347	-0.7827	9	0.02654	T	1	.	0.7125	0.00926	0.2623:0.1881:0.1298:0.4197	.	1233	Q9NZW4	DSPP_HUMAN	D	1233	ENSP00000382213:E1233D;ENSP00000282478:E1233D	ENSP00000282478:E1233D	E	+	3	2	DSPP	88756537	0.003000	0.15002	0.000000	0.03702	0.000000	0.00434	-2.769000	0.00780	-2.252000	0.00699	-3.496000	0.00033	GAA	.	A|0.500;C|0.500	0.500	weak		0.547	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		C	88537513	A	C	88537513	3	2	15	1	0	0	0	0	1	0	0	0	4784	11	1	5	3713	5	DSPP	4	88537513	Missense_Mutation	SNP	A	TCGA-2Z-A9JL-01A-11D-A42J-10	85581238	88537513	102616763	25	1053											
TAF9	6880	hgsc.bcm.edu	37	chr5	68661336	68661336	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaagactgatcagcgcggcActggattgccaatcgcacat	13	7	10	11	3	1	2	1	1	0	1	2	3	1	3	1	2	2	2	1	2	3	1			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr5:68661336A>G	ENST00000328663.4	-	3	695	c.229T>C	c.(229-231)Tgc>Cgc	p.C77R	TAF9_ENST00000506736.1_Missense_Mutation_p.C77R|TAF9_ENST00000380818.3_Intron|TAF9_ENST00000502819.1_Intron|TAF9_ENST00000217893.5_Missense_Mutation_p.C77R|TAF9_ENST00000512561.1_Intron|TAF9_ENST00000380822.4_Intron	NM_001015892.1	NP_001015892.1	Q16594	TAF9_HUMAN	TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 32kDa	77					cellular response to DNA damage stimulus (GO:0006974)|chromatin organization (GO:0006325)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of cell growth (GO:0030307)|positive regulation of response to cytokine stimulus (GO:0060760)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein stabilization (GO:0050821)|response to interleukin-1 (GO:0070555)|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)|PCAF complex (GO:0000125)|pre-snoRNP complex (GO:0070761)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	activating transcription factor binding (GO:0033613)|C2H2 zinc finger domain binding (GO:0070742)|DNA binding (GO:0003677)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|urinary_tract(1)	8		Lung NSC(167;7.26e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.1e-56)|Epithelial(20;9.54e-53)|all cancers(19;2.2e-48)|Lung(70;0.0176)		TCAGCGCGGCACTGGATTGCC	0.413																																					p.C77R		Atlas-SNP	.											.	TAF9	28	.	0			c.T229C						PASS	.						99	97	98					5																	68661336		2203	4300	6503	SO:0001583	missense	6880	exon3			CGCGGCACTGGAT	U21858	CCDS4001.1, CCDS4002.1, CCDS43324.1	5q13.2	2013-09-26	2002-08-29	2001-12-07	ENSG00000085231	ENSG00000085231			11542	protein-coding gene	gene with protein product		600822	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, G, 32kD"	TAF2G		10191103, 15630091, 16079131	Standard	NM_001015892		Approved	TAFII31, TAFII32, TAFIID32, MGC5067, CGI-137, MGC1603, MGC3647, AD-004	uc003jwa.3	Q16594	OTTHUMG00000099359	ENST00000328663.4:c.229T>C	chr5.hg19:g.68661336A>G	ENSP00000370193:p.Cys77Arg	110.0	0.0	.		73.0	28.0	.	NM_003187	D3DWA3|Q5U0D1|Q9BTS1	Missense_Mutation	SNP	ENST00000328663.4	hg19	CCDS4002.1	.	.	.	.	.	.	.	.	.	.	A	13.52	2.261584	0.39995	.	.	ENSG00000085231	ENST00000506736;ENST00000328663;ENST00000217893;ENST00000503245;ENST00000509462;ENST00000504109;ENST00000512152;ENST00000508954	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	5.69	4.53	0.55603	Histone-fold (2);	0.000000	0.85682	D	0.000000	T	0.42200	0.1192	L	0.47716	1.5	0.80722	D	1	B	0.29432	0.244	B	0.41135	0.348	T	0.35724	-0.9777	10	0.38643	T	0.18	-9.3942	9.4418	0.38673	0.9167:0.0:0.0833:0.0	.	77	Q16594	TAF9_HUMAN	R	77	ENSP00000421873:C77R;ENSP00000370193:C77R;ENSP00000217893:C77R;ENSP00000425944:C77R;ENSP00000427343:C77R;ENSP00000426283:C77R;ENSP00000425798:C77R;ENSP00000427617:C77R	ENSP00000217893:C77R	C	-	1	0	TAF9	68697092	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.840000	0.75369	2.306000	0.77630	0.533000	0.62120	TGC	.	.	.	none		0.413	TAF9-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000216803.1	NM_003187		G	68661336	A	G	68661336	3	3	15	1	0	0	0	0	1	0	0	0	15547	159	6	3	979	3	TAF9	5	68661336	Missense_Mutation	SNP	A	TCGA-2Z-A9JL-01A-11D-A42J-10		68661336	112253924	26	1054											
PCDHB10	56126	hgsc.bcm.edu	37	chr5	140573697	140573697	+	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	0	0	0	0	0	0	0	0	0	tcgctggactacgaggccctGcaggctttcgagttccgcgt	5	10	13	13	5	0	0	0	0	0	0	3	3	1	1	2	3	2	4	2	3	1	3			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr5:140573697G>C	ENST00000239446.4	+	1	1756	c.1572G>C	c.(1570-1572)ctG>ctC	p.L524L		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	524	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)			ACGAGGCCCTGCAGGCTTTCG	0.697																																					p.L524L		Atlas-SNP	.											.	PCDHB10	177	.	0			c.G1572C						PASS	.						87	106	100					5																	140573697		2203	4298	6501	SO:0001819	synonymous_variant	56126	exon1			GGCCCTGCAGGCT	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.1572G>C	chr5.hg19:g.140573697G>C		138.0	0.0	.		114.0	38.0	.	NM_018930	Q96T99	Silent	SNP	ENST00000239446.4	hg19	CCDS4252.1																																																																																			.	.	.	none		0.697	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		C	140573697	G	C	140573697	2	2	15	1	0	0	0	0	0	0	0	1	11542	1306	46	4		4	PCDHB10	5	140573697	Silent	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10	71912361	140573697	40341563	27	1055											
PCDHGA12	26025	hgsc.bcm.edu	37	chr5	140810981	140810981	+	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	ttacggcctccgacgggggcGacccggtgcgcacaggcacc	6	4	15	16	6	0	0	0	0	0	0	1	2	1	0	4	5	2	2	4	5	1	1			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr5:140810981G>C	ENST00000252085.3	+	1	797	c.655G>C	c.(655-657)Gac>Cac	p.D219H	PCDHGA7_ENST00000518325.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGB2_ENST00000522605.1_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	219	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGACGGGGGCGACCCGGTGCG	0.652																																					p.D219H		Atlas-SNP	.											.	PCDHGA12	271	.	0			c.G655C						PASS	.						50	52	51					5																	140810981		2203	4300	6503	SO:0001583	missense	26025	exon1			GGGGGCGACCCGG	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.655G>C	chr5.hg19:g.140810981G>C	ENSP00000252085:p.Asp219His	74.0	0.0	.		61.0	20.0	.	NM_032094	O15100|Q6UW70|Q9Y5D7	Missense_Mutation	SNP	ENST00000252085.3	hg19	CCDS4260.1	.	.	.	.	.	.	.	.	.	.	g	8.895	0.955017	0.18431	.	.	ENSG00000253159	ENST00000252085	T	0.01854	4.6	5.27	2.48	0.30137	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.07007	0.0178	M	0.75264	2.295	0.09310	N	1	B;B	0.33198	0.401;0.163	B;P	0.47573	0.339;0.55	T	0.21042	-1.0257	9	0.56958	D	0.05	.	5.9038	0.18982	0.2123:0.0:0.653:0.1347	.	219;219	O60330-2;O60330	.;PCDGC_HUMAN	H	219	ENSP00000252085:D219H	ENSP00000252085:D219H	D	+	1	0	PCDHGA12	140791165	0.003000	0.15002	0.136000	0.22124	0.024000	0.10985	1.587000	0.36622	0.802000	0.34089	0.655000	0.94253	GAC	.	.	.	none		0.652	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735		C	140810981	G	C	140810981	3	2	15	1	0	0	0	0	1	0	0	0	11560	1058	37	4	657	4	PCDHGA12	5	140810981	Missense_Mutation	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10	237284	140810981	40104279	28	1056											
RARS2	57038	hgsc.bcm.edu	37	chr6	88229389	88229389	+	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	acatctcctcttcgagtcttCattccctgtactactccaaa	9	14	3	15	1	4	0	1	0	3	0	8	1	6	0	3	0	2	1	3	0	3	5			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr6:88229389C>T	ENST00000369536.5	-	14	1194	c.1149G>A	c.(1147-1149)atG>atA	p.M383I	RARS2_ENST00000497828.1_5'Flank	NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	383					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)		TTCGAGTCTTCATTCCCTGTA	0.403																																					p.M383I		Atlas-SNP	.											.	RARS2	61	.	0			c.G1149A						PASS	.						106	99	101					6																	88229389		2203	4300	6503	SO:0001583	missense	57038	exon14			AGTCTTCATTCCC	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.1149G>A	chr6.hg19:g.88229389C>T	ENSP00000358549:p.Met383Ile	117.0	0.0	.		130.0	52.0	.	NM_020320	B2RDT7|Q96FU5|Q9H8K8	Missense_Mutation	SNP	ENST00000369536.5	hg19	CCDS5011.1	.	.	.	.	.	.	.	.	.	.	C	34	5.353278	0.95830	.	.	ENSG00000146282	ENST00000369536	T	0.75260	-0.92	5.97	5.97	0.96955	Arginyl-tRNA synthetase, class Ia, core (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	D	0.86276	0.5894	M	0.81802	2.56	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.85130	0.99;0.997	D	0.85995	0.1491	10	0.62326	D	0.03	.	20.4324	0.99085	0.0:1.0:0.0:0.0	.	383;208	Q5T160;E1P510	SYRM_HUMAN;.	I	383	ENSP00000358549:M383I	ENSP00000358549:M383I	M	-	3	0	RARS2	88286108	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.158000	0.77470	2.833000	0.97629	0.585000	0.79938	ATG	.	.	.	none		0.403	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320		T	88229389	C	T	88229389	3	4	15	1	0	0	0	0	1	0	0	0	13072	826	29	2	615	2	RARS2	6	88229389	Missense_Mutation	SNP	C	TCGA-2Z-A9JL-01A-11D-A42J-10		88229389	82885678	29	1057											
KIAA0415	9907	hgsc.bcm.edu	37	chr7	4827394	4827394	+	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	cctgcttgacggcggtgctgGacctgcagctcaggtgggcc	4	8	16	13	2	1	1	1	1	0	0	1	2	1	2	3	5	4	4	3	5	0	1			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr7:4827394G>T	ENST00000348624.4	+	11	1535	c.1441G>T	c.(1441-1443)Gac>Tac	p.D481Y	MIR4656_ENST00000579503.1_RNA|AP5Z1_ENST00000401897.1_Missense_Mutation_p.D481Y	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	481					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)											GGCGGTGCTGGACCTGCAGCT	0.697																																					p.D481Y		Atlas-SNP	.											.	.	.	.	0			c.G1441T						PASS	.						16	20	19					7																	4827394		2014	3994	6008	SO:0001583	missense	9907	exon11			GTGCTGGACCTGC	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.1441G>T	chr7.hg19:g.4827394G>T	ENSP00000297562:p.Asp481Tyr	24.0	0.0	.		46.0	12.0	.	NM_014855	Q8N3X2|Q96H80	Missense_Mutation	SNP	ENST00000348624.4	hg19	CCDS47528.1	.	.	.	.	.	.	.	.	.	.	G	16.42	3.119517	0.56505	.	.	ENSG00000242802	ENST00000348624;ENST00000401897	T;T	0.45668	0.89;0.89	4.73	3.83	0.44106	.	0.125660	0.53938	D	0.000051	T	0.61098	0.2320	M	0.80982	2.52	0.53688	D	0.999978	D	0.61080	0.989	P	0.59643	0.861	T	0.67114	-0.5752	10	0.66056	D	0.02	.	13.1808	0.59653	0.0:0.0:0.8389:0.1611	.	481	O43299	K0415_HUMAN	Y	481	ENSP00000297562:D481Y;ENSP00000384980:D481Y	ENSP00000297562:D481Y	D	+	1	0	KIAA0415	4793920	1.000000	0.71417	0.993000	0.49108	0.425000	0.31504	7.524000	0.81866	1.095000	0.41419	0.549000	0.68633	GAC	.	.	.	none		0.697	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1			T	4827394	G	T	4827394	3	4	15	1	0	0	0	0	1	0	0	0	8182	1174	41	4	1483	4	KIAA0415	7	4827394	Missense_Mutation	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10		4827394	154311269	30	1058											
PMS2	5395	hgsc.bcm.edu	37	chr7	6018319	6018320	+	Frame_Shift_Del	DEL	GT	GT	-																															taacagcagttaagttgagaGtctgaggtctgaaaaacaca																								rs141893001		TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr7:6018319_6018320delGT	ENST00000265849.7	-	13	2287_2288	c.2182_2183delAC	c.(2182-2184)actfs	p.T728fs	PMS2_ENST00000382321.4_Frame_Shift_Del_p.T327fs|PMS2_ENST00000406569.3_Intron|PMS2_ENST00000441476.2_Frame_Shift_Del_p.T622fs	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	728					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)		TAAGTTGAGAGTCTGAGGTCTG	0.307			"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.728_728del		Atlas-INDEL	.	yes	Rec		"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	7	7p22	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)		E	.	PMS2	88	.	0			c.2183_2184del						PASS	.			85,4141		3,79,2031						2	1			33	1,8179		0,1,4089	no	frameshift	PMS2	NM_000535.5		3,80,6120	A1A1,A1R,RR		0.0122,2.0114,0.6932				86,12320				SO:0001589	frameshift_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	.		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.2182_2183delAC	chr7.hg19:g.6018319_6018320delGT	ENSP00000265849:p.Thr728fs	226.0	0.0	0		517.0	183.0	0.353965	NM_000535	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Frame_Shift_Del	DEL	ENST00000265849.7	hg19	CCDS5343.1																																																																																			.	.	.	none		0.307	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535		-	6018320	GT	-	6018319	7	5	15	1	0	1	0	1	0	0	0	0	12150	1029	36	0	417	0	PMS2	7	6018319	Frame_Shift_Del	DEL	GT	TCGA-2Z-A9JL-01A-11D-A42J-10	1190925	6018319	153120344	31	1059											
WDR91	29062	hgsc.bcm.edu	37	chr7	134890789	134890789	+	Frame_Shift_Del	DEL	T	T	-																															ctctttcttcagtcggtggaTttcagcttgcaatgcaaaaa																										TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr7:134890789delT	ENST00000354475.4	-	5	647	c.616delA	c.(616-618)atcfs	p.I206fs	WDR91_ENST00000344400.5_Frame_Shift_Del_p.I206fs|WDR91_ENST00000485942.1_5'UTR|WDR91_ENST00000423565.1_Frame_Shift_Del_p.I171fs	NM_014149.3	NP_054868.3	A4D1P6	WDR91_HUMAN	WD repeat domain 91	206										breast(3)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	40						AGTCGGTGGATTTCAGCTTGC	0.507																																					p.I206fs		Pindel	.											.	WDR91	82	.	0			c.617delT						PASS	.						270	237	248					7																	134890789		2203	4300	6503	SO:0001589	frameshift_variant	29062	exon5			.	AF161534	CCDS34758.1	7q33	2013-01-09			ENSG00000105875	ENSG00000105875		"WD repeat domain containing"	24997	protein-coding gene	gene with protein product						11042152, 11230166	Standard	NM_014149		Approved	HSPC049	uc003vsp.2	A4D1P6	OTTHUMG00000155414	ENST00000354475.4:c.616delA	chr7.hg19:g.134890789delT	ENSP00000346466:p.Ile206fs	147.0	0.0	.		140.0	59.0	0.421	NM_014149	A6NK54|C9JMI4|Q6FI65|Q6MZQ1|Q6P4I1|Q96AE5|Q96G63|Q9H062|Q9H9B6|Q9NVG7|Q9NZY6	Frame_Shift_Del	DEL	ENST00000354475.4	hg19	CCDS34758.1																																																																																			.	.	.	none		0.507	WDR91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340019.1	NM_014149		-	134890789	T	-	134890789	7	5	15	1	0	1	0	1	0	0	0	0	17350	1493	52	0	1671	0	WDR91	7	134890789	Frame_Shift_Del	DEL	T	TCGA-2Z-A9JL-01A-11D-A42J-10	128872470	134890789	24247874	32	1060											
ZNF212	7988	hgsc.bcm.edu	37	chr7	148947362	148947362	+	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	ttcactctggacggtggtggCcgctattcaggctgtggaga	6	11	15	9	2	3	1	2	0	1	1	3	3	3	2	1	6	0	2	1	6	1	3			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr7:148947362C>A	ENST00000335870.2	+	2	265	c.137C>A	c.(136-138)gCc>gAc	p.A46D		NM_012256.3	NP_036388.2	Q9UDV6	ZN212_HUMAN	zinc finger protein 212	46					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)			ACGGTGGTGGCCGCTATTCAG	0.567																																					p.A46D		Atlas-SNP	.											.	ZNF212	28	.	0			c.C137A						PASS	.						50	52	52					7																	148947362		2203	4300	6503	SO:0001583	missense	7988	exon2			TGGTGGCCGCTAT	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.137C>A	chr7.hg19:g.148947362C>A	ENSP00000338572:p.Ala46Asp	128.0	0.0	.		127.0	65.0	.	NM_012256	B2RCF4|Q13396|Q8N664	Missense_Mutation	SNP	ENST00000335870.2	hg19	CCDS5896.1	.	.	.	.	.	.	.	.	.	.	C	18.61	3.660661	0.67586	.	.	ENSG00000170260	ENST00000335870	T	0.78707	-1.2	5.6	5.6	0.85130	.	0.392655	0.21983	N	0.066263	D	0.87593	0.6216	M	0.74258	2.255	0.39801	D	0.972575	D	0.89917	1.0	D	0.85130	0.997	D	0.89043	0.3450	10	0.87932	D	0	-7.1207	15.118	0.72419	0.0:1.0:0.0:0.0	.	46	Q9UDV6	ZN212_HUMAN	D	46	ENSP00000338572:A46D	ENSP00000338572:A46D	A	+	2	0	ZNF212	148578295	1.000000	0.71417	0.965000	0.40720	0.607000	0.37147	3.387000	0.52501	2.653000	0.90120	0.563000	0.77884	GCC	.	.	.	none		0.567	ZNF212-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352710.1	NM_012256		A	148947362	C	A	148947362	3	1	15	1	0	0	0	0	1	0	0	0	17780	739	26	4	143	4	ZNF212	7	148947362	Missense_Mutation	SNP	C	TCGA-2Z-A9JL-01A-11D-A42J-10	14056573	148947362	10191301	33	1061											
CSMD3	114788	hgsc.bcm.edu	37	chr8	113303751	113303751	+	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	ctacttactgatacattctgGtaaaggtttgtcccattgtc	9	16	7	9	0	1	1	0	1	1	0	3	1	2	1	1	2	3	2	1	2	5	7			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr8:113303751G>T	ENST00000297405.5	-	56	9206	c.8962C>A	c.(8962-8964)Cca>Aca	p.P2988T	CSMD3_ENST00000343508.3_Missense_Mutation_p.P2948T|CSMD3_ENST00000455883.2_Missense_Mutation_p.P2819T|CSMD3_ENST00000352409.3_Missense_Mutation_p.P2918T	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2988	Sushi 20. {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						ATACATTCTGGTAAAGGTTTG	0.328										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.P2988T		Atlas-SNP	.											.	CSMD3	2325	.	0			c.C8962A						PASS	.						84	77	79					8																	113303751		2202	4299	6501	SO:0001583	missense	114788	exon56			ATTCTGGTAAAGG	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.8962C>A	chr8.hg19:g.113303751G>T	ENSP00000297405:p.Pro2988Thr	92.0	0.0	.		103.0	29.0	.	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.633524	0.87660	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	D;D;D;D;D	0.86497	-2.13;-2.13;-2.13;-2.13;-2.13	5.74	5.74	0.90152	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000002	D	0.95427	0.8515	M	0.92923	3.36	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.984	D;D;P	0.97110	0.996;1.0;0.839	D	0.95785	0.8820	10	0.72032	D	0.01	.	19.9351	0.97137	0.0:0.0:1.0:0.0	.	2819;2988;2948	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	T	2948;2988;2258;2819;2918	ENSP00000345799:P2948T;ENSP00000297405:P2988T;ENSP00000341558:P2258T;ENSP00000412263:P2819T;ENSP00000343124:P2918T	ENSP00000297405:P2988T	P	-	1	0	CSMD3	113372927	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.030000	0.88816	2.703000	0.92315	0.655000	0.94253	CCA	.	.	.	none		0.328	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113303751	G	T	113303751	3	4	15	1	0	0	0	0	1	0	0	0	3948	1261	44	4	2225	4	CSMD3	8	113303751	Missense_Mutation	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10		113303751	33060271	34	1062											
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84606600	84606600	+	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	atagagcctgttaacatctcAtttctcagccatgacattct	11	14	5	11	0	3	2	2	1	3	1	5	2	3	2	2	0	3	1	2	0	2	4			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr9:84606600A>T	ENST00000344803.2	+	4	1262	c.1215A>T	c.(1213-1215)tcA>tcT	p.S405S		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	405					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TTAACATCTCATTTCTCAGCC	0.458																																					p.S405S		Atlas-SNP	.											FAM75D4,rectum,carcinoma,0,2	.	.	.	0			c.A1215T						PASS	.						95	82	86					9																	84606600		1852	4102	5954	SO:0001819	synonymous_variant	389763	exon4			CATCTCATTTCTC		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.1215A>T	chr9.hg19:g.84606600A>T		116.0	1.0	.		107.0	7.0	.	NM_001001670		Silent	SNP	ENST00000344803.2	hg19	CCDS47986.1																																																																																			.	.	.	none		0.458	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		T	84606600	A	T	84606600	2	4	15	1	0	0	0	0	0	0	0	1	5939	204	8	5		5	FLJ46321	9	84606600	Silent	SNP	A	TCGA-2Z-A9JL-01A-11D-A42J-10		84606600	56606831	35	1063											
C9orf84	158401	hgsc.bcm.edu	37	chr9	114538143	114538143	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagacttcattgtagtccaTgtgggtgtataaactgacct	12	13	9	7	0	1	2	1	1	0	1	2	2	2	2	2	1	1	2	2	1	5	5			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr9:114538143T>C	ENST00000318737.4	-	3	306	c.178A>G	c.(178-180)Atg>Gtg	p.M60V	C9orf84_ENST00000374287.3_Missense_Mutation_p.M60V|C9orf84_ENST00000374283.5_Missense_Mutation_p.M124V	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	60										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						TTGTAGTCCATGTGGGTGTAT	0.363																																					p.M60V		Atlas-SNP	.											.	C9orf84	207	.	0			c.A178G						PASS	.						104	101	102					9																	114538143		2203	4300	6503	SO:0001583	missense	158401	exon3			AGTCCATGTGGGT	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.178A>G	chr9.hg19:g.114538143T>C	ENSP00000322108:p.Met60Val	140.0	0.0	.		121.0	48.0	.	NM_173521	A2A2V3|Q2M1H8|Q96M73	Missense_Mutation	SNP	ENST00000318737.4	hg19	CCDS6781.3	.	.	.	.	.	.	.	.	.	.	T	9.217	1.032346	0.19590	.	.	ENSG00000165181	ENST00000374287;ENST00000318737;ENST00000374283	T;T;T	0.42513	3.69;3.69;0.97	4.97	-1.86	0.07760	.	1.063880	0.07355	N	0.883056	T	0.20861	0.0502	N	0.08118	0	0.09310	N	1	B;B	0.15930	0.006;0.015	B;B	0.15870	0.001;0.014	T	0.21314	-1.0249	10	0.49607	T	0.09	0.116	5.3357	0.15957	0.0:0.4239:0.1725:0.4037	.	124;60	Q5VXU9-2;Q5VXU9	.;CI084_HUMAN	V	60;60;124	ENSP00000363405:M60V;ENSP00000322108:M60V;ENSP00000363401:M124V	ENSP00000322108:M60V	M	-	1	0	C9orf84	113577964	0.000000	0.05858	0.000000	0.03702	0.173000	0.22820	-0.000000	0.12993	-0.496000	0.06650	0.477000	0.44152	ATG	.	.	.	none		0.363	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521		C	114538143	T	C	114538143	3	2	15	1	0	0	0	0	1	0	0	0	2502	1464	51	3	4389	3	C9orf84	9	114538143	Missense_Mutation	SNP	T	TCGA-2Z-A9JL-01A-11D-A42J-10	29931543	114538143	26675288	36	1064											
RGS3	5998	hgsc.bcm.edu	37	chr9	116345868	116345868	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacaagaccttccacccaacAaggactccccttctgggcag	11	6	8	16	0	1	1	0	0	1	1	3	3	3	2	5	2	1	1	5	2	3	2			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr9:116345868A>G	ENST00000374140.2	+	21	2385	c.2176A>G	c.(2176-2178)Aag>Gag	p.K726E	RGS3_ENST00000350696.5_Missense_Mutation_p.K726E|RP11-168K11.2_ENST00000428429.1_RNA|RGS3_ENST00000343817.5_Missense_Mutation_p.K445E|RGS3_ENST00000394646.3_Intron|RGS3_ENST00000462143.1_Missense_Mutation_p.K47E|RGS3_ENST00000342620.5_Intron|RGS3_ENST00000374134.3_Missense_Mutation_p.K47E	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	726	Pro-rich.				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						TCCACCCAACAAGGACTCCCC	0.622																																					p.K726E		Atlas-SNP	.											.	RGS3	251	.	0			c.A2176G						PASS	.						93	89	90					9																	116345868		2203	4300	6503	SO:0001583	missense	5998	exon21			CCCAACAAGGACT	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.2176A>G	chr9.hg19:g.116345868A>G	ENSP00000363255:p.Lys726Glu	79.0	0.0	.		81.0	29.0	.	NM_144488	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	hg19	CCDS43869.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.42|12.42	1.932043|1.932043	0.34096|0.34096	.|.	.|.	ENSG00000138835|ENSG00000138835	ENST00000374140;ENST00000350696;ENST00000343817;ENST00000474719;ENST00000462143;ENST00000374134;ENST00000471324;ENST00000467805|ENST00000496113	T;T;T;T;T;T|.	0.78481|.	0.91;0.91;0.41;0.28;0.28;-1.18|.	4.82|4.82	-3.87|-3.87	0.04218|0.04218	.|.	0.808466|.	0.10976|.	N|.	0.613237|.	T|T	0.39279|0.39279	0.1072|0.1072	L|L	0.27053|0.27053	0.805|0.805	0.37119|0.37119	D|D	0.900721|0.900721	B;B;B;B;B;B|.	0.20052|.	0.041;0.001;0.01;0.001;0.001;0.001|.	B;B;B;B;B;B|.	0.14578|.	0.011;0.004;0.006;0.003;0.002;0.002|.	T|T	0.39461|0.39461	-0.9613|-0.9613	10|5	0.44086|.	T|.	0.13|.	.|.	9.8023|9.8023	0.40773|0.40773	0.33:0.5866:0.0834:0.0|0.33:0.5866:0.0834:0.0	.|.	65;622;47;445;616;726|.	B4DWF9;P49796-6;Q6ZV17;P49796-4;B3KWG8;P49796|.	.;.;.;.;.;RGS3_HUMAN|.	E|R	726;726;445;47;47;47;47;47|180	ENSP00000363255:K726E;ENSP00000259406:K726E;ENSP00000340284:K445E;ENSP00000420356:K47E;ENSP00000363249:K47E;ENSP00000417994:K47E|.	ENSP00000340284:K445E|.	K|Q	+|+	1|2	0|0	RGS3|RGS3	115385689|115385689	0.003000|0.003000	0.15002|0.15002	0.030000|0.030000	0.17652|0.17652	0.251000|0.251000	0.25915|0.25915	-0.237000|-0.237000	0.08990|0.08990	-0.347000|-0.347000	0.08299|0.08299	0.533000|0.533000	0.62120|0.62120	AAG|CAA	.	.	.	none		0.622	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790		G	116345868	A	G	116345868	3	3	15	1	0	0	0	0	1	0	0	0	13319	131	5	3	2507	3	RGS3	9	116345868	Missense_Mutation	SNP	A	TCGA-2Z-A9JL-01A-11D-A42J-10	1807725	116345868	24867563	37	1065											
RXRA	6256	hgsc.bcm.edu	37	chr9	137323760	137323760	+	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	ctcctctgcagggtgctgacGgagcttgtgtccaagatgcg	6	10	14	11	2	1	2	0	1	1	1	3	3	3	3	2	2	4	3	2	2	1	1			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr9:137323760G>T	ENST00000481739.1	+	8	1105	c.1053G>T	c.(1051-1053)acG>acT	p.T351T	RXRA_ENST00000540193.1_Silent_p.T254T|RXRA_ENST00000356384.4_3'UTR	NM_002957.4	NP_002948.1	P19793	RXRA_HUMAN	retinoid X receptor, alpha	351	Ligand-binding.				camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|cellular lipid metabolic process (GO:0044255)|cholesterol metabolic process (GO:0008203)|embryo implantation (GO:0007566)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|response to retinoic acid (GO:0032526)|retinoic acid receptor signaling pathway (GO:0048384)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|vitamin metabolic process (GO:0006766)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein heterodimerization activity (GO:0046982)|retinoic acid receptor activity (GO:0003708)|retinoic acid-responsive element binding (GO:0044323)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|vitamin D receptor binding (GO:0042809)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19				OV - Ovarian serous cystadenocarcinoma(145;4.66e-08)|Epithelial(140;6.72e-08)|all cancers(34;2.22e-07)	Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Etodolac(DB00749)	GGGTGCTGACGGAGCTTGTGT	0.627																																					p.T351T		Atlas-SNP	.											.	RXRA	52	.	0			c.G1053T						PASS	.						120	93	102					9																	137323760		2203	4300	6503	SO:0001819	synonymous_variant	6256	exon8			GCTGACGGAGCTT	X52773	CCDS35172.1	9q34	2013-01-16			ENSG00000186350	ENSG00000186350		"Nuclear hormone receptors"	10477	protein-coding gene	gene with protein product	"nuclear receptor subfamily 2 group B member 1"	180245				2159111	Standard	XM_005263409		Approved	NR2B1	uc004cfa.1	P19793	OTTHUMG00000020887	ENST00000481739.1:c.1053G>T	chr9.hg19:g.137323760G>T		89.0	0.0	.		77.0	21.0	.	NM_002957	B3KY83|Q2NL52|Q2V504	Silent	SNP	ENST00000481739.1	hg19	CCDS35172.1																																																																																			.	.	.	none		0.627	RXRA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054949.1	NM_002957		T	137323760	G	T	137323760	2	4	15	1	0	0	0	0	0	0	0	1	13776	1103	39	4		4	RXRA	9	137323760	Silent	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10	20977892	137323760	3889671	38	1066											
FRMPD2	143162	hgsc.bcm.edu	37	chr10	49380990	49380999	+	Splice_Site	DEL	ATCTGTCACT	ATCTGTCACT	-																															caattctctcccctctcaccAtctgtcactgagacacagct																								rs367862519|rs138229835	byFrequency	TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	ATCTGTCACT	ATCTGTCACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr10:49380990_49380999delATCTGTCACT	ENST00000374201.3	-	25	3515_3524	c.3213_3222delAGTGACAGAT	c.(3211-3222)tcagtgacagat>tc	p.SVTD1071fs	FRMPD2_ENST00000305531.3_Splice_Site_p.SVTD1046fs|FRMPD2_ENST00000474573.1_Splice_Site_p.SVTD23fs|FRMPD2_ENST00000463706.1_5'UTR|FRMPD2_ENST00000407470.4_Splice_Site_p.SVTD1039fs	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	1071					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)		CCCTCTCACCATCTGTCACTGAGACACAGC	0.5																																					p.1072_1075del		Pindel	.											.	FRMPD2	157	.	0			c.3214_3223del						PASS	.																																			SO:0001630	splice_region_variant	143162	exon25			.	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.3223+1AGTGACAGAT>-	chr10.hg19:g.49380990_49380999delATCTGTCACT		589.0	0.0	.		493.0	23.0	0.047	NM_001018071	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Frame_Shift_Del	DEL	ENST00000374201.3	hg19	CCDS31195.1																																																																																			.	.	.	none		0.5	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428	Frame_Shift_Del	-	49380999	ATCTGTCACT	-	49380990	8	5	15	1	0	1	0	1	0	0	1	0	6065	231	8	0	727	0	FRMPD2	10	49380990	Splice_Site	DEL	ATCTGTCACT	TCGA-2Z-A9JL-01A-11D-A42J-10		49380990	86153757	39	1067											
C10orf57	80195	hgsc.bcm.edu	37	chr10	81850575	81850575	+	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	ataaaggcatcacaagtggtCgggctcagctactctggttc	10	10	11	10	1	3	0	2	0	1	0	5	0	3	0	0	4	2	4	0	4	4	3			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr10:81850575C>T	ENST00000372281.3	+	4	304	c.274C>T	c.(274-276)Cgg>Tgg	p.R92W	TMEM254_ENST00000372274.1_3'UTR|TMEM254_ENST00000372275.1_3'UTR|TMEM254_ENST00000467529.1_3'UTR	NM_001270372.1|NM_025125.3	NP_001257301.1|NP_079401.2	Q8TBM7	TM254_HUMAN	transmembrane protein 254	92						integral component of membrane (GO:0016021)		p.R92W(1)									CACAAGTGGTCGGGCTCAGCT	0.383																																					p.R116W		Atlas-SNP	.											C10orf57,NS,carcinoma,0,1	TMEM254	1	.	1	Substitution - Missense(1)	endometrium(1)	c.C346T						PASS	.						148	136	140					10																	81850575		2203	4300	6503	SO:0001583	missense	80195	exon4			AGTGGTCGGGCTC	BC022252	CCDS7363.1, CCDS58086.1, CCDS58087.1, CCDS73157.1	10q23.1	2012-11-06	2012-11-06	2012-11-06	ENSG00000133678	ENSG00000133678			25804	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 57"	C10orf57		14702039	Standard	NM_025125		Approved	FLJ13263, bA369J21.6	uc010qlw.3	Q8TBM7	OTTHUMG00000018602	ENST00000372281.3:c.274C>T	chr10.hg19:g.81850575C>T	ENSP00000361355:p.Arg92Trp	62.0	0.0	.		52.0	22.0	.	NM_001270367	D3DWC8|Q53HP4|Q5JTC0|Q5JTC1|Q6IA45|Q9H8S6	Missense_Mutation	SNP	ENST00000372281.3	hg19	CCDS7363.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.293|7.293	0.611430|0.611430	0.14066|0.14066	.|.	.|.	ENSG00000133678|ENSG00000133678	ENST00000372281|ENST00000450179	.|.	.|.	.|.	4.22|4.22	2.3|2.3	0.28687|0.28687	.|.	1.156350|.	0.06000|.	N|.	0.647577|.	T|T	0.31888|0.31888	0.0811|0.0811	L|L	0.33485|0.33485	1.01|1.01	0.09310|0.09310	N|N	1|1	B;B|.	0.18741|.	0.025;0.03|.	B;B|.	0.12156|.	0.007;0.003|.	T|T	0.20840|0.20840	-1.0263|-1.0263	9|5	0.42905|.	T|.	0.14|.	-11.936|-11.936	6.4042|6.4042	0.21656|0.21656	0.0:0.7479:0.0:0.2521|0.0:0.7479:0.0:0.2521	.|.	116;92|.	E7ERB9;Q8TBM7|.	.;CJ057_HUMAN|.	W|L	92|69	.|.	ENSP00000361355:R92W|.	R|S	+|+	1|2	2|0	C10orf57|C10orf57	81840555|81840555	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.557000|0.557000	0.35523|0.35523	-0.093000|-0.093000	0.11111|0.11111	0.473000|0.473000	0.27368|0.27368	0.557000|0.557000	0.71058|0.71058	CGG|TCG	.	.	.	none		0.383	TMEM254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049030.1	NM_025125		T	81850575	C	T	81850575	3	4	15	1	0	0	0	0	1	0	0	0	1611	875	31	1	288	1	C10orf57	10	81850575	Missense_Mutation	SNP	C	TCGA-2Z-A9JL-01A-11D-A42J-10	32469585	81850575	53684172	40	1068											
SLC25A28	81894	hgsc.bcm.edu	37	chr10	101379882	101379882	+	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	caccatgtgcgtggtgacagTggctccagccggcagcgcct	6	7	14	14	3	0	1	0	1	0	0	1	1	1	1	4	3	3	2	4	3	0	0			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr10:101379882T>A	ENST00000370495.4	-	1	239	c.211A>T	c.(211-213)Act>Tct	p.T71S	RP11-85A1.3_ENST00000566847.1_RNA|SLC25A28_ENST00000496035.1_Intron	NM_031212.3	NP_112489.3	Q96A46	MFRN2_HUMAN	solute carrier family 25 (mitochondrial iron transporter), member 28	71					ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|stomach(1)	11		Colorectal(252;0.234)		Epithelial(162;2.57e-10)|all cancers(201;2.01e-08)		GTGGTGACAGTGGCTCCAGCC	0.721																																					p.T71S		Atlas-SNP	.											.	SLC25A28	34	.	0			c.A211T						PASS	.						10	13	12					10																	101379882		1896	3945	5841	SO:0001583	missense	81894	exon1			TGACAGTGGCTCC	AF327402	CCDS41559.1	10q24.2	2013-05-22	2012-03-29		ENSG00000155287	ENSG00000155287		"Solute carriers"	23472	protein-coding gene	gene with protein product	"mitoferrin 2"	609767	"solute carrier family 25, member 28"			11297739	Standard	NM_031212		Approved	MRS3/4, MRS4L	uc001kpx.2	Q96A46	OTTHUMG00000018886	ENST00000370495.4:c.211A>T	chr10.hg19:g.101379882T>A	ENSP00000359526:p.Thr71Ser	26.0	0.0	.		19.0	6.0	.	NM_031212	Q4VBZ0|Q5T777|Q86VX5|Q969G8|Q9H2J3	Missense_Mutation	SNP	ENST00000370495.4	hg19	CCDS41559.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	5.859|5.859	0.342667|0.342667	0.11069|0.11069	.|.	.|.	ENSG00000155287|ENSG00000155287	ENST00000434701|ENST00000370495	T|T	0.78481|0.78003	-1.18|-1.14	4.49|4.49	4.49|4.49	0.54785|0.54785	.|Mitochondrial carrier domain (1);	.|0.078181	.|0.51477	.|D	.|0.000096	T|T	0.45756|0.45756	0.1358|0.1358	N|N	0.01686|0.01686	-0.76|-0.76	0.31508|0.31508	N|N	0.663909|0.663909	.|B	.|0.06786	.|0.001	.|B	.|0.12156	.|0.007	T|T	0.48422|0.48422	-0.9037|-0.9037	7|10	0.33141|0.02654	T|T	0.24|1	-51.6351|-51.6351	8.2084|8.2084	0.31469|0.31469	0.0:0.0953:0.0:0.9047|0.0:0.0953:0.0:0.9047	.|.	.|71	.|Q96A46	.|MFRN2_HUMAN	L|S	8|71	ENSP00000399102:H8L|ENSP00000359526:T71S	ENSP00000399102:H8L|ENSP00000359526:T71S	H|T	-|-	2|1	0|0	SLC25A28|SLC25A28	101369872|101369872	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	2.051000|2.051000	0.41307|0.41307	1.873000|1.873000	0.54277|0.54277	0.375000|0.375000	0.23000|0.23000	CAC|ACT	.	.	.	none		0.721	SLC25A28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049801.1	NM_031212		A	101379882	T	A	101379882	3	1	15	1	0	0	0	0	1	0	0	0	14504	1696	59	5	899	5	SLC25A28	10	101379882	Missense_Mutation	SNP	T	TCGA-2Z-A9JL-01A-11D-A42J-10	19529307	101379882	34154865	41	1069											
SEC31B	25956	hgsc.bcm.edu	37	chr10	102265129	102265129	+	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	tacacttacagcaaatgaaaCacctgttggtcttctaatcc	13	12	5	11	0	2	1	0	1	2	0	3	1	3	1	2	1	4	2	2	1	5	5			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr10:102265129C>A	ENST00000370345.3	-	10	1265	c.1168G>T	c.(1168-1170)Gtt>Ttt	p.V390F	SEC31B_ENST00000451524.1_Missense_Mutation_p.V390F	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	390					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)		GCAAATGAAACACCTGTTGGT	0.502																																					p.V390F		Atlas-SNP	.											.	SEC31B	84	.	0			c.G1168T						PASS	.						208	208	208					10																	102265129		2203	4300	6503	SO:0001583	missense	25956	exon10			ATGAAACACCTGT	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.1168G>T	chr10.hg19:g.102265129C>A	ENSP00000359370:p.Val390Phe	81.0	0.0	.		58.0	19.0	.	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Missense_Mutation	SNP	ENST00000370345.3	hg19	CCDS7495.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.509524	0.85282	.	.	ENSG00000075826	ENST00000370345;ENST00000451524	T;T	0.60797	0.44;0.16	5.82	4.91	0.64330	.	0.291232	0.38111	N	0.001804	T	0.76543	0.4002	M	0.83953	2.67	0.80722	D	1	D;D	0.58268	0.982;0.969	D;P	0.64506	0.926;0.845	T	0.81072	-0.1098	10	0.87932	D	0	-3.3194	15.336	0.74255	0.1408:0.8592:0.0:0.0	.	389;390	Q9NQW1-5;Q9NQW1	.;SC31B_HUMAN	F	390	ENSP00000359370:V390F;ENSP00000391178:V390F	ENSP00000359370:V390F	V	-	1	0	SEC31B	102255119	0.997000	0.39634	0.933000	0.37362	0.852000	0.48524	3.525000	0.53502	1.448000	0.47680	0.561000	0.74099	GTT	.	.	.	none		0.502	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490		A	102265129	C	A	102265129	3	1	15	1	0	0	0	0	1	0	0	0	14012	478	17	4	2439	4	SEC31B	10	102265129	Missense_Mutation	SNP	C	TCGA-2Z-A9JL-01A-11D-A42J-10	885247	102265129	33269618	42	1070											
INPP5F	22876	hgsc.bcm.edu	37	chr10	121567442	121567445	+	Splice_Site	DEL	TAGC	TAGC	-																															tccaccaatgtgttcattttAgctgaaaaaattaggtgtga																										TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	TAGC	TAGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr10:121567442_121567445delTAGC	ENST00000361976.2	+	13	1606_1608	c.1440_1442delTAGC	c.(1438-1443)catagc>cac	p.S481fs		NM_014937.3	NP_055752.1	Q01968	OCRL_HUMAN	inositol polyphosphate-5-phosphatase F	792	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)		TGTTCATTTTAGCTGAAAAAATTA	0.387																																					.		Atlas-INDEL	.											.	INPP5F	112	.	0			.						PASS	.																																			SO:0001630	splice_region_variant	22876	.			.	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.1441-1TAGC>-	chr10.hg19:g.121567442_121567445delTAGC		91.0	0.0	0		53.0	17.0	0.320755	.	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	Splice_Site	DEL	ENST00000361976.2	hg19	CCDS7616.1																																																																																			.	.	.	none		0.387	INPP5F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050679.1	NM_014937	Frame_Shift_Del	-	121567445	TAGC	-	121567442	8	5	15	1	0	1	0	1	0	0	1	0	7765	434	15	0	1489	0	INPP5F	10	121567442	Splice_Site	DEL	TAGC	TCGA-2Z-A9JL-01A-11D-A42J-10	19302313	121567442	13967305	43	1071											
AP2A2	161	hgsc.bcm.edu	37	chr11	993296	993296	+	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	cttcgcaggctcttcaggctCccgcgtgccacgagaacctg	6	8	11	16	4	2	1	1	0	1	1	4	2	3	1	3	2	2	3	3	2	1	2			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr11:993296C>T	ENST00000448903.2	+	12	1606	c.1465C>T	c.(1465-1467)Ccc>Tcc	p.P489S	AP2A2_ENST00000534328.1_Intron|AP2A2_ENST00000332231.5_Missense_Mutation_p.P490S	NM_001242837.1|NM_012305.3	NP_001229766.1|NP_036437.1	O94973	AP2A2_HUMAN	adaptor-related protein complex 2, alpha 2 subunit	489					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)	21		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)		TCTTCAGGCTCCCGCGTGCCA	0.622																																					p.P490S		Atlas-SNP	.											.	AP2A2	50	.	0			c.C1468T						PASS	.						35	41	39					11																	993296		1981	4155	6136	SO:0001583	missense	161	exon12			CAGGCTCCCGCGT	AB020706	CCDS44512.1, CCDS73234.1	11p15.5	2008-07-18			ENSG00000183020	ENSG00000183020			562	protein-coding gene	gene with protein product	"alpha-adaptin C; Huntingtin interacting protein J", "adaptin, alpha B", "clathrin-associated/assembly/adaptor protein, large, alpha 2"	607242		CLAPA2, ADTAB		9700202, 2564002	Standard	NM_012305		Approved	DKFZP564D1864, HYPJ, KIAA0899, HIP9	uc001lst.2	O94973	OTTHUMG00000165627	ENST00000448903.2:c.1465C>T	chr11.hg19:g.993296C>T	ENSP00000413234:p.Pro489Ser	48.0	0.0	.		44.0	12.0	.	NM_001242837	O75403|Q53ET1|Q96SI8	Missense_Mutation	SNP	ENST00000448903.2	hg19	CCDS44512.1	.	.	.	.	.	.	.	.	.	.	C	13.51	2.257403	0.39896	.	.	ENSG00000183020	ENST00000448903;ENST00000332231;ENST00000448757;ENST00000529125;ENST00000452310	T;T	0.37915	1.17;1.17	3.66	3.66	0.41972	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.51550	0.1681	L	0.48877	1.53	0.80722	D	1	D;P;P	0.69078	0.997;0.787;0.882	D;P;P	0.77557	0.99;0.469;0.604	T	0.49224	-0.8962	10	0.33141	T	0.24	-10.2646	16.226	0.82293	0.0:1.0:0.0:0.0	.	228;490;489	B7Z1Q4;O94973-2;O94973	.;.;AP2A2_HUMAN	S	489;490;490;226;229	ENSP00000413234:P489S;ENSP00000327694:P490S	ENSP00000327694:P490S	P	+	1	0	AP2A2	983296	1.000000	0.71417	0.248000	0.24265	0.485000	0.33311	4.879000	0.63100	1.979000	0.57680	0.462000	0.41574	CCC	.	.	.	none		0.622	AP2A2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385431.2	NM_012305		T	993296	C	T	993296	3	4	15	1	0	0	0	0	1	0	0	0	740	855	30	2	1511	2	AP2A2	11	993296	Missense_Mutation	SNP	C	TCGA-2Z-A9JL-01A-11D-A42J-10		993296	134013220	44	1072											
PPFIBP2	8495	hgsc.bcm.edu	37	chr11	7660962	7660962	+	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	ctttctctcaccttccaataGgacagccctttcttggcgga	7	13	7	14	1	3	0	1	0	2	0	5	2	4	2	3	3	1	0	3	3	2	5			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr11:7660962G>A	ENST00000299492.4	+	15	1624		c.e15-1		PPFIBP2_ENST00000533792.1_Splice_Site|PPFIBP2_ENST00000530181.1_Splice_Site|PPFIBP2_ENST00000528883.1_Splice_Site|PPFIBP2_ENST00000530582.1_Splice_Site	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)						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)		CCTTCCAATAGGACAGCCCTT	0.493																																					.		Atlas-SNP	.											.	PPFIBP2	87	.	0			c.1237-1G>A						PASS	.						182	189	186					11																	7660962		2201	4296	6497	SO:0001630	splice_region_variant	8495	exon15			CCAATAGGACAGC	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.1237-1G>A	chr11.hg19:g.7660962G>A		135.0	0.0	.		109.0	42.0	.	NM_003621	B7Z433|E9PK77|O75337|Q8WW26	Splice_Site	SNP	ENST00000299492.4	hg19	CCDS31419.1	.	.	.	.	.	.	.	.	.	.	G	11.41	1.631854	0.29068	.	.	ENSG00000166387	ENST00000299492;ENST00000533792;ENST00000537467;ENST00000541115;ENST00000528883;ENST00000530181;ENST00000534409;ENST00000530081	.	.	.	5.78	5.78	0.91487	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5173	0.75833	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PPFIBP2	7617538	1.000000	0.71417	0.995000	0.50966	0.317000	0.28152	6.002000	0.70693	2.731000	0.93534	0.557000	0.71058	.	.	.	.	none		0.493	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621	Intron	A	7660962	G	A	7660962	5	1	15	1	0	0	0	0	0	0	1	0	12321	1014	35	2	1290	2	PPFIBP2	11	7660962	Splice_Site	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10	6667666	7660962	127345554	45	1073											
NAV2	89797	hgsc.bcm.edu	37	chr11	19854129	19854129	+	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	cagatggcgtcctcctggccCagattatccaggttgtgggt	6	11	13	11	1	0	2	0	0	0	2	3	2	3	2	4	4	0	1	4	4	1	2			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr11:19854129C>G	ENST00000396087.3	+	2	466	c.367C>G	c.(367-369)Cag>Gag	p.Q123E	NAV2_ENST00000527559.2_Missense_Mutation_p.Q52E|NAV2_ENST00000349880.4_Missense_Mutation_p.Q123E|NAV2_ENST00000360655.4_Missense_Mutation_p.Q59E|NAV2_ENST00000540292.1_Missense_Mutation_p.Q54E|NAV2_ENST00000396085.1_Missense_Mutation_p.Q123E|NAV2_ENST00000534229.1_3'UTR	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	123	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				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						CCTCCTGGCCCAGATTATCCA	0.527																																					p.Q123E		Atlas-SNP	.											.	NAV2	255	.	0			c.C367G						PASS	.						195	201	199					11																	19854129		2199	4293	6492	SO:0001583	missense	89797	exon2			CTGGCCCAGATTA	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.367C>G	chr11.hg19:g.19854129C>G	ENSP00000379396:p.Gln123Glu	45.0	0.0	.		27.0	8.0	.	NM_145117	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Missense_Mutation	SNP	ENST00000396087.3	hg19	CCDS58126.1	.	.	.	.	.	.	.	.	.	.	C	5.035	0.192111	0.09599	.	.	ENSG00000166833	ENST00000360655;ENST00000396085;ENST00000349880;ENST00000396087;ENST00000527559;ENST00000540292	T;T;T;T;T;T	0.58940	0.3;0.3;0.3;0.3;0.3;0.3	5.83	4.9	0.64082	.	0.100385	0.42964	D	0.000629	T	0.31734	0.0806	N	0.03903	-0.33	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.17868	-1.0355	9	.	.	.	.	13.0026	0.58685	0.0:0.6311:0.3689:0.0	.	123;59	Q8IVL1-3;Q8IVL1-4	.;.	E	59;123;123;123;52;54	ENSP00000353871:Q59E;ENSP00000379394:Q123E;ENSP00000309577:Q123E;ENSP00000379396:Q123E;ENSP00000435395:Q52E;ENSP00000443489:Q54E	.	Q	+	1	0	NAV2	19810705	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.992000	0.56980	2.763000	0.94921	0.561000	0.74099	CAG	.	.	.	none		0.527	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		G	19854129	C	G	19854129	3	3	15	1	0	0	0	0	1	0	0	0	10191	595	21	4	452	4	NAV2	11	19854129	Missense_Mutation	SNP	C	TCGA-2Z-A9JL-01A-11D-A42J-10	12193167	19854129	115152387	46	1074											
GPHA2	170589	hgsc.bcm.edu	37	chr11	64702479	64702479	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaccttcttcaggccactgAtggtgcagcactgagagacg	9	9	11	12	1	3	3	2	2	1	1	3	4	3	3	2	2	2	2	2	2	0	2			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr11:64702479A>G	ENST00000279168.2	-	3	326	c.272T>C	c.(271-273)aTc>aCc	p.I91T	GPHA2_ENST00000533257.1_Missense_Mutation_p.I91T|GPHA2_ENST00000532246.1_Missense_Mutation_p.I91T	NM_130769.3	NP_570125.1	Q96T91	GPHA2_HUMAN	glycoprotein hormone alpha 2	91						extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|prostate(1)	3						CAGGCCACTGATGGTGCAGCA	0.617																																					p.I91T		Atlas-SNP	.											.	GPHA2	13	.	0			c.T272C						PASS	.						118	119	119					11																	64702479		2201	4297	6498	SO:0001583	missense	170589	exon3			CCACTGATGGTGC	AF260739	CCDS8086.1	11q13.1	2008-07-18				ENSG00000149735			18054	protein-coding gene	gene with protein product	"glycoprotein alpha 2", "cysteine knot protein"	609651				11809971	Standard	NM_130769		Approved	GPA2, ZSIG51, A2, MGC126572	uc001oca.3	Q96T91		ENST00000279168.2:c.272T>C	chr11.hg19:g.64702479A>G	ENSP00000279168:p.Ile91Thr	77.0	0.0	.		64.0	24.0	.	NM_130769	Q52LE2	Missense_Mutation	SNP	ENST00000279168.2	hg19	CCDS8086.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.178283	0.78564	.	.	ENSG00000149735	ENST00000279168;ENST00000533257;ENST00000532246	T;T	0.28666	1.6;1.6	4.27	4.27	0.50696	Cystine knot, C-terminal (1);	0.000000	0.64402	D	0.000001	T	0.55545	0.1927	M	0.80616	2.505	0.58432	D	0.999998	D	0.76494	0.999	D	0.83275	0.996	T	0.61633	-0.7023	10	0.87932	D	0	.	11.7091	0.51614	1.0:0.0:0.0:0.0	.	91	Q96T91	GPHA2_HUMAN	T	91	ENSP00000279168:I91T;ENSP00000432918:I91T	ENSP00000279168:I91T	I	-	2	0	GPHA2	64459055	1.000000	0.71417	0.997000	0.53966	0.984000	0.73092	8.005000	0.88553	1.937000	0.56155	0.533000	0.62120	ATC	.	.	.	none		0.617	GPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385470.1	NM_130769		G	64702479	A	G	64702479	3	3	15	1	0	0	0	0	1	0	0	0	6615	333	12	3	125	3	GPHA2	11	64702479	Missense_Mutation	SNP	A	TCGA-2Z-A9JL-01A-11D-A42J-10	44848350	64702479	70304037	47	1075											
NPAS4	266743	hgsc.bcm.edu	37	chr11	66190646	66190646	+	Missense_Mutation	SNP	T	T	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	aactgctttgtaaatcatggTatggactgctgcaccccgag	10	11	10	10	1	1	0	1	0	0	0	1	2	1	1	2	2	4	5	2	2	4	3			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr11:66190646T>G	ENST00000311034.2	+	5	927	c.751T>G	c.(751-753)Tat>Gat	p.Y251D		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	251	PAS 2. {ECO:0000255|PROSITE- ProRule:PRU00140}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|kidney(3)|large_intestine(11)|liver(2)|lung(20)|ovary(1)|prostate(3)|skin(3)	49						TAAATCATGGTATGGACTGCT	0.537																																					p.Y251D		Atlas-SNP	.											.	NPAS4	133	.	0			c.T751G						PASS	.						122	93	103					11																	66190646		2200	4295	6495	SO:0001583	missense	266743	exon5			TCATGGTATGGAC	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.751T>G	chr11.hg19:g.66190646T>G	ENSP00000311196:p.Tyr251Asp	90.0	0.0	.		58.0	23.0	.	NM_178864	B7ZL81|Q8N8S5|Q8N9Q9	Missense_Mutation	SNP	ENST00000311034.2	hg19	CCDS8138.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.572924	0.86542	.	.	ENSG00000174576	ENST00000311034	T	0.19394	2.15	5.65	5.65	0.86999	PAS fold-3 (1);PAS (2);	0.000000	0.49916	D	0.000132	T	0.51890	0.1701	M	0.86343	2.81	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.60047	-0.7339	10	0.87932	D	0	-6.2055	13.8382	0.63421	0.0:0.0:0.0:1.0	.	251	Q8IUM7	NPAS4_HUMAN	D	251	ENSP00000311196:Y251D	ENSP00000311196:Y251D	Y	+	1	0	NPAS4	65947222	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.350000	0.79385	2.150000	0.67090	0.528000	0.53228	TAT	.	.	.	none		0.537	NPAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392634.1	NM_178864		G	66190646	T	G	66190646	3	3	15	1	0	0	0	0	1	0	0	0	10572	1638	57	5	769	5	NPAS4	11	66190646	Missense_Mutation	SNP	T	TCGA-2Z-A9JL-01A-11D-A42J-10	1488167	66190646	68815870	48	1076											
CARNS1	57571	hgsc.bcm.edu	37	chr11	67186483	67186483	+	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	ggagcttcggctgagctggcCcggctgctggaggaccggct	4	7	18	12	3	0	1	0	1	0	0	1	4	0	4	2	7	3	6	2	7	0	1			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr11:67186483C>G	ENST00000307823.3	+	4	704	c.252C>G	c.(250-252)gcC>gcG	p.A84A	CARNS1_ENST00000445895.2_Silent_p.A207A|CARNS1_ENST00000531040.1_Silent_p.A207A|CARNS1_ENST00000423745.2_Silent_p.A84A	NM_020811.1	NP_065862.1	A5YM72	CRNS1_HUMAN	carnosine synthase 1	84					ATP catabolic process (GO:0006200)|carnosine biosynthetic process (GO:0035499)		ATP binding (GO:0005524)|ATPase activity (GO:0016887)|carnosine synthase activity (GO:0047730)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)	11						CTGAGCTGGCCCGGCTGCTGG	0.692																																					p.A207A		Atlas-SNP	.											.	CARNS1	60	.	0			c.C621G						PASS	.						5	8	7					11																	67186483		2021	4137	6158	SO:0001819	synonymous_variant	57571	exon5			GCTGGCCCGGCTG		CCDS44658.1, CCDS53667.1	11q13.1	2010-03-25	2010-03-25	2010-03-25	ENSG00000172508	ENSG00000172508			29268	protein-coding gene	gene with protein product		613368	"ATP-grasp domain containing 1"	ATPGD1		20097752	Standard	NM_020811		Approved	KIAA1394	uc010rpr.2	A5YM72		ENST00000307823.3:c.252C>G	chr11.hg19:g.67186483C>G		45.0	0.0	.		41.0	18.0	.	NM_001166222	A8K1M3|B4DFC6|E9PK38|F5H427|Q8N467|Q9P2F3	Silent	SNP	ENST00000307823.3	hg19	CCDS44658.1																																																																																			.	.	.	none		0.692	CARNS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395501.1	NM_020811		G	67186483	C	G	67186483	2	3	15	1	0	0	0	0	0	0	0	1	2658	610	22	4		4	CARNS1	11	67186483	Silent	SNP	C	TCGA-2Z-A9JL-01A-11D-A42J-10	995837	67186483	67820033	49	1077											
POU2AF1	5450	hgsc.bcm.edu	37	chr11	111229622	111229622	+	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	ggtatggccgggccggggctGgggcttgctccggagctgtg	2	8	21	10	3	0	0	0	0	0	0	1	1	1	1	3	8	2	5	3	8	1	2			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr11:111229622G>A	ENST00000393067.3	-	2	552	c.38C>T	c.(37-39)cCa>cTa	p.P13L		NM_006235.2	NP_006226.2	Q16633	OBF1_HUMAN	POU class 2 associating factor 1	13					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)		GGCCGGGGCTGGGGCTTGCTC	0.632			T	BCL6	NHL																																p.P13L		Atlas-SNP	.		Dom	yes		11	11q23.1	5450	"POU domain, class 2, associating factor 1 (OBF1)"		L	.	POU2AF1	23	.	0			c.C38T						PASS	.						48	49	49					11																	111229622		2201	4297	6498	SO:0001583	missense	5450	exon2			GGGGCTGGGGCTT		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.38C>T	chr11.hg19:g.111229622G>A	ENSP00000376786:p.Pro13Leu	58.0	0.0	.		34.0	8.0	.	NM_006235	B2R8Z9|Q14983	Missense_Mutation	SNP	ENST00000393067.3	hg19	CCDS31675.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.165888	0.78339	.	.	ENSG00000110777	ENST00000393067;ENST00000531398	T;T	0.32753	1.44;1.44	5.0	5.0	0.66597	.	0.238634	0.35936	N	0.002889	T	0.33990	0.0882	L	0.45581	1.43	0.49389	D	0.999781	P	0.48089	0.905	P	0.47941	0.562	T	0.03761	-1.1006	10	0.15499	T	0.54	-1.2837	16.0815	0.81007	0.0:0.0:1.0:0.0	.	13	Q16633	OBF1_HUMAN	L	13;15	ENSP00000376786:P13L;ENSP00000433527:P15L	ENSP00000376786:P13L	P	-	2	0	POU2AF1	110734832	0.999000	0.42202	0.973000	0.42090	0.656000	0.38851	3.990000	0.56965	2.331000	0.79229	0.305000	0.20034	CCA	.	.	.	none		0.632	POU2AF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391002.1	NM_006235		A	111229622	G	A	111229622	3	1	15	1	0	0	0	0	1	0	0	0	12277	1348	47	2	748	2	POU2AF1	11	111229622	Missense_Mutation	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10	44043139	111229622	23776894	50	1078											
PFKM	5213	hgsc.bcm.edu	37	chr12	48536588	48536588	+	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	tgtgaccgcatcaagcagtcAgcagctggcaccaagcgtcg	10	6	12	13	3	2	1	2	1	0	0	3	1	2	1	2	1	4	5	2	1	2	0			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr12:48536588A>T	ENST00000312352.7	+	18	1716	c.1677A>T	c.(1675-1677)tcA>tcT	p.S559S	PFKM_ENST00000551804.1_Silent_p.S528S|PFKM_ENST00000547587.1_Silent_p.S559S|PFKM_ENST00000359794.5_Silent_p.S559S|PFKM_ENST00000340802.6_Silent_p.S630S|PFKM_ENST00000395233.2_Silent_p.S528S	NM_001166687.1	NP_001160159.1	P08237	PFKAM_HUMAN	phosphofructokinase, muscle	559	C-terminal regulatory PFK domain 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|muscle cell cellular homeostasis (GO:0046716)|positive regulation of insulin secretion (GO:0032024)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	6-phosphofructokinase complex (GO:0005945)|apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|sperm principal piece (GO:0097228)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|fructose binding (GO:0070061)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			NS(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						TCAAGCAGTCAGCAGCTGGCA	0.512																																					p.S630S		Atlas-SNP	.											.	PFKM	117	.	0			c.A1890T						PASS	.						137	122	127					12																	48536588		2203	4300	6503	SO:0001819	synonymous_variant	5213	exon20			GCAGTCAGCAGCT	M26066	CCDS8760.1, CCDS53786.1	12q13.11	2014-06-13					2.7.1.11		8877	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 122"	610681	"phosphofructokinase, polypeptide X"	PFKX			Standard	NM_001166686		Approved	PFK-1, PPP1R122	uc001rrb.2	P08237		ENST00000312352.7:c.1677A>T	chr12.hg19:g.48536588A>T		97.0	0.0	.		117.0	65.0	.	NM_001166686	J3KNX3|Q16814|Q16815|Q6ZTT1	Silent	SNP	ENST00000312352.7	hg19	CCDS8760.1																																																																																			.	.	.	none		0.512	PFKM-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406490.1	NM_000289		T	48536588	A	T	48536588	2	4	15	1	0	0	0	0	0	0	0	1	11772	175	7	5		5	PFKM	12	48536588	Silent	SNP	A	TCGA-2Z-A9JL-01A-11D-A42J-10		48536588	85315307	51	1079											
KRT80	144501	hgsc.bcm.edu	37	chr12	52565443	52565443	+	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	tcggggcaagaggactcaccGgttttgcacctggactgcac	8	8	13	12	2	1	1	1	0	0	1	2	3	1	3	2	5	2	4	2	5	1	2			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr12:52565443G>A	ENST00000394815.2	-	8	1330	c.1233C>T	c.(1231-1233)acC>acT	p.T411T	KRT80_ENST00000313234.5_Splice_Site_p.T411T	NM_182507.2	NP_872313.2	Q6KB66	K2C80_HUMAN	keratin 80	411	Tail.					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)		AGGACTCACCGGTTTTGCACC	0.602																																					p.T411T	GBM(178;2309 2916 15678 35873)	Atlas-SNP	.											.	KRT80	68	.	0			c.C1233T						PASS	.						55	43	47					12																	52565443		2200	4298	6498	SO:0001630	splice_region_variant	144501	exon8			CTCACCGGTTTTG	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.1234+1C>T	chr12.hg19:g.52565443G>A		169.0	0.0	.		169.0	88.0	.	NM_182507	Q6P1A5|Q7Z3Q0	Silent	SNP	ENST00000394815.2	hg19	CCDS8821.2																																																																																			.	.	.	none		0.602	KRT80-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316757.1	NM_182507	Silent	A	52565443	G	A	52565443	5	1	15	1	0	0	0	0	0	0	1	0	8501	1130	39	1	168	1	KRT80	12	52565443	Splice_Site	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10	4028855	52565443	81286452	52	1080											
MYO1A	4640	hgsc.bcm.edu	37	chr12	57431392	57431392	+	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	gccagctcccccgaggacatGctcagctcccccaggacctt	7	6	9	19	1	1	0	1	0	0	0	3	3	3	2	6	2	3	3	6	2	0	1			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr12:57431392G>T	ENST00000442789.2	-	20	2282	c.1995C>A	c.(1993-1995)agC>agA	p.S665R	MYO1A_ENST00000544473.1_Missense_Mutation_p.S503R|MYO1A_ENST00000300119.3_Missense_Mutation_p.S665R|MYO1A_ENST00000476795.1_5'Flank	NM_001256041.1	NP_001242970.1	Q9UBC5	MYO1A_HUMAN	myosin IA	665	Myosin motor.				microvillus assembly (GO:0030033)|sensory perception of sound (GO:0007605)|vesicle localization (GO:0051648)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|brush border (GO:0005903)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(7)|urinary_tract(3)	50						CCGAGGACATGCTCAGCTCCC	0.512																																					p.S665R		Atlas-SNP	.											.	MYO1A	122	.	0			c.C1995A						PASS	.						227	233	231					12																	57431392		2203	4300	6503	SO:0001583	missense	4640	exon19			GGACATGCTCAGC	L29137	CCDS8929.1	12q13-q15	2011-09-27			ENSG00000166866	ENSG00000166866		"Myosins / Myosin superfamily : Class I"	7595	protein-coding gene	gene with protein product		601478		MYHL, DFNA48		8884266, 12736868	Standard	NM_001256041		Approved		uc009zpd.3	Q9UBC5	OTTHUMG00000149899	ENST00000442789.2:c.1995C>A	chr12.hg19:g.57431392G>T	ENSP00000393392:p.Ser665Arg	77.0	0.0	.		88.0	23.0	.	NM_005379	Q9UQD7	Missense_Mutation	SNP	ENST00000442789.2	hg19	CCDS8929.1	.	.	.	.	.	.	.	.	.	.	G	8.653	0.898793	0.17686	.	.	ENSG00000166866	ENST00000300119;ENST00000442789;ENST00000544473	D;D;D	0.87412	-2.25;-2.25;-2.25	4.96	0.968	0.19680	Myosin head, motor domain (2);	0.445812	0.26654	N	0.023187	T	0.71728	0.3374	N	0.12182	0.205	0.09310	N	1	B	0.24043	0.096	B	0.28465	0.09	T	0.57923	-0.7727	10	0.23891	T	0.37	.	6.547	0.22412	0.4246:0.0:0.5754:0.0	.	665	Q9UBC5	MYO1A_HUMAN	R	665;665;503	ENSP00000300119:S665R;ENSP00000393392:S665R;ENSP00000440514:S503R	ENSP00000300119:S665R	S	-	3	2	MYO1A	55717659	0.000000	0.05858	0.009000	0.14445	0.955000	0.61496	0.230000	0.17852	0.143000	0.18926	0.591000	0.81541	AGC	.	.	.	none		0.512	MYO1A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313833.2	NM_005379		T	57431392	G	T	57431392	3	4	15	1	0	0	0	0	1	0	0	0	10075	1310	46	4	1176	4	MYO1A	12	57431392	Missense_Mutation	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10	4865949	57431392	76420503	53	1081											
PTPRB	5787	hgsc.bcm.edu	37	chr12	71016216	71016216	+	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	gagtagtcgacaaaacccatGatgtgtctgtaattccagtc	12	11	9	9	1	1	1	0	1	1	0	4	3	2	1	2	0	1	2	2	0	4	3			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr12:71016216G>T	ENST00000550358.1	-	3	687	c.662C>A	c.(661-663)tCa>tAa	p.S221*	PTPRB_ENST00000334414.6_Nonsense_Mutation_p.S221*|PTPRB_ENST00000551525.1_Nonsense_Mutation_p.S220*|PTPRB_ENST00000538174.2_5'UTR			P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	0	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			CAAAACCCATGATGTGTCTGT	0.512																																					p.S221X		Atlas-SNP	.											.	PTPRB	676	.	0			c.C662A						PASS	.						172	184	180					12																	71016216		2051	4200	6251	SO:0001587	stop_gained	5787	exon3			ACCCATGATGTGT	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000550358.1:c.662C>A	chr12.hg19:g.71016216G>T	ENSP00000448058:p.Ser221*	60.0	0.0	.		90.0	44.0	.	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Nonsense_Mutation	SNP	ENST00000550358.1	hg19		.	.	.	.	.	.	.	.	.	.	G	37	6.457421	0.97581	.	.	ENSG00000127329	ENST00000334414;ENST00000550358;ENST00000544694;ENST00000551525;ENST00000548122	.	.	.	5.71	5.71	0.89125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.6503	0.88162	0.0:0.0:1.0:0.0	.	.	.	.	X	221;221;221;220;100	.	ENSP00000334928:S221X	S	-	2	0	PTPRB	69302483	0.599000	0.26891	0.070000	0.20053	0.532000	0.34746	3.878000	0.56130	2.686000	0.91538	0.650000	0.86243	TCA	.	.	.	none		0.512	PTPRB-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404436.1			T	71016216	G	T	71016216	4	4	15	1	0	0	0	0	0	1	0	0	12809	1294	45	4	6171	4	PTPRB	12	71016216	Nonsense_Mutation	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10	13584824	71016216	62835679	54	1082											
NAA25	80018	hgsc.bcm.edu	37	chr12	112478370	112478370	+	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	ctaagaggtcacctttacatTtactgaagacatctgaaaac	15	11	6	9	0	2	4	1	2	1	2	2	4	2	4	1	1	3	0	1	1	6	5			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr12:112478370T>A	ENST00000261745.4	-	21	2701	c.2453A>T	c.(2452-2454)aAa>aTa	p.K818I	MIR3657_ENST00000584818.1_RNA	NM_024953.3	NP_079229.2	Q14CX7	NAA25_HUMAN	N(alpha)-acetyltransferase 25, NatB auxiliary subunit	818						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						ACCTTTACATTTACTGAAGAC	0.284																																					p.K818I		Atlas-SNP	.											.	NAA25	105	.	0			c.A2453T						PASS	.						66	65	65					12																	112478370		2201	4295	6496	SO:0001583	missense	80018	exon21			TTACATTTACTGA	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.2453A>T	chr12.hg19:g.112478370T>A	ENSP00000261745:p.Lys818Ile	51.0	0.0	.		89.0	51.0	.	NM_024953	A0JLU7|Q6MZH1|Q7Z4N6|Q9H911	Missense_Mutation	SNP	ENST00000261745.4	hg19	CCDS9159.1	.	.	.	.	.	.	.	.	.	.	T	14.77	2.633358	0.47049	.	.	ENSG00000111300	ENST00000261745;ENST00000550701	T	0.26957	1.7	5.53	0.105	0.14535	.	0.665279	0.15928	N	0.237786	T	0.13713	0.0332	L	0.27053	0.805	0.28371	N	0.920017	B;B	0.20671	0.047;0.047	B;B	0.15052	0.012;0.012	T	0.14587	-1.0467	10	0.59425	D	0.04	-2.7143	2.7285	0.05220	0.1164:0.1349:0.128:0.6207	.	818;818	A8K8X0;Q14CX7	.;NAA25_HUMAN	I	818;24	ENSP00000261745:K818I	ENSP00000261745:K818I	K	-	2	0	NAA25	110962753	1.000000	0.71417	0.998000	0.56505	0.980000	0.70556	1.657000	0.37366	0.061000	0.16311	0.533000	0.62120	AAA	.	.	.	none		0.284	NAA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405205.1	NM_024953		A	112478370	T	A	112478370	3	1	15	1	0	0	0	0	1	0	0	0	10128	1841	64	5	481	5	NAA25	12	112478370	Missense_Mutation	SNP	T	TCGA-2Z-A9JL-01A-11D-A42J-10	41462154	112478370	21373525	55	1083											
NAA25	80018	hgsc.bcm.edu	37	chr12	112499043	112499043	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaccacactcaatttctgAtttttatccatggtgtggta	9	16	7	9	0	2	2	1	2	1	0	3	2	3	2	2	2	0	1	2	2	3	5			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr12:112499043A>G	ENST00000261745.4	-	12	1547	c.1299T>C	c.(1297-1299)aaT>aaC	p.N433N	RP1-267L14.3_ENST00000551125.1_RNA	NM_024953.3	NP_079229.2	Q14CX7	NAA25_HUMAN	N(alpha)-acetyltransferase 25, NatB auxiliary subunit	433						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						TCAATTTCTGATTTTTATCCA	0.453																																					p.N433N		Atlas-SNP	.											.	NAA25	105	.	0			c.T1299C						PASS	.						121	99	106					12																	112499043		2203	4300	6503	SO:0001819	synonymous_variant	80018	exon12			TTTCTGATTTTTA	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.1299T>C	chr12.hg19:g.112499043A>G		60.0	0.0	.		48.0	23.0	.	NM_024953	A0JLU7|Q6MZH1|Q7Z4N6|Q9H911	Silent	SNP	ENST00000261745.4	hg19	CCDS9159.1																																																																																			.	.	.	none		0.453	NAA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405205.1	NM_024953		G	112499043	A	G	112499043	2	3	15	1	0	0	0	0	0	0	0	1	10128	330	12	3		3	NAA25	12	112499043	Silent	SNP	A	TCGA-2Z-A9JL-01A-11D-A42J-10	20673	112499043	21352852	56	1084											
EP400	57634	hgsc.bcm.edu	37	chr12	132547068	132547068	+	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	tgcacatttccagcttctcaGgcagcagcagcagcagcagc	10	7	10	14	0	1	0	1	0	1	0	3	0	2	0	1	1	8	8	1	1	0	2	rs68030464|rs367737531|rs60930033		TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr12:132547068G>A	ENST00000333577.4	+	48	8373	c.8264G>A	c.(8263-8265)aGg>aAg	p.R2755K	EP400_ENST00000332482.4_Missense_Mutation_p.R2682K|EP400_ENST00000389561.2_Missense_Mutation_p.R2719K|EP400_ENST00000389562.2_Missense_Mutation_p.R2718K|EP400_ENST00000330386.6_Missense_Mutation_p.R2638K			Q96L91	EP400_HUMAN	E1A binding protein p400	2755	Interaction with ZNF42. {ECO:0000250}.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.R2718K(2)		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)		CAGCTTCTCAGgcagcagcag	0.567																																					p.R2719K		Atlas-SNP	.											EP400,NS,carcinoma,0,2	EP400	370	.	2	Substitution - Missense(2)	lung(2)	c.G8156A						PASS	.						48	48	48					12																	132547068		2203	4300	6503	SO:0001583	missense	57634	exon47			TTCTCAGGCAGCA	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.8264G>A	chr12.hg19:g.132547068G>A	ENSP00000333602:p.Arg2755Lys	67.0	1.0	.		108.0	8.0	.	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	hg19		.	.	.	.	.	.	.	.	.	.	G	15.46	2.840128	0.51057	.	.	ENSG00000183495	ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000541296	D;D;D;D;D	0.90133	-2.62;-2.62;-2.62;-2.62;-2.62	4.89	4.89	0.63831	.	0.266539	0.31542	N	0.007465	D	0.91264	0.7246	L	0.27053	0.805	0.26223	N	0.97913	D;D;D	0.53312	0.959;0.959;0.959	D;D;D	0.65684	0.937;0.937;0.937	D	0.84986	0.0891	10	0.29301	T	0.29	.	17.0403	0.86487	0.0:0.0:1.0:0.0	.	2719;2638;2718	Q96L91-2;Q96L91-4;Q96L91-5	.;.;.	K	2755;2719;2718;2682;2638;2719	ENSP00000333602:R2755K;ENSP00000374212:R2719K;ENSP00000374213:R2718K;ENSP00000331737:R2682K;ENSP00000330620:R2638K	ENSP00000330620:R2638K	R	+	2	0	EP400	131113021	1.000000	0.71417	0.878000	0.34440	0.286000	0.27126	5.957000	0.70323	2.236000	0.73375	0.561000	0.74099	AGG	.	.	.	none		0.567	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		A	132547068	G	A	132547068	3	1	15	1	0	0	0	0	1	0	0	0	5151	1000	35	2	8335	2	EP400	12	132547068	Missense_Mutation	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10	20048025	132547068	1304827	57	1085											
C13orf33	84935	hgsc.bcm.edu	37	chr13	31495803	31495803	+	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	tcaaagctgatgcattatttGatttcttctattggtttggg	8	19	9	5	0	3	2	1	2	2	0	3	2	3	2	0	2	2	3	0	2	3	7			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr13:31495803G>T	ENST00000380482.4	+	4	932	c.607G>T	c.(607-609)Gat>Tat	p.D203Y	TEX26-AS1_ENST00000586464.1_RNA|TEX26-AS1_ENST00000590721.1_RNA|TEX26-AS1_ENST00000588726.1_RNA|TEX26-AS1_ENST00000451495.2_RNA|TEX26-AS1_ENST00000592950.1_RNA|TEX26-AS1_ENST00000588425.1_RNA|TEX26-AS1_ENST00000586973.1_RNA|TEX26-AS1_ENST00000590344.1_RNA|TEX26-AS1_ENST00000585870.1_RNA|TEX26-AS1_ENST00000593246.1_RNA	NM_032849.3	NP_116238	Q5VYS4	MEDAG_HUMAN	mesenteric estrogen-dependent adipogenesis	203					positive regulation of fat cell differentiation (GO:0045600)	cytoplasm (GO:0005737)											TGCATTATTTGATTTCTTCTA	0.348																																					p.D203Y		Atlas-SNP	.											.	.	.	.	0			c.G607T						PASS	.						88	90	89					13																	31495803		2203	4300	6503	SO:0001583	missense	84935	exon4			TTATTTGATTTCT	AB055407	CCDS9338.1	13q12.3	2013-10-11	2012-09-26	2012-09-26	ENSG00000102802	ENSG00000102802			25926	protein-coding gene	gene with protein product	"mesenteric estrogen-dependent adipose 4", "activated in W/Wv mouse stomach 3 homolog"		"chromosome 13 open reading frame 33"	C13orf33		22510272	Standard	NM_032849		Approved	FLJ14834, AWMS3, MEDA-4	uc001uth.4	Q5VYS4	OTTHUMG00000016679	ENST00000380482.4:c.607G>T	chr13.hg19:g.31495803G>T	ENSP00000369849:p.Asp203Tyr	118.0	0.0	.		106.0	10.0	.	NM_032849	Q8IXF1|Q96K26|Q96NC8	Missense_Mutation	SNP	ENST00000380482.4	hg19	CCDS9338.1	.	.	.	.	.	.	.	.	.	.	G	17.59	3.427018	0.62733	.	.	ENSG00000102802	ENST00000380482	T	0.60548	0.18	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.67353	0.2884	L	0.32530	0.975	0.43039	D	0.994626	D	0.89917	1.0	D	0.87578	0.998	T	0.70930	-0.4738	10	0.87932	D	0	-23.8071	15.9427	0.79771	0.0:0.0:1.0:0.0	.	203	Q5VYS4	CM033_HUMAN	Y	203	ENSP00000369849:D203Y	ENSP00000369849:D203Y	D	+	1	0	C13orf33	30393803	1.000000	0.71417	1.000000	0.80357	0.763000	0.43281	5.741000	0.68638	2.509000	0.84616	0.462000	0.41574	GAT	.	.	.	none		0.348	MEDAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044375.1	NM_032849		T	31495803	G	T	31495803	3	4	15	1	0	0	0	0	1	0	0	0	1729	1290	45	4	621	4	C13orf33	13	31495803	Missense_Mutation	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10		31495803	83674075	58	1086											
FREM2	341640	hgsc.bcm.edu	37	chr13	39263022	39263022	+	Missense_Mutation	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	tacagtggctgagctggcagCcggccaggtggtctaccagc	7	7	15	12	1	1	1	0	1	1	0	1	1	1	1	3	5	5	3	3	5	2	2			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr13:39263022C>T	ENST00000280481.7	+	1	1757	c.1541C>T	c.(1540-1542)gCc>gTc	p.A514V		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	514					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)		GAGCTGGCAGCCGGCCAGGTG	0.602																																					p.A514V		Atlas-SNP	.											.	FREM2	385	.	0			c.C1541T						PASS	.						25	25	25					13																	39263022		2203	4299	6502	SO:0001583	missense	341640	exon1			TGGCAGCCGGCCA	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.1541C>T	chr13.hg19:g.39263022C>T	ENSP00000280481:p.Ala514Val	70.0	0.0	.		37.0	19.0	.	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	hg19	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	C	12.60	1.985880	0.35036	.	.	ENSG00000150893	ENST00000280481	T	0.21734	1.99	5.4	5.4	0.78164	.	0.174652	0.49916	D	0.000121	T	0.27027	0.0662	M	0.77313	2.365	0.50813	D	0.999898	B	0.31193	0.312	B	0.29524	0.103	T	0.03193	-1.1062	10	0.30854	T	0.27	.	14.0567	0.64774	0.1508:0.8492:0.0:0.0	.	514	Q5SZK8	FREM2_HUMAN	V	514	ENSP00000280481:A514V	ENSP00000280481:A514V	A	+	2	0	FREM2	38161022	1.000000	0.71417	0.192000	0.23308	0.928000	0.56348	4.764000	0.62264	2.538000	0.85594	0.561000	0.74099	GCC	.	.	.	none		0.602	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39263022	C	T	39263022	3	4	15	1	0	0	0	0	1	0	0	0	6052	739	26	2	1543	2	FREM2	13	39263022	Missense_Mutation	SNP	C	TCGA-2Z-A9JL-01A-11D-A42J-10	7767219	39263022	75906856	59	1087											
PHF11	51131	hgsc.bcm.edu	37	chr13	50087269	50087269	+	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	agaagttttgatgtggaatcAgtaaagaaagaaatccagag	18	9	11	3	0	1	5	1	1	0	4	2	6	2	6	1	1	0	2	1	1	6	3			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr13:50087269A>C	ENST00000378319.3	+	3	332	c.291A>C	c.(289-291)tcA>tcC	p.S97S	PHF11_ENST00000357596.3_Silent_p.S58S|PHF11_ENST00000488958.1_Silent_p.S58S	NM_001040443.1	NP_001035533.1	Q9UIL8	PHF11_HUMAN	PHD finger protein 11	97					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			large_intestine(3)|lung(1)	4		Lung NSC(96;2.1e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.38e-09)		ATGTGGAATCAGTAAAGAAAG	0.383																																					p.S97S		Atlas-SNP	.											.	PHF11	20	.	0			c.A291C						PASS	.						119	117	117					13																	50087269		2203	4300	6503	SO:0001819	synonymous_variant	51131	exon3			GGAATCAGTAAAG	AB011031	CCDS31975.1, CCDS41887.1	13q14.11	2014-05-20			ENSG00000136147	ENSG00000136147		"Zinc fingers, PHD-type"	17024	protein-coding gene	gene with protein product	"IgE responsiveness (atopic)"	607796				10508479, 15057823	Standard	XM_005266417		Approved	NY-REN-34, BCAP, IGER	uc001vdb.3	Q9UIL8	OTTHUMG00000016916	ENST00000378319.3:c.291A>C	chr13.hg19:g.50087269A>C		63.0	0.0	.		35.0	7.0	.	NM_001040443	Q5W0A4|Q5W0A6|Q9Y5A2	Silent	SNP	ENST00000378319.3	hg19	CCDS31975.1	.	.	.	.	.	.	.	.	.	.	A	9.279	1.047577	0.19827	.	.	ENSG00000136147	ENST00000426879	.	.	.	4.63	-1.37	0.09056	.	.	.	.	.	T	0.42988	0.1227	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.26985	-1.0087	4	.	.	.	-5.0934	3.6917	0.08348	0.5588:0.0:0.2586:0.1826	.	.	.	.	P	52	.	.	Q	+	2	0	PHF11	48985270	0.999000	0.42202	0.990000	0.47175	0.919000	0.55068	0.740000	0.26188	-0.278000	0.09180	-1.161000	0.01788	CAG	.	.	.	none		0.383	PHF11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044915.1	NM_016119		C	50087269	A	C	50087269	2	2	15	1	0	0	0	0	0	0	0	1	11829	175	7	5		5	PHF11	13	50087269	Silent	SNP	A	TCGA-2Z-A9JL-01A-11D-A42J-10	10824247	50087269	65082609	60	1088											
KIAA0586	9786	hgsc.bcm.edu	37	chr14	59006809	59006809	+	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	tttcaccaggtgatatggatCggacacaaattgagcttaat	13	12	9	7	1	1	2	1	2	0	0	2	4	1	4	1	3	1	1	1	3	3	4			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr14:59006809C>A	ENST00000556134.1	+	31	4679	c.4405C>A	c.(4405-4407)Cgg>Agg	p.R1469R	KIAA0586_ENST00000423743.3_Silent_p.R1440R|KIAA0586_ENST00000261244.5_Silent_p.R1408R|KIAA0586_ENST00000354386.6_Silent_p.R1537R	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	1469					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						TGATATGGATCGGACACAAAT	0.299																																					p.R1537R		Atlas-SNP	.											.	KIAA0586	180	.	0			c.C4609A						PASS	.						69	67	68					14																	59006809		1813	4064	5877	SO:0001819	synonymous_variant	9786	exon32			ATGGATCGGACAC	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.4405C>A	chr14.hg19:g.59006809C>A		134.0	0.0	.		99.0	39.0	.	NM_001244189	B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	Silent	SNP	ENST00000556134.1	hg19	CCDS58321.1																																																																																			.	.	.	none		0.299	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1	NM_014749		A	59006809	C	A	59006809	2	1	15	1	0	0	0	0	0	0	0	1	8193	875	31	4		4	KIAA0586	14	59006809	Silent	SNP	C	TCGA-2Z-A9JL-01A-11D-A42J-10		59006809	48342731	61	1089											
PCNX	22990	hgsc.bcm.edu	37	chr14	71514621	71514621	+	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	ttacagtcatctttactgtgCtgtttttcaaatttgactat	9	20	5	7	0	3	1	2	1	1	0	3	1	3	1	0	0	3	2	0	0	4	7			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr14:71514621C>A	ENST00000304743.2	+	22	4704	c.4258C>A	c.(4258-4260)Ctg>Atg	p.L1420M	PCNX_ENST00000439984.3_Missense_Mutation_p.L1309M|PCNX_ENST00000238570.5_Missense_Mutation_p.L1420M	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1420						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)		CTTTACTGTGCTGTTTTTCAA	0.373																																					p.L1420M		Atlas-SNP	.											.	PCNX	198	.	0			c.C4258A						PASS	.						186	165	172					14																	71514621		2202	4300	6502	SO:0001583	missense	22990	exon22			ACTGTGCTGTTTT	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.4258C>A	chr14.hg19:g.71514621C>A	ENSP00000304192:p.Leu1420Met	58.0	0.0	.		71.0	30.0	.	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	hg19	CCDS9806.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.65|17.65	3.441835|3.441835	0.63067|0.63067	.|.	.|.	ENSG00000100731|ENSG00000100731	ENST00000554691|ENST00000304743;ENST00000238570;ENST00000439984	.|T;T;T	.|0.21932	.|2.37;2.41;1.98	5.32|5.32	5.32|5.32	0.75619|0.75619	.|.	.|0.121727	.|0.56097	.|D	.|0.000021	.|T	.|0.50735	.|0.1633	M|M	0.86651|0.86651	2.83|2.83	0.58432|0.58432	D|D	0.999995|0.999995	.|D;D;D	.|0.89917	.|1.0;0.997;0.999	.|D;D;D	.|0.87578	.|0.998;0.947;0.996	.|T	.|0.56774	.|-0.7923	.|10	.|0.87932	.|D	.|0	.|.	12.679|12.679	0.56912|0.56912	0.0:0.9242:0.0:0.0757|0.0:0.9242:0.0:0.0757	.|.	.|1420;1309;1420	.|Q96RV3-3;B2RTR6;Q96RV3	.|.;.;PCX1_HUMAN	X|M	478|1420;1420;1309	.|ENSP00000304192:L1420M;ENSP00000238570:L1420M;ENSP00000396617:L1309M	.|ENSP00000238570:L1420M	C|L	+|+	3|1	2|2	PCNX|PCNX	70584374|70584374	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.776000|7.776000	0.85560|0.85560	2.640000|2.640000	0.89533|0.89533	0.591000|0.591000	0.81541|0.81541	TGC|CTG	.	.	.	none		0.373	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		A	71514621	C	A	71514621	3	1	15	1	0	0	0	0	1	0	0	0	11598	796	28	4	4344	4	PCNX	14	71514621	Missense_Mutation	SNP	C	TCGA-2Z-A9JL-01A-11D-A42J-10	12507812	71514621	35834919	62	1090											
TTLL5	23093	hgsc.bcm.edu	37	chr14	76156649	76156649	+	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	accttcctcctgccagctgaGtacgcggaattttgtagtaa	9	12	9	11	2	0	1	0	1	0	0	2	2	2	2	4	1	3	4	4	1	4	6	rs374680809		TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr14:76156649G>C	ENST00000298832.9	+	6	691	c.486G>C	c.(484-486)gaG>gaC	p.E162D	TTLL5_ENST00000286650.5_Missense_Mutation_p.E162D|TTLL5_ENST00000557636.1_Missense_Mutation_p.E162D	NM_015072.4	NP_055887.3	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	162	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				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)		TGCCAGCTGAGTACGCGGAAT	0.498																																					p.E162D		Atlas-SNP	.											.	TTLL5	102	.	0			c.G486C						PASS	.						124	97	106					14																	76156649		2203	4300	6503	SO:0001583	missense	23093	exon6			AGCTGAGTACGCG	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.486G>C	chr14.hg19:g.76156649G>C	ENSP00000298832:p.Glu162Asp	105.0	0.0	.		59.0	27.0	.	NM_015072	B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4	Missense_Mutation	SNP	ENST00000298832.9	hg19	CCDS32124.1	.	.	.	.	.	.	.	.	.	.	G	13.79	2.340819	0.41498	.	.	ENSG00000119685	ENST00000557636;ENST00000286650;ENST00000298832	T;T;T	0.05996	3.36;3.51;3.36	5.26	4.37	0.52481	.	0.096661	0.64402	D	0.000001	T	0.05410	0.0143	N	0.20685	0.6	0.80722	D	1	P;P;P	0.40909	0.478;0.732;0.72	B;P;B	0.46975	0.397;0.533;0.373	T	0.46652	-0.9176	10	0.07990	T	0.79	.	7.3204	0.26523	0.2583:0.0:0.7417:0.0	.	162;162;162	G3V2J9;Q6EMB2;Q6EMB2-3	.;TTLL5_HUMAN;.	D	162	ENSP00000450713:E162D;ENSP00000286650:E162D;ENSP00000298832:E162D	ENSP00000286650:E162D	E	+	3	2	TTLL5	75226402	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	3.128000	0.50492	1.204000	0.43247	0.655000	0.94253	GAG	.	.	.	alt		0.498	TTLL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414453.1	NM_015072		C	76156649	G	C	76156649	3	2	15	1	0	0	0	0	1	0	0	0	16742	1020	36	4	504	4	TTLL5	14	76156649	Missense_Mutation	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10	4642028	76156649	31192891	63	1091											
CDAN1	146059	hgsc.bcm.edu	37	chr15	43023515	43023515	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagactgtccatgagatgcTggttaaactggaagctgaga	12	10	12	7	0	1	3	1	2	0	3	2	6	2	4	1	2	3	3	1	2	3	1			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr15:43023515T>C	ENST00000356231.3	-	12	1777	c.1754A>G	c.(1753-1755)cAg>cGg	p.Q585R		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	585					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)		CATGAGATGCTGGTTAAACTG	0.547																																					p.Q585R		Atlas-SNP	.											.	CDAN1	70	.	0			c.A1754G						PASS	.						70	72	72					15																	43023515		2203	4299	6502	SO:0001583	missense	146059	exon12			AGATGCTGGTTAA	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.1754A>G	chr15.hg19:g.43023515T>C	ENSP00000348564:p.Gln585Arg	56.0	0.0	.		41.0	18.0	.	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Missense_Mutation	SNP	ENST00000356231.3	hg19	CCDS32209.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.169073	0.78339	.	.	ENSG00000140326	ENST00000356231;ENST00000267892	D	0.87650	-2.28	5.92	5.92	0.95590	.	0.106801	0.64402	D	0.000003	D	0.82930	0.5144	N	0.26042	0.785	0.58432	D	0.999998	P	0.46142	0.873	B	0.44044	0.439	D	0.84011	0.0348	10	0.45353	T	0.12	-20.3702	16.3648	0.83312	0.0:0.0:0.0:1.0	.	585	Q8IWY9	CDAN1_HUMAN	R	585;583	ENSP00000348564:Q585R	ENSP00000267892:Q583R	Q	-	2	0	CDAN1	40810807	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.393000	0.79851	2.263000	0.75096	0.533000	0.62120	CAG	.	.	.	none		0.547	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300		C	43023515	T	C	43023515	3	2	15	1	0	0	0	0	1	0	0	0	3056	1580	55	3	1997	3	CDAN1	15	43023515	Missense_Mutation	SNP	T	TCGA-2Z-A9JL-01A-11D-A42J-10		43023515	59507877	64	1092											
VPS13C	54832	hgsc.bcm.edu	37	chr15	62277127	62277127	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctgaatttttagtatttcTggaatattcttgttttctct	8	23	5	5	0	4	1	0	1	4	0	5	2	4	2	0	1	0	2	0	1	5	10			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr15:62277127T>C	ENST00000261517.5	-	19	1723	c.1650A>G	c.(1648-1650)ccA>ccG	p.P550P	VPS13C_ENST00000249837.3_Silent_p.P507P|VPS13C_ENST00000395898.3_Silent_p.P507P|VPS13C_ENST00000395896.4_Silent_p.P550P	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						TTAGTATTTCTGGAATATTCT	0.328																																					p.P550P		Atlas-SNP	.											.	VPS13C	506	.	0			c.A1650G						PASS	.						79	79	79					15																	62277127		2203	4300	6503	SO:0001819	synonymous_variant	54832	exon19			TATTTCTGGAATA	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.1650A>G	chr15.hg19:g.62277127T>C		344.0	0.0	.		338.0	122.0	.	NM_020821		Silent	SNP	ENST00000261517.5	hg19	CCDS32257.1																																																																																			.	.	.	none		0.328	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		C	62277127	T	C	62277127	2	2	15	1	0	0	0	0	0	0	0	1	17203	1567	55	3		3	VPS13C	15	62277127	Silent	SNP	T	TCGA-2Z-A9JL-01A-11D-A42J-10	19253612	62277127	40254265	65	1093											
HAGH	3029	hgsc.bcm.edu	37	chr16	1869933	1869933	+	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	gtgagtgatcttgtgagtcaGggccccgatacggtcgtcac	7	10	14	10	3	3	3	2	3	1	0	4	4	3	3	2	2	1	0	2	2	1	2			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr16:1869933G>T	ENST00000397356.3	-	4	803	c.397C>A	c.(397-399)Ctg>Atg	p.L133M	HAGH_ENST00000455446.2_Missense_Mutation_p.L133M|HAGH_ENST00000397353.2_Missense_Mutation_p.L85M|HAGH_ENST00000566709.1_Missense_Mutation_p.L85M	NM_005326.4	NP_005317.2	Q16775	GLO2_HUMAN	hydroxyacylglutathione hydrolase	133					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)	TTGTGAGTCAGGGCCCCGATA	0.617																																					p.L133M	Pancreas(55;1048 1176 25227 40124 41333)	Atlas-SNP	.											.,1	HAGH	20	.	0			c.C397A						PASS	.						122	97	105					16																	1869933		2199	4300	6499	SO:0001583	missense	3029	exon4			GAGTCAGGGCCCC	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.397C>A	chr16.hg19:g.1869933G>T	ENSP00000380514:p.Leu133Met	80.0	0.0	.		62.0	18.0	.	NM_005326	A8K290|B4DP33|B4DRA7|E7EN93	Missense_Mutation	SNP	ENST00000397356.3	hg19	CCDS10447.2	.	.	.	.	.	.	.	.	.	.	G	13.01	2.110487	0.37242	.	.	ENSG00000063854	ENST00000455446;ENST00000397356;ENST00000397353	D;D;D	0.96334	-3.98;-3.98;-3.98	5.02	3.04	0.35103	Beta-lactamase-like (2);	0.081935	0.48767	D	0.000175	D	0.97225	0.9093	M	0.80422	2.495	0.80722	D	1	D;P;P;P	0.56035	0.974;0.945;0.829;0.877	P;P;B;P	0.61070	0.883;0.726;0.341;0.659	D	0.96217	0.9157	10	0.54805	T	0.06	-8.7923	10.1115	0.42565	0.1539:0.0:0.8461:0.0	.	133;130;85;133	E7EN93;B4DT01;Q16775-2;Q16775	.;.;.;GLO2_HUMAN	M	133;133;85	ENSP00000406552:L133M;ENSP00000380514:L133M;ENSP00000380511:L85M	ENSP00000380511:L85M	L	-	1	2	HAGH	1809934	0.997000	0.39634	0.997000	0.53966	0.127000	0.20565	1.296000	0.33389	0.611000	0.30052	0.561000	0.74099	CTG	.	.	.	none		0.617	HAGH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250548.2	NM_005326		T	1869933	G	T	1869933	3	4	15	1	0	0	0	0	1	0	0	0	6952	991	35	4	553	4	HAGH	16	1869933	Missense_Mutation	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10		1869933	88484820	66	1094											
PLEKHG4	25894	hgsc.bcm.edu	37	chr16	67320229	67320229	+	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	caagaataagcctcgctccgAtgccctgatgtcaagctatg	11	9	9	12	2	1	2	1	1	0	1	3	3	2	2	3	0	3	2	3	0	5	2			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr16:67320229A>T	ENST00000360461.5	+	14	5030	c.2495A>T	c.(2494-2496)gAt>gTt	p.D832V	PLEKHG4_ENST00000427155.2_Missense_Mutation_p.D832V|PLEKHG4_ENST00000450733.1_Missense_Mutation_p.D751V|PLEKHG4_ENST00000379344.3_Missense_Mutation_p.D832V	NM_001129727.1|NM_015432.3	NP_001123199.1|NP_056247.1	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4	832	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)		CCTCGCTCCGATGCCCTGATG	0.562																																					p.D832V		Atlas-SNP	.											.	PLEKHG4	94	.	0			c.A2495T						PASS	.						158	120	133					16																	67320229		2198	4300	6498	SO:0001583	missense	25894	exon15			GCTCCGATGCCCT	AK024475	CCDS32466.1, CCDS45512.1	16q22.1	2013-01-11						"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	24501	protein-coding gene	gene with protein product	"puratrophin-1"	609526	"spinocerebellar ataxia 4"	SCA4		16491300, 16001362	Standard	NM_015432		Approved	DKFZP434I216, ARHGEF44	uc010cef.3	Q58EX7		ENST00000360461.5:c.2495A>T	chr16.hg19:g.67320229A>T	ENSP00000353646:p.Asp832Val	65.0	0.0	.		54.0	20.0	.	NM_001129728	Q4G0J8|Q4H485|Q56A69|Q9H7K4|Q9UFW0	Missense_Mutation	SNP	ENST00000360461.5	hg19	CCDS32466.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.332590	0.81801	.	.	ENSG00000196155	ENST00000360461;ENST00000427155;ENST00000379344;ENST00000450733	T;T;T;T	0.61980	0.06;0.06;0.06;0.06	5.44	5.44	0.79542	Dbl homology (DH) domain (5);	0.000000	0.34338	N	0.004055	T	0.73281	0.3567	M	0.64997	1.995	0.80722	D	1	D;D	0.67145	0.995;0.996	D;D	0.66602	0.909;0.945	T	0.76165	-0.3059	10	0.87932	D	0	.	10.3785	0.44096	0.8444:0.0:0.0:0.1556	.	751;832	Q58EX7-2;Q58EX7	.;PKHG4_HUMAN	V	832;832;832;751	ENSP00000353646:D832V;ENSP00000401118:D832V;ENSP00000368649:D832V;ENSP00000398030:D751V	ENSP00000353646:D832V	D	+	2	0	PLEKHG4	65877730	1.000000	0.71417	0.951000	0.38953	0.919000	0.55068	5.193000	0.65120	2.082000	0.62665	0.459000	0.35465	GAT	.	.	.	none		0.562	PLEKHG4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421395.2	NM_015432		T	67320229	A	T	67320229	3	4	15	1	0	0	0	0	1	0	0	0	12078	333	12	5	2549	5	PLEKHG4	16	67320229	Missense_Mutation	SNP	A	TCGA-2Z-A9JL-01A-11D-A42J-10	65450296	67320229	23034524	67	1095											
PRPF8	10594	hgsc.bcm.edu	37	chr17	1564944	1564944	+	Missense_Mutation	SNP	T	T	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	cttgcctcttgagtgcgtacTcagcccagacccgctgagaa	8	9	10	14	2	2	3	1	2	1	2	2	4	2	3	3	0	4	2	3	0	2	3			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr17:1564944T>G	ENST00000572621.1	-	25	4428	c.4163A>C	c.(4162-4164)gAg>gCg	p.E1388A	PRPF8_ENST00000304992.6_Missense_Mutation_p.E1388A			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	1388	Linker.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		GAGTGCGTACTCAGCCCAGAC	0.567																																					p.E1388A		Atlas-SNP	.											.	PRPF8	169	.	0			c.A4163C						PASS	.						105	86	92					17																	1564944		2203	4300	6503	SO:0001583	missense	10594	exon26			GCGTACTCAGCCC	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"PRP8 pre-mRNA processing factor 8 homolog (yeast)", "PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.4163A>C	chr17.hg19:g.1564944T>G	ENSP00000460348:p.Glu1388Ala	76.0	0.0	.		44.0	16.0	.	NM_006445	O14547|O75965	Missense_Mutation	SNP	ENST00000572621.1	hg19	CCDS11010.1	.	.	.	.	.	.	.	.	.	.	t	23.6	4.438695	0.83885	.	.	ENSG00000174231	ENST00000304992	D	0.84370	-1.84	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.94318	0.8174	M	0.92970	3.365	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.95339	0.8436	10	0.87932	D	0	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	1388	Q6P2Q9	PRP8_HUMAN	A	1388	ENSP00000304350:E1388A	ENSP00000304350:E1388A	E	-	2	0	PRPF8	1511694	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.013000	0.88655	2.371000	0.80710	0.533000	0.62120	GAG	.	.	.	none		0.567	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2			G	1564944	T	G	1564944	3	3	15	1	0	0	0	0	1	0	0	0	12585	1551	54	5	2916	5	PRPF8	17	1564944	Missense_Mutation	SNP	T	TCGA-2Z-A9JL-01A-11D-A42J-10		1564944	79630266	68	1096											
WSCD1	23302	hgsc.bcm.edu	37	chr17	6023951	6023951	+	Frame_Shift_Del	DEL	G	G	-																															ctgcgtgaccacaactggacGgggctgcccagggagtatgt																								rs554473306		TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr17:6023951delG	ENST00000574946.1	+	9	2088	c.1698delG	c.(1696-1698)acgfs	p.T566fs	WSCD1_ENST00000573634.1_Frame_Shift_Del_p.T450fs|WSCD1_ENST00000317744.5_Frame_Shift_Del_p.T566fs|WSCD1_ENST00000539421.1_Frame_Shift_Del_p.T566fs|WSCD1_ENST00000574232.1_Frame_Shift_Del_p.T566fs			Q658N2	WSCD1_HUMAN	WSC domain containing 1	566						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						ACAACTGGACGGGGCTGCCCA	0.662																																					p.T566fs		Atlas-Indel,Pindel	.											.	WSCD1	84	.	0			c.1697delC						PASS	.						44	49	47					17																	6023951		2203	4300	6503	SO:0001589	frameshift_variant	23302	exon9			.		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.1698delG	chr17.hg19:g.6023951delG	ENSP00000460825:p.Thr566fs	55.0	0.0	0		35.0	13.0	0.371429	NM_015253	A8K0N8|D3DTM3|O60276|Q96G45	Frame_Shift_Del	DEL	ENST00000574946.1	hg19	CCDS32538.1																																																																																			.	.	.	none		0.662	WSCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438965.4	NM_015253		-	6023951	G	-	6023951	7	5	15	1	0	1	0	1	0	0	0	0	17418	1103	39	0	1728	0	WSCD1	17	6023951	Frame_Shift_Del	DEL	G	TCGA-2Z-A9JL-01A-11D-A42J-10	4459007	6023951	75171259	69	1097											
SLC16A11	162515	hgsc.bcm.edu	37	chr17	6945476	6945476	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggccacagccgcggccagcAggggacccccccagctctct	7	3	12	19	2	1	0	0	0	1	0	2	1	1	1	6	4	3	2	6	4	0	0			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr17:6945476A>G	ENST00000308009.1	-	3	1362	c.1025T>C	c.(1024-1026)cTg>cCg	p.L342P	SLC16A11_ENST00000447225.1_Missense_Mutation_p.L310P	NM_153357.1	NP_699188.1	Q8NCK7	MOT11_HUMAN	solute carrier family 16, member 11	342					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						CGCGGCCAGCAGGGGACCCCC	0.726																																					p.L342P		Atlas-SNP	.											.	SLC16A11	25	.	0			c.T1025C						PASS	.						7	11	10					17																	6945476		2159	4207	6366	SO:0001583	missense	162515	exon3			GCCAGCAGGGGAC	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.1025T>C	chr17.hg19:g.6945476A>G	ENSP00000310490:p.Leu342Pro	63.0	0.0	.		56.0	18.0	.	NM_153357		Missense_Mutation	SNP	ENST00000308009.1	hg19	CCDS11086.1	.	.	.	.	.	.	.	.	.	.	A	17.46	3.395782	0.62177	.	.	ENSG00000174326	ENST00000308009;ENST00000447225	T;T	0.62105	0.05;0.05	4.96	4.96	0.65561	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.64402	D	0.000007	T	0.79347	0.4430	M	0.83603	2.65	0.58432	D	0.999999	D	0.89917	1.0	D	0.75484	0.986	T	0.82629	-0.0363	10	0.87932	D	0	.	12.6448	0.56728	1.0:0.0:0.0:0.0	.	342	Q8NCK7	MOT11_HUMAN	P	342;310	ENSP00000310490:L342P;ENSP00000394449:L310P	ENSP00000310490:L342P	L	-	2	0	SLC16A11	6886200	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	4.801000	0.62532	2.074000	0.62210	0.460000	0.39030	CTG	.	.	.	none		0.726	SLC16A11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219921.1	NM_153357		G	6945476	A	G	6945476	3	3	15	1	0	0	0	0	1	0	0	0	14417	188	7	3	398	3	SLC16A11	17	6945476	Missense_Mutation	SNP	A	TCGA-2Z-A9JL-01A-11D-A42J-10	921525	6945476	74249734	70	1098											
LSMD1	84316	hgsc.bcm.edu	37	chr17	7760532	7760532	+	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	0	0	0	0	0	0	0	0	0	0	gaatcctgcgcggggtgtaaCaagcgctcagaccgcgcagc	9	5	14	13	5	1	1	1	0	0	1	2	2	2	1	2	2	4	3	2	2	3	1			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr17:7760532C>A	ENST00000335155.5	-	2	81				LSMD1_ENST00000570555.1_5'Flank|LSMD1_ENST00000575071.1_Intron|LSMD1_ENST00000333775.5_Missense_Mutation_p.L70F|CYB5D1_ENST00000571846.1_5'Flank|CYB5D1_ENST00000570446.1_5'Flank|LSMD1_ENST00000575208.1_Intron|LSMD1_ENST00000576861.1_Intron|CYB5D1_ENST00000332439.4_5'Flank|LSMD1_ENST00000576384.1_5'UTR|LSMD1_ENST00000575771.1_Intron			Q9BRA0	LSMD1_HUMAN							negative regulation of apoptotic process (GO:0043066)	cytoplasm (GO:0005737)|NatC complex (GO:0031417)|nucleus (GO:0005634)				endometrium(1)|lung(2)|ovary(1)	4		all_cancers(10;0.11)|Prostate(122;0.219)				CGGGGTGTAACAAGCGCTCAG	0.697											OREG0024146	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L70F	GBM(66;626 1401 29924 42527)	Atlas-SNP	.											.	LSMD1	8	.	0			c.G210T						PASS	.						40	43	42					17																	7760532		2203	4295	6498	SO:0001627	intron_variant	84316	exon1			GTGTAACAAGCGC																												ENST00000335155.5:c.82-16G>T	chr17.hg19:g.7760532C>A		49.0	0.0	.	644	43.0	18.0	.	NM_032356	Q8N4M0	Missense_Mutation	SNP	ENST00000335155.5	hg19		.	.	.	.	.	.	.	.	.	.	C	6.764	0.509883	0.12883	.	.	ENSG00000183011	ENST00000333775	T	0.54675	0.56	4.56	3.59	0.41128	.	0.696299	0.11829	N	0.525380	T	0.35711	0.0941	.	.	.	0.21220	N	0.999753	B	0.21905	0.062	B	0.21360	0.034	T	0.18871	-1.0323	8	.	.	.	.	7.9928	0.30250	0.1821:0.6418:0.1761:0.0	.	70	Q9BRA0-2	.	F	70	ENSP00000332103:L70F	.	L	-	3	2	LSMD1	7701257	0.008000	0.16893	0.153000	0.22517	0.082000	0.17680	1.447000	0.35101	1.282000	0.44496	0.448000	0.29417	TTG	.	.	.	none		0.697	LSMD1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				A	7760532	C	A	7760532	1	1	15	0	1	0	0	0	0	0	0	0	9069	477	17	4		4	LSMD1	17	7760532	Intron	SNP	C	TCGA-2Z-A9JL-01A-11D-A42J-10	815056	7760532	73434678	71	1099											
DSC1	1823	hgsc.bcm.edu	37	chr18	28712612	28712612	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctggaaaacatttcttgacTgttctcttagcagtgacaca	11	14	7	9	0	3	2	0	2	3	0	4	3	3	3	0	1	2	2	0	1	3	4			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr18:28712612T>C	ENST00000257198.5	-	14	2418	c.2157A>G	c.(2155-2157)acA>acG	p.T719T	DSC1_ENST00000257197.3_Silent_p.T719T|RP11-408H20.2_ENST00000581836.1_RNA|RP11-408H20.3_ENST00000582307.1_RNA	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	719					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)			ATTTCTTGACTGTTCTCTTAG	0.323																																					p.T719T		Atlas-SNP	.											.	DSC1	240	.	0			c.A2157G						PASS	.						118	110	113					18																	28712612		2202	4300	6502	SO:0001819	synonymous_variant	1823	exon14			CTTGACTGTTCTC	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.2157A>G	chr18.hg19:g.28712612T>C		47.0	0.0	.		45.0	16.0	.	NM_004948	Q9HB01	Silent	SNP	ENST00000257198.5	hg19	CCDS11894.1																																																																																			.	.	.	none		0.323	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421		C	28712612	T	C	28712612	2	2	15	1	0	0	0	0	0	0	0	1	4767	1567	55	3		3	DSC1	18	28712612	Silent	SNP	T	TCGA-2Z-A9JL-01A-11D-A42J-10		28712612	49364636	72	1100											
AMH	268	hgsc.bcm.edu	37	chr19	2251466	2251466	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcctcccgggtctgcctcCggccacagccccgctgctgg	4	6	12	19	3	1	0	0	0	1	0	3	0	3	0	7	3	4	2	7	3	1	0	rs368933314		TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr19:2251466C>T	ENST00000221496.4	+	5	1215	c.1193C>T	c.(1192-1194)cCg>cTg	p.P398L	MIR4321_ENST00000592276.1_RNA	NM_000479.3	NP_000470	P03971	MIS_HUMAN	anti-Mullerian hormone	398					aging (GO:0007568)|cell-cell signaling (GO:0007267)|gonadal mesoderm development (GO:0007506)|Mullerian duct regression (GO:0001880)|positive regulation of gene expression (GO:0010628)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|preantral ovarian follicle growth (GO:0001546)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|sex determination (GO:0007530)|sex differentiation (GO:0007548)|urogenital system development (GO:0001655)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)|receptor binding (GO:0005102)			lung(2)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGTCTGCCTCCGGCCACAGCC	0.776									Persistant Mullerian Duct Syndrome (type I and II)				C|||	1	0.000199681	0	0.0014	5008	,	,		6910	0		0	False		,,,				2504	0				p.P398L		Atlas-SNP	.											.	AMH	12	.	0			c.C1193T						PASS	.						1	1	1					19																	2251466		536	1059	1595	SO:0001583	missense	268	exon5	Familial Cancer Database	PMDS, Persistent Oviduct Syndrome	TGCCTCCGGCCAC	K03474	CCDS12085.1	19p13.3	2014-01-30				ENSG00000104899		"Endogenous ligands"	464	protein-coding gene	gene with protein product		600957				3754790, 18784351	Standard	NM_000479		Approved	MIS	uc002lvh.2	P03971		ENST00000221496.4:c.1193C>T	chr19.hg19:g.2251466C>T	ENSP00000221496:p.Pro398Leu	1.0	0.0	.		6.0	4.0	.	NM_000479	O75246|Q6GTN3	Missense_Mutation	SNP	ENST00000221496.4	hg19	CCDS12085.1	.	.	.	.	.	.	.	.	.	.	C	9.562	1.118713	0.20877	.	.	ENSG00000104899	ENST00000221496	D	0.81579	-1.51	4.12	3.04	0.35103	Anti-Mullerian hormone, N-terminal (1);	0.526148	0.17147	U	0.185215	T	0.74390	0.3710	M	0.64997	1.995	0.09310	N	1	B	0.25441	0.126	B	0.16722	0.016	T	0.65434	-0.6169	10	0.52906	T	0.07	-4.6354	7.4131	0.27029	0.0:0.7283:0.1726:0.0991	.	398	P03971	MIS_HUMAN	L	398	ENSP00000221496:P398L	ENSP00000221496:P398L	P	+	2	0	AMH	2202466	0.000000	0.05858	0.001000	0.08648	0.064000	0.16182	0.232000	0.17891	0.675000	0.31264	0.485000	0.47835	CCG	.	.	.	alt		0.776	AMH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451276.3	NM_000479		T	2251466	C	T	2251466	3	4	15	1	0	0	0	0	1	0	0	0	572	652	23	1	1211	1	AMH	19	2251466	Missense_Mutation	SNP	C	TCGA-2Z-A9JL-01A-11D-A42J-10		2251466	56877517	73	1101											
LRG1	116844	hgsc.bcm.edu	37	chr19	4538577	4538577	+	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	ataccagggtgtccagggtgGctgaggcctggaagaggccc	8	6	17	10	0	0	2	0	1	0	1	1	3	1	3	4	6	1	1	4	6	2	1			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr19:4538577G>C	ENST00000306390.6	-	2	879	c.419C>G	c.(418-420)gCc>gGc	p.A140G	CTB-50L17.14_ENST00000586020.1_Intron|LRG1_ENST00000586883.1_5'UTR	NM_052972.2	NP_443204.1	P02750	A2GL_HUMAN	leucine-rich alpha-2-glycoprotein 1	140					brown fat cell differentiation (GO:0050873)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				NS(1)|endometrium(2)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		GTCCAGGGTGGCTGAGGCCTG	0.642																																					p.A140G		Atlas-SNP	.											.	LRG1	25	.	0			c.C419G						PASS	.						30	35	34					19																	4538577		2191	4284	6475	SO:0001583	missense	116844	exon2			AGGGTGGCTGAGG		CCDS12130.1	19p13.3	2013-09-20			ENSG00000171236	ENSG00000171236			29480	protein-coding gene	gene with protein product	"leucine rich alpha 2 glycoprotein"	611289				3856868, 12223515	Standard	NM_052972		Approved	LRG	uc002mau.3	P02750	OTTHUMG00000182010	ENST00000306390.6:c.419C>G	chr19.hg19:g.4538577G>C	ENSP00000302621:p.Ala140Gly	39.0	0.0	.		33.0	14.0	.	NM_052972	Q8N4F5|Q96QZ4	Missense_Mutation	SNP	ENST00000306390.6	hg19	CCDS12130.1	.	.	.	.	.	.	.	.	.	.	.	14.52	2.560456	0.45590	.	.	ENSG00000171236	ENST00000306390	T	0.57436	0.4	4.71	2.36	0.29203	.	0.604145	0.13808	N	0.361308	T	0.46698	0.1406	N	0.05306	-0.075	0.28685	N	0.904909	D	0.89917	1.0	D	0.74348	0.983	T	0.34030	-0.9845	10	0.44086	T	0.13	-10.711	7.5892	0.28010	0.0:0.1809:0.6323:0.1868	.	140	P02750	A2GL_HUMAN	G	140	ENSP00000302621:A140G	ENSP00000302621:A140G	A	-	2	0	LRG1	4489577	0.000000	0.05858	0.008000	0.14137	0.349000	0.29174	0.645000	0.24782	1.161000	0.42604	0.655000	0.94253	GCC	.	.	.	none		0.642	LRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458654.2	NM_052972		C	4538577	G	C	4538577	3	2	15	1	0	0	0	0	1	0	0	0	8949	1203	42	4	628	4	LRG1	19	4538577	Missense_Mutation	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10	2287111	4538577	54590406	74	1102											
COL5A3	50509	hgsc.bcm.edu	37	chr19	10085009	10085009	+	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	agggccaatcacccccacaaAgcctctgactccgtcatctc	10	7	6	18	1	4	1	2	1	2	0	6	1	5	1	5	1	1	0	5	1	2	0			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr19:10085009A>T	ENST00000264828.3	-	46	3503	c.3418T>A	c.(3418-3420)Ttt>Att	p.F1140I		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1140	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)			ACCCCCACAAAGCCTCTGACT	0.612																																					p.F1140I		Atlas-SNP	.											.	COL5A3	243	.	0			c.T3418A						PASS	.						78	77	78					19																	10085009		2203	4300	6503	SO:0001583	missense	50509	exon46			CCACAAAGCCTCT	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.3418T>A	chr19.hg19:g.10085009A>T	ENSP00000264828:p.Phe1140Ile	120.0	0.0	.		115.0	44.0	.	NM_015719	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	hg19	CCDS12222.1	.	.	.	.	.	.	.	.	.	.	A	31	5.059224	0.93846	.	.	ENSG00000080573	ENST00000264828	D	0.93189	-3.18	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	D	0.91895	0.7434	N	0.16567	0.415	0.46011	D	0.998811	D	0.54207	0.965	P	0.61201	0.885	D	0.91247	0.5026	10	0.35671	T	0.21	.	12.4453	0.55647	1.0:0.0:0.0:0.0	.	1140	P25940	CO5A3_HUMAN	I	1140	ENSP00000264828:F1140I	ENSP00000264828:F1140I	F	-	1	0	COL5A3	9946009	1.000000	0.71417	0.933000	0.37362	0.877000	0.50540	6.360000	0.73064	1.821000	0.53095	0.260000	0.18958	TTT	.	.	.	none		0.612	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719		T	10085009	A	T	10085009	3	4	15	1	0	0	0	0	1	0	0	0	3700	72	3	5	1907	5	COL5A3	19	10085009	Missense_Mutation	SNP	A	TCGA-2Z-A9JL-01A-11D-A42J-10	5546432	10085009	49043974	75	1103											
PDE4A	5141	hgsc.bcm.edu	37	chr19	10572554	10572554	+	Splice_Site	DEL	T	T	-																															gacgcccccttgcccgcaggTgctggccacggacatgtcca																										TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr19:10572554delT	ENST00000352831.6	+	13	1732	c.1622delT	c.(1621-1623)gtg>gg	p.V541fs	PDE4A_ENST00000440014.2_Splice_Site_p.V480fs|PDE4A_ENST00000592685.1_Splice_Site_p.V519fs|PDE4A_ENST00000380702.2_Splice_Site_p.V519fs|PDE4A_ENST00000344979.3_Splice_Site_p.V302fs|PDE4A_ENST00000293683.5_Splice_Site_p.V515fs	NM_001111307.1	NP_001104777.1	P27815	PDE4A_HUMAN	phosphodiesterase 4A, cAMP-specific	541	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)	TGCCCGCAGGTGCTGGCCACG	0.637																																					p.V541fs		Atlas-Indel,Pindel	.											.	PDE4A	236	.	0			c.1621delG						PASS	.						70	64	66					19																	10572554		2203	4300	6503	SO:0001630	splice_region_variant	5141	exon13			.		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.1621-1T>-	chr19.hg19:g.10572554delT		33.0	0.0	0		57.0	21.0	0.368421	NM_001111307	O75522|O76092|Q16255|Q16691|Q5DM53|Q6PMT2|Q8IVA7|Q8WUQ3|Q9H3H2	Frame_Shift_Del	DEL	ENST00000352831.6	hg19	CCDS45961.1																																																																																			.	.	.	none		0.637	PDE4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451244.1		Frame_Shift_Del	-	10572554	T	-	10572554	8	5	15	1	0	1	0	1	0	0	1	0	11646	1710	59	0	2129	0	PDE4A	19	10572554	Splice_Site	DEL	T	TCGA-2Z-A9JL-01A-11D-A42J-10	487545	10572554	48556429	76	1104											
PDE4A	5141	hgsc.bcm.edu	37	chr19	10578237	10578237	+	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	gcctgcgcagggacatttggGgaggacacatccgcactccc	8	6	13	14	2	0	0	0	0	0	0	2	3	2	3	3	4	1	2	3	4	0	1			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr19:10578237G>T	ENST00000352831.6	+	15	2711	c.2601G>T	c.(2599-2601)ggG>ggT	p.G867G	PDE4A_ENST00000440014.2_Silent_p.G806G|PDE4A_ENST00000592685.1_Silent_p.G845G|PDE4A_ENST00000380702.2_Silent_p.G845G|PDE4A_ENST00000344979.3_Silent_p.G628G|PDE4A_ENST00000293683.5_Silent_p.G841G	NM_001111307.1	NP_001104777.1	P27815	PDE4A_HUMAN	phosphodiesterase 4A, cAMP-specific	867					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)	GGACATTTGGGGAGGACACAT	0.692																																					p.G867G		Atlas-SNP	.											.	PDE4A	236	.	0			c.G2601T						PASS	.						44	46	45					19																	10578237		2158	4226	6384	SO:0001819	synonymous_variant	5141	exon15			ATTTGGGGAGGAC		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.2601G>T	chr19.hg19:g.10578237G>T		42.0	0.0	.		52.0	19.0	.	NM_001111307	O75522|O76092|Q16255|Q16691|Q5DM53|Q6PMT2|Q8IVA7|Q8WUQ3|Q9H3H2	Silent	SNP	ENST00000352831.6	hg19	CCDS45961.1																																																																																			.	.	.	none		0.692	PDE4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451244.1			T	10578237	G	T	10578237	2	4	15	1	0	0	0	0	0	0	0	1	11646	1219	43	4		4	PDE4A	19	10578237	Silent	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10	5683	10578237	48550746	77	1105											
SLC5A5	6528	hgsc.bcm.edu	37	chr19	18001737	18001737	+	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	ggccccgggattgttgtggtGggacctcgcacggcagacag	6	7	17	11	3	0	1	0	0	0	1	1	3	0	3	3	5	0	3	3	5	0	2			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr19:18001737G>T	ENST00000222248.3	+	14	2041	c.1694G>T	c.(1693-1695)tGg>tTg	p.W565L		NM_000453.2	NP_000444.1	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium/iodide cotransporter), member 5	565					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)	p.W565*(1)		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						TTGTTGTGGTGGGACCTCGCA	0.597																																					p.W565L	Melanoma(65;1008 1708 7910 46650)	Atlas-SNP	.											SLC5A5,NS,NS,0,1	SLC5A5	67	.	1	Substitution - Nonsense(1)	NS(1)	c.G1694T						PASS	.						112	111	111					19																	18001737		2203	4300	6503	SO:0001583	missense	6528	exon14			TGTGGTGGGACCT		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.1694G>T	chr19.hg19:g.18001737G>T	ENSP00000222248:p.Trp565Leu	52.0	0.0	.		48.0	17.0	.	NM_000453	O43702|Q2M335|Q9NYB6	Missense_Mutation	SNP	ENST00000222248.3	hg19	CCDS12368.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.977884	0.74360	.	.	ENSG00000105641	ENST00000222248	D	0.84800	-1.9	4.71	4.71	0.59529	.	0.133028	0.56097	D	0.000040	T	0.79907	0.4527	L	0.53249	1.67	0.51012	D	0.999901	P	0.36683	0.565	B	0.24006	0.05	T	0.82890	-0.0233	10	0.66056	D	0.02	.	15.1801	0.72947	0.0:0.0:1.0:0.0	.	565	Q92911	SC5A5_HUMAN	L	565	ENSP00000222248:W565L	ENSP00000222248:W565L	W	+	2	0	SLC5A5	17862737	1.000000	0.71417	1.000000	0.80357	0.663000	0.39108	5.732000	0.68563	2.457000	0.83068	0.491000	0.48974	TGG	.	.	.	none		0.597	SLC5A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466690.1			T	18001737	G	T	18001737	3	4	15	1	0	0	0	0	1	0	0	0	14681	1357	47	4	1748	4	SLC5A5	19	18001737	Missense_Mutation	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10	7423500	18001737	41127246	78	1106											
ZNF99	7652	hgsc.bcm.edu	37	chr19	22941432	22941432	+	Missense_Mutation	SNP	A	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	agctttgccacattcttcacAtttgcagggtttctctgcag	7	15	8	11	0	3	0	1	0	2	0	4	0	3	0	1	1	4	4	1	1	0	5			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr19:22941432A>C	ENST00000596209.1	-	4	1369	c.1279T>G	c.(1279-1281)Tgt>Ggt	p.C427G	ZNF99_ENST00000397104.3_Missense_Mutation_p.C336G	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	427					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				CATTCTTCACATTTGCAGGGT	0.373																																					p.C427G		Atlas-SNP	.											.	ZNF99	273	.	0			c.T1279G						PASS	.						49	50	50					19																	22941432		2019	4204	6223	SO:0001583	missense	7652	exon4			CTTCACATTTGCA	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"Zinc fingers, C2H2-type", "-"	13175	protein-coding gene	gene with protein product		603981	"zinc finger protein 99 (F8281)", "chromosome 19 open reading frame 9"	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1279T>G	chr19.hg19:g.22941432A>C	ENSP00000472969:p.Cys427Gly	40.0	0.0	.		44.0	21.0	.	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	hg19	CCDS59369.1	.	.	.	.	.	.	.	.	.	.	N	11.83	1.755283	0.31046	.	.	ENSG00000213973	ENST00000397104	T	0.36878	1.23	1.28	1.28	0.21552	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.62097	0.2400	H	0.97415	4	0.35732	D	0.818029	P	0.41597	0.756	P	0.54174	0.744	T	0.67413	-0.5677	9	0.87932	D	0	.	4.314	0.10984	0.7002:0.0:0.0:0.2998	.	336	A8MXY4	ZNF99_HUMAN	G	336	ENSP00000380293:C336G	ENSP00000380293:C336G	C	-	1	0	ZNF99	22733272	0.726000	0.28059	0.011000	0.14972	0.049000	0.14656	3.018000	0.49625	0.566000	0.29273	0.325000	0.21440	TGT	.	.	.	none		0.373	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124		C	22941432	A	C	22941432	3	2	15	1	0	0	0	0	1	0	0	0	18216	217	8	5	2118	5	ZNF99	19	22941432	Missense_Mutation	SNP	A	TCGA-2Z-A9JL-01A-11D-A42J-10	4939695	22941432	36187551	79	1107											
ZNF529	57711	hgsc.bcm.edu	37	chr19	37038656	37038656	+	Missense_Mutation	SNP	T	T	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	actctttgaagtggagtaacTtttccaactctttcaaaggt	11	15	7	8	0	3	1	1	1	2	0	4	2	4	2	1	2	2	1	1	2	4	5			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr19:37038656T>G	ENST00000591340.1	-	5	962	c.804A>C	c.(802-804)aaA>aaC	p.K268N	ZNF529_ENST00000334116.7_Missense_Mutation_p.K163N	NM_020951.4	NP_066002.3	Q6P280	ZN529_HUMAN	zinc finger protein 529	268					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)	1	Esophageal squamous(110;0.198)					GTGGAGTAACTTTTCCAACTC	0.343																																					p.K268N		Atlas-SNP	.											.	ZNF529	82	.	0			c.A804C						PASS	.						139	137	138					19																	37038656		1869	4115	5984	SO:0001583	missense	57711	exon6			AGTAACTTTTCCA	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.804A>C	chr19.hg19:g.37038656T>G	ENSP00000465578:p.Lys268Asn	69.0	0.0	.		60.0	26.0	.	NM_001145649	K7EKE1|Q9H731|Q9HCF7	Missense_Mutation	SNP	ENST00000591340.1	hg19	CCDS54256.1	.	.	.	.	.	.	.	.	.	.	T	1.646	-0.515161	0.04200	.	.	ENSG00000186020	ENST00000334116	T	0.07908	3.15	3.36	2.29	0.28610	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02418	0.0074	N	0.01631	-0.79	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.47341	-0.9125	9	0.12103	T	0.63	.	3.9738	0.09465	0.3664:0.0:0.1882:0.4453	.	163;235	Q6P280-2;Q6P280	.;ZN529_HUMAN	N	268	ENSP00000334695:K268N	ENSP00000334695:K268N	K	-	3	2	ZNF529	41730496	0.000000	0.05858	0.010000	0.14722	0.321000	0.28281	0.374000	0.20501	0.451000	0.26802	-0.468000	0.05107	AAA	.	.	.	none		0.343	ZNF529-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452730.1	NM_020951		G	37038656	T	G	37038656	3	3	15	1	0	0	0	0	1	0	0	0	17982	1606	56	5	891	5	ZNF529	19	37038656	Missense_Mutation	SNP	T	TCGA-2Z-A9JL-01A-11D-A42J-10	14097224	37038656	22090327	80	1108											
CAPN12	147968	hgsc.bcm.edu	37	chr19	39233092	39233092	+	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	tagccatgctggaaatcctgTccaggagggaccacccggcg	9	6	13	13	2	0	0	0	0	0	0	2	3	2	3	5	4	2	1	5	4	2	1			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr19:39233092T>A	ENST00000328867.4	-	3	692	c.384A>T	c.(382-384)ggA>ggT	p.G128G	CAPN12_ENST00000601953.1_5'UTR|CTD-2540F13.2_ENST00000602255.1_RNA	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	128	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)			GGAAATCCTGTCCAGGAGGGA	0.602																																					p.G128G		Atlas-SNP	.											.	CAPN12	43	.	0			c.A384T						PASS	.						58	51	53					19																	39233092		2203	4300	6503	SO:0001819	synonymous_variant	147968	exon3			ATCCTGTCCAGGA	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.384A>T	chr19.hg19:g.39233092T>A		289.0	0.0	.		265.0	101.0	.	NM_144691		Silent	SNP	ENST00000328867.4	hg19	CCDS12519.1																																																																																			.	.	.	none		0.602	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1			A	39233092	T	A	39233092	2	1	15	1	0	0	0	0	0	0	0	1	2627	1654	58	5		5	CAPN12	19	39233092	Silent	SNP	T	TCGA-2Z-A9JL-01A-11D-A42J-10	2194436	39233092	19895891	81	1109											
PPP2R1A	5518	hgsc.bcm.edu	37	chr19	52714553	52714553	+	Missense_Mutation	SNP	T	T	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	cacagtggaggagacagtggTgcgggacaaggcagtggagt	11	5	19	6	1	0	1	0	0	0	1	0	5	0	4	0	6	1	1	0	6	1	0			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr19:52714553T>G	ENST00000322088.6	+	4	369	c.311T>G	c.(310-312)gTg>gGg	p.V104G	PPP2R1A_ENST00000462990.1_5'UTR|PPP2R1A_ENST00000444322.2_Missense_Mutation_p.V49G|PPP2R1A_ENST00000473455.2_3'UTR	NM_014225.5	NP_055040.2	P30153	2AAA_HUMAN	protein phosphatase 2, regulatory subunit A, alpha	104	PP2A subunit B binding.|Polyoma small and medium T antigens Binding.|SV40 small T antigen binding.				apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|chromosome segregation (GO:0007059)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|inactivation of MAPK activity (GO:0000188)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|negative regulation of cell growth (GO:0030308)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine dephosphorylation (GO:0070262)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein complex assembly (GO:0006461)|protein dephosphorylation (GO:0006470)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of DNA replication (GO:0006275)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|response to organic substance (GO:0010033)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|second-messenger-mediated signaling (GO:0019932)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	antigen binding (GO:0003823)|protein heterodimerization activity (GO:0046982)|protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			NS(1)|breast(4)|cervix(2)|endometrium(62)|kidney(1)|large_intestine(7)|lung(21)|ovary(32)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	135				GBM - Glioblastoma multiforme(134;0.00456)|OV - Ovarian serous cystadenocarcinoma(262;0.015)		GAGACAGTGGTGCGGGACAAG	0.642			Mis		clear cell ovarian carcinoma																																p.V104G		Atlas-SNP	.		Dom?	yes		19	19q13.41	5518	"protein phosphatase 2, regulatory subunit A, alpha"		E	.	PPP2R1A	187	.	0			c.T311G						PASS	.						46	47	47					19																	52714553		2203	4300	6503	SO:0001583	missense	5518	exon4			CAGTGGTGCGGGA		CCDS12849.1	19q13	2010-06-18	2010-04-14		ENSG00000105568	ENSG00000105568	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9302	protein-coding gene	gene with protein product	"protein phosphatase 2A, regulatory subunit A, alpha isoform", "protein phosphatase 2, 65kDa regulatory subunit A"	605983	"protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), alpha isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit A, alpha isoform"				Standard	NR_033500		Approved	PR65A, PP2A-Aalpha	uc002pyp.3	P30153	OTTHUMG00000137367	ENST00000322088.6:c.311T>G	chr19.hg19:g.52714553T>G	ENSP00000324804:p.Val104Gly	76.0	0.0	.		69.0	33.0	.	NM_014225	Q13773|Q6ICQ3|Q96DH3	Missense_Mutation	SNP	ENST00000322088.6	hg19	CCDS12849.1	.	.	.	.	.	.	.	.	.	.	T	14.99	2.699824	0.48307	.	.	ENSG00000105568	ENST00000454220;ENST00000322088;ENST00000444322	T;T;T	0.41758	0.99;0.99;0.99	4.46	4.46	0.54185	Armadillo-like helical (1);Armadillo-type fold (1);	0.225482	0.29192	N	0.012863	T	0.74816	0.3766	H	0.97240	3.965	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77557	0.99;0.983;0.983	T	0.83177	-0.0091	10	0.87932	D	0	-27.762	12.0292	0.53388	0.0:0.0:0.0:1.0	.	49;104;104	F5H3X9;A8K7B7;P30153	.;.;2AAA_HUMAN	G	144;104;49	ENSP00000391905:V144G;ENSP00000324804:V104G;ENSP00000415067:V49G	ENSP00000324804:V104G	V	+	2	0	PPP2R1A	57406365	1.000000	0.71417	1.000000	0.80357	0.033000	0.12548	6.983000	0.76180	2.009000	0.58944	0.533000	0.62120	GTG	.	.	.	none		0.642	PPP2R1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000267967.2	NM_014225		G	52714553	T	G	52714553	3	3	15	1	0	0	0	0	1	0	0	0	12392	1696	59	5	325	5	PPP2R1A	19	52714553	Missense_Mutation	SNP	T	TCGA-2Z-A9JL-01A-11D-A42J-10	13481461	52714553	6414430	82	1110											
TMC4	147798	hgsc.bcm.edu	37	chr19	54667538	54667538	+	Missense_Mutation	SNP	A	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	gaacacgggcggcagcacaaAattgaccccagcgatgaaga	15	3	12	11	3	0	3	0	2	0	1	0	5	0	3	2	2	3	2	2	2	4	1			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr19:54667538A>C	ENST00000376591.4	-	8	1344	c.1213T>G	c.(1213-1215)Ttt>Gtt	p.F405V	TMC4_ENST00000301187.4_Missense_Mutation_p.F399V|TMC4_ENST00000416963.1_5'Flank|TMC4_ENST00000476013.2_5'Flank	NM_001145303.1|NM_144686.2	NP_001138775|NP_653287.2	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4	405					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(7)|large_intestine(4)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	22	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					GGCAGCACAAAATTGACCCCA	0.572											OREG0003641	type=REGULATORY REGION|Gene=AK124406|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.F405V		Atlas-SNP	.											.	TMC4	89	.	0			c.T1213G						PASS	.						102	97	99					19																	54667538		2203	4300	6503	SO:0001583	missense	147798	exon8			GCACAAAATTGAC	AY236492	CCDS12882.1, CCDS46174.1	19q13.42	2008-02-05			ENSG00000167608	ENSG00000167608			22998	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005277069		Approved		uc010erf.3	Q7Z404	OTTHUMG00000066485	ENST00000376591.4:c.1213T>G	chr19.hg19:g.54667538A>C	ENSP00000365776:p.Phe405Val	115.0	0.0	.	1002	129.0	45.0	.	NM_001145303	Q7Z5M3|Q8N5E4|Q8TBS7	Missense_Mutation	SNP	ENST00000376591.4	hg19	CCDS46174.1	.	.	.	.	.	.	.	.	.	.	A	11.06	1.528689	0.27387	.	.	ENSG00000167608	ENST00000301187;ENST00000376591	T;T	0.58652	0.32;0.32	5.14	3.92	0.45320	.	0.155752	0.56097	D	0.000024	T	0.50973	0.1647	M	0.67953	2.075	0.80722	D	1	B;B	0.19331	0.035;0.008	B;B	0.18263	0.021;0.017	T	0.55205	-0.8177	10	0.51188	T	0.08	-23.9714	6.2359	0.20762	0.8154:0.0:0.1846:0.0	.	405;399	Q7Z404;Q7Z404-1	TMC4_HUMAN;.	V	399;405	ENSP00000301187:F399V;ENSP00000365776:F405V	ENSP00000301187:F399V	F	-	1	0	TMC4	59359350	1.000000	0.71417	0.998000	0.56505	0.233000	0.25261	1.333000	0.33816	2.074000	0.62210	0.418000	0.28097	TTT	.	.	.	none		0.572	TMC4-011	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000156164.2			C	54667538	A	C	54667538	3	2	15	1	0	0	0	0	1	0	0	0	15999	14	1	5	957	5	TMC4	19	54667538	Missense_Mutation	SNP	A	TCGA-2Z-A9JL-01A-11D-A42J-10	1952985	54667538	4461445	83	1111											
CENPB	1059	hgsc.bcm.edu	37	chr20	3766089	3766089	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggatcctggccctctagcgCggccatggccttgagcagca	6	7	14	14	2	1	1	0	1	1	0	2	2	2	2	4	4	3	2	4	4	1	2			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr20:3766089C>T	ENST00000379751.4	-	1	1248	c.1042G>A	c.(1042-1044)Gcg>Acg	p.A348T	CDC25B_ENST00000379598.5_5'Flank|CDC25B_ENST00000344256.6_5'Flank	NM_001810.5	NP_001801.1	P07199	CENPB_HUMAN	centromere protein B, 80kDa	348					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						CCCTCTAGCGCGGCCATGGCC	0.677																																					p.A348T		Atlas-SNP	.											.	CENPB	24	.	0			c.G1042A						PASS	.						15	13	13					20																	3766089		2190	4286	6476	SO:0001583	missense	1059	exon1			CTAGCGCGGCCAT	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.1042G>A	chr20.hg19:g.3766089C>T	ENSP00000369075:p.Ala348Thr	61.0	0.0	.		75.0	30.0	.	NM_001810	Q96EI4	Missense_Mutation	SNP	ENST00000379751.4	hg19	CCDS13064.1	.	.	.	.	.	.	.	.	.	.	c	14.43	2.534064	0.45073	.	.	ENSG00000125817	ENST00000379751	T	0.43688	0.94	4.04	3.07	0.35406	.	0.000000	0.38548	U	0.001648	T	0.36496	0.0969	L	0.36672	1.1	0.20764	N	0.999853	P	0.49961	0.93	P	0.52066	0.689	T	0.14531	-1.0469	10	0.12103	T	0.63	-10.6982	6.8906	0.24226	0.2009:0.6041:0.195:0.0	.	348	P07199	CENPB_HUMAN	T	348	ENSP00000369075:A348T	ENSP00000369075:A348T	A	-	1	0	CENPB	3714089	0.275000	0.24201	0.311000	0.25182	0.916000	0.54674	3.011000	0.49567	0.647000	0.30713	0.457000	0.33378	GCG	.	.	.	none		0.677	CENPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077772.2	NM_001810		T	3766089	C	T	3766089	3	4	15	1	0	0	0	0	1	0	0	0	3229	768	27	1	761	1	CENPB	20	3766089	Missense_Mutation	SNP	C	TCGA-2Z-A9JL-01A-11D-A42J-10		3766089	59259431	84	1112											
KIF16B	55614	hgsc.bcm.edu	37	chr20	16486456	16486456	+	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	tgtaaggcacgaaaacttgcTtcttctttgcaagagtattt	11	15	8	7	1	2	1	0	0	2	1	2	2	2	1	0	1	3	5	0	1	5	7			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr20:16486456T>A	ENST00000354981.2	-	9	1068	c.911A>T	c.(910-912)aAg>aTg	p.K304M	KIF16B_ENST00000355755.3_Missense_Mutation_p.K304M|KIF16B_ENST00000408042.1_Missense_Mutation_p.K304M|KIF16B_ENST00000378003.2_De_novo_Start_InFrame	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	304	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						GAAAACTTGCTTCTTCTTTGC	0.363																																					p.K304M		Atlas-SNP	.											.	KIF16B	305	.	0			c.A911T						PASS	.						60	57	58					20																	16486456		2203	4300	6503	SO:0001583	missense	55614	exon9			ACTTGCTTCTTCT	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.911A>T	chr20.hg19:g.16486456T>A	ENSP00000347076:p.Lys304Met	117.0	0.0	.		84.0	32.0	.	NM_001199865	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Missense_Mutation	SNP	ENST00000354981.2	hg19	CCDS13122.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.097820	0.76870	.	.	ENSG00000089177	ENST00000354981;ENST00000355755;ENST00000377997;ENST00000408042	T;T;T	0.76968	-1.06;-1.06;-1.06	5.59	5.59	0.84812	Kinesin, motor domain (3);	0.000000	0.85682	D	0.000000	D	0.89044	0.6603	M	0.89534	3.04	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	0.90593	0.4538	10	0.87932	D	0	.	10.4254	0.44375	0.0:0.0729:0.0:0.9271	.	304;304;304;304	Q96L93-4;Q96L93-2;Q96L93-6;Q96L93	.;.;.;KI16B_HUMAN	M	304	ENSP00000347076:K304M;ENSP00000347995:K304M;ENSP00000384164:K304M	ENSP00000347076:K304M	K	-	2	0	KIF16B	16434456	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	4.962000	0.63687	2.257000	0.74773	0.460000	0.39030	AAG	.	.	.	none		0.363	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683		A	16486456	T	A	16486456	3	1	15	1	0	0	0	0	1	0	0	0	8285	1609	56	5	3114	5	KIF16B	20	16486456	Missense_Mutation	SNP	T	TCGA-2Z-A9JL-01A-11D-A42J-10	12720367	16486456	46539064	85	1113											
B4GALT5	9334	hgsc.bcm.edu	37	chr20	48260082	48260082	+	Missense_Mutation	SNP	T	T	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	ccttccaccgaggcatgcaaTcagaaggcttccagtgacct	10	8	9	14	1	1	2	1	1	0	1	3	3	3	2	5	2	1	3	5	2	2	2			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr20:48260082T>G	ENST00000371711.4	-	4	657	c.470A>C	c.(469-471)gAt>gCt	p.D157A		NM_004776.3	NP_004767.1	O43286	B4GT5_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 5	157					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	20			BRCA - Breast invasive adenocarcinoma(9;2.51e-06)			AGGCATGCAATCAGAAGGCTT	0.478																																					p.D157A		Atlas-SNP	.											.	B4GALT5	40	.	0			c.A470C						PASS	.						172	147	156					20																	48260082		2203	4300	6503	SO:0001583	missense	9334	exon4			ATGCAATCAGAAG	AB004550	CCDS13420.1	20q13.1-q13.2	2013-02-19			ENSG00000158470	ENSG00000158470		"Beta 4-glycosyltransferases"	928	protein-coding gene	gene with protein product	"beta4-GalT IV"	604016				9597550, 9435216	Standard	NM_004776		Approved	beta4GalT-V	uc002xuu.4	O43286	OTTHUMG00000033086	ENST00000371711.4:c.470A>C	chr20.hg19:g.48260082T>G	ENSP00000360776:p.Asp157Ala	133.0	0.0	.		98.0	29.0	.	NM_004776	E1P625|Q2M394|Q9UJQ8	Missense_Mutation	SNP	ENST00000371711.4	hg19	CCDS13420.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.657772	0.88154	.	.	ENSG00000158470	ENST00000371711	T	0.36340	1.26	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.68988	0.3061	M	0.93283	3.4	0.80722	D	1	D	0.60575	0.988	D	0.69142	0.962	T	0.78430	-0.2207	10	0.72032	D	0.01	-29.6221	15.5342	0.75990	0.0:0.0:0.0:1.0	.	157	O43286	B4GT5_HUMAN	A	157	ENSP00000360776:D157A	ENSP00000360776:D157A	D	-	2	0	B4GALT5	47693489	1.000000	0.71417	0.549000	0.28204	0.993000	0.82548	8.036000	0.88901	2.060000	0.61445	0.459000	0.35465	GAT	.	.	.	none		0.478	B4GALT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080543.3	NM_004776		G	48260082	T	G	48260082	3	3	15	1	0	0	0	0	1	0	0	0	1274	1435	50	5	720	5	B4GALT5	20	48260082	Missense_Mutation	SNP	T	TCGA-2Z-A9JL-01A-11D-A42J-10	31773626	48260082	14765438	86	1114											
PRIC285	85441	hgsc.bcm.edu	37	chr20	62190711	62190711	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agagggggcagcagcgcagaAggaggtggtctcctgtgagg	9	5	20	7	1	1	3	0	1	1	2	2	4	1	4	1	6	2	3	1	6	1	0			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr20:62190711A>G	ENST00000467148.1	-	19	7907	c.7838T>C	c.(7837-7839)cTt>cCt	p.L2613P	HELZ2_ENST00000427522.2_Missense_Mutation_p.L2044P	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2613	Interaction with THRAP3.				cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										GCAGCGCAGAAGGAGGTGGTC	0.657																																					p.L2613P		Atlas-SNP	.											.	.	.	.	0			c.T7838C						PASS	.						19	19	19					20																	62190711		2195	4289	6484	SO:0001583	missense	85441	exon20			CGCAGAAGGAGGT	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.7838T>C	chr20.hg19:g.62190711A>G	ENSP00000417401:p.Leu2613Pro	74.0	0.0	.		64.0	30.0	.	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	hg19	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	A	13.09	2.131953	0.37630	.	.	ENSG00000130589	ENST00000427522;ENST00000467148	D;D	0.83163	-1.69;-1.69	3.5	3.5	0.40072	.	0.101169	0.40728	N	0.001025	D	0.89146	0.6632	M	0.77103	2.36	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.91635	0.993;0.999	D	0.89105	0.3492	10	0.87932	D	0	.	8.3308	0.32184	1.0:0.0:0.0:0.0	.	2613;2044	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	P	2044;2613	ENSP00000393257:L2044P;ENSP00000417401:L2613P	ENSP00000393257:L2044P	L	-	2	0	RP4-697K14.7	61661155	0.993000	0.37304	0.961000	0.40146	0.159000	0.22180	4.432000	0.59922	1.481000	0.48307	0.379000	0.24179	CTT	.	.	.	none		0.657	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		G	62190711	A	G	62190711	3	3	15	1	0	0	0	0	1	0	0	0	12495	72	3	3	115	3	PRIC285	20	62190711	Missense_Mutation	SNP	A	TCGA-2Z-A9JL-01A-11D-A42J-10	13930629	62190711	834809	87	1115											
NDUFV3	4731	hgsc.bcm.edu	37	chr21	44324023	44324023	+	Intron	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	acacaaaatcagggttgtctGcgccaccgaagggcagccca	12	5	11	13	2	2	0	1	0	1	0	2	1	2	0	3	2	2	2	3	2	3	1			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr21:44324023G>T	ENST00000340344.4	+	3	235				NDUFV3_ENST00000460259.1_3'UTR|NDUFV3_ENST00000354250.2_Missense_Mutation_p.A301S	NM_001001503.1	NP_001001503.1	P56181	NDUV3_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 3, 10kDa						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|skin(1)	10				STAD - Stomach adenocarcinoma(101;0.0606)		AGGGTTGTCTGCGCCACCGAA	0.517																																					p.A301S		Atlas-SNP	.											.	NDUFV3	23	.	0			c.G901T						PASS	.						68	82	77					21																	44324023		2203	4298	6501	SO:0001627	intron_variant	4731	exon3			TTGTCTGCGCCAC		CCDS33572.1, CCDS33573.1	21q22.3	2011-07-04	2002-08-29		ENSG00000160194	ENSG00000160194	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7719	protein-coding gene	gene with protein product	"complex I 10kDa subunit"	602184	"NADH dehydrogenase (ubiquinone) flavoprotein 3 (10kD)"			9344673	Standard	NM_021075		Approved	CI-10k	uc002zcm.3	P56181	OTTHUMG00000086823	ENST00000340344.4:c.170-4951G>T	chr21.hg19:g.44324023G>T		103.0	0.0	.		87.0	28.0	.	NM_021075	A8K0M1|J3KNX7|Q6FGD3|Q8WU60|Q9HCR5	Missense_Mutation	SNP	ENST00000340344.4	hg19	CCDS33573.1	.	.	.	.	.	.	.	.	.	.	G	14.04	2.417930	0.42918	.	.	ENSG00000160194	ENST00000354250	T	0.41400	1.0	5.21	-7.83	0.01201	.	0.910228	0.09528	N	0.789978	T	0.15782	0.0380	N	0.24115	0.695	0.09310	N	1	P	0.34462	0.454	B	0.20955	0.032	T	0.09930	-1.0652	10	0.25751	T	0.34	-1.6203	3.1029	0.06331	0.2488:0.2257:0.4144:0.1112	.	301	P56181-2	.	S	301	ENSP00000346196:A301S	ENSP00000346196:A301S	A	+	1	0	NDUFV3	43197092	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.078000	0.01370	-1.555000	0.01697	0.655000	0.94253	GCG	.	.	.	none		0.517	NDUFV3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195448.2			T	44324023	G	T	44324023	1	4	15	0	1	0	0	0	0	0	0	0	10308	1319	46	4		4	NDUFV3	21	44324023	Intron	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10		44324023	3805872	88	1116											
TRPM2	7226	hgsc.bcm.edu	37	chr21	45773684	45773684	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggggatggtctccaatctccGgcgcagcaacagcagcctct	8	7	12	14	2	3	0	0	0	3	0	5	1	3	1	3	4	4	3	3	4	2	0			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr21:45773684G>A	ENST00000397928.1	+	1	546	c.101G>A	c.(100-102)cGg>cAg	p.R34Q	TRPM2_ENST00000300481.9_Missense_Mutation_p.R34Q|TRPM2_ENST00000300482.5_Missense_Mutation_p.R34Q|TRPM2_ENST00000397932.2_Missense_Mutation_p.R34Q	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	34					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						TCCAATCTCCGGCGCAGCAAC	0.607																																					p.R34Q		Atlas-SNP	.											.	TRPM2	196	.	0			c.G101A						PASS	.						43	36	38					21																	45773684		2203	4300	6503	SO:0001583	missense	7226	exon1			ATCTCCGGCGCAG	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.101G>A	chr21.hg19:g.45773684G>A	ENSP00000381023:p.Arg34Gln	132.0	0.0	.		117.0	50.0	.	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	hg19	CCDS13710.1	.	.	.	.	.	.	.	.	.	.	G	1.216	-0.628356	0.03610	.	.	ENSG00000142185	ENST00000300482;ENST00000431901;ENST00000397928;ENST00000300481;ENST00000397932	T;T;T;T;T	0.53206	0.74;0.87;0.74;0.76;0.63	4.4	1.6	0.23607	.	0.523002	0.16025	N	0.233105	T	0.22437	0.0541	N	0.05124	-0.11	0.09310	N	0.999991	B;B	0.18863	0.031;0.018	B;B	0.10450	0.005;0.005	T	0.17440	-1.0369	10	0.26408	T	0.33	-24.3716	6.9762	0.24677	0.3902:0.0:0.6098:0.0	.	34;34	E9PGK7;O94759	.;TRPM2_HUMAN	Q	34	ENSP00000300482:R34Q;ENSP00000393982:R34Q;ENSP00000381023:R34Q;ENSP00000300481:R34Q;ENSP00000381026:R34Q	ENSP00000300481:R34Q	R	+	2	0	TRPM2	44598112	0.005000	0.15991	0.046000	0.18839	0.016000	0.09150	-0.128000	0.10531	0.027000	0.15297	-0.254000	0.11334	CGG	.	.	.	none		0.607	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307		A	45773684	G	A	45773684	3	1	15	1	0	0	0	0	1	0	0	0	16598	1116	39	1	103	1	TRPM2	21	45773684	Missense_Mutation	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10	1449661	45773684	2356211	89	1117											
SUMO3	6612	hgsc.bcm.edu	37	chr21	46226870	46226870	+	Missense_Mutation	SNP	A	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	gctggggacgggccctctagAaactgtgccctgccaggctg	6	7	15	13	1	1	1	0	0	1	1	1	2	1	2	3	4	3	2	3	4	2	1			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr21:46226870A>C	ENST00000397898.3	-	4	440	c.358T>G	c.(358-360)Tct>Gct	p.S120A	SUMO3_ENST00000411651.2_Missense_Mutation_p.F141C|SUMO3_ENST00000479153.1_5'UTR|SUMO3_ENST00000332859.6_Missense_Mutation_p.F103C|AL773604.8_ENST00000417820.1_RNA					small ubiquitin-like modifier 3											prostate(1)	1				Colorectal(79;0.058)		GGCCCTCTAGAAACTGTGCCC	0.612																																					p.F103C		Atlas-SNP	.											.	SUMO3	11	.	0			c.T308G						PASS	.						58	55	56					21																	46226870		2203	4300	6503	SO:0001583	missense	6612	exon4			CTCTAGAAACTGT		CCDS33587.1, CCDS68220.1	21q22.3	2013-06-05	2013-06-05	2004-05-19	ENSG00000184900	ENSG00000184900			11124	protein-coding gene	gene with protein product		602231	"SMT3 (suppressor of mif two 3, yeast) homolog 1", "SMT3 suppressor of mif two 3 homolog 3 (yeast)", "SMT3 suppressor of mif two 3 homolog 3 (S. cerevisiae)"	SMT3H1		9119407	Standard	NM_006936		Approved	SMT3A	uc002zfz.1	P55854	OTTHUMG00000090256	ENST00000397898.3:c.358T>G	chr21.hg19:g.46226870A>C	ENSP00000380995:p.Ser120Ala	56.0	0.0	.		52.0	23.0	.	NM_006936		Missense_Mutation	SNP	ENST00000397898.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.27|12.27	1.887953|1.887953	0.33348|0.33348	.|.	.|.	ENSG00000184900|ENSG00000184900	ENST00000332859;ENST00000411651|ENST00000397898	T;T|T	0.27256|0.26957	1.82;1.68|1.7	4.8|4.8	-0.774|-0.774	0.10991|0.10991	.|.	.|.	.|.	.|.	.|.	T|T	0.11410|0.11410	0.0278|0.0278	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	P;B|B	0.43352|0.06786	0.804;0.138|0.001	B;B|B	0.37780|0.08055	0.258;0.037|0.003	T|T	0.26052|0.26052	-1.0114|-1.0114	9|9	0.87932|0.44086	D|T	0|0.13	.|.	5.9778|5.9778	0.19391|0.19391	0.6003:0.2568:0.1429:0.0|0.6003:0.2568:0.1429:0.0	.|.	141;103|120	B4DUW4;P55854|A8MUA9	.;SUMO3_HUMAN|.	C|A	103;141|120	ENSP00000330343:F103C;ENSP00000409666:F141C|ENSP00000380995:S120A	ENSP00000330343:F103C|ENSP00000380995:S120A	F|S	-|-	2|1	0|0	SUMO3|SUMO3	45051298|45051298	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	0.535000|0.535000	0.23114|0.23114	-0.196000|-0.196000	0.10366|0.10366	0.533000|0.533000	0.62120|0.62120	TTC|TCT	.	.	.	none		0.612	SUMO3-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000206561.1			C	46226870	A	C	46226870	3	2	15	1	0	0	0	0	1	0	0	0	15401	246	9	5	7	5	SUMO3	21	46226870	Missense_Mutation	SNP	A	TCGA-2Z-A9JL-01A-11D-A42J-10	453186	46226870	1903025	90	1118											
GNAZ	2781	hgsc.bcm.edu	37	chr22	23465473	23465473	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtctacatccagcggcagtTtgaagacctgaaccgcaaca	12	8	9	12	2	1	3	0	2	1	1	2	3	2	3	3	1	4	3	3	1	4	2			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr22:23465473T>C	ENST00000248996.4	+	3	1589	c.923T>C	c.(922-924)tTt>tCt	p.F308S	RTDR1_ENST00000216036.4_Intron	NM_002073.2	NP_002064.1	P19086	GNAZ_HUMAN	guanine nucleotide binding protein (G protein), alpha z polypeptide	308					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|receptor signaling protein activity (GO:0005057)|signal transducer activity (GO:0004871)			endometrium(3)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(5)|urinary_tract(1)	19	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.166)		CAGCGGCAGTTTGAAGACCTG	0.572																																					p.F308S		Atlas-SNP	.											.	GNAZ	45	.	0			c.T923C						PASS	.						128	100	109					22																	23465473		2203	4300	6503	SO:0001583	missense	2781	exon3			GGCAGTTTGAAGA		CCDS13804.1	22q11.1-q11.2	2008-06-10			ENSG00000128266	ENSG00000128266			4395	protein-coding gene	gene with protein product		139160				2115889	Standard	NM_002073		Approved		uc002zwu.1	P19086	OTTHUMG00000150611	ENST00000248996.4:c.923T>C	chr22.hg19:g.23465473T>C	ENSP00000248996:p.Phe308Ser	87.0	0.0	.		76.0	34.0	.	NM_002073	B2R6C1|Q4QRJ6	Missense_Mutation	SNP	ENST00000248996.4	hg19	CCDS13804.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.849238	0.91277	.	.	ENSG00000128266	ENST00000248996;ENST00000456059	D	0.92199	-2.99	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	D	0.97841	0.9291	H	0.99156	4.45	0.80722	D	1	D	0.64830	0.994	D	0.77557	0.99	D	0.99229	1.0881	10	0.87932	D	0	.	14.4404	0.67311	0.0:0.0:0.0:1.0	.	308	P19086	GNAZ_HUMAN	S	308;256	ENSP00000248996:F308S	ENSP00000248996:F308S	F	+	2	0	GNAZ	21795473	1.000000	0.71417	0.997000	0.53966	0.867000	0.49689	7.824000	0.86668	2.085000	0.62840	0.533000	0.62120	TTT	.	.	.	none		0.572	GNAZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319073.1	NM_002073		C	23465473	T	C	23465473	3	2	15	1	0	0	0	0	1	0	0	0	6521	1841	64	3	929	3	GNAZ	22	23465473	Missense_Mutation	SNP	T	TCGA-2Z-A9JL-01A-11D-A42J-10		23465473	27839093	91	1119											
TNRC6B	23112	hgsc.bcm.edu	37	chr22	40521834	40521834	+	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	ctgttcccatgcaaaccaatGagggagaagtatcggaagaa	15	7	11	8	1	0	3	0	1	0	2	2	5	1	4	2	2	2	3	2	2	6	2			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr22:40521834G>T	ENST00000301923.9	+	3	315	c.13G>T	c.(13-15)Gag>Tag	p.E5*	TNRC6B_ENST00000402203.1_Nonsense_Mutation_p.E5*	NM_001024843.1	NP_001020014.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	0	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						GCAAACCAATGAGGGAGAAGT	0.388																																					p.E5X		Atlas-SNP	.											.	TNRC6B	195	.	0			c.G13T						PASS	.						77	69	71					22																	40521834		1835	4086	5921	SO:0001587	stop_gained	23112	exon3			ACCAATGAGGGAG	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	ENST00000301923.9:c.13G>T	chr22.hg19:g.40521834G>T	ENSP00000306759:p.Glu5*	142.0	0.0	.		122.0	44.0	.	NM_001024843	B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	Nonsense_Mutation	SNP	ENST00000301923.9	hg19	CCDS46712.1	.	.	.	.	.	.	.	.	.	.	G	37	6.303463	0.97458	.	.	ENSG00000100354	ENST00000441751;ENST00000301923;ENST00000402203	.	.	.	5.06	5.06	0.68205	.	0.000000	0.30076	U	0.010480	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.2021	0.86908	0.0:0.0:1.0:0.0	.	.	.	.	X	5	.	ENSP00000306759:E5X	E	+	1	0	TNRC6B	38851780	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.003000	0.70701	2.333000	0.79357	0.655000	0.94253	GAG	.	.	.	none		0.388	TNRC6B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321393.1			T	40521834	G	T	40521834	4	4	15	1	0	0	0	0	0	1	0	0	16353	1291	45	4	15	4	TNRC6B	22	40521834	Nonsense_Mutation	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10	17056361	40521834	10782732	92	1120											
PKDREJ	10343	hgsc.bcm.edu	37	chr22	46658026	46658026	+	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	ttggcctgctcggggtgacaGacttccttgctccccaggat	5	11	12	13	1	0	2	0	1	0	1	3	3	2	3	4	4	2	2	4	4	0	3			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr22:46658026G>T	ENST00000253255.5	-	1	1193	c.1194C>A	c.(1192-1194)gtC>gtA	p.V398V		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	398	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)		CGGGGTGACAGACTTCCTTGC	0.532																																					p.V398V		Atlas-SNP	.											.	PKDREJ	195	.	0			c.C1194A						PASS	.						89	94	92					22																	46658026		2203	4300	6503	SO:0001819	synonymous_variant	10343	exon1			GTGACAGACTTCC	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.1194C>A	chr22.hg19:g.46658026G>T		91.0	0.0	.		83.0	39.0	.	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	hg19	CCDS14073.1																																																																																			.	.	.	none		0.532	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		T	46658026	G	T	46658026	2	4	15	1	0	0	0	0	0	0	0	1	11977	929	33	4		4	PKDREJ	22	46658026	Silent	SNP	G	TCGA-2Z-A9JL-01A-11D-A42J-10	6136192	46658026	4646540	93	1121											
MOV10L1	54456	hgsc.bcm.edu	37	chr22	50528560	50528560	+	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	tggtggccttcttctggaggAcggcggacacccctagggag	6	8	16	11	2	2	0	0	0	2	0	2	4	2	4	3	7	0	0	3	7	1	3			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chr22:50528560A>T	ENST00000262794.5	+	1	126	c.43A>T	c.(43-45)Acg>Tcg	p.T15S	MOV10L1_ENST00000545383.1_Missense_Mutation_p.T15S|MOV10L1_ENST00000395843.1_De_novo_Start_InFrame|MOV10L1_ENST00000395858.3_Missense_Mutation_p.T15S|MOV10L1_ENST00000540615.1_5'Flank	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	15					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		CTTCTGGAGGACGGCGGACAC	0.766																																					p.T15S		Atlas-SNP	.											.	MOV10L1	238	.	0			c.A43T						PASS	.						7	7	7					22																	50528560		1561	2879	4440	SO:0001583	missense	54456	exon1			TGGAGGACGGCGG	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"cardiac helicase activated by MEF2C protein"	605794	"Mov10 (mouse)-like 1", "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.43A>T	chr22.hg19:g.50528560A>T	ENSP00000262794:p.Thr15Ser	43.0	0.0	.		47.0	9.0	.	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Missense_Mutation	SNP	ENST00000262794.5	hg19	CCDS14084.1	.	.	.	.	.	.	.	.	.	.	A	9.737	1.163791	0.21538	.	.	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858	D;D;T	0.83837	-1.77;-1.77;-1.36	4.73	0.995	0.19838	.	0.514876	0.18784	N	0.131244	T	0.68787	0.3039	N	0.19112	0.55	0.80722	D	1	B;B	0.16396	0.017;0.017	B;B	0.09377	0.004;0.004	T	0.56763	-0.7925	10	0.26408	T	0.33	-11.1627	11.8849	0.52596	0.7766:0.2234:0.0:0.0	.	15;15	A8MXC6;Q9BXT6	.;M10L1_HUMAN	S	15	ENSP00000438978:T15S;ENSP00000262794:T15S;ENSP00000379199:T15S	ENSP00000262794:T15S	T	+	1	0	MOV10L1	48870687	0.987000	0.35691	0.666000	0.29783	0.224000	0.24922	1.078000	0.30754	0.249000	0.21456	0.460000	0.39030	ACG	.	.	.	none		0.766	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995		T	50528560	A	T	50528560	3	4	15	1	0	0	0	0	1	0	0	0	9726	275	10	5	45	5	MOV10L1	22	50528560	Missense_Mutation	SNP	A	TCGA-2Z-A9JL-01A-11D-A42J-10	3870534	50528560	776006	94	1122											
ATP1B4	23439	hgsc.bcm.edu	37	chrX	119504978	119504978	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caggagttatgatcagacccTtcgcccatagccttaacttc	10	11	7	13	1	1	2	1	1	0	1	3	3	1	3	3	1	2	1	3	1	3	5			TCGA-2Z-A9JL-01A-11D-A42J-10	TCGA-2Z-A9JL-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d76bb38d-3ef3-4a37-bc21-5b7bc290d112	27a1d440-82fb-44f6-b007-5ad71c7b4cc1	g.chrX:119504978T>C	ENST00000218008.3	+	4	532	c.475T>C	c.(475-477)Ttc>Ctc	p.F159L	ATP1B4_ENST00000361319.3_Missense_Mutation_p.F155L|ATP1B4_ENST00000539306.1_Missense_Mutation_p.F116L	NM_001142447.2	NP_001135919.1	Q9UN42	AT1B4_HUMAN	ATPase, Na+/K+ transporting, beta 4 polypeptide	159					monovalent inorganic cation transport (GO:0015672)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|nuclear inner membrane (GO:0005637)|sodium:potassium-exchanging ATPase complex (GO:0005890)	monovalent inorganic cation transmembrane transporter activity (GO:0015077)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	33						GATCAGACCCTTCGCCCATAG	0.413																																					p.F159L		Atlas-SNP	.											.	ATP1B4	61	.	0			c.T475C						PASS	.						133	109	117					X																	119504978		2203	4300	6503	SO:0001583	missense	23439	exon4			AGACCCTTCGCCC	AF158383	CCDS14598.1, CCDS48158.1	Xq24	2012-10-22	2010-04-20		ENSG00000101892	ENSG00000101892		"ATPases / P-type"	808	protein-coding gene	gene with protein product	"Na,K-ATPase beta m-subunit"		"ATPase, (Na+)/K+ transporting, beta 4 polypeptide"			10456317, 17592128	Standard	NM_012069		Approved		uc004esr.3	Q9UN42	OTTHUMG00000022299	ENST00000218008.3:c.475T>C	chrX.hg19:g.119504978T>C	ENSP00000218008:p.Phe159Leu	72.0	0.0	.		40.0	35.0	.	NM_001142447	Q17RR0|Q9UN41	Missense_Mutation	SNP	ENST00000218008.3	hg19	CCDS48158.1	.	.	.	.	.	.	.	.	.	.	T	13.30	2.194981	0.38806	.	.	ENSG00000101892	ENST00000218008;ENST00000361319;ENST00000539306	T;T;T	0.28255	1.62;1.62;1.62	5.51	5.51	0.81932	.	0.144564	0.64402	D	0.000005	T	0.14743	0.0356	N	0.02751	-0.505	0.40189	D	0.977385	P;B;P;P	0.44877	0.845;0.261;0.729;0.683	B;B;B;B	0.43331	0.416;0.344;0.277;0.181	T	0.16837	-1.0389	10	0.11485	T	0.65	-16.9285	12.2846	0.54786	0.0:0.0:0.0:1.0	.	116;124;159;155	B7ZKW0;B7ZKV9;Q9UN42;Q9UN42-2	.;.;AT1B4_HUMAN;.	L	159;155;116	ENSP00000218008:F159L;ENSP00000355346:F155L;ENSP00000443334:F116L	ENSP00000218008:F159L	F	+	1	0	ATP1B4	119389006	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.467000	0.53078	1.835000	0.53391	0.441000	0.28932	TTC	.	.	.	none		0.413	ATP1B4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058095.1	NM_001142447		C	119504978	T	C	119504978	3	2	15	1	0	0	0	0	1	0	0	0	1135	1609	56	3	489	3	ATP1B4	23	119504978	Missense_Mutation	SNP	T	TCGA-2Z-A9JL-01A-11D-A42J-10		119504978	35765582	95	1123											
SDF4	51150	hgsc.bcm.edu	37	chr1	1163850	1163850	+	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	gcacatggcggcacctacttGgaaaagatgaccatcagctt	12	8	10	11	1	1	2	1	1	0	1	1	3	1	3	2	3	2	3	2	3	3	3			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr1:1163850G>T	ENST00000360001.6	-	2	586	c.324C>A	c.(322-324)tcC>tcA	p.S108S	SDF4_ENST00000545427.1_Silent_p.S108S|SDF4_ENST00000459994.2_5'UTR|SDF4_ENST00000263741.7_Silent_p.S108S			Q9BRK5	CAB45_HUMAN	stromal cell derived factor 4	108	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				calcium ion-dependent exocytosis (GO:0017156)|cerebellum development (GO:0021549)|fat cell differentiation (GO:0045444)|response to ethanol (GO:0045471)|UV protection (GO:0009650)|zymogen granule exocytosis (GO:0070625)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|late endosome (GO:0005770)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	11	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;7.85e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.42e-21)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;4.83e-05)|Kidney(185;0.00252)|BRCA - Breast invasive adenocarcinoma(365;0.00263)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0368)|Lung(427;0.204)		GCACCTACTTGGAAAAGATGA	0.667																																					p.S108S		Atlas-SNP	.											.	SDF4	50	.	0			c.C324A						PASS	.						27	32	31					1																	1163850		2201	4298	6499	SO:0001819	synonymous_variant	51150	exon2			CTACTTGGAAAAG		CCDS12.1, CCDS30553.1	1p36.33	2013-01-10			ENSG00000078808	ENSG00000078808		"EF-hand domain containing"	24188	protein-coding gene	gene with protein product	"calcium binding protein"	614282				9254016, 8609160	Standard	NM_016176		Approved	Cab45	uc001adh.4	Q9BRK5	OTTHUMG00000001812	ENST00000360001.6:c.324C>A	chr1.hg19:g.1163850G>T		49.0	0.0	.		48.0	14.0	.	NM_016547	B1AME5|B1AME6|B2RDF1|B4DSM1|Q53G52|Q53HQ9|Q8NBQ3|Q96AA1|Q9NZP7|Q9UN53	Silent	SNP	ENST00000360001.6	hg19	CCDS30553.1	.	.	.	.	.	.	.	.	.	.	G	12.83	2.055142	0.36277	.	.	ENSG00000078808	ENST00000403997	.	.	.	3.86	1.73	0.24493	.	.	.	.	.	T	0.56016	0.1957	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50849	-0.8779	4	.	.	.	-24.5532	8.5179	0.33257	0.0957:0.0:0.7422:0.1621	.	.	.	.	K	43	.	.	Q	-	1	0	SDF4	1153713	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	2.612000	0.46343	0.828000	0.34709	0.511000	0.50034	CAA	.	.	.	none		0.667	SDF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005064.1	NM_016176		T	1163850	G	T	1163850	2	4	16	1	0	0	0	0	0	0	0	1	13975	1335	47	4		4	SDF4	1	1163850	Silent	SNP	G	TCGA-2Z-A9JM-01A-12D-A42J-10		1163850	248086771	1	1124											
KNCN	148930	hgsc.bcm.edu	37	chr1	47014904	47014905	+	Missense_Mutation	DNP	GG	GG	TC																															gctggatcttccttccccgtGgtctgcccctggatggggat																								rs191194559		TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr1:47014904_47014905GG>TC	ENST00000481882.2	-	3	566_567	c.255_256CC>GA	c.(253-258)gaCCac>gaGAac	p.85_86DH>EN	KNCN_ENST00000524908.1_5'UTR|KNCN_ENST00000396314.3_Missense_Mutation_p.62_63DH>EN|MKNK1-AS1_ENST00000602433.1_RNA			A6PVL3	KNCN_HUMAN	kinocilin	85						apical plasma membrane (GO:0016324)|ciliary basal body (GO:0036064)|cuticular plate (GO:0032437)|integral component of membrane (GO:0016021)|kinocilium (GO:0060091)|neuronal cell body (GO:0043025)				central_nervous_system(1)|endometrium(1)|lung(1)|ovary(1)	4	Acute lymphoblastic leukemia(166;0.155)					CCTTCCCCGTGGTCTGCCCCTG	0.5																																					p.H63N|p.D62E		Atlas-SNP	.											.	KNCN	7	.	0			c.C187A|c.C186G						PASS	.																																			SO:0001583	missense	148930	exon2			CCCCGTGGTCTGC|CCCGTGGTCTGCC	AK056573	CCDS44133.1	1p33	2014-02-12	2006-10-26		ENSG00000162456	ENSG00000162456			26488	protein-coding gene	gene with protein product		611455				15855039	Standard	NM_001097611		Approved	FLJ32011, KINO, L5	uc001cpy.2	A6PVL3	OTTHUMG00000007987	ENST00000481882.2:c.255_256delinsTC	chr1.hg19:g.47014904_47014905delinsTC	ENSP00000419705:p.D85_H86delinsEN	113.0	0.0	.		101.0	30.0	.	NM_001097611	A8MXE3	Missense_Mutation	SNP	ENST00000481882.2	hg19																																																																																				.	.|G|1.000;T|0.000	.	none|alt		0.5	KNCN-002	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000316334.2	NM_182516		TC	47014905	GG	TC	47014904	3	4	16	1	0	0	0	0	1	0	0	0	8432	1348	47	4	126	4	KNCN	1	47014904	Missense_Mutation	DNP	GG	TCGA-2Z-A9JM-01A-12D-A42J-10	45851054	47014904	202235717	2	1125											
SLC44A3	126969	hgsc.bcm.edu	37	chr1	95323000	95323000	+	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	atctggactagtgaattcatCcttgcgtgccagcaaatgac	11	11	9	10	1	2	2	1	2	1	0	3	3	3	3	2	1	3	1	2	1	3	3			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr1:95323000C>A	ENST00000271227.6	+	10	1284	c.1182C>A	c.(1180-1182)atC>atA	p.I394I	SLC44A3_ENST00000532427.1_Silent_p.I314I|SLC44A3_ENST00000529450.1_Silent_p.I362I|SLC44A3_ENST00000467909.1_Silent_p.I346I|SLC44A3_ENST00000530397.1_3'UTR|RP11-465K1.2_ENST00000422162.1_RNA|SLC44A3_ENST00000527077.1_Silent_p.I326I|SLC44A3_ENST00000446120.2_Silent_p.I358I	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	394					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)	GTGAATTCATCCTTGCGTGCC	0.443																																					p.I394I		Atlas-SNP	.											.	SLC44A3	109	.	0			c.C1182A						PASS	.						190	172	178					1																	95323000		2203	4300	6503	SO:0001819	synonymous_variant	126969	exon10			ATTCATCCTTGCG	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.1182C>A	chr1.hg19:g.95323000C>A		121.0	0.0	.		114.0	32.0	.	NM_001114106	B4DVY4|B4E1M4|B7ZA08|E9PJH2|E9PJY8|Q6UWT1|Q7Z6C5|Q9BWY7	Silent	SNP	ENST00000271227.6	hg19	CCDS44176.1																																																																																			.	.	.	none		0.443	SLC44A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029544.3	NM_152369		A	95323000	C	A	95323000	2	1	16	1	0	0	0	0	0	0	0	1	14650	845	30	4		4	SLC44A3	1	95323000	Silent	SNP	C	TCGA-2Z-A9JM-01A-12D-A42J-10	48308096	95323000	153927621	3	1126											
VANGL1	81839	hgsc.bcm.edu	37	chr1	116206833	116206833	+	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	ctgcagcccatgttcacgctGcaggtggtccgctccaccga	6	8	11	16	3	1	0	1	0	0	0	3	1	3	0	4	2	3	5	4	2	0	1			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr1:116206833G>T	ENST00000355485.2	+	4	1027	c.756G>T	c.(754-756)ctG>ctT	p.L252L	VANGL1_ENST00000310260.3_Silent_p.L252L|VANGL1_ENST00000369509.1_Silent_p.L252L|VANGL1_ENST00000369510.4_Silent_p.L250L	NM_001172411.1|NM_138959.2	NP_001165882.1|NP_620409.1	Q8TAA9	VANG1_HUMAN	VANGL planar cell polarity protein 1	252					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)		TGTTCACGCTGCAGGTGGTCC	0.577																																					p.L252L		Atlas-SNP	.											.	VANGL1	65	.	0			c.G756T						PASS	.						60	57	58					1																	116206833		2203	4300	6503	SO:0001819	synonymous_variant	81839	exon4			CACGCTGCAGGTG	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.756G>T	chr1.hg19:g.116206833G>T		36.0	0.0	.		39.0	4.0	.	NM_138959	Q5T1D3|Q5T1D4|Q86WG8|Q8N559	Silent	SNP	ENST00000355485.2	hg19	CCDS883.1																																																																																			.	.	.	none		0.577	VANGL1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033096.1			T	116206833	G	T	116206833	2	4	16	1	0	0	0	0	0	0	0	1	17131	1306	46	4		4	VANGL1	1	116206833	Silent	SNP	G	TCGA-2Z-A9JM-01A-12D-A42J-10	20883833	116206833	133043788	4	1127											
LCE2B	26239	hgsc.bcm.edu	37	chr1	152659505	152659505	+	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	tgtggtcccagctctgggggCtgctgcaactctggggctgg	3	10	17	11	0	2	0	0	0	2	0	3	0	3	0	1	6	4	5	1	6	1	0			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr1:152659505C>T	ENST00000368780.3	+	2	240	c.186C>T	c.(184-186)ggC>ggT	p.G62G	LCE2B_ENST00000417924.2_Silent_p.G62G	NM_014357.4	NP_055172.1	O14633	LCE2B_HUMAN	late cornified envelope 2B	62	Cys-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)			GCTCTGGGGGCTGCTGCAACT	0.662																																					p.G62G		Atlas-SNP	.											.	LCE2B	40	.	0			c.C186T						PASS	.						89	105	99					1																	152659505		2203	4300	6503	SO:0001819	synonymous_variant	26239	exon2			TGGGGGCTGCTGC	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.186C>T	chr1.hg19:g.152659505C>T		110.0	0.0	.		115.0	42.0	.	NM_014357	Q5TA80	Silent	SNP	ENST00000368780.3	hg19	CCDS1020.1																																																																																			.	.	.	none		0.662	LCE2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034524.1	NM_014357		T	152659505	C	T	152659505	2	4	16	1	0	0	0	0	0	0	0	1	8673	784	28	2		2	LCE2B	1	152659505	Silent	SNP	C	TCGA-2Z-A9JM-01A-12D-A42J-10	36452672	152659505	96591116	5	1128											
ISG20L2	81875	hgsc.bcm.edu	37	chr1	156696838	156696838	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctccgttgtagttgacaaTgctacatcgagccaaggaac	12	10	9	10	2	1	1	0	1	1	0	3	3	1	2	2	1	4	4	2	1	5	4			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr1:156696838T>C	ENST00000313146.6	-	1	1389	c.607A>G	c.(607-609)Att>Gtt	p.I203V	ISG20L2_ENST00000472824.2_5'Flank|RRNAD1_ENST00000524343.1_5'Flank|ISG20L2_ENST00000368219.1_Missense_Mutation_p.I203V|RRNAD1_ENST00000368218.4_5'Flank|RRNAD1_ENST00000368216.4_5'Flank	NM_030980.1	NP_112242.1	Q9H9L3	I20L2_HUMAN	interferon stimulated exonuclease gene 20kDa-like 2	203	Exonuclease.				ribosome biogenesis (GO:0042254)	nucleus (GO:0005634)	exonuclease activity (GO:0004527)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TAGTTGACAATGCTACATCGA	0.527											OREG0013885	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I203V		Atlas-SNP	.											.	ISG20L2	43	.	0			c.A607G						PASS	.						187	148	161					1																	156696838		2203	4300	6503	SO:0001583	missense	81875	exon1			TGACAATGCTACA	AK095697	CCDS1153.1	1q23.1	2013-10-11			ENSG00000143319	ENSG00000143319			25745	protein-coding gene	gene with protein product		611930				18065403	Standard	NM_030980		Approved	FLJ12671	uc001fps.1	Q9H9L3	OTTHUMG00000041301	ENST00000313146.6:c.607A>G	chr1.hg19:g.156696838T>C	ENSP00000323424:p.Ile203Val	93.0	0.0	.	1780	91.0	27.0	.	NM_030980	D3DVC6|Q64KA2	Missense_Mutation	SNP	ENST00000313146.6	hg19	CCDS1153.1	.	.	.	.	.	.	.	.	.	.	T	12.19	1.864162	0.32977	.	.	ENSG00000143319	ENST00000313146;ENST00000368219	T;T	0.24538	1.85;1.85	5.17	5.17	0.71159	Exonuclease (1);Exonuclease, RNase T/DNA polymerase III (1);Ribonuclease H-like (1);	0.097133	0.50627	D	0.000111	T	0.13927	0.0337	N	0.16833	0.445	0.43494	D	0.995738	B	0.27910	0.193	B	0.42462	0.388	T	0.19289	-1.0310	10	0.38643	T	0.18	.	13.9797	0.64297	0.0:0.0:0.0:1.0	.	203	Q9H9L3	I20L2_HUMAN	V	203	ENSP00000323424:I203V;ENSP00000357202:I203V	ENSP00000323424:I203V	I	-	1	0	ISG20L2	154963462	1.000000	0.71417	1.000000	0.80357	0.768000	0.43524	1.502000	0.35704	2.175000	0.68902	0.533000	0.62120	ATT	.	.	.	none		0.527	ISG20L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098969.1	NM_030980		C	156696838	T	C	156696838	3	2	16	1	0	0	0	0	1	0	0	0	7862	1464	51	3	466	3	ISG20L2	1	156696838	Missense_Mutation	SNP	T	TCGA-2Z-A9JM-01A-12D-A42J-10	4037333	156696838	92553783	6	1129											
SMG7	9887	hgsc.bcm.edu	37	chr1	183520232	183520232	+	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	gcaacgtcatcctctgagagCagttggcatcaggccagcac	10	7	11	13	1	3	1	2	1	1	1	4	2	4	1	2	2	3	5	2	2	1	1			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr1:183520232C>T	ENST00000347615.2	+	21	3326	c.3207C>T	c.(3205-3207)agC>agT	p.S1069S	SMG7_ENST00000367537.3_Silent_p.S1102S|SMG7_ENST00000515829.2_Silent_p.S1023S|SMG7_ENST00000507469.1_Silent_p.S1073S|SMG7_ENST00000456731.2_Silent_p.S981S|SMG7_ENST00000508461.1_Silent_p.S1077S	NM_173156.2	NP_775179.1	Q92540	SMG7_HUMAN	SMG7 nonsense mediated mRNA decay factor	1069					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(16)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	46						CCTCTGAGAGCAGTTGGCATC	0.493																																					p.S1077S		Atlas-SNP	.											.	SMG7	165	.	0			c.C3231T						PASS	.						81	74	76					1																	183520232		2203	4300	6503	SO:0001819	synonymous_variant	9887	exon21			TGAGAGCAGTTGG	D87437	CCDS1355.1, CCDS41445.1, CCDS41445.2, CCDS53444.1, CCDS53445.1	1q25	2013-07-02	2013-07-02	2006-02-16	ENSG00000116698	ENSG00000116698			16792	protein-coding gene	gene with protein product	"EST1 telomerase component homolog C (S. cerevisiae)"	610964	"chromosome 1 open reading frame 16", "smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C1orf16		14636577, 15721257	Standard	NM_173156		Approved	KIAA0250, EST1C, SGA56M, SMG-7	uc001gqf.3	Q92540	OTTHUMG00000035221	ENST00000347615.2:c.3207C>T	chr1.hg19:g.183520232C>T		154.0	0.0	.		112.0	28.0	.	NM_001174061	B4DRB2|E9PCI0|E9PEH2|Q5T1Q0|Q6PIE0|Q7Z7H9|Q8IXC1|Q8IXC2	Silent	SNP	ENST00000347615.2	hg19	CCDS1355.1																																																																																			.	.	.	none		0.493	SMG7-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000085432.1	NM_014837		T	183520232	C	T	183520232	2	4	16	1	0	0	0	0	0	0	0	1	14811	709	25	2		2	SMG7	1	183520232	Silent	SNP	C	TCGA-2Z-A9JM-01A-12D-A42J-10	26823394	183520232	65730389	7	1130											
DHX57	90957	hgsc.bcm.edu	37	chr2	39050399	39050399	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttatgagcactaaacatctcTaaaattttaattctgaaaag	17	14	4	6	0	2	2	0	2	2	0	3	2	2	2	0	0	2	1	0	0	8	6			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr2:39050399T>C	ENST00000295373.6	-	17	3153	c.3027A>G	c.(3025-3027)ttA>ttG	p.L1009L		NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	1009	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				TAAACATCTCTAAAATTTTAA	0.343																																					p.L1009L	Melanoma(191;1090 2095 4375 23729 47341)	Atlas-SNP	.											.	DHX57	127	.	0			c.A3027G						PASS	.						40	43	42					2																	39050399		2203	4300	6503	SO:0001819	synonymous_variant	90957	exon17			CATCTCTAAAATT	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.3027A>G	chr2.hg19:g.39050399T>C		81.0	0.0	.		74.0	27.0	.	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Silent	SNP	ENST00000295373.6	hg19	CCDS1800.1	.	.	.	.	.	.	.	.	.	.	T	3.584	-0.084978	0.07097	.	.	ENSG00000163214	ENST00000452978	.	.	.	5.62	-2.77	0.05877	.	.	.	.	.	T	0.63581	0.2523	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62530	-0.6835	4	.	.	.	.	13.7596	0.62956	0.0:0.7451:0.0:0.2549	.	.	.	.	G	333	.	.	R	-	1	2	DHX57	38903903	1.000000	0.71417	0.979000	0.43373	0.432000	0.31715	1.023000	0.30065	-0.415000	0.07484	-0.411000	0.06167	AGA	.	.	.	none		0.343	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646		C	39050399	T	C	39050399	2	2	16	1	0	0	0	0	0	0	0	1	4515	1519	53	3		3	DHX57	2	39050399	Silent	SNP	T	TCGA-2Z-A9JM-01A-12D-A42J-10		39050399	204148974	8	1131											
THADA	63892	hgsc.bcm.edu	37	chr2	43519255	43519255	+	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	gggcaaacctttcattggaaGcaatatccatcgtccagatc	12	10	8	11	1	1	1	1	0	0	1	5	2	3	2	3	2	2	2	3	2	4	3			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr2:43519255G>C	ENST00000405006.4	-	33	5276	c.4925C>G	c.(4924-4926)gCt>gGt	p.A1642G	THADA_ENST00000415080.2_Missense_Mutation_p.A1323G|THADA_ENST00000330266.7_Intron|THADA_ENST00000405975.2_Missense_Mutation_p.A1642G	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	1642										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)				TTCATTGGAAGCAATATCCAT	0.488																																					p.A1642G		Atlas-SNP	.											.	THADA	131	.	0			c.C4925G						PASS	.						51	56	55					2																	43519255		1955	4146	6101	SO:0001583	missense	63892	exon33			TTGGAAGCAATAT	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.4925C>G	chr2.hg19:g.43519255G>C	ENSP00000385995:p.Ala1642Gly	90.0	0.0	.		84.0	28.0	.	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Missense_Mutation	SNP	ENST00000405006.4	hg19	CCDS46268.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.1|25.1	4.606563|4.606563	0.87157|0.87157	.|.	.|.	ENSG00000115970|ENSG00000115970	ENST00000405975;ENST00000356975;ENST00000415080;ENST00000405006|ENST00000407351	T;T;T|.	0.18502|.	2.48;2.21;2.48|.	5.18|5.18	5.18|5.18	0.71444|0.71444	.|.	0.320498|.	0.28659|.	N|.	0.014574|.	T|T	0.56746|0.56746	0.2006|0.2006	L|L	0.34521|0.34521	1.04|1.04	0.36371|0.36371	D|D	0.86129|0.86129	D;D|.	0.69078|.	0.997;0.991|.	D;P|.	0.72338|.	0.977;0.793|.	T|T	0.60900|0.60900	-0.7171|-0.7171	10|5	0.35671|.	T|.	0.21|.	-12.1636|-12.1636	15.7003|15.7003	0.77536|0.77536	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1569;1642|.	B6ZDQ0;Q6YHU6|.	.;THADA_HUMAN|.	G|V	1642;1569;1323;1642|882	ENSP00000386088:A1642G;ENSP00000416048:A1323G;ENSP00000385995:A1642G|.	ENSP00000349464:A1569G|.	A|L	-|-	2|1	0|0	THADA|THADA	43372759|43372759	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.973000|0.973000	0.67179|0.67179	4.752000|4.752000	0.62176|0.62176	2.421000|2.421000	0.82119|0.82119	0.644000|0.644000	0.83932|0.83932	GCT|CTT	.	.	.	none		0.488	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065		C	43519255	G	C	43519255	3	2	16	1	0	0	0	0	1	0	0	0	15852	971	34	4	960	4	THADA	2	43519255	Missense_Mutation	SNP	G	TCGA-2Z-A9JM-01A-12D-A42J-10	4468856	43519255	199680118	9	1132											
CWC22	57703	hgsc.bcm.edu	37	chr2	180842978	180842978	+	Missense_Mutation	SNP	T	T	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	aatacttatgttggaaatgtTgactttgttgataaggccat	12	16	9	4	0	0	2	0	2	0	0	0	3	0	3	1	2	1	3	1	2	5	7			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr2:180842978T>G	ENST00000410053.3	-	6	819	c.520A>C	c.(520-522)Aac>Cac	p.N174H	CWC22_ENST00000295749.6_Missense_Mutation_p.N174H	NM_020943.2	NP_065994.1	Q9HCG8	CWC22_HUMAN	CWC22 spliceosome-associated protein	174	MIF4G. {ECO:0000255|PROSITE- ProRule:PRU00698}.				mRNA splicing, via spliceosome (GO:0000398)|regulation of mRNA splicing, via spliceosome (GO:0048024)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(8)|stomach(1)	30						TTGGAAATGTTGACTTTGTTG	0.308																																					p.N174H		Atlas-SNP	.											.	CWC22	62	.	0			c.A520C						PASS	.						69	66	67					2																	180842978		1799	4069	5868	SO:0001583	missense	57703	exon6			AAATGTTGACTTT		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.520A>C	chr2.hg19:g.180842978T>G	ENSP00000387006:p.Asn174His	115.0	0.0	.		171.0	63.0	.	NM_020943	Q05DC2|Q4G135|Q52LF0|Q6PEX2|Q7Z6I0|Q9H5L3|Q9H6Q6	Missense_Mutation	SNP	ENST00000410053.3	hg19	CCDS46465.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.569299	0.86439	.	.	ENSG00000163510	ENST00000410053;ENST00000295749;ENST00000404136	T;T;T	0.22945	1.93;1.93;1.93	5.87	5.87	0.94306	MIF4G-like, type 3 (2);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.000000	0.85682	D	0.000000	T	0.63367	0.2505	H	0.94582	3.555	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74680	-0.3584	10	0.87932	D	0	-26.3331	15.4442	0.75216	0.0:0.0:0.0:1.0	.	174	Q9HCG8	CWC22_HUMAN	H	174	ENSP00000387006:N174H;ENSP00000295749:N174H;ENSP00000384159:N174H	ENSP00000295749:N174H	N	-	1	0	CWC22	180551223	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.806000	0.86020	2.239000	0.73571	0.528000	0.53228	AAC	.	.	.	none		0.308	CWC22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334537.1	NM_020943		G	180842978	T	G	180842978	3	3	16	1	0	0	0	0	1	0	0	0	4070	1812	63	5	2266	5	CWC22	2	180842978	Missense_Mutation	SNP	T	TCGA-2Z-A9JM-01A-12D-A42J-10	137323723	180842978	62356395	10	1133											
IL17RC	84818	hgsc.bcm.edu	37	chr3	9974800	9974800	+	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	gcgcaggggcccgtggcttgGtttcacgcgcagcggcgcca	4	6	17	14	6	1	0	1	0	0	0	1	0	1	0	2	5	1	4	2	5	0	2			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr3:9974800G>C	ENST00000295981.3	+	19	2117	c.1899G>C	c.(1897-1899)tgG>tgC	p.W633C	IL17RC_ENST00000383812.4_Missense_Mutation_p.W547C|IL17RC_ENST00000416074.2_Missense_Mutation_p.W388C|IL17RC_ENST00000455057.1_Missense_Mutation_p.W530C|IL17RC_ENST00000403601.3_Missense_Mutation_p.W562C|IL17RC_ENST00000498214.1_3'UTR|RP11-1020A11.1_ENST00000602411.1_RNA|CRELD1_ENST00000452070.1_5'Flank|CRELD1_ENST00000326434.5_5'Flank|IL17RC_ENST00000413608.1_Missense_Mutation_p.W549C|CRELD1_ENST00000383811.3_5'Flank|CRELD1_ENST00000397170.3_5'Flank	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	633	SEFIR. {ECO:0000255|PROSITE- ProRule:PRU00867}.				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						CCGTGGCTTGGTTTCACGCGC	0.711											OREG0015383	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.W633C		Atlas-SNP	.											.	IL17RC	55	.	0			c.G1899C						PASS	.						17	17	17					3																	9974800		2193	4286	6479	SO:0001583	missense	84818	exon19			GGCTTGGTTTCAC	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.1899G>C	chr3.hg19:g.9974800G>C	ENSP00000295981:p.Trp633Cys	26.0	0.0	.	661	39.0	11.0	.	NM_153461	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Missense_Mutation	SNP	ENST00000295981.3	hg19	CCDS2590.1	.	.	.	.	.	.	.	.	.	.	G	15.44	2.834602	0.50951	.	.	ENSG00000163702	ENST00000383812;ENST00000295981;ENST00000403601;ENST00000416074;ENST00000455057;ENST00000413608	T;T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6;0.6	4.97	3.16	0.36331	SEFIR (1);	0.000000	0.64402	D	0.000001	T	0.64594	0.2612	M	0.62723	1.935	0.52099	D	0.999946	D;B;B;D;D;B;D;D	0.89917	1.0;0.129;0.129;1.0;1.0;0.105;1.0;1.0	D;B;B;D;D;B;D;D	0.97110	0.999;0.114;0.114;1.0;1.0;0.069;0.999;0.999	T	0.62992	-0.6736	10	0.72032	D	0.01	-12.9366	6.6131	0.22763	0.093:0.0:0.7317:0.1753	.	388;530;532;549;388;547;633;562	F5H4Z2;E9PHG1;A8BWD5;E9PHJ6;B4E008;Q8NAC3-3;Q8NAC3;Q8NAC3-2	.;.;.;.;.;.;I17RC_HUMAN;.	C	547;633;562;388;530;549	ENSP00000373323:W547C;ENSP00000295981:W633C;ENSP00000384969:W562C;ENSP00000395315:W388C;ENSP00000407894:W530C;ENSP00000396064:W549C	ENSP00000295981:W633C	W	+	3	0	IL17RC	9949800	1.000000	0.71417	1.000000	0.80357	0.393000	0.30537	5.080000	0.64437	0.496000	0.27904	-0.310000	0.09108	TGG	.	.	.	none		0.711	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732		C	9974800	G	C	9974800	3	2	16	1	0	0	0	0	1	0	0	0	7648	1270	44	4	1973	4	IL17RC	3	9974800	Missense_Mutation	SNP	G	TCGA-2Z-A9JM-01A-12D-A42J-10		9974800	188047630	11	1134											
TIGIT	201633	hgsc.bcm.edu	37	chr3	114026767	114026767	+	Missense_Mutation	SNP	T	T	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	agccctcagaatccattctgTggaaggtgacctcaggagaa	12	8	11	10	0	3	3	2	1	1	2	4	5	4	4	3	3	1	0	3	3	3	1			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr3:114026767T>G	ENST00000486257.1	+	5	781	c.524T>G	c.(523-525)gTg>gGg	p.V175G	TIGIT_ENST00000383671.3_Missense_Mutation_p.V175G|TIGIT_ENST00000481065.1_Missense_Mutation_p.V242G|TIGIT_ENST00000496848.1_3'UTR			Q495A1	TIGIT_HUMAN	T cell immunoreceptor with Ig and ITIM domains	175					negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|positive regulation of interleukin-10 production (GO:0032733)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(7)|prostate(1)	17						ATCCATTCTGTGGAAGGTGAC	0.483																																					p.V175G		Atlas-SNP	.											.	TIGIT	42	.	0			c.T524G						PASS	.						76	80	79					3																	114026767		2203	4300	6503	SO:0001583	missense	201633	exon4			ATTCTGTGGAAGG	AK097192	CCDS2980.1	3q13.31	2013-01-11	2008-10-13	2008-10-13	ENSG00000181847	ENSG00000181847		"Immunoglobulin superfamily / V-set domain containing"	26838	protein-coding gene	gene with protein product		612859	"V-set and immunoglobulin domain containing 9", "V-set and transmembrane domain containing 3"	VSIG9, VSTM3		19011627	Standard	NM_173799		Approved	FLJ39873, DKFZp667A205	uc003ebg.2	Q495A1	OTTHUMG00000159331	ENST00000486257.1:c.524T>G	chr3.hg19:g.114026767T>G	ENSP00000419085:p.Val175Gly	172.0	0.0	.		137.0	36.0	.	NM_173799	Q495A3|Q5JPD8|Q6MZS2|Q8N877	Missense_Mutation	SNP	ENST00000486257.1	hg19	CCDS2980.1	.	.	.	.	.	.	.	.	.	.	T	3.429	-0.116496	0.06838	.	.	ENSG00000181847	ENST00000461158;ENST00000481065;ENST00000486257;ENST00000383671;ENST00000484319	T;T;T;T;T	0.58210	0.35;0.36;0.42;0.42;0.35	4.21	-1.81	0.07882	.	0.851711	0.10155	N	0.709140	T	0.27832	0.0685	N	0.14661	0.345	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.16129	-1.0413	10	0.22706	T	0.39	0.8948	4.6147	0.12420	0.0:0.3506:0.1677:0.4817	.	175	Q495A1	TIGIT_HUMAN	G	154;242;175;175;154	ENSP00000418917:V154G;ENSP00000420552:V242G;ENSP00000419085:V175G;ENSP00000373167:V175G;ENSP00000419706:V154G	ENSP00000373167:V175G	V	+	2	0	TIGIT	115509457	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-0.300000	0.08243	-0.325000	0.08577	0.533000	0.62120	GTG	.	.	.	none		0.483	TIGIT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354690.1	NM_173799		G	114026767	T	G	114026767	3	3	16	1	0	0	0	0	1	0	0	0	15914	1696	59	5	538	5	TIGIT	3	114026767	Missense_Mutation	SNP	T	TCGA-2Z-A9JM-01A-12D-A42J-10	104051967	114026767	83995663	12	1135											
C3orf1	51300	hgsc.bcm.edu	37	chr3	119222809	119222809	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctttttaccagcacagtgaAcactagtctgaatgtatacc	12	12	6	11	0	1	2	0	2	1	0	1	2	1	2	3	0	4	2	3	0	6	6			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr3:119222809A>G	ENST00000494664.1	+	4	660	c.458A>G	c.(457-459)aAc>aGc	p.N153S	TIMMDC1_ENST00000493694.1_Intron	NM_016589.3	NP_057673.2	Q9NPL8	TIDC1_HUMAN	translocase of inner mitochondrial membrane domain containing 1	153						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				autonomic_ganglia(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|stomach(1)|urinary_tract(1)	15						AGCACAGTGAACACTAGTCTG	0.323																																					p.N153S		Atlas-SNP	.											.	TIMMDC1	29	.	0			c.A458G						PASS	.						141	140	141					3																	119222809		2203	4300	6503	SO:0001583	missense	51300	exon4			CAGTGAACACTAG	AF210057	CCDS33831.1	3q13.33	2013-12-05	2011-07-05	2011-07-05	ENSG00000113845	ENSG00000113845			1321	protein-coding gene	gene with protein product		615534	"chromosome 3 open reading frame 1"	C3orf1		11092749	Standard	NM_016589		Approved	FLJ22597	uc003ecn.3	Q9NPL8	OTTHUMG00000159388	ENST00000494664.1:c.458A>G	chr3.hg19:g.119222809A>G	ENSP00000418803:p.Asn153Ser	44.0	0.0	.		55.0	13.0	.	NM_016589	D3DN81|Q6IAJ7|Q6UWU6|Q9NPR3|Q9NPS5|Q9P0Y6	Missense_Mutation	SNP	ENST00000494664.1	hg19	CCDS33831.1	.	.	.	.	.	.	.	.	.	.	A	0.009	-1.808491	0.00606	.	.	ENSG00000113845	ENST00000494664;ENST00000466984	T;T	0.39229	1.56;1.09	4.74	0.905	0.19307	.	0.155895	0.56097	N	0.000037	T	0.15696	0.0378	N	0.11427	0.14	0.80722	D	1	B	0.06786	0.001	B	0.11329	0.006	T	0.28106	-1.0054	10	0.02654	T	1	-8.7525	4.7175	0.12903	0.6328:0.1645:0.2027:0.0	.	153	Q9NPL8	TIDC1_HUMAN	S	153;68	ENSP00000418803:N153S;ENSP00000420122:N68S	ENSP00000264244:N153S	N	+	2	0	TIMMDC1	120705499	1.000000	0.71417	0.995000	0.50966	0.007000	0.05969	2.437000	0.44828	0.004000	0.14682	-1.447000	0.01057	AAC	.	.	.	none		0.323	TIMMDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355077.3	NM_016589		G	119222809	A	G	119222809	3	3	16	1	0	0	0	0	1	0	0	0	2208	43	2	3	472	3	C3orf1	3	119222809	Missense_Mutation	SNP	A	TCGA-2Z-A9JM-01A-12D-A42J-10	5196042	119222809	78799621	13	1136											
ALDH1L1	10840	hgsc.bcm.edu	37	chr3	125854448	125854448	+	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	attctcaaaggcatccttggCtgcggccactgccttgtcga	7	11	10	13	2	1	0	1	0	1	0	4	1	2	0	3	3	2	2	3	3	1	3			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr3:125854448C>T	ENST00000393434.2	-	12	1751	c.1402G>A	c.(1402-1404)Gcc>Acc	p.A468T	ALDH1L1_ENST00000273450.3_Missense_Mutation_p.A478T|ALDH1L1_ENST00000472186.1_Missense_Mutation_p.A468T|ALDH1L1_ENST00000452905.2_Missense_Mutation_p.A367T|ALDH1L1_ENST00000393431.2_Missense_Mutation_p.A468T	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	468	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)	GCATCCTTGGCTGCGGCCACT	0.602																																					p.A478T		Atlas-SNP	.											.	ALDH1L1	138	.	0			c.G1432A						PASS	.						143	111	122					3																	125854448		2203	4300	6503	SO:0001583	missense	10840	exon12			CCTTGGCTGCGGC	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.1402G>A	chr3.hg19:g.125854448C>T	ENSP00000377083:p.Ala468Thr	26.0	0.0	.		38.0	12.0	.	NM_001270364	B4DG36|E9PBX3|Q68CS1	Missense_Mutation	SNP	ENST00000393434.2	hg19	CCDS3034.1	.	.	.	.	.	.	.	.	.	.	C	17.61	3.431432	0.62844	.	.	ENSG00000144908	ENST00000273450;ENST00000472186;ENST00000452905;ENST00000393434;ENST00000393431	D;D;D;D;D	0.90324	-2.65;-2.65;-2.65;-2.65;-2.65	4.16	4.16	0.48862	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.133532	0.47455	D	0.000221	D	0.96987	0.9016	H	0.97983	4.12	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.998	D;D;D	0.76575	0.969;0.988;0.955	D	0.98072	1.0399	10	0.87932	D	0	.	14.3504	0.66697	0.0:1.0:0.0:0.0	.	367;520;468	E9PBX3;Q59G10;O75891	.;.;AL1L1_HUMAN	T	478;468;367;468;468	ENSP00000273450:A478T;ENSP00000420293:A468T;ENSP00000395881:A367T;ENSP00000377083:A468T;ENSP00000377081:A468T	ENSP00000273450:A478T	A	-	1	0	ALDH1L1	127337138	1.000000	0.71417	0.054000	0.19295	0.003000	0.03518	6.729000	0.74775	2.331000	0.79229	0.460000	0.39030	GCC	.	.	.	none		0.602	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190		T	125854448	C	T	125854448	3	4	16	1	0	0	0	0	1	0	0	0	494	797	28	2	1354	2	ALDH1L1	3	125854448	Missense_Mutation	SNP	C	TCGA-2Z-A9JM-01A-12D-A42J-10	6631639	125854448	72167982	14	1137											
CCRL1	51554	hgsc.bcm.edu	37	chr3	132319326	132319326	+	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	atgactacagtcaatatgaaCtgatctgtatcaaagaagat	17	11	7	6	0	3	5	2	3	1	2	3	5	3	5	0	0	2	1	0	0	7	3			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr3:132319326C>T	ENST00000249887.2	+	2	181	c.85C>T	c.(85-87)Ctg>Ttg	p.L29L	ACAD11_ENST00000264990.6_Intron|ACAD11_ENST00000545291.1_Intron|ACAD11_ENST00000355458.3_Intron	NM_016557.2|NM_178445.2	NP_057641.1|NP_848540.1	Q9NPB9	ACKR4_HUMAN	atypical chemokine receptor 4	29					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|scavenger receptor activity (GO:0005044)	p.L29L(1)									TCAATATGAACTGATCTGTAT	0.378																																					p.L29L		Atlas-SNP	.											CCRL1,NS,carcinoma,0,2	CCRL1	30	.	1	Substitution - coding silent(1)	endometrium(1)	c.C85T						PASS	.						58	58	58					3																	132319326		2203	4300	6503	SO:0001819	synonymous_variant	51554	exon1			TATGAACTGATCT	AF110640	CCDS3075.1	3q22	2013-07-17	2013-07-16	2013-07-16	ENSG00000129048	ENSG00000129048		"GPCR / Class A : Chemokine receptors : Atypical"	1611	protein-coding gene	gene with protein product		606065	"chemokine (C-C motif) receptor-like 1"	CCRL1		10767544, 16148	Standard	NM_016557		Approved	CCR11, CCBP2, VSHK1, CCX-CKR, PPR1	uc003eow.3	Q9NPB9	OTTHUMG00000159768	ENST00000249887.2:c.85C>T	chr3.hg19:g.132319326C>T		240.0	1.0	.		231.0	11.0	.	NM_178445	B2R9U7	Silent	SNP	ENST00000249887.2	hg19	CCDS3075.1																																																																																			.	.	.	none		0.378	ACKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357238.2	NM_016557		T	132319326	C	T	132319326	2	4	16	1	0	0	0	0	0	0	0	1	2951	564	20	2		2	CCRL1	3	132319326	Silent	SNP	C	TCGA-2Z-A9JM-01A-12D-A42J-10	6464878	132319326	65703104	15	1138											
RASSF6	166824	hgsc.bcm.edu	37	chr4	74459297	74459297	+	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	gcattccttcaacaattagtTtgccatcttcagtctaagga	11	14	6	10	0	4	0	2	0	2	0	5	1	5	1	2	1	2	2	2	1	4	6			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr4:74459297T>A	ENST00000342081.3	-	4	384	c.254A>T	c.(253-255)aAa>aTa	p.K85I	RASSF6_ENST00000307439.5_Missense_Mutation_p.K53I|RASSF6_ENST00000335049.5_Missense_Mutation_p.K41I|RASSF6_ENST00000395777.2_Missense_Mutation_p.K53I	NM_201431.2	NP_958834.1	Q6ZTQ3	RASF6_HUMAN	Ras association (RalGDS/AF-6) domain family member 6	85					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)			AACAATTAGTTTGCCATCTTC	0.338																																					p.K85I		Atlas-SNP	.											.	RASSF6	68	.	0			c.A254T						PASS	.						102	103	103					4																	74459297		2203	4300	6503	SO:0001583	missense	166824	exon4			ATTAGTTTGCCAT	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.254A>T	chr4.hg19:g.74459297T>A	ENSP00000340578:p.Lys85Ile	57.0	0.0	.		83.0	26.0	.	NM_201431	Q68DT2|Q6PDA6|Q86WG9|Q86WH0	Missense_Mutation	SNP	ENST00000342081.3	hg19	CCDS3558.1	.	.	.	.	.	.	.	.	.	.	T	13.64	2.297478	0.40694	.	.	ENSG00000169435	ENST00000307439;ENST00000342081;ENST00000395777;ENST00000335049	T;T;T;T	0.54071	0.59;0.59;0.59;0.59	5.42	5.42	0.78866	.	0.814802	0.11816	N	0.526735	T	0.53738	0.1815	L	0.38175	1.15	0.09310	N	1	D;P;P	0.54397	0.966;0.797;0.943	P;B;B	0.50708	0.648;0.446;0.352	T	0.48647	-0.9017	10	0.62326	D	0.03	-0.7807	11.8484	0.52397	0.0:0.0:0.0:1.0	.	41;53;85	Q6ZTQ3-3;Q6ZTQ3-4;Q6ZTQ3	.;.;RASF6_HUMAN	I	53;85;53;41	ENSP00000303877:K53I;ENSP00000340578:K85I;ENSP00000379123:K53I;ENSP00000335582:K41I	ENSP00000303877:K53I	K	-	2	0	RASSF6	74678161	0.558000	0.26554	0.022000	0.16811	0.609000	0.37215	2.314000	0.43743	2.071000	0.62044	0.443000	0.29094	AAA	.	.	.	none		0.338	RASSF6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252279.1	NM_177532		A	74459297	T	A	74459297	3	1	16	1	0	0	0	0	1	0	0	0	13103	1841	64	5	887	5	RASSF6	4	74459297	Missense_Mutation	SNP	T	TCGA-2Z-A9JM-01A-12D-A42J-10		74459297	116694979	16	1139											
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5469021	5469021	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctctcaatcggtgattaatAaagcaatgcagttagttgcc	12	13	8	8	1	2	1	1	1	1	0	4	1	2	1	1	1	3	4	1	1	6	4			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr5:5469021A>G	ENST00000296564.7	+	15	6364	c.6142A>G	c.(6142-6144)Aaa>Gaa	p.K2048E		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		2048					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						GGTGATTAATAAAGCAATGCA	0.353																																					p.K2048E		Atlas-SNP	.											.	KIAA0947	301	.	0			c.A6142G						PASS	.						124	120	121					5																	5469021		1853	4090	5943	SO:0001583	missense	23379	exon15			ATTAATAAAGCAA																												ENST00000296564.7:c.6142A>G	chr5.hg19:g.5469021A>G	ENSP00000296564:p.Lys2048Glu	99.0	0.0	.		87.0	27.0	.	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	hg19	CCDS47187.1	.	.	.	.	.	.	.	.	.	.	A	13.20	2.165436	0.38217	.	.	ENSG00000164151	ENST00000296564	T	0.12039	2.72	5.86	3.45	0.39498	.	.	.	.	.	T	0.09949	0.0244	L	0.31926	0.97	0.21782	N	0.999541	B	0.25955	0.138	B	0.21151	0.033	T	0.32052	-0.9921	9	0.33940	T	0.23	3.9123	6.658	0.22998	0.7625:0.1549:0.0826:0.0	.	2048	Q9Y2F5	K0947_HUMAN	E	2048	ENSP00000296564:K2048E	ENSP00000296564:K2048E	K	+	1	0	KIAA0947	5522021	1.000000	0.71417	0.004000	0.12327	0.977000	0.68977	2.140000	0.42159	0.464000	0.27142	0.528000	0.53228	AAA	.	.	.	none		0.353	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			G	5469021	A	G	5469021	3	3	16	1	0	0	0	0	1	0	0	0	8209	363	13	3	6200	3	KIAA0947	5	5469021	Missense_Mutation	SNP	A	TCGA-2Z-A9JM-01A-12D-A42J-10		5469021	175446239	17	1140											
DNAH5	1767	hgsc.bcm.edu	37	chr5	13894791	13894791	+	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	aagtgttttctaaataagccTcaatattcagtgatgtccag	13	14	7	7	0	3	1	2	1	1	0	4	1	4	1	2	0	1	1	2	0	6	6			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr5:13894791T>A	ENST00000265104.4	-	16	2503	c.2399A>T	c.(2398-2400)gAg>gTg	p.E800V	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	800	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)					TAAATAAGCCTCAATATTCAG	0.413									Kartagener syndrome																												p.E800V		Atlas-SNP	.											.	DNAH5	868	.	0			c.A2399T						PASS	.						129	122	125					5																	13894791		2203	4300	6503	SO:0001583	missense	1767	exon16	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	TAAGCCTCAATAT	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.2399A>T	chr5.hg19:g.13894791T>A	ENSP00000265104:p.Glu800Val	103.0	0.0	.		66.0	16.0	.	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	hg19	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	T	10.26	1.301659	0.23736	.	.	ENSG00000039139	ENST00000265104	T	0.57752	0.38	5.23	4.07	0.47477	Dynein heavy chain, domain-1 (1);	0.151463	0.56097	D	0.000021	T	0.49881	0.1583	M	0.66939	2.045	0.36165	D	0.848377	B	0.14805	0.011	B	0.22386	0.039	T	0.53408	-0.8443	10	0.38643	T	0.18	.	10.1183	0.42605	0.0:0.0805:0.0:0.9194	.	800	Q8TE73	DYH5_HUMAN	V	800	ENSP00000265104:E800V	ENSP00000265104:E800V	E	-	2	0	DNAH5	13947791	0.998000	0.40836	0.685000	0.30070	0.043000	0.13939	2.905000	0.48727	0.843000	0.35070	0.402000	0.26972	GAG	.	.	.	none		0.413	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13894791	T	A	13894791	3	1	16	1	0	0	0	0	1	0	0	0	4606	1551	54	5	11731	5	DNAH5	5	13894791	Missense_Mutation	SNP	T	TCGA-2Z-A9JM-01A-12D-A42J-10	8425770	13894791	167020469	18	1141											
SPATS1	221409	hgsc.bcm.edu	37	chr6	44320474	44320474	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgttacaggtgctaattgcAgtgattttctggaatctaag	10	15	11	5	0	2	1	0	1	2	0	2	2	2	2	0	2	3	3	0	2	4	6			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr6:44320474A>G	ENST00000288390.2	+	2	498	c.151A>G	c.(151-153)Agt>Ggt	p.S51G	RP11-444E17.6_ENST00000505802.1_3'UTR|SPATS1_ENST00000323108.8_Missense_Mutation_p.S51G			Q496A3	SPAS1_HUMAN	spermatogenesis associated, serine-rich 1	51										NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(2)|lung(5)|skin(1)|urinary_tract(1)	14	all_lung(25;0.00469)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TGCTAATTGCAGTGATTTTCT	0.358																																					p.S51G		Atlas-SNP	.											.	SPATS1	61	.	0			c.A151G						PASS	.						116	108	111					6																	44320474		2203	4300	6503	SO:0001583	missense	221409	exon3			AATTGCAGTGATT	AK058171	CCDS4911.1	6p21.1	2003-08-08			ENSG00000249481	ENSG00000249481			22957	protein-coding gene	gene with protein product							Standard	NM_145026		Approved	SPATA8, FLJ25442, SRSP1	uc021yzz.1	Q496A3	OTTHUMG00000014764	ENST00000288390.2:c.151A>G	chr6.hg19:g.44320474A>G	ENSP00000424400:p.Ser51Gly	46.0	0.0	.		99.0	32.0	.	NM_145026	Q496A2|Q496A5|Q96LJ0	Missense_Mutation	SNP	ENST00000288390.2	hg19	CCDS4911.1	.	.	.	.	.	.	.	.	.	.	A	6.330	0.428946	0.11987	.	.	ENSG00000249481	ENST00000323108;ENST00000288390	T;T	0.48836	0.8;0.8	3.92	-0.0235	0.13943	.	1.491510	0.04356	N	0.356554	T	0.12305	0.0299	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.11842	-1.0571	10	0.12430	T	0.62	.	6.2149	0.20649	0.628:0.0:0.372:0.0	.	51	Q496A3	SPAS1_HUMAN	G	51	ENSP00000437552:S51G;ENSP00000424400:S51G	ENSP00000424400:S51G	S	+	1	0	SPATS1	44428452	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.147000	0.16202	0.003000	0.14656	-0.290000	0.09829	AGT	.	.	.	none		0.358	SPATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040738.2	NM_145026		G	44320474	A	G	44320474	3	3	16	1	0	0	0	0	1	0	0	0	15030	188	7	3	157	3	SPATS1	6	44320474	Missense_Mutation	SNP	A	TCGA-2Z-A9JM-01A-12D-A42J-10		44320474	126794593	19	1142											
CD109	135228	hgsc.bcm.edu	37	chr6	74502420	74502421	+	Frame_Shift_Ins	INS	-	-	AC																															ttatggctgtggtgaacagaINSacatgataaattttgctcca																										TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr6:74502420_74502421insAC	ENST00000287097.5	+	23	2885_2886	c.2773_2774insAC	c.(2773-2775)aacfs	p.N925fs	CD109_ENST00000474094.1_3'UTR|CD109_ENST00000422508.2_Frame_Shift_Ins_p.N848fs|CD109_ENST00000437994.2_Frame_Shift_Ins_p.N925fs			Q6YHK3	CD109_HUMAN	CD109 molecule	925					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						TGGTGAACAGAACATGATAAAT	0.366																																					p.N925fs		Atlas-Indel,Pindel	.											.	CD109	170	.	0			c.2773_2774insAC						PASS	.																																			SO:0001589	frameshift_variant	135228	exon23			.	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.2774_2775dupAC	chr6.hg19:g.74502421_74502422dupAC	ENSP00000287097:p.Asn925fs	70.0	0.0	0		40.0	14.0	0.35	NM_001159587	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Frame_Shift_Ins	INS	ENST00000287097.5	hg19	CCDS4982.1																																																																																			.	.	.	none		0.366	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493		AC	74502421	-	AC	74502420	7	5	16	1	0	1	1	0	0	0	0	0	2965	246	9	0	2863	0	CD109	6	74502420	Frame_Shift_Ins	INS	-	TCGA-2Z-A9JM-01A-12D-A42J-10	30181946	74502420	96612647	20	1143											
SLC35A1	10559	hgsc.bcm.edu	37	chr6	88187175	88187175	+	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	taagatacacaaggacatcaGacaaagaactctacttttca	18	9	5	9	0	3	3	2	0	1	3	3	4	3	4	0	1	3	0	0	1	6	5			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr6:88187175G>T	ENST00000369552.4	+	2	139	c.112G>T	c.(112-114)Gac>Tac	p.D38Y	SLC35A1_ENST00000464978.1_3'UTR|C6orf165_ENST00000507897.1_3'UTR|C6orf165_ENST00000506888.1_3'UTR|SLC35A1_ENST00000369557.5_Missense_Mutation_p.D38Y|SLC35A1_ENST00000544441.1_5'UTR|SLC35A1_ENST00000369556.3_Missense_Mutation_p.D38Y	NM_006416.4	NP_006407.1	P78382	S35A1_HUMAN	solute carrier family 35 (CMP-sialic acid transporter), member A1	38					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)		AAGGACATCAGACAAAGAACT	0.368																																					p.D38Y	NSCLC(183;214 2117 17033 22638 44782)|Ovarian(87;1008 1343 9644 42916 50932)	Atlas-SNP	.											.	SLC35A1	29	.	0			c.G112T						PASS	.						109	103	105					6																	88187175		2203	4300	6503	SO:0001583	missense	10559	exon2			ACATCAGACAAAG	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.112G>T	chr6.hg19:g.88187175G>T	ENSP00000358565:p.Asp38Tyr	79.0	0.0	.		88.0	41.0	.	NM_006416	Q5W1L8	Missense_Mutation	SNP	ENST00000369552.4	hg19	CCDS5010.1	.	.	.	.	.	.	.	.	.	.	G	13.60	2.284666	0.40394	.	.	ENSG00000164414	ENST00000369556;ENST00000369552;ENST00000429605;ENST00000369557;ENST00000369544	T	0.47869	0.83	5.62	3.78	0.43462	.	0.437967	0.23010	U	0.052966	T	0.17280	0.0415	L	0.43923	1.385	0.18873	N	0.999986	P;P	0.39157	0.533;0.662	B;B	0.29942	0.109;0.109	T	0.04153	-1.0973	10	0.72032	D	0.01	-14.2719	8.7393	0.34547	0.2397:0.0:0.7603:0.0	.	38;38	P78382;Q5W1L8	S35A1_HUMAN;.	Y	38;38;38;38;19	ENSP00000358565:D38Y	ENSP00000358557:D19Y	D	+	1	0	SLC35A1	88243894	1.000000	0.71417	0.969000	0.41365	0.996000	0.88848	2.735000	0.47377	0.666000	0.31087	0.655000	0.94253	GAC	.	.	.	none		0.368	SLC35A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041446.1			T	88187175	G	T	88187175	3	4	16	1	0	0	0	0	1	0	0	0	14583	942	33	4	118	4	SLC35A1	6	88187175	Missense_Mutation	SNP	G	TCGA-2Z-A9JM-01A-12D-A42J-10	13684755	88187175	82927892	21	1144											
NRCAM	4897	hgsc.bcm.edu	37	chr7	107823350	107823350	+	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	aggcctggcccattagattcGaaaccattcaagggctacaa	13	8	9	11	1	1	1	1	0	0	1	2	2	1	1	3	3	2	1	3	3	5	4			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr7:107823350G>A	ENST00000425651.2	-	20	2318	c.2319C>T	c.(2317-2319)ttC>ttT	p.F773F	NRCAM_ENST00000413765.2_Silent_p.F754F|NRCAM_ENST00000379022.4_Silent_p.F773F|NRCAM_ENST00000379028.3_Silent_p.F773F|NRCAM_ENST00000379024.4_Silent_p.F754F|NRCAM_ENST00000351718.4_Silent_p.F757F	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	773	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						CATTAGATTCGAAACCATTCA	0.418																																					p.F773F		Atlas-SNP	.											.	NRCAM	267	.	0			c.C2319T						PASS	.						60	57	58					7																	107823350		2203	4300	6503	SO:0001819	synonymous_variant	4897	exon20			AGATTCGAAACCA		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.2319C>T	chr7.hg19:g.107823350G>A		94.0	0.0	.		120.0	31.0	.	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Silent	SNP	ENST00000425651.2	hg19	CCDS47686.1																																																																																			.	.	.	none		0.418	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		A	107823350	G	A	107823350	2	1	16	1	0	0	0	0	0	0	0	1	10651	1049	37	1		1	NRCAM	7	107823350	Silent	SNP	G	TCGA-2Z-A9JM-01A-12D-A42J-10		107823350	51315313	22	1145											
FBXO16	157574	hgsc.bcm.edu	37	chr8	28331306	28331306	+	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	tacccatttgccaagcagggCtcttctttcttcaaatacct	9	14	5	13	0	4	0	1	0	3	0	4	0	4	0	3	1	4	2	3	1	4	6			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr8:28331306C>T	ENST00000380254.2	-	3	266	c.118G>A	c.(118-120)Gcc>Acc	p.A40T	FBXO16_ENST00000519471.2_Missense_Mutation_p.A40T|FBXO16_ENST00000517436.1_5'UTR|FBXO16_ENST00000346498.2_Intron|FBXO16_ENST00000518734.1_Intron	NM_001258211.1|NM_172366.3	NP_001245140.1|NP_758954.1	Q8IX29	FBX16_HUMAN	F-box protein 16	40										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)		CCAAGCAGGGCTCTTCTTTCT	0.303																																					p.A40T		Atlas-SNP	.											.	FBXO16	29	.	0			c.G118A						PASS	.						57	63	61					8																	28331306		2202	4297	6499	SO:0001583	missense	157574	exon3			GCAGGGCTCTTCT	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.118G>A	chr8.hg19:g.28331306C>T	ENSP00000369604:p.Ala40Thr	206.0	0.0	.		257.0	80.0	.	NM_172366	Q3T1B2|Q3T1B3|Q3T1B4	Missense_Mutation	SNP	ENST00000380254.2	hg19	CCDS6068.1	.	.	.	.	.	.	.	.	.	.	C	18.36	3.608040	0.66558	.	.	ENSG00000214050	ENST00000380254;ENST00000517673;ENST00000519471	T;T	0.43688	2.43;0.94	5.86	4.81	0.61882	.	0.593369	0.15469	U	0.260724	T	0.29093	0.0723	N	0.19112	0.55	0.26393	N	0.976548	B	0.23316	0.083	B	0.21360	0.034	T	0.06481	-1.0824	10	0.19590	T	0.45	-36.1552	14.9653	0.71188	0.0:0.9203:0.0:0.0797	.	40	Q8IX29	FBX16_HUMAN	T	40	ENSP00000369604:A40T;ENSP00000429390:A40T	ENSP00000369604:A40T	A	-	1	0	FBXO16	28387225	0.995000	0.38212	1.000000	0.80357	0.998000	0.95712	2.002000	0.40835	2.771000	0.95319	0.563000	0.77884	GCC	.	.	.	none		0.303	FBXO16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219988.2	NM_172366		T	28331306	C	T	28331306	3	4	16	1	0	0	0	0	1	0	0	0	5736	797	28	2	788	2	FBXO16	8	28331306	Missense_Mutation	SNP	C	TCGA-2Z-A9JM-01A-12D-A42J-10		28331306	118032716	23	1146											
CCL27	10850	hgsc.bcm.edu	37	chr9	34662362	34662362	+	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	tcagtagcttgtctgagagtGgctttcggtagagctgagta	8	13	14	6	1	2	3	1	2	1	2	3	4	2	3	0	2	2	6	0	2	3	5			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr9:34662362G>A	ENST00000259631.4	-	2	180	c.122C>T	c.(121-123)cCa>cTa	p.P41L	CCL27_ENST00000557161.1_5'UTR|RP11-195F19.30_ENST00000564224.1_RNA	NM_006664.2	NP_006655.1	Q9Y4X3	CCL27_HUMAN	chemokine (C-C motif) ligand 27	41					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)		GTCTGAGAGTGGCTTTCGGTA	0.577																																					p.P41L		Atlas-SNP	.											.	CCL27	6	.	0			c.C122T						PASS	.						75	64	68					9																	34662362		2203	4300	6503	SO:0001583	missense	10850	exon2			GAGAGTGGCTTTC	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.122C>T	chr9.hg19:g.34662362G>A	ENSP00000259631:p.Pro41Leu	60.0	0.0	.		62.0	20.0	.	NM_006664		Missense_Mutation	SNP	ENST00000259631.4	hg19	CCDS6569.1	.	.	.	.	.	.	.	.	.	.	G	13.70	2.314771	0.40996	.	.	ENSG00000213927	ENST00000259631	T	0.05139	3.49	5.37	3.42	0.39159	Chemokine interleukin-8-like domain (2);	0.241243	0.29676	N	0.011493	T	0.05273	0.0140	L	0.33485	1.01	0.40928	D	0.984365	P	0.37708	0.606	B	0.38985	0.287	T	0.29397	-1.0013	10	0.40728	T	0.16	-8.2034	5.6242	0.17473	0.0979:0.0:0.7064:0.1957	.	41	Q9Y4X3	CCL27_HUMAN	L	41	ENSP00000259631:P41L	ENSP00000259631:P41L	P	-	2	0	CCL27	34652362	0.989000	0.36119	1.000000	0.80357	0.842000	0.47809	1.349000	0.33998	2.673000	0.90976	0.557000	0.71058	CCA	.	.	.	none		0.577	CCL27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052228.1	NM_006664		A	34662362	G	A	34662362	3	1	16	1	0	0	0	0	1	0	0	0	2901	1348	47	2	224	2	CCL27	9	34662362	Missense_Mutation	SNP	G	TCGA-2Z-A9JM-01A-12D-A42J-10		34662362	106551069	24	1147											
ASAH2	56624	hgsc.bcm.edu	37	chr10	52003053	52003053	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttctgccatgatgaaggcaCgactgtatagcctggtgagg	9	10	14	8	1	1	3	0	3	1	0	1	4	1	3	2	3	2	3	2	3	3	3			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr10:52003053C>T	ENST00000395526.4	-	3	418	c.419G>A	c.(418-420)cGt>cAt	p.R140H	ASAH2_ENST00000443575.1_5'Flank|ASAH2_ENST00000329428.6_Missense_Mutation_p.R121H|ASAH2_ENST00000447815.1_Missense_Mutation_p.R140H	NM_019893.2	NP_063946.2	Q9NR71	ASAH2_HUMAN	N-acylsphingosine amidohydrolase (non-lysosomal ceramidase) 2	140					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						GATGAAGGCACGACTGTATAG	0.507																																					p.R140H		Atlas-SNP	.											.	ASAH2	69	.	0			c.G419A						PASS	.						222	184	197					10																	52003053		2203	4300	6503	SO:0001583	missense	56624	exon3			AAGGCACGACTGT	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.419G>A	chr10.hg19:g.52003053C>T	ENSP00000378897:p.Arg140His	94.0	0.0	.		62.0	22.0	.	NM_019893	Q3KNU1|Q5SNT7|Q5SZP6|Q5SZP7|Q5T1D5|Q71ME6	Missense_Mutation	SNP	ENST00000395526.4	hg19	CCDS7239.2	.	.	.	.	.	.	.	.	.	.	C	26.2	4.717778	0.89205	.	.	ENSG00000188611	ENST00000395526;ENST00000447815;ENST00000329428	T;T;T	0.59906	0.23;0.23;0.23	5.82	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.81484	0.4832	M	0.93720	3.45	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.86317	0.1690	10	0.87932	D	0	.	13.911	0.63866	0.1533:0.8467:0.0:0.0	.	140;140	Q9NR71-2;Q9NR71	.;ASAH2_HUMAN	H	140;140;121	ENSP00000378897:R140H;ENSP00000388206:R140H;ENSP00000329886:R121H	ENSP00000329886:R121H	R	-	2	0	ASAH2	51673059	1.000000	0.71417	0.985000	0.45067	0.785000	0.44390	7.167000	0.77562	1.413000	0.46997	0.557000	0.71058	CGT	.	.	.	none		0.507	ASAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048061.3	NM_019893		T	52003053	C	T	52003053	3	4	16	1	0	0	0	0	1	0	0	0	1007	536	19	1	1995	1	ASAH2	10	52003053	Missense_Mutation	SNP	C	TCGA-2Z-A9JM-01A-12D-A42J-10		52003053	83531694	25	1148											
PPRC1	23082	hgsc.bcm.edu	37	chr10	103900243	103900243	+	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	tgccaccagttgatgctgtcCcgtctggcccagcaccagtt	6	10	10	15	1	1	1	0	1	1	0	2	1	2	1	5	1	3	4	5	1	0	2			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr10:103900243C>T	ENST00000278070.2	+	5	2017	c.1978C>T	c.(1978-1980)Ccg>Tcg	p.P660S	PPRC1_ENST00000413464.2_Missense_Mutation_p.P660S|PPRC1_ENST00000370012.1_5'Flank	NM_015062.3	NP_055877.3	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator-related 1	660					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(10)|lung(19)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		TGATGCTGTCCCGTCTGGCCC	0.547																																					p.P660S		Atlas-SNP	.											.	PPRC1	151	.	0			c.C1978T						PASS	.						96	81	86					10																	103900243		2203	4300	6503	SO:0001583	missense	23082	exon5			GCTGTCCCGTCTG	AF325193	CCDS7529.1, CCDS73186.1	10q24.32	2013-02-12	2006-10-17		ENSG00000148840	ENSG00000148840		"RNA binding motif (RRM) containing"	30025	protein-coding gene	gene with protein product			"peroxisome proliferative activated receptor, gamma, coactivator-related 1"			9628581, 11340167	Standard	XM_005269656		Approved	PRC, KIAA0595, MGC74642	uc001kum.3	Q5VV67	OTTHUMG00000018948	ENST00000278070.2:c.1978C>T	chr10.hg19:g.103900243C>T	ENSP00000278070:p.Pro660Ser	47.0	0.0	.		64.0	27.0	.	NM_015062	Q5VV66|Q6P3U5|Q6P3W1|Q76N31|Q9BUJ3|Q9BZE5|Q9Y4E0	Missense_Mutation	SNP	ENST00000278070.2	hg19	CCDS7529.1	.	.	.	.	.	.	.	.	.	.	C	10.93	1.489648	0.26686	.	.	ENSG00000148840	ENST00000278070;ENST00000413464	T;T	0.20598	2.07;2.06	4.59	1.4	0.22301	.	1.584220	0.03763	N	0.258417	T	0.14570	0.0352	N	0.19112	0.55	0.09310	N	1	B;B;B	0.13594	0.008;0.005;0.008	B;B;B	0.10450	0.003;0.005;0.003	T	0.26677	-1.0096	10	0.44086	T	0.13	.	4.7029	0.12835	0.0:0.5724:0.1946:0.233	.	660;540;660	E7EVG6;Q5VV67-2;Q5VV67	.;.;PPRC1_HUMAN	S	660	ENSP00000278070:P660S;ENSP00000399743:P660S	ENSP00000278070:P660S	P	+	1	0	PPRC1	103890233	0.024000	0.19004	0.001000	0.08648	0.096000	0.18686	0.673000	0.25203	0.161000	0.19458	-0.291000	0.09656	CCG	.	.	.	none		0.547	PPRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050021.1	NM_015062		T	103900243	C	T	103900243	3	4	16	1	0	0	0	0	1	0	0	0	12420	623	22	2	1996	2	PPRC1	10	103900243	Missense_Mutation	SNP	C	TCGA-2Z-A9JM-01A-12D-A42J-10	51897190	103900243	31634504	26	1149											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1272661	1272678	+	In_Frame_Del	DEL	CCGAGCACTATAGCCACC	CCGAGCACTATAGCCACC	-																															ccacctggatcctcacagagCcgagcactatagccaccgtg																								rs201730803|rs377533930|rs372504985|rs573266996|rs201218727|rs200249076		TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	CCGAGCACTATAGCCACC	CCGAGCACTATAGCCACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr11:1272661_1272678delCCGAGCACTATAGCCACC	ENST00000529681.1	+	31	14609_14626	c.14551_14568delCCGAGCACTATAGCCACC	c.(14551-14568)ccgagcactatagccaccdel	p.PSTIAT4851del	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_In_Frame_Del_p.PSTIAT4854del	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4851	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)		CCTCACAGAGCCGAGCACTATAGCCACCGTGATGGTGC	0.624																																					p.4850_4856del		Pindel	.											.	MUC5B	473	.	0			c.14550_14567del						PASS	.																																			SO:0001651	inframe_deletion	727897	exon31			.	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.14551_14568delCCGAGCACTATAGCCACC	chr11.hg19:g.1272661_1272678delCCGAGCACTATAGCCACC	ENSP00000436812:p.Pro4851_Thr4856del	136.0	0.0	.		96.0	15.0	0.156	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	In_Frame_Del	DEL	ENST00000529681.1	hg19	CCDS44515.2																																																																																			.	.	.	none		0.624	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		-	1272678	CCGAGCACTATAGCCACC	-	1272661	7	5	16	1	0	1	0	1	0	0	0	0	9986	739	26	0	14682	0	MUC5B	11	1272661	In_Frame_Del	DEL	CCGAGCACTATAGCCACC	TCGA-2Z-A9JM-01A-12D-A42J-10		1272661	133733855	27	1150	10	3									
MUC5B	727897	hgsc.bcm.edu	37	chr11	1272664	1272668	+	Frame_Shift_Del	DEL	AGCAC	AGCAC	-																															cctggatcctcacagagccgAgcactatagccaccgtgatg																								rs573266996		TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	AGCAC	AGCAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr11:1272664_1272668delAGCAC	ENST00000529681.1	+	31	14612_14616	c.14554_14558delAGCAC	c.(14554-14559)agcactfs	p.ST4852fs	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Frame_Shift_Del_p.ST4855fs	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4852	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)		CACAGAGCCGAGCACTATAGCCACC	0.624																																					p.4851_4853del		Atlas-INDEL	.											.	MUC5B	473	.	0			c.14553_14557del						PASS	.																																			SO:0001589	frameshift_variant	727897	exon31			.	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.14554_14558delAGCAC	chr11.hg19:g.1272664_1272668delAGCAC	ENSP00000436812:p.Ser4852fs	129.0	0.0	0		93.0	14.0	0.150538	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Frame_Shift_Del	DEL	ENST00000529681.1	hg19	CCDS44515.2																																																																																			.	.	.	none		0.624	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		-	1272668	AGCAC	-	1272664	7	5	16	1	0	1	0	1	0	0	0	0	9986	304	11	0	14685	0	MUC5B	11	1272664	Frame_Shift_Del	DEL	AGCAC	TCGA-2Z-A9JM-01A-12D-A42J-10	3	1272664	133733852	28	1151	10	3									
MUC5B	727897	hgsc.bcm.edu	37	chr11	1272670	1272678	+	In_Frame_Del	DEL	ATAGCCACC	ATAGCCACC	-																															tcctcacagagccgagcactAtagccaccgtgatggtgccc																								rs200249076|rs377533930|rs372504985		TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	ATAGCCACC	ATAGCCACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr11:1272670_1272678delATAGCCACC	ENST00000529681.1	+	31	14618_14626	c.14560_14568delATAGCCACC	c.(14560-14568)atagccaccdel	p.IAT4854del	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_In_Frame_Del_p.IAT4857del	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4854	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)		GCCGAGCACTATAGCCACCGTGATGGTGC	0.627																																					p.4853_4856del		Atlas-INDEL	.											.	MUC5B	473	.	0			c.14559_14567del						PASS	.																																			SO:0001651	inframe_deletion	727897	exon31			.	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"Mucins"	7516	protein-coding gene	gene with protein product		600770	"mucin 5, subtype B, tracheobronchial"	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.14560_14568delATAGCCACC	chr11.hg19:g.1272670_1272678delATAGCCACC	ENSP00000436812:p.Ile4854_Thr4856del	130.0	0.0	0		96.0	14.0	0.145833	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	In_Frame_Del	DEL	ENST00000529681.1	hg19	CCDS44515.2																																																																																			.	.	.	none		0.627	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		-	1272678	ATAGCCACC	-	1272670	7	5	16	1	0	1	0	1	0	0	0	0	9986	449	16	0	14691	0	MUC5B	11	1272670	In_Frame_Del	DEL	ATAGCCACC	TCGA-2Z-A9JM-01A-12D-A42J-10	6	1272670	133733846	29	1152	10	3									
OR51B5	282763	hgsc.bcm.edu	37	chr11	5364556	5364556	+	Missense_Mutation	SNP	T	T	G																															cagggccagccccaggtctgTggcagccagcatggccagaa																								rs372207902|rs147062602	byFrequency	TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr11:5364556T>G	ENST00000300773.2	-	1	253	c.199A>C	c.(199-201)Aca>Cca	p.T67P	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	67					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A66fs*48(1)		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)		CCCAGGTCTGTGGCAGCCAGC	0.542																																					p.T67P		Atlas-SNP	.											.	OR51B5	60	.	1	Deletion - Frameshift(1)	upper_aerodigestive_tract(1)	c.A199C						PASS	.						44	50	48					11																	5364556		2191	4293	6484	SO:0001583	missense	282763	exon5			GGTCTGTGGCAGC	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.199A>C	chr11.hg19:g.5364556T>G	ENSP00000300773:p.Thr67Pro	41.0	0.0	.		54.0	7.0	.	NM_001005567	B2RN59	Missense_Mutation	SNP	ENST00000300773.2	hg19	CCDS31378.1	.	.	.	.	.	.	.	.	.	.	T	15.67	2.901629	0.52227	.	.	ENSG00000242180	ENST00000300773	T	0.03004	4.08	4.76	4.76	0.60689	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42420	D	0.000714	T	0.17874	0.0429	M	0.89414	3.03	0.19300	N	0.999978	D	0.67145	0.996	D	0.65874	0.939	T	0.09037	-1.0693	10	0.87932	D	0	.	8.6339	0.33936	0.0:0.0903:0.0:0.9097	.	67	Q9H339	O51B5_HUMAN	P	67	ENSP00000300773:T67P	ENSP00000300773:T67P	T	-	1	0	OR51B5	5321132	0.000000	0.05858	0.612000	0.29024	0.641000	0.38312	0.241000	0.18065	2.017000	0.59298	0.529000	0.55759	ACA	.	.	.	none		0.542	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567		G	5364556	T	G	5364556	3	3	16	1	0	0	0	0	1	0	0	0	11098	1696	59	5	743	5	OR51B5	11	5364556	Missense_Mutation	SNP	T	TCGA-2Z-A9JM-01A-12D-A42J-10	4091886	5364556	129641960	30	1153	11	2									
OR51B5	282763	hgsc.bcm.edu	37	chr11	5364558	5364558	+	Missense_Mutation	SNP	G	G	C																															gggccagccccaggtctgtgGcagccagcatggccagaaag																								rs372207902|rs147062602	byFrequency	TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr11:5364558G>C	ENST00000300773.2	-	1	251	c.197C>G	c.(196-198)gCc>gGc	p.A66G	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	66					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A66fs*48(1)		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)		CAGGTCTGTGGCAGCCAGCAT	0.542																																					p.A66G		Atlas-SNP	.											.	OR51B5	60	.	1	Deletion - Frameshift(1)	upper_aerodigestive_tract(1)	c.C197G						PASS	.						45	51	49					11																	5364558		2191	4293	6484	SO:0001583	missense	282763	exon5			TCTGTGGCAGCCA	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.197C>G	chr11.hg19:g.5364558G>C	ENSP00000300773:p.Ala66Gly	41.0	0.0	.		57.0	8.0	.	NM_001005567	B2RN59	Missense_Mutation	SNP	ENST00000300773.2	hg19	CCDS31378.1	.	.	.	.	.	.	.	.	.	.	G	6.859	0.527720	0.13127	.	.	ENSG00000242180	ENST00000300773	T	0.00551	6.65	4.76	-1.03	0.10102	GPCR, rhodopsin-like superfamily (1);	0.790635	0.10593	N	0.656558	T	0.00440	0.0014	L	0.27975	0.815	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.37361	-0.9709	10	0.45353	T	0.12	.	7.7471	0.28875	0.2155:0.4492:0.3354:0.0	.	66	Q9H339	O51B5_HUMAN	G	66	ENSP00000300773:A66G	ENSP00000300773:A66G	A	-	2	0	OR51B5	5321134	0.000000	0.05858	0.203000	0.23512	0.619000	0.37552	-0.266000	0.08631	-0.037000	0.13646	-0.171000	0.13296	GCC	.	.	.	none		0.542	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567		C	5364558	G	C	5364558	3	2	16	1	0	0	0	0	1	0	0	0	11098	1203	42	4	745	4	OR51B5	11	5364558	Missense_Mutation	SNP	G	TCGA-2Z-A9JM-01A-12D-A42J-10	2	5364558	129641958	31	1154	11	2									
BEST1	7439	hgsc.bcm.edu	37	chr11	61724395	61724396	+	Frame_Shift_Ins	INS	-	-	T																															tctgggtgccctgggtgtggINStttgccaacctgtcaatgaa																										TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr11:61724395_61724396insT	ENST00000378043.4	+	5	1204_1205	c.561_562insT	c.(562-564)tttfs	p.F188fs	BEST1_ENST00000526988.1_Frame_Shift_Ins_p.F82fs|BEST1_ENST00000534553.1_Intron|BEST1_ENST00000435278.2_Frame_Shift_Ins_p.F188fs|BEST1_ENST00000301774.9_Intron|BEST1_ENST00000449131.2_Frame_Shift_Ins_p.F128fs|BEST1_ENST00000378042.3_Frame_Shift_Ins_p.F128fs	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1	188					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						CCTGGGTGTGGTTTGCCAACCT	0.559																																					p.W187fs		Atlas-Indel,Pindel	.											.	BEST1	85	.	0			c.561_562insT						PASS	.																																			SO:0001589	frameshift_variant	7439	exon5			.	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.564dupT	chr11.hg19:g.61724398_61724398dupT	ENSP00000367282:p.Phe188fs	61.0	0.0	0		69.0	19.0	0.275362	NM_004183	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Frame_Shift_Ins	INS	ENST00000378043.4	hg19	CCDS31580.1																																																																																			.	.	.	none		0.559	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1	NM_004183		T	61724396	-	T	61724395	7	5	16	1	0	1	1	0	0	0	0	0	1404	1270	44	0	575	0	BEST1	11	61724395	Frame_Shift_Ins	INS	-	TCGA-2Z-A9JM-01A-12D-A42J-10	56359837	61724395	73282121	32	1155											
SPDYC	387778	hgsc.bcm.edu	37	chr11	64940189	64940189	+	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	gccattccactgggcttggaCtcgggaccggcgcccccacc	5	6	12	18	3	0	0	0	0	0	0	2	2	1	2	6	4	0	1	6	4	0	2			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr11:64940189C>A	ENST00000377185.2	+	6	633	c.551C>A	c.(550-552)aCt>aAt	p.T184N	AP003068.18_ENST00000534819.1_RNA	NM_001008778.1	NP_001008778.1			speedy/RINGO cell cycle regulator family member C											breast(1)|endometrium(3)|large_intestine(2)|lung(9)|prostate(1)	16						TGGGCTTGGACTCGGGACCGG	0.667																																					p.T184N		Atlas-SNP	.											.	SPDYC	31	.	0			c.C551A						PASS	.						43	45	44					11																	64940189		2201	4297	6498	SO:0001583	missense	387778	exon6			CTTGGACTCGGGA	AY820305	CCDS31606.1	11q13.1	2013-05-08	2013-05-08		ENSG00000204710	ENSG00000204710		"Speedy homologs"	32681	protein-coding gene	gene with protein product		614030	"speedy homolog C (Xenopus laevis)"			15611625	Standard	NM_001008778		Approved	Ringo2	uc010rnz.2	Q5MJ68	OTTHUMG00000165611	ENST00000377185.2:c.551C>A	chr11.hg19:g.64940189C>A	ENSP00000366390:p.Thr184Asn	18.0	0.0	.		41.0	13.0	.	NM_001008778		Missense_Mutation	SNP	ENST00000377185.2	hg19	CCDS31606.1	.	.	.	.	.	.	.	.	.	.	C	15.55	2.865824	0.51588	.	.	ENSG00000204710	ENST00000377185	.	.	.	5.09	2.0	0.26442	.	0.251706	0.27289	N	0.020044	T	0.37237	0.0996	L	0.59436	1.845	0.09310	N	0.999995	P	0.48998	0.918	P	0.52386	0.697	T	0.17471	-1.0368	9	0.19590	T	0.45	.	4.07	0.09877	0.3344:0.4858:0.0:0.1798	.	184	Q5MJ68	SPDYC_HUMAN	N	184	.	ENSP00000366390:T184N	T	+	2	0	SPDYC	64696765	0.258000	0.24033	0.044000	0.18714	0.973000	0.67179	0.896000	0.28377	0.122000	0.18314	0.655000	0.94253	ACT	.	.	.	none		0.667	SPDYC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385299.1	NM_001008778		A	64940189	C	A	64940189	3	1	16	1	0	0	0	0	1	0	0	0	15040	565	20	4	573	4	SPDYC	11	64940189	Missense_Mutation	SNP	C	TCGA-2Z-A9JM-01A-12D-A42J-10	3215794	64940189	70066327	33	1156											
SPTBN2	6712	hgsc.bcm.edu	37	chr11	66472844	66472844	+	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	ccgtgattcctccagccgggCccgccgcgccgctgccaact	4	6	11	20	6	0	1	0	1	0	0	2	1	2	1	8	1	3	1	8	1	1	1			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr11:66472844C>T	ENST00000533211.1	-	15	2234	c.1903G>A	c.(1903-1905)Gcc>Acc	p.A635T	SPTBN2_ENST00000309996.2_Missense_Mutation_p.A635T|SPTBN2_ENST00000529997.1_Missense_Mutation_p.A635T			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	635					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)	p.A635S(1)		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						TCCAGCCGGGCCCGCCGCGCC	0.672																																					p.A635T		Atlas-SNP	.											SPTBN2,NS,carcinoma,0,1	SPTBN2	188	.	1	Substitution - Missense(1)	lung(1)	c.G1903A						PASS	.						21	25	24					11																	66472844		2174	4255	6429	SO:0001583	missense	6712	exon14			GCCGGGCCCGCCG	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.1903G>A	chr11.hg19:g.66472844C>T	ENSP00000432568:p.Ala635Thr	92.0	0.0	.		84.0	31.0	.	NM_006946	O14872|O14873	Missense_Mutation	SNP	ENST00000533211.1	hg19	CCDS8150.1	.	.	.	.	.	.	.	.	.	.	C	14.59	2.579927	0.46006	.	.	ENSG00000173898	ENST00000533211;ENST00000309996;ENST00000529997	T;T;T	0.52057	0.68;0.68;0.68	4.45	4.45	0.53987	.	0.395296	0.25277	N	0.031832	T	0.47801	0.1465	M	0.63843	1.955	0.31886	N	0.617861	P	0.47910	0.902	P	0.46208	0.507	T	0.54970	-0.8213	10	0.22706	T	0.39	.	11.2662	0.49112	0.1831:0.8169:0.0:0.0	.	635	O15020	SPTN2_HUMAN	T	635	ENSP00000432568:A635T;ENSP00000311489:A635T;ENSP00000433593:A635T	ENSP00000311489:A635T	A	-	1	0	SPTBN2	66229420	0.350000	0.24878	0.983000	0.44433	0.720000	0.41350	2.898000	0.48672	2.294000	0.77228	0.491000	0.48974	GCC	.	.	.	none		0.672	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946		T	66472844	C	T	66472844	3	4	16	1	0	0	0	0	1	0	0	0	15132	739	26	2	5365	2	SPTBN2	11	66472844	Missense_Mutation	SNP	C	TCGA-2Z-A9JM-01A-12D-A42J-10	1532655	66472844	68533672	34	1157											
FKBP4	2288	hgsc.bcm.edu	37	chr12	2907930	2907930	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaggaagatggcggaatcaTtcgcagaatacagactcgcg	14	6	13	8	4	1	4	1	0	0	4	3	6	1	6	0	3	1	1	0	3	4	2			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr12:2907930T>C	ENST00000001008.4	+	4	639	c.452T>C	c.(451-453)aTt>aCt	p.I151T	RP4-816N1.7_ENST00000547042.1_RNA|RP4-816N1.6_ENST00000547834.1_RNA	NM_002014.3	NP_002005.1	Q02790	FKBP4_HUMAN	FK506 binding protein 4, 59kDa	151					androgen receptor signaling pathway (GO:0030521)|chaperone-mediated protein folding (GO:0061077)|copper ion transport (GO:0006825)|embryo implantation (GO:0007566)|male sex differentiation (GO:0046661)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)|negative regulation of neuron projection development (GO:0010977)|prostate gland development (GO:0030850)|protein complex localization (GO:0031503)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|steroid hormone receptor complex assembly (GO:0006463)	axonal growth cone (GO:0044295)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|FK506 binding (GO:0005528)|GTP binding (GO:0005525)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(1)	14			OV - Ovarian serous cystadenocarcinoma(31;0.00105)			GGCGGAATCATTCGCAGAATA	0.488																																					p.I151T		Atlas-SNP	.											.	FKBP4	29	.	0			c.T452C						PASS	.						162	146	151					12																	2907930		2203	4300	6503	SO:0001583	missense	2288	exon4			GAATCATTCGCAG	M88279	CCDS8512.1	12p13.33	2013-01-10	2002-08-29		ENSG00000004478	ENSG00000004478		"Tetratricopeptide (TTC) repeat domain containing"	3720	protein-coding gene	gene with protein product		600611	"FK506-binding protein 4 (59kD)"			1279700	Standard	NM_002014		Approved	FKBP59, FKBP52	uc001qkz.3	Q02790	OTTHUMG00000090429	ENST00000001008.4:c.452T>C	chr12.hg19:g.2907930T>C	ENSP00000001008:p.Ile151Thr	86.0	0.0	.		125.0	31.0	.	NM_002014	D3DUQ1|Q9UCP1|Q9UCV7	Missense_Mutation	SNP	ENST00000001008.4	hg19	CCDS8512.1	.	.	.	.	.	.	.	.	.	.	T	16.67	3.188948	0.57909	.	.	ENSG00000004478	ENST00000001008	D	0.82167	-1.58	4.87	4.87	0.63330	.	0.154283	0.56097	D	0.000027	T	0.80149	0.4570	L	0.41236	1.265	0.58432	D	0.999998	B	0.30634	0.288	B	0.39904	0.313	T	0.77324	-0.2630	10	0.33141	T	0.24	-16.3236	13.3003	0.60321	0.0:0.0:0.0:1.0	.	151	Q02790	FKBP4_HUMAN	T	151	ENSP00000001008:I151T	ENSP00000001008:I151T	I	+	2	0	FKBP4	2778191	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	5.868000	0.69605	1.819000	0.53055	0.460000	0.39030	ATT	.	.	.	none		0.488	FKBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206861.1			C	2907930	T	C	2907930	3	2	16	1	0	0	0	0	1	0	0	0	5917	1493	52	3	466	3	FKBP4	12	2907930	Missense_Mutation	SNP	T	TCGA-2Z-A9JM-01A-12D-A42J-10		2907930	130943965	35	1158											
ITPR2	3709	hgsc.bcm.edu	37	chr12	26572030	26572030	+	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	aaaaggcccagcatgcaaacCaggacatacgccacgtgata	16	4	9	12	2	0	1	0	1	0	0	0	2	0	2	3	2	4	2	3	2	5	2			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr12:26572030C>A	ENST00000381340.3	-	50	7478	c.7062G>T	c.(7060-7062)ctG>ctT	p.L2354L	RP11-513G19.1_ENST00000535324.1_RNA	NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	2354					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)	GCATGCAAACCAGGACATACG	0.468																																					p.L2354L		Atlas-SNP	.											.	ITPR2	270	.	0			c.G7062T						PASS	.						85	93	91					12																	26572030		2027	4191	6218	SO:0001819	synonymous_variant	3709	exon50			GCAAACCAGGACA	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.7062G>T	chr12.hg19:g.26572030C>A		109.0	0.0	.		125.0	6.0	.	NM_002223	O94773	Silent	SNP	ENST00000381340.3	hg19	CCDS41764.1																																																																																			.	.	.	none		0.468	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		A	26572030	C	A	26572030	2	1	16	1	0	0	0	0	0	0	0	1	7928	581	21	4		4	ITPR2	12	26572030	Silent	SNP	C	TCGA-2Z-A9JM-01A-12D-A42J-10	23664100	26572030	107279865	36	1159											
AMIGO2	91523	hgsc.bcm.edu	37	chr12	47471993	47471993	+	5'Flank	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	ctgacgcgagtgcctggagtCagaccacaggcgacaggtgt	9	6	15	11	3	1	2	1	1	0	1	1	5	1	3	2	3	1	0	2	3	0	0			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr12:47471993C>G	ENST00000546455.1	+	0	0				AMIGO2_ENST00000429635.1_Missense_Mutation_p.D265H|AMIGO2_ENST00000266581.4_Missense_Mutation_p.D265H|AMIGO2_ENST00000321382.3_Missense_Mutation_p.D265H|AMIGO2_ENST00000550413.1_Missense_Mutation_p.D265H			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B								hydrolase activity (GO:0016787)										TGCCTGGAGTCAGACCACAGG	0.478																																					p.D265H		Atlas-SNP	.											.	AMIGO2	50	.	0			c.G793C						PASS	.						78	75	76					12																	47471993		2203	4300	6503	SO:0001631	upstream_gene_variant	347902	exon2			TGGAGTCAGACCA	BC016154	CCDS8752.1	12q13.11	2012-06-11	2012-06-11	2012-06-11	ENSG00000179715	ENSG00000179715			28255	protein-coding gene	gene with protein product			"family with sequence similarity 113, member B"	FAM113B		20056006	Standard	NM_138371		Approved	MGC16044	uc001rpq.3	Q96HM7	OTTHUMG00000169617		chr12.hg19:g.47471993C>G	Exception_encountered	135.0	0.0	.		125.0	34.0	.	NM_181847	Q96B20	Missense_Mutation	SNP	ENST00000546455.1	hg19	CCDS8752.1	.	.	.	.	.	.	.	.	.	.	C	11.05	1.523963	0.27299	.	.	ENSG00000139211	ENST00000266581;ENST00000550413;ENST00000429635;ENST00000321382	T;T;T;T	0.02525	4.26;4.26;4.26;4.26	4.66	3.77	0.43336	Cysteine-rich flanking region, C-terminal (1);	0.521481	0.20836	N	0.084792	T	0.03827	0.0108	L	0.38175	1.15	0.45762	D	0.998651	B	0.22909	0.077	B	0.30782	0.12	T	0.49021	-0.8982	10	0.35671	T	0.21	-3.9557	12.6119	0.56556	0.0:0.9173:0.0:0.0827	.	265	Q86SJ2	AMGO2_HUMAN	H	265	ENSP00000266581:D265H;ENSP00000449034:D265H;ENSP00000406020:D265H;ENSP00000320848:D265H	ENSP00000266581:D265H	D	-	1	0	AMIGO2	45758260	0.975000	0.34042	0.044000	0.18714	0.955000	0.61496	2.630000	0.46494	1.272000	0.44329	0.555000	0.69702	GAC	.	.	.	none		0.478	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371		G	47471993	C	G	47471993	1	3	16	0	1	0	0	0	0	0	0	0	576	826	29	4		4	AMIGO2	12	47471993	5'Flank	SNP	C	TCGA-2Z-A9JM-01A-12D-A42J-10	20899963	47471993	86379902	37	1160											
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-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	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,0,2	KRT3	65	.	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	chr12.hg19:g.53183951C>T	ENSP00000413479:p.Gly588Ser	93.0	0.0	.		116.0	18.0	.	NM_057088	A6NIS2|Q701L8	Missense_Mutation	SNP	ENST00000417996.2	hg19	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	16	1	0	0	0	0	1	0	0	0	8473	652	23	1	128	1	KRT3	12	53183951	Missense_Mutation	SNP	C	TCGA-2Z-A9JM-01A-12D-A42J-10	5711958	53183951	80667944	38	1161			1	2		2	2	29	N	G_C	5.698112e-05
KRT3	3850	hgsc.bcm.edu	37	chr12	53183979	53183979	+	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	ccgctgaaaccgctgctgccGccgccaaatccaccgccgat	8	5	9	19	6	0	1	0	1	0	0	1	2	1	1	8	0	3	3	8	0	2	0			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr12:53183979G>A	ENST00000417996.2	-	9	1808	c.1734C>T	c.(1732-1734)ggC>ggT	p.G578G	KRT3_ENST00000309505.3_Silent_p.G579G	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	578	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						cgctgctgccgccgccaaatc	0.701																																					p.G578G		Atlas-SNP	.											.	KRT3	65	.	0			c.C1734T						PASS	.						12	28	22					12																	53183979		1691	3337	5028	SO:0001819	synonymous_variant	3850	exon9			GCTGCCGCCGCCA		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.1734C>T	chr12.hg19:g.53183979G>A		106.0	0.0	.		123.0	15.0	.	NM_057088	A6NIS2|Q701L8	Silent	SNP	ENST00000417996.2	hg19	CCDS44895.1																																																																																			.	.	.	none		0.701	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1	NM_057088		A	53183979	G	A	53183979	2	1	16	1	0	0	0	0	0	0	0	1	8473	1074	38	1		1	KRT3	12	53183979	Silent	SNP	G	TCGA-2Z-A9JM-01A-12D-A42J-10	28	53183979	80667916	39	1162			1	2		2	2	29	N	G_C	5.698112e-05
PPP1R12A	4659	hgsc.bcm.edu	37	chr12	80214604	80214604	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctcatcttcttcactagagCagctagactcatccttcttt	8	15	4	14	0	6	2	3	0	3	2	7	2	7	2	2	0	2	2	2	0	2	6			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr12:80214604C>T	ENST00000450142.2	-	8	1330	c.1064G>A	c.(1063-1065)tGc>tAc	p.C355Y	PPP1R12A_ENST00000437004.2_Missense_Mutation_p.C355Y|RP11-530C5.2_ENST00000548469.1_RNA|PPP1R12A_ENST00000546369.1_Missense_Mutation_p.C268Y|PPP1R12A_ENST00000261207.5_Missense_Mutation_p.C355Y|PPP1R12A_ENST00000550107.1_Missense_Mutation_p.C355Y	NM_002480.2	NP_002471.1	O14974	MYPT1_HUMAN	protein phosphatase 1, regulatory subunit 12A	355					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						TTCACTAGAGCAGCTAGACTC	0.368																																					p.C355Y		Atlas-SNP	.											.	PPP1R12A	76	.	0			c.G1064A						PASS	.						200	195	196					12																	80214604		1899	4101	6000	SO:0001583	missense	4659	exon8			CTAGAGCAGCTAG	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.1064G>A	chr12.hg19:g.80214604C>T	ENSP00000389168:p.Cys355Tyr	36.0	0.0	.		48.0	12.0	.	NM_002480	B4DZ09|F8VWB4|Q2NKL4|Q569H0|Q86WU3|Q8NFR6|Q9BYH0	Missense_Mutation	SNP	ENST00000450142.2	hg19	CCDS44947.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.061280	0.76187	.	.	ENSG00000058272	ENST00000261207;ENST00000546189;ENST00000360825;ENST00000341878;ENST00000312727;ENST00000450142;ENST00000437004;ENST00000546369;ENST00000550107;ENST00000547330;ENST00000547131	T;T;T;T;T;T;T	0.46819	1.26;1.26;1.26;1.26;1.25;1.23;0.86	5.84	4.96	0.65561	.	0.000000	0.85682	D	0.000000	T	0.47248	0.1435	M	0.62723	1.935	0.80722	D	1	B;B;B;B	0.12630	0.003;0.006;0.003;0.004	B;B;B;B	0.10450	0.004;0.005;0.004;0.002	T	0.41378	-0.9512	10	0.42905	T	0.14	.	14.8529	0.70313	0.0:0.9312:0.0:0.0688	.	355;355;355;355	F8W8Q6;O14974-2;O14974-3;O14974	.;.;.;MYPT1_HUMAN	Y	355;355;355;355;355;355;355;268;355;355;50	ENSP00000261207:C355Y;ENSP00000389168:C355Y;ENSP00000416769:C355Y;ENSP00000449514:C268Y;ENSP00000446855:C355Y;ENSP00000446816:C355Y;ENSP00000450061:C50Y	ENSP00000261207:C355Y	C	-	2	0	PPP1R12A	78738735	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.247000	0.78257	1.471000	0.48121	-0.218000	0.12543	TGC	.	.	.	none		0.368	PPP1R12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407254.2	NM_002480		T	80214604	C	T	80214604	3	4	16	1	0	0	0	0	1	0	0	0	12364	710	25	2	2100	2	PPP1R12A	12	80214604	Missense_Mutation	SNP	C	TCGA-2Z-A9JM-01A-12D-A42J-10	27030625	80214604	53637291	40	1163											
C12orf51	283450	hgsc.bcm.edu	37	chr12	112654883	112654883	+	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	tagataaaagtgccccggggCaggcctcccccagcgctggg	8	5	14	14	2	0	1	0	0	0	1	1	1	1	1	5	4	2	2	5	4	3	2			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr12:112654883C>T	ENST00000430131.2	-	45	7070	c.5925G>A	c.(5923-5925)ctG>ctA	p.L1975L	HECTD4_ENST00000377560.5_Silent_p.L2225L|HECTD4_ENST00000550722.1_Silent_p.L2251L			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	1975					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)										TGCCCCGGGGCAGGCCTCCCC	0.547																																					p.L2263L		Atlas-SNP	.											.	.	.	.	0			c.G6789A						PASS	.						24	27	26					12																	112654883		1917	4130	6047	SO:0001819	synonymous_variant	283450	exon46			CCGGGGCAGGCCT	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.5925G>A	chr12.hg19:g.112654883C>T		250.0	1.0	.		345.0	144.0	.	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	C	9.259	1.042822	0.19748	.	.	ENSG00000173064	ENST00000550968	.	.	.	5.81	1.06	0.20224	.	.	.	.	.	T	0.60932	0.2307	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57142	-0.7862	4	.	.	.	.	12.0519	0.53511	0.5084:0.4018:0.0898:0.0	.	.	.	.	Y	142	.	.	C	-	2	0	C12orf51	111139266	0.864000	0.29904	1.000000	0.80357	0.996000	0.88848	-0.036000	0.12185	0.219000	0.20840	0.655000	0.94253	TGC	.	.	.	none		0.547	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		T	112654883	C	T	112654883	2	4	16	1	0	0	0	0	0	0	0	1	1698	697	25	2		2	C12orf51	12	112654883	Silent	SNP	C	TCGA-2Z-A9JM-01A-12D-A42J-10	32440279	112654883	21197012	41	1164											
LPAR6	10161	hgsc.bcm.edu	37	chr13	48986185	48986185	+	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	tttcttttggttcttagagtCtttgacttaaatgggtagac	8	19	9	5	0	3	3	0	1	3	2	3	3	3	3	0	2	0	2	0	2	4	8			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr13:48986185C>G	ENST00000378434.4	-	7	1999	c.375G>C	c.(373-375)aaG>aaC	p.K125N	RB1_ENST00000267163.4_Intron|LPAR6_ENST00000345941.2_Missense_Mutation_p.K125N	NM_005767.5	NP_005758.2	P43657	LPAR6_HUMAN	lysophosphatidic acid receptor 6	125						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.0?(15)|p.?(4)		NS(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	14						TTCTTAGAGTCTTTGACTTAA	0.418																																					p.K125N		Atlas-SNP	.											.	LPAR6	38	.	19	Whole gene deletion(15)|Unknown(4)	bone(10)|breast(4)|adrenal_gland(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	c.G375C						PASS	.						38	38	38					13																	48986185		2203	4300	6503	SO:0001583	missense	10161	exon5			TAGAGTCTTTGAC	AF000546	CCDS9410.1	13q14	2012-08-08	2009-06-23	2009-06-23	ENSG00000139679	ENSG00000139679		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	15520	protein-coding gene	gene with protein product		609239	"purinergic receptor P2Y, G-protein coupled, 5"	P2RY5		11004484, 9755289, 19386608	Standard	NM_005767		Approved	P2Y5	uc010acu.3	P43657	OTTHUMG00000016895	ENST00000378434.4:c.375G>C	chr13.hg19:g.48986185C>G	ENSP00000367691:p.Lys125Asn	38.0	0.0	.		60.0	23.0	.	NM_001162497	A4FTW9|B3KVF2|F2YGU4|O15133|Q3KPF5|Q53FA0|Q5VW44|Q7Z3S0|Q7Z3S6	Missense_Mutation	SNP	ENST00000378434.4	hg19	CCDS9410.1	.	.	.	.	.	.	.	.	.	.	C	16.35	3.097503	0.56075	.	.	ENSG00000139679	ENST00000378434;ENST00000345941	T;T	0.72167	-0.63;-0.63	6.06	5.21	0.72293	GPCR, rhodopsin-like superfamily (1);	0.051696	0.85682	D	0.000000	T	0.60483	0.2272	N	0.26042	0.785	0.38310	D	0.943225	P	0.37688	0.605	B	0.42959	0.403	T	0.58211	-0.7676	10	0.20046	T	0.44	.	11.8623	0.52474	0.0:0.8662:0.0:0.1338	.	125	P43657	LPAR6_HUMAN	N	125	ENSP00000367691:K125N;ENSP00000344353:K125N	ENSP00000344353:K125N	K	-	3	2	LPAR6	47884186	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.960000	0.40422	2.882000	0.98803	0.655000	0.94253	AAG	.	.	.	none		0.418	LPAR6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276280.2	NM_005767		G	48986185	C	G	48986185	3	3	16	1	0	0	0	0	1	0	0	0	8916	912	32	4	663	4	LPAR6	13	48986185	Missense_Mutation	SNP	C	TCGA-2Z-A9JM-01A-12D-A42J-10		48986185	66183693	42	1165											
GALNTL1	57452	hgsc.bcm.edu	37	chr14	69792741	69792741	+	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	gcctgcgcaatgatcggcggGaaggtgagtccttgcaccct	7	8	14	12	3	0	2	0	2	0	0	2	3	1	3	3	3	2	2	3	3	2	1			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr14:69792741G>A	ENST00000337827.4	+	5	892	c.565G>A	c.(565-567)Gaa>Aaa	p.E189K	GALNT16_ENST00000553669.1_Missense_Mutation_p.E189K|GALNT16_ENST00000448469.3_Missense_Mutation_p.E189K	NM_001168368.1|NM_020692.2	NP_001161840.1|NP_065743.2	Q8N428	GLT16_HUMAN	polypeptide N-acetylgalactosaminyltransferase 16	189	Catalytic subdomain A.				protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)										TGATCGGCGGGAAGGTGAGTC	0.572																																					p.E189K		Atlas-SNP	.											.	GALNT16	8	.	0			c.G565A						PASS	.						110	92	98					14																	69792741		2203	4300	6503	SO:0001583	missense	57452	exon5			CGGCGGGAAGGTG	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.565G>A	chr14.hg19:g.69792741G>A	ENSP00000336729:p.Glu189Lys	64.0	0.0	.		54.0	15.0	.	NM_001168368	Q4KMG3|Q58A55|Q9ULT9	Missense_Mutation	SNP	ENST00000337827.4	hg19	CCDS32107.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.524011	0.85600	.	.	ENSG00000100626	ENST00000337827;ENST00000448469;ENST00000553669	T;T;T	0.61040	0.14;0.14;0.14	5.66	5.66	0.87406	Glycosyl transferase, family 2 (1);	0.046825	0.85682	D	0.000000	T	0.76849	0.4045	M	0.70275	2.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	T	0.78122	-0.2327	10	0.72032	D	0.01	.	19.3316	0.94293	0.0:0.0:1.0:0.0	.	189;189	Q8N428;Q58A55	GLTL1_HUMAN;.	K	189	ENSP00000336729:E189K;ENSP00000402970:E189K;ENSP00000451200:E189K	ENSP00000336729:E189K	E	+	1	0	GALNTL1	68862494	1.000000	0.71417	0.998000	0.56505	0.075000	0.17131	8.849000	0.92178	2.672000	0.90937	0.655000	0.94253	GAA	.	.	.	none		0.572	GALNT16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412434.1	NM_001168368		A	69792741	G	A	69792741	3	1	16	1	0	0	0	0	1	0	0	0	6228	1175	41	2	583	2	GALNTL1	14	69792741	Missense_Mutation	SNP	G	TCGA-2Z-A9JM-01A-12D-A42J-10		69792741	37556799	43	1166											
RPS6KA5	9252	hgsc.bcm.edu	37	chr14	91389482	91389482	+	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	catgtcctgaatctccccctCtgacaatatctggtgccatg	8	12	7	14	0	3	2	0	2	3	0	5	2	4	2	4	1	1	0	4	1	3	1			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr14:91389482C>T	ENST00000261991.3	-	6	850	c.677G>A	c.(676-678)aGa>aAa	p.R226K	RPS6KA5_ENST00000418736.2_Missense_Mutation_p.R226K|RPS6KA5_ENST00000536315.2_Missense_Mutation_p.R147K	NM_004755.2	NP_004746.2	O75582	KS6A5_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 5	226	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|histone H2A-S1 phosphorylation (GO:0043990)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cytokine production (GO:0001818)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R226T(2)		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)		ATCTCCCCCTCTGACAATATC	0.333																																					p.R226K		Atlas-SNP	.											RPS6KA5_ENST00000261991,NS,carcinoma,0,1	RPS6KA5	135	.	2	Substitution - Missense(2)	lung(2)	c.G677A						PASS	.						146	127	133					14																	91389482		2203	4300	6503	SO:0001583	missense	9252	exon6			CCCCCTCTGACAA	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.677G>A	chr14.hg19:g.91389482C>T	ENSP00000261991:p.Arg226Lys	78.0	0.0	.		69.0	22.0	.	NM_182398	O95316|Q96AF7	Missense_Mutation	SNP	ENST00000261991.3	hg19	CCDS9893.1	.	.	.	.	.	.	.	.	.	.	C	10.31	1.314437	0.23908	.	.	ENSG00000100784	ENST00000261991;ENST00000536315;ENST00000418736	T;T;T	0.64991	-0.13;-0.13;-0.13	5.51	3.56	0.40772	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.198563	0.56097	N	0.000040	T	0.41236	0.1150	N	0.17312	0.475	0.34057	D	0.656889	B;B	0.02656	0.0;0.0	B;B	0.12837	0.002;0.008	T	0.40346	-0.9568	10	0.23302	T	0.38	.	7.9107	0.29789	0.0:0.6634:0.0:0.3366	.	226;226	O75582-2;O75582	.;KS6A5_HUMAN	K	226;147;226	ENSP00000261991:R226K;ENSP00000442803:R147K;ENSP00000402787:R226K	ENSP00000261991:R226K	R	-	2	0	RPS6KA5	90459235	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	0.710000	0.25748	0.585000	0.29608	-0.136000	0.14681	AGA	.	.	.	none		0.333	RPS6KA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411442.2	NM_004755		T	91389482	C	T	91389482	3	4	16	1	0	0	0	0	1	0	0	0	13667	913	32	2	1785	2	RPS6KA5	14	91389482	Missense_Mutation	SNP	C	TCGA-2Z-A9JM-01A-12D-A42J-10	21596741	91389482	15960058	44	1167											
MTMR10	54893	hgsc.bcm.edu	37	chr15	31253167	31253167	+	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	ttgatttctctgtcccaatcCgagtaagtttcaaagagtgg	10	14	9	8	1	2	2	1	1	1	1	5	3	4	2	2	1	0	2	2	1	3	4			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr15:31253167C>G	ENST00000435680.1	-	7	772	c.675G>C	c.(673-675)tcG>tcC	p.S225S	MTMR10_ENST00000314404.8_5'UTR|MTMR10_ENST00000563714.1_Silent_p.S143S|MTMR10_ENST00000425768.1_Missense_Mutation_p.R195P	NM_017762.2	NP_060232.2	Q9NXD2	MTMRA_HUMAN	myotubularin related protein 10	225	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)		TGTCCCAATCCGAGTAAGTTT	0.473																																					p.S225S		Atlas-SNP	.											.	MTMR10	74	.	0			c.G675C						PASS	.						79	78	78					15																	31253167		1916	4128	6044	SO:0001819	synonymous_variant	54893	exon7			CCAATCCGAGTAA	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.675G>C	chr15.hg19:g.31253167C>G		32.0	0.0	.		21.0	5.0	.	NM_017762	Q6P4Q6	Silent	SNP	ENST00000435680.1	hg19	CCDS45204.1	.	.	.	.	.	.	.	.	.	.	C	13.65	2.300096	0.40694	.	.	ENSG00000166912	ENST00000425768	T	0.54866	0.55	5.15	-10.3	0.00346	.	.	.	.	.	T	0.34513	0.0900	.	.	.	0.21579	N	0.999631	.	.	.	.	.	.	T	0.43814	-0.9368	6	0.52906	T	0.07	.	2.1171	0.03716	0.3931:0.1394:0.3328:0.1347	.	.	.	.	P	195	ENSP00000412314:R195P	ENSP00000412314:R195P	R	-	2	0	MTMR10	29040459	0.241000	0.23857	0.939000	0.37840	0.959000	0.62525	-0.487000	0.06505	-1.281000	0.02399	-0.440000	0.05779	CGG	.	.	.	none		0.473	MTMR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430747.1	NM_017762		G	31253167	C	G	31253167	2	3	16	1	0	0	0	0	0	0	0	1	9946	639	23	4		4	MTMR10	15	31253167	Silent	SNP	C	TCGA-2Z-A9JM-01A-12D-A42J-10		31253167	71278225	45	1168											
NEDD4	4734	hgsc.bcm.edu	37	chr15	56142779	56142779	+	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	ttgtggtcaataaagaaaggCctcccatttggtgcatgccg	10	11	11	9	1	1	1	1	0	0	1	2	1	2	1	3	3	2	1	3	3	4	3			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr15:56142779C>T	ENST00000508342.1	-	10	2864	c.2565G>A	c.(2563-2565)agG>agA	p.R855R	NEDD4_ENST00000506154.1_Silent_p.R839R|NEDD4_ENST00000338963.2_Silent_p.R783R|NEDD4_ENST00000435532.3_Silent_p.R436R	NM_001284338.1	NP_001271267.1	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	855	Mediates interaction with TNIK. {ECO:0000250}.|WW 3. {ECO:0000255|PROSITE- ProRule:PRU00224}.				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)		TAAAGAAAGGCCTCCCATTTG	0.428																																					p.R783R		Atlas-SNP	.											.	NEDD4	167	.	0			c.G2349A						PASS	.						195	210	205					15																	56142779		2193	4292	6485	SO:0001819	synonymous_variant	4734	exon7			GAAAGGCCTCCCA	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.2565G>A	chr15.hg19:g.56142779C>T		110.0	0.0	.		137.0	55.0	.	NM_198400	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Silent	SNP	ENST00000508342.1	hg19		.	.	.	.	.	.	.	.	.	.	C	0.592	-0.832663	0.02713	.	.	ENSG00000069869	ENST00000508871	.	.	.	5.45	3.54	0.40534	.	.	.	.	.	T	0.59742	0.2216	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57289	-0.7837	4	.	.	.	.	9.8067	0.40797	0.0:0.7725:0.0:0.2275	.	.	.	.	D	446	.	.	G	-	2	0	NEDD4	53930071	0.985000	0.35326	1.000000	0.80357	0.048000	0.14542	0.200000	0.17257	1.438000	0.47492	-0.259000	0.10710	GGC	.	.	.	none		0.428	NEDD4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000359817.1	NM_198400		T	56142779	C	T	56142779	2	4	16	1	0	0	0	0	0	0	0	1	10317	738	26	2		2	NEDD4	15	56142779	Silent	SNP	C	TCGA-2Z-A9JM-01A-12D-A42J-10	24889612	56142779	46388613	46	1169											
PARP6	56965	hgsc.bcm.edu	37	chr15	72533806	72533806	+	Missense_Mutation	SNP	T	T	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	tggggccccctcagtttgtgTaaacctgagttccgatcaca	8	11	10	12	1	2	1	2	1	0	0	3	2	3	1	4	2	1	3	4	2	2	3			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr15:72533806T>G	ENST00000569795.1	-	24	2570	c.1883A>C	c.(1882-1884)tAc>tCc	p.Y628S	PARP6_ENST00000260376.7_3'UTR|PARP6_ENST00000413097.2_5'UTR|PARP6_ENST00000287196.9_Missense_Mutation_p.Y628S			Q2NL67	PARP6_HUMAN	poly (ADP-ribose) polymerase family, member 6	628							NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(8)|skin(1)|urinary_tract(1)	18						TCAGTTTGTGTAAACCTGAGT	0.527																																					p.Y628S		Atlas-SNP	.											.	PARP6	44	.	0			c.A1883C						PASS	.						90	86	87					15																	72533806		1931	4124	6055	SO:0001583	missense	56965	exon23			TTTGTGTAAACCT	AL390093	CCDS10241.2	15q22	2010-02-16			ENSG00000137817	ENSG00000137817		"Poly (ADP-ribose) polymerases"	26921	protein-coding gene	gene with protein product						15273990	Standard	XM_005254557		Approved	pART17	uc002auc.3	Q2NL67	OTTHUMG00000133443	ENST00000569795.1:c.1883A>C	chr15.hg19:g.72533806T>G	ENSP00000456348:p.Tyr628Ser	60.0	0.0	.		45.0	14.0	.	NM_020214	Q9H7C5|Q9H9X6|Q9HAF3|Q9NPS6|Q9UFG4	Missense_Mutation	SNP	ENST00000569795.1	hg19	CCDS10241.2	.	.	.	.	.	.	.	.	.	.	T	17.27	3.348146	0.61183	.	.	ENSG00000137817	ENST00000287196	.	.	.	4.91	4.91	0.64330	.	9.159190	0.01062	N	0.004676	T	0.57961	0.2089	N	0.08118	0	0.80722	D	1	D;D	0.65815	0.995;0.995	D;D	0.70487	0.969;0.969	T	0.52909	-0.8512	9	0.23891	T	0.37	-0.7931	13.9137	0.63883	0.0:0.0:0.0:1.0	.	628;561	Q2NL67;A0PJ50	PARP6_HUMAN;.	S	628	.	ENSP00000287196:Y628S	Y	-	2	0	PARP6	70320860	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.927000	0.75840	2.061000	0.61500	0.528000	0.53228	TAC	.	.	.	none		0.527	PARP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257315.2	NM_020214		G	72533806	T	G	72533806	3	3	16	1	0	0	0	0	1	0	0	0	11471	1638	57	5	13	5	PARP6	15	72533806	Missense_Mutation	SNP	T	TCGA-2Z-A9JM-01A-12D-A42J-10	16391027	72533806	29997586	47	1170											
IGF1R	3480	hgsc.bcm.edu	37	chr15	99500486	99500513	+	Frame_Shift_Del	DEL	CCCTCGGCCTCCTCGTCCTCCCTGCCAC	CCCTCGGCCTCCTCGTCCTCCCTGCCAC	-																															tggagagcgtccccctggacCcctcggcctcctcgtcctcc																								rs561256285|rs144738779|rs188857649|rs542567372|rs369254807	byFrequency	TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	CCCTCGGCCTCCTCGTCCTCCCTGCCAC	CCCTCGGCCTCCTCGTCCTCCCTGCCAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr15:99500486_99500513delCCCTCGGCCTCCTCGTCCTCCCTGCCAC	ENST00000268035.6	+	21	4530_4557	c.3919_3946delCCCTCGGCCTCCTCGTCCTCCCTGCCAC	c.(3919-3948)ccctcggcctcctcgtcctccctgccactgfs	p.PSASSSSLPL1307fs	RP11-654A16.3_ENST00000559468.1_RNA|IGF1R_ENST00000558762.1_Frame_Shift_Del_p.PSASSSSLPL1306fs	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	1307					axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	CCCCCTGGACCCCTCGGCCTCCTCGTCCTCCCTGCCACTGCCCGACAG	0.662																																					p.1306_1315del		Pindel	.											.	IGF1R	147	.	0			c.3918_3945del						PASS	.																																			SO:0001589	frameshift_variant	3480	exon21			.	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"CD molecules", "Fibronectin type III domain containing"	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.3919_3946delCCCTCGGCCTCCTCGTCCTCCCTGCCAC	chr15.hg19:g.99500486_99500513delCCCTCGGCCTCCTCGTCCTCCCTGCCAC	ENSP00000268035:p.Pro1307fs	96.0	0.0	.		71.0	13.0	0.183	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Frame_Shift_Del	DEL	ENST00000268035.6	hg19	CCDS10378.1																																																																																			.	.	.	none		0.662	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875		-	99500513	CCCTCGGCCTCCTCGTCCTCCCTGCCAC	-	99500486	7	5	16	1	0	1	0	1	0	0	0	0	7578	623	22	0	4001	0	IGF1R	15	99500486	Frame_Shift_Del	DEL	CCCTCGGCCTCCTCGTCCTCCCTGCCAC	TCGA-2Z-A9JM-01A-12D-A42J-10	26966680	99500486	3030906	48	1171											
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1268646	1268646	+	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	gacctatggggccggcacccCcttgggtatggtagccagca	7	7	14	13	1	0	0	0	0	0	0	0	1	0	0	5	5	2	4	5	5	3	4			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr16:1268646C>T	ENST00000348261.5	+	33	6130	c.5882C>T	c.(5881-5883)cCc>cTc	p.P1961L	CACNA1H_ENST00000565831.1_Missense_Mutation_p.P1955L|CACNA1H_ENST00000358590.4_Missense_Mutation_p.P1955L	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1961					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)	GCCGGCACCCCCTTGGGTATG	0.672																																					p.P1961L		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C5882T						PASS	.						8	9	9					16																	1268646		1934	4083	6017	SO:0001583	missense	8912	exon33			GCACCCCCTTGGG	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.5882C>T	chr16.hg19:g.1268646C>T	ENSP00000334198:p.Pro1961Leu	65.0	0.0	.		109.0	29.0	.	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	hg19	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	C	12.50	1.955207	0.34471	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.96554	-4.05;-3.99	4.78	2.8	0.32819	.	1.245580	0.06297	U	0.700188	D	0.90563	0.7042	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B	0.16802	0.0;0.019;0.0;0.0;0.0	B;B;B;B;B	0.20184	0.001;0.028;0.001;0.002;0.001	T	0.82121	-0.0614	10	0.31617	T	0.26	.	4.2002	0.10462	0.0:0.6028:0.2199:0.1773	.	707;696;702;1955;1961	A2SX38;A2SX35;A2SX37;O95180-2;O95180	.;.;.;.;CAC1H_HUMAN	L	1961;1955	ENSP00000334198:P1961L;ENSP00000351401:P1955L	ENSP00000334198:P1961L	P	+	2	0	CACNA1H	1208647	0.005000	0.15991	0.014000	0.15608	0.002000	0.02628	0.950000	0.29122	1.003000	0.39130	-0.257000	0.10917	CCC	.	.	.	none		0.672	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		T	1268646	C	T	1268646	3	4	16	1	0	0	0	0	1	0	0	0	2547	623	22	2	6008	2	CACNA1H	16	1268646	Missense_Mutation	SNP	C	TCGA-2Z-A9JM-01A-12D-A42J-10		1268646	89086107	49	1172											
SETD6	79918	hgsc.bcm.edu	37	chr16	58552019	58552019	+	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	tgagattttcaacacttatgGgcaaatggctaactggcaac	13	11	9	8	0	1	1	1	1	0	1	1	2	1	1	0	3	3	3	0	3	5	4			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr16:58552019G>T	ENST00000219315.4	+	6	907	c.857G>T	c.(856-858)gGg>gTg	p.G286V	SETD6_ENST00000418480.1_Intron|SETD6_ENST00000310682.2_Missense_Mutation_p.G262V|SETD6_ENST00000394266.4_Missense_Mutation_p.G217V			Q8TBK2	SETD6_HUMAN	SET domain containing 6	286	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						AACACTTATGGGCAAATGGCT	0.463																																					p.G286V		Atlas-SNP	.											.	SETD6	27	.	0			c.G857T						PASS	.						150	121	131					16																	58552019		2198	4300	6498	SO:0001583	missense	79918	exon6			CTTATGGGCAAAT	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.857G>T	chr16.hg19:g.58552019G>T	ENSP00000219315:p.Gly286Val	129.0	0.0	.		106.0	5.0	.	NM_001160305	A8K380|B5ME38|Q9H787	Missense_Mutation	SNP	ENST00000219315.4	hg19	CCDS54013.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.618020	0.87359	.	.	ENSG00000103037	ENST00000310682;ENST00000394266;ENST00000219315	T;T;T	0.26660	1.72;1.72;1.72	5.72	5.72	0.89469	SET domain (2);	0.000000	0.85682	D	0.000000	T	0.64159	0.2573	M	0.93898	3.47	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.73569	-0.3941	10	0.87932	D	0	-19.1594	18.875	0.92331	0.0:0.0:1.0:0.0	.	286;262	Q8TBK2;Q8TBK2-2	SETD6_HUMAN;.	V	262;217;286	ENSP00000310082:G262V;ENSP00000377809:G217V;ENSP00000219315:G286V	ENSP00000219315:G286V	G	+	2	0	SETD6	57109520	1.000000	0.71417	0.979000	0.43373	0.993000	0.82548	9.219000	0.95173	2.689000	0.91719	0.650000	0.86243	GGG	.	.	.	none		0.463	SETD6-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317274.2	NM_024860		T	58552019	G	T	58552019	3	4	16	1	0	0	0	0	1	0	0	0	14148	1232	43	4	879	4	SETD6	16	58552019	Missense_Mutation	SNP	G	TCGA-2Z-A9JM-01A-12D-A42J-10	57283373	58552019	31802734	50	1173											
BCAR1	9564	hgsc.bcm.edu	37	chr16	75263502	75263502	+	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	accatgtcctgggccgcggaAggcgatgggtactgcaaggc	8	6	16	11	3	0	0	0	0	0	0	1	2	1	1	3	5	2	2	3	5	3	1			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr16:75263502A>T	ENST00000162330.5	-	7	2646	c.2520T>A	c.(2518-2520)ccT>ccA	p.P840P	BCAR1_ENST00000393420.6_Silent_p.P858P|BCAR1_ENST00000535626.2_Silent_p.P692P|BCAR1_ENST00000566982.1_5'UTR|BCAR1_ENST00000418647.3_Silent_p.P886P|BCAR1_ENST00000420641.3_Silent_p.P858P|BCAR1_ENST00000538440.2_Silent_p.P840P|BCAR1_ENST00000546196.1_Silent_p.P811P|BCAR1_ENST00000393422.2_Silent_p.P858P|RP11-331F4.4_ENST00000489723.1_RNA|BCAR1_ENST00000542031.2_Silent_p.P838P	NM_001170717.1|NM_014567.3	NP_001164188.1|NP_055382.2	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	840					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)		GGGCCGCGGAAGGCGATGGGT	0.682																																					p.P886P		Atlas-SNP	.											.	BCAR1	184	.	0			c.T2658A						PASS	.						30	24	26					16																	75263502		2196	4299	6495	SO:0001819	synonymous_variant	9564	exon8			CGCGGAAGGCGAT	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.2520T>A	chr16.hg19:g.75263502A>T		74.0	0.0	.		69.0	28.0	.	NM_001170714	B3KWD7|B4DEV4|B4DGB5|B4DIW5|B7Z7X7|E9PCL5|E9PCV2|F5GXA2|F5GXV6|F5H7Z0|F8WA69|Q6QEF7	Silent	SNP	ENST00000162330.5	hg19	CCDS10915.1																																																																																			.	.	.	none		0.682	BCAR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269017.1	NM_014567		T	75263502	A	T	75263502	2	4	16	1	0	0	0	0	0	0	0	1	1348	59	3	5		5	BCAR1	16	75263502	Silent	SNP	A	TCGA-2Z-A9JM-01A-12D-A42J-10	16711483	75263502	15091251	51	1174											
PHF12	57649	hgsc.bcm.edu	37	chr17	27234650	27234650	+	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	tgtttcccggacacgtagttAcagtgaccatagtttgtaag	10	13	10	8	2	0	1	0	1	0	0	1	2	1	2	2	1	1	5	2	1	4	6			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr17:27234650A>T	ENST00000332830.4	-	13	3309	c.2499T>A	c.(2497-2499)tgT>tgA	p.C833*	PHF12_ENST00000577226.1_3'UTR|PHF12_ENST00000582655.1_5'Flank	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)			ACACGTAGTTACAGTGACCAT	0.537																																					p.C833X		Atlas-SNP	.											.	PHF12	69	.	0			c.T2499A						PASS	.						123	96	105					17																	27234650		2203	4300	6503	SO:0001587	stop_gained	57649	exon13			GTAGTTACAGTGA	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.2499T>A	chr17.hg19:g.27234650A>T	ENSP00000329933:p.Cys833*	57.0	0.0	.		59.0	11.0	.	NM_001033561		Nonsense_Mutation	SNP	ENST00000332830.4	hg19	CCDS32598.1	.	.	.	.	.	.	.	.	.	.	A	46	12.355174	0.99660	.	.	ENSG00000109118	ENST00000332830	.	.	.	4.34	3.27	0.37495	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-22.8096	6.3665	0.21457	0.8029:0.0:0.1971:0.0	.	.	.	.	X	833	.	ENSP00000329933:C833X	C	-	3	2	PHF12	24258776	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.575000	0.53870	0.705000	0.31890	0.383000	0.25322	TGT	.	.	.	none		0.537	PHF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255941.1	NM_020889		T	27234650	A	T	27234650	4	4	16	1	0	0	0	0	0	1	0	0	11830	389	14	5	527	5	PHF12	17	27234650	Nonsense_Mutation	SNP	A	TCGA-2Z-A9JM-01A-12D-A42J-10		27234650	53960560	52	1175											
CACNA1G	8913	hgsc.bcm.edu	37	chr17	48703733	48703733	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctacagcgtggaggcccAgagctgccagcgccggccta	7	5	15	14	3	0	1	0	0	0	1	0	2	0	2	4	3	6	2	4	3	2	2			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr17:48703733A>G	ENST00000359106.5	+	38	6755	c.6755A>G	c.(6754-6756)cAg>cGg	p.Q2252R	CACNA1G_ENST00000515411.1_Missense_Mutation_p.Q2189R|CACNA1G_ENST00000354983.4_Missense_Mutation_p.Q2218R|CACNA1G_ENST00000507510.2_Missense_Mutation_p.Q2207R|CACNA1G_ENST00000360761.4_Missense_Mutation_p.Q2136R|CACNA1G_ENST00000507896.1_Missense_Mutation_p.Q2069R|CACNA1G_ENST00000358244.5_Missense_Mutation_p.Q2046R|CACNA1G_ENST00000502264.1_Missense_Mutation_p.Q2181R|CACNA1G_ENST00000510366.1_Missense_Mutation_p.Q2107R|CACNA1G_ENST00000514717.1_Missense_Mutation_p.Q2102R|CACNA1G_ENST00000429973.2_Missense_Mutation_p.Q2141R|CACNA1G_ENST00000352832.5_Missense_Mutation_p.Q2125R|CTB-22K21.2_ENST00000502435.1_RNA|CACNA1G_ENST00000510115.1_Missense_Mutation_p.Q2173R|CACNA1G_ENST00000513964.1_Missense_Mutation_p.Q2114R|CACNA1G_ENST00000503485.1_Missense_Mutation_p.Q2125R|CACNA1G_ENST00000515165.1_Missense_Mutation_p.Q2159R|CACNA1G_ENST00000515765.1_Missense_Mutation_p.Q2196R|CACNA1G_ENST00000514181.1_Missense_Mutation_p.Q2134R|CACNA1G_ENST00000514079.1_Missense_Mutation_p.Q2166R|CACNA1G_ENST00000505165.1_Missense_Mutation_p.Q2080R|CACNA1G_ENST00000512389.1_Missense_Mutation_p.Q2148R|CACNA1G_ENST00000507609.1_Missense_Mutation_p.Q2152R|CACNA1G_ENST00000513689.2_Missense_Mutation_p.Q2162R|CACNA1G_ENST00000442258.2_Missense_Mutation_p.Q2118R|CACNA1G_ENST00000507336.1_Missense_Mutation_p.Q2241R	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	2252					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)	GTGGAGGCCCAGAGCTGCCAG	0.667											OREG0024569	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q2252R		Atlas-SNP	.											.	CACNA1G	659	.	0			c.A6755G						PASS	.						17	23	21					17																	48703733		2033	4181	6214	SO:0001583	missense	8913	exon38			AGGCCCAGAGCTG	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.6755A>G	chr17.hg19:g.48703733A>G	ENSP00000352011:p.Gln2252Arg	71.0	0.0	.	956	129.0	31.0	.	NM_018896	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Missense_Mutation	SNP	ENST00000359106.5	hg19	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	A	16.51	3.143188	0.57044	.	.	ENSG00000006283	ENST00000360761;ENST00000352832;ENST00000354983;ENST00000442258;ENST00000502264;ENST00000512389;ENST00000513964;ENST00000514717;ENST00000510366;ENST00000503485;ENST00000507510;ENST00000507336;ENST00000513689;ENST00000507609;ENST00000510115;ENST00000515165;ENST00000514181;ENST00000515765;ENST00000514079;ENST00000358244;ENST00000359106;ENST00000429973;ENST00000515411;ENST00000505165;ENST00000507896	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97752	-4.37;-4.35;-4.32;-4.37;-4.45;-4.38;-4.52;-4.48;-4.52;-4.51;-4.41;-4.35;-4.49;-4.36;-4.36;-4.4;-4.36;-4.4;-4.4;-4.4;-4.36;-4.4;-4.39;-4.44;-4.43	5.32	3.06	0.35304	.	1.379610	0.04274	N	0.342662	D	0.98340	0.9449	M	0.61703	1.905	0.42919	D	0.994288	D;B;B;D;D;P;D;P;D;B;B;P;B;P;P;D;D;P;P;B;D;B;P;P;P	0.67145	0.958;0.209;0.087;0.959;0.992;0.949;0.959;0.895;0.959;0.001;0.001;0.936;0.209;0.788;0.926;0.996;0.979;0.887;0.948;0.361;0.958;0.167;0.82;0.893;0.658	D;B;B;D;D;P;D;P;D;B;B;P;B;B;D;D;P;P;P;B;D;B;P;B;P	0.74348	0.943;0.038;0.08;0.956;0.983;0.599;0.935;0.573;0.956;0.001;0.001;0.669;0.056;0.304;0.956;0.936;0.69;0.604;0.7;0.077;0.943;0.04;0.504;0.4;0.645	D	0.91285	0.5054	10	0.51188	T	0.08	.	9.6137	0.39679	0.856:0.0:0.144:0.0	.	2102;2114;2107;2189;2162;2134;2166;2125;2152;2069;2080;2181;2148;2241;2141;2196;2159;2229;2207;2125;2118;2173;2136;2252;2046	Q19QZ5;Q19QZ1;Q19QZ4;Q19R07;Q19QY8;Q19R10;Q19QZ6;Q19QZ3;Q19R06;Q19R00;Q19R04;O43497-10;Q19QZ9;Q19QZ7;Q19R08;Q19QZ8;Q19R03;O43497-4;Q19R02;Q19R12;Q19R17;Q19R11;Q2TAC4;O43497;Q19R13	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;CAC1G_HUMAN;.	R	2136;2125;2218;2118;2181;2148;2114;2102;2107;2125;2207;2241;2162;2152;2173;2159;2134;2196;2166;2046;2252;2141;2189;2080;2069	ENSP00000353990:Q2136R;ENSP00000339302:Q2125R;ENSP00000347078:Q2218R;ENSP00000409759:Q2118R;ENSP00000425522:Q2181R;ENSP00000426261:Q2148R;ENSP00000425451:Q2114R;ENSP00000422407:Q2102R;ENSP00000426814:Q2107R;ENSP00000427238:Q2125R;ENSP00000423112:Q2207R;ENSP00000420918:Q2241R;ENSP00000426172:Q2162R;ENSP00000423045:Q2152R;ENSP00000427173:Q2173R;ENSP00000426098:Q2159R;ENSP00000425698:Q2134R;ENSP00000426232:Q2196R;ENSP00000423317:Q2166R;ENSP00000350979:Q2046R;ENSP00000352011:Q2252R;ENSP00000414388:Q2141R;ENSP00000423155:Q2189R;ENSP00000422268:Q2080R;ENSP00000421518:Q2069R	ENSP00000339302:Q2125R	Q	+	2	0	CACNA1G	46058732	1.000000	0.71417	0.341000	0.25589	0.972000	0.66771	3.389000	0.52516	0.324000	0.23333	0.379000	0.24179	CAG	.	.	.	none		0.667	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		G	48703733	A	G	48703733	3	3	16	1	0	0	0	0	1	0	0	0	2546	188	7	3	7172	3	CACNA1G	17	48703733	Missense_Mutation	SNP	A	TCGA-2Z-A9JM-01A-12D-A42J-10	21469083	48703733	32491477	53	1176											
LPO	4025	hgsc.bcm.edu	37	chr17	56332255	56332255	+	Frame_Shift_Del	DEL	C	C	-																															ataaccggctggccagagaaCtaaagagactcaaccctcag																										TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr17:56332255delC	ENST00000262290.4	+	9	1505	c.1189delC	c.(1189-1191)ctafs	p.L397fs	LPO_ENST00000543544.1_Frame_Shift_Del_p.L338fs|LPO_ENST00000421678.2_Frame_Shift_Del_p.L314fs|LPO_ENST00000582328.1_Frame_Shift_Del_p.L314fs	NM_006151.2	NP_006142.1	P22079	PERL_HUMAN	lactoperoxidase	397					defense response to bacterium (GO:0042742)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|hydrogen peroxide catabolic process (GO:0042744)|response to oxidative stress (GO:0006979)|thiocyanate metabolic process (GO:0018969)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|thiocyanate peroxidase activity (GO:0036393)			breast(5)|cervix(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30						GGCCAGAGAACTAAAGAGACT	0.567																																					p.E396fs		Atlas-Indel,Pindel	.											.	LPO	73	.	0			c.1188delA						PASS	.						104	105	105					17																	56332255		2203	4300	6503	SO:0001589	frameshift_variant	4025	exon9			.	M58151	CCDS32689.1, CCDS54149.1	17q23.1	2008-02-05				ENSG00000167419	1.11.1.7		6678	protein-coding gene	gene with protein product		150205				2222811, 8964511	Standard	NM_006151		Approved	SPO	uc002ivt.3	P22079		ENST00000262290.4:c.1189delC	chr17.hg19:g.56332255delC	ENSP00000262290:p.Leu397fs	107.0	0.0	0		81.0	38.0	0.469136	NM_006151	A5JUY4|E7EMJ3|Q13408|Q3KNQ2	Frame_Shift_Del	DEL	ENST00000262290.4	hg19	CCDS32689.1																																																																																			.	.	.	none		0.567	LPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443961.1			-	56332255	C	-	56332255	7	5	16	1	0	1	0	1	0	0	0	0	8929	564	20	0	1219	0	LPO	17	56332255	Frame_Shift_Del	DEL	C	TCGA-2Z-A9JM-01A-12D-A42J-10	7628522	56332255	24862955	54	1177											
CHMP1B	57132	hgsc.bcm.edu	37	chr18	11852058	11852058	+	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	gggcacgagcgtggcttcggCggagcaggatgaactgtctc	7	7	17	10	4	1	1	0	1	1	0	3	4	1	3	0	5	3	3	0	5	1	1			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr18:11852058C>A	ENST00000526991.2	+	1	664	c.548C>A	c.(547-549)gCg>gAg	p.A183E	GNAL_ENST00000269162.5_Intron|GNAL_ENST00000423027.3_Intron|GNAL_ENST00000535121.1_Intron|GNAL_ENST00000334049.6_Intron|RP11-78A19.3_ENST00000586474.1_RNA	NM_020412.4	NP_065145.2	Q7LBR1	CHM1B_HUMAN	charged multivesicular body protein 1B	183	Interaction with SPAST.|Interaction with VPS4A, MITD1 and STAMBP.|Interaction with VPS4B.|Interaction with VTA1.				cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|protein transport (GO:0015031)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein domain specific binding (GO:0019904)			endometrium(1)|lung(1)|urinary_tract(1)	3						GTGGCTTCGGCGGAGCAGGAT	0.617																																					p.A183E		Atlas-SNP	.											.	CHMP1B	16	.	0			c.C548A						PASS	.						19	24	22					18																	11852058		1963	4151	6114	SO:0001583	missense	57132	exon1			CTTCGGCGGAGCA	AF306520	CCDS54180.1	18p11.21	2011-09-21	2011-09-21		ENSG00000255112	ENSG00000255112		"Charged multivesicular body proteins"	24287	protein-coding gene	gene with protein product		606486	"chromatin modifying protein 1B"			15537668	Standard	NM_020412		Approved	CHMP1.5, C18orf2, Vps46B	uc002kqe.3	Q7LBR1	OTTHUMG00000165820	ENST00000526991.2:c.548C>A	chr18.hg19:g.11852058C>A	ENSP00000432279:p.Ala183Glu	43.0	0.0	.		33.0	10.0	.	NM_020412	Q96E89|Q9HD41	Missense_Mutation	SNP	ENST00000526991.2	hg19	CCDS54180.1	.	.	.	.	.	.	.	.	.	.	C	8.013	0.757866	0.15846	.	.	ENSG00000255112	ENST00000526991	D	0.85955	-2.05	5.21	4.34	0.51931	.	.	.	.	.	T	0.71005	0.3289	N	0.17564	0.495	0.36770	D	0.883757	B	0.02656	0.0	B	0.04013	0.001	T	0.65705	-0.6103	9	0.02654	T	1	.	13.9894	0.64357	0.0:0.8473:0.1526:0.0	.	183	Q7LBR1	CHM1B_HUMAN	E	183	ENSP00000432279:A183E	ENSP00000432279:A183E	A	+	2	0	CHMP1B	11842058	1.000000	0.71417	0.978000	0.43139	0.789000	0.44602	5.333000	0.65917	1.562000	0.49601	0.655000	0.94253	GCG	.	.	.	none		0.617	CHMP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386375.2	NM_020412		A	11852058	C	A	11852058	3	1	16	1	0	0	0	0	1	0	0	0	3355	768	27	4	550	4	CHMP1B	18	11852058	Missense_Mutation	SNP	C	TCGA-2Z-A9JM-01A-12D-A42J-10		11852058	66225190	55	1178											
TNPO2	30000	hgsc.bcm.edu	37	chr19	12816354	12816354	+	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	agggtgacacagcgctggtaGacgggctcacagtaaggcag	11	5	16	9	2	1	2	1	1	0	1	1	2	1	2	0	4	1	5	0	4	2	2			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr19:12816354G>T	ENST00000592287.1	-	16	1923	c.1815C>A	c.(1813-1815)gtC>gtA	p.V605V	TNPO2_ENST00000356861.5_Silent_p.V605V|TNPO2_ENST00000425528.1_Silent_p.V605V|TNPO2_ENST00000450764.2_Silent_p.V605V|TNPO2_ENST00000441499.1_Silent_p.V605V|SNORD41_ENST00000386967.1_RNA|TNPO2_ENST00000588216.1_Silent_p.V605V	NM_001136196.1	NP_001129668.1	O14787	TNPO2_HUMAN	transportin 2	605					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						AGCGCTGGTAGACGGGCTCAC	0.637																																					p.V605V		Atlas-SNP	.											.	TNPO2	108	.	0			c.C1815A						PASS	.						25	29	28					19																	12816354		2119	4218	6337	SO:0001819	synonymous_variant	30000	exon16			CTGGTAGACGGGC	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.1815C>A	chr19.hg19:g.12816354G>T		99.0	0.0	.		128.0	45.0	.	NM_013433	O14655|Q6IN77	Silent	SNP	ENST00000592287.1	hg19	CCDS45991.1																																																																																			.	.	.	none		0.637	TNPO2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450785.1	NM_013433		T	12816354	G	T	12816354	2	4	16	1	0	0	0	0	0	0	0	1	16348	929	33	4		4	TNPO2	19	12816354	Silent	SNP	G	TCGA-2Z-A9JM-01A-12D-A42J-10		12816354	46312629	56	1179											
PAK4	10298	hgsc.bcm.edu	37	chr19	39663570	39663570	+	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	gaccccagaccatcgtgcggGgcagcaaaggtgccaaagat	12	4	13	12	2	0	2	0	0	0	2	1	3	0	2	4	3	3	2	4	3	2	0			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr19:39663570G>C	ENST00000593690.1	+	5	644	c.217G>C	c.(217-219)Ggc>Cgc	p.G73R	PAK4_ENST00000599470.1_Intron|PAK4_ENST00000321944.4_Missense_Mutation_p.G73R|PAK4_ENST00000360442.3_Missense_Mutation_p.G73R|PAK4_ENST00000599386.1_Intron|PAK4_ENST00000358301.3_Missense_Mutation_p.G73R|PAK4_ENST00000435673.2_Missense_Mutation_p.G73R	NM_001014831.2	NP_001014831.1	O96013	PAK4_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 4	73	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)			CATCGTGCGGGGCAGCAAAGG	0.652																																					p.G73R		Atlas-SNP	.											.	PAK4	40	.	0			c.G217C						PASS	.						17	17	17					19																	39663570		2066	3994	6060	SO:0001583	missense	10298	exon3			GTGCGGGGCAGCA	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.217G>C	chr19.hg19:g.39663570G>C	ENSP00000469413:p.Gly73Arg	130.0	0.0	.		122.0	45.0	.	NM_001014832	B4DGG6|Q8N4E1|Q8NCH5|Q8NDE3|Q9BU33|Q9ULS8	Missense_Mutation	SNP	ENST00000593690.1	hg19	CCDS12528.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.204131	0.79127	.	.	ENSG00000130669	ENST00000358301;ENST00000435673;ENST00000360442	T;T;T	0.51325	0.71;0.71;0.71	4.04	4.04	0.47022	.	0.122742	0.56097	D	0.000040	T	0.66655	0.2811	M	0.73598	2.24	0.50813	D	0.999891	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.974	T	0.68700	-0.5339	10	0.45353	T	0.12	.	13.7374	0.62827	0.0:0.0:1.0:0.0	.	73;73	O96013-4;O96013	.;PAK4_HUMAN	R	73	ENSP00000351049:G73R;ENSP00000392753:G73R;ENSP00000353625:G73R	ENSP00000351049:G73R	G	+	1	0	PAK4	44355410	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.256000	0.95535	2.085000	0.62840	0.555000	0.69702	GGC	.	.	.	none		0.652	PAK4-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463823.1			C	39663570	G	C	39663570	3	2	16	1	0	0	0	0	1	0	0	0	11410	1232	43	4	223	4	PAK4	19	39663570	Missense_Mutation	SNP	G	TCGA-2Z-A9JM-01A-12D-A42J-10	26847216	39663570	19465413	57	1180											
RABAC1	10567	hgsc.bcm.edu	37	chr19	42463044	42463044	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggccggatggtcgcgcggCgccgctccagccactcccgg	4	4	16	17	7	0	0	0	0	0	0	3	1	2	1	5	5	1	1	5	5	0	0			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr19:42463044C>T	ENST00000222008.6	-	2	210	c.113G>A	c.(112-114)cGc>cAc	p.R38H	RABAC1_ENST00000601078.1_5'UTR|RABAC1_ENST00000601891.1_Missense_Mutation_p.R38H	NM_006423.2	NP_006414.2	Q9UI14	PRAF1_HUMAN	Rab acceptor 1 (prenylated)	38	Required for interaction with prenylated RAB3A and VAMP2. {ECO:0000250}.					cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|synapse (GO:0045202)	identical protein binding (GO:0042802)			central_nervous_system(1)|kidney(1)|prostate(1)	3						GGTCGCGCGGCGCCGCTCCAG	0.721																																					p.R38H		Atlas-SNP	.											.	RABAC1	6	.	0			c.G113A						PASS	.						20	19	19					19																	42463044		2187	4292	6479	SO:0001583	missense	10567	exon2			GCGCGGCGCCGCT	AJ133534	CCDS12593.1	19q13.2	2012-09-20			ENSG00000105404	ENSG00000105404			9794	protein-coding gene	gene with protein product	"PRA1 domain family 1", "prenylated Rab acceptor 1"	604925				10329441, 10751420	Standard	NM_006423		Approved	PRA1, PRAF1, YIP3	uc002osf.3	Q9UI14		ENST00000222008.6:c.113G>A	chr19.hg19:g.42463044C>T	ENSP00000222008:p.Arg38His	59.0	0.0	.		54.0	18.0	.	NM_006423	Q7Z4Y2|Q9Y3R1	Missense_Mutation	SNP	ENST00000222008.6	hg19	CCDS12593.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.210649	0.79240	.	.	ENSG00000105404	ENST00000222008	T	0.46063	0.88	4.34	4.34	0.51931	.	0.000000	0.85682	D	0.000000	T	0.47600	0.1454	M	0.80847	2.515	0.80722	D	1	B	0.19073	0.033	B	0.19946	0.027	T	0.52442	-0.8575	10	0.51188	T	0.08	-7.2464	14.7269	0.69351	0.0:1.0:0.0:0.0	.	38	Q9UI14	PRAF1_HUMAN	H	38	ENSP00000222008:R38H	ENSP00000222008:R38H	R	-	2	0	RABAC1	47154884	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	4.894000	0.63206	2.413000	0.81919	0.561000	0.74099	CGC	.	.	.	none		0.721	RABAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463388.1	NM_006423		T	42463044	C	T	42463044	3	4	16	1	0	0	0	0	1	0	0	0	12973	768	27	1	460	1	RABAC1	19	42463044	Missense_Mutation	SNP	C	TCGA-2Z-A9JM-01A-12D-A42J-10	2799474	42463044	16665939	58	1181											
ZNF225	7768	hgsc.bcm.edu	37	chr19	44635280	44635280	+	Frame_Shift_Del	DEL	A	A	-																															cttcatcaacaactacagtcAagagagaagtctcatacatg																										TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr19:44635280delA	ENST00000262894.6	+	5	793	c.513delA	c.(511-513)tcafs	p.S171fs	ZNF225_ENST00000590612.1_Frame_Shift_Del_p.S171fs|ZNF225_ENST00000592780.1_3'UTR	NM_013362.2	NP_037494.2	Q9UK10	ZN225_HUMAN	zinc finger protein 225	171					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	16		Prostate(69;0.0352)|all_neural(266;0.202)				AACTACAGTCAAGAGAGAAGT	0.398																																					p.S171X		Atlas-Indel,Pindel	.											.	ZNF225	41	.	0			c.512delC						PASS	.						88	91	90					19																	44635280		2074	4246	6320	SO:0001589	frameshift_variant	7768	exon5			.	AF187991	CCDS46100.1	19q13.31	2013-01-08				ENSG00000256294		"Zinc fingers, C2H2-type", "-"	13018	protein-coding gene	gene with protein product							Standard	NM_013362		Approved		uc002oyj.1	Q9UK10		ENST00000262894.6:c.513delA	chr19.hg19:g.44635280delA	ENSP00000262894:p.Ser171fs	75.0	0.0	0		89.0	11.0	0.123596	NM_013362	A8K8S2|Q53F12|Q9NS46|Q9UID8	Frame_Shift_Del	DEL	ENST00000262894.6	hg19	CCDS46100.1																																																																																			.	.	.	none		0.398	ZNF225-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460581.1			-	44635280	A	-	44635280	7	5	16	1	0	1	0	1	0	0	0	0	17791	117	5	0	527	0	ZNF225	19	44635280	Frame_Shift_Del	DEL	A	TCGA-2Z-A9JM-01A-12D-A42J-10	2172236	44635280	14493703	59	1182											
C20orf26	26074	hgsc.bcm.edu	37	chr20	20243776	20243776	+	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	aactccatcaccacagaaggTaaggatgtcggtaactgtgc	13	8	10	10	1	1	1	1	0	0	1	3	2	2	2	2	3	3	2	2	3	4	2			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr20:20243776T>A	ENST00000245957.5	+	21	2579		c.e21+2		RP5-1096J16.1_ENST00000460400.1_RNA|C20orf26_ENST00000377293.1_Splice_Site|C20orf26_ENST00000389656.3_Splice_Site|C20orf26_ENST00000377309.2_Splice_Site	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN												NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		CCACAGAAGGTAAGGATGTCG	0.383																																					.		Atlas-SNP	.											.	C20orf26	188	.	0			c.2503+2T>A						PASS	.						97	93	94					20																	20243776		2203	4300	6503	SO:0001630	splice_region_variant	26074	exon21			AGAAGGTAAGGAT																												ENST00000245957.5:c.2503+2T>A	chr20.hg19:g.20243776T>A		95.0	0.0	.		125.0	22.0	.	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Splice_Site	SNP	ENST00000245957.5	hg19	CCDS33447.1	.	.	.	.	.	.	.	.	.	.	T	16.98	3.271005	0.59540	.	.	ENSG00000089101	ENST00000343997;ENST00000377309;ENST00000389656;ENST00000389655;ENST00000245957;ENST00000377293	.	.	.	5.31	5.31	0.75309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4346	0.75137	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	C20orf26	20191776	1.000000	0.71417	1.000000	0.80357	0.730000	0.41778	5.997000	0.70646	2.223000	0.72356	0.533000	0.62120	.	.	.	.	none		0.383	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3		Intron	A	20243776	T	A	20243776	5	1	16	1	0	0	0	0	0	0	1	0	2108	1652	57	5	2615	5	C20orf26	20	20243776	Splice_Site	SNP	T	TCGA-2Z-A9JM-01A-12D-A42J-10		20243776	42781744	60	1183											
SDC4	6385	hgsc.bcm.edu	37	chr20	43964542	43964542	+	Missense_Mutation	SNP	T	T	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	taggaggtcctgggggtcgaTgacctcagtctctcggatct	6	11	14	10	2	3	1	1	1	2	0	7	4	4	3	2	5	0	0	2	5	1	1			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr20:43964542T>G	ENST00000372733.3	-	2	118	c.79A>C	c.(79-81)Atc>Ctc	p.I27L	SDC4_ENST00000537976.1_Intron	NM_002999.3	NP_002990.2	P31431	SDC4_HUMAN	syndecan 4	27					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)				TGGGGGTCGATGACCTCAGTC	0.542			T	ROS1	NSCLC																																p.I27L		Atlas-SNP	.		Dom	yes		20	20q12	6385	syndecan 4		E	.	SDC4	16	.	0			c.A79C						PASS	.						58	54	55					20																	43964542		2203	4300	6503	SO:0001583	missense	6385	exon2			GGTCGATGACCTC	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.79A>C	chr20.hg19:g.43964542T>G	ENSP00000361818:p.Ile27Leu	4.0	0.0	.		39.0	26.0	.	NM_002999	O00773|Q16833|Q53FN9|Q6FGN3	Missense_Mutation	SNP	ENST00000372733.3	hg19	CCDS13350.1	.	.	.	.	.	.	.	.	.	.	T	8.734	0.917388	0.17982	.	.	ENSG00000124145	ENST00000372733	T	0.28069	1.63	4.79	3.69	0.42338	.	0.238198	0.44483	D	0.000451	T	0.22126	0.0533	M	0.63428	1.95	0.80722	D	1	B	0.27229	0.172	B	0.16289	0.015	T	0.09357	-1.0678	10	0.02654	T	1	-22.057	7.2188	0.25975	0.0:0.1034:0.0:0.8966	.	27	P31431	SDC4_HUMAN	L	27	ENSP00000361818:I27L	ENSP00000361818:I27L	I	-	1	0	SDC4	43397956	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	2.662000	0.46766	0.795000	0.33922	0.459000	0.35465	ATC	.	.	.	none		0.542	SDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080515.1	NM_002999		G	43964542	T	G	43964542	3	3	16	1	0	0	0	0	1	0	0	0	13967	1464	51	5	533	5	SDC4	20	43964542	Missense_Mutation	SNP	T	TCGA-2Z-A9JM-01A-12D-A42J-10	23720766	43964542	19060978	61	1184											
ZNF335	63925	hgsc.bcm.edu	37	chr20	44588028	44588028	+	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	caggcgcaggttcttcttgtGccgtgtgctgaagtggcagt	5	12	15	9	2	2	1	0	1	2	0	2	1	2	1	1	3	2	4	1	3	1	3			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr20:44588028G>T	ENST00000322927.2	-	15	2165	c.2065C>A	c.(2065-2067)Cac>Aac	p.H689N	ZNF335_ENST00000426788.1_Missense_Mutation_p.H534N	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	689					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				TTCTTCTTGTGCCGTGTGCTG	0.662																																					p.H689N		Atlas-SNP	.											.	ZNF335	115	.	0			c.C2065A						PASS	.						53	40	44					20																	44588028		2203	4300	6503	SO:0001583	missense	63925	exon15			TCTTGTGCCGTGT	AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"Zinc fingers, C2H2-type"	15807	protein-coding gene	gene with protein product	"NRC-interacting factor 1"	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.2065C>A	chr20.hg19:g.44588028G>T	ENSP00000325326:p.His689Asn	86.0	0.0	.		76.0	23.0	.	NM_022095	B4DLG7|Q548D0|Q9H684	Missense_Mutation	SNP	ENST00000322927.2	hg19	CCDS13389.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.809312	0.90707	.	.	ENSG00000198026	ENST00000322927;ENST00000243961;ENST00000426788	T;T	0.01613	4.73;4.73	5.02	5.02	0.67125	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	T	0.06508	0.0167	L	0.35644	1.08	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.78314	0.991;0.98	T	0.48896	-0.8994	10	0.44086	T	0.13	-29.7901	17.5159	0.87773	0.0:0.0:1.0:0.0	.	534;689	Q9H4Z2-2;Q9H4Z2	.;ZN335_HUMAN	N	689;466;534	ENSP00000325326:H689N;ENSP00000397098:H534N	ENSP00000243961:H466N	H	-	1	0	ZNF335	44021435	1.000000	0.71417	0.969000	0.41365	0.943000	0.58893	9.113000	0.94321	2.607000	0.88179	0.561000	0.74099	CAC	.	.	.	none		0.662	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095		T	44588028	G	T	44588028	3	4	16	1	0	0	0	0	1	0	0	0	17864	1319	46	4	2019	4	ZNF335	20	44588028	Missense_Mutation	SNP	G	TCGA-2Z-A9JM-01A-12D-A42J-10	623486	44588028	18437492	62	1185											
ARFRP1	10139	hgsc.bcm.edu	37	chr20	62331971	62331971	+	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	caccctgtgagggccgagcaGgcctgggtcaggcaatctcg	7	6	15	13	2	2	1	1	1	1	0	3	2	2	1	3	4	1	2	3	4	1	0			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr20:62331971G>C	ENST00000359715.5	-	6	1067	c.501C>G	c.(499-501)gcC>gcG	p.A167A	ARFRP1_ENST00000324228.2_Silent_p.A167A|ARFRP1_ENST00000485858.1_5'UTR|ARFRP1_ENST00000609142.1_Silent_p.A167A|ARFRP1_ENST00000440854.1_Silent_p.A167A|ARFRP1_ENST00000607873.1_Silent_p.A120A			Q13795	ARFRP_HUMAN	ADP-ribosylation factor related protein 1	167					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)			GGGCCGAGCAGGCCTGGGTCA	0.662																																					p.A167A		Atlas-SNP	.											.	ARFRP1	17	.	0			c.C501G						PASS	.						48	41	44					20																	62331971		2196	4290	6486	SO:0001819	synonymous_variant	10139	exon7			CGAGCAGGCCTGG	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.501C>G	chr20.hg19:g.62331971G>C		51.0	0.0	.		64.0	18.0	.	NM_001134758	B7ZKX7|E1P5J9|Q6IBQ0	Silent	SNP	ENST00000359715.5	hg19	CCDS13533.1	.	.	.	.	.	.	.	.	.	.	G	10.62	1.400715	0.25291	.	.	ENSG00000101246	ENST00000217224	.	.	.	5.4	3.1	0.35709	.	.	.	.	.	T	0.62159	0.2405	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60475	-0.7256	4	.	.	.	-36.1778	11.6004	0.50999	0.2192:0.0:0.7808:0.0	.	.	.	.	V	95	.	.	L	-	1	2	ARFRP1	61802415	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	0.750000	0.26334	1.274000	0.44362	0.462000	0.41574	CTG	.	.	.	none		0.662	ARFRP1-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472024.1			C	62331971	G	C	62331971	2	2	16	1	0	0	0	0	0	0	0	1	856	987	35	4		4	ARFRP1	20	62331971	Silent	SNP	G	TCGA-2Z-A9JM-01A-12D-A42J-10	17743943	62331971	693549	63	1186											
ZNRF3	84133	hgsc.bcm.edu	37	chr22	29445610	29445610	+	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	tccagggcctcagctacccgGagcaggaggggcagtcccca	8	4	14	15	1	1	0	1	0	0	0	3	2	3	2	5	5	3	3	5	5	1	1			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chr22:29445610G>A	ENST00000544604.2	+	8	1616	c.1441G>A	c.(1441-1443)Gag>Aag	p.E481K	ZNRF3_ENST00000332811.4_Missense_Mutation_p.E381K|ZNRF3_ENST00000402174.1_Missense_Mutation_p.E381K|ZNRF3_ENST00000406323.3_Missense_Mutation_p.E381K	NM_001206998.1	NP_001193927.1	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	481					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						CAGCTACCCGGAGCAGGAGGG	0.657																																					p.E481K		Atlas-SNP	.											.	ZNRF3	75	.	0			c.G1441A						PASS	.						31	35	33					22																	29445610		2098	4197	6295	SO:0001583	missense	84133	exon8			TACCCGGAGCAGG	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.1441G>A	chr22.hg19:g.29445610G>A	ENSP00000443824:p.Glu481Lys	48.0	0.0	.		40.0	10.0	.	NM_001206998	B3KU18|Q6ICH1|Q6NTF8|Q8WU18	Missense_Mutation	SNP	ENST00000544604.2	hg19	CCDS56225.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.309517	0.81247	.	.	ENSG00000183579	ENST00000544604;ENST00000332811;ENST00000462485;ENST00000402174;ENST00000406323	T;T;T;T	0.79554	-1.28;-1.28;-1.28;-1.28	5.53	5.53	0.82687	.	0.154870	0.64402	D	0.000019	T	0.78502	0.4293	L	0.56769	1.78	0.40137	D	0.976783	P	0.51057	0.941	B	0.43478	0.421	T	0.79152	-0.1921	10	0.36615	T	0.2	-10.7636	14.1104	0.65118	0.0:0.1501:0.8499:0.0	.	481	Q9ULT6	ZNRF3_HUMAN	K	481;381;188;381;381	ENSP00000443824:E481K;ENSP00000328614:E381K;ENSP00000384456:E381K;ENSP00000384553:E381K	ENSP00000328614:E381K	E	+	1	0	ZNRF3	27775610	1.000000	0.71417	0.986000	0.45419	0.898000	0.52572	6.564000	0.73969	2.593000	0.87608	0.655000	0.94253	GAG	.	.	.	none		0.657	ZNRF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320943.2	XM_290972		A	29445610	G	A	29445610	3	1	16	1	0	0	0	0	1	0	0	0	18225	1175	41	2	1167	2	ZNRF3	22	29445610	Missense_Mutation	SNP	G	TCGA-2Z-A9JM-01A-12D-A42J-10		29445610	21858956	64	1187											
ZMYM3	9203	hgsc.bcm.edu	37	chrX	70472532	70472532	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtctctcccactgaagggcTaggcggggcatttgggctct	6	10	14	11	1	2	1	0	1	2	0	4	1	3	1	1	5	0	3	1	5	2	2			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chrX:70472532T>C	ENST00000353904.2	-	2	761	c.574A>G	c.(574-576)Agc>Ggc	p.S192G	ZMYM3_ENST00000373988.1_Missense_Mutation_p.S192G|ZMYM3_ENST00000373978.1_Missense_Mutation_p.S192G|ZMYM3_ENST00000373998.1_Missense_Mutation_p.S192G|ZMYM3_ENST00000373982.1_Missense_Mutation_p.S192G|ZMYM3_ENST00000489332.1_5'UTR|ZMYM3_ENST00000373984.3_Missense_Mutation_p.S192G|ZMYM3_ENST00000373981.1_Missense_Mutation_p.S192G|ZMYM3_ENST00000314425.5_Missense_Mutation_p.S192G	NM_005096.3	NP_005087.1	Q14202	ZMYM3_HUMAN	zinc finger, MYM-type 3	192					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)					ACTGAAGGGCTAGGCGGGGCA	0.607																																					p.S192G		Atlas-SNP	.											.	ZMYM3	137	.	0			c.A574G						PASS	.						36	33	34					X																	70472532		2203	4300	6503	SO:0001583	missense	9203	exon2			AAGGGCTAGGCGG	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.574A>G	chrX.hg19:g.70472532T>C	ENSP00000343909:p.Ser192Gly	60.0	0.0	.		69.0	45.0	.	NM_005096	D3DVV3|O15089|Q96E26	Missense_Mutation	SNP	ENST00000353904.2	hg19	CCDS14409.1	.	.	.	.	.	.	.	.	.	.	t	4.052	0.007331	0.07866	.	.	ENSG00000147130	ENST00000314425;ENST00000373998;ENST00000353904;ENST00000373984;ENST00000373988;ENST00000373982;ENST00000373981;ENST00000373978	T;T;T;T;T;T;T	0.47177	1.47;0.88;1.47;1.47;1.47;0.85;0.85	5.08	3.93	0.45458	.	1.057890	0.07351	N	0.882388	T	0.34048	0.0884	N	0.19112	0.55	0.23716	N	0.997031	B;B;B	0.31817	0.0;0.341;0.092	B;B;B	0.32980	0.001;0.156;0.074	T	0.23583	-1.0184	10	0.38643	T	0.18	-5.5579	7.0795	0.25223	0.0:0.1055:0.0:0.8945	.	192;192;192	Q96E26;Q14202-2;Q14202	.;.;ZMYM3_HUMAN	G	192	ENSP00000322845:S192G;ENSP00000363110:S192G;ENSP00000343909:S192G;ENSP00000363096:S192G;ENSP00000363100:S192G;ENSP00000363094:S192G;ENSP00000363093:S192G	ENSP00000322845:S192G	S	-	1	0	ZMYM3	70389257	1.000000	0.71417	1.000000	0.80357	0.025000	0.11179	1.530000	0.36007	1.681000	0.50988	0.352000	0.21897	AGC	.	.	.	none		0.607	ZMYM3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057154.1	NM_201599		C	70472532	T	C	70472532	3	2	16	1	0	0	0	0	1	0	0	0	17713	1522	53	3	3652	3	ZMYM3	23	70472532	Missense_Mutation	SNP	T	TCGA-2Z-A9JM-01A-12D-A42J-10		70472532	84798028	65	1188											
HDAC8	55869	hgsc.bcm.edu	37	chrX	71792527	71792527	+	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	ggggatcttggccagggagtCacacatactgacatactcgg	10	8	13	10	1	2	1	1	1	1	0	3	3	2	3	1	5	2	0	1	5	2	3			TCGA-2Z-A9JM-01A-12D-A42J-10	TCGA-2Z-A9JM-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5f432901-8404-4499-ac42-e4560804eee8	db9c908a-91c7-4c8f-b608-39bc3e98d82b	g.chrX:71792527C>G	ENST00000373573.3	-	1	426	c.85G>C	c.(85-87)Gac>Cac	p.D29H	HDAC8_ENST00000429103.2_5'UTR|HDAC8_ENST00000373571.1_Missense_Mutation_p.D29H|HDAC8_ENST00000373556.3_Missense_Mutation_p.D29H|HDAC8_ENST00000373560.2_Missense_Mutation_p.D29H|HDAC8_ENST00000373554.1_Missense_Mutation_p.D29H|HDAC8_ENST00000439122.2_Missense_Mutation_p.D29H|HDAC8_ENST00000373559.4_Missense_Mutation_p.D29H|HDAC8_ENST00000373583.1_Missense_Mutation_p.D29H|HDAC8_ENST00000373589.4_Missense_Mutation_p.D29H|HDAC8_ENST00000478743.1_5'UTR|HDAC8_ENST00000373561.4_Missense_Mutation_p.D29H	NM_018486.2	NP_060956.1	Q9BY41	HDAC8_HUMAN	histone deacetylase 8	29	Histone deacetylase.				chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cohesin localization to chromatin (GO:0071922)|sister chromatid cohesion (GO:0007062)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	histone deacetylase activity (GO:0004407)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|transcription factor binding (GO:0008134)			breast(3)|cervix(1)|endometrium(1)|lung(4)|prostate(1)	10	Renal(35;0.156)				Vorinostat(DB02546)	GCCAGGGAGTCACACATACTG	0.582																																					p.D29H		Atlas-SNP	.											.	HDAC8	18	.	0			c.G85C						PASS	.						86	79	81					X																	71792527		2203	4300	6503	SO:0001583	missense	55869	exon1			GGGAGTCACACAT	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.85G>C	chrX.hg19:g.71792527C>G	ENSP00000362674:p.Asp29His	93.0	0.0	.		40.0	23.0	.	NM_018486	A6ND12|A6ND61|A6NET3|A6NJR3|A8MQ62|B4DKN0|B4DV22|Q86VC8|Q9NP76|Q9NYH4	Missense_Mutation	SNP	ENST00000373573.3	hg19	CCDS14420.1	.	.	.	.	.	.	.	.	.	.	C	19.37	3.813872	0.70912	.	.	ENSG00000147099	ENST00000373573;ENST00000373583;ENST00000373589;ENST00000373568;ENST00000415409;ENST00000373571;ENST00000439122;ENST00000373560;ENST00000373559;ENST00000373561;ENST00000373556;ENST00000373554	T;T;T;T;T;T;T;T;T;T;T	0.74002	-0.55;-0.8;-0.8;-0.55;-0.55;-0.55;-0.55;-0.8;-0.55;-0.55;-0.55	4.77	4.77	0.60923	Histone deacetylase domain (2);	0.000000	0.85682	D	0.000000	D	0.83188	0.5200	L	0.60957	1.885	0.54753	D	0.999988	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.998;0.971;0.971	D	0.83870	0.0273	10	0.51188	T	0.08	-14.3316	14.8087	0.69977	0.0:1.0:0.0:0.0	.	29;29;29;29	B4DH31;B4DKN0;B4DV22;Q9BY41	.;.;.;HDAC8_HUMAN	H	29	ENSP00000362674:D29H;ENSP00000362691:D29H;ENSP00000362669:D29H;ENSP00000396424:D29H;ENSP00000362672:D29H;ENSP00000414486:D29H;ENSP00000362661:D29H;ENSP00000362660:D29H;ENSP00000362662:D29H;ENSP00000362657:D29H;ENSP00000362655:D29H	ENSP00000362655:D29H	D	-	1	0	HDAC8	71709252	1.000000	0.71417	0.997000	0.53966	0.616000	0.37450	5.895000	0.69814	2.298000	0.77334	0.436000	0.28706	GAC	.	.	.	none		0.582	HDAC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057193.2	NM_018486		G	71792527	C	G	71792527	3	3	16	1	0	0	0	0	1	0	0	0	7020	826	29	4	1178	4	HDAC8	23	71792527	Missense_Mutation	SNP	C	TCGA-2Z-A9JM-01A-12D-A42J-10	1319995	71792527	83478033	66	1189											
CROCC	9696	hgsc.bcm.edu	37	chr1	17297201	17297201	+	Missense_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	agagaagggccgcctggaccGcaccctcacgggggctgagc	8	3	16	14	3	1	2	1	1	0	1	1	4	1	3	4	4	1	2	4	4	1	0	rs150054438		TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr1:17297201G>A	ENST00000375541.5	+	35	5792	c.5723G>A	c.(5722-5724)cGc>cAc	p.R1908H		NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		CGCCTGGACCGCACCCTCACG	0.657																																					p.R1908H		Atlas-SNP	.											.	CROCC	185	.	0			c.G5723A						PASS	.						25	27	26					1																	17297201		2202	4299	6501	SO:0001583	missense	9696	exon35			TGGACCGCACCCT	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"rootletin, ciliary rootlet protein"	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.5723G>A	chr1.hg19:g.17297201G>A	ENSP00000364691:p.Arg1908His	197.0	0.0	.		121.0	5.0	.	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	hg19	CCDS30616.1	.	.	.	.	.	.	.	.	.	.	G	19.19	3.779247	0.70107	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.10668	2.85	4.6	2.7	0.31948	.	.	.	.	.	T	0.16342	0.0393	L	0.47716	1.5	0.47065	D	0.9993	D;P;P	0.59357	0.985;0.937;0.929	P;P;P	0.54460	0.753;0.483;0.651	T	0.01460	-1.1349	9	0.37606	T	0.19	.	9.1203	0.36784	0.1828:0.0:0.8172:0.0	.	1789;1211;1908	B1AKD8;Q5TZA2-2;Q5TZA2	.;.;CROCC_HUMAN	H	1908;1789	ENSP00000364691:R1908H	ENSP00000364691:R1908H	R	+	2	0	CROCC	17169788	1.000000	0.71417	0.998000	0.56505	0.844000	0.47949	3.350000	0.52224	0.487000	0.27698	0.655000	0.94253	CGC	.	G|1.000;T|0.000	.	alt		0.657	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675		A	17297201	G	A	17297201	3	1	17	1	0	0	0	0	1	0	0	0	3895	1087	38	1	5861	1	CROCC	1	17297201	Missense_Mutation	SNP	G	TCGA-2Z-A9JN-01A-21D-A42J-10		17297201	231953420	1	1190											
TAS1R2	80834	hgsc.bcm.edu	37	chr1	19181460	19181460	+	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	accttgtctcgcagctcatcGctgatggcgctgtaggtgat	6	12	12	11	3	2	2	1	2	1	0	4	2	2	2	1	2	1	5	1	2	1	2	rs373438774		TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr1:19181460G>A	ENST00000375371.3	-	3	525	c.504C>T	c.(502-504)agC>agT	p.S168S	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	168					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)	GCAGCTCATCGCTGATGGCGC	0.637																																					p.S168S		Atlas-SNP	.											.	TAS1R2	134	.	0			c.C504T						PASS	.	G		1,4403	2.1+/-5.4	0,1,2201	42	42	42		504	-3.7	0	1		42	0,8598		0,0,4299	no	coding-synonymous	TAS1R2	NM_152232.2		0,1,6500	AA,AG,GG		0.0,0.0227,0.0077		168/840	19181460	1,13001	2202	4299	6501	SO:0001819	synonymous_variant	80834	exon3			CTCATCGCTGATG		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.504C>T	chr1.hg19:g.19181460G>A		59.0	0.0	.		33.0	8.0	.	NM_152232	Q5TZ19	Silent	SNP	ENST00000375371.3	hg19	CCDS187.1																																																																																			.	.	.	none		0.637	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1			A	19181460	G	A	19181460	2	1	17	1	0	0	0	0	0	0	0	1	15575	1078	38	1		1	TAS1R2	1	19181460	Silent	SNP	G	TCGA-2Z-A9JN-01A-21D-A42J-10	1884259	19181460	230069161	2	1191											
CD1A	909	hgsc.bcm.edu	37	chr1	158226807	158226807	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcagctgacctgtcctgtcGggtgaagcacagcagtctag	8	8	14	11	1	1	2	0	2	1	0	3	2	2	2	2	2	3	4	2	2	2	1			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr1:158226807G>A	ENST00000289429.5	+	4	1369	c.836G>A	c.(835-837)cGg>cAg	p.R279Q		NM_001763.2	NP_001754.2	P06126	CD1A_HUMAN	CD1a molecule	279	Ig-like.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)		p.R279Q(1)		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)	CTGTCCTGTCGGGTGAAGCAC	0.612																																					p.R279Q		Atlas-SNP	.											CD1A,bladder,carcinoma,0,2	CD1A	88	.	1	Substitution - Missense(1)	urinary_tract(1)	c.G836A						PASS	.						83	77	79					1																	158226807		2203	4300	6503	SO:0001583	missense	909	exon4			CCTGTCGGGTGAA	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.836G>A	chr1.hg19:g.158226807G>A	ENSP00000289429:p.Arg279Gln	105.0	0.0	.		83.0	9.0	.	NM_001763	D3DVD7|Q13962|Q5TDJ8|Q9UMM4|Q9Y5M5	Missense_Mutation	SNP	ENST00000289429.5	hg19	CCDS1174.1	.	.	.	.	.	.	.	.	.	.	G	13.72	2.320750	0.41096	.	.	ENSG00000158477	ENST00000289429	T	0.02812	4.15	3.84	1.94	0.25998	Immunoglobulin-like (1);MHC class I-like antigen recognition (1);Immunoglobulin C1-set (2);	0.221369	0.23003	N	0.053047	T	0.02304	0.0071	L	0.45137	1.4	0.09310	N	1	D	0.76494	0.999	P	0.59221	0.854	T	0.44065	-0.9352	10	0.54805	T	0.06	-15.6093	6.0141	0.19592	0.2415:0.0:0.7585:0.0	.	279	P06126	CD1A_HUMAN	Q	279	ENSP00000289429:R279Q	ENSP00000289429:R279Q	R	+	2	0	CD1A	156493431	0.000000	0.05858	0.008000	0.14137	0.385000	0.30292	-0.203000	0.09438	0.406000	0.25560	0.491000	0.48974	CGG	.	.	.	none		0.612	CD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046349.2	NM_001763		A	158226807	G	A	158226807	3	1	17	1	0	0	0	0	1	0	0	0	2976	1116	39	1	850	1	CD1A	1	158226807	Missense_Mutation	SNP	G	TCGA-2Z-A9JN-01A-21D-A42J-10	139045347	158226807	91023814	3	1192											
ITPKB	3707	hgsc.bcm.edu	37	chr1	226924884	226924884	+	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	ctgctcacgctactgccgctGctgccgctgccactgccgct	3	9	10	19	4	1	0	1	0	0	0	1	0	1	0	4	0	7	6	4	0	1	1	rs147889095	byFrequency	TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr1:226924884G>A	ENST00000272117.3	-	1	275	c.276C>T	c.(274-276)agC>agT	p.S92S	ITPKB_ENST00000429204.1_Silent_p.S92S|ITPKB_ENST00000366784.1_Silent_p.S92S			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	92					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)				tactgccgctgctgccgctgc	0.751																																					p.S92S	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											.,1	ITPKB	158	.	0			c.C276T						PASS	.						4	5	5					1																	226924884		1803	3692	5495	SO:0001819	synonymous_variant	3707	exon2			GCCGCTGCTGCCG	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.276C>T	chr1.hg19:g.226924884G>A		6.0	0.0	.		8.0	4.0	.	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Silent	SNP	ENST00000272117.3	hg19	CCDS1555.1																																																																																			.	.	.	none		0.751	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221		A	226924884	G	A	226924884	2	1	17	1	0	0	0	0	0	0	0	1	7925	1310	46	2		2	ITPKB	1	226924884	Silent	SNP	G	TCGA-2Z-A9JN-01A-21D-A42J-10	68698077	226924884	22325737	4	1193											
CFC1	653275	hgsc.bcm.edu	37	chr2	131280369	131280376	+	Frame_Shift_Del	DEL	CCGCGCGG	CCGCGCGG	-																															gggtgaccccgcaggtgcgtCcgcgcggccgcgctgctgca																										TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	CCGCGCGG	CCGCGCGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr2:131280369_131280376delCCGCGCGG	ENST00000281882.3	+	4	542_549	c.254_261delCCGCGCGG	c.(253-261)tccgcgcggfs	p.SAR85fs	AC013269.3_ENST00000450486.1_RNA	NM_001079530.1	NP_001072998.1	P0CG36	CFC1B_HUMAN	cripto, FRL-1, cryptic family 1B	85					gastrulation (GO:0007369)	extracellular region (GO:0005576)						Colorectal(110;0.1)					GCAGGTGCGTCCGCGCGGCCGCGCTGCT	0.774																																					p.85_87del		Pindel	.											.	.	.	.	0			c.253_260del						PASS	.																																			SO:0001589	frameshift_variant	653275	exon4			.		CCDS33286.1	2q21.1	2008-09-04			ENSG00000152093	ENSG00000152093			33983	protein-coding gene	gene with protein product							Standard	NM_001079530		Approved		uc002trl.2	P0CG36	OTTHUMG00000153959	ENST00000281882.3:c.254_261delCCGCGCGG	chr2.hg19:g.131280369_131280376delCCGCGCGG	ENSP00000281882:p.Ser85fs	425.0	0.0	.		219.0	57.0	0.260	NM_001079530	B2RCY0|B9EJD3|Q53T05|Q9GZR3	Frame_Shift_Del	DEL	ENST00000281882.3	hg19	CCDS33286.1																																																																																			.	.	.	none		0.774	CFC1B-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254521.1	NM_001079530		-	131280376	CCGCGCGG	-	131280369	7	5	17	1	0	1	0	1	0	0	0	0	3281	855	30	0	268	0	CFC1	2	131280369	Frame_Shift_Del	DEL	CCGCGCGG	TCGA-2Z-A9JN-01A-21D-A42J-10		131280369	111919004	5	1194											
CFC1	55997	hgsc.bcm.edu	37	chr2	131355536	131355543	+	Frame_Shift_Del	DEL	GCGCGGCC	GCGCGGCC	-																															gtaccgccgttcctgcagcaGcgcggccgcgcggacgcacc																										TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	GCGCGGCC	GCGCGGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr2:131355536_131355543delGCGCGGCC	ENST00000259216.4	-	4	522_529	c.260_267delGGCCGCGC	c.(259-267)cggccgcgcfs	p.RPR87fs		NM_032545.3	NP_115934.1	P0CG37	CFC1_HUMAN	cripto, FRL-1, cryptic family 1	87	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)					TCCTGCAGCAGCGCGGCCGCGCGGACGC	0.779																																					p.87_90del		Pindel	.											.	.	.	.	0			c.261_268del						PASS	.																																			SO:0001589	frameshift_variant	653275	exon4			.	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.260_267delGGCCGCGC	chr2.hg19:g.131355536_131355543delGCGCGGCC	ENSP00000259216:p.Arg87fs	389.0	0.0	.		262.0	35.0	0.134	NM_001079530	B2RCY0|B9EJD3|Q53T05|Q9GZR3	Frame_Shift_Del	DEL	ENST00000259216.4	hg19	CCDS2162.1																																																																																			.	.	.	none		0.779	CFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333367.1	NM_032545		-	131355543	GCGCGGCC	-	131355536	7	5	17	1	0	1	0	1	0	0	0	0	3281	958	34	0	1112	0	CFC1	2	131355536	Frame_Shift_Del	DEL	GCGCGGCC	TCGA-2Z-A9JN-01A-21D-A42J-10	75167	131355536	111843837	6	1195											
TMIE	259236	hgsc.bcm.edu	37	chr3	46751076	46751076	+	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	ccctgccccacagaggataaGaagaagaagaagaagaagaa	20	2	11	8	0	0	8	0	0	0	8	0	9	0	9	3	1	1	0	3	1	8	1	rs552239745|rs397817178|rs10578999|rs544504092|rs538183178|rs71619660|rs75020261	byFrequency	TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr3:46751076G>T	ENST00000326431.3	+	4	524	c.369G>T	c.(367-369)aaG>aaT	p.K123N		NM_147196.2	NP_671729.2	Q8NEW7	TMIE_HUMAN	transmembrane inner ear	123	Lys-rich.				inner ear morphogenesis (GO:0042472)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				endometrium(1)|lung(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000688)|KIRC - Kidney renal clear cell carcinoma(197;0.0177)|Kidney(197;0.0208)		CAGAGGATaagaagaagaaga	0.502																																					p.K123N		Atlas-SNP	.											.	TMIE	16	.	0			c.G369T						PASS	.						56	61	60					3																	46751076		1899	4121	6020	SO:0001583	missense	259236	exon4			GGATAAGAAGAAG	AY081842	CCDS43081.1	3p21	2010-01-06	2004-05-19		ENSG00000181585	ENSG00000181585			30800	protein-coding gene	gene with protein product		607237	"deafness, autosomal recessive 6"	DFNB6		12140191, 12145746	Standard	NM_147196		Approved		uc010hjk.1	Q8NEW7	OTTHUMG00000149909	ENST00000326431.3:c.369G>T	chr3.hg19:g.46751076G>T	ENSP00000324775:p.Lys123Asn	119.0	0.0	.		68.0	14.0	.	NM_147196	A0AV93|A8K0R0	Missense_Mutation	SNP	ENST00000326431.3	hg19	CCDS43081.1	.	.	.	.	.	.	.	.	.	.	G	4.335	0.061563	0.08339	.	.	ENSG00000181585	ENST00000326431	D	0.86230	-2.09	.	.	.	.	0.415784	0.26349	N	0.024899	T	0.76821	0.4041	L	0.40543	1.245	0.09310	N	1	B	0.25441	0.126	B	0.06405	0.002	T	0.64765	-0.6330	8	0.48119	T	0.1	-5.4402	.	.	.	.	123	Q8NEW7	TMIE_HUMAN	N	123	ENSP00000324775:K123N	ENSP00000324775:K123N	K	+	3	2	TMIE	46726080	0.976000	0.34144	0.425000	0.26659	0.475000	0.33008	1.894000	0.39768	0.121000	0.18284	0.123000	0.15791	AAG	.	.	.	weak		0.502	TMIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313853.1	NM_147196		T	46751076	G	T	46751076	3	4	17	1	0	0	0	0	1	0	0	0	16241	933	33	4	383	4	TMIE	3	46751076	Missense_Mutation	SNP	G	TCGA-2Z-A9JN-01A-21D-A42J-10		46751076	151271354	7	1196											
SEC24A	10802	hgsc.bcm.edu	37	chr5	134010440	134010440	+	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	accctcttccttgaattaccCaagtgggccacaagccttta	10	11	6	14	0	1	1	0	1	1	0	2	1	2	1	5	1	2	0	5	1	5	5			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr5:134010440C>G	ENST00000398844.2	+	5	1241	c.953C>G	c.(952-954)cCa>cGa	p.P318R	SEC24A_ENST00000322887.4_Missense_Mutation_p.P318R	NM_021982.2	NP_068817.1	O95486	SC24A_HUMAN	SEC24 family member A	318					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of protein secretion (GO:0050714)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045714)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	36			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TTGAATTACCCAAGTGGGCCA	0.418																																					p.P318R		Atlas-SNP	.											.	SEC24A	77	.	0			c.C953G						PASS	.						71	65	66					5																	134010440		1848	4097	5945	SO:0001583	missense	10802	exon5			ATTACCCAAGTGG	AJ131244	CCDS43363.1, CCDS58967.1	5q31.1	2013-10-21	2013-10-21		ENSG00000113615	ENSG00000113615			10703	protein-coding gene	gene with protein product		607183	"SEC24 (S. cerevisiae) related gene family, member A", "SEC24 family, member A (S. cerevisiae)"			10075675, 10329445	Standard	NM_021982		Approved		uc003kzs.3	O95486	OTTHUMG00000163064	ENST00000398844.2:c.953C>G	chr5.hg19:g.134010440C>G	ENSP00000381823:p.Pro318Arg	320.0	0.0	.		268.0	36.0	.	NM_001252231	A8MVW3|Q8WUV2|Q96GP7	Missense_Mutation	SNP	ENST00000398844.2	hg19	CCDS43363.1	.	.	.	.	.	.	.	.	.	.	C	14.70	2.612974	0.46631	.	.	ENSG00000113615	ENST00000398844;ENST00000322887	T;T	0.23147	1.92;1.92	5.03	5.03	0.67393	.	0.438354	0.27185	N	0.020535	T	0.29061	0.0722	L	0.54323	1.7	0.54753	D	0.999988	B;B	0.27068	0.167;0.042	B;B	0.26202	0.067;0.036	T	0.04495	-1.0947	10	0.34782	T	0.22	-7.6797	18.7188	0.91686	0.0:1.0:0.0:0.0	.	82;318	B4E205;O95486	.;SC24A_HUMAN	R	318	ENSP00000381823:P318R;ENSP00000321749:P318R	ENSP00000321749:P318R	P	+	2	0	SEC24A	134038339	0.996000	0.38824	1.000000	0.80357	0.820000	0.46376	1.544000	0.36158	2.478000	0.83669	0.563000	0.77884	CCA	.	.	.	none		0.418	SEC24A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371563.1			G	134010440	C	G	134010440	3	3	17	1	0	0	0	0	1	0	0	0	14007	594	21	4	971	4	SEC24A	5	134010440	Missense_Mutation	SNP	C	TCGA-2Z-A9JN-01A-21D-A42J-10		134010440	46904820	8	1197											
DNAH8	1769	hgsc.bcm.edu	37	chr6	38818151	38818151	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggacaacttttacctcattTacatgagcagttggaagtat	12	13	9	7	0	1	1	1	1	0	0	1	3	1	3	1	2	4	3	1	2	5	6			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr6:38818151T>C	ENST00000359357.3	+	36	4927	c.4673T>C	c.(4672-4674)tTa>tCa	p.L1558S	DNAH8_ENST00000449981.2_Missense_Mutation_p.L1775S|DNAH8_ENST00000441566.1_Missense_Mutation_p.L1558S			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1558					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						TTACCTCATTTACATGAGCAG	0.363																																					p.L1775S		Atlas-SNP	.											.	DNAH8	1239	.	0			c.T5324C						PASS	.						135	127	130					6																	38818151		2203	4300	6503	SO:0001583	missense	1769	exon38			CTCATTTACATGA	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.4673T>C	chr6.hg19:g.38818151T>C	ENSP00000352312:p.Leu1558Ser	46.0	0.0	.		51.0	16.0	.	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	T	24.1	4.493327	0.84962	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.64085	-0.08;-0.08;-0.08	5.66	5.66	0.87406	Dynein heavy chain, domain-2 (1);	0.000000	0.64402	D	0.000004	T	0.75939	0.3918	M	0.81112	2.525	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79017	-0.1975	10	0.54805	T	0.06	.	15.9012	0.79377	0.0:0.0:0.0:1.0	.	1558	Q96JB1	DYH8_HUMAN	S	1763;1763;1558;1558	ENSP00000333363:L1763S;ENSP00000352312:L1558S;ENSP00000402294:L1558S	ENSP00000333363:L1763S	L	+	2	0	DNAH8	38926129	1.000000	0.71417	0.893000	0.35052	0.962000	0.63368	7.886000	0.87288	2.167000	0.68274	0.528000	0.53228	TTA	.	.	.	none		0.363	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		C	38818151	T	C	38818151	3	2	17	1	0	0	0	0	1	0	0	0	4609	1764	61	3	4807	3	DNAH8	6	38818151	Missense_Mutation	SNP	T	TCGA-2Z-A9JN-01A-21D-A42J-10		38818151	132296916	9	1198											
DLK2	65989	hgsc.bcm.edu	37	chr6	43422491	43422491	+	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	ccagcgggcgcgctcacctcGgacaggctgaccgggagccc	6	3	15	17	5	1	1	1	1	0	0	2	3	1	3	4	4	2	2	4	4	0	0			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr6:43422491G>A	ENST00000357338.3	-	2	773	c.73C>T	c.(73-75)Cga>Tga	p.R25*	DLK2_ENST00000372488.3_Nonsense_Mutation_p.R25*|DLK2_ENST00000372485.1_Nonsense_Mutation_p.R25*|DLK2_ENST00000414245.1_Nonsense_Mutation_p.R25*	NM_206539.1	NP_996262.1	Q6UY11	DLK2_HUMAN	delta-like 2 homolog (Drosophila)	25					negative regulation of Notch signaling pathway (GO:0045746)|regulation of fat cell differentiation (GO:0045598)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	7	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			CGCTCACCTCGGACAGGCTGA	0.721											OREG0017451	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R25X		Atlas-SNP	.											.	DLK2	22	.	0			c.C73T						PASS	.						9	12	11					6																	43422491		2139	4177	6316	SO:0001587	stop_gained	65989	exon2			CACCTCGGACAGG	AK055380	CCDS4897.1, CCDS75461.1	6p21.1	2008-02-05	2007-07-05	2007-07-05	ENSG00000171462	ENSG00000171462			21113	protein-coding gene	gene with protein product			"EGF-like-domain, multiple 9"	EGFL9			Standard	NM_001286656		Approved	MGC2487	uc003ovb.3	Q6UY11	OTTHUMG00000014735	ENST00000357338.3:c.73C>T	chr6.hg19:g.43422491G>A	ENSP00000349893:p.Arg25*	112.0	0.0	.	916	54.0	5.0	.	NM_023932	B3KNZ7|Q5T3T8|Q9BQ54	Nonsense_Mutation	SNP	ENST00000357338.3	hg19	CCDS4897.1	.	.	.	.	.	.	.	.	.	.	G	37	6.367189	0.97511	.	.	ENSG00000171462	ENST00000372485;ENST00000372488;ENST00000372496;ENST00000357338;ENST00000414245	.	.	.	4.34	-3.28	0.05033	.	0.857967	0.09956	N	0.734079	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	.	8.7775	0.34771	0.0:0.2362:0.2638:0.5	.	.	.	.	X	25	.	ENSP00000349893:R25X	R	-	1	2	DLK2	43530469	1.000000	0.71417	0.943000	0.38184	0.992000	0.81027	0.597000	0.24059	-0.832000	0.04251	0.555000	0.69702	CGA	.	.	.	none		0.721	DLK2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040618.1	NM_023932		A	43422491	G	A	43422491	4	1	17	1	0	0	0	0	0	1	0	0	4567	1124	39	1	1098	1	DLK2	6	43422491	Nonsense_Mutation	SNP	G	TCGA-2Z-A9JN-01A-21D-A42J-10	4604340	43422491	127692576	10	1199											
ACTB	60	hgsc.bcm.edu	37	chr7	5569022	5569022	+	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	atccttctgacccatgcccaCcatcacgccctgggaaggaa	10	7	8	16	1	2	1	1	1	1	0	3	3	3	3	5	2	1	0	5	2	2	1			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr7:5569022C>T	ENST00000331789.5	-	3	324	c.133G>A	c.(133-135)Gtg>Atg	p.V45M	AC006483.1_ENST00000579427.1_RNA|ACTB_ENST00000464611.1_5'Flank	NM_001101.3	NP_001092.1	P63261	ACTG_HUMAN	actin, beta	45					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)		CCCATGCCCACCATCACGCCC	0.627																																					p.V45M		Atlas-SNP	.											.	ACTB	45	.	0			c.G133A						PASS	.						63	68	66					7																	5569022		2203	4300	6503	SO:0001583	missense	60	exon3			TGCCCACCATCAC	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.133G>A	chr7.hg19:g.5569022C>T	ENSP00000349960:p.Val45Met	204.0	0.0	.		113.0	17.0	.	NM_001101	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000331789.5	hg19	CCDS5341.1	.	.	.	.	.	.	.	.	.	.	C	11.02	1.516604	0.27123	.	.	ENSG00000075624	ENST00000331789;ENST00000445914;ENST00000400179;ENST00000432588;ENST00000443528;ENST00000417101;ENST00000414620	D;D;D;D;D	0.92099	-2.97;-2.97;-2.97;-2.97;-2.97	4.9	3.1	0.35709	.	0.000000	0.53938	D	0.000044	D	0.93733	0.7997	M	0.74546	2.27	0.38415	D	0.94602	B	0.20988	0.05	P	0.44990	0.466	D	0.91871	0.5507	10	0.87932	D	0	.	9.1398	0.36897	0.0:0.8199:0.0:0.1801	.	45	P60709	ACTB_HUMAN	M	45;45;45;45;45;48;45	ENSP00000349960:V45M;ENSP00000407473:V45M;ENSP00000393951:V45M;ENSP00000399487:V48M;ENSP00000401032:V45M	ENSP00000349960:V45M	V	-	1	0	ACTB	5535548	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	5.882000	0.69714	0.490000	0.27771	0.557000	0.71058	GTG	.	.	.	none		0.627	ACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059589.4	NM_001101		T	5569022	C	T	5569022	3	4	17	1	0	0	0	0	1	0	0	0	193	507	18	2	1010	2	ACTB	7	5569022	Missense_Mutation	SNP	C	TCGA-2Z-A9JN-01A-21D-A42J-10		5569022	153569641	11	1200											
ABCA13	154664	hgsc.bcm.edu	37	chr7	48278921	48278921	+	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	gaagctgagaaatggggccaCgttggaggctgccaccctaa	11	6	14	10	1	0	1	0	1	0	1	0	4	0	2	3	4	2	3	3	4	3	2			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr7:48278921C>T	ENST00000435803.1	+	9	1005	c.981C>T	c.(979-981)caC>caT	p.H327H		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	327					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						AATGGGGCCACGTTGGAGGCT	0.498																																					p.H327H		Atlas-SNP	.											.	ABCA13	1192	.	0			c.C981T						PASS	.						69	72	71					7																	48278921		2015	4179	6194	SO:0001819	synonymous_variant	154664	exon9			GGGCCACGTTGGA	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.981C>T	chr7.hg19:g.48278921C>T		58.0	0.0	.		48.0	4.0	.	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	hg19	CCDS47584.1																																																																																			.	.	.	none		0.498	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48278921	C	T	48278921	2	4	17	1	0	0	0	0	0	0	0	1	31	535	19	1		1	ABCA13	7	48278921	Silent	SNP	C	TCGA-2Z-A9JN-01A-21D-A42J-10	42709899	48278921	110859742	12	1201											
FLNC	2318	hgsc.bcm.edu	37	chr7	128492929	128492929	+	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	gggagcacgtggtgagcgtgCgcaagagtggcaagcatgtc	9	6	18	8	3	0	2	0	1	0	1	1	3	0	3	0	3	4	4	0	3	2	0			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr7:128492929C>T	ENST00000325888.8	+	37	6313	c.6052C>T	c.(6052-6054)Cgc>Tgc	p.R2018C	RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Missense_Mutation_p.R1985C	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	2018					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						GGTGAGCGTGCGCAAGAGTGG	0.637																																					p.R2018C		Atlas-SNP	.											.	FLNC	339	.	0			c.C6052T						PASS	.						60	68	66					7																	128492929		2078	4199	6277	SO:0001583	missense	2318	exon37			AGCGTGCGCAAGA	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.6052C>T	chr7.hg19:g.128492929C>T	ENSP00000327145:p.Arg2018Cys	249.0	0.0	.		125.0	16.0	.	NM_001458	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Missense_Mutation	SNP	ENST00000325888.8	hg19	CCDS43644.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.590842	0.86851	.	.	ENSG00000128591	ENST00000325888;ENST00000346177	T;T	0.44881	0.91;0.91	5.73	5.73	0.89815	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.135360	0.48767	D	0.000161	T	0.49881	0.1583	L	0.40543	1.245	0.53005	D	0.999969	D;D	0.76494	0.999;0.995	P;P	0.57846	0.828;0.696	T	0.49881	-0.8892	10	0.87932	D	0	.	12.9057	0.58152	0.2697:0.7303:0.0:0.0	.	1985;2018	Q14315-2;Q14315	.;FLNC_HUMAN	C	2018;1985	ENSP00000327145:R2018C;ENSP00000344002:R1985C	ENSP00000327145:R2018C	R	+	1	0	FLNC	128280165	0.102000	0.21896	1.000000	0.80357	0.986000	0.74619	1.868000	0.39509	2.722000	0.93159	0.655000	0.94253	CGC	.	.	.	none		0.637	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			T	128492929	C	T	128492929	3	4	17	1	0	0	0	0	1	0	0	0	5942	768	27	1	6198	1	FLNC	7	128492929	Missense_Mutation	SNP	C	TCGA-2Z-A9JN-01A-21D-A42J-10	80214008	128492929	30645734	13	1202											
PPP1R3B	79660	hgsc.bcm.edu	37	chr8	8998922	8998922	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctagcgggtcatcgaattcCgagaacactttgaccattgt	10	12	9	10	3	2	2	1	1	1	1	4	4	3	2	2	1	2	0	2	1	3	4			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr8:8998922C>T	ENST00000310455.3	-	2	390	c.240G>A	c.(238-240)tcG>tcA	p.S80S	PPP1R3B_ENST00000519699.1_Silent_p.S80S|RP11-10A14.3_ENST00000520017.1_RNA|RP11-10A14.3_ENST00000522057.1_RNA	NM_001201329.1|NM_024607.3	NP_001188258.1|NP_078883.2	Q86XI6	PPR3B_HUMAN	protein phosphatase 1, regulatory subunit 3B	80					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 phosphatase type 1 complex (GO:0000164)	protein phosphatase regulator activity (GO:0019888)			endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	12				COAD - Colon adenocarcinoma(149;0.0717)|READ - Rectum adenocarcinoma(644;0.241)		CATCGAATTCCGAGAACACTT	0.532																																					p.S80S		Atlas-SNP	.											.	PPP1R3B	30	.	0			c.G240A						PASS	.						117	110	113					8																	8998922		2203	4300	6503	SO:0001819	synonymous_variant	79660	exon2			GAATTCCGAGAAC	AK024067	CCDS5973.1	8p23.1	2012-04-17	2011-10-04		ENSG00000173281	ENSG00000173281		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14942	protein-coding gene	gene with protein product	"PP1 subunit R4", "hepatic glycogen-targeting subunit, G(L)"	610541	"protein phosphatase 1, regulatory (inhibitor) subunit 3B"			11948623, 17555403	Standard	NM_024607		Approved	GL, FLJ14005, PPP1R4	uc003wsn.4	Q86XI6	OTTHUMG00000129329	ENST00000310455.3:c.240G>A	chr8.hg19:g.8998922C>T		68.0	0.0	.		53.0	5.0	.	NM_001201329	B3KTV3|Q9H812	Silent	SNP	ENST00000310455.3	hg19	CCDS5973.1																																																																																			.	.	.	none		0.532	PPP1R3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251472.1	NM_024607		T	8998922	C	T	8998922	2	4	17	1	0	0	0	0	0	0	0	1	12382	639	23	1		1	PPP1R3B	8	8998922	Silent	SNP	C	TCGA-2Z-A9JN-01A-21D-A42J-10		8998922	137365100	14	1203											
FAM73B	84895	hgsc.bcm.edu	37	chr9	131832229	131832229	+	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	aagcctcagcttgctgaagtCtgtgctttcttcaaggtaaa	10	13	9	9	0	4	1	2	1	2	0	4	1	4	1	1	1	4	4	1	1	5	4	rs371991039		TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr9:131832229C>G	ENST00000358369.4	+	15	1786	c.1560C>G	c.(1558-1560)gtC>gtG	p.V520V	FAM73B_ENST00000277475.5_3'UTR|FAM73B_ENST00000406926.2_3'UTR	NM_032809.2	NP_116198.2	Q7L4E1	FA73B_HUMAN	family with sequence similarity 73, member B	520					bone development (GO:0060348)	integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(1)	13						TTGCTGAAGTCTGTGCTTTCT	0.562																																					p.V520V		Atlas-SNP	.											.	FAM73B	37	.	0			c.C1560G						PASS	.						213	204	207					9																	131832229		2203	4300	6503	SO:0001819	synonymous_variant	84895	exon15			TGAAGTCTGTGCT	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.1560C>G	chr9.hg19:g.131832229C>G		74.0	0.0	.		49.0	9.0	.	NM_032809	Q8NBM3|Q8TEJ6|Q969E6	Silent	SNP	ENST00000358369.4	hg19	CCDS6917.1																																																																																			.	.	.	alt		0.562	FAM73B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054542.7	NM_032809		G	131832229	C	G	131832229	2	3	17	1	0	0	0	0	0	0	0	1	5625	900	32	4		4	FAM73B	9	131832229	Silent	SNP	C	TCGA-2Z-A9JN-01A-21D-A42J-10		131832229	9381202	15	1204											
ARRDC1	92714	hgsc.bcm.edu	37	chr9	140508149	140508149	+	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	atccacacgccacggttttcCaaggatcacaagtgcagcct	11	8	8	14	2	1	0	1	0	0	0	3	1	3	1	4	2	2	2	4	2	2	2			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr9:140508149C>G	ENST00000371421.4	+	4	427	c.363C>G	c.(361-363)tcC>tcG	p.S121S	C9orf37_ENST00000496793.1_5'Flank|ARRDC1_ENST00000491911.1_3'UTR	NM_152285.2	NP_689498.1	Q8N5I2	ARRD1_HUMAN	arrestin domain containing 1	121						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(2)|lung(4)|prostate(1)|urinary_tract(1)	13	all_cancers(76;0.106)			OV - Ovarian serous cystadenocarcinoma(145;0.000273)|Epithelial(140;0.000464)		CACGGTTTTCCAAGGATCACA	0.572																																					p.S121S		Atlas-SNP	.											.	ARRDC1	24	.	0			c.C363G						PASS	.						189	162	171					9																	140508149		2203	4300	6503	SO:0001819	synonymous_variant	92714	exon4			GTTTTCCAAGGAT	AJ420420	CCDS7049.1	9q34.3	2013-10-11			ENSG00000197070	ENSG00000197070			28633	protein-coding gene	gene with protein product	"alpha-arrestin 1"					23886940	Standard	XM_005266119		Approved	MGC40555	uc004cns.3	Q8N5I2	OTTHUMG00000020993	ENST00000371421.4:c.363C>G	chr9.hg19:g.140508149C>G		103.0	0.0	.		76.0	25.0	.	NM_152285		Silent	SNP	ENST00000371421.4	hg19	CCDS7049.1																																																																																			.	.	.	none		0.572	ARRDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055358.1	NM_152285		G	140508149	C	G	140508149	2	3	17	1	0	0	0	0	0	0	0	1	982	581	21	4		4	ARRDC1	9	140508149	Silent	SNP	C	TCGA-2Z-A9JN-01A-21D-A42J-10	8675920	140508149	705282	16	1205											
SNX19	399979	hgsc.bcm.edu	37	chr11	130781599	130781599	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaagaactcccgatagcgaCgattcacagtgtggtaggcc	11	8	11	11	3	2	1	2	0	0	1	3	4	3	1	2	2	2	1	2	2	4	3			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr11:130781599C>T	ENST00000265909.4	-	2	2311	c.1742G>A	c.(1741-1743)cGt>cAt	p.R581H	SNX19_ENST00000528555.1_5'UTR|SNX19_ENST00000530356.1_5'UTR|SNX19_ENST00000545537.1_5'Flank|SNX19_ENST00000533214.1_Missense_Mutation_p.R581H|SNX19_ENST00000533318.1_5'UTR|SNX19_ENST00000539184.1_Missense_Mutation_p.R24H	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	581	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		CCGATAGCGACGATTCACAGT	0.512																																					p.R581H		Atlas-SNP	.											.	SNX19	84	.	0			c.G1742A						PASS	.						111	107	108					11																	130781599		2201	4297	6498	SO:0001583	missense	399979	exon2			TAGCGACGATTCA	D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"Sorting nexins"	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.1742G>A	chr11.hg19:g.130781599C>T	ENSP00000265909:p.Arg581His	35.0	0.0	.		46.0	14.0	.	NM_014758	E9PKB9|Q8IV55	Missense_Mutation	SNP	ENST00000265909.4	hg19	CCDS31721.1	.	.	.	.	.	.	.	.	.	.	C	35	5.437081	0.96168	.	.	ENSG00000120451	ENST00000265909;ENST00000539184;ENST00000533214	T;T;T	0.62364	0.03;0.03;0.03	5.53	5.53	0.82687	Phox homologous domain (5);	0.050680	0.85682	D	0.000000	D	0.82440	0.5037	M	0.85710	2.77	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;0.999;1.0	D	0.84878	0.0829	10	0.87932	D	0	-16.4214	19.466	0.94939	0.0:1.0:0.0:0.0	.	24;581;581	F5H5D1;E9PKB9;Q92543	.;.;SNX19_HUMAN	H	581;24;581	ENSP00000265909:R581H;ENSP00000443480:R24H;ENSP00000435390:R581H	ENSP00000265909:R581H	R	-	2	0	SNX19	130286809	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	7.372000	0.79612	2.607000	0.88179	0.655000	0.94253	CGT	.	.	.	none		0.512	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758		T	130781599	C	T	130781599	3	4	17	1	0	0	0	0	1	0	0	0	14903	536	19	1	1276	1	SNX19	11	130781599	Missense_Mutation	SNP	C	TCGA-2Z-A9JN-01A-21D-A42J-10		130781599	4224917	17	1206											
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-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_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,0,66	KRAS	30930	.	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	c.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	chr12.hg19:g.25398284C>A	ENSP00000256078:p.Gly12Val	142.0	0.0	.		128.0	46.0	.	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	hg19	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	17	1	0	0	0	0	1	0	0	0	8445	507	18	4	671	4	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-2Z-A9JN-01A-21D-A42J-10		25398284	108453611	18	1207											
PKP2	5318	hgsc.bcm.edu	37	chr12	32949084	32949084	+	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	ataattttctggatgcccccGgtgtttagaaggtcgcgtgc	7	13	12	9	3	1	1	0	0	1	1	2	2	1	2	2	3	2	1	2	3	3	5	rs369837002		TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr12:32949084G>T	ENST00000070846.6	-	12	2472	c.2448C>A	c.(2446-2448)acC>acA	p.T816T	PKP2_ENST00000340811.4_Silent_p.T772T	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	816					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)					GGATGCCCCCGGTGTTTAGAA	0.498																																					p.T816T		Atlas-SNP	.											.	PKP2	110	.	0			c.C2448A						PASS	.						148	134	139					12																	32949084		2203	4300	6503	SO:0001819	synonymous_variant	5318	exon12			GCCCCCGGTGTTT	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.2448C>A	chr12.hg19:g.32949084G>T		110.0	0.0	.		108.0	5.0	.	NM_004572	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Silent	SNP	ENST00000070846.6	hg19	CCDS8731.1																																																																																			.	.	.	alt		0.498	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572		T	32949084	G	T	32949084	2	4	17	1	0	0	0	0	0	0	0	1	11992	1103	39	4		4	PKP2	12	32949084	Silent	SNP	G	TCGA-2Z-A9JN-01A-21D-A42J-10	7550800	32949084	100902811	19	1208											
PTPRR	5801	hgsc.bcm.edu	37	chr12	71155255	71155255	+	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	tcgtgcaacaacatacctcaGgagagacttctgtaattcca	13	10	7	11	1	2	1	1	0	1	1	4	3	3	2	2	1	4	2	2	1	4	4			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr12:71155255G>A	ENST00000283228.2	-	4	1075	c.623C>T	c.(622-624)cCt>cTt	p.P208L	PTPRR_ENST00000342084.4_Missense_Mutation_p.P96L	NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	208					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)		ACATACCTCAGGAGAGACTTC	0.378																																					p.P208L		Atlas-SNP	.											.	PTPRR	109	.	0			c.C623T						PASS	.						126	129	128					12																	71155255		2203	4300	6503	SO:0001583	missense	5801	exon4			ACCTCAGGAGAGA	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.623C>T	chr12.hg19:g.71155255G>A	ENSP00000283228:p.Pro208Leu	65.0	0.0	.		68.0	25.0	.	NM_002849	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Missense_Mutation	SNP	ENST00000283228.2	hg19	CCDS8998.1	.	.	.	.	.	.	.	.	.	.	G	13.43	2.235084	0.39498	.	.	ENSG00000153233	ENST00000283228;ENST00000342084	T;T	0.32515	1.45;1.45	5.68	5.68	0.88126	.	0.127647	0.35466	U	0.003200	T	0.44664	0.1304	L	0.51422	1.61	0.80722	D	1	P;D	0.56521	0.617;0.976	B;P	0.52481	0.121;0.7	T	0.35351	-0.9792	10	0.87932	D	0	-6.8931	19.7965	0.96487	0.0:0.0:1.0:0.0	.	96;208	F5GXR7;Q15256	.;PTPRR_HUMAN	L	208;96	ENSP00000283228:P208L;ENSP00000339605:P96L	ENSP00000283228:P208L	P	-	2	0	PTPRR	69441522	1.000000	0.71417	1.000000	0.80357	0.144000	0.21451	7.920000	0.87521	2.686000	0.91538	0.448000	0.29417	CCT	.	.	.	none		0.378	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849		A	71155255	G	A	71155255	3	1	17	1	0	0	0	0	1	0	0	0	12823	1000	35	2	1394	2	PTPRR	12	71155255	Missense_Mutation	SNP	G	TCGA-2Z-A9JN-01A-21D-A42J-10	38206171	71155255	62696640	20	1209											
HSPH1	10808	hgsc.bcm.edu	37	chr13	31722181	31722181	+	Frame_Shift_Del	DEL	A	A	-																															ccccttctcagaaaggtgagAactttggagaaaggagcagc																										TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr13:31722181delA	ENST00000320027.5	-	10	1637	c.1293delT	c.(1291-1293)gttfs	p.V431fs	HSPH1_ENST00000429785.2_Frame_Shift_Del_p.V250fs|HSPH1_ENST00000380406.5_Frame_Shift_Del_p.V390fs|HSPH1_ENST00000445273.2_Frame_Shift_Del_p.V433fs|HSPH1_ENST00000380405.4_Frame_Shift_Del_p.V431fs	NM_006644.2	NP_006635.2	Q92598	HS105_HUMAN	heat shock 105kDa/110kDa protein 1	431					chaperone mediated protein folding requiring cofactor (GO:0051085)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of NK T cell activation (GO:0051135)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	27		Lung SC(185;0.0257)		all cancers(112;0.00385)|Epithelial(112;0.0328)|OV - Ovarian serous cystadenocarcinoma(117;0.0375)|GBM - Glioblastoma multiforme(144;0.125)		GAAAGGTGAGAACTTTGGAGA	0.403																																					p.L432fs		Atlas-Indel,Pindel	.											.	HSPH1	65	.	0			c.1294delC						PASS	.						133	149	144					13																	31722181		2203	4300	6503	SO:0001589	frameshift_variant	10808	exon10			.	AB003333	CCDS9340.1, CCDS66525.1, CCDS73559.1	13q12.2-q13.3	2011-09-02			ENSG00000120694	ENSG00000120694		"Heat shock proteins / HSP70"	16969	protein-coding gene	gene with protein product		610703				9610721, 9931472	Standard	XM_005266236		Approved	HSP105B, KIAA0201, HSP105A, NY-CO-25	uc001utj.3	Q92598	OTTHUMG00000016685	ENST00000320027.5:c.1293delT	chr13.hg19:g.31722181delA	ENSP00000318687:p.Val431fs	131.0	0.0	0		164.0	27.0	0.164634	NM_006644	B4DYH1|O95739|Q5TBM6|Q5TBM7|Q5TBM8|Q9UPC4	Frame_Shift_Del	DEL	ENST00000320027.5	hg19	CCDS9340.1																																																																																			.	.	.	none		0.403	HSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044384.1			-	31722181	A	-	31722181	7	5	17	1	0	1	0	1	0	0	0	0	7438	233	9	0	1319	0	HSPH1	13	31722181	Frame_Shift_Del	DEL	A	TCGA-2Z-A9JN-01A-21D-A42J-10		31722181	83447697	21	1210											
IGDCC3	9543	hgsc.bcm.edu	37	chr15	65621833	65621833	+	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	cggcccagctggccccgctgTccccgtctcgccccatttag	3	8	10	20	4	1	0	0	0	1	0	3	0	2	0	7	2	1	2	7	2	1	2	rs375413312		TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr15:65621833T>G	ENST00000327987.4	-	13	2351	c.2100A>C	c.(2098-2100)ggA>ggC	p.G700G	IGDCC3_ENST00000559231.1_5'Flank	NM_004884.3	NP_004875.2	Q8IVU1	IGDC3_HUMAN	immunoglobulin superfamily, DCC subclass, member 3	700					neuromuscular process controlling balance (GO:0050885)	integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(9)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						GGCCCCGCTGTCCCCGTCTCG	0.647																																					p.G700G		Atlas-SNP	.											.	IGDCC3	82	.	0			c.A2100C						PASS	.	G		0,4394		0,0,2197	38	45	43		2100	-8	0	15		43	1,8579		0,1,4289	no	coding-synonymous	IGDCC3	NM_004884.3		0,1,6486	GG,GT,TT		0.0117,0.0,0.0077		700/815	65621833	1,12973	2197	4290	6487	SO:0001819	synonymous_variant	9543	exon13			CCGCTGTCCCCGT	AF063936	CCDS10205.1	15q22.3-q23	2013-02-11	2009-01-08	2009-01-08	ENSG00000174498	ENSG00000174498		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	9700	protein-coding gene	gene with protein product		604184	"putative neuronal cell adhesion molecule"	PUNC		9922388	Standard	NM_004884		Approved	HsT18880	uc002aos.2	Q8IVU1	OTTHUMG00000133137	ENST00000327987.4:c.2100A>C	chr15.hg19:g.65621833T>G		87.0	0.0	.		48.0	18.0	.	NM_004884	O95215	Silent	SNP	ENST00000327987.4	hg19	CCDS10205.1																																																																																			.	.	.	weak		0.647	IGDCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256826.1	NM_004884		G	65621833	T	G	65621833	2	3	17	1	0	0	0	0	0	0	0	1	7575	1654	58	5		5	IGDCC3	15	65621833	Silent	SNP	T	TCGA-2Z-A9JN-01A-21D-A42J-10		65621833	36909559	22	1211											
DNAJA3	9093	hgsc.bcm.edu	37	chr16	4498749	4498752	+	Frame_Shift_Del	DEL	CAGA	CAGA	-																															tatagatcccccctgggactCagacagaccagaagattcgg																								rs368706161		TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	CAGA	CAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr16:4498749_4498752delCAGA	ENST00000262375.6	+	9	1218_1221	c.1141_1144delCAGA	c.(1141-1146)cagacafs	p.QT381fs	DNAJA3_ENST00000431375.2_Frame_Shift_Del_p.QT228fs|DNAJA3_ENST00000355296.4_Frame_Shift_Del_p.QT381fs	NM_005147.5	NP_005138.3	Q96EY1	DNJA3_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 3	381					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation-induced cell death of T cells (GO:0006924)|cell aging (GO:0007569)|mitochondrial DNA replication (GO:0006264)|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 I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of programmed cell death (GO:0043069)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell proliferation (GO:0042102)|protein folding (GO:0006457)|protein stabilization (GO:0050821)|response to heat (GO:0009408)|response to interferon-gamma (GO:0034341)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|small GTPase mediated signal transduction (GO:0007264)|T cell differentiation in thymus (GO:0033077)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of plasma membrane (GO:0019897)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|interferon-gamma receptor binding (GO:0005133)|metal ion binding (GO:0046872)|NF-kappaB binding (GO:0051059)|protein kinase binding (GO:0019901)|small GTPase regulator activity (GO:0005083)|transcription factor binding (GO:0008134)			NS(1)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|upper_aerodigestive_tract(2)	15						CCCTGGGACTCAGACAGACCAGAA	0.461																																					p.380_381del		Atlas-Indel,Pindel	.											.	DNAJA3	52	.	0			c.1140_1143del						PASS	.																																			SO:0001589	frameshift_variant	9093	exon9			.	AF061749	CCDS10515.1, CCDS45400.1, CCDS66930.1	16p13.3	2011-09-02			ENSG00000103423	ENSG00000103423		"Heat shock proteins / DNAJ (HSP40)"	11808	protein-coding gene	gene with protein product		608382		TID1		9683573	Standard	NM_005147		Approved	hTid-1	uc002cwk.3	Q96EY1	OTTHUMG00000129470	ENST00000262375.6:c.1141_1144delCAGA	chr16.hg19:g.4498753_4498756delCAGA	ENSP00000262375:p.Gln381fs	96.0	0.0	0		72.0	13.0	0.180556	NM_001135110	B2RAJ5|B4DI33|E7ES32|O75472|Q8WUJ6|Q8WXJ3|Q96D76|Q96IV1|Q9NYH8	Frame_Shift_Del	DEL	ENST00000262375.6	hg19	CCDS10515.1																																																																																			.	.	.	none		0.461	DNAJA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251633.1			-	4498752	CAGA	-	4498749	7	5	17	1	0	1	0	1	0	0	0	0	4615	827	29	0	1175	0	DNAJA3	16	4498749	Frame_Shift_Del	DEL	CAGA	TCGA-2Z-A9JN-01A-21D-A42J-10		4498749	85856004	23	1212											
CDH8	1006	hgsc.bcm.edu	37	chr16	61687964	61687964	+	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	atctttgataattaatggttCatttttatgccgccgtagag	10	17	8	6	2	2	2	1	1	1	1	2	2	2	2	2	1	1	2	2	1	4	8			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr16:61687964C>A	ENST00000577390.1	-	12	2902	c.1948G>T	c.(1948-1950)Gaa>Taa	p.E650*	CDH8_ENST00000299345.6_Nonsense_Mutation_p.E650*|CDH8_ENST00000577730.1_Nonsense_Mutation_p.E650*	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	650					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)		ATTAATGGTTCATTTTTATGC	0.398																																					p.E650X		Atlas-SNP	.											.	CDH8	273	.	0			c.G1948T						PASS	.						72	71	71					16																	61687964		2203	4300	6503	SO:0001587	stop_gained	1006	exon12			ATGGTTCATTTTT	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.1948G>T	chr16.hg19:g.61687964C>A	ENSP00000462701:p.Glu650*	104.0	0.0	.		149.0	12.0	.	NM_001796	B3KWC1|Q14DC6|Q9ULB2	Nonsense_Mutation	SNP	ENST00000577390.1	hg19	CCDS10802.1	.	.	.	.	.	.	.	.	.	.	C	47	13.421152	0.99741	.	.	ENSG00000150394	ENST00000299345	.	.	.	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.8311	0.92139	0.0:1.0:0.0:0.0	.	.	.	.	X	650	.	ENSP00000299345:E650X	E	-	1	0	CDH8	60245465	1.000000	0.71417	0.851000	0.33527	0.702000	0.40608	7.770000	0.85390	2.679000	0.91253	0.655000	0.94253	GAA	.	.	.	none		0.398	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		A	61687964	C	A	61687964	4	1	17	1	0	0	0	0	0	1	0	0	3118	835	29	4	455	4	CDH8	16	61687964	Nonsense_Mutation	SNP	C	TCGA-2Z-A9JN-01A-21D-A42J-10	57189215	61687964	28666789	24	1213											
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-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	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	chr17.hg19:g.39274266C>T	ENSP00000375232:p.Arg101His	40.0	0.0	.		40.0	5.0	.	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	hg19	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	17	1	0	0	0	0	1	0	0	0	8556	768	27	1	289	1	KRTAP4-11	17	39274266	Missense_Mutation	SNP	C	TCGA-2Z-A9JN-01A-21D-A42J-10		39274266	41920944	25	1214											
ZNF536	9745	hgsc.bcm.edu	37	chr19	30935837	30935837	+	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	agccagctctatggcaagggCgagctgcccatgaaggagaa	12	5	14	10	1	1	2	0	1	1	1	1	4	1	2	2	3	4	3	2	3	4	1			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr19:30935837C>T	ENST00000355537.3	+	2	1515	c.1368C>T	c.(1366-1368)ggC>ggT	p.G456G		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	456					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.G456G(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)					ATGGCAAGGGCGAGCTGCCCA	0.647																																					p.G456G		Atlas-SNP	.											ZNF536,colon,carcinoma,0,1	ZNF536	424	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1368T						PASS	.						28	30	29					19																	30935837		2199	4298	6497	SO:0001819	synonymous_variant	9745	exon2			CAAGGGCGAGCTG		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.1368C>T	chr19.hg19:g.30935837C>T		158.0	0.0	.		87.0	13.0	.	NM_014717	A2RU18	Silent	SNP	ENST00000355537.3	hg19	CCDS32984.1																																																																																			.	.	.	none		0.647	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		T	30935837	C	T	30935837	2	4	17	1	0	0	0	0	0	0	0	1	17986	755	27	1		1	ZNF536	19	30935837	Silent	SNP	C	TCGA-2Z-A9JN-01A-21D-A42J-10		30935837	28193146	26	1215											
OTUD3	23252	hgsc.bcm.edu	37	chr1	20233044	20233044	+	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	gcttaaatgaaggcaggaccGaaaacaataaggcacaggcc	17	4	11	9	1	0	1	0	1	0	0	0	3	0	2	2	4	1	3	2	4	7	2			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr1:20233044G>A	ENST00000375120.3	+	7	956	c.955G>A	c.(955-957)Gaa>Aaa	p.E319K		NM_015207.1	NP_056022.1	Q5T2D3	OTUD3_HUMAN	OTU deubiquitinase 3	319					protein K11-linked deubiquitination (GO:0035871)|protein K6-linked deubiquitination (GO:0044313)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|kidney(2)|large_intestine(4)|lung(1)|skin(1)	9		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000276)|Lung NSC(340;0.000338)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.12e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000142)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.000408)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		AGGCAGGACCGAAAACAATAA	0.517																																					p.E319K		Atlas-SNP	.											.	OTUD3	25	.	0			c.G955A						PASS	.						103	105	104					1																	20233044		1965	4159	6124	SO:0001583	missense	23252	exon7			AGGACCGAAAACA	AB007928	CCDS41279.1	1p36.13	2014-02-24	2014-02-24		ENSG00000169914	ENSG00000169914		"OTU domain containing"	29038	protein-coding gene	gene with protein product		611758	"OTU domain containing 3"			9455484, 23827681	Standard	NM_015207		Approved	KIAA0459, DUBA4	uc001bcs.4	Q5T2D3	OTTHUMG00000002696	ENST00000375120.3:c.955G>A	chr1.hg19:g.20233044G>A	ENSP00000364261:p.Glu319Lys	151.0	0.0	.		126.0	10.0	.	NM_015207	O75047	Missense_Mutation	SNP	ENST00000375120.3	hg19	CCDS41279.1	.	.	.	.	.	.	.	.	.	.	G	6.303	0.424020	0.11928	.	.	ENSG00000169914	ENST00000375120	T	0.22945	1.93	5.88	5.88	0.94601	.	0.213831	0.47852	D	0.000207	T	0.21841	0.0526	L	0.47716	1.5	0.51012	D	0.999906	B	0.28880	0.226	B	0.20184	0.028	T	0.04796	-1.0926	10	0.07990	T	0.79	.	16.9476	0.86233	0.0:0.0:1.0:0.0	.	319	Q5T2D3	OTUD3_HUMAN	K	319	ENSP00000364261:E319K	ENSP00000364261:E319K	E	+	1	0	OTUD3	20105631	0.995000	0.38212	0.187000	0.23214	0.047000	0.14425	4.223000	0.58587	2.785000	0.95823	0.650000	0.86243	GAA	.	.	.	none		0.517	OTUD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007655.1			A	20233044	G	A	20233044	3	1	18	1	0	0	0	0	1	0	0	0	11320	1059	37	1	981	1	OTUD3	1	20233044	Missense_Mutation	SNP	G	TCGA-2Z-A9JO-01A-11D-A42J-10		20233044	229017577	1	1216											
INADL	10207	hgsc.bcm.edu	37	chr1	62253584	62253584	+	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	ggtgacatttcagtcaccccCcctgcccctgcagccttacc	6	9	7	19	0	2	1	2	1	0	0	2	1	2	1	7	1	4	1	7	1	1	2			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr1:62253584C>G	ENST00000371158.2	+	8	1122	c.1008C>G	c.(1006-1008)ccC>ccG	p.P336P	INADL_ENST00000316485.6_Silent_p.P336P	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	336					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						CAGTCACCCCCCCTGCCCCTG	0.502																																					p.P336P		Atlas-SNP	.											.	INADL	179	.	0			c.C1008G						PASS	.						88	80	83					1																	62253584		2203	4300	6503	SO:0001819	synonymous_variant	10207	exon8			CACCCCCCCTGCC	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.1008C>G	chr1.hg19:g.62253584C>G		44.0	0.0	.		46.0	13.0	.	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Silent	SNP	ENST00000371158.2	hg19	CCDS617.2																																																																																			.	.	.	none		0.502	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		G	62253584	C	G	62253584	2	3	18	1	0	0	0	0	0	0	0	1	7738	610	22	4		4	INADL	1	62253584	Silent	SNP	C	TCGA-2Z-A9JO-01A-11D-A42J-10	42020540	62253584	186997037	2	1217											
ATG4C	84938	hgsc.bcm.edu	37	chr1	63294738	63294738	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctgatgtaattgataaacAgagtgcttccatgacttctg	11	15	8	7	0	2	4	0	3	2	1	3	4	3	4	1	0	2	2	1	0	3	6			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr1:63294738A>G	ENST00000317868.4	+	7	1031	c.824A>G	c.(823-825)cAg>cGg	p.Q275R	ATG4C_ENST00000371120.3_Missense_Mutation_p.Q275R	NM_032852.3	NP_116241.2	Q96DT6	ATG4C_HUMAN	autophagy related 4C, cysteine peptidase	275					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						ATTGATAAACAGAGTGCTTCC	0.299																																					p.Q275R		Atlas-SNP	.											.	ATG4C	96	.	0			c.A824G						PASS	.						66	69	68					1																	63294738		2203	4300	6503	SO:0001583	missense	84938	exon7			ATAAACAGAGTGC	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.824A>G	chr1.hg19:g.63294738A>G	ENSP00000322159:p.Gln275Arg	133.0	0.0	.		133.0	37.0	.	NM_178221	A6NLR8|D3DQ58|Q96K04	Missense_Mutation	SNP	ENST00000317868.4	hg19	CCDS623.1	.	.	.	.	.	.	.	.	.	.	A	9.217	1.032295	0.19590	.	.	ENSG00000125703	ENST00000317868;ENST00000371120;ENST00000540025;ENST00000414558	T;T	0.40756	1.02;1.02	5.69	4.49	0.54785	.	0.258613	0.39615	N	0.001310	T	0.26376	0.0644	L	0.54323	1.7	0.38573	D	0.949985	B	0.23650	0.089	B	0.38156	0.266	T	0.09314	-1.0680	10	0.11794	T	0.64	-11.6012	11.6985	0.51556	0.8677:0.0:0.0:0.1323	.	275	Q96DT6	ATG4C_HUMAN	R	275;275;275;19	ENSP00000322159:Q275R;ENSP00000360161:Q275R	ENSP00000322159:Q275R	Q	+	2	0	ATG4C	63067326	1.000000	0.71417	0.934000	0.37439	0.772000	0.43724	5.596000	0.67570	2.162000	0.67917	0.533000	0.62120	CAG	.	.	.	none		0.299	ATG4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025332.2	NM_032852		G	63294738	A	G	63294738	3	3	18	1	0	0	0	0	1	0	0	0	1098	188	7	3	846	3	ATG4C	1	63294738	Missense_Mutation	SNP	A	TCGA-2Z-A9JO-01A-11D-A42J-10	1041154	63294738	185955883	3	1218											
FMO2	2327	hgsc.bcm.edu	37	chr1	171162500	171162500	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtggaagatggccgagcaagTatctatcaatctgtcgttac	11	11	11	8	2	3	1	1	0	2	1	4	3	3	2	1	2	2	3	1	2	6	3			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr1:171162500T>C	ENST00000209929.7	+	3	317	c.159T>C	c.(157-159)agT>agC	p.S53S	FMO2_ENST00000441535.1_Silent_p.S53S|FMO2_ENST00000529935.1_3'UTR			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	53					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)					GCCGAGCAAGTATCTATCAAT	0.348																																					p.S53S		Atlas-SNP	.											.	FMO2	66	.	0			c.T159C						PASS	.						111	111	111					1																	171162500		2203	4300	6503	SO:0001819	synonymous_variant	2327	exon3			AGCAAGTATCTAT	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.159T>C	chr1.hg19:g.171162500T>C		89.0	0.0	.		53.0	21.0	.	NM_001460	Q53XR0	Silent	SNP	ENST00000209929.7	hg19	CCDS1293.1																																																																																			.	.	.	none		0.348	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460		C	171162500	T	C	171162500	2	2	18	1	0	0	0	0	0	0	0	1	5962	1635	57	3		3	FMO2	1	171162500	Silent	SNP	T	TCGA-2Z-A9JO-01A-11D-A42J-10	107867762	171162500	78088121	4	1219											
MAPRE3	22924	hgsc.bcm.edu	37	chr2	27247068	27247072	+	Frame_Shift_Del	DEL	CAACC	CAACC	-																															aactatgatggaaaggattaCaaccctctgctggcgcggca																										TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	CAACC	CAACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr2:27247068_27247072delCAACC	ENST00000233121.2	+	4	570_574	c.372_376delCAACC	c.(370-378)tacaaccctfs	p.NP125fs	MAPRE3_ENST00000402218.1_Frame_Shift_Del_p.NP125fs|MAPRE3_ENST00000405074.3_Frame_Shift_Del_p.NP125fs			Q9UPY8	MARE3_HUMAN	microtubule-associated protein, RP/EB family, member 3	125					mitotic nuclear division (GO:0007067)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of microtubule plus-end binding (GO:1903033)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)	microtubule binding (GO:0008017)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(3)|upper_aerodigestive_tract(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAAAGGATTACAACCCTCTGCTGGC	0.434																																					p.124_125del		Atlas-Indel,Pindel	.											MAPRE3,lymph_node,lymphoid_neoplasm,0,1	MAPRE3	40	.	0			c.371_375del						PASS	.																																			SO:0001589	frameshift_variant	22924	exon4			.	Y11174	CCDS1731.1	2p23.3-p23.1	2008-06-04			ENSG00000084764	ENSG00000084764			6892	protein-coding gene	gene with protein product		605788				9233623	Standard	NM_012326		Approved	RP3, EB3	uc002rhw.3	Q9UPY8	OTTHUMG00000097067	ENST00000233121.2:c.372_376delCAACC	chr2.hg19:g.27247068_27247072delCAACC	ENSP00000233121:p.Asn125fs	123.0	0.0	0		111.0	35.0	0.315315	NM_012326	B7WPK5|O00265|Q6FHB0|Q6FI15|Q9BZP7|Q9BZP8	Frame_Shift_Del	DEL	ENST00000233121.2	hg19	CCDS1731.1																																																																																			.	.	.	none		0.434	MAPRE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214183.1	NM_012326		-	27247072	CAACC	-	27247068	7	5	18	1	0	1	0	1	0	0	0	0	9303	489	17	0	382	0	MAPRE3	2	27247068	Frame_Shift_Del	DEL	CAACC	TCGA-2Z-A9JO-01A-11D-A42J-10		27247068	215952305	5	1220											
ATP6V1E2	90423	hgsc.bcm.edu	37	chr2	46739168	46739179	+	Stop_Codon_Del	DEL	AGGCTTATATAA	AGGCTTATATAA	-																															actagcttcacttcccagagGcttatataaagaactttctg																										TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	AGGCTTATATAA	AGGCTTATATAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr2:46739168_46739179delAGGCTTATATAA	ENST00000306448.4	-	0	1785_1796				ATP6V1E2_ENST00000522587.1_Stop_Codon_Del	NM_080653.3	NP_542384.1	Q96A05	VATE2_HUMAN	ATPase, H+ transporting, lysosomal 31kDa, V1 subunit E2						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)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|proton-transporting two-sector ATPase complex, catalytic domain (GO:0033178)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)	13		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.151)			CTTCCCAGAGGCTTATATAAAGAACTTTCTGT	0.406																																					p.225_227del		Atlas-INDEL	.											.	ATP6V1E2	25	.	0			c.675_1795del						PASS	.																																			SO:0001567	stop_retained_variant	90423	exon2			.	BC008981	CCDS1826.1	2p21	2011-02-10	2006-01-13	2002-06-21	ENSG00000250565	ENSG00000250565		"ATPases / V-type"	18125	protein-coding gene	gene with protein product			"ATPase, H+ transporting, lysosomal (vacuolar proton pump) 31kD-like 2", "ATPase, H+ transporting, lysosomal 31kDa, V1 subunit E isoform 2"	ATP6EL2, ATP6V1EL2		12036578	Standard	NM_080653		Approved	MGC9341, VMA4, ATP6E1	uc002ruy.3	Q96A05	OTTHUMG00000128819	Exception_encountered	chr2.hg19:g.46739168_46739179delAGGCTTATATAA	Exception_encountered	30.0	0.0	0		42.0	10.0	0.238095	NM_080653		Frame_Shift_Del	DEL	ENST00000306448.4	hg19	CCDS1826.1																																																																																			.	.	.	none		0.406	ATP6V1E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250753.1	NM_080653		-	46739179	AGGCTTATATAA	-	46739168	7	5	18	1	0	1	0	1	0	0	0	0	1184	1218	42	0	1	0	ATP6V1E2	2	46739168	Stop_Codon_Del	DEL	AGGCTTATATAA	TCGA-2Z-A9JO-01A-11D-A42J-10	19492100	46739168	196460205	6	1221											
ZAP70	7535	hgsc.bcm.edu	37	chr2	98354318	98354318	+	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	gatgtctggagctatggggtCaccatgtgggaggccttgtc	6	11	16	8	0	2	0	1	0	1	0	3	3	2	2	2	5	1	1	2	5	1	2			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr2:98354318C>T	ENST00000264972.5	+	12	1796	c.1581C>T	c.(1579-1581)gtC>gtT	p.V527V	ZAP70_ENST00000463643.1_3'UTR|ZAP70_ENST00000442208.1_Silent_p.V401V|ZAP70_ENST00000451498.2_Silent_p.V220V	NM_001079.3	NP_001070.2	P43403	ZAP70_HUMAN	zeta-chain (TCR) associated protein kinase 70kDa	527	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						GCTATGGGGTCACCATGTGGG	0.647																																					p.V527V		Atlas-SNP	.											.	ZAP70	77	.	0			c.C1581T						PASS	.						121	129	127					2																	98354318		2203	4300	6503	SO:0001819	synonymous_variant	7535	exon12			TGGGGTCACCATG	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.1581C>T	chr2.hg19:g.98354318C>T		73.0	0.0	.		60.0	22.0	.	NM_001079	A6NFP4|Q6PIA4|Q8IXD6|Q9UBS6	Silent	SNP	ENST00000264972.5	hg19	CCDS33254.1																																																																																			.	.	.	none		0.647	ZAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329278.1			T	98354318	C	T	98354318	2	4	18	1	0	0	0	0	0	0	0	1	17526	813	29	2		2	ZAP70	2	98354318	Silent	SNP	C	TCGA-2Z-A9JO-01A-11D-A42J-10	51615150	98354318	144845055	7	1222											
MYO7B	4648	hgsc.bcm.edu	37	chr2	128390900	128390900	+	Frame_Shift_Del	DEL	A	A	-																															cagagcagaacgtctcccgcAtctgccacaagatctacttc																										TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr2:128390900delA	ENST00000409816.2	+	38	5427	c.5395delA	c.(5395-5397)atcfs	p.I1799fs	MYO7B_ENST00000428314.1_Frame_Shift_Del_p.I1799fs|MYO7B_ENST00000389524.4_Frame_Shift_Del_p.I1800fs|MYO7B_ENST00000409090.1_Frame_Shift_Del_p.I652fs			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1799	FERM 2. {ECO:0000255|PROSITE- ProRule:PRU00084}.|MyTH4 3. {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)		CGTCTCCCGCATCTGCCACAA	0.662																																					p.R1798fs		Atlas-Indel,Pindel	.											.	MYO7B	359	.	0			c.5394delC						PASS	.						49	56	53					2																	128390900		2095	4212	6307	SO:0001589	frameshift_variant	4648	exon39			.		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.5395delA	chr2.hg19:g.128390900delA	ENSP00000386461:p.Ile1799fs	155.0	0.0	0		161.0	41.0	0.254658	NM_001080527	Q14786|Q8TEE1	Frame_Shift_Del	DEL	ENST00000409816.2	hg19	CCDS46405.1																																																																																			.	.	.	none		0.662	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001		-	128390900	A	-	128390900	7	5	18	1	0	1	0	1	0	0	0	0	10090	217	8	0	5545	0	MYO7B	2	128390900	Frame_Shift_Del	DEL	A	TCGA-2Z-A9JO-01A-11D-A42J-10	30036582	128390900	114808473	8	1223											
NEB	4703	hgsc.bcm.edu	37	chr2	152410531	152410531	+	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	ttcttttcataaactgatctGtacaggcgctgtaaagttaa	12	15	7	7	1	3	1	1	1	2	0	3	1	3	1	0	1	2	4	0	1	6	7			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr2:152410531G>T	ENST00000172853.10	-	98	14481	c.14334C>A	c.(14332-14334)taC>taA	p.Y4778*	NEB_ENST00000427231.2_Nonsense_Mutation_p.Y6479*|NEB_ENST00000604864.1_Nonsense_Mutation_p.Y6479*|NEB_ENST00000603639.1_Nonsense_Mutation_p.Y6479*|NEB_ENST00000409198.1_Nonsense_Mutation_p.Y4778*|NEB_ENST00000397345.3_Nonsense_Mutation_p.Y6479*			P20929	NEBU_HUMAN	nebulin	4778					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)		AAACTGATCTGTACAGGCGCT	0.438																																					p.Y6479X		Atlas-SNP	.											.	NEB	1697	.	0			c.C19437A						PASS	.						140	133	135					2																	152410531		1915	4127	6042	SO:0001587	stop_gained	4703	exon126			TGATCTGTACAGG	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.14334C>A	chr2.hg19:g.152410531G>T	ENSP00000172853:p.Tyr4778*	90.0	0.0	.		74.0	4.0	.	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Nonsense_Mutation	SNP	ENST00000172853.10	hg19		.	.	.	.	.	.	.	.	.	.	G	55	24.727022	0.99962	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853	.	.	.	5.48	4.6	0.57074	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.1907	0.65637	0.0716:0.0:0.9284:0.0	.	.	.	.	X	4778;6479;6479;827;1209;4778	.	ENSP00000172853:Y4778X	Y	-	3	2	NEB	152118777	1.000000	0.71417	0.999000	0.59377	0.573000	0.36030	5.221000	0.65272	1.307000	0.44944	0.655000	0.94253	TAC	.	.	.	none		0.438	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152410531	G	T	152410531	4	4	18	1	0	0	0	0	0	1	0	0	10309	1372	48	4	6477	4	NEB	2	152410531	Nonsense_Mutation	SNP	G	TCGA-2Z-A9JO-01A-11D-A42J-10	24019631	152410531	90788842	9	1224											
ALS2CR11	151254	hgsc.bcm.edu	37	chr2	202483729	202483729	+	Frame_Shift_Del	DEL	T	T	-																															aagcctccgaccctttaatgTgcatgatatccgggctgctg																										TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr2:202483729delT	ENST00000286195.3	-	1	169	c.125delA	c.(124-126)cacfs	p.H42fs	ALS2CR11_ENST00000439140.1_Frame_Shift_Del_p.H42fs|ALS2CR11_ENST00000450242.1_Frame_Shift_Del_p.H42fs|ALS2CR11_ENST00000439802.1_Frame_Shift_Del_p.H42fs	NM_152525.5	NP_689738.3	Q53TS8	AL2SA_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11	42										NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(11)|ovary(1)|skin(5)|urinary_tract(3)	33						CCCTTTAATGTGCATGATATC	0.607																																					p.H42fs		Atlas-Indel,Pindel	.											.	ALS2CR11	194	.	0			c.126delC						PASS	.						94	90	91					2																	202483729		2203	4300	6503	SO:0001589	frameshift_variant	151254	exon1			.	AB053313	CCDS2349.1, CCDS54430.1, CCDS54428.1, CCDS54429.1	2q33	2007-12-07			ENSG00000155754	ENSG00000155754			14438	protein-coding gene	gene with protein product						11586298	Standard	NM_152525		Approved	FLJ25351	uc002uyf.3	Q53TS8	OTTHUMG00000132830	ENST00000286195.3:c.125delA	chr2.hg19:g.202483729delT	ENSP00000286195:p.His42fs	107.0	0.0	0		138.0	43.0	0.311594	NM_001168217	C9IZH7|E9PGG4|Q8NCN6|Q96LN4	Frame_Shift_Del	DEL	ENST00000286195.3	hg19	CCDS2349.1																																																																																			.	.	.	none		0.607	ALS2CR11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256296.2	NM_152525		-	202483729	T	-	202483729	7	5	18	1	0	1	0	1	0	0	0	0	552	1696	59	0	5548	0	ALS2CR11	2	202483729	Frame_Shift_Del	DEL	T	TCGA-2Z-A9JO-01A-11D-A42J-10	50073198	202483729	40715644	10	1225											
PROM1	8842	hgsc.bcm.edu	37	chr4	16002183	16002183	+	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	ccacatttgcaccaaagacaAaggtaagaaccacaatgatc	18	6	6	11	0	0	3	0	1	0	2	1	3	0	3	3	1	2	2	3	1	5	2			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr4:16002183A>T	ENST00000510224.1	-	14	1762	c.1514T>A	c.(1513-1515)tTt>tAt	p.F505Y	PROM1_ENST00000539194.1_Missense_Mutation_p.F505Y|PROM1_ENST00000508167.1_Missense_Mutation_p.F496Y|PROM1_ENST00000505450.1_Missense_Mutation_p.F496Y|PROM1_ENST00000540805.1_Missense_Mutation_p.F505Y|PROM1_ENST00000543373.1_Missense_Mutation_p.F496Y|PROM1_ENST00000447510.2_Missense_Mutation_p.F505Y			O43490	PROM1_HUMAN	prominin 1	505					camera-type eye photoreceptor cell differentiation (GO:0060219)|glomerular parietal epithelial cell differentiation (GO:0072139)|glomerular visceral epithelial cell differentiation (GO:0072112)|photoreceptor cell maintenance (GO:0045494)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|retina layer formation (GO:0010842)|retina morphogenesis in camera-type eye (GO:0060042)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actinin binding (GO:0042805)|cadherin binding (GO:0045296)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2)	35						ACCAAAGACAAAGGTAAGAAC	0.343																																					p.F505Y		Atlas-SNP	.											.	PROM1	91	.	0			c.T1514A						PASS	.						76	70	72					4																	16002183		1837	4094	5931	SO:0001583	missense	8842	exon13			AAGACAAAGGTAA	AF027208	CCDS47029.1, CCDS54746.1, CCDS54747.1, CCDS54748.1	4p15	2013-06-06	2001-11-28	2003-03-28	ENSG00000007062	ENSG00000007062		"CD molecules"	9454	protein-coding gene	gene with protein product		604365	"prominin (mouse)-like 1", "macular dystrophy, retinal 2", "Stargardt disease 4 (autosomal dominant)"	PROML1, MCDR2, STGD4		11467842	Standard	NM_006017		Approved	AC133, CD133, RP41, CORD12	uc003goo.2	O43490	OTTHUMG00000160180	ENST00000510224.1:c.1514T>A	chr4.hg19:g.16002183A>T	ENSP00000426809:p.Phe505Tyr	34.0	0.0	.		41.0	15.0	.	NM_006017	Q6SV49|Q6SV50|Q6SV51|Q6SV52|Q6SV53|Q96EN6	Missense_Mutation	SNP	ENST00000510224.1	hg19	CCDS47029.1	.	.	.	.	.	.	.	.	.	.	A	17.22	3.335153	0.60853	.	.	ENSG00000007062	ENST00000447510;ENST00000540805;ENST00000539194;ENST00000505450;ENST00000508167;ENST00000510224;ENST00000543373	T;T;T;T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.80232	0.4585	M	0.83603	2.65	0.54753	D	0.999987	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.998;1.0	D;D;D;D;D;D	0.97110	0.999;0.999;1.0;0.999;0.995;1.0	T	0.83241	-0.0058	10	0.66056	D	0.02	-26.3108	14.25	0.66013	1.0:0.0:0.0:0.0	.	496;505;496;505;496;505	O43490-5;O43490-6;O43490-4;O43490-7;O43490-2;O43490	.;.;.;.;.;PROM1_HUMAN	Y	505;505;505;496;496;505;496	ENSP00000415481:F505Y;ENSP00000438045:F505Y;ENSP00000443620:F505Y;ENSP00000426090:F496Y;ENSP00000427346:F496Y;ENSP00000426809:F505Y;ENSP00000445526:F496Y	ENSP00000415481:F505Y	F	-	2	0	PROM1	15611281	1.000000	0.71417	0.152000	0.22495	0.088000	0.18126	8.629000	0.90983	1.994000	0.58287	0.528000	0.53228	TTT	.	.	.	none		0.343	PROM1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359595.2	NM_006017		T	16002183	A	T	16002183	3	4	18	1	0	0	0	0	1	0	0	0	12565	14	1	5	1139	5	PROM1	4	16002183	Missense_Mutation	SNP	A	TCGA-2Z-A9JO-01A-11D-A42J-10		16002183	175152093	11	1226											
MANBA	4126	hgsc.bcm.edu	37	chr4	103560989	103560989	+	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	ggcggtagaattcagtttctGttttgacacactgggcctgc	7	13	12	9	1	2	2	1	1	1	1	2	2	2	2	1	3	1	3	1	3	2	5	rs142814374		TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr4:103560989G>T	ENST00000226578.4	-	14	1994	c.1895C>A	c.(1894-1896)aCa>aAa	p.T632K	MANBA_ENST00000505239.1_Missense_Mutation_p.T575K	NM_005908.3	NP_005899.3	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal	632					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)		TTCAGTTTCTGTTTTGACACA	0.463																																					p.T632K		Atlas-SNP	.											.	MANBA	78	.	0			c.C1895A						PASS	.						119	102	107					4																	103560989		2203	4300	6503	SO:0001583	missense	4126	exon14			GTTTCTGTTTTGA		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.1895C>A	chr4.hg19:g.103560989G>T	ENSP00000226578:p.Thr632Lys	87.0	0.0	.		82.0	4.0	.	NM_005908	Q96BC3|Q9NYX9	Missense_Mutation	SNP	ENST00000226578.4	hg19	CCDS3658.1	.	.	.	.	.	.	.	.	.	.	G	19.25	3.791881	0.70452	.	.	ENSG00000109323	ENST00000226578;ENST00000505239	T;T	0.55588	0.51;0.51	5.7	2.08	0.27032	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.570170	0.20271	N	0.095654	T	0.64659	0.2618	M	0.90483	3.12	0.34404	D	0.695608	D;P	0.56035	0.974;0.955	P;P	0.50537	0.556;0.643	T	0.74253	-0.3725	10	0.49607	T	0.09	-11.3782	9.088	0.36592	0.3294:0.0:0.6706:0.0	.	575;632	E9PFW2;O00462	.;MANBA_HUMAN	K	632;575	ENSP00000226578:T632K;ENSP00000427322:T575K	ENSP00000226578:T632K	T	-	2	0	MANBA	103780037	0.996000	0.38824	0.996000	0.52242	0.991000	0.79684	0.723000	0.25939	0.363000	0.24346	0.650000	0.86243	ACA	.	.	.	none		0.463	MANBA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253803.2			T	103560989	G	T	103560989	3	4	18	1	0	0	0	0	1	0	0	0	9226	1377	48	4	760	4	MANBA	4	103560989	Missense_Mutation	SNP	G	TCGA-2Z-A9JO-01A-11D-A42J-10	87558806	103560989	87593287	12	1227											
C5orf42	65250	hgsc.bcm.edu	37	chr5	37170251	37170251	+	Missense_Mutation	SNP	A	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	cccattgactgtggtttaatAaaaaatctctccttaagatt	13	15	5	8	0	1	2	0	1	1	1	3	2	2	2	2	1	0	1	2	1	5	6			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr5:37170251A>C	ENST00000508244.1	-	32	6447	c.6354T>G	c.(6352-6354)ttT>ttG	p.F2118L	C5orf42_ENST00000274258.7_Missense_Mutation_p.F998L|C5orf42_ENST00000425232.2_Missense_Mutation_p.F2118L			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2118						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)			GTGGTTTAATAAAAAATCTCT	0.438																																					p.F2118L		Atlas-SNP	.											.	C5orf42	422	.	0			c.T6354G						PASS	.						165	168	167					5																	37170251		2203	4300	6503	SO:0001583	missense	65250	exon33			TTTAATAAAAAAT		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.6354T>G	chr5.hg19:g.37170251A>C	ENSP00000421690:p.Phe2118Leu	108.0	0.0	.		132.0	41.0	.	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	hg19	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	A	12.09	1.833277	0.32421	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.21543	2.01;2.01;2.0;2.01	5.12	-6.03	0.02185	.	1.591830	0.03542	N	0.224092	T	0.12646	0.0307	L	0.38838	1.175	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.24548	-1.0157	10	0.11485	T	0.65	.	4.8926	0.13735	0.4906:0.0:0.278:0.2315	.	2118;998	E9PH94;Q9H799	.;CE042_HUMAN	L	2118;2118;998;1166;998	ENSP00000421690:F2118L;ENSP00000389014:F2118L;ENSP00000274258:F998L;ENSP00000424223:F1166L	ENSP00000274258:F998L	F	-	3	2	C5orf42	37206008	0.000000	0.05858	0.000000	0.03702	0.094000	0.18550	-1.670000	0.01956	-1.006000	0.03412	-0.375000	0.07067	TTT	.	.	.	none		0.438	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		C	37170251	A	C	37170251	3	2	18	1	0	0	0	0	1	0	0	0	2303	359	13	5	3319	5	C5orf42	5	37170251	Missense_Mutation	SNP	A	TCGA-2Z-A9JO-01A-11D-A42J-10		37170251	143745009	13	1228											
LRRC1	55227	hgsc.bcm.edu	37	chr6	53784349	53784349	+	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	gaagttgaaggctctgtggcTatctgacaaccagtcccagc	10	9	11	11	0	2	2	0	2	2	0	3	3	3	2	2	2	2	3	2	2	4	2			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr6:53784349T>A	ENST00000370888.1	+	12	1437	c.1160T>A	c.(1159-1161)cTa>cAa	p.L387Q	RP3-523E19.2_ENST00000474641.2_RNA	NM_018214.4	NP_060684.4	Q9BTT6	LRRC1_HUMAN	leucine rich repeat containing 1	387						cytoplasm (GO:0005737)|membrane (GO:0016020)				cervix(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)		GCTCTGTGGCTATCTGACAAC	0.428																																					p.L387Q		Atlas-SNP	.											.	LRRC1	59	.	0			c.T1160A						PASS	.						87	82	83					6																	53784349		1935	4146	6081	SO:0001583	missense	55227	exon12			TGTGGCTATCTGA	AF332199	CCDS4953.2	6p12.2	2014-07-30	2003-11-19		ENSG00000137269	ENSG00000137269			14307	protein-coding gene	gene with protein product		608195	"leucine-rich repeat-containing 1"				Standard	NM_018214		Approved	dJ523E19.1, LANO, FLJ10775, FLJ11834	uc003pcd.1	Q9BTT6	OTTHUMG00000014885	ENST00000370888.1:c.1160T>A	chr6.hg19:g.53784349T>A	ENSP00000359925:p.Leu387Gln	105.0	0.0	.		91.0	28.0	.	NM_018214	Q5TGN3|Q9HAC0|Q9NVF1	Missense_Mutation	SNP	ENST00000370888.1	hg19	CCDS4953.2	.	.	.	.	.	.	.	.	.	.	T	23.9	4.471168	0.84533	.	.	ENSG00000137269	ENST00000370888	D	0.91068	-2.78	5.69	5.69	0.88448	.	0.177730	0.37761	N	0.001948	D	0.96445	0.8840	H	0.95365	3.66	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.97646	1.0151	10	0.87932	D	0	.	15.135	0.72558	0.0:0.0:0.0:1.0	.	387	Q9BTT6	LRRC1_HUMAN	Q	387	ENSP00000359925:L387Q	ENSP00000359925:L387Q	L	+	2	0	LRRC1	53892308	1.000000	0.71417	0.648000	0.29521	0.953000	0.61014	7.698000	0.84413	2.163000	0.67991	0.533000	0.62120	CTA	.	.	.	none		0.428	LRRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040970.2	NM_025168		A	53784349	T	A	53784349	3	1	18	1	0	0	0	0	1	0	0	0	8973	1522	53	5	1206	5	LRRC1	6	53784349	Missense_Mutation	SNP	T	TCGA-2Z-A9JO-01A-11D-A42J-10		53784349	117330718	14	1229											
MPP6	51678	hgsc.bcm.edu	37	chr7	24690128	24690128	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgacatttagggttgaaaatAatgatctggtaattgcccga	13	13	10	5	1	1	3	0	3	1	0	1	4	1	3	1	2	1	2	1	2	5	6			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr7:24690128A>G	ENST00000222644.5	+	5	698	c.448A>G	c.(448-450)Aat>Gat	p.N150D	MPP6_ENST00000409761.1_Missense_Mutation_p.N38D|MPP6_ENST00000396475.2_Missense_Mutation_p.N150D			Q99547	MPH6_HUMAN	membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)	0					maturation of 5.8S rRNA (GO:0000460)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|skin(2)	20						GGTTGAAAATAATGATCTGGT	0.353																																					p.N150D		Atlas-SNP	.											.	MPP6	62	.	0			c.A448G						PASS	.						69	72	71					7																	24690128		2203	4300	6503	SO:0001583	missense	51678	exon6			GAAAATAATGATC	AF162130	CCDS5388.1	7p15	2007-08-01			ENSG00000105926	ENSG00000105926			18167	protein-coding gene	gene with protein product		606959				10753959, 11311936	Standard	NM_016447		Approved	PALS2, VAM-1, p55T	uc003swx.3	Q9NZW5	OTTHUMG00000023507	ENST00000222644.5:c.448A>G	chr7.hg19:g.24690128A>G	ENSP00000222644:p.Asn150Asp	77.0	0.0	.		81.0	31.0	.	NM_016447	B2RAF0	Missense_Mutation	SNP	ENST00000222644.5	hg19	CCDS5388.1	.	.	.	.	.	.	.	.	.	.	A	15.88	2.962360	0.53400	.	.	ENSG00000105926	ENST00000432190;ENST00000222644;ENST00000409761;ENST00000396475;ENST00000430180	T;T;T;T;T	0.25085	1.82;1.82;1.82;1.82;1.82	6.06	6.06	0.98353	PDZ/DHR/GLGF (4);	0.000000	0.64402	D	0.000009	T	0.14270	0.0345	N	0.04132	-0.27	0.41810	D	0.989969	B	0.09022	0.002	B	0.15484	0.013	T	0.12502	-1.0545	10	0.32370	T	0.25	.	15.1804	0.72952	1.0:0.0:0.0:0.0	.	150	Q9NZW5	MPP6_HUMAN	D	150;150;38;150;150	ENSP00000395859:N150D;ENSP00000222644:N150D;ENSP00000386262:N38D;ENSP00000379737:N150D;ENSP00000391020:N150D	ENSP00000222644:N150D	N	+	1	0	MPP6	24656653	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.920000	0.75799	2.324000	0.78689	0.533000	0.62120	AAT	.	.	.	none		0.353	MPP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250272.4			G	24690128	A	G	24690128	3	3	18	1	0	0	0	0	1	0	0	0	9745	362	13	3	462	3	MPP6	7	24690128	Missense_Mutation	SNP	A	TCGA-2Z-A9JO-01A-11D-A42J-10		24690128	134448535	15	1230											
TBRG4	9238	hgsc.bcm.edu	37	chr7	45148711	45148711	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggaaatgggtgaggtggcTgaggaagtcagagtcttatg	10	10	18	3	0	2	3	1	2	1	1	2	5	2	5	0	5	0	1	0	5	3	1			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr7:45148711T>C	ENST00000258770.3	-	2	247	c.126A>G	c.(124-126)tcA>tcG	p.S42S	TBRG4_ENST00000471142.1_5'UTR|TBRG4_ENST00000361278.3_Silent_p.S42S|TBRG4_ENST00000395655.4_Silent_p.S42S|TBRG4_ENST00000494076.1_Silent_p.S42S	NM_004749.3	NP_004740.2	Q969Z0	TBRG4_HUMAN	transforming growth factor beta regulator 4	42					cell cycle arrest (GO:0007050)|cellular respiration (GO:0045333)|positive regulation of cell proliferation (GO:0008284)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			cervix(1)|endometrium(3)|large_intestine(2)|lung(8)|skin(1)|stomach(2)	17						GTGAGGTGGCTGAGGAAGTCA	0.587																																					p.S53S		Atlas-SNP	.											.	TBRG4	52	.	0			c.A159G						PASS	.						99	90	93					7																	45148711		2203	4300	6503	SO:0001819	synonymous_variant	9238	exon2			GGTGGCTGAGGAA	AB023165	CCDS5501.1, CCDS5502.1	7p13	2006-07-07			ENSG00000136270	ENSG00000136270			17443	protein-coding gene	gene with protein product	"FAST kinase domains 4", "cell cycle progression 2 protein"	611325				9383053	Standard	NM_004749		Approved	Cpr2, KIAA0948, H_TD2522F11.8, FASTKD4	uc011kcd.3	Q969Z0	OTTHUMG00000129247	ENST00000258770.3:c.126A>G	chr7.hg19:g.45148711T>C		87.0	0.0	.		95.0	21.0	.	NM_001261834	A4D2L2|A4D2L3|D3DVL5|D3DVL6|O14710|Q53GI8|Q8NDM4|Q9BUC6|Q9Y2F6	Silent	SNP	ENST00000258770.3	hg19	CCDS5501.1																																																																																			.	.	.	none		0.587	TBRG4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251351.1	NM_030900		C	45148711	T	C	45148711	2	2	18	1	0	0	0	0	0	0	0	1	15661	1567	55	3		3	TBRG4	7	45148711	Silent	SNP	T	TCGA-2Z-A9JO-01A-11D-A42J-10	20458583	45148711	113989952	16	1231											
MTUS1	57509	hgsc.bcm.edu	37	chr8	17611702	17611702	+	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	cactgatgagggtgatgaggCactggtctgctgaggtctgg	7	10	17	7	0	2	5	0	5	2	0	2	5	2	5	0	5	1	2	0	5	0	0			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr8:17611702C>T	ENST00000262102.6	-	2	1839	c.1615G>A	c.(1615-1617)Gcc>Acc	p.A539T	MTUS1_ENST00000381862.3_Missense_Mutation_p.A539T|MTUS1_ENST00000519263.1_Missense_Mutation_p.A539T|MTUS1_ENST00000381869.3_Missense_Mutation_p.A539T	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	539					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)		GGTGATGAGGCACTGGTCTGC	0.423																																					p.A539T		Atlas-SNP	.											.	MTUS1	144	.	0			c.G1615A						PASS	.						219	211	214					8																	17611702		2079	4207	6286	SO:0001583	missense	57509	exon2			ATGAGGCACTGGT	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.1615G>A	chr8.hg19:g.17611702C>T	ENSP00000262102:p.Ala539Thr	44.0	0.0	.		60.0	26.0	.	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	hg19	CCDS43717.1	.	.	.	.	.	.	.	.	.	.	C	10.54	1.378332	0.24944	.	.	ENSG00000129422	ENST00000381869;ENST00000262102;ENST00000519263;ENST00000381862	T;T;T;T	0.35973	3.03;1.28;3.03;2.05	5.1	3.26	0.37387	.	0.753950	0.11344	N	0.573725	T	0.22666	0.0547	N	0.19112	0.55	0.09310	N	1	P;B;B	0.35872	0.525;0.102;0.102	B;B;B	0.36092	0.217;0.08;0.08	T	0.12837	-1.0532	10	0.30854	T	0.27	.	6.8492	0.24005	0.0:0.6996:0.1463:0.1542	.	539;539;539	Q9ULD2-5;Q9ULD2-2;Q9ULD2	.;.;MTUS1_HUMAN	T	539	ENSP00000371293:A539T;ENSP00000262102:A539T;ENSP00000430167:A539T;ENSP00000371286:A539T	ENSP00000262102:A539T	A	-	1	0	MTUS1	17655982	0.000000	0.05858	0.003000	0.11579	0.752000	0.42762	-0.236000	0.09003	0.824000	0.34613	0.650000	0.86243	GCC	.	.	.	none		0.423	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		T	17611702	C	T	17611702	3	4	18	1	0	0	0	0	1	0	0	0	9972	710	25	2	2572	2	MTUS1	8	17611702	Missense_Mutation	SNP	C	TCGA-2Z-A9JO-01A-11D-A42J-10		17611702	128752320	17	1232											
ANK1	286	hgsc.bcm.edu	37	chr8	41583374	41583374	+	Missense_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	gatgtgcagggccgggaggcGcaccttccccttggtgccgt	4	8	16	13	3	0	0	0	0	0	0	1	2	1	1	5	4	2	2	5	4	0	2	rs368414600		TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr8:41583374G>A	ENST00000347528.4	-	6	600	c.517C>T	c.(517-519)Cgc>Tgc	p.R173C	ANK1_ENST00000396942.1_Missense_Mutation_p.R173C|ANK1_ENST00000396945.1_Missense_Mutation_p.R173C|ANK1_ENST00000265709.8_Missense_Mutation_p.R206C|ANK1_ENST00000379758.2_Missense_Mutation_p.R173C|ANK1_ENST00000289734.7_Missense_Mutation_p.R173C|ANK1_ENST00000352337.4_Missense_Mutation_p.R173C	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	173	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)			GCCGGGAGGCGCACCTTCCCC	0.677																																					p.R206C		Atlas-SNP	.											.	ANK1	497	.	0			c.C616T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	0,4406		0,0,2203	85	54	64		517,616,517,517,517	5	1	8		64	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	ANK1	NM_000037.3,NM_001142446.1,NM_020475.2,NM_020476.2,NM_020477.2	180,180,180,180,180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	173/1881,206/1898,173/1857,173/1882,173/1720	41583374	1,13005	2203	4300	6503	SO:0001583	missense	286	exon6			GGAGGCGCACCTT	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.517C>T	chr8.hg19:g.41583374G>A	ENSP00000339620:p.Arg173Cys	81.0	0.0	.		76.0	28.0	.	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Missense_Mutation	SNP	ENST00000347528.4	hg19	CCDS6119.1	.	.	.	.	.	.	.	.	.	.	G	32	5.116615	0.94385	0.0	1.16E-4	ENSG00000029534	ENST00000347528;ENST00000289734;ENST00000379758;ENST00000396945;ENST00000396942;ENST00000352337;ENST00000265709;ENST00000358820	T;T;T;T;T;T;T	0.16073	2.37;2.37;2.37;2.37;2.37;2.37;2.37	5.84	4.96	0.65561	Ankyrin repeat-containing domain (2);	0.000000	0.85682	D	0.000000	T	0.35624	0.0938	L	0.45137	1.4	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;0.993;0.98;1.0	T	0.11567	-1.0582	10	0.72032	D	0.01	.	16.3792	0.83439	0.0:0.0:0.8671:0.1329	.	206;173;173;173;173	P16157-21;P16157-4;P16157;P16157-5;P16157-3	.;.;ANK1_HUMAN;.;.	C	173;173;173;173;173;173;206;173	ENSP00000339620:R173C;ENSP00000289734:R173C;ENSP00000369082:R173C;ENSP00000380149:R173C;ENSP00000380147:R173C;ENSP00000309131:R173C;ENSP00000265709:R206C	ENSP00000265709:R206C	R	-	1	0	ANK1	41702531	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	7.997000	0.88414	1.460000	0.47911	0.551000	0.68910	CGC	.	.	.	weak		0.677	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		A	41583374	G	A	41583374	3	1	18	1	0	0	0	0	1	0	0	0	620	1087	38	1	5630	1	ANK1	8	41583374	Missense_Mutation	SNP	G	TCGA-2Z-A9JO-01A-11D-A42J-10	23971672	41583374	104780648	18	1233											
CACNB2	783	hgsc.bcm.edu	37	chr10	18550223	18550223	+	Intron	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agtgctgcgggctggtgcatCgccggcgagtacgggtgtcc	4	8	18	11	5	0	0	0	0	0	0	2	1	1	0	2	4	4	4	2	4	1	1			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr10:18550223C>T	ENST00000324631.7	+	2	273				CACNB2_ENST00000282343.8_Intron|CACNB2_ENST00000377328.1_Intron|CACNB2_ENST00000377319.3_Missense_Mutation_p.R9C|CACNB2_ENST00000396576.2_Missense_Mutation_p.R9C|CACNB2_ENST00000377331.2_Intron|RP11-109I13.2_ENST00000457058.1_RNA|CACNB2_ENST00000352115.6_Intron	NM_201593.2|NM_201596.2	NP_963887.2|NP_963890.2	Q08289	CACB2_HUMAN	calcium channel, voltage-dependent, beta 2 subunit						axon guidance (GO:0007411)|calcium ion import (GO:0070509)|neuromuscular junction development (GO:0007528)|positive regulation of calcium ion transport (GO:0051928)|synaptic transmission (GO:0007268)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|voltage-gated calcium channel complex (GO:0005891)	calcium channel activity (GO:0005262)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|stomach(2)	31					Amlodipine(DB00381)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GCTGGTGCATCGCCGGCGAGT	0.547																																					p.R9C		Atlas-SNP	.											.	CACNB2	220	.	0			c.C25T						PASS	.						129	117	121					10																	18550223		1994	3661	5655	SO:0001627	intron_variant	783	exon1			GTGCATCGCCGGC	U95019	CCDS7125.1, CCDS7126.1, CCDS7127.1, CCDS7128.1, CCDS7129.1, CCDS41493.1, CCDS41494.1	10p12	2014-09-17			ENSG00000165995	ENSG00000165995		"Calcium channel subunits"	1402	protein-coding gene	gene with protein product		600003		MYSB, CACNLB2		9254841, 8494331	Standard	NM_201596		Approved		uc001ipr.2	Q08289	OTTHUMG00000017764	ENST00000324631.7:c.213+110319C>T	chr10.hg19:g.18550223C>T		84.0	0.0	.		56.0	13.0	.	NM_000724	A6PVM5|A6PVM7|A6PVM8|O00304|Q5QJ99|Q5QJA0|Q5VVG9|Q5VVH0|Q5VWV6|Q6TME1|Q6TME2|Q6TME3|Q8WX81|Q96NZ3|Q96NZ4|Q96NZ5|Q9BWU2|Q9HD32|Q9Y340|Q9Y341	Missense_Mutation	SNP	ENST00000324631.7	hg19	CCDS7125.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344707	0.61073	.	.	ENSG00000165995	ENST00000396576;ENST00000377319	D;D	0.83591	-1.74;-1.73	5.29	5.29	0.74685	.	.	.	.	.	D	0.88544	0.6465	L	0.43152	1.355	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.973;0.988	D	0.89081	0.3476	9	0.72032	D	0.01	.	19.1238	0.93374	0.0:1.0:0.0:0.0	.	20;9	Q59H42;Q08289-6	.;.	C	9	ENSP00000379821:R9C;ENSP00000366536:R9C	ENSP00000366536:R9C	R	+	1	0	CACNB2	18590229	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.481000	0.66826	2.752000	0.94435	0.557000	0.71058	CGC	.	.	.	none		0.547	CACNB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047072.2	NM_000724		T	18550223	C	T	18550223	1	4	18	0	1	0	0	0	0	0	0	0	2555	884	31	1		1	CACNB2	10	18550223	Intron	SNP	C	TCGA-2Z-A9JO-01A-11D-A42J-10		18550223	116984524	19	1234											
C10orf118	55088	hgsc.bcm.edu	37	chr10	115922396	115922396	+	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	taaaggtataaaaaacttacTtttttatgatatgttcctgc	14	17	5	5	0	0	1	0	1	0	0	1	1	1	1	1	1	3	2	1	1	9	9			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr10:115922396T>C	ENST00000369287.3	-	2	898	c.632A>G	c.(631-633)aAg>aGg	p.K211R	C10orf118_ENST00000369286.1_Missense_Mutation_p.K211R|C10orf118_ENST00000369285.3_Missense_Mutation_p.K211R	NM_018017.2	NP_060487.2	Q7Z3E2	CC186_HUMAN		211										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)		AAAAACTTACTTTTTTATGAT	0.313																																					p.K211R		Atlas-SNP	.											.	C10orf118	70	.	0			c.A632G						PASS	.						27	27	27					10																	115922396		2200	4298	6498	SO:0001630	splice_region_variant	55088	exon2			ACTTACTTTTTTA																												ENST00000369287.3:c.632+1A>G	chr10.hg19:g.115922396T>C		67.0	0.0	.		67.0	25.0	.	NM_018017	Q2M2V6|Q3ZB81|Q6NS91|Q7RTP1|Q8N117|Q8N3G3|Q8N6C2|Q9NWA3	Missense_Mutation	SNP	ENST00000369287.3	hg19	CCDS7587.1	.	.	.	.	.	.	.	.	.	.	T	11.50	1.656651	0.29425	.	.	ENSG00000165813	ENST00000369287;ENST00000430353;ENST00000369286;ENST00000369285	T;T;T	0.33216	1.42;1.42;1.42	5.48	1.79	0.24919	.	0.377613	0.32624	N	0.005859	T	0.16342	0.0393	N	0.22421	0.69	0.80722	D	1	B	0.02656	0.0	B	0.08055	0.003	T	0.08848	-1.0702	10	0.30078	T	0.28	.	5.0037	0.14277	0.1337:0.146:0.0:0.7202	.	211	Q7Z3E2	CJ118_HUMAN	R	211;317;211;211	ENSP00000358293:K211R;ENSP00000358292:K211R;ENSP00000358291:K211R	ENSP00000358291:K211R	K	-	2	0	C10orf118	115912386	1.000000	0.71417	0.999000	0.59377	0.879000	0.50718	1.291000	0.33330	0.053000	0.16036	-0.343000	0.07986	AAG	.	.	.	none		0.313	C10orf118-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050455.1		Missense_Mutation	C	115922396	T	C	115922396	5	2	18	1	0	0	0	0	0	0	1	0	1589	1623	56	3	2124	3	C10orf118	10	115922396	Splice_Site	SNP	T	TCGA-2Z-A9JO-01A-11D-A42J-10	97372173	115922396	19612351	20	1235											
FAM160A2	84067	hgsc.bcm.edu	37	chr11	6236092	6236092	+	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	aggaagttgacatagacggaGttctgcagcatgttctcgag	11	10	13	7	2	2	2	0	1	2	1	3	5	2	4	0	2	2	5	0	2	2	4			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr11:6236092G>A	ENST00000449352.2	-	10	2528	c.2265C>T	c.(2263-2265)aaC>aaT	p.N755N	FAM160A2_ENST00000265978.4_Silent_p.N769N|FAM160A2_ENST00000529360.1_5'UTR			Q8N612	F16A2_HUMAN	family with sequence similarity 160, member A2	755					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						CATAGACGGAGTTCTGCAGCA	0.587																																					p.N769N		Atlas-SNP	.											.	FAM160A2	100	.	0			c.C2307T						PASS	.						56	45	49					11																	6236092		2201	4296	6497	SO:0001819	synonymous_variant	84067	exon10			GACGGAGTTCTGC		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.2265C>T	chr11.hg19:g.6236092G>A		59.0	0.0	.		44.0	14.0	.	NM_032127	Q9C0A4|Q9H0N3|Q9H624	Silent	SNP	ENST00000449352.2	hg19	CCDS44530.1																																																																																			.	.	.	none		0.587	FAM160A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383759.1	NM_032127		A	6236092	G	A	6236092	2	1	18	1	0	0	0	0	0	0	0	1	5473	1020	36	2		2	FAM160A2	11	6236092	Silent	SNP	G	TCGA-2Z-A9JO-01A-11D-A42J-10		6236092	128770424	21	1236											
NPAT	4863	hgsc.bcm.edu	37	chr11	108043763	108043763	+	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	agacttggatgcctgagcttCattttctgtatgatttaact	9	17	8	7	0	2	3	1	2	1	1	2	4	2	4	1	1	3	2	1	1	2	7			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr11:108043763C>T	ENST00000278612.8	-	13	2053	c.1948G>A	c.(1948-1950)Gaa>Aaa	p.E650K	NPAT_ENST00000610253.1_5'UTR	NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	650	Required for acceleration of G1 phase.				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)		GCCTGAGCTTCATTTTCTGTA	0.368																																					p.E650K		Atlas-SNP	.											.	NPAT	124	.	0			c.G1948A						PASS	.						53	50	51					11																	108043763		1833	4078	5911	SO:0001583	missense	4863	exon13			GAGCTTCATTTTC	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.1948G>A	chr11.hg19:g.108043763C>T	ENSP00000278612:p.Glu650Lys	53.0	0.0	.		55.0	15.0	.	NM_002519	A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	Missense_Mutation	SNP	ENST00000278612.8	hg19	CCDS41710.1	.	.	.	.	.	.	.	.	.	.	C	7.695	0.691773	0.15039	.	.	ENSG00000149308	ENST00000278612	T	0.04083	3.71	6.08	3.87	0.44632	.	0.657735	0.15963	N	0.236168	T	0.02929	0.0087	N	0.19112	0.55	0.09310	N	1	B;B	0.17268	0.021;0.01	B;B	0.18561	0.022;0.009	T	0.46091	-0.9216	10	0.08179	T	0.78	-15.3657	6.6244	0.22820	0.1802:0.6533:0.0:0.1665	.	650;650	B9EG70;Q14207	.;NPAT_HUMAN	K	650	ENSP00000278612:E650K	ENSP00000278612:E650K	E	-	1	0	NPAT	107548973	0.118000	0.22208	0.385000	0.26158	0.799000	0.45148	0.125000	0.15749	1.555000	0.49500	0.655000	0.94253	GAA	.	.	.	none		0.368	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389506.2	NM_002519		T	108043763	C	T	108043763	3	4	18	1	0	0	0	0	1	0	0	0	10573	835	29	2	2359	2	NPAT	11	108043763	Missense_Mutation	SNP	C	TCGA-2Z-A9JO-01A-11D-A42J-10	101807671	108043763	26962753	22	1237											
FAM113B	91523	hgsc.bcm.edu	37	chr12	47629401	47629401	+	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	cccaagctccggcggcagaaGgccaccttcctgaaaaacga	12	4	10	15	3	0	2	0	1	0	1	2	3	2	2	5	3	2	2	5	3	4	1			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr12:47629401G>T	ENST00000546455.1	+	4	1286	c.555G>T	c.(553-555)aaG>aaT	p.K185N	RP11-493L12.3_ENST00000547748.1_RNA|PCED1B_ENST00000432328.1_Missense_Mutation_p.K185N			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B	185							hydrolase activity (GO:0016787)										GGCGGCAGAAGGCCACCTTCC	0.577																																					p.K185N		Atlas-SNP	.											.	.	.	.	0			c.G555T						PASS	.						32	27	29					12																	47629401		2203	4300	6503	SO:0001583	missense	91523	exon2			GCAGAAGGCCACC	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.555G>T	chr12.hg19:g.47629401G>T	ENSP00000446688:p.Lys185Asn	29.0	0.0	.		45.0	17.0	.	NM_138371	Q96B20	Missense_Mutation	SNP	ENST00000546455.1	hg19	CCDS8752.1	.	.	.	.	.	.	.	.	.	.	G	0.690	-0.794903	0.02862	.	.	ENSG00000179715	ENST00000546455;ENST00000432328;ENST00000548348;ENST00000330951	T;T;T	0.17054	2.3;2.3;2.3	0.427	-0.581	0.11713	Esterase, SGNH hydrolase-type (1);Esterase, SGNH hydrolase-type, subgroup (1);	4.839840	0.00674	N	0.000658	T	0.10035	0.0246	N	0.08118	0	0.09310	N	1	B	0.31503	0.326	B	0.36845	0.234	T	0.14811	-1.0459	9	0.23891	T	0.37	12.6003	.	.	.	.	185	Q96HM7	F113B_HUMAN	N	185;185;65;65	ENSP00000446688:K185N;ENSP00000396040:K185N;ENSP00000448693:K65N	ENSP00000328560:K65N	K	+	3	2	FAM113B	45915668	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.398000	0.02509	-0.370000	0.08016	-0.363000	0.07495	AAG	.	.	.	none		0.577	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371		T	47629401	G	T	47629401	3	4	18	1	0	0	0	0	1	0	0	0	5406	991	35	4	557	4	FAM113B	12	47629401	Missense_Mutation	SNP	G	TCGA-2Z-A9JO-01A-11D-A42J-10		47629401	86222494	23	1238											
EEA1	8411	hgsc.bcm.edu	37	chr12	93171433	93171433	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctatttcaccttctcctttAagacatctggaatagattgc	10	16	5	10	0	4	2	1	0	3	2	5	3	4	3	2	1	1	0	2	1	4	7			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr12:93171433A>G	ENST00000322349.8	-	27	4164	c.3900T>C	c.(3898-3900)ctT>ctC	p.L1300L		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	1300					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						CTTCTCCTTTAAGACATCTGG	0.333																																					p.L1300L		Atlas-SNP	.											.	EEA1	104	.	0			c.T3900C						PASS	.						82	70	74					12																	93171433		2203	4300	6503	SO:0001819	synonymous_variant	8411	exon27			TCCTTTAAGACAT	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.3900T>C	chr12.hg19:g.93171433A>G		58.0	0.0	.		69.0	17.0	.	NM_003566	Q14221	Silent	SNP	ENST00000322349.8	hg19	CCDS31874.1																																																																																			.	.	.	none		0.333	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566		G	93171433	A	G	93171433	2	3	18	1	0	0	0	0	0	0	0	1	4923	349	13	3		3	EEA1	12	93171433	Silent	SNP	A	TCGA-2Z-A9JO-01A-11D-A42J-10	45542032	93171433	40680462	24	1239											
PPP2R5E	5529	hgsc.bcm.edu	37	chr14	63842804	63842804	+	Missense_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	ttttttccacaattcttcacGctccttttctttctttttct	4	24	1	12	1	5	0	1	0	4	0	7	0	7	0	2	0	0	1	2	0	1	10			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr14:63842804G>A	ENST00000337537.3	-	14	1929	c.1327C>T	c.(1327-1329)Cgt>Tgt	p.R443C	PPP2R5E_ENST00000422769.2_Missense_Mutation_p.R367C|PPP2R5E_ENST00000555899.1_Missense_Mutation_p.R438C	NM_001282179.1|NM_001282180.1|NM_001282181.1|NM_001282182.1|NM_006246.2	NP_001269108.1|NP_001269109.1|NP_001269110.1|NP_001269111.1|NP_006237.1	Q16537	2A5E_HUMAN	protein phosphatase 2, regulatory subunit B', epsilon isoform	443					regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)	15				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)		AATTCTTCACGCTCCTTTTCT	0.328																																					p.R443C		Atlas-SNP	.											.	PPP2R5E	43	.	0			c.C1327T						PASS	.						166	145	152					14																	63842804		2203	4298	6501	SO:0001583	missense	5529	exon14			CTTCACGCTCCTT	L76703	CCDS9758.1, CCDS61467.1, CCDS61468.1	14q23.2	2010-06-18	2007-01-22		ENSG00000154001	ENSG00000154001		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9313	protein-coding gene	gene with protein product		601647	"protein phosphatase 2, regulatory subunit B (B56), epsilon isoform"			7592815	Standard	NM_006246		Approved		uc001xgd.1	Q16537	OTTHUMG00000140341	ENST00000337537.3:c.1327C>T	chr14.hg19:g.63842804G>A	ENSP00000337641:p.Arg443Cys	55.0	0.0	.		45.0	13.0	.	NM_006246	A4FU37|B7ZAW5|B7ZKK8|B7ZKK9|J3KQN6|Q52LW4	Missense_Mutation	SNP	ENST00000337537.3	hg19	CCDS9758.1	.	.	.	.	.	.	.	.	.	.	G	14.03	2.413814	0.42817	.	.	ENSG00000154001	ENST00000337537;ENST00000555899;ENST00000422769	.	.	.	5.86	5.86	0.93980	Armadillo-type fold (1);	0.111045	0.56097	D	0.000022	D	0.84633	0.5515	M	0.90019	3.08	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.994	D	0.87143	0.2204	9	0.87932	D	0	-5.744	14.9745	0.71261	0.0:0.0:0.8574:0.1426	.	438;443	B7ZKK9;Q16537	.;2A5E_HUMAN	C	443;438;367	.	ENSP00000337641:R443C	R	-	1	0	PPP2R5E	62912557	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	4.260000	0.58835	2.776000	0.95493	0.650000	0.86243	CGT	.	.	.	none		0.328	PPP2R5E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276973.1	NM_006246		A	63842804	G	A	63842804	3	1	18	1	0	0	0	0	1	0	0	0	12406	1087	38	1	80	1	PPP2R5E	14	63842804	Missense_Mutation	SNP	G	TCGA-2Z-A9JO-01A-11D-A42J-10		63842804	43506736	25	1240											
RCCD1	91433	hgsc.bcm.edu	37	chr15	91500569	91500569	+	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	ccggccggtgaggcccaggcTgggaggctacccctgctgcc	4	5	16	16	2	0	1	0	1	0	0	0	2	0	2	6	6	3	3	6	6	1	1			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr15:91500569T>A	ENST00000394258.2	+	3	595	c.393T>A	c.(391-393)gcT>gcA	p.A131A	RCCD1_ENST00000556774.1_Intron|RCCD1_ENST00000556618.1_Silent_p.A131A|AC068831.6_ENST00000553321.1_RNA|RCCD1_ENST00000555155.1_Silent_p.A131A	NM_001017919.1|NM_033544.2	NP_001017919.1|NP_291022.2	A6NED2	RCCD1_HUMAN	RCC1 domain containing 1	131						cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|kidney(1)|large_intestine(2)	4	Lung NSC(78;0.0987)|all_lung(78;0.175)		Lung(145;0.189)			AGGCCCAGGCTGGGAGGCTAC	0.731																																					p.A131A		Atlas-SNP	.											.	RCCD1	9	.	0			c.T393A						PASS	.						10	9	10					15																	91500569		1982	3924	5906	SO:0001819	synonymous_variant	91433	exon3			CCAGGCTGGGAGG		CCDS32333.1	15q26.1	2005-10-21	2005-10-21			ENSG00000166965			30457	protein-coding gene	gene with protein product						12477932	Standard	XM_006720763		Approved	MGC14386	uc002bqk.3	A6NED2		ENST00000394258.2:c.393T>A	chr15.hg19:g.91500569T>A		58.0	0.0	.		63.0	22.0	.	NM_001017919	B2RTP9|Q29RX6	Silent	SNP	ENST00000394258.2	hg19	CCDS32333.1																																																																																			.	.	.	none		0.731	RCCD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414748.1	NM_033544		A	91500569	T	A	91500569	2	1	18	1	0	0	0	0	0	0	0	1	13188	1567	55	5		5	RCCD1	15	91500569	Silent	SNP	T	TCGA-2Z-A9JO-01A-11D-A42J-10		91500569	11030823	26	1241											
PDILT	204474	hgsc.bcm.edu	37	chr16	20371931	20371931	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agttttgatgtggctttccaGgaagtcagagaagcccttca	10	12	11	8	0	2	2	2	1	0	1	3	4	3	3	2	2	1	2	2	2	2	4			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr16:20371931G>A	ENST00000302451.4	-	11	1713	c.1465C>T	c.(1465-1467)Ctg>Ttg	p.L489L		NM_174924.1	NP_777584.1	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis expressed	489					cell migration (GO:0016477)|cell redox homeostasis (GO:0045454)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|spermatid development (GO:0007286)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(33)|prostate(3)|skin(1)|urinary_tract(1)	61						TGGCTTTCCAGGAAGTCAGAG	0.473																																					p.L489L		Atlas-SNP	.											.	PDILT	120	.	0			c.C1465T						PASS	.						218	198	205					16																	20371931		2203	4300	6503	SO:0001819	synonymous_variant	204474	exon11			TTTCCAGGAAGTC		CCDS10584.1	16p12.3	2011-11-10	2009-02-23		ENSG00000169340	ENSG00000169340		"Protein disulfide isomerases"	27338	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 7", "protein disulfide isomerase-like protein of the testis"					15475357	Standard	NM_174924		Approved	PDIA7	uc002dhc.1	Q8N807	OTTHUMG00000131487	ENST00000302451.4:c.1465C>T	chr16.hg19:g.20371931G>A		84.0	0.0	.		81.0	17.0	.	NM_174924	Q8IVQ5	Silent	SNP	ENST00000302451.4	hg19	CCDS10584.1																																																																																			.	.	.	none		0.473	PDILT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254332.1	NM_174924		A	20371931	G	A	20371931	2	1	18	1	0	0	0	0	0	0	0	1	11681	991	35	2		2	PDILT	16	20371931	Silent	SNP	G	TCGA-2Z-A9JO-01A-11D-A42J-10		20371931	69982822	27	1242											
TK2	7084	hgsc.bcm.edu	37	chr16	66547633	66547633	+	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	ctgtaagggagtcttacttaCcagaacaggggctgccatgg	10	9	13	9	0	1	1	0	0	1	1	1	2	1	2	2	4	4	2	2	4	4	3			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr16:66547633C>G	ENST00000451102.2	-	9	1050		c.e9+1		TK2_ENST00000563369.2_Splice_Site|TK2_ENST00000568170.1_5'Flank|TK2_ENST00000527284.1_Splice_Site|TK2_ENST00000299697.7_Splice_Site|TK2_ENST00000544898.1_Splice_Site|TK2_ENST00000525974.1_Splice_Site|TK2_ENST00000417693.3_Splice_Site|RP11-403P17.5_ENST00000561728.1_Splice_Site|TK2_ENST00000545043.2_Splice_Site|TK2_ENST00000564917.1_Splice_Site|TK2_ENST00000527800.1_Splice_Site			O00142	KITM_HUMAN	thymidine kinase 2, mitochondrial						deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|DNA replication (GO:0006260)|nucleobase-containing compound metabolic process (GO:0006139)|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)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|thymidine kinase activity (GO:0004797)			large_intestine(1)|lung(2)|urinary_tract(1)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0736)|Epithelial(162;0.237)		GTCTTACTTACCAGAACAGGG	0.537																																					.		Atlas-SNP	.											.	TK2	17	.	0			c.408+1G>C						PASS	.						70	61	64					16																	66547633		2201	4300	6501	SO:0001630	splice_region_variant	7084	exon10			TACTTACCAGAAC		CCDS10805.1, CCDS10805.2, CCDS54016.1, CCDS54017.1, CCDS54018.1, CCDS61955.1	16q22-q23.1	2012-10-02			ENSG00000166548	ENSG00000166548	2.7.1.21		11831	protein-coding gene	gene with protein product		188250					Standard	NM_004614		Approved		uc002eos.3	O00142	OTTHUMG00000137499	ENST00000451102.2:c.699+1G>C	chr16.hg19:g.66547633C>G		57.0	0.0	.		56.0	19.0	.	NM_001272050	B4DGJ7|B4DZK7|B7ZAB1|E9PH08|O15238	Splice_Site	SNP	ENST00000451102.2	hg19	CCDS10805.2	.	.	.	.	.	.	.	.	.	.	C	19.00	3.741035	0.69304	.	.	ENSG00000166548	ENST00000299697;ENST00000417693;ENST00000545043;ENST00000451102;ENST00000527800;ENST00000527284;ENST00000544898;ENST00000525974	.	.	.	4.89	4.89	0.63831	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6218	0.76813	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TK2	65105134	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	5.457000	0.66672	2.543000	0.85770	0.650000	0.86243	.	.	.	.	none		0.537	TK2-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268806.4		Intron	G	66547633	C	G	66547633	5	3	18	1	0	0	0	0	0	0	1	0	15945	521	18	4	105	4	TK2	16	66547633	Splice_Site	SNP	C	TCGA-2Z-A9JO-01A-11D-A42J-10	46175702	66547633	23807120	28	1243											
TMCO7	79613	hgsc.bcm.edu	37	chr16	69117519	69117519	+	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	gacatcatgaaaaacttcctGttccctccacagaagctgga	13	9	7	12	0	1	2	1	1	0	1	4	4	4	3	3	1	2	2	3	1	3	2	rs376805485		TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr16:69117519G>A	ENST00000261778.1	+	18	3252	c.3240G>A	c.(3238-3240)ctG>ctA	p.L1080L	TANGO6_ENST00000561931.1_3'UTR	NM_024562.1	NP_078838.1	Q9C0B7	TNG6_HUMAN	transport and golgi organization 6 homolog (Drosophila)	1080						integral component of membrane (GO:0016021)											AAAACTTCCTGTTCCCTCCAC	0.587																																					p.L1080L		Atlas-SNP	.											.	.	.	.	0			c.G3240A						PASS	.						44	46	45					16																	69117519		2029	4182	6211	SO:0001819	synonymous_variant	79613	exon18			CTTCCTGTTCCCT		CCDS45516.1	16q22.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000103047	ENSG00000103047			25749	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 7"	TMCO7		11214970	Standard	NM_024562		Approved	FLJ12688, KIAA1746	uc002ewi.4	Q9C0B7	OTTHUMG00000176743	ENST00000261778.1:c.3240G>A	chr16.hg19:g.69117519G>A		84.0	0.0	.		69.0	4.0	.	NM_024562	Q569F9|Q9H9K1	Silent	SNP	ENST00000261778.1	hg19	CCDS45516.1																																																																																			.	.	.	alt		0.587	TANGO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433471.2	XM_928235.2		A	69117519	G	A	69117519	2	1	18	1	0	0	0	0	0	0	0	1	16013	1364	48	2		2	TMCO7	16	69117519	Silent	SNP	G	TCGA-2Z-A9JO-01A-11D-A42J-10	2569886	69117519	21237234	29	1244											
SUPT6H	6830	hgsc.bcm.edu	37	chr17	27005195	27005195	+	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	gaggccctgggcttcatgcgAaatcagcattttgaggtaac	10	10	12	9	1	2	1	2	1	0	0	2	3	2	1	1	3	3	3	1	3	2	4			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr17:27005195A>C	ENST00000314616.6	+	9	1384	c.1101A>C	c.(1099-1101)cgA>cgC	p.R367R	SUPT6H_ENST00000347486.4_Silent_p.R367R	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	367	Interaction with IWS1. {ECO:0000250}.|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)					GCTTCATGCGAAATCAGCATT	0.493																																					p.R367R		Atlas-SNP	.											.	SUPT6H	165	.	0			c.A1101C						PASS	.						68	67	67					17																	27005195		2203	4300	6503	SO:0001819	synonymous_variant	6830	exon9			CATGCGAAATCAG	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.1101A>C	chr17.hg19:g.27005195A>C		85.0	0.0	.		112.0	35.0	.	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Silent	SNP	ENST00000314616.6	hg19	CCDS32596.1																																																																																			.	.	.	none		0.493	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		C	27005195	A	C	27005195	2	2	18	1	0	0	0	0	0	0	0	1	15412	233	9	5		5	SUPT6H	17	27005195	Silent	SNP	A	TCGA-2Z-A9JO-01A-11D-A42J-10		27005195	54190015	30	1245											
AKAP1	8165	hgsc.bcm.edu	37	chr17	55183561	55183561	+	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	tagagggggaagaagataagGggaagagcagctcatcccag	15	4	16	6	0	1	4	1	0	0	4	2	6	2	6	1	4	2	2	1	4	5	2	rs145117487		TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr17:55183561G>C	ENST00000337714.3	+	2	969	c.736G>C	c.(736-738)Ggg>Cgg	p.G246R	AKAP1_ENST00000539273.1_Missense_Mutation_p.G246R|AKAP1_ENST00000314126.3_Missense_Mutation_p.G246R|AKAP1_ENST00000571629.1_Missense_Mutation_p.G246R|AKAP1_ENST00000572557.1_Missense_Mutation_p.G246R	NM_003488.3	NP_003479.1	Q92667	AKAP1_HUMAN	A kinase (PRKA) anchor protein 1	246					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)					AGAAGATAAGGGGAAGAGCAG	0.542																																					p.G246R		Atlas-SNP	.											.	AKAP1	73	.	0			c.G736C						PASS	.						104	111	109					17																	55183561		2203	4300	6503	SO:0001583	missense	8165	exon3			GATAAGGGGAAGA	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.736G>C	chr17.hg19:g.55183561G>C	ENSP00000337736:p.Gly246Arg	104.0	0.0	.		98.0	30.0	.	NM_001242902	A8K8Q1|D3DTZ0|Q13320|Q9BW14	Missense_Mutation	SNP	ENST00000337714.3	hg19	CCDS11594.1	.	.	.	.	.	.	.	.	.	.	G	11.34	1.609976	0.28712	.	.	ENSG00000121057	ENST00000337714;ENST00000314126;ENST00000427138;ENST00000539273	T;T;T	0.18016	2.5;2.24;2.5	6.05	3.76	0.43208	.	0.785841	0.12432	N	0.469465	T	0.16128	0.0388	L	0.60455	1.87	0.09310	N	1	B	0.15473	0.013	B	0.10450	0.005	T	0.20240	-1.0281	10	0.51188	T	0.08	-8.8734	3.4974	0.07659	0.1622:0.1351:0.5635:0.1392	.	246	Q92667	AKAP1_HUMAN	R	246;246;288;246	ENSP00000337736:G246R;ENSP00000314075:G246R;ENSP00000443139:G246R	ENSP00000314075:G246R	G	+	1	0	AKAP1	52538560	0.001000	0.12720	0.006000	0.13384	0.048000	0.14542	0.325000	0.19628	1.575000	0.49775	0.655000	0.94253	GGG	.	G|1.000;A|0.000	.	alt		0.542	AKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277069.1			C	55183561	G	C	55183561	3	2	18	1	0	0	0	0	1	0	0	0	445	1232	43	4	738	4	AKAP1	17	55183561	Missense_Mutation	SNP	G	TCGA-2Z-A9JO-01A-11D-A42J-10	28178366	55183561	26011649	31	1246											
SOX9	6662	hgsc.bcm.edu	37	chr17	70117912	70117912	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caggaagctcgcggaccagtAcccgcacttgcacaacgccg	10	4	11	16	5	0	0	0	0	0	0	1	2	0	2	3	2	4	4	3	2	3	2			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr17:70117912A>G	ENST00000245479.2	+	1	752	c.380A>G	c.(379-381)tAc>tGc	p.Y127C		NM_000346.3	NP_000337.1	P48436	SOX9_HUMAN	SRY (sex determining region Y)-box 9	127					astrocyte fate commitment (GO:0060018)|branching involved in ureteric bud morphogenesis (GO:0001658)|cAMP-mediated signaling (GO:0019933)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cell fate specification (GO:0001708)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to heparin (GO:0071504)|cellular response to interleukin-1 (GO:0071347)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|chondrocyte hypertrophy (GO:0003415)|chromatin remodeling (GO:0006338)|cochlea morphogenesis (GO:0090103)|cytoskeleton organization (GO:0007010)|endocardial cushion morphogenesis (GO:0003203)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation involved in prostatic bud elongation (GO:0060517)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|heart valve development (GO:0003170)|heart valve formation (GO:0003188)|heart valve morphogenesis (GO:0003179)|intestinal epithelial structure maintenance (GO:0060729)|intrahepatic bile duct development (GO:0035622)|limb bud formation (GO:0060174)|lung epithelial cell differentiation (GO:0060487)|male germ-line sex determination (GO:0019100)|male gonad development (GO:0008584)|mammary gland development (GO:0030879)|metanephric nephron tubule formation (GO:0072289)|morphogenesis of a branching epithelium (GO:0061138)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biomineral tissue development (GO:0070168)|negative regulation of bone mineralization (GO:0030502)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune system process (GO:0002683)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of ossification (GO:0030279)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|notochord development (GO:0030903)|nucleosome assembly (GO:0006334)|oligodendrocyte differentiation (GO:0048709)|ossification (GO:0001503)|otic vesicle formation (GO:0030916)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of extracellular matrix assembly (GO:1901203)|positive regulation of kidney development (GO:0090184)|positive regulation of male gonad development (GO:2000020)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein complex assembly (GO:0006461)|protein kinase B signaling (GO:0043491)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in lung morphogenesis (GO:0061046)|regulation of cell adhesion (GO:0030155)|regulation of cell cycle process (GO:0010564)|regulation of cell proliferation (GO:0042127)|regulation of cell proliferation involved in tissue homeostasis (GO:0060784)|regulation of epithelial cell proliferation involved in lung morphogenesis (GO:2000794)|renal vesicle induction (GO:0072034)|retina development in camera-type eye (GO:0060041)|retinal rod cell differentiation (GO:0060221)|Sertoli cell development (GO:0060009)|Sertoli cell differentiation (GO:0060008)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spermatogenesis (GO:0007283)|tissue homeostasis (GO:0001894)|transcription from RNA polymerase II promoter (GO:0006366)|ureter morphogenesis (GO:0072197)|ureter smooth muscle cell differentiation (GO:0072193)|ureter urothelium development (GO:0072190)	nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enhancer binding (GO:0035326)|enhancer sequence-specific DNA binding (GO:0001158)|pre-mRNA intronic binding (GO:0097157)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase activity (GO:0004672)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(5)|pancreas(1)|upper_aerodigestive_tract(2)	26		Colorectal(1115;0.245)	STAD - Stomach adenocarcinoma(260;0.119)			GCGGACCAGTACCCGCACTTG	0.701																																					p.Y127C	Pancreas(42;83 1041 2320 35205 39456)	Atlas-SNP	.											.	SOX9	91	.	0			c.A380G						PASS	.						21	18	19					17																	70117912		2200	4297	6497	SO:0001583	missense	6662	exon1			ACCAGTACCCGCA	S74506	CCDS11689.1	17q24.3	2013-10-17	2008-07-31		ENSG00000125398	ENSG00000125398		"SRY (sex determining region Y)-boxes"	11204	protein-coding gene	gene with protein product		608160	"campomelic dysplasia, autosomal sex-reversal"	CMD1, CMPD1		8348155	Standard	NM_000346		Approved	SRA1	uc002jiw.3	P48436	OTTHUMG00000166300	ENST00000245479.2:c.380A>G	chr17.hg19:g.70117912A>G	ENSP00000245479:p.Tyr127Cys	242.0	0.0	.		168.0	59.0	.	NM_000346	Q53Y80	Missense_Mutation	SNP	ENST00000245479.2	hg19	CCDS11689.1	.	.	.	.	.	.	.	.	.	.	A	19.61	3.859113	0.71834	.	.	ENSG00000125398	ENST00000245479;ENST00000455872	D	0.97870	-4.58	3.97	2.89	0.33648	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.000000	0.85682	U	0.000000	D	0.96546	0.8873	N	0.21545	0.675	0.80722	D	1	D	0.69078	0.997	D	0.66847	0.947	D	0.95255	0.8363	10	0.87932	D	0	.	8.8963	0.35467	0.9088:0.0:0.0912:0.0	.	127	P48436	SOX9_HUMAN	C	127	ENSP00000245479:Y127C	ENSP00000245479:Y127C	Y	+	2	0	SOX9	67629507	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.049000	0.93837	0.430000	0.26230	0.358000	0.22013	TAC	.	.	.	none		0.701	SOX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389032.1	NM_000346		G	70117912	A	G	70117912	3	3	18	1	0	0	0	0	1	0	0	0	14971	391	14	3	382	3	SOX9	17	70117912	Missense_Mutation	SNP	A	TCGA-2Z-A9JO-01A-11D-A42J-10	14934351	70117912	11077298	32	1247											
FXYD1	5348	hgsc.bcm.edu	37	chr19	35631004	35631004	+	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	atggcgtctcttggccacatCttggttttctgtgtgggtct	3	17	12	9	1	4	0	0	0	4	0	5	0	4	0	1	4	0	1	1	4	0	4			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr19:35631004C>G	ENST00000588081.1	+	1	79	c.21C>G	c.(19-21)atC>atG	p.I7M	FXYD1_ENST00000455515.2_Missense_Mutation_p.I7M|FXYD1_ENST00000588715.1_Missense_Mutation_p.I7M|LGI4_ENST00000493050.1_Intron|CTD-2527I21.4_ENST00000592174.1_RNA|FXYD1_ENST00000351325.4_Missense_Mutation_p.I7M|FXYD1_ENST00000589209.1_Missense_Mutation_p.I7M|FXYD1_ENST00000588607.1_Missense_Mutation_p.I7M			O00168	PLM_HUMAN	FXYD domain containing ion transport regulator 1	7					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|positive regulation of sodium ion export from cell (GO:1903278)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of heart contraction (GO:0008016)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)	chloride channel activity (GO:0005254)|ion channel binding (GO:0044325)|sodium channel regulator activity (GO:0017080)			lung(3)	3	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;2.32e-21)|OV - Ovarian serous cystadenocarcinoma(14;3.17e-20)|all cancers(14;2.43e-18)|LUSC - Lung squamous cell carcinoma(66;0.0849)			TTGGCCACATCTTGGTTTTCT	0.622																																					p.I7M		Atlas-SNP	.											.	FXYD1	6	.	0			c.C21G						PASS	.						161	115	131					19																	35631004		2203	4300	6503	SO:0001583	missense	5348	exon2			CCACATCTTGGTT		CCDS12445.1	19q13.1	2008-08-01	2008-08-01			ENSG00000266964			4025	protein-coding gene	gene with protein product		602359	"phospholemman"	PLM		9169143	Standard	NM_005031		Approved		uc002nyc.3	O00168		ENST00000588081.1:c.21C>G	chr19.hg19:g.35631004C>G	ENSP00000467727:p.Ile7Met	23.0	0.0	.		17.0	6.0	.	NM_005031	A8K196	Missense_Mutation	SNP	ENST00000588081.1	hg19	CCDS12445.1	.	.	.	.	.	.	.	.	.	.	C	12.93	2.085201	0.36758	.	.	ENSG00000221857	ENST00000351325;ENST00000455515	T;T	0.67865	-0.29;-0.29	4.13	3.08	0.35506	.	0.567371	0.14534	N	0.313662	T	0.54498	0.1862	.	.	.	0.80722	D	1	B	0.25169	0.119	B	0.19391	0.025	T	0.54384	-0.8302	9	0.56958	D	0.05	-1.9404	7.9651	0.30094	0.0:0.8864:0.0:0.1136	.	7	O00168	PLM_HUMAN	M	7	ENSP00000343314:I7M;ENSP00000393611:I7M	ENSP00000343314:I7M	I	+	3	3	FXYD1	40322844	0.927000	0.31430	0.815000	0.32552	0.900000	0.52787	3.568000	0.53820	1.096000	0.41439	0.579000	0.79373	ATC	.	.	.	none		0.622	FXYD1-007	KNOWN	alternative_3_UTR|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460761.1	NM_021902		G	35631004	C	G	35631004	3	3	18	1	0	0	0	0	1	0	0	0	6124	903	32	4	23	4	FXYD1	19	35631004	Missense_Mutation	SNP	C	TCGA-2Z-A9JO-01A-11D-A42J-10		35631004	23497979	33	1248											
ZIM3	114026	hgsc.bcm.edu	37	chr19	57646984	57646984	+	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	tttagtatgcattttctgatGttgaaagagatttgacttct	10	19	8	4	0	2	4	0	3	2	1	2	5	2	4	0	0	1	3	0	0	3	8			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr19:57646984G>T	ENST00000269834.1	-	5	1106	c.721C>A	c.(721-723)Cat>Aat	p.H241N	U3_ENST00000516874.1_RNA	NM_052882.1	NP_443114.1	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	241					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			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)		ATTTTCTGATGTTGAAAGAGA	0.378																																					p.H241N		Atlas-SNP	.											.	ZIM3	107	.	0			c.C721A						PASS	.						128	126	127					19																	57646984		2203	4300	6503	SO:0001583	missense	114026	exon5			TCTGATGTTGAAA	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.721C>A	chr19.hg19:g.57646984G>T	ENSP00000269834:p.His241Asn	51.0	0.0	.		31.0	11.0	.	NM_052882	Q14CA6	Missense_Mutation	SNP	ENST00000269834.1	hg19	CCDS33125.1	.	.	.	.	.	.	.	.	.	.	G	10.43	1.347746	0.24426	.	.	ENSG00000141946	ENST00000269834	D	0.86865	-2.18	2.53	1.45	0.22620	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94301	0.8169	H	0.95780	3.72	0.25361	N	0.988781	D	0.71674	0.998	D	0.91635	0.999	D	0.85217	0.1024	9	0.87932	D	0	.	7.1216	0.25448	0.1503:0.0:0.8497:0.0	.	241	Q96PE6	ZIM3_HUMAN	N	241	ENSP00000269834:H241N	ENSP00000269834:H241N	H	-	1	0	ZIM3	62338796	0.986000	0.35501	0.564000	0.28396	0.058000	0.15608	2.728000	0.47319	0.373000	0.24621	0.313000	0.20887	CAT	.	.	.	none		0.378	ZIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465078.1			T	57646984	G	T	57646984	3	4	18	1	0	0	0	0	1	0	0	0	17697	1377	48	4	701	4	ZIM3	19	57646984	Missense_Mutation	SNP	G	TCGA-2Z-A9JO-01A-11D-A42J-10	22015980	57646984	1481999	34	1249											
C22orf13	83606	hgsc.bcm.edu	37	chr22	24942883	24942883	+	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	ggaaagttggggggctcaccAtttctccaccagcaccttgc	8	9	11	13	0	2	0	1	0	1	0	3	1	2	1	4	4	2	3	4	4	1	3			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chr22:24942883A>T	ENST00000407471.3	-	4	575	c.385T>A	c.(385-387)Tgc>Agc	p.C129S	GUCD1_ENST00000490922.1_Intron|GUCD1_ENST00000402766.1_Splice_Site_p.C129S|GUCD1_ENST00000435822.1_Splice_Site_p.C129S|GUCD1_ENST00000447813.2_Splice_Site_p.W129R|GUCD1_ENST00000404664.3_Splice_Site_p.C185S	NM_001284251.1	NP_001271180.1	Q96NT3	GUCD1_HUMAN	guanylyl cyclase domain containing 1	129																	GGGGCTCACCATTTCTCCACC	0.557																																					p.C129S		Atlas-SNP	.											.	.	.	.	0			c.T385A						PASS	.						98	98	98					22																	24942883		2203	4300	6503	SO:0001630	splice_region_variant	83606	exon4			CTCACCATTTCTC	AK054681	CCDS33621.1, CCDS63426.1, CCDS63427.1, CCDS74831.1, CCDS74832.1, CCDS74833.1	22q11.2	2012-11-13	2012-11-13	2012-11-13	ENSG00000138867	ENSG00000138867			14237	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 13"	C22orf13		12477932	Standard	XM_005261761		Approved	MGC1842, LLN4	uc003aah.2	Q96NT3	OTTHUMG00000150728	ENST00000407471.3:c.386+1T>A	chr22.hg19:g.24942883A>T		79.0	0.0	.		55.0	12.0	.	NM_031444	B5MCB8|B5MCL7|Q96Q79|Q9BU32	Missense_Mutation	SNP	ENST00000407471.3	hg19	CCDS33621.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.96|16.96	3.266439|3.266439	0.59540|0.59540	.|.	.|.	ENSG00000138867|ENSG00000138867	ENST00000407471;ENST00000435822;ENST00000404664;ENST00000402766|ENST00000447813	.|.	.|.	.|.	5.8|5.8	5.8|5.8	0.92144|0.92144	.|.	0.048451|.	0.85682|.	D|.	0.000000|.	T|T	0.55033|0.55033	0.1895|0.1895	L|L	0.60455|0.60455	1.87|1.87	0.58432|0.58432	D|D	0.999999|0.999999	D;P;P;P;B|.	0.61697|.	0.99;0.917;0.695;0.611;0.07|.	P;B;B;P;B|.	0.61800|.	0.894;0.425;0.236;0.502;0.051|.	T|T	0.51702|0.51702	-0.8672|-0.8672	9|6	0.30078|0.06494	T|T	0.28|0.89	-25.3709|-25.3709	9.7612|9.7612	0.40532|0.40532	0.9234:0.0:0.0766:0.0|0.9234:0.0:0.0766:0.0	.|.	129;185;193;129;129|.	E9PGZ7;B5MCL7;B4DH83;B4DL90;Q96NT3|.	.;.;.;.;CV013_HUMAN|.	S|R	129;129;185;129|129	.|.	ENSP00000381297:C129S|ENSP00000387867:W129R	C|W	-|-	1|1	0|0	C22orf13|C22orf13	23272883|23272883	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	4.659000|4.659000	0.61504|0.61504	2.212000|2.212000	0.71576|0.71576	0.533000|0.533000	0.62120|0.62120	TGC|TGG	.	.	.	none		0.557	GUCD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319819.1	NM_031444	Missense_Mutation	T	24942883	A	T	24942883	5	4	18	1	0	0	0	0	0	0	1	0	2137	231	8	5	349	5	C22orf13	22	24942883	Splice_Site	SNP	A	TCGA-2Z-A9JO-01A-11D-A42J-10		24942883	26361683	35	1250											
ACE2	59272	hgsc.bcm.edu	37	chrX	15596288	15596288	+	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	gtggctgcagaaagtgacatGatttccccaacagcttcatg	11	10	10	10	0	1	3	1	2	0	1	2	3	2	3	2	1	3	3	2	1	2	2			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chrX:15596288G>A	ENST00000252519.3	-	9	1323	c.1221C>T	c.(1219-1221)atC>atT	p.I407I	ACE2_ENST00000427411.1_Silent_p.I407I			Q9BYF1	ACE2_HUMAN	angiotensin I converting enzyme 2	407					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)	AAAGTGACATGATTTCCCCAA	0.418																																					p.I407I		Atlas-SNP	.											.	ACE2	87	.	0			c.C1221T						PASS	.						126	106	113					X																	15596288		2203	4300	6503	SO:0001819	synonymous_variant	59272	exon10			TGACATGATTTCC	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.1221C>T	chrX.hg19:g.15596288G>A		154.0	0.0	.		129.0	44.0	.	NM_021804	C7ECU1|Q6UWP0|Q86WT0|Q9NRA7|Q9UFZ6	Silent	SNP	ENST00000252519.3	hg19	CCDS14169.1																																																																																			.	.	.	none		0.418	ACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055867.1			A	15596288	G	A	15596288	2	1	18	1	0	0	0	0	0	0	0	1	137	1280	45	2		2	ACE2	23	15596288	Silent	SNP	G	TCGA-2Z-A9JO-01A-11D-A42J-10		15596288	139674272	36	1251											
LANCL3	347404	hgsc.bcm.edu	37	chrX	37431495	37431495	+	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	gccgccttcctgctcgggggCgcgggcgtgtacgccgtggc	1	7	18	15	7	0	0	0	0	0	0	2	0	1	0	4	4	2	2	4	4	1	2			TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chrX:37431495C>T	ENST00000378619.3	+	1	591	c.372C>T	c.(370-372)ggC>ggT	p.G124G	TM4SF2_ENST00000465127.1_Intron|LANCL3_ENST00000378621.3_Silent_p.G124G	NM_001170331.1	NP_001163802.1	Q6ZV70	LANC3_HUMAN	LanC lantibiotic synthetase component C-like 3 (bacterial)	124							catalytic activity (GO:0003824)			lung(4)|pancreas(1)	5						TGCTCGGGGGCGCGGGCGTGT	0.731																																					p.G124G		Atlas-SNP	.											.	LANCL3	42	.	0			c.C372T						PASS	.						2	3	2					X																	37431495		1288	2580	3868	SO:0001819	synonymous_variant	347404	exon1			CGGGGGCGCGGGC	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.372C>T	chrX.hg19:g.37431495C>T		63.0	0.0	.		57.0	16.0	.	NM_001170331	A6NHE3	Silent	SNP	ENST00000378619.3	hg19	CCDS55398.1																																																																																			.	.	.	none		0.731	LANCL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080885.1	NM_198511		T	37431495	C	T	37431495	2	4	18	1	0	0	0	0	0	0	0	1	8629	755	27	1		1	LANCL3	23	37431495	Silent	SNP	C	TCGA-2Z-A9JO-01A-11D-A42J-10	21835207	37431495	117839065	37	1252											
FAM104B	90736	hgsc.bcm.edu	37	chrX	55172645	55172645	+	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	gaactggggaaagtttgcatCgggttcagtaacaatctggt	11	11	13	6	1	2	0	1	0	1	0	3	2	2	1	0	4	3	4	0	4	4	3	rs1047042	byFrequency	TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chrX:55172645C>G	ENST00000358460.4	-	3	373	c.220G>C	c.(220-222)Gat>Cat	p.D74H	FAM104B_ENST00000489298.1_Missense_Mutation_p.D73H|FAM104B_ENST00000425133.2_Missense_Mutation_p.D75H|FAM104B_ENST00000478918.1_5'Flank|FAM104B_ENST00000477847.2_Missense_Mutation_p.D71H|FAM104B_ENST00000472571.2_3'UTR|FAM104B_ENST00000332132.4_Missense_Mutation_p.D75H			Q5XKR9	F104B_HUMAN	family with sequence similarity 104, member B	74				D -> V (in Ref. 1; BAG61768). {ECO:0000305}.						endometrium(3)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	8						AAGTTTGCATCGGGTTCAGTA	0.468													C|||	5	0.0013245	0.0023	0	3775	,	,		14416	0		0	False		,,,				2504	0.002				p.D75H		Atlas-SNP	.											.	FAM104B	28	.	0			c.G223C						PASS	.						136	110	119					X																	55172645		2203	4300	6503	SO:0001583	missense	90736	exon3			TTGCATCGGGTTC	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.220G>C	chrX.hg19:g.55172645C>G	ENSP00000364101:p.Asp74His	52.0	0.0	.		54.0	4.0	.	NM_001166699	A6NEH1|B4DSV6|D6R9S5|D6RDJ5|E9PH40|Q8WVU5|Q9BRA1	Missense_Mutation	SNP	ENST00000358460.4	hg19	CCDS35305.2	.	.	.	.	.	.	.	.	.	.	c	3.193	-0.165363	0.06461	.	.	ENSG00000182518	ENST00000358460;ENST00000332132;ENST00000425133;ENST00000477847;ENST00000489298	T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9	1.59	-1.04	0.10068	.	0.505297	0.17523	U	0.171170	T	0.25044	0.0608	N	0.14661	0.345	0.09310	N	1	B;P;P	0.46859	0.002;0.774;0.885	B;P;B	0.46479	0.001;0.518;0.241	T	0.15065	-1.0450	10	0.56958	D	0.05	-1.547	4.2247	0.10575	0.0:0.4679:0.0:0.5321	.	75;74;75	Q5XKR9-3;Q5XKR9;Q5XKR9-2	.;F104B_HUMAN;.	H	74;75;75;71;73	ENSP00000364101:D74H;ENSP00000333394:D75H;ENSP00000397188:D75H;ENSP00000421161:D71H;ENSP00000423164:D73H	ENSP00000333394:D75H	D	-	1	0	FAM104B	55189370	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.019000	0.12546	-0.355000	0.08199	-0.556000	0.04195	GAT	.	C|0.600;T|0.400	.	alt		0.468	FAM104B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056851.1	NM_138362		G	55172645	C	G	55172645	3	3	18	1	0	0	0	0	1	0	0	0	5390	884	31	4	232	4	FAM104B	23	55172645	Missense_Mutation	SNP	C	TCGA-2Z-A9JO-01A-11D-A42J-10	17741150	55172645	100097915	38	1253											
AR	367	hgsc.bcm.edu	37	chrX	66765176	66765176	+	Missense_Mutation	SNP	A	A	T																															gctgcagcagcagcagcagcAgcagcagcagcagcagcagc																								rs62636527		TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chrX:66765176A>T	ENST00000374690.3	+	1	712	c.188A>T	c.(187-189)cAg>cTg	p.Q63L	AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.Q63L|AR_ENST00000504326.1_Missense_Mutation_p.Q63L	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	63	Gln-rich.|Modulating.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	cagcagcagcagcagcagcag	0.672									Androgen Insensitivity Syndrome																												p.Q63L		Atlas-SNP	.											.	AR	249	.	0			c.A188T						PASS	.						5	8	7					X																	66765176		1640	3236	4876	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	AGCAGCAGCAGCA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.188A>T	chrX.hg19:g.66765176A>T	ENSP00000363822:p.Gln63Leu	148.0	0.0	.		137.0	18.0	.	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	11.08	1.532203	0.27387	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.78246	-1.16;-1.16;-1.16	.	.	.	.	0.479323	0.15343	U	0.267412	T	0.62624	0.2443	N	0.19112	0.55	0.09310	N	0.999992	P;D;.	0.58268	0.755;0.982;.	B;P;.	0.48627	0.089;0.584;.	T	0.56408	-0.7984	8	0.17832	T	0.49	.	.	.	.	rs62636527	63;63;61	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	L	63	ENSP00000363822:Q63L;ENSP00000421155:Q63L;ENSP00000379359:Q63L	ENSP00000363822:Q63L	Q	+	2	0	AR	66681901	0.810000	0.29049	0.871000	0.34182	0.555000	0.35460	1.078000	0.30754	0.000000	0.14550	0.000000	0.15137	CAG	.	A|0.982;T|0.018	0.018	weak		0.672	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		T	66765176	A	T	66765176	3	4	18	1	0	0	0	0	1	0	0	0	836	188	7	5	190	5	AR	23	66765176	Missense_Mutation	SNP	A	TCGA-2Z-A9JO-01A-11D-A42J-10	11592531	66765176	88505384	39	1254	12	2									
AR	367	hgsc.bcm.edu	37	chrX	66765179	66765179	+	Missense_Mutation	SNP	A	A	T																															gcagcagcagcagcagcagcAgcagcagcagcagcagcagc																										TCGA-2Z-A9JO-01A-11D-A42J-10	TCGA-2Z-A9JO-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be2d72cb-f80c-4e4e-898b-bcb53f6fbee6	c3d84203-c64e-4591-bf15-d40efc7076fd	g.chrX:66765179A>T	ENST00000374690.3	+	1	715	c.191A>T	c.(190-192)cAg>cTg	p.Q64L	AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.Q64L|AR_ENST00000504326.1_Missense_Mutation_p.Q64L	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	64	Gln-rich.|Modulating.|Poly-Gln.		Q -> R (in prostate cancer).		androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	cagcagcagcagcagcagcag	0.677									Androgen Insensitivity Syndrome																												p.Q64L		Atlas-SNP	.											.	AR	249	.	0			c.A191T						PASS	.						4	8	7					X																	66765179		1590	3143	4733	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	AGCAGCAGCAGCA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.191A>T	chrX.hg19:g.66765179A>T	ENSP00000363822:p.Gln64Leu	145.0	0.0	.		134.0	19.0	.	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	11.28	1.591655	0.28357	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.67865	-0.29;-0.29;-0.29	.	.	.	.	1.847110	0.03494	N	0.217131	T	0.56124	0.1964	N	0.19112	0.55	0.09310	N	0.999991	P;D;.	0.58268	0.755;0.982;.	B;P;.	0.48627	0.089;0.584;.	T	0.50381	-0.8835	8	0.38643	T	0.18	.	.	.	.	.	64;64;62	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	L	64	ENSP00000363822:Q64L;ENSP00000421155:Q64L;ENSP00000379359:Q64L	ENSP00000363822:Q64L	Q	+	2	0	AR	66681904	0.024000	0.19004	0.883000	0.34634	0.574000	0.36063	-0.145000	0.10265	0.000000	0.14550	0.000000	0.15137	CAG	.	.	.	none		0.677	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		T	66765179	A	T	66765179	3	4	18	1	0	0	0	0	1	0	0	0	836	188	7	5	193	5	AR	23	66765179	Missense_Mutation	SNP	A	TCGA-2Z-A9JO-01A-11D-A42J-10	3	66765179	88505381	40	1255	12	2									
PRDM16	63976	hgsc.bcm.edu	37	chr1	3334463	3334463	+	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	aaggcggactcgggcagctcCctgcagcccctcccccacca	7	4	10	20	2	0	0	0	0	0	0	3	1	2	1	6	3	3	3	6	3	1	0			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr1:3334463C>G	ENST00000270722.5	+	11	2812	c.2763C>G	c.(2761-2763)tcC>tcG	p.S921S	PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000378398.3_Silent_p.S921S|PRDM16_ENST00000378391.2_Silent_p.S921S|PRDM16_ENST00000442529.2_Silent_p.S920S|PRDM16_ENST00000511072.1_Silent_p.S922S|PRDM16_ENST00000514189.1_Silent_p.S921S|PRDM16_ENST00000441472.2_Silent_p.S920S			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	921	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)		CGGGCAGCTCCCTGCAGCCCC	0.602			T	EVI1	"MDS, AML"																																p.S921S		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.C2763G						PASS	.						79	89	86					1																	3334463		2010	4175	6185	SO:0001819	synonymous_variant	63976	exon11			CAGCTCCCTGCAG	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.2763C>G	chr1.hg19:g.3334463C>G		395.0	0.0	.		315.0	109.0	.	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Silent	SNP	ENST00000270722.5	hg19	CCDS41236.2																																																																																			.	.	.	none		0.602	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114		G	3334463	C	G	3334463	2	3	19	1	0	0	0	0	0	0	0	1	12467	610	22	4		4	PRDM16	1	3334463	Silent	SNP	C	TCGA-2Z-A9JP-01A-11D-A42J-10		3334463	245916158	1	1256											
ZMYM6	9204	hgsc.bcm.edu	37	chr1	35452999	35452999	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcttttcttcttcgaagtcGgtgagattattattttggtg	7	19	10	5	2	2	1	0	1	2	1	4	3	2	1	0	2	1	1	0	2	3	8	rs61744849		TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr1:35452999G>A	ENST00000357182.4	-	16	3911	c.3684C>T	c.(3682-3684)acC>acT	p.T1228T	ZMYM6_ENST00000373340.2_Intron|ZMYM6_ENST00000487874.1_Intron|RP11-244H3.1_ENST00000417456.1_RNA|ZMYM6NB_ENST00000373337.3_5'Flank|ZMYM6_ENST00000493328.1_5'UTR	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6	1228					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)				CTTCGAAGTCGGTGAGATTAT	0.358																																					p.T1228T		Atlas-SNP	.											.	ZMYM6	110	.	0			c.C3684T						PASS	.						86	85	85					1																	35452999		1822	4084	5906	SO:0001819	synonymous_variant	9204	exon16			GAAGTCGGTGAGA	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.3684C>T	chr1.hg19:g.35452999G>A		98.0	0.0	.		90.0	4.0	.	NM_007167	B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	Silent	SNP	ENST00000357182.4	hg19	CCDS387.2																																																																																			.	G|0.986;A|0.014	0.014	weak		0.358	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011999.1	NM_007167		A	35452999	G	A	35452999	2	1	19	1	0	0	0	0	0	0	0	1	17716	1103	39	1		1	ZMYM6	1	35452999	Silent	SNP	G	TCGA-2Z-A9JP-01A-11D-A42J-10	32118536	35452999	213797622	2	1257											
FLAD1	80308	hgsc.bcm.edu	37	chr1	154956520	154956520	+	Missense_Mutation	SNP	T	T	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	cgtgacggctggcatcatcaTtgttggagatgagatcctta	9	12	12	8	2	2	3	2	2	0	2	3	5	3	3	1	3	0	3	1	3	1	3			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr1:154956520T>G	ENST00000292180.3	+	1	672	c.350T>G	c.(349-351)aTt>aGt	p.I117S	FLAD1_ENST00000315144.10_Missense_Mutation_p.I20S|FLAD1_ENST00000368433.1_Missense_Mutation_p.I117S|FLAD1_ENST00000487371.1_3'UTR|FLAD1_ENST00000368431.3_De_novo_Start_InFrame|FLAD1_ENST00000368432.1_Missense_Mutation_p.I20S	NM_025207.4	NP_079483.3	Q8NFF5	FAD1_HUMAN	flavin adenine dinucleotide synthetase 1	117	Molybdenum cofactor biosynthesis protein- like.				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)			GGCATCATCATTGTTGGAGAT	0.587																																					p.I117S		Atlas-SNP	.											.	FLAD1	52	.	0			c.T350G						PASS	.						25	23	23					1																	154956520		2203	4300	6503	SO:0001583	missense	80308	exon1			TCATCATTGTTGG		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.350T>G	chr1.hg19:g.154956520T>G	ENSP00000292180:p.Ile117Ser	41.0	0.0	.		54.0	28.0	.	NM_025207	Q8N5J1|Q8N686|Q8WU93|Q8WUJ4|Q96CR8|Q99764|Q9HBN6	Missense_Mutation	SNP	ENST00000292180.3	hg19	CCDS1078.1	.	.	.	.	.	.	.	.	.	.	T	32	5.175833	0.94807	.	.	ENSG00000160688	ENST00000368433;ENST00000315144;ENST00000368432;ENST00000292180	T;T;T;T	0.75477	-0.94;-0.94;-0.94;-0.94	5.45	5.45	0.79879	Molybdopterin binding (4);	0.000000	0.85682	D	0.000000	T	0.72211	0.3432	L	0.49126	1.545	0.80722	D	1	P	0.43287	0.802	P	0.52343	0.696	T	0.76528	-0.2926	10	0.62326	D	0.03	-10.5785	13.7506	0.62906	0.0:0.0:0.0:1.0	.	117	Q8NFF5	FAD1_HUMAN	S	117;20;20;117	ENSP00000357418:I117S;ENSP00000317296:I20S;ENSP00000357417:I20S;ENSP00000292180:I117S	ENSP00000292180:I117S	I	+	2	0	FLAD1	153223144	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.610000	0.74178	2.065000	0.61736	0.454000	0.30748	ATT	.	.	.	none		0.587	FLAD1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091089.1	NM_025207		G	154956520	T	G	154956520	3	3	19	1	0	0	0	0	1	0	0	0	5927	1493	52	5	352	5	FLAD1	1	154956520	Missense_Mutation	SNP	T	TCGA-2Z-A9JP-01A-11D-A42J-10	119503521	154956520	94294101	3	1258											
INSRR	3645	hgsc.bcm.edu	37	chr1	156823981	156823981	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaagctgaggccgcggaagTcctccccggtggctgtgaac	7	6	16	12	3	0	2	0	2	0	0	2	4	2	4	4	5	2	2	4	5	3	0			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr1:156823981T>C	ENST00000368195.3	-	2	596	c.200A>G	c.(199-201)gAc>gGc	p.D67G	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	67					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)					GCCGCGGAAGTCCTCCCCGGT	0.627																																					p.D67G		Atlas-SNP	.											.	INSRR	309	.	0			c.A200G						PASS	.						70	69	69					1																	156823981		2203	4300	6503	SO:0001583	missense	3645	exon2			CGGAAGTCCTCCC	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.200A>G	chr1.hg19:g.156823981T>C	ENSP00000357178:p.Asp67Gly	49.0	0.0	.		63.0	22.0	.	NM_014215	O60724|Q5VZS3	Missense_Mutation	SNP	ENST00000368195.3	hg19	CCDS1160.1	.	.	.	.	.	.	.	.	.	.	T	19.23	3.787541	0.70337	.	.	ENSG00000027644	ENST00000368195	T	0.79749	-1.3	5.06	5.06	0.68205	EGF receptor, L domain (1);	0.000000	0.50627	D	0.000108	T	0.77025	0.4070	.	.	.	0.41280	D	0.986901	P	0.48640	0.913	P	0.48901	0.594	T	0.80919	-0.1167	9	0.62326	D	0.03	.	12.7616	0.57367	0.0:0.0:0.0:1.0	.	67	P14616	INSRR_HUMAN	G	67	ENSP00000357178:D67G	ENSP00000357178:D67G	D	-	2	0	INSRR	155090605	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	3.428000	0.52792	1.918000	0.55548	0.455000	0.32223	GAC	.	.	.	none		0.627	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		C	156823981	T	C	156823981	3	2	19	1	0	0	0	0	1	0	0	0	7781	1667	58	3	3776	3	INSRR	1	156823981	Missense_Mutation	SNP	T	TCGA-2Z-A9JP-01A-11D-A42J-10	1867461	156823981	92426640	4	1259											
KIRREL	55243	hgsc.bcm.edu	37	chr1	158058227	158058227	+	Frame_Shift_Del	DEL	A	A	-																															ccctcactctcacctggaccAaaaaggactcaaatatggta																										TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr1:158058227delA	ENST00000359209.6	+	8	1094	c.1027delA	c.(1027-1029)aaafs	p.K344fs	KIRREL_ENST00000368172.1_Frame_Shift_Del_p.K142fs|KIRREL_ENST00000368173.3_Frame_Shift_Del_p.K344fs|KIRREL_ENST00000392272.2_Frame_Shift_Del_p.K241fs|KIRREL_ENST00000416935.2_Frame_Shift_Del_p.K244fs|KIRREL_ENST00000360089.4_Frame_Shift_Del_p.K180fs			Q96J84	KIRR1_HUMAN	kin of IRRE like (Drosophila)	344	Ig-like C2-type 4.				excretion (GO:0007588)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of actin filament polymerization (GO:0030838)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|dendritic shaft (GO:0043198)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	myosin binding (GO:0017022)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(5)|skin(3)|stomach(1)	38	all_hematologic(112;0.0378)					CACCTGGACCAAAAAGGACTC	0.463																																					p.T342fs		Pindel	.											.	KIRREL	346	.	0			c.1026delC						PASS	.						101	100	100					1																	158058227		2203	4300	6503	SO:0001589	frameshift_variant	55243	exon8			.	AK001707	CCDS1172.2, CCDS72952.1	1q21-q25	2013-01-29			ENSG00000183853	ENSG00000183853		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15734	protein-coding gene	gene with protein product	"nephrin-like protein 1"	607428				12424224	Standard	NM_001286349		Approved	NEPH1	uc001frn.4	Q96J84	OTTHUMG00000022438	ENST00000359209.6:c.1027delA	chr1.hg19:g.158058227delA	ENSP00000352138:p.Lys344fs	136.0	0.0	.		121.0	28.0	0.231	NM_018240	Q5W0F8|Q5XKC6|Q7Z696|Q7Z7N8|Q8TB15|Q9H9N1|Q9NVA5	Frame_Shift_Del	DEL	ENST00000359209.6	hg19	CCDS1172.2																																																																																			.	.	.	none		0.463	KIRREL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058342.3	NM_018240		-	158058227	A	-	158058227	7	5	19	1	0	1	0	1	0	0	0	0	8331	131	5	0	1057	0	KIRREL	1	158058227	Frame_Shift_Del	DEL	A	TCGA-2Z-A9JP-01A-11D-A42J-10	1234246	158058227	91192394	5	1260											
KIAA1804	84451	hgsc.bcm.edu	37	chr1	233518353	233518353	+	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	tgccttcattactggatgctGacgtggaaggtcagagcagg	9	10	14	8	1	2	2	2	1	0	1	2	4	2	4	1	4	4	2	1	4	2	2			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr1:233518353G>T	ENST00000366624.3	+	10	3268	c.3007G>T	c.(3007-3009)Gac>Tac	p.D1003Y	MLK4_ENST00000366622.1_Missense_Mutation_p.D449Y	NM_032435.2	NP_115811.2																					ACTGGATGCTGACGTGGAAGG	0.522																																					p.D1003Y		Atlas-SNP	.											.	KIAA1804	129	.	0			c.G3007T						PASS	.						109	92	98					1																	233518353		2203	4300	6503	SO:0001583	missense	0	exon10			GATGCTGACGTGG																												ENST00000366624.3:c.3007G>T	chr1.hg19:g.233518353G>T	ENSP00000355583:p.Asp1003Tyr	49.0	0.0	.		91.0	33.0	.	NM_032435		Missense_Mutation	SNP	ENST00000366624.3	hg19	CCDS1598.1	.	.	.	.	.	.	.	.	.	.	G	18.64	3.667893	0.67814	.	.	ENSG00000143674	ENST00000366624;ENST00000366622	T;T	0.80214	-1.35;2.71	4.77	2.47	0.30058	.	0.256767	0.28901	N	0.013763	T	0.81621	0.4861	L	0.41492	1.28	0.09310	N	0.999995	D;D	0.89917	1.0;0.966	D;P	0.69479	0.964;0.603	T	0.70590	-0.4830	10	0.87932	D	0	.	6.1916	0.20528	0.1283:0.1738:0.6979:0.0	.	450;1003	Q5TCX8-3;Q5TCX8	.;M3KL4_HUMAN	Y	1003;449	ENSP00000355583:D1003Y;ENSP00000355581:D449Y	ENSP00000355581:D449Y	D	+	1	0	RP5-862P8.2	231584976	0.988000	0.35896	0.000000	0.03702	0.340000	0.28889	3.723000	0.54955	0.379000	0.24794	0.563000	0.77884	GAC	.	.	.	none		0.522	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1			T	233518353	G	T	233518353	3	4	19	1	0	0	0	0	1	0	0	0	8266	1290	45	4	3045	4	KIAA1804	1	233518353	Missense_Mutation	SNP	G	TCGA-2Z-A9JP-01A-11D-A42J-10	75460126	233518353	15732268	6	1261											
GLS	2744	hgsc.bcm.edu	37	chr2	191769861	191769861	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggaaaagagccgagtggacTaagattcaacaaactatttt	16	10	9	6	1	1	2	1	0	0	2	1	5	1	4	1	2	3	0	1	2	6	5			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr2:191769861T>C	ENST00000320717.3	+	6	1205	c.947T>C	c.(946-948)cTa>cCa	p.L316P	GLS_ENST00000338435.4_Missense_Mutation_p.L316P	NM_014905.4	NP_055720.3	O94925	GLSK_HUMAN	glutaminase	316					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)	CCGAGTGGACTAAGATTCAAC	0.328																																					p.L316P		Atlas-SNP	.											.	GLS	47	.	0			c.T947C						PASS	.						106	106	106					2																	191769861		2203	4300	6503	SO:0001583	missense	2744	exon6			GTGGACTAAGATT	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.947T>C	chr2.hg19:g.191769861T>C	ENSP00000317379:p.Leu316Pro	85.0	0.0	.		75.0	4.0	.	NM_014905	Q9UL05|Q9UL06|Q9UL07|Q9UN40	Missense_Mutation	SNP	ENST00000320717.3	hg19	CCDS2308.1	.	.	.	.	.	.	.	.	.	.	T	18.98	3.737804	0.69304	.	.	ENSG00000115419	ENST00000320717;ENST00000338435	T;T	0.44083	0.93;0.93	5.74	5.74	0.90152	Beta-lactamase/transpeptidase-like (1);	0.000000	0.64402	D	0.000001	T	0.59905	0.2228	M	0.84511	2.7	0.80722	D	1	D;D	0.59767	0.978;0.986	P;P	0.52454	0.683;0.699	T	0.62932	-0.6749	10	0.32370	T	0.25	-11.2118	16.3785	0.83418	0.0:0.0:0.0:1.0	.	316;316	O94925;O94925-3	GLSK_HUMAN;.	P	316	ENSP00000317379:L316P;ENSP00000340689:L316P	ENSP00000317379:L316P	L	+	2	0	GLS	191478106	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.997000	0.88414	2.323000	0.78572	0.529000	0.55759	CTA	.	.	.	none		0.328	GLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255999.2			C	191769861	T	C	191769861	3	2	19	1	0	0	0	0	1	0	0	0	6470	1522	53	3	969	3	GLS	2	191769861	Missense_Mutation	SNP	T	TCGA-2Z-A9JP-01A-11D-A42J-10		191769861	51429512	7	1262											
DOCK10	55619	hgsc.bcm.edu	37	chr2	225688357	225688357	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	attcaggaaatctctgaggcCggggaagctaaggaaagaac	15	6	13	7	1	2	2	1	1	1	1	3	5	2	5	1	5	2	1	1	5	5	2	rs375357151		TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr2:225688357C>T	ENST00000258390.7	-	28	3111	c.3044G>A	c.(3043-3045)cGg>cAg	p.R1015Q	DOCK10_ENST00000409592.3_Missense_Mutation_p.R1009Q	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1015					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)		TCTCTGAGGCCGGGGAAGCTA	0.368																																					p.R1015Q		Atlas-SNP	.											.	DOCK10	308	.	0			c.G3044A						PASS	.	C	GLN/ARG	1,3805		0,1,1902	100	96	98		3044	5.9	0.7	2		98	0,8240		0,0,4120	no	missense	DOCK10	NM_014689.2	43	0,1,6022	TT,TC,CC		0.0,0.0263,0.0083	probably-damaging	1015/2187	225688357	1,12045	1903	4120	6023	SO:0001583	missense	55619	exon28			TGAGGCCGGGGAA	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.3044G>A	chr2.hg19:g.225688357C>T	ENSP00000258390:p.Arg1015Gln	27.0	0.0	.		42.0	20.0	.	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	hg19	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	C	32	5.175160	0.94807	2.63E-4	0.0	ENSG00000135905	ENST00000409592;ENST00000258390	T;T	0.03635	3.86;3.86	5.9	5.9	0.94986	.	0.050922	0.85682	D	0.000000	T	0.26011	0.0634	M	0.88775	2.98	0.43287	D	0.995263	D;D	0.89917	1.0;1.0	D;D	0.85130	0.996;0.997	T	0.01280	-1.1397	10	0.87932	D	0	.	20.2799	0.98512	0.0:1.0:0.0:0.0	.	1015;1009	Q96BY6;B3FL70	DOC10_HUMAN;.	Q	1009;1015	ENSP00000386694:R1009Q;ENSP00000258390:R1015Q	ENSP00000258390:R1015Q	R	-	2	0	DOCK10	225396601	1.000000	0.71417	0.705000	0.30386	0.991000	0.79684	6.501000	0.73691	2.800000	0.96347	0.643000	0.83706	CGG	.	.	.	weak		0.368	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			T	225688357	C	T	225688357	3	4	19	1	0	0	0	0	1	0	0	0	4687	652	23	1	3632	1	DOCK10	2	225688357	Missense_Mutation	SNP	C	TCGA-2Z-A9JP-01A-11D-A42J-10	33918496	225688357	17511016	8	1263											
PSMD1	5707	hgsc.bcm.edu	37	chr2	232030606	232030607	+	Frame_Shift_Ins	INS	-	-	A																															tgaggcagagaaaaaggaggINSaaaaagagaagaaaaaagaa																										TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr2:232030606_232030607insA	ENST00000308696.6	+	23	2752_2753	c.2590_2591insA	c.(2590-2592)gaafs	p.E864fs	PSMD1_ENST00000409643.1_Frame_Shift_Ins_p.E833fs|PSMD1_ENST00000373635.4_Frame_Shift_Ins_p.E833fs	NM_002807.3	NP_002798.2	Q99460	PSMD1_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	864					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)	31		Ovarian(221;0.000626)|Medulloblastoma(418;0.0109)|Renal(207;0.0112)|Lung NSC(271;0.0538)|all_lung(227;0.0713)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;4e-26)|LUSC - Lung squamous cell carcinoma(224;0.0138)|Lung(119;0.0168)	Bortezomib(DB00188)	GAAAAAGGAGGAAAAAGAGAAG	0.406																																					p.E864fs		Atlas-INDEL	.											.	PSMD1	77	.	0			c.2590_2591insA						PASS	.																																			SO:0001589	frameshift_variant	5707	exon23			.	D44466	CCDS2482.1, CCDS54436.1	2q37.1	2008-05-22			ENSG00000173692	ENSG00000173692		"Proteasome (prosome, macropain) subunits"	9554	protein-coding gene	gene with protein product						8816993	Standard	NM_002807		Approved	S1, P112, Rpn2	uc002vrn.2	Q99460	OTTHUMG00000133223	ENST00000308696.6:c.2595dupA	chr2.hg19:g.232030611_232030611dupA	ENSP00000309474:p.Glu864fs	41.0	0.0	0		36.0	13.0	0.361111	NM_002807	B8ZZH9|Q24JU0|Q53TI2|Q6GMU5|Q6P2P4|Q6PJM7|Q6PKG9|Q86VU1|Q8IV79	Frame_Shift_Ins	INS	ENST00000308696.6	hg19	CCDS2482.1																																																																																			.	.	.	none		0.406	PSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256958.2			A	232030607	-	A	232030606	7	5	19	1	0	1	1	0	0	0	0	0	12702	1175	41	0	2680	0	PSMD1	2	232030606	Frame_Shift_Ins	INS	-	TCGA-2Z-A9JP-01A-11D-A42J-10	6342249	232030606	11168767	9	1264											
UGT1A7	54577	hgsc.bcm.edu	37	chr2	234590634	234590634	+	Frame_Shift_Del	DEL	G	G	-																															cccctatatgtgtgtctactGctgacctgtggctttgccaa																										TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr2:234590634delG	ENST00000373426.3	+	1	51	c.51delG	c.(49-51)ctgfs	p.L18fs	UGT1A1_ENST00000373450.4_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A10_ENST00000373445.1_Intron	NM_019077.2	NP_061950.2	Q9HAW7	UD17_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A7	18					cellular glucuronidation (GO:0052695)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|excretion (GO:0007588)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	drug binding (GO:0008144)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|retinoic acid binding (GO:0001972)			NS(1)|endometrium(6)|kidney(5)|large_intestine(5)|liver(1)|lung(12)|ovary(1)|prostate(1)|skin(1)	33		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;8.93e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000412)|Lung(119;0.00333)|LUSC - Lung squamous cell carcinoma(224;0.00746)	Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)	TGTGTCTACTGCTGACCTGTG	0.557																																					p.L17fs		Atlas-INDEL	.											.	UGT1A7	74	.	0			c.50delT						PASS	.						133	125	127					2																	234590634		2203	4300	6503	SO:0001589	frameshift_variant	54577	exon1			.	U39570	CCDS2506.1	2q37	2010-03-05	2005-07-20		ENSG00000244122	ENSG00000244122		"UDP glucuronosyltransferases"	12539	other	complex locus constituent		606432	"UDP glycosyltransferase 1 family, polypeptide A6"			9295054, 11434514	Standard	NM_019077		Approved	UGT1G		Q9HAW7	OTTHUMG00000059004	ENST00000373426.3:c.51delG	chr2.hg19:g.234590634delG	ENSP00000362525:p.Leu18fs	50.0	0.0	0		55.0	22.0	0.4	NM_019077	B8K293|O00473	Frame_Shift_Del	DEL	ENST00000373426.3	hg19	CCDS2506.1																																																																																			.	.	.	none		0.557	UGT1A7-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130614.1	NM_019077		-	234590634	G	-	234590634	7	5	19	1	0	1	0	1	0	0	0	0	16962	1306	46	0	53	0	UGT1A7	2	234590634	Frame_Shift_Del	DEL	G	TCGA-2Z-A9JP-01A-11D-A42J-10	2560028	234590634	8608739	10	1265											
RAB17	64284	hgsc.bcm.edu	37	chr2	238494751	238494751	+	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	ccagcttgaacacacggggcTggctgggggcagccctgggc	6	5	17	13	1	0	1	0	1	0	0	0	1	0	1	2	6	3	4	2	6	1	1			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr2:238494751T>A	ENST00000264601.3	-	2	676	c.47A>T	c.(46-48)cAg>cTg	p.Q16L	RAB17_ENST00000409822.1_Intron|RAB17_ENST00000409576.1_Intron|RAB17_ENST00000416106.1_5'UTR|RAB17_ENST00000538644.1_5'UTR	NM_022449.3	NP_071894.1	Q9H0T7	RAB17_HUMAN	RAB17, member RAS oncogene family	16					cilium assembly (GO:0042384)|endocytic recycling (GO:0032456)|establishment of melanosome localization (GO:0032401)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|melanosome transport (GO:0032402)|protein transport (GO:0015031)|regulation of dendrite development (GO:0050773)|regulation of filopodium assembly (GO:0051489)|regulation of synapse assembly (GO:0051963)|small GTPase mediated signal transduction (GO:0007264)|transcytosis (GO:0045056)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|dendrite (GO:0030425)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|melanosome (GO:0042470)|neuronal cell body (GO:0043025)|recycling endosome (GO:0055037)|recycling endosome membrane (GO:0055038)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(1)	4		Renal(207;0.00272)|Breast(86;0.00297)|all_hematologic(139;0.182)|Ovarian(221;0.221)		Epithelial(121;9.36e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.26e-10)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000354)|Lung(119;0.011)|LUSC - Lung squamous cell carcinoma(224;0.026)		CACACGGGGCTGGCTGGGGGC	0.587																																					p.Q16L	Colon(56;987 1029 6466 13943 27336)	Atlas-SNP	.											.	RAB17	17	.	0			c.A47T						PASS	.						47	51	49					2																	238494751		2203	4300	6503	SO:0001583	missense	64284	exon2			CGGGGCTGGCTGG	AK022600	CCDS2520.1	2q37.3	2008-05-23			ENSG00000124839	ENSG00000124839		"RAB, member RAS oncogene"	16523	protein-coding gene	gene with protein product		602206				9624171	Standard	NM_022449		Approved		uc002vwz.2	Q9H0T7	OTTHUMG00000133299	ENST00000264601.3:c.47A>T	chr2.hg19:g.238494751T>A	ENSP00000264601:p.Gln16Leu	103.0	0.0	.		95.0	29.0	.	NM_022449	Q53QV6|Q6IA73|Q6PJZ0|Q9BVU1|Q9H9U9	Missense_Mutation	SNP	ENST00000264601.3	hg19	CCDS2520.1	.	.	.	.	.	.	.	.	.	.	T	15.36	2.811895	0.50527	.	.	ENSG00000124839	ENST00000264601;ENST00000411462	T;T	0.79940	-1.32;-1.32	4.47	0.593	0.17478	.	0.379404	0.19708	N	0.107863	T	0.55816	0.1944	N	0.11000	0.08	0.80722	D	1	P	0.38922	0.651	B	0.32677	0.15	T	0.44636	-0.9315	10	0.44086	T	0.13	-11.2708	5.8348	0.18601	0.0:0.0935:0.347:0.5595	.	16	Q9H0T7	RAB17_HUMAN	L	16	ENSP00000264601:Q16L;ENSP00000400240:Q16L	ENSP00000264601:Q16L	Q	-	2	0	RAB17	238159490	1.000000	0.71417	0.067000	0.19924	0.045000	0.14185	2.158000	0.42329	-0.134000	0.11516	0.482000	0.46254	CAG	.	.	.	none		0.587	RAB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257084.2			A	238494751	T	A	238494751	3	1	19	1	0	0	0	0	1	0	0	0	12915	1580	55	5	611	5	RAB17	2	238494751	Missense_Mutation	SNP	T	TCGA-2Z-A9JP-01A-11D-A42J-10	3904117	238494751	4704622	11	1266											
CACNA1D	776	hgsc.bcm.edu	37	chr3	53845336	53845336	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acaccggcaggactatgagcTacaggactttggtcctggct	9	9	12	11	1	0	1	0	1	0	0	1	3	1	3	2	5	2	3	2	5	2	3			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr3:53845336T>C	ENST00000350061.5	+	48	6900	c.6389T>C	c.(6388-6390)cTa>cCa	p.L2130P	CACNA1D_ENST00000288139.4_Missense_Mutation_p.L2150P|CACNA1D_ENST00000422281.2_Missense_Mutation_p.L2106P	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	2130					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)			breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GACTATGAGCTACAGGACTTT	0.602																																					p.L2150P		Atlas-SNP	.											.	CACNA1D	324	.	0			c.T6449C						PASS	.						68	63	65					3																	53845336		2203	4300	6503	SO:0001583	missense	776	exon49			ATGAGCTACAGGA	AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.6389T>C	chr3.hg19:g.53845336T>C	ENSP00000288133:p.Leu2130Pro	64.0	0.0	.		85.0	29.0	.	NM_000720	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Missense_Mutation	SNP	ENST00000350061.5	hg19	CCDS46848.1	.	.	.	.	.	.	.	.	.	.	T	17.42	3.384600	0.61845	.	.	ENSG00000157388	ENST00000350061;ENST00000288139;ENST00000422281;ENST00000481478	D;D;D;D	0.96265	-3.93;-3.96;-3.95;-3.95	5.56	4.37	0.52481	.	0.786356	0.11452	N	0.562709	D	0.97455	0.9167	M	0.73962	2.25	0.80722	D	1	P;D;D;D	0.65815	0.836;0.994;0.966;0.995	P;P;P;D	0.63957	0.572;0.878;0.642;0.92	D	0.94470	0.7684	10	0.33940	T	0.23	.	12.0173	0.53321	0.1296:0.0:0.0:0.8703	.	2106;1823;2130;2150	B0FYA3;Q59GD8;Q01668;Q01668-2	.;.;CAC1D_HUMAN;.	P	2130;2150;2106;1823	ENSP00000288133:L2130P;ENSP00000288139:L2150P;ENSP00000409174:L2106P;ENSP00000418014:L1823P	ENSP00000288139:L2150P	L	+	2	0	CACNA1D	53820376	1.000000	0.71417	0.997000	0.53966	0.974000	0.67602	7.466000	0.80914	1.010000	0.39314	0.533000	0.62120	CTA	.	.	.	none		0.602	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720		C	53845336	T	C	53845336	3	2	19	1	0	0	0	0	1	0	0	0	2543	1522	53	3	6751	3	CACNA1D	3	53845336	Missense_Mutation	SNP	T	TCGA-2Z-A9JP-01A-11D-A42J-10		53845336	144177094	12	1267											
SHQ1	55164	hgsc.bcm.edu	37	chr3	72842103	72842103	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acacacagtagtctgagatgTagagatcattcagtatgtac	14	11	9	7	0	3	2	2	1	1	2	3	4	3	2	0	0	1	4	0	0	4	5			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr3:72842103T>C	ENST00000325599.8	-	10	1284	c.1145A>G	c.(1144-1146)tAc>tGc	p.Y382C	SHQ1_ENST00000463369.1_Missense_Mutation_p.Y354C|SHQ1_ENST00000468371.1_5'UTR	NM_018130.2	NP_060600.2	Q6PI26	SHQ1_HUMAN	SHQ1, H/ACA ribonucleoprotein assembly factor	382					negative regulation of rRNA processing (GO:2000233)|positive regulation of apoptotic process (GO:0043065)|ribonucleoprotein complex assembly (GO:0022618)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	27		Prostate(10;0.00482)|Lung NSC(201;0.0339)|Myeloproliferative disorder(1037;0.204)		BRCA - Breast invasive adenocarcinoma(55;9.68e-05)|Epithelial(33;0.000563)|LUSC - Lung squamous cell carcinoma(21;0.00229)|Lung(16;0.00688)|KIRC - Kidney renal clear cell carcinoma(39;0.018)|Kidney(39;0.0213)		GTCTGAGATGTAGAGATCATT	0.333																																					p.Y382C		Atlas-SNP	.											.	SHQ1	60	.	0			c.A1145G						PASS	.						85	83	83					3																	72842103		2203	4299	6502	SO:0001583	missense	55164	exon10			GAGATGTAGAGAT	BC025270	CCDS33788.1	3p13	2013-01-08	2013-01-08		ENSG00000144736	ENSG00000144736			25543	protein-coding gene	gene with protein product		613663	"SHQ1 homolog (S. cerevisiae)"			12477932	Standard	NM_018130		Approved	FLJ10539, Shq1p	uc003dpf.3	Q6PI26	OTTHUMG00000158814	ENST00000325599.8:c.1145A>G	chr3.hg19:g.72842103T>C	ENSP00000315182:p.Tyr382Cys	51.0	0.0	.		54.0	17.0	.	NM_018130	B4DL05|Q6MZJ4|Q7Z748|Q9H7E5|Q9NVS8	Missense_Mutation	SNP	ENST00000325599.8	hg19	CCDS33788.1	.	.	.	.	.	.	.	.	.	.	T	19.89	3.911519	0.72983	.	.	ENSG00000144736	ENST00000325599;ENST00000463369	T;T	0.42900	0.99;0.96	5.85	5.85	0.93711	SHQ1 protein (1);	0.129663	0.53938	D	0.000048	T	0.67618	0.2912	M	0.86651	2.83	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.73603	-0.3930	10	0.87932	D	0	-9.0575	11.9499	0.52948	0.1373:0.0:0.0:0.8627	.	382	Q6PI26	SHQ1_HUMAN	C	382;354	ENSP00000315182:Y382C;ENSP00000417452:Y354C	ENSP00000315182:Y382C	Y	-	2	0	SHQ1	72924793	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.194000	0.72082	2.237000	0.73441	0.528000	0.53228	TAC	.	.	.	none		0.333	SHQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352310.1	NM_018130		C	72842103	T	C	72842103	3	2	19	1	0	0	0	0	1	0	0	0	14305	1638	57	3	596	3	SHQ1	3	72842103	Missense_Mutation	SNP	T	TCGA-2Z-A9JP-01A-11D-A42J-10	18996767	72842103	125180327	13	1268											
PIK3CB	5291	hgsc.bcm.edu	37	chr3	138478176	138478176	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaggaggcattatgaaacTgaagcacattcataaccacg	16	7	9	9	1	1	2	1	2	0	0	1	3	1	3	1	2	4	3	1	2	4	3			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr3:138478176T>C	ENST00000477593.1	-	2	83	c.10A>G	c.(10-12)Agt>Ggt	p.S4G	PIK3CB_ENST00000289153.2_Missense_Mutation_p.S4G			P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	4					activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	ATTATGAAACTGAAGCACATT	0.423																																					p.S4G		Atlas-SNP	.											PIK3CB,NS,carcinoma,0,1	PIK3CB	103	.	0			c.A10G						PASS	.						82	79	80					3																	138478176		2203	4300	6503	SO:0001583	missense	5291	exon1			TGAAACTGAAGCA		CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	"phosphoinositide-3-kinase, catalytic, beta polypeptide"	PIK3C1		8246984	Standard	NM_006219		Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.10A>G	chr3.hg19:g.138478176T>C	ENSP00000418143:p.Ser4Gly	222.0	0.0	.		239.0	81.0	.	NM_006219	D3DNF0|Q24JU2	Missense_Mutation	SNP	ENST00000477593.1	hg19	CCDS3104.1	.	.	.	.	.	.	.	.	.	.	T	10.66	1.411956	0.25465	.	.	ENSG00000051382	ENST00000477593;ENST00000289153;ENST00000483968;ENST00000461451;ENST00000465581	T;T;T;T	0.72725	-0.39;-0.39;-0.67;-0.68	5.84	0.546	0.17196	.	0.811304	0.11165	N	0.592607	T	0.41604	0.1166	N	0.08118	0	0.18873	N	0.999989	B	0.15141	0.012	B	0.12156	0.007	T	0.21109	-1.0255	10	0.11794	T	0.64	0.1673	2.9379	0.05820	0.2173:0.0698:0.3812:0.3317	.	4	P42338	PK3CB_HUMAN	G	4	ENSP00000418143:S4G;ENSP00000289153:S4G;ENSP00000419857:S4G;ENSP00000420399:S4G	ENSP00000289153:S4G	S	-	1	0	PIK3CB	139960866	0.002000	0.14202	0.079000	0.20413	0.996000	0.88848	-0.054000	0.11826	-0.128000	0.11641	0.533000	0.62120	AGT	.	.	.	none		0.423	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358019.1			C	138478176	T	C	138478176	3	2	19	1	0	0	0	0	1	0	0	0	11921	1580	55	3	3288	3	PIK3CB	3	138478176	Missense_Mutation	SNP	T	TCGA-2Z-A9JP-01A-11D-A42J-10	65636073	138478176	59544254	14	1269											
EIF4G1	1981	hgsc.bcm.edu	37	chr3	184052524	184052524	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctgcttgcagacctgctgcGgatgttctttgacgcactgt	5	13	11	12	2	1	2	0	1	1	1	1	3	1	3	2	1	4	5	2	1	0	3			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr3:184052524G>A	ENST00000346169.2	+	33	4899	c.4628G>A	c.(4627-4629)cGg>cAg	p.R1543Q	FAM131A_ENST00000418281.1_5'Flank|EIF4G1_ENST00000352767.3_Missense_Mutation_p.R1550Q|EIF4G1_ENST00000424196.1_Missense_Mutation_p.R1550Q|EIF4G1_ENST00000392537.2_Missense_Mutation_p.R1456Q|EIF4G1_ENST00000342981.4_Missense_Mutation_p.R1544Q|FAM131A_ENST00000340957.5_5'Flank|EIF4G1_ENST00000441154.1_Missense_Mutation_p.R1380Q|EIF2B5_ENST00000444495.1_Intron|FAM131A_ENST00000383847.2_5'Flank|EIF4G1_ENST00000350481.5_Missense_Mutation_p.R1379Q|EIF4G1_ENST00000414031.1_Missense_Mutation_p.R1503Q|EIF4G1_ENST00000319274.6_Missense_Mutation_p.R1543Q|FAM131A_ENST00000450976.1_5'Flank|EIF4G1_ENST00000435046.2_Missense_Mutation_p.R1347Q|EIF4G1_ENST00000427845.1_Missense_Mutation_p.R1457Q|EIF4G1_ENST00000382330.3_Missense_Mutation_p.R1550Q|EIF4G1_ENST00000434061.2_Missense_Mutation_p.R1348Q|EIF4G1_ENST00000411531.1_Missense_Mutation_p.R1504Q	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	1543	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)			GACCTGCTGCGGATGTTCTTT	0.597																																					p.R1550Q		Atlas-SNP	.											.	EIF4G1	151	.	0			c.G4649A						PASS	.						103	87	92					3																	184052524		2203	4300	6503	SO:0001583	missense	1981	exon34			TGCTGCGGATGTT	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.4628G>A	chr3.hg19:g.184052524G>A	ENSP00000316879:p.Arg1543Gln	68.0	0.0	.		54.0	19.0	.	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Missense_Mutation	SNP	ENST00000346169.2	hg19	CCDS3259.1	.	.	.	.	.	.	.	.	.	.	G	11.33	1.605908	0.28623	.	.	ENSG00000114867	ENST00000346169;ENST00000414031;ENST00000392537;ENST00000382330;ENST00000350481;ENST00000352767;ENST00000427845;ENST00000342981;ENST00000319274;ENST00000424196;ENST00000411531;ENST00000441154;ENST00000434061;ENST00000435046	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53	4.24	0.0401	0.14207	eIF4-gamma/eIF5/eIF2-epsilon (3);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.139826	0.48767	D	0.000171	T	0.72399	0.3455	L	0.42581	1.335	0.52099	D	0.999947	D;D;D	0.55605	0.972;0.972;0.972	P;B;B	0.45639	0.488;0.384;0.384	T	0.66118	-0.6003	10	0.27785	T	0.31	0.0016	10.3514	0.43939	0.0:0.4071:0.453:0.1399	.	1550;1544;1543	E9PFM1;D3DNT2;Q04637	.;.;IF4G1_HUMAN	Q	1543;1503;1456;1550;1379;1550;1457;1544;1543;1550;1504;1380;1348;1347	ENSP00000316879:R1543Q;ENSP00000391935:R1503Q;ENSP00000376320:R1456Q;ENSP00000371767:R1550Q;ENSP00000317600:R1379Q;ENSP00000338020:R1550Q;ENSP00000407682:R1457Q;ENSP00000343450:R1544Q;ENSP00000323737:R1543Q;ENSP00000416255:R1550Q;ENSP00000395974:R1504Q;ENSP00000399858:R1380Q;ENSP00000411826:R1348Q;ENSP00000404754:R1347Q	ENSP00000323737:R1543Q	R	+	2	0	EIF4G1	185535218	1.000000	0.71417	0.541000	0.28102	0.051000	0.14879	7.719000	0.84751	-0.196000	0.10366	0.555000	0.69702	CGG	.	.	.	none		0.597	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917		A	184052524	G	A	184052524	3	1	19	1	0	0	0	0	1	0	0	0	5038	1116	39	1	4750	1	EIF4G1	3	184052524	Missense_Mutation	SNP	G	TCGA-2Z-A9JP-01A-11D-A42J-10	45574348	184052524	13969906	15	1270											
ARAP2	116984	hgsc.bcm.edu	37	chr4	36179487	36179487	+	Missense_Mutation	SNP	A	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	ccacacactgtttccacttaAcacagtaaaaatttttgcct	13	13	3	12	0	0	0	0	0	0	0	1	0	1	0	3	0	2	2	3	0	4	5			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr4:36179487A>C	ENST00000303965.4	-	9	2308	c.1819T>G	c.(1819-1821)Tta>Gta	p.L607V		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	607	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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						TTTCCACTTAACACAGTAAAA	0.368																																					p.L607V		Atlas-SNP	.											.	ARAP2	210	.	0			c.T1819G						PASS	.						150	148	149					4																	36179487		2203	4300	6503	SO:0001583	missense	116984	exon9			CACTTAACACAGT	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.1819T>G	chr4.hg19:g.36179487A>C	ENSP00000302895:p.Leu607Val	46.0	0.0	.		54.0	20.0	.	NM_015230	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Missense_Mutation	SNP	ENST00000303965.4	hg19	CCDS3441.1	.	.	.	.	.	.	.	.	.	.	A	14.67	2.605214	0.46423	.	.	ENSG00000047365	ENST00000303965	D	0.91686	-2.89	5.34	4.12	0.48240	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.51477	D	0.000090	D	0.91707	0.7378	L	0.37800	1.135	0.32339	N	0.560068	P;D	0.89917	0.699;1.0	P;D	0.87578	0.759;0.998	D	0.89237	0.3581	10	0.34782	T	0.22	.	4.7854	0.13222	0.7056:0.0:0.1545:0.1399	.	537;607	A7E2A5;Q8WZ64	.;ARAP2_HUMAN	V	607	ENSP00000302895:L607V	ENSP00000302895:L607V	L	-	1	2	ARAP2	35855882	0.971000	0.33674	0.999000	0.59377	0.995000	0.86356	1.567000	0.36407	0.838000	0.34948	0.402000	0.26972	TTA	.	.	.	none		0.368	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230		C	36179487	A	C	36179487	3	2	19	1	0	0	0	0	1	0	0	0	839	40	2	5	3395	5	ARAP2	4	36179487	Missense_Mutation	SNP	A	TCGA-2Z-A9JP-01A-11D-A42J-10		36179487	154974789	16	1271											
SLC4A9	83697	hgsc.bcm.edu	37	chr5	139747021	139747021	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagcccacactccctgggcGtggctggctggtgtcacctt	4	9	12	16	1	1	0	1	0	0	0	2	0	2	0	4	4	1	2	4	4	0	1			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr5:139747021G>A	ENST00000230993.6	+	15	2137	c.2102G>A	c.(2101-2103)cGt>cAt	p.R701H	SLC4A9_ENST00000507527.1_Missense_Mutation_p.R701H|SLC4A9_ENST00000506757.2_Missense_Mutation_p.R677H|SLC4A9_ENST00000506545.1_Missense_Mutation_p.R614H|SLC4A9_ENST00000432095.2_Missense_Mutation_p.R663H	NM_001258428.1	NP_001245357.1	Q96Q91	B3A4_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 9	701	Membrane (anion exchange).				bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			endometrium(4)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCCCTGGGCGTGGCTGGCTG	0.587																																					p.R701H		Atlas-SNP	.											.	SLC4A9	125	.	0			c.G2102A						PASS	.						27	30	29					5																	139747021		2069	4197	6266	SO:0001583	missense	83697	exon15			CTGGGCGTGGCTG	AF313465	CCDS47278.1, CCDS58973.1, CCDS58974.1, CCDS58975.1	5q31.3	2013-05-22			ENSG00000113073	ENSG00000113073		"Solute carriers"	11035	protein-coding gene	gene with protein product		610207				11305939	Standard	NM_031467		Approved	AE4	uc003lfk.2	Q96Q91	OTTHUMG00000163352	ENST00000230993.6:c.2102G>A	chr5.hg19:g.139747021G>A	ENSP00000230993:p.Arg701His	18.0	0.0	.		24.0	20.0	.	NM_001258428	B7ZL63|D3DQD4|D3DQD5|D3DQD6|E9PDK1|Q96RM5|Q9BXF2|Q9BXN3	Missense_Mutation	SNP	ENST00000230993.6	hg19	CCDS58973.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.813602	0.90790	.	.	ENSG00000113073	ENST00000230993;ENST00000506757;ENST00000432095;ENST00000506545;ENST00000507527	D;D;D;D;D	0.86562	-2.14;-2.14;-2.14;-2.14;-2.14	5.21	4.34	0.51931	Bicarbonate transporter, C-terminal (1);	0.000000	0.64402	D	0.000002	D	0.95095	0.8411	M	0.94142	3.5	0.58432	D	0.999999	P;D;D;D	0.89917	0.681;1.0;1.0;1.0	B;D;D;D	0.91635	0.168;0.999;0.999;0.999	D	0.96394	0.9291	10	0.87932	D	0	.	14.6165	0.68552	0.0705:0.0:0.9295:0.0	.	614;701;663;677	E9PDK1;Q96Q91;Q96Q91-2;Q96Q91-3	.;B3A4_HUMAN;.;.	H	701;677;663;614;701	ENSP00000230993:R701H;ENSP00000424424:R677H;ENSP00000410056:R663H;ENSP00000422855:R614H;ENSP00000427661:R701H	ENSP00000230993:R701H	R	+	2	0	SLC4A9	139727205	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.786000	0.85741	1.569000	0.49696	0.655000	0.94253	CGT	.	.	.	none		0.587	SLC4A9-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000372823.1	NM_031467		A	139747021	G	A	139747021	3	1	19	1	0	0	0	0	1	0	0	0	14673	1145	40	1	2088	1	SLC4A9	5	139747021	Missense_Mutation	SNP	G	TCGA-2Z-A9JP-01A-11D-A42J-10		139747021	41168239	17	1272											
TINAG	27283	hgsc.bcm.edu	37	chr6	54214540	54214540	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atcccacgcatgctacccacTtttcaaagaccaaaatgcta	14	9	4	14	1	1	1	1	0	0	1	2	1	2	1	3	0	3	3	3	0	5	4			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr6:54214540T>C	ENST00000259782.4	+	7	1022	c.926T>C	c.(925-927)cTt>cCt	p.L309P		NM_014464.3	NP_055279.3	Q9UJW2	TINAG_HUMAN	tubulointerstitial nephritis antigen	309					cell adhesion (GO:0007155)|immune response (GO:0006955)	basement membrane (GO:0005604)	cysteine-type endopeptidase activity (GO:0004197)|nucleotide binding (GO:0000166)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(1)	34	Lung NSC(77;0.0518)		LUSC - Lung squamous cell carcinoma(124;0.246)			TGCTACCCACTTTTCAAAGAC	0.423																																					p.L309P		Atlas-SNP	.											.	TINAG	102	.	0			c.T926C						PASS	.						145	135	138					6																	54214540		2203	4300	6503	SO:0001583	missense	27283	exon7			ACCCACTTTTCAA	AB022277	CCDS4955.1	6p12.1	2008-05-15			ENSG00000137251	ENSG00000137251			14599	protein-coding gene	gene with protein product		606749				10652240	Standard	NM_014464		Approved		uc003pcj.2	Q9UJW2	OTTHUMG00000014893	ENST00000259782.4:c.926T>C	chr6.hg19:g.54214540T>C	ENSP00000259782:p.Leu309Pro	81.0	0.0	.		87.0	43.0	.	NM_014464	Q5T467|Q9UJW1|Q9ULZ4	Missense_Mutation	SNP	ENST00000259782.4	hg19	CCDS4955.1	.	.	.	.	.	.	.	.	.	.	T	19.03	3.748832	0.69533	.	.	ENSG00000137251	ENST00000339741;ENST00000259782	D	0.87179	-2.22	5.87	5.87	0.94306	Peptidase C1A, papain C-terminal (2);	0.129015	0.40064	N	0.001200	D	0.88366	0.6417	L	0.43152	1.355	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.90038	0.4140	10	0.66056	D	0.02	.	12.6692	0.56858	0.0:0.0:0.0:1.0	.	309	Q9UJW2	TINAG_HUMAN	P	168;309	ENSP00000259782:L309P	ENSP00000259782:L309P	L	+	2	0	TINAG	54322499	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	3.982000	0.56909	2.247000	0.74100	0.482000	0.46254	CTT	.	.	.	none		0.423	TINAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040984.1	NM_014464		C	54214540	T	C	54214540	3	2	19	1	0	0	0	0	1	0	0	0	15933	1609	56	3	952	3	TINAG	6	54214540	Missense_Mutation	SNP	T	TCGA-2Z-A9JP-01A-11D-A42J-10		54214540	116900527	18	1273											
DST	667	hgsc.bcm.edu	37	chr6	56494230	56494230	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtctcttttcatctacttcAgatctccattgctaaaatac	10	17	3	11	0	5	1	2	0	3	1	7	1	5	1	1	0	3	1	1	0	4	7			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr6:56494230A>G	ENST00000361203.3	-	28	3667	c.3660T>C	c.(3658-3660)tcT>tcC	p.S1220S	DST_ENST00000370769.4_Silent_p.S1220S|DST_ENST00000421834.2_Silent_p.S1220S|DST_ENST00000446842.2_Silent_p.S894S|DST_ENST00000518935.1_Silent_p.S894S|DST_ENST00000370788.2_Silent_p.S1220S|DST_ENST00000370765.6_Silent_p.S894S|DST_ENST00000244364.6_Silent_p.S894S|DST_ENST00000312431.6_Silent_p.S1220S|DST_ENST00000370754.5_Silent_p.S1398S			Q03001	DYST_HUMAN	dystonin	1220					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)			CATCTACTTCAGATCTCCATT	0.308																																					p.S894S		Atlas-SNP	.											.	DST	1427	.	0			c.T2682C						PASS	.						92	88	89					6																	56494230		2203	4300	6503	SO:0001819	synonymous_variant	667	exon18			TACTTCAGATCTC	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.3660T>C	chr6.hg19:g.56494230A>G		45.0	0.0	.		64.0	26.0	.	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	hg19																																																																																				.	.	.	none		0.308	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		G	56494230	A	G	56494230	2	3	19	1	0	0	0	0	0	0	0	1	4785	175	7	3		3	DST	6	56494230	Silent	SNP	A	TCGA-2Z-A9JP-01A-11D-A42J-10	2279690	56494230	114620837	19	1274											
LAMA4	3910	hgsc.bcm.edu	37	chr6	112430643	112430644	+	Missense_Mutation	DNP	GG	GG	AT																															agctgtgctctgtcatgtcaGgctgctggacaggagttgat																										TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr6:112430643_112430644GG>AT	ENST00000230538.7	-	39	5865_5866	c.5468_5469CC>AT	c.(5467-5469)gCC>gAT	p.A1823D	LAMA4_ENST00000389463.4_Missense_Mutation_p.A1816D|LAMA4_ENST00000424408.2_Missense_Mutation_p.A1816D|LAMA4_ENST00000522006.1_Missense_Mutation_p.A1816D	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	1823					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)		TGTCATGTCAGGCTGCTGGACA	0.52																																					p.A1823A|p.A1823D		Atlas-SNP	.											.	LAMA4	227	.	0			c.C5469T|c.C5468A						PASS	.																																			SO:0001583	missense	3910	exon39			ATGTCAGGCTGCT|TGTCAGGCTGCTG		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.5468_5469delinsAT	chr6.hg19:g.112430643_112430644delinsAT	ENSP00000230538:p.Ala1823Asp	56.0	0.0	.		48.0|49.0	25.0	.	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Silent|Missense_Mutation	SNP	ENST00000230538.7	hg19	CCDS43491.1																																																																																			.	.	.	none		0.52	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206		AT	112430644	GG	AT	112430643	3	1	19	1	0	0	0	0	1	0	0	0	8615	987	35	2	6	2	LAMA4	6	112430643	Missense_Mutation	DNP	GG	TCGA-2Z-A9JP-01A-11D-A42J-10	55936413	112430643	58684424	20	1275											
RAPGEF5	9771	hgsc.bcm.edu	37	chr7	22200190	22200190	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctttcaattctttttcaagtAttggatattcataaacatca	13	18	3	7	0	5	0	4	0	1	0	5	1	5	1	0	1	1	1	0	1	6	9			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr7:22200190A>G	ENST00000401957.2	-	4	810	c.563T>C	c.(562-564)aTa>aCa	p.I188T	RAPGEF5_ENST00000344041.6_Missense_Mutation_p.I338T			Q92565	RPGF5_HUMAN	Rap guanine nucleotide exchange factor (GEF) 5	188	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				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						TTTTTCAAGTATTGGATATTC	0.323																																					p.I338T		Atlas-SNP	.											.	RAPGEF5	96	.	0			c.T1013C						PASS	.						45	42	43					7																	22200190		1788	3990	5778	SO:0001583	missense	9771	exon14			TCAAGTATTGGAT	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	ENST00000401957.2:c.563T>C	chr7.hg19:g.22200190A>G	ENSP00000384044:p.Ile188Thr	29.0	0.0	.		41.0	19.0	.	NM_012294	A4D140|Q8IXU5	Missense_Mutation	SNP	ENST00000401957.2	hg19		.	.	.	.	.	.	.	.	.	.	A	10.32	1.317657	0.23994	.	.	ENSG00000136237	ENST00000344041;ENST00000425852;ENST00000258735;ENST00000401957;ENST00000458533	T;T;T	0.28666	1.6;1.6;1.6	6.03	6.03	0.97812	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (2);	0.495212	0.24470	N	0.038242	T	0.23210	0.0561	N	0.19112	0.55	0.29386	N	0.862978	B;B	0.09022	0.0;0.002	B;B	0.08055	0.003;0.002	T	0.08269	-1.0730	10	0.32370	T	0.25	.	16.5594	0.84535	1.0:0.0:0.0:0.0	.	188;338	Q92565;A8MQ07	RPGF5_HUMAN;.	T	338;188;188;188;76	ENSP00000343656:I338T;ENSP00000384044:I188T;ENSP00000415664:I76T	ENSP00000258735:I188T	I	-	2	0	RAPGEF5	22166715	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.076000	0.64413	2.313000	0.78055	0.519000	0.50382	ATA	.	.	.	none		0.323	RAPGEF5-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000326590.2	NM_012294		G	22200190	A	G	22200190	3	3	19	1	0	0	0	0	1	0	0	0	13060	449	16	3	1231	3	RAPGEF5	7	22200190	Missense_Mutation	SNP	A	TCGA-2Z-A9JP-01A-11D-A42J-10		22200190	136938473	21	1276											
VPS41	27072	hgsc.bcm.edu	37	chr7	38902201	38902201	+	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	aagtaaataaaccttgccatAatgtgtgcccaatgccaaaa	17	9	6	9	0	0	0	0	0	0	0	0	0	0	0	4	0	4	1	4	0	9	4			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr7:38902201A>T	ENST00000310301.4	-	4	244	c.190T>A	c.(190-192)Tat>Aat	p.Y64N	VPS41_ENST00000395969.2_Missense_Mutation_p.Y64N	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	64					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						ACCTTGCCATAATGTGTGCCC	0.308																																					p.Y64N		Atlas-SNP	.											.	VPS41	102	.	0			c.T190A						PASS	.						83	84	83					7																	38902201		2203	4300	6503	SO:0001583	missense	27072	exon4			TGCCATAATGTGT	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.190T>A	chr7.hg19:g.38902201A>T	ENSP00000309457:p.Tyr64Asn	53.0	0.0	.		101.0	35.0	.	NM_080631	E9PF36|Q86TP8|Q99851|Q99852	Missense_Mutation	SNP	ENST00000310301.4	hg19	CCDS5457.1	.	.	.	.	.	.	.	.	.	.	A	12.72	2.023444	0.35701	.	.	ENSG00000006715	ENST00000310301;ENST00000395969;ENST00000414632;ENST00000418457;ENST00000457055	T;T;T;T;T	0.51817	2.5;2.48;3.47;0.69;2.45	5.62	5.62	0.85841	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.168014	0.53938	D	0.000041	T	0.15132	0.0365	N	0.01424	-0.875	0.43994	D	0.99669	P;P;P	0.37864	0.61;0.61;0.61	B;B;B	0.24541	0.054;0.054;0.054	T	0.28267	-1.0049	10	0.09843	T	0.71	-19.4277	10.9878	0.47532	0.8608:0.0:0.0:0.1392	.	64;64;64	B2RB94;E9PF36;P49754	.;.;VPS41_HUMAN	N	64;64;51;14;14	ENSP00000309457:Y64N;ENSP00000379297:Y64N;ENSP00000411919:Y51N;ENSP00000407835:Y14N;ENSP00000398584:Y14N	ENSP00000265745:Y64N	Y	-	1	0	VPS41	38868726	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.754000	0.74909	2.133000	0.65898	0.477000	0.44152	TAT	.	.	.	none		0.308	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3			T	38902201	A	T	38902201	3	4	19	1	0	0	0	0	1	0	0	0	17222	362	13	5	2478	5	VPS41	7	38902201	Missense_Mutation	SNP	A	TCGA-2Z-A9JP-01A-11D-A42J-10	16702011	38902201	120236462	22	1277											
PHF20L1	51105	hgsc.bcm.edu	37	chr8	133823301	133823301	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttctcaaggtttgttggcAtccaaagctgttggggttga	7	16	12	6	0	1	1	1	1	1	0	3	1	2	1	1	4	1	6	1	4	2	6			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr8:133823301A>G	ENST00000395386.2	+	9	1157	c.858A>G	c.(856-858)gcA>gcG	p.A286A	PHF20L1_ENST00000395390.2_Silent_p.A261A|PHF20L1_ENST00000395379.1_Silent_p.A286A|PHF20L1_ENST00000395376.1_Silent_p.A291A|PHF20L1_ENST00000220847.7_5'UTR|PHF20L1_ENST00000337920.4_Silent_p.A260A	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	286							zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			GTTTGTTGGCATCCAAAGCTG	0.338																																					p.A286A		Atlas-SNP	.											.	PHF20L1	129	.	0			c.A858G						PASS	.						142	152	148					8																	133823301		2203	4300	6503	SO:0001819	synonymous_variant	51105	exon9			GTTGGCATCCAAA	AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"Tudor domain containing", "Zinc fingers, PHD-type"	24280	protein-coding gene	gene with protein product	"tudor domain containing 20B"					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.858A>G	chr8.hg19:g.133823301A>G		69.0	0.0	.		84.0	51.0	.	NM_016018	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Silent	SNP	ENST00000395386.2	hg19	CCDS6367.2																																																																																			.	.	.	none		0.338	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018		G	133823301	A	G	133823301	2	3	19	1	0	0	0	0	0	0	0	1	11839	204	8	3		3	PHF20L1	8	133823301	Silent	SNP	A	TCGA-2Z-A9JP-01A-11D-A42J-10		133823301	12540721	23	1278											
RECQL4	9684	hgsc.bcm.edu	37	chr8	145741535	145741535	+	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	0	0	0	0	0	0	0	0	0	0	ccctagcttgactggaggggCtgagtccgtggtacctgggg	5	9	17	10	1	0	2	0	2	0	0	1	3	1	3	3	6	2	3	3	6	2	3			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr8:145741535C>T	ENST00000292524.1	+	0	0				RECQL4_ENST00000428558.2_Missense_Mutation_p.S323N|CTD-2517M22.17_ENST00000580385.1_RNA|LRRC14_ENST00000529022.1_5'Flank|RECQL4_ENST00000532237.1_5'UTR	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)			ACTGGAGGGGCTGAGTCCGTG	0.647																																					p.S323N		Atlas-SNP	.											.	RECQL4	75	.	0			c.G968A						PASS	.						74	92	86					8																	145741535		2086	4208	6294	SO:0001631	upstream_gene_variant	9401	exon5			GAGGGGCTGAGTC	BC011377	CCDS6432.1	8q24.3	2012-08-20			ENSG00000160959	ENSG00000160959			20419	protein-coding gene	gene with protein product						7584026	Standard	NM_001272036		Approved	KIAA0014, LRRC14A	uc003zdk.3	Q15048	OTTHUMG00000165179		chr8.hg19:g.145741535C>T	Exception_encountered	84.0	0.0	.		61.0	37.0	.	NM_004260	A8K0A8|D3DWM8	Missense_Mutation	SNP	ENST00000292524.1	hg19	CCDS6432.1																																																																																			.	.	.	none		0.647	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665		T	145741535	C	T	145741535	1	4	19	0	1	0	0	0	0	0	0	0	13215	797	28	2		2	RECQL4	8	145741535	5'Flank	SNP	C	TCGA-2Z-A9JP-01A-11D-A42J-10	11918234	145741535	622487	24	1279											
TSTD2	158427	hgsc.bcm.edu	37	chr9	100389788	100389788	+	Missense_Mutation	SNP	T	T	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	tttaaatccaggtcagaaaaTcttaaaatgcagttctccag	15	12	6	8	0	3	1	1	0	2	1	5	1	4	1	2	1	1	2	2	1	6	4			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr9:100389788T>G	ENST00000341170.4	-	2	439	c.57A>C	c.(55-57)agA>agC	p.R19S	TSTD2_ENST00000354801.2_5'UTR	NM_139246.4	NP_640339.4	Q5T7W7	TSTD2_HUMAN	thiosulfate sulfurtransferase (rhodanese)-like domain containing 2	19										large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	15						GGTCAGAAAATCTTAAAATGC	0.383																																					p.R19S		Atlas-SNP	.											.	TSTD2	42	.	0			c.A57C						PASS	.						131	134	133					9																	100389788		2203	4300	6503	SO:0001583	missense	158427	exon2			AGAAAATCTTAAA	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.57A>C	chr9.hg19:g.100389788T>G	ENSP00000342499:p.Arg19Ser	74.0	0.0	.		69.0	21.0	.	NM_139246	A6NMJ4|A8K584|Q6ZQZ6|Q8IYM3|Q8WY73|Q96ML6|Q96MU1	Missense_Mutation	SNP	ENST00000341170.4	hg19	CCDS6727.2	.	.	.	.	.	.	.	.	.	.	T	15.64	2.893135	0.52121	.	.	ENSG00000136925	ENST00000341170	T	0.32753	1.44	5.38	0.147	0.14838	.	0.161832	0.42420	D	0.000719	T	0.23846	0.0577	L	0.54323	1.7	0.80722	D	1	B	0.24483	0.104	B	0.22386	0.039	T	0.05818	-1.0862	10	0.72032	D	0.01	-3.0007	5.2921	0.15733	0.0:0.2549:0.1411:0.604	.	19	Q5T7W7	TSTD2_HUMAN	S	19	ENSP00000342499:R19S	ENSP00000342499:R19S	R	-	3	2	TSTD2	99429609	1.000000	0.71417	0.722000	0.30670	0.975000	0.68041	1.016000	0.29976	0.064000	0.16427	0.533000	0.62120	AGA	.	.	.	none		0.383	TSTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053325.4	NM_139246		G	100389788	T	G	100389788	3	3	19	1	0	0	0	0	1	0	0	0	16687	1432	50	5	1529	5	TSTD2	9	100389788	Missense_Mutation	SNP	T	TCGA-2Z-A9JP-01A-11D-A42J-10		100389788	40823643	25	1280											
GATA3	2625	hgsc.bcm.edu	37	chr10	8111467	8111467	+	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	gagagcagggacgtcctgtgCgaactgtcagaccaccacaa	12	5	12	12	2	1	2	1	0	0	2	2	5	2	3	3	1	3	1	3	1	2	0			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr10:8111467C>A	ENST00000346208.3	+	5	1408	c.953C>A	c.(952-954)gCg>gAg	p.A318E	GATA3_ENST00000379328.3_Missense_Mutation_p.A319E|GATA3_ENST00000461472.1_3'UTR			P23771	GATA3_HUMAN	GATA binding protein 3	318					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						ACGTCCTGTGCGAACTGTCAG	0.502			"F, N, S"		breast		"HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE)"																														p.A319E		Atlas-SNP	.		Rec	yes		10	10p15	2625	GATA binding protein 3	yes	E	.	GATA3	182	.	0			c.C956A						PASS	.						156	117	130					10																	8111467		2203	4300	6503	SO:0001583	missense	2625	exon5			CCTGTGCGAACTG	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.953C>A	chr10.hg19:g.8111467C>A	ENSP00000341619:p.Ala318Glu	68.0	0.0	.		60.0	21.0	.	NM_001002295	Q5VWG7|Q5VWG8|Q96J16	Missense_Mutation	SNP	ENST00000346208.3	hg19	CCDS7083.1	.	.	.	.	.	.	.	.	.	.	C	33	5.264336	0.95399	.	.	ENSG00000107485	ENST00000379328;ENST00000346208	D;D	0.99436	-5.9;-5.9	5.21	5.21	0.72293	Zinc finger, NHR/GATA-type (1);Zinc finger, GATA-type (4);	0.000000	0.85682	D	0.000000	D	0.99563	0.9843	M	0.84948	2.725	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.995	D	0.98364	1.0550	10	0.87932	D	0	-22.289	19.1275	0.93391	0.0:1.0:0.0:0.0	.	318;319	P23771;P23771-2	GATA3_HUMAN;.	E	319;318	ENSP00000368632:A319E;ENSP00000341619:A318E	ENSP00000341619:A318E	A	+	2	0	GATA3	8151473	1.000000	0.71417	0.987000	0.45799	0.958000	0.62258	7.776000	0.85560	2.590000	0.87494	0.561000	0.74099	GCG	.	.	.	none		0.502	GATA3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046719.1	NM_001002295		A	8111467	C	A	8111467	3	1	19	1	0	0	0	0	1	0	0	0	6262	768	27	4	970	4	GATA3	10	8111467	Missense_Mutation	SNP	C	TCGA-2Z-A9JP-01A-11D-A42J-10		8111467	127423280	26	1281											
ZNF438	220929	hgsc.bcm.edu	37	chr10	31138190	31138190	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttccgttttcttccttttcTctttgctgctccactgttca	2	21	4	14	1	3	0	1	0	2	0	7	0	6	0	3	0	2	4	3	0	0	8			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr10:31138190T>C	ENST00000361310.3	-	6	1473	c.1144A>G	c.(1144-1146)Aga>Gga	p.R382G	ZNF438_ENST00000436087.2_Missense_Mutation_p.R382G|ZNF438_ENST00000413025.1_Missense_Mutation_p.R382G|ZNF438_ENST00000452305.1_Missense_Mutation_p.R372G|ZNF438_ENST00000444692.2_Missense_Mutation_p.R372G|ZNF438_ENST00000442986.1_Missense_Mutation_p.R382G|ZNF438_ENST00000538351.2_Missense_Mutation_p.R333G|ZNF438_ENST00000375311.1_5'UTR|ZNF438_ENST00000331737.6_Missense_Mutation_p.R372G			Q7Z4V0	ZN438_HUMAN	zinc finger protein 438	382					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)				CTTCCTTTTCTCTTTGCTGCT	0.398																																					p.R382G		Atlas-SNP	.											.	ZNF438	90	.	0			c.A1144G						PASS	.						112	107	109					10																	31138190		2203	4300	6503	SO:0001583	missense	220929	exon7			CTTTTCTCTTTGC	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.1144A>G	chr10.hg19:g.31138190T>C	ENSP00000354663:p.Arg382Gly	65.0	0.0	.		51.0	22.0	.	NM_182755	A2A3J4|A8K9L5|Q5T426|Q658Q4|Q6ZN65	Missense_Mutation	SNP	ENST00000361310.3	hg19	CCDS7168.1	.	.	.	.	.	.	.	.	.	.	T	17.20	3.327742	0.60743	.	.	ENSG00000183621	ENST00000331737;ENST00000361310;ENST00000436087;ENST00000442986;ENST00000413025;ENST00000452305;ENST00000444692;ENST00000538351;ENST00000430896	T;T;T;T;T;T;T;T	0.12879	2.64;2.64;2.64;2.64;2.64;2.64;2.64;2.64	5.73	5.73	0.89815	.	0.090652	0.85682	D	0.000000	T	0.34629	0.0904	M	0.73598	2.24	0.49051	D	0.999748	D;D	0.63046	0.986;0.992	P;P	0.59357	0.722;0.856	T	0.09684	-1.0663	10	0.87932	D	0	-28.0386	15.1883	0.73023	0.0:0.0:0.0:1.0	.	382;372	Q7Z4V0;Q7Z4V0-2	ZN438_HUMAN;.	G	372;382;382;382;382;372;372;333;101	ENSP00000333571:R372G;ENSP00000354663:R382G;ENSP00000406934:R382G;ENSP00000412363:R382G;ENSP00000387546:R382G;ENSP00000413060:R372G;ENSP00000410898:R372G;ENSP00000445461:R333G	ENSP00000333571:R372G	R	-	1	2	ZNF438	31178196	1.000000	0.71417	0.642000	0.29436	0.135000	0.20990	7.162000	0.77515	2.186000	0.69663	0.528000	0.53228	AGA	.	.	.	none		0.398	ZNF438-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277006.1	NM_182755		C	31138190	T	C	31138190	3	2	19	1	0	0	0	0	1	0	0	0	17922	1559	54	3	1350	3	ZNF438	10	31138190	Missense_Mutation	SNP	T	TCGA-2Z-A9JP-01A-11D-A42J-10	23026723	31138190	104396557	27	1282											
PCDH15	65217	hgsc.bcm.edu	37	chr10	56423964	56423964	+	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	ggcccaagcagatttcaaagAgagagcccaggatgatccct	13	6	11	11	0	1	4	1	1	0	3	2	6	2	5	3	2	2	1	3	2	2	1			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr10:56423964A>T	ENST00000320301.6	-	2	453	c.59T>A	c.(58-60)cTc>cAc	p.L20H	PCDH15_ENST00000409834.1_5'UTR|PCDH15_ENST00000373957.3_Missense_Mutation_p.L20H|PCDH15_ENST00000437009.1_Missense_Mutation_p.L20H|PCDH15_ENST00000395433.1_Missense_Mutation_p.L20H|PCDH15_ENST00000395432.2_Missense_Mutation_p.L20H|PCDH15_ENST00000395446.1_Missense_Mutation_p.L20H|PCDH15_ENST00000395440.1_Missense_Mutation_p.L20H|PCDH15_ENST00000395430.1_Missense_Mutation_p.L20H|PCDH15_ENST00000373965.2_Missense_Mutation_p.L20H|PCDH15_ENST00000395438.1_Missense_Mutation_p.L20H|PCDH15_ENST00000373955.1_Missense_Mutation_p.L20H|PCDH15_ENST00000395442.1_Missense_Mutation_p.L20H|PCDH15_ENST00000361849.3_Missense_Mutation_p.L20H|PCDH15_ENST00000395445.1_Missense_Mutation_p.L20H|PCDH15_ENST00000414778.1_Missense_Mutation_p.L20H	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	20					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)				GATTTCAAAGAGAGAGCCCAG	0.383										HNSCC(58;0.16)																											p.L20H		Atlas-SNP	.											.	PCDH15	1715	.	0			c.T59A						PASS	.						80	73	75					10																	56423964		2203	4300	6503	SO:0001583	missense	65217	exon2			TCAAAGAGAGAGC	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.59T>A	chr10.hg19:g.56423964A>T	ENSP00000322604:p.Leu20His	36.0	0.0	.		76.0	27.0	.	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	hg19	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	A	13.70	2.314590	0.40996	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000395445;ENST00000395446;ENST00000395442;ENST00000395440;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955;ENST00000458638	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.68765	0.34;0.34;0.26;0.27;0.25;0.46;0.36;0.19;0.23;-0.35;-0.35;0.24;0.24;0.26;0.39;0.55	5.8	5.8	0.92144	.	.	.	.	.	T	0.72407	0.3456	L	0.40543	1.245	0.19300	N	0.999976	D;D;D;D;D;D;D;D;D;D;D;P;P;D;D	0.67145	0.986;0.986;0.986;0.986;0.992;0.986;0.986;0.981;0.996;0.996;0.996;0.81;0.931;0.975;0.986	P;P;P;P;P;P;P;P;P;P;P;B;P;P;P	0.58873	0.789;0.832;0.832;0.832;0.765;0.832;0.789;0.695;0.847;0.784;0.789;0.378;0.678;0.789;0.832	T	0.66555	-0.5894	9	0.87932	D	0	.	13.6644	0.62387	1.0:0.0:0.0:0.0	.	20;20;20;20;20;20;20;20;20;20;20;20;20;20;20	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	H	20	ENSP00000363076:L20H;ENSP00000410304:L20H;ENSP00000378826:L20H;ENSP00000378832:L20H;ENSP00000378833:L20H;ENSP00000378829:L20H;ENSP00000378827:L20H;ENSP00000378820:L20H;ENSP00000354950:L20H;ENSP00000378821:L20H;ENSP00000363068:L20H;ENSP00000322604:L20H;ENSP00000378818:L20H;ENSP00000412628:L20H;ENSP00000363066:L20H;ENSP00000394465:L20H	ENSP00000322604:L20H	L	-	2	0	PCDH15	56093970	0.993000	0.37304	0.031000	0.17742	0.006000	0.05464	5.603000	0.67619	2.216000	0.71823	0.402000	0.26972	CTC	.	.	.	none		0.383	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		T	56423964	A	T	56423964	3	4	19	1	0	0	0	0	1	0	0	0	11518	304	11	5	7599	5	PCDH15	10	56423964	Missense_Mutation	SNP	A	TCGA-2Z-A9JP-01A-11D-A42J-10	25285774	56423964	79110783	28	1283											
MKI67	4288	hgsc.bcm.edu	37	chr10	129910660	129910660	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctttgtgccttcacttccAcatggatttctgaacctgac	8	14	7	12	0	2	2	1	2	1	0	3	3	3	3	3	1	3	1	3	1	1	4			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr10:129910660A>G	ENST00000368654.3	-	9	2081	c.1706T>C	c.(1705-1707)gTg>gCg	p.V569A	MKI67_ENST00000484853.1_5'UTR|MKI67_ENST00000368653.3_Missense_Mutation_p.V209A	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	569					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)				CTTCACTTCCACATGGATTTC	0.458																																					p.V569A		Atlas-SNP	.											.	MKI67	363	.	0			c.T1706C						PASS	.						133	143	140					10																	129910660		2203	4300	6503	SO:0001583	missense	4288	exon9			ACTTCCACATGGA	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.1706T>C	chr10.hg19:g.129910660A>G	ENSP00000357643:p.Val569Ala	61.0	0.0	.		70.0	30.0	.	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	hg19	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	A	10.71	1.426189	0.25726	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609;ENST00000368652	T;T	0.01446	4.94;4.88	4.05	2.73	0.32206	.	0.976288	0.08358	N	0.958088	T	0.01222	0.0040	N	0.19112	0.55	0.09310	N	1	B;B;B	0.28636	0.218;0.218;0.139	B;B;B	0.24848	0.056;0.056;0.025	T	0.42310	-0.9459	10	0.02654	T	1	.	6.0887	0.19983	0.866:0.0:0.134:0.0	.	569;209;569	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	A	569;209;569;144	ENSP00000357643:V569A;ENSP00000357642:V209A	ENSP00000357641:V144A	V	-	2	0	MKI67	129800650	0.000000	0.05858	0.009000	0.14445	0.003000	0.03518	-0.223000	0.09177	0.593000	0.29745	0.460000	0.39030	GTG	.	.	.	none		0.458	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		G	129910660	A	G	129910660	3	3	19	1	0	0	0	0	1	0	0	0	9605	159	6	3	8092	3	MKI67	10	129910660	Missense_Mutation	SNP	A	TCGA-2Z-A9JP-01A-11D-A42J-10	73486696	129910660	5624087	29	1284											
NLRP14	338323	hgsc.bcm.edu	37	chr11	7083573	7083573	+	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	aattcttacagattgatgggCtgtgttctcactaatgcatg	10	15	9	7	0	2	2	1	1	2	1	3	2	2	2	0	1	2	3	0	1	3	5			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr11:7083573C>A	ENST00000299481.4	+	10	3160	c.2814C>A	c.(2812-2814)ggC>ggA	p.G938G		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	938					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)		GATTGATGGGCTGTGTTCTCA	0.408																																					p.G938G		Atlas-SNP	.											.	NLRP14	187	.	0			c.C2814A						PASS	.						122	118	119					11																	7083573		2201	4296	6497	SO:0001819	synonymous_variant	338323	exon10			GATGGGCTGTGTT	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.2814C>A	chr11.hg19:g.7083573C>A		75.0	0.0	.		94.0	38.0	.	NM_176822	Q7RTR6	Silent	SNP	ENST00000299481.4	hg19	CCDS7776.1																																																																																			.	.	.	none		0.408	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822		A	7083573	C	A	7083573	2	1	19	1	0	0	0	0	0	0	0	1	10483	784	28	4		4	NLRP14	11	7083573	Silent	SNP	C	TCGA-2Z-A9JP-01A-11D-A42J-10		7083573	127922943	30	1285											
CCDC88B	283234	hgsc.bcm.edu	37	chr11	64110796	64110797	+	Splice_Site	INS	-	-	GGCAT																															cggctgggcgaggcccatgcINSggtaaggtagccagagtgat																								rs561918725		TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr11:64110796_64110797insGGCAT	ENST00000356786.5	+	11	1252_1253	c.1208_1209insGGCAT	c.(1207-1212)gcggag>gcGGCATggag	p.E404fs	CCDC88B_ENST00000463837.1_3'UTR|CCDC88B_ENST00000301897.4_5'Flank	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	404						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						GAGGCCCATGCGGTAAGGTAGC	0.639																																					p.A403fs		Atlas-Indel,Pindel	.											.	CCDC88B	89	.	0			c.1208_1209insGGCAT						PASS	.																																			SO:0001630	splice_region_variant	283234	exon11			.	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.1209+1->GGCAT	chr11.hg19:g.64110796_64110797insGGCAT		76.0	0.0	0		76.0	12.0	0.157895	NM_032251	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Frame_Shift_Ins	INS	ENST00000356786.5	hg19	CCDS8072.2																																																																																			.	.	.	none		0.639	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251	Frame_Shift_Ins	GGCAT	64110797	-	GGCAT	64110796	8	5	19	1	0	1	1	0	0	0	1	0	2866	782	27	0	1250	0	CCDC88B	11	64110796	Splice_Site	INS	-	TCGA-2Z-A9JP-01A-11D-A42J-10	57027223	64110796	70895720	31	1286											
NUMA1	10068	hgsc.bcm.edu	37	chr11	71716361	71716361	+	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	0	0	0	0	0	0	0	gctctgcaatgcggttccagTcatccagctgctcaggctca	7	10	10	14	1	4	0	3	0	1	0	6	0	6	0	2	2	4	6	2	2	1	1			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr11:71716361T>C	ENST00000393703.4	+	0	1788				NUMA1_ENST00000358965.6_Missense_Mutation_p.D1902G|NUMA1_ENST00000351960.6_Missense_Mutation_p.D780G|NUMA1_ENST00000393695.3_Missense_Mutation_p.D1916G	NM_001039660.1	NP_001034749.1	O95998	I18BP_HUMAN	interleukin 18 binding protein						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						GCGGTTCCAGTCATCCAGCTG	0.592																																					p.D1916G		Atlas-SNP	.											.	NUMA1	142	.	0			c.A5747G						PASS	.						103	87	92					11																	71716361		2200	4293	6493	SO:0001628	intergenic_variant	4926	exon23			TTCCAGTCATCCA	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		chr11.hg19:g.71716361T>C		41.0	0.0	.		31.0	15.0	.	NM_006185	B3KUZ0|B7WPK4|O95993|O96027|Q9NZA9|Q9UBR7	Missense_Mutation	SNP	ENST00000393703.4	hg19	CCDS8206.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.3|25.3	4.625967|4.625967	0.87560|0.87560	.|.	.|.	ENSG00000137497|ENSG00000137497	ENST00000351960;ENST00000358965;ENST00000393695;ENST00000359652;ENST00000536544|ENST00000541584	T;T;T|.	0.25579|.	1.79;2.22;2.22|.	4.85|4.85	4.85|4.85	0.62838|0.62838	.|.	0.000000|.	0.56097|.	D|.	0.000032|.	T|T	0.53981|0.53981	0.1830|0.1830	L|L	0.29908|0.29908	0.895|0.895	0.47819|0.47819	D|D	0.999521|0.999521	D;D;D;D|.	0.89917|.	1.0;0.998;1.0;1.0|.	D;D;D;D|.	0.91635|.	0.999;0.977;0.999;0.999|.	T|T	0.51076|0.51076	-0.8751|-0.8751	10|5	0.87932|.	D|.	0|.	.|.	14.2872|14.2872	0.66254|0.66254	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1922;1902;1916;780|.	Q4LE64;Q14980-2;Q14980;Q9BTE9|.	.;.;NUMA1_HUMAN;.|.	G|A	780;1902;1916;1465;889|765	ENSP00000260051:D780G;ENSP00000351851:D1902G;ENSP00000377298:D1916G|.	ENSP00000260051:D780G|.	D|T	-|-	2|1	0|0	NUMA1|NUMA1	71394009|71394009	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	6.173000|6.173000	0.71937|0.71937	2.038000|2.038000	0.60285|0.60285	0.533000|0.533000	0.62120|0.62120	GAC|ACT	.	.	.	none		0.592	IL18BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258012.2	NM_173042		C	71716361	T	C	71716361	1	2	19	0	1	0	0	0	0	0	0	0	10757	1667	58	3		3	NUMA1	11	71716361	IGR	SNP	T	TCGA-2Z-A9JP-01A-11D-A42J-10	7605565	71716361	63290155	32	1287											
MMP10	4319	hgsc.bcm.edu	37	chr11	102649966	102649966	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttaactgcaaaagagatcatTatatcagcctctccttcata	14	13	4	10	0	4	1	3	0	1	1	5	2	4	1	2	0	3	1	2	0	6	5			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr11:102649966T>C	ENST00000279441.4	-	3	510	c.474A>G	c.(472-474)atA>atG	p.I158M		NM_002425.2	NP_002416.1	P09238	MMP10_HUMAN	matrix metallopeptidase 10 (stromelysin 2)	158					collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|liver(2)|lung(6)	22	all_epithelial(12;0.00961)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0303)|Lung(13;0.0828)|all cancers(10;0.116)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0145)	Marimastat(DB00786)	AAGAGATCATTATATCAGCCT	0.408																																					p.I158M		Atlas-SNP	.											.	MMP10	44	.	0			c.A474G						PASS	.						150	151	151					11																	102649966		2203	4299	6502	SO:0001583	missense	4319	exon3			GATCATTATATCA	X07820	CCDS8321.1	11q22.3	2008-02-05	2005-08-08		ENSG00000166670	ENSG00000166670	3.4.24.22		7156	protein-coding gene	gene with protein product		185260	"matrix metalloproteinase 10 (stromelysin 2)"	STMY2			Standard	NM_002425		Approved		uc001phg.2	P09238	OTTHUMG00000168083	ENST00000279441.4:c.474A>G	chr11.hg19:g.102649966T>C	ENSP00000279441:p.Ile158Met	56.0	0.0	.		91.0	33.0	.	NM_002425	B2R9X9|Q53HH9	Missense_Mutation	SNP	ENST00000279441.4	hg19	CCDS8321.1	.	.	.	.	.	.	.	.	.	.	t	13.80	2.346268	0.41599	.	.	ENSG00000166670	ENST00000279441;ENST00000539681	T;T	0.36878	1.23;1.23	4.38	-1.36	0.09085	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.000000	0.64402	D	0.000003	T	0.66906	0.2837	H	0.96111	3.77	0.53688	D	0.999972	D	0.69078	0.997	D	0.68483	0.958	T	0.76468	-0.2948	10	0.87932	D	0	.	13.7321	0.62794	0.0:0.0:0.5402:0.4598	.	158	P09238	MMP10_HUMAN	M	158	ENSP00000279441:I158M;ENSP00000441485:I158M	ENSP00000279441:I158M	I	-	3	3	MMP10	102155176	0.952000	0.32445	0.984000	0.44739	0.380000	0.30137	-0.019000	0.12546	-0.302000	0.08869	0.482000	0.46254	ATA	.	.	.	none		0.408	MMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398014.1			C	102649966	T	C	102649966	3	2	19	1	0	0	0	0	1	0	0	0	9656	1744	61	3	988	3	MMP10	11	102649966	Missense_Mutation	SNP	T	TCGA-2Z-A9JP-01A-11D-A42J-10	30933605	102649966	32356550	33	1288											
GRIK4	2900	hgsc.bcm.edu	37	chr11	120745851	120745851	+	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	cactctctcttggacaggtaGaattggaaggtcttaccggc	9	11	11	10	1	3	1	0	0	3	1	4	3	3	3	1	5	1	1	1	5	4	4			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr11:120745851G>A	ENST00000527524.2	+	11	1350	c.1063G>A	c.(1063-1065)Gaa>Aaa	p.E355K	RP11-640N11.2_ENST00000505153.2_RNA|GRIK4_ENST00000438375.2_Missense_Mutation_p.E355K	NM_001282470.1	NP_001269399.1	Q16099	GRIK4_HUMAN	glutamate receptor, ionotropic, kainate 4	355					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)		TGGACAGGTAGAATTGGAAGG	0.478																																					p.E355K		Atlas-SNP	.											.	GRIK4	149	.	0			c.G1063A						PASS	.						108	95	99					11																	120745851		2203	4299	6502	SO:0001583	missense	2900	exon9			CAGGTAGAATTGG	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.1063G>A	chr11.hg19:g.120745851G>A	ENSP00000435648:p.Glu355Lys	44.0	0.0	.		62.0	20.0	.	NM_014619	A8K9L1	Missense_Mutation	SNP	ENST00000527524.2	hg19	CCDS8433.1	.	.	.	.	.	.	.	.	.	.	g	22.6	4.305970	0.81247	.	.	ENSG00000149403	ENST00000527524;ENST00000438375	T;T	0.36157	1.27;1.27	5.92	4.95	0.65309	Extracellular ligand-binding receptor (1);	0.137856	0.64402	D	0.000004	T	0.40222	0.1108	M	0.66939	2.045	0.58432	D	0.999997	B;B	0.34226	0.443;0.309	B;B	0.34346	0.18;0.18	T	0.39583	-0.9607	10	0.56958	D	0.05	.	15.9157	0.79517	0.0:0.0:0.8642:0.1358	.	355;355	A6H8K8;Q16099	.;GRIK4_HUMAN	K	355	ENSP00000435648:E355K;ENSP00000404063:E355K	ENSP00000404063:E355K	E	+	1	0	GRIK4	120251061	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.544000	0.82117	2.793000	0.96121	0.651000	0.88453	GAA	.	.	.	none		0.478	GRIK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109760.4	NM_014619		A	120745851	G	A	120745851	3	1	19	1	0	0	0	0	1	0	0	0	6783	943	33	2	1097	2	GRIK4	11	120745851	Missense_Mutation	SNP	G	TCGA-2Z-A9JP-01A-11D-A42J-10	18095885	120745851	14260665	34	1289											
ITFG2	55846	hgsc.bcm.edu	37	chr12	2929937	2929937	+	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	ccactgggtcttcctgaactGatggtgtctcagccaggttg	6	12	12	11	0	2	2	1	2	2	0	4	2	3	2	3	3	2	1	3	3	1	2			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr12:2929937G>A	ENST00000228799.2	+	6	733	c.594G>A	c.(592-594)ctG>ctA	p.L198L	ITFG2_ENST00000542548.1_Silent_p.L86L|ITFG2_ENST00000419778.2_Silent_p.L21L	NM_018463.3	NP_060933.3	Q969R8	ITFG2_HUMAN	integrin alpha FG-GAP repeat containing 2	198					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)			TTCCTGAACTGATGGTGTCTC	0.562																																					p.L198L		Atlas-SNP	.											.	ITFG2	38	.	0			c.G594A						PASS	.						137	116	123					12																	2929937		2203	4300	6503	SO:0001819	synonymous_variant	55846	exon6			TGAACTGATGGTG	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.594G>A	chr12.hg19:g.2929937G>A		54.0	0.0	.		61.0	22.0	.	NM_018463	A8K4Z5|D3DUQ2|Q6PKU5|Q96SX6	Silent	SNP	ENST00000228799.2	hg19	CCDS8513.1																																																																																			.	.	.	none		0.562	ITFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253091.1	NM_018463		A	2929937	G	A	2929937	2	1	19	1	0	0	0	0	0	0	0	1	7877	1277	45	2		2	ITFG2	12	2929937	Silent	SNP	G	TCGA-2Z-A9JP-01A-11D-A42J-10		2929937	130921958	35	1290											
KLRG1	10219	hgsc.bcm.edu	37	chr12	9161629	9161629	+	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	gattggtctgaggaacaattCtggctggaggtgggaagatg	10	10	17	4	0	2	2	0	1	2	1	2	6	2	5	0	6	1	1	0	6	3	2			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr12:9161629C>G	ENST00000266551.4	+	4	431	c.416C>G	c.(415-417)tCt>tGt	p.S139C	KLRG1_ENST00000356986.3_Missense_Mutation_p.S139C|KLRG1_ENST00000538029.1_3'UTR	NM_005810.3	NP_005801.3	Q96E93	KLRG1_HUMAN	killer cell lectin-like receptor subfamily G, member 1	139	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|kidney(1)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	8						AGGAACAATTCTGGCTGGAGG	0.453																																					p.S139C		Atlas-SNP	.											.	KLRG1	16	.	0			c.C416G						PASS	.						93	90	91					12																	9161629		2203	4300	6503	SO:0001583	missense	10219	exon4			ACAATTCTGGCTG	AF097358	CCDS8599.1	12p13.31	2011-08-30			ENSG00000139187	ENSG00000139187		"Killer cell lectin-like receptors", "C-type lectin domain containing"	6380	protein-coding gene	gene with protein product	"C-type lectin domain family 15, member A"	604874				9862378, 9842918, 16461340, 16140789	Standard	NM_005810		Approved	MAFA, 2F1, MAFA-L, CLEC15A	uc001qvg.3	Q96E93		ENST00000266551.4:c.416C>G	chr12.hg19:g.9161629C>G	ENSP00000266551:p.Ser139Cys	86.0	0.0	.		106.0	46.0	.	NM_005810	B7ZAM2|O43198|O75613	Missense_Mutation	SNP	ENST00000266551.4	hg19		.	.	.	.	.	.	.	.	.	.	C	6.937	0.542572	0.13250	.	.	ENSG00000139187	ENST00000539240;ENST00000356986;ENST00000266551;ENST00000543895	T;T;T;T	0.18657	2.2;2.2;2.2;2.2	3.61	-0.812	0.10853	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	1.481950	0.04134	N	0.318442	T	0.29783	0.0744	L	0.58669	1.825	0.09310	N	1	D;P	0.63880	0.993;0.939	P;B	0.52793	0.709;0.401	T	0.18116	-1.0347	10	0.66056	D	0.02	-6.6127	3.0673	0.06219	0.4231:0.3431:0.0:0.2338	.	139;139	Q96E93;Q96E93-2	KLRG1_HUMAN;.	C	60;139;139;60	ENSP00000445627:S60C;ENSP00000349477:S139C;ENSP00000266551:S139C;ENSP00000443658:S60C	ENSP00000266551:S139C	S	+	2	0	KLRG1	9052896	0.003000	0.15002	0.000000	0.03702	0.116000	0.19942	-0.279000	0.08479	-0.173000	0.10761	0.643000	0.83706	TCT	.	.	.	none		0.453	KLRG1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399145.1	NM_005810		G	9161629	C	G	9161629	3	3	19	1	0	0	0	0	1	0	0	0	8428	913	32	4	430	4	KLRG1	12	9161629	Missense_Mutation	SNP	C	TCGA-2Z-A9JP-01A-11D-A42J-10	6231692	9161629	124690266	36	1291											
PAN2	9924	hgsc.bcm.edu	37	chr12	56718077	56718077	+	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	atttctatcctgatttcataCctgcctccagcacctcgata	9	14	4	14	1	2	1	1	1	1	0	5	2	4	1	5	0	3	1	5	0	3	5			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr12:56718077C>T	ENST00000425394.2	-	12	2305		c.e12+1		PAN2_ENST00000548043.1_Splice_Site|PAN2_ENST00000440411.3_Splice_Site|PAN2_ENST00000257931.5_Splice_Site	NM_001127460.2	NP_001120932	Q9HBH5	RDH14_HUMAN	PAN2 poly(A) specific ribonuclease subunit						osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	41					Vitamin A(DB00162)	TGATTTCATACCTGCCTCCAG	0.453																																					.		Atlas-SNP	.											.	PAN2	107	.	0			c.1928+1G>A						PASS	.						94	96	95					12																	56718077		2203	4300	6503	SO:0001630	splice_region_variant	9924	exon13			TTCATACCTGCCT	AB014610	CCDS8915.1, CCDS44922.1, CCDS53802.1	12q13.2	2014-03-27	2014-03-27	2008-01-08		ENSG00000135473		"Ubiquitin-specific peptidases"	20074	protein-coding gene	gene with protein product	"PAN2 homolog, PABP1 dependent poly A specific ribonuclease subunit (S. cerevisiae)"		"ubiquitin specific protease 52", "ubiquitin specific peptidase 52", "PAN2 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"	USP52		12838346, 14583602	Standard	NM_014871		Approved	KIAA0710, hPAN2	uc001skx.3	Q504Q3	OTTHUMG00000170412	ENST00000425394.2:c.1928+1G>A	chr12.hg19:g.56718077C>T		20.0	0.0	.		28.0	12.0	.	NM_014871		Splice_Site	SNP	ENST00000425394.2	hg19	CCDS44922.1	.	.	.	.	.	.	.	.	.	.	C	15.93	2.977115	0.53720	.	.	ENSG00000135473	ENST00000425394;ENST00000440411;ENST00000257931;ENST00000548043	.	.	.	5.39	4.49	0.54785	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.85	0.63489	0.0:0.8469:0.1531:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PAN2	55004344	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	5.365000	0.66116	1.393000	0.46605	0.557000	0.71058	.	.	.	.	none		0.453	PAN2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409024.1	NM_014871	Intron	T	56718077	C	T	56718077	5	4	19	1	0	0	0	0	0	0	1	0	11421	521	18	2	1739	2	PAN2	12	56718077	Splice_Site	SNP	C	TCGA-2Z-A9JP-01A-11D-A42J-10	47556448	56718077	77133818	37	1292											
LRP1	4035	hgsc.bcm.edu	37	chr12	57548344	57548344	+	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	agaaccgcaccaagctcgtcGacagcaagattgtgtttcct	11	9	9	12	3	0	2	0	0	0	2	3	3	1	2	3	0	3	4	3	0	3	2			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr12:57548344G>A	ENST00000243077.3	+	8	1553	c.1087G>A	c.(1087-1089)Gac>Aac	p.D363N	LRP1_ENST00000554174.1_Missense_Mutation_p.D363N	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	363					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.D363N(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)	CAAGCTCGTCGACAGCAAGAT	0.522																																					p.D363N		Atlas-SNP	.											LRP1,NS,carcinoma,0,1	LRP1	428	.	1	Substitution - Missense(1)	endometrium(1)	c.G1087A						PASS	.						114	80	91					12																	57548344		2203	4300	6503	SO:0001583	missense	4035	exon8			CTCGTCGACAGCA	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.1087G>A	chr12.hg19:g.57548344G>A	ENSP00000243077:p.Asp363Asn	81.0	1.0	.		101.0	33.0	.	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	G	15.05	2.719692	0.48728	.	.	ENSG00000123384	ENST00000243077;ENST00000554174	D;D	0.96104	-3.41;-3.91	4.53	4.53	0.55603	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000001	D	0.95623	0.8577	L	0.38175	1.15	0.43835	D	0.996413	D;D	0.89917	0.999;1.0	D;D	0.72625	0.978;0.978	D	0.93779	0.7082	10	0.23891	T	0.37	.	15.1647	0.72814	0.0:0.0:1.0:0.0	.	363;363	Q07954;Q6PJ72	LRP1_HUMAN;.	N	363	ENSP00000243077:D363N;ENSP00000451737:D363N	ENSP00000243077:D363N	D	+	1	0	LRP1	55834611	1.000000	0.71417	0.977000	0.42913	0.916000	0.54674	9.657000	0.98554	2.521000	0.84997	0.650000	0.86243	GAC	.	.	.	none		0.522	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		A	57548344	G	A	57548344	3	1	19	1	0	0	0	0	1	0	0	0	8958	1058	37	1	1117	1	LRP1	12	57548344	Missense_Mutation	SNP	G	TCGA-2Z-A9JP-01A-11D-A42J-10	830267	57548344	76303551	38	1293											
GLI1	2735	hgsc.bcm.edu	37	chr12	57858618	57858618	+	Missense_Mutation	SNP	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	gcgatgcacatctccaggagGctcctacggtcatctctcca	8	9	9	15	2	3	0	1	0	2	0	7	2	5	1	3	3	2	2	3	3	1	1			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr12:57858618G>A	ENST00000228682.2	+	4	447	c.356G>A	c.(355-357)gGc>gAc	p.G119D	GLI1_ENST00000546141.1_Missense_Mutation_p.G78D|GLI1_ENST00000543426.1_5'UTR	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	119					cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			TCTCCAGGAGGCTCCTACGGT	0.587																																					p.G119D	Pancreas(157;841 1936 10503 41495 50368)	Atlas-SNP	.											.	GLI1	141	.	0			c.G356A						PASS	.						118	102	108					12																	57858618		2203	4300	6503	SO:0001583	missense	2735	exon4			CAGGAGGCTCCTA		CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"Zinc fingers, C2H2-type"	4317	protein-coding gene	gene with protein product		165220	"glioma-associated oncogene homolog 1 (zinc finger protein)", "glioma-associated oncogene family zinc finger 1"	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.356G>A	chr12.hg19:g.57858618G>A	ENSP00000228682:p.Gly119Asp	52.0	0.0	.		33.0	15.0	.	NM_005269	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Missense_Mutation	SNP	ENST00000228682.2	hg19	CCDS8940.1	.	.	.	.	.	.	.	.	.	.	g	23.4	4.417691	0.83449	.	.	ENSG00000111087	ENST00000228682;ENST00000546141;ENST00000528432;ENST00000528467	T;T;T	0.18502	2.21;2.24;2.24	3.62	3.62	0.41486	.	0.000000	0.47852	D	0.000216	T	0.41143	0.1146	M	0.75085	2.285	0.52099	D	0.999942	D	0.76494	0.999	D	0.76071	0.987	T	0.45131	-0.9282	10	0.72032	D	0.01	.	14.557	0.68106	0.0:0.0:1.0:0.0	.	119	P08151	GLI1_HUMAN	D	119;78;119;78	ENSP00000228682:G119D;ENSP00000441006:G78D;ENSP00000434408:G78D	ENSP00000228682:G119D	G	+	2	0	GLI1	56144885	1.000000	0.71417	1.000000	0.80357	0.681000	0.39784	9.508000	0.98000	2.017000	0.59298	0.556000	0.70494	GGC	.	.	.	none		0.587	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269		A	57858618	G	A	57858618	3	1	19	1	0	0	0	0	1	0	0	0	6444	1203	42	2	366	2	GLI1	12	57858618	Missense_Mutation	SNP	G	TCGA-2Z-A9JP-01A-11D-A42J-10	310274	57858618	75993277	39	1294											
USP44	84101	hgsc.bcm.edu	37	chr12	95922715	95922716	+	Missense_Mutation	DNP	CC	CC	TA																															ttgatacctttctggaaactCcaatgacaagtcccagaaag																										TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr12:95922715_95922716CC>TA	ENST00000258499.3	-	3	1779_1780	c.1491_1492GG>TA	c.(1489-1494)ttGGag>ttTAag	p.497_498LE>FK	USP44_ENST00000537435.2_Missense_Mutation_p.497_498LE>FK|USP44_ENST00000552440.1_Intron|USP44_ENST00000393091.2_Missense_Mutation_p.497_498LE>FK	NM_001278393.1|NM_032147.2	NP_001265322.1|NP_115523.2	Q9H0E7	UBP44_HUMAN	ubiquitin specific peptidase 44	497	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						TCTGGAAACTCCAATGACAAGT	0.371																																					p.E498K|p.L497F		Atlas-SNP	.											.	USP44	83	.	0			c.G1492A|c.G1491T						PASS	.																																			SO:0001583	missense	84101	exon3			GAAACTCCAATGA|AAACTCCAATGAC	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.1491_1492delinsTA	chr12.hg19:g.95922715_95922716delinsTA	ENSP00000258499:p.L497_E498delinsFK	68.0|67.0	0.0	.		49.0	21.0	.	NM_032147	B2RDW3	Missense_Mutation	SNP	ENST00000258499.3	hg19	CCDS9053.1																																																																																			.	.	.	none		0.371	USP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408312.1	NM_032147		TA	95922716	CC	TA	95922715	3	4	19	1	0	0	0	0	1	0	0	0	17087	864	30	2	662	2	USP44	12	95922715	Missense_Mutation	DNP	CC	TCGA-2Z-A9JP-01A-11D-A42J-10	38064097	95922715	37929180	40	1295											
CKAP4	10970	hgsc.bcm.edu	37	chr12	106633493	106633493	+	Missense_Mutation	SNP	A	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	gctggcggagctcttcctccAgtctccggatctcctccggg	3	10	12	16	3	3	0	0	0	3	0	8	2	6	2	5	4	1	2	5	4	0	1			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr12:106633493A>C	ENST00000378026.4	-	2	1254	c.1118T>G	c.(1117-1119)cTg>cGg	p.L373R	CKAP4_ENST00000552828.1_5'Flank	NM_006825.3	NP_006816.2	Q07065	CKAP4_HUMAN	cytoskeleton-associated protein 4	373						cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|pancreas(1)|urinary_tract(1)	20						CTCTTCCTCCAGTCTCCGGAT	0.647																																					p.L373R		Atlas-SNP	.											.	CKAP4	49	.	0			c.T1118G						PASS	.						33	37	36					12																	106633493		2201	4300	6501	SO:0001583	missense	10970	exon2			TCCTCCAGTCTCC	X69910	CCDS9103.1	12q23.3	2006-06-23				ENSG00000136026			16991	protein-coding gene	gene with protein product						8314870	Standard	NM_006825		Approved	P63, CLIMP-63, ERGIC-63	uc001tlk.3	Q07065		ENST00000378026.4:c.1118T>G	chr12.hg19:g.106633493A>C	ENSP00000367265:p.Leu373Arg	51.0	0.0	.		44.0	13.0	.	NM_006825	Q504S5|Q53ES6	Missense_Mutation	SNP	ENST00000378026.4	hg19	CCDS9103.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.107665	0.77096	.	.	ENSG00000136026	ENST00000378026	T	0.78816	-1.21	5.82	5.82	0.92795	.	0.216802	0.39210	N	0.001438	D	0.87180	0.6113	M	0.76328	2.33	0.52501	D	0.999951	D	0.89917	1.0	D	0.91635	0.999	D	0.85499	0.1190	10	0.28530	T	0.3	-22.5377	16.19	0.81981	1.0:0.0:0.0:0.0	.	373	Q07065	CKAP4_HUMAN	R	373	ENSP00000367265:L373R	ENSP00000367265:L373R	L	-	2	0	CKAP4	105157623	1.000000	0.71417	0.932000	0.37286	0.809000	0.45718	7.726000	0.84824	2.225000	0.72522	0.460000	0.39030	CTG	.	.	.	none		0.647	CKAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407196.1			C	106633493	A	C	106633493	3	2	19	1	0	0	0	0	1	0	0	0	3446	188	7	5	694	5	CKAP4	12	106633493	Missense_Mutation	SNP	A	TCGA-2Z-A9JP-01A-11D-A42J-10	10710778	106633493	27218402	41	1296											
PARP4	143	hgsc.bcm.edu	37	chr13	25033245	25033245	+	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	acatacggcatctcaatagaCatagtcaaagagaagctagc	17	7	8	9	1	2	2	2	0	1	2	3	3	2	2	0	1	3	2	0	1	7	4			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr13:25033245C>G	ENST00000381989.3	-	20	2466	c.2361G>C	c.(2359-2361)atG>atC	p.M787I	PARP4_ENST00000480576.1_5'UTR	NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	787					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)		TCTCAATAGACATAGTCAAAG	0.299																																					p.M787I		Atlas-SNP	.											.	PARP4	142	.	0			c.G2361C						PASS	.						82	83	83					13																	25033245		2202	4300	6502	SO:0001583	missense	143	exon20			AATAGACATAGTC	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.2361G>C	chr13.hg19:g.25033245C>G	ENSP00000371419:p.Met787Ile	226.0	0.0	.		223.0	84.0	.	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	hg19	CCDS9307.1	.	.	.	.	.	.	.	.	.	.	C	6.984	0.551711	0.13374	.	.	ENSG00000102699	ENST00000381989	T	0.01685	4.69	4.48	2.67	0.31697	.	0.232106	0.48286	D	0.000199	T	0.02533	0.0077	L	0.58669	1.825	0.40080	D	0.976127	B	0.11235	0.004	B	0.08055	0.003	T	0.43180	-0.9407	10	0.49607	T	0.09	-9.9497	9.293	0.37797	0.0:0.8127:0.0:0.1873	.	787	Q9UKK3	PARP4_HUMAN	I	787	ENSP00000371419:M787I	ENSP00000371419:M787I	M	-	3	0	PARP4	23931245	1.000000	0.71417	0.770000	0.31555	0.185000	0.23345	1.818000	0.39012	1.107000	0.41642	0.447000	0.29281	ATG	.	.	.	none		0.299	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437		G	25033245	C	G	25033245	3	3	19	1	0	0	0	0	1	0	0	0	11470	478	17	4	2873	4	PARP4	13	25033245	Missense_Mutation	SNP	C	TCGA-2Z-A9JP-01A-11D-A42J-10		25033245	90136633	42	1297											
TSC22D1	8848	hgsc.bcm.edu	37	chr13	45148240	45148240	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgaagaattggctgctgttgTacatactctgaagcaggatt	11	13	11	6	0	1	3	0	2	1	1	1	4	1	4	0	2	4	5	0	2	5	5			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr13:45148240T>C	ENST00000458659.2	-	1	2461	c.1971A>G	c.(1969-1971)gtA>gtG	p.V657V	TSC22D1_ENST00000460842.1_5'Flank|TSC22D1_ENST00000501704.2_Intron	NM_183422.3	NP_904358.2	Q15714	T22D1_HUMAN	TSC22 domain family, member 1	657	Gln-rich.				negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)		GCTGCTGTTGTACATACTCTG	0.498																																					p.V657V		Atlas-SNP	.											.	TSC22D1	88	.	0			c.A1971G						PASS	.						95	91	92					13																	45148240		2203	4300	6503	SO:0001819	synonymous_variant	8848	exon1			CTGTTGTACATAC	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.1971A>G	chr13.hg19:g.45148240T>C		33.0	0.0	.		42.0	4.0	.	NM_183422	B3KRL7|B9EGI0|O00666|Q6AHX5|Q6IBU1|Q8NCN1|Q96JS5	Silent	SNP	ENST00000458659.2	hg19	CCDS31966.1																																																																																			.	.	.	none		0.498	TSC22D1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044743.2	NM_006022		C	45148240	T	C	45148240	2	2	19	1	0	0	0	0	0	0	0	1	16619	1625	57	3		3	TSC22D1	13	45148240	Silent	SNP	T	TCGA-2Z-A9JP-01A-11D-A42J-10	20114995	45148240	70021638	43	1298											
EXD2	55218	hgsc.bcm.edu	37	chr14	69697226	69697226	+	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	atgggcttagcctgaagtccCtcgctgagactgttttgaac	8	12	11	10	1	0	3	0	3	0	1	2	4	1	3	2	1	2	3	2	1	3	3			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr14:69697226C>A	ENST00000409018.3	+	4	756	c.628C>A	c.(628-630)Ctc>Atc	p.L210I	EXD2_ENST00000409949.1_Missense_Mutation_p.L85I|EXD2_ENST00000312994.5_Missense_Mutation_p.L210I|EXD2_ENST00000409675.1_Missense_Mutation_p.L85I|EXD2_ENST00000409014.1_Missense_Mutation_p.L85I|EXD2_ENST00000449989.1_Missense_Mutation_p.L85I|EXD2_ENST00000492815.1_3'UTR|EXD2_ENST00000409242.1_Missense_Mutation_p.L85I	NM_001193361.1	NP_001180290.1	Q9NVH0	EXD2_HUMAN	exonuclease 3'-5' domain containing 2	210	3'-5' exonuclease.						3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|urinary_tract(1)	14						CCTGAAGTCCCTCGCTGAGAC	0.433																																					p.L210I		Atlas-SNP	.											.	EXD2	43	.	0			c.C628A						PASS	.						166	157	160					14																	69697226		2203	4300	6503	SO:0001583	missense	55218	exon4			AAGTCCCTCGCTG	AK001600	CCDS9793.1, CCDS53902.1	14q24.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000081177	ENSG00000081177			20217	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 114", "exonuclease 3'-5' domain-like 2"	C14orf114, EXDL2			Standard	NM_018199		Approved	FLJ10738	uc001xkv.3	Q9NVH0	OTTHUMG00000154496	ENST00000409018.3:c.628C>A	chr14.hg19:g.69697226C>A	ENSP00000387331:p.Leu210Ile	46.0	0.0	.		58.0	19.0	.	NM_001193361	B4DIH6|G5E947|Q6AWB6|Q8N3D3	Missense_Mutation	SNP	ENST00000409018.3	hg19	CCDS53902.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.515379	0.85389	.	.	ENSG00000081177	ENST00000409018;ENST00000193422;ENST00000409014;ENST00000409675;ENST00000409949;ENST00000409242;ENST00000312994;ENST00000413191;ENST00000449989	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	5.33	5.33	0.75918	-5&apos (1);Ribonuclease H-like (1); exonuclease (1);3&apos (1);	0.000000	0.85682	D	0.000000	D	0.91686	0.7372	M	0.78344	2.41	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.99;0.998	D	0.92163	0.5737	10	0.72032	D	0.01	-13.1435	13.1813	0.59655	0.0:0.9164:0.0:0.0836	.	210;85	G5E947;Q9NVH0	.;EXD2_HUMAN	I	210;210;85;85;85;85;210;85;85	ENSP00000387331:L210I;ENSP00000386915:L85I;ENSP00000386762:L85I;ENSP00000386632:L85I;ENSP00000386839:L85I;ENSP00000313140:L210I;ENSP00000409089:L85I;ENSP00000392177:L85I	ENSP00000193422:L210I	L	+	1	0	EXD2	68766979	0.998000	0.40836	0.971000	0.41717	0.854000	0.48673	3.595000	0.54016	2.637000	0.89404	0.655000	0.94253	CTC	.	.	.	none		0.433	EXD2-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000335504.1			A	69697226	C	A	69697226	3	1	19	1	0	0	0	0	1	0	0	0	5300	681	24	4	259	4	EXD2	14	69697226	Missense_Mutation	SNP	C	TCGA-2Z-A9JP-01A-11D-A42J-10		69697226	37652314	44	1299											
KIF26A	26153	hgsc.bcm.edu	37	chr14	104618786	104618786	+	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	cgggtcaacagcttcctcccGccggcgtgcctggtgagtgt	4	9	14	14	4	1	1	1	1	0	0	3	1	3	1	4	3	3	1	4	3	1	1			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr14:104618786G>A	ENST00000423312.2	+	3	723	c.723G>A	c.(721-723)ccG>ccA	p.P241P	KIF26A_ENST00000315264.7_Silent_p.P102P	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	241					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)		GCTTCCTCCCGCCGGCGTGCC	0.657																																					p.P241P		Atlas-SNP	.											.	KIF26A	84	.	0			c.G723A						PASS	.						6	6	6					14																	104618786		1915	3779	5694	SO:0001819	synonymous_variant	26153	exon3			CCTCCCGCCGGCG	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.723G>A	chr14.hg19:g.104618786G>A		90.0	0.0	.		49.0	15.0	.	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Silent	SNP	ENST00000423312.2	hg19	CCDS45171.1																																																																																			.	.	.	none		0.657	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1			A	104618786	G	A	104618786	2	1	19	1	0	0	0	0	0	0	0	1	8301	1074	38	1		1	KIF26A	14	104618786	Silent	SNP	G	TCGA-2Z-A9JP-01A-11D-A42J-10	34921560	104618786	2730754	45	1300											
PKM2	5315	hgsc.bcm.edu	37	chr15	72502795	72502795	+	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	gctttccgtggctgtgcgcaCattcttgatggtctccgcat	4	14	11	12	3	2	1	0	1	2	0	4	1	3	1	2	2	1	4	2	2	0	3			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr15:72502795C>T	ENST00000335181.5	-	4	374	c.271G>A	c.(271-273)Gtg>Atg	p.V91M	PKM_ENST00000568459.1_Missense_Mutation_p.V91M|PKM_ENST00000319622.6_Missense_Mutation_p.V91M|PKM_ENST00000568883.1_Intron|PKM_ENST00000565184.1_Missense_Mutation_p.V91M|PKM_ENST00000449901.2_Missense_Mutation_p.V76M|PKM_ENST00000565154.1_Missense_Mutation_p.V91M|PKM_ENST00000389093.3_Missense_Mutation_p.V91M	NM_002654.4	NP_002645.3	P14618	KPYM_HUMAN	pyruvate kinase, muscle	91					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)	GCTGTGCGCACATTCTTGATG	0.552																																					p.V165M		Atlas-SNP	.											.	PKM	25	.	0			c.G493A						PASS	.						111	94	100					15																	72502795		2199	4297	6496	SO:0001583	missense	5315	exon5			TGCGCACATTCTT	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.271G>A	chr15.hg19:g.72502795C>T	ENSP00000334983:p.Val91Met	48.0	0.0	.		56.0	23.0	.	NM_001206796	A6NFK3|B2R5N8|B3KRY0|B4DFX8|B4DUU6|P14786|Q53GK4|Q96E76|Q9BWB5|Q9UCV6|Q9UPF2	Missense_Mutation	SNP	ENST00000335181.5	hg19	CCDS32284.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.440858	0.83993	.	.	ENSG00000067225	ENST00000319622;ENST00000335181;ENST00000389093;ENST00000449901	D;D;D;D	0.99591	-6.24;-6.24;-6.24;-6.24	5.38	5.38	0.77491	Pyruvate/Phosphoenolpyruvate kinase (2);Pyruvate kinase, barrel (1);	0.000000	0.85682	D	0.000000	D	0.99732	0.9895	M	0.92923	3.36	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;0.999	D;D;D;D;D	0.97110	1.0;0.994;0.992;0.992;0.986	D	0.97546	1.0089	10	0.87932	D	0	-27.492	19.4991	0.95086	0.0:1.0:0.0:0.0	.	76;91;91;91;91	B4DUU6;B4DRT3;E7EUQ8;P14618;P14618-2	.;.;.;KPYM_HUMAN;.	M	91;91;91;76	ENSP00000320171:V91M;ENSP00000334983:V91M;ENSP00000373745:V91M;ENSP00000403365:V76M	ENSP00000320171:V91M	V	-	1	0	PKM2	70289849	0.982000	0.34865	0.980000	0.43619	0.825000	0.46686	2.637000	0.46553	2.669000	0.90835	0.563000	0.77884	GTG	.	.	.	none		0.552	PKM-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420056.1			T	72502795	C	T	72502795	3	4	19	1	0	0	0	0	1	0	0	0	11984	478	17	2	1527	2	PKM2	15	72502795	Missense_Mutation	SNP	C	TCGA-2Z-A9JP-01A-11D-A42J-10		72502795	30028597	46	1301											
ARIH1	25820	hgsc.bcm.edu	37	chr15	72855824	72855824	+	Missense_Mutation	SNP	A	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	gctaaacctgttcgctgcaaAtgtgggcgccaattttggta	9	12	11	9	2	0	0	0	0	0	0	1	0	0	0	2	2	2	5	2	2	5	5			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr15:72855824A>C	ENST00000379887.4	+	7	1208	c.894A>C	c.(892-894)aaA>aaC	p.K298N		NM_005744.3	NP_005735.2	Q9Y4X5	ARI1_HUMAN	ariadne RBR E3 ubiquitin protein ligase 1	298					cytokine-mediated signaling pathway (GO:0019221)|protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|ubiquitin ligase complex (GO:0000151)	small conjugating protein ligase activity (GO:0019787)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(3)|lung(4)|prostate(1)|skin(1)	14						TTCGCTGCAAATGTGGGCGCC	0.403																																					p.K298N		Atlas-SNP	.											.	ARIH1	42	.	0			c.A894C						PASS	.						111	103	105					15																	72855824		2198	4297	6495	SO:0001583	missense	25820	exon7			CTGCAAATGTGGG	AF072832	CCDS10244.1	15q24	2013-10-03	2013-10-03		ENSG00000166233	ENSG00000166233			689	protein-coding gene	gene with protein product	"ariadne, Drosophila, homolog of"	605624	"ariadne (Drosophila) homolog, ubiquitin-conjugating enzyme E2-binding protein, 1", "ariadne homolog, ubiquitin-conjugating enzyme E2 binding protein, 1 (Drosophila)"			10521492, 24058416	Standard	NM_005744		Approved	HARI, HHARI, UBCH7BP, ARI	uc002aut.4	Q9Y4X5	OTTHUMG00000133474	ENST00000379887.4:c.894A>C	chr15.hg19:g.72855824A>C	ENSP00000369217:p.Lys298Asn	96.0	0.0	.		85.0	30.0	.	NM_005744	B2R6U3|O76026|Q9H3T6|Q9UEN0|Q9UP39	Missense_Mutation	SNP	ENST00000379887.4	hg19	CCDS10244.1	.	.	.	.	.	.	.	.	.	.	A	14.32	2.500753	0.44455	.	.	ENSG00000166233	ENST00000379887;ENST00000299305	T	0.80994	-1.44	5.75	2.12	0.27331	Zinc finger, C6HC-type (2);Zinc finger, RING-type (1);	0.000000	0.85682	D	0.000000	T	0.74943	0.3783	M	0.64170	1.965	0.58432	D	0.999993	P	0.36712	0.566	B	0.36766	0.232	T	0.68224	-0.5465	10	0.42905	T	0.14	.	8.948	0.35771	0.7351:0.0:0.2649:0.0	.	298	Q9Y4X5	ARI1_HUMAN	N	298;268	ENSP00000369217:K298N	ENSP00000299305:K268N	K	+	3	2	ARIH1	70642878	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.418000	0.44662	0.108000	0.17862	0.449000	0.29647	AAA	.	.	.	none		0.403	ARIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257350.1	NM_005744		C	72855824	A	C	72855824	3	2	19	1	0	0	0	0	1	0	0	0	923	98	4	5	920	5	ARIH1	15	72855824	Missense_Mutation	SNP	A	TCGA-2Z-A9JP-01A-11D-A42J-10	353029	72855824	29675568	47	1302											
ITGAX	3687	hgsc.bcm.edu	37	chr16	31371685	31371696	+	In_Frame_Del	DEL	CATTGTCATCAC	CATTGTCATCAC	-																															agggatgccgccaaaattctCattgtcatcactgatgggaa																										TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	CATTGTCATCAC	CATTGTCATCAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr16:31371685_31371696delCATTGTCATCAC	ENST00000268296.4	+	8	883_894	c.762_773delCATTGTCATCAC	c.(760-774)ctcattgtcatcact>ctt	p.IVIT255del	ITGAX_ENST00000562522.1_In_Frame_Del_p.IVIT255del	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	255	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						CCAAAATTCTCATTGTCATCACTGATGGGAAG	0.528																																					p.254_258del		Atlas-Indel,Pindel	.											.	ITGAX	198	.	0			c.761_772del						PASS	.																																			SO:0001651	inframe_deletion	3687	exon8			.	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.762_773delCATTGTCATCAC	chr16.hg19:g.31371685_31371696delCATTGTCATCAC	ENSP00000268296:p.Ile255_Thr258del	49.0	0.0	0		50.0	19.0	0.38	NM_000887	Q8IVA6	In_Frame_Del	DEL	ENST00000268296.4	hg19	CCDS10711.1																																																																																			.	.	.	none		0.528	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887		-	31371696	CATTGTCATCAC	-	31371685	7	5	19	1	0	1	0	1	0	0	0	0	7896	813	29	0	792	0	ITGAX	16	31371685	In_Frame_Del	DEL	CATTGTCATCAC	TCGA-2Z-A9JP-01A-11D-A42J-10		31371685	58983068	48	1303											
KIF1C	10749	hgsc.bcm.edu	37	chr17	4925768	4925768	+	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	gccccggagacgcctggaggGctgtggcccgggatgtctgg	4	6	19	12	3	1	1	0	0	1	1	1	4	1	3	4	6	0	1	4	6	0	0			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr17:4925768G>T	ENST00000320785.5	+	22	2749	c.2392G>T	c.(2392-2394)Gct>Tct	p.A798S	AC109333.10_ENST00000438266.1_RNA	NM_006612.5	NP_006603.2	O43896	KIF1C_HUMAN	kinesin family member 1C	798					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						CGCCTGGAGGGCTGTGGCCCG	0.697																																					p.A798S	Melanoma(96;1023 1447 10250 19259 33730)	Atlas-SNP	.											.	KIF1C	70	.	0			c.G2392T						PASS	.						29	30	30					17																	4925768		2200	4291	6491	SO:0001583	missense	10749	exon22			TGGAGGGCTGTGG	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.2392G>T	chr17.hg19:g.4925768G>T	ENSP00000320821:p.Ala798Ser	90.0	0.0	.		92.0	5.0	.	NM_006612	D3DTL6|O75186|Q5U618	Missense_Mutation	SNP	ENST00000320785.5	hg19	CCDS11065.1	.	.	.	.	.	.	.	.	.	.	G	16.63	3.177065	0.57692	.	.	ENSG00000129250	ENST00000320785	T	0.73681	-0.77	4.67	4.67	0.58626	.	.	.	.	.	T	0.76681	0.4021	N	0.25890	0.77	0.49915	D	0.999834	D	0.63880	0.993	D	0.70227	0.968	T	0.73515	-0.3958	9	0.25751	T	0.34	.	15.1017	0.72284	0.0:0.0:1.0:0.0	.	798	O43896	KIF1C_HUMAN	S	798	ENSP00000320821:A798S	ENSP00000320821:A798S	A	+	1	0	KIF1C	4866492	1.000000	0.71417	0.993000	0.49108	0.886000	0.51366	9.657000	0.98554	2.436000	0.82500	0.655000	0.94253	GCT	.	.	.	none		0.697	KIF1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216916.1			T	4925768	G	T	4925768	3	4	19	1	0	0	0	0	1	0	0	0	8292	1203	42	4	2470	4	KIF1C	17	4925768	Missense_Mutation	SNP	G	TCGA-2Z-A9JP-01A-11D-A42J-10		4925768	76269442	49	1304											
MPDU1	9526	hgsc.bcm.edu	37	chr17	7490749	7490749	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctcttgcaaccaggaaacCggagatcccctgatggctgg	9	8	12	12	1	1	2	0	1	1	1	3	4	2	3	4	4	3	2	4	4	2	1	rs371550829		TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr17:7490749C>T	ENST00000250124.6	+	7	840	c.624C>T	c.(622-624)acC>acT	p.T208T	MPDU1_ENST00000423172.2_Intron|MPDU1_ENST00000396501.4_Missense_Mutation_p.P189L	NM_004870.3	NP_004861.2	O75352	MPU1_HUMAN	mannose-P-dolichol utilization defect 1	208	PQ-loop 2.				dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|oligosaccharide biosynthetic process (GO:0009312)|protein folding (GO:0006457)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)				central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(1)|lung(1)	7						ACCAGGAAACCGGAGATCCCC	0.567																																					p.T208T		Atlas-SNP	.											.	MPDU1	14	.	0			c.C624T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	105	103	104		624	-9.3	0.7	17		104	0,8600		0,0,4300	no	coding-synonymous	MPDU1	NM_004870.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		208/248	7490749	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9526	exon7			GGAAACCGGAGAT	AF038961	CCDS11115.1	17p13.1-p12	2008-07-03			ENSG00000129255	ENSG00000129255			7207	protein-coding gene	gene with protein product		604041				8663248, 9653160, 11733564	Standard	NM_004870		Approved	SL15, Lec35, PQLC5, CDGIf	uc002ghw.3	O75352	OTTHUMG00000108147	ENST00000250124.6:c.624C>T	chr17.hg19:g.7490749C>T		69.0	0.0	.		53.0	19.0	.	NM_004870	B3KQP1|B4DT74|Q9BUU8	Silent	SNP	ENST00000250124.6	hg19	CCDS11115.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.40|12.40	1.925630|1.925630	0.34002|0.34002	2.27E-4|2.27E-4	0.0|0.0	ENSG00000129255|ENSG00000129255	ENST00000396501|ENST00000359822	.|.	.|.	.|.	5.24|5.24	-9.26|-9.26	0.00662|0.00662	.|.	.|1.727610	.|0.03156	.|N	.|0.168713	T|T	0.54481|0.54481	0.1861|0.1861	.|.	.|.	.|.	0.54753|0.54753	D|D	0.99998|0.99998	B|.	0.06786|.	0.001|.	B|.	0.04013|.	0.001|.	T|T	0.59611|0.59611	-0.7422|-0.7422	7|6	0.87932|0.62326	D|D	0|0.03	3.3529|3.3529	6.9724|6.9724	0.24656|0.24656	0.3396:0.4581:0.0:0.2023|0.3396:0.4581:0.0:0.2023	.|.	256|.	B4DLH7|.	.|.	L|W	208|208	.|.	ENSP00000379758:P208L|ENSP00000352876:R208W	P|R	+|+	2|1	0|2	MPDU1|MPDU1	7431473|7431473	0.002000|0.002000	0.14202|0.14202	0.713000|0.713000	0.30519|0.30519	0.941000|0.941000	0.58515|0.58515	-2.148000|-2.148000	0.01292|0.01292	-1.641000|-1.641000	0.01523|0.01523	-0.238000|-0.238000	0.12139|0.12139	CCG|CGG	.	.	.	weak		0.567	MPDU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226950.4			T	7490749	C	T	7490749	2	4	19	1	0	0	0	0	0	0	0	1	9728	639	23	1		1	MPDU1	17	7490749	Silent	SNP	C	TCGA-2Z-A9JP-01A-11D-A42J-10	2564981	7490749	73704461	50	1305											
MAP2K3	5606	hgsc.bcm.edu	37	chr17	21203904	21203904	+	Frame_Shift_Del	DEL	C	C	-																															gtgaccatctcagaactgggCcgtggagcctatggggtggt																										TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr17:21203904delC	ENST00000342679.4	+	4	462	c.213delC	c.(211-213)ggcfs	p.G71fs	MAP2K3_ENST00000316920.6_Frame_Shift_Del_p.G42fs|MAP2K3_ENST00000361818.5_Frame_Shift_Del_p.G42fs	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	71	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)		CAGAACTGGGCCGTGGAGCCT	0.602																																					p.G71fs		Atlas-INDEL	.											.	MAP2K3	135	.	0			c.212delG						PASS	.						60	55	57					17																	21203904		2203	4300	6503	SO:0001589	frameshift_variant	5606	exon4			.	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.213delC	chr17.hg19:g.21203904delC	ENSP00000345083:p.Gly71fs	98.0	0.0	0		140.0	13.0	0.0928571	NM_145109	B3KSK7|Q99441|Q9UE71|Q9UE72	Frame_Shift_Del	DEL	ENST00000342679.4	hg19	CCDS11217.1																																																																																			.	.	.	none		0.602	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259374.2	NM_145109		-	21203904	C	-	21203904	7	5	19	1	0	1	0	1	0	0	0	0	9245	726	26	0	227	0	MAP2K3	17	21203904	Frame_Shift_Del	DEL	C	TCGA-2Z-A9JP-01A-11D-A42J-10	13713155	21203904	59991306	51	1306											
FNDC8	54752	hgsc.bcm.edu	37	chr17	33457438	33457438	+	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	aggctggaggatctggaataCctatttccctgttaaggggg	9	11	14	7	0	1	0	0	0	1	0	2	3	2	3	2	6	1	2	2	6	4	4			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr17:33457438C>T	ENST00000158009.5	+	4	1075	c.960C>T	c.(958-960)taC>taT	p.Y320Y	NLE1_ENST00000586869.1_3'UTR	NM_017559.2	NP_060029.1	Q8TC99	FNDC8_HUMAN	fibronectin type III domain containing 8	320						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)		ATCTGGAATACCTATTTCCCT	0.587																																					p.Y320Y		Atlas-SNP	.											.	FNDC8	28	.	0			c.C960T						PASS	.						45	47	46					17																	33457438		2203	4300	6503	SO:0001819	synonymous_variant	54752	exon4			GGAATACCTATTT	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.960C>T	chr17.hg19:g.33457438C>T		39.0	0.0	.		33.0	6.0	.	NM_017559	B2R9G6|Q9UFC2	Silent	SNP	ENST00000158009.5	hg19	CCDS11290.1																																																																																			.	.	.	none		0.587	FNDC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256459.2	NM_017559		T	33457438	C	T	33457438	2	4	19	1	0	0	0	0	0	0	0	1	5981	518	18	2		2	FNDC8	17	33457438	Silent	SNP	C	TCGA-2Z-A9JP-01A-11D-A42J-10	12253534	33457438	47737772	52	1307											
HNF1B	6928	hgsc.bcm.edu	37	chr17	36104669	36104680	+	In_Frame_Del	DEL	GTGGCCGTTGGT	GTGGCCGTTGGT	-																															ccggacaagcggcccttggcGtggccgttggtgagagtatg																										TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	GTGGCCGTTGGT	GTGGCCGTTGGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr17:36104669_36104680delGTGGCCGTTGGT	ENST00000225893.4	-	1	557_568	c.196_207delACCAACGGCCAC	c.(196-207)accaacggccacdel	p.TNGH66del	HNF1B_ENST00000427275.2_In_Frame_Del_p.TNGH66del|RP11-115K3.1_ENST00000558143.1_RNA|HNF1B_ENST00000560016.1_In_Frame_Del_p.TNGH66del|HNF1B_ENST00000561193.1_In_Frame_Del_p.TNGH66del	NM_000458.2|NM_001165923.1	NP_000449.1|NP_001159395.1	P35680	HNF1B_HUMAN	HNF1 homeobox B	66					anterior/posterior pattern specification (GO:0009952)|branching morphogenesis of an epithelial tube (GO:0048754)|embryonic digestive tract morphogenesis (GO:0048557)|endocrine pancreas development (GO:0031018)|endodermal cell fate specification (GO:0001714)|epithelial cell proliferation (GO:0050673)|genitalia development (GO:0048806)|hepatoblast differentiation (GO:0061017)|hindbrain development (GO:0030902)|inner cell mass cell differentiation (GO:0001826)|insulin secretion (GO:0030073)|kidney development (GO:0001822)|mesonephric duct formation (GO:0072181)|negative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis (GO:0061296)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric nephron tubule development (GO:0039020)|pronephros development (GO:0048793)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of endodermal cell fate specification (GO:0042663)|regulation of pronephros size (GO:0035565)|regulation of Wnt signaling pathway (GO:0030111)|response to glucose (GO:0009749)|ureteric bud elongation (GO:0060677)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(3)|large_intestine(2)|liver(1)|lung(3)|ovary(3)|prostate(1)|skin(2)	28		Breast(25;0.00765)|Ovarian(249;0.15)	STAD - Stomach adenocarcinoma(1;0.0142)			GGCCCTTGGCGTGGCCGTTGGTGAGAGTATGG	0.67																																					p.66_70del	Colon(71;102 1179 9001 27917 43397)	Atlas-Indel,Pindel	.											.	HNF1B	61	.	0			c.197_208del	GRCh37	CD024193	HNF1B	D		PASS	.																																			SO:0001651	inframe_deletion	6928	exon1			.	BC017714	CCDS11324.1, CCDS58538.1	17q12	2014-05-06	2007-08-24	2007-08-24	ENSG00000108753	ENSG00000275410		"Homeoboxes / HNF class"	11630	protein-coding gene	gene with protein product		189907	"transcription factor 2, hepatic; LF-B3; variant hepatic nuclear factor"	TCF2		1677179, 10484768	Standard	NM_000458		Approved	LFB3, VHNF1, HNF1beta, MODY5	uc002hok.4	P35680	OTTHUMG00000188478	ENST00000225893.4:c.196_207delACCAACGGCCAC	chr17.hg19:g.36104669_36104680delGTGGCCGTTGGT	ENSP00000225893:p.Thr66_His69del	96.0	0.0	0		86.0	35.0	0.406977	NM_001165923	B4DKM3|E0YMJ9	In_Frame_Del	DEL	ENST00000225893.4	hg19	CCDS11324.1																																																																																			.	.	.	none		0.67	HNF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256807.3	NM_000458		-	36104680	GTGGCCGTTGGT	-	36104669	7	5	19	1	0	1	0	1	0	0	0	0	7259	1136	40	0	1502	0	HNF1B	17	36104669	In_Frame_Del	DEL	GTGGCCGTTGGT	TCGA-2Z-A9JP-01A-11D-A42J-10	2647231	36104669	45090541	53	1308											
ASB16	92591	hgsc.bcm.edu	37	chr17	42254547	42254547	+	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	tcccccaactgggagcctgaAgtccttttcgccgcactgct	6	10	9	16	2	0	1	0	1	0	0	3	2	2	2	5	1	3	2	5	1	2	2			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr17:42254547A>T	ENST00000293414.1	+	3	1095	c.1011A>T	c.(1009-1011)gaA>gaT	p.E337D	ASB16-AS1_ENST00000591166.1_RNA|ASB16-AS1_ENST00000585457.1_RNA|ASB16-AS1_ENST00000588785.1_RNA|ASB16-AS1_ENST00000592897.1_RNA	NM_080863.4	NP_543139.4	Q96NS5	ASB16_HUMAN	ankyrin repeat and SOCS box containing 16	337					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)		GGGAGCCTGAAGTCCTTTTCG	0.701																																					p.E337D		Atlas-SNP	.											.	ASB16	34	.	0			c.A1011T						PASS	.						2	3	3					17																	42254547		1844	3714	5558	SO:0001583	missense	92591	exon3			GCCTGAAGTCCTT	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.1011A>T	chr17.hg19:g.42254547A>T	ENSP00000293414:p.Glu337Asp	67.0	0.0	.		83.0	21.0	.	NM_080863	B2RBC0|Q8WXK0	Missense_Mutation	SNP	ENST00000293414.1	hg19	CCDS11478.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.37|10.37	1.331654|1.331654	0.24167|0.24167	.|.	.|.	ENSG00000161664|ENSG00000168597	ENST00000293414|ENST00000303061	T|.	0.66460|.	-0.21|.	4.95|4.95	0.684|0.684	0.18003|0.18003	Ankyrin repeat-containing domain (2);|.	0.335476|.	0.34223|.	N|.	0.004160|.	T|T	0.35828|0.35828	0.0945|0.0945	M|M	0.61703|0.61703	1.905|1.905	0.33725|0.33725	D|D	0.617503|0.617503	B|P	0.06786|0.39696	0.001|0.683	B|B	0.06405|0.33295	0.002|0.161	T|T	0.47661|0.47661	-0.9100|-0.9100	10|8	0.42905|0.87932	T|D	0.14|0	-12.3109|-12.3109	2.7739|2.7739	0.05342|0.05342	0.1522:0.2645:0.4472:0.136|0.1522:0.2645:0.4472:0.136	.|.	337|25	Q96NS5|Q495Z4	ASB16_HUMAN|CQ065_HUMAN	D|H	337|25	ENSP00000293414:E337D|.	ENSP00000293414:E337D|ENSP00000366342:L25H	E|L	+|-	3|2	2|0	ASB16|C17orf65	39610073|39610073	0.839000|0.839000	0.29477|0.29477	0.954000|0.954000	0.39281|0.39281	0.094000|0.094000	0.18550|0.18550	1.047000|1.047000	0.30367|0.30367	0.021000|0.021000	0.15133|0.15133	-0.253000|-0.253000	0.11424|0.11424	GAA|CTT	.	.	.	none		0.701	ASB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457703.1			T	42254547	A	T	42254547	3	4	19	1	0	0	0	0	1	0	0	0	1020	72	3	5	1021	5	ASB16	17	42254547	Missense_Mutation	SNP	A	TCGA-2Z-A9JP-01A-11D-A42J-10	6149878	42254547	38940663	54	1309											
JMJD6	23210	hgsc.bcm.edu	37	chr17	74714915	74714915	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcttcctgcggtgcactgTcccatcgccctcggatccag	4	11	9	17	3	1	0	0	0	1	0	6	1	4	1	4	2	2	1	4	2	0	2			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr17:74714915T>C	ENST00000397625.4	-	6	1222	c.1108A>G	c.(1108-1110)Aca>Gca	p.T370A	JMJD6_ENST00000445478.2_Missense_Mutation_p.T370A|JMJD6_ENST00000585429.1_Silent_p.G323G	NM_015167.2	NP_055982.2	Q6NYC1	JMJD6_HUMAN	jumonji domain containing 6	370					cell surface receptor signaling pathway (GO:0007166)|erythrocyte development (GO:0048821)|heart development (GO:0007507)|histone H3-R2 demethylation (GO:0070078)|histone H4-R3 demethylation (GO:0070079)|kidney development (GO:0001822)|lung development (GO:0030324)|macrophage activation (GO:0042116)|mRNA processing (GO:0006397)|peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine (GO:0018395)|recognition of apoptotic cell (GO:0043654)|regulation of mRNA splicing, via spliceosome (GO:0048024)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|RNA splicing (GO:0008380)|sprouting angiogenesis (GO:0002040)|T cell differentiation in thymus (GO:0033077)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone demethylase activity (H3-R2 specific) (GO:0033746)|histone demethylase activity (H4-R3 specific) (GO:0033749)|identical protein binding (GO:0042802)|iron ion binding (GO:0005506)|peptidyl-lysine 5-dioxygenase activity (GO:0070815)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			endometrium(2)|kidney(5)|large_intestine(2)|lung(3)|ovary(2)|skin(2)	16						CGGTGCACTGTCCCATCGCCC	0.567																																					p.T370A		Atlas-SNP	.											.	JMJD6	57	.	0			c.A1108G						PASS	.						85	90	89					17																	74714915		2130	4233	6363	SO:0001583	missense	23210	exon6			GCACTGTCCCATC	AB011157	CCDS42383.1, CCDS42384.1	17q25	2007-11-20	2007-02-16	2007-02-16	ENSG00000070495	ENSG00000070495			19355	protein-coding gene	gene with protein product		604914	"phosphatidylserine receptor"	PTDSR		11877474	Standard	NM_015167		Approved	PTDSR1, KIAA0585	uc002jsn.1	Q6NYC1	OTTHUMG00000169267	ENST00000397625.4:c.1108A>G	chr17.hg19:g.74714915T>C	ENSP00000380750:p.Thr370Ala	63.0	0.0	.		58.0	4.0	.	NM_001081461	B3KMN8|B4DGX1|Q86VY0|Q8IUM5|Q9Y4E2	Missense_Mutation	SNP	ENST00000397625.4	hg19	CCDS42384.1	.	.	.	.	.	.	.	.	.	.	T	11.90	1.775446	0.31411	.	.	ENSG00000070495	ENST00000445478;ENST00000397625	.	.	.	6.17	5.1	0.69264	.	0.345176	0.33959	N	0.004383	T	0.20414	0.0491	N	0.08118	0	0.27217	N	0.959752	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.17684	-1.0361	9	0.06099	T	0.92	-17.7187	12.092	0.53733	0.0:0.0663:0.0:0.9337	.	370;370	Q6NYC1;Q6NYC1-3	JMJD6_HUMAN;.	A	370	.	ENSP00000380750:T370A	T	-	1	0	JMJD6	72226510	0.585000	0.26774	0.030000	0.17652	0.900000	0.52787	2.454000	0.44979	1.160000	0.42584	0.533000	0.62120	ACA	.	.	.	none		0.567	JMJD6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403211.1	NM_015167		C	74714915	T	C	74714915	3	2	19	1	0	0	0	0	1	0	0	0	7960	1667	58	3	148	3	JMJD6	17	74714915	Missense_Mutation	SNP	T	TCGA-2Z-A9JP-01A-11D-A42J-10	32460368	74714915	6480295	55	1310											
SEC14L1	6397	hgsc.bcm.edu	37	chr17	75202482	75202482	+	Splice_Site	DEL	G	G	-																															tttcctgtgctctggacgctGgtgggttgagatgctttttg																										TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr17:75202482delG	ENST00000413679.2	+	12	1644	c.1341delG	c.(1339-1341)ctg>ct	p.L447fs	SEC14L1_ENST00000443798.4_Splice_Site_p.L447fs|SEC14L1_ENST00000392476.2_Splice_Site_p.L447fs|SEC14L1_ENST00000431431.2_Splice_Site_p.L413fs|SEC14L1_ENST00000585618.1_Splice_Site_p.L447fs|SEC14L1_ENST00000591437.1_Splice_Site_p.L413fs|SEC14L1_ENST00000436233.4_Splice_Site_p.L447fs|SEC14L1_ENST00000430767.4_Splice_Site_p.L447fs	NM_001143998.1|NM_001143999.1|NM_003003.3	NP_001137470|NP_001137471|NP_002994	Q92503	S14L1_HUMAN	SEC14-like 1 (S. cerevisiae)	447	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(2)	31						TCTGGACGCTGGTGGGTTGAG	0.517																																					p.L447fs		Atlas-Indel,Pindel	.											.	SEC14L1	81	.	0			c.1340delT						PASS	.						60	56	57					17																	75202482		2203	4300	6503	SO:0001630	splice_region_variant	6397	exon12			.	D67029	CCDS11752.1, CCDS42385.1, CCDS45789.1	17q25.2	2008-02-01	2001-11-28			ENSG00000129657			10698	protein-coding gene	gene with protein product		601504	"SEC14 (S. cerevisiae)-like 1"	SEC14L		8697811	Standard	NM_001143998		Approved	PRELID4A	uc002jto.3	Q92503		ENST00000413679.2:c.1341+1G>-	chr17.hg19:g.75202482delG		62.0	0.0	0		93.0	29.0	0.311828	NM_001143998	A8K4E8|B4DDI5|D5G3K1|Q99780	Frame_Shift_Del	DEL	ENST00000413679.2	hg19	CCDS11752.1																																																																																			.	.	.	none		0.517	SEC14L1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000436240.1	NM_003003	Frame_Shift_Del	-	75202482	G	-	75202482	8	5	19	1	0	1	0	1	0	0	1	0	13994	1362	47	0	1379	0	SEC14L1	17	75202482	Splice_Site	DEL	G	TCGA-2Z-A9JP-01A-11D-A42J-10	487567	75202482	5992728	56	1311											
CHST9	83539	hgsc.bcm.edu	37	chr18	24722672	24722672	+	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	cctgtatgttgttcttcaatCcagacttgcaaatacatgaa	12	14	6	9	0	2	2	1	1	1	1	3	2	3	2	2	0	2	4	2	0	5	6			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr18:24722672C>A	ENST00000284224.8	-	2	379	c.102G>T	c.(100-102)tgG>tgT	p.W34C	CHST9_ENST00000580774.1_Missense_Mutation_p.W34C|CHST9_ENST00000581714.1_Missense_Mutation_p.W34C|AQP4-AS1_ENST00000578701.1_RNA	NM_031422.5	NP_113610.2	Q7L1S5	CHST9_HUMAN	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	34					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)					GTTCTTCAATCCAGACTTGCA	0.348																																					p.W34C		Atlas-SNP	.											.	CHST9	114	.	0			c.G102T						PASS	.						97	90	92					18																	24722672		1834	4082	5916	SO:0001583	missense	83539	exon2			TTCAATCCAGACT	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.102G>T	chr18.hg19:g.24722672C>A	ENSP00000284224:p.Trp34Cys	45.0	0.0	.		30.0	16.0	.	NM_001256316	Q6UX69|Q9BXH3|Q9BXH4|Q9BZW9	Missense_Mutation	SNP	ENST00000284224.8	hg19	CCDS42422.1	.	.	.	.	.	.	.	.	.	.	C	9.223	1.033889	0.19590	.	.	ENSG00000154080	ENST00000284224	T	0.75154	-0.91	5.21	2.32	0.28847	.	0.949413	0.08796	N	0.892524	T	0.56949	0.2020	N	0.12182	0.205	0.50313	D	0.999866	B	0.02656	0.0	B	0.04013	0.001	T	0.35649	-0.9780	10	0.42905	T	0.14	1.249	8.8188	0.35011	0.3043:0.5489:0.1469:0.0	.	34	Q7L1S5	CHST9_HUMAN	C	34	ENSP00000284224:W34C	ENSP00000284224:W34C	W	-	3	0	CHST9	22976670	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	0.897000	0.28390	0.167000	0.19631	0.484000	0.47621	TGG	.	.	.	none		0.348	CHST9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446549.1	NM_031422		A	24722672	C	A	24722672	3	1	19	1	0	0	0	0	1	0	0	0	3413	856	30	4	1249	4	CHST9	18	24722672	Missense_Mutation	SNP	C	TCGA-2Z-A9JP-01A-11D-A42J-10		24722672	53354576	57	1312											
ZNF567	163081	hgsc.bcm.edu	37	chr19	37210602	37210602	+	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	gcctcaagacagccctcactGatcatcagagaacacacaca	15	5	6	15	0	4	3	4	1	0	2	4	4	4	3	2	0	2	0	2	0	2	0			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr19:37210602G>T	ENST00000536254.2	+	6	1198	c.976G>T	c.(976-978)Gat>Tat	p.D326Y	ZNF567_ENST00000360729.4_Missense_Mutation_p.D295Y|ZNF567_ENST00000585696.1_Missense_Mutation_p.D295Y|ZNF567_ENST00000392163.2_Missense_Mutation_p.D295Y|ZNF850_ENST00000589390.1_Intron|ZNF567_ENST00000588311.1_Missense_Mutation_p.D295Y			Q8N184	ZN567_HUMAN	zinc finger protein 567	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)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			AGCCCTCACTGATCATCAGAG	0.438																																					p.D295Y		Atlas-SNP	.											.	ZNF567	61	.	0			c.G883T						PASS	.						64	62	63					19																	37210602		2203	4300	6503	SO:0001583	missense	163081	exon4			CTCACTGATCATC	AK093034	CCDS12495.1, CCDS74349.1	19q13.12	2013-10-08				ENSG00000189042		"Zinc fingers, C2H2-type", "-"	28696	protein-coding gene	gene with protein product						12477932	Standard	XM_006723064		Approved	MGC45586	uc002oep.4	Q8N184		ENST00000536254.2:c.976G>T	chr19.hg19:g.37210602G>T	ENSP00000441838:p.Asp326Tyr	83.0	0.0	.		93.0	21.0	.	NM_152603	B3KX49|Q6N044	Missense_Mutation	SNP	ENST00000536254.2	hg19		.	.	.	.	.	.	.	.	.	.	G	13.05	2.119936	0.37436	.	.	ENSG00000189042	ENST00000536254;ENST00000360729;ENST00000423498;ENST00000392163	T;T;T	0.16073	2.37;2.37;2.37	4.53	1.14	0.20703	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.144563	0.32134	N	0.006533	T	0.09555	0.0235	N	0.05383	-0.06	0.09310	N	0.999994	P;P	0.50710	0.938;0.924	P;P	0.48952	0.596;0.461	T	0.11518	-1.0584	10	0.46703	T	0.11	.	3.8123	0.08802	0.2795:0.1877:0.5328:0.0	.	326;295	Q8N184;F8WEL6	ZN567_HUMAN;.	Y	326;295;325;295	ENSP00000441838:D326Y;ENSP00000353957:D295Y;ENSP00000376003:D295Y	ENSP00000353957:D295Y	D	+	1	0	ZNF567	41902442	0.000000	0.05858	0.938000	0.37757	0.987000	0.75469	-0.067000	0.11579	0.608000	0.30000	0.462000	0.41574	GAT	.	.	.	none		0.438	ZNF567-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000453549.1	NM_152603		T	37210602	G	T	37210602	3	4	19	1	0	0	0	0	1	0	0	0	18010	1290	45	4	893	4	ZNF567	19	37210602	Missense_Mutation	SNP	G	TCGA-2Z-A9JP-01A-11D-A42J-10		37210602	21918381	58	1313											
DMPK	1760	hgsc.bcm.edu	37	chr19	46273845	46273847	+	In_Frame_Del	DEL	AAC	AAC	-																															agggcggcggcacgagacagAacaacggcgaacaggagcag																								rs201332435	byFrequency	TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr19:46273845_46273847delAAC	ENST00000291270.4	-	15	1914_1916	c.1789_1791delGTT	c.(1789-1791)gttdel	p.V597del	AC074212.5_ENST00000592217.2_RNA|AC074212.6_ENST00000586498.1_RNA|SIX5_ENST00000317578.6_5'Flank|AC074212.5_ENST00000559756.1_RNA|AC074212.6_ENST00000591530.1_RNA|AC074212.6_ENST00000590076.1_RNA|AC074212.6_ENST00000586251.1_RNA|DMPK_ENST00000354227.5_3'UTR|DMPK_ENST00000447742.2_In_Frame_Del_p.V592del|DMPK_ENST00000458663.2_In_Frame_Del_p.L590del|SIX5_ENST00000560168.1_5'Flank|DMPK_ENST00000343373.4_In_Frame_Del_p.V607del|DMPK_ENST00000600757.1_In_Frame_Del_p.L600del	NM_004409.3	NP_004400.4	Q09013	DMPK_HUMAN	dystrophia myotonica-protein kinase	597					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)		CACGAGACAGAACAACGGCGAAC	0.695											OREG0025561	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.607_608del	Esophageal Squamous(35;307 869 9153 24033 28903)	Atlas-Indel,Pindel	.											.	DMPK	74	.	0			c.1820_1822del						PASS	.																																			SO:0001651	inframe_deletion	1760	exon14			.	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.1789_1791delGTT	chr19.hg19:g.46273848_46273850delAAC	ENSP00000291270:p.Val597del	335.0	0.0	0	938	210.0	68.0	0.32381	NM_001081563	E5KR08|Q16205|Q6P5Z6	In_Frame_Del	DEL	ENST00000291270.4	hg19	CCDS12674.1																																																																																			.	.	.	none		0.695	DMPK-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460572.1	NM_004409		-	46273847	AAC	-	46273845	7	5	19	1	0	1	0	1	0	0	0	0	4586	246	9	0	109	0	DMPK	19	46273845	In_Frame_Del	DEL	AAC	TCGA-2Z-A9JP-01A-11D-A42J-10	9063243	46273845	12855138	59	1314											
REM1	28954	hgsc.bcm.edu	37	chr20	30064340	30064340	+	Missense_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	cccacggggccaccagcctgGccgcctgagcacagtgcctt	6	5	12	18	2	0	1	0	1	0	0	0	1	0	1	7	3	3	1	7	3	0	1			TCGA-2Z-A9JP-01A-11D-A42J-10	TCGA-2Z-A9JP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fce839b6-a61e-4bd6-9fd4-2c885a257ac7	8f3d9061-9b3b-4029-9155-3d169642c461	g.chr20:30064340G>A	ENST00000201979.2	+	2	385	c.92G>A	c.(91-93)gGc>gAc	p.G31D	DEFB124_ENST00000481595.1_Intron	NM_014012.4	NP_054731.2	O75628	REM1_HUMAN	RAS (RAD and GEM)-like GTP-binding 1	31					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)			kidney(3)|large_intestine(3)|lung(14)|pancreas(2)|upper_aerodigestive_tract(1)	23	all_cancers(5;0.000119)|Lung NSC(7;1.32e-05)|all_lung(7;2.14e-05)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			CACCAGCCTGGCCGCCTGAGC	0.642																																					p.G31D		Atlas-SNP	.											.	REM1	54	.	0			c.G92A						PASS	.						76	87	84					20																	30064340		2203	4300	6503	SO:0001583	missense	28954	exon2			AGCCTGGCCGCCT	AF152863	CCDS13181.1	20q11.21	2014-05-09	2004-04-14	2004-04-16	ENSG00000088320	ENSG00000088320			15922	protein-coding gene	gene with protein product	"GTPase GES"	610388	"RAS (RAD and GEM)-like GTP-binding"	REM		10831614, 14623965	Standard	NM_014012		Approved	GES	uc002wwa.3	O75628	OTTHUMG00000032168	ENST00000201979.2:c.92G>A	chr20.hg19:g.30064340G>A	ENSP00000201979:p.Gly31Asp	118.0	0.0	.		102.0	37.0	.	NM_014012	E1P5L1|Q5TZR7|Q5TZR8|Q9NP57	Missense_Mutation	SNP	ENST00000201979.2	hg19	CCDS13181.1	.	.	.	.	.	.	.	.	.	.	G	13.55	2.271745	0.40194	.	.	ENSG00000088320	ENST00000201979	T	0.64991	-0.13	4.55	3.58	0.41010	.	0.709246	0.12931	N	0.427349	T	0.50939	0.1645	L	0.27053	0.805	0.43338	D	0.99538	B	0.17268	0.021	B	0.23419	0.046	T	0.45614	-0.9249	10	0.49607	T	0.09	.	12.1576	0.54085	0.0:0.174:0.826:0.0	.	31	O75628	REM1_HUMAN	D	31	ENSP00000201979:G31D	ENSP00000201979:G31D	G	+	2	0	REM1	29528001	1.000000	0.71417	0.997000	0.53966	0.943000	0.58893	3.986000	0.56937	1.088000	0.41272	0.655000	0.94253	GGC	.	.	.	none		0.642	REM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078508.2	NM_014012		A	30064340	G	A	30064340	3	1	19	1	0	0	0	0	1	0	0	0	13235	1203	42	2	94	2	REM1	20	30064340	Missense_Mutation	SNP	G	TCGA-2Z-A9JP-01A-11D-A42J-10		30064340	32961180	60	1315											
INADL	10207	hgsc.bcm.edu	37	chr1	62288639	62288639	+	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	gctgcctattcacactctgaGgcttggtgtggaagtggatt	7	13	13	8	0	2	1	1	1	1	0	2	3	2	3	1	4	1	2	1	4	2	4			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr1:62288639G>C	ENST00000371158.2	+	15	1820	c.1706G>C	c.(1705-1707)aGg>aCg	p.R569T	INADL_ENST00000316485.6_Missense_Mutation_p.R569T	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	569	PDZ 4. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)		p.R569M(1)		breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						CACACTCTGAGGCTTGGTGTG	0.438																																					p.R569T		Atlas-SNP	.											INADL,NS,carcinoma,0,1	INADL	179	.	1	Substitution - Missense(1)	lung(1)	c.G1706C						PASS	.						229	208	215					1																	62288639		2203	4300	6503	SO:0001583	missense	10207	exon15			CTCTGAGGCTTGG	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.1706G>C	chr1.hg19:g.62288639G>C	ENSP00000360200:p.Arg569Thr	89.0	0.0	.		92.0	51.0	.	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	hg19	CCDS617.2	.	.	.	.	.	.	.	.	.	.	G	20.4	3.987438	0.74589	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000255202	T;T	0.38560	1.13;1.13	4.99	4.99	0.66335	PDZ/DHR/GLGF (3);	0.000000	0.64402	D	0.000002	T	0.55593	0.1930	L	0.35723	1.085	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.999;0.998;0.962	T	0.53085	-0.8488	10	0.37606	T	0.19	.	17.8838	0.88849	0.0:0.0:1.0:0.0	.	569;569;569	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	T	569	ENSP00000360200:R569T;ENSP00000326199:R569T	ENSP00000255202:R569T	R	+	2	0	INADL	62061227	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.336000	0.90033	2.322000	0.78497	0.561000	0.74099	AGG	.	.	.	none		0.438	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		C	62288639	G	C	62288639	3	2	20	1	0	0	0	0	1	0	0	0	7738	1000	35	4	1760	4	INADL	1	62288639	Missense_Mutation	SNP	G	TCGA-2Z-A9JQ-01A-11D-A42J-10		62288639	186961982	1	1316											
NOTCH2	4853	hgsc.bcm.edu	37	chr1	120464974	120464975	+	Missense_Mutation	DNP	CC	CC	AT																															atgcttacgctttcgttttgCcatgattacccccagcagaa																										TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr1:120464974_120464975CC>AT	ENST00000256646.2	-	28	5316_5317	c.5097_5098GG>AT	c.(5095-5100)atGGca>atATca	p.1699_1700MA>IS	NOTCH2_ENST00000493703.1_5'Flank	NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	1699					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)		TTTCGTTTTGCCATGATTACCC	0.5			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome																												p.A1700S|p.M1699I		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.G5098T|c.G5097A						PASS	.																																			SO:0001583	missense	4853	exon28	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	GTTTTGCCATGAT|TTTTGCCATGATT	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.5097_5098delinsAT	chr1.hg19:g.120464974_120464975delinsAT	ENSP00000256646:p.M1699_A1700delinsIS	89.0|90.0	0.0	.		84.0|83.0	23.0	.	NM_024408	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	hg19	CCDS908.1																																																																																			.	.	.	none		0.5	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		AT	120464975	CC	AT	120464974	3	1	20	1	0	0	0	0	1	0	0	0	10555	739	26	4	2345	4	NOTCH2	1	120464974	Missense_Mutation	DNP	CC	TCGA-2Z-A9JQ-01A-11D-A42J-10	58176335	120464974	128785647	2	1317											
ILF2	3608	hgsc.bcm.edu	37	chr1	153636583	153636584	+	Missense_Mutation	DNP	AG	AG	GA																															aacgaatcctcaagtccttcAgtagtctgatgagaacttta																										TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr1:153636583_153636584AG>GA	ENST00000361891.4	-	10	804_805	c.679_680CT>TC	c.(679-681)CTg>TCg	p.L227S	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	227	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)			CAAGTCCTTCAGTAGTCTGATG	0.411																																					p.L227P|p.L227L		Atlas-SNP	.											.	ILF2	25	.	0			c.T680C|c.C679T						PASS	.																																			SO:0001583	missense	3608	exon10			TCCTTCAGTAGTC|CCTTCAGTAGTCT	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.679_680delinsGA	chr1.hg19:g.153636583_153636584delinsGA	ENSP00000355011:p.Leu227Ser	240.0|239.0	0.0	.		203.0|206.0	72.0|74.0	.	NM_004515	A6NDB0|B2R8G7|Q5SR10|Q5SR11|Q7L7R3|Q9BWD4|Q9P1N0	Missense_Mutation|Silent	SNP	ENST00000361891.4	hg19	CCDS1050.1																																																																																			.	.	.	none		0.411	ILF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090040.1	NM_004515		GA	153636584	AG	GA	153636583	3	3	20	1	0	0	0	0	1	0	0	0	7718	188	7	3	512	3	ILF2	1	153636583	Missense_Mutation	DNP	AG	TCGA-2Z-A9JQ-01A-11D-A42J-10	33171609	153636583	95614038	3	1318											
PEAR1	375033	hgsc.bcm.edu	37	chr1	156876627	156876627	+	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	ccatggggcaccctgcgatcCccagactggagcctgcttct	6	8	11	16	1	1	1	0	0	1	1	2	3	2	2	5	3	3	2	5	3	0	1			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr1:156876627C>T	ENST00000338302.3	+	7	824	c.599C>T	c.(598-600)cCc>cTc	p.P200L	PEAR1_ENST00000292357.7_Missense_Mutation_p.P200L			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	200					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)					CCCTGCGATCCCCAGACTGGA	0.617																																					p.P200L		Atlas-SNP	.											.	PEAR1	118	.	0			c.C599T						PASS	.						49	49	49					1																	156876627		2203	4300	6503	SO:0001583	missense	375033	exon6			GCGATCCCCAGAC	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.599C>T	chr1.hg19:g.156876627C>T	ENSP00000344465:p.Pro200Leu	87.0	0.0	.		45.0	16.0	.	NM_001080471	Q8TEK2	Missense_Mutation	SNP	ENST00000338302.3	hg19	CCDS30892.1	.	.	.	.	.	.	.	.	.	.	C	14.49	2.549844	0.45383	.	.	ENSG00000187800	ENST00000338302;ENST00000292357	T;T	0.58797	0.31;0.31	4.81	2.88	0.33553	.	0.135547	0.34245	N	0.004132	T	0.32071	0.0817	L	0.56769	1.78	0.47994	D	0.999563	B	0.31435	0.323	B	0.27380	0.079	T	0.18116	-1.0347	9	.	.	.	.	9.3744	0.38275	0.0:0.8172:0.0:0.1828	.	200	Q5VY43	PEAR1_HUMAN	L	200	ENSP00000344465:P200L;ENSP00000292357:P200L	.	P	+	2	0	PEAR1	155143251	0.002000	0.14202	1.000000	0.80357	0.985000	0.73830	0.782000	0.26788	1.238000	0.43771	0.561000	0.74099	CCC	.	.	.	none		0.617	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471		T	156876627	C	T	156876627	3	4	20	1	0	0	0	0	1	0	0	0	11719	623	22	2	617	2	PEAR1	1	156876627	Missense_Mutation	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	3240044	156876627	92373994	4	1319											
C1orf106	55765	hgsc.bcm.edu	37	chr1	200869255	200869255	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgacgggcaccttgccagcGgagtatcccctcaaaccagg	9	6	11	15	2	1	1	1	1	0	0	2	2	2	2	5	3	3	2	5	3	2	2			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr1:200869255G>A	ENST00000367342.4	+	4	659	c.459G>A	c.(457-459)gcG>gcA	p.A153A	C1orf106_ENST00000413687.2_Silent_p.A68A	NM_018265.3	NP_060735.3	Q3KP66	CA106_HUMAN	chromosome 1 open reading frame 106	153										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(2)	21						CCTTGCCAGCGGAGTATCCCC	0.627																																					p.A167A		Atlas-SNP	.											.	C1orf106	59	.	0			c.G501A						PASS	.						47	42	44					1																	200869255		2202	4300	6502	SO:0001819	synonymous_variant	55765	exon4			GCCAGCGGAGTAT	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.459G>A	chr1.hg19:g.200869255G>A		239.0	0.0	.		137.0	61.0	.	NM_018265	B4E1K9|E9PFY0|Q9NV65|Q9NVI0	Silent	SNP	ENST00000367342.4	hg19																																																																																				.	.	.	none		0.627	C1orf106-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000087057.2	NM_018265		A	200869255	G	A	200869255	2	1	20	1	0	0	0	0	0	0	0	1	1982	1103	39	1		1	C1orf106	1	200869255	Silent	SNP	G	TCGA-2Z-A9JQ-01A-11D-A42J-10	43992628	200869255	48381366	5	1320											
ZFP36L2	678	hgsc.bcm.edu	37	chr2	43452438	43452438	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggcacttttcgccgtactTgcacgtgccgctctcctcga	4	12	9	16	5	1	0	0	0	1	0	4	1	1	0	3	1	3	4	3	1	1	4			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr2:43452438T>C	ENST00000282388.3	-	2	798	c.505A>G	c.(505-507)Aag>Gag	p.K169E	THADA_ENST00000330266.7_Intron	NM_006887.4	NP_008818.3	P47974	TISD_HUMAN	ZFP36 ring finger protein-like 2	169					cell proliferation (GO:0008283)|definitive hemopoiesis (GO:0060216)|hemopoiesis (GO:0030097)|mRNA catabolic process (GO:0006402)|negative regulation of stem cell differentiation (GO:2000737)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	15		Acute lymphoblastic leukemia(82;0.00323)|all_hematologic(82;0.00824)				TCGCCGTACTTGCACGTGCCG	0.637																																					p.K169E		Atlas-SNP	.											.	ZFP36L2	56	.	0			c.A505G						PASS	.						47	44	45					2																	43452438		2203	4300	6503	SO:0001583	missense	678	exon2			CGTACTTGCACGT	X78992	CCDS1811.1	2p22.3-p21	2012-11-27	2012-11-27	2001-11-23	ENSG00000152518	ENSG00000152518		"RING-type (C3HC4) zinc fingers"	1108	protein-coding gene	gene with protein product		612053	"zinc finger protein 36, C3H type-like 1", "zinc finger protein 36, C3H type-like 2"	BRF2		7835719, 8545129, 14981510, 17172869	Standard	NM_006887		Approved	ERF2, RNF162C, TIS11D	uc002rsv.4	P47974	OTTHUMG00000128642	ENST00000282388.3:c.505A>G	chr2.hg19:g.43452438T>C	ENSP00000282388:p.Lys169Glu	56.0	0.0	.		26.0	16.0	.	NM_006887	Q53TB4|Q9BSJ3	Missense_Mutation	SNP	ENST00000282388.3	hg19	CCDS1811.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.435753	0.83885	.	.	ENSG00000152518	ENST00000282388	T	0.52754	0.65	4.65	4.65	0.58169	Zinc finger, CCCH-type (3);	0.477019	0.21330	N	0.076316	T	0.73567	0.3603	M	0.91818	3.245	0.80722	D	1	D	0.71674	0.998	D	0.72338	0.977	T	0.79997	-0.1567	10	0.87932	D	0	-21.6188	13.1367	0.59413	0.0:0.0:0.0:1.0	.	169	P47974	TISD_HUMAN	E	169	ENSP00000282388:K169E	ENSP00000282388:K169E	K	-	1	0	ZFP36L2	43305942	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	7.528000	0.81941	1.742000	0.51746	0.454000	0.30748	AAG	.	.	.	none		0.637	ZFP36L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250513.2	NM_006887		C	43452438	T	C	43452438	3	2	20	1	0	0	0	0	1	0	0	0	17659	1821	63	3	983	3	ZFP36L2	2	43452438	Missense_Mutation	SNP	T	TCGA-2Z-A9JQ-01A-11D-A42J-10		43452438	199746935	6	1321											
SOCS5	9655	hgsc.bcm.edu	37	chr2	46986775	46986775	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gattgattacatacactgccTcgtgcctgatttgcttcaaa	10	14	7	10	1	1	2	1	2	0	0	2	3	1	2	2	0	5	1	2	0	3	5			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr2:46986775T>C	ENST00000306503.5	+	2	1278	c.1106T>C	c.(1105-1107)cTc>cCc	p.L369P	SOCS5_ENST00000394861.2_Missense_Mutation_p.L369P	NM_014011.4	NP_054730.1	O75159	SOCS5_HUMAN	suppressor of cytokine signaling 5	369					cell growth (GO:0016049)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|JAK-STAT cascade (GO:0007259)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of signal transduction (GO:0009968)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)		receptor tyrosine kinase binding (GO:0030971)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(9)|ovary(2)	22		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			ATACACTGCCTCGTGCCTGAT	0.507																																					p.L369P		Atlas-SNP	.											.	SOCS5	62	.	0			c.T1106C						PASS	.						58	56	57					2																	46986775		2203	4300	6503	SO:0001583	missense	9655	exon2			ACTGCCTCGTGCC	AB014571	CCDS1830.1	2p21	2013-02-14			ENSG00000171150	ENSG00000171150		"Suppressors of cytokine signaling", "SH2 domain containing"	16852	protein-coding gene	gene with protein product		607094				9734811, 11230166	Standard	NM_014011		Approved	KIAA0671, SOCS-5, CIS6, CISH6, Cish5	uc002rvf.3	O75159	OTTHUMG00000128852	ENST00000306503.5:c.1106T>C	chr2.hg19:g.46986775T>C	ENSP00000305133:p.Leu369Pro	128.0	0.0	.		132.0	65.0	.	NM_144949	Q53SD4|Q8IYZ4	Missense_Mutation	SNP	ENST00000306503.5	hg19	CCDS1830.1	.	.	.	.	.	.	.	.	.	.	T	17.31	3.356193	0.61293	.	.	ENSG00000171150	ENST00000306503;ENST00000394861	T;T	0.40476	1.03;1.03	5.43	5.43	0.79202	SH2 motif (1);	0.064994	0.64402	D	0.000007	T	0.59500	0.2198	L	0.52011	1.625	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.62191	-0.6906	10	0.87932	D	0	-16.2224	15.3001	0.73940	0.0:0.0:0.0:1.0	.	369	O75159	SOCS5_HUMAN	P	369	ENSP00000305133:L369P;ENSP00000378330:L369P	ENSP00000305133:L369P	L	+	2	0	SOCS5	46840279	1.000000	0.71417	0.944000	0.38274	0.989000	0.77384	7.868000	0.87116	2.279000	0.76181	0.533000	0.62120	CTC	.	.	.	none		0.507	SOCS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250791.2			C	46986775	T	C	46986775	3	2	20	1	0	0	0	0	1	0	0	0	14930	1551	54	3	1108	3	SOCS5	2	46986775	Missense_Mutation	SNP	T	TCGA-2Z-A9JQ-01A-11D-A42J-10	3534337	46986775	196212598	7	1322											
DCTN1	1639	hgsc.bcm.edu	37	chr2	74597421	74597421	+	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	tggttcttcttttccatgagCttctggagcttcacatgctc	5	17	8	11	0	4	1	1	1	3	0	6	2	5	2	1	2	3	4	1	2	0	6			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr2:74597421C>T	ENST00000361874.3	-	12	1496	c.1179G>A	c.(1177-1179)aaG>aaA	p.K393K	DCTN1_ENST00000409868.1_Silent_p.K376K|DCTN1_ENST00000409438.1_Silent_p.K259K|DCTN1_ENST00000394003.3_Silent_p.K386K|DCTN1_ENST00000409567.3_Silent_p.K373K|DCTN1_ENST00000407639.2_Silent_p.K259K|DCTN1_ENST00000495643.1_5'Flank|DCTN1_ENST00000409240.1_Silent_p.K356K	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	393					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|microtubule-based transport (GO:0010970)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nervous system development (GO:0007399)	cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(1)|skin(3)	45						TTTCCATGAGCTTCTGGAGCT	0.537																																					p.K393K		Atlas-SNP	.											.	DCTN1	110	.	0			c.G1179A						PASS	.						72	66	68					2																	74597421		2203	4300	6503	SO:0001819	synonymous_variant	1639	exon12			CATGAGCTTCTGG		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.1179G>A	chr2.hg19:g.74597421C>T		59.0	0.0	.		39.0	21.0	.	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Silent	SNP	ENST00000361874.3	hg19	CCDS1939.1																																																																																			.	.	.	none		0.537	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082		T	74597421	C	T	74597421	2	4	20	1	0	0	0	0	0	0	0	1	4308	796	28	2		2	DCTN1	2	74597421	Silent	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	27610646	74597421	168601952	8	1323											
VWA3B	200403	hgsc.bcm.edu	37	chr2	98844793	98844793	+	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	gcagaaaaggatggagacagCaagtgagcacctctgcccgc	13	4	13	11	1	1	3	0	1	1	2	1	5	1	4	2	2	3	3	2	2	3	0			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr2:98844793C>T	ENST00000477737.1	+	15	2352	c.2148C>T	c.(2146-2148)agC>agT	p.S716S		NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	716										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						ATGGAGACAGCAAGTGAGCAC	0.522																																					p.S716S		Atlas-SNP	.											.	VWA3B	138	.	0			c.C2148T						PASS	.						73	74	73					2																	98844793		2048	4198	6246	SO:0001819	synonymous_variant	200403	exon15			AGACAGCAAGTGA	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.2148C>T	chr2.hg19:g.98844793C>T		50.0	0.0	.		40.0	12.0	.	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Silent	SNP	ENST00000477737.1	hg19	CCDS42718.1	.	.	.	.	.	.	.	.	.	.	C	4.479	0.088881	0.08583	.	.	ENSG00000168658	ENST00000473149	.	.	.	5.18	-1.5	0.08691	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.0944	0.03664	0.1619:0.4501:0.1904:0.1976	.	.	.	.	X	127	.	.	Q	+	1	0	VWA3B	98211225	0.003000	0.15002	0.052000	0.19188	0.496000	0.33645	-0.656000	0.05342	-0.261000	0.09405	0.467000	0.42956	CAA	.	.	.	none		0.522	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992		T	98844793	C	T	98844793	2	4	20	1	0	0	0	0	0	0	0	1	17253	709	25	2		2	VWA3B	2	98844793	Silent	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	24247372	98844793	144354580	9	1324											
GCC2	9648	hgsc.bcm.edu	37	chr2	109102163	109102164	+	Frame_Shift_Del	DEL	AA	AA	-																															agcaattgcttgtgaaaaccAaaaaggaactggcagattca																										TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr2:109102163_109102164delAA	ENST00000309863.6	+	14	4399_4400	c.3685_3686delAA	c.(3685-3687)aaafs	p.K1230fs		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	1230					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						TGTGAAAACCAAAAAGGAACTG	0.272																																					p.1228_1229del		Atlas-Indel,Pindel	.											.	GCC2	129	.	0			c.3684_3685del						PASS	.																																			SO:0001589	frameshift_variant	9648	exon14			.	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.3685_3686delAA	chr2.hg19:g.109102165_109102166delAA	ENSP00000307939:p.Lys1230fs	545.0	0.0	0		608.0	237.0	0.389803	NM_181453	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Frame_Shift_Del	DEL	ENST00000309863.6	hg19	CCDS33268.1																																																																																			.	.	.	none		0.272	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635		-	109102164	AA	-	109102163	7	5	20	1	0	1	0	1	0	0	0	0	6293	131	5	0	3739	0	GCC2	2	109102163	Frame_Shift_Del	DEL	AA	TCGA-2Z-A9JQ-01A-11D-A42J-10	10257370	109102163	134097210	10	1325											
YSK4	80122	hgsc.bcm.edu	37	chr2	135779307	135779307	+	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	cacttctgctgatgctttgcAagatgatgttttgatttttg	7	19	9	6	0	1	4	0	3	1	1	1	4	1	4	0	0	3	4	0	0	1	6			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr2:135779307A>T	ENST00000375845.3	-	2	146	c.116T>A	c.(115-117)tTg>tAg	p.L39*	MAP3K19_ENST00000392918.3_Nonsense_Mutation_p.L39*|MAP3K19_ENST00000392915.1_Nonsense_Mutation_p.L56*|MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000375844.3_Nonsense_Mutation_p.L39*|MAP3K19_ENST00000392917.3_Nonsense_Mutation_p.L39*|MAP3K19_ENST00000358371.4_Nonsense_Mutation_p.L39*	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	39							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)										GATGCTTTGCAAGATGATGTT	0.373																																					p.L39X		Atlas-SNP	.											.	.	.	.	0			c.T116A						PASS	.						153	137	142					2																	135779307		2203	4300	6503	SO:0001587	stop_gained	80122	exon2			CTTTGCAAGATGA	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.116T>A	chr2.hg19:g.135779307A>T	ENSP00000365005:p.Leu39*	67.0	0.0	.		64.0	25.0	.	NM_025052	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Nonsense_Mutation	SNP	ENST00000375845.3	hg19	CCDS2176.2	.	.	.	.	.	.	.	.	.	.	A	24.6	4.554596	0.86231	.	.	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000375844;ENST00000392918;ENST00000392917;ENST00000392915;ENST00000425952;ENST00000414343	.	.	.	4.44	4.44	0.53790	.	0.000000	0.31010	N	0.008422	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.0351	0.42125	1.0:0.0:0.0:0.0	.	.	.	.	X	39;39;39;39;39;56;11;11	.	ENSP00000351140:L39X	L	-	2	0	YSK4	135495777	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	2.668000	0.46816	1.877000	0.54381	0.477000	0.44152	TTG	.	.	.	none		0.373	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052		T	135779307	A	T	135779307	4	4	20	1	0	0	0	0	0	1	0	0	17507	131	5	5	3906	5	YSK4	2	135779307	Nonsense_Mutation	SNP	A	TCGA-2Z-A9JQ-01A-11D-A42J-10	26677144	135779307	107420066	11	1326											
TTN	7273	hgsc.bcm.edu	37	chr2	179435106	179435106	+	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	ttggcatcaaccacagtccaAactaagcggctggtttctct	10	11	8	12	1	2	0	1	0	1	0	4	0	3	0	2	3	3	3	2	3	3	3			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr2:179435106A>T	ENST00000591111.1	-	276	71054	c.70830T>A	c.(70828-70830)gtT>gtA	p.V23610V	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Silent_p.V22683V|TTN_ENST00000589042.1_Silent_p.V25251V|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.V16378V|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000359218.5_Silent_p.V16311V|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000460472.2_Silent_p.V16186V|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586452.1_RNA			Q8WZ42	TITIN_HUMAN	titin	23610	Fibronectin type-III 71. {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)			CCACAGTCCAAACTAAGCGGC	0.428																																					p.V25251V		Atlas-SNP	.											.	TTN	18412	.	0			c.T75753A						PASS	.						55	53	54					2																	179435106		1921	4128	6049	SO:0001819	synonymous_variant	7273	exon326			AGTCCAAACTAAG	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.70830T>A	chr2.hg19:g.179435106A>T		31.0	0.0	.		79.0	35.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.	.	none		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179435106	A	T	179435106	2	4	20	1	0	0	0	0	0	0	0	1	16747	1	1	5		5	TTN	2	179435106	Silent	SNP	A	TCGA-2Z-A9JQ-01A-11D-A42J-10	43655799	179435106	63764267	12	1327											
CUL3	8452	hgsc.bcm.edu	37	chr2	225378264	225378264	+	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	aaaaaattctgcagacatttCcaaaaaaggagcctcaaaat	20	8	5	8	0	2	1	1	0	1	1	3	2	3	2	2	1	2	1	2	1	8	2			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr2:225378264C>A	ENST00000264414.4	-	5	969	c.631G>T	c.(631-633)Gaa>Taa	p.E211*	CUL3_ENST00000344951.4_Nonsense_Mutation_p.E145*|CUL3_ENST00000432260.2_5'Flank|CUL3_ENST00000409777.1_Nonsense_Mutation_p.E187*|CUL3_ENST00000409096.1_Nonsense_Mutation_p.E187*	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	211					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)		GCAGACATTTCCAAAAAAGGA	0.303																																					p.E217X		Atlas-SNP	.											.	CUL3	96	.	0			c.G649T						PASS	.						57	60	59					2																	225378264		2202	4300	6502	SO:0001587	stop_gained	8452	exon5			ACATTTCCAAAAA	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.631G>T	chr2.hg19:g.225378264C>A	ENSP00000264414:p.Glu211*	190.0	0.0	.		148.0	54.0	.	NM_001257198	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Nonsense_Mutation	SNP	ENST00000264414.4	hg19	CCDS2462.1	.	.	.	.	.	.	.	.	.	.	C	38	6.790642	0.97841	.	.	ENSG00000036257	ENST00000264414;ENST00000344951;ENST00000409096;ENST00000409777	.	.	.	5.77	5.77	0.91146	.	0.095159	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	.	20.0562	0.97651	0.0:1.0:0.0:0.0	.	.	.	.	X	211;145;187;187	.	ENSP00000264414:E211X	E	-	1	0	CUL3	225086508	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	5.738000	0.68613	2.758000	0.94735	0.644000	0.83932	GAA	.	.	.	none		0.303	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2			A	225378264	C	A	225378264	4	1	20	1	0	0	0	0	0	1	0	0	4058	864	30	4	1723	4	CUL3	2	225378264	Nonsense_Mutation	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	45943158	225378264	17821109	13	1328											
AQP12B	653437	hgsc.bcm.edu	37	chr2	241622010	241622010	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtccaaggtgaccccgtgcGccaggaagagcaggaagagc	11	3	15	12	3	0	3	0	1	0	2	1	5	1	5	4	3	3	1	4	3	3	0	rs374703341		TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr2:241622010G>A	ENST00000407834.3	-	1	307	c.245C>T	c.(244-246)gCg>gTg	p.A82V		NM_001102467.1	NP_001095937.1	A6NM10	AQ12B_HUMAN	aquaporin 12B	70						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)		GACCCCGTGCGCCAGGAAGAG	0.672																																					p.A82V		Atlas-SNP	.											.	AQP12B	33	.	0			c.C245T						PASS	.		VAL/ALA	0,4406		0,0,2203	50	51	51		245	-2.4	0.1	2		51	1,8597		0,1,4298	no	missense	AQP12B	NM_001102467.1	64	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	benign	82/308	241622010	1,13003	2203	4299	6502	SO:0001583	missense	653437	exon1			CCGTGCGCCAGGA	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.245C>T	chr2.hg19:g.241622010G>A	ENSP00000384894:p.Ala82Val	155.0	0.0	.		89.0	4.0	.	NM_001102467	A4QPB9	Missense_Mutation	SNP	ENST00000407834.3	hg19	CCDS46560.1	.	.	.	.	.	.	.	.	.	.	.	0.005	-2.119709	0.00346	0.0	1.16E-4	ENSG00000185176	ENST00000407834	T	0.06371	3.31	2.53	-2.36	0.06663	.	0.576494	0.18143	N	0.150341	T	0.02047	0.0064	N	0.03224	-0.385	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.44726	-0.9309	9	.	.	.	-0.5459	5.1467	0.14989	0.2663:0.2058:0.5279:0.0	.	82	A6NM10-2	.	V	82	ENSP00000384894:A82V	.	A	-	2	0	AQP12B	241270683	0.001000	0.12720	0.053000	0.19242	0.111000	0.19643	0.052000	0.14163	-0.484000	0.06763	-0.359000	0.07587	GCG	.	.	.	weak		0.672	AQP12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325625.1			A	241622010	G	A	241622010	3	1	20	1	0	0	0	0	1	0	0	0	825	1087	38	1	690	1	AQP12B	2	241622010	Missense_Mutation	SNP	G	TCGA-2Z-A9JQ-01A-11D-A42J-10	16243746	241622010	1577363	14	1329											
SCN11A	11280	hgsc.bcm.edu	37	chr3	38892111	38892111	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagttgagatggtcaaggatGgatttcatggctttgggttg	8	14	15	4	0	2	1	2	1	0	1	2	4	2	3	0	5	0	3	0	5	1	4			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr3:38892111G>A	ENST00000302328.3	-	25	4386	c.4188C>T	c.(4186-4188)tcC>tcT	p.S1396S	SCN11A_ENST00000450244.1_Silent_p.S1396S|SCN11A_ENST00000456224.3_Silent_p.S1358S|SCN11A_ENST00000444237.2_Silent_p.S1396S	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	1396					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)	GGTCAAGGATGGATTTCATGG	0.398																																					p.S1396S		Atlas-SNP	.											.	SCN11A	296	.	0			c.C4188T						PASS	.						190	171	177					3																	38892111		2203	4300	6503	SO:0001819	synonymous_variant	11280	exon25			AAGGATGGATTTC	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.4188C>T	chr3.hg19:g.38892111G>A		35.0	0.0	.		86.0	34.0	.	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Silent	SNP	ENST00000302328.3	hg19	CCDS33737.1																																																																																			.	.	.	none		0.398	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		A	38892111	G	A	38892111	2	1	20	1	0	0	0	0	0	0	0	1	13926	1335	47	2		2	SCN11A	3	38892111	Silent	SNP	G	TCGA-2Z-A9JQ-01A-11D-A42J-10		38892111	159130319	15	1330											
PLXNB1	5364	hgsc.bcm.edu	37	chr3	48457576	48457576	+	Splice_Site	DEL	C	C	-																															gatggaatggaccttcggatCctgtgggacagacagggaga																										TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr3:48457576delC	ENST00000358536.4	-	18	3750	c.3481delG	c.(3481-3483)gat>at	p.D1161fs	PLXNB1_ENST00000448774.2_Intron|PLXNB1_ENST00000296440.6_Splice_Site_p.D1161fs|PLXNB1_ENST00000358459.4_Splice_Site_p.D978fs|PLXNB1_ENST00000456774.1_Splice_Site_p.D978fs|PLXNB1_ENST00000465117.1_5'Flank	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	1161					axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		ACCTTCGGATCCTGTGGGACA	0.647																																					p.D1161fs		Atlas-Indel,Pindel	.											.	PLXNB1	150	.	0			c.3482delA						PASS	.						20	21	21					3																	48457576		2197	4296	6493	SO:0001630	splice_region_variant	5364	exon18			.	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"Plexins"	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.3481-1G>-	chr3.hg19:g.48457576delC		120.0	0.0	0		109.0	37.0	0.33945	NM_001130082	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Frame_Shift_Del	DEL	ENST00000358536.4	hg19	CCDS2765.1																																																																																			.	.	.	none		0.647	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673	Frame_Shift_Del	-	48457576	C	-	48457576	8	5	20	1	0	1	0	1	0	0	1	0	12130	869	30	0	3010	0	PLXNB1	3	48457576	Splice_Site	DEL	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	9565465	48457576	149564854	16	1331											
QARS	5859	hgsc.bcm.edu	37	chr3	49136634	49136634	+	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	cattcagcacatcacgcacaCaggcttctagaagatgtggc	12	8	9	12	1	3	2	2	0	1	2	3	2	3	2	0	2	1	3	0	2	2	3			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr3:49136634C>A	ENST00000306125.6	-	18	2004	c.1667G>T	c.(1666-1668)tGt>tTt	p.C556F	QARS_ENST00000414533.1_Missense_Mutation_p.C545F|QARS_ENST00000470225.1_5'Flank			P47897	SYQ_HUMAN	glutaminyl-tRNA synthetase	556					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)	ATCACGCACACAGGCTTCTAG	0.542																																					p.C556F		Atlas-SNP	.											.	QARS	55	.	0			c.G1667T						PASS	.						105	102	103					3																	49136634		2203	4300	6503	SO:0001583	missense	5859	exon18			CGCACACAGGCTT	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.1667G>T	chr3.hg19:g.49136634C>A	ENSP00000307567:p.Cys556Phe	77.0	0.0	.		70.0	24.0	.	NM_005051	B4DWJ2	Missense_Mutation	SNP	ENST00000306125.6	hg19	CCDS2788.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.801459	0.90538	.	.	ENSG00000172053	ENST00000453392;ENST00000306125;ENST00000414533	T;T;T	0.17370	2.28;2.28;2.28	6.02	6.02	0.97574	Glutamyl/glutaminyl-tRNA synthetase, class Ib, alpha-bundle domain (1);Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.40670	0.1126	L	0.55017	1.72	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.00766	-1.1575	10	0.38643	T	0.18	-17.8032	20.5407	0.99260	0.0:1.0:0.0:0.0	.	545;556	B4DWJ2;P47897	.;SYQ_HUMAN	F	76;556;545	ENSP00000396326:C76F;ENSP00000307567:C556F;ENSP00000390015:C545F	ENSP00000307567:C556F	C	-	2	0	QARS	49111638	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.579000	0.67457	2.865000	0.98341	0.655000	0.94253	TGT	.	.	.	none		0.542	QARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345689.2	NM_005051		A	49136634	C	A	49136634	3	1	20	1	0	0	0	0	1	0	0	0	12884	478	17	4	688	4	QARS	3	49136634	Missense_Mutation	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	679058	49136634	148885796	17	1332											
CACNA1D	776	hgsc.bcm.edu	37	chr3	53699775	53699775	+	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	ttatttgtaatcataatctaTgctattataggattggaact	13	18	6	4	0	2	0	1	0	1	0	2	2	2	2	0	2	2	2	0	2	8	9			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr3:53699775T>G	ENST00000350061.5	+	6	1366	c.855T>G	c.(853-855)taT>taG	p.Y285*	CACNA1D_ENST00000288139.4_Nonsense_Mutation_p.Y285*|CACNA1D_ENST00000422281.2_Nonsense_Mutation_p.Y285*	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	285					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)			breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TCATAATCTATGCTATTATAG	0.333																																					p.Y285X		Atlas-SNP	.											.	CACNA1D	324	.	0			c.T855G						PASS	.						115	116	116					3																	53699775		2203	4300	6503	SO:0001587	stop_gained	776	exon6			AATCTATGCTATT	AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.855T>G	chr3.hg19:g.53699775T>G	ENSP00000288133:p.Tyr285*	82.0	0.0	.		94.0	36.0	.	NM_001128840	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Nonsense_Mutation	SNP	ENST00000350061.5	hg19	CCDS46848.1	.	.	.	.	.	.	.	.	.	.	T	38	6.984700	0.97983	.	.	ENSG00000157388	ENST00000350061;ENST00000288139;ENST00000422281	.	.	.	5.08	5.08	0.68730	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.0112	0.71552	0.0:0.0:0.0:1.0	.	.	.	.	X	285	.	ENSP00000288139:Y285X	Y	+	3	2	CACNA1D	53674815	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.575000	0.46025	2.125000	0.65367	0.533000	0.62120	TAT	.	.	.	none		0.333	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720		G	53699775	T	G	53699775	4	3	20	1	0	0	0	0	0	1	0	0	2543	1471	51	5	877	5	CACNA1D	3	53699775	Nonsense_Mutation	SNP	T	TCGA-2Z-A9JQ-01A-11D-A42J-10	4563141	53699775	144322655	18	1333											
ARHGAP31	57514	hgsc.bcm.edu	37	chr3	119133437	119133437	+	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	tcagtacaggagccttcagaCtgtgacgaagatgacactgt	12	9	11	9	1	2	4	2	2	0	2	2	6	2	5	1	1	2	1	1	1	2	2			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr3:119133437C>T	ENST00000264245.4	+	12	3193	c.2661C>T	c.(2659-2661)gaC>gaT	p.D887D		NM_020754.2	NP_065805.2	Q2M1Z3	RHG31_HUMAN	Rho GTPase activating protein 31	887					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(3)|large_intestine(11)|lung(29)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	67						AGCCTTCAGACTGTGACGAAG	0.557																																					p.D887D	Pancreas(7;176 297 5394 51128 51241)	Atlas-SNP	.											.	ARHGAP31	175	.	0			c.C2661T						PASS	.						108	111	110					3																	119133437		2075	4217	6292	SO:0001819	synonymous_variant	57514	exon12			TTCAGACTGTGAC		CCDS43135.1	3q13.33	2011-06-29			ENSG00000031081	ENSG00000031081		"Rho GTPase activating proteins"	29216	protein-coding gene	gene with protein product		610911				9786927, 12819203, 16519628	Standard	NM_020754		Approved	CDGAP	uc003ecj.4	Q2M1Z3	OTTHUMG00000159362	ENST00000264245.4:c.2661C>T	chr3.hg19:g.119133437C>T		91.0	0.0	.		112.0	50.0	.	NM_020754	Q9ULL6	Silent	SNP	ENST00000264245.4	hg19	CCDS43135.1																																																																																			.	.	.	none		0.557	ARHGAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354942.2			T	119133437	C	T	119133437	2	4	20	1	0	0	0	0	0	0	0	1	880	564	20	2		2	ARHGAP31	3	119133437	Silent	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	65433662	119133437	78888993	19	1334											
PLS1	5357	hgsc.bcm.edu	37	chr3	142383090	142383090	+	Missense_Mutation	SNP	G	G	T																															ctgtccaaagatggaaaacaGtactactaccatttctcggg																								rs373717334		TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr3:142383090G>T	ENST00000337777.3	+	2	224	c.11G>T	c.(10-12)aGt>aTt	p.S4I	PLS1_ENST00000457734.2_Missense_Mutation_p.S4I|PLS1_ENST00000497002.1_Missense_Mutation_p.S4I	NM_002670.2	NP_002661.2	Q14651	PLSI_HUMAN	plastin 1	4						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.S4N(1)		NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	27						ATGGAAAACAGTACTACTACC	0.323																																					p.S4I		Atlas-SNP	.											PLS1,NS,carcinoma,0,2	PLS1	71	.	1	Substitution - Missense(1)	pancreas(1)	c.G11T						PASS	.						84	85	85					3																	142383090		2203	4300	6503	SO:0001583	missense	5357	exon2			AAAACAGTACTAC	L20826	CCDS3125.1	3q23	2013-01-10	2010-02-10		ENSG00000120756	ENSG00000120756		"EF-hand domain containing"	9090	protein-coding gene	gene with protein product		602734	"plastin 1 (I isoform)"			8139549	Standard	NM_002670		Approved	I-plastin, Plastin-1	uc003euz.3	Q14651	OTTHUMG00000159292	ENST00000337777.3:c.11G>T	chr3.hg19:g.142383090G>T	ENSP00000336831:p.Ser4Ile	165.0	0.0	.		192.0	81.0	.	NM_001172312	A8K2Q1|D3DNG3|Q8NEG6	Missense_Mutation	SNP	ENST00000337777.3	hg19	CCDS3125.1	.	.	.	.	.	.	.	.	.	.	G	14.59	2.581186	0.46006	.	.	ENSG00000120756	ENST00000457734;ENST00000483373;ENST00000475296;ENST00000495744;ENST00000461644;ENST00000464320;ENST00000337777;ENST00000497199;ENST00000497002	T;T;T;T;T;T;T;T;T	0.60040	0.8;0.82;0.22;0.56;0.53;0.33;0.8;0.52;0.8	5.44	3.28	0.37604	.	0.174974	0.64402	D	0.000011	T	0.19366	0.0465	N	0.00347	-1.61	0.28604	N	0.909025	B	0.15141	0.012	B	0.16722	0.016	T	0.10428	-1.0630	10	0.49607	T	0.09	-15.4577	4.5182	0.11947	0.4314:0.0:0.5686:0.0	.	4	Q14651	PLSI_HUMAN	I	4	ENSP00000387890:S4I;ENSP00000419893:S4I;ENSP00000417311:S4I;ENSP00000419531:S4I;ENSP00000419271:S4I;ENSP00000418880:S4I;ENSP00000336831:S4I;ENSP00000417491:S4I;ENSP00000418700:S4I	ENSP00000336831:S4I	S	+	2	0	PLS1	143865780	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	2.794000	0.47853	1.466000	0.48025	0.580000	0.79431	AGT	.	.	.	alt		0.323	PLS1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354435.1	NM_002670		T	142383090	G	T	142383090	3	4	20	1	0	0	0	0	1	0	0	0	12114	1029	36	4	13	4	PLS1	3	142383090	Missense_Mutation	SNP	G	TCGA-2Z-A9JQ-01A-11D-A42J-10	23249653	142383090	55639340	20	1335	13	2									
PLS1	5357	hgsc.bcm.edu	37	chr3	142383093	142383093	+	Frame_Shift_Del	DEL	C	C	-																															tccaaagatggaaaacagtaCtactaccatttctcgggagg																										TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr3:142383093delC	ENST00000337777.3	+	2	227	c.14delC	c.(13-15)actfs	p.T7fs	PLS1_ENST00000457734.2_Frame_Shift_Del_p.T7fs|PLS1_ENST00000497002.1_Frame_Shift_Del_p.T7fs	NM_002670.2	NP_002661.2	Q14651	PLSI_HUMAN	plastin 1	7						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	27						GAAAACAGTACTACTACCATT	0.323																																					p.T5fs		Atlas-INDEL	.											.	PLS1	71	.	0			c.13delA						PASS	.						84	85	85					3																	142383093		2203	4300	6503	SO:0001589	frameshift_variant	5357	exon2			.	L20826	CCDS3125.1	3q23	2013-01-10	2010-02-10		ENSG00000120756	ENSG00000120756		"EF-hand domain containing"	9090	protein-coding gene	gene with protein product		602734	"plastin 1 (I isoform)"			8139549	Standard	NM_002670		Approved	I-plastin, Plastin-1	uc003euz.3	Q14651	OTTHUMG00000159292	ENST00000337777.3:c.14delC	chr3.hg19:g.142383093delC	ENSP00000336831:p.Thr7fs	166.0	0.0	0		193.0	80.0	0.414508	NM_001172312	A8K2Q1|D3DNG3|Q8NEG6	Frame_Shift_Del	DEL	ENST00000337777.3	hg19	CCDS3125.1																																																																																			.	.	.	none		0.323	PLS1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354435.1	NM_002670		-	142383093	C	-	142383093	7	5	20	1	0	1	0	1	0	0	0	0	12114	565	20	0	16	0	PLS1	3	142383093	Frame_Shift_Del	DEL	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	3	142383093	55639337	21	1336	13	2									
TACC3	10460	hgsc.bcm.edu	37	chr4	1729484	1729485	+	Missense_Mutation	DNP	CA	CA	GT																															aaactactcatggaattctaCagaaaccagtggaggctgac																										TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr4:1729484_1729485CA>GT	ENST00000313288.4	+	4	461_462	c.355_356CA>GT	c.(355-357)CAg>GTg	p.Q119V		NM_006342.2	NP_006333.1	Q9Y6A5	TACC3_HUMAN	transforming, acidic coiled-coil containing protein 3	119					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)			TGGAATTCTACAGAAACCAGTG	0.54																																					p.Q119E|p.Q119L	Ovarian(120;482 2294 11894 35824)	Atlas-SNP	.											.	TACC3	69	.	0			c.C355G|c.A356T						PASS	.																																			SO:0001583	missense	10460	exon4			ATTCTACAGAAAC|TTCTACAGAAACC	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	Exception_encountered	chr4.hg19:g.1729484_1729485delinsGT	ENSP00000326550:p.Gln119Val	178.0|181.0	0.0	.		115.0|117.0	63.0	.	NM_006342	Q2NKK4|Q3KQS5|Q9UMQ1	Missense_Mutation	SNP	ENST00000313288.4	hg19	CCDS3352.1																																																																																			.	.	.	none		0.54	TACC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203730.2			GT	1729485	CA	GT	1729484	3	3	20	1	0	0	0	0	1	0	0	0	15515	479	17	4	365	4	TACC3	4	1729484	Missense_Mutation	DNP	CA	TCGA-2Z-A9JQ-01A-11D-A42J-10		1729484	189424792	22	1337											
ATP10D	57205	hgsc.bcm.edu	37	chr4	47574963	47574963	+	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	cttcttgtccatggacactgGtgttatacacggctttccaa	8	14	8	11	1	1	0	0	0	1	0	3	1	3	1	2	3	1	2	2	3	3	5			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr4:47574963G>T	ENST00000273859.3	+	18	3584	c.3315G>T	c.(3313-3315)tgG>tgT	p.W1105C		NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	1105					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						ATGGACACTGGTGTTATACAC	0.448																																					p.W1105C		Atlas-SNP	.											.	ATP10D	168	.	0			c.G3315T						PASS	.						279	263	268					4																	47574963		2203	4300	6503	SO:0001583	missense	57205	exon18			ACACTGGTGTTAT	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.3315G>T	chr4.hg19:g.47574963G>T	ENSP00000273859:p.Trp1105Cys	42.0	0.0	.		55.0	18.0	.	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	hg19	CCDS3476.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.704143	0.88924	.	.	ENSG00000145246	ENST00000273859	T	0.72167	-0.63	6.06	6.06	0.98353	HAD-like domain (1);	0.000000	0.85682	D	0.000000	D	0.89553	0.6748	H	0.94925	3.6	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.91174	0.4971	10	0.87932	D	0	-11.8389	20.6397	0.99537	0.0:0.0:1.0:0.0	.	1105	Q9P241	AT10D_HUMAN	C	1105	ENSP00000273859:W1105C	ENSP00000273859:W1105C	W	+	3	0	ATP10D	47269720	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	8.020000	0.88740	2.880000	0.98712	0.650000	0.86243	TGG	.	.	.	none		0.448	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453		T	47574963	G	T	47574963	3	4	20	1	0	0	0	0	1	0	0	0	1118	1270	44	4	3381	4	ATP10D	4	47574963	Missense_Mutation	SNP	G	TCGA-2Z-A9JQ-01A-11D-A42J-10	45845479	47574963	143579313	23	1338											
ANKRD17	26057	hgsc.bcm.edu	37	chr4	74027050	74027050	+	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	aggctttaccatcagccgtgGacaattttcctattcctatt	9	15	6	11	1	1	0	1	0	0	0	3	1	3	1	4	2	2	1	4	2	4	8			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr4:74027050G>T	ENST00000358602.4	-	3	679	c.563C>A	c.(562-564)tCc>tAc	p.S188Y	ANKRD17_ENST00000330838.6_Missense_Mutation_p.S188Y|ANKRD17_ENST00000509867.2_Missense_Mutation_p.S75Y	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	188					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)			ATCAGCCGTGGACAATTTTCC	0.408																																					p.S188Y		Atlas-SNP	.											ANKRD17,NS,carcinoma,0,1	ANKRD17	214	.	0			c.C563A						PASS	.						102	95	97					4																	74027050		2203	4300	6503	SO:0001583	missense	26057	exon3			GCCGTGGACAATT	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.563C>A	chr4.hg19:g.74027050G>T	ENSP00000351416:p.Ser188Tyr	61.0	0.0	.		82.0	37.0	.	NM_198889	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Missense_Mutation	SNP	ENST00000358602.4	hg19	CCDS34004.1	.	.	.	.	.	.	.	.	.	.	G	31	5.096994	0.94197	.	.	ENSG00000132466	ENST00000358602;ENST00000426990;ENST00000330838;ENST00000509867;ENST00000411811	T;T;T	0.71461	-0.4;-0.27;-0.57	5.54	5.54	0.83059	.	0.000000	0.64402	D	0.000005	T	0.81192	0.4771	L	0.50333	1.59	0.40447	D	0.980101	P;D;D;D	0.64830	0.894;0.994;0.981;0.989	P;D;P;P	0.66716	0.706;0.946;0.825;0.706	T	0.82647	-0.0354	10	0.72032	D	0.01	.	19.4722	0.94967	0.0:0.0:1.0:0.0	.	188;188;188;75	O75179-2;G5E964;O75179;E7EUV3	.;.;ANR17_HUMAN;.	Y	188;188;188;75;188	ENSP00000351416:S188Y;ENSP00000332265:S188Y;ENSP00000427151:S75Y	ENSP00000332265:S188Y	S	-	2	0	ANKRD17	74245914	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.848000	0.99507	2.614000	0.88457	0.591000	0.81541	TCC	.	.	.	none		0.408	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217		T	74027050	G	T	74027050	3	4	20	1	0	0	0	0	1	0	0	0	646	1174	41	4	7376	4	ANKRD17	4	74027050	Missense_Mutation	SNP	G	TCGA-2Z-A9JQ-01A-11D-A42J-10	26452087	74027050	117127226	24	1339											
FRAS1	80144	hgsc.bcm.edu	37	chr4	79229272	79229272	+	Frame_Shift_Del	DEL	G	G	-																															ccaacggagaagcactgcttGgcctgcagagatcccctcca																										TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr4:79229272delG	ENST00000325942.6	+	15	2027	c.1587delG	c.(1585-1587)ttgfs	p.L529fs	FRAS1_ENST00000264895.6_Frame_Shift_Del_p.L529fs|FRAS1_ENST00000264899.6_Frame_Shift_Del_p.L529fs	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	529					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						AGCACTGCTTGGCCTGCAGAG	0.562																																					p.L529fs		Atlas-Indel,Pindel	.											.	FRAS1	779	.	0			c.1586delT						PASS	.						73	79	77					4																	79229272		2133	4246	6379	SO:0001589	frameshift_variant	80144	exon15			.	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.1587delG	chr4.hg19:g.79229272delG	ENSP00000326330:p.Leu529fs	111.0	0.0	0		107.0	41.0	0.383178	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Frame_Shift_Del	DEL	ENST00000325942.6	hg19	CCDS54772.1																																																																																			.	.	.	none		0.562	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			-	79229272	G	-	79229272	7	5	20	1	0	1	0	1	0	0	0	0	6049	1339	47	0	1645	0	FRAS1	4	79229272	Frame_Shift_Del	DEL	G	TCGA-2Z-A9JQ-01A-11D-A42J-10	5202222	79229272	111925004	25	1340											
FRAS1	80144	hgsc.bcm.edu	37	chr4	79387543	79387543	+	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	ccggttcaccttcactgtttCtgatgggacaaaccccttct	7	13	7	14	1	4	1	2	1	2	0	4	2	4	2	4	2	1	2	4	2	1	4			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr4:79387543C>T	ENST00000264895.6	+	50	7651	c.7211C>T	c.(7210-7212)tCt>tTt	p.S2404F		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	2404					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						TTCACTGTTTCTGATGGGACA	0.532																																					p.S2404F		Atlas-SNP	.											.	FRAS1	779	.	0			c.C7211T						PASS	.						64	64	64					4																	79387543		2033	4197	6230	SO:0001583	missense	80144	exon50			CTGTTTCTGATGG	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.7211C>T	chr4.hg19:g.79387543C>T	ENSP00000264895:p.Ser2404Phe	124.0	0.0	.		195.0	78.0	.	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	hg19	CCDS54771.1	.	.	.	.	.	.	.	.	.	.	C	13.07	2.127811	0.37533	.	.	ENSG00000138759	ENST00000264895	T	0.25250	1.81	4.86	4.01	0.46588	.	0.622123	0.16858	N	0.196636	T	0.41719	0.1171	M	0.69823	2.125	0.80722	D	1	P	0.48998	0.918	P	0.50896	0.653	T	0.48479	-0.9032	10	0.87932	D	0	.	15.6258	0.76855	0.0:0.8621:0.1379:0.0	.	2404	E9PHH6	.	F	2404	ENSP00000264895:S2404F	ENSP00000264895:S2404F	S	+	2	0	FRAS1	79606567	0.029000	0.19370	0.707000	0.30419	0.840000	0.47671	2.800000	0.47900	1.398000	0.46701	0.585000	0.79938	TCT	.	.	.	none		0.532	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	79387543	C	T	79387543	3	4	20	1	0	0	0	0	1	0	0	0	6049	913	32	2	7484	2	FRAS1	4	79387543	Missense_Mutation	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	158271	79387543	111766733	26	1341											
POU4F2	5458	hgsc.bcm.edu	37	chr4	147560484	147560484	+	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	ggcggcggcggcggcggcggCggcggcggaggccgaagcag	4	0	25	12	10	0	0	0	0	0	0	0	2	0	1	1	11	1	1	1	11	1	0			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr4:147560484C>A	ENST00000281321.3	+	1	440	c.192C>A	c.(190-192)ggC>ggA	p.G64G	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	64	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)					gcggcggcggcggcggcggag	0.771																																					p.G64G		Atlas-SNP	.											.	POU4F2	83	.	0			c.C192A						PASS	.						3	5	5					4																	147560484		1329	2897	4226	SO:0001819	synonymous_variant	5458	exon1			CGGCGGCGGCGGC	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.192C>A	chr4.hg19:g.147560484C>A		117.0	0.0	.		70.0	5.0	.	NM_004575	B1PJR6|B2RC84|Q13883|Q14987	Silent	SNP	ENST00000281321.3	hg19	CCDS34074.1																																																																																			.	.	.	none		0.771	POU4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367020.1	NM_004575		A	147560484	C	A	147560484	2	1	20	1	0	0	0	0	0	0	0	1	12286	755	27	4		4	POU4F2	4	147560484	Silent	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	68172941	147560484	43593792	27	1342											
TERT	7015	hgsc.bcm.edu	37	chr5	1258735	1258736	+	Missense_Mutation	DNP	TC	TC	CG																															gtacgcctgcagcaggaggaTcttgtagatgttggtgcaca																										TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr5:1258735_1258736TC>CG	ENST00000310581.5	-	13	3066_3067	c.3009_3010GA>CG	c.(3007-3012)aaGAtc>aaCGtc	p.1003_1004KI>NV	TERT_ENST00000334602.6_Missense_Mutation_p.940_941KI>NV|TERT_ENST00000296820.5_3'UTR	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	telomerase reverse transcriptase	1003	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)	AGCAGGAGGATCTTGTAGATGT	0.574									TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis																												p.I1004V|p.K1003N		Atlas-SNP	.											.	TERT	2594	.	0			c.A3010G|c.G3009C						PASS	.																																			SO:0001583	missense	7015	exon13	Familial Cancer Database	;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	GGAGGATCTTGTA|GAGGATCTTGTAG	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.3009_3010delinsCG	chr5.hg19:g.1258735_1258736delinsCG	ENSP00000309572:p.K1003_I1004delinsNV	66.0	0.0	.		43.0|44.0	14.0	.	NM_198253	O14783|Q2XS35|Q8N6C3|Q8NG38|Q8NG46	Missense_Mutation	SNP	ENST00000310581.5	hg19	CCDS3861.2																																																																																			.	.	.	none		0.574	TERT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206729.2			CG	1258736	TC	CG	1258735	3	2	20	1	0	0	0	0	1	0	0	0	15776	1435	50	3	404	3	TERT	5	1258735	Missense_Mutation	DNP	TC	TCGA-2Z-A9JQ-01A-11D-A42J-10		1258735	179656525	28	1343											
SLC45A2	51151	hgsc.bcm.edu	37	chr5	33984582	33984582	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatggccatgctgtgcatgAtgagtctgctggtgggtctt	6	13	14	8	0	2	2	0	2	2	0	2	2	2	2	1	3	3	3	1	3	0	1			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr5:33984582A>G	ENST00000296589.4	-	1	253	c.107T>C	c.(106-108)aTc>aCc	p.I36T	SLC45A2_ENST00000509381.1_Missense_Mutation_p.I36T|SLC45A2_ENST00000342059.3_Missense_Mutation_p.I36T|SLC45A2_ENST00000345083.5_Missense_Mutation_p.I36T|SLC45A2_ENST00000382102.3_Missense_Mutation_p.I36T	NM_016180.3	NP_057264	Q9UMX9	S45A2_HUMAN	solute carrier family 45, member 2	36					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						GCTGTGCATGATGAGTCTGCT	0.582																																					p.I36T	Ovarian(31;380 859 8490 22203 49048)	Atlas-SNP	.											.	SLC45A2	100	.	0			c.T107C						PASS	.						53	51	52					5																	33984582		2203	4300	6503	SO:0001583	missense	51151	exon1			TGCATGATGAGTC	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.107T>C	chr5.hg19:g.33984582A>G	ENSP00000296589:p.Ile36Thr	18.0	0.0	.		22.0	9.0	.	NM_016180	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000296589.4	hg19	CCDS3901.1	.	.	.	.	.	.	.	.	.	.	A	15.86	2.956505	0.53293	.	.	ENSG00000164175	ENST00000296589;ENST00000342059;ENST00000382102;ENST00000509381;ENST00000345083	D;D;D;D;D	0.92545	-3.06;-3.06;-3.06;-3.06;-3.06	5.41	5.41	0.78517	Major facilitator superfamily domain, general substrate transporter (1);	0.360446	0.32386	N	0.006168	D	0.94689	0.8287	M	0.82323	2.585	0.58432	D	0.999993	P;B;P	0.51653	0.947;0.427;0.766	P;P;P	0.52823	0.659;0.462;0.71	D	0.94810	0.7978	10	0.51188	T	0.08	-13.8858	15.4467	0.75235	1.0:0.0:0.0:0.0	.	36;36;36	D6RGY6;Q9UMX9-4;Q9UMX9	.;.;S45A2_HUMAN	T	36	ENSP00000296589:I36T;ENSP00000341014:I36T;ENSP00000371534:I36T;ENSP00000421100:I36T;ENSP00000340444:I36T	ENSP00000296589:I36T	I	-	2	0	SLC45A2	34020339	1.000000	0.71417	0.786000	0.31890	0.432000	0.31715	8.996000	0.93539	2.050000	0.60909	0.450000	0.29827	ATC	.	.	.	none		0.582	SLC45A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207443.2	NM_016180		G	33984582	A	G	33984582	3	3	20	1	0	0	0	0	1	0	0	0	14654	333	12	3	1528	3	SLC45A2	5	33984582	Missense_Mutation	SNP	A	TCGA-2Z-A9JQ-01A-11D-A42J-10	32725847	33984582	146930678	29	1344											
LOX	4015	hgsc.bcm.edu	37	chr5	121413349	121413349	+	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	tggggcggccagcggtgactCcagatgagccggccgtccgc	5	5	17	14	5	0	3	0	2	0	1	2	3	2	3	5	5	2	0	5	5	0	0			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr5:121413349C>G	ENST00000231004.4	-	1	631	c.332G>C	c.(331-333)gGa>gCa	p.G111A	LOX_ENST00000513319.1_5'Flank	NM_001178102.1|NM_002317.5	NP_001171573.1|NP_002308.2	P28300	LYOX_HUMAN	lysyl oxidase	111					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)		AGCGGTGACTCCAGATGAGCC	0.721																																					p.G111A		Atlas-SNP	.											.	LOX	29	.	0			c.G332C						PASS	.						7	9	8					5																	121413349		2060	4113	6173	SO:0001583	missense	4015	exon1			GTGACTCCAGATG		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.332G>C	chr5.hg19:g.121413349C>G	ENSP00000231004:p.Gly111Ala	94.0	0.0	.		79.0	33.0	.	NM_002317	B2R5Q3|Q5FWF0	Missense_Mutation	SNP	ENST00000231004.4	hg19	CCDS4129.1	.	.	.	.	.	.	.	.	.	.	C	0.254	-1.004655	0.02112	.	.	ENSG00000113083	ENST00000231004;ENST00000543620	T	0.21734	1.99	4.35	3.47	0.39725	.	0.917794	0.09424	N	0.804091	T	0.13157	0.0319	N	0.19112	0.55	0.31202	N	0.699664	B	0.13145	0.007	B	0.12837	0.008	T	0.19484	-1.0304	10	0.05620	T	0.96	.	12.4631	0.55743	0.0:0.6775:0.3225:0.0	.	111	P28300	LYOX_HUMAN	A	111;71	ENSP00000231004:G111A	ENSP00000231004:G111A	G	-	2	0	LOX	121441248	0.002000	0.14202	0.020000	0.16555	0.036000	0.12997	1.657000	0.37366	0.779000	0.33543	0.455000	0.32223	GGA	.	.	.	none		0.721	LOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250887.2			G	121413349	C	G	121413349	3	3	20	1	0	0	0	0	1	0	0	0	8905	855	30	4	949	4	LOX	5	121413349	Missense_Mutation	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	87428767	121413349	59501911	30	1345											
PCDHA2	56146	hgsc.bcm.edu	37	chr5	140176343	140176343	+	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	gcgaaggtgcgcgcagtggaCgctgactcaggctacaacgc	9	5	15	12	5	1	1	1	1	0	0	1	3	1	2	0	3	3	3	0	3	3	1			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr5:140176343C>G	ENST00000526136.1	+	1	1794	c.1794C>G	c.(1792-1794)gaC>gaG	p.D598E	PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000520672.2_Missense_Mutation_p.D598E|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000378132.1_Missense_Mutation_p.D598E	NM_018905.2	NP_061728.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	598	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(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)			GCGCAGTGGACGCTGACTCAG	0.657																																					p.D598E		Atlas-SNP	.											.	PCDHA2	404	.	0			c.C1794G						PASS	.						160	144	149					5																	140176343		2203	4300	6503	SO:0001583	missense	56146	exon1			AGTGGACGCTGAC	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.1794C>G	chr5.hg19:g.140176343C>G	ENSP00000431748:p.Asp598Glu	142.0	0.0	.		84.0	33.0	.	NM_031495	O75287|Q9BTV3	Missense_Mutation	SNP	ENST00000526136.1	hg19	CCDS54914.1	.	.	.	.	.	.	.	.	.	.	c	11.04	1.520898	0.27211	.	.	ENSG00000204969	ENST00000520672;ENST00000378132;ENST00000526136	T;T;T	0.61392	0.11;0.11;0.11	3.91	-0.181	0.13291	Cadherin (4);Cadherin-like (1);	0.000000	0.41194	U	0.000923	D	0.82572	0.5066	H	0.99261	4.49	0.27054	N	0.963715	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.999	T	0.73940	-0.3824	10	0.87932	D	0	.	8.5891	0.33677	0.0:0.3705:0.0:0.6295	.	598;598;598	Q9Y5H9-3;Q9Y5H9;Q9Y5H9-2	.;PCDA2_HUMAN;.	E	598	ENSP00000430584:D598E;ENSP00000367372:D598E;ENSP00000431748:D598E	ENSP00000367372:D598E	D	+	3	2	PCDHA2	140156527	0.000000	0.05858	0.783000	0.31826	0.107000	0.19398	-0.793000	0.04589	-0.027000	0.13873	-1.080000	0.02220	GAC	.	.	.	none		0.657	PCDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372877.3	NM_018905		G	140176343	C	G	140176343	3	3	20	1	0	0	0	0	1	0	0	0	11531	535	19	4	1796	4	PCDHA2	5	140176343	Missense_Mutation	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	18762994	140176343	40738917	31	1346											
IRF4	3662	hgsc.bcm.edu	37	chr6	401489	401489	+	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	aggagctgaccacgtccagcCccgagggctgccggatctcc	7	5	13	16	3	1	1	0	1	1	0	3	4	2	3	6	3	3	2	6	3	0	0			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr6:401489C>T	ENST00000380956.4	+	7	937	c.811C>T	c.(811-813)Ccc>Tcc	p.P271S		NM_001195286.1|NM_002460.3	NP_001182215.1|NP_002451.2	Q15306	IRF4_HUMAN	interferon regulatory factor 4	271					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)		CACGTCCAGCCCCGAGGGCTG	0.597			T	IGH@	MM																																p.P271S		Atlas-SNP	.		Dom	yes		6	6p25-p23	3662	interferon regulatory factor 4		L	.	IRF4	65	.	0			c.C811T						PASS	.						61	50	54					6																	401489		2203	4300	6503	SO:0001583	missense	3662	exon7			TCCAGCCCCGAGG	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.811C>T	chr6.hg19:g.401489C>T	ENSP00000370343:p.Pro271Ser	106.0	0.0	.		85.0	30.0	.	NM_002460	Q5VUI7|Q99660	Missense_Mutation	SNP	ENST00000380956.4	hg19	CCDS4469.1	.	.	.	.	.	.	.	.	.	.	C	31	5.095778	0.94197	.	.	ENSG00000137265	ENST00000380956;ENST00000412334	D	0.95690	-3.78	5.76	5.76	0.90799	SMAD domain-like (1);SMAD/FHA domain (1);Interferon regulatory factor-3 (1);	0.000000	0.85682	D	0.000000	D	0.96030	0.8707	M	0.62209	1.925	0.80722	D	1	B;P;B;P	0.44429	0.389;0.645;0.088;0.835	P;P;B;P	0.53518	0.507;0.588;0.127;0.728	D	0.94968	0.8114	10	0.41790	T	0.15	-14.7588	19.9857	0.97347	0.0:1.0:0.0:0.0	.	271;301;270;271	F2Z3D5;Q99419;Q15306-2;Q15306	.;.;.;IRF4_HUMAN	S	271;300	ENSP00000370343:P271S	ENSP00000370343:P271S	P	+	1	0	IRF4	346489	1.000000	0.71417	0.997000	0.53966	0.967000	0.64934	7.440000	0.80464	2.706000	0.92434	0.655000	0.94253	CCC	.	.	.	none		0.597	IRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043638.1			T	401489	C	T	401489	3	4	20	1	0	0	0	0	1	0	0	0	7839	623	22	2	833	2	IRF4	6	401489	Missense_Mutation	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10		401489	170713578	32	1347											
IBTK	25998	hgsc.bcm.edu	37	chr6	82906099	82906099	+	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	actcctgcatagcttccttcAgagtctgatgtcaacagttc	9	13	7	12	0	3	2	2	1	1	1	6	2	5	2	2	0	3	3	2	0	2	4			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr6:82906099A>T	ENST00000306270.7	-	22	3639	c.3090T>A	c.(3088-3090)tcT>tcA	p.S1030S	IBTK_ENST00000503631.1_Silent_p.S829S|IBTK_ENST00000510291.1_Silent_p.S1015S	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	1030					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)			central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		AGCTTCCTTCAGAGTCTGATG	0.358																																					p.S1030S		Atlas-SNP	.											.	IBTK	128	.	0			c.T3090A						PASS	.						86	85	85					6																	82906099		2203	4300	6503	SO:0001819	synonymous_variant	25998	exon22			TCCTTCAGAGTCT	AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	17853	protein-coding gene	gene with protein product		606457	"Bruton agammaglobulinemia tyrosine kinase inhibitor"	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.3090T>A	chr6.hg19:g.82906099A>T		42.0	0.0	.		70.0	24.0	.	NM_015525	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Silent	SNP	ENST00000306270.7	hg19	CCDS34490.1																																																																																			.	.	.	none		0.358	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525		T	82906099	A	T	82906099	2	4	20	1	0	0	0	0	0	0	0	1	7483	175	7	5		5	IBTK	6	82906099	Silent	SNP	A	TCGA-2Z-A9JQ-01A-11D-A42J-10	82504610	82906099	88208968	33	1348											
MDN1	23195	hgsc.bcm.edu	37	chr6	90491213	90491213	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgttcacatccaacagaactAtcactccaagagtgatgttt	13	12	6	10	0	2	3	2	1	0	2	4	3	4	3	2	0	2	2	2	0	4	3			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr6:90491213A>G	ENST00000369393.3	-	10	1663	c.1548T>C	c.(1546-1548)gaT>gaC	p.D516D	MDN1_ENST00000428876.1_Silent_p.D516D			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	516					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)		CAACAGAACTATCACTCCAAG	0.423																																					p.D516D		Atlas-SNP	.											.	MDN1	478	.	0			c.T1548C						PASS	.						139	135	136					6																	90491213		2203	4300	6503	SO:0001819	synonymous_variant	23195	exon10			AGAACTATCACTC	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.1548T>C	chr6.hg19:g.90491213A>G		183.0	0.0	.		158.0	62.0	.	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	hg19	CCDS5024.1																																																																																			.	.	.	none		0.423	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			G	90491213	A	G	90491213	2	3	20	1	0	0	0	0	0	0	0	1	9422	446	16	3		3	MDN1	6	90491213	Silent	SNP	A	TCGA-2Z-A9JQ-01A-11D-A42J-10	7585114	90491213	80623854	34	1349											
PSMB1	5689	hgsc.bcm.edu	37	chr6	170862258	170862258	+	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	cgaaaatcgcagctgcaaagGgcccgcggctctgtgcggtt	8	7	14	12	5	1	0	0	0	1	0	2	1	1	0	1	3	3	5	1	3	3	1	rs60257797	byFrequency	TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr6:170862258G>T	ENST00000262193.6	-	1	171	c.73C>A	c.(73-75)Cct>Act	p.P25T	TBP_ENST00000540980.1_5'Flank|TBP_ENST00000392092.2_5'Flank|PSMB1_ENST00000462957.1_5'Flank|TBP_ENST00000230354.6_5'Flank	NM_002793.3	NP_002784.1	P20618	PSB1_HUMAN	proteasome (prosome, macropain) subunit, beta type, 1	25					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	5		Breast(66;5.08e-05)|Ovarian(120;0.0563)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;7.5e-23)|BRCA - Breast invasive adenocarcinoma(81;4.88e-06)|GBM - Glioblastoma multiforme(31;0.00643)	Bortezomib(DB00188)|Carfilzomib(DB08889)	AGCTGCAAAGGGCCCGCGGCT	0.592																																					p.P25T		Atlas-SNP	.											.	PSMB1	12	.	0			c.C73A						PASS	.						39	38	38					6																	170862258		2203	4299	6502	SO:0001583	missense	5689	exon1			GCAAAGGGCCCGC	D00761	CCDS34577.1	6q27	2008-02-05			ENSG00000008018	ENSG00000008018		"Proteasome (prosome, macropain) subunits"	9537	protein-coding gene	gene with protein product		602017				2025653	Standard	NM_002793		Approved	PMSB1, HC5	uc011ehe.2	P20618	OTTHUMG00000016087	ENST00000262193.6:c.73C>A	chr6.hg19:g.170862258G>T	ENSP00000262193:p.Pro25Thr	82.0	0.0	.		63.0	8.0	.	NM_002793	B5BU76|Q9BWA8	Missense_Mutation	SNP	ENST00000262193.6	hg19	CCDS34577.1	.	.	.	.	.	.	.	.	.	.	G	14.28	2.487058	0.44249	.	.	ENSG00000008018	ENST00000262193;ENST00000392093	T	0.25085	1.82	4.37	3.5	0.40072	.	0.244443	0.41605	D	0.000845	T	0.06508	0.0167	N	0.19112	0.55	0.54753	D	0.999988	P	0.45348	0.856	B	0.38803	0.282	T	0.17561	-1.0365	10	0.35671	T	0.21	-6.038	8.6868	0.34243	0.0863:0.1526:0.761:0.0	.	25	P20618	PSB1_HUMAN	T	25;30	ENSP00000262193:P25T	ENSP00000262193:P25T	P	-	1	0	PSMB1	170704183	1.000000	0.71417	0.769000	0.31535	0.030000	0.12068	4.424000	0.59868	1.054000	0.40438	-0.253000	0.11424	CCT	.	G|0.998;A|0.002	.	alt		0.592	PSMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043278.2	NM_002793		T	170862258	G	T	170862258	3	4	20	1	0	0	0	0	1	0	0	0	12684	1232	43	4	676	4	PSMB1	6	170862258	Missense_Mutation	SNP	G	TCGA-2Z-A9JQ-01A-11D-A42J-10	80371045	170862258	252809	35	1350											
COL28A1	340267	hgsc.bcm.edu	37	chr7	7557428	7557428	+	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	attccagttgtgtacataccCctggacctctttctccagct	7	14	6	14	0	2	0	0	0	2	0	4	1	3	1	5	1	3	3	5	1	2	5			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr7:7557428C>T	ENST00000399429.3	-	7	994	c.854G>A	c.(853-855)gGg>gAg	p.G285E		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	285					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)		TGTACATACCCCTGGACCTCT	0.433																																					p.G285E		Atlas-SNP	.											.	COL28A1	113	.	0			c.G854A						PASS	.						201	194	196					7																	7557428		1875	4116	5991	SO:0001630	splice_region_variant	340267	exon7			CATACCCCTGGAC	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.855+1G>A	chr7.hg19:g.7557428C>T		90.0	0.0	.		246.0	110.0	.	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Missense_Mutation	SNP	ENST00000399429.3	hg19	CCDS43553.1	.	.	.	.	.	.	.	.	.	.	C	0.017	-1.496886	0.01001	.	.	ENSG00000215018	ENST00000399429;ENST00000399419;ENST00000448652	D	0.91577	-2.87	3.8	-0.292	0.12839	.	1.902390	0.03505	U	0.218727	T	0.67306	0.2879	N	0.00729	-1.24	0.20764	N	0.999859	P	0.35468	0.503	B	0.33521	0.165	T	0.69018	-0.5256	10	0.06891	T	0.86	2.2101	3.0593	0.06195	0.3875:0.3932:0.0:0.2193	.	285	Q2UY09	COSA1_HUMAN	E	285	ENSP00000382356:G285E	ENSP00000382347:G285E	G	-	2	0	COL28A1	7523953	0.996000	0.38824	0.410000	0.26471	0.493000	0.33554	0.295000	0.19065	-0.057000	0.13199	0.655000	0.94253	GGG	.	.	.	none		0.433	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	Missense_Mutation	T	7557428	C	T	7557428	5	4	20	1	0	0	0	0	0	0	1	0	3688	637	22	2	2639	2	COL28A1	7	7557428	Splice_Site	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10		7557428	151581235	36	1351											
ZNF479	90827	hgsc.bcm.edu	37	chr7	57188741	57188741	+	Frame_Shift_Del	DEL	T	T	-																															tcacccacacttttacagcaTtttttaaattgtaatttctc																										TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr7:57188741delT	ENST00000331162.4	-	5	651	c.381delA	c.(379-381)aaafs	p.K127fs		NM_033273.1	NP_150376.1	Q96JC4	ZN479_HUMAN	zinc finger protein 479	127					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)			TTTTACAGCATTTTTTAAATT	0.368																																					p.C128fs		Atlas-Indel,Pindel	.											.	ZNF479	193	.	0			c.382delT						PASS	.						90	83	85					7																	57188741		1850	4101	5951	SO:0001589	frameshift_variant	90827	exon5			.	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.381delA	chr7.hg19:g.57188741delT	ENSP00000333776:p.Lys127fs	141.0	0.0	0		376.0	151.0	0.401596	NM_033273		Frame_Shift_Del	DEL	ENST00000331162.4	hg19	CCDS43590.1																																																																																			.	.	.	none		0.368	ZNF479-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345302.1	XM_291202		-	57188741	T	-	57188741	7	5	20	1	0	1	0	1	0	0	0	0	17945	1490	52	0	1197	0	ZNF479	7	57188741	Frame_Shift_Del	DEL	T	TCGA-2Z-A9JQ-01A-11D-A42J-10	49631313	57188741	101949922	37	1352											
MOSPD3	64598	hgsc.bcm.edu	37	chr7	100210558	100210558	+	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	gtattcagggcggaccagcgGagcggaccccgacagctgct	8	5	15	13	4	1	0	1	0	0	0	1	4	1	3	3	4	4	3	3	4	1	2			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr7:100210558G>T	ENST00000393950.2	+	1	426	c.144G>T	c.(142-144)cgG>cgT	p.R48R	MOSPD3_ENST00000424091.2_Silent_p.R48R|MOSPD3_ENST00000223054.4_Silent_p.R48R|MOSPD3_ENST00000379527.2_Silent_p.R48R	NM_023948.4	NP_076438.1	O75425	MSPD3_HUMAN	motile sperm domain containing 3	48	MSP. {ECO:0000255|PROSITE- ProRule:PRU00132}.				heart development (GO:0007507)	integral component of membrane (GO:0016021)	structural molecule activity (GO:0005198)			breast(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					CGGACCAGCGGAGCGGACCCC	0.697																																					p.R48R		Atlas-SNP	.											.	MOSPD3	29	.	0			c.G144T						PASS	.						53	61	58					7																	100210558		2203	4296	6499	SO:0001819	synonymous_variant	64598	exon2			CCAGCGGAGCGGA	BC011653	CCDS5701.1, CCDS47662.1	7q22	2009-11-06			ENSG00000106330	ENSG00000106330			25078	protein-coding gene	gene with protein product		609125				15533722	Standard	XM_005250531		Approved	CDS3, NET30	uc003uvs.3	O75425	OTTHUMG00000159599	ENST00000393950.2:c.144G>T	chr7.hg19:g.100210558G>T		382.0	0.0	.		463.0	213.0	.	NM_001040098	A4D2D1|A6NG17|C9JE89|D6W5W1|O75423|O75424	Silent	SNP	ENST00000393950.2	hg19	CCDS5701.1																																																																																			.	.	.	none		0.697	MOSPD3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356395.1	NM_023948		T	100210558	G	T	100210558	2	4	20	1	0	0	0	0	0	0	0	1	9724	1161	41	4		4	MOSPD3	7	100210558	Silent	SNP	G	TCGA-2Z-A9JQ-01A-11D-A42J-10	43021817	100210558	58928105	38	1353											
CBLL1	79872	hgsc.bcm.edu	37	chr7	107389353	107389354	+	Frame_Shift_Del	DEL	TG	TG	-																															ttacaaggcactaatagttcTggatccttgggtggtcttga																										TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr7:107389353_107389354delTG	ENST00000440859.3	+	2	509_510	c.42_43delTG	c.(40-45)tctggafs	p.G15fs	CBLL1_ENST00000222597.2_Frame_Shift_Del_p.G15fs|CBLL1_ENST00000415884.2_Frame_Shift_Del_p.G15fs	NM_001284291.1|NM_024814.2	NP_001271220.1|NP_079090.2	Q75N03	HAKAI_HUMAN	Cbl proto-oncogene-like 1, E3 ubiquitin protein ligase	15					negative regulation of cell adhesion (GO:0007162)|positive regulation of cell migration (GO:0030335)|positive regulation of endocytosis (GO:0045807)|protein ubiquitination (GO:0016567)|single organismal cell-cell adhesion (GO:0016337)	ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(3)|skin(3)	21						CTAATAGTTCTGGATCCTTGGG	0.366																																					p.14_14del		Atlas-INDEL	.											.	CBLL1	54	.	0			c.41_42del						PASS	.																																			SO:0001589	frameshift_variant	79872	exon2			.	AK026762	CCDS5747.1, CCDS64754.1	7q22.3	2013-07-09	2013-07-09		ENSG00000105879	ENSG00000105879		"RING-type (C3HC4) zinc fingers"	21225	protein-coding gene	gene with protein product	"Casitas B-lineage lymphoma-like"	606872	"Cas-Br-M (murine) ecotropic retroviral transforming sequence-like 1"			11836526, 11944035	Standard	NM_001284291		Approved	HAKAI, FLJ23109, RNF188	uc003veq.3	Q75N03	OTTHUMG00000154809	ENST00000440859.3:c.42_43delTG	chr7.hg19:g.107389353_107389354delTG	ENSP00000401277:p.Gly15fs	169.0	0.0	0		291.0	96.0	0.329897	NM_024814	B7ZM03|Q8TAJ4|Q9H5S6	Frame_Shift_Del	DEL	ENST00000440859.3	hg19	CCDS5747.1																																																																																			.	.	.	none		0.366	CBLL1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337156.2	NM_024814		-	107389354	TG	-	107389353	7	5	20	1	0	1	0	1	0	0	0	0	2705	1567	55	0	48	0	CBLL1	7	107389353	Frame_Shift_Del	DEL	TG	TCGA-2Z-A9JQ-01A-11D-A42J-10	7178795	107389353	51749310	39	1354	14	2									
CBLL1	79872	hgsc.bcm.edu	37	chr7	107389358	107389358	+	Frame_Shift_Del	DEL	C	C	-																															aggcactaatagttctggatCcttgggtggtcttgatgttc																								rs267601227		TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr7:107389358delC	ENST00000440859.3	+	2	514	c.47delC	c.(46-48)tccfs	p.S16fs	CBLL1_ENST00000222597.2_Frame_Shift_Del_p.S16fs|CBLL1_ENST00000415884.2_Frame_Shift_Del_p.S16fs	NM_001284291.1|NM_024814.2	NP_001271220.1|NP_079090.2	Q75N03	HAKAI_HUMAN	Cbl proto-oncogene-like 1, E3 ubiquitin protein ligase	16					negative regulation of cell adhesion (GO:0007162)|positive regulation of cell migration (GO:0030335)|positive regulation of endocytosis (GO:0045807)|protein ubiquitination (GO:0016567)|single organismal cell-cell adhesion (GO:0016337)	ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(3)|skin(3)	21						AGTTCTGGATCCTTGGGTGGT	0.373																																					p.S16fs		Atlas-INDEL	.											.	CBLL1	54	.	0			c.46delT						PASS	.						146	149	148					7																	107389358		2203	4300	6503	SO:0001589	frameshift_variant	79872	exon2			.	AK026762	CCDS5747.1, CCDS64754.1	7q22.3	2013-07-09	2013-07-09		ENSG00000105879	ENSG00000105879		"RING-type (C3HC4) zinc fingers"	21225	protein-coding gene	gene with protein product	"Casitas B-lineage lymphoma-like"	606872	"Cas-Br-M (murine) ecotropic retroviral transforming sequence-like 1"			11836526, 11944035	Standard	NM_001284291		Approved	HAKAI, FLJ23109, RNF188	uc003veq.3	Q75N03	OTTHUMG00000154809	ENST00000440859.3:c.47delC	chr7.hg19:g.107389358delC	ENSP00000401277:p.Ser16fs	169.0	0.0	0		293.0	102.0	0.348123	NM_024814	B7ZM03|Q8TAJ4|Q9H5S6	Frame_Shift_Del	DEL	ENST00000440859.3	hg19	CCDS5747.1																																																																																			.	.	.	none		0.373	CBLL1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337156.2	NM_024814		-	107389358	C	-	107389358	7	5	20	1	0	1	0	1	0	0	0	0	2705	855	30	0	53	0	CBLL1	7	107389358	Frame_Shift_Del	DEL	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	5	107389358	51749305	40	1355	14	2									
MTUS1	57509	hgsc.bcm.edu	37	chr8	17503480	17503480	+	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	gggaaggagcccgaattcctTggtgactgcaaagggatggc	10	7	16	8	1	0	1	0	1	0	0	1	5	1	4	2	5	2	1	2	5	3	2			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr8:17503480T>A	ENST00000262102.6	-	15	3992	c.3768A>T	c.(3766-3768)ccA>ccT	p.P1256P	MTUS1_ENST00000400046.1_Silent_p.P328P|MTUS1_ENST00000519263.1_Silent_p.P1202P|MTUS1_ENST00000544260.1_Silent_p.P401P|MTUS1_ENST00000381869.3_Silent_p.P1202P|MTUS1_ENST00000381861.3_Silent_p.P503P|MTUS1_ENST00000297488.6_Silent_p.P422P	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	1256					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)		CCGAATTCCTTGGTGACTGCA	0.537																																					p.P1256P		Atlas-SNP	.											.	MTUS1	144	.	0			c.A3768T						PASS	.						61	64	63					8																	17503480		1923	4140	6063	SO:0001819	synonymous_variant	57509	exon15			ATTCCTTGGTGAC	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.3768A>T	chr8.hg19:g.17503480T>A		95.0	0.0	.		105.0	45.0	.	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Silent	SNP	ENST00000262102.6	hg19	CCDS43717.1																																																																																			.	.	.	none		0.537	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		A	17503480	T	A	17503480	2	1	20	1	0	0	0	0	0	0	0	1	9972	1799	63	5		5	MTUS1	8	17503480	Silent	SNP	T	TCGA-2Z-A9JQ-01A-11D-A42J-10		17503480	128860542	41	1356											
STC1	6781	hgsc.bcm.edu	37	chr8	23702289	23702289	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taacctctccctggttatgcActctcatgggatgtgcgttt	6	15	9	11	1	2	0	1	0	2	0	4	1	2	1	2	2	3	3	2	2	2	3			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr8:23702289A>G	ENST00000290271.2	-	4	1021	c.738T>C	c.(736-738)agT>agC	p.S246S	STC1_ENST00000524323.1_Silent_p.S177S	NM_003155.2	NP_003146.1	P52823	STC1_HUMAN	stanniocalcin 1	246					bone development (GO:0060348)|cellular calcium ion homeostasis (GO:0006874)|cellular response to cAMP (GO:0071320)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to hypoxia (GO:0071456)|chondrocyte proliferation (GO:0035988)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|endothelial cell morphogenesis (GO:0001886)|growth plate cartilage axis specification (GO:0003421)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of renal phosphate excretion (GO:1903403)|ossification (GO:0001503)|positive regulation of calcium ion import (GO:0090280)|regulation of anion transport (GO:0044070)|regulation of cardiac muscle cell contraction (GO:0086004)|response to vitamin D (GO:0033280)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	26		Prostate(55;0.055)|Breast(100;0.116)		Colorectal(74;0.0155)|COAD - Colon adenocarcinoma(73;0.0632)		CTGGTTATGCACTCTCATGGG	0.498																																					p.S246S		Atlas-SNP	.											.	STC1	49	.	0			c.T738C						PASS	.						95	81	86					8																	23702289		2203	4300	6503	SO:0001819	synonymous_variant	6781	exon4			TTATGCACTCTCA		CCDS6043.1	8p22-p12	2008-06-23			ENSG00000159167	ENSG00000159167			11373	protein-coding gene	gene with protein product		601185		STC		9480753	Standard	NM_003155		Approved		uc003xdw.1	P52823	OTTHUMG00000097853	ENST00000290271.2:c.738T>C	chr8.hg19:g.23702289A>G		19.0	0.0	.		58.0	32.0	.	NM_003155	B4DN22|Q71UE5	Silent	SNP	ENST00000290271.2	hg19	CCDS6043.1																																																																																			.	.	.	none		0.498	STC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215143.1			G	23702289	A	G	23702289	2	3	20	1	0	0	0	0	0	0	0	1	15287	156	6	3		3	STC1	8	23702289	Silent	SNP	A	TCGA-2Z-A9JQ-01A-11D-A42J-10	6198809	23702289	122661733	42	1357											
POLR1E	64425	hgsc.bcm.edu	37	chr9	37500883	37500883	+	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	atcatcaacaccaaactgctGaagcactttacttgcttgac	13	11	5	12	0	2	2	2	2	0	0	2	2	2	2	1	0	6	3	1	0	4	4			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr9:37500883G>T	ENST00000377798.4	+	10	1046	c.933G>T	c.(931-933)ctG>ctT	p.L311L	POLR1E_ENST00000377792.3_Silent_p.L373L|POLR1E_ENST00000442009.2_Silent_p.L241L	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)		CCAAACTGCTGAAGCACTTTA	0.498																																					p.L311L	Ovarian(116;843 1620 18506 32459 34463)	Atlas-SNP	.											.	POLR1E	28	.	0			c.G933T						PASS	.						138	116	123					9																	37500883		2203	4300	6503	SO:0001819	synonymous_variant	64425	exon10			ACTGCTGAAGCAC	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.933G>T	chr9.hg19:g.37500883G>T		108.0	0.0	.		73.0	5.0	.	NM_022490	O75395|Q5JTE3	Silent	SNP	ENST00000377798.4	hg19	CCDS6611.1																																																																																			.	.	.	none		0.498	POLR1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052464.1	NM_022490		T	37500883	G	T	37500883	2	4	20	1	0	0	0	0	0	0	0	1	12220	1277	45	4		4	POLR1E	9	37500883	Silent	SNP	G	TCGA-2Z-A9JQ-01A-11D-A42J-10		37500883	103712548	43	1358											
OBP2B	29989	hgsc.bcm.edu	37	chr9	136082700	136082700	+	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	cctcctgggcagctcctgcaGgtacatgagcttcctgcccc	5	9	10	17	0	0	1	0	1	0	0	3	1	3	1	6	2	5	5	6	2	1	2			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr9:136082700G>C	ENST00000372034.3	-	4	342	c.301C>G	c.(301-303)Ctg>Gtg	p.L101V	OBP2B_ENST00000372032.2_Missense_Mutation_p.P56R|OBP2B_ENST00000461961.1_5'UTR	NM_014581.2	NP_055396.1	Q9NPH6	OBP2B_HUMAN	odorant binding protein 2B	101					chemosensory behavior (GO:0007635)|sensory perception of smell (GO:0007608)|transport (GO:0006810)	extracellular region (GO:0005576)	odorant binding (GO:0005549)			central_nervous_system(2)|large_intestine(1)|lung(3)|skin(1)	7				OV - Ovarian serous cystadenocarcinoma(145;3.41e-06)|Epithelial(140;1.88e-05)		AGCTCCTGCAGGTACATGAGC	0.547																																					p.L101V		Atlas-SNP	.											.	OBP2B	20	.	0			c.C301G						PASS	.						110	83	92					9																	136082700		2203	4300	6503	SO:0001583	missense	29989	exon4			CCTGCAGGTACAT	AJ251026	CCDS6961.1	9q34	2014-01-22			ENSG00000171102	ENSG00000171102		"Lipocalins"	23381	protein-coding gene	gene with protein product		604606					Standard	NM_001288987		Approved	hOBPIIb, LCN14	uc004ccz.3	Q9NPH6	OTTHUMG00000020860	ENST00000372034.3:c.301C>G	chr9.hg19:g.136082700G>C	ENSP00000361104:p.Leu101Val	113.0	0.0	.		50.0	20.0	.	NM_014581	Q5VSP6|Q9NY51|Q9NY52	Missense_Mutation	SNP	ENST00000372034.3	hg19	CCDS6961.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.604|0.604	-0.827969|-0.827969	0.02734|0.02734	.|.	.|.	ENSG00000171102|ENSG00000171102	ENST00000372034|ENST00000372032	T|T	0.05025|0.08102	3.51|3.13	1.91|1.91	-3.82|-3.82	0.04281|0.04281	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);|.	1.036800|.	0.07743|.	N|.	0.947204|.	T|T	0.02727|0.02727	0.0082|0.0082	N|N	0.03194|0.03194	-0.395|-0.395	0.09310|0.09310	N|N	1|1	B|.	0.06786|.	0.001|.	B|.	0.15052|.	0.012|.	T|T	0.36504|0.36504	-0.9745|-0.9745	10|7	0.02654|0.87932	T|D	1|0	-15.1887|-15.1887	0.9011|0.9011	0.01274|0.01274	0.1534:0.1911:0.3106:0.3449|0.1534:0.1911:0.3106:0.3449	.|.	101|.	Q9NPH6|.	OBP2B_HUMAN|.	V|R	101|56	ENSP00000361104:L101V|ENSP00000361102:P56R	ENSP00000361104:L101V|ENSP00000361102:P56R	L|P	-|-	1|2	2|0	OBP2B|OBP2B	135072521|135072521	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-2.234000|-2.234000	0.01203|0.01203	-2.668000|-2.668000	0.00415|0.00415	-2.408000|-2.408000	0.00222|0.00222	CTG|CCT	.	.	.	none		0.547	OBP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054851.1	NM_014581		C	136082700	G	C	136082700	3	2	20	1	0	0	0	0	1	0	0	0	10818	991	35	4	223	4	OBP2B	9	136082700	Missense_Mutation	SNP	G	TCGA-2Z-A9JQ-01A-11D-A42J-10	98581817	136082700	5130731	44	1359											
MTPAP	55149	hgsc.bcm.edu	37	chr10	30615418	30615418	+	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	gagaacctcacgagcggacaCcgggcatttaatattttttg	11	11	10	9	3	1	1	1	0	0	1	1	4	1	2	2	2	2	1	2	2	3	6			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr10:30615418C>T	ENST00000263063.4	-	5	970	c.927G>A	c.(925-927)cgG>cgA	p.R309R	MTPAP_ENST00000358107.4_Silent_p.R439R|MTPAP_ENST00000488290.1_5'UTR	NM_018109.3	NP_060579.3	Q9NVV4	PAPD1_HUMAN	mitochondrial poly(A) polymerase	309					cell death (GO:0008219)|histone mRNA catabolic process (GO:0071044)|mRNA polyadenylation (GO:0006378)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|poly(A) RNA binding (GO:0044822)|polynucleotide adenylyltransferase activity (GO:0004652)|protein homodimerization activity (GO:0042803)|UTP binding (GO:0002134)			breast(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	33						CGAGCGGACACCGGGCATTTA	0.443																																					p.R309R		Atlas-SNP	.											MTPAP_ENST00000358107,right_upper_lobe,carcinoma,0,2	MTPAP	113	.	0			c.G927A						PASS	.						107	115	112					10																	30615418		2203	4300	6503	SO:0001819	synonymous_variant	55149	exon5			CGGACACCGGGCA	AL122121	CCDS7165.1	10p12.1	2014-01-30	2009-01-12	2009-01-12	ENSG00000107951	ENSG00000107951			25532	protein-coding gene	gene with protein product	"TUTase1"	613669	"PAP associated domain containing 1"	PAPD1		12239557, 15769737, 15547249	Standard	NM_018109		Approved	FLJ10486, mtPAP, SPAX4	uc001iva.4	Q9NVV4	OTTHUMG00000017895	ENST00000263063.4:c.927G>A	chr10.hg19:g.30615418C>T		343.0	0.0	.		306.0	135.0	.	NM_018109	D3DRX0|Q659E3|Q6P7E5|Q9HA74	Silent	SNP	ENST00000263063.4	hg19	CCDS7165.1																																																																																			.	.	.	none		0.443	MTPAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047426.2	NM_018109		T	30615418	C	T	30615418	2	4	20	1	0	0	0	0	0	0	0	1	9963	494	18	2		2	MTPAP	10	30615418	Silent	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10		30615418	104919329	45	1360											
SFTPD	6441	hgsc.bcm.edu	37	chr10	81702210	81702210	+	Frame_Shift_Del	DEL	G	G	-																															tatgttcccctgcttccccaGgggaccttctcttccagctg																								rs17878336	byFrequency	TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr10:81702210delG	ENST00000372292.3	-	4	407	c.367delC	c.(367-369)ctgfs	p.L123fs		NM_003019.4	NP_003010.4	P35247	SFTPD_HUMAN	surfactant protein D	123	Collagen-like.		L -> V (in dbSNP:rs17878336). {ECO:0000269|PubMed:19100526, ECO:0000269|Ref.4}.		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)			TGCTTCCCCAGGGGACCTTCT	0.602																																					p.L123fs		Atlas-Indel,Pindel	.											.	SFTPD	43	.	0			c.368delT						PASS	.						77	71	73					10																	81702210		2203	4300	6503	SO:0001589	frameshift_variant	6441	exon4			.	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.367delC	chr10.hg19:g.81702210delG	ENSP00000361366:p.Leu123fs	69.0	0.0	0		47.0	21.0	0.446809	NM_003019	Q5T0M3|Q6FH08|Q86YK9|Q8TCD8|Q9UCJ2|Q9UCJ3	Frame_Shift_Del	DEL	ENST00000372292.3	hg19	CCDS7362.1																																																																																			.	.	.	none		0.602	SFTPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049011.1			-	81702210	G	-	81702210	7	5	20	1	0	1	0	1	0	0	0	0	14206	991	35	0	780	0	SFTPD	10	81702210	Frame_Shift_Del	DEL	G	TCGA-2Z-A9JQ-01A-11D-A42J-10	51086792	81702210	53832537	46	1361											
ANKRD2	26287	hgsc.bcm.edu	37	chr10	99343384	99343384	+	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	tctggcaggctgatacccggCacgccctggagcatcctgag	7	7	13	14	2	1	2	0	2	1	0	2	3	2	3	3	4	2	4	3	4	1	1			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr10:99343384C>T	ENST00000307518.5	+	9	1252	c.985C>T	c.(985-987)Cac>Tac	p.H329Y	PI4K2A_ENST00000370649.3_5'Flank|HOGA1_ENST00000370646.4_5'Flank|ANKRD2_ENST00000455090.1_Missense_Mutation_p.H269Y|ANKRD2_ENST00000298808.5_Missense_Mutation_p.H296Y|HOGA1_ENST00000370647.4_5'Flank|ANKRD2_ENST00000370655.1_Missense_Mutation_p.H302Y|PI4K2A_ENST00000555577.1_5'Flank			Q9GZV1	ANKR2_HUMAN	ankyrin repeat domain 2 (stretch responsive muscle)	329					muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|skeletal muscle cell differentiation (GO:0035914)	cytosol (GO:0005829)|euchromatin (GO:0000791)|I band (GO:0031674)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	protein kinase B binding (GO:0043422)|structural constituent of muscle (GO:0008307)			breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|stomach(1)	7		all_hematologic(284;1.95e-06)|Colorectal(252;0.0163)		Epithelial(162;1.18e-94)|all cancers(201;9.31e-86)|BRCA - Breast invasive adenocarcinoma(275;0.0233)|STAD - Stomach adenocarcinoma(243;0.181)|KIRC - Kidney renal clear cell carcinoma(50;0.206)|Kidney(138;0.241)		TGATACCCGGCACGCCCTGGA	0.647																																					p.H329Y		Atlas-SNP	.											.	ANKRD2	27	.	0			c.C985T						PASS	.						18	18	18					10																	99343384		2200	4298	6498	SO:0001583	missense	26287	exon9			ACCCGGCACGCCC	AJ304805	CCDS7466.1, CCDS44468.1	10q23	2013-01-10			ENSG00000165887	ENSG00000165887		"Ankyrin repeat domain containing"	495	protein-coding gene	gene with protein product		610734				10873377, 15136035, 15677738	Standard	NM_001129981		Approved	ARPP	uc001knw.3	Q9GZV1	OTTHUMG00000018860	ENST00000307518.5:c.985C>T	chr10.hg19:g.99343384C>T	ENSP00000306163:p.His329Tyr	367.0	0.0	.		220.0	90.0	.	NM_020349	Q3B778|Q5T456|Q70EZ9|Q8WUD7|Q96MG0|Q9NQC9	Missense_Mutation	SNP	ENST00000307518.5	hg19	CCDS7466.1	.	.	.	.	.	.	.	.	.	.	C	14.11	2.437522	0.43224	.	.	ENSG00000165887	ENST00000307518;ENST00000298808;ENST00000370655;ENST00000455090	T;T;T;T	0.67171	0.93;-0.25;0.88;-0.25	5.6	2.43	0.29744	.	0.449475	0.21686	N	0.070642	T	0.49813	0.1579	N	0.24115	0.695	0.23950	N	0.996373	B;B	0.27117	0.168;0.072	B;B	0.28139	0.086;0.059	T	0.46470	-0.9189	10	0.59425	D	0.04	-0.4987	8.5035	0.33173	0.5059:0.3605:0.1336:0.0	.	296;329	Q9GZV1-2;Q9GZV1	.;ANKR2_HUMAN	Y	329;296;302;269	ENSP00000306163:H329Y;ENSP00000298808:H296Y;ENSP00000359689:H302Y;ENSP00000403114:H269Y	ENSP00000298808:H296Y	H	+	1	0	ANKRD2	99333374	0.396000	0.25262	0.978000	0.43139	0.887000	0.51463	0.858000	0.27845	0.635000	0.30488	0.561000	0.74099	CAC	.	.	.	none		0.647	ANKRD2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	99343384	C	T	99343384	3	4	20	1	0	0	0	0	1	0	0	0	647	710	25	2	1019	2	ANKRD2	10	99343384	Missense_Mutation	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	17641174	99343384	36191363	47	1362											
NRAP	4892	hgsc.bcm.edu	37	chr10	115401186	115401186	+	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	tctgtccataccaactccttCatagcggcctctcatgtggt	7	13	7	14	1	3	0	2	0	2	0	6	0	5	0	4	2	3	0	4	2	3	3			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr10:115401186C>T	ENST00000359988.3	-	13	1505	c.1261G>A	c.(1261-1263)Gaa>Aaa	p.E421K	NRAP_ENST00000369360.3_Missense_Mutation_p.E386K|NRAP_ENST00000360478.3_Missense_Mutation_p.E386K|NRAP_ENST00000369358.4_Missense_Mutation_p.E421K	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)		CCAACTCCTTCATAGCGGCCT	0.453																																					p.E421K		Atlas-SNP	.											NRAP,NS,carcinoma,0,1	NRAP	208	.	0			c.G1261A						PASS	.						178	159	165					10																	115401186		2203	4300	6503	SO:0001583	missense	4892	exon13			CTCCTTCATAGCG		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.1261G>A	chr10.hg19:g.115401186C>T	ENSP00000353078:p.Glu421Lys	50.0	0.0	.		42.0	21.0	.	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	hg19	CCDS7579.1	.	.	.	.	.	.	.	.	.	.	C	15.95	2.983267	0.53827	.	.	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478;ENST00000369350;ENST00000369343	T;T;T;T	0.31510	1.49;2.55;1.49;2.37	5.49	4.57	0.56435	.	0.215254	0.47852	D	0.000220	T	0.22666	0.0547	L	0.45137	1.4	0.31944	N	0.61052	P;P;P	0.35527	0.507;0.454;0.474	B;B;B	0.35182	0.184;0.197;0.097	T	0.13953	-1.0490	10	0.06757	T	0.87	.	11.3728	0.49711	0.0:0.8029:0.1271:0.0701	.	421;386;421	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	K	421;386;421;386;150;150	ENSP00000358365:E421K;ENSP00000358367:E386K;ENSP00000353078:E421K;ENSP00000353666:E386K	ENSP00000353078:E421K	E	-	1	0	NRAP	115391176	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.648000	0.46647	1.280000	0.44463	0.561000	0.74099	GAA	.	.	.	none		0.453	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175		T	115401186	C	T	115401186	3	4	20	1	0	0	0	0	1	0	0	0	10645	835	29	2	4051	2	NRAP	10	115401186	Missense_Mutation	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	16057802	115401186	20133561	48	1363											
GPR123	84435	hgsc.bcm.edu	37	chr10	134916320	134916320	+	Frame_Shift_Del	DEL	A	A	-																															tgcctggacacagaccagccAccgtaccccaggcagcccct																										TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr10:134916320delA	ENST00000392607.3	+	5	811	c.375delA	c.(373-375)ccafs	p.P126fs	GPR123_ENST00000607359.1_Frame_Shift_Del_p.P846fs|GPR123_ENST00000392606.2_Frame_Shift_Del_p.P29fs	NM_001083909.1	NP_001077378.1	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	126					G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(3)	14		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		CAGACCAGCCACCGTACCCCA	0.622																																					p.P125fs		Atlas-Indel,Pindel	.											.	GPR123	118	.	0			c.374delC						PASS	.						64	48	53					10																	134916320		2203	4300	6503	SO:0001589	frameshift_variant	84435	exon5			.	AB058731	CCDS41580.1	10q26	2014-08-08			ENSG00000197177	ENSG00000197177		"-", "GPCR / Class B : Orphans"	13838	protein-coding gene	gene with protein product		612302				12565841	Standard	XM_005252695		Approved	KIAA1828	uc001llw.3	Q86SQ6	OTTHUMG00000019304	ENST00000392607.3:c.375delA	chr10.hg19:g.134916320delA	ENSP00000376384:p.Pro126fs	58.0	0.0	0		41.0	19.0	0.463415	NM_001083909	A5HL16|A6NG50|Q5T234|Q86SN7|Q96JJ9	Frame_Shift_Del	DEL	ENST00000392607.3	hg19	CCDS41580.1																																																																																			.	.	.	none		0.622	GPR123-003	NOVEL	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051113.2			-	134916320	A	-	134916320	7	5	20	1	0	1	0	1	0	0	0	0	6644	146	6	0	389	0	GPR123	10	134916320	Frame_Shift_Del	DEL	A	TCGA-2Z-A9JQ-01A-11D-A42J-10	19515134	134916320	618427	49	1364											
NAV2	89797	hgsc.bcm.edu	37	chr11	19901514	19901521	+	Frame_Shift_Del	DEL	CACCTCTG	CACCTCTG	-																															ccagaagcagcacctctcctCacctctgccgcccgccgtat																										TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	CACCTCTG	CACCTCTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr11:19901514_19901521delCACCTCTG	ENST00000396087.3	+	5	710_717	c.611_618delCACCTCTG	c.(610-618)tcacctctgfs	p.SPL204fs	NAV2_ENST00000360655.4_Frame_Shift_Del_p.SPL140fs|NAV2_ENST00000349880.4_Frame_Shift_Del_p.SPL204fs|NAV2_ENST00000540292.1_Frame_Shift_Del_p.SPL135fs|NAV2_ENST00000396085.1_Frame_Shift_Del_p.SPL204fs|NAV2_ENST00000534229.1_3'UTR|NAV2_ENST00000527559.2_Frame_Shift_Del_p.SPL133fs	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	204	Gln-rich.				glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						caCCTCTCCTCACCTCTGCCGCCCGCCG	0.654																																					p.204_206del		Pindel	.											.	NAV2	255	.	0			c.610_617del						PASS	.																																			SO:0001589	frameshift_variant	89797	exon5			.	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.611_618delCACCTCTG	chr11.hg19:g.19901514_19901521delCACCTCTG	ENSP00000379396:p.Ser204fs	63.0	0.0	.		50.0	12.0	0.240	NM_145117	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Frame_Shift_Del	DEL	ENST00000396087.3	hg19	CCDS58126.1																																																																																			.	.	.	none		0.654	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		-	19901521	CACCTCTG	-	19901514	7	5	20	1	0	1	0	1	0	0	0	0	10191	838	29	0	708	0	NAV2	11	19901514	Frame_Shift_Del	DEL	CACCTCTG	TCGA-2Z-A9JQ-01A-11D-A42J-10		19901514	115105002	50	1365											
MAP4K2	5871	hgsc.bcm.edu	37	chr11	64557720	64557720	+	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	cagtgtggccgtgggctcgcCctgcatgttgacaatcctca	6	10	12	13	2	1	1	1	1	0	0	3	1	2	1	3	2	1	3	3	2	1	1			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr11:64557720C>T	ENST00000294066.2	-	29	2279	c.2188G>A	c.(2188-2190)Ggc>Agc	p.G730S	MAP4K2_ENST00000377350.3_Missense_Mutation_p.G722S	NM_004579.3	NP_004570.2	Q12851	M4K2_HUMAN	mitogen-activated protein kinase kinase kinase kinase 2	730	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				activation of JUN kinase activity (GO:0007257)|immune response (GO:0006955)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|positive regulation of JNK cascade (GO:0046330)|protein phosphorylation (GO:0006468)|vesicle targeting (GO:0006903)	Golgi membrane (GO:0000139)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			cervix(1)|lung(3)|ovary(1)|pancreas(1)|urinary_tract(2)	8						GTGGGCTCGCCCTGCATGTTG	0.622																																					p.G730S		Atlas-SNP	.											.	MAP4K2	83	.	0			c.G2188A						PASS	.						127	113	118					11																	64557720		2201	4297	6498	SO:0001583	missense	5871	exon29			GCTCGCCCTGCAT	BC047865	CCDS8082.1	11q13.1	2011-06-09			ENSG00000168067	ENSG00000168067		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6864	protein-coding gene	gene with protein product		603166		RAB8IP		7515885	Standard	NM_004579		Approved	GCK, BL44	uc001obh.3	Q12851	OTTHUMG00000045328	ENST00000294066.2:c.2188G>A	chr11.hg19:g.64557720C>T	ENSP00000294066:p.Gly730Ser	79.0	0.0	.		64.0	33.0	.	NM_004579	Q86VU3	Missense_Mutation	SNP	ENST00000294066.2	hg19	CCDS8082.1	.	.	.	.	.	.	.	.	.	.	C	34	5.409908	0.96072	.	.	ENSG00000168067	ENST00000294066;ENST00000377350	T;T	0.36340	1.26;1.26	5.28	5.28	0.74379	Citron-like (3);	0.000000	0.85682	D	0.000000	T	0.61274	0.2334	M	0.76938	2.355	0.53005	D	0.999966	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.65582	-0.6133	10	0.87932	D	0	.	14.4958	0.67685	0.0:1.0:0.0:0.0	.	722;730	Q86VU3;Q12851	.;M4K2_HUMAN	S	730;722	ENSP00000294066:G730S;ENSP00000366567:G722S	ENSP00000294066:G730S	G	-	1	0	MAP4K2	64314296	1.000000	0.71417	0.999000	0.59377	0.976000	0.68499	6.468000	0.73551	2.494000	0.84150	0.555000	0.69702	GGC	.	.	.	none		0.622	MAP4K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105239.1	NM_004579		T	64557720	C	T	64557720	3	4	20	1	0	0	0	0	1	0	0	0	9267	623	22	2	290	2	MAP4K2	11	64557720	Missense_Mutation	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	44656206	64557720	70448796	51	1366											
CNTN5	53942	hgsc.bcm.edu	37	chr11	99690335	99690335	+	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	tgctttgttaagaattaagaAgagttcatcttcatctctct	11	17	6	7	0	5	3	2	0	3	3	6	3	5	3	0	0	1	3	0	0	4	5	rs199945392		TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr11:99690335A>T	ENST00000524871.1	+	4	406	c.116A>T	c.(115-117)aAg>aTg	p.K39M	CNTN5_ENST00000527185.1_Missense_Mutation_p.K39M|CNTN5_ENST00000418526.2_Intron|CNTN5_ENST00000279463.3_Missense_Mutation_p.K39M|CNTN5_ENST00000528682.1_Missense_Mutation_p.K39M	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	39					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)		AGAATTAAGAAGAGTTCATCT	0.398																																					p.K39M		Atlas-SNP	.											.	CNTN5	324	.	0			c.A116T						PASS	.						125	126	125					11																	99690335		1887	4119	6006	SO:0001583	missense	53942	exon3			TTAAGAAGAGTTC	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.116A>T	chr11.hg19:g.99690335A>T	ENSP00000435637:p.Lys39Met	66.0	0.0	.		88.0	14.0	.	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	hg19	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	A	14.84	2.654223	0.47467	.	.	ENSG00000149972	ENST00000527185;ENST00000528682;ENST00000524871;ENST00000279463	T;T;T;T	0.57595	0.39;0.46;0.46;0.46	5.06	3.95	0.45737	.	0.313869	0.30547	N	0.009393	T	0.37999	0.1024	N	0.19112	0.55	0.31267	N	0.692233	P;P	0.39576	0.679;0.679	B;B	0.43916	0.436;0.319	T	0.47249	-0.9132	10	0.72032	D	0.01	.	4.34	0.11105	0.7511:0.0:0.2489:0.0	.	39;39	E9PKE8;O94779	.;CNTN5_HUMAN	M	39	ENSP00000433575:K39M;ENSP00000436185:K39M;ENSP00000435637:K39M;ENSP00000279463:K39M	ENSP00000279463:K39M	K	+	2	0	CNTN5	99195545	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	1.718000	0.38001	2.208000	0.71279	0.528000	0.53228	AAG	.	.	.	alt		0.398	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361		T	99690335	A	T	99690335	3	4	20	1	0	0	0	0	1	0	0	0	3646	72	3	5	122	5	CNTN5	11	99690335	Missense_Mutation	SNP	A	TCGA-2Z-A9JQ-01A-11D-A42J-10	35132615	99690335	35316181	52	1367											
SLC37A4	2542	hgsc.bcm.edu	37	chr11	118898353	118898353	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcacccttcttgccctcagAgggcatggggtccaggttgc	5	10	12	14	0	3	1	2	0	1	1	4	1	4	1	3	4	2	2	3	4	0	3			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr11:118898353A>G	ENST00000545985.1	-	6	1366	c.610T>C	c.(610-612)Tct>Cct	p.S204P	SLC37A4_ENST00000330775.7_Missense_Mutation_p.S203P|SLC37A4_ENST00000538950.1_Missense_Mutation_p.S131P|SLC37A4_ENST00000357590.5_Missense_Mutation_p.S204P|SLC37A4_ENST00000525102.1_5'UTR	NM_001164277.1|NM_001467.5	NP_001157749.1|NP_001458.1	O43826	G6PT1_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 4	204					carbohydrate metabolic process (GO:0005975)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glucose-6-phosphate transport (GO:0015760)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucose-6-phosphate transmembrane transporter activity (GO:0015152)|transporter activity (GO:0005215)			endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|prostate(1)	6	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.58e-05)		TTGCCCTCAGAGGGCATGGGG	0.577																																					p.S204P		Atlas-SNP	.											.	SLC37A4	19	.	0			c.T610C						PASS	.						51	56	54					11																	118898353		2060	4197	6257	SO:0001583	missense	2542	exon5			CCTCAGAGGGCAT	Y15409		11q23.3	2014-09-17	2007-03-28	2003-09-10		ENSG00000137700		"Solute carriers"	4061	protein-coding gene	gene with protein product		602671	"glucose-6-phosphatase, transport (glucose-6-phosphate) protein 1"	G6PT1, G6PT2, G6PT3		9428641, 9463334	Standard	NM_001164277		Approved	GSD1b, GSD1c, GSD1d	uc010ryt.1	O43826		ENST00000545985.1:c.610T>C	chr11.hg19:g.118898353A>G	ENSP00000475241:p.Ser204Pro	119.0	0.0	.		89.0	36.0	.	NM_001467	O96016|Q5J7V4|Q9UI19|Q9UNS4	Missense_Mutation	SNP	ENST00000545985.1	hg19																																																																																				.	.	.	none		0.577	SLC37A4-204	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001467		G	118898353	A	G	118898353	3	3	20	1	0	0	0	0	1	0	0	0	14613	304	11	3	773	3	SLC37A4	11	118898353	Missense_Mutation	SNP	A	TCGA-2Z-A9JQ-01A-11D-A42J-10	19208018	118898353	16108163	53	1368											
PRDM10	56980	hgsc.bcm.edu	37	chr11	129795021	129795021	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctcccgcccatggaagcgtAagtgctggtccagtttgtcc	6	10	11	14	2	0	0	0	0	0	0	3	1	3	1	5	2	2	3	5	2	2	2			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr11:129795021A>G	ENST00000360871.3	-	12	1865	c.1634T>C	c.(1633-1635)tTa>tCa	p.L545S	PRDM10_ENST00000526082.1_Missense_Mutation_p.L463S|PRDM10_ENST00000423662.2_Missense_Mutation_p.L463S|PRDM10_ENST00000528746.1_Missense_Mutation_p.L519S|PRDM10_ENST00000304538.6_Missense_Mutation_p.L459S|PRDM10_ENST00000358825.5_Missense_Mutation_p.L549S	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	549					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)		ATGGAAGCGTAAGTGCTGGTC	0.537																																					p.L549S		Atlas-SNP	.											.	PRDM10	120	.	0			c.T1646C						PASS	.						184	181	182					11																	129795021		2201	4297	6498	SO:0001583	missense	56980	exon13			AAGCGTAAGTGCT	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.1634T>C	chr11.hg19:g.129795021A>G	ENSP00000354118:p.Leu545Ser	109.0	0.0	.		127.0	48.0	.	NM_020228	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Missense_Mutation	SNP	ENST00000360871.3	hg19	CCDS8484.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.172096	0.78452	.	.	ENSG00000170325	ENST00000358825;ENST00000304538;ENST00000360871;ENST00000423662;ENST00000528746;ENST00000526082;ENST00000533431	T;T;T;T;T;T;T	0.09350	2.99;2.99;2.99;2.99;2.99;2.99;2.99	5.41	5.41	0.78517	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.232278	0.37178	N	0.002217	T	0.15739	0.0379	L	0.29908	0.895	0.52501	D	0.999951	P;P;P;P;P;P	0.52692	0.638;0.585;0.638;0.585;0.955;0.585	P;P;P;P;P;P	0.53102	0.61;0.475;0.61;0.475;0.718;0.475	T	0.04737	-1.0930	10	0.28530	T	0.3	-6.6276	15.7411	0.77899	1.0:0.0:0.0:0.0	.	459;545;549;463;459;463	B7ZL72;G3XAE5;Q9NQV6;Q9NQV6-5;Q9NQV6-2;Q9NQV6-1	.;.;PRD10_HUMAN;.;.;.	S	549;459;545;463;519;463;262	ENSP00000351686:L549S;ENSP00000302669:L459S;ENSP00000354118:L545S;ENSP00000398431:L463S;ENSP00000431262:L519S;ENSP00000432237:L463S;ENSP00000435940:L262S	ENSP00000302669:L459S	L	-	2	0	PRDM10	129300231	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.910000	0.92685	2.171000	0.68590	0.533000	0.62120	TTA	.	.	.	none		0.537	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437		G	129795021	A	G	129795021	3	3	20	1	0	0	0	0	1	0	0	0	12461	372	13	3	1876	3	PRDM10	11	129795021	Missense_Mutation	SNP	A	TCGA-2Z-A9JQ-01A-11D-A42J-10	10896668	129795021	5211495	54	1369											
KRT6A	3853	hgsc.bcm.edu	37	chr12	52882218	52882218	+	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	cttcagcagccgggccaggtCctgcttggccttctgcaggg	4	9	14	14	1	2	0	1	0	1	0	3	0	3	0	4	4	4	3	4	4	0	3			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr12:52882218C>G	ENST00000330722.6	-	7	1386	c.1318G>C	c.(1318-1320)Gac>Cac	p.D440H		NM_005554.3	NP_005545.1	P02538	K2C6A_HUMAN	keratin 6A	440	Coil 2.|Rod.				cell differentiation (GO:0030154)|positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	39				BRCA - Breast invasive adenocarcinoma(357;0.189)		CGGGCCAGGTCCTGCTTGGCC	0.622																																					p.D440H		Atlas-SNP	.											.	KRT6A	89	.	0			c.G1318C						PASS	.						101	91	95					12																	52882218		2203	4298	6501	SO:0001583	missense	3853	exon7			CCAGGTCCTGCTT	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.1318G>C	chr12.hg19:g.52882218C>G	ENSP00000369317:p.Asp440His	162.0	0.0	.		101.0	51.0	.	NM_005554	A4QPC1|P48667|Q08AR4|Q6NT67|Q96CL4	Missense_Mutation	SNP	ENST00000330722.6	hg19	CCDS41786.1	.	.	.	.	.	.	.	.	.	.	c	22.1	4.247317	0.80024	.	.	ENSG00000205420	ENST00000330722;ENST00000452121	D	0.89681	-2.55	5.06	5.06	0.68205	Filament (1);	0.000000	0.64402	D	0.000007	D	0.97096	0.9051	H	0.98701	4.305	0.53005	D	0.999968	D	0.89917	1.0	D	0.79108	0.992	D	0.98900	1.0776	10	0.87932	D	0	.	18.799	0.92008	0.0:1.0:0.0:0.0	.	440	P02538	K2C6A_HUMAN	H	440;396	ENSP00000369317:D440H	ENSP00000369317:D440H	D	-	1	0	KRT6A	51168485	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.722000	0.61958	2.501000	0.84356	0.591000	0.81541	GAC	.	.	.	none		0.622	KRT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404978.2	NM_005554		G	52882218	C	G	52882218	3	3	20	1	0	0	0	0	1	0	0	0	8487	855	30	4	388	4	KRT6A	12	52882218	Missense_Mutation	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10		52882218	80969677	55	1370											
KRT72	140807	hgsc.bcm.edu	37	chr12	52985268	52985268	+	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	cttggtctggtacagggtctCagcctcggccttgctcttta	4	14	11	12	1	3	0	1	0	3	0	5	0	3	0	2	4	3	2	2	4	2	5	rs145259719	byFrequency	TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr12:52985268C>A	ENST00000537672.2	-	5	953	c.943G>T	c.(943-945)Gag>Tag	p.E315*	KRT72_ENST00000354310.4_Nonsense_Mutation_p.E315*|KRT72_ENST00000293745.2_Nonsense_Mutation_p.E315*|KRT72_ENST00000398066.3_Nonsense_Mutation_p.E127*	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	315	Coil 2.|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)		TACAGGGTCTCAGCCTCGGCC	0.577																																					p.E315X		Atlas-SNP	.											.	KRT72	70	.	0			c.G943T						PASS	.						128	94	106					12																	52985268		2203	4300	6503	SO:0001587	stop_gained	140807	exon5			GGGTCTCAGCCTC	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.943G>T	chr12.hg19:g.52985268C>A	ENSP00000441160:p.Glu315*	72.0	0.0	.		46.0	17.0	.	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Nonsense_Mutation	SNP	ENST00000537672.2	hg19	CCDS8833.1	.	.	.	.	.	.	.	.	.	.	C	15.55	2.865439	0.51588	.	.	ENSG00000170486	ENST00000537672;ENST00000293745;ENST00000354310;ENST00000398066	.	.	.	4.33	4.33	0.51752	.	0.000000	0.52532	D	0.000061	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	13.6339	0.62210	0.0:0.9208:0.0:0.0792	.	.	.	.	X	315;315;315;127	.	ENSP00000293745:E315X	E	-	1	0	KRT72	51271535	1.000000	0.71417	0.230000	0.23976	0.014000	0.08584	7.561000	0.82288	2.715000	0.92844	0.655000	0.94253	GAG	.	C|1.000;T|0.000	.	alt		0.577	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747		A	52985268	C	A	52985268	4	1	20	1	0	0	0	0	0	1	0	0	8492	835	29	4	612	4	KRT72	12	52985268	Nonsense_Mutation	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	103050	52985268	80866627	56	1371											
APPL2	55198	hgsc.bcm.edu	37	chr12	105582221	105582221	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataaacatctgctgcaaaagAgaatctggaagacagcattt	17	9	8	7	0	2	2	0	0	2	2	2	4	2	3	0	1	4	3	0	1	6	2			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr12:105582221A>G	ENST00000258530.3	-	17	1689	c.1464T>C	c.(1462-1464)tcT>tcC	p.S488S	APPL2_ENST00000539978.2_Silent_p.S445S|APPL2_ENST00000551662.1_Silent_p.S494S	NM_001251904.1|NM_018171.3	NP_001238833.1|NP_060641.2	Q06481	APLP2_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 2	0					cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|midbrain development (GO:0030901)|neuromuscular process controlling balance (GO:0050885)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of protein binding (GO:0043393)|suckling behavior (GO:0001967)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						GCTGCAAAAGAGAATCTGGAA	0.423																																					p.S494S		Atlas-SNP	.											.	APPL2	69	.	0			c.T1482C						PASS	.						74	74	74					12																	105582221		2203	4300	6503	SO:0001819	synonymous_variant	55198	exon17			CAAAAGAGAATCT	AY113704	CCDS9101.1, CCDS58275.1, CCDS58276.1	12q23.3	2014-08-12			ENSG00000136044	ENSG00000136044		"Pleckstrin homology (PH) domain containing"	18242	protein-coding gene	gene with protein product		606231				11431708, 17030088	Standard	NM_001251904		Approved	FLJ10659, DIP13B	uc010swu.1	Q8NEU8	OTTHUMG00000169853	ENST00000258530.3:c.1464T>C	chr12.hg19:g.105582221A>G		50.0	0.0	.		73.0	31.0	.	NM_001251904	B3KXX9|H7BXI4|Q13861|Q14594|Q14662|Q71U10|Q7M4L3|Q9BT36	Silent	SNP	ENST00000258530.3	hg19	CCDS9101.1																																																																																			.	.	.	none		0.423	APPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406238.3	NM_018171		G	105582221	A	G	105582221	2	3	20	1	0	0	0	0	0	0	0	1	818	291	11	3		3	APPL2	12	105582221	Silent	SNP	A	TCGA-2Z-A9JQ-01A-11D-A42J-10	52596953	105582221	28269674	57	1372											
OAS3	4940	hgsc.bcm.edu	37	chr12	113386980	113386982	+	In_Frame_Del	DEL	CTG	CTG	-																															ttgcgctgcctccatgagaaCtgtgttcacaaggcctcaag																										TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr12:113386980_113386982delCTG	ENST00000228928.7	+	6	1523_1525	c.1344_1346delCTG	c.(1342-1347)aactgt>aat	p.C449del	RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	449	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						TCCATGAGAACTGTGTTCACAAG	0.567																																					p.448_449del		Atlas-INDEL	.											.	OAS3	63	.	0			c.1343_1345del						PASS	.																																			SO:0001651	inframe_deletion	4940	exon6			.	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.1344_1346delCTG	chr12.hg19:g.113386980_113386982delCTG	ENSP00000228928:p.Cys449del	41.0	0.0	0		30.0	11.0	0.366667	NM_006187	Q2HJ14|Q9H3P5	In_Frame_Del	DEL	ENST00000228928.7	hg19	CCDS44981.1																																																																																			.	.	.	none		0.567	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1			-	113386982	CTG	-	113386980	7	5	20	1	0	1	0	1	0	0	0	0	10808	564	20	0	1366	0	OAS3	12	113386980	In_Frame_Del	DEL	CTG	TCGA-2Z-A9JQ-01A-11D-A42J-10	7804759	113386980	20464915	58	1373											
PLCB2	5330	hgsc.bcm.edu	37	chr15	40594770	40594770	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttcagcaggaaactgttaTcaggaaagtccatgttgaag	13	11	10	7	0	3	1	2	1	1	0	4	3	4	3	1	2	2	3	1	2	4	3			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr15:40594770T>C	ENST00000260402.3	-	4	521	c.272A>G	c.(271-273)gAt>gGt	p.D91G	PLCB2-AS1_ENST00000559520.1_RNA|PLCB2_ENST00000543785.2_Missense_Mutation_p.D91G|PLCB2_ENST00000557821.1_Missense_Mutation_p.D91G|PLCB2_ENST00000456256.2_Missense_Mutation_p.D91G	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	91					activation of phospholipase C activity (GO:0007202)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|sensory perception of bitter taste (GO:0050913)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(3)	39		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		GAAACTGTTATCAGGAAAGTC	0.572																																					p.D91G		Atlas-SNP	.											.	PLCB2	177	.	0			c.A272G						PASS	.						93	98	96					15																	40594770		2035	4190	6225	SO:0001583	missense	5330	exon4			CTGTTATCAGGAA		CCDS42020.1, CCDS61591.1, CCDS61592.1, CCDS73704.1	15q15.1	2012-01-23			ENSG00000137841	ENSG00000137841	3.1.4.11		9055	protein-coding gene	gene with protein product		604114				1644792, 9925923	Standard	XM_005254448		Approved	FLJ38135	uc001zld.3	Q00722	OTTHUMG00000172412	ENST00000260402.3:c.272A>G	chr15.hg19:g.40594770T>C	ENSP00000260402:p.Asp91Gly	127.0	0.0	.		59.0	16.0	.	NM_004573	A8K6J2|B9EGH5	Missense_Mutation	SNP	ENST00000260402.3	hg19	CCDS42020.1	.	.	.	.	.	.	.	.	.	.	T	14.98	2.697454	0.48202	.	.	ENSG00000137841	ENST00000260402;ENST00000456256;ENST00000543785	T;T;T	0.45276	0.9;0.9;0.9	4.87	3.75	0.43078	.	0.342197	0.32836	N	0.005590	T	0.34483	0.0899	L	0.54323	1.7	0.41896	D	0.990392	P;B;B;B	0.44195	0.828;0.002;0.329;0.002	B;B;B;B	0.39119	0.291;0.008;0.165;0.005	T	0.10245	-1.0638	10	0.20046	T	0.44	.	10.737	0.46130	0.0:0.075:0.0:0.925	.	91;91;91;91	B9EGH5;Q00722-2;Q9BVT6;Q00722	.;.;.;PLCB2_HUMAN	G	91	ENSP00000260402:D91G;ENSP00000411991:D91G;ENSP00000444652:D91G	ENSP00000260402:D91G	D	-	2	0	PLCB2	38382062	1.000000	0.71417	0.999000	0.59377	0.701000	0.40568	4.261000	0.58841	1.008000	0.39264	0.459000	0.35465	GAT	.	.	.	none		0.572	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1			C	40594770	T	C	40594770	3	2	20	1	0	0	0	0	1	0	0	0	12035	1435	50	3	3401	3	PLCB2	15	40594770	Missense_Mutation	SNP	T	TCGA-2Z-A9JQ-01A-11D-A42J-10		40594770	61936622	59	1374											
MAP1A	4130	hgsc.bcm.edu	37	chr15	43818453	43818453	+	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	gataaaaccaggaaaccaaaGatgctagaggaaaaatcccc	20	4	8	9	0	0	2	0	0	0	2	1	5	1	4	4	2	3	1	4	2	7	2			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr15:43818453G>T	ENST00000300231.5	+	4	5232	c.4782G>T	c.(4780-4782)aaG>aaT	p.K1594N	MAP1A_ENST00000399453.1_Missense_Mutation_p.K1594N|MAP1A_ENST00000382031.1_Missense_Mutation_p.K1832N			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1594					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)	GGAAACCAAAGATGCTAGAGG	0.493																																					p.K1594N		Atlas-SNP	.											.	MAP1A	189	.	0			c.G4782T						PASS	.						56	58	58					15																	43818453		1879	4101	5980	SO:0001583	missense	4130	exon4			ACCAAAGATGCTA	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.4782G>T	chr15.hg19:g.43818453G>T	ENSP00000300231:p.Lys1594Asn	142.0	0.0	.		142.0	61.0	.	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	hg19	CCDS42031.1	.	.	.	.	.	.	.	.	.	.	G	2.879	-0.232235	0.05983	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.64803	-0.12;-0.12;-0.12	1.46	-2.47	0.06442	.	.	.	.	.	T	0.48732	0.1516	L	0.32530	0.975	0.09310	N	1	P	0.37330	0.59	B	0.43728	0.429	T	0.42241	-0.9463	9	0.34782	T	0.22	-9.6264	3.4489	0.07491	0.5006:0.2186:0.2808:0.0	.	1594	P78559	MAP1A_HUMAN	N	1832;1594;1594	ENSP00000371462:K1832N;ENSP00000382380:K1594N;ENSP00000300231:K1594N	ENSP00000300231:K1594N	K	+	3	2	MAP1A	41605745	0.000000	0.05858	0.000000	0.03702	0.397000	0.30659	-0.481000	0.06552	-0.776000	0.04578	-0.251000	0.11542	AAG	.	.	.	none		0.493	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373		T	43818453	G	T	43818453	3	4	20	1	0	0	0	0	1	0	0	0	9234	933	33	4	4784	4	MAP1A	15	43818453	Missense_Mutation	SNP	G	TCGA-2Z-A9JQ-01A-11D-A42J-10	3223683	43818453	58712939	60	1375											
HERC1	8925	hgsc.bcm.edu	37	chr15	63918321	63918321	+	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	atactgggggggcactgtgtCaggcaggcccagctgcagag	8	6	17	10	0	1	1	1	0	0	1	1	1	1	1	1	5	3	4	1	5	1	1			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr15:63918321C>G	ENST00000443617.2	-	71	13225	c.13138G>C	c.(13138-13140)Gac>Cac	p.D4380H		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	4380					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						GGCACTGTGTCAGGCAGGCCC	0.532																																					p.D4380H		Atlas-SNP	.											.	HERC1	624	.	0			c.G13138C						PASS	.						36	38	38					15																	63918321		1985	4153	6138	SO:0001583	missense	8925	exon71			CTGTGTCAGGCAG	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.13138G>C	chr15.hg19:g.63918321C>G	ENSP00000390158:p.Asp4380His	58.0	0.0	.		48.0	16.0	.	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	C	16.96	3.266711	0.59540	.	.	ENSG00000103657	ENST00000443617	T	0.25250	1.81	5.23	4.31	0.51392	.	0.138683	0.46442	U	0.000293	T	0.19446	0.0467	N	0.24115	0.695	0.45747	D	0.998648	B	0.32653	0.379	B	0.30782	0.12	T	0.04961	-1.0915	10	0.59425	D	0.04	.	15.57	0.76326	0.1389:0.8611:0.0:0.0	.	4380	Q15751	HERC1_HUMAN	H	4380	ENSP00000390158:D4380H	ENSP00000390158:D4380H	D	-	1	0	HERC1	61705374	0.980000	0.34600	0.198000	0.23420	0.897000	0.52465	4.826000	0.62715	1.321000	0.45227	0.491000	0.48974	GAC	.	.	.	none		0.532	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		G	63918321	C	G	63918321	3	3	20	1	0	0	0	0	1	0	0	0	7064	826	29	4	1479	4	HERC1	15	63918321	Missense_Mutation	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	20099868	63918321	38613071	61	1376											
ST8SIA2	8128	hgsc.bcm.edu	37	chr15	92987897	92987897	+	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	ccccagtacaggagtatgccCgggatgtggggctcaagaca	10	6	14	11	1	1	1	1	0	0	1	1	3	1	3	3	4	2	3	3	4	3	2	rs146396658		TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr15:92987897C>A	ENST00000268164.3	+	5	817	c.580C>A	c.(580-582)Cgg>Agg	p.R194R	ST8SIA2_ENST00000539113.1_Silent_p.R173R	NM_006011.3	NP_006002.1	Q92186	SIA8B_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	194					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|ganglioside biosynthetic process (GO:0001574)|N-glycan processing (GO:0006491)|nervous system development (GO:0007399)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	early endosome (GO:0005769)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|recycling endosome (GO:0055037)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)	p.R194R(1)		endometrium(2)|large_intestine(6)|lung(9)|skin(2)|urinary_tract(1)	20	Lung NSC(78;0.0893)|all_lung(78;0.125)		BRCA - Breast invasive adenocarcinoma(143;0.0355)|OV - Ovarian serous cystadenocarcinoma(32;0.203)			GGAGTATGCCCGGGATGTGGG	0.567																																					p.R194R		Atlas-SNP	.											.	ST8SIA2	41	.	1	Substitution - coding silent(1)	lung(1)	c.C580A						PASS	.						65	69	67					15																	92987897		2198	4298	6496	SO:0001819	synonymous_variant	8128	exon5			TATGCCCGGGATG	U33551	CCDS10372.1	15q26	2013-03-01	2003-01-14	2005-02-07	ENSG00000140557	ENSG00000140557		"Sialyltransferases"	10870	protein-coding gene	gene with protein product		602546	"sialyltransferase 8 (alpha-2, 8-sialytransferase) B"	SIAT8B		7559389	Standard	NM_006011		Approved	STX, ST8SIA-II, HsT19690	uc002bra.3	Q92186	OTTHUMG00000149843	ENST00000268164.3:c.580C>A	chr15.hg19:g.92987897C>A		142.0	0.0	.		110.0	56.0	.	NM_006011	Q4VAZ0|Q92470|Q92746	Silent	SNP	ENST00000268164.3	hg19	CCDS10372.1																																																																																			.	C|1.000;T|0.000	.	alt		0.567	ST8SIA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313526.1	NM_006011		A	92987897	C	A	92987897	2	1	20	1	0	0	0	0	0	0	0	1	15244	643	23	4		4	ST8SIA2	15	92987897	Silent	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	29069576	92987897	9543495	62	1377											
KLHL36	79786	hgsc.bcm.edu	37	chr16	84690911	84690911	+	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	ctcaagcggcttgatgccttCatcgatggcttcatcctgaa	8	12	9	12	2	3	2	3	2	0	0	5	3	4	2	2	2	2	2	2	2	2	3			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr16:84690911C>T	ENST00000564996.1	+	3	639	c.498C>T	c.(496-498)ttC>ttT	p.F166F	KLHL36_ENST00000258157.5_Silent_p.F166F	NM_024731.2	NP_079007.2	Q8N4N3	KLH36_HUMAN	kelch-like family member 36	166	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						TTGATGCCTTCATCGATGGCT	0.562																																					p.F166F		Atlas-SNP	.											.	KLHL36	51	.	0			c.C498T						PASS	.						94	77	83					16																	84690911		2199	4300	6499	SO:0001819	synonymous_variant	79786	exon3			TGCCTTCATCGAT	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.498C>T	chr16.hg19:g.84690911C>T		56.0	0.0	.		65.0	34.0	.	NM_024731	Q8N5G6|Q9H9U6	Silent	SNP	ENST00000564996.1	hg19	CCDS10948.1																																																																																			.	.	.	none		0.562	KLHL36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269084.2			T	84690911	C	T	84690911	2	4	20	1	0	0	0	0	0	0	0	1	8396	825	29	2		2	KLHL36	16	84690911	Silent	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10		84690911	5663842	63	1378											
FANCA	2175	hgsc.bcm.edu	37	chr16	89809242	89809242	+	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	agtccagcttctttagctgcTtcctgatgttttcttccctg	4	18	7	12	0	2	1	0	1	2	0	5	1	5	1	3	0	3	4	3	0	1	7			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr16:89809242T>A	ENST00000389301.3	-	37	3761	c.3731A>T	c.(3730-3732)aAg>aTg	p.K1244M	FANCA_ENST00000568369.1_Missense_Mutation_p.K1244M	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	1244					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)		CTTTAGCTGCTTCCTGATGTT	0.493			"D, Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.K1244M		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"Fanconi anemia, complementation group A"		L	.	FANCA	99	.	0			c.A3731T						PASS	.						114	100	105					16																	89809242		2198	4300	6498	SO:0001583	missense	2175	exon37	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AGCTGCTTCCTGA	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.3731A>T	chr16.hg19:g.89809242T>A	ENSP00000373952:p.Lys1244Met	50.0	0.0	.		62.0	14.0	.	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	hg19	CCDS32515.1	.	.	.	.	.	.	.	.	.	.	T	11.12	1.544860	0.27563	.	.	ENSG00000187741	ENST00000389301;ENST00000305699	D	0.84873	-1.91	4.85	-9.7	0.00521	.	1.958180	0.02194	N	0.061614	T	0.63331	0.2502	N	0.08118	0	0.09310	N	1	B;P;P	0.35600	0.42;0.511;0.511	B;B;B	0.31751	0.096;0.135;0.135	T	0.62110	-0.6923	10	0.51188	T	0.08	4.2992	3.4872	0.07624	0.0912:0.185:0.3755:0.3483	.	221;1244;1244	B7Z6Y4;B4DRI7;O15360	.;.;FANCA_HUMAN	M	1244;221	ENSP00000373952:K1244M	ENSP00000306281:K221M	K	-	2	0	FANCA	88336743	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.517000	0.02248	-1.568000	0.01670	-1.223000	0.01593	AAG	.	.	.	none		0.493	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1			A	89809242	T	A	89809242	3	1	20	1	0	0	0	0	1	0	0	0	5669	1609	56	5	664	5	FANCA	16	89809242	Missense_Mutation	SNP	T	TCGA-2Z-A9JQ-01A-11D-A42J-10	5118331	89809242	545511	64	1379											
KDM6B	23135	hgsc.bcm.edu	37	chr17	7749761	7749761	+	Frame_Shift_Del	DEL	C	C	-																															tggctcctgccagcaccgagCcaaggtcctgcccccactgg																										TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr17:7749761delC	ENST00000448097.2	+	7	831	c.500delC	c.(499-501)gccfs	p.A167fs	KDM6B_ENST00000254846.5_Frame_Shift_Del_p.A167fs			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	167					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						CAGCACCGAGCCAAGGTCCTG	0.642																																					p.A167fs		Atlas-Indel,Pindel	.											.	KDM6B	95	.	0			c.499delG						PASS	.						27	28	28					17																	7749761		2202	4300	6502	SO:0001589	frameshift_variant	23135	exon7			.	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.500delC	chr17.hg19:g.7749761delC	ENSP00000412513:p.Ala167fs	135.0	0.0	0		115.0	30.0	0.26087	NM_001080424	C9IZ40|Q96G33	Frame_Shift_Del	DEL	ENST00000448097.2	hg19																																																																																				.	.	.	none		0.642	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272		-	7749761	C	-	7749761	7	5	20	1	0	1	0	1	0	0	0	0	8145	739	26	0	514	0	KDM6B	17	7749761	Frame_Shift_Del	DEL	C	TCGA-2Z-A9JQ-01A-11D-A42J-10		7749761	73445449	65	1380											
ALOX12B	242	hgsc.bcm.edu	37	chr17	7976157	7976158	+	Frame_Shift_Ins	INS	-	-	G																															gggatgggaaggcacttgttINSgcgctggcggatgtcgtgtg																										TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr17:7976157_7976158insG	ENST00000319144.4	-	15	2297_2298	c.2037_2038insC	c.(2035-2040)cgcaacfs	p.N680fs	ALOX12B_ENST00000577351.1_5'Flank	NM_001139.2	NP_001130.1	O75342	LX12B_HUMAN	arachidonate 12-lipoxygenase, 12R type	680	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|ceramide biosynthetic process (GO:0046513)|establishment of skin barrier (GO:0061436)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipoxygenase pathway (GO:0019372)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|protein lipidation (GO:0006497)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)	arachidonate 12-lipoxygenase activity (GO:0004052)|iron ion binding (GO:0005506)|linoleate 9S-lipoxygenase activity (GO:1990136)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	16						AGGCACTTGTTGCGCTGGCGGA	0.589										Multiple Myeloma(8;0.094)																											p.N680fs		Atlas-Indel,Pindel	.											.	ALOX12B	61	.	0			c.2038_2039insC						PASS	.																																			SO:0001589	frameshift_variant	242	exon15			.	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.2038dupC	chr17.hg19:g.7976158_7976158dupG	ENSP00000315167:p.Asn680fs	162.0	0.0	0		161.0	104.0	0.645963	NM_001139		Frame_Shift_Ins	INS	ENST00000319144.4	hg19	CCDS11129.1																																																																																			.	.	.	none		0.589	ALOX12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226984.3			G	7976158	-	G	7976157	7	5	20	1	0	1	1	0	0	0	0	0	537	1812	63	0	71	0	ALOX12B	17	7976157	Frame_Shift_Ins	INS	-	TCGA-2Z-A9JQ-01A-11D-A42J-10	226396	7976157	73219053	66	1381											
C17orf66	256957	hgsc.bcm.edu	37	chr17	34185488	34185488	+	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	aggatggccttgatgactggGgctgagtgcacgtgcatcac	8	9	15	9	1	1	3	1	3	0	0	1	4	1	4	1	4	2	3	1	4	0	1			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr17:34185488G>T	ENST00000311880.2	-	10	1129	c.981C>A	c.(979-981)gcC>gcA	p.A327A	C17orf66_ENST00000592980.1_Silent_p.A287A	NM_152781.2	NP_689994.2	A2RTY3	HEAT9_HUMAN		327					hematopoietic progenitor cell differentiation (GO:0002244)					breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(6)|lung(11)|skin(2)|stomach(4)	38		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0184)		TGATGACTGGGGCTGAGTGCA	0.582																																					p.A327A		Atlas-SNP	.											.	C17orf66	57	.	0			c.C981A						PASS	.						123	83	96					17																	34185488		2203	4300	6503	SO:0001819	synonymous_variant	256957	exon10			GACTGGGGCTGAG																												ENST00000311880.2:c.981C>A	chr17.hg19:g.34185488G>T		127.0	0.0	.		125.0	23.0	.	NM_152781	B4DX21|B4DXA4|B4DXF0|Q8N4R4|Q96M46	Silent	SNP	ENST00000311880.2	hg19	CCDS11299.1																																																																																			.	.	.	none		0.582	C17orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256487.1			T	34185488	G	T	34185488	2	4	20	1	0	0	0	0	0	0	0	1	1876	1219	43	4		4	C17orf66	17	34185488	Silent	SNP	G	TCGA-2Z-A9JQ-01A-11D-A42J-10	26209331	34185488	47009722	67	1382											
FKBP10	60681	hgsc.bcm.edu	37	chr17	39975893	39975893	+	Frame_Shift_Del	DEL	C	C	-																															gaacgccggagaattaccatCcccccgcacctcgcctatgg																										TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr17:39975893delC	ENST00000321562.4	+	6	1133	c.1029delC	c.(1027-1029)atcfs	p.I343fs	FKBP10_ENST00000544340.1_Frame_Shift_Del_p.I55fs	NM_021939.3	NP_068758.3	Q96AY3	FKB10_HUMAN	FK506 binding protein 10, 65 kDa	343	PPIase FKBP-type 3. {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)		GAATTACCATCCCCCCGCACC	0.617																																					p.I343fs		Atlas-Indel,Pindel	.											.	FKBP10	57	.	0			c.1028delT						PASS	.																																			SO:0001589	frameshift_variant	60681	exon6			.	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.1029delC	chr17.hg19:g.39975893delC	ENSP00000317232:p.Ile343fs	82.0	0.0	0		88.0	24.0	0.272727	NM_021939	Q7Z3R4|Q9H3N3|Q9H6J3|Q9H6N5|Q9UF89	Frame_Shift_Del	DEL	ENST00000321562.4	hg19	CCDS11409.1																																																																																			.	.	.	none		0.617	FKBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257410.2	NM_021939		-	39975893	C	-	39975893	7	5	20	1	0	1	0	1	0	0	0	0	5909	845	30	0	1051	0	FKBP10	17	39975893	Frame_Shift_Del	DEL	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	5790405	39975893	41219317	68	1383											
FDXR	2232	hgsc.bcm.edu	37	chr17	72859031	72859031	+	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	ccgggccacctcctcggcatCcagcttctcccagtctgaga	6	8	9	18	2	2	1	0	1	2	1	6	2	4	1	6	2	1	2	6	2	0	1			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr17:72859031C>T	ENST00000293195.5	-	12	1462	c.1384G>A	c.(1384-1386)Gat>Aat	p.D462N	FDXR_ENST00000413947.2_Missense_Mutation_p.D493N|FDXR_ENST00000581530.1_Missense_Mutation_p.D468N|GRIN2C_ENST00000578159.1_5'Flank|FDXR_ENST00000582944.1_Missense_Mutation_p.D454N|FDXR_ENST00000583917.1_Missense_Mutation_p.D434N|FDXR_ENST00000420580.2_Missense_Mutation_p.D422N|FDXR_ENST00000442102.2_Missense_Mutation_p.D505N|FDXR_ENST00000544854.1_Missense_Mutation_p.D410N|FDXR_ENST00000455107.2_3'UTR|GRIN2C_ENST00000347612.4_5'Flank	NM_001258014.1|NM_004110.3|NM_024417.2	NP_001244943.1|NP_004101.2|NP_077728.2	P22570	ADRO_HUMAN	ferredoxin reductase	462					cholesterol metabolic process (GO:0008203)|generation of precursor metabolites and energy (GO:0006091)|NADPH oxidation (GO:0070995)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ferredoxin-NADP+ reductase activity (GO:0004324)|NADPH binding (GO:0070402)|NADPH-adrenodoxin reductase activity (GO:0015039)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16	all_lung(278;0.172)|Lung NSC(278;0.207)				Flavin adenine dinucleotide(DB03147)	TCCTCGGCATCCAGCTTCTCC	0.657																																					p.D505N		Atlas-SNP	.											.	FDXR	68	.	0			c.G1513A						PASS	.						42	52	49					17																	72859031		2203	4300	6503	SO:0001583	missense	2232	exon12			CGGCATCCAGCTT	J03826	CCDS11707.1, CCDS58591.1, CCDS58592.1, CCDS58593.1, CCDS58594.1, CCDS58595.1, CCDS58596.1	17q25.1	2013-06-18			ENSG00000161513	ENSG00000161513	1.18.1.6		3642	protein-coding gene	gene with protein product	"adrenodoxin-NADP(+) reductase", "adrenodoxin reductase"	103270		ADXR		2969697	Standard	NM_001258014		Approved		uc010wrl.2	P22570	OTTHUMG00000179026	ENST00000293195.5:c.1384G>A	chr17.hg19:g.72859031C>T	ENSP00000293195:p.Asp462Asn	80.0	0.0	.		48.0	34.0	.	NM_001258012	B4DDI7|B4DHX5|B4DQQ4|B4DX24|B7Z7G2|E7EQC1|Q13716|Q4PJI0|Q9BU12	Missense_Mutation	SNP	ENST00000293195.5	hg19	CCDS58593.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.253053	0.59212	.	.	ENSG00000161513	ENST00000420580;ENST00000544854;ENST00000293195;ENST00000442102;ENST00000413947	T;T;T;T	0.23552	2.6;2.64;1.9;1.9	5.05	5.05	0.67936	NAD(P)-binding domain (1);	0.097389	0.64402	D	0.000001	T	0.54271	0.1848	M	0.82323	2.585	0.80722	D	1	D;D;D;D;P;P;P;D;P;D	0.62365	0.984;0.991;0.99;0.979;0.793;0.801;0.665;0.979;0.665;0.988	P;D;P;P;P;B;B;P;B;P	0.65684	0.669;0.937;0.755;0.556;0.689;0.425;0.224;0.556;0.224;0.791	T	0.59768	-0.7392	10	0.52906	T	0.07	-13.8242	17.9977	0.89189	0.0:1.0:0.0:0.0	.	422;505;493;460;410;493;462;454;462;468	B4DQQ4;B4DHX5;E7EQC1;B4DDI9;B7Z7G2;B4DDI7;Q6GSK2;B4DX24;P22570;P22570-2	.;.;.;.;.;.;.;.;ADRO_HUMAN;.	N	422;410;468;505;493	ENSP00000414172:D422N;ENSP00000445432:D410N;ENSP00000416515:D505N;ENSP00000408595:D493N	ENSP00000293195:D468N	D	-	1	0	FDXR	70370626	1.000000	0.71417	1.000000	0.80357	0.079000	0.17450	4.096000	0.57734	2.337000	0.79520	0.407000	0.27541	GAT	.	.	.	none		0.657	FDXR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000444449.1	NM_004110		T	72859031	C	T	72859031	3	4	20	1	0	0	0	0	1	0	0	0	5814	855	30	2	95	2	FDXR	17	72859031	Missense_Mutation	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	32883138	72859031	8336179	69	1384											
UNK	85451	hgsc.bcm.edu	37	chr17	73818652	73818652	+	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	ttcctatcagggccaggggcTgccgagctggcccgacttcg	5	8	14	14	3	1	0	1	0	0	0	3	2	2	0	4	4	2	2	4	4	1	3			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr17:73818652T>A	ENST00000589666.1	+	14	2042	c.1932T>A	c.(1930-1932)gcT>gcA	p.A644A	UNK_ENST00000293218.3_Silent_p.A720A|RP11-552F3.4_ENST00000586808.1_RNA	NM_001080419.2	NP_001073888.2	Q9C0B0	UNK_HUMAN	unkempt family zinc finger	644							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)			GGCCAGGGGCTGCCGAGCTGG	0.627																																					p.A644A		Atlas-SNP	.											.	UNK	87	.	0			c.T1932A						PASS	.						57	66	63					17																	73818652		1970	4147	6117	SO:0001819	synonymous_variant	85451	exon14			AGGGGCTGCCGAG	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.1932T>A	chr17.hg19:g.73818652T>A		82.0	0.0	.		83.0	54.0	.	NM_001080419		Silent	SNP	ENST00000589666.1	hg19	CCDS45778.2																																																																																			.	.	.	none		0.627	UNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448835.1	NM_001080419		A	73818652	T	A	73818652	2	1	20	1	0	0	0	0	0	0	0	1	17012	1567	55	5		5	UNK	17	73818652	Silent	SNP	T	TCGA-2Z-A9JQ-01A-11D-A42J-10	959621	73818652	7376558	70	1385											
TIMP2	7077	hgsc.bcm.edu	37	chr17	76869985	76869985	+	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	tccacttccttctcactgacCgctttggccctgatcactgc	5	13	6	17	1	2	2	2	2	1	0	5	2	4	2	4	1	1	1	4	1	0	3	rs146970059		TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr17:76869985C>A	ENST00000262768.7	-	2	445	c.147G>T	c.(145-147)gcG>gcT	p.A49A	TIMP2_ENST00000536189.2_5'UTR|TIMP2_ENST00000585421.1_5'UTR|TIMP2_ENST00000586057.1_5'UTR	NM_003255.4	NP_003246.1	P16035	TIMP2_HUMAN	TIMP metallopeptidase inhibitor 2	49	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.			VIRAKAV -> GKESGDP (in Ref. 10). {ECO:0000305}.	aging (GO:0007568)|cellular response to organic substance (GO:0071310)|central nervous system development (GO:0007417)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of proteolysis (GO:0045861)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|regulation of Rap protein signal transduction (GO:0032487)|response to cytokine (GO:0034097)|response to drug (GO:0042493)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.194)			TCTCACTGACCGCTTTGGCCC	0.507																																					p.A49A		Atlas-SNP	.											.	TIMP2	27	.	0			c.G147T						PASS	.						144	127	133					17																	76869985		2203	4300	6503	SO:0001819	synonymous_variant	7077	exon2			ACTGACCGCTTTG		CCDS11758.1	17q25	2008-07-18	2005-08-08		ENSG00000035862	ENSG00000035862			11821	protein-coding gene	gene with protein product		188825	"tissue inhibitor of metalloproteinase 2"			1427908	Standard	NM_003255		Approved	CSC-21K	uc002jwf.3	P16035	OTTHUMG00000154517	ENST00000262768.7:c.147G>T	chr17.hg19:g.76869985C>A		68.0	0.0	.		81.0	46.0	.	NM_003255	Q16121|Q93006|Q9UDF7	Silent	SNP	ENST00000262768.7	hg19	CCDS11758.1																																																																																			.	C|1.000;T|0.000	.	alt		0.507	TIMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335662.1	NM_003255		A	76869985	C	A	76869985	2	1	20	1	0	0	0	0	0	0	0	1	15930	639	23	4		4	TIMP2	17	76869985	Silent	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	3051333	76869985	4325225	71	1386											
TXNDC2	84203	hgsc.bcm.edu	37	chr18	9886730	9886730	+	Frame_Shift_Del	DEL	A	A	-																															ggagtctgatgcctcacaggAgggcgatgacctacccaagt																										TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr18:9886730delA	ENST00000306084.6	+	2	453	c.254delA	c.(253-255)gagfs	p.E85fs	TXNDC2_ENST00000426718.3_3'UTR|TXNDC2_ENST00000536353.2_Frame_Shift_Del_p.E18fs|TXNDC2_ENST00000357775.5_Frame_Shift_Del_p.E18fs	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	85					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						GCCTCACAGGAGGGCGATGAC	0.562																																					p.E85fs		Atlas-Indel,Pindel	.											.	TXNDC2	168	.	0			c.253delG						PASS	.						154	101	119					18																	9886730		2203	4300	6503	SO:0001589	frameshift_variant	84203	exon2			.	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.254delA	chr18.hg19:g.9886730delA	ENSP00000304908:p.Glu85fs	114.0	0.0	0		73.0	34.0	0.465753	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Frame_Shift_Del	DEL	ENST00000306084.6	hg19	CCDS42414.1																																																																																			.	.	.	none		0.562	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1			-	9886730	A	-	9886730	7	5	20	1	0	1	0	1	0	0	0	0	16809	304	11	0	260	0	TXNDC2	18	9886730	Frame_Shift_Del	DEL	A	TCGA-2Z-A9JQ-01A-11D-A42J-10		9886730	68190518	72	1387											
ELANE	1991	hgsc.bcm.edu	37	chr19	856058	856058	+	Frame_Shift_Del	DEL	C	C	-																															gctctaccccgatgcctttgCcccggtggcacagtttgtaa																										TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr19:856058delC	ENST00000590230.1	+	6	839	c.698delC	c.(697-699)gccfs	p.A233fs	ELANE_ENST00000263621.1_Frame_Shift_Del_p.A233fs			P08246	ELNE_HUMAN	elastase, neutrophil expressed	233	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		A -> P (in SCN1). {ECO:0000269|PubMed:23463630}.		acute inflammatory response to antigenic stimulus (GO:0002438)|cellular calcium ion homeostasis (GO:0006874)|collagen catabolic process (GO:0030574)|defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of chemotaxis (GO:0050922)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neutrophil mediated killing of fungus (GO:0070947)|phagocytosis (GO:0006909)|positive regulation of immune response (GO:0050778)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein catabolic process (GO:0030163)|proteolysis (GO:0006508)|response to lipopolysaccharide (GO:0032496)|response to UV (GO:0009411)|response to yeast (GO:0001878)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)|transcriptional repressor complex (GO:0017053)	cytokine binding (GO:0019955)|endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|peptidase activity (GO:0008233)|protease binding (GO:0002020)|RNA polymerase II transcription corepressor activity (GO:0001106)|serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(1)|lung(4)|pancreas(1)	13					Alpha-1-proteinase inhibitor(DB00058)|Filgrastim(DB00099)|Pegfilgrastim(DB00019)	GATGCCTTTGCCCCGGTGGCA	0.657																																					p.A233fs		Atlas-Indel,Pindel	.											ELANE,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	ELANE	27	.	0			c.697delG						PASS	.						86	96	93					19																	856058		2203	4300	6503	SO:0001589	frameshift_variant	1991	exon5			.		CCDS12045.1	19p13.3	2014-09-17	2009-05-05	2009-05-05	ENSG00000197561	ENSG00000197561	3.4.21.37		3309	protein-coding gene	gene with protein product	"neutrophil elastase", "leukocyte elastase", "medullasin"	130130	"elastase 2, neutrophil"	ELA2		2902087	Standard	XM_005259517		Approved	NE, HNE, HLE	uc002lqb.3	P08246		ENST00000590230.1:c.698delC	chr19.hg19:g.856058delC	ENSP00000466090:p.Ala233fs	207.0	0.0	0		129.0	70.0	0.542636	NM_001972	P09649|Q6B0D9|Q6LDP5	Frame_Shift_Del	DEL	ENST00000590230.1	hg19	CCDS12045.1																																																																																			.	.	.	none		0.657	ELANE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457890.2	NM_001972		-	856058	C	-	856058	7	5	20	1	0	1	0	1	0	0	0	0	5050	739	26	0	716	0	ELANE	19	856058	Frame_Shift_Del	DEL	C	TCGA-2Z-A9JQ-01A-11D-A42J-10		856058	58272925	73	1388											
KIAA1683	80726	hgsc.bcm.edu	37	chr19	18378080	18378080	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctaccaggatgttcttgaaGgcctggctctcgaccacagc	8	10	10	13	1	3	1	0	1	3	0	4	3	3	2	3	3	2	2	3	3	2	3			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr19:18378080G>A	ENST00000600328.3	-	3	463	c.270C>T	c.(268-270)gcC>gcT	p.A90A	KIAA1683_ENST00000600359.3_Silent_p.A44A|KIAA1683_ENST00000392413.4_Silent_p.A90A			Q9H0B3	K1683_HUMAN	KIAA1683	90						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						TGTTCTTGAAGGCCTGGCTCT	0.632																																					p.A90A		Atlas-SNP	.											.	KIAA1683	190	.	0			c.C270T						PASS	.						81	79	80					19																	18378080		2203	4300	6503	SO:0001819	synonymous_variant	80726	exon3			CTTGAAGGCCTGG	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.270C>T	chr19.hg19:g.18378080G>A		101.0	0.0	.		91.0	43.0	.	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Silent	SNP	ENST00000600328.3	hg19	CCDS32958.1																																																																																			.	.	.	none		0.632	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3			A	18378080	G	A	18378080	2	1	20	1	0	0	0	0	0	0	0	1	8258	987	35	2		2	KIAA1683	19	18378080	Silent	SNP	G	TCGA-2Z-A9JQ-01A-11D-A42J-10	17522022	18378080	40750903	74	1389											
PSG8	440533	hgsc.bcm.edu	37	chr19	43258514	43258514	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttactgtcatggatttggagCtttccttgccagtggctgag	6	15	12	8	0	1	1	1	1	0	0	2	3	2	3	2	3	3	2	2	3	1	4	rs200488282	byFrequency	TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr19:43258514C>T	ENST00000306511.4	-	5	1311	c.1214G>A	c.(1213-1215)aGc>aAc	p.S405N	PSG8_ENST00000401467.2_Missense_Mutation_p.S312N|PSG8_ENST00000406636.3_Missense_Mutation_p.S283N|PSG8_ENST00000404209.4_Missense_Mutation_p.S405N|PSG8_ENST00000600709.1_5'UTR	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	405	Ig-like C2-type 3.					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)				GGATTTGGAGCTTTCCTTGCC	0.468																																					p.S405N		Atlas-SNP	.											.	PSG8	101	.	0			c.G1214A						PASS	.						198	211	207					19																	43258514		2203	4299	6502	SO:0001583	missense	440533	exon5			TTGGAGCTTTCCT	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.1214G>A	chr19.hg19:g.43258514C>T	ENSP00000305005:p.Ser405Asn	64.0	0.0	.		90.0	38.0	.	NM_001130167	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Missense_Mutation	SNP	ENST00000306511.4	hg19	CCDS33037.1	.	.	.	.	.	.	.	.	.	.	N	3.401	-0.122166	0.06795	.	.	ENSG00000124467	ENST00000404209;ENST00000292109;ENST00000406636;ENST00000401467;ENST00000426252;ENST00000407488;ENST00000306511	T;T;T;T	0.12361	2.69;2.69;2.69;2.69	1.62	-1.25	0.09405	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.09202	0.0227	L	0.41961	1.31	0.09310	N	1	B;B;B;B;B;B	0.19583	0.004;0.037;0.003;0.011;0.001;0.001	B;B;B;B;B;B	0.21360	0.018;0.034;0.012;0.023;0.005;0.008	T	0.41502	-0.9505	9	0.20519	T	0.43	.	2.8307	0.05499	0.2599:0.5561:0.0:0.1841	.	283;312;405;312;405;405	Q9UQ74-2;B5MCQ0;Q9UQ74;E7ENH0;Q9UQ74-3;A5PKV3	.;.;PSG8_HUMAN;.;.;.	N	405;187;283;312;217;312;405	ENSP00000385869:S405N;ENSP00000385081:S283N;ENSP00000386090:S312N;ENSP00000305005:S405N	ENSP00000292109:S187N	S	-	2	0	PSG8	47950354	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.061000	0.01391	-0.535000	0.06307	-2.322000	0.00252	AGC	.	C|0.999;A|0.001	.	alt		0.468	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1			T	43258514	C	T	43258514	3	4	20	1	0	0	0	0	1	0	0	0	12671	797	28	2	91	2	PSG8	19	43258514	Missense_Mutation	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	24880434	43258514	15870469	75	1390											
RTN2	6253	hgsc.bcm.edu	37	chr19	46000066	46000066	+	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	tcactgcagtgggcgaagacCggcaggacctgccccatggc	8	5	14	14	2	1	1	1	0	0	1	1	3	1	2	4	4	2	2	4	4	1	0			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr19:46000066C>A	ENST00000245923.4	-	1	253	c.18G>T	c.(16-18)ccG>ccT	p.P6P	RTN2_ENST00000344680.4_Silent_p.P6P|PPM1N_ENST00000396737.2_5'Flank|PPM1N_ENST00000324688.4_5'Flank|PPM1N_ENST00000396735.2_5'Flank|PPM1N_ENST00000456399.2_5'Flank|RTN2_ENST00000589384.1_5'Flank|RTN2_ENST00000590526.1_5'UTR|PPM1N_ENST00000401705.1_Intron|PPM1N_ENST00000451287.2_5'Flank	NM_005619.4	NP_005610.1	O75298	RTN2_HUMAN	reticulon 2	6					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)		GGGCGAAGACCGGCAGGACCT	0.741																																					p.P6P		Atlas-SNP	.											.	RTN2	45	.	0			c.G18T						PASS	.						8	10	10					19																	46000066		2184	4277	6461	SO:0001819	synonymous_variant	6253	exon1			GAAGACCGGCAGG	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.18G>T	chr19.hg19:g.46000066C>A		181.0	0.0	.		148.0	62.0	.	NM_206900	O60509|Q7RTM6|Q7RTN1|Q7RTN2	Silent	SNP	ENST00000245923.4	hg19	CCDS12665.1																																																																																			.	.	.	none		0.741	RTN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459574.1	NM_005619		A	46000066	C	A	46000066	2	1	20	1	0	0	0	0	0	0	0	1	13739	639	23	4		4	RTN2	19	46000066	Silent	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	2741552	46000066	13128917	76	1391											
GLTSCR1	29998	hgsc.bcm.edu	37	chr19	48205073	48205073	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacgggccagatgaacggcAcggtggaccacccgccgcct	8	3	13	17	5	0	2	0	1	0	1	0	3	0	3	6	4	1	1	6	4	1	0			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr19:48205073A>G	ENST00000396720.3	+	15	4278	c.4084A>G	c.(4084-4086)Acg>Gcg	p.T1362A	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	1362										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)		GATGAACGGCACGGTGGACCA	0.776																																					p.T1362A		Atlas-SNP	.											.	GLTSCR1	79	.	0			c.A4084G						PASS	.						1	1	1					19																	48205073		728	2032	2760	SO:0001583	missense	29998	exon15			AACGGCACGGTGG	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.4084A>G	chr19.hg19:g.48205073A>G	ENSP00000379946:p.Thr1362Ala	60.0	0.0	.		44.0	16.0	.	NM_015711	A8MW01	Missense_Mutation	SNP	ENST00000396720.3	hg19	CCDS46134.1	.	.	.	.	.	.	.	.	.	.	A	9.937	1.216338	0.22373	.	.	ENSG00000063169	ENST00000396720	T	0.48522	0.81	2.94	1.86	0.25419	.	.	.	.	.	T	0.45915	0.1366	L	0.32530	0.975	0.30752	N	0.744981	D	0.54964	0.969	P	0.53593	0.73	T	0.49661	-0.8916	9	0.87932	D	0	.	7.9097	0.29782	0.7901:0.2099:0.0:0.0	.	1362	Q9NZM4	GSCR1_HUMAN	A	1362	ENSP00000379946:T1362A	ENSP00000379946:T1362A	T	+	1	0	GLTSCR1	52896885	0.043000	0.20138	0.165000	0.22776	0.352000	0.29268	0.917000	0.28665	0.209000	0.20645	0.260000	0.18958	ACG	.	.	.	none		0.776	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711		G	48205073	A	G	48205073	3	3	20	1	0	0	0	0	1	0	0	0	6481	159	6	3	4134	3	GLTSCR1	19	48205073	Missense_Mutation	SNP	A	TCGA-2Z-A9JQ-01A-11D-A42J-10	2205007	48205073	10923910	77	1392											
NUCB1	4924	hgsc.bcm.edu	37	chr19	49404086	49404086	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggccccgaggaaccctcctTctgttgccgctgctgctgct	3	10	12	16	2	1	0	0	0	1	0	2	2	2	1	5	2	5	5	5	2	1	2			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr19:49404086T>C	ENST00000405315.4	+	2	367	c.33T>C	c.(31-33)ctT>ctC	p.L11L	NUCB1_ENST00000407032.1_Silent_p.L11L|NUCB1_ENST00000263273.5_Silent_p.L11L|TULP2_ENST00000221399.3_5'Flank|NUCB1_ENST00000485798.1_Intron	NM_006184.5	NP_006175.2	Q02818	NUCB1_HUMAN	nucleobindin 1	11						endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			cervix(1)|endometrium(4)|large_intestine(4)|lung(8)	17		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000171)|all cancers(93;0.000333)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0244)		GAACCCTCCTTctgttgccgc	0.647																																					p.L11L		Atlas-SNP	.											.	NUCB1	44	.	0			c.T33C						PASS	.						64	49	54					19																	49404086		2203	4300	6503	SO:0001819	synonymous_variant	4924	exon2			CCTCCTTCTGTTG	BC002356	CCDS12740.1	19q13.33	2013-01-10			ENSG00000104805	ENSG00000104805		"EF-hand domain containing"	8043	protein-coding gene	gene with protein product		601323				8661046	Standard	NM_006184		Approved	NUC, Calnuc	uc002plb.4	Q02818	OTTHUMG00000152514	ENST00000405315.4:c.33T>C	chr19.hg19:g.49404086T>C		68.0	0.0	.		42.0	14.0	.	NM_006184	B2RD64|Q15838|Q7Z4J7|Q9BUR1	Silent	SNP	ENST00000405315.4	hg19	CCDS12740.1	.	.	.	.	.	.	.	.	.	.	T	2.581	-0.297309	0.05532	.	.	ENSG00000104805	ENST00000424608	.	.	.	3.96	-7.43	0.01383	.	.	.	.	.	T	0.25568	0.0622	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.31752	-0.9932	4	.	.	.	.	7.9811	0.30183	0.0:0.2298:0.1296:0.6406	.	.	.	.	S	11	.	.	F	+	2	0	NUCB1	54095898	0.000000	0.05858	0.000000	0.03702	0.093000	0.18481	-1.333000	0.02667	-1.430000	0.01985	-0.463000	0.05309	TTC	.	.	.	none		0.647	NUCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326545.2	NM_006184		C	49404086	T	C	49404086	2	2	20	1	0	0	0	0	0	0	0	1	10725	1770	62	3		3	NUCB1	19	49404086	Silent	SNP	T	TCGA-2Z-A9JQ-01A-11D-A42J-10	1199013	49404086	9724897	78	1393											
ZIM3	114026	hgsc.bcm.edu	37	chr19	57647015	57647015	+	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	tttgacttctgcttgtaggcAtttccacagttctcacattt	7	18	6	10	0	2	1	1	1	2	0	4	1	3	1	1	1	1	4	1	1	1	7	rs7251328	byFrequency	TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr19:57647015A>T	ENST00000269834.1	-	5	1075	c.690T>A	c.(688-690)aaT>aaA	p.N230K	U3_ENST00000516874.1_RNA	NM_052882.1	NP_443114.1	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	230					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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)		GCTTGTAGGCATTTCCACAGT	0.413																																					p.N230K		Atlas-SNP	.											.	ZIM3	107	.	0			c.T690A						PASS	.						142	139	140					19																	57647015		2203	4300	6503	SO:0001583	missense	114026	exon5			GTAGGCATTTCCA	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.690T>A	chr19.hg19:g.57647015A>T	ENSP00000269834:p.Asn230Lys	79.0	0.0	.		51.0	29.0	.	NM_052882	Q14CA6	Missense_Mutation	SNP	ENST00000269834.1	hg19	CCDS33125.1	.	.	.	.	.	.	.	.	.	.	G	0.129	-1.116394	0.01799	.	.	ENSG00000141946	ENST00000269834	T	0.07021	3.23	1.97	-0.339	0.12647	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00845	0.0028	N	0.00014	-2.91	0.46078	P	0.0011440000000000339	B	0.12630	0.006	B	0.18871	0.023	T	0.42515	-0.9447	8	0.02654	T	1	.	0.6984	0.00903	0.1873:0.141:0.2128:0.4589	.	230	Q96PE6	ZIM3_HUMAN	K	230	ENSP00000269834:N230K	ENSP00000269834:N230K	N	-	3	2	ZIM3	62338827	0.000000	0.05858	0.293000	0.24932	0.329000	0.28539	-1.080000	0.03407	-0.562000	0.06086	-0.642000	0.03964	AAT	.	A|0.387;G|0.613	.	alt		0.413	ZIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465078.1			T	57647015	A	T	57647015	3	4	20	1	0	0	0	0	1	0	0	0	17697	214	8	5	732	5	ZIM3	19	57647015	Missense_Mutation	SNP	A	TCGA-2Z-A9JQ-01A-11D-A42J-10	8242929	57647015	1481968	79	1394											
ZNF343	79175	hgsc.bcm.edu	37	chr20	2473416	2473416	+	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	tcctctgctctggactcagtCtcttccattctgcttctgtg	3	17	7	14	0	6	0	1	0	5	0	9	1	8	1	2	1	2	2	2	1	0	3	rs145750724		TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr20:2473416C>T	ENST00000278772.4	-	5	720	c.233G>A	c.(232-234)aGa>aAa	p.R78K	RP4-734P14.4_ENST00000461548.1_Missense_Mutation_p.R78K|ZNF343_ENST00000381253.1_Missense_Mutation_p.R78K|ZNF343_ENST00000358413.2_Missense_Mutation_p.R78K	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	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)			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						TGGACTCAGTCTCTTCCATTC	0.413																																					p.R78K		Atlas-SNP	.											.	ZNF343	47	.	0			c.G233A						PASS	.						224	207	213					20																	2473416		2203	4300	6503	SO:0001583	missense	79175	exon5			CTCAGTCTCTTCC	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.233G>A	chr20.hg19:g.2473416C>T	ENSP00000278772:p.Arg78Lys	39.0	0.0	.		38.0	17.0	.	NM_024325	Q5JXU8|Q5JXU9|Q8N8F2|Q96EX8|Q96NA5|Q9BQB0	Missense_Mutation	SNP	ENST00000278772.4	hg19	CCDS13028.1	.	.	.	.	.	.	.	.	.	.	C	14.85	2.658284	0.47467	.	.	ENSG00000088876	ENST00000278772;ENST00000445484;ENST00000381253;ENST00000358413;ENST00000421216	T;T;T;T;T	0.01725	4.67;4.67;4.67;4.67;4.67	3.96	-0.545	0.11843	Krueppel-associated box (4);	.	.	.	.	T	0.01387	0.0045	L	0.39020	1.185	0.09310	N	1	P	0.42785	0.79	B	0.36335	0.222	T	0.49370	-0.8947	9	0.23891	T	0.37	.	4.6349	0.12520	0.3084:0.5313:0.0:0.1602	.	78	Q6P1L6	ZN343_HUMAN	K	78	ENSP00000278772:R78K;ENSP00000399682:R78K;ENSP00000370652:R78K;ENSP00000351188:R78K;ENSP00000416488:R78K	ENSP00000443337:R78K	R	-	2	0	ZNF343	2421416	0.000000	0.05858	0.000000	0.03702	0.923000	0.55619	-0.408000	0.07169	-0.156000	0.11079	0.585000	0.79938	AGA	.	C|1.000;G|0.000	.	alt		0.413	ZNF343-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077617.1	NM_024325		T	2473416	C	T	2473416	3	4	20	1	0	0	0	0	1	0	0	0	17870	913	32	2	1574	2	ZNF343	20	2473416	Missense_Mutation	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10		2473416	60552104	80	1395											
DHX35	60625	hgsc.bcm.edu	37	chr20	37653904	37653904	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctaaatggtgtcaggaacAtttcctgaattacaagggtc	12	12	9	8	0	2	1	1	1	1	0	4	2	3	2	1	3	2	0	1	3	6	3			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr20:37653904A>G	ENST00000252011.3	+	18	1736	c.1703A>G	c.(1702-1704)cAt>cGt	p.H568R	DHX35_ENST00000373325.2_Missense_Mutation_p.H568R|DHX35_ENST00000373323.4_Missense_Mutation_p.H537R	NM_021931.3	NP_068750.2	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35	568					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	40		Myeloproliferative disorder(115;0.00878)				TGTCAGGAACATTTCCTGAAT	0.413																																					p.H568R		Atlas-SNP	.											.	DHX35	82	.	0			c.A1703G						PASS	.						209	210	209					20																	37653904		2203	4300	6503	SO:0001583	missense	60625	exon18			AGGAACATTTCCT	AK026412	CCDS13310.1, CCDS54463.1	20q11.22-q12	2003-06-13	2003-06-13	2003-06-13	ENSG00000101452	ENSG00000101452		"DEAH-boxes"	15861	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 35"	C20orf15, DDX35			Standard	NM_001190809		Approved	FLJ22759, KAIA0875	uc002xjh.3	Q9H5Z1	OTTHUMG00000032463	ENST00000252011.3:c.1703A>G	chr20.hg19:g.37653904A>G	ENSP00000252011:p.His568Arg	76.0	0.0	.		90.0	37.0	.	NM_021931	A2RTX3|B4E0J0|F5GXM6|Q5THR0|Q9H4H7|Q9H6T6	Missense_Mutation	SNP	ENST00000252011.3	hg19	CCDS13310.1	.	.	.	.	.	.	.	.	.	.	A	12.93	2.086830	0.36855	.	.	ENSG00000101452	ENST00000373325;ENST00000252011;ENST00000373323;ENST00000373321;ENST00000449559	T;T;T;T	0.32023	4.28;4.28;4.28;1.47	5.41	5.41	0.78517	.	0.046837	0.85682	D	0.000000	T	0.28962	0.0719	L	0.55990	1.75	0.80722	D	1	B;B	0.09022	0.001;0.002	B;B	0.09377	0.004;0.003	T	0.11767	-1.0574	10	0.72032	D	0.01	.	9.025	0.36224	0.9159:0.0:0.0841:0.0	.	537;568	F5GXM6;Q9H5Z1	.;DHX35_HUMAN	R	568;568;537;48;32	ENSP00000362422:H568R;ENSP00000252011:H568R;ENSP00000362420:H537R;ENSP00000397997:H32R	ENSP00000252011:H568R	H	+	2	0	DHX35	37087318	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.050000	0.76620	2.045000	0.60652	0.533000	0.62120	CAT	.	.	.	none		0.413	DHX35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079212.2	NM_021931		G	37653904	A	G	37653904	3	3	20	1	0	0	0	0	1	0	0	0	4510	217	8	3	1773	3	DHX35	20	37653904	Missense_Mutation	SNP	A	TCGA-2Z-A9JQ-01A-11D-A42J-10	35180488	37653904	25371616	81	1396											
CDH4	1002	hgsc.bcm.edu	37	chr20	60508065	60508065	+	Missense_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	atggtcctgctgtttgtcatGtggatgaagcggcgagagaa	9	11	15	6	2	1	2	1	1	0	1	2	5	2	3	1	3	2	2	1	3	2	1			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr20:60508065G>A	ENST00000360469.5	+	14	2350	c.2262G>A	c.(2260-2262)atG>atA	p.M754I	CDH4_ENST00000543233.1_Missense_Mutation_p.M680I	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	754					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)			TGTTTGTCATGTGGATGAAGC	0.602																																					p.M754I		Atlas-SNP	.											.	CDH4	172	.	0			c.G2262A						PASS	.						89	62	71					20																	60508065		2203	4300	6503	SO:0001583	missense	1002	exon14			TGTCATGTGGATG	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.2262G>A	chr20.hg19:g.60508065G>A	ENSP00000353656:p.Met754Ile	151.0	0.0	.		108.0	42.0	.	NM_001794	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Missense_Mutation	SNP	ENST00000360469.5	hg19	CCDS13488.1	.	.	.	.	.	.	.	.	.	.	G	15.91	2.972864	0.53614	.	.	ENSG00000179242	ENST00000360469;ENST00000536643;ENST00000543233	T;T	0.54071	0.59;0.6	4.18	3.2	0.36748	.	0.300446	0.31233	N	0.008008	T	0.40619	0.1124	L	0.47716	1.5	0.30164	N	0.801882	B	0.06786	0.001	B	0.04013	0.001	T	0.28004	-1.0057	9	.	.	.	.	8.2275	0.31577	0.2526:0.0:0.7474:0.0	.	754	P55283	CADH4_HUMAN	I	754;662;680	ENSP00000353656:M754I;ENSP00000443301:M680I	.	M	+	3	0	CDH4	59941460	1.000000	0.71417	0.986000	0.45419	0.929000	0.56500	2.612000	0.46343	2.027000	0.59764	0.563000	0.77884	ATG	.	.	.	none		0.602	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794		A	60508065	G	A	60508065	3	1	20	1	0	0	0	0	1	0	0	0	3114	1377	48	2	2316	2	CDH4	20	60508065	Missense_Mutation	SNP	G	TCGA-2Z-A9JQ-01A-11D-A42J-10	22854161	60508065	2517455	82	1397											
TPTE	7179	hgsc.bcm.edu	37	chr21	10959746	10959746	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcaaactgacttactcataTgaagcaacattttcagcatc	14	13	4	10	0	3	2	3	2	0	0	4	2	3	2	0	0	5	2	0	0	5	5	rs369891740		TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr21:10959746T>C	ENST00000361285.4	-	8	557	c.228A>G	c.(226-228)tcA>tcG	p.S76S	TPTE_ENST00000342420.5_Intron|TPTE_ENST00000298232.7_Silent_p.S58S|TPTE_ENST00000415664.2_5'UTR	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	76					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)		CTTACTCATATGAAGCAACAT	0.373																																					p.S76S		Atlas-SNP	.											.	TPTE	513	.	0			c.A228G						PASS	.	T	,,	3,4403	4.2+/-10.8	0,3,2200	70	71	71		174,,228	0.2	0	21		71	0,8590		0,0,4295	no	coding-synonymous,intron,coding-synonymous	TPTE	NM_199259.2,NM_199260.2,NM_199261.2	,,	0,3,6495	CC,CT,TT		0.0,0.0681,0.0231	,,	58/534,,76/552	10959746	3,12993	2203	4295	6498	SO:0001819	synonymous_variant	7179	exon8			CTCATATGAAGCA	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.228A>G	chr21.hg19:g.10959746T>C		510.0	0.0	.		610.0	151.0	.	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Silent	SNP	ENST00000361285.4	hg19	CCDS13560.2																																																																																			.	.	.	weak		0.373	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1			C	10959746	T	C	10959746	2	2	20	1	0	0	0	0	0	0	0	1	16442	1451	51	3		3	TPTE	21	10959746	Silent	SNP	T	TCGA-2Z-A9JQ-01A-11D-A42J-10		10959746	37170149	83	1398											
DSCAM	1826	hgsc.bcm.edu	37	chr21	41725475	41725475	+	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	agctgcctgagtccgaggggCgaatgttctcaatgagcagc	9	8	14	10	2	1	2	1	2	1	0	3	4	2	2	2	2	4	3	2	2	2	1	rs140655651	byFrequency	TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chr21:41725475C>A	ENST00000400454.1	-	5	1328	c.851G>T	c.(850-852)cGc>cTc	p.R284L		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	284	Ig-like C2-type 3.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				GTCCGAGGGGCGAATGTTCTC	0.542																																					p.R284L	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.G851T						PASS	.						81	79	80					21																	41725475		1967	4152	6119	SO:0001583	missense	1826	exon5			GAGGGGCGAATGT	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.851G>T	chr21.hg19:g.41725475C>A	ENSP00000383303:p.Arg284Leu	63.0	0.0	.		67.0	27.0	.	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	hg19	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.493198	0.84962	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.67523	1.59;-0.27	5.53	5.53	0.82687	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.062950	0.64402	D	0.000002	T	0.57344	0.2047	L	0.34521	1.04	0.53005	D	0.999968	P	0.44946	0.846	B	0.36666	0.23	T	0.62201	-0.6904	10	0.49607	T	0.09	.	19.7967	0.96487	0.0:1.0:0.0:0.0	.	284	O60469	DSCAM_HUMAN	L	284;36	ENSP00000383303:R284L;ENSP00000385342:R36L	ENSP00000383303:R284L	R	-	2	0	DSCAM	40647345	1.000000	0.71417	0.691000	0.30163	0.995000	0.86356	4.422000	0.59854	2.744000	0.94065	0.655000	0.94253	CGC	.	C|0.999;T|0.001	.	alt		0.542	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		A	41725475	C	A	41725475	3	1	20	1	0	0	0	0	1	0	0	0	4770	768	27	4	5303	4	DSCAM	21	41725475	Missense_Mutation	SNP	C	TCGA-2Z-A9JQ-01A-11D-A42J-10	30765729	41725475	6404420	84	1399											
EGFL6	25975	hgsc.bcm.edu	37	chrX	13588004	13588004	+	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	cctctgccctggagccttgcGctcccgctgctgctctcctg	1	11	10	19	2	2	0	0	0	2	0	4	1	3	1	5	1	5	4	5	1	0	1			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chrX:13588004G>T	ENST00000361306.1	+	1	281	c.24G>T	c.(22-24)gcG>gcT	p.A8A	EGFL6_ENST00000380602.3_Silent_p.A8A	NM_001167890.1|NM_015507.3	NP_001161362.1|NP_056322.2	Q8IUX8	EGFL6_HUMAN	EGF-like-domain, multiple 6	8					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						GGAGCCTTGCGCTCCCGCTGC	0.706																																					p.A8A		Atlas-SNP	.											.	EGFL6	111	.	0			c.G24T						PASS	.						77	60	66					X																	13588004		2203	4300	6503	SO:0001819	synonymous_variant	25975	exon1			CCTTGCGCTCCCG	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.24G>T	chrX.hg19:g.13588004G>T		116.0	0.0	.		87.0	4.0	.	NM_001167890	B2RCB1|Q6UXJ1|Q8NBV0|Q8WYG3|Q9NY67|Q9NZL7|Q9UFK6	Silent	SNP	ENST00000361306.1	hg19	CCDS14155.1																																																																																			.	.	.	none		0.706	EGFL6-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055800.1	NM_015507		T	13588004	G	T	13588004	2	4	20	1	0	0	0	0	0	0	0	1	4965	1074	38	4		4	EGFL6	23	13588004	Silent	SNP	G	TCGA-2Z-A9JQ-01A-11D-A42J-10		13588004	141682556	85	1400											
FAM122B	159090	hgsc.bcm.edu	37	chrX	133906199	133906199	+	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	gagagatcatccatcaagatGaacgaagagcatgaattgga	17	7	11	6	1	2	5	2	2	0	3	3	9	3	6	1	1	2	1	1	1	4	1			TCGA-2Z-A9JQ-01A-11D-A42J-10	TCGA-2Z-A9JQ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c0bed76f-49c1-44d5-b9eb-c8ef1b6c63bc	72b21503-f17e-4728-8b9c-d0b550371302	g.chrX:133906199G>A	ENST00000370790.1	-	9	1642	c.714C>T	c.(712-714)ttC>ttT	p.F238F	FAM122B_ENST00000493333.1_5'UTR|FAM122B_ENST00000486347.1_Silent_p.F239F|FAM122B_ENST00000298090.6_Intron|FAM122B_ENST00000343004.5_Silent_p.F257F	NM_001166599.2|NM_145284.5	NP_001160071.1|NP_660327.2	Q7Z309	F122B_HUMAN	family with sequence similarity 122B	238										breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|skin(1)	6	Acute lymphoblastic leukemia(192;0.000127)					CCATCAAGATGAACGAAGAGC	0.468																																					p.F257F		Atlas-SNP	.											.	FAM122B	20	.	0			c.C771T						PASS	.						128	98	109					X																	133906199		2203	4300	6503	SO:0001819	synonymous_variant	159090	exon10			CAAGATGAACGAA	BX538218	CCDS14643.1, CCDS55497.1, CCDS55498.1	Xq26.3	2008-02-05			ENSG00000156504	ENSG00000156504			30490	protein-coding gene	gene with protein product						12477932	Standard	NM_145284		Approved	DKFZp686L20116, RP11-308B5.5	uc004exq.3	Q7Z309	OTTHUMG00000022461	ENST00000370790.1:c.714C>T	chrX.hg19:g.133906199G>A		87.0	0.0	.		77.0	61.0	.	NM_001170756	A8K902|Q6PIM2|Q6ZU47|Q6ZV64|Q6ZVE4|Q8TB75	Silent	SNP	ENST00000370790.1	hg19	CCDS55497.1																																																																																			.	.	.	none		0.468	FAM122B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058382.1	NM_145284		A	133906199	G	A	133906199	2	1	20	1	0	0	0	0	0	0	0	1	5424	1281	45	2		2	FAM122B	23	133906199	Silent	SNP	G	TCGA-2Z-A9JQ-01A-11D-A42J-10	120318195	133906199	21364361	86	1401											
PGD	5226	hgsc.bcm.edu	37	chr1	10473152	10473152	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaataagacagagctagacTcattcctgattgaaatcaca	16	9	8	8	0	2	5	2	2	0	3	3	6	3	6	1	1	1	1	1	1	4	4			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr1:10473152T>C	ENST00000270776.8	+	8	726	c.688T>C	c.(688-690)Tca>Cca	p.S230P	PGD_ENST00000541529.1_Missense_Mutation_p.S208P|PGD_ENST00000538557.1_Missense_Mutation_p.S217P	NM_002631.2	NP_002622.2	P52209	6PGD_HUMAN	phosphogluconate dehydrogenase	230					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)	AGAGCTAGACTCATTCCTGAT	0.507																																					p.S230P		Atlas-SNP	.											.	PGD	39	.	0			c.T688C						PASS	.						87	82	83					1																	10473152		2203	4300	6503	SO:0001583	missense	5226	exon8			CTAGACTCATTCC	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.688T>C	chr1.hg19:g.10473152T>C	ENSP00000270776:p.Ser230Pro	56.0	0.0	.		49.0	12.0	.	NM_002631	A8K2Y9|B4DQJ8|Q9BWD8	Missense_Mutation	SNP	ENST00000270776.8	hg19	CCDS113.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.278245	0.80692	.	.	ENSG00000142657	ENST00000541529;ENST00000543846;ENST00000270776;ENST00000538557	T;T;T	0.60797	0.16;0.16;0.16	5.06	5.06	0.68205	6-phosphogluconate dehydrogenase, C-terminal (1);Dehydrogenase, multihelical (1);6-phosphogluconate dehydrogenase, C-terminal-like (1);	0.000000	0.85682	D	0.000000	D	0.86053	0.5841	H	0.99182	4.46	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	0.92004	0.5613	10	0.87932	D	0	-15.9984	15.1463	0.72653	0.0:0.0:0.0:1.0	.	208;230;230	F5H7U0;A8K2Y9;P52209	.;.;6PGD_HUMAN	P	208;176;230;217	ENSP00000442285:S208P;ENSP00000270776:S230P;ENSP00000437822:S217P	ENSP00000270776:S230P	S	+	1	0	PGD	10395739	1.000000	0.71417	0.995000	0.50966	0.903000	0.53119	6.048000	0.71046	2.043000	0.60533	0.519000	0.50382	TCA	.	.	.	none		0.507	PGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005398.1	NM_002631		C	10473152	T	C	10473152	3	2	21	1	0	0	0	0	1	0	0	0	11794	1551	54	3	718	3	PGD	1	10473152	Missense_Mutation	SNP	T	TCGA-2Z-A9JR-01A-12D-A42J-10		10473152	238777469	1	1402											
UBR4	23352	hgsc.bcm.edu	37	chr1	19491316	19491316	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttttcccgaacaatgtatgtGgtcagtaactgcagcagctg	10	12	10	9	1	1	0	1	0	0	0	2	1	2	0	1	1	5	5	1	1	4	4			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr1:19491316G>A	ENST00000375254.3	-	32	4515	c.4488C>T	c.(4486-4488)acC>acT	p.T1496T	UBR4_ENST00000375217.2_Silent_p.T1496T|UBR4_ENST00000375226.2_Silent_p.T1496T|UBR4_ENST00000375267.2_Silent_p.T1496T	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	1496					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)	p.T1496T(1)		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)		CAATGTATGTGGTCAGTAACT	0.488																																					p.T1496T		Atlas-SNP	.											UBR4,NS,carcinoma,0,1	UBR4	415	.	1	Substitution - coding silent(1)	lung(1)	c.C4488T						PASS	.						115	113	114					1																	19491316		2203	4300	6503	SO:0001819	synonymous_variant	23352	exon32			GTATGTGGTCAGT	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.4488C>T	chr1.hg19:g.19491316G>A		54.0	0.0	.		64.0	19.0	.	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	hg19	CCDS189.1																																																																																			.	.	.	none		0.488	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		A	19491316	G	A	19491316	2	1	21	1	0	0	0	0	0	0	0	1	16916	1335	47	2		2	UBR4	1	19491316	Silent	SNP	G	TCGA-2Z-A9JR-01A-12D-A42J-10	9018164	19491316	229759305	2	1403											
CDKN2C	1031	hgsc.bcm.edu	37	chr1	51439795	51439795	+	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	ggccacctccgggtggtggaGttcctggtgaagcacacggc	6	7	16	12	2	0	1	0	1	0	0	2	2	2	2	4	6	1	2	4	6	1	1			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr1:51439795G>A	ENST00000262662.1	+	4	2394	c.360G>A	c.(358-360)gaG>gaA	p.E120E	CDKN2C_ENST00000371761.3_Silent_p.E120E|CDKN2C_ENST00000396148.1_Silent_p.E120E			P42773	CDN2C_HUMAN	cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)	120					cell cycle arrest (GO:0007050)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of phosphorylation (GO:0042326)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|oligodendrocyte differentiation (GO:0048709)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|protein kinase binding (GO:0019901)	p.0?(11)|p.?(1)		central_nervous_system(8)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|thyroid(1)	23				GBM - Glioblastoma multiforme(3;3.61e-13)|all cancers(3;0.00151)		GGGTGGTGGAGTTCCTGGTGA	0.542			D		"glioma, MM"																																p.E120E	Melanoma(47;50 1155 4767 22863 47597)	Atlas-SNP	.		Rec	yes		1	1p32	1031	"cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)"		"O, L"	.	CDKN2C	24	.	12	Whole gene deletion(11)|Unknown(1)	central_nervous_system(6)|haematopoietic_and_lymphoid_tissue(5)|thyroid(1)	c.G360A						PASS	.						62	62	62					1																	51439795		2203	4300	6503	SO:0001819	synonymous_variant	1031	exon3			GGTGGAGTTCCTG	BC000598	CCDS555.1	1p32.3	2013-01-10			ENSG00000123080	ENSG00000123080		"Ankyrin repeat domain containing"	1789	protein-coding gene	gene with protein product		603369				8001816, 9636670	Standard	NM_001262		Approved	INK4C, p18	uc001csg.3	P42773	OTTHUMG00000008046	ENST00000262662.1:c.360G>A	chr1.hg19:g.51439795G>A		89.0	0.0	.		85.0	26.0	.	NM_001262	Q8TB83	Silent	SNP	ENST00000262662.1	hg19	CCDS555.1																																																																																			.	.	.	none		0.542	CDKN2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022058.1	NM_001262		A	51439795	G	A	51439795	2	1	21	1	0	0	0	0	0	0	0	1	3167	1020	36	2		2	CDKN2C	1	51439795	Silent	SNP	G	TCGA-2Z-A9JR-01A-12D-A42J-10	31948479	51439795	197810826	3	1404											
MSH4	4438	hgsc.bcm.edu	37	chr1	76282215	76282218	+	Frame_Shift_Del	DEL	AATA	AATA	-																															aaaaccttgaattgttaattAataatcaagactataggtaa																								rs139179365		TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	AATA	AATA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr1:76282215_76282218delAATA	ENST00000263187.3	+	6	1077_1080	c.973_976delAATA	c.(973-978)aataatfs	p.NN325fs		NM_002440.3	NP_002431.2	O15457	MSH4_HUMAN	mutS homolog 4	325					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|female gamete generation (GO:0007292)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						ATTGTTAATTAATAATCAAGACTA	0.279								Mismatch excision repair (MMR)																													p.324_325del		Pindel	.											.	MSH4	147	.	0			c.972_975del						PASS	.																																			SO:0001589	frameshift_variant	4438	exon6			.	U89293	CCDS670.1	1p31	2013-09-12	2013-09-12		ENSG00000057468	ENSG00000057468			7327	protein-coding gene	gene with protein product		602105	"mutS (E. coli) homolog 4", "mutS homolog 4 (E. coli)"			9299235	Standard	NM_002440		Approved		uc001dhd.2	O15457	OTTHUMG00000009788	ENST00000263187.3:c.973_976delAATA	chr1.hg19:g.76282215_76282218delAATA	ENSP00000263187:p.Asn325fs	254.0	0.0	.		320.0	66.0	0.206	NM_002440	Q5T4U6|Q8NEB3|Q9UNP8	Frame_Shift_Del	DEL	ENST00000263187.3	hg19	CCDS670.1																																																																																			.	.	.	none		0.279	MSH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026983.1	NM_002440		-	76282218	AATA	-	76282215	7	5	21	1	0	1	0	1	0	0	0	0	9879	362	13	0	995	0	MSH4	1	76282215	Frame_Shift_Del	DEL	AATA	TCGA-2Z-A9JR-01A-12D-A42J-10	24842420	76282215	172968406	4	1405											
RPRD2	23248	hgsc.bcm.edu	37	chr1	150390180	150390180	+	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	atcatttgctgatgtacttcCtgaagcagctgctctagtga	9	14	9	9	0	2	3	1	3	1	0	3	3	3	3	1	0	5	5	1	0	3	4			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr1:150390180C>T	ENST00000369068.4	+	2	318	c.314C>T	c.(313-315)cCt>cTt	p.P105L	RPRD2_ENST00000492220.1_3'UTR|RPRD2_ENST00000369067.3_Missense_Mutation_p.P105L|RPRD2_ENST00000401000.4_Missense_Mutation_p.P105L|RPRD2_ENST00000539519.1_Missense_Mutation_p.P105L	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	105	CID. {ECO:0000255|PROSITE- ProRule:PRU00724}.					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						GATGTACTTCCTGAAGCAGCT	0.358																																					p.P105L		Atlas-SNP	.											.	RPRD2	189	.	0			c.C314T						PASS	.						138	128	131					1																	150390180		1853	4106	5959	SO:0001583	missense	23248	exon2			TACTTCCTGAAGC	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.314C>T	chr1.hg19:g.150390180C>T	ENSP00000358064:p.Pro105Leu	77.0	0.0	.		66.0	19.0	.	NM_015203	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Missense_Mutation	SNP	ENST00000369068.4	hg19	CCDS44216.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.026331	0.93518	.	.	ENSG00000163125	ENST00000401000;ENST00000539519;ENST00000369067;ENST00000369068	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	5.52	5.52	0.82312	ENTH/VHS (2);RNA polymerase II, large subunit, CTD (2);Domain of unknown function DUF618 (1);	0.051483	0.85682	N	0.000000	T	0.57844	0.2081	M	0.67517	2.055	0.80722	D	1	D;D;D	0.89917	0.99;0.997;1.0	D;D;D	0.87578	0.933;0.953;0.998	T	0.52071	-0.8624	10	0.39692	T	0.17	-10.8804	19.3847	0.94551	0.0:1.0:0.0:0.0	.	105;105;105	B4E2Q6;Q5VT52;Q5VT52-3	.;RPRD2_HUMAN;.	L	105	ENSP00000383785:P105L;ENSP00000445482:P105L;ENSP00000358063:P105L;ENSP00000358064:P105L	ENSP00000358063:P105L	P	+	2	0	RPRD2	148656804	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.530000	0.67141	2.753000	0.94483	0.650000	0.86243	CCT	.	.	.	none		0.358	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203		T	150390180	C	T	150390180	3	4	21	1	0	0	0	0	1	0	0	0	13630	681	24	2	320	2	RPRD2	1	150390180	Missense_Mutation	SNP	C	TCGA-2Z-A9JR-01A-12D-A42J-10	74107965	150390180	98860441	5	1406											
NAV1	89796	hgsc.bcm.edu	37	chr1	201777104	201777104	+	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	cgaagttccttcaacaaagcGttcagtataaaaaaggggcc	15	8	9	9	2	2	0	2	0	0	0	3	1	3	0	2	2	2	3	2	2	7	5			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr1:201777104G>T	ENST00000367296.4	+	18	4092	c.3672G>T	c.(3670-3672)gcG>gcT	p.A1224A	IPO9-AS1_ENST00000413035.1_RNA|NAV1_ENST00000367295.1_Silent_p.A830A|NAV1_ENST00000367300.3_Silent_p.A1164A|MIR1231_ENST00000408101.1_RNA|NAV1_ENST00000367302.1_Silent_p.A1177A|NAV1_ENST00000367297.4_Silent_p.A1216A|NAV1_ENST00000295624.6_Silent_p.A1221A	NM_020443.4	NP_065176.3	Q8NEY1	NAV1_HUMAN	neuron navigator 1	1224					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						TCAACAAAGCGTTCAGTATAA	0.493																																					p.A1224A		Atlas-SNP	.											.	NAV1	143	.	0			c.G3672T						PASS	.						130	137	135					1																	201777104		2203	4300	6503	SO:0001819	synonymous_variant	89796	exon18			CAAAGCGTTCAGT	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.3672G>T	chr1.hg19:g.201777104G>T		138.0	0.0	.		155.0	49.0	.	NM_020443	A8MS88|Q5SVH1|Q5SVH2|Q5SVH3|Q5SVH7|Q5VUY9|Q8IVL2|Q96II1|Q9H7V9|Q9H9S9|Q9H9T5|Q9UGI1|Q9ULK7|Q9ULR9	Silent	SNP	ENST00000367296.4	hg19	CCDS1414.2	.	.	.	.	.	.	.	.	.	.	g	9.718	1.158971	0.21454	.	.	ENSG00000134369	ENST00000438083	.	.	.	5.28	4.36	0.52297	.	.	.	.	.	T	0.54759	0.1878	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52388	-0.8582	4	.	.	.	-33.8304	5.3519	0.16040	0.1465:0.6295:0.1462:0.0778	.	.	.	.	L	204	.	.	R	+	2	0	NAV1	200043727	0.966000	0.33281	1.000000	0.80357	0.959000	0.62525	0.174000	0.16743	1.223000	0.43536	-0.590000	0.04114	CGT	.	.	.	none		0.493	NAV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087013.1	NM_020443		T	201777104	G	T	201777104	2	4	21	1	0	0	0	0	0	0	0	1	10190	1132	40	4		4	NAV1	1	201777104	Silent	SNP	G	TCGA-2Z-A9JR-01A-12D-A42J-10	51386924	201777104	47473517	6	1407											
CENPF	1063	hgsc.bcm.edu	37	chr1	214819961	214819961	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagagctagagatagccaggAcaaaccaagagcatgcagct	16	4	12	9	0	0	3	0	0	0	3	0	6	0	4	2	1	6	4	2	1	4	2			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr1:214819961A>G	ENST00000366955.3	+	13	7216	c.7048A>G	c.(7048-7050)Aca>Gca	p.T2350A		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2446	2 X 177 AA tandem repeats.|Interaction with NDE1 and NDEL1.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		GATAGCCAGGACAAACCAAGA	0.453																																					p.T2350A	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.A7048G						PASS	.						48	49	49					1																	214819961		2203	4300	6503	SO:0001583	missense	1063	exon13			GCCAGGACAAACC	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.7048A>G	chr1.hg19:g.214819961A>G	ENSP00000355922:p.Thr2350Ala	164.0	0.0	.		224.0	78.0	.	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	hg19	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	A	2.753	-0.259660	0.05791	.	.	ENSG00000117724	ENST00000366955	T	0.39997	1.05	4.18	-2.26	0.06867	Centromere protein Cenp-F, leucine-rich repeat-containing domain (1);	0.797597	0.10598	N	0.656030	T	0.17789	0.0427	N	0.08118	0	0.09310	N	1	B	0.18863	0.031	B	0.14578	0.011	T	0.23261	-1.0193	10	0.21014	T	0.42	.	5.8248	0.18548	0.5509:0.1334:0.3157:0.0	.	2446	P49454	CENPF_HUMAN	A	2350	ENSP00000355922:T2350A	ENSP00000355922:T2350A	T	+	1	0	CENPF	212886584	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.036000	0.13819	-0.437000	0.07243	-0.315000	0.08773	ACA	.	.	.	none		0.453	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		G	214819961	A	G	214819961	3	3	21	1	0	0	0	0	1	0	0	0	3233	275	10	3	7094	3	CENPF	1	214819961	Missense_Mutation	SNP	A	TCGA-2Z-A9JR-01A-12D-A42J-10	13042857	214819961	34430660	7	1408											
CDC42BPA	8476	hgsc.bcm.edu	37	chr1	227216669	227216669	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggacttgaatttctttaaatTttctgtgacgggtcttgctc	7	18	9	7	1	3	2	0	2	3	0	4	3	3	3	0	2	1	1	0	2	3	7			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr1:227216669T>C	ENST00000366769.3	-	29	5307	c.4016A>G	c.(4015-4017)aAa>aGa	p.K1339R	CDC42BPA_ENST00000334218.5_Missense_Mutation_p.K1339R|CDC42BPA_ENST00000366764.2_Missense_Mutation_p.K1311R|CDC42BPA_ENST00000366765.3_Missense_Mutation_p.K1352R|CDC42BPA_ENST00000366766.2_Missense_Mutation_p.K1374R|CDC42BPA_ENST00000535525.1_Missense_Mutation_p.K1319R|CDC42BPA_ENST00000366767.3_Missense_Mutation_p.K1258R	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)				TTCTTTAAATTTTCTGTGACG	0.448																																					p.K1339R		Atlas-SNP	.											.	CDC42BPA	528	.	0			c.A4016G						PASS	.						74	70	71					1																	227216669		2203	4300	6503	SO:0001583	missense	8476	exon29			TTAAATTTTCTGT	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.4016A>G	chr1.hg19:g.227216669T>C	ENSP00000355731:p.Lys1339Arg	33.0	0.0	.		35.0	13.0	.	NM_003607		Missense_Mutation	SNP	ENST00000366769.3	hg19	CCDS1558.1	.	.	.	.	.	.	.	.	.	.	T	11.39	1.624802	0.28889	.	.	ENSG00000143776	ENST00000366769;ENST00000366767;ENST00000334218;ENST00000366766;ENST00000366764;ENST00000366762;ENST00000535525;ENST00000366765	T;T;T;T;T;T;T	0.05447	3.44;3.44;3.44;3.44;3.44;3.44;3.44	5.32	5.32	0.75619	.	0.050462	0.85682	D	0.000000	T	0.06554	0.0168	N	0.21508	0.67	0.48901	D	0.999725	B;B;B;B;B;B;B;B	0.22541	0.027;0.012;0.071;0.009;0.018;0.033;0.058;0.041	B;B;B;B;B;B;B;B	0.33690	0.02;0.009;0.168;0.074;0.036;0.036;0.065;0.06	T	0.38045	-0.9679	10	0.10902	T	0.67	.	15.5875	0.76495	0.0:0.0:0.0:1.0	.	1319;1311;654;236;1258;1339;1374;541	F5H5N0;Q5VT25-4;E9PEF7;Q5T7A7;Q5VT25-3;Q5VT25-5;Q5VT25-2;Q5T799	.;.;.;.;.;.;.;.	R	1339;1258;1339;1374;1311;654;1319;1352	ENSP00000355731:K1339R;ENSP00000355729:K1258R;ENSP00000335341:K1339R;ENSP00000355728:K1374R;ENSP00000355726:K1311R;ENSP00000443275:K1319R;ENSP00000355727:K1352R	ENSP00000335341:K1339R	K	-	2	0	CDC42BPA	225283292	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.691000	0.47010	2.153000	0.67306	0.477000	0.44152	AAA	.	.	.	none		0.448	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826		C	227216669	T	C	227216669	3	2	21	1	0	0	0	0	1	0	0	0	3074	1841	64	3	1175	3	CDC42BPA	1	227216669	Missense_Mutation	SNP	T	TCGA-2Z-A9JR-01A-12D-A42J-10	12396708	227216669	22033952	8	1409											
PEX13	5194	hgsc.bcm.edu	37	chr2	61258902	61258902	+	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	gcctctgtcagtatgatgatGgatgctaccttttcagctgt	7	15	10	9	0	3	2	2	2	1	0	3	3	3	3	2	1	3	3	2	1	2	4			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr2:61258902G>T	ENST00000295030.5	+	2	479	c.441G>T	c.(439-441)atG>atT	p.M147I	PEX13_ENST00000472678.1_3'UTR	NM_002618.3	NP_002609.1	Q92968	PEX13_HUMAN	peroxisomal biogenesis factor 13	147	Targeting to peroxisomes.				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)			GTATGATGATGGATGCTACCT	0.408																																					p.M147I		Atlas-SNP	.											.	PEX13	27	.	0			c.G441T						PASS	.						182	173	176					2																	61258902		2203	4300	6503	SO:0001583	missense	5194	exon2			GATGATGGATGCT	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.441G>T	chr2.hg19:g.61258902G>T	ENSP00000295030:p.Met147Ile	77.0	0.0	.		131.0	47.0	.	NM_002618	B2RCS1	Missense_Mutation	SNP	ENST00000295030.5	hg19	CCDS1866.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.179723	0.78564	.	.	ENSG00000162928	ENST00000295030	T	0.77098	-1.07	5.85	4.96	0.65561	Peroxin 13, N-terminal (1);	0.037439	0.85682	D	0.000000	T	0.76335	0.3973	L	0.39898	1.24	0.80722	D	1	P	0.45348	0.856	P	0.46144	0.505	T	0.78352	-0.2237	10	0.56958	D	0.05	-7.6725	16.9567	0.86261	0.0:0.1277:0.8723:0.0	.	147	Q92968	PEX13_HUMAN	I	147	ENSP00000295030:M147I	ENSP00000295030:M147I	M	+	3	0	PEX13	61112406	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.712000	0.84684	1.443000	0.47586	0.655000	0.94253	ATG	.	.	.	none		0.408	PEX13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251581.3	NM_002618		T	61258902	G	T	61258902	3	4	21	1	0	0	0	0	1	0	0	0	11748	1348	47	4	447	4	PEX13	2	61258902	Missense_Mutation	SNP	G	TCGA-2Z-A9JR-01A-12D-A42J-10		61258902	181940471	9	1410											
RPIA	22934	hgsc.bcm.edu	37	chr2	89036089	89036089	+	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	tcggggatcagtggcacaagGgaatccccatcgaggtcatc	10	7	13	11	2	2	0	2	0	0	0	6	3	3	2	2	5	0	1	2	5	2	0			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr2:89036089G>A	ENST00000283646.4	+	7	689	c.634G>A	c.(634-636)Gga>Aga	p.G212R		NM_144563.2	NP_653164.2	P49247	RPIA_HUMAN	ribose 5-phosphate isomerase A	212					carbohydrate metabolic process (GO:0005975)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|ribose phosphate metabolic process (GO:0019693)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	monosaccharide binding (GO:0048029)|ribose-5-phosphate isomerase activity (GO:0004751)	p.G212R(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|skin(1)	18		Acute lymphoblastic leukemia(2;0.000456)|all_hematologic(2;0.00287)				GTGGCACAAGGGAATCCCCAT	0.488																																					p.G212R		Atlas-SNP	.											RPIA,face,carcinoma,0,1	RPIA	35	.	1	Substitution - Missense(1)	skin(1)	c.G634A						PASS	.						107	112	110					2																	89036089		1967	4158	6125	SO:0001583	missense	22934	exon7			CACAAGGGAATCC	L35035	CCDS2004.2	2p11.2	2008-07-31	2008-07-31		ENSG00000153574	ENSG00000153574	5.3.1.6		10297	protein-coding gene	gene with protein product	"ribose 5-phosphate epimerase"	180430				7758956	Standard	NM_144563		Approved		uc002ste.3	P49247	OTTHUMG00000130333	ENST00000283646.4:c.634G>A	chr2.hg19:g.89036089G>A	ENSP00000283646:p.Gly212Arg	49.0	0.0	.		65.0	22.0	.	NM_144563	Q541P9|Q96BJ6	Missense_Mutation	SNP	ENST00000283646.4	hg19	CCDS2004.2	.	.	.	.	.	.	.	.	.	.	G	33	5.268670	0.95429	.	.	ENSG00000153574	ENST00000283646;ENST00000543560	T	0.75938	-0.98	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	D	0.88175	0.6366	M	0.84511	2.7	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89386	0.3685	10	0.66056	D	0.02	-10.5302	18.9716	0.92716	0.0:0.0:1.0:0.0	.	212	P49247	RPIA_HUMAN	R	212;78	ENSP00000283646:G212R	ENSP00000283646:G212R	G	+	1	0	RPIA	88817204	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.011000	0.93618	2.574000	0.86865	0.563000	0.77884	GGA	.	.	.	none		0.488	RPIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252683.2			A	89036089	G	A	89036089	3	1	21	1	0	0	0	0	1	0	0	0	13566	1233	43	2	660	2	RPIA	2	89036089	Missense_Mutation	SNP	G	TCGA-2Z-A9JR-01A-12D-A42J-10	27777187	89036089	154163284	10	1411											
ZNF35	7584	hgsc.bcm.edu	37	chr3	44701072	44701072	+	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	tagttgtttttcacaccttaTtgtgcaccagagaattcaca	11	15	6	9	0	2	1	2	0	0	1	2	2	2	1	2	0	1	3	2	0	3	7			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr3:44701072T>A	ENST00000396056.2	+	4	1452	c.1217T>A	c.(1216-1218)aTt>aAt	p.I406N	ZNF35_ENST00000296092.3_3'UTR|ZNF35_ENST00000542250.1_Missense_Mutation_p.I246N|RP11-944L7.4_ENST00000457331.1_RNA	NM_003420.3	NP_003411.3	P13682	ZNF35_HUMAN	zinc finger protein 35	406					cellular response to retinoic acid (GO:0071300)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cell (GO:0005623)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(3)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	12		Ovarian(412;0.0228)		OV - Ovarian serous cystadenocarcinoma(275;2.49e-27)|KIRC - Kidney renal clear cell carcinoma(197;0.0475)|Kidney(197;0.0595)		TCACACCTTATTGTGCACCAG	0.443																																					p.I406N		Atlas-SNP	.											.	ZNF35	34	.	0			c.T1217A						PASS	.						98	104	102					3																	44701072		2203	4300	6503	SO:0001583	missense	7584	exon4			ACCTTATTGTGCA	X07289	CCDS2718.2	3p21.32	2013-01-08	2006-05-11		ENSG00000169981	ENSG00000169981		"Zinc fingers, C2H2-type"	13099	protein-coding gene	gene with protein product		194533	"zinc finger protein 35 (clone HF.10)"			2108922, 1572646	Standard	NM_003420		Approved	HF.10, HF10, Zfp105	uc003cnq.3	P13682	OTTHUMG00000133091	ENST00000396056.2:c.1217T>A	chr3.hg19:g.44701072T>A	ENSP00000379368:p.Ile406Asn	80.0	0.0	.		120.0	43.0	.	NM_003420	B2RBU6|Q53Y54|Q96D01	Missense_Mutation	SNP	ENST00000396056.2	hg19	CCDS2718.2	.	.	.	.	.	.	.	.	.	.	T	14.13	2.443523	0.43429	.	.	ENSG00000169981	ENST00000396056;ENST00000542250	T;T	0.07114	3.22;3.22	5.29	4.13	0.48395	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.47093	D	0.000246	T	0.07143	0.0181	N	0.01473	-0.845	0.09310	N	1	D	0.67145	0.996	D	0.67900	0.954	T	0.24404	-1.0161	10	0.54805	T	0.06	-21.1804	7.2269	0.26020	0.134:0.0:0.1536:0.7124	.	406	P13682	ZNF35_HUMAN	N	406;246	ENSP00000379368:I406N;ENSP00000443714:I246N	ENSP00000379368:I406N	I	+	2	0	ZNF35	44676076	0.000000	0.05858	0.600000	0.28864	0.994000	0.84299	-0.001000	0.12947	2.225000	0.72522	0.459000	0.35465	ATT	.	.	.	none		0.443	ZNF35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256749.4	NM_003420		A	44701072	T	A	44701072	3	1	21	1	0	0	0	0	1	0	0	0	17874	1493	52	5	1227	5	ZNF35	3	44701072	Missense_Mutation	SNP	T	TCGA-2Z-A9JR-01A-12D-A42J-10		44701072	153321358	11	1412											
FGF5	2250	hgsc.bcm.edu	37	chr4	81207513	81207513	+	Missense_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	tgactgcaagttcagggagcGttttcaagaaaatagctata	14	11	10	6	1	2	2	2	1	0	1	2	3	2	3	0	1	3	4	0	1	7	6			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr4:81207513G>A	ENST00000312465.7	+	3	720	c.494G>A	c.(493-495)cGt>cAt	p.R165H	FGF5_ENST00000503413.1_3'UTR|FGF5_ENST00000456523.3_3'UTR	NM_004464.3	NP_004455.2	P12034	FGF5_HUMAN	fibroblast growth factor 5	165					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						TTCAGGGAGCGTTTTCAAGAA	0.398																																					p.R165H		Atlas-SNP	.											.	FGF5	49	.	0			c.G494A						PASS	.						133	147	142					4																	81207513		2202	4300	6502	SO:0001583	missense	2250	exon3			GGGAGCGTTTTCA	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.494G>A	chr4.hg19:g.81207513G>A	ENSP00000311697:p.Arg165His	196.0	0.0	.		262.0	18.0	.	NM_004464	B2R554|O75846|Q3Y8M3|Q8NF90	Missense_Mutation	SNP	ENST00000312465.7	hg19	CCDS34021.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.269981	0.80469	.	.	ENSG00000138675	ENST00000312465	D	0.81908	-1.55	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.88078	0.6340	M	0.75777	2.31	0.80722	D	1	P	0.35844	0.524	P	0.44990	0.466	D	0.87668	0.2539	10	0.66056	D	0.02	.	20.0851	0.97797	0.0:0.0:1.0:0.0	.	165	P12034	FGF5_HUMAN	H	165	ENSP00000311697:R165H	ENSP00000311697:R165H	R	+	2	0	FGF5	81426537	1.000000	0.71417	1.000000	0.80357	0.663000	0.39108	7.810000	0.86072	2.758000	0.94735	0.650000	0.86243	CGT	.	.	.	none		0.398	FGF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252627.2			A	81207513	G	A	81207513	3	1	21	1	0	0	0	0	1	0	0	0	5862	1145	40	1	504	1	FGF5	4	81207513	Missense_Mutation	SNP	G	TCGA-2Z-A9JR-01A-12D-A42J-10		81207513	109946763	12	1413											
HERC3	8916	hgsc.bcm.edu	37	chr4	89583701	89583701	+	Frame_Shift_Del	DEL	A	A	-																															gaacacaacaatgcaaatacAatcaagtatgtggctgcttg																										TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr4:89583701delA	ENST00000402738.1	+	11	1505	c.1266delA	c.(1264-1266)acafs	p.T422fs	HERC3_ENST00000543130.1_Intron|HERC3_ENST00000264345.3_Frame_Shift_Del_p.T422fs	NM_001271602.1|NM_014606.1	NP_001258531.1|NP_055421.1	Q15034	HERC3_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 3	422					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|prostate(2)|skin(2)	45				OV - Ovarian serous cystadenocarcinoma(123;0.000319)		ATGCAAATACAATCAAGTATG	0.338																																					p.T422fs		Atlas-Indel,Pindel	.											.	HERC3	82	.	0			c.1265delC						PASS	.						92	87	89					4																	89583701		2203	4300	6503	SO:0001589	frameshift_variant	8916	exon11			.	D25215	CCDS34028.1	4q21	2012-02-23	2012-02-23		ENSG00000138641	ENSG00000138641			4876	protein-coding gene	gene with protein product		605200	"hect domain and RLD 3"			10702688	Standard	NM_014606		Approved	KIAA0032	uc003hrw.2	Q15034	OTTHUMG00000150436	ENST00000402738.1:c.1266delA	chr4.hg19:g.89583701delA	ENSP00000385684:p.Thr422fs	125.0	0.0	0		149.0	46.0	0.308725	NM_014606	A8K1S5|Q8IXX3	Frame_Shift_Del	DEL	ENST00000402738.1	hg19	CCDS34028.1																																																																																			.	.	.	none		0.338	HERC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318081.2	NM_014606		-	89583701	A	-	89583701	7	5	21	1	0	1	0	1	0	0	0	0	7066	117	5	0	1300	0	HERC3	4	89583701	Frame_Shift_Del	DEL	A	TCGA-2Z-A9JR-01A-12D-A42J-10	8376188	89583701	101570575	13	1414											
GSTCD	79807	hgsc.bcm.edu	37	chr4	106746923	106746923	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catttggttcattcaagcaaAtatggaatattttactggga	13	15	8	5	0	2	0	2	0	0	0	2	2	2	2	0	3	2	2	0	3	6	7			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr4:106746923A>G	ENST00000515279.1	+	8	1716	c.1496A>G	c.(1495-1497)aAt>aGt	p.N499S	GSTCD_ENST00000360505.5_Missense_Mutation_p.N499S|RP11-45L9.1_ENST00000506527.1_RNA|GSTCD_ENST00000394730.3_Missense_Mutation_p.N412S|RP11-45L9.1_ENST00000504955.1_RNA|GSTCD_ENST00000394728.3_Missense_Mutation_p.N499S|GSTCD_ENST00000515255.1_3'UTR|RP11-45L9.1_ENST00000509003.1_RNA			Q8NEC7	GSTCD_HUMAN	glutathione S-transferase, C-terminal domain containing	499						extracellular vesicular exosome (GO:0070062)				breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|skin(1)	14		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.15e-07)|READ - Rectum adenocarcinoma(30;0.139)		ATTCAAGCAAATATGGAATAT	0.279																																					p.N499S		Atlas-SNP	.											.	GSTCD	69	.	0			c.A1496G						PASS	.						106	107	107					4																	106746923		1800	4058	5858	SO:0001583	missense	79807	exon8			AAGCAAATATGGA	BC032942	CCDS3672.2, CCDS43257.1	4q24	2008-02-05	2006-05-09		ENSG00000138780	ENSG00000138780			25806	protein-coding gene	gene with protein product		615912	"Glutathione S-transferase, C-terminal domain containing"			12477932	Standard	NM_001031720		Approved	FLJ13273	uc003hxz.4	Q8NEC7	OTTHUMG00000131211	ENST00000515279.1:c.1496A>G	chr4.hg19:g.106746923A>G	ENSP00000422354:p.Asn499Ser	197.0	0.0	.		184.0	60.0	.	NM_001031720	A8K8J0|A8MVD3|H9KV97|Q9H8S3	Missense_Mutation	SNP	ENST00000515279.1	hg19	CCDS43257.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.225240	0.79576	.	.	ENSG00000138780	ENST00000394730;ENST00000515279;ENST00000360505;ENST00000394728	T;T;T;T	0.39592	1.07;1.07;1.07;1.07	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.61236	0.2331	L	0.58925	1.835	0.58432	D	0.999998	D;P	0.89917	1.0;0.943	D;P	0.91635	0.999;0.906	T	0.64588	-0.6372	10	0.72032	D	0.01	-2.438	15.2919	0.73872	1.0:0.0:0.0:0.0	.	499;122	Q8NEC7;B7Z8J7	GSTCD_HUMAN;.	S	412;499;499;499	ENSP00000378218:N412S;ENSP00000422354:N499S;ENSP00000353695:N499S;ENSP00000378216:N499S	ENSP00000353695:N499S	N	+	2	0	GSTCD	106966372	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.602000	0.90868	2.076000	0.62316	0.528000	0.53228	AAT	.	.	.	none		0.279	GSTCD-006	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363981.1	NM_024751		G	106746923	A	G	106746923	3	3	21	1	0	0	0	0	1	0	0	0	6842	101	4	3	1522	3	GSTCD	4	106746923	Missense_Mutation	SNP	A	TCGA-2Z-A9JR-01A-12D-A42J-10	17163222	106746923	84407353	14	1415											
OTUD4	54726	hgsc.bcm.edu	37	chr4	146063415	146063415	+	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	gctggtaaagaaggcaccgcAggagttagatgtacctctgg	11	8	14	8	1	1	2	0	0	1	2	1	3	1	3	2	4	1	6	2	4	5	3			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr4:146063415A>T	ENST00000447906.2	-	18	1942	c.1755T>A	c.(1753-1755)ccT>ccA	p.P585P	OTUD4_ENST00000454497.2_Silent_p.P520P|OTUD4_ENST00000455611.2_5'UTR			Q01804	OTUD4_HUMAN	OTU deubiquitinase 4	585					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)					AAGGCACCGCAGGAGTTAGAT	0.498																																					p.P520P		Atlas-SNP	.											.	OTUD4	120	.	0			c.T1560A						PASS	.						123	130	127					4																	146063415		2203	4300	6503	SO:0001819	synonymous_variant	54726	exon18			CACCGCAGGAGTT		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.1755T>A	chr4.hg19:g.146063415A>T		74.0	0.0	.		98.0	32.0	.	NM_001102653	B4DYS4|Q147U2|Q1ZYK1|Q6PG39|Q96MQ5|Q9NT94|Q9UPV6	Silent	SNP	ENST00000447906.2	hg19																																																																																				.	.	.	none		0.498	OTUD4-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000365117.2	NM_017493		T	146063415	A	T	146063415	2	4	21	1	0	0	0	0	0	0	0	1	11321	175	7	5		5	OTUD4	4	146063415	Silent	SNP	A	TCGA-2Z-A9JR-01A-12D-A42J-10	39316492	146063415	45090861	15	1416											
C5orf42	65250	hgsc.bcm.edu	37	chr5	37183541	37183541	+	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	catgttctctaagctttccaGaaaaactagttagaaatgga	15	12	7	7	0	1	2	0	0	1	2	3	3	2	3	1	1	2	3	1	1	6	5			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr5:37183541G>A	ENST00000508244.1	-	25	4835	c.4742C>T	c.(4741-4743)tCt>tTt	p.S1581F	C5orf42_ENST00000274258.7_Missense_Mutation_p.S462F|C5orf42_ENST00000425232.2_Missense_Mutation_p.S1581F			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	1581						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)			AAGCTTTCCAGAAAAACTAGT	0.318																																					p.S1581F		Atlas-SNP	.											.	C5orf42	422	.	0			c.C4742T						PASS	.						81	81	81					5																	37183541		2202	4300	6502	SO:0001583	missense	65250	exon26			TTTCCAGAAAAAC		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.4742C>T	chr5.hg19:g.37183541G>A	ENSP00000421690:p.Ser1581Phe	190.0	0.0	.		167.0	62.0	.	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	hg19	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	G	25.9	4.681656	0.88542	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.74632	-0.86;-0.86;-0.86;-0.86	5.44	5.44	0.79542	.	0.000000	0.46758	D	0.000271	T	0.79953	0.4535	N	0.24115	0.695	0.50467	D	0.999871	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.82776	-0.0290	10	0.87932	D	0	.	19.2648	0.93982	0.0:0.0:1.0:0.0	.	1581;462	E9PH94;Q9H799	.;CE042_HUMAN	F	1581;1581;462;629;462	ENSP00000421690:S1581F;ENSP00000389014:S1581F;ENSP00000274258:S462F;ENSP00000424223:S629F	ENSP00000274258:S462F	S	-	2	0	C5orf42	37219298	1.000000	0.71417	0.991000	0.47740	0.713000	0.41058	5.236000	0.65354	2.551000	0.86045	0.655000	0.94253	TCT	.	.	.	none		0.318	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		A	37183541	G	A	37183541	3	1	21	1	0	0	0	0	1	0	0	0	2303	942	33	2	4959	2	C5orf42	5	37183541	Missense_Mutation	SNP	G	TCGA-2Z-A9JR-01A-12D-A42J-10		37183541	143731719	16	1417											
PDE8B	8622	hgsc.bcm.edu	37	chr5	76700575	76700575	+	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	attcagatataagaacaggaGgaaagagtccattgacgtga	17	8	11	5	1	1	5	1	2	0	3	2	7	2	7	1	2	1	0	1	2	4	4			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr5:76700575G>A	ENST00000264917.5	+	12	1286	c.1241G>A	c.(1240-1242)aGg>aAg	p.R414K	PDE8B_ENST00000342343.4_Missense_Mutation_p.R394K|PDE8B_ENST00000346042.3_Missense_Mutation_p.R317K|PDE8B_ENST00000333194.4_Missense_Mutation_p.R414K|PDE8B_ENST00000340978.3_Missense_Mutation_p.R367K	NM_003719.3	NP_003710.1	O95263	PDE8B_HUMAN	phosphodiesterase 8B	414					cAMP catabolic process (GO:0006198)|cyclic nucleotide metabolic process (GO:0009187)|negative regulation of insulin secretion (GO:0046676)|negative regulation of steroid hormone biosynthetic process (GO:0090032)|phosphorelay signal transduction system (GO:0000160)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)		GMDS/PDE8B(2)	NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(15)|ovary(1)|prostate(2)|skin(3)	40		all_lung(232;0.00043)|Lung NSC(167;0.00114)|Ovarian(174;0.0107)|Prostate(461;0.0605)		OV - Ovarian serous cystadenocarcinoma(54;2.21e-49)|Epithelial(54;5.82e-43)|all cancers(79;4.06e-38)	Caffeine(DB00201)|Ketotifen(DB00920)	AAGAACAGGAGGAAAGAGTCC	0.368																																					p.R414K		Atlas-SNP	.											.	PDE8B	103	.	0			c.G1241A						PASS	.						95	93	94					5																	76700575		2203	4300	6503	SO:0001583	missense	8622	exon12			ACAGGAGGAAAGA	AF079529	CCDS4037.1, CCDS34190.1, CCDS34191.1, CCDS34192.1, CCDS34193.1	5q14.1	2008-05-15			ENSG00000113231	ENSG00000113231	3.1.4.17	"Phosphodiesterases"	8794	protein-coding gene	gene with protein product		603390				9784418	Standard	NM_003719		Approved		uc003kfa.3	O95263	OTTHUMG00000102170	ENST00000264917.5:c.1241G>A	chr5.hg19:g.76700575G>A	ENSP00000264917:p.Arg414Lys	65.0	0.0	.		77.0	24.0	.	NM_001029852	Q5J7V7|Q86XK8|Q8IUJ7|Q8IUJ8|Q8IUJ9|Q8IUK0|Q8N3T2	Missense_Mutation	SNP	ENST00000264917.5	hg19	CCDS4037.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.030433	0.93575	.	.	ENSG00000113231	ENST00000340978;ENST00000346042;ENST00000264917;ENST00000342343;ENST00000333194	T;T;T;T;T	0.72051	-0.45;-0.61;-0.45;-0.45;-0.62	4.75	4.75	0.60458	.	0.763615	0.12696	N	0.446784	T	0.79257	0.4415	M	0.79123	2.44	0.80722	D	1	P;B;P;P;P	0.48911	0.887;0.2;0.917;0.735;0.616	P;B;P;B;B	0.48189	0.57;0.098;0.547;0.381;0.211	T	0.82118	-0.0615	10	0.66056	D	0.02	.	18.136	0.89619	0.0:0.0:1.0:0.0	.	317;367;414;394;414	O95263-2;O95263-6;O95263-3;O95263-4;O95263	.;.;.;.;PDE8B_HUMAN	K	367;317;414;394;414	ENSP00000345446:R367K;ENSP00000330428:R317K;ENSP00000264917:R414K;ENSP00000345646:R394K;ENSP00000331336:R414K	ENSP00000264917:R414K	R	+	2	0	PDE8B	76736331	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.313000	0.96297	2.341000	0.79615	0.563000	0.77884	AGG	.	.	.	none		0.368	PDE8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000220015.3	NM_003719		A	76700575	G	A	76700575	3	1	21	1	0	0	0	0	1	0	0	0	11661	1000	35	2	1287	2	PDE8B	5	76700575	Missense_Mutation	SNP	G	TCGA-2Z-A9JR-01A-12D-A42J-10	39517034	76700575	104214685	17	1418											
APC	324	hgsc.bcm.edu	37	chr5	112154711	112154711	+	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	tgcttggtactcatgataagGatgatatgtcgcgaactttg	10	14	11	6	2	1	2	1	2	0	0	2	4	1	3	0	2	3	2	0	2	4	5			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr5:112154711G>T	ENST00000457016.1	+	10	1362	c.982G>T	c.(982-984)Gat>Tat	p.D328Y	APC_ENST00000257430.4_Missense_Mutation_p.D328Y|APC_ENST00000508376.2_Missense_Mutation_p.D328Y			P25054	APC_HUMAN	adenomatous polyposis coli	328	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)			NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCATGATAAGGATGATATGTC	0.413		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.D328Y	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"E, M, O"	.	APC	4158	.	0			c.G982T						PASS	.						204	179	187					5																	112154711		2202	4300	6502	SO:0001583	missense	324	exon11	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	GATAAGGATGATA	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.982G>T	chr5.hg19:g.112154711G>T	ENSP00000413133:p.Asp328Tyr	41.0	0.0	.		94.0	22.0	.	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	hg19	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.610052	0.87258	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D;D	0.93953	-2.62;-3.32;-2.62;-2.62;-2.8	5.73	5.73	0.89815	Armadillo-like helical (1);	0.000000	0.85682	D	0.000000	D	0.96648	0.8906	M	0.74881	2.28	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.74674	0.982;0.984	D	0.96682	0.9504	10	0.87932	D	0	-20.9336	19.9616	0.97254	0.0:0.0:1.0:0.0	.	330;328	Q4LE70;P25054	.;APC_HUMAN	Y	328;310;328;328;328	ENSP00000413133:D328Y;ENSP00000423224:D310Y;ENSP00000257430:D328Y;ENSP00000427089:D328Y;ENSP00000423828:D328Y	ENSP00000257430:D328Y	D	+	1	0	APC	112182610	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.722000	0.93159	0.650000	0.86243	GAT	.	.	.	none		0.413	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		T	112154711	G	T	112154711	3	4	21	1	0	0	0	0	1	0	0	0	763	1174	41	4	1016	4	APC	5	112154711	Missense_Mutation	SNP	G	TCGA-2Z-A9JR-01A-12D-A42J-10	35454136	112154711	68760549	18	1419											
CDC25C	995	hgsc.bcm.edu	37	chr5	137626353	137626353	+	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	aaaaatcaccaatcaggtgcCcctggttagaatcttcctcc	12	10	6	13	0	3	1	2	0	1	1	5	1	5	1	5	2	1	1	5	2	5	2			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr5:137626353C>T	ENST00000323760.6	-	9	1117	c.839G>A	c.(838-840)gGg>gAg	p.G280E	CDC25C_ENST00000356505.3_Missense_Mutation_p.G250E|CDC25C_ENST00000514555.1_Missense_Mutation_p.G250E|CDC25C_ENST00000415130.2_Missense_Mutation_p.G207E|CDC25C_ENST00000513970.1_Missense_Mutation_p.G280E|CDC25C_ENST00000357274.3_Missense_Mutation_p.G237E|CDC25C_ENST00000348983.3_Missense_Mutation_p.G207E	NM_001790.3	NP_001781.2	P30307	MPIP3_HUMAN	cell division cycle 25C	280					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)			AATCAGGTGCCCCTGGTTAGA	0.443																																					p.G280E		Atlas-SNP	.											.	CDC25C	37	.	0			c.G839A						PASS	.						91	78	83					5																	137626353		2203	4300	6503	SO:0001583	missense	995	exon9			AGGTGCCCCTGGT	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.839G>A	chr5.hg19:g.137626353C>T	ENSP00000321656:p.Gly280Glu	99.0	0.0	.		130.0	40.0	.	NM_001790	D3DQB8|Q96PL3|Q9H168|Q9H2E8|Q9H2E9|Q9H2F1	Missense_Mutation	SNP	ENST00000323760.6	hg19	CCDS4202.1	.	.	.	.	.	.	.	.	.	.	C	7.187	0.590733	0.13812	.	.	ENSG00000158402	ENST00000323760;ENST00000356505;ENST00000357274;ENST00000348983;ENST00000415130;ENST00000513970;ENST00000534892;ENST00000514555	T;T;T;T;T;T;T	0.20738	2.64;2.64;2.05;2.05;2.05;2.64;2.64	5.19	3.41	0.39046	Rhodanese-like (1);	0.381500	0.24332	N	0.039453	T	0.11495	0.0280	N	0.12182	0.205	0.09310	N	0.999993	B;B;B;B	0.28350	0.11;0.208;0.2;0.067	B;B;B;B	0.27796	0.046;0.063;0.083;0.021	T	0.22661	-1.0210	10	0.32370	T	0.25	-2.6834	10.4344	0.44426	0.0:0.8481:0.0:0.1519	.	297;250;207;280	G3V1P6;P30307-2;P30307-4;P30307	.;.;.;MPIP3_HUMAN	E	280;250;237;207;207;280;297;250	ENSP00000321656:G280E;ENSP00000348898:G250E;ENSP00000349821:G237E;ENSP00000345205:G207E;ENSP00000392631:G207E;ENSP00000424795:G280E;ENSP00000425470:G250E	ENSP00000321656:G280E	G	-	2	0	CDC25C	137654252	0.836000	0.29430	0.031000	0.17742	0.889000	0.51656	1.599000	0.36751	0.766000	0.33244	0.585000	0.79938	GGG	.	.	.	none		0.443	CDC25C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251280.1			T	137626353	C	T	137626353	3	4	21	1	0	0	0	0	1	0	0	0	3066	623	22	2	606	2	CDC25C	5	137626353	Missense_Mutation	SNP	C	TCGA-2Z-A9JR-01A-12D-A42J-10	25471642	137626353	43288907	19	1420											
PCDHB16	57717	hgsc.bcm.edu	37	chr5	140563836	140563836	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgctgtacccgctgcagaacGgctccgcgccctgcactgag	6	7	12	16	4	0	2	0	1	0	1	1	2	1	2	3	1	5	6	3	1	2	1	rs535302272	byFrequency	TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr5:140563836G>A	ENST00000361016.2	+	1	2857	c.1702G>A	c.(1702-1704)Ggc>Agc	p.G568S		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	568	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCTGCAGAACGGCTCCGCGCC	0.711													G|||	2	0.000399361	8e-04	0	5008	,	,		13663	0		0	False		,,,				2504	0.001				p.G568S		Atlas-SNP	.											PCDHB16,NS,carcinoma,0,1	PCDHB16	159	.	0			c.G1702A						PASS	.						14	17	16					5																	140563836		1969	3923	5892	SO:0001583	missense	57717	exon1			CAGAACGGCTCCG	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.1702G>A	chr5.hg19:g.140563836G>A	ENSP00000354293:p.Gly568Ser	45.0	1.0	.		33.0	3.0	.	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	hg19	CCDS4251.1	.	.	.	.	.	.	.	.	.	.	g	12.66	2.005258	0.35415	.	.	ENSG00000196963	ENST00000361016	T	0.60797	0.16	4.12	2.28	0.28536	Cadherin (1);Cadherin-like (1);	1.832600	0.03875	N	0.276324	T	0.41719	0.1171	N	0.20807	0.61	0.09310	N	1	B	0.22003	0.063	B	0.17979	0.02	T	0.27123	-1.0083	10	0.45353	T	0.12	.	3.1416	0.06457	0.2646:0.0:0.4112:0.3242	.	568	Q9NRJ7	PCDBG_HUMAN	S	568	ENSP00000354293:G568S	ENSP00000354293:G568S	G	+	1	0	PCDHB16	140544020	0.000000	0.05858	0.984000	0.44739	0.978000	0.69477	0.941000	0.29005	0.212000	0.20703	0.479000	0.44913	GGC	.	.	.	none		0.711	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		A	140563836	G	A	140563836	3	1	21	1	0	0	0	0	1	0	0	0	11548	1116	39	1	1704	1	PCDHB16	5	140563836	Missense_Mutation	SNP	G	TCGA-2Z-A9JR-01A-12D-A42J-10	2937483	140563836	40351424	20	1421											
ANKS1A	23294	hgsc.bcm.edu	37	chr6	34950966	34950966	+	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	gaactgccttctcaaaagagCcagcaaatagcagcattaat	16	8	7	10	0	1	1	1	0	1	1	2	2	1	1	2	0	6	3	2	0	6	3			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr6:34950966C>A	ENST00000360359.3	+	6	1023	c.885C>A	c.(883-885)agC>agA	p.S295R	ANKS1A_ENST00000535627.1_Missense_Mutation_p.S295R	NM_015245.2	NP_056060.2	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1A	295					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						CTCAAAAGAGCCAGCAAATAG	0.478																																					p.S295R		Atlas-SNP	.											.	ANKS1A	123	.	0			c.C885A						PASS	.						165	166	166					6																	34950966		2203	4300	6503	SO:0001583	missense	23294	exon6			AAAGAGCCAGCAA	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.885C>A	chr6.hg19:g.34950966C>A	ENSP00000353518:p.Ser295Arg	91.0	0.0	.		68.0	24.0	.	NM_015245	A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7	Missense_Mutation	SNP	ENST00000360359.3	hg19	CCDS4798.1	.	.	.	.	.	.	.	.	.	.	C	13.49	2.252437	0.39797	.	.	ENSG00000064999	ENST00000544150;ENST00000360359;ENST00000535627	T;T	0.61392	1.02;0.11	5.66	4.61	0.57282	Ankyrin repeat-containing domain (2);	0.000000	0.56097	D	0.000021	T	0.67599	0.2910	M	0.66378	2.025	0.42555	D	0.993121	D;D	0.71674	0.984;0.998	P;D	0.75484	0.642;0.986	T	0.70392	-0.4884	10	0.72032	D	0.01	-21.6177	13.7604	0.62961	0.0:0.9166:0.0:0.0834	.	295;295	B4DQW8;Q92625	.;ANS1A_HUMAN	R	295	ENSP00000353518:S295R;ENSP00000438752:S295R	ENSP00000353518:S295R	S	+	3	2	ANKS1A	35058944	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.009000	0.29886	2.656000	0.90262	0.655000	0.94253	AGC	.	.	.	none		0.478	ANKS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040262.1	XM_166478		A	34950966	C	A	34950966	3	1	21	1	0	0	0	0	1	0	0	0	688	738	26	4	907	4	ANKS1A	6	34950966	Missense_Mutation	SNP	C	TCGA-2Z-A9JR-01A-12D-A42J-10		34950966	136164101	21	1422											
IGF2R	3482	hgsc.bcm.edu	37	chr6	160461724	160461724	+	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	tgccaccgacgggaagaagcGctatgacctgtccgcgctgg	8	6	14	13	5	0	2	0	1	0	1	1	4	1	3	4	2	2	2	4	2	3	1			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr6:160461724G>C	ENST00000356956.1	+	11	1596	c.1448G>C	c.(1447-1449)cGc>cCc	p.R483P		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	483					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)	GGGAAGAAGCGCTATGACCTG	0.557																																					p.R483P		Atlas-SNP	.											.	IGF2R	251	.	0			c.G1448C						PASS	.						143	125	131					6																	160461724		2203	4300	6503	SO:0001583	missense	3482	exon11			AGAAGCGCTATGA	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.1448G>C	chr6.hg19:g.160461724G>C	ENSP00000349437:p.Arg483Pro	90.0	0.0	.		48.0	15.0	.	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	hg19	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	G	16.75	3.208615	0.58343	.	.	ENSG00000197081	ENST00000356956	T	0.02280	4.36	4.79	3.91	0.45181	Mannose-6-phosphate receptor, binding (1);	0.156802	0.47093	D	0.000244	T	0.05273	0.0140	M	0.73598	2.24	0.43874	D	0.996481	D	0.89917	1.0	D	0.75020	0.985	T	0.29731	-1.0002	10	0.36615	T	0.2	-13.4021	9.8517	0.41061	0.1604:0.0:0.8396:0.0	.	483	P11717	MPRI_HUMAN	P	483	ENSP00000349437:R483P	ENSP00000349437:R483P	R	+	2	0	IGF2R	160381714	0.937000	0.31787	0.893000	0.35052	0.604000	0.37047	1.559000	0.36320	2.210000	0.71456	0.655000	0.94253	CGC	.	.	.	none		0.557	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		C	160461724	G	C	160461724	3	2	21	1	0	0	0	0	1	0	0	0	7583	1087	38	4	1490	4	IGF2R	6	160461724	Missense_Mutation	SNP	G	TCGA-2Z-A9JR-01A-12D-A42J-10	125510758	160461724	10653343	22	1423											
CCDC146	57639	hgsc.bcm.edu	37	chr7	76883839	76883844	+	In_Frame_Del	DEL	ATCATC	ATCATC	-																															gcagcttaaaggaagaaaaaAtcatcatagtaaaagaattt																										TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	ATCATC	ATCATC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr7:76883839_76883844delATCATC	ENST00000285871.4	+	5	593_598	c.466_471delATCATC	c.(466-471)atcatcdel	p.II156del	CCDC146_ENST00000431197.1_5'UTR|AC073635.5_ENST00000476561.2_RNA	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	156										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)				GGAAGAAAAAATCATCATAGTAAAAG	0.286																																					p.155_157del		Atlas-Indel,Pindel	.											.	CCDC146	87	.	0			c.465_470del						PASS	.																																			SO:0001651	inframe_deletion	57639	exon5			.	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.466_471delATCATC	chr7.hg19:g.76883839_76883844delATCATC	ENSP00000285871:p.Ile156_Ile157del	43.0	0.0	0		75.0	19.0	0.253333	NM_020879	A8K8X6|Q9P223	In_Frame_Del	DEL	ENST00000285871.4	hg19	CCDS34671.1																																																																																			.	.	.	none		0.286	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879		-	76883844	ATCATC	-	76883839	7	5	21	1	0	1	0	1	0	0	0	0	2782	101	4	0	480	0	CCDC146	7	76883839	In_Frame_Del	DEL	ATCATC	TCGA-2Z-A9JR-01A-12D-A42J-10		76883839	82254824	23	1424											
MLL5	55904	hgsc.bcm.edu	37	chr7	104742528	104742541	+	Frame_Shift_Del	DEL	AATACTGTACTTAC	AATACTGTACTTAC	-																															cacaacaaaatgatattgaaAatactgtacttacaatagaa																										TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	AATACTGTACTTAC	AATACTGTACTTAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr7:104742528_104742541delAATACTGTACTTAC	ENST00000311117.3	+	17	2628_2641	c.2083_2096delAATACTGTACTTAC	c.(2083-2097)aatactgtacttacafs	p.NTVLT695fs	KMT2E_ENST00000334877.4_Frame_Shift_Del_p.NTVLT695fs|KMT2E_ENST00000334914.7_5'UTR|KMT2E_ENST00000257745.4_Frame_Shift_Del_p.NTVLT695fs|CTB-152G17.6_ENST00000607968.1_RNA	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	695					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										TGATATTGAAAATACTGTACTTACAATAGAACCA	0.383																																					p.694_699del		Atlas-Indel,Pindel	.											.	MLL5	173	.	0			c.2082_2095del						PASS	.																																			SO:0001589	frameshift_variant	55904	exon17			.	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.2083_2096delAATACTGTACTTAC	chr7.hg19:g.104742528_104742541delAATACTGTACTTAC	ENSP00000312379:p.Asn695fs	211.0	0.0	0		379.0	92.0	0.242744	NM_182931	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Frame_Shift_Del	DEL	ENST00000311117.3	hg19	CCDS34723.1																																																																																			.	.	.	none		0.383	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			-	104742541	AATACTGTACTTAC	-	104742528	7	5	21	1	0	1	0	1	0	0	0	0	9631	14	1	0	2141	0	MLL5	7	104742528	Frame_Shift_Del	DEL	AATACTGTACTTAC	TCGA-2Z-A9JR-01A-12D-A42J-10	27858689	104742528	54396135	24	1425											
KCNH2	3757	hgsc.bcm.edu	37	chr7	150655488	150655488	+	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	ccacgtccaccaccacggccCccggggcgcccgcgccgccc	4	1	11	25	7	0	0	0	0	0	0	1	0	1	0	9	3	0	0	9	3	0	0			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr7:150655488C>A	ENST00000262186.5	-	4	976	c.575G>T	c.(574-576)gGg>gTg	p.G192V	KCNH2_ENST00000392968.2_Missense_Mutation_p.G96V|KCNH2_ENST00000430723.3_Missense_Mutation_p.G192V|KCNH2_ENST00000330883.4_5'Flank	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	192					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)	CACCAcggcccccggggcgcc	0.761																																					p.G192V	GBM(137;110 1844 13671 20123 45161)	Atlas-SNP	.											.	KCNH2	157	.	0			c.G575T						PASS	.						1	2	1					7																	150655488		1310	2720	4030	SO:0001583	missense	3757	exon4			ACGGCCCCCGGGG	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.575G>T	chr7.hg19:g.150655488C>A	ENSP00000262186:p.Gly192Val	436.0	0.0	.		187.0	23.0	.	NM_000238	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Missense_Mutation	SNP	ENST00000262186.5	hg19	CCDS5910.1	.	.	.	.	.	.	.	.	.	.	C	11.72	1.723869	0.30593	.	.	ENSG00000055118	ENST00000392968;ENST00000262186;ENST00000430723	D;D;D	0.99167	-4.82;-5.03;-5.51	3.64	3.64	0.41730	.	0.496899	0.15878	N	0.240203	D	0.97949	0.9325	N	0.19112	0.55	0.58432	D	0.999999	D;D;P	0.69078	0.997;0.982;0.613	D;P;B	0.63597	0.916;0.682;0.186	D	0.97044	0.9759	10	0.54805	T	0.06	.	11.0164	0.47691	0.0:1.0:0.0:0.0	.	96;192;192	C4PFH9;G5E9I0;Q12809	.;.;KCNH2_HUMAN	V	96;192;192	ENSP00000376695:G96V;ENSP00000262186:G192V;ENSP00000387657:G192V	ENSP00000262186:G192V	G	-	2	0	KCNH2	150286421	0.981000	0.34729	0.992000	0.48379	0.619000	0.37552	1.898000	0.39809	2.040000	0.60383	0.455000	0.32223	GGG	.	.	.	none		0.761	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	NM_000238		A	150655488	C	A	150655488	3	1	21	1	0	0	0	0	1	0	0	0	8039	623	22	4	3333	4	KCNH2	7	150655488	Missense_Mutation	SNP	C	TCGA-2Z-A9JR-01A-12D-A42J-10	45912960	150655488	8483175	25	1426											
VCPIP1	80124	hgsc.bcm.edu	37	chr8	67577722	67577722	+	Frame_Shift_Del	DEL	A	A	-																															tactttttgccaggttatacAatttccctccaggagccaac																										TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr8:67577722delA	ENST00000310421.4	-	1	1730	c.1472delT	c.(1471-1473)ttgfs	p.L491fs	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	491					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)			CAGGTTATACAATTTCCCTCC	0.413																																					p.L491fs	NSCLC(179;265 2915 6144 43644)	Atlas-Indel,Pindel	.											.	VCPIP1	110	.	0			c.1473delG						PASS	.						140	147	144					8																	67577722		2203	4300	6503	SO:0001589	frameshift_variant	80124	exon1			.	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.1472delT	chr8.hg19:g.67577722delA	ENSP00000309031:p.Leu491fs	92.0	0.0	0		87.0	34.0	0.390805	NM_025054	Q504T4|Q86T93|Q86W01|Q8N3A9|Q9H5R8	Frame_Shift_Del	DEL	ENST00000310421.4	hg19	CCDS6192.1																																																																																			.	.	.	none		0.413	VCPIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379227.1			-	67577722	A	-	67577722	7	5	21	1	0	1	0	1	0	0	0	0	17153	131	5	0	2208	0	VCPIP1	8	67577722	Frame_Shift_Del	DEL	A	TCGA-2Z-A9JR-01A-12D-A42J-10		67577722	78786300	26	1427											
MATN2	4147	hgsc.bcm.edu	37	chr8	99015912	99015912	+	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	tcaactactgtgcactgaacAaaccgggctgtgagcatgag	12	8	11	10	1	1	3	1	3	0	0	1	3	1	3	1	1	6	3	1	1	4	1			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr8:99015912A>T	ENST00000520016.1	+	7	1352	c.1228A>T	c.(1228-1230)Aaa>Taa	p.K410*	MATN2_ENST00000521689.1_Nonsense_Mutation_p.K410*|MATN2_ENST00000524308.1_Nonsense_Mutation_p.K369*|MATN2_ENST00000522025.2_Nonsense_Mutation_p.K126*|MATN2_ENST00000254898.5_Nonsense_Mutation_p.K410*			O00339	MATN2_HUMAN	matrilin 2	410	EGF-like 5. {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)			TGCACTGAACAAACCGGGCTG	0.602																																					p.K410X		Atlas-SNP	.											.	MATN2	165	.	0			c.A1228T						PASS	.						88	95	93					8																	99015912		2147	4263	6410	SO:0001587	stop_gained	4147	exon8			CTGAACAAACCGG	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.1228A>T	chr8.hg19:g.99015912A>T	ENSP00000430487:p.Lys410*	81.0	0.0	.		104.0	23.0	.	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Nonsense_Mutation	SNP	ENST00000520016.1	hg19	CCDS55264.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.92|13.92	2.380389|2.380389	0.42207|0.42207	.|.	.|.	ENSG00000132561|ENSG00000132561	ENST00000521689;ENST00000254898;ENST00000378716;ENST00000524308;ENST00000522025;ENST00000520016;ENST00000522270|ENST00000518154;ENST00000521041	.|.	.|.	.|.	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	0.373442|.	0.26086|.	N|.	0.026440|.	.|T	.|0.62429	.|0.2427	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.70561	.|-0.4838	.|3	0.02654|.	T|.	1|.	-23.8411|-23.8411	12.026|12.026	0.53371|0.53371	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|.	.|.	.|.	X|L	410;410;369;369;126;410;114|192;164	.|.	ENSP00000254898:K410X|.	K|Q	+|+	1|2	0|0	MATN2|MATN2	99085088|99085088	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.465000|0.465000	0.32709|0.32709	5.458000|5.458000	0.66679|0.66679	2.111000|2.111000	0.64477|0.64477	0.379000|0.379000	0.24179|0.24179	AAA|CAA	.	.	.	none		0.602	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1			T	99015912	A	T	99015912	4	4	21	1	0	0	0	0	0	1	0	0	9341	131	5	5	1254	5	MATN2	8	99015912	Nonsense_Mutation	SNP	A	TCGA-2Z-A9JR-01A-12D-A42J-10	31438190	99015912	47348110	27	1428											
TG	7038	hgsc.bcm.edu	37	chr8	133895243	133895243	+	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	caaggggagccgccatcttgTggtgggtttcctctgggggc	4	10	17	10	1	2	0	0	0	2	0	3	1	3	1	3	6	1	1	3	6	1	2			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr8:133895243T>C	ENST00000220616.4	+	8	1114	c.1074T>C	c.(1072-1074)tgT>tgC	p.C358C	TG_ENST00000377869.1_Splice_Site_p.C358C	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	358	Thyroglobulin type-1 4. {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)		CGCCATCTTGTGGTGGGTTTC	0.592																																					p.C358C		Atlas-SNP	.											.	TG	416	.	0			c.T1074C						PASS	.						24	24	24					8																	133895243		2203	4300	6503	SO:0001630	splice_region_variant	7038	exon8			ATCTTGTGGTGGG	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.1075+1T>C	chr8.hg19:g.133895243T>C		65.0	0.0	.		81.0	28.0	.	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	hg19	CCDS34944.1																																																																																			.	.	.	none		0.592	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	Silent	C	133895243	T	C	133895243	5	2	21	1	0	0	0	0	0	0	1	0	15825	1710	59	3	1104	3	TG	8	133895243	Splice_Site	SNP	T	TCGA-2Z-A9JR-01A-12D-A42J-10	34879331	133895243	12468779	28	1429											
VPS13A	23230	hgsc.bcm.edu	37	chr9	79862227	79862227	+	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	cttgatctcaaaattaatttGaaggcttcatatattattgt	13	18	5	5	0	2	2	2	2	1	0	3	2	2	2	0	1	0	1	0	1	7	8			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr9:79862227G>T	ENST00000360280.3	+	20	2213	c.1953G>T	c.(1951-1953)ttG>ttT	p.L651F	VPS13A_ENST00000376634.4_Missense_Mutation_p.L651F|VPS13A_ENST00000357409.5_Missense_Mutation_p.L651F|VPS13A_ENST00000376636.3_Missense_Mutation_p.L651F	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	651					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						AAATTAATTTGAAGGCTTCAT	0.294																																					p.L651F		Atlas-SNP	.											.	VPS13A	735	.	0			c.G1953T						PASS	.						80	89	86					9																	79862227		2202	4287	6489	SO:0001583	missense	23230	exon20			TAATTTGAAGGCT	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.1953G>T	chr9.hg19:g.79862227G>T	ENSP00000353422:p.Leu651Phe	336.0	0.0	.		251.0	86.0	.	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	hg19	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	G	16.89	3.246346	0.59103	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.60040	0.22;0.22;0.22;0.22	5.52	4.61	0.57282	.	0.384693	0.22519	N	0.058988	T	0.66944	0.2841	L	0.61036	1.89	0.80722	D	1	P;P;D;D	0.55800	0.891;0.954;0.973;0.973	P;P;P;P	0.61533	0.603;0.721;0.89;0.89	T	0.67573	-0.5636	10	0.54805	T	0.06	.	7.5233	0.27641	0.1579:0.1492:0.6929:0.0	.	651;651;651;651	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	F	651	ENSP00000365821:L651F;ENSP00000365823:L651F;ENSP00000353422:L651F;ENSP00000349985:L651F	ENSP00000349985:L651F	L	+	3	2	VPS13A	79052047	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.532000	0.23067	1.428000	0.47296	0.563000	0.77884	TTG	.	.	.	none		0.294	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		T	79862227	G	T	79862227	3	4	21	1	0	0	0	0	1	0	0	0	17201	1281	45	4	2031	4	VPS13A	9	79862227	Missense_Mutation	SNP	G	TCGA-2Z-A9JR-01A-12D-A42J-10		79862227	61351204	29	1430											
DAB2IP	153090	hgsc.bcm.edu	37	chr9	124544633	124544633	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcgcattgcctcgttggaTgccgccaatgcccgcctcat	7	9	10	15	4	1	0	1	0	0	0	2	1	1	1	5	1	4	2	5	1	2	2			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr9:124544633T>C	ENST00000408936.3	+	16	3608	c.3426T>C	c.(3424-3426)gaT>gaC	p.D1142D	DAB2IP_ENST00000309989.1_Silent_p.D1018D|DAB2IP_ENST00000259371.2_Silent_p.D1114D			Q5VWQ8	DAB2P_HUMAN	DAB2 interacting protein	1142					activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|angiogenesis (GO:0001525)|cell cycle (GO:0007049)|cell motility involved in cerebral cortex radial glia guided migration (GO:0021814)|cellular protein catabolic process (GO:0044257)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|layer formation in cerebral cortex (GO:0021819)|negative regulation of angiogenesis (GO:0016525)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of GTPase activity (GO:0034260)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase activity (GO:0043553)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuron projection morphogenesis (GO:0048812)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of dendrite development (GO:1900006)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of synapse maturation (GO:0090129)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of ARF GTPase activity (GO:0032312)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein complex assembly (GO:0043254)|response to unfolded protein (GO:0006986)|transformed cell apoptotic process (GO:0006927)|tube formation (GO:0035148)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	axon (GO:0030424)|cerebellar mossy fiber (GO:0044300)|climbing fiber (GO:0044301)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|neuronal cell body (GO:0043025)|neuronal cell body membrane (GO:0032809)|parallel fiber (GO:1990032)|plasma membrane (GO:0005886)	14-3-3 protein binding (GO:0071889)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|mitogen-activated protein kinase kinase binding (GO:0031434)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase 2A binding (GO:0051721)|Ras GTPase activator activity (GO:0005099)|SH3 domain binding (GO:0017124)|signaling adaptor activity (GO:0035591)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(8)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	27						CCTCGTTGGATGCCGCCAATG	0.592																																					p.D1114D		Atlas-SNP	.											.	DAB2IP	150	.	0			c.T3342C						PASS	.						133	118	123					9																	124544633		2203	4300	6503	SO:0001819	synonymous_variant	153090	exon16			GTTGGATGCCGCC	AF367051	CCDS6832.1, CCDS6833.2	9q33.1-q33.3	2008-07-21			ENSG00000136848	ENSG00000136848			17294	protein-coding gene	gene with protein product	"nGAP-like protein", "DOC-2/DAB2 interactive protein", "ASK-interacting protein", "ASK1-interacting protein 1"	609205				11944990, 11812785	Standard	XM_005251721		Approved	AF9Q34, DIP1/2, KIAA1743, AIP1	uc004bln.3	Q5VWQ8	OTTHUMG00000020595	ENST00000408936.3:c.3426T>C	chr9.hg19:g.124544633T>C		147.0	0.0	.		105.0	48.0	.	NM_032552	A6H8V2|A6NHI9|B0QZB1|G3XA90|Q8TDL2|Q96SE1|Q9C0C0	Silent	SNP	ENST00000408936.3	hg19																																																																																				.	.	.	none		0.592	DAB2IP-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317857.1	NM_032552		C	124544633	T	C	124544633	2	2	21	1	0	0	0	0	0	0	0	1	4221	1461	51	3		3	DAB2IP	9	124544633	Silent	SNP	T	TCGA-2Z-A9JR-01A-12D-A42J-10	44682406	124544633	16668798	30	1431											
ANKRD30A	91074	hgsc.bcm.edu	37	chr10	37442571	37442573	+	In_Frame_Del	DEL	AAT	AAT	-																															catcaaaaagaaatagataaAataaatggaaaattagaagg																								rs376853184		TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr10:37442571_37442573delAAT	ENST00000602533.1	+	13	1710_1712	c.1611_1613delAAT	c.(1609-1614)aaaata>aaa	p.I538del	ANKRD30A_ENST00000361713.1_In_Frame_Del_p.I538del|ANKRD30A_ENST00000374660.1_In_Frame_Del_p.I538del			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	594					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						AAATAGATAAAATAAATGGAAAA	0.32																																					p.537_538del		Atlas-INDEL	.											ANKRD30A,colon,carcinoma,0,1	ANKRD30A	448	.	0			c.1610_1612del						PASS	.																																			SO:0001651	inframe_deletion	91074	exon13			.	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.1611_1613delAAT	chr10.hg19:g.37442571_37442573delAAT	ENSP00000473551:p.Ile538del	619.0	0.0	0		675.0	52.0	0.077037	NM_052997	Q5W025	In_Frame_Del	DEL	ENST00000602533.1	hg19																																																																																				.	.	.	none		0.32	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		-	37442573	AAT	-	37442571	7	5	21	1	0	1	0	1	0	0	0	0	658	11	1	0	1661	0	ANKRD30A	10	37442571	In_Frame_Del	DEL	AAT	TCGA-2Z-A9JR-01A-12D-A42J-10		37442571	98092176	31	1432											
ANKRD30A	91074	hgsc.bcm.edu	37	chr10	37478466	37478468	+	In_Frame_Del	DEL	AAT	AAT	-																															catcaaaaagaaatagataaAataaatggaaaattagaagg																										TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr10:37478466_37478468delAAT	ENST00000602533.1	+	25	2424_2426	c.2325_2327delAAT	c.(2323-2328)aaaata>aaa	p.I776del	ANKRD30A_ENST00000361713.1_In_Frame_Del_p.I776del|ANKRD30A_ENST00000475522.1_3'UTR|ANKRD30A_ENST00000374660.1_In_Frame_Del_p.I895del			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	832					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						AAATAGATAAAATAAATGGAAAA	0.305																																					p.775_776del		Atlas-Indel,Pindel	.											ANKRD30A,NS,carcinoma,0,1	ANKRD30A	448	.	0			c.2324_2326del						PASS	.																																			SO:0001651	inframe_deletion	91074	exon25			.	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.2325_2327delAAT	chr10.hg19:g.37478466_37478468delAAT	ENSP00000473551:p.Ile776del	350.0	0.0	0		309.0	43.0	0.139159	NM_052997	Q5W025	In_Frame_Del	DEL	ENST00000602533.1	hg19																																																																																				.	.	.	none		0.305	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		-	37478468	AAT	-	37478466	7	5	21	1	0	1	0	1	0	0	0	0	658	11	1	0	2423	0	ANKRD30A	10	37478466	In_Frame_Del	DEL	AAT	TCGA-2Z-A9JR-01A-12D-A42J-10	35895	37478466	98056281	32	1433											
DNAJB12	54788	hgsc.bcm.edu	37	chr10	74095644	74095644	+	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	tcttctgtgctctgtggtacAtatctgtgtcgccaaagtag	7	15	10	9	1	4	0	0	0	4	0	5	0	4	0	1	1	2	3	1	1	4	4	rs368163344		TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr10:74095644A>T	ENST00000444643.2	-	8	1384	c.1052T>A	c.(1051-1053)aTg>aAg	p.M351K	DNAJB12_ENST00000461919.1_Missense_Mutation_p.M146K|DNAJB12_ENST00000394903.2_Missense_Mutation_p.M385K|DNAJB12_ENST00000338820.3_Missense_Mutation_p.M385K			Q9NXW2	DJB12_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 12	351						integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|skin(1)	4						TCTGTGGTACATATCTGTGTC	0.597																																					p.M385K		Atlas-SNP	.											.	DNAJB12	22	.	0			c.T1154A						PASS	.						149	120	130					10																	74095644		2203	4300	6503	SO:0001583	missense	54788	exon8			TGGTACATATCTG	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.1052T>A	chr10.hg19:g.74095644A>T	ENSP00000403313:p.Met351Lys	84.0	0.0	.		72.0	17.0	.	NM_017626	B7Z7I3|Q9H6H0	Missense_Mutation	SNP	ENST00000444643.2	hg19		.	.	.	.	.	.	.	.	.	.	A	22.4	4.283930	0.80803	.	.	ENSG00000148719	ENST00000338820;ENST00000394903;ENST00000444643	T;T;T	0.38560	1.13;1.13;1.13	5.82	5.82	0.92795	Domain of unknown function DUF1977, DnaJ-like (1);	0.052948	0.85682	D	0.000000	T	0.35008	0.0917	N	0.14661	0.345	0.54753	D	0.999988	P;P	0.36249	0.49;0.545	B;B	0.41646	0.247;0.362	T	0.35574	-0.9783	10	0.87932	D	0	-12.4345	16.17	0.81801	1.0:0.0:0.0:0.0	.	351;351	Q9NXW2-2;Q9NXW2	.;DJB12_HUMAN	K	385;385;351	ENSP00000345575:M385K;ENSP00000378363:M385K;ENSP00000403313:M351K	ENSP00000345575:M385K	M	-	2	0	DNAJB12	73765650	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.962000	0.93254	2.224000	0.72417	0.459000	0.35465	ATG	.	.	.	none		0.597	DNAJB12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048581.2			T	74095644	A	T	74095644	3	4	21	1	0	0	0	0	1	0	0	0	4619	217	8	5	79	5	DNAJB12	10	74095644	Missense_Mutation	SNP	A	TCGA-2Z-A9JR-01A-12D-A42J-10	36617178	74095644	61439103	33	1434											
C10orf76	79591	hgsc.bcm.edu	37	chr10	103717456	103717456	+	Frame_Shift_Del	DEL	T	T	-																															tggccaaaagtacagtctcaTttgacataaggaacttcagc																										TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr10:103717456delT	ENST00000370033.4	-	21	1648	c.1529delA	c.(1528-1530)aatfs	p.N510fs		NM_024541.2	NP_078817.2	Q5T2E6	CJ076_HUMAN	chromosome 10 open reading frame 76	510						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|prostate(2)|upper_aerodigestive_tract(2)	24		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)		TACAGTCTCATTTGACATAAG	0.299																																					p.N510fs		Atlas-Indel,Pindel	.											.	C10orf76	48	.	0			c.1530delT						PASS	.						82	75	77					10																	103717456		1817	4080	5897	SO:0001589	frameshift_variant	79591	exon21			.	AK023176	CCDS41563.1	10q24.32	2008-10-21			ENSG00000120029	ENSG00000120029			25788	protein-coding gene	gene with protein product						14702039	Standard	NM_024541		Approved	FLJ13114	uc009xwy.1	Q5T2E6	OTTHUMG00000018943	ENST00000370033.4:c.1529delA	chr10.hg19:g.103717456delT	ENSP00000359050:p.Asn510fs	44.0	0.0	0		52.0	16.0	0.307692	NM_024541	Q2TB87|Q9H8Z9	Frame_Shift_Del	DEL	ENST00000370033.4	hg19	CCDS41563.1																																																																																			.	.	.	none		0.299	C10orf76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050007.1	NM_024541		-	103717456	T	-	103717456	7	5	21	1	0	1	0	1	0	0	0	0	1618	1493	52	0	564	0	C10orf76	10	103717456	Frame_Shift_Del	DEL	T	TCGA-2Z-A9JR-01A-12D-A42J-10	29621812	103717456	31817291	34	1435											
KRTAP5-4	387267	hgsc.bcm.edu	37	chr11	1643025	1643025	+	Frame_Shift_Del	DEL	C	C	-																															agcccccacaggagccacagCcccccttggaacccccacag																										TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr11:1643025delC	ENST00000399682.1	-	1	343	c.299delG	c.(298-300)ggcfs	p.G100fs		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)		GGAGCCACAGCCCCCCTTGGA	0.682																																					p.G100fs		Atlas-INDEL	.											.	KRTAP5-4	78	.	0			c.300delC						PASS	.						6	12	10					11																	1643025		640	1507	2147	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.299delG	chr11.hg19:g.1643025delC	ENSP00000382590:p.Gly100fs	260.0	0.0	0		189.0	19.0	0.100529	NM_001012709		Frame_Shift_Del	DEL	ENST00000399682.1	hg19																																																																																				.	.	.	none		0.682	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709		-	1643025	C	-	1643025	7	5	21	1	0	1	0	1	0	0	0	0	8570	739	26	0	391	0	KRTAP5-4	11	1643025	Frame_Shift_Del	DEL	C	TCGA-2Z-A9JR-01A-12D-A42J-10		1643025	133363491	35	1436											
STIM1	6786	hgsc.bcm.edu	37	chr11	4095775	4095788	+	Frame_Shift_Del	DEL	AAGGTCCATCTGGA	AAGGTCCATCTGGA	-																															accgcacagtggaggtggagAaggtccatctggaaaagaag																								rs199510481|rs200324686		TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	AAGGTCCATCTGGA	AAGGTCCATCTGGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr11:4095775_4095788delAAGGTCCATCTGGA	ENST00000300737.4	+	7	1404_1417	c.835_848delAAGGTCCATCTGGA	c.(835-849)aaggtccatctggaafs	p.KVHLE279fs	STIM1_ENST00000533977.1_Frame_Shift_Del_p.KVHLE106fs|STIM1_ENST00000527651.1_Frame_Shift_Del_p.KVHLE279fs	NM_003156.3	NP_003147.2	Q13586	STIM1_HUMAN	stromal interaction molecule 1	279	Glu-rich.				activation of store-operated calcium channel activity (GO:0032237)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|regulation of calcium ion transport (GO:0051924)|regulation of store-operated calcium entry (GO:2001256)|store-operated calcium entry (GO:0002115)	cortical endoplasmic reticulum (GO:0032541)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|growth cone (GO:0030426)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of plasma membrane (GO:0005887)|microtubule (GO:0005874)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|microtubule plus-end binding (GO:0051010)|store-operated calcium channel activity (GO:0015279)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|liver(1)|lung(14)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)		GGAGGTGGAGAAGGTCCATCTGGAAAAGAAGCTG	0.607																																					p.278_283del		Atlas-Indel,Pindel	.											.	STIM1	55	.	0			c.834_847del						PASS	.																																			SO:0001589	frameshift_variant	6786	exon7			.	BC021300, U52426	CCDS7749.1, CCDS60706.1, CCDS73247.1	11p15.5	2014-09-17			ENSG00000167323	ENSG00000167323		"Sterile alpha motif (SAM) domain containing"	11386	protein-coding gene	gene with protein product		605921				8921403, 11463338, 11983428	Standard	NM_003156		Approved	GOK, D11S4896E	uc021qco.1	Q13586	OTTHUMG00000133360	ENST00000300737.4:c.835_848delAAGGTCCATCTGGA	chr11.hg19:g.4095775_4095788delAAGGTCCATCTGGA	ENSP00000300737:p.Lys279fs	56.0	0.0	0		59.0	15.0	0.254237	NM_003156	E9PQJ4|Q8N382	Frame_Shift_Del	DEL	ENST00000300737.4	hg19	CCDS7749.1																																																																																			.	.	.	none		0.607	STIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257196.1	NM_003156		-	4095788	AAGGTCCATCTGGA	-	4095775	7	5	21	1	0	1	0	1	0	0	0	0	15295	247	9	0	861	0	STIM1	11	4095775	Frame_Shift_Del	DEL	AAGGTCCATCTGGA	TCGA-2Z-A9JR-01A-12D-A42J-10	2452750	4095775	130910741	36	1437											
RAG2	5897	hgsc.bcm.edu	37	chr11	36615488	36615488	+	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	aagctgcctttgaatgtgcaAgtggctgggtagcgaagagg	10	9	16	6	1	0	2	0	1	0	1	0	3	0	2	1	3	4	4	1	3	5	2			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr11:36615488A>T	ENST00000311485.3	-	2	392	c.231T>A	c.(229-231)acT>acA	p.T77T	C11orf74_ENST00000534635.1_5'Flank|C11orf74_ENST00000347206.4_5'Flank|C11orf74_ENST00000446510.2_5'Flank|C11orf74_ENST00000334307.5_5'Flank|RAG2_ENST00000528428.1_5'Flank	NM_000536.3|NM_001243785.1|NM_001243786.1	NP_000527.2|NP_001230714.1|NP_001230715.1	P55895	RAG2_HUMAN	recombination activating gene 2	77			T -> N (in CHIDG; reduced recombination activity). {ECO:0000269|PubMed:18463379}.		B cell differentiation (GO:0030183)|chromatin modification (GO:0016568)|pre-B cell allelic exclusion (GO:0002331)|T cell differentiation in thymus (GO:0033077)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	32	all_lung(20;0.226)	all_hematologic(20;0.00756)				TGAATGTGCAAGTGGCTGGGT	0.423									Familial Hemophagocytic Lymphohistiocytosis																												p.T77T		Atlas-SNP	.											RAG2,NS,carcinoma,0,1	RAG2	92	.	0			c.T231A						PASS	.						131	137	135					11																	36615488		2202	4298	6500	SO:0001819	synonymous_variant	5897	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	TGTGCAAGTGGCT	AF080577	CCDS7903.1	11p13	2014-09-17				ENSG00000175097			9832	protein-coding gene	gene with protein product		179616				1283330	Standard	NM_000536		Approved		uc001mwv.4	P55895		ENST00000311485.3:c.231T>A	chr11.hg19:g.36615488A>T		89.0	0.0	.		132.0	39.0	.	NM_001243785	A8K9E9|Q8TBL4	Silent	SNP	ENST00000311485.3	hg19	CCDS7903.1																																																																																			.	.	.	none		0.423	RAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389536.1	NM_000536		T	36615488	A	T	36615488	2	4	21	1	0	0	0	0	0	0	0	1	13018	59	3	5		5	RAG2	11	36615488	Silent	SNP	A	TCGA-2Z-A9JR-01A-12D-A42J-10	32519713	36615488	98391028	37	1438											
ASRGL1	80150	hgsc.bcm.edu	37	chr11	62156671	62156671	+	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	gtagcctacgcaacctccacAggcggtatcgttaataaaat	13	9	8	11	3	0	0	0	0	0	0	2	0	1	0	3	2	3	4	3	2	7	5			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr11:62156671A>T	ENST00000415229.2	+	5	773	c.558A>T	c.(556-558)acA>acT	p.T186T	ASRGL1_ENST00000301776.5_Silent_p.T186T|ASRGL1_ENST00000535727.1_Silent_p.T58T|CTD-2531D15.5_ENST00000526045.1_RNA	NM_001083926.1	NP_001077395.1	Q7L266	ASGL1_HUMAN	asparaginase like 1	186					asparagine catabolic process via L-aspartate (GO:0033345)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	asparaginase activity (GO:0004067)|beta-aspartyl-peptidase activity (GO:0008798)			endometrium(1)|kidney(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	7					L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)	CAACCTCCACAGGCGGTATCG	0.542																																					p.T186T		Atlas-SNP	.											.	ASRGL1	25	.	0			c.A558T						PASS	.						128	120	123					11																	62156671		2202	4299	6501	SO:0001819	synonymous_variant	80150	exon5			CTCCACAGGCGGT		CCDS8019.1	11q12.3	2008-07-18			ENSG00000162174	ENSG00000162174			16448	protein-coding gene	gene with protein product	"asparaginase-like 1 protein"	609212					Standard	NM_025080		Approved	FLJ22316, ALP1, ALP	uc001ntf.4	Q7L266	OTTHUMG00000167513	ENST00000415229.2:c.558A>T	chr11.hg19:g.62156671A>T		61.0	0.0	.		81.0	25.0	.	NM_001083926	B2R7Q0|Q567Q4|Q6P1P0|Q8NI34|Q9H6F7	Silent	SNP	ENST00000415229.2	hg19	CCDS8019.1																																																																																			.	.	.	none		0.542	ASRGL1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394865.1	NM_001083926		T	62156671	A	T	62156671	2	4	21	1	0	0	0	0	0	0	0	1	1060	175	7	5		5	ASRGL1	11	62156671	Silent	SNP	A	TCGA-2Z-A9JR-01A-12D-A42J-10	25541183	62156671	72849845	38	1439											
PHLDB1	23187	hgsc.bcm.edu	37	chr11	118526375	118526375	+	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	ggccattgaggaagtgtactAcgaccacctgcgcagtgcag	10	7	13	11	2	0	1	0	1	0	0	0	3	0	2	3	2	4	3	3	2	3	3			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr11:118526375A>T	ENST00000361417.2	+	22	4346	c.3935A>T	c.(3934-3936)tAc>tTc	p.Y1312F	PHLDB1_ENST00000524713.1_Missense_Mutation_p.Y455F|PHLDB1_ENST00000534672.1_3'UTR|PHLDB1_ENST00000527898.1_Missense_Mutation_p.Y363F|PHLDB1_ENST00000356063.5_Missense_Mutation_p.Y1265F	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	1312	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)		GAAGTGTACTACGACCACCTG	0.607																																					p.Y1312F		Atlas-SNP	.											.	PHLDB1	103	.	0			c.A3935T						PASS	.						111	94	99					11																	118526375		2200	4295	6495	SO:0001583	missense	23187	exon21			TGTACTACGACCA		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.3935A>T	chr11.hg19:g.118526375A>T	ENSP00000354498:p.Tyr1312Phe	22.0	0.0	.		42.0	15.0	.	NM_001144758	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Missense_Mutation	SNP	ENST00000361417.2	hg19	CCDS8401.1	.	.	.	.	.	.	.	.	.	.	A	28.4	4.918880	0.92249	.	.	ENSG00000019144	ENST00000361417;ENST00000361465;ENST00000358191;ENST00000356063;ENST00000541457;ENST00000527898;ENST00000524713	T;T;T;T	0.72942	-0.7;-0.7;-0.7;-0.7	5.79	5.79	0.91817	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.79839	0.4515	L	0.42581	1.335	0.80722	D	1	B;D;B;B	0.71674	0.392;0.998;0.33;0.382	P;D;P;P	0.87578	0.47;0.998;0.687;0.598	T	0.81182	-0.1049	10	0.62326	D	0.03	-10.3043	16.1354	0.81481	1.0:0.0:0.0:0.0	.	676;1071;1265;1312	B0YJ65;Q5W9G0;Q86UU1-2;Q86UU1	.;.;.;PHLB1_HUMAN	F	1312;1086;676;1265;47;363;455	ENSP00000354498:Y1312F;ENSP00000348359:Y1265F;ENSP00000435388:Y363F;ENSP00000434905:Y455F	ENSP00000348359:Y1265F	Y	+	2	0	PHLDB1	118031585	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	8.842000	0.92136	2.207000	0.71202	0.533000	0.62120	TAC	.	.	.	none		0.607	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157		T	118526375	A	T	118526375	3	4	21	1	0	0	0	0	1	0	0	0	11858	391	14	5	4013	5	PHLDB1	11	118526375	Missense_Mutation	SNP	A	TCGA-2Z-A9JR-01A-12D-A42J-10	56369704	118526375	16480141	39	1440											
H1FNT	341567	hgsc.bcm.edu	37	chr12	48723566	48723566	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgccagccccttcgcaaggcGgccaggaaggccagagaagt	10	3	14	14	3	0	1	0	0	0	1	1	3	0	2	5	4	1	1	5	4	3	1			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr12:48723566G>A	ENST00000335017.1	+	1	804	c.492G>A	c.(490-492)gcG>gcA	p.A164A		NM_181788.1	NP_861453.1	Q75WM6	H1FNT_HUMAN	H1 histone family, member N, testis-specific	164	Arg-rich.				chromosome condensation (GO:0030261)|multicellular organismal development (GO:0007275)|sperm chromatin condensation (GO:0035092)|spermatid nucleus elongation (GO:0007290)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	13						TTCGCAAGGCGGCCAGGAAGG	0.726																																					p.A164A		Atlas-SNP	.											.	H1FNT	30	.	0			c.G492A						PASS	.						16	16	16					12																	48723566		2173	4250	6423	SO:0001819	synonymous_variant	341567	exon1			CAAGGCGGCCAGG	AY302593	CCDS8762.1	12q13.11	2011-01-27				ENSG00000187166		"Histones / Replication-independent"	24893	protein-coding gene	gene with protein product						15710904	Standard	NM_181788		Approved	HANP1, H1T2	uc001rrm.3	Q75WM6		ENST00000335017.1:c.492G>A	chr12.hg19:g.48723566G>A		152.0	0.0	.		93.0	28.0	.	NM_181788	Q147U8|Q5GKZ5|Q7Z694	Silent	SNP	ENST00000335017.1	hg19	CCDS8762.1																																																																																			.	.	.	none		0.726	H1FNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406516.1	NM_181788		A	48723566	G	A	48723566	2	1	21	1	0	0	0	0	0	0	0	1	6928	1103	39	1		1	H1FNT	12	48723566	Silent	SNP	G	TCGA-2Z-A9JR-01A-12D-A42J-10		48723566	85128329	40	1441											
GABPB1	2553	hgsc.bcm.edu	37	chr15	50593523	50593523	+	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	agcatgtattgtcacagtgtCaggactctctgggtttgtgt	7	15	12	7	0	3	0	2	0	1	0	4	1	3	1	0	2	1	3	0	2	1	3			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr15:50593523C>G	ENST00000220429.8	-	5	682	c.514G>C	c.(514-516)Gac>Cac	p.D172H	GABPB1_ENST00000396464.3_Missense_Mutation_p.D172H|GABPB1_ENST00000543881.1_Missense_Mutation_p.D96H|GABPB1_ENST00000380877.3_Missense_Mutation_p.D172H|GABPB1_ENST00000359031.4_Missense_Mutation_p.D172H|GABPB1_ENST00000429662.2_Missense_Mutation_p.D172H|GABPB1_ENST00000560825.1_Missense_Mutation_p.D172H			Q06547	GABP1_HUMAN	GA binding protein transcription factor, beta subunit 1	172					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(1)|large_intestine(7)|lung(5)	14						GTCACAGTGTCAGGACTCTCT	0.418																																					p.D172H		Atlas-SNP	.											.	GABPB1	33	.	0			c.G514C						PASS	.						261	219	233					15																	50593523		2196	4295	6491	SO:0001583	missense	2553	exon5			CAGTGTCAGGACT	D13316	CCDS10135.1, CCDS10136.1, CCDS32239.1, CCDS45258.1	15q21.2	2013-01-10	2008-02-25	2008-02-25	ENSG00000104064	ENSG00000104064		"Ankyrin repeat domain containing"	4074	protein-coding gene	gene with protein product		600610	"GA binding protein transcription factor, beta subunit 2"	GABPB2		7958862	Standard	NM_016655		Approved	E4TF1-47, GABPB	uc001zyb.3	Q06547	OTTHUMG00000131642	ENST00000220429.8:c.514G>C	chr15.hg19:g.50593523C>G	ENSP00000220429:p.Asp172His	90.0	0.0	.		87.0	33.0	.	NM_016654	A8IE52|Q06545|Q12940|Q12941|Q12942|Q8IYD0	Missense_Mutation	SNP	ENST00000220429.8	hg19	CCDS32239.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.113480	0.77210	.	.	ENSG00000104064	ENST00000220429;ENST00000380877;ENST00000543881;ENST00000396464;ENST00000429662;ENST00000359031	T;T;T;T;T;T	0.72167	-0.63;-0.28;0.66;-0.3;-0.3;-0.3	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.77745	0.4176	L	0.29908	0.895	0.58432	D	0.999997	D;D;D;D;D	0.76494	0.999;0.979;0.987;0.999;0.994	P;P;P;D;P	0.80764	0.908;0.865;0.775;0.994;0.896	T	0.75252	-0.3383	10	0.36615	T	0.2	-11.8081	20.024	0.97514	0.0:1.0:0.0:0.0	.	172;172;172;172;172	B7Z726;Q06547-3;Q06547-4;Q06547;Q06547-2	.;.;.;GABP1_HUMAN;.	H	172;172;96;172;172;172	ENSP00000220429:D172H;ENSP00000370259:D172H;ENSP00000442500:D96H;ENSP00000379728:D172H;ENSP00000395771:D172H;ENSP00000351923:D172H	ENSP00000220429:D172H	D	-	1	0	GABPB1	48380815	1.000000	0.71417	0.994000	0.49952	0.999000	0.98932	5.062000	0.64326	2.809000	0.96659	0.655000	0.94253	GAC	.	.	.	none		0.418	GABPB1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000418294.1			G	50593523	C	G	50593523	3	3	21	1	0	0	0	0	1	0	0	0	6165	826	29	4	741	4	GABPB1	15	50593523	Missense_Mutation	SNP	C	TCGA-2Z-A9JR-01A-12D-A42J-10		50593523	51937869	41	1442											
KIAA0101	9768	hgsc.bcm.edu	37	chr15	64668943	64668943	+	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	ccagaatataaaaacttactTtctctttgcttttcctaagc	12	16	3	10	0	1	1	0	0	1	1	3	1	2	1	2	0	4	1	2	0	7	8			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr15:64668943T>A	ENST00000300035.4	-	3	427	c.289A>T	c.(289-291)Aaa>Taa	p.K97*	KIAA0101_ENST00000380258.2_Intron|CTD-2116N17.1_ENST00000558783.1_5'Flank|KIAA0101_ENST00000559519.1_Splice_Site_p.K70*|KIAA0101_ENST00000558008.1_Splice_Site_p.N97Y	NM_014736.4	NP_055551.1	Q15004	PAF15_HUMAN	KIAA0101	97					cellular response to DNA damage stimulus (GO:0006974)|centrosome organization (GO:0051297)|DNA replication (GO:0006260)|regulation of cell cycle (GO:0051726)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	chromatin binding (GO:0003682)			central_nervous_system(1)|lung(1)|upper_aerodigestive_tract(1)	3						AAAACTTACTTTCTCTTTGCT	0.423																																					p.K97X		Atlas-SNP	.											.	KIAA0101	8	.	0			c.A289T						PASS	.						36	38	37					15																	64668943		2202	4300	6502	SO:0001630	splice_region_variant	9768	exon3			CTTACTTTCTCTT	D14657	CCDS10193.1, CCDS32269.1	15q22	2006-06-22			ENSG00000166803	ENSG00000166803			28961	protein-coding gene	gene with protein product		610696				11313979, 16288740	Standard	NM_001029989		Approved	NS5ATP9, OEATC-1, p15(PAF)	uc002ank.3	Q15004	OTTHUMG00000133017	ENST00000300035.4:c.290+1A>T	chr15.hg19:g.64668943T>A		110.0	0.0	.		112.0	28.0	.	NM_014736	A6NNU5|A8K3Y3|G9G694|G9G696	Nonsense_Mutation	SNP	ENST00000300035.4	hg19	CCDS10193.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.479203	0.84747	.	.	ENSG00000166803	ENST00000300035	.	.	.	5.81	5.81	0.92471	.	0.048857	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.3444	15.1475	0.72667	0.0:0.0:0.0:1.0	.	.	.	.	X	97	.	ENSP00000300035:K97X	K	-	1	0	KIAA0101	62455996	1.000000	0.71417	1.000000	0.80357	0.583000	0.36354	7.006000	0.76329	2.222000	0.72286	0.482000	0.46254	AAA	.	.	.	none		0.423	KIAA0101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256603.1	NM_014736	Nonsense_Mutation	A	64668943	T	A	64668943	5	1	21	1	0	0	0	0	0	0	1	0	8162	1855	64	5	79	5	KIAA0101	15	64668943	Splice_Site	SNP	T	TCGA-2Z-A9JR-01A-12D-A42J-10	14075420	64668943	37862449	42	1443											
ABCA3	21	hgsc.bcm.edu	37	chr16	2329051	2329051	+	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	gggatgccccggagccgagcGtacatgaccagcatctcccg	8	5	13	15	4	1	1	0	1	1	0	2	4	1	3	5	2	5	2	5	2	1	1	rs367951064		TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr16:2329051G>A	ENST00000301732.5	-	29	5140	c.4440C>T	c.(4438-4440)taC>taT	p.Y1480Y	ABCA3_ENST00000382381.3_Silent_p.Y1422Y	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	1480	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)	GGAGCCGAGCGTACATGACCA	0.657																																					p.Y1480Y		Atlas-SNP	.											.	ABCA3	176	.	0			c.C4440T						PASS	.						61	63	62					16																	2329051		2198	4299	6497	SO:0001819	synonymous_variant	21	exon29			CCGAGCGTACATG	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.4440C>T	chr16.hg19:g.2329051G>A		102.0	0.0	.		89.0	26.0	.	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Silent	SNP	ENST00000301732.5	hg19	CCDS10466.1																																																																																			.	.	.	alt		0.657	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089		A	2329051	G	A	2329051	2	1	21	1	0	0	0	0	0	0	0	1	33	1140	40	1		1	ABCA3	16	2329051	Silent	SNP	G	TCGA-2Z-A9JR-01A-12D-A42J-10		2329051	88025702	43	1444											
SRCAP	10847	hgsc.bcm.edu	37	chr16	30732250	30732250	+	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	cctgcatctcggcctcctggCcctgtcctcttgcctccact	2	12	7	20	1	2	0	0	0	2	0	6	0	5	0	7	2	2	1	7	2	0	1			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr16:30732250C>T	ENST00000262518.4	+	20	3589	c.3204C>T	c.(3202-3204)ggC>ggT	p.G1068G	SRCAP_ENST00000395059.2_Silent_p.G1068G|SRCAP_ENST00000344771.4_Silent_p.G1068G	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1068	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)			GGCCTCCTGGCCCTGTCCTCT	0.612																																					p.G1068G		Atlas-SNP	.											.	SRCAP	298	.	0			c.C3204T						PASS	.						57	54	55					16																	30732250		2197	4300	6497	SO:0001819	synonymous_variant	10847	exon20			TCCTGGCCCTGTC	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.3204C>T	chr16.hg19:g.30732250C>T		52.0	0.0	.		50.0	6.0	.	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Silent	SNP	ENST00000262518.4	hg19	CCDS10689.2																																																																																			.	.	.	none		0.612	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		T	30732250	C	T	30732250	2	4	21	1	0	0	0	0	0	0	0	1	15147	726	26	2		2	SRCAP	16	30732250	Silent	SNP	C	TCGA-2Z-A9JR-01A-12D-A42J-10	28403199	30732250	59622503	44	1445											
NFAT5	10725	hgsc.bcm.edu	37	chr16	69724916	69724916	+	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	ctgatgactccactcataccAagcagtatgattaagagtga	14	10	8	9	0	1	5	1	4	0	1	2	5	2	5	2	0	2	2	2	0	4	3			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr16:69724916A>T	ENST00000354436.2	+	11	2112	c.1794A>T	c.(1792-1794)ccA>ccT	p.P598P	NFAT5_ENST00000432919.1_Silent_p.P616P|NFAT5_ENST00000566899.1_Silent_p.P522P|NFAT5_ENST00000567239.1_Silent_p.P615P|NFAT5_ENST00000349945.1_Silent_p.P522P|NFAT5_ENST00000393742.2_Silent_p.P522P	NM_006599.3	NP_006590.1	O94916	NFAT5_HUMAN	nuclear factor of activated T-cells 5, tonicity-responsive	598					cytokine production (GO:0001816)|excretion (GO:0007588)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of calcineurin-NFAT signaling cascade (GO:0070884)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						CACTCATACCAAGCAGTATGA	0.348																																					p.P616P		Atlas-SNP	.											.	NFAT5	184	.	0			c.A1848T						PASS	.						108	107	107					16																	69724916		2198	4298	6496	SO:0001819	synonymous_variant	10725	exon12			CATACCAAGCAGT	AF134870	CCDS10881.1, CCDS10882.1, CCDS45519.1	16q22.1	2009-11-24			ENSG00000102908	ENSG00000102908		"Nuclear factor of activated T-cells"	7774	protein-coding gene	gene with protein product		604708				10377394	Standard	NM_173214		Approved	TONEBP, KIAA0827, NFATL1, OREBP, NFATZ, NF-AT5	uc002exl.2	O94916	OTTHUMG00000137572	ENST00000354436.2:c.1794A>T	chr16.hg19:g.69724916A>T		183.0	0.0	.		227.0	122.0	.	NM_138713	A2RRB4|A6H8V5|E9PHR7|O95693|Q7LA65|Q969Q8|Q96QH3|Q9UN18	Silent	SNP	ENST00000354436.2	hg19	CCDS10881.1																																																																																			.	.	.	none		0.348	NFAT5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268952.2	NM_138714		T	69724916	A	T	69724916	2	4	21	1	0	0	0	0	0	0	0	1	10367	117	5	5		5	NFAT5	16	69724916	Silent	SNP	A	TCGA-2Z-A9JR-01A-12D-A42J-10	38992666	69724916	20629837	45	1446											
KRT25	147183	hgsc.bcm.edu	37	chr17	38907279	38907279	+	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	tttcagtcagctcattccggGctgaggttgtggctccgaca	6	12	12	11	2	3	1	3	1	0	0	5	2	5	1	2	3	1	4	2	3	0	3			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr17:38907279G>T	ENST00000312150.4	-	5	944	c.884C>A	c.(883-885)gCc>gAc	p.A295D		NM_181534.3	NP_853512.1			keratin 25											endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(4)	16		Breast(137;0.00526)				CTCATTCCGGGCTGAGGTTGT	0.463																																					p.A295D		Atlas-SNP	.											.	KRT25	63	.	0			c.C884A						PASS	.						104	101	102					17																	38907279		2203	4300	6503	SO:0001583	missense	147183	exon5			TTCCGGGCTGAGG	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.884C>A	chr17.hg19:g.38907279G>T	ENSP00000310573:p.Ala295Asp	83.0	0.0	.		121.0	28.0	.	NM_181534		Missense_Mutation	SNP	ENST00000312150.4	hg19	CCDS11373.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.348552	0.82132	.	.	ENSG00000204897	ENST00000312150	D	0.90004	-2.6	5.84	5.84	0.93424	Filament (1);	0.000000	0.64402	D	0.000007	D	0.93259	0.7852	M	0.89287	3.02	0.36483	D	0.867994	P	0.51147	0.942	P	0.57620	0.824	D	0.95013	0.8153	9	.	.	.	.	8.1242	0.30988	0.0781:0.0:0.7228:0.1991	.	295	Q7Z3Z0	K1C25_HUMAN	D	295	ENSP00000310573:A295D	.	A	-	2	0	KRT25	36160805	0.072000	0.21174	0.500000	0.27589	0.980000	0.70556	1.074000	0.30703	2.758000	0.94735	0.655000	0.94253	GCC	.	.	.	none		0.463	KRT25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257218.1	NM_181534		T	38907279	G	T	38907279	3	4	21	1	0	0	0	0	1	0	0	0	8469	1203	42	4	484	4	KRT25	17	38907279	Missense_Mutation	SNP	G	TCGA-2Z-A9JR-01A-12D-A42J-10		38907279	42287931	46	1447											
KCNH6	81033	hgsc.bcm.edu	37	chr17	61607776	61607776	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccatcagccagatcccacAgttcacgctcaacttcgtgg	10	8	8	15	2	3	1	3	0	0	1	5	2	4	1	3	1	2	2	3	1	1	2			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr17:61607776A>G	ENST00000583023.1	+	4	559	c.548A>G	c.(547-549)cAg>cGg	p.Q183R	KCNH6_ENST00000314672.5_Missense_Mutation_p.Q183R|KCNH6_ENST00000580652.1_Missense_Mutation_p.Q183R|KCNH6_ENST00000581784.1_Missense_Mutation_p.Q183R|KCNH6_ENST00000456941.2_Missense_Mutation_p.Q183R	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	183					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)	CAGATCCCACAGTTCACGCTC	0.607																																					p.Q183R		Atlas-SNP	.											.	KCNH6	122	.	0			c.A548G						PASS	.						199	145	163					17																	61607776		2203	4300	6503	SO:0001583	missense	81033	exon4			TCCCACAGTTCAC	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.548A>G	chr17.hg19:g.61607776A>G	ENSP00000463533:p.Gln183Arg	291.0	0.0	.		230.0	34.0	.	NM_030779	Q9BRD7	Missense_Mutation	SNP	ENST00000583023.1	hg19	CCDS11638.1	.	.	.	.	.	.	.	.	.	.	A	10.92	1.487431	0.26686	.	.	ENSG00000173826	ENST00000314672;ENST00000456941	D;D	0.92805	-3.11;-3.11	4.69	3.61	0.41365	.	0.181186	0.37761	N	0.001951	D	0.92782	0.7705	L	0.42245	1.32	0.46874	D	0.999236	D;B;B;D;D	0.69078	0.969;0.188;0.002;0.997;0.987	P;B;B;D;P	0.66196	0.805;0.062;0.012;0.942;0.886	D	0.91773	0.5429	10	0.56958	D	0.05	.	10.127	0.42656	0.9209:0.0:0.0791:0.0	.	60;183;183;183;183	B4DPJ3;B4DKC0;Q9H252-2;Q9H252;Q9H252-3	.;.;.;KCNH6_HUMAN;.	R	183	ENSP00000318212:Q183R;ENSP00000396900:Q183R	ENSP00000318212:Q183R	Q	+	2	0	KCNH6	58961508	1.000000	0.71417	0.999000	0.59377	0.811000	0.45836	4.897000	0.63231	0.832000	0.34804	0.379000	0.24179	CAG	.	.	.	none		0.607	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779		G	61607776	A	G	61607776	3	3	21	1	0	0	0	0	1	0	0	0	8043	188	7	3	562	3	KCNH6	17	61607776	Missense_Mutation	SNP	A	TCGA-2Z-A9JR-01A-12D-A42J-10	22700497	61607776	19587434	47	1448											
ATP5H	10476	hgsc.bcm.edu	37	chr17	73038343	73038343	+	Frame_Shift_Del	DEL	G	G	-																															tgtagtaagcccagtcgataGctggtggattctcaggtaaa																										TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr17:73038343delG	ENST00000301587.4	-	3	199	c.152delC	c.(151-153)gctfs	p.A51fs	KCTD2_ENST00000581589.1_Intron|ATP5H_ENST00000344546.4_Frame_Shift_Del_p.A51fs|RN7SL573P_ENST00000485340.2_RNA|KCTD2_ENST00000584767.1_Intron	NM_006356.2	NP_006347.1	O75947	ATP5H_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit d	51					ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) (GO:0000276)|mitochondrion (GO:0005739)	hydrogen ion transmembrane transporter activity (GO:0015078)|transmembrane transporter activity (GO:0022857)			lung(1)|skin(1)	2	all_lung(278;0.226)					CCAGTCGATAGCTGGTGGATT	0.458																																					p.A51fs		Atlas-Indel,Pindel	.											.	ATP5H	5	.	0			c.153delT						PASS	.						73	61	65					17																	73038343		2203	4300	6503	SO:0001589	frameshift_variant	10476	exon3			.	AF087135	CCDS11712.1, CCDS32727.1	17q25	2014-01-24	2010-06-11		ENSG00000167863	ENSG00000167863		"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	845	protein-coding gene	gene with protein product			"ATP synthase, H+ transporting, mitochondrial F0 complex, subunit d"			11042152	Standard	NM_006356		Approved	ATPQ, ATP5JD	uc002jmn.1	O75947	OTTHUMG00000179219	ENST00000301587.4:c.152delC	chr17.hg19:g.73038343delG	ENSP00000301587:p.Ala51fs	87.0	0.0	0		98.0	50.0	0.510204	NM_006356	B2R5L6|Q9H3J4	Frame_Shift_Del	DEL	ENST00000301587.4	hg19	CCDS11712.1																																																																																			.	.	.	none		0.458	ATP5H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445318.1	NM_006356		-	73038343	G	-	73038343	7	5	21	1	0	1	0	1	0	0	0	0	1156	971	34	0	349	0	ATP5H	17	73038343	Frame_Shift_Del	DEL	G	TCGA-2Z-A9JR-01A-12D-A42J-10	11430567	73038343	8156867	48	1449											
SAP30BP	29115	hgsc.bcm.edu	37	chr17	73700857	73700857	+	Missense_Mutation	SNP	T	T	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	caaggcccagaaaattgagaTggacaaattggaaaaggcca	18	5	11	7	0	0	2	0	1	0	2	0	5	0	4	2	4	0	0	2	4	6	2			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr17:73700857T>G	ENST00000584667.1	+	9	880	c.623T>G	c.(622-624)aTg>aGg	p.M208R	SAP30BP_ENST00000355423.3_Missense_Mutation_p.M192R	NM_013260.6	NP_037392.1			SAP30 binding protein											kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)	17	all_cancers(13;6.42e-08)		all cancers(21;4.25e-07)|Epithelial(20;9.57e-07)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			AAAATTGAGATGGACAAATTG	0.512																																					p.M208R		Atlas-SNP	.											.	SAP30BP	30	.	0			c.T623G						PASS	.						120	111	114					17																	73700857		2203	4300	6503	SO:0001583	missense	29115	exon9			TTGAGATGGACAA	AY082382	CCDS11726.1	17q25.1	2006-01-05				ENSG00000161526			30785	protein-coding gene	gene with protein product		610218				15496587	Standard	NM_013260		Approved	HCNGP, HTRG, HTRP	uc002jpe.3	Q9UHR5		ENST00000584667.1:c.623T>G	chr17.hg19:g.73700857T>G	ENSP00000462116:p.Met208Arg	111.0	0.0	.		122.0	16.0	.	NM_013260		Missense_Mutation	SNP	ENST00000584667.1	hg19	CCDS11726.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.447631	0.84101	.	.	ENSG00000161526	ENST00000355423;ENST00000293208	.	.	.	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.72510	0.3469	L	0.56199	1.76	0.80722	D	1	D;D	0.65815	0.994;0.995	D;D	0.70227	0.952;0.968	T	0.67518	-0.5650	9	0.13108	T	0.6	-29.2385	15.8909	0.79296	0.0:0.0:0.0:1.0	.	192;208	Q9UHR5-2;Q9UHR5	.;S30BP_HUMAN	R	208;192	.	ENSP00000293208:M192R	M	+	2	0	SAP30BP	71212452	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.092000	0.76930	2.146000	0.66826	0.533000	0.62120	ATG	.	.	.	none		0.512	SAP30BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448227.1	NM_013260		G	73700857	T	G	73700857	3	3	21	1	0	0	0	0	1	0	0	0	13847	1464	51	5	657	5	SAP30BP	17	73700857	Missense_Mutation	SNP	T	TCGA-2Z-A9JR-01A-12D-A42J-10	662514	73700857	7494353	49	1450											
APC2	10297	hgsc.bcm.edu	37	chr19	1465652	1465652	+	Frame_Shift_Del	DEL	G	G	-																															tttgacgacgacgatgcaccGtcatccctggctgcggccgc																								rs61757708		TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr19:1465652delG	ENST00000535453.1	+	14	4065	c.2352delG	c.(2350-2352)ccgfs	p.P784fs	CTB-25B13.12_ENST00000588225.1_RNA|APC2_ENST00000233607.2_Frame_Shift_Del_p.P784fs|C19orf25_ENST00000588427.1_Intron|APC2_ENST00000238483.4_Frame_Shift_Del_p.P510fs			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)		ACGATGCACCGTCATCCCTGG	0.706																																					p.P784fs		Atlas-Indel,Pindel	.											.	APC2	50	.	0			c.2351delC						PASS	.						8	11	10					19																	1465652		2061	4181	6242	SO:0001589	frameshift_variant	10297	exon15			.		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.2352delG	chr19.hg19:g.1465652delG	ENSP00000442954:p.Pro784fs	160.0	0.0	0		102.0	28.0	0.27451	NM_005883	C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	Frame_Shift_Del	DEL	ENST00000535453.1	hg19	CCDS12068.1																																																																																			.	.	.	none		0.706	APC2-004	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449539.2	NM_005883		-	1465652	G	-	1465652	7	5	21	1	0	1	0	1	0	0	0	0	764	1132	40	0	2406	0	APC2	19	1465652	Frame_Shift_Del	DEL	G	TCGA-2Z-A9JR-01A-12D-A42J-10		1465652	57663331	50	1451											
ZNF91	7644	hgsc.bcm.edu	37	chr19	23545348	23545348	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctctgggcagttgtgagacActggttaagtttattataac	10	14	11	6	0	1	1	0	1	1	1	1	2	1	1	0	2	1	5	0	2	4	6			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr19:23545348A>G	ENST00000300619.7	-	4	638	c.433T>C	c.(433-435)Tgt>Cgt	p.C145R	ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000397082.2_Missense_Mutation_p.C113R	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	145					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)				GTTGTGAGACACTGGTTAAGT	0.323																																					p.C145R		Atlas-SNP	.											.	ZNF91	349	.	0			c.T433C						PASS	.						80	85	83					19																	23545348		2159	4277	6436	SO:0001583	missense	7644	exon4			TGAGACACTGGTT	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.433T>C	chr19.hg19:g.23545348A>G	ENSP00000300619:p.Cys145Arg	129.0	0.0	.		105.0	39.0	.	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	hg19	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.778055	0.00634	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.05717	3.43;3.4	0.428	0.428	0.16499	.	.	.	.	.	T	0.15652	0.0377	M	0.75264	2.295	0.09310	N	1	B;D	0.54964	0.04;0.969	B;P	0.59643	0.034;0.861	T	0.18493	-1.0335	8	0.21014	T	0.42	.	.	.	.	.	113;145	Q05481-2;Q05481	.;ZNF91_HUMAN	R	145;113	ENSP00000300619:C145R;ENSP00000380272:C113R	ENSP00000300619:C145R	C	-	1	0	ZNF91	23337188	0.005000	0.15991	0.003000	0.11579	0.118000	0.20060	0.756000	0.26419	0.368000	0.24481	0.147000	0.16070	TGT	.	.	.	none		0.323	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		G	23545348	A	G	23545348	3	3	21	1	0	0	0	0	1	0	0	0	18212	159	6	3	3146	3	ZNF91	19	23545348	Missense_Mutation	SNP	A	TCGA-2Z-A9JR-01A-12D-A42J-10	22079696	23545348	35583635	51	1452											
PPFIA3	8541	hgsc.bcm.edu	37	chr19	49631270	49631271	+	Missense_Mutation	DNP	GC	GC	TT																															gcgcctgctggagacgctgcGcgaggcacaggacgggttgg																										TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr19:49631270_49631271GC>TT	ENST00000334186.4	+	2	489_490	c.140_141GC>TT	c.(139-141)cGC>cTT	p.R47L	PPFIA3_ENST00000602351.1_Missense_Mutation_p.R47L	NM_003660.2	NP_003651.1	O75145	LIPA3_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 3	47					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|presynaptic active zone (GO:0048786)				NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(16)|pancreas(1)|prostate(1)|skin(4)|urinary_tract(1)	35		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)		GAGACGCTGCGCGAGGCACAGG	0.743																																					p.R47L|p.R47R		Atlas-SNP	.											.	PPFIA3	71	.	0			c.G140T|c.C141T						PASS	.																																			SO:0001583	missense	8541	exon2			CGCTGCGCGAGGC|GCTGCGCGAGGCA	AF034800	CCDS12758.1	19q13.33	2013-09-23			ENSG00000177380	ENSG00000177380		"Sterile alpha motif (SAM) domain containing"	9247	protein-coding gene	gene with protein product	"protein tyrosine phosphatase, receptor type, f polypeptide, alpha 3", "liprin-alpha 3", "liprin"	603144				9624153, 9734811	Standard	NM_003660		Approved	KIAA0654, LPNA3, MGC126567, MGC126569	uc002pmr.3	O75145	OTTHUMG00000183213	Exception_encountered	chr19.hg19:g.49631270_49631271delinsTT	ENSP00000335614:p.Arg47Leu	7.0|8.0	0.0	.		8.0	5.0	.	NM_003660	A8K142|Q3MJA0|Q9H8B5|Q9UEW4	Missense_Mutation|Silent	SNP	ENST00000334186.4	hg19	CCDS12758.1																																																																																			.	.	.	none		0.743	PPFIA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465688.1	NM_003660		TT	49631271	GC	TT	49631270	3	4	21	1	0	0	0	0	1	0	0	0	12318	1087	38	4	142	4	PPFIA3	19	49631270	Missense_Mutation	DNP	GC	TCGA-2Z-A9JR-01A-12D-A42J-10	26085922	49631270	9497713	52	1453											
CTSA	5476	hgsc.bcm.edu	37	chr20	44520635	44520635	+	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	tcccggctgcagctcactagAtgggctcctcacagagcatg	8	8	11	14	1	2	2	2	0	0	2	4	2	4	2	2	2	3	5	2	2	1	1			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr20:44520635A>T	ENST00000372459.2	+	2	468	c.275A>T	c.(274-276)gAt>gTt	p.D92V	NEURL2_ENST00000372518.4_5'Flank|CTSA_ENST00000191018.5_Missense_Mutation_p.D92V|CTSA_ENST00000354880.5_Missense_Mutation_p.D110V|RP3-337O18.9_ENST00000607703.1_RNA|CTSA_ENST00000372484.3_Missense_Mutation_p.D110V			P10619	PPGB_HUMAN	cathepsin A	92					glycosphingolipid metabolic process (GO:0006687)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|enzyme activator activity (GO:0008047)|serine-type carboxypeptidase activity (GO:0004185)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|skin(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.0122)				AGCTCACTAGATGGGCTCCTC	0.602											OREG0025986	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D110V		Atlas-SNP	.											.	CTSA	52	.	0			c.A329T						PASS	.						38	43	41					20																	44520635		2203	4300	6503	SO:0001583	missense	5476	exon3			CACTAGATGGGCT	M22960	CCDS13385.2, CCDS46609.1, CCDS54467.1	20q13.12	2012-02-10	2006-12-05	2006-12-05	ENSG00000064601	ENSG00000064601	3.4.16.5	"Cathepsins"	9251	protein-coding gene	gene with protein product	"carboxypeptidase C", "lysosomal protective protein", "carboxypeptidase-L", "carboxypeptidase Y-like kininase", "deamidase", "lysosomal carboxypeptidase A", "urinary kininase"	613111	"protective protein for beta-galactosidase (galactosialidosis)"	GSL, PPGB		2071143	Standard	NM_000308		Approved		uc002xqh.3	P10619	OTTHUMG00000033078	ENST00000372459.2:c.275A>T	chr20.hg19:g.44520635A>T	ENSP00000361537:p.Asp92Val	84.0	0.0	.	924	30.0	11.0	.	NM_000308	B2R798|Q561W6|Q5JZH1|Q96KJ2|Q9BR08|Q9BW68	Missense_Mutation	SNP	ENST00000372459.2	hg19	CCDS46609.1	.	.	.	.	.	.	.	.	.	.	A	28.6	4.931780	0.92389	.	.	ENSG00000064601	ENST00000354880;ENST00000372484;ENST00000191018;ENST00000419493;ENST00000372459	D;D;D;D;D	0.92348	-3.02;-3.02;-3.02;-3.02;-3.02	5.51	5.51	0.81932	.	0.086182	0.85682	D	0.000000	D	0.93383	0.7890	L	0.59436	1.845	0.80722	D	1	D;P;P	0.54601	0.967;0.744;0.744	P;P;P	0.57548	0.823;0.687;0.592	D	0.91572	0.5272	10	0.20046	T	0.44	.	15.2903	0.73862	1.0:0.0:0.0:0.0	.	109;92;109	B4E324;P10619;Q59EV6	.;PPGB_HUMAN;.	V	110;110;92;92;92	ENSP00000346952:D110V;ENSP00000361562:D110V;ENSP00000191018:D92V;ENSP00000408533:D92V;ENSP00000361537:D92V	ENSP00000191018:D92V	D	+	2	0	CTSA	43954042	1.000000	0.71417	0.729000	0.30791	0.899000	0.52679	5.173000	0.65010	2.088000	0.63022	0.454000	0.30748	GAT	.	.	.	none		0.602	CTSA-012	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471297.2	NM_000308		T	44520635	A	T	44520635	3	4	21	1	0	0	0	0	1	0	0	0	4031	333	12	5	339	5	CTSA	20	44520635	Missense_Mutation	SNP	A	TCGA-2Z-A9JR-01A-12D-A42J-10		44520635	18504885	53	1454											
KCNQ2	3785	hgsc.bcm.edu	37	chr20	62044846	62044846	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacagcatgtccaggtggcCggctgagtactgctcgatga	8	8	15	10	2	0	2	0	2	0	0	2	4	1	3	2	4	3	4	2	4	1	1			TCGA-2Z-A9JR-01A-12D-A42J-10	TCGA-2Z-A9JR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9a5edc5e-790b-41c7-b1c1-49106b297a3d	dea33a63-ced9-4e0a-a451-ffb60520dc94	g.chr20:62044846C>T	ENST00000359125.2	-	15	1894	c.1720G>A	c.(1720-1722)Ggc>Agc	p.G574S	KCNQ2_ENST00000354587.3_Missense_Mutation_p.G546S|KCNQ2_ENST00000359689.1_Missense_Mutation_p.G574S|KCNQ2_ENST00000357249.2_Missense_Mutation_p.G556S|KCNQ2_ENST00000360480.3_Missense_Mutation_p.G546S|KCNQ2_ENST00000344462.4_Missense_Mutation_p.G543S|KCNQ2_ENST00000370224.1_Missense_Mutation_p.G546S	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	574					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)	p.G574S(1)		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)	TCCAGGTGGCCGGCTGAGTAC	0.627																																					p.G574S		Atlas-SNP	.											KCNQ2,NS,carcinoma,0,1	KCNQ2	201	.	1	Substitution - Missense(1)	prostate(1)	c.G1720A						PASS	.						98	85	89					20																	62044846		2203	4300	6503	SO:0001583	missense	3785	exon15			GGTGGCCGGCTGA	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.1720G>A	chr20.hg19:g.62044846C>T	ENSP00000352035:p.Gly574Ser	350.0	0.0	.		192.0	70.0	.	NM_172107	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Missense_Mutation	SNP	ENST00000359125.2	hg19	CCDS13520.1	.	.	.	.	.	.	.	.	.	.	c	35	5.507931	0.96386	.	.	ENSG00000075043	ENST00000357249;ENST00000359125;ENST00000370226;ENST00000354587;ENST00000359689;ENST00000430658;ENST00000360480;ENST00000344462;ENST00000370224;ENST00000370222	D;D;D;D;D;D;D;D;D;D	0.99923	-8.01;-8.01;-8.01;-8.01;-8.01;-8.01;-8.01;-8.01;-8.01;-8.01	4.99	4.99	0.66335	Potassium channel, voltage dependent, KCNQ, C-terminal (1);	0.138723	0.49916	D	0.000125	D	0.99924	0.9965	M	0.87547	2.89	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.95748	0.8789	10	0.62326	D	0.03	-37.6648	18.2551	0.90017	0.0:1.0:0.0:0.0	.	546;556;543;574	O43526-3;O43526-2;O43526-4;O43526	.;.;.;KCNQ2_HUMAN	S	556;574;544;546;574;543;546;534;546;546	ENSP00000349789:G556S;ENSP00000352035:G574S;ENSP00000359246:G544S;ENSP00000346601:G546S;ENSP00000352718:G574S;ENSP00000399612:G543S;ENSP00000353668:G546S;ENSP00000339611:G534S;ENSP00000359244:G546S;ENSP00000359242:G546S	ENSP00000339611:G534S	G	-	1	0	KCNQ2	61515290	1.000000	0.71417	0.937000	0.37676	0.905000	0.53344	7.660000	0.83776	2.323000	0.78572	0.556000	0.70494	GGC	.	.	.	none		0.627	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109		T	62044846	C	T	62044846	3	4	21	1	0	0	0	0	1	0	0	0	8090	652	23	1	910	1	KCNQ2	20	62044846	Missense_Mutation	SNP	C	TCGA-2Z-A9JR-01A-12D-A42J-10	17524211	62044846	980674	54	1455											
MACF1	23499	hgsc.bcm.edu	37	chr1	39550024	39550024	+	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	cccaggggacaccttgccctGgaacctgccactgcatgagc	8	6	11	16	0	0	1	0	1	0	0	0	3	0	3	5	3	5	1	5	3	1	1			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr1:39550024G>C	ENST00000372915.3	+	1	221	c.134G>C	c.(133-135)tGg>tCg	p.W45S	MACF1_ENST00000317713.7_Missense_Mutation_p.W45S|MACF1_ENST00000484793.1_Missense_Mutation_p.W45S|MACF1_ENST00000545844.1_Missense_Mutation_p.W45S|MACF1_ENST00000361689.2_Missense_Mutation_p.W45S|MACF1_ENST00000602421.1_Missense_Mutation_p.W45S|MACF1_ENST00000567887.1_Missense_Mutation_p.W45S|MACF1_ENST00000539005.1_Missense_Mutation_p.W45S			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	45	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)			ACCTTGCCCTGGAACCTGCCA	0.617																																					p.W45S		Atlas-SNP	.											.	MACF1	909	.	0			c.G134C						PASS	.						50	42	45					1																	39550024		2203	4300	6503	SO:0001583	missense	23499	exon3			TGCCCTGGAACCT	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.134G>C	chr1.hg19:g.39550024G>C	ENSP00000362006:p.Trp45Ser	52.0	0.0	.		44.0	15.0	.	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.	.	.	.	.	.	.	.	.	.	G	24.5	4.540445	0.85917	.	.	ENSG00000127603	ENST00000484793;ENST00000545844;ENST00000372915;ENST00000361689;ENST00000404645;ENST00000317713;ENST00000539005	T;T;T;T;T	0.64260	-0.06;0.0;-0.06;-0.09;0.1	5.55	5.55	0.83447	.	.	.	.	.	T	0.68091	0.2963	N	0.19112	0.55	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.71104	-0.4689	9	0.54805	T	0.06	.	17.013	0.86411	0.0:0.0:1.0:0.0	.	45	F8W8Q1	.	S	45;45;45;45;61;45;45	ENSP00000439537:W45S;ENSP00000362006:W45S;ENSP00000354573:W45S;ENSP00000313438:W45S;ENSP00000444364:W45S	ENSP00000313438:W45S	W	+	2	0	MACF1	39322611	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.954000	0.93051	2.611000	0.88343	0.655000	0.94253	TGG	.	.	.	none		0.617	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		C	39550024	G	C	39550024	3	2	22	1	0	0	0	0	1	0	0	0	9151	1357	47	4	136	4	MACF1	1	39550024	Missense_Mutation	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10		39550024	209700597	1	1456											
ZZZ3	26009	hgsc.bcm.edu	37	chr1	78034104	78034104	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttttaaactgtaatagttcTttatattcaggtaaattcct	12	20	4	5	0	2	0	1	0	1	0	3	0	3	0	1	1	1	3	1	1	8	12			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr1:78034104T>C	ENST00000370801.3	-	13	2854	c.2379A>G	c.(2377-2379)aaA>aaG	p.K793K	ZZZ3_ENST00000370798.1_Silent_p.K299K|ZZZ3_ENST00000476275.1_5'UTR	NM_015534.4	NP_056349.1	Q8IYH5	ZZZ3_HUMAN	zinc finger, ZZ-type containing 3	793					chromatin organization (GO:0006325)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|stomach(1)|urinary_tract(2)	39						GTAATAGTTCTTTATATTCAG	0.279																																					p.K793K		Atlas-SNP	.											.	ZZZ3	80	.	0			c.A2379G						PASS	.						63	67	65					1																	78034104		2203	4298	6501	SO:0001819	synonymous_variant	26009	exon13			TAGTTCTTTATAT	AL080063	CCDS677.1	1p31.1	2012-08-13			ENSG00000036549	ENSG00000036549		"Zinc fingers, ZZ-type"	24523	protein-coding gene	gene with protein product	"ATAC component 1 homolog (Drosophila)"					16428443, 21304275	Standard	NM_015534		Approved	DKFZP564I052, ATAC1	uc001dhq.3	Q8IYH5	OTTHUMG00000009652	ENST00000370801.3:c.2379A>G	chr1.hg19:g.78034104T>C		228.0	0.0	.		241.0	114.0	.	NM_015534	B7WPC6|Q6N004|Q6N070|Q8IYP0|Q8IYR1|Q8TEK4|Q9Y4U0	Silent	SNP	ENST00000370801.3	hg19	CCDS677.1																																																																																			.	.	.	none		0.279	ZZZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026615.1	NM_015534		C	78034104	T	C	78034104	2	2	22	1	0	0	0	0	0	0	0	1	18268	1606	56	3		3	ZZZ3	1	78034104	Silent	SNP	T	TCGA-2Z-A9JS-01A-21D-A42J-10	38484080	78034104	171216517	2	1457											
SASS6	163786	hgsc.bcm.edu	37	chr1	100573051	100573051	+	Missense_Mutation	SNP	T	T	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	tagtaactgtattcttcaatTtcaacttacccattaaagtt	13	17	3	8	0	3	0	2	0	1	0	3	0	3	0	1	0	3	3	1	0	8	9			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr1:100573051T>G	ENST00000287482.5	-	11	1345	c.1205A>C	c.(1204-1206)aAa>aCa	p.K402T	SASS6_ENST00000462159.1_5'UTR|SASS6_ENST00000535161.1_Missense_Mutation_p.K235T	NM_194292.1	NP_919268.1	Q6UVJ0	SAS6_HUMAN	spindle assembly 6 homolog (C. elegans)	402					centriole replication (GO:0007099)|centrosome duplication (GO:0051298)	centriole (GO:0005814)|centrosome (GO:0005813)|deuterosome (GO:0098536)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	19		all_epithelial(167;4.58e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.085)|all cancers(265;0.139)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.197)		ATTCTTCAATTTCAACTTACC	0.308																																					p.K402T		Atlas-SNP	.											.	SASS6	61	.	0			c.A1205C						PASS	.						70	73	72					1																	100573051		2201	4290	6491	SO:0001583	missense	163786	exon11			TTCAATTTCAACT	AL834265	CCDS764.1	1p21.3	2008-02-05			ENSG00000156876	ENSG00000156876			25403	protein-coding gene	gene with protein product		609321				15665853, 14654843	Standard	NM_194292		Approved	DKFZp761A078, SAS-6, FLJ22097, SAS6	uc001dsu.3	Q6UVJ0	OTTHUMG00000010754	ENST00000287482.5:c.1205A>C	chr1.hg19:g.100573051T>G	ENSP00000287482:p.Lys402Thr	176.0	0.0	.		181.0	77.0	.	NM_194292	D3DT55|Q8N3K0	Missense_Mutation	SNP	ENST00000287482.5	hg19	CCDS764.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.936841	0.73557	.	.	ENSG00000156876	ENST00000287482;ENST00000539329;ENST00000535161	T;T	0.32988	1.43;1.43	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.50939	0.1645	M	0.82716	2.605	0.58432	D	0.999998	D	0.89917	1.0	D	0.79108	0.992	T	0.56062	-0.8041	10	0.48119	T	0.1	-11.3163	15.8532	0.78952	0.0:0.0:0.0:1.0	.	402	Q6UVJ0	SAS6_HUMAN	T	402;375;235	ENSP00000287482:K402T;ENSP00000440169:K235T	ENSP00000287482:K402T	K	-	2	0	SASS6	100345639	1.000000	0.71417	1.000000	0.80357	0.765000	0.43378	6.990000	0.76225	2.140000	0.66376	0.477000	0.44152	AAA	.	.	.	none		0.308	SASS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029656.2	NM_194292		G	100573051	T	G	100573051	3	3	22	1	0	0	0	0	1	0	0	0	13863	1841	64	5	796	5	SASS6	1	100573051	Missense_Mutation	SNP	T	TCGA-2Z-A9JS-01A-21D-A42J-10	22538947	100573051	148677570	3	1458											
WDR77	79084	hgsc.bcm.edu	37	chr1	111990187	111990187	+	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	attctcatctagttcccacaAttcaacagcacctgttgggg	10	12	7	12	0	3	0	2	0	2	0	5	0	4	0	2	2	2	3	2	2	3	5			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr1:111990187A>T	ENST00000235090.5	-	3	519	c.313T>A	c.(313-315)Ttg>Atg	p.L105M	Y_RNA_ENST00000363020.1_RNA|ATP5F1_ENST00000369722.3_5'Flank|ATP5F1_ENST00000483994.1_5'Flank|WDR77_ENST00000411751.2_Intron|WDR77_ENST00000497278.1_5'Flank	NM_024102.2	NP_077007.1	Q9BQA1	MEP50_HUMAN	WD repeat domain 77	105					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA metabolic process (GO:0016070)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|methylosome (GO:0034709)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			NS(2)|endometrium(2)|kidney(2)|large_intestine(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		all_cancers(81;0.000902)|all_epithelial(167;0.00056)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0238)|Colorectal(144;0.0296)|all cancers(265;0.0488)|Epithelial(280;0.0732)|COAD - Colon adenocarcinoma(174;0.114)|LUSC - Lung squamous cell carcinoma(189;0.135)		AGTTCCCACAATTCAACAGCA	0.428																																					p.L105M		Atlas-SNP	.											.	WDR77	21	.	0			c.T313A						PASS	.						123	103	110					1																	111990187		2203	4300	6503	SO:0001583	missense	79084	exon3			CCCACAATTCAAC	BC016946	CCDS835.1	1p13.2	2013-01-09		2005-08-09	ENSG00000116455	ENSG00000116455		"WD repeat domain containing"	29652	protein-coding gene	gene with protein product		611734				11756452, 8619474	Standard	NM_024102		Approved	MEP50	uc001ebb.3	Q9BQA1	OTTHUMG00000011748	ENST00000235090.5:c.313T>A	chr1.hg19:g.111990187A>T	ENSP00000235090:p.Leu105Met	110.0	0.0	.		88.0	27.0	.	NM_024102	B3KMW6|B4DP38|Q3LID2|Q53FU2|Q6JZZ5|Q96GK4|Q9BWY3	Missense_Mutation	SNP	ENST00000235090.5	hg19	CCDS835.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.4|21.4	4.147877|4.147877	0.78001|0.78001	.|.	.|.	ENSG00000116455|ENSG00000116455	ENST00000235090|ENST00000449340	T|.	0.35973|.	1.28|.	5.76|5.76	3.4|3.4	0.38934|0.38934	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.129654|.	0.53938|.	D|.	0.000056|.	T|T	0.43545|0.43545	0.1252|0.1252	L|L	0.59436|0.59436	1.845|1.845	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	P|.	0.62740|.	0.906|.	T|T	0.44907|0.44907	-0.9297|-0.9297	10|5	0.87932|.	D|.	0|.	-11.3985|-11.3985	4.9088|4.9088	0.13811|0.13811	0.4997:0.0:0.5003:0.0|0.4997:0.0:0.5003:0.0	.|.	105|.	Q9BQA1|.	MEP50_HUMAN|.	M|K	105|41	ENSP00000235090:L105M|.	ENSP00000235090:L105M|.	L|N	-|-	1|3	2|2	WDR77|WDR77	111791710|111791710	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	2.746000|2.746000	0.47467|0.47467	1.003000|1.003000	0.39130|0.39130	0.379000|0.379000	0.24179|0.24179	TTG|AAT	.	.	.	none		0.428	WDR77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032465.1	NM_024102		T	111990187	A	T	111990187	3	4	22	1	0	0	0	0	1	0	0	0	17339	98	4	5	747	5	WDR77	1	111990187	Missense_Mutation	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	11417136	111990187	137260434	4	1459											
MTMR11	10903	hgsc.bcm.edu	37	chr1	149907227	149907227	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caatgttgaccagggcaaaaTcgtattcactgttcaaggga	13	10	10	8	1	2	1	2	1	0	0	3	2	2	2	1	2	0	4	1	2	5	4			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr1:149907227T>C	ENST00000439741.2	-	4	540	c.290A>G	c.(289-291)gAt>gGt	p.D97G	MTMR11_ENST00000406732.3_Missense_Mutation_p.D69G|MTMR11_ENST00000361405.6_Missense_Mutation_p.D97G|MTMR11_ENST00000369140.3_Missense_Mutation_p.D25G|MTMR11_ENST00000492824.1_5'UTR	NM_001145862.1	NP_001139334.1	A4FU01	MTMRB_HUMAN	myotubularin related protein 11	97							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)			CAGGGCAAAATCGTATTCACT	0.527																																					p.D97G		Atlas-SNP	.											.	MTMR11	136	.	0			c.A290G						PASS	.						98	82	87					1																	149907227		2203	4300	6503	SO:0001583	missense	10903	exon4			GCAAAATCGTATT	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.290A>G	chr1.hg19:g.149907227T>C	ENSP00000391668:p.Asp97Gly	196.0	0.0	.		151.0	52.0	.	NM_001145862	B3KUE4|B4DJI6|B4DQF5|B4E3Q6|Q3ZCP7|Q5SZ62|Q6P2Q8|Q99752|Q99753	Missense_Mutation	SNP	ENST00000439741.2	hg19	CCDS53360.1	.	.	.	.	.	.	.	.	.	.	T	18.53	3.644788	0.67358	.	.	ENSG00000014914	ENST00000369140;ENST00000439741;ENST00000361405;ENST00000406732	D;D;D;D	0.83992	-1.79;-1.79;-1.79;-1.79	5.11	5.11	0.69529	.	0.112517	0.64402	D	0.000012	D	0.87434	0.6176	M	0.73962	2.25	0.45554	D	0.998509	D;D;D	0.89917	1.0;0.998;0.997	D;D;D	0.87578	0.998;0.995;0.989	D	0.87975	0.2739	9	.	.	.	.	11.2282	0.48897	0.0:0.0:0.0:1.0	.	69;25;97	A4FU01-6;A4FU01-4;A4FU01	.;.;MTMRB_HUMAN	G	25;97;97;69	ENSP00000358136:D25G;ENSP00000391668:D97G;ENSP00000354941:D97G;ENSP00000383948:D69G	.	D	-	2	0	MTMR11	148173851	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	3.778000	0.55371	2.145000	0.66743	0.528000	0.53228	GAT	.	.	.	none		0.527	MTMR11-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_181873		C	149907227	T	C	149907227	3	2	22	1	0	0	0	0	1	0	0	0	9947	1435	50	3	1934	3	MTMR11	1	149907227	Missense_Mutation	SNP	T	TCGA-2Z-A9JS-01A-21D-A42J-10	37917040	149907227	99343394	5	1460											
BNIPL	149428	hgsc.bcm.edu	37	chr1	151009216	151009216	+	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	gtgaagatgggaactatacaAgaggcaggaaaaaagacaga	20	4	13	4	0	0	5	0	1	0	4	0	7	0	7	0	3	2	1	0	3	8	2			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr1:151009216A>T	ENST00000368931.3	+	1	171	c.15A>T	c.(13-15)caA>caT	p.Q5H	BNIPL_ENST00000295294.7_5'UTR	NM_138278.3	NP_612122.2	Q7Z465	BNIPL_HUMAN	BCL2/adenovirus E1B 19kD interacting protein like	5					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|regulation of growth rate (GO:0040009)	cytosol (GO:0005829)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|endometrium(3)|large_intestine(1)|lung(4)|skin(1)	10	Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			GAACTATACAAGAGGCAGGAA	0.483																																					p.Q5H		Atlas-SNP	.											.	BNIPL	45	.	0			c.A15T						PASS	.						144	140	142					1																	151009216		1898	4125	6023	SO:0001583	missense	149428	exon1			TATACAAGAGGCA	AF193056	CCDS978.2, CCDS53362.1	1q21.2	2008-02-05			ENSG00000163141	ENSG00000163141			16976	protein-coding gene	gene with protein product		611275				12681488, 11741952	Standard	NM_138278		Approved	BNIPl-1, BNIPL-2, PP753	uc001ewl.2	Q7Z465	OTTHUMG00000035157	ENST00000368931.3:c.15A>T	chr1.hg19:g.151009216A>T	ENSP00000357927:p.Gln5His	138.0	0.0	.		127.0	43.0	.	NM_138278	Q6DK43|Q8TCY7|Q8WYG2	Missense_Mutation	SNP	ENST00000368931.3	hg19	CCDS978.2	.	.	.	.	.	.	.	.	.	.	A	16.64	3.180184	0.57800	.	.	ENSG00000163141	ENST00000368931;ENST00000361277	T;T	0.38401	1.15;1.14	4.7	-1.45	0.08828	.	0.594348	0.15154	N	0.277530	T	0.17109	0.0411	M	0.63428	1.95	0.28607	N	0.908861	P	0.37864	0.61	B	0.38712	0.28	T	0.12502	-1.0545	10	0.59425	D	0.04	.	8.6368	0.33953	0.5017:0.0:0.4983:0.0	.	5	Q7Z465	BNIPL_HUMAN	H	5	ENSP00000357927:Q5H;ENSP00000355333:Q5H	ENSP00000355333:Q5H	Q	+	3	2	BNIPL	149275840	0.182000	0.23173	0.101000	0.21167	0.276000	0.26787	-0.720000	0.04969	-0.128000	0.11641	-0.304000	0.09214	CAA	.	.	.	none		0.483	BNIPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085092.1	NM_138279		T	151009216	A	T	151009216	3	4	22	1	0	0	0	0	1	0	0	0	1480	69	3	5	17	5	BNIPL	1	151009216	Missense_Mutation	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	1101989	151009216	98241405	6	1461											
SLC27A3	11000	hgsc.bcm.edu	37	chr1	153751216	153751216	+	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	agcagtccccattcctgggcTatgctggcgggccagagctg	6	8	14	13	1	0	1	0	0	0	1	2	1	2	1	4	3	3	4	4	3	1	2	rs141064582		TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr1:153751216T>A	ENST00000368661.3	+	7	1707	c.1642T>A	c.(1642-1644)Tat>Aat	p.Y548N	SLC27A3_ENST00000271857.2_Missense_Mutation_p.Y629N|SLC27A3_ENST00000484014.1_3'UTR	NM_024330.1	NP_077306.1	Q5K4L6	S27A3_HUMAN	solute carrier family 27 (fatty acid transporter), member 3	548					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)			ATTCCTGGGCTATGCTGGCGG	0.622																																					p.Y548N		Atlas-SNP	.											.	SLC27A3	42	.	0			c.T1642A						PASS	.						41	42	41					1																	153751216		2203	4300	6503	SO:0001583	missense	11000	exon7			CTGGGCTATGCTG	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.1642T>A	chr1.hg19:g.153751216T>A	ENSP00000357650:p.Tyr548Asn	38.0	0.0	.		20.0	8.0	.	NM_024330	Q5VUQ7|Q5VUQ8|Q5VUR3|Q6ZV16|Q8N2X7|Q8TEJ0|Q96SW5|Q9BTJ5|Q9BTY5	Missense_Mutation	SNP	ENST00000368661.3	hg19	CCDS1053.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.381272	0.82792	.	.	ENSG00000143554	ENST00000271857;ENST00000368661	T;T	0.50813	0.73;0.73	5.14	5.14	0.70334	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.76292	0.3967	H	0.98542	4.26	0.51482	D	0.999923	D	0.76494	0.999	D	0.81914	0.995	D	0.85387	0.1123	10	0.87932	D	0	-14.8688	12.9728	0.58522	0.0:0.0:0.0:1.0	.	548	Q5K4L6	S27A3_HUMAN	N	629;548	ENSP00000271857:Y629N;ENSP00000357650:Y548N	ENSP00000271857:Y629N	Y	+	1	0	SLC27A3	152017840	1.000000	0.71417	0.994000	0.49952	0.801000	0.45260	5.950000	0.70265	2.155000	0.67459	0.460000	0.39030	TAT	.	T|1.000;C|0.000	.	alt		0.622	SLC27A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_024330		A	153751216	T	A	153751216	3	1	22	1	0	0	0	0	1	0	0	0	14540	1522	53	5	1668	5	SLC27A3	1	153751216	Missense_Mutation	SNP	T	TCGA-2Z-A9JS-01A-21D-A42J-10	2742000	153751216	95499405	7	1462											
DENND4B	9909	hgsc.bcm.edu	37	chr1	153903435	153903435	+	Missense_Mutation	SNP	A	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	agactcactgtggaccctccAgagcacatagagaggtgggc	11	6	13	11	0	1	3	1	0	0	3	2	5	2	4	2	3	1	1	2	3	1	1			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr1:153903435A>C	ENST00000361217.4	-	25	4520	c.4102T>G	c.(4102-4104)Tgg>Ggg	p.W1368G	DENND4B_ENST00000474386.1_5'UTR	NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	1368					positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			TGGACCCTCCAGAGCACATAG	0.572																																					p.W1368G		Atlas-SNP	.											.	DENND4B	210	.	0			c.T4102G						PASS	.						29	32	31					1																	153903435		1907	4124	6031	SO:0001583	missense	9909	exon25			CCCTCCAGAGCAC	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"DENN/MADD domain containing"	29044	protein-coding gene	gene with protein product			"KIAA0476"	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.4102T>G	chr1.hg19:g.153903435A>C	ENSP00000354597:p.Trp1368Gly	129.0	0.0	.		107.0	40.0	.	NM_014856	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	hg19	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	A	14.77	2.634508	0.47049	.	.	ENSG00000198837	ENST00000361217	T	0.21543	2.0	5.14	4.01	0.46588	.	0.060660	0.64402	N	0.000001	T	0.28532	0.0706	M	0.71871	2.18	0.58432	D	0.999999	D	0.69078	0.997	P	0.60789	0.879	T	0.08806	-1.0704	10	0.87932	D	0	-8.0431	11.3312	0.49477	0.8472:0.1528:0.0:0.0	.	1368	O75064	DEN4B_HUMAN	G	1368	ENSP00000354597:W1368G	ENSP00000354597:W1368G	W	-	1	0	DENND4B	152170059	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	7.584000	0.82572	0.958000	0.37956	-0.461000	0.05368	TGG	.	.	.	none		0.572	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806		C	153903435	A	C	153903435	3	2	22	1	0	0	0	0	1	0	0	0	4436	188	7	5	404	5	DENND4B	1	153903435	Missense_Mutation	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	152219	153903435	95347186	8	1463											
HCN3	57657	hgsc.bcm.edu	37	chr1	155258126	155258126	+	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	atggctctcctgggcgtaagGgatcaggaagtgagcggctg	8	8	17	8	2	2	1	1	1	1	0	3	3	2	3	1	5	1	3	1	5	2	1			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr1:155258126G>A	ENST00000368358.3	+	8	2205	c.2197G>A	c.(2197-2199)Gga>Aga	p.G733R	HCN3_ENST00000496230.1_3'UTR	NM_020897.2	NP_065948.1	Q9P1Z3	HCN3_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 3	733	Pro-rich.				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)			TGGGCGTAAGGGATCAGGAAG	0.692																																					p.G733R		Atlas-SNP	.											.	HCN3	74	.	0			c.G2197A						PASS	.						31	34	33					1																	155258126		2203	4299	6502	SO:0001583	missense	57657	exon8			CGTAAGGGATCAG	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.2197G>A	chr1.hg19:g.155258126G>A	ENSP00000357342:p.Gly733Arg	60.0	0.0	.		47.0	21.0	.	NM_020897	D3DV90|Q4VX12|Q8N6W6|Q9BWQ2	Missense_Mutation	SNP	ENST00000368358.3	hg19	CCDS1108.1	.	.	.	.	.	.	.	.	.	.	G	14.96	2.692523	0.48202	.	.	ENSG00000143630	ENST00000368358	D	0.97888	-4.59	5.01	4.09	0.47781	.	0.126715	0.36101	N	0.002785	D	0.90752	0.7097	N	0.08118	0	0.36001	D	0.837413	P;P	0.44260	0.83;0.733	P;B	0.44946	0.465;0.346	D	0.91322	0.5083	10	0.40728	T	0.16	.	11.3683	0.49686	0.0887:0.0:0.9113:0.0	.	428;733	B7Z5R8;Q9P1Z3	.;HCN3_HUMAN	R	733	ENSP00000357342:G733R	ENSP00000357342:G733R	G	+	1	0	HCN3	153524750	0.967000	0.33354	1.000000	0.80357	0.964000	0.63967	1.074000	0.30703	1.464000	0.47987	0.557000	0.71058	GGA	.	.	.	none		0.692	HCN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087388.1	NM_020897		A	155258126	G	A	155258126	3	1	22	1	0	0	0	0	1	0	0	0	7005	1233	43	2	2227	2	HCN3	1	155258126	Missense_Mutation	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10	1354691	155258126	93992495	9	1464											
PYHIN1	149628	hgsc.bcm.edu	37	chr1	158911893	158911893	+	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	aatcctcagaaaatgagcaaAgaagaatgtttcatgctaca	18	9	7	7	0	2	4	2	1	0	3	3	4	3	4	1	0	3	3	1	0	7	2			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr1:158911893A>C	ENST00000368140.1	+	5	951	c.706A>C	c.(706-708)Aga>Cga	p.R236R	PYHIN1_ENST00000485134.1_3'UTR|PYHIN1_ENST00000368138.3_Silent_p.R227R|PYHIN1_ENST00000392252.3_Silent_p.R227R|PYHIN1_ENST00000392254.2_Silent_p.R236R	NM_152501.4|NM_198928.4|NM_198929.4	NP_689714.2|NP_945146.1|NP_945147.1	Q6K0P9	IFIX_HUMAN	pyrin and HIN domain family, member 1	236	HIN-200. {ECO:0000255|PROSITE- ProRule:PRU00106}.				cell cycle (GO:0007049)	nucleus (GO:0005634)				breast(2)|endometrium(3)|large_intestine(10)|lung(32)|ovary(3)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_hematologic(112;0.0378)					AAATGAGCAAAGAAGAATGTT	0.348																																					p.R236R		Atlas-SNP	.											.	PYHIN1	208	.	0			c.A706C						PASS	.						71	73	72					1																	158911893		2203	4300	6503	SO:0001819	synonymous_variant	149628	exon5			GAGCAAAGAAGAA	AY185344	CCDS1178.1, CCDS1179.1, CCDS30907.1, CCDS30908.1	1q23.1	2008-02-05			ENSG00000163564	ENSG00000163564			28894	protein-coding gene	gene with protein product		612677				15122330	Standard	NM_152501		Approved	IFIX, MGC23885	uc001ftb.3	Q6K0P9	OTTHUMG00000037109	ENST00000368140.1:c.706A>C	chr1.hg19:g.158911893A>C		159.0	0.0	.		217.0	17.0	.	NM_152501	Q5T3W6|Q6K0P6|Q6K0P7|Q6K0P8|Q8WW65	Silent	SNP	ENST00000368140.1	hg19	CCDS1178.1																																																																																			.	.	.	none		0.348	PYHIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090110.1	NM_152501		C	158911893	A	C	158911893	2	2	22	1	0	0	0	0	0	0	0	1	12878	64	3	5		5	PYHIN1	1	158911893	Silent	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	3653767	158911893	90338728	10	1465											
ABCB10	23456	hgsc.bcm.edu	37	chr1	229684985	229684985	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaggagagactgttacctgaAgtttgcatgaggtagacacg	12	9	14	6	1	0	4	0	2	0	2	0	7	0	5	1	2	2	4	1	2	3	3			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr1:229684985A>G	ENST00000344517.4	-	2	756	c.714T>C	c.(712-714)acT>acC	p.T238T	RNA5SP78_ENST00000364622.1_RNA	NM_012089.2	NP_036221.2	Q9NRK6	ABCBA_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 10	238	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)	31	Breast(184;0.143)|Ovarian(103;0.249)	Prostate(94;0.167)				TGTTACCTGAAGTTTGCATGA	0.542																																					p.T238T		Atlas-SNP	.											.	ABCB10	71	.	0			c.T714C						PASS	.						86	77	80					1																	229684985		2203	4300	6503	SO:0001819	synonymous_variant	23456	exon2			ACCTGAAGTTTGC	U18237	CCDS1580.1	1q32	2012-03-14			ENSG00000135776	ENSG00000135776		"ATP binding cassette transporters / subfamily B"	41	protein-coding gene	gene with protein product	"ATP-binding cassette sub-family B member 10, mitochondrial", "ATP-binding cassette transporter 10", "ABC transporter 10 protein", "mitochondrial ATP-binding cassette 2"	605454				7766993	Standard	NM_012089		Approved	EST20237, M-ABC2, MTABC2	uc001htp.4	Q9NRK6	OTTHUMG00000039471	ENST00000344517.4:c.714T>C	chr1.hg19:g.229684985A>G		127.0	0.0	.		124.0	57.0	.	NM_012089	Q13040|Q6P1Q8|Q9H3V0	Silent	SNP	ENST00000344517.4	hg19	CCDS1580.1																																																																																			.	.	.	none		0.542	ABCB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095240.1	NM_012089		G	229684985	A	G	229684985	2	3	22	1	0	0	0	0	0	0	0	1	41	59	3	3		3	ABCB10	1	229684985	Silent	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	70773092	229684985	19565636	11	1466											
ADCY3	109	hgsc.bcm.edu	37	chr2	25042856	25042856	+	Missense_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	cagaggggccattggggaagGtggctagcttatcccgcccc	7	7	15	12	1	0	1	0	0	0	1	1	2	1	2	4	6	1	2	4	6	3	3			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr2:25042856G>A	ENST00000260600.5	-	21	4231	c.3380C>T	c.(3379-3381)aCc>aTc	p.T1127I	CENPO_ENST00000473706.1_3'UTR|CENPO_ENST00000380834.2_3'UTR|ADCY3_ENST00000405392.1_Missense_Mutation_p.T714I	NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	1127					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)					ATTGGGGAAGGTGGCTAGCTT	0.582																																					p.T1127I		Atlas-SNP	.											.	ADCY3	114	.	0			c.C3380T						PASS	.						58	50	53					2																	25042856		2203	4300	6503	SO:0001583	missense	109	exon21			GGGAAGGTGGCTA	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.3380C>T	chr2.hg19:g.25042856G>A	ENSP00000260600:p.Thr1127Ile	132.0	0.0	.		139.0	56.0	.	NM_004036	B3KT86|Q53T54|Q9UDB1	Missense_Mutation	SNP	ENST00000260600.5	hg19	CCDS1715.1	.	.	.	.	.	.	.	.	.	.	G	11.73	1.725137	0.30593	.	.	ENSG00000138031	ENST00000260600;ENST00000405392;ENST00000415879	T;T	0.81330	-1.35;-1.48	5.59	4.72	0.59763	.	0.702099	0.14759	N	0.300131	T	0.74718	0.3753	L	0.39898	1.24	0.28882	N	0.894332	B;B;B	0.17268	0.021;0.021;0.001	B;B;B	0.14023	0.01;0.01;0.002	T	0.67393	-0.5682	10	0.41790	T	0.15	.	14.6206	0.68582	0.0711:0.0:0.9289:0.0	.	1128;1127;714	B7ZLX9;O60266;B3KT86	.;ADCY3_HUMAN;.	I	1127;714;1102	ENSP00000260600:T1127I;ENSP00000384484:T714I	ENSP00000260600:T1127I	T	-	2	0	ADCY3	24896360	1.000000	0.71417	0.788000	0.31933	0.028000	0.11728	6.328000	0.72915	1.499000	0.48617	0.655000	0.94253	ACC	.	.	.	none		0.582	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2			A	25042856	G	A	25042856	3	1	22	1	0	0	0	0	1	0	0	0	295	1261	44	2	58	2	ADCY3	2	25042856	Missense_Mutation	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10		25042856	218156517	12	1467											
BIRC6	57448	hgsc.bcm.edu	37	chr2	32740321	32740321	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttaactgaatcacatttggcTacccttgcttcctcttctca	8	16	4	13	0	3	1	2	1	2	0	5	1	4	1	2	1	3	2	2	1	3	6			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr2:32740321T>C	ENST00000421745.2	+	55	10967	c.10833T>C	c.(10831-10833)gcT>gcC	p.A3611A		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	3611					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)					CACATTTGGCTACCCTTGCTT	0.403																																					p.A3611A	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.T10833C						PASS	.						130	129	129					2																	32740321		2203	4300	6503	SO:0001819	synonymous_variant	57448	exon55			TTTGGCTACCCTT	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.10833T>C	chr2.hg19:g.32740321T>C		80.0	0.0	.		65.0	25.0	.	NM_016252	Q9ULD1	Silent	SNP	ENST00000421745.2	hg19	CCDS33175.2																																																																																			.	.	.	none		0.403	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		C	32740321	T	C	32740321	2	2	22	1	0	0	0	0	0	0	0	1	1438	1509	53	3		3	BIRC6	2	32740321	Silent	SNP	T	TCGA-2Z-A9JS-01A-21D-A42J-10	7697465	32740321	210459052	13	1468											
LIMS1	3987	hgsc.bcm.edu	37	chr2	109292439	109292439	+	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	ggtgcttgccgacggcccatCgaagggcgcgtggtgaacgc	6	6	17	12	6	0	1	0	1	0	0	1	3	0	1	2	4	3	1	2	4	2	1			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr2:109292439C>T	ENST00000393310.1	+	6	767	c.600C>T	c.(598-600)atC>atT	p.I200I	LIMS1_ENST00000409441.1_Silent_p.I237I|LIMS1_ENST00000338045.3_Silent_p.I200I|LIMS1_ENST00000332345.6_Silent_p.I200I|LIMS1_ENST00000410093.1_Silent_p.I204I|AC010095.5_ENST00000411710.1_RNA|LIMS1_ENST00000542845.1_Silent_p.I262I|LIMS1_ENST00000544547.1_Silent_p.I212I	NM_001193488.1	NP_001180417.1	P48059	LIMS1_HUMAN	LIM and senescent cell antigen-like domains 1	200	LIM zinc-binding 4. {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						GACGGCCCATCGAAGGGCGCG	0.547																																					p.I262I		Atlas-SNP	.											.	LIMS1	38	.	0			c.C786T						PASS	.						46	41	42					2																	109292439		2203	4300	6503	SO:0001819	synonymous_variant	3987	exon6			GCCCATCGAAGGG		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.600C>T	chr2.hg19:g.109292439C>T		199.0	0.0	.		163.0	72.0	.	NM_001193485	B2RAJ4|B7Z483|B7Z7R3|B7Z907|Q53TE0|Q9BS44	Silent	SNP	ENST00000393310.1	hg19	CCDS2078.1																																																																																			.	.	.	none		0.547	LIMS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253596.1	NM_004987		T	109292439	C	T	109292439	2	4	22	1	0	0	0	0	0	0	0	1	8810	874	31	1		1	LIMS1	2	109292439	Silent	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10	76552118	109292439	133906934	14	1469											
LRP2	4036	hgsc.bcm.edu	37	chr2	170058161	170058163	+	In_Frame_Del	DEL	TTA	TTA	-																															aatttttctcatctgaagtgTtattatcatggcagttgtct																										TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	TTA	TTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr2:170058161_170058163delTTA	ENST00000263816.3	-	44	8712_8714	c.8427_8429delTAA	c.(8425-8430)aataac>aac	p.2809_2810NN>N		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2809	LDL-receptor class A 18. {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)"	ATCTGAAGTGTTATTATCATGGC	0.379																																					p.2810_2810del		Atlas-Indel,Pindel	.											.	LRP2	751	.	0			c.8428_8430del						PASS	.																																			SO:0001651	inframe_deletion	4036	exon44			.		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.8427_8429delTAA	chr2.hg19:g.170058164_170058166delTTA	ENSP00000263816:p.Asn2810del	57.0	0.0	0		49.0	25.0	0.510204	NM_004525	O00711|Q16215	In_Frame_Del	DEL	ENST00000263816.3	hg19	CCDS2232.1																																																																																			.	.	.	none		0.379	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		-	170058163	TTA	-	170058161	7	5	22	1	0	1	0	1	0	0	0	0	8963	1725	60	0	5682	0	LRP2	2	170058161	In_Frame_Del	DEL	TTA	TCGA-2Z-A9JS-01A-21D-A42J-10	60765722	170058161	73141212	15	1470											
SP3	6670	hgsc.bcm.edu	37	chr2	174820712	174820712	+	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	tgctgaccatctgctgactgGatctgtggtatcacttgata	8	14	10	9	0	3	3	1	3	2	0	3	4	3	4	1	2	2	3	1	2	2	3			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr2:174820712G>A	ENST00000310015.6	-	4	1058	c.528C>T	c.(526-528)atC>atT	p.I176I	SP3_ENST00000455789.2_Silent_p.I123I|SP3_ENST00000483084.1_5'Flank|SP3_ENST00000418194.2_Silent_p.I108I	NM_001172712.1|NM_003111.4	NP_001166183.1|NP_003102.1	Q02447	SP3_HUMAN	Sp3 transcription factor	176	Transactivation domain (Gln-rich).				B cell differentiation (GO:0030183)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|embryonic skeletal system development (GO:0048706)|enucleate erythrocyte differentiation (GO:0043353)|granulocyte differentiation (GO:0030851)|liver development (GO:0001889)|lung development (GO:0030324)|megakaryocyte differentiation (GO:0030219)|monocyte differentiation (GO:0030224)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|T cell differentiation (GO:0030217)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)		EWSR1/SP3(3)	NS(2)|large_intestine(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.185)			CTGCTGACTGGATCTGTGGTA	0.403																																					p.I176I		Atlas-SNP	.											.	SP3	82	.	0			c.C528T						PASS	.						247	244	245					2																	174820712		2203	4300	6503	SO:0001819	synonymous_variant	6670	exon4			TGACTGGATCTGT	M97191	CCDS2254.1, CCDS46452.1	2q31	2013-01-08			ENSG00000172845	ENSG00000172845		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	11208	protein-coding gene	gene with protein product		601804				1341900, 1454515	Standard	NM_003111		Approved	SPR-2	uc002uig.3	Q02447	OTTHUMG00000132333	ENST00000310015.6:c.528C>T	chr2.hg19:g.174820712G>A		127.0	0.0	.		104.0	44.0	.	NM_003111	A0AVL9|B4E2B7|Q69B26|Q69B27|Q8TD56|Q8WWU4|Q9BQR1	Silent	SNP	ENST00000310015.6	hg19	CCDS2254.1	.	.	.	.	.	.	.	.	.	.	G	3.289	-0.145284	0.06627	.	.	ENSG00000172845	ENST00000416195	.	.	.	5.95	4.73	0.59995	.	.	.	.	.	T	0.58807	0.2148	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55829	-0.8079	4	.	.	.	.	8.0434	0.30534	0.77:0.0:0.23:0.0	.	.	.	.	F	133	.	.	S	-	2	0	SP3	174528958	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.317000	0.33631	1.063000	0.40649	-0.440000	0.05779	TCC	.	.	.	none		0.403	SP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255452.1	NM_003111		A	174820712	G	A	174820712	2	1	22	1	0	0	0	0	0	0	0	1	14978	1164	41	2		2	SP3	2	174820712	Silent	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10	4762551	174820712	68378661	16	1471											
MAP2	4133	hgsc.bcm.edu	37	chr2	210561373	210561373	+	Frame_Shift_Del	DEL	C	C	-																															agaaacatagaaaagaaaagCcttttaaaaccgggagaggc																										TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr2:210561373delC	ENST00000360351.4	+	8	4794	c.4288delC	c.(4288-4290)cctfs	p.P1430fs	MAP2_ENST00000475600.1_3'UTR|MAP2_ENST00000392194.1_Intron|MAP2_ENST00000447185.1_Frame_Shift_Del_p.P1426fs|MAP2_ENST00000361559.4_Intron|MAP2_ENST00000199940.6_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	1430					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	AAAAGAAAAGCCTTTTAAAAC	0.403																																					p.K1429fs	Pancreas(27;423 979 28787 29963)	Atlas-Indel,Pindel	.											.	MAP2	372	.	0			c.4287delG						PASS	.						60	66	64					2																	210561373		2203	4300	6503	SO:0001589	frameshift_variant	4133	exon8			.		CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"A-kinase anchor proteins"	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.4288delC	chr2.hg19:g.210561373delC	ENSP00000353508:p.Pro1430fs	400.0	0.0	0		341.0	151.0	0.442815	NM_002374	Q17S04|Q8IUX2|Q99975|Q99976	Frame_Shift_Del	DEL	ENST00000360351.4	hg19	CCDS2384.1																																																																																			.	.	.	none		0.403	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538		-	210561373	C	-	210561373	7	5	22	1	0	1	0	1	0	0	0	0	9242	739	26	0	4306	0	MAP2	2	210561373	Frame_Shift_Del	DEL	C	TCGA-2Z-A9JS-01A-21D-A42J-10	35740661	210561373	32638000	17	1472											
PNKD	25953	hgsc.bcm.edu	37	chr2	219205495	219205496	+	Frame_Shift_Ins	INS	-	-	G																															ccttggtcgccattctgtgtINSactcacaagcactggtaagg																										TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr2:219205495_219205496insG	ENST00000273077.4	+	5	561_562	c.510_511insG	c.(511-513)actfs	p.T171fs	PNKD_ENST00000258362.3_Frame_Shift_Ins_p.T147fs|AC021016.8_ENST00000411433.1_RNA|PNKD_ENST00000436005.2_Frame_Shift_Ins_p.T111fs	NM_015488.4	NP_056303.3	Q8N490	PNKD_HUMAN	paroxysmal nonkinesigenic dyskinesia	171					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)		CCATTCTGTGTACTCACAAGCA	0.604																																					p.C170fs		Atlas-Indel,Pindel	.											.	PNKD	58	.	0			c.510_511insG						PASS	.																																			SO:0001589	frameshift_variant	25953	exon5			.		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	Exception_encountered	chr2.hg19:g.219205495_219205496insG	ENSP00000273077:p.Thr171fs	66.0	0.0	0		61.0	24.0	0.393443	NM_015488	A8K1F2|Q96A48|Q9BU26|Q9NSX4|Q9ULN6|Q9Y4T1	Frame_Shift_Ins	INS	ENST00000273077.4	hg19	CCDS2411.1																																																																																			.	.	.	none		0.604	PNKD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256775.2			G	219205496	-	G	219205495	7	5	22	1	0	1	1	0	0	0	0	0	12153	1644	57	0	893	0	PNKD	2	219205495	Frame_Shift_Ins	INS	-	TCGA-2Z-A9JS-01A-21D-A42J-10	8644122	219205495	23993878	18	1473											
C2orf54	79919	hgsc.bcm.edu	37	chr2	241835325	241835325	+	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	tggaagtcctgggcacgcggCgcctcccgggaccggatggc	5	5	17	14	5	0	0	0	0	0	0	2	3	2	3	4	6	0	1	4	6	1	0			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr2:241835325C>G	ENST00000388934.4	-	1	248	c.90G>C	c.(88-90)gcG>gcC	p.A30A		NM_001085437.1	NP_001078906	Q08AI8	CB054_HUMAN	chromosome 2 open reading frame 54	30										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)		GGGCACGCGGCGCCTCCCGGG	0.687																																					p.A30A		Atlas-SNP	.											.	C2orf54	14	.	0			c.G90C						PASS	.						10	12	12					2																	241835325		2081	4195	6276	SO:0001819	synonymous_variant	79919	exon1			ACGCGGCGCCTCC	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.90G>C	chr2.hg19:g.241835325C>G		48.0	0.0	.		54.0	23.0	.	NM_001085437	B3KPP9|H7BXM3|Q08AI9|Q53QU5|Q9H622	Silent	SNP	ENST00000388934.4	hg19	CCDS42839.1																																																																																			.	.	.	none		0.687	C2orf54-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324353.1	NM_024861, NM_001085437		G	241835325	C	G	241835325	2	3	22	1	0	0	0	0	0	0	0	1	2177	755	27	4		4	C2orf54	2	241835325	Silent	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10	22629830	241835325	1364048	19	1474											
CNTN4	152330	hgsc.bcm.edu	37	chr3	3095549	3095549	+	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	cattgaaacaaataaaacatCggtggagctttctttgcctt	13	13	7	8	1	1	1	0	1	1	0	2	2	1	2	1	2	4	1	1	2	4	5			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr3:3095549C>A	ENST00000397461.1	+	23	3254	c.2870C>A	c.(2869-2871)tCg>tAg	p.S957*	CNTN4_ENST00000358480.3_Nonsense_Mutation_p.S738*|CNTN4-AS1_ENST00000442749.2_RNA|CNTN4_ENST00000397459.2_Nonsense_Mutation_p.S629*|CNTN4_ENST00000448906.2_Nonsense_Mutation_p.S629*|CNTN4_ENST00000418658.1_Nonsense_Mutation_p.S957*|CNTN4_ENST00000427331.1_Nonsense_Mutation_p.S957*	NM_001206955.1	NP_001193884.1	Q8IWV2	CNTN4_HUMAN	contactin 4	957	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		AATAAAACATCGGTGGAGCTT	0.423																																					p.S957X		Atlas-SNP	.											.	CNTN4	335	.	0			c.C2870A						PASS	.						98	106	103					3																	3095549		2203	4300	6503	SO:0001587	stop_gained	152330	exon24			AAACATCGGTGGA	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.2870C>A	chr3.hg19:g.3095549C>A	ENSP00000380602:p.Ser957*	148.0	0.0	.		151.0	131.0	.	NM_175607	B2RAX3|Q8IX14|Q8TC35	Nonsense_Mutation	SNP	ENST00000397461.1	hg19	CCDS43041.1	.	.	.	.	.	.	.	.	.	.	C	40	8.002247	0.98605	.	.	ENSG00000144619	ENST00000418658;ENST00000397461;ENST00000427331;ENST00000358480;ENST00000397459;ENST00000448906	.	.	.	5.14	5.14	0.70334	.	0.067800	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.6165	0.91304	0.0:1.0:0.0:0.0	.	.	.	.	X	957;957;957;738;629;629	.	ENSP00000351267:S738X	S	+	2	0	CNTN4	3070549	1.000000	0.71417	0.753000	0.31225	0.999000	0.98932	5.598000	0.67585	2.377000	0.81083	0.655000	0.94253	TCG	.	.	.	none		0.423	CNTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239236.2			A	3095549	C	A	3095549	4	1	22	1	0	0	0	0	0	1	0	0	3645	893	31	4	2952	4	CNTN4	3	3095549	Nonsense_Mutation	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10		3095549	194926881	20	1475											
HDAC11	79885	hgsc.bcm.edu	37	chr3	13525048	13525048	+	Missense_Mutation	SNP	A	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	ggtggtgcacacgaggcgctAtcttaatgagctcaaggtac	10	9	13	9	2	2	1	1	1	1	0	2	2	2	1	0	4	3	4	0	4	4	3			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr3:13525048A>C	ENST00000295757.3	+	3	419	c.236A>C	c.(235-237)tAt>tCt	p.Y79S	HDAC11_ENST00000402271.1_Missense_Mutation_p.Y79S|HDAC11_ENST00000402259.1_Intron|HDAC11_ENST00000404548.1_Missense_Mutation_p.Y79S|HDAC11_ENST00000522202.1_Missense_Mutation_p.Y51S|HDAC11_ENST00000437379.2_Missense_Mutation_p.Y51S|HDAC11_ENST00000433119.1_Missense_Mutation_p.Y51S|HDAC11_ENST00000404040.1_Missense_Mutation_p.Y79S|HDAC11_ENST00000405025.1_Missense_Mutation_p.Y51S|HDAC11_ENST00000446613.2_Intron	NM_024827.3	NP_079103.2	Q96DB2	HDA11_HUMAN	histone deacetylase 11	79	Histone deacetylase.				chromatin modification (GO:0016568)|histone deacetylation (GO:0016575)|oligodendrocyte development (GO:0014003)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone deacetylase activity (GO:0004407)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|transcription factor binding (GO:0008134)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(4)|prostate(3)	13						ACGAGGCGCTATCTTAATGAG	0.647																																					p.Y79S		Atlas-SNP	.											.	HDAC11	39	.	0			c.A236C						PASS	.						67	76	73					3																	13525048		2203	4300	6503	SO:0001583	missense	79885	exon3			GGCGCTATCTTAA	AK025426	CCDS2615.1, CCDS46760.1	3p25.1	2008-07-18			ENSG00000163517	ENSG00000163517	3.5.1.98		19086	protein-coding gene	gene with protein product		607226				11948178	Standard	NM_001136041		Approved		uc003bxy.3	Q96DB2	OTTHUMG00000129800	ENST00000295757.3:c.236A>C	chr3.hg19:g.13525048A>C	ENSP00000295757:p.Tyr79Ser	129.0	0.0	.		114.0	85.0	.	NM_024827	B4DDK1|Q9H6I7|Q9H6X3|Q9NTC9	Missense_Mutation	SNP	ENST00000295757.3	hg19	CCDS2615.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.683964	0.88639	.	.	ENSG00000163517	ENST00000433119;ENST00000295757;ENST00000402271;ENST00000404548;ENST00000404040;ENST00000458642;ENST00000405478;ENST00000405025;ENST00000522202;ENST00000418189;ENST00000434848;ENST00000416248;ENST00000455904;ENST00000437379	D;D;D;T;D;D;D;T;D;D;D;D	0.84223	-1.76;-1.82;-1.76;-0.66;-1.76;-1.76;-1.76;-0.96;-1.76;-1.76;-1.76;-1.76	5.91	5.91	0.95273	Histone deacetylase domain (2);	0.000000	0.85682	D	0.000000	D	0.95082	0.8407	H	0.97611	4.04	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;1.0	D	0.96466	0.9345	10	0.87932	D	0	0.9856	13.7215	0.62730	1.0:0.0:0.0:0.0	.	51;51;51;79	B4DDK1;Q658J9;B5MCV5;Q96DB2	.;.;.;HDA11_HUMAN	S	51;79;79;79;79;79;51;51;51;98;98;51;51;51	ENSP00000295757:Y79S;ENSP00000384123:Y79S;ENSP00000385528:Y79S;ENSP00000385475:Y79S;ENSP00000405403:Y79S;ENSP00000385252:Y51S;ENSP00000384019:Y51S;ENSP00000429794:Y51S;ENSP00000398651:Y98S;ENSP00000402298:Y51S;ENSP00000396122:Y51S;ENSP00000395188:Y51S	ENSP00000295757:Y79S	Y	+	2	0	HDAC11	13500048	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.260000	0.78391	2.254000	0.74563	0.533000	0.62120	TAT	.	.	.	none		0.647	HDAC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252028.5	NM_024827		C	13525048	A	C	13525048	3	2	22	1	0	0	0	0	1	0	0	0	7013	449	16	5	246	5	HDAC11	3	13525048	Missense_Mutation	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	10429499	13525048	184497382	21	1476											
FGD5	152273	hgsc.bcm.edu	37	chr3	14922083	14922083	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctttcctcccacaggtggAaggacagtccagagcccttg	8	9	10	14	0	1	1	0	0	1	1	4	3	4	3	4	3	1	0	4	3	1	2			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr3:14922083A>G	ENST00000285046.5	+	3	2773	c.2663A>G	c.(2662-2664)gAa>gGa	p.E888G	FGD5_ENST00000543601.1_Missense_Mutation_p.E647G	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	888					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						CCACAGGTGGAAGGACAGTCC	0.527																																					p.E888G		Atlas-SNP	.											.	FGD5	248	.	0			c.A2663G						PASS	.						67	67	67					3																	14922083		2071	4204	6275	SO:0001583	missense	152273	exon3			AGGTGGAAGGACA	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.2663A>G	chr3.hg19:g.14922083A>G	ENSP00000285046:p.Glu888Gly	105.0	0.0	.		99.0	4.0	.	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Missense_Mutation	SNP	ENST00000285046.5	hg19	CCDS46767.1	.	.	.	.	.	.	.	.	.	.	A	14.93	2.681534	0.47991	.	.	ENSG00000154783	ENST00000285046;ENST00000543601	T;T	0.77358	-1.09;-0.93	4.99	4.99	0.66335	Dbl homology (DH) domain (1);	0.232426	0.29822	N	0.011101	T	0.71239	0.3316	L	0.57536	1.79	0.39731	D	0.971604	P;B	0.41475	0.751;0.205	B;B	0.34536	0.185;0.032	T	0.75085	-0.3442	10	0.45353	T	0.12	-13.8278	12.9328	0.58296	1.0:0.0:0.0:0.0	.	647;888	B7ZM68;Q6ZNL6	.;FGD5_HUMAN	G	888;647	ENSP00000285046:E888G;ENSP00000445949:E647G	ENSP00000285046:E888G	E	+	2	0	FGD5	14897087	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	4.065000	0.57513	1.874000	0.54306	0.260000	0.18958	GAA	.	.	.	none		0.527	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536		G	14922083	A	G	14922083	3	3	22	1	0	0	0	0	1	0	0	0	5843	246	9	3	2673	3	FGD5	3	14922083	Missense_Mutation	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	1397035	14922083	183100347	22	1477											
SEC22C	9117	hgsc.bcm.edu	37	chr3	42594897	42594897	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaagagcagcataagcaccAccttcatagtcctggctgga	13	8	9	11	0	1	1	1	0	0	1	2	2	2	2	3	2	3	4	3	2	4	4			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr3:42594897A>G	ENST00000264454.3	-	7	898	c.755T>C	c.(754-756)gTg>gCg	p.V252A	SEC22C_ENST00000417572.1_Intron|SEC22C_ENST00000423701.2_Intron|SEC22C_ENST00000273156.7_Intron|SEC22C_ENST00000536332.1_Intron			Q9BRL7	SC22C_HUMAN	SEC22 vesicle trafficking protein homolog C (S. cerevisiae)	252					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)		CATAAGCACCACCTTCATAGT	0.453																																					p.V252A		Atlas-SNP	.											.	SEC22C	27	.	0			c.T755C						PASS	.						97	95	96					3																	42594897		2203	4300	6503	SO:0001583	missense	9117	exon7			AGCACCACCTTCA	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.755T>C	chr3.hg19:g.42594897A>G	ENSP00000264454:p.Val252Ala	65.0	0.0	.		82.0	71.0	.	NM_032970	O95152|Q68CX3|Q6UW18	Missense_Mutation	SNP	ENST00000264454.3	hg19	CCDS2700.1	.	.	.	.	.	.	.	.	.	.	A	9.808	1.182327	0.21870	.	.	ENSG00000093183	ENST00000264454	T	0.16324	2.35	4.25	3.09	0.35607	.	0.345862	0.29594	N	0.011709	T	0.07954	0.0199	N	0.12182	0.205	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.24870	-1.0148	10	0.20046	T	0.44	-23.3351	6.6199	0.22798	0.7104:0.0:0.2896:0.0	.	252	Q9BRL7	SC22C_HUMAN	A	252	ENSP00000264454:V252A	ENSP00000264454:V252A	V	-	2	0	SEC22C	42569901	0.989000	0.36119	1.000000	0.80357	0.995000	0.86356	1.955000	0.40372	0.790000	0.33803	0.482000	0.46254	GTG	.	.	.	none		0.453	SEC22C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254734.1	NM_004206		G	42594897	A	G	42594897	3	3	22	1	0	0	0	0	1	0	0	0	14003	159	6	3	206	3	SEC22C	3	42594897	Missense_Mutation	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	27672814	42594897	155427533	23	1478											
NCKIPSD	51517	hgsc.bcm.edu	37	chr3	48718979	48718979	+	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	cagaggctgaggttgtaccaGttgccacttcttcttctgca	7	13	10	11	0	3	2	0	1	3	1	3	2	3	2	2	2	3	5	2	2	1	6			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr3:48718979G>C	ENST00000294129.2	-	5	952	c.833C>G	c.(832-834)aCt>aGt	p.T278S	NCKIPSD_ENST00000416649.2_Missense_Mutation_p.T271S|NCKIPSD_ENST00000341520.4_Missense_Mutation_p.T278S	NM_016453.2	NP_057537.1	Q9NZQ3	SPN90_HUMAN	NCK interacting protein with SH3 domain	278					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)		GGTTGTACCAGTTGCCACTTC	0.642																																					p.T278S		Atlas-SNP	.											.	NCKIPSD	52	.	0			c.C833G						PASS	.						82	73	76					3																	48718979		2203	4300	6503	SO:0001583	missense	51517	exon5			GTACCAGTTGCCA	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.833C>G	chr3.hg19:g.48718979G>C	ENSP00000294129:p.Thr278Ser	69.0	0.0	.		62.0	52.0	.	NM_016453	B4DFL5|Q6GU34|Q6SPF3|Q8TC10|Q9UGM8	Missense_Mutation	SNP	ENST00000294129.2	hg19	CCDS2776.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.037|0.037	-1.300432|-1.300432	0.01364|0.01364	.|.	.|.	ENSG00000213672|ENSG00000213672	ENST00000415281|ENST00000341520;ENST00000416649;ENST00000294129;ENST00000439518;ENST00000453349;ENST00000426678	.|T;T;T;T	.|0.41065	.|1.01;1.62;1.64;1.66	5.27|5.27	-4.4|-4.4	0.03600|0.03600	.|.	.|1.160740	.|0.06523	.|U	.|0.739951	T|T	0.16085|0.16085	0.0387|0.0387	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.04013	.|0.0;0.0;0.001	T|T	0.27434|0.27434	-1.0074|-1.0074	5|10	.|0.06365	.|T	.|0.9	.|.	5.1942|5.1942	0.15227|0.15227	0.1384:0.1345:0.5335:0.1936|0.1384:0.1345:0.5335:0.1936	.|.	.|278;278;271	.|C9JSC3;Q9NZQ3;Q9NZQ3-3	.|.;SPN90_HUMAN;.	K|S	13|278;271;278;278;200;162	.|ENSP00000342621:T278S;ENSP00000389059:T271S;ENSP00000294129:T278S;ENSP00000409675:T278S	.|ENSP00000294129:T278S	N|T	-|-	3|2	2|0	NCKIPSD|NCKIPSD	48693983|48693983	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.275000|0.275000	0.26752|0.26752	-0.325000|-0.325000	0.07976|0.07976	-0.772000|-0.772000	0.04602|0.04602	-0.471000|-0.471000	0.05019|0.05019	AAC|ACT	.	.	.	none		0.642	NCKIPSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257520.1	NM_016453		C	48718979	G	C	48718979	3	2	22	1	0	0	0	0	1	0	0	0	10232	1029	36	4	1371	4	NCKIPSD	3	48718979	Missense_Mutation	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10	6124082	48718979	149303451	24	1479											
WDFY3	23001	hgsc.bcm.edu	37	chr4	85716133	85716133	+	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	aactgggcaaaaaaagacatCtattaaagaaaagacaacat	23	6	6	6	0	1	3	0	0	1	3	1	3	1	3	0	1	2	1	0	1	10	2			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr4:85716133C>T	ENST00000295888.4	-	20	3575		c.e20-1		WDFY3_ENST00000322366.6_Splice_Site	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3						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)		AAAAAGACATCTATTAAAGAA	0.398																																					.		Atlas-SNP	.											.	WDFY3	314	.	0			c.3168-1G>A						PASS	.						58	57	58					4																	85716133		2203	4300	6503	SO:0001630	splice_region_variant	23001	exon21			AGACATCTATTAA	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.3168-1G>A	chr4.hg19:g.85716133C>T		367.0	0.0	.		387.0	134.0	.	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Splice_Site	SNP	ENST00000295888.4	hg19	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	C	18.48	3.632744	0.67015	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6264	0.95679	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	WDFY3	85935157	1.000000	0.71417	0.996000	0.52242	0.455000	0.32408	7.445000	0.80570	2.717000	0.92951	0.655000	0.94253	.	.	.	.	none		0.398	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991	Intron	T	85716133	C	T	85716133	5	4	22	1	0	0	0	0	0	0	1	0	17282	927	32	2	7609	2	WDFY3	4	85716133	Splice_Site	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10		85716133	105438143	25	1480											
ARHGAP24	83478	hgsc.bcm.edu	37	chr4	86916381	86916381	+	Missense_Mutation	SNP	A	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	acaagctggagagttaggccAgcacaacagactgtccacct	13	6	10	12	0	0	2	0	0	0	2	1	3	1	2	3	2	3	3	3	2	3	1			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr4:86916381A>C	ENST00000395184.1	+	9	2040	c.1574A>C	c.(1573-1575)cAg>cCg	p.Q525P	ARHGAP24_ENST00000264343.4_Missense_Mutation_p.Q432P|ARHGAP24_ENST00000395183.2_Missense_Mutation_p.Q430P	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	525					activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)			breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		GAGTTAGGCCAGCACAACAGA	0.488																																					p.Q525P		Atlas-SNP	.											.	ARHGAP24	116	.	0			c.A1574C						PASS	.						141	120	127					4																	86916381		2203	4300	6503	SO:0001583	missense	83478	exon9			TAGGCCAGCACAA	AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	25361	protein-coding gene	gene with protein product		610586				11230166, 15254788	Standard	NM_001042669		Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.1574A>C	chr4.hg19:g.86916381A>C	ENSP00000378611:p.Gln525Pro	87.0	0.0	.		113.0	44.0	.	NM_001025616	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	Missense_Mutation	SNP	ENST00000395184.1	hg19	CCDS34025.1	.	.	.	.	.	.	.	.	.	.	A	18.85	3.710859	0.68730	.	.	ENSG00000138639	ENST00000395184;ENST00000395183;ENST00000514229;ENST00000264343	T;T;T;T	0.14516	2.84;2.5;2.5;2.5	5.87	5.87	0.94306	.	0.167043	0.53938	D	0.000042	T	0.30293	0.0760	L	0.54323	1.7	0.58432	D	0.999997	D;P;D	0.67145	0.995;0.934;0.996	P;P;P	0.59703	0.862;0.767;0.794	T	0.00939	-1.1507	10	0.66056	D	0.02	.	16.2567	0.82522	1.0:0.0:0.0:0.0	.	430;432;525	Q8N264-3;Q8N264-2;Q8N264	.;.;RHG24_HUMAN	P	525;430;440;432	ENSP00000378611:Q525P;ENSP00000378610:Q430P;ENSP00000425589:Q440P;ENSP00000264343:Q432P	ENSP00000264343:Q432P	Q	+	2	0	ARHGAP24	87135405	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.581000	0.74045	2.242000	0.73789	0.482000	0.46254	CAG	.	.	.	none		0.488	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252815.2	NM_031305		C	86916381	A	C	86916381	3	2	22	1	0	0	0	0	1	0	0	0	873	188	7	5	1720	5	ARHGAP24	4	86916381	Missense_Mutation	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	1200248	86916381	104237895	26	1481											
POU4F2	5458	hgsc.bcm.edu	37	chr4	147560484	147560484	+	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	ggcggcggcggcggcggcggCggcggcggaggccgaagcag	4	0	25	12	10	0	0	0	0	0	0	0	2	0	1	1	11	1	1	1	11	1	0			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr4:147560484C>A	ENST00000281321.3	+	1	440	c.192C>A	c.(190-192)ggC>ggA	p.G64G	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	64	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)					gcggcggcggcggcggcggag	0.771																																					p.G64G		Atlas-SNP	.											.	POU4F2	83	.	0			c.C192A						PASS	.						3	5	5					4																	147560484		1329	2897	4226	SO:0001819	synonymous_variant	5458	exon1			CGGCGGCGGCGGC	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.192C>A	chr4.hg19:g.147560484C>A		72.0	0.0	.		88.0	7.0	.	NM_004575	B1PJR6|B2RC84|Q13883|Q14987	Silent	SNP	ENST00000281321.3	hg19	CCDS34074.1																																																																																			.	.	.	none		0.771	POU4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367020.1	NM_004575		A	147560484	C	A	147560484	2	1	22	1	0	0	0	0	0	0	0	1	12286	755	27	4		4	POU4F2	4	147560484	Silent	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10	60644103	147560484	43593792	27	1482											
KIAA0922	23240	hgsc.bcm.edu	37	chr4	154523827	154523827	+	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	ccttgtgtgcagacgtggttCcaggacccagctgggaggag	7	8	16	10	1	0	1	0	0	0	1	1	4	1	4	3	4	2	3	3	4	0	2			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr4:154523827C>T	ENST00000409663.3	+	23	2636	c.2584C>T	c.(2584-2586)Cca>Tca	p.P862S	KIAA0922_ENST00000409959.3_Missense_Mutation_p.P863S|KIAA0922_ENST00000440693.1_Missense_Mutation_p.P779S	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	862						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)				AGACGTGGTTCCAGGACCCAG	0.512																																					p.P863S		Atlas-SNP	.											.	KIAA0922	214	.	0			c.C2587T						PASS	.						178	172	174					4																	154523827		2203	4300	6503	SO:0001583	missense	23240	exon23			GTGGTTCCAGGAC	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.2584C>T	chr4.hg19:g.154523827C>T	ENSP00000386574:p.Pro862Ser	110.0	0.0	.		111.0	55.0	.	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	hg19	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	C	28.7	4.944424	0.92593	.	.	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	T;T;T;T	0.24723	2.09;1.84;2.08;1.85	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.58637	0.2136	M	0.86268	2.805	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.997	T	0.63580	-0.6605	10	0.72032	D	0.01	-16.3383	19.6869	0.95982	0.0:1.0:0.0:0.0	.	779;863;862	A2VDJ0-3;A2VDJ0-5;A2VDJ0	.;.;T131L_HUMAN	S	862;779;863;640	ENSP00000386574:P862S;ENSP00000409663:P779S;ENSP00000386787:P863S;ENSP00000240487:P640S	ENSP00000240487:P640S	P	+	1	0	KIAA0922	154743277	1.000000	0.71417	0.883000	0.34634	0.994000	0.84299	7.398000	0.79919	2.726000	0.93360	0.655000	0.94253	CCA	.	.	.	none		0.512	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196		T	154523827	C	T	154523827	3	4	22	1	0	0	0	0	1	0	0	0	8208	855	30	2	2677	2	KIAA0922	4	154523827	Missense_Mutation	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10	6963343	154523827	36630449	28	1483											
AGA	175	hgsc.bcm.edu	37	chr4	178354476	178354476	+	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	tatggttggatcttctcctcTtctcatgtattctacagctt	6	19	6	10	0	5	0	1	0	5	0	7	1	5	1	1	2	2	3	1	2	3	8			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr4:178354476T>A	ENST00000264595.2	-	8	959	c.832A>T	c.(832-834)Aga>Tga	p.R278*	AGA_ENST00000506853.1_5'Flank	NM_000027.3|NM_001171988.1	NP_000018.2|NP_001165459.1	P20933	ASPG_HUMAN	aspartylglucosaminidase	278					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)		TCTTCTCCTCTTCTCATGTAT	0.388																																					p.R278X		Atlas-SNP	.											.	AGA	39	.	0			c.A832T						PASS	.						160	157	158					4																	178354476		2203	4300	6503	SO:0001587	stop_gained	175	exon8			CTCCTCTTCTCAT	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.832A>T	chr4.hg19:g.178354476T>A	ENSP00000264595:p.Arg278*	117.0	0.0	.		72.0	27.0	.	NM_000027	B2R7H2|D3DP47|Q4W5Q2|Q6FHN6|Q9UCK6|Q9UCK7|Q9UCK8	Nonsense_Mutation	SNP	ENST00000264595.2	hg19	CCDS3829.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.327041	0.81690	.	.	ENSG00000038002	ENST00000264595;ENST00000502310	.	.	.	5.98	-9.32	0.00643	.	1.744170	0.02144	N	0.057429	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	-18.6433	7.5456	0.27764	0.0:0.3083:0.2807:0.411	.	.	.	.	X	278;135	.	ENSP00000264595:R278X	R	-	1	2	AGA	178591470	0.000000	0.05858	0.004000	0.12327	0.964000	0.63967	-0.368000	0.07543	-1.547000	0.01715	-1.171000	0.01739	AGA	.	.	.	none		0.388	AGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361916.1	NM_000027		A	178354476	T	A	178354476	4	1	22	1	0	0	0	0	0	1	0	0	365	1617	56	5	216	5	AGA	4	178354476	Nonsense_Mutation	SNP	T	TCGA-2Z-A9JS-01A-21D-A42J-10	23830649	178354476	12799800	29	1484											
FAT1	2195	hgsc.bcm.edu	37	chr4	187539964	187539964	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgctcgaaattgtggtgcAttgtcattgtcatctgtaag	8	16	11	6	1	3	0	2	0	1	0	4	1	3	0	0	1	2	4	0	1	2	5			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr4:187539964A>G	ENST00000441802.2	-	10	7985	c.7776T>C	c.(7774-7776)aaT>aaC	p.N2592N		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2592	Cadherin 23. {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						ATTGTGGTGCATTGTCATTGT	0.463										HNSCC(5;0.00058)																											p.N2592N	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T7776C						PASS	.						58	56	56					4																	187539964		1994	4153	6147	SO:0001819	synonymous_variant	2195	exon10			TGGTGCATTGTCA	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.7776T>C	chr4.hg19:g.187539964A>G		95.0	0.0	.		73.0	29.0	.	NM_005245		Silent	SNP	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.	.	none		0.463	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		G	187539964	A	G	187539964	2	3	22	1	0	0	0	0	0	0	0	1	5696	214	8	3		3	FAT1	4	187539964	Silent	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	9185488	187539964	3614312	30	1485											
CLPTM1L	81037	hgsc.bcm.edu	37	chr5	1338066	1338066	+	Missense_Mutation	SNP	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	ctggtcgatgaacaggatggGcaggtaatgcacggttttcc	9	10	14	8	2	0	1	0	1	0	0	2	3	1	2	1	5	2	4	1	5	2	3			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr5:1338066G>A	ENST00000320895.5	-	5	888	c.631C>T	c.(631-633)Ccc>Tcc	p.P211S	CLPTM1L_ENST00000507807.1_Missense_Mutation_p.P78S|CLPTM1L_ENST00000320927.6_Missense_Mutation_p.P211S	NM_030782.3	NP_110409.2	Q96KA5	CLP1L_HUMAN	CLPTM1-like	211					apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24	Lung NSC(6;5.78e-14)|all_lung(6;4.47e-13)|all_epithelial(6;4.47e-09)		Epithelial(17;0.00931)|OV - Ovarian serous cystadenocarcinoma(19;0.0116)|all cancers(22;0.0181)	KIRC - Kidney renal clear cell carcinoma(5;0.177)|Kidney(13;0.208)		AACAGGATGGGCAGGTAATGC	0.527																																					p.P211S		Atlas-SNP	.											.	CLPTM1L	60	.	0			c.C631T						PASS	.						132	107	116					5																	1338066		2203	4297	6500	SO:0001583	missense	81037	exon5			GGATGGGCAGGTA	AK027306	CCDS3862.1	5p15.33	2008-02-05			ENSG00000049656	ENSG00000049656			24308	protein-coding gene	gene with protein product	"cisplatin resistance related protein"	612585				11162647	Standard	NM_030782		Approved	FLJ14400, CRR9	uc003jch.3	Q96KA5	OTTHUMG00000131015	ENST00000320895.5:c.631C>T	chr5.hg19:g.1338066G>A	ENSP00000313854:p.Pro211Ser	94.0	0.0	.		92.0	32.0	.	NM_030782	D3DTC1|Q658W6|Q7LG29|Q96AZ0|Q9H3N4	Missense_Mutation	SNP	ENST00000320895.5	hg19	CCDS3862.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.680386	0.88542	.	.	ENSG00000049656	ENST00000320895;ENST00000507807;ENST00000320927	T;T;T	0.76448	-0.5;-0.5;-1.02	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	D	0.90758	0.7099	M	0.92122	3.275	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.93044	0.6460	10	0.87932	D	0	-28.9216	16.6738	0.85273	0.0:0.0:1.0:0.0	.	211;78	Q96KA5;G5E9Z2	CLP1L_HUMAN;.	S	211;78;211	ENSP00000313854:P211S;ENSP00000423321:P78S;ENSP00000315196:P211S	ENSP00000313854:P211S	P	-	1	0	CLPTM1L	1391066	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	8.128000	0.89595	2.339000	0.79563	0.655000	0.94253	CCC	.	.	.	none		0.527	CLPTM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253649.2	NM_030782		A	1338066	G	A	1338066	3	1	22	1	0	0	0	0	1	0	0	0	3557	1203	42	2	1037	2	CLPTM1L	5	1338066	Missense_Mutation	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10		1338066	179577194	31	1486											
RAI14	26064	hgsc.bcm.edu	37	chr5	34757673	34757673	+	Missense_Mutation	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	cggcaagaagggggccagtgCcaccaaacacgacagtgagg	13	2	15	11	2	0	2	0	1	0	1	0	3	0	2	3	4	2	1	3	4	3	0			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr5:34757673C>T	ENST00000265109.3	+	3	424	c.137C>T	c.(136-138)gCc>gTc	p.A46V	RAI14_ENST00000515799.1_Missense_Mutation_p.A49V|RAI14_ENST00000506376.1_Missense_Mutation_p.A38V|RAI14_ENST00000428746.2_Missense_Mutation_p.A46V|RAI14_ENST00000512629.1_Missense_Mutation_p.A46V|RAI14_ENST00000503673.1_Missense_Mutation_p.A46V|RAI14_ENST00000507276.1_3'UTR|RAI14_ENST00000397449.1_Missense_Mutation_p.A39V	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	46						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)					GGGGCCAGTGCCACCAAACAC	0.537																																					p.A49V		Atlas-SNP	.											.	RAI14	100	.	0			c.C146T						PASS	.						72	69	70					5																	34757673		2203	4300	6503	SO:0001583	missense	26064	exon5			CCAGTGCCACCAA	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.137C>T	chr5.hg19:g.34757673C>T	ENSP00000265109:p.Ala46Val	45.0	0.0	.		41.0	18.0	.	NM_001145525	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Missense_Mutation	SNP	ENST00000265109.3	hg19	CCDS34142.1	.	.	.	.	.	.	.	.	.	.	C	36	5.647579	0.96714	.	.	ENSG00000039560	ENST00000265109;ENST00000514527;ENST00000513974;ENST00000512629;ENST00000428746;ENST00000514873;ENST00000503673;ENST00000504052;ENST00000512305;ENST00000514036;ENST00000515799;ENST00000508315;ENST00000512625;ENST00000506376;ENST00000397449	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.60040	0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22;0.22	5.72	5.72	0.89469	Ankyrin repeat-containing domain (4);	.	.	.	.	T	0.52322	0.1727	N	0.02391	-0.57	0.58432	D	0.999999	D;D;D;D	0.67145	0.972;0.978;0.995;0.996	P;P;P;D	0.63597	0.797;0.871;0.864;0.916	T	0.61811	-0.6986	9	0.26408	T	0.33	-12.1349	19.8937	0.96942	0.0:1.0:0.0:0.0	.	38;46;49;46	Q9P0K7-3;E9PED3;Q9P0K7-2;Q9P0K7	.;.;.;RAI14_HUMAN	V	46;46;46;46;46;46;46;46;46;46;49;46;46;38;39	ENSP00000265109:A46V;ENSP00000424879:A46V;ENSP00000422112:A46V;ENSP00000422377:A46V;ENSP00000388725:A46V;ENSP00000421424:A46V;ENSP00000422942:A46V;ENSP00000422515:A46V;ENSP00000422114:A46V;ENSP00000424502:A46V;ENSP00000427123:A49V;ENSP00000426770:A46V;ENSP00000425115:A46V;ENSP00000423854:A38V;ENSP00000380591:A39V	ENSP00000265109:A46V	A	+	2	0	RAI14	34793430	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	6.052000	0.71080	2.716000	0.92895	0.650000	0.86243	GCC	.	.	.	none		0.537	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577		T	34757673	C	T	34757673	3	4	22	1	0	0	0	0	1	0	0	0	13021	739	26	2	208	2	RAI14	5	34757673	Missense_Mutation	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10	33419607	34757673	146157587	32	1487											
CMYA5	202333	hgsc.bcm.edu	37	chr5	79034827	79034827	+	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	ccaagtgaagagaggctccgTaatagccctgttcaggatga	12	8	12	9	1	1	3	1	2	0	1	2	5	2	4	3	2	1	3	3	2	4	3			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr5:79034827T>A	ENST00000446378.2	+	2	10270	c.10239T>A	c.(10237-10239)cgT>cgA	p.R3413R		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	3413					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)		AGAGGCTCCGTAATAGCCCTG	0.433																																					p.R3413R		Atlas-SNP	.											.	CMYA5	643	.	0			c.T10239A						PASS	.						86	83	84					5																	79034827		1900	4105	6005	SO:0001819	synonymous_variant	202333	exon2			GCTCCGTAATAGC	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.10239T>A	chr5.hg19:g.79034827T>A		117.0	0.0	.		109.0	45.0	.	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Silent	SNP	ENST00000446378.2	hg19	CCDS47238.1																																																																																			.	.	.	none		0.433	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		A	79034827	T	A	79034827	2	1	22	1	0	0	0	0	0	0	0	1	3592	1625	57	5		5	CMYA5	5	79034827	Silent	SNP	T	TCGA-2Z-A9JS-01A-21D-A42J-10	44277154	79034827	101880433	33	1488											
ANKRD34B	340120	hgsc.bcm.edu	37	chr5	79854839	79854839	+	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	aacagggacttcaatgcattGctgatttccttctgaaagat	12	13	8	8	0	2	3	1	2	1	1	3	4	3	4	1	1	3	2	1	1	3	4			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr5:79854839G>T	ENST00000338682.3	-	5	1672	c.1000C>A	c.(1000-1002)Caa>Aaa	p.Q334K		NM_001004441.2	NP_001004441.2	A5PLL1	AN34B_HUMAN	ankyrin repeat domain 34B	334						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)		TCAATGCATTGCTGATTTCCT	0.393																																					p.Q334K		Atlas-SNP	.											.	ANKRD34B	61	.	0			c.C1000A						PASS	.						77	77	77					5																	79854839		2203	4300	6503	SO:0001583	missense	340120	exon5			TGCATTGCTGATT		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.1000C>A	chr5.hg19:g.79854839G>T	ENSP00000339802:p.Gln334Lys	58.0	0.0	.		51.0	27.0	.	NM_001004441	B2RPH1|Q68D79	Missense_Mutation	SNP	ENST00000338682.3	hg19	CCDS34194.1	.	.	.	.	.	.	.	.	.	.	G	5.706	0.314760	0.10789	.	.	ENSG00000189127	ENST00000338682	T	0.19806	2.12	5.74	3.95	0.45737	.	1.624130	0.04344	U	0.354534	T	0.21145	0.0509	L	0.44542	1.39	0.22571	N	0.998977	B	0.06786	0.001	B	0.04013	0.001	T	0.25572	-1.0128	10	0.33940	T	0.23	-0.2737	7.2927	0.26374	0.0775:0.0:0.5171:0.4055	.	334	A5PLL1	AN34B_HUMAN	K	334	ENSP00000339802:Q334K	ENSP00000339802:Q334K	Q	-	1	0	ANKRD34B	79890595	0.000000	0.05858	0.836000	0.33094	0.988000	0.76386	0.449000	0.21744	0.765000	0.33221	0.655000	0.94253	CAA	.	.	.	none		0.393	ANKRD34B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369475.1	NM_001004441		T	79854839	G	T	79854839	3	4	22	1	0	0	0	0	1	0	0	0	663	1328	46	4	548	4	ANKRD34B	5	79854839	Missense_Mutation	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10	820012	79854839	101060421	34	1489											
RHOBTB3	22836	hgsc.bcm.edu	37	chr5	95119657	95119657	+	Missense_Mutation	SNP	A	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	tgatatagttgacctgcttaAaaaggccaaggtaattgact	14	12	9	6	0	0	3	0	3	0	0	0	3	0	3	2	2	1	3	2	2	7	6			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr5:95119657A>C	ENST00000379982.3	+	10	2121	c.1613A>C	c.(1612-1614)aAa>aCa	p.K538T	GLRX_ENST00000508780.1_Intron|RHOBTB3_ENST00000504179.1_Missense_Mutation_p.K169T|GLRX_ENST00000507605.1_Intron	NM_014899.3	NP_055714.3	O94955	RHBT3_HUMAN	Rho-related BTB domain containing 3	538	Interaction with Rab9.				ATP catabolic process (GO:0006200)|retrograde transport, endosome to Golgi (GO:0042147)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|GTP binding (GO:0005525)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|skin(1)	16		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)		GACCTGCTTAAAAAGGCCAAG	0.358																																					p.K538T		Atlas-SNP	.											.	RHOBTB3	43	.	0			c.A1613C						PASS	.						82	74	76					5																	95119657		2203	4300	6503	SO:0001583	missense	22836	exon10			TGCTTAAAAAGGC	AB020685	CCDS4077.1	5q15	2014-05-09			ENSG00000164292	ENSG00000164292		"BTB/POZ domain containing"	18757	protein-coding gene	gene with protein product		607353				11222756, 17035353	Standard	NM_014899		Approved	KIAA0878	uc003klm.3	O94955	OTTHUMG00000121171	ENST00000379982.3:c.1613A>C	chr5.hg19:g.95119657A>C	ENSP00000369318:p.Lys538Thr	74.0	0.0	.		66.0	19.0	.	NM_014899	A0PJA4|A8K1W9|Q8IW06	Missense_Mutation	SNP	ENST00000379982.3	hg19	CCDS4077.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	12.44|12.44|12.44	1.939487|1.939487|1.939487	0.34189|0.34189|0.34189	.|.|.	.|.|.	ENSG00000164292|ENSG00000164292|ENSG00000164292	ENST00000510313|ENST00000379982;ENST00000504179|ENST00000503737	T|T;T|.	0.80909|0.75154|.	-1.43|-0.16;-0.91|.	5.71|5.71|5.71	4.53|4.53|4.53	0.55603|0.55603|0.55603	.|.|.	0.165681|0.165681|.	0.51477|0.51477|.	D|D|.	0.000098|0.000098|.	T|T|.	0.50956|0.50956|.	0.1646|0.1646|.	L|L|L	0.36672|0.36672|0.36672	1.1|1.1|1.1	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|B|.	.|0.27351|.	.|0.176|.	.|B|.	.|0.19148|.	.|0.024|.	T|T|.	0.42766|0.42766|.	-0.9432|-0.9432|.	8|10|.	0.14656|0.16420|.	T|T|.	0.56|0.52|.	-17.4539|-17.4539|-17.4539	8.0259|8.0259|8.0259	0.30436|0.30436|0.30436	0.7769:0.0:0.2231:0.0|0.7769:0.0:0.2231:0.0|0.7769:0.0:0.2231:0.0	.|.|.	.|538|.	.|O94955|.	.|RHBT3_HUMAN|.	Q|T|Y	120|538;169|40	ENSP00000424844:K120Q|ENSP00000369318:K538T;ENSP00000422360:K169T|.	ENSP00000424844:K120Q|ENSP00000369318:K538T|.	K|K|X	+|+|+	1|2|3	0|0|2	RHOBTB3|RHOBTB3|RHOBTB3	95145413|95145413|95145413	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.997000|0.997000|0.997000	0.53966|0.53966|0.53966	0.808000|0.808000|0.808000	0.45660|0.45660|0.45660	3.440000|3.440000|3.440000	0.52886|0.52886|0.52886	0.952000|0.952000|0.952000	0.37798|0.37798|0.37798	0.459000|0.459000|0.459000	0.35465|0.35465|0.35465	AAA|AAA|TAA	.	.	.	none		0.358	RHOBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241658.1	NM_014899		C	95119657	A	C	95119657	3	2	22	1	0	0	0	0	1	0	0	0	13348	14	1	5	1651	5	RHOBTB3	5	95119657	Missense_Mutation	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	15264818	95119657	85795603	35	1490											
PCSK1	5122	hgsc.bcm.edu	37	chr5	95761539	95761539	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttaccaagtaccattgctgAttccacatgggatcattgaa	12	12	7	10	0	1	2	1	2	0	0	2	3	2	3	3	1	3	2	3	1	4	5			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr5:95761539A>G	ENST00000311106.3	-	3	618	c.381T>C	c.(379-381)aaT>aaC	p.N127N	CTD-2337A12.1_ENST00000502645.2_RNA|PCSK1_ENST00000508626.1_Silent_p.N80N	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	127					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)"	ACCATTGCTGATTCCACATGG	0.408																																					p.N127N		Atlas-SNP	.											.	PCSK1	93	.	0			c.T381C						PASS	.						156	134	141					5																	95761539		2203	4300	6503	SO:0001819	synonymous_variant	5122	exon3			TTGCTGATTCCAC		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.381T>C	chr5.hg19:g.95761539A>G		65.0	0.0	.		49.0	16.0	.	NM_000439	B7Z8T7|E9PHA1|P78478|Q92532	Silent	SNP	ENST00000311106.3	hg19	CCDS4081.1																																																																																			.	.	.	none		0.408	PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1	NM_000439		G	95761539	A	G	95761539	2	3	22	1	0	0	0	0	0	0	0	1	11607	330	12	3		3	PCSK1	5	95761539	Silent	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	641882	95761539	85153721	36	1491											
FEM1C	56929	hgsc.bcm.edu	37	chr5	114860326	114860326	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacattctatcagtattgcAgtaacttgtagagatggaaa	14	12	8	7	0	2	1	1	0	1	1	2	3	2	2	1	1	2	4	1	1	5	7			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr5:114860326A>G	ENST00000274457.3	-	3	2094	c.1533T>C	c.(1531-1533)acT>acC	p.T511T		NM_020177.2	NP_064562.1	Q96JP0	FEM1C_HUMAN	fem-1 homolog c (C. elegans)	511					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(5)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	18		all_cancers(142;0.000575)|all_epithelial(76;9.98e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;2.5e-07)|Epithelial(69;2.66e-07)|all cancers(49;1.39e-05)		TCAGTATTGCAGTAACTTGTA	0.453																																					p.T511T		Atlas-SNP	.											.	FEM1C	50	.	0			c.T1533C						PASS	.						186	175	179					5																	114860326		2202	4300	6502	SO:0001819	synonymous_variant	56929	exon3			TATTGCAGTAACT		CCDS4118.1	5q22	2013-01-10	2006-11-08		ENSG00000145780	ENSG00000145780		"Ankyrin repeat domain containing"	16933	protein-coding gene	gene with protein product		608767				14527725, 11733146	Standard	NM_020177		Approved	KIAA1785, EUROIMAGE686608, EUROIMAGE783647, FEM1A	uc003krb.1	Q96JP0	OTTHUMG00000128895	ENST00000274457.3:c.1533T>C	chr5.hg19:g.114860326A>G		100.0	0.0	.		65.0	26.0	.	NM_020177	B2RE47|Q8N3V8|Q9H704|Q9NPL6|Q9NPL9	Silent	SNP	ENST00000274457.3	hg19	CCDS4118.1																																																																																			.	.	.	none		0.453	FEM1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250857.3	NM_020177		G	114860326	A	G	114860326	2	3	22	1	0	0	0	0	0	0	0	1	5818	175	7	3		3	FEM1C	5	114860326	Silent	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	19098787	114860326	66054934	37	1492											
PDLIM4	8572	hgsc.bcm.edu	37	chr5	131606622	131606622	+	Frame_Shift_Del	DEL	A	A	-																															taataggacggcagcccaacAaccagcaggcggccctcagg																										TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr5:131606622delA	ENST00000253754.3	+	4	406	c.342delA	c.(340-342)acafs	p.T115fs	P4HA2_ENST00000471826.1_Intron|PDLIM4_ENST00000484620.1_3'UTR|PDLIM4_ENST00000379018.3_Frame_Shift_Del_p.T115fs	NM_001131027.1|NM_003687.3	NP_001124499.1|NP_003678.2	P50479	PDLI4_HUMAN	PDZ and LIM domain 4	115							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)			GCAGCCCAACAACCAGCAGGC	0.622																																					p.T114fs		Atlas-Indel,Pindel	.											PDLIM4,NS,carcinoma,0,1	PDLIM4	22	.	0			c.341delC						PASS	.						75	84	81					5																	131606622		2203	4300	6503	SO:0001589	frameshift_variant	8572	exon4			.	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.342delA	chr5.hg19:g.131606622delA	ENSP00000253754:p.Thr115fs	155.0	0.0	0		152.0	72.0	0.473684	NM_001131027	B2R8U1|Q53Y39|Q96AT8|Q9BTW8|Q9Y292	Frame_Shift_Del	DEL	ENST00000253754.3	hg19	CCDS4152.1																																																																																			.	.	.	none		0.622	PDLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132644.2	NM_003687		-	131606622	A	-	131606622	7	5	22	1	0	1	0	1	0	0	0	0	11689	117	5	0	356	0	PDLIM4	5	131606622	Frame_Shift_Del	DEL	A	TCGA-2Z-A9JS-01A-21D-A42J-10	16746296	131606622	49308638	38	1493											
NOTCH4	4855	hgsc.bcm.edu	37	chr6	32168924	32168937	+	Frame_Shift_Del	DEL	AGGGGCTGCGTTTG	AGGGGCTGCGTTTG	-																															gggagtcggtctccttgcccAggggctgcgtttgaggggct																								rs204987	byFrequency	TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	AGGGGCTGCGTTTG	AGGGGCTGCGTTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr6:32168924_32168937delAGGGGCTGCGTTTG	ENST00000375023.3	-	22	4234_4247	c.4096_4109delCAAACGCAGCCCCT	c.(4096-4110)caaacgcagcccctgfs	p.QTQPL1366fs		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1366					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						CTCCTTGCCCAGGGGCTGCGTTTGAGGGGCTGCT	0.598																																					p.1366_1370del		Atlas-Indel,Pindel	.											.	NOTCH4	201	.	0			c.4097_4110del						PASS	.																																			SO:0001589	frameshift_variant	4855	exon22			.		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.4096_4109delCAAACGCAGCCCCT	chr6.hg19:g.32168924_32168937delAGGGGCTGCGTTTG	ENSP00000364163:p.Gln1366fs	100.0	0.0	0		99.0	24.0	0.242424	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Frame_Shift_Del	DEL	ENST00000375023.3	hg19	CCDS34420.1																																																																																			.	.	.	none		0.598	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			-	32168937	AGGGGCTGCGTTTG	-	32168924	7	5	22	1	0	1	0	1	0	0	0	0	10558	188	7	0	1938	0	NOTCH4	6	32168924	Frame_Shift_Del	DEL	AGGGGCTGCGTTTG	TCGA-2Z-A9JS-01A-21D-A42J-10		32168924	138946143	39	1494											
RGL2	5863	hgsc.bcm.edu	37	chr6	33262758	33262758	+	Frame_Shift_Del	DEL	C	C	-																															cccgctagtcactcaccccaCcccgggagccagacctcggg																										TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr6:33262758delC	ENST00000497454.1	-	10	1769	c.1274delG	c.(1273-1275)ggtfs	p.G427fs	PFDN6_ENST00000463584.1_Intron|RGL2_ENST00000444031.2_Frame_Shift_Del_p.G345fs|RGL2_ENST00000437840.2_5'UTR	NM_001243738.1|NM_004761.4	NP_001230667.1|NP_004752.1	O15211	RGL2_HUMAN	ral guanine nucleotide dissociation stimulator-like 2	427	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)	intracellular (GO:0005622)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)			breast(2)|cervix(2)|endometrium(7)|kidney(2)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	34						ACTCACCCCACCCCGGGAGCC	0.597																																					p.G425fs		Atlas-Indel,Pindel	.											.	RGL2	58	.	0			c.1275delT						PASS	.						21	23	22					6																	33262758		2182	4275	6457	SO:0001589	frameshift_variant	5863	exon10			.		CCDS4774.1	6p21.3	2010-02-17	2004-06-11	2004-06-16	ENSG00000237441	ENSG00000237441			9769	protein-coding gene	gene with protein product		602306	"RAB2, member RAS oncogene family-like"	RAB2L		8976381	Standard	NM_001243738		Approved	KE1.5, HKE1.5	uc003odv.3	O15211	OTTHUMG00000031072	ENST00000497454.1:c.1274delG	chr6.hg19:g.33262758delC	ENSP00000420211:p.Gly427fs	134.0	0.0	0		130.0	52.0	0.4	NM_004761	B4DG72|Q5STK0|Q9Y3F3	Frame_Shift_Del	DEL	ENST00000497454.1	hg19	CCDS4774.1																																																																																			.	.	.	none		0.597	RGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076098.2			-	33262758	C	-	33262758	7	5	22	1	0	1	0	1	0	0	0	0	13290	507	18	0	1095	0	RGL2	6	33262758	Frame_Shift_Del	DEL	C	TCGA-2Z-A9JS-01A-21D-A42J-10	1093834	33262758	137852309	40	1495											
DAAM2	23500	hgsc.bcm.edu	37	chr6	39824224	39824224	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccgaacgcagaggagctcaAcatccgctttgcagagctgg	10	6	12	13	3	1	2	1	0	0	2	2	4	2	3	2	2	5	5	2	2	2	1			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr6:39824224A>G	ENST00000398904.2	+	2	328	c.146A>G	c.(145-147)aAc>aGc	p.N49S	DAAM2_ENST00000274867.4_Missense_Mutation_p.N49S|DAAM2_ENST00000494405.1_3'UTR|DAAM2_ENST00000405961.3_Missense_Mutation_p.N49S|DAAM2_ENST00000538976.1_Missense_Mutation_p.N49S			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	49	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)					GAGGAGCTCAACATCCGCTTT	0.607																																					p.N49S		Atlas-SNP	.											.	DAAM2	101	.	0			c.A146G						PASS	.						40	43	42					6																	39824224		2034	4199	6233	SO:0001583	missense	23500	exon2			AGCTCAACATCCG	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.146A>G	chr6.hg19:g.39824224A>G	ENSP00000381876:p.Asn49Ser	105.0	0.0	.		133.0	49.0	.	NM_015345	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	hg19	CCDS56426.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.189591	0.78789	.	.	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976;ENST00000405961	D;D;D;D	0.87334	-2.24;-2.24;-2.24;-2.24	5.99	5.99	0.97316	GTPase-binding/formin homology 3 (1);Armadillo-type fold (1);Diaphanous GTPase-binding (1);	0.096890	0.64402	D	0.000001	D	0.87014	0.6072	L	0.59436	1.845	0.44366	D	0.99726	B;B;P	0.52463	0.341;0.393;0.953	B;B;P	0.54759	0.116;0.185;0.76	D	0.85729	0.1330	10	0.31617	T	0.26	.	15.4718	0.75446	1.0:0.0:0.0:0.0	.	49;49;49	G5EA45;Q86T65;F2Z2Q2	.;DAAM2_HUMAN;.	S	49	ENSP00000274867:N49S;ENSP00000381876:N49S;ENSP00000437808:N49S;ENSP00000384637:N49S	ENSP00000274867:N49S	N	+	2	0	DAAM2	39932202	0.998000	0.40836	0.064000	0.19789	0.780000	0.44128	8.760000	0.91671	2.296000	0.77279	0.533000	0.62120	AAC	.	.	.	none		0.607	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1			G	39824224	A	G	39824224	3	3	22	1	0	0	0	0	1	0	0	0	4218	43	2	3	148	3	DAAM2	6	39824224	Missense_Mutation	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	6561466	39824224	131290843	41	1496											
SNX14	57231	hgsc.bcm.edu	37	chr6	86303311	86303311	+	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	cgttacctgttaagaagcagGgaggcggcgctgagacagag	11	6	16	8	3	0	3	0	1	0	3	0	5	0	4	1	3	2	4	1	3	3	2			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr6:86303311G>T	ENST00000314673.3	-	1	302	c.126C>A	c.(124-126)tcC>tcA	p.S42S	SNX14_ENST00000369627.2_Silent_p.S42S|SNX14_ENST00000513865.1_Silent_p.S42S|SNX14_ENST00000346348.3_Silent_p.S42S|RP11-321N4.5_ENST00000503906.1_Intron|SNX14_ENST00000505648.1_Intron	NM_153816.3	NP_722523.1	Q9Y5W7	SNX14_HUMAN	sorting nexin 14	42					protein transport (GO:0015031)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	integral component of membrane (GO:0016021)	phosphatidylinositol binding (GO:0035091)			NS(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(11)|skin(1)	22		all_cancers(76;4.83e-07)|Acute lymphoblastic leukemia(125;3.3e-08)|Prostate(29;2.55e-07)|all_hematologic(105;3.66e-05)|all_epithelial(107;0.000695)|Lung NSC(302;0.197)|all_lung(197;0.24)		BRCA - Breast invasive adenocarcinoma(108;0.0423)		TAAGAAGCAGGGAGGCGGCGC	0.672																																					p.S42S		Atlas-SNP	.											.	SNX14	58	.	0			c.C126A						PASS	.						28	26	27					6																	86303311		2202	4299	6501	SO:0001819	synonymous_variant	57231	exon1			AAGCAGGGAGGCG	AF121863	CCDS5003.1, CCDS5004.1, CCDS75490.1	6q15	2008-10-22			ENSG00000135317	ENSG00000135317		"Sorting nexins"	14977	protein-coding gene	gene with protein product						11485546, 11736640	Standard	XM_005248738		Approved	RGS-PX2	uc003pkr.3	Q9Y5W7	OTTHUMG00000015140	ENST00000314673.3:c.126C>A	chr6.hg19:g.86303311G>T		126.0	0.0	.		136.0	54.0	.	NM_153816	B4DI55|Q4VBR3|Q5TCF9|Q5TCG0|Q6NUI7|Q6PI37|Q9BSD1	Silent	SNP	ENST00000314673.3	hg19	CCDS5004.1																																																																																			.	.	.	none		0.672	SNX14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041393.2	NM_153816		T	86303311	G	T	86303311	2	4	22	1	0	0	0	0	0	0	0	1	14898	1219	43	4		4	SNX14	6	86303311	Silent	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10	46479087	86303311	84811756	42	1497											
NR2E1	7101	hgsc.bcm.edu	37	chr6	108492734	108492734	+	Missense_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	gcactacggggtctacgcctGcgacggctgctcaggttttt	5	11	13	12	4	2	0	1	0	1	0	2	1	2	0	1	4	4	4	1	4	2	4			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr6:108492734G>A	ENST00000368986.4	+	2	806	c.98G>A	c.(97-99)tGc>tAc	p.C33Y	NR2E1_ENST00000368983.3_Missense_Mutation_p.C70Y	NM_003269.3	NP_003260.1	Q9Y466	NR2E1_HUMAN	nuclear receptor subfamily 2, group E, member 1	33					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)		GTCTACGCCTGCGACGGCTGC	0.562																																					p.C33Y		Atlas-SNP	.											.	NR2E1	57	.	0			c.G98A						PASS	.						120	131	127					6																	108492734		2203	4300	6503	SO:0001583	missense	7101	exon2			ACGCCTGCGACGG	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.98G>A	chr6.hg19:g.108492734G>A	ENSP00000357982:p.Cys33Tyr	88.0	0.0	.		80.0	26.0	.	NM_003269	Q6ZMP8	Missense_Mutation	SNP	ENST00000368986.4	hg19	CCDS5063.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.750777	0.89753	.	.	ENSG00000112333	ENST00000368986;ENST00000368983	D;D	0.99828	-6.99;-6.99	5.39	5.39	0.77823	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (5);	0.084915	0.85682	D	0.000000	D	0.99923	0.9964	H	0.98965	4.385	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95984	0.8980	10	0.87932	D	0	.	18.7646	0.91866	0.0:0.0:1.0:0.0	.	33	Q9Y466	NR2E1_HUMAN	Y	33;70	ENSP00000357982:C33Y;ENSP00000357979:C70Y	ENSP00000357979:C70Y	C	+	2	0	NR2E1	108599427	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.542000	0.85734	0.561000	0.74099	TGC	.	.	.	none		0.562	NR2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041712.2			A	108492734	G	A	108492734	3	1	22	1	0	0	0	0	1	0	0	0	10632	1319	46	2	104	2	NR2E1	6	108492734	Missense_Mutation	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10	22189423	108492734	62622333	43	1498											
THEMIS	387357	hgsc.bcm.edu	37	chr6	128134425	128134425	+	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	ccttcacattgaagggcaaaCggaactgtttacagagctca	13	9	9	10	1	2	2	2	1	0	1	2	3	2	3	1	2	4	3	1	2	4	4			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr6:128134425C>T	ENST00000368248.2	-	4	1509	c.1361G>A	c.(1360-1362)cGt>cAt	p.R454H	THEMIS_ENST00000537166.1_Missense_Mutation_p.R419H|THEMIS_ENST00000368250.1_Missense_Mutation_p.R375H|THEMIS_ENST00000543064.1_Missense_Mutation_p.R454H	NM_001010923.2	NP_001010923.1	Q8N1K5	THMS1_HUMAN	thymocyte selection associated	454	CABIT 2.				negative T cell selection (GO:0043383)|positive T cell selection (GO:0043368)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(3)	60						GAAGGGCAAACGGAACTGTTT	0.483																																					p.R454H		Atlas-SNP	.											.	THEMIS	168	.	0			c.G1361A						PASS	.						86	90	88					6																	128134425		2203	4300	6503	SO:0001583	missense	387357	exon4			GGCAAACGGAACT	AK094863	CCDS34534.1, CCDS55055.1	6q22.33	2012-02-08	2009-06-25	2009-06-25	ENSG00000172673	ENSG00000172673			21569	protein-coding gene	gene with protein product	"thymocyte expressed molecule involved in selection"	613607	"chromosome 6 open reading frame 207", "chromosome 6 open reading frame 190", "thymocyte selection pathway associated"	C6orf207, C6orf190, TSEPA		19597499, 19597498, 19597497	Standard	NM_001010923		Approved	bA325O24.4, FLJ40584, bA325O24.3	uc011ebt.2	Q8N1K5	OTTHUMG00000015534	ENST00000368248.2:c.1361G>A	chr6.hg19:g.128134425C>T	ENSP00000357231:p.Arg454His	92.0	0.0	.		81.0	33.0	.	NM_001010923	A1L4F0|A8K7N1|B3KT31|B3KW32|B3KY07|F5H1J9|Q5T3C4|Q5T3C5|Q6MZT7	Missense_Mutation	SNP	ENST00000368248.2	hg19	CCDS34534.1	.	.	.	.	.	.	.	.	.	.	C	9.748	1.166588	0.21621	.	.	ENSG00000172673	ENST00000368250;ENST00000543064;ENST00000368248;ENST00000537166	T;T;T;T	0.16597	2.33;2.33;2.33;2.33	5.69	-4.82	0.03171	.	0.926991	0.09311	N	0.819555	T	0.02649	0.0080	N	0.12182	0.205	0.09310	N	1	B;B	0.16166	0.016;0.004	B;B	0.08055	0.003;0.003	T	0.47315	-0.9127	10	0.48119	T	0.1	1.4237	9.9298	0.41514	0.0:0.5558:0.1306:0.3135	.	454;454	F5H1J9;Q8N1K5	.;THMS1_HUMAN	H	375;454;454;419	ENSP00000357233:R375H;ENSP00000439594:R454H;ENSP00000357231:R454H;ENSP00000439863:R419H	ENSP00000357231:R454H	R	-	2	0	THEMIS	128176118	0.001000	0.12720	0.051000	0.19133	0.848000	0.48234	-2.321000	0.01119	-0.481000	0.06792	0.563000	0.77884	CGT	.	.	.	none		0.483	THEMIS-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_001010923		T	128134425	C	T	128134425	3	4	22	1	0	0	0	0	1	0	0	0	15872	536	19	1	697	1	THEMIS	6	128134425	Missense_Mutation	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10	19641691	128134425	42980642	44	1499											
ADAP1	11033	hgsc.bcm.edu	37	chr7	959664	959664	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgtcgctcgtacttggccCggatccactgctctcgaagg	5	10	11	15	4	1	0	0	0	1	0	5	2	2	1	3	3	2	3	3	3	2	2	rs373846581		TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr7:959664C>T	ENST00000265846.5	-	4	548	c.329G>A	c.(328-330)cGg>cAg	p.R110Q	ADAP1_ENST00000539900.1_Missense_Mutation_p.R121Q|ADAP1_ENST00000449296.2_Missense_Mutation_p.R38Q|ADAP1_ENST00000463358.1_5'UTR	NM_001284308.1|NM_001284309.1|NM_001284311.1|NM_006869.2	NP_001271237.1|NP_001271238.1|NP_001271240.1|NP_006860	O75689	ADAP1_HUMAN	ArfGAP with dual PH domains 1	110	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				cell surface receptor signaling pathway (GO:0007166)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF GTPase activity (GO:0032312)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)	p.R110Q(1)		endometrium(1)|kidney(1)|lung(3)|upper_aerodigestive_tract(1)	6						GTACTTGGCCCGGATCCACTG	0.682													C|||	1	0.000199681	8e-04	0	5008	,	,		8018	0		0	False		,,,				2504	0				p.R110Q		Atlas-SNP	.											ADAP1,mouth,carcinoma,0,1	ADAP1	23	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.G329A						PASS	.	C	GLN/ARG	0,4404		0,0,2202	38	35	36		329	4.5	1	7		36	1,8591	1.2+/-3.3	0,1,4295	no	missense	ADAP1	NM_006869.2	43	0,1,6497	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	110/375	959664	1,12995	2202	4296	6498	SO:0001583	missense	11033	exon4			TTGGCCCGGATCC	AJ006422	CCDS5318.1, CCDS64576.1, CCDS64577.1, CCDS75558.1	7p22.3	2013-01-10	2008-09-22	2008-09-22	ENSG00000105963	ENSG00000105963		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	16486	protein-coding gene	gene with protein product		608114	"centaurin, alpha 1"	CENTA1		10333475	Standard	NM_006869		Approved	GCS1L	uc003sjo.4	O75689	OTTHUMG00000023380	ENST00000265846.5:c.329G>A	chr7.hg19:g.959664C>T	ENSP00000265846:p.Arg110Gln	26.0	0.0	.		32.0	3.0	.	NM_006869	A4D2Q2|B3KRZ4|B4DVA6|F6XZ68|H7C2Q4	Missense_Mutation	SNP	ENST00000265846.5	hg19	CCDS5318.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	31|31	5.084852|5.084852	0.94100|0.94100	0.0|0.0	1.16E-4|1.16E-4	ENSG00000105963|ENSG00000105963	ENST00000446141;ENST00000437486;ENST00000453823|ENST00000265846;ENST00000449296;ENST00000538188;ENST00000539900;ENST00000435943	.|T;T;T;T	.|0.47528	.|0.84;0.85;0.84;0.84	4.53|4.53	4.53|4.53	0.55603|0.55603	.|.	.|0.112189	.|0.56097	.|D	.|0.000024	T|T	0.68796|0.68796	0.3040|0.3040	M|M	0.80332|0.80332	2.49|2.49	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.70716	.|0.969;0.97	T|T	0.74562|0.74562	-0.3624|-0.3624	5|10	.|0.87932	.|D	.|0	-33.1793|-33.1793	14.5163|14.5163	0.67821|0.67821	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|15;110	.|B4DUZ7;O75689	.|.;ADAP1_HUMAN	R|Q	93;44;53|110;38;15;121;97	.|ENSP00000265846:R110Q;ENSP00000407267:R38Q;ENSP00000442682:R121Q;ENSP00000394973:R97Q	.|ENSP00000265846:R110Q	G|R	-|-	1|2	0|0	ADAP1|ADAP1	926190|926190	0.999000|0.999000	0.42202|0.42202	0.998000|0.998000	0.56505|0.56505	0.816000|0.816000	0.46133|0.46133	4.105000|4.105000	0.57797|0.57797	2.215000|2.215000	0.71742|0.71742	0.549000|0.549000	0.68633|0.68633	GGG|CGG	.	.	.	weak		0.682	ADAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059701.2	NM_006869		T	959664	C	T	959664	3	4	22	1	0	0	0	0	1	0	0	0	279	652	23	1	827	1	ADAP1	7	959664	Missense_Mutation	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10		959664	158178999	45	1500											
FBXL18	80028	hgsc.bcm.edu	37	chr7	5541280	5541280	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaggatggcgccctcgcgcGtgcggtccagaatctcgaag	8	6	15	12	6	1	2	0	0	1	2	4	4	2	3	2	3	1	0	2	3	2	0			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr7:5541280G>A	ENST00000382368.3	-	3	743	c.620C>T	c.(619-621)aCg>aTg	p.T207M	FBXL18_ENST00000453700.3_Missense_Mutation_p.T207M	NM_024963.4	NP_079239.3	Q96ME1	FXL18_HUMAN	F-box and leucine-rich repeat protein 18	207									FBXL18/RNF216(2)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)	21		Ovarian(82;0.0607)		UCEC - Uterine corpus endometrioid carcinoma (126;0.181)|OV - Ovarian serous cystadenocarcinoma(56;3.64e-13)		GCCCTCGCGCGTGCGGTCCAG	0.657																																					p.T207M		Atlas-SNP	.											.	FBXL18	99	.	0			c.C620T						PASS	.						23	28	26					7																	5541280		2059	4209	6268	SO:0001583	missense	80028	exon3			TCGCGCGTGCGGT	AK057042	CCDS43546.1	7p22.2	2011-06-09			ENSG00000155034	ENSG00000155034		"F-boxes / Leucine-rich repeats"	21874	protein-coding gene	gene with protein product		609084					Standard	NM_024963		Approved	FLJ11467, Fbl18	uc003son.4	Q96ME1	OTTHUMG00000151832	ENST00000382368.3:c.620C>T	chr7.hg19:g.5541280G>A	ENSP00000371805:p.Thr207Met	118.0	0.0	.		123.0	5.0	.	NM_024963	Q9BR90|Q9BTC7|Q9HAK7	Missense_Mutation	SNP	ENST00000382368.3	hg19	CCDS43546.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.94|19.94	3.920520|3.920520	0.73213|0.73213	.|.	.|.	ENSG00000155034|ENSG00000155034	ENST00000458142|ENST00000382368;ENST00000312577;ENST00000453700	.|T;T	.|0.51071	.|0.75;0.72	5.4|5.4	5.4|5.4	0.78164|0.78164	.|.	.|0.159486	.|0.53938	.|D	.|0.000047	T|T	0.54382|0.54382	0.1855|0.1855	N|N	0.19112|0.19112	0.55|0.55	0.47476|0.47476	D|D	0.999437|0.999437	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.69824	.|0.966;0.942	T|T	0.53760|0.53760	-0.8393|-0.8393	5|10	.|0.35671	.|T	.|0.21	.|.	18.1629|18.1629	0.89716|0.89716	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|207;207	.|F5H4Z4;Q96ME1-4	.|.;.	C|M	91|207	.|ENSP00000371805:T207M;ENSP00000444797:T207M	.|ENSP00000311990:T207M	R|T	-|-	1|2	0|0	FBXL18|FBXL18	5507806|5507806	1.000000|1.000000	0.71417|0.71417	0.951000|0.951000	0.38953|0.38953	0.898000|0.898000	0.52572|0.52572	5.561000|5.561000	0.67339|0.67339	2.528000|2.528000	0.85240|0.85240	0.655000|0.655000	0.94253|0.94253	CGC|ACG	.	.	.	none		0.657	FBXL18-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324093.1	NM_024963		A	5541280	G	A	5541280	3	1	22	1	0	0	0	0	1	0	0	0	5721	1145	40	1	1548	1	FBXL18	7	5541280	Missense_Mutation	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10	4581616	5541280	153597383	46	1501											
SP4	6671	hgsc.bcm.edu	37	chr7	21468306	21468306	+	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	ttgttgcagatcagaagaagGaggaggaggaggaggcggca	13	5	19	4	1	1	3	1	0	0	3	1	8	1	8	0	7	1	3	0	7	2	2			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr7:21468306G>A	ENST00000222584.3	+	2	237	c.19G>A	c.(19-21)Gag>Aag	p.E7K		NM_003112.3	NP_003103.2	Q02446	SP4_HUMAN	Sp4 transcription factor	7	Poly-Glu.				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						TCAGAAGAAGGAGGAGGAGGA	0.512																																					p.E7K		Atlas-SNP	.											SP4,colon,carcinoma,0,1	SP4	91	.	0			c.G19A						PASS	.						20	20	20					7																	21468306		2171	4251	6422	SO:0001583	missense	6671	exon2			AAGAAGGAGGAGG		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.19G>A	chr7.hg19:g.21468306G>A	ENSP00000222584:p.Glu7Lys	84.0	1.0	.		141.0	8.0	.	NM_003112	O60402|Q32M52	Missense_Mutation	SNP	ENST00000222584.3	hg19	CCDS5373.1	.	.	.	.	.	.	.	.	.	.	G	13.71	2.318989	0.41096	.	.	ENSG00000105866	ENST00000222584;ENST00000446800	T	0.09911	2.93	4.5	4.5	0.54988	.	0.061123	0.64402	N	0.000005	T	0.10937	0.0267	L	0.36672	1.1	0.44142	D	0.996934	P	0.34587	0.458	B	0.39152	0.292	T	0.20907	-1.0261	10	0.23891	T	0.37	.	12.5742	0.56355	0.0:0.0:1.0:0.0	.	7	Q02446	SP4_HUMAN	K	7	ENSP00000222584:E7K	ENSP00000222584:E7K	E	+	1	0	SP4	21434831	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.555000	0.73928	2.345000	0.79718	0.563000	0.77884	GAG	.	.	.	none		0.512	SP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211617.2	NM_003112		A	21468306	G	A	21468306	3	1	22	1	0	0	0	0	1	0	0	0	14979	1175	41	2	25	2	SP4	7	21468306	Missense_Mutation	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10	15927026	21468306	137670357	47	1502											
CPVL	54504	hgsc.bcm.edu	37	chr7	29135788	29135788	+	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	aaacatggatgaacctcccgGcccaccctgtagccagagaa	13	5	9	14	1	0	2	0	1	0	1	1	4	1	3	5	2	3	1	5	2	4	1			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr7:29135788G>T	ENST00000409850.1	-	8	980	c.334C>A	c.(334-336)Ccg>Acg	p.P112T	CPVL_ENST00000265394.5_Missense_Mutation_p.P112T|CPVL_ENST00000488891.2_5'UTR|CPVL_ENST00000396276.3_Missense_Mutation_p.P112T			Q9H3G5	CPVL_HUMAN	carboxypeptidase, vitellogenic-like	112						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						GAACCTCCCGGCCCACCCTGT	0.468																																					p.P112T		Atlas-SNP	.											.	CPVL	60	.	0			c.C334A						PASS	.						138	129	132					7																	29135788		2203	4300	6503	SO:0001583	missense	54504	exon4			CTCCCGGCCCACC	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.334C>A	chr7.hg19:g.29135788G>T	ENSP00000387164:p.Pro112Thr	111.0	0.0	.		146.0	77.0	.	NM_019029	A4D1A4|Q6UX20|Q8NBL7|Q96AR7|Q9HB41	Missense_Mutation	SNP	ENST00000409850.1	hg19	CCDS5419.1	.	.	.	.	.	.	.	.	.	.	G	17.54	3.415714	0.62511	.	.	ENSG00000106066	ENST00000265394;ENST00000396276;ENST00000409850;ENST00000448959;ENST00000447426	D;D;D;D;D	0.99245	-5.62;-5.62;-5.62;-5.62;-5.62	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	D	0.99691	0.9883	H	0.99130	4.44	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97328	0.9948	10	0.87932	D	0	0.0175	13.4872	0.61373	0.0773:0.0:0.9227:0.0	.	112	Q9H3G5	CPVL_HUMAN	T	112;112;112;42;42	ENSP00000265394:P112T;ENSP00000379572:P112T;ENSP00000387164:P112T;ENSP00000409036:P42T;ENSP00000395690:P42T	ENSP00000265394:P112T	P	-	1	0	CPVL	29102313	1.000000	0.71417	0.937000	0.37676	0.458000	0.32498	6.755000	0.74914	2.519000	0.84933	0.491000	0.48974	CCG	.	.	.	none		0.468	CPVL-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328305.1	NM_019029		T	29135788	G	T	29135788	3	4	22	1	0	0	0	0	1	0	0	0	3837	1203	42	4	1136	4	CPVL	7	29135788	Missense_Mutation	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10	7667482	29135788	130002875	48	1503											
POLD2	5425	hgsc.bcm.edu	37	chr7	44156052	44156052	+	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	cagctgcaggaggatctcatCcagcatcttaacagcctcca	11	8	8	14	0	2	0	1	0	2	0	5	2	4	2	3	2	5	3	3	2	1	1			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr7:44156052C>T	ENST00000406581.2	-	8	1487	c.838G>A	c.(838-840)Gat>Aat	p.D280N	POLD2_ENST00000223361.3_Missense_Mutation_p.D280N|POLD2_ENST00000452185.1_Missense_Mutation_p.D280N	NM_001256879.1	NP_001243808.1	P49005	DPOD2_HUMAN	polymerase (DNA directed), delta 2, accessory subunit	280					base-excision repair (GO:0006284)|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)	delta DNA polymerase complex (GO:0043625)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	12						AGGATCTCATCCAGCATCTTA	0.597																																					p.D315N		Atlas-SNP	.											.	POLD2	62	.	0			c.G943A						PASS	.						59	47	51					7																	44156052		2203	4299	6502	SO:0001583	missense	5425	exon7			TCTCATCCAGCAT		CCDS5477.1, CCDS75586.1	7p13	2012-05-18	2012-05-18		ENSG00000106628	ENSG00000106628		"DNA polymerases"	9176	protein-coding gene	gene with protein product	"Pol delta B subunit (p50)", "DNA polymerase delta subunit p50"	600815	"polymerase (DNA directed), delta 2, regulatory subunit (50kD)", "polymerase (DNA directed), delta 2, regulatory subunit 50kDa"			8530069	Standard	NM_001127218		Approved		uc003tkf.5	P49005	OTTHUMG00000022909	ENST00000406581.2:c.838G>A	chr7.hg19:g.44156052C>T	ENSP00000386105:p.Asp280Asn	53.0	0.0	.		84.0	31.0	.	NM_006230	A4D2J4|B2R5S4	Missense_Mutation	SNP	ENST00000406581.2	hg19	CCDS5477.1	.	.	.	.	.	.	.	.	.	.	C	32	5.139271	0.94560	.	.	ENSG00000106628	ENST00000406581;ENST00000223361;ENST00000452185;ENST00000436400;ENST00000436844	T;T;T;T	0.33654	1.4;1.4;1.4;1.4	5.84	5.84	0.93424	DNA polymerase alpha/epsilon, subunit B (1);	0.000000	0.85682	D	0.000000	T	0.70116	0.3187	H	0.95328	3.655	0.80722	D	1	D;D	0.89917	0.997;1.0	P;D	0.70716	0.873;0.97	T	0.78298	-0.2258	10	0.66056	D	0.02	-13.0784	14.3287	0.66537	0.0:0.9273:0.0:0.0726	.	280;280	P49005;F8W8R3	DPOD2_HUMAN;.	N	280;280;280;20;198	ENSP00000386105:D280N;ENSP00000223361:D280N;ENSP00000395231:D280N;ENSP00000416203:D198N	ENSP00000223361:D280N	D	-	1	0	POLD2	44122577	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	4.355000	0.59424	2.778000	0.95560	0.655000	0.94253	GAT	.	.	.	none		0.597	POLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250994.2	NM_001127218		T	44156052	C	T	44156052	3	4	22	1	0	0	0	0	1	0	0	0	12198	855	30	2	591	2	POLD2	7	44156052	Missense_Mutation	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10	15020264	44156052	114982611	49	1504											
ELN	2006	hgsc.bcm.edu	37	chr7	73470631	73470631	+	Frame_Shift_Del	DEL	T	T	-																															cggagtcggagttggaggcaTtcctacttacggggttggag																										TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr7:73470631delT	ENST00000252034.7	+	20	1580	c.1181delT	c.(1180-1182)attfs	p.I394fs	ELN_ENST00000380553.4_Frame_Shift_Del_p.I277fs|ELN_ENST00000380575.4_Frame_Shift_Del_p.I384fs|ELN_ENST00000414324.1_Frame_Shift_Del_p.I389fs|ELN_ENST00000466878.1_3'UTR|ELN_ENST00000320399.6_Frame_Shift_Del_p.I394fs|ELN_ENST00000445912.1_Frame_Shift_Del_p.I394fs|ELN_ENST00000357036.5_Frame_Shift_Del_p.I399fs|ELN_ENST00000380562.4_Frame_Shift_Del_p.I394fs|ELN_ENST00000320492.7_Frame_Shift_Del_p.I358fs|ELN_ENST00000380584.4_Frame_Shift_Del_p.I380fs|ELN_ENST00000380576.5_Frame_Shift_Del_p.I394fs|ELN_ENST00000429192.1_Frame_Shift_Del_p.I399fs|ELN_ENST00000358929.4_Frame_Shift_Del_p.I394fs|ELN_ENST00000458204.1_Frame_Shift_Del_p.I384fs	NM_000501.2|NM_001278915.1	NP_000492.2|NP_001265844.1	P15502	ELN_HUMAN	elastin	394	Ala-rich.				blood circulation (GO:0008015)|blood vessel remodeling (GO:0001974)|cell proliferation (GO:0008283)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|organ morphogenesis (GO:0009887)|regulation of actin filament polymerization (GO:0030833)|respiratory gaseous exchange (GO:0007585)|skeletal muscle tissue development (GO:0007519)|stress fiber assembly (GO:0043149)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(4)|pancreas(2)|prostate(1)|skin(2)|stomach(1)	32		Lung NSC(55;0.159)				GTTGGAGGCATTCCTACTTAC	0.627			T	PAX5	B-ALL		"Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome"																														p.I399fs		Atlas-Indel,Pindel	.		Dom	yes		7	7q11.23	2006	elastin	yes	L	.	ELN	81	.	0			c.1195delA						PASS	.						97	104	102					7																	73470631		2203	4300	6503	SO:0001589	frameshift_variant	2006	exon20			.		CCDS5562.2, CCDS43598.1, CCDS43599.1, CCDS47611.1, CCDS47612.1, CCDS64673.1, CCDS64674.1, CCDS64675.1, CCDS64676.1, CCDS64677.1, CCDS64678.1, CCDS75616.1, CCDS75617.1	7q11.1-q21.1	2008-08-01	2008-08-01		ENSG00000049540	ENSG00000049540			3327	protein-coding gene	gene with protein product	"tropoelastin", "supravalvular aortic stenosis", "Williams-Beuren syndrome"	130160				8096434	Standard	NM_001278939		Approved	WBS, WS, SVAS	uc003tzn.3	P15502	OTTHUMG00000150229	ENST00000252034.7:c.1181delT	chr7.hg19:g.73470631delT	ENSP00000252034:p.Ile394fs	105.0	0.0	0		142.0	85.0	0.598592	NM_001081753	B3KTS6|O15336|O15337|Q14233|Q14234|Q14235|Q14238|Q6P0L4|Q6ZWJ6|Q75MU5|Q7Z316|Q7Z3F5|Q9UMF5	Frame_Shift_Del	DEL	ENST00000252034.7	hg19	CCDS5562.2																																																																																			.	.	.	none		0.627	ELN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316913.1	NM_000501		-	73470631	T	-	73470631	7	5	22	1	0	1	0	1	0	0	0	0	5073	1493	52	0	1274	0	ELN	7	73470631	Frame_Shift_Del	DEL	T	TCGA-2Z-A9JS-01A-21D-A42J-10	29314579	73470631	85668032	50	1505											
PRKAR2B	5577	hgsc.bcm.edu	37	chr7	106685477	106685477	+	Missense_Mutation	SNP	A	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	cttcacccgcctgcagcaggAgaacgagcgcaaaggcaccg	11	3	12	15	4	1	1	1	0	0	1	1	3	1	1	3	2	4	4	3	2	2	1			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr7:106685477A>C	ENST00000265717.4	+	1	384	c.125A>C	c.(124-126)gAg>gCg	p.E42A		NM_002736.2	NP_002727.2	P31323	KAP3_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, beta	42	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)|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						CTGCAGCAGGAGAACGAGCGC	0.716																																					p.E42A		Atlas-SNP	.											.	PRKAR2B	34	.	0			c.A125C						PASS	.						5	6	6					7																	106685477		2082	4111	6193	SO:0001583	missense	5577	exon1			AGCAGGAGAACGA		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.125A>C	chr7.hg19:g.106685477A>C	ENSP00000265717:p.Glu42Ala	66.0	0.0	.		80.0	54.0	.	NM_002736	A4D0R9	Missense_Mutation	SNP	ENST00000265717.4	hg19	CCDS5740.1	.	.	.	.	.	.	.	.	.	.	A	10.55	1.381480	0.24944	.	.	ENSG00000005249	ENST00000265717;ENST00000543645;ENST00000539794	T	0.79454	-1.27	3.91	3.91	0.45181	cAMP-dependent protein kinase, regulatory subunit, type I/II alpha/beta (3);	1.313690	0.04903	N	0.451690	T	0.53174	0.1780	N	0.01250	-0.93	0.35233	D	0.777118	B	0.02656	0.0	B	0.14023	0.01	T	0.49093	-0.8975	10	0.20519	T	0.43	-13.5013	9.0772	0.36529	0.8148:0.1852:0.0:0.0	.	42	P31323	KAP3_HUMAN	A	42	ENSP00000265717:E42A	ENSP00000265717:E42A	E	+	2	0	PRKAR2B	106472713	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.293000	0.43558	1.652000	0.50683	0.374000	0.22700	GAG	.	.	.	none		0.716	PRKAR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268386.1			C	106685477	A	C	106685477	3	2	22	1	0	0	0	0	1	0	0	0	12516	304	11	5	127	5	PRKAR2B	7	106685477	Missense_Mutation	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	33214846	106685477	52453186	51	1506											
PXDNL	137902	hgsc.bcm.edu	37	chr8	52412274	52412274	+	Frame_Shift_Del	DEL	A	A	-																															cttacagtcgctctaatctcAgaaggtctccaaaggtctct																								rs372013787		TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr8:52412274delA	ENST00000356297.4	-	5	537	c.437delT	c.(436-438)ctgfs	p.L146fs	PXDNL_ENST00000543296.1_Frame_Shift_Del_p.L146fs	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	146					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)				CTCTAATCTCAGAAGGTCTCC	0.433																																					p.L146fs		Atlas-Indel,Pindel	.											.	PXDNL	414	.	0			c.438delG						PASS	.						182	175	177					8																	52412274		1869	4105	5974	SO:0001589	frameshift_variant	137902	exon5			.		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.437delT	chr8.hg19:g.52412274delA	ENSP00000348645:p.Leu146fs	57.0	0.0	0		68.0	39.0	0.573529	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Frame_Shift_Del	DEL	ENST00000356297.4	hg19	CCDS47855.1																																																																																			.	.	.	none		0.433	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		-	52412274	A	-	52412274	7	5	22	1	0	1	0	1	0	0	0	0	12861	188	7	0	4030	0	PXDNL	8	52412274	Frame_Shift_Del	DEL	A	TCGA-2Z-A9JS-01A-21D-A42J-10		52412274	93951748	52	1507											
C9orf85	138241	hgsc.bcm.edu	37	chr9	74586475	74586475	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatcacataatgtgcaggccAtgtgcctgtgaacttgaagt	11	12	10	8	0	1	2	1	2	0	0	1	2	1	2	2	1	3	1	2	1	4	3			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr9:74586475A>G	ENST00000377031.3	+	3	454	c.264A>G	c.(262-264)ccA>ccG	p.P88P	C9orf85_ENST00000486911.2_Intron|C9orf85_ENST00000334731.2_Silent_p.P88P			Q96MD7	CI085_HUMAN	chromosome 9 open reading frame 85	88										kidney(2)|large_intestine(1)|lung(4)	7						TGTGCAGGCCATGTGCCTGTG	0.303																																					p.P88P		Atlas-SNP	.											.	C9orf85	28	.	0			c.A264G						PASS	.						145	134	137					9																	74586475		2203	4300	6503	SO:0001819	synonymous_variant	138241	exon3			CAGGCCATGTGCC	BC010179	CCDS6639.1	9q21.2	2012-03-16			ENSG00000155621	ENSG00000155621			28784	protein-coding gene	gene with protein product						12477932	Standard	NM_182505		Approved	MGC61599	uc004ain.3	Q96MD7	OTTHUMG00000020002	ENST00000377031.3:c.264A>G	chr9.hg19:g.74586475A>G		58.0	0.0	.		54.0	17.0	.	NM_182505	Q5W0N1|Q5W0N3|Q6PJW9|Q86U95	Silent	SNP	ENST00000377031.3	hg19																																																																																				.	.	.	none		0.303	C9orf85-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052628.2	NM_182505		G	74586475	A	G	74586475	2	3	22	1	0	0	0	0	0	0	0	1	2503	204	8	3		3	C9orf85	9	74586475	Silent	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10		74586475	66626956	53	1508											
SVEP1	79987	hgsc.bcm.edu	37	chr9	113212406	113212406	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgactgagacactcatcgaCgttctttccacatcgggtac	9	11	8	13	3	2	2	1	2	1	1	5	4	3	2	1	1	1	2	1	1	1	3	rs376449068	byFrequency	TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr9:113212406C>T	ENST00000401783.2	-	24	4372	c.4036G>A	c.(4036-4038)Gtc>Atc	p.V1346I	SVEP1_ENST00000374469.1_Missense_Mutation_p.V1323I|SVEP1_ENST00000302728.8_Missense_Mutation_p.V1346I|SVEP1_ENST00000467821.1_5'UTR	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1346	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						CACTCATCGACGTTCTTTCCA	0.453													C|||	2	0.000399361	0	0	5008	,	,		19558	0		0	False		,,,				2504	0.002				p.V1346I		Atlas-SNP	.											.	SVEP1	326	.	0			c.G4036A						PASS	.	C	ILE/VAL	0,3788		0,0,1894	259	241	247		4036	-10.9	0	9		247	2,8236		0,2,4117	no	missense	SVEP1	NM_153366.3	29	0,2,6011	TT,TC,CC		0.0243,0.0,0.0166	benign	1346/3572	113212406	2,12024	1894	4119	6013	SO:0001583	missense	79987	exon24			CATCGACGTTCTT	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.4036G>A	chr9.hg19:g.113212406C>T	ENSP00000384917:p.Val1346Ile	90.0	0.0	.		112.0	51.0	.	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	C	4.180	0.032029	0.08101	0.0	2.43E-4	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728	D;D;D	0.87103	-2.21;-2.21;-2.21	5.44	-10.9	0.00192	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	1.010870	0.07909	N	0.974027	T	0.56232	0.1971	N	0.03194	-0.395	0.09310	N	1	B;B	0.11235	0.004;0.003	B;B	0.04013	0.001;0.001	T	0.54918	-0.8221	10	0.02654	T	1	.	2.8122	0.05445	0.1765:0.3925:0.1795:0.2514	.	1346;1346	E9PBN8;Q4LDE5	.;SVEP1_HUMAN	I	1346;1323;1346	ENSP00000384917:V1346I;ENSP00000363593:V1323I;ENSP00000304118:V1346I	ENSP00000304118:V1346I	V	-	1	0	SVEP1	112252227	0.078000	0.21339	0.000000	0.03702	0.198000	0.23893	-0.651000	0.05372	-1.719000	0.01382	-0.482000	0.04802	GTC	.	.	.	weak		0.453	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	113212406	C	T	113212406	3	4	22	1	0	0	0	0	1	0	0	0	15432	536	19	1	6779	1	SVEP1	9	113212406	Missense_Mutation	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10	38625931	113212406	28001025	54	1509											
RAB14	51552	hgsc.bcm.edu	37	chr9	123954485	123954485	+	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	ttgatgaagcaagcaagattTtcctactcccatgtcccctg	10	12	7	12	0	0	3	0	2	0	1	3	3	3	3	4	0	3	2	4	0	4	4			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr9:123954485T>A	ENST00000373840.4	-	3	307	c.70A>T	c.(70-72)Aaa>Taa	p.K24*		NM_016322.3	NP_057406.2	P61106	RAB14_HUMAN	RAB14, member RAS oncogene family	24					embryo development (GO:0009790)|endocytic recycling (GO:0032456)|fibroblast growth factor receptor signaling pathway (GO:0008543)|Golgi to endosome transport (GO:0006895)|GTP catabolic process (GO:0006184)|intracellular transport (GO:0046907)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of protein localization (GO:0032880)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|rough endoplasmic reticulum (GO:0005791)|trans-Golgi network transport vesicle (GO:0030140)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	5						AAGCAAGATTTTCCTACTCCC	0.303																																					p.K24X		Atlas-SNP	.											.	RAB14	14	.	0			c.A70T						PASS	.						141	143	142					9																	123954485		2203	4292	6495	SO:0001587	stop_gained	51552	exon3			AAGATTTTCCTAC	AF152463	CCDS6827.1	9q32-q34.11	2008-07-21			ENSG00000119396	ENSG00000119396		"RAB, member RAS oncogene"	16524	protein-coding gene	gene with protein product	"F protein-binding protein 1", "bA165P4.3 (member RAS oncogene family)", "small GTP binding protein RAB14"	612673				9792283, 15004230	Standard	NM_016322		Approved	FBP, RAB-14	uc004blc.3	P61106	OTTHUMG00000020582	ENST00000373840.4:c.70A>T	chr9.hg19:g.123954485T>A	ENSP00000362946:p.Lys24*	30.0	0.0	.		30.0	14.0	.	NM_016322	B3KR31|P35287|Q5JVD4|Q6Q7K5|Q969L0|Q9UI11	Nonsense_Mutation	SNP	ENST00000373840.4	hg19	CCDS6827.1	.	.	.	.	.	.	.	.	.	.	T	38	6.999408	0.97990	.	.	ENSG00000119396	ENST00000373840;ENST00000451303	.	.	.	5.83	5.83	0.93111	.	0.089556	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.3812	0.74658	0.0:0.0:0.0:1.0	.	.	.	.	X	24	.	ENSP00000362946:K24X	K	-	1	0	RAB14	122994306	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.870000	0.87175	2.216000	0.71823	0.460000	0.39030	AAA	.	.	.	none		0.303	RAB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053857.1	NM_016322		A	123954485	T	A	123954485	4	1	22	1	0	0	0	0	0	1	0	0	12913	1850	64	5	601	5	RAB14	9	123954485	Nonsense_Mutation	SNP	T	TCGA-2Z-A9JS-01A-21D-A42J-10	10742079	123954485	17258946	55	1510											
COL5A1	1289	hgsc.bcm.edu	37	chr9	137694764	137694764	+	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	gagaaacgggcccaatgggtGagcgtggccaccctgggccc	8	4	16	13	2	0	2	0	1	0	1	0	3	0	2	4	4	2	0	4	4	2	0			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr9:137694764G>T	ENST00000371817.3	+	39	3451	c.3037G>T	c.(3037-3039)Gag>Tag	p.E1013*		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1013	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CCCAATGGGTGAGCGTGGCCA	0.597																																					p.E1013X		Atlas-SNP	.											.	COL5A1	323	.	0			c.G3037T						PASS	.						24	28	27					9																	137694764		2198	4298	6496	SO:0001587	stop_gained	1289	exon39			ATGGGTGAGCGTG	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.3037G>T	chr9.hg19:g.137694764G>T	ENSP00000360882:p.Glu1013*	108.0	0.0	.		82.0	37.0	.	NM_000093	Q15094|Q5SUX4	Nonsense_Mutation	SNP	ENST00000371817.3	hg19	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	G	46	12.371230	0.99661	.	.	ENSG00000130635	ENST00000371817	.	.	.	4.39	4.39	0.52855	.	0.135437	0.48767	U	0.000174	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	17.3375	0.87286	0.0:0.0:1.0:0.0	.	.	.	.	X	1013	.	ENSP00000360882:E1013X	E	+	1	0	COL5A1	136834585	1.000000	0.71417	0.942000	0.38095	0.908000	0.53690	9.579000	0.98204	2.158000	0.67659	0.551000	0.68910	GAG	.	.	.	none		0.597	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		T	137694764	G	T	137694764	4	4	22	1	0	0	0	0	0	1	0	0	3698	1291	45	4	3191	4	COL5A1	9	137694764	Nonsense_Mutation	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10	13740279	137694764	3518667	56	1511											
OLFM1	10439	hgsc.bcm.edu	37	chr9	138011750	138011750	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccctgcagacctggaacaCgagctaccccaagcgcagcg	11	3	11	16	3	0	1	0	0	0	1	0	4	0	2	4	1	6	3	4	1	3	1			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr9:138011750C>T	ENST00000371793.3	+	6	1435	c.1184C>T	c.(1183-1185)aCg>aTg	p.T395M	OLFM1_ENST00000252854.4_Missense_Mutation_p.T377M|OLFM1_ENST00000371796.3_Missense_Mutation_p.T368M	NM_001282611.1	NP_001269540.1	Q99784	NOE1_HUMAN	olfactomedin 1	395	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)		ACCTGGAACACGAGCTACCCC	0.632																																					p.T377M		Atlas-SNP	.											.	OLFM1	57	.	0			c.C1130T						PASS	.						70	59	63					9																	138011750		2203	4300	6503	SO:0001583	missense	10439	exon6			GGAACACGAGCTA	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.1184C>T	chr9.hg19:g.138011750C>T	ENSP00000360858:p.Thr395Met	74.0	0.0	.		71.0	29.0	.	NM_014279	Q53XZ8|Q6IMJ4|Q6IMJ5|Q8N8R0|Q969S7|Q99452	Missense_Mutation	SNP	ENST00000371793.3	hg19		.	.	.	.	.	.	.	.	.	.	C	23.8	4.459036	0.84317	.	.	ENSG00000130558	ENST00000252854;ENST00000371796;ENST00000371793	D;D;D	0.92397	-3.03;-3.03;-3.03	4.7	4.7	0.59300	Olfactomedin-like (3);Quinonprotein alcohol dehydrogenase-like (1);	0.048581	0.85682	D	0.000000	D	0.97349	0.9133	H	0.95043	3.615	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.98883	1.0770	10	0.87932	D	0	.	17.6361	0.88122	0.0:1.0:0.0:0.0	.	395;377	Q99784;Q6IMJ8	NOE1_HUMAN;.	M	377;368;395	ENSP00000252854:T377M;ENSP00000360861:T368M;ENSP00000360858:T395M	ENSP00000252854:T377M	T	+	2	0	OLFM1	137151571	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	7.590000	0.82653	2.166000	0.68216	0.491000	0.48974	ACG	.	.	.	none		0.632	OLFM1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000054974.1	NM_014279		T	138011750	C	T	138011750	3	4	22	1	0	0	0	0	1	0	0	0	10859	536	19	1	1162	1	OLFM1	9	138011750	Missense_Mutation	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10	316986	138011750	3201681	57	1512											
INPP5E	56623	hgsc.bcm.edu	37	chr9	139333176	139333176	+	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	ggccggccggggcccaggctGctgtgggcccgcaccaggag	4	3	19	15	3	0	0	0	0	0	0	0	1	0	1	5	7	1	3	5	7	0	0	rs536052945		TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr9:139333176G>T	ENST00000371712.3	-	1	1098	c.696C>A	c.(694-696)agC>agA	p.S232R	SEC16A_ENST00000467838.1_5'Flank	NM_019892.4	NP_063945.2	Q10713	MPPA_HUMAN	inositol polyphosphate-5-phosphatase, 72 kDa	0					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|endometrium(1)|lung(4)|skin(3)	9		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.36e-06)|Epithelial(140;1.4e-05)		GGCCCAGGCTGCTGTGGGCCC	0.687																																					p.S232R		Atlas-SNP	.											.	INPP5E	18	.	0			c.C696A						PASS	.						9	12	11					9																	139333176		2166	4259	6425	SO:0001583	missense	56623	exon1			CAGGCTGCTGTGG	AF187891	CCDS7000.1	9q34.3	2011-02-11			ENSG00000148384	ENSG00000148384			21474	protein-coding gene	gene with protein product		613037	"Joubert syndrome 1"	JBTS1		10764818, 10577920, 19668216	Standard	NM_019892		Approved	PPI5PIV, CORS1	uc004cho.3	Q9NRR6	OTTHUMG00000020927	ENST00000371712.3:c.696C>A	chr9.hg19:g.139333176G>T	ENSP00000360777:p.Ser232Arg	100.0	0.0	.		103.0	39.0	.	NM_019892	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Missense_Mutation	SNP	ENST00000371712.3	hg19	CCDS7000.1	.	.	.	.	.	.	.	.	.	.	G	13.09	2.134472	0.37630	.	.	ENSG00000148384	ENST00000371712	D	0.97710	-4.5	3.8	0.925	0.19424	.	0.453580	0.22328	N	0.061505	D	0.94032	0.8088	L	0.43923	1.385	0.35619	D	0.809293	B;B	0.31318	0.319;0.132	B;B	0.30105	0.111;0.017	D	0.90931	0.4790	10	0.29301	T	0.29	-36.6616	8.7927	0.34861	0.274:0.0:0.726:0.0	.	232;232	Q9NRR6-2;Q9NRR6	.;INP5E_HUMAN	R	232	ENSP00000360777:S232R	ENSP00000360777:S232R	S	-	3	2	INPP5E	138452997	1.000000	0.71417	1.000000	0.80357	0.630000	0.37929	2.991000	0.49409	0.396000	0.25283	-0.251000	0.11542	AGC	.	.	.	none		0.687	INPP5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055058.1	NM_019892		T	139333176	G	T	139333176	3	4	22	1	0	0	0	0	1	0	0	0	7764	1310	46	4	1278	4	INPP5E	9	139333176	Missense_Mutation	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10	1321426	139333176	1880255	58	1513											
DIP2C	22982	hgsc.bcm.edu	37	chr10	387190	387190	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacagtaagggtccaggcagAtggccacttctctagagggg	10	7	14	10	0	1	2	0	0	1	2	3	2	2	2	2	5	0	2	2	5	2	3			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr10:387190A>G	ENST00000280886.6	-	29	3620	c.3533T>C	c.(3532-3534)aTc>aCc	p.I1178T		NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1178						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)		GTCCAGGCAGATGGCCACTTC	0.483																																					p.I1178T		Atlas-SNP	.											.	DIP2C	195	.	0			c.T3533C						PASS	.						156	129	138					10																	387190		2203	4300	6503	SO:0001583	missense	22982	exon29			AGGCAGATGGCCA	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.3533T>C	chr10.hg19:g.387190A>G	ENSP00000280886:p.Ile1178Thr	124.0	0.0	.		116.0	54.0	.	NM_014974	B4DPI5|Q5SS78	Missense_Mutation	SNP	ENST00000280886.6	hg19	CCDS7054.1	.	.	.	.	.	.	.	.	.	.	A	18.59	3.656310	0.67586	.	.	ENSG00000151240	ENST00000280886;ENST00000535541;ENST00000381503	T	0.39787	1.06	5.53	5.53	0.82687	AMP-dependent synthetase/ligase (1);	0.048817	0.85682	D	0.000000	T	0.42944	0.1225	L	0.47716	1.5	0.80722	D	1	P	0.37015	0.578	P	0.46208	0.507	T	0.25293	-1.0136	10	0.02654	T	1	-37.9788	15.6619	0.77193	1.0:0.0:0.0:0.0	.	1178	Q9Y2E4	DIP2C_HUMAN	T	1178;103;27	ENSP00000280886:I1178T	ENSP00000280886:I1178T	I	-	2	0	DIP2C	377190	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	9.287000	0.95975	2.106000	0.64143	0.528000	0.53228	ATC	.	.	.	none		0.483	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974		G	387190	A	G	387190	3	3	22	1	0	0	0	0	1	0	0	0	4531	333	12	3	1173	3	DIP2C	10	387190	Missense_Mutation	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10		387190	135147557	59	1514											
DIP2C	22982	hgsc.bcm.edu	37	chr10	390824	390826	+	Missense_Mutation	TNP	GCA	GCA	ATG																															gtgtctgggttgcaaggtttGcagatctgggcaggccgctt																										TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G|C|A	G|C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr10:390824_390826GCA>ATG	ENST00000280886.6	-	28	3463_3465	c.3376_3378TGC>CAT	c.(3376-3378)TGC>CAT	p.C1126H		NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1126						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)		TGCAAGGTTTGCAGATCTGGGCA	0.567																																					p.C1126C|p.C1126Y|p.C1126R		Atlas-SNP	.											.	DIP2C	195	.	0			c.C3378T|c.G3377A|c.T3376C						PASS	.																																			SO:0001583	missense	22982	exon28			AGGTTTGCAGATC|GGTTTGCAGATCT|GTTTGCAGATCTG	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.3376_3378TGC>CAT	chr10.hg19:g.390824GCA>ATG	ENSP00000280886:p.Cys1126His	108.0|111.0|111.0	0.0	.		66.0|65.0|64.0	25.0	.	NM_014974	B4DPI5|Q5SS78	Silent|Missense_Mutation|Missense_Mutation	SNP	ENST00000280886.6	hg19	CCDS7054.1																																																																																			.	.	.	none		0.567	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974		ATG	390826	GCA	ATG	390824	3	1	22	1	0	0	0	0	1	0	0	0	4531	1311	46	2	1332	2	DIP2C	10	390824	Missense_Mutation	TNP	GCA	TCGA-2Z-A9JS-01A-21D-A42J-10	3634	390824	135143923	60	1515											
BICC1	80114	hgsc.bcm.edu	37	chr10	60560020	60560020	+	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	aaaaagtgctgagtgcaaatCacggggatccgtccatccag	13	7	11	10	2	1	1	1	1	0	0	4	2	4	2	3	2	2	2	3	2	3	0			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr10:60560020C>A	ENST00000373886.3	+	13	1796	c.1792C>A	c.(1792-1794)Cac>Aac	p.H598N	BICC1_ENST00000263103.1_Missense_Mutation_p.H224N	NM_001080512.1	NP_001073981.1	Q9H694	BICC1_HUMAN	BicC family RNA binding protein 1	598					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						GAGTGCAAATCACGGGGATCC	0.403																																					p.H598N		Atlas-SNP	.											.	BICC1	121	.	0			c.C1792A						PASS	.						48	45	46					10																	60560020		2203	4300	6503	SO:0001583	missense	80114	exon13			GCAAATCACGGGG	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.1792C>A	chr10.hg19:g.60560020C>A	ENSP00000362993:p.His598Asn	347.0	0.0	.		354.0	159.0	.	NM_001080512		Missense_Mutation	SNP	ENST00000373886.3	hg19	CCDS31206.1	.	.	.	.	.	.	.	.	.	.	C	8.488	0.861398	0.17178	.	.	ENSG00000122870	ENST00000373886;ENST00000263103	T;T	0.48522	1.68;0.81	6.02	6.02	0.97574	.	0.099783	0.64402	D	0.000001	T	0.49864	0.1582	L	0.46157	1.445	0.45806	D	0.99868	D;D	0.55385	0.971;0.971	P;B	0.45712	0.491;0.265	T	0.36138	-0.9760	10	0.33141	T	0.24	-15.3338	20.5407	0.99260	0.0:1.0:0.0:0.0	.	518;598	E7EU62;Q9H694	.;BICC1_HUMAN	N	598;224	ENSP00000362993:H598N;ENSP00000263103:H224N	ENSP00000263103:H224N	H	+	1	0	BICC1	60230026	1.000000	0.71417	0.647000	0.29507	0.124000	0.20399	5.335000	0.65929	2.865000	0.98341	0.655000	0.94253	CAC	.	.	.	none		0.403	BICC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048150.2	NM_025044		A	60560020	C	A	60560020	3	1	22	1	0	0	0	0	1	0	0	0	1427	826	29	4	1842	4	BICC1	10	60560020	Missense_Mutation	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10	60169196	60560020	74974727	61	1516											
ANK3	288	hgsc.bcm.edu	37	chr10	61824009	61824009	+	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	ttttccacacgtatttgattGatttcatccactgaaaaatt	12	17	4	8	1	1	3	1	3	0	0	3	3	3	3	2	0	0	1	2	0	3	7			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr10:61824009G>A	ENST00000280772.2	-	39	12548	c.12357C>T	c.(12355-12357)atC>atT	p.I4119I	ANK3_ENST00000503366.1_Silent_p.I1507I|ANK3_ENST00000373827.2_Silent_p.I1500I|ANK3_ENST00000355288.2_Silent_p.I640I	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	4119	Death. {ECO:0000255|PROSITE- ProRule:PRU00064}.				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						GTATTTGATTGATTTCATCCA	0.328																																					p.I4119I		Atlas-SNP	.											.	ANK3	703	.	0			c.C12357T						PASS	.						76	80	78					10																	61824009		2203	4298	6501	SO:0001819	synonymous_variant	288	exon39			TTGATTGATTTCA	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.12357C>T	chr10.hg19:g.61824009G>A		56.0	0.0	.		51.0	23.0	.	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	hg19	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	G	9.439	1.087582	0.20390	.	.	ENSG00000151150	ENST00000514197;ENST00000511043	.	.	.	5.4	4.5	0.54988	.	.	.	.	.	T	0.54631	0.1870	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52888	-0.8515	4	.	.	.	.	5.1251	0.14880	0.1458:0.0:0.523:0.3312	.	.	.	.	L	13;66	.	.	S	-	2	0	ANK3	61494015	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.138000	0.42140	1.273000	0.44346	-0.152000	0.13540	TCA	.	.	.	none		0.328	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		A	61824009	G	A	61824009	2	1	22	1	0	0	0	0	0	0	0	1	622	1280	45	2		2	ANK3	10	61824009	Silent	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10	1263989	61824009	73710738	62	1517											
STOX1	219736	hgsc.bcm.edu	37	chr10	70652348	70652348	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttttaatatctttaggacAcagagtctgggatctaataa	14	15	7	5	0	3	1	0	0	3	1	3	3	3	3	0	2	0	0	0	2	5	8			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr10:70652348A>G	ENST00000298596.6	+	4	2909	c.2826A>G	c.(2824-2826)acA>acG	p.T942T	STOX1_ENST00000399165.4_Missense_Mutation_p.T223A|STOX1_ENST00000421961.2_Silent_p.T832T|STOX1_ENST00000399162.2_Missense_Mutation_p.H156R|STOX1_ENST00000399169.4_Silent_p.T942T	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	942						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						TCTTTAGGACACAGAGTCTGG	0.353																																					p.T223A		Atlas-SNP	.											.	STOX1	75	.	0			c.A667G						PASS	.						81	79	80					10																	70652348		1836	4096	5932	SO:0001819	synonymous_variant	219736	exon4			TAGGACACAGAGT	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.2826A>G	chr10.hg19:g.70652348A>G		225.0	0.0	.		207.0	82.0	.	NM_001130159	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Missense_Mutation	SNP	ENST00000298596.6	hg19	CCDS41535.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.69|13.69	2.313014|2.313014	0.40895|0.40895	.|.	.|.	ENSG00000165730|ENSG00000165730	ENST00000399162|ENST00000399165	D|D	0.82167|0.82255	-1.58|-1.59	5.81|5.81	1.94|1.94	0.25998|0.25998	.|.	.|0.053934	.|0.64402	.|D	.|0.000001	T|T	0.58047|0.58047	0.2095|0.2095	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	B|B	0.09022|0.11235	0.002|0.004	B|B	0.12156|0.09377	0.007|0.004	T|T	0.45542|0.45542	-0.9254|-0.9254	8|9	0.06891|0.07030	T|T	0.86|0.85	.|.	2.5133|2.5133	0.04662|0.04662	0.5545:0.199:0.1391:0.1075|0.5545:0.199:0.1391:0.1075	.|.	156|223	Q6ZVD7-3|Q6ZVD7-2	.|.	R|A	156|223	ENSP00000382115:H156R|ENSP00000382118:T223A	ENSP00000382115:H156R|ENSP00000382118:T223A	H|T	+|+	2|1	0|0	STOX1|STOX1	70322354|70322354	0.968000|0.968000	0.33430|0.33430	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	0.092000|0.092000	0.15066|0.15066	1.035000|1.035000	0.39972|0.39972	0.533000|0.533000	0.62120|0.62120	CAC|ACA	.	.	.	none		0.353	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709		G	70652348	A	G	70652348	2	3	22	1	0	0	0	0	0	0	0	1	15331	159	6	3		3	STOX1	10	70652348	Silent	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	8828339	70652348	64882399	63	1518											
BTAF1	9044	hgsc.bcm.edu	37	chr10	93722390	93722390	+	Frame_Shift_Del	DEL	A	A	-																															agagctgttgctgcagcatcAttagtgcctgtagtagaaag																										TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr10:93722390delA	ENST00000265990.6	+	12	1667	c.1359delA	c.(1357-1359)tcafs	p.S453fs	BTAF1_ENST00000471217.1_3'UTR	NM_003972.2	NP_003963.1	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170kDa	453					negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(6)	59		Colorectal(252;0.0846)				CTGCAGCATCATTAGTGCCTG	0.333																																					p.S453fs		Pindel	.											.	BTAF1	148	.	0			c.1358delC						PASS	.						59	57	57					10																	93722390		2203	4300	6503	SO:0001589	frameshift_variant	9044	exon12			.	AJ001017	CCDS7419.1	10q22-q23	2013-05-01	2013-05-01		ENSG00000095564	ENSG00000095564			17307	protein-coding gene	gene with protein product	"Mot1 homolog (S. cerevisiae)"	605191	"BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170 kD (Mot1 homolog, S. cerevisiae)"			9342322, 9488487	Standard	NM_003972		Approved	TAFII170, TAF172, MOT1, TAF-172, TAF(II)170	uc001khr.3	O14981	OTTHUMG00000018752	ENST00000265990.6:c.1359delA	chr10.hg19:g.93722390delA	ENSP00000265990:p.Ser453fs	397.0	0.0	.		349.0	87.0	0.249	NM_003972	B4E0W6|O43578	Frame_Shift_Del	DEL	ENST00000265990.6	hg19	CCDS7419.1																																																																																			.	.	.	none		0.333	BTAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049380.4	NM_003972		-	93722390	A	-	93722390	7	5	22	1	0	1	0	1	0	0	0	0	1538	204	8	0	1405	0	BTAF1	10	93722390	Frame_Shift_Del	DEL	A	TCGA-2Z-A9JS-01A-21D-A42J-10	23070042	93722390	41812357	64	1519											
FAM178A	55719	hgsc.bcm.edu	37	chr10	102719193	102719193	+	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	gatatttttaaggtgaaagaCttggtcgccaggatacatgg	12	12	12	5	1	0	2	0	1	0	1	1	4	0	3	1	4	1	0	1	4	4	6			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr10:102719193C>G	ENST00000238961.4	+	19	3968	c.3426C>G	c.(3424-3426)gaC>gaG	p.D1142E	FAM178A_ENST00000370269.3_Missense_Mutation_p.D1142E	NM_018121.3	NP_060591.3	Q8IX21	F178A_HUMAN	family with sequence similarity 178, member A	1142						chromatin (GO:0000785)|extracellular space (GO:0005615)|nucleus (GO:0005634)		p.D1142E(1)									AGGTGAAAGACTTGGTCGCCA	0.358																																					p.D1142E		Atlas-SNP	.											C10orf6,NS,carcinoma,0,1	FAM178A	9	.	1	Substitution - Missense(1)	kidney(1)	c.C3426G						PASS	.						188	196	193					10																	102719193		2203	4300	6503	SO:0001583	missense	55719	exon19			GAAAGACTTGGTC	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.3426C>G	chr10.hg19:g.102719193C>G	ENSP00000238961:p.Asp1142Glu	93.0	0.0	.		89.0	42.0	.	NM_001136123	A8K950|B1AL17|Q5W0L8|Q6GMU6|Q9NPE8	Missense_Mutation	SNP	ENST00000238961.4	hg19	CCDS7500.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.382986	0.82792	.	.	ENSG00000119906	ENST00000238961;ENST00000370269	T;T	0.40756	1.03;1.02	5.98	4.99	0.66335	.	0.245484	0.40064	N	0.001183	T	0.50137	0.1598	M	0.62723	1.935	0.44816	D	0.997823	D;D	0.65815	0.991;0.995	P;P	0.55713	0.782;0.782	T	0.52449	-0.8574	10	0.72032	D	0.01	-12.5499	7.0266	0.24944	0.0:0.8615:0.0:0.1385	.	1142;1142	Q8IX21;B1AL17	F178A_HUMAN;.	E	1142	ENSP00000238961:D1142E;ENSP00000359292:D1142E	ENSP00000238961:D1142E	D	+	3	2	FAM178A	102709183	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	0.744000	0.26245	2.838000	0.97847	0.591000	0.81541	GAC	.	.	.	none		0.358	FAM178A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049897.3			G	102719193	C	G	102719193	3	3	22	1	0	0	0	0	1	0	0	0	5507	564	20	4	3500	4	FAM178A	10	102719193	Missense_Mutation	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10	8996803	102719193	32815554	65	1520											
DPCD	25911	hgsc.bcm.edu	37	chr10	103360566	103360566	+	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	ttgaagtaggagacccagcgCccctaggagcagggaacctg	11	5	14	11	1	0	2	0	1	0	1	0	5	0	4	4	3	3	2	4	3	4	3			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr10:103360566C>T	ENST00000370151.4	+	3	266	c.217C>T	c.(217-219)Ccc>Tcc	p.P73S	MIR3158-1_ENST00000583596.1_RNA|DPCD_ENST00000370147.1_Missense_Mutation_p.P73S|DPCD_ENST00000370148.2_Missense_Mutation_p.P73S	NM_015448.1	NP_056263.1	Q9BVM2	DPCD_HUMAN	deleted in primary ciliary dyskinesia homolog (mouse)	73					determination of left/right symmetry (GO:0007368)|epithelial cilium movement (GO:0003351)|lateral ventricle development (GO:0021670)|left/right pattern formation (GO:0060972)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)	nucleus (GO:0005634)				endometrium(1)|large_intestine(1)|lung(2)|skin(1)	5						AGACCCAGCGCCCCTAGGAGC	0.587																																					p.P73S		Atlas-SNP	.											.	DPCD	15	.	0			c.C217T						PASS	.						73	72	72					10																	103360566		2203	4300	6503	SO:0001583	missense	25911	exon3			CCAGCGCCCCTAG		CCDS7514.1	10q24.32	2012-05-03			ENSG00000166171	ENSG00000166171			24542	protein-coding gene	gene with protein product						14630615	Standard	NM_015448		Approved	DKFZP566F084, RP11-529I10.4	uc001ktn.3	Q9BVM2	OTTHUMG00000018934	ENST00000370151.4:c.217C>T	chr10.hg19:g.103360566C>T	ENSP00000359170:p.Pro73Ser	57.0	0.0	.		78.0	25.0	.	NM_015448	A8K289|Q6QNL3|Q8N5R1|Q9UFY6	Missense_Mutation	SNP	ENST00000370151.4	hg19	CCDS7514.1	.	.	.	.	.	.	.	.	.	.	C	8.646	0.897084	0.17686	.	.	ENSG00000166171	ENST00000370151;ENST00000370147;ENST00000370148;ENST00000370149;ENST00000434727	T;T;T;T	0.30448	1.53;1.53;1.53;1.53	5.96	-1.19	0.09585	.	0.947984	0.08934	N	0.872625	T	0.16514	0.0397	L	0.38531	1.155	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33266	-0.9875	10	0.11485	T	0.65	-20.1397	0.9631	0.01399	0.2025:0.2982:0.2681:0.2312	.	73	Q9BVM2	DPCD_HUMAN	S	73;73;73;38;37	ENSP00000359170:P73S;ENSP00000359166:P73S;ENSP00000359167:P73S;ENSP00000403505:P37S	ENSP00000359166:P73S	P	+	1	0	DPCD	103350556	0.000000	0.05858	0.000000	0.03702	0.448000	0.32197	-1.903000	0.01594	0.094000	0.17404	0.655000	0.94253	CCC	.	.	.	none		0.587	DPCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049958.2			T	103360566	C	T	103360566	3	4	22	1	0	0	0	0	1	0	0	0	4713	739	26	2	227	2	DPCD	10	103360566	Missense_Mutation	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10	641373	103360566	32174181	66	1521											
DNHD1	144132	hgsc.bcm.edu	37	chr11	6589765	6589765	+	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	tgttcacagagattttcgtcTttggcttattgtgcctgcag	6	17	10	8	1	2	1	1	0	1	1	3	2	2	1	1	1	2	3	1	1	1	6			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr11:6589765T>A	ENST00000527990.2	+	36	12620	c.12620T>A	c.(12619-12621)cTt>cAt	p.L4207H	DNHD1_ENST00000254579.6_Missense_Mutation_p.L4207H			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	4207					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)		GATTTTCGTCTTTGGCTTATT	0.488																																					p.L4207H		Atlas-SNP	.											.	DNHD1	198	.	0			c.T12620A						PASS	.						164	150	154					11																	6589765		1944	4151	6095	SO:0001583	missense	144132	exon38			TTCGTCTTTGGCT	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.12620T>A	chr11.hg19:g.6589765T>A	ENSP00000436180:p.Leu4207His	50.0	0.0	.		70.0	26.0	.	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	hg19	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	T	18.46	3.628693	0.67015	.	.	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000525883;ENST00000530197	T;T	0.17054	2.3;2.3	4.77	4.77	0.60923	Dynein heavy chain (1);	0.000000	0.64402	D	0.000012	T	0.38904	0.1058	M	0.69823	2.125	0.33897	D	0.638033	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;1.0;0.999	T	0.55811	-0.8082	10	0.87932	D	0	-10.3556	10.8544	0.46789	0.0:0.0:0.0:1.0	.	3295;475;260;4207	B0I1S4;D3DQT9;Q9NSW8;Q96M86	.;.;.;DNHD1_HUMAN	H	4207;4207;475;475	ENSP00000254579:L4207H;ENSP00000436180:L4207H	ENSP00000254579:L4207H	L	+	2	0	DNHD1	6546341	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.149000	0.42244	2.143000	0.66587	0.459000	0.35465	CTT	.	.	.	none		0.488	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		A	6589765	T	A	6589765	3	1	22	1	0	0	0	0	1	0	0	0	4670	1609	56	5	12771	5	DNHD1	11	6589765	Missense_Mutation	SNP	T	TCGA-2Z-A9JS-01A-21D-A42J-10		6589765	128416751	67	1522											
ARNTL	406	hgsc.bcm.edu	37	chr11	13402758	13402758	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccagcccattgaacatcaCgagtacgcctccccctgatg	9	8	7	17	2	1	2	1	2	0	0	3	3	3	2	5	0	3	1	5	0	2	2			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr11:13402758C>T	ENST00000403290.1	+	18	1929	c.1574C>T	c.(1573-1575)aCg>aTg	p.T525M	ARNTL_ENST00000361003.4_Missense_Mutation_p.T407M|ARNTL_ENST00000389708.3_3'UTR|ARNTL_ENST00000403482.3_Missense_Mutation_p.T523M|ARNTL_ENST00000389707.4_Missense_Mutation_p.T524M|ARNTL_ENST00000403510.3_Missense_Mutation_p.T481M|ARNTL_ENST00000401424.1_Missense_Mutation_p.T482M|ARNTL_ENST00000396441.3_Missense_Mutation_p.T524M			O00327	BMAL1_HUMAN	aryl hydrocarbon receptor nuclear translocator-like	525	Interaction with CIART. {ECO:0000250|UniProtKB:Q9WTL8}.				circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription, DNA-templated (GO:0045892)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|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)|protein import into nucleus, translocation (GO:0000060)|regulation of cell cycle (GO:0051726)|regulation of cellular senescence (GO:2000772)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|nuclear body (GO:0016604)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor binding (GO:0017162)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|Hsp90 protein binding (GO:0051879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|signal transducer activity (GO:0004871)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(2)|large_intestine(11)|lung(5)|upper_aerodigestive_tract(1)	20				Epithelial(150;0.0243)		TTGAACATCACGAGTACGCCT	0.473																																					p.T524M		Atlas-SNP	.											.	ARNTL	46	.	0			c.C1571T						PASS	.						143	130	134					11																	13402758		2200	4294	6494	SO:0001583	missense	406	exon17			ACATCACGAGTAC	D89722	CCDS31430.1, CCDS44543.1, CCDS73259.1	11p15	2013-05-21			ENSG00000133794	ENSG00000133794		"Basic helix-loop-helix proteins"	701	protein-coding gene	gene with protein product		602550				9144434, 9079689	Standard	XM_005252930		Approved	MOP3, JAP3, BMAL1, PASD3, bHLHe5	uc001mkp.3	O00327	OTTHUMG00000150623	ENST00000403290.1:c.1574C>T	chr11.hg19:g.13402758C>T	ENSP00000384517:p.Thr525Met	66.0	0.0	.		49.0	25.0	.	NM_001030272	A2I2N6|A8K645|B5ME11|B7WPG7|D3DQW6|O00313|O00314|O00315|O00316|O00317|Q4G136|Q8IUT4|Q99631|Q99649	Missense_Mutation	SNP	ENST00000403290.1	hg19		.	.	.	.	.	.	.	.	.	.	C	14.02	2.409897	0.42715	.	.	ENSG00000133794	ENST00000396441;ENST00000389707;ENST00000401424;ENST00000403290;ENST00000361003;ENST00000403510;ENST00000339640;ENST00000403482	T;T;T;T;T;T;T	0.35605	1.3;1.3;1.3;1.3;1.3;1.3;1.3	5.49	5.49	0.81192	.	0.097970	0.64402	D	0.000001	T	0.45617	0.1351	L	0.44542	1.39	0.80722	D	1	B;P;D;D;P	0.69078	0.11;0.942;0.99;0.997;0.904	B;P;P;P;B	0.56474	0.027;0.62;0.556;0.799;0.416	T	0.24693	-1.0153	10	0.46703	T	0.11	.	14.2188	0.65812	0.1494:0.8506:0.0:0.0	.	523;482;525;524;481	O00327-7;O00327-1;O00327;O00327-8;A2I2N6	.;.;BMAL1_HUMAN;.;.	M	524;524;482;525;407;481;481;523	ENSP00000379718:T524M;ENSP00000374357:T524M;ENSP00000385915:T482M;ENSP00000384517:T525M;ENSP00000354278:T407M;ENSP00000385581:T481M;ENSP00000385897:T523M	ENSP00000340289:T481M	T	+	2	0	ARNTL	13359334	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.325000	0.59234	2.731000	0.93534	0.650000	0.86243	ACG	.	.	.	none		0.473	ARNTL-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000319173.1	NM_001178		T	13402758	C	T	13402758	3	4	22	1	0	0	0	0	1	0	0	0	967	536	19	1	1640	1	ARNTL	11	13402758	Missense_Mutation	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10	6812993	13402758	121603758	68	1523											
HARBI1	283254	hgsc.bcm.edu	37	chr11	46637239	46637239	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccacggtcattagtgtcccTctaatgtcacacaccatcag	10	11	6	14	1	4	0	3	0	1	0	6	0	6	0	3	1	0	0	3	1	2	2			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr11:46637239T>C	ENST00000326737.3	-	2	796	c.549A>G	c.(547-549)agA>agG	p.R183R	ATG13_ENST00000524625.1_5'Flank|ATG13_ENST00000528494.1_5'Flank|ATG13_ENST00000359513.4_5'Flank|ATG13_ENST00000434074.1_5'Flank|ATG13_ENST00000530500.1_5'Flank|ATG13_ENST00000529655.1_5'Flank|ATG13_ENST00000312040.4_5'Flank|ATG13_ENST00000451945.1_5'Flank|ATG13_ENST00000526508.1_5'Flank	NM_173811.3	NP_776172.1	Q96MB7	HARB1_HUMAN	harbinger transposase derived 1	183						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						TTAGTGTCCCTCTAATGTCAC	0.517																																					p.R183R		Atlas-SNP	.											.	HARBI1	19	.	0			c.A549G						PASS	.						164	168	167					11																	46637239		2201	4299	6500	SO:0001819	synonymous_variant	283254	exon2			TGTCCCTCTAATG	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.549A>G	chr11.hg19:g.46637239T>C		135.0	0.0	.		104.0	47.0	.	NM_173811	D3DQP9	Silent	SNP	ENST00000326737.3	hg19	CCDS7920.1																																																																																			.	.	.	none		0.517	HARBI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390291.1	NM_173811		C	46637239	T	C	46637239	2	2	22	1	0	0	0	0	0	0	0	1	6965	1548	54	3		3	HARBI1	11	46637239	Silent	SNP	T	TCGA-2Z-A9JS-01A-21D-A42J-10	33234481	46637239	88369277	69	1524											
SLC3A2	6520	hgsc.bcm.edu	37	chr11	62650443	62650443	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaactcgtggttctccactcAggttgacactgtggccacca	8	10	10	13	1	2	1	1	1	1	0	4	2	2	1	3	3	1	2	3	3	1	2			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr11:62650443A>G	ENST00000377890.2	+	6	1133	c.965A>G	c.(964-966)cAg>cGg	p.Q322R	SLC3A2_ENST00000377891.2_Missense_Mutation_p.Q323R|SLC3A2_ENST00000377889.2_Missense_Mutation_p.Q260R|SLC3A2_ENST00000377892.1_Missense_Mutation_p.Q353R|SLC3A2_ENST00000536981.1_5'UTR|SLC3A2_ENST00000538682.1_3'UTR|SLC3A2_ENST00000338663.7_Missense_Mutation_p.Q221R|SLC3A2_ENST00000535296.1_Missense_Mutation_p.Q291R	NM_002394.5	NP_002385.3	P08195	4F2_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 2	322					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)	p.Q353R(1)		endometrium(1)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)	22						TTCTCCACTCAGGTTGACACT	0.547																																					p.Q323R		Atlas-SNP	.											SLC3A2,NS,carcinoma,0,1	SLC3A2	55	.	1	Substitution - Missense(1)	kidney(1)	c.A968G						PASS	.						147	117	127					11																	62650443		2201	4298	6499	SO:0001583	missense	6520	exon6			CCACTCAGGTTGA		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.965A>G	chr11.hg19:g.62650443A>G	ENSP00000367122:p.Gln322Arg	66.0	0.0	.		60.0	22.0	.	NM_001012662	Q13543	Missense_Mutation	SNP	ENST00000377890.2	hg19	CCDS8039.2	.	.	.	.	.	.	.	.	.	.	A	15.57	2.872936	0.51695	.	.	ENSG00000168003	ENST00000377892;ENST00000377891;ENST00000377890;ENST00000542007;ENST00000377889;ENST00000535296;ENST00000338663;ENST00000422606	D;D;D;D;D;D	0.98296	-4.85;-4.85;-4.85;-4.85;-4.83;-4.85	4.58	4.58	0.56647	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	1.897130	0.02113	N	0.054979	D	0.97179	0.9078	M	0.63428	1.95	0.09310	N	1	B;B;B;B;B	0.28470	0.159;0.003;0.017;0.007;0.213	B;B;B;B;B	0.28784	0.036;0.015;0.028;0.008;0.094	D	0.87653	0.2529	10	0.14252	T	0.57	-2.611	12.2242	0.54451	1.0:0.0:0.0:0.0	.	260;291;322;221;353	P08195-3;F5GZS6;P08195;P08195-2;P08195-4	.;.;4F2_HUMAN;.;.	R	353;323;322;323;260;291;221;203	ENSP00000367124:Q353R;ENSP00000367123:Q323R;ENSP00000367122:Q322R;ENSP00000367121:Q260R;ENSP00000444236:Q291R;ENSP00000340815:Q221R	ENSP00000340815:Q221R	Q	+	2	0	SLC3A2	62407019	0.020000	0.18652	0.007000	0.13788	0.515000	0.34225	2.014000	0.40951	1.849000	0.53698	0.459000	0.35465	CAG	.	.	.	none		0.547	SLC3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157306.1	NM_001012661		G	62650443	A	G	62650443	3	3	22	1	0	0	0	0	1	0	0	0	14640	188	7	3	1087	3	SLC3A2	11	62650443	Missense_Mutation	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	16013204	62650443	72356073	70	1525											
UCP2	7351	hgsc.bcm.edu	37	chr11	73689030	73689030	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggccggcaaccagcccatTgtagaggcttcgggggccct	7	6	14	14	2	0	1	0	0	0	1	1	1	0	1	4	5	2	3	4	5	2	3			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr11:73689030T>C	ENST00000310473.3	-	4	1080	c.238A>G	c.(238-240)Aat>Gat	p.N80D	UCP2_ENST00000542615.1_5'Flank|UCP2_ENST00000536983.1_Missense_Mutation_p.N80D	NM_003355.2	NP_003346.2	P55851	UCP2_HUMAN	uncoupling protein 2 (mitochondrial, proton carrier)	80					aging (GO:0007568)|cellular metabolic process (GO:0044237)|cellular response to amino acid starvation (GO:0034198)|cellular response to glucose stimulus (GO:0071333)|cellular response to insulin stimulus (GO:0032869)|female pregnancy (GO:0007565)|liver regeneration (GO:0097421)|mitochondrial transport (GO:0006839)|negative regulation of apoptotic process (GO:0043066)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|positive regulation of cell death (GO:0010942)|proton transport (GO:0015992)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|response to fatty acid (GO:0070542)|response to hypoxia (GO:0001666)|response to superoxide (GO:0000303)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				large_intestine(1)|lung(3)|prostate(1)	5	Breast(11;0.000112)					ACCAGCCCATTGTAGAGGCTT	0.607																																					p.N80D	Colon(191;388 2040 43557 45622 48925)	Atlas-SNP	.											.	UCP2	24	.	0			c.A238G						PASS	.						58	59	59					11																	73689030		2200	4293	6493	SO:0001583	missense	7351	exon4			GCCCATTGTAGAG	U76367	CCDS8228.1	11q13	2014-02-12						"Solute carriers"	12518	protein-coding gene	gene with protein product		601693	"body mass index QTL 4", "body mass index quantitative trait 4"	BMIQ4		9196039, 11381268	Standard	NM_003355		Approved	SLC25A8	uc001oup.1	P55851		ENST00000310473.3:c.238A>G	chr11.hg19:g.73689030T>C	ENSP00000312029:p.Asn80Asp	87.0	0.0	.		92.0	20.0	.	NM_003355	Q4PJH8|Q53HM3	Missense_Mutation	SNP	ENST00000310473.3	hg19	CCDS8228.1	.	.	.	.	.	.	.	.	.	.	T	16.74	3.206483	0.58343	.	.	ENSG00000175567	ENST00000310473;ENST00000536983;ENST00000544615	T;T;T	0.78924	-1.22;-1.22;-1.22	6.07	6.07	0.98685	Mitochondrial carrier domain (2);	0.217573	0.53938	D	0.000045	T	0.80470	0.4629	M	0.69185	2.1	0.46678	D	0.999154	B;B	0.15930	0.013;0.015	B;B	0.34242	0.152;0.178	T	0.77297	-0.2640	10	0.56958	D	0.05	-5.0289	15.4529	0.75290	0.0:0.0:0.0:1.0	.	80;80	F5GX45;P55851	.;UCP2_HUMAN	D	80;80;53	ENSP00000312029:N80D;ENSP00000441147:N80D;ENSP00000439951:N53D	ENSP00000312029:N80D	N	-	1	0	UCP2	73366678	1.000000	0.71417	0.989000	0.46669	0.605000	0.37080	6.246000	0.72405	2.326000	0.78906	0.533000	0.62120	AAT	.	.	.	none		0.607	UCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398108.1	NM_003355		C	73689030	T	C	73689030	3	2	22	1	0	0	0	0	1	0	0	0	16943	1812	63	3	711	3	UCP2	11	73689030	Missense_Mutation	SNP	T	TCGA-2Z-A9JS-01A-21D-A42J-10	11038587	73689030	61317486	71	1526											
ENO2	2026	hgsc.bcm.edu	37	chr12	7031532	7031532	+	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	gactggtgccccgtgccgttCtgaacgtctggctaaataca	8	10	11	12	3	2	1	0	1	2	0	2	2	2	1	3	2	4	2	3	2	4	3			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr12:7031532C>T	ENST00000535366.1	+	10	1828	c.1202C>T	c.(1201-1203)tCt>tTt	p.S401F	ENO2_ENST00000534977.1_3'UTR|ENO2_ENST00000545045.2_Missense_Mutation_p.S282F|ENO2_ENST00000544774.1_Missense_Mutation_p.S358F|ENO2_ENST00000538763.1_Missense_Mutation_p.S358F|ENO2_ENST00000229277.1_Missense_Mutation_p.S401F|ENO2_ENST00000541477.1_Missense_Mutation_p.S401F|ATN1_ENST00000356654.4_5'Flank			P09104	ENOG_HUMAN	enolase 2 (gamma, neuronal)	401					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|perikaryon (GO:0043204)|phosphopyruvate hydratase complex (GO:0000015)|photoreceptor inner segment (GO:0001917)|plasma membrane (GO:0005886)	magnesium ion binding (GO:0000287)|phosphopyruvate hydratase activity (GO:0004634)			endometrium(3)|large_intestine(2)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						CCGTGCCGTTCTGAACGTCTG	0.547																																					p.S401F		Atlas-SNP	.											.	ENO2	20	.	0			c.C1202T						PASS	.						94	84	87					12																	7031532		2203	4300	6503	SO:0001583	missense	2026	exon11			GCCGTTCTGAACG	M22349	CCDS8570.1	12p13	2012-10-02				ENSG00000111674	4.2.1.11		3353	protein-coding gene	gene with protein product		131360					Standard	NM_001975		Approved		uc001qru.1	P09104		ENST00000535366.1:c.1202C>T	chr12.hg19:g.7031532C>T	ENSP00000437402:p.Ser401Phe	101.0	0.0	.		133.0	63.0	.	NM_001975	B7Z2X9|Q96J33	Missense_Mutation	SNP	ENST00000535366.1	hg19	CCDS8570.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.590935	0.86851	.	.	ENSG00000111674	ENST00000541477;ENST00000229277;ENST00000538763;ENST00000544774;ENST00000535366;ENST00000545045	T;T;T;T;T;T	0.60171	0.21;0.21;0.21;0.21;0.21;0.21	4.22	4.22	0.49857	Enolase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.82536	0.5058	H	0.95504	3.68	0.80722	D	1	P;D	0.69078	0.566;0.997	P;D	0.71656	0.521;0.974	D	0.88558	0.3121	10	0.72032	D	0.01	-10.0883	17.1386	0.86747	0.0:1.0:0.0:0.0	.	358;401	B7Z2X9;P09104	.;ENOG_HUMAN	F	401;401;358;358;401;282	ENSP00000438873:S401F;ENSP00000229277:S401F;ENSP00000441490:S358F;ENSP00000446195:S358F;ENSP00000437402:S401F;ENSP00000438062:S282F	ENSP00000229277:S401F	S	+	2	0	ENO2	6901793	1.000000	0.71417	0.998000	0.56505	0.939000	0.58152	7.651000	0.83577	2.361000	0.80049	0.455000	0.32223	TCT	.	.	.	none		0.547	ENO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401786.1			T	7031532	C	T	7031532	3	4	22	1	0	0	0	0	1	0	0	0	5124	913	32	2	1240	2	ENO2	12	7031532	Missense_Mutation	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10		7031532	126820363	72	1527											
DIP2B	57609	hgsc.bcm.edu	37	chr12	51108338	51108338	+	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	catcctcatgtgcccccataCatgtgtgacaaacttgccaa	11	10	6	14	0	1	1	1	1	0	0	2	1	2	1	4	0	4	0	4	0	3	2			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr12:51108338C>A	ENST00000301180.5	+	23	2844	c.2810C>A	c.(2809-2811)aCa>aAa	p.T937K		NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	937						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						TGCCCCCATACATGTGTGACA	0.463																																					p.T937K		Atlas-SNP	.											.	DIP2B	167	.	0			c.C2810A						PASS	.						110	102	105					12																	51108338		2203	4300	6503	SO:0001583	missense	57609	exon23			CCCATACATGTGT	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.2810C>A	chr12.hg19:g.51108338C>A	ENSP00000301180:p.Thr937Lys	68.0	0.0	.		56.0	27.0	.	NM_173602	Q6B011|Q8N1L5|Q8NB38	Missense_Mutation	SNP	ENST00000301180.5	hg19	CCDS31799.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.574553	0.86542	.	.	ENSG00000066084	ENST00000301180	T	0.37235	1.21	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.45458	0.1343	M	0.78801	2.425	0.80722	D	1	P	0.45428	0.858	P	0.45794	0.493	T	0.39663	-0.9603	10	0.08837	T	0.75	-13.4949	18.5538	0.91075	0.0:1.0:0.0:0.0	.	937	Q9P265	DIP2B_HUMAN	K	937	ENSP00000301180:T937K	ENSP00000301180:T937K	T	+	2	0	DIP2B	49394605	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.651000	0.83577	2.941000	0.99782	0.655000	0.94253	ACA	.	.	.	none		0.463	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602		A	51108338	C	A	51108338	3	1	22	1	0	0	0	0	1	0	0	0	4530	478	17	4	2900	4	DIP2B	12	51108338	Missense_Mutation	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10	44076806	51108338	82743557	73	1528											
DYRK2	8445	hgsc.bcm.edu	37	chr12	68051341	68051341	+	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	caggtgccccacgatcacgtGgcttacaggtatgaggtcct	8	9	12	12	2	1	1	1	1	0	0	2	2	2	1	3	4	2	2	3	4	2	2			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr12:68051341G>T	ENST00000344096.3	+	3	1067	c.654G>T	c.(652-654)gtG>gtT	p.V218V	DYRK2_ENST00000393555.3_Silent_p.V145V|RP11-335O4.3_ENST00000425371.2_RNA	NM_006482.2	NP_006473.2	Q92630	DYRK2_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	218					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)		ACGATCACGTGGCTTACAGGT	0.547																																					p.V218V		Atlas-SNP	.											.	DYRK2	63	.	0			c.G654T						PASS	.						72	56	61					12																	68051341		2203	4300	6503	SO:0001819	synonymous_variant	8445	exon3			TCACGTGGCTTAC	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.654G>T	chr12.hg19:g.68051341G>T		46.0	0.0	.		50.0	25.0	.	NM_006482	B2R9V9|Q9BRB5	Silent	SNP	ENST00000344096.3	hg19	CCDS8978.1																																																																																			.	.	.	none		0.547	DYRK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402218.1			T	68051341	G	T	68051341	2	4	22	1	0	0	0	0	0	0	0	1	4858	1335	47	4		4	DYRK2	12	68051341	Silent	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10	16943003	68051341	65800554	74	1529											
PTPRB	5787	hgsc.bcm.edu	37	chr12	71016317	71016317	+	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	ctgatgaaggcctctgtggtAttcctaataaggaataccag	12	11	10	8	0	1	2	0	2	1	0	2	3	2	3	3	3	1	1	3	3	6	5			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr12:71016317A>T	ENST00000550358.1	-	3	586	c.561T>A	c.(559-561)aaT>aaA	p.N187K	PTPRB_ENST00000551525.1_Missense_Mutation_p.N186K|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000334414.6_Missense_Mutation_p.N187K			P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	0	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			CCTCTGTGGTATTCCTAATAA	0.478																																					p.N187K		Atlas-SNP	.											.	PTPRB	676	.	0			c.T561A						PASS	.						68	73	71					12																	71016317		1915	4126	6041	SO:0001583	missense	5787	exon3			TGTGGTATTCCTA	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000550358.1:c.561T>A	chr12.hg19:g.71016317A>T	ENSP00000448058:p.Asn187Lys	85.0	0.0	.		83.0	34.0	.	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000550358.1	hg19		.	.	.	.	.	.	.	.	.	.	A	16.59	3.166622	0.57476	.	.	ENSG00000127329	ENST00000334414;ENST00000550358;ENST00000544694;ENST00000551525	T;T;T	0.04275	4.17;4.13;3.66	5.72	-9.02	0.00741	.	.	.	.	.	T	0.07954	0.0199	L	0.27053	0.805	0.20307	N	0.999914	D;D;P;P	0.69078	0.997;0.972;0.873;0.873	P;P;B;B	0.58331	0.837;0.621;0.306;0.306	T	0.10314	-1.0635	9	0.40728	T	0.16	.	17.5824	0.87972	0.7669:0.0:0.2331:0.0	.	187;186;187;187	Q6ZTX7;F8VSD5;P23467-3;F8VU56	.;.;.;.	K	187;187;187;186	ENSP00000334928:N187K;ENSP00000448058:N187K;ENSP00000448349:N186K	ENSP00000334928:N187K	N	-	3	2	PTPRB	69302584	0.066000	0.20996	0.074000	0.20217	0.002000	0.02628	-0.965000	0.03829	-1.631000	0.01543	-0.904000	0.02843	AAT	.	.	.	none		0.478	PTPRB-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404436.1			T	71016317	A	T	71016317	3	4	22	1	0	0	0	0	1	0	0	0	12809	446	16	5	6272	5	PTPRB	12	71016317	Missense_Mutation	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	2964976	71016317	62835578	75	1530											
ACSS3	79611	hgsc.bcm.edu	37	chr12	81627129	81627129	+	Splice_Site	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	tattttttcttgttttcaggGatattatgataccatggatg	9	20	8	4	0	2	1	1	1	1	0	2	3	2	3	1	2	1	1	1	2	4	10			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr12:81627129G>A	ENST00000548058.1	+	13	2508	c.1598G>A	c.(1597-1599)gGa>gAa	p.G533E	ACSS3_ENST00000261206.3_Splice_Site_p.G532E|ACSS3_ENST00000548324.1_Splice_Site_p.G215E			Q9H6R3	ACSS3_HUMAN	acyl-CoA synthetase short-chain family member 3	533						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						TGTTTTCAGGGATATTATGAT	0.308																																					p.G533E		Atlas-SNP	.											.	ACSS3	118	.	0			c.G1598A						PASS	.						214	213	213					12																	81627129		2203	4300	6503	SO:0001630	splice_region_variant	79611	exon13			TTCAGGGATATTA		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.1597-1G>A	chr12.hg19:g.81627129G>A		101.0	0.0	.		96.0	39.0	.	NM_024560	Q8NC66	Missense_Mutation	SNP	ENST00000548058.1	hg19	CCDS9022.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.914047	0.92178	.	.	ENSG00000111058	ENST00000548058;ENST00000261206;ENST00000548324	T;T;T	0.60040	2.07;2.07;0.22	5.84	5.84	0.93424	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	D	0.82360	0.5020	M	0.90870	3.155	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.99;1.0	D	0.85234	0.1034	10	0.72032	D	0.01	-9.1533	19.7715	0.96367	0.0:0.0:1.0:0.0	.	215;533	Q9H6R3-2;Q9H6R3	.;ACSS3_HUMAN	E	533;532;215	ENSP00000449535:G533E;ENSP00000261206:G532E;ENSP00000448965:G215E	ENSP00000261206:G532E	G	+	2	0	ACSS3	80151260	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.282000	0.95840	2.777000	0.95525	0.650000	0.86243	GGA	.	.	.	none		0.308	ACSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407794.1	NM_024560	Missense_Mutation	A	81627129	G	A	81627129	5	1	22	1	0	0	0	0	0	0	1	0	190	1188	41	2	1648	2	ACSS3	12	81627129	Splice_Site	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10	10610812	81627129	52224766	76	1531											
SYCP3	50511	hgsc.bcm.edu	37	chr12	102127402	102127402	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgcatatctaaatcccacTgctgaaacaaagtcagaaac	16	9	5	11	0	3	2	1	1	2	1	4	2	4	2	1	0	4	2	1	0	6	2			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr12:102127402T>C	ENST00000392927.3	-	6	535	c.404A>G	c.(403-405)cAg>cGg	p.Q135R	SYCP3_ENST00000392924.1_Missense_Mutation_p.Q135R|SYCP3_ENST00000266743.2_Missense_Mutation_p.Q135R	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	135	Gln-rich.				male meiosis I (GO:0007141)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(1)	11						TAAATCCCACTGCTGAAACAA	0.323																																					p.Q135R		Atlas-SNP	.											.	SYCP3	19	.	0			c.A404G						PASS	.						146	135	138					12																	102127402		2203	4300	6503	SO:0001583	missense	50511	exon6			TCCCACTGCTGAA	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.404A>G	chr12.hg19:g.102127402T>C	ENSP00000376658:p.Gln135Arg	47.0	0.0	.		36.0	11.0	.	NM_001177949		Missense_Mutation	SNP	ENST00000392927.3	hg19	CCDS9087.1	.	.	.	.	.	.	.	.	.	.	T	11.14	1.552521	0.27739	.	.	ENSG00000139351	ENST00000266743;ENST00000392927;ENST00000392924	.	.	.	5.95	5.95	0.96441	.	0.128110	0.53938	D	0.000053	T	0.49966	0.1588	L	0.39326	1.205	0.48452	D	0.99965	P	0.36010	0.532	B	0.39590	0.304	T	0.48352	-0.9043	9	0.30854	T	0.27	-9.351	10.7032	0.45939	0.0:0.0708:0.0:0.9292	.	135	Q8IZU3	SYCP3_HUMAN	R	135	.	ENSP00000266743:Q135R	Q	-	2	0	SYCP3	100651533	1.000000	0.71417	1.000000	0.80357	0.091000	0.18340	3.569000	0.53827	2.272000	0.75746	0.460000	0.39030	CAG	.	.	.	none		0.323	SYCP3-001	KNOWN	alternative_5_UTR|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316478.2	NM_153694		C	102127402	T	C	102127402	3	2	22	1	0	0	0	0	1	0	0	0	15446	1580	55	3	322	3	SYCP3	12	102127402	Missense_Mutation	SNP	T	TCGA-2Z-A9JS-01A-21D-A42J-10	20500273	102127402	31724493	77	1532											
ANAPC7	51434	hgsc.bcm.edu	37	chr12	110825587	110825587	+	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	gttgtcaccagtgtgcacaaAagcatacgctttgatccaca	12	10	8	11	1	1	1	1	1	0	0	2	1	2	1	2	0	3	4	2	0	3	3			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr12:110825587A>T	ENST00000455511.3	-	5	733	c.733T>A	c.(733-735)Ttt>Att	p.F245I	RP11-478C19.2_ENST00000550231.1_RNA|ANAPC7_ENST00000450008.2_Missense_Mutation_p.F245I	NM_016238.2	NP_057322.2	Q9UJX3	APC7_HUMAN	anaphase promoting complex subunit 7	245					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)			breast(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)	19						GTGTGCACAAAAGCATACGCT	0.473																																					p.F245I		Atlas-SNP	.											.	ANAPC7	68	.	0			c.T733A						PASS	.						137	109	118					12																	110825587		2203	4300	6503	SO:0001583	missense	51434	exon5			GCACAAAAGCATA	AF191340	CCDS9145.2, CCDS44971.1	12q13.12	2013-01-10			ENSG00000196510	ENSG00000196510		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	17380	protein-coding gene	gene with protein product		606949					Standard	NM_016238		Approved	APC7	uc001tqo.2	Q9UJX3	OTTHUMG00000157009	ENST00000455511.3:c.733T>A	chr12.hg19:g.110825587A>T	ENSP00000394394:p.Phe245Ile	91.0	0.0	.		88.0	27.0	.	NM_016238	Q96AC4|Q96GF4|Q9BU24|Q9NT16	Missense_Mutation	SNP	ENST00000455511.3	hg19	CCDS9145.2	.	.	.	.	.	.	.	.	.	.	A	23.2	4.386589	0.82902	.	.	ENSG00000196510;ENSG00000196510;ENSG00000258210	ENST00000455511;ENST00000450008;ENST00000550231	T;T	0.63913	-0.07;0.95	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.66896	0.2836	N	0.22421	0.69	0.80722	D	1	D;B	0.57899	0.981;0.207	D;B	0.69142	0.962;0.05	T	0.64045	-0.6499	10	0.25106	T	0.35	-11.8755	16.6245	0.84952	1.0:0.0:0.0:0.0	.	245;245	Q9UJX3-2;Q9UJX3	.;APC7_HUMAN	I	245;245;144	ENSP00000394394:F245I;ENSP00000402314:F245I	ENSP00000402314:F245I	F	-	1	0	RP11-478C19.2;ANAPC7	109309970	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.958000	0.93099	2.323000	0.78572	0.528000	0.53228	TTT	.	.	.	none		0.473	ANAPC7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347075.3	NM_016238		T	110825587	A	T	110825587	3	4	22	1	0	0	0	0	1	0	0	0	606	14	1	5	1098	5	ANAPC7	12	110825587	Missense_Mutation	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	8698185	110825587	23026308	78	1533											
C12orf51	283450	hgsc.bcm.edu	37	chr12	112664523	112664523	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtatgaattcttcacaaaaTaagctgtcttctaaaagctg	14	14	6	7	0	4	1	1	1	3	0	4	1	4	1	0	0	2	3	0	0	7	6			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr12:112664523T>C	ENST00000430131.2	-	43	6773	c.5628A>G	c.(5626-5628)ttA>ttG	p.L1876L	HECTD4_ENST00000550722.1_Silent_p.L2152L|HECTD4_ENST00000377560.5_Silent_p.L2126L			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	1876					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)										CTTCACAAAATAAGCTGTCTT	0.388																																					p.L2164L		Atlas-SNP	.											.	.	.	.	0			c.A6492G						PASS	.						84	81	82					12																	112664523		1869	4124	5993	SO:0001819	synonymous_variant	283450	exon44			ACAAAATAAGCTG	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.5628A>G	chr12.hg19:g.112664523T>C		40.0	0.0	.		36.0	9.0	.	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	T	9.769	1.172289	0.21704	.	.	ENSG00000173064	ENST00000550968	.	.	.	5.24	-1.38	0.09027	.	.	.	.	.	T	0.57417	0.2052	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54118	-0.8341	4	.	.	.	.	10.8882	0.46978	0.0:0.47:0.0:0.53	.	.	.	.	C	43	.	.	Y	-	2	0	C12orf51	111148906	0.090000	0.21635	0.994000	0.49952	0.996000	0.88848	-0.647000	0.05397	-0.195000	0.10382	0.383000	0.25322	TAT	.	.	.	none		0.388	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		C	112664523	T	C	112664523	2	2	22	1	0	0	0	0	0	0	0	1	1698	1403	49	3		3	C12orf51	12	112664523	Silent	SNP	T	TCGA-2Z-A9JS-01A-21D-A42J-10	1838936	112664523	21187372	79	1534											
PRPF39	55015	hgsc.bcm.edu	37	chr14	45578916	45578916	+	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	aattgaaaatgggactcatgAacgagttgtggttctctttg	11	14	11	5	1	2	2	1	2	1	0	3	4	2	3	0	2	1	2	0	2	4	4			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr14:45578916A>T	ENST00000355765.6	+	8	1279	c.1109A>T	c.(1108-1110)gAa>gTa	p.E370V	SNORD127_ENST00000458892.1_RNA	NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	370					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						GGGACTCATGAACGAGTTGTG	0.338																																					p.E370V		Atlas-SNP	.											.	PRPF39	46	.	0			c.A1109T						PASS	.						75	70	72					14																	45578916		2203	4300	6503	SO:0001583	missense	55015	exon8			CTCATGAACGAGT	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.1109A>T	chr14.hg19:g.45578916A>T	ENSP00000348010:p.Glu370Val	104.0	0.0	.		91.0	47.0	.	NM_017922	Q08AL1|Q08AL2|Q9NUU5	Missense_Mutation	SNP	ENST00000355765.6	hg19	CCDS9682.2	.	.	.	.	.	.	.	.	.	.	A	18.44	3.625017	0.66901	.	.	ENSG00000185246	ENST00000355765	T	0.35421	1.31	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.44265	0.1285	L	0.45285	1.41	0.80722	D	1	P	0.50272	0.933	P	0.52672	0.706	T	0.31447	-0.9943	10	0.48119	T	0.1	-4.5178	14.5457	0.68030	1.0:0.0:0.0:0.0	.	370	Q86UA1	PRP39_HUMAN	V	370	ENSP00000348010:E370V	ENSP00000348010:E370V	E	+	2	0	PRPF39	44648666	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.114000	0.94329	2.124000	0.65301	0.383000	0.25322	GAA	.	.	.	none		0.338	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319683.2			T	45578916	A	T	45578916	3	4	22	1	0	0	0	0	1	0	0	0	12579	246	9	5	1135	5	PRPF39	14	45578916	Missense_Mutation	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10		45578916	61770624	80	1535											
C14orf104	55172	hgsc.bcm.edu	37	chr14	50100020	50100024	+	Frame_Shift_Del	DEL	GTTTA	GTTTA	-																															gttacctccaaagaatcgttGtttacaccataataccactc																										TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	GTTTA	GTTTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr14:50100020_50100024delGTTTA	ENST00000298292.8	-	1	1924_1928	c.1844_1848delTAAAC	c.(1843-1848)gtaaacfs	p.VN615fs	DNAAF2_ENST00000406043.3_Frame_Shift_Del_p.VN615fs	NM_018139.2	NP_060609.2	Q9NVR5	KTU_HUMAN	dynein, axonemal, assembly factor 2	615					axonemal dynein complex assembly (GO:0070286)|bacterial-type flagellum-dependent cell motility (GO:0071973)|cilium-dependent cell motility (GO:0060285)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)				kidney(1)|lung(4)	5						AAGAATCGTTGTTTACACCATAATA	0.429																																					p.615_617del		Atlas-Indel,Pindel	.											.	DNAAF2	47	.	0			c.1845_1849del						PASS	.																																			SO:0001589	frameshift_variant	55172	exon1			.	AK001425	CCDS9691.2, CCDS45100.1	14q21.3	2012-05-03	2011-06-09	2011-06-09	ENSG00000165506	ENSG00000165506			20188	protein-coding gene	gene with protein product	"kintoun"	612517	"chromosome 14 open reading frame 104"	C14orf104			Standard	NM_001083908		Approved	FLJ10563, KTU, PF13, CILD10	uc001wws.4	Q9NVR5	OTTHUMG00000152331	ENST00000298292.8:c.1844_1848delTAAAC	chr14.hg19:g.50100020_50100024delGTTTA	ENSP00000298292:p.Val615fs	131.0	0.0	0		98.0	40.0	0.408163	NM_018139	B9WS54|C0JAP7|Q86TR1|Q86TY8|Q969Z5	Frame_Shift_Del	DEL	ENST00000298292.8	hg19	CCDS9691.2																																																																																			.	.	.	none		0.429	DNAAF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276813.1			-	50100024	GTTTA	-	50100020	7	5	22	1	0	1	0	1	0	0	0	0	1738	1368	48	0	677	0	C14orf104	14	50100020	Frame_Shift_Del	DEL	GTTTA	TCGA-2Z-A9JS-01A-21D-A42J-10	4521104	50100020	57249520	81	1536											
TMEM30B	161291	hgsc.bcm.edu	37	chr14	61747022	61747022	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgatgttgacgcggtaggCgccccgcggcagcccggccg	4	5	18	14	7	0	2	0	2	0	0	0	2	0	2	4	5	1	3	4	5	1	2			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr14:61747022C>T	ENST00000555868.1	-	1	1536	c.844G>A	c.(844-846)Gcc>Acc	p.A282T	TMEM30B_ENST00000557163.1_5'UTR|TMEM30B_ENST00000355702.2_Missense_Mutation_p.A282T	NM_001017970.2	NP_001017970.1	Q3MIR4	CC50B_HUMAN	transmembrane protein 30B	282					lipid transport (GO:0006869)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)	6				OV - Ovarian serous cystadenocarcinoma(108;0.107)|BRCA - Breast invasive adenocarcinoma(234;0.181)		ACGCGGTAGGCGCCCCGCGGC	0.667																																					p.A282T		Atlas-SNP	.											.	TMEM30B	13	.	0			c.G844A						PASS	.						39	40	40					14																	61747022		2202	4300	6502	SO:0001583	missense	161291	exon1			GGTAGGCGCCCCG	AK091169	CCDS32093.1	14q23.1	2006-09-20				ENSG00000182107			27254	protein-coding gene	gene with protein product		611029				15375526	Standard	NM_001017970		Approved	CDC50B	uc001xfl.3	Q3MIR4		ENST00000555868.1:c.844G>A	chr14.hg19:g.61747022C>T	ENSP00000450842:p.Ala282Thr	54.0	0.0	.		62.0	26.0	.	NM_001017970	B3KR84|Q14D00	Missense_Mutation	SNP	ENST00000555868.1	hg19	CCDS32093.1	.	.	.	.	.	.	.	.	.	.	C	12.81	2.049475	0.36181	.	.	ENSG00000182107	ENST00000555868;ENST00000355702	.	.	.	4.67	-2.8	0.05823	.	0.667620	0.14557	N	0.312287	T	0.03136	0.0092	N	0.00201	-1.865	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.34279	-0.9835	9	0.02654	T	1	-16.991	1.474	0.02422	0.1438:0.2798:0.1415:0.4349	.	282	Q3MIR4	CC50B_HUMAN	T	282	.	ENSP00000347930:A282T	A	-	1	0	TMEM30B	60816775	0.001000	0.12720	0.025000	0.17156	0.923000	0.55619	-0.871000	0.04223	-0.491000	0.06697	0.650000	0.86243	GCC	.	.	.	none		0.667	TMEM30B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413358.1	XM_090844		T	61747022	C	T	61747022	3	4	22	1	0	0	0	0	1	0	0	0	16166	768	27	1	215	1	TMEM30B	14	61747022	Missense_Mutation	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10	11647002	61747022	45602518	82	1537											
HSP90AA1	3320	hgsc.bcm.edu	37	chr14	102552294	102552294	+	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	gctttggtcccagacttggcGatagtaccaaggttattgat	9	13	11	8	1	0	2	0	1	0	1	1	3	1	2	2	3	1	3	2	3	4	6			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr14:102552294G>A	ENST00000216281.8	-	3	535	c.330C>T	c.(328-330)atC>atT	p.I110I	HSP90AA1_ENST00000441629.2_Intron|HSP90AA1_ENST00000334701.7_Silent_p.I232I	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1	110					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)	CAGACTTGGCGATAGTACCAA	0.423																																					p.I232I		Atlas-SNP	.											.	HSP90AA1	65	.	0			c.C696T						PASS	.						67	67	67					14																	102552294		2203	4297	6500	SO:0001819	synonymous_variant	3320	exon4			CTTGGCGATAGTA	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.330C>T	chr14.hg19:g.102552294G>A		169.0	0.0	.		152.0	64.0	.	NM_001017963	A8K500|B3KPJ9|Q2PP14|Q5CAQ6|Q5CAQ7|Q9BVQ5	Silent	SNP	ENST00000216281.8	hg19	CCDS9967.1																																																																																			.	.	.	none		0.423	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414952.2	NM_005348		A	102552294	G	A	102552294	2	1	22	1	0	0	0	0	0	0	0	1	7408	1048	37	1		1	HSP90AA1	14	102552294	Silent	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10	40805272	102552294	4797246	83	1538											
INO80	54617	hgsc.bcm.edu	37	chr15	41387985	41387985	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaactccattcagagaataTgtgtttaacattccagaact	15	12	6	8	0	1	3	1	0	0	3	3	4	3	3	2	0	3	1	2	0	5	5			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr15:41387985T>C	ENST00000361937.3	-	3	709	c.285A>G	c.(283-285)acA>acG	p.T95T	INO80_ENST00000401393.3_Silent_p.T95T			Q9ULG1	INO80_HUMAN	INO80 complex subunit	95	Assembles INO80 complex module with putative regulatory components INO80E, INO80F, UCHL5, NFRKB, MCRS1 and IN80D.				ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						TCAGAGAATATGTGTTTAACA	0.428																																					p.T95T		Atlas-SNP	.											INOC1,right_upper_lobe,carcinoma,0,2	INO80	122	.	0			c.A285G						PASS	.						70	75	73					15																	41387985		2203	4300	6503	SO:0001819	synonymous_variant	54617	exon3			AGAATATGTGTTT	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.285A>G	chr15.hg19:g.41387985T>C		73.0	1.0	.		73.0	22.0	.	NM_017553	A6H8X4|Q9NTG6	Silent	SNP	ENST00000361937.3	hg19	CCDS10071.1																																																																																			.	.	.	none		0.428	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252527.2	NM_017553		C	41387985	T	C	41387985	2	2	22	1	0	0	0	0	0	0	0	1	7753	1451	51	3		3	INO80	15	41387985	Silent	SNP	T	TCGA-2Z-A9JS-01A-21D-A42J-10		41387985	61143407	84	1539											
ATP8B4	79895	hgsc.bcm.edu	37	chr15	50168660	50168660	+	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	tttacgcttgttaaaaagcaGattcagctgtcctggtttgt	9	16	9	7	1	1	1	1	0	0	1	2	1	2	1	1	1	3	5	1	1	4	6			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr15:50168660G>T	ENST00000284509.6	-	25	2983	c.2842C>A	c.(2842-2844)Ctg>Atg	p.L948M	ATP8B4_ENST00000559829.1_Missense_Mutation_p.L948M	NM_024837.2	NP_079113.2	Q8TF62	AT8B4_HUMAN	ATPase, class I, type 8B, member 4	948						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)		TTAAAAAGCAGATTCAGCTGT	0.433																																					p.L948M		Atlas-SNP	.											.	ATP8B4	173	.	0			c.C2842A						PASS	.						107	104	105					15																	50168660		2196	4295	6491	SO:0001583	missense	79895	exon25			AAAGCAGATTCAG	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.2842C>A	chr15.hg19:g.50168660G>T	ENSP00000284509:p.Leu948Met	55.0	0.0	.		61.0	31.0	.	NM_024837	Q9H727	Missense_Mutation	SNP	ENST00000284509.6	hg19	CCDS32238.1	.	.	.	.	.	.	.	.	.	.	G	14.25	2.479600	0.44044	.	.	ENSG00000104043	ENST00000284509	T	0.71698	-0.59	5.86	2.95	0.34219	.	0.148044	0.45606	D	0.000351	T	0.76205	0.3955	L	0.56199	1.76	0.38832	D	0.955877	D;P	0.58620	0.983;0.632	D;B	0.70716	0.97;0.291	T	0.73512	-0.3959	10	0.44086	T	0.13	.	7.022	0.24920	0.1502:0.0:0.7096:0.1402	.	26;948	Q6PG43;Q8TF62	.;AT8B4_HUMAN	M	948	ENSP00000284509:L948M	ENSP00000284509:L948M	L	-	1	2	ATP8B4	47955952	1.000000	0.71417	0.993000	0.49108	0.856000	0.48823	5.705000	0.68355	0.374000	0.24650	-0.150000	0.13652	CTG	.	.	.	none		0.433	ATP8B4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418100.1	NM_024837		T	50168660	G	T	50168660	3	4	22	1	0	0	0	0	1	0	0	0	1197	933	33	4	752	4	ATP8B4	15	50168660	Missense_Mutation	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10	8780675	50168660	52362732	85	1540											
MYO9A	4649	hgsc.bcm.edu	37	chr15	72176078	72176078	+	Splice_Site	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	tcatcttagctctctgaggtCtgtttaaagaaataaaggta	13	14	8	6	0	4	2	1	1	3	1	5	2	4	2	0	2	1	3	0	2	7	5			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr15:72176078C>G	ENST00000356056.5	-	28	5728		c.e28-1		MYO9A_ENST00000444904.1_Splice_Site|MYO9A_ENST00000564571.1_Splice_Site|MYO9A_ENST00000424560.1_Splice_Site	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA						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						TCTCTGAGGTCTGTTTAAAGA	0.368																																					.		Atlas-SNP	.											.	MYO9A	203	.	0			c.5256-1G>C						PASS	.						124	123	124					15																	72176078		2199	4297	6496	SO:0001630	splice_region_variant	4649	exon29			TGAGGTCTGTTTA	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.5256-1G>C	chr15.hg19:g.72176078C>G		102.0	0.0	.		85.0	38.0	.	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Splice_Site	SNP	ENST00000356056.5	hg19	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	C	18.97	3.736224	0.69189	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	.	.	.	4.23	4.23	0.50019	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.0021	0.86384	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MYO9A	69963132	1.000000	0.71417	0.996000	0.52242	0.944000	0.59088	6.736000	0.74811	2.061000	0.61500	0.557000	0.71058	.	.	.	.	none		0.368	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901	Intron	G	72176078	C	G	72176078	5	3	22	1	0	0	0	0	0	0	1	0	10091	927	32	4	2451	4	MYO9A	15	72176078	Splice_Site	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10	22007418	72176078	30355314	86	1541											
EDC3	80153	hgsc.bcm.edu	37	chr15	74925259	74925260	+	Missense_Mutation	DNP	GA	GA	AG																															gggcaatccaggcagttgatGaccaggtccacagggctagt																										TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr15:74925259_74925260GA>AG	ENST00000315127.4	-	7	1401_1402	c.1220_1221TC>CT	c.(1219-1221)gTC>gCT	p.V407A	EDC3_ENST00000426797.3_Missense_Mutation_p.V407A|EDC3_ENST00000568176.1_Missense_Mutation_p.V407A	NM_001142444.1|NM_025083.3	NP_001135916.1|NP_079359.2	Q96F86	EDC3_HUMAN	enhancer of mRNA decapping 3	407	YjeF N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00719}.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|membrane (GO:0016020)	identical protein binding (GO:0042802)|RNA binding (GO:0003723)			breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16						GGCAGTTGATGACCAGGTCCAC	0.599											OREG0023286	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V407V|p.V407A		Atlas-SNP	.											.	EDC3	32	.	0			c.C1221T|c.T1220C						PASS	.																																			SO:0001583	missense	80153	exon8			GTTGATGACCAGG|TTGATGACCAGGT	BC011534	CCDS10267.1	15q24.1	2013-05-02	2013-05-02	2006-07-07	ENSG00000179151	ENSG00000179151			26114	protein-coding gene	gene with protein product		609842	"yjeF domain containing (E.coli)", "LSM16 homolog (EDC3, S. cerevisiae)", "enhancer of mRNA decapping 3 homolog (S. cerevisiae)"	YJDC, LSM16		15225602, 17533573, 22483619	Standard	NM_025083		Approved	FLJ21128, hYjeF_N2-15q23, YJEFN2	uc002aym.3	Q96F86	OTTHUMG00000142815	ENST00000315127.4:c.1220_1221delinsAG	chr15.hg19:g.74925259_74925260delinsAG	ENSP00000320503:p.Val407Ala	64.0|63.0	0.0	.	1156	71.0|72.0	33.0	.	NM_001142444	B3KPH0|D3DW61|Q9H797	Silent|Missense_Mutation	SNP	ENST00000315127.4	hg19	CCDS10267.1																																																																																			.	.	.	none		0.599	EDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286399.1	NM_025083		AG	74925260	GA	AG	74925259	3	1	22	1	0	0	0	0	1	0	0	0	4909	1277	45	2	309	2	EDC3	15	74925259	Missense_Mutation	DNP	GA	TCGA-2Z-A9JS-01A-21D-A42J-10	2749181	74925259	27606133	87	1542											
FURIN	5045	hgsc.bcm.edu	37	chr15	91424718	91424718	+	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	tgcctcagctgccccagccaCgcctccttggaccctgtgga	5	8	10	18	1	1	0	1	0	0	0	2	2	2	2	7	2	4	1	7	2	0	1			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr15:91424718C>T	ENST00000268171.3	+	16	2274	c.1995C>T	c.(1993-1995)caC>caT	p.H665H	FES_ENST00000414248.2_5'Flank|FES_ENST00000328850.3_5'Flank|FES_ENST00000394302.1_5'Flank	NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	665					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)			GCCCCAGCCACGCCTCCTTGG	0.706																																					p.H665H		Atlas-SNP	.											.	FURIN	85	.	0			c.C1995T						PASS	.						24	27	26					15																	91424718		2195	4285	6480	SO:0001819	synonymous_variant	5045	exon16			CAGCCACGCCTCC	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.1995C>T	chr15.hg19:g.91424718C>T		66.0	0.0	.		62.0	28.0	.	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Silent	SNP	ENST00000268171.3	hg19	CCDS10364.1																																																																																			.	.	.	none		0.706	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569		T	91424718	C	T	91424718	2	4	22	1	0	0	0	0	0	0	0	1	6106	535	19	1		1	FURIN	15	91424718	Silent	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10	16499459	91424718	11106674	88	1543											
PDIA2	64714	hgsc.bcm.edu	37	chr16	335403	335403	+	Missense_Mutation	SNP	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	gcaccgggagctcctagcggGctttggggaggcagctcccc	5	6	16	14	2	0	0	0	0	0	0	2	2	2	2	4	5	3	5	4	5	1	2			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr16:335403G>A	ENST00000219406.6	+	6	905	c.887G>A	c.(886-888)gGc>gAc	p.G296D	PDIA2_ENST00000404312.1_Missense_Mutation_p.G293D|PDIA2_ENST00000462950.1_3'UTR	NM_006849.2	NP_006840.2	Q13087	PDIA2_HUMAN	protein disulfide isomerase family A, member 2	296					cell redox homeostasis (GO:0045454)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein retention in ER lumen (GO:0006621)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)|steroid binding (GO:0005496)			breast(1)|central_nervous_system(4)|kidney(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	17		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				CTCCTAGCGGGCTTTGGGGAG	0.667																																					p.G296D		Atlas-SNP	.											.	PDIA2	51	.	0			c.G887A						PASS	.						23	26	25					16																	335403		1918	4116	6034	SO:0001583	missense	64714	exon6			TAGCGGGCTTTGG	U19948	CCDS42089.1	16p13.3	2009-11-20	2005-06-29	2005-03-03	ENSG00000185615	ENSG00000185615	5.3.4.1	"Protein disulfide isomerases"	14180	protein-coding gene	gene with protein product		608012	"protein disulfide isomerase, pancreatic", "protein disulfide isomerase-associated 2"	PDIP		8561901	Standard	NM_006849		Approved	PDA2, PDI, PDIR	uc002cgo.1	Q13087	OTTHUMG00000064891	ENST00000219406.6:c.887G>A	chr16.hg19:g.335403G>A	ENSP00000219406:p.Gly296Asp	45.0	0.0	.		52.0	36.0	.	NM_006849	A6ZJ64|B4DI27|Q2WGM4|Q4TT67|Q6B010|Q96KJ6|Q9BW95	Missense_Mutation	SNP	ENST00000219406.6	hg19	CCDS42089.1	.	.	.	.	.	.	.	.	.	.	g	0.082	-1.181702	0.01633	.	.	ENSG00000185615	ENST00000219406;ENST00000455994;ENST00000404312	T;T	0.28069	1.63;1.63	4.03	2.0	0.26442	Thioredoxin-like fold (1);	0.602380	0.17134	N	0.185729	T	0.19167	0.0460	L	0.36672	1.1	0.09310	N	0.99999	B	0.06786	0.001	B	0.11329	0.006	T	0.31364	-0.9946	10	0.10377	T	0.69	.	7.2649	0.26224	0.2953:0.0:0.7047:0.0	.	296	Q13087	PDIA2_HUMAN	D	296;265;293	ENSP00000219406:G296D;ENSP00000384410:G293D	ENSP00000219406:G296D	G	+	2	0	PDIA2	275404	0.009000	0.17119	0.316000	0.25252	0.017000	0.09413	1.175000	0.31944	0.351000	0.24027	-0.348000	0.07805	GGC	.	.	.	none		0.667	PDIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139315.3	NM_006849		A	335403	G	A	335403	3	1	22	1	0	0	0	0	1	0	0	0	11675	1203	42	2	909	2	PDIA2	16	335403	Missense_Mutation	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10		335403	90019350	89	1544											
ANKS3	124401	hgsc.bcm.edu	37	chr16	4747050	4747050	+	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	taggtctcccgccacttcttCccgttcagcacctgcagctt	5	12	7	17	2	3	0	1	0	2	0	5	0	4	0	4	1	3	4	4	1	1	5	rs369166637		TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr16:4747050C>T	ENST00000304283.4	-	17	2244	c.1950G>A	c.(1948-1950)ggG>ggA	p.G650G	ANKS3_ENST00000585773.1_Silent_p.G577G|ANKS3_ENST00000446014.2_Silent_p.G521G	NM_133450.3	NP_597707.1	Q6ZW76	ANKS3_HUMAN	ankyrin repeat and sterile alpha motif domain containing 3	650										endometrium(5)|kidney(4)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	19						GCCACTTCTTCCCGTTCAGCA	0.652																																					p.G650G		Atlas-SNP	.											.	ANKS3	44	.	0			c.G1950A						PASS	.	C	,	1,4393		0,1,2196	77	61	66		1629,1950	2.4	0.2	16		66	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ANKS3	NM_001242929.1,NM_133450.3	,	0,1,6496	TT,TC,CC		0.0,0.0228,0.0077	,	543/550,650/657	4747050	1,12993	2197	4300	6497	SO:0001819	synonymous_variant	124401	exon17			CTTCTTCCCGTTC	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.1950G>A	chr16.hg19:g.4747050C>T		61.0	0.0	.		71.0	17.0	.	NM_133450	B4DWU4|D3DUE2|Q8TF25	Silent	SNP	ENST00000304283.4	hg19	CCDS10520.1																																																																																			.	.	.	weak		0.652	ANKS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251642.3	NM_133450		T	4747050	C	T	4747050	2	4	22	1	0	0	0	0	0	0	0	1	690	842	30	2		2	ANKS3	16	4747050	Silent	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10	4411647	4747050	85607703	90	1545											
SEPT12	124404	hgsc.bcm.edu	37	chr16	4828111	4828111	+	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	taagcaggtctctcaggagaGgaaattcacagtgcgccatg	12	8	12	9	1	3	1	2	0	1	1	4	3	3	2	1	3	2	1	1	3	2	2			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr16:4828111G>T	ENST00000268231.8	-	9	1114	c.851C>A	c.(850-852)cCt>cAt	p.P284H	SEPT12_ENST00000396693.5_Missense_Mutation_p.P238H	NM_144605.4	NP_653206.2	Q8IYM1	SEP12_HUMAN	septin 12	284	Septin-type G.				cell cycle (GO:0007049)|cell division (GO:0051301)	cleavage furrow (GO:0032154)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|sperm annulus (GO:0097227)|spindle (GO:0005819)|stress fiber (GO:0001725)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)			NS(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|skin(2)|stomach(3)	23						TCTCAGGAGAGGAAATTCACA	0.607																																					p.P284H		Atlas-SNP	.											.	SEPT12	40	.	0			c.C851A						PASS	.						80	73	75					16																	4828111		2197	4300	6497	SO:0001583	missense	124404	exon9			AGGAGAGGAAATT	AK058139	CCDS10522.1, CCDS53987.1	16p13.3	2013-01-21			ENSG00000140623	ENSG00000140623		"Septins"	26348	protein-coding gene	gene with protein product		611562				14611653, 15915442	Standard	NM_001154458		Approved	FLJ25410	uc002cxq.3	Q8IYM1	OTTHUMG00000129481	ENST00000268231.8:c.851C>A	chr16.hg19:g.4828111G>T	ENSP00000268231:p.Pro284His	106.0	0.0	.		143.0	39.0	.	NM_144605	Q0P6B0|Q1PBH0|Q96LL0	Missense_Mutation	SNP	ENST00000268231.8	hg19	CCDS10522.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.936273	0.73442	.	.	ENSG00000140623	ENST00000396693;ENST00000268231	T;T	0.50548	0.74;0.74	4.45	3.2	0.36748	.	0.170411	0.50627	D	0.000102	T	0.52805	0.1757	L	0.37561	1.115	0.31027	N	0.717824	D;D	0.65815	0.995;0.993	D;D	0.64687	0.917;0.928	T	0.57159	-0.7859	10	0.87932	D	0	.	9.1566	0.36996	0.1436:0.0:0.8564:0.0	.	238;284	Q8IYM1-2;Q8IYM1	.;SEP12_HUMAN	H	238;284	ENSP00000379922:P238H;ENSP00000268231:P284H	ENSP00000268231:P284H	P	-	2	0	SEPT12	4768112	1.000000	0.71417	0.992000	0.48379	0.994000	0.84299	7.391000	0.79828	0.888000	0.36160	0.561000	0.74099	CCT	.	.	.	none		0.607	SEPT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251645.2	NM_144605		T	4828111	G	T	4828111	3	4	22	1	0	0	0	0	1	0	0	0	14075	1000	35	4	233	4	SEPT12	16	4828111	Missense_Mutation	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10	81061	4828111	85526642	91	1546											
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24801182	24801182	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agatgcctaacaatcagagtAttaactctaaagtgagtggt	15	11	9	6	0	2	3	1	1	1	2	2	3	2	3	1	1	3	1	1	1	6	4			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr16:24801182A>G	ENST00000395799.3	+	6	1348	c.1219A>G	c.(1219-1221)Att>Gtt	p.I407V	TNRC6A_ENST00000315183.7_Missense_Mutation_p.I407V	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	407	Interaction with argonaute family proteins.|Sufficient for interaction with AGO1, AGO3 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)		CAATCAGAGTATTAACTCTAA	0.443																																					p.I407V		Atlas-SNP	.											TNRC6A,NS,carcinoma,0,1	TNRC6A	171	.	0			c.A1219G						PASS	.						72	74	73					16																	24801182		2197	4300	6497	SO:0001583	missense	27327	exon6			CAGAGTATTAACT	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.1219A>G	chr16.hg19:g.24801182A>G	ENSP00000379144:p.Ile407Val	71.0	0.0	.		102.0	57.0	.	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	hg19	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	A	5.172	0.217280	0.09810	.	.	ENSG00000090905	ENST00000315183;ENST00000395799	T;T	0.11277	2.79;2.79	5.94	3.72	0.42706	.	0.130307	0.56097	D	0.000036	T	0.08714	0.0216	L	0.47716	1.5	0.80722	D	1	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.09377	0.004;0.001;0.001	T	0.18023	-1.0350	10	0.17369	T	0.5	-2.9762	6.564	0.22501	0.7316:0.1316:0.1368:0.0	.	154;407;407	Q8NDV7-2;Q8NDV7-6;Q8NDV7	.;.;TNR6A_HUMAN	V	407	ENSP00000326900:I407V;ENSP00000379144:I407V	ENSP00000326900:I407V	I	+	1	0	TNRC6A	24708683	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.862000	0.48388	1.066000	0.40716	0.460000	0.39030	ATT	.	.	.	none		0.443	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		G	24801182	A	G	24801182	3	3	22	1	0	0	0	0	1	0	0	0	16352	449	16	3	1241	3	TNRC6A	16	24801182	Missense_Mutation	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	19973071	24801182	65553571	92	1547											
ZNF778	197320	hgsc.bcm.edu	37	chr16	89294957	89294957	+	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	cactcaaattcacactgatgAgaaacctttctaatgtaaag	16	11	5	9	0	3	2	2	2	1	1	3	3	3	2	1	0	1	1	1	0	5	4			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr16:89294957A>T	ENST00000433976.2	+	6	2509	c.2177A>T	c.(2176-2178)gAg>gTg	p.E726V	RP11-46C24.6_ENST00000563182.1_RNA|ZNF778_ENST00000306502.6_Missense_Mutation_p.E684V	NM_001201407.1|NM_182531.3	NP_001188336.1|NP_872337.2	Q96MU6	ZN778_HUMAN	zinc finger protein 778	726					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|skin(2)	24				BRCA - Breast invasive adenocarcinoma(80;0.0269)		CACACTGATGAGAAACCTTTC	0.393																																					p.E754V		Atlas-SNP	.											.	ZNF778	67	.	0			c.A2261T						PASS	.						54	56	55					16																	89294957		1986	4144	6130	SO:0001583	missense	197320	exon7			CTGATGAGAAACC	AK056437	CCDS45550.1, CCDS73928.1	16q24.3	2014-09-17			ENSG00000170100	ENSG00000170100		"Zinc fingers, C2H2-type", "-"	26479	protein-coding gene	gene with protein product							Standard	NM_182531		Approved	FLJ31875	uc021tms.1	Q96MU6		ENST00000433976.2:c.2177A>T	chr16.hg19:g.89294957A>T	ENSP00000405289:p.Glu726Val	163.0	0.0	.		169.0	91.0	.	NM_001201407	Q08AG0	Missense_Mutation	SNP	ENST00000433976.2	hg19	CCDS45550.1	.	.	.	.	.	.	.	.	.	.	A	8.492	0.862348	0.17178	.	.	ENSG00000170100	ENST00000433976;ENST00000306502	T;T	0.07688	3.25;3.17	0.868	-0.434	0.12283	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08980	0.0222	M	0.63843	1.955	0.23816	N	0.996768	B;B	0.18863	0.031;0.018	B;B	0.17722	0.019;0.008	T	0.33523	-0.9865	9	0.66056	D	0.02	.	4.12	0.10101	0.7413:0.0:0.2587:0.0	.	684;726	Q96MU6-2;Q96MU6	.;ZN778_HUMAN	V	726;684	ENSP00000405289:E726V;ENSP00000305203:E684V	ENSP00000305203:E684V	E	+	2	0	ZNF778	87822458	0.993000	0.37304	0.014000	0.15608	0.037000	0.13140	1.505000	0.35736	-0.160000	0.11002	0.254000	0.18369	GAG	.	.	.	none		0.393	ZNF778-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430383.1	NM_182531		T	89294957	A	T	89294957	3	4	22	1	0	0	0	0	1	0	0	0	18163	304	11	5	2195	5	ZNF778	16	89294957	Missense_Mutation	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	64493775	89294957	1059796	93	1548											
AP2B1	163	hgsc.bcm.edu	37	chr17	33977776	33977776	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggaaggaagtcatggaatTcatcgtaaacacttgccaat	14	10	10	7	1	2	0	2	0	0	0	3	3	2	3	1	3	2	1	1	3	6	3			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr17:33977776T>C	ENST00000262325.7	+	13	2317	c.1764T>C	c.(1762-1764)atT>atC	p.I588I	AP2B1_ENST00000592545.1_Silent_p.I550I|AP2B1_ENST00000537622.2_Silent_p.I588I|AP2B1_ENST00000312678.8_Silent_p.I588I|AP2B1_ENST00000538556.1_Silent_p.I531I|AP2B1_ENST00000589344.1_Silent_p.I588I|AP2B1_ENST00000545922.2_3'UTR	NM_001282.2	NP_001273.1	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1 subunit	588	Pro-rich (stalk region).				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	clathrin binding (GO:0030276)|protein transporter activity (GO:0008565)			NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		GTCATGGAATTCATCGTAAAC	0.438																																					p.I588I		Atlas-SNP	.											.	AP2B1	70	.	0			c.T1764C						PASS	.						134	120	125					17																	33977776		2203	4300	6503	SO:0001819	synonymous_variant	163	exon13			TGGAATTCATCGT	M34175	CCDS32621.1, CCDS32622.1	17q11.2-q12	2010-06-18			ENSG00000006125	ENSG00000006125			563	protein-coding gene	gene with protein product		601025		ADTB2, CLAPB1		8262066, 8595912	Standard	XM_005257937		Approved		uc002hjq.3	P63010		ENST00000262325.7:c.1764T>C	chr17.hg19:g.33977776T>C		103.0	0.0	.		138.0	38.0	.	NM_001282	A6NJP3|P21851|Q7Z451|Q96J19	Silent	SNP	ENST00000262325.7	hg19	CCDS32622.1																																																																																			.	.	.	none		0.438	AP2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448969.1			C	33977776	T	C	33977776	2	2	22	1	0	0	0	0	0	0	0	1	741	1771	62	3		3	AP2B1	17	33977776	Silent	SNP	T	TCGA-2Z-A9JS-01A-21D-A42J-10		33977776	47217434	94	1549											
GPATCH8	23131	hgsc.bcm.edu	37	chr17	42476884	42476884	+	Nonsense_Mutation	SNP	G	G	T																															aatggcgccggccagaccttGagcggctgcgggaatgctca																										TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr17:42476884G>T	ENST00000591680.1	-	8	2591	c.2561C>A	c.(2560-2562)tCa>tAa	p.S854*	GPATCH8_ENST00000434000.1_Nonsense_Mutation_p.S776*	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	854	Ser-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)		GCCAGACCTTGAGCGGCTGCG	0.562																																					p.S854X		Atlas-SNP	.											.	GPATCH8	114	.	0			c.C2561A						PASS	.						143	128	133					17																	42476884		2203	4300	6503	SO:0001587	stop_gained	23131	exon8			GACCTTGAGCGGC	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.2561C>A	chr17.hg19:g.42476884G>T	ENSP00000467556:p.Ser854*	62.0	0.0	.		71.0	46.0	.	NM_001002909	B9EGP9|O60300|Q8TB99	Nonsense_Mutation	SNP	ENST00000591680.1	hg19	CCDS32666.1	.	.	.	.	.	.	.	.	.	.	G	31	5.087860	0.94100	.	.	ENSG00000186566	ENST00000335500;ENST00000434000	.	.	.	5.21	5.21	0.72293	.	0.144795	0.48286	D	0.000183	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	-10.9423	18.5485	0.91055	0.0:0.0:1.0:0.0	.	.	.	.	X	854;776	.	ENSP00000335486:S854X	S	-	2	0	GPATCH8	39832410	1.000000	0.71417	0.876000	0.34364	0.419000	0.31324	8.899000	0.92544	2.716000	0.92895	0.561000	0.74099	TCA	.	.	.	none		0.562	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909		T	42476884	G	T	42476884	4	4	22	1	0	0	0	0	0	1	0	0	6601	1294	45	4	1951	4	GPATCH8	17	42476884	Nonsense_Mutation	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10	8499108	42476884	38718326	95	1550	15	2									
GPATCH8	23131	hgsc.bcm.edu	37	chr17	42476886	42476891	+	In_Frame_Del	DEL	GCGGCT	GCGGCT	-																															tggcgccggccagaccttgaGcggctgcgggaatgctcact																								rs111563656	byFrequency	TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	GCGGCT	GCGGCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr17:42476886_42476891delGCGGCT	ENST00000591680.1	-	8	2584_2589	c.2554_2559delAGCCGC	c.(2554-2559)agccgcdel	p.SR854del	GPATCH8_ENST00000434000.1_In_Frame_Del_p.SR776del	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	854	Ser-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)		CAGACCTTGAGCGGCTGCGGGAATGC	0.553																																					p.852_854del		Atlas-Indel,Pindel	.											.	GPATCH8	114	.	0			c.2555_2560del						PASS	.																																			SO:0001651	inframe_deletion	23131	exon8			.	AB011125	CCDS32666.1	17q21.31	2013-01-28	2006-08-22	2006-12-13	ENSG00000186566	ENSG00000186566		"G patch domain containing"	29066	protein-coding gene	gene with protein product		614396	"KIAA0553"	KIAA0553, GPATC8		9628581	Standard	NM_001002909		Approved		uc002igw.2	Q9UKJ3	OTTHUMG00000181818	ENST00000591680.1:c.2554_2559delAGCCGC	chr17.hg19:g.42476886_42476891delGCGGCT	ENSP00000467556:p.Ser854_Arg855del	63.0	0.0	0		66.0	35.0	0.530303	NM_001002909	B9EGP9|O60300|Q8TB99	In_Frame_Del	DEL	ENST00000591680.1	hg19	CCDS32666.1																																																																																			.	.	.	none		0.553	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909		-	42476891	GCGGCT	-	42476886	7	5	22	1	0	1	0	1	0	0	0	0	6601	958	34	0	1953	0	GPATCH8	17	42476886	In_Frame_Del	DEL	GCGGCT	TCGA-2Z-A9JS-01A-21D-A42J-10	2	42476886	38718324	96	1551	15	2									
WNT9B	7484	hgsc.bcm.edu	37	chr17	44952668	44952668	+	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	tctgagcaacttcctggggtCcaagagaggaaacaaggacc	13	6	12	10	0	1	2	0	1	1	1	3	5	3	4	3	4	3	1	3	4	4	1			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr17:44952668C>T	ENST00000290015.2	+	3	589	c.536C>T	c.(535-537)tCc>tTc	p.S179F	WNT9B_ENST00000393461.2_Missense_Mutation_p.S179F	NM_003396.1	NP_003387.1	O14905	WNT9B_HUMAN	wingless-type MMTV integration site family, member 9B	179					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)			TTCCTGGGGTCCAAGAGAGGA	0.627																																					p.S179F		Atlas-SNP	.											.	WNT9B	37	.	0			c.C536T						PASS	.						60	52	55					17																	44952668		2203	4300	6503	SO:0001583	missense	7484	exon3			TGGGGTCCAAGAG	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.536C>T	chr17.hg19:g.44952668C>T	ENSP00000290015:p.Ser179Phe	204.0	0.0	.		230.0	10.0	.	NM_003396	Q6UXT4|Q96Q09	Missense_Mutation	SNP	ENST00000290015.2	hg19	CCDS11506.1	.	.	.	.	.	.	.	.	.	.	C	17.65	3.441637	0.63067	.	.	ENSG00000158955	ENST00000376843;ENST00000393461;ENST00000290015	T;T	0.76839	-1.05;-1.05	4.91	4.91	0.64330	.	0.113119	0.64402	D	0.000010	T	0.70596	0.3242	L	0.52905	1.665	0.26796	N	0.969307	P;B	0.39157	0.662;0.026	B;B	0.34590	0.186;0.084	T	0.69950	-0.5006	10	0.56958	D	0.05	.	11.2092	0.48788	0.3126:0.6874:0.0:0.0	.	179;179	E7EPC3;O14905	.;WNT9B_HUMAN	F	173;179;179	ENSP00000377105:S179F;ENSP00000290015:S179F	ENSP00000290015:S179F	S	+	2	0	WNT9B	42307667	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.914000	0.56401	2.550000	0.86006	0.462000	0.41574	TCC	.	.	.	none		0.627	WNT9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440433.1	NM_003396		T	44952668	C	T	44952668	3	4	22	1	0	0	0	0	1	0	0	0	17411	855	30	2	546	2	WNT9B	17	44952668	Missense_Mutation	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10	2475782	44952668	36242542	97	1552											
PDK2	5164	hgsc.bcm.edu	37	chr17	48184183	48184187	+	Frame_Shift_Del	DEL	CCCAG	CCCAG	-																															atctttgatggcagcaccaaCccagcccatcccaaacacat																										TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	CCCAG	CCCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr17:48184183_48184187delCCCAG	ENST00000503176.1	+	5	704_708	c.543_547delCCCAG	c.(541-549)aacccagccfs	p.PA182fs	PDK2_ENST00000007708.3_Frame_Shift_Del_p.PA118fs	NM_002611.4	NP_002602.2	Q15119	PDK2_HUMAN	pyruvate dehydrogenase kinase, isozyme 2	182	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.				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)	p.P182S(1)		central_nervous_system(4)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	20						GCAGCACCAACCCAGCCCATCCCAA	0.629									Autosomal Dominant Polycystic Kidney Disease																												p.181_182del		Atlas-Indel,Pindel	.											.	PDK2	41	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.542_546del						PASS	.																																			SO:0001589	frameshift_variant	5164	exon5	Familial Cancer Database	ADPKD	.	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.543_547delCCCAG	chr17.hg19:g.48184183_48184187delCCCAG	ENSP00000420927:p.Pro182fs	119.0	0.0	0		172.0	40.0	0.232558	NM_002611	A8K3A7|B3KNW0|Q6P515|Q9BS05	Frame_Shift_Del	DEL	ENST00000503176.1	hg19	CCDS11559.1																																																																																			.	.	.	none		0.629	PDK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366492.2	NM_002611		-	48184187	CCCAG	-	48184183	7	5	22	1	0	1	0	1	0	0	0	0	11683	506	18	0	561	0	PDK2	17	48184183	Frame_Shift_Del	DEL	CCCAG	TCGA-2Z-A9JS-01A-21D-A42J-10	3231515	48184183	33011027	98	1553											
ACSF2	80221	hgsc.bcm.edu	37	chr17	48540788	48540788	+	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	ttgcggatgatcctgcccaaCcccctgtaccattgcctggg	6	10	10	15	1	0	1	0	1	0	0	1	2	1	2	6	2	5	1	6	2	2	3			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr17:48540788C>A	ENST00000300441.4	+	8	1025	c.921C>A	c.(919-921)aaC>aaA	p.N307K	ACSF2_ENST00000427954.2_Missense_Mutation_p.N332K|ACSF2_ENST00000541920.1_Missense_Mutation_p.N147K|ACSF2_ENST00000502667.1_Missense_Mutation_p.N294K|ACSF2_ENST00000504392.1_Missense_Mutation_p.N264K	NM_025149.4	NP_079425.3	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2	307					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ligase activity (GO:0016874)			endometrium(7)|kidney(3)|large_intestine(1)|lung(1)|stomach(1)	13	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			TCCTGCCCAACCCCCTGTACC	0.582																																					p.N307K		Atlas-SNP	.											.	ACSF2	46	.	0			c.C921A						PASS	.						104	89	94					17																	48540788		2203	4300	6503	SO:0001583	missense	80221	exon8			GCCCAACCCCCTG	AK024573, BC012053	CCDS11567.1, CCDS74103.1, CCDS74104.1, CCDS74105.1	17q21.33	2007-10-17			ENSG00000167107	ENSG00000167107		"Acyl-CoA synthetase family"	26101	protein-coding gene	gene with protein product		610465				17762044	Standard	NM_001288968		Approved	FLJ20920, ACSMW	uc002iqu.2	Q96CM8	OTTHUMG00000162128	ENST00000300441.4:c.921C>A	chr17.hg19:g.48540788C>A	ENSP00000300441:p.Asn307Lys	84.0	0.0	.		124.0	33.0	.	NM_025149	B4DFQ6|B4DHT5|B4DUF5|Q9H7G2	Missense_Mutation	SNP	ENST00000300441.4	hg19	CCDS11567.1	.	.	.	.	.	.	.	.	.	.	C	12.55	1.971738	0.34754	.	.	ENSG00000167107	ENST00000300441;ENST00000541920;ENST00000504392;ENST00000427954;ENST00000502667	T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03	4.8	0.521	0.17046	AMP-dependent synthetase/ligase (1);	0.622353	0.17251	N	0.181166	T	0.36908	0.0984	M	0.61703	1.905	0.20196	N	0.999923	B;B;B;B	0.12630	0.006;0.006;0.006;0.006	B;B;B;B	0.25759	0.063;0.063;0.063;0.063	T	0.39663	-0.9603	10	0.87932	D	0	-1.458	5.5213	0.16933	0.0:0.3735:0.225:0.4015	.	294;332;264;307	B4DHT5;B4DFQ6;E9PF16;Q96CM8	.;.;.;ACSF2_HUMAN	K	307;147;264;332;294	ENSP00000300441:N307K;ENSP00000437987:N147K;ENSP00000425964:N264K;ENSP00000401831:N332K;ENSP00000421884:N294K	ENSP00000300441:N307K	N	+	3	2	ACSF2	45895787	0.007000	0.16637	0.169000	0.22859	0.866000	0.49608	-0.285000	0.08410	-0.007000	0.14345	0.655000	0.94253	AAC	.	.	.	none		0.582	ACSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367423.3	NM_025149		A	48540788	C	A	48540788	3	1	22	1	0	0	0	0	1	0	0	0	175	506	18	4	951	4	ACSF2	17	48540788	Missense_Mutation	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10	356605	48540788	32654422	99	1554											
PSMD12	5718	hgsc.bcm.edu	37	chr17	65343241	65343241	+	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	tatattcttacctgctgccaTttttcactttctgcctgtat	6	20	4	11	0	3	0	1	0	2	0	3	0	3	0	3	0	4	2	3	0	4	8			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr17:65343241T>A	ENST00000356126.3	-	7	893	c.786A>T	c.(784-786)aaA>aaT	p.K262N	PSMD12_ENST00000357146.4_Missense_Mutation_p.K242N	NM_002816.3	NP_002807.1	O00232	PSD12_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	262	PCI.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				breast(1)|large_intestine(4)|lung(6)|pancreas(1)|urinary_tract(1)	13	all_cancers(12;2.38e-11)|all_epithelial(3;8.27e-13)					CCTGCTGCCATTTTTCACTTT	0.328																																					p.K262N		Atlas-SNP	.											.	PSMD12	32	.	0			c.A786T						PASS	.						112	107	108					17																	65343241		2202	4297	6499	SO:0001583	missense	5718	exon7			CTGCCATTTTTCA	AB003103	CCDS11669.1, CCDS11670.1	17q24.3	2008-05-22			ENSG00000197170	ENSG00000197170		"Proteasome (prosome, macropain) subunits"	9557	protein-coding gene	gene with protein product		604450				9426256	Standard	NM_002816		Approved	p55, Rpn5	uc002jfy.3	O00232	OTTHUMG00000140376	ENST00000356126.3:c.786A>T	chr17.hg19:g.65343241T>A	ENSP00000348442:p.Lys262Asn	62.0	0.0	.		80.0	46.0	.	NM_002816	A6NP15|Q53HA2|Q6P053	Missense_Mutation	SNP	ENST00000356126.3	hg19	CCDS11669.1	.	.	.	.	.	.	.	.	.	.	T	18.10	3.548664	0.65311	.	.	ENSG00000197170	ENST00000356126;ENST00000357146	T;T	0.06294	3.32;3.32	5.96	3.99	0.46301	.	0.084304	0.85682	D	0.000000	T	0.14227	0.0344	M	0.83953	2.67	0.80722	D	1	P;P	0.49358	0.923;0.923	P;P	0.47827	0.558;0.558	T	0.01015	-1.1480	10	0.48119	T	0.1	-21.8516	8.416	0.32672	0.0:0.7053:0.0:0.2947	.	242;262	A6NP15;O00232	.;PSD12_HUMAN	N	262;242	ENSP00000348442:K262N;ENSP00000349667:K242N	ENSP00000348442:K262N	K	-	3	2	PSMD12	62773703	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	1.422000	0.34826	0.849000	0.35215	-0.242000	0.12053	AAA	.	.	.	none		0.328	PSMD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277103.1	NM_002816, NM_174871		A	65343241	T	A	65343241	3	1	22	1	0	0	0	0	1	0	0	0	12705	1490	52	5	604	5	PSMD12	17	65343241	Missense_Mutation	SNP	T	TCGA-2Z-A9JS-01A-21D-A42J-10	16802453	65343241	15851969	100	1555											
UNC13D	201294	hgsc.bcm.edu	37	chr17	73826558	73826558	+	Missense_Mutation	SNP	T	T	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	cccagctcctcagaggtggtTtctgcctggggtggggagca	5	9	16	11	0	2	1	1	0	1	1	3	2	3	2	3	6	3	3	3	6	0	1			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr17:73826558T>G	ENST00000207549.4	-	29	3094	c.2715A>C	c.(2713-2715)gaA>gaC	p.E905D	UNC13D_ENST00000412096.2_Missense_Mutation_p.E905D	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	905					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)			CAGAGGTGGTTTCTGCCTGGG	0.697									Familial Hemophagocytic Lymphohistiocytosis		OREG0024741	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E905D		Atlas-SNP	.											.	UNC13D	68	.	0			c.A2715C						PASS	.						26	28	28					17																	73826558		2184	4296	6480	SO:0001583	missense	201294	exon29	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GGTGGTTTCTGCC	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.2715A>C	chr17.hg19:g.73826558T>G	ENSP00000207549:p.Glu905Asp	62.0	0.0	.	1148	98.0	52.0	.	NM_199242	B4DWG9|Q9H7K5	Missense_Mutation	SNP	ENST00000207549.4	hg19	CCDS11730.1	.	.	.	.	.	.	.	.	.	.	T	8.808	0.934637	0.18206	.	.	ENSG00000092929	ENST00000207549;ENST00000412096	T;T	0.70986	-0.51;-0.53	4.71	1.21	0.21127	.	0.403193	0.24722	N	0.036133	T	0.38799	0.1054	N	0.08118	0	0.33043	D	0.531752	B	0.06786	0.001	B	0.04013	0.001	T	0.14090	-1.0485	10	0.16420	T	0.52	-3.4552	0.9409	0.01355	0.1436:0.268:0.2583:0.3301	.	905	Q70J99	UN13D_HUMAN	D	905	ENSP00000207549:E905D;ENSP00000388093:E905D	ENSP00000207549:E905D	E	-	3	2	UNC13D	71338153	0.000000	0.05858	0.982000	0.44146	0.659000	0.38960	-0.243000	0.08915	0.852000	0.35287	0.379000	0.24179	GAA	.	.	.	none		0.697	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950		G	73826558	T	G	73826558	3	3	22	1	0	0	0	0	1	0	0	0	16999	1838	64	5	573	5	UNC13D	17	73826558	Missense_Mutation	SNP	T	TCGA-2Z-A9JS-01A-21D-A42J-10	8483317	73826558	7368652	101	1556											
ARHGAP28	79822	hgsc.bcm.edu	37	chr18	6870695	6870695	+	Missense_Mutation	SNP	G	G	T																															ctaaaaagaaataaacttaaGaaatcagagattaagaaaga																										TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr18:6870695G>T	ENST00000383472.4	+	7	1022	c.918G>T	c.(916-918)aaG>aaT	p.K306N	ARHGAP28_ENST00000532996.1_Missense_Mutation_p.K129N|ARHGAP28_ENST00000314319.3_Missense_Mutation_p.K147N|ARHGAP28_ENST00000262227.3_Missense_Mutation_p.K254N|RP11-146G7.2_ENST00000583659.1_RNA|ARHGAP28_ENST00000531294.1_Missense_Mutation_p.K142N|ARHGAP28_ENST00000400091.2_Missense_Mutation_p.K306N|ARHGAP28_ENST00000419673.2_Missense_Mutation_p.K147N|ARHGAP28_ENST00000418986.1_Missense_Mutation_p.K147N			Q9P2N2	RHG28_HUMAN	Rho GTPase activating protein 28	306					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)				ATAAACTTAAGAAATCAGAGA	0.343																																					p.K147N		Atlas-SNP	.											.	ARHGAP28	181	.	0			c.G441T						PASS	.						68	78	74					18																	6870695		2203	4300	6503	SO:0001583	missense	79822	exon6			ACTTAAGAAATCA	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.918G>T	chr18.hg19:g.6870695G>T	ENSP00000372964:p.Lys306Asn	257.0	0.0	.		237.0	88.0	.	NM_001010000	A8MQB7|A8MU88|Q6P160|Q8N4T3|Q9NW53	Missense_Mutation	SNP	ENST00000383472.4	hg19		.	.	.	.	.	.	.	.	.	.	G	15.45	2.836053	0.50951	.	.	ENSG00000088756	ENST00000400091;ENST00000262227;ENST00000419673;ENST00000531294;ENST00000314319;ENST00000418986;ENST00000532996;ENST00000383472	T;T;T;T;T;T	0.08807	3.2;3.15;3.14;3.12;3.14;3.05	5.22	3.03	0.35002	.	0.543333	0.21383	N	0.075434	T	0.12347	0.0300	L	0.50333	1.59	0.29821	N	0.830846	B;B;B;P	0.52577	0.158;0.057;0.364;0.954	B;B;B;P	0.53809	0.035;0.016;0.192;0.735	T	0.04294	-1.0962	10	0.39692	T	0.17	.	4.3594	0.11194	0.4628:0.0:0.5372:0.0	.	306;138;147;254	Q9P2N2;E9PRP2;F6VKJ9;Q9P2N2-2	RHG28_HUMAN;.;.;.	N	306;254;147;142;147;147;138;129	ENSP00000382963:K306N;ENSP00000262227:K254N;ENSP00000392660:K147N;ENSP00000437262:K142N;ENSP00000313506:K147N;ENSP00000406907:K147N	ENSP00000262227:K254N	K	+	3	2	ARHGAP28	6860695	1.000000	0.71417	0.933000	0.37362	0.975000	0.68041	2.199000	0.42715	1.332000	0.45431	0.655000	0.94253	AAG	.	.	.	none		0.343	ARHGAP28-006	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442123.3	XM_371108		T	6870695	G	T	6870695	3	4	22	1	0	0	0	0	1	0	0	0	877	933	33	4	459	4	ARHGAP28	18	6870695	Missense_Mutation	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10		6870695	71206553	102	1557	16	2									
ARHGAP28	79822	hgsc.bcm.edu	37	chr18	6870698	6870698	+	Missense_Mutation	SNP	A	A	T																															aaaagaaataaacttaagaaAtcagagattaagaaagaaga																										TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr18:6870698A>T	ENST00000383472.4	+	7	1025	c.921A>T	c.(919-921)aaA>aaT	p.K307N	ARHGAP28_ENST00000532996.1_Missense_Mutation_p.K130N|ARHGAP28_ENST00000314319.3_Missense_Mutation_p.K148N|ARHGAP28_ENST00000262227.3_Missense_Mutation_p.K255N|RP11-146G7.2_ENST00000583659.1_RNA|ARHGAP28_ENST00000531294.1_Missense_Mutation_p.K143N|ARHGAP28_ENST00000400091.2_Missense_Mutation_p.K307N|ARHGAP28_ENST00000419673.2_Missense_Mutation_p.K148N|ARHGAP28_ENST00000418986.1_Missense_Mutation_p.K148N			Q9P2N2	RHG28_HUMAN	Rho GTPase activating protein 28	307					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)				AACTTAAGAAATCAGAGATTA	0.348																																					p.K148N		Atlas-SNP	.											.	ARHGAP28	181	.	0			c.A444T						PASS	.						68	78	74					18																	6870698		2203	4299	6502	SO:0001583	missense	79822	exon6			TAAGAAATCAGAG	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.921A>T	chr18.hg19:g.6870698A>T	ENSP00000372964:p.Lys307Asn	253.0	0.0	.		242.0	88.0	.	NM_001010000	A8MQB7|A8MU88|Q6P160|Q8N4T3|Q9NW53	Missense_Mutation	SNP	ENST00000383472.4	hg19		.	.	.	.	.	.	.	.	.	.	A	15.85	2.954762	0.53293	.	.	ENSG00000088756	ENST00000400091;ENST00000262227;ENST00000419673;ENST00000531294;ENST00000314319;ENST00000418986;ENST00000532996;ENST00000383472	T;T;T;T;T;T	0.08720	3.22;3.18;3.14;3.14;3.14;3.06	5.22	-2.37	0.06643	.	0.143359	0.64402	D	0.000007	T	0.09379	0.0231	L	0.27053	0.805	0.32678	N	0.51592	D;B;B;B	0.58620	0.983;0.012;0.02;0.01	P;B;B;B	0.55713	0.782;0.014;0.032;0.01	T	0.11867	-1.0570	10	0.15952	T	0.53	.	13.072	0.59068	0.7418:0.0:0.2582:0.0	.	307;139;148;255	Q9P2N2;E9PRP2;F6VKJ9;Q9P2N2-2	RHG28_HUMAN;.;.;.	N	307;255;148;143;148;148;139;130	ENSP00000382963:K307N;ENSP00000262227:K255N;ENSP00000392660:K148N;ENSP00000437262:K143N;ENSP00000313506:K148N;ENSP00000406907:K148N	ENSP00000262227:K255N	K	+	3	2	ARHGAP28	6860698	0.910000	0.30920	0.633000	0.29310	0.960000	0.62799	-0.038000	0.12144	-0.308000	0.08792	-0.242000	0.12053	AAA	.	.	.	none		0.348	ARHGAP28-006	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442123.3	XM_371108		T	6870698	A	T	6870698	3	4	22	1	0	0	0	0	1	0	0	0	877	98	4	5	462	5	ARHGAP28	18	6870698	Missense_Mutation	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	3	6870698	71206550	103	1558	16	2									
ANKRD30B	374860	hgsc.bcm.edu	37	chr18	14852332	14852332	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgaaaatgcaacgtcatctAaacgagaaaaatgaggaggt	19	7	10	5	2	2	3	1	2	1	1	2	5	2	4	0	2	3	1	0	2	7	1			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr18:14852332A>G	ENST00000358984.4	+	36	4212	c.4032A>G	c.(4030-4032)ctA>ctG	p.L1344L		NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	1344										breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						AACGTCATCTAAACGAGAAAA	0.318																																					p.L1344L		Atlas-SNP	.											.	ANKRD30B	237	.	0			c.A4032G						PASS	.						4	2	3					18																	14852332		592	1263	1855	SO:0001819	synonymous_variant	374860	exon36			TCATCTAAACGAG	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.4032A>G	chr18.hg19:g.14852332A>G		178.0	0.0	.		194.0	81.0	.	NM_001145029	B4DGP1|F8WAG3|Q4G175	Silent	SNP	ENST00000358984.4	hg19	CCDS54182.1																																																																																			.	.	.	none		0.318	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029		G	14852332	A	G	14852332	2	3	22	1	0	0	0	0	0	0	0	1	659	349	13	3		3	ANKRD30B	18	14852332	Silent	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	7981634	14852332	63224916	104	1559											
TNFRSF11A	8792	hgsc.bcm.edu	37	chr18	60036643	60036643	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagcccgaggatggggctgAtgggaggctcccaagctcag	8	5	16	12	1	1	1	1	1	0	0	2	4	2	3	3	5	2	3	3	5	1	0			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr18:60036643A>G	ENST00000586569.1	+	9	1531	c.1493A>G	c.(1492-1494)gAt>gGt	p.D498G	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	498					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)				GATGGGGCTGATGGGAGGCTC	0.637																																					p.D498G		Atlas-SNP	.											.	TNFRSF11A	51	.	0			c.A1493G						PASS	.						38	42	41					18																	60036643		1924	3761	5685	SO:0001583	missense	8792	exon9			GGGCTGATGGGAG	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.1493A>G	chr18.hg19:g.60036643A>G	ENSP00000465500:p.Asp498Gly	47.0	0.0	.		33.0	12.0	.	NM_003839	I4EC36|I4EC38|I4EC39|I7JE63|N0GVH0|Q59EP9	Missense_Mutation	SNP	ENST00000586569.1	hg19	CCDS11980.1	.	.	.	.	.	.	.	.	.	.	A	11.33	1.606631	0.28623	.	.	ENSG00000141655	ENST00000269485	.	.	.	4.51	1.98	0.26296	.	1.695040	0.03041	N	0.153332	T	0.37404	0.1002	L	0.51422	1.61	0.09310	N	1	B	0.18741	0.03	B	0.13407	0.009	T	0.15065	-1.0450	8	.	.	.	-3.3746	4.8605	0.13581	0.6714:0.1652:0.1634:0.0	.	498	Q9Y6Q6	TNR11_HUMAN	G	498	.	.	D	+	2	0	TNFRSF11A	58187623	0.054000	0.20591	0.002000	0.10522	0.046000	0.14306	0.964000	0.29306	0.744000	0.32741	0.460000	0.39030	GAT	.	.	.	none		0.637	TNFRSF11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256186.2			G	60036643	A	G	60036643	3	3	22	1	0	0	0	0	1	0	0	0	16296	333	12	3	1527	3	TNFRSF11A	18	60036643	Missense_Mutation	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	45184311	60036643	18040605	105	1560											
DOT1L	84444	hgsc.bcm.edu	37	chr19	2194549	2194549	+	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	ttcaggaagtggatgaaatgGtatggaaaaaagcatgcaga	17	8	13	3	0	1	2	1	1	0	1	1	5	1	5	0	4	2	3	0	4	6	2			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr19:2194549G>A	ENST00000398665.3	+	7	660	c.624G>A	c.(622-624)tgG>tgA	p.W208*		NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	208	DOT1. {ECO:0000255|PROSITE- ProRule:PRU00902}.				histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGATGAAATGGTATGGAAAAA	0.607																																					p.W208X		Atlas-SNP	.											.	DOT1L	205	.	0			c.G624A						PASS	.						104	108	107					19																	2194549		1949	4144	6093	SO:0001587	stop_gained	84444	exon7			GAAATGGTATGGA	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.624G>A	chr19.hg19:g.2194549G>A	ENSP00000381657:p.Trp208*	52.0	0.0	.		40.0	18.0	.	NM_032482	O60379|Q96JL1	Nonsense_Mutation	SNP	ENST00000398665.3	hg19	CCDS42460.1	.	.	.	.	.	.	.	.	.	.	G	37	6.521979	0.97633	.	.	ENSG00000104885	ENST00000398665;ENST00000221482;ENST00000452696	.	.	.	4.27	4.27	0.50696	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-12.6037	15.8524	0.78943	0.0:0.0:1.0:0.0	.	.	.	.	X	208;208;184	.	ENSP00000221482:W208X	W	+	3	0	DOT1L	2145549	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.122000	0.94380	2.216000	0.71823	0.462000	0.41574	TGG	.	.	.	none		0.607	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482		A	2194549	G	A	2194549	4	1	22	1	0	0	0	0	0	1	0	0	4711	1270	44	2	650	2	DOT1L	19	2194549	Nonsense_Mutation	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10		2194549	56934434	106	1561											
CHERP	10523	hgsc.bcm.edu	37	chr19	16643886	16643886	+	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	ggttgtcaaactcgttcatgTctagctgggtctcctccaga	7	13	10	11	1	4	1	2	0	2	1	7	1	5	1	2	2	2	3	2	2	2	3			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr19:16643886T>A	ENST00000198939.6	-	4	494	c.458A>T	c.(457-459)gAc>gTc	p.D153V	CHERP_ENST00000546361.2_Missense_Mutation_p.D153V|CTD-3222D19.2_ENST00000409035.1_Intron					calcium homeostasis endoplasmic reticulum protein											endometrium(3)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|stomach(1)|urinary_tract(3)	24						CTCGTTCATGTCTAGCTGGGT	0.642																																					p.D153V		Atlas-SNP	.											.	CHERP	70	.	0			c.A458T						PASS	.						95	115	108					19																	16643886		2152	4250	6402	SO:0001583	missense	10523	exon4			TTCATGTCTAGCT	U94836	CCDS42518.1	19p13.1	2013-01-28				ENSG00000085872		"G patch domain containing"	16930	protein-coding gene	gene with protein product						8896557, 10794731	Standard	NM_006387		Approved	ERPROT213-21, DAN16	uc002nei.1	Q8IWX8	OTTHUMG00000169304	ENST00000198939.6:c.458A>T	chr19.hg19:g.16643886T>A	ENSP00000198939:p.Asp153Val	69.0	0.0	.		64.0	30.0	.	NM_006387		Missense_Mutation	SNP	ENST00000198939.6	hg19		.	.	.	.	.	.	.	.	.	.	T	16.10	3.026403	0.54683	.	.	ENSG00000085872	ENST00000546361;ENST00000198939	T;T	0.26518	1.73;1.76	5.08	5.08	0.68730	ENTH/VHS (1);RNA polymerase II, large subunit, CTD (1);	.	.	.	.	T	0.40196	0.1107	L	0.47716	1.5	0.80722	D	1	D	0.69078	0.997	D	0.63488	0.915	T	0.08785	-1.0705	9	0.30854	T	0.27	-28.7397	14.0179	0.64536	0.0:0.0:0.0:1.0	.	153	Q8IWX8	CHERP_HUMAN	V	153	ENSP00000439856:D153V;ENSP00000198939:D153V	ENSP00000198939:D153V	D	-	2	0	CHERP	16504886	1.000000	0.71417	1.000000	0.80357	0.530000	0.34684	5.952000	0.70282	1.922000	0.55676	0.402000	0.26972	GAC	.	.	.	none		0.642	CHERP-003	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000403372.1	NM_006387		A	16643886	T	A	16643886	3	1	22	1	0	0	0	0	1	0	0	0	3338	1667	58	5	2348	5	CHERP	19	16643886	Missense_Mutation	SNP	T	TCGA-2Z-A9JS-01A-21D-A42J-10	14449337	16643886	42485097	107	1562											
UNC13A	23025	hgsc.bcm.edu	37	chr19	17766949	17766949	+	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	tcctcctcctcctccagctcCtcctcatcttcaggcagctc	4	12	4	21	0	3	0	2	0	1	0	11	0	10	0	7	1	2	3	7	1	0	1			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr19:17766949C>A	ENST00000519716.2	-	10	1025	c.1026G>T	c.(1024-1026)gaG>gaT	p.E342D	UNC13A_ENST00000551649.1_Missense_Mutation_p.E342D|UNC13A_ENST00000252773.7_Missense_Mutation_p.E342D|UNC13A_ENST00000552293.1_Missense_Mutation_p.E342D|UNC13A_ENST00000550896.1_Missense_Mutation_p.E342D|UNC13A_ENST00000428389.2_Missense_Mutation_p.E430D	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	342	Glu-rich.				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						cctccagctcctcctcatctt	0.592																																					p.E342D		Atlas-SNP	.											.	UNC13A	299	.	0			c.G1026T						PASS	.						33	37	36					19																	17766949		2097	4132	6229	SO:0001583	missense	23025	exon10			CAGCTCCTCCTCA	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.1026G>T	chr19.hg19:g.17766949C>A	ENSP00000429562:p.Glu342Asp	39.0	0.0	.		61.0	22.0	.	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	hg19	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	C	8.553	0.875969	0.17395	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	D;D;D;T;T;D	0.82433	-1.58;-1.61;-1.58;-1.45;-1.44;-1.57	4.56	2.36	0.29203	.	0.284950	0.21761	U	0.069513	T	0.57315	0.2045	N	0.08118	0	0.22317	N	0.999201	B	0.02656	0.0	B	0.01281	0.0	T	0.44742	-0.9308	10	0.05833	T	0.94	-9.3465	4.585	0.12279	0.0:0.5972:0.1803:0.2226	.	342	Q9UPW8	UN13A_HUMAN	D	342;430;342;342;342;342	ENSP00000429562:E342D;ENSP00000400409:E430D;ENSP00000252773:E342D;ENSP00000447236:E342D;ENSP00000447572:E342D;ENSP00000446831:E342D	ENSP00000252773:E342D	E	-	3	2	UNC13A	17627949	0.000000	0.05858	0.996000	0.52242	0.941000	0.58515	0.549000	0.23329	0.849000	0.35215	0.491000	0.48974	GAG	.	.	.	none		0.592	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		A	17766949	C	A	17766949	3	1	22	1	0	0	0	0	1	0	0	0	16996	680	24	4	4217	4	UNC13A	19	17766949	Missense_Mutation	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10	1123063	17766949	41362034	108	1563											
SLC7A9	11136	hgsc.bcm.edu	37	chr19	33350836	33350836	+	Frame_Shift_Del	DEL	G	G	-																															gatgtagcacgccgtcaccaGggggatcccgatgataatgg																										TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr19:33350836delG	ENST00000023064.4	-	8	975	c.784delC	c.(784-786)ctgfs	p.L262fs	SLC7A9_ENST00000590341.1_Frame_Shift_Del_p.L262fs|RN7SKP22_ENST00000365097.1_RNA|SLC7A9_ENST00000587772.1_Frame_Shift_Del_p.L262fs	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	262					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)	GCCGTCACCAGGGGGATCCCG	0.612																																					p.L262fs	GBM(181;1335 2108 9644 44178 46689)	Atlas-Indel,Pindel	.											.	SLC7A9	78	.	0			c.785delT						PASS	.						99	81	87					19																	33350836		2203	4300	6503	SO:0001589	frameshift_variant	11136	exon8			.	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.784delC	chr19.hg19:g.33350836delG	ENSP00000023064:p.Leu262fs	157.0	0.0	0		158.0	56.0	0.35443	NM_001243036	B2R9A6	Frame_Shift_Del	DEL	ENST00000023064.4	hg19	CCDS12425.1																																																																																			.	.	.	none		0.612	SLC7A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450585.1			-	33350836	G	-	33350836	7	5	22	1	0	1	0	1	0	0	0	0	14718	991	35	0	703	0	SLC7A9	19	33350836	Frame_Shift_Del	DEL	G	TCGA-2Z-A9JS-01A-21D-A42J-10	15583887	33350836	25778147	109	1564											
RYR1	6261	hgsc.bcm.edu	37	chr19	39052079	39052079	+	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	tcagagaccaaccgcgcccaGtgggagatgccccaggtcag	10	4	13	14	2	2	2	2	0	0	2	2	4	2	2	5	2	2	0	5	2	1	0			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr19:39052079G>C	ENST00000359596.3	+	90	12609	c.12609G>C	c.(12607-12609)caG>caC	p.Q4203H	RYR1_ENST00000360985.3_Missense_Mutation_p.Q4198H|RYR1_ENST00000355481.4_Missense_Mutation_p.Q4198H			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4203					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)	ACCGCGCCCAGTGGGAGATGC	0.662																																					p.Q4203H		Atlas-SNP	.											.	RYR1	708	.	0			c.G12609C						PASS	.						38	32	34					19																	39052079		2202	4300	6502	SO:0001583	missense	6261	exon90			CGCCCAGTGGGAG	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.12609G>C	chr19.hg19:g.39052079G>C	ENSP00000352608:p.Gln4203His	25.0	0.0	.		26.0	8.0	.	NM_000540	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	10.92	1.487943	0.26686	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.97553	-4.43;-4.43;-4.43	3.43	2.39	0.29439	.	0.000000	0.64402	U	0.000004	D	0.98333	0.9447	M	0.90542	3.125	0.47819	D	0.999523	D;D;D	0.64830	0.994;0.994;0.99	D;D;D	0.78314	0.991;0.991;0.979	D	0.98411	1.0572	10	0.87932	D	0	.	10.5699	0.45194	0.0988:0.0:0.9012:0.0	.	4198;4198;4203	P21817-3;P21817-2;P21817	.;.;RYR1_HUMAN	H	4203;4198;4198	ENSP00000352608:Q4203H;ENSP00000347667:Q4198H;ENSP00000354254:Q4198H	ENSP00000347667:Q4198H	Q	+	3	2	RYR1	43743919	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	4.668000	0.61568	0.816000	0.34421	0.298000	0.19748	CAG	.	.	.	none		0.662	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			C	39052079	G	C	39052079	3	2	22	1	0	0	0	0	1	0	0	0	13781	1020	36	4	12967	4	RYR1	19	39052079	Missense_Mutation	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10	5701243	39052079	20076904	110	1565											
SCAF1	58506	hgsc.bcm.edu	37	chr19	50155522	50155522	+	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	cttcctcatcgtcgtcctcgAggcgcgagcggcaccgcggg	4	7	14	16	8	1	0	1	0	0	0	6	2	3	0	3	3	1	1	3	3	0	1			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr19:50155522A>T	ENST00000360565.3	+	7	2000	c.1876A>T	c.(1876-1878)Agg>Tgg	p.R626W		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	626	Arg-rich.|Ser-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		GTCGTCCTCGAGGCGCGAGCG	0.751																																					p.R626W		Atlas-SNP	.											.	SCAF1	78	.	0			c.A1876T						PASS	.						2	2	2					19																	50155522		1455	3069	4524	SO:0001583	missense	58506	exon7			TCCTCGAGGCGCG	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.1876A>T	chr19.hg19:g.50155522A>T	ENSP00000353769:p.Arg626Trp	32.0	0.0	.		43.0	22.0	.	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Missense_Mutation	SNP	ENST00000360565.3	hg19	CCDS33074.1	.	.	.	.	.	.	.	.	.	.	A	5.477	0.273021	0.10349	.	.	ENSG00000126461	ENST00000360565	T	0.39229	1.09	3.95	-1.19	0.09585	.	0.000000	0.39475	N	0.001357	T	0.44456	0.1294	L	0.27053	0.805	0.09310	N	0.999997	D	0.71674	0.998	D	0.72338	0.977	T	0.45498	-0.9257	9	.	.	.	-21.7886	11.8881	0.52615	0.3307:0.6693:0.0:0.0	.	626	Q9H7N4	SFR19_HUMAN	W	626	ENSP00000353769:R626W	.	R	+	1	2	SCAF1	54847334	0.854000	0.29725	0.019000	0.16419	0.340000	0.28889	0.835000	0.27531	-0.551000	0.06175	0.459000	0.35465	AGG	.	.	.	none		0.751	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228		T	50155522	A	T	50155522	3	4	22	1	0	0	0	0	1	0	0	0	13881	295	11	5	1898	5	SCAF1	19	50155522	Missense_Mutation	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10	11103443	50155522	8973461	111	1566											
CPT1C	126129	hgsc.bcm.edu	37	chr19	50209661	50209661	+	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	tgctctgctggccggccgggGccatgatcggtgagtgagtc	4	9	17	11	3	1	3	0	3	1	0	3	3	1	3	3	5	2	2	3	5	0	0			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr19:50209661G>C	ENST00000392518.4	+	12	1706	c.1334G>C	c.(1333-1335)gGc>gCc	p.G445A	CPT1C_ENST00000598293.1_Missense_Mutation_p.G445A|CPT1C_ENST00000354199.5_Missense_Mutation_p.G445A|CPT1C_ENST00000323446.5_Missense_Mutation_p.G445A|CPT1C_ENST00000405931.2_Missense_Mutation_p.G434A	NM_001199752.1	NP_001186681.1	Q8TCG5	CPT1C_HUMAN	carnitine palmitoyltransferase 1C	445					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)		GCCGGCCGGGGCCATGATCGG	0.637																																					p.G445A		Atlas-SNP	.											.	CPT1C	93	.	0			c.G1334C						PASS	.						10	12	12					19																	50209661		2184	4276	6460	SO:0001583	missense	126129	exon12			GCCGGGGCCATGA	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.1334G>C	chr19.hg19:g.50209661G>C	ENSP00000376303:p.Gly445Ala	52.0	0.0	.		49.0	22.0	.	NM_001199752	A8K0Z8|Q5K6N5|Q8N6Q9|Q8NDS6|Q8TE84	Missense_Mutation	SNP	ENST00000392518.4	hg19	CCDS12779.1	.	.	.	.	.	.	.	.	.	.	G	2.139	-0.397238	0.04899	.	.	ENSG00000169169	ENST00000392518;ENST00000354199;ENST00000405931;ENST00000323446;ENST00000295404	D;D;D;D	0.90788	-2.73;-2.73;-2.73;-2.73	4.36	3.3	0.37823	.	0.000000	0.48767	D	0.000179	D	0.92984	0.7767	L	0.61218	1.895	0.44652	D	0.997633	D;D;D;D	0.89917	0.999;1.0;0.984;0.988	D;D;P;D	0.91635	0.967;0.999;0.868;0.919	D	0.90301	0.4330	10	0.14656	T	0.56	-29.4364	13.1346	0.59402	0.0:0.1628:0.8372:0.0	.	316;445;434;445	C9IY45;Q8TCG5-3;Q8TCG5-2;Q8TCG5	.;.;.;CPT1C_HUMAN	A	445;445;434;445;316	ENSP00000376303:G445A;ENSP00000346138:G445A;ENSP00000384465:G434A;ENSP00000319343:G445A	ENSP00000295404:G316A	G	+	2	0	CPT1C	54901473	1.000000	0.71417	0.240000	0.24138	0.004000	0.04260	8.802000	0.91910	1.040000	0.40099	-0.181000	0.13052	GGC	.	.	.	none		0.637	CPT1C-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465873.1	NM_152359		C	50209661	G	C	50209661	3	2	22	1	0	0	0	0	1	0	0	0	3835	1203	42	4	1372	4	CPT1C	19	50209661	Missense_Mutation	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10	54139	50209661	8919322	112	1567											
AKT1S1	84335	hgsc.bcm.edu	37	chr19	50374877	50374877	+	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	cccagacgggcacagacacaGgcagggacttggcgtactgc	10	4	14	13	2	0	2	0	0	0	2	0	3	0	3	1	4	2	3	1	4	1	2			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr19:50374877G>T	ENST00000391833.1	-	3	2543	c.554C>A	c.(553-555)cCt>cAt	p.P185H	AKT1S1_ENST00000344175.5_Missense_Mutation_p.P185H|AKT1S1_ENST00000391835.1_Missense_Mutation_p.P205H|AKT1S1_ENST00000391834.2_Missense_Mutation_p.P185H|AKT1S1_ENST00000391831.1_Missense_Mutation_p.P185H|AKT1S1_ENST00000391832.3_Missense_Mutation_p.P185H	NM_001278160.1	NP_001265089.1			AKT1 substrate 1 (proline-rich)											kidney(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	5		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.0132)		CACAGACACAGGCAGGGACTT	0.657																																					p.P205H		Atlas-SNP	.											.	AKT1S1	16	.	0			c.C614A						PASS	.						82	88	86					19																	50374877		2203	4300	6503	SO:0001583	missense	84335	exon4			GACACAGGCAGGG	BC022241	CCDS12784.1, CCDS59410.1	19q13.33	2008-02-05			ENSG00000204673	ENSG00000204673			28426	protein-coding gene	gene with protein product	"proline-rich Akt substrate, 40 kDa"	610221				12524439	Standard	NM_032375		Approved	PRAS40, MGC2865, Lobe	uc031rmg.1	Q96B36	OTTHUMG00000150246	ENST00000391833.1:c.554C>A	chr19.hg19:g.50374877G>T	ENSP00000375709:p.Pro185His	55.0	0.0	.		35.0	11.0	.	NM_032375		Missense_Mutation	SNP	ENST00000391833.1	hg19	CCDS12784.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.200977	0.79015	.	.	ENSG00000204673	ENST00000391833;ENST00000344175;ENST00000391832;ENST00000391834;ENST00000391835;ENST00000391831	D;D;D;D;D;D	0.82711	-1.61;-1.61;-1.61;-1.61;-1.64;-1.61	4.14	4.14	0.48551	.	0.000000	0.85682	D	0.000000	D	0.88764	0.6525	L	0.60067	1.865	0.58432	D	0.999993	D	0.89917	1.0	D	0.87578	0.998	D	0.89888	0.4035	10	0.87932	D	0	-10.2665	14.2818	0.66219	0.0:0.0:1.0:0.0	.	185	Q96B36	AKTS1_HUMAN	H	185;185;185;185;205;185	ENSP00000375709:P185H;ENSP00000341698:P185H;ENSP00000375708:P185H;ENSP00000375710:P185H;ENSP00000375711:P205H;ENSP00000375707:P185H	ENSP00000341698:P185H	P	-	2	0	AKT1S1	55066689	1.000000	0.71417	0.994000	0.49952	0.964000	0.63967	5.823000	0.69272	2.305000	0.77605	0.655000	0.94253	CCT	.	.	.	none		0.657	AKT1S1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317073.1	NM_032375		T	50374877	G	T	50374877	3	4	22	1	0	0	0	0	1	0	0	0	479	1000	35	4	224	4	AKT1S1	19	50374877	Missense_Mutation	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10	165216	50374877	8754106	113	1568											
PCK1	5105	hgsc.bcm.edu	37	chr20	56139426	56139426	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caccatcacgtcctggaagaAtaaggagtggagctcagagg	13	6	13	9	1	2	2	2	0	0	2	3	5	3	5	2	4	1	1	2	4	3	1			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr20:56139426A>G	ENST00000319441.4	+	7	1327	c.1163A>G	c.(1162-1164)aAt>aGt	p.N388S	PCK1_ENST00000535860.1_Missense_Mutation_p.N256S|PCK1_ENST00000543666.1_Missense_Mutation_p.N71S	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	388					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			TCCTGGAAGAATAAGGAGTGG	0.577																																					p.N388S		Atlas-SNP	.											.	PCK1	95	.	0			c.A1163G						PASS	.						84	75	78					20																	56139426		2203	4300	6503	SO:0001583	missense	5105	exon7			GGAAGAATAAGGA		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.1163A>G	chr20.hg19:g.56139426A>G	ENSP00000319814:p.Asn388Ser	143.0	0.0	.		165.0	42.0	.	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Missense_Mutation	SNP	ENST00000319441.4	hg19	CCDS13460.1	.	.	.	.	.	.	.	.	.	.	A	12.83	2.056807	0.36277	.	.	ENSG00000124253	ENST00000540165;ENST00000319441;ENST00000543666;ENST00000535860	T;T;T	0.04049	3.72;3.72;3.72	5.2	4.1	0.47936	.	0.080070	0.85682	D	0.000000	T	0.07863	0.0197	M	0.67397	2.05	0.58432	D	0.999995	B;B	0.11235	0.004;0.002	B;B	0.11329	0.006;0.002	T	0.05146	-1.0903	10	0.87932	D	0	-27.5119	10.481	0.44693	0.9211:0.0:0.0789:0.0	.	71;388	B4DT64;P35558	.;PCKGC_HUMAN	S	70;388;71;256	ENSP00000319814:N388S;ENSP00000445767:N71S;ENSP00000444342:N256S	ENSP00000319814:N388S	N	+	2	0	PCK1	55572832	1.000000	0.71417	0.988000	0.46212	0.324000	0.28378	4.873000	0.63057	0.918000	0.36919	0.533000	0.62120	AAT	.	.	.	none		0.577	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2			G	56139426	A	G	56139426	3	3	22	1	0	0	0	0	1	0	0	0	11588	101	4	3	1185	3	PCK1	20	56139426	Missense_Mutation	SNP	A	TCGA-2Z-A9JS-01A-21D-A42J-10		56139426	6886094	114	1569											
OGFR	11054	hgsc.bcm.edu	37	chr20	61436359	61436359	+	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	aggagtcggaggagccgcggGcggcgcggcccagctcgttc	5	4	19	13	7	0	0	0	0	0	0	3	3	0	3	2	6	2	2	2	6	0	1			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr20:61436359G>C	ENST00000290291.6	+	1	173	c.148G>C	c.(148-150)Gcg>Ccg	p.A50P	OGFR_ENST00000370461.1_5'Flank|OGFR-AS1_ENST00000431361.1_RNA	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	50				AAR -> GPE (in Ref. 2). {ECO:0000305}.|DAGDEDEESEEPRAARPSSFQSRMTGSRNWRATRDMCRYRH NYP -> GARRALGVLGQPGGLQMRLPERHGGPQGSLCLMD PCCPLSLALQ (in Ref. 5). {ECO:0000305}.	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)					GGAGCCGCGGGCGGCGCGGCC	0.801																																					p.A50P		Atlas-SNP	.											.	OGFR	63	.	0			c.G148C						PASS	.						8	12	11					20																	61436359		1504	2710	4214	SO:0001583	missense	11054	exon1			CCGCGGGCGGCGC	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.148G>C	chr20.hg19:g.61436359G>C	ENSP00000290291:p.Ala50Pro	42.0	0.0	.		59.0	15.0	.	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Missense_Mutation	SNP	ENST00000290291.6	hg19	CCDS13504.1	.	.	.	.	.	.	.	.	.	.	G	5.458	0.269520	0.10349	.	.	ENSG00000060491	ENST00000290291;ENST00000370468;ENST00000357163	T;T	0.47177	1.84;0.85	2.24	1.25	0.21368	.	1.107710	0.07007	N	0.824466	T	0.32734	0.0839	N	0.14661	0.345	0.20307	N	0.999915	D	0.61080	0.989	P	0.47573	0.55	T	0.17048	-1.0382	10	0.28530	T	0.3	.	4.5217	0.11962	0.0:0.2882:0.4714:0.2404	.	50	Q9NZT2	OGFR_HUMAN	P	50	ENSP00000290291:A50P;ENSP00000359499:A50P	ENSP00000290291:A50P	A	+	1	0	OGFR	60906804	0.026000	0.19158	0.007000	0.13788	0.045000	0.14185	0.706000	0.25690	0.469000	0.27268	-0.333000	0.08304	GCG	.	.	.	none		0.801	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1			C	61436359	G	C	61436359	3	2	22	1	0	0	0	0	1	0	0	0	10850	1203	42	4	150	4	OGFR	20	61436359	Missense_Mutation	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10	5296933	61436359	1589161	115	1570											
EEF1A2	1917	hgsc.bcm.edu	37	chr20	62126370	62126370	+	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	cagcgtgtaggccagcagggCatgctcccgcgtctgcccat	6	7	13	15	3	1	0	0	0	1	0	2	0	2	0	3	2	4	4	3	2	1	1			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr20:62126370C>T	ENST00000298049.7	-	3	479	c.409G>A	c.(409-411)Gcc>Acc	p.A137T	EEF1A2_ENST00000217182.3_Missense_Mutation_p.A137T			Q05639	EF1A2_HUMAN	eukaryotic translation elongation factor 1 alpha 2	137	tr-type G.				positive regulation of apoptotic process (GO:0043065)|response to inorganic substance (GO:0010035)	eukaryotic translation elongation factor 1 complex (GO:0005853)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)|translation factor activity, nucleic acid binding (GO:0008135)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(14)|stomach(1)	20	all_cancers(38;9.45e-12)		BRCA - Breast invasive adenocarcinoma(10;1.22e-05)			GCCAGCAGGGCATGCTCCCGC	0.657																																					p.A137T		Atlas-SNP	.											.	EEF1A2	60	.	0			c.G409A						PASS	.						94	85	88					20																	62126370		2203	4300	6503	SO:0001583	missense	1917	exon4			GCAGGGCATGCTC	AF163763	CCDS13522.1	20q13.3	2010-06-03			ENSG00000101210	ENSG00000101210			3192	protein-coding gene	gene with protein product		602959	"statin-like", "statin"	STNL, STN		8354261, 8812466	Standard	NM_001958		Approved	EEF1AL, HS1	uc002yfe.2	Q05639	OTTHUMG00000033076	ENST00000298049.7:c.409G>A	chr20.hg19:g.62126370C>T	ENSP00000298049:p.Ala137Thr	64.0	0.0	.		96.0	62.0	.	NM_001958	B5BUF3|E1P5J1|P54266|Q0VGC7	Missense_Mutation	SNP	ENST00000298049.7	hg19	CCDS13522.1	.	.	.	.	.	.	.	.	.	.	C	17.73	3.461676	0.63513	.	.	ENSG00000101210	ENST00000298049;ENST00000217182	T;T	0.71341	-0.56;-0.56	3.88	2.93	0.34026	Protein synthesis factor, GTP-binding (1);	0.125571	0.52532	N	0.000078	T	0.76926	0.4056	L	0.45285	1.41	0.58432	D	0.999999	D;B	0.69078	0.997;0.187	D;B	0.79108	0.992;0.332	T	0.77744	-0.2473	10	0.87932	D	0	-1.4932	11.838	0.52338	0.0:0.9122:0.0:0.0878	.	113;137	Q59GP5;Q05639	.;EF1A2_HUMAN	T	137	ENSP00000298049:A137T;ENSP00000217182:A137T	ENSP00000217182:A137T	A	-	1	0	EEF1A2	61596814	1.000000	0.71417	0.982000	0.44146	0.586000	0.36452	5.950000	0.70265	0.766000	0.33244	-0.671000	0.03813	GCC	.	.	.	none		0.657	EEF1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080495.1	NM_001958		T	62126370	C	T	62126370	3	4	22	1	0	0	0	0	1	0	0	0	4926	710	25	2	1002	2	EEF1A2	20	62126370	Missense_Mutation	SNP	C	TCGA-2Z-A9JS-01A-21D-A42J-10	690011	62126370	899150	116	1571											
MYT1	4661	hgsc.bcm.edu	37	chr20	62843443	62843443	+	Missense_Mutation	SNP	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	gctgaagtgccccactcctgGctgcacaggccagggtcacg	7	6	13	15	1	1	1	1	1	0	0	2	1	2	1	4	3	2	3	4	3	1	0			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr20:62843443G>A	ENST00000328439.1	+	9	1833	c.1469G>A	c.(1468-1470)gGc>gAc	p.G490D	MYT1_ENST00000536311.1_Missense_Mutation_p.G490D|MYT1_ENST00000360149.4_Missense_Mutation_p.G192D	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0	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)			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)					CCCACTCCTGGCTGCACAGGC	0.627																																					p.G490D	GBM(59;481 1041 20555 21139 33705)	Atlas-SNP	.											.	MYT1	152	.	0			c.G1469A						PASS	.						140	129	132					20																	62843443		2203	4300	6503	SO:0001583	missense	4661	exon9			CTCCTGGCTGCAC	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.1469G>A	chr20.hg19:g.62843443G>A	ENSP00000327465:p.Gly490Asp	27.0	0.0	.		59.0	19.0	.	NM_004535	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000328439.1	hg19	CCDS13558.1	.	.	.	.	.	.	.	.	.	.	G	18.03	3.531388	0.64972	.	.	ENSG00000196132	ENST00000360149;ENST00000328439;ENST00000536311	T;T;T	0.68331	-0.13;-0.32;1.64	4.46	4.46	0.54185	.	0.000000	0.85682	D	0.000000	D	0.84170	0.5413	M	0.87456	2.885	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.87870	0.2670	10	0.87932	D	0	-31.1382	17.4965	0.87719	0.0:0.0:1.0:0.0	.	490;490;192	F5H7M8;Q01538;Q6P6D5	.;MYT1_HUMAN;.	D	192;490;490	ENSP00000353269:G192D;ENSP00000327465:G490D;ENSP00000442412:G490D	ENSP00000327465:G490D	G	+	2	0	MYT1	62313887	1.000000	0.71417	0.998000	0.56505	0.757000	0.42996	9.725000	0.98778	2.187000	0.69744	0.557000	0.71058	GGC	.	.	.	none		0.627	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535		A	62843443	G	A	62843443	3	1	22	1	0	0	0	0	1	0	0	0	10113	1203	42	2	1495	2	MYT1	20	62843443	Missense_Mutation	SNP	G	TCGA-2Z-A9JS-01A-21D-A42J-10	717073	62843443	182077	117	1572											
UMODL1	89766	hgsc.bcm.edu	37	chr21	43505510	43505510	+	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	ctcctgaaccacatgcgcctTctgcattccttggtaggtga	7	12	9	13	1	1	2	0	2	1	0	3	2	3	2	4	2	3	2	4	2	2	4			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr21:43505510T>A	ENST00000408910.2	+	4	591	c.591T>A	c.(589-591)ctT>ctA	p.L197L	UMODL1_ENST00000408989.2_Silent_p.L197L|UMODL1_ENST00000400427.1_Silent_p.L125L|UMODL1_ENST00000400424.2_Silent_p.L125L	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	197					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						ACATGCGCCTTCTGCATTCCT	0.607																																					p.L197L	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.T591A						PASS	.						138	142	141					21																	43505510		1939	4137	6076	SO:0001819	synonymous_variant	89766	exon4			GCGCCTTCTGCAT		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.591T>A	chr21.hg19:g.43505510T>A		52.0	0.0	.		51.0	28.0	.	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Silent	SNP	ENST00000408910.2	hg19	CCDS42936.1																																																																																			.	.	.	none		0.607	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2			A	43505510	T	A	43505510	2	1	22	1	0	0	0	0	0	0	0	1	16992	1770	62	5		5	UMODL1	21	43505510	Silent	SNP	T	TCGA-2Z-A9JS-01A-21D-A42J-10		43505510	4624385	118	1573											
TMPRSS6	164656	hgsc.bcm.edu	37	chr22	37462120	37462120	+	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	ctttgcaggggggcagttccTcaggtcaccacttgctggat	6	11	13	11	0	2	0	2	0	0	0	3	1	3	1	2	5	2	4	2	5	0	3			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr22:37462120T>C	ENST00000346753.3	-	18	2552	c.2436A>G	c.(2434-2436)tgA>tgG	p.*812W	TMPRSS6_ENST00000406856.1_Nonstop_Mutation_p.*825W|TMPRSS6_ENST00000381792.2_Nonstop_Mutation_p.*825W|TMPRSS6_ENST00000406725.1_Nonstop_Mutation_p.*803W	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	0					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						GGGCAGTTCCTCAGGTCACCA	0.647																																					p.X812W		Atlas-SNP	.											.	TMPRSS6	99	.	0			c.A2436G						PASS	.						48	52	51					22																	37462120		2203	4300	6503	SO:0001578	stop_lost	164656	exon18			AGTTCCTCAGGTC	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.2436A>G	chr22.hg19:g.37462120T>C	ENSP00000334962:p.*812Cysext*96	72.0	0.0	.		75.0	31.0	.	NM_153609	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Missense_Mutation	SNP	ENST00000346753.3	hg19	CCDS13941.1	.	.	.	.	.	.	.	.	.	.	T	12.06	1.824874	0.32237	.	.	ENSG00000187045	ENST00000381792;ENST00000346753;ENST00000406725;ENST00000406856	.	.	.	4.62	4.62	0.57501	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3168	0.66457	0.0:0.0:0.0:1.0	.	.	.	.	W	825;812;803;825	.	.	X	-	3	0	TMPRSS6	35792066	1.000000	0.71417	0.994000	0.49952	0.458000	0.32498	5.142000	0.64820	1.837000	0.53436	0.482000	0.46254	TGA	.	.	.	none		0.647	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609		C	37462120	T	C	37462120	4	2	22	1	0	0	0	0	0	0	0	0	16263	1564	54	3	3	3	TMPRSS6	22	37462120	Nonstop_Mutation	SNP	T	TCGA-2Z-A9JS-01A-21D-A42J-10		37462120	13842446	119	1574											
FBLN1	2192	hgsc.bcm.edu	37	chr22	45931203	45931203	+	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	tggctttatacaagatgctcTaggcaactgtattggtaaga	12	13	10	6	0	1	2	0	0	1	2	1	2	1	2	0	3	3	5	0	3	7	7			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr22:45931203T>A	ENST00000327858.6	+	8	1003	c.908T>A	c.(907-909)cTa>cAa	p.L303Q	FBLN1_ENST00000442170.2_Missense_Mutation_p.L303Q|FBLN1_ENST00000402984.3_Missense_Mutation_p.L341Q|FBLN1_ENST00000262722.7_Missense_Mutation_p.L303Q|FBLN1_ENST00000340923.5_Missense_Mutation_p.L303Q|FBLN1_ENST00000348697.2_Missense_Mutation_p.L303Q	NM_006486.2	NP_006477	P23142	FBLN1_HUMAN	fibulin 1	303	EGF-like 3; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|viral process (GO:0016032)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|peptidase activator activity (GO:0016504)			biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	30		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		CAAGATGCTCTAGGCAACTGT	0.537																																					p.L303Q		Atlas-SNP	.											.	FBLN1	143	.	0			c.T908A						PASS	.						79	71	74					22																	45931203		2203	4300	6503	SO:0001583	missense	2192	exon8			ATGCTCTAGGCAA		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.908T>A	chr22.hg19:g.45931203T>A	ENSP00000331544:p.Leu303Gln	78.0	0.0	.		70.0	32.0	.	NM_006487	B0QY42|B1AHL4|P23143|P23144|P37888|Q5TIC4|Q8TBH8|Q9HBQ5|Q9UC21|Q9UGR4|Q9UH41	Missense_Mutation	SNP	ENST00000327858.6	hg19	CCDS14067.1	.	.	.	.	.	.	.	.	.	.	t	17.75	3.466305	0.63625	.	.	ENSG00000077942	ENST00000348697;ENST00000402984;ENST00000262722;ENST00000327858;ENST00000442170;ENST00000340923	D;D;D;D;D;D	0.91686	-2.89;-2.89;-2.89;-2.15;-2.89;-2.89	5.47	5.47	0.80525	EGF-like calcium-binding (2);	0.070231	0.64402	D	0.000017	D	0.90800	0.7111	N	0.12637	0.245	0.58432	D	0.999998	D;D;D;D	0.89917	1.0;0.999;0.998;0.999	D;D;D;D	0.77557	0.99;0.985;0.971;0.971	D	0.88285	0.2939	10	0.13470	T	0.59	.	15.6182	0.76784	0.0:0.0:0.0:1.0	.	341;303;303;303	B1AHL2;P23142;B1AHL4;P23142-4	.;FBLN1_HUMAN;.;.	Q	303;341;303;303;303;303	ENSP00000262723:L303Q;ENSP00000385521:L341Q;ENSP00000262722:L303Q;ENSP00000331544:L303Q;ENSP00000393812:L303Q;ENSP00000342212:L303Q	ENSP00000262722:L303Q	L	+	2	0	FBLN1	44309867	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.463000	0.66712	2.101000	0.63845	0.445000	0.29226	CTA	.	.	.	none		0.537	FBLN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322287.1	NM_006486		A	45931203	T	A	45931203	3	1	22	1	0	0	0	0	1	0	0	0	5705	1522	53	5	938	5	FBLN1	22	45931203	Missense_Mutation	SNP	T	TCGA-2Z-A9JS-01A-21D-A42J-10	8469083	45931203	5373363	120	1575											
MLC1	23209	hgsc.bcm.edu	37	chr22	50502534	50502534	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcagccttgcactgacctTgaagcgcacgcactggatgg	8	8	12	13	2	0	2	0	2	0	0	0	3	0	3	2	2	4	4	2	2	1	2			TCGA-2Z-A9JS-01A-21D-A42J-10	TCGA-2Z-A9JS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	db0ca5a7-1470-4807-90f7-ef557c434e28	518e7145-530f-4cb8-a90b-bcf9ecab7b98	g.chr22:50502534T>C	ENST00000311597.5	-	11	1594	c.988A>G	c.(988-990)Aag>Gag	p.K330E	MLC1_ENST00000483836.1_5'UTR|MLC1_ENST00000538737.1_Missense_Mutation_p.K296E|MLC1_ENST00000431262.2_Missense_Mutation_p.K300E|MLC1_ENST00000450140.2_Missense_Mutation_p.K278E|MLC1_ENST00000395876.2_Missense_Mutation_p.K330E|MLC1_ENST00000535444.1_Missense_Mutation_p.K251E	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with subcortical cysts 1	330					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)		GCACTGACCTTGAAGCGCACG	0.677																																					p.K330E		Atlas-SNP	.											.	MLC1	48	.	0			c.A988G						PASS	.						50	46	47					22																	50502534		2203	4300	6503	SO:0001583	missense	23209	exon11			TGACCTTGAAGCG	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.988A>G	chr22.hg19:g.50502534T>C	ENSP00000310375:p.Lys330Glu	69.0	0.0	.		72.0	25.0	.	NM_015166	B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8	Missense_Mutation	SNP	ENST00000311597.5	hg19	CCDS14083.1	.	.	.	.	.	.	.	.	.	.	t	16.64	3.178544	0.57692	.	.	ENSG00000100427	ENST00000395876;ENST00000311597;ENST00000538737;ENST00000431262;ENST00000535444;ENST00000450140	D;D;D;D;D;D	0.94330	-3.4;-3.4;-3.4;-3.4;-3.4;-3.4	3.99	2.9	0.33743	.	0.098520	0.64402	D	0.000002	D	0.94997	0.8381	M	0.68952	2.095	0.49389	D	0.999786	D;D;D;D	0.71674	0.996;0.998;0.996;0.998	D;D;D;D	0.78314	0.987;0.991;0.987;0.991	D	0.93639	0.6963	10	0.87932	D	0	-29.1483	7.6427	0.28303	0.0:0.0:0.2162:0.7838	.	296;300;278;330	F5H1B9;B7Z659;B7Z1X1;Q15049	.;.;.;MLC1_HUMAN	E	330;330;296;300;251;278	ENSP00000379216:K330E;ENSP00000310375:K330E;ENSP00000445805:K296E;ENSP00000415877:K300E;ENSP00000438910:K251E;ENSP00000412448:K278E	ENSP00000310375:K330E	K	-	1	0	MLC1	48844661	0.753000	0.28349	0.958000	0.39756	0.472000	0.32918	0.549000	0.23329	0.616000	0.30141	0.454000	0.30748	AAG	.	.	.	none		0.677	MLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316979.2	NM_015166		C	50502534	T	C	50502534	3	2	22	1	0	0	0	0	1	0	0	0	9619	1821	63	3	153	3	MLC1	22	50502534	Missense_Mutation	SNP	T	TCGA-2Z-A9JS-01A-21D-A42J-10	4571331	50502534	802032	121	1576											
TESK2	10420	hgsc.bcm.edu	37	chr1	45811638	45811638	+	Missense_Mutation	SNP	A	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	ccagggtcttcccaatctccAcaaaagatgggcgcagtttg	10	9	10	12	1	2	1	0	0	2	1	4	1	3	1	3	2	0	2	3	2	3	2			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr1:45811638A>C	ENST00000372086.3	-	10	1308	c.908T>G	c.(907-909)gTg>gGg	p.V303G	TESK2_ENST00000341771.6_Missense_Mutation_p.V274G|TESK2_ENST00000486676.1_5'UTR|TESK2_ENST00000372084.1_Missense_Mutation_p.V274G|TESK2_ENST00000538496.1_Missense_Mutation_p.V220G	NM_007170.2	NP_009101.2	Q96S53	TESK2_HUMAN	testis-specific kinase 2	303	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|focal adhesion assembly (GO:0048041)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	32	Acute lymphoblastic leukemia(166;0.155)					CCCAATCTCCACAAAAGATGG	0.522																																					p.V303G		Atlas-SNP	.											.	TESK2	60	.	0			c.T908G						PASS	.						74	72	73					1																	45811638		1899	4113	6012	SO:0001583	missense	10420	exon10			ATCTCCACAAAAG	AJ132545	CCDS41323.1	1p32	2010-04-27			ENSG00000070759	ENSG00000070759	2.7.12.1		11732	protein-coding gene	gene with protein product		604746				10512679	Standard	NM_007170		Approved		uc001cns.1	Q96S53	OTTHUMG00000007680	ENST00000372086.3:c.908T>G	chr1.hg19:g.45811638A>C	ENSP00000361158:p.Val303Gly	73.0	0.0	.		65.0	15.0	.	NM_007170	Q5T422|Q5T423|Q8N520|Q9Y3Q6	Missense_Mutation	SNP	ENST00000372086.3	hg19	CCDS41323.1	.	.	.	.	.	.	.	.	.	.	A	11.87	1.766844	0.31320	.	.	ENSG00000070759	ENST00000372084;ENST00000372086;ENST00000372083;ENST00000341771;ENST00000538496	T;D;T;D	0.82526	-0.19;-1.62;-0.19;-1.62	5.54	-0.102	0.13613	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.750938	0.12432	N	0.469475	T	0.64450	0.2599	N	0.13272	0.32	0.80722	D	1	B;B	0.14012	0.009;0.002	B;B	0.22152	0.038;0.027	T	0.46610	-0.9179	10	0.20519	T	0.43	-0.5571	4.8888	0.13717	0.4968:0.0:0.3572:0.146	.	274;303	Q96S53-3;Q96S53	.;TESK2_HUMAN	G	274;303;287;274;220	ENSP00000361156:V274G;ENSP00000361158:V303G;ENSP00000343940:V274G;ENSP00000441746:V220G	ENSP00000343940:V274G	V	-	2	0	TESK2	45584225	0.438000	0.25602	1.000000	0.80357	0.997000	0.91878	0.273000	0.18662	0.055000	0.16094	0.456000	0.33151	GTG	.	.	.	none		0.522	TESK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020523.1	NM_007170		C	45811638	A	C	45811638	3	2	23	1	0	0	0	0	1	0	0	0	15780	159	6	5	815	5	TESK2	1	45811638	Missense_Mutation	SNP	A	TCGA-2Z-A9JT-01A-11D-A42J-10		45811638	203438983	1	1577											
AMPD2	271	hgsc.bcm.edu	37	chr1	110168296	110168296	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccccaggagctgttcaccCgctcactggctgagagcgag	7	6	12	16	2	2	1	2	1	0	1	2	4	2	2	4	2	2	4	4	2	0	1			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr1:110168296C>T	ENST00000256578.3	+	3	757	c.397C>T	c.(397-399)Cgc>Tgc	p.R133C	AMPD2_ENST00000528667.1_Missense_Mutation_p.R133C|AMPD2_ENST00000393688.3_Missense_Mutation_p.R14C|AMPD2_ENST00000528454.1_Missense_Mutation_p.R15C|AMPD2_ENST00000526301.1_3'UTR|RP5-1160K1.6_ENST00000369843.3_RNA|AMPD2_ENST00000358729.4_Missense_Mutation_p.R58C|AMPD2_ENST00000342115.4_Missense_Mutation_p.R52C	NM_004037.7	NP_004028.3	Q01433	AMPD2_HUMAN	adenosine monophosphate deaminase 2	133					cell death (GO:0008219)|cyclic purine nucleotide metabolic process (GO:0052652)|energy homeostasis (GO:0097009)|IMP biosynthetic process (GO:0006188)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			breast(1)|large_intestine(3)|ovary(2)|skin(1)	7		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.0425)|all cancers(265;0.0884)|Colorectal(144;0.109)|Epithelial(280;0.111)|LUSC - Lung squamous cell carcinoma(189;0.228)		GCTGTTCACCCGCTCACTGGC	0.672																																					p.R133C		Atlas-SNP	.											AMPD2_ENST00000393689,NS,carcinoma,0,1	AMPD2	75	.	0			c.C397T						PASS	.						49	56	54					1																	110168296		2203	4300	6503	SO:0001583	missense	271	exon3			TTCACCCGCTCAC	S47833	CCDS804.1, CCDS805.1, CCDS30796.1, CCDS58016.1	1p13.3	2014-03-03	2010-02-10		ENSG00000116337	ENSG00000116337	3.5.4.6		469	protein-coding gene	gene with protein product	"AMPD isoform L"	102771	"adenosine monophosphate deaminase 2 (isoform L)"			1400401, 24482476	Standard	NM_004037		Approved	SPG63	uc009wfh.2	Q01433	OTTHUMG00000011649	ENST00000256578.3:c.397C>T	chr1.hg19:g.110168296C>T	ENSP00000256578:p.Arg133Cys	151.0	0.0	.		118.0	7.0	.	NM_004037	B4DK50|B4DZI5|E9PNG0|Q14856|Q14857|Q16686|Q16687|Q16688|Q16729|Q5T693|Q5T695|Q96IA1|Q9UDX8|Q9UDX9|Q9UMU4	Missense_Mutation	SNP	ENST00000256578.3	hg19	CCDS805.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.8|27.8	4.865184|4.865184	0.91511|0.91511	.|.	.|.	ENSG00000116337|ENSG00000116337	ENST00000369840|ENST00000531734;ENST00000342115;ENST00000528667;ENST00000531203;ENST00000256578;ENST00000358729;ENST00000527846;ENST00000528454;ENST00000393688	.|T;T;T;T;T;T;T;D	.|0.87809	.|1.12;1.12;1.12;1.12;1.18;1.12;1.18;-2.3	4.84|4.84	4.84|4.84	0.62591|0.62591	.|.	.|0.164918	.|0.56097	.|D	.|0.000040	D|D	0.90851|0.90851	0.7126|0.7126	L|L	0.60455|0.60455	1.87|1.87	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;0.999;0.999	.|D;D;P;P	.|0.80764	.|0.994;0.911;0.858;0.881	D|D	0.91649|0.91649	0.5333|0.5333	5|10	.|0.72032	.|D	.|0.01	-29.6856|-29.6856	16.8712|16.8712	0.86041|0.86041	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|58;14;133;52	.|Q01433-4;Q01433-3;Q01433;Q01433-2	.|.;.;AMPD2_HUMAN;.	L|C	103|52;52;133;15;133;58;100;15;14	.|ENSP00000433739:R52C;ENSP00000345498:R52C;ENSP00000436541:R133C;ENSP00000256578:R133C;ENSP00000351573:R58C;ENSP00000431904:R100C;ENSP00000437164:R15C;ENSP00000377292:R14C	.|ENSP00000256578:R133C	P|R	+|+	2|1	0|0	AMPD2|AMPD2	109969819|109969819	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.918000|0.918000	0.54935|0.54935	7.353000|7.353000	0.79414|0.79414	2.506000|2.506000	0.84524|0.84524	0.462000|0.462000	0.41574|0.41574	CCG|CGC	.	.	.	none		0.672	AMPD2-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390615.1			T	110168296	C	T	110168296	3	4	23	1	0	0	0	0	1	0	0	0	586	652	23	1	448	1	AMPD2	1	110168296	Missense_Mutation	SNP	C	TCGA-2Z-A9JT-01A-11D-A42J-10	64356658	110168296	139082325	2	1578											
HAO2	51179	hgsc.bcm.edu	37	chr1	119935262	119935263	+	Frame_Shift_Del	DEL	GT	GT	-																															gtgaacatggtgttaaggaaGttttgaacattttaacaaat																										TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr1:119935262_119935263delGT	ENST00000325945.3	+	7	1025_1026	c.952_953delGT	c.(952-954)gttfs	p.V318fs	HAO2_ENST00000482991.1_3'UTR|HAO2_ENST00000361035.4_Frame_Shift_Del_p.V331fs	NM_001005783.1|NM_016527.2	NP_001005783.1|NP_057611.1	Q9NYQ3	HAOX2_HUMAN	hydroxyacid oxidase 2 (long chain)	318	FMN hydroxy acid dehydrogenase. {ECO:0000255|PROSITE-ProRule:PRU00683}.				fatty acid oxidation (GO:0019395)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	(S)-2-hydroxy-acid oxidase activity (GO:0003973)|FMN binding (GO:0010181)|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(6)|kidney(2)|large_intestine(5)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)		Lung(183;0.0155)|LUSC - Lung squamous cell carcinoma(189;0.0856)		TGTTAAGGAAGTTTTGAACATT	0.401																																					p.317_318del		Atlas-Indel,Pindel	.											.	HAO2	62	.	0			c.951_952del						PASS	.																																			SO:0001589	frameshift_variant	51179	exon8			.	AF231917	CCDS901.1	1p13.3-p13.1	2008-07-18			ENSG00000116882	ENSG00000116882	1.1.3.15		4810	protein-coding gene	gene with protein product	"(S)-2-hydroxy-acid oxidase", "glycolate oxidase", "long-chain L-2-hydroxy acid oxidase", "growth-inhibiting protein 16"	605176				10777549	Standard	XM_005270913		Approved	HAOX2, GIG16	uc001ehr.1	Q9NYQ3	OTTHUMG00000012410	ENST00000325945.3:c.952_953delGT	chr1.hg19:g.119935262_119935263delGT	ENSP00000316339:p.Val318fs	107.0	0.0	0		111.0	28.0	0.252252	NM_001005783	Q2TU86|Q5QP00|Q9UJS6	Frame_Shift_Del	DEL	ENST00000325945.3	hg19	CCDS901.1																																																																																			.	.	.	none		0.401	HAO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034984.1	NM_001005783		-	119935263	GT	-	119935262	7	5	23	1	0	1	0	1	0	0	0	0	6959	1029	36	0	974	0	HAO2	1	119935262	Frame_Shift_Del	DEL	GT	TCGA-2Z-A9JT-01A-11D-A42J-10	9766966	119935262	129315359	3	1579											
ITGA10	8515	hgsc.bcm.edu	37	chr1	145536864	145536864	+	Missense_Mutation	SNP	T	T	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	ttccttcaggatacatcagaTtacctccggccagtggcctt	8	12	8	13	1	2	1	2	0	0	1	4	2	4	2	5	3	2	0	5	3	2	5			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr1:145536864T>G	ENST00000369304.3	+	18	2419	c.2244T>G	c.(2242-2244)gaT>gaG	p.D748E	ITGA10_ENST00000539363.1_Missense_Mutation_p.D605E|ITGA10_ENST00000538811.1_Missense_Mutation_p.D617E	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	748					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)					ATACATCAGATTACCTCCGGC	0.468																																					p.D748E		Atlas-SNP	.											.	ITGA10	131	.	0			c.T2244G						PASS	.						190	175	180					1																	145536864		2203	4300	6503	SO:0001583	missense	8515	exon18			ATCAGATTACCTC	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.2244T>G	chr1.hg19:g.145536864T>G	ENSP00000358310:p.Asp748Glu	78.0	0.0	.		86.0	24.0	.	NM_003637	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Missense_Mutation	SNP	ENST00000369304.3	hg19	CCDS918.1	.	.	.	.	.	.	.	.	.	.	T	17.52	3.409932	0.62399	.	.	ENSG00000143127	ENST00000369304;ENST00000543043;ENST00000539363;ENST00000538811	T;T;T	0.78481	-1.18;-1.18;-1.18	5.16	1.57	0.23409	Integrin alpha-2 (1);	0.000000	0.85682	D	0.000000	T	0.75428	0.3848	L	0.55213	1.73	0.41709	D	0.989441	D;D;D;D	0.89917	1.0;0.985;0.991;1.0	D;D;P;D	0.81914	0.987;0.918;0.901;0.995	T	0.75714	-0.3221	10	0.87932	D	0	.	5.9093	0.19018	0.0:0.3292:0.0:0.6708	.	714;617;605;748	F5H3T9;F5GY13;B2RTV5;O75578	.;.;.;ITA10_HUMAN	E	748;714;605;617	ENSP00000358310:D748E;ENSP00000439894:D605E;ENSP00000440011:D617E	ENSP00000358310:D748E	D	+	3	2	ITGA10	144248221	1.000000	0.71417	1.000000	0.80357	0.643000	0.38383	0.925000	0.28791	0.446000	0.26666	0.374000	0.22700	GAT	.	.	.	none		0.468	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637		G	145536864	T	G	145536864	3	3	23	1	0	0	0	0	1	0	0	0	7880	1490	52	5	2314	5	ITGA10	1	145536864	Missense_Mutation	SNP	T	TCGA-2Z-A9JT-01A-11D-A42J-10	25601602	145536864	103713757	4	1580											
TOR1AIP2	163590	hgsc.bcm.edu	37	chr1	179834169	179834169	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caggataacactcaggacaaTaatcagctctgttaatacgg	15	9	8	9	1	3	0	2	0	1	0	3	2	3	2	0	3	3	2	0	3	5	4			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr1:179834169T>C	ENST00000553856.1	-	1	142	c.143A>G	c.(142-144)tAt>tGt	p.Y48C	TOR1AIP2_ENST00000367612.3_Intron|TOR1AIP2_ENST00000609928.1_Intron|TOR1AIP2_ENST00000482587.1_5'UTR	NM_022347.3	NP_071742.1	Q9H496	IFG15_HUMAN		48																	CTCAGGACAATAATCAGCTCT	0.433																																					p.Y48C		Atlas-SNP	.											.	TOR1AIP2	38	.	0			c.A143G						PASS	.						174	171	172					1																	179834169		1888	4104	5992	SO:0001583	missense	163590	exon3			GGACAATAATCAG																												ENST00000553856.1:c.143A>G	chr1.hg19:g.179834169T>C	ENSP00000452581:p.Tyr48Cys	391.0	0.0	.		356.0	108.0	.	NM_022347	Q05BU2	Missense_Mutation	SNP	ENST00000553856.1	hg19	CCDS53439.1	.	.	.	.	.	.	.	.	.	.	T	12.59	1.984540	0.35036	.	.	ENSG00000258664	ENST00000553856	.	.	.	4.79	4.79	0.61399	.	.	.	.	.	T	0.48572	0.1507	N	0.08118	0	0.80722	D	1	D	0.71674	0.998	D	0.69824	0.966	T	0.46303	-0.9201	7	.	.	.	.	11.0179	0.47701	0.0:0.0:0.0:1.0	.	48	Q9H496	.	C	48	.	.	Y	-	2	0	AL359853.3	178100792	1.000000	0.71417	0.999000	0.59377	0.975000	0.68041	2.978000	0.49305	2.371000	0.80710	0.533000	0.62120	TAT	.	.	.	none		0.433	IFRG15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	179834169	T	C	179834169	3	2	23	1	0	0	0	0	1	0	0	0	16385	1406	49	3	1685	3	TOR1AIP2	1	179834169	Missense_Mutation	SNP	T	TCGA-2Z-A9JT-01A-11D-A42J-10	34297305	179834169	69416452	5	1581											
MR1	3140	hgsc.bcm.edu	37	chr1	181021439	181021439	+	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	cagctctcttctgcaaagctCatggcttttaccccccagaa	9	11	6	15	0	3	1	1	0	2	1	4	1	3	1	3	1	4	4	3	1	3	3			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr1:181021439C>T	ENST00000367580.5	+	4	678	c.673C>T	c.(673-675)Cat>Tat	p.H225Y	MR1_ENST00000282990.6_Intron|MR1_ENST00000434571.2_Intron|MR1_ENST00000438435.2_Intron|MR1_ENST00000367579.3_Missense_Mutation_p.H180Y	NM_001531.2	NP_001522.1	Q95460	HMR1_HUMAN	major histocompatibility complex, class I-related	225	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	MHC class I receptor activity (GO:0032393)|peptide antigen binding (GO:0042605)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	18					Antithymocyte globulin(DB00098)	CTGCAAAGCTCATGGCTTTTA	0.428																																					p.H225Y	Colon(174;1412 1962 45296 46549 47110)	Atlas-SNP	.											.	MR1	46	.	0			c.C673T						PASS	.						55	56	56					1																	181021439		2203	4300	6503	SO:0001583	missense	3140	exon5			AAAGCTCATGGCT	AF010446	CCDS1342.1, CCDS53440.1, CCDS53441.1, CCDS53442.1	1q25.3	2013-01-11	2003-03-05	2003-03-07	ENSG00000153029	ENSG00000153029		"Immunoglobulin superfamily / C1-set domain containing"	4975	protein-coding gene	gene with protein product		600764	"major histocompatibility complex, class I-like sequence"	HLALS		7624800, 9784382	Standard	NM_001194999		Approved		uc001goq.2	Q95460	OTTHUMG00000035175	ENST00000367580.5:c.673C>T	chr1.hg19:g.181021439C>T	ENSP00000356552:p.His225Tyr	114.0	0.0	.		87.0	23.0	.	NM_001531	A8K2V9|B4E3B1|O97985|O97986|Q53GM1|Q95HB8|Q9MY23|Q9NPL2|Q9TQB3|Q9TQB9|Q9TQK3	Missense_Mutation	SNP	ENST00000367580.5	hg19	CCDS1342.1	.	.	.	.	.	.	.	.	.	.	C	8.090	0.774344	0.16051	.	.	ENSG00000153029	ENST00000367580;ENST00000367579	T;T	0.02737	4.18;4.18	4.52	-2.19	0.07015	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.629307	0.14989	N	0.286793	T	0.01454	0.0047	N	0.03029	-0.43	0.47476	D	0.999438	B;B	0.02656	0.0;0.0	B;B	0.08055	0.002;0.003	T	0.51004	-0.8760	10	0.87932	D	0	.	10.6879	0.45854	0.0:0.3901:0.0:0.6099	.	180;225	Q95460-2;Q95460	.;HMR1_HUMAN	Y	225;180	ENSP00000356552:H225Y;ENSP00000356551:H180Y	ENSP00000356551:H180Y	H	+	1	0	MR1	179288062	0.021000	0.18746	0.881000	0.34555	0.754000	0.42855	-0.563000	0.05943	-0.583000	0.05921	-1.731000	0.00696	CAT	.	.	.	none		0.428	MR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085134.2	NM_001531		T	181021439	C	T	181021439	3	4	23	1	0	0	0	0	1	0	0	0	9759	826	29	2	687	2	MR1	1	181021439	Missense_Mutation	SNP	C	TCGA-2Z-A9JT-01A-11D-A42J-10	1187270	181021439	68229182	6	1582											
PRKD3	23683	hgsc.bcm.edu	37	chr2	37501808	37501808	+	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	tttgtgaaatctcgtggtgaAgatatgcggagaatttctga	11	14	12	4	2	2	5	0	3	2	2	3	6	2	5	0	2	1	0	0	2	4	3			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr2:37501808A>T	ENST00000379066.1	-	11	2169	c.1407T>A	c.(1405-1407)tcT>tcA	p.S469S	PRKD3_ENST00000234179.2_Silent_p.S469S			O94806	KPCD3_HUMAN	protein kinase D3	469	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)				CTCGTGGTGAAGATATGCGGA	0.323																																					p.S469S	Melanoma(80;621 1355 8613 11814 51767)	Atlas-SNP	.											.	PRKD3	170	.	0			c.T1407A						PASS	.						59	56	57					2																	37501808		2203	4300	6503	SO:0001819	synonymous_variant	23683	exon10			TGGTGAAGATATG	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.1407T>A	chr2.hg19:g.37501808A>T		101.0	0.0	.		93.0	26.0	.	NM_005813	D6W587|Q53TR7|Q8NEL8	Silent	SNP	ENST00000379066.1	hg19	CCDS1789.1																																																																																			.	.	.	none		0.323	PRKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218570.3	NM_005813		T	37501808	A	T	37501808	2	4	23	1	0	0	0	0	0	0	0	1	12530	59	3	5		5	PRKD3	2	37501808	Silent	SNP	A	TCGA-2Z-A9JT-01A-11D-A42J-10		37501808	205697565	7	1583											
ADD2	119	hgsc.bcm.edu	37	chr2	70931469	70931469	+	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	atactcatggaagatgtcggGaagactgcgtgggaggtgct	10	9	16	6	2	1	2	1	0	0	2	2	5	1	5	0	4	3	1	0	4	3	1			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr2:70931469G>A	ENST00000264436.4	-	4	750	c.306C>T	c.(304-306)ttC>ttT	p.F102F	ADD2_ENST00000413157.2_Silent_p.F102F|ADD2_ENST00000407644.2_Silent_p.F102F|ADD2_ENST00000355733.3_Silent_p.F102F|ADD2_ENST00000473232.1_5'Flank|ADD2_ENST00000430656.1_Silent_p.F118F	NM_001617.3	NP_001608.1	P35612	ADDB_HUMAN	adducin 2 (beta)	102					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						AAGATGTCGGGAAGACTGCGT	0.602																																					p.F118F		Atlas-SNP	.											.	ADD2	261	.	0			c.C354T						PASS	.						131	113	119					2																	70931469		2203	4300	6503	SO:0001819	synonymous_variant	119	exon3			TGTCGGGAAGACT	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.306C>T	chr2.hg19:g.70931469G>A		55.0	0.0	.		50.0	12.0	.	NM_001185055	A8K4P2|B4DM17|D6W5G7|D6W5G8|Q13482|Q16412|Q59G82|Q5U5P4|Q6P0P2|Q6PGQ4|Q7Z688|Q7Z689|Q7Z690|Q7Z691	Silent	SNP	ENST00000264436.4	hg19	CCDS1906.1																																																																																			.	.	.	none		0.602	ADD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251918.4	NM_001617		A	70931469	G	A	70931469	2	1	23	1	0	0	0	0	0	0	0	1	305	1165	41	2		2	ADD2	2	70931469	Silent	SNP	G	TCGA-2Z-A9JT-01A-11D-A42J-10	33429661	70931469	172267904	8	1584											
CNNM4	26504	hgsc.bcm.edu	37	chr2	97428100	97428100	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgcactttgtcttccatgAcaccaagttggatgccatgc	8	12	10	11	0	1	1	0	1	1	0	2	2	2	2	3	2	3	2	3	2	1	3			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr2:97428100A>G	ENST00000377075.2	+	1	1462	c.1364A>G	c.(1363-1365)gAc>gGc	p.D455G		NM_020184.3	NP_064569.3	Q6P4Q7	CNNM4_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 4	455	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.				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						GTCTTCCATGACACCAAGTTG	0.527																																					p.D455G		Atlas-SNP	.											.	CNNM4	48	.	0			c.A1364G						PASS	.						103	98	100					2																	97428100		2203	4300	6503	SO:0001583	missense	26504	exon1			TCCATGACACCAA	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.1364A>G	chr2.hg19:g.97428100A>G	ENSP00000366275:p.Asp455Gly	188.0	0.0	.		161.0	48.0	.	NM_020184	B7Z1U0|C7SQM3|C7SQM4|C7SQM5|Q53RE5|Q9H9G3|Q9HCI0|Q9NRN1	Missense_Mutation	SNP	ENST00000377075.2	hg19	CCDS2024.2	.	.	.	.	.	.	.	.	.	.	A	16.78	3.216564	0.58452	.	.	ENSG00000158158	ENST00000377075	D	0.95137	-3.62	5.26	5.26	0.73747	Cystathionine beta-synthase, core (2);	0.000000	0.85682	D	0.000000	D	0.95705	0.8603	L	0.42529	1.33	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96259	0.9189	10	0.87932	D	0	-14.3599	14.1805	0.65572	1.0:0.0:0.0:0.0	.	455	Q6P4Q7	CNNM4_HUMAN	G	455	ENSP00000366275:D455G	ENSP00000366275:D455G	D	+	2	0	CNNM4	96791827	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.281000	0.95811	1.996000	0.58369	0.533000	0.62120	GAC	.	.	.	none		0.527	CNNM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252954.1	NM_020184		G	97428100	A	G	97428100	3	3	23	1	0	0	0	0	1	0	0	0	3617	275	10	3	1366	3	CNNM4	2	97428100	Missense_Mutation	SNP	A	TCGA-2Z-A9JT-01A-11D-A42J-10	26496631	97428100	145771273	9	1585											
MRPS9	64965	hgsc.bcm.edu	37	chr2	105654555	105654555	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctcccacagctaacatggCggcgccctgtgtgtcctacg	7	8	11	15	3	0	0	0	0	0	0	2	0	2	0	3	2	4	2	3	2	2	2	rs149402894	byFrequency	TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr2:105654555C>T	ENST00000258455.3	+	1	115	c.5C>T	c.(4-6)gCg>gTg	p.A2V	AC010884.1_ENST00000456519.1_RNA	NM_182640.2	NP_872578.1	P82933	RT09_HUMAN	mitochondrial ribosomal protein S9	2					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						GCTAACATGGCGGCGCCCTGT	0.677													C|||	3	0.000599042	0	0.0014	5008	,	,		14716	0		0	False		,,,				2504	0.002				p.A2V		Atlas-SNP	.											.	MRPS9	32	.	0			c.C5T						PASS	.	C	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	30	30	30		5	3.9	1	2	dbSNP_134	30	4,8596	3.7+/-12.6	0,4,4296	yes	missense	MRPS9	NM_182640.2	64	0,5,6498	TT,TC,CC		0.0465,0.0227,0.0384	probably-damaging	2/397	105654555	5,13001	2203	4300	6503	SO:0001583	missense	64965	exon1			ACATGGCGGCGCC		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.5C>T	chr2.hg19:g.105654555C>T	ENSP00000258455:p.Ala2Val	122.0	0.0	.		105.0	30.0	.	NM_182640	Q6PG40	Missense_Mutation	SNP	ENST00000258455.3	hg19	CCDS2065.1	.	.	.	.	.	.	.	.	.	.	C	13.32	2.203247	0.38905	2.27E-4	4.65E-4	ENSG00000135972	ENST00000258455	T	0.52754	0.65	4.82	3.94	0.45596	.	0.062495	0.64402	N	0.000007	T	0.45597	0.1350	M	0.79475	2.455	0.41050	D	0.985296	B	0.29232	0.238	B	0.17979	0.02	T	0.52208	-0.8606	10	0.72032	D	0.01	-16.2181	9.4342	0.38628	0.0:0.9023:0.0:0.0977	.	2	P82933	RT09_HUMAN	V	2	ENSP00000258455:A2V	ENSP00000258455:A2V	A	+	2	0	MRPS9	105020987	1.000000	0.71417	0.998000	0.56505	0.265000	0.26407	1.884000	0.39668	1.376000	0.46267	0.655000	0.94253	GCG	.	C|1.000;T|0.000	0.000	weak		0.677	MRPS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253352.1	NM_182640		T	105654555	C	T	105654555	3	4	23	1	0	0	0	0	1	0	0	0	9856	768	27	1	7	1	MRPS9	2	105654555	Missense_Mutation	SNP	C	TCGA-2Z-A9JT-01A-11D-A42J-10	8226455	105654555	137544818	10	1586											
SAP130	79595	hgsc.bcm.edu	37	chr2	128774008	128774008	+	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	ggaatggctgaagcttgaggGatgctactctccatggtaac	10	10	13	8	0	1	2	0	2	1	0	2	4	1	4	1	4	4	4	1	4	4	3			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr2:128774008G>T	ENST00000259235.3	-	4	669	c.540C>A	c.(538-540)atC>atA	p.I180I	SAP130_ENST00000357702.5_Silent_p.I180I|SAP130_ENST00000259234.6_Silent_p.I154I	NM_024545.3	NP_078821.2	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa	180					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)		AAGCTTGAGGGATGCTACTCT	0.493																																					p.I180I		Atlas-SNP	.											.	SAP130	169	.	0			c.C540A						PASS	.						128	120	123					2																	128774008		2203	4300	6503	SO:0001819	synonymous_variant	79595	exon4			TTGAGGGATGCTA	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.540C>A	chr2.hg19:g.128774008G>T		146.0	0.0	.		132.0	32.0	.	NM_001145928	B7ZLM3|C9K0X9|Q4ZFV4|Q53T46|Q8WVW4|Q9H9G8	Silent	SNP	ENST00000259235.3	hg19	CCDS2153.1																																																																																			.	.	.	none		0.493	SAP130-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254436.3	NM_024545		T	128774008	G	T	128774008	2	4	23	1	0	0	0	0	0	0	0	1	13844	1164	41	4		4	SAP130	2	128774008	Silent	SNP	G	TCGA-2Z-A9JT-01A-11D-A42J-10	23119453	128774008	114425365	11	1587											
LRP2	4036	hgsc.bcm.edu	37	chr2	170063527	170063532	+	In_Frame_Del	DEL	TGACAA	TGACAA	-																															cactgccaagccccgtggtgTgacaatgccctctgacacaa																										TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	TGACAA	TGACAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr2:170063527_170063532delTGACAA	ENST00000263816.3	-	39	6983_6988	c.6698_6703delTTGTCA	c.(6697-6705)attgtcaca>aca	p.IV2233del		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2233					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)"	CCCCGTGGTGTGACAATGCCCTCTGA	0.461																																					p.2233_2235del		Atlas-Indel,Pindel	.											.	LRP2	751	.	0			c.6699_6704del						PASS	.																																			SO:0001651	inframe_deletion	4036	exon39			.		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.6698_6703delTTGTCA	chr2.hg19:g.170063527_170063532delTGACAA	ENSP00000263816:p.Ile2233_Val2234del	121.0	0.0	0		146.0	34.0	0.232877	NM_004525	O00711|Q16215	In_Frame_Del	DEL	ENST00000263816.3	hg19	CCDS2232.1																																																																																			.	.	.	none		0.461	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		-	170063532	TGACAA	-	170063527	7	5	23	1	0	1	0	1	0	0	0	0	8963	1696	59	0	7428	0	LRP2	2	170063527	In_Frame_Del	DEL	TGACAA	TCGA-2Z-A9JT-01A-11D-A42J-10	41289519	170063527	73135846	12	1588											
MST1	327	hgsc.bcm.edu	37	chr3	49723551	49723551	+	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	ggtagcaaaaggccgcgcgcAtgccgggccgcagtgtgaag	9	4	17	11	5	0	1	0	1	0	0	0	1	0	1	3	3	2	4	3	3	4	1	rs199957562		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr3:49723551A>G	ENST00000296456.5	+	0	3220				MST1_ENST00000449682.2_Missense_Mutation_p.M364T|AC099668.5_ENST00000563780.1_RNA|MST1_ENST00000494828.2_5'Flank|MST1_ENST00000383728.3_3'UTR	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)	p.M350T(3)		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)		GGCCGCGCGCATGCCGGGCCG	0.667																																					p.M364T		Atlas-SNP	.											MST1,cerebellum,glioma,0,4	MST1	84	.	3	Substitution - Missense(3)	NS(2)|skin(1)	c.T1091C						PASS	.						13	16	15					3																	49723551		2196	4289	6485	SO:0001628	intergenic_variant	4485	exon9			GCGCGCATGCCGG	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"acylaminoacyl-peptidase"	102645	"N-acylaminoacyl-peptide hydrolase"	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		chr3.hg19:g.49723551A>G		91.0	0.0	.		67.0	4.0	.	NM_020998	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	hg19	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	A	15.79	2.937159	0.52972	.	.	ENSG00000173531	ENST00000449682	T	0.61510	0.1	5.4	4.17	0.49024	.	0.132069	0.34338	N	0.004055	T	0.35508	0.0934	N	0.04805	-0.155	0.80722	D	1	B	0.09022	0.002	B	0.17979	0.02	T	0.24083	-1.0170	10	0.51188	T	0.08	.	10.9733	0.47450	0.86:0.0:0.0:0.14	.	364	G3XAK1	.	T	364	ENSP00000414287:M364T	ENSP00000414287:M364T	M	-	2	0	MST1	49698555	1.000000	0.71417	0.995000	0.50966	0.875000	0.50365	7.395000	0.79876	2.042000	0.60477	0.533000	0.62120	ATG	.	.	.	weak		0.667	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			G	49723551	A	G	49723551	1	3	23	0	1	0	0	0	0	0	0	0	9897	217	8	3		3	MST1	3	49723551	IGR	SNP	A	TCGA-2Z-A9JT-01A-11D-A42J-10		49723551	148298879	13	1589											
MAGI1	9223	hgsc.bcm.edu	37	chr3	65425621	65425622	+	Frame_Shift_Del	DEL	CT	CT	-																															tgttgctgctgctgctgctgCtcaagctgcttcttccgttt																										TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr3:65425621_65425622delCT	ENST00000497477.2	-	9	1201_1202	c.1202_1203delAG	c.(1201-1203)gagfs	p.E401fs	MAGI1_ENST00000402939.2_Frame_Shift_Del_p.E401fs|MAGI1_ENST00000330909.8_Frame_Shift_Del_p.E401fs|MAGI1_ENST00000470990.1_5'UTR|MAGI1_ENST00000483466.1_Frame_Shift_Del_p.E401fs			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	401					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)		gctgctgctgctCAAGCTGCTT	0.505											OREG0015658	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.401_402del		Atlas-INDEL	.											.	MAGI1	481	.	0			c.1203_1204del						PASS	.																																			SO:0001589	frameshift_variant	9223	exon9			.	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.1202_1203delAG	chr3.hg19:g.65425621_65425622delCT	ENSP00000424369:p.Glu401fs	28.0	0.0	0	1084	24.0	12.0	0.5	NM_001033057	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Frame_Shift_Del	DEL	ENST00000497477.2	hg19																																																																																				.	.	.	none		0.505	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742		-	65425622	CT	-	65425621	7	5	23	1	0	1	0	1	0	0	0	0	9197	796	28	0	3479	0	MAGI1	3	65425621	Frame_Shift_Del	DEL	CT	TCGA-2Z-A9JT-01A-11D-A42J-10	15702070	65425621	132596809	14	1590											
SKIL	6498	hgsc.bcm.edu	37	chr3	170079027	170079027	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatgtttgcaccccagacgtTtgtgatgcattctcacagat	10	13	8	10	1	1	3	1	1	1	2	2	3	1	3	2	0	2	4	2	0	1	3			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr3:170079027T>C	ENST00000458537.3	+	1	1617	c.908T>C	c.(907-909)tTt>tCt	p.F303S	SKIL_ENST00000426052.2_Missense_Mutation_p.F283S|SKIL_ENST00000413427.2_Missense_Mutation_p.F303S|SKIL_ENST00000259119.4_Missense_Mutation_p.F303S	NM_001145097.2|NM_001248008.1|NM_005414.4	NP_001138569.1|NP_001234937.1|NP_005405.2	P12757	SKIL_HUMAN	SKI-like proto-oncogene	303					blastocyst formation (GO:0001825)|cell cycle arrest (GO:0007050)|gene expression (GO:0010467)|lens fiber cell differentiation (GO:0070306)|lymphocyte homeostasis (GO:0002260)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of axonogenesis (GO:0050772)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|protein heterotrimerization (GO:0070208)|protein homotrimerization (GO:0070207)|regulation of apoptotic process (GO:0042981)|response to antibiotic (GO:0046677)|response to cytokine (GO:0034097)|response to growth factor (GO:0070848)|skeletal muscle tissue development (GO:0007519)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|protein complex binding (GO:0032403)|protein domain specific binding (GO:0019904)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	25	all_cancers(22;7.13e-23)|all_epithelial(15;9.95e-28)|all_lung(20;1.23e-16)|Lung NSC(18;5.15e-16)|Ovarian(172;0.000337)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			CCCCAGACGTTTGTGATGCAT	0.433																																					p.F303S		Atlas-SNP	.											.	SKIL	67	.	0			c.T908C						PASS	.						137	131	133					3																	170079027		2203	4300	6503	SO:0001583	missense	6498	exon1			AGACGTTTGTGAT	X15217	CCDS33890.1, CCDS46953.1, CCDS46954.1	3q26	2014-06-25	2014-06-25		ENSG00000136603	ENSG00000136603		"SKI transcriptional corepressors"	10897	protein-coding gene	gene with protein product		165340	"SKI-like oncogene"			2762147	Standard	NM_005414		Approved	SNO, SnoN, SnoA	uc003fgw.3	P12757	OTTHUMG00000158831	ENST00000458537.3:c.908T>C	chr3.hg19:g.170079027T>C	ENSP00000415243:p.Phe303Ser	105.0	0.0	.		113.0	35.0	.	NM_001248008	A6NGT1|B4DT50|O00464|P12756|Q07501	Missense_Mutation	SNP	ENST00000458537.3	hg19	CCDS33890.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.544136	0.86022	.	.	ENSG00000136603	ENST00000259119;ENST00000426052;ENST00000413427;ENST00000458537	D;D;D;D	0.97994	-4.65;-4.64;-4.58;-4.65	5.83	5.83	0.93111	SAND domain-like (2);c-SKI Smad4-binding (1);	0.045464	0.85682	D	0.000000	D	0.98773	0.9587	M	0.85197	2.74	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.99826	1.1050	10	0.87932	D	0	-22.9726	16.2481	0.82460	0.0:0.0:0.0:1.0	.	303;303	P12757-3;P12757	.;SKIL_HUMAN	S	303;283;303;303	ENSP00000259119:F303S;ENSP00000406520:F283S;ENSP00000400193:F303S;ENSP00000415243:F303S	ENSP00000259119:F303S	F	+	2	0	SKIL	171561721	1.000000	0.71417	0.998000	0.56505	0.949000	0.60115	7.698000	0.84413	2.241000	0.73720	0.524000	0.50904	TTT	.	.	.	none		0.433	SKIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352351.4	NM_005414		C	170079027	T	C	170079027	3	2	23	1	0	0	0	0	1	0	0	0	14371	1841	64	3	910	3	SKIL	3	170079027	Missense_Mutation	SNP	T	TCGA-2Z-A9JT-01A-11D-A42J-10	104653406	170079027	27943403	15	1591											
FAM131A	131408	hgsc.bcm.edu	37	chr3	184062561	184062561	+	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	gcctgggcccactggaggccCaggactcactctacaactcg	8	6	11	16	1	2	0	1	0	1	0	3	2	2	2	3	4	2	0	3	4	2	1			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr3:184062561C>G	ENST00000310585.4	+	3	2175	c.811C>G	c.(811-813)Cag>Gag	p.Q271E	FAM131A_ENST00000418281.1_Missense_Mutation_p.Q179E|FAM131A_ENST00000340957.5_Missense_Mutation_p.Q217E|FAM131A_ENST00000453072.1_Missense_Mutation_p.Q217E|FAM131A_ENST00000450976.1_Missense_Mutation_p.Q217E|FAM131A_ENST00000383847.2_Missense_Mutation_p.Q302E|EIF2B5_ENST00000444495.1_Intron			Q6UXB0	F131A_HUMAN	family with sequence similarity 131, member A	271						extracellular region (GO:0005576)				breast(1)|endometrium(1)|large_intestine(2)|lung(9)|skin(1)	14	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			ACTGGAGGCCCAGGACTCACT	0.687																																					p.Q302E		Atlas-SNP	.											.	FAM131A	37	.	0			c.C904G						PASS	.						43	53	49					3																	184062561		2202	4299	6501	SO:0001583	missense	131408	exon6			GAGGCCCAGGACT	BC026221	CCDS3262.1, CCDS3262.2, CCDS54689.1	3q27.1	2007-03-20	2007-03-20	2007-03-20	ENSG00000175182	ENSG00000175182			28308	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 40"	C3orf40		12975309	Standard	NM_144635		Approved	MGC21688	uc003foe.3	Q6UXB0	OTTHUMG00000156206	ENST00000310585.4:c.811C>G	chr3.hg19:g.184062561C>G	ENSP00000310135:p.Gln271Glu	71.0	0.0	.		74.0	19.0	.	NM_144635	D3DNT6|G5E9B1|Q8TA84	Missense_Mutation	SNP	ENST00000310585.4	hg19		.	.	.	.	.	.	.	.	.	.	c	4.836	0.155381	0.09236	.	.	ENSG00000175182	ENST00000450976;ENST00000418281;ENST00000340957;ENST00000418768;ENST00000383847;ENST00000453072;ENST00000310585	T;T;T;T;T;T;T	0.20463	2.07;2.07;2.07;2.07;2.07;2.07;2.07	4.73	4.73	0.59995	.	0.719434	0.14165	N	0.337106	T	0.12347	0.0300	N	0.22421	0.69	0.34151	D	0.667488	B;B;P	0.38250	0.017;0.035;0.624	B;B;B	0.33960	0.013;0.027;0.173	T	0.03619	-1.1019	10	0.06494	T	0.89	-22.0175	13.4502	0.61167	0.0:0.8428:0.1572:0.0	.	271;302;179	Q6UXB0;G5E9B1;C9JPT9	F131A_HUMAN;.;.	E	217;179;217;217;302;217;271	ENSP00000388551:Q217E;ENSP00000414050:Q179E;ENSP00000340974:Q217E;ENSP00000414913:Q217E;ENSP00000373360:Q302E;ENSP00000390588:Q217E;ENSP00000310135:Q271E	ENSP00000310135:Q271E	Q	+	1	0	FAM131A	185545255	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.805000	0.55575	2.170000	0.68504	0.655000	0.94253	CAG	.	.	.	none		0.687	FAM131A-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000343462.1	NM_144635		G	184062561	C	G	184062561	3	3	23	1	0	0	0	0	1	0	0	0	5443	595	21	4	926	4	FAM131A	3	184062561	Missense_Mutation	SNP	C	TCGA-2Z-A9JT-01A-11D-A42J-10	13983534	184062561	13959869	16	1592											
HGFAC	3083	hgsc.bcm.edu	37	chr4	3446365	3446365	+	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	cccagcttgtctgagcagccCttgcctgaacgggggcacct	6	8	12	15	1	1	2	0	2	1	0	1	2	1	2	4	2	5	3	4	2	1	2			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr4:3446365C>A	ENST00000382774.3	+	7	861	c.746C>A	c.(745-747)cCt>cAt	p.P249H	HGFAC_ENST00000511533.1_Missense_Mutation_p.P249H	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	249	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		CTGAGCAGCCCTTGCCTGAAC	0.716																																					p.P249H		Atlas-SNP	.											.	HGFAC	69	.	0			c.C746A						PASS	.						14	16	15					4																	3446365		2187	4281	6468	SO:0001583	missense	3083	exon7			GCAGCCCTTGCCT	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.746C>A	chr4.hg19:g.3446365C>A	ENSP00000372224:p.Pro249His	85.0	0.0	.		61.0	11.0	.	NM_001528	Q14726|Q2M1W7|Q53X47	Missense_Mutation	SNP	ENST00000382774.3	hg19	CCDS3369.1	.	.	.	.	.	.	.	.	.	.	C	16.93	3.258728	0.59321	.	.	ENSG00000109758	ENST00000382774;ENST00000511533	D;D	0.95171	-3.63;-3.63	3.44	2.59	0.31030	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.96744	0.8937	M	0.89478	3.035	0.43617	D	0.995997	D;D	0.89917	1.0;0.959	D;P	0.79784	0.993;0.772	D	0.95496	0.8573	10	0.87932	D	0	.	6.5776	0.22575	0.0:0.8626:0.0:0.1374	.	249;249	D6RAR4;Q04756	.;HGFA_HUMAN	H	249	ENSP00000372224:P249H;ENSP00000421801:P249H	ENSP00000372224:P249H	P	+	2	0	HGFAC	3416163	0.002000	0.14202	0.962000	0.40283	0.793000	0.44817	0.145000	0.16157	0.782000	0.33613	0.462000	0.41574	CCT	.	.	.	none		0.716	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3			A	3446365	C	A	3446365	3	1	23	1	0	0	0	0	1	0	0	0	7093	681	24	4	772	4	HGFAC	4	3446365	Missense_Mutation	SNP	C	TCGA-2Z-A9JT-01A-11D-A42J-10		3446365	187707911	17	1593											
LRRC66	339977	hgsc.bcm.edu	37	chr4	52861855	52861855	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaggcttagatgaggaaataCttggcgcagatgggtctctg	10	10	15	6	1	1	3	0	1	1	2	2	5	1	4	0	4	1	2	0	4	3	3			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr4:52861855C>T	ENST00000343457.3	-	4	1339	c.1333G>A	c.(1333-1335)Gta>Ata	p.V445I		NM_001024611.1	NP_001019782.1	Q68CR7	LRC66_HUMAN	leucine rich repeat containing 66	445						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						TGAGGAAATACTTGGCGCAGA	0.552																																					p.V445I		Atlas-SNP	.											.	LRRC66	128	.	0			c.G1333A						PASS	.						100	106	104					4																	52861855		2046	4191	6237	SO:0001583	missense	339977	exon4			GAAATACTTGGCG	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.1333G>A	chr4.hg19:g.52861855C>T	ENSP00000341944:p.Val445Ile	64.0	0.0	.		55.0	15.0	.	NM_001024611		Missense_Mutation	SNP	ENST00000343457.3	hg19	CCDS43229.1	.	.	.	.	.	.	.	.	.	.	C	10.40	1.339748	0.24339	.	.	ENSG00000188993	ENST00000343457	T	0.45276	0.9	3.89	-2.63	0.06133	.	1.981150	0.02460	N	0.086453	T	0.20618	0.0496	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.10450	0.005	T	0.06917	-1.0800	10	0.37606	T	0.19	4.8277	1.4223	0.02314	0.1424:0.2988:0.1409:0.4179	.	445	Q68CR7	LRC66_HUMAN	I	445	ENSP00000341944:V445I	ENSP00000341944:V445I	V	-	1	0	LRRC66	52556612	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-0.354000	0.07681	-0.779000	0.04560	0.467000	0.42956	GTA	.	.	.	none		0.552	LRRC66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361473.1	NM_001024611		T	52861855	C	T	52861855	3	4	23	1	0	0	0	0	1	0	0	0	9025	565	20	2	1313	2	LRRC66	4	52861855	Missense_Mutation	SNP	C	TCGA-2Z-A9JT-01A-11D-A42J-10	49415490	52861855	138292421	18	1594											
WDFY3	23001	hgsc.bcm.edu	37	chr4	85642588	85642588	+	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	tccttcctctaacaggcgcaGtaaggtagcattatctgttt	9	14	8	10	1	2	0	0	0	2	0	4	0	4	0	2	2	2	5	2	2	4	6			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr4:85642588G>T	ENST00000295888.4	-	47	7986	c.7579C>A	c.(7579-7581)Ctg>Atg	p.L2527M	WDFY3_ENST00000322366.6_Missense_Mutation_p.L2510M	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	2527	Sufficient for translocalization to p62 bodies/ALIS.				aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		AACAGGCGCAGTAAGGTAGCA	0.428																																					p.L2527M		Atlas-SNP	.											WDFY3,NS,carcinoma,0,1	WDFY3	314	.	0			c.C7579A						PASS	.						211	196	201					4																	85642588		2203	4300	6503	SO:0001583	missense	23001	exon47			GGCGCAGTAAGGT	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.7579C>A	chr4.hg19:g.85642588G>T	ENSP00000295888:p.Leu2527Met	47.0	0.0	.		32.0	7.0	.	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	hg19	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	G	18.08	3.544984	0.65198	.	.	ENSG00000163625	ENST00000322366;ENST00000295888;ENST00000514711	T;T;T	0.67171	-0.25;-0.23;-0.22	5.77	4.93	0.64822	.	0.000000	0.85682	D	0.000000	T	0.59905	0.2228	N	0.24115	0.695	0.80722	D	1	D	0.59357	0.985	P	0.49887	0.625	T	0.57057	-0.7876	10	0.21540	T	0.41	.	15.2503	0.73539	0.0676:0.0:0.9324:0.0	.	2527	Q8IZQ1	WDFY3_HUMAN	M	2510;2527;130	ENSP00000318466:L2510M;ENSP00000295888:L2527M;ENSP00000424987:L130M	ENSP00000295888:L2527M	L	-	1	2	WDFY3	85861612	1.000000	0.71417	0.908000	0.35775	0.810000	0.45777	6.376000	0.73141	1.585000	0.49928	0.585000	0.79938	CTG	.	.	.	none		0.428	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		T	85642588	G	T	85642588	3	4	23	1	0	0	0	0	1	0	0	0	17282	1020	36	4	3089	4	WDFY3	4	85642588	Missense_Mutation	SNP	G	TCGA-2Z-A9JT-01A-11D-A42J-10	32780733	85642588	105511688	19	1595											
SLC38A9	153129	hgsc.bcm.edu	37	chr5	54965109	54965109	+	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	agcaataaagtgttaaaaggCccatcagtatgatgacacac	17	8	8	8	0	1	2	1	2	0	0	1	2	1	2	1	1	1	3	1	1	6	3			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr5:54965109C>G	ENST00000396865.2	-	7	1064	c.473G>C	c.(472-474)gGc>gCc	p.G158A	SLC38A9_ENST00000539768.1_Missense_Mutation_p.G158A|SLC38A9_ENST00000512595.1_Missense_Mutation_p.G131A|SLC38A9_ENST00000416547.2_Missense_Mutation_p.G34A|SLC38A9_ENST00000318672.3_Missense_Mutation_p.G158A|SLC38A9_ENST00000515629.1_Missense_Mutation_p.G95A	NM_173514.3	NP_775785.2	Q8NBW4	S38A9_HUMAN	solute carrier family 38, member 9	158					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	8		Lung NSC(810;0.00122)|Prostate(74;0.0376)|Breast(144;0.181)				TGTTAAAAGGCCCATCAGTAT	0.328																																					p.G158A		Atlas-SNP	.											.	SLC38A9	50	.	0			c.G473C						PASS	.						187	190	189					5																	54965109		2203	4300	6503	SO:0001583	missense	153129	exon7			AAAAGGCCCATCA		CCDS3968.1, CCDS58947.1, CCDS58948.1, CCDS75243.1	5q11.2	2013-05-22			ENSG00000177058	ENSG00000177058		"Solute carriers"	26907	protein-coding gene	gene with protein product							Standard	NM_173514		Approved	FLJ90709	uc003jqf.3	Q8NBW4	OTTHUMG00000131189	ENST00000396865.2:c.473G>C	chr5.hg19:g.54965109C>G	ENSP00000380074:p.Gly158Ala	131.0	0.0	.		113.0	32.0	.	NM_173514	B3KXV1|B7Z7D0|Q0P5S0|Q6MZJ8	Missense_Mutation	SNP	ENST00000396865.2	hg19	CCDS3968.1	.	.	.	.	.	.	.	.	.	.	C	15.94	2.982358	0.53827	.	.	ENSG00000177058	ENST00000396865;ENST00000318672;ENST00000539768;ENST00000515629;ENST00000416547;ENST00000512595;ENST00000511233;ENST00000512208;ENST00000503817	T;T;T;T;T;T;T;T;T	0.02158	4.42;4.42;4.42;4.42;4.42;4.42;4.42;4.42;4.42	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.05686	0.0149	N	0.26130	0.795	0.80722	D	1	D;D	0.67145	0.957;0.996	P;D	0.72075	0.615;0.976	T	0.46582	-0.9181	10	0.02654	T	1	-18.6055	19.3048	0.94157	0.0:1.0:0.0:0.0	.	131;158	B3KXV1;Q8NBW4	.;S38A9_HUMAN	A	158;158;158;95;34;131;158;95;95	ENSP00000380074:G158A;ENSP00000316596:G158A;ENSP00000437771:G158A;ENSP00000420934:G95A;ENSP00000397429:G34A;ENSP00000427335:G131A;ENSP00000423219:G158A;ENSP00000426413:G95A;ENSP00000424918:G95A	ENSP00000316596:G158A	G	-	2	0	SLC38A9	55000866	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.065000	0.76727	2.622000	0.88805	0.650000	0.86243	GGC	.	.	.	none		0.328	SLC38A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253912.2	NM_173514		G	54965109	C	G	54965109	3	3	23	1	0	0	0	0	1	0	0	0	14624	739	26	4	1252	4	SLC38A9	5	54965109	Missense_Mutation	SNP	C	TCGA-2Z-A9JT-01A-11D-A42J-10		54965109	125950151	20	1596											
RASA1	5921	hgsc.bcm.edu	37	chr5	86665669	86665669	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtagttcagcactttagtgaAgaacattacatcttttactt	12	16	6	7	0	2	2	1	1	1	1	2	2	2	2	0	0	4	3	0	0	6	8			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr5:86665669A>G	ENST00000274376.6	+	12	2214	c.1650A>G	c.(1648-1650)gaA>gaG	p.E550E	RASA1_ENST00000456692.2_Silent_p.E373E|RASA1_ENST00000512763.1_Silent_p.E383E|RASA1_ENST00000506290.1_Silent_p.E384E	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	550	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)			NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		ACTTTAGTGAAGAACATTACA	0.303																																					p.E550E		Atlas-SNP	.											.	RASA1	213	.	0			c.A1650G						PASS	.						67	66	67					5																	86665669		2203	4297	6500	SO:0001819	synonymous_variant	5921	exon12			TAGTGAAGAACAT		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.1650A>G	chr5.hg19:g.86665669A>G		462.0	0.0	.		472.0	155.0	.	NM_002890	B2R6W3|Q9UDI1	Silent	SNP	ENST00000274376.6	hg19	CCDS34200.1																																																																																			.	.	.	none		0.303	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890		G	86665669	A	G	86665669	2	3	23	1	0	0	0	0	0	0	0	1	13073	69	3	3		3	RASA1	5	86665669	Silent	SNP	A	TCGA-2Z-A9JT-01A-11D-A42J-10	31700560	86665669	94249591	21	1597											
SEMA6A	57556	hgsc.bcm.edu	37	chr5	115782689	115782689	+	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	ggaagaggagtggtgcatttCcagccgcttgcttagaccgg	8	9	15	9	2	0	2	0	0	0	2	1	4	1	4	3	4	3	3	3	4	2	3			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr5:115782689C>G	ENST00000343348.6	-	19	3500	c.2713G>C	c.(2713-2715)Gaa>Caa	p.E905Q	SEMA6A_ENST00000282394.6_Missense_Mutation_p.E382Q|SEMA6A_ENST00000510263.1_Missense_Mutation_p.E905Q|CTB-118N6.3_ENST00000512128.1_RNA|CTB-118N6.3_ENST00000514214.1_RNA|CTB-118N6.3_ENST00000508424.1_RNA|SEMA6A_ENST00000257414.8_Missense_Mutation_p.E922Q|SEMA6A_ENST00000513137.1_Missense_Mutation_p.E332Q|CTB-118N6.3_ENST00000510682.1_RNA|SEMA6A_ENST00000503865.1_Missense_Mutation_p.E284Q|CTB-118N6.3_ENST00000508640.1_RNA	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	905					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)		TGGTGCATTTCCAGCCGCTTG	0.602																																					p.E905Q		Atlas-SNP	.											.	SEMA6A	93	.	0			c.G2713C						PASS	.						67	75	72					5																	115782689		1955	4151	6106	SO:0001583	missense	57556	exon19			GCATTTCCAGCCG	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.2713G>C	chr5.hg19:g.115782689C>G	ENSP00000345512:p.Glu905Gln	72.0	0.0	.		72.0	26.0	.	NM_020796	Q9P2H9	Missense_Mutation	SNP	ENST00000343348.6	hg19	CCDS47256.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.01|16.01	3.000846|3.000846	0.54254|0.54254	.|.	.|.	ENSG00000092421|ENSG00000092421	ENST00000343348;ENST00000257414;ENST00000513137;ENST00000282394;ENST00000503865;ENST00000510263|ENST00000515129	T;T;T;T;T;T|.	0.50813|.	2.14;2.16;0.73;2.57;0.75;2.14|.	5.22|5.22	5.22|5.22	0.72569|0.72569	.|.	0.531003|.	0.18032|.	N|.	0.153898|.	T|T	0.54870|0.54870	0.1885|0.1885	N|N	0.22421|0.22421	0.69|0.69	0.54753|0.54753	D|D	0.99998|0.99998	B;B;D;P;P;P|.	0.56746|.	0.241;0.376;0.977;0.592;0.856;0.787|.	B;B;P;P;P;P|.	0.52514|.	0.192;0.23;0.701;0.479;0.464;0.479|.	T|T	0.50406|0.50406	-0.8832|-0.8832	10|5	0.51188|.	T|.	0.08|.	.|.	18.3652|18.3652	0.90388|0.90388	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	284;905;449;922;382;332|.	E9PDV9;Q9H2E6;Q96SM8;Q9H2E6-2;E7ERF3;B3KU01|.	.;SEM6A_HUMAN;.;.;.;.|.	Q|C	905;922;332;382;284;905|419	ENSP00000345512:E905Q;ENSP00000257414:E922Q;ENSP00000422997:E332Q;ENSP00000282394:E382Q;ENSP00000425364:E284Q;ENSP00000424388:E905Q|.	ENSP00000257414:E922Q|.	E|W	-|-	1|3	0|0	SEMA6A|SEMA6A	115810588|115810588	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.881000|0.881000	0.50899|0.50899	7.443000|7.443000	0.80521|0.80521	2.436000|2.436000	0.82500|0.82500	0.563000|0.563000	0.77884|0.77884	GAA|TGG	.	.	.	none		0.602	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371270.1	NM_020796		G	115782689	C	G	115782689	3	3	23	1	0	0	0	0	1	0	0	0	14052	864	30	4	383	4	SEMA6A	5	115782689	Missense_Mutation	SNP	C	TCGA-2Z-A9JT-01A-11D-A42J-10	29117020	115782689	65132571	22	1598											
DMXL1	1657	hgsc.bcm.edu	37	chr5	118480323	118480323	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttggcaaagacagcattttAtctaatgcaggtaaggaaga	15	10	10	6	0	1	2	0	0	1	2	1	3	1	3	0	3	2	4	0	3	5	5			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr5:118480323A>G	ENST00000311085.8	+	15	2639	c.2559A>G	c.(2557-2559)ttA>ttG	p.L853L	DMXL1_ENST00000539542.1_Silent_p.L853L	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	853										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)		ACAGCATTTTATCTAATGCAG	0.323																																					p.L853L		Atlas-SNP	.											.	DMXL1	268	.	0			c.A2559G						PASS	.						87	96	93					5																	118480323		2201	4295	6496	SO:0001819	synonymous_variant	1657	exon15			CATTTTATCTAAT	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.2559A>G	chr5.hg19:g.118480323A>G		283.0	0.0	.		328.0	108.0	.	NM_005509		Silent	SNP	ENST00000311085.8	hg19	CCDS4125.1																																																																																			.	.	.	none		0.323	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		G	118480323	A	G	118480323	2	3	23	1	0	0	0	0	0	0	0	1	4596	446	16	3		3	DMXL1	5	118480323	Silent	SNP	A	TCGA-2Z-A9JT-01A-11D-A42J-10	2697634	118480323	62434937	23	1599											
ANKHD1	54882	hgsc.bcm.edu	37	chr5	139919000	139919001	+	Frame_Shift_Ins	INS	-	-	T																															tgcatctcaaatatgtcaacINStaagttagaaggtctttact																										TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr5:139919000_139919001insT	ENST00000360839.2	+	34	7780_7781	c.7626_7627insT	c.(7627-7629)taafs	p.*2543fs	ANKHD1_ENST00000297183.6_Intron|ANKHD1-EIF4EBP3_ENST00000532219.1_Intron|ANKHD1_ENST00000544120.1_Frame_Shift_Ins_p.*867fs	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	0						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)			AATATGTCAACTAAGTTAGAAG	0.371																																					p.N2542fs		Atlas-Indel,Pindel	.											.	ANKHD1	233	.	0			c.7626_7627insT						PASS	.																																			SO:0001589	frameshift_variant	54882	exon34			.	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.7627dupT	chr5.hg19:g.139919001_139919001dupT	ENSP00000354085:p.*2543fs	99.0	0.0	0		95.0	23.0	0.242105	NM_017747	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Frame_Shift_Ins	INS	ENST00000360839.2	hg19	CCDS4225.1																																																																																			.	.	.	none		0.371	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		T	139919001	-	T	139919000	7	5	23	1	0	1	1	0	0	0	0	0	628	564	20	0	7866	0	ANKHD1	5	139919000	Frame_Shift_Ins	INS	-	TCGA-2Z-A9JT-01A-11D-A42J-10	21438677	139919000	40996260	24	1600											
PDE6A	5145	hgsc.bcm.edu	37	chr5	149279060	149279060	+	Missense_Mutation	SNP	T	T	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	tgaaagcacatttttaatcaTccatccagactcatccagag	14	11	5	11	0	2	3	2	1	0	2	5	3	5	3	3	0	1	1	3	0	2	3			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr5:149279060T>G	ENST00000255266.5	-	9	1260	c.1141A>C	c.(1141-1143)Atg>Ctg	p.M381L		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	381	GAF 2.				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)	TTTTTAATCATCCATCCAGAC	0.418																																					p.M381L		Atlas-SNP	.											.	PDE6A	98	.	0			c.A1141C						PASS	.						207	203	205					5																	149279060		2203	4300	6503	SO:0001583	missense	5145	exon9			TAATCATCCATCC		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.1141A>C	chr5.hg19:g.149279060T>G	ENSP00000255266:p.Met381Leu	85.0	0.0	.		116.0	40.0	.	NM_000440	Q0P638	Missense_Mutation	SNP	ENST00000255266.5	hg19	CCDS4299.1	.	.	.	.	.	.	.	.	.	.	T	13.25	2.180514	0.38511	.	.	ENSG00000132915	ENST00000255266	T	0.66280	-0.2	5.49	3.1	0.35709	GAF (2);	0.390516	0.31041	N	0.008361	T	0.35364	0.0929	N	0.08118	0	0.38599	D	0.950611	B	0.02656	0.0	B	0.06405	0.002	T	0.10154	-1.0642	10	0.12430	T	0.62	.	8.5252	0.33300	0.0:0.1603:0.0:0.8397	.	381	P16499	PDE6A_HUMAN	L	381	ENSP00000255266:M381L	ENSP00000255266:M381L	M	-	1	0	PDE6A	149259253	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.207000	0.32333	0.472000	0.27344	0.533000	0.62120	ATG	.	.	.	none		0.418	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2			G	149279060	T	G	149279060	3	3	23	1	0	0	0	0	1	0	0	0	11652	1435	50	5	1497	5	PDE6A	5	149279060	Missense_Mutation	SNP	T	TCGA-2Z-A9JT-01A-11D-A42J-10	9360060	149279060	31636200	25	1601											
RREB1	6239	hgsc.bcm.edu	37	chr6	7189549	7189549	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttaccaccaatgggaacaTgcacaggtgggtgagggcgc	11	7	14	9	1	0	1	0	1	0	0	0	2	0	2	2	4	3	1	2	4	3	2			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr6:7189549T>C	ENST00000349384.6	+	6	733	c.419T>C	c.(418-420)aTg>aCg	p.M140T	RREB1_ENST00000379933.3_Missense_Mutation_p.M140T|RREB1_ENST00000334984.6_Missense_Mutation_p.M140T|RREB1_ENST00000379938.2_Missense_Mutation_p.M140T|Y_RNA_ENST00000364613.1_RNA	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	140					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)				AATGGGAACATGCACAGGTGG	0.592																																					p.M140T		Atlas-SNP	.											.	RREB1	242	.	0			c.T419C						PASS	.						62	49	53					6																	7189549		2203	4299	6502	SO:0001583	missense	6239	exon6			GGAACATGCACAG	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.419T>C	chr6.hg19:g.7189549T>C	ENSP00000305560:p.Met140Thr	48.0	0.0	.		58.0	17.0	.	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	hg19	CCDS34336.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.508313	0.85282	.	.	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000471433;ENST00000349384;ENST00000334984;ENST00000483150	T;T;T;T;T;T	0.07800	3.16;3.16;3.16;3.16;3.16;3.16	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	0.000001	T	0.19805	0.0476	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	0.987;0.99;1.0	D;D;D	0.83275	0.961;0.962;0.996	T	0.00664	-1.1620	10	0.87932	D	0	-58.6326	15.8788	0.79185	0.0:0.0:0.0:1.0	.	140;140;140	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	T	140	ENSP00000369265:M140T;ENSP00000369270:M140T;ENSP00000420299:M140T;ENSP00000305560:M140T;ENSP00000335574:M140T;ENSP00000419511:M140T	ENSP00000335574:M140T	M	+	2	0	RREB1	7134548	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.449000	0.80643	2.155000	0.67459	0.482000	0.46254	ATG	.	.	.	none		0.592	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1			C	7189549	T	C	7189549	3	2	23	1	0	0	0	0	1	0	0	0	13692	1464	51	3	429	3	RREB1	6	7189549	Missense_Mutation	SNP	T	TCGA-2Z-A9JT-01A-11D-A42J-10		7189549	163925518	26	1602											
ZBTB22	9278	hgsc.bcm.edu	37	chr6	33283498	33283498	+	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	aagagggagttggcccccctGagtcatcaagacctgccaca	11	6	11	13	0	2	3	2	1	0	2	2	4	2	4	5	2	1	1	5	2	2	1			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr6:33283498G>T	ENST00000431845.2	-	2	1347	c.1196C>A	c.(1195-1197)tCa>tAa	p.S399*	TAPBP_ENST00000426633.2_5'Flank|ZBTB22_ENST00000418724.1_Nonsense_Mutation_p.S399*|TAPBP_ENST00000456592.2_5'Flank|TAPBP_ENST00000475304.1_5'Flank|TAPBP_ENST00000489157.1_5'Flank|TAPBP_ENST00000434618.2_5'Flank	NM_005453.4	NP_005444.4	O15209	ZBT22_HUMAN	zinc finger and BTB domain containing 22	399					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(3)	21						TGGCCCCCCTGAGTCATCAAG	0.617																																					p.S399X		Atlas-SNP	.											.	ZBTB22	48	.	0			c.C1196A						PASS	.						125	137	133					6																	33283498		2203	4300	6503	SO:0001587	stop_gained	9278	exon2			CCCCCTGAGTCAT	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.1196C>A	chr6.hg19:g.33283498G>T	ENSP00000407545:p.Ser399*	64.0	0.0	.		66.0	22.0	.	NM_001145338	B0V007|Q5HYV4|Q5STL0|Q5STR7|Q8WV82	Nonsense_Mutation	SNP	ENST00000431845.2	hg19	CCDS4775.1	.	.	.	.	.	.	.	.	.	.	G	31	5.089417	0.94149	.	.	ENSG00000236104	ENST00000418724;ENST00000431845	.	.	.	4.09	4.09	0.47781	.	0.318682	0.17604	N	0.168311	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.8509	0.63496	0.0:0.0:1.0:0.0	.	.	.	.	X	399	.	ENSP00000404403:S399X	S	-	2	0	ZBTB22	33391476	0.736000	0.28164	0.670000	0.29842	0.909000	0.53808	2.389000	0.44407	2.107000	0.64212	0.448000	0.29417	TCA	.	.	.	none		0.617	ZBTB22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076183.2			T	33283498	G	T	33283498	4	4	23	1	0	0	0	0	0	1	0	0	17542	1294	45	4	712	4	ZBTB22	6	33283498	Nonsense_Mutation	SNP	G	TCGA-2Z-A9JT-01A-11D-A42J-10	26093949	33283498	137831569	27	1603											
KIFC1	3833	hgsc.bcm.edu	37	chr6	33371727	33371727	+	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	caacactggaggggcatttaGccaaggtacaggcccaggct	11	6	13	11	0	0	0	0	0	0	0	0	1	0	1	2	6	3	3	2	6	4	3			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr6:33371727G>T	ENST00000428849.2	+	6	1027	c.577G>T	c.(577-579)Gcc>Tcc	p.A193S		NM_002263.3	NP_002254.2	Q9BW19	KIFC1_HUMAN	kinesin family member C1	193					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						GGGGCATTTAGCCAAGGTACA	0.607																																					p.A193S		Atlas-SNP	.											.	KIFC1	47	.	0			c.G577T						PASS	.						115	115	115					6																	33371727		2203	4300	6503	SO:0001583	missense	3833	exon6			CATTTAGCCAAGG	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.577G>T	chr6.hg19:g.33371727G>T	ENSP00000393963:p.Ala193Ser	147.0	0.0	.		107.0	5.0	.	NM_002263	O60887|Q14834|Q4KMP0|Q5SU09|Q6GMS7|Q6P4A5|Q9UQP7	Missense_Mutation	SNP	ENST00000428849.2	hg19	CCDS34430.1	.	.	.	.	.	.	.	.	.	.	G	0.208	-1.038804	0.02013	.	.	ENSG00000237649	ENST00000428849	T	0.77750	-1.12	5.17	-0.976	0.10286	.	0.591918	0.18780	N	0.131354	T	0.39306	0.1073	L	0.44542	1.39	0.09310	N	1	B;B	0.14012	0.009;0.005	B;B	0.08055	0.003;0.003	T	0.29305	-1.0016	10	0.12103	T	0.63	-18.0933	5.2986	0.15766	0.4038:0.0:0.4622:0.134	.	185;193	B4E063;Q9BW19	.;KIFC1_HUMAN	S	193	ENSP00000393963:A193S	ENSP00000393963:A193S	A	+	1	0	KIFC1	33479705	0.142000	0.22610	0.355000	0.25773	0.014000	0.08584	0.418000	0.21230	0.085000	0.17107	-0.251000	0.11542	GCC	.	.	.	none		0.607	KIFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076417.1	NM_002263		T	33371727	G	T	33371727	3	4	23	1	0	0	0	0	1	0	0	0	8319	971	34	4	599	4	KIFC1	6	33371727	Missense_Mutation	SNP	G	TCGA-2Z-A9JT-01A-11D-A42J-10	88229	33371727	137743340	28	1604											
UTRN	7402	hgsc.bcm.edu	37	chr6	144843189	144843189	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atcacttcttcctacagattAtctggttgaaattaacaaaa	15	14	4	8	0	3	2	1	1	2	1	4	2	4	2	1	1	2	1	1	1	6	6			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr6:144843189A>G	ENST00000367545.3	+	39	5615	c.5615A>G	c.(5614-5616)tAt>tGt	p.Y1872C		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	1872					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)		CCTACAGATTATCTGGTTGAA	0.333																																					p.Y1872C		Atlas-SNP	.											.	UTRN	327	.	0			c.A5615G						PASS	.						132	139	136					6																	144843189		2203	4300	6503	SO:0001583	missense	7402	exon39			CAGATTATCTGGT	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.5615A>G	chr6.hg19:g.144843189A>G	ENSP00000356515:p.Tyr1872Cys	99.0	0.0	.		77.0	23.0	.	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	hg19	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.124519	0.77436	.	.	ENSG00000152818	ENST00000367545	T	0.68765	-0.35	5.7	5.7	0.88788	.	0.000000	0.49305	D	0.000155	T	0.77458	0.4133	M	0.74881	2.28	0.80722	D	1	D	0.89917	1.0	D	0.71414	0.973	T	0.81169	-0.1055	10	0.87932	D	0	.	15.9596	0.79918	1.0:0.0:0.0:0.0	.	1872	P46939	UTRO_HUMAN	C	1872	ENSP00000356515:Y1872C	ENSP00000356515:Y1872C	Y	+	2	0	UTRN	144884882	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	8.698000	0.91311	2.177000	0.69029	0.459000	0.35465	TAT	.	.	.	none		0.333	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			G	144843189	A	G	144843189	3	3	23	1	0	0	0	0	1	0	0	0	17115	449	16	3	5769	3	UTRN	6	144843189	Missense_Mutation	SNP	A	TCGA-2Z-A9JT-01A-11D-A42J-10	111471462	144843189	26271878	29	1605											
C7orf27	221927	hgsc.bcm.edu	37	chr7	2581812	2581812	+	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	caggccaggggctggagaagGacctggaaggcctgggtcct	8	5	18	10	0	0	1	0	0	0	1	1	4	1	3	4	8	0	1	4	8	2	0			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr7:2581812G>C	ENST00000340611.4	-	7	1213	c.957C>G	c.(955-957)gtC>gtG	p.V319V	BRAT1_ENST00000473879.1_5'Flank	NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	319					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						GCTGGAGAAGGACCTGGAAGG	0.642																																					p.V319V		Atlas-SNP	.											.	BRAT1	57	.	0			c.C957G						PASS	.						31	27	28					7																	2581812		2171	4273	6444	SO:0001819	synonymous_variant	221927	exon7			GAGAAGGACCTGG	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.957C>G	chr7.hg19:g.2581812G>C		223.0	0.0	.		268.0	132.0	.	NM_152743	A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Silent	SNP	ENST00000340611.4	hg19	CCDS5334.1																																																																																			.	.	.	none		0.642	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239305.2	NM_152743		C	2581812	G	C	2581812	2	2	23	1	0	0	0	0	0	0	0	1	2384	1161	41	4		4	C7orf27	7	2581812	Silent	SNP	G	TCGA-2Z-A9JT-01A-11D-A42J-10		2581812	156556851	30	1606											
C7orf36	57002	hgsc.bcm.edu	37	chr7	39610143	39610143	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atagatgctggcaaagcagtTactcttcaacagggcttcaa	13	10	9	9	0	3	1	2	0	1	1	3	1	3	1	0	2	4	5	0	2	5	4			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr7:39610143T>C	ENST00000223273.2	+	2	211	c.168T>C	c.(166-168)gtT>gtC	p.V56V	YAE1D1_ENST00000448268.1_Silent_p.V56V|YAE1D1_ENST00000469737.1_3'UTR|YAE1D1_ENST00000432096.2_Silent_p.V56V	NM_020192.3	NP_064577.1	Q9NRH1	YAED1_HUMAN	Yae1 domain containing 1	56																	GCAAAGCAGTTACTCTTCAAC	0.363																																					p.V56V		Atlas-SNP	.											.	YAE1D1	2	.	0			c.T168C						PASS	.						133	136	135					7																	39610143		2203	4300	6503	SO:0001819	synonymous_variant	57002	exon2			AGCAGTTACTCTT	AF226046	CCDS5459.1, CCDS64630.1	7p14.1	2011-11-24	2011-11-24	2011-11-24	ENSG00000241127	ENSG00000241127			24857	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 36"	C7orf36		12477932	Standard	NM_020192		Approved	GK003	uc003thc.4	Q9NRH1	OTTHUMG00000128689	ENST00000223273.2:c.168T>C	chr7.hg19:g.39610143T>C		146.0	0.0	.		140.0	64.0	.	NM_020192	A4D1W4|B4DE83|Q6IAF7|Q8WVZ5	Silent	SNP	ENST00000223273.2	hg19	CCDS5459.1																																																																																			.	.	.	none		0.363	YAE1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250586.1	NM_020192		C	39610143	T	C	39610143	2	2	23	1	0	0	0	0	0	0	0	1	2392	1741	61	3		3	C7orf36	7	39610143	Silent	SNP	T	TCGA-2Z-A9JT-01A-11D-A42J-10	37028331	39610143	119528520	31	1607											
MBLAC1	255374	hgsc.bcm.edu	37	chr7	99725518	99725518	+	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	gctcgaggtgtgggccacgcCgggccacgggggccagcgcg	4	3	20	14	6	0	0	0	0	0	0	1	1	0	0	4	5	1	1	4	5	0	0	rs35757966		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr7:99725518C>G	ENST00000398075.2	+	2	899	c.500C>G	c.(499-501)cCg>cGg	p.P167R	RP11-506M12.1_ENST00000494221.1_RNA	NM_203397.1	NP_981942.1	A4D2B0	MBLC1_HUMAN	metallo-beta-lactamase domain containing 1	167							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						TGGGCCACGCCGGGCCACGGG	0.741																																					p.P167R		Atlas-SNP	.											.	MBLAC1	13	.	0			c.C500G						PASS	.						20	22	21					7																	99725518		1902	4006	5908	SO:0001583	missense	255374	exon2			CCACGCCGGGCCA	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.500C>G	chr7.hg19:g.99725518C>G	ENSP00000381150:p.Pro167Arg	97.0	0.0	.		89.0	44.0	.	NM_203397	Q8N5X8	Missense_Mutation	SNP	ENST00000398075.2	hg19	CCDS43620.1	.	.	.	.	.	.	.	.	.	.	C	30	5.055427	0.93793	.	.	ENSG00000214309	ENST00000398075	T	0.42513	0.97	4.68	4.68	0.58851	Beta-lactamase-like (2);	0.000000	0.56097	U	0.000031	T	0.67050	0.2852	M	0.82923	2.615	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.72865	-0.4163	10	0.87932	D	0	.	15.1263	0.72486	0.0:1.0:0.0:0.0	.	167	A4D2B0	MBLC1_HUMAN	R	167	ENSP00000381150:P167R	ENSP00000381150:P167R	P	+	2	0	MBLAC1	99563454	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.800000	0.75165	2.440000	0.82611	0.561000	0.74099	CCG	.	.	.	none		0.741	MBLAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337353.1	NM_203397		G	99725518	C	G	99725518	3	3	23	1	0	0	0	0	1	0	0	0	9358	652	23	4	502	4	MBLAC1	7	99725518	Missense_Mutation	SNP	C	TCGA-2Z-A9JT-01A-11D-A42J-10	60115375	99725518	59413145	32	1608											
REPIN1	29803	hgsc.bcm.edu	37	chr7	150068585	150068585	+	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	tgccaggcccggctgcccttGccctgccctgagtgtggccg	2	8	14	17	2	0	1	0	1	0	0	0	1	0	1	6	3	4	1	6	3	0	1			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr7:150068585G>A	ENST00000425389.2	+	1	333	c.255G>A	c.(253-255)ttG>ttA	p.L85L	REPIN1_ENST00000540729.1_Silent_p.L85L|RP4-584D14.5_ENST00000488310.1_RNA|REPIN1_ENST00000466559.1_3'UTR|REPIN1_ENST00000479668.1_3'UTR|REPIN1_ENST00000518514.1_Missense_Mutation_p.A134T|REPIN1_ENST00000444957.1_Silent_p.L85L|REPIN1_ENST00000489432.2_Silent_p.L142L|REPIN1_ENST00000482680.1_3'UTR|REPIN1_ENST00000518462.1_3'UTR|REPIN1_ENST00000397281.2_Silent_p.L85L	NM_014374.3	NP_055189.2	Q9BWE0	REPI1_HUMAN	replication initiator 1	85					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)			GGCTGCCCTTGCCCTGCCCTG	0.692																																					p.L142L		Atlas-SNP	.											.	REPIN1	74	.	0			c.G426A						PASS	.						16	19	18					7																	150068585		2106	4220	6326	SO:0001819	synonymous_variant	29803	exon3			GCCCTTGCCCTGC	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.255G>A	chr7.hg19:g.150068585G>A		54.0	0.0	.		60.0	33.0	.	NM_001099695	C9J3L7|D3DWZ1|Q7LE03|Q9BUZ6|Q9NZH2|Q9UMP5	Silent	SNP	ENST00000425389.2	hg19	CCDS43677.1	.	.	.	.	.	.	.	.	.	.	G	9.998	1.232626	0.22626	.	.	ENSG00000214022	ENST00000518514	.	.	.	5.54	2.6	0.31112	.	.	.	.	.	T	0.58892	0.2154	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59112	-0.7515	5	0.87932	D	0	-3.1465	3.7036	0.08391	0.2659:0.0:0.5615:0.1726	.	.	.	.	T	134	.	ENSP00000428129:A134T	A	+	1	0	REPIN1	149699518	0.000000	0.05858	0.992000	0.48379	0.829000	0.46940	-0.141000	0.10327	0.702000	0.31825	0.462000	0.41574	GCC	.	.	.	none		0.692	REPIN1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376940.1	NM_014374		A	150068585	G	A	150068585	2	1	23	1	0	0	0	0	0	0	0	1	13240	1310	46	2		2	REPIN1	7	150068585	Silent	SNP	G	TCGA-2Z-A9JT-01A-11D-A42J-10	50343067	150068585	9070078	33	1609											
INTS9	55756	hgsc.bcm.edu	37	chr8	28669861	28669861	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tacctgggggtgtgtggtaaGcaaggaggatccagagacat	11	8	16	6	0	0	1	0	0	0	1	1	4	1	3	2	5	2	2	2	5	3	2			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr8:28669861G>A	ENST00000521022.1	-	8	808	c.727C>T	c.(727-729)Ctt>Ttt	p.L243F	INTS9_ENST00000521777.1_Missense_Mutation_p.L219F|INTS9_ENST00000397363.4_Missense_Mutation_p.L137F|INTS9_ENST00000416984.2_Missense_Mutation_p.L222F	NM_018250.3	NP_060720.2	Q9NV88	INT9_HUMAN	integrator complex subunit 9	243					snRNA processing (GO:0016180)	cytoplasm (GO:0005737)|integrator complex (GO:0032039)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|pancreas(2)|prostate(1)|urinary_tract(2)	19		Ovarian(32;0.0439)		KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.152)		TGTGTGGTAAGCAAGGAGGAT	0.463																																					p.L243F		Atlas-SNP	.											.	INTS9	43	.	0			c.C727T						PASS	.						114	105	108					8																	28669861		2203	4300	6503	SO:0001583	missense	55756	exon8			TGGTAAGCAAGGA	BC025267	CCDS34873.1, CCDS55215.1, CCDS55216.1	8p21.1	2008-02-05			ENSG00000104299	ENSG00000104299			25592	protein-coding gene	gene with protein product		611352				16239144	Standard	NM_001172562		Approved	FLJ10871, CPSF2L, RC-74	uc011lav.2	Q9NV88	OTTHUMG00000164030	ENST00000521022.1:c.727C>T	chr8.hg19:g.28669861G>A	ENSP00000429065:p.Leu243Phe	108.0	0.0	.		100.0	32.0	.	NM_018250	B7Z560|B7Z6M5|O00224|Q8TB16	Missense_Mutation	SNP	ENST00000521022.1	hg19	CCDS34873.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.83|18.83	3.707284|3.707284	0.68615|0.68615	.|.	.|.	ENSG00000104299|ENSG00000104299	ENST00000524081|ENST00000521022;ENST00000416984;ENST00000541706;ENST00000521777;ENST00000397363	.|T;T;T;T	.|0.47869	.|0.83;0.84;0.83;0.83	5.84|5.84	5.84|5.84	0.93424|0.93424	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.41673|0.41673	0.1169|0.1169	L|L	0.41415|0.41415	1.275|1.275	0.80722|0.80722	D|D	1|1	.|B;B;B	.|0.28801	.|0.125;0.045;0.223	.|B;B;B	.|0.28553	.|0.091;0.049;0.059	T|T	0.22556|0.22556	-1.0213|-1.0213	5|10	.|0.12766	.|T	.|0.61	-18.4337|-18.4337	19.7483|19.7483	0.96259|0.96259	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|222;243;243	.|B7Z6M5;G3XAN1;Q9NV88	.|.;.;INT9_HUMAN	V|F	205|243;222;87;219;137	.|ENSP00000429065:L243F;ENSP00000398208:L222F;ENSP00000430943:L219F;ENSP00000380520:L137F	.|ENSP00000380520:L137F	A|L	-|-	2|1	0|0	INTS9|INTS9	28725780|28725780	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	9.701000|9.701000	0.98710|0.98710	2.779000|2.779000	0.95612|0.95612	0.655000|0.655000	0.94253|0.94253	GCT|CTT	.	.	.	none		0.463	INTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376846.1	NM_018250		A	28669861	G	A	28669861	3	1	23	1	0	0	0	0	1	0	0	0	7792	971	34	2	1289	2	INTS9	8	28669861	Missense_Mutation	SNP	G	TCGA-2Z-A9JT-01A-11D-A42J-10		28669861	117694161	34	1610											
KIAA0146	23514	hgsc.bcm.edu	37	chr8	48352889	48352889	+	Frame_Shift_Del	DEL	A	A	-																															tttcttcaacttctaggtagAaaatctggtgtattaactgt																										TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr8:48352889delA	ENST00000297423.4	+	8	1266	c.882delA	c.(880-882)agafs	p.R294fs	SPIDR_ENST00000518074.1_Frame_Shift_Del_p.R234fs|SPIDR_ENST00000541342.1_Frame_Shift_Del_p.R224fs|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	294	Necessary for interaction with RAD51.				cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of protein complex assembly (GO:0031334)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of establishment of protein localization to chromosome (GO:0070202)	nuclear chromosome (GO:0000228)											TTCTAGGTAGAAAATCTGGTG	0.393																																					p.R294fs		Atlas-Indel,Pindel	.											.	KIAA0146	64	.	0			c.881delG						PASS	.						67	62	64					8																	48352889		1849	4119	5968	SO:0001589	frameshift_variant	23514	exon8			.	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.882delA	chr8.hg19:g.48352889delA	ENSP00000297423:p.Arg294fs	49.0	0.0	0		77.0	26.0	0.337662	NM_001080394	B4DFV2|B4E0Y6|Q96BI5	Frame_Shift_Del	DEL	ENST00000297423.4	hg19	CCDS43737.1																																																																																			.	.	.	none		0.393	SPIDR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377611.1	NM_001080394		-	48352889	A	-	48352889	7	5	23	1	0	1	0	1	0	0	0	0	8164	243	9	0	912	0	KIAA0146	8	48352889	Frame_Shift_Del	DEL	A	TCGA-2Z-A9JT-01A-11D-A42J-10	19683028	48352889	98011133	35	1611											
VCPIP1	80124	hgsc.bcm.edu	37	chr8	67546979	67546979	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttgcagaagaactcacaacTtctgttttcctttgaggaag	11	14	8	8	0	2	3	1	1	1	2	3	4	3	4	1	1	3	2	1	1	4	5			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr8:67546979T>C	ENST00000310421.4	-	3	3684	c.3426A>G	c.(3424-3426)gaA>gaG	p.E1142E		NM_025054.4	NP_079330.2	Q96JH7	VCIP1_HUMAN	valosin containing protein (p97)/p47 complex interacting protein 1	1142					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)			AACTCACAACTTCTGTTTTCC	0.423																																					p.E1142E	NSCLC(179;265 2915 6144 43644)	Atlas-SNP	.											.	VCPIP1	110	.	0			c.A3426G						PASS	.						97	96	96					8																	67546979		2203	4300	6503	SO:0001819	synonymous_variant	80124	exon3			CACAACTTCTGTT	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.3426A>G	chr8.hg19:g.67546979T>C		82.0	0.0	.		111.0	36.0	.	NM_025054	Q504T4|Q86T93|Q86W01|Q8N3A9|Q9H5R8	Silent	SNP	ENST00000310421.4	hg19	CCDS6192.1																																																																																			.	.	.	none		0.423	VCPIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379227.1			C	67546979	T	C	67546979	2	2	23	1	0	0	0	0	0	0	0	1	17153	1606	56	3		3	VCPIP1	8	67546979	Silent	SNP	T	TCGA-2Z-A9JT-01A-11D-A42J-10	19194090	67546979	78817043	36	1612											
ATP6V1C1	528	hgsc.bcm.edu	37	chr8	104068108	104068109	+	Frame_Shift_Del	DEL	CG	CG	-																															ttctgcaggttaaaccacaaCgactggattaagcagtatga																								rs368547373		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	CG	CG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr8:104068108_104068109delCG	ENST00000395862.3	+	8	744_745	c.585_586delCG	c.(583-588)aacgacfs	p.ND195fs	ATP6V1C1_ENST00000521514.1_Frame_Shift_Del_p.ND120fs|ATP6V1C1_ENST00000518738.1_Frame_Shift_Del_p.ND195fs|ATP6V1C1_ENST00000518857.1_Frame_Shift_Del_p.ND120fs	NM_001695.4	NP_001686.1	P21283	VATC1_HUMAN	ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C1	195					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)	p.D196N(1)		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)			TAAACCACAACGACTGGATTAA	0.361																																					p.195_195del		Atlas-Indel,Pindel	.											.	ATP6V1C1	33	.	1	Substitution - Missense(1)	large_intestine(1)	c.584_585del						PASS	.																																			SO:0001589	frameshift_variant	528	exon8			.	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.585_586delCG	chr8.hg19:g.104068108_104068109delCG	ENSP00000379203:p.Asn195fs	154.0	0.0	0		176.0	55.0	0.3125	NM_001695		Frame_Shift_Del	DEL	ENST00000395862.3	hg19	CCDS6296.1																																																																																			.	.	.	none		0.361	ATP6V1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380101.1	NM_001695		-	104068109	CG	-	104068108	7	5	23	1	0	1	0	1	0	0	0	0	1180	535	19	0	611	0	ATP6V1C1	8	104068108	Frame_Shift_Del	DEL	CG	TCGA-2Z-A9JT-01A-11D-A42J-10	36521129	104068108	42295914	37	1613											
KIF24	347240	hgsc.bcm.edu	37	chr9	34256932	34256932	+	Frame_Shift_Del	DEL	G	G	-																															gggtccctggagtccacccaGcttttagttagatctttctt																										TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr9:34256932delG	ENST00000402558.2	-	10	2697	c.2673delC	c.(2671-2673)agcfs	p.S891fs	KIF24_ENST00000345050.2_Frame_Shift_Del_p.S757fs|KIF24_ENST00000379166.2_Frame_Shift_Del_p.S891fs|KIF24_ENST00000379174.3_Frame_Shift_Del_p.S757fs			Q5T7B8	KIF24_HUMAN	kinesin family member 24	891					ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)	centriole (GO:0005814)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(13)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	32			LUSC - Lung squamous cell carcinoma(29;0.0107)			AGTCCACCCAGCTTTTAGTTA	0.547																																					p.W892fs		Atlas-Indel,Pindel	.											.	KIF24	64	.	0			c.2674delT						PASS	.						71	73	72					9																	34256932		2203	4300	6503	SO:0001589	frameshift_variant	347240	exon11			.	AK001795	CCDS6551.2	9p13.3	2013-01-10			ENSG00000186638	ENSG00000186638		"Kinesins", "Sterile alpha motif (SAM) domain containing"	19916	protein-coding gene	gene with protein product		613747	"chromosome 9 open reading frame 48"	C9orf48		12477932	Standard	NM_194313		Approved	bA571F15.4, FLJ10933, FLJ43884	uc003zua.4	Q5T7B8	OTTHUMG00000019810	ENST00000402558.2:c.2673delC	chr9.hg19:g.34256932delG	ENSP00000384433:p.Ser891fs	82.0	0.0	0		103.0	35.0	0.339806	NM_194313	Q2TB93|Q5T7B5|Q5T7B7|Q6ZU97|Q6ZUZ2|Q86XZ0|Q9NV43	Frame_Shift_Del	DEL	ENST00000402558.2	hg19	CCDS6551.2																																																																																			.	.	.	none		0.547	KIF24-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052150.5			-	34256932	G	-	34256932	7	5	23	1	0	1	0	1	0	0	0	0	8299	962	34	0	1445	0	KIF24	9	34256932	Frame_Shift_Del	DEL	G	TCGA-2Z-A9JT-01A-11D-A42J-10		34256932	106956499	38	1614											
ZFAND5	7763	hgsc.bcm.edu	37	chr9	74975669	74975669	+	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	tgctacacagcatgggccccGgggtctggttagtctcctga	6	10	13	12	1	2	1	0	1	2	0	3	1	2	1	3	4	3	3	3	4	2	2			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr9:74975669G>T	ENST00000237937.3	-	2	583	c.26C>A	c.(25-27)cCg>cAg	p.P9Q	ZFAND5_ENST00000343431.2_Missense_Mutation_p.P9Q|ZFAND5_ENST00000376962.5_Missense_Mutation_p.P9Q|ZFAND5_ENST00000376960.4_Missense_Mutation_p.P9Q|ZFAND5_ENST00000488164.1_5'UTR	NM_001102421.1|NM_001278243.1|NM_001278244.1|NM_001278245.1|NM_006007.2	NP_001095891.1|NP_001265172.1|NP_001265173.1|NP_001265174.1|NP_005998.1	O76080	ZFAN5_HUMAN	zinc finger, AN1-type domain 5	9					face development (GO:0060324)|fibroblast migration (GO:0010761)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|respiratory system process (GO:0003016)|skeletal system morphogenesis (GO:0048705)|smooth muscle tissue development (GO:0048745)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			cervix(1)|kidney(2)|lung(2)|prostate(1)	6						CATGGGCCCCGGGGTCTGGTT	0.403																																					p.P9Q		Atlas-SNP	.											.	ZFAND5	14	.	0			c.C26A						PASS	.						88	94	92					9																	74975669		2203	4297	6500	SO:0001583	missense	7763	exon2			GGCCCCGGGGTCT	AF062072	CCDS6642.1	9q13-q21	2008-05-02	2006-07-07	2006-07-07	ENSG00000107372	ENSG00000107372		"Zinc fingers, AN1-type domain containing"	13008	protein-coding gene	gene with protein product		604761	"zinc finger protein 216", "zinc finger, A20 domain containing 2"	ZNF216, ZA20D2		9758550	Standard	NM_001278243		Approved	ZFAND5A	uc004aiy.2	O76080	OTTHUMG00000020008	ENST00000237937.3:c.26C>A	chr9.hg19:g.74975669G>T	ENSP00000237937:p.Pro9Gln	95.0	0.0	.		65.0	14.0	.	NM_001102421	A8K484	Missense_Mutation	SNP	ENST00000237937.3	hg19	CCDS6642.1	.	.	.	.	.	.	.	.	.	.	G	3.765	-0.048781	0.07407	.	.	ENSG00000107372	ENST00000237937;ENST00000376960;ENST00000376962;ENST00000343431;ENST00000376956	.	.	.	5.89	5.89	0.94794	Zinc finger, A20-type (1);	.	.	.	.	T	0.18215	0.0437	N	0.00174	-1.93	0.80722	D	1	B	0.25904	0.137	B	0.26310	0.068	T	0.50874	-0.8776	8	0.02654	T	1	-5.8486	20.2561	0.98419	0.0:0.0:1.0:0.0	.	9	O76080	ZFAN5_HUMAN	Q	9;9;9;9;61	.	ENSP00000237937:P9Q	P	-	2	0	ZFAND5	74165489	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.483000	0.66838	2.797000	0.96272	0.563000	0.77884	CCG	.	.	.	none		0.403	ZFAND5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052644.1			T	74975669	G	T	74975669	3	4	23	1	0	0	0	0	1	0	0	0	17642	1116	39	4	635	4	ZFAND5	9	74975669	Missense_Mutation	SNP	G	TCGA-2Z-A9JT-01A-11D-A42J-10	40718737	74975669	66237762	39	1615											
SVIL	6840	hgsc.bcm.edu	37	chr10	29760115	29760115	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctccccgagtgcaccaccaTccccccctggaaacactgca	9	5	6	21	1	0	0	0	0	0	0	2	2	2	1	8	1	3	2	8	1	1	0			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr10:29760115T>C	ENST00000355867.4	-	31	6339	c.5587A>G	c.(5587-5589)Atg>Gtg	p.M1863V	PTCHD3P1_ENST00000414457.1_RNA|SVIL_ENST00000375398.2_Missense_Mutation_p.M1863V|PTCHD3P1_ENST00000423223.1_RNA|SVIL_ENST00000460007.1_5'Flank|SVIL_ENST00000375400.3_Missense_Mutation_p.M1437V|PTCHD3P1_ENST00000413405.1_RNA|PTCHD3P1_ENST00000455774.1_RNA|PTCHD3P1_ENST00000446807.1_RNA|SVIL_ENST00000535393.1_Missense_Mutation_p.M777V	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1863					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)				TGCACCACCATCCCCCCCTGG	0.527																																					p.M1863V		Atlas-SNP	.											.,1	SVIL	226	.	0			c.A5587G						PASS	.						77	63	68					10																	29760115		2203	4300	6503	SO:0001583	missense	6840	exon31			CCACCATCCCCCC	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.5587A>G	chr10.hg19:g.29760115T>C	ENSP00000348128:p.Met1863Val	198.0	2.0	.		150.0	42.0	.	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	hg19	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.800002	0.90538	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867;ENST00000535393	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.60090	0.2242	M	0.73598	2.24	0.80722	D	1	P;P;D	0.55605	0.875;0.72;0.972	P;P;P	0.55222	0.771;0.692;0.616	T	0.64676	-0.6351	10	0.87932	D	0	-31.3148	16.5582	0.84512	0.0:0.0:0.0:1.0	.	777;1437;1863	F5H2Q5;O95425-2;O95425	.;.;SVIL_HUMAN	V	1437;1863;1863;777	ENSP00000364549:M1437V;ENSP00000364547:M1863V;ENSP00000348128:M1863V;ENSP00000445472:M777V	ENSP00000348128:M1863V	M	-	1	0	SVIL	29800121	1.000000	0.71417	0.969000	0.41365	0.958000	0.62258	7.901000	0.87382	2.308000	0.77769	0.533000	0.62120	ATG	.	.	.	none		0.527	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			C	29760115	T	C	29760115	3	2	23	1	0	0	0	0	1	0	0	0	15433	1435	50	3	1089	3	SVIL	10	29760115	Missense_Mutation	SNP	T	TCGA-2Z-A9JT-01A-11D-A42J-10		29760115	105774632	40	1616											
ABCC2	1244	hgsc.bcm.edu	37	chr10	101595920	101595920	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtccccaatctactctcacTtcagcgagaccgtatcaggt	9	10	8	14	2	4	1	3	0	2	1	6	2	5	1	3	2	2	1	3	2	3	3			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr10:101595920T>C	ENST00000370449.4	+	25	3600	c.3487T>C	c.(3487-3489)Ttc>Ctc	p.F1163L		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	1163	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				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)	CTACTCTCACTTCAGCGAGAC	0.493																																					p.F1163L		Atlas-SNP	.											.	ABCC2	160	.	0			c.T3487C						PASS	.						149	135	140					10																	101595920		2203	4300	6503	SO:0001583	missense	1244	exon25			TCTCACTTCAGCG	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.3487T>C	chr10.hg19:g.101595920T>C	ENSP00000359478:p.Phe1163Leu	198.0	0.0	.		179.0	58.0	.	NM_000392	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Missense_Mutation	SNP	ENST00000370449.4	hg19	CCDS7484.1	.	.	.	.	.	.	.	.	.	.	T	34	5.351795	0.95830	.	.	ENSG00000023839	ENST00000370449	D	0.88277	-2.36	5.78	5.78	0.91487	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	0.94368	0.8189	M	0.77313	2.365	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94944	0.8094	10	0.87932	D	0	-9.1981	16.1127	0.81273	0.0:0.0:0.0:1.0	.	1163	Q92887	MRP2_HUMAN	L	1163	ENSP00000359478:F1163L	ENSP00000359478:F1163L	F	+	1	0	ABCC2	101585910	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	8.037000	0.88933	2.212000	0.71576	0.260000	0.18958	TTC	.	.	.	none		0.493	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392		C	101595920	T	C	101595920	3	2	23	1	0	0	0	0	1	0	0	0	53	1609	56	3	3585	3	ABCC2	10	101595920	Missense_Mutation	SNP	T	TCGA-2Z-A9JT-01A-11D-A42J-10	71835805	101595920	33938827	41	1617											
POLL	27343	hgsc.bcm.edu	37	chr10	103343263	103343263	+	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	aggggctgagccagggtgtgAcctgttggtaccacatctgg	7	9	16	9	0	1	2	0	2	1	0	1	2	1	2	3	5	2	3	3	5	1	2			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr10:103343263A>C	ENST00000370162.3	-	6	1560		c.e6+1		POLL_ENST00000463515.1_5'Flank|POLL_ENST00000436284.2_3'UTR|DPCD_ENST00000416979.2_Intron|POLL_ENST00000299206.4_Splice_Site|POLL_ENST00000370158.3_Splice_Site|DPCD_ENST00000470165.1_Intron|POLL_ENST00000370169.1_Splice_Site|POLL_ENST00000456836.2_Splice_Site|POLL_ENST00000339310.3_Splice_Site|POLL_ENST00000370168.3_5'Flank|POLL_ENST00000370172.1_Splice_Site	NM_001174084.1|NM_001174085.1|NM_013274.3	NP_001167555.1|NP_001167556.1|NP_037406.1	Q9UGP5	DPOLL_HUMAN	polymerase (DNA directed), lambda						DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|nucleotide-excision repair (GO:0006289)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|lyase activity (GO:0016829)|metal ion binding (GO:0046872)			biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(2)	19		Colorectal(252;0.234)		Epithelial(162;1.55e-08)|all cancers(201;6.64e-07)		CCAGGGTGTGACCTGTTGGTA	0.567								DNA polymerases (catalytic subunits)																													.		Atlas-SNP	.											.	POLL	43	.	0			c.789+2T>G						PASS	.						102	85	90					10																	103343263		2203	4300	6503	SO:0001630	splice_region_variant	27343	exon7			GGTGTGACCTGTT	AF161019	CCDS7513.1	10q23	2012-05-18			ENSG00000166169	ENSG00000166169		"DNA polymerases"	9184	protein-coding gene	gene with protein product		606343				17686665	Standard	NM_001174084		Approved		uc001kti.2	Q9UGP5	OTTHUMG00000018933	ENST00000370162.3:c.1065+1T>G	chr10.hg19:g.103343263A>C		54.0	0.0	.		50.0	12.0	.	NM_001174085	D3DR76|Q5JQP5|Q6NUM2|Q9BTN8|Q9HA10|Q9HB35	Splice_Site	SNP	ENST00000370162.3	hg19	CCDS7513.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.158773	0.78226	.	.	ENSG00000166169	ENST00000299206;ENST00000370174;ENST00000370169;ENST00000339310;ENST00000370172;ENST00000370162;ENST00000370158;ENST00000370157;ENST00000456836;ENST00000415897;ENST00000429502	.	.	.	5.83	5.83	0.93111	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2147	0.82198	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	POLL	103333253	1.000000	0.71417	0.994000	0.49952	0.842000	0.47809	8.908000	0.92640	2.231000	0.72958	0.460000	0.39030	.	.	.	.	none		0.567	POLL-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049946.1	NM_013274	Intron	C	103343263	A	C	103343263	5	2	23	1	0	0	0	0	0	0	1	0	12212	289	10	5	676	5	POLL	10	103343263	Splice_Site	SNP	A	TCGA-2Z-A9JT-01A-11D-A42J-10	1747343	103343263	32191484	42	1618											
PAMR1	25891	hgsc.bcm.edu	37	chr11	35456322	35456326	+	Frame_Shift_Del	DEL	GGAGC	GGAGC	-																															agcgcaacccttgggtctttGgagcagtgatgttctcaatt																								rs559149381		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	GGAGC	GGAGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr11:35456322_35456326delGGAGC	ENST00000378880.2	-	10	1805_1809	c.1360_1364delGCTCC	c.(1360-1365)gctccafs	p.AP454fs	PAMR1_ENST00000278360.3_Frame_Shift_Del_p.AP471fs|PAMR1_ENST00000532848.1_Frame_Shift_Del_p.AP414fs|PAMR1_ENST00000378878.3_Frame_Shift_Del_p.AP343fs	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN	peptidase domain containing associated with muscle regeneration 1	454	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	26						TTGGGTCTTTGGAGCAGTGATGTTC	0.527																																					p.471_472del		Atlas-Indel,Pindel	.											.	PAMR1	85	.	0			c.1412_1416del						PASS	.																																			SO:0001589	frameshift_variant	25891	exon11			.		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.1360_1364delGCTCC	chr11.hg19:g.35456322_35456326delGGAGC	ENSP00000368158:p.Ala454fs	53.0	0.0	0		54.0	17.0	0.314815	NM_015430	A8MQ58|B7ZA73|Q5EBL7|Q5JPI4|Q6N062|Q71RE9|Q96JW2|Q9Y432	Frame_Shift_Del	DEL	ENST00000378880.2	hg19	CCDS31460.1																																																																																			.	.	.	none		0.527	PAMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389177.1	NM_015430		-	35456326	GGAGC	-	35456322	7	5	23	1	0	1	0	1	0	0	0	0	11420	1348	47	0	806	0	PAMR1	11	35456322	Frame_Shift_Del	DEL	GGAGC	TCGA-2Z-A9JT-01A-11D-A42J-10		35456322	99550194	43	1619											
EXT2	2132	hgsc.bcm.edu	37	chr11	44129501	44129501	+	Frame_Shift_Del	DEL	G	G	-																															cgacagtcccatcccagagcGgggggatctcagttgcagaa																										TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr11:44129501delG	ENST00000343631.3	+	2	368	c.239delG	c.(238-240)cggfs	p.R80fs	EXT2_ENST00000395673.3_Frame_Shift_Del_p.R113fs|EXT2_ENST00000533608.1_Frame_Shift_Del_p.R80fs|EXT2_ENST00000358681.4_Frame_Shift_Del_p.R80fs			Q93063	EXT2_HUMAN	exostosin glycosyltransferase 2	80					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						ATCCCAGAGCGGGGGGATCTC	0.498			"Mis, N, F, S"			"exostoses, osteosarcoma"			Hereditary Multiple Exostoses																												p.R113fs		Atlas-Indel,Pindel	.	yes	Rec		Multiple Exostoses Type 2	11	11p12-p11	2132	multiple exostoses type 2 gene		M	.	EXT2	129	.	0			c.337delC						PASS	.						80	72	75					11																	44129501		2203	4300	6503	SO:0001589	frameshift_variant	2132	exon2	Familial Cancer Database	HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	.		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.239delG	chr11.hg19:g.44129501delG	ENSP00000342656:p.Arg80fs	141.0	0.0	0		149.0	43.0	0.288591	NM_000401	B2R5Z6|C9JU51|J3KPT2|O15288	Frame_Shift_Del	DEL	ENST00000343631.3	hg19	CCDS7908.1																																																																																			.	.	.	none		0.498	EXT2-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390074.1	NM_000401		-	44129501	G	-	44129501	7	5	23	1	0	1	0	1	0	0	0	0	5326	1116	39	0	344	0	EXT2	11	44129501	Frame_Shift_Del	DEL	G	TCGA-2Z-A9JT-01A-11D-A42J-10	8673179	44129501	90877015	44	1620											
SAPS3	55291	hgsc.bcm.edu	37	chr11	68305152	68305152	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catgttttggaaatttgatcTtcactcatcatcccacatag	11	15	5	10	0	4	1	3	1	1	0	5	2	5	2	1	1	0	1	1	1	2	5			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr11:68305152T>C	ENST00000393800.2	+	3	274	c.20T>C	c.(19-21)cTt>cCt	p.L7P	PPP6R3_ENST00000393801.3_Missense_Mutation_p.L7P|PPP6R3_ENST00000524904.1_Missense_Mutation_p.L7P|PPP6R3_ENST00000265637.4_Missense_Mutation_p.L7P|PPP6R3_ENST00000524845.1_Missense_Mutation_p.L7P|PPP6R3_ENST00000393799.2_Missense_Mutation_p.L7P|PPP6R3_ENST00000534534.1_Intron|PPP6R3_ENST00000265636.5_Missense_Mutation_p.L7P|PPP6R3_ENST00000529710.1_Missense_Mutation_p.L7P|PPP6R3_ENST00000527403.2_Missense_Mutation_p.L7P	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	7					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						AAATTTGATCTTCACTCATCA	0.318																																					p.L7P		Atlas-SNP	.											.	PPP6R3	159	.	0			c.T20C						PASS	.						86	77	80					11																	68305152		2200	4294	6494	SO:0001583	missense	55291	exon3			TTGATCTTCACTC	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.20T>C	chr11.hg19:g.68305152T>C	ENSP00000377389:p.Leu7Pro	207.0	0.0	.		236.0	60.0	.	NM_001164162	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Missense_Mutation	SNP	ENST00000393800.2	hg19	CCDS53672.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.301170	0.81136	.	.	ENSG00000110075	ENST00000393799;ENST00000393800;ENST00000528635;ENST00000533127;ENST00000529344;ENST00000524845;ENST00000265637;ENST00000524904;ENST00000393801;ENST00000265636;ENST00000529710;ENST00000527403;ENST00000531244	T;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;0.44	4.68	4.68	0.58851	.	0.000000	0.85682	D	0.000000	T	0.76744	0.4030	M	0.90814	3.15	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;0.998;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.993;0.987;0.997;0.984;1.0;0.997	T	0.82232	-0.0559	9	.	.	.	.	14.3003	0.66341	0.0:0.0:0.0:1.0	.	7;7;7;7;7;7	Q5H9R7-3;Q5H9R7-6;Q5H9R7-2;Q5H9R7;Q5H9R7-5;Q5H9R7-4	.;.;.;PP6R3_HUMAN;.;.	P	7	ENSP00000377388:L7P;ENSP00000377389:L7P;ENSP00000433768:L7P;ENSP00000433551:L7P;ENSP00000431415:L7P;ENSP00000265637:L7P;ENSP00000433058:L7P;ENSP00000377390:L7P;ENSP00000265636:L7P;ENSP00000437329:L7P;ENSP00000433565:L7P;ENSP00000432837:L7P	.	L	+	2	0	PPP6R3	68061728	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.774000	0.85478	1.973000	0.57446	0.455000	0.32223	CTT	.	.	.	none		0.318	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1	NM_018312		C	68305152	T	C	68305152	3	2	23	1	0	0	0	0	1	0	0	0	13851	1609	56	3	22	3	SAPS3	11	68305152	Missense_Mutation	SNP	T	TCGA-2Z-A9JT-01A-11D-A42J-10	24175651	68305152	66701364	45	1621											
DDX25	29118	hgsc.bcm.edu	37	chr11	125787115	125787115	+	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	gtgcaacatttatggcagcaTcaccattggtcaggccatca	11	10	9	11	0	3	0	3	0	0	0	3	0	3	0	2	3	3	3	2	3	2	3			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr11:125787115T>A	ENST00000263576.6	+	9	1162	c.1007T>A	c.(1006-1008)aTc>aAc	p.I336N	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	336	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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)		TATGGCAGCATCACCATTGGT	0.502																																					p.I336N		Atlas-SNP	.											.	DDX25	65	.	0			c.T1007A						PASS	.						38	37	38					11																	125787115		2128	4248	6376	SO:0001583	missense	29118	exon9			GCAGCATCACCAT	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.1007T>A	chr11.hg19:g.125787115T>A	ENSP00000263576:p.Ile336Asn	46.0	0.0	.		58.0	14.0	.	NM_013264	B2R6Z0|Q5XVN2|Q86W81|Q8IYP1	Missense_Mutation	SNP	ENST00000263576.6	hg19	CCDS44766.1	.	.	.	.	.	.	.	.	.	.	T	14.72	2.618207	0.46736	.	.	ENSG00000109832	ENST00000525943;ENST00000263576;ENST00000526875	T	0.04917	3.53	5.89	5.89	0.94794	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.13713	0.0332	L	0.28694	0.88	0.80722	D	1	D;D	0.76494	0.999;0.999	P;P	0.58928	0.848;0.848	T	0.01030	-1.1475	10	0.87932	D	0	-23.2211	15.9893	0.80188	0.0:0.0:0.0:1.0	.	336;336	B4DHI6;Q9UHL0	.;DDX25_HUMAN	N	222;336;202	ENSP00000263576:I336N	ENSP00000263576:I336N	I	+	2	0	DDX25	125292325	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.621000	0.83083	2.254000	0.74563	0.533000	0.62120	ATC	.	.	.	none		0.502	DDX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386736.3	NM_013264		A	125787115	T	A	125787115	3	1	23	1	0	0	0	0	1	0	0	0	4354	1435	50	5	1041	5	DDX25	11	125787115	Missense_Mutation	SNP	T	TCGA-2Z-A9JT-01A-11D-A42J-10	57481963	125787115	9219401	46	1622											
SLC6A13	6540	hgsc.bcm.edu	37	chr12	369149	369149	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagggtgccatcttcctcctTcttttccatgactggataca	7	14	7	13	0	2	1	0	1	2	0	5	2	5	2	4	2	2	0	4	2	1	5			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr12:369149T>C	ENST00000343164.4	-	2	122	c.70A>G	c.(70-72)Aag>Gag	p.K24E	SLC6A13_ENST00000445055.2_Missense_Mutation_p.K24E|RP11-283I3.4_ENST00000540868.1_RNA|SLC6A13_ENST00000436453.1_Missense_Mutation_p.K24E	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	24				Missing (in Ref. 1; AAF64247). {ECO:0000305}.	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)			TCTTCCTCCTTCTTTTCCATG	0.522																																					p.K24E		Atlas-SNP	.											.	SLC6A13	62	.	0			c.A70G						PASS	.						237	218	224					12																	369149		2203	4300	6503	SO:0001583	missense	6540	exon2			CCTCCTTCTTTTC	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.70A>G	chr12.hg19:g.369149T>C	ENSP00000339260:p.Lys24Glu	94.0	0.0	.		153.0	79.0	.	NM_016615	B4DJL1|Q8TCC2|Q8WW56	Missense_Mutation	SNP	ENST00000343164.4	hg19	CCDS8502.1	.	.	.	.	.	.	.	.	.	.	T	0.012	-1.687081	0.00738	.	.	ENSG00000010379	ENST00000445055;ENST00000343164;ENST00000546319;ENST00000436453	T;T;T;T	0.73363	-0.7;-0.74;0.13;0.46	5.94	1.65	0.23941	.	1.192160	0.05617	N	0.579148	T	0.49423	0.1556	N	0.03608	-0.345	0.19775	N	0.999955	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.30060	-0.9991	10	0.05351	T	0.99	.	10.5688	0.45188	0.0:0.6942:0.0:0.3058	.	24;24;24	B4DJL1;Q8WW56;Q9NSD5	.;.;S6A13_HUMAN	E	24	ENSP00000407104:K24E;ENSP00000339260:K24E;ENSP00000444606:K24E;ENSP00000389316:K24E	ENSP00000339260:K24E	K	-	1	0	SLC6A13	239410	0.712000	0.27916	0.864000	0.33941	0.053000	0.15095	0.179000	0.16840	-0.052000	0.13311	-2.020000	0.00432	AAG	.	.	.	none		0.522	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615		C	369149	T	C	369149	3	2	23	1	0	0	0	0	1	0	0	0	14689	1792	62	3	1794	3	SLC6A13	12	369149	Missense_Mutation	SNP	T	TCGA-2Z-A9JT-01A-11D-A42J-10		369149	133482746	47	1623											
LTBR	4055	hgsc.bcm.edu	37	chr12	6494235	6494235	+	Missense_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	gcatccgggacacagtttgtGccacatgtgccgagaattcc	9	9	11	12	2	0	1	0	0	0	1	2	3	2	2	4	1	2	2	4	1	1	2			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr12:6494235G>A	ENST00000228918.4	+	3	567	c.241G>A	c.(241-243)Gcc>Acc	p.A81T	LTBR_ENST00000546296.1_3'UTR|LTBR_ENST00000543190.1_5'UTR|LTBR_ENST00000539925.1_Missense_Mutation_p.A62T|LTBR_ENST00000541102.1_5'Flank	NM_002342.2	NP_002333.1	P36941	TNR3_HUMAN	lymphotoxin beta receptor (TNFR superfamily, member 3)	81					apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|cervix(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	15						CACAGTTTGTGCCACATGTGC	0.587																																					p.A81T		Atlas-SNP	.											.	LTBR	30	.	0			c.G241A						PASS	.						139	128	132					12																	6494235		2203	4300	6503	SO:0001583	missense	4055	exon3			GTTTGTGCCACAT	L04270	CCDS8544.1, CCDS59233.1	12p13	2013-05-22				ENSG00000111321		"Tumor necrosis factor receptor superfamily"	6718	protein-coding gene	gene with protein product		600979		D12S370		8171323, 8486360	Standard	NM_002342		Approved	TNFCR, TNFR-RP, TNFR2-RP, TNF-R-III, TNFRSF3	uc001qny.2	P36941		ENST00000228918.4:c.241G>A	chr12.hg19:g.6494235G>A	ENSP00000228918:p.Ala81Thr	64.0	0.0	.		80.0	18.0	.	NM_002342	B7Z1D2|D3DUR2|F5GXE7	Missense_Mutation	SNP	ENST00000228918.4	hg19	CCDS8544.1	.	.	.	.	.	.	.	.	.	.	G	11.39	1.624615	0.28889	.	.	ENSG00000111321	ENST00000539925;ENST00000228918;ENST00000536876	T;T;T	0.69685	-0.42;-0.42;-0.42	4.64	-3.91	0.04168	.	0.671765	0.13866	N	0.357310	T	0.44371	0.1290	L	0.37561	1.115	0.20926	N	0.99983	B;B;B	0.24721	0.11;0.027;0.024	B;B;B	0.17433	0.018;0.006;0.005	T	0.25152	-1.0140	10	0.19147	T	0.46	0.0217	4.8169	0.13371	0.4152:0.0:0.3823:0.2026	.	62;62;81	F5GXE7;B7Z1D2;P36941	.;.;TNR3_HUMAN	T	62;81;76	ENSP00000440875:A62T;ENSP00000228918:A81T;ENSP00000437647:A76T	ENSP00000228918:A81T	A	+	1	0	LTBR	6364496	0.000000	0.05858	0.000000	0.03702	0.077000	0.17291	-1.019000	0.03622	-0.623000	0.05618	-0.367000	0.07326	GCC	.	.	.	none		0.587	LTBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399422.1			A	6494235	G	A	6494235	3	1	23	1	0	0	0	0	1	0	0	0	9084	1319	46	2	251	2	LTBR	12	6494235	Missense_Mutation	SNP	G	TCGA-2Z-A9JT-01A-11D-A42J-10	6125086	6494235	127357660	48	1624											
PEX5	5830	hgsc.bcm.edu	37	chr12	7351609	7351609	+	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	cttctctgctccttgcagacCccttgtctgtgtcccctgcc	2	14	7	18	0	2	1	0	0	2	1	5	1	4	1	6	0	3	2	6	0	0	3			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr12:7351609C>A	ENST00000455147.2	+	7	1031	c.451C>A	c.(451-453)Ccc>Acc	p.P151T	PEX5_ENST00000266563.5_Missense_Mutation_p.P151T|PEX5_ENST00000420616.2_Missense_Mutation_p.P151T|PEX5_ENST00000266564.3_Missense_Mutation_p.P151T|PEX5_ENST00000412720.2_Missense_Mutation_p.P172T|PEX5_ENST00000545220.1_Intron|PEX5_ENST00000434354.2_Missense_Mutation_p.P166T	NM_001131026.1	NP_001124498.1	P50542	PEX5_HUMAN	peroxisomal biogenesis factor 5	151					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						CCTTGCAGACCCCTTGTCTGT	0.542																																					p.P166T		Atlas-SNP	.											.	PEX5	63	.	0			c.C496A						PASS	.						67	60	62					12																	7351609		2203	4300	6503	SO:0001583	missense	5830	exon6			GCAGACCCCTTGT	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.451C>A	chr12.hg19:g.7351609C>A	ENSP00000400647:p.Pro151Thr	62.0	0.0	.		83.0	38.0	.	NM_001131023	A8K891|B4DZ45|B7ZAD5|D3DUT8|Q15115|Q15266|Q96FN7	Missense_Mutation	SNP	ENST00000455147.2	hg19	CCDS44823.1	.	.	.	.	.	.	.	.	.	.	C	14.33	2.504553	0.44558	.	.	ENSG00000139197	ENST00000536883;ENST00000542539;ENST00000455147;ENST00000266563;ENST00000543974;ENST00000434354;ENST00000545574;ENST00000420616;ENST00000412720;ENST00000396637;ENST00000266564;ENST00000545845	D;D;D;D;D;D;D	0.88201	-2.3;-2.35;-2.32;-2.3;-2.32;-2.18;-2.32	5.91	4.99	0.66335	.	0.149257	0.45606	D	0.000347	D	0.85008	0.5599	L	0.33485	1.01	0.58432	D	0.999999	P;B;B;B;B	0.48407	0.91;0.073;0.205;0.307;0.138	P;B;B;B;B	0.45099	0.469;0.028;0.032;0.069;0.023	D	0.83524	0.0087	10	0.31617	T	0.26	.	14.2253	0.65855	0.0:0.9262:0.0:0.0738	.	172;166;151;151;151	B4E0T2;B4DZ45;P50542;P50542-3;P50542-2	.;.;PEX5_HUMAN;.;.	T	68;151;151;151;68;166;139;151;172;166;151;68	ENSP00000400647:P151T;ENSP00000266563:P151T;ENSP00000407401:P166T;ENSP00000410159:P151T;ENSP00000391601:P172T;ENSP00000379877:P166T;ENSP00000266564:P151T	ENSP00000266563:P151T	P	+	1	0	PEX5	7242876	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.918000	0.63376	1.434000	0.47414	0.655000	0.94253	CCC	.	.	.	none		0.542	PEX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398611.1	NM_000319		A	7351609	C	A	7351609	3	1	23	1	0	0	0	0	1	0	0	0	11755	623	22	4	514	4	PEX5	12	7351609	Missense_Mutation	SNP	C	TCGA-2Z-A9JT-01A-11D-A42J-10	857374	7351609	126500286	49	1625											
SUOX	6821	hgsc.bcm.edu	37	chr12	56397604	56397604	+	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	ggccctctatgctgttcacaAccagtcccatgtgcgtgagt	7	11	10	13	1	2	1	1	1	1	0	3	1	3	1	3	1	3	2	3	1	2	2			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr12:56397604A>T	ENST00000394109.3	+	3	1155	c.431A>T	c.(430-432)aAc>aTc	p.N144I	SUOX_ENST00000550478.1_3'UTR|SUOX_ENST00000548274.1_Missense_Mutation_p.N144I|SUOX_ENST00000394115.2_Missense_Mutation_p.N144I|SUOX_ENST00000266971.3_Missense_Mutation_p.N144I|SUOX_ENST00000551841.2_Intron|SUOX_ENST00000356124.4_Missense_Mutation_p.N144I			P51687	SUOX_HUMAN	sulfite oxidase	144	Cytochrome b5 heme-binding. {ECO:0000255|PROSITE-ProRule:PRU00279}.				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)			GCTGTTCACAACCAGTCCCAT	0.557																																					p.N144I		Atlas-SNP	.											.	SUOX	33	.	0			c.A431T						PASS	.						99	97	97					12																	56397604		2203	4300	6503	SO:0001583	missense	6821	exon6			TTCACAACCAGTC	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.431A>T	chr12.hg19:g.56397604A>T	ENSP00000377668:p.Asn144Ile	161.0	0.0	.		180.0	74.0	.	NM_000456		Missense_Mutation	SNP	ENST00000394109.3	hg19	CCDS8901.2	.	.	.	.	.	.	.	.	.	.	A	15.77	2.932930	0.52866	.	.	ENSG00000139531	ENST00000356124;ENST00000266971;ENST00000394115;ENST00000548274;ENST00000546833;ENST00000394109	T;T;T;T;T;T	0.80909	-1.43;-1.43;-1.43;-1.43;-1.43;-1.43	4.46	2.08	0.27032	Cytochrome b5 (4);	0.103271	0.64402	D	0.000005	T	0.79924	0.4530	M	0.68317	2.08	0.45403	D	0.99838	B	0.32526	0.374	B	0.42593	0.392	T	0.74228	-0.3733	10	0.40728	T	0.16	-6.0079	8.0486	0.30564	0.8148:0.0:0.1852:0.0	.	144	P51687	SUOX_HUMAN	I	144	ENSP00000348440:N144I;ENSP00000266971:N144I;ENSP00000377674:N144I;ENSP00000450245:N144I;ENSP00000449872:N144I;ENSP00000377668:N144I	ENSP00000266971:N144I	N	+	2	0	SUOX	54683871	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.061000	0.49963	0.463000	0.27118	0.533000	0.62120	AAC	.	.	.	none		0.557	SUOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250309.1	NM_000456		T	56397604	A	T	56397604	3	4	23	1	0	0	0	0	1	0	0	0	15407	43	2	5	441	5	SUOX	12	56397604	Missense_Mutation	SNP	A	TCGA-2Z-A9JT-01A-11D-A42J-10	49045995	56397604	77454291	50	1626											
RAB21	23011	hgsc.bcm.edu	37	chr12	72167772	72167772	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcaaagaattacggaaaatgTtgggaaatgaaatctgttta	17	12	9	3	1	2	2	1	1	1	1	2	4	2	4	0	2	1	2	0	2	8	4			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr12:72167772T>C	ENST00000261263.3	+	4	617	c.361T>C	c.(361-363)Ttg>Ctg	p.L121L		NM_014999.2	NP_055814.1	Q9UL25	RAB21_HUMAN	RAB21, member RAS oncogene family	121					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						ACGGAAAATGTTGGGAAATGA	0.294																																					p.L121L		Atlas-SNP	.											.	RAB21	17	.	0			c.T361C						PASS	.						75	80	78					12																	72167772		2203	4294	6497	SO:0001819	synonymous_variant	23011	exon4			AAAATGTTGGGAA	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.361T>C	chr12.hg19:g.72167772T>C		132.0	0.0	.		147.0	75.0	.	NM_014999	Q14466|Q569H3	Silent	SNP	ENST00000261263.3	hg19	CCDS9003.1																																																																																			.	.	.	none		0.294	RAB21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404855.1			C	72167772	T	C	72167772	2	2	23	1	0	0	0	0	0	0	0	1	12921	1722	60	3		3	RAB21	12	72167772	Silent	SNP	T	TCGA-2Z-A9JT-01A-11D-A42J-10	15770168	72167772	61684123	51	1627											
NAP1L1	4673	hgsc.bcm.edu	37	chr12	76462722	76462722	+	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	ttcttcaccagtttcctcttCttctacttcttcaacatcat	7	19	1	14	0	8	0	3	0	5	0	9	0	9	0	2	0	2	1	2	0	2	8			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr12:76462722C>A	ENST00000261182.8	-	3	556	c.70G>T	c.(70-72)Gaa>Taa	p.E24*	NAP1L1_ENST00000544816.1_Intron|NAP1L1_ENST00000393263.3_Nonsense_Mutation_p.E24*|NAP1L1_ENST00000542344.1_Intron|NAP1L1_ENST00000431879.3_5'UTR|NAP1L1_ENST00000535020.2_Nonsense_Mutation_p.E24*|NAP1L1_ENST00000549596.1_Nonsense_Mutation_p.E24*|NAP1L1_ENST00000547773.1_Intron|NAP1L1_ENST00000548044.1_5'UTR|NAP1L1_ENST00000552342.1_Nonsense_Mutation_p.E24*	NM_004537.4|NM_139207.2	NP_004528.1|NP_631946.1	P55209	NP1L1_HUMAN	nucleosome assembly protein 1-like 1	24	Asp/Glu-rich (acidic).				DNA replication (GO:0006260)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	9		Colorectal(145;0.09)				GTTTCCTCTTCTTCTACTTCT	0.358																																					p.E24X		Atlas-SNP	.											.	NAP1L1	33	.	0			c.G70T						PASS	.						215	212	213					12																	76462722		2203	4300	6503	SO:0001587	stop_gained	4673	exon3			CCTCTTCTTCTAC		CCDS9013.1	12q21.1	2010-03-17			ENSG00000187109	ENSG00000187109			7637	protein-coding gene	gene with protein product		164060				8297347	Standard	NM_004537		Approved	NRP, NAP1, NAP1L, MGC8688, MGC23410	uc001sxx.2	P55209		ENST00000261182.8:c.70G>T	chr12.hg19:g.76462722C>A	ENSP00000261182:p.Glu24*	80.0	0.0	.		93.0	42.0	.	NM_004537	B3KNT8	Nonsense_Mutation	SNP	ENST00000261182.8	hg19	CCDS9013.1	.	.	.	.	.	.	.	.	.	.	C	38	6.800209	0.97849	.	.	ENSG00000187109	ENST00000261182;ENST00000552056;ENST00000393263;ENST00000535020;ENST00000549596;ENST00000552342;ENST00000550934;ENST00000551992;ENST00000551600;ENST00000547704;ENST00000547479	.	.	.	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	.	19.7353	0.96200	0.0:1.0:0.0:0.0	.	.	.	.	X	24;18;24;24;24;24;24;24;24;24;24	.	ENSP00000261182:E24X	E	-	1	0	NAP1L1	74748989	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.979000	0.70508	2.743000	0.94032	0.655000	0.94253	GAA	.	.	.	none		0.358	NAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405850.3	NM_139207		A	76462722	C	A	76462722	4	1	23	1	0	0	0	0	0	1	0	0	10163	922	32	4	1157	4	NAP1L1	12	76462722	Nonsense_Mutation	SNP	C	TCGA-2Z-A9JT-01A-11D-A42J-10	4294950	76462722	57389173	52	1628											
MED13L	23389	hgsc.bcm.edu	37	chr12	116453057	116453057	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaaccaggtgactggcagcActctgcatacctccactctc	10	8	8	15	0	2	1	0	1	2	0	4	2	3	1	3	2	4	3	3	2	2	1			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr12:116453057A>G	ENST00000281928.3	-	8	1238	c.1032T>C	c.(1030-1032)agT>agC	p.S344S		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	344						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)		GACTGGCAGCACTCTGCATAC	0.428																																					p.S344S		Atlas-SNP	.											.	MED13L	193	.	0			c.T1032C						PASS	.						148	132	137					12																	116453057		2203	4300	6503	SO:0001819	synonymous_variant	23389	exon8			GGCAGCACTCTGC	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.1032T>C	chr12.hg19:g.116453057A>G		106.0	0.0	.		153.0	68.0	.	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Silent	SNP	ENST00000281928.3	hg19	CCDS9177.1																																																																																			.	.	.	none		0.428	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3			G	116453057	A	G	116453057	2	3	23	1	0	0	0	0	0	0	0	1	9438	156	6	3		3	MED13L	12	116453057	Silent	SNP	A	TCGA-2Z-A9JT-01A-11D-A42J-10	39990335	116453057	17398838	53	1629											
PXN	5829	hgsc.bcm.edu	37	chr12	120660781	120660781	+	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	acggtgggtgaaggctcagcTgatttctgcttgttggggaa	7	12	16	6	1	2	2	1	2	1	0	2	3	2	3	0	5	2	4	0	5	2	3			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr12:120660781T>G	ENST00000228307.7	-	4	519	c.378A>C	c.(376-378)tcA>tcC	p.S126S	PXN_ENST00000267257.7_Silent_p.S126S|PXN_ENST00000538144.1_5'UTR|PXN_ENST00000424649.2_Silent_p.S126S|PXN_ENST00000536957.1_Silent_p.S124S|PXN_ENST00000458477.2_5'UTR	NM_001080855.2	NP_001074324.1	P49023	PAXI_HUMAN	paxillin	126					activation of MAPK activity (GO:0000187)|branching morphogenesis of an epithelial tube (GO:0048754)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cellular component movement (GO:0006928)|cellular response to reactive oxygen species (GO:0034614)|cytoskeleton organization (GO:0007010)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|growth hormone receptor signaling pathway (GO:0060396)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|muscle contraction (GO:0006936)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of cell shape (GO:0008360)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	beta-catenin binding (GO:0008013)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AAGGCTCAGCTGATTTCTGCT	0.532																																					p.S126S		Atlas-SNP	.											.	PXN	69	.	0			c.A378C						PASS	.						104	106	105					12																	120660781		2035	4186	6221	SO:0001819	synonymous_variant	5829	exon4			CTCAGCTGATTTC	U14588	CCDS44996.1, CCDS44997.1, CCDS44998.1, CCDS58281.1	12q24	2006-01-23			ENSG00000089159	ENSG00000089159			9718	protein-coding gene	gene with protein product		602505				7534286	Standard	NM_001080855		Approved		uc001txv.3	P49023	OTTHUMG00000169169	ENST00000228307.7:c.378A>C	chr12.hg19:g.120660781T>G		125.0	0.0	.		163.0	43.0	.	NM_001080855	B2RAI3|B7ZMB4|O14970|O14971|O60360|Q5HYA4	Silent	SNP	ENST00000228307.7	hg19	CCDS44997.1																																																																																			.	.	.	none		0.532	PXN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402679.4	NM_002859		G	120660781	T	G	120660781	2	3	23	1	0	0	0	0	0	0	0	1	12865	1567	55	5		5	PXN	12	120660781	Silent	SNP	T	TCGA-2Z-A9JT-01A-11D-A42J-10	4207724	120660781	13191114	54	1630											
KNTC1	9735	hgsc.bcm.edu	37	chr12	123075197	123075201	+	Frame_Shift_Del	DEL	ACTGC	ACTGC	-																															tcttgacctggcgttgggttActgcactctcttacctcaaa																										TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	ACTGC	ACTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr12:123075197_123075201delACTGC	ENST00000333479.7	+	41	4220_4224	c.4043_4047delACTGC	c.(4042-4047)tactgcfs	p.YC1348fs	KNTC1_ENST00000450485.2_Intron	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	1348					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)		GCGTTGGGTTACTGCACTCTCTTAC	0.385																																					p.1348_1349del		Atlas-Indel,Pindel	.											.	KNTC1	182	.	0			c.4042_4046del						PASS	.																																			SO:0001589	frameshift_variant	9735	exon41			.		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.4043_4047delACTGC	chr12.hg19:g.123075197_123075201delACTGC	ENSP00000328236:p.Tyr1348fs	136.0	0.0	0		126.0	45.0	0.357143	NM_014708	A7E2C4|B3KSG2	Frame_Shift_Del	DEL	ENST00000333479.7	hg19	CCDS45002.1																																																																																			.	.	.	none		0.385	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2			-	123075201	ACTGC	-	123075197	7	5	23	1	0	1	0	1	0	0	0	0	8435	391	14	0	4201	0	KNTC1	12	123075197	Frame_Shift_Del	DEL	ACTGC	TCGA-2Z-A9JT-01A-11D-A42J-10	2414416	123075197	10776698	55	1631											
NALCN	259232	hgsc.bcm.edu	37	chr13	102047671	102047671	+	Frame_Shift_Del	DEL	A	A	-																															tggcgtattcatacaaacagAaatgacgctgatgatggcac																								rs188237867		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr13:102047671delA	ENST00000251127.6	-	3	235	c.154delT	c.(154-156)tctfs	p.S52fs	NALCN_ENST00000376200.5_Frame_Shift_Del_p.S52fs|NALCN_ENST00000376196.3_Frame_Shift_Del_p.S52fs|NALCN_ENST00000470333.1_5'UTR	NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	52					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					ATACAAACAGAAATGACGCTG	0.443																																					p.S52fs		Atlas-Indel,Pindel	.											.	NALCN	431	.	0			c.155delC						PASS	.						143	113	123					13																	102047671		2203	4300	6503	SO:0001589	frameshift_variant	259232	exon3			.	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.154delT	chr13.hg19:g.102047671delA	ENSP00000251127:p.Ser52fs	84.0	0.0	0		104.0	29.0	0.278846	NM_052867	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Frame_Shift_Del	DEL	ENST00000251127.6	hg19	CCDS9498.1																																																																																			.	.	.	none		0.443	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		-	102047671	A	-	102047671	7	5	23	1	0	1	0	1	0	0	0	0	10155	246	9	0	5230	0	NALCN	13	102047671	Frame_Shift_Del	DEL	A	TCGA-2Z-A9JT-01A-11D-A42J-10		102047671	13122207	56	1632											
LTK	4058	hgsc.bcm.edu	37	chr15	41804906	41804906	+	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	acctccgccgtgcacttacaGatactggccagggcccggca	8	6	11	16	3	0	1	0	0	0	1	1	1	1	1	5	3	3	2	5	3	2	2			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr15:41804906G>A	ENST00000263800.6	-	3	454	c.358C>T	c.(358-360)Ctg>Ttg	p.L120L	LTK_ENST00000355166.5_Splice_Site_p.L120L|LTK_ENST00000561619.1_Intron|LTK_ENST00000453182.2_Splice_Site_p.L120L	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	120					cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		TGCACTTACAGATACTGGCCA	0.667										TSP Lung(18;0.14)																											p.L120L		Atlas-SNP	.											LTK_ENST00000263800,NS,carcinoma,0,2	LTK	117	.	0			c.C358T						PASS	.						11	12	11					15																	41804906		2183	4252	6435	SO:0001630	splice_region_variant	4058	exon3			CTTACAGATACTG	D16105	CCDS10077.1, CCDS10078.1, CCDS45237.1	15q15.1-q21.1	2009-07-10	2008-01-23		ENSG00000062524	ENSG00000062524	2.7.10.1		6721	protein-coding gene	gene with protein product		151520	"leukocyte tyrosine kinase"			2320375	Standard	NM_206961		Approved	TYK1	uc001zoa.3	P29376	OTTHUMG00000130339	ENST00000263800.6:c.359+1C>T	chr15.hg19:g.41804906G>A		62.0	0.0	.		44.0	14.0	.	NM_001135685	A6NNJ8|B4DL89|E9PFX4	Silent	SNP	ENST00000263800.6	hg19	CCDS10077.1																																																																																			.	.	.	none		0.667	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2		Silent	A	41804906	G	A	41804906	5	1	23	1	0	0	0	0	0	0	1	0	9087	956	33	2	2308	2	LTK	15	41804906	Splice_Site	SNP	G	TCGA-2Z-A9JT-01A-11D-A42J-10		41804906	60726486	57	1633											
TSPAN3	10099	hgsc.bcm.edu	37	chr15	77346604	77346612	+	In_Frame_Del	DEL	ATCAACCTC	ATCAACCTC	-																															tacactttctgaatgctgcgAtcaacctcattttccacctg																										TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	ATCAACCTC	ATCAACCTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr15:77346604_77346612delATCAACCTC	ENST00000267970.4	-	4	613_621	c.340_348delGAGGTTGAT	c.(340-348)gaggttgatdel	p.EVD114del	TSPAN3_ENST00000561277.1_5'UTR|TSPAN3_ENST00000346495.2_In_Frame_Del_p.EVD89del|TSPAN3_ENST00000424443.3_In_Frame_Del_p.EVD50del|TSPAN3_ENST00000559494.1_In_Frame_Del_p.EVD25del|TSPAN3_ENST00000558394.1_5'UTR|TSPAN3_ENST00000558745.1_5'UTR	NM_001168412.1|NM_005724.5|NM_198902.2	NP_001161884.1|NP_005715.1|NP_944492.1	O60637	TSN3_HUMAN	tetraspanin 3	114						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(6)|urinary_tract(1)	10				all cancers(203;1.14e-19)		GAATGCTGCGATCAACCTCATTTTCCACC	0.388																																					p.114_117del		Atlas-Indel,Pindel	.											.	TSPAN3	21	.	0			c.341_349del						PASS	.																																			SO:0001651	inframe_deletion	10099	exon4			.		CCDS10292.1, CCDS10293.1, CCDS53963.1	15q23	2013-02-14	2005-03-21	2005-03-21	ENSG00000140391	ENSG00000140391		"Tetraspanins"	17752	protein-coding gene	gene with protein product		613134	"transmembrane 4 superfamily member 8"	TM4SF8			Standard	NM_005724		Approved	TM4-A, TSPAN-3	uc002bcj.3	O60637	OTTHUMG00000143728	ENST00000267970.4:c.340_348delGAGGTTGAT	chr15.hg19:g.77346604_77346612delATCAACCTC	ENSP00000267970:p.Glu114_Asp116del	58.0	0.0	0		52.0	10.0	0.192308	NM_005724	A6NEH4|B3KQQ2|B4DP19|Q9BW22|Q9NVX9	In_Frame_Del	DEL	ENST00000267970.4	hg19	CCDS10292.1																																																																																			.	.	.	none		0.388	TSPAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289792.3	NM_005724		-	77346612	ATCAACCTC	-	77346604	7	5	23	1	0	1	0	1	0	0	0	0	16657	330	12	0	429	0	TSPAN3	15	77346604	In_Frame_Del	DEL	ATCAACCTC	TCGA-2Z-A9JT-01A-11D-A42J-10	35541698	77346604	25184788	58	1634											
ZNF598	90850	hgsc.bcm.edu	37	chr16	2053710	2053710	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggatggtggcaaaggcaggaAgcttcttcccaaagaccacc	12	6	12	11	0	1	1	0	0	1	1	2	3	2	3	3	5	1	3	3	5	3	2			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr16:2053710A>G	ENST00000563630.1	-	2	319	c.77T>C	c.(76-78)cTt>cCt	p.L26P	ZNF598_ENST00000562103.1_Missense_Mutation_p.L26P|ZNF598_ENST00000431526.1_Missense_Mutation_p.L81P			Q86UK7	ZN598_HUMAN	zinc finger protein 598	81							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						AAAGGCAGGAAGCTTCTTCCC	0.537											OREG0023548	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L81P		Atlas-SNP	.											.	ZNF598	55	.	0			c.T242C						PASS	.						97	103	101					16																	2053710		2078	4219	6297	SO:0001583	missense	90850	exon4			GCAGGAAGCTTCT	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.77T>C	chr16.hg19:g.2053710A>G	ENSP00000455882:p.Leu26Pro	119.0	0.0	.	600	90.0	28.0	.	NM_178167	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000563630.1	hg19		.	.	.	.	.	.	.	.	.	.	.	14.36	2.511915	0.44660	.	.	ENSG00000167962	ENST00000431526	T	0.28255	1.62	5.05	5.05	0.67936	.	0.145740	0.48767	D	0.000168	T	0.19446	0.0467	N	0.16708	0.43	0.80722	D	1	P	0.37500	0.597	B	0.34873	0.191	T	0.05750	-1.0866	10	0.30854	T	0.27	-18.4695	13.9561	0.64150	1.0:0.0:0.0:0.0	.	81	Q86UK7	ZN598_HUMAN	P	81	ENSP00000411409:L81P	ENSP00000411409:L81P	L	-	2	0	ZNF598	1993711	1.000000	0.71417	0.990000	0.47175	0.934000	0.57294	5.859000	0.69539	1.911000	0.55334	0.402000	0.26972	CTT	.	.	.	none		0.537	ZNF598-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000434439.1	NM_178167		G	2053710	A	G	2053710	3	3	23	1	0	0	0	0	1	0	0	0	18040	72	3	3	2516	3	ZNF598	16	2053710	Missense_Mutation	SNP	A	TCGA-2Z-A9JT-01A-11D-A42J-10		2053710	88301043	59	1635											
NAGPA	51172	hgsc.bcm.edu	37	chr16	5075564	5075564	+	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	tcatctcctgcagcgggtggTatgcatagtccccatgcagg	7	10	12	12	1	2	0	1	0	1	0	4	0	3	0	3	3	4	4	3	3	2	2			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr16:5075564T>A	ENST00000312251.3	-	10	1482	c.1463A>T	c.(1462-1464)tAc>tTc	p.Y488F	RP11-165E7.1_ENST00000588778.1_RNA|NAGPA_ENST00000381955.3_Missense_Mutation_p.Y454F	NM_016256.3	NP_057340.2	Q9UK23	NAGPA_HUMAN	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase	488					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|lysosome organization (GO:0007040)|protein glycosylation (GO:0006486)|protein targeting to lysosome (GO:0006622)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase activity (GO:0003944)			endometrium(4)|large_intestine(4)|lung(3)|urinary_tract(1)	12					N-Acetyl-D-glucosamine(DB00141)	CAGCGGGTGGTATGCATAGTC	0.637																																					p.Y488F		Atlas-SNP	.											.	NAGPA	30	.	0			c.A1463T						PASS	.						67	75	72					16																	5075564		2197	4300	6497	SO:0001583	missense	51172	exon10			GGGTGGTATGCAT	AF187072	CCDS10527.1	16p13.3	2008-02-05			ENSG00000103174	ENSG00000103174	3.1.4.45		17378	protein-coding gene	gene with protein product		607985				10551838, 12058031	Standard	NM_016256		Approved	APAA, UCE	uc002cyg.3	Q9UK23	OTTHUMG00000090515	ENST00000312251.3:c.1463A>T	chr16.hg19:g.5075564T>A	ENSP00000310998:p.Tyr488Phe	99.0	0.0	.		122.0	56.0	.	NM_016256	B2RAS1|Q96EJ8	Missense_Mutation	SNP	ENST00000312251.3	hg19	CCDS10527.1	.	.	.	.	.	.	.	.	.	.	T	17.13	3.311544	0.60414	.	.	ENSG00000103174	ENST00000312251;ENST00000381955	T;T	0.52057	2.2;0.68	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.66386	0.2784	M	0.72894	2.215	0.38705	D	0.953078	D;D	0.76494	0.999;0.996	D;D	0.78314	0.991;0.99	T	0.72669	-0.4223	10	0.72032	D	0.01	-43.9859	12.7796	0.57469	0.0:0.0:0.0:1.0	.	488;454	Q9UK23;Q9UK23-2	NAGPA_HUMAN;.	F	488;454	ENSP00000310998:Y488F;ENSP00000371381:Y454F	ENSP00000310998:Y488F	Y	-	2	0	NAGPA	5015565	1.000000	0.71417	0.996000	0.52242	0.066000	0.16364	3.790000	0.55461	1.962000	0.57031	0.459000	0.35465	TAC	.	.	.	none		0.637	NAGPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207003.1	NM_016256		A	5075564	T	A	5075564	3	1	23	1	0	0	0	0	1	0	0	0	10151	1638	57	5	88	5	NAGPA	16	5075564	Missense_Mutation	SNP	T	TCGA-2Z-A9JT-01A-11D-A42J-10	3021854	5075564	85279189	60	1636											
ATP2A1	487	hgsc.bcm.edu	37	chr16	28914368	28914368	+	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	cagcctgtccgagaaccagtCcctgctgcggatgccaccct	7	7	10	17	2	0	1	0	0	0	1	2	3	2	2	6	1	5	1	6	1	1	0			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr16:28914368C>T	ENST00000357084.3	+	20	3029	c.2762C>T	c.(2761-2763)tCc>tTc	p.S921F	ATP2A1_ENST00000536376.1_Missense_Mutation_p.S796F|ATP2A1_ENST00000395503.4_Missense_Mutation_p.S921F	NM_173201.3	NP_775293.1	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	921					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						GAGAACCAGTCCCTGCTGCGG	0.632																																					p.S921F		Atlas-SNP	.											.	ATP2A1	116	.	0			c.C2762T						PASS	.						101	82	89					16																	28914368		2197	4300	6497	SO:0001583	missense	487	exon20			ACCAGTCCCTGCT		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.2762C>T	chr16.hg19:g.28914368C>T	ENSP00000349595:p.Ser921Phe	35.0	0.0	.		59.0	17.0	.	NM_004320	A8K5J9|B3KY17|O14984	Missense_Mutation	SNP	ENST00000357084.3	hg19	CCDS10643.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.542099	0.85917	.	.	ENSG00000196296	ENST00000357084;ENST00000395503;ENST00000536376	D;D;D	0.90261	-2.64;-2.64;-2.52	4.74	4.74	0.60224	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.97117	0.9058	H	0.97291	3.975	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.997	D	0.98541	1.0632	10	0.87932	D	0	.	16.6475	0.85180	0.0:1.0:0.0:0.0	.	796;921;921	B3KY17;O14983;O14983-2	.;AT2A1_HUMAN;.	F	921;921;796	ENSP00000349595:S921F;ENSP00000378879:S921F;ENSP00000443101:S796F	ENSP00000349595:S921F	S	+	2	0	ATP2A1	28821869	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.608000	0.82898	2.456000	0.83038	0.561000	0.74099	TCC	.	.	.	none		0.632	ATP2A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254686.2	NM_004320		T	28914368	C	T	28914368	3	4	23	1	0	0	0	0	1	0	0	0	1136	855	30	2	2840	2	ATP2A1	16	28914368	Missense_Mutation	SNP	C	TCGA-2Z-A9JT-01A-11D-A42J-10	23838804	28914368	61440385	61	1637											
OR1E2	8388	hgsc.bcm.edu	37	chr17	3336754	3336754	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcggtgtagtgcatggggaAgcagatggccacatagcggt	9	7	18	7	2	0	1	0	0	0	1	0	2	0	2	1	6	3	3	1	6	3	2			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr17:3336754A>G	ENST00000248384.1	-	1	381	c.382T>C	c.(382-384)Ttc>Ctc	p.F128L		NM_003554.1	NP_003545.1	P47887	OR1E2_HUMAN	olfactory receptor, family 1, subfamily E, member 2	128					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						TGCATGGGGAAGCAGATGGCC	0.557																																					p.F128L		Atlas-SNP	.											.	OR1E2	25	.	0			c.T382C						PASS	.						98	80	86					17																	3336754		2203	4300	6503	SO:0001583	missense	8388	exon1			TGGGGAAGCAGAT	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.382T>C	chr17.hg19:g.3336754A>G	ENSP00000248384:p.Phe128Leu	149.0	0.0	.		195.0	86.0	.	NM_003554	O43877|O95632|Q0VAD5|Q0VAD6|Q9UL13	Missense_Mutation	SNP	ENST00000248384.1	hg19	CCDS11026.1	.	.	.	.	.	.	.	.	.	.	-	13.49	2.253554	0.39797	.	.	ENSG00000127780	ENST00000248384;ENST00000454364	T	0.00388	7.59	5.47	1.98	0.26296	GPCR, rhodopsin-like superfamily (1);	0.300607	0.29355	N	0.012388	T	0.00144	0.0004	N	0.05050	-0.12	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.44832	-0.9302	10	0.72032	D	0.01	.	3.5344	0.07789	0.473:0.0:0.354:0.1731	.	128	P47887	OR1E2_HUMAN	L	128;127	ENSP00000248384:F128L	ENSP00000248384:F128L	F	-	1	0	OR1E2	3283504	0.000000	0.05858	0.884000	0.34674	0.914000	0.54420	-1.011000	0.03652	0.517000	0.28361	0.528000	0.53228	TTC	.	.	.	none		0.557	OR1E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207311.1			G	3336754	A	G	3336754	3	3	23	1	0	0	0	0	1	0	0	0	10962	72	3	3	592	3	OR1E2	17	3336754	Missense_Mutation	SNP	A	TCGA-2Z-A9JT-01A-11D-A42J-10		3336754	77858456	62	1638											
CTNS	1497	hgsc.bcm.edu	37	chr17	3563642	3563642	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtttgtacagaaagagaccGgggtatgaccagctgaacta	13	9	12	7	1	0	4	0	2	0	2	0	5	0	4	2	2	3	4	2	2	5	4	rs371189196	byFrequency	TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr17:3563642G>A	ENST00000046640.3	+	12	1676	c.1083G>A	c.(1081-1083)ccG>ccA	p.P361P	RP11-235E17.6_ENST00000575741.1_RNA|CTNS_ENST00000381870.3_Silent_p.P361P|CTNS_ENST00000441220.2_Silent_p.P253P|CTNS_ENST00000414524.2_Silent_p.P214P	NM_004937.2	NP_004928.2	O60931	CTNS_HUMAN	cystinosin, lysosomal cystine transporter	361					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)	p.P361P(2)		NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)	10				COAD - Colon adenocarcinoma(5;0.0829)	L-Cystine(DB00138)	GAAAGAGACCGGGGTATGACC	0.582													G|||	2	0.000399361	0	0	5008	,	,		18448	0		0.001	False		,,,				2504	0.001				p.P361P		Atlas-SNP	.											CTNS,NS,carcinoma,+1,1	CTNS	42	.	2	Substitution - coding silent(2)	endometrium(2)	c.G1083A						PASS	.						92	95	94					17																	3563642		2203	4300	6503	SO:0001819	synonymous_variant	1497	exon12			GAGACCGGGGTAT	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.1083G>A	chr17.hg19:g.3563642G>A		90.0	0.0	.		90.0	51.0	.	NM_001031681	D3DTJ5|Q8IZ01|Q9UNK6	Silent	SNP	ENST00000046640.3	hg19	CCDS11031.1																																																																																			.	.	.	weak		0.582	CTNS-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317696.1	NM_004937		A	3563642	G	A	3563642	2	1	23	1	0	0	0	0	0	0	0	1	4023	1103	39	1		1	CTNS	17	3563642	Silent	SNP	G	TCGA-2Z-A9JT-01A-11D-A42J-10	226888	3563642	77631568	63	1639											
KCTD11	147040	hgsc.bcm.edu	37	chr17	7256855	7256855	+	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	ggcaccccaagcttcctggaGgaggtgctgcgggtggctct	5	8	16	12	1	1	0	0	0	1	0	2	2	2	2	3	6	3	4	3	6	1	1			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr17:7256855G>T	ENST00000333751.3	+	1	1648	c.594G>T	c.(592-594)gaG>gaT	p.E198D	RP11-542C16.1_ENST00000572417.1_RNA|TMEM95_ENST00000576060.1_5'Flank|TMEM95_ENST00000330767.4_5'Flank|TMEM95_ENST00000389982.4_5'Flank	NM_001002914.2	NP_001002914.1	Q693B1	KCD11_HUMAN	potassium channel tetramerization domain containing 11	198					cell cycle (GO:0007049)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)				kidney(1)|large_intestine(2)|lung(1)	4		Prostate(122;0.157)				GCTTCCTGGAGGAGGTGCTGC	0.667																																					p.E198D		Atlas-SNP	.											.	KCTD11	17	.	0			c.G594T						PASS	.						18	21	20					17																	7256855		2175	4269	6444	SO:0001583	missense	147040	exon1			CCTGGAGGAGGTG	AK056227	CCDS32545.1	17p13.2	2013-06-20	2013-06-20	2003-11-26	ENSG00000213859	ENSG00000213859			21302	protein-coding gene	gene with protein product		609848	"chromosome 17 open reading frame 36", "potassium channel tetramerisation domain containing 11"	C17orf36		12186855, 21472142	Standard	NM_001002914		Approved	REN, KCASH1	uc002gge.4	Q693B1	OTTHUMG00000132061	ENST00000333751.3:c.594G>T	chr17.hg19:g.7256855G>T	ENSP00000328352:p.Glu198Asp	38.0	0.0	.		43.0	10.0	.	NM_001002914	B3KPE0	Missense_Mutation	SNP	ENST00000333751.3	hg19	CCDS32545.1	.	.	.	.	.	.	.	.	.	.	G	19.79	3.893530	0.72639	.	.	ENSG00000213859	ENST00000333751	T	0.79033	-1.23	4.79	1.74	0.24563	.	0.000000	0.46442	U	0.000295	T	0.76300	0.3968	L	0.29908	0.895	0.32060	N	0.595776	D	0.63880	0.993	D	0.67548	0.952	T	0.75184	-0.3407	10	0.46703	T	0.11	.	6.6193	0.22794	0.298:0.0:0.702:0.0	.	198	Q693B1	KCD11_HUMAN	D	198	ENSP00000328352:E198D	ENSP00000328352:E198D	E	+	3	2	KCTD11	7197579	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	1.616000	0.36933	0.258000	0.21686	-0.379000	0.06801	GAG	.	.	.	none		0.667	KCTD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255084.2	NM_001002914		T	7256855	G	T	7256855	3	4	23	1	0	0	0	0	1	0	0	0	8105	991	35	4	596	4	KCTD11	17	7256855	Missense_Mutation	SNP	G	TCGA-2Z-A9JT-01A-11D-A42J-10	3693213	7256855	73938355	64	1640											
NF1	4763	hgsc.bcm.edu	37	chr17	29687644	29687644	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttaccctcctgcactgcAgagccagcttagtatcactg	8	11	7	15	0	1	1	1	0	0	1	3	1	3	1	4	0	5	4	4	0	3	3			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr17:29687644A>G	ENST00000358273.4	+	57	8683	c.8300A>G	c.(8299-8301)cAg>cGg	p.Q2767R	NF1_ENST00000444181.2_Missense_Mutation_p.Q560R|NF1_ENST00000356175.3_Missense_Mutation_p.Q2746R	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	2767					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)		CCTGCACTGCAGAGCCAGCTT	0.458			"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.Q2767R		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.A8300G						PASS	.						219	198	205					17																	29687644		2203	4300	6503	SO:0001583	missense	4763	exon57	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	CACTGCAGAGCCA		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.8300A>G	chr17.hg19:g.29687644A>G	ENSP00000351015:p.Gln2767Arg	89.0	0.0	.		133.0	74.0	.	NM_001042492	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	hg19	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.889195	0.91889	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735;ENST00000444181	T;T;T;T	0.48836	3.15;3.29;2.98;0.8	5.87	5.87	0.94306	.	0.057056	0.64402	D	0.000001	T	0.43188	0.1236	N	0.24115	0.695	0.80722	D	1	D;B;B	0.56968	0.978;0.206;0.131	P;B;B	0.47402	0.546;0.085;0.039	T	0.41520	-0.9504	10	0.52906	T	0.07	.	16.27	0.82612	1.0:0.0:0.0:0.0	.	560;2746;2767	B4DXH1;P21359-2;P21359	.;.;NF1_HUMAN	R	2767;2746;2412;560	ENSP00000351015:Q2767R;ENSP00000348498:Q2746R;ENSP00000389907:Q2412R;ENSP00000396481:Q560R	ENSP00000348498:Q2746R	Q	+	2	0	NF1	26711770	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.000000	0.76290	2.248000	0.74166	0.533000	0.62120	CAG	.	.	.	none		0.458	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		G	29687644	A	G	29687644	3	3	23	1	0	0	0	0	1	0	0	0	10363	188	7	3	8587	3	NF1	17	29687644	Missense_Mutation	SNP	A	TCGA-2Z-A9JT-01A-11D-A42J-10	22430789	29687644	51507566	65	1641											
ABCA10	10349	hgsc.bcm.edu	37	chr17	67146187	67146187	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctccacaggtaacttatacGccattaaagaggaatatctg	14	10	7	10	1	1	1	0	0	1	1	2	2	2	2	3	2	2	1	3	2	7	5			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr17:67146187G>A	ENST00000269081.4	-	38	5324	c.4415C>T	c.(4414-4416)gCg>gTg	p.A1472V	ABCA10_ENST00000416101.2_3'UTR|ABCA10_ENST00000519732.1_5'UTR	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	1472					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)					TAACTTATACGCCATTAAAGA	0.363																																					p.A1472V		Atlas-SNP	.											.	ABCA10	209	.	0			c.C4415T						PASS	.						75	74	75					17																	67146187		2203	4300	6503	SO:0001583	missense	10349	exon38			TTATACGCCATTA	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.4415C>T	chr17.hg19:g.67146187G>A	ENSP00000269081:p.Ala1472Val	127.0	0.0	.		163.0	34.0	.	NM_080282	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Missense_Mutation	SNP	ENST00000269081.4	hg19	CCDS11684.1	.	.	.	.	.	.	.	.	.	.	G	0.086	-1.175617	0.01646	.	.	ENSG00000154263	ENST00000269081	D	0.82526	-1.62	3.15	-5.77	0.02369	.	0.651141	0.11480	U	0.559768	T	0.49115	0.1538	N	0.00869	-1.13	0.44067	D	0.99681	B;B	0.15719	0.007;0.014	B;B	0.09377	0.004;0.002	T	0.48410	-0.9038	10	0.02654	T	1	.	13.728	0.62769	0.6887:0.0:0.3113:0.0	.	464;1472	B4DPV2;Q8WWZ4	.;ABCAA_HUMAN	V	1472	ENSP00000269081:A1472V	ENSP00000269081:A1472V	A	-	2	0	ABCA10	64657782	0.001000	0.12720	0.000000	0.03702	0.064000	0.16182	-0.130000	0.10498	-1.288000	0.02378	-0.369000	0.07265	GCG	.	.	.	none		0.363	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282		A	67146187	G	A	67146187	3	1	23	1	0	0	0	0	1	0	0	0	29	1087	38	1	228	1	ABCA10	17	67146187	Missense_Mutation	SNP	G	TCGA-2Z-A9JT-01A-11D-A42J-10	37458543	67146187	14049023	66	1642											
C17orf95	124512	hgsc.bcm.edu	37	chr17	74729620	74729620	+	Missense_Mutation	SNP	A	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	aagtgctgactggtcacttgAagctttactctacaaatggg	11	12	10	8	0	2	2	1	2	1	0	2	2	2	2	0	2	4	2	0	2	5	4			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr17:74729620A>C	ENST00000341249.6	+	5	757	c.425A>C	c.(424-426)gAa>gCa	p.E142A	METTL23_ENST00000591571.1_3'UTR|METTL23_ENST00000586738.1_3'UTR|MFSD11_ENST00000588460.1_5'Flank|MFSD11_ENST00000586622.1_5'Flank|MIR636_ENST00000384825.1_RNA|METTL23_ENST00000586752.1_Missense_Mutation_p.E75A|METTL23_ENST00000590964.1_Missense_Mutation_p.E75A|METTL23_ENST00000588783.1_3'UTR|METTL23_ENST00000588302.1_3'UTR|METTL23_ENST00000586200.1_Missense_Mutation_p.E23A|METTL23_ENST00000588822.1_Missense_Mutation_p.E75A|RP11-318A15.7_ENST00000587459.1_Intron	NM_001206984.1	NP_001193913.1	Q86XA0	MET23_HUMAN	methyltransferase like 23	142						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	methyltransferase activity (GO:0008168)			large_intestine(2)|lung(1)	3						TGGTCACTTGAAGCTTTACTC	0.348																																					p.E142A		Atlas-SNP	.											.	METTL23	19	.	0			c.A425C						PASS	.						207	205	206					17																	74729620		1855	4090	5945	SO:0001583	missense	124512	exon5			CACTTGAAGCTTT		CCDS45787.1, CCDS59298.1	17q25.2	2011-03-03	2011-03-03	2011-03-03	ENSG00000181038	ENSG00000181038			26988	protein-coding gene	gene with protein product		615262	"chromosome 17 open reading frame 95"	C17orf95		12477932	Standard	NM_001080510		Approved	LOC124512	uc021udl.1	Q86XA0		ENST00000341249.6:c.425A>C	chr17.hg19:g.74729620A>C	ENSP00000341543:p.Glu142Ala	179.0	0.0	.		192.0	87.0	.	NM_001206984	H9ZYJ0|K7EK32	Missense_Mutation	SNP	ENST00000341249.6	hg19	CCDS45787.1	.	.	.	.	.	.	.	.	.	.	A	15.89	2.965668	0.53507	.	.	ENSG00000181038	ENST00000317409;ENST00000341249	T	0.24723	1.84	5.93	3.68	0.42216	.	0.279419	0.39615	N	0.001306	T	0.22244	0.0536	L	0.46157	1.445	0.51767	D	0.999939	B	0.16396	0.017	B	0.23852	0.049	T	0.03807	-1.1002	10	0.33940	T	0.23	-13.1078	8.6686	0.34137	0.8037:0.13:0.0664:0.0	.	142	Q86XA0	MET23_HUMAN	A	221;142	ENSP00000341543:E142A	ENSP00000316862:E221A	E	+	2	0	METTL23	72241215	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	5.715000	0.68430	0.480000	0.27534	0.533000	0.62120	GAA	.	.	.	none		0.348	METTL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451002.1	NM_001080510		C	74729620	A	C	74729620	3	2	23	1	0	0	0	0	1	0	0	0	1894	246	9	5	439	5	C17orf95	17	74729620	Missense_Mutation	SNP	A	TCGA-2Z-A9JT-01A-11D-A42J-10	7583433	74729620	6465590	67	1643											
ZNF750	79755	hgsc.bcm.edu	37	chr17	80789569	80789569	+	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	agcaggtaaggcgagtagatGgtggccagcccgtgctctgt	8	8	16	9	2	1	1	0	0	1	1	1	2	1	1	2	4	3	4	2	4	2	2			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr17:80789569G>C	ENST00000269394.3	-	2	1595	c.762C>G	c.(760-762)acC>acG	p.T254T	TBCD_ENST00000539345.2_Intron|TBCD_ENST00000355528.4_Intron|ZNF750_ENST00000572562.1_Intron|TBCD_ENST00000397466.2_Intron	NM_024702.2	NP_078978.2	Q32MQ0	ZN750_HUMAN	zinc finger protein 750	254					cell differentiation (GO:0030154)|epidermis development (GO:0008544)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	31	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0514)|all_epithelial(8;0.0748)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.149)			GCGAGTAGATGGTGGCCAGCC	0.582																																					p.T254T		Atlas-SNP	.											.	ZNF750	60	.	0			c.C762G						PASS	.						64	69	67					17																	80789569		2203	4300	6503	SO:0001819	synonymous_variant	79755	exon2			GTAGATGGTGGCC	AK023903	CCDS11819.1	17q25.3	2008-05-02				ENSG00000141579			25843	protein-coding gene	gene with protein product		610226				16751772	Standard	NM_024702		Approved	FLJ13841, Zfp750	uc002kga.3	Q32MQ0		ENST00000269394.3:c.762C>G	chr17.hg19:g.80789569G>C		88.0	0.0	.		113.0	33.0	.	NM_024702	Q9H899	Silent	SNP	ENST00000269394.3	hg19	CCDS11819.1																																																																																			.	.	.	none		0.582	ZNF750-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439074.2	NM_024702		C	80789569	G	C	80789569	2	2	23	1	0	0	0	0	0	0	0	1	18144	1335	47	4		4	ZNF750	17	80789569	Silent	SNP	G	TCGA-2Z-A9JT-01A-11D-A42J-10	6059949	80789569	405641	68	1644											
MYOM1	8736	hgsc.bcm.edu	37	chr18	3067525	3067525	+	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	acacctccggaggcgggtctCcccacacgttgcaagtgaga	9	6	12	14	3	1	1	0	1	1	1	3	3	2	2	4	3	1	2	4	3	1	1			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr18:3067525C>G	ENST00000356443.4	-	38	5126	c.4793G>C	c.(4792-4794)gGa>gCa	p.G1598A	MYOM1_ENST00000400569.3_Missense_Mutation_p.G1598A|MYOM1_ENST00000261606.7_Missense_Mutation_p.G1502A	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1598	Ig-like C2-type 5.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						AGGCGGGTCTCCCCACACGTT	0.527																																					p.G1598A		Atlas-SNP	.											.	MYOM1	192	.	0			c.G4793C						PASS	.						41	46	44					18																	3067525		2112	4239	6351	SO:0001583	missense	8736	exon38			GGGTCTCCCCACA	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.4793G>C	chr18.hg19:g.3067525C>G	ENSP00000348821:p.Gly1598Ala	61.0	0.0	.		88.0	26.0	.	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	hg19	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.340439	0.81911	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.79141	-1.24;-1.24;-1.24	5.79	5.79	0.91817	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.89529	0.6741	M	0.82433	2.59	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	D	0.89108	0.3494	10	0.51188	T	0.08	.	20.0371	0.97565	0.0:1.0:0.0:0.0	.	1502;1598	P52179-2;P52179	.;MYOM1_HUMAN	A	1598;1598;1502	ENSP00000348821:G1598A;ENSP00000383413:G1598A;ENSP00000261606:G1502A	ENSP00000261606:G1502A	G	-	2	0	MYOM1	3057525	1.000000	0.71417	0.967000	0.41034	0.469000	0.32828	7.818000	0.86416	2.734000	0.93682	0.655000	0.94253	GGA	.	.	.	none		0.527	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		G	3067525	C	G	3067525	3	3	23	1	0	0	0	0	1	0	0	0	10098	855	30	4	268	4	MYOM1	18	3067525	Missense_Mutation	SNP	C	TCGA-2Z-A9JT-01A-11D-A42J-10		3067525	75009723	69	1645											
ASXL3	80816	hgsc.bcm.edu	37	chr18	31325189	31325189	+	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	cagtgggtaaaacagcaccaGagagaaacgttgaaattccg	16	6	11	8	2	0	3	0	1	0	2	1	4	1	3	2	1	3	3	2	1	4	3			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr18:31325189G>C	ENST00000269197.5	+	12	5377	c.5377G>C	c.(5377-5379)Gag>Cag	p.E1793Q		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	1793					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						AACAGCACCAGAGAGAAACGT	0.488																																					p.E1793Q		Atlas-SNP	.											.	ASXL3	405	.	0			c.G5377C						PASS	.						70	70	70					18																	31325189		1894	4124	6018	SO:0001583	missense	80816	exon12			GCACCAGAGAGAA	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.5377G>C	chr18.hg19:g.31325189G>C	ENSP00000269197:p.Glu1793Gln	85.0	0.0	.		99.0	34.0	.	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	hg19	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	G	14.87	2.663192	0.47572	.	.	ENSG00000141431	ENST00000269197	T	0.18174	2.23	5.7	5.7	0.88788	.	.	.	.	.	T	0.19525	0.0469	N	0.24115	0.695	0.31181	N	0.702038	D	0.54397	0.966	P	0.46479	0.518	T	0.01829	-1.1265	9	0.54805	T	0.06	.	19.8478	0.96722	0.0:0.0:1.0:0.0	.	1793	Q9C0F0	ASXL3_HUMAN	Q	1793	ENSP00000269197:E1793Q	ENSP00000269197:E1793Q	E	+	1	0	ASXL3	29579187	1.000000	0.71417	0.953000	0.39169	0.708000	0.40852	4.103000	0.57783	2.698000	0.92095	0.655000	0.94253	GAG	.	.	.	none		0.488	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			C	31325189	G	C	31325189	3	2	23	1	0	0	0	0	1	0	0	0	1068	943	33	4	5423	4	ASXL3	18	31325189	Missense_Mutation	SNP	G	TCGA-2Z-A9JT-01A-11D-A42J-10	28257664	31325189	46752059	70	1646											
CTDP1	9150	hgsc.bcm.edu	37	chr18	77440069	77440069	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggagggtggcggcgggcgCggccgtgcgcatcggctcgg	2	5	23	11	8	0	0	0	0	0	0	2	1	0	1	1	8	1	2	1	8	0	0			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr18:77440069C>T	ENST00000299543.7	+	1	269	c.122C>T	c.(121-123)gCg>gTg	p.A41V	CTDP1_ENST00000075430.7_Missense_Mutation_p.A41V|RP11-567M16.3_ENST00000317008.4_lincRNA	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	41					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)		GCGGCGGGCGCGGCCGTGCGC	0.796																																					p.A41V		Atlas-SNP	.											.	CTDP1	67	.	0			c.C122T						PASS	.																																			SO:0001583	missense	9150	exon1			CGGGCGCGGCCGT	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.122C>T	chr18.hg19:g.77440069C>T	ENSP00000299543:p.Ala41Val	35.0	0.0	.		26.0	12.0	.	NM_004715	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	Missense_Mutation	SNP	ENST00000299543.7	hg19	CCDS12017.1	.	.	.	.	.	.	.	.	.	.	C	18.89	3.719634	0.68844	.	.	ENSG00000060069	ENST00000299543;ENST00000075430	T;T	0.10763	2.85;2.84	3.86	3.86	0.44501	.	0.208152	0.41294	D	0.000914	T	0.19604	0.0471	M	0.75085	2.285	0.49213	D	0.999765	D;P	0.55605	0.972;0.952	P;B	0.47626	0.552;0.349	T	0.10154	-1.0642	10	0.28530	T	0.3	-27.8058	15.3998	0.74830	0.0:1.0:0.0:0.0	.	41;41	Q9Y5B0-4;Q9Y5B0	.;CTDP1_HUMAN	V	41	ENSP00000299543:A41V;ENSP00000075430:A41V	ENSP00000075430:A41V	A	+	2	0	CTDP1	75541057	0.999000	0.42202	1.000000	0.80357	0.671000	0.39405	3.115000	0.50391	1.694000	0.51137	0.484000	0.47621	GCG	.	.	.	none		0.796	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715		T	77440069	C	T	77440069	3	4	23	1	0	0	0	0	1	0	0	0	4004	768	27	1	124	1	CTDP1	18	77440069	Missense_Mutation	SNP	C	TCGA-2Z-A9JT-01A-11D-A42J-10	46114880	77440069	637179	71	1647											
ABCA7	10347	hgsc.bcm.edu	37	chr19	1051189	1051189	+	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	gcacgtctggttctatgggcGgctgaagggtctgagtgccg	5	10	17	9	3	3	2	0	2	3	0	3	2	3	2	1	4	1	3	1	4	2	2	rs545859049		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr19:1051189G>T	ENST00000263094.6	+	20	2951	c.2720G>T	c.(2719-2721)cGg>cTg	p.R907L	ABCA7_ENST00000433129.1_Missense_Mutation_p.R907L|ABCA7_ENST00000435683.2_Missense_Mutation_p.R769L	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	907	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)		TTCTATGGGCGGCTGAAGGGT	0.652																																					p.R907L		Atlas-SNP	.											.	ABCA7	174	.	0			c.G2720T						PASS	.						59	56	57					19																	1051189		2188	4290	6478	SO:0001583	missense	10347	exon20			ATGGGCGGCTGAA	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.2720G>T	chr19.hg19:g.1051189G>T	ENSP00000263094:p.Arg907Leu	59.0	0.0	.		48.0	11.0	.	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	hg19	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	G	15.01	2.707765	0.48412	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	T;T	0.80480	-1.38;-1.38	4.37	4.37	0.52481	ATPase, AAA+ type, core (1);ABC transporter-like (2);	.	.	.	.	D	0.85340	0.5674	L	0.56769	1.78	0.34708	D	0.727406	D;B	0.54047	0.964;0.05	P;B	0.59221	0.854;0.062	D	0.89415	0.3706	9	0.48119	T	0.1	.	14.3646	0.66799	0.0:0.0:1.0:0.0	.	769;907	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	L	907	ENSP00000263094:R907L;ENSP00000414062:R907L	ENSP00000263094:R907L	R	+	2	0	ABCA7	1002189	0.064000	0.20934	0.833000	0.33012	0.101000	0.19017	2.144000	0.42197	1.984000	0.57885	0.305000	0.20034	CGG	.	.	.	none		0.652	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		T	1051189	G	T	1051189	3	4	23	1	0	0	0	0	1	0	0	0	37	1116	39	4	2794	4	ABCA7	19	1051189	Missense_Mutation	SNP	G	TCGA-2Z-A9JT-01A-11D-A42J-10		1051189	58077794	72	1648											
FBN3	84467	hgsc.bcm.edu	37	chr19	8130912	8130912	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtggctcaccacctccagcCggtaggttccaggccccggc	5	7	12	17	2	1	0	1	0	0	0	3	0	3	0	7	5	1	3	7	5	1	2	rs139098536		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr19:8130912C>T	ENST00000600128.1	-	64	8735	c.8321G>A	c.(8320-8322)cGg>cAg	p.R2774Q	FBN3_ENST00000601739.1_Missense_Mutation_p.R2774Q|FBN3_ENST00000270509.2_Missense_Mutation_p.R2774Q			Q75N90	FBN3_HUMAN	fibrillin 3	2774						proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.R2774L(1)		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						CACCTCCAGCCGGTAGGTTCC	0.677													C|||	1	0.000199681	0	0	5008	,	,		15911	0		0.001	False		,,,				2504	0				p.R2774Q		Atlas-SNP	.											FBN3,NS,carcinoma,0,1	FBN3	300	.	1	Substitution - Missense(1)	lung(1)	c.G8321A						PASS	.	C	GLN/ARG	3,4401		0,3,2199	37	40	39		8321	-0.4	1	19	dbSNP_134	39	0,8594		0,0,4297	no	missense	FBN3	NM_032447.3	43	0,3,6496	TT,TC,CC		0.0,0.0681,0.0231	benign	2774/2810	8130912	3,12995	2202	4297	6499	SO:0001583	missense	84467	exon63			TCCAGCCGGTAGG		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.8321G>A	chr19.hg19:g.8130912C>T	ENSP00000470498:p.Arg2774Gln	123.0	1.0	.		104.0	38.0	.	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	hg19	CCDS12196.1	.	.	.	.	.	.	.	.	.	.	C	3.458	-0.110482	0.06924	6.81E-4	0.0	ENSG00000142449	ENST00000270509;ENST00000341066	D	0.86694	-2.16	4.55	-0.394	0.12434	.	0.739374	0.12731	N	0.443827	T	0.64427	0.2597	N	0.03608	-0.345	0.22066	N	0.999389	B;B	0.10296	0.0;0.003	B;B	0.04013	0.0;0.001	T	0.52260	-0.8599	10	0.14252	T	0.57	.	3.819	0.08827	0.1372:0.4926:0.1402:0.2301	.	2774;837	Q75N90;Q6ZNB8	FBN3_HUMAN;.	Q	2774;837	ENSP00000270509:R2774Q	ENSP00000270509:R2774Q	R	-	2	0	FBN3	8036912	0.000000	0.05858	0.987000	0.45799	0.104000	0.19210	-0.211000	0.09332	-0.062000	0.13088	-0.238000	0.12139	CGG	.	C|1.000;T|0.000	0.000	weak		0.677	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		T	8130912	C	T	8130912	3	4	23	1	0	0	0	0	1	0	0	0	5711	652	23	1	112	1	FBN3	19	8130912	Missense_Mutation	SNP	C	TCGA-2Z-A9JT-01A-11D-A42J-10	7079723	8130912	50998071	73	1649											
CAPNS1	826	hgsc.bcm.edu	37	chr19	36631958	36631958	+	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	aagggcggcggcggcggcggCgggggaggcgggggcctggg	3	1	28	9	7	0	0	0	0	0	0	0	1	0	1	1	12	0	0	1	12	1	0	rs567500165		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr19:36631958C>G	ENST00000246533.3	+	2	643	c.45C>G	c.(43-45)ggC>ggG	p.G15G	CAPNS1_ENST00000589146.1_Silent_p.G15G|CAPNS1_ENST00000587718.1_Silent_p.G15G|CAPNS1_ENST00000590874.1_Silent_p.G15G|CAPNS1_ENST00000588815.1_Silent_p.G15G|CAPNS1_ENST00000588780.1_Silent_p.G15G	NM_001003962.1|NM_001749.2	NP_001003962.1|NP_001740.1	P04632	CPNS1_HUMAN	calpain, small subunit 1	15	Gly-rich (hydrophobic).|Poly-Gly.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell proliferation (GO:0008284)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			cervix(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	5	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			gcggcggcggcgggggaggcg	0.736													C|||	1	0.000199681	0	0	5008	,	,		3971	0.001		0	False		,,,				2504	0				p.G15G	Esophageal Squamous(129;1541 1691 5780 18353 34150)	Atlas-SNP	.											.	CAPNS1	19	.	0			c.C45G						PASS	.						6	7	7					19																	36631958		1958	3947	5905	SO:0001819	synonymous_variant	826	exon2			CGGCGGCGGGGGA	X04106	CCDS12489.1	19q13.1	2013-01-10		2001-08-10	ENSG00000126247	ENSG00000126247	3.4.22.52	"EF-hand domain containing"	1481	protein-coding gene	gene with protein product		114170		CAPN4		3024120, 3016651	Standard	NM_001003962		Approved	CANP, CANPS, 30K, CDPS	uc002odj.3	P04632		ENST00000246533.3:c.45C>G	chr19.hg19:g.36631958C>G		84.0	0.0	.		65.0	4.0	.	NM_001749	A8K0P1|Q8WTX3|Q96EW0	Silent	SNP	ENST00000246533.3	hg19	CCDS12489.1																																																																																			.	.	.	none		0.736	CAPNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457411.2			G	36631958	C	G	36631958	2	3	23	1	0	0	0	0	0	0	0	1	2635	755	27	4		4	CAPNS1	19	36631958	Silent	SNP	C	TCGA-2Z-A9JT-01A-11D-A42J-10	28501046	36631958	22497025	74	1650											
LILRB4	11006	hgsc.bcm.edu	37	chr19	55175397	55175397	+	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	acaaggccagattctccatcCcatccatgacagaggactat	13	8	7	13	0	1	3	0	1	1	2	4	4	3	4	4	2	0	0	4	2	2	2			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr19:55175397C>T	ENST00000391736.1	+	5	571	c.256C>T	c.(256-258)Cca>Tca	p.P86S	LILRB4_ENST00000270452.2_Missense_Mutation_p.P86S|LILRB4_ENST00000391733.3_Missense_Mutation_p.P86S|LILRB4_ENST00000391734.3_Missense_Mutation_p.P86S|LILRB4_ENST00000430952.2_Missense_Mutation_p.P86S	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	86	Ig-like C2-type 1.				immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		ATTCTCCATCCCATCCATGAC	0.582																																					p.P86S		Atlas-SNP	.											.	LILRB4	86	.	0			c.C256T						PASS	.						313	275	288					19																	55175397		2203	4300	6503	SO:0001583	missense	11006	exon3			TCCATCCCATCCA	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.256C>T	chr19.hg19:g.55175397C>T	ENSP00000375616:p.Pro86Ser	120.0	0.0	.		135.0	32.0	.	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	hg19	CCDS12902.1	.	.	.	.	.	.	.	.	.	.	C	2.499	-0.315654	0.05422	.	.	ENSG00000186818	ENST00000420271;ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391734;ENST00000391733;ENST00000434286	T;T;T;T;T;T	0.13420	2.59;2.59;2.59;2.59;2.59;2.59	2.43	-3.34	0.04943	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.07324	0.0185	L	0.35593	1.075	0.09310	N	1	B;B;B;B;B;P	0.45283	0.133;0.07;0.173;0.002;0.009;0.855	B;B;B;B;B;B	0.40199	0.029;0.016;0.017;0.006;0.01;0.322	T	0.25710	-1.0124	9	0.22706	T	0.39	.	2.2596	0.04063	0.4231:0.2687:0.0:0.3081	.	86;86;86;86;86;127	A8MUE1;C9JST2;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6;C9JHA6	.;.;.;.;LIRB4_HUMAN;.	S	127;86;86;86;86;86;86	ENSP00000375616:P86S;ENSP00000270452:P86S;ENSP00000408995:P86S;ENSP00000375614:P86S;ENSP00000375613:P86S;ENSP00000401962:P86S	ENSP00000270452:P86S	P	+	1	0	LILRB4	59867209	0.000000	0.05858	0.005000	0.12908	0.017000	0.09413	-4.855000	0.00177	-0.487000	0.06735	0.407000	0.27541	CCA	.	.	.	none		0.582	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3			T	55175397	C	T	55175397	3	4	23	1	0	0	0	0	1	0	0	0	8800	623	22	2	266	2	LILRB4	19	55175397	Missense_Mutation	SNP	C	TCGA-2Z-A9JT-01A-11D-A42J-10	18543439	55175397	3953586	75	1651											
ZSCAN22	342945	hgsc.bcm.edu	37	chr19	58850450	58850450	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaagccctacaagtgtgacGcgtgtggccgagccttcagc	9	7	13	12	3	1	2	1	1	0	1	1	3	1	2	3	1	4	0	3	1	3	2	rs138721519		TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr19:58850450G>A	ENST00000329665.4	+	3	1381	c.1234G>A	c.(1234-1236)Gcg>Acg	p.A412T		NM_181846.2	NP_862829.1	P10073	ZSC22_HUMAN	zinc finger and SCAN domain containing 22	412					transcription, DNA-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)		CAAGTGTGACGCGTGTGGCCG	0.582																																					p.A412T		Atlas-SNP	.											.	ZSCAN22	47	.	0			c.G1234A						PASS	.	G	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	87	79	82		1234	0.6	0	19	dbSNP_134	82	0,8600		0,0,4300	no	missense	ZSCAN22	NM_181846.2	58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	412/492	58850450	1,13005	2203	4300	6503	SO:0001583	missense	342945	exon3			TGTGACGCGTGTG	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.1234G>A	chr19.hg19:g.58850450G>A	ENSP00000332433:p.Ala412Thr	79.0	0.0	.		80.0	6.0	.	NM_181846	Q15922|Q7Z3L8	Missense_Mutation	SNP	ENST00000329665.4	hg19	CCDS12975.1	.	.	.	.	.	.	.	.	.	.	G	5.713	0.316043	0.10789	2.27E-4	0.0	ENSG00000182318	ENST00000329665	T	0.07567	3.18	3.84	0.551	0.17225	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03011	0.0089	N	0.02539	-0.55	0.09310	N	1	B	0.29766	0.256	B	0.16722	0.016	T	0.40997	-0.9533	9	0.66056	D	0.02	.	7.5259	0.27656	0.3122:0.0:0.6878:0.0	.	412	P10073	ZSC22_HUMAN	T	412	ENSP00000332433:A412T	ENSP00000332433:A412T	A	+	1	0	ZSCAN22	63542262	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.917000	0.28665	0.410000	0.25675	-1.010000	0.02471	GCG	.	G|1.000;A|0.000	0.000	weak		0.582	ZSCAN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466765.1	NM_181846		A	58850450	G	A	58850450	3	1	23	1	0	0	0	0	1	0	0	0	18246	1087	38	1	1240	1	ZSCAN22	19	58850450	Missense_Mutation	SNP	G	TCGA-2Z-A9JT-01A-11D-A42J-10	3675053	58850450	278533	76	1652											
SON	6651	hgsc.bcm.edu	37	chr21	34926409	34926409	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctactctcagtttagttaaTaaatatgatgttgatttatc	12	19	5	5	0	2	2	1	2	2	0	4	2	2	2	0	0	1	3	0	0	7	9			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr21:34926409T>C	ENST00000356577.4	+	3	5347	c.4872T>C	c.(4870-4872)aaT>aaC	p.N1624N	SON_ENST00000290239.6_Silent_p.N1624N|SON_ENST00000381679.4_Silent_p.N1624N|SON_ENST00000381692.2_Intron|SON_ENST00000300278.4_Silent_p.N1624N	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	1624					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						GTTTAGTTAATAAATATGATG	0.383																																					p.N1624N		Atlas-SNP	.											.	SON	343	.	0			c.T4872C						PASS	.						55	56	56					21																	34926409		2203	4300	6503	SO:0001819	synonymous_variant	6651	exon3			AGTTAATAAATAT	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.4872T>C	chr21.hg19:g.34926409T>C		137.0	0.0	.		90.0	52.0	.	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Silent	SNP	ENST00000356577.4	hg19	CCDS13629.1	.	.	.	.	.	.	.	.	.	.	T	2.148	-0.395098	0.04899	.	.	ENSG00000159140	ENST00000436227	.	.	.	5.0	3.84	0.44239	.	.	.	.	.	T	0.47488	0.1448	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.39663	-0.9603	4	.	.	.	.	3.8858	0.09097	0.1818:0.1031:0.0:0.7151	.	.	.	.	T	619	.	.	I	+	2	0	SON	33848279	0.995000	0.38212	0.941000	0.38009	0.950000	0.60333	0.655000	0.24933	0.909000	0.36697	0.482000	0.46254	ATA	.	.	.	none		0.383	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		C	34926409	T	C	34926409	2	2	23	1	0	0	0	0	0	0	0	1	14939	1403	49	3		3	SON	21	34926409	Silent	SNP	T	TCGA-2Z-A9JT-01A-11D-A42J-10		34926409	13203486	77	1653											
RIPK4	54101	hgsc.bcm.edu	37	chr21	43176834	43176834	+	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	ccatggcaatggctccgaagCcagcagcttttccagggagc	9	7	12	13	1	0	0	0	0	0	0	2	2	2	1	4	3	4	4	4	3	2	2			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr21:43176834C>A	ENST00000352483.2	-	2	389	c.325G>T	c.(325-327)Gct>Tct	p.A109S	RIPK4_ENST00000544709.1_Missense_Mutation_p.A46S|RIPK4_ENST00000542057.1_Missense_Mutation_p.A46S|RIPK4_ENST00000332512.3_Missense_Mutation_p.A109S			P57078	RIPK4_HUMAN	receptor-interacting serine-threonine kinase 4	109	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						GGCTCCGAAGCCAGCAGCTTT	0.607																																					p.A109S		Atlas-SNP	.											.	RIPK4	151	.	0			c.G325T						PASS	.						81	77	78					21																	43176834		2203	4300	6503	SO:0001583	missense	54101	exon2			CCGAAGCCAGCAG	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.325G>T	chr21.hg19:g.43176834C>A	ENSP00000330161:p.Ala109Ser	106.0	0.0	.		66.0	29.0	.	NM_020639	Q96KH0	Missense_Mutation	SNP	ENST00000352483.2	hg19		.	.	.	.	.	.	.	.	.	.	C	16.16	3.043353	0.55003	.	.	ENSG00000183421	ENST00000332512;ENST00000352483;ENST00000544709;ENST00000542057	T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1	4.97	4.97	0.65823	.	0.000000	0.56097	D	0.000021	T	0.61048	0.2316	N	0.11023	0.085	0.58432	D	0.999999	D	0.71674	0.998	D	0.80764	0.994	T	0.61407	-0.7069	10	0.28530	T	0.3	-33.7177	14.1534	0.65401	0.1503:0.8497:0.0:0.0	.	109	P57078-2	.	S	109;109;46;46	ENSP00000332454:A109S;ENSP00000330161:A109S;ENSP00000441754:A46S;ENSP00000442901:A46S	ENSP00000332454:A109S	A	-	1	0	RIPK4	42049903	1.000000	0.71417	0.980000	0.43619	0.369000	0.29798	5.852000	0.69488	2.466000	0.83321	0.563000	0.77884	GCT	.	.	.	none		0.607	RIPK4-201	KNOWN	basic	protein_coding	protein_coding		NM_020639		A	43176834	C	A	43176834	3	1	23	1	0	0	0	0	1	0	0	0	13396	739	26	4	2057	4	RIPK4	21	43176834	Missense_Mutation	SNP	C	TCGA-2Z-A9JT-01A-11D-A42J-10	8250425	43176834	4953061	78	1654											
KRTAP12-1	353332	hgsc.bcm.edu	37	chr21	46101934	46101934	+	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	ggcttgaagctcacgggcacGcacacggaggactggcagcc	9	4	15	13	3	1	1	1	1	0	0	1	3	1	3	1	5	2	5	1	5	1	1	rs56135164	byFrequency	TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr21:46101934G>T	ENST00000391617.1	-	1	144	c.105C>A	c.(103-105)tgC>tgA	p.C35*	TSPEAR_ENST00000323084.4_Intron	NM_181686.1	NP_859014.1	P59990	KR121_HUMAN	keratin associated protein 12-1	35	14 X 5 AA approximate repeats.					keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(1)|skin(2)	5						TCACGGGCACGCACACGGAGG	0.687																																					p.C35X		Atlas-SNP	.											.	KRTAP12-1	9	.	0			c.C105A						PASS	.						58	68	64					21																	46101934		2189	4272	6461	SO:0001587	stop_gained	353332	exon1			GGGCACGCACACG	AJ566388	CCDS42966.1	21q22.3	2006-03-13			ENSG00000187175	ENSG00000187175		"Keratin associated proteins"	20529	protein-coding gene	gene with protein product							Standard	NM_181686		Approved	KRTAP12.1, KAP12.1	uc002zfv.3	P59990	OTTHUMG00000057639	ENST00000391617.1:c.105C>A	chr21.hg19:g.46101934G>T	ENSP00000375475:p.Cys35*	115.0	0.0	.		96.0	4.0	.	NM_181686	Q0VAS3	Nonsense_Mutation	SNP	ENST00000391617.1	hg19	CCDS42966.1	.	.	.	.	.	.	.	.	.	.	a	8.104	0.777274	0.16120	.	.	ENSG00000187175	ENST00000391617	.	.	.	2.88	-1.66	0.08265	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999998	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.4733	0.32999	0.5179:0.0:0.4821:0.0	.	.	.	.	X	35	.	ENSP00000375475:C35X	C	-	3	2	KRTAP12-1	44926362	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	-0.346000	0.07760	-1.005000	0.03417	-3.231000	0.00052	TGC	.	G|0.954;A|0.046	.	alt		0.687	KRTAP12-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128043.1	NM_181686		T	46101934	G	T	46101934	4	4	23	1	0	0	0	0	0	1	0	0	8525	1079	38	4	189	4	KRTAP12-1	21	46101934	Nonsense_Mutation	SNP	G	TCGA-2Z-A9JT-01A-11D-A42J-10	2925100	46101934	2027961	79	1655											
MICAL3	57553	hgsc.bcm.edu	37	chr22	18383762	18383762	+	Splice_Site	DEL	C	C	-																															cggaattctttccgacgaaaCcctggagggaaataaatttt																										TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr22:18383762delC	ENST00000441493.2	-	6	1045	c.693delG	c.(691-693)ggg>gg	p.G231fs	MICAL3_ENST00000429452.1_Splice_Site_p.G231fs|MICAL3_ENST00000585038.1_Splice_Site_p.G231fs|MICAL3_ENST00000444520.1_Splice_Site_p.G231fs|MICAL3_ENST00000414725.2_Splice_Site_p.G231fs|MICAL3_ENST00000207726.7_Splice_Site_p.G231fs|MICAL3_ENST00000400561.2_Splice_Site_p.G231fs|MICAL3_ENST00000383094.3_Splice_Site_p.G231fs	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	231	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)		TCCGACGAAACCCTGGAGGGA	0.438																																					p.F232fs		Atlas-Indel,Pindel	.											.	MICAL3	53	.	0			c.694delT						PASS	.						115	101	105					22																	18383762		1568	3582	5150	SO:0001630	splice_region_variant	57553	exon6			.	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.692-1G>-	chr22.hg19:g.18383762delC		72.0	0.0	0		73.0	18.0	0.246575	NM_001136004	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Frame_Shift_Del	DEL	ENST00000441493.2	hg19	CCDS46659.1																																																																																			.	.	.	none		0.438	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1		Frame_Shift_Del	-	18383762	C	-	18383762	8	5	23	1	0	1	0	1	0	0	1	0	9578	521	18	0	6160	0	MICAL3	22	18383762	Splice_Site	DEL	C	TCGA-2Z-A9JT-01A-11D-A42J-10		18383762	32920804	80	1656											
L3MBTL2	83746	hgsc.bcm.edu	37	chr22	41616759	41616759	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtatcgggtgctgcttcggtAtgaaggctttgaaaatgacg	9	12	14	6	3	0	3	0	3	0	0	2	3	0	3	0	3	2	5	0	3	5	4			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr22:41616759A>G	ENST00000216237.5	+	7	898	c.740A>G	c.(739-741)tAt>tGt	p.Y247C		NM_031488.4	NP_113676.2	Q969R5	LMBL2_HUMAN	l(3)mbt-like 2 (Drosophila)	247					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CTGCTTCGGTATGAAGGCTTT	0.498																																					p.Y247C		Atlas-SNP	.											.	L3MBTL2	61	.	0			c.A740G						PASS	.						120	105	110					22																	41616759		2203	4300	6503	SO:0001583	missense	83746	exon7			TTCGGTATGAAGG	AJ305226	CCDS14011.1	22q13.31-q13.33	2008-06-11			ENSG00000100395	ENSG00000100395			18594	protein-coding gene	gene with protein product		611865				11682070	Standard	NM_031488		Approved	H-l(3)mbt-l, DKFZP761I141, dJ756G23.3	uc003azo.3	Q969R5	OTTHUMG00000150942	ENST00000216237.5:c.740A>G	chr22.hg19:g.41616759A>G	ENSP00000216237:p.Tyr247Cys	62.0	0.0	.		40.0	12.0	.	NM_031488	Q8TEN1|Q96SC4|Q9BQI2|Q9UGS4	Missense_Mutation	SNP	ENST00000216237.5	hg19	CCDS14011.1	.	.	.	.	.	.	.	.	.	.	A	13.67	2.306926	0.40795	.	.	ENSG00000100395	ENST00000216237	T	0.53423	0.62	5.37	5.37	0.77165	.	0.335401	0.36101	N	0.002788	T	0.72244	0.3436	M	0.86178	2.8	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.975;0.997	T	0.77778	-0.2460	10	0.87932	D	0	.	15.677	0.77336	1.0:0.0:0.0:0.0	.	247;247	Q969R5-3;Q969R5	.;LMBL2_HUMAN	C	247	ENSP00000216237:Y247C	ENSP00000216237:Y247C	Y	+	2	0	L3MBTL2	39946705	1.000000	0.71417	0.933000	0.37362	0.815000	0.46073	9.279000	0.95777	2.169000	0.68431	0.374000	0.22700	TAT	.	.	.	none		0.498	L3MBTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320613.1	NM_031488		G	41616759	A	G	41616759	3	3	23	1	0	0	0	0	1	0	0	0	8599	449	16	3	766	3	L3MBTL2	22	41616759	Missense_Mutation	SNP	A	TCGA-2Z-A9JT-01A-11D-A42J-10	23232997	41616759	9687807	81	1657											
SAPS2	9701	hgsc.bcm.edu	37	chr22	50860699	50860699	+	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	acaggacagagggcttggtgGactccttttctcagggactg	8	10	14	9	0	1	1	1	0	1	1	3	4	2	4	1	5	0	1	1	5	0	3			TCGA-2Z-A9JT-01A-11D-A42J-10	TCGA-2Z-A9JT-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a0ad5b36-8f0c-4c60-9ff2-0992e47d1368	bcef5136-1bb4-4cff-a8db-659687674ecd	g.chr22:50860699G>A	ENST00000216061.5	+	10	1232	c.862G>A	c.(862-864)Gac>Aac	p.D288N	PPP6R2_ENST00000359139.3_Missense_Mutation_p.D288N|PPP6R2_ENST00000395744.3_Missense_Mutation_p.D288N|PPP6R2_ENST00000395741.3_Missense_Mutation_p.D289N			O75170	PP6R2_HUMAN	protein phosphatase 6, regulatory subunit 2	288						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						GGGCTTGGTGGACTCCTTTTC	0.582																																					p.D289N		Atlas-SNP	.											.	PPP6R2	71	.	0			c.G865A						PASS	.						102	99	100					22																	50860699		2203	4300	6503	SO:0001583	missense	9701	exon9			TTGGTGGACTCCT	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.862G>A	chr22.hg19:g.50860699G>A	ENSP00000216061:p.Asp288Asn	76.0	0.0	.		71.0	15.0	.	NM_001242899	A6PVG3|B7Z7T3|Q5U5P3|Q7Z2L2|Q7Z5G5|Q7Z731|Q9UGB9	Missense_Mutation	SNP	ENST00000216061.5	hg19		.	.	.	.	.	.	.	.	.	.	G	18.28	3.589334	0.66105	.	.	ENSG00000100239	ENST00000359139;ENST00000395741;ENST00000395744;ENST00000216061	T;T;T;T	0.32753	1.45;1.49;1.45;1.44	5.32	5.32	0.75619	.	0.135251	0.64402	D	0.000003	T	0.30230	0.0758	L	0.44542	1.39	0.40878	D	0.983972	B;B;B;B;B	0.15473	0.01;0.013;0.005;0.01;0.005	B;B;B;B;B	0.31869	0.084;0.137;0.03;0.084;0.03	T	0.09751	-1.0660	10	0.36615	T	0.2	-27.8965	11.6177	0.51099	0.0:0.0:0.8222:0.1778	.	288;288;289;288;288	O75170-5;O75170;O75170-3;O75170-4;O75170-2	.;PP6R2_HUMAN;.;.;.	N	288;289;288;288	ENSP00000352051:D288N;ENSP00000379090:D289N;ENSP00000379093:D288N;ENSP00000216061:D288N	ENSP00000216061:D288N	D	+	1	0	PPP6R2	49207565	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.233000	0.95337	2.498000	0.84270	0.456000	0.33151	GAC	.	.	.	none		0.582	PPP6R2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316809.1	NM_014678		A	50860699	G	A	50860699	3	1	23	1	0	0	0	0	1	0	0	0	13850	1174	41	2	888	2	SAPS2	22	50860699	Missense_Mutation	SNP	G	TCGA-2Z-A9JT-01A-11D-A42J-10	9243940	50860699	443867	82	1658											
C1orf93	127281	hgsc.bcm.edu	37	chr1	2518720	2518720	+	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	gcaggagttcctggacggcgActacttcgcgggaggtgcgt	6	8	17	10	5	0	0	0	0	0	0	2	4	1	3	1	5	2	2	1	5	1	3			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr1:2518720A>T	ENST00000378425.5	+	2	330	c.254A>T	c.(253-255)gAc>gTc	p.D85V	FAM213B_ENST00000537325.1_Missense_Mutation_p.D115V|RP3-395M20.9_ENST00000424215.1_RNA|FAM213B_ENST00000484099.1_3'UTR|FAM213B_ENST00000419916.2_Missense_Mutation_p.D115V|FAM213B_ENST00000444521.2_Missense_Mutation_p.D85V|FAM213B_ENST00000378424.4_Missense_Mutation_p.D115V			Q8TBF2	PGFS_HUMAN	family with sequence similarity 213, member B	85					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|myelin sheath (GO:0043209)	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|prostaglandin-F synthase activity (GO:0047017)										CTGGACGGCGACTACTTCGCG	0.706																																					p.D115V		Atlas-SNP	.											.	.	.	.	0			c.A344T						PASS	.						17	18	18					1																	2518720		2183	4281	6464	SO:0001583	missense	127281	exon2			ACGGCGACTACTT	AK075273	CCDS44.1, CCDS44.2, CCDS55564.1, CCDS72690.1, CCDS72691.1	1p36.32	2011-12-08	2011-11-24	2011-11-24	ENSG00000157870	ENSG00000157870	1.11.1.20		28390	protein-coding gene	gene with protein product	"prostamide/prostaglandin F synthase"		"chromosome 1 open reading frame 93"	C1orf93		18006499	Standard	NM_152371		Approved	MGC26818	uc001ajv.2	Q8TBF2	OTTHUMG00000000847	ENST00000378425.5:c.254A>T	chr1.hg19:g.2518720A>T	ENSP00000367682:p.Asp85Val	68.0	0.0	.		58.0	31.0	.	NM_001195736	A8K793|B3KPY3|B4DQR9|B4E0S5|B7ZAC8|B9DI90|B9DI92|J3KQD0|Q8N2H0	Missense_Mutation	SNP	ENST00000378425.5	hg19		.	.	.	.	.	.	.	.	.	.	A	10.52	1.372724	0.24857	.	.	ENSG00000157870	ENST00000419916;ENST00000378424;ENST00000537325;ENST00000378425;ENST00000444521	T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01	3.88	1.78	0.24846	.	0.350346	0.29403	N	0.012249	T	0.22627	0.0546	N	0.14661	0.345	0.34956	D	0.751689	B;B;P;B;B;B	0.35821	0.147;0.001;0.523;0.049;0.057;0.071	B;B;B;B;B;B	0.37267	0.009;0.002;0.245;0.005;0.118;0.187	T	0.21724	-1.0237	10	0.54805	T	0.06	-4.8025	4.8945	0.13744	0.3022:0.0:0.6978:0.0	.	115;85;115;85;85;85	Q8TBF2-5;Q8TBF2-4;Q8TBF2-6;Q8TBF2-2;Q8TBF2-3;Q8TBF2	.;.;.;.;.;PGFS_HUMAN	V	115;115;115;85;85	ENSP00000394405:D115V;ENSP00000367681:D115V;ENSP00000443605:D115V;ENSP00000367682:D85V;ENSP00000413218:D85V	ENSP00000367681:D115V	D	+	2	0	C1orf93	2508580	1.000000	0.71417	0.999000	0.59377	0.013000	0.08279	2.355000	0.44107	0.830000	0.34757	-0.381000	0.06696	GAC	.	.	.	none		0.706	FAM213B-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152371		T	2518720	A	T	2518720	3	4	24	1	0	0	0	0	1	0	0	0	2072	275	10	5	260	5	C1orf93	1	2518720	Missense_Mutation	SNP	A	TCGA-4A-A93W-01A-11D-A36X-10		2518720	246731901	1	1659											
UBE4B	10277	hgsc.bcm.edu	37	chr1	10177640	10177640	+	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	ttcgaccgagttggaatagaGgaaaaaaaagcaccaaaggt	18	6	11	6	2	0	1	0	0	0	1	1	5	0	3	2	3	1	2	2	3	7	3			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr1:10177640G>C	ENST00000253251.8	+	7	1772	c.933G>C	c.(931-933)gaG>gaC	p.E311D	UBE4B_ENST00000377157.3_Missense_Mutation_p.E195D|UBE4B_ENST00000475795.1_3'UTR|UBE4B_ENST00000343090.6_Missense_Mutation_p.E440D					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)		TTGGAATAGAGGAAAAAAAAG	0.373																																					p.E440D		Atlas-SNP	.											.	UBE4B	233	.	0			c.G1320C						PASS	.						49	50	49					1																	10177640		2203	4300	6503	SO:0001583	missense	10277	exon8			AATAGAGGAAAAA	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.933G>C	chr1.hg19:g.10177640G>C	ENSP00000253251:p.Glu311Asp	319.0	1.0	.		355.0	154.0	.	NM_001105562		Missense_Mutation	SNP	ENST00000253251.8	hg19	CCDS110.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.209310	0.79240	.	.	ENSG00000130939	ENST00000253251;ENST00000377157;ENST00000343090	T;T;T	0.49139	0.79;0.79;0.79	6.03	3.17	0.36434	.	0.000000	0.85682	D	0.000000	T	0.60766	0.2294	M	0.61703	1.905	0.54753	D	0.999985	D;D	0.69078	0.997;0.974	D;D	0.72625	0.978;0.969	T	0.57797	-0.7749	10	0.51188	T	0.08	-29.0009	8.8347	0.35104	0.337:0.0:0.663:0.0	.	440;311	O95155;O95155-2	UBE4B_HUMAN;.	D	311;195;440	ENSP00000253251:E311D;ENSP00000366362:E195D;ENSP00000343001:E440D	ENSP00000253251:E311D	E	+	3	2	UBE4B	10100227	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.338000	0.43957	0.441000	0.26529	0.655000	0.94253	GAG	.	.	.	none		0.373	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048		C	10177640	G	C	10177640	3	2	24	1	0	0	0	0	1	0	0	0	16895	991	35	4	1350	4	UBE4B	1	10177640	Missense_Mutation	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10	7658920	10177640	239072981	2	1660											
MAP3K6	9064	hgsc.bcm.edu	37	chr1	27689486	27689486	+	Frame_Shift_Del	DEL	T	T	-																															gcagcagcacagacagggccTtcgcccggtccccaggcctg																										TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr1:27689486delT	ENST00000493901.1	-	8	1237	c.998delA	c.(997-999)aagfs	p.K333fs	MAP3K6_ENST00000374040.3_Frame_Shift_Del_p.K325fs|MAP3K6_ENST00000357582.2_Frame_Shift_Del_p.K333fs	NM_004672.3	NP_004663.3	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase 6	333					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)		AGACAGGGCCTTCGCCCGGTC	0.607																																					p.K333fs		Atlas-Indel,Pindel	.											.	MAP3K6	134	.	0			c.999delG						PASS	.						33	38	36					1																	27689486		2203	4300	6503	SO:0001589	frameshift_variant	9064	exon7			.	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.998delA	chr1.hg19:g.27689486delT	ENSP00000419591:p.Lys333fs	187.0	0.0	0		170.0	70.0	0.411765	NM_004672	A2ACE8|A2VDG4|A2VDG5|Q59HF4|Q5SSD4|Q75PK3|Q96B75	Frame_Shift_Del	DEL	ENST00000493901.1	hg19	CCDS299.1																																																																																			.	.	.	none		0.607	MAP3K6-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013469.2	NM_004672		-	27689486	T	-	27689486	7	5	24	1	0	1	0	1	0	0	0	0	9261	1609	56	0	2960	0	MAP3K6	1	27689486	Frame_Shift_Del	DEL	T	TCGA-4A-A93W-01A-11D-A36X-10	17511846	27689486	221561135	3	1661											
S100A6	6277	hgsc.bcm.edu	37	chr1	153507304	153507304	+	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	gcaatttcagcatcctgcagCttctaatgtgttagaatgtg	10	14	9	8	0	2	1	1	0	1	1	3	1	3	1	1	0	3	5	1	0	4	4			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr1:153507304C>T	ENST00000368720.2	-	4	443	c.141G>A	c.(139-141)aaG>aaA	p.K47K	S100A6_ENST00000496817.1_Silent_p.K47K|S100A6_ENST00000368719.4_Silent_p.K47K|BX470102.3_ENST00000420695.1_RNA			P06703	S10A6_HUMAN	S100 calcium binding protein A6	47	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				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)			CATCCTGCAGCTTCTAATGTG	0.522																																					p.K47K		Atlas-SNP	.											.	S100A6	8	.	0			c.G141A						PASS	.						106	101	102					1																	153507304		2203	4300	6503	SO:0001819	synonymous_variant	6277	exon3			CTGCAGCTTCTAA	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.141G>A	chr1.hg19:g.153507304C>T		78.0	0.0	.		72.0	38.0	.	NM_014624	D3DV39|Q5RHS4	Silent	SNP	ENST00000368720.2	hg19	CCDS1040.1																																																																																			.	.	.	none		0.522	S100A6-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037723.2	NM_014624		T	153507304	C	T	153507304	2	4	24	1	0	0	0	0	0	0	0	1	13795	796	28	2		2	S100A6	1	153507304	Silent	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10	125817818	153507304	95743317	4	1662											
C1orf43	25912	hgsc.bcm.edu	37	chr1	154180025	154180025	+	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	ttctgactggaggggaggtaTgtcacctggatggttgttgg	6	13	17	5	0	2	1	1	1	1	0	2	4	2	4	1	7	0	3	1	7	1	4			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr1:154180025T>G	ENST00000368521.5	-	7	864	c.666A>C	c.(664-666)acA>acC	p.T222T	C1orf43_ENST00000350592.3_Silent_p.T188T|C1orf43_ENST00000362076.4_Silent_p.T170T|C1orf189_ENST00000368525.3_5'Flank|C1orf43_ENST00000483282.1_5'UTR|C1orf43_ENST00000368519.1_Silent_p.T204T	NM_001098616.1	NP_001092086.1	Q9BWL3	CA043_HUMAN	chromosome 1 open reading frame 43	222						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)					AGGGGAGGTATGTCACCTGGA	0.493																																					p.T222T		Atlas-SNP	.											.	C1orf43	36	.	0			c.A666C						PASS	.						222	210	214					1																	154180025		2203	4300	6503	SO:0001819	synonymous_variant	25912	exon7			GAGGTATGTCACC	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.666A>C	chr1.hg19:g.154180025T>G		154.0	0.0	.		112.0	40.0	.	NM_001098616	A8K3G8|D3DV72|D3DV74|Q5M801|Q5VU73|Q5VU83|Q96HP7|Q9UFU2|Q9UGL7|Q9UGL8|Q9Y2R6	Silent	SNP	ENST00000368521.5	hg19	CCDS41404.1																																																																																			.	.	.	none		0.493	C1orf43-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087664.2	NM_015449		G	154180025	T	G	154180025	2	3	24	1	0	0	0	0	0	0	0	1	2042	1451	51	5		5	C1orf43	1	154180025	Silent	SNP	T	TCGA-4A-A93W-01A-11D-A36X-10	672721	154180025	95070596	5	1663											
YY1AP1	55249	hgsc.bcm.edu	37	chr1	155646420	155646420	+	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	acttccttacactggggtttAaccttctctacctccttctg	6	16	5	14	0	2	0	0	0	2	0	5	0	4	0	4	2	3	1	4	2	3	7			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr1:155646420A>C	ENST00000295566.4	-	5	464	c.441T>G	c.(439-441)gtT>gtG	p.V147V	YY1AP1_ENST00000535662.1_5'UTR|YY1AP1_ENST00000359205.5_Silent_p.V70V|YY1AP1_ENST00000368339.5_Silent_p.V219V|MSTO1_ENST00000452804.2_Intron|YY1AP1_ENST00000368330.2_Silent_p.V81V|YY1AP1_ENST00000438245.2_Silent_p.V81V|YY1AP1_ENST00000405763.3_Silent_p.V219V|YY1AP1_ENST00000361831.5_Silent_p.V70V|YY1AP1_ENST00000404643.1_Silent_p.V81V|YY1AP1_ENST00000347088.5_Silent_p.V81V|YY1AP1_ENST00000476093.1_5'UTR|YY1AP1_ENST00000311573.5_Silent_p.V70V|YY1AP1_ENST00000355499.4_Silent_p.V81V|YY1AP1_ENST00000368340.5_Silent_p.V219V|YY1AP1_ENST00000407221.1_Silent_p.V70V|MSTO1_ENST00000538143.1_Intron	NM_001198906.1|NM_139118.2	NP_001185835.1|NP_620829.1	Q9H869	YYAP1_HUMAN	YY1 associated protein 1	147					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)					ACTGGGGTTTAACCTTCTCTA	0.458																																					p.V219V		Atlas-SNP	.											.	YY1AP1	104	.	0			c.T657G						PASS	.						270	218	235					1																	155646420		2203	4300	6503	SO:0001819	synonymous_variant	55249	exon4			GGGTTTAACCTTC	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.441T>G	chr1.hg19:g.155646420A>C		85.0	0.0	.		92.0	8.0	.	NM_001198904	B0QZ54|B4DMP2|B4E0I0|D3DV96|D3DV98|H7BY62|Q5VYZ1|Q5VYZ4|Q5VYZ7|Q7L4C3|Q7L5E2|Q8IXA6|Q8TEW5|Q8TF04|Q96HB6|Q9BQ64|Q9NV84	Silent	SNP	ENST00000295566.4	hg19	CCDS1115.1																																																																																			.	.	.	none		0.458	YY1AP1-043	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000086027.1	NM_139118		C	155646420	A	C	155646420	2	2	24	1	0	0	0	0	0	0	0	1	17520	349	13	5		5	YY1AP1	1	155646420	Silent	SNP	A	TCGA-4A-A93W-01A-11D-A36X-10	1466395	155646420	93604201	6	1664											
LHX4	89884	hgsc.bcm.edu	37	chr1	180235629	180235629	+	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	cacctgcactgctttgcttgCatcatctgcaaccggcagct	7	11	8	15	1	2	0	1	0	1	0	2	0	2	0	2	1	7	7	2	1	1	2			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr1:180235629C>A	ENST00000263726.2	+	3	595	c.351C>A	c.(349-351)tgC>tgA	p.C117*		NM_033343.3	NP_203129.1	Q969G2	LHX4_HUMAN	LIM homeobox 4	117	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				medial motor column neuron differentiation (GO:0021526)|motor neuron axon guidance (GO:0008045)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|placenta development (GO:0001890)|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)			endometrium(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)	16						GCTTTGCTTGCATCATCTGCA	0.607																																					p.C117X		Atlas-SNP	.											.	LHX4	36	.	0			c.C351A						PASS	.						70	68	68					1																	180235629		2203	4300	6503	SO:0001587	stop_gained	89884	exon3			TGCTTGCATCATC	AB037683	CCDS1338.1	1q25.3	2011-06-20			ENSG00000121454	ENSG00000121454		"Homeoboxes / LIM class"	21734	protein-coding gene	gene with protein product		602146				11844481, 11567216	Standard	NM_033343		Approved	Gsh4	uc001goe.2	Q969G2	OTTHUMG00000035115	ENST00000263726.2:c.351C>A	chr1.hg19:g.180235629C>A	ENSP00000263726:p.Cys117*	110.0	0.0	.		113.0	49.0	.	NM_033343	Q8NHE0|Q8NHM1|Q8TCJ1|Q8WWX2|Q969W2	Nonsense_Mutation	SNP	ENST00000263726.2	hg19	CCDS1338.1	.	.	.	.	.	.	.	.	.	.	C	37	6.072372	0.97256	.	.	ENSG00000121454	ENST00000263726	.	.	.	5.25	2.39	0.29439	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.0658	0.30659	0.0:0.6782:0.0:0.3218	.	.	.	.	X	117	.	ENSP00000263726:C117X	C	+	3	2	LHX4	178502252	1.000000	0.71417	0.998000	0.56505	0.853000	0.48598	1.245000	0.32790	0.243000	0.21327	-0.768000	0.03414	TGC	.	.	.	none		0.607	LHX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084995.2	NM_033343		A	180235629	C	A	180235629	4	1	24	1	0	0	0	0	0	1	0	0	8780	718	25	4	361	4	LHX4	1	180235629	Nonsense_Mutation	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10	24589209	180235629	69014992	7	1665											
IARS2	55699	hgsc.bcm.edu	37	chr1	220267580	220267580	+	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	tgcgttgggggctgcgccctCgcgggccgggcgcggccgcc	0	5	20	16	8	0	0	0	0	0	0	1	0	0	0	4	5	2	2	4	5	0	1			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr1:220267580C>T	ENST00000302637.5	+	1	126	c.22C>T	c.(22-24)Cgc>Tgc	p.R8C	IARS2_ENST00000366922.1_5'UTR	NM_018060.3	NP_060530.3	Q9NSE4	SYIM_HUMAN	isoleucyl-tRNA synthetase 2, mitochondrial	8					gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)			NS(1)|breast(1)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(7)|lung(17)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)	GCTGCGCCCTcgcgggccggg	0.731																																					p.R8C		Atlas-SNP	.											.	IARS2	106	.	0			c.C22T						PASS	.						6	8	8					1																	220267580		1994	4041	6035	SO:0001583	missense	55699	exon1			CGCCCTCGCGGGC	AK022665	CCDS1523.1	1q41	2011-07-01	2007-02-26		ENSG00000067704	ENSG00000067704	6.1.1.5	"Aminoacyl tRNA synthetases / Class I"	29685	protein-coding gene	gene with protein product	"isoleucine tRNA ligase 2, mitochondrial"	612801					Standard	NM_018060		Approved	FLJ10326	uc001hmc.3	Q9NSE4	OTTHUMG00000037287	ENST00000302637.5:c.22C>T	chr1.hg19:g.220267580C>T	ENSP00000303279:p.Arg8Cys	89.0	0.0	.		76.0	19.0	.	NM_018060	B2RPG8|Q1M2P9|Q6PI85|Q7L439|Q86WU9|Q96D91|Q9H9Q8|Q9NW42	Missense_Mutation	SNP	ENST00000302637.5	hg19	CCDS1523.1	.	.	.	.	.	.	.	.	.	.	C	14.46	2.543372	0.45280	.	.	ENSG00000067704	ENST00000302637	T	0.18174	2.23	4.13	1.07	0.20283	.	1.149520	0.06488	N	0.734164	T	0.14787	0.0357	L	0.46157	1.445	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38542	-0.9656	10	0.87932	D	0	-5.9953	2.5425	0.04730	0.1499:0.5218:0.1466:0.1817	.	8	Q9NSE4	SYIM_HUMAN	C	8	ENSP00000303279:R8C	ENSP00000303279:R8C	R	+	1	0	IARS2	218334203	0.000000	0.05858	0.042000	0.18584	0.137000	0.21094	-0.922000	0.04004	0.933000	0.37291	0.591000	0.81541	CGC	.	.	.	none		0.731	IARS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018060		T	220267580	C	T	220267580	3	4	24	1	0	0	0	0	1	0	0	0	7481	884	31	1	24	1	IARS2	1	220267580	Missense_Mutation	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10	40031951	220267580	28983041	8	1666											
TLR5	7100	hgsc.bcm.edu	37	chr1	223285550	223285550	+	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	atgtgttctggtcaggatctTtgatgttatggaagccaaac	10	14	11	6	0	3	1	1	1	2	0	3	3	3	3	1	3	2	2	1	3	3	3			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr1:223285550T>A	ENST00000540964.1	-	4	1285	c.824A>T	c.(823-825)aAa>aTa	p.K275I	TLR5_ENST00000342210.6_Missense_Mutation_p.K275I			O60602	TLR5_HUMAN	toll-like receptor 5	275					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)		GTCAGGATCTTTGATGTTATG	0.483																																					p.K275I		Atlas-SNP	.											.	TLR5	86	.	0			c.A824T						PASS	.						87	79	81					1																	223285550		2203	4300	6503	SO:0001583	missense	7100	exon6			GGATCTTTGATGT		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.824A>T	chr1.hg19:g.223285550T>A	ENSP00000440643:p.Lys275Ile	157.0	0.0	.		147.0	62.0	.	NM_003268	B1AZ05|B3Y633|B9VJ63|D1CS80|D3DTB8|O15456|Q32MI2|Q32MI3	Missense_Mutation	SNP	ENST00000540964.1	hg19	CCDS31033.1	.	.	.	.	.	.	.	.	.	.	T	14.97	2.692938	0.48202	.	.	ENSG00000187554	ENST00000540964;ENST00000366881;ENST00000342210	T;T;T	0.38401	1.14;1.14;1.14	5.27	-1.58	0.08479	.	0.412136	0.25484	N	0.030354	T	0.53867	0.1823	M	0.79258	2.445	0.09310	N	1	P	0.47910	0.902	D	0.63597	0.916	T	0.52586	-0.8556	10	0.72032	D	0.01	.	11.276	0.49168	0.0:0.4375:0.0:0.5625	.	275	O60602	TLR5_HUMAN	I	275	ENSP00000440643:K275I;ENSP00000355846:K275I;ENSP00000340089:K275I	ENSP00000340089:K275I	K	-	2	0	TLR5	221352173	0.002000	0.14202	0.001000	0.08648	0.734000	0.41952	0.246000	0.18160	-0.591000	0.05859	0.533000	0.62120	AAA	.	.	.	none		0.483	TLR5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003268		A	223285550	T	A	223285550	3	1	24	1	0	0	0	0	1	0	0	0	15966	1841	64	5	1756	5	TLR5	1	223285550	Missense_Mutation	SNP	T	TCGA-4A-A93W-01A-11D-A36X-10	3017970	223285550	25965071	9	1667											
RYR2	6262	hgsc.bcm.edu	37	chr1	237713903	237713903	+	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	actcttctggatgaccgaacCaagaaatccaacaaggacag	16	6	8	11	1	2	2	0	1	2	1	3	5	3	4	3	2	2	0	3	2	5	1			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr1:237713903C>A	ENST00000366574.2	+	27	3443	c.3126C>A	c.(3124-3126)acC>acA	p.T1042T	RYR2_ENST00000360064.6_Silent_p.T1040T|RYR2_ENST00000542537.1_Silent_p.T1026T	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1042	4 X approximate repeats.|B30.2/SPRY 2. {ECO:0000255|PROSITE- ProRule:PRU00548}.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			ATGACCGAACCAAGAAATCCA	0.507																																					p.T1042T		Atlas-SNP	.											.	RYR2	1273	.	0			c.C3126A						PASS	.						117	109	112					1																	237713903		1927	4150	6077	SO:0001819	synonymous_variant	6262	exon27			CCGAACCAAGAAA	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.3126C>A	chr1.hg19:g.237713903C>A		175.0	0.0	.		180.0	83.0	.	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.	.	none		0.507	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237713903	C	A	237713903	2	1	24	1	0	0	0	0	0	0	0	1	13782	581	21	4		4	RYR2	1	237713903	Silent	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10	14428353	237713903	11536718	10	1668											
GRHL1	29841	hgsc.bcm.edu	37	chr2	10105481	10105481	+	Missense_Mutation	SNP	T	T	C																															ttgcgtataacgccatttccTtcacatgggacatcaacgat																										TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr2:10105481T>C	ENST00000324907.9	+	8	1217	c.1081T>C	c.(1081-1083)Ttc>Ctc	p.F361L	GRHL1_ENST00000324883.5_Missense_Mutation_p.F172L|GRHL1_ENST00000405379.2_Missense_Mutation_p.F361L	NM_198182.2	NP_937825.2	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1 (Drosophila)	361					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)		CGCCATTTCCTTCACATGGGA	0.443																																					p.F361L		Atlas-SNP	.											.	GRHL1	95	.	0			c.T1081C						PASS	.						139	132	135					2																	10105481		2203	4300	6503	SO:0001583	missense	29841	exon8			ATTTCCTTCACAT	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.1081T>C	chr2.hg19:g.10105481T>C	ENSP00000324693:p.Phe361Leu	86.0	0.0	.		85.0	38.0	.	NM_198182	A6NLA4|B2R7E4|B5MEC2|Q53T93|Q6NWN7|Q6NWN8|Q6NWN9|Q8NI33	Missense_Mutation	SNP	ENST00000324907.9	hg19	CCDS33144.2	.	.	.	.	.	.	.	.	.	.	T	32	5.124591	0.94429	.	.	ENSG00000134317	ENST00000405379;ENST00000324883;ENST00000324907	T;T;T	0.18810	2.19;2.19;2.19	5.46	5.46	0.80206	CP2 transcription factor (1);	0.000000	0.85682	D	0.000000	T	0.54791	0.1880	M	0.90019	3.08	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.998;0.999	T	0.65158	-0.6236	10	0.72032	D	0.01	-1.3111	15.5346	0.75993	0.0:0.0:0.0:1.0	.	172;361	Q9NZI5-2;Q9NZI5	.;GRHL1_HUMAN	L	361;172;361	ENSP00000384209:F361L;ENSP00000324494:F172L;ENSP00000324693:F361L	ENSP00000324494:F172L	F	+	1	0	GRHL1	10022932	1.000000	0.71417	1.000000	0.80357	0.788000	0.44548	7.992000	0.88273	2.054000	0.61138	0.528000	0.53228	TTC	.	.	.	none		0.443	GRHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323543.2	NM_014552		C	10105481	T	C	10105481	3	2	24	1	0	0	0	0	1	0	0	0	6770	1609	56	3	1111	3	GRHL1	2	10105481	Missense_Mutation	SNP	T	TCGA-4A-A93W-01A-11D-A36X-10		10105481	233093892	11	1669	17	2									
GRHL1	29841	hgsc.bcm.edu	37	chr2	10105483	10105483	+	Silent	SNP	C	C	T																															gcgtataacgccatttccttCacatgggacatcaacgatga																										TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr2:10105483C>T	ENST00000324907.9	+	8	1219	c.1083C>T	c.(1081-1083)ttC>ttT	p.F361F	GRHL1_ENST00000324883.5_Silent_p.F172F|GRHL1_ENST00000405379.2_Silent_p.F361F	NM_198182.2	NP_937825.2	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1 (Drosophila)	361					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)		CCATTTCCTTCACATGGGACA	0.443																																					p.F361F		Atlas-SNP	.											.	GRHL1	95	.	0			c.C1083T						PASS	.						138	130	133					2																	10105483		2203	4300	6503	SO:0001819	synonymous_variant	29841	exon8			TTCCTTCACATGG	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.1083C>T	chr2.hg19:g.10105483C>T		87.0	0.0	.		87.0	38.0	.	NM_198182	A6NLA4|B2R7E4|B5MEC2|Q53T93|Q6NWN7|Q6NWN8|Q6NWN9|Q8NI33	Silent	SNP	ENST00000324907.9	hg19	CCDS33144.2																																																																																			.	.	.	none		0.443	GRHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323543.2	NM_014552		T	10105483	C	T	10105483	2	4	24	1	0	0	0	0	0	0	0	1	6770	825	29	2		2	GRHL1	2	10105483	Silent	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10	2	10105483	233093890	12	1670	17	2									
ADCY3	109	hgsc.bcm.edu	37	chr2	25095499	25095499	+	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	agcgactggcgggcctccagGaaggccttgcggtgcttgcg	5	7	17	12	4	0	0	0	0	0	0	1	2	1	1	3	5	4	1	3	5	1	2			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr2:25095499G>A	ENST00000260600.5	-	2	1616	c.765C>T	c.(763-765)ttC>ttT	p.F255F		NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	255					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)					GGGCCTCCAGGAAGGCCTTGC	0.632																																					p.F255F		Atlas-SNP	.											.	ADCY3	114	.	0			c.C765T						PASS	.						84	84	84					2																	25095499		2203	4300	6503	SO:0001819	synonymous_variant	109	exon2			CTCCAGGAAGGCC	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.765C>T	chr2.hg19:g.25095499G>A		182.0	0.0	.		135.0	7.0	.	NM_004036	B3KT86|Q53T54|Q9UDB1	Silent	SNP	ENST00000260600.5	hg19	CCDS1715.1																																																																																			.	.	.	none		0.632	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2			A	25095499	G	A	25095499	2	1	24	1	0	0	0	0	0	0	0	1	295	1165	41	2		2	ADCY3	2	25095499	Silent	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10	14990016	25095499	218103874	13	1671											
SULT1C4	27233	hgsc.bcm.edu	37	chr2	108999668	108999668	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tattttgagacttttctggcTgggaaaggtgagagaattta	11	15	12	3	0	1	3	0	2	1	2	1	6	1	4	0	3	0	1	0	3	4	7			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr2:108999668T>C	ENST00000272452.2	+	4	839	c.513T>C	c.(511-513)gcT>gcC	p.A171A	SULT1C4_ENST00000409309.3_Intron	NM_006588.2	NP_006579.2	O75897	ST1C4_HUMAN	sulfotransferase family, cytosolic, 1C, member 4	171					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	sulfotransferase activity (GO:0008146)			endometrium(1)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	12						CTTTTCTGGCTGGGAAAGGTG	0.423																																					p.A171A		Atlas-SNP	.											.	SULT1C4	41	.	0			c.T513C						PASS	.						106	103	104					2																	108999668		2203	4300	6503	SO:0001819	synonymous_variant	27233	exon4			TCTGGCTGGGAAA	AF055584	CCDS2077.1	2q12.3	2008-09-04	2007-03-16	2007-03-16	ENSG00000198075	ENSG00000198075		"Sulfotransferases, cytosolic"	11457	protein-coding gene	gene with protein product		608357	"sulfotransferase family, cytosolic, 1C, member 2"	SULT1C2		10783263, 9852044	Standard	NM_006588		Approved	SULT1C	uc002tea.1	O75897	OTTHUMG00000130958	ENST00000272452.2:c.513T>C	chr2.hg19:g.108999668T>C		146.0	0.0	.		126.0	40.0	.	NM_006588	Q069I8|Q08AS5|Q53S63	Silent	SNP	ENST00000272452.2	hg19	CCDS2077.1																																																																																			.	.	.	none		0.423	SULT1C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253561.1	NM_006588		C	108999668	T	C	108999668	2	2	24	1	0	0	0	0	0	0	0	1	15391	1567	55	3		3	SULT1C4	2	108999668	Silent	SNP	T	TCGA-4A-A93W-01A-11D-A36X-10	83904169	108999668	134199705	14	1672											
MERTK	10461	hgsc.bcm.edu	37	chr2	112767644	112767644	+	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	gattggagacaggaccaaagGtaatgatctccttgtgttac	12	11	11	7	0	1	2	0	1	1	1	2	5	1	3	2	3	1	2	2	3	3	4			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr2:112767644G>C	ENST00000295408.4	+	15	2336		c.e15+1		MERTK_ENST00000409780.1_Splice_Site|MERTK_ENST00000421804.2_Splice_Site			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase						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						AGGACCAAAGGTAATGATCTC	0.448																																					.		Atlas-SNP	.											.	MERTK	112	.	0			c.2079+1G>C						PASS	.						140	135	137					2																	112767644		2203	4300	6503	SO:0001630	splice_region_variant	10461	exon15			CCAAAGGTAATGA	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.2079+1G>C	chr2.hg19:g.112767644G>C		52.0	0.0	.		54.0	16.0	.	NM_006343	Q9HBB4	Splice_Site	SNP	ENST00000295408.4	hg19	CCDS2094.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.737730	0.89573	.	.	ENSG00000153208	ENST00000295408;ENST00000421804;ENST00000409780	.	.	.	6.04	6.04	0.98038	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.1899	0.98228	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MERTK	112484115	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	8.731000	0.91529	2.873000	0.98535	0.563000	0.77884	.	.	.	.	none		0.448	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2		Intron	C	112767644	G	C	112767644	5	2	24	1	0	0	0	0	0	0	1	0	9486	1275	44	4	2138	4	MERTK	2	112767644	Splice_Site	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10	3767976	112767644	130431729	15	1673											
KLHL23	151230	hgsc.bcm.edu	37	chr2	170592248	170592248	+	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	taaaaacagccttaggccttCaaagaagctgcctgctcacc	13	8	7	13	0	2	1	2	0	0	1	2	1	2	1	4	1	5	2	4	1	6	3			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr2:170592248C>T	ENST00000392647.2	+	2	968	c.724C>T	c.(724-726)Caa>Taa	p.Q242*	KLHL23_ENST00000272797.4_Nonsense_Mutation_p.Q242*|KLHL23_ENST00000602521.1_Intron	NM_144711.5	NP_653312.2	Q8NBE8	KLH23_HUMAN	kelch-like family member 23	242										breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(4)|skin(1)|urinary_tract(1)	16						CTTAGGCCTTCAAAGAAGCTG	0.403																																					p.Q242X		Atlas-SNP	.											.	KLHL23	52	.	0			c.C724T						PASS	.						61	64	63					2																	170592248		2203	4299	6502	SO:0001587	stop_gained	151230	exon2			GGCCTTCAAAGAA	BC010437	CCDS2236.1	2q31.1	2013-01-30	2013-01-30		ENSG00000213160	ENSG00000213160		"Kelch-like", "BTB/POZ domain containing"	27506	protein-coding gene	gene with protein product			"kelch-like 23 (Drosophila)"				Standard	NM_144711		Approved	MGC2610, FLJ37812, MGC22679	uc002ufi.2	Q8NBE8	OTTHUMG00000132213	ENST00000392647.2:c.724C>T	chr2.hg19:g.170592248C>T	ENSP00000376419:p.Gln242*	301.0	0.0	.		277.0	127.0	.	NM_144711	Q8N9B9|Q96FT8	Nonsense_Mutation	SNP	ENST00000392647.2	hg19	CCDS2236.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.617647	0.87359	.	.	ENSG00000213160	ENST00000272797;ENST00000392647;ENST00000437875	.	.	.	5.81	5.81	0.92471	.	0.177188	0.52532	D	0.000070	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	.	14.2573	0.66060	0.0:0.9292:0.0:0.0708	.	.	.	.	X	242;242;63	.	ENSP00000272797:Q242X	Q	+	1	0	KLHL23	170300494	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.335000	0.52105	2.738000	0.93877	0.655000	0.94253	CAA	.	.	.	none		0.403	KLHL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255271.2	NM_144711		T	170592248	C	T	170592248	4	4	24	1	0	0	0	0	0	1	0	0	8385	827	29	2	726	2	KLHL23	2	170592248	Nonsense_Mutation	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10	57824604	170592248	72607125	16	1674											
MYO3B	140469	hgsc.bcm.edu	37	chr2	171319897	171319898	+	Frame_Shift_Ins	INS	-	-	A																															gtggacactctggaggtgatINSacggcatccggaagaaacca																										TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr2:171319897_171319898insA	ENST00000408978.4	+	24	2893_2894	c.2750_2751insA	c.(2749-2754)atacggfs	p.R918fs	MYO3B_ENST00000409044.3_Frame_Shift_Ins_p.R918fs|MYO3B_ENST00000334231.6_Frame_Shift_Ins_p.R927fs|MYO3B_ENST00000602629.1_Intron	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	918	Myosin motor.		R -> Q (in dbSNP:rs55769829). {ECO:0000269|PubMed:17344846}.		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						CTGGAGGTGATACGGCATCCGG	0.49																																					p.I917fs		Atlas-Indel,Pindel	.											.	MYO3B	320	.	0			c.2750_2751insA						PASS	.																																			SO:0001589	frameshift_variant	140469	exon24			.		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.2751dupA	chr2.hg19:g.171319898_171319898dupA	ENSP00000386213:p.Arg918fs	123.0	0.0	0		108.0	50.0	0.462963	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Frame_Shift_Ins	INS	ENST00000408978.4	hg19	CCDS42773.1																																																																																			.	.	.	none		0.49	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1			A	171319898	-	A	171319897	7	5	24	1	0	1	1	0	0	0	0	0	10084	1406	49	0	2844	0	MYO3B	2	171319897	Frame_Shift_Ins	INS	-	TCGA-4A-A93W-01A-11D-A36X-10	727649	171319897	71879476	17	1675											
TTN	7273	hgsc.bcm.edu	37	chr2	179506980	179506980	+	Missense_Mutation	SNP	T	T	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	ataccgcttttcagaacaacTtcttcctttggttcaggttt	8	17	6	10	1	3	1	2	0	1	1	4	1	4	1	2	2	3	3	2	2	3	8			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr2:179506980T>G	ENST00000591111.1	-	169	35843	c.35619A>C	c.(35617-35619)gaA>gaC	p.E11873D	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000418062.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.E13514D|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.E4574D|TTN_ENST00000460472.2_Missense_Mutation_p.E4449D|TTN_ENST00000342175.6_Missense_Mutation_p.E4641D|TTN_ENST00000342992.6_Missense_Mutation_p.E10946D|RP11-171I2.3_ENST00000605021.1_lincRNA			Q8WZ42	TITIN_HUMAN	titin	11873	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)			TCAGAACAACTTCTTCCTTTG	0.328																																					p.E13514D		Atlas-SNP	.											.	TTN	18412	.	0			c.A40542C						PASS	.						55	52	53					2																	179506980		1811	4066	5877	SO:0001583	missense	7273	exon219			AACAACTTCTTCC	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.35619A>C	chr2.hg19:g.179506980T>G	ENSP00000465570:p.Glu11873Asp	120.0	0.0	.		123.0	55.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	17.18	3.324057	0.60634	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000414766;ENST00000434777	T;T;T;T	0.70399	-0.48;0.16;0.1;0.13	5.55	4.4	0.53042	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.74283	0.3696	L	0.46157	1.445	0.35153	D	0.769946	B;B;B;B;D	0.65815	0.256;0.256;0.256;0.38;0.995	B;B;B;B;P	0.57371	0.133;0.133;0.133;0.133;0.819	T	0.81068	-0.1100	9	0.87932	D	0	.	10.6265	0.45510	0.0:0.0763:0.0:0.9237	.	4449;4574;4641;11873;10640	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-5	.;.;.;TITIN_HUMAN;.	D	10946;4449;4641;4574;4449;835;173	ENSP00000343764:E10946D;ENSP00000434586:E4449D;ENSP00000340554:E4641D;ENSP00000352154:E4574D	ENSP00000340554:E4641D	E	-	3	2	TTN	179215225	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.633000	0.54295	0.953000	0.37825	0.482000	0.46254	GAA	.	.	.	none		0.328	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179506980	T	G	179506980	3	3	24	1	0	0	0	0	1	0	0	0	16747	1606	56	5	67727	5	TTN	2	179506980	Missense_Mutation	SNP	T	TCGA-4A-A93W-01A-11D-A36X-10	8187083	179506980	63692393	18	1676											
INO80D	54891	hgsc.bcm.edu	37	chr2	206921321	206921321	+	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	actaaagtgctcttgtcgaaCttttaaaatctctgtctctc	10	16	5	10	1	3	0	0	0	3	0	7	1	3	0	0	0	2	1	0	0	5	4			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr2:206921321C>G	ENST00000403263.1	-	4	969	c.565G>C	c.(565-567)Gtt>Ctt	p.V189L		NM_017759.4	NP_060229.3	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	189					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						TCTTGTCGAACTTTTAAAATC	0.502																																					p.V189L		Atlas-SNP	.											.	INO80D	134	.	0			c.G565C						PASS	.						44	47	46					2																	206921321		2046	4186	6232	SO:0001583	missense	54891	exon4			GTCGAACTTTTAA		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.565G>C	chr2.hg19:g.206921321C>G	ENSP00000384198:p.Val189Leu	89.0	0.0	.		76.0	38.0	.	NM_017759	B3KU68|B9EG77|Q6PJC6|Q6PJU1|Q6PKA1|Q9NXD5	Missense_Mutation	SNP	ENST00000403263.1	hg19	CCDS46500.1	.	.	.	.	.	.	.	.	.	.	C	13.40	2.227209	0.39399	.	.	ENSG00000114933	ENST00000403263;ENST00000233270;ENST00000424117	T;T	0.29917	1.55;1.55	5.7	5.7	0.88788	.	0.195959	0.45126	D	0.000397	T	0.26919	0.0659	N	0.19112	0.55	0.40562	D	0.981221	P	0.40834	0.73	B	0.41202	0.35	T	0.02654	-1.1128	10	0.36615	T	0.2	.	19.8388	0.96673	0.0:1.0:0.0:0.0	.	189	Q53TQ3-2	.	L	189;189;84	ENSP00000384198:V189L;ENSP00000402369:V84L	ENSP00000233270:V189L	V	-	1	0	INO80D	206629566	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.880000	0.39628	2.695000	0.91970	0.561000	0.74099	GTT	.	.	.	none		0.502	INO80D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336459.1	NM_017759		G	206921321	C	G	206921321	3	3	24	1	0	0	0	0	1	0	0	0	7756	565	20	4	2550	4	INO80D	2	206921321	Missense_Mutation	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10	27414341	206921321	36278052	19	1677											
DGKD	8527	hgsc.bcm.edu	37	chr2	234343452	234343452	+	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	ggaccacttctcagggatgcAcaattggtacgcctgttccc	8	10	10	13	1	1	0	1	0	1	0	3	2	2	2	3	3	2	3	3	3	2	4			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr2:234343452A>T	ENST00000264057.2	+	5	503	c.491A>T	c.(490-492)cAc>cTc	p.H164L	DGKD_ENST00000409813.3_Missense_Mutation_p.H120L	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	164					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)	TCAGGGATGCACAATTGGTAC	0.537																																					p.H164L		Atlas-SNP	.											.	DGKD	106	.	0			c.A491T						PASS	.						196	171	179					2																	234343452		2203	4300	6503	SO:0001583	missense	8527	exon5			GGATGCACAATTG	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.491A>T	chr2.hg19:g.234343452A>T	ENSP00000264057:p.His164Leu	75.0	0.0	.		69.0	22.0	.	NM_152879	Q14158|Q6PK55|Q8NG53	Missense_Mutation	SNP	ENST00000264057.2	hg19	CCDS2504.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.772147	0.90108	.	.	ENSG00000077044	ENST00000264057;ENST00000427930;ENST00000447484;ENST00000409813	D;D;T;D	0.99719	-6.52;-6.52;1.65;-6.52	4.92	4.92	0.64577	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);	0.166625	0.39759	N	0.001280	D	0.99819	0.9920	H	0.96691	3.865	0.80722	D	1	P;D;D;B	0.89917	0.763;1.0;0.999;0.055	P;D;D;B	0.97110	0.656;1.0;0.994;0.081	D	0.96723	0.9534	10	0.87932	D	0	.	15.0541	0.71897	1.0:0.0:0.0:0.0	.	48;100;120;164	Q53SE4;C9JY42;Q16760-2;Q16760	.;.;.;DGKD_HUMAN	L	164;100;134;120	ENSP00000264057:H164L;ENSP00000407938:H100L;ENSP00000395530:H134L;ENSP00000386455:H120L	ENSP00000264057:H164L	H	+	2	0	DGKD	234008191	1.000000	0.71417	0.998000	0.56505	0.940000	0.58332	8.631000	0.90991	2.200000	0.70718	0.460000	0.39030	CAC	.	.	.	none		0.537	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648		T	234343452	A	T	234343452	3	4	24	1	0	0	0	0	1	0	0	0	4469	159	6	5	533	5	DGKD	2	234343452	Missense_Mutation	SNP	A	TCGA-4A-A93W-01A-11D-A36X-10	27422131	234343452	8855921	20	1678											
CHL1	10752	hgsc.bcm.edu	37	chr3	433428	433428	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gccactttatcttggggactAcctaagaaattaaatggaaa	15	11	8	7	0	1	1	0	0	1	1	1	3	1	3	2	3	1	0	2	3	7	6			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr3:433428A>G	ENST00000256509.2	+	23	3504	c.2862A>G	c.(2860-2862)ctA>ctG	p.L954L	CHL1_ENST00000397491.2_Silent_p.L938L	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)		CTTGGGGACTACCTAAGAAAT	0.313																																					p.L954L		Atlas-SNP	.											.	CHL1	242	.	0			c.A2862G						PASS	.						84	85	85					3																	433428		2203	4300	6503	SO:0001819	synonymous_variant	10752	exon21			GGGACTACCTAAG	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.2862A>G	chr3.hg19:g.433428A>G		106.0	0.0	.		117.0	5.0	.	NM_001253388	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Silent	SNP	ENST00000256509.2	hg19	CCDS2556.1	.	.	.	.	.	.	.	.	.	.	A	6.380	0.438192	0.12104	.	.	ENSG00000134121	ENST00000445697	.	.	.	5.62	-5.76	0.02376	.	.	.	.	.	T	0.34832	0.0911	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43360	-0.9396	4	.	.	.	.	0.6894	0.00888	0.2664:0.179:0.3048:0.2498	.	.	.	.	C	141	.	.	Y	+	2	0	CHL1	408428	0.026000	0.19158	0.042000	0.18584	0.811000	0.45836	-0.893000	0.04127	-0.543000	0.06240	0.528000	0.53228	TAC	.	.	.	none		0.313	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614		G	433428	A	G	433428	2	3	24	1	0	0	0	0	0	0	0	1	3351	378	14	3		3	CHL1	3	433428	Silent	SNP	A	TCGA-4A-A93W-01A-11D-A36X-10		433428	197589002	21	1679											
CNTN6	27255	hgsc.bcm.edu	37	chr3	1424739	1424739	+	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	tcatctgtggaatcatcaagGtttgtctacagaaatgaaag	14	12	9	6	0	5	2	3	1	2	1	5	3	5	3	0	2	1	1	0	2	5	2			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr3:1424739G>A	ENST00000446702.2	+	18	2907	c.2280G>A	c.(2278-2280)agG>agA	p.R760R	CNTN6_ENST00000539053.1_Silent_p.R688R|CNTN6_ENST00000350110.2_Silent_p.R760R			Q9UQ52	CNTN6_HUMAN	contactin 6	760	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.R760S(1)		breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		AATCATCAAGGTTTGTCTACA	0.458																																					p.R760R		Atlas-SNP	.											CNTN6,NS,carcinoma,+1,1	CNTN6	245	.	1	Substitution - Missense(1)	lung(1)	c.G2280A						PASS	.						167	153	158					3																	1424739		2203	4300	6503	SO:0001819	synonymous_variant	27255	exon18			ATCAAGGTTTGTC	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	2176	protein-coding gene	gene with protein product	"neural adhesion molecule"	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.2280G>A	chr3.hg19:g.1424739G>A		279.0	0.0	.		243.0	90.0	.	NM_014461	Q2KHM2	Silent	SNP	ENST00000446702.2	hg19	CCDS2557.1																																																																																			.	.	.	none		0.458	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461		A	1424739	G	A	1424739	2	1	24	1	0	0	0	0	0	0	0	1	3647	1252	44	2		2	CNTN6	3	1424739	Silent	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10	991311	1424739	196597691	22	1680											
CXCR6	10663	hgsc.bcm.edu	37	chr3	45988986	45988986	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccacaatgtggaggccaccaGcatgttccagttataggcct	10	9	10	12	0	0	0	0	0	0	0	1	1	1	1	5	3	1	3	5	3	3	3			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr3:45988986G>A	ENST00000458629.1	+	1	2476	c.1013G>A	c.(1012-1014)aGc>aAc	p.S338N	FYCO1_ENST00000438446.1_Intron|CXCR6_ENST00000438735.1_Missense_Mutation_p.S338N|FYCO1_ENST00000296137.2_Intron|CXCR6_ENST00000304552.4_Missense_Mutation_p.S338N|FYCO1_ENST00000535325.1_Intron|CXCR6_ENST00000457814.1_Missense_Mutation_p.S338N			O00574	CXCR6_HUMAN	chemokine (C-X-C motif) receptor 6	338					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)		GAGGCCACCAGCATGTTCCAG	0.498																																					p.S338N	Esophageal Squamous(63;1005 1117 15521 45762 47089)	Atlas-SNP	.											.	CXCR6	17	.	0			c.G1013A						PASS	.						72	69	70					3																	45988986		2203	4300	6503	SO:0001583	missense	10663	exon2			CCACCAGCATGTT	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.1013G>A	chr3.hg19:g.45988986G>A	ENSP00000395704:p.Ser338Asn	98.0	0.0	.		113.0	40.0	.	NM_006564	O00575|Q9HCA5	Missense_Mutation	SNP	ENST00000458629.1	hg19	CCDS2735.1	.	.	.	.	.	.	.	.	.	.	G	14.59	2.580107	0.46006	.	.	ENSG00000172215	ENST00000438735;ENST00000304552;ENST00000458629;ENST00000457814	T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25	5.58	0.378	0.16204	.	0.374134	0.28940	N	0.013651	T	0.57184	0.2036	M	0.62723	1.935	0.30459	N	0.774467	B	0.10296	0.003	B	0.09377	0.004	T	0.55205	-0.8177	10	0.66056	D	0.02	.	6.2004	0.20573	0.275:0.3366:0.3884:0.0	.	338	O00574	CXCR6_HUMAN	N	338	ENSP00000396218:S338N;ENSP00000304414:S338N;ENSP00000395704:S338N;ENSP00000396886:S338N	ENSP00000304414:S338N	S	+	2	0	CXCR6	45963990	0.980000	0.34600	0.998000	0.56505	0.982000	0.71751	0.153000	0.16323	0.040000	0.15660	0.561000	0.74099	AGC	.	.	.	none		0.498	CXCR6-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344395.1			A	45988986	G	A	45988986	3	1	24	1	0	0	0	0	1	0	0	0	4097	971	34	2	1015	2	CXCR6	3	45988986	Missense_Mutation	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10	44564247	45988986	152033444	23	1681											
PHF7	51533	hgsc.bcm.edu	37	chr3	52456291	52456291	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcagacttatatcagcgctAtcagcactgtgatgccccca	10	10	7	14	1	3	2	3	1	0	1	3	2	3	2	2	0	3	2	2	0	3	3			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr3:52456291A>G	ENST00000327906.3	+	9	1394	c.734A>G	c.(733-735)tAt>tGt	p.Y245C	PHF7_ENST00000347025.2_Intron	NM_016483.4	NP_057567.3	Q9BWX1	PHF7_HUMAN	PHD finger protein 7	245						Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			breast(2)|large_intestine(4)|lung(3)	9				BRCA - Breast invasive adenocarcinoma(193;1.71e-05)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)|OV - Ovarian serous cystadenocarcinoma(275;0.0275)		TATCAGCGCTATCAGCACTGT	0.498																																					p.Y245C		Atlas-SNP	.											.	PHF7	29	.	0			c.A734G						PASS	.						98	94	95					3																	52456291		2203	4300	6503	SO:0001583	missense	51533	exon9			AGCGCTATCAGCA	AY014283	CCDS2854.1, CCDS2855.1	3p21.31	2013-01-28			ENSG00000010318	ENSG00000010318		"Zinc fingers, PHD-type"	18458	protein-coding gene	gene with protein product						11042152, 11829468	Standard	NM_016483		Approved	NYD-SP6, HSPC226	uc003ddy.3	Q9BWX1	OTTHUMG00000158495	ENST00000327906.3:c.734A>G	chr3.hg19:g.52456291A>G	ENSP00000333024:p.Tyr245Cys	89.0	0.0	.		102.0	38.0	.	NM_016483	K4DI82	Missense_Mutation	SNP	ENST00000327906.3	hg19	CCDS2854.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.70|19.70	3.876288|3.876288	0.72180|0.72180	.|.	.|.	ENSG00000010318|ENSG00000010318	ENST00000461861|ENST00000478707;ENST00000327906;ENST00000394916	.|T;T	.|0.09163	.|3.01;3.01	5.75|5.75	5.75|5.75	0.90469|0.90469	.|Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE/PHD-type (1);	.|0.120863	.|0.64402	.|D	.|0.000016	T|T	0.24470|0.24470	0.0593|0.0593	M|M	0.68317|0.68317	2.08|2.08	0.80722|0.80722	D|D	1|1	.|D	.|0.67145	.|0.996	.|P	.|0.57371	.|0.819	T|T	0.00888|0.00888	-1.1526|-1.1526	5|10	.|0.34782	.|T	.|0.22	-0.6876|-0.6876	12.4509|12.4509	0.55677|0.55677	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|245	.|Q9BWX1	.|PHF7_HUMAN	V|C	205|245;245;154	.|ENSP00000419316:Y245C;ENSP00000333024:Y245C	.|ENSP00000333024:Y245C	I|Y	+|+	1|2	0|0	PHF7|PHF7	52431331|52431331	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.358000|5.358000	0.66064|0.66064	2.196000|2.196000	0.70406|0.70406	0.533000|0.533000	0.62120|0.62120	ATC|TAT	.	.	.	none		0.498	PHF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351155.1	NM_016483		G	52456291	A	G	52456291	3	3	24	1	0	0	0	0	1	0	0	0	11846	449	16	3	764	3	PHF7	3	52456291	Missense_Mutation	SNP	A	TCGA-4A-A93W-01A-11D-A36X-10	6467305	52456291	145566139	24	1682											
ITIH3	3699	hgsc.bcm.edu	37	chr3	52835082	52835082	+	Frame_Shift_Del	DEL	T	T	-																															gcaacaatctgaattataacTtcctggagaacatggccctg																										TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr3:52835082delT	ENST00000449956.2	+	11	1309	c.1303delT	c.(1303-1305)ttcfs	p.F435fs	ITIH3_ENST00000416872.2_Frame_Shift_Del_p.F435fs	NM_002217.3	NP_002208.3	Q06033	ITIH3_HUMAN	inter-alpha-trypsin inhibitor heavy chain 3	435	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(6)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		GAATTATAACTTCCTGGAGAA	0.502																																					p.N434fs		Atlas-Indel,Pindel	.											.	ITIH3	132	.	0			c.1302delC						PASS	.						102	105	104					3																	52835082		1922	4124	6046	SO:0001589	frameshift_variant	3699	exon11			.		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.1303delT	chr3.hg19:g.52835082delT	ENSP00000415769:p.Phe435fs	170.0	0.0	0		153.0	59.0	0.385621	NM_002217	Q3B7H5|Q53F06|Q6LAM2|Q99085	Frame_Shift_Del	DEL	ENST00000449956.2	hg19	CCDS46845.1																																																																																			.	.	.	none		0.502	ITIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352668.2	NM_002217		-	52835082	T	-	52835082	7	5	24	1	0	1	0	1	0	0	0	0	7912	1609	56	0	1345	0	ITIH3	3	52835082	Frame_Shift_Del	DEL	T	TCGA-4A-A93W-01A-11D-A36X-10	378791	52835082	145187348	25	1683											
ABI3BP	25890	hgsc.bcm.edu	37	chr3	100565235	100565235	+	Silent	SNP	T	T	C																															ccaggtttggtgtgtgtcacTtctgggctgagagggatttt																										TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr3:100565235T>C	ENST00000284322.5	-	18	1687	c.1578A>G	c.(1576-1578)gaA>gaG	p.E526E	ABI3BP_ENST00000383691.4_5'UTR|ABI3BP_ENST00000495063.1_Silent_p.E575E|ABI3BP_ENST00000471714.1_Silent_p.E575E	NM_015429.3	NP_056244.2	Q7Z7G0	TARSH_HUMAN	ABI family, member 3 (NESH) binding protein	526	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						TGTGTGTCACTTCTGGGCTGA	0.333																																					p.E526E		Atlas-SNP	.											.	ABI3BP	305	.	0			c.A1578G						PASS	.						74	69	71					3																	100565235		1807	4064	5871	SO:0001819	synonymous_variant	25890	exon18			TGTCACTTCTGGG	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.1578A>G	chr3.hg19:g.100565235T>C		109.0	0.0	.		134.0	62.0	.	NM_015429	B3KSL4|Q6ZW20|Q6ZW22|Q9C082|Q9UFI6	Silent	SNP	ENST00000284322.5	hg19	CCDS46880.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	7.023|7.023	0.559028|0.559028	0.13436|0.13436	.|.	.|.	ENSG00000154175|ENSG00000154175	ENST00000495591;ENST00000528490;ENST00000533855|ENST00000466947	.|.	.|.	.|.	5.58|5.58	-1.95|-1.95	0.07548|0.07548	.|.	.|.	.|.	.|.	.|.	T|T	0.18509|0.18509	0.0444|0.0444	.|.	.|.	.|.	0.19300|0.19300	N|N	0.999973|0.999973	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.23797|0.23797	-1.0178|-1.0178	4|4	.|.	.|.	.|.	-1.12|-1.12	1.3054|1.3054	0.02087|0.02087	0.2159:0.1298:0.3307:0.3236|0.2159:0.1298:0.3307:0.3236	.|.	.|.	.|.	.|.	R|G	13;43;204|14	.|.	.|.	K|S	-|-	2|1	0|0	ABI3BP|ABI3BP	102047925|102047925	0.001000|0.001000	0.12720|0.12720	0.098000|0.098000	0.21074|0.21074	0.996000|0.996000	0.88848|0.88848	0.181000|0.181000	0.16880|0.16880	-0.457000|-0.457000	0.07033|0.07033	0.477000|0.477000	0.44152|0.44152	AAG|AGT	.	.	.	none		0.333	ABI3BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353260.1			C	100565235	T	C	100565235	2	2	24	1	0	0	0	0	0	0	0	1	91	1606	56	3		3	ABI3BP	3	100565235	Silent	SNP	T	TCGA-4A-A93W-01A-11D-A36X-10	47730153	100565235	97457195	26	1684	18	2									
ABI3BP	25890	hgsc.bcm.edu	37	chr3	100565237	100565237	+	Frame_Shift_Del	DEL	C	C	-																															aggtttggtgtgtgtcacttCtgggctgagagggattttag																										TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr3:100565237delC	ENST00000284322.5	-	18	1685	c.1576delG	c.(1576-1578)gaafs	p.E526fs	ABI3BP_ENST00000383691.4_5'UTR|ABI3BP_ENST00000495063.1_Frame_Shift_Del_p.E575fs|ABI3BP_ENST00000471714.1_Frame_Shift_Del_p.E575fs	NM_015429.3	NP_056244.2	Q7Z7G0	TARSH_HUMAN	ABI family, member 3 (NESH) binding protein	526	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						TGTGTCACTTCTGGGCTGAGA	0.333																																					p.E526fs		Atlas-INDEL	.											.	ABI3BP	305	.	0			c.1577delA						PASS	.						74	69	71					3																	100565237		1806	4066	5872	SO:0001589	frameshift_variant	25890	exon18			.	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.1576delG	chr3.hg19:g.100565237delC	ENSP00000284322:p.Glu526fs	108.0	0.0	0		133.0	60.0	0.451128	NM_015429	B3KSL4|Q6ZW20|Q6ZW22|Q9C082|Q9UFI6	Frame_Shift_Del	DEL	ENST00000284322.5	hg19	CCDS46880.1																																																																																			.	.	.	none		0.333	ABI3BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353260.1			-	100565237	C	-	100565237	7	5	24	1	0	1	0	1	0	0	0	0	91	922	32	0	1723	0	ABI3BP	3	100565237	Frame_Shift_Del	DEL	C	TCGA-4A-A93W-01A-11D-A36X-10	2	100565237	97457193	27	1685	18	2									
PLOD2	5352	hgsc.bcm.edu	37	chr3	145806425	145806425	+	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	ttgggtaatccagtgtcaacAatatgtccagaaaccgaggt	13	10	10	8	1	1	1	1	0	0	1	3	2	3	1	3	2	2	1	3	2	5	3	rs367818257		TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr3:145806425A>T	ENST00000360060.3	-	9	1130	c.953T>A	c.(952-954)tTg>tAg	p.L318*	RP11-274H2.2_ENST00000480247.1_RNA|PLOD2_ENST00000282903.5_Nonsense_Mutation_p.L318*|PLOD2_ENST00000461497.1_5'Flank|PLOD2_ENST00000494950.1_Nonsense_Mutation_p.L263*	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	318					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)	CAGTGTCAACAATATGTCCAG	0.313																																					p.L318X		Atlas-SNP	.											.	PLOD2	81	.	0			c.T953A						PASS	.						84	79	81					3																	145806425		2202	4298	6500	SO:0001587	stop_gained	5352	exon9			GTCAACAATATGT	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.953T>A	chr3.hg19:g.145806425A>T	ENSP00000353170:p.Leu318*	386.0	1.0	.		434.0	187.0	.	NM_182943	B3KWS3|Q59ED2|Q8N170	Nonsense_Mutation	SNP	ENST00000360060.3	hg19	CCDS3131.1	.	.	.	.	.	.	.	.	.	.	A	37	6.340514	0.97489	.	.	ENSG00000152952	ENST00000282903;ENST00000360060;ENST00000494950	.	.	.	5.33	5.33	0.75918	.	0.069303	0.56097	D	0.000040	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-30.431	15.3138	0.74056	1.0:0.0:0.0:0.0	.	.	.	.	X	318;318;263	.	ENSP00000282903:L318X	L	-	2	0	PLOD2	147289115	0.998000	0.40836	0.669000	0.29828	0.277000	0.26821	8.938000	0.92943	2.016000	0.59253	0.528000	0.53228	TTG	.	.	.	alt		0.313	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935		T	145806425	A	T	145806425	4	4	24	1	0	0	0	0	0	1	0	0	12109	131	5	5	1371	5	PLOD2	3	145806425	Nonsense_Mutation	SNP	A	TCGA-4A-A93W-01A-11D-A36X-10	45241188	145806425	52216005	28	1686											
PRKCI	5584	hgsc.bcm.edu	37	chr3	170016826	170016826	+	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	tccctttaaaccaaatatttCtggggaatttggtttggaca	11	15	8	7	0	1	0	0	0	1	0	2	2	2	2	2	4	1	1	2	4	5	6			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr3:170016826C>A	ENST00000295797.4	+	17	1936	c.1631C>A	c.(1630-1632)tCt>tAt	p.S544Y		NM_002740.5	NP_002731.4	P41743	KPCI_HUMAN	protein kinase C, iota	544	AGC-kinase C-terminal.				actin filament organization (GO:0007015)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell junction organization (GO:0045216)|cellular response to insulin stimulus (GO:0032869)|cytoskeleton organization (GO:0007010)|establishment of apical/basal cell polarity (GO:0035089)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|eye photoreceptor cell development (GO:0042462)|Golgi vesicle budding (GO:0048194)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of glucose import (GO:0046326)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein phosphorylation (GO:0006468)|protein targeting to membrane (GO:0006612)|response to interleukin-1 (GO:0070555)|secretion (GO:0046903)|tight junction assembly (GO:0070830)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Schmidt-Lanterman incisure (GO:0043220)	ATP binding (GO:0005524)|phospholipid binding (GO:0005543)|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)|endometrium(5)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	36	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|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;0.197)		Tamoxifen(DB00675)	CCAAATATTTCTGGGGAATTT	0.388																																					p.S544Y		Atlas-SNP	.											PRKCI,NS,carcinoma,0,1	PRKCI	82	.	0			c.C1631A						PASS	.						88	87	88					3																	170016826		2203	4300	6503	SO:0001583	missense	5584	exon17			ATATTTCTGGGGA		CCDS3212.2	3q26.3	2008-07-18			ENSG00000163558	ENSG00000163558	2.7.11.13		9404	protein-coding gene	gene with protein product		600539		DXS1179E		7607695, 11978974	Standard	NM_002740		Approved	PKCI	uc003fgs.2	P41743	OTTHUMG00000150214	ENST00000295797.4:c.1631C>A	chr3.hg19:g.170016826C>A	ENSP00000295797:p.Ser544Tyr	99.0	0.0	.		140.0	70.0	.	NM_002740	D3DNQ4|Q8WW06	Missense_Mutation	SNP	ENST00000295797.4	hg19	CCDS3212.2	.	.	.	.	.	.	.	.	.	.	C	26.5	4.739807	0.89573	.	.	ENSG00000163558	ENST00000295797	T	0.62639	0.01	5.22	5.22	0.72569	Protein kinase, C-terminal (1);AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	0.059408	0.64402	D	0.000001	T	0.67211	0.2869	L	0.52126	1.63	0.80722	D	1	D	0.57257	0.979	P	0.50860	0.652	T	0.66052	-0.6019	9	.	.	.	.	19.1471	0.93473	0.0:1.0:0.0:0.0	.	544	P41743	KPCI_HUMAN	Y	544	ENSP00000295797:S544Y	.	S	+	2	0	PRKCI	171499520	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.456000	0.80751	2.578000	0.87016	0.650000	0.86243	TCT	.	.	.	none		0.388	PRKCI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316866.3	NM_002740		A	170016826	C	A	170016826	3	1	24	1	0	0	0	0	1	0	0	0	12524	913	32	4	1697	4	PRKCI	3	170016826	Missense_Mutation	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10	24210401	170016826	28005604	29	1687											
PEX5L	51555	hgsc.bcm.edu	37	chr3	179615950	179615950	+	Frame_Shift_Del	DEL	G	G	-																															ctgtgatgtcatagtaaggaGgggcttttcttcagcagact																										TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr3:179615950delG	ENST00000467460.1	-	3	508	c.178delC	c.(178-180)ctcfs	p.L61fs	PEX5L_ENST00000464614.1_Frame_Shift_Del_p.L18fs|PEX5L_ENST00000472994.1_Intron|PEX5L_ENST00000465751.1_Frame_Shift_Del_p.L37fs|PEX5L_ENST00000263962.8_Frame_Shift_Del_p.L59fs|PEX5L_ENST00000468741.1_Intron|PEX5L_ENST00000392649.3_Frame_Shift_Del_p.L18fs|PEX5L_ENST00000476138.1_Frame_Shift_Del_p.L18fs|PEX5L_ENST00000485199.1_Intron|PEX5L-AS2_ENST00000462801.1_RNA	NM_001256751.1|NM_016559.2	NP_001243680.1|NP_057643.1	Q8IYB4	PEX5R_HUMAN	peroxisomal biogenesis factor 5-like	61					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)			ATAGTAAGGAGGGGCTTTTCT	0.438																																					p.L60fs		Atlas-Indel,Pindel	.											.	PEX5L	104	.	0			c.179delT						PASS	.						111	105	107					3																	179615950		2203	4300	6503	SO:0001589	frameshift_variant	51555	exon3			.	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.178delC	chr3.hg19:g.179615950delG	ENSP00000419975:p.Leu61fs	98.0	0.0	0		112.0	45.0	0.401786	NM_016559	B7Z2A5|B7Z305|B7Z318|B7Z5Z5|B7Z8P2|E7EUV8|E7EUZ0|E9PEC1|E9PH97|Q9NQD1|Q9P2U3|Q9P2U4	Frame_Shift_Del	DEL	ENST00000467460.1	hg19	CCDS3236.1																																																																																			.	.	.	none		0.438	PEX5L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348577.1	NM_016559		-	179615950	G	-	179615950	7	5	24	1	0	1	0	1	0	0	0	0	11756	1000	35	0	1754	0	PEX5L	3	179615950	Frame_Shift_Del	DEL	G	TCGA-4A-A93W-01A-11D-A36X-10	9599124	179615950	18406480	30	1688											
C4orf46	201725	hgsc.bcm.edu	37	chr4	159592804	159592804	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccacttcctccagctggtcCaccgttgggccgctgctcct	3	11	9	18	2	0	0	0	0	0	0	5	0	5	0	7	2	2	4	7	2	0	2			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr4:159592804C>T	ENST00000379205.4	-	1	394	c.150G>A	c.(148-150)gtG>gtA	p.V50V	C4orf46_ENST00000508836.1_Intron|ETFDH_ENST00000307738.5_5'Flank|ETFDH_ENST00000511912.1_5'Flank|C4orf46_ENST00000508457.1_Silent_p.V50V	NM_001008393.2	NP_001008394.1	Q504U0	CD046_HUMAN	chromosome 4 open reading frame 46	50										kidney(1)|lung(3)|skin(1)	5						CCAGCTGGTCCACCGTTGGGC	0.692																																					p.V50V		Atlas-SNP	.											.	C4orf46	11	.	0			c.G150A						PASS	.						35	30	31					4																	159592804		2203	4300	6503	SO:0001819	synonymous_variant	201725	exon1			CTGGTCCACCGTT		CCDS34088.1	4q32.1	2014-07-30			ENSG00000205208	ENSG00000205208			27320	protein-coding gene	gene with protein product	"renal cancer differentiation gene 1"						Standard	NM_001008393		Approved	LOC201725, RCDG1	uc003iqa.3	Q504U0	OTTHUMG00000161919	ENST00000379205.4:c.150G>A	chr4.hg19:g.159592804C>T		236.0	0.0	.		226.0	100.0	.	NM_001008393	B3KNH7	Silent	SNP	ENST00000379205.4	hg19	CCDS34088.1																																																																																			.	.	.	none		0.692	C4orf46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366378.1	NM_001008393		T	159592804	C	T	159592804	2	4	24	1	0	0	0	0	0	0	0	1	2276	581	21	2		2	C4orf46	4	159592804	Silent	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10		159592804	31561472	31	1689											
MFAP3L	9848	hgsc.bcm.edu	37	chr4	170913146	170913146	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgatggggatgcgcttggCgatctcaaatgccttctgca	8	11	13	9	2	2	1	1	1	2	0	3	4	2	2	1	3	3	2	1	3	1	2			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr4:170913146C>T	ENST00000361618.3	-	3	920	c.613G>A	c.(613-615)Gcc>Acc	p.A205T	MFAP3L_ENST00000393704.3_Missense_Mutation_p.A102T|RP11-6E9.4_ENST00000508955.1_RNA	NM_021647.6	NP_067679.6	O75121	MFA3L_HUMAN	microfibrillar-associated protein 3-like	205						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)		ATGCGCTTGGCGATCTCAAAT	0.512																																					p.A205T		Atlas-SNP	.											MFAP3L,caecum,carcinoma,0,1	MFAP3L	59	.	0			c.G613A						PASS	.						135	140	138					4																	170913146		2203	4300	6503	SO:0001583	missense	9848	exon3			GCTTGGCGATCTC	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.613G>A	chr4.hg19:g.170913146C>T	ENSP00000354583:p.Ala205Thr	137.0	0.0	.		122.0	44.0	.	NM_021647	A8K1X6|D3DP35|Q4W5N7|Q4W5N9|Q6TNA8|Q9BVE1|Q9BXK0	Missense_Mutation	SNP	ENST00000361618.3	hg19	CCDS34103.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.710617	0.89112	.	.	ENSG00000198948	ENST00000393704;ENST00000361618;ENST00000512698	D;D;D	0.98835	-5.17;-1.96;-4.95	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	D	0.98887	0.9623	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99391	1.0925	10	0.34782	T	0.22	-32.4843	19.4847	0.95025	0.0:1.0:0.0:0.0	.	205	O75121	MFA3L_HUMAN	T	102;205;102	ENSP00000377307:A102T;ENSP00000354583:A205T;ENSP00000422791:A102T	ENSP00000354583:A205T	A	-	1	0	MFAP3L	171149721	1.000000	0.71417	0.999000	0.59377	0.846000	0.48090	7.818000	0.86416	2.602000	0.87976	0.555000	0.69702	GCC	.	.	.	none		0.512	MFAP3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363043.2	NM_021647		T	170913146	C	T	170913146	3	4	24	1	0	0	0	0	1	0	0	0	9523	768	27	1	620	1	MFAP3L	4	170913146	Missense_Mutation	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10	11320342	170913146	20241130	32	1690											
SV2C	22987	hgsc.bcm.edu	37	chr5	75427885	75427885	+	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	ccagtatgaaccaagcgaagGacagcatcgtgtcagtgggg	12	6	14	9	2	1	1	1	1	0	0	2	3	1	2	2	3	3	2	2	3	4	1			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr5:75427885G>C	ENST00000502798.2	+	2	752	c.310G>C	c.(310-312)Gac>Cac	p.D104H	SV2C_ENST00000322285.7_Missense_Mutation_p.D104H	NM_014979.1	NP_055794.1	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	104					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		CCAAGCGAAGGACAGCATCGT	0.557																																					p.D104H		Atlas-SNP	.											.	SV2C	97	.	0			c.G310C						PASS	.						86	90	89					5																	75427885		2109	4241	6350	SO:0001583	missense	22987	exon2			GCGAAGGACAGCA	AB028977	CCDS43331.1, CCDS75261.1	5q13	2008-02-05			ENSG00000122012	ENSG00000122012			30670	protein-coding gene	gene with protein product		610291				10470851, 9801366	Standard	XM_005248470		Approved		uc003kei.1	Q496J9	OTTHUMG00000162384	ENST00000502798.2:c.310G>C	chr5.hg19:g.75427885G>C	ENSP00000423541:p.Asp104His	117.0	0.0	.		123.0	49.0	.	NM_014979	Q496K1|Q9UPU8	Missense_Mutation	SNP	ENST00000502798.2	hg19	CCDS43331.1	.	.	.	.	.	.	.	.	.	.	G	15.21	2.767148	0.49574	.	.	ENSG00000122012	ENST00000502798;ENST00000322285	T;T	0.33216	1.42;1.42	5.76	5.76	0.90799	Major facilitator superfamily domain, general substrate transporter (1);	0.218772	0.47093	D	0.000256	T	0.37517	0.1006	L	0.51422	1.61	0.80722	D	1	P	0.41393	0.748	B	0.42882	0.401	T	0.06356	-1.0831	10	0.46703	T	0.11	-21.7026	19.9694	0.97278	0.0:0.0:1.0:0.0	.	104	Q496J9	SV2C_HUMAN	H	104	ENSP00000423541:D104H;ENSP00000316983:D104H	ENSP00000316983:D104H	D	+	1	0	SV2C	75463641	1.000000	0.71417	0.790000	0.31976	0.526000	0.34562	6.822000	0.75277	2.719000	0.93026	0.655000	0.94253	GAC	.	.	.	none		0.557	SV2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368700.4			C	75427885	G	C	75427885	3	2	24	1	0	0	0	0	1	0	0	0	15431	1174	41	4	312	4	SV2C	5	75427885	Missense_Mutation	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10		75427885	105487375	33	1691											
MEF2C	4208	hgsc.bcm.edu	37	chr5	88027620	88027620	+	Missense_Mutation	SNP	A	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	tttacggttattcattcctaAattcattgggggaggagatt	10	16	10	5	1	2	1	2	0	0	1	3	3	3	2	1	4	1	1	1	4	4	9			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr5:88027620A>C	ENST00000437473.2	-	7	1153	c.736T>G	c.(736-738)Tta>Gta	p.L246V	MEF2C_ENST00000514015.1_Missense_Mutation_p.L246V|MEF2C_ENST00000539796.1_Missense_Mutation_p.L198V|MEF2C_ENST00000508569.1_Missense_Mutation_p.L246V|MEF2C_ENST00000504921.2_Missense_Mutation_p.L246V|MEF2C_ENST00000510942.1_Missense_Mutation_p.L246V|MEF2C_ENST00000503554.1_5'Flank|MEF2C_ENST00000514028.1_Missense_Mutation_p.L246V|MEF2C_ENST00000340208.5_Missense_Mutation_p.L264V|MEF2C_ENST00000424173.2_Missense_Mutation_p.L244V|MEF2C_ENST00000506554.1_Missense_Mutation_p.L246V	NM_001193350.1|NM_002397.4	NP_001180279.1|NP_002388.2	Q06413	MEF2C_HUMAN	myocyte enhancer factor 2C	246					apoptotic process (GO:0006915)|B cell homeostasis (GO:0001782)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac ventricle formation (GO:0003211)|cartilage morphogenesis (GO:0060536)|cell morphogenesis involved in neuron differentiation (GO:0048667)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|cellular response to fluid shear stress (GO:0071498)|cellular response to glucose stimulus (GO:0071333)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to trichostatin A (GO:0035984)|chondrocyte differentiation (GO:0002062)|dentate gyrus development (GO:0021542)|embryonic viscerocranium morphogenesis (GO:0048703)|endochondral ossification (GO:0001958)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|germinal center formation (GO:0002467)|glomerulus morphogenesis (GO:0072102)|heart development (GO:0007507)|heart looping (GO:0001947)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|MAPK cascade (GO:0000165)|melanocyte differentiation (GO:0030318)|monocyte differentiation (GO:0030224)|muscle cell differentiation (GO:0042692)|muscle cell fate determination (GO:0007521)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myotube differentiation (GO:0014902)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of ossification (GO:0030279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nephron tubule epithelial cell differentiation (GO:0072160)|nervous system development (GO:0007399)|neural crest cell differentiation (GO:0014033)|neuron development (GO:0048666)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|osteoblast differentiation (GO:0001649)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|platelet formation (GO:0030220)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of behavioral fear response (GO:2000987)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation in bone marrow (GO:0071864)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|primary heart field specification (GO:0003138)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of dendritic spine development (GO:0060998)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of germinal center formation (GO:0002634)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron apoptotic process (GO:0043523)|regulation of neurotransmitter secretion (GO:0046928)|regulation of sarcomere organization (GO:0060297)|regulation of synapse assembly (GO:0051963)|regulation of synaptic activity (GO:0060025)|regulation of synaptic plasticity (GO:0048167)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|renal tubule morphogenesis (GO:0061333)|response to ischemia (GO:0002931)|response to virus (GO:0009615)|response to vitamin E (GO:0033197)|secondary heart field specification (GO:0003139)|sinoatrial valve morphogenesis (GO:0003185)|skeletal muscle tissue development (GO:0007519)|smooth muscle cell differentiation (GO:0051145)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac muscle cell differentiation (GO:0055012)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|sarcomere (GO:0030017)	activating transcription factor binding (GO:0033613)|AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|miRNA binding (GO:0035198)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	40		all_cancers(142;6.67e-05)|all_epithelial(76;7.77e-07)|Lung NSC(167;0.00566)|all_lung(232;0.00732)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;1.04e-33)|Epithelial(54;1.6e-28)|all cancers(79;2.9e-25)		TTCATTCCTAAATTCATTGGG	0.428										HNSCC(66;0.2)																											p.L264V		Atlas-SNP	.											.	MEF2C	184	.	0			c.T790G						PASS	.						99	97	98					5																	88027620		1851	4087	5938	SO:0001583	missense	4208	exon9			TTCCTAAATTCAT	AL833268	CCDS47244.1, CCDS47245.1, CCDS54877.1, CCDS54878.1	5q14.3	2013-07-03	2007-04-24		ENSG00000081189	ENSG00000081189		"Myocyte enhancer factors"	6996	protein-coding gene	gene with protein product		600662				8455629	Standard	NM_002397		Approved		uc003kjl.3	Q06413	OTTHUMG00000162634	ENST00000437473.2:c.736T>G	chr5.hg19:g.88027620A>C	ENSP00000396219:p.Leu246Val	92.0	0.0	.		81.0	5.0	.	NM_001193347	C9JMZ0|D7F7N5|F8W7V7	Missense_Mutation	SNP	ENST00000437473.2	hg19	CCDS47245.1	.	.	.	.	.	.	.	.	.	.	A	15.52	2.856714	0.51376	.	.	ENSG00000081189	ENST00000340208;ENST00000424173;ENST00000504921;ENST00000514028;ENST00000437473;ENST00000510942;ENST00000506554;ENST00000508569;ENST00000514015;ENST00000539796	T;T;T;T;T;T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5	6.17	1.18	0.20946	.	0.000000	0.85682	D	0.000000	T	0.25717	0.0626	L	0.35644	1.08	0.52501	D	0.999959	B;P;P;P	0.45126	0.215;0.851;0.552;0.603	B;P;B;B	0.44447	0.071;0.45;0.257;0.421	T	0.02326	-1.1176	10	0.52906	T	0.07	-3.6707	9.8788	0.41220	0.5416:0.0:0.4584:0.0	.	244;264;246;246	C9JMZ0;F8W7V7;Q06413;Q06413-2	.;.;MEF2C_HUMAN;.	V	264;244;246;246;246;246;246;246;246;198	ENSP00000340874:L264V;ENSP00000389610:L244V;ENSP00000421925:L246V;ENSP00000426665:L246V;ENSP00000396219:L246V;ENSP00000422390:L246V;ENSP00000425636:L246V;ENSP00000423597:L246V;ENSP00000424606:L246V;ENSP00000441153:L198V	ENSP00000340874:L264V	L	-	1	2	MEF2C	88063376	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	0.696000	0.25541	0.204000	0.20548	0.533000	0.62120	TTA	.	.	.	none		0.428	MEF2C-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369817.1	NM_002397		C	88027620	A	C	88027620	3	2	24	1	0	0	0	0	1	0	0	0	9464	11	1	5	705	5	MEF2C	5	88027620	Missense_Mutation	SNP	A	TCGA-4A-A93W-01A-11D-A36X-10	12599735	88027620	92887640	34	1692											
GPR98	84059	hgsc.bcm.edu	37	chr5	89949370	89949370	+	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	gtcaccacagtggaacggatGctttgtactttaccggacta	10	11	10	10	2	1	0	1	0	0	0	1	3	1	3	2	3	4	2	2	3	4	5			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr5:89949370G>C	ENST00000405460.2	+	20	4075	c.3979G>C	c.(3979-3981)Gct>Cct	p.A1327P		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1327					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)		TGGAACGGATGCTTTGTACTT	0.448																																					p.A1327P		Atlas-SNP	.											.	GPR98	605	.	0			c.G3979C						PASS	.						127	116	120					5																	89949370		1958	4141	6099	SO:0001583	missense	84059	exon20			ACGGATGCTTTGT	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.3979G>C	chr5.hg19:g.89949370G>C	ENSP00000384582:p.Ala1327Pro	149.0	0.0	.		151.0	69.0	.	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.1|21.1	4.091508|4.091508	0.76756|0.76756	.|.	.|.	ENSG00000164199|ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000399043|ENST00000504142	T|.	0.03441|.	3.93|.	5.38|5.38	5.38|5.38	0.77491|0.77491	Concanavalin A-like lectin/glucanase (1);|.	0.147481|.	0.64402|.	D|.	0.000008|.	T|T	0.75170|0.75170	0.3813|0.3813	M|M	0.65975|0.65975	2.015|2.015	0.80722|0.80722	D|D	1|1	D|.	0.63046|.	0.992|.	D|.	0.64410|.	0.925|.	T|T	0.72896|0.72896	-0.4153|-0.4153	10|5	0.51188|.	T|.	0.08|.	.|.	19.4938|19.4938	0.95064|0.95064	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1327|.	Q8WXG9|.	GPR98_HUMAN|.	P|S	1327|915	ENSP00000384582:A1327P|.	ENSP00000296619:A1327P|.	A|C	+|+	1|2	0|0	GPR98|GPR98	89985126|89985126	1.000000|1.000000	0.71417|0.71417	0.982000|0.982000	0.44146|0.44146	0.952000|0.952000	0.60782|0.60782	6.159000|6.159000	0.71856|0.71856	2.691000|2.691000	0.91804|0.91804	0.650000|0.650000	0.86243|0.86243	GCT|TGC	.	.	.	none		0.448	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		C	89949370	G	C	89949370	3	2	24	1	0	0	0	0	1	0	0	0	6728	1319	46	4	4057	4	GPR98	5	89949370	Missense_Mutation	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10	1921750	89949370	90965890	35	1693											
FGFR4	2264	hgsc.bcm.edu	37	chr5	176518791	176518791	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgggcagcatccgctataacTacctgctagatgtgctgggt	8	11	12	10	1	0	1	0	0	0	1	1	1	1	1	2	2	5	5	2	2	4	4			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr5:176518791T>C	ENST00000292408.4	+	6	954	c.709T>C	c.(709-711)Tac>Cac	p.Y237H	FGFR4_ENST00000393637.1_Missense_Mutation_p.Y237H|FGFR4_ENST00000393648.2_Missense_Mutation_p.Y237H|FGFR4_ENST00000292410.3_Missense_Mutation_p.Y237H|FGFR4_ENST00000502906.1_Missense_Mutation_p.Y237H	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4	237	Ig-like C2-type 2.				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)	CCGCTATAACTACCTGCTAGA	0.617										TSP Lung(9;0.080)																											p.Y237H		Atlas-SNP	.											.	FGFR4	174	.	0			c.T709C						PASS	.						90	81	84					5																	176518791		2203	4300	6503	SO:0001583	missense	2264	exon5			TATAACTACCTGC	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.709T>C	chr5.hg19:g.176518791T>C	ENSP00000292408:p.Tyr237His	91.0	0.0	.		86.0	29.0	.	NM_022963	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Missense_Mutation	SNP	ENST00000292408.4	hg19	CCDS4410.1	.	.	.	.	.	.	.	.	.	.	T	15.66	2.900458	0.52227	.	.	ENSG00000160867	ENST00000292408;ENST00000393648;ENST00000502906;ENST00000292410;ENST00000393637;ENST00000377207	T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54	4.13	4.13	0.48395	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.49440	0.1557	L	0.55103	1.725	0.53005	D	0.999962	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;0.997;0.999	T	0.52756	-0.8533	10	0.87932	D	0	.	13.2525	0.60060	0.0:0.0:0.0:1.0	.	237;237;237;237	B5A965;B4DVP5;P22455-2;P22455	.;.;.;FGFR4_HUMAN	H	237;237;237;237;237;349	ENSP00000292408:Y237H;ENSP00000377259:Y237H;ENSP00000424960:Y237H;ENSP00000292410:Y237H;ENSP00000377254:Y237H	ENSP00000292408:Y237H	Y	+	1	0	FGFR4	176451397	1.000000	0.71417	0.994000	0.49952	0.090000	0.18270	7.825000	0.86693	1.867000	0.54127	0.402000	0.26972	TAC	.	.	.	none		0.617	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1			C	176518791	T	C	176518791	3	2	24	1	0	0	0	0	1	0	0	0	5875	1522	53	3	727	3	FGFR4	5	176518791	Missense_Mutation	SNP	T	TCGA-4A-A93W-01A-11D-A36X-10	86569421	176518791	4396469	36	1694											
ZKSCAN4	387032	hgsc.bcm.edu	37	chr6	28213691	28213692	+	Frame_Shift_Del	DEL	GC	GC	-																															caggtggcatatcttcccatGctccttttctggaagcttct																										TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr6:28213691_28213692delGC	ENST00000377294.2	-	5	1083_1084	c.840_841delGC	c.(838-843)gagcatfs	p.H281fs	ZKSCAN4_ENST00000423974.2_Frame_Shift_Del_p.H126fs	NM_019110.3	NP_061983.2	Q969J2	ZKSC4_HUMAN	zinc finger with KRAB and SCAN domains 4	281	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)			endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						ATCTTCCCATGCTCCTTTTCTG	0.49																																					p.281_281del		Atlas-Indel,Pindel	.											.	ZKSCAN4	42	.	0			c.841_842del						PASS	.																																			SO:0001589	frameshift_variant	387032	exon5			.	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.840_841delGC	chr6.hg19:g.28213691_28213692delGC	ENSP00000366509:p.His281fs	108.0	0.0	0		85.0	36.0	0.423529	NM_019110	B2RE32|Q5U7L4	Frame_Shift_Del	DEL	ENST00000377294.2	hg19	CCDS4647.1																																																																																			.	.	.	none		0.49	ZKSCAN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040179.1	NM_019110		-	28213692	GC	-	28213691	7	5	24	1	0	1	0	1	0	0	0	0	17701	1319	46	0	800	0	ZKSCAN4	6	28213691	Frame_Shift_Del	DEL	GC	TCGA-4A-A93W-01A-11D-A36X-10		28213691	142901376	37	1695											
SLC22A1	6580	hgsc.bcm.edu	37	chr6	160560884	160560884	+	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	gggcagcctgcctcgtcatgAtttttatctcacctggtaag	7	13	10	11	1	2	1	2	1	1	0	4	1	2	1	3	2	2	2	3	2	2	4			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr6:160560884A>T	ENST00000366963.4	+	7	1408	c.1261A>T	c.(1261-1263)Att>Ttt	p.I421F	SLC22A1_ENST00000324965.4_Missense_Mutation_p.I421F|SLC22A1_ENST00000457470.2_Missense_Mutation_p.I421F	NM_003057.2|NM_153187.1	NP_003048.1|NP_694857.1	O15245	S22A1_HUMAN	solute carrier family 22 (organic cation transporter), member 1	421					dopamine transport (GO:0015872)|drug transmembrane transport (GO:0006855)|epinephrine transport (GO:0048241)|establishment or maintenance of transmembrane electrochemical gradient (GO:0010248)|norepinephrine transport (GO:0015874)|organic cation transport (GO:0015695)|protein homooligomerization (GO:0051260)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	acetylcholine transmembrane transporter activity (GO:0005277)|dopamine transmembrane transporter activity (GO:0005329)|norepinephrine transmembrane transporter activity (GO:0005333)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|secondary active organic cation transmembrane transporter activity (GO:0008513)		SLC22A1/CUTA(2)	breast(1)|endometrium(3)|large_intestine(3)|lung(13)|upper_aerodigestive_tract(1)	21		Breast(66;0.000776)|Ovarian(120;0.00556)		OV - Ovarian serous cystadenocarcinoma(65;2.73e-17)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)	Acebutolol(DB01193)|Acepromazine(DB01614)|Aciclovir(DB00787)|Amantadine(DB00915)|Amiloride(DB00594)|Aminohippurate(DB00345)|Caspofungin(DB00520)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Choline(DB00122)|Cimetidine(DB00501)|Cladribine(DB00242)|Clonidine(DB00575)|Codeine(DB00318)|Cytarabine(DB00987)|Desipramine(DB01151)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dopamine(DB00988)|Epinephrine(DB00668)|Estradiol(DB00783)|Estropipate(DB04574)|Ganciclovir(DB01004)|Gentian Violet(DB00406)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Lamivudine(DB00709)|Latanoprost(DB00654)|Metformin(DB00331)|Midazolam(DB00683)|Nelfinavir(DB00220)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Pancuronium(DB01337)|Phenformin(DB00914)|Phenoxybenzamine(DB00925)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Prazosin(DB00457)|Probenecid(DB01032)|Procainamide(DB01035)|Progesterone(DB00396)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rocuronium(DB00728)|Saquinavir(DB01232)|Spermine(DB00127)|Testosterone(DB00624)|Thiamine(DB00152)|Thioproperazine(DB01622)|Thiothixene(DB01623)|Tubocurarine(DB01199)|Vecuronium(DB01339)|Verapamil(DB00661)	CCTCGTCATGATTTTTATCTC	0.527																																					p.I421F		Atlas-SNP	.											SLC22A1,colon,carcinoma,0,1	SLC22A1	69	.	0			c.A1261T						PASS	.						62	58	59					6																	160560884		2203	4299	6502	SO:0001583	missense	6580	exon7			GTCATGATTTTTA	U77086	CCDS5274.1, CCDS5275.1	6q25.3	2013-05-22			ENSG00000175003	ENSG00000175003		"Solute carriers"	10963	protein-coding gene	gene with protein product		602607				9605850	Standard	NM_003057		Approved	OCT1	uc003qtc.3	O15245	OTTHUMG00000015947	ENST00000366963.4:c.1261A>T	chr6.hg19:g.160560884A>T	ENSP00000355930:p.Ile421Phe	35.0	2.0	.		32.0	4.0	.	NM_153187	A6NFF3|A8K1H2|C9JSU6|O15395|Q9NQD4	Missense_Mutation	SNP	ENST00000366963.4	hg19	CCDS5274.1	.	.	.	.	.	.	.	.	.	.	A	14.77	2.634717	0.47049	.	.	ENSG00000175003	ENST00000366963;ENST00000324965;ENST00000457470	T;T;T	0.73469	-0.75;0.32;0.32	5.08	-10.2	0.00374	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.782081	0.11578	N	0.550023	T	0.46756	0.1409	M	0.66439	2.03	0.09310	N	0.999999	P;B	0.39940	0.696;0.302	B;B	0.38921	0.254;0.285	T	0.47509	-0.9112	10	0.29301	T	0.29	.	12.514	0.56021	0.1707:0.2871:0.5423:0.0	.	421;421	O15245-2;O15245	.;S22A1_HUMAN	F	421	ENSP00000355930:I421F;ENSP00000318103:I421F;ENSP00000409557:I421F	ENSP00000318103:I421F	I	+	1	0	SLC22A1	160480874	0.104000	0.21937	0.003000	0.11579	0.012000	0.07955	0.127000	0.15790	-2.186000	0.00760	-0.441000	0.05720	ATT	.	.	.	none		0.527	SLC22A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042938.2			T	160560884	A	T	160560884	3	4	24	1	0	0	0	0	1	0	0	0	14453	333	12	5	1287	5	SLC22A1	6	160560884	Missense_Mutation	SNP	A	TCGA-4A-A93W-01A-11D-A36X-10	132347193	160560884	10554183	38	1696											
FAM20C	56975	hgsc.bcm.edu	37	chr7	208933	208933	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacgcagctgaagctcatcAtgaccttccagaattacggg	11	8	10	12	2	2	3	2	2	0	1	3	3	3	3	2	1	3	4	2	1	3	2			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr7:208933A>G	ENST00000313766.5	+	3	1051	c.820A>G	c.(820-822)Atg>Gtg	p.M274V		NM_020223.3	NP_064608.2	Q8IXL6	DMP4_HUMAN	family with sequence similarity 20, member C	274				MTFQNYGQALFKPMK -> FLSDKPFLFLSCFLR (in Ref. 6; CAB99089). {ECO:0000305}.	dentinogenesis (GO:0097187)|enamel mineralization (GO:0070166)|odontoblast differentiation (GO:0071895)|osteoclast maturation (GO:0036179)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|protein phosphorylation (GO:0006468)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of phosphorus metabolic process (GO:0051174)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|lung(2)|urinary_tract(1)	4		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.57e-17)|Epithelial(4;1.26e-16)|all cancers(6;4.79e-14)		GAAGCTCATCATGACCTTCCA	0.612																																					p.M274V		Atlas-SNP	.											.	FAM20C	18	.	0			c.A820G						PASS	.						52	58	56					7																	208933		2076	4193	6269	SO:0001583	missense	56975	exon3			CTCATCATGACCT	BC040074	CCDS47522.1	7p22.3	2012-11-29			ENSG00000177706	ENSG00000177706			22140	protein-coding gene	gene with protein product	"dentin matrix protein 4"	611061				17369251, 17924334	Standard	NM_020223		Approved	IMAGE:4942737, DKFZp547D065, DMP4	uc003sip.3	Q8IXL6	OTTHUMG00000151401	ENST00000313766.5:c.820A>G	chr7.hg19:g.208933A>G	ENSP00000322323:p.Met274Val	84.0	0.0	.		112.0	36.0	.	NM_020223	A4D2Q5|L8B5W8|Q5I0W9|Q7Z4I0|Q9NPT2	Missense_Mutation	SNP	ENST00000313766.5	hg19	CCDS47522.1	.	.	.	.	.	.	.	.	.	.	A	13.96	2.391528	0.42410	.	.	ENSG00000177706	ENST00000313766	T	0.75938	-0.98	5.23	4.06	0.47325	.	0.000000	0.64402	D	0.000003	T	0.66208	0.2766	L	0.54965	1.715	0.47584	D	0.999468	B	0.22983	0.078	B	0.20577	0.03	T	0.61959	-0.6955	10	0.51188	T	0.08	.	6.9119	0.24340	0.6948:0.1559:0.0:0.1493	.	274	Q8IXL6	DMP4_HUMAN	V	274	ENSP00000322323:M274V	ENSP00000322323:M274V	M	+	1	0	FAM20C	304016	1.000000	0.71417	0.996000	0.52242	0.974000	0.67602	5.854000	0.69503	0.806000	0.34183	0.533000	0.62120	ATG	.	.	.	none		0.612	FAM20C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322476.2	NM_020223		G	208933	A	G	208933	3	3	24	1	0	0	0	0	1	0	0	0	5543	217	8	3	830	3	FAM20C	7	208933	Missense_Mutation	SNP	A	TCGA-4A-A93W-01A-11D-A36X-10		208933	158929730	39	1697											
TNS3	64759	hgsc.bcm.edu	37	chr7	47451362	47451362	+	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	gaagctgggccggctcgatgAcgatgcagatcctgctgggg	7	7	17	10	3	0	2	0	1	0	1	2	5	1	2	2	4	3	4	2	4	1	0			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr7:47451362A>T	ENST00000398879.1	-	13	1052	c.686T>A	c.(685-687)gTc>gAc	p.V229D	TNS3_ENST00000442536.2_Missense_Mutation_p.V229D|TNS3_ENST00000355730.3_Missense_Mutation_p.V229D|TNS3_ENST00000311160.9_Missense_Mutation_p.V229D|TNS3_ENST00000458317.2_Missense_Mutation_p.V229D			Q68CZ2	TENS3_HUMAN	tensin 3	229	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				cell migration (GO:0016477)|lung alveolus development (GO:0048286)|positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(17)|endometrium(5)|kidney(4)|large_intestine(7)|liver(1)|lung(16)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	64						CGGCTCGATGACGATGCAGAT	0.522																																					p.V229D		Atlas-SNP	.											.	TNS3	140	.	0			c.T686A						PASS	.						67	74	72					7																	47451362		2036	4178	6214	SO:0001583	missense	64759	exon13			TCGATGACGATGC	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.686T>A	chr7.hg19:g.47451362A>T	ENSP00000381854:p.Val229Asp	116.0	0.0	.		160.0	102.0	.	NM_022748	B2RNV1|Q6IPQ2|Q8IZW7|Q8NAD0|Q96PE0|Q96S48	Missense_Mutation	SNP	ENST00000398879.1	hg19	CCDS5506.2	.	.	.	.	.	.	.	.	.	.	a	8.595	0.885502	0.17540	.	.	ENSG00000136205	ENST00000311160;ENST00000538633;ENST00000398879;ENST00000355730;ENST00000457718;ENST00000450444;ENST00000442536;ENST00000458317	D;D;D;D;D;D;D	0.86694	-2.16;-2.16;-2.16;-2.16;-2.16;-2.16;-2.16	5.17	0.24	0.15489	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.537282	0.20705	N	0.087184	T	0.77343	0.4116	L	0.29908	0.895	0.19300	N	0.999977	B;B	0.21071	0.043;0.051	B;B	0.24006	0.049;0.05	T	0.61594	-0.7031	10	0.29301	T	0.29	-17.3607	9.5619	0.39373	0.3035:0.0:0.6965:0.0	.	229;229	Q68CZ2-4;Q68CZ2	.;TENS3_HUMAN	D	229;339;229;229;332;318;229;229	ENSP00000312143:V229D;ENSP00000381854:V229D;ENSP00000347968:V229D;ENSP00000414358:V332D;ENSP00000396914:V318D;ENSP00000389285:V229D;ENSP00000388318:V229D	ENSP00000312143:V229D	V	-	2	0	TNS3	47417887	0.924000	0.31332	0.001000	0.08648	0.372000	0.29890	1.604000	0.36804	-0.257000	0.09459	-1.216000	0.01612	GTC	.	.	.	none		0.522	TNS3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157253.1	NM_022748		T	47451362	A	T	47451362	3	4	24	1	0	0	0	0	1	0	0	0	16356	275	10	5	3727	5	TNS3	7	47451362	Missense_Mutation	SNP	A	TCGA-4A-A93W-01A-11D-A36X-10	47242429	47451362	111687301	40	1698											
PTCD1	26024	hgsc.bcm.edu	37	chr7	99023210	99023210	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tagctgtcccggctcggctgTagccctagactcagcatcag	7	9	11	14	2	2	1	2	0	0	1	4	1	3	1	2	2	3	5	2	2	3	3			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr7:99023210T>C	ENST00000292478.4	-	6	1195	c.945A>G	c.(943-945)ctA>ctG	p.L315L	ATP5J2-PTCD1_ENST00000413834.1_Silent_p.L364L|PTCD1_ENST00000555673.1_Silent_p.L364L	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	315					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)			GGCTCGGCTGTAGCCCTAGAC	0.647																																					p.L364L		Atlas-SNP	.											.	.	.	.	0			c.A1092G						PASS	.						11	11	11					7																	99023210		2179	4271	6450	SO:0001819	synonymous_variant	100526740	exon7			CGGCTGTAGCCCT	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.945A>G	chr7.hg19:g.99023210T>C		64.0	0.0	.		70.0	37.0	.	NM_001198879	Q3ZB78|Q66K60|Q9UDV2	Silent	SNP	ENST00000292478.4	hg19	CCDS34691.1																																																																																			.	.	.	none		0.647	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1	NM_015545		C	99023210	T	C	99023210	2	2	24	1	0	0	0	0	0	0	0	1	12737	1625	57	3		3	PTCD1	7	99023210	Silent	SNP	T	TCGA-4A-A93W-01A-11D-A36X-10	51571848	99023210	60115453	41	1699											
MET	4233	hgsc.bcm.edu	37	chr7	116417457	116417457	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcacagggcattttggttgtGtatatcatgggactttgttg	7	16	13	5	0	1	0	1	0	0	0	1	1	1	1	0	3	0	5	0	3	2	7			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr7:116417457G>A	ENST00000318493.6	+	16	3515	c.3328G>A	c.(3328-3330)Gta>Ata	p.V1110I	MET_ENST00000539704.1_5'UTR|MET_ENST00000397752.3_Missense_Mutation_p.V1092I			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)			TTTTGGTTGTGTATATCATGG	0.338			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.V1110I		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.G3328A	GRCh37	CM990852	MET	M		PASS	.						191	176	180					7																	116417457		1827	4084	5911	SO:0001583	missense	4233	exon16	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	GGTTGTGTATATC	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.3328G>A	chr7.hg19:g.116417457G>A	ENSP00000317272:p.Val1110Ile	140.0	0.0	.		153.0	95.0	.	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.834124	0.91036	.	.	ENSG00000105976	ENST00000397752;ENST00000318493	T;T	0.64991	-0.13;-0.13	5.16	5.16	0.70880	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.81178	0.4768	M	0.80422	2.495	0.80722	D	1	D;D	0.76494	0.999;0.99	D;D	0.85130	0.997;0.99	D	0.83726	0.0195	10	0.87932	D	0	.	19.0107	0.92871	0.0:0.0:1.0:0.0	.	1110;1092	P08581-2;P08581	.;MET_HUMAN	I	1092;1110	ENSP00000380860:V1092I;ENSP00000317272:V1110I	ENSP00000317272:V1110I	V	+	1	0	MET	116204693	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	9.813000	0.99286	2.560000	0.86352	0.563000	0.77884	GTA	.	.	.	none		0.338	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			A	116417457	G	A	116417457	3	1	24	1	0	0	0	0	1	0	0	0	9492	1377	48	2	3386	2	MET	7	116417457	Missense_Mutation	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10	17394247	116417457	42721206	42	1700											
RNF32	140545	hgsc.bcm.edu	37	chr7	156451243	156451243	+	Frame_Shift_Del	DEL	A	A	-																															cccacagatgccaagttaagAaaaaaattctttgaaaaaaa																										TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr7:156451243delA	ENST00000405335.1	+	8	1072	c.663delA	c.(661-663)agafs	p.R221fs	AC005534.8_ENST00000455709.1_RNA|RNF32_ENST00000432459.2_Frame_Shift_Del_p.R221fs|RNF32_ENST00000392743.2_Frame_Shift_Del_p.R221fs|RNF32_ENST00000343665.4_Frame_Shift_Del_p.R197fs|RNF32_ENST00000480011.1_3'UTR|RNF32_ENST00000311822.8_Frame_Shift_Del_p.R221fs|RNF32_ENST00000392741.2_Frame_Shift_Del_p.R221fs|RNF32_ENST00000317955.5_Frame_Shift_Del_p.R221fs			Q9H0A6	RNF32_HUMAN	ring finger protein 32	221						aggresome (GO:0016235)|endosome (GO:0005768)	zinc ion binding (GO:0008270)			cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(2)	15	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00291)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		CCAAGTTAAGAAAAAAATTCT	0.423																																					p.R221fs		Atlas-Indel,Pindel	.											.	RNF32	77	.	0			c.662delG						PASS	.						76	82	80					7																	156451243		2203	4300	6503	SO:0001589	frameshift_variant	140545	exon7			.		CCDS5944.1	7q36	2013-08-05			ENSG00000105982	ENSG00000105982		"RING-type (C3HC4) zinc fingers"	17118	protein-coding gene	gene with protein product		610241				11890671	Standard	NM_001184996		Approved	FKSG33, HSD15, LMBR2	uc003wmr.3	Q9H0A6	OTTHUMG00000151440	ENST00000405335.1:c.663delA	chr7.hg19:g.156451243delA	ENSP00000385285:p.Arg221fs	125.0	0.0	0		204.0	103.0	0.504902	NM_030936	Q6FIB3|Q6X7T4|Q8N6V8|Q8TDG0|Q96BM5|Q9Y6U1	Frame_Shift_Del	DEL	ENST00000405335.1	hg19	CCDS5944.1																																																																																			.	.	.	none		0.423	RNF32-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322660.2	NM_030936		-	156451243	A	-	156451243	7	5	24	1	0	1	0	1	0	0	0	0	13501	243	9	0	685	0	RNF32	7	156451243	Frame_Shift_Del	DEL	A	TCGA-4A-A93W-01A-11D-A36X-10	40033786	156451243	2687420	43	1701											
BMP1	649	hgsc.bcm.edu	37	chr8	22069171	22069171	+	Missense_Mutation	SNP	T	T	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	gttccactcggatgacaccaTcaccaaaaaaggtttccacc	13	8	6	14	1	1	1	1	1	0	0	4	2	3	2	5	2	0	2	5	2	3	2			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr8:22069171T>G	ENST00000306385.5	+	20	3561	c.2891T>G	c.(2890-2892)aTc>aGc	p.I964S	BMP1_ENST00000354870.5_3'UTR	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1	964	CUB 5. {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)		GATGACACCATCACCAAAAAA	0.567																																					p.I964S		Atlas-SNP	.											.	BMP1	131	.	0			c.T2891G						PASS	.						142	119	127					8																	22069171		2203	4300	6503	SO:0001583	missense	649	exon20			ACACCATCACCAA		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.2891T>G	chr8.hg19:g.22069171T>G	ENSP00000305714:p.Ile964Ser	79.0	0.0	.		88.0	35.0	.	NM_006129	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Missense_Mutation	SNP	ENST00000306385.5	hg19	CCDS6026.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.970260	0.74246	.	.	ENSG00000168487	ENST00000306385	T	0.34072	1.38	4.7	4.7	0.59300	CUB (5);	0.000000	0.37012	U	0.002298	T	0.48822	0.1521	M	0.74881	2.28	0.80722	D	1	P	0.39748	0.686	P	0.48334	0.574	T	0.48603	-0.9021	10	0.38643	T	0.18	.	13.295	0.60292	0.0:0.0:0.0:1.0	.	964	P13497	BMP1_HUMAN	S	964	ENSP00000305714:I964S	ENSP00000305714:I964S	I	+	2	0	BMP1	22125116	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.848000	0.86902	1.977000	0.57605	0.533000	0.62120	ATC	.	.	.	none		0.567	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132		G	22069171	T	G	22069171	3	3	24	1	0	0	0	0	1	0	0	0	1456	1435	50	5	3059	5	BMP1	8	22069171	Missense_Mutation	SNP	T	TCGA-4A-A93W-01A-11D-A36X-10		22069171	124294851	44	1702											
LYN	4067	hgsc.bcm.edu	37	chr8	56922657	56922657	+	Missense_Mutation	SNP	G	G	C																															gccacggaagggcaataccaGcagcagccttagagcacagg																										TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr8:56922657G>C	ENST00000519728.1	+	13	1823	c.1527G>C	c.(1525-1527)caG>caC	p.Q509H	LYN_ENST00000520220.2_Missense_Mutation_p.Q488H	NM_002350.3	NP_002341.1	P07948	LYN_HUMAN	LYN proto-oncogene, Src family tyrosine kinase	509					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)	GGCAATACCAGCAGCAGCCTT	0.483																																					p.Q509H		Atlas-SNP	.											.	LYN	54	.	0			c.G1527C						PASS	.						72	69	70					8																	56922657		2203	4300	6503	SO:0001583	missense	4067	exon13			ATACCAGCAGCAG	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.1527G>C	chr8.hg19:g.56922657G>C	ENSP00000428924:p.Gln509His	187.0	0.0	.		173.0	59.0	.	NM_002350	A0AVQ5	Missense_Mutation	SNP	ENST00000519728.1	hg19	CCDS6162.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.963785	0.74131	.	.	ENSG00000254087	ENST00000519728;ENST00000520220	T;T	0.75050	-0.86;-0.9	5.95	2.85	0.33270	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.79656	0.4483	L	0.55990	1.75	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.984	T	0.77923	-0.2406	10	0.59425	D	0.04	.	7.0536	0.25087	0.4347:0.0:0.5652:0.0	.	579;509	Q6NUK7;P07948	.;LYN_HUMAN	H	509;488	ENSP00000428924:Q509H;ENSP00000428424:Q488H	ENSP00000428924:Q509H	Q	+	3	2	LYN	57085211	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	1.705000	0.37867	0.863000	0.35553	0.655000	0.94253	CAG	.	.	.	none		0.483	LYN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378155.1	NM_002350		C	56922657	G	C	56922657	3	2	24	1	0	0	0	0	1	0	0	0	9114	962	34	4	1573	4	LYN	8	56922657	Missense_Mutation	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10	34853486	56922657	89441365	45	1703	19	2									
LYN	4067	hgsc.bcm.edu	37	chr8	56922659	56922659	+	Missense_Mutation	SNP	A	A	T																															cacggaagggcaataccagcAgcagccttagagcacaggga																										TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr8:56922659A>T	ENST00000519728.1	+	13	1825	c.1529A>T	c.(1528-1530)cAg>cTg	p.Q510L	LYN_ENST00000520220.2_Missense_Mutation_p.Q489L	NM_002350.3	NP_002341.1	P07948	LYN_HUMAN	LYN proto-oncogene, Src family tyrosine kinase	510					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)	CAATACCAGCAGCAGCCTTAG	0.483																																					p.Q510L		Atlas-SNP	.											.	LYN	54	.	0			c.A1529T						PASS	.						70	68	68					8																	56922659		2203	4300	6503	SO:0001583	missense	4067	exon13			ACCAGCAGCAGCC	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.1529A>T	chr8.hg19:g.56922659A>T	ENSP00000428924:p.Gln510Leu	184.0	0.0	.		171.0	59.0	.	NM_002350	A0AVQ5	Missense_Mutation	SNP	ENST00000519728.1	hg19	CCDS6162.1	.	.	.	.	.	.	.	.	.	.	A	15.60	2.882332	0.51908	.	.	ENSG00000254087	ENST00000519728;ENST00000520220	T;T	0.74315	-0.78;-0.83	5.95	5.95	0.96441	Protein kinase-like domain (1);	0.050322	0.85682	D	0.000000	T	0.50171	0.1600	N	0.01352	-0.895	0.80722	D	1	B;B	0.10296	0.003;0.002	B;B	0.12837	0.008;0.004	T	0.50642	-0.8804	10	0.37606	T	0.19	.	16.4237	0.83790	1.0:0.0:0.0:0.0	.	580;510	Q6NUK7;P07948	.;LYN_HUMAN	L	510;489	ENSP00000428924:Q510L;ENSP00000428424:Q489L	ENSP00000428924:Q510L	Q	+	2	0	LYN	57085213	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	6.107000	0.71517	2.279000	0.76181	0.533000	0.62120	CAG	.	.	.	none		0.483	LYN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378155.1	NM_002350		T	56922659	A	T	56922659	3	4	24	1	0	0	0	0	1	0	0	0	9114	188	7	5	1575	5	LYN	8	56922659	Missense_Mutation	SNP	A	TCGA-4A-A93W-01A-11D-A36X-10	2	56922659	89441363	46	1704	19	2									
DECR1	1666	hgsc.bcm.edu	37	chr8	91055027	91055027	+	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	accagggcctataaaaaccaAagtaagttgtattttgcttg	14	12	8	7	0	0	0	0	0	0	0	0	0	0	0	3	1	2	4	3	1	7	8			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr8:91055027A>C	ENST00000220764.2	+	7	825	c.737A>C	c.(736-738)aAa>aCa	p.K246T	DECR1_ENST00000522161.1_Splice_Site_p.K237T	NM_001359.1	NP_001350.1	Q16698	DECR_HUMAN	2,4-dienoyl CoA reductase 1, mitochondrial	246					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	2,4-dienoyl-CoA reductase (NADPH) activity (GO:0008670)|NADPH binding (GO:0070402)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)	p.K246T(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	15			BRCA - Breast invasive adenocarcinoma(11;0.00953)			ATAAAAACCAAAGTAAGTTGT	0.338																																					p.K246T		Atlas-SNP	.											DECR1,colon,carcinoma,0,1	DECR1	37	.	1	Substitution - Missense(1)	large_intestine(1)	c.A737C						PASS	.						159	152	155					8																	91055027		2203	4300	6503	SO:0001630	splice_region_variant	1666	exon7			AAACCAAAGTAAG	L26050	CCDS6250.1	8q21.3	2011-09-14			ENSG00000104325	ENSG00000104325		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	2753	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 18C, member 1"	222745		DECR		7818482, 19027726	Standard	NM_001359		Approved	SDR18C1	uc003yek.1	Q16698	OTTHUMG00000163829	ENST00000220764.2:c.738+1A>C	chr8.hg19:g.91055027A>C		64.0	0.0	.		79.0	35.0	.	NM_001359	B7Z6B8|Q2M304|Q93085	Missense_Mutation	SNP	ENST00000220764.2	hg19	CCDS6250.1	.	.	.	.	.	.	.	.	.	.	A	15.20	2.763756	0.49574	.	.	ENSG00000104325	ENST00000220764;ENST00000522161	T;T	0.22134	1.97;1.97	5.24	5.24	0.73138	NAD(P)-binding domain (1);	0.044737	0.85682	D	0.000000	T	0.32941	0.0846	N	0.26042	0.785	0.80722	D	1	D;B	0.76494	0.999;0.06	D;B	0.76575	0.988;0.224	T	0.04723	-1.0931	10	0.35671	T	0.21	.	15.4185	0.74991	1.0:0.0:0.0:0.0	.	237;246	B7Z6B8;Q16698	.;DECR_HUMAN	T	246;237	ENSP00000220764:K246T;ENSP00000429779:K237T	ENSP00000220764:K246T	K	+	2	0	DECR1	91124203	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.733000	0.91539	2.109000	0.64355	0.528000	0.53228	AAA	.	.	.	none		0.338	DECR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375822.1		Missense_Mutation	C	91055027	A	C	91055027	5	2	24	1	0	0	0	0	0	0	1	0	4384	28	1	5	763	5	DECR1	8	91055027	Splice_Site	SNP	A	TCGA-4A-A93W-01A-11D-A36X-10	34132368	91055027	55308995	47	1705											
RBM12B	389677	hgsc.bcm.edu	37	chr8	94748429	94748429	+	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	gccttgctactaagaaagagCtctacagatgaatccttgat	13	11	8	9	0	1	5	0	2	1	3	2	5	2	5	2	0	4	2	2	0	5	5			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr8:94748429C>G	ENST00000399300.2	-	3	423	c.210G>C	c.(208-210)gaG>gaC	p.E70D	RP11-10N23.4_ENST00000517998.1_RNA|RBM12B_ENST00000517700.1_Missense_Mutation_p.E70D|RBM12B_ENST00000520961.1_Intron	NM_203390.2	NP_976324.2	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	70							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	30	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			TAAGAAAGAGCTCTACAGATG	0.443																																					p.E70D		Atlas-SNP	.											.	RBM12B	78	.	0			c.G210C						PASS	.						180	171	174					8																	94748429		1831	4091	5922	SO:0001583	missense	389677	exon3			AAAGAGCTCTACA		CCDS43755.1	8q22	2014-05-20			ENSG00000183808	ENSG00000183808		"RNA binding motif (RRM) containing"	32310	protein-coding gene	gene with protein product							Standard	NM_203390		Approved		uc003yfz.3	Q8IXT5	OTTHUMG00000164317	ENST00000399300.2:c.210G>C	chr8.hg19:g.94748429C>G	ENSP00000382239:p.Glu70Asp	100.0	0.0	.		105.0	45.0	.	NM_203390	A8MYB5	Missense_Mutation	SNP	ENST00000399300.2	hg19	CCDS43755.1	.	.	.	.	.	.	.	.	.	.	C	14.57	2.574938	0.45902	.	.	ENSG00000183808	ENST00000399300;ENST00000517700;ENST00000519109;ENST00000518597;ENST00000520560;ENST00000521947	T;T;T;T;T;T	0.34667	2.57;2.6;1.8;1.84;1.96;1.35	5.71	3.92	0.45320	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.64402	D	0.000018	T	0.48150	0.1484	M	0.63428	1.95	0.31929	N	0.612458	P	0.38223	0.623	P	0.49953	0.627	T	0.59139	-0.7510	10	0.56958	D	0.05	-22.8351	11.8401	0.52348	0.0:0.8573:0.0:0.1427	.	70	Q8IXT5	RB12B_HUMAN	D	70	ENSP00000382239:E70D;ENSP00000427729:E70D;ENSP00000430474:E70D;ENSP00000428269:E70D;ENSP00000429807:E70D;ENSP00000430466:E70D	ENSP00000382239:E70D	E	-	3	2	RBM12B	94817605	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	0.543000	0.23237	0.764000	0.33197	0.655000	0.94253	GAG	.	.	.	none		0.443	RBM12B-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383603.1	NM_203390		G	94748429	C	G	94748429	3	3	24	1	0	0	0	0	1	0	0	0	13127	796	28	4	2799	4	RBM12B	8	94748429	Missense_Mutation	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10	3693402	94748429	51615593	48	1706											
RC3H2	54542	hgsc.bcm.edu	37	chr9	125612011	125612011	+	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	ttgccagcactgacagatgtGgtgatggggaggcaacttgc	9	9	15	8	0	0	3	0	2	0	1	0	4	0	4	1	4	4	2	1	4	1	2			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr9:125612011G>C	ENST00000373670.1	-	20	4071	c.3471C>G	c.(3469-3471)acC>acG	p.T1157T	RC3H2_ENST00000357244.2_Silent_p.T1157T			Q9HBD1	RC3H2_HUMAN	ring finger and CCCH-type domains 2	1157					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						TGACAGATGTGGTGATGGGGA	0.423																																					p.T1157T		Atlas-SNP	.											.	RC3H2	150	.	0			c.C3471G						PASS	.						79	75	76					9																	125612011		1888	4136	6024	SO:0001819	synonymous_variant	54542	exon21			AGATGTGGTGATG	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.3471C>G	chr9.hg19:g.125612011G>C		187.0	0.0	.		150.0	58.0	.	NM_001100588	Q4VXB1|Q5JPD7|Q86ST6|Q8N3D6|Q96F27|Q9H5J2|Q9HBD2|Q9NWN9|Q9NXE1	Silent	SNP	ENST00000373670.1	hg19	CCDS43874.1																																																																																			.	.	.	none		0.423	RC3H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053966.1	NM_018835		C	125612011	G	C	125612011	2	2	24	1	0	0	0	0	0	0	0	1	13180	1335	47	4		4	RC3H2	9	125612011	Silent	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10		125612011	15601420	49	1707											
ANXA7	310	hgsc.bcm.edu	37	chr10	75156296	75156296	+	Missense_Mutation	SNP	T	T	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	cctgactagggtaagtaggtTgtcctccaggatactgagaa	11	10	12	8	0	0	2	0	2	0	1	2	4	2	3	3	3	1	3	3	3	5	5	rs534428824	byFrequency	TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr10:75156296T>G	ENST00000372921.5	-	5	472	c.416A>C	c.(415-417)cAa>cCa	p.Q139P	ANXA7_ENST00000535178.1_Missense_Mutation_p.Q9P|ANXA7_ENST00000492380.1_5'UTR	NM_001156.3	NP_001147.1	P20073	ANXA7_HUMAN	annexin A7	139	Repeat-rich region.				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)					GTAAGTAGGTTGTCCTCCAGG	0.393																																					p.Q139P		Atlas-SNP	.											.	ANXA7	50	.	0			c.A416C						PASS	.						73	68	70					10																	75156296		2203	4300	6503	SO:0001583	missense	310	exon5			GTAGGTTGTCCTC	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.416A>C	chr10.hg19:g.75156296T>G	ENSP00000362012:p.Gln139Pro	324.0	0.0	.		355.0	149.0	.	NM_004034	Q5F2H3|Q5T0M6|Q5T0M7	Missense_Mutation	SNP	ENST00000372921.5	hg19	CCDS7325.1	.	.	.	.	.	.	.	.	.	.	T	11.46	1.645066	0.29246	.	.	ENSG00000138279	ENST00000372921;ENST00000372919;ENST00000535178;ENST00000394847	T;T;T	0.04706	3.57;4.44;3.57	5.45	4.29	0.51040	.	1.042900	0.07566	N	0.917788	T	0.06735	0.0172	L	0.29908	0.895	0.35337	D	0.786159	B;P;P;P;B	0.49090	0.003;0.867;0.778;0.919;0.003	B;B;B;P;B	0.47044	0.001;0.334;0.184;0.535;0.006	T	0.41413	-0.9510	10	0.21540	T	0.41	.	9.6326	0.39789	0.0:0.0:0.1757:0.8243	.	139;139;66;139;139	Q53HM8;B2R7L2;B4DWU2;P20073-2;P20073	.;.;.;.;ANXA7_HUMAN	P	139;139;9;139	ENSP00000362012:Q139P;ENSP00000362010:Q139P;ENSP00000442864:Q9P	ENSP00000362010:Q139P	Q	-	2	0	ANXA7	74826302	0.985000	0.35326	0.960000	0.40013	0.982000	0.71751	2.182000	0.42556	0.967000	0.38186	0.528000	0.53228	CAA	.	.	.	none		0.393	ANXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048646.2	NM_001156		G	75156296	T	G	75156296	3	3	24	1	0	0	0	0	1	0	0	0	723	1812	63	5	1090	5	ANXA7	10	75156296	Missense_Mutation	SNP	T	TCGA-4A-A93W-01A-11D-A36X-10		75156296	60378451	50	1708											
PSMD13	5719	hgsc.bcm.edu	37	chr11	244701	244701	+	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	agtagtgatgaggcagtgatCctgtgtaaaacagcaattgg	13	10	13	5	0	0	3	0	3	0	0	1	3	1	3	1	2	2	4	1	2	4	3			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr11:244701C>G	ENST00000532097.1	+	6	840	c.336C>G	c.(334-336)atC>atG	p.I112M	PSMD13_ENST00000431206.2_Missense_Mutation_p.I114M|PSMD13_ENST00000352303.5_Missense_Mutation_p.I112M	NM_002817.3	NP_002808.3	Q9UNM6	PSD13_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 13	112					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|meiosis I (GO:0007127)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				NS(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	10		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.79e-27)|Epithelial(43;4e-26)|OV - Ovarian serous cystadenocarcinoma(40;6.02e-21)|BRCA - Breast invasive adenocarcinoma(625;3.93e-05)|Lung(200;0.112)|LUSC - Lung squamous cell carcinoma(625;0.129)		AGGCAGTGATCCTGTGTAAAA	0.373																																					p.I114M		Atlas-SNP	.											.	PSMD13	53	.	0			c.C342G						PASS	.						92	95	94					11																	244701		2203	4300	6503	SO:0001583	missense	5719	exon4			AGTGATCCTGTGT	AB009398	CCDS7692.1, CCDS44504.1	11p15.5	2008-05-22			ENSG00000185627	ENSG00000185627		"Proteasome (prosome, macropain) subunits"	9558	protein-coding gene	gene with protein product		603481				9714768, 8811196	Standard	NM_002817		Approved	p40.5, Rpn9	uc001loo.2	Q9UNM6	OTTHUMG00000119072	ENST00000532097.1:c.336C>G	chr11.hg19:g.244701C>G	ENSP00000436186:p.Ile112Met	377.0	0.0	.		359.0	143.0	.	NM_175932	B3KT15|O75831|Q53XU2|Q9UNV3	Missense_Mutation	SNP	ENST00000532097.1	hg19	CCDS7692.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.95|16.95	3.262842|3.262842	0.59431|0.59431	.|.	.|.	ENSG00000185627|ENSG00000185627	ENST00000532097;ENST00000538343;ENST00000431206;ENST00000528906;ENST00000352303|ENST00000526783	T;T;T;T|.	0.20463|.	2.12;2.07;2.1;2.11|.	5.6|5.6	3.74|3.74	0.42951|0.42951	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72771|0.72771	0.3502|0.3502	M|M	0.83483|0.83483	2.645|2.645	0.51233|0.51233	D|D	0.999919|0.999919	D;P;D;D|.	0.76494|.	0.999;0.941;0.963;0.963|.	D;P;P;P|.	0.71870|.	0.975;0.804;0.74;0.74|.	T|T	0.72401|0.72401	-0.4305|-0.4305	10|5	0.48119|.	T|.	0.1|.	.|.	8.8689|8.8689	0.35303|0.35303	0.0:0.7051:0.0:0.2949|0.0:0.7051:0.0:0.2949	.|.	114;47;112;112|.	Q9UNM6-2;B4DJ66;B2RBM7;Q9UNM6|.	.;.;.;PSD13_HUMAN|.	M|C	112;47;114;74;112|23	ENSP00000436186:I112M;ENSP00000396937:I114M;ENSP00000433364:I74M;ENSP00000333811:I112M|.	ENSP00000333811:I112M|.	I|S	+|+	3|2	3|0	PSMD13|PSMD13	234701|234701	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	1.777000|1.777000	0.38604|0.38604	0.852000|0.852000	0.35287|0.35287	-0.253000|-0.253000	0.11424|0.11424	ATC|TCC	.	.	.	none		0.373	PSMD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239286.2	NM_002817		G	244701	C	G	244701	3	3	24	1	0	0	0	0	1	0	0	0	12706	845	30	4	439	4	PSMD13	11	244701	Missense_Mutation	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10		244701	134761815	51	1709											
OR51A7	119687	hgsc.bcm.edu	37	chr11	4929473	4929473	+	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	ttatgaaccccattgtgtacTgtgtaaagactcgacaaatc	13	12	7	9	1	0	2	0	1	0	1	2	3	0	2	2	0	2	2	2	0	6	4			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr11:4929473T>A	ENST00000359350.4	+	1	874	c.874T>A	c.(874-876)Tgt>Agt	p.C292S	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004749.1	NP_001004749.1	Q8NH64	O51A7_HUMAN	olfactory receptor, family 51, subfamily A, member 7	292						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(7)|lung(13)|ovary(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		CATTGTGTACTGTGTAAAGAC	0.418																																					p.C292S		Atlas-SNP	.											.	OR51A7	86	.	0			c.T874A						PASS	.						133	126	128					11																	4929473		2201	4298	6499	SO:0001583	missense	119687	exon1			GTGTACTGTGTAA	AB065525	CCDS31364.1	11p15.4	2012-08-09			ENSG00000176895	ENSG00000176895		"GPCR / Class A : Olfactory receptors"	15188	protein-coding gene	gene with protein product							Standard	NM_001004749		Approved		uc010qyq.2	Q8NH64	OTTHUMG00000066502	ENST00000359350.4:c.874T>A	chr11.hg19:g.4929473T>A	ENSP00000352305:p.Cys292Ser	116.0	0.0	.		102.0	44.0	.	NM_001004749	Q6IFH8	Missense_Mutation	SNP	ENST00000359350.4	hg19	CCDS31364.1	.	.	.	.	.	.	.	.	.	.	T	0.006	-2.092179	0.00364	.	.	ENSG00000176895	ENST00000359350;ENST00000545959;ENST00000544684	T	0.35236	1.32	5.02	5.02	0.67125	.	0.128592	0.36200	N	0.002737	T	0.12944	0.0314	N	0.04018	-0.295	0.26535	N	0.974196	B	0.12630	0.006	B	0.14578	0.011	T	0.33752	-0.9856	10	0.02654	T	1	.	5.9373	0.19173	0.1627:0.0:0.1696:0.6677	.	292	Q8NH64	O51A7_HUMAN	S	292;292;281	ENSP00000352305:C292S	ENSP00000352305:C292S	C	+	1	0	OR51A7	4886049	0.000000	0.05858	0.998000	0.56505	0.134000	0.20937	-1.501000	0.02281	2.098000	0.63641	0.533000	0.62120	TGT	.	.	.	none		0.418	OR51A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142175.1	NM_001004749		A	4929473	T	A	4929473	3	1	24	1	0	0	0	0	1	0	0	0	11095	1580	55	5	876	5	OR51A7	11	4929473	Missense_Mutation	SNP	T	TCGA-4A-A93W-01A-11D-A36X-10	4684772	4929473	130077043	52	1710											
ELP4	26610	hgsc.bcm.edu	37	chr11	31531372	31531372	+	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	cggtagtgttgccgcgagtaCtgggtctgcagtggcgacag	6	9	17	9	4	1	0	0	0	1	0	1	2	1	0	1	3	3	4	1	3	2	3			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr11:31531372C>G	ENST00000350638.5	+	1	76	c.41C>G	c.(40-42)aCt>aGt	p.T14S	IMMP1L_ENST00000526776.1_5'Flank|ELP4_ENST00000395934.2_Missense_Mutation_p.T14S|IMMP1L_ENST00000532287.1_5'Flank|ELP4_ENST00000379163.5_Missense_Mutation_p.T14S|IMMP1L_ENST00000528161.1_5'Flank|IMMP1L_ENST00000533642.1_5'Flank|IMMP1L_ENST00000534812.1_5'Flank|IMMP1L_ENST00000278200.1_5'Flank	NM_019040.3	NP_061913.3	Q96EB1	ELP4_HUMAN	elongator acetyltransferase complex subunit 4	14					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)			breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(3)	20	Lung SC(675;0.225)					GCCGCGAGTACTGGGTCTGCA	0.592																																					p.T14S		Atlas-SNP	.											.	ELP4	78	.	0			c.C41G						PASS	.						43	50	47					11																	31531372		2108	4240	6348	SO:0001583	missense	26610	exon1			CGAGTACTGGGTC	AJ276005	CCDS7875.2, CCDS73271.1, CCDS73272.1	11p13	2012-08-14	2012-08-08	2002-05-24	ENSG00000109911	ENSG00000109911		"Elongator acetyltransferase complex subunits"	1171	protein-coding gene	gene with protein product		606985	"chromosome 11 open reading frame 19", "elongation protein 4 homolog (S. cerevisiae)"	C11orf19		11889558, 11435442	Standard	XM_005252865		Approved	PAXNEB	uc001mtb.3	Q96EB1	OTTHUMG00000142919	ENST00000350638.5:c.41C>G	chr11.hg19:g.31531372C>G	ENSP00000298937:p.Thr14Ser	114.0	0.0	.		88.0	45.0	.	NM_019040	B4E3W0|E7EPZ6|Q9H4E8|Q9NX11	Missense_Mutation	SNP	ENST00000350638.5	hg19	CCDS7875.2	.	.	.	.	.	.	.	.	.	.	C	6.234	0.411373	0.11812	.	.	ENSG00000109911	ENST00000350638;ENST00000379163;ENST00000395934	T;T;T	0.43294	1.01;0.95;1.52	5.32	-0.0982	0.13629	.	1.001760	0.08046	N	0.995845	T	0.17280	0.0415	N	0.11427	0.14	0.09310	N	1	B;B;B	0.10296	0.0;0.003;0.0	B;B;B	0.10450	0.001;0.005;0.001	T	0.25152	-1.0140	10	0.06494	T	0.89	-13.6166	2.3958	0.04389	0.1418:0.4226:0.2756:0.16	.	14;14;14	B4E3W0;G5E9D4;Q96EB1	.;.;ELP4_HUMAN	S	14	ENSP00000298937:T14S;ENSP00000368461:T14S;ENSP00000379267:T14S	ENSP00000298937:T14S	T	+	2	0	ELP4	31487948	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.092000	0.11129	-0.191000	0.10448	-0.263000	0.10527	ACT	.	.	.	none		0.592	ELP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286640.1	NM_019040		G	31531372	C	G	31531372	3	3	24	1	0	0	0	0	1	0	0	0	5084	565	20	4	43	4	ELP4	11	31531372	Missense_Mutation	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10	26601899	31531372	103475144	53	1711											
DAGLA	747	hgsc.bcm.edu	37	chr11	61507009	61507009	+	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	aggaggtagaggtgaccaccCtggccagcacgcggctctgg	8	5	16	12	2	1	2	0	1	1	1	1	3	1	3	3	6	1	3	3	6	1	1			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr11:61507009C>A	ENST00000257215.5	+	17	1845	c.1729C>A	c.(1729-1731)Ctg>Atg	p.L577M		NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	577					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)		GGTGACCACCCTGGCCAGCAC	0.657																																					p.L577M		Atlas-SNP	.											.	DAGLA	109	.	0			c.C1729A						PASS	.						131	117	122					11																	61507009		2202	4299	6501	SO:0001583	missense	747	exon17			ACCACCCTGGCCA	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.1729C>A	chr11.hg19:g.61507009C>A	ENSP00000257215:p.Leu577Met	97.0	0.0	.		73.0	35.0	.	NM_006133	A7E233|Q6WQJ0	Missense_Mutation	SNP	ENST00000257215.5	hg19	CCDS31578.1	.	.	.	.	.	.	.	.	.	.	C	11.66	1.703596	0.30232	.	.	ENSG00000134780	ENST00000257215	T	0.25414	1.8	4.23	1.89	0.25635	.	0.239340	0.36519	N	0.002560	T	0.13030	0.0316	L	0.27053	0.805	0.29500	N	0.854976	B	0.06786	0.001	B	0.06405	0.002	T	0.07290	-1.0780	10	0.33940	T	0.23	-13.8817	1.9957	0.03455	0.3039:0.3924:0.1987:0.105	.	577	Q9Y4D2	DGLA_HUMAN	M	577	ENSP00000257215:L577M	ENSP00000257215:L577M	L	+	1	2	DAGLA	61263585	0.797000	0.28877	0.985000	0.45067	0.968000	0.65278	1.386000	0.34419	0.875000	0.35847	0.462000	0.41574	CTG	.	.	.	none		0.657	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133		A	61507009	C	A	61507009	3	1	24	1	0	0	0	0	1	0	0	0	4228	680	24	4	1791	4	DAGLA	11	61507009	Missense_Mutation	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10	29975637	61507009	73499507	54	1712											
C11orf48	79081	hgsc.bcm.edu	37	chr11	62432403	62432403	+	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	gtgcctcagacgccgctcccGattcaacacccgccggcgtt	6	7	10	18	6	2	1	2	0	0	1	3	2	3	1	5	1	2	2	5	1	1	2			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr11:62432403G>A	ENST00000431002.2	-	3	2392	c.659C>T	c.(658-660)tCg>tTg	p.S220L	C11orf48_ENST00000354588.3_Missense_Mutation_p.S194L|C11orf48_ENST00000525675.1_Missense_Mutation_p.R28W|C11orf48_ENST00000524958.1_Missense_Mutation_p.R28W|C11orf48_ENST00000532208.1_Missense_Mutation_p.S194L|RP11-831H9.11_ENST00000528405.1_Missense_Mutation_p.R28W|METTL12_ENST00000532971.1_5'Flank|SNORA57_ENST00000383870.1_RNA			Q9BQE6	CK048_HUMAN	chromosome 11 open reading frame 48	220										endometrium(1)|lung(5)|urinary_tract(1)	7						CGCCGCTCCCGATTCAACACC	0.632																																					p.S194L		Atlas-SNP	.											.	C11orf48	18	.	0			c.C581T						PASS	.						27	28	28					11																	62432403		2202	4297	6499	SO:0001583	missense	79081	exon5			GCTCCCGATTCAA	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.659C>T	chr11.hg19:g.62432403G>A	ENSP00000416856:p.Ser220Leu	76.0	0.0	.		95.0	36.0	.	NM_024099	Q96NA4	Missense_Mutation	SNP	ENST00000431002.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.3|21.3	4.124301|4.124301	0.77436|0.77436	.|.	.|.	ENSG00000255432;ENSG00000162194;ENSG00000162194;ENSG00000162194|ENSG00000162194	ENST00000528405;ENST00000524958;ENST00000525675;ENST00000415855|ENST00000354588;ENST00000431002;ENST00000532208	.|.	.|.	.|.	4.84|4.84	3.9|3.9	0.45041|0.45041	.|.	.|.	.|.	.|.	.|.	T|T	0.21227|0.21227	0.0511|0.0511	N|N	0.14661|0.14661	0.345|0.345	0.27538|0.27538	N|N	0.950884|0.950884	.|B	.|0.33904	.|0.431	.|B	.|0.26770	.|0.073	T|T	0.08006|0.08006	-1.0743|-1.0743	6|8	0.87932|0.40728	D|T	0|0.16	-1.3326|-1.3326	12.4856|12.4856	0.55871|0.55871	0.0:0.0:0.825:0.175|0.0:0.0:0.825:0.175	.|.	.|194	.|Q9BQE6-2	.|.	W|L	28;28;28;64|194;220;194	.|.	ENSP00000410979:R64W|ENSP00000346600:S194L	R|S	-|-	1|2	2|0	C11orf48;RP11-831H9.11|C11orf48	62188979|62188979	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.497000|0.497000	0.33675|0.33675	1.639000|1.639000	0.37176|0.37176	1.307000|1.307000	0.44944|0.44944	0.655000|0.655000	0.94253|0.94253	CGG|TCG	.	.	.	none		0.632	C11orf48-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000395233.1	NM_024099		A	62432403	G	A	62432403	3	1	24	1	0	0	0	0	1	0	0	0	1646	1059	37	1	222	1	C11orf48	11	62432403	Missense_Mutation	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10	925394	62432403	72574113	55	1713											
BSCL2	2785	hgsc.bcm.edu	37	chr11	62474607	62474607	+	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	tttgtccggtcctttgatctGgtctccgcacacctcttttt	3	18	7	13	2	3	1	0	1	3	0	6	1	5	1	4	2	0	1	4	2	0	4			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr11:62474607G>A	ENST00000294117.5	+	0	0				BSCL2_ENST00000433053.1_Nonsense_Mutation_p.Q21*|BSCL2_ENST00000405837.1_Nonsense_Mutation_p.Q21*|BSCL2_ENST00000537604.1_5'Flank|HNRNPUL2-BSCL2_ENST00000403734.2_3'UTR|BSCL2_ENST00000360796.5_Nonsense_Mutation_p.Q21*|BSCL2_ENST00000407022.3_5'Flank|BSCL2_ENST00000278893.7_5'Flank|BSCL2_ENST00000421906.1_5'Flank|BSCL2_ENST00000403550.1_5'Flank	NM_012202.4	NP_036334.1	P63215	GBG3_HUMAN	guanine nucleotide binding protein (G protein), gamma 3						activation of MAPK activity (GO:0000187)|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)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	GTPase activity (GO:0003924)|signal transducer activity (GO:0004871)			kidney(1)|large_intestine(1)|lung(2)|urinary_tract(1)	5						CCTTTGATCTGGTCTCCGCAC	0.542																																					p.Q21X		Atlas-SNP	.											.	BSCL2	35	.	0			c.C61T						PASS	.						249	216	226					11																	62474607		692	1591	2283	SO:0001631	upstream_gene_variant	26580	exon1			TGATCTGGTCTCC	AF075042	CCDS8032.1	11p11	2008-07-18				ENSG00000162188			4405	protein-coding gene	gene with protein product	"guanine nucleotide-binding protein gamma-3 subunit", "NBP gamma-3"	608941				10644457	Standard	NM_012202		Approved		uc001nuv.4	P63215			chr11.hg19:g.62474607G>A	Exception_encountered	114.0	0.0	.		108.0	46.0	.	NM_001122955	B2R4S7|P29798|Q61014	Nonsense_Mutation	SNP	ENST00000294117.5	hg19	CCDS8032.1	.	.	.	.	.	.	.	.	.	.	G	14.82	2.648671	0.47258	.	.	ENSG00000168000	ENST00000405837;ENST00000433053;ENST00000360796;ENST00000531524;ENST00000524862;ENST00000525000;ENST00000532818;ENST00000464544;ENST00000530009;ENST00000528874	.	.	.	4.28	4.28	0.50868	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-0.9783	12.5249	0.56081	0.0:0.0:1.0:0.0	.	.	.	.	X	21;21;21;21;21;4;21;21;21;21	.	ENSP00000301781:Q21X	Q	-	1	0	BSCL2	62231183	0.872000	0.30054	0.340000	0.25575	0.344000	0.29017	3.627000	0.54252	2.665000	0.90641	0.655000	0.94253	CAG	.	.	.	none		0.542	GNG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395020.1	NM_012202		A	62474607	G	A	62474607	1	1	24	0	1	0	0	0	0	0	0	0	1529	1357	47	2		2	BSCL2	11	62474607	5'Flank	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10	42204	62474607	72531909	56	1714											
IGSF9B	22997	hgsc.bcm.edu	37	chr11	133805518	133805518	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacccctactcacactgcaCggtcaggtacgccgaggcgg	8	5	12	16	4	2	0	2	0	0	0	2	1	2	0	3	4	3	3	3	4	2	2			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr11:133805518C>T	ENST00000321016.8	-	7	1191	c.961G>A	c.(961-963)Gtg>Atg	p.V321M	IGSF9B_ENST00000533871.2_Missense_Mutation_p.V321M			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	321					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)		TCACACTGCACGGTCAGGTAC	0.632																																					p.V321M		Atlas-SNP	.											.	IGSF9B	290	.	0			c.G961A						PASS	.						18	21	20					11																	133805518		1988	4151	6139	SO:0001583	missense	22997	exon7			ACTGCACGGTCAG	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.961G>A	chr11.hg19:g.133805518C>T	ENSP00000317980:p.Val321Met	48.0	0.0	.		59.0	19.0	.	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	hg19		.	.	.	.	.	.	.	.	.	.	C	28.2	4.902639	0.92035	.	.	ENSG00000080854	ENST00000321016;ENST00000533871;ENST00000527648	T;T;T	0.61158	0.13;0.13;0.13	5.36	5.36	0.76844	Immunoglobulin I-set (1);Fibronectin, type III (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.84474	0.5480	H	0.96333	3.805	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89501	0.3764	9	0.87932	D	0	.	19.0883	0.93215	0.0:1.0:0.0:0.0	.	321	Q9UPX0	TUTLB_HUMAN	M	321;163;321	ENSP00000317980:V321M;ENSP00000436552:V163M;ENSP00000436576:V321M	ENSP00000317980:V321M	V	-	1	0	IGSF9B	133310728	1.000000	0.71417	0.986000	0.45419	0.947000	0.59692	7.406000	0.80017	2.500000	0.84329	0.561000	0.74099	GTG	.	.	.	none		0.632	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		T	133805518	C	T	133805518	3	4	24	1	0	0	0	0	1	0	0	0	7613	536	19	1	3140	1	IGSF9B	11	133805518	Missense_Mutation	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10	71330911	133805518	1200998	57	1715											
ING4	51147	hgsc.bcm.edu	37	chr12	6760546	6760546	+	Frame_Shift_Del	DEL	G	G	-																															gcaaaatggaaccactcaatGgaacactggaagaggaagaa																								rs371902029		TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr12:6760546delG	ENST00000396807.4	-	7	692	c.654delC	c.(652-654)tccfs	p.S218fs	ING4_ENST00000423703.2_Frame_Shift_Del_p.P169fs|ING4_ENST00000444704.2_Frame_Shift_Del_p.S194fs|ING4_ENST00000412586.2_Frame_Shift_Del_p.S215fs|ING4_ENST00000486287.1_5'UTR|ING4_ENST00000341550.4_Frame_Shift_Del_p.S217fs|ING4_ENST00000446105.2_Frame_Shift_Del_p.S214fs	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	218					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						ACCACTCAATGGAACACTGGA	0.532																																					p.I219fs		Atlas-INDEL	.											.	ING4	31	.	0			c.655delA						PASS	.						88	74	79					12																	6760546		2203	4300	6503	SO:0001589	frameshift_variant	51147	exon7			.	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.654delC	chr12.hg19:g.6760546delG	ENSP00000380024:p.Ser218fs	103.0	0.0	0		164.0	13.0	0.0792683	NM_001127582	A4KYM4|A4KYM6|D3DUR8|Q0EF62|Q0EF63|Q4VBQ6|Q96E15|Q9H3J0	Frame_Shift_Del	DEL	ENST00000396807.4	hg19	CCDS44813.1																																																																																			.	.	.	none		0.532	ING4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280467.2	NM_198287		-	6760546	G	-	6760546	7	5	24	1	0	1	0	1	0	0	0	0	7745	1348	47	0	103	0	ING4	12	6760546	Frame_Shift_Del	DEL	G	TCGA-4A-A93W-01A-11D-A36X-10		6760546	127091349	58	1716											
HOXC6	3223	hgsc.bcm.edu	37	chr12	54422675	54422675	+	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	aagccagtatccagatttacCcctggatgcagcgaatgaat	13	9	9	10	1	0	2	0	1	0	1	1	4	1	3	4	1	4	2	4	1	5	3	rs80157375		TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr12:54422675C>A	ENST00000243108.4	+	1	534	c.370C>A	c.(370-372)Ccc>Acc	p.P124T	HOXC6_ENST00000394331.3_Missense_Mutation_p.P42T|RP11-834C11.12_ENST00000513209.1_Intron|RP11-834C11.14_ENST00000512206.1_RNA|HOXC4_ENST00000303406.4_Intron	NM_004503.3	NP_004494.1	P09630	HXC6_HUMAN	homeobox C6	124					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						CCAGATTTACCCCTGGATGCA	0.473																																					p.P124T		Atlas-SNP	.											.	HOXC6	30	.	0			c.C370A						PASS	.						88	94	92					12																	54422675		2203	4300	6503	SO:0001583	missense	3223	exon1			ATTTACCCCTGGA		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.370C>A	chr12.hg19:g.54422675C>A	ENSP00000243108:p.Pro124Thr	42.0	0.0	.		35.0	16.0	.	NM_004503	B2RBV2|Q6DK09	Missense_Mutation	SNP	ENST00000243108.4	hg19	CCDS8871.1	.	.	.	.	.	.	.	.	.	.	C	18.59	3.656619	0.67586	.	.	ENSG00000197757	ENST00000504315;ENST00000509328;ENST00000394331;ENST00000243108	D;D	0.95622	-3.76;-3.76	5.53	5.53	0.82687	Homeobox protein, antennapedia type, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.98223	0.9412	M	0.91406	3.205	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.98802	1.0740	10	0.87932	D	0	.	18.396	0.90499	0.0:1.0:0.0:0.0	.	124	P09630	HXC6_HUMAN	T	42;42;42;124	ENSP00000377864:P42T;ENSP00000243108:P124T	ENSP00000243108:P124T	P	+	1	0	HOXC6	52708942	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.238000	0.78173	2.882000	0.98803	0.655000	0.94253	CCC	.	C|1.000;T|0.000	.	alt		0.473	HOXC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358943.2			A	54422675	C	A	54422675	3	1	24	1	0	0	0	0	1	0	0	0	7322	623	22	4	372	4	HOXC6	12	54422675	Missense_Mutation	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10	47662129	54422675	79429220	59	1717											
HNRNPA1	3178	hgsc.bcm.edu	37	chr12	54675281	54675282	+	Frame_Shift_Del	DEL	TG	TG	-																															aatggggaacgctcacggacTgtgtggtaagatttggaagg																										TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr12:54675281_54675282delTG	ENST00000340913.6	+	2	180_181	c.127_128delTG	c.(127-129)tgtfs	p.C43fs	HNRNPA1_ENST00000330752.8_Frame_Shift_Del_p.C43fs|CBX5_ENST00000209875.4_5'Flank|RP11-968A15.2_ENST00000547177.1_RNA|HNRNPA1_ENST00000546500.1_Frame_Shift_Del_p.C43fs|RP11-968A15.8_ENST00000553061.1_RNA|HNRNPA1_ENST00000547276.1_Frame_Shift_Del_p.C43fs	NM_002136.2|NM_031157.2	NP_002127.1|NP_112420.1	P09651	ROA1_HUMAN	heterogeneous nuclear ribonucleoprotein A1	43	Globular A domain.|RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				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						GCTCACGGACTGTGTGGTAAGA	0.47																																					p.42_43del	Colon(83;502 1289 8436 16406 24870)	Atlas-Indel,Pindel	.											.	HNRNPA1	72	.	0			c.126_127del						PASS	.																																			SO:0001589	frameshift_variant	3178	exon2			.	BC009600	CCDS41793.1, CCDS44909.1	12q13.1	2013-10-11		2007-08-16	ENSG00000135486	ENSG00000135486		"RNA binding motif (RRM) containing"	5031	protein-coding gene	gene with protein product		164017		HNRPA1		1733858	Standard	XR_245923		Approved	hnRNPA1, hnRNP-A1	uc001sfl.3	P09651		ENST00000340913.6:c.127_128delTG	chr12.hg19:g.54675285_54675286delTG	ENSP00000341826:p.Cys43fs	31.0	0.0	0		36.0	16.0	0.444444	NM_002136	A8K4Z8|Q3MIB7|Q6PJZ7	Frame_Shift_Del	DEL	ENST00000340913.6	hg19	CCDS44909.1																																																																																			.	.	.	none		0.47	HNRNPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000405480.1	NM_031157		-	54675282	TG	-	54675281	7	5	24	1	0	1	0	1	0	0	0	0	7264	1580	55	0	133	0	HNRNPA1	12	54675281	Frame_Shift_Del	DEL	TG	TCGA-4A-A93W-01A-11D-A36X-10	252606	54675281	79176614	60	1718											
ARHGAP9	64333	hgsc.bcm.edu	37	chr12	57871296	57871296	+	Missense_Mutation	SNP	A	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	gacttgcagccagtcagtgaAtttatgtagaagcagcgtcc	11	10	11	9	1	1	2	1	1	0	1	2	3	2	2	2	0	4	3	2	0	4	4			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr12:57871296A>C	ENST00000356411.2	-	4	840	c.702T>G	c.(700-702)aaT>aaG	p.N234K	ARHGAP9_ENST00000550454.1_5'UTR|ARHGAP9_ENST00000393791.3_Missense_Mutation_p.N234K|ARHGAP9_ENST00000424809.2_Missense_Mutation_p.N234K|ARHGAP9_ENST00000430041.2_Missense_Mutation_p.N50K|ARHGAP9_ENST00000550288.1_Missense_Mutation_p.N313K|ARHGAP9_ENST00000393797.2_Missense_Mutation_p.N305K			Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9	234	WW. {ECO:0000255|PROSITE- ProRule:PRU00224}.				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)			CAGTCAGTGAATTTATGTAGA	0.637																																					p.N234K		Atlas-SNP	.											.	ARHGAP9	79	.	0			c.T702G						PASS	.						57	63	61					12																	57871296		2203	4300	6503	SO:0001583	missense	64333	exon3			CAGTGAATTTATG	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.702T>G	chr12.hg19:g.57871296A>C	ENSP00000348782:p.Asn234Lys	274.0	0.0	.		201.0	82.0	.	NM_001080157	B4DVI3|E9PDX9|Q8NAF3|Q8TCJ3|Q8WYR0|Q96EZ2|Q96S74	Missense_Mutation	SNP	ENST00000356411.2	hg19		.	.	.	.	.	.	.	.	.	.	A	8.988	0.977083	0.18812	.	.	ENSG00000123329	ENST00000393791;ENST00000356411;ENST00000424809;ENST00000393797;ENST00000340423;ENST00000430041;ENST00000548139;ENST00000552604;ENST00000551452;ENST00000552066;ENST00000549602	T;T;T;T;T;T;T;T;T;D	0.92149	-1.35;-1.35;-1.35;-1.35;-1.35;0.35;0.35;0.35;0.35;-2.98	3.29	-3.24	0.05094	WW/Rsp5/WWP (2);	0.185494	0.43416	N	0.000565	D	0.89291	0.6673	M	0.85710	2.77	0.20074	N	0.999939	P;P;B;P;B;B	0.46784	0.608;0.884;0.361;0.799;0.008;0.023	B;B;B;B;B;B	0.37888	0.202;0.179;0.086;0.26;0.004;0.01	D	0.83749	0.0208	10	0.54805	T	0.06	.	9.9059	0.41375	0.3394:0.0:0.6606:0.0	.	234;313;234;234;234;50	B4E248;Q6ZN13;Q9BRR9;Q9BRR9-2;E9PDX9;B4DVI3	.;.;RHG09_HUMAN;.;.;.	K	234;234;234;305;283;50;50;50;87;50;50	ENSP00000377380:N234K;ENSP00000348782:N234K;ENSP00000394307:N234K;ENSP00000377386:N305K;ENSP00000397950:N50K;ENSP00000449829:N50K;ENSP00000450256:N50K;ENSP00000446932:N87K;ENSP00000448424:N50K;ENSP00000450223:N50K	ENSP00000344852:N283K	N	-	3	2	ARHGAP9	56157563	0.887000	0.30362	0.042000	0.18584	0.034000	0.12701	0.087000	0.14958	-0.743000	0.04784	-0.899000	0.02877	AAT	.	.	.	none		0.637	ARHGAP9-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_032496		C	57871296	A	C	57871296	3	2	24	1	0	0	0	0	1	0	0	0	889	98	4	5	1553	5	ARHGAP9	12	57871296	Missense_Mutation	SNP	A	TCGA-4A-A93W-01A-11D-A36X-10	3196015	57871296	75980599	61	1719											
NAV3	89795	hgsc.bcm.edu	37	chr12	78562567	78562567	+	Missense_Mutation	SNP	T	T	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	atagaactaagagaaaccatTgaaatgctgaaggctcagaa	19	7	9	6	0	1	5	1	2	0	3	1	6	1	5	1	1	3	2	1	1	7	3			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr12:78562567T>G	ENST00000397909.2	+	24	5075	c.4902T>G	c.(4900-4902)atT>atG	p.I1634M	NAV3_ENST00000536525.2_Missense_Mutation_p.I1634M|NAV3_ENST00000228327.6_Missense_Mutation_p.I1634M|NAV3_ENST00000266692.7_Missense_Mutation_p.I1457M			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1634						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						GAGAAACCATTGAAATGCTGA	0.408										HNSCC(70;0.22)																											p.I1634M		Atlas-SNP	.											.	NAV3	506	.	0			c.T4902G						PASS	.						77	78	78					12																	78562567		1812	4077	5889	SO:0001583	missense	89795	exon24			AACCATTGAAATG	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.4902T>G	chr12.hg19:g.78562567T>G	ENSP00000381007:p.Ile1634Met	207.0	0.0	.		209.0	84.0	.	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.70|16.70	3.195863|3.195863	0.58126|0.58126	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692;ENST00000378640;ENST00000550788|ENST00000552895	D;D;D;D;D|.	0.94650|.	-3.48;-3.48;-3.48;-3.48;-3.48|.	5.41|5.41	2.89|2.89	0.33648|0.33648	.|.	0.000000|.	0.40385|.	U|.	0.001119|.	T|.	0.63212|.	0.2492|.	M|M	0.75085|0.75085	2.285|2.285	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.76494|.	0.977;0.997;0.977;0.999|.	P;D;P;D|.	0.83275|.	0.863;0.994;0.703;0.996|.	T|.	0.61133|.	-0.7124|.	10|.	0.66056|.	D|.	0.02|.	-9.4096|-9.4096	6.1373|6.1373	0.20241|0.20241	0.2374:0.0707:0.0:0.6919|0.2374:0.0707:0.0:0.6919	.|.	1634;1457;1634;1634|.	E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2|.	.;.;NAV3_HUMAN;.|.	M|G	1634;1634;1634;1457;255;263|529	ENSP00000446132:I1634M;ENSP00000381007:I1634M;ENSP00000228327:I1634M;ENSP00000266692:I1457M;ENSP00000448303:I263M|.	ENSP00000228327:I1634M|.	I|X	+|+	3|1	3|0	NAV3|NAV3	77086698|77086698	0.992000|0.992000	0.36948|0.36948	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	0.197000|0.197000	0.17197|0.17197	0.995000|0.995000	0.38917|0.38917	0.528000|0.528000	0.53228|0.53228	ATT|TGA	.	.	.	none		0.408	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		G	78562567	T	G	78562567	3	3	24	1	0	0	0	0	1	0	0	0	10192	1800	63	5	4996	5	NAV3	12	78562567	Missense_Mutation	SNP	T	TCGA-4A-A93W-01A-11D-A36X-10	20691271	78562567	55289328	62	1720											
SOHLH2	54937	hgsc.bcm.edu	37	chr13	36744692	36744692	+	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	cagttgggatgtgtagtgcaCgtctggcccaacccagaagt	9	9	13	10	1	1	1	0	0	1	1	1	2	1	2	2	2	2	3	2	2	3	2			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr13:36744692C>T	ENST00000379881.3	-	10	1321	c.1233G>A	c.(1231-1233)acG>acA	p.T411T	SOHLH2_ENST00000554962.1_Silent_p.T488T|CCDC169-SOHLH2_ENST00000511166.1_Silent_p.T488T	NM_017826.2	NP_060296.2	Q9NX45	SOLH2_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 2	411					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;4.63e-08)|Epithelial(112;2.67e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00272)|BRCA - Breast invasive adenocarcinoma(63;0.00685)|GBM - Glioblastoma multiforme(144;0.0273)		GTGTAGTGCACGTCTGGCCCA	0.512																																					p.T488T		Atlas-SNP	.											.	.	.	.	0			c.G1464A						PASS	.						75	61	65					13																	36744692		2203	4300	6503	SO:0001819	synonymous_variant	100526761	exon15			AGTGCACGTCTGG	AK000456	CCDS9355.1, CCDS61309.1	13q13.3	2013-05-21			ENSG00000120669	ENSG00000120669		"Basic helix-loop-helix proteins"	26026	protein-coding gene	gene with protein product	"spermatogenesis associated 28"					12477932	Standard	NM_017826		Approved	FLJ20449, TEB1, bHLHe81, SPATA28		Q9NX45	OTTHUMG00000016728	ENST00000379881.3:c.1233G>A	chr13.hg19:g.36744692C>T		129.0	0.0	.		135.0	66.0	.	NM_001198910	B4DX90|Q5EGC3|Q8TC74|Q96QX4	Silent	SNP	ENST00000379881.3	hg19	CCDS9355.1																																																																																			.	.	.	none		0.512	SOHLH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044477.2	NM_017826		T	36744692	C	T	36744692	2	4	24	1	0	0	0	0	0	0	0	1	14937	523	19	1		1	SOHLH2	13	36744692	Silent	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10		36744692	78425186	63	1721											
DGKH	160851	hgsc.bcm.edu	37	chr13	42733507	42733507	+	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	cattatagaagatgaagatgGcgtaagctgctgctctgtct	11	12	11	7	1	2	4	0	1	2	3	2	4	2	4	0	1	3	4	0	1	5	3			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr13:42733507G>A	ENST00000337343.4	+	6	749	c.728G>A	c.(727-729)gGc>gAc	p.G243D	DGKH_ENST00000540693.1_Splice_Site_p.G243D|DGKH_ENST00000536612.1_Splice_Site_p.G107D|DGKH_ENST00000538674.1_Intron|DGKH_ENST00000379274.2_Splice_Site_p.G107D|DGKH_ENST00000261491.5_Splice_Site_p.G243D|DGKH_ENST00000498255.2_3'UTR	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	243					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)		GATGAAGATGGCGTAAGCTGC	0.423																																					p.G243D		Atlas-SNP	.											.	DGKH	106	.	0			c.G728A						PASS	.						84	65	72					13																	42733507		2203	4300	6503	SO:0001630	splice_region_variant	160851	exon7			AAGATGGCGTAAG	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.729+1G>A	chr13.hg19:g.42733507G>A		88.0	0.0	.		93.0	45.0	.	NM_001204504	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Missense_Mutation	SNP	ENST00000337343.4	hg19	CCDS9381.1	.	.	.	.	.	.	.	.	.	.	G	17.06	3.292173	0.59976	.	.	ENSG00000102780	ENST00000540693;ENST00000337343;ENST00000261491;ENST00000379274;ENST00000536612	D;D;D;D;D	0.84516	-1.86;-1.86;-1.86;-1.86;-1.86	5.31	4.46	0.54185	.	0.000000	0.85682	D	0.000000	D	0.89945	0.6862	L	0.55743	1.74	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.978	D;D;P	0.97110	0.998;1.0;0.841	D	0.90134	0.4208	10	0.56958	D	0.05	.	13.9054	0.63831	0.0737:0.0:0.9263:0.0	.	107;243;243	Q86XP1-3;Q86XP1-2;Q86XP1	.;.;DGKH_HUMAN	D	243;243;243;107;107	ENSP00000440823:G243D;ENSP00000337572:G243D;ENSP00000261491:G243D;ENSP00000368576:G107D;ENSP00000445114:G107D	ENSP00000261491:G243D	G	+	2	0	DGKH	41631507	1.000000	0.71417	0.693000	0.30195	0.158000	0.22134	9.416000	0.97383	1.224000	0.43551	0.655000	0.94253	GGC	.	.	.	none		0.423	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009	Missense_Mutation	A	42733507	G	A	42733507	5	1	24	1	0	0	0	0	0	0	1	0	4472	1217	42	2	750	2	DGKH	13	42733507	Splice_Site	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10	5988815	42733507	72436371	64	1722											
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77642846	77642846	+	Missense_Mutation	SNP	A	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	ctcaaagcagtaggcatcagAggaggcatcttcatcatttg	12	10	10	9	0	5	1	4	0	1	1	5	2	5	2	0	3	1	4	0	3	2	3			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr13:77642846A>C	ENST00000544440.2	-	70	11928	c.11911T>G	c.(11911-11913)Tct>Gct	p.S3971A	MYCBP2_ENST00000407578.2_Missense_Mutation_p.S4009A|MYCBP2_ENST00000357337.6_Missense_Mutation_p.S3971A					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)		TAGGCATCAGAGGAGGCATCT	0.473																																					p.S4009A		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.T12025G						PASS	.						242	190	208					13																	77642846		2203	4300	6503	SO:0001583	missense	23077	exon70			CATCAGAGGAGGC	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.11911T>G	chr13.hg19:g.77642846A>C	ENSP00000444596:p.Ser3971Ala	108.0	0.0	.		117.0	46.0	.	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.26|15.26	2.780536|2.780536	0.49891|0.49891	.|.	.|.	ENSG00000005810|ENSG00000005810	ENST00000429715|ENST00000357337;ENST00000407578;ENST00000544440	.|T;T;T	.|0.65732	.|-0.17;-0.17;-0.17	5.84|5.84	4.63|4.63	0.57726|0.57726	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.46814|0.46814	0.1412|0.1412	N|N	0.21448|0.21448	0.665|0.665	0.51012|0.51012	D|D	0.999903|0.999903	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.28170|0.28170	-1.0052|-1.0052	5|10	.|0.23302	.|T	.|0.38	.|.	12.9953|12.9953	0.58644|0.58644	0.8651:0.1349:0.0:0.0|0.8651:0.1349:0.0:0.0	.|.	.|3971	.|O75592	.|MYCB2_HUMAN	R|A	391|3971;4009;3971	.|ENSP00000349892:S3971A;ENSP00000384288:S4009A;ENSP00000444596:S3971A	.|ENSP00000349892:S3971A	L|S	-|-	2|1	0|0	MYCBP2|MYCBP2	76540847|76540847	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.998000|0.998000	0.95712|0.95712	8.906000|8.906000	0.92626|0.92626	0.991000|0.991000	0.38814|0.38814	0.528000|0.528000	0.53228|0.53228	CTC|TCT	.	.	.	none		0.473	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		C	77642846	A	C	77642846	3	2	24	1	0	0	0	0	1	0	0	0	10025	304	11	5	2067	5	MYCBP2	13	77642846	Missense_Mutation	SNP	A	TCGA-4A-A93W-01A-11D-A36X-10	34909339	77642846	37527032	65	1723											
NYNRIN	57523	hgsc.bcm.edu	37	chr14	24868618	24868618	+	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	cctacttctggctacagctcGaggggccccgagagaacatg	9	7	12	13	2	1	1	0	0	1	1	2	4	1	1	3	3	4	2	3	3	3	3			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr14:24868618G>T	ENST00000382554.3	+	2	484	c.166G>T	c.(166-168)Gag>Tag	p.E56*		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	56					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						GCTACAGCTCGAGGGGCCCCG	0.627																																					p.E56X		Atlas-SNP	.											.	NYNRIN	120	.	0			c.G166T						PASS	.						20	26	25					14																	24868618		1904	4111	6015	SO:0001587	stop_gained	57523	exon2			CAGCTCGAGGGGC	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.166G>T	chr14.hg19:g.24868618G>T	ENSP00000371994:p.Glu56*	124.0	0.0	.		106.0	45.0	.	NM_025081	Q6P153|Q86TR3|Q9HAC4	Nonsense_Mutation	SNP	ENST00000382554.3	hg19	CCDS45090.1	.	.	.	.	.	.	.	.	.	.	G	39	7.662585	0.98419	.	.	ENSG00000205978	ENST00000382554	.	.	.	4.46	1.38	0.22167	.	0.538297	0.11631	U	0.544789	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	3.1501	0.06485	0.0954:0.3385:0.392:0.1741	.	.	.	.	X	56	.	ENSP00000371994:E56X	E	+	1	0	NYNRIN	23938458	0.972000	0.33761	0.982000	0.44146	0.993000	0.82548	0.917000	0.28665	0.089000	0.17243	0.491000	0.48974	GAG	.	.	.	none		0.627	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1			T	24868618	G	T	24868618	4	4	24	1	0	0	0	0	0	1	0	0	10803	1059	37	4	168	4	NYNRIN	14	24868618	Nonsense_Mutation	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10		24868618	82480922	66	1724											
PPP1R13B	23368	hgsc.bcm.edu	37	chr14	104206573	104206573	+	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	ccagggtgttgaagcgctggTacagcagcttctggatgttg	7	11	15	8	1	1	1	0	1	1	0	1	2	1	2	1	3	4	6	1	3	2	4			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr14:104206573T>A	ENST00000202556.9	-	12	2462	c.2180A>T	c.(2179-2181)tAc>tTc	p.Y727F	PPP1R13B_ENST00000423488.2_Missense_Mutation_p.Y146F|PPP1R13B_ENST00000555391.1_5'UTR	NM_015316.2	NP_056131.2	Q96KQ4	ASPP1_HUMAN	protein phosphatase 1, regulatory subunit 13B	727	Pro-rich.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(6)|kidney(2)|large_intestine(7)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.173)|all_epithelial(191;0.131)|Melanoma(154;0.155)				GAAGCGCTGGTACAGCAGCTT	0.662																																					p.Y727F		Atlas-SNP	.											.	PPP1R13B	72	.	0			c.A2180T						PASS	.						47	56	53					14																	104206573		1954	4129	6083	SO:0001583	missense	23368	exon12			CGCTGGTACAGCA	AB018314	CCDS41997.1	14q32.33	2013-01-10	2011-10-04		ENSG00000088808	ENSG00000088808		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	14950	protein-coding gene	gene with protein product		606455	"protein phosphatase 1, regulatory (inhibitor) subunit 13B"			9872452	Standard	NM_015316		Approved	p53BP2-like, KIAA0771, p85, ASPP1	uc001yof.1	Q96KQ4	OTTHUMG00000171647	ENST00000202556.9:c.2180A>T	chr14.hg19:g.104206573T>A	ENSP00000202556:p.Tyr727Phe	55.0	0.0	.		53.0	27.0	.	NM_015316	B2RMX5|O94870	Missense_Mutation	SNP	ENST00000202556.9	hg19	CCDS41997.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.849691	0.91277	.	.	ENSG00000088808	ENST00000202556;ENST00000423488	T;T	0.76839	-0.44;-1.05	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.86426	0.5930	M	0.67700	2.07	0.53005	D	0.99996	D	0.69078	0.997	D	0.70716	0.97	D	0.87435	0.2391	10	0.59425	D	0.04	.	15.6938	0.77477	0.0:0.0:0.0:1.0	.	727	Q96KQ4	ASPP1_HUMAN	F	727;146	ENSP00000202556:Y727F;ENSP00000395213:Y146F	ENSP00000202556:Y727F	Y	-	2	0	PPP1R13B	103276326	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.678000	0.84035	2.102000	0.63906	0.448000	0.29417	TAC	.	.	.	none		0.662	PPP1R13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414591.1	NM_015316		A	104206573	T	A	104206573	3	1	24	1	0	0	0	0	1	0	0	0	12367	1638	57	5	1116	5	PPP1R13B	14	104206573	Missense_Mutation	SNP	T	TCGA-4A-A93W-01A-11D-A36X-10	79337955	104206573	3142967	67	1725											
ASPG	374569	hgsc.bcm.edu	37	chr14	104559866	104559866	+	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	gaggattctctacaccgtgcTggagtgccagcccctcttcg	6	10	11	14	2	2	0	0	0	2	0	4	3	2	2	4	2	4	1	4	2	1	3			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr14:104559866T>A	ENST00000551177.1	+	3	322	c.230T>A	c.(229-231)cTg>cAg	p.L77Q	ASPG_ENST00000546892.2_Missense_Mutation_p.L77Q|ASPG_ENST00000455920.2_Missense_Mutation_p.L77Q	NM_001080464.2	NP_001073933.2	Q86U10	LPP60_HUMAN	asparaginase	77	Asparaginase.|Asparaginase/glutaminase. {ECO:0000255|PROSITE-ProRule:PRU01068}.				asparagine metabolic process (GO:0006528)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)		1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)|asparaginase activity (GO:0004067)|lysophospholipase activity (GO:0004622)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	11						TACACCGTGCTGGAGTGCCAG	0.632																																					p.L77Q		Atlas-SNP	.											.	ASPG	34	.	0			c.T230A						PASS	.						77	89	85					14																	104559866		2068	4187	6255	SO:0001583	missense	374569	exon3			CCGTGCTGGAGTG		CCDS45170.1, CCDS45170.2	14q32.33	2014-03-14	2014-03-14	2008-11-06	ENSG00000166183	ENSG00000166183	3.1.1.5, 3.5.1.1	"Ankyrin repeat domain containing"	20123	protein-coding gene	gene with protein product	"60-kDa-lysophospholipase"		"chromosome 14 open reading frame 76", "asparaginase homolog (S. cerevisiae)"	C14orf76			Standard	NM_001080464		Approved		uc001yoq.2	Q86U10		ENST00000551177.1:c.230T>A	chr14.hg19:g.104559866T>A	ENSP00000450040:p.Leu77Gln	78.0	0.0	.		57.0	23.0	.	NM_001080464	B9EGQ2|Q8IV80	Missense_Mutation	SNP	ENST00000551177.1	hg19	CCDS45170.2	.	.	.	.	.	.	.	.	.	.	T	13.99	2.402521	0.42613	.	.	ENSG00000166183	ENST00000551177;ENST00000299234;ENST00000546892;ENST00000455920	T;T;T	0.24151	1.87;1.87;1.87	3.57	3.57	0.40892	.	0.156561	0.42821	D	0.000653	T	0.46014	0.1371	M	0.73753	2.245	0.45183	D	0.998195	P;D;D;D	0.58620	0.942;0.975;0.968;0.983	P;P;P;D	0.66497	0.8;0.886;0.819;0.944	T	0.40553	-0.9557	10	0.38643	T	0.18	-8.8351	11.416	0.49951	0.0:0.0:0.0:1.0	.	77;77;77;105	G3V1Y8;Q86U10;Q86U10-3;E5RFC2	.;LPP60_HUMAN;.;.	Q	77;105;77;77	ENSP00000450040:L77Q;ENSP00000448911:L77Q;ENSP00000389003:L77Q	ENSP00000299234:L105Q	L	+	2	0	ASPG	103629619	1.000000	0.71417	0.994000	0.49952	0.644000	0.38419	4.913000	0.63341	1.406000	0.46857	0.402000	0.26972	CTG	.	.	.	none		0.632	ASPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407005.1	NM_001080464		A	104559866	T	A	104559866	3	1	24	1	0	0	0	0	1	0	0	0	1052	1580	55	5	240	5	ASPG	14	104559866	Missense_Mutation	SNP	T	TCGA-4A-A93W-01A-11D-A36X-10	353293	104559866	2789674	68	1726											
MAPKBP1	23005	hgsc.bcm.edu	37	chr15	42114511	42114511	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatgaagaagaggaagaagaGgagggaggcatgggccccta	15	3	18	5	0	0	5	0	1	0	4	0	9	0	8	2	5	0	1	2	5	5	1			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr15:42114511G>A	ENST00000456763.2	+	27	3334	c.3138G>A	c.(3136-3138)gaG>gaA	p.E1046E	MAPKBP1_ENST00000260357.7_Silent_p.E879E|MAPKBP1_ENST00000457542.2_Silent_p.E1040E|RP11-23P13.4_ENST00000510176.1_RNA|MAPKBP1_ENST00000514566.1_Silent_p.E1040E|MAPKBP1_ENST00000221214.6_Silent_p.E923E	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	1046	Poly-Glu.									breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		AGGAAGAAGAGGAGGGAGGCA	0.587																																					p.E1046E		Atlas-SNP	.											.	MAPKBP1	120	.	0			c.G3138A						PASS	.						44	45	45					15																	42114511		2203	4300	6503	SO:0001819	synonymous_variant	23005	exon27			AGAAGAGGAGGGA	AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"WD repeat domain containing"	29536	protein-coding gene	gene with protein product			"mitogen activated protein kinase binding protein 1"			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.3138G>A	chr15.hg19:g.42114511G>A		49.0	0.0	.		55.0	27.0	.	NM_001128608	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Silent	SNP	ENST00000456763.2	hg19	CCDS45239.1																																																																																			.	.	.	none		0.587	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359745.1	NM_014994		A	42114511	G	A	42114511	2	1	24	1	0	0	0	0	0	0	0	1	9299	991	35	2		2	MAPKBP1	15	42114511	Silent	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10		42114511	60416881	69	1727											
IGDCC4	57722	hgsc.bcm.edu	37	chr15	65676599	65676599	+	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	cctggatccccaacacccgaGatgagatcaggagcctctgg	10	6	11	14	1	2	2	1	1	1	2	3	6	3	4	5	3	2	0	5	3	1	0			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr15:65676599G>T	ENST00000352385.2	-	20	3710	c.3501C>A	c.(3499-3501)atC>atA	p.I1167I	IGDCC4_ENST00000558048.1_5'UTR	NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	1167						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						CAACACCCGAGATGAGATCAG	0.622																																					p.I1167I		Atlas-SNP	.											.	IGDCC4	95	.	0			c.C3501A						PASS	.						29	32	31					15																	65676599		2201	4299	6500	SO:0001819	synonymous_variant	57722	exon20			ACCCGAGATGAGA		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.3501C>A	chr15.hg19:g.65676599G>T		143.0	0.0	.		101.0	38.0	.	NM_020962	Q9HCE4	Silent	SNP	ENST00000352385.2	hg19	CCDS10206.1																																																																																			.	.	.	none		0.622	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962		T	65676599	G	T	65676599	2	4	24	1	0	0	0	0	0	0	0	1	7576	932	33	4		4	IGDCC4	15	65676599	Silent	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10	23562088	65676599	36854793	70	1728											
FSD2	123722	hgsc.bcm.edu	37	chr15	83428118	83428118	+	Frame_Shift_Del	DEL	T	T	-																															ttctaatagaaagtgacatgTtttggcattgaaatgccatt																										TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr15:83428118delT	ENST00000334574.8	-	13	2413	c.2232delA	c.(2230-2232)aaafs	p.K744fs	RP11-752G15.6_ENST00000561107.1_RNA|RP11-752G15.6_ENST00000558174.1_RNA|RP11-752G15.6_ENST00000559366.1_RNA|FSD2_ENST00000541889.1_Frame_Shift_Del_p.K699fs			A1L4K1	FSD2_HUMAN	fibronectin type III and SPRY domain containing 2	744	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.									breast(2)|central_nervous_system(1)|large_intestine(5)|lung(10)	18						AAGTGACATGTTTTGGCATTG	0.438																																					p.H745fs		Atlas-Indel,Pindel	.											.	FSD2	45	.	0			c.2233delC						PASS	.						71	75	73					15																	83428118		1968	4158	6126	SO:0001589	frameshift_variant	123722	exon13			.	AK122875	CCDS45332.1, CCDS61738.1	15q25.2	2013-02-11	2006-01-11	2006-01-11		ENSG00000186628		"Fibronectin type III domain containing"	18024	protein-coding gene	gene with protein product			"SPRY domain containing 1"	SPRYD1			Standard	NM_001007122		Approved	RP11-127F21	uc002bjd.2	A1L4K1		ENST00000334574.8:c.2232delA	chr15.hg19:g.83428118delT	ENSP00000335651:p.Lys744fs	80.0	0.0	0		67.0	34.0	0.507463	NM_001007122	B3KVG1|B7ZM02	Frame_Shift_Del	DEL	ENST00000334574.8	hg19	CCDS45332.1																																																																																			.	.	.	none		0.438	FSD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418385.1	NM_001007122		-	83428118	T	-	83428118	7	5	24	1	0	1	0	1	0	0	0	0	6078	1722	60	0	21	0	FSD2	15	83428118	Frame_Shift_Del	DEL	T	TCGA-4A-A93W-01A-11D-A36X-10	17751519	83428118	19103274	71	1729											
WDR24	84219	hgsc.bcm.edu	37	chr16	734812	734812	+	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	cacttcatgatgtgctgcagGtggccgccgtggctgcagcc	5	9	14	13	2	1	1	1	1	0	0	1	1	1	1	3	3	4	4	3	3	0	1			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr16:734812G>T	ENST00000248142.6	-	13	2684	c.2685C>A	c.(2683-2685)caC>caA	p.H895Q	JMJD8_ENST00000293882.4_5'Flank|WDR24_ENST00000293883.4_Missense_Mutation_p.H765Q|JMJD8_ENST00000609261.1_5'Flank|JMJD8_ENST00000562824.1_5'Flank|JMJD8_ENST00000412368.2_5'Flank|JMJD8_ENST00000454700.1_5'Flank|JMJD8_ENST00000562111.1_5'Flank			Q96S15	WDR24_HUMAN	WD repeat domain 24	895										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)				TGTGCTGCAGGTGGCCGCCGT	0.677																																					p.H765Q		Atlas-SNP	.											.	WDR24	111	.	0			c.C2295A						PASS	.						16	14	14					16																	734812		2152	4256	6408	SO:0001583	missense	84219	exon9			CTGCAGGTGGCCG	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.2685C>A	chr16.hg19:g.734812G>T	ENSP00000248142:p.His895Gln	106.0	0.0	.		77.0	42.0	.	NM_032259	A2IDB8|D3DU59|Q96GC7|Q9H0B7	Missense_Mutation	SNP	ENST00000248142.6	hg19		.	.	.	.	.	.	.	.	.	.	g	13.02	2.111265	0.37242	.	.	ENSG00000127580	ENST00000248142;ENST00000293883	D;D	0.98419	-4.92;-3.35	4.77	-1.03	0.10102	.	0.000000	0.85682	D	0.000000	D	0.98817	0.9601	M	0.92923	3.36	0.53005	D	0.999969	D	0.76494	0.999	D	0.78314	0.991	D	0.98611	1.0663	10	0.87932	D	0	-36.2207	9.962	0.41701	0.4486:0.0:0.5514:0.0	.	765	Q96S15-2	.	Q	895;765	ENSP00000248142:H895Q;ENSP00000293883:H765Q	ENSP00000248142:H895Q	H	-	3	2	WDR24	674813	0.998000	0.40836	0.998000	0.56505	0.957000	0.61999	0.387000	0.20718	-0.015000	0.14150	-0.360000	0.07572	CAC	.	.	.	none		0.677	WDR24-201	KNOWN	basic	protein_coding	protein_coding		NM_032259		T	734812	G	T	734812	3	4	24	1	0	0	0	0	1	0	0	0	17293	1252	44	4	81	4	WDR24	16	734812	Missense_Mutation	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10		734812	89619941	72	1730											
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24801496	24801496	+	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	tctcaccttagcaatggagaGtcaaaaagtggaggctctta	13	10	10	8	0	3	1	2	0	2	1	4	3	3	2	1	3	1	2	1	3	5	2			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr16:24801496G>A	ENST00000395799.3	+	6	1662	c.1533G>A	c.(1531-1533)gaG>gaA	p.E511E	TNRC6A_ENST00000315183.7_Silent_p.E511E	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	511	Interaction with argonaute family proteins.|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)		GCAATGGAGAGTCAAAAAGTG	0.483																																					p.E511E		Atlas-SNP	.											.	TNRC6A	171	.	0			c.G1533A						PASS	.						107	104	105					16																	24801496		2197	4300	6497	SO:0001819	synonymous_variant	27327	exon6			TGGAGAGTCAAAA	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.1533G>A	chr16.hg19:g.24801496G>A		133.0	0.0	.		100.0	36.0	.	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Silent	SNP	ENST00000395799.3	hg19	CCDS10624.2																																																																																			.	.	.	none		0.483	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		A	24801496	G	A	24801496	2	1	24	1	0	0	0	0	0	0	0	1	16352	1020	36	2		2	TNRC6A	16	24801496	Silent	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10	24066684	24801496	65553257	73	1731											
ELMO3	1874	hgsc.bcm.edu	37	chr16	67233133	67233133	+	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	aggtcaggtctcggaaagggAggacctcctcgtccccaggg	8	6	15	12	2	2	0	1	0	1	0	6	3	4	3	4	6	0	0	4	6	1	0			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr16:67233133A>G	ENST00000379378.3	+	0	2096				ELMO3_ENST00000360833.1_Silent_p.G21G|ELMO3_ENST00000477898.1_5'Flank|ELMO3_ENST00000393997.2_Silent_p.G21G	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)		TCGGAAAGGGAGGACCTCCTC	0.692																																					p.G21G		Atlas-SNP	.											ELMO3,caecum,carcinoma,0,1	ELMO3	41	.	0			c.A63G						PASS	.						21	30	27					16																	67233133		2078	4199	6277	SO:0001628	intergenic_variant	79767	exon1			AAAGGGAGGACCT	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		chr16.hg19:g.67233133A>G		141.0	0.0	.		124.0	41.0	.	NM_024712	A6NGR8|B5BU56|Q12991|Q15328	Silent	SNP	ENST00000379378.3	hg19	CCDS32464.1																																																																																			.	.	.	none		0.692	E2F4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421565.1	NM_001950		G	67233133	A	G	67233133	1	3	24	0	1	0	0	0	0	0	0	0	5069	291	11	3		3	ELMO3	16	67233133	IGR	SNP	A	TCGA-4A-A93W-01A-11D-A36X-10	42431637	67233133	23121620	74	1732											
ZDHHC7	55625	hgsc.bcm.edu	37	chr16	85012877	85012877	+	Frame_Shift_Del	DEL	C	C	-																															gatgatccattttccgaataCatcttttgcaaatactgaaa																										TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr16:85012877delC	ENST00000313732.4	-	5	807	c.455delG	c.(454-456)tgtfs	p.C152fs	ZDHHC7_ENST00000564466.1_Frame_Shift_Del_p.C189fs|ZDHHC7_ENST00000569488.1_5'UTR	NM_017740.2	NP_060210.2	Q9NXF8	ZDHC7_HUMAN	zinc finger, DHHC-type containing 7	152					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						TTTCCGAATACATCTTTTGCA	0.348																																					p.C189X		Atlas-Indel,Pindel	.											.	ZDHHC7	55	.	0			c.567delT						PASS	.						104	101	102					16																	85012877		2199	4300	6499	SO:0001589	frameshift_variant	55625	exon6			.	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.455delG	chr16.hg19:g.85012877delC	ENSP00000315604:p.Cys152fs	256.0	0.0	0		207.0	90.0	0.434783	NM_001145548	D3DUM1|Q8WV42|Q9NVD8	Frame_Shift_Del	DEL	ENST00000313732.4	hg19	CCDS10950.1																																																																																			.	.	.	none		0.348	ZDHHC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269087.1	NM_017740		-	85012877	C	-	85012877	7	5	24	1	0	1	0	1	0	0	0	0	17632	478	17	0	487	0	ZDHHC7	16	85012877	Frame_Shift_Del	DEL	C	TCGA-4A-A93W-01A-11D-A36X-10	17779744	85012877	5341876	75	1733											
JPH3	57338	hgsc.bcm.edu	37	chr16	87724046	87724046	+	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	agccccggttgctgcgttggGacttgaccttctccccgccc	3	10	11	17	3	1	1	0	1	1	0	2	2	1	2	6	2	3	3	6	2	0	4			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr16:87724046G>T	ENST00000284262.2	+	4	2322	c.2080G>T	c.(2080-2082)Gac>Tac	p.D694Y	JPH3_ENST00000563609.1_3'UTR	NM_020655.2	NP_065706.2	Q8WXH2	JPH3_HUMAN	junctophilin 3	694					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)		GCTGCGTTGGGACTTGACCTT	0.662																																					p.D694Y		Atlas-SNP	.											.	JPH3	95	.	0			c.G2080T						PASS	.						13	12	12					16																	87724046		2172	4276	6448	SO:0001583	missense	57338	exon4			CGTTGGGACTTGA	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.2080G>T	chr16.hg19:g.87724046G>T	ENSP00000284262:p.Asp694Tyr	93.0	0.0	.		87.0	27.0	.	NM_020655	D3DUN2|Q8N471|Q9HDC3|Q9HDC4	Missense_Mutation	SNP	ENST00000284262.2	hg19	CCDS10962.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.931957	0.73442	.	.	ENSG00000154118	ENST00000537256;ENST00000284262	T	0.58210	0.35	4.3	4.3	0.51218	.	0.000000	0.85682	D	0.000000	T	0.62502	0.2433	L	0.34521	1.04	0.58432	D	0.999999	D	0.89917	1.0	D	0.76071	0.987	T	0.67457	-0.5666	10	0.72032	D	0.01	.	15.8177	0.78615	0.0:0.0:1.0:0.0	.	694	Q8WXH2	JPH3_HUMAN	Y	557;694	ENSP00000284262:D694Y	ENSP00000284262:D694Y	D	+	1	0	JPH3	86281547	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.048000	0.93830	1.972000	0.57404	0.650000	0.86243	GAC	.	.	.	none		0.662	JPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269108.2			T	87724046	G	T	87724046	3	4	24	1	0	0	0	0	1	0	0	0	7969	1174	41	4	2094	4	JPH3	16	87724046	Missense_Mutation	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10	2711169	87724046	2630707	76	1734											
ANKRD11	29123	hgsc.bcm.edu	37	chr16	89348979	89348979	+	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	ctccaggtggctccgtgaaaGagacctccaggaaggcagtc	10	6	13	12	1	0	2	0	1	0	1	4	4	3	3	4	4	0	2	4	4	2	0			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr16:89348979G>A	ENST00000301030.4	-	9	4431	c.3971C>T	c.(3970-3972)tCt>tTt	p.S1324F	ANKRD11_ENST00000378330.2_Missense_Mutation_p.S1324F	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1324	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)		CTCCGTGAAAGAGACCTCCAG	0.582																																					p.S1324F		Atlas-SNP	.											.	ANKRD11	195	.	0			c.C3971T						PASS	.						38	39	39					16																	89348979		2198	4299	6497	SO:0001583	missense	29123	exon9			GTGAAAGAGACCT	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.3971C>T	chr16.hg19:g.89348979G>A	ENSP00000301030:p.Ser1324Phe	58.0	0.0	.		52.0	26.0	.	NM_001256183	Q6NTG1|Q6QMF8	Missense_Mutation	SNP	ENST00000301030.4	hg19	CCDS32513.1	.	.	.	.	.	.	.	.	.	.	G	13.33	2.204556	0.38905	.	.	ENSG00000167522	ENST00000301030;ENST00000378330	T;T	0.51325	0.71;0.71	5.21	5.21	0.72293	.	0.484210	0.22246	N	0.062606	T	0.63010	0.2475	M	0.67953	2.075	0.53688	D	0.999977	D	0.62365	0.991	P	0.55161	0.77	T	0.67162	-0.5740	10	0.87932	D	0	.	18.7133	0.91666	0.0:0.0:1.0:0.0	.	1324	Q6UB99	ANR11_HUMAN	F	1324	ENSP00000301030:S1324F;ENSP00000367581:S1324F	ENSP00000301030:S1324F	S	-	2	0	ANKRD11	87876480	0.998000	0.40836	0.044000	0.18714	0.062000	0.15995	5.689000	0.68234	2.577000	0.86979	0.563000	0.77884	TCT	.	.	.	none		0.582	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		A	89348979	G	A	89348979	3	1	24	1	0	0	0	0	1	0	0	0	639	942	33	2	4040	2	ANKRD11	16	89348979	Missense_Mutation	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10	1624933	89348979	1005774	77	1735											
ZNF594	84622	hgsc.bcm.edu	37	chr17	5086715	5086715	+	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	tgatgtgggacaaggtgtgaActttgactgaacatctgtcc	10	12	12	7	0	1	4	0	4	1	0	2	5	2	5	1	2	2	0	1	2	3	1			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr17:5086715A>T	ENST00000399604.4	-	1	977	c.837T>A	c.(835-837)agT>agA	p.S279R	ZNF594_ENST00000575779.1_Missense_Mutation_p.S279R			Q96JF6	ZN594_HUMAN	zinc finger protein 594	279					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						CAAGGTGTGAACTTTGACTGA	0.413																																					p.S279R		Atlas-SNP	.											.	ZNF594	89	.	0			c.T837A						PASS	.						78	81	80					17																	5086715		2191	4295	6486	SO:0001583	missense	84622	exon2			GTGTGAACTTTGA	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.837T>A	chr17.hg19:g.5086715A>T	ENSP00000382513:p.Ser279Arg	35.0	0.0	.		44.0	31.0	.	NM_032530	Q6RFS0	Missense_Mutation	SNP	ENST00000399604.4	hg19	CCDS42241.1	.	.	.	.	.	.	.	.	.	.	A	0.815	-0.750550	0.03041	.	.	ENSG00000180626	ENST00000399604	T	0.35973	1.28	2.5	0.216	0.15258	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.18882	0.0453	N	0.21282	0.65	0.09310	N	1	P	0.46621	0.881	B	0.42653	0.394	T	0.09185	-1.0686	9	0.15499	T	0.54	.	2.072	0.03615	0.4378:0.0:0.3138:0.2484	.	279	Q96JF6	ZN594_HUMAN	R	279	ENSP00000382513:S279R	ENSP00000382513:S279R	S	-	3	2	ZNF594	5027439	0.000000	0.05858	0.994000	0.49952	0.847000	0.48162	-1.795000	0.01752	0.217000	0.20800	0.379000	0.24179	AGT	.	.	.	none		0.413	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737		T	5086715	A	T	5086715	3	4	24	1	0	0	0	0	1	0	0	0	18036	40	2	5	1590	5	ZNF594	17	5086715	Missense_Mutation	SNP	A	TCGA-4A-A93W-01A-11D-A36X-10		5086715	76108495	78	1736											
KRT17	3872	hgsc.bcm.edu	37	chr17	39780421	39780421	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtaccagtcacggatcttcAcctccagctcagtgttggcc	7	10	10	14	1	4	0	3	0	1	0	5	1	5	1	4	3	2	3	4	3	1	3			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr17:39780421A>G	ENST00000311208.8	-	1	408	c.341T>C	c.(340-342)gTg>gCg	p.V114A	JUP_ENST00000540235.1_Intron|KRT42P_ENST00000438131.1_RNA	NM_000422.2	NP_000413.1	Q04695	K1C17_HUMAN	keratin 17	114	Coil 1A.|Peptide epitope S1; induces T-cell and keratinocyte proliferation and IFN-gamma production.|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)				ACGGATCTTCACCTCCAGCTC	0.617																																					p.V114A	Pancreas(92;1242 2086 39193 50508)	Atlas-SNP	.											.	KRT17	57	.	0			c.T341C						PASS	.						99	110	106					17																	39780421		2203	4300	6503	SO:0001583	missense	3872	exon1			ATCTTCACCTCCA	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.341T>C	chr17.hg19:g.39780421A>G	ENSP00000308452:p.Val114Ala	175.0	0.0	.		262.0	79.0	.	NM_000422	A5Z1M9|A5Z1N0|A5Z1N1|A5Z1N2|A6NDV6|A6NKQ2|Q6IP98|Q8N1P6	Missense_Mutation	SNP	ENST00000311208.8	hg19	CCDS11402.1	.	.	.	.	.	.	.	.	.	.	A	7.338	0.620347	0.14193	.	.	ENSG00000128422	ENST00000311208	D	0.88124	-2.34	4.77	4.77	0.60923	Filament (1);	0.651197	0.12932	N	0.427268	T	0.76737	0.4029	N	0.21583	0.68	0.80722	D	1	B	0.20550	0.046	B	0.28991	0.097	T	0.65911	-0.6053	10	0.08837	T	0.75	.	6.9946	0.24774	0.7002:0.1529:0.0:0.1469	.	114	Q04695	K1C17_HUMAN	A	114	ENSP00000308452:V114A	ENSP00000308452:V114A	V	-	2	0	KRT17	37033947	0.988000	0.35896	1.000000	0.80357	0.572000	0.35998	1.849000	0.39318	2.132000	0.65825	0.260000	0.18958	GTG	.	.	.	none		0.617	KRT17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257460.1	NM_000422		G	39780421	A	G	39780421	3	3	24	1	0	0	0	0	1	0	0	0	8461	159	6	3	989	3	KRT17	17	39780421	Missense_Mutation	SNP	A	TCGA-4A-A93W-01A-11D-A36X-10	34693706	39780421	41414789	79	1737											
ASB16	92591	hgsc.bcm.edu	37	chr17	42249482	42249482	+	Missense_Mutation	SNP	A	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	tcgctacagcccgaggctacAcagactgtgctcgacacctg	9	7	10	15	3	0	1	0	0	0	1	2	3	0	1	2	1	4	3	2	1	2	2			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr17:42249482A>C	ENST00000293414.1	+	2	454	c.370A>C	c.(370-372)Aca>Cca	p.T124P		NM_080863.4	NP_543139.4	Q96NS5	ASB16_HUMAN	ankyrin repeat and SOCS box containing 16	124					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)		CCGAGGCTACACAGACTGTGC	0.632																																					p.T124P		Atlas-SNP	.											.	ASB16	34	.	0			c.A370C						PASS	.						59	54	56					17																	42249482		2203	4300	6503	SO:0001583	missense	92591	exon2			GGCTACACAGACT	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.370A>C	chr17.hg19:g.42249482A>C	ENSP00000293414:p.Thr124Pro	44.0	0.0	.		54.0	36.0	.	NM_080863	B2RBC0|Q8WXK0	Missense_Mutation	SNP	ENST00000293414.1	hg19	CCDS11478.1	.	.	.	.	.	.	.	.	.	.	A	13.17	2.157459	0.38119	.	.	ENSG00000161664	ENST00000293414	T	0.65178	-0.14	5.55	4.48	0.54585	Ankyrin repeat-containing domain (4);	0.366498	0.31734	N	0.007154	T	0.48059	0.1479	N	0.16833	0.445	0.09310	N	0.99999	P	0.42941	0.794	P	0.46629	0.522	T	0.42050	-0.9474	10	0.62326	D	0.03	-3.1755	4.6071	0.12383	0.6723:0.1645:0.1631:0.0	.	124	Q96NS5	ASB16_HUMAN	P	124	ENSP00000293414:T124P	ENSP00000293414:T124P	T	+	1	0	ASB16	39605008	0.001000	0.12720	0.589000	0.28718	0.238000	0.25445	0.447000	0.21710	1.127000	0.42034	0.533000	0.62120	ACA	.	.	.	none		0.632	ASB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457703.1			C	42249482	A	C	42249482	3	2	24	1	0	0	0	0	1	0	0	0	1020	159	6	5	376	5	ASB16	17	42249482	Missense_Mutation	SNP	A	TCGA-4A-A93W-01A-11D-A36X-10	2469061	42249482	38945728	80	1738											
OSBPL1A	114876	hgsc.bcm.edu	37	chr18	21761235	21761235	+	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	ataactggcatcgtgatcttGgatagttcctatttaaccag	11	14	8	8	1	1	1	0	1	1	0	3	2	2	2	2	2	2	2	2	2	4	7			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr18:21761235G>T	ENST00000319481.3	-	19	1892	c.1686C>A	c.(1684-1686)tcC>tcA	p.S562S	OSBPL1A_ENST00000357041.4_Silent_p.S180S|OSBPL1A_ENST00000399443.3_Silent_p.S49S	NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A	562					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)					TCGTGATCTTGGATAGTTCCT	0.388																																					p.S562S		Atlas-SNP	.											.	OSBPL1A	94	.	0			c.C1686A						PASS	.						111	101	104					18																	21761235		2203	4300	6503	SO:0001819	synonymous_variant	114876	exon19			GATCTTGGATAGT	AF392449, AF274714	CCDS11884.1, CCDS11885.1, CCDS56056.1	18q11.2	2014-06-03	2014-06-03	2014-06-03	ENSG00000141447	ENSG00000141447		"Oxysterol binding proteins", "Ankyrin repeat domain containing"	16398	protein-coding gene	gene with protein product		606730	"oxysterol binding protein-like 1B"	OSBPL1B		11279184, 10588946	Standard	NM_080597		Approved	ORP-1, ORP1	uc002kve.3	Q9BXW6	OTTHUMG00000131944	ENST00000319481.3:c.1686C>A	chr18.hg19:g.21761235G>T		66.0	0.0	.		84.0	38.0	.	NM_080597	B7Z7D3|Q9BZF5|Q9NW87	Silent	SNP	ENST00000319481.3	hg19	CCDS11884.1																																																																																			.	.	.	none		0.388	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254902.1	NM_080597		T	21761235	G	T	21761235	2	4	24	1	0	0	0	0	0	0	0	1	11284	1335	47	4		4	OSBPL1A	18	21761235	Silent	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10		21761235	56316013	81	1739											
SOCS6	9306	hgsc.bcm.edu	37	chr18	67992862	67992862	+	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	tgctacctccaatgcagaatAatcaaatccaaaggaacttc	16	9	5	11	0	1	1	1	0	0	1	4	2	3	2	3	1	4	2	3	1	7	3			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr18:67992862A>T	ENST00000397942.3	+	2	1274	c.958A>T	c.(958-960)Aat>Tat	p.N320Y	SOCS6_ENST00000582322.1_Missense_Mutation_p.N320Y	NM_004232.3	NP_004223.2	O14544	SOCS6_HUMAN	suppressor of cytokine signaling 6	320					defense response (GO:0006952)|JAK-STAT cascade (GO:0007259)|negative regulation of signal transduction (GO:0009968)|negative regulation of T cell activation (GO:0050868)|proteasomal protein catabolic process (GO:0010498)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|immunological synapse (GO:0001772)				NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)	22		Esophageal squamous(42;0.129)|Colorectal(73;0.152)				AATGCAGAATAATCAAATCCA	0.512																																					p.N320Y	Melanoma(84;1024 1361 24382 36583 42651)	Atlas-SNP	.											.	SOCS6	54	.	0			c.A958T						PASS	.						75	72	73					18																	67992862		2203	4300	6503	SO:0001583	missense	9306	exon2			CAGAATAATCAAA	AB006968	CCDS11998.1	18q22	2013-02-14	2004-02-25	2004-02-27	ENSG00000170677	ENSG00000170677		"Suppressors of cytokine signaling", "SH2 domain containing"	16833	protein-coding gene	gene with protein product		605118	"suppressor of cytokine signaling 4"	SOCS4		9344848, 11042152	Standard	NM_004232		Approved	CIS4, SSI4, HSPC060, STATI4, STAI4, Cish4	uc002lkr.1	O14544	OTTHUMG00000132816	ENST00000397942.3:c.958A>T	chr18.hg19:g.67992862A>T	ENSP00000381034:p.Asn320Tyr	88.0	0.0	.		84.0	35.0	.	NM_004232	Q8WUM3	Missense_Mutation	SNP	ENST00000397942.3	hg19	CCDS11998.1	.	.	.	.	.	.	.	.	.	.	A	11.13	1.546894	0.27652	.	.	ENSG00000170677	ENST00000397942	T	0.27256	1.68	5.08	1.26	0.21427	.	0.395352	0.23121	N	0.051698	T	0.15392	0.0371	L	0.27053	0.805	0.40211	D	0.977624	B	0.30455	0.28	B	0.26693	0.072	T	0.07028	-1.0794	10	0.72032	D	0.01	-7.4994	7.6716	0.28462	0.6301:0.2986:0.0713:0.0	.	320	O14544	SOCS6_HUMAN	Y	320	ENSP00000381034:N320Y	ENSP00000381034:N320Y	N	+	1	0	SOCS6	66143842	0.999000	0.42202	0.004000	0.12327	0.961000	0.63080	3.127000	0.50484	-0.029000	0.13827	-0.466000	0.05196	AAT	.	.	.	none		0.512	SOCS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256270.2			T	67992862	A	T	67992862	3	4	24	1	0	0	0	0	1	0	0	0	14931	362	13	5	960	5	SOCS6	18	67992862	Missense_Mutation	SNP	A	TCGA-4A-A93W-01A-11D-A36X-10	46231627	67992862	10084386	82	1740											
ATP8B3	148229	hgsc.bcm.edu	37	chr19	1802569	1802569	+	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	ggttgccaatgtccagggagTatttcttgtcattccattcc	7	15	9	10	0	2	0	1	0	1	0	5	1	5	1	4	2	1	2	4	2	2	6			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr19:1802569T>A	ENST00000310127.6	-	11	1218	c.980A>T	c.(979-981)tAc>tTc	p.Y327F	ATP8B3_ENST00000539485.1_Missense_Mutation_p.Y327F|ATP8B3_ENST00000525591.1_Missense_Mutation_p.Y274F|ATP8B3_ENST00000526092.2_Missense_Mutation_p.Y274F	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	327					binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTCCAGGGAGTATTTCTTGTC	0.577																																					p.Y327F		Atlas-SNP	.											.	ATP8B3	108	.	0			c.A980T						PASS	.						130	141	138					19																	1802569		2127	4225	6352	SO:0001583	missense	148229	exon11			AGGGAGTATTTCT	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.980A>T	chr19.hg19:g.1802569T>A	ENSP00000311336:p.Tyr327Phe	56.0	0.0	.		55.0	30.0	.	NM_138813	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Missense_Mutation	SNP	ENST00000310127.6	hg19	CCDS45901.1	.	.	.	.	.	.	.	.	.	.	t	4.280	0.051064	0.08243	.	.	ENSG00000130270	ENST00000310127;ENST00000539485;ENST00000525591;ENST00000526092;ENST00000382339	T;T;T;T	0.75367	-0.93;-0.93;-0.93;-0.93	3.72	3.72	0.42706	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.450694	0.23629	U	0.046144	T	0.70500	0.3231	L	0.48362	1.52	0.09310	N	1	D;P;P	0.53312	0.959;0.891;0.695	B;P;P	0.48400	0.444;0.494;0.576	T	0.61118	-0.7127	10	0.23302	T	0.38	.	11.7676	0.51939	0.0:0.0:0.0:1.0	.	274;327;274	F5H3R9;O60423;Q7Z485	.;AT8B3_HUMAN;.	F	327;327;274;274;274	ENSP00000311336:Y327F;ENSP00000443574:Y327F;ENSP00000437115:Y274F;ENSP00000445204:Y274F	ENSP00000311336:Y327F	Y	-	2	0	ATP8B3	1753569	0.219000	0.23619	0.600000	0.28864	0.209000	0.24338	3.028000	0.49705	1.569000	0.49696	0.370000	0.22315	TAC	.	.	.	none		0.577	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813		A	1802569	T	A	1802569	3	1	24	1	0	0	0	0	1	0	0	0	1196	1638	57	5	3046	5	ATP8B3	19	1802569	Missense_Mutation	SNP	T	TCGA-4A-A93W-01A-11D-A36X-10		1802569	57326414	83	1741											
ATCAY	85300	hgsc.bcm.edu	37	chr19	3905489	3905489	+	Frame_Shift_Del	DEL	C	C	-																															taagaggaagacgctggtggCcccagagatcaacatttctc																										TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr19:3905489delC	ENST00000450849.2	+	4	661	c.194delC	c.(193-195)gccfs	p.A65fs	ATCAY_ENST00000301260.6_Frame_Shift_Del_p.A65fs|ATCAY_ENST00000398448.3_Frame_Shift_Del_p.A71fs|ATCAY_ENST00000600960.1_Frame_Shift_Del_p.A65fs	NM_033064.4	NP_149053.1	Q86WG3	ATCAY_HUMAN	ataxia, cerebellar, Cayman type	65					apoptotic process (GO:0006915)|mitochondrion distribution (GO:0048311)|negative regulation of glutamate metabolic process (GO:2000212)|neuron projection development (GO:0031175)|regulation of protein localization (GO:0032880)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrial membrane (GO:0031966)|neuron projection (GO:0043005)|synapse (GO:0045202)	kinesin binding (GO:0019894)	p.A65V(2)		breast(1)|endometrium(2)|kidney(2)|lung(2)	7		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00485)|STAD - Stomach adenocarcinoma(1328;0.183)		ACGCTGGTGGCCCCAGAGATC	0.488																																					p.A65fs		Atlas-Indel,Pindel	.											.	ATCAY	84	.	2	Substitution - Missense(2)	kidney(2)	c.193delG						PASS	.						66	67	66					19																	3905489		1958	4142	6100	SO:0001589	frameshift_variant	85300	exon4			.		CCDS45923.1	19p13.3	2014-06-24	2008-07-18		ENSG00000167654	ENSG00000167654			779	protein-coding gene	gene with protein product	"Cayman ataxia", "caytaxin"	608179				8845847, 14556008	Standard	NM_033064		Approved		uc002lyy.4	Q86WG3	OTTHUMG00000181836	ENST00000450849.2:c.194delC	chr19.hg19:g.3905489delC	ENSP00000390941:p.Ala65fs	127.0	0.0	0		115.0	43.0	0.373913	NM_033064	Q8NAQ2|Q8TAQ3|Q96HC6|Q96JF5	Frame_Shift_Del	DEL	ENST00000450849.2	hg19	CCDS45923.1																																																																																			.	.	.	none		0.488	ATCAY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457872.2			-	3905489	C	-	3905489	7	5	24	1	0	1	0	1	0	0	0	0	1077	739	26	0	204	0	ATCAY	19	3905489	Frame_Shift_Del	DEL	C	TCGA-4A-A93W-01A-11D-A36X-10	2102920	3905489	55223494	84	1742											
SIPA1L3	23094	hgsc.bcm.edu	37	chr19	38631838	38631838	+	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	ccccaggggttggccggagaCctacgacatgaatacctcgg	9	6	13	13	3	0	2	0	1	0	1	1	4	0	2	5	5	2	1	5	5	3	3			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr19:38631838C>G	ENST00000222345.6	+	11	3667	c.3158C>G	c.(3157-3159)aCc>aGc	p.T1053S		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	1053					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)			TGGCCGGAGACCTACGACATG	0.622																																					p.T1053S		Atlas-SNP	.											.	SIPA1L3	150	.	0			c.C3158G						PASS	.						57	53	54					19																	38631838		2203	4299	6502	SO:0001583	missense	23094	exon11			CGGAGACCTACGA	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.3158C>G	chr19.hg19:g.38631838C>G	ENSP00000222345:p.Thr1053Ser	121.0	0.0	.		124.0	62.0	.	NM_015073	Q2TV87	Missense_Mutation	SNP	ENST00000222345.6	hg19	CCDS33007.1	.	.	.	.	.	.	.	.	.	.	C	11.89	1.773459	0.31411	.	.	ENSG00000105738	ENST00000222345	T	0.60299	0.2	4.96	4.96	0.65561	.	0.255793	0.40469	N	0.001090	T	0.50752	0.1634	L	0.50333	1.59	0.34666	D	0.723161	B	0.11235	0.004	B	0.12837	0.008	T	0.54892	-0.8225	10	0.10111	T	0.7	-40.2674	17.133	0.86730	0.0:1.0:0.0:0.0	.	1053	O60292	SI1L3_HUMAN	S	1053	ENSP00000222345:T1053S	ENSP00000222345:T1053S	T	+	2	0	SIPA1L3	43323678	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	2.167000	0.42415	2.583000	0.87209	0.460000	0.39030	ACC	.	.	.	none		0.622	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278		G	38631838	C	G	38631838	3	3	24	1	0	0	0	0	1	0	0	0	14344	507	18	4	3192	4	SIPA1L3	19	38631838	Missense_Mutation	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10	34726349	38631838	20497145	85	1743											
FBXO17	115290	hgsc.bcm.edu	37	chr19	39435737	39435737	+	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	gcagccgcagttctctcgagCgccccacctgccaggcagca	7	5	11	18	3	1	0	0	0	1	0	3	1	1	0	5	1	4	5	5	1	0	1			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr19:39435737C>A	ENST00000292852.4	-	5	906	c.565G>T	c.(565-567)Gct>Tct	p.A189S	FBXO17_ENST00000595329.1_Missense_Mutation_p.A189S|SARS2_ENST00000448145.2_Missense_Mutation_p.A24S|CTC-360G5.8_ENST00000599996.1_Missense_Mutation_p.R93L	NM_024907.5	NP_079183.4	Q96EF6	FBX17_HUMAN	F-box protein 17	189	FBA. {ECO:0000255|PROSITE- ProRule:PRU00482}.					SCF ubiquitin ligase complex (GO:0019005)	glycoprotein binding (GO:0001948)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)	7	all_cancers(60;8.37e-07)|all_lung(34;3.71e-07)|Lung NSC(34;4.17e-07)|all_epithelial(25;1.13e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			TTCTCTCGAGCGCCCCACCTG	0.627																																					p.A198S		Atlas-SNP	.											.	FBXO17	42	.	0			c.G592T						PASS	.						53	50	51					19																	39435737		2203	4300	6503	SO:0001583	missense	115290	exon5			CTCGAGCGCCCCA	AF386743	CCDS12526.1	19q13.2	2010-07-02	2004-06-15	2004-06-16		ENSG00000269190		"F-boxes /  "other""	18754	protein-coding gene	gene with protein product	"F-box only protein 26"	609094	"F-box only protein 17"	FBXO26			Standard	NM_148169		Approved	FBG4, FLJ25205, MGC9379, FLJ11798, Fbx17		Q96EF6		ENST00000292852.4:c.565G>T	chr19.hg19:g.39435737C>A	ENSP00000292852:p.Ala189Ser	65.0	0.0	.		87.0	32.0	.	NM_148169	Q96LQ4	Missense_Mutation	SNP	ENST00000292852.4	hg19	CCDS12526.1	.	.	.	.	.	.	.	.	.	.	C	10.86	1.470041	0.26423	.	.	ENSG00000104835	ENST00000448145;ENST00000392076;ENST00000292852	T;T	0.29655	1.56;1.56	4.58	4.58	0.56647	Galactose-binding domain-like (1);F-box associated (FBA) domain (2);	0.118955	0.35870	N	0.002926	T	0.44912	0.1316	L	0.60455	1.87	.	.	.	P;D	0.76494	0.657;0.999	B;D	0.85130	0.271;0.997	T	0.43458	-0.9390	9	0.09590	T	0.72	.	10.9909	0.47549	0.0:0.8108:0.1892:0.0	.	24;189	E7EX87;Q96EF6	.;FBX17_HUMAN	S	24;198;189	ENSP00000399330:A24S;ENSP00000292852:A189S	ENSP00000292852:A189S	A	-	1	0	FBXO17	44127577	0.879000	0.30193	0.861000	0.33841	0.182000	0.23217	1.427000	0.34881	2.530000	0.85305	0.467000	0.42956	GCT	.	.	.	none		0.627	FBXO17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463273.1	NM_024907		A	39435737	C	A	39435737	3	1	24	1	0	0	0	0	1	0	0	0	5737	768	27	4	279	4	FBXO17	19	39435737	Missense_Mutation	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10	803899	39435737	19693246	86	1744											
EGLN2	112398	hgsc.bcm.edu	37	chr19	41306764	41306764	+	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	gccgctgcagagtgaaggcgCtgcagcgctggtcaccaagg	8	5	16	12	3	1	2	1	1	0	1	1	2	1	2	2	3	3	5	2	3	2	0			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr19:41306764C>T	ENST00000593726.1	+	1	1315	c.287C>T	c.(286-288)gCt>gTt	p.A96V	EGLN2_ENST00000303961.4_Missense_Mutation_p.A96V|CTC-490E21.12_ENST00000601627.1_5'Flank|EGLN2_ENST00000406058.2_Missense_Mutation_p.A96V|EGLN2_ENST00000594140.1_5'Flank|RAB4B-EGLN2_ENST00000594136.1_3'UTR			Q96KS0	EGLN2_HUMAN	egl-9 family hypoxia-inducible factor 2	96	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)	AGTGAAGGCGCTGCAGCGCTG	0.682																																					p.A96V		Atlas-SNP	.											.	EGLN2	31	.	0			c.C287T						PASS	.						15	17	17					19																	41306764		2199	4295	6494	SO:0001583	missense	112398	exon2			AAGGCGCTGCAGC	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.287C>T	chr19.hg19:g.41306764C>T	ENSP00000469686:p.Ala96Val	79.0	0.0	.		72.0	37.0	.	NM_053046	A8K5S0|Q8WWY4|Q9BV14	Missense_Mutation	SNP	ENST00000593726.1	hg19	CCDS12567.1	.	.	.	.	.	.	.	.	.	.	C	18.22	3.576639	0.65878	.	.	ENSG00000171570	ENST00000303961;ENST00000406058	T;T	0.28255	1.62;1.62	4.04	4.04	0.47022	.	0.091223	0.43416	D	0.000568	T	0.19087	0.0458	N	0.19112	0.55	0.26530	N	0.974273	B	0.26935	0.164	B	0.22753	0.041	T	0.15435	-1.0437	10	0.62326	D	0.03	-8.2587	10.0167	0.42018	0.0:0.7939:0.2061:0.0	.	96	Q96KS0	EGLN2_HUMAN	V	96	ENSP00000307080:A96V;ENSP00000385253:A96V	ENSP00000307080:A96V	A	+	2	0	EGLN2	45998604	0.086000	0.21541	0.992000	0.48379	0.870000	0.49936	1.134000	0.31442	2.250000	0.74265	0.491000	0.48974	GCT	.	.	.	none		0.682	EGLN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463218.1			T	41306764	C	T	41306764	3	4	24	1	0	0	0	0	1	0	0	0	4971	797	28	2	289	2	EGLN2	19	41306764	Missense_Mutation	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10	1871027	41306764	17822219	87	1745											
CYP2S1	29785	hgsc.bcm.edu	37	chr19	41703754	41703754	+	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	atgcttgctctgcgggacctGggcatggggaagcgagaagg	8	7	18	8	2	1	1	0	0	1	1	1	4	1	3	1	5	4	3	1	5	2	1			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr19:41703754G>C	ENST00000310054.4	+	3	630	c.414G>C	c.(412-414)ctG>ctC	p.L138L	CYP2S1_ENST00000542619.1_Intron	NM_030622.6	NP_085125.1	Q96SQ9	CP2S1_HUMAN	cytochrome P450, family 2, subfamily S, polypeptide 1	138					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						TGCGGGACCTGGGCATGGGGA	0.617																																					p.L138L		Atlas-SNP	.											.	CYP2S1	47	.	0			c.G414C						PASS	.						77	74	75					19																	41703754		2203	4300	6503	SO:0001819	synonymous_variant	29785	exon3			GGACCTGGGCATG	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.414G>C	chr19.hg19:g.41703754G>C		79.0	0.0	.		77.0	22.0	.	NM_030622	Q9BZ66	Silent	SNP	ENST00000310054.4	hg19	CCDS12573.1																																																																																			.	.	.	none		0.617	CYP2S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463287.1			C	41703754	G	C	41703754	2	2	24	1	0	0	0	0	0	0	0	1	4176	1335	47	4		4	CYP2S1	19	41703754	Silent	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10	396990	41703754	17425229	88	1746											
ZNF649	65251	hgsc.bcm.edu	37	chr19	52400157	52400157	+	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	atcacatcccggtacaggtcCttctgagcagggctcaggaa	10	8	11	12	1	3	1	2	1	1	0	5	2	5	2	2	4	2	3	2	4	2	2			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr19:52400157C>G	ENST00000354957.3	-	3	374	c.90G>C	c.(88-90)aaG>aaC	p.K30N	CTC-429C10.2_ENST00000600329.1_RNA|ZNF649_ENST00000600738.1_Missense_Mutation_p.K30N	NM_023074.3	NP_075562.2	Q9BS31	ZN649_HUMAN	zinc finger protein 649	30	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)		GGTACAGGTCCTTCTGAGCAG	0.547																																					p.K30N		Atlas-SNP	.											.	ZNF649	72	.	0			c.G90C						PASS	.						189	174	179					19																	52400157		2203	4300	6503	SO:0001583	missense	65251	exon3			CAGGTCCTTCTGA	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.90G>C	chr19.hg19:g.52400157C>G	ENSP00000347043:p.Lys30Asn	147.0	0.0	.		127.0	47.0	.	NM_023074	A8MYJ5|B2RDC4|Q9H9N2	Missense_Mutation	SNP	ENST00000354957.3	hg19	CCDS12843.1	.	.	.	.	.	.	.	.	.	.	C	6.417	0.445140	0.12164	.	.	ENSG00000198093	ENST00000354957	T	0.02944	4.1	2.51	2.51	0.30379	Krueppel-associated box (4);	.	.	.	.	T	0.16471	0.0396	H	0.95079	3.62	0.19945	N	0.99994	D	0.58620	0.983	P	0.57502	0.822	T	0.05162	-1.0902	9	0.87932	D	0	.	8.5183	0.33259	0.0:1.0:0.0:0.0	.	30	Q9BS31	ZN649_HUMAN	N	30	ENSP00000347043:K30N	ENSP00000347043:K30N	K	-	3	2	ZNF649	57091969	0.071000	0.21146	0.242000	0.24170	0.005000	0.04900	0.529000	0.23019	1.402000	0.46780	0.543000	0.68304	AAG	.	.	.	none		0.547	ZNF649-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461097.1	NM_023074		G	52400157	C	G	52400157	3	3	24	1	0	0	0	0	1	0	0	0	18076	680	24	4	1439	4	ZNF649	19	52400157	Missense_Mutation	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10	10696403	52400157	6728826	89	1747											
U2AF2	11338	hgsc.bcm.edu	37	chr19	56180949	56180949	+	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	gctgctggacgacgaggagtAtgaggagatcgtggaggacg	10	6	19	6	4	0	2	0	1	0	1	1	9	0	6	0	5	1	3	0	5	1	1			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr19:56180949A>T	ENST00000308924.4	+	11	1224	c.1184A>T	c.(1183-1185)tAt>tTt	p.Y395F	CTD-2537I9.12_ENST00000589456.1_RNA|U2AF2_ENST00000590551.1_Missense_Mutation_p.Y227F|U2AF2_ENST00000450554.2_Missense_Mutation_p.Y391F|CTD-2537I9.13_ENST00000592252.1_RNA|CTD-2537I9.12_ENST00000585940.1_RNA			P26368	U2AF2_HUMAN	U2 small nuclear RNA auxiliary factor 2	395	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.Y395F(1)		biliary_tract(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(2)	21		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		GACGAGGAGTATGAGGAGATC	0.642																																					p.Y395F		Atlas-SNP	.											U2AF2,NS,carcinoma,0,1	U2AF2	62	.	1	Substitution - Missense(1)	lung(1)	c.A1184T						PASS	.						154	136	142					19																	56180949		2203	4300	6503	SO:0001583	missense	11338	exon11			AGGAGTATGAGGA	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.1184A>T	chr19.hg19:g.56180949A>T	ENSP00000307863:p.Tyr395Phe	173.0	0.0	.		145.0	62.0	.	NM_007279	Q96HC5	Missense_Mutation	SNP	ENST00000308924.4	hg19	CCDS12933.1	.	.	.	.	.	.	.	.	.	.	A	16.71	3.199227	0.58126	.	.	ENSG00000063244	ENST00000308924;ENST00000450554	T;T	0.15834	2.43;2.39	4.72	4.72	0.59763	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.000000	0.64402	D	0.000001	T	0.32346	0.0826	L	0.56396	1.775	0.80722	D	1	B;P	0.39326	0.214;0.668	P;P	0.54856	0.462;0.762	T	0.02244	-1.1189	10	0.29301	T	0.29	-7.7435	13.4951	0.61421	1.0:0.0:0.0:0.0	.	395;391	P26368;P26368-2	U2AF2_HUMAN;.	F	395;391	ENSP00000307863:Y395F;ENSP00000388475:Y391F	ENSP00000307863:Y395F	Y	+	2	0	U2AF2	60872761	1.000000	0.71417	0.884000	0.34674	0.008000	0.06430	8.801000	0.91905	1.911000	0.55334	0.533000	0.62120	TAT	.	.	.	none		0.642	U2AF2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453599.1	NM_007279		T	56180949	A	T	56180949	3	4	24	1	0	0	0	0	1	0	0	0	16835	449	16	5	1226	5	U2AF2	19	56180949	Missense_Mutation	SNP	A	TCGA-4A-A93W-01A-11D-A36X-10	3780792	56180949	2948034	90	1748											
ZNF543	125919	hgsc.bcm.edu	37	chr19	57840518	57840518	+	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	tcatactgggagaaaccctaCcattgtaacagatgtgggaa	14	9	10	8	0	1	2	1	0	0	2	1	4	1	3	2	2	4	1	2	2	5	4			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr19:57840518C>A	ENST00000321545.4	+	4	2033	c.1688C>A	c.(1687-1689)aCc>aAc	p.T563N		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	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)			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)		AGAAACCCTACCATTGTAACA	0.428																																					p.T563N		Atlas-SNP	.											.	ZNF543	61	.	0			c.C1688A						PASS	.						94	87	89					19																	57840518		2203	4300	6503	SO:0001583	missense	125919	exon4			ACCCTACCATTGT	AL834534	CCDS33130.1	19q13.43	2013-01-08				ENSG00000178229		"Zinc fingers, C2H2-type", "-"	25281	protein-coding gene	gene with protein product							Standard	NM_213598		Approved	DKFZp434H055	uc002qoi.2	Q08ER8		ENST00000321545.4:c.1688C>A	chr19.hg19:g.57840518C>A	ENSP00000322545:p.Thr563Asn	165.0	0.0	.		230.0	11.0	.	NM_213598	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	Missense_Mutation	SNP	ENST00000321545.4	hg19	CCDS33130.1	.	.	.	.	.	.	.	.	.	.	C	9.223	1.033879	0.19590	.	.	ENSG00000178229	ENST00000321545	T	0.06608	3.28	2.35	-1.29	0.09288	.	.	.	.	.	T	0.01976	0.0062	N	0.01576	-0.805	0.09310	N	1	B	0.32731	0.382	B	0.29176	0.099	T	0.41324	-0.9515	9	0.72032	D	0.01	.	3.2089	0.06676	0.1777:0.2393:0.0:0.5829	.	563	Q08ER8	ZN543_HUMAN	N	563	ENSP00000322545:T563N	ENSP00000322545:T563N	T	+	2	0	ZNF543	62532330	0.000000	0.05858	0.000000	0.03702	0.175000	0.22909	-0.247000	0.08866	-0.402000	0.07633	-0.379000	0.06801	ACC	.	.	.	none		0.428	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865		A	57840518	C	A	57840518	3	1	24	1	0	0	0	0	1	0	0	0	17988	507	18	4	1702	4	ZNF543	19	57840518	Missense_Mutation	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10	1659569	57840518	1288465	91	1749											
SMOX	54498	hgsc.bcm.edu	37	chr20	4167467	4167467	+	Intron	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	cagcccctggatgctaacagGggcgccgtaaaggtttgtca	9	8	13	11	2	1	0	1	0	0	0	1	1	1	1	3	4	3	3	3	4	3	3			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr20:4167467G>C	ENST00000305958.4	+	7	1755				SMOX_ENST00000339123.6_Intron|SMOX_ENST00000278795.3_Missense_Mutation_p.R483S|SMOX_ENST00000379460.2_Intron|SMOX_ENST00000346595.2_Intron	NM_175839.2	NP_787033.1	Q9NWM0	SMOX_HUMAN	spermine oxidase						cellular nitrogen compound metabolic process (GO:0034641)|oxidation-reduction process (GO:0055114)|polyamine biosynthetic process (GO:0006596)|polyamine catabolic process (GO:0006598)|polyamine metabolic process (GO:0006595)|small molecule metabolic process (GO:0044281)|spermine catabolic process (GO:0046208)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	N1-acetylspermine:oxygen oxidoreductase (N1-acetylspermidine-forming) activity (GO:0052895)|norspermine:oxygen oxidoreductase activity (GO:0052894)|polyamine oxidase activity (GO:0046592)|spermine:oxygen oxidoreductase (spermidine-forming) activity (GO:0052901)			breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(7)|lung(5)|skin(2)|urinary_tract(1)	26					Spermine(DB00127)	atgctaacaggggcgccgtaa	0.473																																					p.R536S		Atlas-SNP	.											.	SMOX	119	.	0			c.G1608C						PASS	.						70	69	69					20																	4167467		2203	4300	6503	SO:0001627	intron_variant	54498	exon7			TAACAGGGGCGCC	AK000753	CCDS13075.1, CCDS13076.1, CCDS13077.1, CCDS13078.1, CCDS74702.1	20p13	2003-10-15	2003-10-15	2003-10-15	ENSG00000088826	ENSG00000088826			15862	protein-coding gene	gene with protein product		615854	"chromosome 20 open reading frame 16"	C20orf16		11454677, 12398765	Standard	NM_175839		Approved	FLJ20746, dJ779E11.1, PAO, PAOh1, MGC1010, SMO	uc002wkp.3	Q9NWM0	OTTHUMG00000031777	ENST00000305958.4:c.1531-450G>C	chr20.hg19:g.4167467G>C		54.0	0.0	.		92.0	30.0	.	NM_001270691	A2A2P5|A2A2P6|A8BE87|D3DVZ4|Q5TE26|Q5TE27|Q6UY28|Q8IX00|Q96LC3|Q96LC4|Q96QT3|Q9BW38|Q9H6H1|Q9NP51|Q9NPY1|Q9NPY2	Missense_Mutation	SNP	ENST00000305958.4	hg19	CCDS13075.1	.	.	.	.	.	.	.	.	.	.	G	5.907	0.351463	0.11182	.	.	ENSG00000088826	ENST00000278795;ENST00000457205	T;T	0.28895	1.59;1.6	3.49	0.43	0.16515	.	.	.	.	.	T	0.12008	0.0292	.	.	.	0.80722	D	1	B;B	0.30889	0.299;0.072	B;B	0.15052	0.012;0.008	T	0.19614	-1.0300	8	0.10377	T	0.69	.	5.7954	0.18383	0.3566:0.0:0.6434:0.0	.	536;483	Q9NWM0-6;Q9NWM0-4	.;.	S	483;393	ENSP00000278795:R483S;ENSP00000407269:R393S	ENSP00000278795:R483S	R	+	3	2	SMOX	4115467	1.000000	0.71417	0.992000	0.48379	0.923000	0.55619	2.300000	0.43620	0.127000	0.18452	-0.140000	0.14226	AGG	.	.	.	none		0.473	SMOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077806.1	NM_175842		C	4167467	G	C	4167467	1	2	24	0	1	0	0	0	0	0	0	0	14816	1223	43	4		4	SMOX	20	4167467	Intron	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10		4167467	58858053	92	1750											
PAX1	5075	hgsc.bcm.edu	37	chr20	21695396	21695396	+	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	tggccggacccaccacacttCctttattggtctgggttttt	5	15	9	12	1	1	0	0	0	1	0	2	1	2	1	4	4	0	1	4	4	1	6	rs368125977		TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr20:21695396C>T	ENST00000398485.2	+	5	1614	c.1560C>T	c.(1558-1560)ttC>ttT	p.F520F	PAX1_ENST00000444366.2_3'UTR	NM_001257096.1|NM_006192.4	NP_001244025.1|NP_006183.2	P15863	PAX1_HUMAN	paired box 1	520					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						CACCACACTTCCTTTATTGGT	0.632																																					p.F520F		Atlas-SNP	.											.	PAX1	152	.	0			c.C1560T						PASS	.						62	56	58					20																	21695396		2203	4300	6503	SO:0001819	synonymous_variant	5075	exon5			ACACTTCCTTTAT		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.1560C>T	chr20.hg19:g.21695396C>T		76.0	0.0	.		88.0	59.0	.	NM_006192	B4E0D6|Q642X9|Q6NTC0|Q9Y558	Silent	SNP	ENST00000398485.2	hg19	CCDS13146.2																																																																																			.	.	.	weak		0.632	PAX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078282.3			T	21695396	C	T	21695396	2	4	24	1	0	0	0	0	0	0	0	1	11485	854	30	2		2	PAX1	20	21695396	Silent	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10	17527929	21695396	41330124	93	1751											
SLC32A1	140679	hgsc.bcm.edu	37	chr20	37356236	37356236	+	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	acgaggagaatgaagacggcGaggtggtgcgcgtgcgggac	10	4	20	7	6	0	3	0	1	0	2	0	7	0	4	0	5	2	0	0	5	2	0			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr20:37356236G>T	ENST00000217420.1	+	2	795	c.532G>T	c.(532-534)Gag>Tag	p.E178*		NM_080552.2	NP_542119.1	Q9H598	VIAAT_HUMAN	solute carrier family 32 (GABA vesicular transporter), member 1	178					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)	p.E178*(1)		breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(16)|urinary_tract(1)	38		Myeloproliferative disorder(115;0.00878)			Glycine(DB00145)	TGAAGACGGCGAGGTGGTGCG	0.637																																					p.E178X		Atlas-SNP	.											SLC32A1,NS,carcinoma,0,2	SLC32A1	81	.	1	Substitution - Nonsense(1)	lung(1)	c.G532T						PASS	.						79	63	68					20																	37356236		2203	4300	6503	SO:0001587	stop_gained	140679	exon2			GACGGCGAGGTGG	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.532G>T	chr20.hg19:g.37356236G>T	ENSP00000217420:p.Glu178*	30.0	0.0	.		44.0	2.0	.	NM_080552	Q8N489	Nonsense_Mutation	SNP	ENST00000217420.1	hg19	CCDS13307.1	.	.	.	.	.	.	.	.	.	.	G	37	6.235027	0.97399	.	.	ENSG00000101438	ENST00000217420	.	.	.	4.13	3.16	0.36331	.	0.058315	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	-13.9018	11.7879	0.52053	0.0:0.1796:0.8204:0.0	.	.	.	.	X	178	.	ENSP00000217420:E178X	E	+	1	0	SLC32A1	36789650	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	4.814000	0.62627	1.081000	0.41110	-0.302000	0.09304	GAG	.	.	.	none		0.637	SLC32A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079206.1	NM_080552		T	37356236	G	T	37356236	4	4	24	1	0	0	0	0	0	1	0	0	14578	1059	37	4	538	4	SLC32A1	20	37356236	Nonsense_Mutation	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10	15660840	37356236	25669284	94	1752											
PTPRT	11122	hgsc.bcm.edu	37	chr20	40790019	40790019	+	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	tcctccttgaacccgtagccCtggcctctcttcatctgcgt	4	13	7	17	2	3	1	1	1	2	0	6	1	5	1	5	1	3	1	5	1	2	3			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr20:40790019C>G	ENST00000373187.1	-	17	2654	c.2655G>C	c.(2653-2655)caG>caC	p.Q885H	PTPRT_ENST00000373190.1_Missense_Mutation_p.Q884H|PTPRT_ENST00000356100.2_Missense_Mutation_p.Q894H|PTPRT_ENST00000373201.1_Missense_Mutation_p.Q875H|PTPRT_ENST00000373184.1_Missense_Mutation_p.Q875H|PTPRT_ENST00000373198.4_Missense_Mutation_p.Q904H|PTPRT_ENST00000373193.3_Missense_Mutation_p.Q888H			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	885					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)				ACCCGTAGCCCTGGCCTCTCT	0.557																																					p.Q904H		Atlas-SNP	.											.	PTPRT	372	.	0			c.G2712C						PASS	.						64	68	67					20																	40790019		2105	4252	6357	SO:0001583	missense	11122	exon18			GTAGCCCTGGCCT	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.2655G>C	chr20.hg19:g.40790019C>G	ENSP00000362283:p.Gln885His	108.0	0.0	.		148.0	48.0	.	NM_133170	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	ENST00000373187.1	hg19	CCDS42874.1	.	.	.	.	.	.	.	.	.	.	C	17.72	3.459433	0.63401	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	T;T;T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54;1.54;1.54	5.2	0.45	0.16624	.	0.057706	0.64402	N	0.000001	T	0.38188	0.1031	L	0.54323	1.7	0.58432	D	0.999998	P;P	0.52692	0.955;0.845	P;B	0.56088	0.791;0.382	T	0.17961	-1.0352	10	0.87932	D	0	.	8.101	0.30857	0.0:0.6568:0.1185:0.2247	.	907;885	O14522-1;O14522	.;PTPRT_HUMAN	H	884;885;888;894;907;875;875	ENSP00000362286:Q884H;ENSP00000362283:Q885H;ENSP00000362289:Q888H;ENSP00000348408:Q894H;ENSP00000362294:Q907H;ENSP00000362280:Q875H;ENSP00000362297:Q875H	ENSP00000348408:Q894H	Q	-	3	2	PTPRT	40223433	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.886000	0.28241	0.201000	0.20466	-0.182000	0.12963	CAG	.	.	.	none		0.557	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			G	40790019	C	G	40790019	3	3	24	1	0	0	0	0	1	0	0	0	12825	680	24	4	1730	4	PTPRT	20	40790019	Missense_Mutation	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10	3433783	40790019	22235501	95	1753											
PTGIS	5740	hgsc.bcm.edu	37	chr20	48129710	48129710	+	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	cgcaggttgaattctcgcccGtctgccatgggcatggccag	6	9	13	13	3	2	1	0	1	2	0	3	1	2	1	3	3	1	3	3	3	1	2	rs561620152		TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr20:48129710G>A	ENST00000244043.4	-	8	1142	c.1113C>T	c.(1111-1113)gaC>gaT	p.D371D	PTGIS_ENST00000478971.1_5'UTR	NM_000961.3	NP_000952.1	Q16647	PTGIS_HUMAN	prostaglandin I2 (prostacyclin) synthase	371					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)	p.D371D(1)		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)	ATTCTCGCCCGTCTGCCATGG	0.602													G|||	1	0.000199681	0	0.0014	5008	,	,		16866	0		0	False		,,,				2504	0				p.D371D		Atlas-SNP	.											PTGIS,colon,carcinoma,0,1	PTGIS	60	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1113T						PASS	.						97	86	89					20																	48129710		2203	4300	6503	SO:0001819	synonymous_variant	5740	exon8			TCGCCCGTCTGCC		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.1113C>T	chr20.hg19:g.48129710G>A		75.0	0.0	.		109.0	34.0	.	NM_000961	Q3MII8|Q9HAX2|Q9HAX3|Q9HAX4	Silent	SNP	ENST00000244043.4	hg19	CCDS13419.1																																																																																			.	.	.	none		0.602	PTGIS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080496.2			A	48129710	G	A	48129710	2	1	24	1	0	0	0	0	0	0	0	1	12763	1136	40	1		1	PTGIS	20	48129710	Silent	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10	7339691	48129710	14895810	96	1754											
PHACTR3	116154	hgsc.bcm.edu	37	chr20	58415459	58415459	+	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	cagagcaggaagaaagaagaGaaatcaagcaaagattgaca	22	3	11	5	0	1	6	1	1	0	5	1	8	1	7	0	1	2	2	0	1	6	1			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr20:58415459G>A	ENST00000371015.1	+	10	1887	c.1420G>A	c.(1420-1422)Gaa>Aaa	p.E474K	PHACTR3_ENST00000359926.3_Missense_Mutation_p.E471K|PHACTR3_ENST00000355648.4_Missense_Mutation_p.E433K|PHACTR3_ENST00000395639.4_Missense_Mutation_p.E363K|PHACTR3_ENST00000395636.2_Missense_Mutation_p.E433K|PHACTR3_ENST00000541461.1_Missense_Mutation_p.E433K|PHACTR3_ENST00000361300.4_Missense_Mutation_p.E363K	NM_001281507.1|NM_080672.3	NP_001268436.1|NP_542403.1	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3	474	Required for PP1CA binding and inhibition of PP1 activity.					nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|liver(2)|lung(32)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	59	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			AGAAAGAAGAGAAATCAAGCA	0.358																																					p.E474K		Atlas-SNP	.											.	PHACTR3	104	.	0			c.G1420A						PASS	.						138	129	132					20																	58415459		2203	4300	6503	SO:0001583	missense	116154	exon10			AGAAGAGAAATCA	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.1420G>A	chr20.hg19:g.58415459G>A	ENSP00000360054:p.Glu474Lys	244.0	0.0	.		334.0	87.0	.	NM_080672	B1AKX0|B1AN68|B1AN69|B2RB46|Q32P33|Q707P6|Q9H4T4	Missense_Mutation	SNP	ENST00000371015.1	hg19	CCDS13480.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.700042	0.88924	.	.	ENSG00000087495	ENST00000359926;ENST00000371015;ENST00000395639;ENST00000541461;ENST00000355648;ENST00000395636;ENST00000361300	T;T;T;T;T;T;T	0.37058	1.51;1.4;1.22;1.53;1.53;1.53;1.22	5.55	4.59	0.56863	.	0.000000	0.85682	D	0.000000	T	0.59676	0.2211	M	0.71581	2.175	0.80722	D	1	D;D;P;D	0.89917	1.0;0.999;0.869;0.987	D;D;P;D	0.85130	0.997;0.996;0.587;0.937	T	0.64198	-0.6464	10	0.62326	D	0.03	-21.4747	15.4682	0.75419	0.0:0.139:0.861:0.0	.	433;363;474;471	B1AN68;Q96KR7-3;Q96KR7;B1AKX0	.;.;PHAR3_HUMAN;.	K	471;474;363;433;433;433;363	ENSP00000353002:E471K;ENSP00000360054:E474K;ENSP00000379001:E363K;ENSP00000442483:E433K;ENSP00000347866:E433K;ENSP00000378998:E433K;ENSP00000354555:E363K	ENSP00000347866:E433K	E	+	1	0	PHACTR3	57848854	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	9.609000	0.98334	1.333000	0.45449	0.655000	0.94253	GAA	.	.	.	none		0.358	PHACTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079923.3	NM_080672		A	58415459	G	A	58415459	3	1	24	1	0	0	0	0	1	0	0	0	11818	943	33	2	1458	2	PHACTR3	20	58415459	Missense_Mutation	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10	10285749	58415459	4610061	97	1755											
C22orf42	150297	hgsc.bcm.edu	37	chr22	32555136	32555136	+	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	ctcatggcagggtcccacatCtggcctgcagcagtcacagt	8	8	11	14	0	3	0	2	0	1	0	4	0	4	0	2	3	2	3	2	3	0	0			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr22:32555136C>T	ENST00000382097.3	-	1	139	c.67G>A	c.(67-69)Gat>Aat	p.D23N	RP1-90G24.8_ENST00000426354.1_lincRNA	NM_001010859.1	NP_001010859.1	Q6IC83	CV042_HUMAN	chromosome 22 open reading frame 42	23										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(2)	24						GGTCCCACATCTGGCCTGCAG	0.557																																					p.D23N		Atlas-SNP	.											.	C22orf42	37	.	0			c.G67A						PASS	.						78	72	74					22																	32555136		2203	4300	6503	SO:0001583	missense	150297	exon1			CCACATCTGGCCT	BC040263	CCDS33639.1	22q12.3	2009-03-05			ENSG00000205856	ENSG00000205856			27160	protein-coding gene	gene with protein product						12477932	Standard	XM_005261369		Approved		uc003amd.3	Q6IC83	OTTHUMG00000030380	ENST00000382097.3:c.67G>A	chr22.hg19:g.32555136C>T	ENSP00000371529:p.Asp23Asn	62.0	0.0	.		80.0	34.0	.	NM_001010859	A4QPH5	Missense_Mutation	SNP	ENST00000382097.3	hg19	CCDS33639.1	.	.	.	.	.	.	.	.	.	.	C	3.630	-0.075776	0.07184	.	.	ENSG00000205856	ENST00000382097	T	0.26067	1.76	0.131	-0.261	0.12963	.	.	.	.	.	T	0.17534	0.0421	N	0.08118	0	0.09310	N	1	P	0.46395	0.877	P	0.53518	0.728	T	0.13899	-1.0492	8	0.54805	T	0.06	.	.	.	.	.	23	Q6IC83	CV042_HUMAN	N	23	ENSP00000371529:D23N	ENSP00000371529:D23N	D	-	1	0	C22orf42	30885136	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-1.069000	0.03444	-1.313000	0.02303	-1.326000	0.01283	GAT	.	.	.	none		0.557	C22orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075268.2	NM_001010859		T	32555136	C	T	32555136	3	4	24	1	0	0	0	0	1	0	0	0	2151	913	32	2	724	2	C22orf42	22	32555136	Missense_Mutation	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10		32555136	18749430	98	1756											
NOL12	79159	hgsc.bcm.edu	37	chr22	38087326	38087326	+	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	gccgtctcacaggcaaagcaCggcacagcggggagtgagac	11	3	15	12	3	1	1	1	1	1	1	2	3	1	2	1	4	2	3	1	4	1	0			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chr22:38087326C>A	ENST00000359114.4	+	6	695	c.625C>A	c.(625-627)Cgg>Agg	p.R209R	NOL12_ENST00000493862.1_3'UTR	NM_024313.2	NP_077289.1	Q9UGY1	NOL12_HUMAN	nucleolar protein 12	209						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|rRNA binding (GO:0019843)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)	8	Melanoma(58;0.0574)					AGGCAAAGCACGGCACAGCGG	0.657																																					p.R209R		Atlas-SNP	.											.	NOL12	22	.	0			c.C625A						PASS	.						39	39	39					22																	38087326		2203	4300	6503	SO:0001819	synonymous_variant	79159	exon6			AAAGCACGGCACA	Z83844	CCDS13955.1	22q13.1	2012-05-02			ENSG00000256872	ENSG00000273899			28585	protein-coding gene	gene with protein product						12477932	Standard	NM_024313		Approved	MGC3731, Nop25, RRP17	uc003atp.3	Q9UGY1	OTTHUMG00000150660	ENST00000359114.4:c.625C>A	chr22.hg19:g.38087326C>A		253.0	1.0	.		240.0	108.0	.	NM_024313		Silent	SNP	ENST00000359114.4	hg19	CCDS13955.1																																																																																			.	.	.	none		0.657	NOL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319476.1	NM_024313		A	38087326	C	A	38087326	2	1	24	1	0	0	0	0	0	0	0	1	10529	527	19	4		4	NOL12	22	38087326	Silent	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10	5532190	38087326	13217240	99	1757											
HUWE1	10075	hgsc.bcm.edu	37	chrX	53566667	53566667	+	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	tctagttcctttagacactcCccaagcatgtcccacagctc	9	11	5	16	0	1	1	0	0	1	1	5	1	4	1	4	0	2	3	4	0	3	4			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chrX:53566667C>A	ENST00000342160.3	-	74	12040	c.11583G>T	c.(11581-11583)ggG>ggT	p.G3861G	HUWE1_ENST00000262854.6_Silent_p.G3861G			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	3861					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						TTAGACACTCCCCAAGCATGT	0.562																																					p.G3861G		Atlas-SNP	.											.	HUWE1	724	.	0			c.G11583T						PASS	.						118	95	103					X																	53566667		2203	4300	6503	SO:0001819	synonymous_variant	10075	exon75			ACACTCCCCAAGC	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.11583G>T	chrX.hg19:g.53566667C>A		100.0	0.0	.		107.0	52.0	.	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Silent	SNP	ENST00000342160.3	hg19	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	C	10.57	1.386343	0.25031	.	.	ENSG00000086758	ENST00000427052;ENST00000426907	.	.	.	5.81	1.61	0.23674	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	5.6485	0.17602	0.0:0.3479:0.3332:0.3189	.	.	.	.	X	2895;684	.	ENSP00000403236:G684X	G	-	1	0	HUWE1	53583392	0.730000	0.28100	1.000000	0.80357	0.992000	0.81027	-0.225000	0.09151	0.149000	0.19098	0.600000	0.82982	GGA	.	.	.	none		0.562	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		A	53566667	C	A	53566667	2	1	24	1	0	0	0	0	0	0	0	1	7468	610	22	4		4	HUWE1	23	53566667	Silent	SNP	C	TCGA-4A-A93W-01A-11D-A36X-10		53566667	101703893	100	1758											
MAGEE1	57692	hgsc.bcm.edu	37	chrX	75651091	75651091	+	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	atatgtggccagaatccacaGaaaggaaccacaggactggc	15	5	11	10	0	0	2	0	0	0	2	1	4	1	4	3	4	1	0	3	4	4	1			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chrX:75651091G>A	ENST00000361470.2	+	1	3046	c.2768G>A	c.(2767-2769)aGa>aAa	p.R923K		NM_020932.2	NP_065983.1	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	923	Interaction with DTNA. {ECO:0000250}.|MAGE 2. {ECO:0000255|PROSITE- ProRule:PRU00127}.					dendrite (GO:0030425)|dystrophin-associated glycoprotein complex (GO:0016010)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	51						AGAATCCACAGAAAGGAACCA	0.493																																					p.R923K		Atlas-SNP	.											.	MAGEE1	236	.	0			c.G2768A						PASS	.						71	66	68					X																	75651091		2203	4300	6503	SO:0001583	missense	57692	exon1			TCCACAGAAAGGA	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.2768G>A	chrX.hg19:g.75651091G>A	ENSP00000354912:p.Arg923Lys	426.0	0.0	.		367.0	130.0	.	NM_020932	Q5JXC7|Q86TG0|Q8TD92|Q9H216	Missense_Mutation	SNP	ENST00000361470.2	hg19	CCDS14433.1	.	.	.	.	.	.	.	.	.	.	.	4.934	0.173547	0.09391	.	.	ENSG00000198934	ENST00000361470	T	0.03272	3.99	2.21	1.33	0.21861	.	.	.	.	.	T	0.01353	0.0044	N	0.04508	-0.205	0.22001	N	0.999426	B	0.27286	0.174	B	0.19148	0.024	T	0.44757	-0.9307	9	0.02654	T	1	.	4.1401	0.10189	0.216:0.0:0.784:0.0	.	923	Q9HCI5	MAGE1_HUMAN	K	923	ENSP00000354912:R923K	ENSP00000354912:R923K	R	+	2	0	MAGEE1	75567495	1.000000	0.71417	0.766000	0.31476	0.977000	0.68977	0.700000	0.25601	0.369000	0.24510	0.529000	0.55759	AGA	.	.	.	none		0.493	MAGEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057298.1	NM_020932		A	75651091	G	A	75651091	3	1	24	1	0	0	0	0	1	0	0	0	9192	942	33	2	2770	2	MAGEE1	23	75651091	Missense_Mutation	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10	22084424	75651091	79619469	101	1759											
TCEAL3	85012	hgsc.bcm.edu	37	chrX	102864302	102864302	+	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	ccgaaaagcgcccggctgaaGattatgtgccccggaaagca	12	5	12	12	4	0	2	0	1	0	1	0	4	0	3	4	2	3	2	4	2	5	1			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chrX:102864302G>C	ENST00000372628.1	+	3	668	c.310G>C	c.(310-312)Gat>Cat	p.D104H	TCEAL3_ENST00000372627.5_Missense_Mutation_p.D104H|TCEAL3_ENST00000243286.3_Missense_Mutation_p.D104H|TCEAL3_ENST00000477014.1_Intron			Q969E4	TCAL3_HUMAN	transcription elongation factor A (SII)-like 3	104					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						CCCGGCTGAAGATTATGTGCC	0.607																																					p.D104H		Atlas-SNP	.											.	TCEAL3	24	.	0			c.G310C						PASS	.						80	82	82					X																	102864302		2203	4300	6503	SO:0001583	missense	85012	exon3			GCTGAAGATTATG	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.310G>C	chrX.hg19:g.102864302G>C	ENSP00000361711:p.Asp104His	318.0	0.0	.		275.0	120.0	.	NM_001006933	D3DXA4	Missense_Mutation	SNP	ENST00000372628.1	hg19	CCDS14511.1	.	.	.	.	.	.	.	.	.	.	G	19.58	3.854858	0.71719	.	.	ENSG00000196507	ENST00000372628;ENST00000372627;ENST00000243286	T;T;T	0.10573	2.86;2.86;2.86	4.47	4.47	0.54385	.	0.198219	0.25114	N	0.033032	T	0.28067	0.0692	M	0.68952	2.095	0.38999	D	0.959307	D	0.71674	0.998	D	0.68943	0.961	T	0.01998	-1.1232	10	0.72032	D	0.01	.	11.4217	0.49985	0.0:0.0:1.0:0.0	.	104	Q969E4	TCAL3_HUMAN	H	104	ENSP00000361711:D104H;ENSP00000361710:D104H;ENSP00000243286:D104H	ENSP00000243286:D104H	D	+	1	0	TCEAL3	102750958	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	2.021000	0.41020	2.468000	0.83385	0.538000	0.68166	GAT	.	.	.	none		0.607	TCEAL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057737.1	NM_032926		C	102864302	G	C	102864302	3	2	24	1	0	0	0	0	1	0	0	0	15684	942	33	4	312	4	TCEAL3	23	102864302	Missense_Mutation	SNP	G	TCGA-4A-A93W-01A-11D-A36X-10	27213211	102864302	52406258	102	1760											
SASH3	54440	hgsc.bcm.edu	37	chrX	128922424	128922424	+	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	cagattccagaagatgactcAggtgtccccaccccagaaga	13	6	9	13	0	1	6	1	1	0	5	3	6	3	6	5	1	0	0	5	1	2	1			TCGA-4A-A93W-01A-11D-A36X-10	TCGA-4A-A93W-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c87c7ca-a0f4-4ba3-93f2-2d9f3a1db03a	afcc0a63-8340-47fc-a4da-380a1f4fda4a	g.chrX:128922424A>C	ENST00000356892.3	+	3	285	c.171A>C	c.(169-171)tcA>tcC	p.S57S		NM_018990.3	NP_061863.1	O75995	SASH3_HUMAN	SAM and SH3 domain containing 3	57					homeostasis of number of cells within a tissue (GO:0048873)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of immunoglobulin production (GO:0002639)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of organ growth (GO:0046622)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tumor necrosis factor production (GO:0032760)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	12						AAGATGACTCAGGTGTCCCCA	0.552																																					p.S57S		Atlas-SNP	.											.	SASH3	35	.	0			c.A171C						PASS	.						78	64	69					X																	128922424		2203	4300	6503	SO:0001819	synonymous_variant	54440	exon3			TGACTCAGGTGTC	BC051881	CCDS14614.1	Xq26	2013-01-10	2008-02-18	2008-02-18	ENSG00000122122	ENSG00000122122		"SAM and SH3 domain containing", "Sterile alpha motif (SAM) domain containing"	15975	protein-coding gene	gene with protein product		300441	"chromosome X open reading frame 9"	CXorf9		11470164	Standard	NM_018990		Approved	SLY, 753P9, SH3D6C, HACS2	uc004euu.3	O75995	OTTHUMG00000022372	ENST00000356892.3:c.171A>C	chrX.hg19:g.128922424A>C		404.0	0.0	.		350.0	27.0	.	NM_018990	A6NCH1|A8K7K8|Q5JZ38	Silent	SNP	ENST00000356892.3	hg19	CCDS14614.1																																																																																			.	.	.	none		0.552	SASH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058208.1	NM_018990		C	128922424	A	C	128922424	2	2	24	1	0	0	0	0	0	0	0	1	13862	175	7	5		5	SASH3	23	128922424	Silent	SNP	A	TCGA-4A-A93W-01A-11D-A36X-10	26058122	128922424	26348136	103	1761											
C1orf86	199990	hgsc.bcm.edu	37	chr1	2116880	2116880	+	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	agtggcgcctgccccacatcTcagacgcaacccacacgtag	10	5	9	17	3	1	1	1	0	1	1	2	1	1	1	4	1	2	2	4	1	2	1			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr1:2116880T>A	ENST00000400919.3	-	8	1349	c.281A>T	c.(280-282)gAg>gTg	p.E94V	RP11-181G12.2_ENST00000444529.1_RNA|RP11-181G12.2_ENST00000333854.2_RNA|RP11-181G12.2_ENST00000536678.1_RNA	NM_001282671.1	NP_001269600.1	Q6NZ36	FAP20_HUMAN	chromosome 1 open reading frame 86	93					cellular response to DNA damage stimulus (GO:0006974)|interstrand cross-link repair (GO:0036297)|translesion synthesis (GO:0019985)	cell junction (GO:0030054)|chromosome (GO:0005694)|Fanconi anaemia nuclear complex (GO:0043240)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|metal ion binding (GO:0046872)|polyubiquitin binding (GO:0031593)|ubiquitin binding (GO:0043130)			central_nervous_system(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4	all_cancers(77;0.000134)|all_epithelial(69;4.45e-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;1.09e-37)|OV - Ovarian serous cystadenocarcinoma(86;1.5e-23)|GBM - Glioblastoma multiforme(42;1.61e-08)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00437)|STAD - Stomach adenocarcinoma(132;0.0134)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)		GCCCCACATCTCAGACGCAAC	0.567																																					p.E177V		Atlas-SNP	.											.	C1orf86	20	.	0			c.A530T						PASS	.						131	109	116					1																	2116880		692	1591	2283	SO:0001583	missense	199990	exon8			CACATCTCAGACG	AK126870	CCDS38.2, CCDS57965.1, CCDS72686.1, CCDS72687.1	1p36.33	2013-05-22			ENSG00000162585	ENSG00000162585			26428	protein-coding gene	gene with protein product		615183				14702039	Standard	NM_182533		Approved	FLJ31031, FAAP20	uc031pkt.1	Q6NZ36	OTTHUMG00000001404	ENST00000400919.3:c.281A>T	chr1.hg19:g.2116880T>A	ENSP00000383710:p.Glu94Val	317.0	0.0	.		192.0	168.0	.	NM_001146310	A6PW39|A6PW40|A6PW41|A8MQT6|F2Z2L4|Q6ZT64|Q71M24|Q96ND7	Missense_Mutation	SNP	ENST00000400919.3	hg19		.	.	.	.	.	.	.	.	.	.	T	7.453	0.643019	0.14451	.	.	ENSG00000162585	ENST00000400919	.	.	.	3.14	-1.25	0.09405	.	.	.	.	.	T	0.12135	0.0295	N	0.08118	0	0.09310	N	1	P	0.41848	0.763	B	0.35550	0.205	T	0.15492	-1.0435	8	0.87932	D	0	.	4.5477	0.12088	0.0:0.2199:0.228:0.552	.	177	Q6ZRT9	.	V	94	.	ENSP00000383710:E94V	E	-	2	0	C1orf86	2106740	0.006000	0.16342	0.000000	0.03702	0.010000	0.07245	0.022000	0.13511	-0.138000	0.11434	-0.366000	0.07423	GAG	.	.	.	none		0.567	C1orf86-202	KNOWN	basic	protein_coding	protein_coding		NM_182533		A	2116880	T	A	2116880	3	1	25	1	0	0	0	0	1	0	0	0	2065	1551	54	5	166	5	C1orf86	1	2116880	Missense_Mutation	SNP	T	TCGA-4A-A93X-01A-11D-A36X-10		2116880	247133741	1	1762											
ANKRD13C	81573	hgsc.bcm.edu	37	chr1	70819813	70819813	+	Silent	SNP	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	gggttggtgccggccagaagGgccggggactgggagttggc	5	6	22	8	2	0	1	0	0	0	1	0	3	0	3	3	8	1	2	3	8	1	2			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr1:70819813G>A	ENST00000370944.4	-	1	592	c.279C>T	c.(277-279)gcC>gcT	p.A93A	HHLA3_ENST00000531950.1_5'Flank|ANKRD13C_ENST00000262346.6_Silent_p.A93A|HHLA3_ENST00000370940.5_5'Flank|HHLA3_ENST00000432224.1_5'Flank|HHLA3_ENST00000359875.5_5'Flank|HHLA3_ENST00000361764.4_5'Flank	NM_030816.4	NP_110443.3	Q8N6S4	AN13C_HUMAN	ankyrin repeat domain 13C	93					protein retention in ER lumen (GO:0006621)|regulation of anoikis (GO:2000209)|regulation of receptor biosynthetic process (GO:0010869)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	receptor binding (GO:0005102)			endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|prostate(2)|skin(1)|urinary_tract(1)	19						CGGCCAGAAGGGCCGGGGACT	0.677																																					p.A93A		Atlas-SNP	.											.	ANKRD13C	36	.	0			c.C279T						PASS	.						40	53	49					1																	70819813		2203	4299	6502	SO:0001819	synonymous_variant	81573	exon1			CAGAAGGGCCGGG		CCDS648.2	1p32.3-p31.3	2013-01-10			ENSG00000118454	ENSG00000118454		"Ankyrin repeat domain containing"	25374	protein-coding gene	gene with protein product		615125				11230166	Standard	NM_030816		Approved	DKFZP566D1346, dJ677H15.3	uc001dex.4	Q8N6S4	OTTHUMG00000009343	ENST00000370944.4:c.279C>T	chr1.hg19:g.70819813G>A		91.0	0.0	.		92.0	79.0	.	NM_030816	B3KQ97|Q5VYH4|Q5VYH5|Q6PJE4|Q9H0N9	Silent	SNP	ENST00000370944.4	hg19	CCDS648.2																																																																																			.	.	.	none		0.677	ANKRD13C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025903.1	NM_030816		A	70819813	G	A	70819813	2	1	25	1	0	0	0	0	0	0	0	1	643	1219	43	2		2	ANKRD13C	1	70819813	Silent	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	68702933	70819813	178430808	2	1763											
FCER1A	2205	hgsc.bcm.edu	37	chr1	159277544	159277544	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgttccactacagctccgcGtgagaagtactggctacaat	10	10	10	11	2	0	1	0	1	0	1	2	2	2	1	2	1	4	4	2	1	5	4			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr1:159277544G>A	ENST00000368115.1	+	6	695	c.596G>A	c.(595-597)cGt>cAt	p.R199H	FCER1A_ENST00000368114.1_Missense_Mutation_p.R166H	NM_002001.3	NP_001992.1	P12319	FCERA_HUMAN	Fc fragment of IgE, high affinity I, receptor for; alpha polypeptide	199					activation of JUN kinase activity (GO:0007257)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|leukotriene biosynthetic process (GO:0019370)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-3 biosynthetic process (GO:0045401)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of type I hypersensitivity (GO:0001812)|serotonin secretion (GO:0001820)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	IgE receptor activity (GO:0019767)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(19)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	33	all_hematologic(112;0.0429)				Benzylpenicilloyl Polylysine(DB00895)|Omalizumab(DB00043)	ACAGCTCCGCGTGAGAAGTAC	0.413																																					p.R199H		Atlas-SNP	.											.	FCER1A	74	.	0			c.G596A						PASS	.						116	104	108					1																	159277544		2203	4300	6503	SO:0001583	missense	2205	exon6			CTCCGCGTGAGAA	BC015195	CCDS1184.1	1q23	2013-01-11			ENSG00000179639	ENSG00000179639		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3609	protein-coding gene	gene with protein product		147140		FCE1A		8245459	Standard	NM_002001		Approved		uc001ftq.3	P12319	OTTHUMG00000037176	ENST00000368115.1:c.596G>A	chr1.hg19:g.159277544G>A	ENSP00000357097:p.Arg199His	97.0	0.0	.		95.0	5.0	.	NM_002001		Missense_Mutation	SNP	ENST00000368115.1	hg19	CCDS1184.1	.	.	.	.	.	.	.	.	.	.	G	10.76	1.441382	0.25900	.	.	ENSG00000179639	ENST00000368115;ENST00000368114	T;T	0.02050	4.82;4.48	5.37	-8.56	0.00904	.	9.584880	0.00166	N	0.000000	T	0.00356	0.0011	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45963	-0.9225	10	0.42905	T	0.14	.	0.8386	0.01145	0.2503:0.329:0.2067:0.214	.	199	P12319	FCERA_HUMAN	H	199;166	ENSP00000357097:R199H;ENSP00000357096:R166H	ENSP00000357096:R166H	R	+	2	0	FCER1A	157544168	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.697000	0.05098	-1.271000	0.02430	-2.604000	0.00161	CGT	.	.	.	none		0.413	FCER1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090328.2	NM_002001		A	159277544	G	A	159277544	3	1	25	1	0	0	0	0	1	0	0	0	5781	1145	40	1	614	1	FCER1A	1	159277544	Missense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	88457731	159277544	89973077	3	1764											
ASAP2	8853	hgsc.bcm.edu	37	chr2	9528626	9528626	+	Silent	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	cctcccgcccagcctgcagcCcccagcaccaccagcgcccc	6	2	7	26	2	0	0	0	0	0	0	1	0	1	0	10	0	5	2	10	0	0	0			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr2:9528626C>T	ENST00000281419.3	+	22	2674	c.2334C>T	c.(2332-2334)gcC>gcT	p.A778A	ASAP2_ENST00000315273.4_Silent_p.A778A|ASAP2_ENST00000491413.1_3'UTR	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	778	Pro-rich.				positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						AGCCTGCAGCCCCCAGCACCA	0.582																																					p.A778A		Atlas-SNP	.											.	ASAP2	91	.	0			c.C2334T						PASS	.						26	31	29					2																	9528626		2203	4300	6503	SO:0001819	synonymous_variant	8853	exon22			TGCAGCCCCCAGC	AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2721	protein-coding gene	gene with protein product	"centaurin, beta 3"	603817	"development and differentiation enhancing factor 2"	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.2334C>T	chr2.hg19:g.9528626C>T		192.0	0.0	.		111.0	54.0	.	NM_001135191	D6W4Y8	Silent	SNP	ENST00000281419.3	hg19	CCDS1661.1																																																																																			.	.	.	none		0.582	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887		T	9528626	C	T	9528626	2	4	25	1	0	0	0	0	0	0	0	1	1011	610	22	2		2	ASAP2	2	9528626	Silent	SNP	C	TCGA-4A-A93X-01A-11D-A36X-10		9528626	233670747	4	1765											
CCDC121	79635	hgsc.bcm.edu	37	chr2	27850763	27850763	+	5'UTR	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	ctatgatacggtggaaggagCcttctggggccctcagcaaa	10	8	13	10	1	2	1	1	1	1	0	2	3	2	3	2	5	3	1	2	5	4	3	rs555033711	byFrequency	TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr2:27850763C>A	ENST00000324364.3	-	0	84				GPN1_ENST00000424214.1_5'Flank|CCDC121_ENST00000394775.3_Missense_Mutation_p.R130S|GPN1_ENST00000610189.1_5'Flank|GPN1_ENST00000264718.3_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|GPN1_ENST00000503738.1_5'Flank|GPN1_ENST00000458167.2_5'Flank|GPN1_ENST00000407583.3_5'Flank|ZNF512_ENST00000556601.1_Intron|GPN1_ENST00000515877.1_5'Flank	NM_024584.4	NP_078860.2	Q6ZUS5	CC121_HUMAN	coiled-coil domain containing 121											breast(1)|endometrium(3)|large_intestine(2)|lung(6)|prostate(2)	14	Acute lymphoblastic leukemia(172;0.155)					GTGGAAGGAGCCTTCTGGGGC	0.408													C|||	2	0.000399361	0	0	5008	,	,		20467	0		0	False		,,,				2504	0.002				p.R130S		Atlas-SNP	.											.	CCDC121	43	.	0			c.G390T						PASS	.						31	22	25					2																	27850763		692	1591	2283	SO:0001623	5_prime_UTR_variant	79635	exon2			AAGGAGCCTTCTG	AK125354	CCDS1759.1, CCDS46247.1	2p23.2	2008-02-05			ENSG00000176714	ENSG00000176714			25833	protein-coding gene	gene with protein product							Standard	NM_024584		Approved	FLJ43364, FLJ13646	uc002rld.3	Q6ZUS5	OTTHUMG00000128427	ENST00000324364.3:c.-97G>T	chr2.hg19:g.27850763C>A		90.0	0.0	.		80.0	24.0	.	NM_001142683	B3KW66|J3KQZ8|Q9H8G6	Missense_Mutation	SNP	ENST00000324364.3	hg19	CCDS1759.1	.	.	.	.	.	.	.	.	.	.	C	12.28	1.890746	0.33348	.	.	ENSG00000176714	ENST00000394775;ENST00000522876	.	.	.	4.67	-3.58	0.04597	.	.	.	.	.	T	0.15392	0.0371	N	0.19112	0.55	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.35574	-0.9783	8	0.05959	T	0.93	-2.1927	5.3223	0.15887	0.2861:0.4149:0.0:0.299	.	132	E5RHR4	.	S	130;132	.	ENSP00000412150:R130S	R	-	3	2	CCDC121	27704267	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.249000	0.00540	-0.367000	0.08052	-0.467000	0.05162	AGG	.	.	.	none		0.408	CCDC121-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250215.1	NM_024584		A	27850763	C	A	27850763	1	1	25	0	1	0	0	0	0	0	0	0	2759	738	26	4		4	CCDC121	2	27850763	5'UTR	SNP	C	TCGA-4A-A93X-01A-11D-A36X-10	18322137	27850763	215348610	5	1766											
IL1RL2	8808	hgsc.bcm.edu	37	chr2	102808484	102808484	+	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	ttaccaaatttatcagatgaGtacaagcaaatattacatct	17	13	4	7	0	2	2	1	1	1	1	2	2	2	2	1	0	4	2	1	0	8	6			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr2:102808484G>C	ENST00000264257.2	+	4	519	c.393G>C	c.(391-393)gaG>gaC	p.E131D	IL1RL2_ENST00000441515.2_Intron|IL1RL2_ENST00000539491.1_Missense_Mutation_p.E131D|IL1RL2_ENST00000481806.1_Intron	NM_003854.2	NP_003845.2	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2	131	Ig-like C2-type 2.				cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of T cell differentiation (GO:0045582)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)			breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|liver(2)|lung(8)|ovary(2)|prostate(1)	26						TATCAGATGAGTACAAGCAAA	0.373																																					p.E131D		Atlas-SNP	.											.	IL1RL2	118	.	0			c.G393C						PASS	.						108	104	105					2																	102808484		2203	4299	6502	SO:0001583	missense	8808	exon4			AGATGAGTACAAG	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.393G>C	chr2.hg19:g.102808484G>C	ENSP00000264257:p.Glu131Asp	372.0	0.0	.		316.0	147.0	.	NM_003854	A4FU63|Q13525|Q45H74|Q53TU8|Q587I8	Missense_Mutation	SNP	ENST00000264257.2	hg19	CCDS2056.1	.	.	.	.	.	.	.	.	.	.	G	11.27	1.590415	0.28357	.	.	ENSG00000115598	ENST00000264257;ENST00000421464;ENST00000539491	T;T;T	0.14516	2.5;2.5;2.5	4.87	-0.423	0.12325	Immunoglobulin subtype (1);Immunoglobulin-like (1);	0.696055	0.13195	N	0.406431	T	0.10078	0.0247	L	0.46157	1.445	0.09310	N	1	B	0.26708	0.157	B	0.29663	0.105	T	0.37174	-0.9717	10	0.19590	T	0.45	.	4.3376	0.11094	0.2773:0.3204:0.4023:0.0	.	131	Q9HB29	ILRL2_HUMAN	D	131	ENSP00000264257:E131D;ENSP00000387611:E131D;ENSP00000442184:E131D	ENSP00000264257:E131D	E	+	3	2	IL1RL2	102174916	0.000000	0.05858	0.069000	0.20011	0.782000	0.44232	-0.972000	0.03802	0.069000	0.16605	0.655000	0.94253	GAG	.	.	.	none		0.373	IL1RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253290.1	NM_003854		C	102808484	G	C	102808484	3	2	25	1	0	0	0	0	1	0	0	0	7671	1020	36	4	403	4	IL1RL2	2	102808484	Missense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	74957721	102808484	140390889	6	1767											
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160289282	160289282	+	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	aataacctgattggctgtcaTcagattcatcatcttcatca	12	14	5	10	0	7	2	6	1	1	1	7	2	7	2	1	1	1	1	1	1	2	4			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr2:160289282T>A	ENST00000392783.2	-	9	2381	c.1886A>T	c.(1885-1887)gAt>gTt	p.D629V	BAZ2B_ENST00000392782.1_Missense_Mutation_p.D627V|BAZ2B_ENST00000355831.2_Missense_Mutation_p.D629V|BAZ2B_ENST00000343439.5_Missense_Mutation_p.D627V	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	629	Asp/Glu-rich (acidic).				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						TTGGCTGTCATCAGAttcatc	0.313																																					p.D629V		Atlas-SNP	.											.	BAZ2B	196	.	0			c.A1886T						PASS	.						52	51	52					2																	160289282		1964	4171	6135	SO:0001583	missense	29994	exon9			CTGTCATCAGATT	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.1886A>T	chr2.hg19:g.160289282T>A	ENSP00000376534:p.Asp629Val	74.0	0.0	.		56.0	22.0	.	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	hg19	CCDS2209.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.733|9.733	1.162697|1.162697	0.21538|0.21538	.|.	.|.	ENSG00000123636|ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439|ENST00000441143	T;T;T;T|.	0.26518|.	2.59;2.59;2.59;1.73|.	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	0.473584|.	0.15421|.	U|.	0.263251|.	T|.	0.56046|.	0.1959|.	L|L	0.29908|0.29908	0.895|0.895	0.36147|0.36147	D|D	0.847176|0.847176	D;D;D;D;D|.	0.89917|.	1.0;0.999;0.998;0.996;0.993|.	D;D;D;D;P|.	0.79108|.	0.992;0.951;0.948;0.923;0.84|.	T|.	0.61019|.	-0.7147|.	10|.	0.54805|.	T|.	0.06|.	-7.9381|-7.9381	16.0396|16.0396	0.80654|0.80654	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	629;433;627;627;629|.	Q9UIF8-3;Q9UIF8-4;Q9UIF8-2;Q9UIF8-5;Q9UIF8|.	.;.;.;.;BAZ2B_HUMAN|.	V|C	627;629;629;627|60	ENSP00000376533:D627V;ENSP00000376534:D629V;ENSP00000348087:D629V;ENSP00000339670:D627V|.	ENSP00000339670:D627V|.	D|X	-|-	2|3	0|0	BAZ2B|BAZ2B	159997528|159997528	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	5.412000|5.412000	0.66392|0.66392	2.274000|2.274000	0.75844|0.75844	0.533000|0.533000	0.62120|0.62120	GAT|TGA	.	.	.	none		0.313	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			A	160289282	T	A	160289282	3	1	25	1	0	0	0	0	1	0	0	0	1332	1435	50	5	4736	5	BAZ2B	2	160289282	Missense_Mutation	SNP	T	TCGA-4A-A93X-01A-11D-A36X-10	57480798	160289282	82910091	7	1768											
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160289383	160289383	+	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	ttactactgggaatgtctgaAtctgttcctctgaattgttc	8	17	8	8	0	3	2	0	2	3	0	5	3	4	3	1	1	2	2	1	1	5	5			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr2:160289383A>T	ENST00000392783.2	-	9	2280	c.1785T>A	c.(1783-1785)gaT>gaA	p.D595E	BAZ2B_ENST00000392782.1_Missense_Mutation_p.D593E|BAZ2B_ENST00000355831.2_Missense_Mutation_p.D595E|BAZ2B_ENST00000343439.5_Missense_Mutation_p.D593E	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	595	Asp/Glu-rich (acidic).				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						GAATGTCTGAATCTGTTCCTC	0.378																																					p.D595E		Atlas-SNP	.											.	BAZ2B	196	.	0			c.T1785A						PASS	.						154	147	149					2																	160289383		1947	4173	6120	SO:0001583	missense	29994	exon9			GTCTGAATCTGTT	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.1785T>A	chr2.hg19:g.160289383A>T	ENSP00000376534:p.Asp595Glu	98.0	0.0	.		64.0	25.0	.	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	hg19	CCDS2209.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.22|14.22	2.469691|2.469691	0.43839|0.43839	.|.	.|.	ENSG00000123636|ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439|ENST00000441143	T;T;T;T|.	0.40476|.	1.03;1.03;1.03;1.03|.	5.92|5.92	3.56|3.56	0.40772|0.40772	.|.	0.000000|.	0.38164|.	U|.	0.001790|.	T|T	0.49745|0.49745	0.1575|0.1575	L|L	0.46157|0.46157	1.445|1.445	0.33282|0.33282	D|D	0.562345|0.562345	P;P;P;P;P|.	0.44946|.	0.846;0.734;0.607;0.607;0.473|.	P;B;B;B;B|.	0.49276|.	0.605;0.301;0.146;0.146;0.069|.	T|T	0.56974|0.56974	-0.7890|-0.7890	10|5	0.09590|.	T|.	0.72|.	-16.1747|-16.1747	8.3651|8.3651	0.32382|0.32382	0.6993:0.0:0.3007:0.0|0.6993:0.0:0.3007:0.0	.|.	595;399;593;593;595|.	Q9UIF8-3;Q9UIF8-4;Q9UIF8-2;Q9UIF8-5;Q9UIF8|.	.;.;.;.;BAZ2B_HUMAN|.	E|I	593;595;595;593|27	ENSP00000376533:D593E;ENSP00000376534:D595E;ENSP00000348087:D595E;ENSP00000339670:D593E|.	ENSP00000339670:D593E|.	D|F	-|-	3|1	2|0	BAZ2B|BAZ2B	159997629|159997629	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	1.568000|1.568000	0.36418|0.36418	0.504000|0.504000	0.28082|0.28082	0.533000|0.533000	0.62120|0.62120	GAT|TTC	.	.	.	none		0.378	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			T	160289383	A	T	160289383	3	4	25	1	0	0	0	0	1	0	0	0	1332	98	4	5	4837	5	BAZ2B	2	160289383	Missense_Mutation	SNP	A	TCGA-4A-A93X-01A-11D-A36X-10	101	160289383	82909990	8	1769											
SLC4A10	57282	hgsc.bcm.edu	37	chr2	162762260	162762260	+	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	agttcccttgtctgctacatCactcggtttactgaagaagc	9	13	8	11	1	2	2	1	1	1	1	4	2	3	2	1	1	4	3	1	1	4	5			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr2:162762260C>T	ENST00000446997.1	+	15	1953	c.1860C>T	c.(1858-1860)atC>atT	p.I620I	SLC4A10_ENST00000375514.5_Silent_p.I601I|SLC4A10_ENST00000421911.1_Silent_p.I620I|SLC4A10_ENST00000272716.5_Silent_p.I590I|SLC4A10_ENST00000415876.2_Silent_p.I590I	NM_001178015.1	NP_001171486.1	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate transporter, member 10	620					bicarbonate transport (GO:0015701)|chloride transport (GO:0006821)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|symporter activity (GO:0015293)			endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(35)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60					Sodium bicarbonate(DB01390)	TCTGCTACATCACTCGGTTTA	0.423																																					p.I620I		Atlas-SNP	.											.	SLC4A10	309	.	0			c.C1860T						PASS	.						155	154	154					2																	162762260		2070	4248	6318	SO:0001819	synonymous_variant	57282	exon15			CTACATCACTCGG		CCDS46438.1, CCDS54411.1, CCDS54412.1	2q24.2	2013-05-22	2008-09-15		ENSG00000144290	ENSG00000144290		"Solute carriers"	13811	protein-coding gene	gene with protein product		605556	"solute carrier family 4, sodium bicarbonate transporter-like, member 10"			10964153, 18319254	Standard	NM_022058		Approved	NBCn2, NCBE	uc002ubx.4	Q6U841	OTTHUMG00000153938	ENST00000446997.1:c.1860C>T	chr2.hg19:g.162762260C>T		145.0	0.0	.		132.0	58.0	.	NM_001178015	B7Z1R0|B7Z2J0|B7ZLC5|B9EG69|F8W675|Q4ZFX6|Q8TCP2|Q9HCQ6	Silent	SNP	ENST00000446997.1	hg19	CCDS54411.1																																																																																			.	.	.	none		0.423	SLC4A10-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333090.1	NM_022058		T	162762260	C	T	162762260	2	4	25	1	0	0	0	0	0	0	0	1	14664	816	29	2		2	SLC4A10	2	162762260	Silent	SNP	C	TCGA-4A-A93X-01A-11D-A36X-10	2472877	162762260	80437113	9	1770											
ITGA6	3655	hgsc.bcm.edu	37	chr2	173352755	173352755	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtggttattgaactgcttttAtcggtctcggggtaagtgtt	6	17	13	5	2	1	1	0	1	1	0	3	1	1	1	0	4	2	4	0	4	4	6			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr2:173352755A>G	ENST00000264106.6	+	19	2711	c.2508A>G	c.(2506-2508)ttA>ttG	p.L836L	ITGA6_ENST00000409080.1_Silent_p.L797L|ITGA6_ENST00000264107.7_Silent_p.L797L|AC093818.1_ENST00000442417.1_RNA|ITGA6_ENST00000409532.1_Silent_p.L678L|ITGA6_ENST00000343713.4_Silent_p.L792L|ITGA6_ENST00000375221.2_Silent_p.L836L			P23229	ITA6_HUMAN	integrin, alpha 6	836					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)			AACTGCTTTTATCGGTCTCGG	0.328																																					p.L797L		Atlas-SNP	.											.	ITGA6	171	.	0			c.A2391G						PASS	.						176	171	173					2																	173352755		2203	4300	6503	SO:0001819	synonymous_variant	3655	exon18			GCTTTTATCGGTC		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.2508A>G	chr2.hg19:g.173352755A>G		212.0	0.0	.		150.0	65.0	.	NM_000210	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Silent	SNP	ENST00000264106.6	hg19																																																																																				.	.	.	none		0.328	ITGA6-201	KNOWN	basic	protein_coding	protein_coding				G	173352755	A	G	173352755	2	3	25	1	0	0	0	0	0	0	0	1	7887	446	16	3		3	ITGA6	2	173352755	Silent	SNP	A	TCGA-4A-A93X-01A-11D-A36X-10	10590495	173352755	69846618	10	1771											
NFE2L2	4780	hgsc.bcm.edu	37	chr2	178098799	178098799	+	Missense_Mutation	SNP	T	T	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	gctggctgaattgggagaaaTtcacctgtctcttcatctag	9	13	10	9	0	4	2	2	1	2	1	5	3	4	2	1	2	0	2	1	2	3	4			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr2:178098799T>G	ENST00000397062.3	-	2	800	c.246A>C	c.(244-246)gaA>gaC	p.E82D	NFE2L2_ENST00000423513.1_Missense_Mutation_p.E66D|NFE2L2_ENST00000446151.2_Missense_Mutation_p.E66D|NFE2L2_ENST00000464747.1_Missense_Mutation_p.E66D|NFE2L2_ENST00000397063.4_Missense_Mutation_p.E66D	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	82					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E82D(8)|p.G81_F83delGEF(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			TTGGGAGAAATTCACCTGTCT	0.433			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.E82D		Atlas-SNP	.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	NFE2L2,NS,carcinoma,0,9	NFE2L2	225	.	9	Substitution - Missense(8)|Deletion - In frame(1)	endometrium(3)|liver(2)|upper_aerodigestive_tract(1)|cervix(1)|oesophagus(1)|kidney(1)	c.A246C						PASS	.						138	137	137					2																	178098799		1903	4104	6007	SO:0001583	missense	4780	exon2			GAGAAATTCACCT		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.246A>C	chr2.hg19:g.178098799T>G	ENSP00000380252:p.Glu82Asp	70.0	0.0	.		58.0	21.0	.	NM_006164	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	hg19	CCDS42782.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.706902	0.89018	.	.	ENSG00000116044	ENST00000397063;ENST00000397062;ENST00000446151;ENST00000448782;ENST00000421929;ENST00000423513	T;T;T;T;T;T	0.30448	1.53;1.53;1.53;1.67;1.67;1.53	5.78	4.63	0.57726	.	0.000000	0.85682	D	0.000000	T	0.58395	0.2119	M	0.87180	2.865	0.54753	D	0.999981	D;D;D;D	0.89917	0.999;0.997;1.0;0.999	D;D;D;D	0.83275	0.991;0.978;0.996;0.991	T	0.64976	-0.6280	10	0.72032	D	0.01	.	11.2269	0.48888	0.0:0.0712:0.0:0.9288	.	66;66;66;82	E9PGJ7;B4DNB0;C9JFL6;Q16236	.;.;.;NF2L2_HUMAN	D	66;82;66;66;66;66	ENSP00000380253:E66D;ENSP00000380252:E82D;ENSP00000411575:E66D;ENSP00000400073:E66D;ENSP00000412191:E66D;ENSP00000410015:E66D	ENSP00000380252:E82D	E	-	3	2	NFE2L2	177807045	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.909000	0.39917	2.210000	0.71456	0.460000	0.39030	GAA	.	.	.	none		0.433	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		G	178098799	T	G	178098799	3	3	25	1	0	0	0	0	1	0	0	0	10375	1490	52	5	1587	5	NFE2L2	2	178098799	Missense_Mutation	SNP	T	TCGA-4A-A93X-01A-11D-A36X-10	4746044	178098799	65100574	11	1772											
TTN	7273	hgsc.bcm.edu	37	chr2	179470170	179470170	+	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	cttgtatgactacattaagaGgtagggatggttcactttca	11	14	10	6	0	2	2	2	1	0	1	2	3	2	3	0	3	1	3	0	3	4	7			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr2:179470170G>T	ENST00000591111.1	-	229	49153	c.48929C>A	c.(48928-48930)cCt>cAt	p.P16310H	TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.P15383H|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P9011H|TTN_ENST00000460472.2_Missense_Mutation_p.P8886H|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P9078H|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.P17951H|TTN-AS1_ENST00000589234.1_RNA			Q8WZ42	TITIN_HUMAN	titin	16310	Fibronectin type-III 18. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TACATTAAGAGGTAGGGATGG	0.348																																					p.P17951H		Atlas-SNP	.											.	TTN	18412	.	0			c.C53852A						PASS	.						88	81	83					2																	179470170		1864	4103	5967	SO:0001583	missense	7273	exon279			TTAAGAGGTAGGG	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.48929C>A	chr2.hg19:g.179470170G>T	ENSP00000465570:p.Pro16310His	149.0	0.0	.		101.0	11.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	13.93	2.384204	0.42308	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56776	0.44;0.44;0.44;0.44	5.74	5.74	0.90152	Fibronectin, type III (2);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.72755	0.3500	M	0.70108	2.13	0.58432	D	0.999991	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.67231	0.95;0.95;0.95;0.95	T	0.74515	-0.3640	9	0.87932	D	0	.	19.9346	0.97133	0.0:0.0:1.0:0.0	.	8886;9011;9078;16310	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	H	15383;8886;9078;9011;8886	ENSP00000343764:P15383H;ENSP00000434586:P8886H;ENSP00000340554:P9078H;ENSP00000352154:P9011H	ENSP00000340554:P9078H	P	-	2	0	TTN	179178415	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	9.728000	0.98792	2.712000	0.92718	0.563000	0.77884	CCT	.	.	.	none		0.348	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179470170	G	T	179470170	3	4	25	1	0	0	0	0	1	0	0	0	16747	1000	35	4	54177	4	TTN	2	179470170	Missense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	1371371	179470170	63729203	12	1773											
SETD2	29072	hgsc.bcm.edu	37	chr3	47144870	47144870	+	Missense_Mutation	SNP	T	T	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	aatttggttcacagctgtgaTtcatgaaacgagagcaattt	13	13	9	6	1	2	3	2	2	0	1	2	4	2	3	0	1	3	3	0	1	3	4			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr3:47144870T>G	ENST00000409792.3	-	7	4925	c.4883A>C	c.(4882-4884)aAt>aCt	p.N1628T		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1628	Inhibitor binding.|S-adenosyl-L-methionine binding.|SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		ACAGCTGTGATTCATGAAACG	0.328			"N, F, S, Mis"		clear cell renal carcinoma																																p.N1628T		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.A4883C						PASS	.						170	157	161					3																	47144870		2203	4300	6503	SO:0001583	missense	29072	exon7			CTGTGATTCATGA	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4883A>C	chr3.hg19:g.47144870T>G	ENSP00000386759:p.Asn1628Thr	134.0	0.0	.		129.0	75.0	.	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	T	27.5	4.841046	0.91197	.	.	ENSG00000181555	ENST00000451092;ENST00000543224;ENST00000409792	D	0.95238	-3.65	5.83	5.83	0.93111	SET domain (3);	0.000000	0.56097	D	0.000022	D	0.98732	0.9574	H	0.99800	4.79	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	D	0.99208	1.0875	10	0.87932	D	0	.	14.7708	0.69675	0.0:0.0:0.0:1.0	.	1628;1628	F2Z317;Q9BYW2	.;SETD2_HUMAN	T	1628	ENSP00000386759:N1628T	ENSP00000386759:N1628T	N	-	2	0	SETD2	47119874	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.638000	0.83328	2.240000	0.73641	0.528000	0.53228	AAT	.	.	.	none		0.328	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		G	47144870	T	G	47144870	3	3	25	1	0	0	0	0	1	0	0	0	14144	1493	52	5	2871	5	SETD2	3	47144870	Missense_Mutation	SNP	T	TCGA-4A-A93X-01A-11D-A36X-10		47144870	150877560	13	1774											
PBRM1	55193	hgsc.bcm.edu	37	chr3	52598065	52598065	+	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	cttaagtttttcaagctttaCctgaagtagtaaatttcatc	12	17	5	7	0	2	1	2	1	0	0	3	1	2	1	1	0	2	4	1	0	7	8			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr3:52598065C>T	ENST00000296302.7	-	23	3877		c.e23+1		PBRM1_ENST00000410007.1_Splice_Site|PBRM1_ENST00000356770.4_Splice_Site|PBRM1_ENST00000337303.4_Splice_Site|PBRM1_ENST00000409114.3_Splice_Site|PBRM1_ENST00000394830.3_Splice_Site|PBRM1_ENST00000409057.1_Splice_Site|SMIM4_ENST00000476842.1_Intron|PBRM1_ENST00000409767.1_Splice_Site			Q86U86	PB1_HUMAN	polybromo 1						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)	p.?(3)		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)		TCAAGCTTTACCTGAAGTAGT	0.343			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																.		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	3	Unknown(3)	kidney(3)	c.3800+1G>A						PASS	.						85	84	84					3																	52598065		2203	4300	6503	SO:0001630	splice_region_variant	55193	exon25			GCTTTACCTGAAG	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.3875+1G>A	chr3.hg19:g.52598065C>T		71.0	0.0	.		57.0	17.0	.	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Splice_Site	SNP	ENST00000296302.7	hg19		.	.	.	.	.	.	.	.	.	.	C	24.8	4.571270	0.86542	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351	.	.	.	5.32	5.32	0.75619	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.0144	0.92888	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PBRM1	52573105	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.818000	0.86416	2.493000	0.84123	0.655000	0.94253	.	.	.	.	none		0.343	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165	Intron	T	52598065	C	T	52598065	5	4	25	1	0	0	0	0	0	0	1	0	11498	521	18	2	1056	2	PBRM1	3	52598065	Splice_Site	SNP	C	TCGA-4A-A93X-01A-11D-A36X-10	5453195	52598065	145424365	14	1775											
PBRM1	55193	hgsc.bcm.edu	37	chr3	52643768	52643768	+	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	gttggccatcatgtgacttcGaattttttccatgtccatgg	7	16	9	9	1	1	1	1	1	0	0	4	2	3	1	3	2	0	1	3	2	1	5			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr3:52643768G>A	ENST00000296302.7	-	16	2129	c.2128C>T	c.(2128-2130)Cga>Tga	p.R710*	PBRM1_ENST00000410007.1_Nonsense_Mutation_p.R710*|PBRM1_ENST00000356770.4_Nonsense_Mutation_p.R678*|PBRM1_ENST00000337303.4_Nonsense_Mutation_p.R710*|PBRM1_ENST00000409114.3_Nonsense_Mutation_p.R725*|PBRM1_ENST00000394830.3_Nonsense_Mutation_p.R710*|PBRM1_ENST00000409057.1_Nonsense_Mutation_p.R710*|PBRM1_ENST00000409767.1_Nonsense_Mutation_p.R725*			Q86U86	PB1_HUMAN	polybromo 1	710	Bromo 5. {ECO:0000255|PROSITE- ProRule:PRU00035}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.R710*(2)|p.R678*(1)		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)		ATGTGACTTCGAATTTTTTCC	0.438			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.R710X		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	PBRM1_ENST00000356770,colon,carcinoma,0,5	PBRM1	1252	.	3	Substitution - Nonsense(3)	kidney(3)	c.C2128T						PASS	.						147	143	144					3																	52643768		2203	4300	6503	SO:0001587	stop_gained	55193	exon17			GACTTCGAATTTT	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.2128C>T	chr3.hg19:g.52643768G>A	ENSP00000296302:p.Arg710*	184.0	0.0	.		205.0	126.0	.	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Nonsense_Mutation	SNP	ENST00000296302.7	hg19		.	.	.	.	.	.	.	.	.	.	G	38	7.040996	0.98021	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103	.	.	.	6.17	3.13	0.36017	.	0.055075	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-27.7405	15.7	0.77536	0.0:0.0:0.6414:0.3586	.	.	.	.	X	678;710;710;710;710;710;725;725;710;669	.	ENSP00000296302:R710X	R	-	1	2	PBRM1	52618808	0.994000	0.37717	1.000000	0.80357	0.998000	0.95712	0.705000	0.25675	1.587000	0.49959	0.655000	0.94253	CGA	.	.	.	none		0.438	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		A	52643768	G	A	52643768	4	1	25	1	0	0	0	0	0	1	0	0	11498	1066	37	1	2832	1	PBRM1	3	52643768	Nonsense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	45703	52643768	145378662	15	1776											
TOMM70A	9868	hgsc.bcm.edu	37	chr3	100093911	100093911	+	Missense_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	tctgaggatcgatgtcagcaGccatgttaaaatcttgagtg	11	12	11	7	1	3	2	1	2	2	0	4	4	3	3	1	1	2	2	1	1	2	2			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr3:100093911G>A	ENST00000284320.5	-	7	1626	c.1178C>T	c.(1177-1179)gCt>gTt	p.A393V		NM_014820.4	NP_055635.3	O94826	TOM70_HUMAN	translocase of outer mitochondrial membrane 70 homolog A (S. cerevisiae)	393					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|protein transmembrane transport (GO:0071806)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane translocase complex (GO:0005742)|mitochondrion (GO:0005739)	protein transmembrane transporter activity (GO:0008320)			endometrium(11)|large_intestine(5)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	32						GATGTCAGCAGCCATGTTAAA	0.448																																					p.A393V		Atlas-SNP	.											.	TOMM70A	65	.	0			c.C1178T						PASS	.						133	124	127					3																	100093911		2203	4300	6503	SO:0001583	missense	9868	exon7			TCAGCAGCCATGT	AB018262	CCDS33807.1	3q12.2	2013-01-10	2006-04-04		ENSG00000154174	ENSG00000154174		"Tetratricopeptide (TTC) repeat domain containing"	11985	protein-coding gene	gene with protein product		606081	"translocase of outer mitochondrial membrane 70 (yeast) homolog A", "translocase of outer mitochondrial membrane 70 homolog A (yeast)"			10582581	Standard	NM_014820		Approved	KIAA0719	uc003dtw.3	O94826	OTTHUMG00000159065	ENST00000284320.5:c.1178C>T	chr3.hg19:g.100093911G>A	ENSP00000284320:p.Ala393Val	102.0	0.0	.		95.0	29.0	.	NM_014820	D3DN48	Missense_Mutation	SNP	ENST00000284320.5	hg19	CCDS33807.1	.	.	.	.	.	.	.	.	.	.	G	35	5.553185	0.96501	.	.	ENSG00000154174	ENST00000284320;ENST00000544924	T	0.74106	-0.81	5.76	5.76	0.90799	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	D	0.87688	0.6240	M	0.81112	2.525	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87951	0.2723	10	0.62326	D	0.03	-9.8008	19.9574	0.97228	0.0:0.0:1.0:0.0	.	393	O94826	TOM70_HUMAN	V	393;286	ENSP00000284320:A393V	ENSP00000284320:A393V	A	-	2	0	TOMM70A	101576601	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.404000	0.97306	2.715000	0.92844	0.561000	0.74099	GCT	.	.	.	none		0.448	TOMM70A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353141.2			A	100093911	G	A	100093911	3	1	25	1	0	0	0	0	1	0	0	0	16374	971	34	2	672	2	TOMM70A	3	100093911	Missense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	47450143	100093911	97928519	16	1777											
ACAD11	84129	hgsc.bcm.edu	37	chr3	132361614	132361614	+	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	acggggaatccaattgaaaaCaaggctttctggactttaaa	15	10	9	7	1	1	1	0	1	1	0	2	3	2	3	1	4	1	1	1	4	7	4	rs144139484		TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr3:132361614C>T	ENST00000264990.6	-	3	1253	c.282G>A	c.(280-282)ttG>ttA	p.L94L	ACAD11_ENST00000489991.1_Intron|ACAD11_ENST00000355458.3_Silent_p.L94L|ACAD11_ENST00000545291.1_5'UTR|ACAD11_ENST00000481970.2_Silent_p.L94L	NM_032169.4	NP_115545	Q709F0	ACD11_HUMAN	acyl-CoA dehydrogenase family, member 11	94					fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)	mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|peroxisome (GO:0005777)	flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|medium-chain-acyl-CoA dehydrogenase activity (GO:0070991)|transferase activity, transferring phosphorus-containing groups (GO:0016772)|very-long-chain-acyl-CoA dehydrogenase activity (GO:0017099)			breast(2)|endometrium(6)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	36						CAATTGAAAACAAGGCTTTCT	0.318																																					p.L94L		Atlas-SNP	.											.	ACAD11	78	.	0			c.G282A						PASS	.	C		0,4406		0,0,2203	91	96	94		282	2.2	0.9	3	dbSNP_134	94	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ACAD11	NM_032169.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		94/781	132361614	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	84129	exon3			TGAAAACAAGGCT	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.282G>A	chr3.hg19:g.132361614C>T		404.0	0.0	.		430.0	264.0	.	NM_032169	Q08AF0|Q658N9|Q658Y2|Q6ZND2|Q8WUT6|Q9H9R3	Silent	SNP	ENST00000264990.6	hg19	CCDS3074.1																																																																																			.	C|1.000;T|0.000	0.000	weak		0.318	ACAD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357279.2	NM_032169		T	132361614	C	T	132361614	2	4	25	1	0	0	0	0	0	0	0	1	109	477	17	2		2	ACAD11	3	132361614	Silent	SNP	C	TCGA-4A-A93X-01A-11D-A36X-10	32267703	132361614	65660816	17	1778											
LSG1	55341	hgsc.bcm.edu	37	chr3	194380833	194380833	+	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	atctaaacaggagtgggtttCgagcatctactatctggacc	11	11	10	9	1	3	0	0	0	3	0	4	3	3	2	1	3	3	2	1	3	4	4	rs537601352		TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr3:194380833C>T	ENST00000265245.5	-	6	865	c.551G>A	c.(550-552)cGa>cAa	p.R184Q		NM_018385.2	NP_060855.2	Q9H089	LSG1_HUMAN	large 60S subunit nuclear export GTPase 1	184	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)		GAGTGGGTTTCGAGCATCTAC	0.423													C|||	1	0.000199681	0	0	5008	,	,		21403	0.001		0	False		,,,				2504	0				p.R184Q		Atlas-SNP	.											.	LSG1	38	.	0			c.G551A						PASS	.						143	125	131					3																	194380833		2203	4300	6503	SO:0001583	missense	55341	exon6			GGGTTTCGAGCAT		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.551G>A	chr3.hg19:g.194380833C>T	ENSP00000265245:p.Arg184Gln	121.0	0.0	.		132.0	6.0	.	NM_018385	A0JLT4|A0PJK3|A6NI18|Q7L9H8|Q9NUK8	Missense_Mutation	SNP	ENST00000265245.5	hg19	CCDS33922.1	.	.	.	.	.	.	.	.	.	.	C	34	5.302207	0.95601	.	.	ENSG00000041802	ENST00000265245	T	0.55588	0.51	5.24	4.36	0.52297	.	0.000000	0.85682	D	0.000000	T	0.80204	0.4580	H	0.95611	3.695	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86713	0.1937	10	0.87932	D	0	.	14.7734	0.69696	0.0:0.9293:0.0:0.0707	.	184	Q9H089	LSG1_HUMAN	Q	184	ENSP00000265245:R184Q	ENSP00000265245:R184Q	R	-	2	0	LSG1	195862122	1.000000	0.71417	0.998000	0.56505	0.982000	0.71751	7.242000	0.78210	1.535000	0.49220	-0.150000	0.13652	CGA	.	.	.	none		0.423	LSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342740.1	NM_018385		T	194380833	C	T	194380833	3	4	25	1	0	0	0	0	1	0	0	0	9056	884	31	1	1461	1	LSG1	3	194380833	Missense_Mutation	SNP	C	TCGA-4A-A93X-01A-11D-A36X-10	62019219	194380833	3641597	18	1779											
FRYL	285527	hgsc.bcm.edu	37	chr4	48550800	48550800	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atcagtcaaaaggatcactgCtatgttacacctatgacaaa	16	10	6	9	0	3	1	3	1	0	0	3	2	3	2	1	1	2	2	1	1	6	3			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr4:48550800C>T	ENST00000503238.1	-	37	4794	c.4795G>A	c.(4795-4797)Gca>Aca	p.A1599T	FRYL_ENST00000358350.4_Missense_Mutation_p.A1599T|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000537810.1_Missense_Mutation_p.A1599T|FRYL_ENST00000507873.2_5'UTR			O94915	FRYL_HUMAN	FRY-like	1599					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						AGGATCACTGCTATGTTACAC	0.333																																					p.A1599T		Atlas-SNP	.											.	FRYL	242	.	0			c.G4795A						PASS	.						76	70	72					4																	48550800		1866	4101	5967	SO:0001583	missense	285527	exon40			TCACTGCTATGTT	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.4795G>A	chr4.hg19:g.48550800C>T	ENSP00000426064:p.Ala1599Thr	270.0	0.0	.		208.0	87.0	.	NM_015030	O95640|Q8WTZ5|Q9NT40	Missense_Mutation	SNP	ENST00000503238.1	hg19	CCDS43227.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.445247|5.445247	0.96187|0.96187	.|.	.|.	ENSG00000075539|ENSG00000075539	ENST00000503238;ENST00000358350;ENST00000537810|ENST00000514617	T;T;T|.	0.07800|.	3.16;3.16;3.16|.	5.32|5.32	5.32|5.32	0.75619|0.75619	Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.77089|0.77089	0.4079|0.4079	M|M	0.73962|0.73962	2.25|2.25	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	0.998;1.0;1.0|.	D;D;D|.	0.91635|.	0.994;0.997;0.999|.	T|T	0.76231|0.76231	-0.3035|-0.3035	10|5	0.72032|.	D|.	0.01|.	.|.	19.3791|19.3791	0.94525|0.94525	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	430;1599;1599|.	Q6ZR29;O94915;F5GX82|.	.;FRYL_HUMAN;.|.	T|N	1599|469	ENSP00000426064:A1599T;ENSP00000351113:A1599T;ENSP00000441114:A1599T|.	ENSP00000351113:A1599T|.	A|S	-|-	1|2	0|0	FRYL|FRYL	48245557|48245557	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.950000|0.950000	0.60333|0.60333	7.424000|7.424000	0.80242|0.80242	2.644000|2.644000	0.89710|0.89710	0.561000|0.561000	0.74099|0.74099	GCA|AGC	.	.	.	none		0.333	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			T	48550800	C	T	48550800	3	4	25	1	0	0	0	0	1	0	0	0	6071	797	28	2	4346	2	FRYL	4	48550800	Missense_Mutation	SNP	C	TCGA-4A-A93X-01A-11D-A36X-10		48550800	142603476	19	1780											
GSTCD	79807	hgsc.bcm.edu	37	chr4	106744194	106744194	+	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	taacaaatcaggccaaacctGgtgacagaattgtggatttc	14	10	9	8	0	1	2	1	1	0	1	2	3	1	3	2	3	2	0	2	3	4	3			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr4:106744194G>T	ENST00000515279.1	+	6	1544	c.1324G>T	c.(1324-1326)Ggt>Tgt	p.G442C	GSTCD_ENST00000360505.5_Missense_Mutation_p.G442C|GSTCD_ENST00000515255.1_3'UTR|RP11-45L9.1_ENST00000509003.1_RNA|GSTCD_ENST00000394730.3_Missense_Mutation_p.G355C|RP11-45L9.1_ENST00000506527.1_RNA|GSTCD_ENST00000394728.3_Missense_Mutation_p.G442C|RP11-45L9.1_ENST00000504955.1_RNA			Q8NEC7	GSTCD_HUMAN	glutathione S-transferase, C-terminal domain containing	442						extracellular vesicular exosome (GO:0070062)				breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|skin(1)	14		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.15e-07)|READ - Rectum adenocarcinoma(30;0.139)		GGCCAAACCTGGTGACAGAAT	0.388																																					p.G442C		Atlas-SNP	.											.	GSTCD	69	.	0			c.G1324T						PASS	.						172	155	161					4																	106744194		2203	4300	6503	SO:0001583	missense	79807	exon6			AAACCTGGTGACA	BC032942	CCDS3672.2, CCDS43257.1	4q24	2008-02-05	2006-05-09		ENSG00000138780	ENSG00000138780			25806	protein-coding gene	gene with protein product		615912	"Glutathione S-transferase, C-terminal domain containing"			12477932	Standard	NM_001031720		Approved	FLJ13273	uc003hxz.4	Q8NEC7	OTTHUMG00000131211	ENST00000515279.1:c.1324G>T	chr4.hg19:g.106744194G>T	ENSP00000422354:p.Gly442Cys	178.0	0.0	.		136.0	56.0	.	NM_001031720	A8K8J0|A8MVD3|H9KV97|Q9H8S3	Missense_Mutation	SNP	ENST00000515279.1	hg19	CCDS43257.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.239681	0.79800	.	.	ENSG00000138780	ENST00000394730;ENST00000515279;ENST00000360505;ENST00000394728	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	4.99	4.99	0.66335	.	0.054220	0.64402	D	0.000001	T	0.73737	0.3625	M	0.92555	3.32	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.987	T	0.81462	-0.0922	10	0.87932	D	0	-14.8311	18.625	0.91334	0.0:0.0:1.0:0.0	.	442;65	Q8NEC7;B7Z8J7	GSTCD_HUMAN;.	C	355;442;442;442	ENSP00000378218:G355C;ENSP00000422354:G442C;ENSP00000353695:G442C;ENSP00000378216:G442C	ENSP00000353695:G442C	G	+	1	0	GSTCD	106963643	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.092000	0.71414	2.467000	0.83353	0.585000	0.79938	GGT	.	.	.	none		0.388	GSTCD-006	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363981.1	NM_024751		T	106744194	G	T	106744194	3	4	25	1	0	0	0	0	1	0	0	0	6842	1348	47	4	1342	4	GSTCD	4	106744194	Missense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	58193394	106744194	84410082	20	1781											
FAT1	2195	hgsc.bcm.edu	37	chr4	187539082	187539082	+	Missense_Mutation	SNP	T	T	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	ccatgatctgatgcaaccacTttaatctggtaattgtctct	10	15	6	10	0	3	2	0	2	3	0	4	2	3	2	2	1	2	2	2	1	3	4			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr4:187539082T>G	ENST00000441802.2	-	10	8867	c.8658A>C	c.(8656-8658)aaA>aaC	p.K2886N		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2886	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						ATGCAACCACTTTAATCTGGT	0.433										HNSCC(5;0.00058)																											p.K2886N	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.A8658C						PASS	.						182	165	171					4																	187539082		1976	4160	6136	SO:0001583	missense	2195	exon10			AACCACTTTAATC	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.8658A>C	chr4.hg19:g.187539082T>G	ENSP00000406229:p.Lys2886Asn	102.0	0.0	.		79.0	26.0	.	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	hg19	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	T	5.728	0.318720	0.10845	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.50277	0.75	4.86	1.01	0.19927	Cadherin (4);Cadherin-like (1);	0.707453	0.14542	N	0.313219	T	0.22589	0.0545	N	0.11845	0.185	0.28042	N	0.933699	B	0.22746	0.074	B	0.23852	0.049	T	0.13845	-1.0494	10	0.25751	T	0.34	.	1.6164	0.02705	0.137:0.1549:0.1427:0.5654	.	2886	Q14517	FAT1_HUMAN	N	2886;2888	ENSP00000406229:K2886N	ENSP00000260147:K2888N	K	-	3	2	FAT1	187776076	0.750000	0.28316	0.560000	0.28344	0.930000	0.56654	0.640000	0.24705	0.097000	0.17492	-0.256000	0.11100	AAA	.	.	.	none		0.433	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		G	187539082	T	G	187539082	3	3	25	1	0	0	0	0	1	0	0	0	5696	1606	56	5	5180	5	FAT1	4	187539082	Missense_Mutation	SNP	T	TCGA-4A-A93X-01A-11D-A36X-10	80794888	187539082	3615194	21	1782											
CDH18	1016	hgsc.bcm.edu	37	chr5	19473699	19473699	+	Missense_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	tcaaggctgtgatgtcaaagGcctctgtgtcttcctctccg	6	13	10	12	1	5	1	2	1	3	0	7	1	6	1	3	2	0	1	3	2	2	1			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr5:19473699G>A	ENST00000507958.1	-	15	2999	c.2009C>T	c.(2008-2010)gCc>gTc	p.A670V	CDH18_ENST00000274170.4_Missense_Mutation_p.A670V|CDH18_ENST00000506372.1_3'UTR|CDH18_ENST00000510297.1_5'UTR|CDH18_ENST00000502796.1_3'UTR|CDH18_ENST00000382275.1_Missense_Mutation_p.A670V			Q13634	CAD18_HUMAN	cadherin 18, type 2	670					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)					GATGTCAAAGGCCTCTGTGTC	0.517																																					p.A670V		Atlas-SNP	.											.	CDH18	561	.	0			c.C2009T						PASS	.						153	147	149					5																	19473699		2203	4300	6503	SO:0001583	missense	1016	exon13			TCAAAGGCCTCTG	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.2009C>T	chr5.hg19:g.19473699G>A	ENSP00000425093:p.Ala670Val	104.0	0.0	.		101.0	36.0	.	NM_004934	A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	hg19	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	G	34	5.410909	0.96072	.	.	ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170	T;T;T	0.80393	-1.37;-1.37;-1.37	6.16	6.16	0.99307	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	D	0.91503	0.7317	M	0.88906	2.99	0.80722	D	1	D	0.67145	0.996	D	0.70016	0.967	D	0.91416	0.5155	9	.	.	.	.	19.4236	0.94732	0.0:0.0:1.0:0.0	.	670	Q13634	CAD18_HUMAN	V	670	ENSP00000371710:A670V;ENSP00000425093:A670V;ENSP00000274170:A670V	.	A	-	2	0	CDH18	19509456	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	9.863000	0.99569	2.937000	0.99478	0.650000	0.86243	GCC	.	.	.	none		0.517	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		A	19473699	G	A	19473699	3	1	25	1	0	0	0	0	1	0	0	0	3105	1203	42	2	367	2	CDH18	5	19473699	Missense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10		19473699	161441561	22	1783											
FBXO4	26272	hgsc.bcm.edu	37	chr5	41925546	41925546	+	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	agcaaggagagggtggcgcgTacgacctcacgggaggaggt	10	4	19	8	4	1	1	1	0	0	1	1	5	1	3	1	6	2	2	1	6	2	1			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr5:41925546T>A	ENST00000281623.3	+	1	191	c.135T>A	c.(133-135)cgT>cgA	p.R45R	FBXO4_ENST00000296812.2_Silent_p.R45R|FBXO4_ENST00000509134.1_Silent_p.R45R	NM_012176.2	NP_036308.1	Q9UKT5	FBX4_HUMAN	F-box protein 4	45					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)				GGGTGGCGCGTACGACCTCAC	0.741																																					p.R45R		Atlas-SNP	.											.	FBXO4	42	.	0			c.T135A						PASS	.						8	8	8					5																	41925546		1807	3416	5223	SO:0001819	synonymous_variant	26272	exon1			GGCGCGTACGACC	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.135T>A	chr5.hg19:g.41925546T>A		242.0	0.0	.		288.0	137.0	.	NM_033484	Q68CU8|Q86VT8|Q9UK98	Silent	SNP	ENST00000281623.3	hg19	CCDS3938.1																																																																																			.	.	.	none		0.741	FBXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211614.1			A	41925546	T	A	41925546	2	1	25	1	0	0	0	0	0	0	0	1	5755	1625	57	5		5	FBXO4	5	41925546	Silent	SNP	T	TCGA-4A-A93X-01A-11D-A36X-10	22451847	41925546	138989714	23	1784											
NNT	23530	hgsc.bcm.edu	37	chr5	43628360	43628360	+	Missense_Mutation	SNP	A	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	agcccttggaggtggacttgAaggaatctggtgagggacaa	11	8	16	6	0	1	2	0	2	1	0	1	6	1	6	1	6	1	0	1	6	3	2			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr5:43628360A>C	ENST00000264663.5	+	7	1056	c.835A>C	c.(835-837)Aag>Cag	p.K279Q	NNT_ENST00000512996.2_Missense_Mutation_p.K148Q|NNT_ENST00000344920.4_Missense_Mutation_p.K279Q	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	279					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					GGTGGACTTGAAGGAATCTGG	0.448																																					p.K279Q		Atlas-SNP	.											.	NNT	92	.	0			c.A835C						PASS	.						123	117	119					5																	43628360		2203	4300	6503	SO:0001583	missense	23530	exon7			GACTTGAAGGAAT	U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.835A>C	chr5.hg19:g.43628360A>C	ENSP00000264663:p.Lys279Gln	174.0	0.0	.		257.0	134.0	.	NM_182977	Q16796|Q2TB60|Q8N3V4	Missense_Mutation	SNP	ENST00000264663.5	hg19	CCDS3949.1	.	.	.	.	.	.	.	.	.	.	A	13.23	2.175032	0.38413	.	.	ENSG00000112992	ENST00000264663;ENST00000344920;ENST00000512996	D;D;D	0.83163	-1.69;-1.69;-1.69	5.91	5.91	0.95273	Alanine dehydrogenase/PNT, C-terminal (1);	0.086607	0.85682	D	0.000000	T	0.72431	0.3459	N	0.17922	0.545	0.58432	D	0.999995	B	0.14805	0.011	B	0.23150	0.044	T	0.67280	-0.5710	10	0.10902	T	0.67	-15.1084	16.3432	0.83101	1.0:0.0:0.0:0.0	.	279	Q13423	NNTM_HUMAN	Q	279;279;148	ENSP00000264663:K279Q;ENSP00000343873:K279Q;ENSP00000426343:K148Q	ENSP00000264663:K279Q	K	+	1	0	NNT	43664117	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.413000	0.52686	2.263000	0.75096	0.377000	0.23210	AAG	.	.	.	none		0.448	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977		C	43628360	A	C	43628360	3	2	25	1	0	0	0	0	1	0	0	0	10517	247	9	5	857	5	NNT	5	43628360	Missense_Mutation	SNP	A	TCGA-4A-A93X-01A-11D-A36X-10	1702814	43628360	137286900	24	1785											
PELO	53918	hgsc.bcm.edu	37	chr5	52096713	52096713	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catgaccctcactcgggccaAggtggaggtgaacatcccta	10	7	11	13	1	1	2	1	2	0	0	3	3	2	3	3	4	1	0	3	4	3	1			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr5:52096713A>G	ENST00000274311.2	+	2	1470	c.485A>G	c.(484-486)aAg>aGg	p.K162R	ITGA1_ENST00000282588.6_Intron|PELO_ENST00000506949.1_Intron|ITGA1_ENST00000504086.1_Intron	NM_015946.4	NP_057030.3	Q9BRX2	PELO_HUMAN	pelota homolog (Drosophila)	162					cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|chromosome organization (GO:0051276)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|nuclear-transcribed mRNA catabolic process, non-stop decay (GO:0070481)|RNA surveillance (GO:0071025)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	11		Lung NSC(810;4.94e-05)|Breast(144;0.0848)				ACTCGGGCCAAGGTGGAGGTG	0.587																																					p.K162R		Atlas-SNP	.											.	PELO	25	.	0			c.A485G						PASS	.						83	74	77					5																	52096713		2203	4300	6503	SO:0001583	missense	53918	exon2			GGGCCAAGGTGGA		CCDS3956.1	5q11.2	2008-07-18	2001-11-28		ENSG00000152684	ENSG00000152684			8829	protein-coding gene	gene with protein product		605757	"pelota (Drosophila) homolog"			11060452	Standard	NM_015946		Approved		uc003jos.3	Q9BRX2	OTTHUMG00000096973	ENST00000274311.2:c.485A>G	chr5.hg19:g.52096713A>G	ENSP00000274311:p.Lys162Arg	125.0	0.0	.		198.0	86.0	.	NM_015946	Q9GZS6|Q9Y306	Missense_Mutation	SNP	ENST00000274311.2	hg19	CCDS3956.1	.	.	.	.	.	.	.	.	.	.	A	7.663	0.685319	0.14973	.	.	ENSG00000152684	ENST00000274311	T	0.44482	0.92	5.4	4.21	0.49690	eRF1 domain 2 (1);	0.000000	0.85682	U	0.000000	T	0.32041	0.0816	L	0.36672	1.1	0.80722	D	1	B	0.24721	0.11	B	0.29353	0.101	T	0.05616	-1.0874	10	0.14252	T	0.57	-18.997	11.3444	0.49552	0.8638:0.0:0.0:0.1362	.	162	Q9BRX2	PELO_HUMAN	R	162	ENSP00000274311:K162R	ENSP00000274311:K162R	K	+	2	0	PELO	52132470	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.187000	0.89708	1.014000	0.39417	0.460000	0.39030	AAG	.	.	.	none		0.587	PELO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214040.1	NM_015946		G	52096713	A	G	52096713	3	3	25	1	0	0	0	0	1	0	0	0	11731	72	3	3	487	3	PELO	5	52096713	Missense_Mutation	SNP	A	TCGA-4A-A93X-01A-11D-A36X-10	8468353	52096713	128818547	25	1786											
DMXL1	1657	hgsc.bcm.edu	37	chr5	118582763	118582763	+	Missense_Mutation	SNP	A	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	tcggcagtccatttttagaaAtattggaactggagtgatgc	11	13	11	6	1	0	2	0	1	0	1	2	4	1	4	1	3	2	1	1	3	4	5			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr5:118582763A>C	ENST00000311085.8	+	43	9013	c.8933A>C	c.(8932-8934)aAt>aCt	p.N2978T	DMXL1_ENST00000539542.1_Missense_Mutation_p.N2999T|DMXL1_ENST00000505312.1_3'UTR	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	2978										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)		ATTTTTAGAAATATTGGAACT	0.403																																					p.N2978T		Atlas-SNP	.											.	DMXL1	268	.	0			c.A8933C						PASS	.						107	106	106					5																	118582763		2202	4300	6502	SO:0001583	missense	1657	exon43			TTAGAAATATTGG	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.8933A>C	chr5.hg19:g.118582763A>C	ENSP00000309690:p.Asn2978Thr	126.0	0.0	.		146.0	67.0	.	NM_005509		Missense_Mutation	SNP	ENST00000311085.8	hg19	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	A	18.68	3.675682	0.67928	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.10860	2.84;2.83	5.82	5.82	0.92795	WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.14614	0.0353	L	0.60845	1.875	0.80722	D	1	P;P	0.36144	0.48;0.539	B;B	0.34722	0.188;0.093	T	0.01413	-1.1361	10	0.44086	T	0.13	-26.4503	16.1802	0.81892	1.0:0.0:0.0:0.0	.	2999;2978	F5H269;Q9Y485	.;DMXL1_HUMAN	T	2978;2999	ENSP00000309690:N2978T;ENSP00000439479:N2999T	ENSP00000309690:N2978T	N	+	2	0	DMXL1	118610662	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.957000	0.93082	2.220000	0.72140	0.533000	0.62120	AAT	.	.	.	none		0.403	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		C	118582763	A	C	118582763	3	2	25	1	0	0	0	0	1	0	0	0	4596	101	4	5	9103	5	DMXL1	5	118582763	Missense_Mutation	SNP	A	TCGA-4A-A93X-01A-11D-A36X-10	66486050	118582763	62332497	26	1787											
ATXN1	6310	hgsc.bcm.edu	37	chr6	16327888	16327888	+	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	tgctgctgctgctgctgctgCtgctgctgctgctgctgctg	0	14	14	13	0	0	0	0	0	0	0	0	0	0	0	0	0	13	13	0	0	0	0	rs573371188	byFrequency	TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr6:16327888C>A	ENST00000244769.4	-	8	1590	c.654G>T	c.(652-654)caG>caT	p.Q218H	ATXN1_ENST00000436367.1_Missense_Mutation_p.Q218H	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	218	Poly-Gln.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				gctgctgctgctgctgctgct	0.657													-|||	5	0.000998403	0	0	5008	,	,		12853	0.003		0.002	False		,,,				2504	0				p.Q218H		Atlas-SNP	.											.	ATXN1	117	.	0			c.G654T						PASS	.						5	8	7					6																	16327888		1257	2848	4105	SO:0001583	missense	6310	exon7			CTGCTGCTGCTGC	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"Ataxins"	10548	protein-coding gene	gene with protein product		601556	"spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.654G>T	chr6.hg19:g.16327888C>A	ENSP00000244769:p.Gln218His	40.0	0.0	.		63.0	19.0	.	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	hg19	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	-	6.816	0.519699	0.13005	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.37752	1.18;1.18	0.86	0.86	0.19042	.	.	.	.	.	T	0.05090	0.0136	N	0.08118	0	0.09310	N	1	B	0.28713	0.22	B	0.17979	0.02	T	0.28490	-1.0042	9	0.40728	T	0.16	.	3.149	0.06481	0.0:0.6895:0.0:0.3104	.	218	P54253	ATX1_HUMAN	H	218	ENSP00000244769:Q218H;ENSP00000416360:Q218H	ENSP00000244769:Q218H	Q	-	3	2	ATXN1	16435867	0.092000	0.21681	0.008000	0.14137	0.146000	0.21551	0.245000	0.18142	0.726000	0.32339	0.205000	0.17691	CAG	.	.	.	none		0.657	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332		A	16327888	C	A	16327888	3	1	25	1	0	0	0	0	1	0	0	0	1209	796	28	4	1801	4	ATXN1	6	16327888	Missense_Mutation	SNP	C	TCGA-4A-A93X-01A-11D-A36X-10		16327888	154787179	27	1788											
FLOT1	10211	hgsc.bcm.edu	37	chr6	30698809	30698809	+	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	tcctgctcctgcactgccacCtgctgggcccgctccaccac	4	8	8	21	1	0	0	0	0	0	0	3	0	3	0	7	1	4	4	7	1	0	0			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr6:30698809C>G	ENST00000376389.3	-	9	1012	c.792G>C	c.(790-792)caG>caC	p.Q264H	FLOT1_ENST00000456573.2_Missense_Mutation_p.Q216H	NM_005803.2	NP_005794.1	P41440	S19A1_HUMAN	flotillin 1	243					folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|methotrexate transporter activity (GO:0015350)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|prostate(1)	13					Methotrexate(DB00563)|Pralatrexate(DB06813)	GCACTGCCACCTGCTGGGCCC	0.667																																					p.Q264H		Atlas-SNP	.											.	FLOT1	28	.	0			c.G792C						PASS	.						55	62	60					6																	30698809		2203	4300	6503	SO:0001583	missense	10211	exon9			TGCCACCTGCTGG	AF089750	CCDS4688.1	6p21.3	2010-02-17			ENSG00000137312	ENSG00000137312			3757	protein-coding gene	gene with protein product		606998					Standard	XM_005248780		Approved		uc003nrm.3	O75955	OTTHUMG00000031151	ENST00000376389.3:c.792G>C	chr6.hg19:g.30698809C>G	ENSP00000365569:p.Gln264His	29.0	0.0	.		48.0	22.0	.	NM_005803	B2R7U8|B7Z8C3|E9PFY4|O00553|O60227|Q13026|Q9BTX8	Missense_Mutation	SNP	ENST00000376389.3	hg19	CCDS4688.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.552759	0.86127	.	.	ENSG00000137312	ENST00000376389;ENST00000456573;ENST00000413165	T;T	0.37584	1.24;1.19	4.5	3.63	0.41609	.	0.132901	0.52532	D	0.000065	T	0.51109	0.1655	M	0.90650	3.135	0.48830	D	0.999717	D;D	0.61080	0.98;0.989	P;P	0.58577	0.841;0.841	T	0.60021	-0.7344	10	0.87932	D	0	-12.4051	10.3081	0.43693	0.0:0.9015:0.0:0.0985	.	216;264	B4DVY7;O75955	.;FLOT1_HUMAN	H	264;216;201	ENSP00000365569:Q264H;ENSP00000394375:Q216H	ENSP00000365569:Q264H	Q	-	3	2	FLOT1	30806788	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.475000	0.60210	2.511000	0.84671	0.650000	0.86243	CAG	.	.	.	none		0.667	FLOT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076276.2			G	30698809	C	G	30698809	3	3	25	1	0	0	0	0	1	0	0	0	5943	680	24	4	511	4	FLOT1	6	30698809	Missense_Mutation	SNP	C	TCGA-4A-A93X-01A-11D-A36X-10	14370921	30698809	140416258	28	1789											
KIAA0240	23506	hgsc.bcm.edu	37	chr6	42790539	42790539	+	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	tcctctcttttctagagaccCacaagcattgaactattttc	10	15	4	12	0	2	2	0	1	2	1	5	3	3	2	2	0	2	1	2	0	4	7			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr6:42790539C>T	ENST00000314073.5	+	4	223	c.47C>T	c.(46-48)cCa>cTa	p.P16L	GLTSCR1L_ENST00000394168.1_Missense_Mutation_p.P16L			Q6AI39	GSC1L_HUMAN	GLTSCR1-like	16																	TCTAGAGACCCACAAGCATTG	0.279																																					p.P16L		Atlas-SNP	.											.	.	.	.	0			c.C47T						PASS	.						86	86	86					6																	42790539		2202	4299	6501	SO:0001583	missense	23506	exon3			GAGACCCACAAGC	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.47C>T	chr6.hg19:g.42790539C>T	ENSP00000313933:p.Pro16Leu	198.0	0.0	.		252.0	106.0	.	NM_015349	A1L3W2|Q5TFZ3|Q92514	Missense_Mutation	SNP	ENST00000314073.5	hg19	CCDS34451.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.299089	0.81025	.	.	ENSG00000112624	ENST00000394167;ENST00000536004;ENST00000314073;ENST00000394168	T;T	0.61742	0.08;0.08	5.83	5.83	0.93111	.	0.000000	0.64402	D	0.000003	T	0.61702	0.2368	L	0.55481	1.735	0.58432	D	0.999995	P;D;D	0.56287	0.75;0.975;0.975	B;P;P	0.53861	0.235;0.736;0.672	T	0.62676	-0.6804	10	0.59425	D	0.04	-14.1586	20.1224	0.97967	0.0:1.0:0.0:0.0	.	16;16;16	F5H616;Q6AI39;B7Z2G7	.;K0240_HUMAN;.	L	16	ENSP00000313933:P16L;ENSP00000377723:P16L	ENSP00000313933:P16L	P	+	2	0	KIAA0240	42898517	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.714000	0.61902	2.749000	0.94314	0.650000	0.86243	CCA	.	.	.	none		0.279	GLTSCR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040562.3	NM_015349		T	42790539	C	T	42790539	3	4	25	1	0	0	0	0	1	0	0	0	8171	594	21	2	53	2	KIAA0240	6	42790539	Missense_Mutation	SNP	C	TCGA-4A-A93X-01A-11D-A36X-10	12091730	42790539	128324528	29	1790											
UBE2CBP	90025	hgsc.bcm.edu	37	chr6	83767689	83767689	+	Missense_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	ttcaggggttttcatctggaGtgaagatggcattatggaaa	11	13	13	4	0	3	2	2	1	1	1	3	4	3	4	0	5	0	2	0	5	3	4			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr6:83767689G>A	ENST00000369747.3	-	2	252	c.130C>T	c.(130-132)Ctc>Ttc	p.L44F		NM_198920.1	NP_944602.1	Q7Z6J8	UBE3D_HUMAN	ubiquitin protein ligase E3D	44					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)										TTCATCTGGAGTGAAGATGGC	0.428											OREG0017549	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L44F		Atlas-SNP	.											.	.	.	.	0			c.C130T						PASS	.						70	66	67					6																	83767689		2203	4300	6503	SO:0001583	missense	90025	exon2			TCTGGAGTGAAGA	AL137544	CCDS34491.1	6q15	2012-02-24	2012-02-24	2012-02-24	ENSG00000118420	ENSG00000118420			21381	protein-coding gene	gene with protein product	"UBCH10 binding protein with a hect-like domain"	612495	"chromosome 6 open reading frame 157", "ubiquitin-conjugating enzyme E2C binding protein"	C6orf157, UBE2CBP		15749827	Standard	NM_198920		Approved	DKFZp434A1520, H10BH, YJR141W	uc003pjp.2	Q7Z6J8	OTTHUMG00000015108	ENST00000369747.3:c.130C>T	chr6.hg19:g.83767689G>A	ENSP00000358762:p.Leu44Phe	119.0	0.0	.	1224	135.0	67.0	.	NM_198920	B4DP63|Q5T4W2|Q6IPR4|Q75UG0|Q9NT42	Missense_Mutation	SNP	ENST00000369747.3	hg19	CCDS34491.1	.	.	.	.	.	.	.	.	.	.	G	14.45	2.538080	0.45176	.	.	ENSG00000118420	ENST00000369747	T	0.33216	1.42	5.31	1.32	0.21799	.	0.204209	0.42964	N	0.000627	T	0.29491	0.0735	M	0.69823	2.125	0.23913	N	0.99649	D;D	0.76494	0.999;0.999	D;D	0.77557	0.986;0.99	T	0.09079	-1.0691	10	0.62326	D	0.03	-3.8166	2.1836	0.03880	0.1648:0.2847:0.4041:0.1463	.	44;44	D6RD24;Q7Z6J8	.;UB2CB_HUMAN	F	44	ENSP00000358762:L44F	ENSP00000358762:L44F	L	-	1	0	UBE2CBP	83824408	0.084000	0.21492	0.016000	0.15963	0.011000	0.07611	0.531000	0.23052	0.338000	0.23692	0.650000	0.86243	CTC	.	.	.	none		0.428	UBE3D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041347.7	NM_198920		A	83767689	G	A	83767689	3	1	25	1	0	0	0	0	1	0	0	0	16859	1029	36	2	1075	2	UBE2CBP	6	83767689	Missense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	40977150	83767689	87347378	30	1791											
GJA10	84694	hgsc.bcm.edu	37	chr6	90604946	90604946	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagtgagggcattgaggaTgaaacaggccctccattcca	12	7	12	10	0	0	3	0	3	0	0	2	4	2	4	3	3	2	2	3	3	1	2			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr6:90604946T>C	ENST00000369352.1	+	1	759	c.759T>C	c.(757-759)gaT>gaC	p.D253D		NM_032602.1	NP_115991.1	P57773	CXA9_HUMAN	gap junction protein, alpha 10, 62kDa	253					cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(17)|ovary(1)|skin(3)|urinary_tract(1)	37		all_cancers(76;5.71e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.0915)		GCATTGAGGATGAAACAGGCC	0.393																																					p.D253D		Atlas-SNP	.											.	GJA10	83	.	0			c.T759C						PASS	.						88	82	84					6																	90604946		2203	4300	6503	SO:0001819	synonymous_variant	84694	exon1			TGAGGATGAAACA	AF296766	CCDS5025.1	6q15-q16	2008-02-05			ENSG00000135355	ENSG00000135355		"Ion channels / Gap junction proteins (connexins)"	16995	protein-coding gene	gene with protein product	"connexin 62"	611924					Standard	NM_032602		Approved	CX62	uc011eaa.2	Q969M2	OTTHUMG00000015210	ENST00000369352.1:c.759T>C	chr6.hg19:g.90604946T>C		74.0	0.0	.		98.0	45.0	.	NM_032602	B2R722|B3KVQ2|Q5TA63|Q96KG0	Silent	SNP	ENST00000369352.1	hg19	CCDS5025.1																																																																																			.	.	.	none		0.393	GJA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041505.1	NM_032602		C	90604946	T	C	90604946	2	2	25	1	0	0	0	0	0	0	0	1	6408	1461	51	3		3	GJA10	6	90604946	Silent	SNP	T	TCGA-4A-A93X-01A-11D-A36X-10	6837257	90604946	80510121	31	1792											
EPM2A	7957	hgsc.bcm.edu	37	chr6	145948580	145948580	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tacacacagaagaacgaaccTtcccaaatttctggaaaaaa	19	7	5	10	1	1	2	0	0	1	2	2	4	2	3	2	1	3	0	2	1	8	3			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr6:145948580T>C	ENST00000367519.3	-	4	1493	c.968A>G	c.(967-969)aAg>aGg	p.K323R		NM_005670.3	NP_005661.1	O95278	EPM2A_HUMAN	epilepsy, progressive myoclonus type 2A, Lafora disease (laforin)	323					autophagy (GO:0006914)|carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen metabolic process (GO:0005977)|habituation (GO:0046959)|inositol phosphate dephosphorylation (GO:0046855)|nervous system development (GO:0007399)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polysome (GO:0005844)	carbohydrate phosphatase activity (GO:0019203)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|starch binding (GO:2001070)			kidney(1)|large_intestine(2)|lung(2)|pancreas(1)|skin(1)	7		Ovarian(120;0.162)		OV - Ovarian serous cystadenocarcinoma(155;3.38e-07)|GBM - Glioblastoma multiforme(68;0.0203)		AGAACGAACCTTCCCAAATTT	0.517																																					p.K323R		Atlas-SNP	.											.	EPM2A	21	.	0			c.A968G						PASS	.						101	109	107					6																	145948580		2203	4300	6503	SO:0001583	missense	7957	exon4			CGAACCTTCCCAA	AF284580	CCDS5206.1	6q24	2011-06-09			ENSG00000112425	ENSG00000112425		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	3413	protein-coding gene	gene with protein product		607566	"epilepsy, progressive myoclonus type 2, Lafora disease (laforin)"			9222970, 7485240	Standard	XM_006715564		Approved	LDE, LD	uc003qkw.3	B3EWF7	OTTHUMG00000015747	ENST00000367519.3:c.968A>G	chr6.hg19:g.145948580T>C	ENSP00000356489:p.Lys323Arg	76.0	0.0	.		85.0	38.0	.	NM_005670	B3KMU5|B4DRZ2|O95483|Q5T3F5|Q6IS15|Q8IU96|Q8IX24|Q8IX25|Q9BS66|Q9UEN2	Missense_Mutation	SNP	ENST00000367519.3	hg19	CCDS5206.1	.	.	.	.	.	.	.	.	.	.	T	11.02	1.515139	0.27123	.	.	ENSG00000112425	ENST00000367519;ENST00000324857	D	0.95756	-3.8	5.89	5.89	0.94794	.	0.324340	0.38326	N	0.001727	D	0.87362	0.6158	L	0.38531	1.155	0.29866	N	0.827263	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.79174	-0.1912	10	0.31617	T	0.26	-26.7267	13.1249	0.59349	0.0:0.0:0.1994:0.8006	.	323;185	O95278;E1P599	EPM2A_HUMAN;.	R	323	ENSP00000356489:K323R	ENSP00000320279:K323R	K	-	2	0	EPM2A	145990273	0.998000	0.40836	0.950000	0.38849	0.698000	0.40448	2.545000	0.45769	2.257000	0.74773	0.460000	0.39030	AAG	.	.	.	none		0.517	EPM2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042564.1			C	145948580	T	C	145948580	3	2	25	1	0	0	0	0	1	0	0	0	5185	1609	56	3	65	3	EPM2A	6	145948580	Missense_Mutation	SNP	T	TCGA-4A-A93X-01A-11D-A36X-10	55343634	145948580	25166487	32	1793											
MEOX2	4223	hgsc.bcm.edu	37	chr7	15725803	15725803	+	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	tgctgatggtggtgatggtgGtggtggtggtggtggtggtg	2	14	24	1	0	0	2	0	2	0	0	0	2	0	2	0	10	1	1	0	10	0	0			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr7:15725803G>A	ENST00000262041.5	-	1	634	c.225C>T	c.(223-225)caC>caT	p.H75H	AC005550.4_ENST00000442176.1_lincRNA|AC005550.5_ENST00000438923.1_lincRNA	NM_005924.4	NP_005915.2	P50222	MEOX2_HUMAN	mesenchyme homeobox 2	75	Poly-His.				angiogenesis (GO:0001525)|blood circulation (GO:0008015)|limb development (GO:0060173)|multicellular organismal development (GO:0007275)|neuron death (GO:0070997)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle tissue development (GO:0007519)|somite specification (GO:0001757)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding (GO:0043565)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (126;0.0822)		ggtgatggtggtggtggtggt	0.602																																					p.H75H	Esophageal Squamous(140;197 1769 16409 18257 29929)	Atlas-SNP	.											MEOX2,caecum,carcinoma,0,1	MEOX2	68	.	0			c.C225T						PASS	.						21	22	22					7																	15725803		2203	4299	6502	SO:0001819	synonymous_variant	4223	exon1			ATGGTGGTGGTGG		CCDS34605.1	7p22.1-p21.3	2014-07-15	2005-12-22		ENSG00000106511	ENSG00000106511		"Homeoboxes / ANTP class : HOXL subclass"	7014	protein-coding gene	gene with protein product	"growth arrest-specific homeobox"	600535	"mesenchyme homeo box 2 (growth arrest-specific homeo box)", "mesenchyme homeobox 2 (growth arrest-specific homeo box)"	GAX		7713505	Standard	NM_005924		Approved	MOX2	uc003stc.3	P50222	OTTHUMG00000152390	ENST00000262041.5:c.225C>T	chr7.hg19:g.15725803G>A		52.0	0.0	.		71.0	3.0	.	NM_005924	B2R8I7|O75263|Q9UPL6	Silent	SNP	ENST00000262041.5	hg19	CCDS34605.1																																																																																			.	.	.	none		0.602	MEOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326058.2	NM_005924		A	15725803	G	A	15725803	2	1	25	1	0	0	0	0	0	0	0	1	9481	1252	44	2		2	MEOX2	7	15725803	Silent	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10		15725803	143412860	33	1794											
PLEKHA8	84725	hgsc.bcm.edu	37	chr7	30092325	30092325	+	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	tccttttaaaaaatttgcagGcaaatggagttgagcacttg	13	13	9	6	0	0	1	0	1	0	0	1	2	1	2	1	2	2	4	1	2	4	5			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr7:30092325G>A	ENST00000449726.1	+	7	989	c.639G>A	c.(637-639)agG>agA	p.R213R	PLEKHA8_ENST00000396257.2_Splice_Site_p.R213R|PLEKHA8_ENST00000258679.7_Splice_Site_p.R213R|PLEKHA8_ENST00000396259.1_Splice_Site_p.R213R	NM_001197027.1	NP_001183956.1	Q96JA3	PKHA8_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8	213					ER to Golgi ceramide transport (GO:0035621)|lipid transport (GO:0006869)|protein transport (GO:0015031)	membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ceramide binding (GO:0097001)|glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)|phosphatidylinositol-4-phosphate binding (GO:0070273)	p.?(1)		breast(4)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)	17						AAATTTGCAGGCAAATGGAGT	0.318																																					p.R213R		Atlas-SNP	.											.	PLEKHA8	68	.	1	Unknown(1)	breast(1)	c.G639A						PASS	.						25	27	27					7																	30092325		2189	4291	6480	SO:0001630	splice_region_variant	84725	exon7			TTGCAGGCAAATG	BC053990	CCDS5424.1, CCDS56473.1, CCDS75574.1	7p21-p11.2	2013-01-10			ENSG00000106086	ENSG00000106086		"Pleckstrin homology (PH) domain containing"	30037	protein-coding gene	gene with protein product		608639				11001876	Standard	NM_001197027		Approved	FAPP2, MGC3358	uc003taq.3	Q96JA3	OTTHUMG00000097751	ENST00000449726.1:c.639-1G>A	chr7.hg19:g.30092325G>A		350.0	1.0	.		503.0	234.0	.	NM_001197027	B4DH00|Q7Z5V8|Q9BU78|Q9H274|Q9H8Z7	Silent	SNP	ENST00000449726.1	hg19	CCDS56473.1																																																																																			.	.	.	none		0.318	PLEKHA8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032639	Silent	A	30092325	G	A	30092325	5	1	25	1	0	0	0	0	0	0	1	0	12069	1217	42	2	665	2	PLEKHA8	7	30092325	Splice_Site	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	14366522	30092325	129046338	34	1795											
NPC1L1	29881	hgsc.bcm.edu	37	chr7	44560616	44560616	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggacatttgatgttgggccGgtcgttcaggaaccagggaa	9	9	16	7	2	1	1	1	1	0	0	2	4	1	4	2	5	1	2	2	5	2	3			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr7:44560616G>A	ENST00000289547.4	-	13	3110	c.3055C>T	c.(3055-3057)Cgg>Tgg	p.R1019W	NPC1L1_ENST00000546276.1_Missense_Mutation_p.R973W|NPC1L1_ENST00000381160.3_Missense_Mutation_p.R1019W	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	1019					cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	ATGTTGGGCCGGTCGTTCAGG	0.542																																					p.R1019W		Atlas-SNP	.											.	NPC1L1	141	.	0			c.C3055T						PASS	.						159	163	162					7																	44560616		2203	4300	6503	SO:0001583	missense	29881	exon13			TGGGCCGGTCGTT		CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"NPC1 (Niemann-Pick disease, type C1, gene)-like 1"			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.3055C>T	chr7.hg19:g.44560616G>A	ENSP00000289547:p.Arg1019Trp	100.0	0.0	.		103.0	7.0	.	NM_001101648	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Missense_Mutation	SNP	ENST00000289547.4	hg19	CCDS5491.1	.	.	.	.	.	.	.	.	.	.	G	8.430	0.848378	0.17034	.	.	ENSG00000015520	ENST00000289547;ENST00000381160;ENST00000546276	D;D;D	0.93488	-3.11;-3.12;-3.23	5.35	-4.42	0.03579	.	2.832230	0.01137	N	0.006105	D	0.87842	0.6279	N	0.24115	0.695	0.09310	N	1	P;P;D;D	0.69078	0.93;0.865;0.994;0.997	P;B;B;P	0.46452	0.489;0.133;0.409;0.517	T	0.80518	-0.1347	10	0.66056	D	0.02	-1.1573	3.5307	0.07775	0.1295:0.4695:0.1562:0.2448	.	973;1019;1019;1019	B7ZLE6;Q17RV5;D3DVK9;Q9UHC9	.;.;.;NPCL1_HUMAN	W	1019;1019;973	ENSP00000289547:R1019W;ENSP00000370552:R1019W;ENSP00000438033:R973W	ENSP00000289547:R1019W	R	-	1	2	NPC1L1	44527141	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.366000	0.07563	-0.360000	0.08138	0.650000	0.86243	CGG	.	.	.	none		0.542	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389		A	44560616	G	A	44560616	3	1	25	1	0	0	0	0	1	0	0	0	10578	1115	39	1	1056	1	NPC1L1	7	44560616	Missense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	14468291	44560616	114578047	35	1796											
DMTF1	9988	hgsc.bcm.edu	37	chr7	86813800	86813800	+	Missense_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	aggtgacatagtcacacaggGtgtgtcttgggcagctgtgg	8	10	16	7	0	2	1	1	1	1	0	2	1	2	1	0	4	1	2	0	4	1	2			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr7:86813800G>A	ENST00000394703.5	+	13	1471	c.908G>A	c.(907-909)gGt>gAt	p.G303D	DMTF1_ENST00000414194.2_Missense_Mutation_p.G37D|DMTF1_ENST00000413276.2_Missense_Mutation_p.G303D|DMTF1_ENST00000331242.7_Missense_Mutation_p.G303D|DMTF1_ENST00000432937.2_Missense_Mutation_p.G215D	NM_021145.3	NP_066968.3	Q9Y222	DMTF1_HUMAN	cyclin D binding myb-like transcription factor 1	303	HTH myb-type. {ECO:0000255|PROSITE- ProRule:PRU00625}.|Interaction with CCND1, CCND2 and CCND3. {ECO:0000250}.|Required for DNA-binding. {ECO:0000250}.				cell cycle (GO:0007049)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)	16	Esophageal squamous(14;0.0058)					GTCACACAGGGTGTGTCTTGG	0.483																																					p.G303D		Atlas-SNP	.											.	DMTF1	48	.	0			c.G908A						PASS	.						94	76	82					7																	86813800		2203	4300	6503	SO:0001583	missense	9988	exon11			CACAGGGTGTGTC	AF084530	CCDS5601.1, CCDS47633.1	7q21	2014-06-25			ENSG00000135164	ENSG00000135164			14603	protein-coding gene	gene with protein product	"cyclin D-binding Myb-like protein"	608491				10095122, 24958102	Standard	NR_024549		Approved	DMP1, DMTF, hDMP1, MRUL	uc003uih.3	Q9Y222	OTTHUMG00000154135	ENST00000394703.5:c.908G>A	chr7.hg19:g.86813800G>A	ENSP00000378193:p.Gly303Asp	97.0	0.0	.		153.0	70.0	.	NM_001142327	B2RBE1|B4DJS5|Q05C48|Q59G79|Q6IS13|Q969T2|Q9H2Z2|Q9H2Z3	Missense_Mutation	SNP	ENST00000394703.5	hg19	CCDS5601.1	.	.	.	.	.	.	.	.	.	.	G	30	5.056379	0.93793	.	.	ENSG00000135164	ENST00000331242;ENST00000413276;ENST00000432937;ENST00000394703;ENST00000414194	T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58	6.17	6.17	0.99709	Transcription regulator HTH, Myb-type, DNA-binding (1);Myb, DNA-binding (1);SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	T	0.65749	0.2721	L	0.38175	1.15	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.58691	-0.7592	10	0.33940	T	0.23	-11.4511	19.8676	0.96824	0.0:0.0:1.0:0.0	.	303	Q9Y222	DMTF1_HUMAN	D	303;303;215;303;37	ENSP00000332171:G303D;ENSP00000402627:G303D;ENSP00000412532:G215D;ENSP00000378193:G303D;ENSP00000415910:G37D	ENSP00000332171:G303D	G	+	2	0	DMTF1	86651736	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.624000	0.98398	2.941000	0.99782	0.655000	0.94253	GGT	.	.	.	none		0.483	DMTF1-002	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334025.5	NM_021145		A	86813800	G	A	86813800	3	1	25	1	0	0	0	0	1	0	0	0	4594	1261	44	2	942	2	DMTF1	7	86813800	Missense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	42253184	86813800	72324863	36	1797											
HEPACAM2	253012	hgsc.bcm.edu	37	chr7	92821636	92821636	+	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	ctgtactgtgcaaatcttgcCccgatacacaatcagaggct	11	10	8	12	1	2	1	1	0	1	1	2	2	2	1	2	1	4	3	2	1	4	3			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr7:92821636C>A	ENST00000394468.2	-	9	1393	c.1316G>T	c.(1315-1317)gGg>gTg	p.G439V	HEPACAM2_ENST00000492616.1_5'UTR|HEPACAM2_ENST00000453812.2_Missense_Mutation_p.G462V|HEPACAM2_ENST00000341723.4_Missense_Mutation_p.G427V|HEPACAM2_ENST00000440868.1_Missense_Mutation_p.G419C	NM_001039372.1	NP_001034461.1	A8MVW5	HECA2_HUMAN	HEPACAM family member 2	439					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|midbody (GO:0030496)|spindle (GO:0005819)				breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(4)|skin(1)	28						CAAATCTTGCCCCGATACACA	0.403																																					p.G439V		Atlas-SNP	.											.	HEPACAM2	132	.	0			c.G1316T						PASS	.						137	121	126					7																	92821636		2203	4300	6503	SO:0001583	missense	253012	exon9			TCTTGCCCCGATA	AK096002	CCDS5629.1, CCDS43616.1, CCDS75631.1, CCDS75632.1	7q21.3	2013-01-29	2008-07-11		ENSG00000188175	ENSG00000188175		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	27364	protein-coding gene	gene with protein product		614133				12975309	Standard	NM_001288804		Approved	FLJ38683	uc003umm.3	A8MVW5	OTTHUMG00000131732	ENST00000394468.2:c.1316G>T	chr7.hg19:g.92821636C>A	ENSP00000377980:p.Gly439Val	61.0	0.0	.		97.0	22.0	.	NM_001039372	B3KTT4|B4DPJ1|B9EG93|E9PDV5|Q6UXI0	Missense_Mutation	SNP	ENST00000394468.2	hg19	CCDS43616.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.77|12.77	2.036754|2.036754	0.35893|0.35893	.|.	.|.	ENSG00000188175|ENSG00000188175	ENST00000440868|ENST00000394468;ENST00000341723;ENST00000453812	T|T;T;T	0.62941|0.53206	-0.01|0.65;0.67;0.63	4.55|4.55	3.64|3.64	0.41730|0.41730	.|.	0.328676|0.328676	0.31859|0.31859	N|N	0.006945|0.006945	T|T	0.47655|0.47655	0.1457|0.1457	N|N	0.19112|0.19112	0.55|0.55	0.53688|0.53688	D|D	0.999979|0.999979	P|D;P;P	0.50710|0.64830	0.938|0.994;0.802;0.875	B|P;P;P	0.42882|0.59115	0.401|0.852;0.481;0.68	T|T	0.49082|0.49082	-0.8976|-0.8976	10|10	0.38643|0.48119	T|T	0.18|0.1	-7.8122|-7.8122	13.1162|13.1162	0.59301|0.59301	0.0:0.8391:0.1609:0.0|0.0:0.8391:0.1609:0.0	.|.	419|462;439;427	C9JN07|E9PDV5;A8MVW5;A8MVW5-2	.|.;HECA2_HUMAN;.	C|V	419|439;427;462	ENSP00000389592:G419C|ENSP00000377980:G439V;ENSP00000340532:G427V;ENSP00000390204:G462V	ENSP00000389592:G419C|ENSP00000340532:G427V	G|G	-|-	1|2	0|0	HEPACAM2|HEPACAM2	92659572|92659572	0.998000|0.998000	0.40836|0.40836	0.549000|0.549000	0.28204|0.28204	0.003000|0.003000	0.03518|0.03518	1.524000|1.524000	0.35942|0.35942	1.214000|1.214000	0.43395|0.43395	0.563000|0.563000	0.77884|0.77884	GGC|GGG	.	.	.	none		0.403	HEPACAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254651.1	NM_198151		A	92821636	C	A	92821636	3	1	25	1	0	0	0	0	1	0	0	0	7060	623	22	4	80	4	HEPACAM2	7	92821636	Missense_Mutation	SNP	C	TCGA-4A-A93X-01A-11D-A36X-10	6007836	92821636	66317027	37	1798											
GPC2	221914	hgsc.bcm.edu	37	chr7	99768943	99768943	+	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	ttttcattctggccgtggccGcccggagctgtagccgacgc	4	10	13	14	5	2	0	1	0	1	0	2	2	2	1	4	3	2	2	4	3	1	4			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr7:99768943G>T	ENST00000292377.2	-	9	1594	c.1427C>A	c.(1426-1428)gCg>gAg	p.A476E	GPC2_ENST00000471050.1_5'UTR|GAL3ST4_ENST00000360039.4_5'Flank|GAL3ST4_ENST00000423751.1_5'Flank	NM_152742.1	NP_689955.1	Q8N158	GPC2_HUMAN	glypican 2	476					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)					GGCCGTGGCCGCCCGGAGCTG	0.721																																					p.A476E		Atlas-SNP	.											.	GPC2	49	.	0			c.C1427A						PASS	.						8	10	9					7																	99768943		2101	4142	6243	SO:0001583	missense	221914	exon9			GTGGCCGCCCGGA	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.1427C>A	chr7.hg19:g.99768943G>T	ENSP00000292377:p.Ala476Glu	125.0	0.0	.		172.0	42.0	.	NM_152742	A4D2A7	Missense_Mutation	SNP	ENST00000292377.2	hg19	CCDS5689.1	.	.	.	.	.	.	.	.	.	.	G	16.41	3.116661	0.56505	.	.	ENSG00000213420	ENST00000292377	T	0.49139	0.79	4.26	4.26	0.50523	.	0.369108	0.25316	N	0.031543	T	0.45377	0.1339	L	0.46741	1.465	0.25189	N	0.99014	D	0.54772	0.968	P	0.54664	0.758	T	0.34875	-0.9811	10	0.05959	T	0.93	-20.9711	8.1197	0.30963	0.1128:0.0:0.8872:0.0	.	476	Q8N158	GPC2_HUMAN	E	476	ENSP00000292377:A476E	ENSP00000292377:A476E	A	-	2	0	GPC2	99606879	0.262000	0.24073	0.280000	0.24747	0.630000	0.37929	1.545000	0.36169	1.919000	0.55581	0.313000	0.20887	GCG	.	.	.	none		0.721	GPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337556.1	NM_152742		T	99768943	G	T	99768943	3	4	25	1	0	0	0	0	1	0	0	0	6605	1087	38	4	320	4	GPC2	7	99768943	Missense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	6947307	99768943	59369720	38	1799											
PLOD3	8985	hgsc.bcm.edu	37	chr7	100855146	100855146	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctgttctcctcaatgaggaTacgcagggtctgcaggttgg	7	11	13	10	1	3	1	1	1	2	0	4	2	3	2	2	4	2	4	2	4	2	3			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr7:100855146T>C	ENST00000223127.3	-	11	1611	c.1213A>G	c.(1213-1215)Atc>Gtc	p.I405V		NM_001084.4	NP_001075.1	O60568	PLOD3_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3	405					basement membrane assembly (GO:0070831)|cellular protein modification process (GO:0006464)|cellular response to hormone stimulus (GO:0032870)|collagen fibril organization (GO:0030199)|endothelial cell morphogenesis (GO:0001886)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|in utero embryonic development (GO:0001701)|lung morphogenesis (GO:0060425)|neural tube development (GO:0021915)|protein localization (GO:0008104)|vasodilation (GO:0042311)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen galactosyltransferase activity (GO:0050211)|procollagen glucosyltransferase activity (GO:0033823)|procollagen-lysine 5-dioxygenase activity (GO:0008475)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	31	Lung NSC(181;0.168)|all_lung(186;0.215)				Succinic acid(DB00139)|Vitamin C(DB00126)	TCAATGAGGATACGCAGGGTC	0.667																																					p.I405V		Atlas-SNP	.											.	PLOD3	79	.	0			c.A1213G						PASS	.						40	36	37					7																	100855146		2203	4300	6503	SO:0001583	missense	8985	exon11			TGAGGATACGCAG	AF046889	CCDS5715.1	7q22.1	2011-08-24			ENSG00000106397	ENSG00000106397	1.14.11.4		9083	protein-coding gene	gene with protein product	"lysyl hydroxlase 3"	603066				9724729, 9582318	Standard	NM_001084		Approved	LH3	uc003uyd.3	O60568	OTTHUMG00000157111	ENST00000223127.3:c.1213A>G	chr7.hg19:g.100855146T>C	ENSP00000223127:p.Ile405Val	91.0	0.0	.		105.0	53.0	.	NM_001084	B2R6W6|Q540C3	Missense_Mutation	SNP	ENST00000223127.3	hg19	CCDS5715.1	.	.	.	.	.	.	.	.	.	.	T	5.673	0.308822	0.10733	.	.	ENSG00000106397	ENST00000223127	D	0.84730	-1.89	4.26	1.62	0.23740	.	0.294746	0.29853	N	0.011034	T	0.75421	0.3847	L	0.45698	1.435	0.23519	N	0.997508	B	0.02656	0.0	B	0.08055	0.003	T	0.57780	-0.7752	10	0.23302	T	0.38	-13.9258	5.6522	0.17622	0.0:0.0967:0.1704:0.7329	.	405	O60568	PLOD3_HUMAN	V	405	ENSP00000223127:I405V	ENSP00000223127:I405V	I	-	1	0	PLOD3	100641866	0.023000	0.18921	0.983000	0.44433	0.250000	0.25880	0.019000	0.13444	0.046000	0.15833	0.374000	0.22700	ATC	.	.	.	none		0.667	PLOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347470.1			C	100855146	T	C	100855146	3	2	25	1	0	0	0	0	1	0	0	0	12110	1406	49	3	1039	3	PLOD3	7	100855146	Missense_Mutation	SNP	T	TCGA-4A-A93X-01A-11D-A36X-10	1086203	100855146	58283517	39	1800											
NAPEPLD	222236	hgsc.bcm.edu	37	chr7	102760435	102760435	+	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	tgataaggaccgcatctattGgagggagttcacttattgtg	10	13	12	6	1	2	1	1	1	1	0	2	4	2	4	1	3	0	2	1	3	3	6			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr7:102760435G>A	ENST00000417955.1	-	3	684	c.530C>T	c.(529-531)cCa>cTa	p.P177L	NAPEPLD_ENST00000465647.1_Missense_Mutation_p.P177L|NAPEPLD_ENST00000427257.1_Missense_Mutation_p.P177L|NAPEPLD_ENST00000341533.4_Missense_Mutation_p.P177L|NAPEPLD_ENST00000455523.2_Missense_Mutation_p.P250L			Q6IQ20	NAPEP_HUMAN	N-acyl phosphatidylethanolamine phospholipase D	177					phospholipid catabolic process (GO:0009395)	extracellular vesicular exosome (GO:0070062)|photoreceptor outer segment membrane (GO:0042622)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						CGCATCTATTGGAGGGAGTTC	0.458																																					p.P177L		Atlas-SNP	.											.	NAPEPLD	49	.	0			c.C530T						PASS	.						222	205	211					7																	102760435		2203	4300	6503	SO:0001583	missense	222236	exon3			TCTATTGGAGGGA	BC037350, AY357337	CCDS5729.1	7q22.1	2014-03-14			ENSG00000161048	ENSG00000161048	3.1.4.54		21683	protein-coding gene	gene with protein product	"chromosome 7 open reading frame 18, N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D"	612334				14634025, 15820312, 18067139	Standard	NM_198990		Approved	FMP30, C7orf18, NAPE-PLD	uc003vbd.2	Q6IQ20	OTTHUMG00000157204	ENST00000417955.1:c.530C>T	chr7.hg19:g.102760435G>A	ENSP00000407112:p.Pro177Leu	120.0	0.0	.		176.0	77.0	.	NM_001122838	Q5CZ87|Q769K1	Missense_Mutation	SNP	ENST00000417955.1	hg19	CCDS5729.1	.	.	.	.	.	.	.	.	.	.	G	13.98	2.398813	0.42512	.	.	ENSG00000161048	ENST00000341533;ENST00000417955;ENST00000465647;ENST00000427257;ENST00000455523	D;D;D;D;D	0.96856	-4.15;-4.15;-4.15;-4.15;-4.15	5.93	-5.61	0.02489	.	0.892883	0.10026	N	0.725409	D	0.92857	0.7728	M	0.62088	1.915	0.09310	N	1	P;B	0.34562	0.457;0.091	B;B	0.36030	0.216;0.102	D	0.86063	0.1533	10	0.44086	T	0.13	-10.4644	5.9653	0.19322	0.0653:0.381:0.139:0.4147	.	250;177	B4E3B0;Q6IQ20	.;NAPEP_HUMAN	L	177;177;177;177;250	ENSP00000340093:P177L;ENSP00000407112:P177L;ENSP00000419188:P177L;ENSP00000392775:P177L;ENSP00000414364:P250L	ENSP00000340093:P177L	P	-	2	0	NAPEPLD	102547671	0.000000	0.05858	0.001000	0.08648	0.773000	0.43773	-0.455000	0.06762	-0.678000	0.05224	-0.282000	0.10007	CCA	.	.	.	none		0.458	NAPEPLD-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347904.1	NM_198990		A	102760435	G	A	102760435	3	1	25	1	0	0	0	0	1	0	0	0	10170	1348	47	2	663	2	NAPEPLD	7	102760435	Missense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	1905289	102760435	56378228	40	1801											
PAXIP1	22976	hgsc.bcm.edu	37	chr7	154738247	154738247	+	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	cctctggcaaaatattctcgGcataaatgaaggtcattttc	12	13	7	9	1	3	1	1	1	2	0	5	1	3	1	1	3	0	2	1	3	6	5			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr7:154738247G>T	ENST00000404141.1	-	19	3262	c.3108C>A	c.(3106-3108)tgC>tgA	p.C1036*	PAXIP1_ENST00000397192.1_Nonsense_Mutation_p.C1036*|PAXIP1_ENST00000473219.1_5'UTR			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	1036	BRCT 6. {ECO:0000255|PROSITE- ProRule:PRU00033}.|Interaction with TP53BP1.				adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		AATATTCTCGGCATAAATGAA	0.413																																					p.C1036X		Atlas-SNP	.											.	PAXIP1	150	.	0			c.C3108A						PASS	.						66	64	65					7																	154738247		1893	4119	6012	SO:0001587	stop_gained	22976	exon19			TTCTCGGCATAAA	U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"PAX transcription activation domain interacting protein 1 like"	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.3108C>A	chr7.hg19:g.154738247G>T	ENSP00000384048:p.Cys1036*	154.0	0.0	.		256.0	107.0	.	NM_007349	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Nonsense_Mutation	SNP	ENST00000404141.1	hg19	CCDS47753.1	.	.	.	.	.	.	.	.	.	.	G	39	7.444800	0.98289	.	.	ENSG00000157212	ENST00000404141;ENST00000397192;ENST00000357094;ENST00000323199	.	.	.	5.34	-0.931	0.10438	.	0.000000	0.64402	U	0.000009	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.841	13.5779	0.61885	0.418:0.0:0.582:0.0	.	.	.	.	X	1036;1036;860;989	.	ENSP00000319149:C989X	C	-	3	2	PAXIP1	154369180	0.998000	0.40836	0.504000	0.27639	0.641000	0.38312	0.608000	0.24223	-0.428000	0.07339	-0.378000	0.06908	TGC	.	.	.	none		0.413	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349		T	154738247	G	T	154738247	4	4	25	1	0	0	0	0	0	1	0	0	11494	1195	42	4	113	4	PAXIP1	7	154738247	Nonsense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	51977812	154738247	4400416	41	1802											
ARHGEF10	9639	hgsc.bcm.edu	37	chr8	1814770	1814770	+	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	aacacagcctggatggagagTaagttccccagctgcccaca	12	6	10	13	0	0	1	0	0	0	1	1	3	1	2	4	2	4	3	4	2	2	2			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr8:1814770T>G	ENST00000398564.1	+	6	697		c.e6+2		ARHGEF10_ENST00000520359.1_Splice_Site|ARHGEF10_ENST00000398560.1_Splice_Site|ARHGEF10_ENST00000262112.6_Splice_Site|ARHGEF10_ENST00000518288.1_Splice_Site|ARHGEF10_ENST00000349830.3_Splice_Site			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10						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)		GGATGGAGAGTAAGTTCCCCA	0.577																																					.		Atlas-SNP	.											.	ARHGEF10	255	.	0			c.622+2T>G						PASS	.						78	86	83					8																	1814770		2203	4300	6503	SO:0001630	splice_region_variant	9639	exon6			GGAGAGTAAGTTC	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.697+2T>G	chr8.hg19:g.1814770T>G		22.0	0.0	.		20.0	13.0	.	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Splice_Site	SNP	ENST00000398564.1	hg19		.	.	.	.	.	.	.	.	.	.	T	21.5	4.162508	0.78226	.	.	ENSG00000104728	ENST00000349830;ENST00000520359;ENST00000518288;ENST00000398560;ENST00000398564;ENST00000262112	.	.	.	5.1	5.1	0.69264	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1393	0.72599	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARHGEF10	1802177	1.000000	0.71417	0.968000	0.41197	0.818000	0.46254	5.561000	0.67339	2.029000	0.59856	0.477000	0.44152	.	.	.	.	none		0.577	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			Intron	G	1814770	T	G	1814770	5	3	25	1	0	0	0	0	0	0	1	0	894	1652	57	5	642	5	ARHGEF10	8	1814770	Splice_Site	SNP	T	TCGA-4A-A93X-01A-11D-A36X-10		1814770	144549252	42	1803											
MYOM2	9172	hgsc.bcm.edu	37	chr8	1998968	1998968	+	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	ttcaaacacggtacctgctgGacgaatatgcgtcaaaaaag	15	8	9	9	3	2	0	2	0	0	0	2	2	2	1	1	2	4	2	1	2	7	3			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr8:1998968G>A	ENST00000262113.4	+	2	229	c.88G>A	c.(88-90)Gac>Aac	p.D30N	MYOM2_ENST00000523438.1_Intron	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	30					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)		GTACCTGCTGGACGAATATGC	0.488																																					p.D30N		Atlas-SNP	.											.	MYOM2	251	.	0			c.G88A						PASS	.						111	84	93					8																	1998968		2203	4300	6503	SO:0001583	missense	9172	exon2			CTGCTGGACGAAT		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.88G>A	chr8.hg19:g.1998968G>A	ENSP00000262113:p.Asp30Asn	90.0	0.0	.		75.0	53.0	.	NM_003970	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	hg19	CCDS5957.1	.	.	.	.	.	.	.	.	.	.	G	9.371	1.070617	0.20147	.	.	ENSG00000036448	ENST00000262113	T	0.50548	0.74	5.78	-3.17	0.05202	.	0.876047	0.10049	N	0.722425	T	0.36386	0.0965	L	0.57536	1.79	0.09310	N	0.999996	B	0.09022	0.002	B	0.06405	0.002	T	0.35992	-0.9766	10	0.40728	T	0.16	.	4.5719	0.12214	0.2464:0.1783:0.4935:0.0818	.	30	P54296	MYOM2_HUMAN	N	30	ENSP00000262113:D30N	ENSP00000262113:D30N	D	+	1	0	MYOM2	1986375	1.000000	0.71417	0.005000	0.12908	0.069000	0.16628	1.006000	0.29847	-0.172000	0.10779	0.563000	0.77884	GAC	.	.	.	none		0.488	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970		A	1998968	G	A	1998968	3	1	25	1	0	0	0	0	1	0	0	0	10099	1174	41	2	90	2	MYOM2	8	1998968	Missense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	184198	1998968	144365054	43	1804											
AP3M2	10947	hgsc.bcm.edu	37	chr8	42012262	42012262	+	Missense_Mutation	SNP	T	T	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	gacattttcctggagaaacaTtggaaaagtgtggtcagccg	12	10	12	7	1	1	1	1	0	0	1	2	4	2	2	2	3	2	0	2	3	3	3			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr8:42012262T>G	ENST00000518421.1	+	3	348	c.57T>G	c.(55-57)caT>caG	p.H19Q	AP3M2_ENST00000520685.1_Intron|RP11-589C21.5_ENST00000564481.1_RNA|AP3M2_ENST00000517922.1_Missense_Mutation_p.H19Q|AP3M2_ENST00000396926.3_Missense_Mutation_p.H19Q|AP3M2_ENST00000174653.3_Missense_Mutation_p.H19Q	NM_001134296.1	NP_001127768.1	P53677	AP3M2_HUMAN	adaptor-related protein complex 3, mu 2 subunit	19					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)				endometrium(3)|kidney(1)|large_intestine(1)|lung(10)|prostate(1)|stomach(1)	17	all_cancers(6;8.14e-25)|all_epithelial(6;2.41e-27)|all_lung(13;5.09e-13)|Lung NSC(13;8.38e-12)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|Colorectal(10;0.00165)|OV - Ovarian serous cystadenocarcinoma(14;0.00346)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024)			TGGAGAAACATTGGAAAAGTG	0.453																																					p.H19Q		Atlas-SNP	.											.	AP3M2	41	.	0			c.T57G						PASS	.						80	79	80					8																	42012262		2203	4300	6503	SO:0001583	missense	10947	exon3			GAAACATTGGAAA	D38293	CCDS6125.1	8p11.2	2008-07-07			ENSG00000070718	ENSG00000070718			570	protein-coding gene	gene with protein product		610469				7601449	Standard	NM_006803		Approved	CLA20, AP47B	uc003xoo.3	P53677	OTTHUMG00000164060	ENST00000518421.1:c.57T>G	chr8.hg19:g.42012262T>G	ENSP00000428787:p.His19Gln	70.0	0.0	.		75.0	25.0	.	NM_001134296	B2RCR0|D3DSY2|Q7Z472	Missense_Mutation	SNP	ENST00000518421.1	hg19	CCDS6125.1	.	.	.	.	.	.	.	.	.	.	T	17.94	3.510545	0.64522	.	.	ENSG00000070718	ENST00000518421;ENST00000174653;ENST00000396926;ENST00000522288;ENST00000517922	T;T;T;T	0.76060	-0.99;-0.99;-0.99;-0.98	5.36	-1.64	0.08318	Longin-like (1);AP complex, mu/sigma subunit (1);	0.000000	0.85682	D	0.000000	T	0.81143	0.4761	M	0.69185	2.1	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.77351	-0.2620	10	0.51188	T	0.08	-21.5389	11.0086	0.47649	0.0:0.6489:0.0:0.3511	.	19;19	E7ER80;P53677	.;AP3M2_HUMAN	Q	19	ENSP00000428787:H19Q;ENSP00000174653:H19Q;ENSP00000380132:H19Q;ENSP00000429435:H19Q	ENSP00000174653:H19Q	H	+	3	2	AP3M2	42131419	0.970000	0.33590	0.966000	0.40874	0.990000	0.78478	0.183000	0.16919	-0.697000	0.05092	-0.239000	0.12128	CAT	.	.	.	none		0.453	AP3M2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376996.1			G	42012262	T	G	42012262	3	3	25	1	0	0	0	0	1	0	0	0	748	1490	52	5	59	5	AP3M2	8	42012262	Missense_Mutation	SNP	T	TCGA-4A-A93X-01A-11D-A36X-10	40013294	42012262	104351760	44	1805											
TRPA1	8989	hgsc.bcm.edu	37	chr8	72987583	72987583	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtccggcacatcctcatagAcaacgccctggggctccttc	7	8	9	17	3	1	1	1	0	0	1	5	1	4	1	4	3	1	2	4	3	2	2			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr8:72987583A>G	ENST00000262209.4	-	1	269	c.62T>C	c.(61-63)gTc>gCc	p.V21A		NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	21					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	ATCCTCATAGACAACGCCCTG	0.637																																					p.V21A		Atlas-SNP	.											.	TRPA1	256	.	0			c.T62C						PASS	.						101	104	103					8																	72987583		2203	4300	6503	SO:0001583	missense	8989	exon1			TCATAGACAACGC	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	497	protein-coding gene	gene with protein product		604775	"ankyrin-like with transmembrane domains 1"	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.62T>C	chr8.hg19:g.72987583A>G	ENSP00000262209:p.Val21Ala	22.0	0.0	.		39.0	12.0	.	NM_007332	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	hg19	CCDS34908.1	.	.	.	.	.	.	.	.	.	.	A	3.912	-0.019798	0.07634	.	.	ENSG00000104321	ENST00000262209	T	0.41758	0.99	4.58	-1.05	0.10036	.	0.559178	0.19035	N	0.124452	T	0.24431	0.0592	L	0.50333	1.59	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16158	-1.0412	10	0.13108	T	0.6	-0.0577	0.093	0.00041	0.3267:0.1568:0.2116:0.3049	.	21	O75762	TRPA1_HUMAN	A	21	ENSP00000262209:V21A	ENSP00000262209:V21A	V	-	2	0	TRPA1	73150137	0.004000	0.15560	0.004000	0.12327	0.007000	0.05969	-0.206000	0.09398	-0.240000	0.09696	0.482000	0.46254	GTC	.	.	.	none		0.637	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332		G	72987583	A	G	72987583	3	3	25	1	0	0	0	0	1	0	0	0	16589	275	10	3	3405	3	TRPA1	8	72987583	Missense_Mutation	SNP	A	TCGA-4A-A93X-01A-11D-A36X-10	30975321	72987583	73376439	45	1806											
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77776566	77776571	+	In_Frame_Del	DEL	CTTCTC	CTTCTC	-																															agcgtctgccaggagagctgCttctcccccttcttctcctc																										TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	CTTCTC	CTTCTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr8:77776566_77776571delCTTCTC	ENST00000521891.2	+	11	11064_11069	c.10616_10621delCTTCTC	c.(10615-10623)gcttctccc>gcc	p.SP3540del	ZFHX4_ENST00000518282.1_In_Frame_Del_p.SP3514del|ZFHX4_ENST00000050961.6_In_Frame_Del_p.SP3491del|ZFHX4_ENST00000455469.2_In_Frame_Del_p.SP3495del	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	3491					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)			AGGAGAGCTGCTTCTCCCCCTTCTTC	0.49										HNSCC(33;0.089)																											p.3539_3540del		Atlas-Indel,Pindel	.											ZFHX4,NS,carcinoma,0,1	ZFHX4	878	.	0			c.10615_10620del						PASS	.																																			SO:0001651	inframe_deletion	79776	exon11			.		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"Homeoboxes / ZF class"	30939	protein-coding gene	gene with protein product		606940	"zinc finger homeodomain 4"			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.10616_10621delCTTCTC	chr8.hg19:g.77776566_77776571delCTTCTC	ENSP00000430497:p.Ser3540_Pro3541del	121.0	0.0	0		146.0	74.0	0.506849	NM_024721	G3V138|Q18PS0|Q6ZN20	In_Frame_Del	DEL	ENST00000521891.2	hg19	CCDS47878.2																																																																																			.	.	.	none		0.49	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		-	77776571	CTTCTC	-	77776566	7	5	25	1	0	1	0	1	0	0	0	0	17647	797	28	0	10654	0	ZFHX4	8	77776566	In_Frame_Del	DEL	CTTCTC	TCGA-4A-A93X-01A-11D-A36X-10	4788983	77776566	68587456	46	1807											
C9orf106	414318	hgsc.bcm.edu	37	chr9	132084554	132084554	+	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	tgggtggggaaccacgtttcCccagcacatcggcaggccct	7	7	13	14	2	0	0	0	0	0	0	2	1	1	1	4	5	2	3	4	5	1	1			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr9:132084554C>T	ENST00000316786.1	+	0	515							Q8NAJ2	CI106_HUMAN	chromosome 9 open reading frame 106											large_intestine(1)|lung(1)|ovary(1)|skin(1)	4		Ovarian(14;0.00556)|Medulloblastoma(224;0.235)				ACCACGTTTCCCCAGCACATC	0.612																																					p.S154S		Atlas-SNP	.											.	C9orf106	7	.	0			c.C462T						PASS	.						47	49	49					9																	132084554		2012	4166	6178			414318	exon2			CGTTTCCCCAGCA	AK092588		9q34.11	2013-12-05	2013-12-05	2013-12-05	ENSG00000179082	ENSG00000179082			31370	other	unknown							Standard	NM_001012715		Approved	bA65J3.5	uc004bxs.2	Q8NAJ2	OTTHUMG00000020781		chr9.hg19:g.132084554C>T		50.0	0.0	.		30.0	18.0	.	NM_001012715		Silent	SNP	ENST00000316786.1	hg19																																																																																				.	.	.	none		0.612	C9orf106-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000054576.2			T	132084554	C	T	132084554	1	4	25	0	1	0	0	0	0	0	0	0	2449	610	22	2		2	C9orf106	9	132084554	RNA	SNP	C	TCGA-4A-A93X-01A-11D-A36X-10		132084554	9128877	47	1808											
TSC1	7248	hgsc.bcm.edu	37	chr9	135804182	135804183	+	Frame_Shift_Del	DEL	TG	TG	-																															aggttctctttaaagacagcTgtcacgtcgtcccgcacacc																										TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr9:135804182_135804183delTG	ENST00000298552.3	-	3	298_299	c.77_78delCA	c.(76-78)acafs	p.T26fs	TSC1_ENST00000475903.1_5'UTR|TSC1_ENST00000403810.1_Frame_Shift_Del_p.T26fs|TSC1_ENST00000545250.1_Frame_Shift_Del_p.T26fs|TSC1_ENST00000440111.2_Frame_Shift_Del_p.T26fs	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	26					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)		TAAAGACAGCTGTCACGTCGTC	0.475			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.26_27del		Atlas-Indel,Pindel	.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"E, O"	.	TSC1	167	.	0			c.78_79del						PASS	.																																			SO:0001589	frameshift_variant	7248	exon3	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	.	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.77_78delCA	chr9.hg19:g.135804182_135804183delTG	ENSP00000298552:p.Thr26fs	50.0	0.0	0		39.0	15.0	0.384615	NM_000368	B7Z897|Q5VVN5	Frame_Shift_Del	DEL	ENST00000298552.3	hg19	CCDS6956.1																																																																																			.	.	.	none		0.475	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1			-	135804183	TG	-	135804182	7	5	25	1	0	1	0	1	0	0	0	0	16617	1567	55	0	3500	0	TSC1	9	135804182	Frame_Shift_Del	DEL	TG	TCGA-4A-A93X-01A-11D-A36X-10	3719628	135804182	5409249	48	1809											
KLF6	1316	hgsc.bcm.edu	37	chr10	3824256	3824257	+	Frame_Shift_Ins	INS	-	-	A																															atgagagtgtcctctggaggINSactggaagatatcttcagtt																										TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr10:3824256_3824257insA	ENST00000497571.1	-	2	512_513	c.252_253insT	c.(250-255)agtcctfs	p.P85fs	KLF6_ENST00000542957.1_Frame_Shift_Ins_p.P85fs|KLF6_ENST00000173785.4_5'Flank|KLF6_ENST00000469435.1_Frame_Shift_Ins_p.P85fs	NM_001160124.1|NM_001300.5	NP_001153596.1|NP_001291.3	Q99612	KLF6_HUMAN	Kruppel-like factor 6	85					B cell differentiation (GO:0030183)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(3)|endometrium(1)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16				Colorectal(1;0.238)		TCCTCTGGAGGACTGGAAGATA	0.485											OREG0019980	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P85fs		Pindel	.											.	KLF6	38	.	0			c.253_254insT						PASS	.																																			SO:0001589	frameshift_variant	1316	exon2			.	U51869	CCDS7060.1, CCDS53490.1	10p15	2013-01-08	2004-11-29	2004-12-01	ENSG00000067082	ENSG00000067082		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	2235	protein-coding gene	gene with protein product	"GC-rich binding factor"	602053	"core promoter element binding protein"	BCD1, ST12, COPEB		9503030, 9685731	Standard	NM_001300		Approved	CPBP, GBF, Zf9, PAC1	uc001iha.3	Q99612	OTTHUMG00000017567	ENST00000497571.1:c.253dupT	chr10.hg19:g.3824257_3824257dupA	ENSP00000419923:p.Pro85fs	84.0	0.0	.	614	99.0	35.0	0.354	NM_001300	B2RE86|B4DDN0|D3DRR1|F5H3M5|Q5VUT7|Q5VUT8|Q9BT79	Frame_Shift_Ins	INS	ENST00000497571.1	hg19	CCDS7060.1																																																																																			.	.	.	none		0.485	KLF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046495.1			A	3824257	-	A	3824256	7	5	25	1	0	1	1	0	0	0	0	0	8357	1174	41	0	610	0	KLF6	10	3824256	Frame_Shift_Ins	INS	-	TCGA-4A-A93X-01A-11D-A36X-10		3824256	131710491	49	1810											
ARMC3	219681	hgsc.bcm.edu	37	chr10	23287144	23287145	+	Frame_Shift_Ins	INS	-	-	T																															tagtaaacgagatggagccaINSttgccaacgctgctacagta																										TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr10:23287144_23287145insT	ENST00000298032.5	+	11	1327_1328	c.1243_1244insT	c.(1243-1245)attfs	p.I415fs	ARMC3_ENST00000409049.3_Frame_Shift_Ins_p.I415fs|ARMC3_ENST00000376528.4_Frame_Shift_Ins_p.I152fs|ARMC3_ENST00000409983.3_Frame_Shift_Ins_p.I415fs|RNA5SP304_ENST00000411199.1_RNA	NM_173081.3	NP_775104.2	Q5W041	ARMC3_HUMAN	armadillo repeat containing 3	415						extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						AGATGGAGCCATTGCCAACGCT	0.46																																					p.I415fs		Atlas-Indel,Pindel	.											.	ARMC3	102	.	0			c.1243_1244insT						PASS	.																																			SO:0001589	frameshift_variant	219681	exon11			.	AK057389	CCDS7142.1, CCDS60499.1, CCDS60500.1, CCDS73073.1	10p12.31	2013-02-14			ENSG00000165309	ENSG00000165309		"Armadillo repeat containing"	30964	protein-coding gene	gene with protein product	"cancer/testis antigen 81"	611226					Standard	XM_005252380		Approved	FLJ32827, CT81	uc001irm.4	Q5W041	OTTHUMG00000017811	ENST00000298032.5:c.1245dupT	chr10.hg19:g.23287146_23287146dupT	ENSP00000298032:p.Ile415fs	82.0	0.0	0		76.0	53.0	0.697368	NM_173081	A0PG76|A6NH64|B4DZL3|B7ZBN6|B7ZBN7|Q8IXS5|Q8N7B0|Q96M49	Frame_Shift_Ins	INS	ENST00000298032.5	hg19	CCDS7142.1																																																																																			.	.	.	none		0.46	ARMC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047197.2	NM_173081		T	23287145	-	T	23287144	7	5	25	1	0	1	1	0	0	0	0	0	952	217	8	0	1281	0	ARMC3	10	23287144	Frame_Shift_Ins	INS	-	TCGA-4A-A93X-01A-11D-A36X-10	19462888	23287144	112247603	50	1811											
PGBD3	267004	hgsc.bcm.edu	37	chr10	50725003	50725003	+	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	tgtgcaacaaagaacctggcAgattatttattgttccacct	12	13	7	9	0	0	2	0	0	0	2	1	2	1	2	3	1	3	3	3	1	5	5			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr10:50725003A>T	ENST00000374127.3	-	2	359	c.158T>A	c.(157-159)cTg>cAg	p.L53Q	PGBD3_ENST00000603152.1_Missense_Mutation_p.L521Q|ERCC6_ENST00000355832.5_Intron|ERCC6-PGBD3_ENST00000515869.1_Missense_Mutation_p.L521Q|ERCC6-PGBD3_ENST00000447839.2_Missense_Mutation_p.L521Q|PGBD3_ENST00000508005.2_Missense_Mutation_p.L53Q	NM_170753.2	NP_736609.2	Q8N328	PGBD3_HUMAN	piggyBac transposable element derived 3	53										breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|lung(16)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	33						AGAACCTGGCAGATTATTTAT	0.428																																					p.Q53Q		Atlas-SNP	.											.	PGBD3	58	.	0			c.A158A						PASS	.						153	151	152					10																	50725003		2203	4300	6503	SO:0001583	missense	267004	exon2			CCTGGCAGATTAT	AK074682	CCDS7230.1	10q11	2011-03-24			ENSG00000243251	ENSG00000243251			19400	protein-coding gene	gene with protein product							Standard	NM_170753		Approved	FLJ90201		Q8N328	OTTHUMG00000018193	ENST00000374127.3:c.158T>A	chr10.hg19:g.50725003A>T	ENSP00000363242:p.Leu53Gln	86.0	0.0	.		93.0	24.0	.	NM_170753	B3KQC4|Q5W0M0|Q6PIH0	Silent	SNP	ENST00000374127.3	hg19	CCDS7230.1	.	.	.	.	.	.	.	.	.	.	A	18.81	3.703019	0.68501	.	.	ENSG00000243251;ENSG00000243251;ENSG00000258838;ENSG00000258838	ENST00000374127;ENST00000508005;ENST00000515869;ENST00000447839	T;T;T;T	0.26373	1.74;1.74;2.72;2.72	0.468	0.468	0.16732	.	.	.	.	.	T	0.21631	0.0521	N	0.08118	0	0.22562	N	0.998986	D;D	0.58970	0.984;0.984	P;P	0.62435	0.902;0.902	T	0.23655	-1.0182	8	0.22109	T	0.4	-27.2962	.	.	.	.	521;53	E7EV46;Q8N328	.;PGBD3_HUMAN	Q	53;53;521;521	ENSP00000363242:L53Q;ENSP00000426963:L53Q;ENSP00000423550:L521Q;ENSP00000387966:L521Q	ENSP00000387966:L521Q	L	-	2	0	PGBD3;RP11-123B3.6	50395009	0.976000	0.34144	0.985000	0.45067	0.983000	0.72400	1.864000	0.39469	0.413000	0.25759	0.402000	0.26972	CTG	.	.	.	none		0.428	PGBD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047988.1			T	50725003	A	T	50725003	3	4	25	1	0	0	0	0	1	0	0	0	11789	188	7	5	1627	5	PGBD3	10	50725003	Missense_Mutation	SNP	A	TCGA-4A-A93X-01A-11D-A36X-10	27437859	50725003	84809744	51	1812											
TMEM26	219623	hgsc.bcm.edu	37	chr10	63170397	63170397	+	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	gacaaggaaggggccatcttGtatgaagacgctgattccga	12	8	13	8	2	1	3	0	2	1	1	2	6	2	4	2	3	0	2	2	3	4	3			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr10:63170397G>T	ENST00000399298.3	-	6	1158	c.790C>A	c.(790-792)Caa>Aaa	p.Q264K	TMEM26_ENST00000507507.1_5'UTR	NM_178505.6	NP_848600.2	Q6ZUK4	TMM26_HUMAN	transmembrane protein 26	264						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	18	Prostate(12;0.0112)					GGGCCATCTTGTATGAAGACG	0.507																																					p.Q264K		Atlas-SNP	.											.	TMEM26	47	.	0			c.C790A						PASS	.						76	79	78					10																	63170397		2109	4237	6346	SO:0001583	missense	219623	exon6			CATCTTGTATGAA	BC042872	CCDS41530.1	10q21.3	2008-10-20			ENSG00000196932	ENSG00000196932			28550	protein-coding gene	gene with protein product						12477932	Standard	NM_178505		Approved	MGC35010, Em:AC068892.1	uc001jlo.2	Q6ZUK4	OTTHUMG00000018293	ENST00000399298.3:c.790C>A	chr10.hg19:g.63170397G>T	ENSP00000382237:p.Gln264Lys	198.0	0.0	.		217.0	136.0	.	NM_178505	Q6ZVM0|Q8IVN9	Missense_Mutation	SNP	ENST00000399298.3	hg19	CCDS41530.1	.	.	.	.	.	.	.	.	.	.	G	35	5.516645	0.96402	.	.	ENSG00000196932	ENST00000399298	.	.	.	6.17	6.17	0.99709	.	0.254374	0.41938	D	0.000784	D	0.85173	0.5636	M	0.85630	2.765	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.85636	0.1273	9	0.87932	D	0	-16.2012	20.8794	0.99867	0.0:0.0:1.0:0.0	.	264	Q6ZUK4	TMM26_HUMAN	K	264	.	ENSP00000382237:Q264K	Q	-	1	0	TMEM26	62840403	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	9.476000	0.97823	2.941000	0.99782	0.655000	0.94253	CAA	.	.	.	none		0.507	TMEM26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359121.1	NM_178505		T	63170397	G	T	63170397	3	4	25	1	0	0	0	0	1	0	0	0	16163	1386	48	4	320	4	TMEM26	10	63170397	Missense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	12445394	63170397	72364350	52	1813											
DLG5	9231	hgsc.bcm.edu	37	chr10	79579728	79579728	+	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	aggcgagtaaggtgcccactCctggagctccggggagagtt	8	7	16	10	2	0	1	0	0	0	1	2	4	2	2	3	5	2	3	3	5	1	2			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr10:79579728C>G	ENST00000372391.2	-	16	3456	c.3451G>C	c.(3451-3453)Gag>Cag	p.E1151Q	DLG5_ENST00000459739.1_5'UTR|DLG5_ENST00000372388.2_Missense_Mutation_p.E811Q	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	1151					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)			GGTGCCCACTCCTGGAGCTCC	0.632																																					p.E1151Q		Atlas-SNP	.											.	DLG5	154	.	0			c.G3451C						PASS	.						60	67	65					10																	79579728		2203	4300	6503	SO:0001583	missense	9231	exon16			CCCACTCCTGGAG	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.3451G>C	chr10.hg19:g.79579728C>G	ENSP00000361467:p.Glu1151Gln	63.0	0.0	.		55.0	13.0	.	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Missense_Mutation	SNP	ENST00000372391.2	hg19	CCDS7353.2	.	.	.	.	.	.	.	.	.	.	C	17.64	3.440688	0.63067	.	.	ENSG00000151208	ENST00000372391;ENST00000424842;ENST00000372388	T;T;T	0.05139	3.56;3.49;3.71	5.73	5.73	0.89815	.	0.400058	0.18419	N	0.141810	T	0.11281	0.0275	L	0.27053	0.805	0.42181	D	0.991686	B;B;D	0.59357	0.116;0.215;0.985	B;B;P	0.53689	0.124;0.094;0.732	T	0.26643	-1.0097	10	0.29301	T	0.29	.	18.083	0.89447	0.0:1.0:0.0:0.0	.	1041;1151;811	Q8TDM6-4;Q8TDM6;Q8TDM6-2	.;DLG5_HUMAN;.	Q	1151;112;811	ENSP00000361467:E1151Q;ENSP00000394797:E112Q;ENSP00000361464:E811Q	ENSP00000361464:E811Q	E	-	1	0	DLG5	79249734	1.000000	0.71417	0.999000	0.59377	0.161000	0.22273	5.585000	0.67497	2.722000	0.93159	0.655000	0.94253	GAG	.	.	.	none		0.632	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2			G	79579728	C	G	79579728	3	3	25	1	0	0	0	0	1	0	0	0	4560	864	30	4	2376	4	DLG5	10	79579728	Missense_Mutation	SNP	C	TCGA-4A-A93X-01A-11D-A36X-10	16409331	79579728	55955019	53	1814											
C10orf28	27291	hgsc.bcm.edu	37	chr10	99968077	99968077	+	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	taaagacaaaccggaggctcGaagactaaatatcaatcctg	17	7	8	9	2	1	2	1	0	0	2	3	4	2	3	2	2	1	1	2	2	8	3	rs373657280	byFrequency	TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr10:99968077G>C	ENST00000298999.3	+	5	509	c.206G>C	c.(205-207)cGa>cCa	p.R69P	R3HCC1L_ENST00000314594.5_5'UTR|R3HCC1L_ENST00000370586.2_Intron|R3HCC1L_ENST00000370584.3_Missense_Mutation_p.R69P	NM_014472.4	NP_055287	Q7Z5L2	R3HCL_HUMAN	R3H domain and coiled-coil containing 1-like	69							nucleotide binding (GO:0000166)										CCGGAGGCTCGAAGACTAAAT	0.353																																					p.R69P		Atlas-SNP	.											C10orf28,colon,carcinoma,0,1	R3HCC1L	3	.	0			c.G206C						PASS	.						71	78	76					10																	99968077		2203	4299	6502	SO:0001583	missense	27291	exon4			AGGCTCGAAGACT	AF525304	CCDS31267.1, CCDS58093.1, CCDS73178.1	10q24.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166024	ENSG00000166024			23512	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 28"	C10orf28			Standard	NM_014472		Approved	GIDRP86, PSORT	uc001kox.4	Q7Z5L2	OTTHUMG00000018873	ENST00000298999.3:c.206G>C	chr10.hg19:g.99968077G>C	ENSP00000298999:p.Arg69Pro	203.0	0.0	.		183.0	26.0	.	NM_001256620	O60598|Q5W0B4|Q5W0B5|Q86VT9|Q8N9H0	Missense_Mutation	SNP	ENST00000298999.3	hg19	CCDS31267.1	.	.	.	.	.	.	.	.	.	.	G	0.274	-0.991016	0.02162	.	.	ENSG00000166024	ENST00000370584;ENST00000538495;ENST00000298999	T;T	0.07800	3.16;3.16	5.81	0.746	0.18365	.	0.578419	0.16601	N	0.207353	T	0.02230	0.0069	N	0.00926	-1.1	0.09310	N	0.999992	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.47736	-0.9094	9	.	.	.	0.9296	7.6295	0.28230	0.6631:0.2621:0.0748:0.0	.	69;69	Q7Z5L2;Q7Z5L2-2	GIDRP_HUMAN;.	P	69	ENSP00000359616:R69P;ENSP00000298999:R69P	.	R	+	2	0	C10orf28	99958067	0.046000	0.20272	0.000000	0.03702	0.003000	0.03518	0.453000	0.21811	-0.094000	0.12374	-2.142000	0.00338	CGA	.	.	.	none		0.353	R3HCC1L-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049764.1	NM_014472		C	99968077	G	C	99968077	3	2	25	1	0	0	0	0	1	0	0	0	1603	1058	37	4	208	4	C10orf28	10	99968077	Missense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	20388349	99968077	35566670	54	1815											
C10orf137	26098	hgsc.bcm.edu	37	chr10	127411654	127411654	+	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	tagctttggcatggcatatgActttattgattcagtgggaa	10	15	11	5	0	1	2	1	2	0	0	1	3	1	3	0	3	1	3	0	3	4	7			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr10:127411654A>T	ENST00000356792.4	+	3	567	c.335A>T	c.(334-336)gAc>gTc	p.D112V	C10orf137_ENST00000337623.3_Missense_Mutation_p.D112V	NM_001202438.1	NP_001189367.1	Q3B7T1	EDRF1_HUMAN		112					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)				ATGGCATATGACTTTATTGAT	0.373																																					p.D112V		Atlas-SNP	.											.	C10orf137	153	.	0			c.A335T						PASS	.						392	357	369					10																	127411654		2203	4300	6503	SO:0001583	missense	26098	exon3			CATATGACTTTAT																												ENST00000356792.4:c.335A>T	chr10.hg19:g.127411654A>T	ENSP00000349244:p.Asp112Val	143.0	0.0	.		178.0	65.0	.	NM_015608	B2RC65|Q3KR40|Q4G190|Q5VZQ4|Q8IZ74|Q9Y3W4	Missense_Mutation	SNP	ENST00000356792.4	hg19	CCDS55733.1	.	.	.	.	.	.	.	.	.	.	A	13.19	2.163705	0.38217	.	.	ENSG00000107938	ENST00000356792;ENST00000392732;ENST00000337623	.	.	.	5.7	4.57	0.56435	.	0.091287	0.85682	D	0.000000	T	0.52322	0.1727	L	0.36672	1.1	0.80722	D	1	P;P;P	0.50272	0.933;0.933;0.933	P;P;P	0.52957	0.542;0.714;0.542	T	0.44345	-0.9334	9	0.30078	T	0.28	.	11.7725	0.51967	0.9311:0.0:0.0689:0.0	.	112;112;112	Q3B7T1;Q3B7T1-5;Q3B7T1-3	EDRF1_HUMAN;.;.	V	112	.	ENSP00000336727:D112V	D	+	2	0	C10orf137	127401644	1.000000	0.71417	0.998000	0.56505	0.375000	0.29983	6.824000	0.75288	0.988000	0.38734	-0.274000	0.10170	GAC	.	.	.	none		0.373	C10orf137-007	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388539.1			T	127411654	A	T	127411654	3	4	25	1	0	0	0	0	1	0	0	0	1596	275	10	5	345	5	C10orf137	10	127411654	Missense_Mutation	SNP	A	TCGA-4A-A93X-01A-11D-A36X-10	27443577	127411654	8123093	55	1816											
TMEM132A	54972	hgsc.bcm.edu	37	chr11	60703543	60703543	+	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	atgtggctctgcacccgcccGagccctgccgccggggccgc	3	5	14	19	5	1	0	0	0	1	0	1	1	1	0	6	3	3	2	6	3	0	0			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr11:60703543G>T	ENST00000453848.2	+	11	2394	c.2236G>T	c.(2236-2238)Gag>Tag	p.E746*	TMEM132A_ENST00000005286.4_Nonsense_Mutation_p.E747*			Q24JP5	T132A_HUMAN	transmembrane protein 132A	746	Binds to HSPA5/GRP78. {ECO:0000250}.|Confers cellular localization similar to full-length form. {ECO:0000250}.					endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|prostate(1)|skin(3)	32						GCACCCGCCCGAGCCCTGCCG	0.746																																					p.E747X		Atlas-SNP	.											.	TMEM132A	135	.	0			c.G2239T						PASS	.						9	12	11					11																	60703543		2130	4118	6248	SO:0001587	stop_gained	54972	exon11			CCGCCCGAGCCCT	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.2236G>T	chr11.hg19:g.60703543G>T	ENSP00000405823:p.Glu746*	45.0	0.0	.		30.0	13.0	.	NM_017870	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Nonsense_Mutation	SNP	ENST00000453848.2	hg19	CCDS44618.1	.	.	.	.	.	.	.	.	.	.	G	40	8.074232	0.98640	.	.	ENSG00000006118	ENST00000444690;ENST00000453848;ENST00000005286	.	.	.	4.72	4.72	0.59763	.	0.306688	0.27393	N	0.019579	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	15.0866	0.72158	0.0:0.0:1.0:0.0	.	.	.	.	X	497;746;747	.	ENSP00000005286:E747X	E	+	1	0	TMEM132A	60460119	1.000000	0.71417	0.955000	0.39395	0.985000	0.73830	6.464000	0.73534	2.620000	0.88729	0.561000	0.74099	GAG	.	.	.	none		0.746	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870		T	60703543	G	T	60703543	4	4	25	1	0	0	0	0	0	1	0	0	16057	1059	37	4	2281	4	TMEM132A	11	60703543	Nonsense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10		60703543	74302973	56	1817											
HEPHL1	341208	hgsc.bcm.edu	37	chr11	93754630	93754630	+	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	accagaacgtactacattggGattgtggaagaatactggaa	15	9	11	6	1	0	2	0	0	0	2	0	5	0	5	1	3	4	1	1	3	7	5	rs267603252		TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr11:93754630G>T	ENST00000315765.9	+	1	104	c.96G>T	c.(94-96)ggG>ggT	p.G32G		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	32	Plastocyanin-like 1.				copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				ACTACATTGGGATTGTGGAAG	0.473																																					p.G32G		Atlas-SNP	.											.	HEPHL1	144	.	0			c.G96T						PASS	.						161	157	158					11																	93754630		1911	4120	6031	SO:0001819	synonymous_variant	341208	exon1			CATTGGGATTGTG	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.96G>T	chr11.hg19:g.93754630G>T		80.0	0.0	.		50.0	22.0	.	NM_001098672	Q3C1W7	Silent	SNP	ENST00000315765.9	hg19	CCDS44710.1																																																																																			.	.	.	none		0.473	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947		T	93754630	G	T	93754630	2	4	25	1	0	0	0	0	0	0	0	1	7062	1161	41	4		4	HEPHL1	11	93754630	Silent	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	33051087	93754630	41251886	57	1818											
MLL	4297	hgsc.bcm.edu	37	chr11	118352545	118352545	+	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	cctaccccatcagcaagagaGgatcctgccccaaagaaaag	15	4	8	14	0	1	2	1	0	0	2	2	4	2	3	6	1	3	1	6	1	5	1			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr11:118352545G>T	ENST00000389506.5	+	7	3750	c.3750G>T	c.(3748-3750)gaG>gaT	p.E1250D	KMT2A_ENST00000354520.4_Missense_Mutation_p.E1250D|KMT2A_ENST00000534358.1_Missense_Mutation_p.E1250D			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	1250					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)										CAGCAAGAGAGGATCCTGCCC	0.502																																					p.E1250D		Atlas-SNP	.											.	MLL	548	.	0			c.G3750T						PASS	.						107	98	101					11																	118352545		2200	4296	6496	SO:0001583	missense	4297	exon7			AAGAGAGGATCCT	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.3750G>T	chr11.hg19:g.118352545G>T	ENSP00000374157:p.Glu1250Asp	236.0	0.0	.		165.0	80.0	.	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	hg19	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	G	16.06	3.016979	0.54576	.	.	ENSG00000118058	ENST00000534358;ENST00000531904;ENST00000389506;ENST00000354520;ENST00000359313	D;T;D;D	0.83075	-1.68;0.92;-1.68;-1.63	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.76990	0.4065	L	0.47716	1.5	0.41753	D	0.989671	B;B	0.27351	0.176;0.176	B;B	0.22386	0.039;0.039	T	0.72564	-0.4255	10	0.28530	T	0.3	.	13.4678	0.61266	0.0806:0.0:0.9194:0.0	.	1250;1250	E9PQG7;Q03164	.;MLL1_HUMAN	D	1250;1283;1250;1250;160	ENSP00000436786:E1250D;ENSP00000432391:E1283D;ENSP00000374157:E1250D;ENSP00000346516:E1250D	ENSP00000346516:E1250D	E	+	3	2	MLL	117857755	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.989000	0.40707	2.680000	0.91292	0.563000	0.77884	GAG	.	.	.	none		0.502	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		T	118352545	G	T	118352545	3	4	25	1	0	0	0	0	1	0	0	0	9627	991	35	4	3776	4	MLL	11	118352545	Missense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	24597915	118352545	16653971	58	1819											
ERC1	23085	hgsc.bcm.edu	37	chr12	1192643	1192643	+	Missense_Mutation	SNP	A	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	ttctgccaaggctaccgaggAagaccatgagagaacaagac	15	5	11	10	1	1	4	0	1	1	3	1	7	1	5	3	2	3	1	3	2	5	2			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr12:1192643A>C	ENST00000397203.2	+	3	1389	c.983A>C	c.(982-984)gAa>gCa	p.E328A	ERC1_ENST00000589028.1_Missense_Mutation_p.E328A|ERC1_ENST00000543086.3_Missense_Mutation_p.E328A|ERC1_ENST00000546231.2_Missense_Mutation_p.E328A|ERC1_ENST00000355446.5_Missense_Mutation_p.E328A|ERC1_ENST00000360905.4_Missense_Mutation_p.E328A			Q8IUD2	RB6I2_HUMAN	ELKS/RAB6-interacting/CAST family member 1	328					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)			GCTACCGAGGAAGACCATGAG	0.458																																					p.E328A		Atlas-SNP	.											.	ERC1	95	.	0			c.A983C						PASS	.						88	86	87					12																	1192643		2203	4300	6503	SO:0001583	missense	23085	exon3			CCGAGGAAGACCA	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.983A>C	chr12.hg19:g.1192643A>C	ENSP00000380386:p.Glu328Ala	103.0	0.0	.		127.0	46.0	.	NM_178039	A2RU77|A7E295|D3DUP7|D3DUP8|Q6NVK2|Q8IUD3|Q8IUD4|Q8IUD5|Q8NAS1|Q9NXN5|Q9UIK7|Q9UPS1	Missense_Mutation	SNP	ENST00000397203.2	hg19	CCDS8508.1	.	.	.	.	.	.	.	.	.	.	A	17.45	3.393749	0.62066	.	.	ENSG00000082805	ENST00000347735;ENST00000397203;ENST00000454194;ENST00000537890;ENST00000543086;ENST00000542302;ENST00000546231;ENST00000355446;ENST00000360905;ENST00000440394;ENST00000538971	T;T;T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.57873	0.2083	L	0.49350	1.555	0.58432	D	0.999999	B;D;D;D	0.76494	0.3;0.999;0.999;0.975	B;D;D;P	0.80764	0.297;0.994;0.994;0.78	T	0.52419	-0.8578	10	0.27785	T	0.31	-20.1362	15.9948	0.80232	1.0:0.0:0.0:0.0	.	104;328;328;328	F5H327;Q8IUD2-2;Q8IUD2-3;Q8IUD2	.;.;.;RB6I2_HUMAN	A	328;328;328;328;328;328;328;328;328;328;104	ENSP00000340054:E328A;ENSP00000380386:E328A;ENSP00000438546:E328A;ENSP00000445336:E328A;ENSP00000442739:E328A;ENSP00000347621:E328A;ENSP00000354158:E328A;ENSP00000410064:E328A	ENSP00000340054:E328A	E	+	2	0	ERC1	1062904	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.277000	0.78572	2.234000	0.73211	0.533000	0.62120	GAA	.	.	.	none		0.458	ERC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398380.2	NM_015064		C	1192643	A	C	1192643	3	2	25	1	0	0	0	0	1	0	0	0	5212	246	9	5	989	5	ERC1	12	1192643	Missense_Mutation	SNP	A	TCGA-4A-A93X-01A-11D-A36X-10		1192643	132659252	59	1820											
LRP6	4040	hgsc.bcm.edu	37	chr12	12301888	12301888	+	Missense_Mutation	SNP	T	T	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	taacataccctttctctgggTttaccacaacggctcgaggt	9	12	8	12	2	1	0	0	0	1	0	3	1	1	0	2	3	4	2	2	3	4	5			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr12:12301888T>G	ENST00000261349.4	-	14	3270	c.3194A>C	c.(3193-3195)aAc>aCc	p.N1065T	LRP6_ENST00000543091.1_Missense_Mutation_p.N1065T	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1065	Beta-propeller 4.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				TTTCTCTGGGTTTACCACAAC	0.453																																					p.N1065T		Atlas-SNP	.											.	LRP6	170	.	0			c.A3194C						PASS	.						184	167	173					12																	12301888		2203	4300	6503	SO:0001583	missense	4040	exon14			TCTGGGTTTACCA	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.3194A>C	chr12.hg19:g.12301888T>G	ENSP00000261349:p.Asn1065Thr	94.0	0.0	.		85.0	59.0	.	NM_002336	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	hg19	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	T	19.70	3.876601	0.72180	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.91068	-2.78;-2.78	4.82	4.82	0.62117	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	U	0.000011	D	0.92639	0.7661	L	0.49126	1.545	0.80722	D	1	D;P	0.71674	0.998;0.632	D;B	0.74674	0.984;0.325	D	0.90702	0.4621	10	0.25106	T	0.35	.	13.3996	0.60874	0.0:0.0:0.0:1.0	.	1065;1065	F5H7J9;O75581	.;LRP6_HUMAN	T	1065	ENSP00000261349:N1065T;ENSP00000442472:N1065T	ENSP00000261349:N1065T	N	-	2	0	LRP6	12193155	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.970000	0.70431	2.146000	0.66826	0.528000	0.53228	AAC	.	.	.	none		0.453	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			G	12301888	T	G	12301888	3	3	25	1	0	0	0	0	1	0	0	0	8969	1725	60	5	1687	5	LRP6	12	12301888	Missense_Mutation	SNP	T	TCGA-4A-A93X-01A-11D-A36X-10	11109245	12301888	121550007	60	1821											
IFNG	3458	hgsc.bcm.edu	37	chr12	68551700	68551700	+	Missense_Mutation	SNP	T	T	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	taaatagcctcaccgaataaTtagtcagcttttcgaagtca	14	12	6	9	2	3	0	3	0	0	0	4	2	3	0	2	0	2	1	2	0	7	6			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr12:68551700T>G	ENST00000229135.3	-	3	490	c.359A>C	c.(358-360)aAt>aCt	p.N120T	IFNG-AS1_ENST00000536914.1_RNA	NM_000619.2	NP_000610.2	P01579	IFNG_HUMAN	interferon, gamma	120					adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|apoptotic process (GO:0006915)|CD8-positive, alpha-beta T cell differentiation involved in immune response (GO:0002302)|cell cycle arrest (GO:0007050)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to interleukin-18 (GO:0071351)|cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endoplasmic reticulum unfolded protein response (GO:0030968)|extrinsic apoptotic signaling pathway (GO:0097191)|humoral immune response (GO:0006959)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of myelination (GO:0031642)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neutrophil apoptotic process (GO:0001781)|neutrophil chemotaxis (GO:0030593)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity (GO:0060550)|positive regulation of fructose 1,6-bisphosphate metabolic process (GO:0060552)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-23 production (GO:0032747)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000309)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of vitamin D biosynthetic process (GO:0060557)|protein import into nucleus, translocation (GO:0000060)|regulation of insulin secretion (GO:0050796)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of the force of heart contraction (GO:0002026)|response to drug (GO:0042493)|response to virus (GO:0009615)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|interferon-gamma receptor binding (GO:0005133)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000829)	Glucosamine(DB01296)|Olsalazine(DB01250)	CACCGAATAATTAGTCAGCTT	0.368																																					p.N120T		Atlas-SNP	.											.	IFNG	38	.	0			c.A359C						PASS	.						156	151	153					12																	68551700		2203	4299	6502	SO:0001583	missense	3458	exon3			GAATAATTAGTCA		CCDS8980.1	12q14	2007-10-17			ENSG00000111537	ENSG00000111537		"Interferons"	5438	protein-coding gene	gene with protein product		147570					Standard	NM_000619		Approved		uc001stw.1	P01579	OTTHUMG00000169113	ENST00000229135.3:c.359A>C	chr12.hg19:g.68551700T>G	ENSP00000229135:p.Asn120Thr	85.0	0.0	.		74.0	43.0	.	NM_000619	B5BU88|Q53ZV4	Missense_Mutation	SNP	ENST00000229135.3	hg19	CCDS8980.1	.	.	.	.	.	.	.	.	.	.	T	9.875	1.199940	0.22121	.	.	ENSG00000111537	ENST00000229135	T	0.43294	0.95	5.38	-1.2	0.09554	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	1.425740	0.04038	N	0.302620	T	0.23886	0.0578	N	0.12182	0.205	0.09310	N	1	B	0.24721	0.11	B	0.28465	0.09	T	0.13818	-1.0495	9	.	.	.	-2.0684	4.3675	0.11232	0.1454:0.3309:0.0:0.5238	.	120	P01579	IFNG_HUMAN	T	120	ENSP00000229135:N120T	.	N	-	2	0	IFNG	66837967	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.502000	0.06390	-0.370000	0.08016	-1.157000	0.01802	AAT	.	.	.	none		0.368	IFNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402301.1			G	68551700	T	G	68551700	3	3	25	1	0	0	0	0	1	0	0	0	7555	1493	52	5	149	5	IFNG	12	68551700	Missense_Mutation	SNP	T	TCGA-4A-A93X-01A-11D-A36X-10	56249812	68551700	65300195	61	1822											
ATXN2	6311	hgsc.bcm.edu	37	chr12	111893835	111893835	+	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	ggctaaagctggtattacctGaggtacgtgggccatgtggg	8	10	16	7	1	0	1	0	1	0	0	0	1	0	1	2	5	3	4	2	5	5	4			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr12:111893835G>T	ENST00000377617.3	-	23	3903	c.3742C>A	c.(3742-3744)Cag>Aag	p.Q1248K	ATXN2_ENST00000389153.4_Missense_Mutation_p.Q985K|ATXN2_ENST00000535949.1_Missense_Mutation_p.Q941K|ATXN2_ENST00000608853.1_Missense_Mutation_p.Q1088K|ATXN2_ENST00000542287.2_Missense_Mutation_p.Q983K|ATXN2_ENST00000550104.1_3'UTR	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	1248					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						GGTATTACCTGAGGTACGTGG	0.502																																					p.Q1248K		Atlas-SNP	.											.	ATXN2	99	.	0			c.C3742A						PASS	.						245	226	232					12																	111893835		2203	4300	6503	SO:0001583	missense	6311	exon23			TTACCTGAGGTAC	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.3742C>A	chr12.hg19:g.111893835G>T	ENSP00000366843:p.Gln1248Lys	153.0	0.0	.		177.0	106.0	.	NM_002973	A6NLD4|Q6ZQZ7|Q99493	Missense_Mutation	SNP	ENST00000377617.3	hg19	CCDS31902.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.968319	0.92855	.	.	ENSG00000204842	ENST00000389154;ENST00000389153;ENST00000377617;ENST00000482777;ENST00000542287;ENST00000535949;ENST00000550844	D	0.81821	-1.54	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	D	0.86100	0.5852	L	0.36672	1.1	0.80722	D	1	P;B;B;D;D	0.63880	0.792;0.435;0.139;0.993;0.982	B;B;B;D;D	0.75020	0.415;0.115;0.056;0.985;0.968	D	0.86104	0.1558	10	0.56958	D	0.05	-6.4193	19.9595	0.97236	0.0:0.0:1.0:0.0	.	249;1248;941;983;985	Q99700-3;Q99700;Q24JQ7;F8VQP2;F8WB06	.;ATX2_HUMAN;.;.;.	K	303;985;1248;249;983;941;173	ENSP00000366843:Q1248K	ENSP00000366843:Q1248K	Q	-	1	0	ATXN2	110378218	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.974000	0.93433	2.797000	0.96272	0.563000	0.77884	CAG	.	.	.	none		0.502	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973		T	111893835	G	T	111893835	3	4	25	1	0	0	0	0	1	0	0	0	1211	1299	45	4	211	4	ATXN2	12	111893835	Missense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	43342135	111893835	21958060	62	1823											
OAS3	4940	hgsc.bcm.edu	37	chr12	113405314	113405314	+	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	ggcgagtactccacctgcttCacagagctacaacgggactt	10	8	10	13	2	1	1	1	0	0	1	2	3	2	2	2	2	5	3	2	2	3	4			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr12:113405314C>G	ENST00000228928.7	+	13	2960	c.2781C>G	c.(2779-2781)ttC>ttG	p.F927L	RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	927	OAS domain 3.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|nucleobase-containing compound metabolic process (GO:0006139)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|skin(2)	27						CCACCTGCTTCACAGAGCTAC	0.577																																					p.F927L		Atlas-SNP	.											.	OAS3	63	.	0			c.C2781G						PASS	.						60	63	62					12																	113405314		2139	4269	6408	SO:0001583	missense	4940	exon13			CTGCTTCACAGAG	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.2781C>G	chr12.hg19:g.113405314C>G	ENSP00000228928:p.Phe927Leu	155.0	0.0	.		137.0	44.0	.	NM_006187	Q2HJ14|Q9H3P5	Missense_Mutation	SNP	ENST00000228928.7	hg19	CCDS44981.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.11|15.11	2.736400|2.736400	0.49045|0.49045	.|.	.|.	ENSG00000111331|ENSG00000111331	ENST00000228928;ENST00000323881|ENST00000546973	T|.	0.55588|.	0.51|.	4.15|4.15	4.15|4.15	0.48705|0.48705	-oligoadenylate synthetase 1, domain 2/C-terminal (2);-5&apos (2);2&apos (2);|.	0.000000|.	0.35936|.	U|.	0.002889|.	T|.	0.70928|.	0.3280|.	M|M	0.71581|0.71581	2.175|2.175	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.83275|.	0.996|.	T|.	0.71159|.	-0.4674|.	10|.	0.87932|.	D|.	0|.	.|.	12.1472|12.1472	0.54029|0.54029	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	927|.	Q9Y6K5|.	OAS3_HUMAN|.	L|X	927;926|99	ENSP00000228928:F927L|.	ENSP00000228928:F927L|.	F|S	+|+	3|2	2|0	OAS3|OAS3	111889697|111889697	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.053000|0.053000	0.15095|0.15095	1.391000|1.391000	0.34475|0.34475	2.301000|2.301000	0.77427|0.77427	0.558000|0.558000	0.71614|0.71614	TTC|TCA	.	.	.	none		0.577	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1			G	113405314	C	G	113405314	3	3	25	1	0	0	0	0	1	0	0	0	10808	825	29	4	2831	4	OAS3	12	113405314	Missense_Mutation	SNP	C	TCGA-4A-A93X-01A-11D-A36X-10	1511479	113405314	20446581	63	1824											
DNAH10	196385	hgsc.bcm.edu	37	chr12	124323139	124323140	+	Frame_Shift_Ins	INS	-	-	A																															gactacttagattcgaagagINSaaatgctttcccaaggttct																										TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr12:124323139_124323140insA	ENST00000409039.3	+	28	4710_4711	c.4685_4686insA	c.(4684-4689)agaaatfs	p.N1563fs		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1563	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)		GATTCGAAGAGAAATGCTTTCC	0.515																																					p.R1562fs		Atlas-Indel,Pindel	.											DNAH10_same_name,NS,carcinoma,0,6	DNAH10	888	.	0			c.4685_4686insA						PASS	.																																			SO:0001589	frameshift_variant	196385	exon28			.	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.4688dupA	chr12.hg19:g.124323142_124323142dupA	ENSP00000386770:p.Asn1563fs	90.0	0.0	0		119.0	28.0	0.235294	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Frame_Shift_Ins	INS	ENST00000409039.3	hg19	CCDS9255.2																																																																																			.	.	.	none		0.515	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			A	124323140	-	A	124323139	7	5	25	1	0	1	1	0	0	0	0	0	4600	942	33	0	4795	0	DNAH10	12	124323139	Frame_Shift_Ins	INS	-	TCGA-4A-A93X-01A-11D-A36X-10	10917825	124323139	9528756	64	1825											
BRI3BP	140707	hgsc.bcm.edu	37	chr12	125509745	125509745	+	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	tcctgcgtgtacatcctgcaCaagtacgagggcgagccgga	9	7	13	12	4	0	0	0	0	0	0	2	3	2	1	3	2	5	3	3	2	3	2			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr12:125509745C>T	ENST00000341446.8	+	3	616	c.525C>T	c.(523-525)caC>caT	p.H175H		NM_080626.5	NP_542193.3			BRI3 binding protein											large_intestine(1)|lung(8)|ovary(1)	10	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.35e-05)|Epithelial(86;0.000426)|all cancers(50;0.00576)		ACATCCTGCACAAGTACGAGG	0.617																																					p.H175H		Atlas-SNP	.											.	BRI3BP	18	.	0			c.C525T						PASS	.						127	97	107					12																	125509745		2203	4300	6503	SO:0001819	synonymous_variant	140707	exon3			CCTGCACAAGTAC	AF284094	CCDS9262.1	12q24.1	2008-08-04			ENSG00000184992	ENSG00000184992			14251	protein-coding gene	gene with protein product		615627				11860200, 17765869	Standard	NM_080626		Approved	BNAS1, KG19, HCCR-2	uc001uha.1	Q8WY22	OTTHUMG00000168548	ENST00000341446.8:c.525C>T	chr12.hg19:g.125509745C>T		75.0	0.0	.		95.0	32.0	.	NM_080626		Silent	SNP	ENST00000341446.8	hg19	CCDS9262.1																																																																																			.	.	.	none		0.617	BRI3BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400200.2	NM_080626		T	125509745	C	T	125509745	2	4	25	1	0	0	0	0	0	0	0	1	1515	477	17	2		2	BRI3BP	12	125509745	Silent	SNP	C	TCGA-4A-A93X-01A-11D-A36X-10	1186606	125509745	8342150	65	1826											
SPERT	220082	hgsc.bcm.edu	37	chr13	46288259	46288259	+	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	gagagatgaggcaggcgctgCaggccctgctcaaggagaac	11	4	16	10	1	1	3	1	1	0	2	1	6	1	3	1	4	3	4	1	4	2	0			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr13:46288259C>T	ENST00000310521.1	+	3	1179	c.1099C>T	c.(1099-1101)Cag>Tag	p.Q367*	SPERT_ENST00000378966.3_Nonsense_Mutation_p.Q331*	NM_152719.1	NP_689932.1	Q8NA61	SPERT_HUMAN	spermatid associated	367						cytoplasmic membrane-bounded vesicle (GO:0016023)				NS(1)|central_nervous_system(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	15		Breast(56;0.000819)|Lung NSC(96;0.00227)|Prostate(109;0.00703)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;7.26e-05)		GCAGGCGCTGCAGGCCCTGCT	0.692																																					p.Q367X		Atlas-SNP	.											.	SPERT	54	.	0			c.C1099T						PASS	.						8	9	9					13																	46288259		2181	4250	6431	SO:0001587	stop_gained	220082	exon3			GCGCTGCAGGCCC	AK093129	CCDS9399.1, CCDS66540.1	13q14.13	2010-03-23			ENSG00000174015	ENSG00000174015			30720	protein-coding gene	gene with protein product	"spermatid flower-like structure protein", "testis specific leucine zipper protein nurit", "chibby homolog 2 (Drosophila)"					12204287, 20096028	Standard	NM_001286341		Approved	NURIT, CBY2	uc001van.1	Q8NA61	OTTHUMG00000016861	ENST00000310521.1:c.1099C>T	chr13.hg19:g.46288259C>T	ENSP00000309189:p.Gln367*	111.0	0.0	.		127.0	59.0	.	NM_152719	A8K8I5|Q8NHV2	Nonsense_Mutation	SNP	ENST00000310521.1	hg19	CCDS9399.1	.	.	.	.	.	.	.	.	.	.	C	39	7.802377	0.98498	.	.	ENSG00000174015	ENST00000310521;ENST00000378966	.	.	.	4.83	4.83	0.62350	.	0.121108	0.37669	N	0.001987	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	.	14.7672	0.69648	0.0:1.0:0.0:0.0	.	.	.	.	X	367;331	.	ENSP00000309189:Q367X	Q	+	1	0	SPERT	45186260	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	2.125000	0.42016	2.502000	0.84385	0.609000	0.83330	CAG	.	.	.	none		0.692	SPERT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044786.2	NM_152719		T	46288259	C	T	46288259	4	4	25	1	0	0	0	0	0	1	0	0	15051	711	25	2	1109	2	SPERT	13	46288259	Nonsense_Mutation	SNP	C	TCGA-4A-A93X-01A-11D-A36X-10		46288259	68881619	66	1827											
INTS6	26512	hgsc.bcm.edu	37	chr13	51952390	51952390	+	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	attaccttattcagcaaagcAacttggaacccagtgtattc	13	12	6	10	0	1	0	1	0	0	0	2	1	1	1	2	1	5	3	2	1	6	6			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr13:51952390A>T	ENST00000311234.4	-	12	2059	c.1587T>A	c.(1585-1587)gtT>gtA	p.V529V	INTS6_ENST00000497989.1_Silent_p.V351V|INTS6_ENST00000490542.1_Silent_p.V213V|INTS6_ENST00000463928.1_Intron|INTS6_ENST00000398119.2_Silent_p.V516V|INTS6_ENST00000425000.1_Silent_p.V97V	NM_012141.2	NP_036273.1	Q9UL03	INT6_HUMAN	integrator complex subunit 6	529					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)		TCAGCAAAGCAACTTGGAACC	0.363																																					p.V529V		Atlas-SNP	.											.	INTS6	72	.	0			c.T1587A						PASS	.						152	146	148					13																	51952390		2203	4300	6503	SO:0001819	synonymous_variant	26512	exon12			CAAAGCAACTTGG	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.1587T>A	chr13.hg19:g.51952390A>T		111.0	0.0	.		174.0	86.0	.	NM_012141	Q0P664|Q6PJP4|Q9UFK0|Q9Y5M9	Silent	SNP	ENST00000311234.4	hg19	CCDS9428.1																																																																																			.	.	.	none		0.363	INTS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045023.1	NM_012141		T	51952390	A	T	51952390	2	4	25	1	0	0	0	0	0	0	0	1	7789	117	5	5		5	INTS6	13	51952390	Silent	SNP	A	TCGA-4A-A93X-01A-11D-A36X-10	5664131	51952390	63217488	67	1828											
EML5	161436	hgsc.bcm.edu	37	chr14	89093338	89093338	+	Missense_Mutation	SNP	T	T	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	gtatctgaatctggtcggaaTtctgccacaaaaatacgttg	12	12	9	8	2	3	1	0	1	3	0	4	2	3	2	1	2	2	2	1	2	6	4			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr14:89093338T>G	ENST00000380664.5	-	33	4559	c.4560A>C	c.(4558-4560)gaA>gaC	p.E1520D	EML5_ENST00000554922.1_Missense_Mutation_p.E1528D|EML5_ENST00000553320.1_5'Flank|EML5_ENST00000352093.5_Missense_Mutation_p.E1482D			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	1520						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						CTGGTCGGAATTCTGCCACAA	0.428																																					p.E1528D		Atlas-SNP	.											.	EML5	141	.	0			c.A4584C						PASS	.						138	131	133					14																	89093338		1850	4106	5956	SO:0001583	missense	161436	exon34			TCGGAATTCTGCC	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.4560A>C	chr14.hg19:g.89093338T>G	ENSP00000370039:p.Glu1520Asp	68.0	0.0	.		77.0	24.0	.	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	hg19	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	T	14.45	2.538746	0.45176	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.49432	0.78;0.78;0.78	5.04	3.87	0.44632	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.120772	0.56097	D	0.000030	T	0.50905	0.1643	L	0.43646	1.37	0.39864	D	0.973418	B;D	0.69078	0.179;0.997	B;D	0.63283	0.121;0.913	T	0.47407	-0.9120	10	0.15499	T	0.54	-29.3795	8.3227	0.32138	0.0:0.1541:0.0:0.8459	.	1528;1520	Q05BV3-5;Q05BV3	.;EMAL5_HUMAN	D	1528;1482;1520	ENSP00000451998:E1528D;ENSP00000298315:E1482D;ENSP00000370039:E1520D	ENSP00000298315:E1482D	E	-	3	2	EML5	88163091	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.593000	0.36686	0.924000	0.37069	0.533000	0.62120	GAA	.	.	.	none		0.428	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			G	89093338	T	G	89093338	3	3	25	1	0	0	0	0	1	0	0	0	5102	1490	52	5	1389	5	EML5	14	89093338	Missense_Mutation	SNP	T	TCGA-4A-A93X-01A-11D-A36X-10		89093338	18256202	68	1829											
HSP90AA1	3320	hgsc.bcm.edu	37	chr14	102551272	102551273	+	Frame_Shift_Ins	INS	-	-	TTCT																															tcttctttttctttttcttcINSttctttgtcttccttttctt																										TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr14:102551272_102551273insTTCT	ENST00000216281.8	-	5	931_932	c.726_727insAGAA	c.(724-729)gaagaafs	p.E243fs	HSP90AA1_ENST00000441629.2_Frame_Shift_Ins_p.E64fs|HSP90AA1_ENST00000334701.7_Frame_Shift_Ins_p.E365fs	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1	243					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)	tctttttcttcttctttgtctt	0.386																																					p.E365fs		Atlas-Indel,Pindel	.											.	HSP90AA1	65	.	0			c.1093_1094insAGAA						PASS	.																																			SO:0001589	frameshift_variant	3320	exon6			.	M27024	CCDS9967.1, CCDS32160.1	14q32.33	2011-09-02	2006-02-24	2006-02-24	ENSG00000080824	ENSG00000080824		"Heat shock proteins / HSPC"	5253	protein-coding gene	gene with protein product		140571	"heat shock 90kD protein 1, alpha", "heat shock 90kDa protein 1, alpha"	HSPC1, HSPCA		2527334, 16269234	Standard	NM_001017963		Approved	Hsp89, Hsp90, FLJ31884, HSP90N	uc001ykv.4	P07900		ENST00000216281.8:c.727_730dupAGAA	chr14.hg19:g.102551273_102551276dupTTCT	ENSP00000216281:p.Glu243fs	148.0	0.0	0		158.0	30.0	0.189873	NM_001017963	A8K500|B3KPJ9|Q2PP14|Q5CAQ6|Q5CAQ7|Q9BVQ5	Frame_Shift_Ins	INS	ENST00000216281.8	hg19	CCDS9967.1																																																																																			.	.	.	none		0.386	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414952.2	NM_005348		TTCT	102551273	-	TTCT	102551272	7	5	25	1	0	1	1	0	0	0	0	0	7408	922	32	0	1499	0	HSP90AA1	14	102551272	Frame_Shift_Ins	INS	-	TCGA-4A-A93X-01A-11D-A36X-10	13457934	102551272	4798268	69	1830											
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105406085	105406085	+	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	gtttgacccagaaacaaggaActctttgactttagctgctg	11	12	9	9	0	1	3	0	2	1	1	1	4	1	4	1	1	4	3	1	1	4	4			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr14:105406085A>T	ENST00000333244.5	-	7	15822	c.15703T>A	c.(15703-15705)Ttc>Atc	p.F5235I	AHNAK2_ENST00000557457.1_Missense_Mutation_p.F233I	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	5235						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)			GAAACAAGGAACTCTTTGACT	0.547																																					p.F5235I		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T15703A						PASS	.						260	282	275					14																	105406085		2065	4199	6264	SO:0001583	missense	113146	exon7			CAAGGAACTCTTT	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.15703T>A	chr14.hg19:g.105406085A>T	ENSP00000353114:p.Phe5235Ile	72.0	0.0	.		55.0	39.0	.	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	hg19	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	A	9.688	1.151129	0.21371	.	.	ENSG00000185567	ENST00000557457;ENST00000333244	T;T	0.02737	4.18;5.4	3.73	-3.5	0.04710	.	4.827340	0.01750	U	0.029844	T	0.01592	0.0051	N	0.08118	0	0.09310	N	1	B	0.13145	0.007	B	0.08055	0.003	T	0.44003	-0.9356	10	0.21014	T	0.42	.	2.4033	0.04407	0.2008:0.301:0.3769:0.1213	.	5235	Q8IVF2	AHNK2_HUMAN	I	233;5235	ENSP00000450998:F233I;ENSP00000353114:F5235I	ENSP00000353114:F5235I	F	-	1	0	AHNAK2	104477130	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.436000	0.06922	-0.671000	0.05274	-0.441000	0.05720	TTC	.	.	.	none		0.547	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		T	105406085	A	T	105406085	3	4	25	1	0	0	0	0	1	0	0	0	415	43	2	5	1688	5	AHNAK2	14	105406085	Missense_Mutation	SNP	A	TCGA-4A-A93X-01A-11D-A36X-10	2854813	105406085	1943455	70	1831											
GCOM1	100820829	hgsc.bcm.edu	37	chr15	57967233	57967233	+	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	caagactgaagtggaaaccaGagagataggagtgggctgtg	14	6	16	5	0	0	4	0	1	0	3	0	7	0	6	1	3	1	1	1	3	4	1			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr15:57967233G>T	ENST00000267853.5	+	12	1365	c.1271G>T	c.(1270-1272)aGa>aTa	p.R424I	GCOM1_ENST00000396180.1_Missense_Mutation_p.R393I|GCOM1_ENST00000572390.1_Missense_Mutation_p.R396I|MYZAP_ENST00000380565.4_Missense_Mutation_p.R396I|GCOM1_ENST00000380569.2_Missense_Mutation_p.R424I|GCOM1_ENST00000587652.1_Missense_Mutation_p.R424I|GCOM1_ENST00000380568.3_Missense_Mutation_p.R424I|GCOM1_ENST00000574161.1_Missense_Mutation_p.R424I|POLR2M_ENST00000380563.2_5'UTR|GCOM1_ENST00000380561.2_Missense_Mutation_p.R365I|GCOM1_ENST00000380560.2_Missense_Mutation_p.R355I			P0CAP1	MYZAP_HUMAN	myocardial zonula adherens protein	424					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)											GTGGAAACCAGAGAGATAGGA	0.368																																					p.R424I		Atlas-SNP	.											.	GCOM1	66	.	0			c.G1271T						PASS	.						103	105	104					15																	57967233		2192	4292	6484	SO:0001583	missense	145781	exon12			AAACCAGAGAGAT	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.1271G>T	chr15.hg19:g.57967233G>T	ENSP00000267853:p.Arg424Ile	196.0	0.0	.		117.0	48.0	.	NM_001018090	D2E9U7|Q6EER8|Q6EES2|Q6EEV3|Q6EF00|Q6EF01|Q6EF02|Q6EF46|Q6EFN8|Q6EM48|Q6K046|Q6K050|Q6K051|Q6ZQZ3|Q8NC58|Q8NCF3|Q96DI5|Q96JB7|Q96NF5	Missense_Mutation	SNP	ENST00000267853.5	hg19	CCDS10162.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.229693	0.79688	.	.	ENSG00000137878	ENST00000380569;ENST00000380561;ENST00000396180;ENST00000380560;ENST00000267853;ENST00000380565;ENST00000380568	T;T;T;T;T;T;T	0.36699	1.5;1.47;1.53;1.54;1.46;1.24;1.49	5.55	5.55	0.83447	.	0.090649	0.85682	D	0.000000	T	0.49440	0.1557	L	0.34521	1.04	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;1.0;1.0	D;D;D;D	0.76575	0.977;0.931;0.988;0.988	T	0.49312	-0.8953	10	0.72032	D	0.01	-17.4231	14.9994	0.71459	0.0:0.0:1.0:0.0	.	424;424;396;424	P0CAP1-2;P0CAP1-11;P0CAP1-4;P0CAP1	.;.;.;GCOM1_HUMAN	I	424;365;393;355;424;396;424	ENSP00000369943:R424I;ENSP00000369935:R365I;ENSP00000379483:R393I;ENSP00000369933:R355I;ENSP00000267853:R424I;ENSP00000369939:R396I;ENSP00000369942:R424I	ENSP00000267853:R424I	R	+	2	0	GCOM1	55754525	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.192000	0.72069	2.598000	0.87819	0.655000	0.94253	AGA	.	.	.	none		0.368	MYZAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255716.2	NM_001018100		T	57967233	G	T	57967233	3	4	25	1	0	0	0	0	1	0	0	0	6311	942	33	4	1317	4	GCOM1	15	57967233	Missense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10		57967233	44564159	71	1832											
RAB26	25837	hgsc.bcm.edu	37	chr16	2203146	2203146	+	Splice_Site	DEL	G	G	-																															gctggcagcagctgtttacaGgagtatggactgcccttcat																										TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr16:2203146delG	ENST00000210187.6	+	8	751		c.e8-1		RAB26_ENST00000541451.1_Splice_Site|TRAF7_ENST00000326181.6_5'Flank|SNORD60_ENST00000383903.1_RNA|RP11-304L19.5_ENST00000563192.1_lincRNA	NM_014353.4	NP_055168.2	Q9ULW5	RAB26_HUMAN	RAB26, member RAS oncogene family						exocrine system development (GO:0035272)|Golgi to plasma membrane protein transport (GO:0043001)|regulated secretory pathway (GO:0045055)|regulation of exocytosis (GO:0017157)|small GTPase mediated signal transduction (GO:0007264)	Golgi membrane (GO:0000139)|intrinsic component of plasma membrane (GO:0031226)|secretory granule membrane (GO:0030667)	GMP binding (GO:0019002)|GTP binding (GO:0005525)			kidney(1)|large_intestine(1)|lung(3)	5						GCTGTTTACAGGAGTATGGAC	0.637																																					.		Atlas-Indel,Pindel	.											.	RAB26	9	.	0			c.592-2G>-						PASS	.						58	56	56					16																	2203146		2197	4300	6497	SO:0001630	splice_region_variant	25837	exon8			.	AB027137	CCDS10460.1	16p13.3	2008-07-28			ENSG00000167964	ENSG00000167964		"RAB, member RAS oncogene"	14259	protein-coding gene	gene with protein product		605455				11043516	Standard	NM_014353		Approved		uc002cou.3	Q9ULW5	OTTHUMG00000128829	ENST00000210187.6:c.592-1G>-	chr16.hg19:g.2203146delG		144.0	0.0	0		117.0	34.0	0.290598	NM_014353	B2RAA6|Q3L6K5|Q6NXS7	Splice_Site	DEL	ENST00000210187.6	hg19	CCDS10460.1																																																																																			.	.	.	none		0.637	RAB26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250767.2		Intron	-	2203146	G	-	2203146	8	5	25	1	0	1	0	1	0	0	1	0	12926	1014	35	0	621	0	RAB26	16	2203146	Splice_Site	DEL	G	TCGA-4A-A93X-01A-11D-A36X-10		2203146	88151607	72	1833											
SRRM2	23524	hgsc.bcm.edu	37	chr16	2814199	2814199	+	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	ggtcatctccagaaacaaaaGagcaaaatagtgcattgcct	16	8	8	9	0	2	2	1	0	1	2	3	2	2	2	2	1	4	2	2	1	6	2			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr16:2814199G>T	ENST00000301740.8	+	11	4219	c.3670G>T	c.(3670-3672)Gag>Tag	p.E1224*		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	1224	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						AGAAACAAAAGAGCAAAATAG	0.473																																					p.E1224X		Atlas-SNP	.											.	SRRM2	263	.	0			c.G3670T						PASS	.						120	124	123					16																	2814199		2198	4300	6498	SO:0001587	stop_gained	23524	exon11			ACAAAAGAGCAAA	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.3670G>T	chr16.hg19:g.2814199G>T	ENSP00000301740:p.Glu1224*	115.0	0.0	.		110.0	65.0	.	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Nonsense_Mutation	SNP	ENST00000301740.8	hg19	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	G	39	7.886209	0.98542	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	.	.	.	6.17	5.13	0.70059	.	0.266442	0.32785	N	0.005652	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	-1.4439	9.3053	0.37872	0.1728:0.0:0.8272:0.0	.	.	.	.	X	1224;1224;476	.	ENSP00000301740:E1224X	E	+	1	0	SRRM2	2754200	1.000000	0.71417	0.983000	0.44433	0.167000	0.22549	1.237000	0.32695	1.463000	0.47967	0.655000	0.94253	GAG	.	.	.	none		0.473	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			T	2814199	G	T	2814199	4	4	25	1	0	0	0	0	0	1	0	0	15181	943	33	4	3708	4	SRRM2	16	2814199	Nonsense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	611053	2814199	87540554	73	1834											
PDPR	55066	hgsc.bcm.edu	37	chr16	70190605	70190606	+	Frame_Shift_Ins	INS	-	-	A																															gctttgtgcacaatttttctINSgaggacacgggggaagagca																										TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr16:70190605_70190606insA	ENST00000288050.4	+	19	3420_3421	c.2463_2464insA	c.(2464-2466)gagfs	p.E822fs	PDPR_ENST00000542659.1_Frame_Shift_Ins_p.E167fs|PDPR_ENST00000398122.3_Frame_Shift_Ins_p.E722fs|RP11-296I10.3_ENST00000502126.1_RNA|RP11-296I10.3_ENST00000566989.1_RNA|PDPR_ENST00000562100.1_3'UTR|PDPR_ENST00000567046.1_Frame_Shift_Ins_p.E180fs|PDPR_ENST00000568530.1_Frame_Shift_Ins_p.E822fs	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	822					cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		ACAATTTTTCTGAGGACACGGG	0.55																																					p.S821fs		Atlas-INDEL	.											.	PDPR	66	.	0			c.2463_2464insA						PASS	.																																			SO:0001589	frameshift_variant	55066	exon19			.		CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857			30264	protein-coding gene	gene with protein product						9395502	Standard	NM_017990		Approved	PDP3	uc002eyf.1	Q8NCN5		Exception_encountered	chr16.hg19:g.70190605_70190606insA	ENSP00000288050:p.Glu822fs	117.0	0.0	0		135.0	14.0	0.103704	NM_017990	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Frame_Shift_Ins	INS	ENST00000288050.4	hg19	CCDS45520.1																																																																																			.	.	.	none		0.55	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1	NM_017990		A	70190606	-	A	70190605	7	5	25	1	0	1	1	0	0	0	0	0	11696	1567	55	0	2529	0	PDPR	16	70190605	Frame_Shift_Ins	INS	-	TCGA-4A-A93X-01A-11D-A36X-10	67376406	70190605	20164148	74	1835											
SCARF1	8578	hgsc.bcm.edu	37	chr17	1543778	1543778	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagggtcacagcgctgacagTggccagtatctggctcacag	9	7	13	12	1	3	1	2	1	1	0	3	1	3	1	1	3	1	3	1	3	1	1			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr17:1543778T>C	ENST00000263071.4	-	5	1023	c.974A>G	c.(973-975)cAc>cGc	p.H325R	SCARF1_ENST00000574545.1_5'Flank|SCARF1_ENST00000348987.3_Missense_Mutation_p.H325R|SCARF1_ENST00000571272.1_Missense_Mutation_p.H325R	NM_003693.2|NM_145350.1	NP_003684.2|NP_663325.1	Q14162	SREC_HUMAN	scavenger receptor class F, member 1	325	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)		GCGCTGACAGTGGCCAGTATC	0.662																																					p.H325R		Atlas-SNP	.											.	SCARF1	46	.	0			c.A974G						PASS	.						15	13	14					17																	1543778		2182	4287	6469	SO:0001583	missense	8578	exon5			TGACAGTGGCCAG	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.974A>G	chr17.hg19:g.1543778T>C	ENSP00000263071:p.His325Arg	156.0	0.0	.		155.0	43.0	.	NM_145350	A8MQ05|O43701|Q8NHD2|Q8NHD3|Q8NHD4|Q8NHD5	Missense_Mutation	SNP	ENST00000263071.4	hg19	CCDS11007.1	.	.	.	.	.	.	.	.	.	.	T	14.43	2.533044	0.45073	.	.	ENSG00000074660	ENST00000263071;ENST00000348987;ENST00000434376	T;T;T	0.33216	1.42;1.42;1.42	5.24	5.24	0.73138	Growth factor, receptor (1);Epidermal growth factor-like (1);	0.000000	0.49305	D	0.000150	T	0.28400	0.0702	L	0.28344	0.845	0.22796	N	0.998725	D;P;B	0.53462	0.96;0.751;0.028	P;B;B	0.51016	0.656;0.139;0.113	T	0.11084	-1.0602	10	0.22706	T	0.39	-13.5328	10.626	0.45508	0.0:0.0:0.2943:0.7057	.	325;325;325	Q14162-2;Q14162;Q14162-3	.;SREC_HUMAN;.	R	325	ENSP00000263071:H325R;ENSP00000323964:H325R;ENSP00000411167:H325R	ENSP00000263071:H325R	H	-	2	0	SCARF1	1490528	0.001000	0.12720	0.995000	0.50966	0.941000	0.58515	0.362000	0.20284	2.199000	0.70637	0.533000	0.62120	CAC	.	.	.	none		0.662	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207081.4	NM_003693		C	1543778	T	C	1543778	3	2	25	1	0	0	0	0	1	0	0	0	13896	1696	59	3	1546	3	SCARF1	17	1543778	Missense_Mutation	SNP	T	TCGA-4A-A93X-01A-11D-A36X-10		1543778	79651432	75	1836											
CORO6	84940	hgsc.bcm.edu	37	chr17	27943974	27943974	+	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	accttgccacacaggtagacGatgctggagtcgggatcgta	10	8	13	10	3	0	1	0	0	0	1	2	4	0	3	2	3	2	3	2	3	2	3			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr17:27943974G>A	ENST00000445145.2	-	6	841	c.840C>T	c.(838-840)atC>atT	p.I280I	CORO6_ENST00000456796.3_Silent_p.I46I|CORO6_ENST00000580212.1_Silent_p.I240I|RP11-68I3.2_ENST00000581474.1_RNA|CORO6_ENST00000577909.1_Intron|CORO6_ENST00000345068.5_Silent_p.I280I|CORO6_ENST00000584969.1_Silent_p.I280I|CORO6_ENST00000388767.3_Silent_p.I280I			Q6QEF8	CORO6_HUMAN	coronin 6	280					actin cytoskeleton organization (GO:0030036)	actin cytoskeleton (GO:0015629)	actin filament binding (GO:0051015)			breast(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(2)	14						ACAGGTAGACGATGCTGGAGT	0.617																																					p.I280I		Atlas-SNP	.											.	CORO6	34	.	0			c.C840T						PASS	.						171	159	163					17																	27943974		2203	4300	6503	SO:0001819	synonymous_variant	84940	exon6			GTAGACGATGCTG	AF193039	CCDS11252.2	17q11.2	2013-01-10			ENSG00000167549	ENSG00000167549		"Coronins", "WD repeat domain containing"	21356	protein-coding gene	gene with protein product							Standard	NM_032854		Approved	FLJ14871	uc002hel.2	Q6QEF8	OTTHUMG00000132732	ENST00000445145.2:c.840C>T	chr17.hg19:g.27943974G>A		85.0	0.0	.		90.0	58.0	.	NM_032854	B3KU26|Q71MF3|Q8WYH7|Q96K02	Silent	SNP	ENST00000445145.2	hg19																																																																																				.	.	.	none		0.617	CORO6-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000447831.1	NM_032854		A	27943974	G	A	27943974	2	1	25	1	0	0	0	0	0	0	0	1	3760	1048	37	1		1	CORO6	17	27943974	Silent	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	26400196	27943974	53251236	76	1837											
MYO1D	4642	hgsc.bcm.edu	37	chr17	30932207	30932207	+	Missense_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	tgaggtctttgttgtctttcGtatggaacactacaagttgg	8	16	11	6	1	2	1	0	1	2	0	3	2	2	2	0	3	2	3	0	3	4	6			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr17:30932207G>A	ENST00000318217.5	-	21	3066	c.2762C>T	c.(2761-2763)aCg>aTg	p.T921M	MYO1D_ENST00000579584.1_Missense_Mutation_p.T921M|MYO1D_ENST00000394649.4_Missense_Mutation_p.T833M	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID	921	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)			GTTGTCTTTCGTATGGAACAC	0.423																																					p.T921M		Atlas-SNP	.											MYO1D,colon,carcinoma,0,1	MYO1D	93	.	0			c.C2762T						PASS	.						130	110	117					17																	30932207		2203	4300	6503	SO:0001583	missense	4642	exon21			TCTTTCGTATGGA	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.2762C>T	chr17.hg19:g.30932207G>A	ENSP00000324527:p.Thr921Met	115.0	0.0	.		140.0	10.0	.	NM_015194	A6H8V3|Q8NHP9	Missense_Mutation	SNP	ENST00000318217.5	hg19	CCDS32615.1	.	.	.	.	.	.	.	.	.	.	G	16.39	3.109801	0.56398	.	.	ENSG00000176658	ENST00000318217;ENST00000394649	T	0.36699	1.24	4.88	4.88	0.63580	Myosin tail 2 (1);	0.000000	0.40640	U	0.001050	T	0.26846	0.0657	N	0.25647	0.755	0.80722	D	1	P;P	0.38565	0.637;0.637	B;B	0.34301	0.179;0.118	T	0.09100	-1.0690	10	0.48119	T	0.1	.	15.8776	0.79178	0.0:0.0:1.0:0.0	.	832;921	Q7Z3N6;O94832	.;MYO1D_HUMAN	M	921;113	ENSP00000324527:T921M	ENSP00000324527:T921M	T	-	2	0	MYO1D	27956320	1.000000	0.71417	0.995000	0.50966	0.956000	0.61745	7.605000	0.82844	2.421000	0.82119	0.655000	0.94253	ACG	.	.	.	none		0.423	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1			A	30932207	G	A	30932207	3	1	25	1	0	0	0	0	1	0	0	0	10078	1145	40	1	266	1	MYO1D	17	30932207	Missense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	2988233	30932207	50263003	77	1838											
CACNB1	782	hgsc.bcm.edu	37	chr17	37340296	37340296	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggctcacccaggctggagcGtgtgttggagcgctcaatga	8	8	15	10	2	2	1	2	1	0	0	2	3	2	3	1	4	2	4	1	4	1	1			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr17:37340296G>A	ENST00000394303.3	-	10	1093	c.886C>T	c.(886-888)Cgc>Tgc	p.R296C	CACNB1_ENST00000394310.3_Missense_Mutation_p.R296C|CACNB1_ENST00000344140.5_Missense_Mutation_p.R341C|CACNB1_ENST00000582877.1_5'Flank	NM_000723.4	NP_000714.3	Q02641	CACB1_HUMAN	calcium channel, voltage-dependent, beta 1 subunit	296				SNTR -> LQHT (in Ref. 3; AAA36167). {ECO:0000305}.	axon guidance (GO:0007411)|protein targeting to membrane (GO:0006612)|transport (GO:0006810)	sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	16					Dronedarone(DB04855)|Ibutilide(DB00308)|Magnesium Sulfate(DB00653)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	AGGCTGGAGCGTGTGTTGGAG	0.587																																					p.R341C	Esophageal Squamous(5;100 366 38393 41452 45827)	Atlas-SNP	.											.	CACNB1	89	.	0			c.C1021T						PASS	.						119	102	108					17																	37340296		2203	4300	6503	SO:0001583	missense	782	exon10			TGGAGCGTGTGTT		CCDS11334.1, CCDS42311.1, CCDS45665.1	17q21-q22	2013-03-20			ENSG00000067191	ENSG00000067191		"Calcium channel subunits"	1401	protein-coding gene	gene with protein product		114207		CACNLB1		8381767, 8395940	Standard	NM_000723		Approved		uc002hrm.2	Q02641	OTTHUMG00000133217	ENST00000394303.3:c.886C>T	chr17.hg19:g.37340296G>A	ENSP00000377840:p.Arg296Cys	73.0	0.0	.		61.0	41.0	.	NM_199247	A8K114|O15331|Q02639|Q02640|Q8N3X9|Q9C085|Q9UD79	Missense_Mutation	SNP	ENST00000394303.3	hg19	CCDS42311.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.415693	0.83449	.	.	ENSG00000067191	ENST00000539338;ENST00000394303;ENST00000344140;ENST00000394310;ENST00000536613	T;T;T	0.44083	0.93;0.93;0.93	5.42	5.42	0.78866	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (1);	0.000000	0.85682	D	0.000000	T	0.72137	0.3423	M	0.89715	3.055	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.994;0.979;0.997	T	0.78507	-0.2177	10	0.87932	D	0	-13.5845	17.986	0.89156	0.0:0.0:1.0:0.0	.	341;296;296	Q02641-2;Q02641-3;Q02641	.;.;CACB1_HUMAN	C	246;296;341;296;247	ENSP00000377840:R296C;ENSP00000345461:R341C;ENSP00000377847:R296C	ENSP00000345461:R341C	R	-	1	0	CACNB1	34593822	1.000000	0.71417	0.985000	0.45067	0.959000	0.62525	7.579000	0.82511	2.562000	0.86427	0.491000	0.48974	CGC	.	.	.	none		0.587	CACNB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256945.3			A	37340296	G	A	37340296	3	1	25	1	0	0	0	0	1	0	0	0	2554	1145	40	1	1035	1	CACNB1	17	37340296	Missense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	6408089	37340296	43854914	78	1839											
SCRN2	90507	hgsc.bcm.edu	37	chr17	45916327	45916327	+	Missense_Mutation	SNP	A	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	gctccgggtgttgggccgagAtgtccgtgccaatgctcagc	5	9	15	12	3	1	1	1	0	0	1	3	2	3	1	4	2	3	3	4	2	1	1			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr17:45916327A>C	ENST00000290216.9	-	5	727	c.602T>G	c.(601-603)aTc>aGc	p.I201S	SCRN2_ENST00000584123.1_Missense_Mutation_p.I209S|SCRN2_ENST00000407215.3_Missense_Mutation_p.I201S	NM_001145023.1|NM_138355.3	NP_001138495.1|NP_612364.2	Q96FV2	SCRN2_HUMAN	secernin 2	201						extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)			cervix(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	14						TTGGGCCGAGATGTCCGTGCC	0.587																																					p.I201S		Atlas-SNP	.											.	SCRN2	35	.	0			c.T602G						PASS	.						84	88	87					17																	45916327		2203	4300	6503	SO:0001583	missense	90507	exon5			GCCGAGATGTCCG	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.602T>G	chr17.hg19:g.45916327A>C	ENSP00000290216:p.Ile201Ser	54.0	0.0	.		55.0	33.0	.	NM_138355	A8K3N1|B7Z8S7|E9PBV5|Q96AC3|Q9BU04	Missense_Mutation	SNP	ENST00000290216.9	hg19	CCDS11519.1	.	.	.	.	.	.	.	.	.	.	A	16.58	3.162687	0.57368	.	.	ENSG00000141295	ENST00000290216;ENST00000407215	T;T	0.22945	1.93;1.93	5.52	5.52	0.82312	.	0.204208	0.50627	D	0.000110	T	0.44767	0.1309	M	0.90759	3.145	0.53688	D	0.999973	P;P;P	0.47484	0.81;0.896;0.81	P;P;P	0.49887	0.625;0.625;0.625	T	0.52786	-0.8529	10	0.52906	T	0.07	-16.3059	9.1893	0.37189	0.9175:0.0:0.0825:0.0	.	201;201;201	E9PBV5;Q96FV2;B7Z8S7	.;SCRN2_HUMAN;.	S	201	ENSP00000290216:I201S;ENSP00000383935:I201S	ENSP00000290216:I201S	I	-	2	0	SCRN2	43271326	1.000000	0.71417	1.000000	0.80357	0.148000	0.21650	7.472000	0.80996	2.091000	0.63221	0.533000	0.62120	ATC	.	.	.	none		0.587	SCRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441383.1	NM_138355		C	45916327	A	C	45916327	3	2	25	1	0	0	0	0	1	0	0	0	13952	333	12	5	709	5	SCRN2	17	45916327	Missense_Mutation	SNP	A	TCGA-4A-A93X-01A-11D-A36X-10	8576031	45916327	35278883	79	1840											
LUC7L3	51747	hgsc.bcm.edu	37	chr17	48827997	48827998	+	Frame_Shift_Ins	INS	-	-	T																															accagtgaagacattaaatcINStgaaggtgacactcagtcca																										TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr17:48827997_48827998insT	ENST00000505658.1	+	10	1463_1464	c.1274_1275insT	c.(1273-1278)tctgaafs	p.E426fs	LUC7L3_ENST00000240304.1_Frame_Shift_Ins_p.E426fs|LUC7L3_ENST00000393227.2_Frame_Shift_Ins_p.E426fs|LUC7L3_ENST00000544170.1_Frame_Shift_Ins_p.E350fs			O95232	LC7L3_HUMAN	LUC7-like 3 (S. cerevisiae)	426					mRNA splice site selection (GO:0006376)|RNA splicing (GO:0008380)	focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|U1 snRNP (GO:0005685)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	12						GACATTAAATCTGAAGGTGACA	0.396																																					p.S425fs		Atlas-Indel,Pindel	.											.	LUC7L3	32	.	0			c.1274_1275insT						PASS	.																																			SO:0001589	frameshift_variant	51747	exon10			.		CCDS11573.1	17q21.33	2010-02-17			ENSG00000108848	ENSG00000108848			24309	protein-coding gene	gene with protein product	"cisplatin resistance associated overexpressed protein", "CRE-associated protein"	609434				10631324, 12565863	Standard	NM_016424		Approved	LUC7A, CROP, OA48-18, CREAP-1, FLJ11063, CRA, hLuc7A	uc002iss.3	O95232	OTTHUMG00000162257	ENST00000505658.1:c.1275dupT	chr17.hg19:g.48827998_48827998dupT	ENSP00000425092:p.Glu426fs	296.0	0.0	0		297.0	93.0	0.313131	NM_006107	B3KN54|D3DTY1|Q6PHR9|Q9NUY0|Q9P2S7	Frame_Shift_Ins	INS	ENST00000505658.1	hg19	CCDS11573.1																																																																																			.	.	.	none		0.396	LUC7L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368205.2	NM_016424		T	48827998	-	T	48827997	7	5	25	1	0	1	1	0	0	0	0	0	9091	913	32	0	1312	0	LUC7L3	17	48827997	Frame_Shift_Ins	INS	-	TCGA-4A-A93X-01A-11D-A36X-10	2911670	48827997	32367213	80	1841											
ABCA8	10351	hgsc.bcm.edu	37	chr17	66915445	66915445	+	Missense_Mutation	SNP	T	T	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	ttaacatatttttgtacctcTttatccacttcttgtggcag	8	19	5	9	0	2	0	0	0	2	0	3	0	3	0	2	1	2	2	2	1	4	9			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr17:66915445T>G	ENST00000269080.2	-	13	1922	c.1785A>C	c.(1783-1785)aaA>aaC	p.K595N	ABCA8_ENST00000430352.2_Missense_Mutation_p.K595N|ABCA8_ENST00000586539.1_Missense_Mutation_p.K595N	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	595	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)					TTTGTACCTCTTTATCCACTT	0.318																																					p.K595N		Atlas-SNP	.											.	ABCA8	213	.	0			c.A1785C						PASS	.						120	121	121					17																	66915445		2203	4300	6503	SO:0001583	missense	10351	exon13			TACCTCTTTATCC	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.1785A>C	chr17.hg19:g.66915445T>G	ENSP00000269080:p.Lys595Asn	57.0	0.0	.		49.0	14.0	.	NM_007168	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	hg19	CCDS11680.1	.	.	.	.	.	.	.	.	.	.	T	4.610	0.113350	0.08831	.	.	ENSG00000141338	ENST00000269080;ENST00000430352;ENST00000541225	T;D	0.93859	1.11;-3.3	4.54	2.25	0.28309	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.926293	0.09012	N	0.861352	D	0.83746	0.5321	N	0.11284	0.12	0.28435	N	0.917098	B;B;B;B;B	0.09022	0.002;0.0;0.002;0.0;0.0	B;B;B;B;B	0.12837	0.005;0.005;0.008;0.003;0.005	T	0.73597	-0.3932	10	0.56958	D	0.05	.	2.3391	0.04255	0.1542:0.0848:0.1604:0.6006	.	534;595;595;595;595	F5H6Z4;A1L3U3;B4DJ11;C9JQE6;O94911	.;.;.;.;ABCA8_HUMAN	N	595;595;534	ENSP00000269080:K595N;ENSP00000402814:K595N	ENSP00000269080:K595N	K	-	3	2	ABCA8	64427040	0.000000	0.05858	0.501000	0.27601	0.038000	0.13279	-0.684000	0.05173	0.331000	0.23511	0.482000	0.46254	AAA	.	.	.	none		0.318	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		G	66915445	T	G	66915445	3	3	25	1	0	0	0	0	1	0	0	0	38	1606	56	5	3064	5	ABCA8	17	66915445	Missense_Mutation	SNP	T	TCGA-4A-A93X-01A-11D-A36X-10	18087448	66915445	14279765	81	1842											
UNC13D	201294	hgsc.bcm.edu	37	chr17	73832109	73832109	+	Frame_Shift_Del	DEL	C	C	-																															tcacttgtggaagatcttgtCccatgtgcgctggcactggt																										TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr17:73832109delC	ENST00000207549.4	-	17	1907	c.1528delG	c.(1528-1530)gacfs	p.D510fs	UNC13D_ENST00000412096.2_Frame_Shift_Del_p.D510fs	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	510	Interaction with RAB27A.				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)			AAGATCTTGTCCCATGTGCGC	0.617									Familial Hemophagocytic Lymphohistiocytosis																												p.D510fs		Atlas-Indel,Pindel	.											.	UNC13D	68	.	0			c.1529delA						PASS	.						153	148	150					17																	73832109		2203	4300	6503	SO:0001589	frameshift_variant	201294	exon17	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	.	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.1528delG	chr17.hg19:g.73832109delC	ENSP00000207549:p.Asp510fs	84.0	0.0	0		66.0	22.0	0.333333	NM_199242	B4DWG9|Q9H7K5	Frame_Shift_Del	DEL	ENST00000207549.4	hg19	CCDS11730.1																																																																																			.	.	.	none		0.617	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950		-	73832109	C	-	73832109	7	5	25	1	0	1	0	1	0	0	0	0	16999	855	30	0	1808	0	UNC13D	17	73832109	Frame_Shift_Del	DEL	C	TCGA-4A-A93X-01A-11D-A36X-10	6916664	73832109	7363101	82	1843											
UBE2O	63893	hgsc.bcm.edu	37	chr17	74391863	74391863	+	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	ggcagtgaggtagccagcagCgccatctccttccgcactgt	7	8	12	14	2	1	1	0	1	1	0	3	1	2	1	4	2	3	4	4	2	1	2			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr17:74391863C>T	ENST00000319380.7	-	15	2953	c.2889G>A	c.(2887-2889)gcG>gcA	p.A963A	UBE2O_ENST00000587581.1_5'Flank	NM_022066.3	NP_071349.3	Q9C0C9	UBE2O_HUMAN	ubiquitin-conjugating enzyme E2O	963					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						TAGCCAGCAGCGCCATCTCCT	0.502																																					p.A963A		Atlas-SNP	.											.	UBE2O	207	.	0			c.G2889A						PASS	.						126	111	116					17																	74391863		2203	4300	6503	SO:0001819	synonymous_variant	63893	exon15			CAGCAGCGCCATC	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.2889G>A	chr17.hg19:g.74391863C>T		66.0	0.0	.		57.0	21.0	.	NM_022066	A6NDU5|Q69YP4|Q6PIZ2|Q86UA4|Q8N425|Q8TBN1|Q9BSW1|Q9H6E6|Q9H7E4|Q9H9B2	Silent	SNP	ENST00000319380.7	hg19	CCDS32742.1																																																																																			.	.	.	none		0.502	UBE2O-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450123.1	NM_022066		T	74391863	C	T	74391863	2	4	25	1	0	0	0	0	0	0	0	1	16880	755	27	1		1	UBE2O	17	74391863	Silent	SNP	C	TCGA-4A-A93X-01A-11D-A36X-10	559754	74391863	6803347	83	1844											
WDR18	57418	hgsc.bcm.edu	37	chr19	991092	991092	+	Silent	SNP	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	ccttcgcagcccggacagagGgagaggagcttccacccaga	10	4	13	14	2	0	3	0	0	0	3	2	6	1	5	4	3	2	2	4	3	0	2			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr19:991092G>A	ENST00000251289.5	+	6	776	c.753G>A	c.(751-753)agG>agA	p.R251R	WDR18_ENST00000587001.2_Silent_p.R251R	NM_024100.3	NP_077005.2	Q9BV38	WDR18_HUMAN	WD repeat domain 18	251					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|lung(2)|skin(2)	7		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCGGACAGAGGGAGAGGAGCT	0.706																																					p.R251R		Atlas-SNP	.											.	WDR18	20	.	0			c.G753A						PASS	.						42	36	38					19																	991092		2190	4291	6481	SO:0001819	synonymous_variant	57418	exon6			ACAGAGGGAGAGG		CCDS12051.1	19p13.3	2013-01-09				ENSG00000065268		"WD repeat domain containing"	17956	protein-coding gene	gene with protein product	"Involved in Processing ITS2 3 homolog (S. cerevisiae)"					22190735	Standard	NM_024100		Approved	Ipi3	uc002lqm.1	Q9BV38		ENST00000251289.5:c.753G>A	chr19.hg19:g.991092G>A		88.0	0.0	.		73.0	44.0	.	NM_024100	O60390|Q9BWR2	Silent	SNP	ENST00000251289.5	hg19	CCDS12051.1																																																																																			.	.	.	none		0.706	WDR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458225.2			A	991092	G	A	991092	2	1	25	1	0	0	0	0	0	0	0	1	17290	1223	43	2		2	WDR18	19	991092	Silent	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10		991092	58137891	84	1845											
ZNF556	80032	hgsc.bcm.edu	37	chr19	2877861	2877861	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctactgctgggcaacatcctTtcaacgacacgtgagaattc	11	10	8	12	2	1	1	1	1	0	1	3	3	2	1	1	1	4	2	1	1	4	3			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr19:2877861T>C	ENST00000307635.2	+	4	992	c.905T>C	c.(904-906)tTt>tCt	p.F302S	ZNF556_ENST00000586426.1_Missense_Mutation_p.F301S	NM_024967.1	NP_079243.1	Q9HAH1	ZN556_HUMAN	zinc finger protein 556	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)			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)		GCAACATCCTTTCAACGACAC	0.507																																					p.F302S		Atlas-SNP	.											.	ZNF556	73	.	0			c.T905C						PASS	.						61	57	58					19																	2877861		2203	4300	6503	SO:0001583	missense	80032	exon4			CATCCTTTCAACG	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.905T>C	chr19.hg19:g.2877861T>C	ENSP00000302603:p.Phe302Ser	145.0	0.0	.		135.0	78.0	.	NM_024967	Q96GM3	Missense_Mutation	SNP	ENST00000307635.2	hg19	CCDS12097.1	.	.	.	.	.	.	.	.	.	.	T	16.39	3.110252	0.56398	.	.	ENSG00000172000	ENST00000307635	T	0.18810	2.19	2.3	2.3	0.28687	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.16938	0.0407	L	0.47078	1.49	0.09310	N	1	B	0.25850	0.136	B	0.24394	0.053	T	0.26608	-1.0098	9	0.87932	D	0	.	3.8674	0.09022	0.0:0.1859:0.0:0.8141	.	302	Q9HAH1	ZN556_HUMAN	S	302	ENSP00000302603:F302S	ENSP00000302603:F302S	F	+	2	0	ZNF556	2828861	0.000000	0.05858	0.210000	0.23637	0.362000	0.29581	-0.203000	0.09438	0.902000	0.36520	0.334000	0.21626	TTT	.	.	.	none		0.507	ZNF556-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451638.2	NM_024967		C	2877861	T	C	2877861	3	2	25	1	0	0	0	0	1	0	0	0	17999	1841	64	3	919	3	ZNF556	19	2877861	Missense_Mutation	SNP	T	TCGA-4A-A93X-01A-11D-A36X-10	1886769	2877861	56251122	85	1846											
PNPLA6	10908	hgsc.bcm.edu	37	chr19	7623951	7623951	+	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	gtgtgcggcagctagaggttGtcaagtccagctcctactgc	7	10	13	11	1	1	1	1	0	0	1	3	1	3	1	2	2	5	4	2	2	3	3			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr19:7623951G>T	ENST00000221249.6	+	31	3930	c.3499G>T	c.(3499-3501)Gtc>Ttc	p.V1167F	PNPLA6_ENST00000450331.3_Missense_Mutation_p.V1167F|PNPLA6_ENST00000545201.2_Missense_Mutation_p.V1140F|PNPLA6_ENST00000414982.3_Missense_Mutation_p.V1215F|PNPLA6_ENST00000600737.1_Missense_Mutation_p.V1205F	NM_006702.4	NP_006693.3	Q8IY17	PLPL6_HUMAN	patatin-like phospholipase domain containing 6	1206					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						GCTAGAGGTTGTCAAGTCCAG	0.572																																					p.V1215F		Atlas-SNP	.											.	PNPLA6	163	.	0			c.G3643T						PASS	.						89	66	74					19																	7623951		2203	4300	6503	SO:0001583	missense	10908	exon30			GAGGTTGTCAAGT	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.3499G>T	chr19.hg19:g.7623951G>T	ENSP00000221249:p.Val1167Phe	93.0	0.0	.		63.0	22.0	.	NM_001166111	A6NGQ0|B4DFB9|B7Z7T2|F5H5K9|J3KQS3|O60859|Q86W58|Q9UG58	Missense_Mutation	SNP	ENST00000221249.6	hg19	CCDS32891.1	.	.	.	.	.	.	.	.	.	.	g	24.7	4.563922	0.86335	.	.	ENSG00000032444	ENST00000221249;ENST00000545201;ENST00000414982;ENST00000450331	T;T;T;T	0.35789	1.29;1.29;1.29;1.29	4.78	4.78	0.61160	Acyl transferase/acyl hydrolase/lysophospholipase (1);	0.000000	0.85682	D	0.000000	T	0.64316	0.2587	M	0.85630	2.765	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.97110	0.999;1.0;1.0;0.945	T	0.71530	-0.4565	10	0.87932	D	0	-43.7646	15.3194	0.74109	0.0:0.0:1.0:0.0	.	1206;1140;1205;1167	Q8IY17;F5H5K9;Q8IY17-3;Q8IY17-2	PLPL6_HUMAN;.;.;.	F	1167;1140;1215;1167	ENSP00000221249:V1167F;ENSP00000443323:V1140F;ENSP00000407509:V1215F;ENSP00000394348:V1167F	ENSP00000221249:V1167F	V	+	1	0	PNPLA6	7529951	1.000000	0.71417	0.819000	0.32651	0.952000	0.60782	9.869000	0.99810	2.209000	0.71365	0.561000	0.74099	GTC	.	.	.	none		0.572	PNPLA6-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459275.1	NM_006702		T	7623951	G	T	7623951	3	4	25	1	0	0	0	0	1	0	0	0	12176	1377	48	4	3757	4	PNPLA6	19	7623951	Missense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	4746090	7623951	51505032	86	1847											
TMED1	11018	hgsc.bcm.edu	37	chr19	10945735	10945735	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaacaccagcttctcggagaTggtgctgaaggagttgtcaa	11	9	13	8	1	2	2	1	1	1	1	3	5	2	3	1	3	3	3	1	3	3	2			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr19:10945735T>C	ENST00000214869.2	-	3	438	c.340A>G	c.(340-342)Atc>Gtc	p.I114V	TMED1_ENST00000588289.1_5'UTR|C19orf38_ENST00000592854.1_5'Flank|TMED1_ENST00000591695.1_Intron	NM_006858.2	NP_006849.1	Q13445	TMED1_HUMAN	transmembrane emp24 protein transport domain containing 1	114	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.				cell-cell signaling (GO:0007267)|protein transport (GO:0015031)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|lung(2)|ovary(3)|prostate(1)|skin(1)	10						TTCTCGGAGATGGTGCTGAAG	0.587																																					p.I114V		Atlas-SNP	.											.	TMED1	22	.	0			c.A340G						PASS	.						109	107	107					19																	10945735		2203	4300	6503	SO:0001583	missense	11018	exon3			CGGAGATGGTGCT	U41804	CCDS12249.1	19p13.2	2008-02-05	2005-08-26			ENSG00000099203			17291	protein-coding gene	gene with protein product		605395	"transmembrane emp24 domain containing 1"			11466339, 8621446	Standard	NM_006858		Approved	ST2L, MGC1270, IL1RL1LG, Il1rl1l	uc002mpy.3	Q13445		ENST00000214869.2:c.340A>G	chr19.hg19:g.10945735T>C	ENSP00000214869:p.Ile114Val	83.0	0.0	.		99.0	30.0	.	NM_006858		Missense_Mutation	SNP	ENST00000214869.2	hg19	CCDS12249.1	.	.	.	.	.	.	.	.	.	.	T	13.53	2.263688	0.39995	.	.	ENSG00000099203	ENST00000214869	T	0.41758	0.99	5.15	5.15	0.70609	GOLD (3);	0.107611	0.64402	D	0.000005	T	0.36663	0.0975	L	0.39467	1.215	0.80722	D	1	B	0.18741	0.03	B	0.24701	0.055	T	0.13176	-1.0519	10	0.32370	T	0.25	-31.9399	13.9713	0.64242	0.0:0.0:0.0:1.0	.	114	Q13445	TMED1_HUMAN	V	114	ENSP00000214869:I114V	ENSP00000214869:I114V	I	-	1	0	TMED1	10806735	0.963000	0.33076	0.999000	0.59377	0.984000	0.73092	1.642000	0.37207	1.950000	0.56595	0.459000	0.35465	ATC	.	.	.	none		0.587	TMED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452614.1	NM_006858		C	10945735	T	C	10945735	3	2	25	1	0	0	0	0	1	0	0	0	16014	1464	51	3	351	3	TMED1	19	10945735	Missense_Mutation	SNP	T	TCGA-4A-A93X-01A-11D-A36X-10	3321784	10945735	48183248	87	1848											
ZNF675	171392	hgsc.bcm.edu	37	chr19	23836072	23836072	+	Missense_Mutation	SNP	T	T	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	ctctccagtatgtattttttTatgtttagtaaggtttgcag	8	20	8	5	0	1	0	0	0	1	0	2	0	1	0	1	1	1	6	1	1	5	10			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr19:23836072T>G	ENST00000359788.4	-	4	1831	c.1663A>C	c.(1663-1665)Aaa>Caa	p.K555Q	ZNF675_ENST00000600313.1_Intron|ZNF675_ENST00000596211.1_Intron|ZNF675_ENST00000601935.1_Intron	NM_138330.2	NP_612203.2	Q8TD23	ZN675_HUMAN	zinc finger protein 675	555					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)				TGTATTTTTTTATGTTTAGTA	0.308																																					p.K555Q		Atlas-SNP	.											.	ZNF675	88	.	0			c.A1663C						PASS	.						99	101	100					19																	23836072		2202	4299	6501	SO:0001583	missense	171392	exon4			TTTTTTTATGTTT		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.1663A>C	chr19.hg19:g.23836072T>G	ENSP00000352836:p.Lys555Gln	87.0	0.0	.		92.0	63.0	.	NM_138330	Q8N211	Missense_Mutation	SNP	ENST00000359788.4	hg19	CCDS32981.1	.	.	.	.	.	.	.	.	.	.	.	0.038	-1.297753	0.01364	.	.	ENSG00000197372	ENST00000359788	T	0.36340	1.26	0.886	-1.54	0.08584	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12817	0.0311	N	0.03115	-0.41	0.20821	N	0.999848	P	0.40875	0.731	B	0.42163	0.378	T	0.14868	-1.0457	9	0.02654	T	1	.	5.3645	0.16105	0.0:0.0:0.4182:0.5818	.	555	Q8TD23	ZN675_HUMAN	Q	555	ENSP00000352836:K555Q	ENSP00000352836:K555Q	K	-	1	0	ZNF675	23627912	0.001000	0.12720	0.220000	0.23810	0.218000	0.24690	-0.209000	0.09358	0.257000	0.21650	0.254000	0.18369	AAA	.	.	.	none		0.308	ZNF675-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466433.1	NM_138330		G	23836072	T	G	23836072	3	3	25	1	0	0	0	0	1	0	0	0	18094	1763	61	5	47	5	ZNF675	19	23836072	Missense_Mutation	SNP	T	TCGA-4A-A93X-01A-11D-A36X-10	12890337	23836072	35292911	88	1849											
RPS16	6217	hgsc.bcm.edu	37	chr19	39923961	39923961	+	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	cgggcaccagggcctccaaaCtttttggactcgcagcgacg	8	7	12	14	4	0	0	0	0	0	0	2	2	1	1	3	3	2	2	3	3	1	2			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr19:39923961C>G	ENST00000251453.3	-	5	445	c.393G>C	c.(391-393)aaG>aaC	p.K131N	RPS16_ENST00000601655.1_Missense_Mutation_p.K114N|RPS16_ENST00000599539.1_3'UTR|RPS16_ENST00000339471.4_3'UTR	NM_001020.4	NP_001011.1	P62249	RS16_HUMAN	ribosomal protein S16	131					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal small subunit biogenesis (GO:0042274)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|large_intestine(2)|lung(2)|skin(2)	7	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;4.14e-26)|all cancers(26;2.68e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			GGCCTCCAAACTTTTTGGACT	0.502																																					p.K131N		Atlas-SNP	.											.	RPS16	12	.	0			c.G393C						PASS	.						59	62	61					19																	39923961		2203	4300	6503	SO:0001583	missense	6217	exon5			TCCAAACTTTTTG	M60854	CCDS12535.1	19q13.1	2011-04-05				ENSG00000105193		"S ribosomal proteins"	10396	protein-coding gene	gene with protein product	"40S ribosomal protein S16"	603675				2016298, 9582194	Standard	XM_005259137		Approved	S16	uc002olk.3	P62249		ENST00000251453.3:c.393G>C	chr19.hg19:g.39923961C>G	ENSP00000251453:p.Lys131Asn	102.0	0.0	.		130.0	84.0	.	NM_001020	B2RDD5|P17008	Missense_Mutation	SNP	ENST00000251453.3	hg19	CCDS12535.1	.	.	.	.	.	.	.	.	.	.	C	16.95	3.263913	0.59431	.	.	ENSG00000105193	ENST00000251453	.	.	.	4.42	3.38	0.38709	Ribosomal protein S5 domain 2-type fold (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);	.	.	.	.	D	0.87881	0.6289	H	0.99783	4.775	0.80722	D	1	D	0.60575	0.988	D	0.67103	0.949	D	0.87512	0.2440	7	.	.	.	.	6.8709	0.24121	0.0:0.7925:0.0:0.2075	.	131	P62249	RS16_HUMAN	N	131	.	.	K	-	3	2	RPS16	44615801	1.000000	0.71417	1.000000	0.80357	0.592000	0.36648	2.064000	0.41432	1.057000	0.40506	0.579000	0.79373	AAG	.	.	.	none		0.502	RPS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464511.1	NM_001020		G	39923961	C	G	39923961	3	3	25	1	0	0	0	0	1	0	0	0	13640	564	20	4	51	4	RPS16	19	39923961	Missense_Mutation	SNP	C	TCGA-4A-A93X-01A-11D-A36X-10	16087889	39923961	19205022	89	1850											
SPTBN4	57731	hgsc.bcm.edu	37	chr19	41072264	41072264	+	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	ctctctgcggcgcctgaccaCggtcagctccccagatactg	6	8	10	17	3	2	2	1	1	1	1	4	2	3	2	4	2	3	1	4	2	1	1			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr19:41072264C>T	ENST00000352632.3	+	30	6421	c.6335C>T	c.(6334-6336)aCg>aTg	p.T2112M	SPTBN4_ENST00000598249.1_Splice_Site_p.T2112M|SPTBN4_ENST00000392025.1_Splice_Site_p.T855M|SPTBN4_ENST00000338932.3_Splice_Site_p.T2112M			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	2112					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)			CGCCTGACCACGGTCAGCTCC	0.612																																					p.T2112M		Atlas-SNP	.											.	SPTBN4	213	.	0			c.C6335T						PASS	.						13	15	14					19																	41072264		2192	4279	6471	SO:0001630	splice_region_variant	57731	exon30			TGACCACGGTCAG	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.6336+1C>T	chr19.hg19:g.41072264C>T		47.0	0.0	.		63.0	36.0	.	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Missense_Mutation	SNP	ENST00000352632.3	hg19	CCDS12559.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.646036	0.87958	.	.	ENSG00000160460	ENST00000428507;ENST00000352632;ENST00000338932;ENST00000392025	T;T;T	0.78707	0.7;-1.2;0.7	4.95	4.95	0.65309	.	0.000000	0.64402	D	0.000004	D	0.85566	0.5726	L	0.54323	1.7	0.80722	D	1	D;D	0.89917	0.991;1.0	P;D	0.77557	0.749;0.99	D	0.86750	0.1960	10	0.72032	D	0.01	.	17.0938	0.86628	0.0:1.0:0.0:0.0	.	855;2112	C9JY79;Q9H254	.;SPTN4_HUMAN	M	2112;2112;2112;855	ENSP00000263373:T2112M;ENSP00000340345:T2112M;ENSP00000375879:T855M	ENSP00000340345:T2112M	T	+	2	0	SPTBN4	45764104	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	7.474000	0.81024	2.566000	0.86566	0.561000	0.74099	ACG	.	.	.	none		0.612	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2		Missense_Mutation	T	41072264	C	T	41072264	5	4	25	1	0	0	0	0	0	0	1	0	15133	550	19	1	6543	1	SPTBN4	19	41072264	Splice_Site	SNP	C	TCGA-4A-A93X-01A-11D-A36X-10	1148303	41072264	18056719	90	1851											
BCKDHA	593	hgsc.bcm.edu	37	chr19	41928639	41928639	+	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	ccgacggcgggctgtggcagAgaaccagcccttcctcatcg	7	6	13	15	4	1	1	1	0	0	1	3	3	2	1	4	3	2	2	4	3	1	1			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr19:41928639A>T	ENST00000269980.2	+	7	1327	c.959A>T	c.(958-960)gAg>gTg	p.E320V	CTC-435M10.6_ENST00000598887.1_RNA|BCKDHA_ENST00000595085.1_Missense_Mutation_p.E354V|BCKDHA_ENST00000457836.2_Missense_Mutation_p.E298V|BCKDHA_ENST00000535632.1_3'UTR|CTC-435M10.3_ENST00000540732.1_Missense_Mutation_p.E354V	NM_000709.3|NM_001164783.1	NP_000700.1|NP_001158255.1	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha polypeptide	320					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						GCTGTGGCAGAGAACCAGCCC	0.612																																					p.E320V		Atlas-SNP	.											.	BCKDHA	36	.	0			c.A959T						PASS	.						60	58	59					19																	41928639		2203	4300	6503	SO:0001583	missense	593	exon7			TGGCAGAGAACCA	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.959A>T	chr19.hg19:g.41928639A>T	ENSP00000269980:p.Glu320Val	38.0	0.0	.		37.0	16.0	.	NM_000709	B4DP47|E7EW46|Q16034|Q16472	Missense_Mutation	SNP	ENST00000269980.2	hg19	CCDS12581.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.543401	0.86022	.	.	ENSG00000255730;ENSG00000248098;ENSG00000248098;ENSG00000248098	ENST00000540732;ENST00000269980;ENST00000542943;ENST00000457836	D;D;D;D	0.95853	-3.83;-3.83;-3.83;-3.83	5.69	5.69	0.88448	Dehydrogenase, E1 component (1);	0.000000	0.85682	D	0.000000	D	0.97396	0.9148	M	0.83603	2.65	0.80722	D	1	D;P;P;P	0.63880	0.993;0.946;0.914;0.882	P;P;P;P	0.62089	0.898;0.615;0.618;0.619	D	0.97889	1.0296	10	0.66056	D	0.02	-52.8066	14.9376	0.70970	1.0:0.0:0.0:0.0	.	298;319;320;354	B4DP47;Q59EI3;P12694;F5H5P2	.;.;ODBA_HUMAN;.	V	354;320;291;298	ENSP00000443246:E354V;ENSP00000269980:E320V;ENSP00000440345:E291V;ENSP00000416000:E298V	ENSP00000269980:E320V	E	+	2	0	BCKDHA;CTC-435M10.3	46620479	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	8.521000	0.90569	2.181000	0.69327	0.459000	0.35465	GAG	.	.	.	none		0.612	BCKDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398313.3	NM_000709		T	41928639	A	T	41928639	3	4	25	1	0	0	0	0	1	0	0	0	1359	304	11	5	985	5	BCKDHA	19	41928639	Missense_Mutation	SNP	A	TCGA-4A-A93X-01A-11D-A36X-10	856375	41928639	17200344	91	1852											
GLTSCR1	29998	hgsc.bcm.edu	37	chr19	48205408	48205408	+	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	cccgggctgccccctgccaaGcggcgcaagtccgagtcgcc	5	4	13	19	5	0	0	0	0	0	0	2	1	1	0	6	2	3	2	6	2	2	0			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr19:48205408G>A	ENST00000396720.3	+	15	4613	c.4419G>A	c.(4417-4419)aaG>aaA	p.K1473K	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	1473										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)		CCCCTGCCAAGCGGCGCAAGT	0.726																																					p.K1473K		Atlas-SNP	.											.	GLTSCR1	79	.	0			c.G4419A						PASS	.						4	5	4					19																	48205408		1993	4017	6010	SO:0001819	synonymous_variant	29998	exon15			TGCCAAGCGGCGC	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.4419G>A	chr19.hg19:g.48205408G>A		62.0	0.0	.		62.0	41.0	.	NM_015711	A8MW01	Silent	SNP	ENST00000396720.3	hg19	CCDS46134.1																																																																																			.	.	.	none		0.726	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711		A	48205408	G	A	48205408	2	1	25	1	0	0	0	0	0	0	0	1	6481	962	34	2		2	GLTSCR1	19	48205408	Silent	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10	6276769	48205408	10923575	92	1853											
ZNF841	284371	hgsc.bcm.edu	37	chr19	52570490	52570491	+	Frame_Shift_Ins	INS	-	-	T																															gtgaagctaaaaaacaattaINSttaactgtcctctcaatttg																										TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr19:52570490_52570491insT	ENST00000426391.2	-	5	847_848	c.296_297insA	c.(295-297)aatfs	p.N99fs	ZNF432_ENST00000598446.1_Intron|ZNF841_ENST00000594295.1_Frame_Shift_Ins_p.N215fs|ZNF841_ENST00000389534.4_Frame_Shift_Ins_p.N215fs|ZNF841_ENST00000359973.2_Frame_Shift_Ins_p.N99fs			Q6ZN19	ZN841_HUMAN	zinc finger protein 841	99					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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						AAAAACAATTATTAACTGTCCT	0.337																																					p.N215fs		Atlas-Indel,Pindel	.											.	ZNF841	183	.	0			c.645_646insA						PASS	.																																			SO:0001589	frameshift_variant	284371	exon7			.	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.297dupA	chr19.hg19:g.52570492_52570492dupT	ENSP00000415453:p.Asn99fs	69.0	0.0	0		89.0	27.0	0.303371	NM_001136499	B9EG58|Q6ZN82|Q6ZP71|Q8N9U7	Frame_Shift_Ins	INS	ENST00000426391.2	hg19																																																																																				.	.	.	none		0.337	ZNF841-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000462435.1	XM_209155		T	52570491	-	T	52570490	7	5	25	1	0	1	1	0	0	0	0	0	18201	446	16	0	2133	0	ZNF841	19	52570490	Frame_Shift_Ins	INS	-	TCGA-4A-A93X-01A-11D-A36X-10	4365082	52570490	6558493	93	1854											
FOXA2	3170	hgsc.bcm.edu	37	chr20	22563153	22563153	+	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	gaacatgttgcccgagtcagGgtgcagggtccagaaggagc	10	6	16	9	1	1	1	1	0	0	1	2	4	2	2	2	3	4	2	2	3	2	1			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr20:22563153G>A	ENST00000377115.4	-	3	890	c.709C>T	c.(709-711)Cct>Tct	p.P237S	FOXA2_ENST00000419308.2_Missense_Mutation_p.P243S	NM_153675.2	NP_710141.1	Q9Y261	FOXA2_HUMAN	forkhead box A2	237					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)					CCCGAGTCAGGGTGCAGGGTC	0.652																																					p.P243S		Atlas-SNP	.											FOXA2,caecum,carcinoma,0,1	FOXA2	48	.	0			c.C727T						PASS	.						25	28	27					20																	22563153		2203	4300	6503	SO:0001583	missense	3170	exon2			AGTCAGGGTGCAG	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.709C>T	chr20.hg19:g.22563153G>A	ENSP00000366319:p.Pro237Ser	116.0	0.0	.		134.0	63.0	.	NM_021784	Q8WUW4|Q96DF7	Missense_Mutation	SNP	ENST00000377115.4	hg19	CCDS13147.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.385733	0.82792	.	.	ENSG00000125798	ENST00000377115;ENST00000419308;ENST00000319993;ENST00000444877	D;D;D	0.95656	-3.77;-3.77;-3.77	4.98	4.98	0.66077	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.64402	U	0.000011	D	0.97430	0.9159	M	0.74881	2.28	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.70227	0.94;0.968	D	0.98254	1.0495	10	0.87932	D	0	.	17.8574	0.88769	0.0:0.0:1.0:0.0	.	237;243	Q9Y261;B0ZTD4	FOXA2_HUMAN;.	S	237;237;243;123	ENSP00000366319:P237S;ENSP00000400341:P237S;ENSP00000315955:P243S	ENSP00000315955:P243S	P	-	1	0	FOXA2	22511153	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	9.688000	0.98670	2.304000	0.77564	0.574000	0.79327	CCT	.	.	.	none		0.652	FOXA2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078289.1			A	22563153	G	A	22563153	3	1	25	1	0	0	0	0	1	0	0	0	5997	1232	43	2	668	2	FOXA2	20	22563153	Missense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10		22563153	40462367	94	1855											
ARFGEF2	10564	hgsc.bcm.edu	37	chr20	47648608	47648608	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttgcagtgaagctcttgccTatttcatcactgtgaattct	8	17	7	9	0	4	2	2	2	2	0	4	2	4	2	1	0	3	2	1	0	3	5			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr20:47648608T>C	ENST00000371917.4	+	38	5086	c.5086T>C	c.(5086-5088)Tat>Cat	p.Y1696H		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	1696					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)			AGCTCTTGCCTATTTCATCAC	0.398																																					p.Y1696H	Esophageal Squamous(176;1738 1974 26285 33069 35354)	Atlas-SNP	.											.	ARFGEF2	160	.	0			c.T5086C						PASS	.						182	198	193					20																	47648608		2203	4300	6503	SO:0001583	missense	10564	exon38			CTTGCCTATTTCA	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.5086T>C	chr20.hg19:g.47648608T>C	ENSP00000360985:p.Tyr1696His	84.0	0.0	.		102.0	47.0	.	NM_006420	Q5TFT9|Q9NTS1	Missense_Mutation	SNP	ENST00000371917.4	hg19	CCDS13411.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.545282	0.86022	.	.	ENSG00000124198	ENST00000371917	T	0.67345	-0.26	5.93	5.93	0.95920	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.80914	0.4715	M	0.76002	2.32	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.78443	-0.2202	10	0.25751	T	0.34	.	16.3766	0.83401	0.0:0.0:0.0:1.0	.	1696	Q9Y6D5	BIG2_HUMAN	H	1696	ENSP00000360985:Y1696H	ENSP00000360985:Y1696H	Y	+	1	0	ARFGEF2	47082015	1.000000	0.71417	0.997000	0.53966	0.999000	0.98932	7.708000	0.84633	2.263000	0.75096	0.533000	0.62120	TAT	.	.	.	none		0.398	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420		C	47648608	T	C	47648608	3	2	25	1	0	0	0	0	1	0	0	0	853	1522	53	3	5236	3	ARFGEF2	20	47648608	Missense_Mutation	SNP	T	TCGA-4A-A93X-01A-11D-A36X-10	25085455	47648608	15376912	95	1856											
COL18A1	80781	hgsc.bcm.edu	37	chr21	46900748	46900748	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgtgcctgggcgcgagggTccccccgggtttcctggcct	1	9	17	14	3	0	0	0	0	0	0	2	1	2	0	6	5	1	1	6	5	0	1			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr21:46900748T>C	ENST00000359759.4	+	12	2853	c.2832T>C	c.(2830-2832)ggT>ggC	p.G944G	COL18A1_ENST00000400337.2_Silent_p.G529G|COL18A1_ENST00000355480.5_Silent_p.G709G			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	944	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)		GGCGCGAGGGTCCCCCCGGGT	0.711																																					p.G709G		Atlas-SNP	.											.	COL18A1	129	.	0			c.T2127C						PASS	.						16	22	20					21																	46900748		1952	4118	6070	SO:0001819	synonymous_variant	80781	exon12			CGAGGGTCCCCCC		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.2832T>C	chr21.hg19:g.46900748T>C		111.0	0.0	.		78.0	36.0	.	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	hg19																																																																																				.	.	.	none		0.711	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			C	46900748	T	C	46900748	2	2	25	1	0	0	0	0	0	0	0	1	3677	1654	58	3		3	COL18A1	21	46900748	Silent	SNP	T	TCGA-4A-A93X-01A-11D-A36X-10		46900748	1229147	96	1857											
CHEK2	11200	hgsc.bcm.edu	37	chr22	29121248	29121248	+	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	taccctgaaaatccgaaagtGtttcttgctgtatgttcggt	9	15	9	8	2	1	1	0	1	1	0	3	2	2	1	2	1	2	4	2	1	5	5			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr22:29121248G>T	ENST00000405598.1	-	4	618	c.427C>A	c.(427-429)Cac>Aac	p.H143N	CHEK2_ENST00000382566.1_Missense_Mutation_p.H143N|CHEK2_ENST00000402731.1_Missense_Mutation_p.H143N|CHEK2_ENST00000382578.1_Intron|CHEK2_ENST00000328354.6_Missense_Mutation_p.H143N|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000544772.1_5'UTR|CHEK2_ENST00000404276.1_Missense_Mutation_p.H143N|CHEK2_ENST00000382580.2_Missense_Mutation_p.H186N|CHEK2_ENST00000403642.1_Intron|CHEK2_ENST00000348295.3_Missense_Mutation_p.H143N			O96017	CHK2_HUMAN	checkpoint kinase 2	143	FHA. {ECO:0000255|PROSITE- ProRule:PRU00086}.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						ATCCGAAAGTGTTTCTTGCTG	0.378			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																													p.H186N		Atlas-SNP	.	yes	Rec		familial breast cancer	22	22q12.1	11200	CHK2 checkpoint homolog (S. pombe)		E	.	CHEK2	438	.	0			c.C556A	GRCh37	CM077520	CHEK2	M		PASS	.						186	174	178					22																	29121248		2203	4300	6503	SO:0001583	missense	11200	exon4			GAAAGTGTTTCTT	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.427C>A	chr22.hg19:g.29121248G>T	ENSP00000386087:p.His143Asn	147.0	0.0	.		86.0	75.0	.	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	hg19	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.327958	0.81690	.	.	ENSG00000183765	ENST00000348295;ENST00000382566;ENST00000328354;ENST00000404276;ENST00000405598;ENST00000382580;ENST00000402731;ENST00000447421;ENST00000439200;ENST00000398017	D;D;D;D;D;D;D;D;D;D	0.99239	-5.61;-5.61;-5.61;-5.61;-5.61;-5.61;-5.61;-5.61;-5.61;-5.61	5.87	5.87	0.94306	Forkhead-associated (FHA) domain (4);SMAD/FHA domain (1);	0.000000	0.85682	D	0.000000	D	0.99722	0.9892	H	0.98629	4.285	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;0.999;0.999;0.998	D	0.97357	0.9967	10	0.87932	D	0	-12.4286	19.2001	0.93708	0.0:0.0:1.0:0.0	.	143;143;143;143;186	O96017-7;A8JZZ5;O96017-12;O96017;O96017-9	.;.;.;CHK2_HUMAN;.	N	143;143;143;143;143;186;143;143;174;153	ENSP00000329012:H143N;ENSP00000372007:H143N;ENSP00000329178:H143N;ENSP00000385747:H143N;ENSP00000386087:H143N;ENSP00000372023:H186N;ENSP00000384835:H143N;ENSP00000397478:H143N;ENSP00000408065:H174N;ENSP00000381099:H153N	ENSP00000329178:H143N	H	-	1	0	CHEK2	27451248	1.000000	0.71417	0.997000	0.53966	0.869000	0.49853	7.118000	0.77137	2.784000	0.95788	0.585000	0.79938	CAC	.	.	.	none		0.378	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		T	29121248	G	T	29121248	3	4	25	1	0	0	0	0	1	0	0	0	3337	1377	48	4	1256	4	CHEK2	22	29121248	Missense_Mutation	SNP	G	TCGA-4A-A93X-01A-11D-A36X-10		29121248	22183318	97	1858											
CSF2RB	1439	hgsc.bcm.edu	37	chr22	37331470	37331470	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggccctccgcttctgtggcAtctacgggtacaggtgaggg	5	10	15	11	2	2	1	0	1	2	0	3	1	3	1	2	5	2	3	2	5	2	3			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chr22:37331470A>G	ENST00000403662.3	+	11	1615	c.1393A>G	c.(1393-1395)Atc>Gtc	p.I465V	CSF2RB_ENST00000406230.1_Missense_Mutation_p.I471V|CSF2RB_ENST00000262825.5_Missense_Mutation_p.I471V|CSF2RB_ENST00000536485.1_Missense_Mutation_p.I412V			P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	465					cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)|interleukin-5-mediated signaling pathway (GO:0038043)|respiratory gaseous exchange (GO:0007585)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	granulocyte macrophage colony-stimulating factor receptor complex (GO:0030526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(3)|pancreas(1)|skin(5)|upper_aerodigestive_tract(2)	42					Sargramostim(DB00020)	CTTCTGTGGCATCTACGGGTA	0.647																																					p.I465V		Atlas-SNP	.											.	CSF2RB	104	.	0			c.A1393G						PASS	.						115	89	98					22																	37331470		2203	4300	6503	SO:0001583	missense	1439	exon11			TGTGGCATCTACG	M59941	CCDS13936.1	22q12.3	2014-09-09			ENSG00000100368	ENSG00000100368		"CD molecules", "Fibronectin type III domain containing"	2436	protein-coding gene	gene with protein product		138981		IL3RB		1833064, 1424804	Standard	NM_000395		Approved	IL5RB, CD131	uc003aqa.4	P32927	OTTHUMG00000150546	ENST00000403662.3:c.1393A>G	chr22.hg19:g.37331470A>G	ENSP00000384053:p.Ile465Val	64.0	0.0	.		61.0	53.0	.	NM_000395	Q5JZI1|Q6ICE0	Missense_Mutation	SNP	ENST00000403662.3	hg19	CCDS13936.1	.	.	.	.	.	.	.	.	.	.	A	6.866	0.529159	0.13127	.	.	ENSG00000100368	ENST00000403662;ENST00000539104;ENST00000262825;ENST00000406230;ENST00000536485	D;D;D;D	0.91351	-2.32;-2.83;-2.83;-2.83	5.04	-8.6	0.00889	.	1.602080	0.03563	N	0.227412	T	0.74366	0.3707	N	0.08118	0	0.09310	N	1	B;B	0.11235	0.004;0.002	B;B	0.09377	0.004;0.003	T	0.70019	-0.4987	10	0.02654	T	1	-3.7527	9.1387	0.36890	0.3465:0.1842:0.4693:0.0	.	471;465	P32927-2;P32927	.;IL3RB_HUMAN	V	465;465;471;471;412	ENSP00000384053:I465V;ENSP00000262825:I471V;ENSP00000385271:I471V;ENSP00000440003:I412V	ENSP00000262825:I471V	I	+	1	0	CSF2RB	35661416	0.000000	0.05858	0.000000	0.03702	0.995000	0.86356	-0.653000	0.05360	-2.157000	0.00789	0.454000	0.30748	ATC	.	.	.	none		0.647	CSF2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318854.1	NM_000395		G	37331470	A	G	37331470	3	3	25	1	0	0	0	0	1	0	0	0	3937	217	8	3	1431	3	CSF2RB	22	37331470	Missense_Mutation	SNP	A	TCGA-4A-A93X-01A-11D-A36X-10	8210222	37331470	13973096	98	1859											
STAG2	10735	hgsc.bcm.edu	37	chrX	123205104	123205104	+	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	atacccctgattcttcattgCagtctgagttgctcagcttt	7	16	7	11	0	4	2	2	2	2	0	4	2	4	2	2	0	4	4	2	0	1	6			TCGA-4A-A93X-01A-11D-A36X-10	TCGA-4A-A93X-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8ecd194d-3286-4363-9701-6427c66e103c	581486c1-6d50-4794-a2c8-693606b711ff	g.chrX:123205104C>T	ENST00000371160.1	+	25	2754	c.2464C>T	c.(2464-2466)Cag>Tag	p.Q822*	STAG2_ENST00000218089.9_Nonsense_Mutation_p.Q822*|STAG2_ENST00000371157.3_Nonsense_Mutation_p.Q822*|STAG2_ENST00000371144.3_Nonsense_Mutation_p.Q822*|STAG2_ENST00000371145.3_Nonsense_Mutation_p.Q822*|STAG2_ENST00000354548.5_Nonsense_Mutation_p.Q753*|STAG2_ENST00000469481.1_Intron	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	822					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						TTCTTCATTGCAGTCTGAGTT	0.363																																					p.Q822X		Atlas-SNP	.											.	STAG2	309	.	0			c.C2464T						PASS	.						219	188	199					X																	123205104		2203	4300	6503	SO:0001587	stop_gained	10735	exon25			TCATTGCAGTCTG	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.2464C>T	chrX.hg19:g.123205104C>T	ENSP00000360202:p.Gln822*	66.0	0.0	.		43.0	40.0	.	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Nonsense_Mutation	SNP	ENST00000371160.1	hg19	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	C	43	10.338955	0.99387	.	.	ENSG00000101972	ENST00000218089;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	.	.	.	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	-18.2766	18.3649	0.90388	0.0:1.0:0.0:0.0	.	.	.	.	X	822;753;822;822;822;822	.	ENSP00000218089:Q822X	Q	+	1	0	STAG2	123032785	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.818000	0.86416	2.278000	0.76064	0.538000	0.68166	CAG	.	.	.	none		0.363	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		T	123205104	C	T	123205104	4	4	25	1	0	0	0	0	0	1	0	0	15255	711	25	2	2554	2	STAG2	23	123205104	Nonsense_Mutation	SNP	C	TCGA-4A-A93X-01A-11D-A36X-10		123205104	32065456	99	1860											
ARHGEF19	128272	hgsc.bcm.edu	37	chr1	16532674	16532674	+	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	caggccagaccacttcttcaCctctcgctggtgctcttgac	6	11	8	16	1	4	2	1	1	3	1	5	2	4	2	3	2	1	2	3	2	0	3			TCGA-4A-A93Y-01A-11D-A36X-10	TCGA-4A-A93Y-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90	8502bb1a-6a04-42ad-88f1-4559e24b1286	g.chr1:16532674C>T	ENST00000270747.3	-	7	1435		c.e7+1		ARHGEF19_ENST00000478117.1_Splice_Site	NM_153213.3	NP_694945.2	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19						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)		CACTTCTTCACCTCTCGCTGG	0.632																																					.		Atlas-SNP	.											.	ARHGEF19	49	.	0			c.1298+1G>A						PASS	.						42	36	38					1																	16532674		2203	4300	6503	SO:0001630	splice_region_variant	128272	exon8			TCTTCACCTCTCG	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.1298+1G>A	chr1.hg19:g.16532674C>T		111.0	0.0	.		108.0	7.0	.	NM_153213	A6NJ04|Q5TEV2|Q6PJQ4|Q8N244	Splice_Site	SNP	ENST00000270747.3	hg19	CCDS170.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.052337	0.75960	.	.	ENSG00000142632	ENST00000270747;ENST00000421561;ENST00000375607;ENST00000449495;ENST00000441785	.	.	.	4.85	4.85	0.62838	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5392	0.76027	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ARHGEF19	16405261	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	6.992000	0.76238	2.274000	0.75844	0.555000	0.69702	.	.	.	.	none		0.632	ARHGEF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006289.1	NM_153213	Intron	T	16532674	C	T	16532674	5	4	26	1	0	0	0	0	0	0	1	0	902	521	18	2	1149	2	ARHGEF19	1	16532674	Splice_Site	SNP	C	TCGA-4A-A93Y-01A-11D-A36X-10		16532674	232717947	1	1861											
OLFML2B	25903	hgsc.bcm.edu	37	chr1	161953624	161953624	+	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	ttggtgtgggtgtcgaaagcGtaggagatgttggcattccg	7	12	17	5	3	0	1	0	0	0	1	2	3	1	1	1	4	1	3	1	4	2	4	rs150437510	byFrequency	TCGA-4A-A93Y-01A-11D-A36X-10	TCGA-4A-A93Y-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90	8502bb1a-6a04-42ad-88f1-4559e24b1286	g.chr1:161953624G>T	ENST00000294794.3	-	8	2517	c.2094C>A	c.(2092-2094)taC>taA	p.Y698*	OLFML2B_ENST00000367940.2_Nonsense_Mutation_p.Y699*|OLFML2B_ENST00000367938.1_Nonsense_Mutation_p.Y181*	NM_015441.1	NP_056256.1	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B	698	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)			TGTCGAAAGCGTAGGAGATGT	0.552																																					p.Y698X		Atlas-SNP	.											.	OLFML2B	114	.	0			c.C2094A						PASS	.						374	346	355					1																	161953624		2203	4300	6503	SO:0001587	stop_gained	25903	exon8			GAAAGCGTAGGAG	BX648975	CCDS1236.1, CCDS72966.1	1q23.1	2008-02-05			ENSG00000162745	ENSG00000162745			24558	protein-coding gene	gene with protein product							Standard	XM_005245075		Approved	DKFZP586L151	uc001gbu.3	Q68BL8	OTTHUMG00000024047	ENST00000294794.3:c.2094C>A	chr1.hg19:g.161953624G>T	ENSP00000294794:p.Tyr698*	200.0	0.0	.		197.0	13.0	.	NM_015441	B7ZA39|Q5VU96|Q6NX46|Q86X11|Q9Y3X6	Nonsense_Mutation	SNP	ENST00000294794.3	hg19	CCDS1236.1	.	.	.	.	.	.	.	.	.	.	G	39	7.778900	0.98486	.	.	ENSG00000162745	ENST00000294794;ENST00000367940;ENST00000367938	.	.	.	5.36	-2.37	0.06643	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1.000000	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.5642	0.50796	0.6966:0.0:0.3034:0.0	.	.	.	.	X	698;699;181	.	ENSP00000294794:Y698X	Y	-	3	2	OLFML2B	160220248	0.002000	0.14202	0.992000	0.48379	0.968000	0.65278	-1.217000	0.02979	-0.315000	0.08703	-0.224000	0.12420	TAC	.	G|1.000;A|0.000	.	alt		0.552	OLFML2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060552.2	NM_015441		T	161953624	G	T	161953624	4	4	26	1	0	0	0	0	0	1	0	0	10865	1140	40	4	162	4	OLFML2B	1	161953624	Nonsense_Mutation	SNP	G	TCGA-4A-A93Y-01A-11D-A36X-10	145420950	161953624	87296997	2	1862											
BRP44	25874	hgsc.bcm.edu	37	chr1	167893755	167893755	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatttcataattggagcccAgaagaaaactgttctgggac	13	10	9	9	0	2	2	1	0	1	2	2	4	2	4	2	2	2	1	2	2	4	4			TCGA-4A-A93Y-01A-11D-A36X-10	TCGA-4A-A93Y-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90	8502bb1a-6a04-42ad-88f1-4559e24b1286	g.chr1:167893755A>G	ENST00000367846.4	-	2	328	c.130T>C	c.(130-132)Tgg>Cgg	p.W44R	MPC2_ENST00000271373.4_Missense_Mutation_p.W44R	NM_015415.3	NP_056230.1	O95563	MPC2_HUMAN	mitochondrial pyruvate carrier 2	44					cellular metabolic process (GO:0044237)|mitochondrial pyruvate transport (GO:0006850)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	pyruvate transmembrane transporter activity (GO:0050833)										ATTGGAGCCCAGAAGAAAACT	0.303																																					p.W44R		Atlas-SNP	.											.	.	.	.	0			c.T130C						PASS	.						18	19	19					1																	167893755		2201	4288	6489	SO:0001583	missense	25874	exon3			GAGCCCAGAAGAA		CCDS1266.1	1q24	2012-07-30	2012-07-30	2012-07-30	ENSG00000143158	ENSG00000143158			24515	protein-coding gene	gene with protein product		614737	"brain protein 44"	BRP44		3022128, 22628558	Standard	NM_015415		Approved	DKFZP564B167	uc001get.3	O95563	OTTHUMG00000034570	ENST00000367846.4:c.130T>C	chr1.hg19:g.167893755A>G	ENSP00000356820:p.Trp44Arg	552.0	0.0	.		550.0	24.0	.	NM_001143674	A8K261|Q3SXR6|Q6FIF3	Missense_Mutation	SNP	ENST00000367846.4	hg19	CCDS1266.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.298760	0.81025	.	.	ENSG00000143158	ENST00000367846;ENST00000271373;ENST00000458574	D;D;D	0.87179	-2.22;-2.22;-2.22	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	D	0.95182	0.8438	H	0.96833	3.89	0.52099	D	0.999940	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96493	0.9365	9	0.72032	D	0.01	-14.2049	13.8186	0.63308	1.0:0.0:0.0:0.0	.	44;44	B2R4Q7;O95563	.;BR44_HUMAN	R	44	ENSP00000356820:W44R;ENSP00000271373:W44R;ENSP00000392874:W44R	ENSP00000271373:W44R	W	-	1	0	BRP44	166160379	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.363000	0.79516	2.311000	0.77944	0.533000	0.62120	TGG	.	.	.	none		0.303	MPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083652.1	NM_015415		G	167893755	A	G	167893755	3	3	26	1	0	0	0	0	1	0	0	0	1520	188	7	3	269	3	BRP44	1	167893755	Missense_Mutation	SNP	A	TCGA-4A-A93Y-01A-11D-A36X-10	5940131	167893755	81356866	3	1863											
ZNF142	7701	hgsc.bcm.edu	37	chr2	219508733	219508733	+	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	agggcagtgtgggcagcggaAggctcgcccctctccctgga	6	6	16	13	2	1	0	0	0	1	0	3	2	1	2	3	5	1	3	3	5	1	0			TCGA-4A-A93Y-01A-11D-A36X-10	TCGA-4A-A93Y-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90	8502bb1a-6a04-42ad-88f1-4559e24b1286	g.chr2:219508733A>T	ENST00000449707.1	-	8	2927	c.2506T>A	c.(2506-2508)Ttc>Atc	p.F836I	ZNF142_ENST00000411696.2_Missense_Mutation_p.F836I	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	836					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)		GGGCAGCGGAAGGCTCGCCCC	0.612																																					p.F836I	Colon(170;867 1942 8995 15834 18053)	Atlas-SNP	.											.	ZNF142	190	.	0			c.T2506A						PASS	.						152	161	158					2																	219508733		2079	4197	6276	SO:0001583	missense	7701	exon8			AGCGGAAGGCTCG	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.2506T>A	chr2.hg19:g.219508733A>T	ENSP00000408643:p.Phe836Ile	159.0	0.0	.		126.0	10.0	.	NM_001105537	Q92510	Missense_Mutation	SNP	ENST00000449707.1	hg19	CCDS42817.1	.	.	.	.	.	.	.	.	.	.	A	19.54	3.846106	0.71603	.	.	ENSG00000115568	ENST00000449707;ENST00000411696	T;T	0.34667	1.35;1.35	5.22	5.22	0.72569	Zinc finger, C2H2-like (1);	0.119890	0.64402	D	0.000014	T	0.66005	0.2746	M	0.88640	2.97	0.35186	D	0.772903	D;D	0.69078	0.997;0.997	D;D	0.80764	0.994;0.994	T	0.79911	-0.1603	10	0.72032	D	0.01	-4.589	15.2696	0.73689	1.0:0.0:0.0:0.0	.	836;673	P52746;A8MWU9	ZN142_HUMAN;.	I	836	ENSP00000408643:F836I;ENSP00000398798:F836I	ENSP00000398798:F836I	F	-	1	0	ZNF142	219216977	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	4.295000	0.59049	2.196000	0.70406	0.533000	0.62120	TTC	.	.	.	none		0.612	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081		T	219508733	A	T	219508733	3	4	26	1	0	0	0	0	1	0	0	0	17743	72	3	5	2569	5	ZNF142	2	219508733	Missense_Mutation	SNP	A	TCGA-4A-A93Y-01A-11D-A36X-10		219508733	23690640	4	1864											
HEG1	57493	hgsc.bcm.edu	37	chr3	124732430	124732431	+	In_Frame_Ins	INS	-	-	GGAAGAGGAGGAGGAGGA																															gaagaagaagaggaggaggaINSggaagaggaggaggaggagt																								rs374949821		TCGA-4A-A93Y-01A-11D-A36X-10	TCGA-4A-A93Y-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90	8502bb1a-6a04-42ad-88f1-4559e24b1286	g.chr3:124732430_124732431insGGAAGAGGAGGAGGAGGA	ENST00000311127.4	-	6	2059_2060	c.1992_1993insTCCTCCTCCTCCTCTTCC	c.(1990-1995)tcctcc>tccTCCTCCTCCTCCTCTTCCtcc	p.664_665SS>SSSSSSSS	HEG1_ENST00000477536.1_5'UTR	NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	664	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						gaggaggaggaggaagaggagg	0.495																																					p.S665delinsSSSSSSS		Atlas-INDEL	.											.	HEG1	109	.	0			c.1993_1994insTCCTCCTCCTCCTCTTCC						PASS	.																																			SO:0001652	inframe_insertion	57493	exon6			.	AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"heart of glass"	614182	"HEG homolog 1 (zebrafish)"			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.1975_1992dupTCCTCCTCCTCCTCTTCC	chr3.hg19:g.124732430_124732431insGGAAGAGGAGGAGGAGGA	ENSP00000311502:p.Ser670_Ser671dup	95.0	0.0	0		110.0	11.0	0.1	NM_020733	Q6NX66|Q8NC40|Q9BSV0	In_Frame_Ins	INS	ENST00000311127.4	hg19	CCDS46898.1																																																																																			.	.	.	none		0.495	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386		GGAAGAGGAGGAGGAGGA	124732431	-	GGAAGAGGAGGAGGAGGA	124732430	7	5	26	1	0	1	1	0	0	0	0	0	7051	304	11	0	2200	0	HEG1	3	124732430	In_Frame_Ins	INS	-	TCGA-4A-A93Y-01A-11D-A36X-10		124732430	73290000	5	1865											
CXXC4	80319	hgsc.bcm.edu	37	chr4	105412357	105412357	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtctgcagtgttcaggggaTaaggtggagaggaaattagt	11	10	17	3	0	2	1	1	0	1	1	2	4	2	3	0	6	1	2	0	6	3	3			TCGA-4A-A93Y-01A-11D-A36X-10	TCGA-4A-A93Y-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90	8502bb1a-6a04-42ad-88f1-4559e24b1286	g.chr4:105412357T>C	ENST00000426831.1	-	1	110	c.96A>G	c.(94-96)ttA>ttG	p.L32L	CXXC4_ENST00000394767.2_Silent_p.L201L|AC004053.1_ENST00000500179.1_RNA|AC093628.1_ENST00000606234.1_RNA|CXXC4_ENST00000466963.1_Intron			Q9H2H0	CXXC4_HUMAN	CXXC finger protein 4	32					negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)|zygotic specification of dorsal/ventral axis (GO:0007352)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)	DNA binding (GO:0003677)|PDZ domain binding (GO:0030165)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	11				OV - Ovarian serous cystadenocarcinoma(123;3.05e-08)		GTTCAGGGGATAAGGTGGAGA	0.567																																					p.L201L		Atlas-SNP	.											.	CXXC4	20	.	0			c.A603G						PASS	.						139	153	148					4																	105412357		2203	4300	6503	SO:0001819	synonymous_variant	80319	exon2			AGGGGATAAGGTG		CCDS3665.1, CCDS3665.2	4q22-q24	2014-02-18	2011-12-01		ENSG00000168772	ENSG00000168772			24593	protein-coding gene	gene with protein product	"Dvl-binding protein IDAX (inhibition of the Dvl and Axin complex)"	611645				11113207	Standard	NM_025212		Approved	IDAX	uc003hxf.2	Q9H2H0	OTTHUMG00000131121	ENST00000426831.1:c.96A>G	chr4.hg19:g.105412357T>C		78.0	0.0	.		90.0	7.0	.	NM_025212		Silent	SNP	ENST00000426831.1	hg19																																																																																				.	.	.	none		0.567	CXXC4-201	KNOWN	basic	protein_coding	protein_coding		NM_025212		C	105412357	T	C	105412357	2	2	26	1	0	0	0	0	0	0	0	1	4100	1403	49	3		3	CXXC4	4	105412357	Silent	SNP	T	TCGA-4A-A93Y-01A-11D-A36X-10		105412357	85741919	6	1866											
RUNX2	860	hgsc.bcm.edu	37	chr6	45390445	45390445	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagcaacagcagcagcagcaAcagcagcagcagcagcagca	16	0	11	14	0	0	0	0	0	0	0	0	0	0	0	0	0	13	11	0	0	2	0	rs563987595	byFrequency	TCGA-4A-A93Y-01A-11D-A36X-10	TCGA-4A-A93Y-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90	8502bb1a-6a04-42ad-88f1-4559e24b1286	g.chr6:45390445A>G	ENST00000371438.1	+	2	532	c.174A>G	c.(172-174)caA>caG	p.Q58Q	RUNX2_ENST00000352853.5_Silent_p.Q126Q|RUNX2_ENST00000359524.5_Silent_p.Q44Q|RUNX2_ENST00000465038.2_Silent_p.Q58Q|RUNX2_ENST00000371436.6_Silent_p.Q58Q|RUNX2_ENST00000576263.1_Silent_p.Q58Q|RUNX2_ENST00000541979.1_Silent_p.Q126Q|RUNX2_ENST00000371432.3_Silent_p.Q44Q|RP1-244F24.1_ENST00000606796.1_RNA	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	58	Poly-Gln.				BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						agcagcagcaacagcagcagc	0.731													A|||	6	0.00119808	0.0015	0	5008	,	,		8050	0.002		0	False		,,,				2504	0.002				p.Q58Q		Atlas-SNP	.											RUNX2_ENST00000352853,lower_third,carcinoma,0,2	RUNX2	128	.	0			c.A174G						PASS	.						16	24	21					6																	45390445		1589	3298	4887	SO:0001819	synonymous_variant	860	exon3			GCAGCAACAGCAG	AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.174A>G	chr6.hg19:g.45390445A>G		79.0	0.0	.		65.0	3.0	.	NM_001024630	O14614|O14615|O95181	Silent	SNP	ENST00000371438.1	hg19	CCDS43467.2																																																																																			.	.	.	none		0.731	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		G	45390445	A	G	45390445	2	3	26	1	0	0	0	0	0	0	0	1	13761	40	2	3		3	RUNX2	6	45390445	Silent	SNP	A	TCGA-4A-A93Y-01A-11D-A36X-10		45390445	125724622	7	1867											
GPR126	57211	hgsc.bcm.edu	37	chr6	142714109	142714109	+	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	attcaaccttccaaaattggAactacacggtttatgtcgtt	12	14	6	9	2	1	0	1	0	0	0	3	1	2	1	2	2	3	2	2	2	6	7			TCGA-4A-A93Y-01A-11D-A36X-10	TCGA-4A-A93Y-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90	8502bb1a-6a04-42ad-88f1-4559e24b1286	g.chr6:142714109A>T	ENST00000230173.6	+	8	1809	c.1333A>T	c.(1333-1335)Aac>Tac	p.N445Y	GPR126_ENST00000367609.3_Missense_Mutation_p.N445Y|GPR126_ENST00000367608.2_Missense_Mutation_p.N417Y|GPR126_ENST00000296932.8_Missense_Mutation_p.N417Y	NM_020455.5	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126	445					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(12)|lung(10)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		CCAAAATTGGAACTACACGGT	0.294																																					p.N445Y		Atlas-SNP	.											.	GPR126	192	.	0			c.A1333T						PASS	.						77	73	75					6																	142714109		1808	4068	5876	SO:0001583	missense	57211	exon8			AATTGGAACTACA	AK027843	CCDS47489.1, CCDS47490.1, CCDS47491.1, CCDS55064.1	6q23.1-q24.3	2014-08-08			ENSG00000112414	ENSG00000112414		"-", "GPCR / Class B : Orphans"	13841	protein-coding gene	gene with protein product		612243				12565841	Standard	NM_001032395		Approved	FLJ14937	uc010khe.3	Q86SQ4	OTTHUMG00000015709	ENST00000230173.6:c.1333A>T	chr6.hg19:g.142714109A>T	ENSP00000230173:p.Asn445Tyr	149.0	0.0	.		139.0	8.0	.	NM_198569	Q5TGN7|Q6DHZ4|Q6F3F5|Q6F3F6|Q6F3F7|Q6F3F8|Q6MZU7|Q8IXA4|Q8NC14|Q96JW0	Missense_Mutation	SNP	ENST00000230173.6	hg19	CCDS47490.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.125589	0.77436	.	.	ENSG00000112414	ENST00000230173;ENST00000367608;ENST00000296932;ENST00000367609	T;T;T;T	0.50277	0.75;0.75;0.75;0.75	5.69	5.69	0.88448	.	0.000000	0.64402	D	0.000002	T	0.53916	0.1826	L	0.55481	1.735	0.41315	D	0.98713	D;D;D;D	0.62365	0.991;0.991;0.991;0.984	P;P;P;P	0.62560	0.904;0.904;0.904;0.804	T	0.58880	-0.7558	10	0.66056	D	0.02	.	15.9301	0.79651	1.0:0.0:0.0:0.0	.	417;445;417;445	Q86SQ4-4;Q86SQ4-3;Q86SQ4-2;Q86SQ4	.;.;.;GP126_HUMAN	Y	445;417;417;445	ENSP00000230173:N445Y;ENSP00000356580:N417Y;ENSP00000296932:N417Y;ENSP00000356581:N445Y	ENSP00000230173:N445Y	N	+	1	0	GPR126	142755802	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	6.462000	0.73526	2.165000	0.68154	0.528000	0.53228	AAC	.	.	.	none		0.294	GPR126-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042487.2			T	142714109	A	T	142714109	3	4	26	1	0	0	0	0	1	0	0	0	6647	246	9	5	1363	5	GPR126	6	142714109	Missense_Mutation	SNP	A	TCGA-4A-A93Y-01A-11D-A36X-10	97323664	142714109	28400958	8	1868											
SP4	6671	hgsc.bcm.edu	37	chr7	21468306	21468306	+	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	ttgttgcagatcagaagaagGaggaggaggaggaggcggca	13	5	19	4	1	1	3	1	0	0	3	1	8	1	8	0	7	1	3	0	7	2	2			TCGA-4A-A93Y-01A-11D-A36X-10	TCGA-4A-A93Y-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90	8502bb1a-6a04-42ad-88f1-4559e24b1286	g.chr7:21468306G>A	ENST00000222584.3	+	2	237	c.19G>A	c.(19-21)Gag>Aag	p.E7K		NM_003112.3	NP_003103.2	Q02446	SP4_HUMAN	Sp4 transcription factor	7	Poly-Glu.				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						TCAGAAGAAGGAGGAGGAGGA	0.512																																					p.E7K		Atlas-SNP	.											SP4,colon,carcinoma,0,1	SP4	91	.	0			c.G19A						PASS	.						20	20	20					7																	21468306		2171	4251	6422	SO:0001583	missense	6671	exon2			AAGAAGGAGGAGG		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.19G>A	chr7.hg19:g.21468306G>A	ENSP00000222584:p.Glu7Lys	105.0	1.0	.		143.0	6.0	.	NM_003112	O60402|Q32M52	Missense_Mutation	SNP	ENST00000222584.3	hg19	CCDS5373.1	.	.	.	.	.	.	.	.	.	.	G	13.71	2.318989	0.41096	.	.	ENSG00000105866	ENST00000222584;ENST00000446800	T	0.09911	2.93	4.5	4.5	0.54988	.	0.061123	0.64402	N	0.000005	T	0.10937	0.0267	L	0.36672	1.1	0.44142	D	0.996934	P	0.34587	0.458	B	0.39152	0.292	T	0.20907	-1.0261	10	0.23891	T	0.37	.	12.5742	0.56355	0.0:0.0:1.0:0.0	.	7	Q02446	SP4_HUMAN	K	7	ENSP00000222584:E7K	ENSP00000222584:E7K	E	+	1	0	SP4	21434831	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.555000	0.73928	2.345000	0.79718	0.563000	0.77884	GAG	.	.	.	none		0.512	SP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211617.2	NM_003112		A	21468306	G	A	21468306	3	1	26	1	0	0	0	0	1	0	0	0	14979	1175	41	2	25	2	SP4	7	21468306	Missense_Mutation	SNP	G	TCGA-4A-A93Y-01A-11D-A36X-10		21468306	137670357	9	1869											
PLXNA4	91584	hgsc.bcm.edu	37	chr7	131859623	131859623	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atagtccaggaacggaatccCggctccatccaggtcactgg	10	7	11	13	2	1	0	1	0	0	0	5	2	5	2	4	5	1	1	4	5	3	1			TCGA-4A-A93Y-01A-11D-A36X-10	TCGA-4A-A93Y-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90	8502bb1a-6a04-42ad-88f1-4559e24b1286	g.chr7:131859623C>T	ENST00000359827.3	-	21	4893	c.3931G>A	c.(3931-3933)Ggg>Agg	p.G1311R	PLXNA4_ENST00000321063.4_Missense_Mutation_p.G1311R			Q9HCM2	PLXA4_HUMAN	plexin A4	1311					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						AACGGAATCCCGGCTCCATCC	0.582																																					p.G1311R		Atlas-SNP	.											.	PLXNA4	873	.	0			c.G3931A						PASS	.						104	114	111					7																	131859623		2166	4295	6461	SO:0001583	missense	91584	exon21			GAATCCCGGCTCC	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.3931G>A	chr7.hg19:g.131859623C>T	ENSP00000352882:p.Gly1311Arg	94.0	0.0	.		100.0	7.0	.	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	hg19	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	C	34	5.369032	0.95900	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.15603	2.41;2.41	5.59	5.59	0.84812	Plexin, cytoplasmic RasGAP domain (1);	0.000000	0.85682	D	0.000000	T	0.44414	0.1292	M	0.72624	2.21	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.27502	-1.0072	10	0.59425	D	0.04	.	19.5911	0.95511	0.0:1.0:0.0:0.0	.	1311	Q9HCM2	PLXA4_HUMAN	R	1311	ENSP00000323194:G1311R;ENSP00000352882:G1311R	ENSP00000323194:G1311R	G	-	1	0	PLXNA4	131510163	1.000000	0.71417	0.999000	0.59377	0.954000	0.61252	7.792000	0.85828	2.643000	0.89663	0.655000	0.94253	GGG	.	.	.	none		0.582	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		T	131859623	C	T	131859623	3	4	26	1	0	0	0	0	1	0	0	0	12129	652	23	1	1801	1	PLXNA4	7	131859623	Missense_Mutation	SNP	C	TCGA-4A-A93Y-01A-11D-A36X-10	110391317	131859623	27279040	10	1870											
CNTLN	54875	hgsc.bcm.edu	37	chr9	17330790	17330790	+	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	aaagagcatcatgacaagtgCtgaaggaaaacataaggtag	19	6	11	5	0	1	3	1	2	0	1	1	4	1	4	0	2	3	3	0	2	7	2			TCGA-4A-A93Y-01A-11D-A36X-10	TCGA-4A-A93Y-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90	8502bb1a-6a04-42ad-88f1-4559e24b1286	g.chr9:17330790C>A	ENST00000380647.3	+	9	1586	c.1502C>A	c.(1501-1503)gCt>gAt	p.A501D	CNTLN_ENST00000262360.5_Missense_Mutation_p.A501D|CNTLN_ENST00000425824.1_Missense_Mutation_p.A501D			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	501					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)		ATGACAAGTGCTGAAGGAAAA	0.373																																					p.A501D		Atlas-SNP	.											.	CNTLN	128	.	0			c.C1502A						PASS	.						105	99	101					9																	17330790		1877	4098	5975	SO:0001583	missense	54875	exon9			CAAGTGCTGAAGG	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.1502C>A	chr9.hg19:g.17330790C>A	ENSP00000370021:p.Ala501Asp	384.0	0.0	.		367.0	16.0	.	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Missense_Mutation	SNP	ENST00000380647.3	hg19	CCDS43789.1	.	.	.	.	.	.	.	.	.	.	C	10.36	1.327537	0.24080	.	.	ENSG00000044459	ENST00000380647;ENST00000425824;ENST00000262360	T;T;T	0.37752	1.18;1.18;1.18	5.18	4.28	0.50868	.	.	.	.	.	T	0.36468	0.0968	L	0.43152	1.355	0.27282	N	0.958076	B;P;P	0.36837	0.435;0.571;0.571	B;P;P	0.45232	0.154;0.474;0.474	T	0.17048	-1.0382	9	0.14656	T	0.56	.	11.2195	0.48846	0.0:0.8015:0.1273:0.0711	.	501;501;501	Q9NXG0;C9J1F9;Q9NXG0-2	CNTLN_HUMAN;.;.	D	501	ENSP00000370021:A501D;ENSP00000392798:A501D;ENSP00000262360:A501D	ENSP00000262360:A501D	A	+	2	0	CNTLN	17320790	0.179000	0.23135	0.745000	0.31077	0.551000	0.35334	0.445000	0.21677	1.303000	0.44873	-0.157000	0.13467	GCT	.	.	.	none		0.373	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		A	17330790	C	A	17330790	3	1	26	1	0	0	0	0	1	0	0	0	3641	797	28	4	1566	4	CNTLN	9	17330790	Missense_Mutation	SNP	C	TCGA-4A-A93Y-01A-11D-A36X-10		17330790	123882641	11	1871											
SUSD1	64420	hgsc.bcm.edu	37	chr9	114864480	114864480	+	Frame_Shift_Del	DEL	T	T	-																															tacatgtgttctgatccaacTttcctagaacgcctgttcaa																										TCGA-4A-A93Y-01A-11D-A36X-10	TCGA-4A-A93Y-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90	8502bb1a-6a04-42ad-88f1-4559e24b1286	g.chr9:114864480delT	ENST00000374270.3	-	9	1429	c.1257delA	c.(1255-1257)aaafs	p.K419fs	SUSD1_ENST00000374263.3_Frame_Shift_Del_p.K419fs|SUSD1_ENST00000374264.2_Frame_Shift_Del_p.K419fs	NM_022486.3	NP_071931.2	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1	419						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)		SUSD1/ROD1(2)	central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						CTGATCCAACTTTCCTAGAAC	0.328																																					p.V420fs		Atlas-Indel,Pindel	.											.	SUSD1	51	.	0			c.1258delG						PASS	.						85	85	85					9																	114864480		2202	4297	6499	SO:0001589	frameshift_variant	64420	exon9			.	AL137432	CCDS6783.1, CCDS65105.1, CCDS65106.1	9q31.3-q33.1	2008-02-05			ENSG00000106868	ENSG00000106868			25413	protein-coding gene	gene with protein product						12975309	Standard	NM_022486		Approved	DKFZP761E1824	uc004bfu.3	Q6UWL2	OTTHUMG00000020499	ENST00000374270.3:c.1257delA	chr9.hg19:g.114864480delT	ENSP00000363388:p.Lys419fs	252.0	0.0	0		276.0	18.0	0.0652174	NM_022486	A1A4C5|A8KA03|Q5T8V6|Q5T8V7|Q6P9G7|Q8WU83|Q96DM9|Q9H6V2|Q9NTA7	Frame_Shift_Del	DEL	ENST00000374270.3	hg19	CCDS6783.1																																																																																			.	.	.	none		0.328	SUSD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053668.3	NM_022486		-	114864480	T	-	114864480	7	5	26	1	0	1	0	1	0	0	0	0	15419	1606	56	0	1022	0	SUSD1	9	114864480	Frame_Shift_Del	DEL	T	TCGA-4A-A93Y-01A-11D-A36X-10	97533690	114864480	26348951	12	1872											
OR6Q1	219952	hgsc.bcm.edu	37	chr11	57798465	57798465	+	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	ctggacccaggtaactgaatTtgtcatgatgggctttgctg	8	13	12	8	0	1	2	1	2	0	0	1	3	1	3	1	3	2	3	1	3	2	3			TCGA-4A-A93Y-01A-11D-A36X-10	TCGA-4A-A93Y-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90	8502bb1a-6a04-42ad-88f1-4559e24b1286	g.chr11:57798465T>A	ENST00000302622.3	+	1	64	c.41T>A	c.(40-42)tTt>tAt	p.F14Y	OR9Q1_ENST00000335397.3_Intron	NM_001005186.2	NP_001005186.2	Q8NGQ2	OR6Q1_HUMAN	olfactory receptor, family 6, subfamily Q, member 1	14						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			biliary_tract(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(21;0.0707)|all_epithelial(135;0.142)				GTAACTGAATTTGTCATGATG	0.458																																					p.F14Y		Atlas-SNP	.											.	OR6Q1	58	.	0			c.T41A						PASS	.						200	191	194					11																	57798465		2201	4296	6497	SO:0001583	missense	219952	exon1			CTGAATTTGTCAT	AB065737	CCDS31541.1	11q12.1	2012-08-09			ENSG00000172381	ENSG00000172381		"GPCR / Class A : Olfactory receptors"	15302	protein-coding gene	gene with protein product							Standard	NM_001005186		Approved		uc010rjz.2	Q8NGQ2	OTTHUMG00000168831	ENST00000302622.3:c.41T>A	chr11.hg19:g.57798465T>A	ENSP00000307734:p.Phe14Tyr	127.0	0.0	.		145.0	14.0	.	NM_001005186	B9EKW1|Q6IFH1|Q96R34	Missense_Mutation	SNP	ENST00000302622.3	hg19	CCDS31541.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.276285	0.80580	.	.	ENSG00000172381	ENST00000302622	T	0.04360	3.64	5.32	5.32	0.75619	.	0.000000	0.37219	N	0.002183	T	0.30135	0.0755	M	0.93283	3.4	0.31808	N	0.62755	D	0.89917	1.0	D	0.87578	0.998	T	0.54892	-0.8225	10	0.72032	D	0.01	.	14.2577	0.66062	0.0:0.0:0.0:1.0	.	14	Q8NGQ2	OR6Q1_HUMAN	Y	14	ENSP00000307734:F14Y	ENSP00000307734:F14Y	F	+	2	0	OR6Q1	57555041	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.294000	0.65687	2.008000	0.58898	0.523000	0.50628	TTT	.	.	.	none		0.458	OR6Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401257.1	NM_001005186		A	57798465	T	A	57798465	3	1	26	1	0	0	0	0	1	0	0	0	11215	1841	64	5	43	5	OR6Q1	11	57798465	Missense_Mutation	SNP	T	TCGA-4A-A93Y-01A-11D-A36X-10		57798465	77208051	13	1873											
LRP1	4035	hgsc.bcm.edu	37	chr12	57589521	57589521	+	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	agcacttcgtgtgtgaccacGaccgtgactgtgcagatggc	8	9	13	11	3	0	3	0	2	0	1	1	4	0	3	2	1	2	2	2	1	0	1			TCGA-4A-A93Y-01A-11D-A36X-10	TCGA-4A-A93Y-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90	8502bb1a-6a04-42ad-88f1-4559e24b1286	g.chr12:57589521G>T	ENST00000243077.3	+	53	8984	c.8518G>T	c.(8518-8520)Gac>Tac	p.D2840Y	MIR1228_ENST00000408438.1_RNA	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	2840	LDL-receptor class A 18. {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)	GTGTGACCACGACCGTGACTG	0.622																																					p.D2840Y		Atlas-SNP	.											.	LRP1	428	.	0			c.G8518T						PASS	.						140	126	130					12																	57589521		2203	4300	6503	SO:0001583	missense	4035	exon53			GACCACGACCGTG	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.8518G>T	chr12.hg19:g.57589521G>T	ENSP00000243077:p.Asp2840Tyr	119.0	0.0	.		120.0	10.0	.	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	G	17.67	3.446589	0.63178	.	.	ENSG00000123384	ENST00000243077	D	0.95690	-3.78	4.95	4.95	0.65309	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.97455	0.9167	M	0.73598	2.24	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.98001	1.0360	10	0.72032	D	0.01	.	17.1132	0.86681	0.0:0.0:1.0:0.0	.	2840	Q07954	LRP1_HUMAN	Y	2840	ENSP00000243077:D2840Y	ENSP00000243077:D2840Y	D	+	1	0	LRP1	55875788	1.000000	0.71417	0.995000	0.50966	0.728000	0.41692	6.544000	0.73878	2.562000	0.86427	0.561000	0.74099	GAC	.	.	.	none		0.622	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		T	57589521	G	T	57589521	3	4	26	1	0	0	0	0	1	0	0	0	8958	1058	37	4	8728	4	LRP1	12	57589521	Missense_Mutation	SNP	G	TCGA-4A-A93Y-01A-11D-A36X-10		57589521	76262374	14	1874											
LTK	4058	hgsc.bcm.edu	37	chr15	41797955	41797955	+	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	aaatccagctcatcctgaggCgagcagagttctggcagggt	10	8	13	10	1	2	2	1	1	1	1	4	3	4	2	2	3	2	4	2	3	1	1	rs375203744		TCGA-4A-A93Y-01A-11D-A36X-10	TCGA-4A-A93Y-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90	8502bb1a-6a04-42ad-88f1-4559e24b1286	g.chr15:41797955C>T	ENST00000263800.6	-	13	1749	c.1653G>A	c.(1651-1653)tcG>tcA	p.S551S	LTK_ENST00000453182.2_Silent_p.S421S|LTK_ENST00000355166.5_Silent_p.S490S|LTK_ENST00000561619.1_Silent_p.S249S	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	551	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		CATCCTGAGGCGAGCAGAGTT	0.607										TSP Lung(18;0.14)																											p.S551S		Atlas-SNP	.											.	LTK	117	.	0			c.G1653A						PASS	.																																			SO:0001819	synonymous_variant	4058	exon13			CTGAGGCGAGCAG	D16105	CCDS10077.1, CCDS10078.1, CCDS45237.1	15q15.1-q21.1	2009-07-10	2008-01-23		ENSG00000062524	ENSG00000062524	2.7.10.1		6721	protein-coding gene	gene with protein product		151520	"leukocyte tyrosine kinase"			2320375	Standard	NM_206961		Approved	TYK1	uc001zoa.3	P29376	OTTHUMG00000130339	ENST00000263800.6:c.1653G>A	chr15.hg19:g.41797955C>T		250.0	0.0	.		264.0	12.0	.	NM_002344	A6NNJ8|B4DL89|E9PFX4	Silent	SNP	ENST00000263800.6	hg19	CCDS10077.1																																																																																			.	.	.	weak		0.607	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2			T	41797955	C	T	41797955	2	4	26	1	0	0	0	0	0	0	0	1	9087	755	27	1		1	LTK	15	41797955	Silent	SNP	C	TCGA-4A-A93Y-01A-11D-A36X-10		41797955	60733437	15	1875											
CREBBP	1387	hgsc.bcm.edu	37	chr16	3786685	3786685	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgatccgctctgcaaacgccTtgtccagcatctttttgtac	7	14	7	13	2	2	1	0	1	2	0	4	1	4	1	3	0	4	4	3	0	2	4			TCGA-4A-A93Y-01A-11D-A36X-10	TCGA-4A-A93Y-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90	8502bb1a-6a04-42ad-88f1-4559e24b1286	g.chr16:3786685T>C	ENST00000262367.5	-	27	5335	c.4526A>G	c.(4525-4527)aAg>aGg	p.K1509R	CREBBP_ENST00000382070.3_Missense_Mutation_p.K1471R	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1509	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)			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)		TGCAAACGCCTTGTCCAGCAT	0.488			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.K1509R		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.A4526G						PASS	.						304	255	272					16																	3786685		2197	4300	6497	SO:0001583	missense	1387	exon27			AACGCCTTGTCCA	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.4526A>G	chr16.hg19:g.3786685T>C	ENSP00000262367:p.Lys1509Arg	156.0	0.0	.		111.0	5.0	.	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	hg19	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	t	21.9	4.214104	0.79352	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.93906	-3.31;-3.31	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	D	0.96651	0.8907	M	0.82517	2.595	0.80722	D	1	D;D	0.56035	0.974;0.974	D;D	0.75484	0.986;0.986	D	0.97056	0.9767	10	0.62326	D	0.03	-26.9444	14.6308	0.68655	0.0:0.0:0.0:1.0	.	1539;1509	Q4LE28;Q92793	.;CBP_HUMAN	R	1509;1539;1471;98	ENSP00000262367:K1509R;ENSP00000371502:K1471R	ENSP00000262367:K1509R	K	-	2	0	CREBBP	3726686	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.774000	0.85478	2.107000	0.64212	0.459000	0.35465	AAG	.	.	.	none		0.488	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		C	3786685	T	C	3786685	3	2	26	1	0	0	0	0	1	0	0	0	3863	1609	56	3	2822	3	CREBBP	16	3786685	Missense_Mutation	SNP	T	TCGA-4A-A93Y-01A-11D-A36X-10		3786685	86568068	16	1876											
ABCC6	368	hgsc.bcm.edu	37	chr16	16302617	16302618	+	Frame_Shift_Ins	INS	-	-	T																															tgcggttcctcatccactccINSttttcaagccgggaaacaag																										TCGA-4A-A93Y-01A-11D-A36X-10	TCGA-4A-A93Y-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90	8502bb1a-6a04-42ad-88f1-4559e24b1286	g.chr16:16302617_16302618insT	ENST00000205557.7	-	7	790_791	c.761_762insA	c.(760-762)aagfs	p.K254fs	ABCC6_ENST00000574094.1_5'UTR	NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	254					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)	TCATCCACTCCTTTTCAAGCCG	0.55																																					p.K254fs		Pindel	.											.	ABCC6	110	.	0			c.762_763insA						PASS	.																																			SO:0001589	frameshift_variant	368	exon7			.	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.762dupA	chr16.hg19:g.16302621_16302621dupT	ENSP00000205557:p.Lys254fs	459.0	0.0	.		465.0	22.0	0.047	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Frame_Shift_Ins	INS	ENST00000205557.7	hg19	CCDS10568.1																																																																																			.	.	.	none		0.55	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2			T	16302618	-	T	16302617	7	5	26	1	0	1	1	0	0	0	0	0	57	680	24	0	3849	0	ABCC6	16	16302617	Frame_Shift_Ins	INS	-	TCGA-4A-A93Y-01A-11D-A36X-10	12515932	16302617	74052136	17	1877											
CACNG3	10368	hgsc.bcm.edu	37	chr16	24358125	24358125	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gactacgaacaggacacagcCgaatatctcctgcgtaagtt	13	8	9	11	3	1	0	0	0	1	0	2	4	1	1	2	1	4	2	2	1	5	4			TCGA-4A-A93Y-01A-11D-A36X-10	TCGA-4A-A93Y-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90	8502bb1a-6a04-42ad-88f1-4559e24b1286	g.chr16:24358125C>T	ENST00000005284.3	+	2	1484	c.282C>T	c.(280-282)gcC>gcT	p.A94A		NM_006539.3	NP_006530.1	O60359	CCG3_HUMAN	calcium channel, voltage-dependent, gamma subunit 3	94					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|prostate(4)|skin(2)	40				GBM - Glioblastoma multiforme(48;0.0809)		AGGACACAGCCGAATATCTCC	0.557																																					p.A94A		Atlas-SNP	.											.	CACNG3	112	.	0			c.C282T						PASS	.						79	71	74					16																	24358125		2197	4300	6497	SO:0001819	synonymous_variant	10368	exon2			CACAGCCGAATAT	AF131911	CCDS10620.1	16p12.1	2008-05-14			ENSG00000006116	ENSG00000006116		"Calcium channel subunits"	1407	protein-coding gene	gene with protein product		606403				10221464, 10493829	Standard	NM_006539		Approved		uc002dmf.3	O60359	OTTHUMG00000131651	ENST00000005284.3:c.282C>T	chr16.hg19:g.24358125C>T		80.0	0.0	.		96.0	7.0	.	NM_006539		Silent	SNP	ENST00000005284.3	hg19	CCDS10620.1																																																																																			.	.	.	none		0.557	CACNG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254548.1	NM_006539		T	24358125	C	T	24358125	2	4	26	1	0	0	0	0	0	0	0	1	2560	639	23	1		1	CACNG3	16	24358125	Silent	SNP	C	TCGA-4A-A93Y-01A-11D-A36X-10	8055508	24358125	65996628	18	1878											
DHX38	9785	hgsc.bcm.edu	37	chr16	72133644	72133644	+	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	cctgcagcaagccgatcgggAttggtacatgatggacgagg	10	7	15	9	3	0	1	0	1	0	0	1	5	0	3	2	4	4	3	2	4	2	2			TCGA-4A-A93Y-01A-11D-A36X-10	TCGA-4A-A93Y-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90	8502bb1a-6a04-42ad-88f1-4559e24b1286	g.chr16:72133644A>T	ENST00000268482.3	+	8	1483	c.974A>T	c.(973-975)gAt>gTt	p.D325V	DHX38_ENST00000536867.1_Intron	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	325					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)				GCCGATCGGGATTGGTACATG	0.567											OREG0023926	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D325V	Melanoma(97;711 1442 7855 13832 28836)	Atlas-SNP	.											.	DHX38	91	.	0			c.A974T						PASS	.						80	69	72					16																	72133644		2198	4300	6498	SO:0001583	missense	9785	exon8			ATCGGGATTGGTA	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.974A>T	chr16.hg19:g.72133644A>T	ENSP00000268482:p.Asp325Val	118.0	0.0	.	1135	113.0	9.0	.	NM_014003	B4DVG8|D3DWS7|O75212|Q96HN7	Missense_Mutation	SNP	ENST00000268482.3	hg19	CCDS10907.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.128632	0.77549	.	.	ENSG00000140829	ENST00000268482	T	0.03242	4.0	4.69	4.69	0.59074	.	0.055445	0.64402	D	0.000001	T	0.09247	0.0228	M	0.82517	2.595	0.80722	D	1	P	0.42735	0.788	B	0.40410	0.328	T	0.02837	-1.1104	10	0.66056	D	0.02	.	14.4607	0.67448	1.0:0.0:0.0:0.0	.	325	Q92620	PRP16_HUMAN	V	325	ENSP00000268482:D325V	ENSP00000268482:D325V	D	+	2	0	DHX38	70691145	1.000000	0.71417	0.994000	0.49952	0.843000	0.47879	8.822000	0.92013	1.878000	0.54408	0.455000	0.32223	GAT	.	.	.	none		0.567	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003		T	72133644	A	T	72133644	3	4	26	1	0	0	0	0	1	0	0	0	4513	333	12	5	1000	5	DHX38	16	72133644	Missense_Mutation	SNP	A	TCGA-4A-A93Y-01A-11D-A36X-10	47775519	72133644	18221109	19	1879											
NCOR1	9611	hgsc.bcm.edu	37	chr17	15965099	15965099	+	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	tgttttggacacatccatctGgggtgcagaagctgcagcat	9	11	12	9	0	1	1	0	0	1	1	2	2	2	2	1	3	4	5	1	3	1	2			TCGA-4A-A93Y-01A-11D-A36X-10	TCGA-4A-A93Y-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90	8502bb1a-6a04-42ad-88f1-4559e24b1286	g.chr17:15965099G>T	ENST00000268712.3	-	37	5754	c.5497C>A	c.(5497-5499)Cag>Aag	p.Q1833K	NCOR1_ENST00000395851.1_Missense_Mutation_p.Q1849K|NCOR1_ENST00000395857.3_Missense_Mutation_p.Q417K	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1833	Interaction with C1D. {ECO:0000250}.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		ACATCCATCTGGGGTGCAGAA	0.532																																					p.Q1849K		Atlas-SNP	.											.	NCOR1	240	.	0			c.C5545A						PASS	.						58	62	61					17																	15965099		2203	4299	6502	SO:0001583	missense	9611	exon36			CCATCTGGGGTGC	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.5497C>A	chr17.hg19:g.15965099G>T	ENSP00000268712:p.Gln1833Lys	144.0	0.0	.		113.0	5.0	.	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	hg19	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.984237	0.93044	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849;ENST00000395857	T;T;T	0.51325	0.71;1.03;0.74	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.63474	0.2514	L	0.43152	1.355	0.80722	D	1	D;D;D;D;D	0.69078	0.986;0.989;0.969;0.982;0.997	D;D;D;D;D	0.77557	0.979;0.966;0.93;0.968;0.99	T	0.62091	-0.6927	10	0.54805	T	0.06	-9.2428	18.9559	0.92658	0.0:0.0:1.0:0.0	.	643;1737;1833;1849;353	B4DZ48;E7EVK1;O75376;O75376-2;Q86YY1	.;.;NCOR1_HUMAN;.;.	K	1833;1849;1737;417	ENSP00000268712:Q1833K;ENSP00000379192:Q1849K;ENSP00000379198:Q417K	ENSP00000268712:Q1833K	Q	-	1	0	NCOR1	15905824	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.963000	0.93385	2.727000	0.93392	0.650000	0.86243	CAG	.	.	.	none		0.532	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		T	15965099	G	T	15965099	3	4	26	1	0	0	0	0	1	0	0	0	10242	1357	47	4	1865	4	NCOR1	17	15965099	Missense_Mutation	SNP	G	TCGA-4A-A93Y-01A-11D-A36X-10		15965099	65230111	20	1880											
SUZ12	23512	hgsc.bcm.edu	37	chr17	30315477	30315477	+	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	attcagagagtctccatcagGaaaacaagcctggttcagtt	13	10	9	9	0	4	1	3	0	1	1	5	3	4	2	2	2	2	2	2	2	3	3			TCGA-4A-A93Y-01A-11D-A36X-10	TCGA-4A-A93Y-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90	8502bb1a-6a04-42ad-88f1-4559e24b1286	g.chr17:30315477G>T	ENST00000322652.5	+	10	1391	c.1162G>T	c.(1162-1164)Gaa>Taa	p.E388*	SUZ12_ENST00000580398.1_Nonsense_Mutation_p.E365*	NM_015355.2	NP_056170.2	Q15022	SUZ12_HUMAN	SUZ12 polycomb repressive complex 2 subunit	388					histone ubiquitination (GO:0016574)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|histone methyltransferase activity (GO:0042054)|metal ion binding (GO:0046872)|methylated histone binding (GO:0035064)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)		SSH2/SUZ12(2)|JAZF1/SUZ12(133)	breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(5)|skin(1)	21		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.041)|Ovarian(249;0.182)|Breast(31;0.231)				TCTCCATCAGGAAAACAAGCC	0.393			T	JAZF1	endometrial stromal tumours																																p.E388X		Atlas-SNP	.		Dom	yes		17	17q11.2	23512	suppressor of zeste 12 homolog (Drosophila)		M	.	SUZ12	61	.	0			c.G1162T						PASS	.						75	74	75					17																	30315477		2203	4300	6503	SO:0001587	stop_gained	23512	exon10			CATCAGGAAAACA	D63881	CCDS11270.1	17q21	2013-06-05	2013-06-05		ENSG00000178691	ENSG00000178691		"Zinc fingers, C2H2-type"	17101	protein-coding gene	gene with protein product		606245	"suppressor of zeste 12 homolog (Drosophila)"			8590280, 11371647, 18784248	Standard	NM_015355		Approved	JJAZ1, KIAA0160, CHET9	uc002hgs.2	Q15022	OTTHUMG00000132813	ENST00000322652.5:c.1162G>T	chr17.hg19:g.30315477G>T	ENSP00000316578:p.Glu388*	263.0	0.0	.		267.0	14.0	.	NM_015355	Q96BD9	Nonsense_Mutation	SNP	ENST00000322652.5	hg19	CCDS11270.1	.	.	.	.	.	.	.	.	.	.	g	38	7.192437	0.98125	.	.	ENSG00000178691	ENST00000322652	.	.	.	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.17832	T	0.49	-15.3921	19.7638	0.96333	0.0:0.0:1.0:0.0	.	.	.	.	X	388	.	ENSP00000316578:E388X	E	+	1	0	SUZ12	27339590	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.543000	0.73874	2.673000	0.90976	0.650000	0.86243	GAA	.	.	.	none		0.393	SUZ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256260.2	NM_015355		T	30315477	G	T	30315477	4	4	26	1	0	0	0	0	0	1	0	0	15428	1175	41	4	1200	4	SUZ12	17	30315477	Nonsense_Mutation	SNP	G	TCGA-4A-A93Y-01A-11D-A36X-10	14350378	30315477	50879733	21	1881											
SYCP2	10388	hgsc.bcm.edu	37	chr20	58445040	58445040	+	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	tagttggagtatgtctgggcTatgaatgaagacatacaaaa	15	11	11	4	0	1	3	0	2	1	1	1	4	1	4	0	2	1	3	0	2	8	5			TCGA-4A-A93Y-01A-11D-A36X-10	TCGA-4A-A93Y-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90	8502bb1a-6a04-42ad-88f1-4559e24b1286	g.chr20:58445040T>G	ENST00000357552.3	-	36	3781		c.e36-2		SYCP2_ENST00000371001.2_Splice_Site			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2						female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			ATGTCTGGGCTATGAATGAAG	0.318																																					.		Atlas-SNP	.											.	SYCP2	204	.	0			c.3556-2A>C						PASS	.						58	54	55					20																	58445040		2192	4291	6483	SO:0001630	splice_region_variant	10388	exon36			CTGGGCTATGAAT	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.3556-2A>C	chr20.hg19:g.58445040T>G		41.0	0.0	.		71.0	10.0	.	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Splice_Site	SNP	ENST00000357552.3	hg19	CCDS13482.1	.	.	.	.	.	.	.	.	.	.	T	12.49	1.952546	0.34471	.	.	ENSG00000196074	ENST00000371001;ENST00000357552	.	.	.	4.99	4.99	0.66335	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.1113	0.48235	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SYCP2	57878435	0.710000	0.27896	0.907000	0.35723	0.304000	0.27724	2.666000	0.46799	1.873000	0.54277	0.460000	0.39030	.	.	.	.	none		0.318	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258	Intron	G	58445040	T	G	58445040	5	3	26	1	0	0	0	0	0	0	1	0	15444	1536	53	5	1078	5	SYCP2	20	58445040	Splice_Site	SNP	T	TCGA-4A-A93Y-01A-11D-A36X-10		58445040	4580480	22	1882											
MXRA5	25878	hgsc.bcm.edu	37	chrX	3235245	3235246	+	Missense_Mutation	DNP	CC	CC	AA																															agcttgagggttcctccgtaCctgacgtccgtcctccgcgg																										TCGA-4A-A93Y-01A-11D-A36X-10	TCGA-4A-A93Y-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90	8502bb1a-6a04-42ad-88f1-4559e24b1286	g.chrX:3235245_3235246CC>AA	ENST00000217939.6	-	6	6630_6631	c.6476_6477GG>TT	c.(6475-6477)aGG>aTT	p.R2159I		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	2159	Ig-like C2-type 6.					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)				TTCCTCCGTACCTGACGTCCGT	0.683																																					p.R2159S|p.R2159M		Atlas-SNP	.											.	MXRA5	815	.	0			c.G6477T|c.G6476T						PASS	.																																			SO:0001583	missense	25878	exon6			TCCGTACCTGACG|CCGTACCTGACGT	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.6476_6477delinsAA	chrX.hg19:g.3235245_3235246delinsAA	ENSP00000217939:p.Arg2159Ile	201.0|203.0	0.0	.		218.0|219.0	10.0	.	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	hg19	CCDS14124.1																																																																																			.	.	.	none		0.683	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		AA	3235246	CC	AA	3235245	3	1	26	1	0	0	0	0	1	0	0	0	10010	506	18	4	2017	4	MXRA5	23	3235245	Missense_Mutation	DNP	CC	TCGA-4A-A93Y-01A-11D-A36X-10		3235245	152035315	23	1883											
PADI6	353238	hgsc.bcm.edu	37	chr1	17721468	17721468	+	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	gcagagggccgggccatgagTaagaccctccgagacttcct	9	6	13	13	2	0	4	0	1	0	3	2	5	2	4	5	2	0	2	5	2	1	2			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr1:17721468T>C	ENST00000434762.2	+	0	1410							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)	GGGCCATGAGTAAGACCCTCC	0.587																																					p.S453S		Atlas-SNP	.											.	PADI6	51	.	0			c.T1359C						PASS	.						41	45	44					1																	17721468		2104	4264	6368			353238	exon13			CATGAGTAAGACC	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		chr1.hg19:g.17721468T>C		62.0	0.0	.		52.0	18.0	.	NM_207421	Q330K5|Q70SX3	Silent	SNP	ENST00000434762.2	hg19																																																																																				.	.	.	none		0.587	PADI6-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000006804.4	NM_207421		C	17721468	T	C	17721468	1	2	27	0	1	0	0	0	0	0	0	0	11388	1635	57	3		3	PADI6	1	17721468	RNA	SNP	T	TCGA-5P-A9JU-01A-11D-A42J-10		17721468	231529153	1	1884											
NT5C1A	84618	hgsc.bcm.edu	37	chr1	40126872	40126872	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtccccatcgaaggccacgCgcagctgactctgggacaca	9	5	11	16	4	1	1	0	1	1	0	3	3	2	2	3	2	1	2	3	2	1	0	rs572504200		TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr1:40126872C>T	ENST00000235628.1	-	5	619	c.620G>A	c.(619-621)cGc>cAc	p.R207H		NM_032526.1	NP_115915.1	Q9BXI3	5NT1A_HUMAN	5'-nucleotidase, cytosolic IA	207					adenosine metabolic process (GO:0046085)|dephosphorylation (GO:0016311)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|purine nucleobase metabolic process (GO:0006144)|purine nucleoside monophosphate catabolic process (GO:0009128)|purine nucleotide catabolic process (GO:0006195)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)			breast(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)	15	Lung NSC(20;3.81e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;4.3e-17)|all cancers(16;8.48e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			GAAGGCCACGCGCAGCTGACT	0.627													C|||	1	0.000199681	0	0	5008	,	,		19843	0		0	False		,,,				2504	0.001				p.R207H		Atlas-SNP	.											.	NT5C1A	46	.	0			c.G620A						PASS	.						60	52	55					1																	40126872		2203	4300	6503	SO:0001583	missense	84618	exon5			GCCACGCGCAGCT	AF331801	CCDS440.1	1p34.3-p33	2008-07-18			ENSG00000116981	ENSG00000116981			17819	protein-coding gene	gene with protein product	"cytosolic 5' nucleotidase, type 1A", "AMP-specific 5'-NT", "cytosolic 5'-nucleotidase IA"	610525				11133996, 11690631	Standard	NM_032526		Approved	CN-I, CN-IA, CN1A, CN1, MGC119199, MGC119201	uc001cdq.1	Q9BXI3	OTTHUMG00000009244	ENST00000235628.1:c.620G>A	chr1.hg19:g.40126872C>T	ENSP00000235628:p.Arg207His	78.0	0.0	.		75.0	8.0	.	NM_032526	Q3SYB9|Q5TG98|Q9BWT8	Missense_Mutation	SNP	ENST00000235628.1	hg19	CCDS440.1	.	.	.	.	.	.	.	.	.	.	C	35	5.544326	0.96488	.	.	ENSG00000116981	ENST00000235628	.	.	.	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	D	0.87712	0.6246	H	0.95539	3.685	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.91239	0.5020	9	0.72032	D	0.01	-4.9323	18.8667	0.92294	0.0:1.0:0.0:0.0	.	207	Q9BXI3	5NT1A_HUMAN	H	207	.	ENSP00000235628:R207H	R	-	2	0	NT5C1A	39899459	1.000000	0.71417	0.999000	0.59377	0.960000	0.62799	7.792000	0.85828	2.543000	0.85770	0.650000	0.86243	CGC	.	.	.	none		0.627	NT5C1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025626.1	NM_032526		T	40126872	C	T	40126872	3	4	27	1	0	0	0	0	1	0	0	0	10692	768	27	1	494	1	NT5C1A	1	40126872	Missense_Mutation	SNP	C	TCGA-5P-A9JU-01A-11D-A42J-10	22405404	40126872	209123749	2	1885											
TGFBR3	7049	hgsc.bcm.edu	37	chr1	92182200	92182200	+	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	ggaaatccattatcacctgaCtccagatcttcataaccatc	13	11	4	13	0	3	2	2	1	1	1	6	3	5	3	4	1	1	0	4	1	3	3			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr1:92182200C>T	ENST00000525962.1	-	10	1693	c.1632G>A	c.(1630-1632)gaG>gaA	p.E544E	TGFBR3_ENST00000370399.2_Silent_p.E543E|TGFBR3_ENST00000212355.4_Silent_p.E544E			Q03167	TGBR3_HUMAN	transforming growth factor, beta receptor III	544	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				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)		TATCACCTGACTCCAGATCTT	0.463																																					p.E544E		Atlas-SNP	.											.	TGFBR3	103	.	0			c.G1632A						PASS	.						288	298	294					1																	92182200		2203	4300	6503	SO:0001819	synonymous_variant	7049	exon11			ACCTGACTCCAGA	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.1632G>A	chr1.hg19:g.92182200C>T		210.0	0.0	.		215.0	93.0	.	NM_003243	A0AUW8|A8K5N0|B9EG88|Q5T2T4|Q5U731|Q9UGI2	Silent	SNP	ENST00000525962.1	hg19	CCDS30770.1																																																																																			.	.	.	none		0.463	TGFBR3-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382308.1	NM_003243		T	92182200	C	T	92182200	2	4	27	1	0	0	0	0	0	0	0	1	15835	564	20	2		2	TGFBR3	1	92182200	Silent	SNP	C	TCGA-5P-A9JU-01A-11D-A42J-10	52055328	92182200	157068421	3	1886											
GLMN	11146	hgsc.bcm.edu	37	chr1	92712690	92712690	+	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	tatagaacaaagatctttagAtttctgggcctctgtaagag	13	13	9	6	0	3	4	0	0	3	4	3	4	3	4	1	1	1	1	1	1	6	6			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr1:92712690A>T	ENST00000370360.3	-	18	1678	c.1597T>A	c.(1597-1599)Tct>Act	p.S533T	GLMN_ENST00000534881.1_Missense_Mutation_p.S519T	NM_053274.2	NP_444504.1	Q92990	GLMN_HUMAN	glomulin, FKBP associated protein	533					muscle cell differentiation (GO:0042692)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of T cell proliferation (GO:0042130)|neural tube closure (GO:0001843)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of phosphorylation (GO:0042327)|regulation of gene expression, epigenetic (GO:0040029)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|vasculogenesis (GO:0001570)	Cul2-RING ubiquitin ligase complex (GO:0031462)|Cul3-RING ubiquitin ligase complex (GO:0031463)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|cullin-RING ubiquitin ligase complex (GO:0031461)|intracellular (GO:0005622)	hepatocyte growth factor receptor binding (GO:0005171)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase inhibitor activity (GO:0055105)			endometrium(5)|kidney(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)	17		all_lung(203;0.00827)|Lung NSC(277;0.0295)		all cancers(265;0.00702)|GBM - Glioblastoma multiforme(16;0.0381)|Epithelial(280;0.0989)		AGATCTTTAGATTTCTGGGCC	0.338									Multiple Glomus Tumors (of the Skin), Familial																												p.S533T		Atlas-SNP	.											.	GLMN	37	.	0			c.T1597A						PASS	.						109	115	113					1																	92712690		2203	4300	6503	SO:0001583	missense	11146	exon18	Familial Cancer Database	Multiple Familial Glomangiomas, Hereditary Multiple Glomus Tumors, Familial Multiple Glomangiomatosis, Inherited Cutaneous Venous Anomalies, incl. Familial Multiple Glomangiomyoma	CTTTAGATTTCTG	U73704	CCDS738.1	1p22.1	2008-02-05	2004-07-01		ENSG00000174842	ENSG00000174842			14373	protein-coding gene	gene with protein product		601749	"venous malformation with glomus cells"	VMGLOM		8955134	Standard	XM_005270400		Approved	FAP48, GLML, GVM, FKBPAP	uc001dor.3	Q92990	OTTHUMG00000010283	ENST00000370360.3:c.1597T>A	chr1.hg19:g.92712690A>T	ENSP00000359385:p.Ser533Thr	40.0	0.0	.		21.0	6.0	.	NM_053274	Q5VVC3|Q9BVE8	Missense_Mutation	SNP	ENST00000370360.3	hg19	CCDS738.1	.	.	.	.	.	.	.	.	.	.	A	11.11	1.542990	0.27563	.	.	ENSG00000174842	ENST00000370360;ENST00000534881	T;T	0.47528	0.85;0.84	5.97	0.375	0.16188	.	0.644862	0.17527	N	0.171029	T	0.19406	0.0466	L	0.47716	1.5	0.09310	N	0.999993	B;B	0.33777	0.222;0.425	B;B	0.39971	0.122;0.315	T	0.28364	-1.0046	10	0.20046	T	0.44	-1.6953	6.4009	0.21638	0.5904:0.0:0.0699:0.3397	.	519;533	B4DJ85;Q92990	.;GLMN_HUMAN	T	533;519	ENSP00000359385:S533T;ENSP00000440156:S519T	ENSP00000359385:S533T	S	-	1	0	GLMN	92485278	0.746000	0.28272	0.903000	0.35520	0.916000	0.54674	1.332000	0.33805	0.122000	0.18314	-0.327000	0.08410	TCT	.	.	.	none		0.338	GLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028358.1	NM_007070		T	92712690	A	T	92712690	3	4	27	1	0	0	0	0	1	0	0	0	6455	333	12	5	195	5	GLMN	1	92712690	Missense_Mutation	SNP	A	TCGA-5P-A9JU-01A-11D-A42J-10	530490	92712690	156537931	4	1887											
NUF2	83540	hgsc.bcm.edu	37	chr1	163318835	163318835	+	Missense_Mutation	SNP	A	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	aacttggaattcaacaactaAaagatgctgctgaaagggag	17	8	10	6	0	1	2	1	1	0	1	1	4	1	4	0	2	5	2	0	2	7	3			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr1:163318835A>C	ENST00000271452.3	+	13	1504	c.1225A>C	c.(1225-1227)Aaa>Caa	p.K409Q	NUF2_ENST00000367900.3_Missense_Mutation_p.K409Q|NUF2_ENST00000524800.1_Missense_Mutation_p.K362Q	NM_145697.2	NP_663735.2	Q9BZD4	NUF2_HUMAN	NUF2, NDC80 kinetochore complex component	409	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)					TCAACAACTAAAAGATGCTGC	0.323																																					p.K409Q		Atlas-SNP	.											.	NUF2	138	.	0			c.A1225C						PASS	.						58	61	60					1																	163318835		2203	4299	6502	SO:0001583	missense	83540	exon13			CAACTAAAAGATG	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.1225A>C	chr1.hg19:g.163318835A>C	ENSP00000271452:p.Lys409Gln	556.0	0.0	.		567.0	41.0	.	NM_145697	Q8WU69|Q96HJ4|Q96Q78	Missense_Mutation	SNP	ENST00000271452.3	hg19	CCDS1245.1	.	.	.	.	.	.	.	.	.	.	A	10.81	1.455210	0.26161	.	.	ENSG00000143228	ENST00000524800;ENST00000367900;ENST00000271452	T;T;T	0.35973	1.28;1.44;1.44	5.5	3.0	0.34707	.	0.231097	0.49916	D	0.000136	T	0.09069	0.0224	N	0.22421	0.69	0.22982	N	0.998474	B;B	0.14438	0.01;0.01	B;B	0.09377	0.004;0.004	T	0.16276	-1.0408	9	0.17369	T	0.5	-21.3294	10.6004	0.45362	0.6939:0.3061:0.0:0.0	.	362;409	E9PQC4;Q9BZD4	.;NUF2_HUMAN	Q	362;409;409	ENSP00000436888:K362Q;ENSP00000356875:K409Q;ENSP00000271452:K409Q	ENSP00000271452:K409Q	K	+	1	0	NUF2	161585459	0.992000	0.36948	0.215000	0.23724	0.796000	0.44982	3.395000	0.52558	1.047000	0.40274	0.533000	0.62120	AAA	.	.	.	none		0.323	NUF2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000082812.1	NM_145697		C	163318835	A	C	163318835	3	2	27	1	0	0	0	0	1	0	0	0	10754	15	1	5	1271	5	NUF2	1	163318835	Missense_Mutation	SNP	A	TCGA-5P-A9JU-01A-11D-A42J-10	70606145	163318835	85931786	5	1888											
ABL2	27	hgsc.bcm.edu	37	chr1	179078368	179078368	+	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	agttcgtatttcttatggggCtgattctccatttctcggaa	7	17	9	8	2	3	1	0	1	3	0	6	2	3	2	1	3	0	3	1	3	3	6			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr1:179078368C>A	ENST00000502732.1	-	12	2237	c.2034G>T	c.(2032-2034)caG>caT	p.Q678H	ABL2_ENST00000408940.3_Missense_Mutation_p.Q642H|ABL2_ENST00000511413.1_Missense_Mutation_p.Q678H|ABL2_ENST00000507173.1_Missense_Mutation_p.Q657H|ABL2_ENST00000504405.1_Missense_Mutation_p.Q642H|ABL2_ENST00000512653.1_Missense_Mutation_p.Q663H|ABL2_ENST00000367623.4_Missense_Mutation_p.Q657H|ABL2_ENST00000344730.3_Missense_Mutation_p.Q663H	NM_001168236.1|NM_001168237.1|NM_001168238.1|NM_007314.3	NP_001161708.1|NP_001161709.1|NP_001161710.1|NP_009298.1	P42684	ABL2_HUMAN	ABL proto-oncogene 2, non-receptor tyrosine kinase	678					actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|cellular response to retinoic acid (GO:0071300)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phospholipase C activity (GO:0010863)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)			breast(8)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	65					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	TCTTATGGGGCTGATTCTCCA	0.512			T	ETV6	AML																																p.Q678H		Atlas-SNP	.		Dom	yes		1	1q24-q25	27	v-abl Abelson murine leukemia viral oncogene homolog 2		L	.	ABL2	307	.	0			c.G2034T						PASS	.						199	212	208					1																	179078368		2203	4300	6503	SO:0001583	missense	27	exon12			ATGGGGCTGATTC	M14904	CCDS30947.1, CCDS41441.1, CCDS44282.1, CCDS44283.1, CCDS41441.2, CCDS53435.1, CCDS53436.1, CCDS53437.1, CCDS53438.1	1q25.2	2014-06-26	2014-06-26		ENSG00000143322	ENSG00000143322		"SH2 domain containing"	77	protein-coding gene	gene with protein product	"Abelson-related gene"	164690	"v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene)", "v-abl Abelson murine leukemia viral oncogene homolog 2", "c-abl oncogene 2, non-receptor tyrosine kinase"	ABLL		3787260	Standard	NM_001136001		Approved	ARG	uc001gmi.4	P42684	OTTHUMG00000035199	ENST00000502732.1:c.2034G>T	chr1.hg19:g.179078368C>A	ENSP00000427562:p.Gln678His	92.0	0.0	.		108.0	46.0	.	NM_007314	A0M8X0|B7UEF2|B7UEF3|B7UEF4|B7UEF5|Q5T0X6|Q5W0C5|Q6NZY6|Q7Z301	Missense_Mutation	SNP	ENST00000502732.1	hg19	CCDS30947.1	.	.	.	.	.	.	.	.	.	.	C	8.471	0.857571	0.17106	.	.	ENSG00000143322	ENST00000502732;ENST00000408940;ENST00000344730;ENST00000512653;ENST00000504405;ENST00000367623;ENST00000507173;ENST00000511413	T;T;T;T;T;T;T;T	0.13538	2.58;2.58;2.58;2.58;2.58;2.58;2.58;2.58	5.46	3.53	0.40419	.	0.000000	0.49305	D	0.000142	T	0.20170	0.0485	L	0.31752	0.955	0.80722	D	1	D;D;B;D;B;D;B;B	0.76494	0.999;0.998;0.038;0.994;0.052;0.998;0.052;0.069	D;D;B;D;B;D;B;B	0.85130	0.997;0.994;0.018;0.916;0.028;0.994;0.028;0.062	T	0.03608	-1.1020	10	0.26408	T	0.33	.	7.7144	0.28696	0.0:0.74:0.0:0.26	.	657;657;678;642;678;663;642;663	P42684-6;P42684-7;P42684-5;P42684-4;P42684;P42684-3;D1MPS6;P42684-10	.;.;.;.;ABL2_HUMAN;.;.;.	H	678;642;663;663;642;657;657;678	ENSP00000427562:Q678H;ENSP00000386152:Q642H;ENSP00000339209:Q663H;ENSP00000423578:Q663H;ENSP00000426831:Q642H;ENSP00000356595:Q657H;ENSP00000423413:Q657H;ENSP00000424697:Q678H	ENSP00000339209:Q663H	Q	-	3	2	ABL2	177344991	0.998000	0.40836	1.000000	0.80357	0.993000	0.82548	0.656000	0.24948	1.246000	0.43901	0.591000	0.81541	CAG	.	.	.	none		0.512	ABL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085174.3	NM_005158		A	179078368	C	A	179078368	3	1	27	1	0	0	0	0	1	0	0	0	93	796	28	4	1518	4	ABL2	1	179078368	Missense_Mutation	SNP	C	TCGA-5P-A9JU-01A-11D-A42J-10	15759533	179078368	70172253	6	1889											
C1orf25	81627	hgsc.bcm.edu	37	chr1	185106774	185106774	+	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	atccttctgaaaaattctctCttcacaccactgacaatgga	13	12	4	12	0	4	2	1	2	3	0	6	3	5	3	2	1	0	0	2	1	3	3			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr1:185106774C>A	ENST00000367506.5	-	10	1745	c.1477G>T	c.(1477-1479)Gag>Tag	p.E493*	TRMT1L_ENST00000367504.3_Nonsense_Mutation_p.E337*	NM_001202423.1|NM_030934.4	NP_001189352.1|NP_112196.3	Q7Z2T5	TRM1L_HUMAN	tRNA methyltransferase 1 homolog (S. cerevisiae)-like	493	Trm1 methyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00958}.				adult locomotory behavior (GO:0008344)		metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA (guanine-N2-)-methyltransferase activity (GO:0004809)|tRNA binding (GO:0000049)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	21						AAAATTCTCTCTTCACACCAC	0.358																																					p.E493X		Atlas-SNP	.											.	TRMT1L	50	.	0			c.G1477T						PASS	.						141	139	140					1																	185106774		2203	4300	6503	SO:0001587	stop_gained	81627	exon10			TTCTCTCTTCACA	AF288399	CCDS1366.1	1q25.2	2012-06-29	2012-06-29	2011-01-24	ENSG00000121486	ENSG00000121486			16782	protein-coding gene	gene with protein product	"TRM1-like"	611673	"chromosome 1 open reading frame 25", "TRM1 tRNA methyltransferase 1-like"	C1orf25		11318611, 17198746	Standard	NM_030934		Approved		uc001grf.4	Q7Z2T5	OTTHUMG00000035389	ENST00000367506.5:c.1477G>T	chr1.hg19:g.185106774C>A	ENSP00000356476:p.Glu493*	93.0	0.0	.		83.0	26.0	.	NM_030934	Q5TEN0|Q6ZMX0|Q8IWH5|Q8NC68|Q9BZQ1	Nonsense_Mutation	SNP	ENST00000367506.5	hg19	CCDS1366.1	.	.	.	.	.	.	.	.	.	.	C	45	11.739919	0.99597	.	.	ENSG00000121486	ENST00000367504;ENST00000367506;ENST00000458395	.	.	.	5.82	5.82	0.92795	.	0.049538	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	-19.1751	20.0812	0.97776	0.0:1.0:0.0:0.0	.	.	.	.	X	337;493;117	.	ENSP00000356474:E337X	E	-	1	0	TRMT1L	183373397	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.679000	0.84048	2.744000	0.94065	0.585000	0.79938	GAG	.	.	.	none		0.358	TRMT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085787.1	NM_030934		A	185106774	C	A	185106774	4	1	27	1	0	0	0	0	0	1	0	0	2036	922	32	4	748	4	C1orf25	1	185106774	Nonsense_Mutation	SNP	C	TCGA-5P-A9JU-01A-11D-A42J-10	6028406	185106774	64143847	7	1890											
CACNA1S	779	hgsc.bcm.edu	37	chr1	201009812	201009815	+	Frame_Shift_Del	DEL	GCAT	GCAT	-																															ctgggtcagcagtcccttcaGcatctccacacagggtttgc																										TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	GCAT	GCAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr1:201009812_201009815delGCAT	ENST00000362061.3	-	42	5387_5390	c.5161_5164delATGC	c.(5161-5166)atgctgfs	p.ML1721fs	RP11-168O16.2_ENST00000415359.1_RNA|CACNA1S_ENST00000367338.3_Frame_Shift_Del_p.ML1702fs	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1721					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)	AGTCCCTTCAGCATCTCCACACAG	0.613																																					p.1721_1722del		Atlas-Indel,Pindel	.											.	CACNA1S	249	.	0			c.5162_5165del						PASS	.																																			SO:0001589	frameshift_variant	779	exon42			.	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.5161_5164delATGC	chr1.hg19:g.201009812_201009815delGCAT	ENSP00000355192:p.Met1721fs	59.0	0.0	0		45.0	18.0	0.4	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Frame_Shift_Del	DEL	ENST00000362061.3	hg19	CCDS1407.1																																																																																			.	.	.	none		0.613	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		-	201009815	GCAT	-	201009812	7	5	27	1	0	1	0	1	0	0	0	0	2549	962	34	0	469	0	CACNA1S	1	201009812	Frame_Shift_Del	DEL	GCAT	TCGA-5P-A9JU-01A-11D-A42J-10	15903038	201009812	48240809	8	1891											
FAM89A	375061	hgsc.bcm.edu	37	chr1	231155814	231155814	+	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	cccccttgtactcctgaatcGactcgtagaggctgtacagt	8	11	9	13	2	0	2	0	1	0	1	3	3	1	2	3	1	2	4	3	1	4	4	rs147790876		TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr1:231155814G>A	ENST00000366654.4	-	2	384	c.350C>T	c.(349-351)tCg>tTg	p.S117L	FAM89A_ENST00000494111.1_5'UTR|MIR1182_ENST00000408363.1_RNA	NM_198552.2	NP_940954.1	Q96GI7	FA89A_HUMAN	family with sequence similarity 89, member A	117										endometrium(1)|upper_aerodigestive_tract(1)	2	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				CTCCTGAATCGACTCGTAGAG	0.552																																					p.S117L		Atlas-SNP	.											FAM89A,NS,carcinoma,+1,1	FAM89A	8	.	0			c.C350T						PASS	.	G	LEU/SER	0,4406		0,0,2203	72	68	69		350	5.8	1	1	dbSNP_134	69	1,8599	1.2+/-3.3	0,1,4299	no	missense	FAM89A	NM_198552.2	145	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	117/185	231155814	1,13005	2203	4300	6503	SO:0001583	missense	375061	exon2			TGAATCGACTCGT	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.350C>T	chr1.hg19:g.231155814G>A	ENSP00000355614:p.Ser117Leu	43.0	0.0	.		44.0	20.0	.	NM_198552		Missense_Mutation	SNP	ENST00000366654.4	hg19	CCDS1590.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.971514	0.92919	0.0	1.16E-4	ENSG00000182118	ENST00000366654	.	.	.	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.77177	0.4092	M	0.78049	2.395	0.80722	D	1	D	0.76494	0.999	P	0.55667	0.781	T	0.79262	-0.1876	9	0.87932	D	0	-12.6922	20.3277	0.98707	0.0:0.0:1.0:0.0	.	117	Q96GI7	FA89A_HUMAN	L	117	.	ENSP00000355614:S117L	S	-	2	0	FAM89A	229222437	1.000000	0.71417	0.995000	0.50966	0.825000	0.46686	7.783000	0.85696	2.879000	0.98667	0.650000	0.86243	TCG	.	G|1.000;A|0.000	0.000	weak		0.552	FAM89A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092652.1	NM_198552		A	231155814	G	A	231155814	3	1	27	1	0	0	0	0	1	0	0	0	5654	1059	37	1	208	1	FAM89A	1	231155814	Missense_Mutation	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10	30146002	231155814	18094807	9	1892											
ASAP2	8853	hgsc.bcm.edu	37	chr2	9347341	9347342	+	Frame_Shift_Del	DEL	TG	TG	-																															acggcgcagtgccggaacacTgtggcggccatcgaggaggt																										TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr2:9347341_9347342delTG	ENST00000281419.3	+	1	448_449	c.108_109delTG	c.(106-111)actgtgfs	p.V37fs	ASAP2_ENST00000315273.4_Frame_Shift_Del_p.V37fs	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	37					positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						GCCGGAACACTGTGGCGGCCAT	0.718																																					p.36_36del		Atlas-Indel,Pindel	.											.	ASAP2	91	.	0			c.107_108del						PASS	.																																			SO:0001589	frameshift_variant	8853	exon1			.	AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2721	protein-coding gene	gene with protein product	"centaurin, beta 3"	603817	"development and differentiation enhancing factor 2"	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.108_109delTG	chr2.hg19:g.9347343_9347344delTG	ENSP00000281419:p.Val37fs	70.0	0.0	0		96.0	24.0	0.25	NM_001135191	D6W4Y8	Frame_Shift_Del	DEL	ENST00000281419.3	hg19	CCDS1661.1																																																																																			.	.	.	none		0.718	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887		-	9347342	TG	-	9347341	7	5	27	1	0	1	0	1	0	0	0	0	1011	1567	55	0	110	0	ASAP2	2	9347341	Frame_Shift_Del	DEL	TG	TCGA-5P-A9JU-01A-11D-A42J-10		9347341	233852032	10	1893											
NBAS	51594	hgsc.bcm.edu	37	chr2	15534394	15534394	+	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	tctaaccatcagcttgcgtgCctcttctgagctagattgag	8	13	9	11	1	4	3	1	2	3	1	4	3	4	3	2	0	5	2	2	0	2	5			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr2:15534394C>G	ENST00000281513.5	-	28	3239	c.3214G>C	c.(3214-3216)Gca>Cca	p.A1072P	NBAS_ENST00000441750.1_Missense_Mutation_p.A952P	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	1072					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						AGCTTGCGTGCCTCTTCTGAG	0.338																																					p.A1072P		Atlas-SNP	.											.	NBAS	246	.	0			c.G3214C						PASS	.						57	54	55					2																	15534394		2203	4297	6500	SO:0001583	missense	51594	exon28			TGCGTGCCTCTTC	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.3214G>C	chr2.hg19:g.15534394C>G	ENSP00000281513:p.Ala1072Pro	102.0	0.0	.		112.0	28.0	.	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	hg19	CCDS1685.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	29.5|29.5|29.5	5.014392|5.014392|5.014392	0.93404|0.93404|0.93404	.|.|.	.|.|.	ENSG00000151779|ENSG00000151779|ENSG00000151779	ENST00000441750;ENST00000281513;ENST00000441755|ENST00000429842|ENST00000442506	T;T;T|.|.	0.18502|.|.	2.21;2.21;2.21|.|.	5.48|5.48|5.48	5.48|5.48|5.48	0.80851|0.80851|0.80851	Secretory pathway Sec39 (1);|.|.	0.000000|.|.	0.85682|.|.	D|.|.	0.000000|.|.	T|T|T	0.76521|0.76521|0.76521	0.3999|0.3999|0.3999	M|M|M	0.74258|0.74258|0.74258	2.255|2.255|2.255	0.80722|0.80722|0.80722	D|D|D	1|1|1	D;D|.|.	0.89917|.|.	1.0;1.0|.|.	D;D|.|.	0.97110|.|.	0.998;1.0|.|.	T|T|T	0.75941|0.75941|0.75941	-0.3140|-0.3140|-0.3140	10|5|5	0.87932|.|.	D|.|.	0|.|.	.|.|.	18.1585|18.1585|18.1585	0.89701|0.89701|0.89701	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	952;1072|.|.	A2RRP1-2;A2RRP1|.|.	.;NBAS_HUMAN|.|.	P|A|S	952;1072;119|169|119	ENSP00000413201:A952P;ENSP00000281513:A1072P;ENSP00000396501:A119P|.|.	ENSP00000281513:A1072P|.|.	A|G|R	-|-|-	1|2|3	0|0|2	NBAS|NBAS|NBAS	15451845|15451845|15451845	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.997000|0.997000|0.997000	0.53966|0.53966|0.53966	0.864000|0.864000|0.864000	0.49448|0.49448|0.49448	6.752000|6.752000|6.752000	0.74898|0.74898|0.74898	2.572000|2.572000|2.572000	0.86782|0.86782|0.86782	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GCA|GGC|AGG	.	.	.	none		0.338	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		G	15534394	C	G	15534394	3	3	27	1	0	0	0	0	1	0	0	0	10193	739	26	4	4001	4	NBAS	2	15534394	Missense_Mutation	SNP	C	TCGA-5P-A9JU-01A-11D-A42J-10	6187053	15534394	227664979	11	1894											
USP34	9736	hgsc.bcm.edu	37	chr2	61433163	61433164	+	Missense_Mutation	DNP	TT	TT	CA																															gtaacttacctatacaggcaTttctaagttctggaggacta																										TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr2:61433163_61433164TT>CA	ENST00000398571.2	-	72	9218_9219	c.9142_9143AA>TG	c.(9142-9144)AAt>TGt	p.N3048C	USP34_ENST00000472689.1_5'Flank	NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	3048					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)			TATACAGGCATTTCTAAGTTCT	0.381																																					p.N3048S|p.N3048Y		Atlas-SNP	.											.	USP34	334	.	0			c.A9143G|c.A9142T						PASS	.																																			SO:0001583	missense	9736	exon72			CAGGCATTTCTAA|AGGCATTTCTAAG	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.9142_9143delinsCA	chr2.hg19:g.61433163_61433164delinsCA	ENSP00000381577:p.Asn3048Cys	93.0	0.0	.		80.0|82.0	38.0	.	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	hg19	CCDS42686.1																																																																																			.	.	.	none		0.381	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			CA	61433164	TT	CA	61433163	3	2	27	1	0	0	0	0	1	0	0	0	17077	1493	52	3	1533	3	USP34	2	61433163	Missense_Mutation	DNP	TT	TCGA-5P-A9JU-01A-11D-A42J-10	45898769	61433163	181766210	12	1895											
TTC21B	79809	hgsc.bcm.edu	37	chr2	166799781	166799781	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttggagtccctcttcaaaaTacttcagtgcttttttagtg	8	17	7	9	0	3	0	2	0	1	0	4	1	4	1	1	1	2	1	1	1	4	7			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr2:166799781T>C	ENST00000243344.7	-	5	637	c.500A>G	c.(499-501)tAt>tGt	p.Y167C	AC010127.5_ENST00000440322.1_RNA|AC010127.5_ENST00000443032.1_RNA	NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	167					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						CTCTTCAAAATACTTCAGTGC	0.338																																					p.Y167C		Atlas-SNP	.											.	TTC21B	130	.	0			c.A500G						PASS	.						122	115	117					2																	166799781		2203	4300	6503	SO:0001583	missense	79809	exon5			TCAAAATACTTCA	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.500A>G	chr2.hg19:g.166799781T>C	ENSP00000243344:p.Tyr167Cys	120.0	0.0	.		108.0	51.0	.	NM_024753	A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Missense_Mutation	SNP	ENST00000243344.7	hg19	CCDS33315.1	.	.	.	.	.	.	.	.	.	.	T	11.08	1.533262	0.27387	.	.	ENSG00000123607	ENST00000243344	T	0.65364	-0.15	5.33	-0.0208	0.13954	Tetratricopeptide-like helical (1);	0.321357	0.34386	N	0.004013	T	0.49949	0.1587	L	0.49640	1.575	0.80722	D	1	B;B	0.23540	0.087;0.01	B;B	0.26693	0.072;0.01	T	0.30297	-0.9983	10	0.51188	T	0.08	-0.3028	5.7902	0.18357	0.0:0.2217:0.1291:0.6492	.	167;167	Q7Z4L5-2;Q7Z4L5	.;TT21B_HUMAN	C	167	ENSP00000243344:Y167C	ENSP00000243344:Y167C	Y	-	2	0	TTC21B	166508027	0.983000	0.35010	0.127000	0.21898	0.634000	0.38068	0.672000	0.25187	-0.238000	0.09724	-0.408000	0.06270	TAT	.	.	.	none		0.338	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333770.1	NM_024753		C	166799781	T	C	166799781	3	2	27	1	0	0	0	0	1	0	0	0	16700	1406	49	3	3550	3	TTC21B	2	166799781	Missense_Mutation	SNP	T	TCGA-5P-A9JU-01A-11D-A42J-10	105366618	166799781	76399592	13	1896											
PIKFYVE	200576	hgsc.bcm.edu	37	chr2	209150550	209150550	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gacttgaatgctctttcagaTtctgcttgctctgtgtctgt	5	18	9	9	0	5	2	1	1	4	1	5	3	5	2	0	0	3	3	0	0	1	4			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr2:209150550T>C	ENST00000264380.4	+	6	872	c.714T>C	c.(712-714)gaT>gaC	p.D238D	PIKFYVE_ENST00000308862.6_Silent_p.D152D|PIKFYVE_ENST00000392202.3_Silent_p.D141D|PIKFYVE_ENST00000407449.1_Silent_p.D238D	NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	238					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						CTCTTTCAGATTCTGCTTGCT	0.438																																					p.D238D		Atlas-SNP	.											.	PIKFYVE	223	.	0			c.T714C						PASS	.						152	149	150					2																	209150550		2203	4300	6503	SO:0001819	synonymous_variant	200576	exon6			TTCAGATTCTGCT	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.714T>C	chr2.hg19:g.209150550T>C		97.0	0.0	.		95.0	41.0	.	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Silent	SNP	ENST00000264380.4	hg19	CCDS2382.1																																																																																			.	.	.	none		0.438	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040		C	209150550	T	C	209150550	2	2	27	1	0	0	0	0	0	0	0	1	11931	1490	52	3		3	PIKFYVE	2	209150550	Silent	SNP	T	TCGA-5P-A9JU-01A-11D-A42J-10	42350769	209150550	34048823	14	1897											
KIF1A	547	hgsc.bcm.edu	37	chr2	241658507	241658507	+	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	cgctccacggtgtccttgtcGctgttgtacatgtaggcata	6	13	11	11	3	0	0	0	0	0	0	3	0	2	0	2	2	1	6	2	2	3	5	rs553465326		TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr2:241658507G>A	ENST00000320389.7	-	45	4985	c.4827C>T	c.(4825-4827)agC>agT	p.S1609S	KIF1A_ENST00000498729.2_Silent_p.S1710S	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	1609	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)		TGTCCTTGTCGCTGTTGTACA	0.637																																					p.S1710S		Atlas-SNP	.											.	KIF1A	152	.	0			c.C5130T						PASS	.						90	102	98					2																	241658507		2176	4284	6460	SO:0001819	synonymous_variant	547	exon47			CTTGTCGCTGTTG	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.4827C>T	chr2.hg19:g.241658507G>A		102.0	0.0	.		109.0	44.0	.	NM_001244008	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Silent	SNP	ENST00000320389.7	hg19	CCDS46561.1																																																																																			.	.	.	none		0.637	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483		A	241658507	G	A	241658507	2	1	27	1	0	0	0	0	0	0	0	1	8290	1078	38	1		1	KIF1A	2	241658507	Silent	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10	32507957	241658507	1540866	15	1898											
SETD2	29072	hgsc.bcm.edu	37	chr3	47162892	47162892	+	Frame_Shift_Del	DEL	C	C	-																															ggacttgtttcttccatgggCaaagtagaattctttggcac																										TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr3:47162892delC	ENST00000409792.3	-	3	3276	c.3234delG	c.(3232-3234)ttgfs	p.L1078fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1078					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CTTCCATGGGCAAAGTAGAAT	0.413			"N, F, S, Mis"		clear cell renal carcinoma																																p.P1079fs		Atlas-Indel,Pindel	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.3235delC						PASS	.						107	104	105					3																	47162892		2203	4300	6503	SO:0001589	frameshift_variant	29072	exon3			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.3234delG	chr3.hg19:g.47162892delC	ENSP00000386759:p.Leu1078fs	40.0	0.0	0		48.0	41.0	0.854167	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Del	DEL	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.	.	none		0.413	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		-	47162892	C	-	47162892	7	5	27	1	0	1	0	1	0	0	0	0	14144	709	25	0	4536	0	SETD2	3	47162892	Frame_Shift_Del	DEL	C	TCGA-5P-A9JU-01A-11D-A42J-10		47162892	150859538	16	1899											
PBRM1	55193	hgsc.bcm.edu	37	chr3	52597437	52597437	+	Frame_Shift_Del	DEL	A	A	-																															tctccaccttctaactcggcAaatttagcttctagcaactg																										TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr3:52597437delA	ENST00000296302.7	-	24	3949	c.3948delT	c.(3946-3948)tttfs	p.F1316fs	RNU6ATAC16P_ENST00000408591.1_RNA|PBRM1_ENST00000356770.4_Frame_Shift_Del_p.F1284fs|SMIM4_ENST00000476842.1_Intron|PBRM1_ENST00000409057.1_Frame_Shift_Del_p.F1316fs|PBRM1_ENST00000394830.3_Frame_Shift_Del_p.F1291fs|PBRM1_ENST00000410007.1_Frame_Shift_Del_p.F1291fs|PBRM1_ENST00000409767.1_Frame_Shift_Del_p.F1331fs|PBRM1_ENST00000409114.3_Frame_Shift_Del_p.F1331fs|PBRM1_ENST00000337303.4_Frame_Shift_Del_p.F1316fs			Q86U86	PB1_HUMAN	polybromo 1	1316					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)		CTAACTCGGCAAATTTAGCTT	0.423			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.A1292fs		Atlas-Indel,Pindel	.		Rec	yes		3	3p21	55193	polybromo 1		E	.,3	PBRM1	1252	.	0			c.3874delG						PASS	.						148	132	137					3																	52597437		2203	4300	6503	SO:0001589	frameshift_variant	55193	exon25			.	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.3948delT	chr3.hg19:g.52597437delA	ENSP00000296302:p.Phe1316fs	100.0	0.0	0		108.0	89.0	0.824074	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Frame_Shift_Del	DEL	ENST00000296302.7	hg19																																																																																				.	.	.	none		0.423	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		-	52597437	A	-	52597437	7	5	27	1	0	1	0	1	0	0	0	0	11498	127	5	0	980	0	PBRM1	3	52597437	Frame_Shift_Del	DEL	A	TCGA-5P-A9JU-01A-11D-A42J-10	5434545	52597437	145424993	17	1900											
TBC1D23	55773	hgsc.bcm.edu	37	chr3	100025388	100025388	+	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	gcagtatcaattctgttgatGtaagtatatgtagagaatat	14	15	9	3	0	2	2	1	1	1	1	2	3	2	2	0	0	0	6	0	0	8	8			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr3:100025388G>A	ENST00000394144.4	+	13	1420		c.e13+1		TBC1D23_ENST00000475134.1_Splice_Site|TBC1D23_ENST00000486274.1_Splice_Site|TBC1D23_ENST00000344949.5_Splice_Site	NM_001199198.2	NP_001186127.1	Q9NUY8	TBC23_HUMAN	TBC1 domain family, member 23						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						TTCTGTTGATGTAAGTATATG	0.408																																					.		Atlas-SNP	.											TBC1D23_ENST00000394144,right_lower_lobe,carcinoma,0,2	TBC1D23	133	.	0			c.1413+1G>A						PASS	.						92	77	82					3																	100025388		2203	4300	6503	SO:0001630	splice_region_variant	55773	exon13			GTTGATGTAAGTA	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.1413+1G>A	chr3.hg19:g.100025388G>A		63.0	0.0	.		64.0	50.0	.	NM_018309	B9A6M5|Q8TCN8|Q8WUB7|Q96D90|Q9NV75	Splice_Site	SNP	ENST00000394144.4	hg19	CCDS56265.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.609777	0.87258	.	.	ENSG00000036054	ENST00000344949;ENST00000394144;ENST00000475134	.	.	.	5.87	5.87	0.94306	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.712	0.88324	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TBC1D23	101508078	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	8.962000	0.93254	2.785000	0.95823	0.655000	0.94253	.	.	.	.	none		0.408	TBC1D23-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353150.1	NM_018309	Intron	A	100025388	G	A	100025388	5	1	27	1	0	0	0	0	0	0	1	0	15625	1391	48	2	1464	2	TBC1D23	3	100025388	Splice_Site	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10	47427951	100025388	97997042	18	1901											
PCCB	5096	hgsc.bcm.edu	37	chr3	135974705	135974706	+	Frame_Shift_Ins	INS	-	-	A																															gttccattgtagggaaagctINSaacagccagggagaggatca																										TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr3:135974705_135974706insA	ENST00000251654.4	+	2	261_262	c.191_192insA	c.(190-195)ctaacafs	p.T65fs	PCCB_ENST00000462637.1_Frame_Shift_Ins_p.T65fs|PCCB_ENST00000468777.1_Frame_Shift_Ins_p.T65fs|PCCB_ENST00000474833.1_Intron|PCCB_ENST00000466072.1_Frame_Shift_Ins_p.T65fs|PCCB_ENST00000483687.1_Frame_Shift_Ins_p.T65fs|PCCB_ENST00000482086.1_Intron|PCCB_ENST00000478469.1_Frame_Shift_Ins_p.T65fs|PCCB_ENST00000469217.1_Frame_Shift_Ins_p.T65fs|PCCB_ENST00000471595.1_Frame_Shift_Ins_p.T65fs|PCCB_ENST00000490504.1_Frame_Shift_Ins_p.T65fs	NM_000532.4	NP_000523.2	P05166	PCCB_HUMAN	propionyl CoA carboxylase, beta polypeptide	65	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)	TAGGGAAAGCTAACAGCCAGGG	0.48																																					p.L64fs		Atlas-Indel,Pindel	.											.	PCCB	52	.	0			c.191_192insA						PASS	.																																			SO:0001589	frameshift_variant	5096	exon2			.		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.193dupA	chr3.hg19:g.135974707_135974707dupA	ENSP00000251654:p.Thr65fs	110.0	0.0	0		113.0	50.0	0.442478	NM_001178014	B7Z2Z4|Q16813|Q96CX0	Frame_Shift_Ins	INS	ENST00000251654.4	hg19	CCDS3089.1																																																																																			.	.	.	none		0.48	PCCB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000357335.1			A	135974706	-	A	135974705	7	5	27	1	0	1	1	0	0	0	0	0	11512	1522	53	0	197	0	PCCB	3	135974705	Frame_Shift_Ins	INS	-	TCGA-5P-A9JU-01A-11D-A42J-10	35949317	135974705	62047725	19	1902											
WWTR1	25937	hgsc.bcm.edu	37	chr3	149374844	149374844	+	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	cgacgagtgcgagcggacatGctgggcacccccagccagtc	8	4	14	15	4	0	0	0	0	0	0	1	4	0	1	3	2	4	2	3	2	0	0			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr3:149374844G>C	ENST00000465804.1	-	3	506	c.250C>G	c.(250-252)Cat>Gat	p.H84D	WWTR1-AS1_ENST00000495094.1_RNA|WWTR1_ENST00000467467.1_Missense_Mutation_p.H84D|WWTR1-AS1_ENST00000479752.1_RNA|WWTR1-AS1_ENST00000466836.1_RNA|WWTR1_ENST00000360632.3_Missense_Mutation_p.H84D	NM_001168278.1	NP_001161750.1	Q9GZV5	WWTR1_HUMAN	WW domain containing transcription regulator 1	84					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)			GAGCGGACATGCTGGGCACCC	0.726			T	CAMTA1	epitheliod hemangioendothelioma																																p.H84D		Atlas-SNP	.		Dom	yes		3	3q23-q24	607392	WW domain containing transcription regulator 1		M	.	WWTR1	42	.	0			c.C250G						PASS	.						6	8	7					3																	149374844		2132	4104	6236	SO:0001583	missense	25937	exon3			GGACATGCTGGGC	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.250C>G	chr3.hg19:g.149374844G>C	ENSP00000419465:p.His84Asp	55.0	0.0	.		78.0	61.0	.	NM_001168278	D3DNH7|Q8N3P2|Q9Y3W6	Missense_Mutation	SNP	ENST00000465804.1	hg19	CCDS3144.1	.	.	.	.	.	.	.	.	.	.	G	33	5.195253	0.94960	.	.	ENSG00000018408	ENST00000465804;ENST00000360632;ENST00000467467;ENST00000479238;ENST00000485352;ENST00000475579	T;T;T;T	0.53640	0.62;0.62;0.62;0.61	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.69387	0.3105	M	0.74467	2.265	0.80722	D	1	D	0.57899	0.981	D	0.69824	0.966	T	0.72010	-0.4419	10	0.54805	T	0.06	-25.132	18.4973	0.90869	0.0:0.0:1.0:0.0	.	84	Q9GZV5	WWTR1_HUMAN	D	84	ENSP00000419465:H84D;ENSP00000353847:H84D;ENSP00000419234:H84D;ENSP00000418580:H84D	ENSP00000353847:H84D	H	-	1	0	WWTR1	150857534	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	9.333000	0.96459	2.360000	0.80028	0.462000	0.41574	CAT	.	.	.	none		0.726	WWTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356498.1	NM_015472		C	149374844	G	C	149374844	3	2	27	1	0	0	0	0	1	0	0	0	17429	1319	46	4	976	4	WWTR1	3	149374844	Missense_Mutation	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10	13400139	149374844	48647586	20	1903											
ZNF141	7700	hgsc.bcm.edu	37	chr4	367429	367430	+	In_Frame_Ins	INS	-	-	ACA																															acaaatgtgaagaatgtggcINSaaagcctttagacggtccac																										TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr4:367429_367430insACA	ENST00000240499.7	+	4	1352_1353	c.1203_1204insACA	c.(1204-1206)aaa>ACAaaa	p.401_402insT	ZNF141_ENST00000505939.1_Intron|ZNF141_ENST00000512994.1_Intron	NM_003441.2	NP_003432.1	Q15928	ZN141_HUMAN	zinc finger protein 141	401					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						AAGAATGTGGCAAAGCCTTTAG	0.386																																					p.G401delinsGT		Atlas-Indel,Pindel	.											.	ZNF141	48	.	0			c.1203_1204insACA						PASS	.																																			SO:0001652	inframe_insertion	7700	exon4			.	L15309	CCDS33931.1	4p16.3	2013-01-08	2006-06-13			ENSG00000131127		"Zinc fingers, C2H2-type", "-"	12926	protein-coding gene	gene with protein product		194648	"zinc finger protein 141 (clone pHZ-44)"	D4S90		8268908	Standard	NM_003441		Approved	pHZ-44	uc003gaa.2	Q15928		Exception_encountered	chr4.hg19:g.367429_367430insACA	ENSP00000240499:p.Gly401_Lys402insThr	304.0	0.0	0		277.0	110.0	0.397112	NM_003441	Q6DK07	In_Frame_Ins	INS	ENST00000240499.7	hg19	CCDS33931.1																																																																																			.	.	.	none		0.386	ZNF141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357710.1	NM_003441		ACA	367430	-	ACA	367429	7	5	27	1	0	1	1	0	0	0	0	0	17742	697	25	0	1217	0	ZNF141	4	367429	In_Frame_Ins	INS	-	TCGA-5P-A9JU-01A-11D-A42J-10		367429	190786847	21	1904											
FGFRL1	53834	hgsc.bcm.edu	37	chr4	1018294	1018294	+	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	gggcggccagaagtttgtggTgctgcccacgggtgacgtgt	5	9	18	9	3	0	2	0	1	0	1	0	2	0	2	2	4	2	2	2	4	1	1			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr4:1018294T>A	ENST00000398484.2	+	7	1494	c.914T>A	c.(913-915)gTg>gAg	p.V305E	FGFRL1_ENST00000510644.1_Missense_Mutation_p.V305E|FGFRL1_ENST00000264748.6_Missense_Mutation_p.V305E|FGFRL1_ENST00000504138.1_Missense_Mutation_p.V305E			Q8N441	FGRL1_HUMAN	fibroblast growth factor receptor-like 1	305	Ig-like C2-type 3.				diaphragm development (GO:0060539)|heart valve morphogenesis (GO:0003179)|negative regulation of cell proliferation (GO:0008285)|skeletal system development (GO:0001501)|ventricular septum morphogenesis (GO:0060412)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)			endometrium(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	13			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			AAGTTTGTGGTGCTGCCCACG	0.652																																					p.V305E		Atlas-SNP	.											.	FGFRL1	77	.	0			c.T914A						PASS	.						53	53	53					4																	1018294		2203	4298	6501	SO:0001583	missense	53834	exon6			TTGTGGTGCTGCC		CCDS3344.1	4p16	2013-01-11			ENSG00000127418	ENSG00000127418		"Immunoglobulin superfamily / I-set domain containing"	3693	protein-coding gene	gene with protein product		605830					Standard	NM_021923		Approved		uc003gcg.3	Q8N441	OTTHUMG00000118998	ENST00000398484.2:c.914T>A	chr4.hg19:g.1018294T>A	ENSP00000381498:p.Val305Glu	132.0	0.0	.		162.0	55.0	.	NM_001004356	B2RAU9|Q6PJN1|Q9BXN7|Q9H4D7	Missense_Mutation	SNP	ENST00000398484.2	hg19	CCDS3344.1	.	.	.	.	.	.	.	.	.	.	t	26.7	4.758736	0.89843	.	.	ENSG00000127418	ENST00000398484;ENST00000542622;ENST00000510644;ENST00000504138;ENST00000264748	T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57	5.45	5.45	0.79879	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.83945	0.5364	M	0.83312	2.635	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.83076	-0.0140	10	0.26408	T	0.33	-23.5219	14.6694	0.68932	0.0:0.0:0.0:1.0	.	305	Q8N441	FGRL1_HUMAN	E	305;275;305;305;305	ENSP00000381498:V305E;ENSP00000425025:V305E;ENSP00000423091:V305E;ENSP00000264748:V305E	ENSP00000264748:V305E	V	+	2	0	FGFRL1	1008294	1.000000	0.71417	1.000000	0.80357	0.740000	0.42216	4.872000	0.63050	2.062000	0.61559	0.478000	0.44815	GTG	.	.	.	none		0.652	FGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239195.2	NM_021923		A	1018294	T	A	1018294	3	1	27	1	0	0	0	0	1	0	0	0	5876	1696	59	5	932	5	FGFRL1	4	1018294	Missense_Mutation	SNP	T	TCGA-5P-A9JU-01A-11D-A42J-10	650865	1018294	190135982	22	1905											
DSPP	1834	hgsc.bcm.edu	37	chr4	88536436	88536436	+	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	agcgatagcagtgacagcagCaacagcagtgacagcagtga	15	4	13	9	1	0	3	0	3	0	0	0	4	0	3	0	0	7	5	0	0	2	1			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr4:88536436C>T	ENST00000282478.7	+	4	2655	c.2622C>T	c.(2620-2622)agC>agT	p.S874S	DSPP_ENST00000399271.1_Silent_p.S874S|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	874	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gtgacagcagcaacagcagtg	0.502																																					p.S874S		Atlas-SNP	.											.	DSPP	174	.	0			c.C2622T						PASS	.						70	85	79					4																	88536436		1641	2936	4577	SO:0001819	synonymous_variant	1834	exon5			CAGCAGCAACAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2622C>T	chr4.hg19:g.88536436C>T		224.0	0.0	.		233.0	23.0	.	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	hg19	CCDS43248.1																																																																																			.	.	.	none		0.502	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		T	88536436	C	T	88536436	2	4	27	1	0	0	0	0	0	0	0	1	4784	709	25	2		2	DSPP	4	88536436	Silent	SNP	C	TCGA-5P-A9JU-01A-11D-A42J-10	87518142	88536436	102617840	23	1906											
GLRB	2743	hgsc.bcm.edu	37	chr4	157999276	157999277	+	In_Frame_Ins	INS	-	-	AGAAGCAGTATCTATGCCCATCGTATGTTCTTCATGTCTTATATT																															aaagaaagggaaggggaaaaINSagaagcagtatctatgccca																										TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr4:157999276_157999277insAGAAGCAGTATCTATGCCCATCGTATGTTCTTCATGTCTTATATT	ENST00000264428.4	+	2	370_371	c.100_101insAGAAGCAGTATCTATGCCCATCGTATGTTCTTCATGTCTTATATT	c.(100-102)aag>aAGAAGCAGTATCTATGCCCATCGTATGTTCTTCATGTCTTATATTag	p.34_35insKQYLCPSYVLHVLY*	GLRB_ENST00000512619.1_In_Frame_Ins_p.34_35insKQYLCPSYVLHVLY*|GLRB_ENST00000541722.1_In_Frame_Ins_p.34_35insKQYLCPSYVLHVLY*|GLRB_ENST00000509282.1_In_Frame_Ins_p.34_35insKQYLCPSYVLHVLY*	NM_000824.4	NP_000815.1	P48167	GLRB_HUMAN	glycine receptor, beta	34					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)	GAAGGGGAAAAAGAAGCAGTAT	0.337																																					p.K34delinsKKQYLCPSYVLHVLYX		Pindel	.											.	GLRB	74	.	0			c.100_101insAGAAGCAGTATCTATGCCCATCGTATGTTCTTCATGTCTTATATT						PASS	.																																			SO:0001652	inframe_insertion	2743	exon2			.	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	Exception_encountered	chr4.hg19:g.157999276_157999277insAGAAGCAGTATCTATGCCCATCGTATGTTCTTCATGTCTTATATT	ENSP00000264428:p.Lys34_Lys35insLysGlnTyrLeuCysProSerTyrValLeuHisValLeuTyr*	129.0	0.0	.		111.0	21.0	0.189	NM_000824	A8K3K2|D3DP23|F5GWE1	In_Frame_Ins	INS	ENST00000264428.4	hg19	CCDS3796.1																																																																																			.	.	.	none		0.337	GLRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366507.1	NM_000824		AGAAGCAGTATCTATGCCCATCGTATGTTCTTCATGTCTTATATT	157999277	-	AGAAGCAGTATCTATGCCCATCGTATGTTCTTCATGTCTTATATT	157999276	7	5	27	1	0	1	1	0	0	0	0	0	6465	15	1	0	102	0	GLRB	4	157999276	In_Frame_Ins	INS	-	TCGA-5P-A9JU-01A-11D-A42J-10	69462840	157999276	33155000	24	1907											
SLC12A7	10723	hgsc.bcm.edu	37	chr5	1094341	1094342	+	In_Frame_Ins	INS	-	-	TTT																															cattgttgaggaatgggctgINSttttctcttggatttccatc																								rs376148374		TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr5:1094341_1094342insTTT	ENST00000264930.5	-	2	189_190	c.146_147insAAA	c.(145-147)aac>aaAAAc	p.48_49insK		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	48					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)	GGAATGGGCTGTTTTCTCTTGG	0.421																																					p.N49delinsKN		Atlas-Indel,Pindel	.											.	SLC12A7	97	.	0			c.147_148insAAA						PASS	.																																			SO:0001652	inframe_insertion	10723	exon2			.	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.144_146dupAAA	chr5.hg19:g.1094342_1094344dupTTT	ENSP00000264930:p.Glu48_Asn49insLys	86.0	0.0	0		84.0	35.0	0.416667	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	In_Frame_Ins	INS	ENST00000264930.5	hg19	CCDS34129.1																																																																																			.	.	.	none		0.421	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598		TTT	1094342	-	TTT	1094341	7	5	27	1	0	1	1	0	0	0	0	0	14401	1368	48	0	3196	0	SLC12A7	5	1094341	In_Frame_Ins	INS	-	TCGA-5P-A9JU-01A-11D-A42J-10		1094341	179820919	25	1908											
FAM172A	83989	hgsc.bcm.edu	37	chr5	93217216	93217216	+	Frame_Shift_Del	DEL	T	T	-																															tttctttttctctttgggggTtacgatacttctcatagaaa																										TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr5:93217216delT	ENST00000395965.3	-	7	888	c.746delA	c.(745-747)aacfs	p.N249fs	FAM172A_ENST00000509163.1_Frame_Shift_Del_p.N203fs|FAM172A_ENST00000505869.1_Frame_Shift_Del_p.N139fs|FAM172A_ENST00000509739.1_Frame_Shift_Del_p.N102fs	NM_032042.5	NP_114431.2	Q8WUF8	F172A_HUMAN	family with sequence similarity 172, member A	249						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)				endometrium(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	9						TCTTTGGGGGTTACGATACTT	0.318																																					p.N249fs		Atlas-Indel,Pindel	.											.	FAM172A	38	.	0			c.747delC						PASS	.						183	177	179					5																	93217216		2203	4299	6502	SO:0001589	frameshift_variant	83989	exon7			.		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.746delA	chr5.hg19:g.93217216delT	ENSP00000379294:p.Asn249fs	75.0	0.0	0		88.0	35.0	0.397727	NM_032042	B2R7C6|B4DJ14|B4DLG5|Q9H0U8	Frame_Shift_Del	DEL	ENST00000395965.3	hg19	CCDS4069.1																																																																																			.	.	.	none		0.318	FAM172A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254100.3	NM_032042		-	93217216	T	-	93217216	7	5	27	1	0	1	0	1	0	0	0	0	5496	1725	60	0	524	0	FAM172A	5	93217216	Frame_Shift_Del	DEL	T	TCGA-5P-A9JU-01A-11D-A42J-10	92122875	93217216	87698044	26	1909											
RNF216	54476	hgsc.bcm.edu	37	chr7	5792508	5792510	+	In_Frame_Del	DEL	TCT	TCT	-																															tgacatcatcatccaggtccTcttcttcatgctgctgagga																								rs370004752		TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr7:5792508_5792510delTCT	ENST00000425013.2	-	3	392_394	c.168_170delAGA	c.(166-171)gaagag>gag	p.56_57EE>E	RNF216_ENST00000389902.3_In_Frame_Del_p.56_57EE>E	NM_207111.3|NM_207116.2	NP_996994.1|NP_996999.1	Q9NWF9	RN216_HUMAN	ring finger protein 216	56					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)		ATCCAGGTCCTCTTCTTCATGCT	0.453																																					p.57_57del		Atlas-Indel,Pindel	.											.	RNF216	71	.	0			c.169_171del						PASS	.																																			SO:0001651	inframe_deletion	54476	exon3			.	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.168_170delAGA	chr7.hg19:g.5792511_5792513delTCT	ENSP00000404602:p.Glu57del	53.0	0.0	0		104.0	20.0	0.192308	NM_207111	Q6Y691|Q75ML7|Q7Z2H7|Q7Z7C1|Q8NHW7|Q9NYT1	In_Frame_Del	DEL	ENST00000425013.2	hg19	CCDS34595.1																																																																																			.	.	.	none		0.453	RNF216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340374.1	NM_207111		-	5792510	TCT	-	5792508	7	5	27	1	0	1	0	1	0	0	0	0	13493	1551	54	0	2661	0	RNF216	7	5792508	In_Frame_Del	DEL	TCT	TCGA-5P-A9JU-01A-11D-A42J-10		5792508	153346155	27	1910											
PCLO	27445	hgsc.bcm.edu	37	chr7	82581488	82581488	+	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	gcggttaaatcaacgggtttTtcatcttctattattttggt	8	19	8	6	2	4	0	2	0	2	0	4	0	4	0	0	3	1	2	0	3	5	8	rs10630259|rs10694231	byFrequency	TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr7:82581488T>A	ENST00000333891.9	-	5	9118	c.8781A>T	c.(8779-8781)gaA>gaT	p.E2927D	PCLO_ENST00000423517.2_Missense_Mutation_p.E2927D|PCLO_ENST00000437081.1_5'Flank	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CAACGGGTTTTTCATCTTCTA	0.433																																					p.E2927D		Atlas-SNP	.											Q9Y6V0-3,colon,carcinoma,0,3	PCLO	1506	.	0			c.A8781T						PASS	.						123	122	123					7																	82581488		1902	4128	6030	SO:0001583	missense	27445	exon5			GGGTTTTTCATCT	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.8781A>T	chr7.hg19:g.82581488T>A	ENSP00000334319:p.Glu2927Asp	57.0	0.0	.		89.0	6.0	.	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	8.487	0.861147	0.17178	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.20881	2.1;2.04	5.67	0.321	0.15883	.	.	.	.	.	T	0.08980	0.0222	N	0.11201	0.11	0.80722	D	1	B;B	0.14012	0.009;0.009	B;B	0.12156	0.007;0.007	T	0.18587	-1.0332	9	0.87932	D	0	.	2.0445	0.03557	0.1172:0.1463:0.2418:0.4947	.	2927;2927	Q9Y6V0-5;Q9Y6V0-6	.;.	D	2858;2927;2927	ENSP00000334319:E2927D;ENSP00000388393:E2927D	ENSP00000334319:E2927D	E	-	3	2	PCLO	82419424	0.964000	0.33143	0.999000	0.59377	0.737000	0.42083	0.165000	0.16564	0.413000	0.25759	0.455000	0.32223	GAA	.	.	.	none		0.433	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82581488	T	A	82581488	3	1	27	1	0	0	0	0	1	0	0	0	11590	1838	64	5	6748	5	PCLO	7	82581488	Missense_Mutation	SNP	T	TCGA-5P-A9JU-01A-11D-A42J-10	76788980	82581488	76557175	28	1911											
TRIP6	7205	hgsc.bcm.edu	37	chr7	100468243	100468243	+	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	tggttggggatggggctgggGttgtggcccttgatcgcgtc	2	12	20	7	2	0	1	0	1	0	0	2	2	0	2	1	8	0	3	1	8	0	3			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr7:100468243G>C	ENST00000200457.4	+	6	1237	c.877G>C	c.(877-879)Gtt>Ctt	p.V293L		NM_003302.2	NP_003293.2	Q15654	TRIP6_HUMAN	thyroid hormone receptor interactor 6	293	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				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)					TGGGGCTGGGGTTGTGGCCCT	0.602																																					p.V293L		Atlas-SNP	.											.	TRIP6	45	.	0			c.G877C						PASS	.						195	176	182					7																	100468243		2203	4300	6503	SO:0001583	missense	7205	exon6			GCTGGGGTTGTGG	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.877G>C	chr7.hg19:g.100468243G>C	ENSP00000200457:p.Val293Leu	47.0	0.0	.		87.0	25.0	.	NM_003302	A4D2E7|F2ZC07|F2ZC08|O15170|O15275|Q9BTB2|Q9BUE5|Q9BXP3|Q9UNT4	Missense_Mutation	SNP	ENST00000200457.4	hg19	CCDS5708.1	.	.	.	.	.	.	.	.	.	.	g	24.6	4.552765	0.86127	.	.	ENSG00000087077	ENST00000200457	T	0.42900	0.96	5.79	5.79	0.91817	Zinc finger, LIM-type (5);	0.119641	0.64402	D	0.000019	T	0.41811	0.1175	N	0.13235	0.315	0.39933	D	0.974314	P	0.50819	0.939	P	0.57720	0.826	T	0.38200	-0.9672	10	0.46703	T	0.11	.	12.4811	0.55842	0.0:0.0:0.8328:0.1672	.	293	Q15654	TRIP6_HUMAN	L	293	ENSP00000200457:V293L	ENSP00000200457:V293L	V	+	1	0	TRIP6	100306179	1.000000	0.71417	0.969000	0.41365	0.832000	0.47134	5.454000	0.66651	2.737000	0.93849	0.645000	0.84053	GTT	.	.	.	none		0.602	TRIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347151.2	NM_003302		C	100468243	G	C	100468243	3	2	27	1	0	0	0	0	1	0	0	0	16571	1261	44	4	899	4	TRIP6	7	100468243	Missense_Mutation	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10	17886755	100468243	58670420	29	1912											
SSPO	23145	hgsc.bcm.edu	37	chr7	149476014	149476014	+	RNA	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggcctctgtgggctctacaAtggctggccagagggtaagt	8	9	15	9	0	2	1	0	0	2	1	2	1	2	1	2	5	1	3	2	5	3	2			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr7:149476014A>G	ENST00000378016.2	+	0	980							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)			GGGCTCTACAATGGCTGGCCA	0.627																																					p.N327S		Atlas-SNP	.											.	.	.	.	0			c.A980G						PASS	.						119	138	131					7																	149476014		2025	4190	6215			23145	exon7			TCTACAATGGCTG	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149476014A>G		115.0	0.0	.		142.0	63.0	.	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	hg19																																																																																				.	.	.	none		0.627	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				G	149476014	A	G	149476014	1	3	27	0	1	0	0	0	0	0	0	0	15201	101	4	3		3	SSPO	7	149476014	RNA	SNP	A	TCGA-5P-A9JU-01A-11D-A42J-10	49007771	149476014	9662649	30	1913											
RP1L1	94137	hgsc.bcm.edu	37	chr8	10466011	10466031	+	In_Frame_Del	DEL	TCCCCTTCAGCCTCCTGGGCA	TCCCCTTCAGCCTCCTGGGCA	-																															cttctgactctggctgggccTccccttcagcctcctgggca																								rs199577777|rs199959237|rs535482422|rs558932296|rs527932965|rs542254783	byFrequency	TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	TCCCCTTCAGCCTCCTGGGCA	TCCCCTTCAGCCTCCTGGGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr8:10466011_10466031delTCCCCTTCAGCCTCCTGGGCA	ENST00000382483.3	-	4	5800_5820	c.5577_5597delTGCCCAGGAGGCTGAAGGGGA	c.(5575-5598)gatgcccaggaggctgaaggggag>gag	p.DAQEAEG1859del		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1939					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)		p.E1862E(1)|p.D1859E(1)|p.Q1861P(1)|p.A1863D(1)		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)		TGGCTGGGCCTCCCCTTCAGCCTCCTGGGCATCCCCTTCTG	0.629																																					p.1860_1866del		Atlas-INDEL	.											RP1L1,NS,malignant_melanoma,0,1	RP1L1	453	.	4	Substitution - Missense(3)|Substitution - coding silent(1)	lung(4)	c.5578_5598del						PASS	.																																			SO:0001651	inframe_deletion	94137	exon4			.	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.5577_5597delTGCCCAGGAGGCTGAAGGGGA	chr8.hg19:g.10466011_10466031delTCCCCTTCAGCCTCCTGGGCA	ENSP00000371923:p.Asp1859_Gly1865del	38.0	0.0	0		45.0	14.0	0.311111	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	In_Frame_Del	DEL	ENST00000382483.3	hg19	CCDS43708.1																																																																																			.	.	.	none		0.629	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			-	10466031	TCCCCTTCAGCCTCCTGGGCA	-	10466011	7	5	27	1	0	1	0	1	0	0	0	0	13546	1551	54	0	1609	0	RP1L1	8	10466011	In_Frame_Del	DEL	TCCCCTTCAGCCTCCTGGGCA	TCGA-5P-A9JU-01A-11D-A42J-10		10466011	135898011	31	1914											
INTS8	55656	hgsc.bcm.edu	37	chr8	95835690	95835690	+	Missense_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	aggcggcggaccgggaggcgGccacctccagccggccctgc	5	2	17	17	5	0	0	0	0	0	0	1	2	1	2	6	7	2	0	6	7	0	0			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr8:95835690G>A	ENST00000523731.1	+	1	164	c.31G>A	c.(31-33)Gcc>Acc	p.A11T	INTS8_ENST00000447247.1_Missense_Mutation_p.A11T	NM_017864.2	NP_060334.2	Q75QN2	INT8_HUMAN	integrator complex subunit 8	11					snRNA processing (GO:0016180)	integrator complex (GO:0032039)				breast(3)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	28	Breast(36;1.05e-06)					CCGGGAGGCGGCCACCTCCAG	0.706																																					p.A11T		Atlas-SNP	.											.	INTS8	92	.	0			c.G31A						PASS	.						7	8	8					8																	95835690		1952	3843	5795	SO:0001583	missense	55656	exon1			GAGGCGGCCACCT	AK091278	CCDS34925.1	8q22.1	2007-05-03	2006-03-15	2006-03-15	ENSG00000164941	ENSG00000164941			26048	protein-coding gene	gene with protein product		611351	"chromosome 8 open reading frame 52"	C8orf52		16239144	Standard	NM_017864		Approved	FLJ20530, INT8, MGC131633	uc003yhb.4	Q75QN2	OTTHUMG00000164695	ENST00000523731.1:c.31G>A	chr8.hg19:g.95835690G>A	ENSP00000430338:p.Ala11Thr	68.0	0.0	.		113.0	44.0	.	NM_017864	B2RN92|Q5RKZ3|Q6P1R5|Q7Z314|Q9NVS6|Q9NWY7	Missense_Mutation	SNP	ENST00000523731.1	hg19	CCDS34925.1	.	.	.	.	.	.	.	.	.	.	g	14.75	2.627809	0.46944	.	.	ENSG00000164941	ENST00000519457;ENST00000523731;ENST00000447247	.	.	.	5.09	3.23	0.37069	.	0.221578	0.46442	N	0.000289	T	0.51719	0.1691	L	0.44542	1.39	0.44937	D	0.997952	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	T	0.53265	-0.8463	9	0.54805	T	0.06	-16.2241	10.3689	0.44042	0.0715:0.0:0.7951:0.1334	.	11;11	Q75QN2;Q75QN2-2	INT8_HUMAN;.	T	11	.	ENSP00000343274:A11T	A	+	1	0	INTS8	95904866	1.000000	0.71417	1.000000	0.80357	0.039000	0.13416	6.519000	0.73768	1.347000	0.45714	-0.187000	0.12897	GCC	.	.	.	none		0.706	INTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379794.1	NM_017864		A	95835690	G	A	95835690	3	1	27	1	0	0	0	0	1	0	0	0	7791	1203	42	2	33	2	INTS8	8	95835690	Missense_Mutation	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10	85369679	95835690	50528332	32	1915											
DSCC1	79075	hgsc.bcm.edu	37	chr8	120854141	120854141	+	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	attctgaagtagcattcgtgCtgctgctctacatattttat	9	17	7	8	1	2	1	0	1	2	0	3	1	2	1	0	0	5	5	0	0	5	7			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr8:120854141C>A	ENST00000313655.4	-	7	1031	c.817G>T	c.(817-819)Gca>Tca	p.A273S		NM_024094.2	NP_076999.2	Q9BVC3	DCC1_HUMAN	DNA replication and sister chromatid cohesion 1	273					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)			AGCATTCGTGCTGCTGCTCTA	0.358																																					p.A273S		Atlas-SNP	.											.	DSCC1	40	.	0			c.G817T						PASS	.						107	92	97					8																	120854141		2203	4300	6503	SO:0001583	missense	79075	exon7			TTCGTGCTGCTGC		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.817G>T	chr8.hg19:g.120854141C>A	ENSP00000322180:p.Ala273Ser	74.0	0.0	.		90.0	26.0	.	NM_024094	Q969N5	Missense_Mutation	SNP	ENST00000313655.4	hg19	CCDS6330.1	.	.	.	.	.	.	.	.	.	.	c	24.4	4.524072	0.85600	.	.	ENSG00000136982	ENST00000313655	T	0.56444	0.46	6.14	6.14	0.99180	.	0.000000	0.85682	D	0.000000	T	0.79082	0.4386	M	0.89414	3.03	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.80324	-0.1430	10	0.62326	D	0.03	-18.737	20.8449	0.99727	0.0:1.0:0.0:0.0	.	273	Q9BVC3	DCC1_HUMAN	S	273	ENSP00000322180:A273S	ENSP00000322180:A273S	A	-	1	0	DSCC1	120923322	1.000000	0.71417	0.537000	0.28052	0.354000	0.29330	7.342000	0.79310	2.933000	0.99390	0.645000	0.84053	GCA	.	.	.	none		0.358	DSCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381443.1	NM_024094		A	120854141	C	A	120854141	3	1	27	1	0	0	0	0	1	0	0	0	4772	797	28	4	376	4	DSCC1	8	120854141	Missense_Mutation	SNP	C	TCGA-5P-A9JU-01A-11D-A42J-10	25018451	120854141	25509881	33	1916											
FAM91A1	157769	hgsc.bcm.edu	37	chr8	124811759	124811759	+	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	ttaactgttttatgattgtaGcatattggaccagctatccc	10	16	7	8	0	0	1	0	1	0	0	1	2	1	2	2	1	3	4	2	1	5	8			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr8:124811759G>A	ENST00000334705.7	+	17	1806		c.e17-1		FAM91A1_ENST00000521166.1_Splice_Site	NM_144963.2	NP_659400	Q658Y4	F91A1_HUMAN	family with sequence similarity 91, member A1											breast(4)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28	Lung NSC(37;8.76e-13)|Ovarian(258;0.00744)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00192)			TATGATTGTAGCATATTGGAC	0.358																																					.		Atlas-SNP	.											.	FAM91A1	77	.	0			c.1561-1G>A						PASS	.						107	95	99					8																	124811759		1869	4092	5961	SO:0001630	splice_region_variant	157769	exon17			ATTGTAGCATATT	AK074370	CCDS6346.2	8q24.13	2005-10-04			ENSG00000176853	ENSG00000176853			26306	protein-coding gene	gene with protein product						12477932	Standard	XM_005250806		Approved	FLJ23790	uc003yqv.3	Q658Y4	OTTHUMG00000133021	ENST00000334705.7:c.1561-1G>A	chr8.hg19:g.124811759G>A		75.0	0.0	.		60.0	16.0	.	NM_144963	B6YY23|Q658T5|Q8TE89	Splice_Site	SNP	ENST00000334705.7	hg19	CCDS6346.2	.	.	.	.	.	.	.	.	.	.	G	24.2	4.505033	0.85282	.	.	ENSG00000176853	ENST00000521166;ENST00000334705	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6151	0.95630	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FAM91A1	124880940	1.000000	0.71417	0.998000	0.56505	0.886000	0.51366	7.885000	0.87282	2.710000	0.92621	0.643000	0.83706	.	.	.	.	none		0.358	FAM91A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256607.1	NM_144963	Intron	A	124811759	G	A	124811759	5	1	27	1	0	0	0	0	0	0	1	0	5658	985	34	2	1626	2	FAM91A1	8	124811759	Splice_Site	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10	3957618	124811759	21552263	34	1917											
C8orf73	642475	hgsc.bcm.edu	37	chr8	144653908	144653908	+	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	tgctccagggccagtgcgctCagcactcgcagggccgccct	5	6	13	17	3	1	0	1	0	0	0	3	0	2	0	4	2	3	4	4	2	0	0			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr8:144653908C>T	ENST00000398882.3	-	3	787	c.531G>A	c.(529-531)ctG>ctA	p.L177L	MROH6_ENST00000533679.1_5'Flank|RP11-661A12.9_ENST00000531730.1_RNA|MROH6_ENST00000534459.1_5'Flank|MROH6_ENST00000524906.1_5'Flank	NM_001100878.1	NP_001094348.1	A6NGR9	MROH6_HUMAN	maestro heat-like repeat family member 6	177																	CCAGTGCGCTCAGCACTCGCA	0.726																																					p.L177L		Atlas-SNP	.											.	.	.	.	0			c.G531A						PASS	.						10	15	13					8																	144653908		2065	4106	6171	SO:0001819	synonymous_variant	642475	exon3			TGCGCTCAGCACT	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.531G>A	chr8.hg19:g.144653908C>T		106.0	0.0	.		200.0	61.0	.	NM_001100878	A8MWB1	Silent	SNP	ENST00000398882.3	hg19	CCDS47928.1																																																																																			.	.	.	none		0.726	MROH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382330.3	NM_001100878		T	144653908	C	T	144653908	2	4	27	1	0	0	0	0	0	0	0	1	2437	813	29	2		2	C8orf73	8	144653908	Silent	SNP	C	TCGA-5P-A9JU-01A-11D-A42J-10	19842149	144653908	1710114	35	1918											
C9orf86	55684	hgsc.bcm.edu	37	chr9	139718091	139718091	+	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	acaggagatccaggtcaccaGcatccactggagctacaaga	14	5	10	12	0	1	2	1	0	0	2	3	4	3	3	3	3	3	2	3	3	2	1			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr9:139718091G>T	ENST00000311502.7	+	2	481	c.245G>T	c.(244-246)aGc>aTc	p.S82I	RABL6_ENST00000432842.2_Missense_Mutation_p.S44I|RABL6_ENST00000371663.4_Missense_Mutation_p.S82I|RP11-216L13.18_ENST00000471502.1_RNA|RABL6_ENST00000357466.2_Missense_Mutation_p.S82I|RABL6_ENST00000371671.4_Missense_Mutation_p.S82I|RABL6_ENST00000371675.3_5'Flank			Q3YEC7	RABL6_HUMAN	RAB, member RAS oncogene family-like 6	82	Small GTPase-like.				small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)										CAGGTCACCAGCATCCACTGG	0.637																																					p.S82I		Atlas-SNP	.											.	.	.	.	0			c.G245T						PASS	.						37	44	42					9																	139718091		2061	4181	6242	SO:0001583	missense	55684	exon2			TCACCAGCATCCA	AK094382	CCDS48058.1, CCDS55352.1, CCDS55353.1	9q34.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000196642	ENSG00000196642			24703	protein-coding gene	gene with protein product	"Rab-like protein 1", "partner of ARF"	610615	"chromosome 9 open reading frame 86"	C9orf86		14702039, 16582619, 17962191, 19433581	Standard	NM_024718		Approved	FLJ10101, FLJ13045, pp8875, bA216L13.9, Parf, RBEL1	uc004cjj.1	Q3YEC7	OTTHUMG00000020947	ENST00000311502.7:c.245G>T	chr9.hg19:g.139718091G>T	ENSP00000311134:p.Ser82Ile	46.0	0.0	.		62.0	30.0	.	NM_024718	A8QVZ7|A8QVZ8|C6K8I4|C6K8I5|Q4F968|Q5T5R7|Q8IWK1|Q8TCL4|Q8WU94|Q96SR8|Q9BU21|Q9H935	Missense_Mutation	SNP	ENST00000311502.7	hg19	CCDS48058.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.64|18.64	3.667015|3.667015	0.67814|0.67814	.|.	.|.	ENSG00000196642|ENSG00000196642	ENST00000436380|ENST00000371673;ENST00000371663;ENST00000371671;ENST00000311502;ENST00000357466;ENST00000432842	.|T;T;T;T;T	.|0.66815	.|-0.23;-0.23;-0.23;-0.23;-0.23	4.31|4.31	4.31|4.31	0.51392|0.51392	.|Mitochondrial Rho-like (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.82029|0.82029	0.4948|0.4948	M|M	0.80332|0.80332	2.49|2.49	0.80722|0.80722	D|D	1|1	.|D;D;D;D;P	.|0.76494	.|0.998;0.993;0.999;0.999;0.745	.|D;D;D;D;P	.|0.87578	.|0.986;0.958;0.997;0.998;0.447	D|D	0.85292|0.85292	0.1068|0.1068	5|10	.|0.72032	.|D	.|0.01	-22.9255|-22.9255	15.3476|15.3476	0.74350|0.74350	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|82;82;82;82;82	.|A8QVZ8;C6K8I5;Q3YEC7-2;Q3YEC7;C6K8I4	.|.;.;.;PARF_HUMAN;.	H|I	38|82;82;82;82;82;44	.|ENSP00000360727:S82I;ENSP00000360736:S82I;ENSP00000311134:S82I;ENSP00000350056:S82I;ENSP00000414081:S44I	.|ENSP00000311134:S82I	Q|S	+|+	3|2	2|0	C9orf86|C9orf86	138837912|138837912	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.899000|0.899000	0.52679|0.52679	9.203000|9.203000	0.95033|0.95033	1.935000|1.935000	0.56089|0.56089	0.313000|0.313000	0.20887|0.20887	CAG|AGC	.	.	.	none		0.637	RABL6-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055141.4	NM_024718		T	139718091	G	T	139718091	3	4	27	1	0	0	0	0	1	0	0	0	2504	971	34	4	251	4	C9orf86	9	139718091	Missense_Mutation	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10		139718091	1495340	36	1919											
ZNF248	57209	hgsc.bcm.edu	37	chr10	38120750	38120750	+	Missense_Mutation	SNP	T	T	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	ttctccccagtgtgagttctTtgatgtacaatgaggtttga	8	16	10	7	0	2	4	0	4	2	0	3	4	2	4	2	1	1	3	2	1	2	5			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr10:38120750T>G	ENST00000395867.3	-	6	2083	c.1533A>C	c.(1531-1533)caA>caC	p.Q511H	ZNF248_ENST00000374648.3_Intron|ZNF248_ENST00000494133.1_Intron|AL135791.1_ENST00000583461.1_RNA|ZNF248_ENST00000357328.4_Missense_Mutation_p.Q511H	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	511					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						TGTGAGTTCTTTGATGTACAA	0.423																																					p.Q511H		Atlas-SNP	.											.	ZNF248	61	.	0			c.A1533C						PASS	.						111	107	108					10																	38120750		2203	4299	6502	SO:0001583	missense	57209	exon6			AGTTCTTTGATGT	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.1533A>C	chr10.hg19:g.38120750T>G	ENSP00000379208:p.Gln511His	87.0	0.0	.		56.0	41.0	.	NM_001267597	Q8NDV8|Q9UMP3	Missense_Mutation	SNP	ENST00000395867.3	hg19	CCDS7194.1	.	.	.	.	.	.	.	.	.	.	T	13.20	2.165662	0.38217	.	.	ENSG00000198105	ENST00000395867;ENST00000357328	T;T	0.36520	1.25;1.25	4.52	-0.28	0.12886	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.47455	D	0.000237	T	0.38081	0.1027	L	0.43923	1.385	0.28002	N	0.935245	D	0.61080	0.989	P	0.56127	0.792	T	0.25572	-1.0128	10	0.51188	T	0.08	.	8.0331	0.30476	0.0:0.4007:0.0:0.5993	.	511	Q8NDW4	ZN248_HUMAN	H	511	ENSP00000379208:Q511H;ENSP00000349882:Q511H	ENSP00000349882:Q511H	Q	-	3	2	ZNF248	38160756	0.187000	0.23238	0.999000	0.59377	0.997000	0.91878	0.299000	0.19138	0.059000	0.16252	0.528000	0.53228	CAA	.	.	.	none		0.423	ZNF248-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047609.1	NM_021045		G	38120750	T	G	38120750	3	3	27	1	0	0	0	0	1	0	0	0	17805	1838	64	5	210	5	ZNF248	10	38120750	Missense_Mutation	SNP	T	TCGA-5P-A9JU-01A-11D-A42J-10		38120750	97413997	37	1920											
CCAR1	55749	hgsc.bcm.edu	37	chr10	70550999	70550999	+	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	gaagacaaagatcaaaaatcCaaggagaatggtgccagtgt	18	6	11	6	0	1	3	1	0	0	3	2	5	2	3	2	2	1	0	2	2	6	0			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr10:70550999C>G	ENST00000265872.6	+	25	3548	c.3429C>G	c.(3427-3429)tcC>tcG	p.S1143S	CCAR1_ENST00000543719.1_Silent_p.S1128S|CCAR1_ENST00000535016.1_Silent_p.S1128S	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	1143					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						ATCAAAAATCCAAGGAGAATG	0.264																																					p.S1143S		Atlas-SNP	.											.	CCAR1	118	.	0			c.C3429G						PASS	.						69	76	74					10																	70550999		2200	4285	6485	SO:0001819	synonymous_variant	55749	exon25			AAAATCCAAGGAG	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.3429C>G	chr10.hg19:g.70550999C>G		582.0	0.0	.		361.0	237.0	.	NM_018237	A0JLT7|A1L4P7|A8K9D4|B4DNP8|B4DRK8|Q32NE3|Q5EBM3|Q5VUP6|Q6PIZ0|Q6X935|Q9H8N4|Q9NVA7|Q9NVQ0|Q9NWM6	Silent	SNP	ENST00000265872.6	hg19	CCDS7282.1																																																																																			.	.	.	none		0.264	CCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048356.2	NM_018237		G	70550999	C	G	70550999	2	3	27	1	0	0	0	0	0	0	0	1	2732	581	21	4		4	CCAR1	10	70550999	Silent	SNP	C	TCGA-5P-A9JU-01A-11D-A42J-10	32430249	70550999	64983748	38	1921											
GPR26	2849	hgsc.bcm.edu	37	chr10	125447637	125447637	+	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	cactcctctggcctcacaggCgactctcacagccagaacat	10	7	7	17	1	3	1	2	0	2	1	5	2	4	1	3	2	2	0	3	2	1	0			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr10:125447637C>T	ENST00000284674.1	+	3	1028	c.975C>T	c.(973-975)ggC>ggT	p.G325G		NM_153442.3	NP_703143.1	Q8NDV2	GPR26_HUMAN	G protein-coupled receptor 26	325					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)				GCCTCACAGGCGACTCTCACA	0.562																																					p.G325G		Atlas-SNP	.											.	GPR26	47	.	0			c.C975T						PASS	.						47	43	44					10																	125447637		2203	4300	6503	SO:0001819	synonymous_variant	2849	exon3			CACAGGCGACTCT		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.975C>T	chr10.hg19:g.125447637C>T		51.0	0.0	.		37.0	20.0	.	NM_153442	Q2M2E2	Silent	SNP	ENST00000284674.1	hg19	CCDS7636.1																																																																																			.	.	.	none		0.562	GPR26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050850.1			T	125447637	C	T	125447637	2	4	27	1	0	0	0	0	0	0	0	1	6691	755	27	1		1	GPR26	10	125447637	Silent	SNP	C	TCGA-5P-A9JU-01A-11D-A42J-10	54896638	125447637	10087110	39	1922											
PTDSS2	81490	hgsc.bcm.edu	37	chr11	460237	460243	+	Frame_Shift_Del	DEL	ATGTGAC	ATGTGAC	-																															cctcacctgtacgcttggctAtgtgacgctgctggaggaaa																										TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	ATGTGAC	ATGTGAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr11:460237_460243delATGTGAC	ENST00000308020.5	+	2	409_415	c.233_239delATGTGAC	c.(232-240)tatgtgacgfs	p.YVT78fs	RP13-317D12.3_ENST00000525893.1_RNA	NM_030783.1	NP_110410.1	Q9BVG9	PTSS2_HUMAN	phosphatidylserine synthase 2	78					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CDP-diacylglycerol-serine O-phosphatidyltransferase activity (GO:0003882)			autonomic_ganglia(1)|breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(1)	9		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;2.76e-26)|Epithelial(43;2.56e-25)|OV - Ovarian serous cystadenocarcinoma(40;7.54e-20)|BRCA - Breast invasive adenocarcinoma(625;8.76e-05)|Lung(200;0.0407)|LUSC - Lung squamous cell carcinoma(625;0.0735)	Phosphatidylserine(DB00144)	ACGCTTGGCTATGTGACGCTGCTGGAG	0.56																																					p.78_80del		Atlas-Indel,Pindel	.											.	PTDSS2	27	.	0			c.232_238del						PASS	.																																			SO:0001589	frameshift_variant	81490	exon2			.	BC001210	CCDS7696.1	11p15	2008-05-02			ENSG00000174915	ENSG00000174915			15463	protein-coding gene	gene with protein product		612793				14984733	Standard	NM_030783		Approved	PSS2	uc001lpj.3	Q9BVG9	OTTHUMG00000119087	ENST00000308020.5:c.233_239delATGTGAC	chr11.hg19:g.460237_460243delATGTGAC	ENSP00000308258:p.Tyr78fs	148.0	0.0	0		111.0	32.0	0.288288	NM_030783		Frame_Shift_Del	DEL	ENST00000308020.5	hg19	CCDS7696.1																																																																																			.	.	.	none		0.56	PTDSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239301.2			-	460243	ATGTGAC	-	460237	7	5	27	1	0	1	0	1	0	0	0	0	12747	449	16	0	239	0	PTDSS2	11	460237	Frame_Shift_Del	DEL	ATGTGAC	TCGA-5P-A9JU-01A-11D-A42J-10		460237	134546279	40	1923											
IRF7	3665	hgsc.bcm.edu	37	chr11	613956	613956	+	Missense_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	ccctacccctctcacctgtcGttagtgccgcgggctggggc	3	9	12	17	3	1	0	1	0	1	0	3	0	1	0	5	3	2	2	5	3	2	2	rs571836045		TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr11:613956G>A	ENST00000397574.2	-	7	1130	c.761C>T	c.(760-762)aCg>aTg	p.T254M	IRF7_ENST00000330243.5_Missense_Mutation_p.T267M|IRF7_ENST00000397570.1_Intron|IRF7_ENST00000348655.6_Intron|IRF7_ENST00000525445.1_Missense_Mutation_p.T148M|IRF7_ENST00000397566.1_Missense_Mutation_p.T267M|IRF7_ENST00000397562.3_De_novo_Start_OutOfFrame	NM_001572.3	NP_001563.2	Q92985	IRF7_HUMAN	interferon regulatory factor 7	254					cellular response to DNA damage stimulus (GO:0006974)|cytokine-mediated signaling pathway (GO:0019221)|establishment of viral latency (GO:0019043)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interferon-alpha production (GO:0032607)|interferon-beta production (GO:0032608)|interferon-gamma-mediated signaling pathway (GO:0060333)|MDA-5 signaling pathway (GO:0039530)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of adaptive immune response (GO:0002819)|regulation of immune response (GO:0050776)|regulation of monocyte differentiation (GO:0045655)|regulation of MyD88-dependent toll-like receptor signaling pathway (GO:0034124)|regulation of MyD88-independent toll-like receptor signaling pathway (GO:0034127)|regulation of type I interferon production (GO:0032479)|response to virus (GO:0009615)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(49;1.69e-08)|all_epithelial(84;1.65e-05)|Breast(177;0.000231)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;7.68e-28)|Epithelial(43;7.44e-27)|OV - Ovarian serous cystadenocarcinoma(40;3.53e-21)|BRCA - Breast invasive adenocarcinoma(625;6.96e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTCACCTGTCGTTAGTGCCGC	0.697													g|||	1	0.000199681	8e-04	0	5008	,	,		8770	0		0	False		,,,				2504	0				p.T267M		Atlas-SNP	.											.	IRF7	23	.	0			c.C800T						PASS	.						14	18	16					11																	613956		2195	4293	6488	SO:0001583	missense	3665	exon5			CCTGTCGTTAGTG	U53830	CCDS7703.1, CCDS7704.1, CCDS7705.1	11p15.5	2005-10-10			ENSG00000185507	ENSG00000185507			6122	protein-coding gene	gene with protein product		605047					Standard	XM_005252906		Approved		uc001lqh.3	Q92985	OTTHUMG00000132019	ENST00000397574.2:c.761C>T	chr11.hg19:g.613956G>A	ENSP00000380704:p.Thr254Met	79.0	0.0	.		88.0	10.0	.	NM_004031	B9EGL3|O00331|O00332|O00333|O75924|Q9UE79	Missense_Mutation	SNP	ENST00000397574.2	hg19	CCDS7703.1	.	.	.	.	.	.	.	.	.	.	g	5.627	0.300345	0.10678	.	.	ENSG00000185507	ENST00000525445;ENST00000397566;ENST00000397574;ENST00000330243	D;D;D;D	0.96011	-2.92;-3.83;-3.88;-3.83	2.06	-1.94	0.07571	.	.	.	.	.	D	0.84831	0.5559	N	0.03608	-0.345	0.22521	N	0.999023	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.73849	-0.3853	9	0.30854	T	0.27	.	6.3773	0.21515	0.5791:0.0:0.4209:0.0	.	148;254;267	E9PSE3;Q92985;Q92985-4	.;IRF7_HUMAN;.	M	148;267;254;267	ENSP00000434009:T148M;ENSP00000380697:T267M;ENSP00000380704:T254M;ENSP00000329411:T267M	ENSP00000329411:T267M	T	-	2	0	IRF7	603956	0.000000	0.05858	0.002000	0.10522	0.033000	0.12548	-2.121000	0.01322	-0.521000	0.06426	-0.994000	0.02522	ACG	.	.	.	none		0.697	IRF7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255026.1	NM_001572		A	613956	G	A	613956	3	1	27	1	0	0	0	0	1	0	0	0	7842	1145	40	1	770	1	IRF7	11	613956	Missense_Mutation	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10	153719	613956	134392560	41	1924											
MUC2	4583	hgsc.bcm.edu	37	chr11	1093323	1093323	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accccaaccccaacacccacCggcacacagaccccaacccc	13	0	3	25	1	0	1	0	0	0	1	0	1	0	1	10	1	3	1	10	1	3	0	rs7948036		TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr11:1093323C>T	ENST00000441003.2	+	30	5169	c.5142C>T	c.(5140-5142)acC>acT	p.T1714T	MUC2_ENST00000359061.5_Silent_p.T1681T|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_Silent_p.T2T	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)	caacacccaccggcacacaga	0.637																																					p.T1714T		Atlas-SNP	.											.	MUC2	614	.	0			c.C5142T						PASS	.	C		29,3837		0,29,1904	171	218	202		5139	-0.5	0	11	dbSNP_116	202	60,7230		0,60,3585	no	coding-synonymous	MUC2	NM_002457.2		0,89,5489	TT,TC,CC		0.823,0.7501,0.7978		1713/2813	1093323	89,11067	1933	3645	5578	SO:0001819	synonymous_variant	4583	exon30			ACCCACCGGCACA	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.5142C>T	chr11.hg19:g.1093323C>T		24.0	0.0	.		31.0	4.0	.	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	hg19																																																																																				.	.	.	weak		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1093323	C	T	1093323	2	4	27	1	0	0	0	0	0	0	0	1	9982	639	23	1		1	MUC2	11	1093323	Silent	SNP	C	TCGA-5P-A9JU-01A-11D-A42J-10	479367	1093323	133913193	42	1925											
OR51B4	79339	hgsc.bcm.edu	37	chr11	5323073	5323073	+	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	tgccatttccaaaaaggacgGagaagtagatgacaaagaag	18	6	11	6	1	0	4	0	1	0	3	1	6	1	5	2	2	1	1	2	2	6	2			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr11:5323073G>A	ENST00000380224.1	-	1	153	c.104C>T	c.(103-105)tCc>tTc	p.S35F	HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron	NM_033179.2	NP_149419.2	Q9Y5P0	O51B4_HUMAN	olfactory receptor, family 51, subfamily B, member 4	35					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AAAAAGGACGGAGAAGTAGAT	0.498																																					p.S35F		Atlas-SNP	.											.	OR51B4	64	.	0			c.C104T						PASS	.						93	93	93					11																	5323073		2201	4297	6498	SO:0001583	missense	79339	exon1			AGGACGGAGAAGT	BC069094	CCDS7757.1	11p15.4	2012-08-09			ENSG00000183251	ENSG00000183251		"GPCR / Class A : Olfactory receptors"	14708	protein-coding gene	gene with protein product							Standard	NM_033179		Approved		uc010qza.2	Q9Y5P0	OTTHUMG00000066665	ENST00000380224.1:c.104C>T	chr11.hg19:g.5323073G>A	ENSP00000369573:p.Ser35Phe	166.0	0.0	.		210.0	96.0	.	NM_033179	A7MAV5|Q6NTD7	Missense_Mutation	SNP	ENST00000380224.1	hg19	CCDS7757.1	.	.	.	.	.	.	.	.	.	.	G	9.110	1.006205	0.19199	.	.	ENSG00000183251	ENST00000380224	T	0.03242	4.0	4.39	-0.842	0.10748	.	0.448981	0.18455	N	0.140712	T	0.02727	0.0082	N	0.25485	0.75	0.09310	N	1	B	0.17268	0.021	B	0.19946	0.027	T	0.38308	-0.9667	10	0.59425	D	0.04	.	5.8023	0.18420	0.3677:0.2394:0.3928:0.0	.	35	Q9Y5P0	O51B4_HUMAN	F	35	ENSP00000369573:S35F	ENSP00000369573:S35F	S	-	2	0	OR51B4	5279649	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.874000	0.28065	-0.689000	0.05149	-0.795000	0.03280	TCC	.	.	.	none		0.498	OR51B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142956.2	NM_033179		A	5323073	G	A	5323073	3	1	27	1	0	0	0	0	1	0	0	0	11097	1174	41	2	831	2	OR51B4	11	5323073	Missense_Mutation	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10	4229750	5323073	129683443	43	1926											
TTC17	55761	hgsc.bcm.edu	37	chr11	43469573	43469573	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaaaaacgtgactaccagcGtctgggatggcccagcccgg	12	5	12	12	3	1	1	0	1	1	0	1	2	1	2	3	3	4	0	3	3	4	1	rs150211914		TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr11:43469573G>A	ENST00000039989.4	+	19	2701	c.2687G>A	c.(2686-2688)cGt>cAt	p.R896H		NM_018259.5	NP_060729.2	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17	896					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						GACTACCAGCGTCTGGGATGG	0.498																																					p.R896H		Atlas-SNP	.											.	TTC17	112	.	0			c.G2687A						PASS	.	G	HIS/ARG	2,4404	2.1+/-5.4	0,2,2201	85	80	82		2687	6.1	1	11	dbSNP_134	82	0,8600		0,0,4300	no	missense	TTC17	NM_018259.5	29	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	possibly-damaging	896/1142	43469573	2,13004	2203	4300	6503	SO:0001583	missense	55761	exon19			ACCAGCGTCTGGG	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.2687G>A	chr11.hg19:g.43469573G>A	ENSP00000039989:p.Arg896His	83.0	0.0	.		92.0	19.0	.	NM_018259	G3XAB3|Q8NEC0	Missense_Mutation	SNP	ENST00000039989.4	hg19	CCDS31466.1	.	.	.	.	.	.	.	.	.	.	G	17.10	3.303374	0.60195	4.54E-4	0.0	ENSG00000052841	ENST00000039989	T	0.30182	1.54	6.07	6.07	0.98685	.	0.040651	0.85682	D	0.000000	T	0.12774	0.0310	N	0.08118	0	0.29721	N	0.838639	P	0.49559	0.925	B	0.29353	0.101	T	0.09796	-1.0658	10	0.33141	T	0.24	-6.402	13.8057	0.63230	0.0695:0.0:0.9305:0.0	.	896	Q96AE7	TTC17_HUMAN	H	896	ENSP00000039989:R896H	ENSP00000039989:R896H	R	+	2	0	TTC17	43426149	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.092000	0.76930	2.885000	0.99019	0.655000	0.94253	CGT	.	G|1.000;A|0.000	0.000	weak		0.498	TTC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389577.2	NM_018259		A	43469573	G	A	43469573	3	1	27	1	0	0	0	0	1	0	0	0	16696	1145	40	1	2761	1	TTC17	11	43469573	Missense_Mutation	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10	38146500	43469573	91536943	44	1927											
CDC42BPG	55561	hgsc.bcm.edu	37	chr11	64601408	64601408	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtccttacctctgagctccGgaaggacaggaagggaatca	11	7	13	10	1	2	1	1	1	1	0	4	5	4	5	3	5	2	1	3	5	4	1			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr11:64601408G>A	ENST00000342711.5	-	21	2454	c.2455C>T	c.(2455-2457)Cgg>Tgg	p.R819W	CDC42BPG_ENST00000491280.1_5'Flank	NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						TCTGAGCTCCGGAAGGACAGG	0.597																																					p.R819W		Atlas-SNP	.											.	CDC42BPG	101	.	0			c.C2455T						PASS	.						192	203	199					11																	64601408		2201	4297	6498	SO:0001583	missense	55561	exon21			AGCTCCGGAAGGA	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.2455C>T	chr11.hg19:g.64601408G>A	ENSP00000345133:p.Arg819Trp	131.0	0.0	.		124.0	47.0	.	NM_017525		Missense_Mutation	SNP	ENST00000342711.5	hg19	CCDS31601.1	.	.	.	.	.	.	.	.	.	.	G	11.38	1.620693	0.28889	.	.	ENSG00000171219	ENST00000342711	T	0.68331	-0.32	5.08	-1.14	0.09741	.	1.156120	0.06554	N	0.745533	T	0.44540	0.1298	N	0.08118	0	0.23773	N	0.996881	B	0.06786	0.001	B	0.04013	0.001	T	0.25745	-1.0123	10	0.37606	T	0.19	.	8.5718	0.33574	0.5624:0.0:0.4376:0.0	.	819	Q6DT37	MRCKG_HUMAN	W	819	ENSP00000345133:R819W	ENSP00000345133:R819W	R	-	1	2	CDC42BPG	64357984	0.933000	0.31639	0.989000	0.46669	0.825000	0.46686	-0.228000	0.09114	-0.385000	0.07833	-0.258000	0.10820	CGG	.	.	.	none		0.597	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516		A	64601408	G	A	64601408	3	1	27	1	0	0	0	0	1	0	0	0	3076	1115	39	1	2268	1	CDC42BPG	11	64601408	Missense_Mutation	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10	21131835	64601408	70405108	45	1928											
TIMM8B	26521	hgsc.bcm.edu	37	chr11	111956122	111956122	+	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	agagacaattttcagtgcgaGagtctaggcgattccctggc	10	10	12	9	2	2	2	1	0	1	2	3	5	3	2	1	2	1	0	1	2	2	4			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr11:111956122G>A	ENST00000504148.2	-	2	220	c.149C>T	c.(148-150)tCt>tTt	p.S50F	SDHD_ENST00000532699.1_5'Flank|SDHD_ENST00000528182.1_5'Flank|SDHD_ENST00000525291.1_5'Flank|TIMM8B_ENST00000507614.1_5'UTR|SDHD_ENST00000528021.1_5'Flank|TIMM8B_ENST00000541231.1_Missense_Mutation_p.S65F|SDHD_ENST00000526592.1_5'Flank|SDHD_ENST00000528048.1_5'Flank|SDHD_ENST00000375549.3_5'Flank	NM_012459.2	NP_036591.2	Q9Y5J9	TIM8B_HUMAN	translocase of inner mitochondrial membrane 8 homolog B (yeast)	50					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein transport (GO:0072321)|protein targeting to mitochondrion (GO:0006626)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space protein transporter complex (GO:0042719)	zinc ion binding (GO:0008270)			large_intestine(1)	1		all_cancers(61;1.84e-10)|all_epithelial(67;9.33e-06)|Melanoma(852;4.01e-05)|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;6.01e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;1.03e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0512)		TTCAGTGCGAGAGTCTAGGCG	0.473																																					p.S65F		Atlas-SNP	.											.	TIMM8B	13	.	0			c.C194T						PASS	.						136	109	118					11																	111956122		2201	4297	6498	SO:0001583	missense	26521	exon2			GTGCGAGAGTCTA	AF150087	CCDS8357.1, CCDS8357.2	11q23.1-q23.2	2010-11-23	2001-11-28		ENSG00000150779	ENSG00000150779			11818	protein-coding gene	gene with protein product	"mitochondrial import inner membrane translocase subunit Tim8 B"	606659	"translocase of inner mitochondrial membrane 8 (yeast) homolog B"			10552927	Standard	NM_012459		Approved	TIM8B, DDP2, FLJ21744, MGC102866, MGC117373	uc001pmx.3	Q9Y5J9	OTTHUMG00000162261	ENST00000504148.2:c.149C>T	chr11.hg19:g.111956122G>A	ENSP00000422122:p.Ser50Phe	104.0	0.0	.		76.0	27.0	.	NM_012459	B0YJA5|Q3KQS9|Q9UN04	Missense_Mutation	SNP	ENST00000504148.2	hg19		.	.	.	.	.	.	.	.	.	.	G	21.2	4.110278	0.77210	.	.	ENSG00000150779	ENST00000504148;ENST00000541231	T;T	0.66460	-0.21;-0.21	5.56	5.56	0.83823	.	0.293556	0.38663	N	0.001618	T	0.75443	0.3850	.	.	.	0.45239	D	0.998241	D	0.53745	0.962	P	0.51615	0.675	T	0.78489	-0.2184	9	0.87932	D	0	-15.0727	18.3499	0.90335	0.0:0.0:1.0:0.0	.	50	Q9Y5J9	TIM8B_HUMAN	F	50;65	ENSP00000422122:S50F;ENSP00000438455:S65F	ENSP00000422122:S50F	S	-	2	0	TIMM8B	111461332	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.523000	0.53488	2.645000	0.89757	0.549000	0.68633	TCT	.	.	.	none		0.473	TIMM8B-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000368270.2	NM_012459		A	111956122	G	A	111956122	3	1	27	1	0	0	0	0	1	0	0	0	15927	942	33	2	106	2	TIMM8B	11	111956122	Missense_Mutation	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10	47354714	111956122	23050394	46	1929											
WNK1	65125	hgsc.bcm.edu	37	chr12	1005251	1005251	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatcaggtttctgttgcagcAgacggtgcccagaaagaggg	10	9	14	8	1	2	3	1	0	1	3	2	3	2	3	1	3	3	4	1	3	2	3			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr12:1005251A>G	ENST00000315939.6	+	24	6241	c.5598A>G	c.(5596-5598)gcA>gcG	p.A1866A	WNK1_ENST00000530271.2_Silent_p.A2364A|WNK1_ENST00000535572.1_Silent_p.A1618A|WNK1_ENST00000537687.1_Silent_p.A2126A|WNK1_ENST00000340908.4_Silent_p.A1459A	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1866					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)			CTGTTGCAGCAGACGGTGCCC	0.358																																					p.A2126A	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.A6378G						PASS	.						73	75	75					12																	1005251		2203	4300	6503	SO:0001819	synonymous_variant	65125	exon24			TGCAGCAGACGGT	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.5598A>G	chr12.hg19:g.1005251A>G		144.0	0.0	.		149.0	59.0	.	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Silent	SNP	ENST00000315939.6	hg19	CCDS8506.1																																																																																			.	.	.	none		0.358	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		G	1005251	A	G	1005251	2	3	27	1	0	0	0	0	0	0	0	1	17389	175	7	3		3	WNK1	12	1005251	Silent	SNP	A	TCGA-5P-A9JU-01A-11D-A42J-10		1005251	132846644	47	1930											
SCNN1A	6337	hgsc.bcm.edu	37	chr12	6472823	6472823	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttgtacaggtcaaagagcGtctgctctgtgatgcggtcc	8	12	12	9	2	3	2	1	1	2	1	4	2	4	2	1	2	4	2	1	2	2	2			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr12:6472823G>A	ENST00000228916.2	-	3	568	c.470C>T	c.(469-471)aCg>aTg	p.T157M	SCNN1A_ENST00000358945.3_Missense_Mutation_p.T157M|SCNN1A_ENST00000540037.1_De_novo_Start_OutOfFrame|SCNN1A_ENST00000396966.2_Missense_Mutation_p.T157M|SCNN1A_ENST00000360168.3_Missense_Mutation_p.T216M|SCNN1A_ENST00000543768.1_Missense_Mutation_p.T180M|SCNN1A_ENST00000538979.1_Intron	NM_001038.5	NP_001029.1	P37088	SCNNA_HUMAN	sodium channel, non-voltage-gated 1 alpha subunit	157					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)	GTCAAAGAGCGTCTGCTCTGT	0.647																																					p.T216M		Atlas-SNP	.											.	SCNN1A	54	.	0			c.C647T						PASS	.						34	38	37					12																	6472823		2203	4300	6503	SO:0001583	missense	6337	exon2			AAGAGCGTCTGCT	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.470C>T	chr12.hg19:g.6472823G>A	ENSP00000228916:p.Thr157Met	86.0	0.0	.		86.0	32.0	.	NM_001159576	A5X2U9|B4E2Q5|C5HTZ0|O43271|Q6GSQ6|Q9UM64	Missense_Mutation	SNP	ENST00000228916.2	hg19	CCDS8543.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.009860	0.75046	.	.	ENSG00000111319	ENST00000360168;ENST00000358945;ENST00000228916;ENST00000396966;ENST00000543768	T;T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06;-0.06	5.46	5.46	0.80206	.	0.000000	0.64402	D	0.000003	T	0.75064	0.3799	M	0.82517	2.595	0.47819	D	0.999528	D;D;D	0.63880	0.993;0.993;0.976	P;P;B	0.52109	0.69;0.56;0.301	T	0.80188	-0.1486	10	0.87932	D	0	-10.8711	16.8039	0.85621	0.0:0.0:1.0:0.0	.	180;157;216	B4E2Q5;P37088;P37088-2	.;SCNNA_HUMAN;.	M	216;157;157;157;180	ENSP00000353292:T216M;ENSP00000351825:T157M;ENSP00000228916:T157M;ENSP00000380166:T157M;ENSP00000438739:T180M	ENSP00000228916:T157M	T	-	2	0	SCNN1A	6343084	1.000000	0.71417	1.000000	0.80357	0.451000	0.32288	4.654000	0.61469	2.535000	0.85469	0.561000	0.74099	ACG	.	.	.	none		0.647	SCNN1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399055.1			A	6472823	G	A	6472823	3	1	27	1	0	0	0	0	1	0	0	0	13940	1145	40	1	1583	1	SCNN1A	12	6472823	Missense_Mutation	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10	5467572	6472823	127379072	48	1931											
ITGA5	3678	hgsc.bcm.edu	37	chr12	54792434	54792434	+	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	gattcggtagggcatcttcaGggctttgtacacagcctcac	8	11	11	11	1	3	0	2	0	1	0	4	1	3	0	1	3	2	4	1	3	2	5			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr12:54792434G>C	ENST00000293379.4	-	28	3151	c.2890C>G	c.(2890-2892)Ctg>Gtg	p.L964V	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)	964					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						GGCATCTTCAGGGCTTTGTAC	0.572																																					p.L964V		Atlas-SNP	.											.	ITGA5	99	.	0			c.C2890G						PASS	.						105	91	95					12																	54792434		2203	4300	6503	SO:0001583	missense	3678	exon28			TCTTCAGGGCTTT		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.2890C>G	chr12.hg19:g.54792434G>C	ENSP00000293379:p.Leu964Val	82.0	0.0	.		94.0	36.0	.	NM_002205	Q96HA5	Missense_Mutation	SNP	ENST00000293379.4	hg19	CCDS8880.1	.	.	.	.	.	.	.	.	.	.	G	14.49	2.552305	0.45487	.	.	ENSG00000161638	ENST00000293379	T	0.21932	1.98	5.36	1.45	0.22620	.	0.287995	0.31897	N	0.006894	T	0.10809	0.0264	L	0.34521	1.04	0.22601	N	0.998941	P	0.44986	0.847	B	0.35278	0.199	T	0.22312	-1.0220	10	0.31617	T	0.26	.	5.3109	0.15829	0.2368:0.0:0.6205:0.1427	.	964	P08648	ITA5_HUMAN	V	964	ENSP00000293379:L964V	ENSP00000293379:L964V	L	-	1	2	ITGA5	53078701	0.361000	0.24972	0.984000	0.44739	0.992000	0.81027	1.036000	0.30228	0.069000	0.16605	0.655000	0.94253	CTG	.	.	.	none		0.572	ITGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406174.1			C	54792434	G	C	54792434	3	2	27	1	0	0	0	0	1	0	0	0	7886	991	35	4	271	4	ITGA5	12	54792434	Missense_Mutation	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10	48319611	54792434	79059461	49	1932											
UBE3B	89910	hgsc.bcm.edu	37	chr12	109961880	109961880	+	Frame_Shift_Del	DEL	C	C	-																															ctcggtggatgaactgccttCtctggactccgagttctata																										TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr12:109961880delC	ENST00000342494.3	+	22	3057	c.2462delC	c.(2461-2463)tctfs	p.S821fs	UBE3B_ENST00000434735.2_Frame_Shift_Del_p.S821fs	NM_130466.3	NP_569733.2	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B	821	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						GAACTGCCTTCTCTGGACTCC	0.527																																					p.S821fs		Atlas-Indel,Pindel	.											.	UBE3B	116	.	0			c.2461delT						PASS	.						129	109	116					12																	109961880		2203	4300	6503	SO:0001589	frameshift_variant	89910	exon22			.	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.2462delC	chr12.hg19:g.109961880delC	ENSP00000340596:p.Ser821fs	81.0	0.0	0		63.0	19.0	0.301587	NM_183415	A5D8Z3|Q05BX9|Q659F7|Q7Z7Q1|Q9BXZ4	Frame_Shift_Del	DEL	ENST00000342494.3	hg19	CCDS9129.1																																																																																			.	.	.	none		0.527	UBE3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403119.1	NM_183415		-	109961880	C	-	109961880	7	5	27	1	0	1	0	1	0	0	0	0	16892	913	32	0	2540	0	UBE3B	12	109961880	Frame_Shift_Del	DEL	C	TCGA-5P-A9JU-01A-11D-A42J-10	55169446	109961880	23890015	50	1933											
ATP7B	540	hgsc.bcm.edu	37	chr13	52516678	52516679	+	Frame_Shift_Ins	INS	-	-	T																															gtgcagtatcccaaggtctcINStgttccaagttcctgggaag																										TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr13:52516678_52516679insT	ENST00000242839.4	-	15	3411_3412	c.3255_3256insA	c.(3253-3258)acagagfs	p.E1086fs	ATP7B_ENST00000344297.5_Frame_Shift_Ins_p.E879fs|ATP7B_ENST00000418097.2_Frame_Shift_Ins_p.E1021fs|ATP7B_ENST00000400370.3_Frame_Shift_Ins_p.E656fs|ATP7B_ENST00000417240.2_Frame_Shift_Ins_p.E297fs|ATP7B_ENST00000448424.2_Frame_Shift_Ins_p.E1008fs|ATP7B_ENST00000482841.1_5'UTR|ATP7B_ENST00000400366.3_Frame_Shift_Ins_p.E975fs	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	1086					cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	CCCAAGGTCTCTGTTCCAAGTT	0.579									Wilson disease																												p.E1086fs		Atlas-Indel,Pindel	.											.	ATP7B	123	.	0			c.3256_3257insA						PASS	.																																			SO:0001589	frameshift_variant	540	exon15	Familial Cancer Database		.	U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"ATPases / P-type"	870	protein-coding gene	gene with protein product	"Wilson disease", "copper pump 2", "copper-transporting ATPase 2"	606882	"ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.3256dupA	chr13.hg19:g.52516679_52516679dupT	ENSP00000242839:p.Glu1086fs	57.0	0.0	0		42.0	15.0	0.357143	NM_000053	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Frame_Shift_Ins	INS	ENST00000242839.4	hg19	CCDS41892.1																																																																																			.	.	.	none		0.579	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053		T	52516679	-	T	52516678	7	5	27	1	0	1	1	0	0	0	0	0	1191	922	32	0	1169	0	ATP7B	13	52516678	Frame_Shift_Ins	INS	-	TCGA-5P-A9JU-01A-11D-A42J-10		52516678	62653200	51	1934											
EFS	10278	hgsc.bcm.edu	37	chr14	23828684	23828684	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgggggtgggggcagaggccGgtcctggatgctgcccttcc	3	8	19	11	1	0	1	0	0	0	1	2	2	2	2	4	7	2	2	4	7	0	1	rs147068550		TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr14:23828684G>A	ENST00000216733.3	-	4	1610	c.1003C>T	c.(1003-1005)Cgg>Tgg	p.R335W	EFS_ENST00000429593.2_Missense_Mutation_p.R166W|RP11-124D2.3_ENST00000554010.1_RNA|EFS_ENST00000351354.3_Missense_Mutation_p.R242W	NM_005864.2	NP_005855.1	O43281	EFS_HUMAN	embryonal Fyn-associated substrate	335	Pro-rich.				cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			endometrium(2)|kidney(1)|large_intestine(1)|liver(1)|lung(5)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)	16	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00649)		GGCAGAGGCCGGTCCTGGATG	0.721																																					p.R335W		Atlas-SNP	.											.	EFS	37	.	0			c.C1003T						PASS	.	G	TRP/ARG,TRP/ARG	0,3888		0,0,1944	22	24	23		1003,724	1.2	1	14	dbSNP_134	23	2,7684		0,2,3841	no	missense,missense	EFS	NM_005864.2,NM_032459.1	101,101	0,2,5785	AA,AG,GG		0.026,0.0,0.0173	probably-damaging,probably-damaging	335/562,242/469	23828684	2,11572	1944	3843	5787	SO:0001583	missense	10278	exon4			GAGGCCGGTCCTG	AB001466	CCDS9595.1, CCDS9596.1, CCDS61404.1	14q11.2-q12	2011-04-13			ENSG00000100842	ENSG00000100842		"Cas scaffolding proteins"	16898	protein-coding gene	gene with protein product	"Cas scaffolding protein family member 3"	609906				9349509	Standard	NM_005864		Approved	EFS2, EFS1, HEFS, SIN, CASS3	uc001wjo.4	O43281	OTTHUMG00000028741	ENST00000216733.3:c.1003C>T	chr14.hg19:g.23828684G>A	ENSP00000216733:p.Arg335Trp	25.0	0.0	.		39.0	14.0	.	NM_005864	B2RAJ7|B4DJ56|E9PGU2|O43282	Missense_Mutation	SNP	ENST00000216733.3	hg19	CCDS9595.1	.	.	.	.	.	.	.	.	.	.	G	18.46	3.629049	0.67015	0.0	2.6E-4	ENSG00000100842	ENST00000216733;ENST00000351354;ENST00000429593	T;T;T	0.69926	-0.44;0.28;0.39	5.43	1.23	0.21249	.	0.510812	0.18859	N	0.129190	T	0.71945	0.3400	L	0.34521	1.04	0.41759	D	0.989702	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79784	0.993;0.942;0.976	T	0.71820	-0.4477	10	0.72032	D	0.01	-19.2141	14.0841	0.64944	0.0:0.0:0.4685:0.5314	.	166;242;335	B4DJ56;O43281-2;O43281	.;.;EFS_HUMAN	W	335;242;166	ENSP00000216733:R335W;ENSP00000340607:R242W;ENSP00000416684:R166W	ENSP00000216733:R335W	R	-	1	2	EFS	22898524	0.979000	0.34478	0.998000	0.56505	0.996000	0.88848	0.152000	0.16302	-0.050000	0.13356	0.655000	0.94253	CGG	.	G|1.000;A|0.000	0.000	weak		0.721	EFS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071770.2			A	23828684	G	A	23828684	3	1	27	1	0	0	0	0	1	0	0	0	4961	1115	39	1	694	1	EFS	14	23828684	Missense_Mutation	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10		23828684	83520856	52	1935											
RIPK3	11035	hgsc.bcm.edu	37	chr14	24807103	24807103	+	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	gaaggagggtctgtccttggGctcactgctccagcagagct	7	9	14	11	0	2	1	1	0	1	1	4	3	4	2	2	3	3	4	2	3	1	1			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr14:24807103G>T	ENST00000216274.5	-	6	1026	c.808C>A	c.(808-810)Ccc>Acc	p.P270T	RP11-934B9.3_ENST00000555591.1_5'Flank|RIPK3_ENST00000554338.1_5'Flank|ADCY4_ENST00000554068.2_5'Flank|ADCY4_ENST00000558563.1_5'Flank|ADCY4_ENST00000310677.4_5'Flank	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	270	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|amyloid fibril formation (GO:1990000)|apoptotic signaling pathway (GO:0097190)|cellular protein modification process (GO:0006464)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of ligase activity (GO:0051351)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein deacetylation (GO:0090312)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of activated T cell proliferation (GO:0046006)|regulation of activation-induced cell death of T cells (GO:0070235)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000452)|regulation of interferon-gamma production (GO:0032649)|regulation of T cell mediated cytotoxicity (GO:0001914)|signal transduction (GO:0007165)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|NF-kappaB-inducing kinase activity (GO:0004704)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				GBM - Glioblastoma multiforme(265;0.0181)		CTGTCCTTGGGCTCACTGCTC	0.572																																					p.P270T	Pancreas(58;918 1191 4668 13304 15331)	Atlas-SNP	.											.	RIPK3	43	.	0			c.C808A						PASS	.						63	65	64					14																	24807103		2203	4300	6503	SO:0001583	missense	11035	exon6			CCTTGGGCTCACT	AF156884	CCDS9628.1	14q12	2006-05-15			ENSG00000129465	ENSG00000129465			10021	protein-coding gene	gene with protein product		605817				10339433, 10358032	Standard	NM_006871		Approved	RIP3	uc001wpb.3	Q9Y572	OTTHUMG00000029349	ENST00000216274.5:c.808C>A	chr14.hg19:g.24807103G>T	ENSP00000216274:p.Pro270Thr	97.0	0.0	.		81.0	31.0	.	NM_006871	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Missense_Mutation	SNP	ENST00000216274.5	hg19	CCDS9628.1	.	.	.	.	.	.	.	.	.	.	G	15.31	2.797112	0.50208	.	.	ENSG00000129465	ENST00000216274	T	0.70986	-0.53	4.46	2.59	0.31030	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.278577	0.26268	N	0.025359	D	0.83760	0.5324	M	0.90252	3.1	0.09310	N	0.999996	D	0.71674	0.998	D	0.68353	0.957	T	0.74494	-0.3647	10	0.72032	D	0.01	-9.3819	9.2661	0.37641	0.1827:0.0:0.8173:0.0	.	270	Q9Y572	RIPK3_HUMAN	T	270	ENSP00000216274:P270T	ENSP00000216274:P270T	P	-	1	0	RIPK3	23876943	0.994000	0.37717	0.031000	0.17742	0.005000	0.04900	2.658000	0.46733	0.789000	0.33779	0.655000	0.94253	CCC	.	.	.	none		0.572	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871		T	24807103	G	T	24807103	3	4	27	1	0	0	0	0	1	0	0	0	13395	1203	42	4	768	4	RIPK3	14	24807103	Missense_Mutation	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10	978419	24807103	82542437	53	1936											
SYT16	83851	hgsc.bcm.edu	37	chr14	62462841	62462842	+	Missense_Mutation	DNP	TA	TA	AT																															ccagcaagcaggagatatgtTatctgcttcgctggttaaca																										TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	T|A	T|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr14:62462841_62462842TA>AT	ENST00000430451.2	+	1	301_302	c.104_105TA>AT	c.(103-105)tTA>tAT	p.L35Y	SYT16_ENST00000446982.2_Missense_Mutation_p.L35Y	NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	35					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)		GGAGATATGTTATCTGCTTCGC	0.421																																					p.L35X|p.L35F		Atlas-SNP	.											.	SYT16	144	.	0			c.T104A|c.A105T						PASS	.																																			SO:0001583	missense	83851	exon1			ATATGTTATCTGC|TATGTTATCTGCT	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	Exception_encountered	chr14.hg19:g.62462841_62462842delinsAT	ENSP00000394700:p.Leu35Tyr	133.0	0.0	.		136.0	47.0|46.0	.	NM_031914	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000430451.2	hg19	CCDS45121.1																																																																																			.	.	.	none		0.421	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914		AT	62462842	TA	AT	62462841	3	1	27	1	0	0	0	0	1	0	0	0	15484	1764	61	5	106	5	SYT16	14	62462841	Missense_Mutation	DNP	TA	TCGA-5P-A9JU-01A-11D-A42J-10	37655738	62462841	44886699	54	1937											
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105408237	105408237	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcctggacctccaggtcggcGgaaggggcctgaatgcggag	7	5	18	11	3	0	1	0	1	0	0	2	4	1	4	4	7	1	0	4	7	2	0	rs574414313		TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr14:105408237G>A	ENST00000333244.5	-	7	13670	c.13551C>T	c.(13549-13551)tcC>tcT	p.S4517S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4517						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)			CCAGGTCGGCGGAAGGGGCCT	0.622													-|||	1	0.000199681	0	0	5008	,	,		19322	0		0.001	False		,,,				2504	0				p.S4517S		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C13551T						PASS	.						107	116	113					14																	105408237		1972	4154	6126	SO:0001819	synonymous_variant	113146	exon7			GTCGGCGGAAGGG	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.13551C>T	chr14.hg19:g.105408237G>A		143.0	0.0	.		117.0	54.0	.	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	hg19	CCDS45177.1																																																																																			.	.	.	none		0.622	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105408237	G	A	105408237	2	1	27	1	0	0	0	0	0	0	0	1	415	1103	39	1		1	AHNAK2	14	105408237	Silent	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10	42945396	105408237	1941303	55	1938											
TRPM1	4308	hgsc.bcm.edu	37	chr15	31330016	31330017	+	Frame_Shift_Del	DEL	CT	CT	-																															tgctcgttctcctcatccccCtttcttgagccagcatctgc																										TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr15:31330016_31330017delCT	ENST00000256552.6	-	20	2615_2616	c.2468_2469delAG	c.(2467-2469)aagfs	p.K823fs	TRPM1_ENST00000397795.2_Frame_Shift_Del_p.K801fs|RP11-348B17.1_ENST00000558755.1_RNA|TRPM1_ENST00000542188.1_Frame_Shift_Del_p.K840fs|RP11-348B17.1_ENST00000561299.1_RNA	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		CCTCATCCCCCTTTCTTGAGCC	0.48																																					p.840_841del		Atlas-Indel,Pindel	.											TRPM1,colon,carcinoma,0,1	TRPM1	183	.	0			c.2520_2521del						PASS	.																																			SO:0001589	frameshift_variant	4308	exon19			.	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.2468_2469delAG	chr15.hg19:g.31330016_31330017delCT	ENSP00000256552:p.Lys823fs	63.0	0.0	0		87.0	30.0	0.344828	NM_001252020		Frame_Shift_Del	DEL	ENST00000256552.6	hg19	CCDS58346.1																																																																																			.	.	.	none		0.48	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420		-	31330017	CT	-	31330016	7	5	27	1	0	1	0	1	0	0	0	0	16597	680	24	0	2444	0	TRPM1	15	31330016	Frame_Shift_Del	DEL	CT	TCGA-5P-A9JU-01A-11D-A42J-10		31330016	71201376	56	1939											
VPS39	23339	hgsc.bcm.edu	37	chr15	42456665	42456665	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctcaccctcttcctctccAgctgggactggggttttgcc	4	12	10	15	0	3	0	1	0	2	0	5	1	4	1	4	3	3	3	4	3	0	3			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr15:42456665A>G	ENST00000348544.4	-	20	1949	c.1950T>C	c.(1948-1950)gcT>gcC	p.A650A	VPS39_ENST00000318006.5_Silent_p.A639A			Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39 homolog (S. cerevisiae)	650					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	endosome (GO:0005768)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	small GTPase regulator activity (GO:0005083)			breast(2)|kidney(5)|large_intestine(4)|lung(8)|ovary(1)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;3.05e-06)		CTTCCTCTCCAGCTGGGACTG	0.493																																					p.A639A		Atlas-SNP	.											.	VPS39	53	.	0			c.T1917C						PASS	.						61	61	61					15																	42456665		2203	4299	6502	SO:0001819	synonymous_variant	23339	exon19			CTCTCCAGCTGGG	AF280814	CCDS10083.1, CCDS73710.1	15q14	2008-02-05	2006-12-19		ENSG00000166887	ENSG00000166887			20593	protein-coding gene	gene with protein product		612188	"vacuolar protein sorting 39 (yeast)"			11448994	Standard	XM_005254259		Approved	KIAA0770, VAM6	uc001zpc.3	Q96JC1	OTTHUMG00000130467	ENST00000348544.4:c.1950T>C	chr15.hg19:g.42456665A>G		61.0	0.0	.		77.0	31.0	.	NM_015289	O94869|Q71SQ6|Q7Z3V3|Q96B93|Q96RM0	Silent	SNP	ENST00000348544.4	hg19	CCDS10083.1																																																																																			.	.	.	none		0.493	VPS39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000420472.1	NM_015289		G	42456665	A	G	42456665	2	3	27	1	0	0	0	0	0	0	0	1	17221	175	7	3		3	VPS39	15	42456665	Silent	SNP	A	TCGA-5P-A9JU-01A-11D-A42J-10	11126649	42456665	60074727	57	1940											
DUOXA1	90527	hgsc.bcm.edu	37	chr15	45411430	45411430	+	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	gaccggtagcgggggctcagGagtccaccttcctcaggact	7	7	14	13	2	2	0	2	0	0	0	4	3	4	2	4	5	1	2	4	5	1	2			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr15:45411430G>A	ENST00000560572.1	-	6	911	c.906C>T	c.(904-906)ctC>ctT	p.L302L	DUOXA1_ENST00000430224.2_Silent_p.L257L|DUOXA1_ENST00000267803.4_Silent_p.L302L|DUOXA1_ENST00000558422.1_Silent_p.L257L|DUOXA1_ENST00000559014.1_Silent_p.L302L|DUOXA1_ENST00000558996.1_Silent_p.L257L	NM_001276266.1	NP_001263195.1	Q1HG43	DOXA1_HUMAN	dual oxidase maturation factor 1	302					hydrogen peroxide metabolic process (GO:0042743)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein transport (GO:0015031)|regulation of inflammatory response (GO:0050727)|regulation of thyroid hormone generation (GO:2000609)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	16		all_cancers(109;6.02e-08)|all_epithelial(112;1.83e-06)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.82e-18)|GBM - Glioblastoma multiforme(94;4.39e-07)|COAD - Colon adenocarcinoma(120;0.0676)|Colorectal(133;0.0686)		GGGGGCTCAGGAGTCCACCTT	0.597																																					p.L302L		Atlas-SNP	.											.	DUOXA1	32	.	0			c.C906T						PASS	.						76	74	75					15																	45411430		2198	4298	6496	SO:0001819	synonymous_variant	90527	exon9			GCTCAGGAGTCCA	BC029819	CCDS10119.1, CCDS61619.1, CCDS61620.1, CCDS61621.1	15q21.1	2006-11-29	2006-01-23	2006-07-25	ENSG00000140254	ENSG00000140254			26507	protein-coding gene	gene with protein product		612771				16651268	Standard	NM_144565		Approved	FLJ32334, NUMBIP, NIP, mol	uc010bec.4	Q1HG43	OTTHUMG00000131352	ENST00000560572.1:c.906C>T	chr15.hg19:g.45411430G>A		79.0	0.0	.		130.0	56.0	.	NM_144565	Q8N6K9|Q96MI4	Silent	SNP	ENST00000560572.1	hg19																																																																																				.	.	.	none		0.597	DUOXA1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000416242.1	NM_144565		A	45411430	G	A	45411430	2	1	27	1	0	0	0	0	0	0	0	1	4804	1161	41	2		2	DUOXA1	15	45411430	Silent	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10	2954765	45411430	57119962	58	1941											
PLEKHO2	80301	hgsc.bcm.edu	37	chr15	65157740	65157740	+	Frame_Shift_Del	DEL	C	C	-																															caacaacatccacagcactgCccccctgggacctgccacct																										TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr15:65157740delC	ENST00000323544.4	+	6	1254	c.1126delC	c.(1126-1128)cccfs	p.P377fs	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	377	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						CACAGCACTGCCCCCCTGGGA	0.632																																					p.L375fs		Atlas-Indel,Pindel	.											.	PLEKHO2	50	.	0			c.1125delG						PASS	.						81	80	80					15																	65157740		2202	4299	6501	SO:0001589	frameshift_variant	80301	exon6			.	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.1126delC	chr15.hg19:g.65157740delC	ENSP00000326706:p.Pro377fs	43.0	0.0	0		54.0	24.0	0.444444	NM_025201	Q7L4H4|Q8WYS8	Frame_Shift_Del	DEL	ENST00000323544.4	hg19	CCDS10196.1																																																																																			.	.	.	none		0.632	PLEKHO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256659.1	NM_025201		-	65157740	C	-	65157740	7	5	27	1	0	1	0	1	0	0	0	0	12092	739	26	0	1148	0	PLEKHO2	15	65157740	Frame_Shift_Del	DEL	C	TCGA-5P-A9JU-01A-11D-A42J-10	19746310	65157740	37373652	59	1942											
MYO9A	4649	hgsc.bcm.edu	37	chr15	72192260	72192260	+	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	acgccaggaagcttggagaaGagcagctgcactagccataa	14	5	12	10	1	0	2	0	0	0	2	0	4	0	3	2	2	5	4	2	2	4	3			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr15:72192260G>C	ENST00000356056.5	-	24	3710	c.3238C>G	c.(3238-3240)Ctt>Gtt	p.L1080V	MYO9A_ENST00000563542.1_5'UTR|MYO9A_ENST00000564571.1_Missense_Mutation_p.L1080V|MYO9A_ENST00000566885.1_Missense_Mutation_p.L700V|MYO9A_ENST00000444904.1_Missense_Mutation_p.L1061V|MYO9A_ENST00000424560.1_Missense_Mutation_p.L1080V	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1080	IQ 3. {ECO:0000255|PROSITE- ProRule:PRU00116}.|Neck or regulatory domain.				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						GCTTGGAGAAGAGCAGCTGCA	0.488																																					p.L1080V		Atlas-SNP	.											.	MYO9A	203	.	0			c.C3238G						PASS	.						63	63	63					15																	72192260		2199	4297	6496	SO:0001583	missense	4649	exon24			GGAGAAGAGCAGC	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.3238C>G	chr15.hg19:g.72192260G>C	ENSP00000348349:p.Leu1080Val	58.0	0.0	.		72.0	28.0	.	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	hg19	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	G	4.193	0.034411	0.08101	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904;ENST00000261864	T;T;T	0.71817	-0.58;-0.59;-0.6	5.66	-1.37	0.09056	.	.	.	.	.	T	0.44435	0.1293	N	0.11927	0.2	0.09310	N	1	B;B;B	0.09022	0.001;0.0;0.002	B;B;B	0.10450	0.003;0.002;0.005	T	0.23797	-1.0178	9	0.17832	T	0.49	.	4.621	0.12449	0.0687:0.2989:0.1867:0.4456	.	1061;1061;1080	B2RTY4-2;B7WP69;B2RTY4	.;.;MYO9A_HUMAN	V	1080;1080;1061;1061	ENSP00000348349:L1080V;ENSP00000399162:L1080V;ENSP00000398250:L1061V	ENSP00000261864:L1061V	L	-	1	0	MYO9A	69979314	0.000000	0.05858	0.020000	0.16555	0.931000	0.56810	-0.735000	0.04888	0.087000	0.17167	0.655000	0.94253	CTT	.	.	.	none		0.488	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		C	72192260	G	C	72192260	3	2	27	1	0	0	0	0	1	0	0	0	10091	942	33	4	4484	4	MYO9A	15	72192260	Missense_Mutation	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10	7034520	72192260	30339132	60	1943											
SLC28A1	9154	hgsc.bcm.edu	37	chr15	85452001	85452001	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcgtgtttggggaggcgcTggtcaaggatgtctttgcct	4	14	15	8	2	2	0	1	0	1	0	3	2	2	2	1	5	1	2	1	5	1	3			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr15:85452001T>C	ENST00000286749.3	+	8	860	c.770T>C	c.(769-771)cTg>cCg	p.L257P	SLC28A1_ENST00000537624.1_Missense_Mutation_p.L257P|SLC28A1_ENST00000537216.1_Missense_Mutation_p.L257P|SLC28A1_ENST00000394573.1_Missense_Mutation_p.L257P|SLC28A1_ENST00000537703.1_Missense_Mutation_p.L179P|SLC28A1_ENST00000538177.1_Missense_Mutation_p.L257P			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	257					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)	GGGGAGGCGCTGGTCAAGGAT	0.547																																					p.L257P		Atlas-SNP	.											.	SLC28A1	118	.	0			c.T770C						PASS	.						81	79	80					15																	85452001		2203	4299	6502	SO:0001583	missense	9154	exon9			AGGCGCTGGTCAA	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.770T>C	chr15.hg19:g.85452001T>C	ENSP00000286749:p.Leu257Pro	49.0	0.0	.		56.0	24.0	.	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Missense_Mutation	SNP	ENST00000286749.3	hg19	CCDS10334.1	.	.	.	.	.	.	.	.	.	.	T	11.25	1.582919	0.28268	.	.	ENSG00000156222	ENST00000537216;ENST00000538177;ENST00000537624;ENST00000286749;ENST00000394573;ENST00000537703	T;T;T;T;T;T	0.04603	4.33;4.06;4.52;4.5;4.5;3.59	4.59	4.59	0.56863	.	0.071749	0.56097	D	0.000021	T	0.23727	0.0574	M	0.88310	2.945	0.80722	D	1	D;B;D;B;D	0.89917	1.0;0.149;1.0;0.106;1.0	D;B;D;B;D	0.87578	0.992;0.115;0.998;0.183;0.991	T	0.01360	-1.1375	10	0.72032	D	0.01	-2.9199	10.289	0.43584	0.0:0.0:0.0:1.0	.	257;257;257;179;257	B7Z533;F5H560;B7Z3L6;B7Z3M4;O00337	.;.;.;.;S28A1_HUMAN	P	257;257;257;257;257;179	ENSP00000440546:L257P;ENSP00000443752:L257P;ENSP00000444700:L257P;ENSP00000286749:L257P;ENSP00000378074:L257P;ENSP00000443764:L179P	ENSP00000286749:L257P	L	+	2	0	SLC28A1	83253005	1.000000	0.71417	0.955000	0.39395	0.184000	0.23303	5.694000	0.68272	1.930000	0.55929	0.459000	0.35465	CTG	.	.	.	none		0.547	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2			C	85452001	T	C	85452001	3	2	27	1	0	0	0	0	1	0	0	0	14544	1580	55	3	867	3	SLC28A1	15	85452001	Missense_Mutation	SNP	T	TCGA-5P-A9JU-01A-11D-A42J-10	13259741	85452001	17079391	61	1944											
AKAP13	11214	hgsc.bcm.edu	37	chr15	86122639	86122639	+	Missense_Mutation	SNP	A	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	cagtggagatgctgtgcttcAgagagacttggtcatggagc	9	10	15	7	0	2	3	2	0	0	3	2	6	2	4	0	3	3	2	0	3	0	2			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr15:86122639A>C	ENST00000394518.2	+	7	1435	c.1340A>C	c.(1339-1341)cAg>cCg	p.Q447P	AKAP13_ENST00000361243.2_Missense_Mutation_p.Q447P|RP11-815J21.2_ENST00000561409.1_RNA	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	447					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						GCTGTGCTTCAGAGAGACTTG	0.517																																					p.Q447P	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.A1340C						PASS	.						63	67	65					15																	86122639		2202	4299	6501	SO:0001583	missense	11214	exon7			TGCTTCAGAGAGA	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.1340A>C	chr15.hg19:g.86122639A>C	ENSP00000378026:p.Gln447Pro	159.0	0.0	.		207.0	94.0	.	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	hg19	CCDS32319.1	.	.	.	.	.	.	.	.	.	.	A	10.85	1.467257	0.26335	.	.	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540	T;T	0.12361	2.71;2.69	5.3	-3.83	0.04269	.	.	.	.	.	T	0.08403	0.0209	L	0.29908	0.895	0.09310	N	0.999999	B;B	0.06786	0.0;0.001	B;B	0.08055	0.001;0.003	T	0.33650	-0.9860	9	0.51188	T	0.08	.	5.4318	0.16458	0.2672:0.5391:0.0749:0.1188	.	447;447	Q12802;Q12802-2	AKP13_HUMAN;.	P	447;447;446;446	ENSP00000354718:Q447P;ENSP00000378026:Q447P	ENSP00000354718:Q447P	Q	+	2	0	AKAP13	83923643	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.075000	0.11431	-0.915000	0.03823	-0.374000	0.07098	CAG	.	.	.	none		0.517	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		C	86122639	A	C	86122639	3	2	27	1	0	0	0	0	1	0	0	0	449	188	7	5	1362	5	AKAP13	15	86122639	Missense_Mutation	SNP	A	TCGA-5P-A9JU-01A-11D-A42J-10	670638	86122639	16408753	62	1945											
TMC5	79838	hgsc.bcm.edu	37	chr16	19474683	19474683	+	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	attcagtgtctgaactccatTtcccgggtaagtcagtaaaa	12	12	8	9	1	3	1	2	1	1	0	5	1	5	1	2	1	1	2	2	1	4	4			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr16:19474683T>A	ENST00000396229.2	+	7	1979	c.1230T>A	c.(1228-1230)atT>atA	p.I410I	TMC5_ENST00000219821.5_Silent_p.I164I|TMC5_ENST00000381414.4_Silent_p.I410I|TMC5_ENST00000561503.1_Silent_p.I51I|TMC5_ENST00000541464.1_Silent_p.I410I|TMC5_ENST00000564959.1_Silent_p.I93I|TMC5_ENST00000542583.2_Silent_p.I410I	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	410					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						TGAACTCCATTTCCCGGGTAA	0.458																																					p.I410I		Atlas-SNP	.											.	TMC5	169	.	0			c.T1230A						PASS	.						118	108	111					16																	19474683		2197	4300	6497	SO:0001819	synonymous_variant	79838	exon7			CTCCATTTCCCGG	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.1230T>A	chr16.hg19:g.19474683T>A		109.0	0.0	.		78.0	30.0	.	NM_001105249	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Silent	SNP	ENST00000396229.2	hg19	CCDS45431.1																																																																																			.	.	.	none		0.458	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780		A	19474683	T	A	19474683	2	1	27	1	0	0	0	0	0	0	0	1	16000	1829	64	5		5	TMC5	16	19474683	Silent	SNP	T	TCGA-5P-A9JU-01A-11D-A42J-10		19474683	70880070	63	1946											
RBBP6	5930	hgsc.bcm.edu	37	chr16	24578519	24578519	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacagaggactcaaggcccgTcactaccagcaactccagtc	12	5	8	16	1	2	1	2	0	0	1	4	2	3	2	3	2	3	1	3	2	3	1			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr16:24578519T>C	ENST00000319715.4	+	15	2077	c.1645T>C	c.(1645-1647)Tca>Cca	p.S549P	RBBP6_ENST00000348022.2_Missense_Mutation_p.S549P|RBBP6_ENST00000381039.3_Intron	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	549					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)		TCAAGGCCCGTCACTACCAGC	0.488																																					p.S549P		Atlas-SNP	.											.	RBBP6	158	.	0			c.T1645C						PASS	.						169	155	160					16																	24578519		2197	4300	6497	SO:0001583	missense	5930	exon15			GGCCCGTCACTAC		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.1645T>C	chr16.hg19:g.24578519T>C	ENSP00000317872:p.Ser549Pro	108.0	0.0	.		125.0	40.0	.	NM_018703	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Missense_Mutation	SNP	ENST00000319715.4	hg19	CCDS10621.1	.	.	.	.	.	.	.	.	.	.	T	12.47	1.949100	0.34377	.	.	ENSG00000122257	ENST00000319715;ENST00000348022	T;T	0.14893	2.47;2.47	5.8	5.8	0.92144	.	0.000000	0.41396	D	0.000886	T	0.11836	0.0288	N	0.19112	0.55	0.33759	D	0.621639	B;B	0.11235	0.004;0.002	B;B	0.11329	0.006;0.003	T	0.13710	-1.0499	10	0.32370	T	0.25	-13.6566	11.5317	0.50614	0.1922:0.0:0.0:0.8078	.	549;549	Q7Z6E9-2;Q7Z6E9	.;RBBP6_HUMAN	P	549	ENSP00000317872:S549P;ENSP00000316291:S549P	ENSP00000317872:S549P	S	+	1	0	RBBP6	24486020	0.989000	0.36119	1.000000	0.80357	0.991000	0.79684	1.675000	0.37555	2.209000	0.71365	0.460000	0.39030	TCA	.	.	.	none		0.488	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910		C	24578519	T	C	24578519	3	2	27	1	0	0	0	0	1	0	0	0	13116	1667	58	3	1757	3	RBBP6	16	24578519	Missense_Mutation	SNP	T	TCGA-5P-A9JU-01A-11D-A42J-10	5103836	24578519	65776234	64	1947											
BCKDK	10295	hgsc.bcm.edu	37	chr16	31121525	31121525	+	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	tcatgactctgtgacctgcaGatcaaggaccaggcggacga	11	7	12	11	2	3	3	2	2	1	1	3	6	3	5	2	3	1	1	2	3	1	0			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr16:31121525G>T	ENST00000394951.1	+	7	1046		c.e7-1		AC135050.1_ENST00000517000.2_RNA|BCKDK_ENST00000219794.6_Splice_Site|BCKDK_ENST00000394950.3_Splice_Site|BCKDK_ENST00000287507.3_Splice_Site			O14874	BCKD_HUMAN	branched chain ketoacid dehydrogenase kinase						branched-chain amino acid catabolic process (GO:0009083)|cellular amino acid catabolic process (GO:0009063)|phosphorylation (GO:0016310)|protein phosphorylation (GO:0006468)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrion (GO:0005739)	[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity (GO:0047323)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|stomach(1)	2						GTGACCTGCAGATCAAGGACC	0.617																																					.		Atlas-SNP	.											.	BCKDK	52	.	0			c.424-1G>T						PASS	.						93	91	92					16																	31121525		2197	4300	6497	SO:0001630	splice_region_variant	10295	exon6			CCTGCAGATCAAG	AF026548	CCDS10705.1, CCDS45467.1, CCDS61917.1	16p11.2	2008-05-14			ENSG00000103507	ENSG00000103507			16902	protein-coding gene	gene with protein product		614901				1889817	Standard	NM_005881		Approved		uc002eaw.5	O14874	OTTHUMG00000047356	ENST00000394951.1:c.424-1G>T	chr16.hg19:g.31121525G>T		79.0	0.0	.		78.0	32.0	.	NM_001271926	A8MY43|Q6FGL4|Q96G95|Q96IN5	Splice_Site	SNP	ENST00000394951.1	hg19	CCDS10705.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.947194	0.73672	.	.	ENSG00000103507	ENST00000394951;ENST00000219794;ENST00000394950;ENST00000287507	.	.	.	5.45	5.45	0.79879	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4154	0.90568	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BCKDK	31029026	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	8.797000	0.91882	2.720000	0.93068	0.655000	0.94253	.	.	.	.	none		0.617	BCKDK-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108514.1	NM_005881	Intron	T	31121525	G	T	31121525	5	4	27	1	0	0	0	0	0	0	1	0	1361	956	33	4	441	4	BCKDK	16	31121525	Splice_Site	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10	6543006	31121525	59233228	65	1948											
SRR	63826	hgsc.bcm.edu	37	chr17	2226627	2226627	+	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	gatatcttcactgtcacagaGgatgaaattaaggtgaggct	13	11	11	6	0	3	3	2	2	1	1	3	5	3	4	0	3	0	1	0	3	3	3			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr17:2226627G>T	ENST00000344595.5	+	7	1110	c.792G>T	c.(790-792)gaG>gaT	p.E264D	SRR_ENST00000576848.1_Missense_Mutation_p.E38D|TSR1_ENST00000301364.5_3'UTR	NM_021947.1	NP_068766.1	Q9GZT4	SRR_HUMAN	serine racemase	264					aging (GO:0007568)|brain development (GO:0007420)|D-serine biosynthetic process (GO:0070179)|D-serine metabolic process (GO:0070178)|L-serine metabolic process (GO:0006563)|protein homotetramerization (GO:0051289)|pyruvate biosynthetic process (GO:0042866)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|serine family amino acid metabolic process (GO:0009069)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|D-serine ammonia-lyase activity (GO:0008721)|glycine binding (GO:0016594)|L-serine ammonia-lyase activity (GO:0003941)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|serine racemase activity (GO:0030378)|threonine racemase activity (GO:0018114)			NS(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	8		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;3.24e-06)|READ - Rectum adenocarcinoma(1115;0.0649)	L-Serine(DB00133)	CTGTCACAGAGGATGAAATTA	0.448																																					p.E264D		Atlas-SNP	.											.	SRR	21	.	0			c.G792T						PASS	.						103	97	99					17																	2226627		2203	4300	6503	SO:0001583	missense	63826	exon7			CACAGAGGATGAA	AF169974	CCDS11017.1	17p13	2007-01-18			ENSG00000167720	ENSG00000167720			14398	protein-coding gene	gene with protein product		606477				17067558, 15953485, 15193426	Standard	NM_021947		Approved	ILV1, ISO1	uc002fue.1	Q9GZT4	OTTHUMG00000090583	ENST00000344595.5:c.792G>T	chr17.hg19:g.2226627G>T	ENSP00000339435:p.Glu264Asp	172.0	0.0	.		144.0	17.0	.	NM_021947	D3DTI5|Q6IA55	Missense_Mutation	SNP	ENST00000344595.5	hg19	CCDS11017.1	.	.	.	.	.	.	.	.	.	.	G	11.03	1.517749	0.27123	.	.	ENSG00000167720	ENST00000344595	D	0.96365	-3.99	5.88	2.55	0.30701	Pyridoxal phosphate-dependent enzyme, beta subunit (2);	0.000000	0.85682	D	0.000000	D	0.92041	0.7478	L	0.35487	1.065	0.80722	D	1	B	0.28713	0.22	B	0.37422	0.249	D	0.83449	0.0047	10	0.06365	T	0.9	-30.1951	9.8933	0.41302	0.2377:0.0:0.7623:0.0	.	264	Q9GZT4	SRR_HUMAN	D	264	ENSP00000339435:E264D	ENSP00000339435:E264D	E	+	3	2	SRR	2173377	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	2.152000	0.42272	0.297000	0.22615	0.555000	0.69702	GAG	.	.	.	none		0.448	SRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207129.2	NM_021947		T	2226627	G	T	2226627	3	4	27	1	0	0	0	0	1	0	0	0	15178	991	35	4	814	4	SRR	17	2226627	Missense_Mutation	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10		2226627	78968583	66	1949											
ZNF594	84622	hgsc.bcm.edu	37	chr17	5085263	5085263	+	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	aaggtcctactacactgattAcaccaataaactttcttttc	13	14	3	11	0	1	1	0	1	1	0	3	1	2	1	2	1	4	0	2	1	7	7			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr17:5085263A>T	ENST00000399604.4	-	1	2429	c.2289T>A	c.(2287-2289)tgT>tgA	p.C763*	ZNF594_ENST00000575779.1_Nonsense_Mutation_p.C763*			Q96JF6	ZN594_HUMAN	zinc finger protein 594	763					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						TACACTGATTACACCAATAAA	0.408																																					p.C763X		Atlas-SNP	.											.	ZNF594	89	.	0			c.T2289A						PASS	.						208	210	209					17																	5085263		1983	4172	6155	SO:0001587	stop_gained	84622	exon2			CTGATTACACCAA	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.2289T>A	chr17.hg19:g.5085263A>T	ENSP00000382513:p.Cys763*	90.0	0.0	.		94.0	33.0	.	NM_032530	Q6RFS0	Nonsense_Mutation	SNP	ENST00000399604.4	hg19	CCDS42241.1	.	.	.	.	.	.	.	.	.	.	A	29.6	5.023323	0.93462	.	.	ENSG00000180626	ENST00000399604	.	.	.	1.04	1.04	0.20106	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999997	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.9142	0.19045	1.0:0.0:0.0:0.0	.	.	.	.	X	763	.	ENSP00000382513:C763X	C	-	3	2	ZNF594	5025987	0.055000	0.20627	0.019000	0.16419	0.154000	0.21943	0.151000	0.16283	0.418000	0.25898	0.248000	0.18094	TGT	.	.	.	none		0.408	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737		T	5085263	A	T	5085263	4	4	27	1	0	0	0	0	0	1	0	0	18036	389	14	5	138	5	ZNF594	17	5085263	Nonsense_Mutation	SNP	A	TCGA-5P-A9JU-01A-11D-A42J-10	2858636	5085263	76109947	67	1950											
CASC3	22794	hgsc.bcm.edu	37	chr17	38297029	38297030	+	Frame_Shift_Del	DEL	GT	GT	-																															aagagtgctgaggagtcggaGtgtgtgagtgcgcgcaggcg																										TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr17:38297029_38297030delGT	ENST00000264645.7	+	1	454_455	c.228_229delGT	c.(226-231)gagtgtfs	p.C77fs		NM_007359.4	NP_031385.2	O15234	CASC3_HUMAN	cancer susceptibility candidate 3	77					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						AGGAGTCGGAGTGTGTGAGTGC	0.703																																					p.76_76del		Atlas-Indel,Pindel	.											.	CASC3	39	.	0			c.227_228del						PASS	.																																			SO:0001589	frameshift_variant	22794	exon1			.	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.228_229delGT	chr17.hg19:g.38297033_38297034delGT	ENSP00000264645:p.Cys77fs	106.0	0.0	0		114.0	34.0	0.298246	NM_007359	A8K8R0	Frame_Shift_Del	DEL	ENST00000264645.7	hg19	CCDS11362.1																																																																																			.	.	.	none		0.703	CASC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257127.3	NM_007359		-	38297030	GT	-	38297029	7	5	27	1	0	1	0	1	0	0	0	0	2663	1020	36	0	230	0	CASC3	17	38297029	Frame_Shift_Del	DEL	GT	TCGA-5P-A9JU-01A-11D-A42J-10	33211766	38297029	42898181	68	1951											
GRN	2896	hgsc.bcm.edu	37	chr17	42427873	42427873	+	Missense_Mutation	SNP	A	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	ccttctgcgacctggttcacAcccgctgcatcacacccacg	7	8	7	19	3	3	0	2	0	1	0	3	1	3	0	4	1	2	3	4	1	0	2			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr17:42427873A>C	ENST00000053867.3	+	6	588	c.526A>C	c.(526-528)Acc>Ccc	p.T176P	GRN_ENST00000589265.1_Intron	NM_002087.2	NP_002078.1	P28799	GRN_HUMAN	granulin	176					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)		CCTGGTTCACACCCGCTGCAT	0.617											OREG0024459	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T176P		Atlas-SNP	.											.	GRN	51	.	0			c.A526C						PASS	.						116	111	112					17																	42427873		2203	4300	6503	SO:0001583	missense	2896	exon6			GTTCACACCCGCT	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.526A>C	chr17.hg19:g.42427873A>C	ENSP00000053867:p.Thr176Pro	54.0	0.0	.	908	62.0	8.0	.	NM_002087	D3DX55|P23781|P23782|P23783|P23784|Q53HQ8|Q53Y88|Q540U8|Q9BWE7|Q9H8S1|Q9UCH0	Missense_Mutation	SNP	ENST00000053867.3	hg19	CCDS11483.1	.	.	.	.	.	.	.	.	.	.	A	8.948	0.967566	0.18659	.	.	ENSG00000030582	ENST00000053867;ENST00000357351	T	0.72615	-0.67	4.43	-0.595	0.11660	Granulin (2);	1.360170	0.04868	N	0.445459	T	0.60932	0.2307	L	0.34521	1.04	0.09310	N	1	B	0.33238	0.403	B	0.41691	0.364	T	0.48906	-0.8993	10	0.24483	T	0.36	-3.2852	2.7752	0.05345	0.2261:0.0:0.3737:0.4002	.	176	P28799	GRN_HUMAN	P	176	ENSP00000053867:T176P	ENSP00000053867:T176P	T	+	1	0	GRN	39783399	0.004000	0.15560	0.004000	0.12327	0.017000	0.09413	1.212000	0.32394	0.021000	0.15133	-0.464000	0.05259	ACC	.	.	.	none		0.617	GRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457766.1	NM_002087		C	42427873	A	C	42427873	3	2	27	1	0	0	0	0	1	0	0	0	6811	159	6	5	544	5	GRN	17	42427873	Missense_Mutation	SNP	A	TCGA-5P-A9JU-01A-11D-A42J-10	4130844	42427873	38767337	69	1952											
ESCO1	114799	hgsc.bcm.edu	37	chr18	19154134	19154134	+	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	tcttctgaggacacttttcaGatccttgcgtgcattgagaa	9	14	9	9	1	3	3	1	2	2	2	4	5	4	4	1	1	2	1	1	1	1	5			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr18:19154134G>A	ENST00000269214.5	-	4	1608	c.671C>T	c.(670-672)tCt>tTt	p.S224F		NM_052911.2	NP_443143.2	Q5FWF5	ESCO1_HUMAN	establishment of sister chromatid cohesion N-acetyltransferase 1	224					mitotic cell cycle (GO:0000278)|post-translational protein acetylation (GO:0034421)|regulation of DNA replication (GO:0006275)|sister chromatid cohesion (GO:0007062)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|transferase activity, transferring acyl groups (GO:0016746)			breast(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(10)|prostate(3)|upper_aerodigestive_tract(1)	35						ACACTTTTCAGATCCTTGCGT	0.408																																					p.S224F		Atlas-SNP	.											.	ESCO1	89	.	0			c.C671T						PASS	.						167	163	164					18																	19154134		2203	4300	6503	SO:0001583	missense	114799	exon4			TTTTCAGATCCTT	AL832041	CCDS32800.1	18q11.2	2013-05-02	2013-05-02		ENSG00000141446	ENSG00000141446			24645	protein-coding gene	gene with protein product		609674	"establishment of cohesion 1 homolog 1 (S. cerevisiae)"			11572484, 14576321, 15958495	Standard	NM_052911		Approved	ESO1, EFO1, KIAA1911	uc002kth.1	Q5FWF5		ENST00000269214.5:c.671C>T	chr18.hg19:g.19154134G>A	ENSP00000269214:p.Ser224Phe	52.0	0.0	.		50.0	20.0	.	NM_052911	B0YJ11|B0YJ12|Q69YG4|Q69YS3|Q6IMD7|Q8N3Z5|Q8NBG2|Q96PX7	Missense_Mutation	SNP	ENST00000269214.5	hg19	CCDS32800.1	.	.	.	.	.	.	.	.	.	.	G	10.77	1.443142	0.25987	.	.	ENSG00000141446	ENST00000269214;ENST00000383276	T;T	0.63255	-0.03;1.49	4.98	3.2	0.36748	.	0.917970	0.09279	N	0.824061	T	0.57946	0.2088	M	0.62723	1.935	0.24024	N	0.996137	P	0.48162	0.906	B	0.41723	0.365	T	0.52193	-0.8608	10	0.87932	D	0	-10.7597	5.6599	0.17662	0.1623:0.0:0.6812:0.1565	.	224	Q5FWF5	ESCO1_HUMAN	F	224	ENSP00000269214:S224F;ENSP00000372763:S224F	ENSP00000269214:S224F	S	-	2	0	ESCO1	17408132	0.149000	0.22717	0.976000	0.42696	0.380000	0.30137	1.587000	0.36622	0.710000	0.31997	-0.140000	0.14226	TCT	.	.	.	none		0.408	ESCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443942.1	NM_052911		A	19154134	G	A	19154134	3	1	27	1	0	0	0	0	1	0	0	0	5250	942	33	2	1887	2	ESCO1	18	19154134	Missense_Mutation	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10		19154134	58923114	70	1953											
MEX3C	51320	hgsc.bcm.edu	37	chr18	48703464	48703464	+	5'UTR	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gccaccttcaaagcttacatCggtaccattgtaatggaaat	13	11	7	10	1	1	0	1	0	0	0	2	1	1	1	3	2	3	3	3	2	5	5			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr18:48703464C>T	ENST00000591040.1	-	0	525							Q5U5Q3	MEX3C_HUMAN	mex-3 RNA binding family member C						chondrocyte hypertrophy (GO:0003415)|energy homeostasis (GO:0097009)|regulation of fat cell differentiation (GO:0045598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(11)|ovary(1)|skin(1)	17		Colorectal(6;0.003)|all_epithelial(6;0.0473)		Colorectal(16;0.0175)|READ - Rectum adenocarcinoma(32;0.15)		AAGCTTACATCGGTACCATTG	0.443																																					p.D413N		Atlas-SNP	.											.	MEX3C	77	.	0			c.G1237A						PASS	.						103	97	99					18																	48703464		2203	4300	6503	SO:0001623	5_prime_UTR_variant	51320	exon2			TTACATCGGTACC	BC041122	CCDS11951.2	18q21.1	2013-08-21	2013-08-21	2007-07-18	ENSG00000176624	ENSG00000176624		"RING-type (C3HC4) zinc fingers", "Mex-3 homologs"	28040	protein-coding gene	gene with protein product		611005	"ring finger and KH domain containing 2", "mex-3 homolog C (C. elegans)"	RKHD2		17267406	Standard	NM_016626		Approved	FLJ38871, RNF194	uc002lfc.4	Q5U5Q3	OTTHUMG00000132693	ENST00000591040.1:c.-274G>A	chr18.hg19:g.48703464C>T		75.0	0.0	.		76.0	4.0	.	NM_016626	A1L022|Q9NZE3	Missense_Mutation	SNP	ENST00000591040.1	hg19		.	.	.	.	.	.	.	.	.	.	C	26.5	4.744251	0.89663	.	.	ENSG00000176624	ENST00000406189	T	0.51574	0.7	5.97	5.97	0.96955	.	0.044645	0.85682	D	0.000000	T	0.67496	0.2899	M	0.68952	2.095	0.58432	D	0.999999	D	0.89917	1.0	D	0.64506	0.926	T	0.67189	-0.5733	10	0.62326	D	0.03	-15.0661	19.2102	0.93751	0.0:1.0:0.0:0.0	.	413	Q5U5Q3	MEX3C_HUMAN	N	413	ENSP00000385610:D413N	ENSP00000385610:D413N	D	-	1	0	MEX3C	46957462	1.000000	0.71417	0.631000	0.29282	0.995000	0.86356	7.818000	0.86416	2.836000	0.97738	0.655000	0.94253	GAT	.	.	.	none		0.443	MEX3C-003	KNOWN	mRNA_end_NF|basic	processed_transcript	protein_coding	OTTHUMT00000449559.1	NM_016626		T	48703464	C	T	48703464	1	4	27	0	1	0	0	0	0	0	0	0	9518	884	31	1		1	MEX3C	18	48703464	5'UTR	SNP	C	TCGA-5P-A9JU-01A-11D-A42J-10	29549330	48703464	29373784	71	1954											
ZNF77	58492	hgsc.bcm.edu	37	chr19	2936619	2936620	+	Frame_Shift_Ins	INS	-	-	A																															tcacttcctgtgaactttacINSaatctcttcatcattggata																										TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr19:2936619_2936620insA	ENST00000314531.4	-	3	305_306	c.213_214insT	c.(211-216)attgtafs	p.V72fs	ZNF77_ENST00000588050.1_5'Flank	NM_021217.2	NP_067040.1	Q15935	ZNF77_HUMAN	zinc finger protein 77	72	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|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)		GTGAACTTTACAATCTCTTCAT	0.391																																					p.V72fs		Atlas-Indel,Pindel	.											.	ZNF77	47	.	0			c.214_215insT						PASS	.																																			SO:0001589	frameshift_variant	58492	exon3			.	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.214dupT	chr19.hg19:g.2936621_2936621dupA	ENSP00000319053:p.Val72fs	68.0	0.0	0		80.0	30.0	0.375	NM_021217	Q86XJ3|Q9NPP0	Frame_Shift_Ins	INS	ENST00000314531.4	hg19	CCDS12099.1																																																																																			.	.	.	none		0.391	ZNF77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451924.1	NM_021217		A	2936620	-	A	2936619	7	5	27	1	0	1	1	0	0	0	0	0	18154	478	17	0	1431	0	ZNF77	19	2936619	Frame_Shift_Ins	INS	-	TCGA-5P-A9JU-01A-11D-A42J-10		2936619	56192364	72	1955											
NFIC	4782	hgsc.bcm.edu	37	chr19	3381992	3381992	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaagaaggcgccgggctgcGtgctctccaaccccgaccag	8	4	13	16	4	1	1	0	0	1	1	2	2	1	1	5	2	3	3	5	2	3	0			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr19:3381992G>A	ENST00000443272.2	+	2	364	c.313G>A	c.(313-315)Gtg>Atg	p.V105M	NFIC_ENST00000341919.3_Missense_Mutation_p.V105M|NFIC_ENST00000586919.1_Missense_Mutation_p.V96M|NFIC_ENST00000589123.1_Missense_Mutation_p.V96M|NFIC_ENST00000346156.5_Missense_Mutation_p.V96M|NFIC_ENST00000395111.3_Missense_Mutation_p.V96M|NFIC_ENST00000590282.1_Missense_Mutation_p.V105M	NM_001245002.1	NP_001231931.1	P08651	NFIC_HUMAN	nuclear factor I/C (CCAAT-binding transcription factor)	105					DNA replication (GO:0006260)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)|nucleus (GO:0005634)	core promoter proximal region DNA binding (GO:0001159)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.8e-05)|Epithelial(107;2.94e-108)|BRCA - Breast invasive adenocarcinoma(158;0.00154)|STAD - Stomach adenocarcinoma(1328;0.191)		GCCGGGCTGCGTGCTCTCCAA	0.672																																					p.V105M		Atlas-SNP	.											.	NFIC	36	.	0			c.G313A						PASS	.						76	81	79					19																	3381992		2203	4300	6503	SO:0001583	missense	4782	exon2			GGCTGCGTGCTCT	X12492	CCDS12107.1, CCDS45914.1, CCDS58640.1, CCDS59330.1, CCDS59331.1	19p13.3	2008-02-05				ENSG00000141905			7786	protein-coding gene	gene with protein product		600729		NFI		3398920, 7590749	Standard	NM_205843		Approved	CTF, NF-I, CTF5	uc010xhi.2	P08651		ENST00000443272.2:c.313G>A	chr19.hg19:g.3381992G>A	ENSP00000396843:p.Val105Met	60.0	0.0	.		68.0	7.0	.	NM_001245004	A8K1H0|B7Z4U5|B7Z9C3|K7EMU1|P08652|Q14932|Q9UPJ3|Q9UPJ9|Q9UPK0|Q9UPK1	Missense_Mutation	SNP	ENST00000443272.2	hg19	CCDS59330.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.420303	0.83559	.	.	ENSG00000141905	ENST00000443272;ENST00000395111;ENST00000346156;ENST00000341919;ENST00000343825;ENST00000269778	T;T;T	0.81078	-1.45;-1.45;-1.45	3.88	3.88	0.44766	MAD homology 1, Dwarfin-type (2);CTF transcription factor/nuclear factor 1, DNA-binding domain (1);	0.000000	0.64402	D	0.000002	D	0.87200	0.6118	L	0.59436	1.845	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.998;0.998;0.998	D	0.88894	0.3348	10	0.87932	D	0	-20.5809	14.8198	0.70062	0.0:0.0:1.0:0.0	.	105;105;96;105;96	B7Z4U5;P08651;P08651-3;P08651-5;P08651-2	.;NFIC_HUMAN;.;.;.	M	96;96;96;105;105;105	ENSP00000378543:V96M;ENSP00000301935:V96M;ENSP00000342194:V105M	ENSP00000269778:V105M	V	+	1	0	NFIC	3332992	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.472000	0.97709	1.879000	0.54435	0.467000	0.42956	GTG	.	.	.	none		0.672	NFIC-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452834.1	NM_005597		A	3381992	G	A	3381992	3	1	27	1	0	0	0	0	1	0	0	0	10379	1145	40	1	326	1	NFIC	19	3381992	Missense_Mutation	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10	445373	3381992	55746991	73	1956											
CYP2A13	1553	hgsc.bcm.edu	37	chr19	41596036	41596037	+	Missense_Mutation	DNP	GC	GC	TT																															gggttttggcgtgggcaagcGcggcatcgaggaacgcatcc																										TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr19:41596036_41596037GC>TT	ENST00000330436.3	+	3	428_429	c.428_429GC>TT	c.(427-429)cGC>cTT	p.R143L		NM_000766.4	NP_000757.2	Q16696	CP2AD_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 13	143					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)	p.R143H(1)		breast(3)|endometrium(6)|kidney(4)|large_intestine(8)|lung(13)|ovary(3)|prostate(3)|skin(2)	42					Methoxsalen(DB00553)|Nicotine(DB00184)|Testosterone(DB00624)	GTGGGCAAGCGCGGCATCGAGG	0.698																																					p.R143L|p.R143R		Atlas-SNP	.											CYP2A13,NS,carcinoma,0,1|.	CYP2A13	90	.	1	Substitution - Missense(1)	prostate(1)	c.G428T|c.C429T						PASS	.																																			SO:0001583	missense	1553	exon3			GCAAGCGCGGCAT|CAAGCGCGGCATC	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	Exception_encountered	chr19.hg19:g.41596036_41596037delinsTT	ENSP00000332679:p.Arg143Leu	146.0|144.0	0.0	.		176.0	20.0	.	NM_000766	Q53YR8|Q6R569|Q6R570|Q9H2X2	Missense_Mutation|Silent	SNP	ENST00000330436.3	hg19	CCDS12571.1																																																																																			.	.	.	none		0.698	CYP2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463505.1	NM_000766		TT	41596037	GC	TT	41596036	3	4	27	1	0	0	0	0	1	0	0	0	4163	1087	38	4	438	4	CYP2A13	19	41596036	Missense_Mutation	DNP	GC	TCGA-5P-A9JU-01A-11D-A42J-10	38214044	41596036	17532947	74	1957											
HNRNPUL1	11100	hgsc.bcm.edu	37	chr19	41808585	41808585	+	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	cctagccaacttcacgttgcCagatgttggggacttcctgg	7	11	11	12	1	1	1	1	0	0	1	2	2	2	2	4	3	3	2	4	3	2	5			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr19:41808585C>A	ENST00000392006.3	+	12	1876	c.1703C>A	c.(1702-1704)cCa>cAa	p.P568Q	HNRNPUL1_ENST00000263367.3_Missense_Mutation_p.P479Q|HNRNPUL1_ENST00000352456.3_Missense_Mutation_p.P468Q|HNRNPUL1_ENST00000602130.1_Missense_Mutation_p.P568Q|HNRNPUL1_ENST00000378215.4_Missense_Mutation_p.P454Q|HNRNPUL1_ENST00000595018.1_Missense_Mutation_p.P468Q|HNRNPUL1_ENST00000593587.1_Missense_Mutation_p.P468Q	NM_007040.3	NP_008971.2	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1	568	Necessary for interaction with BRD7 and transcriptional activation.|Necessary for interaction with TP53.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	29						TTCACGTTGCCAGATGTTGGG	0.547																																					p.P568Q		Atlas-SNP	.											.	HNRNPUL1	73	.	0			c.C1703A						PASS	.						80	79	79					19																	41808585		2203	4298	6501	SO:0001583	missense	11100	exon12			CGTTGCCAGATGT	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.1703C>A	chr19.hg19:g.41808585C>A	ENSP00000375863:p.Pro568Gln	85.0	0.0	.		82.0	23.0	.	NM_007040	B3KMW7|O76022|Q6ZSZ0|Q7L8P4|Q8N6Z4|Q96G37|Q9HAL3|Q9UG75	Missense_Mutation	SNP	ENST00000392006.3	hg19	CCDS12576.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.567631	0.86439	.	.	ENSG00000105323	ENST00000352456;ENST00000392006;ENST00000378215;ENST00000263367	T;T;T;T	0.59083	0.29;0.29;0.29;0.29	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.81044	0.4741	M	0.90082	3.085	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;0.991;0.999;1.0;1.0	D	0.84535	0.0635	10	0.87932	D	0	-7.3032	17.9067	0.88920	0.0:1.0:0.0:0.0	.	479;468;568;92;454;568;468	B7Z4B8;A8K3W4;Q9BUJ2-2;Q9BUJ2-5;Q9BUJ2-3;Q9BUJ2;Q9BUJ2-4	.;.;.;.;.;HNRL1_HUMAN;.	Q	468;568;454;479	ENSP00000340857:P468Q;ENSP00000375863:P568Q;ENSP00000367460:P454Q;ENSP00000263367:P479Q	ENSP00000263367:P479Q	P	+	2	0	HNRNPUL1	46500425	1.000000	0.71417	0.412000	0.26496	0.984000	0.73092	7.283000	0.78640	2.837000	0.97791	0.591000	0.81541	CCA	.	.	.	none		0.547	HNRNPUL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463406.1	NM_144732, NM_007040		A	41808585	C	A	41808585	3	1	27	1	0	0	0	0	1	0	0	0	7281	594	21	4	1749	4	HNRNPUL1	19	41808585	Missense_Mutation	SNP	C	TCGA-5P-A9JU-01A-11D-A42J-10	212549	41808585	17320398	75	1958											
BCAM	4059	hgsc.bcm.edu	37	chr19	45322442	45322442	+	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	actcagctggagccaattggGgggcagcgtaagggaccttc	9	7	15	10	1	1	0	1	0	0	0	2	2	1	2	2	5	3	3	2	5	2	3	rs577903824	byFrequency	TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr19:45322442G>A	ENST00000270233.6	+	11	1488	c.1466G>A	c.(1465-1467)gGg>gAg	p.G489E	BCAM_ENST00000589651.1_Missense_Mutation_p.G489E	NM_001013257.2|NM_005581.4	NP_001013275.1|NP_005572.2	P50895	BCAM_HUMAN	basal cell adhesion molecule (Lutheran blood group)	489	Ig-like C2-type 3.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	laminin binding (GO:0043236)|laminin receptor activity (GO:0005055)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				AGCCAATTGGGGGGCAGCGTA	0.602													G|||	2	0.000399361	0	0	5008	,	,		15204	0		0	False		,,,				2504	0.002				p.G489E		Atlas-SNP	.											.	BCAM	53	.	0			c.G1466A						PASS	.						82	86	84					19																	45322442		2203	4300	6503	SO:0001583	missense	4059	exon11			AATTGGGGGGCAG	X83425	CCDS12644.1, CCDS42575.1	19q12-q13	2014-07-18	2006-02-23	2006-01-12		ENSG00000187244		"CD molecules", "Blood group antigens", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6722	protein-coding gene	gene with protein product		612773	"Lutheran blood group (Auberger b antigen included)", "basal cell adhesion molecule (Lu and Au blood groups)"	LU			Standard	NM_005581		Approved	CD239	uc002ozu.4	P50895		ENST00000270233.6:c.1466G>A	chr19.hg19:g.45322442G>A	ENSP00000270233:p.Gly489Glu	85.0	0.0	.		79.0	37.0	.	NM_001013257	A8MYF9|A9YWT5|A9YWT6|Q86VC7	Missense_Mutation	SNP	ENST00000270233.6	hg19	CCDS12644.1	.	.	.	.	.	.	.	.	.	.	.	12.24	1.878110	0.33162	.	.	ENSG00000187244	ENST00000270233;ENST00000391955	T;T	0.15718	2.4;2.4	4.37	3.33	0.38152	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.38746	0.1052	M	0.78637	2.42	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.15896	-1.0421	9	0.25106	T	0.35	-6.5398	10.0929	0.42458	0.0:0.0:0.7988:0.2012	.	489	P50895	BCAM_HUMAN	E	489	ENSP00000270233:G489E;ENSP00000375817:G489E	ENSP00000270233:G489E	G	+	2	0	BCAM	50014282	0.736000	0.28164	0.004000	0.12327	0.000000	0.00434	1.570000	0.36439	0.983000	0.38602	-0.349000	0.07799	GGG	.	.	.	none		0.602	BCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453220.1	NM_005581		A	45322442	G	A	45322442	3	1	27	1	0	0	0	0	1	0	0	0	1344	1232	43	2	1508	2	BCAM	19	45322442	Missense_Mutation	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10	3513857	45322442	13806541	76	1959											
CD3EAP	10849	hgsc.bcm.edu	37	chr19	45911526	45911526	+	Frame_Shift_Del	DEL	G	G	-																															ctgctggccccctcaacggaGgcaggaggtggactcacctg																										TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr19:45911526delG	ENST00000309424.3	+	3	788	c.300delG	c.(298-300)gagfs	p.E100fs	ERCC1_ENST00000300853.3_3'UTR|CD3EAP_ENST00000589804.1_Frame_Shift_Del_p.E102fs|PPP1R13L_ENST00000418234.2_5'Flank|ERCC1_ENST00000423698.2_3'UTR|ERCC1_ENST00000588738.1_5'Flank	NM_012099.1	NP_036231.1	O15446	RPA34_HUMAN	CD3e molecule, epsilon associated protein	100					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)		CCTCAACGGAGGCAGGAGGTG	0.642																																					p.E100fs		Atlas-Indel,Pindel	.											.	CD3EAP	27	.	0			c.299delA						PASS	.						56	62	60					19																	45911526		2203	4300	6503	SO:0001589	frameshift_variant	10849	exon3			.	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.300delG	chr19.hg19:g.45911526delG	ENSP00000310966:p.Glu100fs	51.0	0.0	0		70.0	32.0	0.457143	NM_012099	Q32N11|Q7Z5U2|Q9UPF6	Frame_Shift_Del	DEL	ENST00000309424.3	hg19	CCDS12661.1																																																																																			.	.	.	none		0.642	CD3EAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459538.1	NM_012099		-	45911526	G	-	45911526	7	5	27	1	0	1	0	1	0	0	0	0	3014	991	35	0	310	0	CD3EAP	19	45911526	Frame_Shift_Del	DEL	G	TCGA-5P-A9JU-01A-11D-A42J-10	589084	45911526	13217457	77	1960											
AP2A1	160	hgsc.bcm.edu	37	chr19	50305265	50305285	+	In_Frame_Del	DEL	CTGGGGCTGCGGGCAGCCCCT	CTGGGGCTGCGGGCAGCCCCT	-																															cctcgccctccgccgacctcCtggggctgcgggcagcccct																										TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	CTGGGGCTGCGGGCAGCCCCT	CTGGGGCTGCGGGCAGCCCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr19:50305265_50305285delCTGGGGCTGCGGGCAGCCCCT	ENST00000359032.5	+	15	1981_2001	c.1981_2001delCTGGGGCTGCGGGCAGCCCCT	c.(1981-2001)ctggggctgcgggcagcccctdel	p.LGLRAAP661del	AP2A1_ENST00000354293.5_In_Frame_Del_p.LGLRAAP661del	NM_014203.2	NP_055018.2	O95782	AP2A1_HUMAN	adaptor-related protein complex 2, alpha 1 subunit	661					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	AP-2 adaptor complex (GO:0030122)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)	19		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0023)|GBM - Glioblastoma multiforme(134;0.0157)		CGCCGACCTCCTGGGGCTGCGGGCAGCCCCTCCCCCGGCAG	0.756																																					p.660_667del		Atlas-Indel,Pindel	.											.	AP2A1	108	.	0			c.1980_2000del						PASS	.																																			SO:0001651	inframe_deletion	160	exon15			.	AA993745	CCDS46148.1, CCDS46149.1	19q13.3	2008-05-23				ENSG00000196961			561	protein-coding gene	gene with protein product		601026		CLAPA1, ADTAA		2564002	Standard	NM_014203		Approved		uc002ppn.3	O95782		ENST00000359032.5:c.1981_2001delCTGGGGCTGCGGGCAGCCCCT	chr19.hg19:g.50305265_50305285delCTGGGGCTGCGGGCAGCCCCT	ENSP00000351926:p.Leu661_Pro667del	82.0	0.0	0		58.0	13.0	0.224138	NM_130787	Q96CI7|Q96PP6|Q96PP7|Q9H070	In_Frame_Del	DEL	ENST00000359032.5	hg19	CCDS46148.1																																																																																			.	.	.	none		0.756	AP2A1-008	NOVEL	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465809.1			-	50305285	CTGGGGCTGCGGGCAGCCCCT	-	50305265	7	5	27	1	0	1	0	1	0	0	0	0	739	680	24	0	2039	0	AP2A1	19	50305265	In_Frame_Del	DEL	CTGGGGCTGCGGGCAGCCCCT	TCGA-5P-A9JU-01A-11D-A42J-10	4393739	50305265	8823718	78	1961											
USP29	57663	hgsc.bcm.edu	37	chr19	57640983	57640984	+	Missense_Mutation	DNP	CT	CT	AA																															catcttttgctgatgacttaCtcactcaaggtgtcccatgg																										TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr19:57640983_57640984CT>AA	ENST00000254181.4	+	4	1394_1395	c.940_941CT>AA	c.(940-942)CTc>AAc	p.L314N	USP29_ENST00000598197.1_Missense_Mutation_p.L314N	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	314	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)		TGATGACTTACTCACTCAAGGT	0.421																																					p.L314I|p.L314H		Atlas-SNP	.											.	USP29	186	.	0			c.C940A|c.T941A						PASS	.																																			SO:0001583	missense	57663	exon4			GACTTACTCACTC|ACTTACTCACTCA		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		Exception_encountered	chr19.hg19:g.57640983_57640984delinsAA	ENSP00000254181:p.Leu314Asn	120.0	0.0	.		127.0|128.0	42.0|45.0	.	NM_020903		Missense_Mutation	SNP	ENST00000254181.4	hg19	CCDS33124.1																																																																																			.	.	.	none		0.421	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1			AA	57640984	CT	AA	57640983	3	1	27	1	0	0	0	0	1	0	0	0	17071	565	20	4	942	4	USP29	19	57640983	Missense_Mutation	DNP	CT	TCGA-5P-A9JU-01A-11D-A42J-10	7335718	57640983	1488000	79	1962											
VN1R1	57191	hgsc.bcm.edu	37	chr19	57967199	57967199	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaaatataagactgcatgtAatgagctaaatctctttgat	17	13	6	5	0	1	3	0	2	1	1	2	3	1	3	0	0	2	3	0	0	7	5			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr19:57967199A>G	ENST00000321039.3	-	1	655	c.656T>C	c.(655-657)tTa>tCa	p.L219S	AC004076.9_ENST00000596831.1_Intron|AC004076.9_ENST00000415705.3_Intron	NM_020633.3	NP_065684.1	Q9GZP7	VN1R1_HUMAN	vomeronasal 1 receptor 1	219					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)		GACTGCATGTAATGAGCTAAA	0.398																																					p.L219S		Atlas-SNP	.											.	VN1R1	48	.	0			c.T656C						PASS	.						106	100	102					19																	57967199		2203	4300	6503	SO:0001583	missense	57191	exon1			GCATGTAATGAGC	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.656T>C	chr19.hg19:g.57967199A>G	ENSP00000322339:p.Leu219Ser	91.0	0.0	.		100.0	38.0	.	NM_020633	B3KSV5|Q7Z5H8|Q7Z5H9	Missense_Mutation	SNP	ENST00000321039.3	hg19	CCDS12951.1	.	.	.	.	.	.	.	.	.	.	A	14.22	2.469117	0.43839	.	.	ENSG00000178201	ENST00000321039	T	0.39056	1.1	4.11	3.0	0.34707	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.55257	0.1909	M	0.67625	2.065	0.09310	N	1	D	0.58268	0.982	D	0.63381	0.914	T	0.40534	-0.9558	9	0.87932	D	0	.	6.4555	0.21928	0.783:0.0:0.0:0.217	.	219	Q9GZP7	VN1R1_HUMAN	S	219	ENSP00000322339:L219S	ENSP00000322339:L219S	L	-	2	0	VN1R1	62659011	0.012000	0.17670	0.002000	0.10522	0.002000	0.02628	1.890000	0.39728	1.885000	0.54596	0.481000	0.45027	TTA	.	.	.	none		0.398	VN1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466464.1	NM_020633		G	57967199	A	G	57967199	3	3	27	1	0	0	0	0	1	0	0	0	17190	372	13	3	409	3	VN1R1	19	57967199	Missense_Mutation	SNP	A	TCGA-5P-A9JU-01A-11D-A42J-10	326216	57967199	1161784	80	1963											
ZNF341	84905	hgsc.bcm.edu	37	chr20	32376749	32376749	+	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	agagacacatgttgatccacGagcccttcaagaaatacaaa	17	7	7	10	1	1	3	1	1	0	2	2	5	2	3	2	0	2	1	2	0	4	3			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr20:32376749G>A	ENST00000375200.1	+	13	2298	c.1933G>A	c.(1933-1935)Gag>Aag	p.E645K	ZNF341_ENST00000342427.2_Missense_Mutation_p.E638K|RP4-553F4.6_ENST00000423074.1_RNA|RP4-553F4.6_ENST00000443171.1_RNA|RP4-553F4.6_ENST00000439444.1_RNA	NM_001282933.1	NP_001269862.1	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	645					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(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						GTTGATCCACGAGCCCTTCAA	0.552																																					p.E638K		Atlas-SNP	.											.	ZNF341	73	.	0			c.G1912A						PASS	.						120	99	106					20																	32376749		2203	4300	6503	SO:0001583	missense	84905	exon13			ATCCACGAGCCCT	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.1933G>A	chr20.hg19:g.32376749G>A	ENSP00000364346:p.Glu645Lys	209.0	0.0	.		199.0	24.0	.	NM_032819	A2RUF4|B2RXE5|B7ZM09|Q5JXM8|Q96ST5	Missense_Mutation	SNP	ENST00000375200.1	hg19		.	.	.	.	.	.	.	.	.	.	G	21.8	4.207734	0.79240	.	.	ENSG00000131061	ENST00000342427;ENST00000375200	T;T	0.08008	3.14;3.14	4.7	4.7	0.59300	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.061993	0.64402	D	0.000007	T	0.10380	0.0254	N	0.04355	-0.22	0.54753	D	0.999989	D;D;D;D	0.76494	0.999;0.957;0.999;0.999	P;B;P;P	0.56751	0.727;0.198;0.727;0.805	T	0.44847	-0.9301	10	0.72032	D	0.01	-30.0808	18.1856	0.89791	0.0:0.0:1.0:0.0	.	586;497;645;638	Q504V9;B3KU97;Q9BYN7;Q9BYN7-2	.;.;ZN341_HUMAN;.	K	638;645	ENSP00000344308:E638K;ENSP00000364346:E645K	ENSP00000344308:E638K	E	+	1	0	ZNF341	31840410	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	7.413000	0.80104	2.624000	0.88883	0.555000	0.69702	GAG	.	.	.	none		0.552	ZNF341-201	KNOWN	basic	protein_coding	protein_coding				A	32376749	G	A	32376749	3	1	27	1	0	0	0	0	1	0	0	0	17869	1059	37	1	1962	1	ZNF341	20	32376749	Missense_Mutation	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10		32376749	30648771	81	1964											
ADNP	23394	hgsc.bcm.edu	37	chr20	49510165	49510165	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aactgctttacagactgagaTtgttgaggaatggaaactgg	13	11	12	5	0	0	3	0	2	0	2	0	6	0	5	0	3	4	2	0	3	4	4			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr20:49510165T>C	ENST00000396029.3	-	5	1653	c.1086A>G	c.(1084-1086)caA>caG	p.Q362Q	ADNP_ENST00000349014.3_Silent_p.Q362Q|ADNP_ENST00000396032.3_Silent_p.Q362Q|ADNP_ENST00000371602.4_Silent_p.Q362Q	NM_001282531.1|NM_015339.2	NP_001269460.1|NP_056154.1	Q9H2P0	ADNP_HUMAN	activity-dependent neuroprotector homeobox	362					negative regulation of neuron apoptotic process (GO:0043524)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|endometrium(7)|kidney(1)|large_intestine(13)|lung(7)|ovary(2)|prostate(2)|skin(2)	39						CAGACTGAGATTGTTGAGGAA	0.498																																					p.Q362Q		Atlas-SNP	.											.	ADNP	106	.	0			c.A1086G						PASS	.						142	134	137					20																	49510165		2203	4300	6503	SO:0001819	synonymous_variant	23394	exon5			CTGAGATTGTTGA	AF250860	CCDS13433.1	20q13.13	2011-06-20	2007-07-17		ENSG00000101126	ENSG00000101126		"Homeoboxes / ZF class"	15766	protein-coding gene	gene with protein product	"ADNP homeobox 1"	611386	"activity-dependent neuroprotector"			9872452, 11013255	Standard	NM_015339		Approved	KIAA0784, ADNP1	uc002xvu.1	Q9H2P0	OTTHUMG00000032737	ENST00000396029.3:c.1086A>G	chr20.hg19:g.49510165T>C		66.0	0.0	.		63.0	22.0	.	NM_015339	E1P5Y2|O94881|Q5BKU2|Q9UG34	Silent	SNP	ENST00000396029.3	hg19	CCDS13433.1																																																																																			.	.	.	none		0.498	ADNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079705.2	NM_181442		C	49510165	T	C	49510165	2	2	27	1	0	0	0	0	0	0	0	1	323	1490	52	3		3	ADNP	20	49510165	Silent	SNP	T	TCGA-5P-A9JU-01A-11D-A42J-10	17133416	49510165	13515355	82	1965											
ABCG1	9619	hgsc.bcm.edu	37	chr21	43693428	43693428	+	Frame_Shift_Del	DEL	G	G	-																															tgcagggagacgggcatgaaGggggccgtcctcatcaacgg																										TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr21:43693428delG	ENST00000361802.2	+	4	565	c.420delG	c.(418-420)aagfs	p.K140fs	ABCG1_ENST00000347800.2_Frame_Shift_Del_p.K137fs|ABCG1_ENST00000462050.1_3'UTR|ABCG1_ENST00000398457.2_Frame_Shift_Del_p.K142fs|ABCG1_ENST00000343687.3_Frame_Shift_Del_p.K151fs|ABCG1_ENST00000398449.3_Frame_Shift_Del_p.K140fs|ABCG1_ENST00000398437.1_Frame_Shift_Del_p.K286fs|ABCG1_ENST00000340588.4_Frame_Shift_Del_p.K248fs	NM_004915.3	NP_004906.3	P45844	ABCG1_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 1	140	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				amyloid precursor protein catabolic process (GO:0042987)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|detection of hormone stimulus (GO:0009720)|glycoprotein transport (GO:0034436)|high-density lipoprotein particle remodeling (GO:0034375)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of cholesterol efflux (GO:0010875)|regulation of cholesterol esterification (GO:0010872)|regulation of transcription, DNA-templated (GO:0006355)|response to high density lipoprotein particle (GO:0055099)|response to lipid (GO:0033993)|response to organic substance (GO:0010033)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|glycoprotein transporter activity (GO:0034437)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sterol-transporting ATPase activity (GO:0034041)|toxin transporter activity (GO:0019534)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|ovary(3)|prostate(2)|stomach(1)	29					Adenosine triphosphate(DB00171)	CGGGCATGAAGGGGGCCGTCC	0.657																																					p.K151fs		Atlas-Indel,Pindel	.											.	ABCG1	140	.	0			c.452delA						PASS	.						60	65	64					21																	43693428		2203	4300	6503	SO:0001589	frameshift_variant	9619	exon4			.	U34919	CCDS13681.1, CCDS13682.1, CCDS13683.1, CCDS42937.1, CCDS42938.1	21q22.3	2012-03-14			ENSG00000160179	ENSG00000160179		"ATP binding cassette transporters / subfamily G"	73	protein-coding gene	gene with protein product	"ATP-binding cassette transporter 8"	603076				8659545, 16870176	Standard	NM_016818		Approved	ABC8	uc002zaq.3	P45844	OTTHUMG00000086791	ENST00000361802.2:c.420delG	chr21.hg19:g.43693428delG	ENSP00000354995:p.Lys140fs	55.0	0.0	0		84.0	33.0	0.392857	NM_207174	Q86SU8|Q96L76|Q9BXK6|Q9BXK7|Q9BXK8|Q9BXK9|Q9BXL0|Q9BXL1|Q9BXL2|Q9BXL3|Q9BXL4	Frame_Shift_Del	DEL	ENST00000361802.2	hg19	CCDS13682.1																																																																																			.	.	.	none		0.657	ABCG1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195318.2	NM_207174		-	43693428	G	-	43693428	7	5	27	1	0	1	0	1	0	0	0	0	68	991	35	0	602	0	ABCG1	21	43693428	Frame_Shift_Del	DEL	G	TCGA-5P-A9JU-01A-11D-A42J-10		43693428	4436467	83	1966											
SMARCB1	6598	hgsc.bcm.edu	37	chr22	24176330	24176330	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccccactcctcttccaggcGgatgaggcgtcttgccaaca	7	9	9	16	2	2	1	0	1	2	0	5	2	5	2	5	3	2	0	5	3	1	2			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chr22:24176330G>A	ENST00000263121.7	+	9	1317	c.1121G>A	c.(1120-1122)cGg>cAg	p.R374Q	SMARCB1_ENST00000407082.3_Missense_Mutation_p.R328Q|DERL3_ENST00000464023.1_5'Flank|SMARCB1_ENST00000407422.3_Missense_Mutation_p.R365Q|SMARCB1_ENST00000344921.6_Missense_Mutation_p.R383Q	NM_003073.3	NP_003064.2	Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	374					ATP-dependent chromatin remodeling (GO:0043044)|blastocyst hatching (GO:0001835)|cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|DNA integration (GO:0015074)|DNA repair (GO:0006281)|mitotic cell cycle phase transition (GO:0044772)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	p53 binding (GO:0002039)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)	p.?(2)|p.R374Q(1)|p.L266_*386del(1)		bone(4)|central_nervous_system(198)|endometrium(4)|haematopoietic_and_lymphoid_tissue(25)|kidney(3)|large_intestine(5)|liver(2)|lung(5)|meninges(5)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|soft_tissue(194)	458		Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05)				TCTTCCAGGCGGATGAGGCGT	0.662			"D, N, F, S"		malignant rhabdoid	malignant rhabdoid																															p.R374Q		Atlas-SNP	.	yes	Rec	yes	Rhabdoid predisposition syndrome	22	22q11	6598	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1"		M	SMARCB1_ENST00000344921,NS,carcinoma,0,4	SMARCB1	586	.	4	Unknown(2)|Substitution - Missense(1)|Deletion - In frame(1)	central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)	c.G1121A						PASS	.						34	26	29					22																	24176330		2194	4299	6493	SO:0001583	missense	6598	exon9			CCAGGCGGATGAG	U04847	CCDS13817.1, CCDS46671.1	22q11.23	2014-09-17			ENSG00000099956	ENSG00000099956			11103	protein-coding gene	gene with protein product	"sucrose nonfermenting, yeast, homolog-like 1", "integrase interactor 1", "malignant rhabdoid tumor suppressor", "protein phosphatase 1, regulatory subunit 144"	601607		SNF5L1		7801128, 10319872, 10365963	Standard	NM_003073		Approved	BAF47, Ini1, Snr1, hSNFS, Sfh1p, RDT, PPP1R144	uc002zyb.3	Q12824	OTTHUMG00000150737	ENST00000263121.7:c.1121G>A	chr22.hg19:g.24176330G>A	ENSP00000263121:p.Arg374Gln	98.0	0.0	.		64.0	44.0	.	NM_003073	O75784|O95474|Q17S11|Q38GA1|Q76N08|Q9UBH2	Missense_Mutation	SNP	ENST00000263121.7	hg19	CCDS13817.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.551141	0.86127	.	.	ENSG00000099956	ENST00000344921;ENST00000263121;ENST00000407422;ENST00000407082	D;D;D;D	0.97352	-4.27;-4.35;-4.3;-4.18	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	D	0.97996	0.9340	M	0.76574	2.34	0.80722	D	1	D;D;D	0.71674	0.998;0.997;0.998	P;P;P	0.61397	0.888;0.598;0.776	D	0.98914	1.0781	10	0.87932	D	0	-9.4379	17.5847	0.87978	0.0:0.0:1.0:0.0	.	383;365;374	G5E975;Q17S11;Q12824	.;.;SNF5_HUMAN	Q	383;374;365;328	ENSP00000340883:R383Q;ENSP00000263121:R374Q;ENSP00000383984:R365Q;ENSP00000385226:R328Q	ENSP00000263121:R374Q	R	+	2	0	SMARCB1	22506330	1.000000	0.71417	0.998000	0.56505	0.252000	0.25951	9.473000	0.97714	2.475000	0.83589	0.442000	0.29010	CGG	.	.	.	none		0.662	SMARCB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319872.1	NM_003073		A	24176330	G	A	24176330	3	1	27	1	0	0	0	0	1	0	0	0	14787	1116	39	1	1155	1	SMARCB1	22	24176330	Missense_Mutation	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10		24176330	27128236	84	1967											
VSIG4	11326	hgsc.bcm.edu	37	chrX	65253395	65253395	+	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	tgccaggtgacttcacacgtGtagtggctccggtcatccat	7	11	11	12	2	2	1	2	1	0	0	4	1	4	1	3	3	1	2	3	3	1	2			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chrX:65253395G>A	ENST00000374737.4	-	2	441	c.333C>T	c.(331-333)taC>taT	p.Y111Y	VSIG4_ENST00000412866.2_Silent_p.Y111Y|VSIG4_ENST00000455586.2_Silent_p.Y111Y	NM_001257403.1|NM_007268.2	NP_001244332.1|NP_009199.1	Q9Y279	VSIG4_HUMAN	V-set and immunoglobulin domain containing 4	111	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						CTTCACACGTGTAGTGGCTCC	0.547																																					p.Y111Y		Atlas-SNP	.											.	VSIG4	54	.	0			c.C333T						PASS	.						140	121	128					X																	65253395		2203	4300	6503	SO:0001819	synonymous_variant	11326	exon2			ACACGTGTAGTGG	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.333C>T	chrX.hg19:g.65253395G>A		91.0	0.0	.		133.0	104.0	.	NM_001100431	Q6UXI4	Silent	SNP	ENST00000374737.4	hg19	CCDS14383.1	.	.	.	.	.	.	.	.	.	.	G	0.087	-1.173588	0.01646	.	.	ENSG00000155659	ENST00000427538	.	.	.	4.89	2.08	0.27032	.	.	.	.	.	T	0.48537	0.1505	.	.	.	0.34643	D	0.720888	.	.	.	.	.	.	T	0.53760	-0.8393	4	.	.	.	-14.3402	7.2184	0.25973	0.3107:0.0:0.6893:0.0	.	.	.	.	Y	38	.	.	H	-	1	0	VSIG4	65170120	0.637000	0.27216	0.623000	0.29173	0.038000	0.13279	0.292000	0.19011	0.318000	0.23185	0.600000	0.82982	CAC	.	.	.	none		0.547	VSIG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056986.1	NM_007268		A	65253395	G	A	65253395	2	1	27	1	0	0	0	0	0	0	0	1	17237	1372	48	2		2	VSIG4	23	65253395	Silent	SNP	G	TCGA-5P-A9JU-01A-11D-A42J-10		65253395	90017165	85	1968											
AMOT	154796	hgsc.bcm.edu	37	chrX	112065566	112065566	+	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	tggttcaggcgatgctcactAtagaagtgccctggctcttg	7	12	12	10	1	3	1	2	0	1	1	3	2	3	1	1	3	2	3	1	3	3	4			TCGA-5P-A9JU-01A-11D-A42J-10	TCGA-5P-A9JU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d6969c41-5fa5-4853-95a0-0e473b44a505	f87abecd-d116-48b1-bf22-7584bab45053	g.chrX:112065566A>T	ENST00000524145.1	-	2	863	c.789T>A	c.(787-789)taT>taA	p.Y263*	AMOT_ENST00000462114.1_5'Flank|AMOT_ENST00000371958.1_Nonsense_Mutation_p.Y31*|AMOT_ENST00000371959.3_Nonsense_Mutation_p.Y263*|AMOT_ENST00000304758.1_Intron|AMOT_ENST00000371962.1_Nonsense_Mutation_p.Y31*			Q4VCS5	AMOT_HUMAN	angiomotin	263					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						GATGCTCACTATAGAAGTGCC	0.557																																					p.Y263X		Atlas-SNP	.											.	AMOT	204	.	0			c.T789A						PASS	.						99	84	89					X																	112065566		692	1591	2283	SO:0001587	stop_gained	154796	exon1			CTCACTATAGAAG	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.789T>A	chrX.hg19:g.112065566A>T	ENSP00000429013:p.Tyr263*	63.0	0.0	.		62.0	49.0	.	NM_001113490	Q504X5|Q9HD27|Q9UPT1	Nonsense_Mutation	SNP	ENST00000524145.1	hg19	CCDS48154.1	.	.	.	.	.	.	.	.	.	.	A	32	5.111330	0.94339	.	.	ENSG00000126016	ENST00000371959;ENST00000371962;ENST00000524145;ENST00000371958	.	.	.	5.36	3.02	0.34903	.	0.059683	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.9868	8.5979	0.33727	0.8525:0.0:0.1475:0.0	.	.	.	.	X	263;31;263;31	.	ENSP00000361026:Y31X	Y	-	3	2	AMOT	111952222	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.688000	0.54699	1.798000	0.52647	0.430000	0.28490	TAT	.	.	.	none		0.557	AMOT-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378570.1	NM_133265		T	112065566	A	T	112065566	4	4	27	1	0	0	0	0	0	1	0	0	582	456	16	5	2509	5	AMOT	23	112065566	Nonsense_Mutation	SNP	A	TCGA-5P-A9JU-01A-11D-A42J-10	46812171	112065566	43204994	86	1969											
ARHGEF19	128272	hgsc.bcm.edu	37	chr1	16532449	16532449	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcgctggtaggtgcgctcCtggtaggcctggttggtgac	4	10	18	9	2	0	1	0	1	0	0	1	1	1	1	2	7	1	5	2	7	2	3			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr1:16532449C>T	ENST00000270747.3	-	8	1564	c.1428G>A	c.(1426-1428)caG>caA	p.Q476Q	ARHGEF19_ENST00000478117.1_5'UTR	NM_153213.3	NP_694945.2	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19	476	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				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)		AGGTGCGCTCCTGGTAGGCCT	0.662																																					p.Q476Q		Atlas-SNP	.											.	ARHGEF19	49	.	0			c.G1428A						PASS	.						41	40	40					1																	16532449		2203	4300	6503	SO:0001819	synonymous_variant	128272	exon8			GCGCTCCTGGTAG	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.1428G>A	chr1.hg19:g.16532449C>T		80.0	0.0	.		98.0	23.0	.	NM_153213	A6NJ04|Q5TEV2|Q6PJQ4|Q8N244	Silent	SNP	ENST00000270747.3	hg19	CCDS170.1	.	.	.	.	.	.	.	.	.	.	C	9.573	1.121595	0.20877	.	.	ENSG00000142632	ENST00000449495	.	.	.	4.88	2.62	0.31277	.	.	.	.	.	T	0.59252	0.2180	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55749	-0.8092	4	.	.	.	.	10.0467	0.42190	0.0:0.7963:0.0:0.2037	.	.	.	.	K	165	.	.	R	-	2	0	ARHGEF19	16405036	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.513000	0.45494	1.044000	0.40200	-0.254000	0.11334	AGG	.	.	.	none		0.662	ARHGEF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006289.1	NM_153213		T	16532449	C	T	16532449	2	4	28	1	0	0	0	0	0	0	0	1	902	680	24	2		2	ARHGEF19	1	16532449	Silent	SNP	C	TCGA-5P-A9JV-01A-12D-A42J-10		16532449	232718172	1	1970											
SFPQ	6421	hgsc.bcm.edu	37	chr1	35657046	35657046	+	Missense_Mutation	SNP	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	atcctccgtgatatcagcagGtagattcccaacaaacaacc	14	8	6	13	1	1	2	1	1	0	1	4	2	4	2	4	1	4	2	4	1	5	3			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr1:35657046G>A	ENST00000357214.5	-	2	1011	c.913C>T	c.(913-915)Cct>Tct	p.P305S		NM_005066.2	NP_005057.1	P23246	SFPQ_HUMAN	splicing factor proline/glutamine-rich	305	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				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)				ATATCAGCAGGTAGATTCCCA	0.388			T	TFE3	papillary renal cell																																p.P305S		Atlas-SNP	.		Dom	yes		1	1p34.3	6421	splicing factor proline/glutamine rich(polypyrimidine tract binding protein associated)		E	.	SFPQ	51	.	0			c.C913T						PASS	.						103	104	104					1																	35657046		2203	4300	6503	SO:0001583	missense	6421	exon2			CAGCAGGTAGATT	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.913C>T	chr1.hg19:g.35657046G>A	ENSP00000349748:p.Pro305Ser	126.0	0.0	.		134.0	31.0	.	NM_005066	P30808|Q5SZ71	Missense_Mutation	SNP	ENST00000357214.5	hg19	CCDS388.1	.	.	.	.	.	.	.	.	.	.	G	33	5.223348	0.95139	.	.	ENSG00000116560	ENST00000357214	T	0.08807	3.05	5.26	5.26	0.73747	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.22475	0.0542	L	0.35644	1.08	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00770	-1.1573	10	0.66056	D	0.02	-12.496	18.8921	0.92408	0.0:0.0:1.0:0.0	.	305	P23246	SFPQ_HUMAN	S	305	ENSP00000349748:P305S	ENSP00000349748:P305S	P	-	1	0	SFPQ	35429633	1.000000	0.71417	0.990000	0.47175	0.996000	0.88848	9.807000	0.99171	2.439000	0.82584	0.563000	0.77884	CCT	.	.	.	none		0.388	SFPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011984.4	NM_005066		A	35657046	G	A	35657046	3	1	28	1	0	0	0	0	1	0	0	0	14173	1261	44	2	1246	2	SFPQ	1	35657046	Missense_Mutation	SNP	G	TCGA-5P-A9JV-01A-12D-A42J-10	19124597	35657046	213593575	2	1971											
KIF14	9928	hgsc.bcm.edu	37	chr1	200587031	200587031	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attttgtaggtgttctttttTctaagctcccaaatttattt	8	22	5	6	0	2	0	0	0	2	0	3	0	3	0	1	1	1	3	1	1	4	11			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr1:200587031T>C	ENST00000367350.4	-	2	1259	c.821A>G	c.(820-822)gAa>gGa	p.E274G		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	274	Required for PRC1-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						TGTTCTTTTTTCTAAGCTCCC	0.383																																					p.E274G		Atlas-SNP	.											.	KIF14	156	.	0			c.A821G						PASS	.						203	199	200					1																	200587031		2203	4300	6503	SO:0001583	missense	9928	exon2			CTTTTTTCTAAGC	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.821A>G	chr1.hg19:g.200587031T>C	ENSP00000356319:p.Glu274Gly	79.0	0.0	.		96.0	32.0	.	NM_014875	Q14CI8|Q4G0A5|Q5T1W3	Missense_Mutation	SNP	ENST00000367350.4	hg19	CCDS30963.1	.	.	.	.	.	.	.	.	.	.	T	12.93	2.085732	0.36758	.	.	ENSG00000118193	ENST00000367350	T	0.76186	-1.0	5.24	2.91	0.33838	.	0.398430	0.23777	N	0.044665	T	0.61223	0.2330	L	0.29908	0.895	0.27788	N	0.94291	B	0.15141	0.012	B	0.11329	0.006	T	0.55939	-0.8061	10	0.72032	D	0.01	.	9.4118	0.38496	0.0:0.1458:0.0:0.8542	.	274	Q15058	KIF14_HUMAN	G	274	ENSP00000356319:E274G	ENSP00000356319:E274G	E	-	2	0	KIF14	198853654	0.991000	0.36638	0.168000	0.22838	0.811000	0.45836	2.660000	0.46749	0.321000	0.23259	0.477000	0.44152	GAA	.	.	.	none		0.383	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875		C	200587031	T	C	200587031	3	2	28	1	0	0	0	0	1	0	0	0	8283	1783	62	3	4241	3	KIF14	1	200587031	Missense_Mutation	SNP	T	TCGA-5P-A9JV-01A-12D-A42J-10	164929985	200587031	48663590	3	1972											
ADCY3	109	hgsc.bcm.edu	37	chr2	25062898	25062898	+	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	tcttggtcttctcccgcacaTacctgccaggtacacacaga	9	10	7	15	1	3	1	0	0	3	1	4	1	3	1	3	2	3	2	3	2	2	4			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr2:25062898T>A	ENST00000260600.5	-	6	2050	c.1199A>T	c.(1198-1200)tAt>tTt	p.Y400F	ADCY3_ENST00000405392.1_Missense_Mutation_p.Y11F	NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	400					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)					CTCCCGCACATACCTGCCAGG	0.637																																					p.Y400F		Atlas-SNP	.											.	ADCY3	114	.	0			c.A1199T						PASS	.						85	94	91					2																	25062898		2203	4300	6503	SO:0001583	missense	109	exon6			CGCACATACCTGC	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.1199A>T	chr2.hg19:g.25062898T>A	ENSP00000260600:p.Tyr400Phe	66.0	0.0	.		85.0	23.0	.	NM_004036	B3KT86|Q53T54|Q9UDB1	Missense_Mutation	SNP	ENST00000260600.5	hg19	CCDS1715.1	.	.	.	.	.	.	.	.	.	.	T	18.04	3.535166	0.64972	.	.	ENSG00000138031	ENST00000260600;ENST00000405392;ENST00000415879;ENST00000454027;ENST00000427849;ENST00000435135	T;T;T;T;T	0.80994	-1.44;-1.44;-1.44;-1.44;-1.44	5.05	5.05	0.67936	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.125643	0.56097	D	0.000028	D	0.83266	0.5217	L	0.33245	0.995	0.37564	D	0.919179	D;D;D	0.76494	0.999;0.999;0.992	D;D;D	0.79108	0.992;0.992;0.966	D	0.84410	0.0565	10	0.36615	T	0.2	.	13.0155	0.58754	0.0:0.0:0.0:1.0	.	400;400;11	B7ZLX9;O60266;B3KT86	.;ADCY3_HUMAN;.	F	400;11;375;26;156;350	ENSP00000260600:Y400F;ENSP00000384484:Y11F;ENSP00000410120:Y26F;ENSP00000399275:Y156F;ENSP00000389799:Y350F	ENSP00000260600:Y400F	Y	-	2	0	ADCY3	24916402	1.000000	0.71417	0.995000	0.50966	0.925000	0.55904	3.945000	0.56637	1.885000	0.54596	0.448000	0.29417	TAT	.	.	.	none		0.637	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2			A	25062898	T	A	25062898	3	1	28	1	0	0	0	0	1	0	0	0	295	1406	49	5	2299	5	ADCY3	2	25062898	Missense_Mutation	SNP	T	TCGA-5P-A9JV-01A-12D-A42J-10		25062898	218136475	4	1973											
GTF2A1L	11036	hgsc.bcm.edu	37	chr2	48896944	48896944	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caagtagatggaagcggtgaTacatcttccaatgaagaaat	16	9	10	6	1	1	4	0	2	1	2	2	5	2	5	1	2	2	1	1	2	7	3			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr2:48896944T>C	ENST00000403751.3	+	7	1099	c.1062T>C	c.(1060-1062)gaT>gaC	p.D354D	STON1-GTF2A1L_ENST00000394751.3_Silent_p.D1011D|STON1-GTF2A1L_ENST00000405008.1_Silent_p.D1058D|LHCGR_ENST00000420913.3_5'Flank|GTF2A1L_ENST00000430487.2_Silent_p.D320D|STON1-GTF2A1L_ENST00000394754.1_Silent_p.D1058D|STON1-GTF2A1L_ENST00000402114.2_Silent_p.D1058D|STON1-GTF2A1L_ENST00000309827.2_Silent_p.D1058D	NM_006872.3	NP_006863.2	Q9UNN4	TF2AY_HUMAN	general transcription factor IIA, 1-like	354					cognition (GO:0050890)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			lung(7)	7		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GAAGCGGTGATACATCTTCCA	0.373																																					p.D1058D		Atlas-SNP	.											.	STON1-GTF2A1L	180	.	0			c.T3174C						PASS	.						109	116	114					2																	48896944		2203	4300	6503	SO:0001819	synonymous_variant	286749	exon9			CGGTGATACATCT	AF106857	CCDS46281.1, CCDS54359.1	2p16.3	2007-08-02			ENSG00000242441	ENSG00000242441			30727	protein-coding gene	gene with protein product	"TFIIA alpha/beta like factor"	605358				10364255, 11889132, 16525715	Standard	NM_006872		Approved	ALF		Q9UNN4	OTTHUMG00000152038	ENST00000403751.3:c.1062T>C	chr2.hg19:g.48896944T>C		203.0	0.0	.		199.0	36.0	.	NM_001198593	B4DY14|Q53FD9|Q5D050	Silent	SNP	ENST00000403751.3	hg19	CCDS46281.1																																																																																			.	.	.	none		0.373	GTF2A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323852.4	NM_006872		C	48896944	T	C	48896944	2	2	28	1	0	0	0	0	0	0	0	1	6860	1403	49	3		3	GTF2A1L	2	48896944	Silent	SNP	T	TCGA-5P-A9JV-01A-12D-A42J-10	23834046	48896944	194302429	5	1974											
ALMS1	7840	hgsc.bcm.edu	37	chr2	73613036	73613036	+	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	catggccgggcgagctggagGaggaggaggaggaggaggag	10	2	24	5	2	0	0	0	0	0	0	0	9	0	8	1	10	1	1	1	10	0	0	rs61156725|rs72319667|rs3074417	byFrequency	TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr2:73613036G>C	ENST00000264448.6	+	1	151	c.40G>C	c.(40-42)Gag>Cag	p.E14Q	ALMS1_ENST00000409009.1_Missense_Mutation_p.E14Q|ALMS1_ENST00000377715.1_Missense_Mutation_p.E14Q	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	14	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CGAGCTggaggaggaggagga	0.692																																					p.E14Q		Atlas-SNP	.											.	ALMS1	384	.	1	Deletion - In frame(1)	ovary(1)	c.G40C						PASS	.						3	4	4					2																	73613036		1509	3234	4743	SO:0001583	missense	7840	exon1			CTGGAGGAGGAGG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.40G>C	chr2.hg19:g.73613036G>C	ENSP00000264448:p.Glu14Gln	177.0	0.0	.		255.0	13.0	.	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.731519	0.48939	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.26373	2.4;2.61;1.74	3.19	3.19	0.36642	.	0.259523	0.20097	U	0.099311	T	0.32436	0.0829	N	0.19112	0.55	0.22317	N	0.999202	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.03493	-1.1031	10	0.87932	D	0	.	10.1262	0.42652	0.0:0.0:1.0:0.0	.	14;14	B8ZZJ3;Q8TCU4	.;ALMS1_HUMAN	Q	14	ENSP00000386627:E14Q;ENSP00000264448:E14Q;ENSP00000366944:E14Q	ENSP00000264448:E14Q	E	+	1	0	ALMS1	73466544	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	2.034000	0.41145	2.070000	0.61991	0.484000	0.47621	GAG	.	.	.	none		0.692	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		C	73613036	G	C	73613036	3	2	28	1	0	0	0	0	1	0	0	0	535	1175	41	4	42	4	ALMS1	2	73613036	Missense_Mutation	SNP	G	TCGA-5P-A9JV-01A-12D-A42J-10	24716092	73613036	169586337	6	1975											
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125367417	125367417	+	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	cgaggtgtacaggcaccaggGgaatacagccggcttcttct	9	8	13	11	2	2	0	0	0	2	0	2	2	2	1	2	5	3	3	2	5	3	4			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr2:125367417G>A	ENST00000431078.1	+	12	2157	c.1793G>A	c.(1792-1794)gGg>gAg	p.G598E		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	598	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		AGGCACCAGGGGAATACAGCC	0.532																																					p.G598E		Atlas-SNP	.											.	CNTNAP5	405	.	0			c.G1793A						PASS	.						72	71	71					2																	125367417		1870	4106	5976	SO:0001583	missense	129684	exon12			ACCAGGGGAATAC	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.1793G>A	chr2.hg19:g.125367417G>A	ENSP00000399013:p.Gly598Glu	68.0	0.0	.		71.0	17.0	.	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	hg19	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.828320	0.90955	.	.	ENSG00000155052	ENST00000431078	T	0.21734	1.99	5.66	5.66	0.87406	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (2);	0.000000	0.50627	D	0.000105	T	0.56645	0.1999	M	0.89785	3.06	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.63664	-0.6586	10	0.72032	D	0.01	.	18.6671	0.91495	0.0:0.0:1.0:0.0	.	598	Q8WYK1	CNTP5_HUMAN	E	598	ENSP00000399013:G598E	ENSP00000399013:G598E	G	+	2	0	CNTNAP5	125083887	1.000000	0.71417	0.993000	0.49108	0.731000	0.41821	8.884000	0.92432	2.826000	0.97356	0.655000	0.94253	GGG	.	.	.	none		0.532	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			A	125367417	G	A	125367417	3	1	28	1	0	0	0	0	1	0	0	0	3652	1232	43	2	1839	2	CNTNAP5	2	125367417	Missense_Mutation	SNP	G	TCGA-5P-A9JV-01A-12D-A42J-10	51754381	125367417	117831956	7	1976											
NGEF	25791	hgsc.bcm.edu	37	chr2	233785268	233785268	+	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	cgatttcttggagagtcgatTtatctcggtattcctgatac	8	16	9	8	3	2	2	0	1	2	1	5	5	3	2	1	2	1	1	1	2	3	7			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr2:233785268T>A	ENST00000264051.3	-	5	832	c.554A>T	c.(553-555)aAa>aTa	p.K185I	NGEF_ENST00000373552.4_Missense_Mutation_p.K93I|NGEF_ENST00000409079.1_Missense_Mutation_p.K93I	NM_019850.2	NP_062824.2	Q8N5V2	NGEF_HUMAN	neuronal guanine nucleotide exchange factor	185	Regulatory region; modulates activity toward RHOA, RAC1 and CDC42. {ECO:0000250}.				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)		GAGAGTCGATTTATCTCGGTA	0.443																																					p.K185I		Atlas-SNP	.											.	NGEF	198	.	0			c.A554T						PASS	.						84	90	88					2																	233785268		2203	4300	6503	SO:0001583	missense	25791	exon5			GTCGATTTATCTC	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.554A>T	chr2.hg19:g.233785268T>A	ENSP00000264051:p.Lys185Ile	55.0	0.0	.		56.0	9.0	.	NM_019850	B4DMB8|B9A045|E9PC42|Q53QQ4|Q53ST7|Q6GMQ5|Q9NQD6	Missense_Mutation	SNP	ENST00000264051.3	hg19	CCDS2500.1	.	.	.	.	.	.	.	.	.	.	T	14.55	2.569333	0.45798	.	.	ENSG00000066248	ENST00000264051;ENST00000373552;ENST00000541023;ENST00000409079	T;T	0.72725	-0.5;-0.68	5.01	5.01	0.66863	.	0.052813	0.85682	D	0.000000	T	0.75295	0.3830	L	0.29908	0.895	0.80722	D	1	B;D;P	0.71674	0.323;0.998;0.952	B;D;B	0.78314	0.079;0.991;0.438	T	0.74934	-0.3495	10	0.36615	T	0.2	-13.8527	14.714	0.69254	0.0:0.0:0.0:1.0	.	93;93;185	E9PC42;B4DMB8;Q8N5V2	.;.;NGEF_HUMAN	I	185;93;75;93	ENSP00000264051:K185I;ENSP00000362653:K93I	ENSP00000264051:K185I	K	-	2	0	NGEF	233493512	1.000000	0.71417	0.997000	0.53966	0.981000	0.71138	4.295000	0.59049	1.887000	0.54652	0.402000	0.26972	AAA	.	.	.	none		0.443	NGEF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257051.2	XM_044799		A	233785268	T	A	233785268	3	1	28	1	0	0	0	0	1	0	0	0	10401	1841	64	5	1622	5	NGEF	2	233785268	Missense_Mutation	SNP	T	TCGA-5P-A9JV-01A-12D-A42J-10	108417851	233785268	9414105	8	1977											
ZNF385D	79750	hgsc.bcm.edu	37	chr3	21465455	21465455	+	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	tcttgcaaaatgacactcacCcccagtggatgtgctgtctt	9	12	8	12	0	3	1	1	1	2	0	3	2	3	2	2	1	2	2	2	1	2	2			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr3:21465455C>A	ENST00000281523.2	-	7	1472	c.954G>T	c.(952-954)ggG>ggT	p.G318G		NM_024697.2	NP_078973.1	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	318						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						TGACACTCACCCCCAGTGGAT	0.453																																					p.G318G		Atlas-SNP	.											.	ZNF385D	93	.	0			c.G954T						PASS	.						141	141	141					3																	21465455		2203	4300	6503	SO:0001630	splice_region_variant	79750	exon7			ACTCACCCCCAGT	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.954+1G>T	chr3.hg19:g.21465455C>A		122.0	0.0	.		141.0	30.0	.	NM_024697		Silent	SNP	ENST00000281523.2	hg19	CCDS2636.1																																																																																			.	.	.	none		0.453	ZNF385D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252884.1	NM_024697	Silent	A	21465455	C	A	21465455	5	1	28	1	0	0	0	0	0	0	1	0	17890	637	22	4	241	4	ZNF385D	3	21465455	Splice_Site	SNP	C	TCGA-5P-A9JV-01A-12D-A42J-10		21465455	176556975	9	1978											
ZNF197	10168	hgsc.bcm.edu	37	chr3	44671000	44671000	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggctgtggccctggtagaGgagctgcagaaagaccttga	10	7	16	8	0	0	4	0	1	0	3	0	6	0	5	2	4	2	4	2	4	2	2			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr3:44671000G>A	ENST00000396058.1	+	1	521	c.354G>A	c.(352-354)gaG>gaA	p.E118E	ZNF197_ENST00000383745.2_Silent_p.E118E|RP11-944L7.4_ENST00000457331.1_RNA|ZNF197_ENST00000344387.4_Silent_p.E118E|ZNF197_ENST00000383744.4_Silent_p.E118E			O14709	ZN197_HUMAN	zinc finger protein 197	118	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(1)	25				KIRC - Kidney renal clear cell carcinoma(197;0.0478)|Kidney(197;0.0598)		CCCTGGTAGAGGAGCTGCAGA	0.567																																					p.E118E		Atlas-SNP	.											.	ZNF197	81	.	0			c.G354A						PASS	.						43	43	43					3																	44671000		2203	4300	6503	SO:0001819	synonymous_variant	10168	exon2			GGTAGAGGAGCTG	AF011573	CCDS2717.1, CCDS33743.1	3p21	2013-01-09	2003-10-07		ENSG00000186448	ENSG00000186448		"Zinc fingers, C2H2-type", "-", "-", "-"	12988	protein-coding gene	gene with protein product			"zinc finger protein 166"	ZNF166		9380504, 8353497	Standard	XM_005264783		Approved	P18, D3S1363E, ZKSCAN9, ZSCAN41	uc003cnm.3	O14709	OTTHUMG00000133089	ENST00000396058.1:c.354G>A	chr3.hg19:g.44671000G>A		181.0	0.0	.		255.0	55.0	.	NM_001024855	B2RAH8|Q86VG0	Silent	SNP	ENST00000396058.1	hg19	CCDS2717.1																																																																																			.	.	.	none		0.567	ZNF197-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256747.4	NM_006991		A	44671000	G	A	44671000	2	1	28	1	0	0	0	0	0	0	0	1	17771	991	35	2		2	ZNF197	3	44671000	Silent	SNP	G	TCGA-5P-A9JV-01A-12D-A42J-10	23205545	44671000	153351430	10	1979											
TWF2	11344	hgsc.bcm.edu	37	chr3	52266117	52266117	+	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	agcggcctactggctcctgcGaggcacccagcacgagctgc	7	5	13	16	3	0	0	0	0	0	0	1	2	1	0	3	3	6	4	3	3	1	1			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr3:52266117G>A	ENST00000305533.5	-	3	368	c.125C>T	c.(124-126)tCg>tTg	p.S42L	TLR9_ENST00000597542.1_5'UTR|TLR9_ENST00000494383.1_5'Flank|TWF2_ENST00000499914.2_Missense_Mutation_p.S42L	NM_007284.3	NP_009215.1	Q6IBS0	TWF2_HUMAN	twinfilin actin-binding protein 2	42	ADF-H 1. {ECO:0000255|PROSITE- ProRule:PRU00599}.				barbed-end actin filament capping (GO:0051016)|cell projection organization (GO:0030030)|cellular response to growth factor stimulus (GO:0071363)|cellular response to retinoic acid (GO:0071300)|negative regulation of actin filament polymerization (GO:0030837)|positive regulation of axon extension (GO:0045773)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of microvillus length (GO:0032532)|sequestering of actin monomers (GO:0042989)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|myofibril (GO:0030016)|perinuclear region of cytoplasm (GO:0048471)|stereocilium (GO:0032420)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|poly(A) RNA binding (GO:0044822)|protein kinase C binding (GO:0005080)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|stomach(1)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;2.43e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		TGGCTCCTGCGAGGCACCCAG	0.697											OREG0015610	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S42L		Atlas-SNP	.											.	TWF2	33	.	0			c.C125T						PASS	.						28	28	28					3																	52266117		2200	4297	6497	SO:0001583	missense	11344	exon3			TCCTGCGAGGCAC	Y17169	CCDS2849.1	3p21.1	2013-04-25	2013-04-25	2006-11-13	ENSG00000247596	ENSG00000247596			9621	protein-coding gene	gene with protein product		607433	"protein tyrosine kinase 9-like (A6-related protein)", "PTK9L protein tyrosine kinase 9-like (A6-related protein)", "twinfilin, actin-binding protein, homolog 2 (Drosophila)"	PTK9L		10406962, 12807912	Standard	NM_007284		Approved	A6RP, A6r		Q6IBS0	OTTHUMG00000158105	ENST00000305533.5:c.125C>T	chr3.hg19:g.52266117G>A	ENSP00000303908:p.Ser42Leu	85.0	0.0	.	983	96.0	6.0	.	NM_007284	Q9Y3F5	Missense_Mutation	SNP	ENST00000305533.5	hg19	CCDS2849.1	.	.	.	.	.	.	.	.	.	.	G	12.26	1.883869	0.33255	.	.	ENSG00000247596	ENST00000305533;ENST00000499914	T;T	0.28454	1.61;1.61	5.61	1.31	0.21738	Actin-binding, cofilin/tropomyosin type (3);	.	.	.	.	T	0.11452	0.0279	N	0.17082	0.46	0.32664	N	0.517723	B;P	0.35542	0.309;0.508	B;B	0.24701	0.036;0.055	T	0.23261	-1.0193	9	0.10902	T	0.67	.	3.575	0.07932	0.2903:0.0:0.4331:0.2766	.	42;42	D6RG15;Q6IBS0	.;TWF2_HUMAN	L	42	ENSP00000303908:S42L;ENSP00000426464:S42L	ENSP00000303908:S42L	S	-	2	0	TWF2	52241157	0.998000	0.40836	0.818000	0.32626	0.944000	0.59088	2.573000	0.46007	0.733000	0.32492	0.455000	0.32223	TCG	.	.	.	none		0.697	TWF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350199.2			A	52266117	G	A	52266117	3	1	28	1	0	0	0	0	1	0	0	0	16794	1059	37	1	952	1	TWF2	3	52266117	Missense_Mutation	SNP	G	TCGA-5P-A9JV-01A-12D-A42J-10	7595117	52266117	145756313	11	1980											
PRR23B	389151	hgsc.bcm.edu	37	chr3	138739039	138739039	+	Nonsense_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	tcggggtccgcgtcctcctcGtaggcctcttcctgggcggc	1	10	14	16	5	1	0	0	0	1	0	7	0	5	0	5	5	0	1	5	5	1	2			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr3:138739039G>C	ENST00000329447.5	-	1	729	c.465C>G	c.(463-465)taC>taG	p.Y155*	MRPS22_ENST00000495075.1_Intron	NM_001013650.2	NP_001013672.1	Q6ZRT6	PR23B_HUMAN	proline rich 23B	155										NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CGTCCTCCTCGTAGGCCTCTT	0.632																																					p.Y155X		Atlas-SNP	.											.	PRR23B	56	.	0			c.C465G						PASS	.						38	44	42					3																	138739039		2203	4300	6503	SO:0001587	stop_gained	389151	exon1			CTCCTCGTAGGCC	BC137146	CCDS33868.1	3q22.3	2014-06-03			ENSG00000184814	ENSG00000184814			33764	protein-coding gene	gene with protein product							Standard	NM_001013650		Approved	FLJ46116	uc003esy.1	Q6ZRT6	OTTHUMG00000160633	ENST00000329447.5:c.465C>G	chr3.hg19:g.138739039G>C	ENSP00000328768:p.Tyr155*	153.0	0.0	.		175.0	39.0	.	NM_001013650	B2RNV9	Nonsense_Mutation	SNP	ENST00000329447.5	hg19	CCDS33868.1	.	.	.	.	.	.	.	.	.	.	G	19.53	3.845131	0.71603	.	.	ENSG00000184814	ENST00000329447	.	.	.	2.41	-3.3	0.05003	.	3.020250	0.01139	N	0.006140	.	.	.	.	.	.	0.58432	D	0.999995	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.8996	0.29727	0.6481:0.0:0.3519:0.0	.	.	.	.	X	155	.	ENSP00000328768:Y155X	Y	-	3	2	PRR23B	140221729	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	-1.259000	0.02861	-0.945000	0.03681	0.456000	0.33151	TAC	.	.	.	none		0.632	PRR23B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361501.1	NM_001013650		C	138739039	G	C	138739039	4	2	28	1	0	0	0	0	0	1	0	0	12605	1140	40	4	336	4	PRR23B	3	138739039	Nonsense_Mutation	SNP	G	TCGA-5P-A9JV-01A-12D-A42J-10	86472922	138739039	59283391	12	1981											
FAM193A	8603	hgsc.bcm.edu	37	chr4	2696771	2696771	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaggacagctgctctgagcAcagctccagcacctcgacct	9	7	10	15	1	1	2	0	2	1	0	3	4	2	3	3	1	5	5	3	1	0	0			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr4:2696771A>G	ENST00000324666.5	+	15	2669	c.2318A>G	c.(2317-2319)cAc>cGc	p.H773R	FAM193A_ENST00000382839.3_Missense_Mutation_p.H773R|FAM193A_ENST00000502458.1_Missense_Mutation_p.H795R|FAM193A_ENST00000545951.1_Missense_Mutation_p.H773R|FAM193A_ENST00000505311.1_Missense_Mutation_p.H773R	NM_001256666.1	NP_001243595.1	P78312	F193A_HUMAN	family with sequence similarity 193, member A	773										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						TGCTCTGAGCACAGCTCCAGC	0.597																																					p.H795R		Atlas-SNP	.											.	FAM193A	103	.	0			c.A2384G						PASS	.						101	71	81					4																	2696771		2203	4300	6503	SO:0001583	missense	8603	exon16			CTGAGCACAGCTC	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.2318A>G	chr4.hg19:g.2696771A>G	ENSP00000324587:p.His773Arg	78.0	0.0	.		76.0	15.0	.	NM_001256667	B7ZM85|B9EGR0|E9PFA1|O43607|P78311|P78313|Q9UEG8	Missense_Mutation	SNP	ENST00000324666.5	hg19	CCDS58875.1	.	.	.	.	.	.	.	.	.	.	A	18.58	3.655329	0.67586	.	.	ENSG00000125386	ENST00000382839;ENST00000324666;ENST00000545951;ENST00000502458;ENST00000513350	T;T;T;T;T	0.39997	1.05;1.05;1.05;1.05;1.05	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.46190	0.1380	N	0.20685	0.6	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.999	D;D;D;D;D	0.75484	0.986;0.986;0.986;0.961;0.986	T	0.30851	-0.9964	10	0.10902	T	0.67	-19.6886	14.9019	0.70687	1.0:0.0:0.0:0.0	.	773;795;773;795;773	B9EGR0;E9PFA1;P78312;B7ZM85;P78312-2	.;.;F193A_HUMAN;.;.	R	773;773;773;795;627	ENSP00000372290:H773R;ENSP00000324587:H773R;ENSP00000443617:H773R;ENSP00000427505:H795R;ENSP00000427260:H627R	ENSP00000324587:H773R	H	+	2	0	FAM193A	2666569	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.338000	0.79269	2.108000	0.64289	0.533000	0.62120	CAC	.	.	.	none		0.597	FAM193A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360903.1	NM_003704		G	2696771	A	G	2696771	3	3	28	1	0	0	0	0	1	0	0	0	5528	159	6	3	2368	3	FAM193A	4	2696771	Missense_Mutation	SNP	A	TCGA-5P-A9JV-01A-12D-A42J-10		2696771	188457505	13	1982											
BOD1L	259282	hgsc.bcm.edu	37	chr4	13605661	13605662	+	Frame_Shift_Ins	INS	-	-	T																															tcaactttagacttacgctgINStttttctgagtcattttctt																										TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr4:13605661_13605662insT	ENST00000040738.5	-	10	2997_2998	c.2862_2863insA	c.(2860-2865)aaacagfs	p.Q955fs		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	955	Lys-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)										GACTTACGCTGTTTTTCTGAGT	0.386																																					p.Q955fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.2863_2864insA						PASS	.																																			SO:0001589	frameshift_variant	259282	exon10			.	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.2863dupA	chr4.hg19:g.13605666_13605666dupT	ENSP00000040738:p.Gln955fs	100.0	0.0	0		101.0	24.0	0.237624	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Frame_Shift_Ins	INS	ENST00000040738.5	hg19	CCDS3411.2																																																																																			.	.	.	none		0.386	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		T	13605662	-	T	13605661	7	5	28	1	0	1	1	0	0	0	0	0	1483	1386	48	0	6360	0	BOD1L	4	13605661	Frame_Shift_Ins	INS	-	TCGA-5P-A9JV-01A-12D-A42J-10	10908890	13605661	177548615	14	1983											
PAPSS1	9061	hgsc.bcm.edu	37	chr4	108615096	108615096	+	Missense_Mutation	SNP	A	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	catccagagtgtagcatggaAtaccatgacaaaccaggtac	15	7	9	10	0	0	2	0	1	0	1	1	3	1	3	3	2	4	3	3	2	5	3			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr4:108615096A>C	ENST00000265174.4	-	3	514	c.242T>G	c.(241-243)aTt>aGt	p.I81S	PAPSS1_ENST00000511304.1_Intron	NM_005443.4	NP_005434.4	O43252	PAPS1_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 1	81					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)		GTAGCATGGAATACCATGACA	0.443																																					p.I81S		Atlas-SNP	.											.	PAPSS1	57	.	0			c.T242G						PASS	.						114	103	107					4																	108615096		2203	4300	6503	SO:0001583	missense	9061	exon3			CATGGAATACCAT	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.242T>G	chr4.hg19:g.108615096A>C	ENSP00000265174:p.Ile81Ser	55.0	0.0	.		64.0	13.0	.	NM_005443	O43841|O75332|Q96FB1|Q96TF4|Q9P1P9|Q9UE98	Missense_Mutation	SNP	ENST00000265174.4	hg19	CCDS3676.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.718287	0.89205	.	.	ENSG00000138801	ENST00000265174	T	0.77098	-1.07	5.67	5.67	0.87782	Adenylylsulphate kinase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.89801	0.6820	M	0.88512	2.96	0.80722	D	1	D	0.67145	0.996	D	0.91635	0.999	D	0.91416	0.5155	10	0.62326	D	0.03	-29.0903	15.9108	0.79473	1.0:0.0:0.0:0.0	.	81	O43252	PAPS1_HUMAN	S	81	ENSP00000265174:I81S	ENSP00000265174:I81S	I	-	2	0	PAPSS1	108834545	1.000000	0.71417	0.972000	0.41901	0.985000	0.73830	8.789000	0.91839	2.156000	0.67533	0.454000	0.30748	ATT	.	.	.	none		0.443	PAPSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253946.2			C	108615096	A	C	108615096	3	2	28	1	0	0	0	0	1	0	0	0	11441	101	4	5	1672	5	PAPSS1	4	108615096	Missense_Mutation	SNP	A	TCGA-5P-A9JV-01A-12D-A42J-10	95009435	108615096	82539180	15	1984											
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123207818	123207818	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaaccttccccctgttaccAtgtcagggaaatatataatg	12	13	6	10	0	1	0	1	0	0	0	2	1	2	1	4	1	2	1	4	1	6	6			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr4:123207818A>G	ENST00000264501.4	+	53	9533	c.9160A>G	c.(9160-9162)Atg>Gtg	p.M3054V	KIAA1109_ENST00000455637.1_Missense_Mutation_p.M3054V|KIAA1109_ENST00000388738.3_Missense_Mutation_p.M3054V			Q2LD37	K1109_HUMAN	KIAA1109	3054					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CCCTGTTACCATGTCAGGGAA	0.403																																					p.M3054V		Atlas-SNP	.											.	KIAA1109	424	.	0			c.A9160G						PASS	.						148	139	142					4																	123207818		1896	4124	6020	SO:0001583	missense	84162	exon51			GTTACCATGTCAG	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.9160A>G	chr4.hg19:g.123207818A>G	ENSP00000264501:p.Met3054Val	233.0	0.0	.		256.0	58.0	.	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.80|10.80	1.453953|1.453953	0.26161|0.26161	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000419325|ENST00000264501;ENST00000388738;ENST00000455637	.|T;T;T	.|0.18502	.|2.8;2.8;2.21	5.63|5.63	5.63|5.63	0.86233|0.86233	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.17066|0.17066	0.0410|0.0410	N|N	0.11560|0.11560	0.145|0.145	0.47511|0.47511	D|D	0.999445|0.999445	.|B;P	.|0.40332	.|0.452;0.713	.|P;P	.|0.54815	.|0.557;0.761	T|T	0.03443|0.03443	-1.1036|-1.1036	5|10	.|0.02654	.|T	.|1	.|.	15.8352|15.8352	0.78793|0.78793	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|3054;3054	.|Q2LD37-6;Q2LD37	.|.;K1109_HUMAN	R|V	1011|3054	.|ENSP00000264501:M3054V;ENSP00000373390:M3054V;ENSP00000389925:M3054V	.|ENSP00000264501:M3054V	H|M	+|+	2|1	0|0	KIAA1109|KIAA1109	123427268|123427268	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.975000|0.975000	0.68041|0.68041	8.815000|8.815000	0.91973|0.91973	2.149000|2.149000	0.67028|0.67028	0.528000|0.528000	0.53228|0.53228	CAT|ATG	.	.	.	none		0.403	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		G	123207818	A	G	123207818	3	3	28	1	0	0	0	0	1	0	0	0	8215	217	8	3	9362	3	KIAA1109	4	123207818	Missense_Mutation	SNP	A	TCGA-5P-A9JV-01A-12D-A42J-10	14592722	123207818	67946458	16	1985											
FAT4	79633	hgsc.bcm.edu	37	chr4	126411503	126411503	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgggctgtgcctgccatcgTgggcagctgcgcaaccgtct	4	9	15	13	3	1	0	0	0	1	0	2	0	1	0	3	2	5	4	3	2	1	0			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr4:126411503T>C	ENST00000394329.3	+	17	13539	c.13526T>C	c.(13525-13527)gTg>gCg	p.V4509A	FAT4_ENST00000335110.5_Missense_Mutation_p.V2750A	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4509					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						CCTGCCATCGTGGGCAGCTGC	0.572																																					p.V4509A		Atlas-SNP	.											.	FAT4	1752	.	0			c.T13526C						PASS	.						67	67	67					4																	126411503		2203	4300	6503	SO:0001583	missense	79633	exon17			CCATCGTGGGCAG	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.13526T>C	chr4.hg19:g.126411503T>C	ENSP00000377862:p.Val4509Ala	54.0	0.0	.		75.0	19.0	.	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	T	17.80	3.477797	0.63849	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.76968	-0.82;-1.06	5.17	4.0	0.46444	.	0.000000	0.31233	U	0.008019	T	0.71178	0.3309	L	0.58583	1.82	0.48632	D	0.999688	B;B;B	0.20780	0.041;0.048;0.041	B;B;B	0.17433	0.012;0.018;0.012	T	0.68697	-0.5340	10	0.38643	T	0.18	.	9.6102	0.39659	0.0:0.0821:0.0:0.9179	.	2750;4509;4508	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	A	4509;2750	ENSP00000377862:V4509A;ENSP00000335169:V2750A	ENSP00000335169:V2750A	V	+	2	0	FAT4	126630953	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.897000	0.63231	1.941000	0.56285	0.459000	0.35465	GTG	.	.	.	none		0.572	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		C	126411503	T	C	126411503	3	2	28	1	0	0	0	0	1	0	0	0	5699	1696	59	3	13592	3	FAT4	4	126411503	Missense_Mutation	SNP	T	TCGA-5P-A9JV-01A-12D-A42J-10	3203685	126411503	64742773	17	1986											
TDO2	6999	hgsc.bcm.edu	37	chr4	156831319	156831319	+	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	aaggagaagaaaatgaactgCtacttaaatctgagcaggaa	19	7	10	5	0	1	4	0	2	1	2	1	6	1	5	0	2	4	2	0	2	9	2			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr4:156831319C>G	ENST00000536354.2	+	6	638	c.574C>G	c.(574-576)Cta>Gta	p.L192V		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)		AAATGAACTGCTACTTAAATC	0.333																																					p.L192V	Colon(57;928 1036 2595 6946 26094)	Atlas-SNP	.											.	TDO2	51	.	0			c.C574G						PASS	.						73	78	76					4																	156831319		2203	4300	6503	SO:0001583	missense	6999	exon6			GAACTGCTACTTA		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.574C>G	chr4.hg19:g.156831319C>G	ENSP00000444788:p.Leu192Val	127.0	0.0	.		114.0	23.0	.	NM_005651		Missense_Mutation	SNP	ENST00000536354.2	hg19	CCDS34086.1	.	.	.	.	.	.	.	.	.	.	C	8.259	0.810699	0.16537	.	.	ENSG00000151790	ENST00000536354	.	.	.	4.92	4.06	0.47325	.	0.069633	0.64402	D	0.000014	T	0.46756	0.1409	L	0.35288	1.05	0.53688	D	0.999978	B	0.31009	0.303	B	0.35727	0.209	T	0.33548	-0.9864	8	.	.	.	-10.8364	11.2334	0.48925	0.0:0.8473:0.0:0.1527	.	192	P48775	T23O_HUMAN	V	192	.	.	L	+	1	2	TDO2	157050769	0.987000	0.35691	0.113000	0.21522	0.342000	0.28953	1.693000	0.37742	1.174000	0.42811	0.644000	0.83932	CTA	.	.	.	none		0.333	TDO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366209.3	NM_005651		G	156831319	C	G	156831319	3	3	28	1	0	0	0	0	1	0	0	0	15739	796	28	4	596	4	TDO2	4	156831319	Missense_Mutation	SNP	C	TCGA-5P-A9JV-01A-12D-A42J-10	30419816	156831319	34322957	18	1987											
PRKAA1	5562	hgsc.bcm.edu	37	chr5	40764924	40764924	+	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	tatcatttggtcgactttgaCttctaattcctaaatgccat	10	17	5	9	1	2	1	1	1	1	0	4	2	3	1	2	1	1	0	2	1	4	7			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr5:40764924C>A	ENST00000397128.2	-	7	1246	c.1238G>T	c.(1237-1239)aGt>aTt	p.S413I	PRKAA1_ENST00000354209.3_Missense_Mutation_p.S428I	NM_006251.5|NM_206907.3	NP_006242.5|NP_996790.3	Q13131	AAPK1_HUMAN	protein kinase, AMP-activated, alpha 1 catalytic subunit	413					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)	p.S428T(1)		breast(1)	1					Acetylsalicylic acid(DB00945)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Phenformin(DB00914)	TCGACTTTGACTTCTAATTCC	0.358																																					p.S428I		Atlas-SNP	.											PRKAA1,NS,carcinoma,0,2	PRKAA1	27	.	1	Substitution - Missense(1)	lung(1)	c.G1283T						PASS	.						123	108	113					5																	40764924		1853	4113	5966	SO:0001583	missense	5562	exon8			CTTTGACTTCTAA		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.1238G>T	chr5.hg19:g.40764924C>A	ENSP00000380317:p.Ser413Ile	116.0	0.0	.		124.0	28.0	.	NM_206907	A8MTQ6|B2R7E1|O00286|Q5D0E1|Q86VS1|Q9UNQ4	Missense_Mutation	SNP	ENST00000397128.2	hg19	CCDS3932.2	.	.	.	.	.	.	.	.	.	.	C	25.7	4.668512	0.88348	.	.	ENSG00000132356	ENST00000397128;ENST00000354209	D;D	0.84070	-1.67;-1.8	6.01	6.01	0.97437	.	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	M	0.91663	3.23	0.80722	D	1	D;D	0.71674	0.996;0.998	P;D	0.66602	0.883;0.945	D	0.93633	0.6958	10	0.87932	D	0	-15.1947	20.5211	0.99222	0.0:1.0:0.0:0.0	.	413;428	Q13131;Q13131-2	AAPK1_HUMAN;.	I	413;428	ENSP00000380317:S413I;ENSP00000346148:S428I	ENSP00000346148:S428I	S	-	2	0	AC008810.1	40800681	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.861000	0.98227	0.650000	0.86243	AGT	.	.	.	none		0.358	PRKAA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253833.2	NM_006251		A	40764924	C	A	40764924	3	1	28	1	0	0	0	0	1	0	0	0	12503	565	20	4	453	4	PRKAA1	5	40764924	Missense_Mutation	SNP	C	TCGA-5P-A9JV-01A-12D-A42J-10		40764924	140150336	19	1988											
TTC37	9652	hgsc.bcm.edu	37	chr5	94814018	94814018	+	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	cagacttttaatgcaagtagTgctagtctcaacagacttga	13	12	8	8	0	1	3	1	1	1	2	2	3	1	3	0	0	3	3	0	0	5	5			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr5:94814018T>A	ENST00000358746.2	-	40	4639	c.4341A>T	c.(4339-4341)gcA>gcT	p.A1447A		NM_014639.3	NP_055454.1	Q6PGP7	TTC37_HUMAN	tetratricopeptide repeat domain 37	1447						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						ATGCAAGTAGTGCTAGTCTCA	0.378																																					p.A1447A		Atlas-SNP	.											.	TTC37	128	.	0			c.A4341T						PASS	.						89	81	84					5																	94814018		2203	4300	6503	SO:0001819	synonymous_variant	9652	exon40			AAGTAGTGCTAGT	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.4341A>T	chr5.hg19:g.94814018T>A		156.0	0.0	.		146.0	32.0	.	NM_014639	O15077|Q6PJI3	Silent	SNP	ENST00000358746.2	hg19	CCDS4072.1																																																																																			.	.	.	none		0.378	TTC37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241651.1	NM_014639		A	94814018	T	A	94814018	2	1	28	1	0	0	0	0	0	0	0	1	16717	1683	59	5		5	TTC37	5	94814018	Silent	SNP	T	TCGA-5P-A9JV-01A-12D-A42J-10	54049094	94814018	86101242	20	1989											
SPATA9	83890	hgsc.bcm.edu	37	chr5	94994606	94994606	+	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	accttcttcagcacagcattAacacagactgcctatacaat	14	10	4	13	0	2	1	1	0	1	1	2	1	2	1	2	0	5	2	2	0	4	5			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr5:94994606A>T	ENST00000274432.8	-	5	627	c.486T>A	c.(484-486)gtT>gtA	p.V162V	SPATA9_ENST00000477047.2_5'UTR|RFESD_ENST00000508206.1_Intron	NM_031952.3	NP_114158.2	Q9BWV2	SPAT9_HUMAN	spermatogenesis associated 9	162					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)		GCACAGCATTAACACAGACTG	0.343																																					p.V162V		Atlas-SNP	.											.	SPATA9	17	.	0			c.T486A						PASS	.						104	101	102					5																	94994606		2203	4300	6503	SO:0001819	synonymous_variant	83890	exon5			AGCATTAACACAG	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.486T>A	chr5.hg19:g.94994606A>T		78.0	0.0	.		108.0	21.0	.	NM_031952	A8K8H3|Q4G122|Q86X33|Q8NA28	Silent	SNP	ENST00000274432.8	hg19	CCDS4076.1																																																																																			.	.	.	none		0.343	SPATA9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304036.1	NM_031952		T	94994606	A	T	94994606	2	4	28	1	0	0	0	0	0	0	0	1	15028	349	13	5		5	SPATA9	5	94994606	Silent	SNP	A	TCGA-5P-A9JV-01A-12D-A42J-10	180588	94994606	85920654	21	1990											
GABRG2	2566	hgsc.bcm.edu	37	chr5	161495091	161495091	+	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	aatgacggtgtggattctgcTcctgctgtcgctctaccctg	5	13	11	12	2	2	1	0	1	2	0	4	2	3	2	2	2	3	3	2	2	2	2			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr5:161495091T>A	ENST00000361925.4	+	1	306	c.86T>A	c.(85-87)cTc>cAc	p.L29H	GABRG2_ENST00000414552.2_Missense_Mutation_p.L29H|GABRG2_ENST00000393933.4_5'UTR|GABRG2_ENST00000356592.3_Missense_Mutation_p.L29H			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	29					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TGGATTCTGCTCCTGCTGTCG	0.493																																					p.L29H		Atlas-SNP	.											.	GABRG2	142	.	0			c.T86A						PASS	.						92	83	86					5																	161495091		2203	4300	6503	SO:0001583	missense	2566	exon1			TTCTGCTCCTGCT		CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4087	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma 2"	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.86T>A	chr5.hg19:g.161495091T>A	ENSP00000354651:p.Leu29His	74.0	0.0	.		95.0	29.0	.	NM_198904	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Missense_Mutation	SNP	ENST00000361925.4	hg19	CCDS4358.1	.	.	.	.	.	.	.	.	.	.	T	15.93	2.977680	0.53720	.	.	ENSG00000113327	ENST00000356592;ENST00000414552;ENST00000361925	D;T;D	0.81821	-1.54;-1.06;-1.54	5.08	5.08	0.68730	.	0.601929	0.18116	N	0.151218	D	0.83119	0.5185	L	0.57536	1.79	0.80722	D	1	P;P;P	0.44260	0.828;0.69;0.83	P;B;P	0.50860	0.652;0.219;0.569	T	0.82794	-0.0281	10	0.46703	T	0.11	.	12.8183	0.57677	0.0:0.0:0.0:1.0	.	29;29;29	F5HB82;P18507;P18507-2	.;GBRG2_HUMAN;.	H	29	ENSP00000349000:L29H;ENSP00000410732:L29H;ENSP00000354651:L29H	ENSP00000349000:L29H	L	+	2	0	GABRG2	161427669	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.764000	0.62264	1.917000	0.55516	0.402000	0.26972	CTC	.	.	.	none		0.493	GABRG2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252706.1			A	161495091	T	A	161495091	3	1	28	1	0	0	0	0	1	0	0	0	6179	1551	54	5	88	5	GABRG2	5	161495091	Missense_Mutation	SNP	T	TCGA-5P-A9JV-01A-12D-A42J-10	66500485	161495091	19420169	22	1991											
PHIP	55023	hgsc.bcm.edu	37	chr6	79655729	79655729	+	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	gagtcttacttgttttccctGgtattgcagatgcattagct	7	17	9	8	0	1	1	0	0	1	1	2	2	2	1	1	1	4	5	1	1	3	7			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr6:79655729G>C	ENST00000275034.4	-	38	4786	c.4619C>G	c.(4618-4620)cCa>cGa	p.P1540R	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1540					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)		TGTTTTCCCTGGTATTGCAGA	0.343																																					p.P1540R		Atlas-SNP	.											.	PHIP	177	.	0			c.C4619G						PASS	.						96	94	95					6																	79655729		2203	4300	6503	SO:0001583	missense	55023	exon38			TTCCCTGGTATTG	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.4619C>G	chr6.hg19:g.79655729G>C	ENSP00000275034:p.Pro1540Arg	82.0	0.0	.		97.0	21.0	.	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	hg19	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	G	12.56	1.973618	0.34848	.	.	ENSG00000146247	ENST00000275034;ENST00000355098	T	0.39592	1.07	6.11	6.11	0.99139	.	0.406312	0.26369	N	0.024775	T	0.17450	0.0419	N	0.19112	0.55	0.38749	D	0.954061	B;B	0.29085	0.232;0.232	B;B	0.23716	0.048;0.048	T	0.05484	-1.0882	9	.	.	.	-14.0131	19.298	0.94131	0.0:0.0:1.0:0.0	.	1540;1540	A7J992;Q8WWQ0	.;PHIP_HUMAN	R	1540;266	ENSP00000275034:P1540R	.	P	-	2	0	PHIP	79712448	1.000000	0.71417	1.000000	0.80357	0.807000	0.45602	4.951000	0.63610	2.906000	0.99361	0.655000	0.94253	CCA	.	.	.	none		0.343	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			C	79655729	G	C	79655729	3	2	28	1	0	0	0	0	1	0	0	0	11849	1348	47	4	858	4	PHIP	6	79655729	Missense_Mutation	SNP	G	TCGA-5P-A9JV-01A-12D-A42J-10		79655729	91459338	23	1992											
PRDM13	59336	hgsc.bcm.edu	37	chr6	100062606	100062606	+	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	acgaccagagcgaccccgagGttgggggcggcggggagcgc	7	2	20	12	6	0	1	0	0	0	1	0	5	0	2	3	6	2	1	3	6	0	1	rs543525191	byFrequency	TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr6:100062606G>T	ENST00000369215.4	+	4	2400	c.2095G>T	c.(2095-2097)Gtt>Ttt	p.V699F		NM_021620.3	NP_067633.2	Q9H4Q3	PRD13_HUMAN	PR domain containing 13	699					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurogenesis (GO:0022008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(9)|prostate(1)	17		all_cancers(76;1.64e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0128)|Colorectal(196;0.069)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0598)		CGACCCCGAGGTTGGGGGCGG	0.657													G|||	2	0.000399361	0	0	5008	,	,		14126	0.002		0	False		,,,				2504	0				p.V699F		Atlas-SNP	.											.	PRDM13	65	.	0			c.G2095T						PASS	.						32	35	35					6																	100062606		1536	3504	5040	SO:0001583	missense	59336	exon4			CCCGAGGTTGGGG	AY004253	CCDS43487.1	6q16.2	2012-03-28			ENSG00000112238	ENSG00000112238			13998	protein-coding gene	gene with protein product							Standard	NM_021620		Approved		uc003pqg.1	Q9H4Q3	OTTHUMG00000015269	ENST00000369215.4:c.2095G>T	chr6.hg19:g.100062606G>T	ENSP00000358217:p.Val699Phe	173.0	0.0	.		141.0	33.0	.	NM_021620	Q5TGC1|Q5TGC2	Missense_Mutation	SNP	ENST00000369215.4	hg19	CCDS43487.1	.	.	.	.	.	.	.	.	.	.	G	12.48	1.950907	0.34471	.	.	ENSG00000112238	ENST00000369215;ENST00000369214	T;T	0.05717	3.4;3.4	5.66	4.69	0.59074	.	0.355912	0.20414	N	0.092810	T	0.01320	0.0043	N	0.08118	0	0.23862	N	0.996637	B	0.18863	0.031	B	0.22753	0.041	T	0.45804	-0.9236	10	0.72032	D	0.01	-9.2832	6.5857	0.22620	0.2509:0.0:0.7491:0.0	.	699	Q9H4Q3	PRD13_HUMAN	F	699;709	ENSP00000358217:V699F;ENSP00000358216:V709F	ENSP00000358216:V709F	V	+	1	0	PRDM13	100169327	0.496000	0.26059	0.965000	0.40720	0.399000	0.30720	0.923000	0.28757	2.680000	0.91292	0.561000	0.74099	GTT	.	.	.	none		0.657	PRDM13-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041619.2			T	100062606	G	T	100062606	3	4	28	1	0	0	0	0	1	0	0	0	12464	1261	44	4	2109	4	PRDM13	6	100062606	Missense_Mutation	SNP	G	TCGA-5P-A9JV-01A-12D-A42J-10	20406877	100062606	71052461	24	1993											
EIF3B	8662	hgsc.bcm.edu	37	chr7	2415106	2415106	+	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	actacatggcttccgacgtcGaatgggatcctactgggcgc	8	9	12	12	4	0	0	0	0	0	0	3	3	2	1	2	3	2	1	2	3	3	3			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr7:2415106G>A	ENST00000360876.4	+	14	2028	c.1972G>A	c.(1972-1974)Gaa>Aaa	p.E658K	EIF3B_ENST00000397011.2_Missense_Mutation_p.E658K	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)		TTCCGACGTCGAATGGGATCC	0.547																																					p.E658K		Atlas-SNP	.											.	EIF3B	54	.	0			c.G1972A						PASS	.						199	143	162					7																	2415106		2203	4300	6503	SO:0001583	missense	8662	exon14			GACGTCGAATGGG	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.1972G>A	chr7.hg19:g.2415106G>A	ENSP00000354125:p.Glu658Lys	107.0	0.0	.		125.0	35.0	.	NM_001037283		Missense_Mutation	SNP	ENST00000360876.4	hg19	CCDS5332.1	.	.	.	.	.	.	.	.	.	.	G	17.38	3.375384	0.61735	.	.	ENSG00000106263	ENST00000314800;ENST00000360876;ENST00000397011;ENST00000489558	T;T	0.05513	3.43;3.43	5.46	5.46	0.80206	Translation initiation factor 2A, beta propellor-like domain (1);Six-bladed beta-propeller, TolB-like (1);	0.089506	0.85682	D	0.000000	T	0.15305	0.0369	M	0.86028	2.79	0.80722	D	1	P	0.41345	0.746	B	0.38264	0.269	T	0.02457	-1.1156	10	0.72032	D	0.01	-48.6025	18.9193	0.92519	0.0:0.0:1.0:0.0	.	658	P55884	EIF3B_HUMAN	K	658;658;658;582	ENSP00000354125:E658K;ENSP00000380206:E658K	ENSP00000316638:E658K	E	+	1	0	EIF3B	2381632	1.000000	0.71417	0.944000	0.38274	0.019000	0.09904	9.670000	0.98625	2.571000	0.86741	0.655000	0.94253	GAA	.	.	.	none		0.547	EIF3B-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207006.1			A	2415106	G	A	2415106	3	1	28	1	0	0	0	0	1	0	0	0	5015	1059	37	1	2026	1	EIF3B	7	2415106	Missense_Mutation	SNP	G	TCGA-5P-A9JV-01A-12D-A42J-10		2415106	156723557	25	1994											
DYNC1I1	1780	hgsc.bcm.edu	37	chr7	95439731	95439731	+	Missense_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	tgcagcagaagaaagaacccGttcaggacgactctgatctg	13	7	11	10	2	3	4	1	1	2	3	3	6	3	5	1	1	3	3	1	1	3	1			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr7:95439731G>A	ENST00000324972.6	+	3	329	c.136G>A	c.(136-138)Gtt>Att	p.V46I	DYNC1I1_ENST00000437599.1_Missense_Mutation_p.V46I|DYNC1I1_ENST00000537881.1_Missense_Mutation_p.V46I|DYNC1I1_ENST00000447467.2_Missense_Mutation_p.V46I|DYNC1I1_ENST00000457059.1_Missense_Mutation_p.V46I|DYNC1I1_ENST00000413338.1_Missense_Mutation_p.V46I|DYNC1I1_ENST00000359388.4_Missense_Mutation_p.V46I	NM_004411.4	NP_004402.1	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	46	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)			GAAAGAACCCGTTCAGGACGA	0.433																																					p.V46I		Atlas-SNP	.											DYNC1I1,NS,carcinoma,0,1	DYNC1I1	111	.	0			c.G136A						PASS	.						80	79	80					7																	95439731		2202	4300	6502	SO:0001583	missense	1780	exon3			GAACCCGTTCAGG	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.136G>A	chr7.hg19:g.95439731G>A	ENSP00000320130:p.Val46Ile	105.0	0.0	.		112.0	37.0	.	NM_004411	B4DME3|F5H050|G5E9K1|Q8TBF7|Q9Y2X1	Missense_Mutation	SNP	ENST00000324972.6	hg19	CCDS5644.1	.	.	.	.	.	.	.	.	.	.	G	11.10	1.538558	0.27475	.	.	ENSG00000158560	ENST00000447467;ENST00000524053;ENST00000324972;ENST00000537881;ENST00000437599;ENST00000359388;ENST00000413338;ENST00000518089;ENST00000457059	T;T;T;T;T;T;T	0.73897	-0.59;2.65;-0.79;-0.59;-0.56;2.65;-0.59	4.76	2.96	0.34315	.	0.420143	0.24601	N	0.037126	T	0.52338	0.1728	N	0.14661	0.345	0.22933	N	0.998548	B;B;B;B;B	0.06786	0.001;0.0;0.001;0.0;0.001	B;B;B;B;B	0.08055	0.0;0.002;0.001;0.001;0.003	T	0.31138	-0.9954	10	0.19590	T	0.45	-13.6404	7.9351	0.29925	0.3129:0.0:0.6871:0.0	.	46;46;46;46;46	Q7Z6M0;G5E9K1;O14576-2;O14576;O14576-3	.;.;.;DC1I1_HUMAN;.	I	46	ENSP00000392337:V46I;ENSP00000320130:V46I;ENSP00000438377:V46I;ENSP00000398118:V46I;ENSP00000352348:V46I;ENSP00000428273:V46I;ENSP00000412444:V46I	ENSP00000320130:V46I	V	+	1	0	DYNC1I1	95277667	0.998000	0.40836	0.205000	0.23548	0.885000	0.51271	3.060000	0.49955	0.731000	0.32448	0.655000	0.94253	GTT	.	.	.	none		0.433	DYNC1I1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333432.1	NM_004411		A	95439731	G	A	95439731	3	1	28	1	0	0	0	0	1	0	0	0	4844	1145	40	1	142	1	DYNC1I1	7	95439731	Missense_Mutation	SNP	G	TCGA-5P-A9JV-01A-12D-A42J-10	93024625	95439731	63698932	26	1995											
NOBOX	135935	hgsc.bcm.edu	37	chr7	144096177	144096177	+	Silent	SNP	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	tcggcccttcgcacaggtggGgggctgaagagtgggggggt	5	7	21	8	2	0	2	0	1	0	1	2	2	0	2	1	8	0	2	1	8	1	1			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr7:144096177G>A	ENST00000467773.1	-	8	1334	c.1335C>T	c.(1333-1335)ccC>ccT	p.P445P	NOBOX_ENST00000483238.1_Silent_p.P413P|NOBOX_ENST00000223140.5_Silent_p.P328P	NM_001080413.3	NP_001073882.3	O60393	NOBOX_HUMAN	NOBOX oogenesis homeobox	445	Pro-rich.				oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	26	Melanoma(164;0.14)					GCACAGGTGGGGGGCTGAAGA	0.632																																					p.P445P		Atlas-SNP	.											.	NOBOX	130	.	0			c.C1335T						PASS	.						11	12	11					7																	144096177		1824	3970	5794	SO:0001819	synonymous_variant	135935	exon8			AGGTGGGGGGCTG			7q35	2011-06-20			ENSG00000106410	ENSG00000106410		"Homeoboxes / PRD class"	22448	protein-coding gene	gene with protein product	"newborn ovary homeobox-encoding gene"	610934				11804785, 16597639	Standard	NM_001080413		Approved	OG2, Og2x	uc022aoj.1	O60393	OTTHUMG00000158051	ENST00000467773.1:c.1335C>T	chr7.hg19:g.144096177G>A		75.0	0.0	.		99.0	23.0	.	NM_001080413	A6NCD3|A8MZN5	Silent	SNP	ENST00000467773.1	hg19																																																																																				.	.	.	none		0.632	NOBOX-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000350095.1	XM_001134420		A	144096177	G	A	144096177	2	1	28	1	0	0	0	0	0	0	0	1	10519	1219	43	2		2	NOBOX	7	144096177	Silent	SNP	G	TCGA-5P-A9JV-01A-12D-A42J-10	48656446	144096177	15042486	27	1996											
TCEB1	6921	hgsc.bcm.edu	37	chr8	74858968	74858968	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgttagtgtagcgaaccttgTacgtaaaatacatgcatact	13	13	8	7	2	0	0	0	0	0	0	0	1	0	0	1	0	6	5	1	0	8	7			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr8:74858968T>C	ENST00000522337.1	-	5	555	c.236A>G	c.(235-237)tAc>tGc	p.Y79C	TCEB1_ENST00000523815.1_Missense_Mutation_p.Y79C|TCEB1_ENST00000520242.1_Missense_Mutation_p.Y79C|TCEB1_ENST00000519487.1_Missense_Mutation_p.Y79C|TCEB1_ENST00000518127.1_Missense_Mutation_p.Y79C|TCEB1_ENST00000284811.8_Missense_Mutation_p.Y79C|TCEB1_ENST00000602840.1_Intron|TCEB1_ENST00000520210.1_Missense_Mutation_p.Y63C			Q15369	ELOC_HUMAN	transcription elongation factor B (SIII), polypeptide 1 (15kDa, elongin C)	79					cellular response to hypoxia (GO:0071456)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|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 elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)		p.Y79F(1)|p.Y79L(1)		endometrium(2)|kidney(3)|lung(1)|prostate(1)	7	Breast(64;0.0311)		Epithelial(68;0.0136)|all cancers(69;0.0431)|BRCA - Breast invasive adenocarcinoma(89;0.0499)			GCGAACCTTGTACGTAAAATA	0.413																																					p.Y79C		Atlas-SNP	.											TCEB1,NS,carcinoma,0,5	TCEB1	16	.	2	Substitution - Missense(2)	kidney(2)	c.A236G						PASS	.						95	77	83					8																	74858968		2203	4300	6503	SO:0001583	missense	6921	exon4			ACCTTGTACGTAA	L34587	CCDS34910.1, CCDS56539.1	8q13.3	2010-04-21	2002-08-29		ENSG00000154582	ENSG00000154582			11617	protein-coding gene	gene with protein product		600788	"transcription elongation factor B (SIII), polypeptide 1 (15kD, elongin C)"			7821821, 7660122	Standard	NM_005648		Approved	SIII	uc003xzx.2	Q15369	OTTHUMG00000164501	ENST00000522337.1:c.236A>G	chr8.hg19:g.74858968T>C	ENSP00000429906:p.Tyr79Cys	223.0	2.0	.		193.0	58.0	.	NM_005648	E5RGD9|Q567Q6	Missense_Mutation	SNP	ENST00000522337.1	hg19	CCDS34910.1	.	.	.	.	.	.	.	.	.	.	T	15.63	2.889194	0.52014	.	.	ENSG00000154582	ENST00000518127;ENST00000520210;ENST00000520242;ENST00000519487;ENST00000284811;ENST00000522337;ENST00000523815;ENST00000519082	T;T;T;T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85	5.66	5.66	0.87406	BTB/POZ fold (2);	0.000000	0.48286	D	0.000198	T	0.64778	0.2629	H	0.94264	3.515	0.80722	D	1	B	0.26195	0.144	B	0.31614	0.133	T	0.70230	-0.4929	10	0.87932	D	0	-1.9844	15.8997	0.79362	0.0:0.0:0.0:1.0	.	79	Q15369	ELOC_HUMAN	C	79;63;79;79;79;79;79;79	ENSP00000428334:Y79C;ENSP00000430224:Y63C;ENSP00000428171:Y79C;ENSP00000429596:Y79C;ENSP00000284811:Y79C;ENSP00000429906:Y79C;ENSP00000428074:Y79C;ENSP00000429789:Y79C	ENSP00000284811:Y79C	Y	-	2	0	TCEB1	75021522	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.513000	0.81739	2.157000	0.67596	0.482000	0.46254	TAC	.	.	.	none		0.413	TCEB1-010	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000379020.1	NM_005648		C	74858968	T	C	74858968	3	2	28	1	0	0	0	0	1	0	0	0	15691	1638	57	3	106	3	TCEB1	8	74858968	Missense_Mutation	SNP	T	TCGA-5P-A9JV-01A-12D-A42J-10		74858968	71505054	28	1997											
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110439255	110439255	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccccgctgctgtgtcagctgCagatctgcagtttgcactcc	5	11	10	15	1	2	1	1	0	1	1	3	1	3	1	3	0	5	7	3	0	0	1	rs35375999	byFrequency	TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr8:110439255C>T	ENST00000378402.5	+	25	2974	c.2870C>T	c.(2869-2871)gCa>gTa	p.A957V		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	957			A -> E (in dbSNP:rs35375999).		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)			GTGTCAGCTGCAGATCTGCAG	0.557										HNSCC(38;0.096)																											p.A957V		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.C2870T						PASS	.						74	76	76					8																	110439255		1980	4166	6146	SO:0001583	missense	93035	exon25			CAGCTGCAGATCT	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.2870C>T	chr8.hg19:g.110439255C>T	ENSP00000367655:p.Ala957Val	83.0	0.0	.		71.0	9.0	.	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	hg19	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	C	12.88	2.071060	0.36566	.	.	ENSG00000205038	ENST00000378402	D	0.85861	-2.04	5.45	1.06	0.20224	.	0.770532	0.12118	N	0.497923	T	0.71108	0.3301	N	0.25426	0.745	0.23823	N	0.996742	B	0.09022	0.002	B	0.08055	0.003	T	0.52305	-0.8593	10	0.13108	T	0.6	.	6.1929	0.20534	0.0:0.5062:0.0:0.4938	.	957	Q86WI1	PKHL1_HUMAN	V	957	ENSP00000367655:A957V	ENSP00000367655:A957V	A	+	2	0	PKHD1L1	110508431	0.004000	0.15560	0.997000	0.53966	0.897000	0.52465	0.192000	0.17096	0.279000	0.22186	-0.225000	0.12378	GCA	.	C|0.985;A|0.015	.	alt		0.557	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		T	110439255	C	T	110439255	3	4	28	1	0	0	0	0	1	0	0	0	11979	710	25	2	2968	2	PKHD1L1	8	110439255	Missense_Mutation	SNP	C	TCGA-5P-A9JV-01A-12D-A42J-10	35580287	110439255	35924767	29	1998											
AKR1C1	1645	hgsc.bcm.edu	37	chr10	5008141	5008141	+	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	gctttagaggccaccaaattGgcaattgaagctggcttccg	10	10	11	10	1	0	2	0	1	0	1	1	2	1	2	3	3	1	4	3	3	4	5			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr10:5008141G>T	ENST00000380872.4	+	2	312	c.120G>T	c.(118-120)ttG>ttT	p.L40F	AKR1C1_ENST00000434459.2_Missense_Mutation_p.L40F|AKR1C1_ENST00000477661.1_3'UTR|AKR1C1_ENST00000380859.1_Missense_Mutation_p.L42F	NM_001353.5	NP_001344.2	Q04828	AK1C1_HUMAN	aldo-keto reductase family 1, member C1	40					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)	CCACCAAATTGGCAATTGAAG	0.448																																					p.L40F	Colon(130;2054 2316 13360 15380)	Atlas-SNP	.											.	AKR1C1	39	.	0			c.G120T						PASS	.						92	84	87					10																	5008141		2203	4300	6503	SO:0001583	missense	1645	exon2			CAAATTGGCAATT	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.120G>T	chr10.hg19:g.5008141G>T	ENSP00000370254:p.Leu40Phe	155.0	0.0	.		184.0	20.0	.	NM_001353	P52896|Q5SR15|Q7M4N2|Q9UCX2	Missense_Mutation	SNP	ENST00000380872.4	hg19	CCDS7061.1	.	.	.	.	.	.	.	.	.	.	G	0.039	-1.290978	0.01375	.	.	ENSG00000187134	ENST00000434459;ENST00000380872;ENST00000380859	T;T;T	0.25414	1.8;1.8;1.8	2.48	-3.93	0.04143	NADP-dependent oxidoreductase domain (3);	1.106620	0.07086	N	0.837917	T	0.11879	0.0289	N	0.16478	0.41	0.18873	N	0.999983	B;B;B	0.13594	0.008;0.001;0.001	B;B;B	0.21360	0.034;0.004;0.009	T	0.36529	-0.9744	10	0.12766	T	0.61	.	4.7478	0.13045	0.248:0.0:0.5559:0.1961	.	40;40;40	B4E0M1;Q2XPP3;Q04828	.;.;AK1C1_HUMAN	F	40;40;42	ENSP00000412248:L40F;ENSP00000370254:L40F;ENSP00000370240:L42F	ENSP00000370240:L42F	L	+	3	2	AKR1C1	4998141	0.002000	0.14202	0.003000	0.11579	0.009000	0.06853	-0.301000	0.08232	-0.700000	0.05070	0.305000	0.20034	TTG	.	.	.	none		0.448	AKR1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046523.2	NM_001353		T	5008141	G	T	5008141	3	4	28	1	0	0	0	0	1	0	0	0	469	1339	47	4	126	4	AKR1C1	10	5008141	Missense_Mutation	SNP	G	TCGA-5P-A9JV-01A-12D-A42J-10		5008141	130526606	30	1999											
UPF2	26019	hgsc.bcm.edu	37	chr10	11985132	11985132	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctgtattctcttcctcctcTtcttctccctcatcatcatc	4	19	1	17	0	8	0	3	0	5	0	13	0	10	0	3	0	0	1	3	0	1	5			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr10:11985132T>C	ENST00000356352.2	-	16	3683	c.3210A>G	c.(3208-3210)gaA>gaG	p.E1070E	UPF2_ENST00000357604.5_Silent_p.E1070E|UPF2_ENST00000397053.2_Silent_p.E1070E			Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog (yeast)	1070	Glu-rich.|Sufficient for interaction with EIF4A1 and EIF1.				gene expression (GO:0010467)|liver development (GO:0001889)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|organ regeneration (GO:0031100)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(14)|lung(17)|ovary(2)|skin(3)|urinary_tract(2)	56		Renal(717;0.228)				CTTCCTCCTCTTCTTCTCCCT	0.328																																					p.E1070E		Atlas-SNP	.											.	UPF2	111	.	0			c.A3210G						PASS	.						159	142	147					10																	11985132		2202	4300	6502	SO:0001819	synonymous_variant	26019	exon17			CTCCTCTTCTTCT	AB037829	CCDS7086.1	10p14-p13	2011-06-21			ENSG00000151461	ENSG00000151461			17854	protein-coding gene	gene with protein product	"smg-3 homolog, nonsense mediated mRNA decay factor (C. elegans)"	605529				11073994, 11113196	Standard	NM_080599		Approved	RENT2, DKFZP434D222, KIAA1408, smg-3	uc001ilb.3	Q9HAU5	OTTHUMG00000017678	ENST00000356352.2:c.3210A>G	chr10.hg19:g.11985132T>C		43.0	0.0	.		75.0	19.0	.	NM_080599	A6NLJ5|D3DRS0|Q14BM1|Q5W0J4|Q8N8U1|Q9H1J2|Q9NWL1|Q9P2D9|Q9Y4M9	Silent	SNP	ENST00000356352.2	hg19	CCDS7086.1																																																																																			.	.	.	none		0.328	UPF2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046783.1			C	11985132	T	C	11985132	2	2	28	1	0	0	0	0	0	0	0	1	17016	1606	56	3		3	UPF2	10	11985132	Silent	SNP	T	TCGA-5P-A9JV-01A-12D-A42J-10	6976991	11985132	123549615	31	2000											
MARCH8	220972	hgsc.bcm.edu	37	chr10	45953921	45953921	+	Frame_Shift_Del	DEL	A	A	-																															actttacactgaacatacatAaaaagaagtcctccggtgaa																										TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr10:45953921delA	ENST00000319836.3	-	7	1391	c.642delT	c.(640-642)tttfs	p.F214fs	MARCH8_ENST00000476962.1_5'UTR|MARCH8_ENST00000395769.2_Frame_Shift_Del_p.F214fs|MARCH8_ENST00000453424.2_Frame_Shift_Del_p.F496fs|MARCH8_ENST00000395771.3_Frame_Shift_Del_p.F214fs	NM_145021.4	NP_659458.2	Q5T0T0	MARH8_HUMAN	membrane-associated ring finger (C3HC4) 8, E3 ubiquitin protein ligase	214					immune system process (GO:0002376)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(5)|lung(4)	12						GAACATACATAAAAAGAAGTC	0.408																																					p.M215fs	NSCLC(102;658 1594 2173 16344 34808)	Atlas-Indel,Pindel	.											.	MARCH8	29	.	0			c.643delA						PASS	.						84	86	85					10																	45953921		2203	4300	6503	SO:0001589	frameshift_variant	220972	exon7			.	AL833316	CCDS7213.1, CCDS60519.1	10q11.22	2013-01-09	2012-02-23	2005-01-27	ENSG00000165406	ENSG00000165406		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	23356	protein-coding gene	gene with protein product		613335	"c-mir, cellular modulator of immune recognition", "membrane-associated ring finger (C3HC4) 8"	MIR		12582153, 14722266	Standard	XM_005271804		Approved	c-MIR, MARCH-VIII, RNF178	uc001jch.2	Q5T0T0	OTTHUMG00000019345	ENST00000319836.3:c.642delT	chr10.hg19:g.45953921delA	ENSP00000317087:p.Phe214fs	95.0	0.0	0		85.0	19.0	0.223529	NM_001002266	B2R8E7|H0Y7C6|Q5T0S8|Q8TC72	Frame_Shift_Del	DEL	ENST00000319836.3	hg19	CCDS7213.1																																																																																			.	.	.	none		0.408	MARCH8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051217.1	NM_145021		-	45953921	A	-	45953921	7	5	28	1	0	1	0	1	0	0	0	0	9314	359	13	0	237	0	MARCH8	10	45953921	Frame_Shift_Del	DEL	A	TCGA-5P-A9JV-01A-12D-A42J-10	33968789	45953921	89580826	32	2001											
SLC16A9	220963	hgsc.bcm.edu	37	chr10	61413535	61413535	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacagtcttcgtggtcacatAtggaaagatggaccaattac	13	10	9	9	1	2	1	1	0	1	1	3	3	2	3	1	3	1	0	1	3	4	3	rs372708622		TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr10:61413535A>G	ENST00000395348.3	-	5	1885	c.1249T>C	c.(1249-1251)Tat>Cat	p.Y417H	SLC16A9_ENST00000395347.1_Missense_Mutation_p.Y417H	NM_194298.2	NP_919274.1	Q7RTY1	MOT9_HUMAN	solute carrier family 16, member 9	417					urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			kidney(3)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	23						GTGGTCACATATGGAAAGATG	0.443																																					p.Y417H		Atlas-SNP	.											.	SLC16A9	58	.	0			c.T1249C						PASS	.	A	HIS/TYR	1,4405	2.1+/-5.4	0,1,2202	116	108	111		1249	5.2	1	10		111	0,8600		0,0,4300	no	missense	SLC16A9	NM_194298.2	83	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	probably-damaging	417/510	61413535	1,13005	2203	4300	6503	SO:0001583	missense	220963	exon5			TCACATATGGAAA	AK125791	CCDS7256.1	10q21.3	2013-07-18	2013-07-18	2004-01-21	ENSG00000165449	ENSG00000165449		"Solute carriers"	23520	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 9"	614242	"chromosome 10 open reading frame 36", "solute carrier family 16 (monocarboxylic acid transporters), member 9", "solute carrier family 16, member 9 (monocarboxylic acid transporter 9)"	C10orf36			Standard	NM_194298		Approved	FLJ43803, MCT9	uc010qig.1	Q7RTY1	OTTHUMG00000018283	ENST00000395348.3:c.1249T>C	chr10.hg19:g.61413535A>G	ENSP00000378757:p.Tyr417His	90.0	0.0	.		109.0	22.0	.	NM_194298	Q6ZMI2|Q9UFH8	Missense_Mutation	SNP	ENST00000395348.3	hg19	CCDS7256.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.109161	0.77096	2.27E-4	0.0	ENSG00000165449	ENST00000395348;ENST00000395347	T;T	0.58940	0.3;0.3	5.2	5.2	0.72013	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.107752	0.64402	D	0.000003	T	0.72630	0.3484	M	0.68317	2.08	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.70407	-0.4880	10	0.26408	T	0.33	.	15.0446	0.71816	1.0:0.0:0.0:0.0	.	417	Q7RTY1	MOT9_HUMAN	H	417	ENSP00000378757:Y417H;ENSP00000378756:Y417H	ENSP00000378756:Y417H	Y	-	1	0	SLC16A9	61083541	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.962000	0.93254	1.956000	0.56807	0.482000	0.46254	TAT	.	.	.	none		0.443	SLC16A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048174.2	NM_194298		G	61413535	A	G	61413535	3	3	28	1	0	0	0	0	1	0	0	0	14428	449	16	3	288	3	SLC16A9	10	61413535	Missense_Mutation	SNP	A	TCGA-5P-A9JV-01A-12D-A42J-10	15459614	61413535	74121212	33	2002											
WDR11	55717	hgsc.bcm.edu	37	chr10	122650370	122650370	+	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	gatgtctatgaagtctgcgtGctttagaatggatgaacaag	12	12	12	5	1	2	3	0	2	2	1	2	5	2	4	0	1	3	1	0	1	6	3			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr10:122650370G>T	ENST00000263461.6	+	19	2732	c.2486G>T	c.(2485-2487)tGc>tTc	p.C829F	WDR11_ENST00000604509.1_Intron	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						AAGTCTGCGTGCTTTAGAATG	0.433																																					p.C829F		Atlas-SNP	.											.	WDR11	95	.	0			c.G2486T						PASS	.						206	192	197					10																	122650370		2203	4300	6503	SO:0001583	missense	55717	exon19			CTGCGTGCTTTAG	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.2486G>T	chr10.hg19:g.122650370G>T	ENSP00000263461:p.Cys829Phe	108.0	0.0	.		127.0	26.0	.	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000263461.6	hg19	CCDS7619.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.568063	0.86439	.	.	ENSG00000120008	ENST00000263461	D	0.90788	-2.73	5.51	5.51	0.81932	WD40/YVTN repeat-like-containing domain (1);	0.094012	0.85682	D	0.000000	D	0.82889	0.5135	N	0.22421	0.69	0.58432	D	0.999999	B;B;P;B	0.47604	0.41;0.139;0.898;0.167	B;B;B;B	0.37550	0.205;0.016;0.253;0.034	T	0.81854	-0.0741	10	0.10636	T	0.68	-13.3	19.4182	0.94710	0.0:0.0:1.0:0.0	.	829;829;120;358	Q9BZH6;B2RCJ6;Q9NWV7;Q659C9	WDR11_HUMAN;.;.;.	F	829	ENSP00000263461:C829F	ENSP00000263461:C829F	C	+	2	0	WDR11	122640360	1.000000	0.71417	0.025000	0.17156	0.888000	0.51559	9.296000	0.96104	2.575000	0.86900	0.655000	0.94253	TGC	.	.	.	none		0.433	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2			T	122650370	G	T	122650370	3	4	28	1	0	0	0	0	1	0	0	0	17285	1319	46	4	2560	4	WDR11	10	122650370	Missense_Mutation	SNP	G	TCGA-5P-A9JV-01A-12D-A42J-10	61236835	122650370	12884377	34	2003											
OR51E2	81285	hgsc.bcm.edu	37	chr11	4703537	4703537	+	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	tgggctgttactgtattgttGagcactgcagcatggcgcag	7	12	14	8	1	0	1	0	1	0	0	0	1	0	1	0	2	4	8	0	2	2	4			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr11:4703537G>T	ENST00000396950.3	-	2	644	c.405C>A	c.(403-405)ctC>ctA	p.L135L		NM_030774.3	NP_110401.1	Q9H255	O51E2_HUMAN	olfactory receptor, family 51, subfamily E, member 2	135					cellular response to fatty acid (GO:0071398)|detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|positive regulation of blood pressure (GO:0045777)|positive regulation of renin secretion into blood stream (GO:1900135)|steroid hormone mediated signaling pathway (GO:0043401)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|signaling receptor activity (GO:0038023)|steroid hormone receptor activity (GO:0003707)			NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(3)	23		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;3e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00476)|LUSC - Lung squamous cell carcinoma(625;0.2)		CTGTATTGTTGAGCACTGCAG	0.557																																					p.L135L		Atlas-SNP	.											.	OR51E2	77	.	0			c.C405A						PASS	.						59	49	52					11																	4703537		2201	4298	6499	SO:0001819	synonymous_variant	81285	exon2			ATTGTTGAGCACT	AY033942	CCDS7751.1	11p15	2012-08-09			ENSG00000167332	ENSG00000167332		"GPCR / Class A : Olfactory receptors"	15195	protein-coding gene	gene with protein product		611268				11118034	Standard	NM_030774		Approved	PSGR	uc001lzk.2	Q9H255	OTTHUMG00000133362	ENST00000396950.3:c.405C>A	chr11.hg19:g.4703537G>T		77.0	0.0	.		95.0	25.0	.	NM_030774	B2RA63|Q6IF94	Silent	SNP	ENST00000396950.3	hg19	CCDS7751.1																																																																																			.	.	.	none		0.557	OR51E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257198.1	NM_030774		T	4703537	G	T	4703537	2	4	28	1	0	0	0	0	0	0	0	1	11102	1277	45	4		4	OR51E2	11	4703537	Silent	SNP	G	TCGA-5P-A9JV-01A-12D-A42J-10		4703537	130302979	35	2004											
CKAP5	9793	hgsc.bcm.edu	37	chr11	46799725	46799725	+	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	tcattgagtcgacccttcaaGgcagttggaagttcacctat	10	12	9	10	1	3	1	3	1	0	0	4	3	3	2	2	2	0	3	2	2	3	5			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr11:46799725G>T	ENST00000529230.1	-	22	2758	c.2712C>A	c.(2710-2712)gcC>gcA	p.A904A	CKAP5_ENST00000354558.3_Silent_p.A904A|CKAP5_ENST00000312055.5_Silent_p.A904A|CKAP5_ENST00000415402.1_Silent_p.A904A			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	904					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						GACCCTTCAAGGCAGTTGGAA	0.403																																					p.A904A	Ovarian(4;85 273 2202 4844 13323)	Atlas-SNP	.											.	CKAP5	134	.	0			c.C2712A						PASS	.						145	152	149					11																	46799725		2201	4299	6500	SO:0001819	synonymous_variant	9793	exon22			CTTCAAGGCAGTT		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.2712C>A	chr11.hg19:g.46799725G>T		105.0	0.0	.		92.0	20.0	.	NM_001008938	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	Silent	SNP	ENST00000529230.1	hg19	CCDS31477.1																																																																																			.	.	.	none		0.403	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	NM_014756		T	46799725	G	T	46799725	2	4	28	1	0	0	0	0	0	0	0	1	3447	987	35	4		4	CKAP5	11	46799725	Silent	SNP	G	TCGA-5P-A9JV-01A-12D-A42J-10	42096188	46799725	88206791	36	2005											
RPS6KB2	6199	hgsc.bcm.edu	37	chr11	67201948	67201948	+	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	cagcgagagtgccaaccaggCcttcctggtgagtgcggggg	7	6	17	11	2	0	2	0	1	0	1	1	3	1	2	4	4	4	0	4	4	1	1	rs369245928		TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr11:67201948C>G	ENST00000312629.5	+	13	1193	c.1148C>G	c.(1147-1149)gCc>gGc	p.A383G	AP003419.16_ENST00000535922.1_RNA	NM_003952.2	NP_003943.2	Q9UBS0	KS6B2_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide 2	383	AGC-kinase C-terminal.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of translational initiation (GO:0045948)|protein kinase B signaling (GO:0043491)|signal transduction (GO:0007165)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(3)|salivary_gland(1)|stomach(2)	25			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			GCCAACCAGGCCTTCCTGGTG	0.647																																					p.A383G		Atlas-SNP	.											.	RPS6KB2	92	.	0			c.C1148G						PASS	.						24	28	27					11																	67201948		2080	4189	6269	SO:0001583	missense	6199	exon13			ACCAGGCCTTCCT	AB019245	CCDS41677.1	11q13.1	2011-04-05	2002-08-29		ENSG00000175634	ENSG00000175634			10437	protein-coding gene	gene with protein product		608939	"ribosomal protein S6 kinase, 70kD, polypeptide 2"			9878560, 9804755	Standard	XM_005274164		Approved	p70S6Kb, P70-BETA, STK14B, KLS	uc001old.3	Q9UBS0	OTTHUMG00000167673	ENST00000312629.5:c.1148C>G	chr11.hg19:g.67201948C>G	ENSP00000308413:p.Ala383Gly	42.0	0.0	.		47.0	4.0	.	NM_003952	B2RMZ9|B4DML8|O94809|Q9UEC1	Missense_Mutation	SNP	ENST00000312629.5	hg19	CCDS41677.1	.	.	.	.	.	.	.	.	.	.	C	13.04	2.119441	0.37436	.	.	ENSG00000175634	ENST00000312629	T	0.58060	0.36	4.52	4.52	0.55395	Protein kinase, C-terminal (1);AGC-kinase, C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.50086	0.1595	M	0.62088	1.915	0.80722	D	1	B;B	0.15719	0.014;0.005	B;B	0.22601	0.04;0.012	T	0.54622	-0.8266	10	0.87932	D	0	.	10.6873	0.45850	0.0:0.9105:0.0:0.0895	.	383;383	Q9BRS0;Q9UBS0	.;KS6B2_HUMAN	G	383	ENSP00000308413:A383G	ENSP00000308413:A383G	A	+	2	0	RPS6KB2	66958524	1.000000	0.71417	1.000000	0.80357	0.391000	0.30476	1.875000	0.39578	2.339000	0.79563	0.313000	0.20887	GCC	.	.	.	alt		0.647	RPS6KB2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395508.1	NM_003952		G	67201948	C	G	67201948	3	3	28	1	0	0	0	0	1	0	0	0	13670	739	26	4	1198	4	RPS6KB2	11	67201948	Missense_Mutation	SNP	C	TCGA-5P-A9JV-01A-12D-A42J-10	20402223	67201948	67804568	37	2006											
CARD17	440068	hgsc.bcm.edu	37	chr11	104971430	104971430	+	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	agcacccttgtctccaataaTtcacccagtaagccatttat	12	12	4	13	0	2	0	1	0	1	0	3	0	2	0	4	0	2	2	4	0	4	6			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr11:104971430T>A	ENST00000375707.1	-	2	100	c.84A>T	c.(82-84)gaA>gaT	p.E28D	CASP1_ENST00000598974.1_Intron|CASP1_ENST00000594519.1_Intron|CASP1_ENST00000593315.1_Intron|CARD16_ENST00000525374.1_Intron|CASP1_ENST00000415981.2_Intron	NM_001007232.1	NP_001007233.1	Q5XLA6	CAR17_HUMAN	caspase recruitment domain family, member 17	28	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				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						TCTCCAATAATTCACCCAGTA	0.438																																					p.E28D		Atlas-SNP	.											.	CARD17	15	.	0			c.A84T						PASS	.						198	187	191					11																	104971430		2202	4299	6501	SO:0001583	missense	440068	exon2			CAATAATTCACCC		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.84A>T	chr11.hg19:g.104971430T>A	ENSP00000364859:p.Glu28Asp	95.0	0.0	.		125.0	36.0	.	NM_001007232		Missense_Mutation	SNP	ENST00000375707.1	hg19	CCDS31662.1	.	.	.	.	.	.	.	.	.	.	.	4.355	0.065284	0.08388	.	.	ENSG00000255221	ENST00000375707	T	0.20069	2.1	2.92	-3.18	0.05186	DEATH-like (2);Caspase Recruitment (3);	.	.	.	.	T	0.12390	0.0301	N	0.24115	0.695	0.09310	N	1	B	0.29481	0.245	B	0.44044	0.439	T	0.40961	-0.9535	9	0.02654	T	1	.	0.3399	0.00332	0.3708:0.1307:0.1905:0.3079	.	28	Q5XLA6	CAR17_HUMAN	D	28	ENSP00000364859:E28D	ENSP00000364859:E28D	E	-	3	2	CARD17	104476640	0.000000	0.05858	0.026000	0.17262	0.040000	0.13550	-1.024000	0.03603	-0.391000	0.07763	0.418000	0.28097	GAA	.	.	.	none		0.438	CARD17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388181.1	NM_001007232		A	104971430	T	A	104971430	3	1	28	1	0	0	0	0	1	0	0	0	2650	1490	52	5	256	5	CARD17	11	104971430	Missense_Mutation	SNP	T	TCGA-5P-A9JV-01A-12D-A42J-10	37769482	104971430	30035086	38	2007											
ARF3	377	hgsc.bcm.edu	37	chr12	49332835	49332835	+	Silent	SNP	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	taccagttacggtgacgaagGgaatgcaggcccagcttgtc	10	8	13	10	2	0	1	0	1	0	0	1	3	0	2	2	3	4	3	2	3	4	3			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr12:49332835G>A	ENST00000256682.4	-	5	775	c.441C>T	c.(439-441)tcC>tcT	p.S147S	ARF3_ENST00000541967.1_5'Flank|ARF3_ENST00000541959.1_Silent_p.S147S|AC073610.5_ENST00000537495.1_Silent_p.S22S|RP11-302B13.5_ENST00000398092.4_Intron|ARF3_ENST00000447318.2_Silent_p.S110S	NM_001659.2	NP_001650.1	P61204	ARF3_HUMAN	ADP-ribosylation factor 3	147					GTP catabolic process (GO:0006184)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|lung(2)|skin(1)	4						GGTGACGAAGGGAATGCAGGC	0.537																																					p.S147S	Pancreas(189;1862 2134 4419 30933 49364)	Atlas-SNP	.											.	ARF3	11	.	0			c.C441T						PASS	.						145	124	131					12																	49332835		2203	4300	6503	SO:0001819	synonymous_variant	377	exon5			ACGAAGGGAATGC	M74491	CCDS8774.1	12q13.12	2013-01-22			ENSG00000134287	ENSG00000134287		"ADP-ribosylation factors"	654	protein-coding gene	gene with protein product	"small GTP binding protein"	103190				8661066	Standard	NM_001659		Approved		uc001rsr.2	P61204	OTTHUMG00000168080	ENST00000256682.4:c.441C>T	chr12.hg19:g.49332835G>A		98.0	0.0	.		116.0	28.0	.	NM_001659	A8K6G8|B7ZB63|P16587	Silent	SNP	ENST00000256682.4	hg19	CCDS8774.1																																																																																			.	.	.	none		0.537	ARF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258242.2	NM_001659		A	49332835	G	A	49332835	2	1	28	1	0	0	0	0	0	0	0	1	845	1219	43	2		2	ARF3	12	49332835	Silent	SNP	G	TCGA-5P-A9JV-01A-12D-A42J-10		49332835	84519060	39	2008											
VTI1B	10490	hgsc.bcm.edu	37	chr14	68126460	68126460	+	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	aaacttaccatatgctcattCtctacagcatatatgccata	14	13	3	11	0	2	0	1	0	1	0	3	0	2	0	2	0	6	2	2	0	7	7			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr14:68126460C>A	ENST00000554659.1	-	3	695	c.354G>T	c.(352-354)gaG>gaT	p.E118D	RP11-1012A1.4_ENST00000554493.1_5'Flank|5S_rRNA_ENST00000607639.1_RNA	NM_006370.2	NP_006361.1	Q9UEU0	VTI1B_HUMAN	vesicle transport through interaction with t-SNAREs 1B	118					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)		TATGCTCATTCTCTACAGCAT	0.408																																					p.E118D		Atlas-SNP	.											.	VTI1B	15	.	0			c.G354T						PASS	.						84	74	78					14																	68126460		2203	4300	6503	SO:0001583	missense	10490	exon3			CTCATTCTCTACA	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.354G>T	chr14.hg19:g.68126460C>A	ENSP00000450731:p.Glu118Asp	36.0	0.0	.		51.0	19.0	.	NM_006370	O43547|Q96J28	Missense_Mutation	SNP	ENST00000554659.1	hg19	CCDS9786.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.08|12.08	1.829916|1.829916	0.32329|0.32329	.|.	.|.	ENSG00000100568|ENSG00000100568	ENST00000554659|ENST00000554636;ENST00000556461	.|.	.|.	.|.	5.12|5.12	0.197|0.197	0.15164|0.15164	.|.	0.239820|0.239820	0.44285|0.44285	D|D	0.000468|0.000468	T|.	0.30386|.	0.0763|.	N|N	0.08118|0.08118	0|0	0.44104|0.44104	D|D	0.996874|0.996874	P;P|.	0.52463|.	0.953;0.919|.	P;P|.	0.47603|.	0.551;0.45|.	T|.	0.03344|.	-1.1046|.	9|.	0.15066|.	T|.	0.55|.	.|.	9.4955|9.4955	0.38986|0.38986	0.0:0.3897:0.0:0.6103|0.0:0.3897:0.0:0.6103	.|.	118;118|.	A8K6M4;Q9UEU0|.	.;VTI1B_HUMAN|.	D|X	118|17;35	.|.	ENSP00000216456:E118D|.	E|E	-|-	3|1	2|0	VTI1B|VTI1B	67196213|67196213	0.996000|0.996000	0.38824|0.38824	0.964000|0.964000	0.40570|0.40570	0.573000|0.573000	0.36030|0.36030	0.404000|0.404000	0.20999|0.20999	-0.060000|-0.060000	0.13132|0.13132	-0.244000|-0.244000	0.11960|0.11960	GAG|GAA	.	.	.	none		0.408	VTI1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412558.2			A	68126460	C	A	68126460	3	1	28	1	0	0	0	0	1	0	0	0	17248	912	32	4	360	4	VTI1B	14	68126460	Missense_Mutation	SNP	C	TCGA-5P-A9JV-01A-12D-A42J-10		68126460	39223080	40	2009											
DCI	1632	hgsc.bcm.edu	37	chr16	2301546	2301546	+	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	cagaacgcgcgccgggactcGcacagaagccaccagcgcca	11	1	12	17	6	0	2	0	0	0	2	1	3	0	3	4	1	3	1	4	1	2	0			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr16:2301546G>T	ENST00000301729.4	-	1	69	c.22C>A	c.(22-24)Cga>Aga	p.R8R	ECI1_ENST00000562238.1_Silent_p.R8R|ECI1_ENST00000570258.1_Intron|AC009065.1_ENST00000454671.1_5'Flank	NM_001919.3	NP_001910.2	P42126	ECI1_HUMAN	enoyl-CoA delta isomerase 1	8					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						GCCGGGACTCGCACAGAAGCC	0.736																																					p.R8R		Atlas-SNP	.											.	ECI1	20	.	0			c.C22A						PASS	.						3	5	5					16																	2301546		1966	3980	5946	SO:0001819	synonymous_variant	1632	exon1			GGACTCGCACAGA		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.22C>A	chr16.hg19:g.2301546G>T		97.0	0.0	.		108.0	22.0	.	NM_001178029	A8K512|Q13290|Q7Z2L6|Q7Z2L7|Q9BUB8|Q9BW05|Q9UDG6	Silent	SNP	ENST00000301729.4	hg19	CCDS10464.1																																																																																			.	.	.	none		0.736	ECI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250768.1			T	2301546	G	T	2301546	2	4	28	1	0	0	0	0	0	0	0	1	4291	1095	38	4		4	DCI	16	2301546	Silent	SNP	G	TCGA-5P-A9JV-01A-12D-A42J-10		2301546	88053207	41	2010											
PPL	5493	hgsc.bcm.edu	37	chr16	4935927	4935927	+	Missense_Mutation	SNP	T	T	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	gggtgctcttgacctcgttcTccagctgccgcctccgctca	3	11	10	17	3	3	1	1	1	2	0	6	1	4	1	5	1	3	4	5	1	0	2			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr16:4935927T>G	ENST00000345988.2	-	22	2818	c.2729A>C	c.(2728-2730)gAg>gCg	p.E910A	PPL_ENST00000590782.2_Missense_Mutation_p.E908A	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	910					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						GACCTCGTTCTCCAGCTGCCG	0.577																																					p.E910A		Atlas-SNP	.											.	PPL	168	.	0			c.A2729C						PASS	.						81	85	84					16																	4935927		2197	4300	6497	SO:0001583	missense	5493	exon22			TCGTTCTCCAGCT	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.2729A>C	chr16.hg19:g.4935927T>G	ENSP00000340510:p.Glu910Ala	28.0	0.0	.		38.0	9.0	.	NM_002705	O60314|O60454|Q14C98	Missense_Mutation	SNP	ENST00000345988.2	hg19	CCDS10526.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.035131	0.75617	.	.	ENSG00000118898	ENST00000345988	T	0.55588	0.51	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.71005	0.3289	M	0.72118	2.19	0.58432	D	0.999999	D	0.69078	0.997	D	0.77004	0.989	T	0.74990	-0.3475	10	0.72032	D	0.01	.	14.8296	0.70137	0.0:0.0:0.0:1.0	.	910	O60437	PEPL_HUMAN	A	910	ENSP00000340510:E910A	ENSP00000340510:E910A	E	-	2	0	PPL	4875928	1.000000	0.71417	0.994000	0.49952	0.575000	0.36095	8.003000	0.88520	1.918000	0.55548	0.374000	0.22700	GAG	.	.	.	none		0.577	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705		G	4935927	T	G	4935927	3	3	28	1	0	0	0	0	1	0	0	0	12344	1551	54	5	2545	5	PPL	16	4935927	Missense_Mutation	SNP	T	TCGA-5P-A9JV-01A-12D-A42J-10	2634381	4935927	85418826	42	2011											
CACNG3	10368	hgsc.bcm.edu	37	chr16	24372986	24372986	+	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	tcccgagacctgtcccccatCagcaaaggcttccacaccat	10	7	6	18	1	1	1	1	0	0	1	4	2	4	1	6	1	1	2	6	1	1	1	rs148951012		TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr16:24372986C>T	ENST00000005284.3	+	4	1952	c.750C>T	c.(748-750)atC>atT	p.I250I		NM_006539.3	NP_006530.1	O60359	CCG3_HUMAN	calcium channel, voltage-dependent, gamma subunit 3	250					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|prostate(4)|skin(2)	40				GBM - Glioblastoma multiforme(48;0.0809)		TGTCCCCCATCAGCAAAGGCT	0.587																																					p.I250I		Atlas-SNP	.											.	CACNG3	112	.	0			c.C750T						PASS	.			0,4394		0,0,2197	96	101	100		750	4	1	16	dbSNP_134	100	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CACNG3	NM_006539.3		0,1,6496	TT,TC,CC		0.0116,0.0,0.0077		250/316	24372986	1,12993	2197	4300	6497	SO:0001819	synonymous_variant	10368	exon4			CCCCATCAGCAAA	AF131911	CCDS10620.1	16p12.1	2008-05-14			ENSG00000006116	ENSG00000006116		"Calcium channel subunits"	1407	protein-coding gene	gene with protein product		606403				10221464, 10493829	Standard	NM_006539		Approved		uc002dmf.3	O60359	OTTHUMG00000131651	ENST00000005284.3:c.750C>T	chr16.hg19:g.24372986C>T		125.0	0.0	.		121.0	23.0	.	NM_006539		Silent	SNP	ENST00000005284.3	hg19	CCDS10620.1																																																																																			.	C|1.000;T|0.000	0.000	weak		0.587	CACNG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254548.1	NM_006539		T	24372986	C	T	24372986	2	4	28	1	0	0	0	0	0	0	0	1	2560	816	29	2		2	CACNG3	16	24372986	Silent	SNP	C	TCGA-5P-A9JV-01A-12D-A42J-10	19437059	24372986	65981767	43	2012											
HES7	84667	hgsc.bcm.edu	37	chr17	8024974	8024974	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtgaggcggcggtggcggcGgcagcagtccggtgaggggc	4	5	23	9	5	0	2	0	2	0	0	1	2	1	2	1	9	1	2	1	9	0	0			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr17:8024974G>A	ENST00000317814.4	-	4	592	c.593C>T	c.(592-594)cCg>cTg	p.P198L	ALOXE3_ENST00000318227.3_5'Flank|HES7_ENST00000541682.2_Missense_Mutation_p.P203L			Q9BYE0	HES7_HUMAN	hes family bHLH transcription factor 7	198	Pro-rich.				mesoderm development (GO:0007498)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|post-anal tail morphogenesis (GO:0036342)|regulation of somitogenesis (GO:0014807)|rhythmic process (GO:0048511)|skeletal system development (GO:0001501)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription factor binding (GO:0008134)										CGGTGGCGGCGGCAGCAGTCC	0.761																																					p.P203L		Atlas-SNP	.											.	.	.	.	0			c.C608T						PASS	.						1	1	1					17																	8024974		690	1880	2570	SO:0001583	missense	84667	exon4			GGCGGCGGCAGCA	AB049064	CCDS42258.1, CCDS54085.1	17p13.1	2013-10-17	2013-10-17			ENSG00000179111		"Basic helix-loop-helix proteins"	15977	protein-coding gene	gene with protein product	"bHLH factor Hes7"	608059	"hairy and enhancer of split 7 (Drosophila)"			11260262	Standard	NM_032580		Approved	bHLHb37	uc002gkb.2	Q9BYE0		ENST00000317814.4:c.593C>T	chr17.hg19:g.8024974G>A	ENSP00000314774:p.Pro198Leu	361.0	0.0	.		386.0	89.0	.	NM_001165967	F8VPC9	Missense_Mutation	SNP	ENST00000317814.4	hg19	CCDS42258.1	.	.	.	.	.	.	.	.	.	.	G	16.69	3.192157	0.58017	.	.	ENSG00000179111	ENST00000541682;ENST00000317814	T;T	0.79454	-1.27;-1.16	5.1	4.1	0.47936	.	1.346370	0.05201	N	0.505001	T	0.79913	0.4528	N	0.19112	0.55	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.69824	0.925;0.966	T	0.66176	-0.5989	10	0.20519	T	0.43	-7.0736	10.6303	0.45532	0.0:0.0:0.8077:0.1923	.	198;203	Q9BYE0;F8VPC9	HES7_HUMAN;.	L	203;198	ENSP00000446205:P203L;ENSP00000314774:P198L	ENSP00000314774:P198L	P	-	2	0	HES7	7965699	1.000000	0.71417	1.000000	0.80357	0.810000	0.45777	1.887000	0.39698	1.075000	0.40932	0.460000	0.39030	CCG	.	.	.	none		0.761	HES7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441479.1	NM_032580		A	8024974	G	A	8024974	3	1	28	1	0	0	0	0	1	0	0	0	7078	1116	39	1	88	1	HES7	17	8024974	Missense_Mutation	SNP	G	TCGA-5P-A9JV-01A-12D-A42J-10		8024974	73170236	44	2013											
MYH3	4621	hgsc.bcm.edu	37	chr17	10538254	10538254	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacctctccttgcagcctcTgcttggtcttctccagtgaa	5	13	7	16	0	4	1	0	1	4	0	6	1	4	1	5	1	3	2	5	1	1	3			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr17:10538254T>C	ENST00000583535.1	-	31	4346	c.4259A>G	c.(4258-4260)cAg>cGg	p.Q1420R	MYH3_ENST00000226209.7_Missense_Mutation_p.Q1420R	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	1420					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						TTGCAGCCTCTGCTTGGTCTT	0.483																																					p.Q1420R		Atlas-SNP	.											.	MYH3	227	.	0			c.A4259G						PASS	.						121	111	114					17																	10538254		2203	4300	6503	SO:0001583	missense	4621	exon31			AGCCTCTGCTTGG		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"Myosins / Myosin superfamily : Class II"	7573	protein-coding gene	gene with protein product	"myosin, skeletal, heavy chain, embryonic 1", "muscle embryonic myosin heavy chain 3"	160720	"myosin, heavy polypeptide 3, skeletal muscle, embryonic"			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.4259A>G	chr17.hg19:g.10538254T>C	ENSP00000464317:p.Gln1420Arg	97.0	0.0	.		105.0	34.0	.	NM_002470	Q15492	Missense_Mutation	SNP	ENST00000583535.1	hg19	CCDS11157.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.843566	0.91197	.	.	ENSG00000109063	ENST00000226209	T	0.77750	-1.12	5.27	5.27	0.74061	Myosin tail (1);	.	.	.	.	D	0.87075	0.6087	M	0.85777	2.775	0.45056	D	0.998071	D	0.52996	0.957	P	0.57468	0.821	D	0.88963	0.3395	9	0.59425	D	0.04	.	15.4719	0.75446	0.0:0.0:0.0:1.0	.	1420	P11055	MYH3_HUMAN	R	1420	ENSP00000226209:Q1420R	ENSP00000226209:Q1420R	Q	-	2	0	MYH3	10478979	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.291000	0.59025	2.104000	0.64026	0.533000	0.62120	CAG	.	.	.	none		0.483	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470		C	10538254	T	C	10538254	3	2	28	1	0	0	0	0	1	0	0	0	10043	1580	55	3	1607	3	MYH3	17	10538254	Missense_Mutation	SNP	T	TCGA-5P-A9JV-01A-12D-A42J-10	2513280	10538254	70656956	45	2014											
RAI1	10743	hgsc.bcm.edu	37	chr17	17701402	17701402	+	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	accctgaacactgcctccccAaaaagaagccaaaactcaag	17	4	5	15	0	1	2	1	1	0	1	2	2	2	2	5	0	4	0	5	0	7	0			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr17:17701402A>T	ENST00000353383.1	+	3	5609	c.5140A>T	c.(5140-5142)Aaa>Taa	p.K1714*	RAI1_ENST00000261641.6_Intron	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	1714					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)		CTGCCTCCCCAAAAAGAAGCC	0.577																																					p.K1714X		Atlas-SNP	.											.	RAI1	121	.	0			c.A5140T						PASS	.						53	57	56					17																	17701402		2203	4300	6503	SO:0001587	stop_gained	10743	exon3			CTCCCCAAAAAGA	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.5140A>T	chr17.hg19:g.17701402A>T	ENSP00000323074:p.Lys1714*	146.0	0.0	.		165.0	36.0	.	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Nonsense_Mutation	SNP	ENST00000353383.1	hg19	CCDS11188.1	.	.	.	.	.	.	.	.	.	.	A	48	13.919646	0.99770	.	.	ENSG00000108557	ENST00000353383;ENST00000395776;ENST00000315321	.	.	.	5.09	4.01	0.46588	.	0.073600	0.56097	D	0.000029	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.1809	0.54211	0.8568:0.1432:0.0:0.0	.	.	.	.	X	1714;1714;1602	.	ENSP00000322928:K1602X	K	+	1	0	RAI1	17642127	1.000000	0.71417	1.000000	0.80357	0.836000	0.47400	4.724000	0.61972	0.794000	0.33899	-0.375000	0.07067	AAA	.	.	.	none		0.577	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665		T	17701402	A	T	17701402	4	4	28	1	0	0	0	0	0	1	0	0	13020	131	5	5	5142	5	RAI1	17	17701402	Nonsense_Mutation	SNP	A	TCGA-5P-A9JV-01A-12D-A42J-10	7163148	17701402	63493808	46	2015											
CDK5RAP3	80279	hgsc.bcm.edu	37	chr17	46048728	46048728	+	Splice_Site	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	ctcaccgtgtttcccgccagGaccatcagcacgtgcccatc	7	8	8	18	3	2	0	2	0	0	0	4	1	3	1	5	1	2	2	5	1	0	1			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr17:46048728G>T	ENST00000338399.4	+	2	113	c.7G>T	c.(7-9)Gac>Tac	p.D3Y	RP11-6N17.9_ENST00000582262.1_RNA|CDK5RAP3_ENST00000536708.2_Splice_Site_p.D28Y	NM_176096.1	NP_788276.1	Q96JB5	CK5P3_HUMAN	CDK5 regulatory subunit associated protein 3	3					brain development (GO:0007420)|protein ufmylation (GO:0071569)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of neuron differentiation (GO:0045664)	membrane (GO:0016020)	protein kinase binding (GO:0019901)			NS(1)|central_nervous_system(2)|cervix(3)|endometrium(3)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	18						TTCCCGCCAGGACCATCAGCA	0.682																																					p.D3Y		Atlas-SNP	.											.	CDK5RAP3	38	.	0			c.G7T						PASS	.						27	31	30					17																	46048728		2089	4198	6287	SO:0001630	splice_region_variant	80279	exon2			CGCCAGGACCATC	AF110322	CCDS42356.1, CCDS62232.1	17q21.2	2008-07-18				ENSG00000108465			18673	protein-coding gene	gene with protein product	"ischemic heart CDK5 activator-binding protein C53", "LXXLL/leucine-zipper-containing ARFbinding protein"	608202				10721722	Standard	NM_176096		Approved	MST016, FLJ13660, C53, IC53, HSF-27, OK/SW-cl.114, LZAP	uc010wlc.3	Q96JB5		ENST00000338399.4:c.7-1G>T	chr17.hg19:g.46048728G>T		114.0	0.0	.		141.0	39.0	.	NM_176096	B7Z6N4|D3DTU1|D3DTU2|F5H3I5|Q53FA2|Q9H3F8|Q9H8G0|Q9HBR9	Missense_Mutation	SNP	ENST00000338399.4	hg19	CCDS42356.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.316083	0.81469	.	.	ENSG00000108465	ENST00000536708;ENST00000338399	T;T	0.53640	0.61;0.61	5.0	5.0	0.66597	.	0.051123	0.85682	D	0.000000	T	0.57431	0.2053	M	0.71036	2.16	0.80722	D	1	P	0.45474	0.859	P	0.50440	0.641	T	0.58634	-0.7602	9	.	.	.	4.6964	13.7672	0.63002	0.0:0.0:1.0:0.0	.	3	Q96JB5	CK5P3_HUMAN	Y	28;3	ENSP00000438886:D28Y;ENSP00000344683:D3Y	.	D	+	1	0	CDK5RAP3	43403727	1.000000	0.71417	0.999000	0.59377	0.780000	0.44128	6.238000	0.72350	2.337000	0.79520	0.561000	0.74099	GAC	.	.	.	none		0.682	CDK5RAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442913.1	NM_176096	Missense_Mutation	T	46048728	G	T	46048728	5	4	28	1	0	0	0	0	0	0	1	0	3149	1188	41	4	13	4	CDK5RAP3	17	46048728	Splice_Site	SNP	G	TCGA-5P-A9JV-01A-12D-A42J-10	28347326	46048728	35146482	47	2016											
CD7	924	hgsc.bcm.edu	37	chr17	80274160	80274160	+	Missense_Mutation	SNP	C	C	T																															cgcagggagggcagaggctgCtggcgggtcagggagggcag																								rs200504177		TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr17:80274160C>T	ENST00000312648.3	-	3	629	c.523G>A	c.(523-525)Gca>Aca	p.A175T	CD7_ENST00000584284.1_Missense_Mutation_p.A175T|CD7_ENST00000578509.1_Missense_Mutation_p.A75T|CD7_ENST00000583376.1_Missense_Mutation_p.A75T	NM_006137.6	NP_006128.1	P09564	CD7_HUMAN	CD7 molecule	175	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)			GCAGAGGCTGCTGGCGGGTCA	0.716																																					p.A175T	Pancreas(45;804 1068 19702 28207 28798)	Atlas-SNP	.											.	CD7	25	.	0			c.G523A						PASS	.						11	13	13					17																	80274160		2157	4241	6398	SO:0001583	missense	924	exon3			AGGCTGCTGGCGG	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.523G>A	chr17.hg19:g.80274160C>T	ENSP00000312027:p.Ala175Thr	42.0	0.0	.		83.0	25.0	.	NM_006137		Missense_Mutation	SNP	ENST00000312648.3	hg19	CCDS11807.1	.	.	.	.	.	.	.	.	.	.	c	7.421	0.636759	0.14386	.	.	ENSG00000173762	ENST00000312648	T	0.23552	1.9	2.36	-1.28	0.09318	.	.	.	.	.	T	0.10337	0.0253	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	0.35992	-0.9766	9	0.19590	T	0.45	3.6689	5.816	0.18492	0.0:0.4734:0.0:0.5266	.	175;175	Q29VG3;P09564	.;CD7_HUMAN	T	175	ENSP00000312027:A175T	ENSP00000312027:A175T	A	-	1	0	CD7	77867449	0.227000	0.23707	0.003000	0.11579	0.013000	0.08279	0.220000	0.17660	-0.330000	0.08514	-1.031000	0.02408	GCA	.	.	.	weak		0.716	CD7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442826.1	NM_006137		T	80274160	C	T	80274160	3	4	28	1	0	0	0	0	1	0	0	0	3034	797	28	2	207	2	CD7	17	80274160	Missense_Mutation	SNP	C	TCGA-5P-A9JV-01A-12D-A42J-10	34225432	80274160	921050	48	2017	20	2									
CD7	924	hgsc.bcm.edu	37	chr17	80274162	80274162	+	Missense_Mutation	SNP	G	G	T																															cagggagggcagaggctgctGgcgggtcagggagggcagag																								rs201027731|rs555569626	byFrequency	TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr17:80274162G>T	ENST00000312648.3	-	3	627	c.521C>A	c.(520-522)cCa>cAa	p.P174Q	CD7_ENST00000584284.1_Missense_Mutation_p.P174Q|CD7_ENST00000578509.1_Missense_Mutation_p.P74Q|CD7_ENST00000583376.1_Missense_Mutation_p.P74Q	NM_006137.6	NP_006128.1	P09564	CD7_HUMAN	CD7 molecule	174	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)			AGAGGCTGCTGGCGGGTCAGG	0.716																																					p.P174Q	Pancreas(45;804 1068 19702 28207 28798)	Atlas-SNP	.											.,1	CD7	25	.	0			c.C521A						PASS	.						11	14	13					17																	80274162		2162	4241	6403	SO:0001583	missense	924	exon3			GCTGCTGGCGGGT	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.521C>A	chr17.hg19:g.80274162G>T	ENSP00000312027:p.Pro174Gln	46.0	0.0	.		81.0	9.0	.	NM_006137		Missense_Mutation	SNP	ENST00000312648.3	hg19	CCDS11807.1	.	.	.	.	.	.	.	.	.	.	G	4.195	0.034900	0.08101	.	.	ENSG00000173762	ENST00000312648	T	0.19806	2.12	1.69	-3.31	0.04988	.	.	.	.	.	T	0.07503	0.0189	N	0.08118	0	0.09310	N	1	P;P	0.34724	0.465;0.465	B;B	0.30646	0.118;0.118	T	0.36601	-0.9741	9	0.16896	T	0.51	-2.5328	6.7819	0.23650	0.3361:0.0:0.6639:0.0	.	174;174	Q29VG3;P09564	.;CD7_HUMAN	Q	174	ENSP00000312027:P174Q	ENSP00000312027:P174Q	P	-	2	0	CD7	77867451	0.791000	0.28800	0.003000	0.11579	0.009000	0.06853	0.125000	0.15749	-0.861000	0.04094	0.306000	0.20318	CCA	.	.	.	weak		0.716	CD7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442826.1	NM_006137		T	80274162	G	T	80274162	3	4	28	1	0	0	0	0	1	0	0	0	3034	1348	47	4	209	4	CD7	17	80274162	Missense_Mutation	SNP	G	TCGA-5P-A9JV-01A-12D-A42J-10	2	80274162	921048	49	2018	20	2									
MAP2K7	5609	hgsc.bcm.edu	37	chr19	7975205	7975205	+	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	agatgggcagcggcacctgcGgccaggtgtggaagatgcgc	8	5	18	10	3	0	2	0	0	0	2	0	3	0	3	2	5	3	2	2	5	1	0			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr19:7975205G>T	ENST00000397979.3	+	4	448	c.394G>T	c.(394-396)Ggc>Tgc	p.G132C	MAP2K7_ENST00000545011.1_Missense_Mutation_p.G174C|CTD-3193O13.13_ENST00000595655.1_RNA|MAP2K7_ENST00000397983.3_Missense_Mutation_p.G148C|MAP2K7_ENST00000397981.3_Missense_Mutation_p.G132C	NM_145185.2	NP_660186.1	O14733	MP2K7_HUMAN	mitogen-activated protein kinase kinase 7	132	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of neuron apoptotic process (GO:0043525)|response to heat (GO:0009408)|response to osmotic stress (GO:0006970)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|magnesium ion binding (GO:0000287)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(2)|central_nervous_system(3)|endometrium(1)|large_intestine(8)|lung(4)|ovary(1)	19						CGGCACCTGCGGCCAGGTGTG	0.667																																					p.G132C		Atlas-SNP	.											MAP2K7,NS,carcinoma,0,1	MAP2K7	66	.	0			c.G394T						PASS	.						32	39	37					19																	7975205		2033	4174	6207	SO:0001583	missense	5609	exon4			ACCTGCGGCCAGG	AF006689	CCDS42491.1, CCDS74277.1, CCDS74278.1	19p13.3-p13.2	2011-06-09			ENSG00000076984	ENSG00000076984	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6847	protein-coding gene	gene with protein product		603014		PRKMK7		9312068	Standard	XM_005272489		Approved	MKK7, Jnkk2	uc002mit.3	O14733	OTTHUMG00000137368	ENST00000397979.3:c.394G>T	chr19.hg19:g.7975205G>T	ENSP00000381066:p.Gly132Cys	134.0	0.0	.		153.0	40.0	.	NM_145185	B2R9S5|D6W659|O14648|O14816|O60452|O60453|Q1PG43|Q8IY10	Missense_Mutation	SNP	ENST00000397979.3	hg19	CCDS42491.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.016907	0.93404	.	.	ENSG00000076984	ENST00000397981;ENST00000397983;ENST00000545011;ENST00000425613;ENST00000397979	T;T;T;T	0.80738	-1.41;-1.41;-1.41;-1.41	5.31	5.31	0.75309	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.94345	0.8182	H	0.99156	4.45	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96653	0.9483	10	0.87932	D	0	-12.8954	16.4609	0.84044	0.0:0.0:1.0:0.0	.	132;132	O14733-4;O14733	.;MP2K7_HUMAN	C	132;148;174;148;132	ENSP00000381068:G132C;ENSP00000381070:G148C;ENSP00000443946:G174C;ENSP00000381066:G132C	ENSP00000381066:G132C	G	+	1	0	MAP2K7	7881205	1.000000	0.71417	0.995000	0.50966	0.918000	0.54935	9.407000	0.97325	2.502000	0.84385	0.561000	0.74099	GGC	.	.	.	none		0.667	MAP2K7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000267980.1			T	7975205	G	T	7975205	3	4	28	1	0	0	0	0	1	0	0	0	9249	1116	39	4	408	4	MAP2K7	19	7975205	Missense_Mutation	SNP	G	TCGA-5P-A9JV-01A-12D-A42J-10		7975205	51153778	50	2019											
MUC16	94025	hgsc.bcm.edu	37	chr19	9045908	9045908	+	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	cagtttggggcttatcagttGttatagaggcactggaaagc	10	12	13	6	0	1	1	1	0	0	1	1	2	1	2	0	4	1	5	0	4	4	5			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr19:9045908G>C	ENST00000397910.4	-	5	35926	c.35723C>G	c.(35722-35724)aCa>aGa	p.T11908R		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11910	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						CTTATCAGTTGTTATAGAGGC	0.517																																					p.T11908R		Atlas-SNP	.											.	MUC16	4315	.	0			c.C35723G						PASS	.						99	94	95					19																	9045908		1901	4127	6028	SO:0001583	missense	94025	exon5			TCAGTTGTTATAG	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.35723C>G	chr19.hg19:g.9045908G>C	ENSP00000381008:p.Thr11908Arg	90.0	0.0	.		121.0	31.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	G	6.583	0.475972	0.12521	.	.	ENSG00000181143	ENST00000397910	T	0.02258	4.37	3.79	1.67	0.24075	.	.	.	.	.	T	0.04588	0.0125	N	0.24115	0.695	.	.	.	D	0.76494	0.999	D	0.72075	0.976	T	0.38415	-0.9662	8	0.87932	D	0	.	5.8956	0.18937	0.2331:0.0:0.7669:0.0	.	11908	B5ME49	.	R	11908	ENSP00000381008:T11908R	ENSP00000381008:T11908R	T	-	2	0	MUC16	8906908	0.019000	0.18553	0.002000	0.10522	0.008000	0.06430	1.589000	0.36644	0.584000	0.29591	0.555000	0.69702	ACA	.	.	.	none		0.517	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9045908	G	C	9045908	3	2	28	1	0	0	0	0	1	0	0	0	9980	1377	48	4	8120	4	MUC16	19	9045908	Missense_Mutation	SNP	G	TCGA-5P-A9JV-01A-12D-A42J-10	1070703	9045908	50083075	51	2020											
PRKCG	5582	hgsc.bcm.edu	37	chr19	54385763	54385763	+	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	ggggccatggctggtctgggCcccggcgtaggcgattcaga	5	7	18	11	3	2	1	1	0	1	1	2	2	2	1	3	7	0	2	3	7	1	2			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr19:54385763C>T	ENST00000263431.3	+	1	297	c.15C>T	c.(13-15)ggC>ggT	p.G5G	PRKCG_ENST00000536044.1_Silent_p.G5G|PRKCG_ENST00000540413.1_Silent_p.G5G|PRKCG_ENST00000542049.1_5'Flank	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	5					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)	CTGGTCTGGGCCCCGGCGTAG	0.617																																					p.G5G		Atlas-SNP	.											.	PRKCG	246	.	0			c.C15T						PASS	.						71	85	80					19																	54385763		2200	4298	6498	SO:0001819	synonymous_variant	5582	exon1			TCTGGGCCCCGGC	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.15C>T	chr19.hg19:g.54385763C>T		109.0	0.0	.		124.0	27.0	.	NM_002739	B7Z8Q0	Silent	SNP	ENST00000263431.3	hg19	CCDS12867.1																																																																																			.	.	.	none		0.617	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739		T	54385763	C	T	54385763	2	4	28	1	0	0	0	0	0	0	0	1	12522	726	26	2		2	PRKCG	19	54385763	Silent	SNP	C	TCGA-5P-A9JV-01A-12D-A42J-10	45339855	54385763	4743220	52	2021											
TMC2	117532	hgsc.bcm.edu	37	chr20	2618194	2618194	+	Missense_Mutation	SNP	A	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	gattcagaggacacacctaaAagcagctccaaaaatgccac	17	5	7	12	0	1	1	1	0	0	1	2	3	2	2	3	1	3	2	3	1	4	2	rs186977735		TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chr20:2618194A>C	ENST00000358864.1	+	19	2475	c.2460A>C	c.(2458-2460)aaA>aaC	p.K820N		NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	820					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						ACACACCTAAAAGCAGCTCCA	0.438																																					p.K820N		Atlas-SNP	.											.	TMC2	121	.	0			c.A2460C						PASS	.						154	145	148					20																	2618194		2203	4300	6503	SO:0001583	missense	117532	exon19			ACCTAAAAGCAGC	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.2460A>C	chr20.hg19:g.2618194A>C	ENSP00000351732:p.Lys820Asn	105.0	0.0	.		83.0	11.0	.	NM_080751	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Missense_Mutation	SNP	ENST00000358864.1	hg19	CCDS13029.2	.	.	.	.	.	.	.	.	.	.	a	6.895	0.534564	0.13188	.	.	ENSG00000149488	ENST00000358864	T	0.64991	-0.13	4.88	-0.0212	0.13952	.	0.456200	0.22845	N	0.054932	T	0.42607	0.1210	L	0.44542	1.39	0.09310	N	1	B	0.25521	0.128	B	0.14023	0.01	T	0.13764	-1.0497	10	0.22109	T	0.4	-3.5909	3.5807	0.07952	0.5572:0.0:0.2825:0.1603	.	820	Q8TDI7	TMC2_HUMAN	N	820	ENSP00000351732:K820N	ENSP00000351732:K820N	K	+	3	2	TMC2	2566194	0.000000	0.05858	0.000000	0.03702	0.645000	0.38454	0.406000	0.21032	-0.110000	0.12022	-0.386000	0.06593	AAA	.	A|1.000;G|0.000	.	alt		0.438	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2			C	2618194	A	C	2618194	3	2	28	1	0	0	0	0	1	0	0	0	15997	11	1	5	2534	5	TMC2	20	2618194	Missense_Mutation	SNP	A	TCGA-5P-A9JV-01A-12D-A42J-10		2618194	60407326	53	2022											
FAM48B1	100130302	hgsc.bcm.edu	37	chrX	24382426	24382426	+	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	0	0	0	0	0	0	0	0	0	ctgctgctgctgctgctgctGctcctgctcctgctctagct	1	14	10	16	0	1	0	0	0	1	0	3	0	3	0	2	0	10	10	2	0	1	1			TCGA-5P-A9JV-01A-12D-A42J-10	TCGA-5P-A9JV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	16f56910-a925-41a1-8bbc-d8554292616a	d2370805-678e-421c-83ac-49a5cec3cf51	g.chrX:24382426G>C								AC004552.1 (15403 upstream) : PDK3 (100911 downstream)																							tgctgctgctgctcctgctcc	0.627																																					p.A517P		Atlas-SNP	.											.	.	.	.	0			c.G1549C						PASS	.						2	2	2					X																	24382426		1073	2483	3556	SO:0001628	intergenic_variant	100130302	exon1			GCTGCTGCTCCTG																													chrX.hg19:g.24382426G>C		80.0	0.0	.		86.0	11.0	.	NM_001136234		Missense_Mutation	SNP		hg19																																																																																				.	.	.	none	0	0.627									C	24382426	G	C	24382426	1	2	28	0	1	0	0	0	0	0	0	0	5580	1319	46	4		4	FAM48B1	23	24382426	IGR	SNP	G	TCGA-5P-A9JV-01A-12D-A42J-10		24382426	130888134	54	2023											
ATP13A2	23400	hgsc.bcm.edu	37	chr1	17328590	17328590	+	Missense_Mutation	SNP	A	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	tgatcacgttggggccgtaaAtggccttcctggaagagggg	8	9	16	8	2	1	2	1	1	0	1	2	3	2	3	3	6	0	2	3	6	3	3			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr1:17328590A>C	ENST00000326735.8	-	8	677	c.644T>G	c.(643-645)aTt>aGt	p.I215S	ATP13A2_ENST00000452699.1_Missense_Mutation_p.I210S|RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000502860.1_5'Flank|ATP13A2_ENST00000341676.5_Missense_Mutation_p.I210S			Q9NQ11	AT132_HUMAN	ATPase type 13A2	215					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		GGGGCCGTAAATGGCCTTCCT	0.637																																					p.I215S		Atlas-SNP	.											.	ATP13A2	85	.	0			c.T644G						PASS	.						64	58	60					1																	17328590		2203	4300	6503	SO:0001583	missense	23400	exon8			CCGTAAATGGCCT	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"ATPases / P-type", "Parkinson disease"	30213	protein-coding gene	gene with protein product		610513	"Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.644T>G	chr1.hg19:g.17328590A>C	ENSP00000327214:p.Ile215Ser	227.0	0.0	.		277.0	85.0	.	NM_022089	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Missense_Mutation	SNP	ENST00000326735.8	hg19	CCDS175.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.02|13.02	2.111352|2.111352	0.37242|0.37242	.|.	.|.	ENSG00000159363|ENSG00000159363	ENST00000510069;ENST00000508222|ENST00000326735;ENST00000341676;ENST00000452699;ENST00000511957	.|D;D;D;D	.|0.88896	.|-2.44;-2.44;-2.44;-2.44	4.89|4.89	4.89|4.89	0.63831|0.63831	.|ATPase, P-type cation-transporter, N-terminal (1);	.|0.405796	.|0.29594	.|N	.|0.011708	D|D	0.90553|0.90553	0.7039|0.7039	M|M	0.90425|0.90425	3.115|3.115	0.23416|0.23416	N|N	0.997725|0.997725	.|P;P;P	.|0.44776	.|0.784;0.843;0.756	.|B;B;B	.|0.41723	.|0.326;0.365;0.288	D|D	0.86293|0.86293	0.1675|0.1675	5|10	.|0.51188	.|T	.|0.08	-5.3789|-5.3789	12.0045|12.0045	0.53251|0.53251	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|210;210;215	.|Q5JXY1;Q6S9Z9;Q9NQ11	.|.;.;AT132_HUMAN	Q|S	189;121|215;210;210;119	.|ENSP00000327214:I215S;ENSP00000341115:I210S;ENSP00000413307:I210S;ENSP00000427241:I119S	.|ENSP00000327214:I215S	H|I	-|-	3|2	2|0	ATP13A2|ATP13A2	17201177|17201177	1.000000|1.000000	0.71417|0.71417	0.085000|0.085000	0.20634|0.20634	0.421000|0.421000	0.31385|0.31385	6.664000|6.664000	0.74437|0.74437	2.065000|2.065000	0.61736|0.61736	0.459000|0.459000	0.35465|0.35465	CAT|ATT	.	.	.	none		0.637	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089		C	17328590	A	C	17328590	3	2	29	1	0	0	0	0	1	0	0	0	1124	101	4	5	3222	5	ATP13A2	1	17328590	Missense_Mutation	SNP	A	TCGA-5P-A9JW-01A-11D-A42J-10		17328590	231922031	1	2024											
RPA2	6118	hgsc.bcm.edu	37	chr1	28240584	28240584	+	Missense_Mutation	SNP	T	T	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	ttcaacctactgatttctttTcggcttgagaaggtgcgggc	7	14	11	9	2	2	2	1	2	1	1	3	3	2	2	1	3	3	1	1	3	3	6			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr1:28240584T>G	ENST00000373912.3	-	2	406	c.107A>C	c.(106-108)gAa>gCa	p.E36A	RPA2_ENST00000313433.7_Missense_Mutation_p.E124A|RPA2_ENST00000373909.3_Missense_Mutation_p.E44A	NM_002946.3	NP_002937.1	P15927	RFA2_HUMAN	replication protein A2, 32kDa	36					base-excision repair (GO:0006284)|DNA recombinase assembly (GO:0000730)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|mitotic G1 DNA damage checkpoint (GO:0031571)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of DNA damage checkpoint (GO:2000001)|regulation of double-strand break repair via homologous recombination (GO:0010569)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor A complex (GO:0005662)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|enzyme binding (GO:0019899)|protein phosphatase binding (GO:0019903)|single-stranded DNA binding (GO:0003697)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|prostate(3)|skin(1)	11		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00588)|all_lung(284;0.00645)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0429)|OV - Ovarian serous cystadenocarcinoma(117;3.62e-24)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;1.75e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00294)|STAD - Stomach adenocarcinoma(196;0.00308)|BRCA - Breast invasive adenocarcinoma(304;0.00613)|READ - Rectum adenocarcinoma(331;0.0649)		TGATTTCTTTTCGGCTTGAGA	0.498								Direct reversal of damage;Nucleotide excision repair (NER)																													p.E36A		Atlas-SNP	.											.	RPA2	34	.	0			c.A107C						PASS	.						62	71	68					1																	28240584		2203	4300	6503	SO:0001583	missense	6118	exon2			TTCTTTTCGGCTT	BC021257	CCDS314.1, CCDS72740.1	1p35	2008-02-05	2002-08-29		ENSG00000117748	ENSG00000117748			10290	protein-coding gene	gene with protein product		179836	"replication protein A2 (32kD)"			8454588	Standard	XM_005245965		Approved		uc001bpe.1	P15927	OTTHUMG00000003915	ENST00000373912.3:c.107A>C	chr1.hg19:g.28240584T>G	ENSP00000363021:p.Glu36Ala	97.0	0.0	.		99.0	27.0	.	NM_002946	Q52II0|Q5TEI9|Q5TEJ5	Missense_Mutation	SNP	ENST00000373912.3	hg19	CCDS314.1	.	.	.	.	.	.	.	.	.	.	T	11.95	1.790742	0.31685	.	.	ENSG00000117748	ENST00000373912;ENST00000373909;ENST00000313433;ENST00000444045	T;T;T;T	0.22134	2.29;2.28;2.25;1.97	4.59	4.59	0.56863	.	0.048023	0.85682	D	0.000000	T	0.20577	0.0495	L	0.58101	1.795	0.50467	D	0.999874	B;B	0.24043	0.001;0.096	B;B	0.20184	0.003;0.028	T	0.04140	-1.0974	10	0.14656	T	0.56	-13.889	13.2408	0.59995	0.0:0.0:0.0:1.0	.	36;44	P15927;P15927-2	RFA2_HUMAN;.	A	36;44;124;40	ENSP00000363021:E36A;ENSP00000363017:E44A;ENSP00000363015:E124A;ENSP00000387649:E40A	ENSP00000363015:E124A	E	-	2	0	RPA2	28113171	0.998000	0.40836	0.963000	0.40424	0.220000	0.24768	3.230000	0.51286	1.834000	0.53371	0.454000	0.30748	GAA	.	.	.	none		0.498	RPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011179.1	NM_002946		G	28240584	T	G	28240584	3	3	29	1	0	0	0	0	1	0	0	0	13550	1783	62	5	737	5	RPA2	1	28240584	Missense_Mutation	SNP	T	TCGA-5P-A9JW-01A-11D-A42J-10	10911994	28240584	221010037	2	2025											
DENND2C	163259	hgsc.bcm.edu	37	chr1	115143493	115143493	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgtgatggtgcgtccaggaGctgggaaaggagcttccatg	8	9	16	8	1	0	1	0	1	0	0	2	4	2	4	2	4	3	2	2	4	1	1			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr1:115143493G>A	ENST00000393274.1	-	14	2529	c.1904C>T	c.(1903-1905)gCt>gTt	p.A635V	DENND2C_ENST00000481894.1_5'UTR|DENND2C_ENST00000393277.1_Missense_Mutation_p.A635V|DENND2C_ENST00000393276.3_Missense_Mutation_p.A578V	NM_001256404.1	NP_001243333.1	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	635	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|breast(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|skin(3)	37	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GCGTCCAGGAGCTGGGAAAGG	0.448																																					p.A635V		Atlas-SNP	.											.	DENND2C	105	.	0			c.C1904T						PASS	.						128	124	125					1																	115143493		2203	4300	6503	SO:0001583	missense	163259	exon14			CCAGGAGCTGGGA		CCDS875.1, CCDS58018.1	1p13.2-p13.1	2012-10-03			ENSG00000175984	ENSG00000175984		"DENN/MADD domain containing"	24748	protein-coding gene	gene with protein product							Standard	NM_198459		Approved	FLJ37099, DKFZp686G0351, DKFZp779P1149, dJ1156J9.1, RP5-1156J9.1	uc001efd.1	Q68D51	OTTHUMG00000011893	ENST00000393274.1:c.1904C>T	chr1.hg19:g.115143493G>A	ENSP00000376955:p.Ala635Val	136.0	0.0	.		116.0	28.0	.	NM_001256404	B1AL26|Q5TCX6|Q6P3R3	Missense_Mutation	SNP	ENST00000393274.1	hg19	CCDS58018.1	.	.	.	.	.	.	.	.	.	.	G	35	5.559025	0.96514	.	.	ENSG00000175984	ENST00000393276;ENST00000393274;ENST00000369540;ENST00000393277	T;T;T	0.12465	2.68;2.68;2.68	5.18	5.18	0.71444	DENN (3);	0.000000	0.49916	U	0.000121	T	0.31389	0.0795	M	0.72576	2.205	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.986	T	0.08743	-1.0707	10	0.87932	D	0	.	18.7701	0.91888	0.0:0.0:1.0:0.0	.	635;578	Q68D51;Q68D51-3	DEN2C_HUMAN;.	V	578;635;635;635	ENSP00000376957:A578V;ENSP00000376955:A635V;ENSP00000376958:A635V	ENSP00000358553:A635V	A	-	2	0	DENND2C	114945016	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.431000	0.82371	0.650000	0.86243	GCT	.	.	.	none		0.448	DENND2C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000314822.1	NM_198459		A	115143493	G	A	115143493	3	1	29	1	0	0	0	0	1	0	0	0	4432	971	34	2	914	2	DENND2C	1	115143493	Missense_Mutation	SNP	G	TCGA-5P-A9JW-01A-11D-A42J-10	86902909	115143493	134107128	3	2026											
RGL1	23179	hgsc.bcm.edu	37	chr1	183876147	183876147	+	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	gcccccttctctttctcagcTatgccctgtcatgtgagatt	5	15	7	14	0	3	1	2	1	2	1	5	2	3	1	3	0	2	1	3	0	1	4			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr1:183876147T>G	ENST00000360851.3	+	14	1652	c.1474T>G	c.(1474-1476)Tat>Gat	p.Y492D	RGL1_ENST00000536277.1_Splice_Site_p.Y490D|RGL1_ENST00000539189.1_Splice_Site_p.Y463D|RGL1_ENST00000304685.4_Splice_Site_p.Y527D			Q9NZL6	RGL1_HUMAN	ral guanine nucleotide dissociation stimulator-like 1	492	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				cellular lipid metabolic process (GO:0044255)|positive regulation of Ral GTPase activity (GO:0032852)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(5)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(17)|ovary(4)|prostate(3)|stomach(1)	51						CTTTCTCAGCTATGCCCTGTC	0.493																																					p.Y527D		Atlas-SNP	.											.	RGL1	91	.	0			c.T1579G						PASS	.						52	48	50					1																	183876147		2203	4300	6503	SO:0001630	splice_region_variant	23179	exon15			CTCAGCTATGCCC	AF186780	CCDS1359.1, CCDS72992.1	1q25.2	2008-02-05			ENSG00000143344	ENSG00000143344			30281	protein-coding gene	gene with protein product		605667				10760592, 10231032	Standard	XM_005245010		Approved	RGL	uc001gqm.3	Q9NZL6	OTTHUMG00000035328	ENST00000360851.3:c.1473-1T>G	chr1.hg19:g.183876147T>G		59.0	0.0	.		63.0	17.0	.	NM_015149	Q5SXQ2|Q5SXQ6|Q9HBY3|Q9HBY4|Q9NZL5|Q9UG43|Q9Y2G6	Missense_Mutation	SNP	ENST00000360851.3	hg19		.	.	.	.	.	.	.	.	.	.	T	23.7	4.452241	0.84209	.	.	ENSG00000143344	ENST00000304685;ENST00000367531;ENST00000536277;ENST00000543395;ENST00000360851;ENST00000539189	T;T;T;T;T	0.37752	1.18;1.18;1.18;1.18;1.18	5.1	5.1	0.69264	Guanine-nucleotide dissociation stimulator CDC25 (3);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.71668	0.3367	H	0.95884	3.735	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.998;0.997;0.998;0.998	D;D;D;D;D	0.85130	0.997;0.994;0.986;0.994;0.994	T	0.81920	-0.0712	10	0.87932	D	0	.	14.5673	0.68185	0.0:0.0:0.0:1.0	.	463;490;297;492;527	F5H6U6;B7Z2W5;F5H3C3;Q9NZL6;Q5SXQ6	.;.;.;RGL1_HUMAN;.	D	527;527;490;297;492;463	ENSP00000303192:Y527D;ENSP00000356501:Y527D;ENSP00000438662:Y490D;ENSP00000354097:Y492D;ENSP00000437355:Y463D	ENSP00000303192:Y527D	Y	+	1	0	RGL1	182142770	1.000000	0.71417	0.991000	0.47740	0.929000	0.56500	7.564000	0.82326	1.920000	0.55613	0.459000	0.35465	TAT	.	.	.	none		0.493	RGL1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000085742.1	NM_015149	Missense_Mutation	G	183876147	T	G	183876147	5	3	29	1	0	0	0	0	0	0	1	0	13289	1536	53	5	1633	5	RGL1	1	183876147	Splice_Site	SNP	T	TCGA-5P-A9JW-01A-11D-A42J-10	68732654	183876147	65374474	4	2027											
AHCTF1	25909	hgsc.bcm.edu	37	chr1	247070993	247070993	+	Frame_Shift_Del	DEL	C	C	-																															aactggaaacacagatggcgCccttgtctcattacactttc																										TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr1:247070993delC	ENST00000391829.2	-	5	747	c.624delG	c.(622-624)gggfs	p.G208fs	AHCTF1_ENST00000366508.1_Frame_Shift_Del_p.G243fs|AHCTF1_ENST00000326225.3_Frame_Shift_Del_p.G217fs			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	208	Necessary for cytoplasmic localization. {ECO:0000250}.|Seven-bladed beta propeller repeats. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			ACAGATGGCGCCCTTGTCTCA	0.388																																					p.R218fs	Colon(145;197 1800 4745 15099 26333)	Atlas-Indel,Pindel	.											AHCTF1,colon,carcinoma,0,1	AHCTF1	187	.	0			c.652delC						PASS	.						134	126	129					1																	247070993		2203	4300	6503	SO:0001589	frameshift_variant	25909	exon5			.		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.624delG	chr1.hg19:g.247070993delC	ENSP00000375705:p.Gly208fs	231.0	0.0	0		229.0	55.0	0.240175	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Frame_Shift_Del	DEL	ENST00000391829.2	hg19																																																																																				.	.	.	none		0.388	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446		-	247070993	C	-	247070993	7	5	29	1	0	1	0	1	0	0	0	0	408	726	26	0	6304	0	AHCTF1	1	247070993	Frame_Shift_Del	DEL	C	TCGA-5P-A9JW-01A-11D-A42J-10	63194846	247070993	2179628	5	2028											
EPCAM	4072	hgsc.bcm.edu	37	chr2	47601159	47601159	+	Missense_Mutation	SNP	A	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	gaacagacaaggacactgaaAtaacctgctctgagcgagtg	15	6	11	9	1	1	3	0	2	1	1	1	6	1	4	1	1	4	1	1	1	4	1			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr2:47601159A>C	ENST00000263735.4	+	3	755	c.397A>C	c.(397-399)Ata>Cta	p.I133L	EPCAM_ENST00000405271.1_Missense_Mutation_p.I161L	NM_002354.2	NP_002345.2	P16422	EPCAM_HUMAN	epithelial cell adhesion molecule	133	Thyroglobulin type-1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction involved in regulation of gene expression (GO:0023019)|stem cell differentiation (GO:0048863)|ureteric bud development (GO:0001657)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	protein complex binding (GO:0032403)	p.0?(2)|p.?(1)		endometrium(3)|large_intestine(1)|liver(2)|lung(7)|skin(1)|stomach(1)	15						GGACACTGAAATAACCTGCTC	0.453																																					p.I133L		Atlas-SNP	.											.	EPCAM	27	.	3	Whole gene deletion(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(3)	c.A397C						PASS	.						61	56	58					2																	47601159		2203	4300	6503	SO:0001583	missense	4072	exon3			ACTGAAATAACCT	M33011	CCDS1833.1	2p21	2014-09-17	2008-12-16	2008-12-16	ENSG00000119888	ENSG00000119888		"CD molecules"	11529	protein-coding gene	gene with protein product		185535	"antigen identified by monoclonal antibody AUA1", "tumor-associated calcium signal transducer 1"	M4S1, MIC18, TACSTD1		8382772, 11306819	Standard	NM_002354		Approved	Ly74, TROP1, GA733-2, EGP34, EGP40, EGP-2, KSA, CD326, Ep-CAM, HEA125, KS1/4, MK-1, MH99, MOC31, 323/A3, 17-1A, TACST-1, CO-17A, ESA	uc002rvx.3	P16422	OTTHUMG00000128853	ENST00000263735.4:c.397A>C	chr2.hg19:g.47601159A>C	ENSP00000263735:p.Ile133Leu	134.0	0.0	.		115.0	34.0	.	NM_002354	P18180|Q6FG26|Q6FG49|Q96C47|Q9UCD0	Missense_Mutation	SNP	ENST00000263735.4	hg19	CCDS1833.1	.	.	.	.	.	.	.	.	.	.	A	6.234	0.411217	0.11812	.	.	ENSG00000119888	ENST00000405271;ENST00000263735	T;T	0.61510	0.1;0.1	5.93	5.93	0.95920	Thyroglobulin type-1 (4);	0.396683	0.28414	N	0.015423	T	0.33760	0.0874	N	0.13327	0.33	0.33639	D	0.60697	B;B	0.17465	0.022;0.022	B;B	0.19946	0.027;0.027	T	0.38564	-0.9655	10	0.02654	T	1	-14.877	8.4191	0.32690	0.7393:0.1257:0.0:0.135	.	133;161	P16422;B5MCA4	EPCAM_HUMAN;.	L	161;133	ENSP00000385476:I161L;ENSP00000263735:I133L	ENSP00000263735:I133L	I	+	1	0	EPCAM	47454663	0.876000	0.30132	0.840000	0.33206	0.979000	0.70002	1.427000	0.34881	2.281000	0.76405	0.533000	0.62120	ATA	.	.	.	none		0.453	EPCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250792.2			C	47601159	A	C	47601159	3	2	29	1	0	0	0	0	1	0	0	0	5164	101	4	5	407	5	EPCAM	2	47601159	Missense_Mutation	SNP	A	TCGA-5P-A9JW-01A-11D-A42J-10		47601159	195598214	6	2029											
SMEK2	57223	hgsc.bcm.edu	37	chr2	55826141	55826141	+	Missense_Mutation	SNP	T	T	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	cagattcatcaatgaggtccTgtgtgacttccactgatggg	9	12	11	9	0	2	4	2	3	0	1	4	4	4	4	2	2	0	0	2	2	1	2			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr2:55826141T>G	ENST00000345102.5	-	4	633	c.332A>C	c.(331-333)cAg>cCg	p.Q111P	SMEK2_ENST00000272313.5_Missense_Mutation_p.Q111P|SMEK2_ENST00000407823.3_Missense_Mutation_p.Q111P	NM_001122964.1	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	111					positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			AATGAGGTCCTGTGTGACTTC	0.348																																					p.Q111P		Atlas-SNP	.											.	SMEK2	86	.	0			c.A332C						PASS	.						114	123	120					2																	55826141		2203	4300	6503	SO:0001583	missense	57223	exon4			AGGTCCTGTGTGA	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.332A>C	chr2.hg19:g.55826141T>G	ENSP00000339769:p.Gln111Pro	29.0	0.0	.		50.0	11.0	.	NM_001122964	Q6P9B0|Q86XB8|Q9BQJ0|Q9BRK2|Q9H913|Q9P2G0	Missense_Mutation	SNP	ENST00000345102.5	hg19	CCDS46289.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.982446	0.74474	.	.	ENSG00000138041	ENST00000272313;ENST00000407823;ENST00000345102	T;T;T	0.44083	0.93;0.93;0.93	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.60779	0.2295	M	0.67397	2.05	0.80722	D	1	D;D;D	0.67145	0.98;0.996;0.991	P;D;P	0.65323	0.844;0.934;0.844	T	0.58819	-0.7569	10	0.34782	T	0.22	-7.2839	16.0711	0.80936	0.0:0.0:0.0:1.0	.	111;111;111	Q5MIZ7-2;Q5MIZ7;Q5MIZ7-3	.;P4R3B_HUMAN;.	P	111	ENSP00000272313:Q111P;ENSP00000385912:Q111P;ENSP00000339769:Q111P	ENSP00000272313:Q111P	Q	-	2	0	SMEK2	55679645	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.040000	0.89188	2.197000	0.70478	0.482000	0.46254	CAG	.	.	.	none		0.348	SMEK2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251483.1	NM_020463		G	55826141	T	G	55826141	3	3	29	1	0	0	0	0	1	0	0	0	14807	1580	55	5	2273	5	SMEK2	2	55826141	Missense_Mutation	SNP	T	TCGA-5P-A9JW-01A-11D-A42J-10	8224982	55826141	187373232	7	2030											
STARD7	56910	hgsc.bcm.edu	37	chr2	96852507	96852507	+	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	gcagggccacagctgccctcGttctttcgctcagaggactg	6	9	12	14	2	2	1	1	0	1	1	4	2	2	2	2	2	2	4	2	2	0	2	rs114169229	byFrequency	TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr2:96852507G>T	ENST00000337288.5	-	8	1457	c.1074C>A	c.(1072-1074)aaC>aaA	p.N358K	STARD7_ENST00000462501.1_5'UTR	NM_020151.3	NP_064536.2	Q9NQZ5	STAR7_HUMAN	StAR-related lipid transfer (START) domain containing 7	358						mitochondrion (GO:0005739)	lipid binding (GO:0008289)			endometrium(2)|kidney(1)|large_intestine(1)|lung(8)|stomach(2)	14						AGCTGCCCTCGTTCTTTCGCT	0.502																																					p.N358K		Atlas-SNP	.											.	STARD7	49	.	0			c.C1074A						PASS	.						74	69	71					2																	96852507		2203	4300	6503	SO:0001583	missense	56910	exon8			GCCCTCGTTCTTT	AF270647	CCDS2017.2	2p11.1	2011-09-12	2007-08-16		ENSG00000084090	ENSG00000084090		"StAR-related lipid transfer (START) domain containing"	18063	protein-coding gene	gene with protein product			"START domain containing 7"				Standard	NM_020151		Approved	GTT1	uc002svm.4	Q9NQZ5	OTTHUMG00000130457	ENST00000337288.5:c.1074C>A	chr2.hg19:g.96852507G>T	ENSP00000338030:p.Asn358Lys	110.0	0.0	.		104.0	32.0	.	NM_020151	D3DXG9|Q53T44|Q6GU43|Q969M6	Missense_Mutation	SNP	ENST00000337288.5	hg19	CCDS2017.2	.	.	.	.	.	.	.	.	.	.	G	12.13	1.845469	0.32606	.	.	ENSG00000084090	ENST00000337288	T	0.42131	0.98	5.84	-7.15	0.01521	.	0.464535	0.25375	N	0.031122	T	0.18551	0.0445	N	0.14661	0.345	0.31229	N	0.696539	B	0.02656	0.0	B	0.04013	0.001	T	0.22277	-1.0221	10	0.15066	T	0.55	-2.3782	13.2244	0.59907	0.1327:0.0:0.7731:0.0942	.	358	Q9NQZ5	STAR7_HUMAN	K	358	ENSP00000338030:N358K	ENSP00000338030:N358K	N	-	3	2	STARD7	96216234	0.000000	0.05858	0.020000	0.16555	0.505000	0.33919	-1.852000	0.01667	-1.229000	0.02564	-0.302000	0.09304	AAC	.	G|0.998;A|0.002	.	alt		0.502	STARD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252848.2			T	96852507	G	T	96852507	3	4	29	1	0	0	0	0	1	0	0	0	15274	1136	40	4	42	4	STARD7	2	96852507	Missense_Mutation	SNP	G	TCGA-5P-A9JW-01A-11D-A42J-10	41026366	96852507	146346866	8	2031											
CCDC148	130940	hgsc.bcm.edu	37	chr2	159170296	159170296	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcctagatttgtgaggaaaaTatctttgtaacatgtccaga	13	13	9	6	0	1	3	0	1	1	2	2	4	2	4	2	1	1	1	2	1	5	5			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr2:159170296T>C	ENST00000283233.5	-	8	1188	c.875A>G	c.(874-876)tAt>tGt	p.Y292C	CCDC148_ENST00000409187.1_Missense_Mutation_p.Y301C|CCDC148_ENST00000536771.1_Missense_Mutation_p.Y206C	NM_138803.3	NP_620158.3	Q8NFR7	CC148_HUMAN	coiled-coil domain containing 148	292										endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23						GTGAGGAAAATATCTTTGTAA	0.378																																					p.Y292C		Atlas-SNP	.											.	CCDC148	64	.	0			c.A875G						PASS	.						110	111	111					2																	159170296		2203	4300	6503	SO:0001583	missense	130940	exon8			GGAAAATATCTTT		CCDS33304.1	2q24.1	2007-12-07			ENSG00000153237	ENSG00000153237			25191	protein-coding gene	gene with protein product							Standard	NM_138803		Approved	MGC125588	uc002tzq.3	Q8NFR7	OTTHUMG00000153973	ENST00000283233.5:c.875A>G	chr2.hg19:g.159170296T>C	ENSP00000283233:p.Tyr292Cys	68.0	0.0	.		99.0	32.0	.	NM_138803	F5H839|Q3B7I3|Q3B7I4|Q3KR41|Q4ZG12|Q4ZG23|Q53TM6|Q96BN5|Q96LM2	Missense_Mutation	SNP	ENST00000283233.5	hg19	CCDS33304.1	.	.	.	.	.	.	.	.	.	.	T	11.37	1.618527	0.28801	.	.	ENSG00000153237	ENST00000283233;ENST00000375617;ENST00000409187;ENST00000536771	T;T;T	0.31510	1.94;1.94;1.49	5.25	2.81	0.32909	.	.	.	.	.	T	0.39410	0.1077	L	0.35288	1.05	0.28868	N	0.895142	D;D;D;B;B	0.89917	1.0;1.0;1.0;0.003;0.001	D;D;D;B;B	0.73380	0.98;0.98;0.98;0.005;0.003	T	0.14448	-1.0472	9	0.38643	T	0.18	-1.2543	8.4684	0.32971	0.0:0.1691:0.0:0.8309	.	206;140;140;301;292	F5H839;C9JR76;Q8NFR7-2;B8ZZV3;Q8NFR7	.;.;.;.;CC148_HUMAN	C	292;140;301;206	ENSP00000283233:Y292C;ENSP00000386674:Y301C;ENSP00000443740:Y206C	ENSP00000283233:Y292C	Y	-	2	0	CCDC148	158878542	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	0.803000	0.27083	0.841000	0.35020	0.460000	0.39030	TAT	.	.	.	none		0.378	CCDC148-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333270.1	NM_138803		C	159170296	T	C	159170296	3	2	29	1	0	0	0	0	1	0	0	0	2784	1406	49	3	980	3	CCDC148	2	159170296	Missense_Mutation	SNP	T	TCGA-5P-A9JW-01A-11D-A42J-10	62317789	159170296	84029077	9	2032											
SP3	6670	hgsc.bcm.edu	37	chr2	174829164	174829164	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgccgccgccaccgcaccgTttccgtgctgttgctgctgc	2	10	11	18	5	0	0	0	0	0	0	1	0	1	0	6	0	5	6	6	0	0	2			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr2:174829164T>C	ENST00000310015.6	-	2	655	c.125A>G	c.(124-126)aAc>aGc	p.N42S	SP3_ENST00000483084.1_5'Flank|SP3_ENST00000455789.2_Missense_Mutation_p.N30S|SP3_ENST00000418194.2_5'Flank	NM_001172712.1|NM_003111.4	NP_001166183.1|NP_003102.1	Q02447	SP3_HUMAN	Sp3 transcription factor	42					B cell differentiation (GO:0030183)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|embryonic skeletal system development (GO:0048706)|enucleate erythrocyte differentiation (GO:0043353)|granulocyte differentiation (GO:0030851)|liver development (GO:0001889)|lung development (GO:0030324)|megakaryocyte differentiation (GO:0030219)|monocyte differentiation (GO:0030224)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|T cell differentiation (GO:0030217)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)		EWSR1/SP3(3)	NS(2)|large_intestine(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.185)			CACCGCACCGTTTCCGTGCTG	0.721																																					p.N42S		Atlas-SNP	.											.	SP3	82	.	0			c.A125G						PASS	.						2	3	3					2																	174829164		1635	3328	4963	SO:0001583	missense	6670	exon2			GCACCGTTTCCGT	M97191	CCDS2254.1, CCDS46452.1	2q31	2013-01-08			ENSG00000172845	ENSG00000172845		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	11208	protein-coding gene	gene with protein product		601804				1341900, 1454515	Standard	NM_003111		Approved	SPR-2	uc002uig.3	Q02447	OTTHUMG00000132333	ENST00000310015.6:c.125A>G	chr2.hg19:g.174829164T>C	ENSP00000310301:p.Asn42Ser	41.0	0.0	.		30.0	7.0	.	NM_001172712	A0AVL9|B4E2B7|Q69B26|Q69B27|Q8TD56|Q8WWU4|Q9BQR1	Missense_Mutation	SNP	ENST00000310015.6	hg19	CCDS2254.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	11.88|11.88	1.770428|1.770428	0.31320|0.31320	.|.	.|.	ENSG00000172845|ENSG00000172845	ENST00000310015;ENST00000455789|ENST00000416195	T;T|.	0.05996|.	3.58;3.36|.	2.46|2.46	2.46|2.46	0.29980|0.29980	.|.	1.639320|.	0.04616|.	U|.	0.401148|.	T|T	0.19046|0.19046	0.0457|0.0457	N|N	0.08118|0.08118	0|0	0.20307|0.20307	N|N	0.999915|0.999915	B;B;B|.	0.26445|.	0.092;0.092;0.149|.	B;B;B|.	0.15052|.	0.007;0.007;0.012|.	T|T	0.23440|0.23440	-1.0188|-1.0188	10|5	0.14656|.	T|.	0.56|.	.|.	9.5141|9.5141	0.39095|0.39095	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	42;42;30|.	B7ZLN9;Q02447;Q02447-6|.	.;SP3_HUMAN;.|.	S|A	42;30|40	ENSP00000310301:N42S;ENSP00000388903:N30S|.	ENSP00000310301:N42S|.	N|T	-|-	2|1	0|0	SP3|SP3	174537410|174537410	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.709000|0.709000	0.40893|0.40893	1.163000|1.163000	0.31798|0.31798	0.925000|0.925000	0.37094|0.37094	0.353000|0.353000	0.21931|0.21931	AAC|ACG	.	.	.	none		0.721	SP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255452.1	NM_003111		C	174829164	T	C	174829164	3	2	29	1	0	0	0	0	1	0	0	0	14978	1725	60	3	2244	3	SP3	2	174829164	Missense_Mutation	SNP	T	TCGA-5P-A9JW-01A-11D-A42J-10	15658868	174829164	68370209	10	2033											
NDUFA10	4705	hgsc.bcm.edu	37	chr2	240954246	240954246	+	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	ggcaggtaatcgcagatggtGacgctcttcacctcgttgta	8	11	12	10	3	2	2	1	1	1	1	4	2	2	2	1	3	0	6	1	3	2	4			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr2:240954246G>A	ENST00000252711.2	-	5	679	c.579C>T	c.(577-579)gtC>gtT	p.V193V	NDUFA10_ENST00000404554.1_Silent_p.V193V|NDUFA10_ENST00000307300.4_Silent_p.V233V	NM_004544.3	NP_004535.1	O95299	NDUAA_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 10, 42kDa	193					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	ATP binding (GO:0005524)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|nucleoside kinase activity (GO:0019206)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)	16		all_epithelial(40;4.26e-15)|Breast(86;4.4e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0396)|Lung NSC(271;0.128)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(121;7.82e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.5e-13)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;2.39e-05)|Lung(119;0.00519)|LUSC - Lung squamous cell carcinoma(224;0.0202)		CGCAGATGGTGACGCTCTTCA	0.552																																					p.V193V		Atlas-SNP	.											.	NDUFA10	40	.	0			c.C579T						PASS	.						121	103	109					2																	240954246		2203	4300	6503	SO:0001819	synonymous_variant	4705	exon5			GATGGTGACGCTC	AF087661	CCDS2531.1	2q37.3	2011-07-04	2002-08-29		ENSG00000130414	ENSG00000130414		"Mitochondrial respiratory chain complex / Complex I"	7684	protein-coding gene	gene with protein product	"complex I 42kDa subunit"	603835	"NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 10 (42kD)"			9878551	Standard	NM_004544		Approved	CI-42k	uc002vyn.3	O95299	OTTHUMG00000133350	ENST00000252711.2:c.579C>T	chr2.hg19:g.240954246G>A		111.0	0.0	.		134.0	33.0	.	NM_004544	Q8WXC9	Silent	SNP	ENST00000252711.2	hg19	CCDS2531.1																																																																																			.	.	.	none		0.552	NDUFA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257180.2	NM_004544		A	240954246	G	A	240954246	2	1	29	1	0	0	0	0	0	0	0	1	10267	1277	45	2		2	NDUFA10	2	240954246	Silent	SNP	G	TCGA-5P-A9JW-01A-11D-A42J-10	66125082	240954246	2245127	11	2034											
SETMAR	6419	hgsc.bcm.edu	37	chr3	4355443	4355443	+	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	cctgcaagcgattgacccttGaggtgagtctgttcagtgat	8	12	12	9	1	2	4	1	4	1	0	2	5	2	4	2	1	2	2	2	1	1	3			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr3:4355443G>C	ENST00000358065.4	+	2	1085	c.1018G>C	c.(1018-1020)Gag>Cag	p.E340Q	SETMAR_ENST00000430981.1_Missense_Mutation_p.E340Q|SETMAR_ENST00000425863.1_Missense_Mutation_p.E201Q|SUMF1_ENST00000534863.1_Intron	NM_006515.3	NP_006506.3	Q53H47	SETMR_HUMAN	SET domain and mariner transposase fusion gene	340	Histone-lysine N-methyltransferase.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA integration (GO:0015074)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of chromosome organization (GO:2001251)|positive regulation of double-strand break repair via nonhomologous end joining (GO:2001034)|transposition, DNA-mediated (GO:0006313)	chromosome (GO:0005694)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|histone-lysine N-methyltransferase activity (GO:0018024)|protein homodimerization activity (GO:0042803)|structure-specific DNA binding (GO:0043566)|transposase activity (GO:0004803)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)	9		Melanoma(143;0.0657)		Epithelial(13;0.0025)|OV - Ovarian serous cystadenocarcinoma(96;0.011)|all cancers(10;0.0114)		ATTGACCCTTGAGGTGAGTCT	0.502								Chromatin Structure																													p.E340Q		Atlas-SNP	.											.	SETMAR	30	.	0			c.G1018C						PASS	.						95	89	91					3																	4355443		2203	4300	6503	SO:0001583	missense	6419	exon2			ACCCTTGAGGTGA	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.1018G>C	chr3.hg19:g.4355443G>C	ENSP00000373354:p.Glu340Gln	76.0	0.0	.		91.0	29.0	.	NM_006515	B4DY74|E7EN68|Q13579|Q1G668|Q96F41	Missense_Mutation	SNP	ENST00000358065.4	hg19	CCDS2563.2	.	.	.	.	.	.	.	.	.	.	G	10.53	1.376893	0.24857	.	.	ENSG00000170364	ENST00000358065;ENST00000430981;ENST00000425863;ENST00000358950	D;D;T	0.95447	-3.65;-3.71;0.48	3.52	-3.91	0.04168	.	.	.	.	.	D	0.83959	0.5367	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.25105	0.118;0.068;0.068;0.043;0.004	B;B;B;B;B	0.18263	0.015;0.021;0.014;0.003;0.002	T	0.73500	-0.3963	9	0.40728	T	0.16	.	0.2421	0.00193	0.346:0.1408:0.2007:0.3125	.	84;201;327;85;340	B4DND2;E7EN68;Q53H47;Q96H41;C9JHK2	.;.;SETMR_HUMAN;.;.	Q	340;340;201;104	ENSP00000373354:E340Q;ENSP00000403000:E340Q;ENSP00000403145:E201Q	ENSP00000373354:E340Q	E	+	1	0	SETMAR	4330443	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-4.345000	0.00249	-0.959000	0.03618	0.655000	0.94253	GAG	.	.	.	none		0.502	SETMAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206587.4	NM_006515		C	4355443	G	C	4355443	3	2	29	1	0	0	0	0	1	0	0	0	14153	1291	45	4	1024	4	SETMAR	3	4355443	Missense_Mutation	SNP	G	TCGA-5P-A9JW-01A-11D-A42J-10		4355443	193666987	12	2035											
STAB1	23166	hgsc.bcm.edu	37	chr3	52539392	52539395	+	Frame_Shift_Del	DEL	CTGG	CTGG	-																															tcagccgctttgaaaccatcCtggaggtaagctcgggggag																										TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	CTGG	CTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr3:52539392_52539395delCTGG	ENST00000321725.6	+	14	1652_1655	c.1576_1579delCTGG	c.(1576-1581)ctggagfs	p.LE526fs		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	526	FAS1 2. {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)		TGAAACCATCCTGGAGGTAAGCTC	0.593																																					p.525_526del		Atlas-INDEL	.											.	STAB1	178	.	0			c.1575_1578del						PASS	.																																			SO:0001589	frameshift_variant	23166	exon14			.	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.1576_1579delCTGG	chr3.hg19:g.52539392_52539395delCTGG	ENSP00000312946:p.Leu526fs	174.0	0.0	0		157.0	31.0	0.197452	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Frame_Shift_Del	DEL	ENST00000321725.6	hg19	CCDS33768.1																																																																																			.	.	.	none		0.593	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		-	52539395	CTGG	-	52539392	7	5	29	1	0	1	0	1	0	0	0	0	15249	680	24	0	1630	0	STAB1	3	52539392	Frame_Shift_Del	DEL	CTGG	TCGA-5P-A9JW-01A-11D-A42J-10	48183949	52539392	145483038	13	2036	21	2									
STAB1	23166	hgsc.bcm.edu	37	chr3	52539397	52539397	+	Splice_Site	DEL	G	G	-																															cgctttgaaaccatcctggaGgtaagctcgggggaggggtc																										TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr3:52539397delG	ENST00000321725.6	+	14	1657	c.1581delG	c.(1579-1581)gag>ga	p.E527fs		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	527	FAS1 2. {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)		CCATCCTGGAGGTAAGCTCGG	0.587																																					p.E527fs		Atlas-INDEL	.											.	STAB1	178	.	0			c.1580delA						PASS	.						36	38	37					3																	52539397		2202	4300	6502	SO:0001630	splice_region_variant	23166	exon14			.	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.1581+1G>-	chr3.hg19:g.52539397delG		171.0	0.0	0		151.0	31.0	0.205298	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Frame_Shift_Del	DEL	ENST00000321725.6	hg19	CCDS33768.1																																																																																			.	.	.	none		0.587	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136	Frame_Shift_Del	-	52539397	G	-	52539397	8	5	29	1	0	1	0	1	0	0	1	0	15249	1014	35	0	1635	0	STAB1	3	52539397	Splice_Site	DEL	G	TCGA-5P-A9JW-01A-11D-A42J-10	5	52539397	145483033	14	2037	21	2									
CACNA1D	776	hgsc.bcm.edu	37	chr3	53694259	53694259	+	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	gatgtcaaagccctccgtgcCtttcgagtgttgcgaccact	7	11	10	13	3	1	0	1	0	0	0	3	3	2	0	4	0	3	1	4	0	1	2			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr3:53694259C>A	ENST00000350061.5	+	5	1234	c.723C>A	c.(721-723)gcC>gcA	p.A241A	CACNA1D_ENST00000288139.4_Silent_p.A241A|CACNA1D_ENST00000422281.2_Silent_p.A241A	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	241					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)			breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CCCTCCGTGCCTTTCGAGTGT	0.473																																					p.A241A		Atlas-SNP	.											.	CACNA1D	324	.	0			c.C723A						PASS	.						66	62	64					3																	53694259		2203	4300	6503	SO:0001819	synonymous_variant	776	exon5			CCGTGCCTTTCGA	AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.723C>A	chr3.hg19:g.53694259C>A		112.0	0.0	.		95.0	29.0	.	NM_001128840	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Silent	SNP	ENST00000350061.5	hg19	CCDS46848.1																																																																																			.	.	.	none		0.473	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720		A	53694259	C	A	53694259	2	1	29	1	0	0	0	0	0	0	0	1	2543	668	24	4		4	CACNA1D	3	53694259	Silent	SNP	C	TCGA-5P-A9JW-01A-11D-A42J-10	1154862	53694259	144328171	15	2038											
QTRTD1	79691	hgsc.bcm.edu	37	chr3	113786834	113786834	+	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	tcttttttgtgtttatacagGcatgccagaatcactcttgt	8	18	7	8	0	3	1	1	0	2	1	3	1	3	1	1	1	2	2	1	1	3	7			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr3:113786834G>A	ENST00000281273.4	+	5	514	c.257G>A	c.(256-258)gGc>gAc	p.G86D	QTRTD1_ENST00000466050.1_Intron|QTRTD1_ENST00000493014.1_Intron|QTRTD1_ENST00000479882.1_Intron|QTRTD1_ENST00000485050.1_Splice_Site_p.G98D	NM_024638.3	NP_078914.1			queuine tRNA-ribosyltransferase domain containing 1											central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|skin(2)	10						GTTTATACAGGCATGCCAGAA	0.458																																					p.G98D		Atlas-SNP	.											.	QTRTD1	29	.	0			c.G293A						PASS	.						201	180	187					3																	113786834		2203	4300	6503	SO:0001630	splice_region_variant	79691	exon4			ATACAGGCATGCC	AK023022	CCDS33828.1, CCDS58846.1, CCDS58845.1, CCDS58844.1	3q13.31	2010-11-16			ENSG00000151576	ENSG00000151576			25771	protein-coding gene	gene with protein product						12477932	Standard	NM_024638		Approved	FLJ12960	uc003eaz.4	Q9H974	OTTHUMG00000159336	ENST00000281273.4:c.257-1G>A	chr3.hg19:g.113786834G>A		74.0	0.0	.		71.0	24.0	.	NM_001256835		Missense_Mutation	SNP	ENST00000281273.4	hg19	CCDS33828.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.978009	0.92982	.	.	ENSG00000151576	ENST00000472599;ENST00000485050;ENST00000281273;ENST00000482307	.	.	.	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	D	0.84220	0.5424	M	0.82517	2.595	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.81914	0.995;0.98	T	0.83339	-0.0009	8	.	.	.	.	20.6634	0.99662	0.0:0.0:1.0:0.0	.	100;86	C9JJ71;Q9H974	.;QTRD1_HUMAN	D	100;98;86;86	.	.	G	+	2	0	QTRTD1	115269524	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	8.916000	0.92745	2.894000	0.99253	0.655000	0.94253	GGC	.	.	.	none		0.458	QTRTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354708.2	NM_024638	Missense_Mutation	A	113786834	G	A	113786834	5	1	29	1	0	0	0	0	0	0	1	0	12899	1217	42	2	267	2	QTRTD1	3	113786834	Splice_Site	SNP	G	TCGA-5P-A9JW-01A-11D-A42J-10	60092575	113786834	84235596	16	2039											
MYLK	4638	hgsc.bcm.edu	37	chr3	123452791	123452791	+	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	ctcttggttccggctgaactCttgcggcctgcagggtgatg	4	12	14	11	2	2	2	0	2	2	0	3	2	3	2	2	4	3	3	2	4	1	3			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr3:123452791C>T	ENST00000475616.1	-	7	1051	c.1052G>A	c.(1051-1053)aGa>aAa	p.R351K	MYLK_ENST00000360304.3_Missense_Mutation_p.R351K|MYLK_ENST00000346322.5_Missense_Mutation_p.R351K|MYLK_ENST00000360772.3_Missense_Mutation_p.R351K|MYLK_ENST00000359169.1_Missense_Mutation_p.R351K			Q15746	MYLK_HUMAN	myosin light chain kinase	351					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)		CGGCTGAACTCTTGCGGCCTG	0.632																																					p.R351K		Atlas-SNP	.											.	MYLK	224	.	0			c.G1052A						PASS	.						74	80	78					3																	123452791		2203	4300	6503	SO:0001583	missense	4638	exon10			TGAACTCTTGCGG	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.1052G>A	chr3.hg19:g.123452791C>T	ENSP00000418335:p.Arg351Lys	312.0	0.0	.		359.0	122.0	.	NM_053025	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Missense_Mutation	SNP	ENST00000475616.1	hg19	CCDS46896.1	.	.	.	.	.	.	.	.	.	.	C	2.490	-0.317658	0.05386	.	.	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000475616	T;T;T;T;T	0.64085	-0.08;-0.03;-0.08;0.05;-0.03	5.43	-2.45	0.06481	.	.	.	.	.	T	0.32704	0.0838	N	0.04880	-0.145	0.09310	N	0.999993	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;0.001;0.001	T	0.32798	-0.9893	9	0.02654	T	1	.	11.7978	0.52110	0.0:0.561:0.0:0.439	.	351;351;351;351;351	Q15746-6;Q15746-4;Q15746-3;Q15746-2;Q15746	.;.;.;.;MYLK_HUMAN	K	351	ENSP00000354004:R351K;ENSP00000353452:R351K;ENSP00000352088:R351K;ENSP00000320622:R351K;ENSP00000418335:R351K	ENSP00000320622:R351K	R	-	2	0	MYLK	124935481	0.326000	0.24669	0.000000	0.03702	0.004000	0.04260	0.159000	0.16442	-0.306000	0.08818	-0.136000	0.14681	AGA	.	.	.	none		0.632	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025		T	123452791	C	T	123452791	3	4	29	1	0	0	0	0	1	0	0	0	10063	913	32	2	4792	2	MYLK	3	123452791	Missense_Mutation	SNP	C	TCGA-5P-A9JW-01A-11D-A42J-10	9665957	123452791	74569639	17	2040											
CCDC14	64770	hgsc.bcm.edu	37	chr3	123663747	123663747	+	Missense_Mutation	SNP	T	T	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	gttgcatggccagtgctatcTcaacttgaatatctgtgttt	8	16	9	8	0	2	1	1	1	2	0	3	1	2	1	1	1	3	4	1	1	4	5			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr3:123663747T>G	ENST00000488653.2	-	9	1526	c.1436A>C	c.(1435-1437)gAg>gCg	p.E479A	CCDC14_ENST00000485727.1_Missense_Mutation_p.E279A|CCDC14_ENST00000310351.4_Missense_Mutation_p.E319A|CCDC14_ENST00000489746.1_Missense_Mutation_p.E279A|CCDC14_ENST00000433542.2_Missense_Mutation_p.E438A|CCDC14_ENST00000483247.1_Intron			Q49A88	CCD14_HUMAN	coiled-coil domain containing 14	479					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)		CAGTGCTATCTCAACTTGAAT	0.378																																					p.E438A		Atlas-SNP	.											.	CCDC14	97	.	0			c.A1313C						PASS	.						158	128	138					3																	123663747		2203	4300	6503	SO:0001583	missense	64770	exon8			GCTATCTCAACTT	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.1436A>C	chr3.hg19:g.123663747T>G	ENSP00000420180:p.Glu479Ala	162.0	0.0	.		168.0	47.0	.	NM_022757	B7Z2T2|B8ZZ41|B8ZZ58|D3DN98|Q7Z3N3|Q86T30|Q8IWF8|Q8WUJ8|Q96K47|Q9H9A3|Q9UFH0	Missense_Mutation	SNP	ENST00000488653.2	hg19		.	.	.	.	.	.	.	.	.	.	T	14.04	2.416581	0.42918	.	.	ENSG00000175455	ENST00000488653;ENST00000310351;ENST00000485727;ENST00000489746;ENST00000433542;ENST00000409697;ENST00000419247	T;T;T;T;T;T;T	0.56776	0.44;0.44;0.44;0.44;0.44;0.44;0.44	5.09	5.09	0.68999	.	0.192154	0.35805	N	0.002962	T	0.69486	0.3116	M	0.65498	2.005	0.47476	D	0.999439	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.998;0.998	T	0.69855	-0.5032	10	0.44086	T	0.13	.	14.2744	0.66170	0.0:0.0:0.0:1.0	.	479;438;279;320	Q49A88;Q49A88-6;Q49A88-4;Q49A88-5	CCD14_HUMAN;.;.;.	A	479;319;279;279;438;460;120	ENSP00000420180:E479A;ENSP00000312031:E319A;ENSP00000418002:E279A;ENSP00000418403:E279A;ENSP00000395706:E438A;ENSP00000386866:E460A;ENSP00000400957:E120A	ENSP00000312031:E319A	E	-	2	0	CCDC14	125146437	1.000000	0.71417	1.000000	0.80357	0.003000	0.03518	5.326000	0.65875	2.267000	0.75376	0.383000	0.25322	GAG	.	.	.	none		0.378	CCDC14-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_022757		G	123663747	T	G	123663747	3	3	29	1	0	0	0	0	1	0	0	0	2775	1551	54	5	1445	5	CCDC14	3	123663747	Missense_Mutation	SNP	T	TCGA-5P-A9JW-01A-11D-A42J-10	210956	123663747	74358683	18	2041											
CEP135	9662	hgsc.bcm.edu	37	chr4	56841058	56841058	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagagctagagagactccaaCatataatacagcgaagatct	18	7	8	8	1	1	4	0	0	1	4	2	6	2	4	1	0	4	1	1	0	7	4			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr4:56841058C>T	ENST00000257287.4	+	11	1520	c.1396C>T	c.(1396-1398)Cat>Tat	p.H466Y		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	466					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)					GAGACTCCAACATATAATACA	0.353																																					p.H466Y		Atlas-SNP	.											.	CEP135	115	.	0			c.C1396T						PASS	.						78	80	80					4																	56841058		2203	4300	6503	SO:0001583	missense	9662	exon11			CTCCAACATATAA	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.1396C>T	chr4.hg19:g.56841058C>T	ENSP00000257287:p.His466Tyr	334.0	0.0	.		309.0	100.0	.	NM_025009	B2RMY0|O75130|Q58F25|Q9H8H7	Missense_Mutation	SNP	ENST00000257287.4	hg19	CCDS33986.1	.	.	.	.	.	.	.	.	.	.	C	13.67	2.304988	0.40795	.	.	ENSG00000174799	ENST00000257287	T	0.41758	0.99	5.89	4.97	0.65823	.	0.426257	0.26948	N	0.021687	T	0.38321	0.1036	L	0.44542	1.39	0.23632	N	0.997242	B	0.28258	0.205	B	0.30495	0.116	T	0.40270	-0.9572	10	0.66056	D	0.02	.	13.7008	0.62608	0.2299:0.7701:0.0:0.0	.	466	Q66GS9	CP135_HUMAN	Y	466	ENSP00000257287:H466Y	ENSP00000257287:H466Y	H	+	1	0	CEP135	56535815	0.973000	0.33851	0.989000	0.46669	0.725000	0.41563	2.255000	0.43222	2.781000	0.95711	0.555000	0.69702	CAT	.	.	.	none		0.353	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009		T	56841058	C	T	56841058	3	4	29	1	0	0	0	0	1	0	0	0	3249	478	17	2	1434	2	CEP135	4	56841058	Missense_Mutation	SNP	C	TCGA-5P-A9JW-01A-11D-A42J-10		56841058	134313218	19	2042											
C4orf22	255119	hgsc.bcm.edu	37	chr4	81256926	81256926	+	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	cggccgaggataccgcaatgGatcaggaagaggggctgaag	12	4	17	8	3	1	2	1	1	0	1	1	6	1	5	2	6	1	2	2	6	4	1			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr4:81256926G>C	ENST00000358105.3	+	1	53	c.4G>C	c.(4-6)Gat>Cat	p.D2H	C4orf22_ENST00000508675.1_Missense_Mutation_p.D2H|C4orf22_ENST00000512931.1_3'UTR	NM_152770.2	NP_689983.2	Q6V702	CD022_HUMAN	chromosome 4 open reading frame 22	2								p.D2Y(1)		NS(1)|large_intestine(3)|lung(5)|prostate(1)|skin(5)	15						TACCGCAATGGATCAGGAAGA	0.542											OREG0016247	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D2H		Atlas-SNP	.											C4orf22,NS,carcinoma,0,1	C4orf22	35	.	1	Substitution - Missense(1)	lung(1)	c.G4C						PASS	.						99	89	92					4																	81256926		2203	4300	6503	SO:0001583	missense	255119	exon1			GCAATGGATCAGG	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.4G>C	chr4.hg19:g.81256926G>C	ENSP00000350818:p.Asp2His	29.0	0.0	.	1204	38.0	9.0	.	NM_152770	E7EQ13|Q6ZQY4|Q8N4G9	Missense_Mutation	SNP	ENST00000358105.3	hg19	CCDS3587.1	.	.	.	.	.	.	.	.	.	.	G	13.59	2.283543	0.40394	.	.	ENSG00000197826	ENST00000358105;ENST00000508675	T;T	0.35605	1.3;1.33	5.37	4.53	0.55603	.	0.656132	0.14642	N	0.307175	T	0.35307	0.0927	L	0.36672	1.1	0.36933	D	0.891999	P;P	0.44946	0.846;0.755	P;P	0.45610	0.487;0.487	T	0.41378	-0.9512	10	0.72032	D	0.01	.	11.1806	0.48625	0.0853:0.0:0.9147:0.0	.	2;2	E7EQ13;Q6V702	.;CD022_HUMAN	H	2	ENSP00000350818:D2H;ENSP00000425786:D2H	ENSP00000350818:D2H	D	+	1	0	C4orf22	81475950	1.000000	0.71417	0.988000	0.46212	0.010000	0.07245	2.982000	0.49337	1.505000	0.48720	0.655000	0.94253	GAT	.	.	.	none		0.542	C4orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252629.2	NM_152770		C	81256926	G	C	81256926	3	2	29	1	0	0	0	0	1	0	0	0	2257	1174	41	4	6	4	C4orf22	4	81256926	Missense_Mutation	SNP	G	TCGA-5P-A9JW-01A-11D-A42J-10	24415868	81256926	109897350	20	2043											
ELF2	1998	hgsc.bcm.edu	37	chr4	140046428	140046428	+	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	catagccctgctctaatctgGcacttggaactggctccaca	9	10	8	14	0	2	0	0	0	2	0	3	1	3	1	2	3	3	3	2	3	3	3			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr4:140046428G>T	ENST00000394235.2	-	4	630	c.128C>A	c.(127-129)gCc>gAc	p.A43D	ELF2_ENST00000379550.1_Missense_Mutation_p.A43D|ELF2_ENST00000265495.4_Missense_Mutation_p.A43D	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)					CTCTAATCTGGCACTTGGAAC	0.398																																					p.A43D		Atlas-SNP	.											.	ELF2	43	.	0			c.C128A						PASS	.						149	142	144					4																	140046428		2203	4300	6503	SO:0001583	missense	1998	exon3			AATCTGGCACTTG	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.128C>A	chr4.hg19:g.140046428G>T	ENSP00000377782:p.Ala43Asp	108.0	0.0	.		89.0	13.0	.	NM_201999		Missense_Mutation	SNP	ENST00000394235.2	hg19	CCDS3744.1	.	.	.	.	.	.	.	.	.	.	G	31	5.100421	0.94245	.	.	ENSG00000109381	ENST00000394235;ENST00000379550;ENST00000265495	T;T;T	0.57752	0.38;0.38;0.38	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.67135	0.2861	M	0.75264	2.295	0.80722	D	1	P	0.50369	0.934	P	0.51999	0.687	T	0.66578	-0.5888	9	.	.	.	.	19.8298	0.96631	0.0:0.0:1.0:0.0	.	43	Q15723-1	.	D	43	ENSP00000377782:A43D;ENSP00000368868:A43D;ENSP00000265495:A43D	.	A	-	2	0	ELF2	140265878	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.211000	0.95120	2.687000	0.91594	0.591000	0.81541	GCC	.	.	.	none		0.398	ELF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257233.2	NM_006874		T	140046428	G	T	140046428	3	4	29	1	0	0	0	0	1	0	0	0	5056	1203	42	4	1743	4	ELF2	4	140046428	Missense_Mutation	SNP	G	TCGA-5P-A9JW-01A-11D-A42J-10	58789502	140046428	51107848	21	2044											
WDR17	116966	hgsc.bcm.edu	37	chr4	177098210	177098210	+	Splice_Site	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	ttccttttcacacgttcagtCagctattaaaacgtcgggag	10	13	8	10	3	3	0	3	0	0	0	5	1	4	1	1	1	2	2	1	1	3	6			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr4:177098210C>A	ENST00000280190.4	+	29	3724	c.3568C>A	c.(3568-3570)Cag>Aag	p.Q1190K	WDR17_ENST00000508596.1_Splice_Site_p.Q1151K|WDR17_ENST00000393643.2_Splice_Site_p.Q1166K|WDR17_ENST00000507824.2_Splice_Site_p.Q1165K			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	1190										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)		CACGTTCAGTCAGCTATTAAA	0.348																																					p.Q1190K		Atlas-SNP	.											.	WDR17	198	.	0			c.C3568A						PASS	.						62	62	62					4																	177098210		2203	4300	6503	SO:0001630	splice_region_variant	116966	exon29			TTCAGTCAGCTAT	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.3567-1C>A	chr4.hg19:g.177098210C>A		97.0	0.0	.		84.0	20.0	.	NM_170710	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	hg19	CCDS3825.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.53|19.53	3.844105|3.844105	0.71488|0.71488	.|.	.|.	ENSG00000150627|ENSG00000150627	ENST00000508596;ENST00000393643;ENST00000280190;ENST00000507824|ENST00000443118	T;T;T|.	0.54479|.	0.57;0.57;0.57|.	5.85|5.85	5.85|5.85	0.93711|0.93711	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.76435|.	0.3987|.	M|M	0.70595|0.70595	2.14|2.14	0.80722|0.80722	D|D	1|1	P;D;D|.	0.61080|.	0.925;0.989;0.989|.	P;D;D|.	0.69824|.	0.48;0.966;0.966|.	T|.	0.72465|.	-0.4285|.	10|.	0.38643|0.35671	T|T	0.18|0.21	-12.2134|-12.2134	20.2184|20.2184	0.98308|0.98308	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1166;1151;1190|.	E7EP77;E7EQX0;Q8IZU2|.	.;.;WDR17_HUMAN|.	K|X	1151;1166;1190;1166|424	ENSP00000422763:Q1151K;ENSP00000377258:Q1166K;ENSP00000280190:Q1190K|.	ENSP00000280190:Q1190K|ENSP00000426985:S424X	Q|S	+|+	1|2	0|0	WDR17|WDR17	177335204|177335204	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.858000|0.858000	0.48976|0.48976	7.004000|7.004000	0.76317|0.76317	2.775000|2.775000	0.95449|0.95449	0.644000|0.644000	0.83932|0.83932	CAG|TCA	.	.	.	none		0.348	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2		Missense_Mutation	A	177098210	C	A	177098210	5	1	29	1	0	0	0	0	0	0	1	0	17289	840	29	4	3678	4	WDR17	4	177098210	Splice_Site	SNP	C	TCGA-5P-A9JW-01A-11D-A42J-10	37051782	177098210	14056066	22	2045											
MLF1IP	79682	hgsc.bcm.edu	37	chr4	185637572	185637572	+	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	gattgactttctattgccaaGttctctttttcaacagaggg	9	16	8	8	0	3	2	1	1	2	1	4	3	3	2	1	1	2	1	1	1	3	7			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr4:185637572G>A	ENST00000281453.5	-	6	667	c.597C>T	c.(595-597)aaC>aaT	p.N199N	MLF1IP_ENST00000506535.1_5'Flank|MLF1IP_ENST00000541971.1_Silent_p.N199N	NM_024629.3	NP_078905.2														endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|stomach(1)	13		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Hepatocellular(41;0.000519)|Colorectal(36;0.00172)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.0299)|all_hematologic(60;0.0592)|Medulloblastoma(177;0.146)		all cancers(43;7.83e-28)|Epithelial(43;2.56e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-11)|Colorectal(24;3.27e-06)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.16e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000252)|COAD - Colon adenocarcinoma(29;0.000512)|LUSC - Lung squamous cell carcinoma(40;0.01)|READ - Rectum adenocarcinoma(43;0.0419)		CTATTGCCAAGTTCTCTTTTT	0.428																																					p.N199N		Atlas-SNP	.											.	MLF1IP	33	.	0			c.C597T						PASS	.						72	71	71					4																	185637572		2203	4300	6503	SO:0001819	synonymous_variant	79682	exon6			TGCCAAGTTCTCT																												ENST00000281453.5:c.597C>T	chr4.hg19:g.185637572G>A		92.0	0.0	.		110.0	38.0	.	NM_024629		Silent	SNP	ENST00000281453.5	hg19	CCDS3838.1																																																																																			.	.	.	none		0.428	MLF1IP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360841.2			A	185637572	G	A	185637572	2	1	29	1	0	0	0	0	0	0	0	1	9622	1020	36	2		2	MLF1IP	4	185637572	Silent	SNP	G	TCGA-5P-A9JW-01A-11D-A42J-10	8539362	185637572	5516704	23	2046											
SEMA5A	9037	hgsc.bcm.edu	37	chr5	9052121	9052121	+	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	gcttcacactcagaccagtcCgaccactccgaccagctctc	9	7	6	19	2	3	1	2	0	1	1	6	3	5	1	5	0	1	2	5	0	0	1			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr5:9052121C>G	ENST00000382496.5	-	20	3374	c.2709G>C	c.(2707-2709)tcG>tcC	p.S903S	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	903	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						CAGACCAGTCCGACCACTCCG	0.592																																					p.S903S		Atlas-SNP	.											.	SEMA5A	236	.	0			c.G2709C						PASS	.						28	30	29					5																	9052121		2203	4300	6503	SO:0001819	synonymous_variant	9037	exon20			CCAGTCCGACCAC	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.2709G>C	chr5.hg19:g.9052121C>G		140.0	0.0	.		142.0	48.0	.	NM_003966	D3DTC6|O60408|Q1RLL9	Silent	SNP	ENST00000382496.5	hg19	CCDS3875.1																																																																																			.	.	.	none		0.592	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2			G	9052121	C	G	9052121	2	3	29	1	0	0	0	0	0	0	0	1	14050	639	23	4		4	SEMA5A	5	9052121	Silent	SNP	C	TCGA-5P-A9JW-01A-11D-A42J-10		9052121	171863139	24	2047											
HTR1A	3350	hgsc.bcm.edu	37	chr5	63257506	63257506	+	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	tctcaaagggagccggtggtGatgtggtgttgttgccctga	6	12	16	7	1	1	2	1	2	1	0	2	3	1	3	2	4	2	2	2	4	1	2			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr5:63257506G>T	ENST00000323865.3	-	1	274	c.41C>A	c.(40-42)tCa>tAa	p.S14*	RP11-158J3.2_ENST00000502882.1_RNA	NM_000524.3	NP_000515.2	P08908	5HT1A_HUMAN	5-hydroxytryptamine (serotonin) receptor 1A, G protein-coupled	14					adenylate cyclase-inhibiting serotonin receptor signaling pathway (GO:0007198)|behavioral fear response (GO:0001662)|cell proliferation (GO:0008283)|exploration behavior (GO:0035640)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cell proliferation (GO:0008284)|regulation of behavior (GO:0050795)|regulation of dopamine metabolic process (GO:0042053)|regulation of hormone secretion (GO:0046883)|regulation of serotonin secretion (GO:0014062)|serotonin metabolic process (GO:0042428)|serotonin receptor signaling pathway (GO:0007210)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)			cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(29)|ovary(2)|pancreas(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	56		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0575)|Colorectal(97;0.234)		Lung(70;0.105)	Acepromazine(DB01614)|Alprenolol(DB00866)|Alverine(DB01616)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinitapride(DB08810)|Clozapine(DB00363)|Desipramine(DB01151)|Dopamine(DB00988)|Doxepin(DB01142)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Methysergide(DB00247)|Mianserin(DB06148)|Molindone(DB01618)|Naratriptan(DB00952)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Ondansetron(DB00904)|Paliperidone(DB01267)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sumatriptan(DB00669)|Thioproperazine(DB01622)|Trazodone(DB00656)|Trimipramine(DB00726)|Vilazodone(DB06684)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	AGCCGGTGGTGATGTGGTGTT	0.622																																					p.S14X		Atlas-SNP	.											.	HTR1A	128	.	0			c.C41A						PASS	.						100	94	96					5																	63257506		2203	4300	6503	SO:0001587	stop_gained	3350	exon1			GGTGGTGATGTGG	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.41C>A	chr5.hg19:g.63257506G>T	ENSP00000316244:p.Ser14*	197.0	0.0	.		224.0	71.0	.	NM_000524	Q6LAE7	Nonsense_Mutation	SNP	ENST00000323865.3	hg19	CCDS34168.1	.	.	.	.	.	.	.	.	.	.	G	19.23	3.788319	0.70337	.	.	ENSG00000178394	ENST00000323865;ENST00000506598	.	.	.	4.48	4.48	0.54585	.	1.590520	0.03632	N	0.238045	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	.	16.1532	0.81636	0.0:0.0:1.0:0.0	.	.	.	.	X	14	.	ENSP00000316244:S14X	S	-	2	0	HTR1A	63293262	0.019000	0.18553	0.013000	0.15412	0.101000	0.19017	1.258000	0.32944	2.053000	0.61076	0.561000	0.74099	TCA	.	.	.	none		0.622	HTR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368397.1	NM_000524		T	63257506	G	T	63257506	4	4	29	1	0	0	0	0	0	1	0	0	7443	1294	45	4	1230	4	HTR1A	5	63257506	Nonsense_Mutation	SNP	G	TCGA-5P-A9JW-01A-11D-A42J-10	54205385	63257506	117657754	25	2048											
MAN2A1	4124	hgsc.bcm.edu	37	chr5	109183439	109183439	+	Frame_Shift_Del	DEL	T	T	-																															aggtatccaggataacaagaTtacagctaatctatttcgaa																										TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr5:109183439delT	ENST00000261483.4	+	19	3976	c.2924delT	c.(2923-2925)attfs	p.I975fs		NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	975					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		GATAACAAGATTACAGCTAAT	0.348																																					p.I975fs		Atlas-Indel,Pindel	.											.	MAN2A1	136	.	0			c.2923delA						PASS	.						107	101	103					5																	109183439		2200	4299	6499	SO:0001589	frameshift_variant	4124	exon19			.		CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"golgi integral membrane protein 7"	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.2924delT	chr5.hg19:g.109183439delT	ENSP00000261483:p.Ile975fs	96.0	0.0	0		74.0	28.0	0.378378	NM_002372	Q16767	Frame_Shift_Del	DEL	ENST00000261483.4	hg19	CCDS34209.1																																																																																			.	.	.	none		0.348	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1			-	109183439	T	-	109183439	7	5	29	1	0	1	0	1	0	0	0	0	9221	1493	52	0	2998	0	MAN2A1	5	109183439	Frame_Shift_Del	DEL	T	TCGA-5P-A9JW-01A-11D-A42J-10	45925933	109183439	71731821	26	2049											
SEPT8	23176	hgsc.bcm.edu	37	chr5	132099512	132099512	+	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	tcatggtagtcgaagagcgaGcggcggatcttcagctcctc	8	9	13	11	4	3	1	2	0	1	1	6	4	4	2	1	3	3	2	1	3	2	2			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr5:132099512G>T	ENST00000378719.2	-	4	657	c.420C>A	c.(418-420)cgC>cgA	p.R140R	SEPT8_ENST00000378699.2_Silent_p.R80R|SEPT8_ENST00000448933.1_Silent_p.R80R|SEPT8_ENST00000458488.2_Silent_p.R140R|SEPT8_ENST00000481030.1_5'Flank|SEPT8_ENST00000378701.1_Silent_p.R138R|SEPT8_ENST00000378721.4_Silent_p.R138R|SEPT8_ENST00000378706.1_Silent_p.R140R|SEPT8_ENST00000296873.7_Silent_p.R140R	NM_001098811.1	NP_001092281.1	Q92599	SEPT8_HUMAN	septin 8	140	Septin-type G.				cell cycle (GO:0007049)	septin complex (GO:0031105)	GTP binding (GO:0005525)		SEPT8/AFF4(2)	kidney(2)|lung(5)|ovary(2)|skin(1)|urinary_tract(1)	11		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CGAAGAGCGAGCGGCGGATCT	0.517											OREG0003468	type=REGULATORY REGION|Gene=LOC540614|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.R140R		Atlas-SNP	.											.	SEPT8	28	.	0			c.C420A						PASS	.						158	161	160					5																	132099512		2001	4182	6183	SO:0001819	synonymous_variant	23176	exon4			GAGCGAGCGGCGG	AF179995	CCDS43358.1, CCDS43359.1, CCDS43360.1, CCDS47262.1, CCDS75298.1	5q31	2013-01-21			ENSG00000164402	ENSG00000164402		"Septins"	16511	protein-coding gene	gene with protein product		608418				9039502, 9149945	Standard	NM_001098812		Approved	KIAA0202, SEP2	uc003kxr.2	Q92599	OTTHUMG00000059735	ENST00000378719.2:c.420C>A	chr5.hg19:g.132099512G>T		109.0	0.0	.	1592	126.0	36.0	.	NM_015146	A6NC65|A6NKP6|F6W7K9|Q8IX36|Q8IX37|Q9BVB3	Silent	SNP	ENST00000378719.2	hg19	CCDS43358.1																																																																																			.	.	.	none		0.517	SEPT8-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132827.2	XM_034872		T	132099512	G	T	132099512	2	4	29	1	0	0	0	0	0	0	0	1	14083	958	34	4		4	SEPT8	5	132099512	Silent	SNP	G	TCGA-5P-A9JW-01A-11D-A42J-10	22916073	132099512	48815748	27	2050											
NR3C1	2908	hgsc.bcm.edu	37	chr5	142675051	142675052	+	Frame_Shift_Del	DEL	AT	AT	-																															agagaagcagtaaggttttcAtacagagatactcttcataa																										TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr5:142675051_142675052delAT	ENST00000343796.2	-	7	2989_2990	c.1996_1997delAT	c.(1996-1998)atgfs	p.M666fs	NR3C1_ENST00000504572.1_Frame_Shift_Del_p.M667fs|NR3C1_ENST00000231509.3_Frame_Shift_Del_p.M667fs|NR3C1_ENST00000415690.2_Frame_Shift_Del_p.M666fs|NR3C1_ENST00000503201.1_Frame_Shift_Del_p.M666fs|NR3C1_ENST00000394466.2_Frame_Shift_Del_p.M667fs|NR3C1_ENST00000424646.2_Frame_Shift_Del_p.M640fs|NR3C1_ENST00000394464.2_Frame_Shift_Del_p.M666fs|NR3C1_ENST00000416954.2_Frame_Shift_Del_p.M269fs	NM_001018074.1|NM_001018075.1|NM_001018077.1	NP_001018084.1|NP_001018085.1|NP_001018087.1	P04150	GCR_HUMAN	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)	666	Interaction with CLOCK.|Interaction with CRY1.|Steroid-binding.				adrenal gland development (GO:0030325)|chromatin modification (GO:0016568)|gene expression (GO:0010467)|glucocorticoid metabolic process (GO:0008211)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of glucocorticoid mediated signaling pathway (GO:1900170)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucocorticoid biosynthetic process (GO:0031946)|regulation of gluconeogenesis (GO:0006111)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	glucocorticoid receptor activity (GO:0004883)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|zinc ion binding (GO:0008270)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	35		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Alclometasone(DB00240)|Amcinonide(DB00288)|Beclomethasone(DB00394)|Betamethasone(DB00443)|Budesonide(DB01222)|Ciclesonide(DB01410)|Clobetasol propionate(DB01013)|Clocortolone(DB00838)|Cortisone acetate(DB01380)|Desonide(DB01260)|Desoximetasone(DB00547)|Dexamethasone(DB01234)|Diflorasone(DB00223)|Difluprednate(DB06781)|Fludrocortisone(DB00687)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Fluoxymesterone(DB01185)|Flurandrenolide(DB00846)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol(DB00873)|Medrysone(DB00253)|Megestrol acetate(DB00351)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Paramethasone(DB01384)|Prednicarbate(DB01130)|Prednisolone(DB00860)|Prednisone(DB00635)|Rimexolone(DB00896)|Spironolactone(DB00421)|Triamcinolone(DB00620)	TAAGGTTTTCATACAGAGATAC	0.381																																					p.667_667del		Atlas-Indel,Pindel	.											.	NR3C1	124	.	0			c.2000_2001del						PASS	.																																			SO:0001589	frameshift_variant	2908	exon7			.	X03225	CCDS4278.1, CCDS34258.1, CCDS47298.1	5q31-q32	2013-01-16	2002-08-27		ENSG00000113580	ENSG00000113580		"Nuclear hormone receptors"	7978	protein-coding gene	gene with protein product		138040	"nuclear receptor subfamily 3, group C, member 1"	GRL		2867473	Standard	NM_001204258		Approved	GR	uc003lnb.3	P04150	OTTHUMG00000129677	ENST00000343796.2:c.1996_1997delAT	chr5.hg19:g.142675051_142675052delAT	ENSP00000343205:p.Met666fs	70.0	0.0	0		79.0	30.0	0.379747	NM_001024094	A0ZXF9|B0LPG8|D3DQF4|P04151|Q53EP5|Q6N0A4	Frame_Shift_Del	DEL	ENST00000343796.2	hg19	CCDS4278.1																																																																																			.	.	.	none		0.381	NR3C1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370829.1			-	142675052	AT	-	142675051	7	5	29	1	0	1	0	1	0	0	0	0	10637	217	8	0	400	0	NR3C1	5	142675051	Frame_Shift_Del	DEL	AT	TCGA-5P-A9JW-01A-11D-A42J-10	10575539	142675051	38240209	28	2051											
NEU1	4758	hgsc.bcm.edu	37	chr6	31829963	31829963	+	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	tgctccatggtcaccagcggCtgcacctgtcatgggaggag	7	8	14	12	1	2	0	2	0	0	0	3	2	3	2	3	4	3	3	3	4	0	0			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr6:31829963C>T	ENST00000375631.4	-	2	294	c.165G>A	c.(163-165)caG>caA	p.Q55Q		NM_000434.3	NP_000425.1	Q99519	NEUR1_HUMAN	sialidase 1 (lysosomal sialidase)	55					glycosphingolipid metabolic process (GO:0006687)|lipid catabolic process (GO:0016042)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)|exo-alpha-sialidase activity (GO:0004308)			kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	10					Oseltamivir(DB00198)	TCACCAGCGGCTGCACCTGTC	0.587																																					p.Q55Q		Atlas-SNP	.											.	NEU1	21	.	0			c.G165A						PASS	.						68	44	52					6																	31829963		1510	2709	4219	SO:0001819	synonymous_variant	4758	exon2			CAGCGGCTGCACC	AF040958	CCDS4723.1	6p21	2012-10-02			ENSG00000204386	ENSG00000204386	3.2.1.18		7758	protein-coding gene	gene with protein product		608272		NEU		9054950	Standard	NM_000434		Approved		uc003nxq.4	Q99519	OTTHUMG00000031284	ENST00000375631.4:c.165G>A	chr6.hg19:g.31829963C>T		100.0	0.0	.		117.0	24.0	.	NM_000434		Silent	SNP	ENST00000375631.4	hg19	CCDS4723.1																																																																																			.	.	.	none		0.587	NEU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076616.2			T	31829963	C	T	31829963	2	4	29	1	0	0	0	0	0	0	0	1	10348	796	28	2		2	NEU1	6	31829963	Silent	SNP	C	TCGA-5P-A9JW-01A-11D-A42J-10		31829963	139285104	29	2052											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51889838	51889838	+	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	cctgtgccctctatggtcaaGaggcttccaccatgtaagct	8	11	9	13	0	2	1	1	0	1	1	3	1	3	1	4	2	2	3	4	2	3	3			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr6:51889838G>C	ENST00000371117.3	-	32	5045	c.4770C>G	c.(4768-4770)ctC>ctG	p.L1590L	PKHD1_ENST00000340994.4_Silent_p.L1590L	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1590	IPT/TIG 11.				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)					CTATGGTCAAGAGGCTTCCAC	0.473																																					p.L1590L		Atlas-SNP	.											.	PKHD1	927	.	0			c.C4770G						PASS	.						111	101	104					6																	51889838		2203	4300	6503	SO:0001819	synonymous_variant	5314	exon32			GGTCAAGAGGCTT	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.4770C>G	chr6.hg19:g.51889838G>C		71.0	0.0	.		73.0	19.0	.	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	hg19	CCDS4935.1																																																																																			.	.	.	none		0.473	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		C	51889838	G	C	51889838	2	2	29	1	0	0	0	0	0	0	0	1	11978	929	33	4		4	PKHD1	6	51889838	Silent	SNP	G	TCGA-5P-A9JW-01A-11D-A42J-10	20059875	51889838	119225229	30	2053											
C6orf150	115004	hgsc.bcm.edu	37	chr6	74161674	74161674	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctttttggcgcgggccccAgttgcgcggacgggcggcct	2	8	17	14	6	0	0	0	0	0	0	0	1	0	1	4	5	1	1	4	5	0	3			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr6:74161674A>G	ENST00000370315.3	-	1	325	c.231T>C	c.(229-231)acT>acC	p.T77T	MB21D1_ENST00000370318.1_Silent_p.T77T	NM_138441.2	NP_612450.2	Q8N884	CGAS_HUMAN	Mab-21 domain containing 1	77					activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|cyclic nucleotide biosynthetic process (GO:0009190)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of type I interferon production (GO:0032481)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cyclic-GMP-AMP synthase activity (GO:0061501)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|lung(1)	6						CGCGGGCCCCAGTTGCGCGGA	0.726																																					p.T77T		Atlas-SNP	.											.	MB21D1	33	.	0			c.T231C						PASS	.						4	4	4					6																	74161674		1811	3645	5456	SO:0001819	synonymous_variant	115004	exon1			GGCCCCAGTTGCG	BC012928	CCDS4978.1	6q13	2011-02-23	2011-02-23	2011-02-23	ENSG00000164430	ENSG00000164430			21367	protein-coding gene	gene with protein product		613973	"chromosome 6 open reading frame 150"	C6orf150			Standard	NM_138441		Approved		uc003pgx.1	Q8N884	OTTHUMG00000015034	ENST00000370315.3:c.231T>C	chr6.hg19:g.74161674A>G		138.0	0.0	.		151.0	31.0	.	NM_138441	L0L2J9|Q14CV6|Q32NC9|Q5SWL0|Q5SWL1|Q96E45	Silent	SNP	ENST00000370315.3	hg19	CCDS4978.1																																																																																			.	.	.	none		0.726	MB21D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041221.5	NM_138441		G	74161674	A	G	74161674	2	3	29	1	0	0	0	0	0	0	0	1	2339	175	7	3		3	C6orf150	6	74161674	Silent	SNP	A	TCGA-5P-A9JW-01A-11D-A42J-10	22271836	74161674	96953393	31	2054											
CD164	8763	hgsc.bcm.edu	37	chr6	109697298	109697298	+	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	tgtagaattggctgttggcaCtggagtggccgtggaaacta	9	11	15	6	1	0	1	0	0	0	1	0	3	0	3	1	5	1	4	1	5	4	4			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr6:109697298C>T	ENST00000310786.4	-	4	414	c.349G>A	c.(349-351)Gtg>Atg	p.V117M	CD164_ENST00000512821.1_Missense_Mutation_p.V117M|CD164_ENST00000368961.5_Intron|CD164_ENST00000275080.7_Intron|CD164_ENST00000413644.2_Missense_Mutation_p.V117M|CD164_ENST00000324953.5_Missense_Mutation_p.V117M|CD164_ENST00000506649.1_5'UTR|CD164_ENST00000504373.1_Missense_Mutation_p.V83M	NM_001142404.1|NM_006016.4	NP_001135876.1|NP_006007.2	Q04900	MUC24_HUMAN	CD164 molecule, sialomucin	117	Thr-rich.				cell adhesion (GO:0007155)|hemopoiesis (GO:0030097)|heterophilic cell-cell adhesion (GO:0007157)|immune response (GO:0006955)|multicellular organismal development (GO:0007275)|muscle organ development (GO:0007517)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|plasma membrane (GO:0005886)				breast(1)|lung(2)	3		all_cancers(87;4.65e-22)|all_epithelial(87;2.54e-20)|all_lung(197;1.6e-05)|Lung NSC(302;2.92e-05)|Colorectal(196;3.46e-05)|Ovarian(999;0.0175)		Epithelial(106;7.83e-46)|all cancers(137;1.15e-45)|OV - Ovarian serous cystadenocarcinoma(136;2.89e-26)|BRCA - Breast invasive adenocarcinoma(108;0.00128)|GBM - Glioblastoma multiforme(226;0.16)		GCTGTTGGCACTGGAGTGGCC	0.323																																					p.V117M		Atlas-SNP	.											.	CD164	10	.	0			c.G349A						PASS	.						54	56	55					6																	109697298		2203	4300	6503	SO:0001583	missense	8763	exon4			TTGGCACTGGAGT	AF106518	CCDS5073.1, CCDS47462.1, CCDS47463.1, CCDS47464.1, CCDS47465.1	6q21	2014-09-05	2006-03-28		ENSG00000135535	ENSG00000135535		"CD molecules"	1632	protein-coding gene	gene with protein product		603356	"CD164 antigen, sialomucin"			9680353, 9763543	Standard	NM_006016		Approved	MUC-24, MGC-24	uc003pte.3	Q04900	OTTHUMG00000015339	ENST00000310786.4:c.349G>A	chr6.hg19:g.109697298C>T	ENSP00000309376:p.Val117Met	58.0	0.0	.		39.0	11.0	.	NM_006016	B4DQ85|E1P5E7|E1P5E8|E1P5E9|O95413|Q5JSU6|Q9BPV0|Q9NR26	Missense_Mutation	SNP	ENST00000310786.4	hg19	CCDS5073.1	.	.	.	.	.	.	.	.	.	.	C	8.205	0.799104	0.16397	.	.	ENSG00000135535	ENST00000413644;ENST00000324953;ENST00000310786;ENST00000512821;ENST00000504373	T;T;T;T;T	0.59364	0.27;0.27;0.27;0.27;0.27	4.56	-3.14	0.05250	.	1.016850	0.07895	N	0.971727	T	0.16385	0.0394	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.16802	0.015;0.015;0.019;0.015	B;B;B;B	0.18561	0.015;0.022;0.016;0.009	T	0.24728	-1.0152	10	0.45353	T	0.12	3.8623	4.7218	0.12922	0.3874:0.178:0.0:0.4346	.	117;117;117;117	Q04900-5;Q04900-4;Q04900;Q04900-2	.;.;MUC24_HUMAN;.	M	117;117;117;117;83	ENSP00000402237:V117M;ENSP00000314177:V117M;ENSP00000309376:V117M;ENSP00000427546:V117M;ENSP00000422999:V83M	ENSP00000309376:V117M	V	-	1	0	CD164	109803991	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	-0.149000	0.10204	-0.711000	0.04995	-1.115000	0.02055	GTG	.	.	.	none		0.323	CD164-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041742.1	NM_006016		T	109697298	C	T	109697298	3	4	29	1	0	0	0	0	1	0	0	0	2971	565	20	2	307	2	CD164	6	109697298	Missense_Mutation	SNP	C	TCGA-5P-A9JW-01A-11D-A42J-10	35535624	109697298	61417769	32	2055											
STK17A	9263	hgsc.bcm.edu	37	chr7	43663376	43663376	+	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	cttaggcaatgataaacaagAaacattcttaaacatctcac	18	10	4	9	0	2	2	1	1	2	1	3	2	2	2	0	1	3	1	0	1	8	4			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr7:43663376A>T	ENST00000319357.5	+	6	988	c.809A>T	c.(808-810)gAa>gTa	p.E270V		NM_004760.2	NP_004751.2	Q9UEE5	ST17A_HUMAN	serine/threonine kinase 17a	270	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast apoptotic process (GO:2000271)|protein phosphorylation (GO:0006468)|regulation of reactive oxygen species metabolic process (GO:2000377)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	11						GATAAACAAGAAACATTCTTA	0.318																																					p.E270V		Atlas-SNP	.											.	STK17A	31	.	0			c.A809T						PASS	.						97	98	98					7																	43663376		2202	4293	6495	SO:0001583	missense	9263	exon6			AACAAGAAACATT	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.809A>T	chr7.hg19:g.43663376A>T	ENSP00000319192:p.Glu270Val	65.0	0.0	.		71.0	17.0	.	NM_004760	A4D1V6|Q8IVC8	Missense_Mutation	SNP	ENST00000319357.5	hg19	CCDS5470.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.612206	0.87258	.	.	ENSG00000164543	ENST00000319357	T	0.66638	-0.22	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	0.48767	D	0.000167	T	0.79528	0.4461	M	0.69523	2.12	0.80722	D	1	D	0.69078	0.997	D	0.65573	0.936	T	0.82464	-0.0444	10	0.87932	D	0	.	14.6526	0.68808	1.0:0.0:0.0:0.0	.	270	Q9UEE5	ST17A_HUMAN	V	270	ENSP00000319192:E270V	ENSP00000319192:E270V	E	+	2	0	STK17A	43629901	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.695000	0.91298	1.844000	0.53588	0.455000	0.32223	GAA	.	.	.	none		0.318	STK17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250902.1	NM_004760		T	43663376	A	T	43663376	3	4	29	1	0	0	0	0	1	0	0	0	15302	246	9	5	831	5	STK17A	7	43663376	Missense_Mutation	SNP	A	TCGA-5P-A9JW-01A-11D-A42J-10		43663376	115475287	33	2056											
PCLO	27445	hgsc.bcm.edu	37	chr7	82465003	82465003	+	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	cttgcattctggacaaccatGacttgactgcattgattcca	10	13	7	11	0	1	3	0	3	1	0	2	4	2	4	2	1	3	2	2	1	1	5			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr7:82465003G>A	ENST00000333891.9	-	16	14566	c.14229C>T	c.(14227-14229)gtC>gtT	p.V4743V	PCLO_ENST00000426442.2_Intron|PCLO_ENST00000423517.2_Silent_p.V4743V	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						GGACAACCATGACTTGACTGC	0.373																																					p.V4743V		Atlas-SNP	.											.	PCLO	1506	.	0			c.C14229T						PASS	.						59	58	58					7																	82465003		1877	4123	6000	SO:0001819	synonymous_variant	27445	exon16			AACCATGACTTGA	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.14229C>T	chr7.hg19:g.82465003G>A		139.0	0.0	.		97.0	29.0	.	NM_014510		Silent	SNP	ENST00000333891.9	hg19	CCDS47630.1																																																																																			.	.	.	none		0.373	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82465003	G	A	82465003	2	1	29	1	0	0	0	0	0	0	0	1	11590	1277	45	2		2	PCLO	7	82465003	Silent	SNP	G	TCGA-5P-A9JW-01A-11D-A42J-10	38801627	82465003	76673660	34	2057											
TRPV6	55503	hgsc.bcm.edu	37	chr7	142574503	142574503	+	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	agctcttacccagggagtccTgggcccggatgtcagctcca	7	8	12	14	1	2	0	1	0	1	0	4	2	4	2	4	3	3	2	4	3	1	1			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr7:142574503T>A	ENST00000359396.3	-	5	820	c.575A>T	c.(574-576)cAg>cTg	p.Q192L	RP11-114L10.2_ENST00000438839.1_RNA	NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	192					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)					CAGGGAGTCCTGGGCCCGGAT	0.612																																					p.Q192L		Atlas-SNP	.											.	TRPV6	108	.	0			c.A575T						PASS	.						95	85	88					7																	142574503		2203	4300	6503	SO:0001583	missense	55503	exon5			GAGTCCTGGGCCC	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.575A>T	chr7.hg19:g.142574503T>A	ENSP00000352358:p.Gln192Leu	84.0	0.0	.		92.0	27.0	.	NM_018646	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Missense_Mutation	SNP	ENST00000359396.3	hg19	CCDS5874.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.63|18.63	3.665013|3.665013	0.67700|0.67700	.|.	.|.	ENSG00000165125|ENSG00000165125	ENST00000311470|ENST00000359396	.|T	.|0.65364	.|-0.15	4.67|4.67	3.52|3.52	0.40303|0.40303	.|Ankyrin repeat-containing domain (4);	.|0.059353	.|0.64402	.|D	.|0.000001	.|T	.|0.71634	.|0.3363	L|L	0.53561|0.53561	1.675|1.675	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.83275	.|0.996	.|T	.|0.70317	.|-0.4905	.|10	.|0.56958	.|D	.|0.05	.|-20.3379	9.2268|9.2268	0.37412|0.37412	0.0:0.0863:0.0:0.9137|0.0:0.0863:0.0:0.9137	.|.	.|192	.|Q9H1D0	.|TRPV6_HUMAN	.|L	-1|192	.|ENSP00000352358:Q192L	.|ENSP00000352358:Q192L	.|Q	-|-	.|2	.|0	TRPV6|TRPV6	142284625|142284625	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.535000|0.535000	0.34838|0.34838	7.799000|7.799000	0.85936|0.85936	0.661000|0.661000	0.30985|0.30985	0.533000|0.533000	0.62120|0.62120	.|CAG	.	.	.	none		0.612	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274		A	142574503	T	A	142574503	3	1	29	1	0	0	0	0	1	0	0	0	16612	1580	55	5	1646	5	TRPV6	7	142574503	Missense_Mutation	SNP	T	TCGA-5P-A9JW-01A-11D-A42J-10	60109500	142574503	16564160	35	2058											
ABP1	26	hgsc.bcm.edu	37	chr7	150554433	150554433	+	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	caagccccgcggggacttccCcagccccatccatgtgagcg	7	5	11	18	3	0	1	0	1	0	0	2	2	2	2	7	2	3	0	7	2	1	1	rs532287637		TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr7:150554433C>A	ENST00000493429.1	+	4	1459	c.875C>A	c.(874-876)cCc>cAc	p.P292H	AOC1_ENST00000416793.2_Missense_Mutation_p.P292H|AOC1_ENST00000467291.1_Missense_Mutation_p.P292H|AOC1_ENST00000360937.4_Missense_Mutation_p.P292H			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	292					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)	GGGGACTTCCCCAGCCCCATC	0.701																																					p.P292H		Atlas-SNP	.											.	ABP1	92	.	0			c.C875A						PASS	.						12	15	14					7																	150554433		1987	4141	6128	SO:0001583	missense	26	exon2			ACTTCCCCAGCCC	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.875C>A	chr7.hg19:g.150554433C>A	ENSP00000418614:p.Pro292His	60.0	0.0	.		63.0	16.0	.	NM_001091	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Missense_Mutation	SNP	ENST00000493429.1	hg19	CCDS43679.1	.	.	.	.	.	.	.	.	.	.	C	4.108	0.018074	0.07959	.	.	ENSG00000002726	ENST00000493429;ENST00000467291;ENST00000360937;ENST00000416793;ENST00000437714;ENST00000483043	T;T;T;T;T	0.18657	2.2;2.2;2.2;2.2;2.2	5.01	3.15	0.36227	Copper amine oxidase, C-terminal (1);Copper amine oxidase, N-terminal (1);	0.511218	0.18147	N	0.150202	T	0.18800	0.0451	L	0.58101	1.795	0.09310	N	1	B;B	0.14012	0.009;0.006	B;B	0.09377	0.004;0.004	T	0.18713	-1.0328	10	0.39692	T	0.17	-36.7946	5.7513	0.18148	0.3563:0.5521:0.0:0.0915	.	292;292	C9J690;P19801	.;ABP1_HUMAN	H	292;292;292;292;168;292	ENSP00000418614:P292H;ENSP00000418328:P292H;ENSP00000354193:P292H;ENSP00000411613:P292H;ENSP00000417392:P292H	ENSP00000354193:P292H	P	+	2	0	ABP1	150185366	0.000000	0.05858	0.007000	0.13788	0.321000	0.28281	0.542000	0.23222	0.660000	0.30964	0.561000	0.74099	CCC	.	.	.	none		0.701	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091		A	150554433	C	A	150554433	3	1	29	1	0	0	0	0	1	0	0	0	98	623	22	4	877	4	ABP1	7	150554433	Missense_Mutation	SNP	C	TCGA-5P-A9JW-01A-11D-A42J-10	7979930	150554433	8584230	36	2059											
LPL	4023	hgsc.bcm.edu	37	chr8	19809403	19809405	+	In_Frame_Del	DEL	GCG	GCG	-																															aggagcattacccagtgtccGcgggctacaccaaactggtg																								rs199675233		TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	GCG	GCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr8:19809403_19809405delGCG	ENST00000311322.8	+	3	843_845	c.373_375delGCG	c.(373-375)gcgdel	p.A125del		NM_000237.2	NP_000228.1	P06858	LIPL_HUMAN	lipoprotein lipase	125					chylomicron remodeling (GO:0034371)|fatty acid biosynthetic process (GO:0006633)|lipoprotein metabolic process (GO:0042157)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of sequestering of triglyceride (GO:0010890)|response to cold (GO:0009409)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|triglyceride metabolic process (GO:0006641)|very-low-density lipoprotein particle remodeling (GO:0034372)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|lipoprotein lipase activity (GO:0004465)|phospholipase activity (GO:0004620)|receptor binding (GO:0005102)|triglyceride binding (GO:0017129)|triglyceride lipase activity (GO:0004806)	p.A125T(1)|p.A125A(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	36				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	AST-120(DB05269)|Tyloxapol(DB06439)	CCCAGTGTCCGCGGGCTACACCA	0.532																																					p.124_125del		Atlas-Indel,Pindel	.											.	LPL	78	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)|prostate(1)	c.372_374del	GRCh37	HM971397	LPL	M		PASS	.																																			SO:0001651	inframe_deletion	4023	exon3			.		CCDS6012.1	8p22	2012-10-02			ENSG00000175445	ENSG00000175445	3.1.1.34		6677	protein-coding gene	gene with protein product		609708		LIPD			Standard	NM_000237		Approved		uc003wzk.4	P06858	OTTHUMG00000036645	ENST00000311322.8:c.373_375delGCG	chr8.hg19:g.19809403_19809405delGCG	ENSP00000309757:p.Ala125del	143.0	0.0	0		159.0	52.0	0.327044	NM_000237	B2R5T9|Q16282|Q16283|Q96FC4	In_Frame_Del	DEL	ENST00000311322.8	hg19	CCDS6012.1																																																																																			.	.	.	none		0.532	LPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089113.3			-	19809405	GCG	-	19809403	7	5	29	1	0	1	0	1	0	0	0	0	8928	1087	38	0	383	0	LPL	8	19809403	In_Frame_Del	DEL	GCG	TCGA-5P-A9JW-01A-11D-A42J-10		19809403	126554619	37	2060											
GFRA2	2675	hgsc.bcm.edu	37	chr8	21608372	21608372	+	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	taggaggagcgcagcttcttGcagttgtcattcaggttgca	8	12	13	8	1	3	0	2	0	1	0	3	2	3	2	0	3	4	6	0	3	1	6			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr8:21608372G>T	ENST00000524240.1	-	4	1172	c.522C>A	c.(520-522)tgC>tgA	p.C174*	GFRA2_ENST00000517328.1_Nonsense_Mutation_p.C174*|GFRA2_ENST00000400782.4_Nonsense_Mutation_p.C69*|GFRA2_ENST00000518077.1_Nonsense_Mutation_p.C41*	NM_001495.4	NP_001486.4	O00451	GFRA2_HUMAN	GDNF family receptor alpha 2	174					negative regulation of protein autophosphorylation (GO:0031953)|nervous system development (GO:0007399)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	anchored component of membrane (GO:0031225)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|prostate(1)|skin(1)	7				Colorectal(74;0.0189)|COAD - Colon adenocarcinoma(73;0.0727)		GCAGCTTCTTGCAGTTGTCAT	0.617																																					p.C174X		Atlas-SNP	.											.	GFRA2	23	.	0			c.C522A						PASS	.						40	46	44					8																	21608372		2197	4297	6494	SO:0001587	stop_gained	2675	exon4			CTTCTTGCAGTTG	AF002700	CCDS47816.1, CCDS55207.1	8p21.3	2008-05-02			ENSG00000168546	ENSG00000168546			4244	protein-coding gene	gene with protein product		601956				9177201	Standard	NM_001165038		Approved	RETL2, GDNFRB, NTNRA, TRNR2	uc003wzu.1	O00451	OTTHUMG00000163897	ENST00000524240.1:c.522C>A	chr8.hg19:g.21608372G>T	ENSP00000428518:p.Cys174*	156.0	0.0	.		164.0	59.0	.	NM_001495	E9PD47|O15316|O15328|Q58J92|Q6GTR9|Q7Z5C2	Nonsense_Mutation	SNP	ENST00000524240.1	hg19	CCDS47816.1	.	.	.	.	.	.	.	.	.	.	G	36	5.723754	0.96847	.	.	ENSG00000168546	ENST00000524240;ENST00000400782;ENST00000517328;ENST00000518077;ENST00000517892;ENST00000522071;ENST00000520826	.	.	.	4.76	4.76	0.60689	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.8511	10.9886	0.47537	0.0874:0.0:0.9126:0.0	.	.	.	.	X	174;69;174;41;69;174;166	.	ENSP00000383592:C69X	C	-	3	2	GFRA2	21652652	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	4.934000	0.63491	2.197000	0.70478	0.313000	0.20887	TGC	.	.	.	none		0.617	GFRA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376254.3	NM_001495		T	21608372	G	T	21608372	4	4	29	1	0	0	0	0	0	1	0	0	6355	1311	46	4	896	4	GFRA2	8	21608372	Nonsense_Mutation	SNP	G	TCGA-5P-A9JW-01A-11D-A42J-10	1798969	21608372	124755650	38	2061											
ENTPD4	9583	hgsc.bcm.edu	37	chr8	23294697	23294697	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccattttgctggatttcaTctttaatgtctaggggtagg	7	17	11	6	0	3	0	1	0	2	0	4	1	4	1	1	4	1	2	1	4	3	7			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr8:23294697T>C	ENST00000358689.4	-	10	1359	c.1124A>G	c.(1123-1125)gAt>gGt	p.D375G	ENTPD4_ENST00000356206.6_Missense_Mutation_p.D367G|ENTPD4_ENST00000417069.2_Missense_Mutation_p.D367G|ENTPD4_ENST00000521321.1_5'Flank	NM_001128930.2|NM_004901.4	NP_001122402.1|NP_004892.1	Q9Y227	ENTP4_HUMAN	ectonucleoside triphosphate diphosphohydrolase 4	375					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)		CTGGATTTCATCTTTAATGTC	0.458																																					p.D375G		Atlas-SNP	.											.	ENTPD4	56	.	0			c.A1124G						PASS	.						138	110	119					8																	23294697		2203	4300	6503	SO:0001583	missense	9583	exon10			ATTTCATCTTTAA	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.1124A>G	chr8.hg19:g.23294697T>C	ENSP00000351520:p.Asp375Gly	136.0	0.0	.		155.0	49.0	.	NM_004901	D3DSS3|O15092	Missense_Mutation	SNP	ENST00000358689.4	hg19	CCDS6041.1	.	.	.	.	.	.	.	.	.	.	T	19.36	3.813208	0.70912	.	.	ENSG00000197217	ENST00000356206;ENST00000358689;ENST00000417069	T;T;T	0.10763	2.84;2.84;2.84	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.12987	0.0315	L	0.39245	1.2	0.80722	D	1	P;P;P	0.36354	0.549;0.494;0.549	B;B;B	0.40444	0.329;0.221;0.329	T	0.09271	-1.0682	10	0.31617	T	0.26	-26.8762	14.5422	0.68002	0.0:0.0:0.0:1.0	.	367;367;375	Q8NE73;Q9Y227-2;Q9Y227	.;.;ENTP4_HUMAN	G	367;375;367	ENSP00000348536:D367G;ENSP00000351520:D375G;ENSP00000408573:D367G	ENSP00000348536:D367G	D	-	2	0	ENTPD4	23350642	1.000000	0.71417	1.000000	0.80357	0.799000	0.45148	7.698000	0.84413	2.120000	0.65058	0.260000	0.18958	GAT	.	.	.	none		0.458	ENTPD4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215142.1	NM_004901		C	23294697	T	C	23294697	3	2	29	1	0	0	0	0	1	0	0	0	5143	1435	50	3	742	3	ENTPD4	8	23294697	Missense_Mutation	SNP	T	TCGA-5P-A9JW-01A-11D-A42J-10	1686325	23294697	123069325	39	2062											
NDUFB9	4715	hgsc.bcm.edu	37	chr8	125562081	125562081	+	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	tgcccgaaaggaaggtgattTgcccccactgtggtggtata	9	10	13	9	1	0	1	0	1	0	0	0	3	0	2	3	4	2	1	3	4	4	3			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr8:125562081T>A	ENST00000276689.3	+	4	572	c.488T>A	c.(487-489)tTg>tAg	p.L163*	NDUFB9_ENST00000517830.1_Intron|NDUFB9_ENST00000522532.1_Intron|NDUFB9_ENST00000517367.1_Nonsense_Mutation_p.L152*	NM_001278646.1|NM_005005.2	NP_001265575.1|NP_004996.1	Q9Y6M9	NDUB9_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9, 22kDa	163					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	8	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			GAAGGTGATTTGCCCCCACTG	0.522																																					p.L163X		Atlas-SNP	.											NDUFB9,NS,carcinoma,0,1	NDUFB9	18	.	0			c.T488A						PASS	.						69	62	65					8																	125562081		2203	4300	6503	SO:0001587	stop_gained	4715	exon4			GTGATTTGCCCCC	AF044956	CCDS6352.1	8q24.13	2011-07-04	2002-08-29		ENSG00000147684	ENSG00000147684		"LYR motif containing", "Mitochondrial respiratory chain complex / Complex I"	7704	protein-coding gene	gene with protein product	"complex I B22 subunit"	601445	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9 (22kD, B22)"			8661098	Standard	NM_005005		Approved	B22, UQOR22, LYRM3	uc003yrg.4	Q9Y6M9	OTTHUMG00000165054	ENST00000276689.3:c.488T>A	chr8.hg19:g.125562081T>A	ENSP00000276689:p.Leu163*	91.0	0.0	.		120.0	38.0	.	NM_005005	B2R8M6|Q9UQE8	Nonsense_Mutation	SNP	ENST00000276689.3	hg19	CCDS6352.1	.	.	.	.	.	.	.	.	.	.	T	36	5.696320	0.96802	.	.	ENSG00000147684	ENST00000276689;ENST00000517367	.	.	.	5.01	5.01	0.66863	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.3291	15.004	0.71498	0.0:0.0:0.0:1.0	.	.	.	.	X	163;152	.	ENSP00000276689:L163X	L	+	2	0	NDUFB9	125631262	1.000000	0.71417	0.989000	0.46669	0.961000	0.63080	7.437000	0.80417	2.018000	0.59344	0.260000	0.18958	TTG	.	.	.	none		0.522	NDUFB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381606.1	NM_005005		A	125562081	T	A	125562081	4	1	29	1	0	0	0	0	0	1	0	0	10295	1821	63	5	502	5	NDUFB9	8	125562081	Nonsense_Mutation	SNP	T	TCGA-5P-A9JW-01A-11D-A42J-10	102267384	125562081	20801941	40	2063											
NAPRT1	642475	hgsc.bcm.edu	37	chr8	144657205	144657205	+	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	0	0	0	0	0	0	0	0	0	0	tgtgctcagggctgagtcggCtcagggacagctgggccaag	7	7	17	10	1	2	1	2	1	0	0	3	2	2	2	1	4	2	4	1	4	1	0	rs552997428		TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr8:144657205C>T	ENST00000398882.3	-	0	0				NAPRT1_ENST00000449291.2_Missense_Mutation_p.S502N|NAPRT1_ENST00000435154.3_3'UTR|RP11-661A12.9_ENST00000531730.1_RNA|NAPRT1_ENST00000460623.1_5'UTR|NAPRT1_ENST00000276844.7_Missense_Mutation_p.S502N|NAPRT1_ENST00000426292.3_Missense_Mutation_p.S489N	NM_001100878.1	NP_001094348.1	A6NGR9	MROH6_HUMAN	maestro heat-like repeat family member 6																		GCTGAGTCGGCTCAGGGACAG	0.662													C|||	1	0.000199681	0	0	5008	,	,		17051	0.001		0	False		,,,				2504	0				p.S502N		Atlas-SNP	.											.	NAPRT1	47	.	0			c.G1505A						PASS	.						30	32	31					8																	144657205		692	1591	2283	SO:0001631	upstream_gene_variant	93100	exon12			AGTCGGCTCAGGG	AF289596	CCDS47928.1	8q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000204839	ENSG00000204839		"maestro heat-like repeat containing"	27814	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 73"	C8orf73		12477932	Standard	NM_001100878		Approved		uc010mff.3	A6NGR9	OTTHUMG00000165164		chr8.hg19:g.144657205C>T	Exception_encountered	146.0	0.0	.		198.0	63.0	.	NM_145201	A8MWB1	Missense_Mutation	SNP	ENST00000398882.3	hg19	CCDS47928.1	.	.	.	.	.	.	.	.	.	.	C	14.57	2.576030	0.45902	.	.	ENSG00000147813	ENST00000449291;ENST00000340490;ENST00000426292;ENST00000276844	T;T;T;T	0.43294	0.98;0.95;0.96;0.97	5.69	3.91	0.45181	Quinolinate phosphoribosyl transferase, C-terminal (1);	0.431641	0.29791	N	0.011181	T	0.22003	0.0530	N	0.13168	0.305	0.27755	N	0.944011	B;B;B	0.13594	0.008;0.001;0.003	B;B;B	0.11329	0.006;0.002;0.001	T	0.19321	-1.0309	10	0.15066	T	0.55	-6.2117	7.5749	0.27931	0.0:0.7303:0.0:0.2697	.	502;489;502	G5E977;Q6XQN6-3;Q6XQN6	.;.;PNCB_HUMAN	N	502;502;489;502	ENSP00000401508:S502N;ENSP00000341136:S502N;ENSP00000390949:S489N;ENSP00000276844:S502N	ENSP00000276844:S502N	S	-	2	0	NAPRT1	144728348	0.049000	0.20398	0.756000	0.31282	0.644000	0.38419	0.196000	0.17176	0.764000	0.33197	0.655000	0.94253	AGC	.	.	.	none		0.662	MROH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382330.3	NM_001100878		T	144657205	C	T	144657205	1	4	29	0	1	0	0	0	0	0	0	0	10172	797	28	2		2	NAPRT1	8	144657205	5'Flank	SNP	C	TCGA-5P-A9JW-01A-11D-A42J-10	19095124	144657205	1706817	41	2064											
PRSS3	5646	hgsc.bcm.edu	37	chr9	33797999	33797999	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatcaatgcccgcgtgtccAccatctctctgcccaccacc	7	9	5	20	2	4	0	2	0	2	0	6	0	5	0	6	0	2	0	6	0	1	0	rs142141488		TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr9:33797999A>G	ENST00000361005.5	+	3	544	c.544A>G	c.(544-546)Acc>Gcc	p.T182A	RP11-133O22.6_ENST00000454429.2_RNA|PRSS3_ENST00000342836.4_Missense_Mutation_p.T139A|PRSS3_ENST00000379405.3_Missense_Mutation_p.T125A|PRSS3_ENST00000429677.3_Missense_Mutation_p.T118A	NM_007343.3	NP_031369	P35030	TRY3_HUMAN	protease, serine, 3	182	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)			CCGCGTGTCCACCATCTCTCT	0.567																																					p.T182A		Atlas-SNP	.											.	PRSS3	79	.	0			c.A544G						PASS	.						206	156	173					9																	33797999		2203	4300	6503	SO:0001583	missense	5646	exon3			GTGTCCACCATCT		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.544A>G	chr9.hg19:g.33797999A>G	ENSP00000354280:p.Thr182Ala	106.0	0.0	.		120.0	5.0	.	NM_007343	A8CED1|A8CED3|A9Z1Y4|E7ES07|F8W7P3|P15951|Q15665|Q5VXV0|Q6ISJ4|Q9UQV3	Missense_Mutation	SNP	ENST00000361005.5	hg19	CCDS47958.1	.	.	.	.	.	.	.	.	.	.	A	11.10	1.538604	0.27475	.	.	ENSG00000010438	ENST00000361005;ENST00000457896;ENST00000342836;ENST00000429677;ENST00000379405	T;T;D;T;D	0.92699	0.32;0.23;-3.09;0.32;-3.09	3.62	-7.24	0.01475	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.484707	0.25543	N	0.029949	T	0.73024	0.3534	N	0.04686	-0.185	0.24520	N	0.994162	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.11329	0.002;0.006;0.002	T	0.61242	-0.7102	10	0.44086	T	0.13	.	1.0734	0.01627	0.2023:0.3189:0.2612:0.2176	.	125;182;139	P35030-3;P35030;P35030-4	.;TRY3_HUMAN;.	A	182;137;139;118;125	ENSP00000354280:T182A;ENSP00000401249:T137A;ENSP00000340889:T139A;ENSP00000401828:T118A;ENSP00000368715:T125A	ENSP00000340889:T139A	T	+	1	0	PRSS3	33787999	0.000000	0.05858	0.001000	0.08648	0.164000	0.22412	-0.041000	0.12084	-2.179000	0.00767	0.260000	0.18958	ACC	.	.	.	weak		0.567	PRSS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052121.1	NM_002771		G	33797999	A	G	33797999	3	3	29	1	0	0	0	0	1	0	0	0	12632	159	6	3	598	3	PRSS3	9	33797999	Missense_Mutation	SNP	A	TCGA-5P-A9JW-01A-11D-A42J-10		33797999	107415432	42	2065											
C9orf170	401535	hgsc.bcm.edu	37	chr9	89763782	89763782	+	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	cgggcggggaggcctggcctCctgctcagtcggtgcaaatg	5	7	17	12	3	1	0	1	0	0	0	3	1	2	1	3	6	2	2	3	6	1	0			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr9:89763782C>G	ENST00000375941.2	+	1	224	c.137C>G	c.(136-138)tCc>tGc	p.S46C		NM_001001709.2	NP_001001709.1	A2RU37	CI170_HUMAN	chromosome 9 open reading frame 170	46										large_intestine(3)|lung(2)|prostate(1)	6						GGCCTGGCCTCCTGCTCAGTC	0.602																																					p.S46C		Atlas-SNP	.											.	C9orf170	17	.	0			c.C137G						PASS	.						31	34	33					9																	89763782		2202	4299	6501	SO:0001583	missense	401535	exon1			TGGCCTCCTGCTC	AK127445	CCDS35058.1	9q21.33	2009-02-11			ENSG00000204446	ENSG00000204446			33817	protein-coding gene	gene with protein product							Standard	NM_001001709		Approved	FLJ45537	uc004apa.1	A2RU37	OTTHUMG00000159587	ENST00000375941.2:c.137C>G	chr9.hg19:g.89763782C>G	ENSP00000365108:p.Ser46Cys	280.0	0.0	.		252.0	75.0	.	NM_001001709		Missense_Mutation	SNP	ENST00000375941.2	hg19	CCDS35058.1	.	.	.	.	.	.	.	.	.	.	C	13.13	2.145880	0.37923	.	.	ENSG00000204446	ENST00000375941	.	.	.	4.38	0.178	0.15058	.	.	.	.	.	T	0.13543	0.0328	N	0.08118	0	0.09310	N	1	P	0.35844	0.524	B	0.35550	0.205	T	0.17349	-1.0372	8	0.87932	D	0	.	3.1347	0.06435	0.1702:0.4021:0.3314:0.0963	.	46	A2RU37	CI170_HUMAN	C	46	.	ENSP00000365108:S46C	S	+	2	0	C9orf170	88953602	0.000000	0.05858	0.000000	0.03702	0.274000	0.26718	0.031000	0.13710	0.038000	0.15604	-0.176000	0.13171	TCC	.	.	.	none		0.602	C9orf170-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356346.1	NM_001001709		G	89763782	C	G	89763782	3	3	29	1	0	0	0	0	1	0	0	0	2471	855	30	4	139	4	C9orf170	9	89763782	Missense_Mutation	SNP	C	TCGA-5P-A9JW-01A-11D-A42J-10	55965783	89763782	51449649	43	2066											
OGN	4969	hgsc.bcm.edu	37	chr9	95165578	95165578	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctaaatatggattcttcaaAattatctgttccataatcat	14	16	4	7	0	4	0	2	0	2	0	5	1	5	1	1	1	0	2	1	1	7	7			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr9:95165578A>G	ENST00000262551.4	-	2	532	c.112T>C	c.(112-114)Ttt>Ctt	p.F38L	OGN_ENST00000375561.5_Missense_Mutation_p.F38L|CENPP_ENST00000375587.3_Intron	NM_033014.2	NP_148935.1	P20774	MIME_HUMAN	osteoglycin	38					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|negative regulation of smooth muscle cell proliferation (GO:0048662)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	13						GATTCTTCAAAATTATCTGTT	0.358																																					p.F38L		Atlas-SNP	.											.	OGN	26	.	0			c.T112C						PASS	.						76	76	76					9																	95165578		2203	4300	6503	SO:0001583	missense	4969	exon2			CTTCAAAATTATC	AI424992	CCDS6695.1	9q22	2008-02-05	2007-02-16		ENSG00000106809	ENSG00000106809		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	8126	protein-coding gene	gene with protein product	"mimecan proteoglycan"	602383	"osteoglycin (osteoinductive factor)"			2372374	Standard	NM_033014		Approved	mimecan, OIF, SLRR3A	uc004asa.3	P20774	OTTHUMG00000020224	ENST00000262551.4:c.112T>C	chr9.hg19:g.95165578A>G	ENSP00000262551:p.Phe38Leu	107.0	0.0	.		118.0	35.0	.	NM_033014	Q6FIB0|Q9UF90|Q9UNK5	Missense_Mutation	SNP	ENST00000262551.4	hg19	CCDS6695.1	.	.	.	.	.	.	.	.	.	.	A	9.224	1.034153	0.19590	.	.	ENSG00000106809	ENST00000262551;ENST00000375561;ENST00000447356	T;T;T	0.59083	0.29;0.29;0.31	5.55	4.41	0.53225	.	0.508491	0.20017	N	0.100983	T	0.32852	0.0843	N	0.12182	0.205	0.19945	N	0.999942	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18808	-1.0325	10	0.11182	T	0.66	.	7.0374	0.25000	0.7748:0.1478:0.0774:0.0	.	96;38	B4DI63;P20774	.;MIME_HUMAN	L	38;38;96	ENSP00000262551:F38L;ENSP00000364711:F38L;ENSP00000396709:F96L	ENSP00000262551:F38L	F	-	1	0	OGN	94205399	0.011000	0.17503	0.869000	0.34112	0.689000	0.40095	0.790000	0.26900	1.058000	0.40530	0.533000	0.62120	TTT	.	.	.	none		0.358	OGN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053087.1	NM_024416		G	95165578	A	G	95165578	3	3	29	1	0	0	0	0	1	0	0	0	10853	14	1	3	808	3	OGN	9	95165578	Missense_Mutation	SNP	A	TCGA-5P-A9JW-01A-11D-A42J-10	5401796	95165578	46047853	44	2067											
LRRC8A	56262	hgsc.bcm.edu	37	chr9	131670150	131670150	+	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	gggcgtgctggacaagaaggAgggggagcaagccaaggcgc	11	2	20	8	2	0	1	0	0	0	1	0	4	0	4	1	6	3	2	1	6	4	0			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr9:131670150A>T	ENST00000259324.5	+	3	1230	c.707A>T	c.(706-708)gAg>gTg	p.E236V	LRRC8A_ENST00000372599.3_Missense_Mutation_p.E236V|LRRC8A_ENST00000372600.4_Missense_Mutation_p.E236V	NM_001127244.1	NP_001120716.1	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member A	236					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						GACAAGAAGGAGGGGGAGCAA	0.617																																					p.E236V		Atlas-SNP	.											.	LRRC8A	69	.	0			c.A707T						PASS	.						112	107	109					9																	131670150		2203	4300	6503	SO:0001583	missense	56262	exon3			AGAAGGAGGGGGA	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.707A>T	chr9.hg19:g.131670150A>T	ENSP00000259324:p.Glu236Val	157.0	0.0	.		158.0	14.0	.	NM_001127244	Q6UXM2|Q8NCI0|Q9P2B1	Missense_Mutation	SNP	ENST00000259324.5	hg19	CCDS35155.1	.	.	.	.	.	.	.	.	.	.	A	15.88	2.964061	0.53507	.	.	ENSG00000136802	ENST00000372600;ENST00000372599;ENST00000259324	T;T;T	0.37584	1.19;1.19;1.19	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.60650	0.2285	M	0.74881	2.28	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.65434	-0.6169	10	0.87932	D	0	.	14.6237	0.68605	1.0:0.0:0.0:0.0	.	236	Q8IWT6	LRC8A_HUMAN	V	236	ENSP00000361682:E236V;ENSP00000361680:E236V;ENSP00000259324:E236V	ENSP00000259324:E236V	E	+	2	0	LRRC8A	130709971	1.000000	0.71417	1.000000	0.80357	0.607000	0.37147	9.339000	0.96797	2.052000	0.61016	0.460000	0.39030	GAG	.	.	.	none		0.617	LRRC8A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054516.2	NM_019594		T	131670150	A	T	131670150	3	4	29	1	0	0	0	0	1	0	0	0	9028	304	11	5	709	5	LRRC8A	9	131670150	Missense_Mutation	SNP	A	TCGA-5P-A9JW-01A-11D-A42J-10	36504572	131670150	9543281	45	2068											
ZNF438	220929	hgsc.bcm.edu	37	chr10	31138561	31138561	+	Missense_Mutation	SNP	T	T	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	gatcaacttgttctttaaatTtttcactggcaacagcagaa	13	14	6	8	0	3	1	2	0	1	1	3	2	3	1	0	1	3	3	0	1	5	6			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr10:31138561T>G	ENST00000361310.3	-	6	1102	c.773A>C	c.(772-774)aAa>aCa	p.K258T	ZNF438_ENST00000442986.1_Missense_Mutation_p.K258T|ZNF438_ENST00000452305.1_Missense_Mutation_p.K248T|ZNF438_ENST00000375311.1_Intron|ZNF438_ENST00000413025.1_Missense_Mutation_p.K258T|ZNF438_ENST00000444692.2_Missense_Mutation_p.K248T|ZNF438_ENST00000331737.6_Missense_Mutation_p.K248T|ZNF438_ENST00000538351.2_Missense_Mutation_p.K209T|ZNF438_ENST00000436087.2_Missense_Mutation_p.K258T			Q7Z4V0	ZN438_HUMAN	zinc finger protein 438	258					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)				TTCTTTAAATTTTTCACTGGC	0.428																																					p.K258T		Atlas-SNP	.											.	ZNF438	90	.	0			c.A773C						PASS	.						179	176	177					10																	31138561		2203	4300	6503	SO:0001583	missense	220929	exon7			TTAAATTTTTCAC	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.773A>C	chr10.hg19:g.31138561T>G	ENSP00000354663:p.Lys258Thr	84.0	0.0	.		96.0	31.0	.	NM_182755	A2A3J4|A8K9L5|Q5T426|Q658Q4|Q6ZN65	Missense_Mutation	SNP	ENST00000361310.3	hg19	CCDS7168.1	.	.	.	.	.	.	.	.	.	.	T	14.52	2.560611	0.45590	.	.	ENSG00000183621	ENST00000331737;ENST00000361310;ENST00000436087;ENST00000442986;ENST00000413025;ENST00000452305;ENST00000444692;ENST00000538351	T;T;T;T;T;T;T;T	0.13196	2.61;2.62;2.62;2.62;2.62;2.61;2.61;2.62	4.91	2.41	0.29592	.	0.419792	0.29956	N	0.010780	T	0.13927	0.0337	M	0.62723	1.935	0.09310	N	1	P;P	0.38922	0.651;0.557	B;B	0.39419	0.216;0.299	T	0.15065	-1.0450	10	0.72032	D	0.01	-4.3	4.4384	0.11561	0.0:0.1749:0.1693:0.6558	.	258;248	Q7Z4V0;Q7Z4V0-2	ZN438_HUMAN;.	T	248;258;258;258;258;248;248;209	ENSP00000333571:K248T;ENSP00000354663:K258T;ENSP00000406934:K258T;ENSP00000412363:K258T;ENSP00000387546:K258T;ENSP00000413060:K248T;ENSP00000410898:K248T;ENSP00000445461:K209T	ENSP00000333571:K248T	K	-	2	0	ZNF438	31178567	0.118000	0.22208	0.001000	0.08648	0.032000	0.12392	2.262000	0.43285	0.744000	0.32741	0.533000	0.62120	AAA	.	.	.	none		0.428	ZNF438-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277006.1	NM_182755		G	31138561	T	G	31138561	3	3	29	1	0	0	0	0	1	0	0	0	17922	1841	64	5	1721	5	ZNF438	10	31138561	Missense_Mutation	SNP	T	TCGA-5P-A9JW-01A-11D-A42J-10		31138561	104396186	46	2069											
PANK1	53354	hgsc.bcm.edu	37	chr10	91404533	91404533	+	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	agacgtgcggcggctggactGgcggcggatggaagccgttg	6	6	20	9	6	0	1	0	0	0	1	0	4	0	4	1	7	2	2	1	7	1	1			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr10:91404533G>A	ENST00000307534.4	-	1	682	c.527C>T	c.(526-528)cCa>cTa	p.P176L	PANK1_ENST00000322191.6_5'Flank|RP11-80H5.2_ENST00000454174.1_RNA|RP11-80H5.6_ENST00000428166.1_lincRNA|PANK1_ENST00000488482.1_5'Flank|PANK1_ENST00000342512.3_5'Flank|PANK1_ENST00000371774.2_5'Flank|RP11-80H5.2_ENST00000451733.1_RNA	NM_148977.2	NP_683878.1	Q8TE04	PANK1_HUMAN	pantothenate kinase 1	176					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						CGGCTGGACTGGCGGCGGATG	0.766																																					p.P176L		Atlas-SNP	.											.	PANK1	35	.	0			c.C527T						PASS	.						1	2	2					10																	91404533		1059	2515	3574	SO:0001583	missense	53354	exon1			TGGACTGGCGGCG	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.527C>T	chr10.hg19:g.91404533G>A	ENSP00000302108:p.Pro176Leu	34.0	0.0	.		30.0	10.0	.	NM_148977	A6NIP0|Q7RTX6|Q7Z495|Q8TBQ8	Missense_Mutation	SNP	ENST00000307534.4	hg19	CCDS31244.1	.	.	.	.	.	.	.	.	.	.	G	8.772	0.926188	0.18056	.	.	ENSG00000152782	ENST00000307534;ENST00000371775	D	0.99527	-6.09	4.66	3.75	0.43078	.	0.812759	0.10685	N	0.645879	D	0.97436	0.9161	N	0.19112	0.55	0.52099	D	0.999943	B	0.06786	0.001	B	0.04013	0.001	D	0.94700	0.7882	10	0.54805	T	0.06	.	10.7307	0.46096	0.095:0.0:0.905:0.0	.	176	Q8TE04	PANK1_HUMAN	L	176;39	ENSP00000302108:P176L	ENSP00000302108:P176L	P	-	2	0	PANK1	91394513	0.564000	0.26602	0.018000	0.16275	0.029000	0.11900	1.493000	0.35605	0.953000	0.37825	0.561000	0.74099	CCA	.	.	.	none		0.766	PANK1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				A	91404533	G	A	91404533	3	1	29	1	0	0	0	0	1	0	0	0	11423	1348	47	2	1329	2	PANK1	10	91404533	Missense_Mutation	SNP	G	TCGA-5P-A9JW-01A-11D-A42J-10	60265972	91404533	44130214	47	2070											
MXI1	4601	hgsc.bcm.edu	37	chr10	112044605	112044605	+	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	agattgaagtggatgttgaaAgcacagagttctcccatgga	13	10	12	6	0	1	4	0	2	1	2	2	6	1	6	1	2	1	3	1	2	2	3			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr10:112044605A>T	ENST00000239007.7	+	6	765	c.547A>T	c.(547-549)Agc>Tgc	p.S183C	MXI1_ENST00000393134.1_Missense_Mutation_p.S173C|MXI1_ENST00000332674.5_Missense_Mutation_p.S250C|MXI1_ENST00000485566.1_3'UTR|MXI1_ENST00000369612.1_Missense_Mutation_p.S147C|MXI1_ENST00000361248.4_Missense_Mutation_p.S137C	NM_005962.4	NP_005953.4	P50539	MXI1_HUMAN	MAX interactor 1, dimerization protein	183					cytoplasmic sequestering of transcription factor (GO:0042994)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(1)	10		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;1.33e-05)|all cancers(201;0.000277)|BRCA - Breast invasive adenocarcinoma(275;0.127)		GGATGTTGAAAGCACAGAGTT	0.433																																					p.S250C		Atlas-SNP	.											.	MXI1	17	.	0			c.A748T						PASS	.						98	85	89					10																	112044605		2203	4300	6503	SO:0001583	missense	4601	exon6			GTTGAAAGCACAG	BC016678	CCDS7563.1, CCDS7564.2, CCDS31284.1	10q24-q25	2012-11-15	2012-11-15		ENSG00000119950	ENSG00000119950		"MAX dimerization proteins", "Basic helix-loop-helix proteins"	7534	protein-coding gene	gene with protein product		600020	"MAX interacting protein 1", "MAX interactor 1"			7959753	Standard	NM_130439		Approved	MXD2, MAD2, MXI, bHLHc11	uc001kyy.3	P50539	OTTHUMG00000019033	ENST00000239007.7:c.547A>T	chr10.hg19:g.112044605A>T	ENSP00000239007:p.Ser183Cys	79.0	0.0	.		87.0	27.0	.	NM_130439	B1ANN7|D3DR25|D3DRA9|Q15887|Q6FHW2|Q96E53	Missense_Mutation	SNP	ENST00000239007.7	hg19	CCDS7564.2	.	.	.	.	.	.	.	.	.	.	A	18.38	3.610744	0.66558	.	.	ENSG00000119950	ENST00000332674;ENST00000361248;ENST00000239007;ENST00000369619;ENST00000393134;ENST00000369614;ENST00000369613;ENST00000369612	T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.56630	0.1998	M	0.72118	2.19	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.999;1.0	D;D;D;D	0.87578	0.993;0.997;0.993;0.998	T	0.59369	-0.7467	10	0.72032	D	0.01	-12.6328	16.4439	0.83910	1.0:0.0:0.0:0.0	.	173;147;183;250	B1ANN8;P50539-2;P50539;P50539-3	.;.;MXI1_HUMAN;.	C	250;137;183;173;173;147;147;147	ENSP00000331152:S250C;ENSP00000354606:S137C;ENSP00000239007:S183C;ENSP00000376842:S173C;ENSP00000358625:S147C	ENSP00000239007:S183C	S	+	1	0	MXI1	112034595	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.138000	0.77305	2.282000	0.76494	0.533000	0.62120	AGC	.	.	.	none		0.433	MXI1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050316.1	NM_130439		T	112044605	A	T	112044605	3	4	29	1	0	0	0	0	1	0	0	0	10009	72	3	5	847	5	MXI1	10	112044605	Missense_Mutation	SNP	A	TCGA-5P-A9JW-01A-11D-A42J-10	20640072	112044605	23490142	48	2071											
HSPA12A	259217	hgsc.bcm.edu	37	chr10	118440687	118440687	+	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	tgctttatacagttccttaaGgtgtccctccggtaaccgga	8	13	9	11	2	0	0	0	0	0	0	3	1	3	1	4	3	3	3	4	3	4	6			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr10:118440687G>T	ENST00000369209.3	-	9	1107	c.1003C>A	c.(1003-1005)Ctt>Att	p.L335I		NM_025015.2	NP_079291.2	O43301	HS12A_HUMAN	heat shock 70kDa protein 12A	335						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)		AGTTCCTTAAGGTGTCCCTCC	0.488																																					p.L335I		Atlas-SNP	.											.	HSPA12A	81	.	0			c.C1003A						PASS	.						99	104	102					10																	118440687		1989	4169	6158	SO:0001583	missense	259217	exon9			CCTTAAGGTGTCC	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.1003C>A	chr10.hg19:g.118440687G>T	ENSP00000358211:p.Leu335Ile	79.0	0.0	.		66.0	4.0	.	NM_025015		Missense_Mutation	SNP	ENST00000369209.3	hg19	CCDS41569.1	.	.	.	.	.	.	.	.	.	.	G	17.65	3.441640	0.63067	.	.	ENSG00000165868	ENST00000369209	T	0.31510	1.49	5.78	4.86	0.63082	.	0.125530	0.53938	D	0.000050	T	0.37046	0.0989	L	0.37466	1.105	0.45930	D	0.998764	P	0.45396	0.857	P	0.49999	0.628	T	0.18493	-1.0335	10	0.62326	D	0.03	.	16.0591	0.80826	0.0:0.0:0.8648:0.1352	.	335	O43301	HS12A_HUMAN	I	335	ENSP00000358211:L335I	ENSP00000358211:L335I	L	-	1	0	HSPA12A	118430677	1.000000	0.71417	0.964000	0.40570	0.743000	0.42351	5.429000	0.66495	1.420000	0.47138	0.655000	0.94253	CTT	.	.	.	none		0.488	HSPA12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050530.1	NM_025015		T	118440687	G	T	118440687	3	4	29	1	0	0	0	0	1	0	0	0	7411	1000	35	4	1040	4	HSPA12A	10	118440687	Missense_Mutation	SNP	G	TCGA-5P-A9JW-01A-11D-A42J-10	6396082	118440687	17094060	49	2072											
NAP1L4	4676	hgsc.bcm.edu	37	chr11	2970489	2970489	+	Nonstop_Mutation	SNP	T	T	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	gaatgattaacagacaaaaaTtacacctaaatggggaaaaa	22	7	7	5	0	0	2	0	1	0	1	0	4	0	3	1	2	2	0	1	2	9	3			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr11:2970489T>G	ENST00000380542.4	-	15	1268	c.1128A>C	c.(1126-1128)taA>taC	p.*376Y	NAP1L4_ENST00000469089.1_5'UTR|NAP1L4_ENST00000526115.1_Intron	NM_005969.3	NP_005960.1	Q99733	NP1L4_HUMAN	nucleosome assembly protein 1-like 4	0					nucleosome assembly (GO:0006334)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			endometrium(2)|kidney(3)|large_intestine(1)|lung(6)|ovary(1)	13		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00301)|LUSC - Lung squamous cell carcinoma(625;0.211)		CAGACAAAAATTACACCTAAA	0.328																																					p.X376Y		Atlas-SNP	.											.	NAP1L4	39	.	0			c.A1128C						PASS	.						75	67	69					11																	2970489		1834	4086	5920	SO:0001578	stop_lost	4676	exon15			CAAAAATTACACC	AA573896, BC022090, U77456	CCDS41599.1	11p15.5	2007-12-06			ENSG00000205531	ENSG00000205531			7640	protein-coding gene	gene with protein product		601651				8923002	Standard	NM_005969		Approved	NAP2	uc001lxc.3	Q99733	OTTHUMG00000011009	ENST00000380542.4:c.1128A>C	chr11.hg19:g.2970489T>G		603.0	0.0	.		560.0	166.0	.	NM_005969	B2R6J4|F5HFY4	Missense_Mutation	SNP	ENST00000380542.4	hg19	CCDS41599.1	.	.	.	.	.	.	.	.	.	.	T	11.54	1.669728	0.29693	.	.	ENSG00000205531	ENST00000380542	.	.	.	4.07	4.07	0.47477	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.7709	0.51958	0.0:0.0:0.0:1.0	.	.	.	.	Y	376	.	.	X	-	3	2	NAP1L4	2927065	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.761000	0.62243	1.717000	0.51406	0.533000	0.62120	TAA	.	.	.	none		0.328	NAP1L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030273.3	NM_005969		G	2970489	T	G	2970489	4	3	29	1	0	0	0	0	0	0	0	0	10166	1500	52	5	3	5	NAP1L4	11	2970489	Nonstop_Mutation	SNP	T	TCGA-5P-A9JW-01A-11D-A42J-10		2970489	132036027	50	2073											
GLB1L3	112937	hgsc.bcm.edu	37	chr11	134147653	134147653	+	Frame_Shift_Del	DEL	C	C	-																															tcgatctgtgggacttggaaCtgaaagcacaggtcggggta																										TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr11:134147653delC	ENST00000431683.2	+	3	209	c.209delC	c.(208-210)actfs	p.T70fs	GLB1L3_ENST00000389887.5_Frame_Shift_Del_p.T70fs	NM_001080407.2	NP_001073876.2	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1-like 3	70					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)		GGACTTGGAACTGAAAGCACA	0.567																																					p.T70fs		Atlas-Indel,Pindel	.											.	GLB1L3	102	.	0			c.208delA						PASS	.						38	43	41					11																	134147653		2196	4296	6492	SO:0001589	frameshift_variant	112937	exon3			.		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.209delC	chr11.hg19:g.134147653delC	ENSP00000396615:p.Thr70fs	126.0	0.0	0		139.0	52.0	0.374101	NM_001080407	A6NEM0|A6NN15|Q6P3S3|Q96FF8	Frame_Shift_Del	DEL	ENST00000431683.2	hg19	CCDS44780.1																																																																																			.	.	.	none		0.567	GLB1L3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393625.1	NM_138416		-	134147653	C	-	134147653	7	5	29	1	0	1	0	1	0	0	0	0	6437	565	20	0	219	0	GLB1L3	11	134147653	Frame_Shift_Del	DEL	C	TCGA-5P-A9JW-01A-11D-A42J-10	131177164	134147653	858863	51	2074											
CLSTN3	9746	hgsc.bcm.edu	37	chr12	7303653	7303653	+	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	gcctagccagctcccacagaAactccagtacgtaagcctgg	11	6	9	15	1	0	1	0	0	0	1	2	1	2	1	5	1	5	3	5	1	4	3			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr12:7303653A>T	ENST00000266546.6	+	16	2971	c.2521A>T	c.(2521-2523)Aac>Tac	p.N841Y	CLSTN3_ENST00000537408.1_Missense_Mutation_p.N853Y	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	841					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						CTCCCACAGAAACTCCAGTAC	0.652																																					p.N841Y		Atlas-SNP	.											.	CLSTN3	84	.	0			c.A2521T						PASS	.						21	21	21					12																	7303653		2202	4300	6502	SO:0001583	missense	9746	exon16			CACAGAAACTCCA	AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182		"Cadherins / Cadherin-related"	18371	protein-coding gene	gene with protein product	"cadherin-related family member 14"	611324				12498782	Standard	NM_014718		Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167	ENST00000266546.6:c.2521A>T	chr12.hg19:g.7303653A>T	ENSP00000266546:p.Asn841Tyr	91.0	0.0	.		139.0	40.0	.	NM_014718	D3DUT6|O94831|Q2T9J5|Q5UE57	Missense_Mutation	SNP	ENST00000266546.6	hg19	CCDS8575.1	.	.	.	.	.	.	.	.	.	.	A	8.415	0.845014	0.16963	.	.	ENSG00000139182	ENST00000266546;ENST00000537408	T;T	0.35789	1.29;1.29	5.52	5.52	0.82312	.	0.098878	0.64402	D	0.000002	T	0.36635	0.0974	L	0.29908	0.895	0.50632	D	0.999881	D;B	0.61080	0.989;0.263	P;B	0.50490	0.642;0.091	T	0.09530	-1.0670	10	0.40728	T	0.16	-42.2086	14.2234	0.65843	1.0:0.0:0.0:0.0	.	853;841	Q5UE57;Q9BQT9	.;CSTN3_HUMAN	Y	841;853	ENSP00000266546:N841Y;ENSP00000440679:N853Y	ENSP00000266546:N841Y	N	+	1	0	CLSTN3	7194920	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	8.553000	0.90686	2.086000	0.62901	0.459000	0.35465	AAC	.	.	.	none		0.652	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398560.2	NM_014718		T	7303653	A	T	7303653	3	4	29	1	0	0	0	0	1	0	0	0	3565	14	1	5	2583	5	CLSTN3	12	7303653	Missense_Mutation	SNP	A	TCGA-5P-A9JW-01A-11D-A42J-10		7303653	126548242	52	2075											
ACSM4	341392	hgsc.bcm.edu	37	chr12	7476144	7476144	+	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	acacggcccttctgtttcttCtctaaatatgtggtatgagg	8	15	9	9	1	3	1	0	1	3	0	4	1	3	1	1	3	0	2	1	3	4	6			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr12:7476144C>T	ENST00000399422.4	+	9	1344	c.1296C>T	c.(1294-1296)ttC>ttT	p.F432F		NM_001080454.1	NP_001073923.1	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member 4	432					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						TCTGTTTCTTCTCTAAATAtg	0.413																																					p.F432F		Atlas-SNP	.											.	ACSM4	98	.	0			c.C1296T						PASS	.						62	60	61					12																	7476144		1832	4080	5912	SO:0001819	synonymous_variant	341392	exon9			TTTCTTCTCTAAA		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.1296C>T	chr12.hg19:g.7476144C>T		79.0	0.0	.		66.0	16.0	.	NM_001080454	A8MTI6	Silent	SNP	ENST00000399422.4	hg19	CCDS44825.1																																																																																			.	.	.	none		0.413	ACSM4-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337866.2	NM_001080454		T	7476144	C	T	7476144	2	4	29	1	0	0	0	0	0	0	0	1	186	912	32	2		2	ACSM4	12	7476144	Silent	SNP	C	TCGA-5P-A9JW-01A-11D-A42J-10	172491	7476144	126375751	53	2076											
KRT1	3848	hgsc.bcm.edu	37	chr12	53069229	53069229	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagccatagctgccacctccGgagccgtagctgctacctcc	7	7	10	17	2	0	0	0	0	0	0	2	2	2	1	7	1	7	4	7	1	3	3	rs540699806|rs267607656	byFrequency	TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr12:53069229G>A	ENST00000252244.3	-	9	1741	c.1683C>T	c.(1681-1683)tcC>tcT	p.S561S		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	561	Gly/Ser-rich.|Tail.		Missing (in allele 1B). {ECO:0000269|PubMed:1281859}.		complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						tgccacctccggagccgtagc	0.692																																					p.S561S		Atlas-SNP	.											.	KRT1	110	.	0			c.C1683T						PASS	.						4	4	4					12																	53069229		1797	3656	5453	SO:0001819	synonymous_variant	3848	exon9			ACCTCCGGAGCCG	X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"-", "Intermediate filaments type II, keratins (basic)"	6412	protein-coding gene	gene with protein product		139350	"epidermolytic hyperkeratosis 1"	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.1683C>T	chr12.hg19:g.53069229G>A		4.0	0.0	.		36.0	16.0	.	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Silent	SNP	ENST00000252244.3	hg19	CCDS8836.1																																																																																			.	.	.	none		0.692	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121		A	53069229	G	A	53069229	2	1	29	1	0	0	0	0	0	0	0	1	8454	1103	39	1		1	KRT1	12	53069229	Silent	SNP	G	TCGA-5P-A9JW-01A-11D-A42J-10	45593085	53069229	80782666	54	2077											
PAN2	9924	hgsc.bcm.edu	37	chr12	56722345	56722360	+	Frame_Shift_Del	DEL	CTGCCGAATATCATCA	CTGCCGAATATCATCA	-																															ccattctccaggctctggatCtgccgaatatcatcactgcc																										TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	CTGCCGAATATCATCA	CTGCCGAATATCATCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr12:56722345_56722360delCTGCCGAATATCATCA	ENST00000425394.2	-	3	724_739	c.348_363delTGATGATATTCGGCAG	c.(346-363)agtgatgatattcggcagfs	p.SDDIRQ116fs	PAN2_ENST00000440411.3_Frame_Shift_Del_p.SDDIRQ116fs|PAN2_ENST00000548043.1_Frame_Shift_Del_p.SDDIRQ116fs|PAN2_ENST00000257931.5_Frame_Shift_Del_p.SDDIRQ116fs	NM_001127460.2	NP_001120932	Q9HBH5	RDH14_HUMAN	PAN2 poly(A) specific ribonuclease subunit	0					osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	41					Vitamin A(DB00162)	GGCTCTGGATCTGCCGAATATCATCACTGCCATTGA	0.463																																					p.117_122del		Atlas-Indel,Pindel	.											.	PAN2	107	.	0			c.349_364del						PASS	.																																			SO:0001589	frameshift_variant	9924	exon3			.	AB014610	CCDS8915.1, CCDS44922.1, CCDS53802.1	12q13.2	2014-03-27	2014-03-27	2008-01-08		ENSG00000135473		"Ubiquitin-specific peptidases"	20074	protein-coding gene	gene with protein product	"PAN2 homolog, PABP1 dependent poly A specific ribonuclease subunit (S. cerevisiae)"		"ubiquitin specific protease 52", "ubiquitin specific peptidase 52", "PAN2 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"	USP52		12838346, 14583602	Standard	NM_014871		Approved	KIAA0710, hPAN2	uc001skx.3	Q504Q3	OTTHUMG00000170412	ENST00000425394.2:c.348_363delTGATGATATTCGGCAG	chr12.hg19:g.56722345_56722360delCTGCCGAATATCATCA	ENSP00000401721:p.Ser116fs	86.0	0.0	0		97.0	17.0	0.175258	NM_001127460		Frame_Shift_Del	DEL	ENST00000425394.2	hg19	CCDS44922.1																																																																																			.	.	.	none		0.463	PAN2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409024.1	NM_014871		-	56722360	CTGCCGAATATCATCA	-	56722345	7	5	29	1	0	1	0	1	0	0	0	0	11421	912	32	0	3341	0	PAN2	12	56722345	Frame_Shift_Del	DEL	CTGCCGAATATCATCA	TCGA-5P-A9JW-01A-11D-A42J-10	3653116	56722345	77129550	55	2078											
EEA1	8411	hgsc.bcm.edu	37	chr12	93210107	93210107	+	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	cttctgctcttgtacctggtCatgcaaattctcctgggctt	5	16	8	12	0	4	0	1	0	3	0	5	0	4	0	2	2	3	4	2	2	2	5			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr12:93210107C>A	ENST00000322349.8	-	15	2062	c.1798G>T	c.(1798-1800)Gac>Tac	p.D600Y		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	600	Gln/Glu/Lys-rich.				early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|synaptic vesicle to endosome fusion (GO:0016189)|vesicle fusion (GO:0006906)	axonal spine (GO:0044308)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|recycling endosome (GO:0055037)|serine-pyruvate aminotransferase complex (GO:0005969)	1-phosphatidylinositol binding (GO:0005545)|calmodulin binding (GO:0005516)|GTP-dependent protein binding (GO:0030742)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(11)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	36						TGTACCTGGTCATGCAAATTC	0.388																																					p.D600Y		Atlas-SNP	.											.	EEA1	104	.	0			c.G1798T						PASS	.						251	218	229					12																	93210107		2203	4300	6503	SO:0001583	missense	8411	exon15			CCTGGTCATGCAA	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.1798G>T	chr12.hg19:g.93210107C>A	ENSP00000317955:p.Asp600Tyr	197.0	0.0	.		152.0	46.0	.	NM_003566	Q14221	Missense_Mutation	SNP	ENST00000322349.8	hg19	CCDS31874.1	.	.	.	.	.	.	.	.	.	.	C	17.57	3.422447	0.62622	.	.	ENSG00000102189	ENST00000322349	T	0.46819	0.86	5.27	5.27	0.74061	.	0.109285	0.39146	N	0.001443	T	0.44371	0.1290	N	0.14661	0.345	0.42441	D	0.992715	D	0.57257	0.979	P	0.50490	0.642	T	0.52939	-0.8508	10	0.72032	D	0.01	.	18.8732	0.92324	0.0:1.0:0.0:0.0	.	600	Q15075	EEA1_HUMAN	Y	600	ENSP00000317955:D600Y	ENSP00000317955:D600Y	D	-	1	0	EEA1	91734238	1.000000	0.71417	1.000000	0.80357	0.541000	0.35023	5.668000	0.68074	2.473000	0.83533	0.313000	0.20887	GAC	.	.	.	none		0.388	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566		A	93210107	C	A	93210107	3	1	29	1	0	0	0	0	1	0	0	0	4923	826	29	4	2497	4	EEA1	12	93210107	Missense_Mutation	SNP	C	TCGA-5P-A9JW-01A-11D-A42J-10	36487762	93210107	40641788	56	2079											
NCOR2	9612	hgsc.bcm.edu	37	chr12	124846815	124846815	+	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	tggtgggagctgcgtcctccCgggggggctcatggactttg	3	10	18	10	2	1	0	1	0	0	0	3	2	3	2	2	6	2	2	2	6	0	1			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr12:124846815C>A	ENST00000405201.1	-	22	2957	c.2957G>T	c.(2956-2958)cGg>cTg	p.R986L	NCOR2_ENST00000404621.1_Missense_Mutation_p.R968L|NCOR2_ENST00000356219.3_Missense_Mutation_p.R985L|NCOR2_ENST00000397355.1_Missense_Mutation_p.R969L|NCOR2_ENST00000404121.2_Missense_Mutation_p.R539L|NCOR2_ENST00000429285.2_Missense_Mutation_p.R968L			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	986					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)		TGCGTCCTCCCGGGGGGGCTC	0.652																																					p.R986L		Atlas-SNP	.											.	NCOR2	475	.	0			c.G2957T						PASS	.						13	17	16					12																	124846815		2057	4192	6249	SO:0001583	missense	9612	exon24			TCCTCCCGGGGGG	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.2957G>T	chr12.hg19:g.124846815C>A	ENSP00000384018:p.Arg986Leu	35.0	0.0	.		26.0	11.0	.	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	hg19	CCDS41858.2	.	.	.	.	.	.	.	.	.	.	C	11.05	1.523460	0.27299	.	.	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285;ENST00000458234	T;T;T;T;T;T;T	0.28666	2.24;2.56;2.26;2.56;2.28;2.55;1.6	4.91	3.09	0.35607	.	0.443732	0.21379	N	0.075504	T	0.35970	0.0950	L	0.51422	1.61	0.28323	N	0.922137	D;D;D	0.57571	0.974;0.967;0.98	P;P;P	0.53861	0.628;0.549;0.736	T	0.13818	-1.0495	10	0.28530	T	0.3	-22.5278	8.6723	0.34159	0.0:0.8183:0.0:0.1817	.	968;969;986	C9J0Q5;C9J239;C9JFD3	.;.;.	L	986;968;985;969;985;539;968;986	ENSP00000384018:R986L;ENSP00000384202:R968L;ENSP00000348551:R985L;ENSP00000380513:R969L;ENSP00000385618:R539L;ENSP00000400281:R968L;ENSP00000402808:R986L	ENSP00000348551:R985L	R	-	2	0	NCOR2	123412768	1.000000	0.71417	0.992000	0.48379	0.124000	0.20399	1.273000	0.33121	0.504000	0.28082	-0.448000	0.05591	CGG	.	.	.	none		0.652	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		A	124846815	C	A	124846815	3	1	29	1	0	0	0	0	1	0	0	0	10243	652	23	4	4715	4	NCOR2	12	124846815	Missense_Mutation	SNP	C	TCGA-5P-A9JW-01A-11D-A42J-10	31636708	124846815	9005080	57	2080											
METT11D1	64745	hgsc.bcm.edu	37	chr14	21463350	21463350	+	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	gtggagaatggaacaaaagcTgggcacagccttctcatgga	13	7	13	8	0	1	1	1	0	1	1	2	4	1	3	1	4	3	2	1	4	4	1			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr14:21463350T>A	ENST00000339374.6	+	10	1136	c.903T>A	c.(901-903)gcT>gcA	p.A301A	METTL17_ENST00000556670.2_Silent_p.A301A|METTL17_ENST00000382985.4_Silent_p.A301A|RP11-84C10.4_ENST00000557335.1_RNA	NM_001029991.1|NM_022734.2	NP_001025162.1|NP_073571.1	Q9H7H0	MET17_HUMAN	methyltransferase like 17	301					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	copper ion binding (GO:0005507)|methyltransferase activity (GO:0008168)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|skin(2)	20						GAACAAAAGCTGGGCACAGCC	0.458																																					p.A301A		Atlas-SNP	.											.	METTL17	46	.	0			c.T903A						PASS	.						214	191	199					14																	21463350		2203	4300	6503	SO:0001819	synonymous_variant	64745	exon10			AAAAGCTGGGCAC	AK024512	CCDS9562.1, CCDS41913.1	14q11.2	2011-03-03	2011-03-02	2011-03-02	ENSG00000165792	ENSG00000165792			19280	protein-coding gene	gene with protein product			"methyltransferase 11 domain containing 1"	METT11D1		11278769	Standard	XM_006720235		Approved	FLJ20859	uc001vyn.3	Q9H7H0	OTTHUMG00000029610	ENST00000339374.6:c.903T>A	chr14.hg19:g.21463350T>A		110.0	0.0	.		131.0	40.0	.	NM_022734	Q9BSH1|Q9BZH2|Q9BZH3	Silent	SNP	ENST00000339374.6	hg19	CCDS9562.1																																																																																			.	.	.	none		0.458	METTL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073804.4	NM_022734		A	21463350	T	A	21463350	2	1	29	1	0	0	0	0	0	0	0	1	9498	1567	55	5		5	METT11D1	14	21463350	Silent	SNP	T	TCGA-5P-A9JW-01A-11D-A42J-10		21463350	85886190	58	2081											
CHD8	57680	hgsc.bcm.edu	37	chr14	21868201	21868202	+	Missense_Mutation	DNP	AG	AG	TA																															aataacctcctgcctcaggtAgtatagcattcgtacccgca																										TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr14:21868201_21868202AG>TA	ENST00000557364.1	-	25	5018_5019	c.4755_4756CT>TA	c.(4753-4758)taCTac>taTAac	p.Y1586N	SNORD8_ENST00000363915.1_RNA|CHD8_ENST00000555962.1_5'UTR|CHD8_ENST00000430710.3_Missense_Mutation_p.Y1307N|CHD8_ENST00000399982.2_Missense_Mutation_p.Y1586N			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1586					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)		TGCCTCAGGTAGTATAGCATTC	0.441																																					p.Y1586N|p.Y1585Y		Atlas-SNP	.											.	CHD8	339	.	0			c.T4756A|c.C4755T						PASS	.																																			SO:0001583	missense	57680	exon24			TCAGGTAGTATAG|CAGGTAGTATAGC	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.4755_4756delinsTA	chr14.hg19:g.21868201_21868202delinsTA	ENSP00000451601:p.Tyr1586Asn	127.0|126.0	0.0	.		126.0	36.0|35.0	.	NM_001170629	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Missense_Mutation|Silent	SNP	ENST00000557364.1	hg19	CCDS53885.1																																																																																			.	.	.	none		0.441	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920		TA	21868202	AG	TA	21868201	3	4	29	1	0	0	0	0	1	0	0	0	3333	420	15	5	3045	5	CHD8	14	21868201	Missense_Mutation	DNP	AG	TCGA-5P-A9JW-01A-11D-A42J-10	404851	21868201	85481339	59	2082											
WDHD1	11169	hgsc.bcm.edu	37	chr14	55451547	55451547	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccagctctagcagttgaacTccaaggcactgatccccatc	10	8	7	16	0	1	2	0	2	1	0	4	2	3	2	4	1	3	4	4	1	3	2			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr14:55451547T>C	ENST00000360586.3	-	15	1865	c.1800A>G	c.(1798-1800)ggA>ggG	p.G600G	WDHD1_ENST00000359167.4_Silent_p.G118G|WDHD1_ENST00000420358.2_Silent_p.G477G|WDHD1_ENST00000421192.1_Silent_p.G477G	NM_007086.3	NP_009017.1	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1	600					heterochromatin maintenance (GO:0070829)|regulation of chromosome organization (GO:0033044)|RNA processing (GO:0006396)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(2)	42						GCAGTTGAACTCCAAGGCACT	0.383																																					p.G600G		Atlas-SNP	.											.	WDHD1	82	.	0			c.A1800G						PASS	.						53	55	55					14																	55451547		2203	4300	6503	SO:0001819	synonymous_variant	11169	exon15			TTGAACTCCAAGG	AJ006266	CCDS9721.1, CCDS41955.1	14q22.2	2013-01-09			ENSG00000198554	ENSG00000198554		"WD repeat domain containing"	23170	protein-coding gene	gene with protein product	"CTF4, chromosome transmission fidelity factor 4 homolog (S. cerevisiae)"	608126				9175701, 20028748	Standard	NM_007086		Approved	AND-1, CTF4, CHTF4	uc001xbm.2	O75717	OTTHUMG00000140304	ENST00000360586.3:c.1800A>G	chr14.hg19:g.55451547T>C		479.0	0.0	.		491.0	166.0	.	NM_007086	C9JW18|F6W0U7	Silent	SNP	ENST00000360586.3	hg19	CCDS9721.1																																																																																			.	.	.	none		0.383	WDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276897.2	NM_007086		C	55451547	T	C	55451547	2	2	29	1	0	0	0	0	0	0	0	1	17283	1538	54	3		3	WDHD1	14	55451547	Silent	SNP	T	TCGA-5P-A9JW-01A-11D-A42J-10	33583346	55451547	51897993	60	2083											
C14orf115	55237	hgsc.bcm.edu	37	chr14	74825395	74825395	+	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	tggcagcagcgggtggcaggGatggccggatgctggtgatg	6	7	21	7	2	0	1	0	1	0	0	0	3	0	3	1	7	3	4	1	7	0	0			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr14:74825395G>A	ENST00000256362.4	+	2	2150	c.1909G>A	c.(1909-1911)Gat>Aat	p.D637N		NM_018228.2	NP_060698.2	Q9H8Y1	VRTN_HUMAN	vertebrae development associated	637					transposition, DNA-mediated (GO:0006313)		sequence-specific DNA binding (GO:0043565)|transposase activity (GO:0004803)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(15)|ovary(5)|prostate(2)|skin(1)|urinary_tract(1)	41						GGGTGGCAGGGATGGCCGGAT	0.642																																					p.D637N		Atlas-SNP	.											.	VRTN	79	.	0			c.G1909A						PASS	.						45	39	41					14																	74825395		2203	4300	6503	SO:0001583	missense	55237	exon2			GGCAGGGATGGCC	AK001673	CCDS9830.1	14q24.2	2012-12-07	2012-12-07	2010-10-20	ENSG00000133980	ENSG00000133980			20223	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 115", "vertebrae development homolog (pig)"	C14orf115		21232157	Standard	NM_018228		Approved	FLJ10811, vertnin	uc001xpw.4	Q9H8Y1	OTTHUMG00000171208	ENST00000256362.4:c.1909G>A	chr14.hg19:g.74825395G>A	ENSP00000256362:p.Asp637Asn	92.0	0.0	.		105.0	30.0	.	NM_018228	Q9NVC7	Missense_Mutation	SNP	ENST00000256362.4	hg19	CCDS9830.1	.	.	.	.	.	.	.	.	.	.	G	9.465	1.094217	0.20471	.	.	ENSG00000133980	ENST00000256362	T	0.49139	0.79	4.28	3.29	0.37713	.	0.386356	0.25156	U	0.032704	T	0.18341	0.0440	N	0.04203	-0.255	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.17653	-1.0362	10	0.10902	T	0.67	-8.3907	3.9842	0.09507	0.2604:0.0:0.7396:0.0	.	637	Q9H8Y1	VRTN_HUMAN	N	637	ENSP00000256362:D637N	ENSP00000256362:D637N	D	+	1	0	VRTN	73895148	0.904000	0.30761	0.463000	0.27130	0.242000	0.25591	4.484000	0.60271	2.233000	0.73108	0.485000	0.47835	GAT	.	.	.	none		0.642	VRTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412339.1	NM_018228		A	74825395	G	A	74825395	3	1	29	1	0	0	0	0	1	0	0	0	1742	1174	41	2	1911	2	C14orf115	14	74825395	Missense_Mutation	SNP	G	TCGA-5P-A9JW-01A-11D-A42J-10	19373848	74825395	32524145	61	2084											
TJP1	7082	hgsc.bcm.edu	37	chr15	30001031	30001031	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acttgtatatggttttggtgTgaatcgattgtatgctggag	8	17	13	3	1	0	1	0	1	0	0	1	3	0	2	0	3	1	4	0	3	4	7			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr15:30001031T>C	ENST00000346128.6	-	25	5056	c.4582A>G	c.(4582-4584)Aca>Gca	p.T1528A	TJP1_ENST00000356107.6_Missense_Mutation_p.T1528A|TJP1_ENST00000400011.2_Missense_Mutation_p.T1452A|TJP1_ENST00000545208.2_Missense_Mutation_p.T1448A	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	1528					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)		GGTTTTGGTGTGAATCGATTG	0.413																																					p.T1528A	Melanoma(77;681 1843 6309 6570)	Atlas-SNP	.											.	TJP1	140	.	0			c.A4582G						PASS	.						306	282	289					15																	30001031		1911	4145	6056	SO:0001583	missense	7082	exon25			TTGGTGTGAATCG		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.4582A>G	chr15.hg19:g.30001031T>C	ENSP00000281537:p.Thr1528Ala	130.0	0.0	.		127.0	7.0	.	NM_003257	B4E3K1|Q2NKP3|Q4ZGJ6	Missense_Mutation	SNP	ENST00000346128.6	hg19	CCDS42007.1	.	.	.	.	.	.	.	.	.	.	T	13.72	2.321717	0.41096	.	.	ENSG00000104067	ENST00000346128;ENST00000400011;ENST00000545208;ENST00000400007;ENST00000356107	T;T	0.47869	0.83;0.83	5.65	4.48	0.54585	.	0.158020	0.56097	D	0.000023	T	0.39759	0.1090	L	0.48362	1.52	0.80722	D	1	B;B;B;B	0.32350	0.366;0.264;0.025;0.264	B;B;B;B	0.31101	0.118;0.124;0.021;0.085	T	0.37150	-0.9718	10	0.48119	T	0.1	.	11.3701	0.49694	0.2304:0.0:0.0:0.7696	.	1521;1448;1528;1452	A9CQZ8;Q07157-2;Q07157;G5E9E7	.;.;ZO1_HUMAN;.	A	1528;1452;1528;1448;1448	ENSP00000281537:T1528A;ENSP00000382890:T1452A	ENSP00000281537:T1528A	T	-	1	0	TJP1	27788323	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.604000	0.54081	2.371000	0.80710	0.533000	0.62120	ACA	.	.	.	none		0.413	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		C	30001031	T	C	30001031	3	2	29	1	0	0	0	0	1	0	0	0	15941	1696	59	3	680	3	TJP1	15	30001031	Missense_Mutation	SNP	T	TCGA-5P-A9JW-01A-11D-A42J-10		30001031	72530361	62	2085											
PRTG	283659	hgsc.bcm.edu	37	chr15	55930800	55930800	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaaggactggaaagctgaTccacatgtaatcgaacggca	14	7	10	10	2	0	1	0	1	0	0	3	4	2	3	2	3	2	3	2	3	4	1			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr15:55930800T>C	ENST00000389286.4	-	14	2446	c.2399A>G	c.(2398-2400)gAt>gGt	p.D800G		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)		GGAAAGCTGATCCACATGTAA	0.373																																					p.D800G		Atlas-SNP	.											.	PRTG	110	.	0			c.A2399G						PASS	.						65	63	64					15																	55930800		1854	4105	5959	SO:0001583	missense	283659	exon14			AGCTGATCCACAT	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.2399A>G	chr15.hg19:g.55930800T>C	ENSP00000373937:p.Asp800Gly	151.0	0.0	.		133.0	47.0	.	NM_173814		Missense_Mutation	SNP	ENST00000389286.4	hg19	CCDS42040.1	.	.	.	.	.	.	.	.	.	.	T	13.27	2.185993	0.38609	.	.	ENSG00000166450	ENST00000389286	T	0.51817	0.69	4.99	3.84	0.44239	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.061925	0.64402	D	0.000008	T	0.28962	0.0719	N	0.16708	0.43	0.80722	D	1	B	0.19331	0.035	B	0.12837	0.008	T	0.04991	-1.0913	10	0.22109	T	0.4	-13.4313	10.3573	0.43972	0.0:0.0789:0.0:0.9211	.	800	Q2VWP7	PRTG_HUMAN	G	800	ENSP00000373937:D800G	ENSP00000373937:D800G	D	-	2	0	PRTG	53718092	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.882000	0.48546	0.822000	0.34565	0.477000	0.44152	GAT	.	.	.	none		0.373	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814		C	55930800	T	C	55930800	3	2	29	1	0	0	0	0	1	0	0	0	12648	1435	50	3	1081	3	PRTG	15	55930800	Missense_Mutation	SNP	T	TCGA-5P-A9JW-01A-11D-A42J-10	25929769	55930800	46600592	63	2086											
CCNB2	9133	hgsc.bcm.edu	37	chr15	59417066	59417066	+	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	ccttgcctccccactgatagGaaggtcctaggctgccgtgg	6	9	12	14	1	0	1	0	1	0	0	2	2	2	2	6	4	2	1	6	4	3	3			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr15:59417066G>A	ENST00000288207.2	+	9	1378	c.1187G>A	c.(1186-1188)gGa>gAa	p.G396E	CCNB2_ENST00000559622.1_Missense_Mutation_p.G268E|RP11-59H7.3_ENST00000559026.1_RNA	NM_004701.3	NP_004692.1	O95067	CCNB2_HUMAN	cyclin B2	396					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						CCACTGATAGGAAGGTCCTAG	0.478																																					p.G396E		Atlas-SNP	.											.	CCNB2	23	.	0			c.G1187A						PASS	.						74	58	63					15																	59417066		2191	4291	6482	SO:0001583	missense	9133	exon9			TGATAGGAAGGTC	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.1187G>A	chr15.hg19:g.59417066G>A	ENSP00000288207:p.Gly396Glu	84.0	0.0	.		105.0	35.0	.	NM_004701	B3KM93|Q6FI99	Missense_Mutation	SNP	ENST00000288207.2	hg19	CCDS10170.1	.	.	.	.	.	.	.	.	.	.	G	13.06	2.125044	0.37533	.	.	ENSG00000157456	ENST00000288207	T	0.14516	2.5	5.85	1.77	0.24775	.	0.708046	0.14437	N	0.319603	T	0.11324	0.0276	L	0.40543	1.245	0.21719	N	0.999575	B;B	0.24258	0.1;0.1	B;B	0.21151	0.033;0.014	T	0.22068	-1.0227	10	0.49607	T	0.09	.	8.4873	0.33078	0.1126:0.2451:0.6423:0.0	.	396;396	Q53HG9;O95067	.;CCNB2_HUMAN	E	396	ENSP00000288207:G396E	ENSP00000288207:G396E	G	+	2	0	CCNB2	57204358	0.464000	0.25807	0.005000	0.12908	0.017000	0.09413	0.702000	0.25631	0.076000	0.16826	0.561000	0.74099	GGA	.	.	.	none		0.478	CCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256016.1	NM_004701		A	59417066	G	A	59417066	3	1	29	1	0	0	0	0	1	0	0	0	2915	1174	41	2	1221	2	CCNB2	15	59417066	Missense_Mutation	SNP	G	TCGA-5P-A9JW-01A-11D-A42J-10	3486266	59417066	43114326	64	2087											
VPS13C	54832	hgsc.bcm.edu	37	chr15	62221902	62221902	+	Frame_Shift_Del	DEL	A	A	-																															tcttgtttgtaacttatatcAatcatagaactgttgttatc																										TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr15:62221902delA	ENST00000261517.5	-	51	6157	c.6084delT	c.(6082-6084)attfs	p.I2028fs	VPS13C_ENST00000395896.4_Frame_Shift_Del_p.I2028fs|VPS13C_ENST00000395898.3_Frame_Shift_Del_p.I1985fs|VPS13C_ENST00000249837.3_Frame_Shift_Del_p.I1985fs	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						AACTTATATCAATCATAGAAC	0.313																																					p.D2029fs		Atlas-Indel,Pindel	.											.	VPS13C	506	.	0			c.6085delG						PASS	.						166	143	151					15																	62221902		2203	4300	6503	SO:0001589	frameshift_variant	54832	exon51			.	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.6084delT	chr15.hg19:g.62221902delA	ENSP00000261517:p.Ile2028fs	84.0	0.0	0		91.0	33.0	0.362637	NM_020821		Frame_Shift_Del	DEL	ENST00000261517.5	hg19	CCDS32257.1																																																																																			.	.	.	none		0.313	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		-	62221902	A	-	62221902	7	5	29	1	0	1	0	1	0	0	0	0	17203	126	5	0	5345	0	VPS13C	15	62221902	Frame_Shift_Del	DEL	A	TCGA-5P-A9JW-01A-11D-A42J-10	2804836	62221902	40309490	65	2088											
HERC1	8925	hgsc.bcm.edu	37	chr15	64047449	64047449	+	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	taatcttccaaagtctccttCaccccatgtgtataattccc	10	14	3	14	0	3	0	1	0	2	0	6	0	5	0	5	0	0	1	5	0	4	6			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr15:64047449C>A	ENST00000443617.2	-	6	1696	c.1609G>T	c.(1609-1611)Gaa>Taa	p.E537*		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	537					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						AAGTCTCCTTCACCCCATGTG	0.378																																					p.E537X		Atlas-SNP	.											.	HERC1	624	.	0			c.G1609T						PASS	.						93	83	86					15																	64047449		1913	4119	6032	SO:0001587	stop_gained	8925	exon6			CTCCTTCACCCCA	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.1609G>T	chr15.hg19:g.64047449C>A	ENSP00000390158:p.Glu537*	128.0	0.0	.		90.0	20.0	.	NM_003922	Q8IW65	Nonsense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	C	39	7.360880	0.98235	.	.	ENSG00000103657	ENST00000443617	.	.	.	5.97	5.97	0.96955	.	0.000000	0.85682	U	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	20.0492	0.97617	0.0:1.0:0.0:0.0	.	.	.	.	X	537	.	ENSP00000390158:E537X	E	-	1	0	HERC1	61834502	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.836000	0.97738	0.655000	0.94253	GAA	.	.	.	none		0.378	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		A	64047449	C	A	64047449	4	1	29	1	0	0	0	0	0	1	0	0	7064	835	29	4	13268	4	HERC1	15	64047449	Nonsense_Mutation	SNP	C	TCGA-5P-A9JW-01A-11D-A42J-10	1825547	64047449	38483943	66	2089											
EME2	197342	hgsc.bcm.edu	37	chr16	1823724	1823724	+	Missense_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	agccatcctggaagacgccgGtgccgacgtcctgatggagg	8	6	15	12	4	0	2	0	1	0	1	2	5	2	4	5	4	2	0	5	4	1	0			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr16:1823724G>A	ENST00000568449.1	+	2	287	c.266G>A	c.(265-267)gGt>gAt	p.G89D	MRPS34_ENST00000177742.3_5'Flank|MRPS34_ENST00000397375.2_5'Flank|NME3_ENST00000563498.1_5'Flank|EME2_ENST00000307394.7_Missense_Mutation_p.G89D|NME3_ENST00000219302.3_5'Flank	NM_001257370.1	NP_001244299.1	A4GXA9	EME2_HUMAN	essential meiotic structure-specific endonuclease subunit 2	89					DNA recombination (GO:0006310)|DNA repair (GO:0006281)	nucleus (GO:0005634)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)			central_nervous_system(1)|kidney(2)|lung(5)|pancreas(1)	9						GAAGACGCCGGTGCCGACGTC	0.751								Direct reversal of damage;Homologous recombination																													p.G89D		Atlas-SNP	.											.	EME2	40	.	0			c.G266A						PASS	.						6	4	4					16																	1823724		1756	3568	5324	SO:0001583	missense	197342	exon2			ACGCCGGTGCCGA	AK074080	CCDS58404.1	16p13.3	2013-07-03	2013-07-03			ENSG00000197774			27289	protein-coding gene	gene with protein product	"SLX2 structure-specific endonuclease subunit homolog B (S. cerevisiae)"	610886	"essential meiotic endonuclease 1 homolog 2 (S. pombe)"			12721304	Standard	NM_001257370		Approved	FLJ00151, SLX2B	uc010brw.1	A4GXA9		ENST00000568449.1:c.266G>A	chr16.hg19:g.1823724G>A	ENSP00000457353:p.Gly89Asp	160.0	0.0	.		263.0	121.0	.	NM_001257370	Q8TEP2|Q96RY3	Missense_Mutation	SNP	ENST00000568449.1	hg19	CCDS58404.1	.	.	.	.	.	.	.	.	.	.	G	16.80	3.223506	0.58668	.	.	ENSG00000197774	ENST00000307394;ENST00000454910	T	0.25749	1.78	3.56	3.56	0.40772	ERCC4 domain (2);	0.000000	0.42294	U	0.000733	T	0.49236	0.1545	.	.	.	0.54753	D	0.999982	D	0.89917	1.0	D	0.77004	0.989	T	0.53236	-0.8467	9	0.48119	T	0.1	-9.3726	14.1144	0.65144	0.0:0.0:1.0:0.0	.	89	A4GXA9	EME2_HUMAN	D	89	ENSP00000303779:G89D	ENSP00000303779:G89D	G	+	2	0	EME2	1763725	1.000000	0.71417	0.013000	0.15412	0.808000	0.45660	4.916000	0.63362	1.707000	0.51288	0.306000	0.20318	GGT	.	.	.	none		0.751	EME2-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433185.2	NM_001010865		A	1823724	G	A	1823724	3	1	29	1	0	0	0	0	1	0	0	0	5091	1261	44	2	272	2	EME2	16	1823724	Missense_Mutation	SNP	G	TCGA-5P-A9JW-01A-11D-A42J-10		1823724	88531029	67	2090											
GSPT1	2935	hgsc.bcm.edu	37	chr16	11980375	11980375	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctttgagatttgctccagtAagtcctgagcagggcataaa	11	12	10	8	0	1	2	0	2	1	1	3	3	3	2	2	1	2	4	2	1	3	4			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr16:11980375A>G	ENST00000563468.1	-	7	818	c.792T>C	c.(790-792)ctT>ctC	p.L264L	GSPT1_ENST00000439887.2_Silent_p.L401L|GSPT1_ENST00000420576.2_Silent_p.L264L|RP11-166B2.8_ENST00000574364.1_RNA|GSPT1_ENST00000434724.2_Silent_p.L402L|GSPT1_ENST00000564790.1_5'UTR			P15170	ERF3A_HUMAN	G1 to S phase transition 1	264	G5. {ECO:0000255|PROSITE- ProRule:PRU01059}.|tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				G1/S transition of mitotic cell cycle (GO:0000082)|GTP catabolic process (GO:0006184)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein methylation (GO:0006479)|translational termination (GO:0006415)	intracellular (GO:0005622)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation release factor activity (GO:0003747)			breast(1)|central_nervous_system(1)|kidney(4)|lung(4)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	14						TTGCTCCAGTAAGTCCTGAGC	0.353																																					p.L402L		Atlas-SNP	.											.	GSPT1	71	.	0			c.T1206C						PASS	.						84	82	83					16																	11980375		1956	4168	6124	SO:0001819	synonymous_variant	2935	exon9			TCCAGTAAGTCCT	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.792T>C	chr16.hg19:g.11980375A>G		199.0	0.0	.		244.0	55.0	.	NM_002094	J3KQG6|Q96GF2	Silent	SNP	ENST00000563468.1	hg19	CCDS45414.1																																																																																			.	.	.	none		0.353	GSPT1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421513.1	NM_002094		G	11980375	A	G	11980375	2	3	29	1	0	0	0	0	0	0	0	1	6833	349	13	3		3	GSPT1	16	11980375	Silent	SNP	A	TCGA-5P-A9JW-01A-11D-A42J-10	10156651	11980375	78374378	68	2091											
ACSM2B	348158	hgsc.bcm.edu	37	chr16	20570646	20570646	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atccccacgctgcaggccacAggctcccgagaggatgttgg	8	6	13	14	2	0	1	0	0	0	1	2	3	2	2	4	4	1	4	4	4	0	1			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr16:20570646A>G	ENST00000329697.6	-	3	469	c.301T>C	c.(301-303)Tgt>Cgt	p.C101R	ACSM2B_ENST00000567001.1_Missense_Mutation_p.C101R|ACSM2B_ENST00000565232.1_Missense_Mutation_p.C101R|ACSM2B_ENST00000414188.2_Missense_Mutation_p.C101R|ACSM2B_ENST00000565322.1_Missense_Mutation_p.C22R	NM_001105069.1	NP_001098539.1	Q68CK6	ACS2B_HUMAN	acyl-CoA synthetase medium-chain family member 2B	101					fatty acid metabolic process (GO:0006631)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(33)|ovary(1)|prostate(1)|skin(5)	57						TGCAGGCCACAGGCTCCCGAG	0.577																																					p.C101R		Atlas-SNP	.											ACSM2B,NS,carcinoma,0,1	ACSM2B	121	.	0			c.T301C						PASS	.						42	33	36					16																	20570646		2201	4300	6501	SO:0001583	missense	348158	exon4			GGCCACAGGCTCC	AY160217	CCDS10586.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000066813	ENSG00000066813		"Acyl-CoA synthetase family"	30931	protein-coding gene	gene with protein product	"xenobiotic/medium chain fatty acid:CoA ligase"	614359	"acyl-CoA synthetase medium-chain family member 2"	ACSM2		12616642	Standard	NM_182617		Approved	HXMA, HYST1046	uc002dhk.4	Q68CK6	OTTHUMG00000131555	ENST00000329697.6:c.301T>C	chr16.hg19:g.20570646A>G	ENSP00000327453:p.Cys101Arg	130.0	0.0	.		150.0	81.0	.	NM_182617	Q86YT1	Missense_Mutation	SNP	ENST00000329697.6	hg19	CCDS10586.1	.	.	.	.	.	.	.	.	.	.	A	10.81	1.455754	0.26161	.	.	ENSG00000066813	ENST00000329697;ENST00000414188	T;T	0.45668	0.89;0.89	3.51	2.38	0.29361	AMP-dependent synthetase/ligase (1);	0.000000	0.48286	D	0.000188	T	0.55178	0.1904	M	0.64170	1.965	0.48511	D	0.999664	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.49123	-0.8972	10	0.39692	T	0.17	-4.6887	7.8708	0.29565	0.8022:0.0:0.0:0.1978	.	101;101	A8K051;Q68CK6	.;ACS2B_HUMAN	R	101	ENSP00000327453:C101R;ENSP00000390378:C101R	ENSP00000327453:C101R	C	-	1	0	ACSM2B	20478147	0.985000	0.35326	0.002000	0.10522	0.012000	0.07955	4.017000	0.57167	0.406000	0.25560	0.496000	0.49642	TGT	.	.	.	none		0.577	ACSM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254417.2	NM_182617		G	20570646	A	G	20570646	3	3	29	1	0	0	0	0	1	0	0	0	184	188	7	3	1480	3	ACSM2B	16	20570646	Missense_Mutation	SNP	A	TCGA-5P-A9JW-01A-11D-A42J-10	8590271	20570646	69784107	69	2092											
ALKBH5	54890	hgsc.bcm.edu	37	chr17	18087657	18087680	+	In_Frame_Del	DEL	GCCGCAGCCGCCGTAGCCGCCGCA	GCCGCAGCCGCCGTAGCCGCCGCA	-																															gccgggaggccgccgccgctGccgcagccgccgtagccgcc																										TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	GCCGCAGCCGCCGTAGCCGCCGCA	GCCGCAGCCGCCGTAGCCGCCGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr17:18087657_18087680delGCCGCAGCCGCCGTAGCCGCCGCA	ENST00000399138.4	+	1	105_128	c.100_123delGCCGCAGCCGCCGTAGCCGCCGCA	c.(100-123)gccgcagccgccgtagccgccgcadel	p.AAAAVAAA34del	ALKBH5_ENST00000541285.1_Intron|RP11-258F1.1_ENST00000583062.1_RNA|RP11-258F1.1_ENST00000577847.1_RNA	NM_017758.3	NP_060228.3	Q6P6C2	ALKB5_HUMAN	AlkB family member 5, RNA demethylase	34	Ala-rich.				cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|oxidative single-stranded RNA demethylation (GO:0035553)|response to hypoxia (GO:0001666)|spermatogenesis (GO:0007283)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|oxidative RNA demethylase activity (GO:0035515)|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)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|skin(1)	10	all_neural(463;0.228)					cgccgccgctgccgcagccgccgtagccgccgcagccgcagccg	0.705																																					p.33_41del	Ovarian(166;154 1953 40235 46283 46309)	Pindel	.											.	ALKBH5	24	.	0			c.99_122del						PASS	.																																			SO:0001651	inframe_deletion	54890	exon1			.	AK000315	CCDS42272.1	17p11.2	2014-07-23	2014-07-23	2006-02-09	ENSG00000091542	ENSG00000091542	1.14.11.-	"Alkylation repair homologs"	25996	protein-coding gene	gene with protein product		613303	"oxoglutarate and iron-dependent oxygenase domain containing", "alkB, alkylation repair homolog 5 (E. coli)"	OFOXD1		11997338, 24778178	Standard	NM_017758		Approved	FLJ20308	uc010cpw.3	Q6P6C2	OTTHUMG00000059397	ENST00000399138.4:c.100_123delGCCGCAGCCGCCGTAGCCGCCGCA	chr17.hg19:g.18087657_18087680delGCCGCAGCCGCCGTAGCCGCCGCA	ENSP00000382091:p.Ala34_Ala41del	57.0	0.0	.		53.0	10.0	0.189	NM_017758	B4DVJ4|D3DXC6|Q9NXD6	In_Frame_Del	DEL	ENST00000399138.4	hg19	CCDS42272.1																																																																																			.	.	.	none		0.705	ALKBH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132069.3	NM_017758		-	18087680	GCCGCAGCCGCCGTAGCCGCCGCA	-	18087657	7	5	29	1	0	1	0	1	0	0	0	0	530	1319	46	0	102	0	ALKBH5	17	18087657	In_Frame_Del	DEL	GCCGCAGCCGCCGTAGCCGCCGCA	TCGA-5P-A9JW-01A-11D-A42J-10		18087657	63107553	70	2093											
NOS2	4843	hgsc.bcm.edu	37	chr17	26099337	26099346	+	Frame_Shift_Del	DEL	GGGGTTGAAG	GGGGTTGAAG	-																															tcccactgagccagtaccttGgggttgaaggcacagctgaa																								rs531708405		TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	GGGGTTGAAG	GGGGTTGAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr17:26099337_26099346delGGGGTTGAAG	ENST00000313735.6	-	14	1925_1934	c.1692_1701delCTTCAACCCC	c.(1690-1701)gccttcaaccccfs	p.AFNP564fs		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	564	Flavodoxin-like. {ECO:0000255|PROSITE- ProRule:PRU00088}.				arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	CCAGTACCTTGGGGTTGAAGGCACAGCTGA	0.538																																					p.565_568del		Atlas-Indel,Pindel	.											.	NOS2	113	.	0			c.1693_1702del						PASS	.																																			SO:0001589	frameshift_variant	4843	exon14			.	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.1692_1701delCTTCAACCCC	chr17.hg19:g.26099337_26099346delGGGGTTGAAG	ENSP00000327251:p.Ala564fs	81.0	0.0	0		85.0	10.0	0.117647	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Frame_Shift_Del	DEL	ENST00000313735.6	hg19	CCDS11223.1																																																																																			.	.	.	none		0.538	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625		-	26099346	GGGGTTGAAG	-	26099337	7	5	29	1	0	1	0	1	0	0	0	0	10550	1335	47	0	1816	0	NOS2	17	26099337	Frame_Shift_Del	DEL	GGGGTTGAAG	TCGA-5P-A9JW-01A-11D-A42J-10	8011680	26099337	55095873	71	2094											
C17orf42	79736	hgsc.bcm.edu	37	chr17	29226569	29226570	+	Frame_Shift_Ins	INS	-	-	T																															gttctgaatggaaagtcctgINSttttttccagaacatagaaa																										TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr17:29226569_29226570insT	ENST00000581216.1	-	4	1321_1322	c.700_701insA	c.(700-702)acafs	p.T234fs	TEFM_ENST00000580840.1_3'UTR|TEFM_ENST00000579183.1_5'Flank	NM_024683.3	NP_078959.3	Q96QE5	TEFM_HUMAN	transcription elongation factor, mitochondrial	234					DNA metabolic process (GO:0006259)|oxidative phosphorylation (GO:0006119)|regulation of transcription, DNA-templated (GO:0006355)|transcription from mitochondrial promoter (GO:0006390)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|ribonucleoprotein complex (GO:0030529)	DNA polymerase processivity factor activity (GO:0030337)|poly(A) RNA binding (GO:0044822)										GGAAAGTCCTGTTTTTTCCAGA	0.317																																					p.T234fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.701_702insA						PASS	.																																			SO:0001589	frameshift_variant	79736	exon4			.		CCDS42291.1	17q11.2	2011-12-12	2011-12-12	2011-12-12	ENSG00000172171	ENSG00000172171			26223	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 42"	C17orf42		11468690, 10843809, 21278163	Standard	NM_024683		Approved	FLJ22729	uc002hfu.2	Q96QE5		ENST00000581216.1:c.701dupA	chr17.hg19:g.29226575_29226575dupT	ENSP00000462963:p.Thr234fs	186.0	0.0	0		192.0	56.0	0.291667	NM_024683	E1P655|Q6GPG5|Q6PJ19|Q96H04|Q9H5Z9	Frame_Shift_Ins	INS	ENST00000581216.1	hg19	CCDS42291.1																																																																																			.	.	.	none		0.317	TEFM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444498.1	NM_024683		T	29226570	-	T	29226569	7	5	29	1	0	1	1	0	0	0	0	0	1858	1377	48	0	385	0	C17orf42	17	29226569	Frame_Shift_Ins	INS	-	TCGA-5P-A9JW-01A-11D-A42J-10	3127232	29226569	51968641	72	2095											
EFNA2	1943	hgsc.bcm.edu	37	chr19	1299934	1299934	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccgtgctctggaccctccTgggttcctagtcccagcccc	3	9	9	20	1	1	0	0	0	1	0	4	1	4	1	8	2	2	2	8	2	1	2			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr19:1299934T>C	ENST00000215368.2	+	4	647	c.632T>C	c.(631-633)cTg>cCg	p.L211P	MUM1_ENST00000344663.3_Intron	NM_001405.3	NP_001396.2	O43921	EFNA2_HUMAN	ephrin-A2	211					axon guidance (GO:0007411)|bone remodeling (GO:0046849)|cell-cell signaling (GO:0007267)|ephrin receptor signaling pathway (GO:0048013)|olfactory bulb development (GO:0021772)|osteoclast differentiation (GO:0030316)	anchored component of membrane (GO:0031225)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	ephrin receptor binding (GO:0046875)			lung(2)	2		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)		TGGACCCTCCTGGGTTCCTAG	0.711																																					p.L211P		Atlas-SNP	.											.	EFNA2	8	.	0			c.T632C						PASS	.						32	30	31					19																	1299934		2203	4298	6501	SO:0001583	missense	1943	exon4			CCCTCCTGGGTTC		CCDS12061.1	19p13	2011-03-09			ENSG00000099617	ENSG00000099617		"Ephrins"	3222	protein-coding gene	gene with protein product		602756		EPLG6			Standard	NM_001405		Approved	ELF-1, LERK6	uc002lry.2	O43921		ENST00000215368.2:c.632T>C	chr19.hg19:g.1299934T>C	ENSP00000215368:p.Leu211Pro	23.0	0.0	.		36.0	7.0	.	NM_001405	O76020	Missense_Mutation	SNP	ENST00000215368.2	hg19	CCDS12061.1	.	.	.	.	.	.	.	.	.	.	T	12.22	1.871424	0.33069	.	.	ENSG00000099617	ENST00000215368	D	0.92446	-3.04	3.41	3.41	0.39046	.	0.534302	0.14986	U	0.286944	D	0.84804	0.5553	N	0.19112	0.55	0.54753	D	0.999985	B	0.12013	0.005	B	0.08055	0.003	T	0.81782	-0.0775	10	0.87932	D	0	.	9.6252	0.39746	0.0:0.0:0.0:1.0	.	211	O43921	EFNA2_HUMAN	P	211	ENSP00000215368:L211P	ENSP00000215368:L211P	L	+	2	0	EFNA2	1250934	0.992000	0.36948	0.998000	0.56505	0.592000	0.36648	2.449000	0.44935	1.557000	0.49525	0.402000	0.26972	CTG	.	.	.	none		0.711	EFNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450016.1	NM_001405		C	1299934	T	C	1299934	3	2	29	1	0	0	0	0	1	0	0	0	4953	1580	55	3	646	3	EFNA2	19	1299934	Missense_Mutation	SNP	T	TCGA-5P-A9JW-01A-11D-A42J-10		1299934	57829049	73	2096											
MUC16	94025	hgsc.bcm.edu	37	chr19	9082415	9082415	+	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	agaactctttcttctggctgTgggttctgtgggagaagaga	8	13	14	6	0	4	3	0	0	4	3	4	5	4	3	0	3	1	2	0	3	2	3			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr19:9082415T>A	ENST00000397910.4	-	1	9603	c.9400A>T	c.(9400-9402)Aca>Tca	p.T3134S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3135	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						CTTCTGGCTGTGGGTTCTGTG	0.488																																					p.T3134S		Atlas-SNP	.											.	MUC16	4315	.	0			c.A9400T						PASS	.						194	200	198					19																	9082415		1930	4144	6074	SO:0001583	missense	94025	exon1			TGGCTGTGGGTTC	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.9400A>T	chr19.hg19:g.9082415T>A	ENSP00000381008:p.Thr3134Ser	164.0	0.0	.		197.0	67.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	3.734	-0.054959	0.07362	.	.	ENSG00000181143	ENST00000397910	T	0.02369	4.32	0.235	0.235	0.15431	.	.	.	.	.	T	0.03434	0.0099	N	0.08118	0	.	.	.	P	0.49696	0.927	P	0.56563	0.801	T	0.45614	-0.9249	7	0.87932	D	0	.	.	.	.	.	3134	B5ME49	.	S	3134	ENSP00000381008:T3134S	ENSP00000381008:T3134S	T	-	1	0	MUC16	8943415	0.032000	0.19561	0.024000	0.17045	0.224000	0.24922	1.084000	0.30828	0.263000	0.21812	0.260000	0.18958	ACA	.	.	.	none		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9082415	T	A	9082415	3	1	29	1	0	0	0	0	1	0	0	0	9980	1696	59	5	34459	5	MUC16	19	9082415	Missense_Mutation	SNP	T	TCGA-5P-A9JW-01A-11D-A42J-10	7782481	9082415	50046568	74	2097											
ARRDC2	27106	hgsc.bcm.edu	37	chr19	18121498	18121498	+	Missense_Mutation	SNP	T	T	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	aggcccgttcttcgcctacaTccaagagttccgctaccgcc	7	9	8	17	4	1	1	0	0	1	1	4	1	3	1	6	1	2	3	6	1	3	5			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr19:18121498T>G	ENST00000222250.4	+	7	1273	c.1130T>G	c.(1129-1131)aTc>aGc	p.I377S	ARRDC2_ENST00000379656.3_Missense_Mutation_p.I372S	NM_015683.1	NP_056498.1	Q8TBH0	ARRD2_HUMAN	arrestin domain containing 2	377					signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)	12						TTCGCCTACATCCAAGAGTTC	0.647																																					p.I377S		Atlas-SNP	.											.	ARRDC2	60	.	0			c.T1130G						PASS	.						58	56	56					19																	18121498		2203	4300	6503	SO:0001583	missense	27106	exon7			CCTACATCCAAGA		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.1130T>G	chr19.hg19:g.18121498T>G	ENSP00000222250:p.Ile377Ser	47.0	0.0	.		49.0	16.0	.	NM_015683	B2RBG9|O95895|Q6ZRV9|Q8WYG6	Missense_Mutation	SNP	ENST00000222250.4	hg19	CCDS12370.1	.	.	.	.	.	.	.	.	.	.	T	16.42	3.119026	0.56505	.	.	ENSG00000105643	ENST00000379656;ENST00000222250	T;T	0.16196	2.36;2.36	4.25	4.25	0.50352	.	0.228959	0.44483	D	0.000445	T	0.20861	0.0502	L	0.56199	1.76	0.47905	D	0.999549	B;B	0.32507	0.257;0.373	B;B	0.36666	0.115;0.23	T	0.04900	-1.0919	10	0.72032	D	0.01	-14.6862	12.8566	0.57888	0.0:0.0:0.0:1.0	.	377;372	Q8TBH0;Q8TBH0-2	ARRD2_HUMAN;.	S	372;377	ENSP00000368977:I372S;ENSP00000222250:I377S	ENSP00000222250:I377S	I	+	2	0	ARRDC2	17982498	1.000000	0.71417	0.855000	0.33649	0.157000	0.22087	7.845000	0.86875	1.715000	0.51383	0.402000	0.26972	ATC	.	.	.	none		0.647	ARRDC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466845.1	NM_015683		G	18121498	T	G	18121498	3	3	29	1	0	0	0	0	1	0	0	0	983	1435	50	5	1419	5	ARRDC2	19	18121498	Missense_Mutation	SNP	T	TCGA-5P-A9JW-01A-11D-A42J-10	9039083	18121498	41007485	75	2098											
CAPN12	147968	hgsc.bcm.edu	37	chr19	39224978	39224978	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccgaaacactgcagcagcTgctcacaggtcctgagcccg	9	5	10	17	2	1	1	1	1	0	0	2	2	2	1	4	1	6	4	4	1	1	0			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr19:39224978T>C	ENST00000328867.4	-	16	2104	c.1796A>G	c.(1795-1797)cAg>cGg	p.Q599R	CAPN12_ENST00000601953.1_Missense_Mutation_p.Q450R	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	599	Domain IV.				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)			CTGCAGCAGCTGCTCACAGGT	0.602																																					p.Q599R		Atlas-SNP	.											.	CAPN12	43	.	0			c.A1796G						PASS	.						68	64	65					19																	39224978		2200	4296	6496	SO:0001583	missense	147968	exon16			AGCAGCTGCTCAC	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.1796A>G	chr19.hg19:g.39224978T>C	ENSP00000331636:p.Gln599Arg	80.0	0.0	.		96.0	35.0	.	NM_144691		Missense_Mutation	SNP	ENST00000328867.4	hg19	CCDS12519.1	.	.	.	.	.	.	.	.	.	.	T	11.22	1.574581	0.28092	.	.	ENSG00000182472	ENST00000328867	T	0.28255	1.62	4.92	3.86	0.44501	EF-hand-like domain (1);	0.628804	0.15984	N	0.235145	T	0.24736	0.0600	L	0.42245	1.32	0.32013	N	0.601756	B	0.25105	0.118	B	0.21917	0.037	T	0.19943	-1.0290	10	0.44086	T	0.13	.	7.5877	0.28002	0.1901:0.0:0.0:0.8098	.	599	Q6ZSI9	CAN12_HUMAN	R	599	ENSP00000331636:Q599R	ENSP00000331636:Q599R	Q	-	2	0	CAPN12	43916818	0.998000	0.40836	0.996000	0.52242	0.908000	0.53690	1.294000	0.33365	0.671000	0.31185	0.379000	0.24179	CAG	.	.	.	none		0.602	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1			C	39224978	T	C	39224978	3	2	29	1	0	0	0	0	1	0	0	0	2627	1580	55	3	387	3	CAPN12	19	39224978	Missense_Mutation	SNP	T	TCGA-5P-A9JW-01A-11D-A42J-10	21103480	39224978	19904005	76	2099											
ZNF135	7694	hgsc.bcm.edu	37	chr19	58574844	58574844	+	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	accgaagccgaatgtcatctCcctgctggagcaagaggcag	11	6	12	12	2	2	1	1	0	1	1	3	4	2	2	3	2	3	3	3	2	3	0			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr19:58574844C>G	ENST00000313434.5	+	4	292	c.191C>G	c.(190-192)tCc>tGc	p.S64C	ZNF135_ENST00000359978.6_Missense_Mutation_p.S76C|ZNF135_ENST00000506786.1_Missense_Mutation_p.S22C|ZNF135_ENST00000511556.1_Missense_Mutation_p.S64C|ZNF135_ENST00000439855.2_Missense_Mutation_p.S64C|ZNF135_ENST00000401053.4_Missense_Mutation_p.S76C	NM_003436.3	NP_003427.3	P52742	ZN135_HUMAN	zinc finger protein 135	64	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)		AATGTCATCTCCCTGCTGGAG	0.582																																					p.S76C		Atlas-SNP	.											ZNF135_ENST00000401053,NS,malignant_melanoma,0,2	ZNF135	159	.	0			c.C227G						PASS	.						110	95	100					19																	58574844		2203	4300	6503	SO:0001583	missense	7694	exon3			TCATCTCCCTGCT	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.191C>G	chr19.hg19:g.58574844C>G	ENSP00000321406:p.Ser64Cys	99.0	0.0	.		90.0	28.0	.	NM_007134	B4DHH9|E9PEV2|F5GYY9|I3L0B3|Q5U5L3|Q8N1I7	Missense_Mutation	SNP	ENST00000313434.5	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.26|12.26	1.884823|1.884823	0.33255|0.33255	.|.	.|.	ENSG00000176293|ENSG00000176293	ENST00000391699|ENST00000504540;ENST00000401053;ENST00000359978;ENST00000439855;ENST00000313434;ENST00000511556;ENST00000506786	.|T;T;T;T;T;T	.|0.26223	.|1.75;1.75;1.75;1.75;1.75;1.75	2.25|2.25	-1.15|-1.15	0.09709|0.09709	.|Krueppel-associated box (3);	.|.	.|.	.|.	.|.	T|T	0.26412|0.26412	0.0645|0.0645	M|M	0.72353|0.72353	2.195|2.195	0.09310|0.09310	N|N	1|1	.|P;P;P	.|0.52463	.|0.859;0.859;0.953	.|B;B;B	.|0.44044	.|0.439;0.439;0.431	T|T	0.16778|0.16778	-1.0391|-1.0391	5|9	.|0.56958	.|D	.|0.05	.|.	5.0601|5.0601	0.14553|0.14553	0.0:0.5165:0.0:0.4835|0.0:0.5165:0.0:0.4835	.|.	.|64;64;76	.|E9PEV2;P52742;Q8N1I7	.|.;ZN135_HUMAN;.	A|C	70|76;76;76;64;64;64;22	.|ENSP00000441410:S76C;ENSP00000369437:S76C;ENSP00000444828:S64C;ENSP00000321406:S64C;ENSP00000422074:S64C;ENSP00000427691:S22C	.|ENSP00000321406:S64C	P|S	+|+	1|2	0|0	ZNF135|ZNF135	63266656|63266656	0.116000|0.116000	0.22171|0.22171	0.002000|0.002000	0.10522|0.10522	0.185000|0.185000	0.23345|0.23345	1.256000|1.256000	0.32921|0.32921	-0.176000|-0.176000	0.10707|0.10707	0.563000|0.563000	0.77884|0.77884	CCC|TCC	.	.	.	none		0.582	ZNF135-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000361899.2	NM_003436		G	58574844	C	G	58574844	3	3	29	1	0	0	0	0	1	0	0	0	17737	855	30	4	274	4	ZNF135	19	58574844	Missense_Mutation	SNP	C	TCGA-5P-A9JW-01A-11D-A42J-10	19349866	58574844	554139	77	2100											
MYBL2	4605	hgsc.bcm.edu	37	chr20	42315498	42315498	+	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	gacttttctctaaggtcatcGagctggttaagaagtatggc	10	13	11	7	1	2	1	1	0	1	1	4	3	2	1	0	3	1	3	0	3	4	5			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr20:42315498G>T	ENST00000217026.4	+	5	413	c.286G>T	c.(286-288)Gag>Tag	p.E96*	MYBL2_ENST00000396863.4_Nonsense_Mutation_p.E72*	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	96	HTH myb-type 2. {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)			TAAGGTCATCGAGCTGGTTAA	0.587																																					p.E96X		Atlas-SNP	.											.	MYBL2	82	.	0			c.G286T						PASS	.						58	52	54					20																	42315498		2203	4300	6503	SO:0001587	stop_gained	4605	exon5			GTCATCGAGCTGG		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.286G>T	chr20.hg19:g.42315498G>T	ENSP00000217026:p.Glu96*	79.0	0.0	.		72.0	27.0	.	NM_002466	B2RBS5|B7Z8D9|F8W6N6|Q53F07	Nonsense_Mutation	SNP	ENST00000217026.4	hg19	CCDS13322.1	.	.	.	.	.	.	.	.	.	.	G	34	5.362811	0.95877	.	.	ENSG00000101057	ENST00000396863;ENST00000217026	.	.	.	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	-40.0646	18.2387	0.89958	0.0:0.0:1.0:0.0	.	.	.	.	X	72;96	.	ENSP00000217026:E96X	E	+	1	0	MYBL2	41748912	1.000000	0.71417	0.996000	0.52242	0.368000	0.29767	9.726000	0.98782	2.687000	0.91594	0.462000	0.41574	GAG	.	.	.	none		0.587	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080408.1	NM_002466		T	42315498	G	T	42315498	4	4	29	1	0	0	0	0	0	1	0	0	10017	1059	37	4	304	4	MYBL2	20	42315498	Nonsense_Mutation	SNP	G	TCGA-5P-A9JW-01A-11D-A42J-10		42315498	20710022	78	2101											
ZNF831	128611	hgsc.bcm.edu	37	chr20	57767884	57767884	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccggcaagggcagagcgggcGgcaggaagtgcggccagaga	10	1	20	10	4	0	2	0	0	0	2	0	4	0	3	2	6	2	3	2	6	2	0			TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr20:57767884G>A	ENST00000371030.2	+	1	1810	c.1810G>A	c.(1810-1812)Ggc>Agc	p.G604S		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	604							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)					CAGAGCGGGCGGCAGGAAGTG	0.612																																					p.G604S		Atlas-SNP	.											.	ZNF831	287	.	0			c.G1810A						PASS	.						39	45	43					20																	57767884		2064	4194	6258	SO:0001583	missense	128611	exon1			GCGGGCGGCAGGA	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.1810G>A	chr20.hg19:g.57767884G>A	ENSP00000360069:p.Gly604Ser	195.0	0.0	.		168.0	59.0	.	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	hg19	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	G	4.418	0.077213	0.08485	.	.	ENSG00000124203	ENST00000371030	T	0.04275	3.66	5.52	-6.39	0.01951	.	1.361980	0.05276	N	0.518429	T	0.01730	0.0055	N	0.01576	-0.805	0.09310	N	1	B	0.25312	0.123	B	0.12837	0.008	T	0.47459	-0.9116	10	0.05620	T	0.96	1.2211	15.2673	0.73672	0.7034:0.0:0.2966:0.0	.	604	Q5JPB2	ZN831_HUMAN	S	604	ENSP00000360069:G604S	ENSP00000360069:G604S	G	+	1	0	ZNF831	57201279	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.216000	0.09266	-1.592000	0.01619	-1.074000	0.02243	GGC	.	.	.	none		0.612	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		A	57767884	G	A	57767884	3	1	29	1	0	0	0	0	1	0	0	0	18197	1116	39	1	1812	1	ZNF831	20	57767884	Missense_Mutation	SNP	G	TCGA-5P-A9JW-01A-11D-A42J-10	15452386	57767884	5257636	79	2102											
NPBWR2	2832	hgsc.bcm.edu	37	chr20	62737462	62737473	+	In_Frame_Del	DEL	GGCCCGCAGCCT	GGCCCGCAGCCT	-																															gctccagagcggagccgcacGgcccgcagcctgcgcaggag																								rs201687254|rs139565347|rs147787913	byFrequency	TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	GGCCCGCAGCCT	GGCCCGCAGCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chr20:62737462_62737473delGGCCCGCAGCCT	ENST00000369768.1	-	1	1051_1062	c.712_723delAGGCTGCGGGCC	c.(712-723)aggctgcgggccdel	p.RLRA238del		NM_005286.2	NP_005277.2	P48146	NPBW2_HUMAN	neuropeptides B/W receptor 2	238					G-protein coupled receptor signaling pathway (GO:0007186)|opioid receptor signaling pathway (GO:0038003)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|opioid receptor activity (GO:0004985)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(38;2.58e-11)|all_epithelial(29;6.4e-13)|Lung NSC(23;1.25e-09)|all_lung(23;4.21e-09)					GGAGCCGCACGGCCCGCAGCCTGCGCAGGAGG	0.665																																					p.238_242del		Atlas-Indel,Pindel	.											.	NPBWR2	36	.	0			c.713_724del						PASS	.																																			SO:0001651	inframe_deletion	2832	exon1			.	U22492	CCDS13557.1	20q13.3	2012-08-08	2006-02-15	2006-02-15	ENSG00000125522	ENSG00000125522		"GPCR / Class A : Neuropeptide receptors : W/B"	4530	protein-coding gene	gene with protein product		600731	"G protein-coupled receptor 8"	GPR8		12401809	Standard	NM_005286		Approved		uc011abt.2	P48146	OTTHUMG00000033032	ENST00000369768.1:c.712_723delAGGCTGCGGGCC	chr20.hg19:g.62737462_62737473delGGCCCGCAGCCT	ENSP00000358783:p.Arg238_Ala241del	57.0	0.0	0		65.0	14.0	0.215385	NM_005286	Q6NWQ6|Q9H4K3	In_Frame_Del	DEL	ENST00000369768.1	hg19	CCDS13557.1																																																																																			.	.	.	none		0.665	NPBWR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080300.1	NM_005286		-	62737473	GGCCCGCAGCCT	-	62737462	7	5	29	1	0	1	0	1	0	0	0	0	10576	1103	39	0	281	0	NPBWR2	20	62737462	In_Frame_Del	DEL	GGCCCGCAGCCT	TCGA-5P-A9JW-01A-11D-A42J-10	4969578	62737462	288058	80	2103											
AR	367	hgsc.bcm.edu	37	chrX	66765164	66765164	+	Missense_Mutation	SNP	A	A	T																															cagtttgctgctgctgcagcAgcagcagcagcagcagcagc																										TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	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	chrX.hg19:g.66765164A>T	ENSP00000363822:p.Gln59Leu	56.0	0.0	.		119.0	6.0	.	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	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	29	1	0	0	0	0	1	0	0	0	836	188	7	5	178	5	AR	23	66765164	Missense_Mutation	SNP	A	TCGA-5P-A9JW-01A-11D-A42J-10		66765164	88505396	81	2104	22	2									
AR	367	hgsc.bcm.edu	37	chrX	66765167	66765167	+	Missense_Mutation	SNP	A	A	T																															tttgctgctgctgcagcagcAgcagcagcagcagcagcagc																										TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chrX:66765167A>T	ENST00000374690.3	+	1	703	c.179A>T	c.(178-180)cAg>cTg	p.Q60L	AR_ENST00000504326.1_Missense_Mutation_p.Q60L|AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.Q60L	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	60	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)	CTgcagcagcagcagcagcag	0.677									Androgen Insensitivity Syndrome																												p.Q60L		Atlas-SNP	.											.	AR	249	.	0			c.A179T	GRCh37	CI994028	AR	I		PASS	.						6	9	8					X																	66765167		1971	3901	5872	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	AGCAGCAGCAGCA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.179A>T	chrX.hg19:g.66765167A>T	ENSP00000363822:p.Gln60Leu	52.0	0.0	.		118.0	13.0	.	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	11.27	1.588228	0.28357	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.57436	0.4;0.4;0.4	.	.	.	.	1.241110	0.06210	N	0.684797	T	0.29288	0.0729	N	0.19112	0.55	0.09310	N	0.999999	P;P;.	0.36048	0.534;0.534;.	B;B;.	0.29862	0.08;0.108;.	T	0.11494	-1.0585	8	0.12103	T	0.63	.	.	.	.	.	60;60;58	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	L	60	ENSP00000363822:Q60L;ENSP00000421155:Q60L;ENSP00000379359:Q60L	ENSP00000363822:Q60L	Q	+	2	0	AR	66681892	0.997000	0.39634	0.860000	0.33809	0.513000	0.34164	1.220000	0.32491	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	66765167	A	T	66765167	3	4	29	1	0	0	0	0	1	0	0	0	836	188	7	5	181	5	AR	23	66765167	Missense_Mutation	SNP	A	TCGA-5P-A9JW-01A-11D-A42J-10	3	66765167	88505393	82	2105	22	2									
MST4	51765	hgsc.bcm.edu	37	chrX	131207114	131207114	+	Frame_Shift_Del	DEL	T	T	-																															tgaagaaactaattgaaaaaTttcaaaagtaagttggaaat																										TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chrX:131207114delT	ENST00000354719.6	+	10	1363	c.1147delT	c.(1147-1149)tttfs	p.F383fs	MST4_ENST00000394334.2_Frame_Shift_Del_p.F407fs|MST4_ENST00000496850.1_Frame_Shift_Del_p.F345fs|MST4_ENST00000481105.1_Frame_Shift_Del_p.F429fs|MST4_ENST00000394335.2_Frame_Shift_Del_p.F330fs														p.F407I(1)		endometrium(2)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(192;0.000127)					AATTGAAAAATTTCAAAAGTA	0.343																																					p.K406fs		Atlas-Indel,Pindel	.											.	MST4	61	.	1	Substitution - Missense(1)	prostate(1)	c.1218delA						PASS	.						48	53	51					X																	131207114		2169	4256	6425	SO:0001589	frameshift_variant	0	exon11			.																												ENST00000354719.6:c.1147delT	chrX.hg19:g.131207114delT	ENSP00000346755:p.Phe383fs	326.0	0.0	0		290.0	160.0	0.551724	NM_016542		Frame_Shift_Del	DEL	ENST00000354719.6	hg19																																																																																				.	.	.	none		0.343	MST4-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000058308.2			-	131207114	T	-	131207114	7	5	29	1	0	1	0	1	0	0	0	0	9899	1493	52	0	1257	0	MST4	23	131207114	Frame_Shift_Del	DEL	T	TCGA-5P-A9JW-01A-11D-A42J-10	64441947	131207114	24063446	83	2106	23	2									
MST4	51765	hgsc.bcm.edu	37	chrX	131207118	131207118	+	Missense_Mutation	SNP	A	A	C																															gaaactaattgaaaaatttcAaaagtaagttggaaatgtca																										TCGA-5P-A9JW-01A-11D-A42J-10	TCGA-5P-A9JW-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	82cf23e0-e687-4cf2-b83f-732ce4279056	d59804af-3375-4351-a1ef-125b05396a6f	g.chrX:131207118A>C	ENST00000354719.6	+	10	1367	c.1151A>C	c.(1150-1152)cAa>cCa	p.Q384P	MST4_ENST00000394334.2_Missense_Mutation_p.Q408P|MST4_ENST00000496850.1_Missense_Mutation_p.Q346P|MST4_ENST00000481105.1_Missense_Mutation_p.Q430P|MST4_ENST00000394335.2_Missense_Mutation_p.Q331P																endometrium(2)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(192;0.000127)					GAAAAATTTCAAAAGTAAGTT	0.328																																					p.Q408P		Atlas-SNP	.											.	MST4	61	.	0			c.A1223C						PASS	.						46	51	49					X																	131207118		2162	4248	6410	SO:0001583	missense	0	exon11			AATTTCAAAAGTA																												ENST00000354719.6:c.1151A>C	chrX.hg19:g.131207118A>C	ENSP00000346755:p.Gln384Pro	317.0	1.0	.		279.0	162.0	.	NM_016542		Missense_Mutation	SNP	ENST00000354719.6	hg19		.	.	.	.	.	.	.	.	.	.	a	16.71	3.199273	0.58126	.	.	ENSG00000134602	ENST00000394334;ENST00000481105;ENST00000354719;ENST00000394335;ENST00000496850	T;T;T;T;T	0.37411	1.2;1.2;1.2;1.2;1.2	5.44	5.44	0.79542	.	0.000000	0.64402	D	0.000008	T	0.60971	0.2310	M	0.80422	2.495	0.47949	D	0.999553	D;P;D;D;P	0.64830	0.967;0.91;0.994;0.98;0.91	P;P;D;P;P	0.65443	0.737;0.616;0.935;0.907;0.616	T	0.66838	-0.5822	10	0.72032	D	0.01	.	14.6026	0.68450	1.0:0.0:0.0:0.0	.	430;384;346;331;408	B4E0Y9;Q8NBY1;Q9P289-3;Q9P289-2;Q9P289	.;.;.;.;MST4_HUMAN	P	408;430;384;331;346	ENSP00000377867:Q408P;ENSP00000418753:Q430P;ENSP00000346755:Q384P;ENSP00000377868:Q331P;ENSP00000419702:Q346P	ENSP00000346755:Q384P	Q	+	2	0	AL109749.1	131034799	1.000000	0.71417	1.000000	0.80357	0.790000	0.44656	6.933000	0.75874	1.829000	0.53265	0.422000	0.28245	CAA	.	.	.	none		0.328	MST4-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000058308.2			C	131207118	A	C	131207118	3	2	29	1	0	0	0	0	1	0	0	0	9899	130	5	5	1261	5	MST4	23	131207118	Missense_Mutation	SNP	A	TCGA-5P-A9JW-01A-11D-A42J-10	4	131207118	24063442	84	2107	23	2									
TNFRSF18	8784	hgsc.bcm.edu	37	chr1	1141898	1141898	+	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	cccaggctgagcgcgcacagCagcgccaggccgcacagggc	8	1	15	17	4	0	1	0	1	0	0	0	1	0	1	3	3	3	4	3	3	0	0			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr1:1141898C>A	ENST00000379268.2	-	1	173	c.54G>T	c.(52-54)ctG>ctT	p.L18L	TNFRSF18_ENST00000328596.6_Silent_p.L18L|TNFRSF18_ENST00000379265.5_Silent_p.L18L|TNFRSF18_ENST00000486728.1_5'Flank	NM_004195.2|NM_148902.1	NP_004186.1|NP_683700.1	Q9Y5U5	TNR18_HUMAN	tumor necrosis factor receptor superfamily, member 18	18					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)		GCGCGCACAGCAGCGCCAGGC	0.751																																					p.L18L	GBM(157;472 1934 13810 14591 35952)	Atlas-SNP	.											.	TNFRSF18	13	.	0			c.G54T						PASS	.						3	4	4					1																	1141898		1947	3834	5781	SO:0001819	synonymous_variant	8784	exon1			GCACAGCAGCGCC	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.54G>T	chr1.hg19:g.1141898C>A		106.0	0.0	.		98.0	48.0	.	NM_148902	B1AME1|O95851|Q5U0I4|Q9NYJ9	Silent	SNP	ENST00000379268.2	hg19	CCDS10.1																																																																																			.	.	.	none		0.751	TNFRSF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004083.2	NM_004195		A	1141898	C	A	1141898	2	1	30	1	0	0	0	0	0	0	0	1	16303	697	25	4		4	TNFRSF18	1	1141898	Silent	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10		1141898	248108723	1	2108											
PER3	8863	hgsc.bcm.edu	37	chr1	7845028	7845028	+	Frame_Shift_Del	DEL	T	T	-																															gggagcggtggagccccgagTtccatctgcagaggaaattg																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr1:7845028delT	ENST00000361923.2	+	1	266	c.91delT	c.(91-93)ttcfs	p.F31fs	PER3_ENST00000377541.1_Frame_Shift_Del_p.F31fs|PER3_ENST00000377532.3_Frame_Shift_Del_p.F31fs	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	31					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)		GAGCCCCGAGTTCCATCTGCA	0.672																																					p.E30fs		Atlas-Indel,Pindel	.											.	PER3	95	.	0			c.90delG						PASS	.						28	32	30					1																	7845028		2202	4300	6502	SO:0001589	frameshift_variant	8863	exon1			.	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.91delT	chr1.hg19:g.7845028delT	ENSP00000355031:p.Phe31fs	221.0	0.0	0		209.0	96.0	0.45933	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Frame_Shift_Del	DEL	ENST00000361923.2	hg19	CCDS89.1																																																																																			.	.	.	none		0.672	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831		-	7845028	T	-	7845028	7	5	30	1	0	1	0	1	0	0	0	0	11738	1725	60	0	93	0	PER3	1	7845028	Frame_Shift_Del	DEL	T	TCGA-5P-A9JY-01A-11D-A42J-10	6703130	7845028	241405593	2	2109											
PTCHD2	57540	hgsc.bcm.edu	37	chr1	11562062	11562062	+	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	ctactgctcgccccccagctCgctcatgacctacttttttc	5	13	5	18	2	1	1	1	1	0	0	4	1	1	1	4	0	4	3	4	0	2	5			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr1:11562062C>T	ENST00000294484.6	+	2	1151	c.1013C>T	c.(1012-1014)tCg>tTg	p.S338L	PTCHD2_ENST00000389575.3_Missense_Mutation_p.S338L	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	338					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)		CCCCCCAGCTCGCTCATGACC	0.637																																					p.S338L		Atlas-SNP	.											.	PTCHD2	193	.	0			c.C1013T						PASS	.						36	40	39					1																	11562062		1956	4121	6077	SO:0001583	missense	57540	exon2			CCAGCTCGCTCAT	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.1013C>T	chr1.hg19:g.11562062C>T	ENSP00000294484:p.Ser338Leu	133.0	0.0	.		102.0	45.0	.	NM_020780	Q5VTU9|Q9UJD6	Missense_Mutation	SNP	ENST00000294484.6	hg19	CCDS41247.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.987294	0.93106	.	.	ENSG00000204624	ENST00000294484;ENST00000389575	T;T	0.57752	0.38;0.38	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.63593	0.2524	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.66779	-0.5837	10	0.72032	D	0.01	-14.5988	18.2403	0.89966	0.0:1.0:0.0:0.0	.	338	Q9P2K9	PTHD2_HUMAN	L	338	ENSP00000294484:S338L;ENSP00000374226:S338L	ENSP00000294484:S338L	S	+	2	0	PTCHD2	11484649	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.494000	0.81503	2.542000	0.85734	0.655000	0.94253	TCG	.	.	.	none		0.637	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561		T	11562062	C	T	11562062	3	4	30	1	0	0	0	0	1	0	0	0	12743	893	31	1	1015	1	PTCHD2	1	11562062	Missense_Mutation	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10	3717034	11562062	237688559	3	2110											
PTCHD2	57540	hgsc.bcm.edu	37	chr1	11585336	11585336	+	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	cctgctccttggcaggctgtGtcgcctggggatggagaggt	4	10	17	10	1	0	1	0	0	0	1	2	3	1	2	3	6	1	3	3	6	0	1			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr1:11585336G>T	ENST00000294484.6	+	12	2718	c.2580G>T	c.(2578-2580)gtG>gtT	p.V860V	PTCHD2_ENST00000389575.3_Silent_p.V860V	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	860					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)		GGCAGGCTGTGTCGCCTGGGG	0.637																																					p.V860V		Atlas-SNP	.											.	PTCHD2	193	.	0			c.G2580T						PASS	.						75	76	75					1																	11585336		2021	4177	6198	SO:0001819	synonymous_variant	57540	exon12			GGCTGTGTCGCCT	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.2580G>T	chr1.hg19:g.11585336G>T		95.0	0.0	.		84.0	30.0	.	NM_020780	Q5VTU9|Q9UJD6	Silent	SNP	ENST00000294484.6	hg19	CCDS41247.1																																																																																			.	.	.	none		0.637	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561		T	11585336	G	T	11585336	2	4	30	1	0	0	0	0	0	0	0	1	12743	1364	48	4		4	PTCHD2	1	11585336	Silent	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	23274	11585336	237665285	4	2111											
VPS13D	55187	hgsc.bcm.edu	37	chr1	12318000	12318000	+	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	ggactatttcagctgccgagAatggtggtattttgctttga	8	15	12	6	1	1	2	1	1	0	1	1	4	1	3	1	3	3	3	1	3	3	6			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr1:12318000A>T	ENST00000358136.3	+	10	1080	c.950A>T	c.(949-951)gAa>gTa	p.E317V	VPS13D_ENST00000356315.4_Missense_Mutation_p.E317V	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)		AGCTGCCGAGAATGGTGGTAT	0.448																																					p.E317V		Atlas-SNP	.											.	VPS13D	316	.	0			c.A950T						PASS	.						221	205	210					1																	12318000		2203	4300	6503	SO:0001583	missense	55187	exon10			GCCGAGAATGGTG	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.950A>T	chr1.hg19:g.12318000A>T	ENSP00000350854:p.Glu317Val	110.0	0.0	.		82.0	32.0	.	NM_015378		Missense_Mutation	SNP	ENST00000358136.3	hg19	CCDS30588.1	.	.	.	.	.	.	.	.	.	.	A	16.77	3.214047	0.58452	.	.	ENSG00000048707	ENST00000356315;ENST00000358136	T;T	0.48201	0.82;0.82	5.54	5.54	0.83059	.	0.053588	0.64402	D	0.000001	T	0.40595	0.1123	L	0.48642	1.525	0.80722	D	1	P;P	0.40731	0.655;0.728	B;B	0.35114	0.194;0.196	T	0.30995	-0.9959	10	0.34782	T	0.22	.	15.1606	0.72782	1.0:0.0:0.0:0.0	.	317;317	Q5THJ4-2;Q5THJ4	.;VP13D_HUMAN	V	317	ENSP00000348666:E317V;ENSP00000350854:E317V	ENSP00000348666:E317V	E	+	2	0	VPS13D	12240587	0.997000	0.39634	0.969000	0.41365	0.948000	0.59901	3.680000	0.54641	2.230000	0.72887	0.528000	0.53228	GAA	.	.	.	none		0.448	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		T	12318000	A	T	12318000	3	4	30	1	0	0	0	0	1	0	0	0	17204	246	9	5	984	5	VPS13D	1	12318000	Missense_Mutation	SNP	A	TCGA-5P-A9JY-01A-11D-A42J-10	732664	12318000	236932621	5	2112											
MAP3K6	9064	hgsc.bcm.edu	37	chr1	27685320	27685320	+	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	ttcccatacccgcgtgggccCtggtcaatgatttctggggc	5	11	12	13	2	2	1	1	1	1	0	3	1	3	1	3	4	1	0	3	4	2	3			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr1:27685320C>A	ENST00000493901.1	-	20	2702	c.2463G>T	c.(2461-2463)caG>caT	p.Q821H	MAP3K6_ENST00000374040.3_Missense_Mutation_p.Q813H|MAP3K6_ENST00000357582.2_Missense_Mutation_p.Q821H	NM_004672.3	NP_004663.3	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase 6	821	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)		CGCGTGGGCCCTGGTCAATGA	0.587																																					p.Q821H		Atlas-SNP	.											.	MAP3K6	134	.	0			c.G2463T						PASS	.						82	74	77					1																	27685320		2203	4300	6503	SO:0001583	missense	9064	exon19			TGGGCCCTGGTCA	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.2463G>T	chr1.hg19:g.27685320C>A	ENSP00000419591:p.Gln821His	73.0	0.0	.		69.0	33.0	.	NM_004672	A2ACE8|A2VDG4|A2VDG5|Q59HF4|Q5SSD4|Q75PK3|Q96B75	Missense_Mutation	SNP	ENST00000493901.1	hg19	CCDS299.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.31|18.31	3.596728|3.596728	0.66332|0.66332	.|.	.|.	ENSG00000142733|ENSG00000142733	ENST00000374040;ENST00000493901;ENST00000545447;ENST00000357582|ENST00000472410	T;T;T|.	0.25414|.	1.8;1.8;1.8|.	5.84|5.84	2.54|2.54	0.30619|0.30619	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	0.40979|0.40979	0.1139|0.1139	N|N	0.26162|0.26162	0.8|0.8	0.46798|0.46798	D|D	0.999201|0.999201	D;D|.	0.76494|.	0.999;0.999|.	D;D|.	0.72982|.	0.964;0.979|.	T|T	0.10660|0.10660	-1.0620|-1.0620	9|5	0.42905|.	T|.	0.14|.	.|.	7.3605|7.3605	0.26744|0.26744	0.0:0.5545:0.0:0.4455|0.0:0.5545:0.0:0.4455	.|.	813;821|.	O95382-3;O95382|.	.;M3K6_HUMAN|.	H|M	813;821;544;821|545	ENSP00000363152:Q813H;ENSP00000419591:Q821H;ENSP00000350195:Q821H|.	ENSP00000350195:Q821H|.	Q|R	-|-	3|2	2|0	MAP3K6|MAP3K6	27557907|27557907	0.372000|0.372000	0.25064|0.25064	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	-0.312000|-0.312000	0.08113|0.08113	0.729000|0.729000	0.32403|0.32403	0.561000|0.561000	0.74099|0.74099	CAG|AGG	.	.	.	none		0.587	MAP3K6-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013469.2	NM_004672		A	27685320	C	A	27685320	3	1	30	1	0	0	0	0	1	0	0	0	9261	680	24	4	1447	4	MAP3K6	1	27685320	Missense_Mutation	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10	15367320	27685320	221565301	6	2113											
SFPQ	6421	hgsc.bcm.edu	37	chr1	35657092	35657092	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctgtgtgtaagttttctcTccaggcctcctcaagagaga	8	12	10	11	1	2	2	1	0	1	2	5	3	4	2	3	1	0	3	3	1	2	3			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr1:35657092T>C	ENST00000357214.5	-	2	965	c.867A>G	c.(865-867)ggA>ggG	p.G289G		NM_005066.2	NP_005057.1	P23246	SFPQ_HUMAN	splicing factor proline/glutamine-rich	289					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)				AAGTTTTCTCTCCAGGCCTCC	0.413			T	TFE3	papillary renal cell																																p.G289G		Atlas-SNP	.		Dom	yes		1	1p34.3	6421	splicing factor proline/glutamine rich(polypyrimidine tract binding protein associated)		E	.	SFPQ	51	.	0			c.A867G						PASS	.						83	83	83					1																	35657092		2203	4300	6503	SO:0001819	synonymous_variant	6421	exon2			TTTCTCTCCAGGC	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.867A>G	chr1.hg19:g.35657092T>C		136.0	0.0	.		125.0	49.0	.	NM_005066	P30808|Q5SZ71	Silent	SNP	ENST00000357214.5	hg19	CCDS388.1																																																																																			.	.	.	none		0.413	SFPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011984.4	NM_005066		C	35657092	T	C	35657092	2	2	30	1	0	0	0	0	0	0	0	1	14173	1538	54	3		3	SFPQ	1	35657092	Silent	SNP	T	TCGA-5P-A9JY-01A-11D-A42J-10	7971772	35657092	213593529	7	2114											
AKIRIN1	79647	hgsc.bcm.edu	37	chr1	39469081	39469081	+	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	tgcgacggtatgggacaaggCcaacaagctgtaagtattgc	12	8	13	8	2	0	0	0	0	0	0	0	2	0	1	1	3	4	4	1	3	6	4			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr1:39469081C>A	ENST00000432648.3	+	4	717	c.559C>A	c.(559-561)Cca>Aca	p.P187T	AKIRIN1_ENST00000372984.4_Missense_Mutation_p.P140T|AKIRIN1_ENST00000446189.2_Missense_Mutation_p.P142T	NM_024595.2	NP_078871.1	Q9H9L7	AKIR1_HUMAN	akirin 1	187						nuclear membrane (GO:0031965)|nucleus (GO:0005634)				lung(1)|prostate(1)|skin(1)	3						TGGGACAAGGCCAACAAGCTG	0.373																																					p.P187T		Atlas-SNP	.											.	AKIRIN1	7	.	0			c.C559A						PASS	.						126	106	113					1																	39469081		2203	4300	6503	SO:0001583	missense	79647	exon4			ACAAGGCCAACAA	AK022728	CCDS433.1, CCDS44113.1	1p34.3	2013-10-11	2008-06-23	2008-06-23	ENSG00000174574	ENSG00000174574			25744	protein-coding gene	gene with protein product		615164	"chromosome 1 open reading frame 108"	C1orf108		19200367	Standard	NM_024595		Approved	FLJ12666	uc001ccw.3	Q9H9L7	OTTHUMG00000007496	ENST00000432648.3:c.559C>A	chr1.hg19:g.39469081C>A	ENSP00000392678:p.Pro187Thr	73.0	0.0	.		44.0	16.0	.	NM_024595	B4DZU6|Q0VDB3|Q53FK8	Missense_Mutation	SNP	ENST00000432648.3	hg19	CCDS433.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.185740	0.78789	.	.	ENSG00000174574	ENST00000432648;ENST00000446189;ENST00000372984	.	.	.	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.78375	0.4273	M	0.71206	2.165	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.983	D;D;P	0.87578	0.996;0.998;0.755	T	0.78409	-0.2215	9	0.49607	T	0.09	-31.0616	16.9086	0.86134	0.0:1.0:0.0:0.0	.	140;142;187	B4DQP0;B4DZU6;Q9H9L7	.;.;AKIR1_HUMAN	T	187;142;140	.	ENSP00000362075:P140T	P	+	1	0	AKIRIN1	39241668	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.444000	0.66587	2.657000	0.90304	0.557000	0.71058	CCA	.	.	.	none		0.373	AKIRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019687.2	NM_024595		A	39469081	C	A	39469081	3	1	30	1	0	0	0	0	1	0	0	0	461	739	26	4	573	4	AKIRIN1	1	39469081	Missense_Mutation	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10	3811989	39469081	209781540	8	2115											
USP24	23358	hgsc.bcm.edu	37	chr1	55604356	55604356	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtccatgaaatgaggcaccAtgaggtagaatagttcgtgg	12	10	13	6	1	0	4	0	3	0	1	2	4	1	4	2	3	0	3	2	3	4	3			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr1:55604356A>G	ENST00000294383.6	-	26	2852	c.2853T>C	c.(2851-2853)caT>caC	p.H951H	USP24_ENST00000407756.1_Silent_p.H791H	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	951					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						ATGAGGCACCATGAGGTAGAA	0.368																																					p.H951H		Atlas-SNP	.											.	USP24	323	.	0			c.T2853C						PASS	.						76	72	73					1																	55604356		1901	4114	6015	SO:0001819	synonymous_variant	23358	exon26			GGCACCATGAGGT	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.2853T>C	chr1.hg19:g.55604356A>G		144.0	0.0	.		92.0	46.0	.	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Silent	SNP	ENST00000294383.6	hg19	CCDS44154.2																																																																																			.	.	.	none		0.368	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			G	55604356	A	G	55604356	2	3	30	1	0	0	0	0	0	0	0	1	17067	214	8	3		3	USP24	1	55604356	Silent	SNP	A	TCGA-5P-A9JY-01A-11D-A42J-10	16135275	55604356	193646265	9	2116											
ZRANB2	9406	hgsc.bcm.edu	37	chr1	71532486	71532486	+	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	gtgaccgtgatcttgttcgtCtttttttgcgatcaccagat	6	17	9	9	3	3	3	1	2	2	1	4	4	3	3	2	0	1	1	2	0	0	5			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr1:71532486C>G	ENST00000370920.3	-	9	1203	c.902G>C	c.(901-903)aGa>aCa	p.R301T	ZRANB2-AS1_ENST00000450461.1_RNA|MIR186_ENST00000384988.1_RNA|ZRANB2_ENST00000477096.1_5'UTR|ZRANB2-AS1_ENST00000426999.1_RNA|ZRANB2_ENST00000254821.6_Missense_Mutation_p.R301T	NM_203350.2	NP_976225.1	O95218	ZRAB2_HUMAN	zinc finger, RAN-binding domain containing 2	301	Required for nuclear targeting.				mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(4)|ovary(2)|stomach(1)	15						TCTTGTTCGTCTTTTTTTGCG	0.383																																					p.R301T		Atlas-SNP	.											.	ZRANB2	75	.	0			c.G902C						PASS	.						125	121	122					1																	71532486		2203	4300	6503	SO:0001583	missense	9406	exon9			GTTCGTCTTTTTT	AF065391	CCDS659.1, CCDS660.1	1p31	2008-02-05	2006-06-28	2006-06-28	ENSG00000132485	ENSG00000132485		"Zinc fingers, RAN-binding domain containing"	13058	protein-coding gene	gene with protein product		604347	"zinc finger protein 265"	ZNF265		9931435	Standard	NM_005455		Approved	ZIS, ZIS1, ZIS2	uc001dft.3	O95218	OTTHUMG00000009660	ENST00000370920.3:c.902G>C	chr1.hg19:g.71532486C>G	ENSP00000359958:p.Arg301Thr	139.0	0.0	.		176.0	59.0	.	NM_005455	D3DQ75|Q53GS3|Q59F92|Q5VV33|Q5VV34|Q8IXN6|Q9UP63	Missense_Mutation	SNP	ENST00000370920.3	hg19	CCDS659.1	.	.	.	.	.	.	.	.	.	.	C	14.31	2.496632	0.44352	.	.	ENSG00000132485	ENST00000370920;ENST00000254821	T;T	0.65549	-0.09;-0.16	6.16	5.26	0.73747	.	.	.	.	.	T	0.32194	0.0821	N	0.19112	0.55	0.45097	D	0.998112	B;B	0.30281	0.18;0.275	B;B	0.30855	0.035;0.121	T	0.38866	-0.9641	9	0.56958	D	0.05	.	11.4336	0.50056	0.0:0.8636:0.0:0.1364	.	301;301	O95218;O95218-2	ZRAB2_HUMAN;.	T	301	ENSP00000359958:R301T;ENSP00000254821:R301T	ENSP00000254821:R301T	R	-	2	0	ZRANB2	71305074	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.684000	0.61686	1.623000	0.50342	0.650000	0.86243	AGA	.	.	.	none		0.383	ZRANB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026636.1	NM_203350		G	71532486	C	G	71532486	3	3	30	1	0	0	0	0	1	0	0	0	18235	913	32	4	136	4	ZRANB2	1	71532486	Missense_Mutation	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10	15928130	71532486	177718135	10	2117											
SNX7	51375	hgsc.bcm.edu	37	chr1	99127306	99127307	+	Frame_Shift_Ins	INS	-	-	C																															gatggagggcgagcgccgggINScatcgcaggcgccctcctcg																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr1:99127306_99127307insC	ENST00000306121.3	+	1	28_29	c.19_20insC	c.(19-21)gcafs	p.A7fs	SNX7_ENST00000529992.1_Frame_Shift_Ins_p.A7fs|SNX7_ENST00000370189.5_5'UTR	NM_015976.4	NP_057060.2	Q9UNH6	SNX7_HUMAN	sorting nexin 7	0					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)		CGAGCGCCGGGCATCGCAGGCG	0.802																																					p.A7fs		Pindel	.											.	SNX7	76	.	0			c.19_20insC						PASS	.																																			SO:0001589	frameshift_variant	51375	exon1			.	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.20dupC	chr1.hg19:g.99127307_99127307dupC	ENSP00000304429:p.Ala7fs	36.0	0.0	.		35.0	10.0	0.286	NM_015976	A8KAF3|D3DT50|Q53FQ3|Q5VT09|Q5VT10|Q86U82|Q8WVD4|Q96FW9|Q9Y3Z7	Frame_Shift_Ins	INS	ENST00000306121.3	hg19	CCDS755.2																																																																																			.	.	.	none		0.802	SNX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029609.2			C	99127307	-	C	99127306	7	5	30	1	0	1	1	0	0	0	0	0	14920	1203	42	0	21	0	SNX7	1	99127306	Frame_Shift_Ins	INS	-	TCGA-5P-A9JY-01A-11D-A42J-10	27594820	99127306	150123315	11	2118											
ATP8B2	57198	hgsc.bcm.edu	37	chr1	154315937	154315937	+	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	ccccattcatagtgcggaatCcagaggggaagatccgactc	11	7	11	12	2	1	2	1	0	0	2	4	5	3	4	4	3	1	0	4	3	3	2			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr1:154315937C>G	ENST00000368489.3	+	17	1750	c.1750C>G	c.(1750-1752)Cca>Gca	p.P584A		NM_020452.3	NP_065185.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	570					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)		IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			AGTGCGGAATCCAGAGGGGAA	0.517																																					p.P584A		Atlas-SNP	.											.	ATP8B2	158	.	0			c.C1750G						PASS	.						59	53	55					1																	154315937		2203	4300	6503	SO:0001583	missense	57198	exon17			CGGAATCCAGAGG	AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515		"ATPases / P-type"	13534	protein-coding gene	gene with protein product		605867	"ATPase, class I, type 8B, member 2"			10574461, 11015572	Standard	NM_020452		Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368489.3:c.1750C>G	chr1.hg19:g.154315937C>G	ENSP00000357475:p.Pro584Ala	64.0	0.0	.		66.0	28.0	.	NM_020452	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	Missense_Mutation	SNP	ENST00000368489.3	hg19	CCDS1066.1	.	.	.	.	.	.	.	.	.	.	C	19.50	3.840063	0.71488	.	.	ENSG00000143515	ENST00000368489	T	0.61859	0.07	5.54	4.61	0.57282	.	0.057135	0.64402	D	0.000001	T	0.67011	0.2848	M	0.85462	2.755	0.80722	D	1	P	0.47191	0.891	P	0.54174	0.744	T	0.71062	-0.4701	10	0.62326	D	0.03	.	13.9576	0.64160	0.0:0.9264:0.0:0.0736	.	584	P98198-3	.	A	584	ENSP00000357475:P584A	ENSP00000357475:P584A	P	+	1	0	ATP8B2	152582561	1.000000	0.71417	0.993000	0.49108	0.986000	0.74619	4.739000	0.62080	2.884000	0.98904	0.655000	0.94253	CCA	.	.	.	none		0.517	ATP8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087658.2	NM_020452		G	154315937	C	G	154315937	3	3	30	1	0	0	0	0	1	0	0	0	1195	855	30	4	1946	4	ATP8B2	1	154315937	Missense_Mutation	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10	55188631	154315937	94934684	12	2119											
RD3	343035	hgsc.bcm.edu	37	chr1	211654560	211654576	+	Frame_Shift_Del	DEL	TGTGCTGGCCAGCCAGC	TGTGCTGGCCAGCCAGC	-																															aggtcataggtggaccggggTgtgctggccagccagctgta																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	TGTGCTGGCCAGCCAGC	TGTGCTGGCCAGCCAGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr1:211654560_211654576delTGTGCTGGCCAGCCAGC	ENST00000367002.4	-	2	1345_1361	c.182_198delGCTGGCTGGCCAGCACA	c.(181-198)agctggctggccagcacafs	p.SWLAST61fs	RD3_ENST00000484910.1_Intron	NM_001164688.1|NM_183059.2	NP_001158160.1|NP_898882.1	Q7Z3Z2	RD3_HUMAN	retinal degeneration 3	61					response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)			p.W62L(1)		central_nervous_system(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	10				OV - Ovarian serous cystadenocarcinoma(81;0.00284)|all cancers(67;0.0279)|Epithelial(68;0.0689)		TGGACCGGGGTGTGCTGGCCAGCCAGCTGTAGTCCAC	0.599																																					p.61_67del		Atlas-Indel,Pindel	.											.	RD3	26	.	1	Substitution - Missense(1)	lung(1)	c.183_199del						PASS	.																																			SO:0001589	frameshift_variant	343035	exon2			.	AY191519	CCDS1498.1	1q32.3	2008-02-05	2006-11-13	2006-11-13	ENSG00000198570	ENSG00000198570			19689	protein-coding gene	gene with protein product		180040	"chromosome 1 open reading frame 36"	C1orf36		12914764	Standard	NM_183059		Approved	LCA12	uc001hin.2	Q7Z3Z2	OTTHUMG00000037002	ENST00000367002.4:c.182_198delGCTGGCTGGCCAGCACA	chr1.hg19:g.211654560_211654576delTGTGCTGGCCAGCCAGC	ENSP00000355969:p.Ser61fs	154.0	0.0	0		154.0	43.0	0.279221	NM_183059	A8K595	Frame_Shift_Del	DEL	ENST00000367002.4	hg19	CCDS1498.1																																																																																			.	.	.	none		0.599	RD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089837.1	NM_183059		-	211654576	TGTGCTGGCCAGCCAGC	-	211654560	7	5	30	1	0	1	0	1	0	0	0	0	13200	1683	59	0	397	0	RD3	1	211654560	Frame_Shift_Del	DEL	TGTGCTGGCCAGCCAGC	TCGA-5P-A9JY-01A-11D-A42J-10	57338623	211654560	37596061	13	2120											
ADI1	55256	hgsc.bcm.edu	37	chr2	3523139	3523139	+	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	cgaggcttgggctcgcgtacCttccagtagagcaccccgag	7	7	13	14	4	0	1	0	0	0	1	2	3	1	1	4	2	2	5	4	2	2	4			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr2:3523139C>T	ENST00000327435.6	-	1	368	c.120G>A	c.(118-120)aaG>aaA	p.K40K	ADI1_ENST00000382093.5_5'Flank|AC142528.1_ENST00000450917.1_RNA	NM_018269.3	NP_060739.2			acireductone dioxygenase 1											breast(2)|large_intestine(2)|lung(4)|ovary(1)|stomach(1)	10	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.0729)|Epithelial(75;0.173)|all cancers(51;0.228)		GCTCGCGTACCTTCCAGTAGA	0.771																																					p.K40K		Atlas-SNP	.											.	ADI1	12	.	0			c.G120A						PASS	.						2	2	2					2																	3523139		1436	3148	4584	SO:0001630	splice_region_variant	55256	exon1			GCGTACCTTCCAG		CCDS1653.1	2p25.2	2013-05-29			ENSG00000182551	ENSG00000182551	1.13.11.54		30576	protein-coding gene	gene with protein product	"membrane-type 1 matrix metalloproteinase cytoplasmic tail binding protein-1"	613400				14718544, 15938715	Standard	NM_018269		Approved	SIPL, MTCBP-1, ARD, APL1, FLJ10913, HMFT1638, mtnD	uc002qxp.4	Q9BV57	OTTHUMG00000112441	ENST00000327435.6:c.120+1G>A	chr2.hg19:g.3523139C>T		51.0	0.0	.		59.0	28.0	.	NM_018269		Silent	SNP	ENST00000327435.6	hg19	CCDS1653.1																																																																																			.	.	.	none		0.771	ADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000231914.6	NM_018269	Silent	T	3523139	C	T	3523139	5	4	30	1	0	0	0	0	0	0	1	0	315	695	24	2	435	2	ADI1	2	3523139	Splice_Site	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10		3523139	239676234	14	2121											
BRE	9577	hgsc.bcm.edu	37	chr2	28460154	28460155	+	In_Frame_Ins	INS	-	-	TGCTCACCA																															cgttcctcaagtatgccaccINStgctcaccaacaaggtaaaa																								rs139141828		TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr2:28460154_28460155insTGCTCACCA	ENST00000342045.2	+	9	907_908	c.766_767insTGCTCACCA	c.(766-768)ctg>cTGCTCACCAtg	p.256_257insLTM	BRE_ENST00000379624.1_In_Frame_Ins_p.256_257insLTM|BRE_ENST00000344773.2_In_Frame_Ins_p.256_257insLTM|BRE_ENST00000379632.2_In_Frame_Ins_p.256_257insLTM|BRE_ENST00000361704.2_In_Frame_Ins_p.256_257insLTM	NM_199194.2	NP_954664.1			brain and reproductive organ-expressed (TNFRSF1A modulator)											NS(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(2)	23	Acute lymphoblastic leukemia(172;0.155)					AGTATGCCACCTGCTCACCAAC	0.49																																					p.L256delinsLLTM		Atlas-Indel,Pindel	.											.	BRE	164	.	0			c.766_767insTGCTCACCA						PASS	.																																			SO:0001652	inframe_insertion	9577	exon8			.	AF015767	CCDS1763.1, CCDS1764.1, CCDS1765.1	2p23	2008-02-05			ENSG00000158019	ENSG00000158019			1106	protein-coding gene	gene with protein product	"BRCA1/BRCA2-containing complex, subunit 4"	610497				9737713, 7826398	Standard	NM_004899		Approved	BRCC45, BRCC4	uc002rls.3	Q9NXR7	OTTHUMG00000097831	ENST00000342045.2:c.767_775dupTGCTCACCA	chr2.hg19:g.28460155_28460163dupTGCTCACCA	ENSP00000339371:p.Leu256_Leu257insLeuThrMet	29.0	0.0	0		29.0	11.0	0.37931	NM_199191		In_Frame_Ins	INS	ENST00000342045.2	hg19	CCDS1763.1																																																																																			.	.	.	none		0.49	BRE-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215114.1			TGCTCACCA	28460155	-	TGCTCACCA	28460154	7	5	30	1	0	1	1	0	0	0	0	0	1511	680	24	0	792	0	BRE	2	28460154	In_Frame_Ins	INS	-	TCGA-5P-A9JY-01A-11D-A42J-10	24937015	28460154	214739219	15	2122											
KLRAQ1	129285	hgsc.bcm.edu	37	chr2	48738524	48738524	+	Missense_Mutation	SNP	A	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	gttacgaggatcagttaagtAtgatgagtgaccacctgtgc	11	11	12	7	1	1	3	1	3	0	0	1	5	1	4	2	1	2	3	2	1	3	3			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr2:48738524A>C	ENST00000294952.8	+	21	2387	c.2230A>C	c.(2230-2232)Atg>Ctg	p.M744L	PPP1R21_ENST00000476199.1_3'UTR|PPP1R21_ENST00000449090.2_Missense_Mutation_p.M702L|PPP1R21_ENST00000281394.4_Missense_Mutation_p.M733L	NM_001135629.2	NP_001129101.1	Q6ZMI0	PPR21_HUMAN	protein phosphatase 1, regulatory subunit 21	744						membrane (GO:0016020)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(4)|lung(9)	15						TCAGTTAAGTATGATGAGTGA	0.418																																					p.M744L		Atlas-SNP	.											.	PPP1R21	47	.	0			c.A2230C						PASS	.						235	205	215					2																	48738524		2203	4300	6503	SO:0001583	missense	129285	exon21			TTAAGTATGATGA	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.2230A>C	chr2.hg19:g.48738524A>C	ENSP00000294952:p.Met744Leu	143.0	0.0	.		134.0	58.0	.	NM_001135629	B7ZKY5|B7ZKY7|E1B6W7|Q2TA78|Q6ZMI6|Q8IW83|Q8J029|Q96ES8	Missense_Mutation	SNP	ENST00000294952.8	hg19	CCDS46278.1	.	.	.	.	.	.	.	.	.	.	A	19.29	3.799274	0.70567	.	.	ENSG00000162869	ENST00000281394;ENST00000294952;ENST00000449090	.	.	.	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.73225	0.3560	L	0.52266	1.64	0.58432	D	0.999995	P;P;P	0.49696	0.927;0.856;0.91	D;P;D	0.66602	0.945;0.881;0.909	T	0.68911	-0.5284	9	0.26408	T	0.33	-25.9975	16.4461	0.83932	1.0:0.0:0.0:0.0	.	702;744;733	E1B6W7;Q6ZMI0;Q6ZMI0-2	.;PPR21_HUMAN;.	L	733;744;702	.	ENSP00000281394:M733L	M	+	1	0	KLRAQ1	48592028	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	9.339000	0.96797	2.285000	0.76669	0.528000	0.53228	ATG	.	.	.	none		0.418	PPP1R21-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251238.4	NM_152994		C	48738524	A	C	48738524	3	2	30	1	0	0	0	0	1	0	0	0	8420	449	16	5	2312	5	KLRAQ1	2	48738524	Missense_Mutation	SNP	A	TCGA-5P-A9JY-01A-11D-A42J-10	20278370	48738524	194460849	16	2123											
USP34	9736	hgsc.bcm.edu	37	chr2	61417473	61417473	+	Missense_Mutation	SNP	T	T	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	aatcagactgtaggttctgaTactggcttatcaagtttgta	11	15	9	6	0	3	2	2	1	1	1	3	2	3	2	0	2	1	5	0	2	6	6			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr2:61417473T>G	ENST00000398571.2	-	78	9882	c.9806A>C	c.(9805-9807)tAt>tCt	p.Y3269S	AHSA2_ENST00000394457.3_3'UTR	NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	3269					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)			TAGGTTCTGATACTGGCTTAT	0.383																																					p.Y3269S		Atlas-SNP	.											.	USP34	334	.	0			c.A9806C						PASS	.						101	95	97					2																	61417473		1835	4096	5931	SO:0001583	missense	9736	exon78			TTCTGATACTGGC	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.9806A>C	chr2.hg19:g.61417473T>G	ENSP00000381577:p.Tyr3269Ser	137.0	0.0	.		143.0	63.0	.	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	hg19	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	T	16.74	3.206114	0.58234	.	.	ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571;ENST00000436269	T	0.64260	-0.09	5.87	5.87	0.94306	.	0.109289	0.64402	D	0.000004	T	0.40862	0.1134	N	0.08118	0	0.52501	D	0.999958	B	0.33694	0.421	B	0.25405	0.06	T	0.38972	-0.9636	10	0.27785	T	0.31	.	16.5764	0.84681	0.0:0.0:0.0:1.0	.	3269	Q70CQ2	UBP34_HUMAN	S	3117;3034;3269;147	ENSP00000381577:Y3269S	ENSP00000263989:Y3117S	Y	-	2	0	USP34	61270977	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.483000	0.60264	2.371000	0.80710	0.533000	0.62120	TAT	.	.	.	none		0.383	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			G	61417473	T	G	61417473	3	3	30	1	0	0	0	0	1	0	0	0	17077	1406	49	5	846	5	USP34	2	61417473	Missense_Mutation	SNP	T	TCGA-5P-A9JY-01A-11D-A42J-10	12678949	61417473	181781900	17	2124											
TTN	7273	hgsc.bcm.edu	37	chr2	179391818	179391818	+	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	aactcagggtataaagtccaCcatcttgtttctgtacgtcc	10	13	7	11	1	3	0	1	0	2	0	5	0	5	0	3	1	2	3	3	1	5	5	rs281864933		TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr2:179391818C>A	ENST00000591111.1	-	313	103198	c.102974G>T	c.(102973-102975)gGt>gTt	p.G34325V	TTN_ENST00000589042.1_Missense_Mutation_p.G35966V|TTN-AS1_ENST00000588804.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.G33398V|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.G27026V|TTN_ENST00000460472.2_Missense_Mutation_p.G26901V|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000592161.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000587576.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.G27093V|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	34325	Ig-like 152.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATAAAGTCCACCATCTTGTTT	0.433																																					p.G35966V		Atlas-SNP	.											.	TTN	18412	.	0			c.G107897T						PASS	.						192	177	182					2																	179391818		1948	4153	6101	SO:0001583	missense	7273	exon363			AGTCCACCATCTT	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.102974G>T	chr2.hg19:g.179391818C>A	ENSP00000465570:p.Gly34325Val	106.0	0.0	.		100.0	46.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	14.05	2.420858	0.42918	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21	6.17	5.27	0.74061	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.67325	0.2881	N	0.21324	0.655	0.80722	D	1	D;D;D;D;D	0.65815	0.987;0.987;0.987;0.987;0.995	P;P;P;P;P	0.55055	0.767;0.767;0.767;0.767;0.702	T	0.71174	-0.4670	9	0.87932	D	0	.	17.7197	0.88347	0.0:0.8781:0.1219:0.0	.	26901;27026;27093;34325;33398	D3DPF9;E7EQE6;E7ET18;Q8WZ42;A6NKB1	.;.;.;TITIN_HUMAN;.	V	33398;26901;27093;27026;26898	ENSP00000343764:G33398V;ENSP00000434586:G26901V;ENSP00000340554:G27093V;ENSP00000352154:G27026V	ENSP00000340554:G27093V	G	-	2	0	TTN	179100064	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.170000	0.64990	2.941000	0.99782	0.655000	0.94253	GGT	.	.	.	none		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179391818	C	A	179391818	3	1	30	1	0	0	0	0	1	0	0	0	16747	507	18	4	82	4	TTN	2	179391818	Missense_Mutation	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10	117974345	179391818	63807555	18	2125											
SLC23A3	151295	hgsc.bcm.edu	37	chr2	220027074	220027074	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccagccaggaagatgggcTgtgtcagcagtgagtgcagt	9	8	16	8	0	1	2	1	1	0	1	2	3	2	3	2	2	3	3	2	2	1	0			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr2:220027074T>C	ENST00000409878.3	-	11	1516	c.1484A>G	c.(1483-1485)cAg>cGg	p.Q495R	SLC23A3_ENST00000396775.3_3'UTR|SLC23A3_ENST00000455516.2_Missense_Mutation_p.Q503R|NHEJ1_ENST00000356853.5_5'Flank|SLC23A3_ENST00000295738.7_Missense_Mutation_p.Q378R	NM_001144889.1	NP_001138361.1	Q6PIS1	S23A3_HUMAN	solute carrier family 23, member 3	495					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)		GAAGATGGGCTGTGTCAGCAG	0.557																																					p.Q503R		Atlas-SNP	.											.	SLC23A3	60	.	0			c.A1508G						PASS	.						76	80	79					2																	220027074		2027	4185	6212	SO:0001583	missense	151295	exon11			ATGGGCTGTGTCA	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.1484A>G	chr2.hg19:g.220027074T>C	ENSP00000386473:p.Gln495Arg	65.0	0.0	.		62.0	30.0	.	NM_001144890	B7Z512|Q2PYN6|Q96NA6	Missense_Mutation	SNP	ENST00000409878.3	hg19	CCDS46518.1	.	.	.	.	.	.	.	.	.	.	T	12.59	1.984557	0.35036	.	.	ENSG00000213901	ENST00000295738;ENST00000409878;ENST00000455516	T;T;T	0.42513	0.97;2.3;2.29	3.37	3.37	0.38596	.	0.403835	0.19974	N	0.101924	T	0.18593	0.0446	N	0.08118	0	0.80722	D	1	B;B;B	0.24092	0.097;0.097;0.034	B;B;B	0.19946	0.016;0.016;0.027	T	0.06356	-1.0831	9	.	.	.	.	6.0302	0.19677	0.2296:0.0:0.0:0.7704	.	495;503;378	Q6PIS1;B7Z512;Q6PIS1-2	S23A3_HUMAN;.;.	R	378;495;503	ENSP00000295738:Q378R;ENSP00000386473:Q495R;ENSP00000406546:Q503R	.	Q	-	2	0	SLC23A3	219735318	0.770000	0.28543	0.999000	0.59377	0.984000	0.73092	0.835000	0.27531	1.539000	0.49286	0.374000	0.22700	CAG	.	.	.	none		0.557	SLC23A3-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336331.2	NM_144712		C	220027074	T	C	220027074	3	2	30	1	0	0	0	0	1	0	0	0	14477	1580	55	3	356	3	SLC23A3	2	220027074	Missense_Mutation	SNP	T	TCGA-5P-A9JY-01A-11D-A42J-10	40635256	220027074	23172299	19	2126											
TRIP12	9320	hgsc.bcm.edu	37	chr2	230656737	230656737	+	Frame_Shift_Del	DEL	C	C	-																															aaatgttctccaatataaaaCtgcagcctgtgtcttacatt																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr2:230656737delC	ENST00000283943.5	-	28	4213	c.4035delG	c.(4033-4035)cagfs	p.Q1345fs	TRIP12_ENST00000389044.4_Frame_Shift_Del_p.Q1393fs|TRIP12_ENST00000389045.3_Frame_Shift_Del_p.Q1075fs	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1345					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		CAATATAAAACTGCAGCCTGT	0.403																																					p.F1346fs		Atlas-Indel,Pindel	.											.	TRIP12	207	.	0			c.4036delT						PASS	.						128	126	127					2																	230656737		2203	4300	6503	SO:0001589	frameshift_variant	9320	exon28			.	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.4035delG	chr2.hg19:g.230656737delC	ENSP00000283943:p.Gln1345fs	235.0	0.0	0		205.0	79.0	0.385366	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Frame_Shift_Del	DEL	ENST00000283943.5	hg19	CCDS33391.1																																																																																			.	.	.	none		0.403	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		-	230656737	C	-	230656737	7	5	30	1	0	1	0	1	0	0	0	0	16568	564	20	0	1999	0	TRIP12	2	230656737	Frame_Shift_Del	DEL	C	TCGA-5P-A9JY-01A-11D-A42J-10	10629663	230656737	12542636	20	2127											
TRPM8	79054	hgsc.bcm.edu	37	chr2	234890560	234890561	+	Splice_Site	INS	-	-	TTT																															tataatgctgcagaggatggINStaagagtcaagaatatttgt																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr2:234890560_234890561insTTT	ENST00000324695.4	+	19	2629		c.e19+1		TRPM8_ENST00000433712.2_Splice_Site	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8						calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	GCAGAGGATGGTAAGAGTCAAG	0.376																																					.		Atlas-Indel,Pindel	.											.	TRPM8	146	.	0			c.2589+1->TTT						PASS	.																																			SO:0001630	splice_region_variant	79054	exon19			.	AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"Voltage-gated ion channels / Transient receptor potential cation channels"	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.2589+1->TTT	chr2.hg19:g.234890560_234890561insTTT		122.0	0.0	0		111.0	54.0	0.486486	NM_024080	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Splice_Site	INS	ENST00000324695.4	hg19	CCDS33407.1																																																																																			.	.	.	none		0.376	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080	Intron	TTT	234890561	-	TTT	234890560	8	5	30	1	0	1	1	0	0	0	1	0	16604	1275	44	0	2660	0	TRPM8	2	234890560	Splice_Site	INS	-	TCGA-5P-A9JY-01A-11D-A42J-10	4233823	234890560	8308813	21	2128											
PPARG	5468	hgsc.bcm.edu	37	chr3	12447494	12447494	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acctccgggccctggcaaaaCatttgtatgactcatacata	12	10	7	12	1	1	1	1	1	0	0	2	1	2	1	3	2	2	2	3	2	5	4			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr3:12447494C>T	ENST00000287820.6	+	5	854	c.733C>T	c.(733-735)Cat>Tat	p.H245Y	PPARG_ENST00000539812.1_Missense_Mutation_p.H215Y|PPARG_ENST00000397010.2_Missense_Mutation_p.H217Y|PPARG_ENST00000397026.2_Missense_Mutation_p.H223Y|PPARG_ENST00000397012.2_Missense_Mutation_p.H217Y|PPARG_ENST00000397000.1_Missense_Mutation_p.H217Y|PPARG_ENST00000309576.6_Missense_Mutation_p.H217Y|PPARG_ENST00000397015.2_Missense_Mutation_p.H217Y	NM_015869.4	NP_056953.2	P37231	PPARG_HUMAN	peroxisome proliferator-activated receptor gamma	245	Interaction with FAM120B. {ECO:0000250}.				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)	CCTGGCAAAACATTTGTATGA	0.517			T	PAX8	follicular thyroid		"Insulin resistance ; lipodystrophy, familial partial L;diabetes mellitus, insulin-resistantI, with acanthosis nigricans and hypertension"																														p.H245Y		Atlas-SNP	.		Dom	yes		3	3p25	5468	"peroxisome proliferative activated receptor, gamma"	yes	E	.	PPARG	49	.	0			c.C733T						PASS	.						70	71	71					3																	12447494		2203	4300	6503	SO:0001583	missense	5468	exon5			GCAAAACATTTGT	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.733C>T	chr3.hg19:g.12447494C>T	ENSP00000287820:p.His245Tyr	126.0	0.0	.		137.0	32.0	.	NM_015869	A8K3G6|B5BUA1|O00684|O00710|O14515|Q0QJH8|Q15178|Q15179|Q15180|Q15832|Q86U60|Q96J12	Missense_Mutation	SNP	ENST00000287820.6	hg19	CCDS2609.1	.	.	.	.	.	.	.	.	.	.	C	19.44	3.827607	0.71143	.	.	ENSG00000132170	ENST00000397010;ENST00000309576;ENST00000397015;ENST00000397012;ENST00000397026;ENST00000397000;ENST00000539812;ENST00000287820	T;T;T;T;T;D;D;T	0.90788	-0.45;-0.45;-0.45;-0.45;-0.45;-2.73;-2.73;-0.45	5.81	5.81	0.92471	Nuclear hormone receptor, ligand-binding (1);	0.153557	0.56097	D	0.000022	D	0.90270	0.6957	M	0.74258	2.255	0.58432	D	0.999999	P;B;P	0.44139	0.68;0.184;0.827	B;B;B	0.36418	0.224;0.099;0.149	D	0.91163	0.4962	10	0.59425	D	0.04	.	20.0896	0.97814	0.0:1.0:0.0:0.0	.	245;231;217	P37231;Q4W4C7;E9PFX5	PPARG_HUMAN;.;.	Y	217;217;217;217;223;217;215;245	ENSP00000380205:H217Y;ENSP00000312472:H217Y;ENSP00000380210:H217Y;ENSP00000380207:H217Y;ENSP00000380221:H223Y;ENSP00000380196:H217Y;ENSP00000438940:H215Y;ENSP00000287820:H245Y	ENSP00000287820:H245Y	H	+	1	0	PPARG	12422494	1.000000	0.71417	0.869000	0.34112	0.996000	0.88848	5.579000	0.67457	2.741000	0.93983	0.650000	0.86243	CAT	.	.	.	none		0.517	PPARG-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251979.2	NM_005037		T	12447494	C	T	12447494	3	4	30	1	0	0	0	0	1	0	0	0	12306	478	17	2	751	2	PPARG	3	12447494	Missense_Mutation	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10		12447494	185574936	22	2129											
MYD88	30	hgsc.bcm.edu	37	chr3	38180443	38180443	+	5'Flank	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	tggcagggacgccctggcgcCtctgtaggccgactgctcga	5	7	15	14	4	1	0	0	0	1	0	2	3	1	1	3	4	1	3	3	4	1	1			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr3:38180443C>A	ENST00000333167.8	-	0	0				MYD88_ENST00000443433.2_Silent_p.A97A|ACAA1_ENST00000444607.2_5'Flank|ACAA1_ENST00000301810.7_5'Flank|MYD88_ENST00000495303.1_Silent_p.A97A|ACAA1_ENST00000544624.1_5'Flank|MYD88_ENST00000396334.3_Silent_p.A97A|ACAA1_ENST00000450296.1_5'Flank|MYD88_ENST00000424893.1_Silent_p.A97A|MYD88_ENST00000417037.2_Silent_p.A97A	NM_001607.3	NP_001598.1	P09110	THIK_HUMAN	acetyl-CoA acyltransferase 1						alpha-linolenic acid metabolic process (GO:0036109)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acetyl-CoA C-acyltransferase activity (GO:0003988)|palmitoyl-CoA oxidase activity (GO:0016401)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	9				KIRC - Kidney renal clear cell carcinoma(284;0.0523)|Kidney(284;0.0657)		GCCCTGGCGCCTCTGTAGGCC	0.652																																					p.A97A		Atlas-SNP	.											.	MYD88	900	.	0			c.C291A						PASS	.						37	43	41					3																	38180443		2203	4299	6502	SO:0001631	upstream_gene_variant	4615	exon1			TGGCGCCTCTGTA	X14813	CCDS2673.1, CCDS46794.1	3p22.2	2012-05-16	2010-04-30		ENSG00000060971	ENSG00000060971	2.3.1.16		82	protein-coding gene	gene with protein product	"peroxisomal 3-oxoacyl-Coenzyme A thiolase"	604054	"acetyl-Coenzyme A acyltransferase 1"				Standard	NM_001607		Approved		uc003cht.3	P09110	OTTHUMG00000131087		chr3.hg19:g.38180443C>A	Exception_encountered	54.0	0.0	.		98.0	24.0	.	NM_002468	G5E935|Q96CA6	Silent	SNP	ENST00000333167.8	hg19	CCDS2673.1																																																																																			.	.	.	none		0.652	ACAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342980.1	NM_001607		A	38180443	C	A	38180443	1	1	30	0	1	0	0	0	0	0	0	0	10030	668	24	4		4	MYD88	3	38180443	5'Flank	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10	25732949	38180443	159841987	23	2130											
ACTR8	93973	hgsc.bcm.edu	37	chr3	53914039	53914040	+	Frame_Shift_Del	DEL	AC	AC	-																															gtttgtgtcttcgggcaatgAcgtgaggaatgctggcagga																								rs149728050	byFrequency	TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr3:53914039_53914040delAC	ENST00000335754.3	-	2	320_321	c.220_221delGT	c.(220-222)gtcfs	p.V74fs	ACTR8_ENST00000231909.7_5'Flank|ACTR8_ENST00000482349.1_5'UTR|AC012467.1_ENST00000410956.1_RNA	NM_022899.4	NP_075050.3	Q9H981	ARP8_HUMAN	ARP8 actin-related protein 8 homolog (yeast)	74					chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	ATP binding (GO:0005524)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.000143)|KIRC - Kidney renal clear cell carcinoma(284;0.00544)|Kidney(284;0.00607)|OV - Ovarian serous cystadenocarcinoma(275;0.111)		TCGGGCAATGACGTGAGGAATG	0.475																																					p.74_74del		Atlas-INDEL	.											.	ACTR8	56	.	0			c.221_222del						PASS	.																																			SO:0001589	frameshift_variant	93973	exon2			.		CCDS2875.1	3p21.31	2011-07-06	2001-11-28		ENSG00000113812	ENSG00000113812		"INO80 complex subunits"	14672	protein-coding gene	gene with protein product	"INO80 complex subunit N"		"ARP8 (actin-related protein 8, yeast) homolog"			18163988, 16230350	Standard	NM_022899		Approved	INO80N	uc003dhd.3	Q9H981	OTTHUMG00000158279	ENST00000335754.3:c.220_221delGT	chr3.hg19:g.53914039_53914040delAC	ENSP00000336842:p.Val74fs	122.0	0.0	0		161.0	33.0	0.204969	NM_022899	B3KSW7|Q8N566|Q9H663	Frame_Shift_Del	DEL	ENST00000335754.3	hg19	CCDS2875.1																																																																																			.	.	.	none		0.475	ACTR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350562.2	NM_022899		-	53914040	AC	-	53914039	7	5	30	1	0	1	0	1	0	0	0	0	217	275	10	0	1701	0	ACTR8	3	53914039	Frame_Shift_Del	DEL	AC	TCGA-5P-A9JY-01A-11D-A42J-10	15733596	53914039	144108391	24	2131	24	2									
ACTR8	93973	hgsc.bcm.edu	37	chr3	53914042	53914049	+	Frame_Shift_Del	DEL	TGAGGAAT	TGAGGAAT	-																															tgtgtcttcgggcaatgacgTgaggaatgctggcaggaaga																								rs560149594		TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	TGAGGAAT	TGAGGAAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr3:53914042_53914049delTGAGGAAT	ENST00000335754.3	-	2	311_318	c.211_218delATTCCTCA	c.(211-219)attcctcacfs	p.IPH71fs	ACTR8_ENST00000231909.7_5'Flank|ACTR8_ENST00000482349.1_5'UTR|AC012467.1_ENST00000410956.1_RNA	NM_022899.4	NP_075050.3	Q9H981	ARP8_HUMAN	ARP8 actin-related protein 8 homolog (yeast)	71					chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	ATP binding (GO:0005524)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.000143)|KIRC - Kidney renal clear cell carcinoma(284;0.00544)|Kidney(284;0.00607)|OV - Ovarian serous cystadenocarcinoma(275;0.111)		GGCAATGACGTGAGGAATGCTGGCAGGA	0.466																																					p.71_73del		Atlas-INDEL	.											.	ACTR8	56	.	0			c.212_219del						PASS	.																																			SO:0001589	frameshift_variant	93973	exon2			.		CCDS2875.1	3p21.31	2011-07-06	2001-11-28		ENSG00000113812	ENSG00000113812		"INO80 complex subunits"	14672	protein-coding gene	gene with protein product	"INO80 complex subunit N"		"ARP8 (actin-related protein 8, yeast) homolog"			18163988, 16230350	Standard	NM_022899		Approved	INO80N	uc003dhd.3	Q9H981	OTTHUMG00000158279	ENST00000335754.3:c.211_218delATTCCTCA	chr3.hg19:g.53914042_53914049delTGAGGAAT	ENSP00000336842:p.Ile71fs	118.0	0.0	0		161.0	33.0	0.204969	NM_022899	B3KSW7|Q8N566|Q9H663	Frame_Shift_Del	DEL	ENST00000335754.3	hg19	CCDS2875.1																																																																																			.	.	.	none		0.466	ACTR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350562.2	NM_022899		-	53914049	TGAGGAAT	-	53914042	7	5	30	1	0	1	0	1	0	0	0	0	217	1696	59	0	1704	0	ACTR8	3	53914042	Frame_Shift_Del	DEL	TGAGGAAT	TCGA-5P-A9JY-01A-11D-A42J-10	3	53914042	144108388	25	2132	24	2									
TPRA1	131601	hgsc.bcm.edu	37	chr3	127298938	127298938	+	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	gatgtttggtgccaggggtgGgggtagcgctgtgctcccat	4	11	18	8	1	0	0	0	0	0	0	1	1	1	0	2	5	3	4	2	5	1	2			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr3:127298938G>A	ENST00000355552.3	-	2	428	c.52C>T	c.(52-54)Cca>Tca	p.P18S	TPRA1_ENST00000296210.7_Missense_Mutation_p.P18S|TPRA1_ENST00000450633.2_Missense_Mutation_p.P18S|TPRA1_ENST00000489960.1_Missense_Mutation_p.P18S	NM_001136053.1	NP_001129525.1	Q86W33	TPRA1_HUMAN	transmembrane protein, adipocyte asscociated 1	18					aging (GO:0007568)|G-protein coupled receptor signaling pathway (GO:0007186)|lipid metabolic process (GO:0006629)	integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	9						GCCAGGGGTGGGGGTAGCGCT	0.647																																					p.P18S		Atlas-SNP	.											.	TPRA1	21	.	0			c.C52T						PASS	.						107	85	93					3																	127298938		2203	4300	6503	SO:0001583	missense	131601	exon2			GGGGTGGGGGTAG	AK056759	CCDS3042.1, CCDS46899.1	3q21.2	2012-08-22	2009-07-08	2009-07-08	ENSG00000163870	ENSG00000163870		"GPCR / Unclassified : 7TM orphan receptors"	30413	protein-coding gene	gene with protein product	"transmembrane protein 227"	608336	"G protein-coupled receptor 175"	GPR175		10342878	Standard	NM_001136053		Approved	TPRA40, FLJ32197, TMEM227	uc003ejn.3	Q86W33	OTTHUMG00000159639	ENST00000355552.3:c.52C>T	chr3.hg19:g.127298938G>A	ENSP00000347748:p.Pro18Ser	64.0	0.0	.		69.0	23.0	.	NM_001142646	A8MVB8|D3DNA9|Q8WZ24|Q96AJ6|Q9P2R4	Missense_Mutation	SNP	ENST00000355552.3	hg19	CCDS3042.1	.	.	.	.	.	.	.	.	.	.	G	17.31	3.357003	0.61293	.	.	ENSG00000163870	ENST00000450633;ENST00000296210;ENST00000355552;ENST00000489960;ENST00000490290;ENST00000469111;ENST00000490643;ENST00000462228	.	.	.	5.05	3.18	0.36537	.	0.304279	0.35970	N	0.002879	T	0.32793	0.0841	L	0.27053	0.805	0.37281	D	0.907849	B;B	0.15473	0.013;0.003	B;B	0.12156	0.007;0.001	T	0.20672	-1.0268	9	0.48119	T	0.1	-4.4783	2.1346	0.03758	0.1559:0.1718:0.4957:0.1766	.	18;18	Q86W33-3;Q86W33	.;TPRA1_HUMAN	S	18	.	ENSP00000296210:P18S	P	-	1	0	TPRA1	128781628	0.880000	0.30214	0.033000	0.17914	0.792000	0.44763	1.076000	0.30729	0.576000	0.29452	0.655000	0.94253	CCA	.	.	.	none		0.647	TPRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356624.1	NM_016372		A	127298938	G	A	127298938	3	1	30	1	0	0	0	0	1	0	0	0	16429	1232	43	2	1109	2	TPRA1	3	127298938	Missense_Mutation	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	73384896	127298938	70723492	26	2133											
CHST2	9435	hgsc.bcm.edu	37	chr3	142840750	142840750	+	Frame_Shift_Del	DEL	C	C	-																															agccgagacccgcgagctcaCcgcatgcccttcttggaggc																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr3:142840750delC	ENST00000309575.3	+	2	2476	c.1092delC	c.(1090-1092)cacfs	p.H364fs		NM_004267.4	NP_004258.2	Q9Y4C5	CHST2_HUMAN	carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2	364					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						CGCGAGCTCACCGCATGCCCT	0.697																																					p.H364fs		Atlas-Indel,Pindel	.											.	CHST2	67	.	0			c.1091delA						PASS	.						20	25	23					3																	142840750		2201	4293	6494	SO:0001589	frameshift_variant	9435	exon2			.	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.1092delC	chr3.hg19:g.142840750delC	ENSP00000307911:p.His364fs	72.0	0.0	0		120.0	38.0	0.316667	NM_004267	D3DNG5|Q2M370|Q9GZN5|Q9UED5|Q9Y6F2	Frame_Shift_Del	DEL	ENST00000309575.3	hg19	CCDS3129.1																																																																																			.	.	.	none		0.697	CHST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354850.1	NM_004267		-	142840750	C	-	142840750	7	5	30	1	0	1	0	1	0	0	0	0	3406	506	18	0	1094	0	CHST2	3	142840750	Frame_Shift_Del	DEL	C	TCGA-5P-A9JY-01A-11D-A42J-10	15541812	142840750	55181680	27	2134											
ABCC5	10057	hgsc.bcm.edu	37	chr3	183695342	183695342	+	Frame_Shift_Del	DEL	G	G	-																															ccactgaggcttctgagaggGactttactgaaaacggtgtt																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr3:183695342delG	ENST00000334444.6	-	10	1607	c.1367delC	c.(1366-1368)tccfs	p.S456fs	ABCC5_ENST00000492216.1_5'UTR|ABCC5_ENST00000265586.6_Frame_Shift_Del_p.S456fs	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	456	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	TTCTGAGAGGGACTTTACTGA	0.488																																					p.S456fs		Pindel	.											.	ABCC5	142	.	0			c.1368delC						PASS	.						82	79	80					3																	183695342		1906	4131	6037	SO:0001589	frameshift_variant	10057	exon10			.	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.1367delC	chr3.hg19:g.183695342delG	ENSP00000333926:p.Ser456fs	134.0	0.0	.		163.0	21.0	0.129	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Frame_Shift_Del	DEL	ENST00000334444.6	hg19	CCDS43176.1																																																																																			.	.	.	none		0.488	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688		-	183695342	G	-	183695342	7	5	30	1	0	1	0	1	0	0	0	0	56	1174	41	0	3030	0	ABCC5	3	183695342	Frame_Shift_Del	DEL	G	TCGA-5P-A9JY-01A-11D-A42J-10	40854592	183695342	14327088	28	2135											
HGFAC	3083	hgsc.bcm.edu	37	chr4	3443800	3443800	+	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	0	0	0	0	0	0	0	0	0	cccttcctcctcctcctcctGctgctgctgctgctgccacg	1	12	7	21	1	0	0	0	0	0	0	5	0	5	0	7	0	6	5	7	0	0	1	rs372137428		TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr4:3443800G>C	ENST00000382774.3	+	1	187	c.72G>C	c.(70-72)ctG>ctC	p.L24L	HGFAC_ENST00000511533.1_Silent_p.L24L	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	24					proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		TCCTCCTCCTGCTGCTGCTGC	0.716													G|||	1	0.000199681	8e-04	0	5008	,	,		13355	0		0	False		,,,				2504	0				p.L24L		Atlas-SNP	.											.	HGFAC	69	.	0			c.G72C						PASS	.	G		5,3433		0,5,1714	13	16	15		72	0.1	1	4		15	0,7164		0,0,3582	no	coding-synonymous	HGFAC	NM_001528.2		0,5,5296	CC,CG,GG		0.0,0.1454,0.0472		24/656	3443800	5,10597	1719	3582	5301	SO:0001819	synonymous_variant	3083	exon1			CCTCCTGCTGCTG	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.72G>C	chr4.hg19:g.3443800G>C		56.0	0.0	.		54.0	4.0	.	NM_001528	Q14726|Q2M1W7|Q53X47	Silent	SNP	ENST00000382774.3	hg19	CCDS3369.1																																																																																			.	.	.	weak		0.716	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3			C	3443800	G	C	3443800	2	2	30	1	0	0	0	0	0	0	0	1	7093	1306	46	4		4	HGFAC	4	3443800	Silent	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10		3443800	187710476	29	2136											
AASDH	132949	hgsc.bcm.edu	37	chr4	57215435	57215435	+	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	attcaaaaacttacccaccaCaataaagtttccacacttag	17	10	2	12	0	1	0	1	0	0	0	2	0	2	0	3	0	2	1	3	0	7	5			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr4:57215435C>T	ENST00000205214.6	-	11	2662	c.2482G>A	c.(2482-2484)Gtg>Atg	p.V828M	AASDH_ENST00000502617.1_Missense_Mutation_p.V828M|AASDH_ENST00000513376.1_Missense_Mutation_p.V728M|AASDH_ENST00000451613.1_Missense_Mutation_p.V828M|AASDH_ENST00000434343.2_Missense_Mutation_p.V343M|AASDH_ENST00000602986.1_Missense_Mutation_p.V675M	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	828					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				TTACCCACCACAATAAAGTTT	0.333																																					p.V828M		Atlas-SNP	.											.	AASDH	101	.	0			c.G2482A						PASS	.						55	56	56					4																	57215435		2203	4300	6503	SO:0001583	missense	132949	exon11			CCACCACAATAAA	AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"Acyl-CoA synthetase family"	23993	protein-coding gene	gene with protein product	"acyl-CoA synthetase family member 4"	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.2482G>A	chr4.hg19:g.57215435C>T	ENSP00000205214:p.Val828Met	122.0	0.0	.		91.0	43.0	.	NM_181806	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Missense_Mutation	SNP	ENST00000205214.6	hg19	CCDS3504.1	.	.	.	.	.	.	.	.	.	.	C	17.41	3.381731	0.61845	.	.	ENSG00000157426	ENST00000205214;ENST00000513376;ENST00000434343;ENST00000451613;ENST00000503808;ENST00000502617	T;T;T;T;T	0.59502	0.26;0.26;0.26;0.26;0.26	5.9	-1.03	0.10102	Quinonprotein alcohol dehydrogenase-like (2);	0.658469	0.16385	N	0.216708	T	0.70325	0.3211	M	0.80183	2.485	0.19775	N	0.99995	D;D;D;D	0.63046	0.985;0.992;0.985;0.962	P;D;P;P	0.66196	0.822;0.942;0.853;0.882	T	0.61720	-0.7005	10	0.87932	D	0	-3.5325	8.749	0.34605	0.0:0.5572:0.1027:0.3402	.	675;828;828;828	E9PH98;Q4L235-4;Q4L235-3;Q4L235	.;.;.;ACSF4_HUMAN	M	828;728;343;828;675;828	ENSP00000205214:V828M;ENSP00000423760:V728M;ENSP00000392158:V343M;ENSP00000409656:V828M;ENSP00000421171:V828M	ENSP00000205214:V828M	V	-	1	0	AASDH	56910192	0.001000	0.12720	0.914000	0.36105	0.953000	0.61014	-0.115000	0.10741	-0.101000	0.12219	-0.355000	0.07637	GTG	.	.	.	none		0.333	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806		T	57215435	C	T	57215435	3	4	30	1	0	0	0	0	1	0	0	0	22	478	17	2	834	2	AASDH	4	57215435	Missense_Mutation	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10	53771635	57215435	133938841	30	2137											
HELQ	113510	hgsc.bcm.edu	37	chr4	84376623	84376624	+	Frame_Shift_Ins	INS	-	-	G																															atcaccacctccaaggacgaINSgacattccggggaatctgag																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr4:84376623_84376624insG	ENST00000295488.3	-	1	385_386	c.223_224insC	c.(223-225)ctcfs	p.L75fs	MRPS18C_ENST00000295491.4_5'Flank|MRPS18C_ENST00000507349.1_5'Flank|MRPS18C_ENST00000507019.1_5'Flank|HELQ_ENST00000510985.1_Frame_Shift_Ins_p.L75fs|HELQ_ENST00000440639.2_5'UTR	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	75					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						TCCAAGGACGAGACATTCCGGG	0.574								Other identified genes with known or suspected DNA repair function																													p.L75fs		Atlas-Indel,Pindel	.											.	HELQ	95	.	0			c.224_225insC						PASS	.																																			SO:0001589	frameshift_variant	113510	exon1			.	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.224dupC	chr4.hg19:g.84376624_84376624dupG	ENSP00000295488:p.Leu75fs	165.0	0.0	0		146.0	61.0	0.417808	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Frame_Shift_Ins	INS	ENST00000295488.3	hg19	CCDS3603.1																																																																																			.	.	.	none		0.574	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636		G	84376624	-	G	84376623	7	5	30	1	0	1	1	0	0	0	0	0	7054	304	11	0	3153	0	HELQ	4	84376623	Frame_Shift_Ins	INS	-	TCGA-5P-A9JY-01A-11D-A42J-10	27161188	84376623	106777653	31	2138											
NKX6-1	4825	hgsc.bcm.edu	37	chr4	85418816	85418816	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagccagcggcttggggtacCggcccacggcggccacggcc	5	3	16	17	5	0	0	0	0	0	0	0	0	0	0	5	7	3	2	5	7	1	2			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr4:85418816C>T	ENST00000295886.4	-	1	787	c.566G>A	c.(565-567)cGg>cAg	p.R189Q	NKX6-1_ENST00000515820.2_5'Flank	NM_006168.2	NP_006159.2	P78426	NKX61_HUMAN	NK6 homeobox 1	189	Repressor domain. {ECO:0000250}.				cell proliferation (GO:0008283)|cellular response to cytokine stimulus (GO:0071345)|cellular response to peptide hormone stimulus (GO:0071375)|detection of glucose (GO:0051594)|endocrine pancreas development (GO:0031018)|negative regulation of glial cell differentiation (GO:0045686)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte differentiation (GO:0048709)|organ morphogenesis (GO:0009887)|pancreas development (GO:0031016)|positive regulation of glial cell differentiation (GO:0045687)|positive regulation of insulin secretion (GO:0032024)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of axon extension (GO:0030516)|regulation of neuron migration (GO:2001222)|regulation of transcription from RNA polymerase II promoter involved in spinal cord motor neuron fate specification (GO:0021912)|regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification (GO:0021913)|response to drug (GO:0042493)|response to nicotine (GO:0035094)|smoothened signaling pathway (GO:0007224)|transcription from RNA polymerase II promoter (GO:0006366)|type B pancreatic cell maturation (GO:0072560)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	15		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.0013)		CTTGGGGTACCGGCCCACGGC	0.751																																					p.R189Q		Atlas-SNP	.											.	NKX6-1	38	.	0			c.G566A						PASS	.						5	6	5					4																	85418816		1879	3711	5590	SO:0001583	missense	4825	exon1			GGGTACCGGCCCA	AH007313	CCDS3607.1	4q21.33	2012-03-09	2007-07-09	2002-10-04	ENSG00000163623	ENSG00000163623		"Homeoboxes / ANTP class : NKL subclass"	7839	protein-coding gene	gene with protein product		602563	"NK homeobox (Drosophila), family 6, A", "NK6 transcription factor related, locus 1 (Drosophila)"	NKX6A		9119408	Standard	NM_006168		Approved	Nkx6.1	uc003hpa.1	P78426	OTTHUMG00000130426	ENST00000295886.4:c.566G>A	chr4.hg19:g.85418816C>T	ENSP00000295886:p.Arg189Gln	82.0	0.0	.		80.0	34.0	.	NM_006168		Missense_Mutation	SNP	ENST00000295886.4	hg19	CCDS3607.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.463970	0.84425	.	.	ENSG00000163623	ENST00000295886	D	0.90563	-2.69	3.86	3.86	0.44501	.	0.000000	0.64402	D	0.000007	D	0.92770	0.7701	M	0.62723	1.935	0.80722	D	1	D	0.61697	0.99	D	0.67725	0.953	D	0.90310	0.4336	10	0.11485	T	0.65	-17.2863	14.7331	0.69397	0.0:1.0:0.0:0.0	.	189	P78426	NKX61_HUMAN	Q	189	ENSP00000295886:R189Q	ENSP00000295886:R189Q	R	-	2	0	NKX6-1	85637840	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.960000	0.63673	1.997000	0.58415	0.484000	0.47621	CGG	.	.	.	none		0.751	NKX6-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252814.2	NM_006168		T	85418816	C	T	85418816	3	4	30	1	0	0	0	0	1	0	0	0	10464	652	23	1	549	1	NKX6-1	4	85418816	Missense_Mutation	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10	1042193	85418816	105735460	32	2139											
FAM190A	401145	hgsc.bcm.edu	37	chr4	91229870	91229871	+	Frame_Shift_Ins	INS	-	-	A																															aagagcactcaactaacaagINSaatgtctttataaattgtct																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr4:91229870_91229871insA	ENST00000509176.1	+	2	723_724	c.435_436insA	c.(436-438)aatfs	p.N146fs	CCSER1_ENST00000432775.2_Frame_Shift_Ins_p.N146fs|CCSER1_ENST00000333691.8_Frame_Shift_Ins_p.N146fs	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	146								p.K145N(1)									CAACTAACAAGAATGTCTTTAT	0.376																																					p.K145fs		Atlas-Indel,Pindel	.											FAM190A_ENST00000509176,rectum,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.435_436insA						PASS	.																																			SO:0001589	frameshift_variant	401145	exon2			.		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.437dupA	chr4.hg19:g.91229872_91229872dupA	ENSP00000425040:p.Asn146fs	197.0	0.0	0		157.0	63.0	0.401274	NM_207491	Q4W5M0|Q86V57	Frame_Shift_Ins	INS	ENST00000509176.1	hg19	CCDS47099.1																																																																																			.	.	.	none		0.376	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065		A	91229871	-	A	91229870	7	5	30	1	0	1	1	0	0	0	0	0	5525	933	33	0	437	0	FAM190A	4	91229870	Frame_Shift_Ins	INS	-	TCGA-5P-A9JY-01A-11D-A42J-10	5811054	91229870	99924406	33	2140											
CMBL	134147	hgsc.bcm.edu	37	chr5	10286542	10286543	+	Frame_Shift_Del	DEL	TC	TC	-																															gcagttccaccccagcagaaTcccacgatgccaattttctg																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr5:10286542_10286543delTC	ENST00000296658.3	-	4	809_810	c.389_390delGA	c.(388-390)ggafs	p.G130fs	CMBL_ENST00000510532.1_5'UTR	NM_138809.3	NP_620164.1	Q96DG6	CMBL_HUMAN	carboxymethylenebutenolidase homolog (Pseudomonas)	130						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(1)|lung(9)|skin(1)|stomach(1)	13						CCCAGCAGAATCCCACGATGCC	0.421																																					p.130_131del		Pindel	.											.	CMBL	24	.	0			c.390_391del						PASS	.																																			SO:0001589	frameshift_variant	134147	exon4			.		CCDS3878.1	5p15.2	2010-06-25	2006-09-12		ENSG00000164237	ENSG00000164237	3.1.-.-		25090	protein-coding gene	gene with protein product		613379	"carboxymethylenebutenolidase-like (Pseudomonas)"			3804974, 20177059	Standard	NM_138809		Approved	FLJ23617	uc003jes.3	Q96DG6	OTTHUMG00000131043	ENST00000296658.3:c.389_390delGA	chr5.hg19:g.10286542_10286543delTC	ENSP00000296658:p.Gly130fs	91.0	0.0	.		63.0	23.0	0.365	NM_138809	D3DTC7|Q8TED6	Frame_Shift_Del	DEL	ENST00000296658.3	hg19	CCDS3878.1																																																																																			.	.	.	none		0.421	CMBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253689.1	NM_138809		-	10286543	TC	-	10286542	7	5	30	1	0	1	0	1	0	0	0	0	3578	1422	50	0	359	0	CMBL	5	10286542	Frame_Shift_Del	DEL	TC	TCGA-5P-A9JY-01A-11D-A42J-10		10286542	170628718	34	2141											
EDIL3	10085	hgsc.bcm.edu	37	chr5	83402477	83402477	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	catctgttacctgaatccacGgccatctgtcattttctgca	8	14	6	13	1	4	1	1	1	3	0	5	1	5	1	3	1	2	2	3	1	2	3			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr5:83402477G>A	ENST00000296591.5	-	6	1059	c.641C>T	c.(640-642)cCg>cTg	p.P214L	EDIL3_ENST00000380138.3_Missense_Mutation_p.P204L	NM_005711.3	NP_005702.3	O43854	EDIL3_HUMAN	EGF-like repeats and discoidin I-like domains 3	214	F5/8 type C 1. {ECO:0000255|PROSITE- ProRule:PRU00081}.				cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|prostate(5)|skin(3)	31		Lung NSC(167;0.000121)|all_lung(232;0.000154)|Ovarian(174;0.0425)		OV - Ovarian serous cystadenocarcinoma(54;4.3e-40)|Epithelial(54;4.79e-32)|all cancers(79;1.54e-26)		CTGAATCCACGGCCATCTGTC	0.403																																					p.P214L		Atlas-SNP	.											.	EDIL3	94	.	0			c.C641T						PASS	.						152	140	144					5																	83402477		2203	4300	6503	SO:0001583	missense	10085	exon6			ATCCACGGCCATC	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.641C>T	chr5.hg19:g.83402477G>A	ENSP00000296591:p.Pro214Leu	113.0	0.0	.		93.0	39.0	.	NM_005711	B2R763|O43855|Q5D094|Q8N610	Missense_Mutation	SNP	ENST00000296591.5	hg19	CCDS4062.1	.	.	.	.	.	.	.	.	.	.	G	31	5.072698	0.93950	.	.	ENSG00000164176	ENST00000296591;ENST00000380138	D;D	0.99032	-5.35;-5.35	5.37	5.37	0.77165	Coagulation factor 5/8 C-terminal type domain (4);Galactose-binding domain-like (1);	0.105630	0.64402	N	0.000003	D	0.99296	0.9754	M	0.81179	2.53	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.963;1.0	D	0.99556	1.0967	10	0.87932	D	0	-7.3862	19.114	0.93330	0.0:0.0:1.0:0.0	.	204;214	O43854-2;O43854	.;EDIL3_HUMAN	L	214;204	ENSP00000296591:P214L;ENSP00000369483:P204L	ENSP00000296591:P214L	P	-	2	0	EDIL3	83438233	1.000000	0.71417	0.994000	0.49952	0.954000	0.61252	9.209000	0.95087	2.528000	0.85240	0.650000	0.86243	CCG	.	.	.	none		0.403	EDIL3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239258.1	NM_005711		A	83402477	G	A	83402477	3	1	30	1	0	0	0	0	1	0	0	0	4917	1116	39	1	825	1	EDIL3	5	83402477	Missense_Mutation	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	73115935	83402477	97512783	35	2142											
YTHDC2	64848	hgsc.bcm.edu	37	chr5	112851004	112851005	+	Frame_Shift_Del	DEL	AG	AG	-																															cttctttgaccagtactgaaAgagcctttattcatcgactc																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr5:112851004_112851005delAG	ENST00000161863.4	+	2	436_437	c.223_224delAG	c.(223-225)agafs	p.R75fs	YTHDC2_ENST00000515883.1_Frame_Shift_Del_p.R75fs	NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	75	R3H. {ECO:0000255|PROSITE- ProRule:PRU00382}.				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)		CAGTACTGAAAGAGCCTTTATT	0.327																																					p.74_75del		Atlas-Indel,Pindel	.											.	YTHDC2	118	.	0			c.222_223del						PASS	.																																			SO:0001589	frameshift_variant	64848	exon2			.	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.223_224delAG	chr5.hg19:g.112851006_112851007delAG	ENSP00000161863:p.Arg75fs	137.0	0.0	0		99.0	45.0	0.454545	NM_022828	B2RP66	Frame_Shift_Del	DEL	ENST00000161863.4	hg19	CCDS4113.1																																																																																			.	.	.	none		0.327	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828		-	112851005	AG	-	112851004	7	5	30	1	0	1	0	1	0	0	0	0	17509	64	3	0	229	0	YTHDC2	5	112851004	Frame_Shift_Del	DEL	AG	TCGA-5P-A9JY-01A-11D-A42J-10	29448527	112851004	68064256	36	2143											
COMMD10	51397	hgsc.bcm.edu	37	chr5	115428295	115428295	+	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	cagcagcaattagagaacatTcatcttagacaagacaaagc	18	7	7	9	0	2	3	1	0	1	3	2	4	2	3	0	0	4	2	0	0	6	3			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr5:115428295T>A	ENST00000274458.4	+	4	359	c.297T>A	c.(295-297)atT>atA	p.I99I	COMMD10_ENST00000515539.1_Silent_p.I85I	NM_016144.2	NP_057228.1	Q9Y6G5	COMDA_HUMAN	COMM domain containing 10	99										endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(2)	9		all_cancers(142;0.0834)|all_epithelial(76;0.00314)|Prostate(80;0.0102)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;4.3e-07)|Epithelial(69;8.06e-07)|all cancers(49;4.06e-05)		TAGAGAACATTCATCTTAGAC	0.393																																					p.I99I		Atlas-SNP	.											.	COMMD10	18	.	0			c.T297A						PASS	.						93	85	88					5																	115428295		2202	4300	6502	SO:0001819	synonymous_variant	51397	exon4			GAACATTCATCTT	AY542165	CCDS34215.1	5q23.1	2008-02-05				ENSG00000145781			30201	protein-coding gene	gene with protein product						15799966	Standard	NM_016144		Approved	PTD002	uc003krt.1	Q9Y6G5		ENST00000274458.4:c.297T>A	chr5.hg19:g.115428295T>A		67.0	0.0	.		85.0	42.0	.	NM_016144	D3DT07|Q9P077	Silent	SNP	ENST00000274458.4	hg19	CCDS34215.1																																																																																			.	.	.	none		0.393	COMMD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371033.1	NM_016144		A	115428295	T	A	115428295	2	1	30	1	0	0	0	0	0	0	0	1	3717	1771	62	5		5	COMMD10	5	115428295	Silent	SNP	T	TCGA-5P-A9JY-01A-11D-A42J-10	2577291	115428295	65486965	37	2144											
PCDHGA2	56113	hgsc.bcm.edu	37	chr5	140719649	140719649	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccataattgggctttttaatGtacatgatagagactctggg	11	14	10	6	0	1	2	0	1	1	1	1	3	1	2	1	2	1	2	1	2	4	7			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr5:140719649G>A	ENST00000394576.2	+	1	1111	c.1111G>A	c.(1111-1113)Gta>Ata	p.V371I	PCDHGA1_ENST00000517417.1_Intron	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	371	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)|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)			GCTTTTTAATGTACATGATAG	0.423																																					p.V371I		Atlas-SNP	.											.	PCDHGA2	205	.	0			c.G1111A						PASS	.						79	82	81					5																	140719649		2203	4300	6503	SO:0001583	missense	56113	exon1			TTTAATGTACATG	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.1111G>A	chr5.hg19:g.140719649G>A	ENSP00000378077:p.Val371Ile	79.0	0.0	.		86.0	41.0	.	NM_018915	Q52LL6|Q9Y5D5	Missense_Mutation	SNP	ENST00000394576.2	hg19	CCDS47289.1	.	.	.	.	.	.	.	.	.	.	.	8.322	0.824576	0.16678	.	.	ENSG00000081853	ENST00000394576	T	0.53206	0.63	5.13	3.26	0.37387	Cadherin (4);Cadherin-like (1);	0.000000	0.37261	U	0.002174	T	0.45276	0.1334	L	0.51422	1.61	0.25788	N	0.98465	B;P	0.44044	0.373;0.825	B;P	0.44696	0.169;0.458	T	0.33163	-0.9879	10	0.46703	T	0.11	.	10.9284	0.47203	0.1626:0.0:0.8374:0.0	.	371;371	Q9Y5H1-2;Q9Y5H1	.;PCDG2_HUMAN	I	371	ENSP00000378077:V371I	ENSP00000378077:V371I	V	+	1	0	PCDHGA2	140699833	1.000000	0.71417	0.955000	0.39395	0.005000	0.04900	3.236000	0.51336	0.616000	0.30141	-1.165000	0.01757	GTA	.	.	.	none		0.423	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374738.1	NM_018915		A	140719649	G	A	140719649	3	1	30	1	0	0	0	0	1	0	0	0	11561	1377	48	2	1113	2	PCDHGA2	5	140719649	Missense_Mutation	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	25291354	140719649	40195611	38	2145											
SPARC	6678	hgsc.bcm.edu	37	chr5	151043688	151043688	+	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	ccggcccactcatccagggcGatgtacttgtcattgtccag	7	10	10	14	2	2	0	2	0	0	0	4	1	4	0	4	2	1	1	4	2	1	3			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr5:151043688G>T	ENST00000231061.4	-	9	1156	c.843C>A	c.(841-843)atC>atA	p.I281I	SPARC_ENST00000537849.1_5'Flank	NM_003118.3	NP_003109.1	P09486	SPRC_HUMAN	secreted protein, acidic, cysteine-rich (osteonectin)	281	EF-hand.				blood coagulation (GO:0007596)|bone development (GO:0060348)|cellular response to growth factor stimulus (GO:0071363)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|inner ear development (GO:0048839)|lung development (GO:0030324)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|ossification (GO:0001503)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|regulation of cell morphogenesis (GO:0022604)|response to cadmium ion (GO:0046686)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to gravity (GO:0009629)|response to L-ascorbic acid (GO:0033591)|response to lead ion (GO:0010288)|response to lipopolysaccharide (GO:0032496)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	basement membrane (GO:0005604)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nuclear matrix (GO:0016363)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|platelet alpha granule membrane (GO:0031092)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)			central_nervous_system(3)|large_intestine(5)|lung(5)|ovary(1)|urinary_tract(1)	15		Medulloblastoma(196;0.109)|all_hematologic(541;0.122)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)	OV - Ovarian serous cystadenocarcinoma(192;0.00118)		CATCCAGGGCGATGTACTTGT	0.592																																					p.I281I		Atlas-SNP	.											.	SPARC	38	.	0			c.C843A						PASS	.						114	102	106					5																	151043688		2203	4300	6503	SO:0001819	synonymous_variant	6678	exon9			CAGGGCGATGTAC		CCDS4318.1	5q31-q33	2012-10-02			ENSG00000113140	ENSG00000113140			11219	protein-coding gene	gene with protein product	"cysteine-rich protein", "osteonectin"	182120		ON		2838412, 3410046	Standard	NM_003118		Approved		uc003lui.4	P09486	OTTHUMG00000130122	ENST00000231061.4:c.843C>A	chr5.hg19:g.151043688G>T		87.0	0.0	.		84.0	4.0	.	NM_003118	D3DQH9|Q6IBK4	Silent	SNP	ENST00000231061.4	hg19	CCDS4318.1																																																																																			.	.	.	none		0.592	SPARC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252430.1	NM_003118		T	151043688	G	T	151043688	2	4	30	1	0	0	0	0	0	0	0	1	15007	1048	37	4		4	SPARC	5	151043688	Silent	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	10324039	151043688	29871572	39	2146											
BTN2A1	11120	hgsc.bcm.edu	37	chr6	26459730	26459730	+	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	ccagtttattgtcgtggggcCcactgatcccatcttggcca	6	12	10	13	1	1	1	0	1	1	0	3	1	2	1	4	3	0	1	4	3	1	4			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr6:26459730C>A	ENST00000312541.5	+	3	352	c.104C>A	c.(103-105)cCc>cAc	p.P35H	BTN2A1_ENST00000541522.1_5'UTR|BTN2A1_ENST00000429381.1_Missense_Mutation_p.P35H|BTN2A1_ENST00000469185.1_Missense_Mutation_p.P35H	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	35	Ig-like V-type.				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						GTCGTGGGGCCCACTGATCCC	0.512																																					p.P35H		Atlas-SNP	.											.	BTN2A1	118	.	0			c.C104A						PASS	.						89	80	83					6																	26459730		2203	4300	6503	SO:0001583	missense	11120	exon3			TGGGGCCCACTGA	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.104C>A	chr6.hg19:g.26459730C>A	ENSP00000312158:p.Pro35His	132.0	0.0	.		87.0	39.0	.	NM_001197234	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Missense_Mutation	SNP	ENST00000312541.5	hg19	CCDS4613.1	.	.	.	.	.	.	.	.	.	.	C	11.78	1.742052	0.30865	.	.	ENSG00000112763	ENST00000312541;ENST00000429381;ENST00000265424;ENST00000469185	T;T;T	0.67523	-0.27;-0.27;-0.27	3.12	3.12	0.35913	Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.51477	D	0.000090	T	0.77452	0.4132	M	0.88105	2.93	0.80722	D	1	D;D	0.65815	0.995;0.965	P;P	0.61940	0.896;0.824	T	0.81765	-0.0783	10	0.66056	D	0.02	.	12.4734	0.55799	0.0:1.0:0.0:0.0	.	35;35	Q96AV7;Q7KYR7	.;BT2A1_HUMAN	H	35	ENSP00000312158:P35H;ENSP00000416945:P35H;ENSP00000419043:P35H	ENSP00000265424:P35H	P	+	2	0	BTN2A1	26567709	0.955000	0.32602	0.117000	0.21633	0.002000	0.02628	4.989000	0.63870	2.055000	0.61198	0.561000	0.74099	CCC	.	.	.	none		0.512	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049		A	26459730	C	A	26459730	3	1	30	1	0	0	0	0	1	0	0	0	1562	623	22	4	110	4	BTN2A1	6	26459730	Missense_Mutation	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10		26459730	144655337	40	2147											
TREML1	340205	hgsc.bcm.edu	37	chr6	41119115	41119115	+	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	ccaatcttatgggtctcttcTtcttcctctgtcaggccagg	5	15	8	13	0	6	0	1	0	5	0	8	0	7	0	3	3	0	0	3	3	2	4			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr6:41119115T>A	ENST00000426005.2	-	3	427	c.384A>T	c.(382-384)gaA>gaT	p.E128D	TREML1_ENST00000373127.4_Missense_Mutation_p.E128D|TREML1_ENST00000437044.2_Missense_Mutation_p.E17D	NM_178174.2	NP_835468.1	Q86YW5	TRML1_HUMAN	triggering receptor expressed on myeloid cells-like 1	128	Poly-Glu.				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)					GGGTCTCTTCTTCTTCCTCTG	0.512																																					p.E128D		Atlas-SNP	.											.	TREML1	20	.	0			c.A384T						PASS	.						101	91	94					6																	41119115		2203	4300	6503	SO:0001583	missense	340205	exon3			CTCTTCTTCTTCC	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.384A>T	chr6.hg19:g.41119115T>A	ENSP00000402855:p.Glu128Asp	87.0	0.0	.		75.0	35.0	.	NM_178174	Q496B3|Q8IWY1|Q8IWY2	Missense_Mutation	SNP	ENST00000426005.2	hg19	CCDS4851.1	.	.	.	.	.	.	.	.	.	.	T	4.222	0.040141	0.08148	.	.	ENSG00000161911	ENST00000373127;ENST00000437044;ENST00000426005	T;T;T	0.54479	1.55;0.57;1.69	3.39	-0.928	0.10448	.	0.826859	0.10677	N	0.646874	T	0.38746	0.1052	L	0.53249	1.67	0.09310	N	1	P;P;D	0.63880	0.476;0.608;0.993	B;B;P	0.60789	0.277;0.156;0.879	T	0.32134	-0.9918	10	0.19590	T	0.45	.	6.8523	0.24022	0.0:0.5548:0.0:0.4452	.	17;128;128	Q86YW5-3;Q86YW5;Q86YW5-2	.;TRML1_HUMAN;.	D	128;17;128	ENSP00000362219:E128D;ENSP00000400405:E17D;ENSP00000402855:E128D	ENSP00000362219:E128D	E	-	3	2	TREML1	41227093	0.000000	0.05858	0.002000	0.10522	0.016000	0.09150	-1.599000	0.02085	-0.379000	0.07906	-0.924000	0.02725	GAA	.	.	.	none		0.512	TREML1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043538.2	NM_178174		A	41119115	T	A	41119115	3	1	30	1	0	0	0	0	1	0	0	0	16484	1606	56	5	565	5	TREML1	6	41119115	Missense_Mutation	SNP	T	TCGA-5P-A9JY-01A-11D-A42J-10	14659385	41119115	129995952	41	2148											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51890829	51890829	+	Missense_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	ctggaacagtgggagcgcccGcatcgggtatctggggggct	6	7	18	10	3	1	0	0	0	1	0	2	2	1	2	1	6	2	3	1	6	2	1	rs112182862		TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr6:51890829G>A	ENST00000371117.3	-	32	4054	c.3779C>T	c.(3778-3780)gCg>gTg	p.A1260V	PKHD1_ENST00000340994.4_Missense_Mutation_p.A1260V	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1260	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)					GGGAGCGCCCGCATCGGGTAT	0.592																																					p.A1260V		Atlas-SNP	.											.	PKHD1	927	.	0			c.C3779T						PASS	.						40	42	41					6																	51890829		2203	4300	6503	SO:0001583	missense	5314	exon32			GCGCCCGCATCGG	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.3779C>T	chr6.hg19:g.51890829G>A	ENSP00000360158:p.Ala1260Val	105.0	0.0	.		77.0	25.0	.	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	G	10.03	1.239805	0.22711	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	T;T	0.77489	-1.1;-1.1	5.87	2.04	0.26737	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	1.171700	0.05986	N	0.645227	T	0.48223	0.1488	L	0.47716	1.5	0.09310	N	1	B;B	0.27316	0.145;0.175	B;B	0.19148	0.009;0.024	T	0.35919	-0.9769	10	0.38643	T	0.18	.	3.7884	0.08710	0.2374:0.0:0.452:0.3106	.	1260;1260	P08F94-2;P08F94	.;PKHD1_HUMAN	V	1260	ENSP00000360158:A1260V;ENSP00000341097:A1260V	ENSP00000341097:A1260V	A	-	2	0	PKHD1	51998788	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.611000	0.05622	0.361000	0.24292	0.655000	0.94253	GCG	.	G|0.500;A|0.500	0.500	weak		0.592	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51890829	G	A	51890829	3	1	30	1	0	0	0	0	1	0	0	0	11978	1087	38	1	8628	1	PKHD1	6	51890829	Missense_Mutation	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	10771714	51890829	119224238	42	2149											
PNRC1	10957	hgsc.bcm.edu	37	chr6	89793815	89793815	+	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	ttctcctagtgttcttccaaAgcctcctagtcactggatgg	7	14	8	12	0	3	0	1	0	2	0	6	1	5	1	4	2	1	1	4	2	3	5			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr6:89793815A>T	ENST00000336032.3	+	2	1001	c.884A>T	c.(883-885)aAg>aTg	p.K295M	PNRC1_ENST00000354922.3_Missense_Mutation_p.K110M|PNRC1_ENST00000369472.1_Missense_Mutation_p.K110M	NM_006813.2	NP_006804.1	Q12796	PNRC1_HUMAN	proline-rich nuclear receptor coactivator 1	295					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(1)|large_intestine(2)|lung(3)	6		all_cancers(76;3.64e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.102)		GTTCTTCCAAAGCCTCCTAGT	0.423										Multiple Myeloma(7;0.094)																											p.K295M		Atlas-SNP	.											.	PNRC1	17	.	0			c.A884T						PASS	.						83	85	84					6																	89793815		2203	4300	6503	SO:0001583	missense	10957	exon2			TTCCAAAGCCTCC	U03105	CCDS5018.1	6q16.1	2008-02-05	2003-09-25	2003-09-26	ENSG00000146278	ENSG00000146278			17278	protein-coding gene	gene with protein product		606714	"proline rich 2"	PROL2		7578250	Standard	NM_006813		Approved	B4-2, PRR2	uc003pmv.3	Q12796	OTTHUMG00000015191	ENST00000336032.3:c.884A>T	chr6.hg19:g.89793815A>T	ENSP00000336931:p.Lys295Met	321.0	1.0	.		251.0	105.0	.	NM_006813	B2R6Q0|E1P515|Q5T7J6|Q7Z5N0	Missense_Mutation	SNP	ENST00000336032.3	hg19	CCDS5018.1	.	.	.	.	.	.	.	.	.	.	A	17.98	3.520456	0.64747	.	.	ENSG00000146278	ENST00000369472;ENST00000336032;ENST00000354922	T;T;T	0.63744	0.1;-0.06;0.1	5.64	5.64	0.86602	.	0.048020	0.85682	D	0.000000	T	0.74680	0.3748	M	0.75777	2.31	0.51012	D	0.9999	D	0.89917	1.0	D	0.91635	0.999	T	0.79052	-0.1961	10	0.87932	D	0	-11.794	15.8451	0.78883	1.0:0.0:0.0:0.0	.	295	Q12796	PNRC1_HUMAN	M	110;295;110	ENSP00000358484:K110M;ENSP00000336931:K295M;ENSP00000347000:K110M	ENSP00000336931:K295M	K	+	2	0	PNRC1	89850534	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.453000	0.73488	2.126000	0.65437	0.533000	0.62120	AAG	.	.	.	none		0.423	PNRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041471.1	NM_006813		T	89793815	A	T	89793815	3	4	30	1	0	0	0	0	1	0	0	0	12181	72	3	5	890	5	PNRC1	6	89793815	Missense_Mutation	SNP	A	TCGA-5P-A9JY-01A-11D-A42J-10	37902986	89793815	81321252	43	2150											
SESN1	27244	hgsc.bcm.edu	37	chr6	109315799	109315799	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagggcttcaacctcaaagAaagaatcacttacctgaaga	16	8	8	9	0	3	5	3	2	0	3	3	5	3	5	2	1	2	1	2	1	6	2			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr6:109315799A>G	ENST00000356644.7	-	6	903	c.809T>C	c.(808-810)tTc>tCc	p.F270S	SESN1_ENST00000436639.2_Missense_Mutation_p.F329S|SESN1_ENST00000302071.2_Missense_Mutation_p.F204S	NM_001199933.1	NP_001186862.1	Q9Y6P5	SESN1_HUMAN	sestrin 1	270					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of cell proliferation (GO:0008285)|regulation of protein kinase B signaling (GO:0051896)|regulation of response to reactive oxygen species (GO:1901031)	nucleus (GO:0005634)				cervix(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	10		all_cancers(87;6.45e-05)|Acute lymphoblastic leukemia(125;3.55e-10)|all_hematologic(75;1.68e-07)|all_epithelial(87;0.0106)|Colorectal(196;0.0637)		Epithelial(106;0.0014)|BRCA - Breast invasive adenocarcinoma(108;0.00146)|all cancers(137;0.0031)|OV - Ovarian serous cystadenocarcinoma(136;0.0117)		AACCTCAAAGAAAGAATCACT	0.343																																					p.F329S		Atlas-SNP	.											.	SESN1	29	.	0			c.T986C						PASS	.						79	65	70					6																	109315799		2203	4300	6503	SO:0001583	missense	27244	exon6			TCAAAGAAAGAAT	AF033120	CCDS5070.1, CCDS56444.1, CCDS56445.1	6q21	2008-10-23			ENSG00000080546	ENSG00000080546			21595	protein-coding gene	gene with protein product		606103				9926927, 7938006	Standard	NM_014454		Approved	SEST1, PA26	uc003psu.3	Q9Y6P5	OTTHUMG00000015338	ENST00000356644.7:c.809T>C	chr6.hg19:g.109315799A>G	ENSP00000349061:p.Phe270Ser	91.0	0.0	.		66.0	26.0	.	NM_014454	Q2M2B7|Q5T316|Q9NV00|Q9UPD5|Q9Y6P6	Missense_Mutation	SNP	ENST00000356644.7	hg19	CCDS56445.1	.	.	.	.	.	.	.	.	.	.	A	10.30	1.312418	0.23908	.	.	ENSG00000080546	ENST00000436639;ENST00000302071;ENST00000356644	T;T;T	0.20463	2.07;2.07;2.07	5.7	4.48	0.54585	.	0.284352	0.43579	D	0.000549	T	0.01765	0.0056	N	0.01576	-0.805	0.32805	D	0.500689	B;B	0.06786	0.0;0.001	B;B	0.08055	0.001;0.003	T	0.45056	-0.9287	10	0.07175	T	0.84	-19.8022	7.1186	0.25431	0.7777:0.1489:0.0734:0.0	.	329;270	Q9Y6P5-2;Q9Y6P5	.;SESN1_HUMAN	S	329;204;270	ENSP00000393762:F329S;ENSP00000306734:F204S;ENSP00000349061:F270S	ENSP00000306734:F204S	F	-	2	0	SESN1	109422492	0.998000	0.40836	1.000000	0.80357	0.976000	0.68499	2.829000	0.48128	2.161000	0.67846	0.482000	0.46254	TTC	.	.	.	none		0.343	SESN1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041738.4	NM_014454		G	109315799	A	G	109315799	3	3	30	1	0	0	0	0	1	0	0	0	14137	246	9	3	689	3	SESN1	6	109315799	Missense_Mutation	SNP	A	TCGA-5P-A9JY-01A-11D-A42J-10	19521984	109315799	61799268	44	2151											
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138657620	138657620	+	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	cgtgtctatgacatcattgtGtagccgactcctgttctact	7	15	8	11	2	3	1	1	1	2	0	4	2	4	1	2	0	2	2	2	0	3	5			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr6:138657620G>T	ENST00000251691.4	+	34	6697	c.6531G>T	c.(6529-6531)gtG>gtT	p.V2177V		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)		ACATCATTGTGTAGCCGACTC	0.542																																					p.V2177V		Atlas-SNP	.											.	KIAA1244	236	.	0			c.G6531T						PASS	.						85	75	78					6																	138657620		2203	4300	6503	SO:0001819	synonymous_variant	57221	exon34			CATTGTGTAGCCG	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.6531G>T	chr6.hg19:g.138657620G>T		113.0	0.0	.		75.0	27.0	.	NM_020340		Silent	SNP	ENST00000251691.4	hg19	CCDS5189.2																																																																																			.	.	.	none		0.542	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		T	138657620	G	T	138657620	2	4	30	1	0	0	0	0	0	0	0	1	8224	1364	48	4		4	KIAA1244	6	138657620	Silent	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	29341821	138657620	32457447	45	2152											
C6orf35	729515	hgsc.bcm.edu	37	chr6	157739882	157739887	+	In_Frame_Del	DEL	AGCCCC	AGCCCC	-																															cccacaccatgcatacagggAgccccagcccagagctcgca																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	AGCCCC	AGCCCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr6:157739882_157739887delAGCCCC	ENST00000400788.4	-	3	355_360	c.254_259delGGGGCT	c.(253-261)tggggctcc>tcc	p.WG85del	TMEM242_ENST00000367144.4_In_Frame_Del_p.WG85del	NM_018452.4	NP_060922.2	Q9NWH2	TM242_HUMAN	transmembrane protein 242	85						integral component of membrane (GO:0016021)											GCATACAGGGAGCCCCAGCCCAGAGC	0.495																																					p.85_87del		Pindel	.											.	.	.	.	0			c.255_260del						PASS	.																																			SO:0001651	inframe_deletion	729515	exon3			.	AF217510	CCDS43519.1	6q25.3	2011-11-25	2011-11-25	2011-11-25	ENSG00000215712	ENSG00000215712			17206	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 35"	C6orf35			Standard	NM_018452		Approved	BM033	uc003sih.4	Q9NWH2	OTTHUMG00000015893	ENST00000400788.4:c.254_259delGGGGCT	chr6.hg19:g.157739882_157739887delAGCCCC	ENSP00000383594:p.Trp85_Gly86del	237.0	0.0	.		228.0	67.0	0.294	NM_018452	B9EJD0|Q9NZ88|Q9P094	In_Frame_Del	DEL	ENST00000400788.4	hg19	CCDS43519.1																																																																																			.	.	.	none		0.495	TMEM242-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042837.2			-	157739887	AGCCCC	-	157739882	7	5	30	1	0	1	0	1	0	0	0	0	2365	304	11	0	174	0	C6orf35	6	157739882	In_Frame_Del	DEL	AGCCCC	TCGA-5P-A9JY-01A-11D-A42J-10	19082262	157739882	13375185	46	2153											
SP8	221833	hgsc.bcm.edu	37	chr7	20824956	20824956	+	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	gaggagccgccgccgccgccCccgccgccgccgccgctgcc	2	1	14	24	9	0	0	0	0	0	0	0	2	0	1	11	1	2	1	11	1	0	0	rs201180283		TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	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	chr7.hg19:g.20824956C>G		85.0	0.0	.		154.0	13.0	.	NM_182700	Q7Z615|Q7Z616|Q96MJ1	Silent	SNP	ENST00000361443.4	hg19	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	30	1	0	0	0	0	0	0	0	1	14983	610	22	4		4	SP8	7	20824956	Silent	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10		20824956	138313707	47	2154											
CYP51A1	1595	hgsc.bcm.edu	37	chr7	91761140	91761140	+	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	gacttttcccaaatgctatgGcatgcccaaggaatggaatt	12	11	9	9	0	0	0	0	0	0	0	1	3	1	2	2	3	2	2	2	3	5	4			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr7:91761140G>T	ENST00000003100.8	-	2	404	c.239C>A	c.(238-240)gCc>gAc	p.A80D	LRRD1_ENST00000422722.1_5'UTR|CTB-161K23.1_ENST00000453068.1_RNA|CYP51A1_ENST00000450723.1_5'UTR	NM_000786.3	NP_000777.1	Q16850	CP51A_HUMAN	cytochrome P450, family 51, subfamily A, polypeptide 1	74					cholesterol biosynthetic process (GO:0006695)|cholesterol biosynthetic process via 24,25-dihydrolanosterol (GO:0033488)|demethylation (GO:0070988)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|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)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|sterol 14-demethylase activity (GO:0008398)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|skin(1)	10	all_cancers(62;2.16e-09)|all_epithelial(64;3.86e-08)|Breast(17;0.00206)|all_lung(186;0.169)|all_hematologic(106;0.215)|Lung NSC(181;0.227)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)		Itraconazole(DB01167)|Ketoconazole(DB01026)|Sertaconazole(DB01153)|Tioconazole(DB01007)	AAATGCTATGGCATGCCCAAG	0.323																																					p.A80D	GBM(70;1100 1190 11592 25836 51397)	Atlas-SNP	.											.	CYP51A1	30	.	0			c.C239A						PASS	.						46	47	47					7																	91761140		2203	4298	6501	SO:0001583	missense	1595	exon2			GCTATGGCATGCC	U51685	CCDS5623.1, CCDS55123.1	7q21.2	2012-10-10	2003-02-14	2003-02-28	ENSG00000001630	ENSG00000001630		"Cytochrome P450s"	2649	protein-coding gene	gene with protein product		601637	"cytochrome P450, 51 (lanosterol 14-alpha-demethylase)"	CYP51		8975714	Standard	NM_000786		Approved	CP51, CYPL1, P450L1, LDM, P450-14DM	uc003ulm.4	Q16850	OTTHUMG00000131131	ENST00000003100.8:c.239C>A	chr7.hg19:g.91761140G>T	ENSP00000003100:p.Ala80Asp	446.0	1.0	.		569.0	183.0	.	NM_000786	A4D1F8|B2RAI4|B4DJ55|O00770|O00772|Q16784|Q8N1A8|Q99868	Missense_Mutation	SNP	ENST00000003100.8	hg19	CCDS5623.1	.	.	.	.	.	.	.	.	.	.	G	33	5.213546	0.95069	.	.	ENSG00000001630	ENST00000003100;ENST00000496998;ENST00000435873	T	0.70399	-0.48	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	D	0.86356	0.5913	M	0.90198	3.095	0.80722	D	1	D;D	0.69078	0.996;0.997	P;P	0.62491	0.87;0.903	D	0.89062	0.3463	10	0.72032	D	0.01	.	19.1465	0.93471	0.0:0.0:1.0:0.0	.	20;74	B3KRC6;Q16850	.;CP51A_HUMAN	D	80;20;24	ENSP00000003100:A80D	ENSP00000003100:A80D	A	-	2	0	CYP51A1	91599076	1.000000	0.71417	0.973000	0.42090	0.998000	0.95712	9.062000	0.93920	2.584000	0.87258	0.650000	0.86243	GCC	.	.	.	none		0.323	CYP51A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253812.4			T	91761140	G	T	91761140	3	4	30	1	0	0	0	0	1	0	0	0	4197	1203	42	4	1326	4	CYP51A1	7	91761140	Missense_Mutation	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	70936184	91761140	67377523	48	2155											
LAMB4	22798	hgsc.bcm.edu	37	chr7	107746348	107746348	+	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	attgcaaaagcagcttccccGaacaatcatctcgtacagag	14	8	7	12	2	2	1	1	0	1	1	4	2	3	1	2	0	5	4	2	0	5	3			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr7:107746348G>A	ENST00000388781.3	-	8	867	c.784C>T	c.(784-786)Cgg>Tgg	p.R262W	LAMB4_ENST00000418464.1_Missense_Mutation_p.R262W|LAMB4_ENST00000388780.3_Missense_Mutation_p.R262W|LAMB4_ENST00000414450.2_Missense_Mutation_p.R262W|LAMB4_ENST00000205386.4_Missense_Mutation_p.R262W	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	262	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				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						CAGCTTCCCCGAACAATCATC	0.468																																					p.R262W		Atlas-SNP	.											LAMB4,colon,carcinoma,0,3	LAMB4	253	.	0			c.C784T						PASS	.						128	111	117					7																	107746348		2203	4300	6503	SO:0001583	missense	22798	exon8			TTCCCCGAACAAT	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.784C>T	chr7.hg19:g.107746348G>A	ENSP00000373433:p.Arg262Trp	100.0	0.0	.		127.0	78.0	.	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	hg19	CCDS34732.1	.	.	.	.	.	.	.	.	.	.	G	17.45	3.393627	0.62066	.	.	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000388780;ENST00000418464;ENST00000414450	T;T;T;T;T	0.78364	-1.17;-1.17;-1.17;-1.17;-1.17	4.87	2.02	0.26589	Laminin, N-terminal (3);	0.488989	0.17139	N	0.185530	T	0.81772	0.4893	M	0.83384	2.64	0.39988	D	0.975007	D	0.65815	0.995	P	0.55011	0.766	T	0.78209	-0.2293	10	0.56958	D	0.05	.	3.4717	0.07570	0.1456:0.1338:0.5824:0.1382	.	262	A4D0S4	LAMB4_HUMAN	W	262	ENSP00000205386:R262W;ENSP00000373433:R262W;ENSP00000373432:R262W;ENSP00000402353:R262W;ENSP00000402265:R262W	ENSP00000205386:R262W	R	-	1	2	LAMB4	107533584	0.000000	0.05858	0.024000	0.17045	0.951000	0.60555	0.673000	0.25203	0.233000	0.21120	0.655000	0.94253	CGG	.	.	.	none		0.468	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		A	107746348	G	A	107746348	3	1	30	1	0	0	0	0	1	0	0	0	8620	1057	37	1	4609	1	LAMB4	7	107746348	Missense_Mutation	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	15985208	107746348	51392315	49	2156											
DNAJB9	4189	hgsc.bcm.edu	37	chr7	108213747	108213747	+	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	agcactgcaggactgtcactCaacgaagaggaaatatggtt	14	8	11	8	1	2	1	2	0	0	1	2	4	2	3	0	3	3	3	0	3	4	2			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr7:108213747C>T	ENST00000249356.3	+	3	1168	c.622C>T	c.(622-624)Caa>Taa	p.Q208*	DNAJB9_ENST00000465725.1_Intron	NM_012328.2	NP_036460.1	Q9UBS3	DNJB9_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 9	208					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						GACTGTCACTCAACGAAGAGG	0.378																																					p.Q208X		Atlas-SNP	.											.	DNAJB9	25	.	0			c.C622T						PASS	.						103	102	102					7																	108213747		2203	4300	6503	SO:0001587	stop_gained	4189	exon3			GTCACTCAACGAA	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.622C>T	chr7.hg19:g.108213747C>T	ENSP00000249356:p.Gln208*	62.0	0.0	.		83.0	20.0	.	NM_012328		Nonsense_Mutation	SNP	ENST00000249356.3	hg19	CCDS5752.1	.	.	.	.	.	.	.	.	.	.	C	41	8.877952	0.98988	.	.	ENSG00000128590	ENST00000249356	.	.	.	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.1901	0.93663	0.0:1.0:0.0:0.0	.	.	.	.	X	208	.	.	Q	+	1	0	DNAJB9	108000983	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	7.377000	0.79668	2.776000	0.95493	0.655000	0.94253	CAA	.	.	.	none		0.378	DNAJB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337414.1			T	108213747	C	T	108213747	4	4	30	1	0	0	0	0	0	1	0	0	4629	827	29	2	628	2	DNAJB9	7	108213747	Nonsense_Mutation	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10	467399	108213747	50924916	50	2157											
SLC10A5	347051	hgsc.bcm.edu	37	chr8	82606176	82606176	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaaacagcaaacccaaagcAggaactaagagacccaacag	20	1	7	13	0	0	1	0	0	0	1	0	3	0	2	3	1	6	2	3	1	6	1			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr8:82606176A>G	ENST00000518568.1	-	1	2233	c.1032T>C	c.(1030-1032)ccT>ccC	p.P344P		NM_001010893.2	NP_001010893.1	Q5PT55	NTCP5_HUMAN	solute carrier family 10, member 5	344						integral component of membrane (GO:0016021)	bile acid:sodium symporter activity (GO:0008508)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)	15						AACCCAAAGCAGGAACTAAGA	0.363																																					p.P344P		Atlas-SNP	.											.	SLC10A5	35	.	0			c.T1032C						PASS	.						64	65	65					8																	82606176		2203	4300	6503	SO:0001819	synonymous_variant	347051	exon1			CAAAGCAGGAACT		CCDS34915.1	8q21.13	2013-07-18	2013-07-18		ENSG00000253598	ENSG00000253598		"Solute carriers"	22981	protein-coding gene	gene with protein product							Standard	NM_001010893		Approved		uc011lfs.2	Q5PT55	OTTHUMG00000164683	ENST00000518568.1:c.1032T>C	chr8.hg19:g.82606176A>G		112.0	0.0	.		68.0	36.0	.	NM_001010893	B2RN26	Silent	SNP	ENST00000518568.1	hg19	CCDS34915.1																																																																																			.	.	.	none		0.363	SLC10A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379736.1	XM_294493		G	82606176	A	G	82606176	2	3	30	1	0	0	0	0	0	0	0	1	14390	175	7	3		3	SLC10A5	8	82606176	Silent	SNP	A	TCGA-5P-A9JY-01A-11D-A42J-10		82606176	63757846	51	2158											
ZFAT	57623	hgsc.bcm.edu	37	chr8	135614212	135614212	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgagaatgcaggtctgaggAggagaccacggtggtttcca	10	9	15	7	1	1	3	0	2	1	2	2	6	2	4	2	5	1	2	2	5	1	2			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr8:135614212A>G	ENST00000377838.3	-	6	1924	c.1750T>C	c.(1750-1752)Tcc>Ccc	p.S584P	ZFAT_ENST00000520214.1_Missense_Mutation_p.S572P|ZFAT_ENST00000429442.2_Missense_Mutation_p.S572P|ZFAT_ENST00000523399.1_Missense_Mutation_p.S522P|ZFAT_ENST00000520356.1_Missense_Mutation_p.S572P|ZFAT_ENST00000520727.1_Missense_Mutation_p.S572P|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	584					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)			AGGTCTGAGGAGGAGACCACG	0.587																																					p.S584P		Atlas-SNP	.											.	ZFAT	265	.	0			c.T1750C						PASS	.						30	31	31					8																	135614212		1926	4131	6057	SO:0001583	missense	57623	exon6			CTGAGGAGGAGAC	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.1750T>C	chr8.hg19:g.135614212A>G	ENSP00000367069:p.Ser584Pro	46.0	0.0	.		62.0	35.0	.	NM_020863	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Missense_Mutation	SNP	ENST00000377838.3	hg19	CCDS47924.1	.	.	.	.	.	.	.	.	.	.	A	2.258	-0.369941	0.05069	.	.	ENSG00000066827	ENST00000520356;ENST00000520727;ENST00000429442;ENST00000377838;ENST00000520214;ENST00000318135;ENST00000523399;ENST00000398946	T;T;T;T;T;T	0.09723	3.02;2.95;2.96;2.95;2.95;2.96	5.28	0.00147	0.14046	.	0.688237	0.13587	N	0.376881	T	0.09905	0.0243	L	0.27053	0.805	0.09310	N	1	B;P;D;B	0.53151	0.393;0.901;0.958;0.165	B;P;P;B	0.51229	0.163;0.447;0.663;0.059	T	0.21245	-1.0251	10	0.44086	T	0.13	-0.6841	4.3929	0.11350	0.4893:0.3331:0.1776:0.0	.	522;572;572;584	E9PER3;E9PBN4;Q9P243-3;Q9P243	.;.;.;ZFAT_HUMAN	P	572;572;572;584;572;471;522;572	ENSP00000427879:S572P;ENSP00000427831:S572P;ENSP00000394501:S572P;ENSP00000367069:S584P;ENSP00000428483:S572P;ENSP00000429091:S522P	ENSP00000326997:S471P	S	-	1	0	ZFAT	135683394	0.000000	0.05858	0.003000	0.11579	0.081000	0.17604	-1.550000	0.02180	-0.116000	0.11893	0.533000	0.62120	TCC	.	.	.	none		0.587	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939		G	135614212	A	G	135614212	3	3	30	1	0	0	0	0	1	0	0	0	17644	304	11	3	2025	3	ZFAT	8	135614212	Missense_Mutation	SNP	A	TCGA-5P-A9JY-01A-11D-A42J-10	53008036	135614212	10749810	52	2159											
EPPK1	83481	hgsc.bcm.edu	37	chr8	144947044	144947044	+	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	agggccagcttctcaccgccGtaggggtcaggatagcccgt	7	7	14	13	3	2	0	2	0	1	0	3	1	2	1	4	4	2	2	4	4	2	3	rs377574983	byFrequency	TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr8:144947044G>T	ENST00000525985.1	-	2	449	c.378C>A	c.(376-378)taC>taA	p.Y126*				P58107	EPIPL_HUMAN	epiplakin 1	126						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)			TCTCACCGCCGTAGGGGTCAG	0.667																																					p.Y126X		Atlas-SNP	.											EPPK1,bladder,carcinoma,0,1	EPPK1	199	.	0			c.C378A						PASS	.						28	33	31					8																	144947044		2024	4180	6204	SO:0001587	stop_gained	83481	exon1			ACCGCCGTAGGGG	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.378C>A	chr8.hg19:g.144947044G>T	ENSP00000436337:p.Tyr126*	136.0	0.0	.		139.0	60.0	.	NM_031308	Q76E58|Q9NSU9	Nonsense_Mutation	SNP	ENST00000525985.1	hg19		.	.	.	.	.	.	.	.	.	.	G	12.45	1.940545	0.34283	.	.	ENSG00000227184	ENST00000525985	.	.	.	4.44	-7.55	0.01327	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.0392	0.71774	0.2859:0.0:0.7141:0.0	.	.	.	.	X	126	.	ENSP00000436337:Y126X	Y	-	3	2	EPPK1	145019032	0.803000	0.28956	0.591000	0.28745	0.074000	0.17049	-0.097000	0.11042	-1.541000	0.01727	-0.481000	0.04817	TAC	.	.	.	alt		0.667	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		T	144947044	G	T	144947044	4	4	30	1	0	0	0	0	0	1	0	0	5192	1140	40	4	6888	4	EPPK1	8	144947044	Nonsense_Mutation	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	9332832	144947044	1416978	53	2160											
DDX58	23586	hgsc.bcm.edu	37	chr9	32467857	32467857	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccttcatcagcaactgaggtGgcaatcagaatattgtgatc	12	11	9	9	0	3	3	3	2	0	1	4	3	3	3	1	2	2	2	1	2	4	3			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr9:32467857G>A	ENST00000379883.2	-	15	2245	c.2088C>T	c.(2086-2088)gcC>gcT	p.A696A	DDX58_ENST00000542096.1_Silent_p.A625A|DDX58_ENST00000379868.1_Silent_p.A493A|DDX58_ENST00000545044.1_Silent_p.A493A|DDX58_ENST00000379882.1_Silent_p.A651A	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	696	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.|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)		CAACTGAGGTGGCAATCAGAA	0.438																																					p.A696A		Atlas-SNP	.											.	DDX58	82	.	0			c.C2088T						PASS	.						178	151	160					9																	32467857		2203	4300	6503	SO:0001819	synonymous_variant	23586	exon15			TGAGGTGGCAATC	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.2088C>T	chr9.hg19:g.32467857G>A		107.0	0.0	.		136.0	61.0	.	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Silent	SNP	ENST00000379883.2	hg19	CCDS6526.1																																																																																			.	.	.	none		0.438	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314		A	32467857	G	A	32467857	2	1	30	1	0	0	0	0	0	0	0	1	4377	1335	47	2		2	DDX58	9	32467857	Silent	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10		32467857	108745574	54	2161											
RUSC2	9853	hgsc.bcm.edu	37	chr9	35548396	35548396	+	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	caggtctgtcagggaccccaCtccagtgagatgcctcctgc	7	8	11	15	0	2	1	1	1	1	1	4	3	4	2	5	2	2	0	5	2	0	0			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr9:35548396C>A	ENST00000455600.1	+	2	2447	c.1878C>A	c.(1876-1878)caC>caA	p.H626Q		NM_001135999.1	NP_001129471	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	626						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)	Rab GTPase binding (GO:0017137)			NS(1)|breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(4)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)			AGGGACCCCACTCCAGTGAGA	0.647																																					p.H626Q		Atlas-SNP	.											.	RUSC2	88	.	0			c.C1878A						PASS	.						52	49	50					9																	35548396		2203	4300	6503	SO:0001583	missense	9853	exon2			ACCCCACTCCAGT	AB002373	CCDS35008.1	9p13.2	2003-12-02			ENSG00000198853	ENSG00000198853			23625	protein-coding gene	gene with protein product		611053				9205841	Standard	NM_001135999		Approved	KIAA0375	uc003zww.3	Q8N2Y8	OTTHUMG00000019861	ENST00000455600.1:c.1878C>A	chr9.hg19:g.35548396C>A	ENSP00000393922:p.His626Gln	57.0	0.0	.		47.0	17.0	.	NM_014806	A2RU62|A7E2A9|O15080|Q5W134|Q641Q6|Q6P1W7	Missense_Mutation	SNP	ENST00000455600.1	hg19	CCDS35008.1	.	.	.	.	.	.	.	.	.	.	C	10.24	1.294418	0.23564	.	.	ENSG00000198853	ENST00000361226;ENST00000455600;ENST00000543478	T;T	0.20200	2.09;2.09	5.86	1.69	0.24217	.	0.421346	0.23941	N	0.043043	T	0.04679	0.0127	N	0.01874	-0.695	0.21782	N	0.999545	B	0.02656	0.0	B	0.01281	0.0	T	0.38134	-0.9675	10	0.02654	T	1	-3.2088	1.9507	0.03366	0.2064:0.1172:0.4682:0.2082	.	626	Q8N2Y8	RUSC2_HUMAN	Q	626	ENSP00000355177:H626Q;ENSP00000393922:H626Q	ENSP00000355177:H626Q	H	+	3	2	RUSC2	35538396	0.024000	0.19004	1.000000	0.80357	0.905000	0.53344	0.124000	0.15728	0.823000	0.34589	-0.165000	0.13383	CAC	.	.	.	none		0.647	RUSC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052309.1	XM_048462		A	35548396	C	A	35548396	3	1	30	1	0	0	0	0	1	0	0	0	13764	564	20	4	1880	4	RUSC2	9	35548396	Missense_Mutation	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10	3080539	35548396	105665035	55	2162											
IKBKAP	8518	hgsc.bcm.edu	37	chr9	111642434	111642434	+	Frame_Shift_Del	DEL	A	A	-																															agagtccagaaatgccatatAatttttctgggctggagatg																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr9:111642434delA	ENST00000374647.5	-	32	3665	c.3358delT	c.(3358-3360)tatfs	p.Y1120fs	IKBKAP_ENST00000467959.1_5'UTR|IKBKAP_ENST00000537196.1_Frame_Shift_Del_p.Y771fs	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	1120					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						AATGCCATATAATTTTTCTGG	0.453																																					p.Y1120fs		Atlas-Indel,Pindel	.											.	IKBKAP	122	.	0			c.3359delA						PASS	.						100	99	99					9																	111642434		2203	4300	6503	SO:0001589	frameshift_variant	8518	exon32			.	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.3358delT	chr9.hg19:g.111642434delA	ENSP00000363779:p.Tyr1120fs	110.0	0.0	0		105.0	49.0	0.466667	NM_003640	Q5JSV2|Q9H327|Q9UG87	Frame_Shift_Del	DEL	ENST00000374647.5	hg19	CCDS6773.1																																																																																			.	.	.	none		0.453	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1			-	111642434	A	-	111642434	7	5	30	1	0	1	0	1	0	0	0	0	7617	362	13	0	664	0	IKBKAP	9	111642434	Frame_Shift_Del	DEL	A	TCGA-5P-A9JY-01A-11D-A42J-10	76094038	111642434	29570997	56	2163											
CEL	1056	hgsc.bcm.edu	37	chr9	135939799	135939799	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctccctcgcagctgggcgcCgtgtacacagaaggtgggtt	6	9	14	12	3	1	1	0	0	1	1	3	1	1	1	2	3	2	4	2	3	2	2			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr9:135939799C>T	ENST00000372080.4	+	2	100	c.84C>T	c.(82-84)gcC>gcT	p.A28A	CEL_ENST00000351304.7_Silent_p.A25A	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	25	Heparin-binding.				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)		AGCTGGGCGCCGTGTACACAG	0.647																																					p.A28A		Atlas-SNP	.											.	CEL	71	.	0			c.C84T						PASS	.						60	69	66					9																	135939799		2074	4198	6272	SO:0001819	synonymous_variant	1056	exon2			GGGCGCCGTGTAC	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.84C>T	chr9.hg19:g.135939799C>T		66.0	0.0	.		74.0	5.0	.	NM_001807	Q16398|Q5T7U7|Q9UCH1|Q9UP41	Silent	SNP	ENST00000372080.4	hg19	CCDS43896.1																																																																																			.	.	.	none		0.647	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1			T	135939799	C	T	135939799	2	4	30	1	0	0	0	0	0	0	0	1	3211	639	23	1		1	CEL	9	135939799	Silent	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10	24297365	135939799	5273632	57	2164											
MAN1B1	11253	hgsc.bcm.edu	37	chr9	139996055	139996055	+	Frame_Shift_Del	DEL	G	G	-																															tggacctccgacagcactgtGgccgaggtgaccagcattca																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr9:139996055delG	ENST00000371589.4	+	8	1258	c.1185delG	c.(1183-1185)gtgfs	p.V395fs	MAN1B1_ENST00000474902.1_Frame_Shift_Del_p.V98fs	NM_016219.4	NP_057303.2	Q9UKM7	MA1B1_HUMAN	mannosidase, alpha, class 1B, member 1	395					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)		ACAGCACTGTGGCCGAGGTGA	0.577																																					p.V395fs		Atlas-Indel,Pindel	.											.	MAN1B1	40	.	0			c.1184delT						PASS	.						53	49	50					9																	139996055		2203	4300	6503	SO:0001589	frameshift_variant	11253	exon8			.	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.1185delG	chr9.hg19:g.139996055delG	ENSP00000360645:p.Val395fs	87.0	0.0	0		81.0	32.0	0.395062	NM_016219	Q5VSG3|Q9BRS9|Q9Y5K7	Frame_Shift_Del	DEL	ENST00000371589.4	hg19	CCDS7029.1																																																																																			.	.	.	none		0.577	MAN1B1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055294.2	NM_016219		-	139996055	G	-	139996055	7	5	30	1	0	1	0	1	0	0	0	0	9219	1335	47	0	1215	0	MAN1B1	9	139996055	Frame_Shift_Del	DEL	G	TCGA-5P-A9JY-01A-11D-A42J-10	4056256	139996055	1217376	58	2165											
CACNA1B	774	hgsc.bcm.edu	37	chr9	141016005	141016005	+	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	gtgggcggaggcagctccccCagacgcccctgactccccgc	5	4	13	19	3	0	2	0	1	0	1	2	3	2	3	6	3	1	2	6	3	0	0			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr9:141016005C>T	ENST00000371372.1	+	47	6719	c.6574C>T	c.(6574-6576)Cag>Tag	p.Q2192*	CACNA1B_ENST00000371355.4_Nonsense_Mutation_p.Q2193*|CACNA1B_ENST00000277549.5_Nonsense_Mutation_p.Q1386*|CACNA1B_ENST00000277551.2_Intron|CACNA1B_ENST00000371357.1_Nonsense_Mutation_p.Q2191*|CACNA1B_ENST00000371363.1_Nonsense_Mutation_p.Q2190*	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	2192					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	GCAGCTCCCCCAGACGCCCCT	0.657																																					p.Q2192X		Atlas-SNP	.											.	CACNA1B	266	.	0			c.C6574T						PASS	.						29	34	32					9																	141016005		1959	4128	6087	SO:0001587	stop_gained	774	exon46			CTCCCCCAGACGC	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.6574C>T	chr9.hg19:g.141016005C>T	ENSP00000360423:p.Gln2192*	93.0	0.0	.		73.0	34.0	.	NM_000718	B1AQK5	Nonsense_Mutation	SNP	ENST00000371372.1	hg19	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	C	56	26.872562	0.99970	.	.	ENSG00000148408	ENST00000371372;ENST00000277549;ENST00000371363;ENST00000371357;ENST00000371355	.	.	.	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	.	18.2603	0.90033	0.0:1.0:0.0:0.0	.	.	.	.	X	2192;1386;2190;2191;2193	.	ENSP00000277549:Q1386X	Q	+	1	0	CACNA1B	140135826	1.000000	0.71417	1.000000	0.80357	0.490000	0.33462	7.220000	0.78008	2.315000	0.78130	0.555000	0.69702	CAG	.	.	.	none		0.657	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		T	141016005	C	T	141016005	4	4	30	1	0	0	0	0	0	1	0	0	2541	595	21	2	6756	2	CACNA1B	9	141016005	Nonsense_Mutation	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10	1019950	141016005	197426	59	2166											
PITRM1	10531	hgsc.bcm.edu	37	chr10	3193438	3193438	+	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	aagcgtagcgttcacagtgaCctgtcaggaccacgtccaac	11	7	10	13	3	2	1	2	1	0	0	3	2	3	2	3	1	3	2	3	1	3	2			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr10:3193438C>G	ENST00000224949.4	-	15	1773		c.e15+1		PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000380989.2_Splice_Site|PITRM1-AS1_ENST00000601046.1_RNA|PITRM1_ENST00000451104.2_Splice_Site|PITRM1_ENST00000380994.1_Splice_Site|PITRM1_ENST00000464395.1_5'Flank			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1						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						TTCACAGTGACCTGTCAGGAC	0.502																																					.		Atlas-SNP	.											.	PITRM1	109	.	0			c.1738+1G>C						PASS	.						53	51	52					10																	3193438		1924	4123	6047	SO:0001630	splice_region_variant	10531	exon16			CAGTGACCTGTCA	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.1738+1G>C	chr10.hg19:g.3193438C>G		145.0	0.0	.		121.0	60.0	.	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Splice_Site	SNP	ENST00000224949.4	hg19	CCDS59208.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	14.12|14.12	2.441743|2.441743	0.43326|0.43326	.|.	.|.	ENSG00000107959|ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000380994;ENST00000451104|ENST00000430362	.|.	.|.	.|.	5.67|5.67	5.67|5.67	0.87782|0.87782	.|.	.|.	.|.	.|.	.|.	.|T	.|0.76543	.|0.4002	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.74581	.|-0.3618	.|4	.|.	.|.	.|.	.|.	19.7539|19.7539	0.96283|0.96283	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	.|S	-1|216	.|.	.|.	.|R	-|-	.|3	.|2	PITRM1|PITRM1	3183438|3183438	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.152000|0.152000	0.21847|0.21847	5.524000|5.524000	0.67105|0.67105	2.668000|2.668000	0.90789|0.90789	0.561000|0.561000	0.74099|0.74099	.|AGG	.	.	.	none		0.502	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		Intron	G	3193438	C	G	3193438	5	3	30	1	0	0	0	0	0	0	1	0	11960	521	18	4	1426	4	PITRM1	10	3193438	Splice_Site	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10		3193438	132341309	60	2167											
C10orf68	79741	hgsc.bcm.edu	37	chr10	33017895	33017895	+	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	tccaaatgcaagaaaagaaaCaaataaattctggagtggaa	21	7	8	5	0	1	2	0	0	1	2	2	4	2	4	1	2	2	1	1	2	9	2	rs202220321	byFrequency	TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr10:33017895C>G	ENST00000375030.2	+	12	1312	c.694C>G	c.(694-696)Caa>Gaa	p.Q232E	C10orf68_ENST00000375028.3_Missense_Mutation_p.Q200E|C10orf68_ENST00000375025.4_Missense_Mutation_p.Q224E			Q9H943	CJ068_HUMAN		224										breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(4)	29						AGAAAAGAAACAAATAAATTC	0.294																																					p.Q224E		Atlas-SNP	.											.	C10orf68	75	.	0			c.C670G						PASS	.						57	57	57					10																	33017895		2202	4296	6498	SO:0001583	missense	79741	exon9			AAGAAACAAATAA																												ENST00000375030.2:c.694C>G	chr10.hg19:g.33017895C>G	ENSP00000364170:p.Gln232Glu	348.0	0.0	.		304.0	31.0	.	NM_024688	B0QZ71|Q08AN7|Q8N7T7	Missense_Mutation	SNP	ENST00000375030.2	hg19		.	.	.	.	.	.	.	.	.	.	.	10.24	1.294784	0.23564	.	.	ENSG00000150076	ENST00000302316;ENST00000375030;ENST00000375028;ENST00000375025;ENST00000375037	T;T;T;T	0.27720	1.68;1.65;1.67;1.67	2.21	0.181	0.15073	.	.	.	.	.	T	0.29256	0.0728	L	0.44542	1.39	0.09310	N	1	P;B;P;B	0.43578	0.811;0.039;0.811;0.039	P;B;P;B	0.54924	0.764;0.058;0.764;0.058	T	0.18681	-1.0329	9	0.02654	T	1	.	4.3059	0.10947	0.2495:0.4698:0.2806:0.0	.	141;224;200;232	B4DX58;Q9H943;A2A3B4;A2A3D6	.;CJ068_HUMAN;.;.	E	224;232;200;224;172	ENSP00000303710:Q224E;ENSP00000364170:Q232E;ENSP00000364168:Q200E;ENSP00000364165:Q224E	ENSP00000303710:Q224E	Q	+	1	0	C10orf68	33057901	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.391000	0.07323	0.028000	0.15324	-0.324000	0.08512	CAA	.	.	.	none		0.294	C10orf68-001	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000313999.2			G	33017895	C	G	33017895	3	3	30	1	0	0	0	0	1	0	0	0	1615	479	17	4	696	4	C10orf68	10	33017895	Missense_Mutation	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10	29824457	33017895	102516852	61	2168											
FAM21C	253725	hgsc.bcm.edu	37	chr10	46264959	46264959	+	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	gacagcaggtctaaaggagaAcccagggattctgggaccct	12	6	13	10	0	2	1	0	0	2	1	2	5	2	3	2	4	2	1	2	4	3	2			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr10:46264959A>T	ENST00000336378.4	+	20	2044	c.1926A>T	c.(1924-1926)gaA>gaT	p.E642D	FAM21C_ENST00000537517.1_Missense_Mutation_p.E620D|FAM21C_ENST00000540872.1_Missense_Mutation_p.E644D|FAM21C_ENST00000374362.2_Missense_Mutation_p.E644D|FAM21C_ENST00000359860.4_Missense_Mutation_p.E586D	NM_015262.2	NP_056077.2	Q9Y4E1	FA21C_HUMAN	family with sequence similarity 21, member C	642					retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome (GO:0005768)|plasma membrane (GO:0005886)|WASH complex (GO:0071203)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						CTAAAGGAGAACCCAGGGATT	0.458																																					p.E644D		Atlas-SNP	.											FAM21C,NS,carcinoma,0,1	FAM21C	68	.	0			c.A1932T						PASS	.						14	14	14					10																	46264959		1412	3417	4829	SO:0001583	missense	253725	exon20			AGGAGAACCCAGG		CCDS44374.1, CCDS44374.2, CCDS53528.1, CCDS53529.1	10q11.22	2014-05-09			ENSG00000172661	ENSG00000172661			23414	protein-coding gene	gene with protein product		613631				20498093	Standard	NM_015262		Approved	Em:AC012044.3, KIAA0592	uc001jcu.3	Q9Y4E1	OTTHUMG00000018089	ENST00000336378.4:c.1926A>T	chr10.hg19:g.46264959A>T	ENSP00000337541:p.Glu642Asp	546.0	0.0	.		474.0	168.0	.	NM_015262	B4DZQ6|B9EK53|F5H0J6|F5H871|Q5SQU4|Q5SQU5|Q7L521|Q9UG79	Missense_Mutation	SNP	ENST00000336378.4	hg19		.	.	.	.	.	.	.	.	.	.	A	5.187	0.220030	0.09863	.	.	ENSG00000172661	ENST00000336378;ENST00000540872;ENST00000537517;ENST00000374362;ENST00000399588;ENST00000359860;ENST00000436993	.	.	.	3.08	0.225	0.15325	.	0.636826	0.15981	N	0.235294	T	0.24774	0.0601	L	0.41824	1.3	0.09310	N	0.999993	P;B;B;B	0.43169	0.8;0.013;0.013;0.099	B;B;B;B	0.43331	0.416;0.014;0.014;0.041	T	0.16928	-1.0386	9	0.12766	T	0.61	-5.5005	4.9224	0.13876	0.5671:0.0:0.4329:0.0	.	620;644;642;587	F5H871;Q9Y4E1-4;Q9Y4E1;Q9Y4E1-3	.;.;FA21C_HUMAN;.	D	642;644;620;644;644;586;556	.	ENSP00000337541:E642D	E	+	3	2	FAM21C	45584965	0.420000	0.25457	0.108000	0.21378	0.396000	0.30629	0.238000	0.18004	-0.046000	0.13446	0.448000	0.29417	GAA	.	.	.	none		0.458	FAM21C-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding				T	46264959	A	T	46264959	3	4	30	1	0	0	0	0	1	0	0	0	5546	40	2	5	2010	5	FAM21C	10	46264959	Missense_Mutation	SNP	A	TCGA-5P-A9JY-01A-11D-A42J-10	13247064	46264959	89269788	62	2169											
C10orf71	118461	hgsc.bcm.edu	37	chr10	50532215	50532217	+	In_Frame_Del	DEL	TCA	TCA	-																															agaacctgtgagcaacggtgTcatcctccccaatgggcttg																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	TCA	TCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr10:50532215_50532217delTCA	ENST00000374144.3	+	3	1913_1915	c.1625_1627delTCA	c.(1624-1629)gtcatc>gtc	p.I543del	C10orf71_ENST00000323868.4_In_Frame_Del_p.I543del			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	543										endometrium(1)	1						AGCAACGGTGTCATCCTCCCCAA	0.498																																					p.542_542del		Atlas-Indel,Pindel	.											.	C10orf71	179	.	0			c.1624_1626del						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.1625_1627delTCA	chr10.hg19:g.50532215_50532217delTCA	ENSP00000363259:p.Ile543del	150.0	0.0	0		109.0	41.0	0.376147	NM_001135196	A0AVL8	In_Frame_Del	DEL	ENST00000374144.3	hg19	CCDS44387.1																																																																																			.	.	.	none		0.498	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459		-	50532217	TCA	-	50532215	7	5	30	1	0	1	0	1	0	0	0	0	1616	1667	58	0	1627	0	C10orf71	10	50532215	In_Frame_Del	DEL	TCA	TCGA-5P-A9JY-01A-11D-A42J-10	4267256	50532215	85002532	63	2170											
CDK1	983	hgsc.bcm.edu	37	chr10	62551998	62551998	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caaatggaaaccaggaagccTagcatcccatgtcaaaaact	17	6	7	11	0	1	0	1	0	0	0	2	2	2	2	3	2	4	1	3	2	6	1			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr10:62551998T>C	ENST00000395284.3	+	7	888	c.746T>C	c.(745-747)cTa>cCa	p.L249P	CDK1_ENST00000316629.4_Missense_Mutation_p.L192P|CDK1_ENST00000373809.2_Missense_Mutation_p.L192P|CDK1_ENST00000448257.2_Missense_Mutation_p.L249P	NM_001786.4	NP_001777.1	P06493	CDK1_HUMAN	cyclin-dependent kinase 1	249	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell aging (GO:0007569)|cell migration (GO:0016477)|cellular response to hydrogen peroxide (GO:0070301)|centrosome cycle (GO:0007098)|chromosome condensation (GO:0030261)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell differentiation (GO:0030855)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|MAPK cascade (GO:0000165)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|mitotic G2 DNA damage checkpoint (GO:0007095)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ regeneration (GO:0031100)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|pronuclear fusion (GO:0007344)|protein complex assembly (GO:0006461)|protein localization to kinetochore (GO:0034501)|Ras protein signal transduction (GO:0007265)|regulation of embryonic development (GO:0045995)|regulation of Schwann cell differentiation (GO:0014038)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to activity (GO:0014823)|response to amine (GO:0014075)|response to axon injury (GO:0048678)|response to cadmium ion (GO:0046686)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to organic cyclic compound (GO:0014070)|response to toxic substance (GO:0009636)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac muscle cell development (GO:0055015)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|midbody (GO:0030496)|mitochondrion (GO:0005739)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|histone kinase activity (GO:0035173)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			ovary(1)	1						CCAGGAAGCCTAGCATCCCAT	0.393																																					p.L249P		Atlas-SNP	.											.	CDK1	24	.	0			c.T746C						PASS	.						90	89	89					10																	62551998		2203	4300	6503	SO:0001583	missense	983	exon7			GAAGCCTAGCATC	BC014563	CCDS7260.1, CCDS44408.1	10q21.2	2011-11-08	2009-12-16	2009-12-16	ENSG00000170312	ENSG00000170312		"Cyclin-dependent kinases"	1722	protein-coding gene	gene with protein product		116940	"cell division cycle 2, G1 to S and G2 to M"	CDC2		3553962, 19884882	Standard	NM_001786		Approved	CDC28A	uc001jld.3	P06493	OTTHUMG00000018290	ENST00000395284.3:c.746T>C	chr10.hg19:g.62551998T>C	ENSP00000378699:p.Leu249Pro	107.0	0.0	.		103.0	39.0	.	NM_001786	A8K7C4|C9J497|O60764	Missense_Mutation	SNP	ENST00000395284.3	hg19	CCDS44408.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.231155	0.79688	.	.	ENSG00000170312	ENST00000395284;ENST00000316629;ENST00000448257;ENST00000373809	T;T;T;T	0.47177	0.85;0.85;0.85;0.85	6.02	4.85	0.62838	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.66867	0.2833	M	0.73962	2.25	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.986;0.992;0.988	T	0.70648	-0.4814	10	0.72032	D	0.01	-9.4912	12.7155	0.57113	0.1229:0.0:0.0:0.8771	.	192;255;249	P06493-2;Q5H9N4;P06493	.;.;CDK1_HUMAN	P	249;192;249;192	ENSP00000378699:L249P;ENSP00000325970:L192P;ENSP00000397973:L249P;ENSP00000362915:L192P	ENSP00000325970:L192P	L	+	2	0	CDK1	62222004	1.000000	0.71417	0.636000	0.29352	0.988000	0.76386	6.281000	0.72632	2.311000	0.77944	0.533000	0.62120	CTA	.	.	.	none		0.393	CDK1-007	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048211.2	NM_001786		C	62551998	T	C	62551998	3	2	30	1	0	0	0	0	1	0	0	0	3126	1522	53	3	780	3	CDK1	10	62551998	Missense_Mutation	SNP	T	TCGA-5P-A9JY-01A-11D-A42J-10	12019783	62551998	72982749	64	2171											
NEUROG3	50674	hgsc.bcm.edu	37	chr10	71332599	71332599	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgctcttaggccggctgcgTcccccgcgccgtgcccggag	2	7	14	18	7	1	0	0	0	1	0	3	1	2	1	5	3	2	2	5	3	1	1			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr10:71332599T>C	ENST00000242462.4	-	2	230	c.201A>G	c.(199-201)ggA>ggG	p.G67G	RP11-343J3.2_ENST00000428753.1_RNA	NM_020999.3	NP_066279.2	Q9Y4Z2	NGN3_HUMAN	neurogenin 3	67					central nervous system development (GO:0007417)|endocrine pancreas development (GO:0031018)|epithelial cell differentiation (GO:0030855)|forebrain development (GO:0030900)|hindbrain development (GO:0030902)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|peripheral nervous system development (GO:0007422)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of dendrite morphogenesis (GO:0048814)|spinal cord development (GO:0021510)|transdifferentiation (GO:0060290)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription coactivator activity (GO:0003713)			endometrium(4)|large_intestine(2)|lung(6)|prostate(1)	13						GCCGGCTGCGTCCCCCGCGCC	0.697																																					p.G67G		Atlas-SNP	.											.	NEUROG3	33	.	0			c.A201G						PASS	.						35	23	27					10																	71332599		2200	4298	6498	SO:0001819	synonymous_variant	50674	exon2			GCTGCGTCCCCCG	AJ133776	CCDS31212.1	10q21.3	2013-05-21			ENSG00000122859	ENSG00000122859		"Basic helix-loop-helix proteins"	13806	protein-coding gene	gene with protein product		604882				9000438, 10677506	Standard	NM_020999		Approved	Atoh5, Math4B, ngn3, bHLHa7	uc001jpp.3	Q9Y4Z2	OTTHUMG00000018391	ENST00000242462.4:c.201A>G	chr10.hg19:g.71332599T>C		57.0	0.0	.		78.0	4.0	.	NM_020999	Q5VVI0|Q6DJX6|Q9BY24	Silent	SNP	ENST00000242462.4	hg19	CCDS31212.1																																																																																			.	.	.	none		0.697	NEUROG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048464.1	NM_020999		C	71332599	T	C	71332599	2	2	30	1	0	0	0	0	0	0	0	1	10361	1654	58	3		3	NEUROG3	10	71332599	Silent	SNP	T	TCGA-5P-A9JY-01A-11D-A42J-10	8780601	71332599	64202148	65	2172											
CYP2C18	1562	hgsc.bcm.edu	37	chr10	96447962	96447962	+	Frame_Shift_Del	DEL	A	A	-																															tgcggaattttgggatggggAagaggagcatcgaggaccgt																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr10:96447962delA	ENST00000285979.6	+	3	611	c.412delA	c.(412-414)aagfs	p.K138fs	CYP2C18_ENST00000339022.5_Frame_Shift_Del_p.K138fs|CYP2C19_ENST00000464755.1_3'UTR	NM_000772.2	NP_000763.1	P33260	CP2CI_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 18	138					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxygen binding (GO:0019825)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	26		Colorectal(252;0.09)		all cancers(201;2.8e-06)|KIRC - Kidney renal clear cell carcinoma(50;0.0646)|Kidney(138;0.0805)	Aminophenazone(DB01424)|Antipyrine(DB01435)|Buprenorphine(DB00921)|Clobazam(DB00349)|Clotiazepam(DB01559)|Cyclophosphamide(DB00531)|Dapsone(DB00250)|Desipramine(DB01151)|Diazepam(DB00829)|Diclofenac(DB00586)|Diphenhydramine(DB01075)|Ifosfamide(DB01181)|Imipramine(DB00458)|Lansoprazole(DB00448)|Lidocaine(DB00281)|Methadone(DB00333)|Omeprazole(DB00338)|Pegvisomant(DB00082)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Propofol(DB00818)|Tolbutamide(DB01124)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vilazodone(DB06684)|Warfarin(DB00682)	TGGGATGGGGAAGAGGAGCAT	0.473																																					p.G137fs		Atlas-INDEL	.											.	CYP2C18	79	.	0			c.411delG						PASS	.						124	116	119					10																	96447962		2203	4300	6503	SO:0001589	frameshift_variant	1562	exon3			.	M61853	CCDS7435.1, CCDS44460.1	10q24	2003-11-12	2003-01-14		ENSG00000108242	ENSG00000108242		"Cytochrome P450s"	2620	protein-coding gene	gene with protein product		601131	"cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 18"	CYP2C17		1896026, 2009263	Standard	NM_000772		Approved	P450IIC17, CPCI, CYP2C		P33260	OTTHUMG00000018796	ENST00000285979.6:c.412delA	chr10.hg19:g.96447962delA	ENSP00000285979:p.Lys138fs	202.0	0.0	0		182.0	70.0	0.384615	NM_000772	B2R8K2|Q16703|Q16751|Q4VAT5|Q6GRG1	Frame_Shift_Del	DEL	ENST00000285979.6	hg19	CCDS7435.1																																																																																			.	.	.	none		0.473	CYP2C18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049486.1	NM_000772		-	96447962	A	-	96447962	7	5	30	1	0	1	0	1	0	0	0	0	4167	247	9	0	422	0	CYP2C18	10	96447962	Frame_Shift_Del	DEL	A	TCGA-5P-A9JY-01A-11D-A42J-10	25115363	96447962	39086785	66	2173	25	3									
CYP2C18	1562	hgsc.bcm.edu	37	chr10	96447963	96447965	+	In_Frame_Del	DEL	AGA	AGA	-																															gcggaattttgggatggggaAgaggagcatcgaggaccgtg																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr10:96447963_96447965delAGA	ENST00000285979.6	+	3	612_614	c.413_415delAGA	c.(412-417)aagagg>agg	p.K138del	CYP2C18_ENST00000339022.5_In_Frame_Del_p.K138del|CYP2C19_ENST00000464755.1_3'UTR	NM_000772.2	NP_000763.1	P33260	CP2CI_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 18	138					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)	p.R139G(2)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	26		Colorectal(252;0.09)		all cancers(201;2.8e-06)|KIRC - Kidney renal clear cell carcinoma(50;0.0646)|Kidney(138;0.0805)	Aminophenazone(DB01424)|Antipyrine(DB01435)|Buprenorphine(DB00921)|Clobazam(DB00349)|Clotiazepam(DB01559)|Cyclophosphamide(DB00531)|Dapsone(DB00250)|Desipramine(DB01151)|Diazepam(DB00829)|Diclofenac(DB00586)|Diphenhydramine(DB01075)|Ifosfamide(DB01181)|Imipramine(DB00458)|Lansoprazole(DB00448)|Lidocaine(DB00281)|Methadone(DB00333)|Omeprazole(DB00338)|Pegvisomant(DB00082)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Propofol(DB00818)|Tolbutamide(DB01124)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vilazodone(DB06684)|Warfarin(DB00682)	GGGATGGGGAAGAGGAGCATCGA	0.468																																					p.138_138del		Pindel	.											.	CYP2C18	79	.	2	Substitution - Missense(2)	lung(2)	c.412_414del						PASS	.																																			SO:0001651	inframe_deletion	1562	exon3			.	M61853	CCDS7435.1, CCDS44460.1	10q24	2003-11-12	2003-01-14		ENSG00000108242	ENSG00000108242		"Cytochrome P450s"	2620	protein-coding gene	gene with protein product		601131	"cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 18"	CYP2C17		1896026, 2009263	Standard	NM_000772		Approved	P450IIC17, CPCI, CYP2C		P33260	OTTHUMG00000018796	ENST00000285979.6:c.413_415delAGA	chr10.hg19:g.96447963_96447965delAGA	ENSP00000285979:p.Lys138del	207.0	0.0	.		182.0	54.0	0.297	NM_000772	B2R8K2|Q16703|Q16751|Q4VAT5|Q6GRG1	In_Frame_Del	DEL	ENST00000285979.6	hg19	CCDS7435.1																																																																																			.	.	.	none		0.468	CYP2C18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049486.1	NM_000772		-	96447965	AGA	-	96447963	7	5	30	1	0	1	0	1	0	0	0	0	4167	72	3	0	423	0	CYP2C18	10	96447963	In_Frame_Del	DEL	AGA	TCGA-5P-A9JY-01A-11D-A42J-10	1	96447963	39086784	67	2174	25	3									
CYP2C18	1562	hgsc.bcm.edu	37	chr10	96447965	96447965	+	Frame_Shift_Del	DEL	A	A	-																															ggaattttgggatggggaagAggagcatcgaggaccgtgtt																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr10:96447965delA	ENST00000285979.6	+	3	614	c.415delA	c.(415-417)aggfs	p.R139fs	CYP2C18_ENST00000339022.5_Frame_Shift_Del_p.R139fs|CYP2C19_ENST00000464755.1_3'UTR	NM_000772.2	NP_000763.1	P33260	CP2CI_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 18	139					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)	p.R139G(2)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	26		Colorectal(252;0.09)		all cancers(201;2.8e-06)|KIRC - Kidney renal clear cell carcinoma(50;0.0646)|Kidney(138;0.0805)	Aminophenazone(DB01424)|Antipyrine(DB01435)|Buprenorphine(DB00921)|Clobazam(DB00349)|Clotiazepam(DB01559)|Cyclophosphamide(DB00531)|Dapsone(DB00250)|Desipramine(DB01151)|Diazepam(DB00829)|Diclofenac(DB00586)|Diphenhydramine(DB01075)|Ifosfamide(DB01181)|Imipramine(DB00458)|Lansoprazole(DB00448)|Lidocaine(DB00281)|Methadone(DB00333)|Omeprazole(DB00338)|Pegvisomant(DB00082)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Propofol(DB00818)|Tolbutamide(DB01124)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vilazodone(DB06684)|Warfarin(DB00682)	GATGGGGAAGAGGAGCATCGA	0.468																																					p.K138fs		Atlas-INDEL	.											.	CYP2C18	79	.	2	Substitution - Missense(2)	lung(2)	c.414delG						PASS	.						124	117	120					10																	96447965		2203	4300	6503	SO:0001589	frameshift_variant	1562	exon3			.	M61853	CCDS7435.1, CCDS44460.1	10q24	2003-11-12	2003-01-14		ENSG00000108242	ENSG00000108242		"Cytochrome P450s"	2620	protein-coding gene	gene with protein product		601131	"cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 18"	CYP2C17		1896026, 2009263	Standard	NM_000772		Approved	P450IIC17, CPCI, CYP2C		P33260	OTTHUMG00000018796	ENST00000285979.6:c.415delA	chr10.hg19:g.96447965delA	ENSP00000285979:p.Arg139fs	206.0	0.0	0		180.0	71.0	0.394444	NM_000772	B2R8K2|Q16703|Q16751|Q4VAT5|Q6GRG1	Frame_Shift_Del	DEL	ENST00000285979.6	hg19	CCDS7435.1																																																																																			.	.	.	none		0.468	CYP2C18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049486.1	NM_000772		-	96447965	A	-	96447965	7	5	30	1	0	1	0	1	0	0	0	0	4167	295	11	0	425	0	CYP2C18	10	96447965	Frame_Shift_Del	DEL	A	TCGA-5P-A9JY-01A-11D-A42J-10	2	96447965	39086782	68	2175	25	3									
CNNM2	54805	hgsc.bcm.edu	37	chr10	104679232	104679232	+	Frame_Shift_Del	DEL	T	T	-																															ggtcaacaccacgctcaccaTcctgctcgacgacatcgccg																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr10:104679232delT	ENST00000369878.4	+	1	1183	c.995delT	c.(994-996)atcfs	p.I332fs	CNNM2_ENST00000433628.2_Frame_Shift_Del_p.I332fs|CNNM2_ENST00000369875.3_Frame_Shift_Del_p.I332fs	NM_017649.4	NP_060119.3	Q9H8M5	CNNM2_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 2	332	DUF21.				magnesium ion homeostasis (GO:0010960)|magnesium ion transport (GO:0015693)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	adenyl nucleotide binding (GO:0030554)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		ACGCTCACCATCCTGCTCGAC	0.627																																					p.I332fs		Atlas-Indel,Pindel	.											.	CNNM2	119	.	0			c.994delA						PASS	.						70	60	63					10																	104679232		2203	4299	6502	SO:0001589	frameshift_variant	54805	exon1			.	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.995delT	chr10.hg19:g.104679232delT	ENSP00000358894:p.Ile332fs	36.0	0.0	0		40.0	20.0	0.5	NM_199076	Q5T569|Q5T570|Q8WU59|Q9H952|Q9NRK5|Q9NXT4	Frame_Shift_Del	DEL	ENST00000369878.4	hg19	CCDS44474.1																																																																																			.	.	.	none		0.627	CNNM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050113.3	NM_017649		-	104679232	T	-	104679232	7	5	30	1	0	1	0	1	0	0	0	0	3615	1435	50	0	997	0	CNNM2	10	104679232	Frame_Shift_Del	DEL	T	TCGA-5P-A9JY-01A-11D-A42J-10	8231267	104679232	30855515	69	2176											
PHRF1	57661	hgsc.bcm.edu	37	chr11	605692	605692	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccctgcagtcccaccagccCgtggccaggcccgtctccgt	4	6	11	20	3	1	0	0	0	1	0	3	0	2	0	7	2	2	1	7	2	0	0	rs374393458		TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr11:605692C>T	ENST00000264555.5	+	12	1550	c.1422C>T	c.(1420-1422)ccC>ccT	p.P474P	PHRF1_ENST00000533464.1_Silent_p.P470P|PHRF1_ENST00000413872.2_Silent_p.P472P|PHRF1_ENST00000416188.2_Silent_p.P473P	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	474					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						CCCACCAGCCCGTGGCCAGGC	0.637																																					p.P473P		Atlas-SNP	.											.	PHRF1	188	.	0			c.C1419T						PASS	.	C		1,3837		0,1,1918	47	53	51		1419	-9.6	0.8	11		51	0,8238		0,0,4119	no	coding-synonymous	PHRF1	NM_020901.2		0,1,6037	TT,TC,CC		0.0,0.0261,0.0083		473/1649	605692	1,12075	1919	4119	6038	SO:0001819	synonymous_variant	57661	exon12			CCAGCCCGTGGCC	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.1422C>T	chr11.hg19:g.605692C>T		37.0	0.0	.		51.0	21.0	.	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Silent	SNP	ENST00000264555.5	hg19																																																																																				.	.	.	weak		0.637	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901		T	605692	C	T	605692	2	4	30	1	0	0	0	0	0	0	0	1	11868	639	23	1		1	PHRF1	11	605692	Silent	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10		605692	134400824	70	2177											
OSBPL5	114879	hgsc.bcm.edu	37	chr11	3111822	3111822	+	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	ccatcctgctcctcgtctgaGagctctgggcaggactcagg	6	9	12	14	1	3	1	1	1	2	1	6	3	5	2	3	3	2	3	3	3	0	0			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr11:3111822G>C	ENST00000263650.7	-	20	2523	c.2364C>G	c.(2362-2364)ctC>ctG	p.L788L	OSBPL5_ENST00000525498.1_Silent_p.L699L|OSBPL5_ENST00000478260.1_Silent_p.L242L|OSBPL5_ENST00000348039.5_Silent_p.L720L|OSBPL5_ENST00000542243.1_Silent_p.L419L|OSBPL5_ENST00000389989.3_Silent_p.L720L	NM_020896.3	NP_065947.1	Q9H0X9	OSBL5_HUMAN	oxysterol binding protein-like 5	788					cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|Golgi to plasma membrane transport (GO:0006893)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|oxysterol binding (GO:0008142)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	25		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		CCTCGTCTGAGAGCTCTGGGC	0.677																																					p.L788L		Atlas-SNP	.											.	OSBPL5	78	.	0			c.C2364G						PASS	.						67	65	66					11																	3111822		2202	4298	6500	SO:0001819	synonymous_variant	114879	exon20			GTCTGAGAGCTCT	AF392453	CCDS31343.1, CCDS31344.1	11p15.4	2013-01-10			ENSG00000021762	ENSG00000021762		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16392	protein-coding gene	gene with protein product		606733					Standard	NM_145638		Approved	KIAA1534, ORP5	uc001lxk.2	Q9H0X9	OTTHUMG00000011702	ENST00000263650.7:c.2364C>G	chr11.hg19:g.3111822G>C		178.0	0.0	.		204.0	109.0	.	NM_020896	A6NDP0|A6NJS8|Q54A90|Q8N596|Q9BZB0|Q9P1Z4	Silent	SNP	ENST00000263650.7	hg19	CCDS31344.1																																																																																			.	.	.	none		0.677	OSBPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032332.2			C	3111822	G	C	3111822	2	2	30	1	0	0	0	0	0	0	0	1	11287	929	33	4		4	OSBPL5	11	3111822	Silent	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	2506130	3111822	131894694	71	2178											
RRM1	6240	hgsc.bcm.edu	37	chr11	4143450	4143450	+	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	atttgagaaactatatgcaaGgtatgggaaaaatatgaaag	19	10	10	2	0	0	2	0	2	0	1	0	4	0	3	0	2	2	2	0	2	9	5			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr11:4143450G>C	ENST00000300738.5	+	11	1322	c.1118G>C	c.(1117-1119)aGt>aCt	p.S373T	RRM1_ENST00000423050.2_Splice_Site_p.S276T|RRM1_ENST00000537197.1_Splice_Site_p.S35T|RRM1_ENST00000534285.1_Splice_Site_p.S151T|RRM1_ENST00000528470.1_3'UTR	NM_001033.3	NP_001024.1	P23921	RIR1_HUMAN	ribonucleotide reductase M1	373					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)	CTATATGCAAGGTATGGGAAA	0.353																																					p.S373T	NSCLC(45;1345 1376 6258 22925)|Ovarian(34;894 1053 6175 12768)	Atlas-SNP	.											.	RRM1	31	.	0			c.G1118C						PASS	.						143	136	138					11																	4143450		2201	4298	6499	SO:0001630	splice_region_variant	6240	exon11			ATGCAAGGTATGG	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.1118+1G>C	chr11.hg19:g.4143450G>C		79.0	0.0	.		72.0	28.0	.	NM_001033	Q9UNN2	Missense_Mutation	SNP	ENST00000300738.5	hg19	CCDS7750.1	.	.	.	.	.	.	.	.	.	.	G	13.67	2.307194	0.40795	.	.	ENSG00000167325	ENST00000300738;ENST00000423050;ENST00000536894;ENST00000534285;ENST00000543838;ENST00000537197	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	5.7	4.79	0.61399	Ribonucleoside-diphosphate reductase, alpha subunit (1);Ribonucleotide reductase large subunit, C-terminal (1);	0.340623	0.37530	N	0.002041	T	0.33089	0.0851	L	0.34521	1.04	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.11084	-1.0602	10	0.59425	D	0.04	-3.1579	11.9367	0.52878	0.0801:0.0:0.9199:0.0	.	373	P23921	RIR1_HUMAN	T	373;276;286;151;151;35	ENSP00000300738:S373T;ENSP00000390539:S276T;ENSP00000431464:S151T;ENSP00000442148:S35T	ENSP00000300738:S373T	S	+	2	0	RRM1	4100026	1.000000	0.71417	1.000000	0.80357	0.836000	0.47400	4.984000	0.63838	1.409000	0.46915	0.557000	0.71058	AGT	.	.	.	none		0.353	RRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257197.1	NM_001033	Missense_Mutation	C	4143450	G	C	4143450	5	2	30	1	0	0	0	0	0	0	1	0	13694	1014	35	4	1160	4	RRM1	11	4143450	Splice_Site	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	1031628	4143450	130863066	72	2179											
TCP11L1	55346	hgsc.bcm.edu	37	chr11	33083259	33083259	+	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	gaagtgggaccacctccagaGgccgttccccgaagtaggtc	9	6	13	13	2	0	1	0	0	0	1	3	4	2	2	6	3	0	2	6	3	3	2			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr11:33083259G>T	ENST00000334274.4	+	7	1359	c.959G>T	c.(958-960)aGg>aTg	p.R320M	TCP11L1_ENST00000432887.1_Missense_Mutation_p.R320M|TCP11L1_ENST00000531632.2_Missense_Mutation_p.R320M|TCP11L1_ENST00000324357.9_Missense_Mutation_p.R99M	NM_018393.3	NP_060863.3	Q9NUJ3	T11L1_HUMAN	t-complex 11, testis-specific-like 1	320						microtubule (GO:0005874)				kidney(1)|liver(2)|lung(2)|skin(1)	6						CACCTCCAGAGGCCGTTCCCC	0.532																																					p.R320M		Atlas-SNP	.											.	TCP11L1	40	.	0			c.G959T						PASS	.						32	30	31					11																	33083259		2202	4298	6500	SO:0001583	missense	55346	exon7			TCCAGAGGCCGTT	BC041696	CCDS7882.1	11p13	2014-08-12	2012-09-20		ENSG00000176148	ENSG00000176148			25655	protein-coding gene	gene with protein product			"t-complex 11 (mouse) like 1"				Standard	NM_001145541		Approved	FLJ11336	uc010rei.2	Q9NUJ3	OTTHUMG00000165303	ENST00000334274.4:c.959G>T	chr11.hg19:g.33083259G>T	ENSP00000335595:p.Arg320Met	151.0	0.0	.		155.0	68.0	.	NM_001145541	D3DR01|Q8IVX4	Missense_Mutation	SNP	ENST00000334274.4	hg19	CCDS7882.1	.	.	.	.	.	.	.	.	.	.	G	10.24	1.295641	0.23564	.	.	ENSG00000176148	ENST00000334274;ENST00000531632;ENST00000432887;ENST00000324357	T;T;T;T	0.11821	2.74;2.74;2.74;2.74	5.42	1.52	0.23074	.	0.300219	0.42548	D	0.000689	T	0.17831	0.0428	M	0.64997	1.995	0.09310	N	1	P	0.42941	0.794	P	0.45377	0.478	T	0.06144	-1.0843	10	0.72032	D	0.01	-4.844	8.6816	0.34212	0.4363:0.0:0.5637:0.0	.	320	Q9NUJ3	T11L1_HUMAN	M	320;320;320;99	ENSP00000335595:R320M;ENSP00000433067:R320M;ENSP00000395070:R320M;ENSP00000316279:R99M	ENSP00000316279:R99M	R	+	2	0	TCP11L1	33039835	0.995000	0.38212	0.002000	0.10522	0.003000	0.03518	1.522000	0.35921	0.275000	0.22094	-0.143000	0.13931	AGG	.	.	.	none		0.532	TCP11L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383377.4	NM_018393		T	33083259	G	T	33083259	3	4	30	1	0	0	0	0	1	0	0	0	15726	1000	35	4	981	4	TCP11L1	11	33083259	Missense_Mutation	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	28939809	33083259	101923257	73	2180											
MMP27	64066	hgsc.bcm.edu	37	chr11	102562558	102562558	+	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	caaaaataaacaagcttaaaCtcttatgatacaatatcttt	19	13	2	7	0	2	1	0	1	2	0	2	1	2	1	0	0	4	1	0	0	11	6			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr11:102562558C>G	ENST00000260229.4	-	10	1572	c.1481G>C	c.(1480-1482)aGt>aCt	p.S494T		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	494	Required for retention in the endoplasmic reticulum. {ECO:0000269|PubMed:24548619}.				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)	CAAGCTTAAACTCTTATGATA	0.299																																					p.S494T		Atlas-SNP	.											.	MMP27	84	.	0			c.G1481C						PASS	.						114	113	113					11																	102562558		2203	4295	6498	SO:0001583	missense	64066	exon10			CTTAAACTCTTAT	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.1481G>C	chr11.hg19:g.102562558C>G	ENSP00000260229:p.Ser494Thr	136.0	0.0	.		107.0	17.0	.	NM_022122	Q6UWK6	Missense_Mutation	SNP	ENST00000260229.4	hg19	CCDS8319.1	.	.	.	.	.	.	.	.	.	.	C	10.81	1.456849	0.26161	.	.	ENSG00000137675	ENST00000260229	T	0.13538	2.58	5.83	1.67	0.24075	.	0.496244	0.18873	N	0.128791	T	0.07638	0.0192	L	0.34521	1.04	0.09310	N	1	B	0.27498	0.18	B	0.22601	0.04	T	0.41016	-0.9532	10	0.02654	T	1	.	8.7498	0.34609	0.0:0.6807:0.0:0.3193	.	494	Q9H306	MMP27_HUMAN	T	494	ENSP00000260229:S494T	ENSP00000260229:S494T	S	-	2	0	MMP27	102067768	0.001000	0.12720	0.045000	0.18777	0.845000	0.48019	0.104000	0.15313	0.026000	0.15269	0.563000	0.77884	AGT	.	.	.	none		0.299	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122		G	102562558	C	G	102562558	3	3	30	1	0	0	0	0	1	0	0	0	9671	565	20	4	64	4	MMP27	11	102562558	Missense_Mutation	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10	69479299	102562558	32443958	74	2181											
IFT46	56912	hgsc.bcm.edu	37	chr11	118416523	118416523	+	Missense_Mutation	SNP	T	T	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	ctcaccacagatcatgtcaaTgtactctgccaggctgcaat	11	10	7	13	0	4	1	3	0	1	1	4	1	4	1	2	1	3	3	2	1	3	1			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr11:118416523T>G	ENST00000264021.3	-	10	1136	c.718A>C	c.(718-720)Att>Ctt	p.I240L	IFT46_ENST00000530872.1_Missense_Mutation_p.I291L|TMEM25_ENST00000354284.4_Intron|IFT46_ENST00000264020.2_Missense_Mutation_p.I291L|TMEM25_ENST00000442938.2_Intron	NM_001168618.1	NP_001162089.1	Q9NQC8	IFT46_HUMAN	intraflagellar transport 46	240					cilium assembly (GO:0042384)|intraciliary transport (GO:0042073)|protein stabilization (GO:0050821)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|motile primary cilium (GO:0031512)	protein C-terminus binding (GO:0008022)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	9						ATCATGTCAATGTACTCTGCC	0.507																																					p.I291L		Atlas-SNP	.											.	IFT46	19	.	0			c.A871C						PASS	.						179	148	158					11																	118416523		2200	4295	6495	SO:0001583	missense	56912	exon11			TGTCAATGTACTC	AL136934	CCDS8399.1, CCDS53718.1	11q23.3	2014-07-18	2014-07-03	2010-04-22	ENSG00000118096	ENSG00000118096		"Intraflagellar transport homologs"	26146	protein-coding gene	gene with protein product	"cilia and flagella associated protein 32"		"chromosome 11 open reading frame 60", "intraflagellar transport 46 homolog (Chlamydomonas)"	C11orf60		10873569, 19253336	Standard	NM_020153		Approved	C11orf2, FLJ21827, CFAP32	uc001pto.2	Q9NQC8	OTTHUMG00000166408	ENST00000264021.3:c.718A>C	chr11.hg19:g.118416523T>G	ENSP00000264021:p.Ile240Leu	125.0	0.0	.		112.0	8.0	.	NM_020153	A8K0F6|Q9H6V5	Missense_Mutation	SNP	ENST00000264021.3	hg19	CCDS53718.1	.	.	.	.	.	.	.	.	.	.	T	16.64	3.180313	0.57800	.	.	ENSG00000118096	ENST00000264021;ENST00000264020;ENST00000530872	T;T;T	0.46819	0.87;0.86;0.86	6.03	3.76	0.43208	.	0.364645	0.29335	N	0.012458	T	0.43277	0.1240	M	0.65975	2.015	0.37231	D	0.905678	B;P;B	0.34462	0.139;0.454;0.114	B;B;B	0.31016	0.06;0.123;0.078	T	0.53078	-0.8489	10	0.62326	D	0.03	-8.0521	9.6786	0.40056	0.0:0.1401:0.0:0.8599	.	291;240;291	E9PR06;Q9NQC8;Q9NQC8-2	.;IFT46_HUMAN;.	L	240;291;291	ENSP00000264021:I240L;ENSP00000264020:I291L;ENSP00000432384:I291L	ENSP00000264020:I291L	I	-	1	0	IFT46	117921733	1.000000	0.71417	0.997000	0.53966	0.835000	0.47333	1.106000	0.31098	1.109000	0.41680	0.533000	0.62120	ATT	.	.	.	none		0.507	IFT46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389627.1	NM_020153		G	118416523	T	G	118416523	3	3	30	1	0	0	0	0	1	0	0	0	7567	1464	51	5	208	5	IFT46	11	118416523	Missense_Mutation	SNP	T	TCGA-5P-A9JY-01A-11D-A42J-10	15853965	118416523	16589993	75	2182											
NOP2	4839	hgsc.bcm.edu	37	chr12	6672800	6672803	+	Frame_Shift_Del	DEL	GGGG	GGGG	-																															cctgctccatctccccagcaGggggcagcacaaatggttcc																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	GGGG	GGGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr12:6672800_6672803delGGGG	ENST00000322166.5	-	7	786_789	c.665_668delCCCC	c.(664-669)ccccctfs	p.PP222fs	NOP2_ENST00000545200.1_Frame_Shift_Del_p.PP218fs|NOP2_ENST00000537442.1_Frame_Shift_Del_p.PP222fs|NOP2_ENST00000541778.1_Frame_Shift_Del_p.PP218fs|NOP2_ENST00000542015.1_Intron|NOP2_ENST00000382421.3_Frame_Shift_Del_p.PP255fs|NOP2_ENST00000399466.2_Frame_Shift_Del_p.PP218fs	NM_001258308.1|NM_006170.3	NP_001245237.1|NP_006161.2	P46087	NOP2_HUMAN	NOP2 nucleolar protein	222					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						CTCCCCAGCAGGGGGCAGCACAAA	0.559											OREG0021630	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.255_256del		Atlas-Indel,Pindel	.											.	NOP2	44	.	0			c.765_768del						PASS	.																																			SO:0001589	frameshift_variant	4839	exon8			.		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.665_668delCCCC	chr12.hg19:g.6672800_6672803delGGGG	ENSP00000313272:p.Pro222fs	81.0	0.0	0	635	79.0	33.0	0.417722	NM_001258309	A1A4Z3|B3KPD6|Q05BA7|Q0P5S5|Q3KQS4|Q58F30	Frame_Shift_Del	DEL	ENST00000322166.5	hg19	CCDS58203.1																																																																																			.	.	.	none		0.559	NOP2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402614.1	NM_006170		-	6672803	GGGG	-	6672800	7	5	30	1	0	1	0	1	0	0	0	0	10545	1000	35	0	1810	0	NOP2	12	6672800	Frame_Shift_Del	DEL	GGGG	TCGA-5P-A9JY-01A-11D-A42J-10		6672800	127179095	76	2183											
CAND1	55832	hgsc.bcm.edu	37	chr12	67696393	67696393	+	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	ctttaacaatgcttcagagtCaggtgggttttaaagtaaag	13	13	10	5	0	2	1	2	0	0	1	2	1	2	1	0	2	2	3	0	2	6	6			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr12:67696393C>A	ENST00000545606.1	+	8	1728	c.1291C>A	c.(1291-1293)Cag>Aag	p.Q431K		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	431					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)		GCTTCAGAGTCAGGTGGGTTT	0.363																																					p.Q431K		Atlas-SNP	.											.	CAND1	100	.	0			c.C1291A						PASS	.						88	78	81					12																	67696393		2203	4300	6503	SO:0001583	missense	55832	exon8			CAGAGTCAGGTGG		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.1291C>A	chr12.hg19:g.67696393C>A	ENSP00000442318:p.Gln431Lys	119.0	0.0	.		99.0	39.0	.	NM_018448	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Missense_Mutation	SNP	ENST00000545606.1	hg19	CCDS8977.1	.	.	.	.	.	.	.	.	.	.	C	30	5.051857	0.93793	.	.	ENSG00000111530	ENST00000545606;ENST00000299218;ENST00000540047;ENST00000544619	T;T	0.65364	-0.15;-0.15	5.4	5.4	0.78164	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.80555	0.4645	M	0.85630	2.765	0.80722	D	1	P;D	0.61697	0.593;0.99	P;P	0.61397	0.828;0.888	T	0.82116	-0.0616	9	.	.	.	-6.9157	19.547	0.95302	0.0:1.0:0.0:0.0	.	431;431	Q86VP6-2;Q86VP6	.;CAND1_HUMAN	K	431;431;273;139	ENSP00000442318:Q431K;ENSP00000444089:Q139K	.	Q	+	1	0	CAND1	65982660	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	7.719000	0.84751	2.699000	0.92147	0.555000	0.69702	CAG	.	.	.	none		0.363	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448		A	67696393	C	A	67696393	3	1	30	1	0	0	0	0	1	0	0	0	2617	827	29	4	1321	4	CAND1	12	67696393	Missense_Mutation	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10	61023593	67696393	66155502	77	2184											
NAV3	89795	hgsc.bcm.edu	37	chr12	78593299	78593299	+	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	tggaaacacacagttcttctGacgttaccattggtgagttc	10	13	9	9	1	2	2	0	2	2	0	3	3	2	3	1	2	2	3	1	2	2	5			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr12:78593299G>T	ENST00000397909.2	+	37	6876	c.6703G>T	c.(6703-6705)Gac>Tac	p.D2235Y	NAV3_ENST00000541270.1_Missense_Mutation_p.D65Y|NAV3_ENST00000266692.7_Missense_Mutation_p.D2036Y|NAV3_ENST00000228327.6_Missense_Mutation_p.D2213Y|NAV3_ENST00000536525.2_Missense_Mutation_p.D2213Y			Q8IVL0	NAV3_HUMAN	neuron navigator 3	2235						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						CAGTTCTTCTGACGTTACCAT	0.383										HNSCC(70;0.22)																											p.D2213Y		Atlas-SNP	.											.	NAV3	506	.	0			c.G6637T						PASS	.						80	78	79					12																	78593299		1863	4091	5954	SO:0001583	missense	89795	exon36			TCTTCTGACGTTA	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.6703G>T	chr12.hg19:g.78593299G>T	ENSP00000381007:p.Asp2235Tyr	178.0	0.0	.		128.0	47.0	.	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.4|20.4	3.985795|3.985795	0.74589|0.74589	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692;ENST00000541270|ENST00000552895;ENST00000551162	T;T;T;T;T|.	0.53206|.	1.3;1.31;1.3;1.28;0.63|.	5.71|5.71	5.71|5.71	0.89125|0.89125	.|.	0.000000|.	0.41396|.	U|.	0.000895|.	D|.	0.84593|.	0.5506|.	M|M	0.87900|0.87900	2.915|2.915	0.80722|0.80722	D|D	1|1	D;D;P;D|.	0.89917|.	0.974;1.0;0.911;1.0|.	P;D;P;D|.	0.91635|.	0.829;0.998;0.504;0.999|.	D|.	0.85408|.	0.1135|.	10|.	0.87932|.	D|.	0|.	-21.054|-21.054	20.2245|20.2245	0.98337|0.98337	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	2213;2036;2235;2213|.	E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2|.	.;.;NAV3_HUMAN;.|.	Y|L	2213;2235;2213;2036;65|1107;102	ENSP00000446132:D2213Y;ENSP00000381007:D2235Y;ENSP00000228327:D2213Y;ENSP00000266692:D2036Y;ENSP00000444918:D65Y|.	ENSP00000228327:D2213Y|.	D|X	+|+	1|2	0|2	NAV3|NAV3	77117430|77117430	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	9.813000|9.813000	0.99286|0.99286	2.861000|2.861000	0.98227|0.98227	0.650000|0.650000	0.86243|0.86243	GAC|TGA	.	.	.	none		0.383	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		T	78593299	G	T	78593299	3	4	30	1	0	0	0	0	1	0	0	0	10192	1290	45	4	6779	4	NAV3	12	78593299	Missense_Mutation	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	10896906	78593299	55258596	78	2185											
RBM19	9904	hgsc.bcm.edu	37	chr12	114377884	114377884	+	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	caggctgccaaaatggccgaAggtctcctgcagctgggccg	8	6	14	13	2	1	0	0	0	1	0	2	1	1	0	4	4	3	3	4	4	3	0			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr12:114377884A>T	ENST00000545145.2	-	15	1897	c.1819T>A	c.(1819-1821)Ttc>Atc	p.F607I	RBM19_ENST00000392561.3_Missense_Mutation_p.F607I|RP11-780K2.1_ENST00000550206.1_RNA|RBM19_ENST00000261741.5_Missense_Mutation_p.F607I	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	607	RRM 4. {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)					AAATGGCCGAAGGTCTCCTGC	0.637																																					p.F607I		Atlas-SNP	.											.	RBM19	117	.	0			c.T1819A						PASS	.						66	71	69					12																	114377884		2203	4300	6503	SO:0001583	missense	9904	exon15			GGCCGAAGGTCTC	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.1819T>A	chr12.hg19:g.114377884A>T	ENSP00000442053:p.Phe607Ile	86.0	0.0	.		78.0	11.0	.	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	hg19	CCDS9172.1	.	.	.	.	.	.	.	.	.	.	A	17.41	3.382304	0.61845	.	.	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.15139	2.45;2.45;2.45	4.3	4.3	0.51218	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.000000	0.85682	D	0.000000	T	0.55386	0.1917	H	0.96943	3.91	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.71695	-0.4515	10	0.87932	D	0	-14.4911	13.458	0.61210	1.0:0.0:0.0:0.0	.	607	Q9Y4C8	RBM19_HUMAN	I	607	ENSP00000442053:F607I;ENSP00000376344:F607I;ENSP00000261741:F607I	ENSP00000261741:F607I	F	-	1	0	RBM19	112862267	1.000000	0.71417	0.249000	0.24280	0.148000	0.21650	8.500000	0.90498	1.600000	0.50102	0.459000	0.35465	TTC	.	.	.	none		0.637	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196		T	114377884	A	T	114377884	3	4	30	1	0	0	0	0	1	0	0	0	13134	72	3	5	1103	5	RBM19	12	114377884	Missense_Mutation	SNP	A	TCGA-5P-A9JY-01A-11D-A42J-10	35784585	114377884	19474011	79	2186											
KNTC1	9735	hgsc.bcm.edu	37	chr12	123052914	123052914	+	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	cacagtatctttggcttcgaCatcgggtaacatgttttaca	10	14	8	9	2	1	0	0	0	1	0	3	1	1	0	0	2	2	4	0	2	3	6			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr12:123052914C>T	ENST00000333479.7	+	21	1888	c.1711C>T	c.(1711-1713)Cat>Tat	p.H571Y	KNTC1_ENST00000450485.2_Missense_Mutation_p.H534Y	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	571					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)		TTGGCTTCGACATCGGGTAAC	0.343																																					p.H571Y		Atlas-SNP	.											.	KNTC1	182	.	0			c.C1711T						PASS	.						150	145	147					12																	123052914		1859	4093	5952	SO:0001583	missense	9735	exon21			CTTCGACATCGGG		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.1711C>T	chr12.hg19:g.123052914C>T	ENSP00000328236:p.His571Tyr	212.0	0.0	.		158.0	73.0	.	NM_014708	A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	hg19	CCDS45002.1	.	.	.	.	.	.	.	.	.	.	C	13.89	2.370581	0.42003	.	.	ENSG00000184445	ENST00000450485;ENST00000333479	T;T	0.32272	1.46;1.9	5.36	5.36	0.76844	.	0.178872	0.50627	D	0.000105	T	0.33381	0.0861	L	0.55103	1.725	0.80722	D	1	B;B	0.32071	0.068;0.355	B;B	0.29267	0.009;0.1	T	0.12016	-1.0564	10	0.51188	T	0.08	-13.3748	19.0977	0.93260	0.0:1.0:0.0:0.0	.	534;571	E7ES84;P50748	.;KNTC1_HUMAN	Y	534;571	ENSP00000397992:H534Y;ENSP00000328236:H571Y	ENSP00000328236:H571Y	H	+	1	0	KNTC1	121618867	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	2.016000	0.40971	2.516000	0.84829	0.460000	0.39030	CAT	.	.	.	none		0.343	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2			T	123052914	C	T	123052914	3	4	30	1	0	0	0	0	1	0	0	0	8435	478	17	2	1789	2	KNTC1	12	123052914	Missense_Mutation	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10	8675030	123052914	10798981	80	2187											
HSPH1	10808	hgsc.bcm.edu	37	chr13	31728852	31728852	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaacaacatggctgttatcTgctccacactaaatagatgt	13	12	6	10	0	2	1	1	0	1	1	3	1	3	1	1	1	3	3	1	1	6	3			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr13:31728852T>C	ENST00000320027.5	-	4	691	c.347A>G	c.(346-348)cAg>cGg	p.Q116R	HSPH1_ENST00000380406.5_Intron|HSPH1_ENST00000380405.4_Missense_Mutation_p.Q116R|HSPH1_ENST00000429785.2_Missense_Mutation_p.Q13R|HSPH1_ENST00000445273.2_Missense_Mutation_p.Q118R	NM_006644.2	NP_006635.2	Q92598	HS105_HUMAN	heat shock 105kDa/110kDa protein 1	116					chaperone mediated protein folding requiring cofactor (GO:0051085)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of NK T cell activation (GO:0051135)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	27		Lung SC(185;0.0257)		all cancers(112;0.00385)|Epithelial(112;0.0328)|OV - Ovarian serous cystadenocarcinoma(117;0.0375)|GBM - Glioblastoma multiforme(144;0.125)		GGCTGTTATCTGCTCCACACT	0.343																																					p.Q116R		Atlas-SNP	.											.	HSPH1	65	.	0			c.A347G						PASS	.						157	137	144					13																	31728852		2203	4300	6503	SO:0001583	missense	10808	exon4			GTTATCTGCTCCA	AB003333	CCDS9340.1, CCDS66525.1, CCDS73559.1	13q12.2-q13.3	2011-09-02			ENSG00000120694	ENSG00000120694		"Heat shock proteins / HSP70"	16969	protein-coding gene	gene with protein product		610703				9610721, 9931472	Standard	XM_005266236		Approved	HSP105B, KIAA0201, HSP105A, NY-CO-25	uc001utj.3	Q92598	OTTHUMG00000016685	ENST00000320027.5:c.347A>G	chr13.hg19:g.31728852T>C	ENSP00000318687:p.Gln116Arg	92.0	0.0	.		77.0	37.0	.	NM_006644	B4DYH1|O95739|Q5TBM6|Q5TBM7|Q5TBM8|Q9UPC4	Missense_Mutation	SNP	ENST00000320027.5	hg19	CCDS9340.1	.	.	.	.	.	.	.	.	.	.	T	13.43	2.235880	0.39498	.	.	ENSG00000120694	ENST00000320027;ENST00000380405;ENST00000445273;ENST00000429785;ENST00000438061	T;T;T;T	0.05717	5.3;5.3;5.3;3.4	6.08	6.08	0.98989	.	0.134584	0.50627	D	0.000112	T	0.27697	0.0681	M	0.77103	2.36	0.32658	N	0.518415	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	0.992;1.0;1.0;1.0;1.0;1.0	T	0.30621	-0.9972	10	0.66056	D	0.02	-17.9521	16.643	0.85134	0.0:0.0:0.0:1.0	.	13;167;167;118;116;116	B4DY72;E7EUG1;B4DZB4;B4DYH1;Q92598-2;Q92598	.;.;.;.;.;HS105_HUMAN	R	116;116;118;13;167	ENSP00000318687:Q116R;ENSP00000369768:Q116R;ENSP00000396090:Q118R;ENSP00000388778:Q13R	ENSP00000318687:Q116R	Q	-	2	0	HSPH1	30626852	1.000000	0.71417	1.000000	0.80357	0.016000	0.09150	7.698000	0.84413	2.330000	0.79161	0.533000	0.62120	CAG	.	.	.	none		0.343	HSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044384.1			C	31728852	T	C	31728852	3	2	30	1	0	0	0	0	1	0	0	0	7438	1580	55	3	2289	3	HSPH1	13	31728852	Missense_Mutation	SNP	T	TCGA-5P-A9JY-01A-11D-A42J-10		31728852	83441026	81	2188											
HNRNPC	3183	hgsc.bcm.edu	37	chr14	21679430	21679430	+	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	tctctgtcatcctctccttcCtcagcctctttttcatcatc	4	18	2	17	0	7	0	4	0	3	0	12	0	9	0	4	0	1	0	4	0	0	3			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr14:21679430C>A	ENST00000320084.7	-	8	1112	c.873G>T	c.(871-873)gaG>gaT	p.E291D	HNRNPC_ENST00000554455.1_Missense_Mutation_p.E291D|HNRNPC_ENST00000420743.2_Missense_Mutation_p.E291D|HNRNPC_ENST00000336053.6_3'UTR|HNRNPC_ENST00000555914.1_Missense_Mutation_p.E277D|HNRNPC_ENST00000556628.1_Missense_Mutation_p.E211D|HNRNPC_ENST00000449098.1_Missense_Mutation_p.E278D|HNRNPC_ENST00000553753.1_3'UTR|HNRNPC_ENST00000555883.1_Missense_Mutation_p.E235D|HNRNPC_ENST00000430246.2_Missense_Mutation_p.E278D|HNRNPC_ENST00000556142.1_3'UTR|HNRNPC_ENST00000555309.1_Missense_Mutation_p.E290D|HNRNPC_ENST00000556897.1_Missense_Mutation_p.E278D|HNRNPC_ENST00000556513.1_3'UTR|HNRNPC_ENST00000554969.1_Missense_Mutation_p.E278D|HNRNPC_ENST00000553300.1_Missense_Mutation_p.E278D|HNRNPC_ENST00000557201.1_Missense_Mutation_p.E291D	NM_001077442.1	NP_001070910.1	P07910	HNRPC_HUMAN	heterogeneous nuclear ribonucleoprotein C (C1/C2)	291	Asp/Glu-rich (acidic).				3'-UTR-mediated mRNA stabilization (GO:0070935)|ATP-dependent chromatin remodeling (GO:0043044)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|spliceosomal complex (GO:0005681)	identical protein binding (GO:0042802)|mRNA 3'-UTR binding (GO:0003730)|nucleosomal DNA binding (GO:0031492)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)			breast(1)|liver(1)|lung(6)|skin(1)	9	all_cancers(95;0.00176)		Epithelial(56;1.08e-06)|all cancers(55;8.95e-06)	GBM - Glioblastoma multiforme(265;0.00783)		CCTCTCCTTCCTCAGCCTCTT	0.488																																					p.E291D	NSCLC(108;607 2244 12726 38757)	Atlas-SNP	.											.	HNRNPC	31	.	0			c.G873T						PASS	.						124	134	131					14																	21679430		2138	4253	6391	SO:0001583	missense	3183	exon9			TCCTTCCTCAGCC		CCDS41915.1, CCDS45079.1	14q11.2	2013-06-12		2007-08-16	ENSG00000092199	ENSG00000092199		"RNA binding motif (RRM) containing"	5035	protein-coding gene	gene with protein product		164020		HNRPC		3457372	Standard	NM_031314		Approved	hnRNPC	uc001waa.3	P07910	OTTHUMG00000170757	ENST00000320084.7:c.873G>T	chr14.hg19:g.21679430C>A	ENSP00000319690:p.Glu291Asp	124.0	0.0	.		102.0	42.0	.	NM_031314	D3DS19|D3DS22|P22628|Q53EX2|Q59FD3|Q5FWE8|Q86SF8|Q86U45|Q96HK7|Q96HM4|Q96IY5|Q9BTS3	Missense_Mutation	SNP	ENST00000320084.7	hg19	CCDS41915.1	.	.	.	.	.	.	.	.	.	.	C	17.39	3.377766	0.61735	.	.	ENSG00000092199	ENST00000320084;ENST00000449098;ENST00000554969;ENST00000554455;ENST00000430246;ENST00000400042;ENST00000555914;ENST00000555309;ENST00000556628;ENST00000555883;ENST00000557201;ENST00000553300;ENST00000556897;ENST00000420743;ENST00000557157;ENST00000445284;ENST00000554539	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.15603	3.0;2.83;2.83;3.0;2.83;2.83;3.0;2.41;2.57;3.0;2.83;2.83;3.0;2.65;2.41	5.85	4.78	0.61160	.	0.170959	0.35179	U	0.003390	T	0.35098	0.0920	M	0.66939	2.045	0.39716	D	0.971396	D;D;D;P;D	0.71674	0.992;0.998;0.974;0.956;0.974	D;D;D;D;D	0.80764	0.986;0.994;0.969;0.931;0.969	T	0.07385	-1.0775	10	0.56958	D	0.05	.	7.8423	0.29406	0.0:0.7836:0.0:0.2164	.	211;235;277;291;278	P07910-3;P07910-4;G3V4C1;P07910;P07910-2	.;.;.;HNRPC_HUMAN;.	D	291;278;278;291;278;87;277;290;211;235;291;278;278;291;199;291;175	ENSP00000319690:E291D;ENSP00000404559:E278D;ENSP00000450725:E278D;ENSP00000451291:E291D;ENSP00000442816:E278D;ENSP00000451708:E277D;ENSP00000450790:E290D;ENSP00000451652:E211D;ENSP00000450629:E235D;ENSP00000452276:E291D;ENSP00000450544:E278D;ENSP00000451176:E278D;ENSP00000404848:E291D;ENSP00000450601:E199D;ENSP00000452545:E175D	ENSP00000319690:E291D	E	-	3	2	HNRNPC	20749270	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.775000	0.38584	2.755000	0.94549	0.655000	0.94253	GAG	.	.	.	none		0.488	HNRNPC-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410235.1			A	21679430	C	A	21679430	3	1	30	1	0	0	0	0	1	0	0	0	7269	680	24	4	51	4	HNRNPC	14	21679430	Missense_Mutation	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10		21679430	85670110	82	2189											
WDR20	91833	hgsc.bcm.edu	37	chr14	102675867	102675867	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagtgtcatggacggggccAttgcttctggggtcagcaaa	8	9	15	9	1	3	0	2	0	1	0	3	1	3	1	1	5	2	3	1	5	1	2	rs374240865		TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr14:102675867A>G	ENST00000342702.3	+	3	1391	c.1360A>G	c.(1360-1362)Att>Gtt	p.I454V	WDR20_ENST00000499851.2_Missense_Mutation_p.I197V|WDR20_ENST00000322340.5_Intron|WDR20_ENST00000335263.5_Missense_Mutation_p.I454V|WDR20_ENST00000299135.6_3'UTR|WDR20_ENST00000545563.1_Missense_Mutation_p.I281V|WDR20_ENST00000556807.1_Missense_Mutation_p.I393V|WDR20_ENST00000556511.2_Missense_Mutation_p.I393V|WDR20_ENST00000424963.2_Missense_Mutation_p.I330V|WDR20_ENST00000454394.2_Missense_Mutation_p.I485V	NM_001242418.1|NM_144574.3	NP_001229347.1|NP_653175.2	Q8TBZ3	WDR20_HUMAN	WD repeat domain 20	454										breast(1)|large_intestine(2)|lung(4)|prostate(1)	8						GGACGGGGCCATTGCTTCTGG	0.532											OREG0022939	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I485V		Atlas-SNP	.											.	WDR20	35	.	0			c.A1453G						PASS	.	A	,,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	1,4405	2.1+/-5.4	0,1,2202	102	101	102		,,1177,1453,1396,1360,1360,1177	-0.9	0.9	14		102	0,8600		0,0,4300	no	utr-3,intron,missense,missense,missense,missense,missense,missense	WDR20	NM_001242414.1,NM_001242415.1,NM_001242416.1,NM_001242417.1,NM_001242418.1,NM_144574.3,NM_181291.2,NM_181308.2	,,29,29,29,29,29,29	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	,,benign,benign,benign,benign,benign,benign	,,393/521,485/601,466/582,454/570,454/582,393/509	102675867	1,13005	2203	4300	6503	SO:0001583	missense	91833	exon4			GGGGCCATTGCTT	BC028387	CCDS9968.1, CCDS9969.1, CCDS9970.1, CCDS55942.1, CCDS55943.1, CCDS55944.1, CCDS55945.1	14q32.31	2013-01-09				ENSG00000140153		"WD repeat domain containing"	19667	protein-coding gene	gene with protein product							Standard	NM_181291		Approved	DMR, MGC33177, FLJ33659	uc010txu.2	Q8TBZ3		ENST00000342702.3:c.1360A>G	chr14.hg19:g.102675867A>G	ENSP00000341037:p.Ile454Val	134.0	0.0	.	1368	126.0	70.0	.	NM_001242417	B4DN18|E7EUY8|F8W9S4|G3V2F8|G3V5R0|H0YJJ1|Q86TU2|Q8NCN7|Q8WXX2|Q9UF86	Missense_Mutation	SNP	ENST00000342702.3	hg19	CCDS9969.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.973|0.973	-0.699494|-0.699494	0.03279|0.03279	2.27E-4|2.27E-4	0.0|0.0	ENSG00000140153|ENSG00000140153	ENST00000556511|ENST00000335263;ENST00000299135;ENST00000424963;ENST00000342702;ENST00000556807;ENST00000499851;ENST00000454394;ENST00000401892;ENST00000545563	.|T;T;T;T;T;T;T	.|0.57107	.|0.42;0.42;0.42;0.42;0.42;0.42;0.42	5.73|5.73	-0.897|-0.897	0.10553|0.10553	.|.	.|0.202343	.|0.51477	.|N	.|0.000097	T|T	0.31358|0.31358	0.0794|0.0794	L|L	0.34521|0.34521	1.04|1.04	0.45883|0.45883	D|D	0.998733|0.998733	.|B;B;B;B;B;B;B	.|0.06786	.|0.0;0.0;0.0;0.0;0.0;0.001;0.0	.|B;B;B;B;B;B;B	.|0.04013	.|0.001;0.0;0.001;0.001;0.001;0.0;0.0	T|T	0.10222|0.10222	-1.0639|-1.0639	5|10	.|0.12430	.|T	.|0.62	.|.	6.2989|6.2989	0.21101|0.21101	0.6201:0.1198:0.2601:0.0|0.6201:0.1198:0.2601:0.0	.|.	.|485;466;393;454;393;330;454	.|E7EUY8;Q5JPH5;G3V2F8;Q8TBZ3-2;F8W9S4;B3KR43;Q8TBZ3	.|.;.;.;.;.;.;WDR20_HUMAN	R|V	384|454;393;330;454;393;197;485;384;281	.|ENSP00000335434:I454V;ENSP00000395793:I330V;ENSP00000341037:I454V;ENSP00000450636:I393V;ENSP00000443641:I197V;ENSP00000406084:I485V;ENSP00000437927:I281V	.|ENSP00000299135:I393V	H|I	+|+	2|1	0|0	WDR20|WDR20	101745620|101745620	1.000000|1.000000	0.71417|0.71417	0.860000|0.860000	0.33809|0.33809	0.999000|0.999000	0.98932|0.98932	1.243000|1.243000	0.32767|0.32767	-0.385000|-0.385000	0.07833|0.07833	0.533000|0.533000	0.62120|0.62120	CAT|ATT	.	.	.	weak		0.532	WDR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414963.1	NM_181291		G	102675867	A	G	102675867	3	3	30	1	0	0	0	0	1	0	0	0	17292	217	8	3	1387	3	WDR20	14	102675867	Missense_Mutation	SNP	A	TCGA-5P-A9JY-01A-11D-A42J-10	80996437	102675867	4673673	83	2190											
AQR	9716	hgsc.bcm.edu	37	chr15	35196623	35196623	+	Missense_Mutation	SNP	T	T	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	tccattttgtatagtattggTcatatcttgttgatactggt	8	20	8	5	0	2	1	1	1	1	0	3	1	3	1	1	2	1	3	1	2	5	10			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr15:35196623T>G	ENST00000156471.5	-	19	2140	c.1915A>C	c.(1915-1917)Acc>Ccc	p.T639P		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	639					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		ATAGTATTGGTCATATCTTGT	0.348																																					p.T639P		Atlas-SNP	.											.	AQR	139	.	0			c.A1915C						PASS	.						111	101	104					15																	35196623		1810	4073	5883	SO:0001583	missense	9716	exon19			TATTGGTCATATC	AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 164"	610548	"aquarius homolog (mouse)"			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.1915A>C	chr15.hg19:g.35196623T>G	ENSP00000156471:p.Thr639Pro	181.0	0.0	.		138.0	70.0	.	NM_014691	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Missense_Mutation	SNP	ENST00000156471.5	hg19	CCDS42013.1	.	.	.	.	.	.	.	.	.	.	T	13.74	2.328239	0.41197	.	.	ENSG00000021776	ENST00000156471;ENST00000543879	D	0.93763	-3.28	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	D	0.91226	0.7235	M	0.61703	1.905	0.48975	D	0.999738	P	0.46706	0.883	B	0.38458	0.274	D	0.91292	0.5060	10	0.42905	T	0.14	-16.3603	15.4615	0.75359	0.0:0.0:0.0:1.0	.	639	O60306	AQR_HUMAN	P	639	ENSP00000156471:T639P	ENSP00000156471:T639P	T	-	1	0	AQR	32983915	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.608000	0.82898	2.117000	0.64856	0.533000	0.62120	ACC	.	.	.	none		0.348	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691		G	35196623	T	G	35196623	3	3	30	1	0	0	0	0	1	0	0	0	835	1667	58	5	2610	5	AQR	15	35196623	Missense_Mutation	SNP	T	TCGA-5P-A9JY-01A-11D-A42J-10		35196623	67334769	84	2191											
RTF1	23168	hgsc.bcm.edu	37	chr15	41709461	41709461	+	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	agaagcggaaaggccgcgtcGtgatcgactcggacacagag	12	4	15	10	6	0	3	0	1	0	2	3	6	0	5	1	3	1	0	1	3	2	0			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr15:41709461G>C	ENST00000389629.4	+	1	160	c.148G>C	c.(148-150)Gtg>Ctg	p.V50L	RTF1_ENST00000462276.1_3'UTR	NM_015138.4	NP_055953.3	Q92541	RTF1_HUMAN	Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	50					DNA-templated transcription, initiation (GO:0006352)|endodermal cell fate commitment (GO:0001711)|histone H3-K4 trimethylation (GO:0080182)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)	18		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)		AGGCCGCGTCGTGATCGACTC	0.721																																					p.V50L		Atlas-SNP	.											.	RTF1	76	.	0			c.G148C						PASS	.						18	22	21					15																	41709461		692	1591	2283	SO:0001583	missense	23168	exon1			CGCGTCGTGATCG	D87440	CCDS32200.2	15q14	2004-03-03	2005-07-20	2005-07-20	ENSG00000137815	ENSG00000137815			28996	protein-coding gene	gene with protein product		611633	"KIAA0252"	KIAA0252		15632063	Standard	NM_015138		Approved		uc001zny.3	Q92541	OTTHUMG00000133744	ENST00000389629.4:c.148G>C	chr15.hg19:g.41709461G>C	ENSP00000374280:p.Val50Leu	243.0	0.0	.		172.0	78.0	.	NM_015138	Q96BX6	Missense_Mutation	SNP	ENST00000389629.4	hg19	CCDS32200.2	.	.	.	.	.	.	.	.	.	.	G	14.44	2.537417	0.45176	.	.	ENSG00000137815	ENST00000389629	.	.	.	4.06	4.06	0.47325	.	0.093110	0.41500	U	0.000876	T	0.39462	0.1079	N	0.16790	0.44	0.37411	D	0.913231	B	0.06786	0.001	B	0.04013	0.001	T	0.36286	-0.9754	9	0.26408	T	0.33	-1.56	12.7087	0.57078	0.0:0.2172:0.7828:0.0	.	50	Q92541	RTF1_HUMAN	L	50	.	ENSP00000374280:V50L	V	+	1	0	RTF1	39496753	1.000000	0.71417	0.992000	0.48379	0.993000	0.82548	5.349000	0.66010	2.252000	0.74401	0.462000	0.41574	GTG	.	.	.	none		0.721	RTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258111.1	NM_015138		C	41709461	G	C	41709461	3	2	30	1	0	0	0	0	1	0	0	0	13734	1145	40	4	150	4	RTF1	15	41709461	Missense_Mutation	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	6512838	41709461	60821931	85	2192											
CA12	771	hgsc.bcm.edu	37	chr15	63632589	63632589	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggtagcggtaatattcagcGgtcctctccggaagcagctc	8	9	12	12	4	2	0	1	0	1	0	5	1	3	1	2	4	4	4	2	4	4	4			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr15:63632589G>A	ENST00000178638.3	-	7	1085	c.645C>T	c.(643-645)acC>acT	p.T215T	CA12_ENST00000344366.3_Silent_p.T215T|CA12_ENST00000422263.2_Silent_p.T155T	NM_001218.3	NP_001209.1	O43570	CAH12_HUMAN	carbonic anhydrase XII	215					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	16					Benzthiazide(DB00562)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Zonisamide(DB00909)	AATATTCAGCGGTCCTCTCCG	0.567																																					p.T215T		Atlas-SNP	.											CA12,NS,carcinoma,0,1	CA12	33	.	0			c.C645T						PASS	.						90	79	83					15																	63632589		2203	4300	6503	SO:0001819	synonymous_variant	771	exon7			TTCAGCGGTCCTC	AF051882	CCDS10185.1, CCDS10186.1	15q22	2004-01-19			ENSG00000074410	ENSG00000074410		"Carbonic anhydrases"	1371	protein-coding gene	gene with protein product		603263				9636197	Standard	NM_001218		Approved	HsT18816	uc002amc.3	O43570	OTTHUMG00000132881	ENST00000178638.3:c.645C>T	chr15.hg19:g.63632589G>A		160.0	0.0	.		138.0	33.0	.	NM_206925	B2RE24|Q53YE5|Q9BWG2	Silent	SNP	ENST00000178638.3	hg19	CCDS10185.1																																																																																			.	.	.	none		0.567	CA12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256370.1	NM_001218		A	63632589	G	A	63632589	2	1	30	1	0	0	0	0	0	0	0	1	2515	1103	39	1		1	CA12	15	63632589	Silent	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	21923128	63632589	38898803	86	2193											
SLC24A1	9187	hgsc.bcm.edu	37	chr15	65943145	65943145	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaagaggaggaggaggaggaGgaagaggaggagaagggaaa	18	0	23	0	0	0	3	0	0	0	3	0	13	0	11	0	9	0	0	0	9	4	0			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr15:65943145G>A	ENST00000261892.6	+	7	2945	c.2658G>A	c.(2656-2658)gaG>gaA	p.E886E	SLC24A1_ENST00000339868.6_Silent_p.E868E|SLC24A1_ENST00000544319.2_Silent_p.E772E|SLC24A1_ENST00000537259.1_Silent_p.E868E|SLC24A1_ENST00000399033.4_Silent_p.E886E|SLC24A1_ENST00000546330.1_Silent_p.E868E|SLC24A1_ENST00000449142.2_3'UTR	NM_001254740.1|NM_004727.2	NP_001241669.1|NP_004718.1	O60721	NCKX1_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 1	886	Poly-Glu.				calcium ion transport (GO:0006816)|ion transport (GO:0006811)|phototransduction, visible light (GO:0007603)|response to light intensity (GO:0009642)|rhodopsin mediated signaling pathway (GO:0016056)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|outer membrane (GO:0019867)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						aggaggaggaggaagaggagg	0.567																																					p.E886E		Atlas-SNP	.											.	SLC24A1	58	.	0			c.G2658A						PASS	.						44	49	48					15																	65943145		2194	4289	6483	SO:0001819	synonymous_variant	9187	exon7			GGAGGAGGAAGAG	AF062922	CCDS45284.1, CCDS73742.1, CCDS73743.1, CCDS73744.1	15q22.31	2014-01-28			ENSG00000074621	ENSG00000074621		"Solute carriers"	10975	protein-coding gene	gene with protein product		603617				9856482	Standard	NM_004727		Approved	NCKX1, NCKX, RODX, KIAA0702, HsT17412, CSNB1D	uc010ujf.2	O60721	OTTHUMG00000167960	ENST00000261892.6:c.2658G>A	chr15.hg19:g.65943145G>A		77.0	0.0	.		84.0	4.0	.	NM_004727	O43485|O75184|Q17RM9	Silent	SNP	ENST00000261892.6	hg19	CCDS45284.1																																																																																			.	.	.	none		0.567	SLC24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397304.1	NM_004727		A	65943145	G	A	65943145	2	1	30	1	0	0	0	0	0	0	0	1	14478	991	35	2		2	SLC24A1	15	65943145	Silent	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	2310556	65943145	36588247	87	2194											
PPCDC	60490	hgsc.bcm.edu	37	chr15	75341008	75341009	+	Frame_Shift_Del	DEL	TT	TT	-																															aggtagaccagctcaaggccTttggctatgtcgagatcccc																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr15:75341008_75341009delTT	ENST00000342932.3	+	5	619_620	c.475_476delTT	c.(475-477)tttfs	p.F159fs	PPCDC_ENST00000563393.1_Frame_Shift_Del_p.F36fs|PPCDC_ENST00000568649.1_Frame_Shift_Del_p.F116fs|PPCDC_ENST00000564923.1_Frame_Shift_Del_p.F84fs|PPCDC_ENST00000567336.1_Frame_Shift_Del_p.F127fs	NM_021823.3	NP_068595.3	Q96CD2	COAC_HUMAN	phosphopantothenoylcysteine decarboxylase	159					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)	phosphopantothenoylcysteine decarboxylase activity (GO:0004633)			breast(1)|cervix(1)	2						GCTCAAGGCCTTTGGCTATGTC	0.619																																					p.158_159del		Atlas-Indel,Pindel	.											.	PPCDC	12	.	0			c.474_475del						PASS	.																																			SO:0001589	frameshift_variant	60490	exon5			.	AK027491	CCDS10275.1, CCDS73761.1, CCDS73759.1, CCDS73760.1	15q24.2	2005-08-16			ENSG00000138621	ENSG00000138621	4.1.1.36		28107	protein-coding gene	gene with protein product		609854				12975309, 11923312	Standard	XM_005254579		Approved	MDS018, FLJ14585	uc002azo.3	Q96CD2	OTTHUMG00000142824	ENST00000342932.3:c.475_476delTT	chr15.hg19:g.75341008_75341009delTT	ENSP00000343190:p.Phe159fs	129.0	0.0	0		62.0	22.0	0.354839	NM_021823	Q96SX0|Q9HC17	Frame_Shift_Del	DEL	ENST00000342932.3	hg19	CCDS10275.1																																																																																			.	.	.	none		0.619	PPCDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286416.1	NM_021823		-	75341009	TT	-	75341008	7	5	30	1	0	1	0	1	0	0	0	0	12311	1609	56	0	489	0	PPCDC	15	75341008	Frame_Shift_Del	DEL	TT	TCGA-5P-A9JY-01A-11D-A42J-10	9397863	75341008	27190384	88	2195											
GNG13	51764	hgsc.bcm.edu	37	chr16	849062	849062	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctttcttcatctgtggcaCgtcccactcctccatggggt	4	14	8	15	1	4	0	1	0	3	0	7	0	7	0	3	3	0	1	3	3	0	2			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr16:849062C>T	ENST00000248150.4	-	2	117	c.16G>A	c.(16-18)Gtg>Atg	p.V6M		NM_016541.2	NP_057625.1	Q9P2W3	GBG13_HUMAN	guanine nucleotide binding protein (G protein), gamma 13	6					cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|sensory perception of taste (GO:0050909)|small molecule metabolic process (GO:0044281)	heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|signal transducer activity (GO:0004871)			ovary(1)	1		Hepatocellular(780;0.00335)				ATCTGTGGCACGTCCCACTCC	0.647																																					p.V6M		Atlas-SNP	.											.	GNG13	8	.	0			c.G16A						PASS	.						111	88	96					16																	849062		2198	4298	6496	SO:0001583	missense	51764	exon2			GTGGCACGTCCCA	AB030207	CCDS10427.1	16p13.3	2008-08-01			ENSG00000127588	ENSG00000127588			14131	protein-coding gene	gene with protein product	"G gamma subunit, clone:h2-35"	607298				10570481	Standard	NM_016541		Approved	h2-35, G(gamma)13	uc002ckh.4	Q9P2W3	OTTHUMG00000047839	ENST00000248150.4:c.16G>A	chr16.hg19:g.849062C>T	ENSP00000248150:p.Val6Met	30.0	0.0	.		58.0	33.0	.	NM_016541	B2R5C8|Q52LX0|Q9UJJ3	Missense_Mutation	SNP	ENST00000248150.4	hg19	CCDS10427.1	.	.	.	.	.	.	.	.	.	.	C	12.17	1.857389	0.32791	.	.	ENSG00000127588	ENST00000248150	T	0.24723	1.84	5.57	3.63	0.41609	G-protein gamma domain (4);	0.498697	0.22298	N	0.061909	T	0.14570	0.0352	.	.	.	0.23632	N	0.997248	P	0.43412	0.806	B	0.32090	0.14	T	0.17471	-1.0368	9	0.56958	D	0.05	-22.0611	7.2617	0.26207	0.0:0.701:0.1418:0.1572	.	6	Q9P2W3	GBG13_HUMAN	M	6	ENSP00000248150:V6M	ENSP00000248150:V6M	V	-	1	0	GNG13	789063	0.135000	0.22499	0.674000	0.29902	0.804000	0.45430	1.921000	0.40035	1.369000	0.46134	-0.221000	0.12465	GTG	.	.	.	none		0.647	GNG13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109062.3	NM_016541		T	849062	C	T	849062	3	4	30	1	0	0	0	0	1	0	0	0	6533	536	19	1	195	1	GNG13	16	849062	Missense_Mutation	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10		849062	89505691	89	2196											
NLRC3	197358	hgsc.bcm.edu	37	chr16	3594306	3594306	+	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	ccaccgcacacgctccgtcaTccccgatggcgttctcctgt	5	9	8	19	5	2	0	1	0	1	0	5	1	4	0	6	1	0	3	6	1	0	1			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr16:3594306T>C	ENST00000301749.7	-	0	3200				NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000603507.1_RNA|LA16c-390H2.4_ENST00000573820.1_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						CGCTCCGTCATCCCCGATGGC	0.592																																					p.D932G		Atlas-SNP	.											.	NLRC3	103	.	0			c.A2795G						PASS	.						71	76	74					16																	3594306		2092	4224	6316			197358	exon17			CCGTCATCCCCGA	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		chr16.hg19:g.3594306T>C		87.0	0.0	.		113.0	69.0	.	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	hg19		.	.	.	.	.	.	.	.	.	.	T	16.86	3.238733	0.58995	.	.	ENSG00000167984	ENST00000301749;ENST00000359128;ENST00000448023	T;T;T	0.70516	-0.49;-0.49;-0.49	5.28	5.28	0.74379	.	0.062992	0.64402	D	0.000007	T	0.81098	0.4752	M	0.82323	2.585	0.27170	N	0.960946	D	0.56521	0.976	P	0.57152	0.814	T	0.77216	-0.2669	10	0.72032	D	0.01	.	11.5799	0.50885	0.0:0.0:0.0:1.0	.	978	C9JLH9	.	G	932;903;978	ENSP00000301749:D932G;ENSP00000352039:D903G;ENSP00000414415:D978G	ENSP00000301749:D932G	D	-	2	0	NLRC3	3534307	1.000000	0.71417	0.993000	0.49108	0.342000	0.28953	5.519000	0.67074	2.235000	0.73313	0.524000	0.50904	GAT	.	.	.	none		0.592	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844		C	3594306	T	C	3594306	1	2	30	0	1	0	0	0	0	0	0	0	10475	1435	50	3		3	NLRC3	16	3594306	RNA	SNP	T	TCGA-5P-A9JY-01A-11D-A42J-10	2745244	3594306	86760447	90	2197											
UBN1	29855	hgsc.bcm.edu	37	chr16	4927063	4927068	+	In_Frame_Del	DEL	CATCGT	CATCGT	-																															gcaggggtctccaaggatgcCatcgtcacaggccctgcccc																								rs141880836|rs191007074		TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	CATCGT	CATCGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr16:4927063_4927068delCATCGT	ENST00000396658.4	+	15	3919_3924	c.3216_3221delCATCGT	c.(3214-3222)gccatcgtc>gcc	p.IV1073del	UBN1_ENST00000545171.1_In_Frame_Del_p.IV1073del|UBN1_ENST00000590769.1_In_Frame_Del_p.IV1073del|UBN1_ENST00000262376.6_In_Frame_Del_p.IV1073del	NM_016936.3	NP_058632.2	Q9NPG3	UBN1_HUMAN	ubinuclein 1	1073					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						CCAAGGATGCCATCGTCACAGGCCCT	0.578																																					p.1072_1074del		Atlas-Indel,Pindel	.											.	UBN1	88	.	0			c.3215_3220del						PASS	.																																			SO:0001651	inframe_deletion	29855	exon16			.	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.3216_3221delCATCGT	chr16.hg19:g.4927063_4927068delCATCGT	ENSP00000379894:p.Ile1073_Val1074del	73.0	0.0	0		82.0	35.0	0.426829	NM_001079514	B7Z6D3|D3DUE8|Q13079|Q9P1P7	In_Frame_Del	DEL	ENST00000396658.4	hg19	CCDS10525.1																																																																																			.	.	.	none		0.578	UBN1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251719.1	NM_016936		-	4927068	CATCGT	-	4927063	7	5	30	1	0	1	0	1	0	0	0	0	16904	581	21	0	3274	0	UBN1	16	4927063	In_Frame_Del	DEL	CATCGT	TCGA-5P-A9JY-01A-11D-A42J-10	1332757	4927063	85427690	91	2198											
C16orf72	29035	hgsc.bcm.edu	37	chr16	9196862	9196862	+	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	aagcgtggatacccatcaacGaagttttgatattggaattc	13	12	9	7	2	1	1	1	1	0	0	2	4	1	3	1	2	3	1	1	2	6	6			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr16:9196862G>A	ENST00000327827.7	+	3	726	c.329G>A	c.(328-330)cGa>cAa	p.R110Q	RP11-473I1.5_ENST00000565648.1_RNA|RP11-473I1.9_ENST00000574285.1_RNA	NM_014117.2	NP_054836.2	Q14CZ0	CP072_HUMAN	chromosome 16 open reading frame 72	110										endometrium(4)|large_intestine(2)|lung(2)	8						ACCCATCAACGAAGTTTTGAT	0.373																																					p.R110Q		Atlas-SNP	.											.	C16orf72	26	.	0			c.G329A						PASS	.						91	91	91					16																	9196862		2197	4300	6497	SO:0001583	missense	29035	exon3			ATCAACGAAGTTT	AK123266	CCDS10538.1	16p13.2	2012-11-19			ENSG00000182831	ENSG00000182831			30103	protein-coding gene	gene with protein product						8889548	Standard	NM_014117		Approved	FLJ41272, PRO0149	uc002czm.3	Q14CZ0	OTTHUMG00000178147	ENST00000327827.7:c.329G>A	chr16.hg19:g.9196862G>A	ENSP00000331720:p.Arg110Gln	86.0	0.0	.		153.0	51.0	.	NM_014117		Missense_Mutation	SNP	ENST00000327827.7	hg19	CCDS10538.1	.	.	.	.	.	.	.	.	.	.	G	32	5.171478	0.94807	.	.	ENSG00000182831	ENST00000327827	T	0.50277	0.75	5.98	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.65995	0.2745	M	0.78801	2.425	0.58432	D	0.999999	D	0.76494	0.999	P	0.57425	0.82	T	0.71852	-0.4467	10	0.62326	D	0.03	-1.7932	17.2125	0.86935	0.0:0.1261:0.8739:0.0	.	110	Q14CZ0	CP072_HUMAN	Q	110	ENSP00000331720:R110Q	ENSP00000331720:R110Q	R	+	2	0	C16orf72	9104363	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.751000	0.98889	1.514000	0.48869	0.591000	0.81541	CGA	.	.	.	none		0.373	C16orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440760.2	NM_014117		A	9196862	G	A	9196862	3	1	30	1	0	0	0	0	1	0	0	0	1833	1058	37	1	339	1	C16orf72	16	9196862	Missense_Mutation	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	4269799	9196862	81157891	92	2199											
SNX29	92017	hgsc.bcm.edu	37	chr16	12571579	12571579	+	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	tttctctttcttgacaggtcTacatccggataaaagacgat	11	14	7	9	2	3	2	0	1	3	1	5	4	4	3	1	2	1	0	1	2	3	5			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr16:12571579T>A	ENST00000566228.1	+	19	2110	c.2041T>A	c.(2041-2043)Tac>Aac	p.Y681N	SNX29_ENST00000323433.4_Missense_Mutation_p.Y296N|SNX29_ENST00000306030.3_Missense_Mutation_p.Y296N	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	681	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.					extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						TTGACAGGTCTACATCCGGAT	0.413																																					p.Y681N		Atlas-SNP	.											.	SNX29	60	.	0			c.T2041A						PASS	.						78	72	74					16																	12571579		1851	4094	5945	SO:0001583	missense	92017	exon19			CAGGTCTACATCC	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.2041T>A	chr16.hg19:g.12571579T>A	ENSP00000456480:p.Tyr681Asn	273.0	1.0	.		295.0	173.0	.	NM_032167	B5MDW2|Q8N2X2|Q9HA26	Missense_Mutation	SNP	ENST00000566228.1	hg19	CCDS10553.2	.	.	.	.	.	.	.	.	.	.	T	17.14	3.312908	0.60414	.	.	ENSG00000048471	ENST00000306030;ENST00000323433	T;T	0.38240	1.15;1.15	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.41119	0.1145	L	0.37850	1.14	0.38631	D	0.951388	.	.	.	.	.	.	T	0.37079	-0.9721	8	0.45353	T	0.12	-15.4993	13.9674	0.64218	0.0:0.0:0.0:1.0	.	.	.	.	N	296	ENSP00000306940:Y296N;ENSP00000322226:Y296N	ENSP00000306940:Y296N	Y	+	1	0	SNX29	12479080	1.000000	0.71417	1.000000	0.80357	0.236000	0.25371	7.508000	0.81686	2.180000	0.69256	0.533000	0.62120	TAC	.	.	.	none		0.413	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422622.1			A	12571579	T	A	12571579	3	1	30	1	0	0	0	0	1	0	0	0	14911	1522	53	5	928	5	SNX29	16	12571579	Missense_Mutation	SNP	T	TCGA-5P-A9JY-01A-11D-A42J-10	3374717	12571579	77783174	93	2200											
APOB48R	55911	hgsc.bcm.edu	37	chr16	28507402	28507402	+	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	ctcaggcggggaggctgggaCagcctcaggaggggaggagg	8	3	22	8	1	2	0	2	0	0	0	2	5	2	5	1	10	1	1	1	10	0	0	rs148114931|rs62034314		TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr16:28507402C>T	ENST00000431282.1	+	2	1050	c.1040C>T	c.(1039-1041)aCa>aTa	p.T347I	CLN3_ENST00000567160.1_5'Flank|APOBR_ENST00000328423.5_Missense_Mutation_p.T347I|APOBR_ENST00000564831.1_Missense_Mutation_p.T347I|CLN3_ENST00000569430.1_5'Flank			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor	347	Glu-rich.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						GAGGCTGGGACAGCCTCAGGA	0.711																																					p.T347I		Atlas-SNP	.											.	APOBR	89	.	0			c.C1040T						PASS	.						9	11	10					16																	28507402		1844	3986	5830	SO:0001583	missense	55911	exon2			CTGGGACAGCCTC	AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"apolipoprotein B48 receptor", "apolipoprotein B100 receptor"	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83		ENST00000431282.1:c.1040C>T	chr16.hg19:g.28507402C>T	ENSP00000416094:p.Thr347Ile	27.0	0.0	.		40.0	6.0	.	NM_018690	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Missense_Mutation	SNP	ENST00000431282.1	hg19		.	.	.	.	.	.	.	.	.	.	c	13.05	2.120378	0.37436	.	.	ENSG00000184730	ENST00000328423;ENST00000431282	T;T	0.60424	0.19;0.19	3.61	-7.21	0.01490	.	.	.	.	.	T	0.34513	0.0900	N	0.19112	0.55	0.09310	N	1	.	.	.	.	.	.	T	0.35724	-0.9777	7	0.38643	T	0.18	.	3.7838	0.08692	0.2212:0.2578:0.4267:0.0943	rs62034314	.	.	.	I	347	ENSP00000327669:T347I;ENSP00000416094:T347I	ENSP00000327669:T347I	T	+	2	0	APOBR	28414903	0.002000	0.14202	0.000000	0.03702	0.006000	0.05464	-0.337000	0.07852	-0.824000	0.04295	0.455000	0.32223	ACA	.	C|0.500;T|0.500	0.500	weak		0.711	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_182804		T	28507402	C	T	28507402	3	4	30	1	0	0	0	0	1	0	0	0	786	478	17	2	1046	2	APOB48R	16	28507402	Missense_Mutation	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10	15935823	28507402	61847351	94	2201											
CPNE2	221184	hgsc.bcm.edu	37	chr16	57147302	57147317	+	Frame_Shift_Del	DEL	CTCTTTGACCAGGACA	CTCTTTGACCAGGACA	-																															tacagaagctcaagttcgcgCtctttgaccaggacaagtcc																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	CTCTTTGACCAGGACA	CTCTTTGACCAGGACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr16:57147302_57147317delCTCTTTGACCAGGACA	ENST00000535318.2	+	4	644_659	c.283_298delCTCTTTGACCAGGACA	c.(283-300)ctctttgaccaggacaagfs	p.LFDQDK95fs	CPNE2_ENST00000537605.1_5'UTR|CPNE2_ENST00000565874.1_Frame_Shift_Del_p.LFDQDK95fs|CPNE2_ENST00000290776.8_Frame_Shift_Del_p.LFDQDK95fs			Q96FN4	CPNE2_HUMAN	copine II	95	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)				CAAGTTCGCGCTCTTTGACCAGGACAAGTCCAGTAT	0.593																																					p.94_99del		Atlas-Indel,Pindel	.											.	CPNE2	48	.	0			c.282_297del						PASS	.																																			SO:0001589	frameshift_variant	221184	exon3			.		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.283_298delCTCTTTGACCAGGACA	chr16.hg19:g.57147302_57147317delCTCTTTGACCAGGACA	ENSP00000439018:p.Leu95fs	99.0	0.0	0		126.0	15.0	0.119048	NM_152727	Q68D19|Q719H8|Q86XP9	Frame_Shift_Del	DEL	ENST00000535318.2	hg19	CCDS10774.1																																																																																			.	.	.	none		0.593	CPNE2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432986.2	NM_152727		-	57147317	CTCTTTGACCAGGACA	-	57147302	7	5	30	1	0	1	0	1	0	0	0	0	3814	797	28	0	289	0	CPNE2	16	57147302	Frame_Shift_Del	DEL	CTCTTTGACCAGGACA	TCGA-5P-A9JY-01A-11D-A42J-10	28639900	57147302	33207451	95	2202											
SPAG7	9552	hgsc.bcm.edu	37	chr17	4871090	4871090	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctcaggatggagcccagtaGgtccgccatcttgggagtga	8	8	15	10	1	2	1	1	1	1	0	3	4	3	4	3	4	1	2	3	4	1	2			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr17:4871090G>A	ENST00000206020.3	-	1	77	c.10C>T	c.(10-12)Cta>Tta	p.L4L	RP5-1050D4.3_ENST00000576752.1_RNA|SPAG7_ENST00000575142.1_5'Flank|SPAG7_ENST00000573366.1_5'Flank|SPAG7_ENST00000571023.1_5'UTR	NM_004890.2	NP_004881.2	O75391	SPAG7_HUMAN	sperm associated antigen 7	4						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			central_nervous_system(1)|endometrium(1)|kidney(2)|lung(3)|ovary(2)|urinary_tract(1)	10						GAGCCCAGTAGGTCCGCCATC	0.617																																					p.L4L		Atlas-SNP	.											.	SPAG7	22	.	0			c.C10T						PASS	.						70	76	74					17																	4871090		1970	4148	6118	SO:0001819	synonymous_variant	9552	exon1			CCAGTAGGTCCGC	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.10C>T	chr17.hg19:g.4871090G>A		45.0	0.0	.		74.0	20.0	.	NM_004890	Q96EU5	Silent	SNP	ENST00000206020.3	hg19	CCDS42240.1																																																																																			.	.	.	none		0.617	SPAG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438747.1	NM_004890		A	4871090	G	A	4871090	2	1	30	1	0	0	0	0	0	0	0	1	14996	991	35	2		2	SPAG7	17	4871090	Silent	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10		4871090	76324120	96	2203											
MYH10	4628	hgsc.bcm.edu	37	chr17	8404183	8404183	+	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	tgctctgagagctcctccagGgctgttgcgtgtctttgtct	3	15	12	11	1	3	1	0	1	3	1	5	2	5	1	2	1	3	4	2	1	0	2			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr17:8404183G>T	ENST00000269243.4	-	27	3750	c.3612C>A	c.(3610-3612)gcC>gcA	p.A1204A	MYH10_ENST00000360416.3_Silent_p.A1235A|MYH10_ENST00000396239.1_Silent_p.A1225A|MYH10_ENST00000379980.4_Silent_p.A1220A	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	1204					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						GCTCCTCCAGGGCTGTTGCGT	0.547																																					p.A1235A		Atlas-SNP	.											.	MYH10	148	.	0			c.C3705A						PASS	.						176	158	164					17																	8404183		2203	4300	6503	SO:0001819	synonymous_variant	4628	exon29			CTCCAGGGCTGTT	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.3612C>A	chr17.hg19:g.8404183G>T		39.0	0.0	.		42.0	15.0	.	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	hg19	CCDS11144.1																																																																																			.	.	.	none		0.547	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			T	8404183	G	T	8404183	2	4	30	1	0	0	0	0	0	0	0	1	10037	1219	43	4		4	MYH10	17	8404183	Silent	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	3533093	8404183	72791027	97	2204											
DNAH9	1770	hgsc.bcm.edu	37	chr17	11672607	11672607	+	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	aggcatacctggtgaaaaacGtgccattcaactactacacc	14	8	7	12	1	1	1	1	1	0	0	1	1	1	1	3	2	6	1	3	2	6	4	rs61744697	byFrequency	TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr17:11672607G>C	ENST00000262442.4	+	38	7581	c.7513G>C	c.(7513-7515)Gtg>Ctg	p.V2505L	DNAH9_ENST00000454412.2_Missense_Mutation_p.V2505L	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2505	AAA 3. {ECO:0000250}.			V -> L (in Ref. 1; AAF69004). {ECO:0000305}.	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)		GGTGAAAAACGTGCCATTCAA	0.627																																					p.V2505L		Atlas-SNP	.											.	DNAH9	695	.	0			c.G7513C						PASS	.						61	53	56					17																	11672607		2203	4300	6503	SO:0001583	missense	1770	exon38			AAAAACGTGCCAT	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.7513G>C	chr17.hg19:g.11672607G>C	ENSP00000262442:p.Val2505Leu	74.0	0.0	.		98.0	58.0	.	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.782584	0.90282	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.46063	0.88;0.88	5.41	4.42	0.53409	ATPase, AAA+ type, core (1);	0.072443	0.53938	D	0.000045	T	0.53449	0.1797	L	0.50847	1.595	0.80722	D	1	D	0.56521	0.976	P	0.60173	0.87	T	0.47289	-0.9129	10	0.37606	T	0.19	.	15.0436	0.71811	0.0722:0.0:0.9278:0.0	.	2505	Q9NYC9	DYH9_HUMAN	L	2505;2505;1087	ENSP00000262442:V2505L;ENSP00000414874:V2505L	ENSP00000262442:V2505L	V	+	1	0	DNAH9	11613332	1.000000	0.71417	0.998000	0.56505	0.899000	0.52679	6.624000	0.74243	2.696000	0.92011	0.655000	0.94253	GTG	.	G|0.901;T|0.099	.	alt		0.627	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		C	11672607	G	C	11672607	3	2	30	1	0	0	0	0	1	0	0	0	4610	1145	40	4	7663	4	DNAH9	17	11672607	Missense_Mutation	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	3268424	11672607	69522603	98	2205											
NF1	4763	hgsc.bcm.edu	37	chr17	29654742	29654742	+	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	ttcatatccggacccgctggGaactgtcacagcccgactct	8	9	9	15	3	3	0	2	0	1	0	4	3	4	2	3	2	2	1	3	2	2	2			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr17:29654742G>A	ENST00000358273.4	+	38	5877	c.5494G>A	c.(5494-5496)Gaa>Aaa	p.E1832K	NF1_ENST00000581113.2_3'UTR|NF1_ENST00000356175.3_Missense_Mutation_p.E1811K	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1832	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)		GACCCGCTGGGAACTGTCACA	0.512			"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.E1832K		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.G5494A						PASS	.						122	117	119					17																	29654742		2203	4300	6503	SO:0001583	missense	4763	exon38	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	CGCTGGGAACTGT		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.5494G>A	chr17.hg19:g.29654742G>A	ENSP00000351015:p.Glu1832Lys	159.0	0.0	.		262.0	70.0	.	NM_001042492	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	hg19	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.829086	0.90955	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	D;D;D	0.96427	-4.01;-4.01;-4.01	5.8	5.8	0.92144	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.96371	0.8816	L	0.33137	0.985	0.80722	D	1	B;D;P	0.54964	0.001;0.969;0.939	B;D;P	0.64321	0.001;0.924;0.657	D	0.94673	0.7858	10	0.21014	T	0.42	.	19.049	0.93034	0.0:0.0:1.0:0.0	.	861;1811;1832	Q59FX3;P21359-2;P21359	.;.;NF1_HUMAN	K	1832;1811;1477	ENSP00000351015:E1832K;ENSP00000348498:E1811K;ENSP00000389907:E1477K	ENSP00000348498:E1811K	E	+	1	0	NF1	26678868	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	9.434000	0.97515	2.733000	0.93635	0.650000	0.86243	GAA	.	.	.	none		0.512	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		A	29654742	G	A	29654742	3	1	30	1	0	0	0	0	1	0	0	0	10363	1175	41	2	5705	2	NF1	17	29654742	Missense_Mutation	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	17982135	29654742	51540468	99	2206											
PCGF2	7703	hgsc.bcm.edu	37	chr17	36891478	36891482	+	Stop_Codon_Del	DEL	AAGTT	AAGTT	-																															gggagagggtccctggcctcAagttaaggggggcacgggag																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	AAGTT	AAGTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr17:36891478_36891482delAAGTT	ENST00000580830.1	-	0	1730_1734				PCGF2_ENST00000360797.2_Stop_Codon_Del|PCGF2_ENST00000579882.1_3'UTR|PCGF2_ENST00000578109.1_3'UTR|PCGF2_ENST00000581345.1_Stop_Codon_Del|PCGF2_ENST00000585100.1_3'UTR			P35227	PCGF2_HUMAN	polycomb group ring finger 2						anterior/posterior pattern specification (GO:0009952)|cellular response to hydrogen peroxide (GO:0070301)|embryonic skeletal system morphogenesis (GO:0048704)|histone acetylation (GO:0016573)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	10	Breast(7;9.07e-22)					CCCTGGCCTCAAGTTAAGGGGGGCA	0.595											OREG0024367	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.344_345del		Atlas-Indel,Pindel	.											.	PCGF2	24	.	0			c.1030_1034del						PASS	.																																			SO:0001567	stop_retained_variant	7703	exon11			.	D13969	CCDS32638.1	17q12	2013-01-09	2005-01-17	2005-01-19		ENSG00000277258		"RING-type (C3HC4) zinc fingers", "Polycomb group ring fingers"	12929	protein-coding gene	gene with protein product		600346	"ring finger protein 110"	ZNF144, RNF110		8325509	Standard	NM_007144		Approved	MEL-18	uc002hqp.1	P35227		Exception_encountered	chr17.hg19:g.36891478_36891482delAAGTT	Exception_encountered	137.0	0.0	0	866	225.0	54.0	0.24	NM_007144	A6NGD8	Frame_Shift_Del	DEL	ENST00000580830.1	hg19	CCDS32638.1																																																																																			.	.	.	none		0.595	PCGF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442246.2	NM_007144		-	36891482	AAGTT	-	36891478	7	5	30	1	0	1	0	1	0	0	0	0	11582	143	5	0	5	0	PCGF2	17	36891478	Stop_Codon_Del	DEL	AAGTT	TCGA-5P-A9JY-01A-11D-A42J-10	7236736	36891478	44303732	100	2207											
KRTAP4-3	85290	hgsc.bcm.edu	37	chr17	39324382	39324382	+	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	ctggccgagaccttgaccacAgctctggtcagagcagacag	10	6	12	13	1	2	4	1	1	1	3	2	5	2	4	3	2	2	2	3	2	0	1			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr17:39324382A>T	ENST00000391356.2	-	1	42	c.43T>A	c.(43-45)Tgt>Agt	p.C15S		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	15					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)			CCTTGACCACAGCTCTGGTCA	0.627																																					p.C15S		Atlas-SNP	.											KRTAP4-3,colon,carcinoma,0,1	KRTAP4-3	40	.	0			c.T43A						PASS	.						30	32	31					17																	39324382		2201	4293	6494	SO:0001583	missense	85290	exon1			GACCACAGCTCTG	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.43T>A	chr17.hg19:g.39324382A>T	ENSP00000375151:p.Cys15Ser	109.0	0.0	.		152.0	106.0	.	NM_033187		Missense_Mutation	SNP	ENST00000391356.2	hg19	CCDS42331.1	.	.	.	.	.	.	.	.	.	.	.	12.59	1.983700	0.35036	.	.	ENSG00000196156	ENST00000391356	T	0.00619	6.18	4.74	4.74	0.60224	.	.	.	.	.	T	0.03477	0.0100	M	0.81341	2.54	0.34605	D	0.716949	D	0.89917	1.0	D	0.83275	0.996	T	0.27365	-1.0076	9	0.62326	D	0.03	.	12.478	0.55825	1.0:0.0:0.0:0.0	.	15	Q9BYR4	KRA43_HUMAN	S	15	ENSP00000375151:C15S	ENSP00000375151:C15S	C	-	1	0	KRTAP4-3	36577908	0.986000	0.35501	1.000000	0.80357	0.191000	0.23601	0.183000	0.16919	1.867000	0.54127	0.533000	0.62120	TGT	.	.	.	none		0.627	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1			T	39324382	A	T	39324382	3	4	30	1	0	0	0	0	1	0	0	0	8559	188	7	5	548	5	KRTAP4-3	17	39324382	Missense_Mutation	SNP	A	TCGA-5P-A9JY-01A-11D-A42J-10	2432904	39324382	41870828	101	2208											
ATP6V0A1	535	hgsc.bcm.edu	37	chr17	40629677	40629677	+	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	gctgaattgcatcatcagcaGatggcggatccagacttgtt	10	11	11	9	1	2	3	2	1	0	2	3	4	3	4	1	2	2	4	1	2	1	3			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr17:40629677G>T	ENST00000343619.4	+	6	546		c.e6-1		ATP6V0A1_ENST00000393829.2_Splice_Site|ATP6V0A1_ENST00000537728.1_Splice_Site|ATP6V0A1_ENST00000585525.1_Splice_Site|ATP6V0A1_ENST00000264649.6_Missense_Mutation_p.Q148H|ATP6V0A1_ENST00000546249.1_Splice_Site|ATP6V0A1_ENST00000544137.1_Intron	NM_001130021.1	NP_001123493.1	Q93050	VPP1_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a1						ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|urinary_tract(3)	26		all_cancers(22;1.18e-05)|Breast(137;0.000105)|all_epithelial(22;0.000254)		BRCA - Breast invasive adenocarcinoma(366;0.137)		ATCATCAGCAGATGGCGGATC	0.458																																					p.Q148H		Atlas-SNP	.											.	ATP6V0A1	67	.	0			c.G444T						PASS	.						134	117	123					17																	40629677		2203	4300	6503	SO:0001630	splice_region_variant	535	exon6			TCAGCAGATGGCG	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.424-1G>T	chr17.hg19:g.40629677G>T		98.0	0.0	.		139.0	77.0	.	NM_001130020	B7Z3B7|Q8N5G7|Q9NSX0	Missense_Mutation	SNP	ENST00000343619.4	hg19	CCDS45684.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.3|28.3	4.909417|4.909417	0.92107|0.92107	.|.	.|.	ENSG00000033627|ENSG00000033627	ENST00000343619;ENST00000546249;ENST00000393829;ENST00000537728|ENST00000264649	.|D	.|0.86297	.|-2.1	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	.|0.382752	.|0.15363	.|U	.|0.266279	.|D	.|0.83972	.|0.5370	N|N	0.12502|0.12502	0.225|0.225	0.80722|0.80722	D|D	1|1	.|P	.|0.37176	.|0.586	.|P	.|0.45506	.|0.483	.|T	.|0.82705	.|-0.0325	.|10	.|0.39692	.|T	.|0.17	.|-2.6871	20.0498|20.0498	0.97621|0.97621	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|148	.|B7Z3B7	.|.	.|H	-1|148	.|ENSP00000264649:Q148H	.|ENSP00000264649:Q148H	.|Q	+|+	.|3	.|2	ATP6V0A1|ATP6V0A1	37883203|37883203	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.820000|9.820000	0.99359|0.99359	2.753000|2.753000	0.94483|0.94483	0.557000|0.557000	0.71058|0.71058	.|CAG	.	.	.	none		0.458	ATP6V0A1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450364.1	NM_001130020	Intron	T	40629677	G	T	40629677	5	4	30	1	0	0	0	0	0	0	1	0	1168	956	33	4	462	4	ATP6V0A1	17	40629677	Splice_Site	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	1305295	40629677	40565533	102	2209											
RNF213	57674	hgsc.bcm.edu	37	chr17	78356798	78356798	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcttttaaattttgacacAgaattgtcaactaaagaaat	16	13	7	5	0	1	3	1	1	0	2	1	3	1	3	0	1	1	1	0	1	7	6			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr17:78356798A>G	ENST00000582970.1	+	58	14141	c.13998A>G	c.(13996-13998)acA>acG	p.T4666T	CTD-2047H16.4_ENST00000573394.1_RNA|RNF213_ENST00000336301.6_Silent_p.T2739T|RNF213_ENST00000508628.2_Silent_p.T4715T|RNF213_ENST00000427003.3_3'UTR|CTD-2047H16.4_ENST00000575034.1_RNA|CTD-2047H16.4_ENST00000572151.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	4666					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)			ATTTTGACACAGAATTGTCAA	0.403																																					p.T4666T		Atlas-SNP	.											.	RNF213	766	.	0			c.A13998G						PASS	.						96	91	92					17																	78356798		2203	4300	6503	SO:0001819	synonymous_variant	57674	exon58			TGACACAGAATTG	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.13998A>G	chr17.hg19:g.78356798A>G		97.0	0.0	.		161.0	99.0	.	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	hg19	CCDS58606.1																																																																																			.	.	.	none		0.403	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		G	78356798	A	G	78356798	2	3	30	1	0	0	0	0	0	0	0	1	13490	175	7	3		3	RNF213	17	78356798	Silent	SNP	A	TCGA-5P-A9JY-01A-11D-A42J-10	37727121	78356798	2838412	103	2210											
SERPINB3	6317	hgsc.bcm.edu	37	chr18	61324647	61324647	+	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	aattaggtttttaattttttCtgcaagggaaagaataaaag	16	15	8	2	0	1	1	0	0	1	1	1	2	1	2	0	2	1	2	0	2	8	8			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr18:61324647C>T	ENST00000283752.5	-	6	613		c.e6-1		SERPINB3_ENST00000332821.8_Splice_Site|SERPINB11_ENST00000489748.1_RNA	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3						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						TTAATTTTTTCTGCAAGGGAA	0.368																																					.		Atlas-SNP	.											.	SERPINB3	90	.	0			c.470-1G>A						PASS	.						79	82	81					18																	61324647		2203	4300	6503	SO:0001630	splice_region_variant	6317	exon7			TTTTTTCTGCAAG	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.470-1G>A	chr18.hg19:g.61324647C>T		359.0	0.0	.		291.0	105.0	.	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Splice_Site	SNP	ENST00000283752.5	hg19	CCDS11987.1	.	.	.	.	.	.	.	.	.	.	C	14.48	2.549363	0.45383	.	.	ENSG00000057149	ENST00000283752;ENST00000332821	.	.	.	2.74	2.74	0.32292	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.6068	0.62052	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SERPINB3	59475627	1.000000	0.71417	0.463000	0.27130	0.269000	0.26545	6.973000	0.76116	1.841000	0.53522	0.455000	0.32223	.	.	.	.	none		0.368	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919	Intron	T	61324647	C	T	61324647	5	4	30	1	0	0	0	0	0	0	1	0	14115	927	32	2	715	2	SERPINB3	18	61324647	Splice_Site	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10		61324647	16752601	104	2211											
ARID3A	1820	hgsc.bcm.edu	37	chr19	932539	932539	+	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	aggggctgggccccccaggcCctgccagcttgggcaccacg	5	4	15	17	1	0	0	0	0	0	0	0	0	0	0	6	5	2	3	6	5	0	1			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr19:932539C>T	ENST00000263620.3	+	3	817	c.490C>T	c.(490-492)Cct>Tct	p.P164S		NM_005224.2	NP_005215.1	Q99856	ARI3A_HUMAN	AT rich interactive domain 3A (BRIGHT-like)	164						cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCCCCAGGCCCTGCCAGCTT	0.697																																					p.P164S	Pancreas(29;54 1022 32760 50921)	Atlas-SNP	.											.	ARID3A	35	.	0			c.C490T						PASS	.						11	7	8					19																	932539		2071	4150	6221	SO:0001583	missense	1820	exon3			CCAGGCCCTGCCA	U88047	CCDS12050.1	19p13.3	2013-02-07	2006-11-08	2004-01-30		ENSG00000116017		"-"	3031	protein-coding gene	gene with protein product		603265	"dead ringer-like 1 (Drosophila)", "AT rich interactive domain 3A (BRIGHT- like)"	DRIL1		9722953	Standard	NM_005224		Approved	BRIGHT	uc002lql.3	Q99856		ENST00000263620.3:c.490C>T	chr19.hg19:g.932539C>T	ENSP00000263620:p.Pro164Ser	114.0	0.0	.		128.0	62.0	.	NM_005224	Q5I858|Q6P9C6|Q8IZA7|Q8N4Z3	Missense_Mutation	SNP	ENST00000263620.3	hg19	CCDS12050.1	.	.	.	.	.	.	.	.	.	.	C	0.013	-1.619291	0.00828	.	.	ENSG00000116017	ENST00000263620	T	0.36157	1.27	3.79	-3.67	0.04476	.	6.078050	0.01060	U	0.004623	T	0.12178	0.0296	N	0.01576	-0.805	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.18053	-1.0349	10	0.10377	T	0.69	-3.8161	5.4637	0.16632	0.0:0.1949:0.4491:0.356	.	164	Q99856	ARI3A_HUMAN	S	164	ENSP00000263620:P164S	ENSP00000263620:P164S	P	+	1	0	ARID3A	883539	0.005000	0.15991	0.000000	0.03702	0.384000	0.30261	0.223000	0.17719	-0.955000	0.03636	0.443000	0.29094	CCT	.	.	.	none		0.697	ARID3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458219.1	NM_005224		T	932539	C	T	932539	3	4	30	1	0	0	0	0	1	0	0	0	916	623	22	2	496	2	ARID3A	19	932539	Missense_Mutation	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10		932539	58196444	105	2212											
TLE2	7089	hgsc.bcm.edu	37	chr19	3019295	3019295	+	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	actcacctctggacccctcgGcctccacgcccgcacggtcc	5	6	8	22	4	2	0	1	0	1	0	5	1	4	1	7	3	0	1	7	3	0	0			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr19:3019295G>T	ENST00000262953.6	-	7	798	c.536C>A	c.(535-537)gCc>gAc	p.A179D	TLE2_ENST00000591529.1_Missense_Mutation_p.A193D|TLE2_ENST00000443826.3_Intron|TLE2_ENST00000586422.1_Intron|TLE2_ENST00000590536.1_Missense_Mutation_p.A180D|TLE2_ENST00000587217.1_5'UTR|TLE2_ENST00000455444.2_Intron|TLE2_ENST00000447365.2_5'UTR|TLE2_ENST00000426948.2_Missense_Mutation_p.A193D	NM_003260.4	NP_003251.2	Q04725	TLE2_HUMAN	transducin-like enhancer of split 2	179	Gly/Pro-rich.				negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|prostate(1)	13				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGACCCCTCGGCCTCCACGCC	0.697																																					p.A193D		Atlas-SNP	.											.	TLE2	35	.	0			c.C578A						PASS	.						6	8	7					19																	3019295		2030	4111	6141	SO:0001583	missense	7089	exon8			CCCTCGGCCTCCA	M99436	CCDS45911.1, CCDS45912.1, CCDS45913.1, CCDS74255.1	19p13.3	2014-03-07	2014-03-07					"WD repeat domain containing"	11838	protein-coding gene	gene with protein product	"enhancer of split groucho 2"	601041	"transducin-like enhancer of split 2, homolog of Drosophila E(sp1)", "transducin-like enhancer of split 2 (E(sp1) homolog, Drosophila)"			8808280	Standard	NM_003260		Approved	ESG2, GRG2, ESG, FLJ41188	uc002lww.3	Q04725		ENST00000262953.6:c.536C>A	chr19.hg19:g.3019295G>T	ENSP00000262953:p.Ala179Asp	66.0	0.0	.		43.0	19.0	.	NM_001144761	B4DE03|E9PEV7|F8WCH2|Q8WVY0|Q9Y6S0	Missense_Mutation	SNP	ENST00000262953.6	hg19	CCDS45911.1	.	.	.	.	.	.	.	.	.	.	G	6.782	0.513219	0.12944	.	.	ENSG00000065717	ENST00000262953;ENST00000450017;ENST00000426948	T;T	0.55234	0.53;0.76	4.43	4.43	0.53597	.	0.274149	0.32884	N	0.005534	T	0.37705	0.1013	N	0.19112	0.55	0.09310	N	1	B;B	0.23058	0.076;0.079	B;B	0.23574	0.047;0.023	T	0.27400	-1.0075	10	0.37606	T	0.19	-19.2454	12.9084	0.58166	0.0:0.0:1.0:0.0	.	193;179	F8WCH2;Q04725	.;TLE2_HUMAN	D	179;173;193	ENSP00000262953:A179D;ENSP00000392869:A193D	ENSP00000262953:A179D	A	-	2	0	TLE2	2970295	0.045000	0.20229	0.939000	0.37840	0.212000	0.24457	1.274000	0.33132	2.177000	0.69029	0.491000	0.48974	GCC	.	.	.	none		0.697	TLE2-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452194.2	NM_003260		T	3019295	G	T	3019295	3	4	30	1	0	0	0	0	1	0	0	0	15951	1203	42	4	1751	4	TLE2	19	3019295	Missense_Mutation	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	2086756	3019295	56109688	106	2213											
MPND	84954	hgsc.bcm.edu	37	chr19	4357350	4357351	+	Frame_Shift_Del	DEL	AG	AG	-																															tctgcaggacatcgacgcacAgatggactaccagctgcggc																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr19:4357350_4357351delAG	ENST00000262966.8	+	9	1164_1165	c.1097_1098delAG	c.(1096-1098)cagfs	p.Q366fs	MPND_ENST00000359935.4_Frame_Shift_Del_p.Q316fs|AC007292.3_ENST00000593524.1_RNA|MPND_ENST00000599840.1_Frame_Shift_Del_p.Q366fs	NM_032868.4	NP_116257.2	Q8N594	MPND_HUMAN	MPN domain containing	366	MPN.						peptidase activity (GO:0008233)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)	8				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		ATCGACGCACAGATGGACTACC	0.663																																					p.366_366del		Atlas-INDEL	.											.	MPND	28	.	0			c.1096_1097del						PASS	.																																			SO:0001589	frameshift_variant	84954	exon9			.		CCDS42470.1, CCDS54200.1, CCDS74261.1	19p13.3	2014-08-12			ENSG00000008382				25934	protein-coding gene	gene with protein product							Standard	XM_005259663		Approved	FLJ14981	uc002mae.3	Q8N594	OTTHUMG00000181914	ENST00000262966.8:c.1097_1098delAG	chr19.hg19:g.4357350_4357351delAG	ENSP00000262966:p.Gln366fs	76.0	0.0	0		92.0	33.0	0.358696	NM_032868	Q96SJ0|Q9Y2P1|Q9Y2P2	Frame_Shift_Del	DEL	ENST00000262966.8	hg19	CCDS42470.1																																																																																			.	.	.	none		0.663	MPND-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458292.1	NM_032868		-	4357351	AG	-	4357350	7	5	30	1	0	1	0	1	0	0	0	0	9738	188	7	0	1131	0	MPND	19	4357350	Frame_Shift_Del	DEL	AG	TCGA-5P-A9JY-01A-11D-A42J-10	1338055	4357350	54771633	107	2214	26	3									
MPND	84954	hgsc.bcm.edu	37	chr19	4357351	4357354	+	Frame_Shift_Del	DEL	GATG	GATG	-																															ctgcaggacatcgacgcacaGatggactaccagctgcggct																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	GATG	GATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr19:4357351_4357354delGATG	ENST00000262966.8	+	9	1165_1168	c.1098_1101delGATG	c.(1096-1101)cagatgfs	p.QM366fs	MPND_ENST00000359935.4_Frame_Shift_Del_p.QM316fs|AC007292.3_ENST00000593524.1_RNA|MPND_ENST00000599840.1_Frame_Shift_Del_p.QM366fs	NM_032868.4	NP_116257.2	Q8N594	MPND_HUMAN	MPN domain containing	366	MPN.						peptidase activity (GO:0008233)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)	8				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		TCGACGCACAGATGGACTACCAGC	0.672																																					p.366_367del		Pindel	.											.	MPND	28	.	0			c.1097_1100del						PASS	.																																			SO:0001589	frameshift_variant	84954	exon9			.		CCDS42470.1, CCDS54200.1, CCDS74261.1	19p13.3	2014-08-12			ENSG00000008382				25934	protein-coding gene	gene with protein product							Standard	XM_005259663		Approved	FLJ14981	uc002mae.3	Q8N594	OTTHUMG00000181914	ENST00000262966.8:c.1098_1101delGATG	chr19.hg19:g.4357351_4357354delGATG	ENSP00000262966:p.Gln366fs	77.0	0.0	.		92.0	25.0	0.272	NM_032868	Q96SJ0|Q9Y2P1|Q9Y2P2	Frame_Shift_Del	DEL	ENST00000262966.8	hg19	CCDS42470.1																																																																																			.	.	.	none		0.672	MPND-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458292.1	NM_032868		-	4357354	GATG	-	4357351	7	5	30	1	0	1	0	1	0	0	0	0	9738	933	33	0	1132	0	MPND	19	4357351	Frame_Shift_Del	DEL	GATG	TCGA-5P-A9JY-01A-11D-A42J-10	1	4357351	54771632	108	2215	26	3									
MPND	84954	hgsc.bcm.edu	37	chr19	4357354	4357354	+	Frame_Shift_Del	DEL	G	G	-																															caggacatcgacgcacagatGgactaccagctgcggctgca																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr19:4357354delG	ENST00000262966.8	+	9	1168	c.1101delG	c.(1099-1101)atgfs	p.M367fs	MPND_ENST00000359935.4_Frame_Shift_Del_p.M317fs|AC007292.3_ENST00000593524.1_RNA|MPND_ENST00000599840.1_Frame_Shift_Del_p.M367fs	NM_032868.4	NP_116257.2	Q8N594	MPND_HUMAN	MPN domain containing	367	MPN.						peptidase activity (GO:0008233)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)	8				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		ACGCACAGATGGACTACCAGC	0.677																																					p.M367fs		Atlas-INDEL	.											.	MPND	28	.	0			c.1100delT						PASS	.						21	23	23					19																	4357354		2017	4181	6198	SO:0001589	frameshift_variant	84954	exon9			.		CCDS42470.1, CCDS54200.1, CCDS74261.1	19p13.3	2014-08-12			ENSG00000008382				25934	protein-coding gene	gene with protein product							Standard	XM_005259663		Approved	FLJ14981	uc002mae.3	Q8N594	OTTHUMG00000181914	ENST00000262966.8:c.1101delG	chr19.hg19:g.4357354delG	ENSP00000262966:p.Met367fs	77.0	0.0	0		88.0	34.0	0.386364	NM_032868	Q96SJ0|Q9Y2P1|Q9Y2P2	Frame_Shift_Del	DEL	ENST00000262966.8	hg19	CCDS42470.1																																																																																			.	.	.	none		0.677	MPND-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458292.1	NM_032868		-	4357354	G	-	4357354	7	5	30	1	0	1	0	1	0	0	0	0	9738	1348	47	0	1135	0	MPND	19	4357354	Frame_Shift_Del	DEL	G	TCGA-5P-A9JY-01A-11D-A42J-10	3	4357354	54771629	109	2216	26	3									
DPP9	91039	hgsc.bcm.edu	37	chr19	4700253	4700253	+	Missense_Mutation	SNP	T	T	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	cctggctgtcagtctggaacTcagccagtttcaaggcaatc	9	10	10	12	0	4	0	3	0	1	0	5	1	4	1	2	3	2	3	2	3	3	1			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr19:4700253T>G	ENST00000598800.1	-	11	1467	c.962A>C	c.(961-963)gAg>gCg	p.E321A	DPP9_ENST00000262960.9_Missense_Mutation_p.E350A|DPP9_ENST00000597849.1_Missense_Mutation_p.E350A|DPP9_ENST00000594671.1_Missense_Mutation_p.E321A			Q86TI2	DPP9_HUMAN	dipeptidyl-peptidase 9	321						cytoplasm (GO:0005737)|membrane (GO:0016020)	aminopeptidase activity (GO:0004177)|identical protein binding (GO:0042802)|serine-type peptidase activity (GO:0008236)			cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)		AGTCTGGAACTCAGCCAGTTT	0.577																																					p.E350A		Atlas-SNP	.											.	DPP9	59	.	0			c.A1049C						PASS	.						43	45	44					19																	4700253		1931	4135	6066	SO:0001583	missense	91039	exon10			TGGAACTCAGCCA	AF452102	CCDS45928.1	19p13.3	2014-06-11	2006-01-12		ENSG00000142002	ENSG00000142002			18648	protein-coding gene	gene with protein product		608258	"dipeptidylpeptidase 9"				Standard	NM_139159		Approved		uc002mba.3	Q86TI2	OTTHUMG00000182040	ENST00000598800.1:c.962A>C	chr19.hg19:g.4700253T>G	ENSP00000469603:p.Glu321Ala	87.0	0.0	.		67.0	32.0	.	NM_139159	O75273|O75868|Q1ZZB8|Q6AI37|Q6UAL0|Q6ZMT2|Q6ZNJ5|Q8N2J7|Q8N3F5|Q8WXD8|Q96NT8|Q9BVR3	Missense_Mutation	SNP	ENST00000598800.1	hg19		.	.	.	.	.	.	.	.	.	.	T	14.87	2.665127	0.47677	.	.	ENSG00000142002	ENST00000357909;ENST00000381797;ENST00000262960	T	0.30182	1.54	4.5	4.5	0.54988	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.052580	0.64402	D	0.000001	T	0.49609	0.1567	L	0.58583	1.82	0.80722	D	1	P;D	0.89917	0.943;1.0	P;D	0.83275	0.854;0.996	T	0.44802	-0.9304	10	0.39692	T	0.17	-24.9386	13.1304	0.59377	0.0:0.0:0.0:1.0	.	321;350	Q86TI2;Q1ZZB8	DPP9_HUMAN;.	A	429;291;350	ENSP00000262960:E350A	ENSP00000262960:E350A	E	-	2	0	DPP9	4651253	1.000000	0.71417	0.144000	0.22314	0.018000	0.09664	7.573000	0.82421	1.891000	0.54761	0.459000	0.35465	GAG	.	.	.	none		0.577	DPP9-026	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000459343.2			G	4700253	T	G	4700253	3	3	30	1	0	0	0	0	1	0	0	0	4735	1551	54	5	1681	5	DPP9	19	4700253	Missense_Mutation	SNP	T	TCGA-5P-A9JY-01A-11D-A42J-10	342899	4700253	54428730	110	2217											
MYO1F	4542	hgsc.bcm.edu	37	chr19	8615148	8615148	+	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	cacattgatggactcgctgcGcccgccccagcggctgtcca	6	7	11	17	4	0	1	0	1	0	0	2	2	1	2	4	2	2	2	4	2	0	1			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr19:8615148G>C	ENST00000338257.8	-	10	1264	c.997C>G	c.(997-999)Cgc>Ggc	p.R333G	AC092316.1_ENST00000598703.1_RNA	NM_012335.3	NP_036467.2	O00160	MYO1F_HUMAN	myosin IF	333	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						GACTCGCTGCGCCCGCCCCAG	0.647																																					p.R333G		Atlas-SNP	.											MYO1F,NS,carcinoma,0,1	MYO1F	128	.	0			c.C997G						PASS	.						27	32	30					19																	8615148		2056	4215	6271	SO:0001583	missense	4542	exon10			CGCTGCGCCCGCC	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.997C>G	chr19.hg19:g.8615148G>C	ENSP00000344871:p.Arg333Gly	90.0	2.0	.		87.0	36.0	.	NM_012335	Q8WWN7	Missense_Mutation	SNP	ENST00000338257.8	hg19	CCDS42494.1	.	.	.	.	.	.	.	.	.	.	G	15.00	2.701939	0.48307	.	.	ENSG00000142347	ENST00000305795;ENST00000338257	D	0.88431	-2.38	4.82	4.82	0.62117	Myosin head, motor domain (2);	0.229852	0.37623	N	0.002016	D	0.89280	0.6670	L	0.48986	1.54	0.50632	D	0.999883	P;P	0.37594	0.601;0.601	B;P	0.44597	0.339;0.454	D	0.90617	0.4556	10	0.87932	D	0	.	16.9171	0.86154	0.0:0.0:1.0:0.0	.	333;333	B0I1T1;O00160	.;MYO1F_HUMAN	G	378;333	ENSP00000344871:R333G	ENSP00000304899:R378G	R	-	1	0	MYO1F	8521148	1.000000	0.71417	0.671000	0.29857	0.673000	0.39480	4.746000	0.62133	2.227000	0.72691	0.563000	0.77884	CGC	.	.	.	none		0.647	MYO1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342716.2			C	8615148	G	C	8615148	3	2	30	1	0	0	0	0	1	0	0	0	10080	1087	38	4	2375	4	MYO1F	19	8615148	Missense_Mutation	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	3914895	8615148	50513835	111	2218											
ANO8	57719	hgsc.bcm.edu	37	chr19	17440636	17440637	+	Frame_Shift_Del	DEL	TG	TG	-																															tcaggtacgagttgacaaacTggaactgcaggaaggaggca																								rs377317921		TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr19:17440636_17440637delTG	ENST00000159087.4	-	12	1491_1492	c.1333_1334delCA	c.(1333-1335)cagfs	p.Q445fs		NM_020959.2	NP_066010.1	Q9HCE9	ANO8_HUMAN	anoctamin 8	445	Leu-rich.				chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			autonomic_ganglia(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(3)	27						GTTGACAAACTGGAACTGCAGG	0.604																																					p.445_445del		Pindel	.											.	ANO8	67	.	0			c.1334_1335del						PASS	.																																			SO:0001589	frameshift_variant	57719	exon12			.	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.1333_1334delCA	chr19.hg19:g.17440636_17440637delTG	ENSP00000159087:p.Gln445fs	133.0	0.0	.		129.0	36.0	0.279	NM_020959	A6NIJ0	Frame_Shift_Del	DEL	ENST00000159087.4	hg19	CCDS32949.1																																																																																			.	.	.	none		0.604	ANO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462943.1	XM_050644		-	17440637	TG	-	17440636	7	5	30	1	0	1	0	1	0	0	0	0	703	1580	55	0	2392	0	ANO8	19	17440636	Frame_Shift_Del	DEL	TG	TCGA-5P-A9JY-01A-11D-A42J-10	8825488	17440636	41688347	112	2219											
FCHO1	23149	hgsc.bcm.edu	37	chr19	17881335	17881335	+	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	aactacctgaaccgttgcatGgaccaggagcggctgcggag	10	6	14	11	3	0	1	0	1	0	0	0	4	0	4	3	4	6	3	3	4	3	2			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr19:17881335G>C	ENST00000596536.1	+	8	721	c.438G>C	c.(436-438)atG>atC	p.M146I	FCHO1_ENST00000595033.1_Missense_Mutation_p.M96I|FCHO1_ENST00000596951.1_Missense_Mutation_p.M146I|FCHO1_ENST00000597512.1_Missense_Mutation_p.M153I|FCHO1_ENST00000252771.7_Missense_Mutation_p.M146I|FCHO1_ENST00000600676.1_Missense_Mutation_p.M146I|FCHO1_ENST00000539407.1_Missense_Mutation_p.M146I|FCHO1_ENST00000389133.4_Missense_Mutation_p.M146I|FCHO1_ENST00000594202.1_Missense_Mutation_p.M146I	NM_015122.2	NP_055937.1	O14526	FCHO1_HUMAN	FCH domain only 1	146	Mediates membrane-binding.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	AP-2 adaptor complex binding (GO:0035612)			NS(2)|breast(1)|large_intestine(6)|liver(1)|lung(12)	22						ACCGTTGCATGGACCAGGAGC	0.632																																					p.M146I		Atlas-SNP	.											.	FCHO1	69	.	0			c.G438C						PASS	.						49	48	48					19																	17881335		2203	4300	6503	SO:0001583	missense	23149	exon7			TTGCATGGACCAG	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.438G>C	chr19.hg19:g.17881335G>C	ENSP00000470731:p.Met146Ile	78.0	0.0	.		68.0	28.0	.	NM_001161358	A6NHE6|A8K5U5|B4E120|Q05C93|Q8IW22	Missense_Mutation	SNP	ENST00000596536.1	hg19	CCDS32955.1	.	.	.	.	.	.	.	.	.	.	G	12.27	1.888439	0.33348	.	.	ENSG00000130475	ENST00000252771;ENST00000389133;ENST00000539407	T;T;T	0.41400	1.0;1.0;1.0	4.56	3.53	0.40419	.	0.470084	0.24165	N	0.040958	T	0.28532	0.0706	L	0.29908	0.895	0.37133	D	0.901365	B;B;B	0.11235	0.001;0.001;0.004	B;B;B	0.15052	0.005;0.002;0.012	T	0.15521	-1.0434	10	0.37606	T	0.19	-18.5905	7.9831	0.30196	0.1112:0.0:0.8888:0.0	.	96;146;146	B4E120;O14526;O14526-2	.;FCHO1_HUMAN;.	I	146	ENSP00000252771:M146I;ENSP00000373785:M146I;ENSP00000437978:M146I	ENSP00000252771:M146I	M	+	3	0	FCHO1	17742335	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.314000	0.59166	1.148000	0.42385	0.491000	0.48974	ATG	.	.	.	none		0.632	FCHO1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466946.2	NM_015122		C	17881335	G	C	17881335	3	2	30	1	0	0	0	0	1	0	0	0	5794	1348	47	4	456	4	FCHO1	19	17881335	Missense_Mutation	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	440699	17881335	41247648	113	2220											
ZNF146	7705	hgsc.bcm.edu	37	chr19	36727964	36727964	+	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	tacatgtgaggattcattcaGgtgataaaccttacgaatgc	13	12	9	7	1	2	2	2	2	0	0	2	4	2	3	1	2	4	0	1	2	5	5			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr19:36727964G>T	ENST00000443387.2	+	4	1614	c.622G>T	c.(622-624)Ggt>Tgt	p.G208C	ZNF565_ENST00000355114.5_Intron|ZNF146_ENST00000456324.1_Missense_Mutation_p.G208C	NM_007145.2	NP_009076.2	Q15072	OZF_HUMAN	zinc finger protein 146	208					regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	11	Esophageal squamous(110;0.162)					GATTCATTCAGGTGATAAACC	0.438																																					p.G208C		Atlas-SNP	.											.	ZNF146	32	.	0			c.G622T						PASS	.						196	162	173					19																	36727964		2203	4300	6503	SO:0001583	missense	7705	exon3			CATTCAGGTGATA	X70394	CCDS12492.1	19q13.1	2013-01-08				ENSG00000167635		"Zinc fingers, C2H2-type"	12931	protein-coding gene	gene with protein product		601505				10449921, 8641144	Standard	NM_001099639		Approved	OZF	uc010eeu.3	Q15072		ENST00000443387.2:c.622G>T	chr19.hg19:g.36727964G>T	ENSP00000392095:p.Gly208Cys	94.0	0.0	.		90.0	32.0	.	NM_001099638	Q2TB94	Missense_Mutation	SNP	ENST00000443387.2	hg19	CCDS12492.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.400015	0.62177	.	.	ENSG00000167635	ENST00000443387;ENST00000456324	T;T	0.42900	0.96;0.96	4.48	4.48	0.54585	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.41001	D	0.000980	T	0.71854	0.3389	M	0.91663	3.23	0.50039	D	0.999848	D	0.89917	1.0	D	0.97110	1.0	T	0.79027	-0.1971	10	0.87932	D	0	-7.7826	17.1134	0.86682	0.0:0.0:1.0:0.0	.	208	Q15072	OZF_HUMAN	C	208	ENSP00000392095:G208C;ENSP00000400391:G208C	ENSP00000392095:G208C	G	+	1	0	ZNF146	41419804	1.000000	0.71417	1.000000	0.80357	0.494000	0.33585	8.947000	0.93000	2.780000	0.95670	0.561000	0.74099	GGT	.	.	.	none		0.438	ZNF146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451706.1	NM_007145		T	36727964	G	T	36727964	3	4	30	1	0	0	0	0	1	0	0	0	17745	1000	35	4	624	4	ZNF146	19	36727964	Missense_Mutation	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10	18846629	36727964	22401019	114	2221											
BTBD3	22903	hgsc.bcm.edu	37	chr20	11898938	11898938	+	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	gtactcatggtagatgacaaGgaaaagaacatgaaatgtct	17	9	10	5	0	2	4	1	2	1	2	2	5	2	5	0	2	2	2	0	2	7	2			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr20:11898938G>T	ENST00000405977.1	+	2	640	c.15G>T	c.(13-15)aaG>aaT	p.K5N	BTBD3_ENST00000399006.2_Intron|BTBD3_ENST00000254977.3_Intron|BTBD3_ENST00000378226.2_Missense_Mutation_p.K5N|RP4-742J24.2_ENST00000439529.1_RNA	NM_001282550.1|NM_001282552.1|NM_001282554.1	NP_001269479.1|NP_001269481.1|NP_001269483.1	Q9Y2F9	BTBD3_HUMAN	BTB (POZ) domain containing 3	5					cerebral cortex development (GO:0021987)|dendrite morphogenesis (GO:0048813)	cytosol (GO:0005829)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(18)|ovary(3)|skin(2)	34						TAGATGACAAGGAAAAGAACA	0.413																																					p.K5N		Atlas-SNP	.											.	BTBD3	92	.	0			c.G15T						PASS	.						193	201	199					20																	11898938		2203	4300	6503	SO:0001583	missense	22903	exon1			TGACAAGGAAAAG	AB023169	CCDS13113.1, CCDS13114.1	20p12.2	2013-01-08			ENSG00000132640	ENSG00000132640		"BTB/POZ domain containing"	15854	protein-coding gene	gene with protein product		615566					Standard	NM_001282551		Approved	KIAA0952, dJ742J24.1	uc002wnz.3	Q9Y2F9	OTTHUMG00000031889	ENST00000405977.1:c.15G>T	chr20.hg19:g.11898938G>T	ENSP00000384545:p.Lys5Asn	42.0	0.0	.		64.0	9.0	.	NM_014962	D3DW19|Q5JY73	Missense_Mutation	SNP	ENST00000405977.1	hg19	CCDS13113.1	.	.	.	.	.	.	.	.	.	.	G	12.64	1.997866	0.35226	.	.	ENSG00000132640	ENST00000405977;ENST00000378226	T;T	0.80653	-1.4;-1.4	6.17	5.22	0.72569	.	0.052693	0.64402	D	0.000001	T	0.66137	0.2759	N	0.14661	0.345	0.48762	D	0.9997	B	0.02656	0.0	B	0.01281	0.0	T	0.63462	-0.6632	10	0.66056	D	0.02	.	10.1626	0.42860	0.1676:0.0:0.8324:0.0	.	5	Q9Y2F9	BTBD3_HUMAN	N	5	ENSP00000384545:K5N;ENSP00000367471:K5N	ENSP00000367471:K5N	K	+	3	2	BTBD3	11846938	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.552000	0.53705	1.598000	0.50083	0.655000	0.94253	AAG	.	.	.	none		0.413	BTBD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078021.3			T	11898938	G	T	11898938	3	4	30	1	0	0	0	0	1	0	0	0	1546	991	35	4	17	4	BTBD3	20	11898938	Missense_Mutation	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10		11898938	51126582	115	2222											
KCNQ2	3785	hgsc.bcm.edu	37	chr20	62038497	62038497	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggacactggacagggggcgCggccgggggcgccgagaagt	7	2	21	11	6	0	1	0	0	0	1	0	4	0	3	2	7	0	0	2	7	1	0	rs543477138		TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr20:62038497C>T	ENST00000359125.2	-	17	2293	c.2119G>A	c.(2119-2121)Gcg>Acg	p.A707T	KCNQ2_ENST00000357249.2_Missense_Mutation_p.A689T|KCNQ2_ENST00000344462.4_Missense_Mutation_p.A676T|KCNQ2_ENST00000354587.3_Missense_Mutation_p.A715T|KCNQ2_ENST00000359689.1_Missense_Mutation_p.A707T|KCNQ2_ENST00000370224.1_Missense_Mutation_p.A715T|KCNQ2_ENST00000360480.3_Missense_Mutation_p.A679T	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	707					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)	ACAgggggcgcggccgggggc	0.711																																					p.A707T		Atlas-SNP	.											KCNQ2,colon,carcinoma,0,2	KCNQ2	201	.	0			c.G2119A						PASS	.						5	6	5					20																	62038497		2041	4078	6119	SO:0001583	missense	3785	exon17			GGGGCGCGGCCGG	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.2119G>A	chr20.hg19:g.62038497C>T	ENSP00000352035:p.Ala707Thr	280.0	0.0	.		372.0	45.0	.	NM_172107	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Missense_Mutation	SNP	ENST00000359125.2	hg19	CCDS13520.1	.	.	.	.	.	.	.	.	.	.	C	3.761	-0.049564	0.07407	.	.	ENSG00000075043	ENST00000357249;ENST00000359125;ENST00000370226;ENST00000354587;ENST00000359689;ENST00000430658;ENST00000360480;ENST00000344462;ENST00000370224	D;D;D;D;D;D;D;D;D	0.99005	-5.17;-5.32;-5.32;-5.11;-5.32;-5.17;-5.17;-5.26;-5.11	4.5	0.844	0.18943	.	0.510450	0.17649	U	0.166750	D	0.92948	0.7756	N	0.02539	-0.55	0.09310	N	1	B;B;B;B	0.06786	0.001;0.001;0.001;0.0	B;B;B;B	0.06405	0.001;0.002;0.001;0.0	D	0.87991	0.2749	10	0.15066	T	0.55	-18.663	8.3989	0.32574	0.0:0.5829:0.0:0.4171	.	679;689;676;707	O43526-3;O43526-2;O43526-4;O43526	.;.;.;KCNQ2_HUMAN	T	689;707;677;715;707;676;679;703;715	ENSP00000349789:A689T;ENSP00000352035:A707T;ENSP00000359246:A677T;ENSP00000346601:A715T;ENSP00000352718:A707T;ENSP00000399612:A676T;ENSP00000353668:A679T;ENSP00000339611:A703T;ENSP00000359244:A715T	ENSP00000339611:A703T	A	-	1	0	KCNQ2	61508941	0.000000	0.05858	0.004000	0.12327	0.148000	0.21650	0.648000	0.24828	0.331000	0.23511	0.491000	0.48974	GCG	.	.	.	none		0.711	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109		T	62038497	C	T	62038497	3	4	30	1	0	0	0	0	1	0	0	0	8090	768	27	1	503	1	KCNQ2	20	62038497	Missense_Mutation	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10	50139559	62038497	987023	116	2223											
KCNJ15	3772	hgsc.bcm.edu	37	chr21	39671467	39671468	+	Frame_Shift_Ins	INS	-	-	A																															gcgtttattcatggggacttINSagaacccggtgagcccattt																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr21:39671467_39671468insA	ENST00000328656.4	+	4	587_588	c.284_285insA	c.(283-288)ttagaafs	p.E96fs	KCNJ15_ENST00000398930.1_Frame_Shift_Ins_p.E96fs|KCNJ15_ENST00000398938.2_Frame_Shift_Ins_p.E96fs|KCNJ15_ENST00000398932.1_Frame_Shift_Ins_p.E96fs|KCNJ15_ENST00000398934.1_Frame_Shift_Ins_p.E96fs	NM_001276437.1|NM_001276438.1|NM_001276439.1|NM_002243.3	NP_001263366.1|NP_001263367.1|NP_001263368.1|NP_002234.2	Q99712	KCJ15_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 15	96					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	24					Yohimbine(DB01392)	CATGGGGACTTAGAACCCGGTG	0.48																																					p.I95fs		Atlas-Indel,Pindel	.											.	KCNJ15	43	.	0			c.284_285insA						PASS	.																																			SO:0001589	frameshift_variant	3772	exon3			.	Y10745	CCDS13656.1	21q22.2	2011-07-05			ENSG00000157551	ENSG00000157551		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6261	protein-coding gene	gene with protein product		602106				9299242, 8995301, 16382105	Standard	NM_170736		Approved	Kir4.2, Kir1.3, IRKK	uc002ywx.4	Q99712	OTTHUMG00000090609	ENST00000328656.4:c.285dupA	chr21.hg19:g.39671468_39671468dupA	ENSP00000331698:p.Glu96fs	90.0	0.0	0		50.0	30.0	0.6	NM_170736	D3DSH5|O00564|Q96L28|Q99446	Frame_Shift_Ins	INS	ENST00000328656.4	hg19	CCDS13656.1																																																																																			.	.	.	none		0.48	KCNJ15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207181.2	NM_002243		A	39671468	-	A	39671467	7	5	30	1	0	1	1	0	0	0	0	0	8056	1764	61	0	286	0	KCNJ15	21	39671467	Frame_Shift_Ins	INS	-	TCGA-5P-A9JY-01A-11D-A42J-10		39671467	8458428	117	2224											
KRTAP10-7	386675	hgsc.bcm.edu	37	chr21	46021419	46021419	+	Missense_Mutation	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	gccagcagtctagctgccagCcggcttgctgcaccacctcc	6	7	10	18	1	1	0	0	0	1	0	2	0	2	0	6	1	6	5	6	1	1	2			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr21:46021419C>T	ENST00000380102.2	+	1	923	c.898C>T	c.(898-900)Ccg>Tcg	p.P300S	TSPEAR_ENST00000323084.4_Intron	NM_198689.2	NP_941962.1	P60409	KR107_HUMAN	keratin associated protein 10-7	300	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						TAGCTGCCAGCCGGCTTGCTG	0.672																																					p.P295S		Atlas-SNP	.											.	KRTAP10-7	41	.	0			c.C883T						PASS	.						89	82	84					21																	46021419		2203	4296	6499	SO:0001583	missense	386675	exon2			TGCCAGCCGGCTT	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.898C>T	chr21.hg19:g.46021419C>T	ENSP00000369445:p.Pro300Ser	46.0	0.0	.		23.0	14.0	.	NM_198689	Q0VDJ8|Q70LJ2	Missense_Mutation	SNP	ENST00000380102.2	hg19		.	.	.	.	.	.	.	.	.	.	c	8.469	0.857149	0.17106	.	.	ENSG00000205441	ENST00000380102	T	0.01887	4.58	3.25	2.34	0.29019	.	.	.	.	.	T	0.03136	0.0092	L	0.55481	1.735	0.21290	N	0.99973	B	0.25312	0.123	B	0.25759	0.063	T	0.41484	-0.9506	9	0.24483	T	0.36	.	10.1685	0.42895	0.0:0.777:0.223:0.0	.	295	P60409-2	.	S	300	ENSP00000369445:P300S	ENSP00000369445:P300S	P	+	1	0	KRTAP10-7	44845847	0.101000	0.21875	0.244000	0.24202	0.501000	0.33797	2.782000	0.47758	0.445000	0.26639	0.467000	0.42956	CCG	.	.	.	none		0.672	KRTAP10-7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128038.1	NM_198689		T	46021419	C	T	46021419	3	4	30	1	0	0	0	0	1	0	0	0	8521	739	26	2	889	2	KRTAP10-7	21	46021419	Missense_Mutation	SNP	C	TCGA-5P-A9JY-01A-11D-A42J-10	6349952	46021419	2108476	118	2225											
LZTR1	8216	hgsc.bcm.edu	37	chr22	21348913	21348913	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgagcttccagttgtgccGcctggagcagctgtgccgcc	5	9	13	14	2	0	1	0	1	0	0	1	2	1	2	5	1	5	4	5	1	0	2			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr22:21348913G>A	ENST00000215739.8	+	15	2041	c.1682G>A	c.(1681-1683)cGc>cAc	p.R561H	LZTR1_ENST00000479606.1_3'UTR|LZTR1_ENST00000389355.3_Missense_Mutation_p.R542H	NM_006767.3	NP_006758.2	Q8N653	LZTR1_HUMAN	leucine-zipper-like transcription regulator 1	561					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)			CAGTTGTGCCGCCTGGAGCAG	0.632																																					p.R561H		Atlas-SNP	.											.	LZTR1	99	.	0			c.G1682A						PASS	.						63	49	54					22																	21348913		2202	4300	6502	SO:0001583	missense	8216	exon15			TGTGCCGCCTGGA	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.1682G>A	chr22.hg19:g.21348913G>A	ENSP00000215739:p.Arg561His	42.0	0.0	.		29.0	6.0	.	NM_006767	Q14776|Q20WK0	Missense_Mutation	SNP	ENST00000215739.8	hg19	CCDS33606.1	.	.	.	.	.	.	.	.	.	.	g	32	5.180499	0.94846	.	.	ENSG00000099949	ENST00000539817;ENST00000215739;ENST00000389355	T;T	0.67523	-0.27;-0.27	4.72	4.72	0.59763	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (1);	0.000000	0.85682	D	0.000000	T	0.81054	0.4743	M	0.76170	2.325	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.993;0.989;0.996	D	0.83385	0.0014	10	0.72032	D	0.01	-35.0718	15.2289	0.73372	0.0:0.0:1.0:0.0	.	542;561;520	B7Z3T9;Q8N653;F5GXU8	.;LZTR1_HUMAN;.	H	520;561;542	ENSP00000215739:R561H;ENSP00000374006:R542H	ENSP00000215739:R561H	R	+	2	0	LZTR1	19678913	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.743000	0.85020	2.444000	0.82710	0.457000	0.33378	CGC	.	.	.	none		0.632	LZTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320387.1	NM_006767		A	21348913	G	A	21348913	3	1	30	1	0	0	0	0	1	0	0	0	9144	1087	38	1	1740	1	LZTR1	22	21348913	Missense_Mutation	SNP	G	TCGA-5P-A9JY-01A-11D-A42J-10		21348913	29955653	119	2226											
KDELR3	11015	hgsc.bcm.edu	37	chr22	38877266	38877267	+	Missense_Mutation	DNP	AG	AG	TA																															atcagtggctatcctgccccAgctcttcatgatcagcaaga																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr22:38877266_38877267AG>TA	ENST00000216014.4	+	4	573_574	c.401_402AG>TA	c.(400-402)cAG>cTA	p.Q134L	KDELR3_ENST00000471268.1_3'UTR|KDELR3_ENST00000409006.3_Missense_Mutation_p.Q134L	NM_006855.2	NP_006846.1	O43731	ERD23_HUMAN	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3	134					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein retention in ER lumen (GO:0006621)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ER retention sequence binding (GO:0046923)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)	13	Melanoma(58;0.0286)					ATCCTGCCCCAGCTCTTCATGA	0.505																																					p.Q134L|p.Q134Q	Ovarian(11;103 529 24120 28493 32980)	Atlas-SNP	.											.	KDELR3	39	.	0			c.A401T|c.G402A						PASS	.																																			SO:0001583	missense	11015	exon4			TGCCCCAGCTCTT|GCCCCAGCTCTTC	AL035081	CCDS13972.1, CCDS46705.1	22q13	2008-05-02			ENSG00000100196	ENSG00000100196			6306	protein-coding gene	gene with protein product							Standard	NM_006855		Approved		uc003avu.3	O43731	OTTHUMG00000153520	Exception_encountered	chr22.hg19:g.38877266_38877267delinsTA	ENSP00000216014:p.Gln134Leu	118.0|117.0	0.0	.		83.0	49.0	.	NM_016657	A8K7T7|B8ZZ26|O95557|Q4V750|Q4V767|Q53FP4|Q53GK1	Missense_Mutation|Silent	SNP	ENST00000216014.4	hg19	CCDS13972.1																																																																																			.	.	.	none		0.505	KDELR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331474.1			TA	38877267	AG	TA	38877266	3	4	30	1	0	0	0	0	1	0	0	0	8128	188	7	5	415	5	KDELR3	22	38877266	Missense_Mutation	DNP	AG	TCGA-5P-A9JY-01A-11D-A42J-10	17528353	38877266	12427300	120	2227											
DMC1	11144	hgsc.bcm.edu	37	chr22	38958351	38958351	+	Frame_Shift_Del	DEL	A	A	-																															ttcctcttttcactatactcAaatgcagtcaagaatcctgg																										TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chr22:38958351delA	ENST00000216024.2	-	5	543	c.267delT	c.(265-267)tttfs	p.F89fs	DMC1_ENST00000428462.2_Frame_Shift_Del_p.F89fs	NM_007068.2	NP_008999.2	Q14565	DMC1_HUMAN	DNA meiotic recombinase 1	89					female gamete generation (GO:0007292)|male meiosis I (GO:0007141)|meiotic nuclear division (GO:0007126)|oocyte maturation (GO:0001556)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	chromosome (GO:0005694)|chromosome, telomeric region (GO:0000781)|condensed nuclear chromosome (GO:0000794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)			large_intestine(5)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	11	Melanoma(58;0.0286)					CACTATACTCAAATGCAGTCA	0.328								Homologous recombination																													p.E90fs		Atlas-Indel,Pindel	.											.	DMC1	33	.	0			c.268delG						PASS	.						114	112	113					22																	38958351		2203	4300	6503	SO:0001589	frameshift_variant	11144	exon5			.	D63882	CCDS13973.1, CCDS63477.1	22q13.1	2013-05-02	2013-05-02		ENSG00000100206	ENSG00000100206			2927	protein-coding gene	gene with protein product		602721	"DMC1 (dosage suppressor of mck1, yeast homolog) meiosis-specific homologous recombination", "DMC1 dosage suppressor of mck1 homolog, meiosis-specific homologous recombination (yeast)"			8602360, 8590282, 17541404	Standard	NM_007068		Approved	LIM15	uc003avz.2	Q14565	OTTHUMG00000151088	ENST00000216024.2:c.267delT	chr22.hg19:g.38958351delA	ENSP00000216024:p.Phe89fs	116.0	0.0	0		122.0	54.0	0.442623	NM_007068	A8K9A2|B4DMW6|Q08AI1|Q99498|Q9UH11	Frame_Shift_Del	DEL	ENST00000216024.2	hg19	CCDS13973.1																																																																																			.	.	.	none		0.328	DMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321246.2	NM_007068		-	38958351	A	-	38958351	7	5	30	1	0	1	0	1	0	0	0	0	4581	127	5	0	795	0	DMC1	22	38958351	Frame_Shift_Del	DEL	A	TCGA-5P-A9JY-01A-11D-A42J-10	81085	38958351	12346215	121	2228											
MED14	9282	hgsc.bcm.edu	37	chrX	40526005	40526005	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaaactggcccctggtcctaTtgagattccatgcgaggatg	10	10	11	10	1	0	1	0	1	0	1	2	4	2	2	4	3	2	0	4	3	3	3			TCGA-5P-A9JY-01A-11D-A42J-10	TCGA-5P-A9JY-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d3702abb-947d-4b7c-93d3-30102121f09b	f6bea4da-a48b-4082-b9aa-e19d3af1ac5c	g.chrX:40526005T>C	ENST00000324817.1	-	24	3350	c.3232A>G	c.(3232-3234)Ata>Gta	p.I1078V		NM_004229.3	NP_004220.2	O60244	MED14_HUMAN	mediator complex subunit 14	1078	Pro-rich.				androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(2)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CCTGGTCCTATTGAGATTCCA	0.478																																					p.I1078V		Atlas-SNP	.											.	MED14	108	.	0			c.A3232G						PASS	.						48	41	43					X																	40526005		2203	4300	6503	SO:0001583	missense	9282	exon24			GTCCTATTGAGAT	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.3232A>G	chrX.hg19:g.40526005T>C	ENSP00000323720:p.Ile1078Val	195.0	0.0	.		138.0	14.0	.	NM_004229	Q4KMR7|Q9UNB3	Missense_Mutation	SNP	ENST00000324817.1	hg19	CCDS14254.1	.	.	.	.	.	.	.	.	.	.	T	12.03	1.817087	0.32145	.	.	ENSG00000180182	ENST00000324817	.	.	.	5.75	4.59	0.56863	.	0.041131	0.85682	D	0.000000	T	0.25531	0.0621	N	0.08118	0	0.34054	D	0.656508	B	0.02656	0.0	B	0.01281	0.0	T	0.23940	-1.0174	9	0.17369	T	0.5	.	10.6482	0.45632	0.0:0.0753:0.0:0.9247	.	1078	O60244	MED14_HUMAN	V	1078	.	ENSP00000323720:I1078V	I	-	1	0	MED14	40410949	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	7.496000	0.81526	0.810000	0.34279	0.402000	0.26972	ATA	.	.	.	none		0.478	MED14-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060692.1	NM_004229		C	40526005	T	C	40526005	3	2	30	1	0	0	0	0	1	0	0	0	9439	1493	52	3	1164	3	MED14	23	40526005	Missense_Mutation	SNP	T	TCGA-5P-A9JY-01A-11D-A42J-10		40526005	114744555	122	2229											
TMEM52	339456	hgsc.bcm.edu	37	chr1	1850654	1850654	+	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	aggagcggcaggagcggcagGagcggcagcagcagccgcag	10	0	20	11	4	0	0	0	0	0	0	0	3	0	3	1	6	6	6	1	6	0	0			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr1:1850654G>C	ENST00000310991.3	-	1	58	c.51C>G	c.(49-51)ctC>ctG	p.L17L	TMEM52_ENST00000378602.3_5'Flank	NM_178545.3	NP_848640.1	Q8NDY8	TMM52_HUMAN	transmembrane protein 52	17						integral component of membrane (GO:0016021)				NS(1)|prostate(1)|stomach(1)	3	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)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.82e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.75e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		ggagcggcaggagcggcagca	0.771																																					p.L17L		Atlas-SNP	.											TMEM52,NS,carcinoma,0,1	TMEM52	21	.	0			c.C51G						PASS	.						1	2	1					1																	1850654		671	1684	2355	SO:0001819	synonymous_variant	339456	exon1			CGGCAGGAGCGGC	AJ278736	CCDS35.1	1p36.33	2008-02-05			ENSG00000178821	ENSG00000178821			27916	protein-coding gene	gene with protein product							Standard	NM_178545		Approved		uc001aij.2	Q8NDY8	OTTHUMG00000000944	ENST00000310991.3:c.51C>G	chr1.hg19:g.1850654G>C		9.0	1.0	.		10.0	2.0	.	NM_178545	Q4VXS6|Q6UX25	Silent	SNP	ENST00000310991.3	hg19	CCDS35.1	.	.	.	.	.	.	.	.	.	.	.	4.530	0.098402	0.08681	.	.	ENSG00000178821	ENST00000378598	.	.	.	0.149	0.149	0.14863	.	.	.	.	.	T	0.39489	0.1080	.	.	.	0.22446	N	0.999091	.	.	.	.	.	.	T	0.39035	-0.9633	4	0.87932	D	0	.	.	.	.	.	.	.	.	C	15	.	ENSP00000367861:S15C	S	-	2	0	TMEM52	1840514	0.001000	0.12720	0.009000	0.14445	0.010000	0.07245	0.286000	0.18902	0.192000	0.20272	0.195000	0.17529	TCC	.	.	.	none		0.771	TMEM52-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000002781.1	NM_178545		C	1850654	G	C	1850654	2	2	31	1	0	0	0	0	0	0	0	1	16190	1161	41	4		4	TMEM52	1	1850654	Silent	SNP	G	TCGA-5P-A9JZ-01A-11D-A42J-10		1850654	247399967	1	2230											
PTCH2	8643	hgsc.bcm.edu	37	chr1	45295617	45295617	+	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	gggggtctctggccatgcctCccagcagcaattcctcctgc	5	9	11	16	0	1	0	0	0	1	0	5	0	4	0	5	3	4	2	5	3	1	1			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr1:45295617C>T	ENST00000372192.3	-	7	1029	c.899G>A	c.(898-900)gGa>gAa	p.G300E	PTCH2_ENST00000447098.2_Missense_Mutation_p.G300E	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	300					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)					GGCCATGCCTCCCAGCAGCAA	0.587									Basal Cell Nevus syndrome																												p.G300E		Atlas-SNP	.											.	PTCH2	96	.	0			c.G899A						PASS	.						37	37	37					1																	45295617		2203	4300	6503	SO:0001583	missense	8643	exon7	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	ATGCCTCCCAGCA	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.899G>A	chr1.hg19:g.45295617C>T	ENSP00000361266:p.Gly300Glu	102.0	0.0	.		95.0	42.0	.	NM_001166292	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	Missense_Mutation	SNP	ENST00000372192.3	hg19	CCDS516.1	.	.	.	.	.	.	.	.	.	.	C	31	5.096188	0.94197	.	.	ENSG00000117425	ENST00000447098;ENST00000372192	D;D	0.97731	-4.44;-4.51	4.78	4.78	0.61160	.	0.000000	0.51477	D	0.000084	D	0.98845	0.9610	M	0.89095	3.005	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99701	1.1004	10	0.87932	D	0	-14.0582	16.7386	0.85454	0.0:1.0:0.0:0.0	.	300	Q9Y6C5	PTC2_HUMAN	E	300	ENSP00000389703:G300E;ENSP00000361266:G300E	ENSP00000361266:G300E	G	-	2	0	PTCH2	45068204	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.071000	0.76770	2.480000	0.83734	0.561000	0.74099	GGA	.	.	.	none		0.587	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	NM_003738		T	45295617	C	T	45295617	3	4	31	1	0	0	0	0	1	0	0	0	12741	855	30	2	2796	2	PTCH2	1	45295617	Missense_Mutation	SNP	C	TCGA-5P-A9JZ-01A-11D-A42J-10	43444963	45295617	203955004	2	2231											
C8A	731	hgsc.bcm.edu	37	chr1	57372456	57372456	+	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	attgtaaaaaatttggaggtGgcaaaactggcaagtgttta	15	12	11	3	0	0	0	0	0	0	0	0	1	0	1	0	4	1	4	0	4	7	5			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr1:57372456G>A	ENST00000361249.3	+	8	1309	c.1213G>A	c.(1213-1215)Ggc>Agc	p.G405S		NM_000562.2	NP_000553.1	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	405	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						ATTTGGAGGTGGCAAAACTGG	0.403																																					p.G405S		Atlas-SNP	.											.	C8A	103	.	0			c.G1213A						PASS	.						108	108	108					1																	57372456		2203	4300	6503	SO:0001583	missense	731	exon8			GGAGGTGGCAAAA	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.1213G>A	chr1.hg19:g.57372456G>A	ENSP00000354458:p.Gly405Ser	153.0	0.0	.		139.0	56.0	.	NM_000562	A2RUI4|A2RUI5|Q13668|Q9H130	Missense_Mutation	SNP	ENST00000361249.3	hg19	CCDS606.1	.	.	.	.	.	.	.	.	.	.	G	10.61	1.398516	0.25205	.	.	ENSG00000157131	ENST00000361249	D	0.83250	-1.7	4.87	4.87	0.63330	Membrane attack complex component/perforin (MACPF) domain (3);	0.711573	0.14889	N	0.292511	T	0.78748	0.4332	L	0.58302	1.8	0.19575	N	0.999965	P	0.35527	0.507	B	0.37550	0.253	T	0.66991	-0.5783	10	0.06494	T	0.89	-25.6441	13.709	0.62656	0.0:0.0:1.0:0.0	.	405	P07357	CO8A_HUMAN	S	405	ENSP00000354458:G405S	ENSP00000354458:G405S	G	+	1	0	C8A	57145044	0.061000	0.20836	0.154000	0.22540	0.399000	0.30720	2.056000	0.41355	2.711000	0.92665	0.561000	0.74099	GGC	.	.	.	none		0.403	C8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022890.1	NM_000562		A	57372456	G	A	57372456	3	1	31	1	0	0	0	0	1	0	0	0	2418	1348	47	2	1243	2	C8A	1	57372456	Missense_Mutation	SNP	G	TCGA-5P-A9JZ-01A-11D-A42J-10	12076839	57372456	191878165	3	2232											
TCHH	7062	hgsc.bcm.edu	37	chr1	152084174	152084174	+	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	ctcctcttgctcccgccttaGttgctgctcgcgcctctcct	1	14	7	19	3	2	0	0	0	2	0	6	0	4	0	5	0	3	4	5	0	1	3			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr1:152084174G>C	ENST00000368804.1	-	2	1518	c.1519C>G	c.(1519-1521)Cta>Gta	p.L507V		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	507	9 X 28 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCCCGCCTTAGTTGCTGCTCG	0.652																																					p.L507V		Atlas-SNP	.											.	TCHH	275	.	0			c.C1519G						PASS	.						63	70	67					1																	152084174		2062	4193	6255	SO:0001583	missense	7062	exon3			GCCTTAGTTGCTG	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.1519C>G	chr1.hg19:g.152084174G>C	ENSP00000357794:p.Leu507Val	30.0	0.0	.		37.0	6.0	.	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	g	7.583	0.669162	0.14776	.	.	ENSG00000159450	ENST00000368804	T	0.06528	3.29	1.93	0.956	0.19608	.	.	.	.	.	T	0.01061	0.0035	N	0.08118	0	0.09310	N	1	B	0.25904	0.137	B	0.29440	0.102	T	0.48305	-0.9047	9	0.29301	T	0.29	.	7.6375	0.28274	0.0:0.0:0.7453:0.2547	.	507	Q07283	TRHY_HUMAN	V	507	ENSP00000357794:L507V	ENSP00000357794:L507V	L	-	1	2	TCHH	150350798	0.000000	0.05858	0.002000	0.10522	0.099000	0.18886	0.376000	0.20535	0.398000	0.25338	0.109000	0.15622	CTA	.	.	.	none		0.652	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		C	152084174	G	C	152084174	3	2	31	1	0	0	0	0	1	0	0	0	15712	1020	36	4	4316	4	TCHH	1	152084174	Missense_Mutation	SNP	G	TCGA-5P-A9JZ-01A-11D-A42J-10	94711718	152084174	97166447	4	2233			1	3		2	2	48	N	G_A	7.439135e-05
TCHH	7062	hgsc.bcm.edu	37	chr1	152084221	152084221	+	Missense_Mutation	SNP	A	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	cgcgcctctcctcctcctcgAgcttcagccaacgttcgcgc	4	9	8	20	6	2	0	1	0	1	0	7	1	4	0	5	0	3	2	5	0	1	2	rs202112040		TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr1:152084221A>C	ENST00000368804.1	-	2	1471	c.1472T>G	c.(1471-1473)cTc>cGc	p.L491R		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	491	9 X 28 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCCTCCTCGAGCTTCAGCCA	0.672																																					p.L491R		Atlas-SNP	.											.	TCHH	275	.	0			c.T1472G						PASS	.						63	70	68					1																	152084221		2106	4220	6326	SO:0001583	missense	7062	exon3			TCCTCGAGCTTCA	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"EF-hand domain containing"	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.1472T>G	chr1.hg19:g.152084221A>C	ENSP00000357794:p.Leu491Arg	22.0	0.0	.		42.0	8.0	.	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	a	0.064	-1.216147	0.01542	.	.	ENSG00000159450	ENST00000368804	T	0.04603	3.59	2.11	-4.23	0.03789	.	.	.	.	.	T	0.00524	0.0017	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.43491	-0.9388	9	0.12430	T	0.62	.	7.0185	0.24900	0.2982:0.5613:0.0:0.1406	.	491	Q07283	TRHY_HUMAN	R	491	ENSP00000357794:L491R	ENSP00000357794:L491R	L	-	2	0	TCHH	150350845	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-1.154000	0.03166	-2.764000	0.00368	-1.533000	0.00918	CTC	.	.	.	weak		0.672	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		C	152084221	A	C	152084221	3	2	31	1	0	0	0	0	1	0	0	0	15712	304	11	5	4363	5	TCHH	1	152084221	Missense_Mutation	SNP	A	TCGA-5P-A9JZ-01A-11D-A42J-10	47	152084221	97166400	5	2234			1	3		2	2	48	N	G_A	7.439135e-05
SEMA4A	64218	hgsc.bcm.edu	37	chr1	156130786	156130786	+	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	cgagtttgacttctttgagaGgctccacacatcgcgggtgg	7	11	13	10	3	1	2	0	2	1	1	3	4	2	2	1	3	0	2	1	3	0	3			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr1:156130786G>C	ENST00000368285.3	+	8	1043	c.776G>C	c.(775-777)aGg>aCg	p.R259T	SEMA4A_ENST00000355014.2_Missense_Mutation_p.R259T|SEMA4A_ENST00000368284.1_Missense_Mutation_p.R127T|SEMA4A_ENST00000368282.1_Missense_Mutation_p.R259T|SEMA4A_ENST00000487358.1_3'UTR|SEMA4A_ENST00000368286.2_Missense_Mutation_p.R127T	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	259	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				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)					TTCTTTGAGAGGCTCCACACA	0.622																																					p.R259T		Atlas-SNP	.											.	SEMA4A	75	.	0			c.G776C						PASS	.						112	126	121					1																	156130786		2203	4300	6503	SO:0001583	missense	64218	exon8			TTGAGAGGCTCCA	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.776G>C	chr1.hg19:g.156130786G>C	ENSP00000357268:p.Arg259Thr	37.0	0.0	.		57.0	17.0	.	NM_001193300	B2RDH8|B3KR76|Q5TCI5|Q5TCJ6|Q8WUA9	Missense_Mutation	SNP	ENST00000368285.3	hg19	CCDS1132.1	.	.	.	.	.	.	.	.	.	.	G	15.32	2.798929	0.50208	.	.	ENSG00000196189	ENST00000435124;ENST00000414683;ENST00000355014;ENST00000368285;ENST00000368284;ENST00000368283;ENST00000544376;ENST00000368286;ENST00000438830;ENST00000368282	T;T;T;T;T;T;T;T	0.10763	2.84;2.84;2.84;2.84;2.84;2.84;2.84;2.84	5.65	-0.876	0.10624	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.435314	0.24776	N	0.035696	T	0.02571	0.0078	L	0.39898	1.24	0.25989	N	0.982277	B;B	0.27264	0.041;0.173	B;B	0.29440	0.065;0.102	T	0.38929	-0.9638	10	0.48119	T	0.1	.	5.6603	0.17664	0.5503:0.1361:0.3136:0.0	.	127;259	Q5TCJ6;Q9H3S1	.;SEM4A_HUMAN	T	259;160;259;259;127;221;221;127;226;259	ENSP00000401391:R259T;ENSP00000399230:R160T;ENSP00000347117:R259T;ENSP00000357268:R259T;ENSP00000357267:R127T;ENSP00000357269:R127T;ENSP00000392865:R226T;ENSP00000357265:R259T	ENSP00000347117:R259T	R	+	2	0	SEMA4A	154397410	0.916000	0.31088	0.889000	0.34880	0.729000	0.41735	1.624000	0.37018	-0.096000	0.12329	-0.391000	0.06502	AGG	.	.	.	none		0.622	SEMA4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039484.2	NM_022367		C	156130786	G	C	156130786	3	2	31	1	0	0	0	0	1	0	0	0	14044	1000	35	4	802	4	SEMA4A	1	156130786	Missense_Mutation	SNP	G	TCGA-5P-A9JZ-01A-11D-A42J-10	4046565	156130786	93119835	6	2235											
CNTN2	6900	hgsc.bcm.edu	37	chr1	205033767	205033767	+	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	acagagtgactgtaactccaGatggcaccttgatcataaga	14	9	9	9	0	1	5	1	2	0	3	2	5	2	5	2	1	1	2	2	1	2	3			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr1:205033767G>C	ENST00000331830.4	+	12	1692	c.1408G>C	c.(1408-1410)Gat>Cat	p.D470H	AL583832.1_ENST00000515887.1_RNA	NM_005076.3	NP_005067.1	Q02246	CNTN2_HUMAN	contactin 2 (axonal)	470	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)			TGTAACTCCAGATGGCACCTT	0.517																																					p.D470H	Melanoma(183;2548 2817 37099 41192)	Atlas-SNP	.											.	CNTN2	116	.	0			c.G1408C						PASS	.						128	109	115					1																	205033767		2203	4300	6503	SO:0001583	missense	6900	exon12			ACTCCAGATGGCA	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.1408G>C	chr1.hg19:g.205033767G>C	ENSP00000330633:p.Asp470His	95.0	0.0	.		114.0	44.0	.	NM_005076	P78432|Q5T054	Missense_Mutation	SNP	ENST00000331830.4	hg19	CCDS1449.1	.	.	.	.	.	.	.	.	.	.	G	18.52	3.641312	0.67244	.	.	ENSG00000184144	ENST00000331830	T	0.79554	-1.28	5.47	4.56	0.56223	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.248655	0.28047	N	0.016801	D	0.89822	0.6826	M	0.90595	3.13	0.46317	D	0.998986	D;D	0.76494	0.983;0.999	D;D	0.78314	0.965;0.991	D	0.90037	0.4139	10	0.72032	D	0.01	.	8.2648	0.31808	0.239:0.0:0.761:0.0	.	470;361	Q02246;Q68DA2	CNTN2_HUMAN;.	H	470	ENSP00000330633:D470H	ENSP00000330633:D470H	D	+	1	0	CNTN2	203300390	1.000000	0.71417	0.678000	0.29963	0.959000	0.62525	5.421000	0.66447	1.316000	0.45131	0.561000	0.74099	GAT	.	.	.	none		0.517	CNTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090080.3	NM_005076		C	205033767	G	C	205033767	3	2	31	1	0	0	0	0	1	0	0	0	3643	942	33	4	1450	4	CNTN2	1	205033767	Missense_Mutation	SNP	G	TCGA-5P-A9JZ-01A-11D-A42J-10	48902981	205033767	44216854	7	2236											
CEP68	23177	hgsc.bcm.edu	37	chr2	65299543	65299543	+	Missense_Mutation	SNP	T	T	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	tgatatgggctctccccagcTaaggacacgggacagagggt	10	7	14	10	1	1	2	0	1	1	1	2	4	1	4	2	4	1	2	2	4	2	2			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr2:65299543T>G	ENST00000377990.2	+	3	1516	c.1313T>G	c.(1312-1314)cTa>cGa	p.L438R	CEP68_ENST00000537589.1_Missense_Mutation_p.L50R|RAB1A_ENST00000494188.1_Intron|CEP68_ENST00000546106.1_Missense_Mutation_p.L438R|CEP68_ENST00000497039.1_3'UTR|CEP68_ENST00000260569.4_Missense_Mutation_p.L438R	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	438					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						TCTCCCCAGCTAAGGACACGG	0.637																																					p.L438R		Atlas-SNP	.											.	CEP68	69	.	0			c.T1313G						PASS	.						46	49	48					2																	65299543		2203	4300	6503	SO:0001583	missense	23177	exon3			CCCAGCTAAGGAC	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.1313T>G	chr2.hg19:g.65299543T>G	ENSP00000367229:p.Leu438Arg	61.0	0.0	.		70.0	29.0	.	NM_015147	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Missense_Mutation	SNP	ENST00000377990.2	hg19	CCDS1880.2	.	.	.	.	.	.	.	.	.	.	T	16.41	3.115090	0.56505	.	.	ENSG00000011523	ENST00000377990;ENST00000546106;ENST00000537589;ENST00000260569;ENST00000545501	T;T;T;T	0.26067	2.39;2.38;1.76;2.39	5.78	-1.46	0.08800	.	1.328540	0.05425	N	0.544888	T	0.38878	0.1057	M	0.62723	1.935	0.09310	N	1	B;B;D;D;B	0.76494	0.102;0.102;0.98;0.999;0.102	B;B;P;D;B	0.67548	0.051;0.051;0.804;0.952;0.051	T	0.28964	-1.0027	10	0.45353	T	0.12	0.0022	0.6239	0.00783	0.3256:0.1216:0.2231:0.3297	.	426;438;438;438;438	F5H3N9;F5H2Y2;Q76N32;Q76N32-2;Q05C09	.;.;CEP68_HUMAN;.;.	R	438;438;50;438;426	ENSP00000367229:L438R;ENSP00000438306:L438R;ENSP00000443357:L50R;ENSP00000260569:L438R	ENSP00000260569:L438R	L	+	2	0	CEP68	65153047	0.000000	0.05858	0.002000	0.10522	0.086000	0.17979	0.206000	0.17375	-0.173000	0.10761	-0.468000	0.05107	CTA	.	.	.	none		0.637	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147		G	65299543	T	G	65299543	3	3	31	1	0	0	0	0	1	0	0	0	3260	1522	53	5	1319	5	CEP68	2	65299543	Missense_Mutation	SNP	T	TCGA-5P-A9JZ-01A-11D-A42J-10		65299543	177899830	8	2237											
SPEG	10290	hgsc.bcm.edu	37	chr2	220342166	220342166	+	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	gcagagttggctgtgcattcAggtaggcaggagttccggag	8	9	17	7	1	1	1	1	0	0	1	2	3	2	3	1	5	1	7	1	5	1	4			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr2:220342166A>G	ENST00000312358.7	+	20	4860	c.4728A>G	c.(4726-4728)tcA>tcG	p.S1576S	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1576					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)		CTGTGCATTCAGGTAGGCAGG	0.622																																					p.S1576S		Atlas-SNP	.											.	SPEG	272	.	0			c.A4728G						PASS	.						32	37	35					2																	220342166		2094	4215	6309	SO:0001630	splice_region_variant	10290	exon20			GCATTCAGGTAGG	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.4729+1A>G	chr2.hg19:g.220342166A>G		78.0	0.0	.		65.0	24.0	.	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Silent	SNP	ENST00000312358.7	hg19	CCDS42824.1																																																																																			.	.	.	none		0.622	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	Silent	G	220342166	A	G	220342166	5	3	31	1	0	0	0	0	0	0	1	0	15048	202	7	3	4818	3	SPEG	2	220342166	Splice_Site	SNP	A	TCGA-5P-A9JZ-01A-11D-A42J-10	155042623	220342166	22857207	9	2238											
C4orf23	152992	hgsc.bcm.edu	37	chr4	8470057	8470057	+	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	tctcgaaatgggagtttgaaGacctggaatgggggaggtaa	12	9	16	4	1	1	2	0	1	1	1	2	6	1	5	1	5	0	2	1	5	4	2			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr4:8470057G>T	ENST00000389737.4	+	9	1911	c.1911G>T	c.(1909-1911)aaG>aaT	p.K637N	TRMT44_ENST00000513449.2_Missense_Mutation_p.K396N	NM_152544.2	NP_689757.2	Q8IYL2	TRM44_HUMAN	tRNA methyltransferase 44 homolog (S. cerevisiae)	637					tRNA processing (GO:0008033)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)										GGAGTTTGAAGACCTGGAATG	0.473																																					p.K637N		Atlas-SNP	.											.	TRMT44	7	.	0			c.G1911T						PASS	.						60	69	66					4																	8470057		2203	4300	6503	SO:0001583	missense	152992	exon9			TTTGAAGACCTGG	AK093044	CCDS3402.1, CCDS3402.2	4p16.1	2012-06-12	2012-06-12	2012-06-12	ENSG00000155275	ENSG00000155275			26653	protein-coding gene	gene with protein product	"tRNA methyltransferase 44 homolog (S. cerevisiae)"	614309	"chromosome 4 open reading frame 23", "methyltransferase like 19"	C4orf23, METTL19		21658913	Standard	NM_152544		Approved	FLJ35725, TRM44	uc003glg.2	Q8IYL2	OTTHUMG00000160935	ENST00000389737.4:c.1911G>T	chr4.hg19:g.8470057G>T	ENSP00000374387:p.Lys637Asn	79.0	0.0	.		101.0	41.0	.	NM_152544	Q8NA95	Missense_Mutation	SNP	ENST00000389737.4	hg19	CCDS3402.2	.	.	.	.	.	.	.	.	.	.	G	10.35	1.325276	0.24080	.	.	ENSG00000155275	ENST00000513449;ENST00000389737;ENST00000285635	T;T	0.18657	2.21;2.2	4.05	3.2	0.36748	.	1.211260	0.05647	N	0.584554	T	0.19604	0.0471	L	0.45137	1.4	0.09310	N	1	B;B	0.18461	0.026;0.028	B;B	0.24701	0.028;0.055	T	0.21177	-1.0253	10	0.40728	T	0.16	-4.6458	4.3664	0.11227	0.093:0.1435:0.5957:0.1679	.	637;396	Q8IYL2;Q8IYL2-2	TRM44_HUMAN;.	N	396;637;245	ENSP00000424643:K396N;ENSP00000374387:K637N	ENSP00000285635:K245N	K	+	3	2	METTL19	8520957	0.088000	0.21588	0.029000	0.17559	0.088000	0.18126	0.592000	0.23984	2.274000	0.75844	0.462000	0.41574	AAG	.	.	.	none		0.473	TRMT44-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359197.2	NM_152544		T	8470057	G	T	8470057	3	4	31	1	0	0	0	0	1	0	0	0	2258	933	33	4	1945	4	C4orf23	4	8470057	Missense_Mutation	SNP	G	TCGA-5P-A9JZ-01A-11D-A42J-10		8470057	182684219	10	2239											
CC2D2A	57545	hgsc.bcm.edu	37	chr4	15539635	15539635	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccctccagagcccactgaTcgggcagtgatagagcagga	11	5	13	12	1	0	4	0	2	0	2	2	5	1	5	3	2	3	2	3	2	1	1			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr4:15539635T>C	ENST00000503292.1	+	17	2058	c.1878T>C	c.(1876-1878)gaT>gaC	p.D626D	CC2D2A_ENST00000424120.1_Silent_p.D626D|CC2D2A_ENST00000513811.1_3'UTR|CC2D2A_ENST00000413206.1_Silent_p.D626D|CC2D2A_ENST00000389652.5_Silent_p.D577D	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	626					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|urinary_tract(2)	32						AGCCCACTGATCGGGCAGTGA	0.607																																					p.D626D		Atlas-SNP	.											.	CC2D2A	158	.	0			c.T1878C						PASS	.						44	53	50					4																	15539635		2098	4229	6327	SO:0001819	synonymous_variant	57545	exon17			CACTGATCGGGCA	AB037766, EU450799	CCDS47026.1, CCDS47027.1, CCDS47027.2, CCDS54744.1	4p15.33	2014-09-17	2007-10-19		ENSG00000048342	ENSG00000048342			29253	protein-coding gene	gene with protein product	"Meckel syndrome, type 6"	612013				10718198, 18513680	Standard	NM_001080522		Approved	KIAA1345, MKS6, JBTS9	uc010idv.2	Q9P2K1	OTTHUMG00000160255	ENST00000503292.1:c.1878T>C	chr4.hg19:g.15539635T>C		165.0	0.0	.		143.0	49.0	.	NM_001080522	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	Silent	SNP	ENST00000503292.1	hg19	CCDS47026.1																																																																																			.	.	.	none		0.607	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2	NM_001080522		C	15539635	T	C	15539635	2	2	31	1	0	0	0	0	0	0	0	1	2730	1432	50	3		3	CC2D2A	4	15539635	Silent	SNP	T	TCGA-5P-A9JZ-01A-11D-A42J-10	7069578	15539635	175614641	11	2240											
DNAJC21	134218	hgsc.bcm.edu	37	chr5	34945005	34945005	+	Silent	SNP	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	gagaagtcaaagaagcatcgGgaaatggtggccttgctaaa	15	7	13	6	1	1	2	1	0	0	2	2	4	1	3	1	3	2	2	1	3	6	2			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr5:34945005G>A	ENST00000342382.4	+	8	1244	c.1017G>A	c.(1015-1017)cgG>cgA	p.R339R	DNAJC21_ENST00000303525.7_Silent_p.R339R|DNAJC21_ENST00000382021.2_Silent_p.R339R			Q5F1R6	DJC21_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 21	339	Glu-rich.				protein folding (GO:0006457)	ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(31;7.08e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)			AGAAGCATCGGGAAATGGTGG	0.418																																					p.R339R		Atlas-SNP	.											.	DNAJC21	54	.	0			c.G1017A						PASS	.						142	143	143					5																	34945005		2203	4300	6503	SO:0001819	synonymous_variant	134218	exon8			GCATCGGGAAATG		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.1017G>A	chr5.hg19:g.34945005G>A		603.0	0.0	.		564.0	206.0	.	NM_001012339	Q3B7J9|Q6P086|Q6ZS43|Q86VC6	Silent	SNP	ENST00000342382.4	hg19	CCDS34144.1																																																																																			.	.	.	none		0.418	DNAJC21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157337.1	NM_194283		A	34945005	G	A	34945005	2	1	31	1	0	0	0	0	0	0	0	1	4642	1219	43	2		2	DNAJC21	5	34945005	Silent	SNP	G	TCGA-5P-A9JZ-01A-11D-A42J-10		34945005	145970255	12	2241											
CAPN11	11131	hgsc.bcm.edu	37	chr6	44137019	44137019	+	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	ctttttttttcttaagcagaGcccacttttactgatacggg	8	17	7	9	1	1	2	0	1	1	1	1	2	1	2	1	1	4	1	1	1	3	8			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr6:44137019G>A	ENST00000398776.1	+	3	128	c.90G>A	c.(88-90)gaG>gaA	p.E30E	CAPN11_ENST00000542245.1_Splice_Site_p.E30E	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11	30					proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)			breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CTTAAGCAGAGCCCACTTTTA	0.483																																					p.E30E		Atlas-SNP	.											.	CAPN11	66	.	0			c.G90A						PASS	.						24	24	24					6																	44137019		1861	4093	5954	SO:0001630	splice_region_variant	11131	exon3			AGCAGAGCCCACT	AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225		"EF-hand domain containing"	1478	protein-coding gene	gene with protein product		604822				10409436	Standard	NM_007058		Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.89-1G>A	chr6.hg19:g.44137019G>A		194.0	0.0	.		200.0	75.0	.	NM_007058	B2RA64|Q5T3G1|Q8N4R5	Silent	SNP	ENST00000398776.1	hg19	CCDS47436.1																																																																																			.	.	.	none		0.483	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3		Silent	A	44137019	G	A	44137019	5	1	31	1	0	0	0	0	0	0	1	0	2626	985	34	2	100	2	CAPN11	6	44137019	Splice_Site	SNP	G	TCGA-5P-A9JZ-01A-11D-A42J-10		44137019	126978048	13	2242											
SMAP1	60682	hgsc.bcm.edu	37	chr6	71567632	71567633	+	Frame_Shift_Del	DEL	TA	TA	-																															ttttgtggtgcaggtgtattTatgggacccacaaatatacc																										TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr6:71567632_71567633delTA	ENST00000370455.3	+	10	1217_1218	c.969_970delTA	c.(967-972)tttatgfs	p.M324fs	SMAP1_ENST00000370452.3_Frame_Shift_Del_p.M297fs|SMAP1_ENST00000316999.5_Frame_Shift_Del_p.M297fs|B3GAT2_ENST00000230053.6_3'UTR	NM_001044305.1|NM_001281440.1	NP_001037770.1|NP_001268369.1	Q8IYB5	SMAP1_HUMAN	small ArfGAP 1	324					positive regulation of erythrocyte differentiation (GO:0045648)|regulation of ARF GTPase activity (GO:0032312)|regulation of clathrin-mediated endocytosis (GO:2000369)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(1)|urinary_tract(1)	15						CAGGTGTATTTATGGGACCCAC	0.45																																					p.323_323del		Atlas-Indel,Pindel	.											.	SMAP1	77	.	0			c.968_969del						PASS	.																																			SO:0001589	frameshift_variant	60682	exon10			.	AK023221	CCDS4973.1, CCDS43478.1, CCDS64459.1, CCDS75478.1	6q12-q13	2009-11-30	2008-09-05		ENSG00000112305	ENSG00000112305		"ADP-ribosylation factor GTPase activating proteins"	19651	protein-coding gene	gene with protein product		611372	"stromal membrane-associated protein 1", "stromal membrane-associated GTPase-activating protein 1"			9644265, 12119110	Standard	NM_001044305		Approved	FLJ13159, SMAP-1	uc003pfr.3	Q8IYB5	OTTHUMG00000014996	ENST00000370455.3:c.969_970delTA	chr6.hg19:g.71567632_71567633delTA	ENSP00000359484:p.Met324fs	64.0	0.0	0		60.0	23.0	0.383333	NM_001044305	Q53H70|Q5SYQ2|Q6PK24|Q8NDH4|Q96L38|Q96L39|Q9H8X4	Frame_Shift_Del	DEL	ENST00000370455.3	hg19	CCDS43478.1																																																																																			.	.	.	none		0.45	SMAP1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041149.1	NM_001044305		-	71567633	TA	-	71567632	7	5	31	1	0	1	0	1	0	0	0	0	14779	1751	61	0	1007	0	SMAP1	6	71567632	Frame_Shift_Del	DEL	TA	TCGA-5P-A9JZ-01A-11D-A42J-10	27430613	71567632	99547435	14	2243											
EGFR	1956	hgsc.bcm.edu	37	chr7	55221781	55221781	+	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	ctctacaaccccaccacgtaCcagatggatgtgaaccccga	12	6	7	16	2	1	2	0	1	1	1	1	4	1	3	6	1	4	1	6	1	4	2			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr7:55221781C>T	ENST00000275493.2	+	7	1002	c.825C>T	c.(823-825)taC>taT	p.Y275Y	EGFR_ENST00000454757.2_Silent_p.Y222Y|EGFR_ENST00000344576.2_Silent_p.Y275Y|EGFR_ENST00000420316.2_Silent_p.Y275Y|EGFR_ENST00000455089.1_Silent_p.Y230Y|EGFR_ENST00000342916.3_Silent_p.Y275Y|EGFR_ENST00000442591.1_Silent_p.Y275Y	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	275			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)	CCACCACGTACCAGATGGATG	0.587		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																											p.Y275Y		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.C825T						PASS	.						198	156	170					7																	55221781		2203	4300	6503	SO:0001819	synonymous_variant	1956	exon7	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	CACGTACCAGATG		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.825C>T	chr7.hg19:g.55221781C>T		118.0	0.0	.		327.0	94.0	.	NM_201283	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	hg19	CCDS5514.1																																																																																			.	.	.	none		0.587	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		T	55221781	C	T	55221781	2	4	31	1	0	0	0	0	0	0	0	1	4969	518	18	2		2	EGFR	7	55221781	Silent	SNP	C	TCGA-5P-A9JZ-01A-11D-A42J-10		55221781	103916882	15	2244											
DLX6	1750	hgsc.bcm.edu	37	chr7	96635450	96635450	+	Missense_Mutation	SNP	A	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	gccgccgccgccgccgccgcAgccgcactcgcagcagagct	5	2	13	21	8	0	1	0	0	0	1	1	1	0	1	7	0	3	5	7	0	0	0	rs563784519	byFrequency	TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr7:96635450A>C	ENST00000518156.2	+	1	591	c.161A>C	c.(160-162)cAg>cCg	p.Q54P	DLX6-AS2_ENST00000606174.1_RNA|DLX6-AS1_ENST00000430027.3_RNA|DLX6-AS1_ENST00000431497.2_RNA|DLX6-AS1_ENST00000437331.2_RNA|DLX6_ENST00000007660.5_Intron|DLX6_ENST00000555308.1_5'Flank|DLX6-AS1_ENST00000437541.1_RNA|DLX6-AS1_ENST00000452769.2_RNA|DLX6-AS1_ENST00000605417.1_RNA|DLX6-AS1_ENST00000458352.2_RNA|DLX6-AS1_ENST00000430404.2_RNA			P56179	DLX6_HUMAN	distal-less homeobox 6	0					anatomical structure formation involved in morphogenesis (GO:0048646)|embryonic limb morphogenesis (GO:0030326)|epithelial cell differentiation (GO:0030855)|head development (GO:0060322)|inner ear morphogenesis (GO:0042472)|nervous system development (GO:0007399)|palate development (GO:0060021)|positive regulation of epithelial cell proliferation (GO:0050679)|skeletal system development (GO:0001501)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|large_intestine(1)|liver(2)|lung(4)|ovary(2)|urinary_tract(1)	12	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					ccgccgccgcagccgcACTCG	0.736													A|||	29	0.00579073	0.0015	0.0058	5008	,	,		5002	0.001		0.006	False		,,,				2504	0.0164				p.Q54P		Atlas-SNP	.											.	DLX6	37	.	0			c.A161C						PASS	.						2	2	2					7																	96635450		849	2293	3142	SO:0001583	missense	1750	exon1			CGCCGCAGCCGCA		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.161A>C	chr7.hg19:g.96635450A>C	ENSP00000428480:p.Gln54Pro	45.0	0.0	.		89.0	5.0	.	NM_005222	A4D1I2|B3KSQ0|J3KR92|Q3ZAR6|Q9UPL2	Missense_Mutation	SNP	ENST00000518156.2	hg19	CCDS47647.2	.	.	.	.	.	.	.	.	.	.	a	0.105	-1.146361	0.01714	.	.	ENSG00000006377	ENST00000518156	T	0.20200	2.09	3.38	0.713	0.18173	.	.	.	.	.	T	0.24586	0.0596	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.03673	-1.1014	6	0.34782	T	0.22	.	8.4116	0.32646	0.3776:0.6224:0.0:0.0	.	.	.	.	P	54	ENSP00000428480:Q54P	ENSP00000428480:Q54P	Q	+	2	0	DLX6	96473386	1.000000	0.71417	0.997000	0.53966	0.962000	0.63368	1.464000	0.35288	0.377000	0.24735	0.414000	0.27820	CAG	.	.	.	none		0.736	DLX6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334373.4	NM_005222		C	96635450	A	C	96635450	3	2	31	1	0	0	0	0	1	0	0	0	4577	188	7	5	163	5	DLX6	7	96635450	Missense_Mutation	SNP	A	TCGA-5P-A9JZ-01A-11D-A42J-10	41413669	96635450	62503213	16	2245											
CDHR3	222256	hgsc.bcm.edu	37	chr7	105624700	105624700	+	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	tttaccaggttgaggccttcGatccagaagacacaagccga	12	8	10	11	2	0	3	0	1	0	2	2	5	1	3	4	2	2	1	4	2	3	4			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr7:105624700G>A	ENST00000317716.9	+	4	558	c.478G>A	c.(478-480)Gat>Aat	p.D160N	CDHR3_ENST00000542731.1_Missense_Mutation_p.D160N|CDHR3_ENST00000541203.1_Intron|CDHR3_ENST00000478080.1_Missense_Mutation_p.D72N|CDHR3_ENST00000470188.1_3'UTR|CDHR3_ENST00000343407.5_5'UTR	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	160	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						TGAGGCCTTCGATCCAGAAGA	0.458																																					p.D160N		Atlas-SNP	.											.	CDHR3	153	.	0			c.G478A						PASS	.						63	64	64					7																	105624700		1907	4124	6031	SO:0001583	missense	222256	exon4			GCCTTCGATCCAG	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.478G>A	chr7.hg19:g.105624700G>A	ENSP00000325954:p.Asp160Asn	118.0	0.0	.		293.0	40.0	.	NM_152750	Q8TCI7	Missense_Mutation	SNP	ENST00000317716.9	hg19	CCDS47684.1	.	.	.	.	.	.	.	.	.	.	G	17.55	3.417404	0.62622	.	.	ENSG00000128536	ENST00000542731;ENST00000317716;ENST00000478080	T;T;T	0.78003	-1.14;-1.14;-1.14	4.56	4.56	0.56223	Cadherin (4);Cadherin-like (1);	0.137563	0.47455	D	0.000228	D	0.89150	0.6633	M	0.90977	3.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.88819	0.3297	10	0.33940	T	0.23	-25.4541	12.9987	0.58662	0.0:0.0:1.0:0.0	.	147;160	B3KYA0;Q6ZTQ4	.;CDHR3_HUMAN	N	160;160;72	ENSP00000439766:D160N;ENSP00000325954:D160N;ENSP00000417771:D72N	ENSP00000325954:D160N	D	+	1	0	CDHR3	105411936	1.000000	0.71417	0.963000	0.40424	0.334000	0.28698	4.753000	0.62183	2.522000	0.85027	0.655000	0.94253	GAT	.	.	.	none		0.458	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750		A	105624700	G	A	105624700	3	1	31	1	0	0	0	0	1	0	0	0	3122	1058	37	1	492	1	CDHR3	7	105624700	Missense_Mutation	SNP	G	TCGA-5P-A9JZ-01A-11D-A42J-10	8989250	105624700	53513963	17	2246											
FAM71F1	84691	hgsc.bcm.edu	37	chr7	128363339	128363339	+	Frame_Shift_Del	DEL	T	T	-																															gagtgaagccctgtctcagaTttttgccgacttacaccagc																										TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr7:128363339delT	ENST00000315184.5	+	4	829	c.776delT	c.(775-777)attfs	p.I259fs	FAM71F1_ENST00000485070.1_Frame_Shift_Del_p.I160fs|FAM71F1_ENST00000469348.1_3'UTR	NM_001282788.1|NM_032599.2	NP_001269717.1|NP_115988.1	Q96KD3	F71F1_HUMAN	family with sequence similarity 71, member F1	259										NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18						CTGTCTCAGATTTTTGCCGAC	0.498																																					p.I259fs		Atlas-Indel,Pindel	.											.	FAM71F1	42	.	0			c.775delA						PASS	.						121	119	120					7																	128363339		2203	4300	6503	SO:0001589	frameshift_variant	84691	exon4			.	AF367470	CCDS5804.1, CCDS64763.1	7q32.1	2007-11-20	2007-11-20	2007-11-20	ENSG00000135248	ENSG00000135248			30704	protein-coding gene	gene with protein product			"family with sequence similarity 137, member A"	FAM137A		12477932	Standard	XM_005250645		Approved	NYD-SP18	uc003vno.1	Q96KD3	OTTHUMG00000158276	ENST00000315184.5:c.776delT	chr7.hg19:g.128363339delT	ENSP00000326652:p.Ile259fs	131.0	0.0	0		96.0	33.0	0.34375	NM_032599	Q8IY75|Q8NA48	Frame_Shift_Del	DEL	ENST00000315184.5	hg19	CCDS5804.1																																																																																			.	.	.	none		0.498	FAM71F1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350544.2	NM_032599		-	128363339	T	-	128363339	7	5	31	1	0	1	0	1	0	0	0	0	5619	1493	52	0	790	0	FAM71F1	7	128363339	Frame_Shift_Del	DEL	T	TCGA-5P-A9JZ-01A-11D-A42J-10	22738639	128363339	30775324	18	2247											
OR2A1	346528	hgsc.bcm.edu	37	chr7	144015742	144015744	+	In_Frame_Del	DEL	CTT	CTT	-																															gggcctcatgaaatcaaccaCttcttctgtgaaatcctgtc																										TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr7:144015742_144015744delCTT	ENST00000408951.1	+	1	525_527	c.525_527delCTT	c.(523-528)cacttc>cac	p.F177del	OR2A1-AS1_ENST00000475089.1_RNA|OR2A1-AS1_ENST00000463561.1_RNA|OR2A1-AS1_ENST00000478925.1_RNA|OR2A1-AS1_ENST00000461843.1_RNA|OR2A1-AS1_ENST00000478806.1_RNA|OR2A1-AS1_ENST00000476560.1_RNA|OR2A1-AS1_ENST00000488041.1_RNA|OR2A1-AS1_ENST00000487102.1_RNA|OR2A1-AS1_ENST00000489488.1_RNA|OR2A1-AS1_ENST00000486094.1_RNA|OR2A1-AS1_ENST00000493539.1_RNA|OR2A1-AS1_ENST00000496968.1_RNA|OR2A1-AS1_ENST00000467944.1_RNA	NM_001005287.1	NP_001005287.1	Q8NGT9	OR2A1_HUMAN	olfactory receptor, family 2, subfamily A, member 1	177						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(1)|lung(3)|skin(2)	6	Melanoma(164;0.14)					AAATCAACCACTTCTTCTGTGAA	0.581																																					p.175_176del		Atlas-INDEL	.											.	OR2A1	10	.	0			c.524_526del						PASS	.																																			SO:0001651	inframe_deletion	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.525_527delCTT	chr7.hg19:g.144015745_144015747delCTT	ENSP00000386175:p.Phe177del	400.0	0.0	0		594.0	68.0	0.114478	NM_001005287	Q6IF44|Q96R46	In_Frame_Del	DEL	ENST00000408951.1	hg19	CCDS43673.1																																																																																			.	.	.	none		0.581	OR2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349985.1			-	144015744	CTT	-	144015742	7	5	31	1	0	1	0	1	0	0	0	0	10981	564	20	0	527	0	OR2A1	7	144015742	In_Frame_Del	DEL	CTT	TCGA-5P-A9JZ-01A-11D-A42J-10	15652403	144015742	15122921	19	2248											
C7orf33	202865	hgsc.bcm.edu	37	chr7	148311173	148311173	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acatgaaccgggggatggaaTttattgctcctgtatcagct	10	12	11	8	1	1	1	1	1	0	0	2	3	2	3	2	3	3	3	2	3	4	4			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr7:148311173T>C	ENST00000307003.2	+	2	605	c.244T>C	c.(244-246)Ttt>Ctt	p.F82L		NM_145304.2	NP_660347.1	Q8WU49	CG033_HUMAN	chromosome 7 open reading frame 33	82										central_nervous_system(1)|large_intestine(4)|lung(7)|prostate(2)	14	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			GGGGATGGAATTTATTGCTCC	0.478																																					p.F82L		Atlas-SNP	.											.	C7orf33	28	.	0			c.T244C						PASS	.						90	88	88					7																	148311173		2203	4300	6503	SO:0001583	missense	202865	exon2			ATGGAATTTATTG	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.244T>C	chr7.hg19:g.148311173T>C	ENSP00000304071:p.Phe82Leu	42.0	0.0	.		113.0	74.0	.	NM_145304		Missense_Mutation	SNP	ENST00000307003.2	hg19	CCDS5890.1	.	.	.	.	.	.	.	.	.	.	T	3.680	-0.065801	0.07273	.	.	ENSG00000170279	ENST00000307003	.	.	.	1.06	1.06	0.20224	.	.	.	.	.	T	0.20577	0.0495	N	0.19112	0.55	0.09310	N	1	B	0.23185	0.081	B	0.17433	0.018	T	0.21827	-1.0234	8	0.87932	D	0	.	4.3208	0.11016	0.0:0.0:0.0:1.0	.	82	Q8WU49	CG033_HUMAN	L	82	.	ENSP00000304071:F82L	F	+	1	0	C7orf33	147942106	0.002000	0.14202	0.002000	0.10522	0.003000	0.03518	0.586000	0.23894	0.718000	0.32166	0.368000	0.22195	TTT	.	.	.	none		0.478	C7orf33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327684.1	NM_145304		C	148311173	T	C	148311173	3	2	31	1	0	0	0	0	1	0	0	0	2390	1493	52	3	250	3	C7orf33	7	148311173	Missense_Mutation	SNP	T	TCGA-5P-A9JZ-01A-11D-A42J-10	4295431	148311173	10827490	20	2249											
DNAJB6	10049	hgsc.bcm.edu	37	chr7	157160104	157160104	+	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	agtccatttgaatttggcttCacattccgtaacccagatga	11	13	7	10	1	1	3	1	2	0	1	3	3	3	3	3	1	1	2	3	1	2	5			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr7:157160104C>A	ENST00000262177.4	+	5	478	c.273C>A	c.(271-273)ttC>ttA	p.F91L	DNAJB6_ENST00000429029.2_Missense_Mutation_p.F91L|DNAJB6_ENST00000452797.2_Missense_Mutation_p.F42L|DNAJB6_ENST00000443280.1_Missense_Mutation_p.F91L	NM_058246.3	NP_490647.1	O75190	DNJB6_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 6	91	Gly/Phe-rich.|Interaction with HSP70.				intermediate filament organization (GO:0045109)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of ATPase activity (GO:0032781)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	ATPase activator activity (GO:0001671)|chaperone binding (GO:0051087)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|lung(1)|ovary(2)|stomach(1)	5	all_neural(206;0.181)	all_epithelial(9;0.000606)|all_hematologic(28;0.00287)|Acute lymphoblastic leukemia(9;0.0647)|Ovarian(593;0.196)	OV - Ovarian serous cystadenocarcinoma(82;0.00399)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		AATTTGGCTTCACATTCCGTA	0.388																																					p.F91L	Esophageal Squamous(46;195 967 1350 20350 43814)	Atlas-SNP	.											.	DNAJB6	39	.	0			c.C273A						PASS	.						160	149	153					7																	157160104		2203	4299	6502	SO:0001583	missense	10049	exon5			TGGCTTCACATTC	AB014888	CCDS5946.1, CCDS47755.1	7q36.3	2014-02-03			ENSG00000105993	ENSG00000105993		"Heat shock proteins / DNAJ (HSP40)"	14888	protein-coding gene	gene with protein product		611332	"limb girdle muscular dystrophy 1D (autosomal dominant)"	LGMD1D		10319584, 9915854, 22366786	Standard	NM_005494		Approved	MRJ	uc003wnk.3	O75190	OTTHUMG00000157242	ENST00000262177.4:c.273C>A	chr7.hg19:g.157160104C>A	ENSP00000262177:p.Phe91Leu	91.0	0.0	.		101.0	6.0	.	NM_058246	A4D232|A8K7D8|A8KAG0|B4DN73|E9PCZ2|O95806|Q53EN8|Q59EF2|Q6FIC8|Q75MA2|Q9UIK6	Missense_Mutation	SNP	ENST00000262177.4	hg19	CCDS5946.1	.	.	.	.	.	.	.	.	.	.	C	16.17	3.046573	0.55110	.	.	ENSG00000105993	ENST00000441561;ENST00000429029;ENST00000262177;ENST00000417758;ENST00000452797;ENST00000443280;ENST00000421417;ENST00000412557;ENST00000453383	T;T;T;T;T;T;T;T	0.79454	-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27	4.58	0.533	0.17121	Heat shock protein DnaJ, N-terminal (1);	0.131004	0.32190	U	0.006450	D	0.83959	0.5367	M	0.71296	2.17	0.51767	D	0.999933	B;D;P;P;D	0.71674	0.427;0.998;0.589;0.942;0.996	B;D;B;P;D	0.80764	0.235;0.994;0.347;0.816;0.98	T	0.81400	-0.0950	10	0.66056	D	0.02	.	9.0446	0.36338	0.0:0.3955:0.0:0.6045	.	91;42;91;91;91	E9PH18;B4DN73;A8KAG0;O75190;O75190-2	.;.;.;DNJB6_HUMAN;.	L	91;91;91;91;42;91;91;91;91	ENSP00000410643:F91L;ENSP00000397556:F91L;ENSP00000262177:F91L;ENSP00000400665:F91L;ENSP00000402270:F42L;ENSP00000396267:F91L;ENSP00000403407:F91L;ENSP00000396240:F91L	ENSP00000262177:F91L	F	+	3	2	DNAJB6	156852865	1.000000	0.71417	0.997000	0.53966	0.963000	0.63663	1.038000	0.30254	-0.130000	0.11599	-0.137000	0.14449	TTC	.	.	.	none		0.388	DNAJB6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000348119.2			A	157160104	C	A	157160104	3	1	31	1	0	0	0	0	1	0	0	0	4626	825	29	4	287	4	DNAJB6	7	157160104	Missense_Mutation	SNP	C	TCGA-5P-A9JZ-01A-11D-A42J-10	8848931	157160104	1978559	21	2250											
MTSS1	9788	hgsc.bcm.edu	37	chr8	125580765	125580765	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgtccaactgaggctggAtatcacctctccctgcaaaa	11	9	7	14	0	2	1	1	1	1	0	4	2	3	2	3	2	2	2	3	2	4	1			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr8:125580765A>G	ENST00000518547.1	-	7	946	c.473T>C	c.(472-474)aTc>aCc	p.I158T	MTSS1_ENST00000378017.3_Missense_Mutation_p.I158T|MTSS1_ENST00000325064.5_Missense_Mutation_p.I162T|MTSS1_ENST00000395508.2_5'Flank|MTSS1_ENST00000431961.2_5'UTR|MTSS1_ENST00000354184.4_5'UTR|MTSS1_ENST00000524090.1_Missense_Mutation_p.I48T	NM_001282971.1|NM_014751.4	NP_001269900.1|NP_055566.3	O43312	MTSS1_HUMAN	metastasis suppressor 1	158	IMD. {ECO:0000255|PROSITE- ProRule:PRU00668}.				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)			CTGAGGCTGGATATCACCTCT	0.493																																					p.I158T	Esophageal Squamous(160;622 1893 3862 8546 12509)	Atlas-SNP	.											.	MTSS1	79	.	0			c.T473C						PASS	.						69	65	67					8																	125580765		2203	4300	6503	SO:0001583	missense	9788	exon7			GGCTGGATATCAC	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.473T>C	chr8.hg19:g.125580765A>G	ENSP00000429064:p.Ile158Thr	75.0	0.0	.		88.0	7.0	.	NM_014751	J3KNK6|Q8TCA2|Q96RX2	Missense_Mutation	SNP	ENST00000518547.1	hg19	CCDS6353.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.12|17.12	3.306988|3.306988	0.60305|0.60305	.|.	.|.	ENSG00000170873|ENSG00000170873	ENST00000378017;ENST00000518547;ENST00000325064;ENST00000524090|ENST00000522162	T;T;T;T|.	0.33216|.	1.51;1.5;1.51;1.42|.	5.45|5.45	5.45|5.45	0.79879|0.79879	IRSp53/MIM homology domain (IMD) (3);|.	0.055995|.	0.64402|.	D|.	0.000001|.	T|T	0.60130|0.60130	0.2245|0.2245	L|L	0.39898|0.39898	1.24|1.24	0.80722|0.80722	D|D	1|1	D;P;B;P|.	0.61697|.	0.99;0.523;0.021;0.731|.	P;B;B;P|.	0.60236|.	0.871;0.391;0.248;0.486|.	T|T	0.56691|0.56691	-0.7937|-0.7937	10|5	0.14252|.	T|.	0.57|.	-27.9499|-27.9499	15.806|15.806	0.78513|0.78513	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	48;158;158;158|.	E7EWW5;A5YM41;O43312;O43312-4|.	.;.;MTSS1_HUMAN;.|.	T|P	158;158;162;48|153	ENSP00000367256:I158T;ENSP00000429064:I158T;ENSP00000322804:I162T;ENSP00000428319:I48T|.	ENSP00000322804:I162T|.	I|S	-|-	2|1	0|0	MTSS1|MTSS1	125649946|125649946	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.934000|0.934000	0.57294|0.57294	9.181000|9.181000	0.94874|0.94874	2.196000|2.196000	0.70406|0.70406	0.533000|0.533000	0.62120|0.62120	ATC|TCC	.	.	.	none		0.493	MTSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109625.3	NM_014751		G	125580765	A	G	125580765	3	3	31	1	0	0	0	0	1	0	0	0	9969	333	12	3	1826	3	MTSS1	8	125580765	Missense_Mutation	SNP	A	TCGA-5P-A9JZ-01A-11D-A42J-10		125580765	20783257	22	2251											
MFSD3	113655	hgsc.bcm.edu	37	chr8	145736222	145736222	+	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	gcagcacttcttgggaggccTggtcaccacagtcaccttca	8	9	10	14	0	4	0	3	0	1	0	4	1	4	1	3	3	1	2	3	3	0	3			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr8:145736222T>A	ENST00000301327.4	+	4	1261	c.1001T>A	c.(1000-1002)cTg>cAg	p.L334Q	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	334	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)			TTGGGAGGCCTGGTCACCACA	0.627																																					p.L334Q		Atlas-SNP	.											.	MFSD3	17	.	0			c.T1001A						PASS	.						53	52	52					8																	145736222		2202	4297	6499	SO:0001583	missense	113655	exon4			GAGGCCTGGTCAC		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.1001T>A	chr8.hg19:g.145736222T>A	ENSP00000301327:p.Leu334Gln	35.0	0.0	.		22.0	9.0	.	NM_138431		Missense_Mutation	SNP	ENST00000301327.4	hg19	CCDS6431.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.987542	0.74589	.	.	ENSG00000167700	ENST00000301327	T	0.59083	0.29	5.25	3.88	0.44766	Major facilitator superfamily domain, general substrate transporter (1);	0.328159	0.28549	N	0.014948	T	0.69142	0.3078	M	0.72894	2.215	0.32062	N	0.595635	D	0.56746	0.977	D	0.64321	0.924	T	0.73742	-0.3887	10	0.48119	T	0.1	.	9.3368	0.38056	0.0:0.1009:0.0:0.8991	.	334	Q96ES6	MFSD3_HUMAN	Q	334	ENSP00000301327:L334Q	ENSP00000301327:L334Q	L	+	2	0	MFSD3	145707030	0.856000	0.29760	1.000000	0.80357	0.936000	0.57629	1.128000	0.31369	1.986000	0.57962	0.379000	0.24179	CTG	.	.	.	none		0.627	MFSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382478.2	NM_138431		A	145736222	T	A	145736222	3	1	31	1	0	0	0	0	1	0	0	0	9539	1580	55	5	1015	5	MFSD3	8	145736222	Missense_Mutation	SNP	T	TCGA-5P-A9JZ-01A-11D-A42J-10	20155457	145736222	627800	23	2252											
DPP7	29952	hgsc.bcm.edu	37	chr9	140006480	140006481	+	Splice_Site	DNP	GC	GC	TA																															tcaggttgatctcggtgcagGcctgcaggtgccccagcctg																										TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr9:140006480_140006481GC>TA	ENST00000371579.2	-	10	1055_1056	c.1051_1052GC>TA	c.(1051-1053)GCc>TAc	p.A351Y		NM_013379.2	NP_037511.2	Q9UHL4	DPP2_HUMAN	dipeptidyl-peptidase 7	351						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)		CTCGGTGCAGGCCTGCAGGTGC	0.658																																					p.A351D|p.A351S		Atlas-SNP	.											.	DPP7	22	.	0			c.C1052A|c.G1051T						PASS	.																																			SO:0001630	splice_region_variant	29952	exon10			GTGCAGGCCTGCA|TGCAGGCCTGCAG	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.1051_1052delinsTA	chr9.hg19:g.140006480_140006481delinsTA		118.0|119.0	0.0	.		96.0|97.0	38.0	.	NM_013379	A8K7U7|Q5VSF1|Q969X4	Missense_Mutation	SNP	ENST00000371579.2	hg19	CCDS7030.1																																																																																			.	.	.	none		0.658	DPP7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055279.1	NM_013379	Missense_Mutation	TA	140006481	GC	TA	140006480	5	4	31	1	0	0	0	0	0	0	1	0	4733	1217	42	4	442	4	DPP7	9	140006480	Splice_Site	DNP	GC	TCGA-5P-A9JZ-01A-11D-A42J-10		140006480	1206951	24	2253											
ITGB1	3688	hgsc.bcm.edu	37	chr10	33199326	33199326	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgttaaaataggaacattcCtgtgtgcatgtgtctttctt	10	17	8	6	0	2	0	0	0	2	0	3	1	3	1	1	1	2	2	1	1	4	5			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr10:33199326C>T	ENST00000396033.2	-	14	2124	c.1989G>A	c.(1987-1989)caG>caA	p.Q663Q	ITGB1_ENST00000374956.4_Silent_p.Q663Q|ITGB1_ENST00000423113.1_Silent_p.Q663Q|ITGB1_ENST00000302278.3_Silent_p.Q663Q	NM_133376.2	NP_596867.1	P05556	ITB1_HUMAN	integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)	663					axon extension (GO:0048675)|axon guidance (GO:0007411)|B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cardiac muscle cell differentiation (GO:0055007)|cell fate specification (GO:0001708)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular calcium ion homeostasis (GO:0006874)|cellular defense response (GO:0006968)|cellular response to ionizing radiation (GO:0071479)|cellular response to mechanical stimulus (GO:0071260)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|formation of radial glial scaffolds (GO:0021943)|G1/S transition of mitotic cell cycle (GO:0000082)|germ cell migration (GO:0008354)|heterotypic cell-cell adhesion (GO:0034113)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|maternal process involved in female pregnancy (GO:0060135)|mesodermal cell differentiation (GO:0048333)|negative regulation of anoikis (GO:2000811)|negative regulation of cell projection organization (GO:0031345)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of apoptotic process (GO:0043065)|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 endocytosis (GO:0045807)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein transport within lipid bilayer (GO:0032594)|regulation of cell cycle (GO:0051726)|regulation of collagen catabolic process (GO:0010710)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of immune response (GO:0050776)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|response to transforming growth factor beta (GO:0071559)|sarcomere organization (GO:0045214)|tight junction assembly (GO:0070830)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	acrosomal vesicle (GO:0001669)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha1-beta1 complex (GO:0034665)|integrin alpha10-beta1 complex (GO:0034680)|integrin alpha11-beta1 complex (GO:0034681)|integrin alpha2-beta1 complex (GO:0034666)|integrin alpha3-beta1 complex (GO:0034667)|integrin alpha7-beta1 complex (GO:0034677)|integrin alpha8-beta1 complex (GO:0034678)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|intercalated disc (GO:0014704)|invadopodium membrane (GO:0071438)|membrane (GO:0016020)|membrane raft (GO:0045121)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|cell adhesion molecule binding (GO:0050839)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|peptide binding (GO:0042277)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|virus receptor activity (GO:0001618)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Ovarian(717;1.34e-05)|Breast(68;0.0634)			Antithymocyte globulin(DB00098)	AGGAACATTCCTGTGTGCATG	0.378																																					p.Q663Q		Atlas-SNP	.											.	ITGB1	156	.	0			c.G1989A						PASS	.						49	50	49					10																	33199326		2203	4297	6500	SO:0001819	synonymous_variant	3688	exon14			ACATTCCTGTGTG	BC020057	CCDS7174.1	10p11.2	2010-10-13			ENSG00000150093	ENSG00000150093		"CD molecules", "Integrins"	6153	protein-coding gene	gene with protein product		135630		FNRB, MSK12, MDF2		2524991	Standard	NM_033668		Approved	CD29, GPIIA	uc001iwt.4	P05556	OTTHUMG00000017928	ENST00000396033.2:c.1989G>A	chr10.hg19:g.33199326C>T		497.0	0.0	.		549.0	211.0	.	NM_002211	A8K6N2|D3DRX9|D3DRY3|D3DRY4|D3DRY5|P78466|P78467|Q13089|Q13090|Q13091|Q13212|Q14622|Q14647|Q29RW2|Q7Z3V1|Q8WUM6	Silent	SNP	ENST00000396033.2	hg19	CCDS7174.1																																																																																			.	.	.	none		0.378	ITGB1-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047496.1	NM_002211		T	33199326	C	T	33199326	2	4	31	1	0	0	0	0	0	0	0	1	7897	680	24	2		2	ITGB1	10	33199326	Silent	SNP	C	TCGA-5P-A9JZ-01A-11D-A42J-10		33199326	102335421	25	2254											
FAM175B	23172	hgsc.bcm.edu	37	chr10	126515171	126515171	+	Missense_Mutation	SNP	T	T	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	acttttctttcagaaagtcaTtgggtggtacagattccggc	9	14	10	8	1	3	2	2	0	1	2	4	2	4	2	1	3	1	1	1	3	2	6			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr10:126515171T>G	ENST00000298492.5	+	5	320	c.275T>G	c.(274-276)aTt>aGt	p.I92S		NM_032182.3	NP_115558.3	Q15018	F175B_HUMAN	family with sequence similarity 175, member B	92	MPN-like.				cellular response to freezing (GO:0071497)	BRISC complex (GO:0070552)|cytoplasm (GO:0005737)	polyubiquitin binding (GO:0031593)			NS(1)	1						CAGAAAGTCATTGGGTGGTAC	0.453																																					p.I92S		Atlas-SNP	.											.	FAM175B	39	.	0			c.T275G						PASS	.						108	103	105					10																	126515171		2203	4300	6503	SO:0001583	missense	23172	exon5			AAGTCATTGGGTG	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.275T>G	chr10.hg19:g.126515171T>G	ENSP00000298492:p.Ile92Ser	98.0	0.0	.		80.0	20.0	.	NM_032182	B4DKR2|Q96H11	Missense_Mutation	SNP	ENST00000298492.5	hg19	CCDS31308.2	.	.	.	.	.	.	.	.	.	.	T	25.4	4.630040	0.87660	.	.	ENSG00000165660	ENST00000298492	T	0.44881	0.91	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.65903	0.2736	M	0.74647	2.275	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.69731	-0.5066	10	0.87932	D	0	-36.1308	16.1986	0.82053	0.0:0.0:0.0:1.0	.	92	Q15018	F175B_HUMAN	S	92	ENSP00000298492:I92S	ENSP00000298492:I92S	I	+	2	0	FAM175B	126505161	1.000000	0.71417	0.373000	0.26003	0.829000	0.46940	8.027000	0.88791	2.227000	0.72691	0.455000	0.32223	ATT	.	.	.	none		0.453	FAM175B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050891.2	NM_032182		G	126515171	T	G	126515171	3	3	31	1	0	0	0	0	1	0	0	0	5502	1493	52	5	293	5	FAM175B	10	126515171	Missense_Mutation	SNP	T	TCGA-5P-A9JZ-01A-11D-A42J-10	93315845	126515171	9019576	26	2255											
ATG2A	23130	hgsc.bcm.edu	37	chr11	64677319	64677320	+	Frame_Shift_Ins	INS	-	-	AA																															gccgcaggtcggcaatggggINSaagcgcagccgcagcgtggc																										TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr11:64677319_64677320insAA	ENST00000377264.3	-	14	2052_2053	c.1940_1941insTT	c.(1939-1941)ttcfs	p.F647fs	ATG2A_ENST00000421419.2_Frame_Shift_Ins_p.F647fs	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	647					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						CGGCAATGGGGAAGCGCAGCCG	0.703																																					p.F647fs		Atlas-Indel,Pindel	.											.	ATG2A	133	.	0			c.1941_1942insTT						PASS	.																																			SO:0001589	frameshift_variant	23130	exon14			.		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.1939_1940dupTT	chr11.hg19:g.64677320_64677321dupAA	ENSP00000366475:p.Phe647fs	74.0	0.0	0		96.0	37.0	0.385417	NM_015104	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Frame_Shift_Ins	INS	ENST00000377264.3	hg19	CCDS31602.1																																																																																			.	.	.	none		0.703	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104		AA	64677320	-	AA	64677319	7	5	31	1	0	1	1	0	0	0	0	0	1093	1165	41	0	3987	0	ATG2A	11	64677319	Frame_Shift_Ins	INS	-	TCGA-5P-A9JZ-01A-11D-A42J-10		64677319	70329197	27	2256											
PCF11	51585	hgsc.bcm.edu	37	chr11	82877690	82877690	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggcactgaaccaaaggagaAtgtagaaaactggcaaagtt	18	6	11	6	0	0	3	0	1	0	2	0	4	0	3	1	3	2	4	1	3	7	2			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr11:82877690A>G	ENST00000298281.4	+	5	2203	c.1751A>G	c.(1750-1752)aAt>aGt	p.N584S		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	584					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						CCAAAGGAGAATGTAGAAAAC	0.393																																					p.N584S		Atlas-SNP	.											PCF11_ENST00000298281,NS,carcinoma,0,4	PCF11	220	.	0			c.A1751G						PASS	.						66	66	66					11																	82877690		1824	4044	5868	SO:0001583	missense	51585	exon5			AGGAGAATGTAGA	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.1751A>G	chr11.hg19:g.82877690A>G	ENSP00000298281:p.Asn584Ser	339.0	1.0	.		312.0	126.0	.	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	hg19	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	A	13.22	2.172383	0.38315	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.50813	1.68;0.74;0.73	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000005	T	0.34483	0.0899	N	0.19112	0.55	0.29519	N	0.853609	P;P	0.43788	0.473;0.817	B;B	0.38500	0.091;0.275	T	0.25433	-1.0132	9	.	.	.	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	584;584	E9PQ01;O94913	.;PCF11_HUMAN	S	584	ENSP00000298281:N584S;ENSP00000434540:N584S;ENSP00000431567:N584S	.	N	+	2	0	PCF11	82555338	1.000000	0.71417	0.991000	0.47740	0.967000	0.64934	3.827000	0.55745	2.326000	0.78906	0.533000	0.62120	AAT	.	.	.	none		0.393	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		G	82877690	A	G	82877690	3	3	31	1	0	0	0	0	1	0	0	0	11580	101	4	3	1769	3	PCF11	11	82877690	Missense_Mutation	SNP	A	TCGA-5P-A9JZ-01A-11D-A42J-10	18200371	82877690	52128826	28	2257											
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-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	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_ENST00000525532.1_Missense_Mutation_p.A1115T|SORL1_ENST00000532694.1_Missense_Mutation_p.A1017T|SORL1_ENST00000527934.1_Missense_Mutation_p.A786T	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	chr11.hg19:g.121498410G>A	ENSP00000260197:p.Ala2171Thr	63.0	0.0	.		80.0	34.0	.	NM_003105	B2RNX7|Q92856	Missense_Mutation	SNP	ENST00000260197.7	hg19	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	31	1	0	0	0	0	1	0	0	0	14947	1087	38	1	6697	1	SORL1	11	121498410	Missense_Mutation	SNP	G	TCGA-5P-A9JZ-01A-11D-A42J-10	38620720	121498410	13508106	29	2258											
OR10G7	390265	hgsc.bcm.edu	37	chr11	123909026	123909026	+	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	tgtgcctcccctctgaggtgCggatccgcaggatggaacag	7	8	14	12	2	1	1	0	1	1	0	3	4	3	4	4	4	3	1	4	4	1	0			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr11:123909026C>T	ENST00000330487.5	-	1	691	c.683G>A	c.(682-684)cGc>cAc	p.R228H		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	228						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)		CTCTGAGGTGCGGATCCGCAG	0.537																																					p.R228H		Atlas-SNP	.											.	OR10G7	103	.	0			c.G683A						PASS	.						138	119	126					11																	123909026		2201	4299	6500	SO:0001583	missense	390265	exon1			GAGGTGCGGATCC	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.683G>A	chr11.hg19:g.123909026C>T	ENSP00000329689:p.Arg228His	173.0	0.0	.		192.0	15.0	.	NM_001004463	Q6IFE8	Missense_Mutation	SNP	ENST00000330487.5	hg19	CCDS31705.1	.	.	.	.	.	.	.	.	.	.	C	3.124	-0.179813	0.06380	.	.	ENSG00000182634	ENST00000330487	T	0.39229	1.09	3.38	1.49	0.22878	GPCR, rhodopsin-like superfamily (1);	0.566427	0.16064	N	0.231343	T	0.25568	0.0622	L	0.28556	0.865	0.20074	N	0.999935	B	0.09022	0.002	B	0.17979	0.02	T	0.20042	-1.0287	10	0.20046	T	0.44	.	5.6004	0.17351	0.0:0.5333:0.2729:0.1938	.	228	Q8NGN6	O10G7_HUMAN	H	228	ENSP00000329689:R228H	ENSP00000329689:R228H	R	-	2	0	OR10G7	123414236	0.000000	0.05858	0.974000	0.42286	0.400000	0.30750	-1.370000	0.02575	0.271000	0.22005	-0.232000	0.12228	CGC	.	.	.	weak		0.537	OR10G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387271.1	NM_001004463		T	123909026	C	T	123909026	3	4	31	1	0	0	0	0	1	0	0	0	10909	768	27	1	256	1	OR10G7	11	123909026	Missense_Mutation	SNP	C	TCGA-5P-A9JZ-01A-11D-A42J-10	2410616	123909026	11097490	30	2259											
KRT1	3848	hgsc.bcm.edu	37	chr12	53069229	53069229	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagccatagctgccacctccGgagccgtagctgctacctcc	7	7	10	17	2	0	0	0	0	0	0	2	2	2	1	7	1	7	4	7	1	3	3	rs540699806|rs267607656	byFrequency	TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr12:53069229G>A	ENST00000252244.3	-	9	1741	c.1683C>T	c.(1681-1683)tcC>tcT	p.S561S		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	561	Gly/Ser-rich.|Tail.		Missing (in allele 1B). {ECO:0000269|PubMed:1281859}.		complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						tgccacctccggagccgtagc	0.692																																					p.S561S		Atlas-SNP	.											.	KRT1	110	.	0			c.C1683T						PASS	.						4	4	4					12																	53069229		1797	3656	5453	SO:0001819	synonymous_variant	3848	exon9			ACCTCCGGAGCCG	X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"-", "Intermediate filaments type II, keratins (basic)"	6412	protein-coding gene	gene with protein product		139350	"epidermolytic hyperkeratosis 1"	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.1683C>T	chr12.hg19:g.53069229G>A		21.0	0.0	.		41.0	6.0	.	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Silent	SNP	ENST00000252244.3	hg19	CCDS8836.1																																																																																			.	.	.	none		0.692	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121		A	53069229	G	A	53069229	2	1	31	1	0	0	0	0	0	0	0	1	8454	1103	39	1		1	KRT1	12	53069229	Silent	SNP	G	TCGA-5P-A9JZ-01A-11D-A42J-10		53069229	80782666	31	2260											
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-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	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,0,2	KRT3	65	.	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	chr12.hg19:g.53183951C>T	ENSP00000413479:p.Gly588Ser	86.0	1.0	.		105.0	19.0	.	NM_057088	A6NIS2|Q701L8	Missense_Mutation	SNP	ENST00000417996.2	hg19	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	31	1	0	0	0	0	1	0	0	0	8473	652	23	1	128	1	KRT3	12	53183951	Missense_Mutation	SNP	C	TCGA-5P-A9JZ-01A-11D-A42J-10	114722	53183951	80667944	32	2261			2	4		2	2	29	N	G_C	4.431892e-05
KRT3	3850	hgsc.bcm.edu	37	chr12	53183979	53183979	+	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	ccgctgaaaccgctgctgccGccgccaaatccaccgccgat	8	5	9	19	6	0	1	0	1	0	0	1	2	1	1	8	0	3	3	8	0	2	0			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr12:53183979G>A	ENST00000417996.2	-	9	1808	c.1734C>T	c.(1732-1734)ggC>ggT	p.G578G	KRT3_ENST00000309505.3_Silent_p.G579G	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	578	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						cgctgctgccgccgccaaatc	0.701																																					p.G578G		Atlas-SNP	.											.	KRT3	65	.	0			c.C1734T						PASS	.						12	28	22					12																	53183979		1691	3337	5028	SO:0001819	synonymous_variant	3850	exon9			GCTGCCGCCGCCA		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.1734C>T	chr12.hg19:g.53183979G>A		98.0	0.0	.		124.0	9.0	.	NM_057088	A6NIS2|Q701L8	Silent	SNP	ENST00000417996.2	hg19	CCDS44895.1																																																																																			.	.	.	none		0.701	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1	NM_057088		A	53183979	G	A	53183979	2	1	31	1	0	0	0	0	0	0	0	1	8473	1074	38	1		1	KRT3	12	53183979	Silent	SNP	G	TCGA-5P-A9JZ-01A-11D-A42J-10	28	53183979	80667916	33	2262			2	4		2	2	29	N	G_C	4.431892e-05
UHRF1BP1L	23074	hgsc.bcm.edu	37	chr12	100453755	100453755	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acagaaattgatttaaccatAgaatgcttctttcatccaca	15	13	4	9	0	2	3	1	1	1	2	3	3	3	3	2	0	2	1	2	0	4	6			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr12:100453755A>G	ENST00000279907.7	-	13	1828	c.1616T>C	c.(1615-1617)cTa>cCa	p.L539P	UHRF1BP1L_ENST00000545232.2_Missense_Mutation_p.L189P	NM_015054.1	NP_055869.1	A0JNW5	UH1BL_HUMAN	UHRF1 binding protein 1-like	539										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(21)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	50						ATTTAACCATAGAATGCTTCT	0.348																																					p.L539P		Atlas-SNP	.											.	UHRF1BP1L	144	.	0			c.T1616C						PASS	.						89	85	87					12																	100453755		2203	4300	6503	SO:0001583	missense	23074	exon13			AACCATAGAATGC		CCDS31882.1, CCDS31883.1	12q23.1	2011-04-15	2008-08-15		ENSG00000111647	ENSG00000111647			29102	protein-coding gene	gene with protein product							Standard	XM_005268737		Approved	KIAA0701	uc001tgq.3	A0JNW5	OTTHUMG00000170195	ENST00000279907.7:c.1616T>C	chr12.hg19:g.100453755A>G	ENSP00000279907:p.Leu539Pro	146.0	0.0	.		150.0	53.0	.	NM_015054	A0PJE5|O75183|Q8NDL1|Q96C30|Q9BTS5|Q9H0F1	Missense_Mutation	SNP	ENST00000279907.7	hg19	CCDS31882.1	.	.	.	.	.	.	.	.	.	.	A	17.24	3.339180	0.60963	.	.	ENSG00000111647	ENST00000279907;ENST00000545232	T;T	0.22743	2.13;1.94	5.49	5.49	0.81192	.	0.071978	0.56097	D	0.000025	T	0.47021	0.1423	M	0.73217	2.22	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.48937	-0.8990	10	0.87932	D	0	-5.8001	15.5763	0.76392	1.0:0.0:0.0:0.0	.	539	A0JNW5	UH1BL_HUMAN	P	539;189	ENSP00000279907:L539P;ENSP00000444824:L189P	ENSP00000279907:L539P	L	-	2	0	UHRF1BP1L	98977886	1.000000	0.71417	0.988000	0.46212	0.913000	0.54294	9.339000	0.96797	2.091000	0.63221	0.477000	0.44152	CTA	.	.	.	none		0.348	UHRF1BP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407875.1	NM_001006947		G	100453755	A	G	100453755	3	3	31	1	0	0	0	0	1	0	0	0	16981	420	15	3	2814	3	UHRF1BP1L	12	100453755	Missense_Mutation	SNP	A	TCGA-5P-A9JZ-01A-11D-A42J-10	47269776	100453755	33398140	34	2263											
MTUS2	23281	hgsc.bcm.edu	37	chr13	29674966	29674967	+	Missense_Mutation	DNP	GG	GG	TT																															aatccaatctcccgaaatctGgtctccgtcctcccggatac																										TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr13:29674966_29674967GG>TT	ENST00000431530.3	+	3	2591_2592	c.2533_2534GG>TT	c.(2533-2535)GGt>TTt	p.G845F		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	835	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						CCCGAAATCTGGTCTCCGTCCT	0.475																																					p.G845C|p.G845V		Atlas-SNP	.											.	MTUS2	279	.	0			c.G2533T|c.G2534T						PASS	.																																			SO:0001583	missense	23281	exon3			AAATCTGGTCTCC|AATCTGGTCTCCG	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	Exception_encountered	chr13.hg19:g.29674966_29674967delinsTT	ENSP00000392057:p.Gly845Phe	219.0|221.0	0.0	.		232.0|233.0	71.0|72.0	.	NM_001033602	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Missense_Mutation	SNP	ENST00000431530.3	hg19	CCDS45022.1																																																																																			.	.	.	none		0.475	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270		TT	29674967	GG	TT	29674966	3	4	31	1	0	0	0	0	1	0	0	0	9973	1348	47	4	2543	4	MTUS2	13	29674966	Missense_Mutation	DNP	GG	TCGA-5P-A9JZ-01A-11D-A42J-10		29674966	85494912	35	2264											
MYH7	4625	hgsc.bcm.edu	37	chr14	23886164	23886164	+	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	agctcatggatagtctttccGctggaacccaactgctcagt	9	11	9	12	1	3	0	2	0	1	0	4	2	4	2	2	2	4	3	2	2	3	2	rs150552664		TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr14:23886164G>T	ENST00000355349.3	-	33	4719	c.4557C>A	c.(4555-4557)agC>agA	p.S1519R	MIR208B_ENST00000401172.1_RNA|CTD-2201G16.1_ENST00000557368.1_RNA	NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1519			S -> C. {ECO:0000269|PubMed:15858117}.		adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)	p.S1519S(1)		NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		TAGTCTTTCCGCTGGAACCCA	0.587																																					p.S1519R		Atlas-SNP	.											MYH7,NS,carcinoma,0,1	MYH7	349	.	1	Substitution - coding silent(1)	endometrium(1)	c.C4557A						PASS	.						118	106	110					14																	23886164		2203	4300	6503	SO:0001583	missense	4625	exon33			CTTTCCGCTGGAA	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.4557C>A	chr14.hg19:g.23886164G>T	ENSP00000347507:p.Ser1519Arg	63.0	0.0	.		60.0	3.0	.	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	hg19	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	G	10.59	1.391880	0.25118	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	D	0.82619	-1.63	5.01	-6.56	0.01848	Myosin tail (1);	.	.	.	.	D	0.87083	0.6089	M	0.86573	2.825	0.23893	N	0.996541	B	0.24882	0.113	P	0.47864	0.559	D	0.84711	0.0734	9	0.72032	D	0.01	.	3.7721	0.08646	0.3606:0.1824:0.3674:0.0896	.	1519	P12883	MYH7_HUMAN	R	1519;1524	ENSP00000347507:S1519R	ENSP00000347507:S1519R	S	-	3	2	MYH7	22956004	0.000000	0.05858	0.023000	0.16930	0.057000	0.15508	-4.112000	0.00292	-0.848000	0.04163	-1.405000	0.01134	AGC	.	G|1.000;A|0.000	.	alt		0.587	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		T	23886164	G	T	23886164	3	4	31	1	0	0	0	0	1	0	0	0	10046	1078	38	4	1282	4	MYH7	14	23886164	Missense_Mutation	SNP	G	TCGA-5P-A9JZ-01A-11D-A42J-10		23886164	83463376	36	2265											
PPP1R13B	23368	hgsc.bcm.edu	37	chr14	104219447	104219447	+	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	ctttaaatcttccaattgctGactaagctgatcaaccctta	12	14	4	11	0	2	2	1	2	1	0	3	2	3	2	2	0	3	2	2	0	6	6			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr14:104219447G>T	ENST00000202556.9	-	7	1000	c.718C>A	c.(718-720)Cag>Aag	p.Q240K		NM_015316.2	NP_056131.2	Q96KQ4	ASPP1_HUMAN	protein phosphatase 1, regulatory subunit 13B	240	Gln-rich.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(6)|kidney(2)|large_intestine(7)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.173)|all_epithelial(191;0.131)|Melanoma(154;0.155)				TCCAATTGCTGACTAAGCTGA	0.423																																					p.Q240K		Atlas-SNP	.											.	PPP1R13B	72	.	0			c.C718A						PASS	.						156	141	145					14																	104219447		1859	4097	5956	SO:0001583	missense	23368	exon7			ATTGCTGACTAAG	AB018314	CCDS41997.1	14q32.33	2013-01-10	2011-10-04		ENSG00000088808	ENSG00000088808		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	14950	protein-coding gene	gene with protein product		606455	"protein phosphatase 1, regulatory (inhibitor) subunit 13B"			9872452	Standard	NM_015316		Approved	p53BP2-like, KIAA0771, p85, ASPP1	uc001yof.1	Q96KQ4	OTTHUMG00000171647	ENST00000202556.9:c.718C>A	chr14.hg19:g.104219447G>T	ENSP00000202556:p.Gln240Lys	119.0	0.0	.		93.0	30.0	.	NM_015316	B2RMX5|O94870	Missense_Mutation	SNP	ENST00000202556.9	hg19	CCDS41997.1	.	.	.	.	.	.	.	.	.	.	G	16.90	3.250172	0.59212	.	.	ENSG00000088808	ENST00000202556;ENST00000380023	T	0.28454	1.61	5.74	5.74	0.90152	.	0.168163	0.52532	D	0.000063	T	0.29817	0.0745	L	0.32530	0.975	0.80722	D	1	B	0.24618	0.107	B	0.27076	0.076	T	0.02975	-1.1087	10	0.38643	T	0.18	.	19.9238	0.97097	0.0:0.0:1.0:0.0	.	240	Q96KQ4	ASPP1_HUMAN	K	240;107	ENSP00000202556:Q240K	ENSP00000202556:Q240K	Q	-	1	0	PPP1R13B	103289200	1.000000	0.71417	0.997000	0.53966	0.981000	0.71138	5.915000	0.69973	2.712000	0.92718	0.650000	0.86243	CAG	.	.	.	none		0.423	PPP1R13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414591.1	NM_015316		T	104219447	G	T	104219447	3	4	31	1	0	0	0	0	1	0	0	0	12367	1299	45	4	2598	4	PPP1R13B	14	104219447	Missense_Mutation	SNP	G	TCGA-5P-A9JZ-01A-11D-A42J-10	80333283	104219447	3130093	37	2266											
HERC2	8924	hgsc.bcm.edu	37	chr15	28377879	28377879	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccccatgtgtagaggtcccCggctgctgtgacacaggcgc	6	7	14	14	2	0	2	0	1	0	1	1	2	1	2	4	3	1	3	4	3	1	1			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr15:28377879C>T	ENST00000261609.7	-	80	12436	c.12328G>A	c.(12328-12330)Ggg>Agg	p.G4110R		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)		TAGAGGTCCCCGGCTGCTGTG	0.642																																					p.G4110R		Atlas-SNP	.											.	HERC2	501	.	0			c.G12328A						PASS	.						66	72	70					15																	28377879		2203	4300	6503	SO:0001583	missense	8924	exon80			GGTCCCCGGCTGC	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.12328G>A	chr15.hg19:g.28377879C>T	ENSP00000261609:p.Gly4110Arg	181.0	0.0	.		215.0	77.0	.	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	C	34	5.370568	0.95900	.	.	ENSG00000128731	ENST00000261609	D	0.98060	-4.69	4.86	4.86	0.63082	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	D	0.000000	D	0.99281	0.9749	H	0.98048	4.135	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.98643	1.0676	10	0.87932	D	0	.	18.3848	0.90463	0.0:1.0:0.0:0.0	.	4110	O95714	HERC2_HUMAN	R	4110	ENSP00000261609:G4110R	ENSP00000261609:G4110R	G	-	1	0	HERC2	26051474	1.000000	0.71417	0.978000	0.43139	0.966000	0.64601	7.765000	0.85310	2.418000	0.82041	0.555000	0.69702	GGG	.	.	.	none		0.642	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		T	28377879	C	T	28377879	3	4	31	1	0	0	0	0	1	0	0	0	7065	652	23	1	2232	1	HERC2	15	28377879	Missense_Mutation	SNP	C	TCGA-5P-A9JZ-01A-11D-A42J-10		28377879	74153513	38	2267											
CAPN3	825	hgsc.bcm.edu	37	chr15	42678446	42678446	+	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	agtcataccccatgatcaaaGtttcatcgaaaactacgcag	15	9	6	11	2	3	1	3	1	0	0	4	2	3	1	2	0	3	2	2	0	5	3			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr15:42678446G>C	ENST00000397163.3	+	3	680	c.461G>C	c.(460-462)aGt>aCt	p.S154T	CAPN3_ENST00000357568.3_Missense_Mutation_p.S154T|RP11-164J13.1_ENST00000495723.1_RNA|CAPN3_ENST00000349748.3_Missense_Mutation_p.S154T|CAPN3_ENST00000356316.3_Missense_Mutation_p.S67T|CAPN3_ENST00000318023.7_Missense_Mutation_p.S154T	NM_000070.2	NP_000061.1	P20807	CAN3_HUMAN	calpain 3, (p94)	154	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)		CATGATCAAAGTTTCATCGAA	0.567											OREG0023085	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S154T		Atlas-SNP	.											.	CAPN3	172	.	0			c.G461C						PASS	.						127	106	113					15																	42678446		2203	4299	6502	SO:0001583	missense	825	exon3			ATCAAAGTTTCAT	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.461G>C	chr15.hg19:g.42678446G>C	ENSP00000380349:p.Ser154Thr	110.0	0.0	.	910	95.0	43.0	.	NM_000070	A6H8K6|Q7L4R0|Q9BQC8|Q9BTU4|Q9Y5S6|Q9Y5S7	Missense_Mutation	SNP	ENST00000397163.3	hg19	CCDS45245.1	.	.	.	.	.	.	.	.	.	.	G	15.93	2.976764	0.53720	.	.	ENSG00000092529	ENST00000356316;ENST00000397163;ENST00000357568;ENST00000349748;ENST00000318023	D;D;D;D;D	0.89123	-2.47;-2.47;-2.47;-2.47;-2.47	6.07	5.14	0.70334	Peptidase C2, calpain, catalytic domain (3);	0.233701	0.41396	U	0.000881	D	0.87962	0.6310	M	0.81112	2.525	0.53005	D	0.999969	B;B;B;B;B;B	0.12013	0.001;0.005;0.001;0.003;0.004;0.001	B;B;B;B;B;B	0.17722	0.01;0.01;0.006;0.011;0.019;0.005	D	0.84491	0.0611	10	0.59425	D	0.04	.	8.4683	0.32969	0.0892:0.2647:0.6461:0.0	.	67;67;154;154;154;67	C6EVS4;C6EVS3;P20807-2;P20807-3;P20807;Q762C8	.;.;.;.;CAN3_HUMAN;.	T	67;154;154;154;154	ENSP00000348667:S67T;ENSP00000380349:S154T;ENSP00000350181:S154T;ENSP00000183936:S154T;ENSP00000326281:S154T	ENSP00000326281:S154T	S	+	2	0	CAPN3	40465738	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.094000	0.64523	2.890000	0.99128	0.650000	0.86243	AGT	.	.	.	none		0.567	CAPN3-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421075.1			C	42678446	G	C	42678446	3	2	31	1	0	0	0	0	1	0	0	0	2630	1029	36	4	523	4	CAPN3	15	42678446	Missense_Mutation	SNP	G	TCGA-5P-A9JZ-01A-11D-A42J-10	14300567	42678446	59852946	39	2268											
MAP1A	4130	hgsc.bcm.edu	37	chr15	43816966	43816966	+	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	cagcacaggataaagcaataGtctttgagattatggaggca	15	9	11	6	0	1	1	0	1	1	1	1	4	1	3	0	3	2	3	0	3	5	4			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr15:43816966G>C	ENST00000300231.5	+	4	3745	c.3295G>C	c.(3295-3297)Gtc>Ctc	p.V1099L	MAP1A_ENST00000399453.1_Missense_Mutation_p.V1099L|MAP1A_ENST00000382031.1_Missense_Mutation_p.V1337L			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1099					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)	TAAAGCAATAGTCTTTGAGAT	0.547																																					p.V1099L		Atlas-SNP	.											MAP1A,caecum,carcinoma,0,1	MAP1A	189	.	0			c.G3295C						PASS	.						84	87	86					15																	43816966		1940	4122	6062	SO:0001583	missense	4130	exon4			GCAATAGTCTTTG	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.3295G>C	chr15.hg19:g.43816966G>C	ENSP00000300231:p.Val1099Leu	99.0	0.0	.		113.0	38.0	.	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	hg19	CCDS42031.1	.	.	.	.	.	.	.	.	.	.	G	11.14	1.551496	0.27739	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.01685	4.69;4.7;4.7	5.22	4.31	0.51392	.	0.000000	0.31145	N	0.008170	T	0.02767	0.0083	M	0.75447	2.3	0.28523	N	0.912969	B	0.32101	0.356	B	0.31290	0.127	T	0.16958	-1.0385	10	0.32370	T	0.25	-17.6786	6.9319	0.24445	0.1487:0.0:0.8513:0.0	.	1099	P78559	MAP1A_HUMAN	L	1337;1099;1099	ENSP00000371462:V1337L;ENSP00000382380:V1099L;ENSP00000300231:V1099L	ENSP00000300231:V1099L	V	+	1	0	MAP1A	41604258	0.744000	0.28250	0.999000	0.59377	0.576000	0.36127	1.627000	0.37050	2.894000	0.99253	0.655000	0.94253	GTC	.	.	.	none		0.547	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373		C	43816966	G	C	43816966	3	2	31	1	0	0	0	0	1	0	0	0	9234	1029	36	4	3297	4	MAP1A	15	43816966	Missense_Mutation	SNP	G	TCGA-5P-A9JZ-01A-11D-A42J-10	1138520	43816966	58714426	40	2269											
TM4SF5	9032	hgsc.bcm.edu	37	chr17	4686223	4686223	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtggtcccctggaatgtgaCgctcttctcgctgctggtgg	3	12	14	12	3	2	1	0	1	2	0	4	2	3	2	2	4	1	3	2	4	1	1			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr17:4686223C>T	ENST00000270560.3	+	4	501	c.470C>T	c.(469-471)aCg>aTg	p.T157M		NM_003963.2	NP_003954.2	O14894	T4S5_HUMAN	transmembrane 4 L six family member 5	157						integral component of plasma membrane (GO:0005887)				large_intestine(2)|lung(3)|ovary(1)	6						TGGAATGTGACGCTCTTCTCG	0.637																																					p.T157M		Atlas-SNP	.											.	TM4SF5	26	.	0			c.C470T						PASS	.						76	72	73					17																	4686223		2203	4300	6503	SO:0001583	missense	9032	exon4			ATGTGACGCTCTT	AF027204	CCDS11054.1	17p13.3	2007-01-06	2005-03-21		ENSG00000142484	ENSG00000142484			11857	protein-coding gene	gene with protein product		604657	"transmembrane 4 superfamily member 5"			9479038	Standard	NM_003963		Approved		uc002fyw.1	O14894	OTTHUMG00000090776	ENST00000270560.3:c.470C>T	chr17.hg19:g.4686223C>T	ENSP00000270560:p.Thr157Met	97.0	0.0	.		148.0	83.0	.	NM_003963	Q17RW9|Q6IB79	Missense_Mutation	SNP	ENST00000270560.3	hg19	CCDS11054.1	.	.	.	.	.	.	.	.	.	.	C	14.98	2.698656	0.48307	.	.	ENSG00000142484	ENST00000270560	T	0.33865	1.39	5.71	2.51	0.30379	.	0.225720	0.44902	D	0.000418	T	0.51618	0.1685	M	0.82823	2.61	0.29698	N	0.840385	D	0.64830	0.994	P	0.60886	0.88	T	0.51888	-0.8648	10	0.72032	D	0.01	-3.5111	4.4304	0.11524	0.0:0.5775:0.1699:0.2526	.	157	O14894	T4S5_HUMAN	M	157	ENSP00000270560:T157M	ENSP00000270560:T157M	T	+	2	0	TM4SF5	4632970	0.833000	0.29383	0.764000	0.31436	0.125000	0.20455	1.159000	0.31749	1.413000	0.46997	0.655000	0.94253	ACG	.	.	.	none		0.637	TM4SF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207558.2			T	4686223	C	T	4686223	3	4	31	1	0	0	0	0	1	0	0	0	15983	536	19	1	484	1	TM4SF5	17	4686223	Missense_Mutation	SNP	C	TCGA-5P-A9JZ-01A-11D-A42J-10		4686223	76508987	41	2270											
PFAS	5198	hgsc.bcm.edu	37	chr17	8170960	8170960	+	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	cgtgggcggcttcagctatgCagatgtcctgggctctgcca	5	10	14	12	2	2	1	1	0	1	1	3	1	3	1	2	3	3	4	2	3	1	2			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr17:8170960C>A	ENST00000314666.6	+	26	3492	c.3359C>A	c.(3358-3360)gCa>gAa	p.A1120E	PFAS_ENST00000545834.1_Missense_Mutation_p.A696E	NM_012393.2	NP_036525.1	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	1120	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)	TTCAGCTATGCAGATGTCCTG	0.607																																					p.A1120E		Atlas-SNP	.											.	PFAS	91	.	0			c.C3359A						PASS	.						121	108	112					17																	8170960		2203	4300	6503	SO:0001583	missense	5198	exon26			GCTATGCAGATGT	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.3359C>A	chr17.hg19:g.8170960C>A	ENSP00000313490:p.Ala1120Glu	94.0	0.0	.		114.0	33.0	.	NM_012393	A6H8V8	Missense_Mutation	SNP	ENST00000314666.6	hg19	CCDS11136.1	.	.	.	.	.	.	.	.	.	.	C	18.89	3.719074	0.68844	.	.	ENSG00000178921	ENST00000545834;ENST00000314666;ENST00000546020	T;T	0.30448	1.53;2.26	5.68	5.68	0.88126	Glutamine amidotransferase type 1 (1);	0.000000	0.85682	D	0.000000	T	0.60805	0.2297	M	0.82923	2.615	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.65134	-0.6242	10	0.87932	D	0	-12.8738	17.2855	0.87140	0.0:1.0:0.0:0.0	.	1120;1120	A8K8N7;O15067	.;PUR4_HUMAN	E	696;1120;529	ENSP00000441706:A696E;ENSP00000313490:A1120E	ENSP00000313490:A1120E	A	+	2	0	PFAS	8111685	1.000000	0.71417	0.784000	0.31847	0.066000	0.16364	5.285000	0.65633	2.688000	0.91661	0.563000	0.77884	GCA	.	.	.	none		0.607	PFAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226994.2			A	8170960	C	A	8170960	3	1	31	1	0	0	0	0	1	0	0	0	11761	710	25	4	3457	4	PFAS	17	8170960	Missense_Mutation	SNP	C	TCGA-5P-A9JZ-01A-11D-A42J-10	3484737	8170960	73024250	42	2271											
PGS1	9489	hgsc.bcm.edu	37	chr17	76411070	76411070	+	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	tggaggcccagattgcgatcGtgacggagaaccaggccctg	9	6	15	11	3	0	3	0	1	0	2	1	6	0	4	3	4	2	0	3	4	1	1	rs372229822		TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr17:76411070G>T	ENST00000262764.6	+	8	1539	c.1513G>T	c.(1513-1515)Gtg>Ttg	p.V505L	PGS1_ENST00000588281.1_3'UTR|PGS1_ENST00000329897.7_Missense_Mutation_p.V370L	NM_024419.3	NP_077733.3	Q32NB8	PGPS1_HUMAN	phosphatidylglycerophosphate synthase 1	505					cardiolipin biosynthetic process (GO:0032049)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity (GO:0008444)			cervix(2)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	10			BRCA - Breast invasive adenocarcinoma(99;0.00144)|OV - Ovarian serous cystadenocarcinoma(97;0.031)			GATTGCGATCGTGACGGAGAA	0.627																																					p.V505L	Esophageal Squamous(45;182 1126 10685 43198)	Atlas-SNP	.											.	PGS1	30	.	0			c.G1513T						PASS	.						53	56	55					17																	76411070		2050	4218	6268	SO:0001583	missense	9489	exon8			GCGATCGTGACGG		CCDS42391.1	17q25.3	2006-02-09							30029	protein-coding gene	gene with protein product		614942				9880566	Standard	XR_243691		Approved	DKFZP762M186	uc002jvm.3	Q32NB8		ENST00000262764.6:c.1513G>T	chr17.hg19:g.76411070G>T	ENSP00000262764:p.Val505Leu	97.0	0.0	.		87.0	23.0	.	NM_024419	B7ZA32|Q8IYK9|Q8TA85|Q96A75|Q9H7G9|Q9NPW7	Missense_Mutation	SNP	ENST00000262764.6	hg19	CCDS42391.1	.	.	.	.	.	.	.	.	.	.	G	18.19	3.569404	0.65765	.	.	ENSG00000087157	ENST00000262764;ENST00000329897	T;T	0.12984	2.63;2.63	4.52	4.52	0.55395	.	32.001500	0.00769	N	0.001196	T	0.23532	0.0569	L	0.60845	1.875	0.80722	D	1	P	0.48694	0.914	B	0.39935	0.314	T	0.45571	-0.9252	10	0.59425	D	0.04	-16.446	17.458	0.87612	0.0:0.0:1.0:0.0	.	505	Q32NB8	PGPS1_HUMAN	L	505;370	ENSP00000262764:V505L;ENSP00000330039:V370L	ENSP00000262764:V505L	V	+	1	0	PGS1	73922665	1.000000	0.71417	1.000000	0.80357	0.563000	0.35712	9.112000	0.94314	2.337000	0.79520	0.561000	0.74099	GTG	.	.	.	alt		0.627	PGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437301.1	NM_024419		T	76411070	G	T	76411070	3	4	31	1	0	0	0	0	1	0	0	0	11815	1145	40	4	1543	4	PGS1	17	76411070	Missense_Mutation	SNP	G	TCGA-5P-A9JZ-01A-11D-A42J-10	68240110	76411070	4784140	43	2272											
PRKCSH	5589	hgsc.bcm.edu	37	chr19	11558373	11558373	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaggaggaggaggaggaggaAgaagaggctgaagaagagga	17	1	22	1	0	0	5	0	1	0	4	0	13	0	12	0	8	0	1	0	8	4	0			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr19:11558373A>G	ENST00000589838.1	+	10	969	c.969A>G	c.(967-969)gaA>gaG	p.E323E	PRKCSH_ENST00000592741.1_Silent_p.E323E|PRKCSH_ENST00000587327.1_Silent_p.E323E|PRKCSH_ENST00000252455.2_Silent_p.E323E|PRKCSH_ENST00000591462.1_Silent_p.E323E|PRKCSH_ENST00000412601.1_Silent_p.E323E			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	323	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)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(3)	19						aggaggaggaagaagaggctg	0.642																																					p.E323E		Atlas-SNP	.											PRKCSH,colon,carcinoma,0,1	PRKCSH	55	.	0			c.A969G						PASS	.																																			SO:0001819	synonymous_variant	5589	exon11			GGAGGAAGAAGAG		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.969A>G	chr19.hg19:g.11558373A>G		93.0	0.0	.		106.0	7.0	.	NM_001001329	A8K318|Q96BU9|Q96D06|Q9P0W9	Silent	SNP	ENST00000589838.1	hg19	CCDS32911.1																																																																																			.	.	.	none		0.642	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1			G	11558373	A	G	11558373	2	3	31	1	0	0	0	0	0	0	0	1	12526	69	3	3		3	PRKCSH	19	11558373	Silent	SNP	A	TCGA-5P-A9JZ-01A-11D-A42J-10		11558373	47570610	44	2273											
RNASEH2A	10535	hgsc.bcm.edu	37	chr19	12921202	12921202	+	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	gacttggatactgattatggCtcaggctaccccaatggtga	10	11	11	9	0	1	2	1	2	0	0	1	4	1	3	2	4	2	2	2	4	4	4			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr19:12921202C>A	ENST00000221486.4	+	6	715	c.621C>A	c.(619-621)ggC>ggA	p.G207G		NM_006397.2	NP_006388.2	O75792	RNH2A_HUMAN	ribonuclease H2, subunit A	207					DNA replication (GO:0006260)|mismatch repair (GO:0006298)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	nucleus (GO:0005634)|ribonuclease H2 complex (GO:0032299)	metal ion binding (GO:0046872)|ribonuclease activity (GO:0004540)|RNA binding (GO:0003723)|RNA-DNA hybrid ribonuclease activity (GO:0004523)			breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|skin(1)|urinary_tract(1)	14						CTGATTATGGCTCAGGCTACC	0.512																																					p.G207G		Atlas-SNP	.											.	RNASEH2A	25	.	0			c.C621A						PASS	.						98	90	93					19																	12921202		2203	4300	6503	SO:0001819	synonymous_variant	10535	exon6			TTATGGCTCAGGC	Z97029	CCDS12282.1	19p13.13	2014-09-17	2006-08-17			ENSG00000104889	3.1.26.-		18518	protein-coding gene	gene with protein product		606034	"ribonuclease H2, large subunit", "Aicardi-Goutieres syndrome 4"			9789007, 16845400	Standard	NM_006397		Approved	RNASEHI, RNHIA, RNHL, AGS4	uc002mvg.1	O75792		ENST00000221486.4:c.621C>A	chr19.hg19:g.12921202C>A		96.0	0.0	.		121.0	49.0	.	NM_006397	B2RCY1|Q96F11	Silent	SNP	ENST00000221486.4	hg19	CCDS12282.1																																																																																			.	.	.	none		0.512	RNASEH2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451507.1	NM_006397		A	12921202	C	A	12921202	2	1	31	1	0	0	0	0	0	0	0	1	13425	784	28	4		4	RNASEH2A	19	12921202	Silent	SNP	C	TCGA-5P-A9JZ-01A-11D-A42J-10	1362829	12921202	46207781	45	2274											
PTPRH	5794	hgsc.bcm.edu	37	chr19	55710166	55710166	+	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	cagtcatgccttccctgaccCatgagacccagtagctgtag	9	9	9	14	0	1	2	1	2	0	1	2	3	2	2	4	0	2	3	4	0	2	3			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr19:55710166C>T	ENST00000376350.3	-	8	1557	c.1535G>A	c.(1534-1536)tGg>tAg	p.W512*	PTPRH_ENST00000588559.1_5'UTR|PTPRH_ENST00000263434.5_Nonsense_Mutation_p.W334*	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	512	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		TTCCCTGACCCATGAGACCCA	0.587																																					p.W512X		Atlas-SNP	.											.	PTPRH	139	.	0			c.G1535A						PASS	.						130	110	116					19																	55710166		2203	4300	6503	SO:0001587	stop_gained	5794	exon8			CTGACCCATGAGA		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.1535G>A	chr19.hg19:g.55710166C>T	ENSP00000365528:p.Trp512*	40.0	0.0	.		55.0	23.0	.	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Nonsense_Mutation	SNP	ENST00000376350.3	hg19	CCDS33110.1	.	.	.	.	.	.	.	.	.	.	C	17.94	3.511395	0.64522	.	.	ENSG00000080031	ENST00000376350;ENST00000263434	.	.	.	3.19	2.14	0.27477	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	.	7.8788	0.29610	0.2465:0.7535:0.0:0.0	.	.	.	.	X	512;334	.	ENSP00000263434:W334X	W	-	2	0	PTPRH	60401978	0.001000	0.12720	0.001000	0.08648	0.009000	0.06853	0.767000	0.26575	0.935000	0.37341	-0.219000	0.12488	TGG	.	.	.	none		0.587	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1			T	55710166	C	T	55710166	4	4	31	1	0	0	0	0	0	1	0	0	12816	595	21	2	1864	2	PTPRH	19	55710166	Nonsense_Mutation	SNP	C	TCGA-5P-A9JZ-01A-11D-A42J-10	42788964	55710166	3418817	46	2275											
SF3A1	10291	hgsc.bcm.edu	37	chr22	30731504	30731513	+	Frame_Shift_Del	DEL	AATCTTCACC	AATCTTCACC	-																															ggcatgcctgtggcttcatgAatcttcaccttaatgacaga																										TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	AATCTTCACC	AATCTTCACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chr22:30731504_30731513delAATCTTCACC	ENST00000215793.8	-	15	2377_2386	c.2223_2232delGGTGAAGATT	c.(2221-2232)aaggtgaagattfs	p.KVKI741fs	SF3A1_ENST00000439242.1_Frame_Shift_Del_p.KVKI676fs	NM_005877.4	NP_005868.1	Q15459	SF3A1_HUMAN	splicing factor 3a, subunit 1, 120kDa	741	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U2-type spliceosomal complex (GO:0005684)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|urinary_tract(1)	29						TGGCTTCATGAATCTTCACCTTAATGACAG	0.514																																					p.742_745del		Atlas-Indel,Pindel	.											.	SF3A1	61	.	0			c.2224_2233del						PASS	.																																			SO:0001589	frameshift_variant	10291	exon15			.	X85237	CCDS13875.1	22q12.2	2014-09-17	2002-08-29		ENSG00000099995	ENSG00000099995			10765	protein-coding gene	gene with protein product		605595	"splicing factor 3a, subunit 1, 120kD"			7489498	Standard	NM_005877		Approved	SF3a120, SAP114, PRPF21, Prp21	uc003ahl.3	Q15459	OTTHUMG00000151005	ENST00000215793.8:c.2223_2232delGGTGAAGATT	chr22.hg19:g.30731504_30731513delAATCTTCACC	ENSP00000215793:p.Lys741fs	105.0	0.0	0		103.0	29.0	0.281553	NM_005877	E9PAW1	Frame_Shift_Del	DEL	ENST00000215793.8	hg19	CCDS13875.1																																																																																			.	.	.	none		0.514	SF3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320916.2	NM_005877		-	30731513	AATCTTCACC	-	30731504	7	5	31	1	0	1	0	1	0	0	0	0	14159	242	9	0	157	0	SF3A1	22	30731504	Frame_Shift_Del	DEL	AATCTTCACC	TCGA-5P-A9JZ-01A-11D-A42J-10		30731504	20573062	47	2276											
AR	367	hgsc.bcm.edu	37	chrX	66765152	66765152	+	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	acctcccggcgccagtttgcTgctgctgcagcagcagcagc	6	7	12	16	2	0	0	0	0	0	0	1	0	1	0	3	1	8	8	3	1	0	1			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chrX:66765152T>A	ENST00000374690.3	+	1	688	c.164T>A	c.(163-165)cTg>cAg	p.L55Q	AR_ENST00000513847.1_3'UTR|AR_ENST00000504326.1_Missense_Mutation_p.L55Q|AR_ENST00000396044.3_Missense_Mutation_p.L55Q	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	55	Modulating.|Poly-Leu.				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)	GCCAGTTTGCTGCTGCTgcag	0.662									Androgen Insensitivity Syndrome																												p.L55Q		Atlas-SNP	.											.	AR	249	.	0			c.T164A						PASS	.						11	14	13					X																	66765152		2169	4252	6421	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	GTTTGCTGCTGCT	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.164T>A	chrX.hg19:g.66765152T>A	ENSP00000363822:p.Leu55Gln	244.0	0.0	.		249.0	13.0	.	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	N	7.392	0.630975	0.14322	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.58797	0.31;0.31;0.31	.	.	.	.	0.268702	0.26919	N	0.021823	T	0.26666	0.0652	N	0.08118	0	0.09310	N	0.999996	B;B	0.17852	0.006;0.024	B;B	0.04013	0.0;0.001	T	0.17107	-1.0380	8	0.10111	T	0.7	.	.	.	.	.	55;55	E7EVX6;D3YPQ2	.;.	Q	55	ENSP00000363822:L55Q;ENSP00000421155:L55Q;ENSP00000379359:L55Q	ENSP00000363822:L55Q	L	+	2	0	AR	66681877	0.998000	0.40836	0.922000	0.36590	0.480000	0.33159	0.009000	0.13219	0.000000	0.14550	0.000000	0.15137	CTG	.	.	.	none		0.662	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		A	66765152	T	A	66765152	3	1	31	1	0	0	0	0	1	0	0	0	836	1580	55	5	166	5	AR	23	66765152	Missense_Mutation	SNP	T	TCGA-5P-A9JZ-01A-11D-A42J-10		66765152	88505408	48	2277											
GPR50	9248	hgsc.bcm.edu	37	chrX	150349201	150349201	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctggccaccccgaccgtgcCtctggccaccctaagcccca	6	5	9	21	2	1	0	0	0	1	0	1	1	1	0	9	2	2	1	9	2	1	1			TCGA-5P-A9JZ-01A-11D-A42J-10	TCGA-5P-A9JZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	52e2c3e0-b7fa-491c-b9ab-525d210a1837	b000234d-c290-4ae5-9ce1-305e268770ab	g.chrX:150349201C>T	ENST00000218316.3	+	2	1215	c.1146C>T	c.(1144-1146)gcC>gcT	p.A382A	GPR50-AS1_ENST00000454196.1_RNA|AF003625.3_ENST00000602313.1_lincRNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	382	Pro-rich.				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)					CCGACCGTGCCTCTGGCCACC	0.582																																					p.A382A		Atlas-SNP	.											.	GPR50	195	.	0			c.C1146T						PASS	.						94	106	102					X																	150349201		2140	4224	6364	SO:0001819	synonymous_variant	9248	exon2			CCGTGCCTCTGGC	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.1146C>T	chrX.hg19:g.150349201C>T		109.0	0.0	.		85.0	29.0	.	NM_004224	Q0VGG3|Q3ZAR0	Silent	SNP	ENST00000218316.3	hg19	CCDS44012.1																																																																																			.	.	.	none		0.582	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060874.1	NM_004224		T	150349201	C	T	150349201	2	4	31	1	0	0	0	0	0	0	0	1	6704	668	24	2		2	GPR50	23	150349201	Silent	SNP	C	TCGA-5P-A9JZ-01A-11D-A42J-10	83584049	150349201	4921359	49	2278											
PIK3CD	5293	hgsc.bcm.edu	37	chr1	9781589	9781589	+	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	tgcgagctgaccaaattcctGctggaccgggccctggccaa	8	7	12	14	2	0	1	0	1	0	0	1	3	1	2	5	3	3	2	5	3	2	1			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr1:9781589G>A	ENST00000377346.4	+	15	2094	c.1899G>A	c.(1897-1899)ctG>ctA	p.L633L	PIK3CD_ENST00000361110.2_Silent_p.L657L|PIK3CD_ENST00000536656.1_Silent_p.L657L|PIK3CD_ENST00000543390.1_Silent_p.L300L	NM_005026.3	NP_005017.3	O00329	PK3CD_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta	633	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				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)	CCAAATTCCTGCTGGACCGGG	0.617											OREG0013082	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L633L		Atlas-SNP	.											.	PIK3CD	86	.	0			c.G1899A						PASS	.						58	59	59					1																	9781589		2203	4300	6503	SO:0001819	synonymous_variant	5293	exon15			ATTCCTGCTGGAC		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.1899G>A	chr1.hg19:g.9781589G>A		54.0	0.0	.	659	39.0	19.0	.	NM_005026	A6NCG0|G1FFP1|O15445|Q5SR49	Silent	SNP	ENST00000377346.4	hg19	CCDS104.1																																																																																			.	.	.	none		0.617	PIK3CD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004235.1	NM_005026		A	9781589	G	A	9781589	2	1	32	1	0	0	0	0	0	0	0	1	11922	1306	46	2		2	PIK3CD	1	9781589	Silent	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10		9781589	239469032	1	2279											
GPSM2	29899	hgsc.bcm.edu	37	chr1	109440639	109440645	+	Frame_Shift_Del	DEL	GTTTTGG	GTTTTGG	-																															gtatcatgccaaagggaaaaGttttggttgccctggtcccc																										TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	GTTTTGG	GTTTTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr1:109440639_109440645delGTTTTGG	ENST00000406462.2	+	6	1246_1252	c.473_479delGTTTTGG	c.(472-480)agttttggtfs	p.SFG158fs	AKNAD1_ENST00000357393.4_Intron|GPSM2_ENST00000264126.3_Frame_Shift_Del_p.SFG158fs			P81274	GPSM2_HUMAN	G-protein signaling modulator 2	158					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)		AAAGGGAAAAGTTTTGGTTGCCCTGGT	0.449																																					p.158_160del		Atlas-Indel,Pindel	.											.	GPSM2	56	.	0			c.472_478del						PASS	.																																			SO:0001589	frameshift_variant	29899	exon5			.	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.473_479delGTTTTGG	chr1.hg19:g.109440639_109440645delGTTTTGG	ENSP00000385510:p.Ser158fs	113.0	0.0	0		58.0	16.0	0.275862	NM_013296	Q5T1N8|Q6IBL7|Q8N0Z5	Frame_Shift_Del	DEL	ENST00000406462.2	hg19	CCDS792.2																																																																																			.	.	.	none		0.449	GPSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032400.3	NM_013296		-	109440645	GTTTTGG	-	109440639	7	5	32	1	0	1	0	1	0	0	0	0	6742	1029	36	0	487	0	GPSM2	1	109440639	Frame_Shift_Del	DEL	GTTTTGG	TCGA-5P-A9K0-01A-11D-A42J-10	99659050	109440639	139809982	2	2280											
BCL9	607	hgsc.bcm.edu	37	chr1	147086326	147086331	+	In_Frame_Del	DEL	CCATGG	CCATGG	-																															cccaggtcttctaccccctcCcatggccaaactactgccac																										TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	CCATGG	CCATGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr1:147086326_147086331delCCATGG	ENST00000234739.3	+	6	1211_1216	c.471_476delCCATGG	c.(469-477)tcccatggc>tcc	p.HG158del	BCL9_ENST00000473292.1_3'UTR	NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	158					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)					CTACCCCCTCCCATGGCCAAACTACT	0.51			T	"IGH@, IGL@"	B-ALL																																p.157_159del		Atlas-Indel,Pindel	.		Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	.	BCL9	150	.	0			c.470_475del						PASS	.																																			SO:0001651	inframe_deletion	607	exon6			.	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.471_476delCCATGG	chr1.hg19:g.147086326_147086331delCCATGG	ENSP00000234739:p.His158_Gly159del	128.0	0.0	0		81.0	27.0	0.333333	NM_004326	Q5T489	In_Frame_Del	DEL	ENST00000234739.3	hg19	CCDS30833.1																																																																																			.	.	.	none		0.51	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326		-	147086331	CCATGG	-	147086326	7	5	32	1	0	1	0	1	0	0	0	0	1381	610	22	0	481	0	BCL9	1	147086326	In_Frame_Del	DEL	CCATGG	TCGA-5P-A9K0-01A-11D-A42J-10	37645687	147086326	102164295	3	2281											
ECM1	1893	hgsc.bcm.edu	37	chr1	150483676	150483676	+	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	agagtgtgccaaacttgtggTaaggttgggttcttgatgcc	8	13	14	6	0	1	2	0	1	1	1	1	2	1	2	2	3	3	3	2	3	2	5			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr1:150483676T>A	ENST00000369047.4	+	6	833		c.e6+2		ECM1_ENST00000470432.1_3'UTR|ECM1_ENST00000369049.4_Splice_Site|ECM1_ENST00000346569.6_Splice_Site	NM_004425.3	NP_004416.2	Q16610	ECM1_HUMAN	extracellular matrix protein 1						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)			AAACTTGTGGTAAGGTTGGGT	0.547																																					.	Melanoma(156;1696 2560 11093 19685)	Atlas-SNP	.											.	ECM1	96	.	0			c.708+2T>A						PASS	.						74	79	77					1																	150483676		2203	4300	6503	SO:0001630	splice_region_variant	1893	exon6			TTGTGGTAAGGTT	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.708+2T>A	chr1.hg19:g.150483676T>A		46.0	0.0	.		31.0	11.0	.	NM_004425	A8K8S0|B4DW49|B4DY60|O43266|Q5T5G4|Q5T5G5|Q5T5G6|Q8IZ60	Splice_Site	SNP	ENST00000369047.4	hg19	CCDS953.1	.	.	.	.	.	.	.	.	.	.	T	10.52	1.374014	0.24857	.	.	ENSG00000143369	ENST00000369049;ENST00000369047;ENST00000346569	.	.	.	4.83	4.83	0.62350	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.7152	0.46008	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ECM1	148750300	1.000000	0.71417	0.999000	0.59377	0.164000	0.22412	3.764000	0.55264	2.046000	0.60703	0.533000	0.62120	.	.	.	.	none		0.547	ECM1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035832.2	NM_004425	Intron	A	150483676	T	A	150483676	5	1	32	1	0	0	0	0	0	0	1	0	4899	1652	57	5	732	5	ECM1	1	150483676	Splice_Site	SNP	T	TCGA-5P-A9K0-01A-11D-A42J-10	3397350	150483676	98766945	4	2282											
GLUL	2752	hgsc.bcm.edu	37	chr1	182357774	182357774	+	Frame_Shift_Del	DEL	G	G	-																															agtccttctccagtaccatcGatccagatatacatggcctg																										TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr1:182357774delG	ENST00000331872.6	-	2	639	c.99delC	c.(97-99)atcfs	p.I33fs	GLUL_ENST00000417584.2_Frame_Shift_Del_p.I33fs|GLUL_ENST00000491322.1_5'UTR|GLUL_ENST00000339526.4_Frame_Shift_Del_p.I33fs|GLUL_ENST00000311223.5_Frame_Shift_Del_p.I33fs	NM_001033044.2	NP_001028216.1	P15104	GLNA_HUMAN	glutamate-ammonia ligase	33					cell proliferation (GO:0008283)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to starvation (GO:0009267)|glutamate catabolic process (GO:0006538)|glutamine biosynthetic process (GO:0006542)|neurotransmitter uptake (GO:0001504)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of insulin secretion (GO:0032024)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein homooligomerization (GO:0051260)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glial cell projection (GO:0097386)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perikaryon (GO:0043204)|protein complex (GO:0043234)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|glutamate-ammonia ligase activity (GO:0004356)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)	p.I33I(1)		endometrium(2)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(1)	16					Ceftriaxone(DB01212)|Diazoxide(DB01119)|L-Glutamine(DB00130)|L-Methionine(DB00134)|Pegvisomant(DB00082)	CAGTACCATCGATCCAGATAT	0.537																																					p.D34fs		Atlas-Indel,Pindel	.											.	GLUL	38	.	1	Substitution - coding silent(1)	large_intestine(1)	c.100delG						PASS	.						164	146	152					1																	182357774		2203	4300	6503	SO:0001589	frameshift_variant	2752	exon2			.	AL161952	CCDS1344.1	1q31	2010-05-04	2010-05-04		ENSG00000135821	ENSG00000135821	6.3.1.2		4341	protein-coding gene	gene with protein product	"glutamine synthetase"	138290	"glutamate-ammonia ligase (glutamine synthase)"	GLNS		1681907, 2888076	Standard	NM_002065		Approved		uc001gpa.2	P15104	OTTHUMG00000037407	ENST00000331872.6:c.99delC	chr1.hg19:g.182357774delG	ENSP00000356537:p.Ile33fs	91.0	0.0	0		100.0	34.0	0.34	NM_001033056	Q499Y9|Q5T9Z1|Q7Z3W4|Q8IZ17	Frame_Shift_Del	DEL	ENST00000331872.6	hg19	CCDS1344.1																																																																																			.	.	.	none		0.537	GLUL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091043.1	NM_002065		-	182357774	G	-	182357774	7	5	32	1	0	1	0	1	0	0	0	0	6485	1048	37	0	1046	0	GLUL	1	182357774	Frame_Shift_Del	DEL	G	TCGA-5P-A9K0-01A-11D-A42J-10	31874098	182357774	66892847	5	2283											
OR14C36	127066	hgsc.bcm.edu	37	chr1	248512735	248512735	+	Missense_Mutation	SNP	T	T	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	caggtcttacattcacatctTttcgaccgtgctcgggtttc	6	15	8	12	3	3	0	1	0	2	0	6	1	3	0	1	2	2	2	1	2	1	5			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr1:248512735T>G	ENST00000317861.1	+	1	659	c.659T>G	c.(658-660)tTt>tGt	p.F220C		NM_001001918.1	NP_001001918.1	Q8NHC7	O14CZ_HUMAN	olfactory receptor, family 14, subfamily C, member 36	220						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(2)|lung(20)|ovary(2)|prostate(3)|skin(7)|upper_aerodigestive_tract(2)	43						ATTCACATCTTTTCGACCGTG	0.502																																					p.F220C		Atlas-SNP	.											.	OR14C36	113	.	0			c.T659G						PASS	.						189	156	167					1																	248512735		2203	4300	6503	SO:0001583	missense	127066	exon1			ACATCTTTTCGAC	BK004466	CCDS31112.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000177174	ENSG00000177174		"GPCR / Class A : Olfactory receptors"	15026	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily BF, member 1"	OR5BF1			Standard	NM_001001918		Approved		uc010pzl.2	Q8NHC7	OTTHUMG00000040463	ENST00000317861.1:c.659T>G	chr1.hg19:g.248512735T>G	ENSP00000324534:p.Phe220Cys	81.0	0.0	.		68.0	26.0	.	NM_001001918	Q6IEZ6	Missense_Mutation	SNP	ENST00000317861.1	hg19	CCDS31112.1	.	.	.	.	.	.	.	.	.	.	T	10.62	1.400474	0.25291	.	.	ENSG00000177174	ENST00000317861	T	0.00211	8.54	3.91	3.91	0.45181	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000198	T	0.00468	0.0015	M	0.78456	2.415	0.09310	N	1	D	0.89917	1.0	D	0.79108	0.992	T	0.41016	-0.9532	10	0.66056	D	0.02	.	7.653	0.28358	0.0:0.0991:0.0:0.9009	.	220	Q8NHC7	O14CZ_HUMAN	C	220	ENSP00000324534:F220C	ENSP00000324534:F220C	F	+	2	0	OR14C36	246579358	0.003000	0.15002	0.981000	0.43875	0.279000	0.26890	1.430000	0.34914	1.654000	0.50703	0.324000	0.21423	TTT	.	.	.	none		0.502	OR14C36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097359.1	NM_001001918		G	248512735	T	G	248512735	3	3	32	1	0	0	0	0	1	0	0	0	10953	1841	64	5	661	5	OR14C36	1	248512735	Missense_Mutation	SNP	T	TCGA-5P-A9K0-01A-11D-A42J-10	66154961	248512735	737886	6	2284											
HNRPLL	92906	hgsc.bcm.edu	37	chr2	38812955	38812955	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcagcaaatgtcacacatTctttggcactatctatgttt	10	15	6	10	0	3	0	1	0	2	0	3	0	3	0	0	1	2	4	0	1	3	5			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr2:38812955T>C	ENST00000449105.3	-	3	716	c.377A>G	c.(376-378)gAa>gGa	p.E126G	HNRNPLL_ENST00000608859.1_Missense_Mutation_p.E126G|HNRNPLL_ENST00000409636.1_Missense_Mutation_p.E121G|HNRNPLL_ENST00000378915.3_Missense_Mutation_p.E126G|HNRNPLL_ENST00000409328.1_Missense_Mutation_p.E126G|HNRNPLL_ENST00000410076.1_Missense_Mutation_p.E121G|HNRNPLL_ENST00000358367.4_Missense_Mutation_p.E126G			Q8WVV9	HNRLL_HUMAN	heterogeneous nuclear ribonucleoprotein L-like	126	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|positive regulation of RNA splicing (GO:0033120)	membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)										TGTCACACATTCTTTGGCACT	0.408																																					p.E126G		Atlas-SNP	.											.	HNRPLL	19	.	0			c.A377G						PASS	.						165	148	153					2																	38812955		2203	4300	6503	SO:0001583	missense	92906	exon3			ACACATTCTTTGG	BC008217	CCDS46261.1, CCDS1796.2	2p22	2014-02-10		2013-06-12	ENSG00000143889	ENSG00000143889		"RNA binding motif (RRM) containing"	25127	protein-coding gene	gene with protein product		611208		HNRPLL		18669861	Standard	NM_138394		Approved		uc021vgc.1	Q8WVV9	OTTHUMG00000102075	ENST00000449105.3:c.377A>G	chr2.hg19:g.38812955T>C	ENSP00000390625:p.Glu126Gly	64.0	0.0	.		47.0	23.0	.	NM_138394	Q53T80|Q5JB51|Q5JB52|Q659B9|Q8IVH5|Q8IVH6|Q96HR5	Missense_Mutation	SNP	ENST00000449105.3	hg19		.	.	.	.	.	.	.	.	.	.	T	13.11	2.138987	0.37728	.	.	ENSG00000143889	ENST00000449105;ENST00000409636;ENST00000378915;ENST00000409328;ENST00000358367;ENST00000410076;ENST00000425682	T;T;T;T;T;T;T	0.08720	3.06;3.06;3.06;3.06;3.06;3.06;3.06	5.99	4.84	0.62591	.	0.378699	0.30602	N	0.009261	T	0.10078	0.0247	L	0.56280	1.765	0.32157	N	0.58347	B;B	0.14012	0.009;0.009	B;B	0.14023	0.01;0.01	T	0.04005	-1.0985	10	0.30854	T	0.27	.	11.8201	0.52235	0.0:0.0677:0.0:0.9323	.	121;126	C9J9G0;D6W592	.;.	G	126;121;126;126;126;121;65	ENSP00000390625:E126G;ENSP00000387088:E121G;ENSP00000368195:E126G;ENSP00000386575:E126G;ENSP00000351136:E126G;ENSP00000386695:E121G;ENSP00000396669:E65G	ENSP00000351136:E126G	E	-	2	0	HNRPLL	38666459	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.046000	0.57376	1.100000	0.41517	0.533000	0.62120	GAA	.	.	.	none		0.408	HNRNPLL-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000219887.2	NM_138394		C	38812955	T	C	38812955	3	2	32	1	0	0	0	0	1	0	0	0	7284	1783	62	3	1295	3	HNRPLL	2	38812955	Missense_Mutation	SNP	T	TCGA-5P-A9K0-01A-11D-A42J-10		38812955	204386418	7	2285											
OXER1	165140	hgsc.bcm.edu	37	chr2	42990746	42990746	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtggggctgcaccaccttcaGgtagcggttgagtgcgatgg	6	9	17	9	2	1	1	1	1	0	0	1	2	1	1	2	5	3	4	2	5	1	3			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr2:42990746G>A	ENST00000378661.2	-	1	655	c.574C>T	c.(574-576)Ctg>Ttg	p.L192L		NM_148962.4	NP_683765.1	Q8TDS5	OXER1_HUMAN	oxoeicosanoid (OXE) receptor 1	192					G-protein coupled receptor signaling pathway (GO:0007186)|regulation of cAMP biosynthetic process (GO:0030817)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	5(S)-hydroxyperoxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050648)|5-hydroxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050647)|5-oxo-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050646)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	10						ACCACCTTCAGGTAGCGGTTG	0.657																																					p.L192L		Atlas-SNP	.											.	OXER1	33	.	0			c.C574T						PASS	.						47	38	42					2																	42990746		2203	4300	6503	SO:0001819	synonymous_variant	165140	exon1			CCTTCAGGTAGCG	AB083055	CCDS1810.1	2p22.1	2012-08-10			ENSG00000162881	ENSG00000162881		"GPCR / Class A : Leukotriene receptors"	24884	protein-coding gene	gene with protein product	"5-oxo-ETE acid G-protein-coupled receptor 1"					12065583, 15001665	Standard	NM_148962		Approved	GPCR, TG1019, GPR170	uc002rss.3	Q8TDS5	OTTHUMG00000128643	ENST00000378661.2:c.574C>T	chr2.hg19:g.42990746G>A		57.0	0.0	.		48.0	12.0	.	NM_148962	Q86WP7|Q8NGW4	Silent	SNP	ENST00000378661.2	hg19	CCDS1810.1																																																																																			.	.	.	none		0.657	OXER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250514.1	NM_148962		A	42990746	G	A	42990746	2	1	32	1	0	0	0	0	0	0	0	1	11338	991	35	2		2	OXER1	2	42990746	Silent	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10	4177791	42990746	200208627	8	2286											
ATP6V1E2	90423	hgsc.bcm.edu	37	chr2	46739823	46739824	+	Missense_Mutation	DNP	TT	TT	GA																															catcatgtgcttaatctgctTtttcacatcgacatcactca																										TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr2:46739823_46739824TT>GA	ENST00000306448.4	-	2	1140_1141	c.27_28AA>TC	c.(25-30)aaAAag>aaTCag	p.9_10KK>NQ	ATP6V1E2_ENST00000522587.1_Missense_Mutation_p.9_10KK>NQ	NM_080653.3	NP_542384.1	Q96A05	VATE2_HUMAN	ATPase, H+ transporting, lysosomal 31kDa, V1 subunit E2	9					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)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|proton-transporting two-sector ATPase complex, catalytic domain (GO:0033178)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)	13		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.151)			TTAATCTGCTTTTTCACATCGA	0.49																																					p.K10Q|p.K9N		Atlas-SNP	.											.	ATP6V1E2	25	.	0			c.A28C|c.A27T						PASS	.																																			SO:0001583	missense	90423	exon2			TCTGCTTTTTCAC|CTGCTTTTTCACA	BC008981	CCDS1826.1	2p21	2011-02-10	2006-01-13	2002-06-21	ENSG00000250565	ENSG00000250565		"ATPases / V-type"	18125	protein-coding gene	gene with protein product			"ATPase, H+ transporting, lysosomal (vacuolar proton pump) 31kD-like 2", "ATPase, H+ transporting, lysosomal 31kDa, V1 subunit E isoform 2"	ATP6EL2, ATP6V1EL2		12036578	Standard	NM_080653		Approved	MGC9341, VMA4, ATP6E1	uc002ruy.3	Q96A05	OTTHUMG00000128819	ENST00000306448.4:c.27_28delinsGA	chr2.hg19:g.46739823_46739824delinsGA	ENSP00000304891:p.K9_K10delinsNQ	43.0	0.0	.		29.0	10.0|9.0	.	NM_080653		Missense_Mutation	SNP	ENST00000306448.4	hg19	CCDS1826.1																																																																																			.	.	.	none		0.49	ATP6V1E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250753.1	NM_080653		GA	46739824	TT	GA	46739823	3	3	32	1	0	0	0	0	1	0	0	0	1184	1850	64	5	656	5	ATP6V1E2	2	46739823	Missense_Mutation	DNP	TT	TCGA-5P-A9K0-01A-11D-A42J-10	3749077	46739823	196459550	9	2287											
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125204404	125204404	+	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	tcctggatgaccagcactggCactcggtcctcattgagcgg	7	9	12	13	2	1	2	1	2	0	0	4	3	3	3	3	4	2	2	3	4	0	1			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr2:125204404C>G	ENST00000431078.1	+	6	1172	c.808C>G	c.(808-810)Cac>Gac	p.H270D		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	270	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.H270N(1)		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)		CCAGCACTGGCACTCGGTCCT	0.607																																					p.H270D		Atlas-SNP	.											CNTNAP5,NS,carcinoma,0,1	CNTNAP5	405	.	1	Substitution - Missense(1)	lung(1)	c.C808G						PASS	.						73	77	76					2																	125204404		2165	4283	6448	SO:0001583	missense	129684	exon6			CACTGGCACTCGG	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.808C>G	chr2.hg19:g.125204404C>G	ENSP00000399013:p.His270Asp	119.0	0.0	.		85.0	29.0	.	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	hg19	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.607383	0.87157	.	.	ENSG00000155052	ENST00000431078	D	0.86956	-2.19	5.87	5.87	0.94306	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.53938	D	0.000053	D	0.96034	0.8708	H	0.96518	3.835	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96573	0.9424	10	0.87932	D	0	.	19.5705	0.95413	0.0:1.0:0.0:0.0	.	270	Q8WYK1	CNTP5_HUMAN	D	270	ENSP00000399013:H270D	ENSP00000399013:H270D	H	+	1	0	CNTNAP5	124920874	1.000000	0.71417	1.000000	0.80357	0.654000	0.38779	7.666000	0.83877	2.941000	0.99782	0.655000	0.94253	CAC	.	.	.	none		0.607	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			G	125204404	C	G	125204404	3	3	32	1	0	0	0	0	1	0	0	0	3652	710	25	4	830	4	CNTNAP5	2	125204404	Missense_Mutation	SNP	C	TCGA-5P-A9K0-01A-11D-A42J-10	78464581	125204404	117994969	10	2288											
SF3B1	23451	hgsc.bcm.edu	37	chr2	198272752	198272752	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctgggaacatagcatctaaTtcctcatcagaaagtgggcg	12	10	10	9	1	4	1	2	0	2	1	5	2	5	2	1	2	2	1	1	2	4	3			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr2:198272752T>C	ENST00000335508.6	-	9	1300	c.1209A>G	c.(1207-1209)gaA>gaG	p.E403E		NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	403	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)			TAGCATCTAATTCCTCATCAG	0.363			Mis		myelodysplastic syndrome																																p.E403E		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1	1038	.	0			c.A1209G						PASS	.						92	90	91					2																	198272752		2203	4300	6503	SO:0001819	synonymous_variant	23451	exon9			ATCTAATTCCTCA	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.1209A>G	chr2.hg19:g.198272752T>C		55.0	0.0	.		47.0	11.0	.	NM_012433	E9PCH3	Silent	SNP	ENST00000335508.6	hg19	CCDS33356.1																																																																																			.	.	.	none		0.363	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			C	198272752	T	C	198272752	2	2	32	1	0	0	0	0	0	0	0	1	14162	1490	52	3		3	SF3B1	2	198272752	Silent	SNP	T	TCGA-5P-A9K0-01A-11D-A42J-10	73068348	198272752	44926621	11	2289											
TNS1	7145	hgsc.bcm.edu	37	chr2	218683236	218683236	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggcaccgtgtggacgccAgccacactgaactgagctcg	9	5	12	15	3	0	2	0	2	0	0	1	3	0	3	4	2	3	2	4	2	1	0			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr2:218683236A>G	ENST00000171887.4	-	24	3959	c.3507T>C	c.(3505-3507)gcT>gcC	p.A1169A	TNS1_ENST00000430930.1_Silent_p.A1148A|TNS1_ENST00000419504.1_Silent_p.A1156A	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1169					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)		TGTGGACGCCAGCCACACTGA	0.632																																					p.A1169A		Atlas-SNP	.											.	TNS1	251	.	0			c.T3507C						PASS	.						51	55	54					2																	218683236		2203	4300	6503	SO:0001819	synonymous_variant	7145	exon24			GACGCCAGCCACA	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.3507T>C	chr2.hg19:g.218683236A>G		58.0	0.0	.		71.0	22.0	.	NM_022648	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	hg19	CCDS2407.1																																																																																			.	.	.	none		0.632	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		G	218683236	A	G	218683236	2	3	32	1	0	0	0	0	0	0	0	1	16355	175	7	3		3	TNS1	2	218683236	Silent	SNP	A	TCGA-5P-A9K0-01A-11D-A42J-10	20410484	218683236	24516137	12	2290											
TNS1	7145	hgsc.bcm.edu	37	chr2	218712606	218712607	+	Frame_Shift_Ins	INS	-	-	A																															tcagtggatgggactgacggINSgaggatccagagaggggctg																								rs1364641	byFrequency	TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr2:218712606_218712607insA	ENST00000171887.4	-	17	2710_2711	c.2258_2259insT	c.(2257-2259)tccfs	p.S753fs	TNS1_ENST00000480665.1_5'Flank|TNS1_ENST00000430930.1_Frame_Shift_Ins_p.S753fs|TNS1_ENST00000419504.1_Frame_Shift_Ins_p.S753fs	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	753					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)		GGGACTGACGGGAGGATCCAGA	0.653																																					p.S753fs		Atlas-Indel,Pindel	.											.	TNS1	251	.	0			c.2259_2260insT						PASS	.																																			SO:0001589	frameshift_variant	7145	exon17			.	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.2258_2259insT	chr2.hg19:g.218712606_218712607insA	ENSP00000171887:p.Ser753fs	67.0	0.0	0		59.0	26.0	0.440678	NM_022648	Q4ZG71|Q6IPI5	Frame_Shift_Ins	INS	ENST00000171887.4	hg19	CCDS2407.1																																																																																			.	.	.	none		0.653	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		A	218712607	-	A	218712606	7	5	32	1	0	1	1	0	0	0	0	0	16355	1219	43	0	3016	0	TNS1	2	218712606	Frame_Shift_Ins	INS	-	TCGA-5P-A9K0-01A-11D-A42J-10	29370	218712606	24486767	13	2291											
CRTAP	10491	hgsc.bcm.edu	37	chr3	33155650	33155650	+	Missense_Mutation	SNP	A	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	ctgcgcgccgggcgcgcccaAtacgaacgctacagcttccg	7	5	12	17	8	0	0	0	0	0	0	1	1	1	0	3	1	5	2	3	1	4	3			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr3:33155650A>C	ENST00000320954.6	+	1	180	c.81A>C	c.(79-81)caA>caC	p.Q27H	CRTAP_ENST00000449224.1_Missense_Mutation_p.Q27H	NM_006371.4	NP_006362.1	O75718	CRTAP_HUMAN	cartilage associated protein	27					chaperone-mediated protein folding (GO:0061077)|extracellular matrix organization (GO:0030198)|negative regulation of post-translational protein modification (GO:1901874)|peptidyl-proline hydroxylation to 3-hydroxy-L-proline (GO:0018400)|protein stabilization (GO:0050821)|spermatogenesis (GO:0007283)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular space (GO:0005615)|macromolecular complex (GO:0032991)|proteinaceous extracellular matrix (GO:0005578)	protein complex binding (GO:0032403)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	9						GGCGCGCCCAATACGAACGCT	0.736																																					p.Q27H		Atlas-SNP	.											.	CRTAP	16	.	0			c.A81C						PASS	.						9	9	9					3																	33155650		2106	4146	6252	SO:0001583	missense	10491	exon1			CGCCCAATACGAA	AJ006470	CCDS2657.1	3p22	2014-09-17			ENSG00000170275	ENSG00000170275			2379	protein-coding gene	gene with protein product	"leprecan-like 3"	605497				9217321, 10429950	Standard	NM_006371		Approved	CASP, LEPREL3	uc003cfl.4	O75718	OTTHUMG00000130746	ENST00000320954.6:c.81A>C	chr3.hg19:g.33155650A>C	ENSP00000323696:p.Gln27His	580.0	0.0	.		556.0	254.0	.	NM_006371	B2RBL6	Missense_Mutation	SNP	ENST00000320954.6	hg19	CCDS2657.1	.	.	.	.	.	.	.	.	.	.	A	18.07	3.540586	0.65085	.	.	ENSG00000170275	ENST00000320954;ENST00000509775;ENST00000539684;ENST00000449224;ENST00000423366	T;T	0.76968	-1.06;-1.06	4.13	2.28	0.28536	.	0.000000	0.85682	D	0.000000	D	0.86167	0.5868	M	0.81497	2.545	0.52099	D	0.99994	D;D	0.64830	0.994;0.994	D;D	0.78314	0.991;0.991	D	0.86505	0.1806	10	0.87932	D	0	-0.1463	10.1	0.42499	0.2355:0.0:0.7645:0.0	.	27;27	C9JP16;O75718	.;CRTAP_HUMAN	H	27	ENSP00000323696:Q27H;ENSP00000409997:Q27H	ENSP00000323696:Q27H	Q	+	3	2	CRTAP	33130654	1.000000	0.71417	1.000000	0.80357	0.327000	0.28475	2.883000	0.48554	0.946000	0.37632	-0.407000	0.06327	CAA	.	.	.	none		0.736	CRTAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253246.3			C	33155650	A	C	33155650	3	2	32	1	0	0	0	0	1	0	0	0	3900	98	4	5	83	5	CRTAP	3	33155650	Missense_Mutation	SNP	A	TCGA-5P-A9K0-01A-11D-A42J-10		33155650	164866780	14	2292											
ACAA1	30	hgsc.bcm.edu	37	chr3	38167691	38167691	+	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	ctgggatggcataggcaggtCcaatgcccatgatgtcaggt	9	9	14	9	0	1	1	1	1	0	0	2	2	2	2	2	5	1	2	2	5	2	1			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr3:38167691C>G	ENST00000333167.8	-	9	1131	c.959G>C	c.(958-960)gGa>gCa	p.G320A	ACAA1_ENST00000450296.1_Missense_Mutation_p.G279A|ACAA1_ENST00000301810.7_Intron|Y_RNA_ENST00000365095.1_RNA|ACAA1_ENST00000544624.1_3'UTR|ACAA1_ENST00000480865.1_5'UTR	NM_001607.3	NP_001598.1	P09110	THIK_HUMAN	acetyl-CoA acyltransferase 1	320					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)		ATAGGCAGGTCCAATGCCCAT	0.572																																					p.G320A		Atlas-SNP	.											.	ACAA1	32	.	0			c.G959C						PASS	.						89	71	77					3																	38167691		2203	4300	6503	SO:0001583	missense	30	exon9			GCAGGTCCAATGC	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.959G>C	chr3.hg19:g.38167691C>G	ENSP00000333664:p.Gly320Ala	116.0	0.0	.		106.0	49.0	.	NM_001607	G5E935|Q96CA6	Missense_Mutation	SNP	ENST00000333167.8	hg19	CCDS2673.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.6|29.6	5.017968|5.017968	0.93404|0.93404	.|.	.|.	ENSG00000060971|ENSG00000060971	ENST00000421218|ENST00000333167;ENST00000450296;ENST00000358122	.|D;D	.|0.92805	.|-3.11;-3.11	5.11|5.11	5.11|5.11	0.69529|0.69529	.|Thiolase-like, subgroup (1);Thiolase-like (1);Thiolase, C-terminal (1);	.|0.053952	.|0.64402	.|D	.|0.000001	D|D	0.95452|0.95452	0.8523|0.8523	M|M	0.68728|0.68728	2.09|2.09	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.65815	.|0.991;0.995;0.993	.|D;D;D	.|0.69142	.|0.92;0.962;0.952	D|D	0.95909|0.95909	0.8921|0.8921	5|10	.|0.87932	.|D	.|0	-17.279|-17.279	18.5603|18.5603	0.91097|0.91097	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|252;279;320	.|F5GXL8;C9JDE9;P09110	.|.;.;THIK_HUMAN	H|A	210|320;279;252	.|ENSP00000333664:G320A;ENSP00000395183:G279A	.|ENSP00000333664:G320A	D|G	-|-	1|2	0|0	ACAA1|ACAA1	38142695|38142695	1.000000|1.000000	0.71417|0.71417	0.953000|0.953000	0.39169|0.39169	0.935000|0.935000	0.57460|0.57460	7.320000|7.320000	0.79064|0.79064	2.371000|2.371000	0.80710|0.80710	0.650000|0.650000	0.86243|0.86243	GAC|GGA	.	.	.	none		0.572	ACAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342980.1	NM_001607		G	38167691	C	G	38167691	3	3	32	1	0	0	0	0	1	0	0	0	104	855	30	4	331	4	ACAA1	3	38167691	Missense_Mutation	SNP	C	TCGA-5P-A9K0-01A-11D-A42J-10	5012041	38167691	159854739	15	2293											
USP4	7375	hgsc.bcm.edu	37	chr3	49338037	49338037	+	Missense_Mutation	SNP	A	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	agcacattctgggcaaaccaAagtagatttgaagaggccat	15	8	10	8	0	1	3	0	1	1	2	1	3	1	3	2	2	2	3	2	2	4	3			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr3:49338037A>C	ENST00000265560.4	-	11	1421	c.1375T>G	c.(1375-1377)Ttg>Gtg	p.L459V	USP4_ENST00000351842.4_Missense_Mutation_p.L412V|USP4_ENST00000488520.1_5'UTR	NM_003363.3	NP_003354.2	Q13107	UBP4_HUMAN	ubiquitin specific peptidase 4 (proto-oncogene)	459	Necessary for interaction with RB1 and RBL2. {ECO:0000250}.|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)		GGGCAAACCAAAGTAGATTTG	0.463																																					p.L459V		Atlas-SNP	.											.	USP4	72	.	0			c.T1375G						PASS	.						126	108	114					3																	49338037		2203	4300	6503	SO:0001583	missense	7375	exon11			AAACCAAAGTAGA	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.1375T>G	chr3.hg19:g.49338037A>C	ENSP00000265560:p.Leu459Val	123.0	0.0	.		114.0	48.0	.	NM_003363	A8K6Y0|C9IY91|O43452|O43453|Q08AK8	Missense_Mutation	SNP	ENST00000265560.4	hg19	CCDS2793.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.14|19.14	3.769182|3.769182	0.69992|0.69992	.|.	.|.	ENSG00000114316|ENSG00000114316	ENST00000431357|ENST00000351842;ENST00000265560	.|T;T	.|0.35048	.|1.33;1.33	5.93|5.93	2.34|2.34	0.29019|0.29019	.|Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.46870|0.46870	0.1415|0.1415	L|L	0.46614|0.46614	1.455|1.455	0.80722|0.80722	D|D	1|1	.|P;B;D	.|0.76494	.|0.939;0.218;0.999	.|P;P;D	.|0.87578	.|0.714;0.489;0.998	T|T	0.33214|0.33214	-0.9877|-0.9877	5|10	.|0.52906	.|T	.|0.07	-15.2249|-15.2249	7.059|7.059	0.25115|0.25115	0.6063:0.0:0.3937:0.0|0.6063:0.0:0.3937:0.0	.|.	.|412;459;459	.|Q13107-2;Q13107;Q08AK7	.|.;UBP4_HUMAN;.	C|V	197|412;459	.|ENSP00000341028:L412V;ENSP00000265560:L459V	.|ENSP00000265560:L459V	F|L	-|-	2|1	0|2	USP4|USP4	49313041|49313041	0.942000|0.942000	0.31987|0.31987	0.976000|0.976000	0.42696|0.42696	0.954000|0.954000	0.61252|0.61252	1.828000|1.828000	0.39111|0.39111	0.501000|0.501000	0.28013|0.28013	0.459000|0.459000	0.35465|0.35465	TTT|TTG	.	.	.	none		0.463	USP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346069.1	NM_199443		C	49338037	A	C	49338037	3	2	32	1	0	0	0	0	1	0	0	0	17083	11	1	5	1564	5	USP4	3	49338037	Missense_Mutation	SNP	A	TCGA-5P-A9K0-01A-11D-A42J-10	11170346	49338037	148684393	16	2294											
RBM15B	29890	hgsc.bcm.edu	37	chr3	51431290	51431290	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccggtctgcagaggcggctTctcaggaacctggtctccta	6	9	12	14	2	3	1	1	0	3	1	5	2	3	2	3	5	2	2	3	5	2	2			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr3:51431290T>C	ENST00000323686.4	+	1	2560	c.2460T>C	c.(2458-2460)ctT>ctC	p.L820L		NM_013286.4	NP_037418.3	Q8NDT2	RB15B_HUMAN	RNA binding motif protein 15B	820	Interaction with Epstein-Barr virus BMLF1.|SPOC. {ECO:0000255|PROSITE- ProRule:PRU00249}.				mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|large_intestine(5)|lung(3)	12				BRCA - Breast invasive adenocarcinoma(193;0.000224)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		AGAGGCGGCTTCTCAGGAACC	0.637																																					p.L820L		Atlas-SNP	.											.	RBM15B	47	.	0			c.T2460C						PASS	.						26	30	29					3																	51431290		2203	4300	6503	SO:0001819	synonymous_variant	29890	exon1			GCGGCTTCTCAGG	AL831838	CCDS33764.1	3p21.1	2013-02-12			ENSG00000179837	ENSG00000259956		"RNA binding motif (RRM) containing"	24303	protein-coding gene	gene with protein product		612602				16129689	Standard	NM_013286		Approved	HUMAGCGB, OTT3	uc003dbd.3	Q8NDT2	OTTHUMG00000156896	ENST00000323686.4:c.2460T>C	chr3.hg19:g.51431290T>C		64.0	0.0	.		63.0	22.0	.	NM_013286	A4QPG7|Q6QE19|Q9BV96	Silent	SNP	ENST00000323686.4	hg19	CCDS33764.1																																																																																			.	.	.	none		0.637	RBM15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346489.1	NM_013286		C	51431290	T	C	51431290	2	2	32	1	0	0	0	0	0	0	0	1	13130	1770	62	3		3	RBM15B	3	51431290	Silent	SNP	T	TCGA-5P-A9K0-01A-11D-A42J-10	2093253	51431290	146591140	17	2295											
PRR23A	729627	hgsc.bcm.edu	37	chr3	138724832	138724832	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcaggatgagggtgtgtccAtcgagagacactcgcaggat	11	8	14	8	2	1	2	1	1	0	1	4	6	2	4	1	3	0	1	1	3	0	0			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr3:138724832A>G	ENST00000383163.2	-	1	278	c.279T>C	c.(277-279)gaT>gaC	p.D93D	MRPS22_ENST00000495075.1_5'UTR	NM_001134659.1	NP_001128131.1	A6NEV1	PR23A_HUMAN	proline rich 23A	93										endometrium(3)|kidney(1)|lung(7)	11						GGGTGTGTCCATCGAGAGACA	0.642																																					p.D93D		Atlas-SNP	.											.	PRR23A	35	.	0			c.T279C						PASS	.						25	25	25					3																	138724832		692	1591	2283	SO:0001819	synonymous_variant	729627	exon1			GTGTCCATCGAGA		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.279T>C	chr3.hg19:g.138724832A>G		196.0	0.0	.		142.0	59.0	.	NM_001134659		Silent	SNP	ENST00000383163.2	hg19	CCDS46923.1																																																																																			.	.	.	none		0.642	PRR23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361503.1	NM_001134659		G	138724832	A	G	138724832	2	3	32	1	0	0	0	0	0	0	0	1	12604	214	8	3		3	PRR23A	3	138724832	Silent	SNP	A	TCGA-5P-A9K0-01A-11D-A42J-10	87293542	138724832	59297598	18	2296											
SLITRK3	22865	hgsc.bcm.edu	37	chr3	164906764	164906764	+	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	ggctggggattctccagctgGtgcaacgtgcagcatctctg	6	10	14	11	1	2	0	0	0	2	0	4	1	2	1	1	4	5	5	1	4	1	1			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr3:164906764G>T	ENST00000475390.1	-	2	2298	c.1855C>A	c.(1855-1857)Cca>Aca	p.P619T	SLITRK3_ENST00000241274.3_Missense_Mutation_p.P619T			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	619					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						TCTCCAGCTGGTGCAACGTGC	0.567										HNSCC(40;0.11)																											p.P619T		Atlas-SNP	.											.	SLITRK3	263	.	0			c.C1855A						PASS	.						42	42	42					3																	164906764		2203	4300	6503	SO:0001583	missense	22865	exon2			CAGCTGGTGCAAC	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.1855C>A	chr3.hg19:g.164906764G>T	ENSP00000420091:p.Pro619Thr	71.0	0.0	.		59.0	15.0	.	NM_014926	Q1RMY6	Missense_Mutation	SNP	ENST00000475390.1	hg19	CCDS3197.1	.	.	.	.	.	.	.	.	.	.	G	4.489	0.090753	0.08632	.	.	ENSG00000121871	ENST00000475390;ENST00000241274	T;T	0.54866	0.55;0.55	5.23	5.23	0.72850	.	0.211812	0.23924	N	0.043211	T	0.37073	0.0990	N	0.17082	0.46	0.30130	N	0.804861	B	0.14012	0.009	B	0.10450	0.005	T	0.26052	-1.0114	10	0.38643	T	0.18	-4.1785	13.2744	0.60180	0.0:0.2728:0.7272:0.0	.	619	O94933	SLIK3_HUMAN	T	619	ENSP00000420091:P619T;ENSP00000241274:P619T	ENSP00000241274:P619T	P	-	1	0	SLITRK3	166389458	0.975000	0.34042	0.589000	0.28718	0.655000	0.38815	2.147000	0.42226	2.871000	0.98454	0.655000	0.94253	CCA	.	.	.	none		0.567	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926		T	164906764	G	T	164906764	3	4	32	1	0	0	0	0	1	0	0	0	14757	1261	44	4	1082	4	SLITRK3	3	164906764	Missense_Mutation	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10	26181932	164906764	33115666	19	2297											
ZBBX	79740	hgsc.bcm.edu	37	chr3	167086364	167086364	+	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	tcgcagttcttgagcatttcTgaagacataagatttaaatg	13	14	8	6	1	2	4	0	2	2	2	3	4	2	4	0	0	1	3	0	0	4	6			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr3:167086364T>A	ENST00000392766.2	-	5	409		c.e5-2		ZBBX_ENST00000469220.1_Intron|ZBBX_ENST00000392764.1_Splice_Site|ZBBX_ENST00000392767.2_Splice_Site|ZBBX_ENST00000307529.5_Splice_Site|ZBBX_ENST00000455345.2_Splice_Site	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing							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						TGAGCATTTCTGAAGACATAA	0.318																																					.		Atlas-SNP	.											.	ZBBX	299	.	0			c.69-2A>T						PASS	.						113	97	102					3																	167086364		1801	4061	5862	SO:0001630	splice_region_variant	79740	exon6			CATTTCTGAAGAC	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.69-2A>T	chr3.hg19:g.167086364T>A		27.0	0.0	.		37.0	17.0	.	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Splice_Site	SNP	ENST00000392766.2	hg19	CCDS3199.2	.	.	.	.	.	.	.	.	.	.	T	12.73	2.026562	0.35797	.	.	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000474464	.	.	.	5.21	5.21	0.72293	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.4867	0.50358	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	ZBBX	168569058	1.000000	0.71417	0.937000	0.37676	0.328000	0.28507	5.110000	0.64622	1.972000	0.57404	0.477000	0.44152	.	.	.	.	none		0.318	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	Intron	A	167086364	T	A	167086364	5	1	32	1	0	0	0	0	0	0	1	0	17528	1594	55	5	2403	5	ZBBX	3	167086364	Splice_Site	SNP	T	TCGA-5P-A9K0-01A-11D-A42J-10	2179600	167086364	30936066	20	2298											
SEC62	7095	hgsc.bcm.edu	37	chr3	169701000	169701000	+	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	aaactaagaaaaaattcaaaCttgagccacatgatgatcag	20	8	6	7	0	2	4	2	3	0	1	2	4	2	4	1	0	3	0	1	0	6	3			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr3:169701000C>G	ENST00000337002.4	+	5	566	c.508C>G	c.(508-510)Ctt>Gtt	p.L170V	SEC62_ENST00000480708.1_Missense_Mutation_p.L170V|SEC62-AS1_ENST00000479626.1_RNA	NM_003262.3	NP_003253.1	Q99442	SEC62_HUMAN	SEC62 homolog (S. cerevisiae)	170					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						AAAATTCAAACTTGAGCCACA	0.348																																					p.L170V		Atlas-SNP	.											.	SEC62	27	.	0			c.C508G						PASS	.						71	76	74					3																	169701000		2203	4298	6501	SO:0001583	missense	7095	exon5			TTCAAACTTGAGC	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.508C>G	chr3.hg19:g.169701000C>G	ENSP00000337688:p.Leu170Val	333.0	0.0	.		261.0	81.0	.	NM_003262	D3DNQ0|O00682|O00729	Missense_Mutation	SNP	ENST00000337002.4	hg19	CCDS3210.1	.	.	.	.	.	.	.	.	.	.	C	31	5.072916	0.93950	.	.	ENSG00000008952	ENST00000337002;ENST00000480708	T;T	0.02421	4.3;4.3	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.18509	0.0444	M	0.79693	2.465	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	T	0.00021	-1.2347	10	0.54805	T	0.06	-9.9639	20.3431	0.98773	0.0:1.0:0.0:0.0	.	170	Q99442	SEC62_HUMAN	V	170	ENSP00000337688:L170V;ENSP00000420331:L170V	ENSP00000337688:L170V	L	+	1	0	SEC62	171183694	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.411000	0.66386	2.880000	0.98712	0.650000	0.86243	CTT	.	.	.	none		0.348	SEC62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352043.1			G	169701000	C	G	169701000	3	3	32	1	0	0	0	0	1	0	0	0	14017	565	20	4	526	4	SEC62	3	169701000	Missense_Mutation	SNP	C	TCGA-5P-A9K0-01A-11D-A42J-10	2614636	169701000	28321430	21	2299											
DVL3	1857	hgsc.bcm.edu	37	chr3	183887831	183887831	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccacgatcacgatggctcCagtggcgcctctgaccagga	8	7	11	15	3	2	1	1	1	1	0	4	4	4	2	4	3	0	1	4	3	0	0			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr3:183887831C>T	ENST00000313143.3	+	14	1784	c.1536C>T	c.(1534-1536)tcC>tcT	p.S512S	DVL3_ENST00000431765.1_Silent_p.S495S|EIF2B5_ENST00000444495.1_Intron	NM_004423.3	NP_004414.3	Q92997	DVL3_HUMAN	dishevelled segment polarity protein 3	512					canonical Wnt signaling pathway (GO:0060070)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|intracellular signal transduction (GO:0035556)|non-canonical Wnt signaling pathway (GO:0035567)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|outflow tract septum morphogenesis (GO:0003148)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	cell cortex (GO:0005938)	beta-catenin binding (GO:0008013)|frizzled binding (GO:0005109)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(6)|liver(1)|lung(13)|ovary(1)|prostate(1)	35	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.08e-34)|OV - Ovarian serous cystadenocarcinoma(80;1.31e-22)			ACGATGGCTCCAGTGGCGCCT	0.662																																					p.S512S		Atlas-SNP	.											.	DVL3	68	.	0			c.C1536T						PASS	.						73	63	66					3																	183887831		2203	4300	6503	SO:0001819	synonymous_variant	1857	exon14			TGGCTCCAGTGGC	D86963	CCDS3253.1	3q27	2013-05-22	2013-05-22		ENSG00000161202	ENSG00000161202		"Dishevelled homologs"	3087	protein-coding gene	gene with protein product		601368	"dishevelled 3 (homologous to Drosophila dsh)", "dishevelled, dsh homolog 3 (Drosophila)"			8817329	Standard	NM_004423		Approved	KIAA0208	uc003fms.3	Q92997	OTTHUMG00000156841	ENST00000313143.3:c.1536C>T	chr3.hg19:g.183887831C>T		121.0	0.0	.		112.0	48.0	.	NM_004423	B4E3E5|D3DNT0|O14642|Q13531|Q8N5E9|Q92607	Silent	SNP	ENST00000313143.3	hg19	CCDS3253.1																																																																																			.	.	.	none		0.662	DVL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346184.1	NM_004423		T	183887831	C	T	183887831	2	4	32	1	0	0	0	0	0	0	0	1	4839	581	21	2		2	DVL3	3	183887831	Silent	SNP	C	TCGA-5P-A9K0-01A-11D-A42J-10	14186831	183887831	14134599	22	2300											
VPS8	23355	hgsc.bcm.edu	37	chr3	184654055	184654055	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aactcgtgtccctgaagcctTgtaaagctgcggagctggtt	8	11	12	10	2	0	1	0	1	0	0	2	2	1	2	2	2	5	4	2	2	4	3			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr3:184654055T>C	ENST00000437079.3	+	35	3091	c.2920T>C	c.(2920-2922)Tgt>Cgt	p.C974R	VPS8_ENST00000436792.2_Missense_Mutation_p.C972R|VPS8_ENST00000287546.4_Missense_Mutation_p.C974R|VPS8_ENST00000446204.2_Missense_Mutation_p.C882R	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	974							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)			CCTGAAGCCTTGTAAAGCTGC	0.413																																					p.C974R		Atlas-SNP	.											.	VPS8	109	.	0			c.T2920C						PASS	.						63	60	61					3																	184654055		1870	4103	5973	SO:0001583	missense	23355	exon34			AAGCCTTGTAAAG	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.2920T>C	chr3.hg19:g.184654055T>C	ENSP00000397879:p.Cys974Arg	66.0	0.0	.		55.0	24.0	.	NM_001009921	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Missense_Mutation	SNP	ENST00000437079.3	hg19	CCDS46971.1	.	.	.	.	.	.	.	.	.	.	T	5.373	0.254065	0.10185	.	.	ENSG00000156931	ENST00000287546;ENST00000437079;ENST00000436792;ENST00000446204	T;T;T;T	0.15834	2.39;2.39;2.39;2.39	5.11	5.11	0.69529	Quinonprotein alcohol dehydrogenase-like (1);	0.373852	0.29225	N	0.012776	T	0.08492	0.0211	N	0.11427	0.14	0.54753	D	0.999988	B;B;B	0.21381	0.002;0.055;0.003	B;B;B	0.22753	0.002;0.041;0.004	T	0.27971	-1.0058	10	0.12766	T	0.61	-10.8263	9.6614	0.39958	0.1556:0.0:0.0:0.8444	.	974;882;972	Q8N3P4;Q8N3P4-2;Q8N3P4-3	VPS8_HUMAN;.;.	R	974;974;972;882	ENSP00000287546:C974R;ENSP00000397879:C974R;ENSP00000404704:C972R;ENSP00000405483:C882R	ENSP00000287546:C974R	C	+	1	0	VPS8	186136749	0.826000	0.29277	0.998000	0.56505	0.560000	0.35617	1.018000	0.30002	2.265000	0.75225	0.533000	0.62120	TGT	.	.	.	none		0.413	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015303		C	184654055	T	C	184654055	3	2	32	1	0	0	0	0	1	0	0	0	17230	1812	63	3	3050	3	VPS8	3	184654055	Missense_Mutation	SNP	T	TCGA-5P-A9K0-01A-11D-A42J-10	766224	184654055	13368375	23	2301											
MASP1	5648	hgsc.bcm.edu	37	chr3	186961355	186961355	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgtggtgaggttgttccttGtagagaaggtgatcagcccg	8	12	15	6	1	1	3	1	2	0	1	2	4	2	3	2	3	1	3	2	3	2	4			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr3:186961355G>A	ENST00000337774.5	-	9	1534	c.1145C>T	c.(1144-1146)aCa>aTa	p.T382I	MASP1_ENST00000296280.6_Missense_Mutation_p.T382I|MASP1_ENST00000392472.2_Missense_Mutation_p.T269I|MASP1_ENST00000495249.1_Intron	NM_001879.5	NP_001870.3	P48740	MASP1_HUMAN	mannan-binding lectin serine peptidase 1 (C4/C2 activating component of Ra-reactive factor)	382	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|negative regulation of complement activation (GO:0045916)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|peptidase activity (GO:0008233)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(27)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	60	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)		GTTGTTCCTTGTAGAGAAGGT	0.478																																					p.T382I		Atlas-SNP	.											.	MASP1	240	.	0			c.C1145T						PASS	.						237	216	223					3																	186961355		2203	4300	6503	SO:0001583	missense	5648	exon9			TTCCTTGTAGAGA	D28593	CCDS33907.1, CCDS33908.1, CCDS33909.1	3q27-q28	2014-09-17	2005-08-17		ENSG00000127241	ENSG00000127241		"Serine peptidases / Serine peptidases"	6901	protein-coding gene	gene with protein product		600521	"mannan-binding lectin serine protease 1 (C4/C2 activating component of Ra-reactive factor)"	CRARF, PRSS5		8018603, 8240317	Standard	NR_033519		Approved	MASP	uc003fri.3	P48740	OTTHUMG00000156461	ENST00000337774.5:c.1145C>T	chr3.hg19:g.186961355G>A	ENSP00000336792:p.Thr382Ile	72.0	0.0	.		69.0	23.0	.	NM_139125	A8K542|A8K6M1|B4E2L7|O95570|Q68D21|Q8IUV8|Q96RS4|Q9UF09	Missense_Mutation	SNP	ENST00000337774.5	hg19	CCDS33907.1	.	.	.	.	.	.	.	.	.	.	G	16.32	3.089268	0.55968	.	.	ENSG00000127241	ENST00000337774;ENST00000296280;ENST00000392472;ENST00000541896	T;T;T	0.64803	0.76;-0.12;-0.12	5.56	4.66	0.58398	Complement control module (2);Sushi/SCR/CCP (3);	0.308438	0.38436	N	0.001698	T	0.72078	0.3416	M	0.85462	2.755	0.80722	D	1	B;P;P	0.39964	0.139;0.697;0.48	B;P;B	0.44860	0.16;0.462;0.331	T	0.76719	-0.2856	10	0.59425	D	0.04	.	15.3089	0.74016	0.0:0.1404:0.8596:0.0	.	269;382;382	P48740-4;P48740-2;P48740	.;.;MASP1_HUMAN	I	382;382;269;269	ENSP00000336792:T382I;ENSP00000296280:T382I;ENSP00000376264:T269I	ENSP00000296280:T382I	T	-	2	0	MASP1	188444049	1.000000	0.71417	0.956000	0.39512	0.993000	0.82548	4.068000	0.57534	1.311000	0.45024	0.561000	0.74099	ACA	.	.	.	none		0.478	MASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344262.1	NM_001879		A	186961355	G	A	186961355	3	1	32	1	0	0	0	0	1	0	0	0	9329	1377	48	2	1874	2	MASP1	3	186961355	Missense_Mutation	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10	2307300	186961355	11061075	24	2302											
TFRC	7037	hgsc.bcm.edu	37	chr3	195800989	195800990	+	Frame_Shift_Ins	INS	-	-	AT																															aatagcccaagtagccaatcINSataaatcctaaagagacaaa																										TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr3:195800989_195800990insAT	ENST00000360110.4	-	4	414_415	c.245_246insAT	c.(244-246)atgfs	p.M82fs	TFRC_ENST00000420415.1_Start_Codon_Ins|RNU7-18P_ENST00000516365.1_RNA|TFRC_ENST00000540528.1_Stop_Codon_Ins|TFRC_ENST00000535031.1_Intron|TFRC_ENST00000392396.3_Frame_Shift_Ins_p.M82fs	NM_001128148.1	NP_001121620.1	P02786	TFR1_HUMAN	transferrin receptor	82					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)	AGTAGCCAATCATAAATCCTAA	0.421			T	BCL6	NHL																																p.M82fs		Atlas-Indel,Pindel	.		Dom	yes		3	3q29	7037	"transferrin receptor (p90, CD71)"		L	.	TFRC	54	.	0			c.246_247insAT						PASS	.																																			SO:0001589	frameshift_variant	7037	exon4			.	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.244_245dupAT	chr3.hg19:g.195800990_195800991dupAT	ENSP00000353224:p.Met82fs	83.0	0.0	0		73.0	20.0	0.273973	NM_001128148	D3DXB0|Q1HE24|Q59G55|Q9UCN0|Q9UCU5|Q9UDF9|Q9UK21	Frame_Shift_Ins	INS	ENST00000360110.4	hg19	CCDS3312.1																																																																																			.	.	.	none		0.421	TFRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341346.1			AT	195800990	-	AT	195800989	7	5	32	1	0	1	1	0	0	0	0	0	15824	826	29	0	2100	0	TFRC	3	195800989	Frame_Shift_Ins	INS	-	TCGA-5P-A9K0-01A-11D-A42J-10	8839634	195800989	2221441	25	2303											
LRRC66	339977	hgsc.bcm.edu	37	chr4	52861896	52861896	+	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	ggtgtggtgtgtgccccgcaGcttccatgtcatcgtagaag	6	11	14	10	2	1	1	1	0	0	1	3	1	2	1	3	2	2	3	3	2	2	2			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr4:52861896G>T	ENST00000343457.3	-	4	1298	c.1292C>A	c.(1291-1293)gCt>gAt	p.A431D		NM_001024611.1	NP_001019782.1	Q68CR7	LRC66_HUMAN	leucine rich repeat containing 66	431						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						GTGCCCCGCAGCTTCCATGTC	0.537																																					p.A431D		Atlas-SNP	.											.	LRRC66	128	.	0			c.C1292A						PASS	.						117	124	121					4																	52861896		2046	4191	6237	SO:0001583	missense	339977	exon4			CCCGCAGCTTCCA	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.1292C>A	chr4.hg19:g.52861896G>T	ENSP00000341944:p.Ala431Asp	42.0	0.0	.		55.0	26.0	.	NM_001024611		Missense_Mutation	SNP	ENST00000343457.3	hg19	CCDS43229.1	.	.	.	.	.	.	.	.	.	.	G	14.64	2.596364	0.46318	.	.	ENSG00000188993	ENST00000343457	T	0.47177	0.85	4.03	1.23	0.21249	.	0.494819	0.17140	N	0.185495	T	0.49490	0.1560	L	0.43152	1.355	0.09310	N	1	D	0.69078	0.997	P	0.59221	0.854	T	0.32481	-0.9905	10	0.72032	D	0.01	-1.8392	5.792	0.18365	0.1098:0.387:0.5031:0.0	.	431	Q68CR7	LRC66_HUMAN	D	431	ENSP00000341944:A431D	ENSP00000341944:A431D	A	-	2	0	LRRC66	52556653	0.000000	0.05858	0.015000	0.15790	0.002000	0.02628	-0.287000	0.08388	0.428000	0.26173	0.467000	0.42956	GCT	.	.	.	none		0.537	LRRC66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361473.1	NM_001024611		T	52861896	G	T	52861896	3	4	32	1	0	0	0	0	1	0	0	0	9025	971	34	4	1354	4	LRRC66	4	52861896	Missense_Mutation	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10		52861896	138292380	26	2304											
TECRL	253017	hgsc.bcm.edu	37	chr4	65274879	65274880	+	Frame_Shift_Ins	INS	-	-	T																															ccttgtttgagcatcaaataINStttcaatctcaaagtgagtc																										TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr4:65274879_65274880insT	ENST00000381210.3	-	1	300_301	c.190_191insA	c.(190-192)atafs	p.I64fs	TECRL_ENST00000507440.1_Frame_Shift_Ins_p.I64fs	NM_001010874.4	NP_001010874.2	Q5HYJ1	TECRL_HUMAN	trans-2,3-enoyl-CoA reductase-like	64					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						AGCATCAAATATTTCAATCTCA	0.347																																					p.I64fs		Atlas-Indel,Pindel	.											.	TECRL	106	.	0			c.191_192insA						PASS	.																																			SO:0001589	frameshift_variant	253017	exon1			.	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.191dupA	chr4.hg19:g.65274882_65274882dupT	ENSP00000370607:p.Ile64fs	45.0	0.0	0		38.0	15.0	0.394737	NM_001010874		Frame_Shift_Ins	INS	ENST00000381210.3	hg19	CCDS33990.1																																																																																			.	.	.	none		0.347	TECRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361705.4	NM_001010874		T	65274880	-	T	65274879	7	5	32	1	0	1	1	0	0	0	0	0	15758	449	16	0	948	0	TECRL	4	65274879	Frame_Shift_Ins	INS	-	TCGA-5P-A9K0-01A-11D-A42J-10	12412983	65274879	125879397	27	2305											
EPHA5	2044	hgsc.bcm.edu	37	chr4	66230803	66230803	+	Frame_Shift_Del	DEL	C	C	-																															gtcccatgatacttgcttcaCctaggaaatctctgcgttgc																								rs374393697		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr4:66230803delC	ENST00000273854.3	-	12	2768	c.2168delG	c.(2167-2169)ggtfs	p.G723fs	EPHA5_ENST00000354839.4_Frame_Shift_Del_p.G701fs|EPHA5_ENST00000432638.2_Frame_Shift_Del_p.G560fs|EPHA5_ENST00000511294.1_Frame_Shift_Del_p.G724fs	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	723	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						ACTTGCTTCACCTAGGAAATC	0.393										TSP Lung(17;0.13)																											p.G723fs		Atlas-INDEL	.											.	EPHA5	315	.	0			c.2169delT						PASS	.						235	224	228					4																	66230803		2203	4300	6503	SO:0001589	frameshift_variant	2044	exon12			.	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.2168delG	chr4.hg19:g.66230803delC	ENSP00000273854:p.Gly723fs	83.0	0.0	0		80.0	24.0	0.3	NM_004439	Q7Z3F2	Frame_Shift_Del	DEL	ENST00000273854.3	hg19	CCDS3513.1																																																																																			.	.	.	none		0.393	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		-	66230803	C	-	66230803	7	5	32	1	0	1	0	1	0	0	0	0	5172	507	18	0	973	0	EPHA5	4	66230803	Frame_Shift_Del	DEL	C	TCGA-5P-A9K0-01A-11D-A42J-10	955924	66230803	124923473	28	2306	27	3									
EPHA5	2044	hgsc.bcm.edu	37	chr4	66230804	66230806	+	In_Frame_Del	DEL	CTA	CTA	-																															tcccatgatacttgcttcacCtaggaaatctctgcgttgct																										TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	CTA	CTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr4:66230804_66230806delCTA	ENST00000273854.3	-	12	2765_2767	c.2165_2167delTAG	c.(2164-2169)ctaggt>cgt	p.722_723LG>R	EPHA5_ENST00000354839.4_In_Frame_Del_p.700_701LG>R|EPHA5_ENST00000432638.2_In_Frame_Del_p.559_560LG>R|EPHA5_ENST00000511294.1_In_Frame_Del_p.723_724LG>R	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	722	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						CTTGCTTCACCTAGGAAATCTCT	0.389										TSP Lung(17;0.13)																											p.722_723del		Pindel	.											.	EPHA5	315	.	0			c.2166_2168del						PASS	.																																			SO:0001651	inframe_deletion	2044	exon12			.	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.2165_2167delTAG	chr4.hg19:g.66230804_66230806delCTA	ENSP00000273854:p.Leu722_Gly723delinsArg	83.0	0.0	.		81.0	21.0	0.259	NM_004439	Q7Z3F2	In_Frame_Del	DEL	ENST00000273854.3	hg19	CCDS3513.1																																																																																			.	.	.	none		0.389	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		-	66230806	CTA	-	66230804	7	5	32	1	0	1	0	1	0	0	0	0	5172	681	24	0	974	0	EPHA5	4	66230804	In_Frame_Del	DEL	CTA	TCGA-5P-A9K0-01A-11D-A42J-10	1	66230804	124923472	29	2307	27	3									
EPHA5	2044	hgsc.bcm.edu	37	chr4	66230806	66230806	+	Missense_Mutation	SNP	A	A	T																															ccatgatacttgcttcacctAggaaatctctgcgttgcttt																										TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr4:66230806A>T	ENST00000273854.3	-	12	2765	c.2165T>A	c.(2164-2166)cTa>cAa	p.L722Q	EPHA5_ENST00000354839.4_Missense_Mutation_p.L700Q|EPHA5_ENST00000432638.2_Missense_Mutation_p.L559Q|EPHA5_ENST00000511294.1_Missense_Mutation_p.L723Q	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	722	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						TGCTTCACCTAGGAAATCTCT	0.388										TSP Lung(17;0.13)																											p.L722Q		Atlas-SNP	.											.	EPHA5	315	.	0			c.T2165A						PASS	.						231	221	224					4																	66230806		2203	4300	6503	SO:0001583	missense	2044	exon12			TCACCTAGGAAAT	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.2165T>A	chr4.hg19:g.66230806A>T	ENSP00000273854:p.Leu722Gln	83.0	0.0	.		81.0	25.0	.	NM_004439	Q7Z3F2	Missense_Mutation	SNP	ENST00000273854.3	hg19	CCDS3513.1	.	.	.	.	.	.	.	.	.	.	A	25.7	4.663442	0.88251	.	.	ENSG00000145242	ENST00000273854;ENST00000432638;ENST00000354839;ENST00000511294	D;D;D;D	0.84223	-1.82;-1.82;-1.82;-1.82	5.76	5.76	0.90799	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.45126	D	0.000384	D	0.91891	0.7433	M	0.75264	2.295	0.58432	D	0.999999	D;D;D;D	0.89917	0.993;1.0;0.992;0.998	D;D;D;D	0.72625	0.95;0.978;0.917;0.935	D	0.92786	0.6244	10	0.87932	D	0	.	16.0723	0.80943	1.0:0.0:0.0:0.0	.	701;723;700;722	B7ZKW7;B7ZKJ3;P54756-2;P54756	.;.;.;EPHA5_HUMAN	Q	722;559;700;723	ENSP00000273854:L722Q;ENSP00000389208:L559Q;ENSP00000346899:L700Q;ENSP00000427638:L723Q	ENSP00000273854:L722Q	L	-	2	0	EPHA5	65913401	1.000000	0.71417	0.992000	0.48379	0.953000	0.61014	9.297000	0.96120	2.199000	0.70637	0.528000	0.53228	CTA	.	.	.	none		0.388	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		T	66230806	A	T	66230806	3	4	32	1	0	0	0	0	1	0	0	0	5172	420	15	5	976	5	EPHA5	4	66230806	Missense_Mutation	SNP	A	TCGA-5P-A9K0-01A-11D-A42J-10	2	66230806	124923470	30	2308	27	3									
SLC9A3	6550	hgsc.bcm.edu	37	chr5	483552	483552	+	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	gtggccgactgctccgagatGttggccttcacatacttctg	6	12	11	12	2	2	1	1	0	1	1	3	3	3	1	3	2	2	2	3	2	1	4			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr5:483552G>A	ENST00000264938.3	-	6	987	c.978C>T	c.(976-978)aaC>aaT	p.N326N	CTD-2228K2.7_ENST00000606288.1_RNA|SLC9A3_ENST00000514375.1_Silent_p.N326N|CTD-2228K2.7_ENST00000607286.1_RNA	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	326					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)			GCTCCGAGATGTTGGCCTTCA	0.622																																					p.N326N		Atlas-SNP	.											.	SLC9A3	89	.	0			c.C978T						PASS	.						47	34	38					5																	483552		2195	4296	6491	SO:0001819	synonymous_variant	6550	exon6			CGAGATGTTGGCC		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.978C>T	chr5.hg19:g.483552G>A		147.0	0.0	.		119.0	36.0	.	NM_004174	B7ZKR2|E9PF67|Q3MIW3	Silent	SNP	ENST00000264938.3	hg19	CCDS3855.1																																																																																			.	.	.	none		0.622	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174		A	483552	G	A	483552	2	1	32	1	0	0	0	0	0	0	0	1	14726	1368	48	2		2	SLC9A3	5	483552	Silent	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10		483552	180431708	31	2309											
C5orf42	65250	hgsc.bcm.edu	37	chr5	37226992	37226993	+	Missense_Mutation	DNP	GT	GT	TC																															acttttctggatagaatgcaGttctgtaatggttctatctg																										TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G|T	G|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr5:37226992_37226993GT>TC	ENST00000508244.1	-	11	1797_1798	c.1704_1705AC>GA	c.(1702-1707)gaACtg>gaGAtg	p.L569M	C5orf42_ENST00000274258.7_De_novo_Start_InFrame|C5orf42_ENST00000425232.2_Missense_Mutation_p.L569M			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	569						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)			ATAGAATGCAGTTCTGTAATGG	0.337																																					p.L569M|p.E568E		Atlas-SNP	.											.	C5orf42	422	.	0			c.C1705A|c.A1704G						PASS	.																																			SO:0001583	missense	65250	exon12			AATGCAGTTCTGT|ATGCAGTTCTGTA		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.1704_1705delinsTC	chr5.hg19:g.37226992_37226993delinsTC	ENSP00000421690:p.Leu569Met	132.0	0.0	.		102.0|101.0	45.0|44.0	.	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation|Silent	SNP	ENST00000508244.1	hg19	CCDS34146.2																																																																																			.	.	.	none		0.337	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		TC	37226993	GT	TC	37226992	3	4	32	1	0	0	0	0	1	0	0	0	2303	1020	36	4	8052	4	C5orf42	5	37226992	Missense_Mutation	DNP	GT	TCGA-5P-A9K0-01A-11D-A42J-10	36743440	37226992	143688268	32	2310											
ANKRD55	79722	hgsc.bcm.edu	37	chr5	55439741	55439741	+	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	gttgtggaaagccgcccagtGgagtggtgtcattccctgca	7	10	14	10	1	1	0	1	0	0	0	2	2	2	2	3	3	2	2	3	3	1	2			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr5:55439741G>A	ENST00000341048.4	-	7	650	c.499C>T	c.(499-501)Cac>Tac	p.H167Y	ANKRD55_ENST00000504958.2_Intron|ANKRD55_ENST00000513241.2_Missense_Mutation_p.H138Y|RNA5SP184_ENST00000411071.1_RNA|ANKRD55_ENST00000505970.2_5'UTR	NM_024669.2	NP_078945.2	Q3KP44	ANR55_HUMAN	ankyrin repeat domain 55	167										breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(1)	34		Lung NSC(810;8.69e-05)|Prostate(74;0.00634)|Breast(144;0.0334)|Ovarian(174;0.223)				GCCGCCCAGTGGAGTGGTGTC	0.532																																					p.H167Y		Atlas-SNP	.											.	ANKRD55	70	.	0			c.C499T						PASS	.						220	219	219					5																	55439741		2203	4300	6503	SO:0001583	missense	79722	exon7			CCCAGTGGAGTGG	AK021857	CCDS34161.1	5q11.2	2013-01-10			ENSG00000164512	ENSG00000164512		"Ankyrin repeat domain containing"	25681	protein-coding gene	gene with protein product		615189					Standard	XM_005248599		Approved	FLJ11795	uc003jqu.3	Q3KP44	OTTHUMG00000162305	ENST00000341048.4:c.499C>T	chr5.hg19:g.55439741G>A	ENSP00000342295:p.His167Tyr	57.0	0.0	.		33.0	14.0	.	NM_024669	B3KVT8|Q3KP45|Q9HAD3	Missense_Mutation	SNP	ENST00000341048.4	hg19	CCDS34161.1	.	.	.	.	.	.	.	.	.	.	G	19.01	3.743502	0.69418	.	.	ENSG00000164512	ENST00000507283;ENST00000341048;ENST00000513241	D;D	0.87179	-2.22;-2.22	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	D	0.94128	0.8117	M	0.84948	2.725	0.58432	D	0.999992	D	0.89917	1.0	D	0.87578	0.998	D	0.93582	0.6913	10	0.41790	T	0.15	.	18.7597	0.91845	0.0:0.0:1.0:0.0	.	167	B3KVT8	.	Y	167;167;138	ENSP00000342295:H167Y;ENSP00000423507:H138Y	ENSP00000342295:H167Y	H	-	1	0	ANKRD55	55475498	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.934000	0.87649	2.518000	0.84900	0.650000	0.86243	CAC	.	.	.	none		0.532	ANKRD55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368510.4	NM_024669		A	55439741	G	A	55439741	3	1	32	1	0	0	0	0	1	0	0	0	681	1348	47	2	1369	2	ANKRD55	5	55439741	Missense_Mutation	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10	18212749	55439741	125475519	33	2311											
CDC23	8697	hgsc.bcm.edu	37	chr5	137527594	137527594	+	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	tgagtttctcgtaacattctCctaaagcaaccagcatgcga	12	11	7	11	2	2	1	0	1	2	0	4	2	2	1	2	0	5	4	2	0	4	4			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr5:137527594C>G	ENST00000394886.2	-	12	1349	c.1319G>C	c.(1318-1320)gGa>gCa	p.G440A		NM_004661.3	NP_004652.2	Q9UJX2	CDC23_HUMAN	cell division cycle 23	440					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)			GTAACATTCTCCTAAAGCAAC	0.408																																					p.G440A		Atlas-SNP	.											.	CDC23	46	.	0			c.G1319C						PASS	.						121	120	120					5																	137527594		2203	4300	6503	SO:0001583	missense	8697	exon12			CATTCTCCTAAAG	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.1319G>C	chr5.hg19:g.137527594C>G	ENSP00000378350:p.Gly440Ala	110.0	0.0	.		111.0	39.0	.	NM_004661	A8K6E5|B4E3A2|B7WP05|D3DQB7|O75433|Q53FN2|Q9BS73	Missense_Mutation	SNP	ENST00000394886.2	hg19	CCDS4200.2	.	.	.	.	.	.	.	.	.	.	C	24.7	4.563709	0.86335	.	.	ENSG00000094880	ENST00000394886	T	0.79653	-1.29	5.9	5.9	0.94986	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	D	0.89167	0.6638	M	0.72353	2.195	0.80722	D	1	D	0.55800	0.973	D	0.67382	0.951	D	0.86877	0.2039	10	0.38643	T	0.18	-13.154	20.275	0.98485	0.0:1.0:0.0:0.0	.	440	Q9UJX2	CDC23_HUMAN	A	440	ENSP00000378350:G440A	ENSP00000378350:G440A	G	-	2	0	CDC23	137555493	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.711000	0.68400	2.800000	0.96347	0.455000	0.32223	GGA	.	.	.	none		0.408	CDC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251275.2			G	137527594	C	G	137527594	3	3	32	1	0	0	0	0	1	0	0	0	3063	855	30	4	494	4	CDC23	5	137527594	Missense_Mutation	SNP	C	TCGA-5P-A9K0-01A-11D-A42J-10	82087853	137527594	43387666	34	2312											
C6orf145	221749	hgsc.bcm.edu	37	chr6	3723879	3723879	+	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	ccaaatgtctgtctcgaaggGgaccaggtggtaatatgaca	12	9	12	8	1	2	1	0	1	2	0	3	3	2	2	2	4	0	1	2	4	4	2			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr6:3723879G>T	ENST00000380283.4	-	5	1164	c.670C>A	c.(670-672)Ccc>Acc	p.P224T	PXDC1_ENST00000477592.2_5'UTR	NM_183373.3	NP_899229.2	Q5TGL8	PXDC1_HUMAN	PX domain containing 1	224							phosphatidylinositol binding (GO:0035091)										GTCTCGAAGGGGACCAGGTGG	0.557																																					p.P224T		Atlas-SNP	.											.	.	.	.	0			c.C670A						PASS	.						180	151	161					6																	3723879		2203	4300	6503	SO:0001583	missense	221749	exon5			CGAAGGGGACCAG	AJ420534	CCDS4486.1	6p25.1	2011-11-25	2011-11-25	2011-11-25	ENSG00000168994	ENSG00000168994			21361	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 145"	C6orf145			Standard	NM_183373		Approved		uc003mvt.2	Q5TGL8	OTTHUMG00000014146	ENST00000380283.4:c.670C>A	chr6.hg19:g.3723879G>T	ENSP00000369636:p.Pro224Thr	80.0	0.0	.		97.0	40.0	.	NM_183373	A8K0N3|Q6PGP0|Q86XB7	Missense_Mutation	SNP	ENST00000380283.4	hg19	CCDS4486.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.687792	0.88639	.	.	ENSG00000168994	ENST00000380283	T	0.50001	0.76	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.66406	0.2786	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.69423	-0.5149	9	0.72032	D	0.01	-31.499	18.5146	0.90931	0.0:0.0:1.0:0.0	.	224	Q5TGL8	CF145_HUMAN	T	224	ENSP00000369636:P224T	ENSP00000369636:P224T	P	-	1	0	C6orf145	3668878	1.000000	0.71417	0.898000	0.35279	0.956000	0.61745	8.431000	0.90285	2.662000	0.90505	0.555000	0.69702	CCC	.	.	.	none		0.557	PXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039688.1	NM_183373		T	3723879	G	T	3723879	3	4	32	1	0	0	0	0	1	0	0	0	2336	1232	43	4	29	4	C6orf145	6	3723879	Missense_Mutation	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10		3723879	167391188	35	2313											
NHLRC1	378884	hgsc.bcm.edu	37	chr6	18121925	18121925	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaaaggtatccacttggcCgacaagctgcatacttgagc	11	8	9	13	1	0	1	0	1	0	0	1	2	1	1	3	2	4	3	3	2	4	4			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr6:18121925C>T	ENST00000340650.3	-	1	926	c.913G>A	c.(913-915)Ggc>Agc	p.G305S		NM_198586.2	NP_940988.2	Q6VVB1	NHLC1_HUMAN	NHL repeat containing E3 ubiquitin protein ligase 1	305					autophagy (GO:0006914)|carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|positive regulation of protein ubiquitination (GO:0031398)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(3)|lung(3)|skin(1)|urinary_tract(2)	11	Ovarian(93;0.016)|Breast(50;0.0245)	all_hematologic(90;0.165)	all cancers(50;0.0451)|Epithelial(50;0.0493)			TCCACTTGGCCGACAAGCTGC	0.557																																					p.G305S		Atlas-SNP	.											.	NHLRC1	42	.	0			c.G913A						PASS	.						67	64	65					6																	18121925		2203	4300	6503	SO:0001583	missense	378884	exon1			CTTGGCCGACAAG	AY324849	CCDS4542.1	6p22.3	2014-01-28	2013-12-12		ENSG00000187566	ENSG00000187566			21576	protein-coding gene	gene with protein product	"epilepsy, progressive myoclonus type 2B"	608072	"NHL repeat containing 1"			12958597	Standard	NM_198586		Approved	bA204B7.2, EPM2B, malin	uc003ncl.1	Q6VVB1	OTTHUMG00000014315	ENST00000340650.3:c.913G>A	chr6.hg19:g.18121925C>T	ENSP00000345464:p.Gly305Ser	52.0	0.0	.		49.0	21.0	.	NM_198586	Q3SYB1|Q5VUK7|Q6IMH1	Missense_Mutation	SNP	ENST00000340650.3	hg19	CCDS4542.1	.	.	.	.	.	.	.	.	.	.	C	1.321	-0.599467	0.03744	.	.	ENSG00000187566	ENST00000340650	D	0.97114	-4.25	5.67	0.632	0.17705	Six-bladed beta-propeller, TolB-like (1);	0.324151	0.34088	N	0.004275	D	0.89567	0.6752	M	0.71581	2.175	0.24490	N	0.994308	B	0.20671	0.047	B	0.13407	0.009	T	0.80946	-0.1155	10	0.22109	T	0.4	-14.9657	5.8977	0.18949	0.0:0.5163:0.1219:0.3618	.	305	Q6VVB1	NHLC1_HUMAN	S	305	ENSP00000345464:G305S	ENSP00000345464:G305S	G	-	1	0	NHLRC1	18229904	0.001000	0.12720	0.219000	0.23793	0.057000	0.15508	-0.025000	0.12413	-0.195000	0.10382	-0.794000	0.03295	GGC	.	.	.	none		0.557	NHLRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039958.1			T	18121925	C	T	18121925	3	4	32	1	0	0	0	0	1	0	0	0	10412	652	23	1	278	1	NHLRC1	6	18121925	Missense_Mutation	SNP	C	TCGA-5P-A9K0-01A-11D-A42J-10	14398046	18121925	152993142	36	2314											
ABT1	29777	hgsc.bcm.edu	37	chr6	26597296	26597296	+	Missense_Mutation	SNP	A	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	actagatgcggaggaggagcAggaggaatccgaagaagcgg	14	3	18	6	3	0	2	0	0	0	2	1	8	1	7	1	6	3	1	1	6	4	1			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr6:26597296A>C	ENST00000274849.1	+	1	117	c.86A>C	c.(85-87)cAg>cCg	p.Q29P		NM_013375.3	NP_037507.1	Q9ULW3	ABT1_HUMAN	activator of basal transcription 1	29					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						GAGGAGGAGCAGGAGGAATCC	0.607																																					p.Q29P		Atlas-SNP	.											.	ABT1	39	.	0			c.A86C						PASS	.						75	84	81					6																	26597296		2203	4300	6503	SO:0001583	missense	29777	exon1			AGGAGCAGGAGGA	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.86A>C	chr6.hg19:g.26597296A>C	ENSP00000274849:p.Gln29Pro	148.0	0.0	.		134.0	57.0	.	NM_013375		Missense_Mutation	SNP	ENST00000274849.1	hg19	CCDS4616.1	.	.	.	.	.	.	.	.	.	.	A	14.05	2.421177	0.42918	.	.	ENSG00000146109	ENST00000274849	.	.	.	4.27	3.09	0.35607	.	0.579965	0.17698	N	0.165036	T	0.11537	0.0281	N	0.25647	0.755	0.24539	N	0.994079	B	0.02656	0.0	B	0.01281	0.0	T	0.21008	-1.0258	9	0.29301	T	0.29	-11.7293	8.6559	0.34062	0.6171:0.3829:0.0:0.0	.	29	Q9ULW3	ABT1_HUMAN	P	29	.	ENSP00000274849:Q29P	Q	+	2	0	ABT1	26705275	0.002000	0.14202	0.989000	0.46669	0.697000	0.40408	-0.309000	0.08145	0.959000	0.37980	-0.313000	0.08912	CAG	.	.	.	none		0.607	ABT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043698.1			C	26597296	A	C	26597296	3	2	32	1	0	0	0	0	1	0	0	0	101	188	7	5	88	5	ABT1	6	26597296	Missense_Mutation	SNP	A	TCGA-5P-A9K0-01A-11D-A42J-10	8475371	26597296	144517771	37	2315											
PGC	5225	hgsc.bcm.edu	37	chr6	41704737	41704737	+	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	actcccacggtgcagtagccGttgttctgctcaacaaagaa	11	9	9	12	2	2	1	1	0	1	1	3	1	3	1	2	1	4	5	2	1	4	3			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr6:41704737G>A	ENST00000373025.3	-	9	1082	c.1020C>T	c.(1018-1020)aaC>aaT	p.N340N	RP11-298J23.5_ENST00000438967.1_RNA|TFEB_ENST00000230323.4_5'Flank|TFEB_ENST00000420312.1_5'Flank|TFEB_ENST00000373033.1_5'Flank|TFEB_ENST00000358871.2_5'Flank|TFEB_ENST00000403298.4_5'Flank	NM_002630.3	NP_002621.1	P20142	PEPC_HUMAN	progastricsin (pepsinogen C)	340					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)			TGCAGTAGCCGTTGTTCTGCT	0.587																																					p.N340N		Atlas-SNP	.											.	PGC	56	.	0			c.C1020T						PASS	.						53	52	52					6																	41704737		2203	4300	6503	SO:0001819	synonymous_variant	5225	exon9			GTAGCCGTTGTTC		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.1020C>T	chr6.hg19:g.41704737G>A		76.0	0.0	.		65.0	21.0	.	NM_002630	B4DVZ3|Q5T3D7|Q5T3D8	Silent	SNP	ENST00000373025.3	hg19	CCDS4859.1																																																																																			.	.	.	none		0.587	PGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040521.2			A	41704737	G	A	41704737	2	1	32	1	0	0	0	0	0	0	0	1	11792	1136	40	1		1	PGC	6	41704737	Silent	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10	15107441	41704737	129410330	38	2316											
FAM184A	79632	hgsc.bcm.edu	37	chr6	119345322	119345322	+	Frame_Shift_Del	DEL	A	A	-																															gcctgtaggctttctgctgtAaaaagctgtgaccttttcaa																										TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr6:119345322delA	ENST00000338891.7	-	2	1259	c.816delT	c.(814-816)tttfs	p.F272fs	FAM184A_ENST00000368475.4_Frame_Shift_Del_p.F152fs|FAM184A_ENST00000352896.5_Frame_Shift_Del_p.F152fs|FAM184A_ENST00000522284.1_Frame_Shift_Del_p.F152fs|RP11-351A11.1_ENST00000518570.1_RNA|FAM184A_ENST00000521531.1_Frame_Shift_Del_p.F272fs	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	272						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						TTTCTGCTGTAAAAAGCTGTG	0.358																																					p.T273fs		Atlas-Indel,Pindel	.											.	FAM184A	109	.	0			c.817delA						PASS	.						85	79	81					6																	119345322		1824	4081	5905	SO:0001589	frameshift_variant	79632	exon2			.	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.816delT	chr6.hg19:g.119345322delA	ENSP00000342604:p.Phe272fs	70.0	0.0	0		87.0	30.0	0.344828	NM_024581	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Frame_Shift_Del	DEL	ENST00000338891.7	hg19	CCDS43499.1																																																																																			.	.	.	none		0.358	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		-	119345322	A	-	119345322	7	5	32	1	0	1	0	1	0	0	0	0	5515	359	13	0	2674	0	FAM184A	6	119345322	Frame_Shift_Del	DEL	A	TCGA-5P-A9K0-01A-11D-A42J-10	77640585	119345322	51769745	39	2317											
HEBP2	23593	hgsc.bcm.edu	37	chr6	138727155	138727155	+	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	tgacaagctacgtggagcctGgttcaggtccttttagtgag	8	12	13	8	1	1	2	1	2	0	0	2	3	2	3	2	3	3	2	2	3	3	4			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr6:138727155G>T	ENST00000607197.1	+	3	563	c.286G>T	c.(286-288)Ggt>Tgt	p.G96C	HEBP2_ENST00000448741.1_Missense_Mutation_p.G107C|HEBP2_ENST00000367697.3_Missense_Mutation_p.G96C	NM_014320.2	NP_055135.1	Q9Y5Z4	HEBP2_HUMAN	heme binding protein 2	96					negative regulation of mitochondrial membrane potential (GO:0010917)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of necrotic cell death (GO:0010940)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|lung(3)	5	Breast(32;0.0933)			GBM - Glioblastoma multiforme(68;0.000732)|OV - Ovarian serous cystadenocarcinoma(155;0.00171)		CGTGGAGCCTGGTTCAGGTCC	0.393																																					p.G96C		Atlas-SNP	.											HEBP2,NS,malignant_melanoma,0,1	HEBP2	12	.	0			c.G286T						PASS	.						136	126	129					6																	138727155		2203	4300	6503	SO:0001583	missense	23593	exon3			GAGCCTGGTTCAG	AF117616	CCDS5191.1	6q24	2008-08-29	2002-09-23	2002-09-27	ENSG00000051620	ENSG00000051620			15716	protein-coding gene	gene with protein product		605825	"chromosome 6 open reading frame 34"	C6orf34		10640688, 17098234	Standard	NM_014320		Approved	SOUL	uc003qhw.1	Q9Y5Z4	OTTHUMG00000015671	ENST00000607197.1:c.286G>T	chr6.hg19:g.138727155G>T	ENSP00000475750:p.Gly96Cys	124.0	0.0	.		111.0	36.0	.	NM_014320	Q96P57	Missense_Mutation	SNP	ENST00000607197.1	hg19	CCDS5191.1	.	.	.	.	.	.	.	.	.	.	G	10.22	1.291247	0.23564	.	.	ENSG00000051620	ENST00000448741;ENST00000058691;ENST00000367697	T;T;T	0.22539	1.95;1.95;1.95	5.55	5.55	0.83447	Regulatory factor, effector, bacterial (1);	0.142267	0.64402	D	0.000005	T	0.44685	0.1305	M	0.86268	2.805	0.54753	D	0.999988	D	0.89917	1.0	D	0.97110	1.0	T	0.46512	-0.9186	10	0.56958	D	0.05	.	16.3966	0.83607	0.0:0.0:1.0:0.0	.	96	Q9Y5Z4	HEBP2_HUMAN	C	107;96;96	ENSP00000392101:G107C;ENSP00000058691:G96C;ENSP00000356670:G96C	ENSP00000058691:G96C	G	+	1	0	HEBP2	138768848	1.000000	0.71417	0.140000	0.22221	0.541000	0.35023	6.709000	0.74665	2.615000	0.88500	0.491000	0.48974	GGT	.	.	.	none		0.393	HEBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042426.2			T	138727155	G	T	138727155	3	4	32	1	0	0	0	0	1	0	0	0	7044	1348	47	4	296	4	HEBP2	6	138727155	Missense_Mutation	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10	19381833	138727155	32387912	40	2318											
IQCE	23288	hgsc.bcm.edu	37	chr7	2617955	2617955	+	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	ggaggaaaacagcaggaaggAccggcagatagagcagctcc	15	2	15	9	1	0	2	0	0	0	2	1	6	1	6	2	5	4	4	2	5	4	1			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr7:2617955A>T	ENST00000402050.2	+	7	729	c.545A>T	c.(544-546)gAc>gTc	p.D182V	IQCE_ENST00000438376.2_Missense_Mutation_p.D166V|IQCE_ENST00000404984.1_Missense_Mutation_p.D131V|IQCE_ENST00000325979.7_Missense_Mutation_p.D117V	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	182						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)		AGCAGGAAGGACCGGCAGATA	0.622																																					p.D182V		Atlas-SNP	.											.	IQCE	66	.	0			c.A545T						PASS	.						59	68	65					7																	2617955		2086	4217	6303	SO:0001583	missense	23288	exon7			GGAAGGACCGGCA	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.545A>T	chr7.hg19:g.2617955A>T	ENSP00000385597:p.Asp182Val	65.0	0.0	.		82.0	40.0	.	NM_152558	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Missense_Mutation	SNP	ENST00000402050.2	hg19	CCDS43542.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.107831	0.77096	.	.	ENSG00000106012	ENST00000402050;ENST00000404984;ENST00000415271;ENST00000438376;ENST00000325979;ENST00000423395;ENST00000422276	T;T;T;T;T;T	0.10960	2.82;2.82;2.82;2.82;2.82;2.82	5.5	4.33	0.51752	.	0.050251	0.85682	D	0.000000	T	0.30823	0.0777	M	0.75264	2.295	0.58432	D	0.999997	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;0.999;1.0;0.997;0.999;0.999	T	0.01488	-1.1342	10	0.52906	T	0.07	-18.5907	11.0308	0.47772	0.8605:0.0:0.0:0.1395	.	117;166;117;182;182;166	B4DXN1;B4DDX4;Q6IPM2-2;Q6IPM2;B3KRY4;Q6IPM2-4	.;.;.;IQCE_HUMAN;.;.	V	182;131;218;166;117;117;117	ENSP00000385597:D182V;ENSP00000385945:D131V;ENSP00000404643:D218V;ENSP00000396178:D166V;ENSP00000313772:D117V;ENSP00000413570:D117V	ENSP00000313772:D117V	D	+	2	0	IQCE	2584481	1.000000	0.71417	0.997000	0.53966	0.975000	0.68041	6.359000	0.73060	0.893000	0.36288	0.460000	0.39030	GAC	.	.	.	none		0.622	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558		T	2617955	A	T	2617955	3	4	32	1	0	0	0	0	1	0	0	0	7813	275	10	5	571	5	IQCE	7	2617955	Missense_Mutation	SNP	A	TCGA-5P-A9K0-01A-11D-A42J-10		2617955	156520708	41	2319											
KIAA1429	25962	hgsc.bcm.edu	37	chr8	95539042	95539042	+	Missense_Mutation	SNP	A	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	tgatcactcctgcttgtagcAgtcctgtaactccttgagcc	7	13	8	13	0	1	2	1	2	0	0	4	2	4	2	4	0	4	4	4	0	2	4			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr8:95539042A>C	ENST00000297591.5	-	8	1505	c.1430T>G	c.(1429-1431)cTg>cGg	p.L477R	KIAA1429_ENST00000437199.1_Missense_Mutation_p.L477R|KIAA1429_ENST00000421249.2_Missense_Mutation_p.L477R	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	477					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			TGCTTGTAGCAGTCCTGTAAC	0.443																																					p.L477R		Atlas-SNP	.											.	KIAA1429	176	.	0			c.T1430G						PASS	.						98	96	96					8																	95539042		2203	4300	6503	SO:0001583	missense	25962	exon8			TGTAGCAGTCCTG	AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 121"					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.1430T>G	chr8.hg19:g.95539042A>C	ENSP00000297591:p.Leu477Arg	54.0	0.0	.		62.0	22.0	.	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Missense_Mutation	SNP	ENST00000297591.5	hg19	CCDS34923.1	.	.	.	.	.	.	.	.	.	.	A	15.11	2.736385	0.49045	.	.	ENSG00000164944	ENST00000297591;ENST00000437199;ENST00000421249	T;T;T	0.57595	0.4;0.41;0.39	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.70780	0.3263	M	0.62723	1.935	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.85130	0.997;0.997	T	0.73600	-0.3931	10	0.87932	D	0	-6.7927	16.2285	0.82315	1.0:0.0:0.0:0.0	.	477;477	Q69YN4-4;Q69YN4	.;VIR_HUMAN	R	477	ENSP00000297591:L477R;ENSP00000395600:L477R;ENSP00000398390:L477R	ENSP00000297591:L477R	L	-	2	0	KIAA1429	95608218	1.000000	0.71417	0.930000	0.37139	0.300000	0.27592	8.962000	0.93254	2.235000	0.73313	0.460000	0.39030	CTG	.	.	.	none		0.443	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496		C	95539042	A	C	95539042	3	2	32	1	0	0	0	0	1	0	0	0	8238	188	7	5	4130	5	KIAA1429	8	95539042	Missense_Mutation	SNP	A	TCGA-5P-A9K0-01A-11D-A42J-10		95539042	50824980	42	2320											
C9orf93	203238	hgsc.bcm.edu	37	chr9	15666301	15666301	+	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	gaaaagcataatgcacaagaGagctttgcaaaactaaattt	19	9	7	6	0	0	1	0	0	0	1	0	3	0	1	0	0	5	4	0	0	8	4			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr9:15666301G>C	ENST00000380701.3	+	9	1384	c.1056G>C	c.(1054-1056)gaG>gaC	p.E352D	CCDC171_ENST00000297641.3_Missense_Mutation_p.E352D	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	352	Glu-rich.																ATGCACAAGAGAGCTTTGCAA	0.294																																					p.E352D		Atlas-SNP	.											.	.	.	.	0			c.G1056C						PASS	.						51	52	52					9																	15666301		2203	4300	6503	SO:0001583	missense	203238	exon9			ACAAGAGAGCTTT	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.1056G>C	chr9.hg19:g.15666301G>C	ENSP00000370077:p.Glu352Asp	75.0	0.0	.		43.0	18.0	.	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Missense_Mutation	SNP	ENST00000380701.3	hg19	CCDS6481.1	.	.	.	.	.	.	.	.	.	.	G	17.57	3.421902	0.62622	.	.	ENSG00000164989	ENST00000297641;ENST00000380701	T;T	0.14893	2.47;2.47	4.98	4.08	0.47627	.	0.323937	0.32357	N	0.006202	T	0.22898	0.0553	L	0.27053	0.805	0.80722	D	1	D;D;D	0.64830	0.994;0.994;0.99	P;P;P	0.60789	0.879;0.831;0.717	T	0.02226	-1.1192	10	0.21540	T	0.41	-13.6304	13.1746	0.59619	0.0778:0.0:0.9222:0.0	.	352;352;352	B7ZM22;Q6TFL3-3;Q6TFL3	.;.;CI093_HUMAN	D	352	ENSP00000297641:E352D;ENSP00000370077:E352D	ENSP00000297641:E352D	E	+	3	2	C9orf93	15656301	1.000000	0.71417	1.000000	0.80357	0.788000	0.44548	0.815000	0.27253	1.217000	0.43442	0.591000	0.81541	GAG	.	.	.	none		0.294	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550		C	15666301	G	C	15666301	3	2	32	1	0	0	0	0	1	0	0	0	2508	933	33	4	1086	4	C9orf93	9	15666301	Missense_Mutation	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10		15666301	125547130	43	2321											
EGFL7	51162	hgsc.bcm.edu	37	chr9	139566407	139566407	+	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	ctggtgctggccccactgcaCagcctggcctcgcaggcact	5	7	12	17	1	0	0	0	0	0	0	1	0	0	0	4	4	3	4	4	4	0	0			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr9:139566407C>A	ENST00000371699.1	+	9	1577	c.666C>A	c.(664-666)caC>caA	p.H222Q	MIR126_ENST00000362291.1_RNA|EGFL7_ENST00000406555.3_Missense_Mutation_p.H222Q|EGFL7_ENST00000308874.7_Missense_Mutation_p.H222Q|EGFL7_ENST00000371698.3_Missense_Mutation_p.H222Q|EGFL7_ENST00000492002.1_3'UTR			Q9UHF1	EGFL7_HUMAN	EGF-like-domain, multiple 7	222					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)		CCCCACTGCACAGCCTGGCCT	0.706											OREG0019619	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H222Q		Atlas-SNP	.											.	EGFL7	11	.	0			c.C666A						PASS	.						6	7	7					9																	139566407		1851	3602	5453	SO:0001583	missense	51162	exon10			ACTGCACAGCCTG	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.666C>A	chr9.hg19:g.139566407C>A	ENSP00000360764:p.His222Gln	34.0	0.0	.	1649	33.0	7.0	.	NM_016215	B3KRP0|M9VTX9|Q5M7Y5|Q5VUD5|Q96EG0	Missense_Mutation	SNP	ENST00000371699.1	hg19	CCDS7002.1	.	.	.	.	.	.	.	.	.	.	C	13.57	2.276313	0.40294	.	.	ENSG00000172889	ENST00000371699;ENST00000308874;ENST00000406555;ENST00000371698	D;D;D;D	0.83163	-1.69;-1.69;-1.69;-1.69	4.15	1.18	0.20946	.	0.475986	0.22547	N	0.058656	T	0.66597	0.2805	L	0.32530	0.975	0.31471	N	0.668321	B	0.29988	0.264	B	0.23150	0.044	T	0.57871	-0.7736	10	0.20519	T	0.43	-26.4872	4.9643	0.14082	0.0:0.5813:0.1503:0.2684	.	222	Q9UHF1	EGFL7_HUMAN	Q	222	ENSP00000360764:H222Q;ENSP00000307843:H222Q;ENSP00000385639:H222Q;ENSP00000360763:H222Q	ENSP00000307843:H222Q	H	+	3	2	EGFL7	138686228	0.647000	0.27304	1.000000	0.80357	0.832000	0.47134	-0.224000	0.09164	0.236000	0.21180	0.561000	0.74099	CAC	.	.	.	none		0.706	EGFL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055094.1	NM_016215		A	139566407	C	A	139566407	3	1	32	1	0	0	0	0	1	0	0	0	4966	477	17	4	692	4	EGFL7	9	139566407	Missense_Mutation	SNP	C	TCGA-5P-A9K0-01A-11D-A42J-10	123900106	139566407	1647024	44	2322											
C10orf27	219793	hgsc.bcm.edu	37	chr10	72534001	72534001	+	Missense_Mutation	SNP	T	T	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	tcttgcttctcttgaggaggTtcatgcacttctggaagctg	6	15	11	9	0	4	1	1	1	3	0	5	3	4	3	0	3	3	4	0	3	1	5			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr10:72534001T>G	ENST00000299290.1	-	9	1274	c.885A>C	c.(883-885)gaA>gaC	p.E295D	TBATA_ENST00000394982.2_5'Flank|TBATA_ENST00000456372.2_3'UTR	NM_152710.2	NP_689923	Q96M53	TBATA_HUMAN	thymus, brain and testes associated	295					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|nucleus (GO:0005634)											CTTGAGGAGGTTCATGCACTT	0.622																																					p.E295D		Atlas-SNP	.											.	.	.	.	0			c.A885C						PASS	.						70	67	68					10																	72534001		2203	4300	6503	SO:0001583	missense	219793	exon9			AGGAGGTTCATGC	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.885A>C	chr10.hg19:g.72534001T>G	ENSP00000299290:p.Glu295Asp	59.0	0.0	.		56.0	23.0	.	NM_152710	A4QPA8|B2RPQ2|Q5T4G2	Missense_Mutation	SNP	ENST00000299290.1	hg19	CCDS7308.1	.	.	.	.	.	.	.	.	.	.	T	8.123	0.781331	0.16120	.	.	ENSG00000166220	ENST00000299290	T	0.45668	0.89	4.19	-8.38	0.00973	.	1.349240	0.04739	N	0.422520	T	0.20210	0.0486	L	0.31207	0.915	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.002;0.002;0.002	T	0.16453	-1.0402	10	0.16420	T	0.52	-0.0633	0.5239	0.00616	0.3677:0.2095:0.2498:0.173	.	294;296;295	B7ZMN4;B7ZMN5;Q96M53	.;.;SPATL_HUMAN	D	295	ENSP00000299290:E295D	ENSP00000299290:E295D	E	-	3	2	C10orf27	72204007	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-3.090000	0.00609	-1.149000	0.02843	0.482000	0.46254	GAA	.	.	.	none		0.622	TBATA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048519.1	NM_152710		G	72534001	T	G	72534001	3	3	32	1	0	0	0	0	1	0	0	0	1602	1722	60	5	182	5	C10orf27	10	72534001	Missense_Mutation	SNP	T	TCGA-5P-A9K0-01A-11D-A42J-10		72534001	63000746	45	2323											
MINPP1	9562	hgsc.bcm.edu	37	chr10	89311958	89311958	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctaacagcgtacaattacaAaaaacaaatgcatcggaagt	19	7	6	9	2	0	0	0	0	0	0	1	1	0	1	1	1	6	2	1	1	9	3			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr10:89311958A>G	ENST00000371996.4	+	5	1228	c.1187A>G	c.(1186-1188)aAa>aGa	p.K396R	MINPP1_ENST00000536010.1_Missense_Mutation_p.K195R|MINPP1_ENST00000371994.4_3'UTR|MINPP1_ENST00000472891.1_3'UTR	NM_004897.4	NP_004888.2	Q9UNW1	MINP1_HUMAN	multiple inositol-polyphosphate phosphatase 1	396					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)		TACAATTACAAAAAACAAATG	0.433																																					p.K396R		Atlas-SNP	.											.	MINPP1	22	.	0			c.A1187G						PASS	.						132	124	127					10																	89311958		2203	4300	6503	SO:0001583	missense	9562	exon5			ATTACAAAAAACA	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.1187A>G	chr10.hg19:g.89311958A>G	ENSP00000361064:p.Lys396Arg	104.0	0.0	.		85.0	26.0	.	NM_004897	F5H683|O95172|O95286|Q59EJ2|Q9UGA3	Missense_Mutation	SNP	ENST00000371996.4	hg19	CCDS7384.1	.	.	.	.	.	.	.	.	.	.	A	8.904	0.957056	0.18507	.	.	ENSG00000107789	ENST00000371996;ENST00000546140;ENST00000536010	T;T	0.76448	-1.02;-1.02	6.08	4.94	0.65067	.	0.679605	0.15713	N	0.248324	T	0.59074	0.2167	N	0.25890	0.77	0.22866	N	0.998632	B	0.06786	0.001	B	0.14578	0.011	T	0.38779	-0.9645	10	0.15499	T	0.54	-10.4064	2.702	0.05152	0.5775:0.1255:0.0718:0.2253	.	396	Q9UNW1	MINP1_HUMAN	R	396;255;195	ENSP00000361064:K396R;ENSP00000437823:K195R	ENSP00000361064:K396R	K	+	2	0	MINPP1	89301938	0.010000	0.17322	0.995000	0.50966	0.760000	0.43138	2.185000	0.42584	2.333000	0.79357	0.482000	0.46254	AAA	.	.	.	none		0.433	MINPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049221.1			G	89311958	A	G	89311958	3	3	32	1	0	0	0	0	1	0	0	0	9595	14	1	3	1243	3	MINPP1	10	89311958	Missense_Mutation	SNP	A	TCGA-5P-A9K0-01A-11D-A42J-10	16777957	89311958	46222789	46	2324											
FAM160B1	57700	hgsc.bcm.edu	37	chr10	116615097	116615097	+	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	gaatgggaagaattcttgatCaggtaatacattttaaaata	17	13	8	3	0	2	2	1	1	1	1	2	4	2	3	0	2	1	1	0	2	8	7			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr10:116615097C>A	ENST00000369248.4	+	14	2280	c.1945C>A	c.(1945-1947)Cag>Aag	p.Q649K	FAM160B1_ENST00000369250.3_Missense_Mutation_p.Q649K	NM_020940.3	NP_065991.3	Q5W0V3	F16B1_HUMAN	family with sequence similarity 160, member B1	649										NS(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)	25						AATTCTTGATCAGGTAATACA	0.318																																					p.Q649K		Atlas-SNP	.											.	FAM160B1	107	.	0			c.C1945A						PASS	.						61	63	62					10																	116615097		2203	4300	6503	SO:0001583	missense	57700	exon14			CTTGATCAGGTAA	AB046820	CCDS31290.1, CCDS44480.1	10q26.11	2008-06-05	2008-06-05	2008-06-05	ENSG00000151553	ENSG00000151553			29320	protein-coding gene	gene with protein product			"KIAA1600"	KIAA1600		10997877	Standard	NM_020940		Approved	bA106M7.3	uc001lcb.3	Q5W0V3	OTTHUMG00000019092	ENST00000369248.4:c.1945C>A	chr10.hg19:g.116615097C>A	ENSP00000358251:p.Gln649Lys	53.0	0.0	.		37.0	11.0	.	NM_020940	Q5H9P7|Q5W0V2|Q8IY76|Q9HCH2	Missense_Mutation	SNP	ENST00000369248.4	hg19	CCDS31290.1	.	.	.	.	.	.	.	.	.	.	C	33	5.231626	0.95207	.	.	ENSG00000151553	ENST00000369248;ENST00000369250	T;T	0.62498	0.02;0.02	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.79482	0.4453	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	0.74318	-0.3704	10	0.26408	T	0.33	-21.742	20.1076	0.97898	0.0:1.0:0.0:0.0	.	649;649	Q5W0V3-2;Q5W0V3	.;F16B1_HUMAN	K	649	ENSP00000358251:Q649K;ENSP00000358253:Q649K	ENSP00000358251:Q649K	Q	+	1	0	FAM160B1	116605087	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.612000	0.82975	2.823000	0.97156	0.650000	0.86243	CAG	.	.	.	none		0.318	FAM160B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050499.1	XM_049351		A	116615097	C	A	116615097	3	1	32	1	0	0	0	0	1	0	0	0	5474	827	29	4	1999	4	FAM160B1	10	116615097	Missense_Mutation	SNP	C	TCGA-5P-A9K0-01A-11D-A42J-10	27303139	116615097	18919650	47	2325											
NANOS1	340719	hgsc.bcm.edu	37	chr10	120789990	120789990	+	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	caacaaggaggcgatggcgcTctacaccacccatatcctca	12	6	8	15	2	2	0	1	0	1	0	3	2	3	1	3	3	2	1	3	3	4	2	rs137998752		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr10:120789990T>A	ENST00000425699.1	+	1	763	c.677T>A	c.(676-678)cTc>cAc	p.L226H		NM_199461.2	NP_955631.1	Q8WY41	NANO1_HUMAN	nanos homolog 1 (Drosophila)	226					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)			lung(1)	1		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0193)		GCGATGGCGCTCTACACCACC	0.721																																					p.L226H		Atlas-SNP	.											.	NANOS1	1	.	0			c.T677A						PASS	.						25	21	22					10																	120789990		2130	4209	6339	SO:0001583	missense	340719	exon1			TGGCGCTCTACAC	AF275269	CCDS7607.1	10q26.13	2003-12-01			ENSG00000188613	ENSG00000188613			23044	protein-coding gene	gene with protein product		608226				12690449	Standard	NM_199461		Approved	NOS1	uc009xzf.1	Q8WY41	OTTHUMG00000019141	ENST00000425699.1:c.677T>A	chr10.hg19:g.120789990T>A	ENSP00000393275:p.Leu226His	11.0	0.0	.		13.0	10.0	.	NM_199461		Missense_Mutation	SNP	ENST00000425699.1	hg19	CCDS7607.1	.	.	.	.	.	.	.	.	.	.	T	16.47	3.131880	0.56828	.	.	ENSG00000188613	ENST00000425699;ENST00000340087	T;T	0.46451	0.87;0.87	5.08	5.08	0.68730	Zinc finger, nanos-type (2);	0.090635	0.46145	D	0.000318	T	0.47838	0.1467	N	0.17474	0.49	0.53688	D	0.999973	D	0.65815	0.995	D	0.69824	0.966	T	0.53330	-0.8454	10	0.56958	D	0.05	-16.2297	14.4916	0.67654	0.0:0.0:0.0:1.0	.	226	Q8WY41	NANO1_HUMAN	H	226;18	ENSP00000393275:L226H;ENSP00000345924:L18H	ENSP00000345924:L18H	L	+	2	0	NANOS1	120779980	1.000000	0.71417	0.998000	0.56505	0.377000	0.30045	5.891000	0.69782	1.902000	0.55061	0.402000	0.26972	CTC	.	T|1.000;G|0.000	.	alt		0.721	NANOS1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000110794.1			A	120789990	T	A	120789990	3	1	32	1	0	0	0	0	1	0	0	0	10158	1551	54	5	679	5	NANOS1	10	120789990	Missense_Mutation	SNP	T	TCGA-5P-A9K0-01A-11D-A42J-10	4174893	120789990	14744757	48	2326											
KNDC1	85442	hgsc.bcm.edu	37	chr10	135013101	135013101	+	Silent	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	aacgggcaggcgtcaccctcCccaaggtgggtgcccagttc	7	6	13	15	2	1	0	1	0	0	0	3	0	2	0	4	4	2	2	4	4	2	1			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr10:135013101C>T	ENST00000304613.3	+	15	2919	c.2898C>T	c.(2896-2898)tcC>tcT	p.S966S	KNDC1_ENST00000368571.2_Silent_p.S901S|KNDC1_ENST00000368572.2_Silent_p.S968S			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	966					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)		CGTCACCCTCCCCAAGGTGGG	0.627																																					p.S966S		Atlas-SNP	.											.	KNDC1	155	.	0			c.C2898T						PASS	.						91	88	89					10																	135013101		2203	4300	6503	SO:0001819	synonymous_variant	85442	exon15			ACCCTCCCCAAGG	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.2898C>T	chr10.hg19:g.135013101C>T		63.0	0.0	.		73.0	37.0	.	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Silent	SNP	ENST00000304613.3	hg19	CCDS7674.1																																																																																			.	.	.	none		0.627	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		T	135013101	C	T	135013101	2	4	32	1	0	0	0	0	0	0	0	1	8433	610	22	2		2	KNDC1	10	135013101	Silent	SNP	C	TCGA-5P-A9K0-01A-11D-A42J-10	14223111	135013101	521646	49	2327											
FAM160A2	84067	hgsc.bcm.edu	37	chr11	6238643	6238643	+	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	ctggttgagagtccgcaaagGgctgctgaggaaggggccag	9	6	18	8	1	0	2	0	2	0	1	1	4	1	3	2	5	1	4	2	5	2	1			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr11:6238643G>T	ENST00000449352.2	-	9	2436	c.2173C>A	c.(2173-2175)Cct>Act	p.P725T	FAM160A2_ENST00000529360.1_5'Flank|FAM160A2_ENST00000265978.4_Missense_Mutation_p.P739T|FAM160A2_ENST00000524416.1_Missense_Mutation_p.P725T			Q8N612	F16A2_HUMAN	family with sequence similarity 160, member A2	725					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						GTCCGCAAAGGGCTGCTGAGG	0.587																																					p.P739T		Atlas-SNP	.											.	FAM160A2	100	.	0			c.C2215A						PASS	.						55	56	56					11																	6238643		2201	4296	6497	SO:0001583	missense	84067	exon9			GCAAAGGGCTGCT		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.2173C>A	chr11.hg19:g.6238643G>T	ENSP00000416918:p.Pro725Thr	32.0	0.0	.		28.0	11.0	.	NM_032127	Q9C0A4|Q9H0N3|Q9H624	Missense_Mutation	SNP	ENST00000449352.2	hg19	CCDS44530.1	.	.	.	.	.	.	.	.	.	.	G	16.98	3.271449	0.59649	.	.	ENSG00000051009	ENST00000449352;ENST00000442917;ENST00000265978;ENST00000524416	T;T;T	0.71817	-0.6;-0.6;-0.6	5.11	5.11	0.69529	.	0.102616	0.64402	D	0.000002	T	0.80221	0.4583	L	0.57536	1.79	0.36080	D	0.842696	D;D;D	0.76494	0.999;0.983;0.965	D;P;P	0.78314	0.991;0.637;0.719	T	0.80254	-0.1459	10	0.25751	T	0.34	-25.4407	15.3805	0.74651	0.0:0.0:1.0:0.0	.	725;725;739	E9PJK5;Q8N612;Q8N612-2	.;F16A2_HUMAN;.	T	725;650;739;725	ENSP00000416918:P725T;ENSP00000265978:P739T;ENSP00000431773:P725T	ENSP00000265978:P739T	P	-	1	0	FAM160A2	6195219	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.027000	0.76463	2.663000	0.90544	0.561000	0.74099	CCT	.	.	.	none		0.587	FAM160A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383759.1	NM_032127		T	6238643	G	T	6238643	3	4	32	1	0	0	0	0	1	0	0	0	5473	1232	43	4	761	4	FAM160A2	11	6238643	Missense_Mutation	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10		6238643	128767873	50	2328											
NRXN2	9379	hgsc.bcm.edu	37	chr11	64410176	64410176	+	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	caacagcggcaacagcggcaGcagaggtggcggcggcggcg	9	1	19	12	6	0	1	0	0	0	1	0	1	0	1	0	7	5	3	0	7	2	0			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr11:64410176G>A	ENST00000377551.1	-	16	3615				NRXN2_ENST00000409571.1_Intron|NRXN2_ENST00000265459.6_Intron|NRXN2_ENST00000301894.2_Silent_p.L34L|NRXN2_ENST00000377559.3_Intron			Q9P2S2	NRX2A_HUMAN	neurexin 2						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						aacagcggcagcagAggtggc	0.786																																					p.L34L		Atlas-SNP	.											.	NRXN2	247	.	0			c.C100T						PASS	.						8	9	9					11																	64410176		2086	4108	6194	SO:0001627	intron_variant	9379	exon1			GCGGCAGCAGAGG		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.3403+5514C>T	chr11.hg19:g.64410176G>A		19.0	0.0	.		29.0	10.0	.	NM_138734	A7E2C1|Q9Y2D6	Silent	SNP	ENST00000377551.1	hg19	CCDS8077.1																																																																																			.	.	.	none		0.786	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104967.3	NM_015080		A	64410176	G	A	64410176	1	1	32	0	1	0	0	0	0	0	0	0	10673	962	34	2		2	NRXN2	11	64410176	Intron	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10	58171533	64410176	70596340	51	2329											
C1RL	51279	hgsc.bcm.edu	37	chr12	7261763	7261763	+	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	agagatatttcccccacactCtgggtccaggcatctggaac	10	9	9	13	0	2	1	0	0	2	1	4	3	4	2	3	3	1	1	3	3	2	2			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr12:7261763C>T	ENST00000266542.4	-	1	106	c.14G>A	c.(13-15)aGa>aAa	p.R5K	C1RL-AS1_ENST00000536679.1_RNA|C1RL_ENST00000545280.1_Missense_Mutation_p.R5K|C1RL_ENST00000545337.1_Missense_Mutation_p.R5K|C1RL-AS1_ENST00000541775.1_RNA|C1RL_ENST00000544702.1_Missense_Mutation_p.R5K|C1RL-AS1_ENST00000382215.3_RNA|C1RL-AS1_ENST00000435921.2_RNA	NM_016546.2	NP_057630.2	Q9NZP8	C1RL_HUMAN	complement component 1, r subcomponent-like	5					complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						CCCCCACACTCTGGGTCCAGG	0.602											OREG0021648	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R5K		Atlas-SNP	.											.	C1RL	39	.	0			c.G14A						PASS	.						40	33	35					12																	7261763		2203	4300	6503	SO:0001583	missense	51279	exon1			CACACTCTGGGTC	AF178985	CCDS8573.1, CCDS73431.1	12p13.31	2008-02-05				ENSG00000139178			21265	protein-coding gene	gene with protein product		608974				12838346	Standard	XM_005253385		Approved	C1r-LP, C1RL1	uc001qsn.3	Q9NZP8		ENST00000266542.4:c.14G>A	chr12.hg19:g.7261763C>T	ENSP00000266542:p.Arg5Lys	59.0	0.0	.	640	55.0	9.0	.	NM_016546	Q53GX9	Missense_Mutation	SNP	ENST00000266542.4	hg19	CCDS8573.1	.	.	.	.	.	.	.	.	.	.	C	9.654	1.142312	0.21205	.	.	ENSG00000139178	ENST00000545280;ENST00000266542;ENST00000396661;ENST00000544702;ENST00000543933;ENST00000545337	D;T;T;T	0.86694	-2.16;1.37;1.94;1.64	3.69	0.697	0.18081	.	0.188541	0.27023	N	0.021317	T	0.75451	0.3851	L	0.29908	0.895	0.09310	N	1	B;B;B	0.19331	0.035;0.035;0.002	B;B;B	0.17098	0.017;0.017;0.003	T	0.60606	-0.7230	10	0.32370	T	0.25	.	6.2753	0.20977	0.0:0.491:0.4009:0.1081	.	5;5;5	F5GWF3;F5H7C8;Q9NZP8	.;.;C1RL_HUMAN	K	5	ENSP00000266542:R5K;ENSP00000441885:R5K;ENSP00000437398:R5K;ENSP00000442611:R5K	ENSP00000266542:R5K	R	-	2	0	C1RL	7153039	0.000000	0.05858	0.017000	0.16124	0.149000	0.21700	-0.454000	0.06770	0.143000	0.18926	0.400000	0.26472	AGA	.	.	.	none		0.602	C1RL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398367.1	NM_016546		T	7261763	C	T	7261763	3	4	32	1	0	0	0	0	1	0	0	0	1975	913	32	2	1473	2	C1RL	12	7261763	Missense_Mutation	SNP	C	TCGA-5P-A9K0-01A-11D-A42J-10		7261763	126590132	52	2330											
COL2A1	1280	hgsc.bcm.edu	37	chr12	48379569	48379569	+	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	ggtcaccgttggctcccttgGggccagcaagaccactgggc	6	7	14	14	1	1	1	1	0	0	1	2	1	2	1	4	5	1	3	4	5	1	2			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr12:48379569G>C	ENST00000380518.3	-	25	1786	c.1622C>G	c.(1621-1623)cCc>cGc	p.P541R	COL2A1_ENST00000493991.1_5'UTR|COL2A1_ENST00000337299.6_Missense_Mutation_p.P472R	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	541	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)	GGCTCCCTTGGGGCCAGCAAG	0.632																																					p.P541R		Atlas-SNP	.											.	COL2A1	368	.	0			c.C1622G						PASS	.						44	45	45					12																	48379569		2203	4300	6503	SO:0001583	missense	1280	exon25			CCCTTGGGGCCAG	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.1622C>G	chr12.hg19:g.48379569G>C	ENSP00000369889:p.Pro541Arg	61.0	0.0	.		78.0	49.0	.	NM_001844	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Missense_Mutation	SNP	ENST00000380518.3	hg19	CCDS41778.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.964237	0.74131	.	.	ENSG00000139219	ENST00000380518;ENST00000395281;ENST00000337299	D;D	0.98684	-5.07;-5.07	5.48	4.58	0.56647	.	0.064020	0.64402	D	0.000007	D	0.98670	0.9554	M	0.62209	1.925	0.80722	D	1	D;D	0.67145	0.996;0.993	D;D	0.79784	0.993;0.985	D	0.98492	1.0610	10	0.62326	D	0.03	.	12.6214	0.56605	0.0814:0.0:0.9186:0.0	.	472;541	P02458-1;P02458	.;CO2A1_HUMAN	R	541;472;472	ENSP00000369889:P541R;ENSP00000338213:P472R	ENSP00000338213:P472R	P	-	2	0	COL2A1	46665836	1.000000	0.71417	0.998000	0.56505	0.711000	0.40976	6.740000	0.74832	2.572000	0.86782	0.609000	0.83330	CCC	.	.	.	none		0.632	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844		C	48379569	G	C	48379569	3	2	32	1	0	0	0	0	1	0	0	0	3689	1232	43	4	2961	4	COL2A1	12	48379569	Missense_Mutation	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10	41117806	48379569	85472326	53	2331											
FAM71C	196472	hgsc.bcm.edu	37	chr12	100042138	100042138	+	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	agaggagaagtgattgacgtGcacaaccgtgcccgaatggt	12	7	14	8	3	0	4	0	2	0	2	0	6	0	4	2	2	3	1	2	2	3	1			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr12:100042138G>T	ENST00000324341.1	+	1	608	c.186G>T	c.(184-186)gtG>gtT	p.V62V	ANKS1B_ENST00000329257.7_Intron|ANKS1B_ENST00000547776.2_Intron|ANKS1B_ENST00000547010.1_Intron	NM_153364.3	NP_699195.1	Q8NEG0	FA71C_HUMAN	family with sequence similarity 71, member C	62										breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(2;0.00733)|Epithelial(2;0.0385)|all cancers(2;0.19)		TGATTGACGTGCACAACCGTG	0.522																																					p.V62V		Atlas-SNP	.											.	FAM71C	48	.	0			c.G186T						PASS	.						151	129	136					12																	100042138		2203	4300	6503	SO:0001819	synonymous_variant	196472	exon1			TGACGTGCACAAC		CCDS9072.1	12q23.1	2006-02-03				ENSG00000180219			28594	protein-coding gene	gene with protein product						12477932	Standard	NM_153364		Approved	MGC39520	uc001tgn.3	Q8NEG0		ENST00000324341.1:c.186G>T	chr12.hg19:g.100042138G>T		71.0	0.0	.		99.0	26.0	.	NM_153364	B2R6Y6	Silent	SNP	ENST00000324341.1	hg19	CCDS9072.1																																																																																			.	.	.	none		0.522	FAM71C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408458.1	NM_153364		T	100042138	G	T	100042138	2	4	32	1	0	0	0	0	0	0	0	1	5616	1306	46	4		4	FAM71C	12	100042138	Silent	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10	51662569	100042138	33809757	54	2332											
IFT88	8100	hgsc.bcm.edu	37	chr13	21217615	21217615	+	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	tatgaattaatggaaaatccCagtcaagctattgaatggct	15	12	8	6	0	1	2	1	2	0	0	2	3	2	3	1	2	1	2	1	2	8	4			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr13:21217615C>G	ENST00000319980.6	+	21	2058	c.1731C>G	c.(1729-1731)ccC>ccG	p.P577P	IFT88_ENST00000351808.5_Silent_p.P568P|IFT88_ENST00000382778.4_Silent_p.P577P|IFT88_ENST00000537103.1_Silent_p.P549P	NM_175605.3	NP_783195.2	Q13099	IFT88_HUMAN	intraflagellar transport 88	577					anterior/posterior pattern specification (GO:0009952)|cardiac muscle cell differentiation (GO:0055007)|cardiac septum morphogenesis (GO:0060411)|cilium morphogenesis (GO:0060271)|cochlea development (GO:0090102)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|embryonic digit morphogenesis (GO:0042733)|epidermal stem cell homeostasis (GO:0036334)|epidermis development (GO:0008544)|epithelial cell morphogenesis (GO:0003382)|eye development (GO:0001654)|forebrain morphogenesis (GO:0048853)|heart formation (GO:0060914)|inner ear receptor stereocilium organization (GO:0060122)|kidney development (GO:0001822)|liver development (GO:0001889)|lung vasculature development (GO:0060426)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|protein localization (GO:0008104)|regulation of autophagic vacuole assembly (GO:2000785)|regulation of cilium assembly (GO:1902017)|regulation of fat cell differentiation (GO:0045598)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of protein processing (GO:0070613)|regulation of smoothened signaling pathway (GO:0008589)|response to fluid shear stress (GO:0034405)|smoothened signaling pathway (GO:0007224)|sperm axoneme assembly (GO:0007288)|spermatid nucleus elongation (GO:0007290)|spinal cord dorsal/ventral patterning (GO:0021513)|telencephalon development (GO:0021537)	acrosomal membrane (GO:0002080)|apical part of cell (GO:0045177)|axonemal basal plate (GO:0097541)|centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|kinocilium (GO:0060091)|motile cilium (GO:0031514)|motile primary cilium (GO:0031512)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	27		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)		TGGAAAATCCCAGTCAAGCTA	0.328																																					p.P577P		Atlas-SNP	.											.	IFT88	83	.	0			c.C1731G						PASS	.						108	106	106					13																	21217615		2203	4300	6503	SO:0001819	synonymous_variant	8100	exon21			AAATCCCAGTCAA	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.1731C>G	chr13.hg19:g.21217615C>G		81.0	0.0	.		57.0	21.0	.	NM_175605	A2A491|B4DUS2|Q5SZJ6|Q8N719	Silent	SNP	ENST00000319980.6	hg19	CCDS31944.1																																																																																			.	.	.	none		0.328	IFT88-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044075.3	NM_006531		G	21217615	C	G	21217615	2	3	32	1	0	0	0	0	0	0	0	1	7573	581	21	4		4	IFT88	13	21217615	Silent	SNP	C	TCGA-5P-A9K0-01A-11D-A42J-10		21217615	93952263	55	2333											
PAN3	255967	hgsc.bcm.edu	37	chr13	28830508	28830508	+	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	tctcctgctcccagaagaagAagtcacactccaaatccagc	13	7	6	15	0	2	3	1	0	1	3	6	3	5	3	4	0	2	1	4	0	4	0	rs372499998		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr13:28830508A>T	ENST00000380958.3	+	7	1232	c.1080A>T	c.(1078-1080)agA>agT	p.R360S	PAN3_ENST00000483842.1_3'UTR|PAN3_ENST00000282391.5_Missense_Mutation_p.R48S|PAN3_ENST00000399613.1_Missense_Mutation_p.R160S	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)		CCAGAAGAAGAAGTCACACTC	0.458																																					p.R360S		Atlas-SNP	.											.	PAN3	123	.	0			c.A1080T						PASS	.	A	SER/ARG	0,4406		0,0,2203	196	176	183		1080	4.6	1	13		183	1,8599	1.2+/-3.3	0,1,4299	no	missense	PAN3	NM_175854.7	110	0,1,6502	TT,TA,AA		0.0116,0.0,0.0077	probably-damaging	360/888	28830508	1,13005	2203	4300	6503	SO:0001583	missense	255967	exon7			AAGAAGAAGTCAC	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.1080A>T	chr13.hg19:g.28830508A>T	ENSP00000370345:p.Arg360Ser	66.0	0.0	.		57.0	22.0	.	NM_175854		Missense_Mutation	SNP	ENST00000380958.3	hg19	CCDS9329.2	.	.	.	.	.	.	.	.	.	.	A	18.98	3.736859	0.69304	0.0	1.16E-4	ENSG00000152520	ENST00000380958;ENST00000399613;ENST00000282391	T;T;T	0.42131	0.98;1.0;0.98	5.8	4.63	0.57726	.	0.043039	0.85682	D	0.000000	T	0.41190	0.1148	N	0.24115	0.695	0.58432	D	0.999999	D;D;D;D	0.67145	0.991;0.996;0.981;0.981	P;D;D;D	0.77557	0.64;0.99;0.943;0.943	T	0.43589	-0.9382	10	0.05436	T	0.98	-15.7444	8.7714	0.34735	0.8559:0.0:0.1441:0.0	.	360;360;48;306	Q58A45-4;Q58A45;Q58A45-2;Q58A45-3	.;PAN3_HUMAN;.;.	S	360;160;48	ENSP00000370345:R360S;ENSP00000382522:R160S;ENSP00000282391:R48S	ENSP00000282391:R48S	R	+	3	2	PAN3	27728508	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.930000	0.40124	1.028000	0.39785	0.528000	0.53228	AGA	.	.	.	weak		0.458	PAN3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044318.4	NM_175854		T	28830508	A	T	28830508	3	4	32	1	0	0	0	0	1	0	0	0	11422	243	9	5	1106	5	PAN3	13	28830508	Missense_Mutation	SNP	A	TCGA-5P-A9K0-01A-11D-A42J-10	7612893	28830508	86339370	56	2334											
ZC3H13	23091	hgsc.bcm.edu	37	chr13	46554017	46554017	+	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	ggaagaatcccttgcttgatCtctgttgtctctttcaggat	7	16	9	9	0	3	2	1	1	2	1	6	4	4	4	1	2	1	2	1	2	2	4			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr13:46554017C>A	ENST00000242848.4	-	11	2191	c.1843G>T	c.(1843-1845)Gat>Tat	p.D615Y	ZC3H13_ENST00000282007.3_Missense_Mutation_p.D615Y			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	615	Arg/Ser-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)		CTTGCTTGATCTCTGTTGTCT	0.398																																					p.D615Y	Esophageal Squamous(187;747 2077 11056 31291 44172)	Atlas-SNP	.											.	ZC3H13	197	.	0			c.G1843T						PASS	.						192	169	177					13																	46554017		2203	4300	6503	SO:0001583	missense	23091	exon11			CTTGATCTCTGTT	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.1843G>T	chr13.hg19:g.46554017C>A	ENSP00000242848:p.Asp615Tyr	65.0	0.0	.		70.0	22.0	.	NM_015070	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Missense_Mutation	SNP	ENST00000242848.4	hg19		.	.	.	.	.	.	.	.	.	.	C	14.81	2.646156	0.47258	.	.	ENSG00000123200	ENST00000242848;ENST00000282007;ENST00000431251	T;T	0.32988	2.41;1.43	5.73	5.73	0.89815	.	0.180213	0.38663	N	0.001610	T	0.42404	0.1201	L	0.29908	0.895	0.80722	D	1	D;D	0.63046	0.986;0.992	P;P	0.59761	0.733;0.863	T	0.08597	-1.0714	10	0.38643	T	0.18	.	19.9162	0.97063	0.0:1.0:0.0:0.0	.	615;615	Q5T200;Q5T200-2	ZC3HD_HUMAN;.	Y	615;615;431	ENSP00000242848:D615Y;ENSP00000282007:D615Y	ENSP00000242848:D615Y	D	-	1	0	ZC3H13	45452018	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.104000	0.71498	2.710000	0.92621	0.650000	0.86243	GAT	.	.	.	none		0.398	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070		A	46554017	C	A	46554017	3	1	32	1	0	0	0	0	1	0	0	0	17577	913	32	4	2879	4	ZC3H13	13	46554017	Missense_Mutation	SNP	C	TCGA-5P-A9K0-01A-11D-A42J-10	17723509	46554017	68615861	57	2335											
TPP2	7174	hgsc.bcm.edu	37	chr13	103301430	103301430	+	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	tttgcacttctagggaagaaGaaatcaagcaatttgacatt	15	12	8	6	0	2	3	1	1	1	2	2	4	2	4	0	1	2	2	0	1	6	5			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr13:103301430G>A	ENST00000376065.4	+	22	2838	c.2802G>A	c.(2800-2802)aaG>aaA	p.K934K	TPP2_ENST00000376052.3_Silent_p.K934K	NM_003291.2	NP_003282.2	P29144	TPP2_HUMAN	tripeptidyl peptidase II	934					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)					TAGGGAAGAAGAAATCAAGCA	0.333																																					p.K934K		Atlas-SNP	.											.	TPP2	124	.	0			c.G2802A						PASS	.						145	140	141					13																	103301430		2203	4300	6503	SO:0001819	synonymous_variant	7174	exon22			GAAGAAGAAATCA	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.2802G>A	chr13.hg19:g.103301430G>A		81.0	0.0	.		49.0	16.0	.	NM_003291	Q5VZU8	Silent	SNP	ENST00000376065.4	hg19	CCDS9502.1																																																																																			.	.	.	none		0.333	TPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045683.2			A	103301430	G	A	103301430	2	1	32	1	0	0	0	0	0	0	0	1	16424	933	33	2		2	TPP2	13	103301430	Silent	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10	56747413	103301430	11868448	58	2336											
FANCM	57697	hgsc.bcm.edu	37	chr14	45628482	45628482	+	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	tacccagaaggagcaactggAggtaattatttttggaattg	13	12	11	5	0	0	1	0	0	0	1	0	4	0	4	1	4	3	2	1	4	6	6			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr14:45628482A>G	ENST00000267430.5	+	9	1665	c.1580A>G	c.(1579-1581)gAg>gGg	p.E527G	FANCM_ENST00000542564.2_Splice_Site_p.E501G|FANCM_ENST00000556036.1_Splice_Site_p.E527G	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	527	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						GAGCAACTGGAGGTAATTATT	0.353								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.E527G		Atlas-SNP	.											.	FANCM	225	.	0			c.A1580G						PASS	.						34	35	34					14																	45628482		2203	4299	6502	SO:0001630	splice_region_variant	57697	exon9	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AACTGGAGGTAAT	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.1581+1A>G	chr14.hg19:g.45628482A>G		90.0	0.0	.		101.0	23.0	.	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	hg19	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	A	16.51	3.144462	0.57044	.	.	ENSG00000187790	ENST00000556036;ENST00000267430;ENST00000542564;ENST00000556250	T;T;T;T	0.77877	-1.13;-1.13;-1.13;3.42	5.28	4.1	0.47936	Helicase, C-terminal (3);	0.243934	0.40640	N	0.001051	T	0.77274	0.4106	L	0.35341	1.055	0.44439	D	0.997363	P;P;P	0.51240	0.943;0.943;0.907	P;P;P	0.55508	0.777;0.698;0.586	T	0.77507	-0.2562	10	0.66056	D	0.02	.	10.9842	0.47513	0.9244:0.0:0.0756:0.0	.	501;527;527	B2RTQ9;Q8IYD8;Q8IYD8-2	.;FANCM_HUMAN;.	G	527;527;501;112	ENSP00000450596:E527G;ENSP00000267430:E527G;ENSP00000442493:E501G;ENSP00000452033:E112G	ENSP00000267430:E527G	E	+	2	0	FANCM	44698232	1.000000	0.71417	0.995000	0.50966	0.600000	0.36913	7.179000	0.77665	0.798000	0.33994	0.460000	0.39030	GAG	.	.	.	none		0.353	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128	Missense_Mutation	G	45628482	A	G	45628482	5	3	32	1	0	0	0	0	0	0	1	0	5678	318	11	3	1614	3	FANCM	14	45628482	Splice_Site	SNP	A	TCGA-5P-A9K0-01A-11D-A42J-10		45628482	61721058	59	2337											
SIX6	4990	hgsc.bcm.edu	37	chr14	60976418	60976418	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acactaccaggaggctgagaAgctgcgtggaagacccctgg	11	5	14	11	1	0	2	0	1	0	2	0	5	0	4	3	4	3	2	3	4	3	1			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr14:60976418A>G	ENST00000327720.5	+	1	750	c.302A>G	c.(301-303)aAg>aGg	p.K101R		NM_007374.2	NP_031400.2	O95475	SIX6_HUMAN	SIX homeobox 6	101					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)		GAGGCTGAGAAGCTGCGTGGA	0.577																																					p.K101R		Atlas-SNP	.											.	SIX6	27	.	0			c.A302G						PASS	.						48	51	50					14																	60976418		2203	4300	6503	SO:0001583	missense	4990	exon1			CTGAGAAGCTGCG	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.302A>G	chr14.hg19:g.60976418A>G	ENSP00000328596:p.Lys101Arg	348.0	0.0	.		335.0	120.0	.	NM_007374	Q6NT42|Q9P1X8	Missense_Mutation	SNP	ENST00000327720.5	hg19	CCDS9747.1	.	.	.	.	.	.	.	.	.	.	A	9.599	1.128074	0.20959	.	.	ENSG00000184302	ENST00000327720	D	0.97232	-4.3	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	D	0.93729	0.7996	L	0.27975	0.815	0.80722	D	1	B	0.17038	0.02	B	0.16722	0.016	D	0.90866	0.4742	10	0.48119	T	0.1	.	14.7304	0.69377	1.0:0.0:0.0:0.0	.	101	O95475	SIX6_HUMAN	R	101	ENSP00000328596:K101R	ENSP00000328596:K101R	K	+	2	0	SIX6	60046171	1.000000	0.71417	1.000000	0.80357	0.226000	0.24999	9.139000	0.94554	2.263000	0.75096	0.379000	0.24179	AAG	.	.	.	none		0.577	SIX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276952.2			G	60976418	A	G	60976418	3	3	32	1	0	0	0	0	1	0	0	0	14364	72	3	3	304	3	SIX6	14	60976418	Missense_Mutation	SNP	A	TCGA-5P-A9K0-01A-11D-A42J-10	15347936	60976418	46373122	60	2338											
MYO5A	4644	hgsc.bcm.edu	37	chr15	52699526	52699526	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcctagtatgtgccatctcCtttgcatcatccactccttc	6	15	5	15	0	2	0	1	0	1	0	6	0	4	0	5	0	3	2	5	0	2	4			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr15:52699526C>T	ENST00000399231.3	-	8	1152	c.909G>A	c.(907-909)aaG>aaA	p.K303K	MYO5A_ENST00000399233.2_Silent_p.K303K|MYO5A_ENST00000553916.1_Silent_p.K303K|MYO5A_ENST00000356338.6_Silent_p.K303K|MYO5A_ENST00000358212.6_Silent_p.K303K	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	303	Myosin motor.				actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		GTGCCATCTCCTTTGCATCAT	0.378																																					p.K303K		Atlas-SNP	.											.	MYO5A	145	.	0			c.G909A						PASS	.						142	130	134					15																	52699526		1968	4156	6124	SO:0001819	synonymous_variant	4644	exon8			CATCTCCTTTGCA		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.909G>A	chr15.hg19:g.52699526C>T		65.0	0.0	.		69.0	23.0	.	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Silent	SNP	ENST00000399231.3	hg19	CCDS42037.1																																																																																			.	.	.	none		0.378	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259		T	52699526	C	T	52699526	2	4	32	1	0	0	0	0	0	0	0	1	10085	680	24	2		2	MYO5A	15	52699526	Silent	SNP	C	TCGA-5P-A9K0-01A-11D-A42J-10		52699526	49831866	61	2339											
PARP16	54956	hgsc.bcm.edu	37	chr15	65563347	65563347	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccaggtcccaggcccgttTgtggttgtctccggaggact	5	10	13	13	2	1	0	0	0	1	0	3	2	2	2	4	5	0	2	4	5	0	2			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr15:65563347T>C	ENST00000261888.6	-	2	683	c.238A>G	c.(238-240)Aaa>Gaa	p.K80E	PARP16_ENST00000558873.1_5'UTR|PARP16_ENST00000444347.2_Intron	NM_017851.4	NP_060321.3	Q8N5Y8	PAR16_HUMAN	poly (ADP-ribose) polymerase family, member 16	80	PARP alpha-helical.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cell death (GO:0060548)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum tubular network (GO:0071782)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)	kinase binding (GO:0019900)|NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|protein serine/threonine kinase activator activity (GO:0043539)			kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	9						CAGGCCCGTTTGTGGTTGTCT	0.522																																					p.K80E	NSCLC(50;885 1163 13509 21242 41978)	Atlas-SNP	.											.	PARP16	23	.	0			c.A238G						PASS	.						165	161	162					15																	65563347		2201	4299	6500	SO:0001583	missense	54956	exon2			CCCGTTTGTGGTT	AK000516	CCDS10204.1	15q22.2	2010-02-16	2004-08-25	2004-08-25	ENSG00000138617	ENSG00000138617		"Poly (ADP-ribose) polymerases"	26040	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 30"	C15orf30		15273990	Standard	NM_017851		Approved	FLJ20509, FLJ25281, pART15	uc002aoq.3	Q8N5Y8	OTTHUMG00000133138	ENST00000261888.6:c.238A>G	chr15.hg19:g.65563347T>C	ENSP00000261888:p.Lys80Glu	96.0	0.0	.		93.0	38.0	.	NM_017851	Q6PK64|Q9NX03	Missense_Mutation	SNP	ENST00000261888.6	hg19	CCDS10204.1	.	.	.	.	.	.	.	.	.	.	T	0.539	-0.854339	0.02630	.	.	ENSG00000138617	ENST00000261888	T	0.44482	0.92	5.8	-1.38	0.09027	Poly(ADP-ribose) polymerase, catalytic domain (1);	0.766439	0.13541	N	0.380223	T	0.23370	0.0565	N	0.14661	0.345	0.09310	N	0.999995	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.20042	-1.0287	10	0.21014	T	0.42	0.0022	12.9664	0.58485	0.0:0.0646:0.633:0.3023	.	80;80	Q8N5Y8-3;Q8N5Y8	.;PAR16_HUMAN	E	80	ENSP00000261888:K80E	ENSP00000261888:K80E	K	-	1	0	PARP16	63350400	0.006000	0.16342	0.023000	0.16930	0.334000	0.28698	-0.018000	0.12568	-0.153000	0.11137	0.533000	0.62120	AAA	.	.	.	none		0.522	PARP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256827.2	NM_017851		C	65563347	T	C	65563347	3	2	32	1	0	0	0	0	1	0	0	0	11467	1821	63	3	753	3	PARP16	15	65563347	Missense_Mutation	SNP	T	TCGA-5P-A9K0-01A-11D-A42J-10	12863821	65563347	36968045	62	2340											
ITGA11	22801	hgsc.bcm.edu	37	chr15	68620582	68620582	+	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	aagtggaggctggcattgatCtgaaccactgggcgggacct	9	8	15	9	1	1	2	0	2	1	0	1	4	1	4	2	5	1	2	2	5	2	1			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr15:68620582C>T	ENST00000315757.7	-	16	2006	c.1920G>A	c.(1918-1920)caG>caA	p.Q640Q	ITGA11_ENST00000423218.2_Silent_p.Q640Q	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	640					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						TGGCATTGATCTGAACCACTG	0.612																																					p.Q640Q		Atlas-SNP	.											.	ITGA11	110	.	0			c.G1920A						PASS	.						86	92	90					15																	68620582		2021	4166	6187	SO:0001819	synonymous_variant	22801	exon16			ATTGATCTGAACC	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.1920G>A	chr15.hg19:g.68620582C>T		55.0	0.0	.		53.0	25.0	.	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Silent	SNP	ENST00000315757.7	hg19	CCDS45291.1																																																																																			.	.	.	none		0.612	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211		T	68620582	C	T	68620582	2	4	32	1	0	0	0	0	0	0	0	1	7881	912	32	2		2	ITGA11	15	68620582	Silent	SNP	C	TCGA-5P-A9K0-01A-11D-A42J-10	3057235	68620582	33910810	63	2341											
GRIN2A	2903	hgsc.bcm.edu	37	chr16	10274246	10274246	+	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	gggccggcagcaccagcaggGtccaatagcccactctgccc	8	4	12	17	1	1	0	0	0	1	0	2	0	2	0	5	3	4	3	5	3	2	1			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr16:10274246G>T	ENST00000396573.2	-	3	332	c.23C>A	c.(22-24)aCc>aAc	p.T8N	GRIN2A_ENST00000562109.1_Missense_Mutation_p.T8N|GRIN2A_ENST00000404927.2_Missense_Mutation_p.T8N|GRIN2A_ENST00000330684.3_Missense_Mutation_p.T8N|GRIN2A_ENST00000396575.2_Missense_Mutation_p.T8N	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	8					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)	CACCAGCAGGGTCCAATAGCC	0.662																																					p.T8N		Atlas-SNP	.											.	GRIN2A	366	.	0			c.C23A						PASS	.						13	15	14					16																	10274246		2191	4288	6479	SO:0001583	missense	2903	exon3			AGCAGGGTCCAAT		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.23C>A	chr16.hg19:g.10274246G>T	ENSP00000379818:p.Thr8Asn	28.0	0.0	.		35.0	11.0	.	NM_000833	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	hg19	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	G	19.51	3.840531	0.71488	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000330684;ENST00000396575	T;T;T;T	0.11712	2.76;2.75;2.76;2.76	4.54	4.54	0.55810	.	0.328981	0.24520	N	0.037803	T	0.13713	0.0332	N	0.22421	0.69	0.80722	D	1	D;B;B	0.57899	0.981;0.149;0.149	P;B;B	0.52109	0.69;0.065;0.065	T	0.12993	-1.0526	9	.	.	.	.	16.2901	0.82747	0.0:0.0:1.0:0.0	.	8;8;8	Q547U9;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	N	8	ENSP00000379818:T8N;ENSP00000385872:T8N;ENSP00000332549:T8N;ENSP00000379820:T8N	.	T	-	2	0	GRIN2A	10181747	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.990000	0.63876	2.088000	0.63022	0.561000	0.74099	ACC	.	.	.	none		0.662	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			T	10274246	G	T	10274246	3	4	32	1	0	0	0	0	1	0	0	0	6786	1261	44	4	4419	4	GRIN2A	16	10274246	Missense_Mutation	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10		10274246	80080507	64	2342											
TGFB1I1	7041	hgsc.bcm.edu	37	chr16	31486006	31486014	+	In_Frame_Del	DEL	CCTCAGCCG	CCTCAGCCG	-																															ctggggctgctgcagtccgaCctcagccgccggggtgttcc																								rs199879867		TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	CCTCAGCCG	CCTCAGCCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr16:31486006_31486014delCCTCAGCCG	ENST00000394863.3	+	7	772_780	c.642_650delCCTCAGCCG	c.(640-651)gacctcagccgc>gac	p.LSR215del	TGFB1I1_ENST00000567607.1_In_Frame_Del_p.LSR198del|TGFB1I1_ENST00000394858.2_In_Frame_Del_p.LSR198del|TGFB1I1_ENST00000361773.3_In_Frame_Del_p.LSR198del	NM_001042454.2	NP_001035919.1	O43294	TGFI1_HUMAN	transforming growth factor beta 1 induced transcript 1	215	Interaction with PTK2B/PYK2.				androgen receptor signaling pathway (GO:0030521)|cell adhesion (GO:0007155)|cell fate commitment (GO:0045165)|epithelial cell differentiation (GO:0030855)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|response to heat (GO:0009408)|transcription from RNA polymerase II promoter (GO:0006366)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|I-SMAD binding (GO:0070411)|Roundabout binding (GO:0048495)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			lung(8)|upper_aerodigestive_tract(1)	9						TGCAGTCCGACCTCAGCCGCCGGGGTGTT	0.622																																					p.214_217del		Atlas-Indel,Pindel	.											.	TGFB1I1	60	.	0			c.641_649del						PASS	.																																			SO:0001651	inframe_deletion	7041	exon7			.	AB007836	CCDS10713.1, CCDS42156.1	16p11	2008-02-05			ENSG00000140682	ENSG00000140682			11767	protein-coding gene	gene with protein product		602353				9422762, 10075738	Standard	NM_015927		Approved	Hic-5, TSC-5, ARA55, HIC-5	uc002ecd.2	O43294	OTTHUMG00000132467	ENST00000394863.3:c.642_650delCCTCAGCCG	chr16.hg19:g.31486006_31486014delCCTCAGCCG	ENSP00000378332:p.Leu215_Arg217del	40.0	0.0	0		65.0	27.0	0.415385	NM_001042454	B2R8D5|Q9BPW3|Q9Y2V5	In_Frame_Del	DEL	ENST00000394863.3	hg19	CCDS42156.1																																																																																			.	.	.	none		0.622	TGFB1I1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255630.3			-	31486014	CCTCAGCCG	-	31486006	7	5	32	1	0	1	0	1	0	0	0	0	15829	506	18	0	668	0	TGFB1I1	16	31486006	In_Frame_Del	DEL	CCTCAGCCG	TCGA-5P-A9K0-01A-11D-A42J-10	21211760	31486006	58868747	65	2343											
NLRC5	84166	hgsc.bcm.edu	37	chr16	57099127	57099127	+	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	gtccccttctgtgacagggtGcaggagccgtgggcggacag	6	7	17	11	2	1	1	0	1	1	0	2	3	2	3	3	4	2	1	3	4	0	1			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr16:57099127G>A	ENST00000262510.6	+	33	4383	c.4158G>A	c.(4156-4158)gtG>gtA	p.V1386V	NLRC5_ENST00000308149.7_Silent_p.V1357V|NLRC5_ENST00000436936.1_Silent_p.V1386V|NLRC5_ENST00000539144.1_Silent_p.V1357V	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	1386					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)				GTGACAGGGTGCAGGAGCCGT	0.617																																					p.V1386V		Atlas-SNP	.											.	NLRC5	186	.	0			c.G4158A						PASS	.						27	28	27					16																	57099127		2198	4300	6498	SO:0001819	synonymous_variant	84166	exon32			CAGGGTGCAGGAG	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.4158G>A	chr16.hg19:g.57099127G>A		30.0	0.0	.		28.0	15.0	.	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Silent	SNP	ENST00000262510.6	hg19	CCDS10773.1																																																																																			.	.	.	none		0.617	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206		A	57099127	G	A	57099127	2	1	32	1	0	0	0	0	0	0	0	1	10477	1306	46	2		2	NLRC5	16	57099127	Silent	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10	25613121	57099127	33255626	66	2344											
SLC38A8	146167	hgsc.bcm.edu	37	chr16	84050195	84050197	+	In_Frame_Del	DEL	AAC	AAC	-																															tctcgctgaggtcaggcataAacagcgccatggcgagcgtc																										TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr16:84050195_84050197delAAC	ENST00000299709.3	-	8	1088_1090	c.1089_1091delGTT	c.(1087-1092)ctgttt>ctt	p.F364del		NM_001080442.1	NP_001073911.1	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8	364					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						GTCAGGCATAAACAGCGCCATGG	0.631																																					p.364_364del		Atlas-Indel,Pindel	.											.	SLC38A8	60	.	0			c.1090_1092del						PASS	.																																			SO:0001651	inframe_deletion	146167	exon8			.		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.1089_1091delGTT	chr16.hg19:g.84050195_84050197delAAC	ENSP00000299709:p.Phe364del	69.0	0.0	0		66.0	28.0	0.424242	NM_001080442		In_Frame_Del	DEL	ENST00000299709.3	hg19	CCDS32495.1																																																																																			.	.	.	none		0.631	SLC38A8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432623.1	NM_001080442		-	84050197	AAC	-	84050195	7	5	32	1	0	1	0	1	0	0	0	0	14623	14	1	0	228	0	SLC38A8	16	84050195	In_Frame_Del	DEL	AAC	TCGA-5P-A9K0-01A-11D-A42J-10	26951068	84050195	6304558	67	2345											
MAP2K4	6416	hgsc.bcm.edu	37	chr17	12028658	12028658	+	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	cgacaaggatatgatgtccgCtctgatgtctggagtttggg	8	12	14	7	2	2	2	0	2	2	0	3	5	3	4	1	3	0	2	1	3	2	2			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr17:12028658C>T	ENST00000353533.5	+	8	924	c.861C>T	c.(859-861)cgC>cgT	p.R287R	MAP2K4_ENST00000415385.3_Silent_p.R298R	NM_003010.2	NP_003001.1	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4	287	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron apoptotic process (GO:0043525)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|nucleus (GO:0005634)|perikaryon (GO:0043204)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.0?(10)|p.?(3)		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)		ATGATGTCCGCTCTGATGTCT	0.393			"D, Mis, N"		"pancreatic, breast, colorectal"																																p.R287R		Atlas-SNP	.		Rec	yes		17	17p11.2	6416	mitogen-activated protein kinase kinase 4		E	.	MAP2K4	176	.	13	Whole gene deletion(10)|Unknown(3)	breast(4)|ovary(4)|lung(2)|biliary_tract(1)|large_intestine(1)|pancreas(1)	c.C861T						PASS	.						251	196	214					17																	12028658		2203	4300	6503	SO:0001819	synonymous_variant	6416	exon8			TGTCCGCTCTGAT	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.861C>T	chr17.hg19:g.12028658C>T		70.0	0.0	.		82.0	42.0	.	NM_003010	B2R7N7|B3KYB2|D3DTS5|Q5U0B8|Q6FHX4|Q6P9H2|Q6PIE6	Silent	SNP	ENST00000353533.5	hg19	CCDS11162.1																																																																																			.	.	.	none		0.393	MAP2K4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441226.1			T	12028658	C	T	12028658	2	4	32	1	0	0	0	0	0	0	0	1	9246	784	28	2		2	MAP2K4	17	12028658	Silent	SNP	C	TCGA-5P-A9K0-01A-11D-A42J-10		12028658	69166552	68	2346											
WSB1	26118	hgsc.bcm.edu	37	chr17	25639388	25639388	+	Missense_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	tttggagtttctctcgtatcGtatttagaagattctgcctt	7	19	8	7	2	2	2	0	0	2	2	5	3	2	3	1	1	1	3	1	1	4	8			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr17:25639388G>A	ENST00000262394.2	+	9	1575	c.1259G>A	c.(1258-1260)cGt>cAt	p.R420H	WSB1_ENST00000348811.2_Missense_Mutation_p.R274H|RP11-173M1.8_ENST00000578929.1_lincRNA	NM_015626.8	NP_056441.6	Q9Y6I7	WSB1_HUMAN	WD repeat and SOCS box containing 1	420	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	intracellular (GO:0005622)				lung(3)	3	all_cancers(1;2e-13)|all_epithelial(1;4.8e-15)|Lung NSC(42;0.00152)		BRCA - Breast invasive adenocarcinoma(3;0.0152)	UCEC - Uterine corpus endometrioid carcinoma (53;0.154)		CTCTCGTATCGTATTTAGAAG	0.423																																					p.R420H		Atlas-SNP	.											.	WSB1	29	.	0			c.G1259A						PASS	.						217	204	208					17																	25639388		2203	4300	6503	SO:0001583	missense	26118	exon9			CGTATCGTATTTA	AF069313	CCDS11220.1, CCDS11221.1	17q11.2	2013-01-09	2011-01-25		ENSG00000109046	ENSG00000109046		"WD repeat domain containing"	19221	protein-coding gene	gene with protein product		610091	"WD repeat and SOCS box-containing 1"			10354473, 12076535	Standard	XR_243778		Approved	DKFZp564A122, DKFZp564B0482, SWIP1	uc002gzd.1	Q9Y6I7	OTTHUMG00000132293	ENST00000262394.2:c.1259G>A	chr17.hg19:g.25639388G>A	ENSP00000262394:p.Arg420His	78.0	0.0	.		107.0	5.0	.	NM_015626	Q9NRB1|Q9UBH9|Q9UG25|Q9UNN6|Q9Y656	Missense_Mutation	SNP	ENST00000262394.2	hg19	CCDS11220.1	.	.	.	.	.	.	.	.	.	.	G	11.34	1.609183	0.28623	.	.	ENSG00000109046	ENST00000262394;ENST00000348811	T;T	0.45668	0.89;0.89	5.61	-0.349	0.12609	SOCS protein, C-terminal (4);	0.380726	0.25467	N	0.030468	T	0.37348	0.1000	M	0.77103	2.36	0.25069	N	0.991007	P;P	0.47409	0.895;0.808	B;B	0.39258	0.289;0.295	T	0.36696	-0.9737	10	0.59425	D	0.04	-0.7374	7.4606	0.27294	0.5866:0.0:0.4134:0.0	.	274;420	Q9Y6I7-2;Q9Y6I7	.;WSB1_HUMAN	H	420;274	ENSP00000262394:R420H;ENSP00000327055:R274H	ENSP00000262394:R420H	R	+	2	0	WSB1	22663515	0.713000	0.27926	0.021000	0.16686	0.394000	0.30568	0.916000	0.28651	0.129000	0.18514	-0.812000	0.03155	CGT	.	.	.	none		0.423	WSB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255391.4	NM_015626		A	25639388	G	A	25639388	3	1	32	1	0	0	0	0	1	0	0	0	17416	1145	40	1	1293	1	WSB1	17	25639388	Missense_Mutation	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10	13610730	25639388	55555822	69	2347											
KRT23	25984	hgsc.bcm.edu	37	chr17	39084730	39084730	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccaagtgtccaagtctcgatGcttcttctttattataagct	9	16	6	10	1	3	0	0	0	3	0	5	1	4	0	2	0	2	2	2	0	5	6			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr17:39084730G>A	ENST00000209718.3	-	5	1190	c.766C>T	c.(766-768)Cat>Tat	p.H256Y	KRT23_ENST00000436344.3_Missense_Mutation_p.H119Y|AC004231.2_ENST00000418393.1_RNA	NM_015515.3	NP_056330.3	Q9C075	K1C23_HUMAN	keratin 23 (histone deacetylase inducible)	256	Coil 2.|Rod.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Breast(137;0.000301)|Ovarian(249;0.15)				AAGTCTCGATGCTTCTTCTTT	0.423																																					p.H256Y		Atlas-SNP	.											.	KRT23	59	.	0			c.C766T						PASS	.						238	237	238					17																	39084730		2203	4300	6503	SO:0001583	missense	25984	exon5			CTCGATGCTTCTT	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.766C>T	chr17.hg19:g.39084730G>A	ENSP00000209718:p.His256Tyr	55.0	0.0	.		50.0	9.0	.	NM_015515	A8K084|B7Z7J2|I3L3Q6|Q9NUR6	Missense_Mutation	SNP	ENST00000209718.3	hg19	CCDS11380.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.410931	0.83340	.	.	ENSG00000108244	ENST00000209718;ENST00000436344	D;D	0.88664	-2.41;-2.41	5.82	4.83	0.62350	Filament (1);	0.236010	0.29932	N	0.010825	D	0.88175	0.6366	L	0.40543	1.245	0.36524	D	0.870343	P	0.48911	0.917	P	0.48166	0.569	D	0.91444	0.5176	10	0.87932	D	0	.	16.0906	0.81088	0.0:0.0:0.8649:0.1351	.	256	Q9C075	K1C23_HUMAN	Y	256;119	ENSP00000209718:H256Y;ENSP00000414056:H119Y	ENSP00000209718:H256Y	H	-	1	0	KRT23	36338256	1.000000	0.71417	0.976000	0.42696	0.947000	0.59692	6.419000	0.73345	1.417000	0.47077	0.655000	0.94253	CAT	.	.	.	none		0.423	KRT23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257223.1			A	39084730	G	A	39084730	3	1	32	1	0	0	0	0	1	0	0	0	8467	1319	46	2	522	2	KRT23	17	39084730	Missense_Mutation	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10	13445342	39084730	42110480	70	2348											
TANC2	26115	hgsc.bcm.edu	37	chr17	61498264	61498264	+	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	gccaagtagcccattcaatgGccagtaaataccagtcttca	13	9	7	12	0	3	0	2	0	1	0	3	0	3	0	4	1	2	2	4	1	6	5			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr17:61498264G>T	ENST00000424789.2	+	25	4925	c.4921G>T	c.(4921-4923)Gcc>Tcc	p.A1641S	TANC2_ENST00000389520.4_Missense_Mutation_p.A1651S|RP11-269G24.3_ENST00000583552.1_RNA	NM_025185.3	NP_079461.2	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	1641					in utero embryonic development (GO:0001701)					breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|upper_aerodigestive_tract(3)	44						CCATTCAATGGCCAGTAAATA	0.547																																					p.A1641S		Atlas-SNP	.											.	TANC2	266	.	0			c.G4921T						PASS	.						76	82	80					17																	61498264		2162	4277	6439	SO:0001583	missense	26115	exon25			TCAATGGCCAGTA	AB032974	CCDS45754.1	17q23.3	2013-01-11				ENSG00000170921		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30212	protein-coding gene	gene with protein product	"rolling pebbles homolog B (Drosophila)"	615047					Standard	NM_025185		Approved	DKFZP564D166, FLJ10215, FLJ11824, KIAA1148, KIAA1636, rols, ROLSA	uc002jal.4	Q9HCD6		ENST00000424789.2:c.4921G>T	chr17.hg19:g.61498264G>T	ENSP00000387593:p.Ala1641Ser	67.0	0.0	.		94.0	16.0	.	NM_025185	Q9HAC3|Q9NW88|Q9NXY9|Q9ULS2	Missense_Mutation	SNP	ENST00000424789.2	hg19	CCDS45754.1	.	.	.	.	.	.	.	.	.	.	G	4.811	0.150774	0.09185	.	.	ENSG00000170921	ENST00000389520;ENST00000424789	T;T	0.65364	-0.15;-0.15	5.2	5.2	0.72013	.	0.139271	0.48767	D	0.000169	T	0.39226	0.1070	N	0.04508	-0.205	0.37296	D	0.908467	B	0.29766	0.256	B	0.23419	0.046	T	0.42032	-0.9475	10	0.11485	T	0.65	.	19.093	0.93235	0.0:0.0:1.0:0.0	.	1641	Q9HCD6	TANC2_HUMAN	S	1651;1641	ENSP00000374171:A1651S;ENSP00000387593:A1641S	ENSP00000374171:A1651S	A	+	1	0	TANC2	58851996	1.000000	0.71417	0.998000	0.56505	0.337000	0.28794	5.335000	0.65929	2.600000	0.87896	0.561000	0.74099	GCC	.	.	.	none		0.547	TANC2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444765.1			T	61498264	G	T	61498264	3	4	32	1	0	0	0	0	1	0	0	0	15557	1203	42	4	5019	4	TANC2	17	61498264	Missense_Mutation	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10	22413534	61498264	19696946	71	2349											
NOL11	25926	hgsc.bcm.edu	37	chr17	65720229	65720229	+	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	cttaaccaaatatacactctTacttggacaagacgaaaact	17	10	4	10	1	1	1	0	0	1	1	1	3	1	2	1	1	4	0	1	1	8	5			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr17:65720229T>G	ENST00000253247.4	+	6	699	c.584T>G	c.(583-585)tTa>tGa	p.L195*	NOL11_ENST00000535137.1_Nonsense_Mutation_p.L13*	NM_015462.3	NP_056277.2	Q9H8H0	NOL11_HUMAN	nucleolar protein 11	195					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)			TATACACTCTTACTTGGACAA	0.299																																					p.L195X		Atlas-SNP	.											.	NOL11	48	.	0			c.T584G						PASS	.						94	95	95					17																	65720229		2203	4299	6502	SO:0001587	stop_gained	25926	exon6			CACTCTTACTTGG	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.584T>G	chr17.hg19:g.65720229T>G	ENSP00000253247:p.Leu195*	27.0	0.0	.		55.0	28.0	.	NM_015462	B7Z5V9|Q7L5S1|Q9UG18	Nonsense_Mutation	SNP	ENST00000253247.4	hg19	CCDS11671.1	.	.	.	.	.	.	.	.	.	.	T	18.68	3.675567	0.67928	.	.	ENSG00000130935	ENST00000253247;ENST00000535137	.	.	.	4.54	3.46	0.39613	.	0.551131	0.17882	N	0.158838	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.4969	6.8539	0.24030	0.0:0.1084:0.0:0.8916	.	.	.	.	X	195;13	.	ENSP00000253247:L195X	L	+	2	0	NOL11	63150691	0.411000	0.25384	0.967000	0.41034	0.223000	0.24884	1.047000	0.30367	0.710000	0.31997	0.377000	0.23210	TTA	.	.	.	none		0.299	NOL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448074.1	NM_015462		G	65720229	T	G	65720229	4	3	32	1	0	0	0	0	0	1	0	0	10528	1764	61	5	606	5	NOL11	17	65720229	Nonsense_Mutation	SNP	T	TCGA-5P-A9K0-01A-11D-A42J-10	4221965	65720229	15474981	72	2350											
KPNA2	3838	hgsc.bcm.edu	37	chr17	66039316	66039316	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgagcagattcttcctacctTagttcggctcctgcatcatg	7	14	8	12	1	2	2	1	1	1	1	5	2	4	2	3	1	3	4	3	1	2	5			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr17:66039316T>C	ENST00000537025.2	+	7	1387	c.767T>C	c.(766-768)tTa>tCa	p.L256S	KPNA2_ENST00000330459.3_Missense_Mutation_p.L256S			P52292	IMA1_HUMAN	karyopherin alpha 2 (RAG cohort 1, importin alpha 1)	256					cytokine-mediated signaling pathway (GO:0019221)|DNA metabolic process (GO:0006259)|NLS-bearing protein import into nucleus (GO:0006607)|regulation of DNA recombination (GO:0000018)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone deacetylase binding (GO:0042826)|nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|kidney(2)|lung(9)|prostate(1)|urinary_tract(2)	22	all_cancers(12;1.18e-09)		BRCA - Breast invasive adenocarcinoma(8;1.03e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			CTTCCTACCTTAGTTCGGCTC	0.458																																					p.L256S		Atlas-SNP	.											.	KPNA2	55	.	0			c.T767C						PASS	.						178	185	183					17																	66039316		2203	4300	6503	SO:0001583	missense	3838	exon7			CTACCTTAGTTCG	U09559	CCDS32713.1	17q24.2	2013-02-14						"Importins", "Armadillo repeat containing"	6395	protein-coding gene	gene with protein product		600685		RCH1		8016130, 7754385	Standard	NM_002266		Approved	SRP1alpha, IPOA1, QIP2	uc002jgk.3	P52292		ENST00000537025.2:c.767T>C	chr17.hg19:g.66039316T>C	ENSP00000438483:p.Leu256Ser	55.0	0.0	.		86.0	46.0	.	NM_002266	B9EJD6|Q53YE3|Q9BRU5	Missense_Mutation	SNP	ENST00000537025.2	hg19	CCDS32713.1	.	.	.	.	.	.	.	.	.	.	T	16.62	3.173143	0.57584	.	.	ENSG00000182481	ENST00000330459;ENST00000537025	D;D	0.89746	-2.56;-2.56	5.56	5.56	0.83823	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	U	0.000013	D	0.96012	0.8701	H	0.94183	3.505	0.80722	D	1	D	0.69078	0.997	D	0.76071	0.987	D	0.97172	0.9845	10	0.87932	D	0	.	15.7143	0.77655	0.0:0.0:0.0:1.0	.	256	P52292	IMA2_HUMAN	S	256	ENSP00000332455:L256S;ENSP00000438483:L256S	ENSP00000332455:L256S	L	+	2	0	KPNA2	63469778	1.000000	0.71417	0.762000	0.31397	0.036000	0.12997	7.857000	0.86963	2.105000	0.64084	0.455000	0.32223	TTA	.	.	.	none		0.458	KPNA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448111.1	NM_002266		C	66039316	T	C	66039316	3	2	32	1	0	0	0	0	1	0	0	0	8437	1764	61	3	789	3	KPNA2	17	66039316	Missense_Mutation	SNP	T	TCGA-5P-A9K0-01A-11D-A42J-10	319087	66039316	15155894	73	2351											
NEDD4L	23327	hgsc.bcm.edu	37	chr18	55992364	55992364	+	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	ctatgtcaaccacaacaaccGgaccactcagtggcacagac	14	5	7	15	1	2	1	2	0	0	1	2	2	2	2	3	2	3	1	3	2	4	1			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr18:55992364G>T	ENST00000400345.3	+	9	933	c.650G>T	c.(649-651)cGg>cTg	p.R217L	NEDD4L_ENST00000456173.2_Missense_Mutation_p.R96L|NEDD4L_ENST00000431212.2_Missense_Mutation_p.R96L|NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000586263.1_Missense_Mutation_p.R209L|NEDD4L_ENST00000356462.6_Missense_Mutation_p.R217L|NEDD4L_ENST00000382850.4_Missense_Mutation_p.R217L|NEDD4L_ENST00000456986.1_Missense_Mutation_p.R96L|NEDD4L_ENST00000256832.7_Missense_Mutation_p.R96L|NEDD4L_ENST00000256830.9_Missense_Mutation_p.R217L|NEDD4L_ENST00000357895.5_Missense_Mutation_p.R209L|NEDD4L_ENST00000435432.2_Missense_Mutation_p.R96L	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	217	WW 1. {ECO:0000255|PROSITE- ProRule:PRU00224}.				cellular sodium ion homeostasis (GO:0006883)|excretion (GO:0007588)|gene expression (GO:0010467)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cation channel activity (GO:2001259)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of sodium ion transport (GO:0010765)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane depolarization (GO:0003254)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of protein catabolic process (GO:0042176)|regulation of tight junction assembly (GO:2000810)|response to metal ion (GO:0010038)|response to salt stress (GO:0009651)|sodium ion transport (GO:0006814)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|ventricular cardiac muscle cell action potential (GO:0086005)|viral life cycle (GO:0019058)|viral process (GO:0016032)|water homeostasis (GO:0030104)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ion channel binding (GO:0044325)|ligase activity (GO:0016874)|potassium channel inhibitor activity (GO:0019870)|potassium channel regulator activity (GO:0015459)|sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4)	37						CACAACAACCGGACCACTCAG	0.542																																					p.R217L		Atlas-SNP	.											.	NEDD4L	126	.	0			c.G650T						PASS	.						176	176	176					18																	55992364		2061	4196	6257	SO:0001583	missense	23327	exon9			ACAACCGGACCAC	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.650G>T	chr18.hg19:g.55992364G>T	ENSP00000383199:p.Arg217Leu	84.0	0.0	.		48.0	4.0	.	NM_015277	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Missense_Mutation	SNP	ENST00000400345.3	hg19	CCDS45872.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.972477	0.92919	.	.	ENSG00000049759	ENST00000400345;ENST00000382850;ENST00000356462;ENST00000256830;ENST00000256832;ENST00000456986;ENST00000357895;ENST00000435432;ENST00000456173;ENST00000431212	D;D;D;D;D;D;D;D;D;D	0.84442	-1.85;-1.85;-1.85;-1.85;-1.85;-1.85;-1.85;-1.85;-1.85;-1.85	5.51	5.51	0.81932	WW/Rsp5/WWP (6);	0.107321	0.64402	D	0.000014	D	0.94437	0.8210	H	0.96576	3.845	0.58432	D	0.999999	P;D;D;P;P;D;D	0.67145	0.872;0.996;0.996;0.722;0.493;0.986;0.996	B;D;D;B;B;D;D	0.68621	0.441;0.959;0.959;0.369;0.196;0.941;0.959	D	0.95496	0.8573	10	0.72032	D	0.01	.	12.7259	0.57170	0.0748:0.0:0.9252:0.0	.	217;209;209;96;217;217;217	Q96PU5-3;Q96PU5-6;Q96PU5-7;Q3LSM7;Q96PU5-2;Q96PU5;Q96PU5-5	.;.;.;.;.;NED4L_HUMAN;.	L	217;217;217;217;96;96;209;96;96;96	ENSP00000383199:R217L;ENSP00000372301:R217L;ENSP00000348847:R217L;ENSP00000256830:R217L;ENSP00000256832:R96L;ENSP00000411947:R96L;ENSP00000350569:R209L;ENSP00000393395:R96L;ENSP00000405440:R96L;ENSP00000389406:R96L	ENSP00000256830:R217L	R	+	2	0	NEDD4L	54143344	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.623000	0.83113	2.600000	0.87896	0.655000	0.94253	CGG	.	.	.	none		0.542	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1			T	55992364	G	T	55992364	3	4	32	1	0	0	0	0	1	0	0	0	10318	1116	39	4	712	4	NEDD4L	18	55992364	Missense_Mutation	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10		55992364	22084884	74	2352											
CDH20	28316	hgsc.bcm.edu	37	chr18	59221635	59221635	+	Missense_Mutation	SNP	A	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	ggcaggacatgctgcccgagAtcgagagcctctcccgctac	8	6	12	15	3	1	2	0	0	1	2	3	5	1	3	3	2	4	3	3	2	1	1			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr18:59221635A>C	ENST00000262717.4	+	12	2511	c.2113A>C	c.(2113-2115)Atc>Ctc	p.I705L	CDH20_ENST00000538374.1_Missense_Mutation_p.I705L|CDH20_ENST00000536675.2_Missense_Mutation_p.I705L			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	705					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)				GCTGCCCGAGATCGAGAGCCT	0.677																																					p.I705L		Atlas-SNP	.											.	CDH20	117	.	0			c.A2113C						PASS	.						39	39	39					18																	59221635		2203	4300	6503	SO:0001583	missense	28316	exon11			CCCGAGATCGAGA	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.2113A>C	chr18.hg19:g.59221635A>C	ENSP00000262717:p.Ile705Leu	65.0	0.0	.		67.0	27.0	.	NM_031891	Q495S3	Missense_Mutation	SNP	ENST00000262717.4	hg19	CCDS11977.1	.	.	.	.	.	.	.	.	.	.	A	16.35	3.098802	0.56183	.	.	ENSG00000101542	ENST00000536675;ENST00000538374;ENST00000262717	T;T;T	0.76186	-1.0;-1.0;-1.0	5.78	5.78	0.91487	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	T	0.65903	0.2736	L	0.28274	0.84	0.51767	D	0.999931	P	0.39376	0.67	B	0.43194	0.411	T	0.62310	-0.6881	10	0.10111	T	0.7	.	16.3979	0.83621	1.0:0.0:0.0:0.0	.	705	Q9HBT6	CAD20_HUMAN	L	705	ENSP00000444767:I705L;ENSP00000442226:I705L;ENSP00000262717:I705L	ENSP00000262717:I705L	I	+	1	0	CDH20	57372615	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.218000	0.65257	2.333000	0.79357	0.533000	0.62120	ATC	.	.	.	none		0.677	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891		C	59221635	A	C	59221635	3	2	32	1	0	0	0	0	1	0	0	0	3108	333	12	5	2155	5	CDH20	18	59221635	Missense_Mutation	SNP	A	TCGA-5P-A9K0-01A-11D-A42J-10	3229271	59221635	18855613	75	2353											
TJP3	27134	hgsc.bcm.edu	37	chr19	3740744	3740744	+	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	ccgctacccgccctacgaacGagtggtgttgcgagaaggtg	8	7	14	12	5	0	1	0	0	0	1	0	4	0	1	3	2	4	2	3	2	4	3			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr19:3740744G>A	ENST00000541714.2	+	14	2288	c.1826G>A	c.(1825-1827)cGa>cAa	p.R609Q	TJP3_ENST00000589378.1_Missense_Mutation_p.R618Q|TJP3_ENST00000539908.2_Missense_Mutation_p.R573Q|TJP3_ENST00000382008.3_Missense_Mutation_p.R623Q|TJP3_ENST00000587686.1_Missense_Mutation_p.R628Q|TJP3_ENST00000262968.9_Missense_Mutation_p.R642Q	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	609	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				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)		CCCTACGAACGAGTGGTGTTG	0.642																																					p.R618Q		Atlas-SNP	.											.	TJP3	79	.	0			c.G1853A						PASS	.						17	19	18					19																	3740744		2201	4298	6499	SO:0001583	missense	27134	exon14			ACGAACGAGTGGT	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.1826G>A	chr19.hg19:g.3740744G>A	ENSP00000439278:p.Arg609Gln	113.0	0.0	.		97.0	41.0	.	NM_001267561	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Missense_Mutation	SNP	ENST00000541714.2	hg19	CCDS32873.2	.	.	.	.	.	.	.	.	.	.	G	20.2	3.944565	0.73672	.	.	ENSG00000105289	ENST00000541714;ENST00000539908;ENST00000382008;ENST00000262968	T;T;T;T	0.11385	2.78;2.97;2.78;2.87	5.0	5.0	0.66597	Guanylate kinase/L-type calcium channel (1);	0.000000	0.85682	D	0.000000	T	0.38558	0.1045	M	0.86268	2.805	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.998	D;D;D;P	0.80764	0.988;0.994;0.977;0.889	T	0.41431	-0.9509	10	0.87932	D	0	.	16.8553	0.86004	0.0:0.0:1.0:0.0	.	628;642;623;609	O95049-3;O95049-2;O95049;F5H2X0	.;.;ZO3_HUMAN;.	Q	609;573;623;642	ENSP00000439278:R609Q;ENSP00000439991:R573Q;ENSP00000371438:R623Q;ENSP00000262968:R642Q	ENSP00000262968:R642Q	R	+	2	0	TJP3	3691744	1.000000	0.71417	0.527000	0.27925	0.131000	0.20780	5.430000	0.66501	2.286000	0.76751	0.655000	0.94253	CGA	.	.	.	none		0.642	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1			A	3740744	G	A	3740744	3	1	32	1	0	0	0	0	1	0	0	0	15943	1058	37	1	1975	1	TJP3	19	3740744	Missense_Mutation	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10		3740744	55388239	76	2354											
MPND	84954	hgsc.bcm.edu	37	chr19	4343749	4343749	+	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	gcggtgcgggcgaggaggcgCcggaggaggacgaggacgaa	9	1	23	8	7	0	0	0	0	0	0	0	8	0	5	1	8	1	0	1	8	1	0			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr19:4343749C>A	ENST00000262966.8	+	2	119	c.52C>A	c.(52-54)Ccg>Acg	p.P18T	AC007292.7_ENST00000598582.1_RNA|MPND_ENST00000359935.4_Missense_Mutation_p.P18T|MPND_ENST00000599840.1_Missense_Mutation_p.P18T	NM_032868.4	NP_116257.2	Q8N594	MPND_HUMAN	MPN domain containing	18							peptidase activity (GO:0008233)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)	8				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		CGAGGAGGCGCCGGAGGAGGA	0.776																																					p.P18T		Atlas-SNP	.											.	MPND	28	.	0			c.C52A						PASS	.						2	3	2					19																	4343749		1012	2236	3248	SO:0001583	missense	84954	exon2			GAGGCGCCGGAGG		CCDS42470.1, CCDS54200.1, CCDS74261.1	19p13.3	2014-08-12			ENSG00000008382				25934	protein-coding gene	gene with protein product							Standard	XM_005259663		Approved	FLJ14981	uc002mae.3	Q8N594	OTTHUMG00000181914	ENST00000262966.8:c.52C>A	chr19.hg19:g.4343749C>A	ENSP00000262966:p.Pro18Thr	26.0	0.0	.		27.0	14.0	.	NM_032868	Q96SJ0|Q9Y2P1|Q9Y2P2	Missense_Mutation	SNP	ENST00000262966.8	hg19	CCDS42470.1	.	.	.	.	.	.	.	.	.	.	C	15.88	2.962778	0.53507	.	.	ENSG00000008382	ENST00000262966;ENST00000359935	T;T	0.46819	0.86;0.86	3.52	2.46	0.29980	.	0.228377	0.26079	N	0.026463	T	0.36386	0.0965	L	0.56769	1.78	0.26945	N	0.96617	P;B;B	0.35982	0.531;0.244;0.244	B;B;B	0.29785	0.107;0.05;0.05	T	0.41822	-0.9487	10	0.87932	D	0	-21.8679	5.8373	0.18615	0.0:0.8489:0.0:0.1511	.	18;18;18	Q8N594-2;A6NI36;Q8N594	.;.;MPND_HUMAN	T	18	ENSP00000262966:P18T;ENSP00000353015:P18T	ENSP00000262966:P18T	P	+	1	0	MPND	4294749	0.575000	0.26692	0.970000	0.41538	0.979000	0.70002	0.457000	0.21875	1.493000	0.48517	0.455000	0.32223	CCG	.	.	.	none		0.776	MPND-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458292.1	NM_032868		A	4343749	C	A	4343749	3	1	32	1	0	0	0	0	1	0	0	0	9738	739	26	4	58	4	MPND	19	4343749	Missense_Mutation	SNP	C	TCGA-5P-A9K0-01A-11D-A42J-10	603005	4343749	54785234	77	2355											
SLC5A5	6528	hgsc.bcm.edu	37	chr19	17986910	17986910	+	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	aaccactcccggatcaacctCatggagtgagtgaaaatgca	14	7	9	11	1	2	2	2	2	0	0	3	4	3	4	3	2	3	1	3	2	4	0			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr19:17986910C>A	ENST00000222248.3	+	5	1040	c.693C>A	c.(691-693)ctC>ctA	p.L231L		NM_000453.2	NP_000444.1	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium/iodide cotransporter), member 5	231					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						GGATCAACCTCATGGAGTGAG	0.622																																					p.L231L	Melanoma(65;1008 1708 7910 46650)	Atlas-SNP	.											SLC5A5,right_upper_lobe,carcinoma,0,1	SLC5A5	67	.	0			c.C693A						PASS	.						139	115	123					19																	17986910		2203	4300	6503	SO:0001819	synonymous_variant	6528	exon5			CAACCTCATGGAG		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.693C>A	chr19.hg19:g.17986910C>A		41.0	0.0	.		48.0	27.0	.	NM_000453	O43702|Q2M335|Q9NYB6	Silent	SNP	ENST00000222248.3	hg19	CCDS12368.1																																																																																			.	.	.	none		0.622	SLC5A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466690.1			A	17986910	C	A	17986910	2	1	32	1	0	0	0	0	0	0	0	1	14681	813	29	4		4	SLC5A5	19	17986910	Silent	SNP	C	TCGA-5P-A9K0-01A-11D-A42J-10	13643161	17986910	41142073	78	2356											
RAB3A	5864	hgsc.bcm.edu	37	chr19	18309591	18309591	+	Missense_Mutation	SNP	A	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	acaccacccgctcatcctccAtgtcacacttgtttcctacc	8	11	3	19	1	2	0	2	0	0	0	5	0	5	0	6	0	1	2	6	0	1	3			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr19:18309591A>C	ENST00000222256.4	-	4	594	c.416T>G	c.(415-417)aTg>aGg	p.M139R	RAB3A_ENST00000464076.3_Missense_Mutation_p.M44R	NM_002866.4	NP_002857.1	P20336	RAB3A_HUMAN	RAB3A, member RAS oncogene family	139					axonogenesis (GO:0007409)|constitutive secretory pathway (GO:0045054)|glutamate secretion (GO:0014047)|GTP catabolic process (GO:0006184)|lung development (GO:0030324)|maintenance of presynaptic active zone structure (GO:0048790)|mitochondrion organization (GO:0007005)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|positive regulation of exocytosis (GO:0045921)|post-embryonic development (GO:0009791)|protein transport (GO:0015031)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|respiratory system process (GO:0003016)|response to electrical stimulus (GO:0051602)|sensory perception of touch (GO:0050975)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|synaptic vesicle maturation (GO:0016188)|synaptic vesicle recycling (GO:0036465)	acrosomal vesicle (GO:0001669)|axon (GO:0030424)|clathrin-sculpted acetylcholine transport vesicle membrane (GO:0060201)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|clathrin-sculpted glutamate transport vesicle membrane (GO:0060203)|clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|vesicle (GO:0031982)	ATPase activator activity (GO:0001671)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			NS(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	8						CTCATCCTCCATGTCACACTT	0.577																																					p.M139R		Atlas-SNP	.											.	RAB3A	23	.	0			c.T416G						PASS	.						148	113	125					19																	18309591		2203	4300	6503	SO:0001583	missense	5864	exon4			TCCTCCATGTCAC		CCDS12372.1	19p13.2	2008-07-17			ENSG00000105649	ENSG00000105649		"RAB, member RAS oncogene"	9777	protein-coding gene	gene with protein product	"RAS-associated protein RAB3A"	179490				2687157, 7532276	Standard	NM_002866		Approved		uc002nie.2	P20336	OTTHUMG00000137378	ENST00000222256.4:c.416T>G	chr19.hg19:g.18309591A>C	ENSP00000222256:p.Met139Arg	51.0	0.0	.		40.0	22.0	.	NM_002866	A8K0J4|Q9NYE1	Missense_Mutation	SNP	ENST00000222256.4	hg19	CCDS12372.1	.	.	.	.	.	.	.	.	.	.	A	15.37	2.812370	0.50527	.	.	ENSG00000105649	ENST00000222256	T	0.79454	-1.27	5.24	4.23	0.50019	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.67599	0.2910	L	0.38838	1.175	0.80722	D	1	B	0.09022	0.002	B	0.15484	0.013	T	0.63134	-0.6705	10	0.72032	D	0.01	-41.6067	9.0893	0.36601	0.9116:0.0:0.0884:0.0	.	139	P20336	RAB3A_HUMAN	R	139	ENSP00000222256:M139R	ENSP00000222256:M139R	M	-	2	0	RAB3A	18170591	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.115000	0.94336	0.831000	0.34780	0.459000	0.35465	ATG	.	.	.	none		0.577	RAB3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268056.2	NM_002866		C	18309591	A	C	18309591	3	2	32	1	0	0	0	0	1	0	0	0	12944	217	8	5	254	5	RAB3A	19	18309591	Missense_Mutation	SNP	A	TCGA-5P-A9K0-01A-11D-A42J-10	322681	18309591	40819392	79	2357											
ZNF575	284346	hgsc.bcm.edu	37	chr19	44039436	44039442	+	Frame_Shift_Del	DEL	CGCACAG	CGCACAG	-																															gctggcagcccaccgcctcaCgcacagcggcgcccgcccgc																										TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	CGCACAG	CGCACAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr19:44039436_44039442delCGCACAG	ENST00000314228.5	+	4	847_853	c.335_341delCGCACAG	c.(334-342)acgcacagcfs	p.THS112fs	ZNF575_ENST00000458714.2_Frame_Shift_Del_p.THS211fs|ZNF575_ENST00000601282.1_Frame_Shift_Del_p.THS112fs	NM_174945.2	NP_777605.1	Q86XF7	ZN575_HUMAN	zinc finger protein 575	112					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)				CACCGCCTCACGCACAGCGGCGCCCGC	0.72																																					p.112_114del		Atlas-Indel,Pindel	.											.	ZNF575	14	.	0			c.334_340del						PASS	.																																			SO:0001589	frameshift_variant	284346	exon4			.	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.335_341delCGCACAG	chr19.hg19:g.44039436_44039442delCGCACAG	ENSP00000315870:p.Thr112fs	110.0	0.0	0		81.0	22.0	0.271605	NM_174945	B4DX54	Frame_Shift_Del	DEL	ENST00000314228.5	hg19	CCDS12623.1																																																																																			.	.	.	none		0.72	ZNF575-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463191.1	NM_174945		-	44039442	CGCACAG	-	44039436	7	5	32	1	0	1	0	1	0	0	0	0	18019	536	19	0	341	0	ZNF575	19	44039436	Frame_Shift_Del	DEL	CGCACAG	TCGA-5P-A9K0-01A-11D-A42J-10	25729845	44039436	15089547	80	2358											
RSPH6A	81492	hgsc.bcm.edu	37	chr19	46308112	46308112	+	Missense_Mutation	SNP	T	T	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	caccaggtagctgcgtttgaTtcccaggatcttgccccaga	8	10	10	13	1	1	2	0	1	1	1	2	3	2	3	4	2	3	3	4	2	1	4			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr19:46308112T>G	ENST00000221538.3	-	3	1193	c.1051A>C	c.(1051-1053)Atc>Ctc	p.I351L	RSPH6A_ENST00000597055.1_Missense_Mutation_p.I351L|RSPH6A_ENST00000600188.1_Missense_Mutation_p.I87L	NM_030785.3	NP_110412.1	Q9H0K4	RSH6A_HUMAN	radial spoke head 6 homolog A (Chlamydomonas)	351						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						CTGCGTTTGATTCCCAGGATC	0.612																																					p.I351L		Atlas-SNP	.											.	RSPH6A	70	.	0			c.A1051C						PASS	.						79	63	69					19																	46308112		2203	4300	6503	SO:0001583	missense	81492	exon3			GTTTGATTCCCAG	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.1051A>C	chr19.hg19:g.46308112T>G	ENSP00000221538:p.Ile351Leu	53.0	0.0	.		44.0	16.0	.	NM_030785	Q53FE2|Q6PEZ9	Missense_Mutation	SNP	ENST00000221538.3	hg19	CCDS12675.1	.	.	.	.	.	.	.	.	.	.	T	0.016	-1.539158	0.00942	.	.	ENSG00000104941	ENST00000221538	T	0.15718	2.4	4.08	0.585	0.17428	.	0.639188	0.14459	N	0.318311	T	0.03871	0.0109	N	0.00980	-1.08	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.43458	-0.9390	10	0.02654	T	1	-1.7801	7.385	0.26878	0.0:0.1517:0.3433:0.505	.	351	Q9H0K4	RSH6A_HUMAN	L	351	ENSP00000221538:I351L	ENSP00000221538:I351L	I	-	1	0	RSPH6A	50999952	0.348000	0.24861	0.144000	0.22314	0.492000	0.33523	1.902000	0.39848	0.227000	0.20999	-0.666000	0.03841	ATC	.	.	.	none		0.612	RSPH6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461657.1			G	46308112	T	G	46308112	3	3	32	1	0	0	0	0	1	0	0	0	13720	1493	52	5	1118	5	RSPH6A	19	46308112	Missense_Mutation	SNP	T	TCGA-5P-A9K0-01A-11D-A42J-10	2268676	46308112	12820871	81	2359											
ZNF470	388566	hgsc.bcm.edu	37	chr19	57088479	57088479	+	Silent	SNP	T	T	C																															accgtggagaaaagaaacttTtaaaatgtaatgactgtgag																										TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr19:57088479T>C	ENST00000330619.8	+	6	1368	c.682T>C	c.(682-684)Tta>Cta	p.L228L	ZNF470_ENST00000391709.3_Silent_p.L228L|ZNF470_ENST00000601902.1_Intron	NM_001001668.3	NP_001001668.3	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	228					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|large_intestine(12)|lung(11)|ovary(1)|pancreas(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	41		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)		AAAGAAACTTTTAAAATGTAA	0.318																																					p.L228L		Atlas-SNP	.											.	ZNF470	103	.	0			c.T682C						PASS	.						41	43	42					19																	57088479		2203	4298	6501	SO:0001819	synonymous_variant	388566	exon6			AAACTTTTAAAAT	AK129686	CCDS33122.1	19q13.43	2013-01-08				ENSG00000197016		"Zinc fingers, C2H2-type", "-"	22220	protein-coding gene	gene with protein product						15302581	Standard	NM_001001668		Approved	CZF-1, FLJ26175	uc002qnl.4	Q6ECI4		ENST00000330619.8:c.682T>C	chr19.hg19:g.57088479T>C		116.0	0.0	.		92.0	39.0	.	NM_001001668	A8MTW0|B9EGU1|Q6ZPA1|Q9Y2N9	Silent	SNP	ENST00000330619.8	hg19	CCDS33122.1																																																																																			.	.	.	none		0.318	ZNF470-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459707.2	NM_001001668		C	57088479	T	C	57088479	2	2	32	1	0	0	0	0	0	0	0	1	17941	1838	64	3		3	ZNF470	19	57088479	Silent	SNP	T	TCGA-5P-A9K0-01A-11D-A42J-10	10780367	57088479	2040504	82	2360	28	2									
ZNF470	388566	hgsc.bcm.edu	37	chr19	57088481	57088481	+	Frame_Shift_Del	DEL	A	A	-																															cgtggagaaaagaaacttttAaaatgtaatgactgtgagaa																										TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr19:57088481delA	ENST00000330619.8	+	6	1370	c.684delA	c.(682-684)ttafs	p.L228fs	ZNF470_ENST00000391709.3_Frame_Shift_Del_p.L228fs|ZNF470_ENST00000601902.1_Intron	NM_001001668.3	NP_001001668.3	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	228					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|large_intestine(12)|lung(11)|ovary(1)|pancreas(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	41		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)		AGAAACTTTTAAAATGTAATG	0.318																																					p.L228X		Atlas-Indel,Pindel	.											.	ZNF470	103	.	0			c.683delT						PASS	.						41	43	42					19																	57088481		2202	4298	6500	SO:0001589	frameshift_variant	388566	exon6			.	AK129686	CCDS33122.1	19q13.43	2013-01-08				ENSG00000197016		"Zinc fingers, C2H2-type", "-"	22220	protein-coding gene	gene with protein product						15302581	Standard	NM_001001668		Approved	CZF-1, FLJ26175	uc002qnl.4	Q6ECI4		ENST00000330619.8:c.684delA	chr19.hg19:g.57088481delA	ENSP00000333223:p.Leu228fs	114.0	0.0	0		91.0	37.0	0.406593	NM_001001668	A8MTW0|B9EGU1|Q6ZPA1|Q9Y2N9	Frame_Shift_Del	DEL	ENST00000330619.8	hg19	CCDS33122.1																																																																																			.	.	.	none		0.318	ZNF470-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459707.2	NM_001001668		-	57088481	A	-	57088481	7	5	32	1	0	1	0	1	0	0	0	0	17941	359	13	0	698	0	ZNF470	19	57088481	Frame_Shift_Del	DEL	A	TCGA-5P-A9K0-01A-11D-A42J-10	2	57088481	2040502	83	2361	28	2									
CENPB	1059	hgsc.bcm.edu	37	chr20	3766512	3766512	+	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	tccgcacagccccgcggcctGgtcgggcaggaagtcgtacc	6	5	14	16	5	0	0	0	0	0	0	3	1	1	1	5	4	2	3	5	4	2	1			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr20:3766512G>T	ENST00000379751.4	-	1	825	c.619C>A	c.(619-621)Cag>Aag	p.Q207K	CDC25B_ENST00000379598.5_5'Flank|CDC25B_ENST00000344256.6_5'Flank	NM_001810.5	NP_001801.1	P07199	CENPB_HUMAN	centromere protein B, 80kDa	207					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						CCCGCGGCCTGGTCGGGCAGG	0.711																																					p.Q207K		Atlas-SNP	.											.	CENPB	24	.	0			c.C619A						PASS	.						38	42	41					20																	3766512		2053	3965	6018	SO:0001583	missense	1059	exon1			CGGCCTGGTCGGG	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.619C>A	chr20.hg19:g.3766512G>T	ENSP00000369075:p.Gln207Lys	83.0	0.0	.		109.0	64.0	.	NM_001810	Q96EI4	Missense_Mutation	SNP	ENST00000379751.4	hg19	CCDS13064.1	.	.	.	.	.	.	.	.	.	.	g	2.123	-0.400953	0.04865	.	.	ENSG00000125817	ENST00000379751	T	0.41065	1.01	4.04	3.06	0.35304	.	0.329002	0.17525	U	0.171098	T	0.18635	0.0447	N	0.05230	-0.09	0.29031	N	0.885727	B	0.20052	0.041	B	0.22880	0.042	T	0.25745	-1.0123	10	0.02654	T	1	-13.7175	10.5484	0.45072	0.0:0.0:0.8047:0.1952	.	207	P07199	CENPB_HUMAN	K	207	ENSP00000369075:Q207K	ENSP00000369075:Q207K	Q	-	1	0	CENPB	3714512	1.000000	0.71417	0.996000	0.52242	0.238000	0.25445	2.542000	0.45744	0.647000	0.30713	0.457000	0.33378	CAG	.	.	.	none		0.711	CENPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077772.2	NM_001810		T	3766512	G	T	3766512	3	4	32	1	0	0	0	0	1	0	0	0	3229	1357	47	4	1184	4	CENPB	20	3766512	Missense_Mutation	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10		3766512	59259008	84	2362											
RPN2	6185	hgsc.bcm.edu	37	chr20	35864988	35864988	+	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	cacctcttcttgcagctatgCtgggactcatgtatgtctac	7	14	8	12	0	4	0	1	0	3	0	4	1	4	1	1	1	4	4	1	1	3	5			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr20:35864988C>A	ENST00000237530.6	+	16	2070	c.1759C>A	c.(1759-1761)Ctg>Atg	p.L587M	RPN2_ENST00000373622.5_Missense_Mutation_p.L555M|RPN2_ENST00000470352.1_3'UTR	NM_002951.3	NP_002942.2	P04844	RPN2_HUMAN	ribophorin II	587					aging (GO:0007568)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|gene expression (GO:0010467)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	autophagic vacuole membrane (GO:0000421)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|oligosaccharyltransferase complex (GO:0008250)|rough endoplasmic reticulum (GO:0005791)	ribosome binding (GO:0043022)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|skin(2)|stomach(1)	24		Myeloproliferative disorder(115;0.00878)				TGCAGCTATGCTGGGACTCAT	0.463																																					p.L587M		Atlas-SNP	.											.	RPN2	45	.	0			c.C1759A						PASS	.						127	99	108					20																	35864988		2203	4300	6503	SO:0001583	missense	6185	exon16			GCTATGCTGGGAC	Y00282	CCDS13291.1, CCDS46599.1	20q12-q13.1	2013-03-06			ENSG00000118705	ENSG00000118705			10382	protein-coding gene	gene with protein product	"oligosaccharyltransferase complex subunit (non-catalytic)"	180490					Standard	NM_002951		Approved	SWP1, RPNII, RIBIIR, RPN-II	uc002xgp.3	P04844	OTTHUMG00000032409	ENST00000237530.6:c.1759C>A	chr20.hg19:g.35864988C>A	ENSP00000237530:p.Leu587Met	42.0	0.0	.		35.0	11.0	.	NM_002951	Q5JYR6|Q6IBA5|Q96E21|Q9BUQ3|Q9UBE1	Missense_Mutation	SNP	ENST00000237530.6	hg19	CCDS13291.1	.	.	.	.	.	.	.	.	.	.	C	17.82	3.482967	0.63962	.	.	ENSG00000118705	ENST00000237530;ENST00000373622;ENST00000397161;ENST00000437329	T;T;T	0.61980	0.06;0.06;0.06	4.98	4.98	0.66077	.	0.080968	0.50627	D	0.000116	T	0.77850	0.4192	M	0.73962	2.25	0.51767	D	0.999932	D;D	0.89917	1.0;0.999	D;D	0.79784	0.993;0.987	T	0.76966	-0.2763	10	0.38643	T	0.18	-7.2993	15.8004	0.78450	0.0:1.0:0.0:0.0	.	555;587	Q5JYR6;P04844	.;RPN2_HUMAN	M	587;555;94;94	ENSP00000237530:L587M;ENSP00000362724:L555M;ENSP00000409580:L94M	ENSP00000237530:L587M	L	+	1	2	RPN2	35298402	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	2.846000	0.48262	2.584000	0.87258	0.561000	0.74099	CTG	.	.	.	none		0.463	RPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079076.2	NM_002951		A	35864988	C	A	35864988	3	1	32	1	0	0	0	0	1	0	0	0	13621	796	28	4	1821	4	RPN2	20	35864988	Missense_Mutation	SNP	C	TCGA-5P-A9K0-01A-11D-A42J-10	32098476	35864988	27160532	85	2363											
KRTAP8-1	337879	hgsc.bcm.edu	37	chr21	32185474	32185474	+	Frame_Shift_Del	DEL	G	G	-																															agccaacgctatatcccagcGggtagccatagctgccccag																										TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr21:32185474delG	ENST00000329621.4	-	1	96	c.65delC	c.(64-66)ccgfs	p.P22fs		NM_175857.3	NP_787053.1	Q8IUC2	KRA81_HUMAN	keratin associated protein 8-1	22	12 X 2 AA repeats of G-[YCGS].					intermediate filament (GO:0005882)				central_nervous_system(1)|large_intestine(1)|lung(4)	6						ATATCCCAGCGGGTAGCCATA	0.597																																					p.P22fs		Atlas-Indel,Pindel	.											.	KRTAP8-1	20	.	0			c.66delG						PASS	.						83	71	75					21																	32185474		2203	4300	6503	SO:0001589	frameshift_variant	337879	exon1			.	AJ457064	CCDS13607.1	21q22.1	2006-03-13			ENSG00000183640	ENSG00000183640		"Keratin associated proteins"	18935	protein-coding gene	gene with protein product						12359730	Standard	NM_175857		Approved	KAP8.1	uc002you.3	Q8IUC2	OTTHUMG00000057771	ENST00000329621.4:c.65delC	chr21.hg19:g.32185474delG	ENSP00000332805:p.Pro22fs	96.0	0.0	0		94.0	34.0	0.361702	NM_175857	Q3LI57	Frame_Shift_Del	DEL	ENST00000329621.4	hg19	CCDS13607.1																																																																																			.	.	.	none		0.597	KRTAP8-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128223.1			-	32185474	G	-	32185474	7	5	32	1	0	1	0	1	0	0	0	0	8579	1116	39	0	130	0	KRTAP8-1	21	32185474	Frame_Shift_Del	DEL	G	TCGA-5P-A9K0-01A-11D-A42J-10		32185474	15944421	86	2364											
MORC3	23515	hgsc.bcm.edu	37	chr21	37741433	37741433	+	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	aacagtacccccaaacctgcAgtagatcatgatattgacat	15	9	6	11	0	1	3	1	2	0	1	1	3	1	3	3	0	4	3	3	0	5	4			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr21:37741433A>C	ENST00000400485.1	+	15	1843	c.1767A>C	c.(1765-1767)gcA>gcC	p.A589A	MORC3_ENST00000487909.1_3'UTR	NM_015358.2	NP_056173.1	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	589					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						CCAAACCTGCAGTAGATCATG	0.413																																					p.A589A		Atlas-SNP	.											.	MORC3	78	.	0			c.A1767C						PASS	.						205	197	199					21																	37741433		2108	4220	6328	SO:0001819	synonymous_variant	23515	exon15			ACCTGCAGTAGAT	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.1767A>C	chr21.hg19:g.37741433A>C		130.0	0.0	.		126.0	62.0	.	NM_015358	A8KA92|Q9UEZ2	Silent	SNP	ENST00000400485.1	hg19	CCDS42924.1																																																																																			.	.	.	none		0.413	MORC3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000194640.1	NM_015358		C	37741433	A	C	37741433	2	2	32	1	0	0	0	0	0	0	0	1	9710	175	7	5		5	MORC3	21	37741433	Silent	SNP	A	TCGA-5P-A9K0-01A-11D-A42J-10	5555959	37741433	10388462	87	2365											
COMT	1312	hgsc.bcm.edu	37	chr22	19956092	19956092	+	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	tgcggaaggggacagtgctaCtggctgacaacgtgatctgc	9	8	15	9	2	1	2	0	2	1	0	1	4	1	4	0	4	5	2	0	4	3	1			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chr22:19956092C>G	ENST00000361682.6	+	6	1031	c.649C>G	c.(649-651)Ctg>Gtg	p.L217V	COMT_ENST00000407537.1_Missense_Mutation_p.L167V|COMT_ENST00000449653.1_Missense_Mutation_p.L167V|COMT_ENST00000406520.3_Missense_Mutation_p.L217V|COMT_ENST00000403710.1_Missense_Mutation_p.L217V	NM_000754.3	NP_000745.1	P21964	COMT_HUMAN	catechol-O-methyltransferase	217					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)	GACAGTGCTACTGGCTGACAA	0.607																																					p.L217V		Atlas-SNP	.											.	COMT	10	.	0			c.C649G						PASS	.						85	66	73					22																	19956092		2203	4300	6503	SO:0001583	missense	1312	exon6			GTGCTACTGGCTG		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.649C>G	chr22.hg19:g.19956092C>G	ENSP00000354511:p.Leu217Val	40.0	0.0	.		59.0	21.0	.	NM_000754	A8MPV9|Q6IB07|Q6ICE6|Q9BWC7	Missense_Mutation	SNP	ENST00000361682.6	hg19	CCDS13770.1	.	.	.	.	.	.	.	.	.	.	C	7.677	0.688266	0.14973	.	.	ENSG00000093010	ENST00000361682;ENST00000403710;ENST00000407537;ENST00000412786;ENST00000406520;ENST00000449653	T;T;T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.38;-0.38;-0.38	5.2	0.507	0.16967	.	0.078098	0.52532	N	0.000062	T	0.48589	0.1508	N	0.25380	0.74	0.48185	D	0.9996	B	0.33345	0.409	B	0.38225	0.268	T	0.14200	-1.0481	9	.	.	.	-4.4637	5.9261	0.19112	0.0:0.5177:0.2579:0.2243	.	217	P21964	COMT_HUMAN	V	217;217;167;217;217;167	ENSP00000354511:L217V;ENSP00000385917:L217V;ENSP00000384654:L167V;ENSP00000403958:L217V;ENSP00000385150:L217V;ENSP00000416778:L167V	.	L	+	1	2	COMT	18336092	0.931000	0.31567	0.061000	0.19648	0.053000	0.15095	0.873000	0.28052	0.009000	0.14813	0.491000	0.48974	CTG	.	.	.	none		0.607	COMT-011	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318936.2	NM_000754		G	19956092	C	G	19956092	3	3	32	1	0	0	0	0	1	0	0	0	3727	564	20	4	663	4	COMT	22	19956092	Missense_Mutation	SNP	C	TCGA-5P-A9K0-01A-11D-A42J-10		19956092	31348474	88	2366											
KDM6A	7403	hgsc.bcm.edu	37	chrX	44950075	44950075	+	Frame_Shift_Del	DEL	A	A	-																															ggaatatggcacgaaatatcAaggtctcagatccaaagctt																										TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chrX:44950075delA	ENST00000377967.4	+	26	3885	c.3844delA	c.(3844-3846)aagfs	p.K1282fs	KDM6A_ENST00000543216.1_Frame_Shift_Del_p.K1203fs|KDM6A_ENST00000536777.1_Frame_Shift_Del_p.K1237fs|KDM6A_ENST00000382899.4_Frame_Shift_Del_p.K1289fs	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	1282					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						ACGAAATATCAAGGTCTCAGA	0.363			"D, N, F, S"		"renal, oesophageal SCC, MM"																																p.I1281fs	Colon(129;1273 1667 15230 27352 52914)	Atlas-Indel,Pindel	.		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.3843delC						PASS	.						179	155	163					X																	44950075		2203	4300	6503	SO:0001589	frameshift_variant	7403	exon26			.	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.3844delA	chrX.hg19:g.44950075delA	ENSP00000367203:p.Lys1282fs	89.0	0.0	0		95.0	67.0	0.705263	NM_021140	Q52LL9|Q5JVQ7	Frame_Shift_Del	DEL	ENST00000377967.4	hg19	CCDS14265.1																																																																																			.	.	.	none		0.363	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140		-	44950075	A	-	44950075	7	5	32	1	0	1	0	1	0	0	0	0	8144	131	5	0	3946	0	KDM6A	23	44950075	Frame_Shift_Del	DEL	A	TCGA-5P-A9K0-01A-11D-A42J-10		44950075	110320485	89	2367											
PPP1R3F	89801	hgsc.bcm.edu	37	chrX	49126754	49126754	+	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	catggtggagctggaggcgcTgctgccgcctcccggagcgg	4	6	18	13	4	0	0	0	0	0	0	1	3	1	3	3	6	4	3	3	6	0	0			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chrX:49126754T>A	ENST00000055335.6	+	1	438	c.422T>A	c.(421-423)cTg>cAg	p.L141Q	PPP1R3F_ENST00000495799.1_Intron|LL0XNC01-7P3.1_ENST00000602455.1_lincRNA|PPP1R3F_ENST00000438316.1_Intron|PPP1R3F_ENST00000466508.1_Intron	NM_033215.4	NP_149992.3	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory subunit 3F	141	CBM21. {ECO:0000255|PROSITE- ProRule:PRU00491}.				regulation of glycogen (starch) synthase activity (GO:2000465)|regulation of glycogen biosynthetic process (GO:0005979)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycogen binding (GO:2001069)|protein phosphatase binding (GO:0019903)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(4)	27	Ovarian(276;0.236)					CTGGAGGCGCTGCTGCCGCCT	0.761																																					p.L141Q		Atlas-SNP	.											.	PPP1R3F	56	.	0			c.T422A						PASS	.						2	3	3					X																	49126754		1527	3160	4687	SO:0001583	missense	89801	exon1			AGGCGCTGCTGCC		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.422T>A	chrX.hg19:g.49126754T>A	ENSP00000055335:p.Leu141Gln	21.0	0.0	.		15.0	10.0	.	NM_033215	A2VDJ8|B3KPW2|E9PCM3	Missense_Mutation	SNP	ENST00000055335.6	hg19	CCDS35254.1	.	.	.	.	.	.	.	.	.	.	t	17.42	3.385987	0.61956	.	.	ENSG00000049769	ENST00000055335	T	0.60299	0.2	4.24	3.06	0.35304	Putative phosphatase regulatory subunit (1);	0.000000	0.30401	N	0.009707	T	0.55273	0.1910	L	0.33339	1.005	0.80722	D	1	D	0.65815	0.995	P	0.59115	0.852	T	0.57740	-0.7759	10	0.87932	D	0	-6.2371	4.6588	0.12632	0.0:0.2485:0.0:0.7515	.	141	Q6ZSY5	PPR3F_HUMAN	Q	141	ENSP00000055335:L141Q	ENSP00000055335:L141Q	L	+	2	0	PPP1R3F	49013698	0.963000	0.33076	1.000000	0.80357	0.994000	0.84299	0.866000	0.27954	1.504000	0.48704	0.419000	0.28159	CTG	.	.	.	none		0.761	PPP1R3F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060819.2	NM_033215		A	49126754	T	A	49126754	3	1	32	1	0	0	0	0	1	0	0	0	12385	1580	55	5	424	5	PPP1R3F	23	49126754	Missense_Mutation	SNP	T	TCGA-5P-A9K0-01A-11D-A42J-10	4176679	49126754	106143806	90	2368											
HUWE1	10075	hgsc.bcm.edu	37	chrX	53619440	53619440	+	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	tatcctcttctcctcgagacCcctccttctccttgcttagt	4	16	4	17	1	3	1	0	0	3	1	8	2	5	1	6	0	1	1	6	0	2	5			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chrX:53619440C>T	ENST00000342160.3	-	32	4347	c.3890G>A	c.(3889-3891)gGg>gAg	p.G1297E	HUWE1_ENST00000262854.6_Missense_Mutation_p.G1297E|HUWE1_ENST00000218328.8_Missense_Mutation_p.G1297E			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	1297					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						TCCTCGAGACCCCTCCTTCTC	0.547																																					p.G1297E		Atlas-SNP	.											.	HUWE1	724	.	0			c.G3890A						PASS	.						244	192	210					X																	53619440		2203	4300	6503	SO:0001583	missense	10075	exon33			CGAGACCCCTCCT	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.3890G>A	chrX.hg19:g.53619440C>T	ENSP00000340648:p.Gly1297Glu	25.0	0.0	.		15.0	14.0	.	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	hg19	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	C	17.60	3.430637	0.62844	.	.	ENSG00000086758	ENST00000342160;ENST00000262854;ENST00000218328	T;T;T	0.44083	1.22;1.22;0.93	5.88	5.88	0.94601	UBA-like (1);	0.000000	0.85682	D	0.000000	T	0.38719	0.1051	L	0.33485	1.01	0.80722	D	1	B;B	0.29432	0.192;0.244	B;B	0.32211	0.142;0.097	T	0.21415	-1.0246	10	0.56958	D	0.05	.	17.8502	0.88744	0.0:1.0:0.0:0.0	.	1297;1297	Q7Z6Z7;Q7Z6Z7-2	HUWE1_HUMAN;.	E	1297	ENSP00000340648:G1297E;ENSP00000262854:G1297E;ENSP00000218328:G1297E	ENSP00000218328:G1297E	G	-	2	0	HUWE1	53636165	1.000000	0.71417	0.942000	0.38095	0.803000	0.45373	7.121000	0.77160	2.489000	0.83994	0.600000	0.82982	GGG	.	.	.	none		0.547	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		T	53619440	C	T	53619440	3	4	32	1	0	0	0	0	1	0	0	0	7468	623	22	2	9442	2	HUWE1	23	53619440	Missense_Mutation	SNP	C	TCGA-5P-A9K0-01A-11D-A42J-10	4492686	53619440	101651120	91	2369											
ATP1B4	23439	hgsc.bcm.edu	37	chrX	119500447	119500447	+	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	ggaagcagaagaagaggctcGggtgacggtggtgcccaaat	12	5	17	7	2	0	4	0	1	0	3	1	5	0	5	1	5	2	2	1	5	4	0			TCGA-5P-A9K0-01A-11D-A42J-10	TCGA-5P-A9K0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a26d518a-50bf-4b8e-98cb-308952c4b675	35135c15-ac82-41b6-ad60-f04f92bf961f	g.chrX:119500447G>C	ENST00000218008.3	+	2	188	c.131G>C	c.(130-132)cGg>cCg	p.R44P	ATP1B4_ENST00000361319.3_Missense_Mutation_p.R44P|ATP1B4_ENST00000539306.1_Missense_Mutation_p.R44P	NM_001142447.2	NP_001135919.1	Q9UN42	AT1B4_HUMAN	ATPase, Na+/K+ transporting, beta 4 polypeptide	44	Glu-rich.				monovalent inorganic cation transport (GO:0015672)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|nuclear inner membrane (GO:0005637)|sodium:potassium-exchanging ATPase complex (GO:0005890)	monovalent inorganic cation transmembrane transporter activity (GO:0015077)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	33						GAAGAGGCTCGGGTGACGGTG	0.512																																					p.R44P		Atlas-SNP	.											.	ATP1B4	61	.	0			c.G131C						PASS	.						95	89	91					X																	119500447		2203	4300	6503	SO:0001583	missense	23439	exon2			AGGCTCGGGTGAC	AF158383	CCDS14598.1, CCDS48158.1	Xq24	2012-10-22	2010-04-20		ENSG00000101892	ENSG00000101892		"ATPases / P-type"	808	protein-coding gene	gene with protein product	"Na,K-ATPase beta m-subunit"		"ATPase, (Na+)/K+ transporting, beta 4 polypeptide"			10456317, 17592128	Standard	NM_012069		Approved		uc004esr.3	Q9UN42	OTTHUMG00000022299	ENST00000218008.3:c.131G>C	chrX.hg19:g.119500447G>C	ENSP00000218008:p.Arg44Pro	173.0	0.0	.		145.0	115.0	.	NM_001142447	Q17RR0|Q9UN41	Missense_Mutation	SNP	ENST00000218008.3	hg19	CCDS48158.1	.	.	.	.	.	.	.	.	.	.	G	5.008	0.187169	0.09547	.	.	ENSG00000101892	ENST00000218008;ENST00000361319;ENST00000539306	T;T;T	0.09163	3.01;3.01;3.01	5.51	-9.66	0.00534	.	0.985232	0.08295	N	0.967802	T	0.05456	0.0144	N	0.14661	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	0.44711	-0.9310	10	0.66056	D	0.02	-10.7869	10.5975	0.45347	0.6174:0.1732:0.2095:0.0	.	44;44;44;44	B7ZKW0;B7ZKV9;Q9UN42;Q9UN42-2	.;.;AT1B4_HUMAN;.	P	44	ENSP00000218008:R44P;ENSP00000355346:R44P;ENSP00000443334:R44P	ENSP00000218008:R44P	R	+	2	0	ATP1B4	119384475	0.022000	0.18835	0.001000	0.08648	0.175000	0.22909	-2.104000	0.01340	-2.816000	0.00345	-0.912000	0.02778	CGG	.	.	.	none		0.512	ATP1B4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058095.1	NM_001142447		C	119500447	G	C	119500447	3	2	32	1	0	0	0	0	1	0	0	0	1135	1116	39	4	137	4	ATP1B4	23	119500447	Missense_Mutation	SNP	G	TCGA-5P-A9K0-01A-11D-A42J-10	65881007	119500447	35770113	92	2370											
TAS1R3	83756	hgsc.bcm.edu	37	chr1	1268443	1268443	+	Frame_Shift_Del	DEL	G	G	-																															caggctccacgacgtgggcaGgttcaacggcagcctcagga																										TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr1:1268443delG	ENST00000339381.5	+	4	1450	c.1418delG	c.(1417-1419)aggfs	p.R473fs		NM_152228.1	NP_689414	Q7RTX0	TS1R3_HUMAN	taste receptor, type 1, member 3	473					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)		GACGTGGGCAGGTTCAACGGC	0.647																																					p.R473fs		Atlas-Indel,Pindel	.											.	TAS1R3	39	.	0			c.1417delA						PASS	.						52	48	49					1																	1268443		2200	4296	6496	SO:0001589	frameshift_variant	83756	exon4			.	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.1418delG	chr1.hg19:g.1268443delG	ENSP00000344411:p.Arg473fs	85.0	0.0	0		97.0	40.0	0.412371	NM_152228	Q5TA49|Q8NGW9	Frame_Shift_Del	DEL	ENST00000339381.5	hg19	CCDS30556.1																																																																																			.	.	.	none		0.647	TAS1R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008493.1			-	1268443	G	-	1268443	7	5	33	1	0	1	0	1	0	0	0	0	15576	1000	35	0	1432	0	TAS1R3	1	1268443	Frame_Shift_Del	DEL	G	TCGA-5P-A9K2-01A-11D-A42J-10		1268443	247982178	1	2371											
TNFRSF14	8764	hgsc.bcm.edu	37	chr1	2491291	2491291	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgcgcgagccggaactgcTccaggacagagaacgccgtg	9	4	15	13	6	0	1	0	0	0	1	1	5	1	3	3	2	5	1	3	2	2	0			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr1:2491291T>C	ENST00000355716.4	+	4	633	c.334T>C	c.(334-336)Tcc>Ccc	p.S112P	RP3-395M20.8_ENST00000416860.2_RNA|RP3-395M20.8_ENST00000452793.1_RNA|TNFRSF14_ENST00000409119.1_Missense_Mutation_p.S112P	NM_003820.2	NP_003811.2	Q92956	TNR14_HUMAN	tumor necrosis factor receptor superfamily, member 14	112					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)		CCGGAACTGCTCCAGGACAGA	0.687			"Mis, N, F"		follicular lymphoma																																p.S112P		Atlas-SNP	.		Rec	yes		1	1p36.32	8764	"tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)"		L	.	TNFRSF14	89	.	0			c.T334C						PASS	.						32	34	33					1																	2491291		2198	4295	6493	SO:0001583	missense	8764	exon4			AACTGCTCCAGGA	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.334T>C	chr1.hg19:g.2491291T>C	ENSP00000347948:p.Ser112Pro	63.0	0.0	.		119.0	52.0	.	NM_003820	B3KW30|B9DI89|Q6IB95|Q8N634|Q8WXR1|Q96J31|Q9UM65	Missense_Mutation	SNP	ENST00000355716.4	hg19	CCDS44046.1	.	.	.	.	.	.	.	.	.	.	T	11.61	1.689551	0.29962	.	.	ENSG00000157873	ENST00000426449;ENST00000434817;ENST00000435221;ENST00000451778;ENST00000409119;ENST00000355716	D;D;D;D;D;D	0.91068	-2.78;-2.78;-2.78;-2.78;-2.78;-2.78	3.04	1.9	0.25705	TNFR/CD27/30/40/95 cysteine-rich region (4);	.	.	.	.	D	0.93556	0.7943	M	0.77486	2.375	0.25545	N	0.987142	D	0.69078	0.997	D	0.79784	0.993	D	0.84151	0.0423	9	0.72032	D	0.01	-17.456	4.8629	0.13592	0.0:0.1455:0.0:0.8545	.	112	Q92956	TNR14_HUMAN	P	112	ENSP00000411854:S112P;ENSP00000415254:S112P;ENSP00000399292:S112P;ENSP00000399533:S112P;ENSP00000386859:S112P;ENSP00000347948:S112P	ENSP00000347948:S112P	S	+	1	0	TNFRSF14	2483127	0.821000	0.29204	0.619000	0.29118	0.023000	0.10783	0.787000	0.26858	0.572000	0.29383	0.379000	0.24179	TCC	.	.	.	none		0.687	TNFRSF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002088.1			C	2491291	T	C	2491291	3	2	33	1	0	0	0	0	1	0	0	0	16301	1551	54	3	348	3	TNFRSF14	1	2491291	Missense_Mutation	SNP	T	TCGA-5P-A9K2-01A-11D-A42J-10	1222848	2491291	246759330	2	2372											
BAI2	576	hgsc.bcm.edu	37	chr1	32198684	32198684	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggtctgtcatagccaggacGgcagacatccaggtgagcgc	9	6	14	12	3	2	2	1	1	1	1	3	3	3	3	2	4	2	1	2	4	1	1	rs140842802		TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr1:32198684G>A	ENST00000373658.3	-	26	3854	c.3513C>T	c.(3511-3513)gcC>gcT	p.A1171A	BAI2_ENST00000373655.2_Silent_p.A1171A|BAI2_ENST00000398556.3_Silent_p.A1086A|BAI2_ENST00000465256.1_5'UTR|BAI2_ENST00000398542.1_Silent_p.A1071A|BAI2_ENST00000527361.1_Silent_p.A1138A|BAI2_ENST00000398547.1_Silent_p.A1104A|BAI2_ENST00000398538.1_Silent_p.A1159A|BAI2_ENST00000257070.4_Silent_p.A1138A|BAI2_ENST00000440175.2_Silent_p.A780A	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	1171					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)		TAGCCAGGACGGCAGACATCC	0.627																																					p.A1171A		Atlas-SNP	.											.	BAI2	128	.	0			c.C3513T						PASS	.	G		1,4393		0,1,2196	57	42	47		3513	-4.8	0.9	1	dbSNP_134	47	0,8588		0,0,4294	no	coding-synonymous	BAI2	NM_001703.2		0,1,6490	AA,AG,GG		0.0,0.0228,0.0077		1171/1586	32198684	1,12981	2197	4294	6491	SO:0001819	synonymous_variant	576	exon26			CAGGACGGCAGAC	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.3513C>T	chr1.hg19:g.32198684G>A		101.0	0.0	.		146.0	12.0	.	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Silent	SNP	ENST00000373658.3	hg19	CCDS346.2																																																																																			.	G|1.000;A|0.000	0.000	weak		0.627	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703		A	32198684	G	A	32198684	2	1	33	1	0	0	0	0	0	0	0	1	1299	1103	39	1		1	BAI2	1	32198684	Silent	SNP	G	TCGA-5P-A9K2-01A-11D-A42J-10	29707393	32198684	217051937	3	2373											
THRAP3	9967	hgsc.bcm.edu	37	chr1	36751972	36751972	+	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	tttcctttccattccagttcTaggtctcgttccagatcata	7	17	5	12	1	3	1	1	0	2	1	8	1	7	1	4	1	0	2	4	1	2	7			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr1:36751972T>G	ENST00000354618.5	+	4	365	c.141T>G	c.(139-141)tcT>tcG	p.S47S	THRAP3_ENST00000469141.2_Silent_p.S47S	NM_005119.3	NP_005110.2	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	47	Arg-rich.|Required for mRNA splicing activation.|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)				ATTCCAGTTCTAGGTCTCGTT	0.388			T	USP6	aneurysmal bone cysts																																p.S47S	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.T141G						PASS	.						77	80	79					1																	36751972		2202	4300	6502	SO:0001819	synonymous_variant	9967	exon4			CAGTTCTAGGTCT	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.141T>G	chr1.hg19:g.36751972T>G		55.0	0.0	.		62.0	26.0	.	NM_005119	D3DPS5|Q5VTK6	Silent	SNP	ENST00000354618.5	hg19	CCDS405.1																																																																																			.	.	.	none		0.388	THRAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021688.2	NM_005119		G	36751972	T	G	36751972	2	3	33	1	0	0	0	0	0	0	0	1	15886	1509	53	5		5	THRAP3	1	36751972	Silent	SNP	T	TCGA-5P-A9K2-01A-11D-A42J-10	4553288	36751972	212498649	4	2374											
MTF1	4520	hgsc.bcm.edu	37	chr1	38288019	38288019	+	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	gggctggtgctgccacagctGatgccactgccgctgctgat	5	9	14	13	1	0	2	0	2	0	0	0	2	0	2	3	2	6	5	3	2	0	0			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr1:38288019G>A	ENST00000373036.4	-	9	1681	c.1541C>T	c.(1540-1542)tCa>tTa	p.S514L		NM_005955.2	NP_005946.2	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1	514					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cadmium ion (GO:0046686)|response to metal ion (GO:0010038)|response to oxidative stress (GO:0006979)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(3)|kidney(5)|large_intestine(6)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)	31	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				TGCCACAGCTGATGCCACTGC	0.567																																					p.S514L		Atlas-SNP	.											.	MTF1	67	.	0			c.C1541T						PASS	.						44	42	42					1																	38288019		2203	4300	6503	SO:0001583	missense	4520	exon9			ACAGCTGATGCCA	BC014454	CCDS30676.1	1p33	2008-02-05			ENSG00000188786	ENSG00000188786			7428	protein-coding gene	gene with protein product		600172				8065932	Standard	NM_005955		Approved		uc001cce.1	Q14872	OTTHUMG00000004439	ENST00000373036.4:c.1541C>T	chr1.hg19:g.38288019G>A	ENSP00000362127:p.Ser514Leu	85.0	0.0	.		104.0	49.0	.	NM_005955	B2RAK6|Q96CB1	Missense_Mutation	SNP	ENST00000373036.4	hg19	CCDS30676.1	.	.	.	.	.	.	.	.	.	.	G	11.79	1.743385	0.30865	.	.	ENSG00000188786	ENST00000373036	T	0.38722	1.12	4.65	4.65	0.58169	.	0.806293	0.10166	N	0.707756	T	0.34454	0.0898	L	0.29908	0.895	0.09310	N	1	B	0.13594	0.008	B	0.16722	0.016	T	0.07712	-1.0758	10	0.37606	T	0.19	.	13.3481	0.60587	0.0:0.0:1.0:0.0	.	514	Q14872	MTF1_HUMAN	L	514	ENSP00000362127:S514L	ENSP00000362127:S514L	S	-	2	0	MTF1	38060606	0.049000	0.20398	0.028000	0.17463	0.994000	0.84299	2.507000	0.45442	2.873000	0.98535	0.561000	0.74099	TCA	.	.	.	none		0.567	MTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012984.2	NM_005955		A	38288019	G	A	38288019	3	1	33	1	0	0	0	0	1	0	0	0	9929	1294	45	2	732	2	MTF1	1	38288019	Missense_Mutation	SNP	G	TCGA-5P-A9K2-01A-11D-A42J-10	1536047	38288019	210962602	5	2375											
ASH1L	55870	hgsc.bcm.edu	37	chr1	155451901	155451901	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaacacctgctttcctgaTcaaatccttgctaaccaatc	11	11	4	15	0	1	1	1	1	0	0	4	1	3	1	5	0	4	2	5	0	4	3			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr1:155451901T>C	ENST00000368346.3	-	3	1399	c.760A>G	c.(760-762)Atc>Gtc	p.I254V	ASH1L_ENST00000392403.3_Missense_Mutation_p.I254V|ASH1L_ENST00000548830.1_3'UTR			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	254					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)			GCTTTCCTGATCAAATCCTTG	0.443																																					p.I254V		Atlas-SNP	.											ASH1L,NS,carcinoma,0,1	ASH1L	279	.	0			c.A760G						PASS	.						125	118	120					1																	155451901		2203	4300	6503	SO:0001583	missense	55870	exon3			TCCTGATCAAATC	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.760A>G	chr1.hg19:g.155451901T>C	ENSP00000357330:p.Ile254Val	74.0	0.0	.		121.0	43.0	.	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	hg19		.	.	.	.	.	.	.	.	.	.	T	11.90	1.777686	0.31502	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.88975	-2.45;-2.45	4.44	4.44	0.53790	.	0.373475	0.24940	N	0.034388	T	0.69405	0.3107	N	0.19112	0.55	0.80722	D	1	B;B	0.24651	0.066;0.108	B;B	0.20955	0.014;0.032	T	0.69075	-0.5241	10	0.33141	T	0.24	.	10.2656	0.43453	0.0:0.0:0.0:1.0	.	254;254	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	V	254	ENSP00000357330:I254V;ENSP00000376204:I254V	ENSP00000357330:I254V	I	-	1	0	ASH1L	153718525	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.002000	0.40835	2.003000	0.58678	0.460000	0.39030	ATC	.	.	.	none		0.443	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		C	155451901	T	C	155451901	3	2	33	1	0	0	0	0	1	0	0	0	1041	1435	50	3	8238	3	ASH1L	1	155451901	Missense_Mutation	SNP	T	TCGA-5P-A9K2-01A-11D-A42J-10	117163882	155451901	93798720	6	2376											
IARS2	55699	hgsc.bcm.edu	37	chr1	220267813	220267813	+	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	cagcagccggacacggagctGgagatccagcaggtacgggc	10	3	16	12	3	0	1	0	0	0	1	1	4	1	3	2	5	5	4	2	5	1	1			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr1:220267813G>T	ENST00000302637.5	+	1	359	c.255G>T	c.(253-255)ctG>ctT	p.L85L	IARS2_ENST00000366922.1_Silent_p.L13L	NM_018060.3	NP_060530.3	Q9NSE4	SYIM_HUMAN	isoleucyl-tRNA synthetase 2, mitochondrial	85					gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)			NS(1)|breast(1)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(7)|lung(17)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)	ACACGGAGCTGGAGATCCAGC	0.711																																					p.L85L		Atlas-SNP	.											.	IARS2	106	.	0			c.G255T						PASS	.						7	10	9					1																	220267813		2113	4210	6323	SO:0001819	synonymous_variant	55699	exon1			GGAGCTGGAGATC	AK022665	CCDS1523.1	1q41	2011-07-01	2007-02-26		ENSG00000067704	ENSG00000067704	6.1.1.5	"Aminoacyl tRNA synthetases / Class I"	29685	protein-coding gene	gene with protein product	"isoleucine tRNA ligase 2, mitochondrial"	612801					Standard	NM_018060		Approved	FLJ10326	uc001hmc.3	Q9NSE4	OTTHUMG00000037287	ENST00000302637.5:c.255G>T	chr1.hg19:g.220267813G>T		44.0	0.0	.		59.0	21.0	.	NM_018060	B2RPG8|Q1M2P9|Q6PI85|Q7L439|Q86WU9|Q96D91|Q9H9Q8|Q9NW42	Silent	SNP	ENST00000302637.5	hg19	CCDS1523.1																																																																																			.	.	.	none		0.711	IARS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018060		T	220267813	G	T	220267813	2	4	33	1	0	0	0	0	0	0	0	1	7481	1335	47	4		4	IARS2	1	220267813	Silent	SNP	G	TCGA-5P-A9K2-01A-11D-A42J-10	64815912	220267813	28982808	7	2377											
CAD	790	hgsc.bcm.edu	37	chr2	27463149	27463149	+	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	ccagacacctgaaagaccccGccgtggcatcccagggcttc	9	5	10	17	2	0	3	0	1	0	2	2	3	1	3	6	2	0	2	6	2	1	1	rs199572743		TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr2:27463149G>T	ENST00000403525.1	+	34	5468	c.5324G>T	c.(5323-5325)cGc>cTc	p.R1775L	CAD_ENST00000264705.4_Missense_Mutation_p.R1838L			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)					GAAAGACCCCGCCGTGGCATC	0.567																																					p.R1838L		Atlas-SNP	.											.	CAD	199	.	0			c.G5513T						PASS	.						103	115	111					2																	27463149		2203	4300	6503	SO:0001583	missense	790	exon35			GACCCCGCCGTGG	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.5324G>T	chr2.hg19:g.27463149G>T	ENSP00000384510:p.Arg1775Leu	66.0	0.0	.		86.0	33.0	.	NM_004341	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Missense_Mutation	SNP	ENST00000403525.1	hg19		.	.	.	.	.	.	.	.	.	.	G	16.79	3.220193	0.58560	.	.	ENSG00000084774	ENST00000264705;ENST00000403525	D;D	0.98313	-4.86;-4.8	5.28	5.28	0.74379	.	0.120124	0.53938	D	0.000045	D	0.95915	0.8670	L	0.39898	1.24	0.53005	D	0.999967	B;B	0.11235	0.004;0.001	B;B	0.12156	0.007;0.002	D	0.93894	0.7182	10	0.19590	T	0.45	-6.6265	16.4322	0.83853	0.0:0.0:1.0:0.0	.	1775;1838	F8VPD4;P27708	.;PYR1_HUMAN	L	1838;1775	ENSP00000264705:R1838L;ENSP00000384510:R1775L	ENSP00000264705:R1838L	R	+	2	0	CAD	27316653	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	4.863000	0.62983	2.474000	0.83562	0.555000	0.69702	CGC	.	.	.	alt		0.567	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1			T	27463149	G	T	27463149	3	4	33	1	0	0	0	0	1	0	0	0	2567	1087	38	4	5651	4	CAD	2	27463149	Missense_Mutation	SNP	G	TCGA-5P-A9K2-01A-11D-A42J-10		27463149	215736224	8	2378											
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160289719	160289719	+	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	cctaaaagtgcatttgtcaaGaatggatttgggtggttgtt	10	15	12	4	0	1	1	1	0	0	1	1	2	1	2	1	3	1	3	1	3	4	5			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr2:160289719G>C	ENST00000392783.2	-	9	1944	c.1449C>G	c.(1447-1449)ttC>ttG	p.F483L	BAZ2B_ENST00000392782.1_Missense_Mutation_p.F481L|BAZ2B_ENST00000355831.2_Missense_Mutation_p.F483L|BAZ2B_ENST00000343439.5_Missense_Mutation_p.F481L	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	483					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						CATTTGTCAAGAATGGATTTG	0.383																																					p.F483L		Atlas-SNP	.											.	BAZ2B	196	.	0			c.C1449G						PASS	.						320	294	302					2																	160289719		1859	4096	5955	SO:0001583	missense	29994	exon9			TGTCAAGAATGGA	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.1449C>G	chr2.hg19:g.160289719G>C	ENSP00000376534:p.Phe483Leu	83.0	0.0	.		88.0	43.0	.	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	hg19	CCDS2209.2	.	.	.	.	.	.	.	.	.	.	G	15.24	2.775924	0.49786	.	.	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439;ENST00000546335	D;D;D;D	0.88124	-2.34;-2.34;-2.34;-2.34	5.78	0.8	0.18672	.	0.000000	0.38720	U	0.001589	D	0.89188	0.6644	L	0.60455	1.87	0.42787	D	0.993881	D;P;P;P;P	0.58268	0.982;0.936;0.762;0.936;0.894	D;P;B;P;B	0.68943	0.961;0.64;0.391;0.64;0.437	D	0.84632	0.0690	10	0.22109	T	0.4	-9.1949	10.1708	0.42908	0.3245:0.0:0.6755:0.0	.	483;287;481;481;483	Q9UIF8-3;Q9UIF8-4;Q9UIF8-2;Q9UIF8-5;Q9UIF8	.;.;.;.;BAZ2B_HUMAN	L	481;483;483;481;420	ENSP00000376533:F481L;ENSP00000376534:F483L;ENSP00000348087:F483L;ENSP00000339670:F481L	ENSP00000339670:F481L	F	-	3	2	BAZ2B	159997965	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	2.715000	0.47210	0.086000	0.17137	0.655000	0.94253	TTC	.	.	.	none		0.383	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			C	160289719	G	C	160289719	3	2	33	1	0	0	0	0	1	0	0	0	1332	933	33	4	5173	4	BAZ2B	2	160289719	Missense_Mutation	SNP	G	TCGA-5P-A9K2-01A-11D-A42J-10	132826570	160289719	82909654	9	2379											
CD302	9936	hgsc.bcm.edu	37	chr2	160634461	160634461	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttacttacctgataaatattTccttttgtatgggactaaaa	13	17	5	6	0	0	1	0	1	0	0	1	2	1	2	2	1	2	1	2	1	8	9			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr2:160634461T>C	ENST00000259053.4	-	5	527	c.484A>G	c.(484-486)Aaa>Gaa	p.K162E	LY75-CD302_ENST00000505052.1_Missense_Mutation_p.K1747E|LY75_ENST00000554112.1_Missense_Mutation_p.K1803E|CD302_ENST00000429078.2_Missense_Mutation_p.K104E|CD302_ENST00000480212.1_5'UTR|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.K1803E|LY75_ENST00000553424.1_Missense_Mutation_p.K1747E	NM_001198764.1|NM_014880.4	NP_001185693.1|NP_055695.2	Q8IX05	CD302_HUMAN	CD302 molecule	162					phagocytosis (GO:0006909)	cell cortex (GO:0005938)|filopodium (GO:0030175)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|prostate(1)|skin(1)	11						GATAAATATTTCCTTTTGTAT	0.219																																					p.K1803E		Atlas-SNP	.											.	.	.	.	0			c.A5407G						PASS	.						9	10	10					2																	160634461		1861	3919	5780	SO:0001583	missense	100526664	exon38			AATATTTCCTTTT	AY314007	CCDS33308.1, CCDS56139.1, CCDS74595.1	2q24.2	2011-08-30	2006-03-28		ENSG00000241399	ENSG00000241399		"CD molecules", "C-type lectin domain containing"	30843	protein-coding gene	gene with protein product	"C-type lectin domain family 13, member A"	612246	"CD302 antigen"			7584026, 7584028	Standard	NM_014880		Approved	DCL-1, KIAA0022, BIMLEC, CLEC13A		Q8IX05	OTTHUMG00000154080	ENST00000259053.4:c.484A>G	chr2.hg19:g.160634461T>C	ENSP00000259053:p.Lys162Glu	401.0	0.0	.		481.0	199.0	.	NM_001198759	A8K5G4|B4E2T9|Q15009	Missense_Mutation	SNP	ENST00000259053.4	hg19	CCDS33308.1	.	.	.	.	.	.	.	.	.	.	T	17.20	3.329012	0.60743	.	.	ENSG00000241399;ENSG00000241399;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000259053;ENST00000429078;ENST00000554112;ENST00000553424;ENST00000504764;ENST00000505052	T;T;T;T;T;T	0.19105	3.24;2.17;3.01;3.0;3.01;3.0	5.39	5.39	0.77823	.	0.403394	0.25305	N	0.031623	T	0.19725	0.0474	L	0.27053	0.805	0.24410	N	0.994667	D;P;P;B	0.55172	0.97;0.884;0.932;0.172	P;P;P;B	0.48571	0.543;0.503;0.582;0.05	T	0.10019	-1.0648	10	0.27082	T	0.32	-0.1735	12.084	0.53688	0.0:0.0:0.0:1.0	.	104;1747;1803;162	B4E2T9;O60449-3;O60449-2;Q8IX05	.;.;.;CD302_HUMAN	E	162;104;1803;1747;1803;1747	ENSP00000259053:K162E;ENSP00000394301:K104E;ENSP00000451511:K1803E;ENSP00000451446:K1747E;ENSP00000423463:K1803E;ENSP00000421035:K1747E	ENSP00000259053:K162E	K	-	1	0	LY75;CD302;LY75-CD302	160342707	1.000000	0.71417	1.000000	0.80357	0.653000	0.38743	1.390000	0.34464	2.174000	0.68829	0.454000	0.30748	AAA	.	.	.	none		0.219	CD302-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333760.1	NM_014880		C	160634461	T	C	160634461	3	2	33	1	0	0	0	0	1	0	0	0	3005	1792	62	3	222	3	CD302	2	160634461	Missense_Mutation	SNP	T	TCGA-5P-A9K2-01A-11D-A42J-10	344742	160634461	82564912	10	2380											
ABCB11	8647	hgsc.bcm.edu	37	chr2	169787177	169787177	+	Frame_Shift_Del	DEL	C	C	-																															aaaggttgcgtggcttaccaCcttcccttgatcaggatcat																										TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr2:169787177delC	ENST00000263817.6	-	25	3533	c.3409delG	c.(3409-3411)gtgfs	p.V1137fs		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	1137	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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)	TGGCTTACCACCTTCCCTTGA	0.463																																					p.V1137fs		Atlas-Indel,Pindel	.											.	ABCB11	136	.	0			c.3410delT						PASS	.						68	63	65					2																	169787177		1974	4152	6126	SO:0001589	frameshift_variant	8647	exon25			.	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.3409delG	chr2.hg19:g.169787177delC	ENSP00000263817:p.Val1137fs	49.0	0.0	0		64.0	18.0	0.28125	NM_003742	Q53TL2|Q9UNB2	Frame_Shift_Del	DEL	ENST00000263817.6	hg19	CCDS46444.1																																																																																			.	.	.	none		0.463	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742		-	169787177	C	-	169787177	7	5	33	1	0	1	0	1	0	0	0	0	42	507	18	0	572	0	ABCB11	2	169787177	Frame_Shift_Del	DEL	C	TCGA-5P-A9K2-01A-11D-A42J-10	9152716	169787177	73412196	11	2381											
ITGAV	3685	hgsc.bcm.edu	37	chr2	187466865	187466865	+	Missense_Mutation	SNP	A	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	cgccggtgccagccaattgaAtttgatgcaacaggtaaatt	12	10	10	9	2	0	2	0	2	0	0	0	2	0	2	3	2	4	2	3	2	5	4			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr2:187466865A>C	ENST00000261023.3	+	2	577	c.303A>C	c.(301-303)gaA>gaC	p.E101D	ITGAV_ENST00000374907.3_Missense_Mutation_p.E101D|ITGAV_ENST00000433736.2_Missense_Mutation_p.E55D	NM_002210.3	NP_002201	P06756	ITAV_HUMAN	integrin, alpha V	101					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)	AGCCAATTGAATTTGATGCAA	0.408																																					p.E101D	Melanoma(58;108 1995 6081)	Atlas-SNP	.											.	ITGAV	124	.	0			c.A303C						PASS	.						51	52	52					2																	187466865		2203	4300	6503	SO:0001583	missense	3685	exon2			AATTGAATTTGAT		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.303A>C	chr2.hg19:g.187466865A>C	ENSP00000261023:p.Glu101Asp	44.0	0.0	.		69.0	21.0	.	NM_001145000	A0AV67|B0LPF4|B7Z883|B7ZLX0|D3DPG8|E7EWZ6|Q53SK4|Q59EB7|Q6LD15	Missense_Mutation	SNP	ENST00000261023.3	hg19	CCDS2292.1	.	.	.	.	.	.	.	.	.	.	A	11.75	1.731766	0.30684	.	.	ENSG00000138448	ENST00000544640;ENST00000261023;ENST00000374907;ENST00000433736	T;T;T	0.02916	4.11;4.11;4.11	5.15	-1.41	0.08941	.	0.638947	0.16335	N	0.218968	T	0.01765	0.0056	N	0.25201	0.72	0.30054	N	0.811519	B;B;B	0.31125	0.201;0.037;0.309	B;B;B	0.23852	0.049;0.033;0.049	T	0.46775	-0.9167	10	0.18710	T	0.47	.	9.1659	0.37052	0.5777:0.0:0.4223:0.0	.	55;101;101	E7EWZ6;P06756-2;P06756	.;.;ITAV_HUMAN	D	101;101;101;55	ENSP00000261023:E101D;ENSP00000364042:E101D;ENSP00000404291:E55D	ENSP00000261023:E101D	E	+	3	2	ITGAV	187175110	0.924000	0.31332	0.996000	0.52242	0.992000	0.81027	-0.040000	0.12104	-0.253000	0.09514	0.533000	0.62120	GAA	.	.	.	none		0.408	ITGAV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255882.2	NM_002210		C	187466865	A	C	187466865	3	2	33	1	0	0	0	0	1	0	0	0	7895	98	4	5	360	5	ITGAV	2	187466865	Missense_Mutation	SNP	A	TCGA-5P-A9K2-01A-11D-A42J-10	17679688	187466865	55732508	12	2382											
SF3B1	23451	hgsc.bcm.edu	37	chr2	198270054	198270054	+	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	ttaaaaatggaagatttccaGatggctggtcattaacactt	14	13	8	6	0	1	2	1	0	0	2	2	3	2	3	1	3	1	1	1	3	5	4			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr2:198270054G>T	ENST00000335508.6	-	10	1473	c.1382C>A	c.(1381-1383)tCt>tAt	p.S461Y	SNORA4_ENST00000365564.1_RNA|SF3B1_ENST00000462613.1_5'Flank	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	461	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)			AAGATTTCCAGATGGCTGGTC	0.363			Mis		myelodysplastic syndrome																																p.S461Y		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1	1038	.	0			c.C1382A						PASS	.						56	58	57					2																	198270054		2203	4300	6503	SO:0001583	missense	23451	exon10			TTTCCAGATGGCT	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.1382C>A	chr2.hg19:g.198270054G>T	ENSP00000335321:p.Ser461Tyr	173.0	0.0	.		222.0	100.0	.	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	hg19	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	G	17.13	3.311427	0.60414	.	.	ENSG00000115524	ENST00000335508	.	.	.	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.34308	0.0893	N	0.02011	-0.69	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.17592	-1.0364	9	0.24483	T	0.36	.	19.6287	0.95691	0.0:0.0:1.0:0.0	.	461	O75533	SF3B1_HUMAN	Y	461	.	ENSP00000335321:S461Y	S	-	2	0	SF3B1	197978299	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.665000	0.98609	2.710000	0.92621	0.655000	0.94253	TCT	.	.	.	none		0.363	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			T	198270054	G	T	198270054	3	4	33	1	0	0	0	0	1	0	0	0	14162	942	33	4	2596	4	SF3B1	2	198270054	Missense_Mutation	SNP	G	TCGA-5P-A9K2-01A-11D-A42J-10	10803189	198270054	44929319	13	2383											
AGFG1	3267	hgsc.bcm.edu	37	chr2	228356286	228356286	+	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	aggattaaatccaccacacaGggtgaaatctatctccatga	15	9	7	10	0	2	2	0	2	2	0	4	3	3	3	3	2	0	0	3	2	4	2			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr2:228356286G>T	ENST00000310078.8	+	2	451	c.191G>T	c.(190-192)aGg>aTg	p.R64M	AGFG1_ENST00000373671.3_Missense_Mutation_p.R64M|AGFG1_ENST00000409315.1_Missense_Mutation_p.R64M|AGFG1_ENST00000409171.1_Missense_Mutation_p.R64M|AGFG1_ENST00000409979.2_Missense_Mutation_p.R64M	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	64	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				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						CCACCACACAGGGTGAAATCT	0.279																																					p.R64M		Atlas-SNP	.											.	AGFG1	80	.	0			c.G191T						PASS	.						87	96	93					2																	228356286		2202	4297	6499	SO:0001583	missense	3267	exon2			CACACAGGGTGAA		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.191G>T	chr2.hg19:g.228356286G>T	ENSP00000312059:p.Arg64Met	416.0	0.0	.		528.0	223.0	.	NM_004504	B3KUL1|E9PHX7|Q15277|Q4VAS0|Q4VAS1|Q4VAS3|Q53QT8|Q53R11	Missense_Mutation	SNP	ENST00000310078.8	hg19	CCDS2467.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.918260	0.92249	.	.	ENSG00000173744	ENST00000409979;ENST00000542592;ENST00000310078;ENST00000409315;ENST00000373671;ENST00000409171	T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.74935	0.3782	M	0.93939	3.475	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;0.996;1.0	D;D;D;D	0.79784	0.993;0.958;0.938;0.985	T	0.80892	-0.1179	10	0.87932	D	0	.	19.1077	0.93303	0.0:0.0:1.0:0.0	.	64;64;64;64	P52594-2;P52594-3;E9PHX7;P52594	.;.;.;AGFG1_HUMAN	M	64;49;64;64;64;64	ENSP00000387282:R64M;ENSP00000312059:R64M;ENSP00000387154:R64M;ENSP00000362775:R64M;ENSP00000387218:R64M	ENSP00000312059:R64M	R	+	2	0	AGFG1	228064530	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.011000	0.93618	2.814000	0.96858	0.563000	0.77884	AGG	.	.	.	none		0.279	AGFG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256895.2	NM_004504		T	228356286	G	T	228356286	3	4	33	1	0	0	0	0	1	0	0	0	380	1000	35	4	197	4	AGFG1	2	228356286	Missense_Mutation	SNP	G	TCGA-5P-A9K2-01A-11D-A42J-10	30086232	228356286	14843087	14	2384											
IP6K2	51447	hgsc.bcm.edu	37	chr3	48727116	48727116	+	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	ggacacaaggcacctcgtagCgggaagtcaggttttccagt	10	8	13	10	2	1	0	1	0	0	0	3	2	2	2	2	4	1	3	2	4	3	3	rs372776558		TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr3:48727116C>T	ENST00000328631.5	-	5	858	c.635G>A	c.(634-636)cGc>cAc	p.R212H		NM_001005909.2|NM_016291.3	NP_001005909.1|NP_057375.2	Q9UHH9	IP6K2_HUMAN	inositol hexakisphosphate kinase 2	212					cytokine-mediated signaling pathway (GO:0019221)|inositol phosphate metabolic process (GO:0043647)|negative regulation of cell growth (GO:0030308)|phosphate ion transport (GO:0006817)|phosphatidylinositol phosphorylation (GO:0046854)|positive regulation of apoptotic process (GO:0043065)|small molecule metabolic process (GO:0044281)|type I interferon signaling pathway (GO:0060337)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			biliary_tract(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)	15						CACCTCGTAGCGGGAAGTCAG	0.478																																					p.R212H		Atlas-SNP	.											.	IP6K2	63	.	0			c.G635A						PASS	.						126	107	113					3																	48727116		2203	4300	6503	SO:0001583	missense	51447	exon5			TCGTAGCGGGAAG	AF177145	CCDS2777.1, CCDS33752.1, CCDS54579.1, CCDS54580.1, CCDS54581.1	3p21.31	2009-01-05	2009-01-05	2008-12-22	ENSG00000068745	ENSG00000068745			17313	protein-coding gene	gene with protein product		606992	"inositol hexaphosphate kinase 2"	IHPK2		10574768	Standard	NM_016291		Approved		uc003cup.3	Q9UHH9	OTTHUMG00000133543	ENST00000328631.5:c.635G>A	chr3.hg19:g.48727116C>T	ENSP00000331103:p.Arg212His	48.0	0.0	.		91.0	26.0	.	NM_016291	A8K3B1|B4E3G6|G8JLL6|Q6P0N8|Q9BSZ6|Q9BUW3|Q9H4P7|Q9NT63|Q9UFU6	Missense_Mutation	SNP	ENST00000328631.5	hg19	CCDS2777.1	.	.	.	.	.	.	.	.	.	.	C	15.84	2.951641	0.53186	.	.	ENSG00000068745	ENST00000328631	T	0.14144	2.53	5.73	5.73	0.89815	.	0.262087	0.43260	D	0.000582	T	0.25457	0.0619	L	0.31157	0.91	0.80722	D	1	D	0.89917	1.0	D	0.69307	0.963	T	0.02625	-1.1132	10	0.14656	T	0.56	-22.2326	19.8966	0.96963	0.0:1.0:0.0:0.0	.	212	Q9UHH9	IP6K2_HUMAN	H	212	ENSP00000331103:R212H	ENSP00000331103:R212H	R	-	2	0	IP6K2	48702120	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.285000	0.51716	2.700000	0.92200	0.655000	0.94253	CGC	.	.	.	alt		0.478	IP6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257521.2	NM_016291		T	48727116	C	T	48727116	3	4	33	1	0	0	0	0	1	0	0	0	7796	768	27	1	653	1	IP6K2	3	48727116	Missense_Mutation	SNP	C	TCGA-5P-A9K2-01A-11D-A42J-10		48727116	149295314	15	2385											
DOCK3	1795	hgsc.bcm.edu	37	chr3	51251577	51251577	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatcatttctctgcagcttcTtcgtggagacatggaacaga	10	13	9	9	1	3	2	1	0	2	2	5	4	3	3	0	2	3	2	0	2	2	4			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr3:51251577T>C	ENST00000266037.9	+	14	1174	c.1151T>C	c.(1150-1152)cTt>cCt	p.L384P		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	384					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)		CTGCAGCTTCTTCGTGGAGAC	0.373																																					p.L384P		Atlas-SNP	.											.	DOCK3	397	.	0			c.T1151C						PASS	.						97	93	94					3																	51251577		1868	4127	5995	SO:0001583	missense	1795	exon14			AGCTTCTTCGTGG	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.1151T>C	chr3.hg19:g.51251577T>C	ENSP00000266037:p.Leu384Pro	68.0	0.0	.		142.0	6.0	.	NM_004947	O15017	Missense_Mutation	SNP	ENST00000266037.9	hg19	CCDS46835.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.353420	0.82243	.	.	ENSG00000088538	ENST00000266037	T	0.08896	3.04	5.35	5.35	0.76521	.	0.059841	0.64402	D	0.000003	T	0.37919	0.1021	M	0.91300	3.195	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.48948	-0.8989	10	0.87932	D	0	.	15.6362	0.76953	0.0:0.0:0.0:1.0	.	384	Q8IZD9	DOCK3_HUMAN	P	384	ENSP00000266037:L384P	ENSP00000266037:L384P	L	+	2	0	DOCK3	51226617	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.483000	0.81158	2.155000	0.67459	0.533000	0.62120	CTT	.	.	.	none		0.373	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		C	51251577	T	C	51251577	3	2	33	1	0	0	0	0	1	0	0	0	4690	1609	56	3	1205	3	DOCK3	3	51251577	Missense_Mutation	SNP	T	TCGA-5P-A9K2-01A-11D-A42J-10	2524461	51251577	146770853	16	2386											
CCDC48	79825	hgsc.bcm.edu	37	chr3	128720759	128720759	+	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	gcggagggggccaccacggcCgggcaggcagcaggtgacgg	7	1	21	12	4	0	1	0	1	0	0	0	2	0	2	3	8	1	3	3	8	0	0			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr3:128720759C>A	ENST00000480450.1	+	1	288	c.288C>A	c.(286-288)gcC>gcA	p.A96A	KIAA1257_ENST00000510149.1_Intron|EFCC1_ENST00000436022.2_5'UTR			Q9HA90	EFCC1_HUMAN	EF-hand and coiled-coil domain containing 1	96							calcium ion binding (GO:0005509)										CCACCACGGCCGGGCAGGCAG	0.731																																					p.A96A		Atlas-SNP	.											.	.	.	.	0			c.C288A						PASS	.						4	9	7					3																	128720759		615	1457	2072	SO:0001819	synonymous_variant	79825	exon1			CACGGCCGGGCAG	AK022119	CCDS3054.1, CCDS3054.2	3q21.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000114654	ENSG00000114654		"EF-hand domain containing"	25692	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 73", "coiled-coil domain containing 48"	C3orf73, CCDC48			Standard	NM_024768		Approved	FLJ12057	uc011bkt.2	Q9HA90	OTTHUMG00000158996	ENST00000480450.1:c.288C>A	chr3.hg19:g.128720759C>A		63.0	0.0	.		170.0	47.0	.	NM_024768	A8MYE2	Silent	SNP	ENST00000480450.1	hg19	CCDS3054.2																																																																																			.	.	.	none		0.731	EFCC1-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352832.1	NM_024768		A	128720759	C	A	128720759	2	1	33	1	0	0	0	0	0	0	0	1	2821	639	23	4		4	CCDC48	3	128720759	Silent	SNP	C	TCGA-5P-A9K2-01A-11D-A42J-10	77469182	128720759	69301671	17	2387											
IGSF10	285313	hgsc.bcm.edu	37	chr3	151163860	151163860	+	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	ctttttgtacttgagtctttGcttataatactaggaagcat	10	18	7	6	0	1	1	0	1	1	0	1	2	1	2	0	1	4	3	0	1	6	9			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr3:151163860G>T	ENST00000282466.3	-	4	3908	c.3909C>A	c.(3907-3909)agC>agA	p.S1303R		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	1303					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)			TTGAGTCTTTGCTTATAATAC	0.438																																					p.S1303R		Atlas-SNP	.											.	IGSF10	279	.	0			c.C3909A						PASS	.						280	258	266					3																	151163860		2203	4300	6503	SO:0001583	missense	285313	exon4			GTCTTTGCTTATA	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.3909C>A	chr3.hg19:g.151163860G>T	ENSP00000282466:p.Ser1303Arg	87.0	0.0	.		121.0	5.0	.	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	hg19	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	G	8.227	0.803834	0.16467	.	.	ENSG00000152580	ENST00000282466	T	0.69561	-0.41	4.62	2.79	0.32731	.	0.256644	0.26879	N	0.022028	T	0.48040	0.1478	N	0.20986	0.625	0.09310	N	1	B	0.18013	0.025	B	0.17722	0.019	T	0.27872	-1.0061	10	0.23891	T	0.37	.	9.3524	0.38147	0.0777:0.0:0.7791:0.1432	.	1303	Q6WRI0	IGS10_HUMAN	R	1303	ENSP00000282466:S1303R	ENSP00000282466:S1303R	S	-	3	2	IGSF10	152646550	0.000000	0.05858	0.047000	0.18901	0.016000	0.09150	0.760000	0.26475	0.477000	0.27464	0.591000	0.81541	AGC	.	.	.	none		0.438	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		T	151163860	G	T	151163860	3	4	33	1	0	0	0	0	1	0	0	0	7604	1310	46	4	4022	4	IGSF10	3	151163860	Missense_Mutation	SNP	G	TCGA-5P-A9K2-01A-11D-A42J-10	22443101	151163860	46858570	18	2388											
FRYL	285527	hgsc.bcm.edu	37	chr4	48581047	48581047	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtatgcaaacatccaagcaTagctcacagctgtagagcag	14	8	9	10	0	1	1	1	0	0	1	2	1	2	1	1	0	6	7	1	0	5	3	rs544935208		TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr4:48581047T>C	ENST00000503238.1	-	20	2470	c.2471A>G	c.(2470-2472)tAt>tGt	p.Y824C	FRYL_ENST00000537810.1_Missense_Mutation_p.Y824C|FRYL_ENST00000507711.1_Missense_Mutation_p.Y824C|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000358350.4_Missense_Mutation_p.Y824C			O94915	FRYL_HUMAN	FRY-like	824					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						CATCCAAGCATAGCTCACAGC	0.378													T|||	1	0.000199681	0	0.0014	5008	,	,		18848	0		0	False		,,,				2504	0				p.Y824C		Atlas-SNP	.											.	FRYL	242	.	0			c.A2471G						PASS	.						115	106	109					4																	48581047		1846	4094	5940	SO:0001583	missense	285527	exon23			CAAGCATAGCTCA	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.2471A>G	chr4.hg19:g.48581047T>C	ENSP00000426064:p.Tyr824Cys	80.0	0.0	.		129.0	54.0	.	NM_015030	O95640|Q8WTZ5|Q9NT40	Missense_Mutation	SNP	ENST00000503238.1	hg19	CCDS43227.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.239029	0.79800	.	.	ENSG00000075539	ENST00000503238;ENST00000358350;ENST00000537810;ENST00000507711	T;T;T;T	0.46451	1.86;1.86;1.86;0.87	6.05	6.05	0.98169	.	0.000000	0.64402	U	0.000002	T	0.64148	0.2572	M	0.71036	2.16	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74674	0.984;0.975	T	0.63699	-0.6578	10	0.44086	T	0.13	.	16.5993	0.84807	0.0:0.0:0.0:1.0	.	824;824	F2Z2S2;O94915	.;FRYL_HUMAN	C	824	ENSP00000426064:Y824C;ENSP00000351113:Y824C;ENSP00000441114:Y824C;ENSP00000421584:Y824C	ENSP00000351113:Y824C	Y	-	2	0	FRYL	48275804	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	5.949000	0.70257	2.311000	0.77944	0.528000	0.53228	TAT	.	.	.	none		0.378	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			C	48581047	T	C	48581047	3	2	33	1	0	0	0	0	1	0	0	0	6071	1406	49	3	6738	3	FRYL	4	48581047	Missense_Mutation	SNP	T	TCGA-5P-A9K2-01A-11D-A42J-10		48581047	142573229	19	2389											
FIP1L1	81608	hgsc.bcm.edu	37	chr4	54248495	54248495	+	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	aactgctgaaaatggtgtacCaaaaccggtaacataaggct	16	8	9	8	1	0	1	0	1	0	0	0	1	0	1	2	3	5	4	2	3	8	3			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr4:54248495C>G	ENST00000337488.6	+	4	415	c.221C>G	c.(220-222)cCa>cGa	p.P74R	FIP1L1_ENST00000507922.1_Missense_Mutation_p.P59R|FIP1L1_ENST00000507166.1_Missense_Mutation_p.P74R|FIP1L1_ENST00000358575.5_Missense_Mutation_p.P59R|FIP1L1_ENST00000306932.6_Missense_Mutation_p.P59R|FIP1L1_ENST00000510668.1_3'UTR	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	74	Necessary for stimulating PAPOLA activity.|Sufficient for interaction with PAPOLA.				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)			AATGGTGTACCAAAACCGGTA	0.358			T	PDGFRA	idiopathic hypereosinophilic syndrome																																p.P74R		Atlas-SNP	.		Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	.	FIP1L1	60	.	0			c.C221G						PASS	.						154	140	145					4																	54248495		2203	4300	6503	SO:0001583	missense	81608	exon4			GTGTACCAAAACC	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.221C>G	chr4.hg19:g.54248495C>G	ENSP00000336752:p.Pro74Arg	63.0	0.0	.		86.0	29.0	.	NM_030917	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Missense_Mutation	SNP	ENST00000337488.6	hg19	CCDS3491.1	.	.	.	.	.	.	.	.	.	.	C	10.95	1.494563	0.26774	.	.	ENSG00000145216	ENST00000337488;ENST00000358575;ENST00000507922;ENST00000306932;ENST00000507166	T	0.76968	-1.06	5.48	4.63	0.57726	.	0.519843	0.18037	N	0.153726	T	0.55816	0.1944	N	0.08118	0	0.25163	N	0.990332	B;B;B;P	0.36282	0.071;0.018;0.083;0.546	B;B;B;B	0.38954	0.285;0.034;0.027;0.286	T	0.46470	-0.9189	10	0.16420	T	0.52	-2.5771	5.3271	0.15913	0.1739:0.672:0.0:0.1541	.	59;59;74;59	G3XAD6;Q6UN15-3;Q6UN15;Q6UN15-4	.;.;FIP1_HUMAN;.	R	74;59;59;59;74	ENSP00000423325:P74R	ENSP00000302993:P59R	P	+	2	0	FIP1L1	53943252	0.926000	0.31397	0.995000	0.50966	0.989000	0.77384	1.814000	0.38972	1.279000	0.44446	0.655000	0.94253	CCA	.	.	.	none		0.358	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250602.1	NM_030917		G	54248495	C	G	54248495	3	3	33	1	0	0	0	0	1	0	0	0	5903	594	21	4	235	4	FIP1L1	4	54248495	Missense_Mutation	SNP	C	TCGA-5P-A9K2-01A-11D-A42J-10	5667448	54248495	136905781	20	2390											
PRDM5	11107	hgsc.bcm.edu	37	chr4	121828665	121828665	+	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	taatccatattttcatccaaGtcttcaggcattctcttctc	9	17	3	12	0	5	0	2	0	3	0	9	0	7	0	2	1	0	1	2	1	3	7			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr4:121828665G>A	ENST00000264808.3	-	2	381	c.141C>T	c.(139-141)gaC>gaT	p.D47D	PRDM5_ENST00000515109.1_Silent_p.D47D|PRDM5_ENST00000394435.2_Silent_p.D47D|PRDM5_ENST00000428209.2_Silent_p.D47D	NM_018699.2	NP_061169.2	Q9NQX1	PRDM5_HUMAN	PR domain containing 5	47	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				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						TTTCATCCAAGTCTTCAGGCA	0.328																																					p.D47D		Atlas-SNP	.											.	PRDM5	76	.	0			c.C141T						PASS	.						153	152	152					4																	121828665		2203	4300	6503	SO:0001819	synonymous_variant	11107	exon2			ATCCAAGTCTTCA	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.141C>T	chr4.hg19:g.121828665G>A		159.0	0.0	.		162.0	74.0	.	NM_018699	Q0VAI9|Q0VAJ0|Q6NXQ7	Silent	SNP	ENST00000264808.3	hg19	CCDS3716.1																																																																																			.	.	.	none		0.328	PRDM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256528.2			A	121828665	G	A	121828665	2	1	33	1	0	0	0	0	0	0	0	1	12470	1020	36	2		2	PRDM5	4	121828665	Silent	SNP	G	TCGA-5P-A9K2-01A-11D-A42J-10	67580170	121828665	69325611	21	2391											
TRPC3	7222	hgsc.bcm.edu	37	chr4	122825529	122825529	+	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	caattagcatgttgagtaaaAcgaccaccatagttacattg	15	11	7	8	1	0	1	0	1	0	0	0	2	0	1	2	0	3	4	2	0	6	6			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr4:122825529A>T	ENST00000379645.3	-	8	2274	c.2201T>A	c.(2200-2202)gTt>gAt	p.V734D	TRPC3_ENST00000513531.1_Missense_Mutation_p.V606D|TRPC3_ENST00000264811.5_Missense_Mutation_p.V661D	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	649					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						GTTGAGTAAAACGACCACCAT	0.328																																					p.V734D		Atlas-SNP	.											.	TRPC3	201	.	0			c.T2201A						PASS	.						100	96	97					4																	122825529		2203	4299	6502	SO:0001583	missense	7222	exon8			AGTAAAACGACCA	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.2201T>A	chr4.hg19:g.122825529A>T	ENSP00000368966:p.Val734Asp	183.0	0.0	.		218.0	64.0	.	NM_001130698	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Missense_Mutation	SNP	ENST00000379645.3	hg19	CCDS47130.1	.	.	.	.	.	.	.	.	.	.	A	25.7	4.668125	0.88348	.	.	ENSG00000138741	ENST00000264811;ENST00000379645;ENST00000513531	D;D;D	0.98849	-5.18;-5.18;-5.18	5.52	5.52	0.82312	Ion transport (1);	0.000000	0.64402	D	0.000002	D	0.99378	0.9781	H	0.94698	3.57	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.998	D	0.98652	1.0680	10	0.87932	D	0	-35.6827	15.9239	0.79597	1.0:0.0:0.0:0.0	.	649;606;734	Q13507;E9PCJ9;Q5G1L5	TRPC3_HUMAN;.;.	D	661;734;606	ENSP00000264811:V661D;ENSP00000368966:V734D;ENSP00000426899:V606D	ENSP00000264811:V661D	V	-	2	0	TRPC3	123044979	1.000000	0.71417	0.993000	0.49108	0.997000	0.91878	9.174000	0.94824	2.207000	0.71202	0.533000	0.62120	GTT	.	.	.	none		0.328	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305		T	122825529	A	T	122825529	3	4	33	1	0	0	0	0	1	0	0	0	16591	43	2	5	584	5	TRPC3	4	122825529	Missense_Mutation	SNP	A	TCGA-5P-A9K2-01A-11D-A42J-10	996864	122825529	68328747	22	2392			1	5		2	2	16	A		3.876303e-05
TRPC3	7222	hgsc.bcm.edu	37	chr4	122825544	122825544	+	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	gtaaaacgaccaccatagttAcattgtatattccataaaga	17	11	5	8	1	0	1	0	0	0	1	1	2	1	1	3	0	2	3	3	0	8	8			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr4:122825544A>T	ENST00000379645.3	-	8	2259	c.2186T>A	c.(2185-2187)gTa>gAa	p.V729E	TRPC3_ENST00000513531.1_Missense_Mutation_p.V601E|TRPC3_ENST00000264811.5_Missense_Mutation_p.V656E	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	644					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						CACCATAGTTACATTGTATAT	0.328																																					p.V729E		Atlas-SNP	.											.	TRPC3	201	.	0			c.T2186A						PASS	.						96	92	93					4																	122825544		2203	4299	6502	SO:0001583	missense	7222	exon8			ATAGTTACATTGT	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.2186T>A	chr4.hg19:g.122825544A>T	ENSP00000368966:p.Val729Glu	200.0	0.0	.		217.0	68.0	.	NM_001130698	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Missense_Mutation	SNP	ENST00000379645.3	hg19	CCDS47130.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.677827	0.88445	.	.	ENSG00000138741	ENST00000264811;ENST00000379645;ENST00000513531	D;D;D	0.98762	-5.12;-5.12;-5.12	5.52	5.52	0.82312	Ion transport (1);	0.000000	0.64402	D	0.000002	D	0.99312	0.9759	M	0.92555	3.32	0.80722	D	1	D;D;D	0.89917	0.998;0.998;1.0	D;D;D	0.80764	0.968;0.981;0.994	D	0.98934	1.0788	10	0.87932	D	0	-23.7439	15.9239	0.79597	1.0:0.0:0.0:0.0	.	644;601;729	Q13507;E9PCJ9;Q5G1L5	TRPC3_HUMAN;.;.	E	656;729;601	ENSP00000264811:V656E;ENSP00000368966:V729E;ENSP00000426899:V601E	ENSP00000264811:V656E	V	-	2	0	TRPC3	123044994	1.000000	0.71417	0.988000	0.46212	0.941000	0.58515	9.174000	0.94824	2.207000	0.71202	0.533000	0.62120	GTA	.	.	.	none		0.328	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305		T	122825544	A	T	122825544	3	4	33	1	0	0	0	0	1	0	0	0	16591	391	14	5	599	5	TRPC3	4	122825544	Missense_Mutation	SNP	A	TCGA-5P-A9K2-01A-11D-A42J-10	15	122825544	68328732	23	2393			1	5		2	2	16	A		3.876303e-05
FAM198B	51313	hgsc.bcm.edu	37	chr4	159092466	159092466	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccagagcttacgcacccgcGggacgcacagggagcagatg	10	4	14	13	4	0	2	0	0	0	2	1	4	1	4	2	2	3	4	2	2	1	1			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr4:159092466G>A	ENST00000296530.8	-	2	683	c.62C>T	c.(61-63)cCg>cTg	p.P21L	FAM198B_ENST00000592057.1_Missense_Mutation_p.P21L|RP11-597D13.9_ENST00000503611.1_RNA|FAM198B_ENST00000589306.1_Intron|RP11-597D13.9_ENST00000505532.1_RNA|FAM198B_ENST00000393807.5_Missense_Mutation_p.P21L|RP11-597D13.9_ENST00000509463.1_RNA|RP11-597D13.9_ENST00000514381.1_RNA|FAM198B_ENST00000585682.1_Missense_Mutation_p.P21L	NM_016613.6	NP_057697.2	Q6UWH4	F198B_HUMAN	family with sequence similarity 198, member B	21						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						ACGCACCCGCGGGACGCACAG	0.587																																					p.P21L		Atlas-SNP	.											.	FAM198B	134	.	0			c.C62T						PASS	.						41	41	41					4																	159092466		2201	4299	6500	SO:0001583	missense	51313	exon2			ACCCGCGGGACGC		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.62C>T	chr4.hg19:g.159092466G>A	ENSP00000296530:p.Pro21Leu	61.0	0.0	.		52.0	23.0	.	NM_016613	Q498Z3|Q6IAF9|Q6ZMF2|Q86XL0	Missense_Mutation	SNP	ENST00000296530.8	hg19	CCDS3798.1	.	.	.	.	.	.	.	.	.	.	G	12.83	2.055019	0.36277	.	.	ENSG00000164125	ENST00000337222;ENST00000296530;ENST00000393807;ENST00000417442	T;T	0.31510	1.5;1.49	5.31	3.57	0.40892	.	0.540389	0.20073	N	0.099828	T	0.25457	0.0619	L	0.54323	1.7	0.21967	N	0.999447	B;B;B	0.32968	0.392;0.068;0.028	B;B;B	0.28232	0.087;0.012;0.012	T	0.24548	-1.0157	10	0.87932	D	0	-0.7468	6.6971	0.23205	0.1449:0.0:0.71:0.145	.	21;21;21	Q6UWH4-3;Q6UWH4-2;Q6UWH4	.;.;F198B_HUMAN	L	21	ENSP00000296530:P21L;ENSP00000377396:P21L	ENSP00000296530:P21L	P	-	2	0	FAM198B	159311916	0.990000	0.36364	0.275000	0.24674	0.855000	0.48748	2.335000	0.43929	0.799000	0.34018	0.655000	0.94253	CCG	.	.	.	none		0.587	FAM198B-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365230.1	NM_001031700, NM_016613		A	159092466	G	A	159092466	3	1	33	1	0	0	0	0	1	0	0	0	5533	1116	39	1	1618	1	FAM198B	4	159092466	Missense_Mutation	SNP	G	TCGA-5P-A9K2-01A-11D-A42J-10	36266922	159092466	32061810	24	2394											
CDKN2AIP	55602	hgsc.bcm.edu	37	chr4	184366090	184366090	+	Frame_Shift_Del	DEL	C	C	-																															tcgcaacgccggggacctggCccccgctggcggcgctgcct																										TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr4:184366090delC	ENST00000504169.1	+	1	347	c.140delC	c.(139-141)gccfs	p.A47fs	CDKN2AIP_ENST00000510928.1_Frame_Shift_Del_p.A47fs|CDKN2AIP_ENST00000302350.4_Frame_Shift_Del_p.A47fs	NM_017632.2	NP_060102.1	Q9NXV6	CARF_HUMAN	CDKN2A interacting protein	47					negative regulation of cell growth (GO:0030308)|positive regulation of signal transduction (GO:0009967)|regulation of protein stability (GO:0031647)	cytoplasm (GO:0005737)|granular component (GO:0001652)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	p53 binding (GO:0002039)|RNA binding (GO:0003723)			endometrium(1)|kidney(2)|large_intestine(2)|lung(1)	6		all_lung(41;6.9e-12)|Lung NSC(41;1.28e-11)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;1.15e-26)|Epithelial(43;2.98e-22)|OV - Ovarian serous cystadenocarcinoma(60;7.64e-10)|GBM - Glioblastoma multiforme(59;4.22e-06)|Colorectal(24;5.87e-06)|STAD - Stomach adenocarcinoma(60;2.09e-05)|COAD - Colon adenocarcinoma(29;5.15e-05)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)		GGGGACCTGGCCCCCGCTGGC	0.687																																					p.A47fs		Atlas-Indel,Pindel	.											.	CDKN2AIP	31	.	0			c.139delG						PASS	.																																			SO:0001589	frameshift_variant	55602	exon1			.	AK000043	CCDS34110.1	4q35.1	2008-02-05			ENSG00000168564	ENSG00000168564			24325	protein-coding gene	gene with protein product	"collaborates/cooperates with ARF (alternate reading frame) protein"	615914				12154087, 16803988	Standard	NM_017632		Approved	FLJ20036, CARF	uc003ivp.1	Q9NXV6	OTTHUMG00000160626	ENST00000504169.1:c.140delC	chr4.hg19:g.184366090delC	ENSP00000427108:p.Ala47fs	83.0	0.0	0		150.0	60.0	0.4	NM_017632	Q8TBM5|Q9NYH0	Frame_Shift_Del	DEL	ENST00000504169.1	hg19	CCDS34110.1																																																																																			.	.	.	none		0.687	CDKN2AIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361488.1	NM_017632		-	184366090	C	-	184366090	7	5	33	1	0	1	0	1	0	0	0	0	3164	739	26	0	142	0	CDKN2AIP	4	184366090	Frame_Shift_Del	DEL	C	TCGA-5P-A9K2-01A-11D-A42J-10	25273624	184366090	6788186	25	2395											
FAM81B	153643	hgsc.bcm.edu	37	chr5	94783981	94783981	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcttttacaggaaaagtcTgaaaataaaatggaagaaaa	20	10	7	4	0	2	2	0	1	2	1	3	4	2	4	0	2	1	0	0	2	10	3			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr5:94783981T>C	ENST00000283357.5	+	9	1084	c.1038T>C	c.(1036-1038)tcT>tcC	p.S346S		NM_152548.2	NP_689761	Q96LP2	FA81B_HUMAN	family with sequence similarity 81, member B	346						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)		AGGAAAAGTCTGAAAATAAAA	0.294																																					p.S346S		Atlas-SNP	.											.	FAM81B	51	.	0			c.T1038C						PASS	.						44	40	41					5																	94783981		1799	4069	5868	SO:0001819	synonymous_variant	153643	exon9			AAAGTCTGAAAAT		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.1038T>C	chr5.hg19:g.94783981T>C		309.0	0.0	.		386.0	167.0	.	NM_152548		Silent	SNP	ENST00000283357.5	hg19	CCDS43341.1																																																																																			.	.	.	none		0.294	FAM81B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370690.1	NM_152548		C	94783981	T	C	94783981	2	2	33	1	0	0	0	0	0	0	0	1	5636	1567	55	3		3	FAM81B	5	94783981	Silent	SNP	T	TCGA-5P-A9K2-01A-11D-A42J-10		94783981	86131279	26	2396											
GRAMD3	65983	hgsc.bcm.edu	37	chr5	125808993	125808993	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagaaagaaatactataccAaggaaagctctttgtatcag	18	9	7	7	0	2	2	1	0	1	2	2	3	2	3	1	1	3	2	1	1	8	5			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr5:125808993A>G	ENST00000285689.3	+	5	880	c.419A>G	c.(418-420)cAa>cGa	p.Q140R	GRAMD3_ENST00000542322.1_Missense_Mutation_p.Q148R|GRAMD3_ENST00000513040.1_Missense_Mutation_p.Q155R|GRAMD3_ENST00000543198.1_Missense_Mutation_p.Q117R|GRAMD3_ENST00000544396.1_Missense_Mutation_p.Q36R|GRAMD3_ENST00000511134.1_Missense_Mutation_p.Q124R|GRAMD3_ENST00000502348.1_Missense_Mutation_p.Q31R|GRAMD3_ENST00000515200.1_Missense_Mutation_p.Q117R|RP11-517I3.1_ENST00000515808.1_RNA	NM_023927.2	NP_076416.2	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3	140	GRAM.					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)		ATACTATACCAAGGAAAGCTC	0.328																																					p.Q155R		Atlas-SNP	.											.	GRAMD3	30	.	0			c.A464G						PASS	.						54	59	57					5																	125808993		2202	4299	6501	SO:0001583	missense	65983	exon5			TATACCAAGGAAA	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.419A>G	chr5.hg19:g.125808993A>G	ENSP00000285689:p.Gln140Arg	173.0	0.0	.		216.0	90.0	.	NM_001146319	B7Z1F2|B7Z3R1|B7Z6D8|B7Z8T2|D3DSZ3|Q9H753	Missense_Mutation	SNP	ENST00000285689.3	hg19	CCDS4136.1	.	.	.	.	.	.	.	.	.	.	A	29.2	4.989266	0.93106	.	.	ENSG00000155324	ENST00000513040;ENST00000506445;ENST00000543367;ENST00000285689;ENST00000515200;ENST00000542322;ENST00000544396;ENST00000543198;ENST00000502348;ENST00000511134	D;D;D;D;D;D;D;D;D	0.87729	-2.29;-2.29;-2.29;-2.29;-2.29;-2.29;-2.29;-2.29;-2.29	6.04	6.04	0.98038	GRAM (2);	0.047859	0.85682	D	0.000000	D	0.95608	0.8572	H	0.95679	3.705	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.997;1.0	D;D;D;D;D	0.97110	0.998;1.0;1.0;0.994;0.998	D	0.96686	0.9507	10	0.72032	D	0.01	.	16.2378	0.82389	1.0:0.0:0.0:0.0	.	124;36;148;155;140	B7Z8T2;B7Z1F2;B7Z3R1;B7Z6D8;Q96HH9	.;.;.;.;GRAM3_HUMAN	R	155;154;124;140;117;148;36;117;31;124	ENSP00000426120:Q155R;ENSP00000424985:Q154R;ENSP00000285689:Q140R;ENSP00000426143:Q117R;ENSP00000441876:Q148R;ENSP00000444049:Q36R;ENSP00000442902:Q117R;ENSP00000427596:Q31R;ENSP00000426088:Q124R	ENSP00000285689:Q140R	Q	+	2	0	GRAMD3	125836892	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.224000	0.95209	2.317000	0.78254	0.459000	0.35465	CAA	.	.	.	none		0.328	GRAMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250922.2	NM_023927		G	125808993	A	G	125808993	3	3	33	1	0	0	0	0	1	0	0	0	6758	130	5	3	651	3	GRAMD3	5	125808993	Missense_Mutation	SNP	A	TCGA-5P-A9K2-01A-11D-A42J-10	31025012	125808993	55106267	27	2397											
RREB1	6239	hgsc.bcm.edu	37	chr6	7249194	7249198	+	Frame_Shift_Del	DEL	TGGAG	TGGAG	-																															cgcctcccagctcgtggggaTggagtgacagcctcagtccc																										TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	TGGAG	TGGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr6:7249194_7249198delTGGAG	ENST00000349384.6	+	12	5371_5375	c.5057_5061delTGGAG	c.(5056-5061)atggagfs	p.ME1686fs	RREB1_ENST00000334984.6_Frame_Shift_Del_p.ME1475fs|RREB1_ENST00000379938.2_Frame_Shift_Del_p.ME1741fs|RREB1_ENST00000379933.3_Frame_Shift_Del_p.ME1686fs	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1686					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)				CTCGTGGGGATGGAGTGACAGCCTC	0.634																																					p.1741_1742del		Atlas-Indel,Pindel	.											.	RREB1	242	.	0			c.5221_5225del						PASS	.																																			SO:0001589	frameshift_variant	6239	exon13			.	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.5057_5061delTGGAG	chr6.hg19:g.7249194_7249198delTGGAG	ENSP00000305560:p.Met1686fs	22.0	0.0	0		30.0	10.0	0.333333	NM_001003699	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Frame_Shift_Del	DEL	ENST00000349384.6	hg19	CCDS34336.1																																																																																			.	.	.	none		0.634	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1			-	7249198	TGGAG	-	7249194	7	5	33	1	0	1	0	1	0	0	0	0	13692	1464	51	0	5260	0	RREB1	6	7249194	Frame_Shift_Del	DEL	TGGAG	TCGA-5P-A9K2-01A-11D-A42J-10		7249194	163865873	28	2398											
ZNF184	7738	hgsc.bcm.edu	37	chr6	27420389	27420389	+	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	ctgaacaagatgggtcctctGactaaaggctttcccacatt	11	11	8	11	0	1	3	0	2	1	1	3	3	3	3	2	2	1	1	2	2	4	3			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr6:27420389G>T	ENST00000211936.6	-	6	1233	c.949C>A	c.(949-951)Cag>Aag	p.Q317K	ZNF184_ENST00000377419.1_Missense_Mutation_p.Q317K	NM_007149.2	NP_009080.2	Q99676	ZN184_HUMAN	zinc finger protein 184	317					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|kidney(9)|large_intestine(13)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						TGGGTCCTCTGACTAAAGGCT	0.413																																					p.Q317K		Atlas-SNP	.											.	ZNF184	89	.	0			c.C949A						PASS	.						52	53	53					6																	27420389		2203	4300	6503	SO:0001583	missense	7738	exon6			TCCTCTGACTAAA	U66561	CCDS4624.1	6p21.3	2013-01-08	2006-06-28		ENSG00000096654	ENSG00000096654		"Zinc fingers, C2H2-type", "-"	12975	protein-coding gene	gene with protein product		602277	"zinc finger protein 184 (Kruppel-like)"				Standard	NM_007149		Approved		uc003nji.3	Q99676	OTTHUMG00000014478	ENST00000211936.6:c.949C>A	chr6.hg19:g.27420389G>T	ENSP00000211936:p.Gln317Lys	55.0	0.0	.		63.0	22.0	.	NM_007149	B2R715|O60792|Q8TBA9	Missense_Mutation	SNP	ENST00000211936.6	hg19	CCDS4624.1	.	.	.	.	.	.	.	.	.	.	G	14.54	2.566236	0.45694	.	.	ENSG00000096654	ENST00000211936;ENST00000377419;ENST00000341087;ENST00000538681	T;T	0.07327	3.2;3.2	4.99	4.1	0.47936	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.44902	D	0.000405	T	0.01387	0.0045	N	0.12637	0.245	0.32231	N	0.574014	P	0.50710	0.938	B	0.34590	0.186	T	0.52449	-0.8574	10	0.24483	T	0.36	.	9.5393	0.39242	0.0989:0.0:0.9011:0.0	.	317	Q99676	ZN184_HUMAN	K	317;317;317;5	ENSP00000211936:Q317K;ENSP00000366636:Q317K	ENSP00000211936:Q317K	Q	-	1	0	ZNF184	27528368	0.000000	0.05858	1.000000	0.80357	0.976000	0.68499	-0.289000	0.08365	2.591000	0.87537	0.455000	0.32223	CAG	.	.	.	none		0.413	ZNF184-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040146.1	NM_007149		T	27420389	G	T	27420389	3	4	33	1	0	0	0	0	1	0	0	0	17763	1299	45	4	1310	4	ZNF184	6	27420389	Missense_Mutation	SNP	G	TCGA-5P-A9K2-01A-11D-A42J-10	20171195	27420389	143694678	29	2399											
HLA-C	3107	hgsc.bcm.edu	37	chr6	31239839	31239839	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggagggctcggggcgccaTgacccgcatctcggcctctg	5	6	16	14	4	2	1	0	1	2	0	4	3	2	2	3	5	0	2	3	5	0	0			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr6:31239839T>C	ENST00000376228.5	-	1	24	c.10A>G	c.(10-12)Atg>Gtg	p.M4V	HLA-C_ENST00000383329.3_Missense_Mutation_p.M4V	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	4					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						CGGGGCGCCATGACCCGCATC	0.667																																					p.M4V		Atlas-SNP	.											.	HLA-C	92	.	0			c.A10G						PASS	.						18	19	19					6																	31239839		1511	2709	4220	SO:0001583	missense	3107	exon1			GCGCCATGACCCG	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.10A>G	chr6.hg19:g.31239839T>C	ENSP00000365402:p.Met4Val	69.0	0.0	.		84.0	30.0	.	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	hg19	CCDS34393.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	3.391|3.391	-0.124293|-0.124293	0.06795|0.06795	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000415537|ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	.|T;T	.|0.00730	.|5.78;5.77	2.38|2.38	-0.236|-0.236	0.13067|0.13067	.|.	.|.	.|.	.|.	.|.	T|T	0.00440|0.00440	0.0014|0.0014	M|M	0.78456|0.78456	2.415|2.415	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.11235	.|0.003;0.001;0.003;0.004	.|B;B;B;B	.|0.19391	.|0.019;0.011;0.011;0.025	T|T	0.42189|0.42189	-0.9466|-0.9466	5|9	.|0.66056	.|D	.|0.02	.|.	2.6949|2.6949	0.05132|0.05132	0.0:0.1644:0.2772:0.5584|0.0:0.1644:0.2772:0.5584	.|.	.|4;4;4;4	.|A2AEA4;A6H578;A2AEA2;P10321	.|.;.;.;1C07_HUMAN	R|V	3|4	.|ENSP00000365402:M4V;ENSP00000372819:M4V	.|ENSP00000365402:M4V	H|M	-|-	2|1	0|0	HLA-C|HLA-C	31347818|31347818	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.016000|0.016000	0.09150|0.09150	-0.065000|-0.065000	0.11617|0.11617	-0.041000|-0.041000	0.13558|0.13558	0.254000|0.254000	0.18369|0.18369	CAT|ATG	.	.	.	none		0.667	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117		C	31239839	T	C	31239839	3	2	33	1	0	0	0	0	1	0	0	0	7204	1464	51	3	1122	3	HLA-C	6	31239839	Missense_Mutation	SNP	T	TCGA-5P-A9K2-01A-11D-A42J-10	3819450	31239839	139875228	30	2400											
KLC4	89953	hgsc.bcm.edu	37	chr6	43039962	43039962	+	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	gctggaggctgctgagacccTggaggaatgtgccctgcggt	6	8	17	10	1	0	1	0	1	0	1	0	5	0	4	2	5	3	3	2	5	1	0			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr6:43039962T>A	ENST00000394056.2	+	13	1952	c.1457T>A	c.(1456-1458)cTg>cAg	p.L486Q	KLC4_ENST00000347162.5_Missense_Mutation_p.L486Q|KLC4_ENST00000259708.3_Missense_Mutation_p.L504Q|KLC4_ENST00000394058.1_Missense_Mutation_p.L486Q|KLC4_ENST00000453940.2_Missense_Mutation_p.L409Q|KLC4_ENST00000479388.1_Missense_Mutation_p.L486Q|RP11-387M24.5_ENST00000606123.1_RNA			Q9NSK0	KLC4_HUMAN	kinesin light chain 4	486						cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			endometrium(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(4)	23			all cancers(41;0.00169)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0376)|KIRC - Kidney renal clear cell carcinoma(2;0.0453)			GCTGAGACCCTGGAGGAATGT	0.602																																					p.L504Q		Atlas-SNP	.											.	KLC4	89	.	0			c.T1511A						PASS	.						62	68	66					6																	43039962		2203	4300	6503	SO:0001583	missense	89953	exon12			AGACCCTGGAGGA	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.1457T>A	chr6.hg19:g.43039962T>A	ENSP00000377620:p.Leu486Gln	38.0	0.0	.		53.0	22.0	.	NM_201523	B3KNY4|B3KPI3|B3KSQ3|B4DME9|Q66K28|Q96EG6	Missense_Mutation	SNP	ENST00000394056.2	hg19	CCDS4883.1	.	.	.	.	.	.	.	.	.	.	T	32	5.142869	0.94560	.	.	ENSG00000137171	ENST00000347162;ENST00000453940;ENST00000259708;ENST00000479388;ENST00000394056;ENST00000394058	D;T;D;D;D;D	0.83506	-1.73;1.13;-1.73;-1.73;-1.73;-1.73	6.04	6.04	0.98038	Tetratricopeptide-like helical (1);	0.000000	0.47852	D	0.000205	D	0.90573	0.7045	M	0.84326	2.69	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.91635	0.999;0.997;0.998	D	0.91944	0.5565	10	0.87932	D	0	-20.1899	16.5763	0.84648	0.0:0.0:0.0:1.0	.	409;504;486	B4DME9;Q9NSK0-3;Q9NSK0	.;.;KLC4_HUMAN	Q	486;409;504;486;486;486	ENSP00000340221:L486Q;ENSP00000395806:L409Q;ENSP00000259708:L504Q;ENSP00000418031:L486Q;ENSP00000377620:L486Q;ENSP00000377622:L486Q	ENSP00000259708:L504Q	L	+	2	0	KLC4	43147940	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	8.040000	0.89188	2.317000	0.78254	0.459000	0.35465	CTG	.	.	.	none		0.602	KLC4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040579.2	NM_138343		A	43039962	T	A	43039962	3	1	33	1	0	0	0	0	1	0	0	0	8343	1580	55	5	1626	5	KLC4	6	43039962	Missense_Mutation	SNP	T	TCGA-5P-A9K2-01A-11D-A42J-10	11800123	43039962	128075105	31	2401											
RIMS1	22999	hgsc.bcm.edu	37	chr6	72892828	72892828	+	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	gctgcgaggacgtggagctgGagagcgagagcgtcagcgag	9	4	20	8	5	1	2	1	0	0	2	1	8	1	4	0	3	5	2	0	3	0	0			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr6:72892828G>C	ENST00000521978.1	+	6	1654	c.1654G>C	c.(1654-1656)Gag>Cag	p.E552Q	RIMS1_ENST00000491071.2_Missense_Mutation_p.E552Q|RIMS1_ENST00000264839.7_Missense_Mutation_p.E552Q|RIMS1_ENST00000517960.1_Missense_Mutation_p.E552Q|RIMS1_ENST00000348717.5_Missense_Mutation_p.E552Q|RIMS1_ENST00000520567.1_Missense_Mutation_p.E552Q|RIMS1_ENST00000518273.1_Missense_Mutation_p.E552Q|RIMS1_ENST00000522291.1_Missense_Mutation_p.E552Q	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	552					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)				CGTGGAGCTGGAGAGCGAGAG	0.657																																					p.E552Q		Atlas-SNP	.											.	RIMS1	278	.	0			c.G1654C						PASS	.						8	9	8					6																	72892828		2004	4128	6132	SO:0001583	missense	22999	exon6			GAGCTGGAGAGCG	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.1654G>C	chr6.hg19:g.72892828G>C	ENSP00000428417:p.Glu552Gln	80.0	0.0	.		87.0	29.0	.	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	hg19	CCDS47449.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.33|16.33	3.092994|3.092994	0.56075|0.56075	.|.	.|.	ENSG00000079841|ENSG00000079841	ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978|ENST00000517433	T;T;T;T;T;T;T;T|.	0.18016|.	2.24;2.37;2.3;2.38;2.36;2.37;2.37;2.29|.	4.05|4.05	3.15|3.15	0.36227|0.36227	.|.	0.000000|.	0.64402|.	D|.	0.000013|.	T|T	0.59514|0.59514	0.2199|0.2199	M|M	0.69358|0.69358	2.11|2.11	0.80722|0.80722	D|D	1|1	B;B;B|.	0.30114|.	0.269;0.062;0.22|.	B;B;B|.	0.30105|.	0.111;0.029;0.05|.	T|T	0.60419|0.60419	-0.7267|-0.7267	10|5	0.72032|.	D|.	0.01|.	0.0102|0.0102	13.3578|13.3578	0.60638|0.60638	0.0:0.1599:0.8401:0.0|0.0:0.1599:0.8401:0.0	.|.	552;552;552|.	E9PHR1;C9JNW6;Q86UR5|.	.;.;RIMS1_HUMAN|.	Q|A	552|125	ENSP00000430101:E552Q;ENSP00000275037:E552Q;ENSP00000264839:E552Q;ENSP00000429959:E552Q;ENSP00000430408:E552Q;ENSP00000430502:E552Q;ENSP00000430932:E552Q;ENSP00000428417:E552Q|.	ENSP00000264839:E552Q|.	E|G	+|+	1|2	0|0	RIMS1|RIMS1	72949549|72949549	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.977000|0.977000	0.68977|0.68977	9.414000|9.414000	0.97362|0.97362	0.633000|0.633000	0.30452|0.30452	0.455000|0.455000	0.32223|0.32223	GAG|GGA	.	.	.	none		0.657	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			C	72892828	G	C	72892828	3	2	33	1	0	0	0	0	1	0	0	0	13380	1175	41	4	1676	4	RIMS1	6	72892828	Missense_Mutation	SNP	G	TCGA-5P-A9K2-01A-11D-A42J-10	29852866	72892828	98222239	32	2402											
POU3F2	5454	hgsc.bcm.edu	37	chr6	99283832	99283832	+	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	cggaaaaagcggacctccatCgaggtgagcgtcaagggggc	11	4	16	10	4	1	1	1	1	0	0	3	4	2	3	2	5	2	0	2	5	3	0			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr6:99283832C>A	ENST00000328345.5	+	1	1253	c.1083C>A	c.(1081-1083)atC>atA	p.I361I		NM_005604.3	NP_005595.2	P20265	PO3F2_HUMAN	POU class 3 homeobox 2	361					astrocyte development (GO:0014002)|cellular response to organic substance (GO:0071310)|cerebral cortex radially oriented cell migration (GO:0021799)|epidermis development (GO:0008544)|forebrain ventricular zone progenitor cell division (GO:0021869)|hypothalamus cell differentiation (GO:0021979)|myelination in peripheral nervous system (GO:0022011)|neurohypophysis development (GO:0021985)|neuron differentiation (GO:0030182)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of axonogenesis (GO:0050770)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	identical protein binding (GO:0042802)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(3)|lung(5)	10		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0355)		GGACCTCCATCGAGGTGAGCG	0.617																																					p.I361I		Atlas-SNP	.											.	POU3F2	33	.	0			c.C1083A						PASS	.						65	73	70					6																	99283832		2203	4300	6503	SO:0001819	synonymous_variant	5454	exon1			CTCCATCGAGGTG	Z11933	CCDS5040.1	6q16.2	2011-06-20	2007-07-13		ENSG00000184486	ENSG00000184486		"Homeoboxes / POU class"	9215	protein-coding gene	gene with protein product		600494	"POU domain class 3, transcription factor 2"	OTF7		8441633	Standard	NM_005604		Approved	POUF3, BRN2, OCT7	uc003ppe.3	P20265	OTTHUMG00000015258	ENST00000328345.5:c.1083C>A	chr6.hg19:g.99283832C>A		70.0	0.0	.		96.0	30.0	.	NM_005604	Q14960|Q86V54|Q9UJL0	Silent	SNP	ENST00000328345.5	hg19	CCDS5040.1																																																																																			.	.	.	none		0.617	POU3F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041586.2			A	99283832	C	A	99283832	2	1	33	1	0	0	0	0	0	0	0	1	12282	874	31	4		4	POU3F2	6	99283832	Silent	SNP	C	TCGA-5P-A9K2-01A-11D-A42J-10	26391004	99283832	71831235	33	2403											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152470766	152470766	+	Missense_Mutation	SNP	A	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	cttgggcaattatctgctcaAtcttattgtggttcagtgaa	9	16	9	7	0	4	1	2	1	2	0	4	1	4	1	0	2	1	3	0	2	5	5	rs139643725		TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr6:152470766A>C	ENST00000367255.5	-	136	25089	c.24488T>G	c.(24487-24489)aTt>aGt	p.I8163S	SYNE1_ENST00000354674.4_Missense_Mutation_p.I318S|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000448038.1_Missense_Mutation_p.I8092S|SYNE1_ENST00000341594.5_Missense_Mutation_p.I7775S|SYNE1_ENST00000265368.4_Missense_Mutation_p.I8163S|SYNE1_ENST00000423061.1_Missense_Mutation_p.I8092S|SYNE1_ENST00000539504.1_Missense_Mutation_p.I318S|SYNE1_ENST00000356820.4_Missense_Mutation_p.I2687S	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8163					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)		TATCTGCTCAATCTTATTGTG	0.433										HNSCC(10;0.0054)																											p.I8163S		Atlas-SNP	.											.	SYNE1	3227	.	0			c.T24488G						PASS	.						103	102	102					6																	152470766		2203	4300	6503	SO:0001583	missense	23345	exon136			TGCTCAATCTTAT	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.24488T>G	chr6.hg19:g.152470766A>C	ENSP00000356224:p.Ile8163Ser	25.0	0.0	.		38.0	16.0	.	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	A	28.0	4.878417	0.91740	.	.	ENSG00000131018	ENST00000367255;ENST00000539504;ENST00000367257;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000313630;ENST00000367247;ENST00000367251;ENST00000354674	T;T;T;T;T;T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55	5.86	5.86	0.93980	.	0.000000	0.64402	D	0.000013	T	0.63450	0.2512	L	0.59436	1.845	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.994	D;D;D;D;D	0.77004	0.984;0.989;0.982;0.989;0.965	T	0.67952	-0.5537	10	0.87932	D	0	.	16.2453	0.82441	1.0:0.0:0.0:0.0	.	8163;8163;8092;8092;365	Q8NF91;E7EQI5;Q8NF91-4;E9PEL9;B7Z9Y6	SYNE1_HUMAN;.;.;.;.	S	8163;318;809;8092;8163;8092;7775;2687;325;320;1085;318	ENSP00000356224:I8163S;ENSP00000441052:I318S;ENSP00000356226:I809S;ENSP00000396024:I8092S;ENSP00000265368:I8163S;ENSP00000390975:I8092S;ENSP00000341887:I7775S;ENSP00000349276:I2687S;ENSP00000356220:I1085S;ENSP00000346701:I318S	ENSP00000265368:I8163S	I	-	2	0	SYNE1	152512459	1.000000	0.71417	0.990000	0.47175	0.994000	0.84299	9.108000	0.94275	2.241000	0.73720	0.533000	0.62120	ATT	.	A|1.000;G|0.000	.	alt		0.433	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		C	152470766	A	C	152470766	3	2	33	1	0	0	0	0	1	0	0	0	15457	101	4	5	2022	5	SYNE1	6	152470766	Missense_Mutation	SNP	A	TCGA-5P-A9K2-01A-11D-A42J-10	53186934	152470766	18644301	34	2404											
TBP	6908	hgsc.bcm.edu	37	chr6	170871004	170871004	+	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	gagcaacaaaggcagcagcaGcaacaacaacagcagcagca	19	0	10	12	0	0	0	0	0	0	0	0	1	0	0	0	1	11	8	0	1	5	0			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr6:170871004G>A	ENST00000392092.2	+	3	459	c.180G>A	c.(178-180)caG>caA	p.Q60Q	TBP_ENST00000230354.6_Silent_p.Q60Q|TBP_ENST00000540980.1_Silent_p.Q40Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	60	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		Ggcagcagcagcaacaacaac	0.542																																					p.Q60Q		Atlas-SNP	.											.	TBP	58	.	0			c.G180A						PASS	.						43	45	44					6																	170871004		2203	4300	6503	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAACAA	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"General transcription factors"	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.180G>A	chr6.hg19:g.170871004G>A		50.0	0.0	.		29.0	5.0	.	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	hg19	CCDS5315.1																																																																																			.	.	.	none		0.542	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		A	170871004	G	A	170871004	2	1	33	1	0	0	0	0	0	0	0	1	15656	962	34	2		2	TBP	6	170871004	Silent	SNP	G	TCGA-5P-A9K2-01A-11D-A42J-10	18400238	170871004	244063	35	2405											
DDC	1644	hgsc.bcm.edu	37	chr7	50544331	50544331	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcccacttacccggtagtcAgtgataagccctggagaaaa	12	8	9	12	1	1	2	1	1	0	1	2	3	2	2	3	2	2	1	3	2	5	3			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr7:50544331A>G	ENST00000444124.2	-	11	1232	c.1032T>C	c.(1030-1032)acT>acC	p.T344T	DDC_ENST00000431062.1_Silent_p.T251T|DDC_ENST00000357936.5_Silent_p.T344T|DDC_ENST00000426377.1_Silent_p.T266T	NM_001082971.1	NP_001076440	P20711	DDC_HUMAN	dopa decarboxylase (aromatic L-amino acid decarboxylase)	344					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)	CCCGGTAGTCAGTGATAAGCC	0.448																																					p.T344T		Atlas-SNP	.											.	DDC	100	.	0			c.T1032C						PASS	.						66	63	64					7																	50544331		2203	4300	6503	SO:0001819	synonymous_variant	1644	exon11			GTAGTCAGTGATA		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.1032T>C	chr7.hg19:g.50544331A>G		25.0	0.0	.		35.0	18.0	.	NM_001082971	C9IYA0|E7ER62|E7EU95|Q16723|Q5W5T9|Q75MJ6	Silent	SNP	ENST00000444124.2	hg19	CCDS5511.1	.	.	.	.	.	.	.	.	.	.	A	7.728	0.698663	0.15106	.	.	ENSG00000132437	ENST00000430300	.	.	.	5.4	-1.93	0.07594	.	.	.	.	.	T	0.40040	0.1101	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29427	-1.0012	4	.	.	.	-0.6052	2.1317	0.03752	0.3061:0.4032:0.16:0.1307	.	.	.	.	P	225	.	.	L	-	2	0	DDC	50511825	0.242000	0.23868	0.997000	0.53966	0.675000	0.39556	-0.925000	0.03992	-0.142000	0.11354	0.528000	0.53228	CTG	.	.	.	none		0.448	DDC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342593.1			G	50544331	A	G	50544331	2	3	33	1	0	0	0	0	0	0	0	1	4327	175	7	3		3	DDC	7	50544331	Silent	SNP	A	TCGA-5P-A9K2-01A-11D-A42J-10		50544331	108594332	36	2406											
ZNF394	84124	hgsc.bcm.edu	37	chr7	99092213	99092213	+	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	cgcttcttctaaaatttgttGcattggaatcaactctttgt	9	18	6	8	1	4	0	1	0	3	0	4	1	4	1	0	1	2	3	0	1	4	7			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr7:99092213G>A	ENST00000337673.6	-	3	828	c.625C>T	c.(625-627)Caa>Taa	p.Q209*	ZNF789_ENST00000494186.1_Intron|ZNF394_ENST00000394177.3_5'UTR|ZNF789_ENST00000493485.1_Intron|ZNF394_ENST00000426306.2_3'UTR	NM_032164.2	NP_115540.2	Q53GI3	ZN394_HUMAN	zinc finger protein 394	209	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(5)|stomach(1)|urinary_tract(1)	16	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					AAAATTTGTTGCATTGGAATC	0.473																																					p.Q209X	Ovarian(24;589 697 9939 12704 40742)	Atlas-SNP	.											.	ZNF394	48	.	0			c.C625T						PASS	.						70	73	72					7																	99092213		2200	4300	6500	SO:0001587	stop_gained	84124	exon3			TTTGTTGCATTGG	BC025241	CCDS5666.1	7q22.1	2014-01-28			ENSG00000160908	ENSG00000160908		"Zinc fingers, C2H2-type", "-", "-", "-"	18832	protein-coding gene	gene with protein product							Standard	NM_032164		Approved	ZKSCAN14, FLJ12298, ZSCAN46	uc003uqs.3	Q53GI3	OTTHUMG00000154660	ENST00000337673.6:c.625C>T	chr7.hg19:g.99092213G>A	ENSP00000337363:p.Gln209*	26.0	0.0	.		23.0	14.0	.	NM_032164	A4D281|Q05DA6|Q6P5X9|Q8TB27|Q9HA37|Q9UD51	Nonsense_Mutation	SNP	ENST00000337673.6	hg19	CCDS5666.1	.	.	.	.	.	.	.	.	.	.	G	15.31	2.796123	0.50208	.	.	ENSG00000160908	ENST00000337673	.	.	.	4.15	1.19	0.21007	.	0.713278	0.12205	N	0.489912	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05721	T	0.95	.	7.4057	0.26989	0.0:0.346:0.4733:0.1808	.	.	.	.	X	209	.	ENSP00000337363:Q209X	Q	-	1	0	ZNF394	98930149	0.061000	0.20836	0.486000	0.27416	0.517000	0.34286	0.594000	0.24014	0.246000	0.21394	0.655000	0.94253	CAA	.	.	.	none		0.473	ZNF394-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336498.1	NM_032164		A	99092213	G	A	99092213	4	1	33	1	0	0	0	0	0	1	0	0	17892	1328	46	2	1064	2	ZNF394	7	99092213	Nonsense_Mutation	SNP	G	TCGA-5P-A9K2-01A-11D-A42J-10	48547882	99092213	60046450	37	2407											
ZC3HAV1	56829	hgsc.bcm.edu	37	chr7	138738235	138738235	+	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	catgagtttcatgtaggaaaCtgtcaaaattattcgaacag	15	12	8	6	1	2	1	2	1	0	0	3	3	2	2	0	1	2	2	0	1	6	4			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr7:138738235C>G	ENST00000242351.5	-	12	2727	c.2411G>C	c.(2410-2412)aGt>aCt	p.S804T	ZC3HAV1_ENST00000464606.1_Missense_Mutation_p.S926T	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	804	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				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						ATGTAGGAAACTGTCAAAATT	0.388																																					p.S804T		Atlas-SNP	.											.	ZC3HAV1	75	.	0			c.G2411C						PASS	.						143	144	143					7																	138738235		2203	4300	6503	SO:0001583	missense	56829	exon12			AGGAAACTGTCAA	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.2411G>C	chr7.hg19:g.138738235C>G	ENSP00000242351:p.Ser804Thr	56.0	0.0	.		102.0	47.0	.	NM_020119	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Missense_Mutation	SNP	ENST00000242351.5	hg19	CCDS5851.1	.	.	.	.	.	.	.	.	.	.	C	11.89	1.772816	0.31411	.	.	ENSG00000105939	ENST00000242351;ENST00000464606	T;T	0.13420	2.59;2.59	5.2	3.36	0.38483	Poly(ADP-ribose) polymerase, catalytic domain (2);	0.612362	0.14791	N	0.298256	T	0.08088	0.0202	N	0.14661	0.345	0.58432	D	0.999993	B	0.06786	0.001	B	0.11329	0.006	T	0.18398	-1.0338	10	0.34782	T	0.22	.	8.3898	0.32522	0.0:0.8094:0.0:0.1906	.	804	Q7Z2W4	ZCCHV_HUMAN	T	804;926	ENSP00000242351:S804T;ENSP00000418385:S926T	ENSP00000242351:S804T	S	-	2	0	ZC3HAV1	138388775	0.999000	0.42202	0.028000	0.17463	0.004000	0.04260	2.248000	0.43160	1.323000	0.45263	0.563000	0.77884	AGT	.	.	.	none		0.388	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119		G	138738235	C	G	138738235	3	3	33	1	0	0	0	0	1	0	0	0	17587	565	20	4	305	4	ZC3HAV1	7	138738235	Missense_Mutation	SNP	C	TCGA-5P-A9K2-01A-11D-A42J-10	39646022	138738235	20400428	38	2408											
HIPK2	28996	hgsc.bcm.edu	37	chr7	139316430	139316430	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcccagggaccacatgtcaAttgcctcacaaaatggtaaa	15	7	8	11	0	2	0	2	0	0	0	2	1	2	1	3	2	2	1	3	2	5	2			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr7:139316430A>G	ENST00000406875.3	-	3	1239	c.1145T>C	c.(1144-1146)aTt>aCt	p.I382T	HIPK2_ENST00000428878.2_Missense_Mutation_p.I382T|HIPK2_ENST00000342645.6_Missense_Mutation_p.I382T	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	382	Interaction with DAXX.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)			breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					CCACATGTCAATTGCCTCACA	0.468																																					p.I382T		Atlas-SNP	.											.	HIPK2	192	.	0			c.T1145C						PASS	.						99	95	96					7																	139316430		1992	4197	6189	SO:0001583	missense	28996	exon3			ATGTCAATTGCCT	AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"homeodomain-interacting protein kinase 2"			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.1145T>C	chr7.hg19:g.139316430A>G	ENSP00000385571:p.Ile382Thr	53.0	0.0	.		95.0	55.0	.	NM_022740	Q75MR7|Q8WWI4|Q9H2Y1	Missense_Mutation	SNP	ENST00000406875.3	hg19		.	.	.	.	.	.	.	.	.	.	A	23.1	4.378002	0.82682	.	.	ENSG00000064393	ENST00000406875;ENST00000428878;ENST00000342645	T;T;T	0.20200	2.09;2.09;2.09	5.18	5.18	0.71444	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	0.47985	0.1475	.	.	.	0.58432	D	0.999998	P;D	0.61080	0.946;0.989	P;D	0.75020	0.659;0.985	T	0.52518	-0.8565	8	0.87932	D	0	.	15.2032	0.73157	1.0:0.0:0.0:0.0	.	382;382	Q9H2X6;Q9H2X6-3	HIPK2_HUMAN;.	T	382	ENSP00000385571:I382T;ENSP00000413724:I382T;ENSP00000343108:I382T	ENSP00000343108:I382T	I	-	2	0	HIPK2	138966970	1.000000	0.71417	0.903000	0.35520	0.964000	0.63967	8.974000	0.93433	2.180000	0.69256	0.383000	0.25322	ATT	.	.	.	none		0.468	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740		G	139316430	A	G	139316430	3	3	33	1	0	0	0	0	1	0	0	0	7124	101	4	3	2503	3	HIPK2	7	139316430	Missense_Mutation	SNP	A	TCGA-5P-A9K2-01A-11D-A42J-10	578195	139316430	19822233	39	2409											
EPHB6	2051	hgsc.bcm.edu	37	chr7	142562074	142562074	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcctcctcctcctcctcCtcttcttcctctgcagcgtg	1	15	4	21	1	3	0	0	0	3	0	11	0	11	0	8	0	2	1	8	0	0	2			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr7:142562074C>T	ENST00000392957.2	+	7	1303	c.516C>T	c.(514-516)tcC>tcT	p.S172S	EPHB6_ENST00000411471.2_Intron|EPHB6_ENST00000442129.1_Silent_p.S172S	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	172	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.|Poly-Ser.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					cctcctcctcctcttcttcct	0.622																																					p.S172S		Atlas-SNP	.											.	EPHB6	168	.	0			c.C516T						PASS	.						83	98	93					7																	142562074		2200	4299	6499	SO:0001819	synonymous_variant	2051	exon7			CTCCTCCTCTTCT	D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3396	protein-coding gene	gene with protein product		602757	"EphB6"				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.516C>T	chr7.hg19:g.142562074C>T		52.0	0.0	.		87.0	4.0	.	NM_004445	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Silent	SNP	ENST00000392957.2	hg19	CCDS5873.2																																																																																			.	.	.	none		0.622	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			T	142562074	C	T	142562074	2	4	33	1	0	0	0	0	0	0	0	1	5180	668	24	2		2	EPHB6	7	142562074	Silent	SNP	C	TCGA-5P-A9K2-01A-11D-A42J-10	3245644	142562074	16576589	40	2410											
RGS3	5998	hgsc.bcm.edu	37	chr9	116276826	116276826	+	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	gtgcagaccatgaagggccaCgggaactaccaaaactgccc	13	4	11	13	1	0	2	0	1	0	1	0	3	0	3	4	2	5	1	4	2	5	1			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr9:116276826C>A	ENST00000374140.2	+	16	1775	c.1566C>A	c.(1564-1566)caC>caA	p.H522Q	RGS3_ENST00000317613.6_Missense_Mutation_p.H410Q|RGS3_ENST00000394646.3_Missense_Mutation_p.H241Q|RGS3_ENST00000374136.1_Missense_Mutation_p.H148Q|RGS3_ENST00000343817.5_Missense_Mutation_p.H241Q|RGS3_ENST00000350696.5_Missense_Mutation_p.H522Q	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	522					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						TGAAGGGCCACGGGAACTACC	0.572																																					p.H522Q		Atlas-SNP	.											.	RGS3	251	.	0			c.C1566A						PASS	.						128	99	109					9																	116276826		2203	4300	6503	SO:0001583	missense	5998	exon16			GGGCCACGGGAAC	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.1566C>A	chr9.hg19:g.116276826C>A	ENSP00000363255:p.His522Gln	68.0	0.0	.		97.0	38.0	.	NM_144488	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	hg19	CCDS43869.1	.	.	.	.	.	.	.	.	.	.	C	14.28	2.487145	0.44249	.	.	ENSG00000138835	ENST00000374140;ENST00000350696;ENST00000317613;ENST00000343817;ENST00000394646;ENST00000374136	T;T;T;T;T	0.64438	0.83;0.83;1.21;0.34;-0.1	5.08	-10.2	0.00374	.	0.175530	0.51477	D	0.000089	T	0.36908	0.0984	N	0.14661	0.345	0.37206	D	0.904586	B;B;P;P;P;P	0.41673	0.026;0.302;0.754;0.64;0.759;0.729	B;B;B;B;B;B	0.40940	0.012;0.059;0.344;0.186;0.237;0.318	T	0.68788	-0.5316	10	0.72032	D	0.01	.	12.3146	0.54948	0.0997:0.6511:0.0:0.2493	.	241;148;241;412;410;522	B3KUB2;Q5VXC0;P49796-4;B3KWG8;P49796-5;P49796	.;.;.;.;.;RGS3_HUMAN	Q	522;522;410;241;241;148	ENSP00000363255:H522Q;ENSP00000259406:H522Q;ENSP00000312844:H410Q;ENSP00000340284:H241Q;ENSP00000378141:H241Q	ENSP00000312844:H410Q	H	+	3	2	RGS3	115316647	0.003000	0.15002	0.040000	0.18447	0.978000	0.69477	-1.926000	0.01562	-2.740000	0.00379	-0.340000	0.08031	CAC	.	.	.	none		0.572	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790		A	116276826	C	A	116276826	3	1	33	1	0	0	0	0	1	0	0	0	13319	535	19	4	1765	4	RGS3	9	116276826	Missense_Mutation	SNP	C	TCGA-5P-A9K2-01A-11D-A42J-10		116276826	24936605	41	2411											
PAPPA	5069	hgsc.bcm.edu	37	chr9	118969802	118969802	+	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	gatcaacacatctcaatattTtctttgcaaaatcctcagag	14	13	4	10	0	4	1	3	0	2	1	6	2	5	1	1	0	2	1	1	0	5	4			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr9:118969802T>A	ENST00000328252.3	+	3	1915	c.1546T>A	c.(1546-1548)Ttc>Atc	p.F516I	PAPPA_ENST00000534838.1_Intron	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	516	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						TCTCAATATTTTCTTTGCAAA	0.423																																					p.F516I		Atlas-SNP	.											.	PAPPA	243	.	0			c.T1546A						PASS	.						78	77	77					9																	118969802		2203	4300	6503	SO:0001583	missense	5069	exon3			AATATTTTCTTTG		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.1546T>A	chr9.hg19:g.118969802T>A	ENSP00000330658:p.Phe516Ile	40.0	0.0	.		56.0	27.0	.	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Missense_Mutation	SNP	ENST00000328252.3	hg19	CCDS6813.1	.	.	.	.	.	.	.	.	.	.	T	36	5.692924	0.96793	.	.	ENSG00000182752	ENST00000328252;ENST00000443904	T	0.02345	4.33	6.17	6.17	0.99709	Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.15998	0.0385	M	0.78049	2.395	0.80722	D	1	D;D	0.76494	0.999;0.984	D;P	0.68943	0.961;0.844	T	0.00036	-1.2256	10	0.87932	D	0	-24.8985	16.8222	0.85835	0.0:0.0:0.0:1.0	.	58;516	E7EMD3;Q13219	.;PAPP1_HUMAN	I	516;58	ENSP00000330658:F516I	ENSP00000330658:F516I	F	+	1	0	PAPPA	118009623	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.008000	0.88588	2.371000	0.80710	0.533000	0.62120	TTC	.	.	.	none		0.423	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		A	118969802	T	A	118969802	3	1	33	1	0	0	0	0	1	0	0	0	11439	1841	64	5	1556	5	PAPPA	9	118969802	Missense_Mutation	SNP	T	TCGA-5P-A9K2-01A-11D-A42J-10	2692976	118969802	22243629	42	2412											
GLT6D1	360203	hgsc.bcm.edu	37	chr9	138516059	138516059	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttctttgatgaagtctaaaaTattatggggtgtgccaccaa	12	14	9	6	0	2	2	0	2	2	0	2	2	2	2	2	2	1	0	2	2	6	5			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr9:138516059T>C	ENST00000371763.1	-	5	968	c.715A>G	c.(715-717)Att>Gtt	p.I239V		NM_182974.2	NP_892019.2	Q7Z4J2	GL6D1_HUMAN	glycosyltransferase 6 domain containing 1	239					carbohydrate metabolic process (GO:0005975)	integral component of membrane (GO:0016021)	transferase activity, transferring hexosyl groups (GO:0016758)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	15		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;4.3e-07)|Epithelial(140;1.58e-06)|all cancers(34;5.36e-05)		AAGTCTAAAATATTATGGGGT	0.403																																					p.I239V		Atlas-SNP	.											.	GLT6D1	56	.	0			c.A715G						PASS	.						122	120	121					9																	138516059		1857	4098	5955	SO:0001583	missense	360203	exon5			CTAAAATATTATG	AY336054	CCDS43900.1	9q34.3	2013-02-22	2004-09-16	2004-09-17	ENSG00000204007	ENSG00000204007		"Glycosyltransferase family 6 domain containing"	23671	protein-coding gene	gene with protein product		613699	"galactosyltransferase family 6 domain containing 1"	GLTDC1			Standard	NM_182974		Approved		uc010nbd.1	Q7Z4J2	OTTHUMG00000020911	ENST00000371763.1:c.715A>G	chr9.hg19:g.138516059T>C	ENSP00000360829:p.Ile239Val	56.0	0.0	.		64.0	25.0	.	NM_182974		Missense_Mutation	SNP	ENST00000371763.1	hg19	CCDS43900.1	.	.	.	.	.	.	.	.	.	.	T	0.011	-1.711905	0.00712	.	.	ENSG00000204007	ENST00000371763	T	0.00949	5.51	3.49	-4.46	0.03536	.	1.290870	0.05318	N	0.526126	T	0.00300	0.0009	N	0.00252	-1.77	0.09310	N	1	B	0.14438	0.01	B	0.15870	0.014	T	0.46148	-0.9212	10	0.02654	T	1	-13.1181	6.5445	0.22398	0.132:0.229:0.0:0.639	.	239	Q7Z4J2	GL6D1_HUMAN	V	239	ENSP00000360829:I239V	ENSP00000360829:I239V	I	-	1	0	GLT6D1	137655880	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.867000	0.04241	-1.120000	0.02953	-0.912000	0.02778	ATT	.	.	.	none		0.403	GLT6D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055005.2	NM_182974		C	138516059	T	C	138516059	3	2	33	1	0	0	0	0	1	0	0	0	6475	1406	49	3	119	3	GLT6D1	9	138516059	Missense_Mutation	SNP	T	TCGA-5P-A9K2-01A-11D-A42J-10	19546257	138516059	2697372	43	2413											
TET1	80312	hgsc.bcm.edu	37	chr10	70404540	70404540	+	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	tcatggggaagaacaaaaatTggaattgaacccacatactg	17	8	9	7	0	1	2	1	1	0	1	1	4	1	4	1	3	3	0	1	3	7	3			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr10:70404540T>A	ENST00000373644.4	+	4	2263	c.2054T>A	c.(2053-2055)tTg>tAg	p.L685*		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	685					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						GAACAAAAATTGGAATTGAAC	0.393																																					p.L685X		Atlas-SNP	.											.	TET1	255	.	0			c.T2054A						PASS	.						64	60	62					10																	70404540		2203	4300	6503	SO:0001587	stop_gained	80312	exon4			AAAAATTGGAATT	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.2054T>A	chr10.hg19:g.70404540T>A	ENSP00000362748:p.Leu685*	229.0	0.0	.		260.0	104.0	.	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Nonsense_Mutation	SNP	ENST00000373644.4	hg19	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	T	39	7.512099	0.98329	.	.	ENSG00000138336	ENST00000373644	.	.	.	5.93	2.37	0.29283	.	0.975799	0.08385	N	0.953916	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.8223	0.40889	0.0:0.1927:0.0:0.8073	.	.	.	.	X	685	.	ENSP00000362748:L685X	L	+	2	0	TET1	70074546	1.000000	0.71417	0.927000	0.36925	0.820000	0.46376	2.257000	0.43240	0.161000	0.19458	-1.054000	0.02325	TTG	.	.	.	none		0.393	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		A	70404540	T	A	70404540	4	1	33	1	0	0	0	0	0	1	0	0	15781	1821	63	5	2064	5	TET1	10	70404540	Nonsense_Mutation	SNP	T	TCGA-5P-A9K2-01A-11D-A42J-10		70404540	65130207	44	2414											
DENND5A	23258	hgsc.bcm.edu	37	chr11	9165682	9165682	+	Frame_Shift_Del	DEL	A	A	-																															agatggtaacaagcctccggAtgacactgggggactgctgc																										TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr11:9165682delA	ENST00000328194.3	-	19	3586	c.3266delT	c.(3265-3267)atcfs	p.I1089fs	DENND5A_ENST00000527700.1_Frame_Shift_Del_p.I432fs|DENND5A_ENST00000530044.1_Frame_Shift_Del_p.I1089fs	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A	1089					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						AAGCCTCCGGATGACACTGGG	0.607																																					p.I1089fs		Atlas-Indel,Pindel	.											.	DENND5A	84	.	0			c.3267delC						PASS	.						88	86	87					11																	9165682		2201	4296	6497	SO:0001589	frameshift_variant	23258	exon19			.	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.3266delT	chr11.hg19:g.9165682delA	ENSP00000328524:p.Ile1089fs	22.0	0.0	0		41.0	17.0	0.414634	NM_001243254	B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	Frame_Shift_Del	DEL	ENST00000328194.3	hg19	CCDS31423.1																																																																																			.	.	.	none		0.607	DENND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385910.2	NM_015213		-	9165682	A	-	9165682	7	5	33	1	0	1	0	1	0	0	0	0	4438	333	12	0	617	0	DENND5A	11	9165682	Frame_Shift_Del	DEL	A	TCGA-5P-A9K2-01A-11D-A42J-10		9165682	125840834	45	2415											
CTR9	9646	hgsc.bcm.edu	37	chr11	10789494	10789494	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctatgctagcccttggcaacGtgtggctccaaactttacat	9	12	8	12	1	0	0	0	0	0	0	1	0	1	0	2	2	5	3	2	2	5	5			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr11:10789494G>A	ENST00000361367.2	+	14	2254	c.1828G>A	c.(1828-1830)Gtg>Atg	p.V610M		NM_014633.3	NP_055448.1	Q6PD62	CTR9_HUMAN	CTR9, Paf1/RNA polymerase II complex component	610					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)		CCTTGGCAACGTGTGGCTCCA	0.428																																					p.V610M		Atlas-SNP	.											.	CTR9	94	.	0			c.G1828A						PASS	.						186	174	178					11																	10789494		2201	4294	6495	SO:0001583	missense	9646	exon14			GGCAACGTGTGGC	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.1828G>A	chr11.hg19:g.10789494G>A	ENSP00000355013:p.Val610Met	77.0	0.0	.		105.0	32.0	.	NM_014633	D3DQV8|Q15015	Missense_Mutation	SNP	ENST00000361367.2	hg19	CCDS7805.1	.	.	.	.	.	.	.	.	.	.	G	18.15	3.559522	0.65538	.	.	ENSG00000198730	ENST00000361367	T	0.47528	0.84	5.56	5.56	0.83823	Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.47116	0.1428	M	0.64404	1.975	0.80722	D	1	B	0.32526	0.374	B	0.20955	0.032	T	0.49360	-0.8948	10	0.54805	T	0.06	-10.6378	19.5083	0.95130	0.0:0.0:1.0:0.0	.	610	Q6PD62	CTR9_HUMAN	M	610	ENSP00000355013:V610M	ENSP00000355013:V610M	V	+	1	0	CTR9	10746070	1.000000	0.71417	0.995000	0.50966	0.980000	0.70556	9.792000	0.99085	2.620000	0.88729	0.467000	0.42956	GTG	.	.	.	none		0.428	CTR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386215.1	NM_014633		A	10789494	G	A	10789494	3	1	33	1	0	0	0	0	1	0	0	0	4026	1145	40	1	1882	1	CTR9	11	10789494	Missense_Mutation	SNP	G	TCGA-5P-A9K2-01A-11D-A42J-10	1623812	10789494	124217022	46	2416											
EHBP1L1	254102	hgsc.bcm.edu	37	chr11	65349066	65349066	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccagcccctcggctccggaAaggctctgatgccctccggc	5	6	11	19	3	1	1	0	1	1	0	4	2	3	2	6	4	2	2	6	4	1	0			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr11:65349066A>G	ENST00000309295.4	+	9	1188	c.923A>G	c.(922-924)aAa>aGa	p.K308R		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	308						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						CGGCTCCGGAAAGGCTCTGAT	0.682																																					p.K308R		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.A923G						PASS	.						8	9	8					11																	65349066		1828	4032	5860	SO:0001583	missense	254102	exon9			TCCGGAAAGGCTC	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.923A>G	chr11.hg19:g.65349066A>G	ENSP00000312671:p.Lys308Arg	62.0	0.0	.		89.0	41.0	.	NM_001099409	Q8TB89|Q9H7M7	Missense_Mutation	SNP	ENST00000309295.4	hg19	CCDS44649.1	.	.	.	.	.	.	.	.	.	.	A	17.47	3.396496	0.62177	.	.	ENSG00000173442	ENST00000309295;ENST00000533237	T;D	0.82255	-0.41;-1.59	4.13	2.98	0.34508	.	0.537435	0.17622	N	0.167700	D	0.83170	0.5196	L	0.36672	1.1	0.80722	D	1	D	0.63880	0.993	D	0.70935	0.971	T	0.81538	-0.0887	10	0.54805	T	0.06	.	4.8457	0.13512	0.855:0.0:0.145:0.0	.	308	Q8N3D4	EH1L1_HUMAN	R	308	ENSP00000312671:K308R;ENSP00000431996:K308R	ENSP00000312671:K308R	K	+	2	0	EHBP1L1	65105642	0.996000	0.38824	1.000000	0.80357	0.736000	0.42039	0.565000	0.23578	1.744000	0.51775	0.459000	0.35465	AAA	.	.	.	none		0.682	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658		G	65349066	A	G	65349066	3	3	33	1	0	0	0	0	1	0	0	0	4978	14	1	3	957	3	EHBP1L1	11	65349066	Missense_Mutation	SNP	A	TCGA-5P-A9K2-01A-11D-A42J-10	54559572	65349066	69657450	47	2417											
BIRC2	329	hgsc.bcm.edu	37	chr11	102221170	102221170	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttacctaccatatgtggccAttaacttttttgtcaccatc	9	16	4	12	0	1	0	1	0	0	0	2	0	1	0	4	1	3	0	4	1	4	7			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr11:102221170A>G	ENST00000227758.2	+	2	1984	c.585A>G	c.(583-585)ccA>ccG	p.P195P	BIRC2_ENST00000532672.1_Silent_p.P174P|BIRC2_ENST00000530675.1_Silent_p.P146P|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	195					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)		ATATGTGGCCATTAACTTTTT	0.428																																					p.P195P		Atlas-SNP	.											.	BIRC2	51	.	0			c.A585G						PASS	.						114	115	115					11																	102221170		2203	4299	6502	SO:0001819	synonymous_variant	329	exon2			GTGGCCATTAACT	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.585A>G	chr11.hg19:g.102221170A>G		55.0	0.0	.		54.0	18.0	.	NM_001256163	B4E026|Q16516|Q4TTG0	Silent	SNP	ENST00000227758.2	hg19	CCDS8316.1																																																																																			.	.	.	none		0.428	BIRC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394170.1	NM_001166		G	102221170	A	G	102221170	2	3	33	1	0	0	0	0	0	0	0	1	1435	204	8	3		3	BIRC2	11	102221170	Silent	SNP	A	TCGA-5P-A9K2-01A-11D-A42J-10	36872104	102221170	32785346	48	2418											
SLC4A8	9498	hgsc.bcm.edu	37	chr12	51844689	51844689	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctgtatgtgggagttcggAtgccgcttggccggcagagc	5	10	16	10	3	1	1	0	0	1	1	2	3	1	3	2	4	2	4	2	4	1	3			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr12:51844689A>G	ENST00000453097.2	+	3	377	c.160A>G	c.(160-162)Atg>Gtg	p.M54V	SLC4A8_ENST00000394856.1_Start_Codon_SNP_p.M1V|SLC4A8_ENST00000535225.2_Start_Codon_SNP_p.M1V|SLC4A8_ENST00000358657.3_Missense_Mutation_p.M81V|SLC4A8_ENST00000514353.3_Start_Codon_SNP_p.M1V	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)		GGGAGTTCGGATGCCGCTTGG	0.552																																					p.M54V		Atlas-SNP	.											.	SLC4A8	292	.	0			c.A160G						PASS	.						28	28	28					12																	51844689		2203	4299	6502	SO:0001583	missense	9498	exon3			GTTCGGATGCCGC	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.160A>G	chr12.hg19:g.51844689A>G	ENSP00000405812:p.Met54Val	124.0	0.0	.		158.0	67.0	.	NM_001039960		Missense_Mutation	SNP	ENST00000453097.2	hg19	CCDS44890.1	.	.	.	.	.	.	.	.	.	.	A	14.95	2.687601	0.48097	.	.	ENSG00000050438	ENST00000535225;ENST00000358657;ENST00000453097;ENST00000394856;ENST00000319957;ENST00000514353;ENST00000547697;ENST00000551071	T;T;T;T;T	0.73681	-0.25;-0.77;-0.76;-0.23;-0.23	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.50905	0.1643	N	0.05510	-0.035	0.80722	D	1	B;B;B;B;B;B;B	0.09022	0.002;0.0;0.0;0.0;0.0;0.0;0.002	B;B;B;B;B;B;B	0.06405	0.001;0.002;0.001;0.001;0.002;0.002;0.002	T	0.51244	-0.8730	10	0.02654	T	1	.	14.0718	0.64865	1.0:0.0:0.0:0.0	.	1;81;1;54;54;54;1	E7EML0;Q2Y0W8-2;F5GZ31;Q2Y0W8;Q2Y0W8-3;Q2Y0W8-6;F8VSA8	.;.;.;S4A8_HUMAN;.;.;.	V	1;81;54;1;54;1;1;1	ENSP00000441520:M1V;ENSP00000351483:M81V;ENSP00000405812:M54V;ENSP00000378325:M1V;ENSP00000442561:M1V	ENSP00000315789:M54V	M	+	1	0	SLC4A8	50130956	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.797000	0.75150	2.039000	0.60335	0.379000	0.24179	ATG	.	.	.	none		0.552	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858		G	51844689	A	G	51844689	3	3	33	1	0	0	0	0	1	0	0	0	14672	333	12	3	170	3	SLC4A8	12	51844689	Missense_Mutation	SNP	A	TCGA-5P-A9K2-01A-11D-A42J-10		51844689	82007206	49	2419											
ANKLE2	23141	hgsc.bcm.edu	37	chr12	133331516	133331516	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgtgggtcctggctgagagCtgtgacacctgcctcatggt	5	12	14	10	0	1	2	1	2	0	1	2	3	2	2	3	3	2	2	3	3	0	1			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr12:133331516C>T	ENST00000357997.5	-	2	474	c.385G>A	c.(385-387)Gct>Act	p.A129T	ANKLE2_ENST00000337516.5_Missense_Mutation_p.A129T|ANKLE2_ENST00000539605.1_Missense_Mutation_p.A67T	NM_015114.1	NP_055929.1	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	129					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|negative regulation of phosphorylation (GO:0042326)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	protein phosphatase 2A binding (GO:0051721)|protein phosphatase type 2A regulator activity (GO:0008601)			NS(2)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(20)|ovary(1)|urinary_tract(2)	45	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)		TGGCTGAGAGCTGTGACACCT	0.468																																					p.A129T		Atlas-SNP	.											.	ANKLE2	76	.	0			c.G385A						PASS	.						62	63	62					12																	133331516		1925	4138	6063	SO:0001583	missense	23141	exon2			TGAGAGCTGTGAC	AB014592	CCDS41869.1	12q24.33	2013-01-11	2008-03-25	2008-03-25	ENSG00000176915	ENSG00000176915		"Ankyrin repeat domain containing"	29101	protein-coding gene	gene with protein product	"LEM domain containing 7"		"KIAA0692"	KIAA0692		9734811	Standard	XM_005266159		Approved	LEMD7, Lem4	uc001ukx.2	Q86XL3	OTTHUMG00000168046	ENST00000357997.5:c.385G>A	chr12.hg19:g.133331516C>T	ENSP00000350686:p.Ala129Thr	64.0	0.0	.		98.0	35.0	.	NM_015114	A8KAG3|B3KN97|B3KSF8|O75176|Q6P6A5|Q8TAZ9|Q96DH4	Missense_Mutation	SNP	ENST00000357997.5	hg19	CCDS41869.1	.	.	.	.	.	.	.	.	.	.	c	10.97	1.501322	0.26861	.	.	ENSG00000176915	ENST00000539605;ENST00000357997;ENST00000337516	T;T;T	0.31769	1.91;1.89;1.48	5.27	-1.39	0.08997	.	0.968721	0.08558	N	0.927956	T	0.18130	0.0435	L	0.37561	1.115	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.001;0.002	T	0.30736	-0.9968	10	0.20519	T	0.43	-4.831	1.7839	0.03038	0.2934:0.4018:0.096:0.2088	.	129;129	Q86XL3-2;Q86XL3	.;ANKL2_HUMAN	T	67;129;129	ENSP00000446268:A67T;ENSP00000350686:A129T;ENSP00000337651:A129T	ENSP00000337651:A129T	A	-	1	0	ANKLE2	131841589	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.313000	0.02718	-1.011000	0.03391	-2.167000	0.00324	GCT	.	.	.	none		0.468	ANKLE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397712.1			T	133331516	C	T	133331516	3	4	33	1	0	0	0	0	1	0	0	0	633	797	28	2	2479	2	ANKLE2	12	133331516	Missense_Mutation	SNP	C	TCGA-5P-A9K2-01A-11D-A42J-10	81486827	133331516	520379	50	2420											
USP12	219333	hgsc.bcm.edu	37	chr13	27669947	27669947	+	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	gaattcatgggcatcttgttGcatgtagttgtcaaaaagct	11	14	10	6	0	3	0	2	0	1	0	3	1	3	0	0	1	2	6	0	1	4	5			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr13:27669947G>T	ENST00000282344.6	-	4	620	c.364C>A	c.(364-366)Caa>Aaa	p.Q122K		NM_182488.3	NP_872294.2	O75317	UBP12_HUMAN	ubiquitin specific peptidase 12	122	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Lung SC(185;0.0161)		all cancers(112;0.0508)|GBM - Glioblastoma multiforme(144;0.168)|Epithelial(112;0.244)|OV - Ovarian serous cystadenocarcinoma(117;0.246)		GCATCTTGTTGCATGTAGTTG	0.264																																					p.Q122K	Ovarian(37;808 911 7590 44442 44991)	Atlas-SNP	.											.	USP12	35	.	0			c.C364A						PASS	.						39	41	40					13																	27669947		2201	4295	6496	SO:0001583	missense	219333	exon4			CTTGTTGCATGTA	AL049221	CCDS31952.1	13q12.13	2010-05-12	2005-08-08	2003-10-08	ENSG00000152484	ENSG00000152484		"Ubiquitin-specific peptidases"	20485	protein-coding gene	gene with protein product			"ubiquitin specific protease 12 like 1", "ubiquitin specific protease 12"	USP12L1		12838346	Standard	NM_182488		Approved		uc001uqy.3	O75317	OTTHUMG00000016626	ENST00000282344.6:c.364C>A	chr13.hg19:g.27669947G>T	ENSP00000282344:p.Gln122Lys	51.0	0.0	.		51.0	12.0	.	NM_182488	A8K0X0|Q5VZV3|Q8TC49	Missense_Mutation	SNP	ENST00000282344.6	hg19	CCDS31952.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.992997	0.93167	.	.	ENSG00000152484	ENST00000282344	T	0.56776	0.44	5.54	5.54	0.83059	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	D	0.85566	0.5726	H	0.99535	4.615	0.80722	D	1	D	0.76494	0.999	D	0.74348	0.983	D	0.91509	0.5225	10	0.72032	D	0.01	-19.9417	19.8379	0.96666	0.0:0.0:1.0:0.0	.	122	O75317	UBP12_HUMAN	K	122	ENSP00000282344:Q122K	ENSP00000282344:Q122K	Q	-	1	0	USP12	26567947	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.700000	0.98707	2.765000	0.95021	0.655000	0.94253	CAA	.	.	.	none		0.264	USP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044264.1	NM_182488		T	27669947	G	T	27669947	3	4	33	1	0	0	0	0	1	0	0	0	17055	1328	46	4	772	4	USP12	13	27669947	Missense_Mutation	SNP	G	TCGA-5P-A9K2-01A-11D-A42J-10		27669947	87499931	51	2421											
FLRT2	23768	hgsc.bcm.edu	37	chr14	86088353	86088353	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attagcctcaaattgttgttTttgtctaagaatcacctgag	11	16	7	7	0	3	2	2	1	1	1	3	2	3	2	2	0	1	2	2	0	4	6			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr14:86088353T>C	ENST00000330753.4	+	2	1262	c.495T>C	c.(493-495)ttT>ttC	p.F165F	FLRT2_ENST00000554746.1_Silent_p.F165F	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	165					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)		AATTGTTGTTTTTGTCTAAGA	0.498																																					p.F165F		Atlas-SNP	.											.	FLRT2	168	.	0			c.T495C						PASS	.						59	61	61					14																	86088353		2203	4300	6503	SO:0001819	synonymous_variant	23768	exon2			GTTGTTTTTGTCT	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.495T>C	chr14.hg19:g.86088353T>C		44.0	0.0	.		62.0	20.0	.	NM_013231	A0AV84|B7ZLP3	Silent	SNP	ENST00000330753.4	hg19	CCDS9877.1																																																																																			.	.	.	none		0.498	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			C	86088353	T	C	86088353	2	2	33	1	0	0	0	0	0	0	0	1	5946	1838	64	3		3	FLRT2	14	86088353	Silent	SNP	T	TCGA-5P-A9K2-01A-11D-A42J-10		86088353	21261187	52	2422											
WDR25	79446	hgsc.bcm.edu	37	chr14	100996202	100996202	+	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	agtgctccccaggcggtgacTtgctggtgacgggcagcgcc	5	7	16	13	3	0	2	0	2	0	0	1	2	1	2	3	4	3	3	3	4	0	1			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr14:100996202T>A	ENST00000335290.6	+	7	1685	c.1459T>A	c.(1459-1461)Ttg>Atg	p.L487M	WDR25_ENST00000554998.1_Missense_Mutation_p.L487M|WDR25_ENST00000542471.2_Missense_Mutation_p.L230M|WDR25_ENST00000557502.1_3'UTR|WDR25_ENST00000402312.3_Missense_Mutation_p.L487M	NM_024515.4	NP_078791.3	Q64LD2	WDR25_HUMAN	WD repeat domain 25	487										central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|skin(1)	20		Melanoma(154;0.212)				AGGCGGTGACTTGCTGGTGAC	0.662																																					p.L487M		Atlas-SNP	.											.	WDR25	37	.	0			c.T1459A						PASS	.						63	60	61					14																	100996202		2203	4300	6503	SO:0001583	missense	79446	exon7			GGTGACTTGCTGG	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.1459T>A	chr14.hg19:g.100996202T>A	ENSP00000334148:p.Leu487Met	36.0	0.0	.		53.0	19.0	.	NM_001161476	A8K7E5|Q6NVV6|Q86TQ4|Q9BTK5	Missense_Mutation	SNP	ENST00000335290.6	hg19	CCDS32157.1	.	.	.	.	.	.	.	.	.	.	T	12.17	1.858302	0.32791	.	.	ENSG00000176473	ENST00000554998;ENST00000402312;ENST00000335290;ENST00000542471	T;T;T;T	0.01455	4.87;4.87;4.87;4.87	4.83	0.608	0.17569	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.375063	0.24571	N	0.037382	T	0.03959	0.0111	L	0.49350	1.555	0.26397	N	0.97649	P;D	0.54964	0.655;0.969	B;P	0.60541	0.269;0.876	T	0.32428	-0.9907	10	0.49607	T	0.09	-14.2158	3.7184	0.08446	0.136:0.5689:0.1327:0.1624	.	230;487	Q64LD2-2;Q64LD2	.;WDR25_HUMAN	M	487;487;487;230	ENSP00000450661:L487M;ENSP00000385540:L487M;ENSP00000334148:L487M;ENSP00000441903:L230M	ENSP00000334148:L487M	L	+	1	2	WDR25	100065955	0.519000	0.26242	0.987000	0.45799	0.242000	0.25591	1.074000	0.30703	0.547000	0.28938	-0.132000	0.14878	TTG	.	.	.	none		0.662	WDR25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414312.1	NM_024515		A	100996202	T	A	100996202	3	1	33	1	0	0	0	0	1	0	0	0	17294	1606	56	5	1481	5	WDR25	14	100996202	Missense_Mutation	SNP	T	TCGA-5P-A9K2-01A-11D-A42J-10	14907849	100996202	6353338	53	2423											
CYFIP1	23191	hgsc.bcm.edu	37	chr15	22991163	22991163	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatcctgcagtacgtgaagaCgctgatggaggtgatgccca	11	8	13	9	2	0	4	0	3	0	1	1	5	1	5	2	2	3	3	2	2	3	1			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr15:22991163C>T	ENST00000313077.7	+	25	2977	c.2852C>T	c.(2851-2853)aCg>aTg	p.T951M	CYFIP1_ENST00000435939.2_Missense_Mutation_p.T520M|CYFIP1_ENST00000560848.1_Missense_Mutation_p.T951M	NM_014608.2	NP_055423.1			cytoplasmic FMR1 interacting protein 1											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(1)|lung(14)|ovary(4)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	40		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		TACGTGAAGACGCTGATGGAG	0.652																																					p.T951M		Atlas-SNP	.											.	CYFIP1	159	.	0			c.C2852T						PASS	.						70	51	58					15																	22991163		2203	4300	6503	SO:0001583	missense	23191	exon25			TGAAGACGCTGAT	D38549	CCDS73695.1, CCDS73696.1	15q11	2008-07-18			ENSG00000068793	ENSG00000273749			13759	protein-coding gene	gene with protein product	"selective hybridizing clone", "cytoplasmic FMRP interacting protein 1"	606322				11438699	Standard	XM_005272543		Approved	KIAA0068, P140SRA-1, SHYC	uc001yus.3	Q7L576	OTTHUMG00000129100	ENST00000313077.7:c.2852C>T	chr15.hg19:g.22991163C>T	ENSP00000324549:p.Thr951Met	11.0	0.0	.		24.0	13.0	.	NM_014608		Missense_Mutation	SNP	ENST00000313077.7	hg19	CCDS10009.1	.	.	.	.	.	.	.	.	.	.	C	34	5.373132	0.95923	.	.	ENSG00000068793	ENST00000313077;ENST00000412127;ENST00000435939	T;T	0.24151	1.87;1.87	5.57	5.57	0.84162	.	0.000000	0.64402	D	0.000001	T	0.53626	0.1808	M	0.70595	2.14	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.87578	0.998;0.953;0.946	T	0.52260	-0.8599	10	0.62326	D	0.03	-26.4779	19.9018	0.96988	0.0:1.0:0.0:0.0	.	979;520;951	E7EQ04;Q7L576-2;Q7L576	.;.;CYFP1_HUMAN	M	951;979;520	ENSP00000324549:T951M;ENSP00000405956:T520M	ENSP00000324549:T951M	T	+	2	0	CYFIP1	20542604	1.000000	0.71417	0.983000	0.44433	0.994000	0.84299	7.645000	0.83430	2.787000	0.95880	0.555000	0.69702	ACG	.	.	.	none		0.652	CYFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251136.2	NM_014608		T	22991163	C	T	22991163	3	4	33	1	0	0	0	0	1	0	0	0	4139	536	19	1	3327	1	CYFIP1	15	22991163	Missense_Mutation	SNP	C	TCGA-5P-A9K2-01A-11D-A42J-10		22991163	79540229	54	2424											
PARN	5073	hgsc.bcm.edu	37	chr16	14704668	14704668	+	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	tgatttaaatatggaattccTaaacacgattttaaaaagaa	19	13	5	4	1	0	2	0	1	0	1	1	4	1	3	1	1	1	0	1	1	10	7			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr16:14704668T>G	ENST00000437198.2	-	7	530		c.e7-2		PARN_ENST00000341484.7_Splice_Site|PARN_ENST00000566021.1_Splice_Site|PARN_ENST00000539279.1_Intron|PARN_ENST00000420015.2_Splice_Site	NM_001134477.2|NM_002582.3	NP_001127949.1|NP_002573.1	O95453	PARN_HUMAN	poly(A)-specific ribonuclease						female gamete generation (GO:0007292)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA metabolic process (GO:0016070)|RNA modification (GO:0009451)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|nuclease activity (GO:0004518)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(A)-specific ribonuclease activity (GO:0004535)|protein kinase binding (GO:0019901)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|urinary_tract(1)	21						ATGGAATTCCTAAACACGATT	0.338																																					.		Atlas-SNP	.											.	PARN	72	.	0			c.251-2A>C						PASS	.						135	130	131					16																	14704668		1838	4100	5938	SO:0001630	splice_region_variant	5073	exon7			AATTCCTAAACAC	AJ005698	CCDS45419.1, CCDS45420.1, CCDS58425.1	16p13	2014-08-08	2011-07-07		ENSG00000140694	ENSG00000140694	3.1.13.4		8609	protein-coding gene	gene with protein product	"deadenylation nuclease"	604212	"poly(A)-specific ribonuclease (deadenylation nuclease)"			10640832	Standard	NM_002582		Approved	DAN	uc010uzd.2	O95453	OTTHUMG00000173199	ENST00000437198.2:c.389-2A>C	chr16.hg19:g.14704668T>G		32.0	0.0	.		62.0	21.0	.	NM_001242992	B2RCB3|B4DDG8|B4DWR4|B4E1H6	Splice_Site	SNP	ENST00000437198.2	hg19	CCDS45419.1	.	.	.	.	.	.	.	.	.	.	T	16.06	3.015177	0.54468	.	.	ENSG00000140694	ENST00000437198;ENST00000341484;ENST00000420015;ENST00000538472	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1186	0.72423	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PARN	14612169	1.000000	0.71417	0.986000	0.45419	0.714000	0.41099	6.526000	0.73799	2.222000	0.72286	0.533000	0.62120	.	.	.	.	none		0.338	PARN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422383.1	NM_002582	Intron	G	14704668	T	G	14704668	5	3	33	1	0	0	0	0	0	0	1	0	11460	1536	53	5	1604	5	PARN	16	14704668	Splice_Site	SNP	T	TCGA-5P-A9K2-01A-11D-A42J-10		14704668	75650085	55	2425											
ACSM1	116285	hgsc.bcm.edu	37	chr16	20651870	20651870	+	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	ttgggcaacacgacctccccGccagtatagcagtgctccag	9	7	10	15	2	0	0	0	0	0	0	2	1	2	0	5	1	3	4	5	1	3	3	rs377637288	byFrequency	TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr16:20651870G>A	ENST00000307493.4	-	7	1096	c.1029C>T	c.(1027-1029)ggC>ggT	p.G343G	ACSM1_ENST00000520010.1_Silent_p.G343G|ACSM1_ENST00000219151.4_5'UTR	NM_052956.2	NP_443188.2	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member 1	343					benzoate metabolic process (GO:0018874)|butyrate metabolic process (GO:0019605)|cholesterol homeostasis (GO:0042632)|energy derivation by oxidation of organic compounds (GO:0015980)|fatty acid biosynthetic process (GO:0006633)|fatty acid oxidation (GO:0019395)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	blood microparticle (GO:0072562)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	acyl-CoA ligase activity (GO:0003996)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(23)|skin(3)|upper_aerodigestive_tract(2)	42						CGACCTCCCCGCCAGTATAGC	0.572													G|||	3	0.000599042	0	0	5008	,	,		18070	0		0	False		,,,				2504	0.0031				p.G343G		Atlas-SNP	.											ACSM1,caecum,carcinoma,0,1	ACSM1	118	.	0			c.C1029T						PASS	.	G		0,4402		0,0,2201	94	77	83		1029	-8.5	0	16		83	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ACSM1	NM_052956.2		0,1,6500	AA,AG,GG		0.0116,0.0,0.0077		343/578	20651870	1,13001	2201	4300	6501	SO:0001819	synonymous_variant	116285	exon7			CTCCCCGCCAGTA	AB059429	CCDS10587.1	16p12.3	2008-02-05	2005-09-08	2005-09-08	ENSG00000166743	ENSG00000166743	6.2.1.2	"Acyl-CoA synthetase family"	18049	protein-coding gene	gene with protein product		614357	"butyryl Coenzyme A synthetase 1"	BUCS1		11470804, 12654705	Standard	NM_052956		Approved	MACS1	uc002dhm.1	Q08AH1	OTTHUMG00000131550	ENST00000307493.4:c.1029C>T	chr16.hg19:g.20651870G>A		70.0	0.0	.		119.0	69.0	.	NM_052956	Q08AH2|Q96A20	Silent	SNP	ENST00000307493.4	hg19	CCDS10587.1	.	.	.	.	.	.	.	.	.	.	G	3.898	-0.022674	0.07634	0.0	1.16E-4	ENSG00000166743	ENST00000524149	.	.	.	4.83	-8.51	0.00923	.	.	.	.	.	T	0.36082	0.0954	.	.	.	0.30763	N	0.743914	.	.	.	.	.	.	T	0.42103	-0.9471	4	.	.	.	.	11.4682	0.50252	0.6558:0.0947:0.2495:0.0	.	.	.	.	V	49	.	.	A	-	2	0	ACSM1	20559371	0.000000	0.05858	0.013000	0.15412	0.000000	0.00434	-3.438000	0.00471	-2.125000	0.00821	-1.821000	0.00599	GCG	.	.	.	weak		0.572	ACSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254412.1	NM_052956		A	20651870	G	A	20651870	2	1	33	1	0	0	0	0	0	0	0	1	182	1074	38	1		1	ACSM1	16	20651870	Silent	SNP	G	TCGA-5P-A9K2-01A-11D-A42J-10	5947202	20651870	69702883	56	2426											
LRRC36	55282	hgsc.bcm.edu	37	chr16	67405136	67405137	+	Frame_Shift_Del	DEL	AG	AG	-																															catggtttccaagatgctacAggcagcgaggcaagtgttgg																										TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr16:67405136_67405137delAG	ENST00000329956.6	+	9	1504_1505	c.1485_1486delAG	c.(1483-1488)acaggcfs	p.G496fs	LRRC36_ENST00000290940.7_Frame_Shift_Del_p.G228fs|LRRC36_ENST00000541146.1_Frame_Shift_Del_p.R20fs|LRRC36_ENST00000435835.3_Frame_Shift_Del_p.G375fs|LRRC36_ENST00000563189.1_Frame_Shift_Del_p.G375fs	NM_018296.5	NP_060766.5	Q1X8D7	LRC36_HUMAN	leucine rich repeat containing 36	496										endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	24		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0669)|Epithelial(162;0.161)		AAGATGCTACAGGCAGCGAGGC	0.47																																					p.495_495del		Atlas-Indel,Pindel	.											.	LRRC36	68	.	0			c.1484_1485del						PASS	.																																			SO:0001589	frameshift_variant	55282	exon9			.	BC026156	CCDS32467.1, CCDS58474.1	16q22.1	2008-02-05				ENSG00000159708			25615	protein-coding gene	gene with protein product						12477932	Standard	NM_001161575		Approved	FLJ11004	uc002esv.3	Q1X8D7		ENST00000329956.6:c.1485_1486delAG	chr16.hg19:g.67405136_67405137delAG	ENSP00000329943:p.Gly496fs	51.0	0.0	0		113.0	37.0	0.327434	NM_018296	A4FTV6|A6NDE9|A8K8E6|Q7Z5K5	Frame_Shift_Del	DEL	ENST00000329956.6	hg19	CCDS32467.1																																																																																			.	.	.	none		0.47	LRRC36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421770.1	NM_018296		-	67405137	AG	-	67405136	7	5	33	1	0	1	0	1	0	0	0	0	8997	175	7	0	1547	0	LRRC36	16	67405136	Frame_Shift_Del	DEL	AG	TCGA-5P-A9K2-01A-11D-A42J-10	46753266	67405136	22949617	57	2427											
TAT	6898	hgsc.bcm.edu	37	chr16	71607494	71607494	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aataagaagcaatctcctccCgactggataggaagcctgaa	15	7	9	10	1	1	2	0	1	1	1	3	5	2	4	3	2	2	1	3	2	7	2			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr16:71607494C>T	ENST00000355962.4	-	4	489	c.356G>A	c.(355-357)cGg>cAg	p.R119Q	RP11-432I5.1_ENST00000561529.1_RNA	NM_000353.2	NP_000344.1	P17735	ATTY_HUMAN	tyrosine aminotransferase	119					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)	AATCTCCTCCCGACTGGATAG	0.473																																					p.R119Q	Melanoma(198;542 2142 10292 21661 50033)|Esophageal Squamous(48;487 1013 5572 44395 52594)	Atlas-SNP	.											.	TAT	80	.	0			c.G356A						PASS	.						60	55	56					16																	71607494		2187	4269	6456	SO:0001583	missense	6898	exon4			TCCTCCCGACTGG		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.356G>A	chr16.hg19:g.71607494C>T	ENSP00000348234:p.Arg119Gln	59.0	0.0	.		95.0	32.0	.	NM_000353	B2R8I1|D3DWS2	Missense_Mutation	SNP	ENST00000355962.4	hg19	CCDS10903.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.454470	0.84209	.	.	ENSG00000198650	ENST00000355962	D	0.91686	-2.89	6.01	6.01	0.97437	Tyrosine aminotransferase (1);Aminotransferase, class I/classII (1);Tyrosine/nicotianamine aminotransferase (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.97589	0.9210	H	0.96333	3.805	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.98231	1.0483	10	0.87932	D	0	-18.9801	18.7017	0.91623	0.0:1.0:0.0:0.0	.	119	P17735	ATTY_HUMAN	Q	119	ENSP00000348234:R119Q	ENSP00000348234:R119Q	R	-	2	0	TAT	70164995	1.000000	0.71417	0.995000	0.50966	0.491000	0.33493	5.645000	0.67909	2.861000	0.98227	0.650000	0.86243	CGG	.	.	.	none		0.473	TAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268989.1			T	71607494	C	T	71607494	3	4	33	1	0	0	0	0	1	0	0	0	15602	652	23	1	1044	1	TAT	16	71607494	Missense_Mutation	SNP	C	TCGA-5P-A9K2-01A-11D-A42J-10	4202358	71607494	18747259	58	2428											
ZCCHC14	23174	hgsc.bcm.edu	37	chr16	87445572	87445572	+	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	gcacacaatgcagcctggcgGgggtggggcgggctgcgggg	5	4	22	10	3	0	0	0	0	0	0	0	0	0	0	1	8	3	3	1	8	1	0			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr16:87445572G>A	ENST00000268616.4	-	12	2561	c.2344C>T	c.(2344-2346)Ccg>Tcg	p.P782S		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	782	Poly-Pro.						nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		CAGCCTGGCGGGGGTGGGGCG	0.672																																					p.P782S		Atlas-SNP	.											.	ZCCHC14	87	.	0			c.C2344T						PASS	.						5	7	6					16																	87445572		1877	3794	5671	SO:0001583	missense	23174	exon12			CTGGCGGGGGTGG	AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"Zinc fingers, CCHC domain containing", "Sterile alpha motif (SAM) domain containing"	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.2344C>T	chr16.hg19:g.87445572G>A	ENSP00000268616:p.Pro782Ser	35.0	0.0	.		64.0	39.0	.	NM_015144	D3DUN1|O60324|Q3MJD8|Q9UFP0	Missense_Mutation	SNP	ENST00000268616.4	hg19	CCDS10961.1	.	.	.	.	.	.	.	.	.	.	G	0.776	-0.763986	0.02996	.	.	ENSG00000140948	ENST00000268616	T	0.17213	2.29	5.55	4.57	0.56435	.	0.199338	0.43110	D	0.000616	T	0.14700	0.0355	N	0.08118	0	0.09310	N	1	P;D	0.53151	0.939;0.958	P;P	0.52758	0.708;0.609	T	0.11251	-1.0595	10	0.34782	T	0.22	-26.68	12.1873	0.54247	0.0:0.1722:0.8278:0.0	.	782;782	Q8WYQ9-2;Q8WYQ9	.;ZCH14_HUMAN	S	782	ENSP00000268616:P782S	ENSP00000268616:P782S	P	-	1	0	ZCCHC14	86003073	1.000000	0.71417	0.038000	0.18304	0.006000	0.05464	4.357000	0.59436	1.290000	0.44636	0.643000	0.83706	CCG	.	.	.	none		0.672	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269107.1	NM_015144		A	87445572	G	A	87445572	3	1	33	1	0	0	0	0	1	0	0	0	17595	1232	43	2	513	2	ZCCHC14	16	87445572	Missense_Mutation	SNP	G	TCGA-5P-A9K2-01A-11D-A42J-10	15838078	87445572	2909181	59	2429											
SLC25A11	8402	hgsc.bcm.edu	37	chr17	4841167	4841167	+	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	caggctgaagaagccctcgtAgcggacaactttgaacagca	13	6	11	11	2	0	3	0	2	0	1	1	4	0	4	1	2	5	3	1	2	5	2			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr17:4841167A>T	ENST00000225665.7	-	8	1154	c.814T>A	c.(814-816)Tac>Aac	p.Y272N	RNF167_ENST00000575111.1_5'Flank|RNF167_ENST00000572430.1_5'Flank|SLC25A11_ENST00000544061.2_Missense_Mutation_p.Y221N|RNF167_ENST00000576229.1_5'Flank|RNF167_ENST00000262482.6_5'Flank|RNF167_ENST00000571816.1_5'Flank	NM_001165417.1|NM_003562.4	NP_001158889.1|NP_003553.2	Q02978	M2OM_HUMAN	solute carrier family 25 (mitochondrial carrier; oxoglutarate carrier), member 11	272					alpha-ketoglutarate transport (GO:0015742)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxoglutarate:malate antiporter activity (GO:0015367)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)	10						AAGCCCTCGTAGCGGACAACT	0.597																																					p.Y272N	Esophageal Squamous(144;1178 2388 18010 48797)	Atlas-SNP	.											.	SLC25A11	22	.	0			c.T814A						PASS	.						79	87	84					17																	4841167		2203	4300	6503	SO:0001583	missense	8402	exon8			CCTCGTAGCGGAC	X66114	CCDS11059.1, CCDS54069.1	17p13.3	2013-05-22			ENSG00000108528	ENSG00000108528		"Solute carriers"	10981	protein-coding gene	gene with protein product		604165		SLC20A4		10072597, 1457818	Standard	NM_003562		Approved	OGC	uc002fzo.2	Q02978	OTTHUMG00000099395	ENST00000225665.7:c.814T>A	chr17.hg19:g.4841167A>T	ENSP00000225665:p.Tyr272Asn	37.0	0.0	.		92.0	23.0	.	NM_003562	F5GY65|O75537|Q969P7	Missense_Mutation	SNP	ENST00000225665.7	hg19	CCDS11059.1	.	.	.	.	.	.	.	.	.	.	A	0.781	-0.762405	0.02996	.	.	ENSG00000108528	ENST00000225665;ENST00000544061	T;T	0.77358	-1.09;-1.09	5.16	5.16	0.70880	Mitochondrial carrier domain (2);	0.206543	0.41712	D	0.000829	T	0.36690	0.0976	N	0.00102	-2.13	0.38778	D	0.954692	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.56565	-0.7958	10	0.02654	T	1	-5.1413	12.9924	0.58627	1.0:0.0:0.0:0.0	.	272;272	Q6IBH0;Q02978	.;M2OM_HUMAN	N	272;221	ENSP00000225665:Y272N;ENSP00000440804:Y221N	ENSP00000225665:Y272N	Y	-	1	0	SLC25A11	4781912	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	3.939000	0.56591	2.164000	0.68074	0.533000	0.62120	TAC	.	.	.	none		0.597	SLC25A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216852.4	NM_003562		T	4841167	A	T	4841167	3	4	33	1	0	0	0	0	1	0	0	0	14486	420	15	5	134	5	SLC25A11	17	4841167	Missense_Mutation	SNP	A	TCGA-5P-A9K2-01A-11D-A42J-10		4841167	76354043	60	2430											
CCDC144A	9720	hgsc.bcm.edu	37	chr17	16667486	16667487	+	Missense_Mutation	DNP	GA	GA	AG																															gacatggagagctacttgttGaaggttagctatcttttttc																										TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr17:16667486_16667487GA>AG	ENST00000360524.8	+	15	4171_4172	c.4095_4096GA>AG	c.(4093-4098)ttGAag>ttAGag	p.K1366E	CCDC144A_ENST00000456009.1_Missense_Mutation_p.K1132E|RP11-219A15.1_ENST00000448331.3_Missense_Mutation_p.K1366E|CCDC144A_ENST00000443444.2_Missense_Mutation_p.K1366E|CCDC144A_ENST00000399273.1_Missense_Mutation_p.K1366E	NM_014695.1	NP_055510.1	A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A	1366																	GCTACTTGTTGAAGGTTAGCTA	0.351																																					p.L1365L|p.K1366E		Atlas-SNP	.											.	CCDC144A	53	.	0			c.G4095A|c.A4096G						PASS	.																																			SO:0001583	missense	9720	exon15			CTTGTTGAAGGTT|TTGTTGAAGGTTA	BC133019	CCDS45621.1	17p11.2	2008-10-23			ENSG00000170160	ENSG00000170160			29072	protein-coding gene	gene with protein product						9628581, 11997339	Standard	NM_014695		Approved	KIAA0565, FLJ43983	uc002gqk.1	A2RUR9	OTTHUMG00000059178	Exception_encountered	chr17.hg19:g.16667486_16667487delinsAG	ENSP00000353717:p.Lys1366Glu	116.0|113.0	0.0	.		179.0|173.0	37.0|36.0	.	NM_014695	O60311|Q6ZU57	Silent|Missense_Mutation	SNP	ENST00000360524.8	hg19	CCDS45621.1																																																																																			.	.	.	none		0.351	CCDC144A-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000444093.1			AG	16667487	GA	AG	16667486	3	1	33	1	0	0	0	0	1	0	0	0	2779	1281	45	2	4153	2	CCDC144A	17	16667486	Missense_Mutation	DNP	GA	TCGA-5P-A9K2-01A-11D-A42J-10	11826319	16667486	64527724	61	2431											
ZNF207	7756	hgsc.bcm.edu	37	chr17	30696690	30696690	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccccgtatgggcagggacCgccaatggtgcccccttacc	6	6	12	17	2	0	0	0	0	0	0	0	1	0	1	7	3	2	2	7	3	3	2			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr17:30696690C>T	ENST00000321233.6	+	11	1503	c.1349C>T	c.(1348-1350)cCg>cTg	p.P450L	ZNF207_ENST00000394673.2_Missense_Mutation_p.P435L|ZNF207_ENST00000394670.4_Missense_Mutation_p.P466L|ZNF207_ENST00000577908.1_Missense_Mutation_p.P466L|ZNF207_ENST00000342555.6_Missense_Mutation_p.P469L|ZNF207_ENST00000341711.6_Missense_Mutation_p.P367L	NM_003457.3	NP_003448.1	O43670	ZN207_HUMAN	zinc finger protein 207	450					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)			GGGCAGGGACCGCCAATGGTG	0.522																																					p.P466L		Atlas-SNP	.											ZNF207,NS,malignant_melanoma,0,1	ZNF207	32	.	0			c.C1397T						PASS	.						73	65	68					17																	30696690		2203	4300	6503	SO:0001583	missense	7756	exon12			AGGGACCGCCAAT	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.1349C>T	chr17.hg19:g.30696690C>T	ENSP00000322777:p.Pro450Leu	41.0	0.0	.		67.0	18.0	.	NM_001098507	A8K6Y6|E1P660|E1P661|E1P662|Q53XS9|Q96HW5|Q9BUQ7	Missense_Mutation	SNP	ENST00000321233.6	hg19	CCDS11271.1	.	.	.	.	.	.	.	.	.	.	C	15.03	2.711425	0.48517	.	.	ENSG00000010244	ENST00000394670;ENST00000394673;ENST00000394679;ENST00000321233;ENST00000341711;ENST00000342555	T;T	0.49720	0.83;0.77	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.39911	0.1096	N	0.24115	0.695	0.80722	D	1	B;B;B;B;B	0.21688	0.059;0.012;0.012;0.012;0.012	B;B;B;B;B	0.15870	0.014;0.009;0.009;0.009;0.003	T	0.20140	-1.0284	10	0.72032	D	0.01	.	20.1322	0.98003	0.0:1.0:0.0:0.0	.	419;469;466;435;450	A8MTG3;Q59G94;E1P660;O43670-2;O43670	.;.;.;.;ZN207_HUMAN	L	466;419;469;435;367;450	ENSP00000378165:P466L;ENSP00000344913:P367L	ENSP00000322777:P435L	P	+	2	0	ZNF207	27720803	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.640000	0.61368	2.765000	0.95021	0.484000	0.47621	CCG	.	.	.	none		0.522	ZNF207-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256251.2			T	30696690	C	T	30696690	3	4	33	1	0	0	0	0	1	0	0	0	17777	652	23	1	1443	1	ZNF207	17	30696690	Missense_Mutation	SNP	C	TCGA-5P-A9K2-01A-11D-A42J-10	14029204	30696690	50498520	62	2432											
PSMD11	5717	hgsc.bcm.edu	37	chr17	30806379	30806379	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgatccgagtcattgagccTttttccagagtacaggtgag	9	12	11	9	1	1	4	1	3	0	1	3	5	3	4	3	1	2	1	3	1	1	4			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr17:30806379T>C	ENST00000261712.3	+	10	1286	c.1023T>C	c.(1021-1023)ccT>ccC	p.P341P	PSMD11_ENST00000457654.2_Silent_p.P341P	NM_001270482.1|NM_002815.3	NP_001257411.1|NP_002806.2	O00231	PSD11_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 11	341	PCI.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome assembly (GO:0043248)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stem cell differentiation (GO:0048863)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	19		Breast(31;0.159)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.109)			TCATTGAGCCTTTTTCCAGAG	0.507																																					p.P341P	Ovarian(130;1038 1716 9294 11987 19279)	Atlas-SNP	.											.	PSMD11	41	.	0			c.T1023C						PASS	.						121	117	118					17																	30806379		2203	4300	6503	SO:0001819	synonymous_variant	5717	exon10			TGAGCCTTTTTCC	AB003102	CCDS11272.1	17q12	2008-05-22			ENSG00000108671	ENSG00000108671		"Proteasome (prosome, macropain) subunits"	9556	protein-coding gene	gene with protein product		604449				9426256, 9119060	Standard	NM_001270482		Approved	S9, p44.5, MGC3844, Rpn6	uc010cta.2	O00231	OTTHUMG00000132811	ENST00000261712.3:c.1023T>C	chr17.hg19:g.30806379T>C		57.0	0.0	.		75.0	4.0	.	NM_002815	A8K3I7|E1P663|O00495|Q53FT5	Silent	SNP	ENST00000261712.3	hg19	CCDS11272.1	.	.	.	.	.	.	.	.	.	.	T	9.740	1.164650	0.21538	.	.	ENSG00000108671	ENST00000457654	.	.	.	5.41	0.333	0.15943	.	.	.	.	.	T	0.50257	0.1605	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35500	-0.9786	4	.	.	.	-8.2709	4.7365	0.12991	0.1519:0.3938:0.0:0.4542	.	.	.	.	L	79	.	.	F	+	1	0	PSMD11	27830492	0.938000	0.31826	0.999000	0.59377	0.989000	0.77384	0.064000	0.14437	0.101000	0.17610	0.459000	0.35465	TTT	.	.	.	none		0.507	PSMD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256252.2	NM_002815		C	30806379	T	C	30806379	2	2	33	1	0	0	0	0	0	0	0	1	12704	1596	56	3		3	PSMD11	17	30806379	Silent	SNP	T	TCGA-5P-A9K2-01A-11D-A42J-10	109689	30806379	50388831	63	2433											
RSAD1	55316	hgsc.bcm.edu	37	chr17	48557272	48557272	+	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	tgttctttggtggggggaccCccagtctagccagtccccac	5	10	12	14	0	2	0	0	0	2	0	3	1	3	1	5	4	1	1	5	4	1	3			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr17:48557272C>A	ENST00000258955.2	+	3	386	c.301C>A	c.(301-303)Ccc>Acc	p.P101T		NM_018346.1	NP_060816.1	Q9HA92	RSAD1_HUMAN	radical S-adenosyl methionine domain containing 1	101					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)			TGGGGGGACCCCCAGTCTAGC	0.612											OREG0024566	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P101T		Atlas-SNP	.											.	RSAD1	36	.	0			c.C301A						PASS	.						42	53	49					17																	48557272		2203	4300	6503	SO:0001583	missense	55316	exon3			GGGACCCCCAGTC	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.301C>A	chr17.hg19:g.48557272C>A	ENSP00000258955:p.Pro101Thr	57.0	0.0	.	955	118.0	68.0	.	NM_018346	B4DMW0|Q53HV8|Q86VC4|Q9BRY7|Q9NUS7	Missense_Mutation	SNP	ENST00000258955.2	hg19	CCDS11569.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.899032	0.91962	.	.	ENSG00000136444	ENST00000258955;ENST00000510554	D	0.87179	-2.22	4.64	4.64	0.57946	Elongator protein 3/MiaB/NifB (1);Radical SAM, alpha/beta horseshoe (1);Radical SAM (1);	0.000000	0.85682	D	0.000000	D	0.96436	0.8837	H	0.98738	4.315	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98372	1.0554	10	0.87932	D	0	-27.8023	17.2877	0.87146	0.0:1.0:0.0:0.0	.	101;101	B4DEV9;Q9HA92	.;RSAD1_HUMAN	T	101;31	ENSP00000258955:P101T	ENSP00000258955:P101T	P	+	1	0	RSAD1	45912271	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	7.345000	0.79337	2.397000	0.81536	0.491000	0.48974	CCC	.	.	.	none		0.612	RSAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367413.1	NM_018346		A	48557272	C	A	48557272	3	1	33	1	0	0	0	0	1	0	0	0	13707	623	22	4	311	4	RSAD1	17	48557272	Missense_Mutation	SNP	C	TCGA-5P-A9K2-01A-11D-A42J-10	17750893	48557272	32637938	64	2434											
AXIN2	8313	hgsc.bcm.edu	37	chr17	63533850	63533850	+	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	gatcgtccagtatcgtctgcGggtcttcctcgtagctgccg	4	12	12	13	5	2	0	0	0	2	0	7	1	4	0	3	1	3	3	3	1	2	3			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr17:63533850G>T	ENST00000375702.5	-	5	1412	c.1304C>A	c.(1303-1305)cCg>cAg	p.P435Q	AXIN2_ENST00000307078.5_Missense_Mutation_p.P435Q			Q9Y2T1	AXIN2_HUMAN	axin 2	435	Interaction with beta-catenin. {ECO:0000250}.				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						TATCGTCTGCGGGTCTTCCTC	0.672									Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome																												p.P435Q		Atlas-SNP	.											AXIN2,colon,carcinoma,0,1	AXIN2	92	.	0			c.C1304A						PASS	.						16	18	17					17																	63533850		2175	4255	6430	SO:0001583	missense	8313	exon6	Familial Cancer Database	Oligodontia-Colorectal Cancer syndrome, Tooth Agenesis-Colorectal Cancer Syndrome	GTCTGCGGGTCTT	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.1304C>A	chr17.hg19:g.63533850G>T	ENSP00000364854:p.Pro435Gln	22.0	0.0	.		42.0	2.0	.	NM_004655	Q3MJ88|Q9H3M6|Q9UH84	Missense_Mutation	SNP	ENST00000375702.5	hg19		.	.	.	.	.	.	.	.	.	.	G	20.9	4.071338	0.76301	.	.	ENSG00000168646	ENST00000307078;ENST00000375702	T;T	0.69306	-0.39;-0.38	4.93	3.96	0.45880	Axin beta-catenin binding (1);	0.055629	0.85682	D	0.000000	T	0.79701	0.4491	M	0.71036	2.16	0.53688	D	0.999974	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.81693	-0.0817	10	0.87932	D	0	-8.8725	12.9793	0.58554	0.0796:0.0:0.9204:0.0	.	435;435	Q9Y2T1;E7ES00	AXIN2_HUMAN;.	Q	435	ENSP00000302625:P435Q;ENSP00000364854:P435Q	ENSP00000302625:P435Q	P	-	2	0	AXIN2	60964312	1.000000	0.71417	0.977000	0.42913	0.948000	0.59901	7.269000	0.78482	1.093000	0.41377	0.650000	0.86243	CCG	.	.	.	none		0.672	AXIN2-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000445901.1	NM_004655		T	63533850	G	T	63533850	3	4	33	1	0	0	0	0	1	0	0	0	1237	1116	39	4	1251	4	AXIN2	17	63533850	Missense_Mutation	SNP	G	TCGA-5P-A9K2-01A-11D-A42J-10	14976578	63533850	17661360	65	2435											
ZNF407	55628	hgsc.bcm.edu	37	chr18	72776216	72776216	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagctgcccccaggggtgcAggacgagccgggcctgtact	7	5	16	13	2	0	1	0	0	0	1	0	3	0	2	4	4	5	3	4	4	1	1			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr18:72776216A>G	ENST00000299687.5	+	8	6539	c.6539A>G	c.(6538-6540)cAg>cGg	p.Q2180R		NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	2180					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)		CCAGGGGTGCAGGACGAGCCG	0.692																																					p.Q2180R		Atlas-SNP	.											.	ZNF407	231	.	0			c.A6539G						PASS	.						17	23	21					18																	72776216		2088	4212	6300	SO:0001583	missense	55628	exon8			GGGTGCAGGACGA	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.6539A>G	chr18.hg19:g.72776216A>G	ENSP00000299687:p.Gln2180Arg	29.0	0.0	.		35.0	16.0	.	NM_017757	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	hg19	CCDS45885.1	.	.	.	.	.	.	.	.	.	.	a	6.142	0.394484	0.11638	.	.	ENSG00000215421	ENST00000299687	T	0.12147	2.71	4.63	-1.48	0.08745	.	.	.	.	.	T	0.16981	0.0408	M	0.61703	1.905	0.24952	N	0.99179	B	0.10296	0.003	B	0.12156	0.007	T	0.42666	-0.9438	9	0.72032	D	0.01	.	14.9676	0.71208	0.3463:0.6537:0.0:0.0	.	2180	Q9C0G0	ZN407_HUMAN	R	2180	ENSP00000299687:Q2180R	ENSP00000299687:Q2180R	Q	+	2	0	ZNF407	70905204	0.994000	0.37717	0.013000	0.15412	0.036000	0.12997	2.459000	0.45023	0.362000	0.24319	0.457000	0.33378	CAG	.	.	.	none		0.692	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		G	72776216	A	G	72776216	3	3	33	1	0	0	0	0	1	0	0	0	17899	188	7	3	6699	3	ZNF407	18	72776216	Missense_Mutation	SNP	A	TCGA-5P-A9K2-01A-11D-A42J-10		72776216	5301032	66	2436			2	6		2	2	25	A		6.202012e-05
ZNF407	55628	hgsc.bcm.edu	37	chr18	72776240	72776240	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgagccgggcctgtactcccAcaccgtgctggagactgcgg	6	6	14	15	4	0	1	0	0	0	1	1	3	1	1	4	3	4	2	4	3	1	1			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr18:72776240A>G	ENST00000299687.5	+	8	6563	c.6563A>G	c.(6562-6564)cAc>cGc	p.H2188R		NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	2188					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)		CTGTACTCCCACACCGTGCTG	0.692																																					p.H2188R		Atlas-SNP	.											.	ZNF407	231	.	0			c.A6563G						PASS	.						14	19	17					18																	72776240		2039	4186	6225	SO:0001583	missense	55628	exon8			ACTCCCACACCGT	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.6563A>G	chr18.hg19:g.72776240A>G	ENSP00000299687:p.His2188Arg	29.0	0.0	.		34.0	13.0	.	NM_017757	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	hg19	CCDS45885.1	.	.	.	.	.	.	.	.	.	.	a	14.35	2.510614	0.44660	.	.	ENSG00000215421	ENST00000299687	T	0.13538	2.58	4.77	4.77	0.60923	.	.	.	.	.	T	0.36524	0.0970	M	0.71581	2.175	0.80722	D	1	D	0.71674	0.998	D	0.83275	0.996	T	0.15752	-1.0426	9	0.87932	D	0	.	14.3168	0.66457	1.0:0.0:0.0:0.0	.	2188	Q9C0G0	ZN407_HUMAN	R	2188	ENSP00000299687:H2188R	ENSP00000299687:H2188R	H	+	2	0	ZNF407	70905228	1.000000	0.71417	0.841000	0.33234	0.047000	0.14425	4.479000	0.60236	2.194000	0.70268	0.457000	0.33378	CAC	.	.	.	none		0.692	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		G	72776240	A	G	72776240	3	3	33	1	0	0	0	0	1	0	0	0	17899	159	6	3	6723	3	ZNF407	18	72776240	Missense_Mutation	SNP	A	TCGA-5P-A9K2-01A-11D-A42J-10	24	72776240	5301008	67	2437			2	6		2	2	25	A		6.202012e-05
WDR18	57418	hgsc.bcm.edu	37	chr19	994054	994056	+	In_Frame_Del	DEL	GCT	GCT	-																															tacctggaccgcacggagcaGctgcaggccgtcctgtgcag																										TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	GCT	GCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr19:994054_994056delGCT	ENST00000251289.5	+	9	1157_1159	c.1134_1136delGCT	c.(1132-1137)cagctg>cag	p.L379del	WDR18_ENST00000587001.2_Intron	NM_024100.3	NP_077005.2	Q9BV38	WDR18_HUMAN	WD repeat domain 18	379					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|lung(2)|skin(2)	7		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCACGGAGCAGCTGCAGGCCGTC	0.7																																					p.378_379del		Atlas-Indel,Pindel	.											.	WDR18	20	.	0			c.1133_1135del						PASS	.																																			SO:0001651	inframe_deletion	57418	exon9			.		CCDS12051.1	19p13.3	2013-01-09				ENSG00000065268		"WD repeat domain containing"	17956	protein-coding gene	gene with protein product	"Involved in Processing ITS2 3 homolog (S. cerevisiae)"					22190735	Standard	NM_024100		Approved	Ipi3	uc002lqm.1	Q9BV38		ENST00000251289.5:c.1134_1136delGCT	chr19.hg19:g.994054_994056delGCT	ENSP00000251289:p.Leu379del	60.0	0.0	0		53.0	24.0	0.45283	NM_024100	O60390|Q9BWR2	In_Frame_Del	DEL	ENST00000251289.5	hg19	CCDS12051.1																																																																																			.	.	.	none		0.7	WDR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458225.2			-	994056	GCT	-	994054	7	5	33	1	0	1	0	1	0	0	0	0	17290	962	34	0	1168	0	WDR18	19	994054	In_Frame_Del	DEL	GCT	TCGA-5P-A9K2-01A-11D-A42J-10		994054	58134929	68	2438											
SAFB2	9667	hgsc.bcm.edu	37	chr19	5587272	5587272	+	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	acttagtagcggcgggtgaaGtgggggtacggggggggatg	7	7	23	4	3	0	1	0	1	0	0	0	2	0	2	0	8	2	2	0	8	4	3			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr19:5587272G>T	ENST00000252542.4	-	21	3108	c.2844C>A	c.(2842-2844)caC>caA	p.H948Q		NM_014649.2	NP_055464.1	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	948	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)		GGCGGGTGAAgtgggggtacg	0.647																																					p.H948Q	Ovarian(127;888 1728 23957 44128 52668)	Atlas-SNP	.											.	SAFB2	90	.	0			c.C2844A						PASS	.						21	23	22					19																	5587272		2203	4299	6502	SO:0001583	missense	9667	exon21			GGTGAAGTGGGGG	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.2844C>A	chr19.hg19:g.5587272G>T	ENSP00000252542:p.His948Gln	95.0	0.0	.		114.0	46.0	.	NM_014649	B4DKG3|Q8TB13	Missense_Mutation	SNP	ENST00000252542.4	hg19	CCDS32879.1	.	.	.	.	.	.	.	.	.	.	g	13.86	2.363959	0.41902	.	.	ENSG00000130254	ENST00000252542	T	0.08282	3.11	3.73	3.73	0.42828	.	0.618569	0.14577	N	0.311114	T	0.07143	0.0181	L	0.36672	1.1	0.30505	N	0.769985	B	0.30482	0.281	B	0.26517	0.07	T	0.07121	-1.0789	10	0.59425	D	0.04	-9.5501	7.3079	0.26457	0.1263:0.0:0.8737:0.0	.	948	Q14151	SAFB2_HUMAN	Q	948	ENSP00000252542:H948Q	ENSP00000252542:H948Q	H	-	3	2	SAFB2	5538272	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	0.856000	0.27818	1.614000	0.50241	0.561000	0.74099	CAC	.	.	.	none		0.647	SAFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451016.1	NM_014649		T	5587272	G	T	5587272	3	4	33	1	0	0	0	0	1	0	0	0	13820	1020	36	4	21	4	SAFB2	19	5587272	Missense_Mutation	SNP	G	TCGA-5P-A9K2-01A-11D-A42J-10	4593218	5587272	53541711	69	2439											
ZNF709	163051	hgsc.bcm.edu	37	chr19	12575957	12575957	+	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	aagtttggtaatatctgaaaGcttttccacattgtttacat	12	17	6	6	0	1	1	0	1	1	0	2	1	2	1	1	1	2	4	1	1	5	8			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr19:12575957G>C	ENST00000397732.3	-	4	950	c.779C>G	c.(778-780)gCt>gGt	p.A260G	CTD-3105H18.18_ENST00000598753.1_Intron|ZNF709_ENST00000428311.1_Missense_Mutation_p.A260G	NM_152601.3	NP_689814.1	Q8N972	ZN709_HUMAN	zinc finger protein 709	260					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|upper_aerodigestive_tract(3)	6						ATATCTGAAAGCTTTTCCACA	0.388																																					p.A260G	GBM(33;565 669 12371 29134 51667)	Atlas-SNP	.											.	ZNF709	80	.	0			c.C779G						PASS	.						50	52	52					19																	12575957		2158	4284	6442	SO:0001583	missense	163051	exon4			CTGAAAGCTTTTC	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.779C>G	chr19.hg19:g.12575957G>C	ENSP00000380840:p.Ala260Gly	72.0	0.0	.		63.0	23.0	.	NM_152601	A8K4E6	Missense_Mutation	SNP	ENST00000397732.3	hg19	CCDS42504.1	.	.	.	.	.	.	.	.	.	.	G	17.92	3.506577	0.64410	.	.	ENSG00000242852;ENSG00000196826	ENST00000397732;ENST00000428311	T;T	0.19669	2.13;2.13	2.8	0.387	0.16259	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	1.011620	0.07961	N	0.982440	T	0.12433	0.0302	N	0.13098	0.295	0.09310	N	1	B	0.15719	0.014	B	0.15052	0.012	T	0.33420	-0.9869	10	0.59425	D	0.04	.	6.852	0.24020	0.0:0.4983:0.3262:0.1756	.	260	Q8N972	ZN709_HUMAN	G	260	ENSP00000380840:A260G;ENSP00000404127:A260G	ENSP00000404127:A260G	A	-	2	0	ZNF709;CTD-2192J16.17	12436957	0.000000	0.05858	0.007000	0.13788	0.904000	0.53231	-0.765000	0.04730	0.198000	0.20407	0.467000	0.42956	GCT	.	.	.	none		0.388	ZNF709-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344088.1	NM_152601		C	12575957	G	C	12575957	3	2	33	1	0	0	0	0	1	0	0	0	18125	971	34	4	1150	4	ZNF709	19	12575957	Missense_Mutation	SNP	G	TCGA-5P-A9K2-01A-11D-A42J-10	6988685	12575957	46553026	70	2440											
ERF	2077	hgsc.bcm.edu	37	chr19	42754700	42754700	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgactctggcttgtaggcccAatccgggaaggcaaaccctg	9	7	12	13	2	1	0	0	0	1	0	2	2	2	1	3	4	1	3	3	4	4	2			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr19:42754700A>G	ENST00000222329.4	-	2	197	c.40T>C	c.(40-42)Tgg>Cgg	p.W14R	ERF_ENST00000440177.2_5'UTR|AC006486.9_ENST00000594664.1_Intron|ERF_ENST00000595941.1_5'UTR	NM_006494.2	NP_006485.2	P50548	ERF_HUMAN	Ets2 repressor factor	14					cell cycle (GO:0007049)|cell differentiation (GO:0030154)|chorio-allantoic fusion (GO:0060710)|ectodermal cell differentiation (GO:0010668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|trophoblast giant cell differentiation (GO:0060707)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	17		Prostate(69;0.00682)				TTGTAGGCCCAATCCGGGAAG	0.647																																					p.W14R		Atlas-SNP	.											.	ERF	47	.	0			c.T40C						PASS	.						38	33	35					19																	42754700		2202	4300	6502	SO:0001583	missense	2077	exon2			AGGCCCAATCCGG	U58535	CCDS12600.1	19q13	2008-07-16				ENSG00000105722			3444	protein-coding gene	gene with protein product	"Ets2 repressor factor"	611888				7588608, 9192842	Standard	XM_005258644		Approved	PE-2, PE2	uc002ote.4	P50548		ENST00000222329.4:c.40T>C	chr19.hg19:g.42754700A>G	ENSP00000222329:p.Trp14Arg	65.0	0.0	.		94.0	35.0	.	NM_006494	B2RAP1|B7Z4R0|Q59G38|Q9UPI7	Missense_Mutation	SNP	ENST00000222329.4	hg19	CCDS12600.1	.	.	.	.	.	.	.	.	.	.	A	18.88	3.716679	0.68844	.	.	ENSG00000105722	ENST00000222329	T	0.08896	3.04	5.37	5.37	0.77165	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.26991	0.0661	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.00715	-1.1597	10	0.87932	D	0	.	13.6266	0.62168	1.0:0.0:0.0:0.0	.	14	P50548	ERF_HUMAN	R	14	ENSP00000222329:W14R	ENSP00000222329:W14R	W	-	1	0	ERF	47446540	1.000000	0.71417	0.980000	0.43619	0.992000	0.81027	7.293000	0.78740	2.170000	0.68504	0.533000	0.62120	TGG	.	.	.	none		0.647	ERF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463684.1	NM_006494		G	42754700	A	G	42754700	3	3	33	1	0	0	0	0	1	0	0	0	5223	130	5	3	1618	3	ERF	19	42754700	Missense_Mutation	SNP	A	TCGA-5P-A9K2-01A-11D-A42J-10	30178743	42754700	16374283	71	2441											
ZNF221	7638	hgsc.bcm.edu	37	chr19	44466901	44466901	+	Missense_Mutation	SNP	T	T	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	gatttcaccttcacttgaacTgcttcattcaggactctgca	9	14	6	12	0	5	1	4	1	1	0	5	3	5	2	1	1	3	2	1	1	1	5			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr19:44466901T>G	ENST00000251269.5	+	3	351	c.23T>G	c.(22-24)cTg>cGg	p.L8R	ZNF221_ENST00000592350.1_Missense_Mutation_p.L8R|ZNF221_ENST00000587682.1_Missense_Mutation_p.L8R	NM_013359.2	NP_037491	Q9UK13	ZN221_HUMAN	zinc finger protein 221	8					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(11)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	30		Prostate(69;0.0352)				TCACTTGAACTGCTTCATTCA	0.428																																					p.L8R		Atlas-SNP	.											.	ZNF221	59	.	0			c.T23G						PASS	.						145	124	131					19																	44466901		2203	4300	6503	SO:0001583	missense	7638	exon3			TTGAACTGCTTCA	AF187987	CCDS12633.1	19q13.31	2013-01-08				ENSG00000159905		"Zinc fingers, C2H2-type", "-"	13014	protein-coding gene	gene with protein product							Standard	NM_013359		Approved		uc002oxx.2	Q9UK13		ENST00000251269.5:c.23T>G	chr19.hg19:g.44466901T>G	ENSP00000251269:p.Leu8Arg	40.0	0.0	.		62.0	19.0	.	NM_013359	B2RAI6|Q2M2H2|Q9P1U8	Missense_Mutation	SNP	ENST00000251269.5	hg19	CCDS12633.1	.	.	.	.	.	.	.	.	.	.	T	11.42	1.634816	0.29068	.	.	ENSG00000159905	ENST00000251269	T	0.07444	3.19	2.04	2.04	0.26737	.	.	.	.	.	T	0.06416	0.0165	N	0.22421	0.69	0.09310	N	1	D	0.58620	0.983	B	0.43838	0.433	T	0.32613	-0.9900	9	0.72032	D	0.01	.	6.0601	0.19832	0.0:0.0:0.0:1.0	.	8	Q9UK13	ZN221_HUMAN	R	8	ENSP00000251269:L8R	ENSP00000251269:L8R	L	+	2	0	ZNF221	49158741	0.066000	0.20996	0.002000	0.10522	0.002000	0.02628	1.349000	0.33998	1.167000	0.42706	0.379000	0.24179	CTG	.	.	.	none		0.428	ZNF221-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460068.1			G	44466901	T	G	44466901	3	3	33	1	0	0	0	0	1	0	0	0	17787	1580	55	5	25	5	ZNF221	19	44466901	Missense_Mutation	SNP	T	TCGA-5P-A9K2-01A-11D-A42J-10	1712201	44466901	14662082	72	2442											
GLTSCR2	29997	hgsc.bcm.edu	37	chr19	48248919	48248919	+	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	cttcggtggacccagcgctgAggcggcggcggcgaggccca	5	4	18	14	6	0	1	0	1	0	0	1	3	0	2	2	7	1	1	2	7	0	1			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr19:48248919A>C	ENST00000246802.5	+	1	141	c.103A>C	c.(103-105)Agg>Cgg	p.R35R	GLTSCR2_ENST00000598681.1_3'UTR	NM_015710.4	NP_056525.2	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	35						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)		CCCAGCGCTGAGGCGGCGGCG	0.677																																					p.R35R	Colon(58;613 1041 9473 10089 15241)	Atlas-SNP	.											.	GLTSCR2	45	.	0			c.A103C						PASS	.						39	48	45					19																	48248919		2203	4300	6503	SO:0001819	synonymous_variant	29997	exon1			GCGCTGAGGCGGC	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.103A>C	chr19.hg19:g.48248919A>C		103.0	0.0	.		172.0	70.0	.	NM_015710	Q9BTC6|Q9HAX6|Q9NPP1|Q9NPR4|Q9UFI2	Silent	SNP	ENST00000246802.5	hg19	CCDS12705.1																																																																																			.	.	.	none		0.677	GLTSCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464870.1	NM_015710		C	48248919	A	C	48248919	2	2	33	1	0	0	0	0	0	0	0	1	6482	295	11	5		5	GLTSCR2	19	48248919	Silent	SNP	A	TCGA-5P-A9K2-01A-11D-A42J-10	3782018	48248919	10880064	73	2443											
CNOT3	4849	hgsc.bcm.edu	37	chr19	54652449	54652449	+	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	caggccttgggccccccttcCggcccccacaacccacctcc	5	5	7	24	1	0	0	0	0	0	0	2	0	2	0	10	3	1	0	10	3	1	2			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr19:54652449C>G	ENST00000406403.1	+	11	2980	c.1377C>G	c.(1375-1377)tcC>tcG	p.S459S	CNOT3_ENST00000358389.3_Silent_p.S278S|CNOT3_ENST00000221232.5_Silent_p.S459S			O75175	CNOT3_HUMAN	CCR4-NOT transcription complex, subunit 3	459	Pro-rich.				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)					GCCCCCCTTCCGGCCCCCACA	0.652																																					p.S459S		Atlas-SNP	.											.	CNOT3	133	.	0			c.C1377G						PASS	.						20	23	22					19																	54652449		2203	4299	6502	SO:0001819	synonymous_variant	4849	exon12			CCCTTCCGGCCCC	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.1377C>G	chr19.hg19:g.54652449C>G		107.0	0.0	.		155.0	61.0	.	NM_014516	Q9NZN7|Q9UF76	Silent	SNP	ENST00000406403.1	hg19	CCDS12880.1																																																																																			.	.	.	none		0.652	CNOT3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142130.3	NM_014516		G	54652449	C	G	54652449	2	3	33	1	0	0	0	0	0	0	0	1	3622	639	23	4		4	CNOT3	19	54652449	Silent	SNP	C	TCGA-5P-A9K2-01A-11D-A42J-10	6403530	54652449	4476534	74	2444											
TTYH1	57348	hgsc.bcm.edu	37	chr19	54930303	54930303	+	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	atgtcacccccttccccaggCcttgttgctggtggcggcct	3	11	11	16	1	1	0	1	0	0	0	2	0	2	0	6	4	1	2	6	4	0	3			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr19:54930303C>A	ENST00000376530.3	+	2	231	c.128C>A	c.(127-129)gCc>gAc	p.A43D	TTYH1_ENST00000301194.4_Splice_Site_p.A43D|TTYH1_ENST00000376531.3_Splice_Site_p.A43D|TTYH1_ENST00000391739.3_Splice_Site_p.A92D	NM_001201461.1|NM_020659.3	NP_001188390.1|NP_065710.1	Q9H313	TTYH1_HUMAN	tweety family member 1	43					cell-substrate adhesion (GO:0031589)|chloride transport (GO:0006821)|filopodium assembly (GO:0046847)|ion transmembrane transport (GO:0034220)|iron ion transmembrane transport (GO:0034755)|iron ion transport (GO:0006826)|mitotic nuclear division (GO:0007067)|regulation of anion transport (GO:0044070)|single organismal cell-cell adhesion (GO:0016337)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|filopodium membrane (GO:0031527)|filopodium tip (GO:0032433)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum membrane (GO:0030868)	calcium ion binding (GO:0005509)|iron ion transmembrane transporter activity (GO:0005381)|volume-sensitive chloride channel activity (GO:0072320)			endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0767)		CTTCCCCAGGCCTTGTTGCTG	0.662																																					p.A43D		Atlas-SNP	.											.	TTYH1	78	.	0			c.C128A						PASS	.						77	81	80					19																	54930303		2203	4299	6502	SO:0001630	splice_region_variant	57348	exon2			CCCAGGCCTTGTT	AF177909	CCDS12893.1, CCDS33106.1, CCDS56102.1	19q13.4	2013-09-02	2013-09-02		ENSG00000167614	ENSG00000167614			13476	protein-coding gene	gene with protein product		605784	"tweety (Drosophila) homolog 1", "tweety homolog 1 (Drosophila)"			10950931	Standard	NM_020659		Approved		uc002qfr.3	Q9H313	OTTHUMG00000065544	ENST00000376530.3:c.127-1C>A	chr19.hg19:g.54930303C>A		35.0	0.0	.		56.0	19.0	.	NM_020659	B0VJY3|B0VJY4|B0VJY5|B2VAL9|Q5U682|Q68A17|Q6L750|Q6ZTE5|Q8WUU2	Missense_Mutation	SNP	ENST00000376530.3	hg19	CCDS12893.1	.	.	.	.	.	.	.	.	.	.	C	18.15	3.560585	0.65538	.	.	ENSG00000167614	ENST00000444661;ENST00000423529;ENST00000301194;ENST00000376530;ENST00000445095;ENST00000391739;ENST00000376531	T;T;T;T;T;T	0.14022	2.54;2.54;2.54;2.54;2.54;2.54	3.5	2.45	0.29901	.	0.078315	0.51477	D	0.000087	T	0.28001	0.0690	L	0.55990	1.75	0.42190	D	0.99172	D;D;D;D	0.89917	0.995;1.0;1.0;0.999	D;D;D;D	0.87578	0.912;0.998;0.998;0.997	T	0.01566	-1.1323	10	0.72032	D	0.01	-17.3171	8.7249	0.34463	0.0:0.8838:0.0:0.1162	.	92;43;43;43	B7Z1H9;Q9H313-2;Q9H313-3;Q9H313	.;.;.;TTYH1_HUMAN	D	15;39;43;43;92;92;43	ENSP00000391282:A39D;ENSP00000301194:A43D;ENSP00000365713:A43D;ENSP00000393592:A92D;ENSP00000375619:A92D;ENSP00000365714:A43D	ENSP00000301194:A43D	A	+	2	0	TTYH1	59622115	1.000000	0.71417	1.000000	0.80357	0.552000	0.35366	5.153000	0.64888	0.818000	0.34468	0.555000	0.69702	GCC	.	.	.	none		0.662	TTYH1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140498.1		Missense_Mutation	A	54930303	C	A	54930303	5	1	33	1	0	0	0	0	0	0	1	0	16751	753	26	4	134	4	TTYH1	19	54930303	Splice_Site	SNP	C	TCGA-5P-A9K2-01A-11D-A42J-10	277854	54930303	4198680	75	2445											
GZF1	64412	hgsc.bcm.edu	37	chr20	23345062	23345062	+	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	ctggaatccaaatcctccccAtttaacctactgcatgagat	12	11	5	13	0	0	1	0	1	0	1	3	3	3	2	5	1	3	1	5	1	4	3			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr20:23345062A>C	ENST00000338121.5	+	2	119	c.42A>C	c.(40-42)ccA>ccC	p.P14P	GZF1_ENST00000544236.1_Intron|GZF1_ENST00000542987.1_Intron|GZF1_ENST00000377051.2_Silent_p.P14P			Q9H116	GZF1_HUMAN	GDNF-inducible zinc finger protein 1	14					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)					AATCCTCCCCATTTAACCTAC	0.478																																					p.P14P		Atlas-SNP	.											.	GZF1	61	.	0			c.A42C						PASS	.						86	89	88					20																	23345062		2203	4300	6503	SO:0001819	synonymous_variant	64412	exon1			CTCCCCATTTAAC	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.42A>C	chr20.hg19:g.23345062A>C		33.0	0.0	.		40.0	29.0	.	NM_022482	A8K199|B2RBC3|B3KPL4|B4DF58|D3DW39|Q54A22|Q96N08|Q9BQK9|Q9H117|Q9H6W6	Silent	SNP	ENST00000338121.5	hg19	CCDS13151.1																																																																																			.	.	.	none		0.478	GZF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078333.1	NM_022482		C	23345062	A	C	23345062	2	2	33	1	0	0	0	0	0	0	0	1	6921	204	8	5		5	GZF1	20	23345062	Silent	SNP	A	TCGA-5P-A9K2-01A-11D-A42J-10		23345062	39680458	76	2446											
PRIC285	85441	hgsc.bcm.edu	37	chr20	62200744	62200744	+	Frame_Shift_Del	DEL	T	T	-																															cagggtggccgagcgccagaTtcctgcagggtcctgggcga																										TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr20:62200744delT	ENST00000467148.1	-	4	914	c.845delA	c.(844-846)aatfs	p.N282fs	HELZ2_ENST00000479540.1_5'Flank|HELZ2_ENST00000427522.2_5'Flank	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	282					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)										GAGCGCCAGATTCCTGCAGGG	0.682																																					p.N282fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.846delT						PASS	.						19	23	22					20																	62200744		2190	4297	6487	SO:0001589	frameshift_variant	85441	exon5			.	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.845delA	chr20.hg19:g.62200744delT	ENSP00000417401:p.Asn282fs	51.0	0.0	0		80.0	44.0	0.55	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Frame_Shift_Del	DEL	ENST00000467148.1	hg19	CCDS33508.1																																																																																			.	.	.	none		0.682	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		-	62200744	T	-	62200744	7	5	33	1	0	1	0	1	0	0	0	0	12495	1493	52	0	7191	0	PRIC285	20	62200744	Frame_Shift_Del	DEL	T	TCGA-5P-A9K2-01A-11D-A42J-10	38855682	62200744	824776	77	2447											
ZGPAT	84619	hgsc.bcm.edu	37	chr20	62365029	62365029	+	Missense_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	cggcatcctgcccccactgcGcacagaggccacagagtccg	8	4	11	18	3	0	2	0	0	0	2	2	2	2	2	5	2	2	2	5	2	0	0	rs376773744		TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr20:62365029G>A	ENST00000328969.5	+	4	936	c.809G>A	c.(808-810)cGc>cAc	p.R270H	ZGPAT_ENST00000355969.6_Missense_Mutation_p.R270H|ZGPAT_ENST00000357119.4_Missense_Mutation_p.R270H|LIME1_ENST00000309546.3_5'Flank|ZGPAT_ENST00000369967.3_Missense_Mutation_p.R270H|ZGPAT_ENST00000448100.2_Missense_Mutation_p.R270H|RP4-583P15.15_ENST00000490623.2_Missense_Mutation_p.A176T|ZGPAT_ENST00000478385.1_3'UTR	NM_032527.4	NP_115916.3	Q8N5A5	ZGPAT_HUMAN	zinc finger, CCCH-type with G patch domain	270					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)					CCCCCACTGCGCACAGAGGCC	0.637																																					p.R270H		Atlas-SNP	.											.	ZGPAT	57	.	0			c.G809A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	110	106	108		809,809,809,809,809	4.7	0.6	20		108	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	ZGPAT	NM_001083113.1,NM_001195653.1,NM_001195654.1,NM_032527.4,NM_181485.2	29,29,29,29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	270/512,270/512,270/503,270/532,270/512	62365029	1,13005	2203	4300	6503	SO:0001583	missense	84619	exon4			CACTGCGCACAGA	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.809G>A	chr20.hg19:g.62365029G>A	ENSP00000332013:p.Arg270His	40.0	0.0	.		73.0	48.0	.	NM_032527	E1P5K1|Q4VXN9|Q5JWI9|Q5JWJ0|Q8NC55|Q8WUV4|Q96JI0|Q96JU4|Q9H401	Missense_Mutation	SNP	ENST00000328969.5	hg19	CCDS13534.1	.	.	.	.	.	.	.	.	.	.	G	37	6.080234	0.97267	0.0	1.16E-4	ENSG00000197114	ENST00000448100;ENST00000355969;ENST00000357119;ENST00000369967;ENST00000328969	T;T;T;T;T	0.24538	1.88;1.88;1.85;1.88;1.86	5.65	4.7	0.59300	.	0.050728	0.85682	N	0.000000	T	0.48750	0.1517	M	0.76328	2.33	0.46901	D	0.999241	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.44528	-0.9322	10	0.30854	T	0.27	-4.7504	12.8179	0.57675	0.0758:0.0:0.9242:0.0	.	270;270;270	Q8N5A5-3;Q8N5A5;Q8N5A5-2	.;ZGPAT_HUMAN;.	H	270	ENSP00000391176:R270H;ENSP00000348242:R270H;ENSP00000349634:R270H;ENSP00000358984:R270H;ENSP00000332013:R270H	ENSP00000332013:R270H	R	+	2	0	ZGPAT	61835473	1.000000	0.71417	0.555000	0.28281	0.949000	0.60115	6.831000	0.75324	1.387000	0.46486	0.591000	0.81541	CGC	.	.	.	weak		0.637	ZGPAT-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080214.1	NM_181484		A	62365029	G	A	62365029	3	1	33	1	0	0	0	0	1	0	0	0	17686	1087	38	1	819	1	ZGPAT	20	62365029	Missense_Mutation	SNP	G	TCGA-5P-A9K2-01A-11D-A42J-10	164285	62365029	660491	78	2448											
C20orf135	140701	hgsc.bcm.edu	37	chr20	62494129	62494129	+	Frame_Shift_Del	DEL	G	G	-																															gaagaggagctggagggcgaGgaggccctggggccacacgg																										TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr20:62494129delG	ENST00000369916.3	+	1	1564	c.1236delG	c.(1234-1236)gagfs	p.E413fs	C20ORF135_ENST00000601296.1_5'Flank|TPD52L2_ENST00000346249.4_5'Flank|TPD52L2_ENST00000369927.4_5'Flank|TPD52L2_ENST00000348257.5_5'Flank|TPD52L2_ENST00000351424.4_5'Flank|TPD52L2_ENST00000352482.4_5'Flank|TPD52L2_ENST00000358548.4_5'Flank|TPD52L2_ENST00000217121.5_5'Flank	NM_080622.3	NP_542189.1	Q9H3Z7	ABHGB_HUMAN	abhydrolase domain containing 16B	413							hydrolase activity (GO:0016787)			endometrium(2)|kidney(1)|lung(3)	6						TGGAGGGCGAGGAGGCCCTGG	0.721																																					p.E412fs		Atlas-Indel,Pindel	.											.	ABHD16B	22	.	0			c.1235delA						PASS	.						11	10	11					20																	62494129		1954	3816	5770	SO:0001589	frameshift_variant	140701	exon1			.		CCDS13539.1	20q13.33	2013-01-17	2010-12-09	2010-12-09	ENSG00000183260	ENSG00000183260		"Abhydrolase domain containing"	16128	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 135"	C20orf135			Standard	NM_080622		Approved	dJ591C20.1	uc002ygx.1	Q9H3Z7	OTTHUMG00000033010	ENST00000369916.3:c.1236delG	chr20.hg19:g.62494129delG	ENSP00000358932:p.Glu413fs	26.0	0.0	0		39.0	17.0	0.435897	NM_080622		Frame_Shift_Del	DEL	ENST00000369916.3	hg19	CCDS13539.1																																																																																			.	.	.	none		0.721	ABHD16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080254.1			-	62494129	G	-	62494129	7	5	33	1	0	1	0	1	0	0	0	0	2090	991	35	0	1238	0	C20orf135	20	62494129	Frame_Shift_Del	DEL	G	TCGA-5P-A9K2-01A-11D-A42J-10	129100	62494129	531391	79	2449											
ADARB1	104	hgsc.bcm.edu	37	chr21	46603314	46603314	+	Missense_Mutation	SNP	T	T	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	aaagatccatctttcagaaaTcagagcgaggggggtttagg	13	9	13	6	1	3	3	2	0	1	3	4	4	4	3	1	4	1	1	1	4	3	3			TCGA-5P-A9K2-01A-11D-A42J-10	TCGA-5P-A9K2-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13f52db0-17b0-499c-ab9f-dd9c49a5ee2d	59a2e838-4559-4580-8f5f-07db42390e4d	g.chr21:46603314T>G	ENST00000360697.3	+	5	1300	c.1285T>G	c.(1285-1287)Tca>Gca	p.S429A	ADARB1_ENST00000348831.4_Missense_Mutation_p.S429A|ADARB1_ENST00000539173.1_Missense_Mutation_p.S429A|ADARB1_ENST00000437626.1_3'UTR|ADARB1_ENST00000389863.4_Missense_Mutation_p.S429A			P78563	RED1_HUMAN	adenosine deaminase, RNA-specific, B1	429	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				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)			endometrium(4)|kidney(1)|large_intestine(3)|lung(8)|skin(1)	17				Colorectal(79;0.115)		CTTTCAGAAATCAGAGCGAGG	0.393																																					p.S429A		Atlas-SNP	.											.	ADARB1	81	.	0			c.T1285G						PASS	.						56	59	58					21																	46603314		2203	4300	6503	SO:0001583	missense	104	exon7			CAGAAATCAGAGC	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.1285T>G	chr21.hg19:g.46603314T>G	ENSP00000353920:p.Ser429Ala	51.0	0.0	.		43.0	19.0	.	NM_001160230	A6NFK8|A6NJ84|C3TTQ1|C3TTQ2|C9JUP4|G5E9B4|O00395|O00465|O00691|O00692|P78555|Q4AE79|Q6P0M9|Q8NFD1	Missense_Mutation	SNP	ENST00000360697.3	hg19	CCDS33589.1	.	.	.	.	.	.	.	.	.	.	T	14.41	2.525933	0.44969	.	.	ENSG00000197381	ENST00000539173;ENST00000539917;ENST00000389863;ENST00000348831;ENST00000360697	D;D;D;D	0.93307	-3.2;-3.2;-3.2;-3.2	5.63	5.63	0.86233	Adenosine deaminase/editase (3);	0.115843	0.64402	D	0.000012	D	0.84754	0.5542	N	0.11201	0.11	0.80722	D	1	B;B;B;B	0.18310	0.027;0.005;0.008;0.004	B;B;B;B	0.24269	0.038;0.052;0.045;0.022	T	0.79995	-0.1568	10	0.07325	T	0.83	-28.2484	14.0959	0.65021	0.0:0.0:0.0:1.0	.	429;429;457;429	P78563;Q4AE77;G5E9B4;P78563-3	RED1_HUMAN;.;.;.	A	429	ENSP00000441897:S429A;ENSP00000374513:S429A;ENSP00000015877:S429A;ENSP00000353920:S429A	ENSP00000015877:S429A	S	+	1	0	ADARB1	45427742	1.000000	0.71417	0.850000	0.33497	0.990000	0.78478	5.882000	0.69714	2.279000	0.76181	0.533000	0.62120	TCA	.	.	.	none		0.393	ADARB1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206648.2	NM_015833		G	46603314	T	G	46603314	3	3	33	1	0	0	0	0	1	0	0	0	282	1435	50	5	1303	5	ADARB1	21	46603314	Missense_Mutation	SNP	T	TCGA-5P-A9K2-01A-11D-A42J-10		46603314	1526581	80	2450											
PLEKHG5	57449	hgsc.bcm.edu	37	chr1	6529206	6529206	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcctcctcctcctcctcCtcttcctcctcctgctcatc	1	15	1	24	0	2	0	1	0	1	0	13	0	12	0	10	0	1	1	10	0	0	1			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr1:6529206C>T	ENST00000400915.3	-	20	2379	c.2313G>A	c.(2311-2313)gaG>gaA	p.E771E	PLEKHG5_ENST00000377725.1_Silent_p.E715E|PLEKHG5_ENST00000537245.1_Silent_p.E794E|PLEKHG5_ENST00000377740.3_Silent_p.E792E|TNFRSF25_ENST00000377782.3_5'Flank|PLEKHG5_ENST00000340850.5_Silent_p.E715E|PLEKHG5_ENST00000377732.1_Silent_p.E752E|PLEKHG5_ENST00000377748.1_Silent_p.E792E|PLEKHG5_ENST00000400913.1_Silent_p.E715E|PLEKHG5_ENST00000377728.3_Silent_p.E715E|PLEKHG5_ENST00000377737.2_Silent_p.E715E|PLEKHG5_ENST00000544978.1_Silent_p.E715E|TNFRSF25_ENST00000351959.5_5'Flank|TNFRSF25_ENST00000356876.3_5'Flank|PLEKHG5_ENST00000535355.1_Silent_p.E784E	NM_001042663.1	NP_001036128.1	O94827	PKHG5_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 5	771	Glu-rich.				apoptotic signaling pathway (GO:0097190)|endothelial cell chemotaxis (GO:0035767)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			liver(1)	1	Ovarian(185;0.02)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;5.51e-35)|GBM - Glioblastoma multiforme(13;3.57e-27)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419)		cctcctcctcctcttcctcct	0.637																																					p.E794E		Atlas-SNP	.											PLEKHG5_ENST00000377748,colon,carcinoma,0,1	PLEKHG5	66	.	0			c.G2382A						PASS	.						75	76	76					1																	6529206		2203	4300	6503	SO:0001819	synonymous_variant	57449	exon20			CTCCTCCTCTTCC	AK024676	CCDS79.1, CCDS41240.1, CCDS41241.1, CCDS57967.1, CCDS57968.1, CCDS57969.1	1p36.31	2014-09-17		2005-08-09	ENSG00000171680	ENSG00000171680		"Pleckstrin homology (PH) domain containing"	29105	protein-coding gene	gene with protein product	"synectin-binding guanine exchange factor"	611101				17564964	Standard	NM_001042663		Approved	KIAA0720, Syx, GEF720, Tech	uc010nzr.1	O94827	OTTHUMG00000000905	ENST00000400915.3:c.2313G>A	chr1.hg19:g.6529206C>T		30.0	1.0	.		28.0	5.0	.	NM_001265592	B3KU07|B7Z2M3|B7Z5X2|F5GZ21|F5H1I0|Q5SY17|Q5T8W5|Q5T8W9|Q6ZNM0|Q7Z436|Q86YD8|Q96BS1	Silent	SNP	ENST00000400915.3	hg19	CCDS41241.1																																																																																			.	.	.	none		0.637	PLEKHG5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002631.1	NM_020631		T	6529206	C	T	6529206	2	4	34	1	0	0	0	0	0	0	0	1	12080	680	24	2		2	PLEKHG5	1	6529206	Silent	SNP	C	TCGA-5P-A9K3-01A-11D-A42J-10		6529206	242721415	1	2451											
GBP2	2634	hgsc.bcm.edu	37	chr1	89587538	89587538	+	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	cacaatcgccaccaccaccaCaggctgcgtaattgcagata	13	6	7	15	2	0	1	0	0	0	1	1	1	0	1	4	1	2	3	4	1	3	3			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr1:89587538C>G	ENST00000370466.3	-	2	380	c.112G>C	c.(112-114)Gtg>Ctg	p.V38L	GBP2_ENST00000463660.1_5'Flank	NM_004120.3	NP_004111.2	P32456	GBP2_HUMAN	guanylate binding protein 2, interferon-inducible	38	GB1/RHD3-type G.|GTPase domain (Globular). {ECO:0000250}.				cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(1)	20		Lung NSC(277;0.0908)		all cancers(265;0.0151)|Epithelial(280;0.0284)		ACCACCACCACAGGCTGCGTA	0.522																																					p.V38L		Atlas-SNP	.											.	GBP2	58	.	0			c.G112C						PASS	.						162	146	151					1																	89587538		2203	4300	6503	SO:0001583	missense	2634	exon2			CCACCACAGGCTG	BC073163	CCDS719.1	1p22.2	2008-02-05			ENSG00000162645	ENSG00000162645			4183	protein-coding gene	gene with protein product		600412				1715024	Standard	NM_004120		Approved		uc001dmz.1	P32456	OTTHUMG00000010662	ENST00000370466.3:c.112G>C	chr1.hg19:g.89587538C>G	ENSP00000359497:p.Val38Leu	83.0	0.0	.		77.0	60.0	.	NM_004120	Q6GPH0|Q6IAU2|Q86TB0	Missense_Mutation	SNP	ENST00000370466.3	hg19	CCDS719.1	.	.	.	.	.	.	.	.	.	.	C	12.90	2.075367	0.36662	.	.	ENSG00000162645	ENST00000370466	T	0.79033	-1.23	3.43	2.48	0.30137	Guanylate-binding protein, N-terminal (1);	0.099287	0.38837	U	0.001553	T	0.56001	0.1956	L	0.46670	1.46	0.25639	N	0.986223	B	0.27316	0.175	B	0.33339	0.162	T	0.53358	-0.8450	10	0.44086	T	0.13	-12.4763	10.4347	0.44428	0.0:0.7988:0.2012:0.0	.	38	P32456	GBP2_HUMAN	L	38	ENSP00000359497:V38L	ENSP00000359497:V38L	V	-	1	0	GBP2	89360126	0.602000	0.26916	0.012000	0.15200	0.166000	0.22503	1.376000	0.34306	0.730000	0.32425	0.491000	0.48974	GTG	.	.	.	none		0.522	GBP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029406.2	NM_004120		G	89587538	C	G	89587538	3	3	34	1	0	0	0	0	1	0	0	0	6281	478	17	4	1703	4	GBP2	1	89587538	Missense_Mutation	SNP	C	TCGA-5P-A9K3-01A-11D-A42J-10	83058332	89587538	159663083	2	2452											
HMCN1	83872	hgsc.bcm.edu	37	chr1	186072734	186072734	+	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	tggatgaaagatggccggccCcttccacagacggatcaagt	11	7	12	11	2	1	3	1	1	0	2	2	5	2	5	4	4	0	0	4	4	2	1			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr1:186072734C>G	ENST00000271588.4	+	69	10933	c.10704C>G	c.(10702-10704)ccC>ccG	p.P3568P	HMCN1_ENST00000367492.2_Silent_p.P3568P	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3568	Ig-like C2-type 34.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						ATGGCCGGCCCCTTCCACAGA	0.428																																					p.P3568P		Atlas-SNP	.											.	HMCN1	797	.	0			c.C10704G						PASS	.						69	72	71					1																	186072734		2203	4299	6502	SO:0001819	synonymous_variant	83872	exon69			CCGGCCCCTTCCA	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.10704C>G	chr1.hg19:g.186072734C>G		103.0	0.0	.		133.0	66.0	.	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.	.	none		0.428	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		G	186072734	C	G	186072734	2	3	34	1	0	0	0	0	0	0	0	1	7227	610	22	4		4	HMCN1	1	186072734	Silent	SNP	C	TCGA-5P-A9K3-01A-11D-A42J-10	96485196	186072734	63177887	3	2453											
KCNT2	343450	hgsc.bcm.edu	37	chr1	196448320	196448320	+	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	ataacttaccttataactaaGataaccaagtaatattgttt	17	15	3	6	0	0	1	0	0	0	1	0	1	0	1	2	0	4	2	2	0	9	10			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr1:196448320G>C	ENST00000294725.9	-	5	1288	c.373C>G	c.(373-375)Ctt>Gtt	p.L125V	KCNT2_ENST00000367433.5_Missense_Mutation_p.L125V|KCNT2_ENST00000609185.1_Missense_Mutation_p.L125V|KCNT2_ENST00000367431.4_Missense_Mutation_p.L125V|KCNT2_ENST00000451324.2_De_novo_Start_OutOfFrame			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	125					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						TTATAACTAAGATAACCAAGT	0.299																																					p.L125V		Atlas-SNP	.											KCNT2,NS,carcinoma,0,1	KCNT2	243	.	0			c.C373G						PASS	.						52	52	52					1																	196448320		2200	4299	6499	SO:0001583	missense	343450	exon5			AACTAAGATAACC	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.373C>G	chr1.hg19:g.196448320G>C	ENSP00000294725:p.Leu125Val	458.0	0.0	.		549.0	196.0	.	NM_198503	Q3SY59|Q5VTN1|Q6ZMT3	Missense_Mutation	SNP	ENST00000294725.9	hg19	CCDS1384.1	.	.	.	.	.	.	.	.	.	.	G	14.98	2.696345	0.48202	.	.	ENSG00000162687	ENST00000367433;ENST00000367431;ENST00000294725	T;T;T	0.21191	2.02;2.08;2.28	5.06	4.14	0.48551	.	0.000000	0.53938	D	0.000047	T	0.35508	0.0934	M	0.79343	2.45	0.80722	D	1	P;P;P;P	0.45634	0.739;0.83;0.863;0.739	B;P;P;B	0.51324	0.443;0.646;0.666;0.443	T	0.03423	-1.1038	10	0.41790	T	0.15	-12.8857	11.2789	0.49181	0.0906:0.0:0.9094:0.0	.	125;125;125;125	A9LNM6;Q6UVM3-2;Q6UVM3-3;Q6UVM3	.;.;.;KCNT2_HUMAN	V	125	ENSP00000356403:L125V;ENSP00000356401:L125V;ENSP00000294725:L125V	ENSP00000294725:L125V	L	-	1	0	KCNT2	194714943	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.775000	0.62346	2.791000	0.96007	0.591000	0.81541	CTT	.	.	.	none		0.299	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503		C	196448320	G	C	196448320	3	2	34	1	0	0	0	0	1	0	0	0	8099	942	33	4	3130	4	KCNT2	1	196448320	Missense_Mutation	SNP	G	TCGA-5P-A9K3-01A-11D-A42J-10	10375586	196448320	52802301	4	2454											
BTG2	7832	hgsc.bcm.edu	37	chr1	203276494	203276495	+	Frame_Shift_Ins	INS	-	-	A																															ccgcctcctgtgggctcctcINSacctgcaagaaccaagtgct																										TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr1:203276494_203276495insA	ENST00000290551.4	+	2	476_477	c.405_406insA	c.(406-408)accfs	p.T136fs	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	136					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)			GTGGGCTCCTCACCTGCAAGAA	0.668																																					p.L135fs		Atlas-Indel,Pindel	.											.	BTG2	16	.	0			c.405_406insA						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.406dupA	chr1.hg19:g.203276495_203276495dupA	ENSP00000290551:p.Thr136fs	55.0	0.0	0		85.0	22.0	0.258824	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Frame_Shift_Ins	INS	ENST00000290551.4	hg19	CCDS1437.1																																																																																			.	.	.	none		0.668	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		A	203276495	-	A	203276494	7	5	34	1	0	1	1	0	0	0	0	0	1556	813	29	0	411	0	BTG2	1	203276494	Frame_Shift_Ins	INS	-	TCGA-5P-A9K3-01A-11D-A42J-10	6828174	203276494	45974127	5	2455											
BPNT1	10380	hgsc.bcm.edu	37	chr1	220232335	220232335	+	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	atggatatcggttaacttgcCtatagaaaaacatcaatcaa	17	11	6	7	1	2	1	2	0	0	1	3	2	2	2	1	2	3	1	1	2	8	5			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr1:220232335C>G	ENST00000469520.2	-	10	1228		c.e10-1		BPNT1_ENST00000322067.7_Splice_Site|BPNT1_ENST00000544404.1_Splice_Site|BPNT1_ENST00000414869.2_Splice_Site|BPNT1_ENST00000354807.3_Splice_Site			O95861	BPNT1_HUMAN	3'(2'), 5'-bisphosphate nucleotidase 1						3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|dephosphorylation (GO:0016311)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|phosphatidylinositol phosphorylation (GO:0046854)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3'(2'),5'-bisphosphate nucleotidase activity (GO:0008441)|inositol-1,4-bisphosphate 1-phosphatase activity (GO:0004441)|magnesium ion binding (GO:0000287)			breast(1)|endometrium(1)|large_intestine(1)|lung(9)|ovary(1)|skin(1)	14				GBM - Glioblastoma multiforme(131;0.0558)		GTTAACTTGCCTATAGAAAAA	0.383																																					.		Atlas-SNP	.											.	BPNT1	29	.	0			c.779-1G>C						PASS	.						116	107	110					1																	220232335		1899	4122	6021	SO:0001630	splice_region_variant	10380	exon10			ACTTGCCTATAGA	AF125042	CCDS41469.1, CCDS65787.1, CCDS65788.1	1q42	2008-02-05			ENSG00000162813	ENSG00000162813	3.1.3.7		1096	protein-coding gene	gene with protein product		604053				10224133	Standard	XM_005272998		Approved		uc001hma.3	O95861	OTTHUMG00000037435	ENST00000469520.2:c.779-1G>C	chr1.hg19:g.220232335C>G		42.0	0.0	.		70.0	15.0	.	NM_006085	A8K7C8|B4DPS5|B4DUS9|D3DTA9|Q8WVL5|Q9UGJ3	Splice_Site	SNP	ENST00000469520.2	hg19	CCDS41469.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.621110	0.87460	.	.	ENSG00000162813	ENST00000322067;ENST00000469520;ENST00000354807;ENST00000302686;ENST00000544404;ENST00000414869	.	.	.	5.28	5.28	0.74379	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.28	0.94050	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	BPNT1	218298958	1.000000	0.71417	0.997000	0.53966	0.974000	0.67602	7.682000	0.84083	2.643000	0.89663	0.555000	0.69702	.	.	.	.	none		0.383	BPNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091137.2	NM_006085	Intron	G	220232335	C	G	220232335	5	3	34	1	0	0	0	0	0	0	1	0	1496	695	24	4	152	4	BPNT1	1	220232335	Splice_Site	SNP	C	TCGA-5P-A9K3-01A-11D-A42J-10	16955841	220232335	29018286	6	2456											
SETD2	29072	hgsc.bcm.edu	37	chr3	47079260	47079260	+	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	ccaagtaggaggatcccactGagtctgcctagaaagagaca	14	6	11	10	0	1	3	0	1	1	2	2	6	2	5	3	2	1	1	3	2	4	2			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr3:47079260G>A	ENST00000409792.3	-	18	7288	c.7246C>T	c.(7246-7248)Cag>Tag	p.Q2416*		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2416	WW. {ECO:0000255|PROSITE- ProRule:PRU00224}.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		GGATCCCACTGAGTCTGCCTA	0.458			"N, F, S, Mis"		clear cell renal carcinoma																																p.Q2416X		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	SETD2_ENST00000409792,NS,carcinoma,0,2	SETD2	721	.	0			c.C7246T						PASS	.						100	88	92					3																	47079260		2203	4300	6503	SO:0001587	stop_gained	29072	exon18			CCCACTGAGTCTG	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.7246C>T	chr3.hg19:g.47079260G>A	ENSP00000386759:p.Gln2416*	63.0	0.0	.		31.0	18.0	.	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Nonsense_Mutation	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	G	48	14.016458	0.99775	.	.	ENSG00000181555	ENST00000451092;ENST00000409792	.	.	.	5.93	5.93	0.95920	.	0.000000	0.52532	D	0.000061	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	20.3539	0.98825	0.0:0.0:1.0:0.0	.	.	.	.	X	2416	.	ENSP00000386759:Q2416X	Q	-	1	0	SETD2	47054264	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.717000	0.98755	2.826000	0.97356	0.655000	0.94253	CAG	.	.	.	none		0.458	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		A	47079260	G	A	47079260	4	1	34	1	0	0	0	0	0	1	0	0	14144	1299	45	2	464	2	SETD2	3	47079260	Nonsense_Mutation	SNP	G	TCGA-5P-A9K3-01A-11D-A42J-10		47079260	150943170	7	2457											
PBRM1	55193	hgsc.bcm.edu	37	chr3	52613184	52613184	+	Frame_Shift_Del	DEL	T	T	-																															agtggcaacctggttcaccaTtggacatttccacagggaca																								rs373854321		TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr3:52613184delT	ENST00000296302.7	-	21	3420	c.3419delA	c.(3418-3420)aatfs	p.N1140fs	PBRM1_ENST00000394830.3_Frame_Shift_Del_p.N1115fs|PBRM1_ENST00000409767.1_Frame_Shift_Del_p.N1155fs|PBRM1_ENST00000410007.1_Frame_Shift_Del_p.N1115fs|SMIM4_ENST00000476842.1_3'UTR|PBRM1_ENST00000356770.4_Frame_Shift_Del_p.N1108fs|PBRM1_ENST00000337303.4_Frame_Shift_Del_p.N1140fs|PBRM1_ENST00000409114.3_Frame_Shift_Del_p.N1155fs|PBRM1_ENST00000409057.1_Frame_Shift_Del_p.N1140fs			Q86U86	PB1_HUMAN	polybromo 1	1140					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)	p.N1140fs*19(2)|p.N1108fs*19(1)		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)		TGGTTCACCATTGGACATTTC	0.443			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.N1115fs		Atlas-Indel,Pindel	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	3	Deletion - Frameshift(3)	kidney(3)	c.3345delT						PASS	.						165	141	149					3																	52613184		2203	4300	6503	SO:0001589	frameshift_variant	55193	exon22			.	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.3419delA	chr3.hg19:g.52613184delT	ENSP00000296302:p.Asn1140fs	75.0	0.0	0		82.0	61.0	0.743902	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Frame_Shift_Del	DEL	ENST00000296302.7	hg19																																																																																				.	.	.	none		0.443	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		-	52613184	T	-	52613184	7	5	34	1	0	1	0	1	0	0	0	0	11498	1493	52	0	1521	0	PBRM1	3	52613184	Frame_Shift_Del	DEL	T	TCGA-5P-A9K3-01A-11D-A42J-10	5533924	52613184	145409246	8	2458											
COL6A6	131873	hgsc.bcm.edu	37	chr3	130290142	130290142	+	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	ggagctgttagccatggcagGatcaagcgacaagtacttct	11	9	12	9	1	2	0	1	0	1	0	2	3	2	2	1	3	4	4	1	3	4	3			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr3:130290142G>A	ENST00000358511.6	+	6	2913	c.2882G>A	c.(2881-2883)gGa>gAa	p.G961E	COL6A6_ENST00000453409.2_Missense_Mutation_p.G961E	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	961	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						GCCATGGCAGGATCAAGCGAC	0.498																																					p.G961E		Atlas-SNP	.											.	COL6A6	497	.	0			c.G2882A						PASS	.						52	50	51					3																	130290142		1978	4174	6152	SO:0001583	missense	131873	exon6			TGGCAGGATCAAG	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.2882G>A	chr3.hg19:g.130290142G>A	ENSP00000351310:p.Gly961Glu	146.0	0.0	.		177.0	63.0	.	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	hg19	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	G	16.07	3.018725	0.54576	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.78364	-1.17;-1.17	4.82	4.82	0.62117	von Willebrand factor, type A (3);	0.000000	0.53938	D	0.000046	T	0.78604	0.4309	M	0.80508	2.5	0.30392	N	0.780931	P	0.47484	0.896	P	0.44394	0.448	T	0.79662	-0.1710	10	0.41790	T	0.15	.	10.0767	0.42364	0.132:0.0:0.868:0.0	.	961	A6NMZ7	CO6A6_HUMAN	E	961	ENSP00000351310:G961E;ENSP00000399236:G961E	ENSP00000351310:G961E	G	+	2	0	COL6A6	131772832	1.000000	0.71417	0.763000	0.31416	0.909000	0.53808	4.785000	0.62418	2.403000	0.81681	0.561000	0.74099	GGA	.	.	.	none		0.498	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		A	130290142	G	A	130290142	3	1	34	1	0	0	0	0	1	0	0	0	3705	1174	41	2	2904	2	COL6A6	3	130290142	Missense_Mutation	SNP	G	TCGA-5P-A9K3-01A-11D-A42J-10	77676958	130290142	67732288	9	2459											
NLGN1	22871	hgsc.bcm.edu	37	chr3	173997169	173997169	+	Frame_Shift_Del	DEL	T	T	-																															gaaagacattactggctttgTttacggaccatcagtgggtg																										TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr3:173997169delT	ENST00000457714.1	+	6	1807	c.1378delT	c.(1378-1380)tttfs	p.F460fs	NLGN1_ENST00000361589.4_Frame_Shift_Del_p.F460fs|NLGN1_ENST00000401917.3_Frame_Shift_Del_p.F500fs|NLGN1_ENST00000545397.1_Frame_Shift_Del_p.F460fs	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	477					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)			ACTGGCTTTGTTTACGGACCA	0.448																																					p.L459fs		Atlas-Indel,Pindel	.											NLGN1,NS,carcinoma,0,1	NLGN1	209	.	0			c.1377delG						PASS	.						97	93	95					3																	173997169		2203	4300	6503	SO:0001589	frameshift_variant	22871	exon6			.	AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.1378delT	chr3.hg19:g.173997169delT	ENSP00000392500:p.Phe460fs	153.0	0.0	0		180.0	50.0	0.277778	NM_014932	Q9UPT2	Frame_Shift_Del	DEL	ENST00000457714.1	hg19	CCDS3222.1																																																																																			.	.	.	none		0.448	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932		-	173997169	T	-	173997169	7	5	34	1	0	1	0	1	0	0	0	0	10468	1725	60	0	1392	0	NLGN1	3	173997169	Frame_Shift_Del	DEL	T	TCGA-5P-A9K3-01A-11D-A42J-10	43707027	173997169	24025261	10	2460											
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178916725	178916725	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tagtgactttagaatgcctcCgtgaggctacattaataacc	12	12	8	9	1	0	3	0	2	0	1	1	3	1	3	3	1	3	1	3	1	6	6			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr3:178916725C>T	ENST00000263967.3	+	2	269	c.112C>T	c.(112-114)Cgt>Tgt	p.R38C		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	38	PI3K-ABD. {ECO:0000255|PROSITE- ProRule:PRU00877}.		R -> H (in CRC; likely involved in disease pathogenesis; shows an increase in lipid kinase activity; may disrupt the interaction between the PI3K-ABD domain and the N-terminal lobe of PI3K/PI4K kinase domain possibly affecting the conformation of the kinase domain).		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.R38G(1)|p.R38S(1)|p.R38C(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)	AGAATGCCTCCGTGAGGCTAC	0.393		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.R38C	Colon(199;1504 1750 3362 26421 31210 32040)	Atlas-SNP	.		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	PIK3CA_ENST00000263967,caecum,carcinoma,0,17	PIK3CA	8460	.	3	Substitution - Missense(3)	large_intestine(1)|stomach(1)|central_nervous_system(1)	c.C112T						PASS	.						76	74	75					3																	178916725		1845	4085	5930	SO:0001583	missense	5290	exon2			TGCCTCCGTGAGG		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.112C>T	chr3.hg19:g.178916725C>T	ENSP00000263967:p.Arg38Cys	158.0	0.0	.		265.0	137.0	.	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	hg19	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	C	19.88	3.909863	0.72983	.	.	ENSG00000121879	ENST00000263967;ENST00000468036	T;T	0.73363	-0.74;-0.74	5.44	5.44	0.79542	Phosphatidylinositol 3-kinase, p85-binding (2);	0.000000	0.85682	D	0.000000	D	0.84019	0.5380	L	0.56199	1.76	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.82665	-0.0345	9	.	.	.	-9.214	19.2635	0.93977	0.0:1.0:0.0:0.0	.	38	P42336	PK3CA_HUMAN	C	38	ENSP00000263967:R38C;ENSP00000417479:R38C	.	R	+	1	0	PIK3CA	180399419	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.642000	0.67888	2.547000	0.85894	0.555000	0.69702	CGT	.	.	.	none		0.393	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			T	178916725	C	T	178916725	3	4	34	1	0	0	0	0	1	0	0	0	11920	652	23	1	114	1	PIK3CA	3	178916725	Missense_Mutation	SNP	C	TCGA-5P-A9K3-01A-11D-A42J-10	4919556	178916725	19105705	11	2461											
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-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr3:178936082G>A	ENST00000263967.3	+	10	1781	c.1624G>A	c.(1624-1626)Gaa>Aaa	p.E542K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	542	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> K (in CLOVE, KERSEB, CRC and BC; also found in glioblastoma multiforme and endometrial carcinoma; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N- terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|E -> Q (found in an endometrial carcinoma sample; unknown pathological significance). {ECO:0000269|PubMed:16322209}.|E -> V (in BC; unknown pathological significance). {ECO:0000269|PubMed:16353168}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E542K(545)|p.E542Q(10)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TCCTCTCTCTGAAATCACTGA	0.333	E542K(BT483_BREAST)|E542K(CAL51_BREAST)|E542K(HGC27_STOMACH)|E542K(IM95_STOMACH)|E542K(JHUEM1_ENDOMETRIUM)|E542K(NCIH1341_LUNG)|E542K(SW948_LARGE_INTESTINE)|E542K(T84_LARGE_INTESTINE)|E542K(VMCUB1_URINARY_TRACT)	57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.E542K	Colon(199;1504 1750 3362 26421 31210 32040)	Atlas-SNP	.		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	PIK3CA_ENST00000263967,NS,carcinoma,0,2	PIK3CA	8460	.	555	Substitution - Missense(555)	breast(176)|large_intestine(166)|urinary_tract(45)|endometrium(37)|skin(19)|lung(18)|stomach(16)|ovary(16)|thyroid(14)|upper_aerodigestive_tract(9)|central_nervous_system(7)|cervix(6)|liver(6)|oesophagus(5)|penis(4)|kidney(3)|soft_tissue(2)|haematopoietic_and_lymphoid_tissue(2)|prostate(2)|biliary_tract(1)|pituitary(1)	c.G1624A						PASS	.						56	56	56					3																	178936082		1809	4069	5878	SO:0001583	missense	5290	exon10			CTCTCTGAAATCA		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1624G>A	chr3.hg19:g.178936082G>A	ENSP00000263967:p.Glu542Lys	360.0	1.0	.		542.0	259.0	.	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	hg19	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	34	5.360420	0.95877	.	.	ENSG00000121879	ENST00000263967	T	0.62105	0.05	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69287	0.3094	L	0.41356	1.27	0.80722	D	1	D	0.65815	0.995	D	0.63192	0.912	T	0.60296	-0.7291	10	0.09843	T	0.71	-23.9623	20.0024	0.97423	0.0:0.0:1.0:0.0	.	542	P42336	PK3CA_HUMAN	K	542	ENSP00000263967:E542K	ENSP00000263967:E542K	E	+	1	0	PIK3CA	180418776	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAA	.	.	.	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	34	1	0	0	0	0	1	0	0	0	11920	1291	45	2	1658	2	PIK3CA	3	178936082	Missense_Mutation	SNP	G	TCGA-5P-A9K3-01A-11D-A42J-10	19357	178936082	19086348	12	2462											
ADD1	118	hgsc.bcm.edu	37	chr4	2930015	2930015	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cggcttcccaatgttagagaAggaggaggaagcccatagac	13	6	13	9	1	0	2	0	0	0	2	1	6	1	5	2	4	1	2	2	4	5	3			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr4:2930015A>G	ENST00000398129.1	+	14	1999	c.1979A>G	c.(1978-1980)aAg>aGg	p.K660R	ADD1_ENST00000398125.1_3'UTR|ADD1_ENST00000503455.2_3'UTR|ADD1_ENST00000264758.7_Missense_Mutation_p.K691R|ADD1_ENST00000513328.2_3'UTR|ADD1_ENST00000355842.3_3'UTR|ADD1_ENST00000446856.1_Missense_Mutation_p.K660R|ADD1_ENST00000398123.2_3'UTR			P35611	ADDA_HUMAN	adducin 1 (alpha)	660					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)		ATGTTAGAGAAGGAGGAGGAA	0.607																																					p.K691R	Esophageal Squamous(71;505 1201 20414 34538 37449)	Atlas-SNP	.											.	ADD1	56	.	0			c.A2072G						PASS	.						96	113	107					4																	2930015		2203	4300	6503	SO:0001583	missense	118	exon15			TAGAGAAGGAGGA	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.1979A>G	chr4.hg19:g.2930015A>G	ENSP00000381197:p.Lys660Arg	178.0	0.0	.		102.0	47.0	.	NM_014189	A2A3N8|A2A3P0|B4DI79|D3DVR3|D3DVR4|D3DVR5|Q13734|Q14729|Q16156|Q86XM2|Q9UJB6	Missense_Mutation	SNP	ENST00000398129.1	hg19	CCDS43205.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	4.319|4.319	0.058597|0.058597	0.08339|0.08339	.|.	.|.	ENSG00000087274|ENSG00000087274	ENST00000264758;ENST00000446856;ENST00000398129|ENST00000514940	T;T;T|.	0.06294|.	3.32;3.36;3.36|.	4.9|4.9	0.371|0.371	0.16168|0.16168	.|.	1.249810|.	0.05914|.	N|.	0.632241|.	T|T	0.23249|0.23249	0.0562|0.0562	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	1|1	B;B|.	0.17038|.	0.012;0.02|.	B;B|.	0.16289|.	0.007;0.015|.	T|T	0.27706|0.27706	-1.0066|-1.0066	10|5	0.08837|.	T|.	0.75|.	-1.4542|-1.4542	6.947|6.947	0.24524|0.24524	0.6262:0.1198:0.0:0.254|0.6262:0.1198:0.0:0.254	.|.	660;691|.	P35611;P35611-3|.	ADDA_HUMAN;.|.	R|G	691;660;660|397	ENSP00000264758:K691R;ENSP00000399828:K660R;ENSP00000381197:K660R|.	ENSP00000264758:K691R|.	K|R	+|+	2|1	0|2	ADD1|ADD1	2899813|2899813	1.000000|1.000000	0.71417|0.71417	0.003000|0.003000	0.11579|0.11579	0.266000|0.266000	0.26442|0.26442	3.998000|3.998000	0.57024|0.57024	-0.114000|-0.114000	0.11936|0.11936	0.533000|0.533000	0.62120|0.62120	AAG|AGG	.	.	.	none		0.607	ADD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242840.1	NM_014189		G	2930015	A	G	2930015	3	3	34	1	0	0	0	0	1	0	0	0	304	72	3	3	2164	3	ADD1	4	2930015	Missense_Mutation	SNP	A	TCGA-5P-A9K3-01A-11D-A42J-10		2930015	188224261	13	2463											
PKD2	5311	hgsc.bcm.edu	37	chr4	88929118	88929118	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcggcctccccttctcctcCgctctcgtcgtgctcccggc	0	10	9	22	6	2	0	0	0	2	0	8	0	5	0	6	2	1	2	6	2	0	1			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr4:88929118C>T	ENST00000237596.2	+	1	299	c.233C>T	c.(232-234)cCg>cTg	p.P78L		NM_000297.3	NP_000288.1	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)		CCTTCTCCTCCGCTCTCGTCG	0.731																																					p.P78L		Atlas-SNP	.											.	PKD2	82	.	0			c.C233T						PASS	.						1	1	1					4																	88929118		872	2057	2929	SO:0001583	missense	5311	exon1			CTCCTCCGCTCTC	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	ENST00000237596.2:c.233C>T	chr4.hg19:g.88929118C>T	ENSP00000237596:p.Pro78Leu	333.0	0.0	.		245.0	140.0	.	NM_000297	Q8TB08|Q9P0T6|Q9Y3X8	Missense_Mutation	SNP	ENST00000237596.2	hg19	CCDS3627.1	.	.	.	.	.	.	.	.	.	.	C	16.46	3.130467	0.56828	.	.	ENSG00000118762	ENST00000237596	D	0.82167	-1.58	2.77	1.9	0.25705	.	0.000000	0.64402	U	0.000001	T	0.68137	0.2968	L	0.36672	1.1	0.80722	D	1	P	0.51240	0.943	B	0.32149	0.141	T	0.66960	-0.5791	10	0.87932	D	0	-7.5048	9.3789	0.38301	0.0:0.7799:0.2201:0.0	.	78	Q13563	PKD2_HUMAN	L	78	ENSP00000237596:P78L	ENSP00000237596:P78L	P	+	2	0	PKD2	89148142	1.000000	0.71417	0.333000	0.25482	0.349000	0.29174	3.011000	0.49567	0.331000	0.23511	0.313000	0.20887	CCG	.	.	.	none		0.731	PKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253042.4	NM_000297		T	88929118	C	T	88929118	3	4	34	1	0	0	0	0	1	0	0	0	11973	652	23	1	235	1	PKD2	4	88929118	Missense_Mutation	SNP	C	TCGA-5P-A9K3-01A-11D-A42J-10	85999103	88929118	102225158	14	2464											
CASP6	839	hgsc.bcm.edu	37	chr4	110624544	110624544	+	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	ccctgcggagccccgaggccGagctcattgcagccaaacgc	8	4	12	17	4	1	0	1	0	0	0	1	3	1	1	5	2	6	2	5	2	1	1	rs376919922		TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr4:110624544G>C	ENST00000265164.2	-	1	85	c.8C>G	c.(7-9)tCg>tGg	p.S3W	CASP6_ENST00000352981.3_Missense_Mutation_p.S3W|CASP6_ENST00000505486.1_Missense_Mutation_p.S3W	NM_001226.3	NP_001217.2	P55212	CASP6_HUMAN	caspase 6, apoptosis-related cysteine peptidase	3					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|epithelial cell differentiation (GO:0030855)|proteolysis (GO:0006508)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|identical protein binding (GO:0042802)			breast(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	8		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000171)		CCCCGAGGCCGAGCTCATTGC	0.726																																					p.S3W		Atlas-SNP	.											.	CASP6	25	.	0			c.C8G						PASS	.						24	30	28					4																	110624544		2201	4296	6497	SO:0001583	missense	839	exon1			GAGGCCGAGCTCA	U20536	CCDS3684.1, CCDS3685.1	4q25	2008-02-05	2005-08-17		ENSG00000138794	ENSG00000138794		"Caspases"	1507	protein-coding gene	gene with protein product		601532	"caspase 6, apoptosis-related cysteine protease"			8780721, 7796396	Standard	XM_005263271		Approved	MCH2	uc003hzn.1	P55212	OTTHUMG00000131914	ENST00000265164.2:c.8C>G	chr4.hg19:g.110624544G>C	ENSP00000265164:p.Ser3Trp	251.0	0.0	.		227.0	135.0	.	NM_001226	Q9BQE7	Missense_Mutation	SNP	ENST00000265164.2	hg19	CCDS3684.1	.	.	.	.	.	.	.	.	.	.	G	11.08	1.533971	0.27387	.	.	ENSG00000138794	ENST00000352981;ENST00000265164;ENST00000505486	T;T;T	0.54071	3.64;4.26;0.59	2.22	1.36	0.22044	.	3.831530	0.01273	U	0.009503	T	0.40067	0.1102	L	0.29908	0.895	0.09310	N	0.999992	P;P	0.48640	0.913;0.627	B;B	0.38880	0.284;0.257	T	0.38714	-0.9648	10	0.66056	D	0.02	.	4.5637	0.12172	0.1898:0.0:0.8102:0.0	.	3;3	P55212-2;P55212	.;CASP6_HUMAN	W	3	ENSP00000285333:S3W;ENSP00000265164:S3W;ENSP00000424080:S3W	ENSP00000265164:S3W	S	-	2	0	CASP6	110843993	0.870000	0.30015	0.140000	0.22221	0.018000	0.09664	2.136000	0.42121	0.497000	0.27926	0.484000	0.47621	TCG	.	.	.	alt		0.726	CASP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254866.1	NM_001226		C	110624544	G	C	110624544	3	2	34	1	0	0	0	0	1	0	0	0	2677	1059	37	4	901	4	CASP6	4	110624544	Missense_Mutation	SNP	G	TCGA-5P-A9K3-01A-11D-A42J-10	21695426	110624544	80529732	15	2465											
GIN1	54826	hgsc.bcm.edu	37	chr5	102423700	102423700	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatcaatggagagattttcgTatttctatattctaatagtt	12	19	6	4	1	3	1	1	0	2	1	4	3	3	2	0	1	0	2	0	1	7	11			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr5:102423700T>C	ENST00000399004.2	-	8	1565	c.1471A>G	c.(1471-1473)Acg>Gcg	p.T491A	GIN1_ENST00000508629.1_3'UTR	NM_017676.2	NP_060146.2	Q9NXP7	GIN1_HUMAN	gypsy retrotransposon integrase 1	491					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)		GAGATTTTCGTATTTCTATAT	0.343																																					p.T491A		Atlas-SNP	.											.	GIN1	53	.	0			c.A1471G						PASS	.						113	105	108					5																	102423700		1833	4086	5919	SO:0001583	missense	54826	exon8			TTTTCGTATTTCT	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.1471A>G	chr5.hg19:g.102423700T>C	ENSP00000381970:p.Thr491Ala	71.0	0.0	.		74.0	27.0	.	NM_017676	B2RXF7|B4DIV4|Q6AI03|Q96BR2	Missense_Mutation	SNP	ENST00000399004.2	hg19	CCDS43349.1	.	.	.	.	.	.	.	.	.	.	T	3.219	-0.159979	0.06502	.	.	ENSG00000145723	ENST00000399004	T	0.15718	2.4	5.64	-3.05	0.05396	.	1.062550	0.07572	N	0.918705	T	0.04407	0.0121	N	0.03608	-0.345	0.48452	D	0.99965	B	0.02656	0.0	B	0.01281	0.0	T	0.51926	-0.8643	10	0.05351	T	0.99	-28.7686	1.0916	0.01664	0.2638:0.3554:0.1004:0.2803	.	491	Q9NXP7	GIN1_HUMAN	A	491	ENSP00000381970:T491A	ENSP00000381970:T491A	T	-	1	0	GIN1	102451599	0.005000	0.15991	0.872000	0.34217	0.230000	0.25150	-0.560000	0.05964	-0.199000	0.10317	-0.366000	0.07423	ACG	.	.	.	none		0.343	GIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370478.3	NM_017676		C	102423700	T	C	102423700	3	2	34	1	0	0	0	0	1	0	0	0	6393	1638	57	3	101	3	GIN1	5	102423700	Missense_Mutation	SNP	T	TCGA-5P-A9K3-01A-11D-A42J-10		102423700	78491560	16	2466											
ANKS1A	23294	hgsc.bcm.edu	37	chr6	35047434	35047434	+	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	tgaagaacctctgggagctaGagctcgtcaatgtgagtagt	11	10	13	7	1	2	4	1	2	1	2	3	5	2	5	1	1	3	3	1	1	5	2			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr6:35047434G>A	ENST00000360359.3	+	15	2563	c.2425G>A	c.(2425-2427)Gag>Aag	p.E809K	ANKS1A_ENST00000535627.1_Intron|ANKS1A_ENST00000470698.1_3'UTR	NM_015245.2	NP_056060.2	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1A	809	SAM 2. {ECO:0000255|PROSITE- ProRule:PRU00184}.				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						CTGGGAGCTAGAGCTCGTCAA	0.607																																					p.E809K		Atlas-SNP	.											.	ANKS1A	123	.	0			c.G2425A						PASS	.						72	69	70					6																	35047434		2203	4300	6503	SO:0001583	missense	23294	exon15			GAGCTAGAGCTCG	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.2425G>A	chr6.hg19:g.35047434G>A	ENSP00000353518:p.Glu809Lys	64.0	0.0	.		83.0	36.0	.	NM_015245	A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7	Missense_Mutation	SNP	ENST00000360359.3	hg19	CCDS4798.1	.	.	.	.	.	.	.	.	.	.	G	34	5.398429	0.96030	.	.	ENSG00000064999	ENST00000360359;ENST00000373990	T	0.52754	0.65	5.17	5.17	0.71159	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.000000	0.49916	D	0.000138	T	0.65647	0.2711	M	0.76328	2.33	0.80722	D	1	P;D;D	0.76494	0.865;0.995;0.999	P;D;D	0.85130	0.541;0.976;0.997	T	0.69573	-0.5109	10	0.87932	D	0	-26.8262	19.1108	0.93315	0.0:0.0:1.0:0.0	.	135;135;809	Q49AR9;E7EM84;Q92625	.;.;ANS1A_HUMAN	K	809;135	ENSP00000353518:E809K	ENSP00000353518:E809K	E	+	1	0	ANKS1A	35155412	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	9.717000	0.98755	2.573000	0.86826	0.556000	0.70494	GAG	.	.	.	none		0.607	ANKS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040262.1	XM_166478		A	35047434	G	A	35047434	3	1	34	1	0	0	0	0	1	0	0	0	688	943	33	2	2483	2	ANKS1A	6	35047434	Missense_Mutation	SNP	G	TCGA-5P-A9K3-01A-11D-A42J-10		35047434	136067633	17	2467											
DNAH8	1769	hgsc.bcm.edu	37	chr6	38919137	38919137	+	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	tttttcaagcaagaaagtatAttgcagattctttggaggag	13	14	10	4	0	2	2	1	0	1	2	2	4	2	4	0	2	2	3	0	2	5	7			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr6:38919137A>T	ENST00000359357.3	+	80	11895	c.11641A>T	c.(11641-11643)Att>Ttt	p.I3881F	RP1-207H1.3_ENST00000416948.1_RNA|DNAH8_ENST00000449981.2_Missense_Mutation_p.I4098F|DNAH8_ENST00000441566.1_Missense_Mutation_p.I3845F			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	3881	AAA 6. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|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						AAGAAAGTATATTGCAGATTC	0.378																																					p.I4098F		Atlas-SNP	.											.	DNAH8	1239	.	0			c.A12292T						PASS	.						134	142	139					6																	38919137		2203	4300	6503	SO:0001583	missense	1769	exon82			AAGTATATTGCAG	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.11641A>T	chr6.hg19:g.38919137A>T	ENSP00000352312:p.Ile3881Phe	120.0	0.0	.		131.0	55.0	.	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	A	20.3	3.970636	0.74246	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.12984	2.63;2.63;2.63	5.6	4.41	0.53225	Dynein heavy chain (1);	0.162449	0.52532	D	0.000067	T	0.43942	0.1270	H	0.98612	4.28	0.58432	D	0.999999	D;D	0.71674	0.997;0.998	D;D	0.72625	0.962;0.978	T	0.65100	-0.6250	10	0.87932	D	0	.	12.1872	0.54245	0.8718:0.0:0.0:0.1282	.	3845;3881	Q96JB1-2;Q96JB1	.;DYH8_HUMAN	F	4086;4086;3881;3845	ENSP00000333363:I4086F;ENSP00000352312:I3881F;ENSP00000402294:I3845F	ENSP00000333363:I4086F	I	+	1	0	DNAH8	39027115	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	6.045000	0.71020	1.027000	0.39758	0.533000	0.62120	ATT	.	.	.	none		0.378	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		T	38919137	A	T	38919137	3	4	34	1	0	0	0	0	1	0	0	0	4609	449	16	5	11951	5	DNAH8	6	38919137	Missense_Mutation	SNP	A	TCGA-5P-A9K3-01A-11D-A42J-10	3871703	38919137	132195930	18	2468											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51524419	51524419	+	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	agacgtgggggctctggagcTcatggtagaatacagccaag	11	7	15	8	1	2	2	1	0	1	2	2	3	2	3	1	4	3	3	1	4	4	2			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr6:51524419T>A	ENST00000371117.3	-	61	10780	c.10505A>T	c.(10504-10506)gAg>gTg	p.E3502V		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3502			E -> V (in ARPKD). {ECO:0000269|PubMed:12846734}.		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)					GCTCTGGAGCTCATGGTAGAA	0.443																																					p.E3502V		Atlas-SNP	.											.	PKHD1	927	.	0			c.A10505T	GRCh37	CM032337	PKHD1	M		PASS	.						64	65	64					6																	51524419		2203	4300	6503	SO:0001583	missense	5314	exon61			TGGAGCTCATGGT	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.10505A>T	chr6.hg19:g.51524419T>A	ENSP00000360158:p.Glu3502Val	107.0	0.0	.		138.0	58.0	.	NM_138694	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	T	17.90	3.502052	0.64298	.	.	ENSG00000170927	ENST00000371117	D	0.86366	-2.11	5.72	5.72	0.89469	.	0.080901	0.52532	D	0.000070	D	0.84995	0.5596	L	0.32530	0.975	0.80722	D	1	D	0.76494	0.999	D	0.71414	0.973	D	0.84626	0.0687	10	0.30854	T	0.27	.	11.2211	0.48855	0.0:0.0:0.1531:0.8469	.	3502	P08F94	PKHD1_HUMAN	V	3502	ENSP00000360158:E3502V	ENSP00000360158:E3502V	E	-	2	0	PKHD1	51632378	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	3.238000	0.51352	2.177000	0.69029	0.533000	0.62120	GAG	.	.	.	none		0.443	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51524419	T	A	51524419	3	1	34	1	0	0	0	0	1	0	0	0	11978	1551	54	5	1747	5	PKHD1	6	51524419	Missense_Mutation	SNP	T	TCGA-5P-A9K3-01A-11D-A42J-10	12605282	51524419	119590648	19	2469											
ZNF92	168374	hgsc.bcm.edu	37	chr7	64863907	64863907	+	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	gtgaagaatgtggcaaggccTttaaccagttctcgattctt	10	13	10	8	1	2	2	0	1	2	1	3	3	2	2	2	2	1	2	2	2	4	5			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr7:64863907T>A	ENST00000328747.7	+	4	1079	c.880T>A	c.(880-882)Ttt>Att	p.F294I	ZNF92_ENST00000450302.2_Missense_Mutation_p.F225I|ZNF92_ENST00000431504.1_Missense_Mutation_p.F218I|ZNF92_ENST00000357512.2_Missense_Mutation_p.F262I	NM_152626.2	NP_689839.1	Q03936	ZNF92_HUMAN	zinc finger protein 92	294					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(3)|lung(4)|pancreas(1)|skin(1)|stomach(1)	13		Lung NSC(55;0.159)				TGGCAAGGCCTTTAACCAGTT	0.358																																					p.F294I		Atlas-SNP	.											.	ZNF92	68	.	0			c.T880A						PASS	.						33	37	36					7																	64863907		2198	4290	6488	SO:0001583	missense	168374	exon4			AAGGCCTTTAACC	M61872	CCDS34646.1, CCDS47596.1, CCDS75608.1, CCDS75609.1	7q11.21	2013-01-08	2006-05-12		ENSG00000146757	ENSG00000146757		"Zinc fingers, C2H2-type", "-"	13168	protein-coding gene	gene with protein product		603974	"zinc finger protein 92 (HTF12)"			8467795	Standard	NM_001287533		Approved	HPF12, TF12	uc003ttz.3	Q03936	OTTHUMG00000156557	ENST00000328747.7:c.880T>A	chr7.hg19:g.64863907T>A	ENSP00000332595:p.Phe294Ile	78.0	0.0	.		103.0	46.0	.	NM_152626	A6NNF9|Q8N492|Q8NB35	Missense_Mutation	SNP	ENST00000328747.7	hg19	CCDS34646.1	.	.	.	.	.	.	.	.	.	.	T	15.03	2.711240	0.48517	.	.	ENSG00000146757	ENST00000328747;ENST00000431504;ENST00000357512;ENST00000450302	T;T;T;T	0.47528	0.87;0.84;0.84;0.84	0.427	0.427	0.16489	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.65091	0.2658	M	0.85373	2.75	0.34231	D	0.676527	D;D	0.89917	0.999;1.0	D;D	0.97110	0.932;1.0	T	0.69308	-0.5179	9	0.66056	D	0.02	.	5.1591	0.15050	0.0:1.0E-4:0.0:0.9999	.	262;294	Q03936-3;Q03936	.;ZNF92_HUMAN	I	294;218;262;225	ENSP00000332595:F294I;ENSP00000400495:F218I;ENSP00000350113:F262I;ENSP00000396126:F225I	ENSP00000332595:F294I	F	+	1	0	ZNF92	64501342	1.000000	0.71417	0.022000	0.16811	0.022000	0.10575	5.518000	0.67068	0.388000	0.25054	0.383000	0.25322	TTT	.	.	.	none		0.358	ZNF92-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344589.2	NM_152626		A	64863907	T	A	64863907	3	1	34	1	0	0	0	0	1	0	0	0	18213	1609	56	5	894	5	ZNF92	7	64863907	Missense_Mutation	SNP	T	TCGA-5P-A9K3-01A-11D-A42J-10		64863907	94274756	20	2470											
CYP51A1	1595	hgsc.bcm.edu	37	chr7	91755569	91755569	+	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	tatattctttatccatacctGaaactaggcaaaggcagcca	14	11	6	10	0	1	1	0	1	1	0	2	1	2	1	3	2	3	2	3	2	7	7			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr7:91755569G>T	ENST00000003100.8	-	5	933	c.768C>A	c.(766-768)ttC>ttA	p.F256L	CYP51A1_ENST00000450723.1_Missense_Mutation_p.F151L|LRRD1_ENST00000422722.1_5'UTR	NM_000786.3	NP_000777.1	Q16850	CP51A_HUMAN	cytochrome P450, family 51, subfamily A, polypeptide 1	250					cholesterol biosynthetic process (GO:0006695)|cholesterol biosynthetic process via 24,25-dihydrolanosterol (GO:0033488)|demethylation (GO:0070988)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|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)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|sterol 14-demethylase activity (GO:0008398)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|skin(1)	10	all_cancers(62;2.16e-09)|all_epithelial(64;3.86e-08)|Breast(17;0.00206)|all_lung(186;0.169)|all_hematologic(106;0.215)|Lung NSC(181;0.227)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)		Itraconazole(DB01167)|Ketoconazole(DB01026)|Sertaconazole(DB01153)|Tioconazole(DB01007)	ATCCATACCTGAAACTAGGCA	0.373																																					p.F256L	GBM(70;1100 1190 11592 25836 51397)	Atlas-SNP	.											.	CYP51A1	30	.	0			c.C768A						PASS	.						31	27	29					7																	91755569		2203	4299	6502	SO:0001583	missense	1595	exon5			ATACCTGAAACTA	U51685	CCDS5623.1, CCDS55123.1	7q21.2	2012-10-10	2003-02-14	2003-02-28	ENSG00000001630	ENSG00000001630		"Cytochrome P450s"	2649	protein-coding gene	gene with protein product		601637	"cytochrome P450, 51 (lanosterol 14-alpha-demethylase)"	CYP51		8975714	Standard	NM_000786		Approved	CP51, CYPL1, P450L1, LDM, P450-14DM	uc003ulm.4	Q16850	OTTHUMG00000131131	ENST00000003100.8:c.768C>A	chr7.hg19:g.91755569G>T	ENSP00000003100:p.Phe256Leu	60.0	0.0	.		97.0	29.0	.	NM_000786	A4D1F8|B2RAI4|B4DJ55|O00770|O00772|Q16784|Q8N1A8|Q99868	Missense_Mutation	SNP	ENST00000003100.8	hg19	CCDS5623.1	.	.	.	.	.	.	.	.	.	.	G	36	5.667382	0.96745	.	.	ENSG00000001630	ENST00000003100;ENST00000496998;ENST00000450723	T;T	0.68025	-0.3;-0.3	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.81767	0.4892	M	0.83118	2.625	0.80722	D	1	P;P	0.51240	0.929;0.943	P;P	0.57776	0.712;0.827	T	0.82989	-0.0183	10	0.54805	T	0.06	.	19.6188	0.95647	0.0:0.0:1.0:0.0	.	196;250	B3KRC6;Q16850	.;CP51A_HUMAN	L	256;196;151	ENSP00000003100:F256L;ENSP00000406757:F151L	ENSP00000003100:F256L	F	-	3	2	CYP51A1	91593505	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.788000	0.99064	2.699000	0.92147	0.650000	0.86243	TTC	.	.	.	none		0.373	CYP51A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253812.4			T	91755569	G	T	91755569	3	4	34	1	0	0	0	0	1	0	0	0	4197	1281	45	4	785	4	CYP51A1	7	91755569	Missense_Mutation	SNP	G	TCGA-5P-A9K3-01A-11D-A42J-10	26891662	91755569	67383094	21	2471											
TRIM4	89122	hgsc.bcm.edu	37	chr7	99516791	99516791	+	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	cccgggggcacggggcccagGcgccggcgctgcgtcttctc	2	5	17	17	6	2	0	0	0	2	0	3	0	2	0	3	6	1	2	3	6	0	1			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr7:99516791G>A	ENST00000355947.2	-	1	363	c.234C>T	c.(232-234)cgC>cgT	p.R78R	TRIM4_ENST00000354241.5_Silent_p.R78R|TRIM4_ENST00000349062.2_Silent_p.R78R	NM_033017.3	NP_148977.2	Q9C037	TRIM4_HUMAN	tripartite motif containing 4	78					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)				CGGGGCCCAGGCGCCGGCGCT	0.751																																					p.R78R		Atlas-SNP	.											.	TRIM4	33	.	0			c.C234T						PASS	.						2	2	2					7																	99516791		1472	3021	4493	SO:0001819	synonymous_variant	89122	exon1			GCCCAGGCGCCGG	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.234C>T	chr7.hg19:g.99516791G>A		45.0	0.0	.		57.0	24.0	.	NM_033017	A4D298|Q75MK1|Q96F06|Q9C036	Silent	SNP	ENST00000355947.2	hg19	CCDS5679.1																																																																																			.	.	.	none		0.751	TRIM4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345050.1	NM_033017		A	99516791	G	A	99516791	2	1	34	1	0	0	0	0	0	0	0	1	16526	1190	42	2		2	TRIM4	7	99516791	Silent	SNP	G	TCGA-5P-A9K3-01A-11D-A42J-10	7761222	99516791	59621872	22	2472											
PARP12	64761	hgsc.bcm.edu	37	chr7	139762578	139762578	+	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	caagcggcgccgcagctcggGcaactccagggcgcccccgg	6	2	15	18	6	0	0	0	0	0	0	2	0	1	0	4	4	3	3	4	4	2	0	rs201640031	byFrequency	TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr7:139762578G>C	ENST00000263549.3	-	1	943	c.70C>G	c.(70-72)Ccc>Gcc	p.P24A		NM_022750.2	NP_073587.1	Q9H0J9	PAR12_HUMAN	poly (ADP-ribose) polymerase family, member 12	24						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)					CGCAGCTCGGGCAACTCCAGG	0.786													G|||	11	0.00219649	0	0.0072	5008	,	,		7612	0		0.006	False		,,,				2504	0				p.P24A		Atlas-SNP	.											.	PARP12	59	.	0			c.C70G						PASS	.						1	2	1					7																	139762578		1047	2218	3265	SO:0001583	missense	64761	exon1			GCTCGGGCAACTC	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.70C>G	chr7.hg19:g.139762578G>C	ENSP00000263549:p.Pro24Ala	0.0	0.0	.		5.0	4.0	.	NM_022750	Q9H610|Q9NP36|Q9NTI3	Missense_Mutation	SNP	ENST00000263549.3	hg19	CCDS5857.1	.	.	.	.	.	.	.	.	.	.	G	0.080	-1.186107	0.01620	.	.	ENSG00000059378	ENST00000263549	T	0.27720	1.65	3.29	-1.02	0.10135	.	0.997579	0.08113	N	0.995896	T	0.08582	0.0213	N	0.01048	-1.04	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35126	-0.9801	10	0.08599	T	0.76	.	6.7623	0.23548	0.0:0.5216:0.314:0.1644	.	24	Q9H0J9	PAR12_HUMAN	A	24	ENSP00000263549:P24A	ENSP00000263549:P24A	P	-	1	0	PARP12	139409047	0.008000	0.16893	0.000000	0.03702	0.001000	0.01503	0.832000	0.27490	-0.419000	0.07439	0.561000	0.74099	CCC	.	.	.	weak		0.786	PARP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348413.1	NM_022750		C	139762578	G	C	139762578	3	2	34	1	0	0	0	0	1	0	0	0	11464	1203	42	4	2083	4	PARP12	7	139762578	Missense_Mutation	SNP	G	TCGA-5P-A9K3-01A-11D-A42J-10	40245787	139762578	19376085	23	2473											
RNF19A	25897	hgsc.bcm.edu	37	chr8	101300044	101300044	+	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	caatttgtttgctgatggaaGttaatccattgtcagaagag	12	14	10	5	0	1	3	1	1	0	2	2	4	2	4	1	1	1	3	1	1	4	4			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr8:101300044G>C	ENST00000519449.1	-	3	675	c.359C>G	c.(358-360)aCt>aGt	p.T120S	RNF19A_ENST00000341084.2_Missense_Mutation_p.T120S	NM_001280539.1|NM_015435.3	NP_001267468.1|NP_056250.3	Q9NV58	RN19A_HUMAN	ring finger protein 19A, RBR E3 ubiquitin protein ligase	120					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)			GCTGATGGAAGTTAATCCATT	0.378																																					p.T120S		Atlas-SNP	.											.	RNF19A	67	.	0			c.C359G						PASS	.						112	112	112					8																	101300044		2203	4300	6503	SO:0001583	missense	25897	exon3			ATGGAAGTTAATC	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.359C>G	chr8.hg19:g.101300044G>C	ENSP00000428968:p.Thr120Ser	63.0	0.0	.		85.0	29.0	.	NM_015435	A3KCU9|Q52LG1|Q9H5H9|Q9H8M8|Q9UFG0|Q9UFX6|Q9Y4Y1	Missense_Mutation	SNP	ENST00000519449.1	hg19	CCDS6286.1	.	.	.	.	.	.	.	.	.	.	G	13.13	2.145412	0.37825	.	.	ENSG00000034677	ENST00000519449;ENST00000341084;ENST00000519527;ENST00000523167	D;D	0.82984	-1.67;-1.67	5.57	5.57	0.84162	.	0.287283	0.38005	N	0.001857	T	0.70237	0.3201	N	0.16478	0.41	0.41573	D	0.988693	B	0.02656	0.0	B	0.01281	0.0	T	0.64997	-0.6275	10	0.14656	T	0.56	.	14.8593	0.70366	0.0:0.0:0.8558:0.1442	.	120	Q9NV58	RN19A_HUMAN	S	120	ENSP00000428968:T120S;ENSP00000342667:T120S	ENSP00000342667:T120S	T	-	2	0	RNF19A	101369220	1.000000	0.71417	0.984000	0.44739	0.975000	0.68041	3.867000	0.56047	2.606000	0.88127	0.650000	0.86243	ACT	.	.	.	none		0.378	RNF19A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380004.1	NM_015435		C	101300044	G	C	101300044	3	2	34	1	0	0	0	0	1	0	0	0	13483	1029	36	4	2193	4	RNF19A	8	101300044	Missense_Mutation	SNP	G	TCGA-5P-A9K3-01A-11D-A42J-10		101300044	45063978	24	2474											
ZC3H3	23144	hgsc.bcm.edu	37	chr8	144522390	144522390	+	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	aggaagcgggaggggatgagGaggaggaggaggaggaggaa	14	1	25	1	1	0	1	0	1	0	0	0	11	0	11	0	11	1	0	0	11	2	0	rs267601811		TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr8:144522390G>T	ENST00000262577.5	-	11	2667	c.2636C>A	c.(2635-2637)tCc>tAc	p.S879Y		NM_015117.2	NP_055932.2	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3	879	Poly-Ser.				mRNA polyadenylation (GO:0006378)|poly(A)+ mRNA export from nucleus (GO:0016973)|regulation of mRNA export from nucleus (GO:0010793)	nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.S879F(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23	all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107)			aggggatgaggaggaggagga	0.657																																					p.S879Y		Atlas-SNP	.											ZC3H3,NS,malignant_melanoma,0,1	ZC3H3	75	.	1	Substitution - Missense(1)	skin(1)	c.C2636A						PASS	.						30	29	29					8																	144522390		2203	4298	6501	SO:0001583	missense	23144	exon11			GATGAGGAGGAGG	D63484	CCDS6402.1	8q24.3	2012-07-05	2005-06-02	2005-06-02	ENSG00000014164	ENSG00000014164		"Zinc fingers, CCCH-type domain containing"	28972	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 3"	ZC3HDC3		8590280	Standard	NM_015117		Approved	KIAA0150	uc003yyd.2	Q8IXZ2	OTTHUMG00000165127	ENST00000262577.5:c.2636C>A	chr8.hg19:g.144522390G>T	ENSP00000262577:p.Ser879Tyr	82.0	0.0	.		109.0	0.0	.	NM_015117	Q14163|Q8N4E2|Q9BUS4	Missense_Mutation	SNP	ENST00000262577.5	hg19	CCDS6402.1	.	.	.	.	.	.	.	.	.	.	G	16.95	3.263668	0.59431	.	.	ENSG00000014164	ENST00000262577	T	0.58210	0.35	4.04	4.04	0.47022	.	0.788333	0.10701	N	0.643991	T	0.45716	0.1356	L	0.27053	0.805	0.09310	N	1	P	0.50943	0.94	P	0.44860	0.462	T	0.37244	-0.9714	10	0.66056	D	0.02	-3.2232	12.9046	0.58145	0.0:0.0:1.0:0.0	.	879	Q8IXZ2	ZC3H3_HUMAN	Y	879	ENSP00000262577:S879Y	ENSP00000262577:S879Y	S	-	2	0	ZC3H3	144593533	0.025000	0.19082	0.006000	0.13384	0.122000	0.20287	2.137000	0.42130	1.831000	0.53308	0.467000	0.42956	TCC	.	.	.	none		0.657	ZC3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382011.2	NM_015117		T	144522390	G	T	144522390	3	4	34	1	0	0	0	0	1	0	0	0	17581	1174	41	4	218	4	ZC3H3	8	144522390	Missense_Mutation	SNP	G	TCGA-5P-A9K3-01A-11D-A42J-10	43222346	144522390	1841632	25	2475											
ZNF16	7564	hgsc.bcm.edu	37	chr8	146157588	146157588	+	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	accccctcatgaccagttagGtccacactgtgctggaaact	10	9	8	14	0	1	1	1	1	0	0	2	2	2	2	4	2	2	2	4	2	2	1			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr8:146157588G>A	ENST00000276816.4	-	4	771	c.585C>T	c.(583-585)gaC>gaT	p.D195D	ZNF16_ENST00000394909.2_Silent_p.D195D	NM_001029976.2	NP_001025147.2	P17020	ZNF16_HUMAN	zinc finger protein 16	195	Necessary for transcription activation.				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)		GACCAGTTAGGTCCACACTGT	0.493																																					p.D195D		Atlas-SNP	.											.	ZNF16	80	.	0			c.C585T						PASS	.						121	114	116					8																	146157588		2203	4300	6503	SO:0001819	synonymous_variant	7564	exon3			AGTTAGGTCCACA	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.585C>T	chr8.hg19:g.146157588G>A		76.0	0.0	.		87.0	37.0	.	NM_006958	B3KXM4|D3DWP2|Q45SH7|Q96FG0|Q9NRA4	Silent	SNP	ENST00000276816.4	hg19	CCDS6437.1																																																																																			.	.	.	none		0.493	ZNF16-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000382978.1	NM_006958		A	146157588	G	A	146157588	2	1	34	1	0	0	0	0	0	0	0	1	17750	1252	44	2		2	ZNF16	8	146157588	Silent	SNP	G	TCGA-5P-A9K3-01A-11D-A42J-10	1635198	146157588	206434	26	2476											
SECISBP2	79048	hgsc.bcm.edu	37	chr9	91961869	91961869	+	Frame_Shift_Del	DEL	C	C	-																															ccgcatgagtcaaatgaagaCcccgcacaatcccttggact																										TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr9:91961869delC	ENST00000375807.3	+	11	1579	c.1508delC	c.(1507-1509)accfs	p.T503fs	SECISBP2_ENST00000339901.4_Frame_Shift_Del_p.T430fs|SECISBP2_ENST00000534113.2_Frame_Shift_Del_p.T435fs	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	503					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						CAAATGAAGACCCCGCACAAT	0.552																																					p.T503fs		Atlas-Indel,Pindel	.											.	SECISBP2	64	.	0			c.1507delA						PASS	.						87	82	84					9																	91961869		2203	4300	6503	SO:0001589	frameshift_variant	79048	exon11			.	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.1508delC	chr9.hg19:g.91961869delC	ENSP00000364965:p.Thr503fs	63.0	0.0	0		95.0	27.0	0.284211	NM_024077	F8W892|Q5HYY1|Q8IYC0|Q9H0A1	Frame_Shift_Del	DEL	ENST00000375807.3	hg19	CCDS6683.1																																																																																			.	.	.	none		0.552	SECISBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052990.3	NM_024077		-	91961869	C	-	91961869	7	5	34	1	0	1	0	1	0	0	0	0	14019	507	18	0	1550	0	SECISBP2	9	91961869	Frame_Shift_Del	DEL	C	TCGA-5P-A9K3-01A-11D-A42J-10		91961869	49251562	27	2477											
C9orf172	389813	hgsc.bcm.edu	37	chr9	139741257	139741257	+	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	cccctgggcagctacgcgcgCgagctggcggccgctgggcg	3	4	18	16	7	0	0	0	0	0	0	0	1	0	0	3	4	3	4	3	4	1	1			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr9:139741257C>T	ENST00000436881.1	+	1	2391	c.2391C>T	c.(2389-2391)cgC>cgT	p.R797R	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	797										endometrium(2)|large_intestine(1)|lung(6)	9						GCTACGCGCGCGAGCTGGCGG	0.721																																					p.R797R		Atlas-SNP	.											.	C9orf172	23	.	0			c.C2391T						PASS	.						8	8	8					9																	139741257		1367	3002	4369	SO:0001819	synonymous_variant	389813	exon1			CGCGCGCGAGCTG		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.2391C>T	chr9.hg19:g.139741257C>T		49.0	0.0	.		33.0	12.0	.	NM_001080482		Silent	SNP	ENST00000436881.1	hg19	CCDS48059.1																																																																																			.	.	.	none		0.721	C9orf172-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080482		T	139741257	C	T	139741257	2	4	34	1	0	0	0	0	0	0	0	1	2473	755	27	1		1	C9orf172	9	139741257	Silent	SNP	C	TCGA-5P-A9K3-01A-11D-A42J-10	47779388	139741257	1472174	28	2478											
IDE	3416	hgsc.bcm.edu	37	chr10	94250353	94250353	+	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	atttagaaactatggcaaccCtagagatagaaaaaacaaac	21	7	6	7	0	0	3	0	0	0	3	0	4	0	3	1	1	4	1	1	1	10	5			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr10:94250353C>T	ENST00000265986.6	-	12	1487		c.e12-1		IDE_ENST00000496903.1_Splice_Site|IDE_ENST00000371581.5_Splice_Site	NM_004969.3	NP_004960.2	P14735	IDE_HUMAN	insulin-degrading enzyme						beta-amyloid metabolic process (GO:0050435)|bradykinin catabolic process (GO:0010815)|determination of adult lifespan (GO:0008340)|hormone catabolic process (GO:0042447)|insulin catabolic process (GO:1901143)|insulin metabolic process (GO:1901142)|insulin receptor signaling pathway (GO:0008286)|negative regulation of proteolysis (GO:0045861)|positive regulation of protein oligomerization (GO:0032461)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|ubiquitin homeostasis (GO:0010992)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|beta-amyloid binding (GO:0001540)|beta-endorphin binding (GO:0031626)|glycoprotein binding (GO:0001948)|insulin binding (GO:0043559)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|urinary_tract(2)	33					"""Insulin(DB00071)|Bacitracin(DB00626)|Insulin Regular(DB00030)"	TATGGCAACCCTAGAGATAGA	0.348																																					.		Atlas-SNP	.											IDE,colon,carcinoma,0,1	IDE	77	.	0			c.1431-1G>A						PASS	.						133	133	133					10																	94250353		2203	4300	6503	SO:0001630	splice_region_variant	3416	exon13			GCAACCCTAGAGA	M21188	CCDS7421.1, CCDS53554.1	10q23-q25	2007-03-27			ENSG00000119912	ENSG00000119912			5381	protein-coding gene	gene with protein product	"insulysin"	146680				2293021	Standard	NM_004969		Approved		uc001kia.3	P14735	OTTHUMG00000018759	ENST00000265986.6:c.1431-1G>A	chr10.hg19:g.94250353C>T		51.0	0.0	.		62.0	25.0	.	NM_004969	B2R721|B7ZAU2|D3DR35|Q5T5N2	Splice_Site	SNP	ENST00000265986.6	hg19	CCDS7421.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.195005	0.78902	.	.	ENSG00000119912	ENST00000265986	.	.	.	4.83	4.83	0.62350	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.803	0.88593	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	IDE	94240333	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	7.272000	0.78516	2.616000	0.88540	0.655000	0.94253	.	.	.	.	none		0.348	IDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049393.1	NM_004969	Intron	T	94250353	C	T	94250353	5	4	34	1	0	0	0	0	0	0	1	0	7500	695	24	2	1685	2	IDE	10	94250353	Splice_Site	SNP	C	TCGA-5P-A9K3-01A-11D-A42J-10		94250353	41284394	29	2479											
CNNM2	54805	hgsc.bcm.edu	37	chr10	104678741	104678741	+	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	cacatcattctcaaccgccgCacctcgggcatcatcgagat	10	8	7	16	4	3	1	3	0	1	1	6	2	3	1	3	1	1	2	3	1	1	1			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr10:104678741C>T	ENST00000369878.4	+	1	692	c.504C>T	c.(502-504)cgC>cgT	p.R168R	CNNM2_ENST00000433628.2_Silent_p.R168R|CNNM2_ENST00000369875.3_Silent_p.R168R	NM_017649.4	NP_060119.3	Q9H8M5	CNNM2_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 2	168					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)		TCAACCGCCGCACCTCGGGCA	0.642																																					p.R168R		Atlas-SNP	.											.	CNNM2	119	.	0			c.C504T						PASS	.						130	141	137					10																	104678741		2199	4299	6498	SO:0001819	synonymous_variant	54805	exon1			CCGCCGCACCTCG	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.504C>T	chr10.hg19:g.104678741C>T		128.0	0.0	.		160.0	59.0	.	NM_199076	Q5T569|Q5T570|Q8WU59|Q9H952|Q9NRK5|Q9NXT4	Silent	SNP	ENST00000369878.4	hg19	CCDS44474.1																																																																																			.	.	.	none		0.642	CNNM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050113.3	NM_017649		T	104678741	C	T	104678741	2	4	34	1	0	0	0	0	0	0	0	1	3615	697	25	2		2	CNNM2	10	104678741	Silent	SNP	C	TCGA-5P-A9K3-01A-11D-A42J-10	10428388	104678741	30856006	30	2480											
PDZD8	118987	hgsc.bcm.edu	37	chr10	119044221	119044221	+	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	tgattcccatgtttgacggtCgtccgaactgtccttagtag	7	14	10	10	3	0	2	0	2	0	0	4	3	3	2	3	1	1	2	3	1	3	4			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr10:119044221C>T	ENST00000334464.5	-	5	2262	c.2023G>A	c.(2023-2025)Gac>Aac	p.D675N	PDZD8_ENST00000482496.1_5'UTR	NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	675					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)		GTTTGACGGTCGTCCGAACTG	0.428																																					p.D675N		Atlas-SNP	.											.	PDZD8	85	.	0			c.G2023A						PASS	.						98	96	97					10																	119044221		2203	4300	6503	SO:0001583	missense	118987	exon5			GACGGTCGTCCGA	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.2023G>A	chr10.hg19:g.119044221C>T	ENSP00000334642:p.Asp675Asn	110.0	0.0	.		142.0	48.0	.	NM_173791	Q86WE0|Q86WE5|Q9UFF1	Missense_Mutation	SNP	ENST00000334464.5	hg19	CCDS7600.1	.	.	.	.	.	.	.	.	.	.	C	16.56	3.156972	0.57259	.	.	ENSG00000165650	ENST00000334464	D	0.88975	-2.45	5.87	5.87	0.94306	.	0.100838	0.64402	D	0.000002	D	0.91168	0.7218	L	0.32530	0.975	0.54753	D	0.999988	D	0.76494	0.999	P	0.61275	0.886	D	0.91308	0.5072	10	0.59425	D	0.04	-20.2619	20.2043	0.98273	0.0:1.0:0.0:0.0	.	675	Q8NEN9	PDZD8_HUMAN	N	675	ENSP00000334642:D675N	ENSP00000334642:D675N	D	-	1	0	PDZD8	119034211	1.000000	0.71417	1.000000	0.80357	0.370000	0.29829	5.774000	0.68906	2.779000	0.95612	0.591000	0.81541	GAC	.	.	.	none		0.428	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791		T	119044221	C	T	119044221	3	4	34	1	0	0	0	0	1	0	0	0	11712	884	31	1	1445	1	PDZD8	10	119044221	Missense_Mutation	SNP	C	TCGA-5P-A9K3-01A-11D-A42J-10	14365480	119044221	16490526	31	2481											
DENND5A	23258	hgsc.bcm.edu	37	chr11	9187516	9187517	+	Splice_Site	INS	-	-	AGAA																															ggcttcctggatgtacttctINSatatcaaacagaaaaataaa																										TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr11:9187516_9187517insAGAA	ENST00000328194.3	-	11	2472		c.e11-2		DENND5A_ENST00000527700.1_Splice_Site|DENND5A_ENST00000530044.1_Splice_Site	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A						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						GATGTACTTCTATATCAAACAG	0.45																																					.		Atlas-Indel,Pindel	.											.	DENND5A	84	.	0			c.2152-2->TTCT						PASS	.																																			SO:0001630	splice_region_variant	23258	exon12			.	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.2152-2->TTCT	chr11.hg19:g.9187516_9187517insAGAA		61.0	0.0	0		80.0	20.0	0.25	NM_001243254	B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	Splice_Site	INS	ENST00000328194.3	hg19	CCDS31423.1																																																																																			.	.	.	none		0.45	DENND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385910.2	NM_015213	Intron	AGAA	9187517	-	AGAA	9187516	8	5	34	1	0	1	1	0	0	0	1	0	4438	1536	53	0	1765	0	DENND5A	11	9187516	Splice_Site	INS	-	TCGA-5P-A9K3-01A-11D-A42J-10		9187516	125819000	32	2482											
PRPF19	27339	hgsc.bcm.edu	37	chr11	60666069	60666069	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctgttccaaagatgagtcCgtcagggtggaactgtgcac	9	10	12	10	1	1	2	1	1	0	1	4	3	4	3	3	2	2	2	3	2	2	1			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr11:60666069C>T	ENST00000227524.4	-	13	1289	c.1084G>A	c.(1084-1086)Gga>Aga	p.G362R		NM_014502.4	NP_055317.1			pre-mRNA processing factor 19											haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	22						AAGATGAGTCCGTCAGGGTGG	0.562																																					p.G362R		Atlas-SNP	.											.	PRPF19	62	.	0			c.G1084A						PASS	.						95	84	88					11																	60666069		2203	4299	6502	SO:0001583	missense	27339	exon13			TGAGTCCGTCAGG	BC018698	CCDS7995.1	11q12.2	2014-05-20	2013-06-10	2005-04-01	ENSG00000110107	ENSG00000110107		"WD repeat domain containing", "U-box domain containing"	17896	protein-coding gene	gene with protein product	"nuclear matrix protein NMP200 related to splicing factor PRP19", "psoralen 4"	608330	"PRP19/PSO4 homolog (S. cerevisiae)", "PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae)"	PRP19		12960389	Standard	NM_014502		Approved	UBOX4, NMP200, PSO4, hPSO4	uc001nqf.3	Q9UMS4	OTTHUMG00000167798	ENST00000227524.4:c.1084G>A	chr11.hg19:g.60666069C>T	ENSP00000227524:p.Gly362Arg	91.0	0.0	.		91.0	4.0	.	NM_014502		Missense_Mutation	SNP	ENST00000227524.4	hg19	CCDS7995.1	.	.	.	.	.	.	.	.	.	.	C	33	5.267928	0.95429	.	.	ENSG00000110107	ENST00000227524;ENST00000535326	D;T	0.84873	-1.91;4.45	5.17	5.17	0.71159	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);Ricin B lectin (1);	0.000000	0.85682	D	0.000000	D	0.94548	0.8244	M	0.93420	3.415	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95597	0.8659	10	0.87932	D	0	-9.6313	18.4838	0.90821	0.0:1.0:0.0:0.0	.	362	Q9UMS4	PRP19_HUMAN	R	362;34	ENSP00000227524:G362R;ENSP00000445435:G34R	ENSP00000227524:G362R	G	-	1	0	PRPF19	60422645	1.000000	0.71417	0.991000	0.47740	0.950000	0.60333	7.296000	0.78790	2.683000	0.91414	0.655000	0.94253	GGA	.	.	.	none		0.562	PRPF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396334.1	NM_014502		T	60666069	C	T	60666069	3	4	34	1	0	0	0	0	1	0	0	0	12574	661	23	1	446	1	PRPF19	11	60666069	Missense_Mutation	SNP	C	TCGA-5P-A9K3-01A-11D-A42J-10	51478553	60666069	74340447	33	2483											
SART1	9092	hgsc.bcm.edu	37	chr11	65744127	65744127	+	Splice_Site	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	cctggtcttttgtgccccagGactttgaacgggatgaggag	7	11	14	9	1	1	2	0	2	1	0	1	5	1	5	3	4	2	0	3	4	1	3			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr11:65744127G>C	ENST00000312397.5	+	14	1839	c.1747G>C	c.(1747-1749)Gac>Cac	p.D583H		NM_005146.4	NP_005137.1	O43290	SNUT1_HUMAN	squamous cell carcinoma antigen recognized by T cells	583					cell cycle arrest (GO:0007050)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of cytotoxic T cell differentiation (GO:0045585)|spliceosomal snRNP assembly (GO:0000387)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						TGTGCCCCAGGACTTTGAACG	0.667																																					p.D583H		Atlas-SNP	.											.	SART1	41	.	0			c.G1747C						PASS	.						28	28	28					11																	65744127		2201	4296	6497	SO:0001630	splice_region_variant	9092	exon14			CCCCAGGACTTTG	AB006198	CCDS31611.1	11q13.1	2009-01-06	2006-12-07		ENSG00000175467	ENSG00000175467			10538	protein-coding gene	gene with protein product	"small nuclear ribonucleoprotein 110kDa (U4/U6.U5)"	605941	"squamous cell carcinoma antigen recognised by T cells"			9449708	Standard	NM_005146		Approved	Ara1, Snu66, SNRNP110	uc001ogl.3	O43290	OTTHUMG00000166771	ENST00000312397.5:c.1747-1G>C	chr11.hg19:g.65744127G>C		86.0	0.0	.		104.0	34.0	.	NM_005146	A6NDN1|Q53GB5	Missense_Mutation	SNP	ENST00000312397.5	hg19	CCDS31611.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.123380	0.56613	.	.	ENSG00000175467	ENST00000312397;ENST00000542816	T	0.25250	1.81	4.11	4.11	0.48088	.	0.000000	0.85682	D	0.000000	T	0.49321	0.1550	M	0.74546	2.27	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.50849	-0.8779	9	.	.	.	-25.3255	13.9074	0.63845	0.0:0.0:1.0:0.0	.	583	O43290	SNUT1_HUMAN	H	583;425	ENSP00000310448:D583H	.	D	+	1	0	SART1	65500703	1.000000	0.71417	0.959000	0.39883	0.111000	0.19643	8.804000	0.91921	2.131000	0.65755	0.491000	0.48974	GAC	.	.	.	none		0.667	SART1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391409.1		Missense_Mutation	C	65744127	G	C	65744127	5	2	34	1	0	0	0	0	0	0	1	0	13859	1188	41	4	1801	4	SART1	11	65744127	Splice_Site	SNP	G	TCGA-5P-A9K3-01A-11D-A42J-10	5078058	65744127	69262389	34	2484											
LRFN4	78999	hgsc.bcm.edu	37	chr11	66627359	66627359	+	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	ggctgccttactggtcttcaCtgtggccttgctggttcggg	2	14	14	11	1	2	0	1	0	1	0	3	0	2	0	2	5	3	3	2	5	1	4			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr11:66627359C>G	ENST00000309602.4	+	2	1844	c.1601C>G	c.(1600-1602)aCt>aGt	p.T534S	PC_ENST00000393960.1_Intron|PC_ENST00000393955.2_Intron|LRFN4_ENST00000393952.3_Intron|PC_ENST00000393958.2_Intron	NM_024036.4	NP_076941.2	Q6PJG9	LRFN4_HUMAN	leucine rich repeat and fibronectin type III domain containing 4	534						integral component of membrane (GO:0016021)				breast(1)|lung(1)|prostate(1)	3						CTGGTCTTCACTGTGGCCTTG	0.716																																					p.T534S		Atlas-SNP	.											.	LRFN4	25	.	0			c.C1601G						PASS	.						36	29	31					11																	66627359		2190	4283	6473	SO:0001583	missense	78999	exon2			TCTTCACTGTGGC	BC007718	CCDS8153.1	11q13.1	2013-02-11				ENSG00000173621		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	28456	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 6"	612810				16495444, 16828986	Standard	NM_024036		Approved	MGC3103, SALM3., FIGLER6	uc001ojr.3	Q6PJG9		ENST00000309602.4:c.1601C>G	chr11.hg19:g.66627359C>G	ENSP00000312535:p.Thr534Ser	66.0	0.0	.		98.0	39.0	.	NM_024036	Q4VBZ3|Q59GV4|Q8N644|Q9BWJ0	Missense_Mutation	SNP	ENST00000309602.4	hg19	CCDS8153.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.003128	0.74932	.	.	ENSG00000173621	ENST00000309602	T	0.49139	0.79	4.79	3.88	0.44766	.	0.399801	0.18584	N	0.136948	T	0.44052	0.1275	L	0.29908	0.895	0.80722	D	1	P	0.52170	0.951	P	0.52031	0.688	T	0.11891	-1.0569	10	0.23891	T	0.37	.	10.7673	0.46301	0.0:0.9054:0.0:0.0946	.	534	Q6PJG9	LRFN4_HUMAN	S	534	ENSP00000312535:T534S	ENSP00000312535:T534S	T	+	2	0	LRFN4	66383935	0.587000	0.26791	1.000000	0.80357	0.997000	0.91878	1.223000	0.32527	1.023000	0.39654	0.462000	0.41574	ACT	.	.	.	none		0.716	LRFN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393127.1	NM_024036		G	66627359	C	G	66627359	3	3	34	1	0	0	0	0	1	0	0	0	8947	565	20	4	1607	4	LRFN4	11	66627359	Missense_Mutation	SNP	C	TCGA-5P-A9K3-01A-11D-A42J-10	883232	66627359	68379157	35	2485											
LRRC32	2615	hgsc.bcm.edu	37	chr11	76372150	76372150	+	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	gaaggtgtggcgggtgaggcGagtcagactgttctccgcca	7	8	17	9	3	2	2	1	1	1	1	3	4	2	2	2	4	0	1	2	4	1	1			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr11:76372150G>A	ENST00000407242.2	-	3	729	c.487C>T	c.(487-489)Cgc>Tgc	p.R163C	LRRC32_ENST00000464145.1_Intron|AP001189.4_ENST00000447519.1_RNA|LRRC32_ENST00000404995.1_Missense_Mutation_p.R163C|LRRC32_ENST00000260061.5_Missense_Mutation_p.R163C	NM_005512.2	NP_005503.1	Q14392	LRC32_HUMAN	leucine rich repeat containing 32	163					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						CGGGTGAGGCGAGTCAGACTG	0.642																																					p.R163C		Atlas-SNP	.											LRRC32,brain,glioma,0,2	LRRC32	74	.	0			c.C487T						PASS	.						70	70	70					11																	76372150		2200	4292	6492	SO:0001583	missense	2615	exon3			TGAGGCGAGTCAG	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.487C>T	chr11.hg19:g.76372150G>A	ENSP00000384126:p.Arg163Cys	38.0	0.0	.		62.0	11.0	.	NM_005512	Q86V06	Missense_Mutation	SNP	ENST00000407242.2	hg19	CCDS8245.1	.	.	.	.	.	.	.	.	.	.	G	14.94	2.685814	0.47991	.	.	ENSG00000137507	ENST00000260061;ENST00000407242;ENST00000404995;ENST00000421973	T;T;T;T	0.80123	-1.34;-1.34;-1.34;0.34	4.43	4.43	0.53597	.	0.344997	0.29028	N	0.013367	D	0.82559	0.5063	L	0.58925	1.835	0.20196	N	0.999927	D;D	0.71674	0.996;0.998	P;P	0.57846	0.828;0.828	T	0.73717	-0.3895	10	0.45353	T	0.12	.	7.4961	0.27490	0.0:0.145:0.5544:0.3006	.	163;163	C9JYU3;Q14392	.;LRC32_HUMAN	C	163	ENSP00000260061:R163C;ENSP00000384126:R163C;ENSP00000385766:R163C;ENSP00000413331:R163C	ENSP00000260061:R163C	R	-	1	0	LRRC32	76049798	0.793000	0.28825	0.183000	0.23137	0.772000	0.43724	2.399000	0.44495	2.306000	0.77630	0.462000	0.41574	CGC	.	.	.	none		0.642	LRRC32-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257926.2	NM_005512		A	76372150	G	A	76372150	3	1	34	1	0	0	0	0	1	0	0	0	8994	1058	37	1	1505	1	LRRC32	11	76372150	Missense_Mutation	SNP	G	TCGA-5P-A9K3-01A-11D-A42J-10	9744791	76372150	58634366	36	2486											
MYO7A	4647	hgsc.bcm.edu	37	chr11	76872079	76872079	+	Missense_Mutation	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	tcaacgcagcaatttacaagCctccctcccaggatgtgaag	12	8	8	13	1	1	1	1	1	0	0	3	2	3	2	3	1	4	2	3	1	5	2			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr11:76872079C>T	ENST00000409709.3	+	12	1533	c.1261C>T	c.(1261-1263)Cct>Tct	p.P421S	MYO7A_ENST00000409893.1_Missense_Mutation_p.P421S|MYO7A_ENST00000409619.2_Missense_Mutation_p.P410S|MYO7A_ENST00000458637.2_Missense_Mutation_p.P421S	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	421	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						AATTTACAAGCCTCCCTCCCA	0.562																																					p.P421S		Atlas-SNP	.											.	MYO7A	164	.	0			c.C1261T						PASS	.						100	110	107					11																	76872079		2051	4183	6234	SO:0001583	missense	4647	exon12			TACAAGCCTCCCT	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.1261C>T	chr11.hg19:g.76872079C>T	ENSP00000386331:p.Pro421Ser	88.0	0.0	.		120.0	47.0	.	NM_001127179	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	hg19	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.965660	0.74131	.	.	ENSG00000137474	ENST00000409709;ENST00000409893;ENST00000458637;ENST00000409619;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000343419	T;T;T;T	0.71103	-0.54;-0.54;-0.54;-0.54	5.34	5.34	0.76211	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	T	0.72716	0.3495	L	0.60957	1.885	0.80722	D	1	B;B;B	0.28128	0.201;0.107;0.197	B;B;B	0.35278	0.199;0.127;0.113	T	0.71237	-0.4652	10	0.48119	T	0.1	.	19.0292	0.92948	0.0:1.0:0.0:0.0	.	421;421;421	B9A012;F8VUN5;Q13402	.;.;MYO7A_HUMAN	S	421;421;421;410;420;420;343;420	ENSP00000386331:P421S;ENSP00000386689:P421S;ENSP00000392185:P421S;ENSP00000386635:P410S	ENSP00000345075:P343S	P	+	1	0	MYO7A	76549727	1.000000	0.71417	0.998000	0.56505	0.957000	0.61999	6.006000	0.70724	2.486000	0.83907	0.585000	0.79938	CCT	.	.	.	none		0.562	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		T	76872079	C	T	76872079	3	4	34	1	0	0	0	0	1	0	0	0	10089	739	26	2	1303	2	MYO7A	11	76872079	Missense_Mutation	SNP	C	TCGA-5P-A9K3-01A-11D-A42J-10	499929	76872079	58134437	37	2487											
CLEC1A	51267	hgsc.bcm.edu	37	chr12	10251426	10251426	+	Missense_Mutation	SNP	A	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	cctgtgcgccggggctctggAtgccgagttgtggcagagcc	4	8	17	12	3	1	1	0	0	1	1	1	3	1	2	4	4	3	3	4	4	0	1			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr12:10251426A>C	ENST00000315330.4	-	1	158	c.96T>G	c.(94-96)caT>caG	p.H32Q	CLEC1A_ENST00000457018.2_Missense_Mutation_p.H32Q|CLEC1A_ENST00000420265.2_Missense_Mutation_p.H32Q	NM_016511.2	NP_057595.2	Q8NC01	CLC1A_HUMAN	C-type lectin domain family 1, member A	32					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	23						GGGGCTCTGGATGCCGAGTTG	0.542																																					p.H32Q		Atlas-SNP	.											.	CLEC1A	48	.	0			c.T96G						PASS	.						82	71	75					12																	10251426		2203	4300	6503	SO:0001583	missense	51267	exon1			CTCTGGATGCCGA	AY358587	CCDS8612.1, CCDS73443.1	12p13.31	2005-02-09				ENSG00000150048		"C-type lectin domain containing"	24355	protein-coding gene	gene with protein product		606782				10671229, 11745369	Standard	XM_005253383		Approved	CLEC1, MGC34328	uc001qxb.3	Q8NC01		ENST00000315330.4:c.96T>G	chr12.hg19:g.10251426A>C	ENSP00000326407:p.His32Gln	104.0	0.0	.		124.0	32.0	.	NM_016511	Q8IUW7|Q9NZH3	Missense_Mutation	SNP	ENST00000315330.4	hg19	CCDS8612.1	.	.	.	.	.	.	.	.	.	.	A	9.945	1.218431	0.22373	.	.	ENSG00000150048	ENST00000315330;ENST00000457018;ENST00000420265;ENST00000414501	T;T;T;T	0.41065	5.06;5.17;5.01;1.01	5.55	-5.06	0.02946	.	0.256382	0.26851	N	0.022167	T	0.11879	0.0289	N	0.04959	-0.14	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	0.17501	-1.0367	10	0.13853	T	0.58	.	0.9013	0.01274	0.2277:0.2131:0.3272:0.232	.	32;32;32	E7ESV9;E9PFB4;Q8NC01	.;.;CLC1A_HUMAN	Q	32	ENSP00000326407:H32Q;ENSP00000415048:H32Q;ENSP00000417010:H32Q;ENSP00000396272:H32Q	ENSP00000326407:H32Q	H	-	3	2	CLEC1A	10142693	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.426000	0.02443	-0.573000	0.05998	-0.173000	0.13275	CAT	.	.	.	none		0.542	CLEC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399924.1	NM_016511		C	10251426	A	C	10251426	3	2	34	1	0	0	0	0	1	0	0	0	3507	330	12	5	770	5	CLEC1A	12	10251426	Missense_Mutation	SNP	A	TCGA-5P-A9K3-01A-11D-A42J-10		10251426	123600469	38	2488											
SLC2A13	114134	hgsc.bcm.edu	37	chr12	40422123	40422134	+	In_Frame_Del	DEL	TCCTCTTCAATG	TCCTCTTCAATG	-																															ctgagccaacctctttttccTcctcttcaatgttgtttttg																								rs375574046		TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	TCCTCTTCAATG	TCCTCTTCAATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr12:40422123_40422134delTCCTCTTCAATG	ENST00000280871.4	-	3	944_955	c.894_905delCATTGAAGAGGA	c.(892-906)aacattgaagaggag>aag	p.298_302NIEEE>K	SLC2A13_ENST00000380858.1_In_Frame_Del_p.298_302NIEEE>K	NM_052885.3	NP_443117.3	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 13	298					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	29		Lung NSC(34;0.105)|all_lung(34;0.123)				CTCTTTTTCCTCCTCTTCAATGTTGTTTTTGA	0.363										HNSCC(50;0.14)																											p.299_302del		Atlas-Indel,Pindel	.											.	SLC2A13	91	.	0			c.895_906del						PASS	.																																			SO:0001651	inframe_deletion	114134	exon3			.	AJ315644	CCDS8736.2	12q12	2013-05-22			ENSG00000151229	ENSG00000151229		"Solute carriers"	15956	protein-coding gene	gene with protein product	"H(+)-myo-inositol symporter"	611036				11500374	Standard	NM_052885		Approved	HMIT	uc010skm.2	Q96QE2	OTTHUMG00000059743	ENST00000280871.4:c.894_905delCATTGAAGAGGA	chr12.hg19:g.40422123_40422134delTCCTCTTCAATG	ENSP00000280871:p.Asn298_Glu302delinsLys	67.0	0.0	0		46.0	12.0	0.26087	NM_052885	Q17S07	In_Frame_Del	DEL	ENST00000280871.4	hg19	CCDS8736.2																																																																																			.	.	.	none		0.363	SLC2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132849.2			-	40422134	TCCTCTTCAATG	-	40422123	7	5	34	1	0	1	0	1	0	0	0	0	14555	1551	54	0	1073	0	SLC2A13	12	40422123	In_Frame_Del	DEL	TCCTCTTCAATG	TCGA-5P-A9K3-01A-11D-A42J-10	30170697	40422123	93429772	39	2489											
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43896178	43896178	+	Missense_Mutation	SNP	A	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	tcatgttgctgtaggtatgaAagggtaaactggtttccttt	9	16	11	5	0	1	1	1	1	0	0	2	1	2	1	1	3	2	6	1	3	5	6			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr12:43896178A>C	ENST00000389420.3	-	4	643	c.644T>G	c.(643-645)tTt>tGt	p.F215C	ADAMTS20_ENST00000553158.1_Missense_Mutation_p.F215C	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	215					extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		GTAGGTATGAAAGGGTAAACT	0.313																																					p.F215C		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.T644G						PASS	.						145	161	155					12																	43896178		2203	4299	6502	SO:0001583	missense	80070	exon4			GTATGAAAGGGTA	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.644T>G	chr12.hg19:g.43896178A>C	ENSP00000374071:p.Phe215Cys	56.0	0.0	.		82.0	24.0	.	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	hg19	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	A	9.204	1.029127	0.19512	.	.	ENSG00000173157	ENST00000389420;ENST00000553158;ENST00000389417	T;T	0.61274	0.29;0.12	4.66	2.31	0.28768	.	0.677370	0.13497	N	0.383543	T	0.39545	0.1082	L	0.27053	0.805	0.21184	N	0.999766	B	0.06786	0.001	B	0.10450	0.005	T	0.23833	-1.0177	10	0.38643	T	0.18	.	4.8737	0.13646	0.6866:0.0:0.1669:0.1464	.	215	P59510	ATS20_HUMAN	C	215	ENSP00000374071:F215C;ENSP00000448341:F215C	ENSP00000374068:F215C	F	-	2	0	ADAMTS20	42182445	1.000000	0.71417	0.012000	0.15200	0.175000	0.22909	2.224000	0.42945	0.379000	0.24794	0.533000	0.62120	TTT	.	.	.	none		0.313	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		C	43896178	A	C	43896178	3	2	34	1	0	0	0	0	1	0	0	0	266	14	1	5	5231	5	ADAMTS20	12	43896178	Missense_Mutation	SNP	A	TCGA-5P-A9K3-01A-11D-A42J-10	3474055	43896178	89955717	40	2490											
FKBP11	51303	hgsc.bcm.edu	37	chr12	49317595	49317596	+	Frame_Shift_Del	DEL	CA	CA	-																															tggtggaaatccccgttttcCataggccaagtgagaaggaa																										TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr12:49317595_49317596delCA	ENST00000550765.1	-	5	755_756	c.357_358delTG	c.(355-360)tatggafs	p.YG119fs	CCDC65_ENST00000266984.5_Intron|FKBP11_ENST00000444214.2_Frame_Shift_Del_p.YG17fs|AC073610.5_ENST00000537495.1_Intron|RP11-302B13.5_ENST00000398092.4_Intron|FKBP11_ENST00000552878.1_Frame_Shift_Del_p.YG119fs|FKBP11_ENST00000453172.2_Frame_Shift_Del_p.YG119fs	NM_016594.2	NP_057678.1	Q9NYL4	FKB11_HUMAN	FK506 binding protein 11, 19 kDa	119	PPIase FKBP-type. {ECO:0000255|PROSITE- ProRule:PRU00277}.				chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			kidney(1)|large_intestine(3)|lung(1)	5						CCCCGTTTTCCATAGGCCAAGT	0.51																																					p.120_120del		Atlas-Indel,Pindel	.											.	FKBP11	12	.	0			c.358_359del						PASS	.																																			SO:0001589	frameshift_variant	51303	exon5			.	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.357_358delTG	chr12.hg19:g.49317595_49317596delCA	ENSP00000449751:p.Tyr119fs	103.0	0.0	0		107.0	41.0	0.383178	NM_016594	B4DWB7	Frame_Shift_Del	DEL	ENST00000550765.1	hg19	CCDS8773.1																																																																																			.	.	.	none		0.51	FKBP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408927.1	NM_016594		-	49317596	CA	-	49317595	7	5	34	1	0	1	0	1	0	0	0	0	5910	603	21	0	312	0	FKBP11	12	49317595	Frame_Shift_Del	DEL	CA	TCGA-5P-A9K3-01A-11D-A42J-10	5421417	49317595	84534300	41	2491											
PPP1R12A	4659	hgsc.bcm.edu	37	chr12	80182551	80182551	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgatcaccagctgatgtagaActggtttcatatcttcaaaa	13	12	7	9	1	4	2	3	1	1	1	4	3	4	2	1	1	2	3	1	1	5	4			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr12:80182551A>G	ENST00000450142.2	-	21	2945	c.2679T>C	c.(2677-2679)agT>agC	p.S893S	PPP1R12A_ENST00000437004.2_Silent_p.S893S|PPP1R12A_ENST00000550107.1_Silent_p.S837S|PPP1R12A_ENST00000546369.1_Silent_p.S806S|PPP1R12A_ENST00000261207.5_Silent_p.S893S	NM_002480.2	NP_002471.1	O14974	MYPT1_HUMAN	protein phosphatase 1, regulatory subunit 12A	893					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						CTGATGTAGAACTGGTTTCAT	0.348																																					p.S893S		Atlas-SNP	.											.	PPP1R12A	76	.	0			c.T2679C						PASS	.						39	37	38					12																	80182551		1805	4080	5885	SO:0001819	synonymous_variant	4659	exon21			TGTAGAACTGGTT	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.2679T>C	chr12.hg19:g.80182551A>G		45.0	0.0	.		69.0	27.0	.	NM_002480	B4DZ09|F8VWB4|Q2NKL4|Q569H0|Q86WU3|Q8NFR6|Q9BYH0	Silent	SNP	ENST00000450142.2	hg19	CCDS44947.1	.	.	.	.	.	.	.	.	.	.	A	9.444	1.088753	0.20390	.	.	ENSG00000058272	ENST00000550299	.	.	.	5.94	3.48	0.39840	.	.	.	.	.	T	0.55114	0.1900	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50457	-0.8826	4	.	.	.	.	6.2542	0.20864	0.7244:0.0:0.0767:0.1988	.	.	.	.	A	76	.	.	V	-	2	0	PPP1R12A	78706682	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	2.692000	0.47018	1.079000	0.41038	0.528000	0.53228	GTT	.	.	.	none		0.348	PPP1R12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407254.2	NM_002480		G	80182551	A	G	80182551	2	3	34	1	0	0	0	0	0	0	0	1	12364	40	2	3		3	PPP1R12A	12	80182551	Silent	SNP	A	TCGA-5P-A9K3-01A-11D-A42J-10	30864956	80182551	53669344	42	2492											
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77742691	77742691	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtgctatctgtcgactgatTagggttgaaggcaggcggtg	7	11	17	6	2	1	2	0	2	1	0	2	3	1	2	0	5	1	3	0	5	3	3			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr13:77742691T>C	ENST00000544440.2	-	40	5889	c.5872A>G	c.(5872-5874)Aat>Gat	p.N1958D	MYCBP2_ENST00000407578.2_Missense_Mutation_p.N1996D|MYCBP2_ENST00000357337.6_Missense_Mutation_p.N1958D|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)		GTCGACTGATTAGGGTTGAAG	0.498																																					p.N1996D		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.A5986G						PASS	.						226	195	205					13																	77742691		2203	4300	6503	SO:0001583	missense	23077	exon40			ACTGATTAGGGTT	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.5872A>G	chr13.hg19:g.77742691T>C	ENSP00000444596:p.Asn1958Asp	94.0	0.0	.		105.0	40.0	.	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	hg19		.	.	.	.	.	.	.	.	.	.	T	19.02	3.745961	0.69418	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	T;T;T	0.28454	1.62;1.61;1.62	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.42108	0.1188	L	0.29908	0.895	0.58432	D	0.999997	P	0.52842	0.956	D	0.65010	0.931	T	0.13150	-1.0520	10	0.29301	T	0.29	.	16.1459	0.81569	0.0:0.0:0.0:1.0	.	1958	O75592	MYCB2_HUMAN	D	1958;1996;1958	ENSP00000349892:N1958D;ENSP00000384288:N1996D;ENSP00000444596:N1958D	ENSP00000349892:N1958D	N	-	1	0	MYCBP2	76640692	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	2.221000	0.72209	0.528000	0.53228	AAT	.	.	.	none		0.498	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		C	77742691	T	C	77742691	3	2	34	1	0	0	0	0	1	0	0	0	10025	1754	61	3	8226	3	MYCBP2	13	77742691	Missense_Mutation	SNP	T	TCGA-5P-A9K3-01A-11D-A42J-10		77742691	37427187	43	2493											
ADCY4	196883	hgsc.bcm.edu	37	chr14	24787720	24787720	+	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	tttcaccttgatgacaccccGgctgtagcaggtgtagccca	8	10	10	13	1	1	2	1	2	0	0	1	2	1	2	4	2	2	4	4	2	2	4			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr14:24787720G>T	ENST00000310677.4	-	26	3249	c.3136C>A	c.(3136-3138)Cgg>Agg	p.R1046R	ADCY4_ENST00000418030.2_Silent_p.R1046R|ADCY4_ENST00000554068.2_Silent_p.R1046R	NM_001198568.1|NM_001198592.1|NM_139247.3	NP_001185497.1|NP_001185521.1|NP_640340.2	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4	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)|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)		ATGACACCCCGGCTGTAGCAG	0.562																																					p.R1046R		Atlas-SNP	.											.	ADCY4	86	.	0			c.C3136A						PASS	.						113	102	106					14																	24787720		2203	4300	6503	SO:0001819	synonymous_variant	196883	exon26			CACCCCGGCTGTA	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.3136C>A	chr14.hg19:g.24787720G>T		78.0	0.0	.		95.0	4.0	.	NM_001198592	B3KV74|D3DS75|Q17R40|Q6ZTM6|Q96ML7	Silent	SNP	ENST00000310677.4	hg19	CCDS9627.1																																																																																			.	.	.	none		0.562	ADCY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073200.4			T	24787720	G	T	24787720	2	4	34	1	0	0	0	0	0	0	0	1	296	1115	39	4		4	ADCY4	14	24787720	Silent	SNP	G	TCGA-5P-A9K3-01A-11D-A42J-10		24787720	82561820	44	2494											
NIN	51199	hgsc.bcm.edu	37	chr14	51208398	51208398	+	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	tcgtaggtcagatttcatccGggacatttgcaggtttacat	9	14	10	8	2	2	1	2	0	0	1	4	2	3	2	1	3	2	3	1	3	2	5	rs142213280		TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr14:51208398G>T	ENST00000382041.3	-	25	5540	c.5350C>A	c.(5350-5352)Cgg>Agg	p.R1784R	NIN_ENST00000389868.3_Silent_p.R1071R|NIN_ENST00000324330.9_Silent_p.R1784R|NIN_ENST00000530997.2_Silent_p.R1784R|NIN_ENST00000245441.5_Silent_p.R1784R|NIN_ENST00000382043.4_Silent_p.R1071R|NIN_ENST00000453196.1_Silent_p.R1784R	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	1784					centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					GATTTCATCCGGGACATTTGC	0.423			T	PDGFRB	MPD																																p.R1784R		Atlas-SNP	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN	475	.	0			c.C5350A						PASS	.						194	183	187					14																	51208398		2203	4300	6503	SO:0001819	synonymous_variant	51199	exon25			TCATCCGGGACAT	AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"EF-hand domain containing"	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.5350C>A	chr14.hg19:g.51208398G>T		56.0	0.0	.		80.0	29.0	.	NM_020921	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Silent	SNP	ENST00000382041.3	hg19	CCDS32079.1	.	.	.	.	.	.	.	.	.	.	G	3.994	-0.003957	0.07773	.	.	ENSG00000100503	ENST00000530997;ENST00000389869;ENST00000530853	.	.	.	5.38	4.48	0.54585	.	.	.	.	.	T	0.70954	0.3283	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.70769	-0.4782	4	.	.	.	0.3126	15.3972	0.74805	0.0:0.1395:0.8605:0.0	.	.	.	.	Q	1274	.	.	P	-	2	0	NIN	50278148	0.565000	0.26610	0.240000	0.24138	0.475000	0.33008	1.835000	0.39181	1.404000	0.46819	0.563000	0.77884	CCG	.	G|1.000;A|0.000	.	alt		0.423	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946		T	51208398	G	T	51208398	2	4	34	1	0	0	0	0	0	0	0	1	10424	1115	39	4		4	NIN	14	51208398	Silent	SNP	G	TCGA-5P-A9K3-01A-11D-A42J-10	26420678	51208398	56141142	45	2495											
PLD4	122618	hgsc.bcm.edu	37	chr14	105395668	105395668	+	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	aggctcttctgcagaagctgCagcagctgctgggcaggaac	9	7	14	11	0	2	1	0	0	2	1	2	2	2	2	0	3	7	8	0	3	2	1			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr14:105395668C>T	ENST00000392593.4	+	5	661	c.493C>T	c.(493-495)Cag>Tag	p.Q165*	PLD4_ENST00000553861.1_5'Flank|PLD4_ENST00000540372.1_Nonsense_Mutation_p.Q172*	NM_138790.2	NP_620145.2	Q96BZ4	PLD4_HUMAN	phospholipase D family, member 4	165					glycerophospholipid biosynthetic process (GO:0046474)|hematopoietic progenitor cell differentiation (GO:0002244)|inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phagocytosis (GO:0006909)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|trans-Golgi network membrane (GO:0032588)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase D activity (GO:0004630)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	13		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.00067)|OV - Ovarian serous cystadenocarcinoma(23;0.00976)|Epithelial(46;0.0201)|GBM - Glioblastoma multiforme(11;0.116)			GCAGAAGCTGCAGCAGCTGCT	0.647																																					p.Q165X		Atlas-SNP	.											.	PLD4	46	.	0			c.C493T						PASS	.						14	18	16					14																	105395668		2015	4160	6175	SO:0001587	stop_gained	122618	exon5			AAGCTGCAGCAGC		CCDS9995.2	14q32.33	2014-01-28	2005-05-20	2005-05-20	ENSG00000166428	ENSG00000166428			23792	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 175"	C14orf175			Standard	XM_006720024		Approved		uc001ypu.1	Q96BZ4	OTTHUMG00000144167	ENST00000392593.4:c.493C>T	chr14.hg19:g.105395668C>T	ENSP00000376372:p.Gln165*	123.0	0.0	.		171.0	67.0	.	NM_138790	Q6UWD2	Nonsense_Mutation	SNP	ENST00000392593.4	hg19	CCDS9995.2	.	.	.	.	.	.	.	.	.	.	C	32	5.126145	0.94429	.	.	ENSG00000166428	ENST00000540372;ENST00000392593;ENST00000557573	.	.	.	4.16	0.899	0.19271	.	0.479596	0.20954	N	0.082696	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	0.003	12.7242	0.57162	0.0:0.305:0.695:0.0	.	.	.	.	X	172;165;163	.	ENSP00000376372:Q165X	Q	+	1	0	PLD4	104466713	0.000000	0.05858	0.992000	0.48379	0.986000	0.74619	-0.621000	0.05559	0.190000	0.20209	0.479000	0.44913	CAG	.	.	.	none		0.647	PLD4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000291348.2	NM_138790		T	105395668	C	T	105395668	4	4	34	1	0	0	0	0	0	1	0	0	12055	711	25	2	507	2	PLD4	14	105395668	Nonsense_Mutation	SNP	C	TCGA-5P-A9K3-01A-11D-A42J-10	54187270	105395668	1953872	46	2496											
TRPM7	54822	hgsc.bcm.edu	37	chr15	50904942	50904942	+	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	aagttcattaagtggataagGaaagcgcttggtttctggat	12	13	12	4	1	2	0	1	0	1	0	2	3	2	3	0	4	1	3	0	4	4	5			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr15:50904942G>A	ENST00000313478.7	-	16	2136	c.1855C>T	c.(1855-1857)Cct>Tct	p.P619S	TRPM7_ENST00000560955.1_Missense_Mutation_p.P619S	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	619					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)		AGTGGATAAGGAAAGCGCTTG	0.383																																					p.P619S		Atlas-SNP	.											.	TRPM7	145	.	0			c.C1855T						PASS	.						193	195	194					15																	50904942		1842	4084	5926	SO:0001583	missense	54822	exon16			GATAAGGAAAGCG	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.1855C>T	chr15.hg19:g.50904942G>A	ENSP00000320239:p.Pro619Ser	59.0	0.0	.		79.0	30.0	.	NM_017672	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	Missense_Mutation	SNP	ENST00000313478.7	hg19	CCDS42035.1	.	.	.	.	.	.	.	.	.	.	G	9.636	1.137653	0.21123	.	.	ENSG00000092439	ENST00000313478	T	0.73681	-0.77	5.44	3.55	0.40652	.	0.000000	0.85682	D	0.000000	T	0.60560	0.2278	L	0.32530	0.975	0.49213	D	0.999769	P	0.35745	0.518	B	0.37650	0.255	T	0.51012	-0.8759	10	0.12430	T	0.62	-7.7048	9.4445	0.38688	0.134:0.1185:0.7475:0.0	.	619	Q96QT4	TRPM7_HUMAN	S	619	ENSP00000320239:P619S	ENSP00000320239:P619S	P	-	1	0	TRPM7	48692234	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	3.773000	0.55333	0.765000	0.33221	0.585000	0.79938	CCT	.	.	.	none		0.383	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672		A	50904942	G	A	50904942	3	1	34	1	0	0	0	0	1	0	0	0	16603	1174	41	2	3838	2	TRPM7	15	50904942	Missense_Mutation	SNP	G	TCGA-5P-A9K3-01A-11D-A42J-10		50904942	51626450	47	2497											
THSD4	79875	hgsc.bcm.edu	37	chr15	72037466	72037466	+	Missense_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	atcgcagtaccctattttccGctgtgtgcacagaagcactc	9	11	8	13	2	0	1	0	0	0	1	3	1	1	1	2	0	3	5	2	0	3	4	rs374464107		TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr15:72037466G>A	ENST00000355327.3	+	12	2062	c.1928G>A	c.(1927-1929)cGc>cAc	p.R643H	THSD4_ENST00000357769.4_Missense_Mutation_p.R283H|THSD4_ENST00000261862.6_Missense_Mutation_p.R643H|THSD4_ENST00000567838.1_3'UTR			Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4	643					elastic fiber assembly (GO:0048251)	extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						CCTATTTTCCGCTGTGTGCAC	0.542																																					p.R643H		Atlas-SNP	.											.	THSD4	75	.	0			c.G1928A						PASS	.	G	HIS/ARG	0,4006		0,0,2003	297	300	299		1928	2.9	1	15		299	1,8345		0,1,4172	no	missense	THSD4	NM_024817.2	29	0,1,6175	AA,AG,GG		0.012,0.0,0.0081	benign	643/1019	72037466	1,12351	2003	4173	6176	SO:0001583	missense	79875	exon11			TTTTCCGCTGTGT	AK023772	CCDS10238.2, CCDS66817.1	15q23	2009-11-09			ENSG00000187720	ENSG00000187720			25835	protein-coding gene	gene with protein product		614476				19734141	Standard	NM_001286429		Approved	FVSY9334, PRO34005, FLJ13710, ADAMTSL6	uc002atb.1	Q6ZMP0	OTTHUMG00000133389	ENST00000355327.3:c.1928G>A	chr15.hg19:g.72037466G>A	ENSP00000347484:p.Arg643His	52.0	0.0	.		64.0	18.0	.	NM_024817	B2RTY3|B4DR13|Q6MZI3|Q6UXZ8|Q9H8E4	Missense_Mutation	SNP	ENST00000355327.3	hg19	CCDS10238.2	.	.	.	.	.	.	.	.	.	.	G	7.907	0.735646	0.15574	0.0	1.2E-4	ENSG00000187720	ENST00000355327;ENST00000261862;ENST00000357769	T;T;T	0.61040	0.14;0.14;0.14	4.96	2.87	0.33458	.	.	.	.	.	T	0.34077	0.0885	N	0.14661	0.345	0.37248	D	0.906434	B;B	0.19445	0.017;0.036	B;B	0.14023	0.004;0.01	T	0.17806	-1.0357	9	0.14252	T	0.57	.	8.2784	0.31885	0.2135:0.0:0.7865:0.0	.	283;643	B4DR13;Q6ZMP0	.;THSD4_HUMAN	H	643;643;283	ENSP00000347484:R643H;ENSP00000261862:R643H;ENSP00000350413:R283H	ENSP00000261862:R643H	R	+	2	0	THSD4	69824520	0.648000	0.27313	0.997000	0.53966	0.996000	0.88848	0.393000	0.20817	1.249000	0.43950	0.491000	0.48974	CGC	.	.	.	weak		0.542	THSD4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257253.2	NM_024817		A	72037466	G	A	72037466	3	1	34	1	0	0	0	0	1	0	0	0	15890	1087	38	1	1970	1	THSD4	15	72037466	Missense_Mutation	SNP	G	TCGA-5P-A9K3-01A-11D-A42J-10	21132524	72037466	30493926	48	2498											
KIAA0556	23247	hgsc.bcm.edu	37	chr16	27751558	27751558	+	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	caaaggcacccatgagatggCtggtgccagcggggacaagg	11	4	16	10	1	0	1	0	1	0	1	0	3	0	2	2	6	2	2	2	6	2	0			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr16:27751558C>T	ENST00000261588.4	+	15	1959	c.1940C>T	c.(1939-1941)gCt>gTt	p.A647V		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	647						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						CATGAGATGGCTGGTGCCAGC	0.537																																					p.A647V		Atlas-SNP	.											.	KIAA0556	348	.	0			c.C1940T						PASS	.						67	64	65					16																	27751558		2197	4300	6497	SO:0001583	missense	23247	exon15			AGATGGCTGGTGC	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.1940C>T	chr16.hg19:g.27751558C>T	ENSP00000261588:p.Ala647Val	98.0	0.0	.		106.0	6.0	.	NM_015202	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	hg19	CCDS32415.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.484756	0.44147	.	.	ENSG00000047578	ENST00000261588	T	0.10860	2.83	5.39	2.35	0.29111	.	0.712332	0.14666	N	0.305670	T	0.09512	0.0234	L	0.54323	1.7	0.09310	N	1	P	0.38078	0.617	B	0.34242	0.178	T	0.18999	-1.0319	10	0.41790	T	0.15	-6.6671	5.8366	0.18611	0.1594:0.6626:0.0:0.178	.	647	O60303	K0556_HUMAN	V	647	ENSP00000261588:A647V	ENSP00000261588:A647V	A	+	2	0	KIAA0556	27659059	0.000000	0.05858	0.014000	0.15608	0.110000	0.19582	0.116000	0.15561	1.269000	0.44280	0.655000	0.94253	GCT	.	.	.	none		0.537	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202		T	27751558	C	T	27751558	3	4	34	1	0	0	0	0	1	0	0	0	8190	797	28	2	1998	2	KIAA0556	16	27751558	Missense_Mutation	SNP	C	TCGA-5P-A9K3-01A-11D-A42J-10		27751558	62603195	49	2499											
CTCF	10664	hgsc.bcm.edu	37	chr16	67645250	67645250	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtggttaaagtgggggccaAtggagaggtggagacactag	11	7	19	4	0	0	2	0	0	0	2	0	4	0	2	1	7	0	1	1	7	4	2			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr16:67645250A>G	ENST00000264010.4	+	3	959	c.515A>G	c.(514-516)aAt>aGt	p.N172S	CTCF_ENST00000401394.1_Intron	NM_006565.3	NP_006556.1	P49711	CTCF_HUMAN	CCCTC-binding factor (zinc finger protein)	172					chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|DNA methylation (GO:0006306)|maintenance of DNA methylation (GO:0010216)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome positioning (GO:0016584)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone acetylation (GO:0035065)|regulation of histone methylation (GO:0031060)|regulation of molecular function, epigenetic (GO:0040030)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin insulator sequence binding (GO:0043035)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(6)|central_nervous_system(2)|cervix(1)|endometrium(34)|haematopoietic_and_lymphoid_tissue(7)|kidney(3)|large_intestine(9)|liver(1)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	79		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)		GTGGGGGCCAATGGAGAGGTG	0.493																																					p.N172S	Colon(175;1200 1966 6945 23069 27405)	Atlas-SNP	.											.	CTCF	193	.	0			c.A515G						PASS	.						54	57	56					16																	67645250		2198	4300	6498	SO:0001583	missense	10664	exon3			GGGCCAATGGAGA	U25435	CCDS10841.1, CCDS54029.1	16q21-q22.3	2013-01-08			ENSG00000102974	ENSG00000102974		"Zinc fingers, C2H2-type"	13723	protein-coding gene	gene with protein product	"11 zinc finger transcriptional repressor"	604167				8649389, 18550811	Standard	NM_006565		Approved		uc002etl.3	P49711	OTTHUMG00000137539	ENST00000264010.4:c.515A>G	chr16.hg19:g.67645250A>G	ENSP00000264010:p.Asn172Ser	204.0	0.0	.		256.0	105.0	.	NM_006565	B5MC38|Q53XI7|Q59EL8	Missense_Mutation	SNP	ENST00000264010.4	hg19	CCDS10841.1	.	.	.	.	.	.	.	.	.	.	A	15.52	2.859178	0.51376	.	.	ENSG00000102974	ENST00000264010	T	0.09255	3.0	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.20292	0.0488	N	0.24115	0.695	0.80722	D	1	D	0.63880	0.993	D	0.68192	0.956	T	0.01988	-1.1234	10	0.62326	D	0.03	-4.254	15.5629	0.76262	1.0:0.0:0.0:0.0	.	172	P49711	CTCF_HUMAN	S	172	ENSP00000264010:N172S	ENSP00000264010:N172S	N	+	2	0	CTCF	66202751	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.361000	0.66092	2.261000	0.74972	0.533000	0.62120	AAT	.	.	.	none		0.493	CTCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268870.2	NM_006565		G	67645250	A	G	67645250	3	3	34	1	0	0	0	0	1	0	0	0	4002	101	4	3	517	3	CTCF	16	67645250	Missense_Mutation	SNP	A	TCGA-5P-A9K3-01A-11D-A42J-10	39893692	67645250	22709503	50	2500											
TCF25	22980	hgsc.bcm.edu	37	chr16	89940088	89940089	+	Frame_Shift_Ins	INS	-	-	C																															cggtcctatgtcgcgccgggINSccctccggaggctgaggggg																										TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr16:89940088_89940089insC	ENST00000263346.8	+	1	69_70	c.13_14insC	c.(13-15)gccfs	p.A5fs		NM_014972.2	NP_055787.1	Q9BQ70	TCF25_HUMAN	transcription factor 25 (basic helix-loop-helix)	5					heart development (GO:0007507)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|large_intestine(1)|lung(8)|ovary(3)|skin(1)|urinary_tract(2)	18		all_cancers(9;4.71e-08)|Lung NSC(15;0.000192)|all_lung(18;0.000319)|all_neural(9;0.0122)|all_hematologic(23;0.027)		BRCA - Breast invasive adenocarcinoma(80;0.0288)		GTCGCGCCGGGCCCTCCGGAGG	0.678																																					p.A5fs		Atlas-Indel,Pindel	.											.	TCF25	61	.	0			c.13_14insC						PASS	.																																			SO:0001589	frameshift_variant	22980	exon1			.	AF322111	CCDS10987.1	16q24.3	2008-02-05			ENSG00000141002	ENSG00000141002			29181	protein-coding gene	gene with protein product		612326				12107429, 16574069	Standard	NM_014972		Approved	Nulp1, KIAA1049	uc002fpb.2	Q9BQ70	OTTHUMG00000138986	ENST00000263346.8:c.16dupC	chr16.hg19:g.89940091_89940091dupC	ENSP00000263346:p.Ala5fs	88.0	0.0	0		93.0	36.0	0.387097	NM_014972	Q2MK75|Q9UPV3	Frame_Shift_Ins	INS	ENST00000263346.8	hg19	CCDS10987.1																																																																																			.	.	.	none		0.678	TCF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272875.2	NM_014972		C	89940089	-	C	89940088	7	5	34	1	0	1	1	0	0	0	0	0	15705	1203	42	0	15	0	TCF25	16	89940088	Frame_Shift_Ins	INS	-	TCGA-5P-A9K3-01A-11D-A42J-10	22294838	89940088	414665	51	2501											
TP53	7157	hgsc.bcm.edu	37	chr17	7579355	7579355	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccagaatgcaagaagcccAgacggaaaccgtagctgccc	13	4	10	14	2	0	3	0	0	0	3	1	4	1	4	4	1	5	3	4	1	5	1			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr17:7579355A>G	ENST00000269305.4	-	4	521	c.332T>C	c.(331-333)cTg>cCg	p.L111P	TP53_ENST00000455263.2_Missense_Mutation_p.L111P|TP53_ENST00000359597.4_Missense_Mutation_p.L111P|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.L111P|TP53_ENST00000413465.2_Missense_Mutation_p.L111P|TP53_ENST00000445888.2_Missense_Mutation_p.L111P	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	111	Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		L -> M (in a sporadic cancer; somatic mutation).|L -> P (in sporadic cancers; somatic mutation).|L -> Q (in sporadic cancers; somatic mutation).|L -> R (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.L111R(11)|p.0?(8)|p.L111Q(7)|p.L111P(6)|p.G59fs*23(3)|p.V73fs*9(1)|p.G105_T125del21(1)|p.Y107fs*44(1)|p.L111fs*10(1)|p.Y103_G112>C(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.Y103_L111>L(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)	CAAGAAGCCCAGACGGAAACC	0.617		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.L111P	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,carcinoma,0,38	TP53	33396	.	43	Substitution - Missense(24)|Whole gene deletion(8)|Deletion - Frameshift(7)|Complex - deletion inframe(2)|Deletion - In frame(1)|Complex - frameshift(1)	lung(9)|upper_aerodigestive_tract(7)|liver(6)|large_intestine(5)|central_nervous_system(4)|bone(4)|breast(4)|haematopoietic_and_lymphoid_tissue(2)|stomach(1)|urinary_tract(1)	c.T332C	GRCh37	CX942126	TP53	X		PASS	.						64	60	61					17																	7579355		2203	4300	6503	SO:0001583	missense	7157	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AAGCCCAGACGGA	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.332T>C	chr17.hg19:g.7579355A>G	ENSP00000269305:p.Leu111Pro	148.0	0.0	.		123.0	74.0	.	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	19.91	3.915273	0.73098	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591	D;D;D;D;D;D;D;D	0.99837	-7.06;-7.06;-7.06;-7.06;-7.06;-7.06;-7.06;-7.06	4.75	4.75	0.60458	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.64402	D	0.000001	D	0.99760	0.9903	M	0.81942	2.565	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.994;0.992;1.0;0.997;1.0;1.0;0.996	D	0.96946	0.9691	10	0.87932	D	0	-10.3745	12.5363	0.56144	1.0:0.0:0.0:0.0	.	72;111;111;111;111;111;111	B4E095;E7EMR6;P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	P	111	ENSP00000410739:L111P;ENSP00000352610:L111P;ENSP00000269305:L111P;ENSP00000398846:L111P;ENSP00000391127:L111P;ENSP00000391478:L111P;ENSP00000424104:L111P;ENSP00000426252:L111P	ENSP00000269305:L111P	L	-	2	0	TP53	7520080	0.739000	0.28196	0.244000	0.24202	0.958000	0.62258	7.389000	0.79806	2.125000	0.65367	0.533000	0.62120	CTG	.	.	.	none		0.617	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		G	7579355	A	G	7579355	3	3	34	1	0	0	0	0	1	0	0	0	16393	188	7	3	970	3	TP53	17	7579355	Missense_Mutation	SNP	A	TCGA-5P-A9K3-01A-11D-A42J-10		7579355	73615855	52	2502											
FBXO47	494188	hgsc.bcm.edu	37	chr17	37099134	37099134	+	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	tgtttccacttagcattaggAgacgtgcattattctctaga	10	15	8	8	1	1	2	0	0	1	2	3	3	2	2	1	1	2	3	1	1	4	6			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr17:37099134A>T	ENST00000378079.2	-	9	1179	c.980T>A	c.(979-981)cTc>cAc	p.L327H		NM_001008777.2	NP_001008777.2	Q5MNV8	FBX47_HUMAN	F-box protein 47	327										NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)	20						TAGCATTAGGAGACGTGCATT	0.403																																					p.L327H		Atlas-SNP	.											.	FBXO47	34	.	0			c.T980A						PASS	.						98	91	93					17																	37099134		2203	4300	6503	SO:0001583	missense	494188	exon9			ATTAGGAGACGTG		CCDS32639.1	17q12	2014-08-12			ENSG00000204952	ENSG00000204952		"F-boxes /  "other""	31969	protein-coding gene	gene with protein product		609498				15723337	Standard	NM_001008777		Approved		uc002hrc.2	Q5MNV8	OTTHUMG00000178945	ENST00000378079.2:c.980T>A	chr17.hg19:g.37099134A>T	ENSP00000367319:p.Leu327His	78.0	0.0	.		103.0	21.0	.	NM_001008777	B2RTZ4	Missense_Mutation	SNP	ENST00000378079.2	hg19	CCDS32639.1	.	.	.	.	.	.	.	.	.	.	A	18.14	3.558184	0.65538	.	.	ENSG00000204952	ENST00000378079	T	0.61158	0.13	5.9	4.8	0.61643	.	0.254055	0.40385	N	0.001113	T	0.71609	0.3360	M	0.66939	2.045	0.34792	D	0.735817	D	0.89917	1.0	D	0.67231	0.95	T	0.80763	-0.1237	10	0.87932	D	0	-13.2646	12.1337	0.53957	0.8566:0.1434:0.0:0.0	.	327	Q5MNV8	FBX47_HUMAN	H	327	ENSP00000367319:L327H	ENSP00000367319:L327H	L	-	2	0	FBXO47	34352660	1.000000	0.71417	0.996000	0.52242	0.995000	0.86356	7.161000	0.77505	1.013000	0.39391	0.482000	0.46254	CTC	.	.	.	none		0.403	FBXO47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444073.1	NM_001008777		T	37099134	A	T	37099134	3	4	34	1	0	0	0	0	1	0	0	0	5763	304	11	5	390	5	FBXO47	17	37099134	Missense_Mutation	SNP	A	TCGA-5P-A9K3-01A-11D-A42J-10	29519779	37099134	44096076	53	2503											
RAB40B	10966	hgsc.bcm.edu	37	chr17	80656364	80656364	+	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	gtacggggactcggccgcgcCatcctgcaggctcgccagga	6	5	15	15	5	0	0	0	0	0	0	3	2	1	2	4	5	2	3	4	5	1	1			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr17:80656364C>G	ENST00000571995.1	-	1	240	c.109G>C	c.(109-111)Ggc>Cgc	p.G37R	RAB40B_ENST00000269347.6_5'UTR|RAB40B_ENST00000538809.2_Missense_Mutation_p.G37R	NM_006822.2	NP_006813.1	Q12829	RB40B_HUMAN	RAB40B, member RAS oncogene family	37					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)			TCGGCCGCGCCATCCTGCAGG	0.771																																					p.G37R		Atlas-SNP	.											.	RAB40B	24	.	0			c.G109C						PASS	.						20	20	20					17																	80656364		2193	4292	6485	SO:0001583	missense	10966	exon1			CCGCGCCATCCTG	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.109G>C	chr17.hg19:g.80656364C>G	ENSP00000461785:p.Gly37Arg	86.0	0.0	.		92.0	22.0	.	NM_006822	Q8WVG3	Missense_Mutation	SNP	ENST00000571995.1	hg19	CCDS11816.1	.	.	.	.	.	.	.	.	.	.	c	22.0	4.225081	0.79576	.	.	ENSG00000141542	ENST00000269347;ENST00000538809	.	.	.	3.06	0.941	0.19519	Small GTP-binding protein domain (1);	0.086007	0.44902	U	0.000415	T	0.62648	0.2445	L	0.42581	1.335	0.50039	D	0.999846	D	0.71674	0.998	D	0.74674	0.984	T	0.60505	-0.7250	9	0.62326	D	0.03	.	7.9072	0.29769	0.0:0.7395:0.1633:0.0972	.	37	Q12829	RB40B_HUMAN	R	37;71	.	ENSP00000269347:G37R	G	-	1	0	RAB40B	78249653	1.000000	0.71417	0.997000	0.53966	0.886000	0.51366	3.169000	0.50809	0.312000	0.23038	-0.738000	0.03535	GGC	.	.	.	none		0.771	RAB40B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439007.1			G	80656364	C	G	80656364	3	3	34	1	0	0	0	0	1	0	0	0	12954	594	21	4	751	4	RAB40B	17	80656364	Missense_Mutation	SNP	C	TCGA-5P-A9K3-01A-11D-A42J-10	43557230	80656364	538846	54	2504											
LAMA3	3909	hgsc.bcm.edu	37	chr18	21530086	21530086	+	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	aatacacatcggaagtcagcCcgggaagcacttatgtgttt	12	10	10	9	2	1	0	1	0	0	0	2	2	1	2	1	2	3	2	1	2	5	3			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr18:21530086C>T	ENST00000313654.9	+	72	9846	c.9605C>T	c.(9604-9606)cCc>cTc	p.P3202L	LAMA3_ENST00000587184.1_Missense_Mutation_p.P1537L|LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000269217.6_Missense_Mutation_p.P1593L|LAMA3_ENST00000399516.3_Missense_Mutation_p.P3146L	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	3202	Laminin G-like 5. {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)					GGAAGTCAGCCCGGGAAGCAC	0.498																																					p.P3202L		Atlas-SNP	.											.	LAMA3	397	.	0			c.C9605T						PASS	.						106	103	104					18																	21530086		2203	4300	6503	SO:0001583	missense	3909	exon72			GTCAGCCCGGGAA	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.9605C>T	chr18.hg19:g.21530086C>T	ENSP00000324532:p.Pro3202Leu	72.0	0.0	.		32.0	18.0	.	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	hg19	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	C	13.34	2.208505	0.39003	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000269217	T;T;T	0.79554	-1.28;-1.28;-1.28	5.7	1.77	0.24775	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	T	0.75781	0.3896	L	0.31294	0.92	0.09310	N	1	P;P;P;D	0.53462	0.822;0.734;0.849;0.96	B;B;B;P	0.54965	0.419;0.342;0.438;0.765	T	0.62525	-0.6836	9	0.36615	T	0.2	.	4.5329	0.12013	0.3242:0.3871:0.2215:0.0672	.	1537;1593;3146;3202	Q6VU69;B0YJ33;Q6VU67;Q16787	.;.;.;LAMA3_HUMAN	L	3202;3146;1593	ENSP00000324532:P3202L;ENSP00000382432:P3146L;ENSP00000269217:P1593L	ENSP00000269217:P1593L	P	+	2	0	LAMA3	19784084	0.000000	0.05858	0.000000	0.03702	0.299000	0.27559	-0.439000	0.06897	0.036000	0.15547	0.655000	0.94253	CCC	.	.	.	none		0.498	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		T	21530086	C	T	21530086	3	4	34	1	0	0	0	0	1	0	0	0	8614	623	22	2	10066	2	LAMA3	18	21530086	Missense_Mutation	SNP	C	TCGA-5P-A9K3-01A-11D-A42J-10		21530086	56547162	55	2505											
CALR	811	hgsc.bcm.edu	37	chr19	13050917	13050917	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggttcatgtcatcttcaacTacaagggcaagaacgtgctg	12	10	10	9	1	4	1	3	0	1	1	4	1	4	1	0	2	4	3	0	2	5	3			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr19:13050917T>C	ENST00000316448.5	+	4	521	c.448T>C	c.(448-450)Tac>Cac	p.Y150H		NM_004343.3	NP_004334.1	P27797	CALR_HUMAN	calreticulin	150	N-domain.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|cellular response to lithium ion (GO:0071285)|cellular senescence (GO:0090398)|chaperone-mediated protein folding (GO:0061077)|cortical actin cytoskeleton organization (GO:0030866)|endoplasmic reticulum unfolded protein response (GO:0030968)|glucocorticoid receptor signaling pathway (GO:0042921)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|peptide antigen assembly with MHC class I protein complex (GO:0002502)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of phagocytosis (GO:0050766)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|post-translational protein modification (GO:0043687)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein localization to nucleus (GO:0034504)|protein maturation by protein folding (GO:0022417)|protein N-linked glycosylation via asparagine (GO:0018279)|protein stabilization (GO:0050821)|regulation of apoptotic process (GO:0042981)|regulation of meiosis (GO:0040020)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to testosterone (GO:0033574)|sequestering of calcium ion (GO:0051208)|spermatogenesis (GO:0007283)	acrosomal vesicle (GO:0001669)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|intracellular (GO:0005622)|membrane (GO:0016020)|MHC class I peptide loading complex (GO:0042824)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasmic reticulum (GO:0016529)	androgen receptor binding (GO:0050681)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|chaperone binding (GO:0051087)|complement component C1q binding (GO:0001849)|DNA binding (GO:0003677)|glycoprotein binding (GO:0001948)|hormone binding (GO:0042562)|integrin binding (GO:0005178)|iron ion binding (GO:0005506)|mRNA binding (GO:0003729)|peptide binding (GO:0042277)|poly(A) RNA binding (GO:0044822)|protein binding involved in protein folding (GO:0044183)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(1)	10					Antihemophilic Factor(DB00025)|Melatonin(DB01065)|Tenecteplase(DB00031)	CATCTTCAACTACAAGGGCAA	0.532																																					p.Y150H		Atlas-SNP	.											.	CALR	31	.	0			c.T448C						PASS	.						124	102	109					19																	13050917		2203	4300	6503	SO:0001583	missense	811	exon4			TTCAACTACAAGG	M84739	CCDS12288.1	19p13.3-p13.2	2014-09-17				ENSG00000179218			1455	protein-coding gene	gene with protein product	"Sicca syndrome antigen A (autoantigen Ro; calreticulin)", "autoantigen Ro"	109091				2365822	Standard	NM_004343		Approved	RO, SSA, cC1qR, CRT, FLJ26680	uc002mvu.2	P27797		ENST00000316448.5:c.448T>C	chr19.hg19:g.13050917T>C	ENSP00000320866:p.Tyr150His	105.0	0.0	.		155.0	10.0	.	NM_004343	Q6IAT4|Q9UDG2	Missense_Mutation	SNP	ENST00000316448.5	hg19	CCDS12288.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.004029	0.74932	.	.	ENSG00000179218	ENST00000316448;ENST00000539083	T	0.50277	0.75	5.7	5.7	0.88788	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.49253	0.1546	L	0.54323	1.7	0.80722	D	1	B	0.18310	0.027	B	0.32533	0.147	T	0.43605	-0.9381	10	0.37606	T	0.19	-30.8317	14.9384	0.70975	0.0:0.0:0.0:1.0	.	150	P27797	CALR_HUMAN	H	150;29	ENSP00000320866:Y150H	ENSP00000320866:Y150H	Y	+	1	0	CALR	12911917	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.875000	0.87205	2.173000	0.68751	0.459000	0.35465	TAC	.	.	.	none		0.532	CALR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451952.1	NM_004343		C	13050917	T	C	13050917	3	2	34	1	0	0	0	0	1	0	0	0	2594	1522	53	3	462	3	CALR	19	13050917	Missense_Mutation	SNP	T	TCGA-5P-A9K3-01A-11D-A42J-10		13050917	46078066	56	2506											
GADD45GIP1	90480	hgsc.bcm.edu	37	chr19	13065098	13065098	+	Missense_Mutation	SNP	T	T	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	cagcagctcgcgcctccttcTtccgtttctgtttttcctcc	2	16	6	17	3	2	0	0	0	2	0	7	0	6	0	5	0	2	4	5	0	0	5			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr19:13065098T>G	ENST00000316939.1	-	2	616	c.593A>C	c.(592-594)aAg>aCg	p.K198T		NM_052850.3	NP_443082.2	Q8TAE8	G45IP_HUMAN	growth arrest and DNA-damage-inducible, gamma interacting protein 1	198					cell cycle (GO:0007049)|viral process (GO:0016032)	mitochondrion (GO:0005739)|nucleus (GO:0005634)				ovary(2)|prostate(1)|skin(1)	4						CGCCTCCTTCTTCCGTTTCTG	0.602																																					p.K198T		Atlas-SNP	.											.	GADD45GIP1	11	.	0			c.A593C						PASS	.						71	75	74					19																	13065098		2203	4300	6503	SO:0001583	missense	90480	exon2			TCCTTCTTCCGTT	AF479749	CCDS12290.1	19p13.2	2014-02-12				ENSG00000179271			29996	protein-coding gene	gene with protein product	"papillomavirus L2 interacting nuclear protein 1", "CKII beta binding protein 2", "CR6 interacting factor 1", "p53-responsive gene 6"	605162				10441517, 12482659	Standard	NM_052850		Approved	PLINP-1, MGC4667, MGC4758, CKBBP2, PRG6, Plinp1, CRIF1, CKbetaBP2	uc002mwb.4	Q8TAE8		ENST00000316939.1:c.593A>C	chr19.hg19:g.13065098T>G	ENSP00000323065:p.Lys198Thr	92.0	0.0	.		113.0	10.0	.	NM_052850	Q8IVM3|Q8TE51|Q969P9|Q9BSM6	Missense_Mutation	SNP	ENST00000316939.1	hg19	CCDS12290.1	.	.	.	.	.	.	.	.	.	.	T	14.82	2.648449	0.47258	.	.	ENSG00000179271	ENST00000316939	.	.	.	5.04	4.01	0.46588	.	0.170944	0.48286	D	0.000189	T	0.68613	0.3020	M	0.75777	2.31	0.46701	D	0.999166	D	0.63880	0.993	D	0.63113	0.911	T	0.68557	-0.5377	9	0.72032	D	0.01	-0.2416	5.6027	0.17363	0.1536:0.0847:0.0:0.7617	.	198	Q8TAE8	G45IP_HUMAN	T	198	.	ENSP00000323065:K198T	K	-	2	0	GADD45GIP1	12926098	1.000000	0.71417	0.992000	0.48379	0.382000	0.30200	3.520000	0.53465	0.755000	0.32990	0.456000	0.33151	AAG	.	.	.	none		0.602	GADD45GIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452759.2	NM_052850		G	13065098	T	G	13065098	3	3	34	1	0	0	0	0	1	0	0	0	6191	1609	56	5	79	5	GADD45GIP1	19	13065098	Missense_Mutation	SNP	T	TCGA-5P-A9K3-01A-11D-A42J-10	14181	13065098	46063885	57	2507											
PGLYRP2	114770	hgsc.bcm.edu	37	chr19	15586537	15586537	+	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	tctgccgtcggaagttgctgCggaaccctgggtctctggcc	4	10	14	13	3	2	0	0	0	2	0	4	2	2	2	3	4	4	2	3	4	2	1	rs145689498		TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr19:15586537C>A	ENST00000340880.4	-	2	1424	c.944G>T	c.(943-945)cGc>cTc	p.R315L	PGLYRP2_ENST00000292609.4_Missense_Mutation_p.R315L	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	315					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						GAAGTTGCTGCGGAACCCTGG	0.632																																					p.R315L		Atlas-SNP	.											.	PGLYRP2	116	.	0			c.G944T						PASS	.						41	41	41					19																	15586537		2203	4300	6503	SO:0001583	missense	114770	exon2			TTGCTGCGGAACC	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.944G>T	chr19.hg19:g.15586537C>A	ENSP00000345968:p.Arg315Leu	67.0	0.0	.		74.0	36.0	.	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Missense_Mutation	SNP	ENST00000340880.4	hg19	CCDS12330.2	.	.	.	.	.	.	.	.	.	.	C	18.78	3.696236	0.68386	.	.	ENSG00000161031	ENST00000340880;ENST00000292609	T;T	0.05925	3.39;3.37	5.46	4.41	0.53225	.	0.273852	0.32106	N	0.006569	T	0.14270	0.0345	M	0.69248	2.105	0.25310	N	0.989205	P;P	0.51240	0.943;0.827	P;B	0.53722	0.733;0.391	T	0.05146	-1.0903	10	0.38643	T	0.18	-17.4685	9.327	0.37999	0.0:0.8965:0.0:0.1035	.	315;315	Q96PD5-2;Q96PD5	.;PGRP2_HUMAN	L	315	ENSP00000345968:R315L;ENSP00000292609:R315L	ENSP00000292609:R315L	R	-	2	0	PGLYRP2	15447537	0.419000	0.25449	0.850000	0.33497	0.691000	0.40173	1.661000	0.37408	1.259000	0.44117	0.561000	0.74099	CGC	.	C|1.000;T|0.000	.	alt		0.632	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890		A	15586537	C	A	15586537	3	1	34	1	0	0	0	0	1	0	0	0	11801	768	27	4	802	4	PGLYRP2	19	15586537	Missense_Mutation	SNP	C	TCGA-5P-A9K3-01A-11D-A42J-10	2521439	15586537	43542446	58	2508											
PRX	57716	hgsc.bcm.edu	37	chr19	40900916	40900916	+	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	cattccactgacggccacagCcccctctgccctcccttcct	5	9	5	22	1	1	1	0	1	1	0	4	1	4	1	7	1	2	0	7	1	0	2			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr19:40900916C>A	ENST00000324001.7	-	7	3613	c.3343G>T	c.(3343-3345)Gct>Tct	p.A1115S	PRX_ENST00000291825.7_3'UTR	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	periaxin	1115	Glu-rich (acidic).				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)			ACGGCCACAGCCCCCTCTGCC	0.672																																					p.A1115S		Atlas-SNP	.											.	PRX	151	.	0			c.G3343T						PASS	.						55	53	54					19																	40900916		2203	4300	6503	SO:0001583	missense	57716	exon7			CCACAGCCCCCTC	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.3343G>T	chr19.hg19:g.40900916C>A	ENSP00000326018:p.Ala1115Ser	31.0	0.0	.		35.0	10.0	.	NM_181882	Q9BXL9|Q9HCF2	Missense_Mutation	SNP	ENST00000324001.7	hg19	CCDS33028.1	.	.	.	.	.	.	.	.	.	.	C	0.137	-1.106788	0.01813	.	.	ENSG00000105227	ENST00000324001	T	0.01059	5.39	3.82	2.77	0.32553	.	0.669254	0.13016	N	0.420476	T	0.01189	0.0039	L	0.40543	1.245	0.22017	N	0.999411	B	0.18166	0.026	B	0.11329	0.006	T	0.47560	-0.9108	10	0.21540	T	0.41	-0.4464	5.8736	0.18816	0.0:0.7574:0.0:0.2426	.	1115	Q9BXM0	PRAX_HUMAN	S	1115	ENSP00000326018:A1115S	ENSP00000326018:A1115S	A	-	1	0	PRX	45592756	0.000000	0.05858	0.021000	0.16686	0.018000	0.09664	-1.062000	0.03468	0.812000	0.34326	0.491000	0.48974	GCT	.	.	.	none		0.672	PRX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462582.1	NM_020956		A	40900916	C	A	40900916	3	1	34	1	0	0	0	0	1	0	0	0	12652	739	26	4	1046	4	PRX	19	40900916	Missense_Mutation	SNP	C	TCGA-5P-A9K3-01A-11D-A42J-10	25314379	40900916	18228067	59	2509											
NLRP7	199713	hgsc.bcm.edu	37	chr19	55450484	55450484	+	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	ggcagcccaagacctccttcAggtcggtcacggataagggc	9	6	13	13	2	2	1	2	0	0	1	4	2	3	2	3	5	1	1	3	5	2	2			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr19:55450484A>T	ENST00000590030.1	-	3	1743	c.1703T>A	c.(1702-1704)cTg>cAg	p.L568Q	NLRP7_ENST00000588756.1_Missense_Mutation_p.L568Q|NLRP7_ENST00000446217.1_Missense_Mutation_p.L596Q|NLRP7_ENST00000328092.5_Missense_Mutation_p.L568Q|NLRP7_ENST00000592784.1_Missense_Mutation_p.L568Q|NLRP7_ENST00000448121.2_Missense_Mutation_p.L568Q|NLRP7_ENST00000340844.2_Missense_Mutation_p.L568Q			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	568							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)		GACCTCCTTCAGGTCGGTCAC	0.517																																					p.L568Q		Atlas-SNP	.											.	NLRP7	411	.	0			c.T1703A						PASS	.						80	78	79					19																	55450484		2203	4300	6503	SO:0001583	missense	199713	exon4			TCCTTCAGGTCGG	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.1703T>A	chr19.hg19:g.55450484A>T	ENSP00000465520:p.Leu568Gln	53.0	0.0	.		82.0	14.0	.	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	hg19	CCDS33109.1	.	.	.	.	.	.	.	.	.	.	A	10.36	1.329178	0.24167	.	.	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217;ENST00000399724	T;T;T;T	0.75589	-0.89;-0.89;-0.95;-0.93	2.24	-4.48	0.03515	.	1.148190	0.06821	N	0.792301	T	0.73745	0.3626	L	0.44542	1.39	0.09310	N	1	D;D;D;D	0.65815	0.995;0.985;0.995;0.995	D;P;P;D	0.67900	0.931;0.901;0.901;0.954	T	0.63120	-0.6708	10	0.37606	T	0.19	.	1.4421	0.02357	0.4838:0.15:0.2155:0.1506	.	596;568;568;568	E7EPM2;Q32MH9;Q8WX94;Q8WX94-2	.;.;NALP7_HUMAN;.	Q	568;568;568;596;335	ENSP00000329568:L568Q;ENSP00000409137:L568Q;ENSP00000339491:L568Q;ENSP00000414273:L596Q	ENSP00000329568:L568Q	L	-	2	0	NLRP7	60142296	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.087000	0.14958	-2.141000	0.00805	-0.464000	0.05259	CTG	.	.	.	none		0.517	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		T	55450484	A	T	55450484	3	4	34	1	0	0	0	0	1	0	0	0	10489	188	7	5	1442	5	NLRP7	19	55450484	Missense_Mutation	SNP	A	TCGA-5P-A9K3-01A-11D-A42J-10	14549568	55450484	3678499	60	2510											
ZNF583	147949	hgsc.bcm.edu	37	chr19	56935542	56935542	+	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	aaagcatttagctatagtggAtctcttactctacatcagag	13	13	7	8	0	3	1	1	0	2	1	4	2	3	2	0	1	4	2	0	1	6	6			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr19:56935542A>T	ENST00000333201.9	+	5	1725	c.1515A>T	c.(1513-1515)ggA>ggT	p.G505G	ZNF583_ENST00000585612.1_Intron|ZNF583_ENST00000291598.7_Silent_p.G505G	NM_001159861.1|NM_152478.2	NP_001153333.1|NP_689691.2	Q96ND8	ZN583_HUMAN	zinc finger protein 583	505					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(2)|prostate(1)|skin(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0564)		GCTATAGTGGATCTCTTACTC	0.403																																					p.G505G		Atlas-SNP	.											.	ZNF583	83	.	0			c.A1515T						PASS	.						112	117	115					19																	56935542		2203	4300	6503	SO:0001819	synonymous_variant	147949	exon5			TAGTGGATCTCTT	AK055592	CCDS12943.1	19q13.43	2013-09-20			ENSG00000198440	ENSG00000198440		"Zinc fingers, C2H2-type", "-"	26427	protein-coding gene	gene with protein product							Standard	NM_152478		Approved	FLJ31030	uc010ygl.1	Q96ND8	OTTHUMG00000168874	ENST00000333201.9:c.1515A>T	chr19.hg19:g.56935542A>T		43.0	0.0	.		55.0	24.0	.	NM_001159861	O14850|Q2NKK3	Silent	SNP	ENST00000333201.9	hg19	CCDS12943.1																																																																																			.	.	.	none		0.403	ZNF583-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401453.1	NM_152478		T	56935542	A	T	56935542	2	4	34	1	0	0	0	0	0	0	0	1	18027	320	12	5		5	ZNF583	19	56935542	Silent	SNP	A	TCGA-5P-A9K3-01A-11D-A42J-10	1485058	56935542	2193441	61	2511											
ADAM33	80332	hgsc.bcm.edu	37	chr20	3652297	3652297	+	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	aggtccagctgggcactgggGagtgccaaggctccccgaca	8	5	15	13	1	0	0	0	0	0	0	2	2	2	1	4	5	2	3	4	5	1	0			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr20:3652297G>C	ENST00000356518.2	-	16	2077	c.1836C>G	c.(1834-1836)ctC>ctG	p.L612L	ADAM33_ENST00000379861.4_Silent_p.L612L|ADAM33_ENST00000350009.2_Silent_p.L612L|ADAM33_ENST00000466620.1_5'UTR	NM_025220.2	NP_079496.1	Q9BZ11	ADA33_HUMAN	ADAM metallopeptidase domain 33	612	Cys-rich.		L -> H (in dbSNP:rs41453444). {ECO:0000269|Ref.4}.		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						GGGCACTGGGGAGTGCCAAGG	0.642																																					p.L612L		Atlas-SNP	.											.	ADAM33	76	.	0			c.C1836G						PASS	.						29	23	25					20																	3652297		2197	4293	6490	SO:0001819	synonymous_variant	80332	exon16			ACTGGGGAGTGCC	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.1836C>G	chr20.hg19:g.3652297G>C		44.0	0.0	.		47.0	19.0	.	NM_025220	A0A1K6|Q5JT75|Q5JT76|Q8N0W6	Silent	SNP	ENST00000356518.2	hg19	CCDS13058.1																																																																																			.	.	.	none		0.642	ADAM33-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077763.2	NM_025220		C	3652297	G	C	3652297	2	2	34	1	0	0	0	0	0	0	0	1	250	1161	41	4		4	ADAM33	20	3652297	Silent	SNP	G	TCGA-5P-A9K3-01A-11D-A42J-10		3652297	59373223	62	2512											
ESF1	51575	hgsc.bcm.edu	37	chr20	13763687	13763687	+	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	ggctcgaaatctcttgtcaaTtttgacttttcgatcctttt	7	19	6	9	2	2	1	1	1	1	0	6	3	3	1	1	1	0	1	1	1	2	7			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr20:13763687T>A	ENST00000202816.1	-	2	207	c.100A>T	c.(100-102)Att>Ttt	p.I34F	NDUFAF5_ENST00000463598.1_5'Flank|NDUFAF5_ENST00000378106.5_5'Flank	NM_001276380.1|NM_016649.3	NP_001263309.1|NP_057733.2	Q9H501	ESF1_HUMAN	ESF1, nucleolar pre-rRNA processing protein, homolog (S. cerevisiae)	34					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|skin(1)|stomach(1)	31						CTCTTGTCAATTTTGACTTTT	0.433																																					p.I34F		Atlas-SNP	.											.	ESF1	77	.	0			c.A100T						PASS	.						66	64	65					20																	13763687		2203	4300	6503	SO:0001583	missense	51575	exon2			TGTCAATTTTGAC		CCDS13117.1	20p12.1	2007-02-12	2006-11-13	2006-11-13	ENSG00000089048	ENSG00000089048			15898	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 6"	C20orf6			Standard	NM_016649		Approved	bA526K24.1	uc002wok.2	Q9H501	OTTHUMG00000031906	ENST00000202816.1:c.100A>T	chr20.hg19:g.13763687T>A	ENSP00000202816:p.Ile34Phe	62.0	0.0	.		93.0	35.0	.	NM_001276380	Q86X92|Q9H9Q5|Q9HA35|Q9NX93|Q9P1S6	Missense_Mutation	SNP	ENST00000202816.1	hg19	CCDS13117.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.764628	0.89932	.	.	ENSG00000089048	ENST00000202816;ENST00000541185	T	0.36157	1.27	4.75	4.75	0.60458	.	0.000000	0.85682	D	0.000000	T	0.65460	0.2693	M	0.89478	3.035	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.73569	-0.3941	10	0.87932	D	0	.	13.9559	0.64147	0.0:0.0:0.0:1.0	.	34	Q9H501	ESF1_HUMAN	F	34	ENSP00000202816:I34F	ENSP00000202816:I34F	I	-	1	0	ESF1	13711687	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	1.765000	0.52091	0.383000	0.25322	ATT	.	.	.	none		0.433	ESF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078049.1	NM_016649		A	13763687	T	A	13763687	3	1	34	1	0	0	0	0	1	0	0	0	5253	1493	52	5	2507	5	ESF1	20	13763687	Missense_Mutation	SNP	T	TCGA-5P-A9K3-01A-11D-A42J-10	10111390	13763687	49261833	63	2513											
TUBB1	81027	hgsc.bcm.edu	37	chr20	57599619	57599619	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccatccaagagatctttaaTagggtctctgagcatttctc	10	13	8	10	0	3	2	0	1	3	1	6	3	4	2	2	1	1	1	2	1	3	4			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr20:57599619T>C	ENST00000217133.1	+	4	1406	c.1137T>C	c.(1135-1137)aaT>aaC	p.N379N		NM_030773.3	NP_110400.1	Q9H4B7	TBB1_HUMAN	tubulin, beta 1 class VI	379					'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)	AGATCTTTAATAGGGTCTCTG	0.522																																					p.N379N		Atlas-SNP	.											.	TUBB1	42	.	0			c.T1137C						PASS	.						46	43	44					20																	57599619		2203	4300	6503	SO:0001819	synonymous_variant	81027	exon4			CTTTAATAGGGTC	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.1137T>C	chr20.hg19:g.57599619T>C		44.0	0.0	.		70.0	25.0	.	NM_030773		Silent	SNP	ENST00000217133.1	hg19	CCDS13475.1																																																																																			.	.	.	none		0.522	TUBB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079903.1	NM_030773		C	57599619	T	C	57599619	2	2	34	1	0	0	0	0	0	0	0	1	16765	1403	49	3		3	TUBB1	20	57599619	Silent	SNP	T	TCGA-5P-A9K3-01A-11D-A42J-10	43835932	57599619	5425901	64	2514											
TCP10L	140290	hgsc.bcm.edu	37	chr21	33956569	33956569	+	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	tgggcacgggtcctctgggtGggtgccctctttggggtccc	1	11	17	12	1	2	0	0	0	2	0	4	0	4	0	3	6	1	1	3	6	0	1			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr21:33956569G>A	ENST00000300258.3	-	2	159	c.46C>T	c.(46-48)Cac>Tac	p.H16Y	TCP10L_ENST00000472557.1_Intron|AP000275.65_ENST00000553001.1_Intron	NM_144659.5	NP_653260.1	Q8TDR4	TCP1L_HUMAN	t-complex 10-like	16					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	protein self-association (GO:0043621)|repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)			breast(1)|central_nervous_system(1)|liver(1)|skin(1)	4						TCCTCTGGGTGGGTGCCCTCT	0.632																																					p.H16Y		Atlas-SNP	.											.	TCP10L	24	.	0			c.C46T						PASS	.						52	49	50					21																	33956569		2203	4300	6503	SO:0001583	missense	140290	exon2			CTGGGTGGGTGCC	AF115967	CCDS13616.1	21p22.11	2012-09-20	2012-09-20		ENSG00000242220	ENSG00000242220			11657	protein-coding gene	gene with protein product		608365	"t-complex 10 (a murine tcp homolog)-like", "t-complex 10 (mouse)-like"			10830953	Standard	NM_144659		Approved	PRED77		Q8TDR4	OTTHUMG00000064901	ENST00000300258.3:c.46C>T	chr21.hg19:g.33956569G>A	ENSP00000300258:p.His16Tyr	58.0	0.0	.		72.0	21.0	.	NM_144659	Q53EW0|Q96LN5	Missense_Mutation	SNP	ENST00000300258.3	hg19	CCDS13616.1	.	.	.	.	.	.	.	.	.	.	G	10.95	1.495034	0.26774	.	.	ENSG00000242220	ENST00000300258	T	0.19669	2.13	0.468	0.468	0.16732	.	.	.	.	.	T	0.36771	0.0979	L	0.57536	1.79	0.09310	N	1	D	0.61080	0.989	D	0.70487	0.969	T	0.10800	-1.0614	8	0.87932	D	0	.	.	.	.	.	16	Q8TDR4	TCP1L_HUMAN	Y	16	ENSP00000300258:H16Y	ENSP00000300258:H16Y	H	-	1	0	TCP10L	32878440	0.003000	0.15002	0.033000	0.17914	0.051000	0.14879	-0.046000	0.11983	0.485000	0.27652	0.205000	0.17691	CAC	.	.	.	none		0.632	TCP10L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139350.1	NM_144659		A	33956569	G	A	33956569	3	1	34	1	0	0	0	0	1	0	0	0	15723	1348	47	2	617	2	TCP10L	21	33956569	Missense_Mutation	SNP	G	TCGA-5P-A9K3-01A-11D-A42J-10		33956569	14173326	65	2515											
COL6A2	1292	hgsc.bcm.edu	37	chr21	47546102	47546102	+	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	aacatgacgctgttctccgaCctggtcgctgagaagttcat	9	11	10	11	3	2	2	1	2	1	1	4	4	2	2	2	1	1	4	2	1	2	2			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr21:47546102C>T	ENST00000300527.4	+	26	2477	c.2373C>T	c.(2371-2373)gaC>gaT	p.D791D	COL6A2_ENST00000357838.4_Silent_p.D791D|COL6A2_ENST00000310645.5_Silent_p.D791D|COL6A2_ENST00000397763.1_Silent_p.D791D|COL6A2_ENST00000409416.1_Silent_p.D791D	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	791	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)		TGTTCTCCGACCTGGTCGCTG	0.632																																					p.D791D		Atlas-SNP	.											.	COL6A2	351	.	0			c.C2373T						PASS	.						212	210	211					21																	47546102		2203	4300	6503	SO:0001819	synonymous_variant	1292	exon26			CTCCGACCTGGTC	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.2373C>T	chr21.hg19:g.47546102C>T		26.0	0.0	.		34.0	10.0	.	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Silent	SNP	ENST00000300527.4	hg19	CCDS13728.1																																																																																			.	.	.	none		0.632	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1			T	47546102	C	T	47546102	2	4	34	1	0	0	0	0	0	0	0	1	3702	506	18	2		2	COL6A2	21	47546102	Silent	SNP	C	TCGA-5P-A9K3-01A-11D-A42J-10	13589533	47546102	583793	66	2516											
EP300	2033	hgsc.bcm.edu	37	chr22	41527606	41527606	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatcagcagcctgggcagtcTccccaaggcatgcggcccat	9	6	11	15	1	2	0	1	0	1	0	3	0	2	0	4	3	3	3	4	3	2	0			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr22:41527606T>C	ENST00000263253.7	+	6	2716	c.1497T>C	c.(1495-1497)tcT>tcC	p.S499S		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	499					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						CTGGGCAGTCTCCCCAAGGCA	0.473			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.S499S		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300	367	.	0			c.T1497C						PASS	.						84	82	83					22																	41527606		2203	4300	6503	SO:0001819	synonymous_variant	2033	exon6	Familial Cancer Database	Broad Thumb-Hallux syndrome	GCAGTCTCCCCAA	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.1497T>C	chr22.hg19:g.41527606T>C		78.0	0.0	.		97.0	16.0	.	NM_001429	B1AKC2	Silent	SNP	ENST00000263253.7	hg19	CCDS14010.1																																																																																			.	.	.	none		0.473	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		C	41527606	T	C	41527606	2	2	34	1	0	0	0	0	0	0	0	1	5150	1538	54	3		3	EP300	22	41527606	Silent	SNP	T	TCGA-5P-A9K3-01A-11D-A42J-10		41527606	9776960	67	2517											
MOV10L1	54456	hgsc.bcm.edu	37	chr22	50555698	50555698	+	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	agtcactaattgctgcgcgcGaaccattttcttggaaaaag	12	11	9	9	3	2	0	1	0	1	0	2	2	2	1	1	1	3	1	1	1	4	5			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chr22:50555698G>T	ENST00000262794.5	+	9	1455	c.1372G>T	c.(1372-1374)Gaa>Taa	p.E458*	MOV10L1_ENST00000395858.3_Nonsense_Mutation_p.E458*|MOV10L1_ENST00000540615.1_Nonsense_Mutation_p.E438*|MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000545383.1_Nonsense_Mutation_p.E458*	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	458					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)	p.E458K(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		TGCTGCGCGCGAACCATTTTC	0.423																																					p.E458X		Atlas-SNP	.											MOV10L1,rectum,carcinoma,0,1	MOV10L1	238	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1372T						PASS	.						80	76	77					22																	50555698		2203	4300	6503	SO:0001587	stop_gained	54456	exon9			GCGCGCGAACCAT	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"cardiac helicase activated by MEF2C protein"	605794	"Mov10 (mouse)-like 1", "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.1372G>T	chr22.hg19:g.50555698G>T	ENSP00000262794:p.Glu458*	113.0	2.0	.		110.0	36.0	.	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Nonsense_Mutation	SNP	ENST00000262794.5	hg19	CCDS14084.1	.	.	.	.	.	.	.	.	.	.	G	37	6.499084	0.97616	.	.	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000540615	.	.	.	5.76	5.76	0.90799	.	0.237801	0.43260	D	0.000585	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.16420	T	0.52	-29.9369	18.7444	0.91787	0.0:0.0:1.0:0.0	.	.	.	.	X	458;458;458;438	.	ENSP00000262794:E458X	E	+	1	0	MOV10L1	48897825	0.426000	0.25506	0.468000	0.27192	0.010000	0.07245	2.329000	0.43876	2.716000	0.92895	0.650000	0.86243	GAA	.	.	.	none		0.423	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995		T	50555698	G	T	50555698	4	4	34	1	0	0	0	0	0	1	0	0	9726	1059	37	4	1447	4	MOV10L1	22	50555698	Nonsense_Mutation	SNP	G	TCGA-5P-A9K3-01A-11D-A42J-10	9028092	50555698	748868	68	2518											
FANCB	2187	hgsc.bcm.edu	37	chrX	14862799	14862799	+	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	aattcagggcatagccgggtGatgtgatttgaaaacaagat	14	10	12	5	1	1	4	1	3	0	1	1	4	1	4	1	2	2	1	1	2	5	3			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chrX:14862799G>A	ENST00000324138.3	-	8	2144	c.1991C>T	c.(1990-1992)tCa>tTa	p.S664L	FANCB_ENST00000398334.1_Missense_Mutation_p.S664L	NM_152633.2	NP_689846.1	Q8NB91	FANCB_HUMAN	Fanconi anemia, complementation group B	664					DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24	Hepatocellular(33;0.183)					ATAGCCGGGTGATGTGATTTG	0.368								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.S664L		Atlas-SNP	.											.	FANCB	78	.	0			c.C1991T						PASS	.						77	77	77					X																	14862799		2203	4299	6502	SO:0001583	missense	2187	exon8	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CCGGGTGATGTGA	AK091383	CCDS14161.1	Xp22.2	2014-09-17			ENSG00000181544	ENSG00000181544		"Fanconi anemia, complementation groups"	3583	protein-coding gene	gene with protein product		300515				9382107, 15502827	Standard	NM_152633		Approved	FAB, FLJ34064, FAAP95	uc004cwh.1	Q8NB91	OTTHUMG00000021168	ENST00000324138.3:c.1991C>T	chrX.hg19:g.14862799G>A	ENSP00000326819:p.Ser664Leu	119.0	0.0	.		118.0	89.0	.	NM_152633	B2RMZ4|Q7Z2U2|Q86XG1	Missense_Mutation	SNP	ENST00000324138.3	hg19	CCDS14161.1	.	.	.	.	.	.	.	.	.	.	G	15.26	2.780725	0.49891	.	.	ENSG00000181544	ENST00000324138;ENST00000398334;ENST00000452869	.	.	.	5.5	5.5	0.81552	.	0.068421	0.64402	D	0.000011	T	0.73393	0.3581	L	0.59436	1.845	0.42896	D	0.994218	D	0.63046	0.992	P	0.56865	0.808	T	0.76974	-0.2760	9	0.87932	D	0	-6.2689	18.4174	0.90575	0.0:0.0:1.0:0.0	.	664	Q8NB91	FANCB_HUMAN	L	664	.	ENSP00000326819:S664L	S	-	2	0	FANCB	14772720	1.000000	0.71417	0.040000	0.18447	0.006000	0.05464	6.647000	0.74354	2.289000	0.77006	0.594000	0.82650	TCA	.	.	.	none		0.368	FANCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055835.1	NM_152633		A	14862799	G	A	14862799	3	1	34	1	0	0	0	0	1	0	0	0	5670	1294	45	2	596	2	FANCB	23	14862799	Missense_Mutation	SNP	G	TCGA-5P-A9K3-01A-11D-A42J-10		14862799	140407761	69	2519											
GPKOW	27238	hgsc.bcm.edu	37	chrX	48979991	48979991	+	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	gtcggccagccgcctccgtgCggacgtgcgagtgaagccga	6	5	16	14	7	0	1	0	1	0	0	2	4	1	2	5	2	4	0	5	2	1	0			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chrX:48979991C>A	ENST00000156109.5	-	1	160	c.82G>T	c.(82-84)Gca>Tca	p.A28S		NM_015698.4	NP_056513.2	Q92917	GPKOW_HUMAN	G patch domain and KOW motifs	28						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(2)	21						CGCCTCCGTGCGGACGTGCGA	0.617																																					p.A28S		Atlas-SNP	.											.	GPKOW	38	.	0			c.G82T						PASS	.						26	23	24					X																	48979991		2202	4299	6501	SO:0001583	missense	27238	exon1			TCCGTGCGGACGT	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.82G>T	chrX.hg19:g.48979991C>A	ENSP00000156109:p.Ala28Ser	169.0	0.0	.		222.0	172.0	.	NM_015698	Q59EK5|Q9BQA8	Missense_Mutation	SNP	ENST00000156109.5	hg19	CCDS35251.1	.	.	.	.	.	.	.	.	.	.	C	7.394	0.631345	0.14322	.	.	ENSG00000068394	ENST00000156109	.	.	.	5.39	-2.38	0.06622	.	0.722949	0.14213	N	0.333912	T	0.21962	0.0529	L	0.34521	1.04	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.31052	-0.9957	9	0.07990	T	0.79	.	5.6619	0.17674	0.4884:0.3358:0.0:0.1758	.	28	Q92917	GPKOW_HUMAN	S	28	.	ENSP00000156109:A28S	A	-	1	0	GPKOW	48866935	0.000000	0.05858	0.003000	0.11579	0.742000	0.42306	-0.802000	0.04545	-0.289000	0.09038	0.504000	0.49776	GCA	.	.	.	none		0.617	GPKOW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056535.2	NM_015698		A	48979991	C	A	48979991	3	1	34	1	0	0	0	0	1	0	0	0	6620	768	27	4	1392	4	GPKOW	23	48979991	Missense_Mutation	SNP	C	TCGA-5P-A9K3-01A-11D-A42J-10	34117192	48979991	106290569	70	2520											
SMARCA1	6594	hgsc.bcm.edu	37	chrX	128582334	128582334	+	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	ggagttttagttgcccgtttCttcttttctgctctctctct	2	21	7	11	1	5	0	0	0	5	0	7	1	5	1	1	1	2	4	1	1	1	7			TCGA-5P-A9K3-01A-11D-A42J-10	TCGA-5P-A9K3-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	84a1aab7-7e50-4015-accb-e32579b2fc62	fe756f10-d087-48bf-984d-e9ba64bab839	g.chrX:128582334C>G	ENST00000371122.4	-	24	3246	c.3117G>C	c.(3115-3117)aaG>aaC	p.K1039N	SMARCA1_ENST00000371121.3_Missense_Mutation_p.K1027N|SMARCA1_ENST00000371123.1_Missense_Mutation_p.K1027N	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	1039					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						TTGCCCGTTTCTTCTTTTCTG	0.313																																					p.K1039N		Atlas-SNP	.											.	SMARCA1	126	.	0			c.G3117C						PASS	.						148	136	140					X																	128582334		2203	4297	6500	SO:0001583	missense	6594	exon24			CCGTTTCTTCTTT	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.3117G>C	chrX.hg19:g.128582334C>G	ENSP00000360163:p.Lys1039Asn	54.0	0.0	.		66.0	46.0	.	NM_003069	Q5JV41|Q5JV42	Missense_Mutation	SNP	ENST00000371122.4	hg19	CCDS14612.1	.	.	.	.	.	.	.	.	.	.	C	14.87	2.663123	0.47572	.	.	ENSG00000102038	ENST00000371121;ENST00000371123;ENST00000371122	D;D;D	0.92299	-3.01;-3.01;-2.99	5.87	5.87	0.94306	.	0.000000	0.64402	D	0.000005	D	0.96667	0.8912	M	0.87758	2.905	0.80722	D	1	D;D;D;D	0.69078	0.981;0.997;0.989;0.981	D;D;D;D	0.77004	0.966;0.989;0.985;0.966	D	0.96323	0.9238	10	0.51188	T	0.08	-18.2877	19.3889	0.94570	0.0:1.0:0.0:0.0	.	1018;1039;1027;1039	E9PCY3;B7ZLQ5;P28370-2;P28370	.;.;.;SMCA1_HUMAN	N	1027;1027;1039	ENSP00000360162:K1027N;ENSP00000360164:K1027N;ENSP00000360163:K1039N	ENSP00000360162:K1027N	K	-	3	2	SMARCA1	128410015	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.498000	0.53302	2.618000	0.88619	0.600000	0.82982	AAG	.	.	.	none		0.313	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058206.1	NM_003069		G	128582334	C	G	128582334	3	3	34	1	0	0	0	0	1	0	0	0	14781	912	32	4	51	4	SMARCA1	23	128582334	Missense_Mutation	SNP	C	TCGA-5P-A9K3-01A-11D-A42J-10	79602343	128582334	26688226	71	2521											
HMGCS2	3158	hgsc.bcm.edu	37	chr1	120301769	120301769	+	Frame_Shift_Del	DEL	A	A	-																															cactgattctggatttttttAcggtatgatgtgtaacatcg																										TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr1:120301769delA	ENST00000369406.3	-	4	871	c.822delT	c.(820-822)cgtfs	p.R274fs	HMGCS2_ENST00000544913.2_Frame_Shift_Del_p.R232fs|HMGCS2_ENST00000476640.1_Intron	NM_005518.3	NP_005509.1	P54868	HMCS2_HUMAN	3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)	274					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)		GGATTTTTTTACGGTATGATG	0.468																																					p.K275fs		Atlas-Indel,Pindel	.											.	HMGCS2	58	.	0			c.823delA						PASS	.						130	130	130					1																	120301769		2203	4300	6503	SO:0001589	frameshift_variant	3158	exon4			.	BC044217	CCDS905.1, CCDS53353.1	1p13-p12	2014-09-17	2010-04-30		ENSG00000134240	ENSG00000134240			5008	protein-coding gene	gene with protein product		600234	"3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial)"			7851882, 7893153	Standard	NM_005518		Approved		uc001eid.3	P54868	OTTHUMG00000012101	ENST00000369406.3:c.822delT	chr1.hg19:g.120301769delA	ENSP00000358414:p.Arg274fs	100.0	0.0	0		92.0	23.0	0.25	NM_005518	B7Z8R3|D3Y5K6|Q5SZU2|Q6IBF4	Frame_Shift_Del	DEL	ENST00000369406.3	hg19	CCDS905.1																																																																																			.	.	.	none		0.468	HMGCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033469.2	NM_005518		-	120301769	A	-	120301769	7	5	35	1	0	1	0	1	0	0	0	0	7240	378	14	0	728	0	HMGCS2	1	120301769	Frame_Shift_Del	DEL	A	TCGA-5P-A9K6-01A-11D-A42J-10		120301769	128948852	1	2522											
RALGPS2	55103	hgsc.bcm.edu	37	chr1	178863074	178863074	+	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	ttctgcagaatcagaagattTggcagtacatttatatccag	13	13	8	7	0	2	3	1	0	1	3	3	3	3	3	1	1	2	3	1	1	5	6			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr1:178863074T>A	ENST00000367635.3	+	16	1684	c.1346T>A	c.(1345-1347)tTg>tAg	p.L449*	RALGPS2_ENST00000477383.1_3'UTR|RALGPS2_ENST00000367634.2_Nonsense_Mutation_p.L423*	NM_152663.3	NP_689876.2	Q86X27	RGPS2_HUMAN	Ral GEF with PH domain and SH3 binding motif 2	449					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						TCAGAAGATTTGGCAGTACAT	0.318																																					p.L449X		Atlas-SNP	.											.	RALGPS2	69	.	0			c.T1346A						PASS	.						61	61	61					1																	178863074		2203	4293	6496	SO:0001587	stop_gained	55103	exon16			AAGATTTGGCAGT	AK098470	CCDS1325.1, CCDS65733.1	1q24	2013-01-11			ENSG00000116191	ENSG00000116191		"Pleckstrin homology (PH) domain containing"	30279	protein-coding gene	gene with protein product						10747847, 12102558	Standard	NM_152663		Approved	KIAA0351, FLJ10244, FLJ25604	uc001glz.3	Q86X27	OTTHUMG00000035076	ENST00000367635.3:c.1346T>A	chr1.hg19:g.178863074T>A	ENSP00000356607:p.Leu449*	62.0	0.0	.		54.0	18.0	.	NM_152663	B7Z7B1|Q5T5Z1|Q5VZ67|Q9NW78	Nonsense_Mutation	SNP	ENST00000367635.3	hg19	CCDS1325.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	39|39	7.409622|7.409622	0.98265|0.98265	.|.	.|.	ENSG00000116191|ENSG00000116191	ENST00000367635;ENST00000367634;ENST00000324778;ENST00000535251|ENST00000367632	.|.	.|.	.|.	5.54|5.54	5.54|5.54	0.83059|0.83059	.|.	0.248036|.	0.33875|.	N|.	0.004461|.	.|T	.|0.67655	.|0.2916	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.70974	.|-0.4726	.|3	0.02654|.	T|.	1|.	.|.	15.3383|15.3383	0.74277|0.74277	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	X|R	449;423;414;98|40	.|.	ENSP00000313613:L414X|.	L|W	+|+	2|1	0|0	RALGPS2|RALGPS2	177129697|177129697	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	7.143000|7.143000	0.77348|0.77348	2.102000|2.102000	0.63906|0.63906	0.454000|0.454000	0.30748|0.30748	TTG|TGG	.	.	.	none		0.318	RALGPS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084926.2	NM_152663		A	178863074	T	A	178863074	4	1	35	1	0	0	0	0	0	1	0	0	13031	1821	63	5	1404	5	RALGPS2	1	178863074	Nonsense_Mutation	SNP	T	TCGA-5P-A9K6-01A-11D-A42J-10	58561305	178863074	70387547	2	2523											
C2orf53	339779	hgsc.bcm.edu	37	chr2	27360426	27360426	+	Missense_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	ggggcaggaggggctgcgggGccggaggcacaccaggcata	8	2	21	10	2	0	0	0	0	0	0	0	2	0	2	2	10	1	4	2	10	1	1			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr2:27360426G>A	ENST00000335524.3	-	3	1297	c.772C>T	c.(772-774)Ccc>Tcc	p.P258S	PREB_ENST00000416802.1_5'Flank|PREB_ENST00000260643.2_5'Flank|PREB_ENST00000406567.3_5'Flank	NM_178553.3	NP_848648.2	Q53SZ7	PRR30_HUMAN		258										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)					GGGCTGCGGGGCCGGAGGCAC	0.657																																					p.P258S		Atlas-SNP	.											.	C2orf53	45	.	0			c.C772T						PASS	.						20	22	21					2																	27360426		2081	4142	6223	SO:0001583	missense	339779	exon3			TGCGGGGCCGGAG																												ENST00000335524.3:c.772C>T	chr2.hg19:g.27360426G>A	ENSP00000335017:p.Pro258Ser	156.0	0.0	.		173.0	50.0	.	NM_178553	Q86UE2	Missense_Mutation	SNP	ENST00000335524.3	hg19	CCDS1739.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.302|9.302	1.053391|1.053391	0.19907|0.19907	.|.	.|.	ENSG00000186143|ENSG00000186143	ENST00000432962|ENST00000335524	.|T	.|0.32753	.|1.44	4.67|4.67	3.78|3.78	0.43462|0.43462	.|.	.|0.958574	.|0.08507	.|N	.|0.935541	T|T	0.34774|0.34774	0.0909|0.0909	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	1|1	.|D	.|0.53312	.|0.959	.|P	.|0.51615	.|0.675	T|T	0.21381|0.21381	-1.0247|-1.0247	6|10	0.87932|0.59425	D|D	0|0.04	-2.4184|-2.4184	10.6794|10.6794	0.45804|0.45804	0.0:0.1934:0.8066:0.0|0.0:0.1934:0.8066:0.0	.|.	.|258	.|Q53SZ7	.|CB053_HUMAN	V|S	93|258	.|ENSP00000335017:P258S	ENSP00000393468:A93V|ENSP00000335017:P258S	A|P	-|-	2|1	0|0	C2orf53|C2orf53	27213930|27213930	0.971000|0.971000	0.33674|0.33674	0.163000|0.163000	0.22734|0.22734	0.184000|0.184000	0.23303|0.23303	2.911000|2.911000	0.48774|0.48774	1.153000|1.153000	0.42468|0.42468	0.561000|0.561000	0.74099|0.74099	GCC|CCC	.	.	.	none		0.657	C2orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250188.1			A	27360426	G	A	27360426	3	1	35	1	0	0	0	0	1	0	0	0	2176	1203	42	2	470	2	C2orf53	2	27360426	Missense_Mutation	SNP	G	TCGA-5P-A9K6-01A-11D-A42J-10		27360426	215838947	3	2524											
DPP10	57628	hgsc.bcm.edu	37	chr2	116593770	116593770	+	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	tgcatcaatgatcttaaaatCagatgaaaagctttttaaat	17	14	5	5	0	3	3	2	2	1	1	3	3	3	3	0	0	2	2	0	0	7	4			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr2:116593770C>A	ENST00000410059.1	+	22	2468	c.1988C>A	c.(1987-1989)tCa>tAa	p.S663*	DPP10_ENST00000393147.2_Nonsense_Mutation_p.S667*|DPP10_ENST00000409163.1_Nonsense_Mutation_p.S613*|DPP10_ENST00000310323.8_Nonsense_Mutation_p.S656*	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	663						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						ATCTTAAAATCAGATGAAAAG	0.343																																					p.S667X		Atlas-SNP	.											.	DPP10	415	.	0			c.C2000A						PASS	.						84	82	83					2																	116593770		2203	4300	6503	SO:0001587	stop_gained	57628	exon22			TAAAATCAGATGA	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.1988C>A	chr2.hg19:g.116593770C>A	ENSP00000386565:p.Ser663*	146.0	0.0	.		125.0	30.0	.	NM_001178034	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Nonsense_Mutation	SNP	ENST00000410059.1	hg19	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	C	41	8.960916	0.99018	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393147;ENST00000310323	.	.	.	5.67	5.67	0.87782	.	0.066573	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.2616	18.7538	0.91825	0.0:1.0:0.0:0.0	.	.	.	.	X	663;613;667;656	.	ENSP00000309066:S656X	S	+	2	0	DPP10	116310240	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.472000	0.60189	2.649000	0.89929	0.655000	0.94253	TCA	.	.	.	none		0.343	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		A	116593770	C	A	116593770	4	1	35	1	0	0	0	0	0	1	0	0	4729	838	29	4	2245	4	DPP10	2	116593770	Nonsense_Mutation	SNP	C	TCGA-5P-A9K6-01A-11D-A42J-10	89233344	116593770	126605603	4	2525											
LRP2	4036	hgsc.bcm.edu	37	chr2	169999196	169999197	+	Frame_Shift_Ins	INS	-	-	A																															ctcctacctgcatcacactcINSagtggtgctcccctctataa																								rs367958079		TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr2:169999196_169999197insA	ENST00000263816.3	-	71	13380_13381	c.13095_13096insT	c.(13093-13098)actgagfs	p.E4366fs		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	4366	EGF-like 16. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	GCATCACACTCAGTGGTGCTCC	0.574																																					p.E4366_C4367delinsX		Atlas-Indel,Pindel	.											.	LRP2	751	.	0			c.13096_13097insT						PASS	.																																			SO:0001589	frameshift_variant	4036	exon71			.		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.13096dupT	chr2.hg19:g.169999197_169999197dupA	ENSP00000263816:p.Glu4366fs	53.0	0.0	0		56.0	18.0	0.321429	NM_004525	O00711|Q16215	Frame_Shift_Ins	INS	ENST00000263816.3	hg19	CCDS2232.1																																																																																			.	.	.	none		0.574	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		A	169999197	-	A	169999196	7	5	35	1	0	1	1	0	0	0	0	0	8963	835	29	0	907	0	LRP2	2	169999196	Frame_Shift_Ins	INS	-	TCGA-5P-A9K6-01A-11D-A42J-10	53405426	169999196	73200177	5	2526											
NOP58	51602	hgsc.bcm.edu	37	chr2	203165004	203165004	+	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	tgactccacacttccaacctGttctaaaaaacgcaaaatag	16	9	4	12	1	1	1	0	1	1	0	3	1	3	1	3	0	2	2	3	0	7	4			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr2:203165004G>C	ENST00000264279.5	+	13	1542	c.1316G>C	c.(1315-1317)tGt>tCt	p.C439S		NM_015934.3	NP_057018.1	Q9Y2X3	NOP58_HUMAN	NOP58 ribonucleoprotein	439					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)			breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|lung(4)|prostate(2)	16						CTTCCAACCTGTTCTAAAAAA	0.333																																					p.C439S		Atlas-SNP	.											.	NOP58	41	.	0			c.G1316C						PASS	.						85	89	87					2																	203165004		2203	4299	6502	SO:0001583	missense	51602	exon13			CAACCTGTTCTAA		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.1316G>C	chr2.hg19:g.203165004G>C	ENSP00000264279:p.Cys439Ser	468.0	0.0	.		554.0	177.0	.	NM_015934	Q53SA4|Q6PK08|Q9P036|Q9UFN3	Missense_Mutation	SNP	ENST00000264279.5	hg19	CCDS2353.1	.	.	.	.	.	.	.	.	.	.	G	4.364	0.067124	0.08388	.	.	ENSG00000055044	ENST00000264279	T	0.58210	0.35	6.04	3.99	0.46301	.	0.334108	0.36815	N	0.002398	T	0.23410	0.0566	N	0.03608	-0.345	0.31765	N	0.6328	B	0.10296	0.003	B	0.01281	0.0	T	0.22521	-1.0214	10	0.07813	T	0.8	-8.107	8.6349	0.33941	0.0899:0.0:0.7125:0.1977	.	439	Q9Y2X3	NOP58_HUMAN	S	439	ENSP00000264279:C439S	ENSP00000264279:C439S	C	+	2	0	NOP58	202873249	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.010000	0.40913	1.457000	0.47850	0.563000	0.77884	TGT	.	.	.	none		0.333	NOP58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256313.2	NM_015934		C	203165004	G	C	203165004	3	2	35	1	0	0	0	0	1	0	0	0	10547	1377	48	4	1366	4	NOP58	2	203165004	Missense_Mutation	SNP	G	TCGA-5P-A9K6-01A-11D-A42J-10	33165808	203165004	40034369	6	2527											
TRIM42	287015	hgsc.bcm.edu	37	chr3	140409996	140409996	+	Missense_Mutation	SNP	A	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	tgtttaaagttagagccatcAatgataatggtcctgggcaa	13	12	10	6	0	1	2	1	1	0	1	2	2	2	2	2	2	1	3	2	2	6	4			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr3:140409996A>C	ENST00000286349.3	+	4	2238	c.2047A>C	c.(2047-2049)Aat>Cat	p.N683H		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	683	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(11)|lung(33)|ovary(2)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						TAGAGCCATCAATGATAATGG	0.438																																					p.N683H		Atlas-SNP	.											.	TRIM42	143	.	0			c.A2047C						PASS	.						152	148	149					3																	140409996		2203	4300	6503	SO:0001583	missense	287015	exon4			GCCATCAATGATA	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.2047A>C	chr3.hg19:g.140409996A>C	ENSP00000286349:p.Asn683His	118.0	0.0	.		118.0	30.0	.	NM_152616	A1L4B4|Q8N832|Q8NDL3	Missense_Mutation	SNP	ENST00000286349.3	hg19	CCDS3113.1	.	.	.	.	.	.	.	.	.	.	A	18.79	3.699132	0.68501	.	.	ENSG00000155890	ENST00000286349	T	0.62232	0.04	5.46	5.46	0.80206	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.084638	0.49916	D	0.000130	T	0.66703	0.2816	N	0.24115	0.695	0.36090	D	0.843388	D	0.89917	1.0	D	0.91635	0.999	T	0.75739	-0.3212	10	0.87932	D	0	-29.3416	11.9122	0.52745	1.0:0.0:0.0:0.0	.	683	Q8IWZ5	TRI42_HUMAN	H	683	ENSP00000286349:N683H	ENSP00000286349:N683H	N	+	1	0	TRIM42	141892686	1.000000	0.71417	0.993000	0.49108	0.989000	0.77384	5.754000	0.68743	2.074000	0.62210	0.528000	0.53228	AAT	.	.	.	none		0.438	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616		C	140409996	A	C	140409996	3	2	35	1	0	0	0	0	1	0	0	0	16529	130	5	5	2061	5	TRIM42	3	140409996	Missense_Mutation	SNP	A	TCGA-5P-A9K6-01A-11D-A42J-10		140409996	57612434	7	2528											
EIF4G1	1981	hgsc.bcm.edu	37	chr3	184042785	184042785	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaactgaagatgttaacagaGgcaataatgcatgactgtgt	16	10	10	5	0	0	4	0	2	0	2	0	4	0	4	0	1	3	3	0	1	5	2			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr3:184042785G>A	ENST00000346169.2	+	18	3010	c.2739G>A	c.(2737-2739)gaG>gaA	p.E913E	EIF4G1_ENST00000350481.5_Silent_p.E749E|EIF4G1_ENST00000342981.4_Silent_p.E914E|EIF4G1_ENST00000352767.3_Silent_p.E920E|EIF4G1_ENST00000382330.3_Silent_p.E920E|EIF4G1_ENST00000435046.2_Silent_p.E717E|SNORD66_ENST00000390856.1_RNA|EIF4G1_ENST00000424196.1_Silent_p.E920E|EIF4G1_ENST00000414031.1_Silent_p.E873E|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000441154.1_Silent_p.E750E|EIF4G1_ENST00000427845.1_Silent_p.E827E|EIF4G1_ENST00000392537.2_Silent_p.E826E|EIF4G1_ENST00000434061.2_Silent_p.E718E|EIF4G1_ENST00000411531.1_Silent_p.E874E|EIF4G1_ENST00000319274.6_Silent_p.E913E	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	913	eIF3/EIF4A-binding.				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)			TGTTAACAGAGGCAATAATGC	0.478																																					p.E920E		Atlas-SNP	.											.	EIF4G1	151	.	0			c.G2760A						PASS	.						111	114	113					3																	184042785		2203	4300	6503	SO:0001819	synonymous_variant	1981	exon19			AACAGAGGCAATA	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.2739G>A	chr3.hg19:g.184042785G>A		71.0	0.0	.		67.0	25.0	.	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Silent	SNP	ENST00000346169.2	hg19	CCDS3259.1																																																																																			.	.	.	none		0.478	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917		A	184042785	G	A	184042785	2	1	35	1	0	0	0	0	0	0	0	1	5038	991	35	2		2	EIF4G1	3	184042785	Silent	SNP	G	TCGA-5P-A9K6-01A-11D-A42J-10	43632789	184042785	13979645	8	2529											
NKX3-2	579	hgsc.bcm.edu	37	chr4	13543692	13543692	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tagtacgggtaatagtaggaGggctgcagtggcagaagcga	12	7	17	5	2	0	1	0	0	0	1	0	3	0	2	0	4	3	6	0	4	6	5			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr4:13543692G>A	ENST00000382438.5	-	2	1562	c.927C>T	c.(925-927)ccC>ccT	p.P309P		NM_001189.3	NP_001180.1	P78367	NKX32_HUMAN	NK3 homeobox 2	309					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						AATAGTAGGAGGGCTGCAGTG	0.657																																					p.P309P		Atlas-SNP	.											.	NKX3-2	15	.	0			c.C927T						PASS	.						41	36	38					4																	13543692		2200	4299	6499	SO:0001819	synonymous_variant	579	exon2			GTAGGAGGGCTGC	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.927C>T	chr4.hg19:g.13543692G>A		280.0	0.0	.		335.0	90.0	.	NM_001189	Q2M2I7	Silent	SNP	ENST00000382438.5	hg19	CCDS3410.1																																																																																			.	.	.	none		0.657	NKX3-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207317.3			A	13543692	G	A	13543692	2	1	35	1	0	0	0	0	0	0	0	1	10463	987	35	2		2	NKX3-2	4	13543692	Silent	SNP	G	TCGA-5P-A9K6-01A-11D-A42J-10		13543692	177610584	9	2530											
RUFY3	22902	hgsc.bcm.edu	37	chr4	71660584	71660584	+	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	1	0	0	0	0	0	0	0	0	gacaggagcatcccaggaagGggttcccagaagtcagaatc	13	5	13	10	0	1	2	1	0	0	2	4	5	3	4	2	4	1	2	2	4	3	1			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr4:71660584G>A	ENST00000226328.4	+	0	4233				RUFY3_ENST00000381006.3_Silent_p.R510R|RUFY3_ENST00000502653.1_Silent_p.R457R	NM_014961.3	NP_055776.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3						negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)				endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			TCCCAGGAAGGGGTTCCCAGA	0.388																																					p.R510R		Atlas-SNP	.											.	RUFY3	61	.	0			c.G1530A						PASS	.						132	137	135					4																	71660584		2203	4300	6503	SO:0001628	intergenic_variant	22902	exon14			AGGAAGGGGTTCC	AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189		"Zinc fingers, FYVE domain containing"	30285	protein-coding gene	gene with protein product	"single axon-related 1"	611194				17439943	Standard	NM_001130709		Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910		chr4.hg19:g.71660584G>A		126.0	0.0	.		137.0	49.0	.	NM_001037442	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	Silent	SNP	ENST00000226328.4	hg19	CCDS3547.1																																																																																			.	.	.	none		0.388	RUFY3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252161.2	NM_014961		A	71660584	G	A	71660584	1	1	35	0	1	0	0	0	0	0	0	0	13753	1223	43	2		2	RUFY3	4	71660584	IGR	SNP	G	TCGA-5P-A9K6-01A-11D-A42J-10	58116892	71660584	119493692	10	2531											
HNRPDL	9987	hgsc.bcm.edu	37	chr4	83350614	83350614	+	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	ccgggcgccgcctgcgccctCcctttatagccgccccgccc	2	6	10	23	6	0	0	0	0	0	0	1	0	1	0	9	1	2	0	9	1	2	3			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr4:83350614C>G	ENST00000295470.5	-	1	405	c.230G>C	c.(229-231)gGa>gCa	p.G77A	HNRNPDL_ENST00000602300.1_5'Flank|HNRNPDL_ENST00000514511.1_5'Flank|HNRNPDL_ENST00000349655.4_5'Flank|ENOPH1_ENST00000509635.1_5'Flank|ENOPH1_ENST00000273920.3_5'Flank|HNRNPDL_ENST00000502762.1_Missense_Mutation_p.G77A	NM_001207000.1|NM_031372.3	NP_001193929.1|NP_112740.1	O14979	HNRDL_HUMAN	heterogeneous nuclear ribonucleoprotein D-like	77					regulation of gene expression (GO:0010468)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|single-stranded DNA binding (GO:0003697)										CCTGCGCCCTCCCTTTATAGC	0.741																																					p.G77A		Atlas-SNP	.											.	HNRPDL	35	.	0			c.G230C						PASS	.						7	10	9					4																	83350614		2072	4194	6266	SO:0001583	missense	9987	exon1			CGCCCTCCCTTTA	D89092	CCDS3593.1, CCDS75153.1	4q21.22	2013-06-12		2013-06-12	ENSG00000152795	ENSG00000152795		"RNA binding motif (RRM) containing"	5037	protein-coding gene	gene with protein product		607137		HNRPDL		10072754, 9524220	Standard	NM_001207000		Approved	JKTBP, laAUF1	uc003hmr.3	O14979	OTTHUMG00000130299	ENST00000295470.5:c.230G>C	chr4.hg19:g.83350614C>G	ENSP00000295470:p.Gly77Ala	68.0	0.0	.		87.0	32.0	.	NM_031372	Q6SPF2|Q7KZ74|Q7KZ75|Q96IM0|Q96S43	Missense_Mutation	SNP	ENST00000295470.5	hg19	CCDS3593.1	.	.	.	.	.	.	.	.	.	.	c	19.68	3.873638	0.72180	.	.	ENSG00000152795	ENST00000295470;ENST00000502762	T;T	0.66460	-0.21;-0.21	4.37	3.5	0.40072	.	0.357050	0.20341	N	0.094229	T	0.42877	0.1222	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.44877	-0.9299	10	0.87932	D	0	.	6.9493	0.24536	0.0:0.7224:0.1789:0.0988	.	77	O14979	HNRDL_HUMAN	A	77	ENSP00000295470:G77A;ENSP00000422040:G77A	ENSP00000295470:G77A	G	-	2	0	HNRPDL	83569638	0.998000	0.40836	1.000000	0.80357	0.803000	0.45373	0.789000	0.26886	2.132000	0.65825	0.305000	0.20034	GGA	.	.	.	none		0.741	HNRNPDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252644.1	NM_005463		G	83350614	C	G	83350614	3	3	35	1	0	0	0	0	1	0	0	0	7283	855	30	4	1060	4	HNRPDL	4	83350614	Missense_Mutation	SNP	C	TCGA-5P-A9K6-01A-11D-A42J-10	11690030	83350614	107803662	11	2532											
NNT	23530	hgsc.bcm.edu	37	chr5	43613093	43613093	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggcattgtctcctgctggtGttcagaacttggtcaagcag	7	13	12	9	0	3	1	2	0	1	1	4	1	3	1	1	3	3	4	1	3	2	3			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr5:43613093G>A	ENST00000264663.5	+	3	456	c.235G>A	c.(235-237)Gtt>Att	p.V79I	NNT_ENST00000512996.2_5'UTR|NNT_ENST00000344920.4_Missense_Mutation_p.V79I	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	79					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					TCCTGCTGGTGTTCAGAACTT	0.473																																					p.V79I		Atlas-SNP	.											.	NNT	92	.	0			c.G235A						PASS	.						168	169	169					5																	43613093		2203	4300	6503	SO:0001583	missense	23530	exon3			GCTGGTGTTCAGA	U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.235G>A	chr5.hg19:g.43613093G>A	ENSP00000264663:p.Val79Ile	132.0	0.0	.		126.0	54.0	.	NM_182977	Q16796|Q2TB60|Q8N3V4	Missense_Mutation	SNP	ENST00000264663.5	hg19	CCDS3949.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.598252	0.87055	.	.	ENSG00000112992	ENST00000505678;ENST00000512422;ENST00000264663;ENST00000344920	D;D;D;D	0.82984	-1.67;-1.67;-1.67;-1.67	5.7	5.7	0.88788	Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-1 (1);Alanine dehydrogenase/PNT, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.88451	0.6440	M	0.81179	2.53	0.80722	D	1	P	0.46859	0.885	P	0.48901	0.594	D	0.89154	0.3525	10	0.59425	D	0.04	-29.0904	19.8481	0.96728	0.0:0.0:1.0:0.0	.	79	Q13423	NNTM_HUMAN	I	79	ENSP00000427670:V79I;ENSP00000421886:V79I;ENSP00000264663:V79I;ENSP00000343873:V79I	ENSP00000264663:V79I	V	+	1	0	NNT	43648850	1.000000	0.71417	0.979000	0.43373	0.954000	0.61252	9.584000	0.98220	2.705000	0.92388	0.650000	0.86243	GTT	.	.	.	none		0.473	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977		A	43613093	G	A	43613093	3	1	35	1	0	0	0	0	1	0	0	0	10517	1377	48	2	241	2	NNT	5	43613093	Missense_Mutation	SNP	G	TCGA-5P-A9K6-01A-11D-A42J-10		43613093	137302167	12	2533											
CSF1R	1436	hgsc.bcm.edu	37	chr5	149459890	149459890	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctagcacgttccagggcCgggcagggtctagagtagag	8	7	17	9	2	1	2	0	0	1	2	2	2	2	2	2	3	2	5	2	3	3	4	rs535129002		TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr5:149459890C>T	ENST00000286301.3	-	4	608	c.317G>A	c.(316-318)cGg>cAg	p.R106Q	CSF1R_ENST00000543093.1_Missense_Mutation_p.R106Q	NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	106					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)	GTTCCAGGGCCGGGCAGGGTC	0.617																																					p.R106Q		Atlas-SNP	.											.	CSF1R	250	.	0			c.G317A						PASS	.						36	35	35					5																	149459890		2203	4299	6502	SO:0001583	missense	1436	exon4			CAGGGCCGGGCAG	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.317G>A	chr5.hg19:g.149459890C>T	ENSP00000286301:p.Arg106Gln	49.0	0.0	.		67.0	5.0	.	NM_005211	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Missense_Mutation	SNP	ENST00000286301.3	hg19	CCDS4302.1	.	.	.	.	.	.	.	.	.	.	C	12.29	1.892951	0.33442	.	.	ENSG00000182578	ENST00000286301;ENST00000543093	T;T	0.04758	3.56;3.56	4.92	1.53	0.23141	.	0.583037	0.14309	N	0.327833	T	0.07863	0.0197	L	0.56769	1.78	0.09310	N	1	D;D;P	0.63880	0.993;0.987;0.929	P;B;B	0.50049	0.629;0.396;0.211	T	0.28996	-1.0026	10	0.29301	T	0.29	.	5.7207	0.17985	0.0:0.5844:0.0:0.4156	.	106;106;106	B4DG86;B5A955;P07333	.;.;CSF1R_HUMAN	Q	106	ENSP00000286301:R106Q;ENSP00000445282:R106Q	ENSP00000286301:R106Q	R	-	2	0	CSF1R	149440083	0.000000	0.05858	0.015000	0.15790	0.087000	0.18053	-0.169000	0.09911	0.445000	0.26639	0.561000	0.74099	CGG	.	.	.	none		0.617	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211		T	149459890	C	T	149459890	3	4	35	1	0	0	0	0	1	0	0	0	3934	652	23	1	2677	1	CSF1R	5	149459890	Missense_Mutation	SNP	C	TCGA-5P-A9K6-01A-11D-A42J-10	105846797	149459890	31455370	13	2534											
C6orf126	389383	hgsc.bcm.edu	37	chr6	35745347	35745347	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggccagaataaccatgatcTgcttgccccaggtgaggccc	9	7	12	13	0	1	3	0	2	1	1	1	3	1	3	5	3	3	1	5	3	2	2			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr6:35745347T>C	ENST00000403376.3	+	2	196	c.196T>C	c.(196-198)Tgc>Cgc	p.C66R	CLPSL2_ENST00000360454.2_Missense_Mutation_p.C66R|CLPSL2_ENST00000481904.1_3'UTR	NM_207409.2	NP_997292.2	Q6UWE3	COLL2_HUMAN	colipase-like 2	66					digestion (GO:0007586)|lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	enzyme activator activity (GO:0008047)										AACCATGATCTGCTTGCCCCA	0.557																																					p.C66R		Atlas-SNP	.											.	.	.	.	0			c.T196C						PASS	.						42	41	41					6																	35745347		2203	4300	6503	SO:0001583	missense	389383	exon2			ATGATCTGCTTGC		CCDS4810.2, CCDS69095.1	6p21.31	2014-01-28	2012-02-06	2012-02-06	ENSG00000196748	ENSG00000196748			21250	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 126"	C6orf126			Standard	NM_001286550		Approved	dJ510O8.5, UNQ3045	uc010jvz.1	Q6UWE3	OTTHUMG00000014581	ENST00000403376.3:c.196T>C	chr6.hg19:g.35745347T>C	ENSP00000385898:p.Cys66Arg	73.0	0.0	.		70.0	19.0	.	NM_207409	B0QZ45|Q5T9G3	Missense_Mutation	SNP	ENST00000403376.3	hg19	CCDS4810.2	.	.	.	.	.	.	.	.	.	.	T	14.54	2.565760	0.45694	.	.	ENSG00000196748	ENST00000360454;ENST00000403376	.	.	.	3.41	2.2	0.27929	.	0.000000	0.39759	N	0.001275	T	0.61502	0.2352	M	0.75085	2.285	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76071	0.982;0.987	T	0.64428	-0.6410	9	0.87932	D	0	-20.7405	6.6191	0.22792	0.0:0.0:0.2463:0.7537	.	66;66	Q6UWE3;Q6UWE3-2	CF126_HUMAN;.	R	66	.	ENSP00000353639:C66R	C	+	1	0	C6orf126	35853325	0.936000	0.31750	0.532000	0.27989	0.271000	0.26615	1.611000	0.36879	0.645000	0.30675	0.459000	0.35465	TGC	.	.	.	none		0.557	CLPSL2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280618.2	NM_207409		C	35745347	T	C	35745347	3	2	35	1	0	0	0	0	1	0	0	0	2328	1580	55	3	202	3	C6orf126	6	35745347	Missense_Mutation	SNP	T	TCGA-5P-A9K6-01A-11D-A42J-10		35745347	135369720	14	2535											
SLC22A7	10864	hgsc.bcm.edu	37	chr6	43268946	43268946	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccacaggtacttgctccacTgtgccaggctcaatgggcgg	7	8	12	14	1	1	0	1	0	0	0	2	0	2	0	3	4	3	3	3	4	2	2			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr6:43268946T>C	ENST00000372585.5	+	6	996	c.901T>C	c.(901-903)Tgt>Cgt	p.C301R	SLC22A7_ENST00000372574.3_Missense_Mutation_p.C299R|SLC22A7_ENST00000372589.3_Missense_Mutation_p.C299R|SLC22A7_ENST00000487175.1_3'UTR	NM_153320.2	NP_696961.2	Q9Y694	S22A7_HUMAN	solute carrier family 22 (organic anion transporter), member 7	301					organic anion transport (GO:0015711)|response to stilbenoid (GO:0035634)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			NS(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(3)	26			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)		Acetylsalicylic acid(DB00945)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Cimetidine(DB00501)|Clarithromycin(DB01211)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Docetaxel(DB01248)|Enalapril(DB00584)|Erythromycin(DB00199)|Fluorouracil(DB00544)|Ganciclovir(DB01004)|Glyburide(DB01016)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Oxtriphylline(DB01303)|Oxytetracycline(DB00595)|Pravastatin(DB00175)|Probenecid(DB01032)|Rifampicin(DB01045)|Salicylic acid(DB00936)|Testosterone(DB00624)|Tetracycline(DB00759)|Theophylline(DB00277)|Valproic Acid(DB00313)|Zalcitabine(DB00943)|Zidovudine(DB00495)	CTTGCTCCACTGTGCCAGGCT	0.577																																					p.C301R		Atlas-SNP	.											.	SLC22A7	69	.	0			c.T901C						PASS	.						174	158	163					6																	43268946		2203	4300	6503	SO:0001583	missense	10864	exon5			CTCCACTGTGCCA	AF097518	CCDS4892.1, CCDS4893.2	6p21.1	2013-05-22			ENSG00000137204	ENSG00000137204		"Solute carriers"	10971	protein-coding gene	gene with protein product		604995				9650585, 10773670	Standard	XM_006714970		Approved	NLT, OAT2	uc003out.3	Q9Y694	OTTHUMG00000014726	ENST00000372585.5:c.901T>C	chr6.hg19:g.43268946T>C	ENSP00000361666:p.Cys301Arg	35.0	0.0	.		47.0	20.0	.	NM_153320	B2CZX6|Q5T046|Q5T048|Q5T050|Q9H2W5	Missense_Mutation	SNP	ENST00000372585.5	hg19	CCDS4893.2	.	.	.	.	.	.	.	.	.	.	T	17.37	3.373115	0.61624	.	.	ENSG00000137204	ENST00000372589;ENST00000372585;ENST00000372574	T;T;T	0.55413	0.52;0.52;0.52	4.95	4.95	0.65309	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.100743	0.64402	D	0.000001	T	0.66848	0.2831	M	0.86028	2.79	0.80722	D	1	D;D;D	0.67145	0.987;0.984;0.996	D;D;D	0.68943	0.961;0.935;0.96	T	0.74222	-0.3735	10	0.87932	D	0	.	12.1803	0.54208	0.0:0.0:0.0:1.0	.	301;299;299	Q9Y694;Q9Y694-2;Q9Y694-3	S22A7_HUMAN;.;.	R	299;301;299	ENSP00000361670:C299R;ENSP00000361666:C301R;ENSP00000361655:C299R	ENSP00000361655:C299R	C	+	1	0	SLC22A7	43376924	1.000000	0.71417	0.980000	0.43619	0.525000	0.34531	5.033000	0.64146	1.871000	0.54225	0.374000	0.22700	TGT	.	.	.	none		0.577	SLC22A7-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040588.1			C	43268946	T	C	43268946	3	2	35	1	0	0	0	0	1	0	0	0	14472	1580	55	3	919	3	SLC22A7	6	43268946	Missense_Mutation	SNP	T	TCGA-5P-A9K6-01A-11D-A42J-10	7523599	43268946	127846121	15	2536											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152589267	152589267	+	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	actggctactgagcgaaggaGactcttctgctcggctaatt	9	11	11	10	2	2	2	0	1	2	1	3	4	2	2	0	3	3	3	0	3	3	4			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr6:152589267G>T	ENST00000367255.5	-	100	19340	c.18739C>A	c.(18739-18741)Ctc>Atc	p.L6247I	SYNE1_ENST00000356820.4_Missense_Mutation_p.L771I|SYNE1_ENST00000265368.4_Missense_Mutation_p.L6247I|SYNE1_ENST00000448038.1_Missense_Mutation_p.L6176I|SYNE1_ENST00000423061.1_Missense_Mutation_p.L6176I|SYNE1_ENST00000341594.5_Missense_Mutation_p.L5859I	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6247					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)		GAGCGAAGGAGACTCTTCTGC	0.443										HNSCC(10;0.0054)																											p.L6247I		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C18739A						PASS	.						100	100	100					6																	152589267		2203	4300	6503	SO:0001583	missense	23345	exon100			GAAGGAGACTCTT	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.18739C>A	chr6.hg19:g.152589267G>T	ENSP00000356224:p.Leu6247Ile	83.0	0.0	.		87.0	30.0	.	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	18.04	3.534749	0.64972	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820	T;T;T;T;T;T	0.73681	-0.68;-0.7;-0.77;-0.69;-0.4;0.88	5.74	5.74	0.90152	.	0.000000	0.50627	D	0.000101	T	0.70298	0.3208	M	0.72894	2.215	0.49687	D	0.999816	P;P;P	0.46912	0.818;0.818;0.886	B;B;P	0.48677	0.382;0.382;0.586	T	0.70306	-0.4908	10	0.34782	T	0.22	.	11.0403	0.47827	0.0687:0.0:0.8012:0.1301	.	6247;6247;6176	Q8NF91;E7EQI5;Q8NF91-4	SYNE1_HUMAN;.;.	I	6247;6176;6247;6176;5859;771	ENSP00000356224:L6247I;ENSP00000396024:L6176I;ENSP00000265368:L6247I;ENSP00000390975:L6176I;ENSP00000341887:L5859I;ENSP00000349276:L771I	ENSP00000265368:L6247I	L	-	1	0	SYNE1	152630960	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	4.624000	0.61254	2.873000	0.98535	0.563000	0.77884	CTC	.	.	.	none		0.443	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152589267	G	T	152589267	3	4	35	1	0	0	0	0	1	0	0	0	15457	942	33	4	7915	4	SYNE1	6	152589267	Missense_Mutation	SNP	G	TCGA-5P-A9K6-01A-11D-A42J-10	109320321	152589267	18525800	16	2537											
SP8	221833	hgsc.bcm.edu	37	chr7	20824939	20825106	+	In_Frame_Del	DEL	GAGCCGCCGCCGCCGCCCCCGCCGCCGCCGCCGCTGCCCCCGGAAACTCCGGGGGCCTGGAAAACAGAGTAGTCGTTGGCGAAGGGCGAGCTGGAGGCGGCGGCTGCGGCGGCGGCGGCGGCGGCTGCGGCGCTGCTGGAGGTGAGGGAGAAGGCGCTGGAGCCAGGC	GAGCCGCCGCCGCCGCCCCCGCCGCCGCCGCCGCTGCCCCCGGAAACTCCGGGGGCCTGGAAAACAGAGTAGTCGTTGGCGAAGGGCGAGCTGGAGGCGGCGGCTGCGGCGGCGGCGGCGGCGGCTGCGGCGCTGCTGGAGGTGAGGGAGAAGGCGCTGGAGCCAGGC	-																															cgtcctgcgagtgcgcggagGagccgccgccgccgcccccg																								rs185796187|rs550042701|rs372591893|rs201180283	byFrequency	TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	GAGCCGCCGCCGCCGCCCCCGCCGCCGCCGCCGCTGCCCCCGGAAACTCCGGGGGCCTGGAAAACAGAGTAGTCGTTGGCGAAGGGCGAGCTGGAGGCGGCGGCTGCGGCGGCGGCGGCGGCGGCTGCGGCGCTGCTGGAGGTGAGGGAGAAGGCGCTGGAGCCAGGC	GAGCCGCCGCCGCCGCCCCCGCCGCCGCCGCCGCTGCCCCCGGAAACTCCGGGGGCCTGGAAAACAGAGTAGTCGTTGGCGAAGGGCGAGCTGGAGGCGGCGGCTGCGGCGGCGGCGGCGGCGGCTGCGGCGCTGCTGGAGGTGAGGGAGAAGGCGCTGGAGCCAGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr7:20824939_20825106delGAGCCGCCGCCGCCGCCCCCGCCGCCGCCGCCGCTGCCCCCGGAAACTCCGGGGGCCTGGAAAACAGAGTAGTCGTTGGCGAAGGGCGAGCTGGAGGCGGCGGCTGCGGCGGCGGCGGCGGCGGCTGCGGCGCTGCTGGAGGTGAGGGAGAAGGCGCTGGAGCCAGGC	ENST00000361443.4	-	3	513_680	c.276_443delGCCTGGCTCCAGCGCCTTCTCCCTCACCTCCAGCAGCGCCGCAGCCGCCGCCGCCGCCGCCGCAGCCGCCGCCTCCAGCTCGCCCTTCGCCAACGACTACTCTGTTTTCCAGGCCCCCGGAGTTTCCGGGGGCAGCGGCGGCGGCGGCGGGGGCGGCGGCGGCGGCTC	c.(274-444)tcgcctggctccagcgccttctccctcacctccagcagcgccgcagccgccgccgccgccgccgcagccgccgcctccagctcgcccttcgccaacgactactctgttttccaggcccccggagtttccgggggcagcggcggcggcggcgggggcggcggcggcggctcc>tcc	p.92_148SPGSSAFSLTSSSAAAAAAAAAAAASSSPFANDYSVFQAPGVSGGSGGGGGGGGGGS>S	SP8_ENST00000418710.2_In_Frame_Del_p.110_166SPGSSAFSLTSSSAAAAAAAAAAAASSSPFANDYSVFQAPGVSGGSGGGGGGGGGGS>S	NM_198956.2	NP_945194.1	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor	92	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)	p.G165delG(1)|p.G147delG(1)		NS(1)|central_nervous_system(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	8						GTGCGCGGAGGAgccgccgccgccgcccccgccgccgccgccgctgcccccgGAAACTCCGGGGGCCTGGAAAACAGAGTAGTCGTTGGCGAAGGGCGAGCTGGAggcggcggctgcggcggcggcggcggcggctgcggcgCTGCTGGAGGTGAGGGAGAAGGCGCTGGAGCCAGGCGAGCCGCCGC	0.758																																					p.111_166del		Pindel	.											.	SP8	43	.	2	Deletion - In frame(2)	central_nervous_system(2)	c.331_498del						PASS	.																																			SO:0001651	inframe_deletion	221833	exon2			.		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.276_443delGCCTGGCTCCAGCGCCTTCTCCCTCACCTCCAGCAGCGCCGCAGCCGCCGCCGCCGCCGCCGCAGCCGCCGCCTCCAGCTCGCCCTTCGCCAACGACTACTCTGTTTTCCAGGCCCCCGGAGTTTCCGGGGGCAGCGGCGGCGGCGGCGGGGGCGGCGGCGGCGGCTC	chr7.hg19:g.20824939_20825106delGAGCCGCCGCCGCCGCCCCCGCCGCCGCCGCCGCTGCCCCCGGAAACTCCGGGGGCCTGGAAAACAGAGTAGTCGTTGGCGAAGGGCGAGCTGGAGGCGGCGGCTGCGGCGGCGGCGGCGGCGGCTGCGGCGCTGCTGGAGGTGAGGGAGAAGGCGCTGGAGCCAGGC	ENSP00000354482:p.Ser92_Gly147del	50.0	0.0	.		99.0	10.0	0.101	NM_182700	Q7Z615|Q7Z616|Q96MJ1	In_Frame_Del	DEL	ENST00000361443.4	hg19	CCDS5372.1																																																																																			.	.	.	none		0.758	SP8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326904.2			-	20825106	GAGCCGCCGCCGCCGCCCCCGCCGCCGCCGCCGCTGCCCCCGGAAACTCCGGGGGCCTGGAAAACAGAGTAGTCGTTGGCGAAGGGCGAGCTGGAGGCGGCGGCTGCGGCGGCGGCGGCGGCGGCTGCGGCGCTGCTGGAGGTGAGGGAGAAGGCGCTGGAGCCAGGC	-	20824939	7	5	35	1	0	1	0	1	0	0	0	0	14983	1174	41	0	1033	0	SP8	7	20824939	In_Frame_Del	DEL	GAGCCGCCGCCGCCGCCCCCGCCGCCGCCGCCGCTGCCCCCGGAAACTCCGGGGGCCTGGAAAACAGAGTAGTCGTTGGCGAAGGGCGAGCTGGAGGCGGCGGCTGCGGCGGCGGCGGCGGCGGCTGCGGCGCTGCTGGAGGTGAGGGAGAAGGCGCTGGAGCCAGGC	TCGA-5P-A9K6-01A-11D-A42J-10		20824939	138313724	17	2538											
DNAJB9	4189	hgsc.bcm.edu	37	chr7	108213747	108213747	+	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	agcactgcaggactgtcactCaacgaagaggaaatatggtt	14	8	11	8	1	2	1	2	0	0	1	2	4	2	3	0	3	3	3	0	3	4	2			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr7:108213747C>T	ENST00000249356.3	+	3	1168	c.622C>T	c.(622-624)Caa>Taa	p.Q208*	DNAJB9_ENST00000465725.1_Intron	NM_012328.2	NP_036460.1	Q9UBS3	DNJB9_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 9	208					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						GACTGTCACTCAACGAAGAGG	0.378																																					p.Q208X		Atlas-SNP	.											.	DNAJB9	25	.	0			c.C622T						PASS	.						103	102	102					7																	108213747		2203	4300	6503	SO:0001587	stop_gained	4189	exon3			GTCACTCAACGAA	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.622C>T	chr7.hg19:g.108213747C>T	ENSP00000249356:p.Gln208*	46.0	0.0	.		74.0	36.0	.	NM_012328		Nonsense_Mutation	SNP	ENST00000249356.3	hg19	CCDS5752.1	.	.	.	.	.	.	.	.	.	.	C	41	8.877952	0.98988	.	.	ENSG00000128590	ENST00000249356	.	.	.	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.1901	0.93663	0.0:1.0:0.0:0.0	.	.	.	.	X	208	.	.	Q	+	1	0	DNAJB9	108000983	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	7.377000	0.79668	2.776000	0.95493	0.655000	0.94253	CAA	.	.	.	none		0.378	DNAJB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337414.1			T	108213747	C	T	108213747	4	4	35	1	0	0	0	0	0	1	0	0	4629	827	29	2	628	2	DNAJB9	7	108213747	Nonsense_Mutation	SNP	C	TCGA-5P-A9K6-01A-11D-A42J-10	87388808	108213747	50924916	18	2539											
SGK223	157285	hgsc.bcm.edu	37	chr8	8234618	8234618	+	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	cttggccctgggcagcagctGcatgttctatcttggcctgt	4	13	12	12	0	2	0	0	0	2	0	2	0	2	0	2	3	3	5	2	3	1	4			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr8:8234618G>T	ENST00000520004.1	-	3	1565	c.1301C>A	c.(1300-1302)gCa>gAa	p.A434E	SGK223_ENST00000330777.4_Missense_Mutation_p.A434E			Q86YV5	SG223_HUMAN		436							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GGCAGCAGCTGCATGTTCTAT	0.617																																					p.A434E	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.C1301A						PASS	.						61	67	65					8																	8234618		2053	4200	6253	SO:0001583	missense	0	exon2			GCAGCTGCATGTT																												ENST00000520004.1:c.1301C>A	chr8.hg19:g.8234618G>T	ENSP00000428054:p.Ala434Glu	42.0	0.0	.		54.0	15.0	.	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	hg19	CCDS43706.1	.	.	.	.	.	.	.	.	.	.	G	0.011	-1.703006	0.00719	.	.	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.56444	0.46;0.46	4.76	-0.32	0.12721	.	1.566350	0.03920	N	0.283453	T	0.36908	0.0984	L	0.36672	1.1	0.09310	N	1	B	0.31125	0.309	B	0.32289	0.143	T	0.13202	-1.0518	10	0.02654	T	1	.	5.1422	0.14965	0.3301:0.2621:0.4078:0.0	.	434	Q86YV5	SG223_HUMAN	E	434	ENSP00000330930:A434E;ENSP00000428054:A434E	ENSP00000330930:A434E	A	-	2	0	AC068353.1	8272028	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	1.166000	0.31834	-0.162000	0.10964	-0.175000	0.13238	GCA	.	.	.	none		0.617	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1			T	8234618	G	T	8234618	3	4	35	1	0	0	0	0	1	0	0	0	14223	1319	46	4	2923	4	SGK223	8	8234618	Missense_Mutation	SNP	G	TCGA-5P-A9K6-01A-11D-A42J-10		8234618	138129404	19	2540											
PKN3	29941	hgsc.bcm.edu	37	chr9	131477092	131477093	+	Frame_Shift_Ins	INS	-	-	AT																															acagcgcaccaaacgtccccINSatatggagcctaggactcga																										TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr9:131477092_131477093insAT	ENST00000291906.4	+	13	1993_1994	c.1600_1601insAT	c.(1600-1602)catfs	p.H534fs	PKN3_ENST00000485301.1_3'UTR	NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	534	Pro-rich.				epithelial cell migration (GO:0010631)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24						CAAACGTCCCCATATGGAGCCT	0.609																																					p.H534fs		Atlas-Indel,Pindel	.											PKN3,neck,malignant_melanoma,0,1	PKN3	62	.	0			c.1600_1601insAT						PASS	.																																			SO:0001589	frameshift_variant	29941	exon13			.	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.1603_1604dupAT	chr9.hg19:g.131477095_131477096dupAT	ENSP00000291906:p.His534fs	136.0	0.0	0		144.0	41.0	0.284722	NM_013355	Q9UM03	Frame_Shift_Ins	INS	ENST00000291906.4	hg19	CCDS6908.1																																																																																			.	.	.	none		0.609	PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054487.1	NM_013355		AT	131477093	-	AT	131477092	7	5	35	1	0	1	1	0	0	0	0	0	11988	594	21	0	1650	0	PKN3	9	131477092	Frame_Shift_Ins	INS	-	TCGA-5P-A9K6-01A-11D-A42J-10		131477092	9736339	20	2541											
ECD	11319	hgsc.bcm.edu	37	chr10	74920304	74920308	+	Splice_Site	DEL	CACCT	CACCT	-																															gccaaacatatgagcaggaaCacctcctaaaaacaagagaa																										TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	CACCT	CACCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr10:74920304_74920308delCACCT	ENST00000372979.4	-	3	413_417	c.207_211delAGGTG	c.(205-213)ggaggtgtt>ggtt	p.GV70fs	ECD_ENST00000610256.1_5'UTR|ECD_ENST00000454759.2_Splice_Site_p.GV70fs|ECD_ENST00000430082.2_Splice_Site_p.GV70fs	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	70					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)					TGAGCAGGAACACCTCCTAAAAACA	0.337																																					p.70_71del		Atlas-INDEL	.											.	ECD	50	.	0			c.208_212del						PASS	.																																			SO:0001630	splice_region_variant	11319	exon3			.	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.206-1AGGTG>-	chr10.hg19:g.74920304_74920308delCACCT		182.0	0.0	0		210.0	48.0	0.228571	NM_001135752	C9JX46|E9PAW8	Frame_Shift_Del	DEL	ENST00000372979.4	hg19	CCDS7321.1																																																																																			.	.	.	none		0.337	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265	Frame_Shift_Del	-	74920308	CACCT	-	74920304	8	5	35	1	0	1	0	1	0	0	1	0	4890	478	17	0	1874	0	ECD	10	74920304	Splice_Site	DEL	CACCT	TCGA-5P-A9K6-01A-11D-A42J-10		74920304	60614443	21	2542	29	3									
ECD	11319	hgsc.bcm.edu	37	chr10	74920305	74920311	+	Splice_Site	DEL	ACCTCCT	ACCTCCT	-																															ccaaacatatgagcaggaacAcctcctaaaaacaagagaaa																										TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	ACCTCCT	ACCTCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr10:74920305_74920311delACCTCCT	ENST00000372979.4	-	3	412_416	c.206_210delAGGAGGT	c.(205-210)gaggag>g	p.EE69fs	ECD_ENST00000610256.1_5'UTR|ECD_ENST00000454759.2_Splice_Site_p.EE69fs|ECD_ENST00000430082.2_Splice_Site_p.EE69fs	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	69					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)					GAGCAGGAACACCTCCTAAAAACAAGA	0.343																																					p.69_71del		Pindel	.											.	ECD	50	.	0			c.206_211del						PASS	.																																			SO:0001630	splice_region_variant	11319	exon3			.	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.206-1AGGAGGT>-	chr10.hg19:g.74920305_74920311delACCTCCT		179.0	0.0	.		205.0	34.0	0.166	NM_001135752	C9JX46|E9PAW8	In_Frame_Del	DEL	ENST00000372979.4	hg19	CCDS7321.1																																																																																			.	.	.	none		0.343	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265	Frame_Shift_Del	-	74920311	ACCTCCT	-	74920305	8	5	35	1	0	1	0	1	0	0	1	0	4890	146	6	0	1875	0	ECD	10	74920305	Splice_Site	DEL	ACCTCCT	TCGA-5P-A9K6-01A-11D-A42J-10	1	74920305	60614442	22	2543	29	3									
ECD	11319	hgsc.bcm.edu	37	chr10	74920311	74920311	+	Splice_Site	SNP	T	T	G																															atatgagcaggaacacctccTaaaaacaagagaaaagcaac																										TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr10:74920311T>G	ENST00000372979.4	-	3	412		c.e3-2		ECD_ENST00000610256.1_Splice_Site|ECD_ENST00000454759.2_Splice_Site|ECD_ENST00000430082.2_Splice_Site	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)						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)					GAACACCTCCTAAAAACAAGA	0.338																																					.		Atlas-SNP	.											.	ECD	50	.	0			c.206-2A>C						PASS	.						75	69	71					10																	74920311		2203	4300	6503	SO:0001630	splice_region_variant	11319	exon4			ACCTCCTAAAAAC	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.206-2A>C	chr10.hg19:g.74920311T>G		175.0	0.0	.		204.0	49.0	.	NM_001135753	C9JX46|E9PAW8	Splice_Site	SNP	ENST00000372979.4	hg19	CCDS7321.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.063343	0.76187	.	.	ENSG00000122882	ENST00000372979;ENST00000430082;ENST00000454759;ENST00000413026	.	.	.	5.05	5.05	0.67936	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.7558	0.57335	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	ECD	74590317	1.000000	0.71417	0.998000	0.56505	0.938000	0.57974	7.209000	0.77916	1.907000	0.55213	0.533000	0.62120	.	.	.	.	none		0.338	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265	Intron	G	74920311	T	G	74920311	5	3	35	1	0	0	0	0	0	0	1	0	4890	1536	53	5	1881	5	ECD	10	74920311	Splice_Site	SNP	T	TCGA-5P-A9K6-01A-11D-A42J-10	6	74920311	60614436	23	2544	29	3									
INPP5F	79892	hgsc.bcm.edu	37	chr10	121586617	121586617	+	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	ggcagtcggtcccagtctctTagcagcacagatagtagcgt	9	9	12	11	2	1	1	0	0	1	1	4	1	2	1	1	2	3	4	1	2	3	3			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr10:121586617T>C	ENST00000360003.3	-	0	4113				INPP5F_ENST00000361976.2_Silent_p.L908L|INPP5F_ENST00000369080.3_Silent_p.L298L	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)			breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(2)|skin(2)	21						CCCAGTCTCTTAGCAGCACAG	0.478																																					p.L908L		Atlas-SNP	.											.	INPP5F	112	.	0			c.T2724C						PASS	.						127	102	111					10																	121586617		2203	4300	6503	SO:0001628	intergenic_variant	22876	exon20			GTCTCTTAGCAGC	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		chr10.hg19:g.121586617T>C		60.0	0.0	.		51.0	14.0	.	NM_014937	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Silent	SNP	ENST00000360003.3	hg19	CCDS7617.1																																																																																			.	.	.	none		0.478	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834		C	121586617	T	C	121586617	1	2	35	0	1	0	0	0	0	0	0	0	7765	1741	61	3		3	INPP5F	10	121586617	IGR	SNP	T	TCGA-5P-A9K6-01A-11D-A42J-10	46666306	121586617	13948130	24	2545											
AP2A2	161	hgsc.bcm.edu	37	chr11	977190	977190	+	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	ccccatgggcgactggacatCccgagtggtgcacctgctca	7	7	12	15	2	1	0	1	0	0	0	2	3	2	1	4	3	2	2	4	3	0	0			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr11:977190C>T	ENST00000448903.2	+	5	710	c.569C>T	c.(568-570)tCc>tTc	p.S190F	AP2A2_ENST00000534328.1_Missense_Mutation_p.S190F|AP2A2_ENST00000332231.5_Missense_Mutation_p.S190F	NM_001242837.1|NM_012305.3	NP_001229766.1|NP_036437.1	O94973	AP2A2_HUMAN	adaptor-related protein complex 2, alpha 2 subunit	190					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)	21		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)		GACTGGACATCCCGAGTGGTG	0.602																																					p.S190F		Atlas-SNP	.											.	AP2A2	50	.	0			c.C569T						PASS	.						59	67	65					11																	977190		2122	4216	6338	SO:0001583	missense	161	exon5			GGACATCCCGAGT	AB020706	CCDS44512.1, CCDS73234.1	11p15.5	2008-07-18			ENSG00000183020	ENSG00000183020			562	protein-coding gene	gene with protein product	"alpha-adaptin C; Huntingtin interacting protein J", "adaptin, alpha B", "clathrin-associated/assembly/adaptor protein, large, alpha 2"	607242		CLAPA2, ADTAB		9700202, 2564002	Standard	NM_012305		Approved	DKFZP564D1864, HYPJ, KIAA0899, HIP9	uc001lst.2	O94973	OTTHUMG00000165627	ENST00000448903.2:c.569C>T	chr11.hg19:g.977190C>T	ENSP00000413234:p.Ser190Phe	53.0	0.0	.		80.0	21.0	.	NM_012305	O75403|Q53ET1|Q96SI8	Missense_Mutation	SNP	ENST00000448903.2	hg19	CCDS44512.1	.	.	.	.	.	.	.	.	.	.	c	13.17	2.158320	0.38119	.	.	ENSG00000183020	ENST00000525796;ENST00000534328;ENST00000417081;ENST00000448903;ENST00000332231;ENST00000448757;ENST00000534485;ENST00000329626	T;T;T;T;T	0.38722	1.12;1.12;1.12;1.12;1.7	2.8	2.8	0.32819	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.075573	0.56097	D	0.000038	T	0.63616	0.2526	M	0.83603	2.65	0.58432	D	0.999998	P;D;D	0.71674	0.943;0.998;0.997	P;P;D	0.64237	0.86;0.856;0.923	T	0.73161	-0.4070	10	0.72032	D	0.01	-32.6353	14.8145	0.70020	0.0:1.0:0.0:0.0	.	83;190;190	Q59FN8;O94973-2;O94973	.;.;AP2A2_HUMAN	F	30;190;190;190;190;190;180;63	ENSP00000437228:S30F;ENSP00000436059:S190F;ENSP00000413234:S190F;ENSP00000327694:S190F;ENSP00000435756:S180F	ENSP00000328024:S63F	S	+	2	0	AP2A2	967190	1.000000	0.71417	0.102000	0.21198	0.011000	0.07611	7.541000	0.82084	1.895000	0.54865	0.586000	0.80456	TCC	.	.	.	none		0.602	AP2A2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385431.2	NM_012305		T	977190	C	T	977190	3	4	35	1	0	0	0	0	1	0	0	0	740	855	30	2	587	2	AP2A2	11	977190	Missense_Mutation	SNP	C	TCGA-5P-A9K6-01A-11D-A42J-10		977190	134029326	25	2546											
TPH1	7166	hgsc.bcm.edu	37	chr11	18051107	18051107	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatactttcgacgtttacggTagacattgtctttgaagccc	10	14	8	9	3	1	2	0	1	1	1	2	3	1	2	1	1	3	2	1	1	5	7			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr11:18051107T>C	ENST00000250018.2	-	4	984	c.422A>G	c.(421-423)tAc>tGc	p.Y141C	TPH1_ENST00000341556.2_Missense_Mutation_p.Y141C	NM_004179.2	NP_004170.1	P17752	TPH1_HUMAN	tryptophan hydroxylase 1	141					aromatic amino acid family metabolic process (GO:0009072)|bone remodeling (GO:0046849)|cellular nitrogen compound metabolic process (GO:0034641)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|mammary gland alveolus development (GO:0060749)|negative regulation of ossification (GO:0030279)|response to immobilization stress (GO:0035902)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|neuron projection (GO:0043005)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|tryptophan 5-monooxygenase activity (GO:0004510)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(14)|prostate(1)|stomach(1)	25					L-Tryptophan(DB00150)|Tetrahydrobiopterin(DB00360)	ACGTTTACGGTAGACATTGTC	0.264																																					p.Y141C		Atlas-SNP	.											.	TPH1	44	.	0			c.A422G						PASS	.						57	61	60					11																	18051107		2198	4285	6483	SO:0001583	missense	7166	exon4			TTACGGTAGACAT	X52836	CCDS7829.1	11p15.3-p14	2012-10-02	2008-07-31	2003-04-04	ENSG00000129167	ENSG00000129167	1.14.16.4		12008	protein-coding gene	gene with protein product	"tryptophan 5-monooxygenase"	191060	"tryptophan hydroxylase (tryptophan 5-monooxygenase)"	TPRH, TPH		1463016	Standard	NM_004179		Approved		uc001mnp.2	P17752	OTTHUMG00000166421	ENST00000250018.2:c.422A>G	chr11.hg19:g.18051107T>C	ENSP00000250018:p.Tyr141Cys	54.0	0.0	.		54.0	10.0	.	NM_004179	D3DQX6|O95188|O95189|Q16736|Q3KPG8	Missense_Mutation	SNP	ENST00000250018.2	hg19	CCDS7829.1	.	.	.	.	.	.	.	.	.	.	T	19.61	3.860327	0.71834	.	.	ENSG00000129167	ENST00000250018;ENST00000341556;ENST00000528338	D;D;D	0.99795	-6.78;-6.78;-6.78	5.75	5.75	0.90469	Aromatic amino acid hydroxylase, C-terminal (4);	0.000000	0.85682	D	0.000000	D	0.99873	0.9940	H	0.97659	4.05	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96375	0.9277	10	0.87932	D	0	-15.8182	16.0614	0.80839	0.0:0.0:0.0:1.0	.	141	P17752	TPH1_HUMAN	C	141;141;151	ENSP00000250018:Y141C;ENSP00000343550:Y141C;ENSP00000436081:Y151C	ENSP00000250018:Y141C	Y	-	2	0	TPH1	18007683	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.136000	0.71703	2.191000	0.70037	0.528000	0.53228	TAC	.	.	.	none		0.264	TPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389696.1	NM_004179		C	18051107	T	C	18051107	3	2	35	1	0	0	0	0	1	0	0	0	16413	1638	57	3	940	3	TPH1	11	18051107	Missense_Mutation	SNP	T	TCGA-5P-A9K6-01A-11D-A42J-10	17073917	18051107	116955409	26	2547											
ZNF259	8882	hgsc.bcm.edu	37	chr11	116655623	116655623	+	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	ttgcattctgggcagtttgtGctgaactggagcacctggaa	8	12	13	8	0	1	1	0	1	1	0	1	3	1	3	1	3	4	5	1	3	2	3			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr11:116655623G>A	ENST00000227322.3	-	8	827	c.768C>T	c.(766-768)agC>agT	p.S256S		NM_003904.3	NP_003895.1	O75312	ZPR1_HUMAN		256					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)		GGCAGTTTGTGCTGAACTGGA	0.507																																					p.S256S		Atlas-SNP	.											.	ZNF259	27	.	0			c.C768T						PASS	.						121	104	110					11																	116655623		2201	4296	6497	SO:0001819	synonymous_variant	8882	exon8			GTTTGTGCTGAAC																												ENST00000227322.3:c.768C>T	chr11.hg19:g.116655623G>A		98.0	0.0	.		94.0	38.0	.	NM_003904	Q2TAA0	Silent	SNP	ENST00000227322.3	hg19	CCDS8375.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.834|7.834	0.720560|0.720560	0.15372|0.15372	.|.	.|.	ENSG00000109917|ENSG00000109917	ENST00000444935|ENST00000429220	.|.	.|.	.|.	5.92|5.92	3.07|3.07	0.35406|0.35406	.|.	.|.	.|.	.|.	.|.	T|T	0.54143|0.54143	0.1840|0.1840	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.47873|0.47873	-0.9083|-0.9083	4|4	.|.	.|.	.|.	-17.5691|-17.5691	5.7069|5.7069	0.17913|0.17913	0.2102:0.0:0.6522:0.1376|0.2102:0.0:0.6522:0.1376	.|.	.|.	.|.	.|.	V|Y	256|183	.|.	.|.	A|H	-|-	2|1	0|0	ZNF259|ZNF259	116160833|116160833	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.685000|0.685000	0.39939|0.39939	0.961000|0.961000	0.29267|0.29267	0.845000|0.845000	0.35118|0.35118	0.655000|0.655000	0.94253|0.94253	GCA|CAC	.	.	.	none		0.507	ZNF259-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106283.2			A	116655623	G	A	116655623	2	1	35	1	0	0	0	0	0	0	0	1	17813	1310	46	2		2	ZNF259	11	116655623	Silent	SNP	G	TCGA-5P-A9K6-01A-11D-A42J-10	98604516	116655623	18350893	27	2548											
B4GALNT3	283358	hgsc.bcm.edu	37	chr12	668503	668503	+	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	cgggctgcttggcatctacaAgtctgacctggacaggattg	8	10	13	10	1	2	1	0	1	2	0	2	3	2	3	1	4	2	3	1	4	2	3			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr12:668503A>T	ENST00000266383.5	+	19	2817	c.2804A>T	c.(2803-2805)aAg>aTg	p.K935M		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	935					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)			GGCATCTACAAGTCTGACCTG	0.602																																					p.K935M		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.A2804T						PASS	.						127	132	130					12																	668503		2203	4300	6503	SO:0001583	missense	283358	exon19			TCTACAAGTCTGA	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.2804A>T	chr12.hg19:g.668503A>T	ENSP00000266383:p.Lys935Met	125.0	0.0	.		117.0	30.0	.	NM_173593	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	hg19	CCDS8504.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.539637	0.85917	.	.	ENSG00000139044	ENST00000266383	T	0.40756	1.02	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.69531	0.3121	M	0.89095	3.005	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.77024	-0.2741	10	0.87932	D	0	-40.3422	14.6956	0.69118	1.0:0.0:0.0:0.0	.	935	Q6L9W6	B4GN3_HUMAN	M	935	ENSP00000266383:K935M	ENSP00000266383:K935M	K	+	2	0	B4GALNT3	538764	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.223000	0.95203	1.930000	0.55929	0.379000	0.24179	AAG	.	.	.	none		0.602	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593		T	668503	A	T	668503	3	4	35	1	0	0	0	0	1	0	0	0	1268	72	3	5	2878	5	B4GALNT3	12	668503	Missense_Mutation	SNP	A	TCGA-5P-A9K6-01A-11D-A42J-10		668503	133183392	28	2549											
KIAA0528	9847	hgsc.bcm.edu	37	chr12	22606969	22606969	+	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	catggagaaaaccactgactCctccttcctaaataatagtg	14	10	6	11	0	0	2	0	1	0	1	3	3	3	2	4	1	1	0	4	1	6	4			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr12:22606969C>A	ENST00000333957.4	-	24	2987	c.2732G>T	c.(2731-2733)gGa>gTa	p.G911V	C2CD5_ENST00000545552.1_Missense_Mutation_p.G965V|C2CD5_ENST00000396028.2_Missense_Mutation_p.G953V|C2CD5_ENST00000544930.1_Missense_Mutation_p.G767V|C2CD5_ENST00000536386.1_Missense_Mutation_p.G964V|C2CD5_ENST00000542676.1_Missense_Mutation_p.G962V|C2CD5_ENST00000446597.1_Missense_Mutation_p.G962V	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	911					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)										ACCACTGACTCCTCCTTCCTA	0.358																																					p.G911V		Atlas-SNP	.											.	.	.	.	0			c.G2732T						PASS	.						90	80	83					12																	22606969		2203	4300	6503	SO:0001583	missense	9847	exon24			CTGACTCCTCCTT	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.2732G>T	chr12.hg19:g.22606969C>A	ENSP00000334229:p.Gly911Val	49.0	0.0	.		60.0	16.0	.	NM_014802	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Missense_Mutation	SNP	ENST00000333957.4	hg19	CCDS31758.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.3|21.3	4.123537|4.123537	0.77436|0.77436	.|.	.|.	ENSG00000111731|ENSG00000111731	ENST00000539615|ENST00000333957;ENST00000446597;ENST00000536386;ENST00000396028;ENST00000542676;ENST00000545552;ENST00000544930	.|T;T;T;T;T;T	.|0.74209	.|-0.79;-0.79;-0.82;-0.8;-0.79;-0.8	5.41|5.41	4.53|4.53	0.55603|0.55603	.|.	.|0.062767	.|0.64402	.|D	.|0.000005	.|D	.|0.85221	.|0.5647	M|M	0.76170|0.76170	2.325|2.325	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;0.999;1.0;0.988	.|D	.|0.86983	.|0.2105	.|10	.|0.87932	.|D	.|0	-20.1497|-20.1497	14.1353|14.1353	0.65284|0.65284	0.0:0.9278:0.0:0.0722|0.0:0.9278:0.0:0.0722	.|.	.|964;962;767;953;911	.|F5H2A1;B4DRN7;F5H3N1;Q86YS7-2;Q86YS7	.|.;.;.;.;K0528_HUMAN	X|V	212|911;962;964;953;962;965;767	.|ENSP00000334229:G911V;ENSP00000388756:G962V;ENSP00000439392:G964V;ENSP00000379345:G953V;ENSP00000441951:G962V;ENSP00000443204:G965V	.|ENSP00000334229:G911V	E|G	-|-	1|2	0|0	KIAA0528|KIAA0528	22498236|22498236	1.000000|1.000000	0.71417|0.71417	0.934000|0.934000	0.37439|0.37439	0.972000|0.972000	0.66771|0.66771	7.493000|7.493000	0.81493|0.81493	1.281000|1.281000	0.44480|0.44480	0.561000|0.561000	0.74099|0.74099	GAG|GGA	.	.	.	none		0.358	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802		A	22606969	C	A	22606969	3	1	35	1	0	0	0	0	1	0	0	0	8189	855	30	4	278	4	KIAA0528	12	22606969	Missense_Mutation	SNP	C	TCGA-5P-A9K6-01A-11D-A42J-10	21938466	22606969	111244926	29	2550											
KRT84	3890	hgsc.bcm.edu	37	chr12	52776299	52776299	+	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	tcgagatcagacttgttcatGaaagctgcatccacatcctg	11	11	8	11	1	2	3	2	1	0	2	5	4	4	3	2	0	2	3	2	0	1	2			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr12:52776299G>A	ENST00000257951.3	-	4	900	c.834C>T	c.(832-834)ttC>ttT	p.F278F	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	278	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)		ACTTGTTCATGAAAGCTGCAT	0.458																																					p.F278F		Atlas-SNP	.											.	KRT84	61	.	0			c.C834T						PASS	.						131	117	122					12																	52776299		2203	4300	6503	SO:0001819	synonymous_variant	3890	exon4			GTTCATGAAAGCT	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.834C>T	chr12.hg19:g.52776299G>A		45.0	0.0	.		61.0	16.0	.	NM_033045	B2RA43|Q6ISB0|Q701L6	Silent	SNP	ENST00000257951.3	hg19	CCDS8825.1																																																																																			.	.	.	none		0.458	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045		A	52776299	G	A	52776299	2	1	35	1	0	0	0	0	0	0	0	1	8505	1281	45	2		2	KRT84	12	52776299	Silent	SNP	G	TCGA-5P-A9K6-01A-11D-A42J-10	30169330	52776299	81075596	30	2551											
OR4E2	26686	hgsc.bcm.edu	37	chr14	22133689	22133689	+	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	gctatctgcactccactccaCtaccccaatgtgatgaacat	11	10	5	15	0	1	2	0	2	1	0	3	2	3	2	4	0	3	2	4	0	4	2			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr14:22133689C>T	ENST00000408935.1	+	1	393	c.393C>T	c.(391-393)caC>caT	p.H131H		NM_001001912.1	NP_001001912.1	Q8NGC2	OR4E2_HUMAN	olfactory receptor, family 4, subfamily E, member 2	131						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|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)		CTCCACTCCACTACCCCAATG	0.483																																					p.H131H		Atlas-SNP	.											.	OR4E2	44	.	0			c.C393T						PASS	.						191	180	184					14																	22133689		2042	4205	6247	SO:0001819	synonymous_variant	26686	exon1			ACTCCACTACCCC		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.393C>T	chr14.hg19:g.22133689C>T		60.0	0.0	.		56.0	18.0	.	NM_001001912	Q6IET6|Q96R62	Silent	SNP	ENST00000408935.1	hg19	CCDS41916.1																																																																																			.	.	.	none		0.483	OR4E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401874.1			T	22133689	C	T	22133689	2	4	35	1	0	0	0	0	0	0	0	1	11067	564	20	2		2	OR4E2	14	22133689	Silent	SNP	C	TCGA-5P-A9K6-01A-11D-A42J-10		22133689	85215851	31	2552											
G2E3	55632	hgsc.bcm.edu	37	chr14	31085631	31085631	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caagtgtaataactgtttagCaattcccatcaccaatacat	15	12	4	10	0	1	0	1	0	0	0	2	0	2	0	2	0	3	3	2	0	7	6			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr14:31085631C>T	ENST00000206595.6	+	15	2166	c.2012C>T	c.(2011-2013)gCa>gTa	p.A671V	G2E3_ENST00000438909.2_Missense_Mutation_p.A625V|G2E3_ENST00000553504.1_Missense_Mutation_p.A701V	NM_017769.3	NP_060239.2	Q7L622	G2E3_HUMAN	G2/M-phase specific E3 ubiquitin protein ligase	671	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				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						AACTGTTTAGCAATTCCCATC	0.368																																					p.A671V		Atlas-SNP	.											.	G2E3	82	.	0			c.C2012T						PASS	.						65	60	62					14																	31085631		2203	4300	6503	SO:0001583	missense	55632	exon15			GTTTAGCAATTCC	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.2012C>T	chr14.hg19:g.31085631C>T	ENSP00000206595:p.Ala671Val	150.0	0.0	.		139.0	44.0	.	NM_017769	Q9BVR2|Q9H9E9|Q9NXC0|Q9P2L3	Missense_Mutation	SNP	ENST00000206595.6	hg19	CCDS9638.1	.	.	.	.	.	.	.	.	.	.	C	2.276	-0.365809	0.05069	.	.	ENSG00000092140	ENST00000206595;ENST00000438909;ENST00000553504	T;T;T	0.57752	0.38;0.38;0.38	5.8	1.92	0.25849	HECT (3);	0.807701	0.12051	N	0.504113	T	0.27349	0.0671	N	0.17474	0.49	0.09310	N	0.999996	B;B	0.14438	0.01;0.001	B;B	0.17433	0.018;0.003	T	0.29792	-1.0000	10	0.02654	T	1	-1.326	4.2841	0.10846	0.2379:0.4554:0.0:0.3066	.	183;671	Q49AD9;Q7L622	.;G2E3_HUMAN	V	671;625;701	ENSP00000206595:A671V;ENSP00000391068:A625V;ENSP00000451653:A701V	ENSP00000206595:A671V	A	+	2	0	G2E3	30155382	0.968000	0.33430	0.995000	0.50966	0.629000	0.37895	1.333000	0.33816	0.353000	0.24079	0.591000	0.81541	GCA	.	.	.	none		0.368	G2E3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276613.2	NM_017769		T	31085631	C	T	31085631	3	4	35	1	0	0	0	0	1	0	0	0	6147	710	25	2	2066	2	G2E3	14	31085631	Missense_Mutation	SNP	C	TCGA-5P-A9K6-01A-11D-A42J-10	8951942	31085631	76263909	32	2553											
BTBD7	55727	hgsc.bcm.edu	37	chr14	93761032	93761032	+	Missense_Mutation	SNP	T	T	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	ggcttgtagagaaagctcctTtaatgctgatgttccctcat	9	14	9	9	0	1	2	1	1	0	1	3	3	3	2	2	1	2	5	2	1	3	5			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr14:93761032T>G	ENST00000334746.5	-	3	641	c.334A>C	c.(334-336)Aag>Cag	p.K112Q	BTBD7_ENST00000554565.1_Intron|BTBD7_ENST00000555525.1_Missense_Mutation_p.K112Q|BTBD7_ENST00000393170.2_5'Flank|BTBD7_ENST00000298896.3_Missense_Mutation_p.K112Q	NM_001002860.2	NP_001002860.2	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7	112					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)		GAAAGCTCCTTTAATGCTGAT	0.453																																					p.K112Q		Atlas-SNP	.											.	BTBD7	112	.	0			c.A334C						PASS	.						87	77	81					14																	93761032		2203	4300	6503	SO:0001583	missense	55727	exon3			GCTCCTTTAATGC	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.334A>C	chr14.hg19:g.93761032T>G	ENSP00000335615:p.Lys112Gln	80.0	0.0	.		71.0	19.0	.	NM_018167	A8K5V7|Q69Z05|Q7Z308|Q86TS0|Q9HAA4|Q9NVM0	Missense_Mutation	SNP	ENST00000334746.5	hg19	CCDS32146.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.174317	0.78452	.	.	ENSG00000011114	ENST00000334746;ENST00000298896;ENST00000555525	T	0.46819	0.86	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.66096	0.2755	L	0.57536	1.79	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.80764	0.994;0.991;0.991	T	0.68265	-0.5454	10	0.72032	D	0.01	.	16.3224	0.82956	0.0:0.0:0.0:1.0	.	112;112;112	Q9P203-3;G3V3T2;Q9P203	.;.;BTBD7_HUMAN	Q	112	ENSP00000335615:K112Q	ENSP00000298896:K112Q	K	-	1	0	BTBD7	92830785	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.040000	0.89188	2.263000	0.75096	0.533000	0.62120	AAG	.	.	.	none		0.453	BTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412701.1	NM_001002860		G	93761032	T	G	93761032	3	3	35	1	0	0	0	0	1	0	0	0	1548	1850	64	5	3175	5	BTBD7	14	93761032	Missense_Mutation	SNP	T	TCGA-5P-A9K6-01A-11D-A42J-10	62675401	93761032	13588508	33	2554											
FAM98B	283742	hgsc.bcm.edu	37	chr15	38776827	38776827	+	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	ggtggtggtggtggtggtggTggtggtggaggaggtggata	4	11	26	0	0	0	0	0	0	0	0	0	3	0	3	0	13	0	0	0	13	1	1			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr15:38776827T>A	ENST00000491535.1	+	0	3111				FAM98B_ENST00000397609.2_Silent_p.G423G	NM_001042429.1	NP_001035894.1	Q52LJ0	FA98B_HUMAN	family with sequence similarity 98, member B							cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-splicing ligase complex (GO:0072669)	poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|skin(1)	8		all_cancers(109;3.11e-17)|all_epithelial(112;2.64e-15)|Lung NSC(122;2.11e-11)|all_lung(180;5.61e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;9e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0209)		gtggtggtggtggtggtggag	0.443																																					p.G423G		Atlas-SNP	.											FAM98B_ENST00000397609,NS,carcinoma,0,1	FAM98B	53	.	0			c.T1269A						PASS	.						19	18	18					15																	38776827		1515	3413	4928	SO:0001628	intergenic_variant	283742	exon8			TGGTGGTGGTGGT		CCDS10047.2	15q14	2006-11-29		2005-11-20	ENSG00000171262	ENSG00000171262			26773	protein-coding gene	gene with protein product						12477932	Standard	NM_173611		Approved	FLJ38426	uc001zkc.3	Q52LJ0	OTTHUMG00000129831		chr15.hg19:g.38776827T>A		78.0	0.0	.		80.0	10.0	.	NM_173611	A8MUW5|Q8N935	Silent	SNP	ENST00000491535.1	hg19	CCDS42015.1																																																																																			.	.	.	none		0.443	FAM98B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252071.2	NM_173611		A	38776827	T	A	38776827	1	1	35	0	1	0	0	0	0	0	0	0	5664	1683	59	5		5	FAM98B	15	38776827	IGR	SNP	T	TCGA-5P-A9K6-01A-11D-A42J-10		38776827	63754565	34	2555											
TGFB1I1	7041	hgsc.bcm.edu	37	chr16	31488254	31488254	+	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	tgttcgccccgcgctgccagGgctgccagggccccatcctg	3	7	13	18	3	0	0	0	0	0	0	2	0	1	0	7	2	2	3	7	2	0	1			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr16:31488254G>T	ENST00000394863.3	+	10	1172	c.1042G>T	c.(1042-1044)Ggc>Tgc	p.G348C	TGFB1I1_ENST00000361773.3_Missense_Mutation_p.G331C|TGFB1I1_ENST00000394858.2_Missense_Mutation_p.G331C|TGFB1I1_ENST00000567607.1_Missense_Mutation_p.G331C	NM_001042454.2	NP_001035919.1	O43294	TGFI1_HUMAN	transforming growth factor beta 1 induced transcript 1	348	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				androgen receptor signaling pathway (GO:0030521)|cell adhesion (GO:0007155)|cell fate commitment (GO:0045165)|epithelial cell differentiation (GO:0030855)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|response to heat (GO:0009408)|transcription from RNA polymerase II promoter (GO:0006366)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|I-SMAD binding (GO:0070411)|Roundabout binding (GO:0048495)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			lung(8)|upper_aerodigestive_tract(1)	9						GCGCTGCCAGGGCTGCCAGGG	0.692																																					p.G348C		Atlas-SNP	.											.	TGFB1I1	60	.	0			c.G1042T						PASS	.						10	11	11					16																	31488254		2183	4269	6452	SO:0001583	missense	7041	exon10			TGCCAGGGCTGCC	AB007836	CCDS10713.1, CCDS42156.1	16p11	2008-02-05			ENSG00000140682	ENSG00000140682			11767	protein-coding gene	gene with protein product		602353				9422762, 10075738	Standard	NM_015927		Approved	Hic-5, TSC-5, ARA55, HIC-5	uc002ecd.2	O43294	OTTHUMG00000132467	ENST00000394863.3:c.1042G>T	chr16.hg19:g.31488254G>T	ENSP00000378332:p.Gly348Cys	43.0	0.0	.		44.0	26.0	.	NM_001042454	B2R8D5|Q9BPW3|Q9Y2V5	Missense_Mutation	SNP	ENST00000394863.3	hg19	CCDS42156.1	.	.	.	.	.	.	.	.	.	.	G	33	5.216196	0.95104	.	.	ENSG00000140682	ENST00000394863;ENST00000361773;ENST00000394858	D;D;D	0.89050	-2.46;-2.46;-2.46	5.35	4.39	0.52855	Zinc finger, LIM-type (5);	0.049439	0.85682	D	0.000000	D	0.95111	0.8416	M	0.91872	3.25	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95618	0.8678	10	0.87932	D	0	.	12.2376	0.54524	0.0837:0.0:0.9163:0.0	.	348	O43294	TGFI1_HUMAN	C	348;331;331	ENSP00000378332:G348C;ENSP00000355117:G331C;ENSP00000378327:G331C	ENSP00000355117:G331C	G	+	1	0	TGFB1I1	31395755	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.737000	0.98831	1.391000	0.46566	0.484000	0.47621	GGC	.	.	.	none		0.692	TGFB1I1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255630.3			T	31488254	G	T	31488254	3	4	35	1	0	0	0	0	1	0	0	0	15829	1232	43	4	1080	4	TGFB1I1	16	31488254	Missense_Mutation	SNP	G	TCGA-5P-A9K6-01A-11D-A42J-10		31488254	58866499	35	2556											
COG4	25839	hgsc.bcm.edu	37	chr16	70543137	70543137	+	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	tagcttcccctgctcacctgCtggtggtagtccctttgctt	3	15	9	14	0	1	0	1	0	0	0	3	0	3	0	4	2	4	5	4	2	2	5			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr16:70543137C>T	ENST00000323786.5	-	7	1020	c.999G>A	c.(997-999)caG>caA	p.Q333Q	COG4_ENST00000393612.4_Silent_p.Q329Q	NM_001195139.1|NM_015386.2	NP_001182068.1|NP_056201.2	Q9H9E3	COG4_HUMAN	component of oligomeric golgi complex 4	329					Golgi organization (GO:0007030)|Golgi vesicle prefusion complex stabilization (GO:0048213)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|pancreas(1)|prostate(2)	33		Ovarian(137;0.0694)				TGCTCACCTGCTGGTGGTAGT	0.458																																					p.Q333Q		Atlas-SNP	.											.	COG4	64	.	0			c.G999A						PASS	.						163	146	152					16																	70543137		2198	4300	6498	SO:0001819	synonymous_variant	25839	exon7			CACCTGCTGGTGG	AL050101	CCDS10892.2, CCDS73909.1	16q22.1	2013-09-20			ENSG00000103051	ENSG00000103051		"Components of oligomeric golgi complex"	18620	protein-coding gene	gene with protein product		606976				11980916	Standard	NM_015386		Approved	COD1, DKFZP586E1519	uc002ezc.3	Q9H9E3	OTTHUMG00000128515	ENST00000323786.5:c.999G>A	chr16.hg19:g.70543137C>T		47.0	0.0	.		97.0	47.0	.	NM_015386	B4DMN8|C9JS23|Q96D40|Q9BRF0|Q9BVZ2|Q9H5Y4|Q9Y3W3	Silent	SNP	ENST00000323786.5	hg19	CCDS10892.2																																																																																			.	.	.	none		0.458	COG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250326.3			T	70543137	C	T	70543137	2	4	35	1	0	0	0	0	0	0	0	1	3662	796	28	2		2	COG4	16	70543137	Silent	SNP	C	TCGA-5P-A9K6-01A-11D-A42J-10	39054883	70543137	19811616	36	2557											
METT10D	79066	hgsc.bcm.edu	37	chr17	2405596	2405596	+	Missense_Mutation	SNP	T	T	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	ggtttgtccttgtatctattTcttgcatgcattgatttact	6	21	7	7	0	2	1	0	1	2	0	3	1	3	1	1	1	3	4	1	1	3	9			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr17:2405596T>G	ENST00000263092.6	-	2	157	c.30A>C	c.(28-30)agA>agC	p.R10S	METTL16_ENST00000571669.2_Intron|METTL16_ENST00000538844.1_5'UTR	NM_024086.3	NP_076991.3	Q86W50	MET16_HUMAN	methyltransferase like 16	10							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						TGTATCTATTTCTTGCATGCA	0.393																																					p.R10S		Atlas-SNP	.											.	METTL16	75	.	0			c.A30C						PASS	.						179	156	164					17																	2405596		1852	4101	5953	SO:0001583	missense	79066	exon2			TCTATTTCTTGCA	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.30A>C	chr17.hg19:g.2405596T>G	ENSP00000263092:p.Arg10Ser	57.0	0.0	.		72.0	31.0	.	NM_024086	D3DTI8|Q86TE5|Q96T16|Q9BVG7	Missense_Mutation	SNP	ENST00000263092.6	hg19	CCDS42232.1	.	.	.	.	.	.	.	.	.	.	T	19.35	3.810352	0.70797	.	.	ENSG00000127804	ENST00000263092;ENST00000399834	T	0.58940	0.3	5.63	-0.311	0.12761	.	0.000000	0.85682	D	0.000000	T	0.75057	0.3798	M	0.93062	3.375	0.80722	D	1	D;D	0.89917	0.995;1.0	D;D	0.91635	0.972;0.999	T	0.72074	-0.4400	10	0.87932	D	0	-8.5176	5.0389	0.14449	0.1296:0.2868:0.0:0.5836	.	10;10	Q86W50-2;Q86W50	.;MET16_HUMAN	S	10	ENSP00000263092:R10S	ENSP00000263092:R10S	R	-	3	2	METTL16	2352346	0.998000	0.40836	0.999000	0.59377	0.962000	0.63368	0.343000	0.19944	0.081000	0.16988	-0.444000	0.05651	AGA	.	.	.	none		0.393	METTL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437653.2	NM_024086		G	2405596	T	G	2405596	3	3	35	1	0	0	0	0	1	0	0	0	9497	1780	62	5	1694	5	METT10D	17	2405596	Missense_Mutation	SNP	T	TCGA-5P-A9K6-01A-11D-A42J-10		2405596	78789614	37	2558											
MYH10	4628	hgsc.bcm.edu	37	chr17	8438748	8438748	+	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	aatctgtctgatgactggtgCaaaagggtggccacgttgtc	9	11	13	8	1	2	2	0	2	2	0	3	2	2	2	1	3	1	2	1	3	3	1			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr17:8438748C>T	ENST00000269243.4	-	15	1959	c.1821G>A	c.(1819-1821)ttG>ttA	p.L607L	MYH10_ENST00000360416.3_Silent_p.L617L|MYH10_ENST00000396239.1_Silent_p.L607L|MYH10_ENST00000379980.4_Silent_p.L623L	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	607	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						ATGACTGGTGCAAAAGGGTGG	0.443																																					p.L617L		Atlas-SNP	.											.	MYH10	148	.	0			c.G1851A						PASS	.						103	94	97					17																	8438748		2203	4300	6503	SO:0001819	synonymous_variant	4628	exon16			CTGGTGCAAAAGG	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.1821G>A	chr17.hg19:g.8438748C>T		67.0	0.0	.		85.0	47.0	.	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	hg19	CCDS11144.1																																																																																			.	.	.	none		0.443	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			T	8438748	C	T	8438748	2	4	35	1	0	0	0	0	0	0	0	1	10037	709	25	2		2	MYH10	17	8438748	Silent	SNP	C	TCGA-5P-A9K6-01A-11D-A42J-10	6033152	8438748	72756462	38	2559											
RAI1	10743	hgsc.bcm.edu	37	chr17	17697096	17697096	+	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	ggccgcctcagctatgaccaGcagcagcagcagcagcagca	11	3	12	15	1	1	1	1	1	0	0	1	1	1	1	3	1	8	8	3	1	1	1	rs113303801|rs398124422|rs371983878|rs571229335|rs587780431	byFrequency	TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr17:17697096G>C	ENST00000353383.1	+	3	1303	c.834G>C	c.(832-834)caG>caC	p.Q278H	RAI1_ENST00000261641.6_Missense_Mutation_p.Q278H	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	278	Gln-rich.|Poly-Gln.				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)		GCTATGACcagcagcagcagc	0.637																																					p.Q278H		Atlas-SNP	.											.	RAI1	121	.	0			c.G834C						PASS	.						18	23	22					17																	17697096		2081	4107	6188	SO:0001583	missense	10743	exon3			TGACCAGCAGCAG	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.834G>C	chr17.hg19:g.17697096G>C	ENSP00000323074:p.Gln278His	45.0	0.0	.		82.0	6.0	.	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Missense_Mutation	SNP	ENST00000353383.1	hg19	CCDS11188.1	.	.	.	.	.	.	.	.	.	.	g	0.076	-1.192861	0.01607	.	.	ENSG00000108557	ENST00000353383;ENST00000395774;ENST00000395776;ENST00000355970;ENST00000261641;ENST00000315321	T;T;T	0.69806	-0.43;1.41;0.17	4.53	-9.06	0.00727	.	0.597522	0.15390	N	0.264894	T	0.43743	0.1261	L	0.39898	1.24	0.18873	N	0.999987	P	0.37864	0.61	B	0.37198	0.243	T	0.31392	-0.9945	10	0.35671	T	0.21	.	4.0515	0.09798	0.4386:0.1326:0.3468:0.0819	.	278	Q7Z5J4	RAI1_HUMAN	H	278;278;278;278;278;255	ENSP00000323074:Q278H;ENSP00000379120:Q278H;ENSP00000261641:Q278H	ENSP00000261641:Q278H	Q	+	3	2	RAI1	17637821	0.953000	0.32496	0.000000	0.03702	0.311000	0.27955	0.063000	0.14410	-2.722000	0.00388	-1.461000	0.01025	CAG	.	.	.	none		0.637	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665		C	17697096	G	C	17697096	3	2	35	1	0	0	0	0	1	0	0	0	13020	962	34	4	836	4	RAI1	17	17697096	Missense_Mutation	SNP	G	TCGA-5P-A9K6-01A-11D-A42J-10	9258348	17697096	63498114	39	2560											
KRTAP4-11	653240	hgsc.bcm.edu	37	chr17	39274461	39274461	+	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	tggggcgacagtaggtggtcCtgcagcaggtggtctcacag	7	8	17	9	1	1	0	1	0	1	0	3	1	2	0	1	6	2	3	1	6	1	1			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr17:39274461C>G	ENST00000391413.2	-	1	145	c.107G>C	c.(106-108)aGg>aCg	p.R36T		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	36	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)			GTAGGTGGTCCTGCAGCAGGT	0.662																																					p.R36T		Atlas-SNP	.											.	KRTAP4-11	94	.	0			c.G107C						PASS	.						21	24	23					17																	39274461		692	1591	2283	SO:0001583	missense	653240	exon1			GTGGTCCTGCAGC	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.107G>C	chr17.hg19:g.39274461C>G	ENSP00000375232:p.Arg36Thr	54.0	0.0	.		71.0	10.0	.	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	hg19	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	8.971	0.972966	0.18736	.	.	ENSG00000212721	ENST00000391413	T	0.01379	4.96	4.17	0.917	0.19380	.	.	.	.	.	T	0.02727	0.0082	M	0.90145	3.09	0.09310	N	1	B	0.22983	0.078	B	0.25614	0.062	T	0.48410	-0.9038	9	0.14252	T	0.57	.	3.4615	0.07535	0.3471:0.4506:0.0:0.2022	.	36	Q9BYQ6	KR411_HUMAN	T	36	ENSP00000375232:R36T	ENSP00000375232:R36T	R	-	2	0	KRTAP4-11	36527987	0.000000	0.05858	0.607000	0.28956	0.268000	0.26511	-0.865000	0.04250	0.397000	0.25310	-0.243000	0.11985	AGG	.	.	.	none		0.662	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1			G	39274461	C	G	39274461	3	3	35	1	0	0	0	0	1	0	0	0	8556	681	24	4	484	4	KRTAP4-11	17	39274461	Missense_Mutation	SNP	C	TCGA-5P-A9K6-01A-11D-A42J-10	21577365	39274461	41920749	40	2561											
TOM1L1	10040	hgsc.bcm.edu	37	chr17	52990171	52990171	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaatagaatcttgaatttcAttaaggtaagtctgttgtat	14	16	8	3	0	3	3	1	1	2	2	3	3	3	3	0	1	0	3	0	1	7	7			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr17:52990171A>G	ENST00000575882.1	+	4	720	c.367A>G	c.(367-369)Att>Gtt	p.I123V	TOM1L1_ENST00000348161.4_Missense_Mutation_p.I46V|TOM1L1_ENST00000540336.1_Missense_Mutation_p.I46V|TOM1L1_ENST00000572158.1_Missense_Mutation_p.I116V|TOM1L1_ENST00000536554.1_Missense_Mutation_p.I46V|TOM1L1_ENST00000575333.1_Missense_Mutation_p.I123V|TOM1L1_ENST00000570371.1_Missense_Mutation_p.I123V|TOM1L1_ENST00000572405.1_Missense_Mutation_p.I88V|TOM1L1_ENST00000445275.2_Missense_Mutation_p.I123V	NM_005486.2	NP_005477.2	O75674	TM1L1_HUMAN	target of myb1 (chicken)-like 1	123	VHS. {ECO:0000255|PROSITE- ProRule:PRU00218}.				activation of protein kinase activity (GO:0032147)|intracellular protein transport (GO:0006886)|negative regulation of mitosis (GO:0045839)|positive regulation of protein autophosphorylation (GO:0031954)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)	clathrin binding (GO:0030276)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|ubiquitin binding (GO:0043130)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	15						CTTGAATTTCATTAAGGTAAG	0.313																																					p.I123V		Atlas-SNP	.											.	TOM1L1	33	.	0			c.A367G						PASS	.						56	58	57					17																	52990171		2203	4299	6502	SO:0001583	missense	10040	exon4			AATTTCATTAAGG	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.367A>G	chr17.hg19:g.52990171A>G	ENSP00000460823:p.Ile123Val	71.0	0.0	.		74.0	8.0	.	NM_005486	Q53G06|Q8N749	Missense_Mutation	SNP	ENST00000575882.1	hg19	CCDS11582.1	.	.	.	.	.	.	.	.	.	.	A	13.68	2.309181	0.40895	.	.	ENSG00000141198	ENST00000445275;ENST00000540336;ENST00000348161;ENST00000536554	T;T;T;T	0.27104	1.69;1.69;1.69;1.69	5.72	4.65	0.58169	VHS subgroup (1);ENTH/VHS (2);VHS (2);	0.244803	0.33916	N	0.004422	T	0.26919	0.0659	M	0.63428	1.95	0.43673	D	0.996109	P;P;P;P;B;P	0.45396	0.826;0.647;0.685;0.647;0.043;0.857	B;B;B;B;B;B	0.41412	0.338;0.176;0.356;0.19;0.037;0.356	T	0.05053	-1.0909	10	0.56958	D	0.05	-12.0729	9.2264	0.37410	0.9156:0.0:0.0844:0.0	.	46;116;46;123;123;46	B4DUW5;B4E1N0;B7Z9E2;O75674;Q8N749;B4E1M9	.;.;.;TM1L1_HUMAN;.;.	V	123;46;46;46	ENSP00000408958:I123V;ENSP00000441242:I46V;ENSP00000343901:I46V;ENSP00000443099:I46V	ENSP00000343901:I46V	I	+	1	0	TOM1L1	50345170	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	5.061000	0.64319	2.184000	0.69523	0.460000	0.39030	ATT	.	.	.	none		0.313	TOM1L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439029.2	NM_005486		G	52990171	A	G	52990171	3	3	35	1	0	0	0	0	1	0	0	0	16364	217	8	3	381	3	TOM1L1	17	52990171	Missense_Mutation	SNP	A	TCGA-5P-A9K6-01A-11D-A42J-10	13715710	52990171	28205039	41	2562											
TEX14	56155	hgsc.bcm.edu	37	chr17	56670954	56670954	+	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	ctgcttgtttccaaactgtcCttggctccttgagtgcactg	5	15	9	12	0	0	1	0	1	0	0	3	1	3	1	3	1	3	4	3	1	1	4			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr17:56670954C>A	ENST00000240361.8	-	15	2641	c.2556G>T	c.(2554-2556)aaG>aaT	p.K852N	TEX14_ENST00000389934.3_Missense_Mutation_p.K846N|TEX14_ENST00000349033.5_Missense_Mutation_p.K846N			Q8IWB6	TEX14_HUMAN	testis expressed 14	852					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CCAAACTGTCCTTGGCTCCTT	0.418																																					p.K852N		Atlas-SNP	.											.	TEX14	343	.	0			c.G2556T						PASS	.						210	158	176					17																	56670954		2203	4300	6503	SO:0001583	missense	56155	exon15			ACTGTCCTTGGCT	AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"cancer/testis antigen 113"	605792	"testis expressed sequence 14"			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.2556G>T	chr17.hg19:g.56670954C>A	ENSP00000240361:p.Lys852Asn	109.0	0.0	.		152.0	35.0	.	NM_001201457	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	hg19	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	C	10.45	1.352807	0.24512	.	.	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.80566	-1.39;-1.39;-1.34	4.78	0.311	0.15831	.	0.716733	0.13889	N	0.355726	T	0.74253	0.3692	L	0.57536	1.79	0.09310	N	1	P;P;P	0.46142	0.704;0.873;0.804	B;B;P	0.44860	0.162;0.436;0.462	T	0.63065	-0.6720	10	0.38643	T	0.18	-8.5367	4.1126	0.10065	0.0:0.5389:0.1727:0.2884	.	852;846;846	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	N	852;846;846	ENSP00000240361:K852N;ENSP00000374584:K846N;ENSP00000268910:K846N	ENSP00000240361:K852N	K	-	3	2	TEX14	54025953	0.050000	0.20438	0.705000	0.30386	0.036000	0.12997	0.098000	0.15189	0.336000	0.23639	-0.251000	0.11542	AAG	.	.	.	none		0.418	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1			A	56670954	C	A	56670954	3	1	35	1	0	0	0	0	1	0	0	0	15790	680	24	4	2013	4	TEX14	17	56670954	Missense_Mutation	SNP	C	TCGA-5P-A9K6-01A-11D-A42J-10	3680783	56670954	24524256	42	2563											
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2729383	2729383	+	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	aatattaaaaaagaccagacGcttaaagcaagaattgaaat	22	8	6	5	1	0	4	0	1	0	3	0	4	0	4	1	0	1	2	1	0	10	4			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr18:2729383G>A	ENST00000320876.6	+	24	3362	c.3024G>A	c.(3022-3024)acG>acA	p.T1008T	SMCHD1_ENST00000261598.8_Silent_p.T1008T|RP11-703M24.5_ENST00000583546.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1008					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						AAGACCAGACGCTTAAAGCAA	0.313																																					p.T1008T		Atlas-SNP	.											.	SMCHD1	88	.	0			c.G3024A						PASS	.						43	40	41					18																	2729383		1791	4050	5841	SO:0001819	synonymous_variant	23347	exon24			CCAGACGCTTAAA	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.3024G>A	chr18.hg19:g.2729383G>A		57.0	0.0	.		65.0	23.0	.	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Silent	SNP	ENST00000320876.6	hg19	CCDS45822.1																																																																																			.	.	.	none		0.313	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			A	2729383	G	A	2729383	2	1	35	1	0	0	0	0	0	0	0	1	14801	1074	38	1		1	SMCHD1	18	2729383	Silent	SNP	G	TCGA-5P-A9K6-01A-11D-A42J-10		2729383	75347865	43	2564											
C18orf8	29919	hgsc.bcm.edu	37	chr18	21106695	21106695	+	Missense_Mutation	SNP	A	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	tttctcctccagagaaaggaAtgcaagatggtcatcctgtc	11	11	9	10	0	2	2	1	0	1	2	6	4	4	3	3	2	1	1	3	2	3	1			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr18:21106695A>C	ENST00000269221.3	+	13	1265	c.1155A>C	c.(1153-1155)gaA>gaC	p.E385D	C18orf8_ENST00000590868.1_Missense_Mutation_p.E337D	NM_013326.3	NP_037458.3	Q96DM3	MIC1_HUMAN	chromosome 18 open reading frame 8	385						lysosomal membrane (GO:0005765)				endometrium(9)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	21	all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127)					AGAGAAAGGAATGCAAGATGG	0.463																																					p.E385D		Atlas-SNP	.											.	C18orf8	58	.	0			c.A1155C						PASS	.						121	113	116					18																	21106695		2203	4300	6503	SO:0001583	missense	29919	exon13			AAAGGAATGCAAG	AK057192	CCDS32803.1, CCDS74199.1	18q11.2	2013-12-13			ENSG00000141452	ENSG00000141452			24326	protein-coding gene	gene with protein product	"colon cancer associated protein Mic1", "macrophage inhibitory cytokine 1"					12477932	Standard	NM_013326		Approved	MIC1, MIC-1, HsT2591	uc021uie.2	Q96DM3		ENST00000269221.3:c.1155A>C	chr18.hg19:g.21106695A>C	ENSP00000269221:p.Glu385Asp	55.0	0.0	.		61.0	22.0	.	NM_013326	Q9BU17|Q9Y5M0	Missense_Mutation	SNP	ENST00000269221.3	hg19	CCDS32803.1	.	.	.	.	.	.	.	.	.	.	A	9.126	1.010228	0.19277	.	.	ENSG00000141452	ENST00000269221;ENST00000544799;ENST00000540942;ENST00000542734	.	.	.	4.86	-9.72	0.00515	.	0.162119	0.53938	N	0.000044	T	0.08537	0.0212	N	0.00327	-1.64	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.40887	-0.9539	9	0.08179	T	0.78	-8.5287	9.6011	0.39605	0.3022:0.2706:0.4272:0.0	.	228;385	B7Z2Y1;Q96DM3	.;MIC1_HUMAN	D	385;228;337;228	.	ENSP00000269221:E385D	E	+	3	2	C18orf8	19360693	0.997000	0.39634	0.870000	0.34147	0.995000	0.86356	0.548000	0.23314	-1.505000	0.01807	0.533000	0.62120	GAA	.	.	.	none		0.463	C18orf8-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445386.1	NM_013326		C	21106695	A	C	21106695	3	2	35	1	0	0	0	0	1	0	0	0	1909	98	4	5	1205	5	C18orf8	18	21106695	Missense_Mutation	SNP	A	TCGA-5P-A9K6-01A-11D-A42J-10	18377312	21106695	56970553	44	2565											
ZNF562	54811	hgsc.bcm.edu	37	chr19	9763811	9763811	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagggtttctctccagtgtgAtttcgtatgtgtatagcaag	8	16	11	6	1	1	1	0	1	1	0	4	1	2	1	1	1	1	4	1	1	5	6			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr19:9763811A>G	ENST00000448622.1	-	6	1257	c.1095T>C	c.(1093-1095)aaT>aaC	p.N365N	ZNF562_ENST00000453372.2_Silent_p.N365N|ZNF562_ENST00000537617.1_Silent_p.N249N|ZNF562_ENST00000293648.4_Silent_p.N293N|ZNF562_ENST00000590155.1_Silent_p.N364N|ZNF562_ENST00000541032.1_Silent_p.N328N|ZNF562_ENST00000453792.2_Silent_p.N296N	NM_001130031.1|NM_001130032.1	NP_001123503.1|NP_001123504.1	Q6V9R5	ZN562_HUMAN	zinc finger protein 562	365					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	17						CTCCAGTGTGATTTCGTATGT	0.428																																					p.N365N		Atlas-SNP	.											.	ZNF562	72	.	0			c.T1095C						PASS	.						137	129	132					19																	9763811		2203	4300	6503	SO:0001819	synonymous_variant	54811	exon6			AGTGTGATTTCGT	AK000086	CCDS12217.1, CCDS45956.1, CCDS74280.1	19p13.2	2013-09-20			ENSG00000171466	ENSG00000171466		"Zinc fingers, C2H2-type", "-"	25950	protein-coding gene	gene with protein product							Standard	NM_001130031		Approved	FLJ20079	uc010xks.2	Q6V9R5	OTTHUMG00000180205	ENST00000448622.1:c.1095T>C	chr19.hg19:g.9763811A>G		69.0	0.0	.		84.0	27.0	.	NM_001130032	Q32MN2|Q9NXS5	Silent	SNP	ENST00000448622.1	hg19	CCDS45956.1																																																																																			.	.	.	none		0.428	ZNF562-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450239.1	NM_017656		G	9763811	A	G	9763811	2	3	35	1	0	0	0	0	0	0	0	1	18005	330	12	3		3	ZNF562	19	9763811	Silent	SNP	A	TCGA-5P-A9K6-01A-11D-A42J-10		9763811	49365172	45	2566											
AP2S1	1175	hgsc.bcm.edu	37	chr19	47341743	47341743	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atcagcagctgtttcagcacCttcgtctggctggtctctcg	5	13	10	13	2	4	0	2	0	2	0	7	0	4	0	1	2	3	5	1	2	0	2			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr19:47341743C>T	ENST00000263270.6	-	5	615	c.390G>A	c.(388-390)aaG>aaA	p.K130K	AP2S1_ENST00000593442.1_Silent_p.K80K|AP2S1_ENST00000352203.4_Silent_p.K144K|AP2S1_ENST00000601498.1_Silent_p.K146K|AP2S1_ENST00000601649.1_Silent_p.K92K|AP2S1_ENST00000597020.1_Silent_p.K110K|AP2S1_ENST00000599990.1_Silent_p.K132K	NM_004069.3	NP_004060.2	P53680	AP2S1_HUMAN	adaptor-related protein complex 2, sigma 1 subunit	130					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|regulation of endocytosis (GO:0030100)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	AP-2 adaptor complex (GO:0030122)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			central_nervous_system(1)|lung(1)|urinary_tract(1)	3		all_cancers(25;1.24e-06)|all_epithelial(76;1.09e-05)|all_lung(116;0.00019)|Lung NSC(112;0.000601)|Ovarian(192;0.0221)|all_neural(266;0.0459)|Breast(70;0.128)		OV - Ovarian serous cystadenocarcinoma(262;3.86e-05)|all cancers(93;0.000107)|Epithelial(262;0.00325)|GBM - Glioblastoma multiforme(486;0.0336)		GTTTCAGCACCTTCGTCTGGC	0.657																																					p.K130K		Atlas-SNP	.											.	AP2S1	12	.	0			c.G390A						PASS	.						54	45	48					19																	47341743		2203	4300	6503	SO:0001819	synonymous_variant	1175	exon5			CAGCACCTTCGTC	AJ010148	CCDS12693.1, CCDS33062.1	19q13.2-q13.3	2014-02-04				ENSG00000042753			565	protein-coding gene	gene with protein product		602242	"hypocalciuric hypercalcemia 3 (Oklahoma type)"	CLAPS2, HHC3		9040778, 9767099, 23222959	Standard	XM_005258500		Approved	FBHOk, FBH3	uc002pft.1	P53680		ENST00000263270.6:c.390G>A	chr19.hg19:g.47341743C>T		88.0	0.0	.		96.0	35.0	.	NM_004069	B2R4Z4|O75977|Q6PK67	Silent	SNP	ENST00000263270.6	hg19	CCDS33062.1																																																																																			.	.	.	none		0.657	AP2S1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466643.1			T	47341743	C	T	47341743	2	4	35	1	0	0	0	0	0	0	0	1	743	680	24	2		2	AP2S1	19	47341743	Silent	SNP	C	TCGA-5P-A9K6-01A-11D-A42J-10	37577932	47341743	11787240	46	2567											
C19orf18	147685	hgsc.bcm.edu	37	chr19	58472818	58472818	+	Frame_Shift_Del	DEL	C	C	-																															gaagtaggtgcgtggactcaCcctcgtcctctgagccctct																										TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr19:58472818delC	ENST00000314391.3	-	5	574	c.473delG	c.(472-474)ggtfs	p.G158fs		NM_152474.4	NP_689687.1	Q8NEA5	CS018_HUMAN	chromosome 19 open reading frame 18	158						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	8		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;0.017)		CGTGGACTCACCCTCGTCCTC	0.493																																					p.G158fs		Atlas-Indel,Pindel	.											.	C19orf18	27	.	0			c.474delT						PASS	.						176	139	152					19																	58472818		2203	4300	6503	SO:0001589	frameshift_variant	147685	exon5			.	BC033933	CCDS12967.1	19q13.43	2013-03-11			ENSG00000177025	ENSG00000177025			28642	protein-coding gene	gene with protein product						12477932	Standard	NM_152474		Approved	MGC41906	uc002qqv.3	Q8NEA5	OTTHUMG00000183450	ENST00000314391.3:c.473delG	chr19.hg19:g.58472818delC	ENSP00000321519:p.Gly158fs	62.0	0.0	0		81.0	25.0	0.308642	NM_152474		Frame_Shift_Del	DEL	ENST00000314391.3	hg19	CCDS12967.1																																																																																			.	.	.	none		0.493	C19orf18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466704.1	NM_152474		-	58472818	C	-	58472818	7	5	35	1	0	1	0	1	0	0	0	0	1912	507	18	0	182	0	C19orf18	19	58472818	Frame_Shift_Del	DEL	C	TCGA-5P-A9K6-01A-11D-A42J-10	11131075	58472818	656165	47	2568											
ACSS1	84532	hgsc.bcm.edu	37	chr20	25004243	25004243	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accacgcgcccaccccggagTccttggttgaaggtgataac	9	7	11	14	3	0	2	0	2	0	0	1	3	1	3	5	3	1	1	5	3	2	3			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr20:25004243T>C	ENST00000323482.4	-	4	745	c.666A>G	c.(664-666)ggA>ggG	p.G222G	ACSS1_ENST00000542618.1_Silent_p.G101G|ACSS1_ENST00000537502.1_Silent_p.G139G|ACSS1_ENST00000432802.2_Silent_p.G222G	NM_001252675.1|NM_032501.3	NP_001239604.1|NP_115890.2	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	222					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)	CACCCCGGAGTCCTTGGTTGA	0.537																																					p.G222G		Atlas-SNP	.											.	ACSS1	46	.	0			c.A666G						PASS	.						75	65	69					20																	25004243		2203	4300	6503	SO:0001819	synonymous_variant	84532	exon4			CCGGAGTCCTTGG		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.666A>G	chr20.hg19:g.25004243T>C		24.0	0.0	.		57.0	21.0	.	NM_001252677	B3KXL2|B4DJZ3|D3DW48|F5H6F4|F8W7Y1|Q5TF42|Q8IV99|Q8N234|Q96JI1|Q96JX6|Q9NU28	Silent	SNP	ENST00000323482.4	hg19	CCDS13167.1																																																																																			.	.	.	none		0.537	ACSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078386.2	NM_032501		C	25004243	T	C	25004243	2	2	35	1	0	0	0	0	0	0	0	1	188	1654	58	3		3	ACSS1	20	25004243	Silent	SNP	T	TCGA-5P-A9K6-01A-11D-A42J-10		25004243	38021277	48	2569											
C20orf160	140706	hgsc.bcm.edu	37	chr20	30602782	30602782	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgtaggagcagcgtgagcCgccggcccctgcactcgatg	6	6	14	15	4	0	1	0	1	0	0	1	3	0	2	5	2	4	3	5	2	1	1	rs545553537		TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr20:30602782C>T	ENST00000300415.8	+	2	119	c.106C>T	c.(106-108)Cgc>Tgc	p.R36C	CCM2L_ENST00000262659.8_Missense_Mutation_p.R36C			Q9NUG4	CCM2L_HUMAN	cerebral cavernous malformation 2-like	36																	CAGCGTGAGCCGCCGGCCCCT	0.637													C|||	1	0.000199681	0	0.0014	5008	,	,		15977	0		0	False		,,,				2504	0				p.R36C		Atlas-SNP	.											.	.	.	.	0			c.C106T						PASS	.						72	72	72					20																	30602782		2203	4300	6503	SO:0001583	missense	140706	exon2			GTGAGCCGCCGGC	AL031658	CCDS13195.1	20q11.21	2012-10-30	2012-10-30	2012-10-30	ENSG00000101331	ENSG00000101331			16153	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 160"	C20orf160			Standard	NM_080625		Approved	dJ310O13.5	uc002wxf.2	Q9NUG4	OTTHUMG00000032197	ENST00000300415.8:c.106C>T	chr20.hg19:g.30602782C>T	ENSP00000300415:p.Arg36Cys	89.0	0.0	.		113.0	42.0	.	NM_080625	Q5JYR9|Q8N5F1|Q8N6G8|Q96MD5	Missense_Mutation	SNP	ENST00000300415.8	hg19		.	.	.	.	.	.	.	.	.	.	C	29.4	5.007033	0.93287	.	.	ENSG00000101331	ENST00000300415;ENST00000339619;ENST00000262659	T;T	0.60171	0.21;0.21	4.66	4.66	0.58398	.	0.000000	0.85682	D	0.000000	T	0.77377	0.4121	M	0.80422	2.495	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81328	-0.0982	10	0.87932	D	0	-39.7528	16.7122	0.85388	0.0:1.0:0.0:0.0	.	36	Q9NUG4-2	.	C	36	ENSP00000300415:R36C;ENSP00000262659:R36C	ENSP00000262659:R36C	R	+	1	0	C20orf160	30066443	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	5.299000	0.65716	2.418000	0.82041	0.655000	0.94253	CGC	.	.	.	none		0.637	CCM2L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_080625		T	30602782	C	T	30602782	3	4	35	1	0	0	0	0	1	0	0	0	2095	652	23	1	112	1	C20orf160	20	30602782	Missense_Mutation	SNP	C	TCGA-5P-A9K6-01A-11D-A42J-10	5598539	30602782	32422738	49	2570											
MAPK1	5594	hgsc.bcm.edu	37	chr22	22160189	22160189	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gttggaaggcttgaggtcacGgtgcagaacgttagctgaat	10	10	15	6	2	1	3	1	2	0	1	1	4	1	4	0	4	3	5	0	4	4	3			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr22:22160189G>A	ENST00000215832.6	-	3	630	c.442C>T	c.(442-444)Cgt>Tgt	p.R148C	MAPK1_ENST00000398822.3_Missense_Mutation_p.R148C|MAPK1_ENST00000544786.1_Missense_Mutation_p.R148C	NM_002745.4	NP_002736.3	P28482	MK01_HUMAN	mitogen-activated protein kinase 1	148	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|caveolin-mediated endocytosis (GO:0072584)|cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|chemotaxis (GO:0006935)|cytosine metabolic process (GO:0019858)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|labyrinthine layer blood vessel development (GO:0060716)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mammary gland epithelial cell proliferation (GO:0033598)|MAPK cascade (GO:0000165)|MAPK import into nucleus (GO:0000189)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell differentiation (GO:0045596)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|Ras protein signal transduction (GO:0007265)|regulation of cytoskeleton organization (GO:0051493)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of protein stability (GO:0031647)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of stress-activated MAPK cascade (GO:0032872)|response to epidermal growth factor (GO:0070849)|response to estrogen (GO:0043627)|response to exogenous dsRNA (GO:0043330)|response to stress (GO:0006950)|response to toxic substance (GO:0009636)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|protein complex (GO:0043234)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MAP kinase activity (GO:0004707)|phosphatase binding (GO:0019902)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Colorectal(54;0.105)	all_lung(157;3.89e-05)		READ - Rectum adenocarcinoma(21;0.0689)	Arsenic trioxide(DB01169)|Isoprenaline(DB01064)	TTGAGGTCACGGTGCAGAACG	0.428																																					p.R148C		Atlas-SNP	.											.	MAPK1	38	.	0			c.C442T						PASS	.						195	175	182					22																	22160189		2203	4300	6503	SO:0001583	missense	5594	exon3			GGTCACGGTGCAG	M84489	CCDS13795.1	22q11.2	2014-09-17			ENSG00000100030	ENSG00000100030	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6871	protein-coding gene	gene with protein product		176948		PRKM2, PRKM1			Standard	NM_138957		Approved	ERK, ERK2, p41mapk, MAPK2	uc002zvn.3	P28482	OTTHUMG00000030508	ENST00000215832.6:c.442C>T	chr22.hg19:g.22160189G>A	ENSP00000215832:p.Arg148Cys	113.0	0.0	.		116.0	37.0	.	NM_002745	A8CZ64	Missense_Mutation	SNP	ENST00000215832.6	hg19	CCDS13795.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.583812	0.86748	.	.	ENSG00000100030	ENST00000215832;ENST00000415911;ENST00000398822;ENST00000544786	T;T;T	0.64803	-0.12;-0.12;-0.12	4.77	3.76	0.43208	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);	0.050300	0.85682	N	0.000000	T	0.78117	0.4233	M	0.77820	2.39	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.81491	-0.0909	10	0.87932	D	0	0.4712	13.3578	0.60638	0.0765:0.0:0.9235:0.0	.	148;148	A8CZ64;P28482	.;MK01_HUMAN	C	148;136;148;148	ENSP00000215832:R148C;ENSP00000381803:R148C;ENSP00000440842:R148C	ENSP00000215832:R148C	R	-	1	0	MAPK1	20490189	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.654000	0.83653	1.374000	0.46228	0.650000	0.86243	CGT	.	.	.	none		0.428	MAPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000075396.2			A	22160189	G	A	22160189	3	1	35	1	0	0	0	0	1	0	0	0	9278	1116	39	1	664	1	MAPK1	22	22160189	Missense_Mutation	SNP	G	TCGA-5P-A9K6-01A-11D-A42J-10		22160189	29144377	50	2571											
C22orf30	253143	hgsc.bcm.edu	37	chr22	32108919	32108919	+	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	agaggaacaccgtcggtatcTtagcttctgagtcttcatgg	9	12	11	9	2	4	2	1	1	3	1	5	3	4	3	1	3	2	2	1	3	3	4			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chr22:32108919T>G	ENST00000327423.6	-	4	5095	c.4906A>C	c.(4906-4908)Aga>Cga	p.R1636R	PRR14L_ENST00000434485.1_Silent_p.R1636R|PRR14L_ENST00000397493.2_Silent_p.R1636R	NM_173566.2	NP_775837.2	Q5THK1	PR14L_HUMAN	proline rich 14-like	1636										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(5)|skin(1)|urinary_tract(2)	14						CGTCGGTATCTTAGCTTCTGA	0.468											OREG0003533	type=REGULATORY REGION|Gene=BC040859|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.R1636R		Atlas-SNP	.											.	PRR14L	198	.	0			c.A4906C						PASS	.						34	27	29					22																	32108919		692	1591	2283	SO:0001819	synonymous_variant	253143	exon4			GGTATCTTAGCTT	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.4906A>C	chr22.hg19:g.32108919T>G		92.0	0.0	.	829	110.0	41.0	.	NM_173566	Q5THK4|Q6ZNN1|Q6ZWH0|Q8IW74|Q9H5T4	Silent	SNP	ENST00000327423.6	hg19	CCDS13900.2																																																																																			.	.	.	none		0.468	PRR14L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074993.2	NM_173566		G	32108919	T	G	32108919	2	3	35	1	0	0	0	0	0	0	0	1	2144	1617	56	5		5	C22orf30	22	32108919	Silent	SNP	T	TCGA-5P-A9K6-01A-11D-A42J-10	9948730	32108919	19195647	51	2572											
CXorf23	256643	hgsc.bcm.edu	37	chrX	19973668	19973668	+	Missense_Mutation	SNP	A	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	tgacatctgtctctctgtggAatagctagaagcaaccctag	11	11	9	10	0	3	2	0	1	3	1	4	3	3	3	1	1	3	2	1	1	6	3			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chrX:19973668A>C	ENST00000379682.4	-	4	1324	c.1291T>G	c.(1291-1293)Tcc>Gcc	p.S431A	CXorf23_ENST00000379687.3_Missense_Mutation_p.S431A|CXorf23_ENST00000356980.3_Missense_Mutation_p.S431A			A2AJT9	CX023_HUMAN	chromosome X open reading frame 23	431						mitochondrion (GO:0005739)				endometrium(2)|large_intestine(1)|lung(6)|skin(1)|urinary_tract(1)	11						CTCTCTGTGGAATAGCTAGAA	0.333																																					p.S431A		Atlas-SNP	.											.	CXorf23	75	.	0			c.T1291G						PASS	.						97	86	90					X																	19973668		2203	4300	6503	SO:0001583	missense	256643	exon4			CTGTGGAATAGCT	AL833278	CCDS14194.2	Xp22.13	2012-11-27			ENSG00000173681	ENSG00000173681			27413	protein-coding gene	gene with protein product						14702039	Standard	NM_198279		Approved		uc004czp.3	A2AJT9	OTTHUMG00000021226	ENST00000379682.4:c.1291T>G	chrX.hg19:g.19973668A>C	ENSP00000369004:p.Ser431Ala	24.0	0.0	.		18.0	12.0	.	NM_198279	A1A4E8|Q5VSM7|Q5VSN1|Q6ZS60|Q8N1W7	Missense_Mutation	SNP	ENST00000379682.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.73|10.73	1.433061|1.433061	0.25813|0.25813	.|.	.|.	ENSG00000173681|ENSG00000173681	ENST00000340625|ENST00000379687;ENST00000379682;ENST00000356980;ENST00000539038	.|T;T;T	.|0.12774	.|2.65;2.65;2.65	5.05|5.05	3.87|3.87	0.44632|0.44632	.|.	.|.	.|.	.|.	.|.	T|T	0.07638|0.07638	0.0192|0.0192	N|N	0.17800|0.17800	0.525|0.525	0.26427|0.26427	N|N	0.976006|0.976006	.|B;B	.|0.23377	.|0.017;0.084	.|B;B	.|0.18561	.|0.011;0.022	T|T	0.39078|0.39078	-0.9631|-0.9631	5|8	.|.	.|.	.|.	.|.	4.3281|4.3281	0.11050|0.11050	0.6669:0.0:0.0972:0.2358|0.6669:0.0:0.0972:0.2358	.|.	.|431;431	.|A2AJT9-2;A2AJT9	.|.;CX023_HUMAN	C|A	39|431;431;431;319	.|ENSP00000369009:S431A;ENSP00000369004:S431A;ENSP00000349470:S431A	.|.	F|S	-|-	2|1	0|0	CXorf23|CXorf23	19883589|19883589	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.551000|1.551000	0.36233|0.36233	0.578000|0.578000	0.29487|0.29487	0.486000|0.486000	0.48141|0.48141	TTC|TCC	.	.	.	none		0.333	CXorf23-006	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000055991.2	NM_198279		C	19973668	A	C	19973668	3	2	35	1	0	0	0	0	1	0	0	0	4105	246	9	5	789	5	CXorf23	23	19973668	Missense_Mutation	SNP	A	TCGA-5P-A9K6-01A-11D-A42J-10		19973668	135296892	52	2573											
HTATSF1	27336	hgsc.bcm.edu	37	chrX	135593689	135593689	+	Missense_Mutation	SNP	T	T	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	gacaaagagttagaagaaaaTgactctgaaaactccgaatt	19	8	8	6	1	1	5	0	2	1	3	2	7	2	5	1	0	1	1	1	0	8	2			TCGA-5P-A9K6-01A-11D-A42J-10	TCGA-5P-A9K6-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f41aab4-303b-428a-ac0c-df760be57c3e	22f09e94-5687-4bdb-bf4b-f54d47a940ea	g.chrX:135593689T>G	ENST00000218364.4	+	9	1959	c.1785T>G	c.(1783-1785)aaT>aaG	p.N595K	HTATSF1_ENST00000535601.1_Missense_Mutation_p.N595K	NM_014500.4	NP_055315.2	O43719	HTSF1_HUMAN	HIV-1 Tat specific factor 1	595	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)					TAGAAGAAAATGACTCTGAAA	0.383																																					p.N595K		Atlas-SNP	.											.	HTATSF1	66	.	0			c.T1785G						PASS	.						55	60	59					X																	135593689		2201	4298	6499	SO:0001583	missense	27336	exon10			AGAAAATGACTCT	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.1785T>G	chrX.hg19:g.135593689T>G	ENSP00000218364:p.Asn595Lys	133.0	0.0	.		154.0	111.0	.	NM_001163280	D3DWG9|Q59G06|Q99730	Missense_Mutation	SNP	ENST00000218364.4	hg19	CCDS14657.1	.	.	.	.	.	.	.	.	.	.	T	4.431	0.079832	0.08533	.	.	ENSG00000102241	ENST00000535601;ENST00000218364;ENST00000415377	T;T	0.04049	3.72;3.72	3.82	2.65	0.31530	.	0.148955	0.31589	N	0.007382	T	0.03011	0.0089	N	0.19112	0.55	0.09310	N	1	B	0.33694	0.421	B	0.27500	0.08	T	0.41875	-0.9484	10	0.87932	D	0	-11.1441	6.7729	0.23604	0.0:0.1179:0.0:0.8821	.	595	O43719	HTSF1_HUMAN	K	595	ENSP00000442699:N595K;ENSP00000218364:N595K	ENSP00000218364:N595K	N	+	3	2	HTATSF1	135421355	0.295000	0.24389	0.047000	0.18901	0.018000	0.09664	1.393000	0.34497	0.653000	0.30826	0.425000	0.28330	AAT	.	.	.	none		0.383	HTATSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058497.1	NM_014500		G	135593689	T	G	135593689	3	3	35	1	0	0	0	0	1	0	0	0	7440	1461	51	5	1819	5	HTATSF1	23	135593689	Missense_Mutation	SNP	T	TCGA-5P-A9K6-01A-11D-A42J-10	115620021	135593689	19676871	53	2574											
TXNIP	10628	hgsc.bcm.edu	37	chr1	145440061	145440064	+	Frame_Shift_Del	DEL	AAAG	AAAG	-																															cctgtgtctgctaaaaaagaAaagaaagtttcctgcatgtt																										TCGA-5P-A9K8-01A-11D-A42J-10	TCGA-5P-A9K8-10A-01D-A42M-10	AAAG	AAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1dda8cfa-899d-4d02-a2c8-ebb1169560aa	dfacd90a-6863-4d3d-a67d-2a39274e2691	g.chr1:145440061_145440064delAAAG	ENST00000369317.4	+	4	829_832	c.495_498delAAAG	c.(493-498)gaaaagfs	p.EK165fs	TXNIP_ENST00000475171.1_Intron	NM_006472.3	NP_006463.3	Q9H3M7	TXNIP_HUMAN	thioredoxin interacting protein	165					cell cycle (GO:0007049)|cellular response to tumor cell (GO:0071228)|innate immune response (GO:0045087)|keratinocyte differentiation (GO:0030216)|negative regulation of cell division (GO:0051782)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|protein import into nucleus (GO:0006606)|regulation of cell proliferation (GO:0042127)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucose (GO:0009749)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)	enzyme inhibitor activity (GO:0004857)|ubiquitin protein ligase binding (GO:0031625)	p.K166R(1)		breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(1)|lung(5)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	21	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CTAAAAAAGAAAAGAAAGTTTCCT	0.417																																					p.165_166del		Atlas-Indel,Pindel	.											.	TXNIP	51	.	1	Substitution - Missense(1)	ovary(1)	c.494_497del						PASS	.																																			SO:0001589	frameshift_variant	10628	exon4			.	S73591	CCDS72876.1	1q11	2008-07-18			ENSG00000117289	ENSG00000265972			16952	protein-coding gene	gene with protein product	"upregulated by 1,25-dihydroxyvitamin D-3", "thioredoxin binding protein 2"	606599				8086474	Standard	NM_006472		Approved	VDUP1, EST01027, HHCPA78, THIF	uc001enn.4	Q9H3M7	OTTHUMG00000013755	ENST00000369317.4:c.495_498delAAAG	chr1.hg19:g.145440065_145440068delAAAG	ENSP00000358323:p.Glu165fs	46.0	0.0	0		47.0	18.0	0.382979	NM_006472	B4E3D3|Q16226|Q6PML0|Q9BXG9	Frame_Shift_Del	DEL	ENST00000369317.4	hg19	CCDS913.1																																																																																			.	.	.	none		0.417	TXNIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038547.1	NM_006472		-	145440064	AAAG	-	145440061	7	5	36	1	0	1	0	1	0	0	0	0	16815	11	1	0	509	0	TXNIP	1	145440061	Frame_Shift_Del	DEL	AAAG	TCGA-5P-A9K8-01A-11D-A42J-10		145440061	103810560	1	2575											
C1orf9	51430	hgsc.bcm.edu	37	chr1	172558934	172558934	+	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	gcaaaattctacagatctagGatatgctaatggaaatcttg	15	12	8	6	0	3	1	0	0	3	1	3	3	3	3	0	2	2	2	0	2	7	6			TCGA-5P-A9K8-01A-11D-A42J-10	TCGA-5P-A9K8-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1dda8cfa-899d-4d02-a2c8-ebb1169560aa	dfacd90a-6863-4d3d-a67d-2a39274e2691	g.chr1:172558934G>T	ENST00000263688.3	+	18	2912	c.2693G>T	c.(2692-2694)gGa>gTa	p.G898V	SUCO_ENST00000610051.1_Intron|SUCO_ENST00000608151.1_Missense_Mutation_p.G1050V|SUCO_ENST00000367723.4_Missense_Mutation_p.G1049V	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	898					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											ACAGATCTAGGATATGCTAAT	0.358																																					p.G898V		Atlas-SNP	.											.	.	.	.	0			c.G2693T						PASS	.						89	94	92					1																	172558934		2201	4294	6495	SO:0001583	missense	51430	exon18			ATCTAGGATATGC	AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"SUN-like protein 1", "osteopotentia"		"chromosome 1 open reading frame 9"	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.2693G>T	chr1.hg19:g.172558934G>T	ENSP00000263688:p.Gly898Val	84.0	0.0	.		94.0	12.0	.	NM_014283	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Missense_Mutation	SNP	ENST00000263688.3	hg19	CCDS1303.1	.	.	.	.	.	.	.	.	.	.	G	16.65	3.181241	0.57800	.	.	ENSG00000094975	ENST00000367723;ENST00000263688	.	.	.	5.5	4.56	0.56223	.	0.049394	0.85682	N	0.000000	T	0.72399	0.3455	M	0.74258	2.255	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.77593	-0.2530	9	0.72032	D	0.01	-8.9083	14.1563	0.65419	0.0:0.0:0.8488:0.1512	.	898;1050;898	B4DZJ3;Q5H945;Q9UBS9	.;.;OSPT_HUMAN	V	1050;898	.	ENSP00000263688:G898V	G	+	2	0	C1orf9	170825557	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	5.123000	0.64703	1.265000	0.44215	0.655000	0.94253	GGA	.	.	.	none		0.358	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227		T	172558934	G	T	172558934	3	4	36	1	0	0	0	0	1	0	0	0	2069	1174	41	4	2763	4	C1orf9	1	172558934	Missense_Mutation	SNP	G	TCGA-5P-A9K8-01A-11D-A42J-10	27118873	172558934	76691687	2	2576											
MTR	4548	hgsc.bcm.edu	37	chr1	236959019	236959019	+	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	acaacatgtcacccgcgctcCaagacctgtcgcaacccggt	10	6	8	17	4	1	1	1	0	0	1	3	1	2	1	4	1	2	2	4	1	3	0			TCGA-5P-A9K8-01A-11D-A42J-10	TCGA-5P-A9K8-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1dda8cfa-899d-4d02-a2c8-ebb1169560aa	dfacd90a-6863-4d3d-a67d-2a39274e2691	g.chr1:236959019C>T	ENST00000366577.5	+	1	410	c.16C>T	c.(16-18)Caa>Taa	p.Q6*	MTR_ENST00000418145.2_Silent_p.S133S|MTR_ENST00000535889.1_Nonsense_Mutation_p.Q6*	NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase	6					cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|methylation (GO:0032259)|nervous system development (GO:0007399)|pteridine-containing compound metabolic process (GO:0042558)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	cobalamin binding (GO:0031419)|methionine synthase activity (GO:0008705)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	67	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	ACCCGCGCTCCAAGACCTGTC	0.632																																					p.Q6X		Atlas-SNP	.											.	MTR	127	.	0			c.C16T						PASS	.						100	77	85					1																	236959019		2203	4300	6503	SO:0001587	stop_gained	4548	exon1			GCGCTCCAAGACC	U73338	CCDS1614.1, CCDS73054.1	1q43	2011-05-12			ENSG00000116984	ENSG00000116984	2.1.1.13		7468	protein-coding gene	gene with protein product		156570				8968735	Standard	NM_000254		Approved	cblG	uc001hyi.4	Q99707	OTTHUMG00000040060	ENST00000366577.5:c.16C>T	chr1.hg19:g.236959019C>T	ENSP00000355536:p.Gln6*	38.0	0.0	.		50.0	5.0	.	NM_000254	A1L4N8|A9Z1W4|B9EGF7|Q99713|Q99723	Nonsense_Mutation	SNP	ENST00000366577.5	hg19	CCDS1614.1	.	.	.	.	.	.	.	.	.	.	C	42	9.187394	0.99094	.	.	ENSG00000116984	ENST00000417743;ENST00000366577;ENST00000535889	.	.	.	3.06	1.09	0.20402	.	2.563360	0.01436	N	0.014912	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10902	T	0.67	25.1223	5.645	0.17584	0.2278:0.5511:0.221:0.0	.	.	.	.	X	6	.	ENSP00000355536:Q6X	Q	+	1	0	MTR	235025642	0.004000	0.15560	0.001000	0.08648	0.975000	0.68041	1.050000	0.30404	0.290000	0.22444	-0.340000	0.08031	CAA	.	.	.	none		0.632	MTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096632.2	NM_000254		T	236959019	C	T	236959019	4	4	36	1	0	0	0	0	0	1	0	0	9965	595	21	2	18	2	MTR	1	236959019	Nonsense_Mutation	SNP	C	TCGA-5P-A9K8-01A-11D-A42J-10	64400085	236959019	12291602	3	2577											
TLR3	7098	hgsc.bcm.edu	37	chr4	187006026	187006026	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atccaaaaactctgtacattAaatttatttaaatattcaat	18	16	1	6	0	2	0	1	0	1	0	3	0	3	0	1	0	2	1	1	0	10	8			TCGA-5P-A9K8-01A-11D-A42J-10	TCGA-5P-A9K8-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1dda8cfa-899d-4d02-a2c8-ebb1169560aa	dfacd90a-6863-4d3d-a67d-2a39274e2691	g.chr4:187006026A>G	ENST00000296795.3	+	5	2818	c.2714A>G	c.(2713-2715)tAa>tGa	p.*905*	TLR3_ENST00000504367.1_Silent_p.*628*	NM_003265.2	NP_003256.1	O15455	TLR3_HUMAN	toll-like receptor 3	0					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)		TCTGTACATTAAATTTATTTA	0.308																																					p.X905X		Atlas-SNP	.											.	TLR3	83	.	0			c.A2714G						PASS	.						29	32	31					4																	187006026		2196	4298	6494	SO:0001819	synonymous_variant	7098	exon5			TACATTAAATTTA	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.2714A>G	chr4.hg19:g.187006026A>G		102.0	0.0	.		127.0	13.0	.	NM_003265	B2RAI7|B7Z7K0|E6Y0F0|E6Y0F1|E9PGH4|Q4VAL2|Q504W0	Silent	SNP	ENST00000296795.3	hg19	CCDS3846.1																																																																																			.	.	.	none		0.308	TLR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360313.4			G	187006026	A	G	187006026	2	3	36	1	0	0	0	0	0	0	0	1	15964	369	13	3		3	TLR3	4	187006026	Silent	SNP	A	TCGA-5P-A9K8-01A-11D-A42J-10		187006026	4148250	4	2578											
DNAH5	1767	hgsc.bcm.edu	37	chr5	13794140	13794140	+	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	gccatatgttgtacccattcGtttatccacatagctctcta	9	15	5	12	1	1	0	0	0	1	0	4	0	2	0	3	0	2	4	3	0	5	8	rs375053470		TCGA-5P-A9K8-01A-11D-A42J-10	TCGA-5P-A9K8-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1dda8cfa-899d-4d02-a2c8-ebb1169560aa	dfacd90a-6863-4d3d-a67d-2a39274e2691	g.chr5:13794140G>A	ENST00000265104.4	-	48	8019	c.7915C>T	c.(7915-7917)Cga>Tga	p.R2639*		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2639	AAA 3. {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)					GTACCCATTCGTTTATCCACA	0.368									Kartagener syndrome																												p.R2639X		Atlas-SNP	.											.	DNAH5	868	.	0			c.C7915T	GRCh37	CI065821|CM020273	DNAH5	I|M		PASS	.	G	stop/ARG	1,4405	2.1+/-5.4	0,1,2202	103	98	100		7915	5.9	1	5		100	0,8600		0,0,4300	no	stop-gained	DNAH5	NM_001369.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		2639/4625	13794140	1,13005	2203	4300	6503	SO:0001587	stop_gained	1767	exon48	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CCATTCGTTTATC	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.7915C>T	chr5.hg19:g.13794140G>A	ENSP00000265104:p.Arg2639*	137.0	0.0	.		130.0	38.0	.	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Nonsense_Mutation	SNP	ENST00000265104.4	hg19	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	g	50	16.923105	0.99875	2.27E-4	0.0	ENSG00000039139	ENST00000265104	.	.	.	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.2366	0.98359	0.0:0.0:1.0:0.0	.	.	.	.	X	2639	.	ENSP00000265104:R2639X	R	-	1	2	DNAH5	13847140	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.593000	0.54001	2.792000	0.96026	0.557000	0.71058	CGA	.	.	.	weak		0.368	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13794140	G	A	13794140	4	1	36	1	0	0	0	0	0	1	0	0	4606	1153	40	1	6087	1	DNAH5	5	13794140	Nonsense_Mutation	SNP	G	TCGA-5P-A9K8-01A-11D-A42J-10		13794140	167121120	5	2579											
HIST1H2BG	8339	hgsc.bcm.edu	37	chr6	26216532	26216532	+	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	ggtgacagccttggtaccttCggacactgcgtgcttggcca	6	10	13	12	2	0	1	0	1	0	0	1	2	0	2	3	4	4	2	3	4	1	4			TCGA-5P-A9K8-01A-11D-A42J-10	TCGA-5P-A9K8-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1dda8cfa-899d-4d02-a2c8-ebb1169560aa	dfacd90a-6863-4d3d-a67d-2a39274e2691	g.chr6:26216532C>G	ENST00000244601.3	-	1	340	c.340G>C	c.(340-342)Gaa>Caa	p.E114Q	HIST1H2AE_ENST00000303910.2_5'Flank	NM_003518.3	NP_003509.1	P62807	H2B1C_HUMAN	histone cluster 1, H2bg	114					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)				TTGGTACCTTCGGACACTGCG	0.532																																					p.E114Q		Atlas-SNP	.											.	HIST1H2BG	25	.	0			c.G340C						PASS	.						97	97	97					6																	26216532		2203	4300	6503	SO:0001583	missense	8339	exon1			TACCTTCGGACAC	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.340G>C	chr6.hg19:g.26216532C>G	ENSP00000244601:p.Glu114Gln	58.0	0.0	.		85.0	21.0	.	NM_003518	P02278|Q3B872|Q4VB69|Q93078|Q93080	Missense_Mutation	SNP	ENST00000244601.3	hg19	CCDS4594.1	.	.	.	.	.	.	.	.	.	.	.	13.36	2.215310	0.39102	.	.	ENSG00000187990	ENST00000244601	T	0.48836	0.8	3.89	3.89	0.44902	.	0.000000	0.33457	U	0.004887	T	0.54581	0.1867	.	.	.	0.37512	D	0.91718	.	.	.	.	.	.	T	0.62695	-0.6800	7	0.72032	D	0.01	.	15.3699	0.74554	0.0:1.0:0.0:0.0	.	.	.	.	Q	114	ENSP00000244601:E114Q	ENSP00000244601:E114Q	E	-	1	0	HIST1H2BG	26324511	1.000000	0.71417	0.999000	0.59377	0.102000	0.19082	7.499000	0.81566	2.172000	0.68678	0.561000	0.74099	GAA	.	.	.	none		0.532	HIST1H2BG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040109.2	NM_003518		G	26216532	C	G	26216532	3	3	36	1	0	0	0	0	1	0	0	0	7153	893	31	4	44	4	HIST1H2BG	6	26216532	Missense_Mutation	SNP	C	TCGA-5P-A9K8-01A-11D-A42J-10		26216532	144898535	6	2580											
DEFB110	245913	hgsc.bcm.edu	37	chr6	49986773	49986773	+	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	atgacactgatttttacattGaccattacctattctgcact	11	16	4	10	0	1	3	0	3	1	0	1	3	1	3	2	0	3	1	2	0	3	7			TCGA-5P-A9K8-01A-11D-A42J-10	TCGA-5P-A9K8-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1dda8cfa-899d-4d02-a2c8-ebb1169560aa	dfacd90a-6863-4d3d-a67d-2a39274e2691	g.chr6:49986773G>T	ENST00000371148.2	-	2	166	c.121C>A	c.(121-123)Caa>Aaa	p.Q41K	DEFB110_ENST00000393660.2_Intron	NM_001037497.1	NP_001032586.1	Q30KQ9	DB110_HUMAN	defensin, beta 110 locus	41					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(1)|lung(1)|ovary(1)	3	Lung NSC(77;0.042)					TTTTTACATTGACCATTACCT	0.388																																					p.Q41K		Atlas-SNP	.											.	DEFB110	5	.	0			c.C121A						PASS	.						186	163	171					6																	49986773		2203	4300	6503	SO:0001583	missense	245913	exon2			TACATTGACCATT	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.121C>A	chr6.hg19:g.49986773G>T	ENSP00000360190:p.Gln41Lys	54.0	0.0	.		73.0	41.0	.	NM_001037497	Q30KR0	Missense_Mutation	SNP	ENST00000371148.2	hg19	CCDS34475.1	.	.	.	.	.	.	.	.	.	.	G	0.019	-1.456084	0.01071	.	.	ENSG00000203970	ENST00000371148	T	0.10382	2.88	4.77	2.84	0.33178	.	1.041720	0.07626	N	0.927868	T	0.02047	0.0064	.	.	.	0.09310	N	1	B	0.11235	0.004	B	0.12156	0.007	T	0.45190	-0.9278	8	.	.	.	0.3027	7.7772	0.29043	0.0:0.1777:0.6386:0.1837	.	41	Q30KQ9	DB110_HUMAN	K	41	ENSP00000360190:Q41K	.	Q	-	1	0	DEFB110	50094732	0.473000	0.25878	0.887000	0.34795	0.012000	0.07955	1.013000	0.29937	1.191000	0.43056	0.655000	0.94253	CAA	.	.	.	none		0.388	DEFB110-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359664.1	NM_001037728		T	49986773	G	T	49986773	3	4	36	1	0	0	0	0	1	0	0	0	4402	1299	45	4	222	4	DEFB110	6	49986773	Missense_Mutation	SNP	G	TCGA-5P-A9K8-01A-11D-A42J-10	23770241	49986773	121128294	7	2581											
PNLDC1	154197	hgsc.bcm.edu	37	chr6	160239629	160239629	+	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	tcctttcctcagtaccttgaCgtgctggctccttacgtgaa	6	14	8	13	2	1	2	1	2	0	0	4	2	4	2	4	1	3	3	4	1	3	4	rs146349877		TCGA-5P-A9K8-01A-11D-A42J-10	TCGA-5P-A9K8-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1dda8cfa-899d-4d02-a2c8-ebb1169560aa	dfacd90a-6863-4d3d-a67d-2a39274e2691	g.chr6:160239629C>T	ENST00000610273.1	+	16	1338	c.1167C>T	c.(1165-1167)gaC>gaT	p.D389D	PNLDC1_ENST00000392167.3_Silent_p.D400D	NM_001271862.1|NM_173516.1	NP_001258791.1|NP_775787.1	Q8NA58	PNDC1_HUMAN	poly(A)-specific ribonuclease (PARN)-like domain containing 1	389						integral component of membrane (GO:0016021)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	31		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		AGTACCTTGACGTGCTGGCTC	0.562																																					p.D389D		Atlas-SNP	.											.	PNLDC1	66	.	0			c.C1167T						PASS	.	C		0,4406		0,0,2203	90	83	86		1167	-8.8	0.8	6	dbSNP_134	86	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PNLDC1	NM_173516.1		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		389/521	160239629	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	154197	exon16			CCTTGACGTGCTG	AK097559	CCDS5271.1, CCDS5271.2, CCDS64561.1	6q25.3	2008-02-05			ENSG00000146453	ENSG00000146453			21185	protein-coding gene	gene with protein product							Standard	NM_001271862		Approved	FLJ40240, dJ195P10.2	uc003qsy.2	Q8NA58	OTTHUMG00000015941	ENST00000610273.1:c.1167C>T	chr6.hg19:g.160239629C>T		54.0	0.0	.		62.0	12.0	.	NM_173516	Q5TAP7|Q8N7X5	Silent	SNP	ENST00000610273.1	hg19	CCDS5271.1																																																																																			.	C|1.000;T|0.000	0.000	weak		0.562	PNLDC1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_173516		T	160239629	C	T	160239629	2	4	36	1	0	0	0	0	0	0	0	1	12155	535	19	1		1	PNLDC1	6	160239629	Silent	SNP	C	TCGA-5P-A9K8-01A-11D-A42J-10	110252856	160239629	10875438	8	2582											
DRD2	1813	hgsc.bcm.edu	37	chr11	113295145	113295145	+	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	gacgaggaggtcggccactgCgaggctgacgatcaggtagt	9	6	17	9	4	1	1	1	1	0	0	2	6	1	2	1	5	1	2	1	5	1	1			TCGA-5P-A9K8-01A-11D-A42J-10	TCGA-5P-A9K8-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1dda8cfa-899d-4d02-a2c8-ebb1169560aa	dfacd90a-6863-4d3d-a67d-2a39274e2691	g.chr11:113295145C>T	ENST00000362072.3	-	2	573	c.229G>A	c.(229-231)Gca>Aca	p.A77T	DRD2_ENST00000538967.1_Missense_Mutation_p.A77T|DRD2_ENST00000544518.1_Missense_Mutation_p.A77T|DRD2_ENST00000346454.3_Missense_Mutation_p.A77T|DRD2_ENST00000535984.1_5'UTR|DRD2_ENST00000542968.1_Missense_Mutation_p.A77T|DRD2_ENST00000355319.2_Missense_Mutation_p.A77T	NM_000795.3	NP_000786.1	P14416	DRD2_HUMAN	dopamine receptor D2	77					activation of protein kinase activity (GO:0032147)|adenohypophysis development (GO:0021984)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adult walking behavior (GO:0007628)|arachidonic acid secretion (GO:0050482)|associative learning (GO:0008306)|auditory behavior (GO:0031223)|axonogenesis (GO:0007409)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|branching morphogenesis of a nerve (GO:0048755)|cellular calcium ion homeostasis (GO:0006874)|cerebral cortex GABAergic interneuron migration (GO:0021853)|circadian regulation of gene expression (GO:0032922)|dopamine metabolic process (GO:0042417)|feeding behavior (GO:0007631)|G-protein coupled receptor internalization (GO:0002031)|grooming behavior (GO:0007625)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|long-term memory (GO:0007616)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of circadian sleep/wake cycle, sleep (GO:0042321)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of insulin secretion (GO:0046676)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein secretion (GO:0050709)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|neuron-neuron synaptic transmission (GO:0007270)|orbitofrontal cortex development (GO:0021769)|peristalsis (GO:0030432)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|pigmentation (GO:0043473)|positive regulation of cytokinesis (GO:0032467)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of dopamine uptake involved in synaptic transmission (GO:0051586)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of receptor internalization (GO:0002092)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of urine volume (GO:0035810)|prepulse inhibition (GO:0060134)|protein localization (GO:0008104)|regulation of cAMP metabolic process (GO:0030814)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of heart rate (GO:0002027)|regulation of locomotion involved in locomotory behavior (GO:0090325)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of potassium ion transport (GO:0043266)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, GABAergic (GO:0032228)|release of sequestered calcium ion into cytosol (GO:0051209)|response to amphetamine (GO:0001975)|response to axon injury (GO:0048678)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to histamine (GO:0034776)|response to hypoxia (GO:0001666)|response to inactivity (GO:0014854)|response to iron ion (GO:0010039)|response to light stimulus (GO:0009416)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to toxic substance (GO:0009636)|sensory perception of smell (GO:0007608)|striatum development (GO:0021756)|synapse assembly (GO:0007416)|synaptic transmission, dopaminergic (GO:0001963)|temperature homeostasis (GO:0001659)|visual learning (GO:0008542)|Wnt signaling pathway (GO:0016055)	acrosomal vesicle (GO:0001669)|axon (GO:0030424)|axon terminus (GO:0043679)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|sperm flagellum (GO:0036126)|synaptic vesicle membrane (GO:0030672)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity, coupled via Gi/Go (GO:0001591)|drug binding (GO:0008144)|identical protein binding (GO:0042802)|potassium channel regulator activity (GO:0015459)			endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(18)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	39		all_cancers(61;3.91e-16)|all_epithelial(67;2.95e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000977)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0494)		BRCA - Breast invasive adenocarcinoma(274;5.77e-06)|Epithelial(105;6.66e-05)|all cancers(92;0.000307)|OV - Ovarian serous cystadenocarcinoma(223;0.216)	Acepromazine(DB01614)|Acetophenazine(DB01063)|Alizapride(DB01425)|Amantadine(DB00915)|Amisulpride(DB06288)|Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Desipramine(DB01151)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Droperidol(DB00450)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Memantine(DB01043)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Metoclopramide(DB01233)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sertindole(DB06144)|Sulpiride(DB00391)|Tetrabenazine(DB04844)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	TCGGCCACTGCGAGGCTGACG	0.632																																					p.A77T		Atlas-SNP	.											.	DRD2	98	.	0			c.G229A						PASS	.						135	105	115					11																	113295145		2201	4296	6497	SO:0001583	missense	1813	exon2			CCACTGCGAGGCT	M29066	CCDS8361.1, CCDS8362.1	11q22-q23	2012-08-08						"GPCR / Class A : Dopamine receptors"	3023	protein-coding gene	gene with protein product		126450					Standard	NM_000795		Approved		uc001poa.4	P14416		ENST00000362072.3:c.229G>A	chr11.hg19:g.113295145C>T	ENSP00000354859:p.Ala77Thr	59.0	0.0	.		71.0	4.0	.	NM_016574	Q9NZR3|Q9UPA9	Missense_Mutation	SNP	ENST00000362072.3	hg19	CCDS8361.1	.	.	.	.	.	.	.	.	.	.	C	36	5.614408	0.96649	.	.	ENSG00000149295	ENST00000355319;ENST00000346454;ENST00000362072;ENST00000544518;ENST00000542968;ENST00000538967;ENST00000543292	T;T;T;T;T;T;T	0.56103	0.48;0.48;0.48;0.48;0.48;0.48;0.48	5.3	5.3	0.74995	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.86020	0.5833	H	0.99758	4.755	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.999;1.0	D	0.92664	0.6144	10	0.87932	D	0	.	18.9437	0.92613	0.0:1.0:0.0:0.0	.	77;77;77;77	F8VUV1;P14416-3;P14416-2;P14416	.;.;.;DRD2_HUMAN	T	77	ENSP00000347474:A77T;ENSP00000278597:A77T;ENSP00000354859:A77T;ENSP00000441068:A77T;ENSP00000442172:A77T;ENSP00000438215:A77T;ENSP00000438419:A77T	ENSP00000278597:A77T	A	-	1	0	DRD2	112800355	1.000000	0.71417	0.517000	0.27799	0.991000	0.79684	7.758000	0.85224	2.469000	0.83416	0.561000	0.74099	GCA	.	.	.	none		0.632	DRD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395834.1	NM_000795		T	113295145	C	T	113295145	3	4	36	1	0	0	0	0	1	0	0	0	4759	768	27	1	1130	1	DRD2	11	113295145	Missense_Mutation	SNP	C	TCGA-5P-A9K8-01A-11D-A42J-10		113295145	21711371	9	2583											
SARNP	84324	hgsc.bcm.edu	37	chr12	56182870	56182870	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctacattacctttctggagaTtgaagagacattcaaaccaa	15	11	6	9	0	2	3	1	1	1	2	2	5	2	3	2	1	3	0	2	1	5	5	rs138765992		TCGA-5P-A9K8-01A-11D-A42J-10	TCGA-5P-A9K8-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1dda8cfa-899d-4d02-a2c8-ebb1169560aa	dfacd90a-6863-4d3d-a67d-2a39274e2691	g.chr12:56182870T>C	ENST00000336133.3	-	9	544	c.490A>G	c.(490-492)Atc>Gtc	p.I164V	SARNP_ENST00000552080.1_Missense_Mutation_p.I164V|SARNP_ENST00000444631.2_Missense_Mutation_p.I104V|RP11-762I7.5_ENST00000546837.1_Missense_Mutation_p.N476S	NM_033082.3	NP_149073.1	P82979	SARNP_HUMAN	SAP domain containing ribonucleoprotein	164					mRNA export from nucleus (GO:0006406)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|transcription, DNA-templated (GO:0006351)	intracellular membrane-bounded organelle (GO:0043231)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|transcription export complex (GO:0000346)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	6						TTTCTGGAGATTGAAGAGACA	0.368																																					p.I164V		Atlas-SNP	.											.	SARNP	19	.	0			c.A490G						PASS	.	T	VAL/ILE	1,4405	2.1+/-5.4	0,1,2202	113	103	106		490	3.9	1	12	dbSNP_134	106	0,8600		0,0,4300	no	missense	SARNP	NM_033082.3	29	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign	164/211	56182870	1,13005	2203	4300	6503	SO:0001583	missense	84324	exon9			TGGAGATTGAAGA	AJ409089	CCDS8892.1	12q13.2	2009-07-09				ENSG00000205323			24432	protein-coding gene	gene with protein product	"hepatocellular carcinoma 1", "cytokine induced protein 29 kDa"	610049				11356193, 11922608	Standard	NM_033082		Approved	THO1, Hcc-1, CIP29		P82979	OTTHUMG00000170441	ENST00000336133.3:c.490A>G	chr12.hg19:g.56182870T>C	ENSP00000337632:p.Ile164Val	52.0	0.0	.		65.0	7.0	.	NM_033082	A8K393|Q9P066	Missense_Mutation	SNP	ENST00000336133.3	hg19	CCDS8892.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	1.508|1.508	-0.550269|-0.550269	0.03996|0.03996	2.27E-4|2.27E-4	0.0|0.0	ENSG00000205323|ENSG00000257390	ENST00000444631;ENST00000336133;ENST00000552080|ENST00000546837	.|.	.|.	.|.	4.99|4.99	3.87|3.87	0.44632|0.44632	.|.	0.308918|.	0.37304|.	N|.	0.002142|.	T|T	0.11367|0.11367	0.0277|0.0277	N|N	0.01242|0.01242	-0.935|-0.935	0.30568|0.30568	N|N	0.763848|0.763848	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.12837|0.12837	-1.0532|-1.0532	9|5	0.02654|.	T|.	1|.	-16.7878|-16.7878	6.8802|6.8802	0.24168|0.24168	0.0:0.1004:0.0:0.8996|0.0:0.1004:0.0:0.8996	.|.	164|.	P82979|.	SARNP_HUMAN|.	V|S	104;164;164|476	.|.	ENSP00000337632:I164V|.	I|N	-|-	1|2	0|0	SARNP|RP11-762I7.5	54469137|54469137	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	1.389000|1.389000	0.34453|0.34453	2.234000|2.234000	0.73211|0.73211	0.460000|0.460000	0.39030|0.39030	ATC|AAT	.	T|1.000;C|0.000	0.000	weak		0.368	SARNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409159.2	NM_033082		C	56182870	T	C	56182870	3	2	36	1	0	0	0	0	1	0	0	0	13856	1493	52	3	154	3	SARNP	12	56182870	Missense_Mutation	SNP	T	TCGA-5P-A9K8-01A-11D-A42J-10		56182870	77669025	10	2584											
NAV3	89795	hgsc.bcm.edu	37	chr12	78516053	78516053	+	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	gcaggcagcaaggatactccGagctaccagtccatgactag	12	6	11	12	1	0	1	0	1	0	0	2	3	2	2	3	2	4	4	3	2	4	3			TCGA-5P-A9K8-01A-11D-A42J-10	TCGA-5P-A9K8-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1dda8cfa-899d-4d02-a2c8-ebb1169560aa	dfacd90a-6863-4d3d-a67d-2a39274e2691	g.chr12:78516053G>A	ENST00000397909.2	+	16	4256	c.4083G>A	c.(4081-4083)ccG>ccA	p.P1361P	NAV3_ENST00000536525.2_Silent_p.P1361P|NAV3_ENST00000228327.6_Silent_p.P1361P|NAV3_ENST00000266692.7_Intron			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1361	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						AGGATACTCCGAGCTACCAGT	0.577										HNSCC(70;0.22)																											p.P1361P		Atlas-SNP	.											NAV3,NS,carcinoma,0,1	NAV3	506	.	0			c.G4083A						PASS	.						109	105	106					12																	78516053		2014	4184	6198	SO:0001819	synonymous_variant	89795	exon16			TACTCCGAGCTAC	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.4083G>A	chr12.hg19:g.78516053G>A		41.0	0.0	.		57.0	19.0	.	NM_014903	Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	hg19																																																																																				.	.	.	none		0.577	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		A	78516053	G	A	78516053	2	1	36	1	0	0	0	0	0	0	0	1	10192	1045	37	1		1	NAV3	12	78516053	Silent	SNP	G	TCGA-5P-A9K8-01A-11D-A42J-10	22333183	78516053	55335842	11	2585											
IL32	9235	hgsc.bcm.edu	37	chr16	3119278	3119278	+	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	gagctcttcatgtcctctttCcagtcctacggagccccacg	6	11	8	16	2	3	0	1	0	2	0	6	2	6	1	5	1	3	1	5	1	1	3			TCGA-5P-A9K8-01A-11D-A42J-10	TCGA-5P-A9K8-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1dda8cfa-899d-4d02-a2c8-ebb1169560aa	dfacd90a-6863-4d3d-a67d-2a39274e2691	g.chr16:3119278C>A	ENST00000534507.1	+	6	838	c.627C>A	c.(625-627)ttC>ttA	p.F209L	IL32_ENST00000008180.9_Missense_Mutation_p.F143L|IL32_ENST00000531965.1_Missense_Mutation_p.F153L|IL32_ENST00000548652.1_Missense_Mutation_p.F154L|IL32_ENST00000382213.3_Missense_Mutation_p.F154L|IL32_ENST00000551122.1_Intron|IL32_ENST00000525643.2_Missense_Mutation_p.F163L|IL32_ENST00000444393.3_Missense_Mutation_p.F163L|IL32_ENST00000552936.1_Missense_Mutation_p.F187L|IL32_ENST00000552664.1_Missense_Mutation_p.F163L|IL32_ENST00000533097.2_Missense_Mutation_p.F163L|IL32_ENST00000440815.3_Missense_Mutation_p.F163L|IL32_ENST00000549213.1_Intron|IL32_ENST00000526464.2_Missense_Mutation_p.F163L|IL32_ENST00000529550.1_Missense_Mutation_p.F163L|IL32_ENST00000551513.1_Missense_Mutation_p.F200L|IL32_ENST00000530538.2_Missense_Mutation_p.F163L|IL32_ENST00000530890.1_Missense_Mutation_p.F143L|IL32_ENST00000552356.1_Missense_Mutation_p.F143L|IL32_ENST00000528163.2_Missense_Mutation_p.F163L|IL32_ENST00000548476.1_Missense_Mutation_p.F209L|IL32_ENST00000529699.1_Missense_Mutation_p.F143L|IL32_ENST00000396887.3_Intron|RNU1-125P_ENST00000516752.1_RNA|IL32_ENST00000325568.5_Missense_Mutation_p.F163L|IL32_ENST00000548246.1_Missense_Mutation_p.F123L|IL32_ENST00000396890.2_Missense_Mutation_p.F209L			P24001	IL32_HUMAN	interleukin 32	209					cell adhesion (GO:0007155)|defense response (GO:0006952)|immune response (GO:0006955)	extracellular space (GO:0005615)|membrane (GO:0016020)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	15						TGTCCTCTTTCCAGTCCTACG	0.557																																					p.F163L		Atlas-SNP	.											.	IL32	32	.	0			c.C489A						PASS	.						99	125	116					16																	3119278		2197	4300	6497	SO:0001583	missense	9235	exon7			CTCTTTCCAGTCC	M59807	CCDS32377.1, CCDS32378.1, CCDS32379.1, CCDS45394.1	16p13.3	2011-07-21			ENSG00000008517	ENSG00000008517		"Interleukins and interleukin receptors"	16830	protein-coding gene	gene with protein product	"natural killer cell transcript 4"	606001				1729377, 9653642	Standard	XM_005255686		Approved	NK4, TAIF, TAIFb, TAIFd	uc002ctn.3	P24001	OTTHUMG00000167498	ENST00000534507.1:c.627C>A	chr16.hg19:g.3119278C>A	ENSP00000431775:p.Phe209Leu	143.0	0.0	.		176.0	11.0	.	NM_004221	A6NNM0|A8MPX0|B4DJM1|B8Q191|D3DUB0|D3DUB2|Q5VFH7|Q5VFH8|Q8WV38|Q96GK9	Missense_Mutation	SNP	ENST00000534507.1	hg19		.	.	.	.	.	.	.	.	.	.	C	11.24	1.581265	0.28180	.	.	ENSG00000008517	ENST00000325568;ENST00000534507;ENST00000531965;ENST00000529699;ENST00000526464;ENST00000440815;ENST00000529550;ENST00000525643;ENST00000548807;ENST00000528163;ENST00000530890;ENST00000444393;ENST00000533097;ENST00000008180;ENST00000396890;ENST00000548652;ENST00000530538;ENST00000552936;ENST00000548476;ENST00000552664;ENST00000552356;ENST00000551513;ENST00000382213;ENST00000548246	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.39592	1.07;1.07;1.07;1.07;1.07;1.07;1.07;1.07;1.07;1.07;1.07;1.07;1.07;1.07;1.07;1.07;1.07;1.07;1.07;1.07;1.07;1.07;1.07;1.07	1.81	-3.01	0.05463	.	.	.	.	.	T	0.16214	0.0390	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B;B	0.12630	0.002;0.006;0.006;0.006;0.006;0.006	B;B;B;B;B;B	0.06405	0.002;0.002;0.002;0.002;0.002;0.002	T	0.29792	-1.0000	9	0.02654	T	1	.	3.4077	0.07347	0.0:0.3182:0.215:0.4668	.	123;143;154;143;209;163	B8Q191;C6GKH1;A6NNM0;A8MPX0;P24001;P24001-2	.;.;.;.;IL32_HUMAN;.	L	163;209;153;143;163;163;163;163;209;163;143;163;163;143;209;154;163;187;209;163;143;200;154;123	ENSP00000324742:F163L;ENSP00000431775:F209L;ENSP00000433177:F153L;ENSP00000436937:F143L;ENSP00000450364:F163L;ENSP00000405063:F163L;ENSP00000437020:F163L;ENSP00000432218:F163L;ENSP00000448354:F209L;ENSP00000432850:F163L;ENSP00000433747:F143L;ENSP00000411958:F163L;ENSP00000432917:F163L;ENSP00000008180:F143L;ENSP00000380099:F209L;ENSP00000446624:F154L;ENSP00000436929:F163L;ENSP00000447033:F187L;ENSP00000449483:F209L;ENSP00000448683:F163L;ENSP00000446978:F143L;ENSP00000449147:F200L;ENSP00000371648:F154L;ENSP00000447979:F123L	ENSP00000008180:F143L	F	+	3	2	IL32	3059279	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.640000	0.05440	-0.850000	0.04152	-0.320000	0.08662	TTC	.	.	.	none		0.557	IL32-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000394812.2	NM_004221		A	3119278	C	A	3119278	3	1	36	1	0	0	0	0	1	0	0	0	7699	854	30	4	511	4	IL32	16	3119278	Missense_Mutation	SNP	C	TCGA-5P-A9K8-01A-11D-A42J-10		3119278	87235475	12	2586											
WDR59	79726	hgsc.bcm.edu	37	chr16	74976685	74976685	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catggctggtggcaaggcagTtagcattttttttattccat	8	16	10	7	0	0	0	0	0	0	0	1	0	1	0	1	4	1	5	1	4	3	6			TCGA-5P-A9K8-01A-11D-A42J-10	TCGA-5P-A9K8-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1dda8cfa-899d-4d02-a2c8-ebb1169560aa	dfacd90a-6863-4d3d-a67d-2a39274e2691	g.chr16:74976685T>C	ENST00000262144.6	-	7	615	c.485A>G	c.(484-486)aAc>aGc	p.N162S		NM_030581.3	NP_085058.3	Q6PJI9	WDR59_HUMAN	WD repeat domain 59	162										breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)	27						GGCAAGGCAGTTAGCATTTTT	0.502																																					p.N162S		Atlas-SNP	.											.	WDR59	66	.	0			c.A485G						PASS	.						90	82	85					16																	74976685		2198	4300	6498	SO:0001583	missense	79726	exon7			AGGCAGTTAGCAT	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.485A>G	chr16.hg19:g.74976685T>C	ENSP00000262144:p.Asn162Ser	67.0	0.0	.		98.0	7.0	.	NM_030581	B3KRC3|Q71RE7|Q96PW5|Q9BSW6|Q9HA43	Missense_Mutation	SNP	ENST00000262144.6	hg19	CCDS32488.1	.	.	.	.	.	.	.	.	.	.	T	15.56	2.869817	0.51588	.	.	ENSG00000103091	ENST00000262144;ENST00000536050	T	0.70164	-0.46	5.96	5.96	0.96718	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.135443	0.64402	D	0.000005	T	0.57932	0.2087	L	0.35341	1.055	0.47778	D	0.999513	B;B	0.26002	0.042;0.139	B;B	0.21917	0.033;0.037	T	0.55661	-0.8106	10	0.48119	T	0.1	-29.498	16.1099	0.81255	0.0:0.0:0.0:1.0	.	162;162	Q6PJI9-2;Q6PJI9	.;WDR59_HUMAN	S	162;141	ENSP00000262144:N162S	ENSP00000262144:N162S	N	-	2	0	WDR59	73534186	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.564000	0.60830	2.285000	0.76669	0.533000	0.62120	AAC	.	.	.	none		0.502	WDR59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410601.3	NM_030581		C	74976685	T	C	74976685	3	2	36	1	0	0	0	0	1	0	0	0	17320	1725	60	3	2519	3	WDR59	16	74976685	Missense_Mutation	SNP	T	TCGA-5P-A9K8-01A-11D-A42J-10	71857407	74976685	15378068	13	2587											
ZNF521	25925	hgsc.bcm.edu	37	chr18	22805343	22805343	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttctgcacttgctcggaagCtccatttgttccacagttgg	6	15	9	11	1	1	0	0	0	1	0	4	1	3	1	2	2	3	5	2	2	1	5			TCGA-5P-A9K8-01A-11D-A42J-10	TCGA-5P-A9K8-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1dda8cfa-899d-4d02-a2c8-ebb1169560aa	dfacd90a-6863-4d3d-a67d-2a39274e2691	g.chr18:22805343C>T	ENST00000361524.3	-	4	2687	c.2539G>A	c.(2539-2541)Gct>Act	p.A847T	ZNF521_ENST00000538137.2_Missense_Mutation_p.A847T|ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000584787.1_Missense_Mutation_p.A627T	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	847					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)					TGCTCGGAAGCTCCATTTGTT	0.478			T	PAX5	ALL																																p.A847T		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	.	ZNF521	269	.	0			c.G2539A						PASS	.						188	179	182					18																	22805343		2203	4300	6503	SO:0001583	missense	25925	exon4			CGGAAGCTCCATT	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.2539G>A	chr18.hg19:g.22805343C>T	ENSP00000354794:p.Ala847Thr	94.0	0.0	.		110.0	7.0	.	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	hg19	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	C	6.220	0.408661	0.11812	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T;T	0.08984	3.03;3.04	5.93	5.93	0.95920	.	0.055023	0.85682	D	0.000000	T	0.06280	0.0162	N	0.08118	0	0.38015	D	0.934651	B	0.16396	0.017	B	0.14578	0.011	T	0.47837	-0.9086	10	0.23891	T	0.37	-15.1198	20.3539	0.98825	0.0:1.0:0.0:0.0	.	847	Q96K83	ZN521_HUMAN	T	847;881;847	ENSP00000354794:A847T;ENSP00000382352:A847T	ENSP00000354794:A847T	A	-	1	0	ZNF521	21059341	0.995000	0.38212	0.498000	0.27564	0.181000	0.23173	4.541000	0.60670	2.826000	0.97356	0.655000	0.94253	GCT	.	.	.	none		0.478	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		T	22805343	C	T	22805343	3	4	36	1	0	0	0	0	1	0	0	0	17977	797	28	2	1416	2	ZNF521	18	22805343	Missense_Mutation	SNP	C	TCGA-5P-A9K8-01A-11D-A42J-10		22805343	55271905	14	2588											
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385790	58385790	+	Missense_Mutation	SNP	G	G	T																															cacattctccacattcataaGgtcttttcccagtgtgaact																								rs111727691		TCGA-5P-A9K8-01A-11D-A42J-10	TCGA-5P-A9K8-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1dda8cfa-899d-4d02-a2c8-ebb1169560aa	dfacd90a-6863-4d3d-a67d-2a39274e2691	g.chr19:58385790G>T	ENST00000435989.2	-	3	1202	c.968C>A	c.(967-969)cCt>cAt	p.P323H	ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000600634.1_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	chr19.hg19:g.58385790G>T	ENSP00000410545:p.Pro323His	51.0	0.0	.		71.0	9.0	.	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	hg19	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	18188	1000	35	4	1603	4	ZNF814	19	58385790	Missense_Mutation	SNP	G	TCGA-5P-A9K8-01A-11D-A42J-10		58385790	743193	15	2589	30	2									
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385793	58385793	+	Missense_Mutation	SNP	C	C	T																															attctccacattcataaggtCttttcccagtgtgaactctc																								rs113623532		TCGA-5P-A9K8-01A-11D-A42J-10	TCGA-5P-A9K8-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1dda8cfa-899d-4d02-a2c8-ebb1169560aa	dfacd90a-6863-4d3d-a67d-2a39274e2691	g.chr19:58385793C>T	ENST00000435989.2	-	3	1199	c.965G>A	c.(964-966)aGa>aAa	p.R322K	ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000600634.1_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	chr19.hg19:g.58385793C>T	ENSP00000410545:p.Arg322Lys	48.0	0.0	.		69.0	8.0	.	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	hg19	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	18188	913	32	2	1606	2	ZNF814	19	58385793	Missense_Mutation	SNP	C	TCGA-5P-A9K8-01A-11D-A42J-10	3	58385793	743190	16	2590	30	2									
RALGAPB	57148	hgsc.bcm.edu	37	chr20	37163753	37163753	+	Missense_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	agctgctgggctcctgattcGcagcattcatctcgtcaccc	6	11	9	15	2	3	1	2	1	1	0	6	1	4	1	2	1	3	5	2	1	0	2	rs376931767		TCGA-5P-A9K8-01A-11D-A42J-10	TCGA-5P-A9K8-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1dda8cfa-899d-4d02-a2c8-ebb1169560aa	dfacd90a-6863-4d3d-a67d-2a39274e2691	g.chr20:37163753G>A	ENST00000262879.6	+	16	2566	c.2282G>A	c.(2281-2283)cGc>cAc	p.R761H	RALGAPB_ENST00000397038.1_Missense_Mutation_p.R539H|RALGAPB_ENST00000397042.3_Missense_Mutation_p.R757H|RALGAPB_ENST00000397040.1_Missense_Mutation_p.R761H			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	761					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						CTCCTGATTCGCAGCATTCAT	0.502																																					p.R761H		Atlas-SNP	.											.	RALGAPB	134	.	0			c.G2282A						PASS	.	G	HIS/ARG	0,4406		0,0,2203	180	174	176		2282	5.7	1	20		176	1,8599	1.2+/-3.3	0,1,4299	no	missense	RALGAPB	NM_020336.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	761/1495	37163753	1,13005	2203	4300	6503	SO:0001583	missense	57148	exon16			TGATTCGCAGCAT	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.2282G>A	chr20.hg19:g.37163753G>A	ENSP00000262879:p.Arg761His	54.0	0.0	.		79.0	39.0	.	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Missense_Mutation	SNP	ENST00000262879.6	hg19	CCDS13305.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.000557	0.93227	0.0	1.16E-4	ENSG00000170471	ENST00000262879;ENST00000397042;ENST00000304939;ENST00000397038;ENST00000397040;ENST00000438490	.	.	.	5.68	5.68	0.88126	.	0.047499	0.85682	D	0.000000	T	0.77778	0.4181	L	0.60455	1.87	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.77004	0.934;0.989;0.989;0.989	T	0.77983	-0.2382	9	0.62326	D	0.03	.	19.7782	0.96405	0.0:0.0:1.0:0.0	.	589;761;757;761	A2A2F0;Q86X10-4;A2A2E9;Q86X10	.;.;.;RLGPB_HUMAN	H	761;757;761;539;761;589	.	ENSP00000262879:R761H	R	+	2	0	RALGAPB	36597167	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.357000	0.97099	2.668000	0.90789	0.591000	0.81541	CGC	.	.	.	weak		0.502	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336		A	37163753	G	A	37163753	3	1	36	1	0	0	0	0	1	0	0	0	13028	1087	38	1	2340	1	RALGAPB	20	37163753	Missense_Mutation	SNP	G	TCGA-5P-A9K8-01A-11D-A42J-10		37163753	25861767	17	2591											
CCT8L2	150160	hgsc.bcm.edu	37	chr22	17072976	17072976	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gatggatcttccaaaggcccCagagattggatggccaggga	11	7	14	9	0	1	1	0	0	1	1	2	6	2	4	4	5	0	0	4	5	1	2			TCGA-5P-A9K8-01A-11D-A42J-10	TCGA-5P-A9K8-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1dda8cfa-899d-4d02-a2c8-ebb1169560aa	dfacd90a-6863-4d3d-a67d-2a39274e2691	g.chr22:17072976C>T	ENST00000359963.3	-	1	724	c.465G>A	c.(463-465)ctG>ctA	p.L155L		NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2	155					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)				CCAAAGGCCCCAGAGATTGGA	0.647																																					p.L155L		Atlas-SNP	.											.	CCT8L2	150	.	0			c.G465A						PASS	.						53	52	52					22																	17072976		2203	4300	6503	SO:0001819	synonymous_variant	150160	exon1			AGGCCCCAGAGAT	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.465G>A	chr22.hg19:g.17072976C>T		76.0	0.0	.		95.0	7.0	.	NM_014406	A4QPH3|Q9UJS3	Silent	SNP	ENST00000359963.3	hg19	CCDS13738.1																																																																																			.	.	.	none		0.647	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280580.1			T	17072976	C	T	17072976	2	4	36	1	0	0	0	0	0	0	0	1	2963	581	21	2		2	CCT8L2	22	17072976	Silent	SNP	C	TCGA-5P-A9K8-01A-11D-A42J-10		17072976	34231590	18	2592											
PANX2	56666	hgsc.bcm.edu	37	chr22	50615492	50615492	+	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	gacgccagcctgtggccgtcGctgtttgagcacaagttcct	6	10	12	13	3	0	1	0	1	0	0	2	2	1	1	4	1	2	4	4	1	1	2			TCGA-5P-A9K8-01A-11D-A42J-10	TCGA-5P-A9K8-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1dda8cfa-899d-4d02-a2c8-ebb1169560aa	dfacd90a-6863-4d3d-a67d-2a39274e2691	g.chr22:50615492G>A	ENST00000395842.2	+	2	351	c.351G>A	c.(349-351)tcG>tcA	p.S117S	PANX2_ENST00000159647.5_Silent_p.S117S	NM_052839.3	NP_443071.2	Q96RD6	PANX2_HUMAN	pannexin 2	117					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)		TGTGGCCGTCGCTGTTTGAGC	0.701																																					p.S117S		Atlas-SNP	.											.	PANX2	69	.	0			c.G351A						PASS	.						31	26	28					22																	50615492		2195	4292	6487	SO:0001819	synonymous_variant	56666	exon2			GCCGTCGCTGTTT		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.351G>A	chr22.hg19:g.50615492G>A		49.0	0.0	.		75.0	33.0	.	NM_052839	B7Z684|Q96RD5|Q9UGX8	Silent	SNP	ENST00000395842.2	hg19	CCDS14085.2																																																																																			.	.	.	none		0.701	PANX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075010.3	NM_052839		A	50615492	G	A	50615492	2	1	36	1	0	0	0	0	0	0	0	1	11428	1074	38	1		1	PANX2	22	50615492	Silent	SNP	G	TCGA-5P-A9K8-01A-11D-A42J-10	33542516	50615492	689074	19	2593											
TEX11	56159	hgsc.bcm.edu	37	chrX	70099888	70099888	+	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	cctgttgatatttgctatgtCgctgaagagtctatcaattg	9	16	9	7	1	2	3	1	2	1	1	3	3	2	3	1	0	1	3	1	0	5	6			TCGA-5P-A9K8-01A-11D-A42J-10	TCGA-5P-A9K8-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1dda8cfa-899d-4d02-a2c8-ebb1169560aa	dfacd90a-6863-4d3d-a67d-2a39274e2691	g.chrX:70099888C>T	ENST00000395889.2	-	4	309	c.154G>A	c.(154-156)Gac>Aac	p.D52N	TEX11_ENST00000374333.2_Missense_Mutation_p.D37N|TEX11_ENST00000344304.3_Missense_Mutation_p.D52N	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	52					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					TTTGCTATGTCGCTGAAGAGT	0.333																																					p.D52N		Atlas-SNP	.											.	TEX11	132	.	0			c.G154A						PASS	.						144	116	125					X																	70099888		2203	4299	6502	SO:0001583	missense	56159	exon4			CTATGTCGCTGAA	AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"testis expressed sequence 11"			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.154G>A	chrX.hg19:g.70099888C>T	ENSP00000379226:p.Asp52Asn	67.0	0.0	.		64.0	8.0	.	NM_001003811	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Missense_Mutation	SNP	ENST00000395889.2	hg19	CCDS35323.1	.	.	.	.	.	.	.	.	.	.	C	4.294	0.053862	0.08291	.	.	ENSG00000120498	ENST00000374333;ENST00000395889;ENST00000344304	T;T;T	0.32272	1.46;1.46;1.46	5.2	2.38	0.29361	.	0.554058	0.17534	N	0.170796	T	0.14227	0.0344	L	0.27053	0.805	0.09310	N	1	P;B	0.36125	0.538;0.403	B;B	0.24155	0.051;0.023	T	0.15009	-1.0452	9	.	.	.	-1.3832	4.1683	0.10317	0.0:0.5942:0.1888:0.2169	.	37;52	Q8IYF3-3;Q8IYF3	.;TEX11_HUMAN	N	37;52;52	ENSP00000363453:D37N;ENSP00000379226:D52N;ENSP00000340995:D52N	.	D	-	1	0	TEX11	70016613	0.015000	0.18098	0.001000	0.08648	0.196000	0.23810	0.769000	0.26604	0.178000	0.19917	0.594000	0.82650	GAC	.	.	.	none		0.333	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1			T	70099888	C	T	70099888	3	4	36	1	0	0	0	0	1	0	0	0	15786	884	31	1	2780	1	TEX11	23	70099888	Missense_Mutation	SNP	C	TCGA-5P-A9K8-01A-11D-A42J-10		70099888	85170672	20	2594											
PRAMEF18	391003	hgsc.bcm.edu	37	chr1	13475225	13475225	+	Frame_Shift_Del	DEL	A	A	-																															ctcttcatctagggagccatAagttaatgccaatgtctcca																										TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr1:13475225delA	ENST00000376126.2	-	3	903	c.904delT	c.(904-906)tatfs	p.Y302fs		NM_001099850.1	NP_001093320.1	Q5VWM3	PRA18_HUMAN	PRAME family member 18	302					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					lung(2)|ovary(1)	3	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AGGGAGCCATAAGTTAATGCC	0.493																																					p.Y302fs		Atlas-INDEL	.											.	PRAMEF19	6	.	0			c.905delA						PASS	.						3	4	4					1																	13475225		1676	3663	5339	SO:0001589	frameshift_variant	645414	exon3			.			1p36.21	2013-01-17			ENSG00000204491			"-"	30693	protein-coding gene	gene with protein product							Standard			Approved	OTTHUMG00000002932		Q5VWM3	OTTHUMG00000002932	ENST00000376126.2:c.904delT	chr1.hg19:g.13475225delA	ENSP00000365294:p.Tyr302fs	307.0	0.0	0		305.0	92.0	0.301639	NM_001099790		Frame_Shift_Del	DEL	ENST00000376126.2	hg19	CCDS41258.1																																																																																			.	.	.	none		0.493	PRAMEF18-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008177.2	NM_001099850		-	13475225	A	-	13475225	7	5	37	1	0	1	0	1	0	0	0	0	12443	362	13	0	539	0	PRAMEF18	1	13475225	Frame_Shift_Del	DEL	A	TCGA-5P-A9KA-01A-11D-A42J-10		13475225	235775396	1	2595											
PRAMEF18	645414	hgsc.bcm.edu	37	chr1	13696061	13696061	+	Frame_Shift_Del	DEL	A	A	-																															ctcttcatctagggagccatAagttaatgccaatgtctcca																										TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr1:13696061delA	ENST00000376101.2	-	3	696	c.697delT	c.(697-699)tatfs	p.Y233fs	PRAMEF19_ENST00000540591.1_Frame_Shift_Del_p.Y302fs			Q5SWL8	PRA19_HUMAN	PRAME family member 19	233					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					lung(3)	3	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AGGGAGCCATAAGTTAATGCC	0.493																																					p.Y302fs		Atlas-Indel,Pindel	.											.	PRAMEF19	6	.	0			c.905delA						PASS	.						2	2	2					1																	13696061		1123	2538	3661	SO:0001589	frameshift_variant	645414	exon3			.			1p36.21	2013-01-17			ENSG00000204480	ENSG00000204480		"-"	24908	protein-coding gene	gene with protein product							Standard	NM_001099790		Approved	OTTHUMG00000007919	uc009vnu.1	Q5SWL8	OTTHUMG00000007919	ENST00000376101.2:c.697delT	chr1.hg19:g.13696061delA	ENSP00000365269:p.Tyr233fs	323.0	0.0	0		242.0	46.0	0.190083	NM_001099790		Frame_Shift_Del	DEL	ENST00000376101.2	hg19																																																																																				.	.	.	none		0.493	PRAMEF19-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000021794.2	NM_001099790		-	13696061	A	-	13696061	7	5	37	1	0	1	0	1	0	0	0	0	12443	362	13	0	1991	0	PRAMEF18	1	13696061	Frame_Shift_Del	DEL	A	TCGA-5P-A9KA-01A-11D-A42J-10	220836	13696061	235554560	2	2596											
PRDM2	7799	hgsc.bcm.edu	37	chr1	14105118	14105118	+	Missense_Mutation	SNP	G	G	T																															gaggaggaggaagaggaggaGgatgaagaagaagaagaaga																										TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr1:14105118G>T	ENST00000235372.7	+	8	1684	c.828G>T	c.(826-828)gaG>gaT	p.E276D	PRDM2_ENST00000343137.4_Missense_Mutation_p.E75D|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000413440.1_Missense_Mutation_p.E75D|PRDM2_ENST00000311066.5_Missense_Mutation_p.E276D|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000505823.1_Intron	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	276	Asp/Glu-rich (acidic).			EDEEEEEDDDDDELEDEG -> VGGGGGVVVVVSWKARGE (in Ref. 6; AAA87023). {ECO:0000305}.	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)		aagaggaggaggatgaagaag	0.507																																					p.E276D		Atlas-SNP	.											.	PRDM2	147	.	0			c.G828T						PASS	.						53	54	54					1																	14105118		2203	4300	6503	SO:0001583	missense	7799	exon8			GGAGGAGGATGAA	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.828G>T	chr1.hg19:g.14105118G>T	ENSP00000235372:p.Glu276Asp	135.0	0.0	.		139.0	9.0	.	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Missense_Mutation	SNP	ENST00000235372.7	hg19	CCDS150.1	.	.	.	.	.	.	.	.	.	.	G	2.186	-0.386540	0.04966	.	.	ENSG00000116731	ENST00000235372;ENST00000311066;ENST00000400800;ENST00000413440;ENST00000343137;ENST00000407521	T;T;T;T	0.01871	4.71;4.59;4.59;4.59	3.35	-4.1	0.03940	.	0.206931	0.16085	U	0.230348	T	0.00906	0.0030	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	0.44620	-0.9316	10	0.25106	T	0.35	.	0.6861	0.00883	0.2164:0.1476:0.3377:0.2984	.	134;276;276	Q5THJ0;Q13029;Q13029-2	.;PRDM2_HUMAN;.	D	276;276;276;75;75;75	ENSP00000235372:E276D;ENSP00000312352:E276D;ENSP00000411103:E75D;ENSP00000341621:E75D	ENSP00000235372:E276D	E	+	3	2	PRDM2	13977705	0.000000	0.05858	0.076000	0.20297	0.107000	0.19398	-2.098000	0.01347	-0.616000	0.05671	-0.226000	0.12346	GAG	.	.	.	none		0.507	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231		T	14105118	G	T	14105118	3	4	37	1	0	0	0	0	1	0	0	0	12468	991	35	4	854	4	PRDM2	1	14105118	Missense_Mutation	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10	409057	14105118	235145503	3	2597	31	2									
PRDM2	7799	hgsc.bcm.edu	37	chr1	14105121	14105121	+	Missense_Mutation	SNP	T	T	A																															gaggaggaagaggaggaggaTgaagaagaagaagaagatga																								rs199679022		TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr1:14105121T>A	ENST00000235372.7	+	8	1687	c.831T>A	c.(829-831)gaT>gaA	p.D277E	PRDM2_ENST00000343137.4_Missense_Mutation_p.D76E|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000413440.1_Missense_Mutation_p.D76E|PRDM2_ENST00000311066.5_Missense_Mutation_p.D277E|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000505823.1_Intron	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	277	Asp/Glu-rich (acidic).			EDEEEEEDDDDDELEDEG -> VGGGGGVVVVVSWKARGE (in Ref. 6; AAA87023). {ECO:0000305}.	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)		aggaggaggatgaagaagaag	0.498																																					p.D277E		Atlas-SNP	.											PRDM2,colon,carcinoma,0,1	PRDM2	147	.	0			c.T831A						PASS	.						55	56	56					1																	14105121		2203	4300	6503	SO:0001583	missense	7799	exon8			GGAGGATGAAGAA	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.831T>A	chr1.hg19:g.14105121T>A	ENSP00000235372:p.Asp277Glu	134.0	0.0	.		139.0	14.0	.	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Missense_Mutation	SNP	ENST00000235372.7	hg19	CCDS150.1	.	.	.	.	.	.	.	.	.	.	T	0	-2.833500	0.00069	.	.	ENSG00000116731	ENST00000235372;ENST00000311066;ENST00000400800;ENST00000413440;ENST00000343137;ENST00000407521	T;T;T;T	0.01495	4.93;4.83;4.85;4.85	2.72	0.517	0.17025	.	1.614850	0.05616	N	0.579053	T	0.00967	0.0032	N	0.08118	0	0.09310	N	1	B;B;B;B	0.09022	0.001;0.0;0.001;0.002	B;B;B;B	0.04013	0.0;0.0;0.0;0.001	T	0.43637	-0.9379	10	0.02654	T	1	.	3.8016	0.08760	0.1568:0.0:0.5983:0.245	.	277;135;277;277	A8MW16;Q5THJ0;Q13029;Q13029-2	.;.;PRDM2_HUMAN;.	E	277;277;277;76;76;76	ENSP00000235372:D277E;ENSP00000312352:D277E;ENSP00000411103:D76E;ENSP00000341621:D76E	ENSP00000235372:D277E	D	+	3	2	PRDM2	13977708	0.074000	0.21230	0.135000	0.22099	0.097000	0.18754	-1.008000	0.03663	0.237000	0.21200	-0.319000	0.08680	GAT	.	T|0.999;G|0.001	.	alt		0.498	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231		A	14105121	T	A	14105121	3	1	37	1	0	0	0	0	1	0	0	0	12468	1461	51	5	857	5	PRDM2	1	14105121	Missense_Mutation	SNP	T	TCGA-5P-A9KA-01A-11D-A42J-10	3	14105121	235145500	4	2598	31	2									
KIAA0467	23334	hgsc.bcm.edu	37	chr1	43896951	43896951	+	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	ttcaggtcaacatctgaaagCagtgcttcatttccacgatc	11	12	7	11	1	4	1	3	1	1	0	6	2	5	1	1	1	3	2	1	1	2	3			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr1:43896951C>A	ENST00000562955.1	+	33	4761	c.4761C>A	c.(4759-4761)agC>agA	p.S1587R	SZT2_ENST00000372442.1_Missense_Mutation_p.S745R	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	1644					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						CATCTGAAAGCAGTGCTTCAT	0.532																																					p.S1587R		Atlas-SNP	.											.	SZT2	383	.	0			c.C4761A						PASS	.						190	196	194					1																	43896951		2203	4300	6503	SO:0001583	missense	23334	exon33			TGAAAGCAGTGCT	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.4761C>A	chr1.hg19:g.43896951C>A	ENSP00000457168:p.Ser1587Arg	156.0	0.0	.		114.0	32.0	.	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Missense_Mutation	SNP	ENST00000562955.1	hg19	CCDS30694.2	.	.	.	.	.	.	.	.	.	.	C	14.01	2.407481	0.42715	.	.	ENSG00000198198	ENST00000372442	.	.	.	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	T	0.61464	0.2349	L	0.52573	1.65	0.27731	N	0.944803	D	0.89917	1.0	D	0.87578	0.998	T	0.56583	-0.7955	9	0.56958	D	0.05	.	12.4908	0.55899	0.0:0.9231:0.0:0.0769	.	1587	Q5T011-5	.	R	745	.	ENSP00000361519:S745R	S	+	3	2	SZT2	43669538	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.696000	0.47052	2.595000	0.87683	0.563000	0.77884	AGC	.	.	.	none		0.532	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		A	43896951	C	A	43896951	3	1	37	1	0	0	0	0	1	0	0	0	8185	709	25	4	2301	4	KIAA0467	1	43896951	Missense_Mutation	SNP	C	TCGA-5P-A9KA-01A-11D-A42J-10	29791830	43896951	205353670	5	2599											
DIO1	1733	hgsc.bcm.edu	37	chr1	54371929	54371929	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctacgcagcactgcctgagAggctctacataatccaggag	11	8	10	12	1	2	1	0	1	2	1	3	3	3	2	2	2	4	3	2	2	3	3			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr1:54371929A>G	ENST00000361921.3	+	3	667	c.643A>G	c.(643-645)Agg>Ggg	p.R215G	DIO1_ENST00000524406.1_Missense_Mutation_p.R86G|DIO1_ENST00000322679.6_Intron|DIO1_ENST00000525202.1_Missense_Mutation_p.R151G|DIO1_ENST00000388876.3_Missense_Mutation_p.R167G|DIO1_ENST00000532493.1_Intron	NM_000792.5|NM_213593.3	NP_000783.2|NP_998758.1	P49895	IOD1_HUMAN	deiodinase, iodothyronine, type I	215					cellular nitrogen compound metabolic process (GO:0034641)|hormone biosynthetic process (GO:0042446)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	selenium binding (GO:0008430)|thyroxine 5'-deiodinase activity (GO:0004800)			cervix(1)|endometrium(2)|large_intestine(3)|lung(2)|skin(1)	9						ACTGCCTGAGAGGCTCTACAT	0.642																																					p.R167G		Atlas-SNP	.											.	DIO1	66	.	0			c.A499G						PASS	.						37	34	35					1																	54371929		2203	4300	6503	SO:0001583	missense	1733	exon2			CCTGAGAGGCTCT		CCDS30722.1, CCDS41339.1, CCDS41340.1, CCDS53320.1	1p33-p32	2012-03-01			ENSG00000211452	ENSG00000211452	1.97.1.10		2883	protein-coding gene	gene with protein product		147892		TXDI1		8964838	Standard	NM_000792		Approved		uc001cwb.3	P49895	OTTHUMG00000008435	ENST00000361921.3:c.643A>G	chr1.hg19:g.54371929A>G	ENSP00000354643:p.Arg215Gly	146.0	0.0	.		143.0	6.0	.	NM_001039715	Q1RN02|Q3KNP8|Q6Q4C1|Q6Q4C2|Q6Q4C3|Q6Q4C4|Q6Q4C5|Q6Q4C6|Q6Q4C7|Q6Q4C9|Q8WWC6	Missense_Mutation	SNP	ENST00000361921.3	hg19	CCDS41339.1	.	.	.	.	.	.	.	.	.	.	A	18.85	3.710682	0.68730	.	.	ENSG00000211452	ENST00000529589;ENST00000361921;ENST00000525202;ENST00000524406;ENST00000388876	T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72	4.94	2.35	0.29111	Thioredoxin-like fold (1);	0.000000	0.64402	D	0.000004	T	0.71929	0.3398	M	0.91459	3.21	0.35969	D	0.835158	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.989;0.997	T	0.81357	-0.0969	9	.	.	.	.	11.6333	0.51189	0.7221:0.2779:0.0:0.0	.	215;151;167	P49895;P49895-2;P49895-4	IOD1_HUMAN;.;.	G	172;215;151;86;167	ENSP00000432797:R172G;ENSP00000354643:R215G;ENSP00000435725:R151G;ENSP00000434152:R86G;ENSP00000373528:R167G	.	R	+	1	2	DIO1	54144517	1.000000	0.71417	0.983000	0.44433	0.963000	0.63663	1.113000	0.31184	0.794000	0.33899	0.459000	0.35465	AGG	.	.	.	none		0.642	DIO1-001	KNOWN	basic|appris_principal|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000023247.3			G	54371929	A	G	54371929	3	3	37	1	0	0	0	0	1	0	0	0	4526	295	11	3	653	3	DIO1	1	54371929	Missense_Mutation	SNP	A	TCGA-5P-A9KA-01A-11D-A42J-10	10474978	54371929	194878692	6	2600											
PLA2G4A	5321	hgsc.bcm.edu	37	chr1	186880403	186880403	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgcccagacctacgatttaGtatggctctgtgtgatcagg	9	12	11	9	1	2	2	1	1	1	1	2	3	2	2	2	2	2	2	2	2	3	4			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr1:186880403G>A	ENST00000367466.3	+	7	592	c.440G>A	c.(439-441)aGt>aAt	p.S147N	PLA2G4A_ENST00000442353.2_Intron|PLA2G4A_ENST00000466600.1_3'UTR	NM_024420.2	NP_077734	P47712	PA24A_HUMAN	phospholipase A2, group IVA (cytosolic, calcium-dependent)	147	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.|Phospholipid binding. {ECO:0000305}.				arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|blood coagulation (GO:0007596)|cardiolipin acyl-chain remodeling (GO:0035965)|cellular response to antibiotic (GO:0071236)|glycerophospholipid biosynthetic process (GO:0046474)|icosanoid biosynthetic process (GO:0046456)|icosanoid metabolic process (GO:0006690)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|platelet activation (GO:0030168)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|prostate(3)|skin(4)|stomach(1)	53					Aldesleukin(DB00041)|Carbachol(DB00411)|Carbenicillin(DB00578)|Epirubicin(DB00445)|Fluocinolone Acetonide(DB00591)|Fluticasone Propionate(DB00588)|Niflumic Acid(DB04552)|Orlistat(DB01083)|Quinacrine(DB01103)|Streptokinase(DB00086)|Suramin(DB04786)	CTACGATTTAGTATGGCTCTG	0.448																																					p.S147N		Atlas-SNP	.											.	PLA2G4A	125	.	0			c.G440A						PASS	.						162	167	165					1																	186880403		2203	4300	6503	SO:0001583	missense	5321	exon7			GATTTAGTATGGC	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.440G>A	chr1.hg19:g.186880403G>A	ENSP00000356436:p.Ser147Asn	82.0	0.0	.		94.0	20.0	.	NM_024420	B1AKG4|Q29R80	Missense_Mutation	SNP	ENST00000367466.3	hg19	CCDS1372.1	.	.	.	.	.	.	.	.	.	.	G	14.84	2.654167	0.47362	.	.	ENSG00000116711	ENST00000367466	T	0.04706	3.57	5.24	5.24	0.73138	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	0.000000	0.85682	D	0.000000	T	0.06962	0.0177	L	0.53561	1.675	0.80722	D	1	B	0.21821	0.061	B	0.19148	0.024	T	0.30937	-0.9961	10	0.16420	T	0.52	-18.437	16.3228	0.82958	0.0:0.0:1.0:0.0	.	147	P47712	PA24A_HUMAN	N	147	ENSP00000356436:S147N	ENSP00000356436:S147N	S	+	2	0	PLA2G4A	185147026	1.000000	0.71417	0.995000	0.50966	0.993000	0.82548	5.534000	0.67167	2.437000	0.82529	0.650000	0.86243	AGT	.	.	.	none		0.448	PLA2G4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086236.1	NM_024420		A	186880403	G	A	186880403	3	1	37	1	0	0	0	0	1	0	0	0	12008	1029	36	2	462	2	PLA2G4A	1	186880403	Missense_Mutation	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10	132508474	186880403	62370218	7	2601											
PPP2R5A	5525	hgsc.bcm.edu	37	chr1	212534084	212534084	+	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	tagtgcttacaacatgcacaGtattctcagcaatacaagtg	14	11	7	9	0	1	0	1	0	1	0	2	0	1	0	0	0	6	4	0	0	7	5			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr1:212534084G>C	ENST00000261461.2	+	13	2007	c.1433G>C	c.(1432-1434)aGt>aCt	p.S478T	RP11-384C4.2_ENST00000447949.1_RNA|PPP2R5A_ENST00000537030.3_Missense_Mutation_p.S421T	NM_006243.3	NP_006234.1	Q15172	2A5A_HUMAN	protein phosphatase 2, regulatory subunit B', alpha	478					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)		AACATGCACAGTATTCTCAGC	0.343																																					p.S478T		Atlas-SNP	.											.	PPP2R5A	48	.	0			c.G1433C						PASS	.						66	71	70					1																	212534084		2203	4300	6503	SO:0001583	missense	5525	exon13			TGCACAGTATTCT	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.1433G>C	chr1.hg19:g.212534084G>C	ENSP00000261461:p.Ser478Thr	612.0	0.0	.		616.0	68.0	.	NM_006243	B2R6D2|B7Z7L2|D3DT99|Q2NL72|Q5VVB2|Q8TBI9	Missense_Mutation	SNP	ENST00000261461.2	hg19	CCDS1503.1	.	.	.	.	.	.	.	.	.	.	g	8.348	0.830290	0.16749	.	.	ENSG00000066027	ENST00000542178;ENST00000261461;ENST00000537030	.	.	.	5.74	3.63	0.41609	.	0.809925	0.12040	N	0.505128	T	0.14874	0.0359	N	0.08118	0	0.23813	N	0.996775	B;B	0.09022	0.002;0.002	B;B	0.12156	0.004;0.007	T	0.26710	-1.0095	9	0.13853	T	0.58	-12.4512	1.8913	0.03249	0.258:0.0:0.4334:0.3086	.	421;478	B7Z7L2;Q15172	.;2A5A_HUMAN	T	478;478;421	.	ENSP00000261461:S478T	S	+	2	0	PPP2R5A	210600707	1.000000	0.71417	0.991000	0.47740	0.255000	0.26057	1.499000	0.35671	1.408000	0.46895	0.651000	0.88453	AGT	.	.	.	none		0.343	PPP2R5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089302.1	NM_006243		C	212534084	G	C	212534084	3	2	37	1	0	0	0	0	1	0	0	0	12402	1029	36	4	1483	4	PPP2R5A	1	212534084	Missense_Mutation	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10	25653681	212534084	36716537	8	2602											
PGBD2	267002	hgsc.bcm.edu	37	chr1	249210858	249210858	+	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	aagtctgcaaagctgcttgaGgttctgaatgctatggagga	11	11	13	6	0	2	2	0	2	2	0	2	4	2	4	0	3	4	5	0	3	4	3			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr1:249210858G>T	ENST00000329291.5	+	3	222	c.75G>T	c.(73-75)gaG>gaT	p.E25D	PGBD2_ENST00000462488.1_Intron|PGBD2_ENST00000539153.1_Missense_Mutation_p.E22D|PGBD2_ENST00000355360.4_Intron	NM_170725.2	NP_733843.1	Q6P3X8	PGBD2_HUMAN	piggyBac transposable element derived 2	25										NS(1)|endometrium(3)|lung(6)|ovary(1)|skin(3)	14	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.012)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			AGCTGCTTGAGGTTCTGAATG	0.483																																					p.E25D		Atlas-SNP	.											.	PGBD2	103	.	0			c.G75T						PASS	.						81	79	80					1																	249210858		2203	4300	6503	SO:0001583	missense	267002	exon3			GCTTGAGGTTCTG	AF229602	CCDS31128.1, CCDS31129.1	1q	2008-02-05			ENSG00000185220	ENSG00000185220			19399	protein-coding gene	gene with protein product							Standard	XM_005270333		Approved		uc001ifh.3	Q6P3X8	OTTHUMG00000040424	ENST00000329291.5:c.75G>T	chr1.hg19:g.249210858G>T	ENSP00000331643:p.Glu25Asp	91.0	0.0	.		101.0	5.0	.	NM_170725	B3KVR8|Q6MZF8	Missense_Mutation	SNP	ENST00000329291.5	hg19	CCDS31128.1	.	.	.	.	.	.	.	.	.	.	G	16.72	3.201001	0.58234	.	.	ENSG00000185220	ENST00000329291;ENST00000539153	T;T	0.12465	2.68;2.68	4.08	3.16	0.36331	.	0.241764	0.20985	U	0.082152	T	0.12263	0.0298	L	0.47716	1.5	0.24031	N	0.996119	P;P	0.50528	0.936;0.895	P;B	0.44477	0.451;0.264	T	0.13202	-1.0518	10	0.25106	T	0.35	-3.497	7.0352	0.24989	0.1209:0.0:0.8791:0.0	.	22;25	F5H4U7;Q6P3X8	.;PGBD2_HUMAN	D	25;22	ENSP00000331643:E25D;ENSP00000439950:E22D	ENSP00000331643:E25D	E	+	3	2	PGBD2	247177481	1.000000	0.71417	0.998000	0.56505	0.850000	0.48378	0.537000	0.23144	2.272000	0.75746	0.655000	0.94253	GAG	.	.	.	none		0.483	PGBD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000097318.1			T	249210858	G	T	249210858	3	4	37	1	0	0	0	0	1	0	0	0	11788	991	35	4	81	4	PGBD2	1	249210858	Missense_Mutation	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10	36676774	249210858	39763	9	2603											
ZDBF2	57683	hgsc.bcm.edu	37	chr2	207170563	207170563	+	Missense_Mutation	SNP	T	T	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	tccaaggaagtacgtactgaTgtacagtataagaataataa	18	10	8	5	1	0	2	0	1	0	1	1	3	1	3	1	1	3	4	1	1	10	7			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr2:207170563T>G	ENST00000374423.3	+	5	1697	c.1311T>G	c.(1309-1311)gaT>gaG	p.D437E		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	437							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						TACGTACTGATGTACAGTATA	0.338																																					p.D437E		Atlas-SNP	.											.	ZDBF2	531	.	0			c.T1311G						PASS	.						70	68	69					2																	207170563		1844	4091	5935	SO:0001583	missense	57683	exon5			TACTGATGTACAG	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.1311T>G	chr2.hg19:g.207170563T>G	ENSP00000363545:p.Asp437Glu	87.0	0.0	.		92.0	7.0	.	NM_020923	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	hg19	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	T	10.36	1.328042	0.24080	.	.	ENSG00000204186	ENST00000374423	T	0.45668	0.89	3.89	-2.8	0.05823	.	0.201148	0.24681	N	0.036479	T	0.28632	0.0709	L	0.43152	1.355	0.09310	N	1	B	0.26876	0.162	B	0.27076	0.076	T	0.17868	-1.0355	10	0.30854	T	0.27	.	9.0122	0.36148	0.0:0.5221:0.0:0.4779	.	437	Q9HCK1	ZDBF2_HUMAN	E	437	ENSP00000363545:D437E	ENSP00000363545:D437E	D	+	3	2	ZDBF2	206878808	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.004000	0.13106	-0.539000	0.06273	-0.256000	0.11100	GAT	.	.	.	none		0.338	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		G	207170563	T	G	207170563	3	3	37	1	0	0	0	0	1	0	0	0	17611	1461	51	5	1321	5	ZDBF2	2	207170563	Missense_Mutation	SNP	T	TCGA-5P-A9KA-01A-11D-A42J-10		207170563	36028810	10	2604											
FAM134A	79137	hgsc.bcm.edu	37	chr2	220044862	220044862	+	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	gggtcaggcgcccggccgcaCctgctgagtgtgcccgagtt	4	7	16	14	4	1	1	1	1	0	0	1	2	1	1	4	3	2	3	4	3	0	1			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr2:220044862C>G	ENST00000430297.2	+	4	586	c.450C>G	c.(448-450)caC>caG	p.H150Q	CNPPD1_ENST00000409789.1_5'Flank	NM_024293.4	NP_077269.3	Q8NC44	F134A_HUMAN	family with sequence similarity 134, member A	150						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)		CCCGGCCGCACCTGCTGAGTG	0.592																																					p.H150Q		Atlas-SNP	.											.	FAM134A	34	.	0			c.C450G						PASS	.						75	76	76					2																	220044862		2203	4300	6503	SO:0001583	missense	79137	exon4			GCCGCACCTGCTG	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.450C>G	chr2.hg19:g.220044862C>G	ENSP00000395249:p.His150Gln	145.0	0.0	.		145.0	49.0	.	NM_024293	Q6P1P5|Q9H0K7	Missense_Mutation	SNP	ENST00000430297.2	hg19	CCDS2434.1	.	.	.	.	.	.	.	.	.	.	C	16.10	3.026015	0.54683	.	.	ENSG00000144567	ENST00000430297	T	0.39997	1.05	4.53	4.53	0.55603	.	0.167420	0.56097	D	0.000032	T	0.41073	0.1143	N	0.22421	0.69	0.35553	D	0.804029	P	0.52692	0.955	P	0.54759	0.76	T	0.49952	-0.8884	10	0.39692	T	0.17	-10.4898	11.9832	0.53131	0.0:0.9169:0.0:0.0831	.	150	Q8NC44	F134A_HUMAN	Q	150	ENSP00000395249:H150Q	ENSP00000395249:H150Q	H	+	3	2	FAM134A	219753106	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.267000	0.33050	2.342000	0.79632	0.561000	0.74099	CAC	.	.	.	none		0.592	FAM134A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336147.2	NM_024293		G	220044862	C	G	220044862	3	3	37	1	0	0	0	0	1	0	0	0	5449	506	18	4	464	4	FAM134A	2	220044862	Missense_Mutation	SNP	C	TCGA-5P-A9KA-01A-11D-A42J-10	12874299	220044862	23154511	11	2605											
CUL3	8452	hgsc.bcm.edu	37	chr2	225370771	225370771	+	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	atactcaaagtcacccgcaaTagtttgtttaaagagacggt	14	11	8	8	2	2	1	2	0	0	1	2	2	2	1	1	1	1	3	1	1	6	5			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr2:225370771T>A	ENST00000264414.4	-	8	1446	c.1108A>T	c.(1108-1110)Att>Ttt	p.I370F	CUL3_ENST00000409777.1_Missense_Mutation_p.I346F|CUL3_ENST00000344951.4_Missense_Mutation_p.I304F|CUL3_ENST00000409096.1_Missense_Mutation_p.I346F	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	370					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)		TCACCCGCAATAGTTTGTTTA	0.383																																					p.I376F		Atlas-SNP	.											.	CUL3	96	.	0			c.A1126T						PASS	.						75	73	74					2																	225370771		2203	4300	6503	SO:0001583	missense	8452	exon8			CCGCAATAGTTTG	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.1108A>T	chr2.hg19:g.225370771T>A	ENSP00000264414:p.Ile370Phe	318.0	1.0	.		274.0	89.0	.	NM_001257198	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Missense_Mutation	SNP	ENST00000264414.4	hg19	CCDS2462.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.609729	0.87258	.	.	ENSG00000036257	ENST00000264414;ENST00000344951;ENST00000409096;ENST00000409777	T;T;T;T	0.74421	-0.84;-0.84;-0.84;-0.84	5.63	5.63	0.86233	Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.76350	0.3975	M	0.71920	2.185	0.80722	D	1	P;B;P	0.45986	0.87;0.372;0.717	B;B;B	0.43301	0.291;0.415;0.415	T	0.79492	-0.1781	10	0.54805	T	0.06	.	16.1413	0.81528	0.0:0.0:0.0:1.0	.	304;348;370	Q13618-3;Q53S54;Q13618	.;.;CUL3_HUMAN	F	370;304;346;346	ENSP00000264414:I370F;ENSP00000343601:I304F;ENSP00000387200:I346F;ENSP00000386525:I346F	ENSP00000264414:I370F	I	-	1	0	CUL3	225079015	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.655000	0.83696	2.270000	0.75569	0.482000	0.46254	ATT	.	.	.	none		0.383	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2			A	225370771	T	A	225370771	3	1	37	1	0	0	0	0	1	0	0	0	4058	1406	49	5	1234	5	CUL3	2	225370771	Missense_Mutation	SNP	T	TCGA-5P-A9KA-01A-11D-A42J-10	5325909	225370771	17828602	12	2606											
TRIP12	9320	hgsc.bcm.edu	37	chr2	230656640	230656641	+	Missense_Mutation	DNP	CT	CT	TA																															tagaggattgctctcatcatCtgtggattctctttcatctt																										TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr2:230656640_230656641CT>TA	ENST00000283943.5	-	28	4309_4310	c.4131_4132AG>TA	c.(4129-4134)acAGat>acTAat	p.D1378N	TRIP12_ENST00000389045.3_Missense_Mutation_p.D1108N|TRIP12_ENST00000389044.4_Missense_Mutation_p.D1426N	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1378					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		CTCTCATCATCTGTGGATTCTC	0.381																																					p.D1378N|p.T1377T		Atlas-SNP	.											.	TRIP12	207	.	0			c.G4132A|c.A4131T						PASS	.																																			SO:0001583	missense	9320	exon28			CATCATCTGTGGA|ATCATCTGTGGAT	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.4131_4132delinsTA	chr2.hg19:g.230656640_230656641delinsTA	ENSP00000283943:p.Asp1378Asn	205.0|206.0	0.0	.		163.0|161.0	51.0|49.0	.	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Missense_Mutation|Silent	SNP	ENST00000283943.5	hg19	CCDS33391.1																																																																																			.	.	.	none		0.381	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		TA	230656641	CT	TA	230656640	3	4	37	1	0	0	0	0	1	0	0	0	16568	913	32	2	1902	2	TRIP12	2	230656640	Missense_Mutation	DNP	CT	TCGA-5P-A9KA-01A-11D-A42J-10	5285869	230656640	12542733	13	2607											
ITPR1	3708	hgsc.bcm.edu	37	chr3	4704871	4704871	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acggcagaaactgatgagagAacagaatattctcaagcagg	17	6	11	7	1	1	5	1	2	1	3	2	6	1	5	0	2	3	2	0	2	5	2			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr3:4704871A>G	ENST00000443694.2	+	13	1490	c.1490A>G	c.(1489-1491)gAa>gGa	p.E497G	ITPR1_ENST00000423119.2_Missense_Mutation_p.E512G|ITPR1_ENST00000357086.4_Missense_Mutation_p.E512G|ITPR1_ENST00000456211.2_Missense_Mutation_p.E497G|ITPR1_ENST00000302640.8_Missense_Mutation_p.E497G|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000354582.6_Missense_Mutation_p.E512G			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	512					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)	CTGATGAGAGAACAGAATATT	0.453																																					p.E512G		Atlas-SNP	.											.	ITPR1	659	.	0			c.A1535G						PASS	.						112	116	115					3																	4704871		1992	4184	6176	SO:0001583	missense	3708	exon16			TGAGAGAACAGAA	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.1490A>G	chr3.hg19:g.4704871A>G	ENSP00000401671:p.Glu497Gly	102.0	0.0	.		107.0	11.0	.	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	hg19	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.606397	0.87157	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.90732	-2.72;-2.72;-2.72;-2.72;-2.72;-2.72	4.72	4.72	0.59763	Intracellular calcium-release channel (1);	0.098627	0.64402	D	0.000002	D	0.96018	0.8703	M	0.91459	3.21	0.80722	D	1	D;D;D	0.76494	0.999;0.997;0.998	D;D;D	0.80764	0.994;0.992;0.986	D	0.96933	0.9682	10	0.87932	D	0	.	14.3957	0.67010	1.0:0.0:0.0:0.0	.	497;512;512	E7EPX7;Q14643;G5E9P1	.;ITPR1_HUMAN;.	G	512;497;512;512;512;497;497	ENSP00000306253:E497G;ENSP00000346595:E512G;ENSP00000405934:E512G;ENSP00000349597:E512G;ENSP00000397885:E497G;ENSP00000401671:E497G	ENSP00000306253:E497G	E	+	2	0	ITPR1	4679871	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.054000	0.93866	1.990000	0.58119	0.533000	0.62120	GAA	.	.	.	none		0.453	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		G	4704871	A	G	4704871	3	3	37	1	0	0	0	0	1	0	0	0	7927	246	9	3	1589	3	ITPR1	3	4704871	Missense_Mutation	SNP	A	TCGA-5P-A9KA-01A-11D-A42J-10		4704871	193317559	14	2608											
CAND2	23066	hgsc.bcm.edu	37	chr3	12856913	12856913	+	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	cacccagaccggcagcaaccTccatatgctacgtggacagg	11	5	10	15	2	0	1	0	0	0	1	1	2	1	2	4	3	4	3	4	3	3	2			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr3:12856913T>A	ENST00000456430.2	+	8	1321	c.1280T>A	c.(1279-1281)cTc>cAc	p.L427H	CAND2_ENST00000295989.5_Missense_Mutation_p.L334H	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	427					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						GGCAGCAACCTCCATATGCTA	0.602																																					p.L427H	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											.	CAND2	138	.	0			c.T1280A						PASS	.						43	51	49					3																	12856913		2080	4201	6281	SO:0001583	missense	23066	exon8			GCAACCTCCATAT		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"TBP interacting protein"	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.1280T>A	chr3.hg19:g.12856913T>A	ENSP00000387641:p.Leu427His	419.0	0.0	.		418.0	137.0	.	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	hg19	CCDS54554.1	.	.	.	.	.	.	.	.	.	.	T	16.65	3.183403	0.57800	.	.	ENSG00000144712	ENST00000295989;ENST00000456430	D;D	0.90620	-2.7;-2.7	4.7	2.12	0.27331	Armadillo-like helical (1);Armadillo-type fold (1);	0.184696	0.36740	N	0.002429	D	0.92893	0.7739	M	0.72894	2.215	0.80722	D	1	B;D	0.76494	0.439;0.999	B;D	0.81914	0.105;0.995	D	0.88911	0.3359	10	0.19590	T	0.45	-15.1226	9.6264	0.39752	0.0:0.0:0.3388:0.6612	.	427;334	O75155;O75155-2	CAND2_HUMAN;.	H	334;427	ENSP00000295989:L334H;ENSP00000387641:L427H	ENSP00000295989:L334H	L	+	2	0	CAND2	12831913	0.437000	0.25593	0.809000	0.32408	0.782000	0.44232	2.017000	0.40981	0.132000	0.18615	0.459000	0.35465	CTC	.	.	.	none		0.602	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617		A	12856913	T	A	12856913	3	1	37	1	0	0	0	0	1	0	0	0	2618	1551	54	5	1310	5	CAND2	3	12856913	Missense_Mutation	SNP	T	TCGA-5P-A9KA-01A-11D-A42J-10	8152042	12856913	185165517	15	2609											
CCR9	10803	hgsc.bcm.edu	37	chr3	45943247	45943247	+	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	tctatgtttttgtgggtgagAgattccgccgggatctcgtg	5	15	14	7	3	2	2	0	1	2	1	4	4	3	3	2	2	0	1	2	2	1	4			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr3:45943247A>C	ENST00000357632.2	+	3	1147	c.967A>C	c.(967-969)Aga>Cga	p.R323R	Y_RNA_ENST00000364765.1_RNA|CCR9_ENST00000395963.2_Silent_p.R311R|LZTFL1_ENST00000536047.1_Intron|LZTFL1_ENST00000539217.1_Intron|CCR9_ENST00000355983.2_Silent_p.R311R|CCR9_ENST00000422395.1_3'UTR	NM_001256369.1|NM_031200.2	NP_001243298.1|NP_112477.1	P51686	CCR9_HUMAN	chemokine (C-C motif) receptor 9	323					cellular defense response (GO:0006968)|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)	cell surface (GO:0009986)|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(4)|large_intestine(8)|lung(2)|ovary(2)|prostate(2)|skin(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.00118)|KIRC - Kidney renal clear cell carcinoma(197;0.0182)|Kidney(197;0.0214)		TGTGGGTGAGAGATTCCGCCG	0.517																																					p.R323R		Atlas-SNP	.											.	CCR9	45	.	0			c.A967C						PASS	.						107	100	102					3																	45943247		2203	4300	6503	SO:0001819	synonymous_variant	10803	exon3			GGTGAGAGATTCC	AJ132337	CCDS2732.1, CCDS2733.1	3p21.31	2012-09-20			ENSG00000173585	ENSG00000173585		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1610	protein-coding gene	gene with protein product		604738		GPR28		10229797	Standard	NM_006641		Approved	GPR-9-6, CDw199	uc003coz.2	P51686	OTTHUMG00000133450	ENST00000357632.2:c.967A>C	chr3.hg19:g.45943247A>C		101.0	0.0	.		91.0	32.0	.	NM_031200	Q4VBM3|Q549E0|Q9UQQ6	Silent	SNP	ENST00000357632.2	hg19	CCDS2732.1																																																																																			.	.	.	none		0.517	CCR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257323.2			C	45943247	A	C	45943247	2	2	37	1	0	0	0	0	0	0	0	1	2950	296	11	5		5	CCR9	3	45943247	Silent	SNP	A	TCGA-5P-A9KA-01A-11D-A42J-10	33086334	45943247	152079183	16	2610											
HYAL2	8692	hgsc.bcm.edu	37	chr3	50357467	50357467	+	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	tagctggcgtgataaccggcGatacacatctttgtcctgcc	8	11	10	12	3	1	1	0	1	1	0	2	2	2	1	3	2	4	1	3	2	3	4			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr3:50357467G>A	ENST00000447092.1	-	1	2746	c.454C>T	c.(454-456)Cgc>Tgc	p.R152C	TUSC2_ENST00000462137.1_5'UTR|HYAL2_ENST00000357750.4_Missense_Mutation_p.R152C|HYAL2_ENST00000395139.3_Missense_Mutation_p.R152C|HYAL2_ENST00000442581.1_Missense_Mutation_p.R152C			Q12891	HYAL2_HUMAN	hyaluronoglucosaminidase 2	152					carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to interleukin-1 (GO:0071347)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to UV-B (GO:0071493)|defense response to virus (GO:0051607)|fusion of virus membrane with host plasma membrane (GO:0019064)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hematopoietic progenitor cell differentiation (GO:0002244)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|kidney development (GO:0001822)|monocyte activation (GO:0042117)|multicellular organismal aging (GO:0010259)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of cell growth (GO:0030308)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of urine volume (GO:0035810)|renal water absorption (GO:0070295)|response to antibiotic (GO:0046677)|response to reactive oxygen species (GO:0000302)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)|transformation of host cell by virus (GO:0019087)|viral entry into host cell (GO:0046718)	anchored component of external side of plasma membrane (GO:0031362)|anchored component of plasma membrane (GO:0046658)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|lysosome (GO:0005764)|membrane raft (GO:0045121)|microvillus (GO:0005902)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|hyaluronic acid binding (GO:0005540)|hyaluronoglucuronidase activity (GO:0033906)|hyalurononglucosaminidase activity (GO:0004415)|receptor signaling protein tyrosine kinase inhibitor activity (GO:0030294)|receptor tyrosine kinase binding (GO:0030971)|transforming growth factor beta binding (GO:0050431)|virus receptor activity (GO:0001618)			breast(1)|endometrium(2)|kidney(1)|ovary(1)|prostate(1)|skin(1)	7				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		GATAACCGGCGATACACATCT	0.582																																					p.R152C		Atlas-SNP	.											.	HYAL2	31	.	0			c.C454T						PASS	.						100	94	96					3																	50357467		2203	4300	6503	SO:0001583	missense	8692	exon3			ACCGGCGATACAC	AJ000099	CCDS2818.1	3p21.3	2008-07-18			ENSG00000068001	ENSG00000068001			5321	protein-coding gene	gene with protein product	"lysosomal hyaluronidase", "PH-20 homolog", "hyaluronidase 2"	603551				9712871, 9790770	Standard	NM_003773		Approved	LuCa-2, LUCA2	uc003czv.3	Q12891	OTTHUMG00000156876	ENST00000447092.1:c.454C>T	chr3.hg19:g.50357467G>A	ENSP00000401853:p.Arg152Cys	52.0	0.0	.		59.0	19.0	.	NM_033158	B3KRZ2|O15177|Q9BW29	Missense_Mutation	SNP	ENST00000447092.1	hg19	CCDS2818.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.444411	0.83993	.	.	ENSG00000068001	ENST00000447092;ENST00000357750;ENST00000395139;ENST00000442581	T;T;T;T	0.28255	1.62;1.62;1.62;1.62	5.68	5.68	0.88126	Aldolase-type TIM barrel (1);Glycoside hydrolase, superfamily (1);	0.100850	0.64402	D	0.000003	T	0.62270	0.2414	M	0.90145	3.09	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.996	T	0.69217	-0.5203	10	0.87932	D	0	-33.2855	13.3441	0.60561	0.0:0.0:0.8421:0.1579	.	152;152	B3KRZ2;Q12891	.;HYAL2_HUMAN	C	152	ENSP00000401853:R152C;ENSP00000350387:R152C;ENSP00000378571:R152C;ENSP00000406657:R152C	ENSP00000350387:R152C	R	-	1	0	HYAL2	50332471	1.000000	0.71417	1.000000	0.80357	0.677000	0.39632	7.819000	0.86621	2.683000	0.91414	0.455000	0.32223	CGC	.	.	.	none		0.582	HYAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346391.1	NM_003773		A	50357467	G	A	50357467	3	1	37	1	0	0	0	0	1	0	0	0	7471	1058	37	1	979	1	HYAL2	3	50357467	Missense_Mutation	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10	4414220	50357467	147664963	17	2611											
GPR128	84873	hgsc.bcm.edu	37	chr3	100354648	100354648	+	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	ggttggacagatattcaacaCttccagaaatgcttcacctg	12	11	8	10	0	2	2	2	0	0	2	3	3	3	3	2	2	2	2	2	2	3	5			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr3:100354648C>G	ENST00000273352.3	+	5	843	c.575C>G	c.(574-576)aCt>aGt	p.T192S	GPR128_ENST00000475887.1_5'UTR	NM_032787.2	NP_116176.2	Q96K78	GP128_HUMAN	G protein-coupled receptor 128	192					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						ATATTCAACACTTCCAGAAAT	0.368																																					p.T192S	Pancreas(87;185 1975 7223 18722)	Atlas-SNP	.											.	GPR128	126	.	0			c.C575G						PASS	.						73	69	71					3																	100354648		2203	4300	6503	SO:0001583	missense	84873	exon5			TCAACACTTCCAG	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.575C>G	chr3.hg19:g.100354648C>G	ENSP00000273352:p.Thr192Ser	182.0	0.0	.		178.0	71.0	.	NM_032787	Q14D94|Q86SQ2	Missense_Mutation	SNP	ENST00000273352.3	hg19	CCDS2938.1	.	.	.	.	.	.	.	.	.	.	C	4.358	0.065875	0.08388	.	.	ENSG00000144820	ENST00000273352	T	0.38401	1.14	5.65	1.34	0.21922	.	1.897240	0.02251	N	0.066623	T	0.33206	0.0855	L	0.56769	1.78	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.20974	-1.0259	10	0.07644	T	0.81	.	7.141	0.25556	0.5112:0.4042:0.0:0.0846	.	192	Q96K78	GP128_HUMAN	S	192	ENSP00000273352:T192S	ENSP00000273352:T192S	T	+	2	0	GPR128	101837338	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-1.307000	0.02733	0.228000	0.21019	0.591000	0.81541	ACT	.	.	.	none		0.368	GPR128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353236.1			G	100354648	C	G	100354648	3	3	37	1	0	0	0	0	1	0	0	0	6648	565	20	4	593	4	GPR128	3	100354648	Missense_Mutation	SNP	C	TCGA-5P-A9KA-01A-11D-A42J-10	49997181	100354648	97667782	18	2612											
KIAA1524	57650	hgsc.bcm.edu	37	chr3	108271221	108271221	+	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	ttttgttttttgatgcaaatCttaaaagaaaaaaaagtcaa	18	15	5	3	0	2	2	1	1	1	1	2	2	2	2	0	0	1	2	0	0	8	6			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr3:108271221C>A	ENST00000295746.8	-	20	2484		c.e20-1		KIAA1524_ENST00000491772.1_Splice_Site	NM_020890.2	NP_065941.2	Q8TCG1	CIP2A_HUMAN	KIAA1524						positive regulation of neural precursor cell proliferation (GO:2000179)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(21)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TGATGCAAATCTTAAAAGAAA	0.303																																					.		Atlas-SNP	.											.	KIAA1524	82	.	0			c.2408-1G>T						PASS	.						72	69	70					3																	108271221		2195	4296	6491	SO:0001630	splice_region_variant	57650	exon21			GCAAATCTTAAAA	AB040957	CCDS33812.1	3q13.13	2014-01-14			ENSG00000163507	ENSG00000163507			29302	protein-coding gene	gene with protein product	"cancerous inhibitor of protein phosphatase 2A"	610643				10819331, 24214971	Standard	NM_020890		Approved	CIP2A	uc003dxb.4	Q8TCG1	OTTHUMG00000159233	ENST00000295746.8:c.2408-1G>T	chr3.hg19:g.108271221C>A		39.0	0.0	.		34.0	15.0	.	NM_020890	A1L4J7|B9EGC3|Q6P4G6|Q8WVP8|Q96PI2|Q9H9C6|Q9P204	Splice_Site	SNP	ENST00000295746.8	hg19	CCDS33812.1	.	.	.	.	.	.	.	.	.	.	C	18.19	3.569304	0.65765	.	.	ENSG00000163507	ENST00000491772;ENST00000295746	.	.	.	4.91	4.91	0.64330	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.1089	0.89528	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KIAA1524	109753911	1.000000	0.71417	1.000000	0.80357	0.836000	0.47400	4.749000	0.62155	2.244000	0.73946	0.557000	0.71058	.	.	.	.	none		0.303	KIAA1524-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353975.2	NM_020890	Intron	A	108271221	C	A	108271221	5	1	37	1	0	0	0	0	0	0	1	0	8246	927	32	4	318	4	KIAA1524	3	108271221	Splice_Site	SNP	C	TCGA-5P-A9KA-01A-11D-A42J-10	7916573	108271221	89751209	19	2613											
C3orf30	152405	hgsc.bcm.edu	37	chr3	118865256	118865256	+	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	tatttagccaagctaccaacGgagtagctgaacaaaatggg	15	8	10	8	1	0	1	0	1	0	0	0	2	0	2	2	2	6	3	2	2	9	5			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr3:118865256G>C	ENST00000295622.1	+	1	260	c.220G>C	c.(220-222)Gga>Cga	p.G74R	IGSF11_ENST00000441144.2_5'Flank|IGSF11_ENST00000425327.2_5'Flank|RP11-484M3.5_ENST00000490594.1_5'Flank|IGSF11_ENST00000354673.2_5'Flank	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	74										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)		AGCTACCAACGGAGTAGCTGA	0.502																																					p.G74R		Atlas-SNP	.											.	C3orf30	64	.	0			c.G220C						PASS	.						71	55	60					3																	118865256		2203	4300	6503	SO:0001583	missense	152405	exon1			ACCAACGGAGTAG	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.220G>C	chr3.hg19:g.118865256G>C	ENSP00000295622:p.Gly74Arg	174.0	0.0	.		162.0	70.0	.	NM_152539	A1L4B7	Missense_Mutation	SNP	ENST00000295622.1	hg19	CCDS2984.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.49|11.49	1.654796|1.654796	0.29425|0.29425	.|.	.|.	ENSG00000163424|ENSG00000163424	ENST00000295622;ENST00000470341|ENST00000460150	T|.	0.22336|.	1.96|.	3.31|3.31	0.864|0.864	0.19068|0.19068	.|.	.|.	.|.	.|.	.|.	T|T	0.19366|0.19366	0.0465|0.0465	N|N	0.17082|0.17082	0.46|0.46	0.09310|0.09310	N|N	1|1	B;B|.	0.33583|.	0.004;0.418|.	B;B|.	0.26969|.	0.001;0.075|.	T|T	0.24621|0.24621	-1.0155|-1.0155	9|5	0.15952|.	T|.	0.53|.	-1.8244|-1.8244	4.332|4.332	0.11067|0.11067	0.6757:0.2027:0.1216:0.0|0.6757:0.2027:0.1216:0.0	.|.	74;74|.	E9PFE5;Q96M34|.	.;CC030_HUMAN|.	R|P	74|37	ENSP00000295622:G74R|.	ENSP00000295622:G74R|.	G|R	+|+	1|2	0|0	C3orf30|C3orf30	120347946|120347946	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	1.226000|1.226000	0.32563|0.32563	0.176000|0.176000	0.19873|0.19873	-0.471000|-0.471000	0.05019|0.05019	GGA|CGG	.	.	.	none		0.502	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539		C	118865256	G	C	118865256	3	2	37	1	0	0	0	0	1	0	0	0	2222	1117	39	4	222	4	C3orf30	3	118865256	Missense_Mutation	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10	10594035	118865256	79157174	20	2614											
ITGB5	3693	hgsc.bcm.edu	37	chr3	124527967	124527967	+	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	gagattaagatcctcaggctGatcccagactgacaactcca	13	8	8	12	0	1	5	1	2	0	3	4	6	4	5	3	1	1	1	3	1	2	1			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr3:124527967G>T	ENST00000296181.4	-	9	1461	c.1165C>A	c.(1165-1167)Cag>Aag	p.Q389K		NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	389					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|epithelial cell-cell adhesion (GO:0090136)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alphav-beta5 complex (GO:0034684)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	30				GBM - Glioblastoma multiforme(114;0.163)		TCCTCAGGCTGATCCCAGACT	0.488																																					p.Q389K		Atlas-SNP	.											.	ITGB5	66	.	0			c.C1165A						PASS	.						114	111	112					3																	124527967		2203	4300	6503	SO:0001583	missense	3693	exon9			CAGGCTGATCCCA	J05633	CCDS3030.1	3q21.2	2010-03-23			ENSG00000082781	ENSG00000082781		"Integrins"	6160	protein-coding gene	gene with protein product		147561				2211615	Standard	NM_002213		Approved		uc003eho.3	P18084	OTTHUMG00000159432	ENST00000296181.4:c.1165C>A	chr3.hg19:g.124527967G>T	ENSP00000296181:p.Gln389Lys	109.0	0.0	.		117.0	25.0	.	NM_002213	B0LPF8|B2RD70	Missense_Mutation	SNP	ENST00000296181.4	hg19	CCDS3030.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.146|8.146	0.786378|0.786378	0.16189|0.16189	.|.	.|.	ENSG00000082781|ENSG00000082781	ENST00000296181|ENST00000496703	T|.	0.62498|.	0.02|.	5.63|5.63	3.69|3.69	0.42338|0.42338	Integrin beta subunit, N-terminal (2);|.	0.444750|.	0.23612|.	N|.	0.046324|.	T|.	0.30885|.	0.0779|.	N|N	0.21373|0.21373	0.66|0.66	0.29615|0.29615	N|N	0.846611|0.846611	B|.	0.25351|.	0.124|.	B|.	0.27500|.	0.08|.	T|.	0.10497|.	-1.0627|.	10|.	0.23891|.	T|.	0.37|.	.|.	7.7963|7.7963	0.29150|0.29150	0.0:0.1207:0.5314:0.3479|0.0:0.1207:0.5314:0.3479	.|.	389|.	P18084|.	ITB5_HUMAN|.	K|X	389|155	ENSP00000296181:Q389K|.	ENSP00000296181:Q389K|.	Q|S	-|-	1|2	0|0	ITGB5|ITGB5	126010657|126010657	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	4.353000|4.353000	0.59411|0.59411	2.656000|2.656000	0.90262|0.90262	0.655000|0.655000	0.94253|0.94253	CAG|TCA	.	.	.	none		0.488	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3	NM_002213		T	124527967	G	T	124527967	3	4	37	1	0	0	0	0	1	0	0	0	7905	1299	45	4	1262	4	ITGB5	3	124527967	Missense_Mutation	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10	5662711	124527967	73494463	21	2615											
CRMP1	1400	hgsc.bcm.edu	37	chr4	5838634	5838634	+	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	0	0	0	0	0	0	0	0	0	0	ctgtgacctgcaagtccccaCtggcaaggacaaaacaaggt	13	6	10	12	0	0	1	0	1	0	0	1	2	1	2	3	3	2	2	3	3	5	0			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr4:5838634C>A	ENST00000397890.2	-	10	1183		c.e10-1		CRMP1_ENST00000512574.1_Splice_Site|CRMP1_ENST00000511535.1_Splice_Site|CRMP1_ENST00000324989.7_Splice_Site	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1						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)		CAAGTCCCCACTGGCAAGGAC	0.532																																					.		Atlas-SNP	.											.	CRMP1	118	.	0			c.1311-1G>T						PASS	.						80	72	74					4																	5838634		2203	4300	6503	SO:0001630	splice_region_variant	1400	exon11			TCCCCACTGGCAA	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.969-1G>T	chr4.hg19:g.5838634C>A		43.0	0.0	.		47.0	7.0	.	NM_001014809	A0EJG6|Q13024|Q4W5F1|Q96TC8	Splice_Site	SNP	ENST00000397890.2	hg19	CCDS43207.1	.	.	.	.	.	.	.	.	.	.	C	18.65	3.669144	0.67814	.	.	ENSG00000072832	ENST00000324989;ENST00000397890;ENST00000534845;ENST00000512574	.	.	.	4.12	4.12	0.48240	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9555	0.79884	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CRMP1	5889535	1.000000	0.71417	0.990000	0.47175	0.800000	0.45204	7.319000	0.79040	2.325000	0.78763	0.456000	0.33151	.	.	.	.	none		0.532	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313	Intron	A	5838634	C	A	5838634	5	1	37	1	0	0	0	0	0	0	1	0	3892	579	20	4	770	4	CRMP1	4	5838634	Splice_Site	SNP	C	TCGA-5P-A9KA-01A-11D-A42J-10		5838634	185315642	22	2616											
LRBA	987	hgsc.bcm.edu	37	chr4	151935618	151935618	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acaatatccctattggatacTtctccaacttcaaccaaacc	14	11	2	14	0	2	0	1	0	1	0	4	1	3	1	4	1	4	0	4	1	7	6			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr4:151935618T>C	ENST00000357115.3	-	2	420	c.177A>G	c.(175-177)gaA>gaG	p.E59E	LRBA_ENST00000507224.1_Silent_p.E59E|LRBA_ENST00000510413.1_Silent_p.E59E|LRBA_ENST00000535741.1_Silent_p.E59E	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	59						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)					TATTGGATACTTCTCCAACTT	0.438																																					p.E59E		Atlas-SNP	.											.	LRBA	253	.	0			c.A177G						PASS	.						56	55	55					4																	151935618		2203	4300	6503	SO:0001819	synonymous_variant	987	exon2			GGATACTTCTCCA	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.177A>G	chr4.hg19:g.151935618T>C		183.0	0.0	.		152.0	40.0	.	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Silent	SNP	ENST00000357115.3	hg19	CCDS3773.1																																																																																			.	.	.	none		0.438	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			C	151935618	T	C	151935618	2	2	37	1	0	0	0	0	0	0	0	1	8938	1606	56	3		3	LRBA	4	151935618	Silent	SNP	T	TCGA-5P-A9KA-01A-11D-A42J-10	146096984	151935618	39218658	23	2617											
CCDC110	256309	hgsc.bcm.edu	37	chr4	186379896	186379896	+	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	aatctttctttctcttttagCtggattatctctagctggct	6	20	6	9	0	4	0	0	0	4	0	6	1	4	1	0	2	2	3	0	2	4	6			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr4:186379896C>G	ENST00000307588.3	-	6	1920	c.1845G>C	c.(1843-1845)caG>caC	p.Q615H	CCDC110_ENST00000393540.3_Missense_Mutation_p.Q578H|CCDC110_ENST00000507501.1_5'Flank|CCDC110_ENST00000510617.1_Missense_Mutation_p.Q615H	NM_152775.3	NP_689988.1	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110	615						nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(9)	30		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)		TCTCTTTTAGCTGGATTATCT	0.318																																					p.Q615H		Atlas-SNP	.											.	CCDC110	78	.	0			c.G1845C						PASS	.						74	78	76					4																	186379896		2200	4295	6495	SO:0001583	missense	256309	exon6			TTTTAGCTGGATT	AB080722	CCDS3843.1, CCDS47170.1	4q35.1	2010-12-24			ENSG00000168491	ENSG00000168491			28504	protein-coding gene	gene with protein product	"cancer/testis antigen 52"	609488				18160854	Standard	NM_152775		Approved	KM-HN-1, MGC33607, CT52	uc003ixu.4	Q8TBZ0	OTTHUMG00000160415	ENST00000307588.3:c.1845G>C	chr4.hg19:g.186379896C>G	ENSP00000306776:p.Gln615His	73.0	0.0	.		64.0	15.0	.	NM_152775	Q86YI9|Q8N7W0	Missense_Mutation	SNP	ENST00000307588.3	hg19	CCDS3843.1	.	.	.	.	.	.	.	.	.	.	C	12.14	1.848641	0.32699	.	.	ENSG00000168491	ENST00000393540;ENST00000307588;ENST00000510617	T;T;T	0.35421	1.31;1.31;1.31	5.55	1.79	0.24919	.	0.267348	0.27219	N	0.020368	T	0.48040	0.1478	M	0.65975	2.015	0.28722	N	0.902995	D;D;D	0.63880	0.993;0.98;0.993	P;P;P	0.60415	0.874;0.824;0.874	T	0.43523	-0.9386	10	0.72032	D	0.01	-6.7213	6.9762	0.24677	0.0:0.3022:0.0:0.6978	.	615;578;615	B4DZA2;Q8TBZ0-2;Q8TBZ0	.;.;CC110_HUMAN	H	578;615;615	ENSP00000377172:Q578H;ENSP00000306776:Q615H;ENSP00000427246:Q615H	ENSP00000306776:Q615H	Q	-	3	2	CCDC110	186616890	1.000000	0.71417	0.193000	0.23327	0.716000	0.41182	0.893000	0.28336	0.109000	0.17891	0.655000	0.94253	CAG	.	.	.	none		0.318	CCDC110-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360519.2	NM_152775		G	186379896	C	G	186379896	3	3	37	1	0	0	0	0	1	0	0	0	2749	796	28	4	664	4	CCDC110	4	186379896	Missense_Mutation	SNP	C	TCGA-5P-A9KA-01A-11D-A42J-10	34444278	186379896	4774380	24	2618											
PCDHA7	56141	hgsc.bcm.edu	37	chr5	140215838	140215838	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcgagcatcccgttccgcGtggggctgtacactggtgag	5	9	16	11	4	0	1	0	1	0	0	2	2	2	1	2	3	3	4	2	3	1	2			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr5:140215838G>A	ENST00000525929.1	+	1	1870	c.1870G>A	c.(1870-1872)Gtg>Atg	p.V624M	PCDHA7_ENST00000378125.3_Missense_Mutation_p.V624M|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7	624	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|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)			CCCGTTCCGCGTGGGGCTGTA	0.637																																					p.V624M	NSCLC(160;258 2013 5070 22440 28951)	Atlas-SNP	.											PCDHA7_ENST00000525929,colon,carcinoma,0,2	PCDHA7	367	.	0			c.G1870A						PASS	.						105	105	105					5																	140215838		2203	4300	6503	SO:0001583	missense	56141	exon1			TTCCGCGTGGGGC	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.1870G>A	chr5.hg19:g.140215838G>A	ENSP00000436426:p.Val624Met	97.0	0.0	.		97.0	34.0	.	NM_031852	O75282	Missense_Mutation	SNP	ENST00000525929.1	hg19	CCDS54918.1	.	.	.	.	.	.	.	.	.	.	G	11.44	1.640241	0.29157	.	.	ENSG00000204963	ENST00000525929;ENST00000378125	T;T	0.59502	0.26;0.26	3.57	3.57	0.40892	Cadherin (4);Cadherin-like (1);	0.382752	0.15065	U	0.282541	T	0.75398	0.3844	M	0.78223	2.4	0.21386	N	0.999704	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.984	T	0.66019	-0.6027	10	0.87932	D	0	.	13.8776	0.63662	0.0:0.0:1.0:0.0	.	624;624	Q9UN72-2;Q9UN72	.;PCDA7_HUMAN	M	624	ENSP00000436426:V624M;ENSP00000367365:V624M	ENSP00000367365:V624M	V	+	1	0	PCDHA7	140196022	0.411000	0.25384	1.000000	0.80357	0.518000	0.34316	0.668000	0.25127	1.968000	0.57251	0.462000	0.41574	GTG	.	.	.	none		0.637	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	NM_018910		A	140215838	G	A	140215838	3	1	37	1	0	0	0	0	1	0	0	0	11536	1145	40	1	1872	1	PCDHA7	5	140215838	Missense_Mutation	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10		140215838	40699422	25	2619											
PCDH12	51294	hgsc.bcm.edu	37	chr5	141331117	141331117	+	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	tggtttggtttgggctggaaTtggccctgatgcagcaagga	7	12	16	6	0	0	1	0	1	0	0	0	3	0	3	1	6	2	5	1	6	2	3			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr5:141331117T>A	ENST00000231484.3	-	2	4129	c.2919A>T	c.(2917-2919)caA>caT	p.Q973H	AC005740.6_ENST00000607378.1_RNA	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	973					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)			TGGGCTGGAATTGGCCCTGAT	0.547											OREG0016877	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q973H		Atlas-SNP	.											.	PCDH12	133	.	0			c.A2919T						PASS	.						113	104	107					5																	141331117		2203	4300	6503	SO:0001583	missense	51294	exon2			CTGGAATTGGCCC	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.2919A>T	chr5.hg19:g.141331117T>A	ENSP00000231484:p.Gln973His	82.0	0.0	.	1663	104.0	22.0	.	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	hg19	CCDS4269.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.228733	0.79576	.	.	ENSG00000113555	ENST00000231484	T	0.76060	-0.99	6.08	3.72	0.42706	.	0.000000	0.85682	D	0.000000	T	0.82144	0.4973	M	0.74881	2.28	0.44012	D	0.996728	D	0.89917	1.0	D	0.73708	0.981	T	0.80845	-0.1200	10	0.49607	T	0.09	.	6.5721	0.22545	0.0:0.247:0.0:0.753	.	973	Q9NPG4	PCD12_HUMAN	H	973	ENSP00000231484:Q973H	ENSP00000231484:Q973H	Q	-	3	2	PCDH12	141311301	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	1.537000	0.36083	1.117000	0.41842	0.533000	0.62120	CAA	.	.	.	none		0.547	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		A	141331117	T	A	141331117	3	1	37	1	0	0	0	0	1	0	0	0	11517	1490	52	5	647	5	PCDH12	5	141331117	Missense_Mutation	SNP	T	TCGA-5P-A9KA-01A-11D-A42J-10	1115279	141331117	39584143	26	2620											
RANBP17	64901	hgsc.bcm.edu	37	chr5	170289055	170289055	+	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	aagatggcgctgcacttccaGgtcagtgtgctctgcgccgc	6	9	13	13	3	2	1	1	0	1	1	3	1	3	1	2	2	3	3	2	2	1	1			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr5:170289055G>A	ENST00000523189.1	+	1	182	c.18G>A	c.(16-18)caG>caA	p.Q6Q		NM_022897.3	NP_075048.1	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	6					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)			TGCACTTCCAGGTCAGTGTGC	0.781			T	TRD@	ALL																																p.Q6Q		Atlas-SNP	.		Dom	yes		5	5q34	64901	RAN binding protein 17		L	.	RANBP17	108	.	0			c.G18A						PASS	.						2	2	2					5																	170289055		998	1929	2927	SO:0001630	splice_region_variant	64901	exon1			CTTCCAGGTCAGT	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.18+1G>A	chr5.hg19:g.170289055G>A		5.0	0.0	.		6.0	5.0	.	NM_022897	Q8IU74	Silent	SNP	ENST00000523189.1	hg19	CCDS34287.1																																																																																			.	.	.	none		0.781	RANBP17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372036.1	NM_022897	Silent	A	170289055	G	A	170289055	5	1	37	1	0	0	0	0	0	0	1	0	13040	1014	35	2	20	2	RANBP17	5	170289055	Splice_Site	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10	28957938	170289055	10626205	27	2621											
KIAA0319	9856	hgsc.bcm.edu	37	chr6	24551749	24551749	+	Missense_Mutation	SNP	T	T	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	tttcctgattttagtcctttTttgtctgaaaggaacaatga	10	18	7	6	0	1	3	0	3	1	0	3	4	3	4	2	1	1	0	2	1	4	6			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr6:24551749T>G	ENST00000378214.3	-	20	3477	c.2953A>C	c.(2953-2955)Aaa>Caa	p.K985Q	KIAA0319_ENST00000535378.1_Missense_Mutation_p.K976Q|KIAA0319_ENST00000537886.1_Intron|KIAA0319_ENST00000430948.2_Missense_Mutation_p.K940Q|KIAA0319_ENST00000543707.1_Missense_Mutation_p.K985Q	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	985					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						TTAGTCCTTTTTTGTCTGAAA	0.373																																					p.K985Q		Atlas-SNP	.											.	KIAA0319	117	.	0			c.A2953C						PASS	.						234	198	210					6																	24551749		2203	4300	6503	SO:0001583	missense	9856	exon20			TCCTTTTTTGTCT	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.2953A>C	chr6.hg19:g.24551749T>G	ENSP00000367459:p.Lys985Gln	75.0	0.0	.		63.0	22.0	.	NM_001168375	A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Missense_Mutation	SNP	ENST00000378214.3	hg19	CCDS34348.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.041125	0.75732	.	.	ENSG00000137261	ENST00000535378;ENST00000430948;ENST00000378214;ENST00000543707	T;T;T;T	0.10005	2.92;2.93;2.92;2.92	4.55	4.55	0.56014	.	0.143376	0.46758	D	0.000269	T	0.19725	0.0474	L	0.56396	1.775	0.42490	D	0.992892	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.994	T	0.00891	-1.1525	10	0.62326	D	0.03	-16.8042	14.1127	0.65132	0.0:0.0:0.0:1.0	.	976;985	Q5VV43-2;Q5VV43	.;K0319_HUMAN	Q	976;940;985;985	ENSP00000442403:K976Q;ENSP00000401086:K940Q;ENSP00000367459:K985Q;ENSP00000437656:K985Q	ENSP00000367459:K985Q	K	-	1	0	KIAA0319	24659728	1.000000	0.71417	0.972000	0.41901	0.956000	0.61745	3.686000	0.54685	1.906000	0.55180	0.449000	0.29647	AAA	.	.	.	none		0.373	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040009.1	NM_014809		G	24551749	T	G	24551749	3	3	37	1	0	0	0	0	1	0	0	0	8175	1850	64	5	273	5	KIAA0319	6	24551749	Missense_Mutation	SNP	T	TCGA-5P-A9KA-01A-11D-A42J-10		24551749	146563318	28	2622											
HLA-C	3107	hgsc.bcm.edu	37	chr6	31239449	31239450	+	Frame_Shift_Ins	INS	-	-	T																															cctgtgcctggcgcttgtacINSttctgtgtctcccggtccca																								rs28626310	byFrequency	TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr6:31239449_31239450insT	ENST00000376228.5	-	2	283_284	c.269_270insA	c.(268-270)aagfs	p.K90fs	HLA-C_ENST00000383329.3_Frame_Shift_Ins_p.K90fs	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	90	Alpha-1.		K -> N (in dbSNP:rs28626310).		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						GGCGCTTGTACTTCTGTGTCTC	0.698																																					p.K90fs		Atlas-Indel,Pindel	.											.	HLA-C	92	.	0			c.270_271insA						PASS	.																																			SO:0001589	frameshift_variant	3107	exon2			.	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.270dupA	chr6.hg19:g.31239451_31239451dupT	ENSP00000365402:p.Lys90fs	107.0	0.0	0		133.0	31.0	0.233083	NM_002117	O02864|O02958|Q29643|Q9MY30	Frame_Shift_Ins	INS	ENST00000376228.5	hg19	CCDS34393.1																																																																																			.	.	.	none		0.698	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117		T	31239450	-	T	31239449	7	5	37	1	0	1	1	0	0	0	0	0	7204	564	20	0	858	0	HLA-C	6	31239449	Frame_Shift_Ins	INS	-	TCGA-5P-A9KA-01A-11D-A42J-10	6687700	31239449	139875618	29	2623											
FBXL4	26235	hgsc.bcm.edu	37	chr6	99374476	99374476	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gatacacctgttgttcaaaaGtaagttccacatagtcctgg	12	12	8	9	0	1	0	1	0	0	0	3	1	3	0	3	1	1	4	3	1	5	6			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr6:99374476G>A	ENST00000369244.2	-	4	817	c.389C>T	c.(388-390)aCt>aTt	p.T130I	FBXL4_ENST00000229971.1_Missense_Mutation_p.T130I	NM_001278716.1	NP_001265645.1	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4	130					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)		TTGTTCAAAAGTAAGTTCCAC	0.443																																					p.T130I		Atlas-SNP	.											.	FBXL4	54	.	0			c.C389T						PASS	.						95	76	83					6																	99374476		2203	4300	6503	SO:0001583	missense	26235	exon3			TCAAAAGTAAGTT	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.389C>T	chr6.hg19:g.99374476G>A	ENSP00000358247:p.Thr130Ile	161.0	0.0	.		123.0	41.0	.	NM_012160	B2R7Q5|E1P530|O95919|Q5BJH0|Q9UJU0	Missense_Mutation	SNP	ENST00000369244.2	hg19	CCDS5041.1	.	.	.	.	.	.	.	.	.	.	G	13.32	2.202194	0.38905	.	.	ENSG00000112234	ENST00000369244;ENST00000229971	T;T	0.14893	2.47;2.47	5.52	5.52	0.82312	.	0.301455	0.40144	N	0.001178	T	0.07098	0.0180	N	0.19112	0.55	0.36933	D	0.89199	B	0.18166	0.026	B	0.20577	0.03	T	0.18524	-1.0334	10	0.30854	T	0.27	.	19.8176	0.96576	0.0:0.0:1.0:0.0	.	130	Q9UKA2	FBXL4_HUMAN	I	130	ENSP00000358247:T130I;ENSP00000229971:T130I	ENSP00000229971:T130I	T	-	2	0	FBXL4	99481197	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	4.947000	0.63583	2.765000	0.95021	0.650000	0.86243	ACT	.	.	.	none		0.443	FBXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041587.2			A	99374476	G	A	99374476	3	1	37	1	0	0	0	0	1	0	0	0	5728	1029	36	2	1504	2	FBXL4	6	99374476	Missense_Mutation	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10	68135027	99374476	71740591	30	2624											
SESN1	27244	hgsc.bcm.edu	37	chr6	109319902	109319902	+	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	tgatagtgtgtgagtaaaacTactgcatgtaccaattccgc	12	12	9	8	1	0	2	0	2	0	0	1	2	1	2	2	0	4	3	2	0	6	5			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr6:109319902T>G	ENST00000356644.7	-	5	703	c.609A>C	c.(607-609)gtA>gtC	p.V203V	SESN1_ENST00000302071.2_Silent_p.V137V|RP11-787I22.3_ENST00000605885.1_RNA|SESN1_ENST00000436639.2_Silent_p.V262V	NM_001199933.1	NP_001186862.1	Q9Y6P5	SESN1_HUMAN	sestrin 1	203					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of cell proliferation (GO:0008285)|regulation of protein kinase B signaling (GO:0051896)|regulation of response to reactive oxygen species (GO:1901031)	nucleus (GO:0005634)				cervix(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	10		all_cancers(87;6.45e-05)|Acute lymphoblastic leukemia(125;3.55e-10)|all_hematologic(75;1.68e-07)|all_epithelial(87;0.0106)|Colorectal(196;0.0637)		Epithelial(106;0.0014)|BRCA - Breast invasive adenocarcinoma(108;0.00146)|all cancers(137;0.0031)|OV - Ovarian serous cystadenocarcinoma(136;0.0117)		TGAGTAAAACTACTGCATGTA	0.423																																					p.V262V		Atlas-SNP	.											.	SESN1	29	.	0			c.A786C						PASS	.						106	100	102					6																	109319902		2203	4299	6502	SO:0001819	synonymous_variant	27244	exon5			TAAAACTACTGCA	AF033120	CCDS5070.1, CCDS56444.1, CCDS56445.1	6q21	2008-10-23			ENSG00000080546	ENSG00000080546			21595	protein-coding gene	gene with protein product		606103				9926927, 7938006	Standard	NM_014454		Approved	SEST1, PA26	uc003psu.3	Q9Y6P5	OTTHUMG00000015338	ENST00000356644.7:c.609A>C	chr6.hg19:g.109319902T>G		133.0	0.0	.		126.0	31.0	.	NM_014454	Q2M2B7|Q5T316|Q9NV00|Q9UPD5|Q9Y6P6	Silent	SNP	ENST00000356644.7	hg19	CCDS56445.1																																																																																			.	.	.	none		0.423	SESN1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041738.4	NM_014454		G	109319902	T	G	109319902	2	3	37	1	0	0	0	0	0	0	0	1	14137	1509	53	5		5	SESN1	6	109319902	Silent	SNP	T	TCGA-5P-A9KA-01A-11D-A42J-10	9945426	109319902	61795165	31	2625											
TUBE1	51175	hgsc.bcm.edu	37	chr6	112392751	112392751	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcttccatcccttcaactTgtagatagtgatgaaggtga	10	15	8	8	0	2	4	1	3	1	1	4	4	4	4	2	1	1	1	2	1	4	6			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr6:112392751T>C	ENST00000368662.5	-	12	1370	c.1292A>G	c.(1291-1293)cAa>cGa	p.Q431R	TUBE1_ENST00000604814.1_5'UTR	NM_016262.4	NP_057346.1	Q9UJT0	TBE_HUMAN	tubulin, epsilon 1	431					centrosome cycle (GO:0007098)|protein polymerization (GO:0051258)	microtubule (GO:0005874)|pericentriolar material (GO:0000242)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			cervix(1)|endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	12		all_cancers(87;0.0101)|all_hematologic(75;0.000258)|Colorectal(196;0.0466)|all_epithelial(87;0.1)		all cancers(137;0.0217)|OV - Ovarian serous cystadenocarcinoma(136;0.0613)|Epithelial(106;0.0636)|GBM - Glioblastoma multiforme(226;0.0972)|BRCA - Breast invasive adenocarcinoma(108;0.246)	Vinblastine(DB00570)	CCCTTCAACTTGTAGATAGTG	0.358																																					p.Q431R		Atlas-SNP	.											.	TUBE1	49	.	0			c.A1292G						PASS	.						109	100	103					6																	112392751		2203	4300	6503	SO:0001583	missense	51175	exon12			TCAACTTGTAGAT	AF201334	CCDS5100.1	6q21	2005-11-03			ENSG00000074935	ENSG00000074935		"Tubulins"	20775	protein-coding gene	gene with protein product		607345				10620804	Standard	NM_016262		Approved	dJ142L7.2, FLJ22589, TUBE	uc003pvq.3	Q9UJT0	OTTHUMG00000015382	ENST00000368662.5:c.1292A>G	chr6.hg19:g.112392751T>C	ENSP00000357651:p.Gln431Arg	78.0	0.0	.		59.0	13.0	.	NM_016262	Q5H8W8|Q8NEG3	Missense_Mutation	SNP	ENST00000368662.5	hg19	CCDS5100.1	.	.	.	.	.	.	.	.	.	.	T	15.27	2.784984	0.49997	.	.	ENSG00000074935	ENST00000368662	T	0.78595	-1.19	5.62	5.62	0.85841	Tubulin, C-terminal (1);Tubulin/FtsZ, C-terminal (1);	0.175445	0.51477	D	0.000096	T	0.65512	0.2698	L	0.48986	1.54	0.80722	D	1	B	0.13145	0.007	B	0.19946	0.027	T	0.67879	-0.5556	10	0.87932	D	0	.	15.807	0.78520	0.0:0.0:0.0:1.0	.	431	Q9UJT0	TBE_HUMAN	R	431	ENSP00000357651:Q431R	ENSP00000357651:Q431R	Q	-	2	0	TUBE1	112499444	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.903000	0.56318	2.128000	0.65567	0.533000	0.62120	CAA	.	.	.	none		0.358	TUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041867.1	NM_016262		C	112392751	T	C	112392751	3	2	37	1	0	0	0	0	1	0	0	0	16775	1812	63	3	139	3	TUBE1	6	112392751	Missense_Mutation	SNP	T	TCGA-5P-A9KA-01A-11D-A42J-10	3072849	112392751	58722316	32	2626											
TSPYL4	23270	hgsc.bcm.edu	37	chr6	116574508	116574508	+	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	aagctgaaggaaggccctgtCagcctgggcatttacgtttg	9	10	13	9	1	1	1	1	1	0	0	1	2	1	2	2	3	3	3	2	3	4	3			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr6:116574508C>A	ENST00000420283.1	-	1	753	c.664G>T	c.(664-666)Gac>Tac	p.D222Y	RP3-486I3.7_ENST00000448740.2_lincRNA|DSE_ENST00000540275.1_5'Flank	NM_021648.4	NP_067680.3	Q9UJ04	TSYL4_HUMAN	TSPY-like 4	222					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)		AAGGCCCTGTCAGCCTGGGCA	0.537																																					p.D222Y		Atlas-SNP	.											.	TSPYL4	18	.	0			c.G664T						PASS	.						33	34	33					6																	116574508		2017	4176	6193	SO:0001583	missense	23270	exon1			CCCTGTCAGCCTG		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.664G>T	chr6.hg19:g.116574508C>A	ENSP00000410943:p.Asp222Tyr	74.0	0.0	.		73.0	24.0	.	NM_021648	B4DYQ2|O94828|Q96GW8	Missense_Mutation	SNP	ENST00000420283.1	hg19	CCDS5106.1	.	.	.	.	.	.	.	.	.	.	C	19.87	3.906607	0.72868	.	.	ENSG00000187189	ENST00000420283	T	0.26067	1.76	3.98	3.98	0.46160	.	.	.	.	.	T	0.43634	0.1256	M	0.77820	2.39	0.42876	D	0.994152	D	0.69078	0.997	D	0.77557	0.99	T	0.45308	-0.9270	9	0.72032	D	0.01	-19.1634	14.3987	0.67027	0.0:1.0:0.0:0.0	.	222	Q9UJ04	TSYL4_HUMAN	Y	222	ENSP00000410943:D222Y	ENSP00000410943:D222Y	D	-	1	0	TSPYL4	116681201	0.942000	0.31987	0.994000	0.49952	0.993000	0.82548	2.046000	0.41260	2.514000	0.84764	0.462000	0.41574	GAC	.	.	.	none		0.537	TSPYL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041934.2			A	116574508	C	A	116574508	3	1	37	1	0	0	0	0	1	0	0	0	16673	826	29	4	584	4	TSPYL4	6	116574508	Missense_Mutation	SNP	C	TCGA-5P-A9KA-01A-11D-A42J-10	4181757	116574508	54540559	33	2627											
SHPRH	257218	hgsc.bcm.edu	37	chr6	146262786	146262786	+	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	gtgggacactcaaccatctgAgcttcatcaaggcagatcct	11	9	9	12	0	4	2	3	1	1	1	5	3	5	3	2	2	2	2	2	2	2	1			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr6:146262786A>T	ENST00000367505.2	-	10	2727	c.2463T>A	c.(2461-2463)gcT>gcA	p.A821A	SHPRH_ENST00000438092.2_Silent_p.A821A|SHPRH_ENST00000275233.7_Silent_p.A821A|SHPRH_ENST00000367503.3_Silent_p.A821A			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	821	Helicase ATP-binding; second part. {ECO:0000255|PROSITE-ProRule:PRU00541}.				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)		CAACCATCTGAGCTTCATCAA	0.512																																					p.A821A		Atlas-SNP	.											.	SHPRH	169	.	0			c.T2463A						PASS	.						71	75	74					6																	146262786		1977	4155	6132	SO:0001819	synonymous_variant	257218	exon10			CATCTGAGCTTCA	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.2463T>A	chr6.hg19:g.146262786A>T		84.0	0.0	.		60.0	23.0	.	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Silent	SNP	ENST00000367505.2	hg19	CCDS43513.2																																																																																			.	.	.	none		0.512	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082		T	146262786	A	T	146262786	2	4	37	1	0	0	0	0	0	0	0	1	14304	291	11	5		5	SHPRH	6	146262786	Silent	SNP	A	TCGA-5P-A9KA-01A-11D-A42J-10	29688278	146262786	24852281	34	2628											
JAZF1	221895	hgsc.bcm.edu	37	chr7	27872487	27872487	+	Frame_Shift_Del	DEL	G	G	-																															attgattgtgtggtgccgcaGgccctgagctgtcttgtaac																										TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr7:27872487delG	ENST00000283928.5	-	5	829	c.664delC	c.(664-666)ctgfs	p.L222fs	JAZF1_ENST00000466516.1_5'UTR	NM_175061.3	NP_778231.2	Q86VZ6	JAZF1_HUMAN	JAZF zinc finger 1	222					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|transcription corepressor activity (GO:0003714)		JAZF1/SUZ12(133)	endometrium(1)|large_intestine(1)|lung(4)	6						TGGTGCCGCAGGCCCTGAGCT	0.488			T	SUZ12	endometrial stromal tumours																																p.L222fs		Atlas-Indel,Pindel	.		Dom	yes		7	7p15.2-p15.1	221895	juxtaposed with another zinc finger gene 1		M	.	JAZF1	13	.	0			c.665delT						PASS	.						171	154	160					7																	27872487		2203	4300	6503	SO:0001589	frameshift_variant	221895	exon5			.	BC047229	CCDS5416.1	7p15.2-p15.1	2010-04-14			ENSG00000153814	ENSG00000153814		"Zinc fingers, C2H2-type"	28917	protein-coding gene	gene with protein product		606246				8401585	Standard	XM_006715656		Approved	TIP27, DKFZp761K2222, ZNF802	uc003szn.3	Q86VZ6	OTTHUMG00000128545	ENST00000283928.5:c.664delC	chr7.hg19:g.27872487delG	ENSP00000283928:p.Leu222fs	77.0	0.0	0		73.0	20.0	0.273973	NM_175061	A4D195|Q8N3L7	Frame_Shift_Del	DEL	ENST00000283928.5	hg19	CCDS5416.1																																																																																			.	.	.	none		0.488	JAZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250382.2	NM_175061		-	27872487	G	-	27872487	7	5	37	1	0	1	0	1	0	0	0	0	7953	991	35	0	71	0	JAZF1	7	27872487	Frame_Shift_Del	DEL	G	TCGA-5P-A9KA-01A-11D-A42J-10		27872487	131266176	35	2629											
VOPP1	81552	hgsc.bcm.edu	37	chr7	55560085	55560085	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaagccggctccgcagcagAaaagcacgcccatcatcaga	14	3	10	14	3	2	3	2	0	0	3	3	3	3	3	3	1	3	4	3	1	3	0			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr7:55560085A>G	ENST00000285279.5	-	4	418	c.218T>C	c.(217-219)tTc>tCc	p.F73S	VOPP1_ENST00000418904.1_Missense_Mutation_p.F56S|VOPP1_ENST00000471168.1_5'Flank|VOPP1_ENST00000454227.1_Missense_Mutation_p.F10S|VOPP1_ENST00000427700.1_Missense_Mutation_p.F71S|VOPP1_ENST00000453256.1_Missense_Mutation_p.F6S|VOPP1_ENST00000428648.1_Missense_Mutation_p.F6S|VOPP1_ENST00000433959.1_Missense_Mutation_p.F64S|VOPP1_ENST00000545390.1_Missense_Mutation_p.F70S|VOPP1_ENST00000428097.1_Missense_Mutation_p.F6S	NM_001284282.1|NM_030796.3	NP_001271211.1|NP_110423.3	Q96AW1	VOPP1_HUMAN	vesicular, overexpressed in cancer, prosurvival protein 1	73					regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasmic vesicle membrane (GO:0030659)|endosome (GO:0005768)|integral component of organelle membrane (GO:0031301)	signal transducer activity (GO:0004871)			endometrium(1)|lung(4)	5						TCCGCAGCAGAAAAGCACGCC	0.622																																					p.F73S		Atlas-SNP	.											.	VOPP1	14	.	0			c.T218C						PASS	.						17	21	20					7																	55560085		1930	4125	6055	SO:0001583	missense	81552	exon4			CAGCAGAAAAGCA		CCDS47588.1, CCDS64654.1, CCDS64656.1	7p11.2	2010-06-22			ENSG00000154978	ENSG00000154978			34518	protein-coding gene	gene with protein product	"Glioblastoma-amplified secreted protein", "EGFR-coamplified and overexpressed protein"	611915				15735698	Standard	NM_030796		Approved	ECop, GASP, FLJ20532, DKFZp564K0822	uc003tqs.3	Q96AW1	OTTHUMG00000156124	ENST00000285279.5:c.218T>C	chr7.hg19:g.55560085A>G	ENSP00000285279:p.Phe73Ser	163.0	0.0	.		149.0	35.0	.	NM_030796	B0AZU1|B2RAT4|B3KS72|C9JWR3|Q6FIE3|Q8NBN8|Q96RE5|Q9H0W4	Missense_Mutation	SNP	ENST00000285279.5	hg19	CCDS47588.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.551347	0.86127	.	.	ENSG00000154978	ENST00000285279;ENST00000428648;ENST00000433959;ENST00000545390;ENST00000428097;ENST00000418904;ENST00000454227;ENST00000453256;ENST00000427700;ENST00000455023;ENST00000414113;ENST00000417399;ENST00000452832	.	.	.	4.46	4.46	0.54185	.	.	.	.	.	T	0.61702	0.2368	N	0.24115	0.695	0.53688	D	0.999971	D;D;D;D	0.76494	0.999;0.997;0.999;0.999	D;D;D;D	0.80764	0.994;0.991;0.994;0.994	T	0.65890	-0.6058	8	0.72032	D	0.01	-14.8351	11.7138	0.51641	1.0:0.0:0.0:0.0	.	56;70;73;64	C9JWR3;B0AZU1;Q96AW1;B3KS72	.;.;VOPP1_HUMAN;.	S	73;6;64;70;6;56;10;6;71;6;6;6;6	.	ENSP00000285279:F73S	F	-	2	0	VOPP1	55527579	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.730000	0.84881	1.635000	0.50512	0.460000	0.39030	TTC	.	.	.	none		0.622	VOPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343074.1	NM_030796		G	55560085	A	G	55560085	3	3	37	1	0	0	0	0	1	0	0	0	17196	246	9	3	308	3	VOPP1	7	55560085	Missense_Mutation	SNP	A	TCGA-5P-A9KA-01A-11D-A42J-10	27687598	55560085	103578578	36	2630											
ZNF713	349075	hgsc.bcm.edu	37	chr7	56006915	56006915	+	Missense_Mutation	SNP	A	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	ggagagaagccttgagtgtaAtaaatttgcagaaaactgta	16	10	11	4	0	0	3	0	1	0	2	0	5	0	4	1	1	3	3	1	1	7	5			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr7:56006915A>C	ENST00000429591.2	+	4	547	c.509A>C	c.(508-510)aAt>aCt	p.N170T	MRPS17_ENST00000426595.1_Intron	NM_182633.1	NP_872439.1	Q8N859	ZN713_HUMAN	zinc finger protein 713	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)			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)			CTTGAGTGTAATAAATTTGCA	0.383																																					p.N170T		Atlas-SNP	.											.	ZNF713	47	.	0			c.A509C						PASS	.						57	59	58					7																	56006915		2203	4300	6503	SO:0001583	missense	349075	exon4			AGTGTAATAAATT	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.509A>C	chr7.hg19:g.56006915A>C	ENSP00000416662:p.Asn170Thr	245.0	0.0	.		184.0	48.0	.	NM_182633		Missense_Mutation	SNP	ENST00000429591.2	hg19	CCDS34639.1	.	.	.	.	.	.	.	.	.	.	A	0.926	-0.714248	0.03206	.	.	ENSG00000178665	ENST00000429591	T	0.06933	3.24	3.78	0.12	0.14691	.	0.592008	0.14084	N	0.342516	T	0.07728	0.0194	L	0.55481	1.735	0.09310	N	1	B	0.14438	0.01	B	0.11329	0.006	T	0.30327	-0.9982	10	0.49607	T	0.09	.	3.9021	0.09166	0.4915:0.1908:0.3177:0.0	.	170	Q8N859	ZN713_HUMAN	T	170	ENSP00000416662:N170T	ENSP00000416662:N170T	N	+	2	0	ZNF713	55974409	0.000000	0.05858	0.008000	0.14137	0.057000	0.15508	-1.087000	0.03383	0.015000	0.14971	-0.326000	0.08463	AAT	.	.	.	none		0.383	ZNF713-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343297.1	NM_182633		C	56006915	A	C	56006915	3	2	37	1	0	0	0	0	1	0	0	0	18129	101	4	5	523	5	ZNF713	7	56006915	Missense_Mutation	SNP	A	TCGA-5P-A9KA-01A-11D-A42J-10	446830	56006915	103131748	37	2631											
MET	4233	hgsc.bcm.edu	37	chr7	116423474	116423474	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagctgccagtgaagtggaTggctttggaaagtctgcaaa	13	9	13	6	0	1	1	0	1	1	0	1	3	1	3	1	3	3	3	1	3	4	1	rs121913245		TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr7:116423474T>C	ENST00000318493.6	+	19	3990	c.3803T>C	c.(3802-3804)aTg>aCg	p.M1268T	MET_ENST00000539704.1_Missense_Mutation_p.M120T|MET_ENST00000397752.3_Missense_Mutation_p.M1250T			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.M1268T(4)		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)			GTGAAGTGGATGGCTTTGGAA	0.393			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.M1268T		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,rectum,carcinoma,+1,5	MET	412	.	4	Substitution - Missense(4)	kidney(4)	c.T3803C	GRCh37	CM992181	MET	M	rs121913245	PASS	.						93	92	92					7																	116423474		1872	4102	5974	SO:0001583	missense	4233	exon19	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	AGTGGATGGCTTT	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.3803T>C	chr7.hg19:g.116423474T>C	ENSP00000317272:p.Met1268Thr	138.0	0.0	.		136.0	45.0	.	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	T	18.99	3.740165	0.69304	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000539704	T;T;T	0.37752	1.18;1.18;1.18	5.68	5.68	0.88126	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	0.61714	0.2369	M	0.75264	2.295	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;1.0	T	0.65734	-0.6096	10	0.87932	D	0	.	16.2225	0.82267	0.0:0.0:0.0:1.0	.	1268;1250	P08581-2;P08581	.;MET_HUMAN	T	1250;1268;120	ENSP00000380860:M1250T;ENSP00000317272:M1268T;ENSP00000445020:M120T	ENSP00000317272:M1268T	M	+	2	0	MET	116210710	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.997000	0.88414	2.289000	0.77006	0.460000	0.39030	ATG	.	.	.	weak		0.393	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			C	116423474	T	C	116423474	3	2	37	1	0	0	0	0	1	0	0	0	9492	1464	51	3	3873	3	MET	7	116423474	Missense_Mutation	SNP	T	TCGA-5P-A9KA-01A-11D-A42J-10	60416559	116423474	42715189	38	2632											
CTTNBP2	83992	hgsc.bcm.edu	37	chr7	117375153	117375153	+	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	taacattcggacagtccattTcctgaaacaaaccaaaaagc	17	8	5	11	1	0	1	0	1	0	0	3	2	2	2	3	1	4	0	3	1	5	3			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr7:117375153T>A	ENST00000160373.3	-	16	3781	c.3690A>T	c.(3688-3690)ggA>ggT	p.G1230G		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1230					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)		ACAGTCCATTTCCTGAAACAA	0.438																																					p.G1230G		Atlas-SNP	.											.	CTTNBP2	200	.	0			c.A3690T						PASS	.						43	46	45					7																	117375153		2203	4300	6503	SO:0001630	splice_region_variant	83992	exon16			TCCATTTCCTGAA		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.3689-1A>T	chr7.hg19:g.117375153T>A		181.0	0.0	.		188.0	60.0	.	NM_033427	O43389|Q7LG11|Q9C0A5	Silent	SNP	ENST00000160373.3	hg19	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	T	6.108	0.388122	0.11581	.	.	ENSG00000077063	ENST00000446636	.	.	.	5.52	3.13	0.36017	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.7914	0.29123	0.0:0.0682:0.2618:0.67	.	.	.	.	X	718	.	.	K	-	1	0	CTTNBP2	117162389	1.000000	0.71417	0.995000	0.50966	0.166000	0.22503	4.491000	0.60326	0.460000	0.27045	-0.313000	0.08912	AAA	.	.	.	none		0.438	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427	Silent	A	117375153	T	A	117375153	5	1	37	1	0	0	0	0	0	0	1	0	4047	1797	62	5	1333	5	CTTNBP2	7	117375153	Splice_Site	SNP	T	TCGA-5P-A9KA-01A-11D-A42J-10	951679	117375153	41763510	39	2633											
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121616253	121616253	+	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	atctactgctttgatgcggaCcgattttcaagttttgagga	9	15	10	7	2	2	2	1	2	1	0	2	5	2	4	1	2	3	2	1	2	2	6			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr7:121616253C>T	ENST00000393386.2	+	5	894	c.483C>T	c.(481-483)gaC>gaT	p.D161D	PTPRZ1_ENST00000449182.1_Silent_p.D161D	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	161	Alpha-carbonic anhydrase.				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						TTGATGCGGACCGATTTTCAA	0.308																																					p.D161D		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.C483T						PASS	.						112	106	108					7																	121616253		2203	4296	6499	SO:0001819	synonymous_variant	5803	exon5			TGCGGACCGATTT	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.483C>T	chr7.hg19:g.121616253C>T		53.0	0.0	.		75.0	27.0	.	NM_001206838	A4D0W5|C9JFM0|O76043|Q9UDR6	Silent	SNP	ENST00000393386.2	hg19	CCDS34740.1																																																																																			.	.	.	none		0.308	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		T	121616253	C	T	121616253	2	4	37	1	0	0	0	0	0	0	0	1	12827	506	18	2		2	PTPRZ1	7	121616253	Silent	SNP	C	TCGA-5P-A9KA-01A-11D-A42J-10	4241100	121616253	37522410	40	2634											
SLC13A1	6561	hgsc.bcm.edu	37	chr7	122839917	122839917	+	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	ctcaccttggtgtggaggacGatgggcagaggtagtaaaac	11	8	15	7	1	1	1	1	0	0	1	1	4	1	3	1	5	1	3	1	5	3	3			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr7:122839917G>C	ENST00000194130.2	-	1	123	c.84C>G	c.(82-84)atC>atG	p.I28M		NM_022444.3	NP_071889.2	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 1	28					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)	TGTGGAGGACGATGGGCAGAG	0.433																																					p.I28M		Atlas-SNP	.											.	SLC13A1	110	.	0			c.C84G						PASS	.						123	96	105					7																	122839917		2203	4300	6503	SO:0001583	missense	6561	exon1			GAGGACGATGGGC		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.84C>G	chr7.hg19:g.122839917G>C	ENSP00000194130:p.Ile28Met	75.0	0.0	.		95.0	31.0	.	NM_022444	Q9H5Z0	Missense_Mutation	SNP	ENST00000194130.2	hg19	CCDS5786.1	.	.	.	.	.	.	.	.	.	.	G	0.327	-0.958172	0.02267	.	.	ENSG00000081800	ENST00000194130	T	0.03035	4.07	5.73	0.75	0.18387	.	0.275865	0.35525	N	0.003157	T	0.05135	0.0137	M	0.67700	2.07	0.21105	N	0.999788	P	0.43542	0.81	B	0.42495	0.389	T	0.26224	-1.0109	10	0.49607	T	0.09	.	4.9281	0.13903	0.4153:0.0:0.4347:0.15	.	28	Q9BZW2	S13A1_HUMAN	M	28	ENSP00000194130:I28M	ENSP00000194130:I28M	I	-	3	3	SLC13A1	122627153	0.387000	0.25188	0.004000	0.12327	0.004000	0.04260	0.832000	0.27490	0.198000	0.20407	0.655000	0.94253	ATC	.	.	.	none		0.433	SLC13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347404.1	NM_022444		C	122839917	G	C	122839917	3	2	37	1	0	0	0	0	1	0	0	0	14404	1048	37	4	1763	4	SLC13A1	7	122839917	Missense_Mutation	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10	1223664	122839917	36298746	41	2635											
MLL3	58508	hgsc.bcm.edu	37	chr7	151877112	151877112	+	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	ccagtgttgaagaggccctgGatgaggcactgcgggtgagt	8	8	17	8	1	0	4	0	3	0	1	0	5	0	5	2	4	1	2	2	4	1	1			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr7:151877112G>T	ENST00000262189.6	-	37	7467	c.7249C>A	c.(7249-7251)Cca>Aca	p.P2417T	KMT2C_ENST00000355193.2_Missense_Mutation_p.P2417T	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2417	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)										AGAGGCCCTGGATGAGGCACT	0.552																																					p.P2417T		Atlas-SNP	.											.	MLL3	1564	.	0			c.C7249A						PASS	.						246	210	222					7																	151877112		2203	4300	6503	SO:0001583	missense	58508	exon37			GCCCTGGATGAGG	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.7249C>A	chr7.hg19:g.151877112G>T	ENSP00000262189:p.Pro2417Thr	122.0	0.0	.		119.0	41.0	.	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	G	8.065	0.769065	0.15983	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.83591	-1.74;-1.74	5.5	3.67	0.42095	.	0.332800	0.21736	N	0.069896	T	0.73869	0.3642	L	0.59436	1.845	0.26605	N	0.972947	B;B	0.24823	0.008;0.112	B;B	0.17722	0.003;0.019	T	0.57051	-0.7877	10	0.15499	T	0.54	.	5.2311	0.15422	0.0787:0.3973:0.3945:0.1295	.	2417;1478	Q8NEZ4;Q8NEZ4-2	MLL3_HUMAN;.	T	2417	ENSP00000262189:P2417T;ENSP00000347325:P2417T	ENSP00000262189:P2417T	P	-	1	0	MLL3	151508045	0.106000	0.21978	0.035000	0.18076	0.963000	0.63663	0.673000	0.25203	1.294000	0.44707	0.650000	0.86243	CCA	.	.	.	none		0.552	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			T	151877112	G	T	151877112	3	4	37	1	0	0	0	0	1	0	0	0	9629	1174	41	4	7578	4	MLL3	7	151877112	Missense_Mutation	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10	29037195	151877112	7261551	42	2636											
MLL3	58508	hgsc.bcm.edu	37	chr7	151919089	151919091	+	In_Frame_Del	DEL	GCT	GCT	-																															agcatttcaaattttacctaGctcttttacttttgtgacaa																										TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	GCT	GCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr7:151919089_151919091delGCT	ENST00000262189.6	-	22	3712_3714	c.3494_3496delAGC	c.(3493-3498)gagcta>gta	p.1165_1166EL>V	KMT2C_ENST00000355193.2_In_Frame_Del_p.1165_1166EL>V	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1165					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)										ATTTTACCTAGCTCTTTTACTTT	0.315																																					p.1165_1166del		Atlas-Indel,Pindel	.											.	MLL3	1564	.	0			c.3495_3497del						PASS	.																																			SO:0001651	inframe_deletion	58508	exon22			.	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.3494_3496delAGC	chr7.hg19:g.151919089_151919091delGCT	ENSP00000262189:p.Glu1165_Leu1166delinsVal	228.0	0.0	0		182.0	55.0	0.302198	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	In_Frame_Del	DEL	ENST00000262189.6	hg19	CCDS5931.1																																																																																			.	.	.	none		0.315	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			-	151919091	GCT	-	151919089	7	5	37	1	0	1	0	1	0	0	0	0	9629	962	34	0	11391	0	MLL3	7	151919089	In_Frame_Del	DEL	GCT	TCGA-5P-A9KA-01A-11D-A42J-10	41977	151919089	7219574	43	2637											
ZNF572	137209	hgsc.bcm.edu	37	chr8	125988832	125988832	+	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	aagaggaggaaaaacccaatCaccaggaatgggactcagga	18	3	12	8	0	2	1	2	0	0	1	2	6	2	6	2	5	1	0	2	5	5	0			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr8:125988832C>A	ENST00000319286.5	+	3	476	c.322C>A	c.(322-324)Cac>Aac	p.H108N		NM_152412.2	NP_689625.2	Q7Z3I7	ZN572_HUMAN	zinc finger protein 572	108					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			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)			AAAACCCAATCACCAGGAATG	0.418										HNSCC(60;0.17)																											p.H108N		Atlas-SNP	.											.	ZNF572	82	.	0			c.C322A						PASS	.						93	99	97					8																	125988832		2203	4300	6503	SO:0001583	missense	137209	exon3			CCCAATCACCAGG	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.322C>A	chr8.hg19:g.125988832C>A	ENSP00000319305:p.His108Asn	224.0	0.0	.		156.0	44.0	.	NM_152412	A1L4F1|Q8N1Q0	Missense_Mutation	SNP	ENST00000319286.5	hg19	CCDS6354.1	.	.	.	.	.	.	.	.	.	.	C	1.701	-0.501601	0.04261	.	.	ENSG00000180938	ENST00000319286	T	0.07444	3.19	4.56	1.76	0.24704	.	0.869576	0.09725	N	0.763920	T	0.06371	0.0164	N	0.22421	0.69	0.09310	N	1	B	0.16802	0.019	B	0.19391	0.025	T	0.37549	-0.9701	10	0.72032	D	0.01	-0.0456	5.9665	0.19328	0.0:0.6519:0.1632:0.1849	.	108	Q7Z3I7	ZN572_HUMAN	N	108	ENSP00000319305:H108N	ENSP00000319305:H108N	H	+	1	0	ZNF572	126058013	0.054000	0.20591	0.001000	0.08648	0.102000	0.19082	0.699000	0.25586	0.644000	0.30656	0.655000	0.94253	CAC	.	.	.	none		0.418	ZNF572-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381359.1	NM_152412		A	125988832	C	A	125988832	3	1	37	1	0	0	0	0	1	0	0	0	18016	826	29	4	328	4	ZNF572	8	125988832	Missense_Mutation	SNP	C	TCGA-5P-A9KA-01A-11D-A42J-10		125988832	20375190	44	2638											
RANBP6	26953	hgsc.bcm.edu	37	chr9	6012698	6012698	+	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	gtagcaatgacattttttttGgttttggaatttgcacactt	9	19	8	5	0	0	1	0	1	0	0	0	2	0	2	0	2	2	4	0	2	3	9			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr9:6012698G>T	ENST00000259569.5	-	1	2920	c.2910C>A	c.(2908-2910)acC>acA	p.T970T	RANBP6_ENST00000485372.1_5'Flank	NM_001243202.1|NM_001243203.1|NM_012416.3	NP_001230131.1|NP_001230132.1|NP_036548.1	O60518	RNBP6_HUMAN	RAN binding protein 6	970					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.K971fs*1(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(5)|large_intestine(8)|lung(9)|ovary(7)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)		CATTTTTTTTGGTTTTGGAAT	0.368																																					p.T970T		Atlas-SNP	.											.	RANBP6	127	.	1	Insertion - Frameshift(1)	NS(1)	c.C2910A						PASS	.						108	101	104					9																	6012698		2203	4300	6503	SO:0001819	synonymous_variant	26953	exon1			TTTTTTGGTTTTG	AF039023	CCDS6467.1	9p24.1	2008-03-26			ENSG00000137040	ENSG00000137040			9851	protein-coding gene	gene with protein product							Standard	NM_001243202		Approved		uc003zjr.3	O60518	OTTHUMG00000019512	ENST00000259569.5:c.2910C>A	chr9.hg19:g.6012698G>T		81.0	0.0	.		75.0	5.0	.	NM_012416	Q5T7X4|Q7Z3V2|Q96E78	Silent	SNP	ENST00000259569.5	hg19	CCDS6467.1																																																																																			.	.	.	none		0.368	RANBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051650.1	NM_012416		T	6012698	G	T	6012698	2	4	37	1	0	0	0	0	0	0	0	1	13044	1335	47	4		4	RANBP6	9	6012698	Silent	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10		6012698	135200733	45	2639											
PTPLAD2	401494	hgsc.bcm.edu	37	chr9	21008120	21008120	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtgccaaatgattcaaaataAggcagcgattgatagatggc	15	9	11	6	1	1	3	1	2	0	1	1	4	1	3	1	2	2	1	1	2	5	4			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr9:21008120A>G	ENST00000495827.2	-	6	561	c.516T>C	c.(514-516)ccT>ccC	p.P172P	PTPLAD2_ENST00000513293.2_Silent_p.P172P	NM_001010915.3	NP_001010915.2	Q5VWC8	HACD4_HUMAN	protein tyrosine phosphatase-like A domain containing 2	172					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)	10				Lung(24;6.02e-14)|LUSC - Lung squamous cell carcinoma(38;1.29e-10)		ATTCAAAATAAGGCAGCGATT	0.358																																					p.P172P		Atlas-SNP	.											.	PTPLAD2	26	.	0			c.T516C						PASS	.						115	110	111					9																	21008120		1869	4102	5971	SO:0001819	synonymous_variant	401494	exon6			AAAATAAGGCAGC		CCDS43791.1	9p21.3	2008-02-05			ENSG00000188921	ENSG00000188921			20920	protein-coding gene	gene with protein product		615941					Standard	NM_001010915		Approved	Em:AL662879.1, OTTHUMG00000021016	uc010mir.1	Q5VWC8	OTTHUMG00000021016	ENST00000495827.2:c.516T>C	chr9.hg19:g.21008120A>G		178.0	0.0	.		162.0	51.0	.	NM_001010915	Q7Z385	Silent	SNP	ENST00000495827.2	hg19	CCDS43791.1																																																																																			.	.	.	none		0.358	PTPLAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055434.3	NM_001010915		G	21008120	A	G	21008120	2	3	37	1	0	0	0	0	0	0	0	1	12787	59	3	3		3	PTPLAD2	9	21008120	Silent	SNP	A	TCGA-5P-A9KA-01A-11D-A42J-10	14995422	21008120	120205311	46	2640											
NOL6	65083	hgsc.bcm.edu	37	chr9	33467722	33467722	+	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	ggtcgagagtgagccagcagGttcagccgagcccccaggcc	8	4	15	14	2	1	2	1	1	0	1	2	4	1	2	5	3	4	2	5	3	0	1			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr9:33467722G>A	ENST00000379471.2	-	12	1656	c.1569C>T	c.(1567-1569)aaC>aaT	p.N523N	NOL6_ENST00000455041.2_Silent_p.N471N|NOL6_ENST00000464829.1_Intron			Q9H6R4	NOL6_HUMAN	nucleolar protein 6 (RNA-associated)	523					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)		GAGCCAGCAGGTTCAGCCGAG	0.627																																					p.N523N		Atlas-SNP	.											.	NOL6	85	.	0			c.C1569T						PASS	.						27	30	29					9																	33467722		2202	4300	6502	SO:0001819	synonymous_variant	65083	exon12			CAGCAGGTTCAGC	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.1569C>T	chr9.hg19:g.33467722G>A		56.0	0.0	.		68.0	22.0	.	NM_022917	Q5T5M3|Q5T5M4|Q7L4G6|Q8N6I0|Q8TEY9|Q8TEZ0|Q8TEZ1|Q9H675	Silent	SNP	ENST00000379471.2	hg19																																																																																				.	.	.	none		0.627	NOL6-005	NOVEL	non_canonical_TEC|basic	protein_coding	protein_coding	OTTHUMT00000001019.2	NM_022917		A	33467722	G	A	33467722	2	1	37	1	0	0	0	0	0	0	0	1	10532	1252	44	2		2	NOL6	9	33467722	Silent	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10	12459602	33467722	107745709	47	2641											
ZBTB5	9925	hgsc.bcm.edu	37	chr9	37442100	37442100	+	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	ctgagctcacgatgcttagtCccagctgctgtagcataaag	10	10	10	11	1	1	1	1	1	0	0	2	2	2	1	1	0	5	6	1	0	4	3			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr9:37442100C>T	ENST00000307750.4	-	2	637	c.449G>A	c.(448-450)gGa>gAa	p.G150E		NM_014872.2	NP_055687.1	O15062	ZBTB5_HUMAN	zinc finger and BTB domain containing 5	150					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	8				GBM - Glioblastoma multiforme(29;0.00733)|Lung(182;0.226)		GATGCTTAGTCCCAGCTGCTG	0.597																																					p.G150E		Atlas-SNP	.											.	ZBTB5	43	.	0			c.G449A						PASS	.						58	59	58					9																	37442100		2203	4300	6503	SO:0001583	missense	9925	exon2			CTTAGTCCCAGCT	AB002352	CCDS6610.1	9p13.1	2013-01-09			ENSG00000168795	ENSG00000168795		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	23836	protein-coding gene	gene with protein product						9205841	Standard	NM_014872		Approved	KIAA0354	uc003zzx.3	O15062	OTTHUMG00000019918	ENST00000307750.4:c.449G>A	chr9.hg19:g.37442100C>T	ENSP00000307604:p.Gly150Glu	68.0	0.0	.		57.0	19.0	.	NM_014872		Missense_Mutation	SNP	ENST00000307750.4	hg19	CCDS6610.1	.	.	.	.	.	.	.	.	.	.	C	19.60	3.857578	0.71834	.	.	ENSG00000168795	ENST00000307750	T	0.09073	3.02	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.17746	0.0426	N	0.19112	0.55	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.07712	-1.0758	10	0.30854	T	0.27	.	19.6787	0.95950	0.0:1.0:0.0:0.0	.	150	O15062	ZBTB5_HUMAN	E	150	ENSP00000307604:G150E	ENSP00000307604:G150E	G	-	2	0	ZBTB5	37432100	1.000000	0.71417	0.973000	0.42090	0.872000	0.50106	7.226000	0.78060	2.884000	0.98904	0.655000	0.94253	GGA	.	.	.	none		0.597	ZBTB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052462.1	NM_014872		T	37442100	C	T	37442100	3	4	37	1	0	0	0	0	1	0	0	0	17563	855	30	2	1588	2	ZBTB5	9	37442100	Missense_Mutation	SNP	C	TCGA-5P-A9KA-01A-11D-A42J-10	3974378	37442100	103771331	48	2642											
PTGES	9536	hgsc.bcm.edu	37	chr9	132502088	132502090	+	In_Frame_Del	DEL	GAA	GAA	-																															ggacccagaaaggagtagacGaagcccaggaaaaggaaggg																										TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr9:132502088_132502090delGAA	ENST00000340607.4	-	3	293_295	c.259_261delTTC	c.(259-261)ttcdel	p.F87del	PTGES_ENST00000481476.1_5'UTR	NM_004878.4	NP_004869.1	O14684	PTGES_HUMAN	prostaglandin E synthase	87					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)				AGGAGTAGACGAAGCCCAGGAAA	0.596																																					p.87_88del		Atlas-Indel,Pindel	.											.	PTGES	7	.	0			c.260_262del						PASS	.																																			SO:0001651	inframe_deletion	9536	exon3			.	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.259_261delTTC	chr9.hg19:g.132502088_132502090delGAA	ENSP00000342385:p.Phe87del	244.0	0.0	0		231.0	73.0	0.316017	NM_004878	O14900|Q5SZC0	In_Frame_Del	DEL	ENST00000340607.4	hg19	CCDS6927.1																																																																																			.	.	.	none		0.596	PTGES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054599.2	NM_004878		-	132502090	GAA	-	132502088	7	5	37	1	0	1	0	1	0	0	0	0	12757	1049	37	0	201	0	PTGES	9	132502088	In_Frame_Del	DEL	GAA	TCGA-5P-A9KA-01A-11D-A42J-10	95059988	132502088	8711343	49	2643											
GFI1B	8328	hgsc.bcm.edu	37	chr9	135863782	135863782	+	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	cagtcctcttgtgcccagcaCtgagcccgccttggacttca	6	10	9	16	1	2	1	1	1	1	0	3	2	3	2	4	1	3	1	4	1	0	3			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr9:135863782C>T	ENST00000339463.3	+	8	1256	c.437C>T	c.(436-438)aCt>aTt	p.T146I	GFI1B_ENST00000372122.1_Missense_Mutation_p.T146I|GFI1B_ENST00000450530.1_Missense_Mutation_p.T146I|GFI1B_ENST00000534944.1_Missense_Mutation_p.T146I|GFI1B_ENST00000372123.1_Missense_Mutation_p.T146I|GFI1B_ENST00000372124.1_Missense_Mutation_p.T146I			Q5VTD9	GFI1B_HUMAN	growth factor independent 1B transcription repressor	146	Interaction with ARIH2.				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)		GTGCCCAGCACTGAGCCCGCC	0.637																																					p.T146I		Atlas-SNP	.											.	GFI1B	37	.	0			c.C437T						PASS	.						70	54	59					9																	135863782		2203	4300	6503	SO:0001583	missense	8328	exon4			CCAGCACTGAGCC	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.437C>T	chr9.hg19:g.135863782C>T	ENSP00000344782:p.Thr146Ile	52.0	0.0	.		52.0	18.0	.	NM_001135031	O95270|Q5VTD8|Q6FHZ2|Q6T888	Missense_Mutation	SNP	ENST00000339463.3	hg19	CCDS6957.1	.	.	.	.	.	.	.	.	.	.	C	11.54	1.669057	0.29604	.	.	ENSG00000165702	ENST00000372124;ENST00000339463;ENST00000450530;ENST00000534944;ENST00000372123;ENST00000372122	T;T;T;T;T;T	0.09538	3.12;2.97;2.97;3.12;3.12;2.97	4.97	4.97	0.65823	.	0.601268	0.17315	N	0.178721	T	0.12817	0.0311	L	0.36672	1.1	0.20638	N	0.999877	B;B	0.25105	0.118;0.01	B;B	0.29942	0.109;0.013	T	0.15492	-1.0435	10	0.41790	T	0.15	-0.9295	17.229	0.86979	0.0:1.0:0.0:0.0	.	146;146	Q5VTD9-2;Q5VTD9	.;GFI1B_HUMAN	I	146	ENSP00000361197:T146I;ENSP00000344782:T146I;ENSP00000409546:T146I;ENSP00000446134:T146I;ENSP00000361196:T146I;ENSP00000361195:T146I	ENSP00000344782:T146I	T	+	2	0	GFI1B	134853603	0.468000	0.25839	0.029000	0.17559	0.159000	0.22180	5.530000	0.67141	2.276000	0.75962	0.563000	0.77884	ACT	.	.	.	none		0.637	GFI1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393840.1	NM_004188		T	135863782	C	T	135863782	3	4	37	1	0	0	0	0	1	0	0	0	6347	565	20	2	447	2	GFI1B	9	135863782	Missense_Mutation	SNP	C	TCGA-5P-A9KA-01A-11D-A42J-10	3361694	135863782	5349649	50	2644											
AGAP11	119385	hgsc.bcm.edu	37	chr10	88768386	88768386	+	RNA	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	agccatccccattaaacaggGcatgctcttaaagcgaagtg	13	8	9	11	1	1	0	0	0	1	0	2	1	2	0	3	1	4	2	3	1	5	2			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr10:88768386G>C	ENST00000444431.1	+	0	2986				RP11-96C23.5_ENST00000433214.2_RNA|RP11-96C23.10_ENST00000451760.1_RNA|RP11-96C23.14_ENST00000444180.3_RNA			Q8TF27	AGA11_HUMAN	ankyrin repeat and GTPase domain Arf GTPase activating protein 11						regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)										ATTAAACAGGGCATGCTCTTA	0.493																																					p.G126A		Atlas-SNP	.											.	.	.	.	0			c.G377C						PASS	.						174	188	183					10																	88768386		2150	4274	6424			119385	exon12			AACAGGGCATGCT			10q23.2	2013-01-11			ENSG00000151303	ENSG00000151303		"ADP-ribosylation factor GTPase activating proteins", "Ankyrin repeat domain containing"	29421	protein-coding gene	gene with protein product						11853319	Standard	NM_133447		Approved	KIAA1975	uc001kee.2	Q8TF27	OTTHUMG00000018667		chr10.hg19:g.88768386G>C		121.0	0.0	.		114.0	42.0	.	NM_133447	B9EIP7|D3DWE4	Missense_Mutation	SNP	ENST00000444431.1	hg19																																																																																				.	.	.	none		0.493	AGAP11-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000049193.1	NM_133447		C	88768386	G	C	88768386	1	2	37	0	1	0	0	0	0	0	0	0	367	1203	42	4		4	AGAP11	10	88768386	RNA	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10		88768386	46766361	51	2645											
C10orf79	80217	hgsc.bcm.edu	37	chr10	105990410	105990410	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgtagatgagaggttttagcTtccggtcagaaaaagccaca	13	9	11	8	2	1	3	1	1	0	3	2	4	2	3	2	2	2	3	2	2	4	4			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr10:105990410T>C	ENST00000278064.2	-	2	372	c.47A>G	c.(46-48)aAg>aGg	p.K16R	WDR96_ENST00000428666.1_Missense_Mutation_p.K86R|WDR96_ENST00000369719.1_Missense_Mutation_p.K16R|WDR96_ENST00000357060.3_Missense_Mutation_p.K86R|WDR96_ENST00000369720.1_Missense_Mutation_p.K16R																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						AGGTTTTAGCTTCCGGTCAGA	0.433																																					p.K86R		Atlas-SNP	.											.	WDR96	183	.	0			c.A257G						PASS	.						119	110	113					10																	105990410		2203	4300	6503	SO:0001583	missense	80217	exon2			TTTAGCTTCCGGT																												ENST00000278064.2:c.47A>G	chr10.hg19:g.105990410T>C	ENSP00000278064:p.Lys16Arg	121.0	0.0	.		98.0	34.0	.	NM_025145		Missense_Mutation	SNP	ENST00000278064.2	hg19		.	.	.	.	.	.	.	.	.	.	T	5.114	0.206598	0.09704	.	.	ENSG00000197748	ENST00000357060;ENST00000428666;ENST00000278064;ENST00000369720;ENST00000369719	T;T;T;T;T	0.13778	2.56;2.56;2.56;2.56;2.56	4.94	-5.89	0.02282	WD40/YVTN repeat-like-containing domain (1);	1.068010	0.07464	N	0.901047	T	0.07098	0.0180	N	0.16233	0.39	0.09310	N	1	B;B;B	0.20671	0.002;0.047;0.006	B;B;B	0.18561	0.009;0.022;0.009	T	0.44467	-0.9326	10	0.12766	T	0.61	.	11.2618	0.49087	0.0999:0.5681:0.0:0.332	.	86;86;86	Q8NDM7-5;B4DHB6;Q8NDM7	.;.;WDR96_HUMAN	R	86;86;16;16;16	ENSP00000349568:K86R;ENSP00000400289:K86R;ENSP00000278064:K16R;ENSP00000358734:K16R;ENSP00000358733:K16R	ENSP00000278064:K16R	K	-	2	0	WDR96	105980400	0.000000	0.05858	0.000000	0.03702	0.782000	0.44232	-1.097000	0.03349	-1.561000	0.01684	0.397000	0.26171	AAG	.	.	.	none		0.433	WDR96-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050200.1			C	105990410	T	C	105990410	3	2	37	1	0	0	0	0	1	0	0	0	1620	1609	56	3	4888	3	C10orf79	10	105990410	Missense_Mutation	SNP	T	TCGA-5P-A9KA-01A-11D-A42J-10	17222024	105990410	29544337	52	2646											
ATRNL1	26033	hgsc.bcm.edu	37	chr10	117228744	117228744	+	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	ataatataaaggaatacagaGatagtttttcctatgaaaaa	20	12	6	3	0	0	2	0	1	0	1	1	4	1	3	1	1	1	1	1	1	10	8			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr10:117228744G>T	ENST00000355044.3	+	24	3685	c.3559G>T	c.(3559-3561)Gat>Tat	p.D1187Y	ATRNL1_ENST00000303745.7_Intron|ATRNL1_ENST00000423111.2_Missense_Mutation_p.D238Y	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	1187					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)		GGAATACAGAGATAGTTTTTC	0.284																																					p.D1187Y		Atlas-SNP	.											.	ATRNL1	219	.	0			c.G3559T						PASS	.						35	39	38					10																	117228744		2188	4264	6452	SO:0001583	missense	26033	exon24			TACAGAGATAGTT	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.3559G>T	chr10.hg19:g.117228744G>T	ENSP00000347152:p.Asp1187Tyr	234.0	0.0	.		191.0	50.0	.	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Missense_Mutation	SNP	ENST00000355044.3	hg19	CCDS7592.1	.	.	.	.	.	.	.	.	.	.	G	17.53	3.413636	0.62511	.	.	ENSG00000107518	ENST00000355044;ENST00000423111	T;T	0.58652	0.32;0.32	5.73	5.73	0.89815	.	0.092022	0.64402	D	0.000001	T	0.66268	0.2772	L	0.41236	1.265	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.986;0.997	T	0.56848	-0.7911	10	0.02654	T	1	-28.319	19.9112	0.97025	0.0:0.0:1.0:0.0	.	238;1187	B4DH41;Q5VV63	.;ATRN1_HUMAN	Y	1187;238	ENSP00000347152:D1187Y;ENSP00000409624:D238Y	ENSP00000347152:D1187Y	D	+	1	0	ATRNL1	117218734	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.001000	0.88508	2.718000	0.92993	0.585000	0.79938	GAT	.	.	.	none		0.284	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		T	117228744	G	T	117228744	3	4	37	1	0	0	0	0	1	0	0	0	1207	942	33	4	3653	4	ATRNL1	10	117228744	Missense_Mutation	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10	11238334	117228744	18306003	53	2647											
QSER1	79832	hgsc.bcm.edu	37	chr11	32955850	32955850	+	Missense_Mutation	SNP	A	A	G																															ctgttgaagatggtgattctAaatctcattttcagcagtca																										TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr11:32955850A>G	ENST00000399302.2	+	4	2994	c.2659A>G	c.(2659-2661)Aaa>Gaa	p.K887E	QSER1_ENST00000527788.1_Missense_Mutation_p.K648E	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	887										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)					TGGTGATTCTAAATCTCATTT	0.388																																					p.K887E		Atlas-SNP	.											.	QSER1	153	.	0			c.A2659G						PASS	.						79	73	75					11																	32955850		1879	4115	5994	SO:0001583	missense	79832	exon4			GATTCTAAATCTC	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.2659A>G	chr11.hg19:g.32955850A>G	ENSP00000382241:p.Lys887Glu	123.0	0.0	.		121.0	38.0	.	NM_001076786	Q6ZU30|Q6ZUR5	Missense_Mutation	SNP	ENST00000399302.2	hg19	CCDS41631.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.022835	0.75275	.	.	ENSG00000060749	ENST00000399302;ENST00000078652;ENST00000527788	T;T	0.25912	2.1;1.77	5.84	5.84	0.93424	.	0.154150	0.44483	D	0.000455	T	0.49626	0.1568	M	0.64997	1.995	0.51233	D	0.99991	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.997;0.994	T	0.46871	-0.9160	10	0.54805	T	0.06	.	16.2149	0.82206	1.0:0.0:0.0:0.0	.	648;648;887	C9JJ88;Q2KHR3-2;Q2KHR3	.;.;QSER1_HUMAN	E	887;648;648	ENSP00000382241:K887E;ENSP00000432766:K648E	ENSP00000078652:K648E	K	+	1	0	QSER1	32912426	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.923000	0.92808	2.234000	0.73211	0.459000	0.35465	AAA	.	.	.	none		0.388	QSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388448.1	NM_024774		G	32955850	A	G	32955850	3	3	37	1	0	0	0	0	1	0	0	0	12895	363	13	3	2665	3	QSER1	11	32955850	Missense_Mutation	SNP	A	TCGA-5P-A9KA-01A-11D-A42J-10		32955850	102050666	54	2648	32	2									
QSER1	79832	hgsc.bcm.edu	37	chr11	32955852	32955852	+	Missense_Mutation	SNP	A	A	T																															gttgaagatggtgattctaaAtctcattttcagcagtcatt																										TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr11:32955852A>T	ENST00000399302.2	+	4	2996	c.2661A>T	c.(2659-2661)aaA>aaT	p.K887N	QSER1_ENST00000527788.1_Missense_Mutation_p.K648N	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	887										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)					GTGATTCTAAATCTCATTTTC	0.393																																					p.K887N		Atlas-SNP	.											.	QSER1	153	.	0			c.A2661T						PASS	.						79	74	75					11																	32955852		1879	4114	5993	SO:0001583	missense	79832	exon4			TTCTAAATCTCAT	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.2661A>T	chr11.hg19:g.32955852A>T	ENSP00000382241:p.Lys887Asn	124.0	0.0	.		119.0	38.0	.	NM_001076786	Q6ZU30|Q6ZUR5	Missense_Mutation	SNP	ENST00000399302.2	hg19	CCDS41631.1	.	.	.	.	.	.	.	.	.	.	A	15.87	2.961485	0.53400	.	.	ENSG00000060749	ENST00000399302;ENST00000078652;ENST00000527788	T;T	0.26660	2.05;1.72	5.84	-0.203	0.13204	.	0.154150	0.44483	D	0.000455	T	0.42539	0.1207	M	0.64997	1.995	0.35835	D	0.825631	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.997	T	0.48736	-0.9009	10	0.56958	D	0.05	.	10.6404	0.45590	0.5806:0.0:0.4194:0.0	.	648;648;887	C9JJ88;Q2KHR3-2;Q2KHR3	.;.;QSER1_HUMAN	N	887;648;648	ENSP00000382241:K887N;ENSP00000432766:K648N	ENSP00000078652:K648N	K	+	3	2	QSER1	32912428	0.998000	0.40836	0.991000	0.47740	0.993000	0.82548	1.360000	0.34125	-0.056000	0.13221	0.459000	0.35465	AAA	.	.	.	none		0.393	QSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388448.1	NM_024774		T	32955852	A	T	32955852	3	4	37	1	0	0	0	0	1	0	0	0	12895	98	4	5	2667	5	QSER1	11	32955852	Missense_Mutation	SNP	A	TCGA-5P-A9KA-01A-11D-A42J-10	2	32955852	102050664	55	2649	32	2									
IGHMBP2	3508	hgsc.bcm.edu	37	chr11	68703885	68703885	+	Missense_Mutation	SNP	T	T	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	ctttgagtatcttgacgataTtgtcccagaaaactattccc	11	14	6	10	1	1	3	0	2	1	1	3	4	3	3	2	0	1	1	2	0	5	7			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr11:68703885T>G	ENST00000255078.3	+	13	2048	c.1937T>G	c.(1936-1938)aTt>aGt	p.I646S		NM_002180.2	NP_002171.2	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	646	SS DNA-binding. {ECO:0000250}.				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)			CTTGACGATATTGTCCCAGAA	0.547																																					p.I646S		Atlas-SNP	.											.	IGHMBP2	83	.	0			c.T1937G						PASS	.						103	104	104					11																	68703885		2200	4294	6494	SO:0001583	missense	3508	exon13			ACGATATTGTCCC	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.1937T>G	chr11.hg19:g.68703885T>G	ENSP00000255078:p.Ile646Ser	98.0	0.0	.		131.0	43.0	.	NM_002180	A0PJD2|Q00443|Q14177	Missense_Mutation	SNP	ENST00000255078.3	hg19	CCDS8187.1	.	.	.	.	.	.	.	.	.	.	T	12.56	1.973900	0.34848	.	.	ENSG00000132740	ENST00000255078	D	0.90261	-2.64	4.1	4.1	0.47936	.	0.358876	0.27816	N	0.017721	D	0.88089	0.6343	L	0.61218	1.895	0.80722	D	1	B	0.20550	0.046	B	0.15870	0.014	D	0.85819	0.1384	10	0.44086	T	0.13	-22.5874	12.4851	0.55868	0.0:0.0:0.0:1.0	.	646	P38935	SMBP2_HUMAN	S	646	ENSP00000255078:I646S	ENSP00000255078:I646S	I	+	2	0	IGHMBP2	68460461	1.000000	0.71417	0.265000	0.24526	0.788000	0.44548	4.434000	0.59935	1.848000	0.53677	0.459000	0.35465	ATT	.	.	.	none		0.547	IGHMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396862.1	NM_002180		G	68703885	T	G	68703885	3	3	37	1	0	0	0	0	1	0	0	0	7598	1493	52	5	1987	5	IGHMBP2	11	68703885	Missense_Mutation	SNP	T	TCGA-5P-A9KA-01A-11D-A42J-10	35748033	68703885	66302631	56	2650											
SIDT2	51092	hgsc.bcm.edu	37	chr11	117064631	117064631	+	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	atcgtttgcacctccgtggtCtggggcttcgcgctcttctt	2	15	11	13	4	3	0	0	0	3	0	6	0	4	0	2	3	1	4	2	3	0	4			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr11:117064631C>T	ENST00000324225.4	+	24	2805	c.2274C>T	c.(2272-2274)gtC>gtT	p.V758V	SIDT2_ENST00000532062.1_Silent_p.V50V|SIDT2_ENST00000431081.2_Silent_p.V755V	NM_001040455.1	NP_001035545.1	Q8NBJ9	SIDT2_HUMAN	SID1 transmembrane family, member 2	758					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)		CCTCCGTGGTCTGGGGCTTCG	0.617																																					p.V758V		Atlas-SNP	.											.	SIDT2	82	.	0			c.C2274T						PASS	.						100	92	95					11																	117064631		2201	4296	6497	SO:0001819	synonymous_variant	51092	exon24			CGTGGTCTGGGGC	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.2274C>T	chr11.hg19:g.117064631C>T		41.0	0.0	.		39.0	10.0	.	NM_001040455	Q8NBY7|Q9Y357	Silent	SNP	ENST00000324225.4	hg19	CCDS31682.1																																																																																			.	.	.	none		0.617	SIDT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392836.1	NM_015996		T	117064631	C	T	117064631	2	4	37	1	0	0	0	0	0	0	0	1	14316	900	32	2		2	SIDT2	11	117064631	Silent	SNP	C	TCGA-5P-A9KA-01A-11D-A42J-10	48360746	117064631	17941885	57	2651											
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117335821	117335844	+	In_Frame_Del	DEL	GTTGCTGCCGGGGCTGTTCTCTCT	GTTGCTGCCGGGGCTGTTCTCTCT	-																															tccacgatgctgtactgcccGttgctgccggggctgttctc																								rs375180039|rs140840612|rs574227365		TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	GTTGCTGCCGGGGCTGTTCTCTCT	GTTGCTGCCGGGGCTGTTCTCTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr11:117335821_117335844delGTTGCTGCCGGGGCTGTTCTCTCT	ENST00000321322.6	-	17	3260_3283	c.3259_3282delAGAGAGAACAGCCCCGGCAGCAAC	c.(3259-3282)agagagaacagccccggcagcaacdel	p.RENSPGSN1087del	DSCAML1_ENST00000527706.1_In_Frame_Del_p.RENSPGSN817del	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1027	Fibronectin type-III 2. {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)		TGTACTGCCCGTTGCTGCCGGGGCTGTTCTCTCTGTAGCCAATC	0.598																																					p.1087_1095del		Atlas-Indel,Pindel	.											.	DSCAML1	286	.	0			c.3260_3283del						PASS	.																																			SO:0001651	inframe_deletion	57453	exon17			.		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.3259_3282delAGAGAGAACAGCCCCGGCAGCAAC	chr11.hg19:g.117335821_117335844delGTTGCTGCCGGGGCTGTTCTCTCT	ENSP00000315465:p.Arg1087_Asn1094del	105.0	0.0	0		107.0	30.0	0.280374	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	In_Frame_Del	DEL	ENST00000321322.6	hg19	CCDS8384.1																																																																																			.	.	.	none		0.598	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		-	117335844	GTTGCTGCCGGGGCTGTTCTCTCT	-	117335821	7	5	37	1	0	1	0	1	0	0	0	0	4771	1136	40	0	3127	0	DSCAML1	11	117335821	In_Frame_Del	DEL	GTTGCTGCCGGGGCTGTTCTCTCT	TCGA-5P-A9KA-01A-11D-A42J-10	271190	117335821	17670695	58	2652											
RNF26	79102	hgsc.bcm.edu	37	chr11	119206568	119206568	+	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	cagtgacggtgactgtgttgCatccggacttcaccctgagg	7	10	13	11	2	1	3	1	3	0	0	2	4	2	4	2	3	1	2	2	3	0	2			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr11:119206568C>A	ENST00000311413.4	+	1	1332	c.736C>A	c.(736-738)Cat>Aat	p.H246N	RP11-334E6.10_ENST00000501918.2_RNA	NM_032015.4	NP_114404.1	Q9BY78	RNF26_HUMAN	ring finger protein 26	246						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)		GACTGTGTTGCATCCGGACTT	0.612																																					p.H246N		Atlas-SNP	.											.	RNF26	23	.	0			c.C736A						PASS	.						105	99	101					11																	119206568		2199	4295	6494	SO:0001583	missense	79102	exon1			GTGTTGCATCCGG	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.736C>A	chr11.hg19:g.119206568C>A	ENSP00000312439:p.His246Asn	25.0	0.0	.		23.0	4.0	.	NM_032015	Q542Y8	Missense_Mutation	SNP	ENST00000311413.4	hg19	CCDS8419.1	.	.	.	.	.	.	.	.	.	.	C	2.446	-0.327525	0.05314	.	.	ENSG00000173456	ENST00000311413	T	0.25414	1.8	5.21	5.21	0.72293	.	0.069763	0.53938	D	0.000046	T	0.26557	0.0649	N	0.24115	0.695	0.35730	D	0.817828	D	0.53885	0.963	P	0.58873	0.847	T	0.11012	-1.0605	10	0.10636	T	0.68	-14.9067	9.8055	0.40791	0.0:0.9063:0.0:0.0937	.	246	Q9BY78	RNF26_HUMAN	N	246	ENSP00000312439:H246N	ENSP00000312439:H246N	H	+	1	0	RNF26	118711778	1.000000	0.71417	1.000000	0.80357	0.757000	0.42996	2.732000	0.47352	2.432000	0.82394	0.561000	0.74099	CAT	.	.	.	none		0.612	RNF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388220.1	NM_032015		A	119206568	C	A	119206568	3	1	37	1	0	0	0	0	1	0	0	0	13499	710	25	4	738	4	RNF26	11	119206568	Missense_Mutation	SNP	C	TCGA-5P-A9KA-01A-11D-A42J-10	1870747	119206568	15799948	59	2653											
B3GAT1	27087	hgsc.bcm.edu	37	chr11	134253770	134253770	+	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	gcgtctccacgtgcaggtgcGtgtagttgaggccggtgtcg	4	10	17	10	5	1	1	0	1	1	0	3	1	1	1	2	3	2	3	2	3	1	2			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr11:134253770G>C	ENST00000524765.1	-	3	4969	c.425C>G	c.(424-426)aCg>aGg	p.T142R	B3GAT1_ENST00000312527.4_Missense_Mutation_p.T142R|B3GAT1_ENST00000392580.1_Missense_Mutation_p.T142R|B3GAT1_ENST00000537389.1_Missense_Mutation_p.T155R|B3GAT1_ENST00000531510.1_5'Flank			Q9P2W7	B3GA1_HUMAN	beta-1,3-glucuronyltransferase 1	142					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity (GO:0015018)|metal ion binding (GO:0046872)|UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(175;0.127)	all_cancers(12;1.39e-23)|all_epithelial(12;7.17e-17)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|Medulloblastoma(222;0.0125)|all_neural(223;0.0137)|Esophageal squamous(93;0.0559)		Epithelial(10;2.58e-11)|all cancers(11;5.75e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.000879)|Lung(977;0.0864)		GTGCAGGTGCGTGTAGTTGAG	0.726																																					p.T142R		Atlas-SNP	.											.	B3GAT1	49	.	0			c.C425G						PASS	.						30	29	29					11																	134253770		2175	4226	6401	SO:0001583	missense	27087	exon3			AGGTGCGTGTAGT	AB029396	CCDS8500.1	11q25	2014-07-08	2014-07-08		ENSG00000109956	ENSG00000109956	2.4.1.135	"CD molecules", "Beta-1,3-glucuronyltransferases"	921	protein-coding gene	gene with protein product	"galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1", "glucuronosyltransferase P"	151290	"CD57 antigen"	CD57, LEU7			Standard	XM_005271506		Approved	GlcAT-P, HNK-1, NK-1	uc001qhq.3	Q9P2W7	OTTHUMG00000167180	ENST00000524765.1:c.425C>G	chr11.hg19:g.134253770G>C	ENSP00000433847:p.Thr142Arg	53.0	0.0	.		40.0	5.0	.	NM_054025	Q96FS7	Missense_Mutation	SNP	ENST00000524765.1	hg19	CCDS8500.1	.	.	.	.	.	.	.	.	.	.	G	37	6.104294	0.97286	.	.	ENSG00000109956	ENST00000392580;ENST00000312527;ENST00000524765;ENST00000537389	T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.72358	0.3450	L	0.41573	1.285	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.994;1.0	T	0.66822	-0.5826	10	0.23302	T	0.38	-24.5871	19.1576	0.93517	0.0:0.0:1.0:0.0	.	155;142	F5H0S0;Q9P2W7	.;B3GA1_HUMAN	R	142;142;142;155	ENSP00000376359:T142R;ENSP00000307875:T142R;ENSP00000433847:T142R;ENSP00000445983:T155R	ENSP00000307875:T142R	T	-	2	0	B3GAT1	133758980	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	9.822000	0.99363	2.541000	0.85698	0.561000	0.74099	ACG	.	.	.	none		0.726	B3GAT1-002	KNOWN	alternative_3_UTR|alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393639.1	NM_018644		C	134253770	G	C	134253770	3	2	37	1	0	0	0	0	1	0	0	0	1253	1145	40	4	591	4	B3GAT1	11	134253770	Missense_Mutation	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10	15047202	134253770	752746	60	2654											
PEX5	5830	hgsc.bcm.edu	37	chr12	7351708	7351710	+	Splice_Site	DEL	TGG	TGG	-																															agggaacagccaccgatcgcTggtgagttcagatacctctt																										TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	TGG	TGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr12:7351708_7351710delTGG	ENST00000455147.2	+	7	1130_1131	c.550_551delTGG	c.(550-552)tgg>g	p.W184del	PEX5_ENST00000434354.2_Splice_Site_p.W199del|PEX5_ENST00000412720.2_Splice_Site_p.W205del|PEX5_ENST00000545220.1_Intron|PEX5_ENST00000420616.2_Splice_Site_p.W184del|PEX5_ENST00000266563.5_Splice_Site_p.W184del|PEX5_ENST00000266564.3_Splice_Site_p.W184del	NM_001131026.1	NP_001124498.1	P50542	PEX5_HUMAN	peroxisomal biogenesis factor 5	184					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						CACCGATCGCTGGTGAGTTCAGA	0.522																																					p.198_199del		Atlas-Indel,Pindel	.											.	PEX5	63	.	0			c.594_596del						PASS	.																																			SO:0001630	splice_region_variant	5830	exon6			.	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.551+1TGG>-	chr12.hg19:g.7351708_7351710delTGG		53.0	0.0	0		62.0	13.0	0.209677	NM_001131023	A8K891|B4DZ45|B7ZAD5|D3DUT8|Q15115|Q15266|Q96FN7	In_Frame_Del	DEL	ENST00000455147.2	hg19	CCDS44823.1																																																																																			.	.	.	none		0.522	PEX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398611.1	NM_000319	In_Frame_Del	-	7351710	TGG	-	7351708	8	5	37	1	0	1	0	1	0	0	1	0	11755	1594	55	0	613	0	PEX5	12	7351708	Splice_Site	DEL	TGG	TCGA-5P-A9KA-01A-11D-A42J-10		7351708	126500187	61	2655											
PRB4	5545	hgsc.bcm.edu	37	chr12	11461534	11461596	+	In_Frame_Del	DEL	CCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	CCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	-																															ggggacggtgggactggttgCctccttgtgggggtggtctt																								rs11054244|rs59021567|rs11054243|rs551775057|rs12303607|rs199532199|rs148027029|rs71057722|rs59189129|rs536297617	byFrequency	TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	CCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	CCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr12:11461534_11461596delCCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	ENST00000535904.1	-	3	354_416	c.321_383delAAACCAGTCCCAAGGTACCCCACCTCCTCCAGGAAAGCCAGAAAGACCACCCCCACAAGGAGG	c.(319-384)ggaaaccagtcccaaggtaccccacctcctccaggaaagccagaaagaccacccccacaaggaggc>ggc	p.107_128GNQSQGTPPPPGKPERPPPQGG>G	PRB4_ENST00000445719.2_Splice_Site_p.107_112GNQSQG>G|PRB4_ENST00000279575.1_In_Frame_Del_p.107_128GNQSQGTPPPPGKPERPPPQGG>G			P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4	128	9.5 X 21 AA tandem repeats of K-P-[EQ]- [GR]-[PR]-[PR]-P-Q-G-G-N-Q-[PS]-[QH]- [RG]-[PT]-P-P-[PH]-P-G.		Missing (in allele M and allele S).	SR -> RP (in Ref. 7; CAA30542). {ECO:0000305}.		extracellular region (GO:0005576)		p.P115L(1)|p.G118E(1)|p.P117T(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|skin(4)|upper_aerodigestive_tract(3)	30						GGACTGGTTGCCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTTCCTCCTTGTG	0.605										HNSCC(22;0.051)																											p.108_112del		Pindel	.											.	PRB4	59	.	3	Substitution - Missense(3)	lung(1)|kidney(1)|skin(1)	c.322_334del						PASS	.																																			SO:0001651	inframe_deletion	5545	exon3			.		CCDS8641.1, CCDS58208.1	12p13.2	2012-10-02			ENSG00000230657	ENSG00000230657			9340	protein-coding gene	gene with protein product		180990					Standard	NM_002723		Approved		uc001qzt.4	P10163	OTTHUMG00000169116	ENST00000535904.1:c.321_383delAAACCAGTCCCAAGGTACCCCACCTCCTCCAGGAAAGCCAGAAAGACCACCCCCACAAGGAGG	chr12.hg19:g.11461534_11461596delCCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	ENSP00000442834:p.Gly107_Gly127del	96.0	0.0	.		123.0	12.0	0.098	NM_001261399	A1L439|O00600|P02813|P10161|P10162|P81489	Frame_Shift_Del	DEL	ENST00000535904.1	hg19	CCDS8641.1																																																																																			.	.	.	none		0.605	PRB4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402308.1	NM_002723		-	11461596	CCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	-	11461534	7	5	37	1	0	1	0	1	0	0	0	0	12455	739	26	0	364	0	PRB4	12	11461534	In_Frame_Del	DEL	CCTCCTTGTGGGGGTGGTCTTTCTGGCTTTCCTGGAGGAGGTGGGGTACCTTGGGACTGGTTT	TCGA-5P-A9KA-01A-11D-A42J-10	4109826	11461534	122390361	62	2656											
PTPRB	5787	hgsc.bcm.edu	37	chr12	70974991	70974991	+	Missense_Mutation	SNP	T	T	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	atcagtaagacttggtaaaaTtctacgtctccttgtgcctg	10	14	8	9	1	3	1	1	0	2	1	4	1	3	1	2	1	2	2	2	1	4	6			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr12:70974991T>G	ENST00000261266.5	-	8	1778	c.1749A>C	c.(1747-1749)gaA>gaC	p.E583D	PTPRB_ENST00000550358.1_Missense_Mutation_p.E801D|PTPRB_ENST00000550857.1_Missense_Mutation_p.E493D|PTPRB_ENST00000451516.2_Missense_Mutation_p.E493D|PTPRB_ENST00000551525.1_Missense_Mutation_p.E800D|PTPRB_ENST00000334414.6_Missense_Mutation_p.E801D|PTPRB_ENST00000538708.1_Missense_Mutation_p.E583D	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	583	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			CTTGGTAAAATTCTACGTCTC	0.458																																					p.E801D		Atlas-SNP	.											.	PTPRB	676	.	0			c.A2403C						PASS	.						137	136	136					12																	70974991		1932	4140	6072	SO:0001583	missense	5787	exon10			GTAAAATTCTACG	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.1749A>C	chr12.hg19:g.70974991T>G	ENSP00000261266:p.Glu583Asp	151.0	0.0	.		161.0	76.0	.	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	hg19	CCDS44944.1	.	.	.	.	.	.	.	.	.	.	T	0.968	-0.701100	0.03255	.	.	ENSG00000127329	ENST00000334414;ENST00000451516;ENST00000550358;ENST00000544694;ENST00000538708;ENST00000550857;ENST00000261266;ENST00000551525;ENST00000548122	T;T;T;T;T;T;T;T	0.55234	0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53	5.86	-10.8	0.00216	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.192388	0.53938	N	0.000057	T	0.08537	0.0212	N	0.00608	-1.33	0.20196	N	0.999928	B;B;B;B;B;B;B	0.09022	0.0;0.0;0.0;0.001;0.002;0.0;0.001	B;B;B;B;B;B;B	0.08055	0.002;0.002;0.002;0.002;0.003;0.003;0.003	T	0.46414	-0.9193	10	0.02654	T	1	.	1.1909	0.01864	0.1973:0.1989:0.3143:0.2895	.	493;583;680;800;801;583;801	P23467-2;F5H3G6;Q6ZR19;F8VSD5;P23467-3;P23467;F8VU56	.;.;.;.;.;PTPRB_HUMAN;.	D	801;493;801;801;583;493;583;800;680	ENSP00000334928:E801D;ENSP00000393028:E493D;ENSP00000448058:E801D;ENSP00000438927:E583D;ENSP00000447302:E493D;ENSP00000261266:E583D;ENSP00000448349:E800D;ENSP00000446982:E680D	ENSP00000261266:E583D	E	-	3	2	PTPRB	69261258	0.000000	0.05858	0.614000	0.29051	0.388000	0.30384	-2.979000	0.00663	-1.448000	0.01941	-0.309000	0.09137	GAA	.	.	.	none		0.458	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			G	70974991	T	G	70974991	3	3	37	1	0	0	0	0	1	0	0	0	12809	1490	52	5	4344	5	PTPRB	12	70974991	Missense_Mutation	SNP	T	TCGA-5P-A9KA-01A-11D-A42J-10	59513457	70974991	62876904	63	2657											
KNTC1	9735	hgsc.bcm.edu	37	chr12	123034324	123034324	+	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	ttttcttagatgaaaaacctCatggtttattcattacctac	12	17	4	8	0	3	2	2	1	1	1	3	2	3	2	2	1	3	1	2	1	6	8			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr12:123034324C>A	ENST00000333479.7	+	13	1176	c.999C>A	c.(997-999)ctC>ctA	p.L333L	KNTC1_ENST00000450485.2_Silent_p.L296L	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	333					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)		TGAAAAACCTCATGGTTTATT	0.308																																					p.L333L		Atlas-SNP	.											.	KNTC1	182	.	0			c.C999A						PASS	.						44	41	42					12																	123034324		1806	4067	5873	SO:0001819	synonymous_variant	9735	exon13			AAACCTCATGGTT		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.999C>A	chr12.hg19:g.123034324C>A		98.0	0.0	.		122.0	54.0	.	NM_014708	A7E2C4|B3KSG2	Silent	SNP	ENST00000333479.7	hg19	CCDS45002.1																																																																																			.	.	.	none		0.308	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2			A	123034324	C	A	123034324	2	1	37	1	0	0	0	0	0	0	0	1	8435	813	29	4		4	KNTC1	12	123034324	Silent	SNP	C	TCGA-5P-A9KA-01A-11D-A42J-10	52059333	123034324	10817571	64	2658											
PABPC3	5042	hgsc.bcm.edu	37	chr13	25670355	25670366	+	In_Frame_Del	DEL	AGCTACCCAACG	AGCTACCCAACG	-																															gaatgaaccccagcacccccAgctacccaacggcctcgctc																								rs371856829|rs533997128		TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	AGCTACCCAACG	AGCTACCCAACG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr13:25670355_25670366delAGCTACCCAACG	ENST00000281589.3	+	1	56_67	c.19_30delAGCTACCCAACG	c.(19-30)agctacccaacgdel	p.SYPT7del		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	7					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)		CAGCACCCCCAGCTACCCAACGGCCTCGCTCT	0.67																																					p.6_10del		Atlas-INDEL	.											.	PABPC3	129	.	0			c.18_29del						PASS	.																																			SO:0001651	inframe_deletion	5042	exon1			.	AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"RNA binding motif (RRM) containing"	8556	protein-coding gene	gene with protein product	"testis PABP"	604680	"poly(A)-binding protein, cytoplasmic 3"	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.19_30delAGCTACCCAACG	chr13.hg19:g.25670355_25670366delAGCTACCCAACG	ENSP00000281589:p.Ser7_Thr10del	93.0	0.0	0		91.0	16.0	0.175824	NM_030979	Q8NHV0|Q9H086	In_Frame_Del	DEL	ENST00000281589.3	hg19	CCDS9311.1																																																																																			.	.	.	none		0.67	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979		-	25670366	AGCTACCCAACG	-	25670355	7	5	37	1	0	1	0	1	0	0	0	0	11372	188	7	0	21	0	PABPC3	13	25670355	In_Frame_Del	DEL	AGCTACCCAACG	TCGA-5P-A9KA-01A-11D-A42J-10		25670355	89499523	65	2659											
ZIC5	85416	hgsc.bcm.edu	37	chr13	100623797	100623798	+	Missense_Mutation	DNP	CC	CC	GT																															ctgaagcggctggacctgagCcgttgccaaatccgctaatc																										TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr13:100623797_100623798CC>GT	ENST00000267294.4	-	1	365_366	c.132_133GG>AC	c.(130-135)acGGct>acACct	p.A45P		NM_033132.3	NP_149123.2	Q96T25	ZIC5_HUMAN	Zic family member 5	45					cell differentiation (GO:0030154)|forebrain development (GO:0030900)|neural tube closure (GO:0001843)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(1)|lung(2)|prostate(1)|skin(2)	9	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					TGGACCTGAGCCGTTGCCAAAT	0.658																																					p.A45P|p.T44T		Atlas-SNP	.											.	ZIC5	38	.	0			c.G133C|c.G132A						PASS	.																																			SO:0001583	missense	85416	exon1			CCTGAGCCGTTGC|CTGAGCCGTTGCC	AF378304	CCDS9494.2	13q32.2	2013-01-08	2011-05-19		ENSG00000139800	ENSG00000139800		"Zinc fingers, C2H2-type"	20322	protein-coding gene	gene with protein product			"Zic family member 5 (odd-paired homolog, Drosophila)"				Standard	NM_033132		Approved		uc001vom.1	Q96T25	OTTHUMG00000017280	ENST00000267294.4:c.132_133delinsGT	chr13.hg19:g.100623797_100623798delinsGT	ENSP00000267294:p.Ala45Pro	65.0|66.0	0.0	.		69.0	18.0|16.0	.	NM_033132	Q5VYB0	Missense_Mutation|Silent	SNP	ENST00000267294.4	hg19	CCDS9494.2																																																																																			.	.	.	none		0.658	ZIC5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000045623.3	NM_033132		GT	100623798	CC	GT	100623797	3	3	37	1	0	0	0	0	1	0	0	0	17694	739	26	4	1866	4	ZIC5	13	100623797	Missense_Mutation	DNP	CC	TCGA-5P-A9KA-01A-11D-A42J-10	74953442	100623797	14546081	66	2660											
TPP2	7174	hgsc.bcm.edu	37	chr13	103289504	103289504	+	Missense_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	atcttgggttcagtgtcccaGccatttggaactcatgaatc	9	13	9	10	0	3	1	2	1	1	0	5	2	4	2	2	2	2	1	2	2	2	3			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr13:103289504G>A	ENST00000376065.4	+	14	1787	c.1751G>A	c.(1750-1752)aGc>aAc	p.S584N	TPP2_ENST00000376052.3_Missense_Mutation_p.S584N	NM_003291.2	NP_003282.2	P29144	TPP2_HUMAN	tripeptidyl peptidase II	584					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)					CAGTGTCCCAGCCATTTGGAA	0.383																																					p.S584N		Atlas-SNP	.											.	TPP2	124	.	0			c.G1751A						PASS	.						116	112	113					13																	103289504		2203	4300	6503	SO:0001583	missense	7174	exon14			GTCCCAGCCATTT	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.1751G>A	chr13.hg19:g.103289504G>A	ENSP00000365233:p.Ser584Asn	59.0	0.0	.		68.0	22.0	.	NM_003291	Q5VZU8	Missense_Mutation	SNP	ENST00000376065.4	hg19	CCDS9502.1	.	.	.	.	.	.	.	.	.	.	G	14.61	2.587138	0.46110	.	.	ENSG00000134900	ENST00000376065;ENST00000376052	.	.	.	5.92	5.04	0.67666	.	0.178273	0.64402	D	0.000007	T	0.56891	0.2016	L	0.44542	1.39	0.47949	D	0.999558	B	0.18166	0.026	B	0.18561	0.022	T	0.50939	-0.8768	9	0.33141	T	0.24	.	18.5671	0.91120	0.0:0.1842:0.8158:0.0	.	584	P29144	TPP2_HUMAN	N	584	.	ENSP00000365220:S584N	S	+	2	0	TPP2	102087505	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.411000	0.52672	2.822000	0.97130	0.650000	0.86243	AGC	.	.	.	none		0.383	TPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045683.2			A	103289504	G	A	103289504	3	1	37	1	0	0	0	0	1	0	0	0	16424	971	34	2	1805	2	TPP2	13	103289504	Missense_Mutation	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10	2665707	103289504	11880374	67	2661											
TRAPPC6B	122553	hgsc.bcm.edu	37	chr14	39627583	39627583	+	Frame_Shift_Del	DEL	A	A	-																															tgatatctaactcatccttgAaccttgcagtatcttttgta																										TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr14:39627583delA	ENST00000330149.5	-	3	399	c.173delT	c.(172-174)ttcfs	p.F58fs	TRAPPC6B_ENST00000557764.1_Intron|TRAPPC6B_ENST00000347691.5_Frame_Shift_Del_p.F58fs	NM_001079537.1	NP_001073005.1	Q86SZ2	TPC6B_HUMAN	trafficking protein particle complex 6B	58					vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0128)		CTCATCCTTGAACCTTGCAGT	0.313																																					p.F58fs		Atlas-Indel,Pindel	.											.	TRAPPC6B	13	.	0			c.174delC						PASS	.						93	90	91					14																	39627583		2203	4295	6498	SO:0001589	frameshift_variant	122553	exon3			.	AK025437	CCDS9670.1, CCDS41947.1	14q13.3	2011-10-10			ENSG00000182400	ENSG00000182400		"Trafficking protein particle complex"	23066	protein-coding gene	gene with protein product		610397					Standard	NM_177452		Approved		uc001wut.1	Q86SZ2	OTTHUMG00000140259	ENST00000330149.5:c.173delT	chr14.hg19:g.39627583delA	ENSP00000330289:p.Phe58fs	71.0	0.0	0		64.0	29.0	0.453125	NM_001079537	B3KPS2|Q5JPD6|Q86U35|Q86X35	Frame_Shift_Del	DEL	ENST00000330149.5	hg19	CCDS41947.1																																																																																			.	.	.	none		0.313	TRAPPC6B-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276775.1	NM_177452		-	39627583	A	-	39627583	7	5	37	1	0	1	0	1	0	0	0	0	16476	246	9	0	319	0	TRAPPC6B	14	39627583	Frame_Shift_Del	DEL	A	TCGA-5P-A9KA-01A-11D-A42J-10		39627583	67721957	68	2662											
SYNE2	23224	hgsc.bcm.edu	37	chr14	64494496	64494496	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcatctacacgaaagtctTcttcaacaactgcaggtgag	14	9	8	10	1	4	1	1	1	3	0	4	2	4	1	0	1	5	2	0	1	5	3			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr14:64494496T>C	ENST00000344113.4	+	43	6911	c.6699T>C	c.(6697-6699)ctT>ctC	p.L2233L	SYNE2_ENST00000554584.1_Silent_p.L2233L|SYNE2_ENST00000358025.3_Silent_p.L2233L|SYNE2_ENST00000357395.3_5'UTR	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2233					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)		ACGAAAGTCTTCTTCAACAAC	0.378																																					p.L2233L		Atlas-SNP	.											.	SYNE2	577	.	0			c.T6699C						PASS	.						58	53	55					14																	64494496		1847	4099	5946	SO:0001819	synonymous_variant	23224	exon43			AAGTCTTCTTCAA	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.6699T>C	chr14.hg19:g.64494496T>C		165.0	0.0	.		156.0	55.0	.	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.	.	none		0.378	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		C	64494496	T	C	64494496	2	2	37	1	0	0	0	0	0	0	0	1	15458	1770	62	3		3	SYNE2	14	64494496	Silent	SNP	T	TCGA-5P-A9KA-01A-11D-A42J-10	24866913	64494496	42855044	69	2663											
CPSF2	53981	hgsc.bcm.edu	37	chr14	92627590	92627590	+	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	aatcaagtagcagtccgcagAgtaagtgtgttttcaataag	14	11	10	6	1	2	1	2	0	0	1	3	1	3	1	1	0	1	5	1	0	6	5			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr14:92627590A>T	ENST00000298875.4	+	15	2541	c.2256A>T	c.(2254-2256)agA>agT	p.R752S		NM_017437.2	NP_059133.1	Q9P2I0	CPSF2_HUMAN	cleavage and polyadenylation specific factor 2, 100kDa	752					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	RNA binding (GO:0003723)			breast(2)|cervix(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	24		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)		CAGTCCGCAGAGTAAGTGTGT	0.388																																					p.R752S	Ovarian(78;28 1788 18702 44111)	Atlas-SNP	.											.	CPSF2	63	.	0			c.A2256T						PASS	.						152	141	145					14																	92627590		2203	4300	6503	SO:0001630	splice_region_variant	53981	exon15			CCGCAGAGTAAGT	AB037788	CCDS9902.1	14q31.1	2008-07-28	2002-08-29			ENSG00000165934			2325	protein-coding gene	gene with protein product		606028	"cleavage and polyadenylation specific factor 2, 100kD subunit"			7969155, 11124543	Standard	NM_017437		Approved	KIAA1367	uc001yah.2	Q9P2I0		ENST00000298875.4:c.2256+1A>T	chr14.hg19:g.92627590A>T		115.0	0.0	.		102.0	32.0	.	NM_017437	B3KME1|Q6NSJ1|Q9H3W7	Missense_Mutation	SNP	ENST00000298875.4	hg19	CCDS9902.1	.	.	.	.	.	.	.	.	.	.	A	26.7	4.759873	0.89932	.	.	ENSG00000165934	ENST00000298875	T	0.53640	0.61	5.78	0.956	0.19608	.	0.000000	0.85682	D	0.000000	T	0.62950	0.2470	M	0.74467	2.265	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.61936	-0.6960	10	0.87932	D	0	.	8.5209	0.33275	0.4617:0.0:0.5383:0.0	.	752	Q9P2I0	CPSF2_HUMAN	S	752	ENSP00000298875:R752S	ENSP00000298875:R752S	R	+	3	2	CPSF2	91697343	1.000000	0.71417	0.995000	0.50966	0.982000	0.71751	3.124000	0.50461	0.134000	0.18681	0.533000	0.62120	AGA	.	.	.	none		0.388	CPSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412123.1		Missense_Mutation	T	92627590	A	T	92627590	5	4	37	1	0	0	0	0	0	0	1	0	3827	318	11	5	2306	5	CPSF2	14	92627590	Splice_Site	SNP	A	TCGA-5P-A9KA-01A-11D-A42J-10	28133094	92627590	14721950	70	2664											
TLN2	83660	hgsc.bcm.edu	37	chr15	63112730	63112731	+	Frame_Shift_Ins	INS	-	-	A																															ccaactgtcattgcagaaacINSagagttactgggggctgcag																										TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr15:63112730_63112731insA	ENST00000561311.1	+	53	7153_7154	c.6923_6924insA	c.(6922-6927)acagagfs	p.E2309fs	TLN2_ENST00000306829.6_Frame_Shift_Ins_p.E2309fs			Q9Y4G6	TLN2_HUMAN	talin 2	2309	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						ATTGCAGAAACAGAGTTACTGG	0.47																																					p.T2308fs		Atlas-Indel,Pindel	.											.	TLN2	253	.	0			c.6923_6924insA						PASS	.																																			SO:0001589	frameshift_variant	83660	exon51			.	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.6924dupA	chr15.hg19:g.63112731_63112731dupA	ENSP00000453508:p.Glu2309fs	91.0	0.0	0		96.0	25.0	0.260417	NM_015059	A6NLB8	Frame_Shift_Ins	INS	ENST00000561311.1	hg19	CCDS32261.1																																																																																			.	.	.	none		0.47	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			A	63112731	-	A	63112730	7	5	37	1	0	1	1	0	0	0	0	0	15960	478	17	0	7125	0	TLN2	15	63112730	Frame_Shift_Ins	INS	-	TCGA-5P-A9KA-01A-11D-A42J-10		63112730	39418662	71	2665											
TSC2	7249	hgsc.bcm.edu	37	chr16	2112991	2112991	+	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	aggagcgagtcccgaggcgcCgtgcgcatcaaggtgctgga	8	5	17	11	5	1	0	1	0	0	0	2	4	2	2	2	4	3	2	2	4	1	0			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr16:2112991C>G	ENST00000219476.3	+	14	2010	c.1380C>G	c.(1378-1380)gcC>gcG	p.A460A	TSC2_ENST00000401874.2_Silent_p.A460A|TSC2_ENST00000350773.4_Silent_p.A460A|TSC2_ENST00000568454.1_Silent_p.A471A|TSC2_ENST00000382538.6_Silent_p.A411A|TSC2_ENST00000439673.2_Silent_p.A423A|TSC2_ENST00000353929.4_Silent_p.A460A	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	460					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)				CCCGAGGCGCCGTGCGCATCA	0.706			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.A460A		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	.	TSC2	364	.	0			c.C1380G						PASS	.						53	42	46					16																	2112991		1960	3715	5675	SO:0001819	synonymous_variant	7249	exon14	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	AGGCGCCGTGCGC	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.1380C>G	chr16.hg19:g.2112991C>G		40.0	0.0	.		67.0	14.0	.	NM_001114382	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Silent	SNP	ENST00000219476.3	hg19	CCDS10458.1																																																																																			.	.	.	none		0.706	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		G	2112991	C	G	2112991	2	3	37	1	0	0	0	0	0	0	0	1	16618	639	23	4		4	TSC2	16	2112991	Silent	SNP	C	TCGA-5P-A9KA-01A-11D-A42J-10		2112991	88241762	72	2666											
ZC3H7A	29066	hgsc.bcm.edu	37	chr16	11856530	11856530	+	Frame_Shift_Del	DEL	C	C	-																															acacaagagaaaaatacctgCgctccaggtacatttgcttc																								rs571101988		TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr16:11856530delC	ENST00000396516.2	-	16	2273	c.2076delG	c.(2074-2076)gcgfs	p.A692fs	ZC3H7A_ENST00000575984.1_5'Flank|ZC3H7A_ENST00000355758.4_Frame_Shift_Del_p.A692fs			Q8IWR0	Z3H7A_HUMAN	zinc finger CCCH-type containing 7A	692						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.A692A(1)		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						AAAATACCTGCGCTCCAGGTA	0.413																																					p.Q693fs		Atlas-INDEL	.											.	ZC3H7A	72	.	1	Substitution - coding silent(1)	prostate(1)	c.2077delC						PASS	.						115	99	105					16																	11856530		2197	4300	6497	SO:0001589	frameshift_variant	29066	exon17			.	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.2076delG	chr16.hg19:g.11856530delC	ENSP00000379773:p.Ala692fs	64.0	0.0	0		53.0	11.0	0.207547	NM_014153	D3DUG5|Q9NPE9	Frame_Shift_Del	DEL	ENST00000396516.2	hg19	CCDS10550.1																																																																																			.	.	.	none		0.413	ZC3H7A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437066.1	NM_014153		-	11856530	C	-	11856530	7	5	37	1	0	1	0	1	0	0	0	0	17584	755	27	0	867	0	ZC3H7A	16	11856530	Frame_Shift_Del	DEL	C	TCGA-5P-A9KA-01A-11D-A42J-10	9743539	11856530	78498223	73	2667	33	2									
ZC3H7A	29066	hgsc.bcm.edu	37	chr16	11856532	11856534	+	In_Frame_Del	DEL	CTC	CTC	-																															acaagagaaaaatacctgcgCtccaggtacatttgcttcca																										TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr16:11856532_11856534delCTC	ENST00000396516.2	-	16	2269_2271	c.2072_2074delGAG	c.(2071-2076)ggagcg>gcg	p.G691del	ZC3H7A_ENST00000575984.1_5'Flank|ZC3H7A_ENST00000355758.4_In_Frame_Del_p.G691del			Q8IWR0	Z3H7A_HUMAN	zinc finger CCCH-type containing 7A	691						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						AATACCTGCGCTCCAGGTACATT	0.404																																					p.691_692del		Atlas-INDEL	.											ZC3H7A,colon,carcinoma,+1,1	ZC3H7A	72	.	0			c.2073_2075del						PASS	.																																			SO:0001651	inframe_deletion	29066	exon17			.	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.2072_2074delGAG	chr16.hg19:g.11856532_11856534delCTC	ENSP00000379773:p.Gly691del	64.0	0.0	0		55.0	11.0	0.2	NM_014153	D3DUG5|Q9NPE9	In_Frame_Del	DEL	ENST00000396516.2	hg19	CCDS10550.1																																																																																			.	.	.	none		0.404	ZC3H7A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437066.1	NM_014153		-	11856534	CTC	-	11856532	7	5	37	1	0	1	0	1	0	0	0	0	17584	797	28	0	869	0	ZC3H7A	16	11856532	In_Frame_Del	DEL	CTC	TCGA-5P-A9KA-01A-11D-A42J-10	2	11856532	78498221	74	2668	33	2									
ZFHX3	463	hgsc.bcm.edu	37	chr16	72991450	72991450	+	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	aggttcatgttctgggccagGtagtattggtagagctcggc	7	12	15	7	1	2	1	1	0	1	1	3	1	2	1	1	5	1	6	1	5	3	6			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr16:72991450G>A	ENST00000268489.5	-	2	3267	c.2595C>T	c.(2593-2595)taC>taT	p.Y865Y	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	865					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)				TCTGGGCCAGGTAGTATTGGT	0.607																																					p.Y865Y		Atlas-SNP	.											.	ZFHX3	404	.	0			c.C2595T						PASS	.						115	105	108					16																	72991450		2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			GGCCAGGTAGTAT	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.2595C>T	chr16.hg19:g.72991450G>A		77.0	0.0	.		73.0	26.0	.	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	hg19	CCDS10908.1																																																																																			.	.	.	none		0.607	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		A	72991450	G	A	72991450	2	1	37	1	0	0	0	0	0	0	0	1	17646	1256	44	2		2	ZFHX3	16	72991450	Silent	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10	61134918	72991450	17363303	75	2669											
C17orf68	80169	hgsc.bcm.edu	37	chr17	8137889	8137889	+	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	gggcagaagggccttagggtCaaaggaggcccaggccttac	10	5	16	10	0	1	1	1	0	0	1	1	2	1	2	3	6	1	1	3	6	4	2			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr17:8137889C>T	ENST00000315684.8	-	10	1709	c.1702G>A	c.(1702-1704)Gac>Aac	p.D568N	CTC1_ENST00000581671.1_5'Flank	NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	568					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						GCCTTAGGGTCAAAGGAGGCC	0.632																																					p.D568N		Atlas-SNP	.											.	CTC1	75	.	0			c.G1702A						PASS	.						45	53	50					17																	8137889		2051	4182	6233	SO:0001583	missense	80169	exon10			TAGGGTCAAAGGA	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.1702G>A	chr17.hg19:g.8137889C>T	ENSP00000313759:p.Asp568Asn	173.0	0.0	.		188.0	53.0	.	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Missense_Mutation	SNP	ENST00000315684.8	hg19	CCDS42259.1	.	.	.	.	.	.	.	.	.	.	c	11.75	1.732111	0.30684	.	.	ENSG00000178971	ENST00000315684;ENST00000449476	D;D	0.84589	-1.87;-1.87	5.44	4.47	0.54385	.	0.422251	0.23775	N	0.044690	T	0.81550	0.4846	M	0.65975	2.015	0.32033	N	0.599281	B	0.23540	0.087	B	0.25759	0.063	T	0.76926	-0.2778	10	0.16896	T	0.51	-7.7145	10.2272	0.43233	0.0:0.9083:0.0:0.0917	.	568	Q2NKJ3	CTC1_HUMAN	N	568;533	ENSP00000313759:D568N;ENSP00000396018:D533N	ENSP00000313759:D568N	D	-	1	0	CTC1	8078614	0.998000	0.40836	1.000000	0.80357	0.708000	0.40852	0.458000	0.21892	1.328000	0.45358	-0.371000	0.07208	GAC	.	.	.	none		0.632	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099		T	8137889	C	T	8137889	3	4	37	1	0	0	0	0	1	0	0	0	1878	826	29	2	2007	2	C17orf68	17	8137889	Missense_Mutation	SNP	C	TCGA-5P-A9KA-01A-11D-A42J-10		8137889	73057321	76	2670											
USP43	124739	hgsc.bcm.edu	37	chr17	9559778	9559778	+	Frame_Shift_Del	DEL	A	A	-																															ttcccagcacgacgccctggAattcctgctctggttgctgg																										TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr17:9559778delA	ENST00000285199.7	+	2	659	c.563delA	c.(562-564)gaafs	p.E188fs	USP43_ENST00000570827.2_3'UTR|USP43_ENST00000570475.1_Frame_Shift_Del_p.E188fs	NM_001267576.1|NM_153210.4	NP_001254505.1|NP_694942.3	Q70EL4	UBP43_HUMAN	ubiquitin specific peptidase 43	188	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						GACGCCCTGGAATTCCTGCTC	0.522																																					p.E188fs		Atlas-Indel,Pindel	.											.	USP43	65	.	0			c.562delG						PASS	.						75	73	74					17																	9559778		1866	4108	5974	SO:0001589	frameshift_variant	124739	exon2			.	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.563delA	chr17.hg19:g.9559778delA	ENSP00000285199:p.Glu188fs	157.0	0.0	0		146.0	42.0	0.287671	NM_001267576	A6NDT9|B7ZLT9|B7ZVX5|Q8N2C5|Q96DQ6	Frame_Shift_Del	DEL	ENST00000285199.7	hg19	CCDS45610.1																																																																																			.	.	.	none		0.522	USP43-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439855.3	NM_153210		-	9559778	A	-	9559778	7	5	37	1	0	1	0	1	0	0	0	0	17086	246	9	0	569	0	USP43	17	9559778	Frame_Shift_Del	DEL	A	TCGA-5P-A9KA-01A-11D-A42J-10	1421889	9559778	71635432	77	2671											
MYH8	4626	hgsc.bcm.edu	37	chr17	10299694	10299694	+	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	ttcacatttctcttgttctaCttgcttctttattttctcca	5	23	2	11	0	5	0	1	0	4	0	7	0	5	0	1	0	2	2	1	0	2	11			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr17:10299694C>A	ENST00000403437.2	-	33	4700	c.4606G>T	c.(4606-4608)Gta>Tta	p.V1536L	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	1536					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						TCTTGTTCTACTTGCTTCTTT	0.383									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																												p.V1536L		Atlas-SNP	.											.	MYH8	346	.	0			c.G4606T						PASS	.						169	149	156					17																	10299694		2203	4300	6503	SO:0001583	missense	4626	exon33	Familial Cancer Database	Carney Complex Variant	GTTCTACTTGCTT		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.4606G>T	chr17.hg19:g.10299694C>A	ENSP00000384330:p.Val1536Leu	80.0	0.0	.		68.0	19.0	.	NM_002472	Q14910	Missense_Mutation	SNP	ENST00000403437.2	hg19	CCDS11153.1	.	.	.	.	.	.	.	.	.	.	C	1.961	-0.438953	0.04636	.	.	ENSG00000133020	ENST00000252173;ENST00000403437	T	0.55588	0.51	5.26	4.3	0.51218	Myosin tail (1);	0.267575	0.20576	U	0.089628	T	0.14700	0.0355	N	0.00507	-1.42	0.29779	N	0.834145	B	0.02656	0.0	B	0.06405	0.002	T	0.29701	-1.0003	10	0.02654	T	1	.	5.6007	0.17351	0.0:0.6792:0.0:0.3208	.	1536	P13535	MYH8_HUMAN	L	1536	ENSP00000384330:V1536L	ENSP00000252173:V1536L	V	-	1	0	MYH8	10240419	0.000000	0.05858	1.000000	0.80357	0.997000	0.91878	-1.501000	0.02281	1.458000	0.47871	0.650000	0.86243	GTA	.	.	.	none		0.383	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		A	10299694	C	A	10299694	3	1	37	1	0	0	0	0	1	0	0	0	10048	565	20	4	1239	4	MYH8	17	10299694	Missense_Mutation	SNP	C	TCGA-5P-A9KA-01A-11D-A42J-10	739916	10299694	70895516	78	2672											
SPAG5	10615	hgsc.bcm.edu	37	chr17	26906847	26906847	+	Missense_Mutation	SNP	A	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	aagcaagggcacaggagttgAttctggctctaagagaaaaa	16	7	12	6	0	2	2	0	1	2	1	2	4	2	3	0	3	1	4	0	3	5	3			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr17:26906847A>C	ENST00000321765.5	-	17	3138	c.2806T>G	c.(2806-2808)Tca>Gca	p.S936A	ALDOC_ENST00000395321.2_5'Flank|ALDOC_ENST00000226253.4_5'Flank|ALDOC_ENST00000395319.3_5'Flank	NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	936					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)					ACAGGAGTTGATTCTGGCTCT	0.532																																					p.S936A		Atlas-SNP	.											.	SPAG5	92	.	0			c.T2806G						PASS	.						107	111	110					17																	26906847		2203	4300	6503	SO:0001583	missense	10615	exon17			GAGTTGATTCTGG	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.2806T>G	chr17.hg19:g.26906847A>C	ENSP00000323300:p.Ser936Ala	132.0	0.0	.		111.0	29.0	.	NM_006461	O95213|Q9BWE8|Q9NT17|Q9UFE6	Missense_Mutation	SNP	ENST00000321765.5	hg19	CCDS32594.1	.	.	.	.	.	.	.	.	.	.	a	1.508	-0.550368	0.03996	.	.	ENSG00000076382	ENST00000321765	T	0.29142	1.58	5.51	-2.49	0.06403	.	0.926052	0.09003	N	0.862743	T	0.11580	0.0282	N	0.08118	0	0.09310	N	0.999998	B	0.06786	0.001	B	0.06405	0.002	T	0.36625	-0.9740	10	0.07813	T	0.8	0.0217	6.531	0.22326	0.2456:0.4877:0.2668:0.0	.	936	Q96R06	SPAG5_HUMAN	A	936	ENSP00000323300:S936A	ENSP00000323300:S936A	S	-	1	0	SPAG5	23930974	0.320000	0.24616	0.867000	0.34043	0.630000	0.37929	-0.063000	0.11655	-0.336000	0.08438	0.524000	0.50904	TCA	.	.	.	none		0.532	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461		C	26906847	A	C	26906847	3	2	37	1	0	0	0	0	1	0	0	0	14994	333	12	5	807	5	SPAG5	17	26906847	Missense_Mutation	SNP	A	TCGA-5P-A9KA-01A-11D-A42J-10	16607153	26906847	54288363	79	2673											
TBX21	30009	hgsc.bcm.edu	37	chr17	45822709	45822709	+	Frame_Shift_Del	DEL	T	T	-																															ataaggaagctgaaggacagTtttataactattttcccaac																										TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr17:45822709delT	ENST00000177694.1	+	6	1796	c.1585delT	c.(1585-1587)tttfs	p.F529fs		NM_013351.1	NP_037483.1	Q9UL17	TBX21_HUMAN	T-box 21	529					cellular response to organic substance (GO:0071310)|lymphocyte migration (GO:0072676)|multicellular organismal development (GO:0007275)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	neuronal cell body (GO:0043025)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|endometrium(1)|large_intestine(3)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	22						TGAAGGACAGTTTTATAACTA	0.483																																					p.Q528fs		Atlas-Indel,Pindel	.											.	TBX21	50	.	0			c.1584delG						PASS	.						44	50	48					17																	45822709		2199	4298	6497	SO:0001589	frameshift_variant	30009	exon6			.	AF093098	CCDS11514.1	17q21.2	2008-06-23				ENSG00000073861		"T-boxes"	11599	protein-coding gene	gene with protein product		604895					Standard	NM_013351		Approved	TBLYM, T-bet	uc002ilv.1	Q9UL17		ENST00000177694.1:c.1585delT	chr17.hg19:g.45822709delT	ENSP00000177694:p.Phe529fs	51.0	0.0	0		50.0	15.0	0.3	NM_013351		Frame_Shift_Del	DEL	ENST00000177694.1	hg19	CCDS11514.1																																																																																			.	.	.	none		0.483	TBX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441365.1	NM_013351		-	45822709	T	-	45822709	7	5	37	1	0	1	0	1	0	0	0	0	15669	1725	60	0	1607	0	TBX21	17	45822709	Frame_Shift_Del	DEL	T	TCGA-5P-A9KA-01A-11D-A42J-10	18915862	45822709	35372501	80	2674											
LAMA3	3909	hgsc.bcm.edu	37	chr18	21343469	21343469	+	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	ggcatctatgctggtggaggGgtctgcattaactgtcaggt	7	12	15	7	0	3	0	1	0	2	0	3	1	3	1	0	6	3	3	0	6	2	2			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr18:21343469G>T	ENST00000313654.9	+	8	1405	c.1164G>T	c.(1162-1164)ggG>ggT	p.G388G	LAMA3_ENST00000399516.3_Silent_p.G388G	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	388	Domain V.|Laminin EGF-like 2. {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)					CTGGTGGAGGGGTCTGCATTA	0.488																																					p.G388G		Atlas-SNP	.											.	LAMA3	397	.	0			c.G1164T						PASS	.						126	129	128					18																	21343469		2023	4178	6201	SO:0001819	synonymous_variant	3909	exon8			TGGAGGGGTCTGC	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.1164G>T	chr18.hg19:g.21343469G>T		96.0	0.0	.		84.0	23.0	.	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	hg19	CCDS42419.1																																																																																			.	.	.	none		0.488	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		T	21343469	G	T	21343469	2	4	37	1	0	0	0	0	0	0	0	1	8614	1219	43	4		4	LAMA3	18	21343469	Silent	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10		21343469	56733779	81	2675											
C18orf25	147339	hgsc.bcm.edu	37	chr18	43796193	43796193	+	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	gtcttccgcagaagagaatgAaccctctcaggcagaaacgg	13	6	11	11	2	2	4	1	1	2	3	4	5	3	4	2	2	2	2	2	2	4	1			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr18:43796193A>T	ENST00000282059.6	+	2	721	c.347A>T	c.(346-348)gAa>gTa	p.E116V	C18orf25_ENST00000321319.6_Missense_Mutation_p.E116V	NM_145055.3	NP_659492	Q96B23	CR025_HUMAN	chromosome 18 open reading frame 25	116										central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)	11						GAAGAGAATGAACCCTCTCAG	0.522																																					p.E116V		Atlas-SNP	.											.	C18orf25	27	.	0			c.A347T						PASS	.						102	102	102					18																	43796193		1920	4136	6056	SO:0001583	missense	147339	exon2			AGAATGAACCCTC	AL713661	CCDS42430.1, CCDS42431.1	18q21.1	2014-01-03			ENSG00000152242	ENSG00000152242			28172	protein-coding gene	gene with protein product	"ARKadia-like 1"					15722956	Standard	NM_001008239		Approved	MGC12909, ARKL1, RNF111L1	uc002lbw.3	Q96B23		ENST00000282059.6:c.347A>T	chr18.hg19:g.43796193A>T	ENSP00000282059:p.Glu116Val	146.0	0.0	.		144.0	42.0	.	NM_145055	A8K123|A8KAB6|Q5XG78|Q6N058|Q86TB5|Q8TCQ5	Missense_Mutation	SNP	ENST00000282059.6	hg19	CCDS42430.1	.	.	.	.	.	.	.	.	.	.	A	17.05	3.291056	0.59976	.	.	ENSG00000152242	ENST00000282059;ENST00000321319	.	.	.	5.95	5.95	0.96441	.	0.108809	0.64402	D	0.000013	T	0.50514	0.1620	L	0.38175	1.15	0.47737	D	0.9995	B;P	0.45531	0.007;0.86	B;P	0.47075	0.013;0.536	T	0.54556	-0.8276	9	0.72032	D	0.01	-14.0694	12.2973	0.54854	0.8589:0.1411:0.0:0.0	.	116;116	Q96B23-2;Q96B23	.;CR025_HUMAN	V	116	.	ENSP00000282059:E116V	E	+	2	0	C18orf25	42050191	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.954000	0.56708	2.282000	0.76494	0.533000	0.62120	GAA	.	.	.	none		0.522	C18orf25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445242.1	NM_145055		T	43796193	A	T	43796193	3	4	37	1	0	0	0	0	1	0	0	0	1901	246	9	5	349	5	C18orf25	18	43796193	Missense_Mutation	SNP	A	TCGA-5P-A9KA-01A-11D-A42J-10	22452724	43796193	34281055	82	2676											
PHLPP1	23239	hgsc.bcm.edu	37	chr18	60646284	60646284	+	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	aggtgccagcagaggccagtGatgagggcattgtcatcagc	10	7	15	9	0	2	3	2	2	0	1	2	3	2	3	2	3	3	2	2	3	0	1			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr18:60646284G>T	ENST00000262719.5	+	17	5008	c.4774G>T	c.(4774-4776)Gat>Tat	p.D1592Y	PHLPP1_ENST00000400316.4_Missense_Mutation_p.D1080Y			O60346	PHLP1_HUMAN	PH domain and leucine rich repeat protein phosphatase 1	1592					apoptotic process (GO:0006915)|entrainment of circadian clock (GO:0009649)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			endometrium(2)|kidney(2)|lung(13)	17						AGAGGCCAGTGATGAGGGCAT	0.632																																					p.D1592Y		Atlas-SNP	.											.	PHLPP1	164	.	0			c.G4774T						PASS	.						34	39	38					18																	60646284		2098	4215	6313	SO:0001583	missense	23239	exon17			GCCAGTGATGAGG	AB011178	CCDS45881.1, CCDS45881.2	18q21.32	2013-01-11	2009-05-26	2009-05-26	ENSG00000081913	ENSG00000081913		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent", "Pleckstrin homology (PH) domain containing"	20610	protein-coding gene	gene with protein product		609396	"pleckstrin homology domain containing, family E (with leucine rich repeats) member 1", "PH domain and leucine rich repeat protein phosphatase"	PLEKHE1, PHLPP		10570941, 15808505	Standard	NM_194449		Approved	KIAA0606, SCOP	uc021ule.1	O60346	OTTHUMG00000150629	ENST00000262719.5:c.4774G>T	chr18.hg19:g.60646284G>T	ENSP00000262719:p.Asp1592Tyr	110.0	0.0	.		103.0	27.0	.	NM_194449	A1A4F5|Q641Q7|Q6P4C4|Q6PJI6|Q86TN6|Q96FK2|Q9NUY1	Missense_Mutation	SNP	ENST00000262719.5	hg19	CCDS45881.2	.	.	.	.	.	.	.	.	.	.	G	18.89	3.720529	0.68959	.	.	ENSG00000081913	ENST00000400316;ENST00000262719	T;T	0.27890	1.78;1.64	4.18	4.18	0.49190	.	.	.	.	.	T	0.38241	0.1033	N	0.22421	0.69	0.54753	D	0.999982	D	0.67145	0.996	P	0.59703	0.862	T	0.40813	-0.9543	9	0.72032	D	0.01	-19.3796	16.6946	0.85332	0.0:0.0:1.0:0.0	.	1592	O60346	PHLP1_HUMAN	Y	1080;1592	ENSP00000383170:D1080Y;ENSP00000262719:D1592Y	ENSP00000262719:D1592Y	D	+	1	0	PHLPP1	58797264	1.000000	0.71417	0.948000	0.38648	0.894000	0.52154	5.705000	0.68355	2.173000	0.68751	0.561000	0.74099	GAT	.	.	.	none		0.632	PHLPP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319249.2	NM_194449		T	60646284	G	T	60646284	3	4	37	1	0	0	0	0	1	0	0	0	11861	1290	45	4	4840	4	PHLPP1	18	60646284	Missense_Mutation	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10	16850091	60646284	17430964	83	2677											
VAV1	7409	hgsc.bcm.edu	37	chr19	6854009	6854009	+	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	agcccgctatgacttctgcgCccgagaccgatcagagctgt	8	8	11	14	4	2	3	1	1	1	2	2	5	2	3	3	0	3	2	3	0	1	2			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr19:6854009C>T	ENST00000602142.1	+	26	2466	c.2384C>T	c.(2383-2385)gCc>gTc	p.A795V	VAV1_ENST00000599806.1_Missense_Mutation_p.A740V|VAV1_ENST00000596764.1_Missense_Mutation_p.A763V|VAV1_ENST00000539284.1_Missense_Mutation_p.A698V|VAV1_ENST00000304076.2_Missense_Mutation_p.A773V	NM_005428.3	NP_005419.2	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	795	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|reactive oxygen species metabolic process (GO:0072593)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(16)|lung(18)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	62						GACTTCTGCGCCCGAGACCGA	0.547																																					p.A795V		Atlas-SNP	.											.	VAV1	140	.	0			c.C2384T						PASS	.						110	99	103					19																	6854009		2203	4300	6503	SO:0001583	missense	7409	exon26			TCTGCGCCCGAGA		CCDS12174.1, CCDS59341.1, CCDS59342.1	19p13.2	2013-02-14	2007-07-25			ENSG00000141968		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12657	protein-coding gene	gene with protein product		164875	"vav 1 oncogene"	VAV		9438848	Standard	NM_005428		Approved		uc010xjh.2	P15498		ENST00000602142.1:c.2384C>T	chr19.hg19:g.6854009C>T	ENSP00000472929:p.Ala795Val	48.0	0.0	.		38.0	14.0	.	NM_005428	B4DVK9|M0QXX6|Q15860	Missense_Mutation	SNP	ENST00000602142.1	hg19	CCDS12174.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.720792	0.89205	.	.	ENSG00000141968	ENST00000304076;ENST00000539284	T	0.59083	0.29	4.35	4.35	0.52113	Src homology-3 domain (5);	0.000000	0.85682	D	0.000000	T	0.80105	0.4562	M	0.90977	3.165	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;0.999;0.999	D;D;D;D	0.91635	0.998;0.999;0.988;0.981	D	0.84741	0.0751	10	0.66056	D	0.02	.	14.4087	0.67101	0.0:1.0:0.0:0.0	.	698;795;740;795	F5H5P4;B2R8B5;Q96D37;P15498	.;.;.;VAV_HUMAN	V	795;698	ENSP00000443242:A698V	ENSP00000302269:A795V	A	+	2	0	VAV1	6805009	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	6.530000	0.73816	2.278000	0.76064	0.561000	0.74099	GCC	.	.	.	none		0.547	VAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458475.1			T	6854009	C	T	6854009	3	4	37	1	0	0	0	0	1	0	0	0	17143	739	26	2	2486	2	VAV1	19	6854009	Missense_Mutation	SNP	C	TCGA-5P-A9KA-01A-11D-A42J-10		6854009	52274974	84	2678											
C19orf57	79173	hgsc.bcm.edu	37	chr19	14004035	14004035	+	Splice_Site	SNP	A	A	G																															tcctgtttcctcatcaggggAgctatgtaggaaaagataaa																										TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr19:14004035A>G	ENST00000586783.1	-	3	207	c.208T>C	c.(208-210)Tcc>Ccc	p.S70P	C19orf57_ENST00000454313.1_Splice_Site_p.S70P|C19orf57_ENST00000346736.2_Splice_Site_p.S70P|C19orf57_ENST00000591586.1_Splice_Site_p.S70P			Q0VDD7	CS057_HUMAN	chromosome 19 open reading frame 57	70					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)			TCATCAGGGGAGCTATGTAGG	0.587																																					p.S70P		Atlas-SNP	.											.	C19orf57	34	.	0			c.T208C						PASS	.						37	37	37					19																	14004035		2201	4296	6497	SO:0001630	splice_region_variant	79173	exon4			CAGGGGAGCTATG	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.207-1T>C	chr19.hg19:g.14004035A>G		92.0	0.0	.		94.0	32.0	.	NM_024323	Q13411|Q8N825|Q96D63|Q9BU49	Missense_Mutation	SNP	ENST00000586783.1	hg19		.	.	.	.	.	.	.	.	.	.	A	13.17	2.155863	0.38021	.	.	ENSG00000132016	ENST00000454313;ENST00000346736	T;T	0.36878	1.23;1.23	3.65	2.63	0.31362	.	1.390520	0.05098	N	0.486553	T	0.46678	0.1405	L	0.32530	0.975	0.09310	N	1	D	0.76494	0.999	D	0.69479	0.964	T	0.24368	-1.0162	10	0.52906	T	0.07	-2.3155	5.53	0.16978	0.87:0.0:0.13:0.0	.	70	Q0VDD7-2	.	P	70	ENSP00000404382:S70P;ENSP00000254336:S70P	ENSP00000254336:S70P	S	-	1	0	C19orf57	13865035	0.805000	0.28982	0.068000	0.19968	0.011000	0.07611	1.213000	0.32407	0.587000	0.29643	0.459000	0.35465	TCC	.	.	.	none		0.587	C19orf57-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000457947.1	NM_024323	Missense_Mutation	G	14004035	A	G	14004035	5	3	37	1	0	0	0	0	0	0	1	0	1941	318	11	3	1725	3	C19orf57	19	14004035	Splice_Site	SNP	A	TCGA-5P-A9KA-01A-11D-A42J-10	7150026	14004035	45124948	85	2679	34	2									
C19orf57	79173	hgsc.bcm.edu	37	chr19	14004037	14004037	+	Splice_Site	SNP	C	C	T																															ctgtttcctcatcaggggagCtatgtaggaaaagataaaac																										TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr19:14004037C>T	ENST00000586783.1	-	3	206		c.e3-1		C19orf57_ENST00000454313.1_Splice_Site|C19orf57_ENST00000346736.2_Splice_Site|C19orf57_ENST00000591586.1_Splice_Site			Q0VDD7	CS057_HUMAN	chromosome 19 open reading frame 57						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)			ATCAGGGGAGCTATGTAGGAA	0.587																																					.		Atlas-SNP	.											.	C19orf57	34	.	0			c.207-1G>A						PASS	.						37	37	37					19																	14004037		2201	4296	6497	SO:0001630	splice_region_variant	79173	exon5			GGGGAGCTATGTA	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.207-1G>A	chr19.hg19:g.14004037C>T		88.0	0.0	.		93.0	32.0	.	NM_024323	Q13411|Q8N825|Q96D63|Q9BU49	Splice_Site	SNP	ENST00000586783.1	hg19		.	.	.	.	.	.	.	.	.	.	C	9.753	1.167971	0.21621	.	.	ENSG00000132016	ENST00000454313;ENST00000346736	.	.	.	3.41	3.41	0.39046	.	.	.	.	.	.	.	.	.	.	.	0.53005	D	0.999969	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.5024	0.44813	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C19orf57	13865037	1.000000	0.71417	0.114000	0.21550	0.016000	0.09150	2.959000	0.49153	1.917000	0.55516	0.561000	0.74099	.	.	.	.	none		0.587	C19orf57-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000457947.1	NM_024323	Intron	T	14004037	C	T	14004037	5	4	37	1	0	0	0	0	0	0	1	0	1941	811	28	2	1727	2	C19orf57	19	14004037	Splice_Site	SNP	C	TCGA-5P-A9KA-01A-11D-A42J-10	2	14004037	45124946	86	2680	34	2									
ISYNA1	51477	hgsc.bcm.edu	37	chr19	18545729	18545729	+	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	gtgtgaccggggcctcaggtGgtgggcattgggggctcctc	3	9	19	10	1	1	1	1	1	0	0	3	1	2	1	3	7	0	2	3	7	0	1			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr19:18545729G>T	ENST00000338128.8	-	11	1888	c.1671C>A	c.(1669-1671)acC>acA	p.T557T	ISYNA1_ENST00000578963.1_Silent_p.T429T|ISYNA1_ENST00000545187.1_Silent_p.T407T|ISYNA1_ENST00000457269.4_Silent_p.T503T|ISYNA1_ENST00000317018.6_Silent_p.T355T	NM_001170938.1|NM_016368.4	NP_001164409.1|NP_057452.1	Q9NPH2	INO1_HUMAN	inositol-3-phosphate synthase 1	557					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						GGCCTCAGGTGGTGGGCATTG	0.617																																					p.T557T		Atlas-SNP	.											.	ISYNA1	31	.	0			c.C1671A						PASS	.						47	53	51					19																	18545729		2203	4300	6503	SO:0001819	synonymous_variant	51477	exon11			TCAGGTGGTGGGC		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.1671C>A	chr19.hg19:g.18545729G>T		69.0	0.0	.		85.0	29.0	.	NM_016368	B3KRT1|G5E9U0|Q6NXT5|Q7Z525|Q9BT65|Q9H2Y2|Q9NSU0|Q9NVW7	Silent	SNP	ENST00000338128.8	hg19	CCDS12379.1																																																																																			.	.	.	none		0.617	ISYNA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444469.2	NM_016368		T	18545729	G	T	18545729	2	4	37	1	0	0	0	0	0	0	0	1	7874	1335	47	4		4	ISYNA1	19	18545729	Silent	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10	4541692	18545729	40583254	87	2681											
ZNF536	9745	hgsc.bcm.edu	37	chr19	30935607	30935607	+	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	actgctgccagatctgcggcCggcgcttcaaggagccctgg	6	7	14	14	3	2	1	1	0	1	1	2	2	2	2	3	4	4	2	3	4	1	1			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr19:30935607C>A	ENST00000355537.3	+	2	1285	c.1138C>A	c.(1138-1140)Cgg>Agg	p.R380R		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	380					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)					GATCTGCGGCCGGCGCTTCAA	0.597																																					p.R380R		Atlas-SNP	.											.	ZNF536	424	.	0			c.C1138A						PASS	.						66	71	70					19																	30935607		2203	4300	6503	SO:0001819	synonymous_variant	9745	exon2			TGCGGCCGGCGCT		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.1138C>A	chr19.hg19:g.30935607C>A		68.0	0.0	.		82.0	25.0	.	NM_014717	A2RU18	Silent	SNP	ENST00000355537.3	hg19	CCDS32984.1																																																																																			.	.	.	none		0.597	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		A	30935607	C	A	30935607	2	1	37	1	0	0	0	0	0	0	0	1	17986	643	23	4		4	ZNF536	19	30935607	Silent	SNP	C	TCGA-5P-A9KA-01A-11D-A42J-10	12389878	30935607	28193376	88	2682											
ECH1	1891	hgsc.bcm.edu	37	chr19	39321795	39321795	+	Missense_Mutation	SNP	T	T	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	tcgaaatcttgttgaagcacTctaccatctctctgtgaagc	10	13	7	11	1	4	2	0	2	4	0	6	3	4	2	1	0	3	2	1	0	4	3			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr19:39321795T>G	ENST00000221418.4	-	3	504	c.272A>C	c.(271-273)gAg>gCg	p.E91A	ECH1_ENST00000597805.1_5'UTR|AC104534.3_ENST00000594769.1_Missense_Mutation_p.S261R	NM_001398.2	NP_001389.2	Q13011	ECH1_HUMAN	enoyl CoA hydratase 1, peroxisomal	91					fatty acid beta-oxidation (GO:0006635)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	isomerase activity (GO:0016853)|receptor binding (GO:0005102)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	6	all_cancers(60;9.36e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			GTTGAAGCACTCTACCATCTC	0.522																																					p.E91A		Atlas-SNP	.											.	ECH1	14	.	0			c.A272C						PASS	.						131	117	122					19																	39321795		2203	4300	6503	SO:0001583	missense	1891	exon3			AAGCACTCTACCA	U16660	CCDS33014.1	19q13.1	2010-04-30	2010-04-30			ENSG00000104823			3149	protein-coding gene	gene with protein product		600696	"enoyl Coenzyme A hydratase 1, peroxisomal"			7558027	Standard	XM_005258610		Approved	HPXEL		Q13011		ENST00000221418.4:c.272A>C	chr19.hg19:g.39321795T>G	ENSP00000221418:p.Glu91Ala	94.0	0.0	.		76.0	28.0	.	NM_001398	A8K745|Q8WVX0|Q96EZ9	Missense_Mutation	SNP	ENST00000221418.4	hg19	CCDS33014.1	.	.	.	.	.	.	.	.	.	.	T	16.65	3.180975	0.57800	.	.	ENSG00000104823	ENST00000221418	T	0.70045	-0.45	5.73	4.71	0.59529	Crotonase, core (1);	0.403282	0.26631	N	0.023320	T	0.65933	0.2739	N	0.20610	0.595	0.54753	D	0.999986	D;P	0.64830	0.994;0.586	D;P	0.65573	0.936;0.477	T	0.63616	-0.6597	10	0.34782	T	0.22	.	9.8374	0.40977	0.1601:0.0:0.0:0.8399	.	91;91	B4DVS4;Q13011	.;ECH1_HUMAN	A	91	ENSP00000221418:E91A	ENSP00000221418:E91A	E	-	2	0	ECH1	44013635	0.977000	0.34250	0.983000	0.44433	0.956000	0.61745	1.856000	0.39389	0.983000	0.38602	0.533000	0.62120	GAG	.	.	.	none		0.522	ECH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462650.1			G	39321795	T	G	39321795	3	3	37	1	0	0	0	0	1	0	0	0	4894	1551	54	5	746	5	ECH1	19	39321795	Missense_Mutation	SNP	T	TCGA-5P-A9KA-01A-11D-A42J-10	8386188	39321795	19807188	89	2683											
MAP3K10	4294	hgsc.bcm.edu	37	chr19	40721175	40721175	+	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	caagacagcacagtgcccctGtgcggggcccacggctccca	8	4	12	17	2	0	1	0	0	0	1	1	1	1	1	4	3	3	2	4	3	1	0			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr19:40721175G>C	ENST00000253055.3	+	10	3129	c.2841G>C	c.(2839-2841)ctG>ctC	p.L947L		NM_002446.3	NP_002437.2	Q02779	M3K10_HUMAN	mitogen-activated protein kinase kinase kinase 10	947					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|JNK cascade (GO:0007254)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of apoptotic process (GO:0043065)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|bHLH transcription factor binding (GO:0043425)|JUN kinase kinase kinase activity (GO:0004706)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription corepressor activity (GO:0003714)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						CAGTGCCCCTGTGCGGGGCCC	0.701																																					p.L947L		Atlas-SNP	.											.	MAP3K10	70	.	0			c.G2841C						PASS	.						7	5	6					19																	40721175		2053	4054	6107	SO:0001819	synonymous_variant	4294	exon10			GCCCCTGTGCGGG	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.2841G>C	chr19.hg19:g.40721175G>C		115.0	0.0	.		122.0	40.0	.	NM_002446	Q12761|Q14871	Silent	SNP	ENST00000253055.3	hg19	CCDS12549.1																																																																																			.	.	.	none		0.701	MAP3K10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462552.1	NM_002446		C	40721175	G	C	40721175	2	2	37	1	0	0	0	0	0	0	0	1	9251	1364	48	4		4	MAP3K10	19	40721175	Silent	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10	1399380	40721175	18407808	90	2684											
CEACAM5	1048	hgsc.bcm.edu	37	chr19	42219064	42219064	+	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	gtccaatggcaacaggacccTcactctattcaatgtcacaa	13	9	6	13	0	4	0	3	0	1	0	5	1	5	1	2	2	1	1	2	2	5	2			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr19:42219064T>A	ENST00000221992.6	+	3	713	c.599T>A	c.(598-600)cTc>cAc	p.L200H	CEA_ENST00000598976.1_Intron|CEACAM5_ENST00000405816.1_Missense_Mutation_p.L200H|CEACAM5_ENST00000398599.4_Missense_Mutation_p.L200H	NM_004363.2	NP_004354.2	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 5	200	Ig-like 2.				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)		AACAGGACCCTCACTCTATTC	0.517																																					p.L200H		Atlas-SNP	.											.	CEACAM5	84	.	0			c.T599A						PASS	.						184	167	173					19																	42219064		2203	4300	6503	SO:0001583	missense	1048	exon3			GGACCCTCACTCT	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.599T>A	chr19.hg19:g.42219064T>A	ENSP00000221992:p.Leu200His	144.0	0.0	.		138.0	34.0	.	NM_004363	H9KVA7	Missense_Mutation	SNP	ENST00000221992.6	hg19	CCDS12584.1	.	.	.	.	.	.	.	.	.	.	-	7.761	0.705442	0.15172	.	.	ENSG00000105388	ENST00000221992;ENST00000405816	T;T	0.09630	2.96;2.96	2.94	2.94	0.34122	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.44307	0.1287	H	0.97635	4.045	0.24084	N	0.995938	D;B;D	0.89917	1.0;0.277;1.0	D;P;D	0.97110	1.0;0.619;1.0	T	0.37478	-0.9704	9	0.87932	D	0	.	7.7048	0.28644	0.0:0.0:0.0:1.0	.	200;200;200	Q8N4D0;P06731;Q53G30	.;CEAM5_HUMAN;.	H	200	ENSP00000221992:L200H;ENSP00000385072:L200H	ENSP00000221992:L200H	L	+	2	0	CEACAM5	46910904	1.000000	0.71417	0.973000	0.42090	0.044000	0.14063	3.332000	0.52083	1.133000	0.42147	0.164000	0.16699	CTC	.	.	.	none		0.517	CEACAM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321132.2	NM_004363		A	42219064	T	A	42219064	3	1	37	1	0	0	0	0	1	0	0	0	3197	1551	54	5	609	5	CEACAM5	19	42219064	Missense_Mutation	SNP	T	TCGA-5P-A9KA-01A-11D-A42J-10	1497889	42219064	16909919	91	2685											
SYMPK	8189	hgsc.bcm.edu	37	chr19	46324744	46324744	+	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	caaggctgagtttccctcacCtgcagcaggcgggaggaagg	9	6	15	11	1	1	1	1	1	0	0	2	3	2	3	2	5	2	4	2	5	2	1			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr19:46324744C>T	ENST00000245934.7	-	22	3036		c.e22-1		SYMPK_ENST00000598155.1_Splice_Site	NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin						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)		TTTCCCTCACCTGCAGCAGGC	0.557																																					.		Atlas-SNP	.											SYMPK,NS,carcinoma,0,1	SYMPK	104	.	0			c.2792-1G>A						PASS	.						105	83	90					19																	46324744		2203	4300	6503	SO:0001630	splice_region_variant	8189	exon23			CCTCACCTGCAGC	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.2792-1G>A	chr19.hg19:g.46324744C>T		49.0	0.0	.		40.0	14.0	.	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Splice_Site	SNP	ENST00000245934.7	hg19	CCDS12676.2	.	.	.	.	.	.	.	.	.	.	C	14.50	2.553529	0.45487	.	.	ENSG00000125755	ENST00000245934	.	.	.	4.26	4.26	0.50523	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2551	0.66045	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SYMPK	51016584	1.000000	0.71417	1.000000	0.80357	0.302000	0.27658	6.903000	0.75703	2.228000	0.72767	0.555000	0.69702	.	.	.	.	none		0.557	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819	Intron	T	46324744	C	T	46324744	5	4	37	1	0	0	0	0	0	0	1	0	15451	695	24	2	1057	2	SYMPK	19	46324744	Splice_Site	SNP	C	TCGA-5P-A9KA-01A-11D-A42J-10	4105680	46324744	12804239	92	2686											
PPP5C	5536	hgsc.bcm.edu	37	chr19	46888119	46888119	+	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	tgtagaagtgatcctcacccTtttcggcttcaagctcctgt	7	14	8	12	1	2	2	2	1	0	1	5	2	4	2	3	1	1	3	3	1	3	4			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr19:46888119T>A	ENST00000012443.4	+	7	960	c.857T>A	c.(856-858)cTt>cAt	p.L286H	PPP5C_ENST00000391919.1_Missense_Mutation_p.L158H|AC007193.9_ENST00000599645.1_RNA	NM_006247.3	NP_006238.1	P53041	PPP5_HUMAN	protein phosphatase 5, catalytic subunit	286	Catalytic.				cell death (GO:0008219)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein dephosphorylation (GO:0006470)|protein heterooligomerization (GO:0051291)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|RNA binding (GO:0003723)|signal transducer activity (GO:0004871)			endometrium(4)|kidney(1)|large_intestine(5)|liver(2)|lung(4)|ovary(1)|pancreas(1)	18		Ovarian(192;0.0731)|all_neural(266;0.196)		OV - Ovarian serous cystadenocarcinoma(262;0.000196)|all cancers(93;0.00192)|GBM - Glioblastoma multiforme(486;0.0499)|Epithelial(262;0.0504)		ATCCTCACCCTTTTCGGCTTC	0.527																																					p.L286H		Atlas-SNP	.											PPP5C,bladder,carcinoma,0,1	PPP5C	44	.	0			c.T857A						PASS	.						130	108	116					19																	46888119		2203	4300	6503	SO:0001583	missense	5536	exon7			TCACCCTTTTCGG		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.857T>A	chr19.hg19:g.46888119T>A	ENSP00000012443:p.Leu286His	56.0	0.0	.		67.0	14.0	.	NM_006247	Q16722|Q53XV2	Missense_Mutation	SNP	ENST00000012443.4	hg19	CCDS12684.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.336873	0.81801	.	.	ENSG00000011485	ENST00000012443;ENST00000451918;ENST00000391919	T;T	0.14144	2.53;2.53	4.59	4.59	0.56863	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (2);Metallophosphoesterase domain (1);	0.144822	0.46758	D	0.000266	T	0.59197	0.2176	H	0.99937	4.99	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.996;0.999	T	0.77413	-0.2597	10	0.87932	D	0	-8.0808	11.9499	0.52948	0.0:0.0:0.0:1.0	.	144;286;286	B7Z1I1;B2R6R6;P53041	.;.;PPP5_HUMAN	H	286;273;158	ENSP00000012443:L286H;ENSP00000375786:L158H	ENSP00000012443:L286H	L	+	2	0	PPP5C	51579959	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.482000	0.81143	1.706000	0.51276	0.402000	0.26972	CTT	.	.	.	none		0.527	PPP5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258969.2	NM_006247		A	46888119	T	A	46888119	3	1	37	1	0	0	0	0	1	0	0	0	12416	1609	56	5	883	5	PPP5C	19	46888119	Missense_Mutation	SNP	T	TCGA-5P-A9KA-01A-11D-A42J-10	563375	46888119	12240864	93	2687											
CD33	945	hgsc.bcm.edu	37	chr19	51728819	51728820	+	Frame_Shift_Ins	INS	-	-	T																															agaggaagtaccaaatacagINSttacaaatctccccagctct																								rs267605608|rs34919259	byFrequency	TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr19:51728819_51728820insT	ENST00000262262.4	+	2	404_405	c.383_384insT	c.(382-387)agttacfs	p.Y129fs	CD33_ENST00000391796.3_Frame_Shift_Ins_p.Y129fs|CD33_ENST00000436584.2_Intron|CD33_ENST00000421133.2_Intron	NM_001772.3	NP_001763.3	P20138	CD33_HUMAN	CD33 molecule	129	Ig-like V-type.				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)	ACCAAATACAGTTACAAATCTC	0.53																																					p.S128fs		Atlas-Indel,Pindel	.											.	CD33	55	.	0			c.383_384insT						PASS	.																																			SO:0001589	frameshift_variant	945	exon2			.	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.385dupT	chr19.hg19:g.51728821_51728821dupT	ENSP00000262262:p.Tyr129fs	111.0	0.0	0		120.0	35.0	0.291667	NM_001177608	B4E3P8|C9JEN7|F8WAL2|Q8TD24	Frame_Shift_Ins	INS	ENST00000262262.4	hg19	CCDS33084.1																																																																																			.	.	.	none		0.53	CD33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464199.2	NM_001772		T	51728820	-	T	51728819	7	5	37	1	0	1	1	0	0	0	0	0	3007	1029	36	0	389	0	CD33	19	51728819	Frame_Shift_Ins	INS	-	TCGA-5P-A9KA-01A-11D-A42J-10	4840700	51728819	7400164	94	2688											
PPP2R1A	5518	hgsc.bcm.edu	37	chr19	52719042	52719042	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgtctgcagctccagaaagCagtggggcctgagatcacca	10	7	12	12	0	2	2	1	1	1	2	3	3	3	2	3	2	3	3	3	2	1	0			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr19:52719042C>T	ENST00000322088.6	+	7	876	c.818C>T	c.(817-819)gCa>gTa	p.A273V	PPP2R1A_ENST00000462990.1_Missense_Mutation_p.A94V|PPP2R1A_ENST00000444322.2_Missense_Mutation_p.A218V	NM_014225.5	NP_055040.2	P30153	2AAA_HUMAN	protein phosphatase 2, regulatory subunit A, alpha	273	PP2A subunit B binding.|Polyoma small and medium T antigens Binding.				apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|chromosome segregation (GO:0007059)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|inactivation of MAPK activity (GO:0000188)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|negative regulation of cell growth (GO:0030308)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine dephosphorylation (GO:0070262)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein complex assembly (GO:0006461)|protein dephosphorylation (GO:0006470)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of DNA replication (GO:0006275)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|response to organic substance (GO:0010033)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|second-messenger-mediated signaling (GO:0019932)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	antigen binding (GO:0003823)|protein heterodimerization activity (GO:0046982)|protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			NS(1)|breast(4)|cervix(2)|endometrium(62)|kidney(1)|large_intestine(7)|lung(21)|ovary(32)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	135				GBM - Glioblastoma multiforme(134;0.00456)|OV - Ovarian serous cystadenocarcinoma(262;0.015)		CTCCAGAAAGCAGTGGGGCCT	0.577			Mis		clear cell ovarian carcinoma																																p.A273V		Atlas-SNP	.		Dom?	yes		19	19q13.41	5518	"protein phosphatase 2, regulatory subunit A, alpha"		E	.	PPP2R1A	187	.	0			c.C818T						PASS	.						60	59	60					19																	52719042		2203	4300	6503	SO:0001583	missense	5518	exon7			AGAAAGCAGTGGG		CCDS12849.1	19q13	2010-06-18	2010-04-14		ENSG00000105568	ENSG00000105568	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9302	protein-coding gene	gene with protein product	"protein phosphatase 2A, regulatory subunit A, alpha isoform", "protein phosphatase 2, 65kDa regulatory subunit A"	605983	"protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), alpha isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit A, alpha isoform"				Standard	NR_033500		Approved	PR65A, PP2A-Aalpha	uc002pyp.3	P30153	OTTHUMG00000137367	ENST00000322088.6:c.818C>T	chr19.hg19:g.52719042C>T	ENSP00000324804:p.Ala273Val	73.0	0.0	.		77.0	27.0	.	NM_014225	Q13773|Q6ICQ3|Q96DH3	Missense_Mutation	SNP	ENST00000322088.6	hg19	CCDS12849.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.975313	0.74360	.	.	ENSG00000105568	ENST00000423369;ENST00000391791;ENST00000322088;ENST00000444322	T;T	0.04234	3.67;3.67	4.67	4.67	0.58626	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000006	T	0.07818	0.0196	M	0.71581	2.175	0.80722	D	1	P;B;B	0.40144	0.704;0.012;0.012	B;B;B	0.33196	0.159;0.007;0.007	T	0.10753	-1.0616	10	0.49607	T	0.09	-6.7782	15.501	0.75698	0.0:1.0:0.0:0.0	.	218;273;273	F5H3X9;A8K7B7;P30153	.;.;2AAA_HUMAN	V	263;193;273;218	ENSP00000324804:A273V;ENSP00000415067:A218V	ENSP00000324804:A273V	A	+	2	0	PPP2R1A	57410854	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.796000	0.75145	2.595000	0.87683	0.655000	0.94253	GCA	.	.	.	none		0.577	PPP2R1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000267967.2	NM_014225		T	52719042	C	T	52719042	3	4	37	1	0	0	0	0	1	0	0	0	12392	710	25	2	844	2	PPP2R1A	19	52719042	Missense_Mutation	SNP	C	TCGA-5P-A9KA-01A-11D-A42J-10	990223	52719042	6409941	95	2689											
SDCBP2	27111	hgsc.bcm.edu	37	chr20	1293357	1293357	+	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	gctggtccccaaagcgcagcCccacaagggatgcaggggtg	9	4	15	13	1	0	0	0	0	0	0	1	1	1	1	4	4	3	3	4	4	2	0			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr20:1293357C>A	ENST00000360779.3	-	6	607	c.434G>T	c.(433-435)gGg>gTg	p.G145V	SDCBP2_ENST00000339987.3_Missense_Mutation_p.G145V|SDCBP2_ENST00000467129.1_5'Flank|SDCBP2_ENST00000381812.1_Missense_Mutation_p.G145V|SDCBP2_ENST00000381808.3_Missense_Mutation_p.G60V	NM_080489.4	NP_536737.3	Q9H190	SDCB2_HUMAN	syndecan binding protein (syntenin) 2	145	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(3)|lung(1)|skin(1)|stomach(1)	7						AAAGCGCAGCCCCACAAGGGA	0.637																																					p.G145V		Atlas-SNP	.											.	SDCBP2	78	.	0			c.G434T						PASS	.						55	52	53					20																	1293357		2203	4300	6503	SO:0001583	missense	27111	exon6			CGCAGCCCCACAA	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.434G>T	chr20.hg19:g.1293357C>A	ENSP00000354013:p.Gly145Val	43.0	0.0	.		49.0	19.0	.	NM_080489	O95892|Q5W0X1|Q9BZ42|Q9H567|Q9NRY8	Missense_Mutation	SNP	ENST00000360779.3	hg19	CCDS42848.1	.	.	.	.	.	.	.	.	.	.	c	14.90	2.672885	0.47781	.	.	ENSG00000125775	ENST00000381812;ENST00000381808;ENST00000360779;ENST00000339987	D;D;D;D	0.84070	-1.8;-1.8;-1.8;-1.8	4.51	3.56	0.40772	PDZ/DHR/GLGF (4);	0.126644	0.53938	D	0.000055	D	0.93631	0.7966	H	0.96633	3.855	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.95321	0.8420	10	0.87932	D	0	-8.1802	13.8898	0.63731	0.1538:0.8462:0.0:0.0	.	145	Q9H190	SDCB2_HUMAN	V	145;60;145;145	ENSP00000371233:G145V;ENSP00000371229:G60V;ENSP00000354013:G145V;ENSP00000342935:G145V	ENSP00000342935:G145V	G	-	2	0	SDCBP2	1241357	1.000000	0.71417	0.988000	0.46212	0.165000	0.22458	7.545000	0.82128	1.212000	0.43366	-0.314000	0.08810	GGG	.	.	.	none		0.637	SDCBP2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077513.2	NM_080489		A	1293357	C	A	1293357	3	1	37	1	0	0	0	0	1	0	0	0	13969	623	22	4	460	4	SDCBP2	20	1293357	Missense_Mutation	SNP	C	TCGA-5P-A9KA-01A-11D-A42J-10		1293357	61732163	96	2690											
EMILIN3	90187	hgsc.bcm.edu	37	chr20	39990966	39990966	+	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	cgtaagctcatccccggccgGggcaccggggcccctttggg	4	6	15	16	4	1	0	1	0	0	0	2	0	2	0	6	6	1	3	6	6	1	2			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr20:39990966G>T	ENST00000332312.3	-	4	1435	c.1243C>A	c.(1243-1245)Ccg>Acg	p.P415T		NM_052846.1	NP_443078.1	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	415						cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)				biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(3)|urinary_tract(2)	30		Myeloproliferative disorder(115;0.00425)				TCCCCGGCCGGGGCACCGGGG	0.652																																					p.P415T		Atlas-SNP	.											.	EMILIN3	63	.	0			c.C1243A						PASS	.						42	48	46					20																	39990966		2203	4300	6503	SO:0001583	missense	90187	exon4			CGGCCGGGGCACC	AL031667	CCDS13316.1	20q12	2005-11-06	2004-03-02	2004-03-02	ENSG00000183798	ENSG00000183798		"EMI domain containing"	16123	protein-coding gene	gene with protein product	"chromosome 20 open reading frame 130"	608929	"elastin microfibril interfacer 5"	C20orf130, EMILIN5		12221002	Standard	NM_052846		Approved	dJ620E11.4	uc002xjy.1	Q9NT22	OTTHUMG00000046304	ENST00000332312.3:c.1243C>A	chr20.hg19:g.39990966G>T	ENSP00000332806:p.Pro415Thr	49.0	0.0	.		51.0	18.0	.	NM_052846	Q495S5|Q495S6|Q495S7|Q76KT4	Missense_Mutation	SNP	ENST00000332312.3	hg19	CCDS13316.1	.	.	.	.	.	.	.	.	.	.	G	0.009	-1.832401	0.00579	.	.	ENSG00000183798	ENST00000332312	T	0.13089	2.62	5.14	0.703	0.18116	.	1.249350	0.05414	N	0.543007	T	0.12008	0.0292	L	0.44542	1.39	0.09310	N	1	B	0.15141	0.012	B	0.11329	0.006	T	0.36890	-0.9729	9	.	.	.	-1.804	4.9083	0.13809	0.0688:0.1239:0.4241:0.3832	.	415	Q9NT22	EMIL3_HUMAN	T	415	ENSP00000332806:P415T	.	P	-	1	0	EMILIN3	39424380	0.293000	0.24371	0.000000	0.03702	0.005000	0.04900	2.297000	0.43593	0.181000	0.19994	-0.264000	0.10439	CCG	.	.	.	none		0.652	EMILIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106876.2	XM_029741		T	39990966	G	T	39990966	3	4	37	1	0	0	0	0	1	0	0	0	5097	1232	43	4	1061	4	EMILIN3	20	39990966	Missense_Mutation	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10	38697609	39990966	23034554	97	2691											
SIK1	150094	hgsc.bcm.edu	37	chr21	44838412	44838412	+	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	ttgccgtggtggagggggagAcgactatacctgtgggggga	7	8	20	6	2	0	1	0	0	0	1	0	5	0	3	2	7	2	0	2	7	2	3			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr21:44838412A>T	ENST00000270162.6	-	12	1604	c.1472T>A	c.(1471-1473)gTc>gAc	p.V491D		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	491					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)	GGAGGGGGAGACGACTATACC	0.637																																					p.V491D		Atlas-SNP	.											.	SIK1	65	.	0			c.T1472A						PASS	.						27	30	29					21																	44838412		2202	4300	6502	SO:0001583	missense	150094	exon12			GGGGAGACGACTA	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.1472T>A	chr21.hg19:g.44838412A>T	ENSP00000270162:p.Val491Asp	92.0	0.0	.		90.0	23.0	.	NM_173354	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Missense_Mutation	SNP	ENST00000270162.6	hg19	CCDS33575.1	.	.	.	.	.	.	.	.	.	.	A	13.46	2.245017	0.39697	.	.	ENSG00000142178	ENST00000270162	T	0.73575	-0.76	4.79	4.79	0.61399	.	0.429630	0.24920	N	0.034556	T	0.67998	0.2953	L	0.50333	1.59	0.21553	N	0.999647	P	0.46395	0.877	B	0.38562	0.276	T	0.64896	-0.6299	10	0.49607	T	0.09	.	14.3387	0.66608	1.0:0.0:0.0:0.0	.	491	P57059	SIK1_HUMAN	D	491	ENSP00000270162:V491D	ENSP00000270162:V491D	V	-	2	0	SIK1	43662840	1.000000	0.71417	0.004000	0.12327	0.159000	0.22180	5.993000	0.70616	1.790000	0.52503	0.533000	0.62120	GTC	.	.	.	none		0.637	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354		T	44838412	A	T	44838412	3	4	37	1	0	0	0	0	1	0	0	0	14330	275	10	5	891	5	SIK1	21	44838412	Missense_Mutation	SNP	A	TCGA-5P-A9KA-01A-11D-A42J-10		44838412	3291483	98	2692											
TST	7263	hgsc.bcm.edu	37	chr22	37407323	37407323	+	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	tcctcagtcaggaagtccatGaaaggcatgttgacggcacc	11	8	11	11	1	2	2	2	2	0	0	4	3	4	3	3	3	0	3	3	3	2	1			TCGA-5P-A9KA-01A-11D-A42J-10	TCGA-5P-A9KA-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1e5c321a-1ec5-43d8-a9ce-dea256ce836f	88f8e541-dd2d-4548-bad0-c30265b48b79	g.chr22:37407323G>T	ENST00000403892.3	-	2	1373	c.639C>A	c.(637-639)ttC>ttA	p.F213L	Y_RNA_ENST00000516603.1_RNA|TST_ENST00000249042.3_Missense_Mutation_p.F213L	NM_001270483.1	NP_001257412.1	Q16762	THTR_HUMAN	thiosulfate sulfurtransferase (rhodanese)	213	Rhodanese 2. {ECO:0000255|PROSITE- ProRule:PRU00173}.				cellular nitrogen compound metabolic process (GO:0034641)|cyanate catabolic process (GO:0009440)|epithelial cell differentiation (GO:0030855)|rRNA import into mitochondrion (GO:0035928)|rRNA transport (GO:0051029)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	5S rRNA binding (GO:0008097)|thiosulfate sulfurtransferase activity (GO:0004792)			kidney(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)|urinary_tract(1)	7						GGAAGTCCATGAAAGGCATGT	0.582																																					p.F213L		Atlas-SNP	.											.	TST	22	.	0			c.C639A						PASS	.						55	45	49					22																	37407323		2203	4300	6503	SO:0001583	missense	7263	exon3			GTCCATGAAAGGC	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.639C>A	chr22.hg19:g.37407323G>T	ENSP00000385828:p.Phe213Leu	97.0	0.0	.		100.0	41.0	.	NM_003312	B3KRM1|Q6IB06	Missense_Mutation	SNP	ENST00000403892.3	hg19	CCDS13938.1	.	.	.	.	.	.	.	.	.	.	G	17.81	3.481640	0.63849	.	.	ENSG00000128311	ENST00000403892;ENST00000249042;ENST00000413912	T;T	0.38240	1.15;1.15	5.08	4.07	0.47477	Rhodanese-like (5);	0.000000	0.85682	D	0.000000	T	0.52980	0.1768	M	0.75447	2.3	0.58432	D	0.999997	P	0.50943	0.94	P	0.62014	0.897	T	0.53669	-0.8406	10	0.51188	T	0.08	-4.9919	8.164	0.31215	0.289:0.0:0.711:0.0	.	213	Q16762	THTR_HUMAN	L	213	ENSP00000385828:F213L;ENSP00000249042:F213L	ENSP00000249042:F213L	F	-	3	2	TST	35737269	0.999000	0.42202	0.977000	0.42913	0.767000	0.43475	2.480000	0.45206	1.366000	0.46076	0.655000	0.94253	TTC	.	.	.	none		0.582	TST-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318790.1			T	37407323	G	T	37407323	3	4	37	1	0	0	0	0	1	0	0	0	16685	1281	45	4	258	4	TST	22	37407323	Missense_Mutation	SNP	G	TCGA-5P-A9KA-01A-11D-A42J-10		37407323	13897243	99	2693											
MTOR	2475	hgsc.bcm.edu	37	chr1	11269473	11269473	+	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	actcctaagcatccgatgctGgtaaatcaaaggatcctcct	12	10	7	12	1	1	0	1	0	0	0	5	2	5	1	4	2	2	3	4	2	4	2			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr1:11269473G>T	ENST00000361445.4	-	25	3773	c.3697C>A	c.(3697-3699)Cag>Aag	p.Q1233K		NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	1233					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)	ATCCGATGCTGGTAAATCAAA	0.468																																					p.Q1233K		Atlas-SNP	.											.	MTOR	327	.	0			c.C3697A						PASS	.						260	247	251					1																	11269473		2203	4300	6503	SO:0001583	missense	2475	exon25			GATGCTGGTAAAT	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.3697C>A	chr1.hg19:g.11269473G>T	ENSP00000354558:p.Gln1233Lys	63.0	0.0	.		77.0	4.0	.	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	hg19	CCDS127.1	.	.	.	.	.	.	.	.	.	.	G	11.31	1.601119	0.28534	.	.	ENSG00000198793	ENST00000361445;ENST00000539766	T	0.66638	-0.22	5.78	5.78	0.91487	Armadillo-type fold (1);	0.202762	0.43919	D	0.000504	T	0.57169	0.2035	L	0.36672	1.1	0.80722	D	1	B	0.13594	0.008	B	0.14578	0.011	T	0.55082	-0.8196	10	0.07175	T	0.84	.	19.9981	0.97395	0.0:0.0:1.0:0.0	.	1233	P42345	MTOR_HUMAN	K	1233	ENSP00000354558:Q1233K	ENSP00000354558:Q1233K	Q	-	1	0	MTOR	11192060	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.599000	0.82757	2.733000	0.93635	0.561000	0.74099	CAG	.	.	.	none		0.468	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		T	11269473	G	T	11269473	3	4	38	1	0	0	0	0	1	0	0	0	9961	1357	47	4	4088	4	MTOR	1	11269473	Missense_Mutation	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10		11269473	237981148	1	2694											
FAM131C	348487	hgsc.bcm.edu	37	chr1	16388654	16388654	+	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	gccggggcgggatctggagtCggacaggtagccgttggtgg	5	7	21	8	4	1	0	0	0	1	0	2	3	1	3	2	8	1	2	2	8	1	2	rs374242693		TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr1:16388654C>T	ENST00000375662.4	-	4	391	c.208G>A	c.(208-210)Gac>Aac	p.D70N	FAM131C_ENST00000494078.1_5'UTR	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	70								p.D70N(1)		large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		GATCTGGAGTCGGACAGGTAG	0.652																																					p.D70N		Atlas-SNP	.											FAM131C,caecum,carcinoma,0,1	FAM131C	21	.	1	Substitution - Missense(1)	large_intestine(1)	c.G208A						PASS	.	C	ASN/ASP	0,4104		0,0,2052	77	78	78		208	0.4	1	1		78	2,8368		0,2,4183	no	missense	FAM131C	NM_182623.2	23	0,2,6235	TT,TC,CC		0.0239,0.0,0.016	benign	70/281	16388654	2,12472	2052	4185	6237	SO:0001583	missense	348487	exon4			TGGAGTCGGACAG		CCDS41270.1	1p36.13	2008-02-05	2007-03-20	2007-03-20	ENSG00000185519	ENSG00000185519			26717	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 117"	C1orf117		12477932	Standard	NM_182623		Approved	FLJ36766	uc001axz.4	Q96AQ9	OTTHUMG00000009525	ENST00000375662.4:c.208G>A	chr1.hg19:g.16388654C>T	ENSP00000364814:p.Asp70Asn	119.0	0.0	.		103.0	15.0	.	NM_182623	Q5T5Q5|Q8N3X3|Q8N9P9	Missense_Mutation	SNP	ENST00000375662.4	hg19	CCDS41270.1	.	.	.	.	.	.	.	.	.	.	C	11.83	1.755733	0.31046	0.0	2.39E-4	ENSG00000185519	ENST00000375662	T	0.15256	2.44	4.64	0.426	0.16479	.	0.428262	0.22187	N	0.063432	T	0.13670	0.0331	L	0.60455	1.87	0.29394	N	0.862426	B	0.21309	0.054	B	0.12156	0.007	T	0.11036	-1.0604	10	0.37606	T	0.19	.	4.7214	0.12920	0.0:0.5558:0.1572:0.287	.	70	Q96AQ9	F131C_HUMAN	N	70	ENSP00000364814:D70N	ENSP00000364814:D70N	D	-	1	0	FAM131C	16261241	0.075000	0.21258	0.966000	0.40874	0.854000	0.48673	0.068000	0.14531	0.057000	0.16193	-0.379000	0.06801	GAC	.	.	.	none		0.652	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623		T	16388654	C	T	16388654	3	4	38	1	0	0	0	0	1	0	0	0	5445	884	31	1	650	1	FAM131C	1	16388654	Missense_Mutation	SNP	C	TCGA-5P-A9KC-01A-11D-A42J-10	5119181	16388654	232861967	2	2695											
HP1BP3	50809	hgsc.bcm.edu	37	chr1	21091954	21091954	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttctttaggttcacaaaggCgagtaaaggccagtgggagg	11	9	14	7	1	2	0	1	0	1	0	2	2	2	1	1	5	0	2	1	5	4	5			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr1:21091954C>T	ENST00000312239.5	-	8	945	c.806G>A	c.(805-807)cGc>cAc	p.R269H	HP1BP3_ENST00000375003.2_Missense_Mutation_p.R117H	NM_016287.3	NP_057371.2	Q5SSJ5	HP1B3_HUMAN	heterochromatin protein 1, binding protein 3	269	H15 2. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)	nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|prostate(2)|skin(2)|urinary_tract(1)	16		all_lung(284;6.55e-06)|Lung NSC(340;6.59e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.26e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00015)|GBM - Glioblastoma multiforme(114;0.000521)|Kidney(64;0.000529)|STAD - Stomach adenocarcinoma(196;0.00311)|KIRC - Kidney renal clear cell carcinoma(64;0.00687)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.201)		TTCACAAAGGCGAGTAAAGGC	0.418																																					p.R269H		Atlas-SNP	.											.	HP1BP3	47	.	0			c.G806A						PASS	.						123	118	120					1																	21091954		2203	4300	6503	SO:0001583	missense	50809	exon8			CAAAGGCGAGTAA	BC053327	CCDS30621.1	1p36.12	2008-02-05			ENSG00000127483	ENSG00000127483			24973	protein-coding gene	gene with protein product						12477932	Standard	NM_016287		Approved	HP1-BP74	uc001bdw.1	Q5SSJ5	OTTHUMG00000002622	ENST00000312239.5:c.806G>A	chr1.hg19:g.21091954C>T	ENSP00000312625:p.Arg269His	102.0	0.0	.		117.0	35.0	.	NM_016287	A6NI71|A8K5D7|B3KMZ8|B4E210|Q05BI0|Q5SSJ6|Q5SWC6|Q6PIM9|Q8NDF0|Q9UHY0	Missense_Mutation	SNP	ENST00000312239.5	hg19	CCDS30621.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.599025	0.87055	.	.	ENSG00000127483	ENST00000312239;ENST00000375004;ENST00000375003;ENST00000419948;ENST00000438032;ENST00000424732	T;T;T;T;T	0.22336	1.98;1.98;1.98;1.98;1.96	6.1	5.19	0.71726	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.045842	0.85682	D	0.000000	T	0.40094	0.1103	L	0.48362	1.52	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.69824	0.966;0.945	T	0.26018	-1.0115	10	0.87932	D	0	-0.8069	15.6469	0.77063	0.0:0.9343:0.0:0.0657	.	231;269	Q5SSJ5-2;Q5SSJ5	.;HP1B3_HUMAN	H	269;231;117;128;269;231	ENSP00000312625:R269H;ENSP00000364142:R117H;ENSP00000391721:R128H;ENSP00000403039:R269H;ENSP00000402754:R231H	ENSP00000312625:R269H	R	-	2	0	HP1BP3	20964541	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.997000	0.70646	1.593000	0.50029	0.650000	0.86243	CGC	.	.	.	none		0.418	HP1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007457.2	NM_016287		T	21091954	C	T	21091954	3	4	38	1	0	0	0	0	1	0	0	0	7335	768	27	1	879	1	HP1BP3	1	21091954	Missense_Mutation	SNP	C	TCGA-5P-A9KC-01A-11D-A42J-10	4703300	21091954	228158667	3	2696											
COL8A2	1296	hgsc.bcm.edu	37	chr1	36564328	36564328	+	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	cccttggggcctggcagtccTggcatcccatagccagtggg	5	8	14	14	0	0	0	0	0	0	0	2	0	2	0	5	5	1	2	5	5	1	2			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr1:36564328T>G	ENST00000397799.1	-	4	1178	c.954A>C	c.(952-954)ccA>ccC	p.P318P	COL8A2_ENST00000303143.4_Silent_p.P318P|COL8A2_ENST00000481785.1_Silent_p.P253P			P25067	CO8A2_HUMAN	collagen, type VIII, alpha 2	318	Triple-helical region.				angiogenesis (GO:0001525)|camera-type eye morphogenesis (GO:0048593)|collagen catabolic process (GO:0030574)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			NS(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CTGGCAGTCCTGGCATCCCAT	0.716																																					p.P318P		Atlas-SNP	.											.	COL8A2	41	.	0			c.A954C						PASS	.						10	12	12					1																	36564328		2039	4085	6124	SO:0001819	synonymous_variant	1296	exon2			CAGTCCTGGCATC	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.954A>C	chr1.hg19:g.36564328T>G		75.0	0.0	.		82.0	21.0	.	NM_005202	Q5JV31|Q8TEJ5	Silent	SNP	ENST00000397799.1	hg19	CCDS403.1																																																																																			.	.	.	none		0.716	COL8A2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313674.1	NM_005202		G	36564328	T	G	36564328	2	3	38	1	0	0	0	0	0	0	0	1	3708	1567	55	5		5	COL8A2	1	36564328	Silent	SNP	T	TCGA-5P-A9KC-01A-11D-A42J-10	15472374	36564328	212686293	4	2697											
TYW3	127253	hgsc.bcm.edu	37	chr1	75199100	75199100	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgcatcctactccttgacCgggtgaggcccctttgcgcc	4	9	11	17	3	0	2	0	2	0	0	2	2	2	2	7	2	2	1	7	2	1	3			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr1:75199100C>T	ENST00000370867.3	+	1	261	c.172C>T	c.(172-174)Cgg>Tgg	p.R58W	CRYZ_ENST00000370872.3_5'Flank|CRYZ_ENST00000417775.1_5'Flank|CRYZ_ENST00000340866.5_5'Flank|TYW3_ENST00000457880.2_Missense_Mutation_p.R58W|CRYZ_ENST00000370871.3_5'Flank|TYW3_ENST00000421739.2_Missense_Mutation_p.R58W|TYW3_ENST00000479111.1_5'UTR	NM_138467.2	NP_612476.1	Q6IPR3	TYW3_HUMAN	tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)	58					tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)	p.R58W(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|ovary(2)|prostate(1)|skin(1)	15						ACTCCTTGACCGGGTGAGGCC	0.567																																					p.R58W		Atlas-SNP	.											TYW3,NS,carcinoma,0,1	TYW3	36	.	1	Substitution - Missense(1)	prostate(1)	c.C172T						PASS	.						74	65	68					1																	75199100		2203	4300	6503	SO:0001583	missense	127253	exon1			CTTGACCGGGTGA	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.172C>T	chr1.hg19:g.75199100C>T	ENSP00000359904:p.Arg58Trp	47.0	0.0	.		62.0	3.0	.	NM_001162916	B4DSP9|E9PGR7|Q5HYJ0|Q8N7L1	Missense_Mutation	SNP	ENST00000370867.3	hg19	CCDS666.1	.	.	.	.	.	.	.	.	.	.	C	14.95	2.689848	0.48097	.	.	ENSG00000162623	ENST00000457880;ENST00000370867;ENST00000421739	T;T	0.30981	1.51;1.51	5.03	2.11	0.27256	tRNA wybutosine-synthesizing protein (2);	0.702089	0.14447	N	0.318982	T	0.23532	0.0569	L	0.50333	1.59	0.24118	N	0.995819	D;D;D	0.63046	0.99;0.992;0.989	B;P;P	0.49301	0.417;0.498;0.606	T	0.13019	-1.0525	10	0.72032	D	0.01	-0.7708	16.5745	0.84633	0.0:0.5347:0.4653:0.0	.	58;58;58	B4DFU6;E9PGR7;Q6IPR3	.;.;TYW3_HUMAN	W	58	ENSP00000407025:R58W;ENSP00000359904:R58W	ENSP00000359904:R58W	R	+	1	2	TYW3	74971688	0.849000	0.29639	0.878000	0.34440	0.268000	0.26511	0.521000	0.22893	0.288000	0.22398	-0.228000	0.12330	CGG	.	.	.	none		0.567	TYW3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026573.1	NM_138467		T	75199100	C	T	75199100	3	4	38	1	0	0	0	0	1	0	0	0	16832	643	23	1	174	1	TYW3	1	75199100	Missense_Mutation	SNP	C	TCGA-5P-A9KC-01A-11D-A42J-10	38634772	75199100	174051521	5	2698											
GDAP2	54834	hgsc.bcm.edu	37	chr1	118420722	118420723	+	Frame_Shift_Ins	INS	-	-	T																															gaggctgtccacatggtggaINSttttgtccttcagtcctgag																										TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr1:118420722_118420723insT	ENST00000369443.5	-	13	1603_1604	c.1354_1355insA	c.(1354-1356)atcfs	p.I452fs	GDAP2_ENST00000369442.3_Frame_Shift_Ins_p.I452fs	NM_017686.3	NP_060156.1	Q9NXN4	GDAP2_HUMAN	ganglioside induced differentiation associated protein 2	452	CRAL-TRIO.				response to retinoic acid (GO:0032526)	lysosomal membrane (GO:0005765)				kidney(2)|large_intestine(3)|lung(9)|ovary(2)	16		all_cancers(81;0.0156)|all_lung(203;5.81e-05)|Lung NSC(69;0.000446)|all_epithelial(167;0.00295)		Lung(183;0.0583)|LUSC - Lung squamous cell carcinoma(189;0.194)		CACATGGTGGATTTTGTCCTTC	0.401																																					p.I452fs		Atlas-Indel,Pindel	.											.	GDAP2	37	.	0			c.1355_1356insA						PASS	.																																			SO:0001589	frameshift_variant	54834	exon13			.	AK000149	CCDS897.1, CCDS44201.1	1q11	2011-10-20			ENSG00000196505	ENSG00000196505			18010	protein-coding gene	gene with protein product						1021725	Standard	NM_017686		Approved	FLJ20142, dJ776P7.1, MACROD3	uc001ehf.3	Q9NXN4	OTTHUMG00000012199	ENST00000369443.5:c.1355dupA	chr1.hg19:g.118420726_118420726dupT	ENSP00000358451:p.Ile452fs	144.0	0.0	0		160.0	49.0	0.30625	NM_017686	Q96DZ0	Frame_Shift_Ins	INS	ENST00000369443.5	hg19	CCDS897.1																																																																																			.	.	.	none		0.401	GDAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033732.2	NM_017686		T	118420723	-	T	118420722	7	5	38	1	0	1	1	0	0	0	0	0	6316	333	12	0	191	0	GDAP2	1	118420722	Frame_Shift_Ins	INS	-	TCGA-5P-A9KC-01A-11D-A42J-10	43221622	118420722	130829899	6	2699											
PSMD4	5710	hgsc.bcm.edu	37	chr1	151238063	151238063	+	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	tgaatttggagtagatcccaGtgctgatcctgagctggcct	8	12	12	9	0	0	4	0	3	0	1	2	5	2	5	3	2	2	3	3	2	2	2			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr1:151238063G>T	ENST00000368884.3	+	6	712	c.632G>T	c.(631-633)aGt>aTt	p.S211I	PSMD4_ENST00000368881.4_Missense_Mutation_p.S211I	NM_002810.2	NP_002801.1	P55036	PSMD4_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 4	211					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle, base subcomplex (GO:0008540)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|lung(7)	11	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			GTAGATCCCAGTGCTGATCCT	0.507																																					p.S211I		Atlas-SNP	.											.	PSMD4	27	.	0			c.G632T						PASS	.						84	76	79					1																	151238063		2203	4300	6503	SO:0001583	missense	5710	exon6			ATCCCAGTGCTGA	U51007	CCDS991.1	1q21.2	2008-05-22			ENSG00000159352	ENSG00000159352		"Proteasome (prosome, macropain) subunits"	9561	protein-coding gene	gene with protein product		601648				8641424	Standard	XM_005245354		Approved	S5A, AF-1, AF, Rpn10	uc001exl.3	P55036	OTTHUMG00000012349	ENST00000368884.3:c.632G>T	chr1.hg19:g.151238063G>T	ENSP00000357879:p.Ser211Ile	95.0	0.0	.		83.0	23.0	.	NM_002810	D3DV16|Q5VWC5|Q9NS92	Missense_Mutation	SNP	ENST00000368884.3	hg19	CCDS991.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.414949	0.83449	.	.	ENSG00000159352	ENST00000368884;ENST00000368881;ENST00000437736	T;T	0.15834	2.39;2.39	5.7	5.7	0.88788	Ubiquitin interacting motif (3);	0.000000	0.85682	D	0.000000	T	0.32102	0.0818	M	0.65677	2.01	0.58432	D	0.999998	D;D	0.55172	0.97;0.97	P;P	0.60473	0.875;0.875	T	0.02668	-1.1126	10	0.87932	D	0	-15.2977	19.4422	0.94825	0.0:0.0:1.0:0.0	.	211;211	Q5VWC4;P55036	.;PSMD4_HUMAN	I	211;211;196	ENSP00000357879:S211I;ENSP00000357876:S211I	ENSP00000357876:S211I	S	+	2	0	PSMD4	149504687	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.403000	0.73264	2.688000	0.91661	0.655000	0.94253	AGT	.	.	.	none		0.507	PSMD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034409.3	NM_002810		T	151238063	G	T	151238063	3	4	38	1	0	0	0	0	1	0	0	0	12710	1029	36	4	654	4	PSMD4	1	151238063	Missense_Mutation	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10	32817341	151238063	98012558	7	2700											
SMG7	9887	hgsc.bcm.edu	37	chr1	183520249	183520249	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagcagttggcatcaggccaGcactccgagtggcacctgga	9	6	14	12	1	1	0	1	0	0	0	2	3	2	1	3	4	2	5	3	4	0	1			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr1:183520249G>A	ENST00000347615.2	+	21	3343	c.3224G>A	c.(3223-3225)aGc>aAc	p.S1075N	SMG7_ENST00000507469.1_Missense_Mutation_p.S1079N|SMG7_ENST00000515829.2_Missense_Mutation_p.S1029N|SMG7_ENST00000508461.1_Missense_Mutation_p.S1083N|SMG7_ENST00000367537.3_Missense_Mutation_p.S1108N|SMG7_ENST00000456731.2_Missense_Mutation_p.S987N	NM_173156.2	NP_775179.1	Q92540	SMG7_HUMAN	SMG7 nonsense mediated mRNA decay factor	1075					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(16)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	46						CATCAGGCCAGCACTCCGAGT	0.493																																					p.S1083N		Atlas-SNP	.											.	SMG7	165	.	0			c.G3248A						PASS	.						77	71	73					1																	183520249		2203	4300	6503	SO:0001583	missense	9887	exon21			AGGCCAGCACTCC	D87437	CCDS1355.1, CCDS41445.1, CCDS41445.2, CCDS53444.1, CCDS53445.1	1q25	2013-07-02	2013-07-02	2006-02-16	ENSG00000116698	ENSG00000116698			16792	protein-coding gene	gene with protein product	"EST1 telomerase component homolog C (S. cerevisiae)"	610964	"chromosome 1 open reading frame 16", "smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)"	C1orf16		14636577, 15721257	Standard	NM_173156		Approved	KIAA0250, EST1C, SGA56M, SMG-7	uc001gqf.3	Q92540	OTTHUMG00000035221	ENST00000347615.2:c.3224G>A	chr1.hg19:g.183520249G>A	ENSP00000340766:p.Ser1075Asn	101.0	0.0	.		124.0	28.0	.	NM_001174061	B4DRB2|E9PCI0|E9PEH2|Q5T1Q0|Q6PIE0|Q7Z7H9|Q8IXC1|Q8IXC2	Missense_Mutation	SNP	ENST00000347615.2	hg19	CCDS1355.1	.	.	.	.	.	.	.	.	.	.	G	15.74	2.922705	0.52653	.	.	ENSG00000116698	ENST00000456731;ENST00000367537;ENST00000508461;ENST00000347615;ENST00000507469;ENST00000515829	T;T;T;T;T;T	0.20463	2.11;2.09;2.11;2.11;2.07;2.11	5.34	4.43	0.53597	.	0.231216	0.52532	N	0.000077	T	0.10208	0.0250	N	0.19112	0.55	0.37364	D	0.911351	B;B;B;B;B	0.32245	0.181;0.079;0.13;0.181;0.361	B;B;B;B;B	0.27076	0.014;0.021;0.076;0.024;0.054	T	0.09465	-1.0673	10	0.02654	T	1	-2.1512	10.3745	0.44075	0.1495:0.0:0.8505:0.0	.	1083;987;1029;1075;1079	E9PCI0;E9PCE5;Q92540-2;Q92540;E9PEH2	.;.;.;SMG7_HUMAN;.	N	987;1108;1083;1075;1079;1029	ENSP00000407629:S987N;ENSP00000356507:S1108N;ENSP00000426915:S1083N;ENSP00000340766:S1075N;ENSP00000425133:S1079N;ENSP00000421358:S1029N	ENSP00000340766:S1075N	S	+	2	0	SMG7	181786872	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.986000	0.63851	1.373000	0.46208	0.650000	0.86243	AGC	.	.	.	none		0.493	SMG7-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000085432.1	NM_014837		A	183520249	G	A	183520249	3	1	38	1	0	0	0	0	1	0	0	0	14811	971	34	2	3460	2	SMG7	1	183520249	Missense_Mutation	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10	32282186	183520249	65730372	8	2701											
CAMK1G	57172	hgsc.bcm.edu	37	chr1	209778922	209778922	+	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	tgaccggatcctggagcgggGtgtctacacagagaaggatg	10	7	16	8	2	1	2	0	1	1	1	2	6	2	5	2	5	2	0	2	5	2	1			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr1:209778922G>C	ENST00000009105.1	+	5	583	c.338G>C	c.(337-339)gGt>gCt	p.G113A	CAMK1G_ENST00000361322.2_Missense_Mutation_p.G113A			Q96NX5	KCC1G_HUMAN	calcium/calmodulin-dependent protein kinase IG	113	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			breast(2)|central_nervous_system(1)|large_intestine(8)|lung(8)|stomach(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.0475)		CTGGAGCGGGGTGTCTACACA	0.493																																					p.G113A	Ovarian(163;530 1939 9680 28669 48710)	Atlas-SNP	.											.	CAMK1G	49	.	0			c.G338C						PASS	.						146	135	139					1																	209778922		2203	4300	6503	SO:0001583	missense	57172	exon5			AGCGGGGTGTCTA		CCDS1486.1	1q32.2	2012-09-20			ENSG00000008118	ENSG00000008118			14585	protein-coding gene	gene with protein product		614994				12637513	Standard	NM_020439		Approved	VWS1, CLICKIII, dJ272L16.1	uc001hhd.3	Q96NX5	OTTHUMG00000036361	ENST00000009105.1:c.338G>C	chr1.hg19:g.209778922G>C	ENSP00000009105:p.Gly113Ala	42.0	0.0	.		64.0	15.0	.	NM_020439	Q86UH5|Q9Y3J7	Missense_Mutation	SNP	ENST00000009105.1	hg19	CCDS1486.1	.	.	.	.	.	.	.	.	.	.	G	32	5.184022	0.94885	.	.	ENSG00000008118	ENST00000009105;ENST00000423146;ENST00000361322	T;T;T	0.46063	0.88;1.64;0.88	5.34	5.34	0.76211	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.56097	D	0.000035	T	0.66036	0.2749	M	0.72576	2.205	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.77004	0.956;0.989	T	0.68614	-0.5362	10	0.87932	D	0	.	19.4188	0.94712	0.0:0.0:1.0:0.0	.	113;113	Q96NX5-2;Q96NX5	.;KCC1G_HUMAN	A	113	ENSP00000009105:G113A;ENSP00000392173:G113A;ENSP00000354861:G113A	ENSP00000009105:G113A	G	+	2	0	CAMK1G	207845545	1.000000	0.71417	0.994000	0.49952	0.996000	0.88848	9.507000	0.97996	2.664000	0.90586	0.655000	0.94253	GGT	.	.	.	none		0.493	CAMK1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088526.1	NM_020439		C	209778922	G	C	209778922	3	2	38	1	0	0	0	0	1	0	0	0	2600	1261	44	4	352	4	CAMK1G	1	209778922	Missense_Mutation	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10	26258673	209778922	39471699	9	2702											
RHOU	58480	hgsc.bcm.edu	37	chr1	228879035	228879035	+	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	actttgcttggttgcaggatGaatttgacaagctgaggcct	9	13	12	7	0	0	3	0	3	0	0	0	4	0	4	1	3	3	4	1	3	2	4			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr1:228879035G>A	ENST00000366691.3	+	3	991	c.325G>A	c.(325-327)Gaa>Aaa	p.E109K		NM_021205.5	NP_067028.1			ras homolog family member U											breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)|stomach(1)	13	Breast(184;0.162)	Prostate(94;0.183)				GTTGCAGGATGAATTTGACAA	0.448																																					p.E109K		Atlas-SNP	.											.	RHOU	20	.	0			c.G325A						PASS	.						190	199	196					1																	228879035		2203	4300	6503	SO:0001583	missense	58480	exon3			CAGGATGAATTTG		CCDS1575.1	1q42.11-q42.3	2012-02-27	2012-02-27	2004-03-24	ENSG00000116574	ENSG00000116574			17794	protein-coding gene	gene with protein product	"Ryu GTPase", "Wnt-1 responsive Cdc42 homolog", "2310026M05Rik", "GTP-binding protein like 1", "CDC42-like GTPase", "GTP-binding protein SB128", "ras-like gene family member U"	606366	"ras homolog gene family, member U"	ARHU		11459829	Standard	NM_021205		Approved	WRCH-1, DJ646B12.2, FLJ10616, WRCH1, CDC42L1, hG28K, fJ646B12.2	uc001htf.3	Q7L0Q8	OTTHUMG00000037919	ENST00000366691.3:c.325G>A	chr1.hg19:g.228879035G>A	ENSP00000355652:p.Glu109Lys	77.0	0.0	.		78.0	13.0	.	NM_021205		Missense_Mutation	SNP	ENST00000366691.3	hg19	CCDS1575.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.860283	0.91433	.	.	ENSG00000116574	ENST00000366691	T	0.77489	-1.1	4.73	4.73	0.59995	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.78559	0.4302	L	0.50919	1.6	0.80722	D	1	B	0.29508	0.246	B	0.40285	0.325	T	0.80020	-0.1557	10	0.87932	D	0	.	15.2086	0.73198	0.0:0.0:1.0:0.0	.	109	Q7L0Q8	RHOU_HUMAN	K	109	ENSP00000355652:E109K	ENSP00000355652:E109K	E	+	1	0	RHOU	226945658	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.690000	0.84178	2.439000	0.82584	0.655000	0.94253	GAA	.	.	.	none		0.448	RHOU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092555.1	NM_021205		A	228879035	G	A	228879035	3	1	38	1	0	0	0	0	1	0	0	0	13358	1291	45	2	335	2	RHOU	1	228879035	Missense_Mutation	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10	19100113	228879035	20371586	10	2703											
KIF26B	55083	hgsc.bcm.edu	37	chr1	245850297	245850297	+	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	agaagcccaaggccagccccGacaacttgctcatcctgtct	10	7	8	16	1	2	1	1	0	1	1	3	2	3	1	5	1	4	1	5	1	3	1			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr1:245850297G>A	ENST00000407071.2	+	12	4452	c.4012G>A	c.(4012-4014)Gac>Aac	p.D1338N	KIF26B_ENST00000366518.4_Missense_Mutation_p.D957N	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	1338					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)			GGCCAGCCCCGACAACTTGCT	0.567																																					p.D1338N		Atlas-SNP	.											.	KIF26B	343	.	0			c.G4012A						PASS	.						49	54	52					1																	245850297		2051	4213	6264	SO:0001583	missense	55083	exon12			AGCCCCGACAACT	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.4012G>A	chr1.hg19:g.245850297G>A	ENSP00000385545:p.Asp1338Asn	112.0	0.0	.		106.0	29.0	.	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	hg19	CCDS44342.1	.	.	.	.	.	.	.	.	.	.	G	12.95	2.091651	0.36952	.	.	ENSG00000162849	ENST00000407071;ENST00000366518;ENST00000413001	T;T	0.79940	-1.32;-1.31	5.82	3.94	0.45596	.	.	.	.	.	T	0.74122	0.3675	L	0.43152	1.355	0.21386	N	0.9997	B;B	0.16396	0.017;0.004	B;B	0.08055	0.003;0.002	T	0.65294	-0.6203	9	0.51188	T	0.08	.	11.8996	0.52675	0.1401:0.0:0.8599:0.0	.	957;1338	B7WPD9;Q2KJY2	.;KI26B_HUMAN	N	1338;957;954	ENSP00000385545:D1338N;ENSP00000355475:D957N	ENSP00000355475:D957N	D	+	1	0	KIF26B	243916920	0.992000	0.36948	0.356000	0.25785	0.517000	0.34286	3.275000	0.51639	1.462000	0.47948	0.561000	0.74099	GAC	.	.	.	none		0.567	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		A	245850297	G	A	245850297	3	1	38	1	0	0	0	0	1	0	0	0	8302	1058	37	1	4058	1	KIF26B	1	245850297	Missense_Mutation	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10	16971262	245850297	3400324	11	2704											
LPIN1	23175	hgsc.bcm.edu	37	chr2	11959665	11959665	+	Frame_Shift_Del	DEL	A	A	-																															tccagtgtttgacagacatcAaaaacctgtttttccccaac																										TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr2:11959665delA	ENST00000256720.2	+	18	2443	c.2350delA	c.(2350-2352)aaafs	p.K784fs	LPIN1_ENST00000449576.2_Frame_Shift_Del_p.K869fs|LPIN1_ENST00000396099.1_Frame_Shift_Del_p.K826fs|LPIN1_ENST00000396097.1_Frame_Shift_Del_p.K514fs|LPIN1_ENST00000425416.2_Frame_Shift_Del_p.K790fs|LPIN1_ENST00000404113.2_Frame_Shift_Del_p.K285fs	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	784	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)		GACAGACATCAAAAACCTGTT	0.373																																					p.I868fs		Atlas-Indel,Pindel	.											.	LPIN1	99	.	0			c.2604delC						PASS	.						170	175	173					2																	11959665		2203	4300	6503	SO:0001589	frameshift_variant	23175	exon20			.	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.2350delA	chr2.hg19:g.11959665delA	ENSP00000256720:p.Lys784fs	117.0	0.0	0		110.0	37.0	0.336364	NM_001261428	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Frame_Shift_Del	DEL	ENST00000256720.2	hg19	CCDS1682.1																																																																																			.	.	.	none		0.373	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693		-	11959665	A	-	11959665	7	5	38	1	0	1	0	1	0	0	0	0	8925	131	5	0	2416	0	LPIN1	2	11959665	Frame_Shift_Del	DEL	A	TCGA-5P-A9KC-01A-11D-A42J-10		11959665	231239708	12	2705											
PUM2	23369	hgsc.bcm.edu	37	chr2	20482914	20482914	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgctgctgctgtggtggcTgagtgccaattggccgaaac	6	11	15	9	1	0	1	0	1	0	0	0	2	0	1	2	3	5	5	2	3	2	2			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr2:20482914T>C	ENST00000361078.2	-	11	1536	c.1514A>G	c.(1513-1515)cAg>cGg	p.Q505R	PUM2_ENST00000536417.1_Missense_Mutation_p.Q449R|PUM2_ENST00000319801.5_Missense_Mutation_p.Q505R|PUM2_ENST00000403432.1_Missense_Mutation_p.Q505R|PUM2_ENST00000338086.5_Missense_Mutation_p.Q505R			Q8TB72	PUM2_HUMAN	pumilio RNA-binding family member 2	505					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)					CTGTGGTGGCTGAGTGCCAAT	0.453																																					p.Q505R		Atlas-SNP	.											.	PUM2	91	.	0			c.A1514G						PASS	.						71	75	73					2																	20482914		2203	4300	6503	SO:0001583	missense	23369	exon11			GGTGGCTGAGTGC	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.1514A>G	chr2.hg19:g.20482914T>C	ENSP00000354370:p.Gln505Arg	59.0	0.0	.		61.0	10.0	.	NM_015317	B3KSL0|B4E2B6|D6W527|O00234|Q53TV7|Q8WY43|Q9HAN2	Missense_Mutation	SNP	ENST00000361078.2	hg19		.	.	.	.	.	.	.	.	.	.	T	15.48	2.844781	0.51164	.	.	ENSG00000055917	ENST00000338086;ENST00000361078;ENST00000319801;ENST00000440577;ENST00000403432;ENST00000536417	T;T;T;T;T;T	0.19532	2.17;2.45;2.4;2.14;2.17;2.16	6.03	4.81	0.61882	.	0.059994	0.64402	D	0.000002	T	0.33818	0.0876	L	0.43923	1.385	0.51012	D	0.999907	B;D;B	0.54601	0.005;0.967;0.016	B;D;B	0.65140	0.008;0.932;0.017	T	0.01557	-1.1325	10	0.26408	T	0.33	-4.0585	13.0341	0.58860	0.0:0.0:0.1341:0.8659	.	449;505;505	B4E2B6;B7ZL34;Q8TB72-3	.;.;.	R	505;505;505;396;505;449	ENSP00000338173:Q505R;ENSP00000354370:Q505R;ENSP00000326746:Q505R;ENSP00000409905:Q396R;ENSP00000385992:Q505R;ENSP00000440093:Q449R	ENSP00000326746:Q505R	Q	-	2	0	PUM2	20346395	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	2.965000	0.49200	2.313000	0.78055	0.454000	0.30748	CAG	.	.	.	none		0.453	PUM2-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015317		C	20482914	T	C	20482914	3	2	38	1	0	0	0	0	1	0	0	0	12839	1580	55	3	1720	3	PUM2	2	20482914	Missense_Mutation	SNP	T	TCGA-5P-A9KC-01A-11D-A42J-10	8523249	20482914	222716459	13	2706											
CIB4	130106	hgsc.bcm.edu	37	chr2	26805731	26805731	+	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	ttggccattgcatgttcaaaCtctgagaaggacagcatgtt	11	12	10	8	0	2	1	1	1	1	1	2	3	2	2	1	2	3	4	1	2	2	4			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr2:26805731C>G	ENST00000288861.4	-	6	542	c.489G>C	c.(487-489)gaG>gaC	p.E163D	CIB4_ENST00000405346.3_5'UTR	NM_001029881.1	NP_001025052.1	A0PJX0	CIB4_HUMAN	calcium and integrin binding family member 4	163	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CATGTTCAAACTCTGAGAAGG	0.547																																					p.E163D		Atlas-SNP	.											.	CIB4	15	.	0			c.G489C						PASS	.						144	110	121					2																	26805731		2203	4300	6503	SO:0001583	missense	130106	exon6			TTCAAACTCTGAG		CCDS33160.1	2p23.3	2013-01-10			ENSG00000157884	ENSG00000157884		"EF-hand domain containing"	33703	protein-coding gene	gene with protein product		610646				15574431	Standard	NM_001029881		Approved		uc002rhm.3	A0PJX0	OTTHUMG00000151993	ENST00000288861.4:c.489G>C	chr2.hg19:g.26805731C>G	ENSP00000288861:p.Glu163Asp	88.0	0.0	.		69.0	18.0	.	NM_001029881	B2RU18	Missense_Mutation	SNP	ENST00000288861.4	hg19	CCDS33160.1	.	.	.	.	.	.	.	.	.	.	C	17.81	3.479953	0.63849	.	.	ENSG00000157884	ENST00000288861;ENST00000403670;ENST00000405346	D	0.84370	-1.84	5.29	5.29	0.74685	EF-hand-like domain (1);	0.000000	0.64402	D	0.000013	D	0.90484	0.7019	M	0.69248	2.105	0.44366	D	0.997261	D	0.63880	0.993	D	0.72982	0.979	D	0.88822	0.3299	10	0.31617	T	0.26	.	14.503	0.67734	0.0:1.0:0.0:0.0	.	163	A0PJX0	CIB4_HUMAN	D	163;118;165	ENSP00000288861:E163D	ENSP00000288861:E163D	E	-	3	2	CIB4	26659235	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.684000	0.37649	2.491000	0.84063	0.650000	0.86243	GAG	.	.	.	none		0.547	CIB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324709.1			G	26805731	C	G	26805731	3	3	38	1	0	0	0	0	1	0	0	0	3425	564	20	4	76	4	CIB4	2	26805731	Missense_Mutation	SNP	C	TCGA-5P-A9KC-01A-11D-A42J-10	6322817	26805731	216393642	14	2707											
SNX17	9784	hgsc.bcm.edu	37	chr2	27596784	27596784	+	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	gaagtgctgctcagcaacggGcagaaagttctggtcaacgt	11	8	13	9	2	3	1	2	0	1	1	3	2	3	1	0	2	5	5	0	2	4	1			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr2:27596784G>C	ENST00000233575.2	+	5	600	c.378G>C	c.(376-378)ggG>ggC	p.G126G	SNX17_ENST00000537606.1_Silent_p.G101G|SNX17_ENST00000542478.1_5'UTR|SNX17_ENST00000543024.1_5'UTR	NM_001267059.1|NM_001267061.1|NM_014748.3	NP_001253988.1|NP_001253990.1|NP_055563.1	Q15036	SNX17_HUMAN	sorting nexin 17	126	FERM-like.|Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				cholesterol catabolic process (GO:0006707)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|receptor-mediated endocytosis (GO:0006898)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)	low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylinositol binding (GO:0035091)|protein C-terminus binding (GO:0008022)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCAGCAACGGGCAGAAAGTTC	0.562																																					p.G126G		Atlas-SNP	.											.	SNX17	40	.	0			c.G378C						PASS	.						127	108	114					2																	27596784		2203	4300	6503	SO:0001819	synonymous_variant	9784	exon5			CAACGGGCAGAAA	D31764	CCDS1750.1, CCDS58704.1	2p23-p22	2008-05-21			ENSG00000115234	ENSG00000115234		"Sorting nexins"	14979	protein-coding gene	gene with protein product		605963				12169628, 15769472	Standard	NM_014748		Approved	KIAA0064	uc002rkg.2	Q15036	OTTHUMG00000097781	ENST00000233575.2:c.378G>C	chr2.hg19:g.27596784G>C		118.0	0.0	.		72.0	22.0	.	NM_014748	B4DQM7|Q53HN7|Q6IAS3	Silent	SNP	ENST00000233575.2	hg19	CCDS1750.1																																																																																			.	.	.	none		0.562	SNX17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215024.1	NM_014748		C	27596784	G	C	27596784	2	2	38	1	0	0	0	0	0	0	0	1	14901	1190	42	4		4	SNX17	2	27596784	Silent	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10	791053	27596784	215602589	15	2708											
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125320891	125320891	+	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	caagttacactggtgccaccTgccacaactgtgagtagatt	11	10	9	11	0	0	2	0	1	0	1	0	2	0	2	3	1	4	2	3	1	4	3			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr2:125320891T>A	ENST00000431078.1	+	11	2108	c.1744T>A	c.(1744-1746)Tgc>Agc	p.C582S		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	582	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)		TGGTGCCACCTGCCACAACTG	0.483																																					p.C582S		Atlas-SNP	.											.	CNTNAP5	405	.	0			c.T1744A						PASS	.						36	39	38					2																	125320891		1938	4153	6091	SO:0001583	missense	129684	exon11			GCCACCTGCCACA	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.1744T>A	chr2.hg19:g.125320891T>A	ENSP00000399013:p.Cys582Ser	45.0	0.0	.		58.0	20.0	.	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	hg19	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.851039	0.91277	.	.	ENSG00000155052	ENST00000431078	D	0.84730	-1.89	6.07	6.07	0.98685	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (2);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.53938	D	0.000043	D	0.96037	0.8709	H	0.99435	4.565	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.97784	1.0234	10	0.72032	D	0.01	.	15.4647	0.75390	0.0:0.0:0.0:1.0	.	582	Q8WYK1	CNTP5_HUMAN	S	582	ENSP00000399013:C582S	ENSP00000399013:C582S	C	+	1	0	CNTNAP5	125037361	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.316000	0.79007	2.326000	0.78906	0.533000	0.62120	TGC	.	.	.	none		0.483	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			A	125320891	T	A	125320891	3	1	38	1	0	0	0	0	1	0	0	0	3652	1580	55	5	1786	5	CNTNAP5	2	125320891	Missense_Mutation	SNP	T	TCGA-5P-A9KC-01A-11D-A42J-10	97724107	125320891	117878482	16	2709											
UBR3	130507	hgsc.bcm.edu	37	chr2	170871867	170871867	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagcacagctggcaaaaggTcttgtttaagtaagtactaa	15	10	9	7	0	1	0	0	0	1	0	1	0	1	0	0	2	3	6	0	2	7	6			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr2:170871867T>C	ENST00000272793.5	+	30	4494	c.4444T>C	c.(4444-4446)Tct>Cct	p.S1482P	UBR3_ENST00000392631.1_Missense_Mutation_p.S303P|UBR3_ENST00000465630.1_3'UTR|UBR3_ENST00000418381.1_Missense_Mutation_p.S1482P			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	1482					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						TGGCAAAAGGTCTTGTTTAAG	0.318																																					p.S1482P		Atlas-SNP	.											.	UBR3	182	.	0			c.T4444C						PASS	.						80	83	82					2																	170871867		2203	4300	6503	SO:0001583	missense	130507	exon30			AAAAGGTCTTGTT	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.4444T>C	chr2.hg19:g.170871867T>C	ENSP00000272793:p.Ser1482Pro	73.0	0.0	.		44.0	16.0	.	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Missense_Mutation	SNP	ENST00000272793.5	hg19		.	.	.	.	.	.	.	.	.	.	T	21.0	4.083095	0.76642	.	.	ENSG00000144357	ENST00000272793;ENST00000442603;ENST00000418381;ENST00000392631;ENST00000439681	T;T;T;T	0.68331	-0.32;-0.32;-0.32;-0.32	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.78710	0.4326	L	0.59436	1.845	0.48452	D	0.999656	D;D;D	0.76494	0.998;0.999;0.995	D;D;D	0.80764	0.986;0.994;0.979	T	0.76906	-0.2786	10	0.35671	T	0.21	.	16.05	0.80749	0.0:0.0:0.0:1.0	.	1482;303;1482	Q6ZT12;Q6ZT12-2;E7EVK3	UBR3_HUMAN;.;.	P	1482;1482;1482;303;153	ENSP00000272793:S1482P;ENSP00000396068:S1482P;ENSP00000376408:S303P;ENSP00000389097:S153P	ENSP00000272793:S1482P	S	+	1	0	UBR3	170580113	1.000000	0.71417	0.999000	0.59377	0.979000	0.70002	7.353000	0.79414	2.263000	0.75096	0.533000	0.62120	TCT	.	.	.	none		0.318	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070		C	170871867	T	C	170871867	3	2	38	1	0	0	0	0	1	0	0	0	16915	1667	58	3	4562	3	UBR3	2	170871867	Missense_Mutation	SNP	T	TCGA-5P-A9KC-01A-11D-A42J-10	45550976	170871867	72327506	17	2710											
CFLAR	8837	hgsc.bcm.edu	37	chr2	202025647	202025647	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtacctgcagtgcctctcccAgaaactgagacaagaaaggt	13	7	10	11	0	1	3	0	1	1	3	2	4	1	3	3	1	4	2	3	1	4	1			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr2:202025647A>G	ENST00000309955.3	+	9	1801	c.1286A>G	c.(1285-1287)cAg>cGg	p.Q429R	CFLAR_ENST00000479953.2_Missense_Mutation_p.Q333R|CFLAR_ENST00000423241.2_Missense_Mutation_p.Q429R|CFLAR_ENST00000457277.1_Missense_Mutation_p.Q429R|CFLAR_ENST00000341582.6_Missense_Mutation_p.Q394R|CFLAR_ENST00000340870.5_Missense_Mutation_p.Q429R|CFLAR_ENST00000443227.1_Missense_Mutation_p.Q333R|CFLAR_ENST00000355558.4_Intron	NM_001202515.1|NM_003879.5	NP_001189444.1|NP_003870.4	O15519	CFLAR_HUMAN	CASP8 and FADD-like apoptosis regulator	429	Interaction with TRAF1 and TRAF2.|Interaction with caspase-3.|Interaction with caspase-8 subunits p18 and p10.|Interaction with caspase-8.|Not proteolytically processed and involved in apoptosis inhibition.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of myoblast fusion (GO:1901740)|positive regulation of catalytic activity (GO:0043085)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of necroptotic process (GO:0060544)|regulation of satellite cell proliferation (GO:0014842)|skeletal muscle atrophy (GO:0014732)|skeletal muscle tissue development (GO:0007519)|skeletal muscle tissue regeneration (GO:0043403)|skeletal myofibril assembly (GO:0014866)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|ripoptosome (GO:0097342)	cysteine-type peptidase activity (GO:0008234)|death effector domain binding (GO:0035877)|enzyme activator activity (GO:0008047)|protease binding (GO:0002020)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|stomach(1)	13						TGCCTCTCCCAGAAACTGAGA	0.557																																					p.Q429R	Pancreas(16;548 657 22190 32864 42338)	Atlas-SNP	.											.	CFLAR	37	.	0			c.A1286G						PASS	.						38	36	37					2																	202025647		2203	4300	6503	SO:0001583	missense	8837	exon9			TCTCCCAGAAACT	AF005774	CCDS2337.1, CCDS46487.1, CCDS56157.1, CCDS56158.1, CCDS59436.1	2q33-q34	2014-01-30			ENSG00000003402	ENSG00000003402		"Endogenous ligands"	1876	protein-coding gene	gene with protein product		603599		CASP8AP1		9208847, 9217161	Standard	NM_003879		Approved	CASH, Casper, CLARP, FLAME, FLIP, I-FLICE, MRIT, c-FLIP	uc002uxb.4	O15519	OTTHUMG00000132819	ENST00000309955.3:c.1286A>G	chr2.hg19:g.202025647A>G	ENSP00000312455:p.Gln429Arg	66.0	0.0	.		72.0	20.0	.	NM_003879	B4DJE0|B7Z9F9|O14673|O14674|O14675|O15137|O15138|O15356|O15510|O43618|O43619|O43620|O60458|O60459|Q53TS6|Q54AF1|Q96TE4|Q9UEW1	Missense_Mutation	SNP	ENST00000309955.3	hg19	CCDS2337.1	.	.	.	.	.	.	.	.	.	.	A	19.35	3.809868	0.70797	.	.	ENSG00000003402	ENST00000309955;ENST00000443227;ENST00000340870;ENST00000343375;ENST00000341582;ENST00000423241;ENST00000457277	T;T;T;T;T;T	0.03065	4.06;4.06;4.06;4.06;4.06;4.06	5.61	5.61	0.85477	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase precursor p45, core (1);	0.249814	0.40144	N	0.001170	T	0.14527	0.0351	M	0.69248	2.105	0.35533	D	0.802442	D;D;D;D	0.76494	0.963;0.99;0.997;0.999	P;P;D;D	0.70227	0.846;0.856;0.918;0.968	T	0.08411	-1.0723	10	0.41790	T	0.15	-21.5966	12.3315	0.55041	0.859:0.141:0.0:0.0	.	333;429;394;429	O15519-3;O15519-11;O15519-8;O15519	.;.;.;CFLAR_HUMAN	R	429;333;429;315;394;429;429	ENSP00000312455:Q429R;ENSP00000413270:Q333R;ENSP00000339326:Q429R;ENSP00000345807:Q394R;ENSP00000399420:Q429R;ENSP00000411535:Q429R	ENSP00000312455:Q429R	Q	+	2	0	CFLAR	201733892	1.000000	0.71417	0.999000	0.59377	0.875000	0.50365	4.249000	0.58766	2.135000	0.66039	0.454000	0.30748	CAG	.	.	.	none		0.557	CFLAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256276.3	NM_003879		G	202025647	A	G	202025647	3	3	38	1	0	0	0	0	1	0	0	0	3294	188	7	3	1380	3	CFLAR	2	202025647	Missense_Mutation	SNP	A	TCGA-5P-A9KC-01A-11D-A42J-10	31153780	202025647	41173726	18	2711											
ALS2CR8	79800	hgsc.bcm.edu	37	chr2	203817333	203817333	+	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	aggtacttcgtgtaattccaCctacccagacaggaatggca	12	9	9	11	1	0	1	0	0	0	1	2	2	1	2	3	3	2	3	3	3	4	5			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr2:203817333C>T	ENST00000402905.3	+	5	679	c.358C>T	c.(358-360)Cct>Tct	p.P120S	CARF_ENST00000428585.1_Missense_Mutation_p.P44S|CARF_ENST00000414439.1_Missense_Mutation_p.P18S|CARF_ENST00000434998.1_Missense_Mutation_p.P18S|CARF_ENST00000320443.8_Missense_Mutation_p.P120S|WDR12_ENST00000477723.1_Intron|CARF_ENST00000545262.1_Missense_Mutation_p.P44S|CARF_ENST00000456821.2_Missense_Mutation_p.P108S|CARF_ENST00000444724.1_Missense_Mutation_p.P120S|CARF_ENST00000438828.2_Missense_Mutation_p.P120S|CARF_ENST00000471271.1_3'UTR|CARF_ENST00000545253.1_Missense_Mutation_p.P32S	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	120					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)										TGTAATTCCACCTACCCAGAC	0.433																																					p.P120S		Atlas-SNP	.											.	ALS2CR8	56	.	0			c.C358T						PASS	.						135	124	127					2																	203817333		1865	4114	5979	SO:0001583	missense	79800	exon6			ATTCCACCTACCC	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.358C>T	chr2.hg19:g.203817333C>T	ENSP00000384006:p.Pro120Ser	94.0	0.0	.		89.0	23.0	.	NM_024744	B4E1W7|G3V1K7|Q8ND29|Q8WXC0|Q96J78|Q96Q38|Q96Q39|Q9H712	Missense_Mutation	SNP	ENST00000402905.3	hg19	CCDS42801.1	.	.	.	.	.	.	.	.	.	.	C	2.275	-0.366143	0.05069	.	.	ENSG00000138380	ENST00000402905;ENST00000431787;ENST00000444724;ENST00000414857;ENST00000414439;ENST00000428585;ENST00000545253;ENST00000545262;ENST00000447539;ENST00000456821;ENST00000434998;ENST00000320443;ENST00000438828	.	.	.	5.24	-0.0813	0.13703	.	0.079962	0.50627	N	0.000102	T	0.03053	0.0090	N	0.00128	-2.045	0.21184	N	0.999761	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	0.36841	-0.9731	9	0.02654	T	1	-0.7081	2.635	0.04955	0.2506:0.0707:0.1307:0.5481	.	32;44;120;120;120	B4DIA7;G3V1K7;B4DRP6;Q8N187;F6SXV3	.;.;.;AL2S8_HUMAN;.	S	120;90;120;120;18;44;32;44;44;108;18;120;120	.	ENSP00000316224:P120S	P	+	1	0	ALS2CR8	203525578	1.000000	0.71417	0.987000	0.45799	0.917000	0.54804	1.699000	0.37804	-0.235000	0.09767	-1.728000	0.00702	CCT	.	.	.	none		0.433	CARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335768.5	NM_001104586		T	203817333	C	T	203817333	3	4	38	1	0	0	0	0	1	0	0	0	555	507	18	2	368	2	ALS2CR8	2	203817333	Missense_Mutation	SNP	C	TCGA-5P-A9KC-01A-11D-A42J-10	1791686	203817333	39382040	19	2712											
RAF1	5894	hgsc.bcm.edu	37	chr3	12650333	12650333	+	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	gtgctacagtgctcatgaaaTttgtagccacaagtctgaca	12	11	9	9	0	2	2	1	2	1	0	2	2	2	2	1	0	4	3	1	0	4	3	rs561163045		TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr3:12650333T>A	ENST00000251849.4	-	5	952	c.513A>T	c.(511-513)aaA>aaT	p.K171N	RAF1_ENST00000442415.2_Missense_Mutation_p.K171N|RAF1_ENST00000542177.1_Missense_Mutation_p.K90N|RAF1_ENST00000534997.1_5'UTR	NM_002880.3	NP_002871.1	P04049	RAF1_HUMAN	Raf-1 proto-oncogene, serine/threonine kinase	171					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)	GCTCATGAAATTTGTAGCCAC	0.428			T	SRGAP3	pilocytic astrocytoma				Noonan syndrome																												p.K171N		Atlas-SNP	.		Dom	yes		3	3p25	5894	v-raf-1 murine leukemia viral oncogene homolog 1		M	.	RAF1	66	.	0			c.A513T						PASS	.						137	122	127					3																	12650333		2203	4300	6503	SO:0001583	missense	5894	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	ATGAAATTTGTAG	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.513A>T	chr3.hg19:g.12650333T>A	ENSP00000251849:p.Lys171Asn	136.0	0.0	.		131.0	38.0	.	NM_002880	B0LPH8|B2R5N3|Q15278|Q9UC20	Missense_Mutation	SNP	ENST00000251849.4	hg19	CCDS2612.1	.	.	.	.	.	.	.	.	.	.	T	19.80	3.894506	0.72639	.	.	ENSG00000132155	ENST00000251849;ENST00000442415;ENST00000432427;ENST00000542177	D;D;D;D	0.83673	-1.75;-1.75;-1.75;-1.75	5.52	1.27	0.21489	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);Diacylglycerol/phorbol-ester binding (1);	0.100276	0.64402	D	0.000003	T	0.80844	0.4701	N	0.14661	0.345	0.80722	D	1	D;D	0.89917	1.0;0.996	D;D	0.80764	0.994;0.984	T	0.79813	-0.1645	10	0.87932	D	0	.	9.4339	0.38626	0.0:0.3375:0.0:0.6625	.	90;171	B4E0X2;P04049	.;RAF1_HUMAN	N	171;171;83;90	ENSP00000251849:K171N;ENSP00000401888:K171N;ENSP00000398591:K83N;ENSP00000443567:K90N	ENSP00000251849:K171N	K	-	3	2	RAF1	12625333	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.110000	0.31147	0.354000	0.24105	0.460000	0.39030	AAA	.	.	.	none		0.428	RAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252015.2	NM_002880		A	12650333	T	A	12650333	3	1	38	1	0	0	0	0	1	0	0	0	13015	1490	52	5	1485	5	RAF1	3	12650333	Missense_Mutation	SNP	T	TCGA-5P-A9KC-01A-11D-A42J-10		12650333	185372097	20	2713											
ZMYND10	51364	hgsc.bcm.edu	37	chr3	50382584	50382594	+	Frame_Shift_Del	DEL	TGGGCTCGCCC	TGGGCTCGCCC	-																															ggtgaccagcagctcctgaaTgggctcgccctggctgactg																										TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	TGGGCTCGCCC	TGGGCTCGCCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr3:50382584_50382594delTGGGCTCGCCC	ENST00000231749.3	-	2	1434_1444	c.162_172delGGGCGAGCCCA	c.(160-174)cagggcgagcccattfs	p.QGEPI54fs	ZMYND10_ENST00000490675.1_5'Flank|ZMYND10-AS1_ENST00000440013.1_RNA|ZMYND10_ENST00000360165.3_Frame_Shift_Del_p.QGEPI54fs|NPRL2_ENST00000493465.1_5'Flank	NM_015896.2	NP_056980.2	O75800	ZMY10_HUMAN	zinc finger, MYND-type containing 10	54					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)		AGCTCCTGAATGGGCTCGCCCTGGCTGACTG	0.607										TSP Lung(30;0.18)																											p.55_58del		Pindel	.											.	ZMYND10	37	.	0			c.163_173del						PASS	.																																			SO:0001589	frameshift_variant	51364	exon2			.	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.162_172delGGGCGAGCCCA	chr3.hg19:g.50382584_50382594delTGGGCTCGCCC	ENSP00000231749:p.Gln54fs	74.0	0.0	.		50.0	14.0	0.280	NM_015896	A6NK41|B3KU54|O14570|O75801|Q53FE6|Q8N4R6|Q8NDN6	Frame_Shift_Del	DEL	ENST00000231749.3	hg19	CCDS2825.1																																																																																			.	.	.	none		0.607	ZMYND10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346376.1	NM_015896		-	50382594	TGGGCTCGCCC	-	50382584	7	5	38	1	0	1	0	1	0	0	0	0	17717	1464	51	0	1194	0	ZMYND10	3	50382584	Frame_Shift_Del	DEL	TGGGCTCGCCC	TCGA-5P-A9KC-01A-11D-A42J-10	37732251	50382584	147639846	21	2714	35	2									
ZMYND10	51364	hgsc.bcm.edu	37	chr3	50382588	50382598	+	Frame_Shift_Del	DEL	CTCGCCCTGGC	CTCGCCCTGGC	-																															accagcagctcctgaatgggCtcgccctggctgactgtggc																										TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	CTCGCCCTGGC	CTCGCCCTGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr3:50382588_50382598delCTCGCCCTGGC	ENST00000231749.3	-	2	1430_1440	c.158_168delGCCAGGGCGAG	c.(157-168)agccagggcgagfs	p.SQGE53fs	ZMYND10_ENST00000490675.1_5'Flank|ZMYND10-AS1_ENST00000440013.1_RNA|ZMYND10_ENST00000360165.3_Frame_Shift_Del_p.SQGE53fs|NPRL2_ENST00000493465.1_5'Flank	NM_015896.2	NP_056980.2	O75800	ZMY10_HUMAN	zinc finger, MYND-type containing 10	53					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)		CCTGAATGGGCTCGCCCTGGCTGACTGTGGC	0.602										TSP Lung(30;0.18)																											p.53_57del		Atlas-INDEL	.											.	ZMYND10	37	.	0			c.159_169del						PASS	.																																			SO:0001589	frameshift_variant	51364	exon2			.	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.158_168delGCCAGGGCGAG	chr3.hg19:g.50382588_50382598delCTCGCCCTGGC	ENSP00000231749:p.Ser53fs	73.0	0.0	0		45.0	11.0	0.244444	NM_015896	A6NK41|B3KU54|O14570|O75801|Q53FE6|Q8N4R6|Q8NDN6	Frame_Shift_Del	DEL	ENST00000231749.3	hg19	CCDS2825.1																																																																																			.	.	.	none		0.602	ZMYND10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346376.1	NM_015896		-	50382598	CTCGCCCTGGC	-	50382588	7	5	38	1	0	1	0	1	0	0	0	0	17717	796	28	0	1198	0	ZMYND10	3	50382588	Frame_Shift_Del	DEL	CTCGCCCTGGC	TCGA-5P-A9KC-01A-11D-A42J-10	4	50382588	147639842	22	2715	35	2									
ZDHHC23	254887	hgsc.bcm.edu	37	chr3	113673053	113673053	+	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	agggcaggagaagaccaaagGgttccctggggcagacatgt	12	5	16	8	0	0	3	0	0	0	3	1	4	1	3	2	5	0	3	2	5	2	1			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr3:113673053G>C	ENST00000330212.3	+	3	967	c.668G>C	c.(667-669)gGg>gCg	p.G223A	ZDHHC23_ENST00000498275.1_Missense_Mutation_p.G217A	NM_173570.3	NP_775841.2	Q8IYP9	ZDH23_HUMAN	zinc finger, DHHC-type containing 23	223					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						AAGACCAAAGGGTTCCCTGGG	0.562																																					p.G223A		Atlas-SNP	.											.	ZDHHC23	38	.	0			c.G668C						PASS	.						95	97	97					3																	113673053		2203	4300	6503	SO:0001583	missense	254887	exon3			CCAAAGGGTTCCC	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.668G>C	chr3.hg19:g.113673053G>C	ENSP00000330485:p.Gly223Ala	153.0	0.0	.		199.0	43.0	.	NM_173570	D3DN76	Missense_Mutation	SNP	ENST00000330212.3	hg19	CCDS33827.1	.	.	.	.	.	.	.	.	.	.	G	10.94	1.491910	0.26774	.	.	ENSG00000184307	ENST00000330212;ENST00000498275	T;T	0.41400	1.0;1.01	5.64	3.81	0.43845	.	0.364534	0.32687	N	0.005764	T	0.44582	0.1300	L	0.48642	1.525	0.19300	N	0.99997	P	0.52463	0.953	P	0.52454	0.699	T	0.24548	-1.0157	10	0.29301	T	0.29	-14.6686	10.8169	0.46583	0.0706:0.1325:0.7969:0.0	.	223	Q8IYP9	ZDH23_HUMAN	A	223;217	ENSP00000330485:G223A;ENSP00000417840:G217A	ENSP00000330485:G223A	G	+	2	0	ZDHHC23	115155743	1.000000	0.71417	1.000000	0.80357	0.303000	0.27691	3.650000	0.54424	1.352000	0.45808	0.561000	0.74099	GGG	.	.	.	none		0.562	ZDHHC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354702.1	NM_173570		C	113673053	G	C	113673053	3	2	38	1	0	0	0	0	1	0	0	0	17626	1232	43	4	674	4	ZDHHC23	3	113673053	Missense_Mutation	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10	63290465	113673053	84349377	23	2716											
RAB6B	51560	hgsc.bcm.edu	37	chr3	133557104	133557104	+	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	cctcctcgatggttatctgcCtagagatgaggggaaggggg	8	9	16	8	1	1	2	0	1	1	1	3	5	2	3	3	5	1	1	3	5	3	2			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr3:133557104C>T	ENST00000285208.4	-	6	751		c.e6-1		RAB6B_ENST00000543906.1_Splice_Site|RAB6B_ENST00000469959.1_Intron|RAB6B_ENST00000486858.1_Splice_Site	NM_016577.3	NP_057661.3	Q9NRW1	RAB6B_HUMAN	RAB6B, member RAS oncogene family						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						GGTTATCTGCCTAGAGATGAG	0.592																																					.		Atlas-SNP	.											.	RAB6B	36	.	0			c.402-1G>A						PASS	.						112	105	107					3																	133557104		2203	4300	6503	SO:0001630	splice_region_variant	51560	exon7			ATCTGCCTAGAGA	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.402-1G>A	chr3.hg19:g.133557104C>T		42.0	0.0	.		54.0	18.0	.	NM_016577	B2R5Z9|B7Z337|D3DND3|Q92929	Splice_Site	SNP	ENST00000285208.4	hg19	CCDS3082.1	.	.	.	.	.	.	.	.	.	.	C	18.92	3.724693	0.68959	.	.	ENSG00000154917	ENST00000285208;ENST00000543906;ENST00000486858;ENST00000477759;ENST00000460865	.	.	.	4.64	4.64	0.57946	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.9471	0.52934	0.1739:0.8261:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RAB6B	135039794	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	7.013000	0.76373	2.573000	0.86826	0.655000	0.94253	.	.	.	.	none		0.592	RAB6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357152.1		Intron	T	133557104	C	T	133557104	5	4	38	1	0	0	0	0	0	0	1	0	12965	695	24	2	237	2	RAB6B	3	133557104	Splice_Site	SNP	C	TCGA-5P-A9KC-01A-11D-A42J-10	19884051	133557104	64465326	24	2717											
RNF212	285498	hgsc.bcm.edu	37	chr4	1066753	1066753	+	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	ccagggtgccctcagcctgcTggaacggaaacaagacggcc	10	4	13	14	2	1	1	1	0	0	1	1	3	1	3	4	4	5	1	4	4	3	0			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr4:1066753T>A	ENST00000433731.2	-	10	864	c.803A>T	c.(802-804)cAg>cTg	p.Q268L	RNF212_ENST00000382968.5_3'UTR			Q495C1	RN212_HUMAN	ring finger protein 212	268					chiasma assembly (GO:0051026)|meiotic gene conversion (GO:0006311)|protein sumoylation (GO:0016925)|reciprocal meiotic recombination (GO:0007131)	synaptonemal complex (GO:0000795)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	10			OV - Ovarian serous cystadenocarcinoma(23;0.0179)	UCEC - Uterine corpus endometrioid carcinoma (64;0.151)		CTCAGCCTGCTGGAACGGAAA	0.478											OREG0016028	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q268L		Atlas-SNP	.											.	RNF212	69	.	0			c.A803T						PASS	.						87	90	89					4																	1066753		2203	4300	6503	SO:0001583	missense	285498	exon10			GCCTGCTGGAACG	AK096160	CCDS3345.1, CCDS46996.1, CCDS54704.1	4p16.3	2013-02-27	2007-01-19	2007-01-19	ENSG00000178222	ENSG00000178222		"RING-type (C3HC4) zinc fingers"	27729	protein-coding gene	gene with protein product		612041	"hypothetical protein LOC285498"	LOC285498		23396135	Standard	NM_001131034		Approved	FLJ38841	uc003gcj.3	Q495C1	OTTHUMG00000118997	ENST00000433731.2:c.803A>T	chr4.hg19:g.1066753T>A	ENSP00000389709:p.Gln268Leu	198.0	0.0	.	593	190.0	44.0	.	NM_001131034	C9J8N0|Q495C0|Q86W82|Q8IY99|Q8N8U7	Missense_Mutation	SNP	ENST00000433731.2	hg19	CCDS46996.1	.	.	.	.	.	.	.	.	.	.	T	7.107	0.575269	0.13623	.	.	ENSG00000178222	ENST00000433731	T	0.51071	0.72	1.17	-2.34	0.06704	.	.	.	.	.	T	0.19485	0.0468	N	0.08118	0	0.09310	N	0.999999	P	0.34977	0.478	B	0.26614	0.071	T	0.08868	-1.0701	9	0.87932	D	0	.	3.1593	0.06515	0.0:0.231:0.4453:0.3237	.	268	Q495C1	RN212_HUMAN	L	268	ENSP00000389709:Q268L	ENSP00000389709:Q268L	Q	-	2	0	RNF212	1056753	0.001000	0.12720	0.000000	0.03702	0.006000	0.05464	-0.798000	0.04565	-1.036000	0.03287	-0.331000	0.08364	CAG	.	.	.	none		0.478	RNF212-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359124.2	NM_194439		A	1066753	T	A	1066753	3	1	38	1	0	0	0	0	1	0	0	0	13489	1580	55	5	94	5	RNF212	4	1066753	Missense_Mutation	SNP	T	TCGA-5P-A9KC-01A-11D-A42J-10		1066753	190087523	25	2718											
MTTP	4547	hgsc.bcm.edu	37	chr4	100534106	100534106	+	Missense_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	aaggactggaagccttaatcGcagccacccctgacgagggg	11	5	13	12	2	0	1	0	1	0	0	1	4	0	3	4	4	2	1	4	4	3	1			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr4:100534106G>A	ENST00000265517.5	+	15	2229	c.2026G>A	c.(2026-2028)Gca>Aca	p.A676T	MTTP_ENST00000457717.1_Missense_Mutation_p.A676T|MTTP_ENST00000511045.1_Missense_Mutation_p.A703T|RP11-766F14.1_ENST00000508578.1_RNA			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	676					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)	p.A676T(1)		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)	AGCCTTAATCGCAGCCACCCC	0.483																																					p.A676T		Atlas-SNP	.											MTTP,rectum,carcinoma,0,1	MTTP	127	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2026A						PASS	.						136	134	135					4																	100534106		2203	4300	6503	SO:0001583	missense	4547	exon16			TTAATCGCAGCCA		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.2026G>A	chr4.hg19:g.100534106G>A	ENSP00000265517:p.Ala676Thr	41.0	0.0	.		49.0	2.0	.	NM_000253	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	hg19	CCDS3651.1	.	.	.	.	.	.	.	.	.	.	G	36	5.669852	0.96754	.	.	ENSG00000138823	ENST00000511045;ENST00000457717;ENST00000265517	T;T;T	0.64991	-0.13;-0.1;-0.1	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.76751	0.4031	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.914;0.996	T	0.70000	-0.4992	10	0.18276	T	0.48	-15.6636	19.7133	0.96105	0.0:0.0:1.0:0.0	.	703;676	E9PBP6;P55157	.;MTP_HUMAN	T	703;676;676	ENSP00000427679:A703T;ENSP00000400821:A676T;ENSP00000265517:A676T	ENSP00000265517:A676T	A	+	1	0	MTTP	100753129	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.307000	0.96226	2.659000	0.90383	0.650000	0.86243	GCA	.	.	.	none		0.483	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3			A	100534106	G	A	100534106	3	1	38	1	0	0	0	0	1	0	0	0	9971	1087	38	1	2084	1	MTTP	4	100534106	Missense_Mutation	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10	99467353	100534106	90620170	26	2719											
ELOVL6	79071	hgsc.bcm.edu	37	chr4	110980893	110980894	+	Frame_Shift_Del	DEL	CG	CG	-																															acaccatataagcaccagttCgaagagcaccgaatatactt																										TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	CG	CG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr4:110980893_110980894delCG	ENST00000394607.3	-	4	401_402	c.238_239delCG	c.(238-240)cgafs	p.R80fs	ELOVL6_ENST00000506461.1_5'UTR|ELOVL6_ENST00000302274.3_Frame_Shift_Del_p.R80fs			Q9H5J4	ELOV6_HUMAN	ELOVL fatty acid elongase 6	80					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)		AGCACCAGTTCGAAGAGCACCG	0.401																																					p.80_80del		Atlas-Indel,Pindel	.											.	ELOVL6	27	.	0			c.239_240del						PASS	.																																			SO:0001589	frameshift_variant	79071	exon4			.	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.238_239delCG	chr4.hg19:g.110980893_110980894delCG	ENSP00000378105:p.Arg80fs	176.0	0.0	0		169.0	36.0	0.213018	NM_001130721	Q4W5L0|Q8NCD1	Frame_Shift_Del	DEL	ENST00000394607.3	hg19	CCDS3690.1																																																																																			.	.	.	none		0.401	ELOVL6-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255748.1	NM_024090		-	110980894	CG	-	110980893	7	5	38	1	0	1	0	1	0	0	0	0	5080	884	31	0	566	0	ELOVL6	4	110980893	Frame_Shift_Del	DEL	CG	TCGA-5P-A9KC-01A-11D-A42J-10	10446787	110980893	80173383	27	2720											
PDCD6	10016	hgsc.bcm.edu	37	chr5	306756	306756	+	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	caaggccggcgtgaacttcaGcgagttcacgggtgtgtgga	8	8	16	9	4	2	1	2	1	0	0	2	3	2	2	1	4	2	1	1	4	2	2			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr5:306756G>C	ENST00000264933.4	+	4	348	c.248G>C	c.(247-249)aGc>aCc	p.S83T	AHRR_ENST00000316418.5_Intron|AHRR_ENST00000505113.1_Intron|PDCD6_ENST00000507528.1_Missense_Mutation_p.S83T|AHRR_ENST00000512529.1_Intron|PDCD6_ENST00000505221.1_Intron	NM_001267556.1|NM_001267558.1|NM_013232.3	NP_001254485.1|NP_001254487.1|NP_037364.1	O75340	PDCD6_HUMAN	programmed cell death 6	83	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|cellular response to heat (GO:0034605)|intracellular protein transport (GO:0006886)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|proteolysis (GO:0006508)|response to calcium ion (GO:0051592)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	binding, bridging (GO:0060090)|calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|calcium-dependent protein binding (GO:0048306)|protein dimerization activity (GO:0046983)			breast(2)|endometrium(1)|large_intestine(4)|lung(1)	8			Epithelial(17;0.00193)|OV - Ovarian serous cystadenocarcinoma(19;0.00489)|all cancers(22;0.00511)|Lung(60;0.113)			GTGAACTTCAGCGAGTTCACG	0.537																																					p.S83T		Atlas-SNP	.											.	PDCD6	24	.	0			c.G248C						PASS	.						95	79	84					5																	306756		2203	4300	6503	SO:0001583	missense	10016	exon4			ACTTCAGCGAGTT	AF035606	CCDS3854.1, CCDS58940.1, CCDS58941.1, CCDS75222.1, CCDS75223.1	5p15.33	2013-01-10			ENSG00000249915	ENSG00000249915		"EF-hand domain containing"	8765	protein-coding gene	gene with protein product	"apoptosis-linked gene-2"	601057				8560270	Standard	NM_013232		Approved	ALG-2, PEF1B	uc003jat.1	O75340	OTTHUMG00000090283	ENST00000264933.4:c.248G>C	chr5.hg19:g.306756G>C	ENSP00000264933:p.Ser83Thr	76.0	0.0	.		77.0	19.0	.	NM_013232	B2RD16|E7ESR3|Q2YDC2|Q5TZS0	Missense_Mutation	SNP	ENST00000264933.4	hg19	CCDS3854.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	5.045|5.045	0.193946|0.193946	0.09599|0.09599	.|.	.|.	ENSG00000249915|ENSG00000249915	ENST00000502359|ENST00000264933;ENST00000507528	.|T;T	.|0.78481	.|-1.18;-1.18	5.53|5.53	3.75|3.75	0.43078|0.43078	.|EF-hand-like domain (1);	.|.	.|.	.|.	.|.	T|T	0.57873|0.57873	0.2083|0.2083	N|N	0.16567|0.16567	0.415|0.415	0.80722|0.80722	D|D	1|1	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.06405	.|0.002;0.002	T|T	0.43956|0.43956	-0.9359|-0.9359	5|9	.|0.21014	.|T	.|0.42	.|.	6.1331|6.1331	0.20217|0.20217	0.1641:0.1548:0.6811:0.0|0.1641:0.1548:0.6811:0.0	.|.	.|83;83	.|Q2YDC2;O75340	.|.;PDCD6_HUMAN	P|T	14|83	.|ENSP00000264933:S83T;ENSP00000423815:S83T	.|ENSP00000264933:S83T	A|S	+|+	1|2	0|0	PDCD6|PDCD6	359756|359756	0.978000|0.978000	0.34361|0.34361	0.971000|0.971000	0.41717|0.41717	0.011000|0.011000	0.07611|0.07611	2.062000|2.062000	0.41413|0.41413	0.703000|0.703000	0.31848|0.31848	-0.127000|-0.127000	0.14921|0.14921	GCG|AGC	.	.	.	none		0.537	PDCD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206609.2	NM_013232		C	306756	G	C	306756	3	2	38	1	0	0	0	0	1	0	0	0	11630	971	34	4	262	4	PDCD6	5	306756	Missense_Mutation	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10		306756	180608504	28	2721											
FASTKD3	79072	hgsc.bcm.edu	37	chr5	7867443	7867443	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggccacaatatcctccggggTaaatgtttccaatttttcac	10	13	7	11	1	1	0	1	0	0	0	4	0	4	0	4	3	0	2	4	3	5	5			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr5:7867443T>C	ENST00000264669.5	-	2	890	c.754A>G	c.(754-756)Acc>Gcc	p.T252A	FASTKD3_ENST00000513658.1_Intron|MTRR_ENST00000502509.1_Intron|MTRR_ENST00000264668.2_5'Flank|MTRR_ENST00000341013.6_5'Flank|MTRR_ENST00000440940.2_5'Flank	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	252					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						TCCTCCGGGGTAAATGTTTCC	0.363																																					p.T252A		Atlas-SNP	.											.	FASTKD3	88	.	0			c.A754G						PASS	.						79	84	82					5																	7867443		2202	4300	6502	SO:0001583	missense	79072	exon2			CCGGGGTAAATGT	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.754A>G	chr5.hg19:g.7867443T>C	ENSP00000264669:p.Thr252Ala	36.0	0.0	.		43.0	13.0	.	NM_024091	Q9BVD3	Missense_Mutation	SNP	ENST00000264669.5	hg19	CCDS3873.1	.	.	.	.	.	.	.	.	.	.	T	9.962	1.223021	0.22457	.	.	ENSG00000124279	ENST00000264669	T	0.23552	1.9	4.85	-3.71	0.04424	.	0.721105	0.14271	N	0.330147	T	0.09423	0.0232	N	0.13235	0.315	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.38112	-0.9676	10	0.07482	T	0.82	-1.8934	6.0475	0.19768	0.1224:0.3502:0.0:0.5273	.	252	Q14CZ7	FAKD3_HUMAN	A	252	ENSP00000264669:T252A	ENSP00000264669:T252A	T	-	1	0	FASTKD3	7920443	0.617000	0.27043	0.000000	0.03702	0.742000	0.42306	0.512000	0.22755	-0.538000	0.06281	0.528000	0.53228	ACC	.	.	.	none		0.363	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091		C	7867443	T	C	7867443	3	2	38	1	0	0	0	0	1	0	0	0	5694	1638	57	3	1258	3	FASTKD3	5	7867443	Missense_Mutation	SNP	T	TCGA-5P-A9KC-01A-11D-A42J-10	7560687	7867443	173047817	29	2722											
FYB	2533	hgsc.bcm.edu	37	chr5	39153579	39153579	+	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	aacggaggtttaatgtttctGggaggtaggcttgggactgg	8	12	17	4	1	1	0	0	0	1	0	1	3	1	3	0	7	1	4	0	7	3	5			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr5:39153579G>T	ENST00000351578.6	-	3	1453	c.1263C>A	c.(1261-1263)ccC>ccA	p.P421P	FYB_ENST00000505428.1_Silent_p.P421P|FYB_ENST00000515010.1_Silent_p.P421P|FYB_ENST00000512982.1_Silent_p.P421P|FYB_ENST00000540520.1_Silent_p.P431P	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein	421	Interaction with SKAP1.				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)			TAATGTTTCTGGGAGGTAGGC	0.488																																					p.P431P		Atlas-SNP	.											.	FYB	354	.	0			c.C1293A						PASS	.						291	298	296					5																	39153579		2025	4174	6199	SO:0001819	synonymous_variant	2533	exon3			GTTTCTGGGAGGT	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.1263C>A	chr5.hg19:g.39153579G>T		156.0	0.0	.		192.0	55.0	.	NM_001243093	A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Silent	SNP	ENST00000351578.6	hg19	CCDS47200.1																																																																																			.	.	.	none		0.488	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367098.1	NM_001465		T	39153579	G	T	39153579	2	4	38	1	0	0	0	0	0	0	0	1	6131	1335	47	4		4	FYB	5	39153579	Silent	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10	31286136	39153579	141761681	30	2723											
GNB2L1	10399	hgsc.bcm.edu	37	chr5	180670768	180670768	+	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	acccagccgttgtggcccttGagggtgccacgaagggtcat	7	8	14	12	2	1	1	1	1	0	0	1	2	1	1	4	3	2	1	4	3	1	2			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr5:180670768G>C	ENST00000512805.1	-	1	441	c.33C>G	c.(31-33)ctC>ctG	p.L11L	SNORD95_ENST00000579879.1_RNA|GNB2L1_ENST00000456394.2_Silent_p.L11L|SNORD96A_ENST00000606577.1_RNA|GNB2L1_ENST00000376817.4_Silent_p.L11L|GNB2L1_ENST00000505461.1_5'UTR|GNB2L1_ENST00000504726.1_Silent_p.L11L|CTC-338M12.4_ENST00000506340.1_RNA|CTC-338M12.4_ENST00000511331.1_RNA|GNB2L1_ENST00000511566.1_Silent_p.L11L|GNB2L1_ENST00000511900.1_Silent_p.L11L	NM_006098.4	NP_006089.1	P63244	GBLP_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1	11					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)		TGTGGCCCTTGAGGGTGCCAC	0.597																																					p.L11L		Atlas-SNP	.											.	GNB2L1	22	.	0			c.C33G						PASS	.						107	78	88					5																	180670768		2203	4300	6503	SO:0001819	synonymous_variant	10399	exon1			GCCCTTGAGGGTG	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.33C>G	chr5.hg19:g.180670768G>C		88.0	0.0	.		88.0	24.0	.	NM_006098	B3KTJ0|D3DWS0|P25388|P99049|Q53HU2|Q5J8M6|Q5VLR4|Q6FH47	Silent	SNP	ENST00000512805.1	hg19	CCDS34324.1																																																																																			.	.	.	none		0.597	GNB2L1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372943.2	NM_006098		C	180670768	G	C	180670768	2	2	38	1	0	0	0	0	0	0	0	1	6525	1277	45	4		4	GNB2L1	5	180670768	Silent	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10	141517189	180670768	244492	31	2724											
TMEM170B	100113407	hgsc.bcm.edu	37	chr6	11575790	11575797	+	Stop_Codon_Del	DEL	TTTGAGGT	TTTGAGGT	-																															ttcaaggatcctcgctacacTttgaggtttctgtgggaatg																										TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	TTTGAGGT	TTTGAGGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr6:11575790_11575797delTTTGAGGT	ENST00000379426.1	+	0	395_402				TMEM170B_ENST00000543875.1_Stop_Codon_Del	NM_001100829.1	NP_001094299.1	Q5T4T1	T170B_HUMAN	transmembrane protein 170B							integral component of membrane (GO:0016021)				large_intestine(3)|lung(5)	8						CTCGCTACACTTTGAGGTTTCTGTGGGA	0.442																																					p.132_133del		Atlas-INDEL	.											.	TMEM170B	9	.	0			c.394_450del						PASS	.																																			SO:0001567	stop_retained_variant	100113407	exon3			.		CCDS43425.1	6p24.1	2008-08-08			ENSG00000205269	ENSG00000205269			34244	protein-coding gene	gene with protein product							Standard	NM_001100829		Approved		uc010jpa.4	Q5T4T1	OTTHUMG00000014259	Exception_encountered	chr6.hg19:g.11575790_11575797delTTTGAGGT	ENSP00000368737:p.*133Trpext*16	61.0	0.0	0		72.0	10.0	0.138889	NM_001100829		Frame_Shift_Del	DEL	ENST00000379426.1	hg19	CCDS43425.1																																																																																			.	.	.	none		0.442	TMEM170B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000039862.1	NM_001100829		-	11575797	TTTGAGGT	-	11575790	7	5	38	1	0	1	0	1	0	0	0	0	16099	1609	56	0	405	0	TMEM170B	6	11575790	Stop_Codon_Del	DEL	TTTGAGGT	TCGA-5P-A9KC-01A-11D-A42J-10		11575790	159539277	32	2725											
ATXN1	6310	hgsc.bcm.edu	37	chr6	16328017	16328017	+	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	gccagcagagtggaataggcCtccagctgggagcgctggga	9	5	17	10	1	0	1	0	0	0	1	1	4	1	4	3	4	3	3	3	4	2	1			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr6:16328017C>G	ENST00000244769.4	-	8	1461	c.525G>C	c.(523-525)gaG>gaC	p.E175D	ATXN1_ENST00000436367.1_Missense_Mutation_p.E175D	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	175					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)				TGGAATAGGCCTCCAGCTGGG	0.662																																					p.E175D		Atlas-SNP	.											.	ATXN1	117	.	0			c.G525C						PASS	.						33	37	36					6																	16328017		2195	4282	6477	SO:0001583	missense	6310	exon7			ATAGGCCTCCAGC	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.525G>C	chr6.hg19:g.16328017C>G	ENSP00000244769:p.Glu175Asp	34.0	0.0	.		34.0	9.0	.	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	hg19	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	C	16.60	3.169241	0.57584	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.50277	0.75;0.75	5.26	3.47	0.39725	.	0.105649	0.64402	D	0.000007	T	0.23249	0.0562	M	0.63843	1.955	0.42281	D	0.992091	B	0.25441	0.126	B	0.16289	0.015	T	0.08229	-1.0732	10	0.16420	T	0.52	-30.305	11.2182	0.48838	0.0:0.8513:0.0:0.1487	.	175	P54253	ATX1_HUMAN	D	175	ENSP00000244769:E175D;ENSP00000416360:E175D	ENSP00000244769:E175D	E	-	3	2	ATXN1	16435996	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.505000	0.45424	1.211000	0.43351	0.467000	0.42956	GAG	.	.	.	none		0.662	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332		G	16328017	C	G	16328017	3	3	38	1	0	0	0	0	1	0	0	0	1209	680	24	4	1930	4	ATXN1	6	16328017	Missense_Mutation	SNP	C	TCGA-5P-A9KC-01A-11D-A42J-10	4752227	16328017	154787050	33	2726											
C6orf222	389384	hgsc.bcm.edu	37	chr6	36291122	36291122	+	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	ccaacacacaggggcagaaaGctgggcctcttgggtcgtcg	9	6	14	12	2	1	1	0	0	1	1	3	1	1	1	2	4	2	2	2	4	2	1			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr6:36291122G>C	ENST00000437635.2	-	8	1596	c.1419C>G	c.(1417-1419)agC>agG	p.S473R		NM_001010903.4	NP_001010903.3	P0C671	CF222_HUMAN	chromosome 6 open reading frame 222	473										breast(4)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|skin(4)|urinary_tract(4)	26						GGGGCAGAAAGCTGGGCCTCT	0.622																																					p.S473R		Atlas-SNP	.											.	C6orf222	72	.	0			c.C1419G						PASS	.						86	97	93					6																	36291122		2203	4300	6503	SO:0001583	missense	389384	exon8			CAGAAAGCTGGGC		CCDS34439.1	6p21.31	2012-02-22			ENSG00000189325	ENSG00000189325			33769	protein-coding gene	gene with protein product							Standard	NM_001010903		Approved	DKFZp779B1540	uc003oly.3	P0C671	OTTHUMG00000014591	ENST00000437635.2:c.1419C>G	chr6.hg19:g.36291122G>C	ENSP00000418983:p.Ser473Arg	51.0	0.0	.		61.0	15.0	.	NM_001010903	B2RTY8	Missense_Mutation	SNP	ENST00000437635.2	hg19	CCDS34439.1	.	.	.	.	.	.	.	.	.	.	G	15.86	2.958254	0.53400	.	.	ENSG00000189325	ENST00000437635	T	0.55930	0.49	4.68	2.88	0.33553	.	0.339819	0.25964	N	0.027169	T	0.50188	0.1601	M	0.74258	2.255	0.26291	N	0.978125	D	0.57571	0.98	P	0.60068	0.868	T	0.38993	-0.9635	10	0.56958	D	0.05	-16.2355	6.0853	0.19964	0.2203:0.0:0.7797:0.0	.	473	P0C671	CF222_HUMAN	R	473	ENSP00000418983:S473R	ENSP00000418983:S473R	S	-	3	2	C6orf222	36399100	0.989000	0.36119	0.953000	0.39169	0.456000	0.32438	1.288000	0.33296	1.274000	0.44362	0.655000	0.94253	AGC	.	.	.	none		0.622	C6orf222-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040338.2	NM_001010903		C	36291122	G	C	36291122	3	2	38	1	0	0	0	0	1	0	0	0	2358	962	34	4	559	4	C6orf222	6	36291122	Missense_Mutation	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10	19963105	36291122	134823945	34	2727											
NFYA	4800	hgsc.bcm.edu	37	chr6	41051876	41051876	+	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	ggtccaggctgtccctggtgGacaaggtcaaaccatcatgc	9	8	12	12	0	2	0	2	0	0	0	4	1	4	1	3	5	2	1	3	5	2	0			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr6:41051876G>A	ENST00000341376.6	+	4	455	c.254G>A	c.(253-255)gGa>gAa	p.G85E	NFYA_ENST00000353205.5_Missense_Mutation_p.G56E|OARD1_ENST00000480585.1_Intron	NM_002505.4	NP_002496.1	P23511	NFYA_HUMAN	nuclear transcription factor Y, alpha	85	Gln-rich.				cellular lipid metabolic process (GO:0044255)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)	CCAAT-binding factor complex (GO:0016602)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|large_intestine(4)|lung(2)|urinary_tract(1)	9	Ovarian(28;0.0418)|Colorectal(47;0.196)					GTCCCTGGTGGACAAGGTCAA	0.473																																					p.G85E		Atlas-SNP	.											.	NFYA	33	.	0			c.G254A						PASS	.						102	78	86					6																	41051876		2203	4300	6503	SO:0001583	missense	4800	exon4			CTGGTGGACAAGG		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.254G>A	chr6.hg19:g.41051876G>A	ENSP00000345702:p.Gly85Glu	52.0	0.0	.		80.0	16.0	.	NM_002505	Q8IXU0	Missense_Mutation	SNP	ENST00000341376.6	hg19	CCDS4849.1	.	.	.	.	.	.	.	.	.	.	G	19.77	3.888578	0.72524	.	.	ENSG00000001167	ENST00000341376;ENST00000353205	.	.	.	5.76	4.89	0.63831	.	0.046056	0.85682	D	0.000000	T	0.44095	0.1277	L	0.55481	1.735	0.58432	D	0.999995	B;B	0.30236	0.274;0.057	B;B	0.18871	0.023;0.01	T	0.53809	-0.8386	9	0.72032	D	0.01	-8.7123	16.2087	0.82144	0.0:0.1331:0.8669:0.0	.	56;85	P23511-2;P23511	.;NFYA_HUMAN	E	85;56	.	ENSP00000345702:G85E	G	+	2	0	NFYA	41159854	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.792000	0.99085	1.552000	0.49463	0.650000	0.86243	GGA	.	.	.	none		0.473	NFYA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040496.1			A	41051876	G	A	41051876	3	1	38	1	0	0	0	0	1	0	0	0	10396	1174	41	2	264	2	NFYA	6	41051876	Missense_Mutation	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10	4760754	41051876	130063191	35	2728											
HCRTR2	3062	hgsc.bcm.edu	37	chr6	55145137	55145137	+	Missense_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	gcagagtatttgggatgtttGcccatactgaagacagagag	12	10	13	6	0	0	4	0	1	0	3	0	6	0	5	1	1	2	3	1	1	3	4			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr6:55145137G>A	ENST00000370862.3	+	6	1336	c.1000G>A	c.(1000-1002)Gcc>Acc	p.A334T		NM_001526.3	NP_001517.2	O43614	OX2R_HUMAN	hypocretin (orexin) receptor 2	334					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)	p.A334S(1)		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)			TGGGATGTTTGCCCATACTGA	0.368																																					p.A334T		Atlas-SNP	.											HCRTR2,NS,carcinoma,0,1	HCRTR2	112	.	1	Substitution - Missense(1)	lung(1)	c.G1000A						PASS	.						216	207	210					6																	55145137		2203	4300	6503	SO:0001583	missense	3062	exon6			ATGTTTGCCCATA	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.1000G>A	chr6.hg19:g.55145137G>A	ENSP00000359899:p.Ala334Thr	85.0	0.0	.		82.0	24.0	.	NM_001526	Q5VTM0	Missense_Mutation	SNP	ENST00000370862.3	hg19	CCDS4956.1	.	.	.	.	.	.	.	.	.	.	G	2.547	-0.304921	0.05495	.	.	ENSG00000137252	ENST00000370862	T	0.61392	0.11	5.62	-3.24	0.05094	GPCR, rhodopsin-like superfamily (1);	0.482845	0.24143	N	0.041156	T	0.12008	0.0292	N	0.05441	-0.05	0.09310	N	0.999991	B	0.02656	0.0	B	0.04013	0.001	T	0.39143	-0.9628	10	0.13108	T	0.6	.	12.8352	0.57770	0.6041:0.0:0.3959:0.0	.	334	O43614	OX2R_HUMAN	T	334	ENSP00000359899:A334T	ENSP00000359899:A334T	A	+	1	0	HCRTR2	55253096	0.385000	0.25172	0.674000	0.29902	0.116000	0.19942	0.901000	0.28445	-0.455000	0.07054	-0.385000	0.06624	GCC	.	.	.	none		0.368	HCRTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043392.1			A	55145137	G	A	55145137	3	1	38	1	0	0	0	0	1	0	0	0	7009	1319	46	2	1022	2	HCRTR2	6	55145137	Missense_Mutation	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10	14093261	55145137	115969930	36	2729											
SMAP1	60682	hgsc.bcm.edu	37	chr6	71508431	71508431	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagccggcaaaaccacttacAgctgaaaaggtaaaattctt	17	8	7	9	1	1	1	0	1	1	0	1	1	1	1	2	2	4	3	2	2	8	4			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr6:71508431A>G	ENST00000370455.3	+	6	815	c.567A>G	c.(565-567)acA>acG	p.T189T	SMAP1_ENST00000370452.3_Silent_p.T162T|SMAP1_ENST00000316999.5_Silent_p.T162T	NM_001044305.1|NM_001281440.1	NP_001037770.1|NP_001268369.1	Q8IYB5	SMAP1_HUMAN	small ArfGAP 1	189					positive regulation of erythrocyte differentiation (GO:0045648)|regulation of ARF GTPase activity (GO:0032312)|regulation of clathrin-mediated endocytosis (GO:2000369)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(1)|urinary_tract(1)	15						AACCACTTACAGCTGAAAAGG	0.274																																					p.T189T		Atlas-SNP	.											.	SMAP1	77	.	0			c.A567G						PASS	.						37	43	41					6																	71508431		2199	4290	6489	SO:0001819	synonymous_variant	60682	exon6			ACTTACAGCTGAA	AK023221	CCDS4973.1, CCDS43478.1, CCDS64459.1, CCDS75478.1	6q12-q13	2009-11-30	2008-09-05		ENSG00000112305	ENSG00000112305		"ADP-ribosylation factor GTPase activating proteins"	19651	protein-coding gene	gene with protein product		611372	"stromal membrane-associated protein 1", "stromal membrane-associated GTPase-activating protein 1"			9644265, 12119110	Standard	NM_001044305		Approved	FLJ13159, SMAP-1	uc003pfr.3	Q8IYB5	OTTHUMG00000014996	ENST00000370455.3:c.567A>G	chr6.hg19:g.71508431A>G		1050.0	0.0	.		1198.0	310.0	.	NM_001044305	Q53H70|Q5SYQ2|Q6PK24|Q8NDH4|Q96L38|Q96L39|Q9H8X4	Silent	SNP	ENST00000370455.3	hg19	CCDS43478.1	.	.	.	.	.	.	.	.	.	.	A	9.297	1.052127	0.19827	.	.	ENSG00000112305	ENST00000439432	.	.	.	5.28	5.28	0.74379	.	.	.	.	.	T	0.48624	0.1510	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52358	-0.8586	4	.	.	.	-19.7696	8.9897	0.36017	0.9161:0.0:0.0839:0.0	.	.	.	.	G	64	.	.	S	+	1	0	SMAP1	71565152	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.702000	0.37836	2.126000	0.65437	0.529000	0.55759	AGC	.	.	.	none		0.274	SMAP1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041149.1	NM_001044305		G	71508431	A	G	71508431	2	3	38	1	0	0	0	0	0	0	0	1	14779	175	7	3		3	SMAP1	6	71508431	Silent	SNP	A	TCGA-5P-A9KC-01A-11D-A42J-10	16363294	71508431	99606636	37	2730											
SENP6	26054	hgsc.bcm.edu	37	chr6	76388567	76388567	+	Missense_Mutation	SNP	T	T	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	ctccagctaagggaggcatcTctgttaccaatgaggacctg	10	9	11	11	0	1	1	0	1	1	0	3	3	2	3	3	3	2	3	3	3	3	2			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr6:76388567T>G	ENST00000447266.2	+	16	2477	c.1999T>G	c.(1999-2001)Tct>Gct	p.S667A	SENP6_ENST00000370010.2_Missense_Mutation_p.S660A|SENP6_ENST00000541192.1_Missense_Mutation_p.S263A|SENP6_ENST00000327284.8_Missense_Mutation_p.S660A|SENP6_ENST00000370014.3_Missense_Mutation_p.S667A	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	667	Protease.				protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				GGGAGGCATCTCTGTTACCAA	0.323																																					p.S667A		Atlas-SNP	.											.	SENP6	189	.	0			c.T1999G						PASS	.						76	74	75					6																	76388567		1851	4085	5936	SO:0001583	missense	26054	exon16			GGCATCTCTGTTA		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.1999T>G	chr6.hg19:g.76388567T>G	ENSP00000402527:p.Ser667Ala	152.0	0.0	.		165.0	35.0	.	NM_015571	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Missense_Mutation	SNP	ENST00000447266.2	hg19	CCDS47454.1	.	.	.	.	.	.	.	.	.	.	T	16.09	3.024669	0.54683	.	.	ENSG00000112701	ENST00000370010;ENST00000370014;ENST00000327284;ENST00000447266;ENST00000424947;ENST00000541192	T;T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51;1.67	5.98	5.98	0.97165	.	0.099352	0.64402	D	0.000001	T	0.21881	0.0527	L	0.38838	1.175	0.50313	D	0.999867	B;B;P	0.51653	0.167;0.104;0.947	B;B;P	0.47528	0.127;0.059;0.549	T	0.01039	-1.1472	10	0.38643	T	0.18	-15.2821	16.4622	0.84064	0.0:0.0:0.0:1.0	.	660;667;660	Q9GZR1-2;Q9GZR1;F8W6D9	.;SENP6_HUMAN;.	A	660;667;660;667;557;263	ENSP00000359027:S660A;ENSP00000359031:S667A;ENSP00000321820:S660A;ENSP00000402527:S667A;ENSP00000391426:S557A;ENSP00000441715:S263A	ENSP00000321820:S660A	S	+	1	0	SENP6	76445287	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	4.735000	0.62051	2.289000	0.77006	0.533000	0.62120	TCT	.	.	.	none		0.323	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571		G	76388567	T	G	76388567	3	3	38	1	0	0	0	0	1	0	0	0	14063	1551	54	5	2061	5	SENP6	6	76388567	Missense_Mutation	SNP	T	TCGA-5P-A9KC-01A-11D-A42J-10	4880136	76388567	94726500	38	2731											
SASH1	23328	hgsc.bcm.edu	37	chr6	148840743	148840743	+	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	tgaacggtccgccctctactCtggcgtgcacaagaagcccc	8	7	10	16	3	2	2	0	1	2	1	3	2	3	2	4	2	4	1	4	2	4	1			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr6:148840743C>G	ENST00000367467.3	+	10	1398	c.923C>G	c.(922-924)tCt>tGt	p.S308C		NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	308					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)		GCCCTCTACTCTGGCGTGCAC	0.552																																					p.S308C		Atlas-SNP	.											.	SASH1	123	.	0			c.C923G						PASS	.						80	82	81					6																	148840743		2203	4300	6503	SO:0001583	missense	23328	exon10			TCTACTCTGGCGT	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.923C>G	chr6.hg19:g.148840743C>G	ENSP00000356437:p.Ser308Cys	111.0	0.0	.		99.0	27.0	.	NM_015278	Q5TGN5|Q8TAI0|Q9H7R7	Missense_Mutation	SNP	ENST00000367467.3	hg19	CCDS5212.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.136995	0.77775	.	.	ENSG00000111961	ENST00000367467;ENST00000535767	T	0.40476	1.03	5.43	5.43	0.79202	.	0.113799	0.64402	D	0.000008	T	0.42562	0.1208	L	0.27053	0.805	0.44798	D	0.997802	D;D	0.76494	0.999;0.999	P;D	0.64042	0.862;0.921	T	0.45527	-0.9255	10	0.72032	D	0.01	-8.9095	17.4215	0.87516	0.0:1.0:0.0:0.0	.	289;308	Q6P4R9;O94885	.;SASH1_HUMAN	C	308;69	ENSP00000356437:S308C	ENSP00000356437:S308C	S	+	2	0	SASH1	148882436	1.000000	0.71417	0.638000	0.29380	0.954000	0.61252	7.127000	0.77210	2.548000	0.85928	0.655000	0.94253	TCT	.	.	.	none		0.552	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278		G	148840743	C	G	148840743	3	3	38	1	0	0	0	0	1	0	0	0	13861	913	32	4	961	4	SASH1	6	148840743	Missense_Mutation	SNP	C	TCGA-5P-A9KC-01A-11D-A42J-10	72452176	148840743	22274324	39	2732											
MEOX2	4223	hgsc.bcm.edu	37	chr7	15725800	15725800	+	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	tgctgctgatggtggtgatgGtggtggtggtggtggtggtg	2	14	23	2	0	0	2	0	2	0	0	0	2	0	2	0	9	2	2	0	9	0	0	rs113582077	byFrequency	TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr7:15725800G>A	ENST00000262041.5	-	1	637	c.228C>T	c.(226-228)caC>caT	p.H76H	AC005550.5_ENST00000438923.1_lincRNA|AC005550.4_ENST00000442176.1_lincRNA	NM_005924.4	NP_005915.2	P50222	MEOX2_HUMAN	mesenchyme homeobox 2	76	Poly-His.				angiogenesis (GO:0001525)|blood circulation (GO:0008015)|limb development (GO:0060173)|multicellular organismal development (GO:0007275)|neuron death (GO:0070997)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle tissue development (GO:0007519)|somite specification (GO:0001757)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding (GO:0043565)	p.H80delH(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (126;0.0822)		ggtggtgatggtggtggtggt	0.612																																					p.H76H	Esophageal Squamous(140;197 1769 16409 18257 29929)	Atlas-SNP	.											.	MEOX2	68	.	1	Deletion - In frame(1)	stomach(1)	c.C228T						PASS	.						11	13	13					7																	15725800		2192	4293	6485	SO:0001819	synonymous_variant	4223	exon1			GTGATGGTGGTGG		CCDS34605.1	7p22.1-p21.3	2014-07-15	2005-12-22		ENSG00000106511	ENSG00000106511		"Homeoboxes / ANTP class : HOXL subclass"	7014	protein-coding gene	gene with protein product	"growth arrest-specific homeobox"	600535	"mesenchyme homeo box 2 (growth arrest-specific homeo box)", "mesenchyme homeobox 2 (growth arrest-specific homeo box)"	GAX		7713505	Standard	NM_005924		Approved	MOX2	uc003stc.3	P50222	OTTHUMG00000152390	ENST00000262041.5:c.228C>T	chr7.hg19:g.15725800G>A		13.0	0.0	.		34.0	11.0	.	NM_005924	B2R8I7|O75263|Q9UPL6	Silent	SNP	ENST00000262041.5	hg19	CCDS34605.1																																																																																			.	.	.	none		0.612	MEOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326058.2	NM_005924		A	15725800	G	A	15725800	2	1	38	1	0	0	0	0	0	0	0	1	9481	1252	44	2		2	MEOX2	7	15725800	Silent	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10		15725800	143412863	40	2733											
C7orf44	55744	hgsc.bcm.edu	37	chr7	43679188	43679188	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttctgggtcgtctctactccTttttcacttcatcaccgttt	4	19	5	13	2	5	0	3	0	2	0	8	0	6	0	2	1	1	1	2	1	1	6	rs537301566		TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr7:43679188T>C	ENST00000395879.1	-	5	2115	c.434A>G	c.(433-435)aAg>aGg	p.K145R	COA1_ENST00000395880.3_Missense_Mutation_p.K145R|COA1_ENST00000310564.6_Missense_Mutation_p.K145R|COA1_ENST00000223336.6_Missense_Mutation_p.K145R|COA1_ENST00000488813.1_5'UTR			Q9GZY4	COA1_HUMAN	cytochrome c oxidase assembly factor 1 homolog (S. cerevisiae)	145					mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex IV assembly (GO:0033617)	cytoplasm (GO:0005737)|integral component of mitochondrial inner membrane (GO:0031305)|mitochondrion (GO:0005739)											TCTCTACTCCTTTTTCACTTC	0.517																																					p.K145R		Atlas-SNP	.											.	.	.	.	0			c.A434G						PASS	.						169	175	173					7																	43679188		2203	4300	6503	SO:0001583	missense	55744	exon6			TACTCCTTTTTCA	AK001665	CCDS5471.1	7p13	2012-12-05	2012-10-15	2012-06-25	ENSG00000106603	ENSG00000106603		"Mitochondrial respiratory chain complex assembly factors"	21868	protein-coding gene	gene with protein product		614769	"chromosome 7 open reading frame 44"	C7orf44		22356826	Standard	NM_018224		Approved	FLJ10803, MITRAC15	uc003tin.2	Q9GZY4	OTTHUMG00000128949	ENST00000395879.1:c.434A>G	chr7.hg19:g.43679188T>C	ENSP00000379218:p.Lys145Arg	74.0	0.0	.		114.0	5.0	.	NM_018224	A6NJU8|A8KAH8|Q9HAB7|Q9NVD2	Missense_Mutation	SNP	ENST00000395879.1	hg19	CCDS5471.1	.	.	.	.	.	.	.	.	.	.	T	10.24	1.295640	0.23564	.	.	ENSG00000106603	ENST00000395879;ENST00000310564;ENST00000395880;ENST00000223336	.	.	.	3.36	-0.562	0.11781	.	1.528020	0.03663	N	0.242820	T	0.26593	0.0650	N	0.19112	0.55	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.19321	-1.0309	9	0.49607	T	0.09	0.2435	2.7004	0.05146	0.4087:0.1199:0.0:0.4714	.	145	Q9GZY4	CG044_HUMAN	R	145	.	ENSP00000223336:K145R	K	-	2	0	C7orf44	43645713	0.000000	0.05858	0.005000	0.12908	0.073000	0.16967	-0.710000	0.05024	-0.096000	0.12329	0.533000	0.62120	AAG	.	.	.	none		0.517	COA1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313664.1	NM_018224		C	43679188	T	C	43679188	3	2	38	1	0	0	0	0	1	0	0	0	2396	1609	56	3	10	3	C7orf44	7	43679188	Missense_Mutation	SNP	T	TCGA-5P-A9KC-01A-11D-A42J-10	27953388	43679188	115459475	41	2734											
TFPI2	7980	hgsc.bcm.edu	37	chr7	93519981	93519981	+	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	cgacagccccagggggcgagCggggtccatggtgcaggggg	6	3	21	11	3	0	0	0	0	0	0	1	2	1	0	3	7	3	1	3	7	0	0			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr7:93519981C>T	ENST00000222543.5	-	1	322	c.10G>A	c.(10-12)Gct>Act	p.A4T	TFPI2_ENST00000545378.1_Missense_Mutation_p.A4T|GNGT1_ENST00000455502.1_Intron|AC002076.10_ENST00000435257.1_RNA	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	4					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)			AGGGGGCGAGCGGGGTCCATG	0.701																																					p.A4T		Atlas-SNP	.											TFPI2,NS,carcinoma,0,1	TFPI2	37	.	0			c.G10A						PASS	.						18	23	22					7																	93519981		2155	4228	6383	SO:0001583	missense	7980	exon1			GGCGAGCGGGGTC	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.10G>A	chr7.hg19:g.93519981C>T	ENSP00000222543:p.Ala4Thr	163.0	0.0	.		206.0	94.0	.	NM_001271003	Q66ME8|Q8NAK6|Q9UC86	Missense_Mutation	SNP	ENST00000222543.5	hg19	CCDS5632.1	.	.	.	.	.	.	.	.	.	.	C	9.953	1.220665	0.22457	.	.	ENSG00000105825	ENST00000222543;ENST00000545378	T;T	0.55930	0.65;0.49	3.98	-3.56	0.04626	.	1.700580	0.02712	N	0.112974	T	0.29423	0.0733	N	0.17082	0.46	0.09310	N	1	B;B;B	0.11235	0.001;0.004;0.001	B;B;B	0.10450	0.001;0.005;0.001	T	0.22382	-1.0218	10	0.06365	T	0.9	.	4.5229	0.11968	0.2394:0.3512:0.0:0.4095	.	4;4;4	Q8NAK6;F5H3J8;P48307	.;.;TFPI2_HUMAN	T	4	ENSP00000222543:A4T;ENSP00000438861:A4T	ENSP00000222543:A4T	A	-	1	0	TFPI2	93357917	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.016000	0.00645	-1.242000	0.02523	-2.185000	0.00314	GCT	.	.	.	none		0.701	TFPI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254720.2	NM_006528		T	93519981	C	T	93519981	3	4	38	1	0	0	0	0	1	0	0	0	15821	768	27	1	717	1	TFPI2	7	93519981	Missense_Mutation	SNP	C	TCGA-5P-A9KC-01A-11D-A42J-10	49840793	93519981	65618682	42	2735											
HBP1	26959	hgsc.bcm.edu	37	chr7	106829794	106829794	+	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	aagaaagtgtatcatttggcGagtctgtactgaagttgact	12	13	11	5	1	2	3	1	2	1	1	2	4	2	3	0	1	1	3	0	1	5	4			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr7:106829794G>A	ENST00000222574.4	+	7	1009	c.823G>A	c.(823-825)Gag>Aag	p.E275K	HBP1_ENST00000461963.1_Intron|HBP1_ENST00000468410.1_Missense_Mutation_p.E275K|HBP1_ENST00000485846.1_Missense_Mutation_p.E275K	NM_012257.3	NP_036389.2	O60381	HBP1_HUMAN	HMG-box transcription factor 1	275	AXH. {ECO:0000255|PROSITE- ProRule:PRU00496}.				cell cycle arrest (GO:0007050)|positive regulation of potassium ion transport (GO:0043268)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			large_intestine(4)|lung(3)|prostate(1)|skin(2)	10						ATCATTTGGCGAGTCTGTACT	0.373																																					p.E285K		Atlas-SNP	.											.	HBP1	31	.	0			c.G853A						PASS	.						205	173	183					7																	106829794		2203	4300	6503	SO:0001583	missense	26959	exon7			TTTGGCGAGTCTG	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.823G>A	chr7.hg19:g.106829794G>A	ENSP00000222574:p.Glu275Lys	88.0	0.0	.		129.0	60.0	.	NM_001244262	B3KVB7|Q8TBM1|Q8TE93|Q96AJ2	Missense_Mutation	SNP	ENST00000222574.4	hg19	CCDS5741.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.707854	0.89018	.	.	ENSG00000105856	ENST00000468410;ENST00000222574;ENST00000485846;ENST00000498408	D;D;D	0.98978	-5.29;-5.29;-5.29	5.94	5.94	0.96194	Ataxin, AXH domain (1);Ataxin-1/HBP1 module (AXH) (3);	0.045424	0.85682	D	0.000000	D	0.97882	0.9304	L	0.38531	1.155	0.80722	D	1	P;P;B	0.51537	0.946;0.634;0.146	P;B;B	0.45681	0.49;0.121;0.055	D	0.98523	1.0624	10	0.72032	D	0.01	-5.9607	20.3736	0.98901	0.0:0.0:1.0:0.0	.	285;275;275	B4DJ36;O60381-3;O60381	.;.;HBP1_HUMAN	K	275;275;275;267	ENSP00000420500:E275K;ENSP00000222574:E275K;ENSP00000418738:E275K	ENSP00000222574:E275K	E	+	1	0	HBP1	106617030	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.748000	0.74877	2.820000	0.97059	0.650000	0.86243	GAG	.	.	.	none		0.373	HBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349297.1	NM_012257		A	106829794	G	A	106829794	3	1	38	1	0	0	0	0	1	0	0	0	6992	1059	37	1	845	1	HBP1	7	106829794	Missense_Mutation	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10	13309813	106829794	52308869	43	2736											
TMEM176B	28959	hgsc.bcm.edu	37	chr7	150491072	150491072	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaccccgcccagaaggcacAgcctgaggcactcagcacag	12	2	11	16	1	1	3	1	1	0	2	1	3	1	3	4	2	2	3	4	2	1	0			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr7:150491072A>G	ENST00000447204.2	-	3	664	c.292T>C	c.(292-294)Tgt>Cgt	p.C98R	TMEM176B_ENST00000492607.1_Missense_Mutation_p.C98R|TMEM176B_ENST00000429904.2_Missense_Mutation_p.C98R|TMEM176B_ENST00000326442.5_Missense_Mutation_p.C98R|TMEM176B_ENST00000450753.2_Intron|TMEM176B_ENST00000434545.1_Missense_Mutation_p.C98R	NM_014020.3	NP_054739.3	Q3YBM2	T176B_HUMAN	transmembrane protein 176B	98					cell differentiation (GO:0030154)|negative regulation of dendritic cell differentiation (GO:2001199)|organ morphogenesis (GO:0009887)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				cervix(1)|large_intestine(4)|lung(10)|ovary(1)|skin(3)	19			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CAGAAGGCACAGCCTGAGGCA	0.572																																					p.C98R		Atlas-SNP	.											.	TMEM176B	36	.	0			c.T292C						PASS	.						204	180	188					7																	150491072		2203	4300	6503	SO:0001583	missense	28959	exon3			AGGCACAGCCTGA	AF115384	CCDS5908.1, CCDS47746.1	7q36.1	2006-09-04			ENSG00000106565	ENSG00000106565			29596	protein-coding gene	gene with protein product		610385				9922225	Standard	NM_014020		Approved	LR8	uc003whu.4	Q3YBM2	OTTHUMG00000157577	ENST00000447204.2:c.292T>C	chr7.hg19:g.150491072A>G	ENSP00000410269:p.Cys98Arg	141.0	0.0	.		228.0	46.0	.	NM_014020	B2RDK2|D3DWZ7|E9PAV4|Q5BJI2|Q9BT42|Q9Y609	Missense_Mutation	SNP	ENST00000447204.2	hg19	CCDS5908.1	.	.	.	.	.	.	.	.	.	.	a	16.03	3.007339	0.54361	.	.	ENSG00000106565	ENST00000492607;ENST00000326442;ENST00000447204;ENST00000434545;ENST00000429904;ENST00000528038	T;T;T;T;T	0.02498	4.27;4.27;4.27;4.27;4.27	4.93	3.72	0.42706	.	0.150640	0.45126	D	0.000393	T	0.12135	0.0295	M	0.75447	2.3	0.58432	D	0.999992	D	0.89917	1.0	D	0.91635	0.999	T	0.00220	-1.1906	10	0.87932	D	0	-13.3179	8.7774	0.34769	0.8105:0.1895:0.0:0.0	.	98	Q3YBM2	T176B_HUMAN	R	98	ENSP00000419258:C98R;ENSP00000318409:C98R;ENSP00000410269:C98R;ENSP00000413531:C98R;ENSP00000397810:C98R	ENSP00000318409:C98R	C	-	1	0	TMEM176B	150122005	0.774000	0.28592	0.998000	0.56505	0.758000	0.43043	1.283000	0.33237	1.858000	0.53909	0.446000	0.29264	TGT	.	.	.	none		0.572	TMEM176B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349204.1	NM_014020		G	150491072	A	G	150491072	3	3	38	1	0	0	0	0	1	0	0	0	16105	188	7	3	540	3	TMEM176B	7	150491072	Missense_Mutation	SNP	A	TCGA-5P-A9KC-01A-11D-A42J-10	43661278	150491072	8647591	44	2737											
LPL	4023	hgsc.bcm.edu	37	chr8	19805804	19805804	+	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	cagagtccgtggctacctgtCatttcaatcacagcagcaaa	12	9	8	12	1	3	1	3	0	0	1	4	1	4	1	2	1	3	3	2	1	3	2			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr8:19805804C>T	ENST00000311322.8	+	2	672	c.202C>T	c.(202-204)Cat>Tat	p.H68Y	LPL_ENST00000521994.1_3'UTR	NM_000237.2	NP_000228.1	P06858	LIPL_HUMAN	lipoprotein lipase	68					chylomicron remodeling (GO:0034371)|fatty acid biosynthetic process (GO:0006633)|lipoprotein metabolic process (GO:0042157)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of sequestering of triglyceride (GO:0010890)|response to cold (GO:0009409)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|triglyceride metabolic process (GO:0006641)|very-low-density lipoprotein particle remodeling (GO:0034372)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|lipoprotein lipase activity (GO:0004465)|phospholipase activity (GO:0004620)|receptor binding (GO:0005102)|triglyceride binding (GO:0017129)|triglyceride lipase activity (GO:0004806)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	36				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	AST-120(DB05269)|Tyloxapol(DB06439)	GGCTACCTGTCATTTCAATCA	0.517																																					p.H68Y		Atlas-SNP	.											.	LPL	78	.	0			c.C202T						PASS	.						129	111	117					8																	19805804		2203	4300	6503	SO:0001583	missense	4023	exon2			ACCTGTCATTTCA		CCDS6012.1	8p22	2012-10-02			ENSG00000175445	ENSG00000175445	3.1.1.34		6677	protein-coding gene	gene with protein product		609708		LIPD			Standard	NM_000237		Approved		uc003wzk.4	P06858	OTTHUMG00000036645	ENST00000311322.8:c.202C>T	chr8.hg19:g.19805804C>T	ENSP00000309757:p.His68Tyr	111.0	0.0	.		125.0	40.0	.	NM_000237	B2R5T9|Q16282|Q16283|Q96FC4	Missense_Mutation	SNP	ENST00000311322.8	hg19	CCDS6012.1	.	.	.	.	.	.	.	.	.	.	C	13.50	2.256638	0.39896	.	.	ENSG00000175445	ENST00000524029;ENST00000522701;ENST00000311322;ENST00000535763	D;D;D	0.90385	-2.66;-2.66;-2.66	5.53	4.57	0.56435	Lipase, N-terminal (1);	0.381500	0.31963	N	0.006798	D	0.86768	0.6012	L	0.28556	0.865	0.30370	N	0.782972	P	0.45011	0.848	P	0.46885	0.53	D	0.88243	0.2911	8	.	.	.	-18.2601	12.3788	0.55295	0.2421:0.7579:0.0:0.0	.	68	P06858	LIPL_HUMAN	Y	68;68;68;54	ENSP00000428237:H68Y;ENSP00000428557:H68Y;ENSP00000309757:H68Y	.	H	+	1	0	LPL	19850084	0.406000	0.25344	1.000000	0.80357	0.178000	0.23041	1.150000	0.31639	2.599000	0.87857	0.655000	0.94253	CAT	.	.	.	none		0.517	LPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089113.3			T	19805804	C	T	19805804	3	4	38	1	0	0	0	0	1	0	0	0	8928	826	29	2	208	2	LPL	8	19805804	Missense_Mutation	SNP	C	TCGA-5P-A9KC-01A-11D-A42J-10		19805804	126558218	45	2738											
PEBP4	157310	hgsc.bcm.edu	37	chr8	22777789	22777789	+	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	aggaacaaccttgcagccaaTgttccccaactctgggtaga	12	8	9	12	0	1	1	0	0	1	1	2	2	2	2	4	2	5	3	4	2	5	3	rs201637080	byFrequency	TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr8:22777789T>A	ENST00000256404.6	-	3	257	c.166A>T	c.(166-168)Att>Ttt	p.I56F	PEBP4_ENST00000521284.1_5'UTR	NM_144962.2	NP_659399.2	Q96S96	PEBP4_HUMAN	phosphatidylethanolamine-binding protein 4	56						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)		TTGCAGCCAATGTTCCCCAAC	0.537																																					p.I56F		Atlas-SNP	.											.	PEBP4	23	.	0			c.A166T						PASS	.						78	84	82					8																	22777789		1907	4111	6018	SO:0001583	missense	157310	exon3			AGCCAATGTTCCC	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.166A>T	chr8.hg19:g.22777789T>A	ENSP00000256404:p.Ile56Phe	68.0	0.0	.		76.0	26.0	.	NM_144962	Q5EVA1|Q8WW74	Missense_Mutation	SNP	ENST00000256404.6	hg19	CCDS43724.1	.	.	.	.	.	.	.	.	.	.	T	9.085	1.000215	0.19121	.	.	ENSG00000134020	ENST00000256404	T	0.49432	0.78	5.75	-5.55	0.02536	.	0.657684	0.14588	N	0.310461	T	0.33990	0.0882	L	0.29908	0.895	0.09310	N	0.999999	P	0.50066	0.931	P	0.47402	0.546	T	0.35822	-0.9773	10	0.54805	T	0.06	-12.6443	7.9829	0.30194	0.0:0.4548:0.2715:0.2737	.	56	Q96S96	PEBP4_HUMAN	F	56	ENSP00000256404:I56F	ENSP00000256404:I56F	I	-	1	0	PEBP4	22833734	0.005000	0.15991	0.016000	0.15963	0.006000	0.05464	-1.156000	0.03160	-1.083000	0.03097	-0.263000	0.10527	ATT	.	.	.	alt		0.537	PEBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375141.2	NM_144962		A	22777789	T	A	22777789	3	1	38	1	0	0	0	0	1	0	0	0	11721	1464	51	5	537	5	PEBP4	8	22777789	Missense_Mutation	SNP	T	TCGA-5P-A9KC-01A-11D-A42J-10	2971985	22777789	123586233	46	2739											
ZNF250	58500	hgsc.bcm.edu	37	chr8	146106965	146106965	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggttgaaggcacgcccacActccccgcactcatagggct	8	7	10	16	2	1	1	1	1	0	0	2	1	2	1	3	3	0	4	3	3	2	2			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr8:146106965A>G	ENST00000292579.7	-	6	1734	c.1618T>C	c.(1618-1620)Tgt>Cgt	p.C540R	ZNF250_ENST00000417550.2_Missense_Mutation_p.C535R|ZNF250_ENST00000543949.1_Intron|ZNF250_ENST00000342660.6_Intron	NM_001109689.3|NM_021061.4	NP_001103159.1|NP_066405.1	P15622	ZN250_HUMAN	zinc finger protein 250	540					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(2)|lung(8)|skin(1)	15	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;2.53e-38)|OV - Ovarian serous cystadenocarcinoma(54;4.07e-38)|all cancers(56;2.27e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.0654)		GCACGCCCACACTCCCCGCAC	0.542																																					p.C540R	NSCLC(16;520 556 24096 40084 43446)	Atlas-SNP	.											.	ZNF250	37	.	0			c.T1618C						PASS	.						78	61	67					8																	146106965		2203	4300	6503	SO:0001583	missense	58500	exon6			GCCCACACTCCCC	AK095705	CCDS34972.1, CCDS55282.1	8q24.3	2013-01-08	2004-11-08			ENSG00000196150		"Zinc fingers, C2H2-type", "-"	13044	protein-coding gene	gene with protein product			"zinc finger protein 647"	ZNF647		12477932	Standard	NM_021061		Approved	MGC9718, ZFP647	uc003zer.4	P15622		ENST00000292579.7:c.1618T>C	chr8.hg19:g.146106965A>G	ENSP00000292579:p.Cys540Arg	63.0	0.0	.		65.0	16.0	.	NM_021061	D3DWP1|Q59HE9|Q8N942|Q96AH9	Missense_Mutation	SNP	ENST00000292579.7	hg19	CCDS34972.1	.	.	.	.	.	.	.	.	.	.	A	18.89	3.718818	0.68844	.	.	ENSG00000196150	ENST00000292579;ENST00000417550;ENST00000394912	D;D	0.85955	-2.05;-2.05	4.06	4.06	0.47325	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.53938	D	0.000059	D	0.94522	0.8236	H	0.96916	3.905	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.996;0.999	D	0.95711	0.8758	10	0.72032	D	0.01	-18.4303	12.9415	0.58348	1.0:0.0:0.0:0.0	.	535;540	D3DWP1;P15622	.;ZN250_HUMAN	R	540;535;423	ENSP00000292579:C540R;ENSP00000393442:C535R	ENSP00000292579:C540R	C	-	1	0	ZNF250	146077769	0.973000	0.33851	0.998000	0.56505	0.874000	0.50279	4.788000	0.62439	2.077000	0.62373	0.397000	0.26171	TGT	.	.	.	none		0.542	ZNF250-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382968.1	NM_021061		G	146106965	A	G	146106965	3	3	38	1	0	0	0	0	1	0	0	0	17807	159	6	3	68	3	ZNF250	8	146106965	Missense_Mutation	SNP	A	TCGA-5P-A9KC-01A-11D-A42J-10	123329176	146106965	257057	47	2740											
KIAA1432	57589	hgsc.bcm.edu	37	chr9	5763340	5763340	+	Frame_Shift_Del	DEL	T	T	-																															tcccagcggatcatgctgccTttccacatcaacatttaccc																										TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr9:5763340delT	ENST00000414202.2	+	19	2504	c.2313delT	c.(2311-2313)cctfs	p.P771fs	KIAA1432_ENST00000418622.3_Frame_Shift_Del_p.P692fs|KIAA1432_ENST00000381532.2_Frame_Shift_Del_p.P692fs|KIAA1432_ENST00000251879.6_Frame_Shift_Del_p.P771fs|KIAA1432_ENST00000449720.2_Frame_Shift_Del_p.P655fs	NM_001206557.1|NM_020829.3	NP_001193486.1|NP_065880.2														breast(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(23)|prostate(1)|upper_aerodigestive_tract(1)	45		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)		TCATGCTGCCTTTCCACATCA	0.493																																					p.P771fs		Atlas-Indel,Pindel	.											.	KIAA1432	97	.	0			c.2312delC						PASS	.						258	237	244					9																	5763340		2203	4300	6503	SO:0001589	frameshift_variant	57589	exon19			.																												ENST00000414202.2:c.2313delT	chr9.hg19:g.5763340delT	ENSP00000416696:p.Pro771fs	109.0	0.0	0		135.0	44.0	0.325926	NM_001135920		Frame_Shift_Del	DEL	ENST00000414202.2	hg19	CCDS34982.2																																																																																			.	.	.	none		0.493	KIAA1432-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051636.3			-	5763340	T	-	5763340	7	5	38	1	0	1	0	1	0	0	0	0	8240	1596	56	0	2146	0	KIAA1432	9	5763340	Frame_Shift_Del	DEL	T	TCGA-5P-A9KC-01A-11D-A42J-10		5763340	135450091	48	2741											
PFKP	5214	hgsc.bcm.edu	37	chr10	3109839	3109839	+	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	gctccttgcggaagttcctgGagcacctctccggggccggc	4	8	14	15	3	1	0	0	0	1	0	4	2	3	2	5	5	2	3	5	5	1	2			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr10:3109839G>A	ENST00000381125.4	+	1	128	c.52G>A	c.(52-54)Gag>Aag	p.E18K	RP11-118K6.3_ENST00000607898.1_lincRNA|PFKP_ENST00000381075.2_5'Flank	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	18	N-terminal catalytic PFK domain 1.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein complex binding (GO:0032403)			breast(2)|central_nervous_system(4)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		GAAGTTCCTGGAGCACCTCTC	0.746																																					p.E18K		Atlas-SNP	.											.	PFKP	182	.	0			c.G52A						PASS	.						4	4	4					10																	3109839		1949	3792	5741	SO:0001583	missense	5214	exon1			TTCCTGGAGCACC	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.52G>A	chr10.hg19:g.3109839G>A	ENSP00000370517:p.Glu18Lys	76.0	0.0	.		91.0	22.0	.	NM_002627	B3KS15|Q5VSR7|Q5VSR8	Missense_Mutation	SNP	ENST00000381125.4	hg19	CCDS7059.1	.	.	.	.	.	.	.	.	.	.	G	15.93	2.977986	0.53720	.	.	ENSG00000067057	ENST00000381125	T	0.79940	-1.32	3.84	3.84	0.44239	.	0.305787	0.28718	N	0.014375	T	0.67618	0.2912	N	0.20986	0.625	0.80722	D	1	B	0.13145	0.007	B	0.11329	0.006	T	0.62186	-0.6907	10	0.11485	T	0.65	.	15.7657	0.78126	0.0:0.0:1.0:0.0	.	18	Q01813	K6PP_HUMAN	K	18	ENSP00000370517:E18K	ENSP00000370517:E18K	E	+	1	0	PFKP	3099839	1.000000	0.71417	1.000000	0.80357	0.634000	0.38068	6.336000	0.72954	1.876000	0.54355	0.450000	0.29827	GAG	.	.	.	none		0.746	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627		A	3109839	G	A	3109839	3	1	38	1	0	0	0	0	1	0	0	0	11773	1175	41	2	54	2	PFKP	10	3109839	Missense_Mutation	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10		3109839	132424908	49	2742											
POLR3A	11128	hgsc.bcm.edu	37	chr10	79741958	79741958	+	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	gggtgcccttcacaccgtgtGtggccatgactgcccgcagg	5	8	14	14	2	1	1	1	1	0	0	1	1	1	1	4	3	2	1	4	3	0	1	rs200705099		TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr10:79741958G>C	ENST00000372371.3	-	28	3850	c.3713C>G	c.(3712-3714)aCa>aGa	p.T1238R		NM_007055.3	NP_008986.2	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa	1238					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)			CACACCGTGTGTGGCCATGAC	0.557																																					p.T1238R		Atlas-SNP	.											.	POLR3A	104	.	0			c.C3713G						PASS	.						178	140	153					10																	79741958		2203	4300	6503	SO:0001583	missense	11128	exon28			CCGTGTGTGGCCA	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.3713C>G	chr10.hg19:g.79741958G>C	ENSP00000361446:p.Thr1238Arg	90.0	0.0	.		86.0	23.0	.	NM_007055	Q8IW34|Q8TCW5	Missense_Mutation	SNP	ENST00000372371.3	hg19	CCDS7354.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.837201	0.91117	.	.	ENSG00000148606	ENST00000539141;ENST00000372371;ENST00000540842	T	0.67865	-0.29	5.99	5.99	0.97316	RNA polymerase Rpb1, domain 5 (1);	0.000000	0.85682	D	0.000000	D	0.82476	0.5045	M	0.75777	2.31	0.80722	D	1	D	0.69078	0.997	D	0.74674	0.984	T	0.80830	-0.1207	9	.	.	.	-23.5145	20.4488	0.99124	0.0:0.0:1.0:0.0	.	1238	O14802	RPC1_HUMAN	R	54;1238;1217	ENSP00000361446:T1238R	.	T	-	2	0	POLR3A	79411964	1.000000	0.71417	0.953000	0.39169	0.779000	0.44077	9.155000	0.94700	2.843000	0.97960	0.655000	0.94253	ACA	.	G|1.000;A|0.000	.	alt		0.557	POLR3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048923.1	NM_007055		C	79741958	G	C	79741958	3	2	38	1	0	0	0	0	1	0	0	0	12235	1377	48	4	475	4	POLR3A	10	79741958	Missense_Mutation	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10	76632119	79741958	55792789	50	2743											
CNNM1	26507	hgsc.bcm.edu	37	chr10	101090293	101090293	+	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	ggccgcctgctggactgggcGctgcgccaggagataagcac	7	5	16	13	3	0	1	0	0	0	1	0	3	0	2	3	4	3	3	3	4	1	1			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr10:101090293G>C	ENST00000356713.4	+	1	1438	c.1149G>C	c.(1147-1149)gcG>gcC	p.A383A	CNNM1_ENST00000370528.3_Silent_p.A312A|CNNM1_ENST00000370534.4_Silent_p.A18A|CNNM1_ENST00000446890.1_Silent_p.A312A	NM_020348.2	NP_065081.2	Q9NRU3	CNNM1_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 1	383	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)		TGGACTGGGCGCTGCGCCAGG	0.662																																					p.A383A		Atlas-SNP	.											.	CNNM1	101	.	0			c.G1149C						PASS	.						18	16	17					10																	101090293		2202	4294	6496	SO:0001819	synonymous_variant	26507	exon1			CTGGGCGCTGCGC	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.1149G>C	chr10.hg19:g.101090293G>C		91.0	0.0	.		100.0	28.0	.	NM_020348	Q4QQG7|Q4QQH8|Q4QQP9|Q9NT45	Silent	SNP	ENST00000356713.4	hg19	CCDS7478.2																																																																																			.	.	.	none		0.662	CNNM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049792.2	NM_020348		C	101090293	G	C	101090293	2	2	38	1	0	0	0	0	0	0	0	1	3614	1074	38	4		4	CNNM1	10	101090293	Silent	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10	21348335	101090293	34444454	51	2744											
TACC2	10579	hgsc.bcm.edu	37	chr10	123842717	123842717	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagaggctgcaggtggcttTccccctgcagagtccaggca	9	7	13	12	0	0	2	0	0	0	2	2	2	2	2	3	4	2	5	3	4	1	1			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr10:123842717T>C	ENST00000369005.1	+	4	1042	c.702T>C	c.(700-702)ttT>ttC	p.F234F	TACC2_ENST00000515603.1_Silent_p.F234F|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000334433.3_Silent_p.F234F|TACC2_ENST00000453444.2_Silent_p.F234F|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515273.1_Silent_p.F234F	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	234					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)				CAGGTGGCTTTCCCCCTGCAG	0.627																																					p.F234F		Atlas-SNP	.											.	TACC2	271	.	0			c.T702C						PASS	.						31	35	34					10																	123842717		2203	4300	6503	SO:0001819	synonymous_variant	10579	exon4			TGGCTTTCCCCCT	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.702T>C	chr10.hg19:g.123842717T>C		101.0	0.0	.		94.0	4.0	.	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	hg19	CCDS7626.1																																																																																			.	.	.	none		0.627	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			C	123842717	T	C	123842717	2	2	38	1	0	0	0	0	0	0	0	1	15514	1780	62	3		3	TACC2	10	123842717	Silent	SNP	T	TCGA-5P-A9KC-01A-11D-A42J-10	22752424	123842717	11692030	52	2745											
OR5P3	120066	hgsc.bcm.edu	37	chr11	7846802	7846802	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgaggtgggaggtgcaggTggagaaggccttgtggcggc	7	7	22	5	1	0	2	0	1	0	1	0	4	0	3	1	8	1	1	1	8	1	1			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr11:7846802T>C	ENST00000328375.1	-	1	717	c.718A>G	c.(718-720)Acc>Gcc	p.T240A	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153445.1	NP_703146.1	Q8WZ94	OR5P3_HUMAN	olfactory receptor, family 5, subfamily P, 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)			autonomic_ganglia(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(2)|upper_aerodigestive_tract(1)	15				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GAGGTGCAGGTGGAGAAGGCC	0.507																																					p.T240A		Atlas-SNP	.											.	OR5P3	44	.	0			c.A718G						PASS	.						131	110	117					11																	7846802		2190	4296	6486	SO:0001583	missense	120066	exon1			TGCAGGTGGAGAA	AF158377	CCDS7783.1	11p15.4	2012-08-09			ENSG00000182334	ENSG00000182334		"GPCR / Class A : Olfactory receptors"	14784	protein-coding gene	gene with protein product							Standard	NM_153445		Approved	JCG1	uc010rbg.2	Q8WZ94	OTTHUMG00000165669	ENST00000328375.1:c.718A>G	chr11.hg19:g.7846802T>C	ENSP00000332068:p.Thr240Ala	121.0	0.0	.		132.0	37.0	.	NM_153445	Q6IFE1|Q8NGM2	Missense_Mutation	SNP	ENST00000328375.1	hg19	CCDS7783.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.417992	0.83449	.	.	ENSG00000182334	ENST00000328375	T	0.41065	1.01	5.12	5.12	0.69794	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000037	T	0.74245	0.3691	H	0.96365	3.81	0.40222	D	0.977746	D	0.89917	1.0	D	0.97110	1.0	T	0.83182	-0.0088	10	0.87932	D	0	-38.011	12.9161	0.58207	0.0:0.0:0.0:1.0	.	240	Q8WZ94	OR5P3_HUMAN	A	240	ENSP00000332068:T240A	ENSP00000332068:T240A	T	-	1	0	OR5P3	7803378	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.944000	0.70219	2.147000	0.66899	0.528000	0.53228	ACC	.	.	.	none		0.507	OR5P3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385697.1	NM_153445		C	7846802	T	C	7846802	3	2	38	1	0	0	0	0	1	0	0	0	11186	1696	59	3	220	3	OR5P3	11	7846802	Missense_Mutation	SNP	T	TCGA-5P-A9KC-01A-11D-A42J-10		7846802	127159714	53	2746											
TRIM44	54765	hgsc.bcm.edu	37	chr11	35685224	35685224	+	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	atgggcttgatttgagtaccTattgccaggaagataggcag	11	11	13	6	0	0	3	0	2	0	1	0	4	0	4	2	3	2	3	2	3	4	6			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr11:35685224T>A	ENST00000299413.5	+	1	872	c.565T>A	c.(565-567)Tat>Aat	p.Y189N	RP1-276E15.1_ENST00000525573.2_lincRNA	NM_017583.4	NP_060053.2	Q96DX7	TRI44_HUMAN	tripartite motif containing 44	189						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18	all_lung(20;0.0317)|Lung NSC(22;0.0661)|all_epithelial(35;0.115)	all_hematologic(20;0.107)				TTTGAGTACCTATTGCCAGGA	0.498																																					p.Y189N		Atlas-SNP	.											.	TRIM44	29	.	0			c.T565A						PASS	.						134	122	126					11																	35685224		2202	4298	6500	SO:0001583	missense	54765	exon1			AGTACCTATTGCC	BC024031	CCDS31461.1	11p13	2011-04-20	2011-01-25		ENSG00000166326	ENSG00000166326		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19016	protein-coding gene	gene with protein product		612298	"tripartite motif-containing 44"				Standard	NM_017583		Approved	DIPB, MC7	uc001mwi.2	Q96DX7	OTTHUMG00000166312	ENST00000299413.5:c.565T>A	chr11.hg19:g.35685224T>A	ENSP00000299413:p.Tyr189Asn	130.0	0.0	.		132.0	39.0	.	NM_017583	D3DR14|Q96QY2|Q9UGK0	Missense_Mutation	SNP	ENST00000299413.5	hg19	CCDS31461.1	.	.	.	.	.	.	.	.	.	.	T	12.74	2.029805	0.35797	.	.	ENSG00000166326	ENST00000299413	T	0.52754	0.65	4.99	2.61	0.31194	Zinc finger, B-box (3);	0.000000	0.32608	N	0.005868	T	0.50051	0.1593	M	0.88704	2.975	0.42521	D	0.993006	B	0.22146	0.065	B	0.21708	0.036	T	0.50294	-0.8845	10	0.87932	D	0	-6.2404	5.5627	0.17152	0.1523:0.0858:0.0:0.7619	.	189	Q96DX7	TRI44_HUMAN	N	189	ENSP00000299413:Y189N	ENSP00000299413:Y189N	Y	+	1	0	TRIM44	35641800	1.000000	0.71417	0.666000	0.29783	0.021000	0.10359	5.358000	0.66064	0.308000	0.22923	-0.250000	0.11733	TAT	.	.	.	none		0.498	TRIM44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389081.1	NM_017583		A	35685224	T	A	35685224	3	1	38	1	0	0	0	0	1	0	0	0	16531	1522	53	5	567	5	TRIM44	11	35685224	Missense_Mutation	SNP	T	TCGA-5P-A9KC-01A-11D-A42J-10	27838422	35685224	99321292	54	2747											
AHNAK	79026	hgsc.bcm.edu	37	chr11	62294536	62294536	+	Frame_Shift_Del	DEL	G	G	-																															acatcaggcatagaaatattGggggctttgaaatgcatatc																										TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr11:62294536delG	ENST00000378024.4	-	5	7627	c.7353delC	c.(7351-7353)cccfs	p.P2451fs	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	2451					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)				TAGAAATATTGGGGGCTTTGA	0.453																																					p.N2452fs		Atlas-Indel,Pindel	.											.	AHNAK	532	.	0			c.7354delA						PASS	.						123	125	125					11																	62294536		2202	4299	6501	SO:0001589	frameshift_variant	79026	exon5			.	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.7353delC	chr11.hg19:g.62294536delG	ENSP00000367263:p.Pro2451fs	113.0	0.0	0		116.0	33.0	0.284483	NM_001620	A1A586	Frame_Shift_Del	DEL	ENST00000378024.4	hg19	CCDS31584.1																																																																																			.	.	.	none		0.453	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		-	62294536	G	-	62294536	7	5	38	1	0	1	0	1	0	0	0	0	414	1335	47	0	10439	0	AHNAK	11	62294536	Frame_Shift_Del	DEL	G	TCGA-5P-A9KC-01A-11D-A42J-10	26609312	62294536	72711980	55	2748											
SUV420H1	51111	hgsc.bcm.edu	37	chr11	67926523	67926523	+	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	accctggaattatttatatgAgttagcttagatgaggtaga	13	14	10	4	0	0	4	0	2	0	2	0	5	0	5	1	2	1	3	1	2	7	7			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr11:67926523A>C	ENST00000304363.4	-	11	1643	c.1290T>G	c.(1288-1290)acT>acG	p.T430T		NM_017635.3	NP_060105	Q4FZB7	SV421_HUMAN	suppressor of variegation 4-20 homolog 1 (Drosophila)	430					histone H4-K20 trimethylation (GO:0034773)|muscle organ development (GO:0007517)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)	histone methyltransferase activity (H4-K20 specific) (GO:0042799)|histone-lysine N-methyltransferase activity (GO:0018024)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(15)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						TATTTATATGAGTTAGCTTAG	0.388																																					p.T430T		Atlas-SNP	.											.	SUV420H1	125	.	0			c.T1290G						PASS	.						102	106	105					11																	67926523		2199	4294	6493	SO:0001819	synonymous_variant	51111	exon11			TATATGAGTTAGC	AL512763	CCDS31623.1, CCDS44660.1	11q13.2	2011-07-01			ENSG00000110066	ENSG00000110066		"Chromatin-modifying enzymes / K-methyltransferases"	24283	protein-coding gene	gene with protein product		610881				10810093, 11401438	Standard	NM_016028		Approved	CGI-85, KMT5B	uc001onm.1	Q4FZB7	OTTHUMG00000150484	ENST00000304363.4:c.1290T>G	chr11.hg19:g.67926523A>C		82.0	0.0	.		67.0	14.0	.	NM_017635	B7WNX7|Q3SX56|Q4V775|Q6P150|Q96E44|Q9BUL0|Q9H022|Q9H2K3|Q9NXV3|Q9Y393	Silent	SNP	ENST00000304363.4	hg19	CCDS31623.1																																																																																			.	.	.	none		0.388	SUV420H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318319.1	NM_017635		C	67926523	A	C	67926523	2	2	38	1	0	0	0	0	0	0	0	1	15426	291	11	5		5	SUV420H1	11	67926523	Silent	SNP	A	TCGA-5P-A9KC-01A-11D-A42J-10	5631987	67926523	67079993	56	2749											
CNTN5	53942	hgsc.bcm.edu	37	chr11	99941227	99941227	+	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	gccctctccgatgggaatgtAaggctactggaaaacccaga	12	7	11	11	1	1	1	0	0	1	1	2	4	1	3	3	3	2	2	3	3	5	2			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr11:99941227A>T	ENST00000524871.1	+	11	1524	c.1234A>T	c.(1234-1236)Aag>Tag	p.K412*	CNTN5_ENST00000418526.2_Nonsense_Mutation_p.K338*|CNTN5_ENST00000279463.3_Nonsense_Mutation_p.K412*|CNTN5_ENST00000528682.1_Nonsense_Mutation_p.K412*|CNTN5_ENST00000527185.1_Nonsense_Mutation_p.K412*	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	412	Ig-like C2-type 4.				cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		ATGGGAATGTAAGGCTACTGG	0.468																																					p.K412X		Atlas-SNP	.											.	CNTN5	324	.	0			c.A1234T						PASS	.						93	92	92					11																	99941227		1892	4111	6003	SO:0001587	stop_gained	53942	exon10			GAATGTAAGGCTA	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.1234A>T	chr11.hg19:g.99941227A>T	ENSP00000435637:p.Lys412*	79.0	0.0	.		89.0	15.0	.	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Nonsense_Mutation	SNP	ENST00000524871.1	hg19	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	A	40	8.015620	0.98610	.	.	ENSG00000149972	ENST00000527185;ENST00000528682;ENST00000524871;ENST00000418526;ENST00000279463	.	.	.	5.97	5.97	0.96955	.	0.045838	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.6272	0.76870	1.0:0.0:0.0:0.0	.	.	.	.	X	412;412;412;338;412	.	ENSP00000279463:K412X	K	+	1	0	CNTN5	99446437	1.000000	0.71417	0.993000	0.49108	0.844000	0.47949	9.339000	0.96797	2.285000	0.76669	0.528000	0.53228	AAG	.	.	.	none		0.468	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361		T	99941227	A	T	99941227	4	4	38	1	0	0	0	0	0	1	0	0	3646	363	13	5	1268	5	CNTN5	11	99941227	Nonsense_Mutation	SNP	A	TCGA-5P-A9KC-01A-11D-A42J-10	32014704	99941227	35065289	57	2750											
OR8B8	26493	hgsc.bcm.edu	37	chr11	124310809	124310809	+	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	tatagaggaagaagtacataGgggtgtgcaagtgagagttg	14	9	16	2	0	0	3	0	1	0	3	0	5	0	4	0	3	2	3	0	3	7	5			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr11:124310809G>T	ENST00000328064.2	-	1	245	c.173C>A	c.(172-174)cCt>cAt	p.P58H		NM_012378.1	NP_036510.1	Q15620	OR8B8_HUMAN	olfactory receptor, family 8, subfamily B, member 8	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)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		GAAGTACATAGGGGTGTGCAA	0.453																																					p.P58H		Atlas-SNP	.											.	OR8B8	76	.	0			c.C173A						PASS	.						120	123	122					11																	124310809		2201	4299	6500	SO:0001583	missense	26493	exon1			TACATAGGGGTGT	AF238488	CCDS8446.1	11q24.2	2012-08-09			ENSG00000197125	ENSG00000197125		"GPCR / Class A : Olfactory receptors"	8477	protein-coding gene	gene with protein product						9119360	Standard	NM_012378		Approved	TPCR85	uc010sal.2	Q15620	OTTHUMG00000165917	ENST00000328064.2:c.173C>A	chr11.hg19:g.124310809G>T	ENSP00000330280:p.Pro58His	82.0	0.0	.		75.0	28.0	.	NM_012378	A1L446|Q96RC8	Missense_Mutation	SNP	ENST00000328064.2	hg19	CCDS8446.1	.	.	.	.	.	.	.	.	.	.	G	18.79	3.698534	0.68386	.	.	ENSG00000197125	ENST00000328064	T	0.02050	4.48	3.8	2.89	0.33648	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48767	D	0.000161	T	0.20047	0.0482	H	0.97440	4.005	0.48696	D	0.999697	D	0.89917	1.0	D	0.97110	1.0	T	0.24977	-1.0145	10	0.87932	D	0	.	11.8548	0.52431	0.0889:0.0:0.9111:0.0	.	58	Q15620	OR8B8_HUMAN	H	58	ENSP00000330280:P58H	ENSP00000330280:P58H	P	-	2	0	OR8B8	123816019	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.395000	0.79876	1.174000	0.42811	0.557000	0.71058	CCT	.	.	.	none		0.453	OR8B8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387056.1	NM_012378		T	124310809	G	T	124310809	3	4	38	1	0	0	0	0	1	0	0	0	11237	1000	35	4	765	4	OR8B8	11	124310809	Missense_Mutation	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10	24369582	124310809	10695707	58	2751											
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43769218	43769218	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgagatcaattcttatttTgctgaaaacagtgtatccag	13	14	8	6	0	2	2	1	2	1	1	3	3	3	2	1	0	2	2	1	0	5	5			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr12:43769218T>C	ENST00000389420.3	-	36	5409	c.5410A>G	c.(5410-5412)Aaa>Gaa	p.K1804E		NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1804	GON. {ECO:0000255|PROSITE- ProRule:PRU00383}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		ATTCTTATTTTGCTGAAAACA	0.338																																					p.K1804E		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.A5410G						PASS	.						125	120	121					12																	43769218		2203	4300	6503	SO:0001583	missense	80070	exon36			TTATTTTGCTGAA	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.5410A>G	chr12.hg19:g.43769218T>C	ENSP00000374071:p.Lys1804Glu	85.0	0.0	.		111.0	28.0	.	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	hg19	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	T	15.21	2.766630	0.49574	.	.	ENSG00000173157	ENST00000389420	T	0.32515	1.45	4.93	4.93	0.64822	Peptidase M12B, GON-ADAMTSs (2);	0.000000	0.52532	D	0.000076	T	0.62060	0.2397	M	0.88570	2.965	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.70651	-0.4813	10	0.72032	D	0.01	.	15.2892	0.73854	0.0:0.0:0.0:1.0	.	1804	P59510	ATS20_HUMAN	E	1804	ENSP00000374071:K1804E	ENSP00000374071:K1804E	K	-	1	0	ADAMTS20	42055485	1.000000	0.71417	1.000000	0.80357	0.031000	0.12232	6.588000	0.74076	2.150000	0.67090	0.455000	0.32223	AAA	.	.	.	none		0.338	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		C	43769218	T	C	43769218	3	2	38	1	0	0	0	0	1	0	0	0	266	1821	63	3	337	3	ADAMTS20	12	43769218	Missense_Mutation	SNP	T	TCGA-5P-A9KC-01A-11D-A42J-10		43769218	90082677	59	2752											
DDN	23109	hgsc.bcm.edu	37	chr12	49392077	49392077	+	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	gggggcccgggccgccgaccTccccagggccccgcccacgc	3	1	15	22	5	0	0	0	0	0	0	1	1	1	0	9	4	0	0	9	4	0	0			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr12:49392077T>A	ENST00000421952.2	-	2	603	c.582A>T	c.(580-582)ggA>ggT	p.G194G	RP11-386G11.3_ENST00000549516.1_RNA|RP11-386G11.5_ENST00000547866.1_RNA|RP11-386G11.5_ENST00000547395.1_RNA|RP11-386G11.5_ENST00000552284.1_RNA|RP11-386G11.5_ENST00000552933.1_RNA	NM_015086.1	NP_055901.2	O94850	DEND_HUMAN	dendrin	194	Interaction with MAGI2.					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						GCCGCCGACCTCCCCAGGGCC	0.781																																					p.G194G		Atlas-SNP	.											.	DDN	54	.	0			c.A582T						PASS	.						6	7	7					12																	49392077		1658	3517	5175	SO:0001819	synonymous_variant	23109	exon2			CCGACCTCCCCAG	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.582A>T	chr12.hg19:g.49392077T>A		37.0	0.0	.		29.0	7.0	.	NM_015086		Silent	SNP	ENST00000421952.2	hg19	CCDS31791.2																																																																																			.	.	.	none		0.781	DDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343335.1			A	49392077	T	A	49392077	2	1	38	1	0	0	0	0	0	0	0	1	4335	1538	54	5		5	DDN	12	49392077	Silent	SNP	T	TCGA-5P-A9KC-01A-11D-A42J-10	5622859	49392077	84459818	60	2753											
ERBB3	2065	hgsc.bcm.edu	37	chr12	56481697	56481697	+	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	cctcaggacacagactgcttTgtatgtaccctttccattgc	8	13	7	13	0	1	1	1	0	0	1	2	2	2	2	3	1	3	3	3	1	2	5			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr12:56481697T>C	ENST00000267101.3	+	6	1172	c.732T>C	c.(730-732)ttT>ttC	p.F244F	ERBB3_ENST00000450146.2_Intron|ERBB3_ENST00000415288.2_Splice_Site_p.F185F	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	244					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			CAGACTGCTTTGTATGTACCC	0.532																																					p.F244F		Atlas-SNP	.											.	ERBB3	350	.	0			c.T732C						PASS	.						161	158	159					12																	56481697		2203	4300	6503	SO:0001630	splice_region_variant	2065	exon6			CTGCTTTGTATGT	M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"lethal congenital contracture syndrome 2"	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.732+1T>C	chr12.hg19:g.56481697T>C		64.0	0.0	.		91.0	45.0	.	NM_001982	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Silent	SNP	ENST00000267101.3	hg19	CCDS31833.1																																																																																			.	.	.	none		0.532	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3		Silent	C	56481697	T	C	56481697	5	2	38	1	0	0	0	0	0	0	1	0	5210	1826	63	3	885	3	ERBB3	12	56481697	Splice_Site	SNP	T	TCGA-5P-A9KC-01A-11D-A42J-10	7089620	56481697	77370198	61	2754											
R3HDM2	22864	hgsc.bcm.edu	37	chr12	57662177	57662177	+	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	ttgcacagactggctcacagGgaccagcatgggttgctgga	9	8	14	10	0	1	1	1	0	0	1	1	3	1	3	1	4	3	5	1	4	0	2			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr12:57662177G>A	ENST00000347140.3	-	18	2287	c.1897C>T	c.(1897-1899)Cct>Tct	p.P633S	R3HDM2_ENST00000441731.2_Missense_Mutation_p.P328S|R3HDM2_ENST00000546843.1_5'UTR|R3HDM2_ENST00000413953.2_Missense_Mutation_p.P360S|R3HDM2_ENST00000402412.1_Missense_Mutation_p.P647S|R3HDM2_ENST00000403821.2_Missense_Mutation_p.P667S|R3HDM2_ENST00000358907.2_Missense_Mutation_p.P633S|RP11-123K3.4_ENST00000548184.1_3'UTR			Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	633	Gln-rich.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	22						TGGCTCACAGGGACCAGCATG	0.557																																					p.P633S		Atlas-SNP	.											.	R3HDM2	125	.	0			c.C1897T						PASS	.						87	75	79					12																	57662177		2203	4300	6503	SO:0001583	missense	22864	exon16			TCACAGGGACCAG	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.1897C>T	chr12.hg19:g.57662177G>A	ENSP00000317903:p.Pro633Ser	52.0	0.0	.		72.0	17.0	.	NM_014925	Q2M1T9|Q3ZCT5	Missense_Mutation	SNP	ENST00000347140.3	hg19	CCDS8937.2	.	.	.	.	.	.	.	.	.	.	G	23.9	4.475222	0.84640	.	.	ENSG00000179912	ENST00000413953;ENST00000393811;ENST00000347140;ENST00000402412;ENST00000358907;ENST00000441731;ENST00000429355;ENST00000403821;ENST00000548161	T;T;T;T;T;T;T;T	0.49720	0.82;0.8;1.83;1.83;1.83;0.77;1.4;1.72	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.67674	0.2918	M	0.64170	1.965	0.58432	D	0.999992	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.996;0.996;0.996;0.998	T	0.67177	-0.5736	10	0.54805	T	0.06	-10.1624	18.5737	0.91147	0.0:0.0:1.0:0.0	.	667;647;633;360	B5MCG9;B5MCU0;Q9Y2K5;E9PAL1	.;.;R3HD2_HUMAN;.	S	360;360;633;647;633;328;398;667;22	ENSP00000409146:P360S;ENSP00000377400:P360S;ENSP00000317903:P633S;ENSP00000385839:P647S;ENSP00000351784:P633S;ENSP00000408536:P328S;ENSP00000394676:P398S;ENSP00000385169:P667S	ENSP00000317903:P633S	P	-	1	0	R3HDM2	55948444	1.000000	0.71417	0.995000	0.50966	0.754000	0.42855	7.382000	0.79729	2.755000	0.94549	0.650000	0.86243	CCT	.	.	.	none		0.557	R3HDM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326570.2	NM_014925		A	57662177	G	A	57662177	3	1	38	1	0	0	0	0	1	0	0	0	12901	1232	43	2	1061	2	R3HDM2	12	57662177	Missense_Mutation	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10	1180480	57662177	76189718	62	2755											
ASCL4	121549	hgsc.bcm.edu	37	chr12	108169302	108169302	+	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	gagaccacctgccccgggagCtggcagacaagcgcctcagc	9	3	13	16	2	1	2	1	0	0	2	1	4	1	3	5	2	4	2	5	2	1	0			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr12:108169302C>A	ENST00000342331.4	+	1	1141	c.310C>A	c.(310-312)Ctg>Atg	p.L104M		NM_203436.2	NP_982260.2	Q6XD76	ASCL4_HUMAN	achaete-scute family bHLH transcription factor 4	103	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|skin development (GO:0043588)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(1)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	13						GCCCCGGGAGCTGGCAGACAA	0.697																																					p.L104M	GBM(170;776 3695 11650)	Atlas-SNP	.											.	ASCL4	28	.	0			c.C310A						PASS	.						6	7	7					12																	108169302		2116	4159	6275	SO:0001583	missense	121549	exon1			CGGGAGCTGGCAG	AY238895	CCDS31894.2	12q24.11	2013-10-17	2013-10-17		ENSG00000187855	ENSG00000187855		"Basic helix-loop-helix proteins"	24311	protein-coding gene	gene with protein product		609155	"achaete-scute complex-like 4 (Drosophila)", "achaete-scute complex homolog 4 (Drosophila)"				Standard	NM_203436		Approved	HASH4, bHLHa44	uc001tmr.3	Q6XD76	OTTHUMG00000156964	ENST00000342331.4:c.310C>A	chr12.hg19:g.108169302C>A	ENSP00000345420:p.Leu104Met	41.0	0.0	.		38.0	17.0	.	NM_203436	Q7RTS2	Missense_Mutation	SNP	ENST00000342331.4	hg19	CCDS31894.2	.	.	.	.	.	.	.	.	.	.	C	12.88	2.070242	0.36566	.	.	ENSG00000187855	ENST00000342331	D	0.98164	-4.76	4.33	1.4	0.22301	Helix-loop-helix DNA-binding (5);	0.283517	0.28748	N	0.014263	D	0.97717	0.9251	M	0.68317	2.08	0.22648	N	0.998896	P	0.42483	0.781	P	0.57152	0.814	D	0.93422	0.6778	10	0.34782	T	0.22	-17.6037	6.1213	0.20154	0.0:0.6081:0.1363:0.2556	.	103	Q6XD76	ASCL4_HUMAN	M	104	ENSP00000345420:L104M	ENSP00000345420:L104M	L	+	1	2	ASCL4	106693432	1.000000	0.71417	0.994000	0.49952	0.566000	0.35808	0.947000	0.29082	0.057000	0.16193	0.305000	0.20034	CTG	.	.	.	none		0.697	ASCL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346845.1	NM_203436		A	108169302	C	A	108169302	3	1	38	1	0	0	0	0	1	0	0	0	1036	796	28	4	312	4	ASCL4	12	108169302	Missense_Mutation	SNP	C	TCGA-5P-A9KC-01A-11D-A42J-10	50507125	108169302	25682593	63	2756											
PARP4	143	hgsc.bcm.edu	37	chr13	25009275	25009275	+	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	caaaagacaaggaagcaggaCtgtgagcgcgggcagtcggg	13	3	17	8	3	0	2	0	1	0	1	1	4	0	4	0	4	2	2	0	4	4	0			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr13:25009275C>T	ENST00000381989.3	-	31	4109	c.4004G>A	c.(4003-4005)aGt>aAt	p.S1335N		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1335					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)		GGAAGCAGGACTGTGAGCGCG	0.498																																					p.S1335N		Atlas-SNP	.											.	PARP4	142	.	0			c.G4004A						PASS	.						86	92	90					13																	25009275		2203	4300	6503	SO:0001583	missense	143	exon31			GCAGGACTGTGAG	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.4004G>A	chr13.hg19:g.25009275C>T	ENSP00000371419:p.Ser1335Asn	95.0	0.0	.		118.0	36.0	.	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	hg19	CCDS9307.1	.	.	.	.	.	.	.	.	.	.	c	0.841	-0.742013	0.03088	.	.	ENSG00000102699	ENST00000381989	T	0.01821	4.62	2.35	-4.71	0.03279	.	9.944990	0.00691	U	0.000733	T	0.01156	0.0038	N	0.19112	0.55	0.09310	N	1	B	0.24186	0.099	B	0.18263	0.021	T	0.46205	-0.9208	10	0.16420	T	0.52	.	0.5609	0.00679	0.1939:0.2856:0.2729:0.2476	.	1335	Q9UKK3	PARP4_HUMAN	N	1335	ENSP00000371419:S1335N	ENSP00000371419:S1335N	S	-	2	0	PARP4	23907275	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-1.146000	0.03191	-1.910000	0.01083	0.313000	0.20887	AGT	.	.	.	none		0.498	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437		T	25009275	C	T	25009275	3	4	38	1	0	0	0	0	1	0	0	0	11470	565	20	2	1186	2	PARP4	13	25009275	Missense_Mutation	SNP	C	TCGA-5P-A9KC-01A-11D-A42J-10		25009275	90160603	64	2757											
TGDS	23483	hgsc.bcm.edu	37	chr13	95230409	95230409	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtttcttgtttgaagcccTgacccatgaatgcaactaaa	13	12	7	9	0	1	3	0	3	1	0	1	3	1	3	2	0	3	3	2	0	6	4			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr13:95230409T>C	ENST00000261296.5	-	9	795	c.675A>G	c.(673-675)tcA>tcG	p.S225S	TGDS_ENST00000498294.1_5'Flank	NM_014305.2	NP_055120.1	O95455	TGDS_HUMAN	TDP-glucose 4,6-dehydratase	225					nucleotide-sugar metabolic process (GO:0009225)		coenzyme binding (GO:0050662)|dTDP-glucose 4,6-dehydratase activity (GO:0008460)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	8	all_neural(89;0.0684)|Medulloblastoma(90;0.163)					TTTGAAGCCCTGACCCATGAA	0.373																																					p.S225S		Atlas-SNP	.											.	TGDS	24	.	0			c.A675G						PASS	.						77	74	75					13																	95230409		2203	4300	6503	SO:0001819	synonymous_variant	23483	exon9			AAGCCCTGACCCA	AF048686	CCDS9471.1	13q32.1	2012-02-22			ENSG00000088451	ENSG00000088451	4.2.1.46	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	20324	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 2E, member 1"					19027726	Standard	NM_014305		Approved	TDPGD, SDR2E1	uc001vlw.3	O95455	OTTHUMG00000046308	ENST00000261296.5:c.675A>G	chr13.hg19:g.95230409T>C		142.0	0.0	.		134.0	35.0	.	NM_014305	Q05DQ3|Q2TU31|Q5T3Z2|Q9H1T9	Silent	SNP	ENST00000261296.5	hg19	CCDS9471.1																																																																																			.	.	.	none		0.373	TGDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106904.2	NM_014305		C	95230409	T	C	95230409	2	2	38	1	0	0	0	0	0	0	0	1	15826	1567	55	3		3	TGDS	13	95230409	Silent	SNP	T	TCGA-5P-A9KC-01A-11D-A42J-10	70221134	95230409	19939469	65	2758											
SYT16	83851	hgsc.bcm.edu	37	chr14	62547937	62547937	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attctatctcagccacctgcAcccagaaggggaaatgaaag	14	7	9	11	0	2	2	1	1	2	1	3	3	2	3	3	2	2	1	3	2	4	2			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr14:62547937A>G	ENST00000430451.2	+	4	1576	c.1379A>G	c.(1378-1380)cAc>cGc	p.H460R	RP11-355I22.5_ENST00000553990.1_lincRNA	NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	460					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)		AGCCACCTGCACCCAGAAGGG	0.502																																					p.H460R		Atlas-SNP	.											.	SYT16	144	.	0			c.A1379G						PASS	.						30	32	31					14																	62547937		2105	4243	6348	SO:0001583	missense	83851	exon4			ACCTGCACCCAGA	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.1379A>G	chr14.hg19:g.62547937A>G	ENSP00000394700:p.His460Arg	82.0	0.0	.		91.0	24.0	.	NM_031914	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Missense_Mutation	SNP	ENST00000430451.2	hg19	CCDS45121.1	.	.	.	.	.	.	.	.	.	.	A	10.98	1.503479	0.26949	.	.	ENSG00000139973	ENST00000430451	T	0.78003	-1.14	4.88	4.88	0.63580	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.521666	0.22640	N	0.057462	T	0.56156	0.1966	N	0.08118	0	0.80722	D	1	B	0.18310	0.027	B	0.17098	0.017	T	0.53885	-0.8375	10	0.34782	T	0.22	-1.3072	7.2012	0.25881	0.831:0.0:0.169:0.0	.	460	Q17RD7	SYT16_HUMAN	R	460	ENSP00000394700:H460R	ENSP00000394700:H460R	H	+	2	0	SYT16	61617690	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.399000	0.44495	2.164000	0.68074	0.533000	0.62120	CAC	.	.	.	none		0.502	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914		G	62547937	A	G	62547937	3	3	38	1	0	0	0	0	1	0	0	0	15484	159	6	3	1393	3	SYT16	14	62547937	Missense_Mutation	SNP	A	TCGA-5P-A9KC-01A-11D-A42J-10		62547937	44801603	66	2759											
C14orf174	161394	hgsc.bcm.edu	37	chr14	77845295	77845295	+	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	gtgagttcgttcatgaaaagGaagttgtagatttgtcccaa	12	13	11	5	1	1	3	1	2	0	1	3	4	2	4	1	1	0	4	1	1	5	5			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr14:77845295G>T	ENST00000216471.4	+	1	1820	c.1534G>T	c.(1534-1536)Gaa>Taa	p.E512*	SAMD15_ENST00000533095.2_Intron|TMED8_ENST00000216468.7_5'Flank	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	512										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						TCATGAAAAGGAAGTTGTAGA	0.408																																					p.E512X		Atlas-SNP	.											.	SAMD15	60	.	0			c.G1534T						PASS	.						98	96	97					14																	77845295		2203	4300	6503	SO:0001587	stop_gained	161394	exon1			GAAAAGGAAGTTG	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.1534G>T	chr14.hg19:g.77845295G>T	ENSP00000216471:p.Glu512*	168.0	0.0	.		198.0	57.0	.	NM_001010860	Q2M3P3	Nonsense_Mutation	SNP	ENST00000216471.4	hg19	CCDS32126.1	.	.	.	.	.	.	.	.	.	.	G	36	5.723196	0.96847	.	.	ENSG00000100583	ENST00000216471	.	.	.	4.33	-2.85	0.05734	.	1.341590	0.05553	N	0.567955	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	.	5.1042	0.14775	0.3883:0.1822:0.4296:0.0	.	.	.	.	X	512	.	ENSP00000216471:E512X	E	+	1	0	SAMD15	76915048	0.002000	0.14202	0.000000	0.03702	0.020000	0.10135	-0.284000	0.08422	-0.515000	0.06479	-0.459000	0.05422	GAA	.	.	.	none		0.408	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860		T	77845295	G	T	77845295	4	4	38	1	0	0	0	0	0	1	0	0	1761	1175	41	4	1536	4	C14orf174	14	77845295	Nonsense_Mutation	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10	15297358	77845295	29504245	67	2760											
TTC7B	145567	hgsc.bcm.edu	37	chr14	91161915	91161915	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatcttccgactcctcttgTcaagttcctgtgtggacaca	9	13	7	12	1	3	0	1	0	2	0	6	2	6	1	3	1	0	1	3	1	2	3			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr14:91161915T>C	ENST00000328459.6	-	6	827	c.706A>G	c.(706-708)Aca>Gca	p.T236A	RP11-661G16.2_ENST00000553712.1_RNA|TTC7B_ENST00000357056.2_Missense_Mutation_p.T236A	NM_001010854.1	NP_001010854.1	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B	236										NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	36		Melanoma(154;0.222)				ACTCCTCTTGTCAAGTTCCTG	0.383																																					p.T236A		Atlas-SNP	.											.	TTC7B	93	.	0			c.A706G						PASS	.						123	101	108					14																	91161915		2203	4300	6503	SO:0001583	missense	145567	exon6			CTCTTGTCAAGTT	BC035865	CCDS32140.1	14q32.12	2013-01-11	2004-06-02	2004-06-04		ENSG00000165914		"Tetratricopeptide (TTC) repeat domain containing"	19858	protein-coding gene	gene with protein product			"tetratricopeptide repeat domain 7 like 1"	TTC7L1			Standard	XM_005267367		Approved		uc001xyp.3	Q86TV6		ENST00000328459.6:c.706A>G	chr14.hg19:g.91161915T>C	ENSP00000336127:p.Thr236Ala	43.0	0.0	.		50.0	14.0	.	NM_001010854	Q86U24|Q86VT3	Missense_Mutation	SNP	ENST00000328459.6	hg19	CCDS32140.1	.	.	.	.	.	.	.	.	.	.	T	12.89	2.073012	0.36566	.	.	ENSG00000165914	ENST00000555768;ENST00000357056;ENST00000328459;ENST00000557766	T;T	0.37235	1.9;1.21	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.45276	0.1334	L	0.35723	1.085	0.80722	D	1	P	0.52842	0.956	D	0.65010	0.931	T	0.21211	-1.0252	10	0.09084	T	0.74	-16.2664	15.4112	0.74923	0.0:0.0:0.0:1.0	.	236	Q86TV6	TTC7B_HUMAN	A	134;236;236;156	ENSP00000349564:T236A;ENSP00000336127:T236A	ENSP00000336127:T236A	T	-	1	0	TTC7B	90231668	1.000000	0.71417	0.998000	0.56505	0.186000	0.23388	7.386000	0.79775	2.118000	0.64928	0.402000	0.26972	ACA	.	.	.	none		0.383	TTC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411364.2			C	91161915	T	C	91161915	3	2	38	1	0	0	0	0	1	0	0	0	16725	1667	58	3	1885	3	TTC7B	14	91161915	Missense_Mutation	SNP	T	TCGA-5P-A9KC-01A-11D-A42J-10	13316620	91161915	16187625	68	2761											
C15orf2	23742	hgsc.bcm.edu	37	chr15	24924481	24924481	+	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	acatgtctgtttccaacttcCgtaagagcacctgtggttca	9	13	8	11	1	2	1	1	0	1	1	4	1	4	1	3	1	2	4	3	1	2	4			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr15:24924481C>G	ENST00000329468.2	+	1	3941	c.3467C>G	c.(3466-3468)cCg>cGg	p.P1156R		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	1156					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)		p.P1156Q(1)									TTCCAACTTCCGTAAGAGCAC	0.418																																					p.P1156R		Atlas-SNP	.											C15orf2,NS,carcinoma,-1,1	.	.	.	1	Substitution - Missense(1)	lung(1)	c.C3467G						PASS	.						72	63	66					15																	24924481		2203	4298	6501	SO:0001583	missense	23742	exon1			AACTTCCGTAAGA	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.3467C>G	chr15.hg19:g.24924481C>G	ENSP00000333735:p.Pro1156Arg	57.0	0.0	.		83.0	17.0	.	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	hg19	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	10.24	1.295704	0.23564	.	.	ENSG00000185823	ENST00000329468	T	0.09630	2.96	1.77	0.827	0.18835	.	.	.	.	.	T	0.10723	0.0262	N	0.08118	0	0.09310	N	1	D	0.76494	0.999	P	0.62813	0.907	T	0.22208	-1.0223	9	0.87932	D	0	.	4.3207	0.11016	0.0:0.7896:0.0:0.2104	.	1156	Q9NZP6	CO002_HUMAN	R	1156	ENSP00000333735:P1156R	ENSP00000333735:P1156R	P	+	2	0	C15orf2	22475574	0.000000	0.05858	0.004000	0.12327	0.013000	0.08279	0.156000	0.16382	0.304000	0.22809	0.313000	0.20887	CCG	.	.	.	none		0.418	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		G	24924481	C	G	24924481	3	3	38	1	0	0	0	0	1	0	0	0	1786	652	23	4	3469	4	C15orf2	15	24924481	Missense_Mutation	SNP	C	TCGA-5P-A9KC-01A-11D-A42J-10		24924481	77606911	69	2762											
SCAMP2	10066	hgsc.bcm.edu	37	chr15	75165566	75165566	+	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	ggggtttacatccactgggtCcgcgaaggggttggtgtcga	6	10	17	8	3	0	0	0	0	0	0	3	2	2	0	2	6	1	2	2	6	2	3			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr15:75165566C>T	ENST00000268099.9	-	1	140	c.31G>A	c.(31-33)Gac>Aac	p.D11N		NM_005697.3	NP_005688.2	O15127	SCAM2_HUMAN	secretory carrier membrane protein 2	11					post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|recycling endosome membrane (GO:0055038)|trans-Golgi network membrane (GO:0032588)|transport vesicle (GO:0030133)				kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	9						TCCACTGGGTCCGCGAAGGGG	0.682																																					p.D11N		Atlas-SNP	.											.	SCAMP2	18	.	0			c.G31A						PASS	.						48	43	45					15																	75165566		2018	3917	5935	SO:0001583	missense	10066	exon1			CTGGGTCCGCGAA	AF005038	CCDS10271.1	15q23-q25	2013-02-21			ENSG00000140497	ENSG00000140497		"Secretory carrier membrane proteins"	10564	protein-coding gene	gene with protein product		606912				9378760	Standard	NM_005697		Approved		uc002azb.1	O15127	OTTHUMG00000142817	ENST00000268099.9:c.31G>A	chr15.hg19:g.75165566C>T	ENSP00000268099:p.Asp11Asn	40.0	0.0	.		68.0	14.0	.	NM_005697	B2RDF0|Q9BQE8	Missense_Mutation	SNP	ENST00000268099.9	hg19	CCDS10271.1	.	.	.	.	.	.	.	.	.	.	C	34	5.355708	0.95854	.	.	ENSG00000140497	ENST00000268099;ENST00000543345	T	0.20463	2.07	5.19	5.19	0.71726	.	0.108092	0.64402	D	0.000009	T	0.24586	0.0596	L	0.59436	1.845	0.49051	D	0.999744	P	0.39964	0.697	B	0.38500	0.275	T	0.02546	-1.1143	10	0.72032	D	0.01	.	14.1356	0.65287	0.0:1.0:0.0:0.0	.	11	O15127	SCAM2_HUMAN	N	11	ENSP00000268099:D11N	ENSP00000268099:D11N	D	-	1	0	SCAMP2	72952619	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.069000	0.50026	2.716000	0.92895	0.650000	0.86243	GAC	.	.	.	none		0.682	SCAMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286403.3	NM_005697		T	75165566	C	T	75165566	3	4	38	1	0	0	0	0	1	0	0	0	13884	855	30	2	994	2	SCAMP2	15	75165566	Missense_Mutation	SNP	C	TCGA-5P-A9KC-01A-11D-A42J-10	50241085	75165566	27365826	70	2763											
SCAPER	49855	hgsc.bcm.edu	37	chr15	76646306	76646306	+	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	gtacctgaatgaaagtggccAgtaaaacacagctcatctct	14	9	8	10	0	2	2	1	2	1	0	3	2	2	2	2	1	3	3	2	1	5	2			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr15:76646306A>T	ENST00000563290.1	-	30	4126	c.4031T>A	c.(4030-4032)cTg>cAg	p.L1344Q	SCAPER_ENST00000538941.2_Missense_Mutation_p.L1098Q|SCAPER_ENST00000324767.7_Missense_Mutation_p.L1344Q			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	1344						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						GAAAGTGGCCAGTAAAACACA	0.398																																					p.L1344Q		Atlas-SNP	.											.	SCAPER	160	.	0			c.T4031A						PASS	.						116	116	116					15																	76646306		1978	4174	6152	SO:0001583	missense	49855	exon29			GTGGCCAGTAAAA	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.4031T>A	chr15.hg19:g.76646306A>T	ENSP00000454973:p.Leu1344Gln	118.0	0.0	.		110.0	25.0	.	NM_020843	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Missense_Mutation	SNP	ENST00000563290.1	hg19	CCDS53962.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.470147	0.84533	.	.	ENSG00000140386	ENST00000324767;ENST00000538941	T;T	0.58652	0.42;0.32	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.78566	0.4303	M	0.83774	2.66	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.81833	-0.0751	10	0.87932	D	0	.	16.4563	0.84015	1.0:0.0:0.0:0.0	.	1343;1098	Q9BY12;F5H7X8	SCAPE_HUMAN;.	Q	1344;1098	ENSP00000326924:L1344Q;ENSP00000442190:L1098Q	ENSP00000326924:L1344Q	L	-	2	0	SCAPER	74433361	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	8.851000	0.92205	2.343000	0.79666	0.533000	0.62120	CTG	.	.	.	none		0.398	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843		T	76646306	A	T	76646306	3	4	38	1	0	0	0	0	1	0	0	0	13891	188	7	5	183	5	SCAPER	15	76646306	Missense_Mutation	SNP	A	TCGA-5P-A9KC-01A-11D-A42J-10	1480740	76646306	25885086	71	2764											
ERI2	112479	hgsc.bcm.edu	37	chr16	20809656	20809656	+	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	tatctgaacctggatctttgGcttcttttacattataaata	11	18	5	7	0	3	1	0	1	3	0	3	2	3	2	1	2	2	1	1	2	7	8			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr16:20809656G>C	ENST00000357967.4	-	9	1508	c.1466C>G	c.(1465-1467)gCc>gGc	p.A489G	ERI2_ENST00000389345.5_Missense_Mutation_p.A224G|ERI2_ENST00000564349.1_Missense_Mutation_p.A396G|ERI2_ENST00000563117.1_Missense_Mutation_p.A396G|ERI2_ENST00000300005.3_Intron|ERI2_ENST00000569729.1_Intron	NM_001142725.1	NP_001136197.1	A8K979	ERI2_HUMAN	ERI1 exoribonuclease family member 2	489							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						TGGATCTTTGGCTTCTTTTAC	0.353																																					p.A489G		Atlas-SNP	.											.	ERI2	50	.	0			c.C1466G						PASS	.						109	95	99					16																	20809656		692	1591	2283	SO:0001583	missense	112479	exon9			TCTTTGGCTTCTT	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.1466C>G	chr16.hg19:g.20809656G>C	ENSP00000350651:p.Ala489Gly	62.0	0.0	.		75.0	14.0	.	NM_001142725	Q6ZSJ2|Q96FR9|Q9P224|Q9Y6V3	Missense_Mutation	SNP	ENST00000357967.4	hg19	CCDS45436.1	.	.	.	.	.	.	.	.	.	.	G	10.97	1.501882	0.26949	.	.	ENSG00000196678	ENST00000357967;ENST00000389345	T;T	0.20069	2.14;2.1	5.83	3.8	0.43715	.	1.431980	0.04342	N	0.354195	T	0.21881	0.0527	L	0.59436	1.845	0.09310	N	1	B	0.31680	0.335	B	0.28139	0.086	T	0.33523	-0.9865	10	0.66056	D	0.02	1.127	2.2941	0.04145	0.1648:0.2783:0.4135:0.1434	.	489	A8K979	ERI2_HUMAN	G	489;224	ENSP00000350651:A489G;ENSP00000373996:A224G	ENSP00000350651:A489G	A	-	2	0	ERI2	20717157	0.012000	0.17670	0.966000	0.40874	0.901000	0.52897	0.386000	0.20702	0.743000	0.32719	0.655000	0.94253	GCC	.	.	.	none		0.353	ERI2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_080663		C	20809656	G	C	20809656	3	2	38	1	0	0	0	0	1	0	0	0	5230	1203	42	4	880	4	ERI2	16	20809656	Missense_Mutation	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10		20809656	69545097	72	2765											
PFN1	5216	hgsc.bcm.edu	37	chr17	4850000	4850000	+	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	tacgaagatccatgctaaatTccccatcctgcagcagtgag	12	9	8	12	1	0	2	0	1	0	1	3	3	3	2	4	0	4	3	4	0	4	3			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr17:4850000T>A	ENST00000225655.5	-	2	867	c.248A>T	c.(247-249)gAa>gTa	p.E83V	PFN1_ENST00000574872.1_Missense_Mutation_p.E47V	NM_005022.3	NP_005013.1	P07737	PROF1_HUMAN	profilin 1	83					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						CATGCTAAATTCCCCATCCTG	0.532																																					p.E83V		Atlas-SNP	.											.	PFN1	6	.	0			c.A248T						PASS	.						98	100	99					17																	4850000		2203	4300	6503	SO:0001583	missense	5216	exon2			CTAAATTCCCCAT	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.248A>T	chr17.hg19:g.4850000T>A	ENSP00000225655:p.Glu83Val	43.0	0.0	.		62.0	22.0	.	NM_005022	Q53Y44	Missense_Mutation	SNP	ENST00000225655.5	hg19	CCDS11061.1	.	.	.	.	.	.	.	.	.	.	T	16.92	3.255562	0.59321	.	.	ENSG00000108518	ENST00000225655	D	0.86694	-2.16	4.41	4.41	0.53225	.	0.225081	0.37577	N	0.002024	D	0.82323	0.5012	L	0.27053	0.805	0.40895	D	0.984105	P;D	0.57899	0.826;0.981	B;P	0.50860	0.251;0.652	D	0.83494	0.0071	10	0.87932	D	0	.	6.7098	0.23270	0.0:0.1044:0.0:0.8956	.	83;83	P07737;Q53Y44	PROF1_HUMAN;.	V	83	ENSP00000225655:E83V	ENSP00000225655:E83V	E	-	2	0	PFN1	4790745	1.000000	0.71417	0.973000	0.42090	0.877000	0.50540	6.167000	0.71902	1.992000	0.58205	0.379000	0.24179	GAA	.	.	.	none		0.532	PFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216853.1	NM_005022		A	4850000	T	A	4850000	3	1	38	1	0	0	0	0	1	0	0	0	11774	1783	62	5	182	5	PFN1	17	4850000	Missense_Mutation	SNP	T	TCGA-5P-A9KC-01A-11D-A42J-10		4850000	76345210	73	2766											
SLFN13	146857	hgsc.bcm.edu	37	chr17	33768163	33768163	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tactgtgctgagagagggggAaggccactgtgacccaagtg	10	7	16	8	0	0	3	0	2	0	1	0	5	0	4	2	3	2	1	2	3	3	1			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr17:33768163A>G	ENST00000285013.6	-	6	2420	c.2145T>C	c.(2143-2145)ctT>ctC	p.L715L	SLFN13_ENST00000534689.1_Silent_p.L397L|SLFN13_ENST00000533791.1_Silent_p.L715L|SLFN13_ENST00000360502.2_Silent_p.L397L|SLFN13_ENST00000542635.1_Silent_p.L715L|SLFN13_ENST00000526861.1_Silent_p.L715L	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	715						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)		AGAGAGGGGGAAGGCCACTGT	0.458																																					p.L715L		Atlas-SNP	.											.	SLFN13	79	.	0			c.T2145C						PASS	.						135	143	140					17																	33768163		2203	4300	6503	SO:0001819	synonymous_variant	146857	exon6			AGGGGGAAGGCCA	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.2145T>C	chr17.hg19:g.33768163A>G		43.0	0.0	.		72.0	4.0	.	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Silent	SNP	ENST00000285013.6	hg19	CCDS32620.1																																																																																			.	.	.	none		0.458	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682		G	33768163	A	G	33768163	2	3	38	1	0	0	0	0	0	0	0	1	14749	233	9	3		3	SLFN13	17	33768163	Silent	SNP	A	TCGA-5P-A9KC-01A-11D-A42J-10	28918163	33768163	47427047	74	2767											
ACLY	47	hgsc.bcm.edu	37	chr17	40062802	40062802	+	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	tgtacacgacagaggcgccaCccccggccaccatggtccag	9	4	11	17	3	0	1	0	0	0	1	1	2	1	1	6	3	1	1	6	3	1	1			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr17:40062802C>A	ENST00000352035.2	-	8	975	c.845G>T	c.(844-846)gGt>gTt	p.G282V	ACLY_ENST00000393896.2_Missense_Mutation_p.G282V|ACLY_ENST00000353196.1_Missense_Mutation_p.G282V|ACLY_ENST00000537919.1_Intron|ACLY_ENST00000590151.1_Missense_Mutation_p.G282V	NM_001096.2	NP_001087.2	P53396	ACLY_HUMAN	ATP citrate lyase	282					ATP catabolic process (GO:0006200)|cellular carbohydrate metabolic process (GO:0044262)|cellular lipid metabolic process (GO:0044255)|citrate metabolic process (GO:0006101)|coenzyme A metabolic process (GO:0015936)|energy reserve metabolic process (GO:0006112)|lipid biosynthetic process (GO:0008610)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	citrate lyase complex (GO:0009346)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)		NTN1/ACLY(2)	breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	28		Breast(137;0.000143)				AGAGGCGCCACCCCCGGCCAC	0.602																																					p.G282V	Colon(64;807 1396 15971 30971)	Atlas-SNP	.											.	ACLY	85	.	0			c.G845T						PASS	.						111	103	105					17																	40062802		2203	4300	6503	SO:0001583	missense	47	exon8			GCGCCACCCCCGG	X64330	CCDS11412.1, CCDS11413.1	17q21.2	2010-04-27			ENSG00000131473	ENSG00000131473	2.3.3.8		115	protein-coding gene	gene with protein product	"ATP citrate synthase"	108728				1371749, 8088842	Standard	NM_001096		Approved	ATPCL, CLATP, ACL	uc002hyg.3	P53396	OTTHUMG00000133507	ENST00000352035.2:c.845G>T	chr17.hg19:g.40062802C>A	ENSP00000253792:p.Gly282Val	48.0	0.0	.		47.0	13.0	.	NM_001096	B4DIM0|B4E3P0|Q13037|Q9BRL0	Missense_Mutation	SNP	ENST00000352035.2	hg19	CCDS11412.1	.	.	.	.	.	.	.	.	.	.	C	34	5.324101	0.95708	.	.	ENSG00000131473	ENST00000352035;ENST00000401700;ENST00000353196;ENST00000393896	T;T;T	0.70986	-0.53;-0.53;-0.53	6.07	6.07	0.98685	Succinyl-CoA synthetase-like (2);Succinyl-CoA synthetase, beta subunit, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.89230	0.6656	M	0.94101	3.495	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;0.999	D	0.90677	0.4602	10	0.87932	D	0	.	20.6439	0.99570	0.0:1.0:0.0:0.0	.	336;336;282;282	B4DIM0;E7ENH9;G3XAI4;P53396	.;.;.;ACLY_HUMAN	V	282;336;282;282	ENSP00000253792:G282V;ENSP00000345398:G282V;ENSP00000377474:G282V	ENSP00000253792:G282V	G	-	2	0	ACLY	37316328	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.616000	0.83018	2.884000	0.98904	0.655000	0.94253	GGT	.	.	.	none		0.602	ACLY-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257465.1	NM_001096		A	40062802	C	A	40062802	3	1	38	1	0	0	0	0	1	0	0	0	143	507	18	4	2548	4	ACLY	17	40062802	Missense_Mutation	SNP	C	TCGA-5P-A9KC-01A-11D-A42J-10	6294639	40062802	41132408	75	2768											
BRCA1	672	hgsc.bcm.edu	37	chr17	41246841	41246841	+	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	tactgggttgatgatgttcaGtatttgttacatccgtctca	8	17	9	7	1	2	2	2	2	1	0	4	2	3	2	1	1	2	4	1	1	3	6	rs80356990		TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr17:41246841G>C	ENST00000357654.3	-	10	825	c.707C>G	c.(706-708)aCt>aGt	p.T236S	BRCA1_ENST00000471181.2_Missense_Mutation_p.T236S|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000354071.3_Missense_Mutation_p.T236S|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000309486.4_5'UTR|BRCA1_ENST00000493795.1_Missense_Mutation_p.T189S|BRCA1_ENST00000468300.1_Missense_Mutation_p.T236S|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000346315.3_Missense_Mutation_p.T236S|BRCA1_ENST00000491747.2_Missense_Mutation_p.T236S	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	236					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)		ATGATGTTCAGTATTTGTTAC	0.348			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.T236S		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.C707G						PASS	.						40	38	38					17																	41246841		2203	4299	6502	SO:0001583	missense	672	exon9	Familial Cancer Database		TGTTCAGTATTTG	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.707C>G	chr17.hg19:g.41246841G>C	ENSP00000350283:p.Thr236Ser	54.0	0.0	.		53.0	15.0	.	NM_007298	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	hg19	CCDS11453.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.010|0.010	-1.767696|-1.767696	0.00645|0.00645	.|.	.|.	ENSG00000012048|ENSG00000012048	ENST00000473961|ENST00000357654;ENST00000412061;ENST00000354071;ENST00000346315;ENST00000468300;ENST00000393691;ENST00000471181;ENST00000493795;ENST00000491747;ENST00000478531;ENST00000484087;ENST00000493919;ENST00000487825;ENST00000470026;ENST00000477152;ENST00000494123	.|D;D;D;D;D;D;D;D;D;D;D;D;D;D	.|0.97161	.|-2.25;-2.36;-2.35;-2.14;-2.64;-2.25;-2.4;-1.96;-1.79;-2.26;-1.65;-2.81;-4.27;-2.49	4.86|4.86	-0.582|-0.582	0.11709|0.11709	.|.	.|0.962464	.|0.08592	.|N	.|0.922956	D|D	0.93048|0.93048	0.7787|0.7787	L|L	0.44542|0.44542	1.39|1.39	0.18873|0.18873	N|N	0.999988|0.999988	.|B;B;P;B;B;B;P;B;P;B;B	.|0.37864	.|0.058;0.039;0.457;0.146;0.091;0.146;0.592;0.051;0.61;0.41;0.228	.|B;B;B;B;B;B;B;B;B;B;B	.|0.35278	.|0.01;0.02;0.098;0.024;0.024;0.024;0.199;0.016;0.138;0.096;0.053	D|D	0.86464|0.86464	0.1781|0.1781	5|10	.|0.66056	.|D	.|0.02	.|.	3.5881|3.5881	0.07978|0.07978	0.4166:0.0:0.2972:0.2863|0.4166:0.0:0.2972:0.2863	.|.	.|235;189;235;236;195;236;236;236;236;236;236	.|E7EUM2;B4DES0;E7ETR2;E7EMP0;E7ERL4;Q5YLB2;P38398-3;Q6IN79;E9PFC7;P38398;P38398-2	.|.;.;.;.;.;.;.;.;.;BRCA1_HUMAN;.	V|S	102|236;236;236;236;236;189;236;189;235;235;110;189;111;236;210;236	.|ENSP00000350283:T236S;ENSP00000326002:T236S;ENSP00000246907:T236S;ENSP00000417148:T236S;ENSP00000377294:T189S;ENSP00000418960:T236S;ENSP00000418775:T189S;ENSP00000420412:T235S;ENSP00000419481:T110S;ENSP00000418819:T189S;ENSP00000418212:T111S;ENSP00000419274:T236S;ENSP00000419988:T210S;ENSP00000419103:T236S	.|ENSP00000246907:T236S	L|T	-|-	1|2	2|0	BRCA1|BRCA1	38500367|38500367	0.000000|0.000000	0.05858|0.05858	0.106000|0.106000	0.21319|0.21319	0.131000|0.131000	0.20780|0.20780	-0.880000|-0.880000	0.04183|0.04183	-0.208000|-0.208000	0.10171|0.10171	-0.218000|-0.218000	0.12543|0.12543	CTG|ACT	.	.	.	weak		0.348	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		C	41246841	G	C	41246841	3	2	38	1	0	0	0	0	1	0	0	0	1500	1029	36	4	5010	4	BRCA1	17	41246841	Missense_Mutation	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10	1184039	41246841	39948369	76	2769											
ITGB3	3690	hgsc.bcm.edu	37	chr17	45380155	45380156	+	Frame_Shift_Ins	INS	-	-	A																															ctgtgtcgtcagattccagtINSactatgaagattctagtgga																										TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr17:45380155_45380156insA	ENST00000559488.1	+	13	2099_2100	c.2083_2084insA	c.(2083-2085)tacfs	p.Y695fs	RP11-290H9.4_ENST00000576345.1_RNA|ITGB3_ENST00000560629.1_Frame_Shift_Ins_p.L684fs|RP11-290H9.4_ENST00000575039.1_RNA|ITGB3_ENST00000435993.2_Frame_Shift_Ins_p.Y648fs	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	695					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)	CAGATTCCAGTACTATGAAGAT	0.5																																					p.Y695_Y696delinsX		Atlas-Indel,Pindel	.											.	ITGB3	157	.	0			c.2083_2084insA						PASS	.																																			SO:0001589	frameshift_variant	3690	exon13			.		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.2084dupA	chr17.hg19:g.45380156_45380156dupA	ENSP00000452786:p.Tyr695fs	59.0	0.0	0		97.0	29.0	0.298969	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Frame_Shift_Ins	INS	ENST00000559488.1	hg19	CCDS11511.1																																																																																			.	.	.	none		0.5	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212		A	45380156	-	A	45380155	7	5	38	1	0	1	1	0	0	0	0	0	7902	1638	57	0	2133	0	ITGB3	17	45380155	Frame_Shift_Ins	INS	-	TCGA-5P-A9KC-01A-11D-A42J-10	4133314	45380155	35815055	77	2770											
CHAD	1101	hgsc.bcm.edu	37	chr17	48545993	48545993	+	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	cagccagcaccgggaagttgTtgcgctgtaggttgagcagc	8	8	15	10	2	0	1	0	1	0	0	0	2	0	2	2	2	5	7	2	2	2	4			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr17:48545993T>A	ENST00000508540.1	-	1	334	c.182A>T	c.(181-183)aAc>aTc	p.N61I	ACSF2_ENST00000504392.1_Intron|ACSF2_ENST00000427954.2_Intron|ACSF2_ENST00000300441.4_Intron|ACSF2_ENST00000502667.1_Intron|ACSF2_ENST00000506085.1_Intron|CHAD_ENST00000258969.4_Missense_Mutation_p.N61I|ACSF2_ENST00000541920.1_Intron	NM_001267.2	NP_001258.2	O15335	CHAD_HUMAN	chondroadherin	61					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)			CGGGAAGTTGTTGCGCTGTAG	0.622																																					p.N61I		Atlas-SNP	.											.	CHAD	36	.	0			c.A182T						PASS	.						97	81	86					17																	48545993		2203	4300	6503	SO:0001583	missense	1101	exon1			AAGTTGTTGCGCT	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.182A>T	chr17.hg19:g.48545993T>A	ENSP00000423812:p.Asn61Ile	72.0	0.0	.		56.0	14.0	.	NM_001267	A8K812|Q6GTU0|Q96RJ5	Missense_Mutation	SNP	ENST00000508540.1	hg19	CCDS11568.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.250312	0.80024	.	.	ENSG00000136457	ENST00000508540;ENST00000258969	T;T	0.08282	3.11;3.11	4.31	4.31	0.51392	.	0.000000	0.85682	D	0.000000	T	0.44201	0.1282	H	0.98048	4.135	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.65307	-0.6200	10	0.87932	D	0	.	13.6404	0.62246	0.0:0.0:0.0:1.0	.	61	O15335	CHAD_HUMAN	I	61	ENSP00000423812:N61I;ENSP00000258969:N61I	ENSP00000258969:N61I	N	-	2	0	CHAD	45900992	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.774000	0.85478	1.811000	0.52892	0.379000	0.24179	AAC	.	.	.	none		0.622	CHAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367447.3	NM_001267		A	48545993	T	A	48545993	3	1	38	1	0	0	0	0	1	0	0	0	3312	1725	60	5	909	5	CHAD	17	48545993	Missense_Mutation	SNP	T	TCGA-5P-A9KC-01A-11D-A42J-10	3165838	48545993	32649217	78	2771											
TMC8	147138	hgsc.bcm.edu	37	chr17	76130534	76130534	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagcagacccgggcccagacGgcctgccgcctgctctccta	6	5	11	19	3	1	2	0	0	1	2	2	2	1	2	6	2	3	2	6	2	1	1			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr17:76130534G>A	ENST00000318430.5	+	8	1250	c.876G>A	c.(874-876)acG>acA	p.T292T	TMC6_ENST00000322914.3_5'Flank|TMC8_ENST00000589691.1_Silent_p.T69T	NM_152468.4	NP_689681.2	Q8IU68	TMC8_HUMAN	transmembrane channel-like 8	292					ion transport (GO:0006811)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|regulation of cell growth (GO:0001558)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|zinc ion homeostasis (GO:0055069)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	12			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)|OV - Ovarian serous cystadenocarcinoma(97;0.192)			GGGCCCAGACGGCCTGCCGCC	0.672																																					p.T292T		Atlas-SNP	.											.	TMC8	44	.	0			c.G876A						PASS	.						38	42	41					17																	76130534		2203	4300	6503	SO:0001819	synonymous_variant	147138	exon8			CCAGACGGCCTGC	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.876G>A	chr17.hg19:g.76130534G>A		46.0	0.0	.		47.0	13.0	.	NM_152468	Q2YDC0|Q8IWU7|Q8N358|Q8NF04	Silent	SNP	ENST00000318430.5	hg19	CCDS32749.1																																																																																			.	.	.	none		0.672	TMC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436900.3			A	76130534	G	A	76130534	2	1	38	1	0	0	0	0	0	0	0	1	16003	1103	39	1		1	TMC8	17	76130534	Silent	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10	27584541	76130534	5064676	79	2772											
CLUL1	27098	hgsc.bcm.edu	37	chr18	619236	619236	+	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	tttctgaggtgggggagataGatgcagatgaagaggtgaag	12	9	18	2	0	1	7	0	3	1	4	1	8	1	7	0	4	1	1	0	4	3	2			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr18:619236G>A	ENST00000400606.2	+	3	275	c.130G>A	c.(130-132)Gat>Aat	p.D44N	CLUL1_ENST00000580436.1_3'UTR|CLUL1_ENST00000581619.1_Missense_Mutation_p.D69N|CLUL1_ENST00000579494.1_Missense_Mutation_p.D44N|CLUL1_ENST00000540035.1_Missense_Mutation_p.D96N|CLUL1_ENST00000338387.7_Missense_Mutation_p.D44N	NM_014410.4	NP_055225.1	Q15846	CLUL1_HUMAN	clusterin-like 1 (retinal)	44					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						GGGGGAGATAGATGCAGATGA	0.388																																					p.D44N		Atlas-SNP	.											.	CLUL1	57	.	0			c.G130A						PASS	.						133	125	127					18																	619236		1882	4114	5996	SO:0001583	missense	27098	exon3			GAGATAGATGCAG	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.130G>A	chr18.hg19:g.619236G>A	ENSP00000383449:p.Asp44Asn	165.0	0.0	.		154.0	19.0	.	NM_199167	A0FDN7	Missense_Mutation	SNP	ENST00000400606.2	hg19	CCDS42405.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.568182	0.00895	.	.	ENSG00000079101	ENST00000400606;ENST00000540035;ENST00000338387	T;T;T	0.24151	1.87;1.87;1.87	5.07	0.56	0.17279	Clusterin, N-terminal (1);	0.746850	0.13546	N	0.379829	T	0.15522	0.0374	L	0.51422	1.61	0.09310	N	1	B;B	0.17268	0.021;0.006	B;B	0.13407	0.008;0.009	T	0.38908	-0.9639	10	0.02654	T	1	-0.8279	3.5588	0.07874	0.0916:0.1057:0.2609:0.5417	.	96;44	F5GWQ8;Q15846	.;CLUL1_HUMAN	N	44;96;44	ENSP00000383449:D44N;ENSP00000441726:D96N;ENSP00000341128:D44N	ENSP00000341128:D44N	D	+	1	0	CLUL1	609236	0.897000	0.30589	0.007000	0.13788	0.005000	0.04900	1.467000	0.35321	0.154000	0.19237	-0.182000	0.12963	GAT	.	.	.	none		0.388	CLUL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441183.1			A	619236	G	A	619236	3	1	38	1	0	0	0	0	1	0	0	0	3572	942	33	2	136	2	CLUL1	18	619236	Missense_Mutation	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10		619236	77458012	80	2773											
ICAM1	3383	hgsc.bcm.edu	37	chr19	10394341	10394341	+	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	cccgctgaggtcacgaccacGgtgctggtgaggagagatca	9	6	15	11	3	2	3	2	2	0	1	2	6	2	4	2	4	1	2	2	4	0	0			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr19:10394341G>T	ENST00000264832.3	+	3	841	c.516G>T	c.(514-516)acG>acT	p.T172T	ICAM1_ENST00000423829.2_Intron|CTD-2369P2.5_ENST00000592893.1_RNA|CTD-2369P2.8_ENST00000589379.1_RNA	NM_000201.2	NP_000192.2	P05362	ICAM1_HUMAN	intercellular adhesion molecule 1	172	Ig-like C2-type 2.				adhesion of symbiont to host (GO:0044406)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell aging (GO:0007569)|cellular response to alkaloid (GO:0071312)|cellular response to glucose stimulus (GO:0071333)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nutrient levels (GO:0031669)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|establishment of endothelial barrier (GO:0061028)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|membrane to membrane docking (GO:0022614)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|ovarian follicle development (GO:0001541)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cellular extravasation (GO:0002693)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of vasoconstriction (GO:0045907)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of leukocyte mediated cytotoxicity (GO:0001910)|regulation of ruffle assembly (GO:1900027)|response to amino acid (GO:0043200)|response to amphetamine (GO:0001975)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to gonadotropin (GO:0034698)|response to ionizing radiation (GO:0010212)|response to organic cyclic compound (GO:0014070)|response to sulfur dioxide (GO:0010477)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)|T cell antigen processing and presentation (GO:0002457)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;2.81e-06)|all cancers(31;6.56e-06)		Hyaluronan(DB08818)|Natalizumab(DB00108)	TCACGACCACGGTGCTGGTGA	0.657																																					p.T172T		Atlas-SNP	.											ICAM1,NS,carcinoma,0,1	ICAM1	32	.	0			c.G516T						PASS	.						33	34	33					19																	10394341		2203	4300	6503	SO:0001819	synonymous_variant	3383	exon3			GACCACGGTGCTG		CCDS12231.1	19p13.3-p13.2	2014-01-30	2008-07-18			ENSG00000090339		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Endogenous ligands"	5344	protein-coding gene	gene with protein product	"human rhinovirus receptor"	147840				2453850, 3871395	Standard	NM_000201		Approved	BB2, CD54	uc002mnq.2	P05362		ENST00000264832.3:c.516G>T	chr19.hg19:g.10394341G>T		67.0	0.0	.		54.0	4.0	.	NM_000201	B2R6M3|Q5NKV7|Q96B50	Silent	SNP	ENST00000264832.3	hg19	CCDS12231.1																																																																																			.	.	.	none		0.657	ICAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451207.1			T	10394341	G	T	10394341	2	4	38	1	0	0	0	0	0	0	0	1	7486	1103	39	4		4	ICAM1	19	10394341	Silent	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10		10394341	48734642	81	2774											
ZNF226	7769	hgsc.bcm.edu	37	chr19	44677042	44677042	+	Frame_Shift_Del	DEL	C	C	-																															ccttcaaacaagatgtatcaCctatagaaagaaatgagcag																										TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr19:44677042delC	ENST00000590089.1	+	6	539	c.172delC	c.(172-174)cctfs	p.P58fs	ZNF226_ENST00000588742.1_Frame_Shift_Del_p.P58fs|ZNF226_ENST00000300823.6_Frame_Shift_Del_p.P58fs|ZNF226_ENST00000589160.1_Frame_Shift_Del_p.P58fs|ZNF226_ENST00000413984.2_Frame_Shift_Del_p.P58fs|ZNF226_ENST00000454662.2_Frame_Shift_Del_p.P58fs|ZNF226_ENST00000588795.1_Frame_Shift_Del_p.P58fs|ZNF226_ENST00000337433.5_Frame_Shift_Del_p.P58fs|ZNF226_ENST00000588883.1_Frame_Shift_Del_p.P58fs			Q9NYT6	ZN226_HUMAN	zinc finger protein 226	58	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)						Prostate(69;0.0352)|all_neural(266;0.202)				AGATGTATCACCTATAGAAAG	0.363																																					p.S57fs	Pancreas(115;581 1665 13228 19278 50070)	Atlas-Indel,Pindel	.											.	.	.	.	0			c.171delA						PASS	.						73	68	69					19																	44677042		1872	4108	5980	SO:0001589	frameshift_variant	7769	exon5			.	AF024707	CCDS46102.1, CCDS46103.1	19q13.31	2013-01-08	2012-09-11	2012-09-11	ENSG00000167380	ENSG00000167380		"Zinc fingers, C2H2-type", "-"	13019	protein-coding gene	gene with protein product							Standard	NM_001146220		Approved		uc002oyp.3	Q9NYT6		ENST00000590089.1:c.172delC	chr19.hg19:g.44677042delC	ENSP00000465121:p.Pro58fs	273.0	0.0	0		281.0	81.0	0.288256	NM_001032372	Q8WWE6|Q96TE6|Q9NS44	Frame_Shift_Del	DEL	ENST00000590089.1	hg19	CCDS46102.1																																																																																			.	.	.	none		0.363	ZNF226-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460712.1			-	44677042	C	-	44677042	7	5	38	1	0	1	0	1	0	0	0	0	17792	507	18	0	182	0	ZNF226	19	44677042	Frame_Shift_Del	DEL	C	TCGA-5P-A9KC-01A-11D-A42J-10	34282701	44677042	14451941	82	2775											
CEP250	11190	hgsc.bcm.edu	37	chr20	34067123	34067123	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaggaggcaaagcgacaggAagaagtgcttgccagggcag	13	4	16	8	1	1	1	1	0	0	1	1	4	1	3	1	4	3	3	1	4	3	1			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr20:34067123A>G	ENST00000397527.1	+	18	2882	c.2162A>G	c.(2161-2163)gAa>gGa	p.E721G	RP3-477O4.14_ENST00000444933.1_RNA|RP3-477O4.14_ENST00000453914.1_RNA|RP3-477O4.14_ENST00000416260.1_RNA|CEP250_ENST00000342580.4_Missense_Mutation_p.E721G	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	721	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)			AAGCGACAGGAAGAAGTGCTT	0.612																																					p.E721G		Atlas-SNP	.											.	CEP250	141	.	0			c.A2162G						PASS	.						115	99	104					20																	34067123		2203	4300	6503	SO:0001583	missense	11190	exon18			GACAGGAAGAAGT	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.2162A>G	chr20.hg19:g.34067123A>G	ENSP00000380661:p.Glu721Gly	130.0	0.0	.		148.0	46.0	.	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	hg19	CCDS13255.1	.	.	.	.	.	.	.	.	.	.	A	14.68	2.606924	0.46527	.	.	ENSG00000126001	ENST00000397527;ENST00000342580	T;T	0.11169	2.8;2.85	4.74	4.74	0.60224	.	0.093895	0.46442	D	0.000300	T	0.13500	0.0327	M	0.71581	2.175	0.26978	N	0.965431	B	0.14012	0.009	B	0.15484	0.013	T	0.08046	-1.0741	10	0.45353	T	0.12	.	8.6617	0.34097	0.9136:0.0:0.0864:0.0	.	721	Q9BV73	CP250_HUMAN	G	721	ENSP00000380661:E721G;ENSP00000341541:E721G	ENSP00000341541:E721G	E	+	2	0	CEP250	33530537	0.998000	0.40836	0.870000	0.34147	0.519000	0.34347	0.789000	0.26886	2.118000	0.64928	0.533000	0.62120	GAA	.	.	.	none		0.612	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		G	34067123	A	G	34067123	3	3	38	1	0	0	0	0	1	0	0	0	3254	246	9	3	2220	3	CEP250	20	34067123	Missense_Mutation	SNP	A	TCGA-5P-A9KC-01A-11D-A42J-10		34067123	28958397	83	2776											
CHRNA4	1137	hgsc.bcm.edu	37	chr20	61982275	61982275	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggggaagaaggtgacgtcgAtgctgcaggagctcttgtaa	11	8	16	6	2	1	2	0	1	1	1	2	5	1	4	0	4	3	4	0	4	3	2			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr20:61982275A>G	ENST00000370263.4	-	5	709	c.488T>C	c.(487-489)aTc>aCc	p.I163T	CHRNA4_ENST00000463705.1_5'UTR	NM_000744.6|NM_001256573.1	NP_000735.1|NP_001243502.1	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 (neuronal)	163					action potential (GO:0001508)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cognition (GO:0050890)|DNA repair (GO:0006281)|exploration behavior (GO:0035640)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|neurological system process (GO:0050877)|regulation of dopamine secretion (GO:0014059)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(19)|prostate(3)|skin(3)|soft_tissue(1)	33	all_cancers(38;1.71e-10)				Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	GGTGACGTCGATGCTGCAGGA	0.602																																					p.I163T		Atlas-SNP	.											.	CHRNA4	98	.	0			c.T488C						PASS	.						113	103	107					20																	61982275		2202	4300	6502	SO:0001583	missense	1137	exon5			ACGTCGATGCTGC		CCDS13517.1	20q13.33	2013-09-20	2012-02-07		ENSG00000101204	ENSG00000101204		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1958	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 4 (neuronal)"	118504	"cholinergic receptor, nicotinic, alpha polypeptide 4"	EBN, EBN1		1505988	Standard	NM_000744		Approved	BFNC	uc002yes.3	P43681	OTTHUMG00000033080	ENST00000370263.4:c.488T>C	chr20.hg19:g.61982275A>G	ENSP00000359285:p.Ile163Thr	58.0	0.0	.		75.0	13.0	.	NM_000744	Q4JGR7|Q4VAQ5|Q4VAQ6	Missense_Mutation	SNP	ENST00000370263.4	hg19	CCDS13517.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.218747	0.79464	.	.	ENSG00000101204	ENST00000370258;ENST00000370263;ENST00000539366	D	0.81499	-1.5	4.87	4.87	0.63330	Neurotransmitter-gated ion-channel ligand-binding (3);Neurotransmitter-gated ion-channel, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.92192	0.7524	H	0.94462	3.54	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	1.0;1.0	D	0.94266	0.7506	10	0.87932	D	0	.	14.4626	0.67462	1.0:0.0:0.0:0.0	.	92;163	Q4VAQ5;P43681	.;ACHA4_HUMAN	T	69;163;92	ENSP00000359285:I163T	ENSP00000359280:I69T	I	-	2	0	CHRNA4	61452719	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	9.135000	0.94478	1.806000	0.52798	0.459000	0.35465	ATC	.	.	.	none		0.602	CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3			G	61982275	A	G	61982275	3	3	38	1	0	0	0	0	1	0	0	0	3387	333	12	3	1403	3	CHRNA4	20	61982275	Missense_Mutation	SNP	A	TCGA-5P-A9KC-01A-11D-A42J-10	27915152	61982275	1043245	84	2777											
LZTR1	8216	hgsc.bcm.edu	37	chr22	21343964	21343964	+	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	ggaccgagagctcacctgctGggaggaggtgaggggcgtgg	7	5	21	8	2	1	2	1	1	0	1	1	6	1	5	2	7	2	2	2	7	0	0			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr22:21343964G>T	ENST00000215739.8	+	7	1003	c.644G>T	c.(643-645)tGg>tTg	p.W215L	LZTR1_ENST00000479606.1_3'UTR|LZTR1_ENST00000389355.3_Missense_Mutation_p.W196L	NM_006767.3	NP_006758.2	Q8N653	LZTR1_HUMAN	leucine-zipper-like transcription regulator 1	215					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)			CTCACCTGCTgggaggaggtg	0.647																																					p.W215L		Atlas-SNP	.											.	LZTR1	99	.	0			c.G644T						PASS	.						53	42	46					22																	21343964		2203	4300	6503	SO:0001583	missense	8216	exon7			CCTGCTGGGAGGA	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.644G>T	chr22.hg19:g.21343964G>T	ENSP00000215739:p.Trp215Leu	23.0	0.0	.		16.0	6.0	.	NM_006767	Q14776|Q20WK0	Missense_Mutation	SNP	ENST00000215739.8	hg19	CCDS33606.1	.	.	.	.	.	.	.	.	.	.	G	35	5.532619	0.96446	.	.	ENSG00000099949	ENST00000539817;ENST00000215739;ENST00000389355	D;D	0.81659	-1.52;-1.52	5.96	5.96	0.96718	Kelch-type beta propeller (1);	0.366329	0.33712	N	0.004632	D	0.91112	0.7202	M	0.89095	3.005	0.80722	D	1	D;D;D;P	0.71674	0.998;0.996;0.978;0.95	P;D;P;P	0.67900	0.903;0.954;0.832;0.487	D	0.92081	0.5672	10	0.87932	D	0	-8.4501	17.8985	0.88896	0.0:0.0:1.0:0.0	.	196;174;215;174	B7Z3T9;Q6ZSY0;Q8N653;F5GXU8	.;.;LZTR1_HUMAN;.	L	174;215;196	ENSP00000215739:W215L;ENSP00000374006:W196L	ENSP00000215739:W215L	W	+	2	0	LZTR1	19673964	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.497000	0.97970	2.834000	0.97654	0.650000	0.86243	TGG	.	.	.	none		0.647	LZTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320387.1	NM_006767		T	21343964	G	T	21343964	3	4	38	1	0	0	0	0	1	0	0	0	9144	1357	47	4	670	4	LZTR1	22	21343964	Missense_Mutation	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10		21343964	29960602	85	2778											
SMARCB1	6598	hgsc.bcm.edu	37	chr22	24167567	24167568	+	Frame_Shift_Del	DEL	AC	AC	-																															atcgcatacagcatccggggAcagctgagctggcatcagaa																										TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chr22:24167567_24167568delAC	ENST00000263121.7	+	7	1147_1148	c.951_952delAC	c.(949-954)ggacagfs	p.Q318fs	SMARCB1_ENST00000407422.3_Frame_Shift_Del_p.Q309fs|SMARCB1_ENST00000407082.3_Frame_Shift_Del_p.Q272fs|SMARCB1_ENST00000344921.6_Frame_Shift_Del_p.Q327fs	NM_003073.3	NP_003064.2	Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	318	2 X approximate tandem repeats.|Interaction with PPP1R15A.				ATP-dependent chromatin remodeling (GO:0043044)|blastocyst hatching (GO:0001835)|cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|DNA integration (GO:0015074)|DNA repair (GO:0006281)|mitotic cell cycle phase transition (GO:0044772)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	p53 binding (GO:0002039)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)	p.?(6)|p.L266_*386del(1)		bone(4)|central_nervous_system(198)|endometrium(4)|haematopoietic_and_lymphoid_tissue(25)|kidney(3)|large_intestine(5)|liver(2)|lung(5)|meninges(5)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|soft_tissue(194)	458		Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05)				GCATCCGGGGACAGCTGAGCTG	0.545			"D, N, F, S"		malignant rhabdoid	malignant rhabdoid																															p.317_317del		Atlas-Indel,Pindel	.	yes	Rec	yes	Rhabdoid predisposition syndrome	22	22q11	6598	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1"		M	.,3	SMARCB1	586	.	7	Unknown(6)|Deletion - In frame(1)	central_nervous_system(6)|soft_tissue(1)	c.950_951del						PASS	.																																			SO:0001589	frameshift_variant	6598	exon7			.	U04847	CCDS13817.1, CCDS46671.1	22q11.23	2014-09-17			ENSG00000099956	ENSG00000099956			11103	protein-coding gene	gene with protein product	"sucrose nonfermenting, yeast, homolog-like 1", "integrase interactor 1", "malignant rhabdoid tumor suppressor", "protein phosphatase 1, regulatory subunit 144"	601607		SNF5L1		7801128, 10319872, 10365963	Standard	NM_003073		Approved	BAF47, Ini1, Snr1, hSNFS, Sfh1p, RDT, PPP1R144	uc002zyb.3	Q12824	OTTHUMG00000150737	ENST00000263121.7:c.951_952delAC	chr22.hg19:g.24167567_24167568delAC	ENSP00000263121:p.Gln318fs	77.0	0.0	0		40.0	22.0	0.55	NM_003073	O75784|O95474|Q17S11|Q38GA1|Q76N08|Q9UBH2	Frame_Shift_Del	DEL	ENST00000263121.7	hg19	CCDS13817.1																																																																																			.	.	.	none		0.545	SMARCB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319872.1	NM_003073		-	24167568	AC	-	24167567	7	5	38	1	0	1	0	1	0	0	0	0	14787	262	10	0	977	0	SMARCB1	22	24167567	Frame_Shift_Del	DEL	AC	TCGA-5P-A9KC-01A-11D-A42J-10	2823603	24167567	27136999	86	2779											
MPP1	4354	hgsc.bcm.edu	37	chrX	154007573	154007573	+	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	gtgagaggtcaaagtagtgaGcgtactggctgcggatggcc	9	8	17	7	2	1	2	1	2	0	1	1	4	1	3	1	4	3	3	1	4	3	2			TCGA-5P-A9KC-01A-11D-A42J-10	TCGA-5P-A9KC-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6a01a138-dd7b-4d04-b7c1-53e09d984f27	1a9bde7a-dc3e-413a-91fe-bf1fd077ada1	g.chrX:154007573G>C	ENST00000369534.3	-	12	1427	c.1280C>G	c.(1279-1281)gCt>gGt	p.A427G	MPP1_ENST00000413259.3_Missense_Mutation_p.A397G|MPP1_ENST00000393531.1_Missense_Mutation_p.A407G	NM_001166460.1|NM_001166461.1|NM_002436.3	NP_001159932.1|NP_001159933.1|NP_002427.1	Q00013	EM55_HUMAN	membrane protein, palmitoylated 1, 55kDa	427	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.|Interaction with MPP5.				nucleotide phosphorylation (GO:0046939)|regulation of neutrophil chemotaxis (GO:0090022)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cortical cytoskeleton (GO:0030863)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(9)|ovary(2)|prostate(1)	21	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					AAAGTAGTGAGCGTACTGGCT	0.517																																					p.A427G		Atlas-SNP	.											.	MPP1	52	.	0			c.C1280G						PASS	.						101	81	88					X																	154007573		2203	4300	6503	SO:0001583	missense	4354	exon12			TAGTGAGCGTACT		CCDS14762.1, CCDS55544.1, CCDS55545.1	Xq28	2008-03-04	2002-08-29		ENSG00000130830	ENSG00000130830			7219	protein-coding gene	gene with protein product		305360	"membrane protein, palmitoylated 1 (55kD)"	DXS552E		1713685	Standard	NM_002436		Approved	PEMP	uc004fmp.2	Q00013	OTTHUMG00000024244	ENST00000369534.3:c.1280C>G	chrX.hg19:g.154007573G>C	ENSP00000358547:p.Ala427Gly	187.0	0.0	.		183.0	51.0	.	NM_002436	B4DZV5|G3XAI1|Q2TSB6|Q5J7V5	Missense_Mutation	SNP	ENST00000369534.3	hg19	CCDS14762.1	.	.	.	.	.	.	.	.	.	.	G	5.893	0.348929	0.11126	.	.	ENSG00000130830	ENST00000369534;ENST00000413259;ENST00000393531	T;T;T	0.43294	0.95;0.95;0.95	5.86	5.86	0.93980	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (2);	0.154571	0.56097	D	0.000023	T	0.31513	0.0799	N	0.25992	0.78	0.47037	D	0.999298	B;B;B;B	0.12013	0.005;0.0;0.0;0.0	B;B;B;B	0.10450	0.004;0.005;0.003;0.003	T	0.13019	-1.0525	10	0.11182	T	0.66	.	17.5546	0.87887	0.0:0.0:1.0:0.0	.	410;397;407;427	B4E325;B4DZV5;G3XAI1;Q00013	.;.;.;EM55_HUMAN	G	427;397;407	ENSP00000358547:A427G;ENSP00000400155:A397G;ENSP00000377165:A407G	ENSP00000358547:A427G	A	-	2	0	MPP1	153660767	0.997000	0.39634	0.644000	0.29465	0.990000	0.78478	5.737000	0.68606	2.465000	0.83290	0.600000	0.82982	GCT	.	.	.	none		0.517	MPP1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061191.3	NM_002436		C	154007573	G	C	154007573	3	2	38	1	0	0	0	0	1	0	0	0	9740	971	34	4	124	4	MPP1	23	154007573	Missense_Mutation	SNP	G	TCGA-5P-A9KC-01A-11D-A42J-10		154007573	1262987	87	2780											
TMEM52	339456	hgsc.bcm.edu	37	chr1	1850654	1850654	+	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	aggagcggcaggagcggcagGagcggcagcagcagccgcag	10	0	20	11	4	0	0	0	0	0	0	0	3	0	3	1	6	6	6	1	6	0	0			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr1:1850654G>C	ENST00000310991.3	-	1	58	c.51C>G	c.(49-51)ctC>ctG	p.L17L	TMEM52_ENST00000378602.3_5'Flank	NM_178545.3	NP_848640.1	Q8NDY8	TMM52_HUMAN	transmembrane protein 52	17						integral component of membrane (GO:0016021)				NS(1)|prostate(1)|stomach(1)	3	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)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.82e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.75e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		ggagcggcaggagcggcagca	0.771																																					p.L17L		Atlas-SNP	.											TMEM52,NS,carcinoma,0,1	TMEM52	21	.	0			c.C51G						PASS	.						1	2	1					1																	1850654		671	1684	2355	SO:0001819	synonymous_variant	339456	exon1			CGGCAGGAGCGGC	AJ278736	CCDS35.1	1p36.33	2008-02-05			ENSG00000178821	ENSG00000178821			27916	protein-coding gene	gene with protein product							Standard	NM_178545		Approved		uc001aij.2	Q8NDY8	OTTHUMG00000000944	ENST00000310991.3:c.51C>G	chr1.hg19:g.1850654G>C		11.0	0.0	.		9.0	2.0	.	NM_178545	Q4VXS6|Q6UX25	Silent	SNP	ENST00000310991.3	hg19	CCDS35.1	.	.	.	.	.	.	.	.	.	.	.	4.530	0.098402	0.08681	.	.	ENSG00000178821	ENST00000378598	.	.	.	0.149	0.149	0.14863	.	.	.	.	.	T	0.39489	0.1080	.	.	.	0.22446	N	0.999091	.	.	.	.	.	.	T	0.39035	-0.9633	4	0.87932	D	0	.	.	.	.	.	.	.	.	C	15	.	ENSP00000367861:S15C	S	-	2	0	TMEM52	1840514	0.001000	0.12720	0.009000	0.14445	0.010000	0.07245	0.286000	0.18902	0.192000	0.20272	0.195000	0.17529	TCC	.	.	.	none		0.771	TMEM52-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000002781.1	NM_178545		C	1850654	G	C	1850654	2	2	39	1	0	0	0	0	0	0	0	1	16190	1161	41	4		4	TMEM52	1	1850654	Silent	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10		1850654	247399967	1	2781											
CHD5	26038	hgsc.bcm.edu	37	chr1	6212475	6212475	+	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	cacacgcacacactcaccgaGgagcctttcttcctcttgtt	8	11	6	16	2	3	0	1	0	2	0	4	2	4	1	3	1	1	2	3	1	0	4			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr1:6212475G>T	ENST00000262450.3	-	6	966	c.867C>A	c.(865-867)tcC>tcA	p.S289S	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)		cactcacCGAGGAGCCTTTCT	0.552																																					p.S289S		Atlas-SNP	.											.	CHD5	267	.	0			c.C867A						PASS	.						128	103	111					1																	6212475		2203	4300	6503	SO:0001819	synonymous_variant	26038	exon6			CACCGAGGAGCCT	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.867C>A	chr1.hg19:g.6212475G>T		44.0	0.0	.		42.0	7.0	.	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Silent	SNP	ENST00000262450.3	hg19	CCDS57.1																																																																																			.	.	.	none		0.552	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557		T	6212475	G	T	6212475	2	4	39	1	0	0	0	0	0	0	0	1	3330	987	35	4		4	CHD5	1	6212475	Silent	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10	4361821	6212475	243038146	2	2782											
GCLM	2730	hgsc.bcm.edu	37	chr1	94360206	94360206	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtcaacagctgtatgtcaaAttgtttagcaaatgcagtca	14	12	8	7	0	3	0	3	0	0	0	3	0	3	0	0	0	4	5	0	0	5	4			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr1:94360206A>G	ENST00000370238.3	-	6	865	c.619T>C	c.(619-621)Ttt>Ctt	p.F207L	GCLM_ENST00000467772.1_5'UTR	NM_002061.2	NP_002052.1	P48507	GSH0_HUMAN	glutamate-cysteine ligase, modifier subunit	207					apoptotic mitochondrial changes (GO:0008637)|cellular nitrogen compound metabolic process (GO:0034641)|cysteine metabolic process (GO:0006534)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of glutamate-cysteine ligase activity (GO:0035229)|regulation of blood vessel size (GO:0050880)|regulation of mitochondrial depolarization (GO:0051900)|response to drug (GO:0042493)|response to nitrosative stress (GO:0051409)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|glutamate-cysteine ligase complex (GO:0017109)	glutamate-cysteine ligase activity (GO:0004357)|glutamate-cysteine ligase catalytic subunit binding (GO:0035226)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		all_lung(203;0.000815)|Lung NSC(277;0.00363)		all cancers(265;0.00566)|GBM - Glioblastoma multiforme(16;0.0203)|Epithelial(280;0.131)	L-Cysteine(DB00151)	TGTATGTCAAATTGTTTAGCA	0.328																																					p.F207L		Atlas-SNP	.											.	GCLM	20	.	0			c.T619C						PASS	.						149	145	146					1																	94360206		2203	4300	6503	SO:0001583	missense	2730	exon6			TGTCAAATTGTTT	L35546	CCDS746.1	1p21	2008-02-05			ENSG00000023909	ENSG00000023909	6.3.2.2		4312	protein-coding gene	gene with protein product	"gamma-glutamylcysteine synthetase"	601176		GLCLR		7826375	Standard	NM_002061		Approved		uc001dqg.1	P48507	OTTHUMG00000010562	ENST00000370238.3:c.619T>C	chr1.hg19:g.94360206A>G	ENSP00000359258:p.Phe207Leu	81.0	0.0	.		61.0	12.0	.	NM_002061	A8K334|D3DT45|M5A959|Q6FHC1|Q9NPX9|Q9NU74	Missense_Mutation	SNP	ENST00000370238.3	hg19	CCDS746.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.220456	0.79464	.	.	ENSG00000023909	ENST00000370238	T	0.38560	1.13	5.94	5.94	0.96194	NADP-dependent oxidoreductase domain (2);	0.000000	0.85682	D	0.000000	T	0.29423	0.0733	M	0.63428	1.95	0.58432	D	0.999999	B	0.30146	0.27	B	0.31812	0.136	T	0.10543	-1.0625	10	0.24483	T	0.36	.	16.4127	0.83723	1.0:0.0:0.0:0.0	.	207	P48507	GSH0_HUMAN	L	207	ENSP00000359258:F207L	ENSP00000359258:F207L	F	-	1	0	GCLM	94132794	1.000000	0.71417	0.994000	0.49952	0.952000	0.60782	9.251000	0.95483	2.279000	0.76181	0.528000	0.53228	TTT	.	.	.	none		0.328	GCLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029169.1	NM_002061		G	94360206	A	G	94360206	3	3	39	1	0	0	0	0	1	0	0	0	6303	101	4	3	213	3	GCLM	1	94360206	Missense_Mutation	SNP	A	TCGA-5P-A9KE-01A-11D-A42J-10	88147731	94360206	154890415	3	2783											
ATXN7L2	127002	hgsc.bcm.edu	37	chr1	110035211	110035211	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcttgtcttcctgcagtcaAaagcccattaacgagaaagt	12	11	7	11	1	3	1	1	0	2	1	4	2	4	1	2	0	3	1	2	0	4	3			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr1:110035211A>G	ENST00000369870.3	+	11	2173	c.2158A>G	c.(2158-2160)Aaa>Gaa	p.K720E	ATXN7L2_ENST00000459635.1_3'UTR|CYB561D1_ENST00000430195.2_5'Flank|CYB561D1_ENST00000527072.1_5'Flank|CYB561D1_ENST00000420578.2_5'Flank|CYB561D1_ENST00000528785.1_5'Flank|CYB561D1_ENST00000533024.1_5'Flank|CYB561D1_ENST00000310611.4_5'Flank|CYB561D1_ENST00000393709.3_5'Flank|CYB561D1_ENST00000496961.1_5'Flank|CYB561D1_ENST00000369868.3_5'Flank	NM_153340.4	NP_699171.3	Q5T6C5	AT7L2_HUMAN	ataxin 7-like 2	720										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)	17		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0426)|Epithelial(280;0.0675)|READ - Rectum adenocarcinoma(129;0.0693)|all cancers(265;0.071)|LUSC - Lung squamous cell carcinoma(189;0.228)		CCTGCAGTCAAAAGCCCATTA	0.572																																					p.K720E		Atlas-SNP	.											.	ATXN7L2	60	.	0			c.A2158G						PASS	.						166	165	166					1																	110035211		2203	4300	6503	SO:0001583	missense	127002	exon11			CAGTCAAAAGCCC	BC037582	CCDS30794.1	1p13.2	2008-02-05			ENSG00000162650	ENSG00000162650			28713	protein-coding gene	gene with protein product						12477932	Standard	NM_153340		Approved	MGC46534, FLJ00381	uc001dxr.3	Q5T6C5	OTTHUMG00000011027	ENST00000369870.3:c.2158A>G	chr1.hg19:g.110035211A>G	ENSP00000358886:p.Lys720Glu	73.0	0.0	.		74.0	17.0	.	NM_153340		Missense_Mutation	SNP	ENST00000369870.3	hg19	CCDS30794.1	.	.	.	.	.	.	.	.	.	.	A	15.78	2.935311	0.52866	.	.	ENSG00000162650	ENST00000369870;ENST00000369869	T	0.36157	1.27	4.9	4.9	0.64082	.	1.139640	0.06543	N	0.743509	T	0.28764	0.0713	N	0.08118	0	0.36581	D	0.873544	D	0.63880	0.993	D	0.70935	0.971	T	0.09975	-1.0650	10	0.66056	D	0.02	25.5507	10.8481	0.46754	1.0:0.0:0.0:0.0	.	720	Q5T6C5	AT7L2_HUMAN	E	720;347	ENSP00000358886:K720E	ENSP00000358885:K347E	K	+	1	0	ATXN7L2	109836734	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.732000	0.62029	2.064000	0.61679	0.459000	0.35465	AAA	.	.	.	none		0.572	ATXN7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030331.1	NM_153340		G	110035211	A	G	110035211	3	3	39	1	0	0	0	0	1	0	0	0	1217	15	1	3	2200	3	ATXN7L2	1	110035211	Missense_Mutation	SNP	A	TCGA-5P-A9KE-01A-11D-A42J-10	15675005	110035211	139215410	4	2784											
TRIM33	51592	hgsc.bcm.edu	37	chr1	114942184	114942184	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttctgaagcttctttttcacGgtggataaatccattggttt	8	18	8	7	1	3	1	1	1	2	0	4	2	4	2	1	3	1	2	1	3	3	7	rs376287925		TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr1:114942184G>A	ENST00000358465.2	-	18	3098	c.3015C>T	c.(3013-3015)acC>acT	p.T1005T	TRIM33_ENST00000450349.2_Silent_p.T637T|TRIM33_ENST00000369543.2_Silent_p.T1005T	NM_015906.3	NP_056990.3	Q9UPN9	TRI33_HUMAN	tripartite motif containing 33	1005	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	48	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCTTTTTCACGGTGGATAAAT	0.348			T	RET	papillary thyroid								G|||	1	0.000199681	0	0	5008	,	,		13211	0		0	False		,,,				2504	0.001				p.T1005T		Atlas-SNP	.		Dom	yes		1	1p13	51592	" tripartite motif-containing 33 (PTC7,TIF1G)"		E	.	TRIM33	115	.	0			c.C3015T						PASS	.	G	,	0,4406		0,0,2203	120	131	127		3015,3015	-2.2	1	1		127	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	TRIM33	NM_015906.3,NM_033020.2	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	1005/1128,1005/1111	114942184	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	51592	exon18			TTTCACGGTGGAT	AF220136	CCDS872.1, CCDS873.1	1p13.1	2014-02-17	2011-01-25		ENSG00000197323	ENSG00000197323		"Tripartite motif containing / Tripartite motif containing", "Zinc fingers, PHD-type", "RING-type (C3HC4) zinc fingers"	16290	protein-coding gene	gene with protein product	"transcriptional intermediary factor 1 gamma", "ret-fused gene 7"	605769	"tripartite motif-containing 33"			11331580, 10022127	Standard	XM_005270936		Approved	TIF1GAMMA, FLJ11429, KIAA1113, TIFGAMMA, RFG7, TF1G, TIF1G, PTC7	uc001eew.3	Q9UPN9	OTTHUMG00000011891	ENST00000358465.2:c.3015C>T	chr1.hg19:g.114942184G>A		71.0	0.0	.		70.0	19.0	.	NM_033020	O95855|Q5TG72|Q5TG73|Q5TG74|Q9C017|Q9UJ79	Silent	SNP	ENST00000358465.2	hg19	CCDS872.1	.	.	.	.	.	.	.	.	.	.	G	9.579	1.123105	0.20959	0.0	1.16E-4	ENSG00000197323	ENST00000448034	.	.	.	5.61	-2.2	0.06994	.	.	.	.	.	T	0.23532	0.0569	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.32268	-0.9913	4	.	.	.	-9.9523	2.2583	0.04060	0.143:0.2503:0.1421:0.4645	.	.	.	.	L	766	.	.	P	-	2	0	TRIM33	114743707	0.082000	0.21442	0.998000	0.56505	0.999000	0.98932	-0.593000	0.05740	-0.013000	0.14199	0.650000	0.86243	CCG	.	.	.	none		0.348	TRIM33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032854.1	NM_015906		A	114942184	G	A	114942184	2	1	39	1	0	0	0	0	0	0	0	1	16519	1103	39	1		1	TRIM33	1	114942184	Silent	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10	4906973	114942184	134308437	5	2785											
VTCN1	79679	hgsc.bcm.edu	37	chr1	117699520	117699520	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gttcccagctgaggcgacagTagtgactgtgatggagtgtc	8	10	15	8	1	0	3	0	3	0	0	2	5	1	4	1	2	1	3	1	2	1	2			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr1:117699520T>C	ENST00000369458.3	-	3	199	c.121A>G	c.(121-123)Act>Gct	p.T41A	VTCN1_ENST00000539893.1_5'UTR|VTCN1_ENST00000463461.1_5'UTR|VTCN1_ENST00000328189.3_Intron|VTCN1_ENST00000359008.4_Missense_Mutation_p.T44A	NM_024626.3	NP_078902.2			V-set domain containing T cell activation inhibitor 1											large_intestine(7)|lung(4)|upper_aerodigestive_tract(1)	12	Lung SC(450;0.225)	all_cancers(81;6.05e-06)|all_epithelial(167;5.59e-07)|all_lung(203;2.85e-06)|Lung NSC(69;2e-05)		Lung(183;0.0664)|LUSC - Lung squamous cell carcinoma(189;0.214)|Colorectal(144;0.23)		GAGGCGACAGTAGTGACTGTG	0.473																																					p.T41A		Atlas-SNP	.											.	VTCN1	26	.	0			c.A121G						PASS	.						68	65	66					1																	117699520		2203	4300	6503	SO:0001583	missense	79679	exon3			CGACAGTAGTGAC	BX648021	CCDS894.1, CCDS58019.1, CCDS58020.1	1p12	2013-01-29			ENSG00000134258	ENSG00000134258		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	28873	protein-coding gene	gene with protein product	"B7 family member, H4", "B7 superfamily member 1"	608162				12818165, 12818166	Standard	NM_024626		Approved	B7-H4, FLJ22418, B7S1, B7X, B7H4	uc001ehb.3	Q7Z7D3	OTTHUMG00000012118	ENST00000369458.3:c.121A>G	chr1.hg19:g.117699520T>C	ENSP00000358470:p.Thr41Ala	54.0	0.0	.		45.0	13.0	.	NM_024626		Missense_Mutation	SNP	ENST00000369458.3	hg19	CCDS894.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	2.374|2.374	-0.343751|-0.343751	0.05208|0.05208	.|.	.|.	ENSG00000134258|ENSG00000134258	ENST00000369458;ENST00000359008|ENST00000369456	T;T|.	0.06142|.	3.35;3.34|.	5.88|5.88	4.76|4.76	0.60689|0.60689	Immunoglobulin subtype (1);|.	0.094559|.	0.47093|.	D|.	0.000254|.	T|T	0.10035|0.10035	0.0246|0.0246	N|N	0.00926|0.00926	-1.1|-1.1	0.44462|0.44462	D|D	0.997391|0.997391	B|.	0.21381|.	0.055|.	B|.	0.20955|.	0.032|.	T|T	0.10245|0.10245	-1.0638|-1.0638	10|6	0.07813|0.87932	T|D	0.8|0	-7.9789|-7.9789	7.5709|7.5709	0.27907|0.27907	0.0:0.1647:0.0:0.8353|0.0:0.1647:0.0:0.8353	.|.	41|.	Q7Z7D3|.	VTCN1_HUMAN|.	A|C	41;44|68	ENSP00000358470:T41A;ENSP00000351899:T44A|.	ENSP00000351899:T44A|ENSP00000358468:Y68C	T|Y	-|-	1|2	0|0	VTCN1|VTCN1	117501043|117501043	0.964000|0.964000	0.33143|0.33143	0.078000|0.078000	0.20375|0.20375	0.059000|0.059000	0.15707|0.15707	2.478000|2.478000	0.45189|0.45189	1.060000|1.060000	0.40578|0.40578	-0.270000|-0.270000	0.10280|0.10280	ACT|TAC	.	.	.	none		0.473	VTCN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000033500.2	NM_024626		C	117699520	T	C	117699520	3	2	39	1	0	0	0	0	1	0	0	0	17246	1638	57	3	739	3	VTCN1	1	117699520	Missense_Mutation	SNP	T	TCGA-5P-A9KE-01A-11D-A42J-10	2757336	117699520	131551101	6	2786											
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144881617	144881617	+	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	tcacgaggctgggactggttAtccaactgtgaaaggggcca	10	8	14	9	1	1	1	1	1	0	0	2	3	2	2	2	5	1	2	2	5	3	1			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr1:144881617A>T	ENST00000369354.3	-	25	3768	c.3579T>A	c.(3577-3579)gaT>gaA	p.D1193E	PDE4DIP_ENST00000369359.4_Missense_Mutation_p.D1330E|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.D1330E|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.D1193E|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.D1149E			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1193					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)		GGGACTGGTTATCCAACTGTG	0.582			T	PDGFRB	MPD																																p.D1193E		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.T3579A						PASS	.						77	70	73					1																	144881617		2203	4296	6499	SO:0001583	missense	9659	exon25			CTGGTTATCCAAC	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.3579T>A	chr1.hg19:g.144881617A>T	ENSP00000358360:p.Asp1193Glu	65.0	0.0	.		78.0	10.0	.	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	hg19	CCDS30824.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.120|0.120	-1.126364|-1.126364	0.01770|0.01770	.|.	.|.	ENSG00000178104|ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359|ENST00000530592	T;T;T;T;T|.	0.01495|.	4.83;4.91;4.91;4.91;4.91|.	5.44|5.44	-2.4|-2.4	0.06583|0.06583	.|.	.|.	.|.	.|.	.|.	T|.	0.12135|.	0.0295|.	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	0.999995|0.999995	B;B|.	0.12013|.	0.002;0.005|.	B;B|.	0.12156|.	0.004;0.007|.	T|.	0.34378|.	-0.9831|.	9|.	0.07175|.	T|.	0.84|.	.|.	6.5931|6.5931	0.22658|0.22658	0.3516:0.171:0.4774:0.0|0.3516:0.171:0.4774:0.0	.|.	1149;1193|.	Q5VU43-3;Q5VU43|.	.;MYOME_HUMAN|.	E|K	1149;1193;1193;1330;1330|88	ENSP00000327209:D1149E;ENSP00000358360:D1193E;ENSP00000358363:D1193E;ENSP00000435654:D1330E;ENSP00000358366:D1330E|.	ENSP00000327209:D1149E|.	D|X	-|-	3|1	2|0	PDE4DIP|PDE4DIP	143592974|143592974	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.018000|0.018000	0.09664|0.09664	-0.226000|-0.226000	0.09139|0.09139	-0.300000|-0.300000	0.08895|0.08895	-0.256000|-0.256000	0.11100|0.11100	GAT|TAA	.	.	.	none		0.582	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		T	144881617	A	T	144881617	3	4	39	1	0	0	0	0	1	0	0	0	11650	446	16	5	3541	5	PDE4DIP	1	144881617	Missense_Mutation	SNP	A	TCGA-5P-A9KE-01A-11D-A42J-10	27182097	144881617	104369004	7	2787											
CCT3	7203	hgsc.bcm.edu	37	chr1	156279019	156279019	+	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	gccagcatcaggagccccgcCttgccggctctggtcatcgc	5	7	12	17	3	3	0	2	0	1	0	4	1	3	1	5	3	3	2	5	3	0	1			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr1:156279019C>G	ENST00000295688.3	-	14	1889	c.1609G>C	c.(1609-1611)Ggc>Cgc	p.G537R	CCT3_ENST00000368261.3_Missense_Mutation_p.G492R|CCT3_ENST00000472765.2_Missense_Mutation_p.G492R|CCT3_ENST00000368259.2_Missense_Mutation_p.G499R	NM_005998.4	NP_005989.3	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 (gamma)	537					'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)					GGAGCCCCGCCTTGCCGGCTC	0.537																																					p.G537R		Atlas-SNP	.											.	CCT3	61	.	0			c.G1609C						PASS	.						112	119	116					1																	156279019		2203	4300	6503	SO:0001583	missense	7203	exon14			CCCCGCCTTGCCG	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.1609G>C	chr1.hg19:g.156279019C>G	ENSP00000295688:p.Gly537Arg	52.0	0.0	.		39.0	8.0	.	NM_005998	A6NE14|Q5SZY1|Q9BR64	Missense_Mutation	SNP	ENST00000295688.3	hg19	CCDS1140.2	.	.	.	.	.	.	.	.	.	.	C	13.57	2.276772	0.40294	.	.	ENSG00000163468	ENST00000295688;ENST00000368259;ENST00000368261;ENST00000472765	T;T;T;T	0.78481	-1.18;-0.54;-0.61;-0.61	5.43	1.47	0.22746	.	0.687378	0.13466	N	0.385795	T	0.52403	0.1732	L	0.58101	1.795	0.26422	N	0.976086	B;B;B	0.27732	0.187;0.117;0.039	B;B;B	0.32342	0.144;0.068;0.089	T	0.47446	-0.9117	10	0.38643	T	0.18	-0.6586	3.7531	0.08575	0.17:0.5583:0.0:0.2717	.	499;536;537	P49368-2;E9PAQ6;P49368	.;.;TCPG_HUMAN	R	537;499;492;492	ENSP00000295688:G537R;ENSP00000357242:G499R;ENSP00000357244:G492R;ENSP00000431543:G492R	ENSP00000295688:G537R	G	-	1	0	CCT3	154545643	0.035000	0.19736	0.167000	0.22817	0.977000	0.68977	0.217000	0.17603	0.117000	0.18138	0.650000	0.86243	GGC	.	.	.	none		0.537	CCT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060602.3	NM_005998		G	156279019	C	G	156279019	3	3	39	1	0	0	0	0	1	0	0	0	2956	681	24	4	32	4	CCT3	1	156279019	Missense_Mutation	SNP	C	TCGA-5P-A9KE-01A-11D-A42J-10	11397402	156279019	92971602	8	2788											
SPTA1	6708	hgsc.bcm.edu	37	chr1	158621173	158621173	+	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	ttacctgccggatttgagctCcttctggtgttagaagtcct	6	15	10	10	1	1	2	0	1	1	1	3	3	3	3	4	2	3	2	4	2	3	4			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr1:158621173C>G	ENST00000368147.4	-	24	3641	c.3461G>C	c.(3460-3462)gGa>gCa	p.G1154A		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1154					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)					GATTTGAGCTCCTTCTGGTGT	0.438																																					p.G1154A		Atlas-SNP	.											.	SPTA1	720	.	0			c.G3461C						PASS	.						209	207	208					1																	158621173		1885	4104	5989	SO:0001583	missense	6708	exon24			TGAGCTCCTTCTG	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.3461G>C	chr1.hg19:g.158621173C>G	ENSP00000357129:p.Gly1154Ala	104.0	0.0	.		105.0	26.0	.	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	12.62	1.991563	0.35131	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.65178	-0.14;-0.14	4.66	4.66	0.58398	.	.	.	.	.	T	0.28067	0.0692	N	0.05574	-0.02	0.38698	D	0.952926	B	0.15930	0.015	B	0.26614	0.071	T	0.18555	-1.0333	9	0.51188	T	0.08	.	10.5066	0.44836	0.1931:0.8069:0.0:0.0	.	1154	P02549	SPTA1_HUMAN	A	1154	ENSP00000357130:G1154A;ENSP00000357129:G1154A	ENSP00000357129:G1154A	G	-	2	0	SPTA1	156887797	1.000000	0.71417	0.998000	0.56505	0.932000	0.56968	0.505000	0.22642	2.572000	0.86782	0.655000	0.94253	GGA	.	.	.	none		0.438	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		G	158621173	C	G	158621173	3	3	39	1	0	0	0	0	1	0	0	0	15128	855	30	4	3914	4	SPTA1	1	158621173	Missense_Mutation	SNP	C	TCGA-5P-A9KE-01A-11D-A42J-10	2342154	158621173	90629448	9	2789											
C1orf74	148304	hgsc.bcm.edu	37	chr1	209956492	209956492	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagattccagtctgaggaaTggagcctgctgtaggagact	11	9	13	8	0	1	3	0	1	1	2	2	6	2	5	2	3	2	2	2	3	2	2			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr1:209956492T>C	ENST00000294811.1	-	2	744	c.488A>G	c.(487-489)cAt>cGt	p.H163R		NM_152485.2	NP_689698.1	Q96LT6	CA074_HUMAN	chromosome 1 open reading frame 74	163										endometrium(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)	15				OV - Ovarian serous cystadenocarcinoma(81;0.0328)		GTCTGAGGAATGGAGCCTGCT	0.517																																					p.H163R		Atlas-SNP	.											.	C1orf74	30	.	0			c.A488G						PASS	.						83	86	85					1																	209956492		2203	4300	6503	SO:0001583	missense	148304	exon2			GAGGAATGGAGCC	AK057807	CCDS1491.1	1q32.2	2008-02-05			ENSG00000162757	ENSG00000162757			26319	protein-coding gene	gene with protein product						12477932	Standard	NM_152485		Approved	FLJ25078	uc001hhp.1	Q96LT6	OTTHUMG00000036483	ENST00000294811.1:c.488A>G	chr1.hg19:g.209956492T>C	ENSP00000294811:p.His163Arg	117.0	0.0	.		89.0	24.0	.	NM_152485		Missense_Mutation	SNP	ENST00000294811.1	hg19	CCDS1491.1	.	.	.	.	.	.	.	.	.	.	T	6.835	0.523237	0.13066	.	.	ENSG00000162757	ENST00000294811	T	0.41400	1.0	5.51	-1.42	0.08913	.	1.329280	0.04580	N	0.394789	T	0.20861	0.0502	N	0.12746	0.255	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.11012	-1.0605	10	0.25106	T	0.35	0.017	1.6047	0.02681	0.2356:0.0875:0.2398:0.4371	.	163	Q96LT6	CA074_HUMAN	R	163	ENSP00000294811:H163R	ENSP00000294811:H163R	H	-	2	0	C1orf74	208023115	0.000000	0.05858	0.002000	0.10522	0.895000	0.52256	-0.733000	0.04898	-0.187000	0.10516	0.533000	0.62120	CAT	.	.	.	none		0.517	C1orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088745.1	NM_152485		C	209956492	T	C	209956492	3	2	39	1	0	0	0	0	1	0	0	0	2060	1464	51	3	325	3	C1orf74	1	209956492	Missense_Mutation	SNP	T	TCGA-5P-A9KE-01A-11D-A42J-10	51335319	209956492	39294129	10	2790											
USH2A	7399	hgsc.bcm.edu	37	chr1	216595303	216595303	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgatttccaaaaataaaacTtgcagaattgctatgggcgt	14	12	9	6	1	0	2	0	1	0	1	1	2	1	2	1	1	3	2	1	1	6	5			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr1:216595303T>C	ENST00000307340.3	-	2	762	c.376A>G	c.(376-378)Agt>Ggt	p.S126G	USH2A_ENST00000366942.3_Missense_Mutation_p.S126G|USH2A_ENST00000366943.2_Missense_Mutation_p.S126G	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	126					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)		AAAATAAAACTTGCAGAATTG	0.453										HNSCC(13;0.011)																											p.S126G		Atlas-SNP	.											.	USH2A	1168	.	0			c.A376G						PASS	.						96	94	95					1																	216595303		2203	4300	6503	SO:0001583	missense	7399	exon2			TAAAACTTGCAGA	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.376A>G	chr1.hg19:g.216595303T>C	ENSP00000305941:p.Ser126Gly	112.0	0.0	.		110.0	27.0	.	NM_007123	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.050033	0.75846	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.65732	-0.17;-0.17;-0.17	5.42	5.42	0.78866	Concanavalin A-like lectin/glucanase (1);	0.000000	0.49916	U	0.000121	T	0.78329	0.4266	M	0.72118	2.19	0.53688	D	0.99997	D;D	0.89917	0.999;1.0	D;D	0.87578	0.96;0.998	T	0.81123	-0.1076	10	0.87932	D	0	.	15.45	0.75265	0.0:0.0:0.0:1.0	.	126;126	O75445-2;O75445	.;USH2A_HUMAN	G	126	ENSP00000305941:S126G;ENSP00000355910:S126G;ENSP00000355909:S126G	ENSP00000305941:S126G	S	-	1	0	USH2A	214661926	1.000000	0.71417	0.736000	0.30914	0.839000	0.47603	4.527000	0.60573	2.057000	0.61298	0.482000	0.46254	AGT	.	.	.	none		0.453	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		C	216595303	T	C	216595303	3	2	39	1	0	0	0	0	1	0	0	0	17048	1609	56	3	15530	3	USH2A	1	216595303	Missense_Mutation	SNP	T	TCGA-5P-A9KE-01A-11D-A42J-10	6638811	216595303	32655318	11	2791											
SMYD1	150572	hgsc.bcm.edu	37	chr2	88390544	88390544	+	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	tgggtagattaactgcaacgGttttactctcagtgatcaga	11	13	10	7	1	2	3	2	1	1	2	3	3	2	3	0	2	4	3	0	2	4	4			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr2:88390544G>C	ENST00000419482.2	+	4	627	c.542G>C	c.(541-543)gGt>gCt	p.G181A	SMYD1_ENST00000444564.2_Missense_Mutation_p.G181A|SMYD1_ENST00000438570.1_Intron|SMYD1_ENST00000468008.1_3'UTR	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	181	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						AACTGCAACGGTTTTACTCTC	0.493																																					p.G181A		Atlas-SNP	.											.	SMYD1	95	.	0			c.G542C						PASS	.						172	171	171					2																	88390544		2203	4300	6503	SO:0001583	missense	150572	exon4			GCAACGGTTTTAC	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.542G>C	chr2.hg19:g.88390544G>C	ENSP00000393453:p.Gly181Ala	49.0	0.0	.		41.0	10.0	.	NM_198274	A0AV30|A6NE13	Missense_Mutation	SNP	ENST00000419482.2	hg19	CCDS33240.1	.	.	.	.	.	.	.	.	.	.	G	12.35	1.911492	0.33721	.	.	ENSG00000115593	ENST00000419482;ENST00000444564;ENST00000295833	T;T	0.11277	2.79;2.79	5.2	4.26	0.50523	SET domain (2);	0.095655	0.64402	D	0.000001	T	0.07324	0.0185	N	0.05230	-0.09	0.80722	D	1	P	0.36110	0.537	B	0.41332	0.354	T	0.49771	-0.8904	10	0.18276	T	0.48	-12.1291	15.8949	0.79326	0.0:0.217:0.783:0.0	.	181	Q8NB12	SMYD1_HUMAN	A	181;181;15	ENSP00000393453:G181A;ENSP00000407888:G181A	ENSP00000295833:G15A	G	+	2	0	SMYD1	88171659	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.135000	0.57997	2.575000	0.86900	0.561000	0.74099	GGT	.	.	.	none		0.493	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915		C	88390544	G	C	88390544	3	2	39	1	0	0	0	0	1	0	0	0	14834	1261	44	4	556	4	SMYD1	2	88390544	Missense_Mutation	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10		88390544	154808829	12	2792											
DDX18	8886	hgsc.bcm.edu	37	chr2	118578868	118578868	+	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	gtatcagaccacttctggaaGgcaggtatgattaacattga	13	11	10	7	0	2	3	1	2	1	1	2	4	2	4	1	3	1	3	1	3	4	5			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr2:118578868G>A	ENST00000263239.2	+	4	774	c.646G>A	c.(646-648)Ggc>Agc	p.G216S	DDX18_ENST00000474694.1_3'UTR	NM_006773.3	NP_006764.3	Q9NVP1	DDX18_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	216	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(4)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						ACTTCTGGAAGGCAGGTATGA	0.313																																					p.G216S		Atlas-SNP	.											.	DDX18	79	.	0			c.G646A						PASS	.						76	78	77					2																	118578868		2203	4299	6502	SO:0001583	missense	8886	exon4			CTGGAAGGCAGGT	X98743	CCDS2120.1	2q21.2	2008-02-05	2003-06-13		ENSG00000088205	ENSG00000088205		"DEAD-boxes"	2741	protein-coding gene	gene with protein product		606355	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 18 (Myc-regulated)"			8861962	Standard	NM_006773		Approved	MrDb	uc002tlh.1	Q9NVP1	OTTHUMG00000058521	ENST00000263239.2:c.646G>A	chr2.hg19:g.118578868G>A	ENSP00000263239:p.Gly216Ser	233.0	0.0	.		202.0	58.0	.	NM_006773	Q6GTZ9|Q6IAU4|Q92732|Q9BQB7	Missense_Mutation	SNP	ENST00000263239.2	hg19	CCDS2120.1	.	.	.	.	.	.	.	.	.	.	G	33	5.248238	0.95305	.	.	ENSG00000088205	ENST00000263239	T	0.18810	2.19	5.0	5.0	0.66597	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.049310	0.85682	N	0.000000	T	0.50429	0.1615	M	0.85945	2.785	0.80722	D	1	D	0.64830	0.994	D	0.66351	0.943	T	0.56643	-0.7945	10	0.87932	D	0	-0.8536	17.0203	0.86432	0.0:0.0:1.0:0.0	.	216	Q9NVP1	DDX18_HUMAN	S	216	ENSP00000263239:G216S	ENSP00000263239:G216S	G	+	1	0	DDX18	118295338	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.070000	0.93974	2.775000	0.95449	0.650000	0.86243	GGC	.	.	.	none		0.313	DDX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129632.3	NM_006773		A	118578868	G	A	118578868	3	1	39	1	0	0	0	0	1	0	0	0	4347	1000	35	2	660	2	DDX18	2	118578868	Missense_Mutation	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10	30188324	118578868	124620505	13	2793											
LRP2	4036	hgsc.bcm.edu	37	chr2	170062024	170062024	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtagagaaggtcctcttcAtagtccagagtcagcccact	11	9	9	12	0	3	2	2	0	1	2	5	3	5	2	3	1	1	1	3	1	3	3			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr2:170062024A>G	ENST00000263816.3	-	41	7965	c.7680T>C	c.(7678-7680)taT>taC	p.Y2560Y		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2560					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)"	GGTCCTCTTCATAGTCCAGAG	0.483																																					p.Y2560Y		Atlas-SNP	.											.	LRP2	751	.	0			c.T7680C						PASS	.						118	109	112					2																	170062024		2203	4300	6503	SO:0001819	synonymous_variant	4036	exon41			CTCTTCATAGTCC		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.7680T>C	chr2.hg19:g.170062024A>G		62.0	0.0	.		64.0	21.0	.	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	hg19	CCDS2232.1																																																																																			.	.	.	none		0.483	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		G	170062024	A	G	170062024	2	3	39	1	0	0	0	0	0	0	0	1	8963	224	8	3		3	LRP2	2	170062024	Silent	SNP	A	TCGA-5P-A9KE-01A-11D-A42J-10	51483156	170062024	73137349	14	2794											
TTN	7273	hgsc.bcm.edu	37	chr2	179466287	179466287	+	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	agatctttgggtgggcctggTacatctgttggatgtaaatc	8	14	13	6	0	2	1	0	0	2	1	3	2	2	2	1	4	1	3	1	4	3	4			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr2:179466287T>A	ENST00000591111.1	-	237	50738	c.50514A>T	c.(50512-50514)gtA>gtT	p.V16838V	TTN_ENST00000359218.5_Silent_p.V9539V|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000460472.2_Silent_p.V9414V|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000589042.1_Silent_p.V18479V|TTN_ENST00000342992.6_Silent_p.V15911V|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Silent_p.V9606V|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	16838					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)			GTGGGCCTGGTACATCTGTTG	0.393																																					p.V18479V		Atlas-SNP	.											.	TTN	18412	.	0			c.A55437T						PASS	.						190	172	178					2																	179466287		1883	4105	5988	SO:0001819	synonymous_variant	7273	exon287			GCCTGGTACATCT	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.50514A>T	chr2.hg19:g.179466287T>A		38.0	0.0	.		45.0	10.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.	.	none		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179466287	T	A	179466287	2	1	39	1	0	0	0	0	0	0	0	1	16747	1625	57	5		5	TTN	2	179466287	Silent	SNP	T	TCGA-5P-A9KE-01A-11D-A42J-10	9404263	179466287	63733086	15	2795											
CALCRL	10203	hgsc.bcm.edu	37	chr2	188245407	188245407	+	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	tacatttctgcttttacctgAtggatcaaagtcctgaaagt	11	15	7	8	0	2	2	1	2	1	0	3	3	3	3	2	1	3	1	2	1	4	4	rs374525357		TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr2:188245407A>T	ENST00000409998.1	-	7	1073	c.292T>A	c.(292-294)Tca>Aca	p.S98T	AC007319.1_ENST00000453517.1_RNA|CALCRL_ENST00000410068.1_Missense_Mutation_p.S98T|CALCRL_ENST00000392370.3_Missense_Mutation_p.S98T|AC007319.1_ENST00000412276.1_RNA			Q16602	CALRL_HUMAN	calcitonin receptor-like	98					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)	p.S98T(1)		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)			CTTTTACCTGATGGATCAAAG	0.378																																					p.S98T		Atlas-SNP	.											CALCRL,caecum,carcinoma,0,1	CALCRL	73	.	1	Substitution - Missense(1)	large_intestine(1)	c.T292A						PASS	.	A	THR/SER	0,4406		0,0,2203	70	68	68		292	2.8	1	2		68	1,8599	1.2+/-3.3	0,1,4299	no	missense	CALCRL	NM_005795.4	58	0,1,6502	TT,TA,AA		0.0116,0.0,0.0077	benign	98/462	188245407	1,13005	2203	4300	6503	SO:0001583	missense	10203	exon5			TACCTGATGGATC	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.292T>A	chr2.hg19:g.188245407A>T	ENSP00000386972:p.Ser98Thr	150.0	0.0	.		138.0	22.0	.	NM_001271751	A8K6G5|A8KAD3|Q53S02|Q53TS5	Missense_Mutation	SNP	ENST00000409998.1	hg19	CCDS2293.1	.	.	.	.	.	.	.	.	.	.	A	9.664	1.144967	0.21288	0.0	1.16E-4	ENSG00000064989	ENST00000392370;ENST00000409998;ENST00000410068	T;T;T	0.52295	0.67;0.67;0.67	5.3	2.75	0.32379	GPCR, family 2, extracellular hormone receptor domain (3);	0.000000	0.53938	D	0.000056	T	0.20414	0.0491	N	0.04090	-0.28	0.47183	D	0.999341	B	0.09022	0.002	B	0.10450	0.005	T	0.07366	-1.0776	10	0.07813	T	0.8	.	9.1592	0.37012	0.7122:0.0:0.0:0.2878	.	98	Q16602	CALRL_HUMAN	T	98	ENSP00000376177:S98T;ENSP00000386972:S98T;ENSP00000387190:S98T	ENSP00000376177:S98T	S	-	1	0	CALCRL	187953652	1.000000	0.71417	0.993000	0.49108	0.940000	0.58332	5.513000	0.67037	1.005000	0.39183	0.460000	0.39030	TCA	.	.	.	weak		0.378	CALCRL-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334648.1	NM_005795		T	188245407	A	T	188245407	3	4	39	1	0	0	0	0	1	0	0	0	2582	333	12	5	1133	5	CALCRL	2	188245407	Missense_Mutation	SNP	A	TCGA-5P-A9KE-01A-11D-A42J-10	8779120	188245407	54953966	16	2796											
CCNYL1	151195	hgsc.bcm.edu	37	chr2	208576635	208576635	+	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	cttcccatggggaacacgctGacctgttgcgtgtcccccaa	7	9	10	15	2	0	1	0	1	0	0	2	2	2	2	4	2	2	2	4	2	2	2			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr2:208576635G>A	ENST00000295414.3	+	1	226	c.15G>A	c.(13-15)ctG>ctA	p.L5L	CCNYL1_ENST00000339882.5_Silent_p.L5L|CCNYL1_ENST00000392209.3_Intron|CCNYL1_ENST00000420822.1_Silent_p.L5L			Q8N7R7	CCYL1_HUMAN	cyclin Y-like 1	5					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)					endometrium(1)|large_intestine(1)|lung(3)	5				LUSC - Lung squamous cell carcinoma(261;0.0731)|Epithelial(149;0.139)|Lung(261;0.14)		GGAACACGCTGACCTGTTGCG	0.711																																					p.L5L		Atlas-SNP	.											.	CCNYL1	15	.	0			c.G15A						PASS	.						14	25	22					2																	208576635		689	1587	2276	SO:0001819	synonymous_variant	151195	exon1			CACGCTGACCTGT	AK095479	CCDS2377.1, CCDS46503.1	2q33.3	2008-02-05			ENSG00000163249	ENSG00000163249			26868	protein-coding gene	gene with protein product							Standard	NM_152523		Approved	FLJ40432	uc002vci.3	Q8N7R7	OTTHUMG00000132946	ENST00000295414.3:c.15G>A	chr2.hg19:g.208576635G>A		131.0	0.0	.		97.0	24.0	.	NM_001142300	Q6NX60	Silent	SNP	ENST00000295414.3	hg19																																																																																				.	.	.	none		0.711	CCNYL1-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000337062.1	NM_152523		A	208576635	G	A	208576635	2	1	39	1	0	0	0	0	0	0	0	1	2939	1277	45	2		2	CCNYL1	2	208576635	Silent	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10	20331228	208576635	34622738	17	2797											
ITM2C	81618	hgsc.bcm.edu	37	chr2	231741620	231741620	+	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	tggacaagtgctatgtcatcGaactcaacaccaccattgtg	12	10	8	11	1	2	0	2	0	0	0	3	2	2	1	2	1	3	1	2	1	4	2			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr2:231741620G>C	ENST00000326427.6	+	4	625	c.499G>C	c.(499-501)Gaa>Caa	p.E167Q	ITM2C_ENST00000326407.6_Intron|ITM2C_ENST00000409704.2_Missense_Mutation_p.E105Q|ITM2C_ENST00000335005.6_Missense_Mutation_p.E120Q|ITM2C_ENST00000492029.1_3'UTR	NM_030926.4	NP_112188.1	Q9NQX7	ITM2C_HUMAN	integral membrane protein 2C	167	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)		CTATGTCATCGAACTCAACAC	0.577																																					p.E167Q		Atlas-SNP	.											ITM2C,NS,carcinoma,0,3	ITM2C	17	.	0			c.G499C						PASS	.						178	160	166					2																	231741620		2203	4300	6503	SO:0001583	missense	81618	exon4			GTCATCGAACTCA	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.499G>C	chr2.hg19:g.231741620G>C	ENSP00000322730:p.Glu167Gln	61.0	0.0	.		44.0	9.0	.	NM_030926	B3KPG4|Q4G0A8|Q53H84|Q6IAE7|Q86VK5|Q8N288|Q8TAW0|Q9BUP8	Missense_Mutation	SNP	ENST00000326427.6	hg19	CCDS2479.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.949503	0.92660	.	.	ENSG00000135916	ENST00000457215;ENST00000541852;ENST00000326427;ENST00000335005;ENST00000543957;ENST00000409704;ENST00000418408	T;T;T;T;T;T;T	0.79033	-1.23;-1.23;-1.23;-1.23;-1.23;-1.23;-1.23	5.8	5.8	0.92144	BRICHOS (2);	0.000000	0.85682	D	0.000000	D	0.85978	0.5823	L	0.60455	1.87	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.86536	0.1825	10	0.72032	D	0.01	-1.6305	15.5631	0.76266	0.0:0.0:1.0:0.0	.	120;167	Q9NQX7-2;Q9NQX7	.;ITM2C_HUMAN	Q	167;105;167;120;105;105;105	ENSP00000390655:E167Q;ENSP00000440295:E105Q;ENSP00000322730:E167Q;ENSP00000335121:E120Q;ENSP00000444899:E105Q;ENSP00000387242:E105Q;ENSP00000403257:E105Q	ENSP00000322730:E167Q	E	+	1	0	ITM2C	231449864	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.243000	0.72384	2.735000	0.93741	0.655000	0.94253	GAA	.	.	.	none		0.577	ITM2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256954.2	NM_030926		C	231741620	G	C	231741620	3	2	39	1	0	0	0	0	1	0	0	0	7921	1059	37	4	513	4	ITM2C	2	231741620	Missense_Mutation	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10	23164985	231741620	11457753	18	2798											
SEC13	6396	hgsc.bcm.edu	37	chr3	10346761	10346761	+	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	ggtgggcaggccgatggaggGggcccaggccacatctcgaa	8	4	18	11	2	1	0	0	0	1	0	2	3	1	1	3	7	0	1	3	7	1	0			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr3:10346761G>A	ENST00000350697.3	-	7	789	c.664C>T	c.(664-666)Ccc>Tcc	p.P222S	SEC13_ENST00000397109.3_Missense_Mutation_p.P208S|SEC13_ENST00000492602.1_5'Flank|SEC13_ENST00000397117.1_Missense_Mutation_p.P208S|SEC13_ENST00000337354.4_Missense_Mutation_p.P225S|SEC13_ENST00000383801.2_Missense_Mutation_p.P268S	NM_183352.1	NP_899195.1	P55735	SEC13_HUMAN	SEC13 homolog (S. cerevisiae)	222					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)				NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	17						CCGATGGAGGGGGCCCAGGCC	0.612																																					p.P222S		Atlas-SNP	.											.	SEC13	35	.	0			c.C664T						PASS	.						99	91	93					3																	10346761		2203	4300	6503	SO:0001583	missense	6396	exon7			TGGAGGGGGCCCA		CCDS2599.1, CCDS46751.1, CCDS63540.1	3p25-p24	2013-01-10	2006-11-07	2006-11-07	ENSG00000157020	ENSG00000157020		"WD repeat domain containing"	10697	protein-coding gene	gene with protein product		600152	"SEC13 (S. cerevisiae)-like 1", "SEC13-like 1 (S. cerevisiae)"	D3S1231E, SEC13L1		7987303	Standard	NM_183352		Approved	SEC13R, npp-20	uc003bvn.3	P55735	OTTHUMG00000128671	ENST00000350697.3:c.664C>T	chr3.hg19:g.10346761G>A	ENSP00000312122:p.Pro222Ser	35.0	0.0	.		60.0	17.0	.	NM_183352	A8MV37|B4DXJ1|Q5BJF0|Q9BRM6|Q9BUG7	Missense_Mutation	SNP	ENST00000350697.3	hg19	CCDS2599.1	.	.	.	.	.	.	.	.	.	.	G	32	5.123386	0.94429	.	.	ENSG00000157020	ENST00000397109;ENST00000337354;ENST00000350697;ENST00000397117;ENST00000383801	T;T;T;T;T	0.70399	-0.48;-0.48;-0.48;-0.48;-0.48	5.62	5.62	0.85841	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	0.83348	0.5235	M	0.72576	2.205	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.998;1.0	T	0.82995	-0.0180	9	.	.	.	.	17.1466	0.86767	0.0:0.0:1.0:0.0	.	222;208;268;222	E9PHR5;A8MXL6;B4DXJ1;P55735	.;.;.;SEC13_HUMAN	S	208;225;222;208;268	ENSP00000380298:P208S;ENSP00000336566:P225S;ENSP00000312122:P222S;ENSP00000380306:P208S;ENSP00000373312:P268S	.	P	-	1	0	SEC13	10321761	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.727000	0.98787	2.646000	0.89796	0.655000	0.94253	CCC	.	.	.	none		0.612	SEC13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250563.3			A	10346761	G	A	10346761	3	1	39	1	0	0	0	0	1	0	0	0	13993	1232	43	2	316	2	SEC13	3	10346761	Missense_Mutation	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10		10346761	187675669	19	2799											
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41268729	41268729	+	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	tggctagtggtggaccccaaGctttagtaaatataatgagg	12	11	12	6	0	0	1	0	1	0	0	0	2	0	2	2	4	1	3	2	4	7	6			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr3:41268729G>C	ENST00000349496.5	+	7	1247	c.967G>C	c.(967-969)Gct>Cct	p.A323P	CTNNB1_ENST00000405570.1_Missense_Mutation_p.A323P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.A323P|CTNNB1_ENST00000453024.1_Missense_Mutation_p.A316P|CTNNB1_ENST00000396185.3_Missense_Mutation_p.A323P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	323					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TGGACCCCAAGCTTTAGTAAA	0.398		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.A323P	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	.	CTNNB1	4904	.	0			c.G967C						PASS	.						70	74	73					3																	41268729		2203	4300	6503	SO:0001583	missense	1499	exon7	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CCCCAAGCTTTAG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.967G>C	chr3.hg19:g.41268729G>C	ENSP00000344456:p.Ala323Pro	74.0	0.0	.		76.0	20.0	.	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	G	18.44	3.625073	0.66901	.	.	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18	5.5	5.5	0.81552	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.58119	0.2100	L	0.47716	1.5	0.80722	D	1	B;B	0.25105	0.054;0.118	B;B	0.23574	0.032;0.047	T	0.52653	-0.8547	10	0.25751	T	0.34	3.006	19.382	0.94540	0.0:0.0:1.0:0.0	.	251;323	B4DSW9;P35222	.;CTNB1_HUMAN	P	323;323;323;316;323	ENSP00000385604:A323P;ENSP00000379486:A323P;ENSP00000344456:A323P;ENSP00000411226:A316P;ENSP00000379488:A323P	ENSP00000344456:A323P	A	+	1	0	CTNNB1	41243733	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.869000	0.99810	2.591000	0.87537	0.591000	0.81541	GCT	.	.	.	none		0.398	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		C	41268729	G	C	41268729	3	2	39	1	0	0	0	0	1	0	0	0	4018	971	34	4	989	4	CTNNB1	3	41268729	Missense_Mutation	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10	30921968	41268729	156753701	20	2800											
DAG1	1605	hgsc.bcm.edu	37	chr3	49568721	49568721	+	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	gagaatggggcccttctctcCtggaagctgggctgctccct	5	10	13	13	0	1	1	0	0	1	1	4	3	3	2	3	4	2	3	3	4	2	1			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr3:49568721C>G	ENST00000539901.1	+	3	1335	c.777C>G	c.(775-777)tcC>tcG	p.S259S	DAG1_ENST00000545947.1_Silent_p.S259S|DAG1_ENST00000541308.1_Silent_p.S259S|DAG1_ENST00000308775.2_Silent_p.S259S|DAG1_ENST00000515359.2_Silent_p.S259S|DAG1_ENST00000538711.1_Silent_p.S259S	NM_001177644.2	NP_001171115	Q14118	DAG1_HUMAN	dystroglycan 1 (dystrophin-associated glycoprotein 1)	259	Required for laminin recognition.				basement membrane organization (GO:0071711)|branching involved in salivary gland morphogenesis (GO:0060445)|calcium-dependent cell-matrix adhesion (GO:0016340)|commissural neuron axon guidance (GO:0071679)|cytoskeletal anchoring at plasma membrane (GO:0007016)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|microtubule anchoring (GO:0034453)|modulation by virus of host morphology or physiology (GO:0019048)|morphogenesis of an epithelial sheet (GO:0002011)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell migration (GO:0030336)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase B signaling (GO:0051898)|nerve maturation (GO:0021682)|NLS-bearing protein import into nucleus (GO:0006607)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell outer membrane (GO:0009279)|cell-cell adherens junction (GO:0005913)|contractile ring (GO:0070938)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystroglycan complex (GO:0016011)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|node of Ranvier (GO:0033268)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|alpha-actinin binding (GO:0051393)|calcium ion binding (GO:0005509)|laminin-1 binding (GO:0043237)|SH2 domain binding (GO:0042169)|structural constituent of muscle (GO:0008307)|tubulin binding (GO:0015631)|vinculin binding (GO:0017166)|virus receptor activity (GO:0001618)			NS(1)|autonomic_ganglia(2)|breast(2)|endometrium(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	23				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.00241)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		CCCTTCTCTCCTGGAAGCTGG	0.557																																					p.S259S		Atlas-SNP	.											.	DAG1	60	.	0			c.C777G						PASS	.						64	69	67					3																	49568721		2203	4300	6503	SO:0001819	synonymous_variant	1605	exon4			TCTCTCCTGGAAG	L19711	CCDS2799.1	3p21	2014-09-17			ENSG00000173402	ENSG00000173402			2666	protein-coding gene	gene with protein product	"alpha-dystroglycan", "dystrophin-associated glycoprotein-1", "beta-dystroglycan"	128239				7774920, 1741056	Standard	NM_001177643		Approved	A3a, 156DAG, AGRNR, DAG	uc021wyd.1	Q14118	OTTHUMG00000156869	ENST00000539901.1:c.777C>G	chr3.hg19:g.49568721C>G		58.0	0.0	.		60.0	22.0	.	NM_001177642	A8K6M7|Q969J9	Silent	SNP	ENST00000539901.1	hg19	CCDS2799.1																																																																																			.	.	.	none		0.557	DAG1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346326.1			G	49568721	C	G	49568721	2	3	39	1	0	0	0	0	0	0	0	1	4227	668	24	4		4	DAG1	3	49568721	Silent	SNP	C	TCGA-5P-A9KE-01A-11D-A42J-10	8299992	49568721	148453709	21	2801											
CACNA1D	776	hgsc.bcm.edu	37	chr3	53845165	53845165	+	Missense_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	gatatccgaaggcttgggacGctatgcaagggacccaaaat	13	7	12	9	2	0	0	0	0	0	0	1	4	1	2	2	3	1	3	2	3	6	3			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr3:53845165G>A	ENST00000350061.5	+	48	6729	c.6218G>A	c.(6217-6219)cGc>cAc	p.R2073H	CACNA1D_ENST00000544977.1_3'UTR|CACNA1D_ENST00000288139.4_Missense_Mutation_p.R2093H|CACNA1D_ENST00000422281.2_Missense_Mutation_p.R2049H	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	2073					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)			breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GGCTTGGGACGCTATGCAAGG	0.522																																					p.R2093H		Atlas-SNP	.											.	CACNA1D	324	.	0			c.G6278A						PASS	.						100	97	98					3																	53845165		2203	4300	6503	SO:0001583	missense	776	exon49			TGGGACGCTATGC	AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.6218G>A	chr3.hg19:g.53845165G>A	ENSP00000288133:p.Arg2073His	101.0	0.0	.		100.0	27.0	.	NM_000720	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Missense_Mutation	SNP	ENST00000350061.5	hg19	CCDS46848.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.033345	0.54896	.	.	ENSG00000157388	ENST00000350061;ENST00000288139;ENST00000422281;ENST00000481478	T;T;T;T	0.57595	0.39;0.39;0.39;0.39	5.39	5.39	0.77823	.	0.320794	0.25083	N	0.033278	T	0.72391	0.3454	M	0.77103	2.36	0.80722	D	1	D;B;B;D	0.76494	0.996;0.051;0.051;0.999	P;B;B;P	0.62184	0.655;0.009;0.006;0.899	T	0.72937	-0.4140	10	0.48119	T	0.1	.	19.5276	0.95213	0.0:0.0:1.0:0.0	.	2049;1766;2073;2093	B0FYA3;Q59GD8;Q01668;Q01668-2	.;.;CAC1D_HUMAN;.	H	2073;2093;2049;1766	ENSP00000288133:R2073H;ENSP00000288139:R2093H;ENSP00000409174:R2049H;ENSP00000418014:R1766H	ENSP00000288139:R2093H	R	+	2	0	CACNA1D	53820205	1.000000	0.71417	1.000000	0.80357	0.665000	0.39181	3.789000	0.55454	2.710000	0.92621	0.655000	0.94253	CGC	.	.	.	none		0.522	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720		A	53845165	G	A	53845165	3	1	39	1	0	0	0	0	1	0	0	0	2543	1087	38	1	6580	1	CACNA1D	3	53845165	Missense_Mutation	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10	4276444	53845165	144177265	22	2802											
C3orf63	23272	hgsc.bcm.edu	37	chr3	56694957	56694957	+	Missense_Mutation	SNP	A	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	cttaccttcatttggacctaAgtatgtttccttataaaaca	12	16	4	9	0	1	0	1	0	0	0	2	1	2	1	3	1	2	2	3	1	6	8			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr3:56694957A>C	ENST00000493960.2	-	10	1259	c.1249T>G	c.(1249-1251)Tta>Gta	p.L417V	FAM208A_ENST00000355628.5_Missense_Mutation_p.L417V|FAM208A_ENST00000431842.2_Missense_Mutation_p.L21V	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	417							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						TTTGGACCTAAGTATGTTTCC	0.299																																					p.L417V		Atlas-SNP	.											.	FAM208A	113	.	0			c.T1249G						PASS	.						108	109	109					3																	56694957		2202	4299	6501	SO:0001583	missense	23272	exon10			GACCTAAGTATGT	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.1249T>G	chr3.hg19:g.56694957A>C	ENSP00000417509:p.Leu417Val	105.0	0.0	.		65.0	12.0	.	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Missense_Mutation	SNP	ENST00000493960.2	hg19	CCDS46853.1	.	.	.	.	.	.	.	.	.	.	A	3.516	-0.098806	0.07010	.	.	ENSG00000163946	ENST00000431842;ENST00000493960;ENST00000355628	T;T;T	0.11821	2.74;2.88;2.88	5.8	0.493	0.16878	.	0.773939	0.11384	N	0.569476	T	0.05318	0.0141	N	0.05383	-0.06	0.20307	N	0.999914	B;B;B	0.09022	0.002;0.001;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.44726	-0.9309	10	0.15066	T	0.55	-0.0154	4.2051	0.10485	0.3113:0.4663:0.1139:0.1085	.	417;417;21	Q9UK61-3;Q9UK61-4;Q9UK61-2	.;.;.	V	21;417;417	ENSP00000399410:L21V;ENSP00000417509:L417V;ENSP00000347845:L417V	ENSP00000347845:L417V	L	-	1	2	C3orf63	56669997	0.306000	0.24490	0.992000	0.48379	0.983000	0.72400	-0.247000	0.08866	0.067000	0.16545	0.460000	0.39030	TTA	.	.	.	none		0.299	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224		C	56694957	A	C	56694957	3	2	39	1	0	0	0	0	1	0	0	0	2241	69	3	5	3883	5	C3orf63	3	56694957	Missense_Mutation	SNP	A	TCGA-5P-A9KE-01A-11D-A42J-10	2849792	56694957	141327473	23	2803											
PARL	55486	hgsc.bcm.edu	37	chr3	183602589	183602589	+	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	gcccaccgacgcaccccacgCctggccgcagccccagcctc	6	2	9	24	4	0	0	0	0	0	0	1	1	0	0	9	1	2	2	9	1	0	0			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr3:183602589C>A	ENST00000317096.4	-	1	106	c.46G>T	c.(46-48)Gcg>Tcg	p.A16S	PARL_ENST00000311101.5_Missense_Mutation_p.A16S|PARL_ENST00000435888.1_Missense_Mutation_p.A16S|RP11-315J22.5_ENST00000445165.1_RNA|MIR4448_ENST00000584360.1_RNA	NM_018622.5	NP_061092.3	Q9H300	PARL_HUMAN	presenilin associated, rhomboid-like	16					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)			GCACCCCACGCCTGGCCGCAG	0.711											OREG0015941	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A16S		Atlas-SNP	.											.	PARL	32	.	0			c.G46T						PASS	.						8	9	9					3																	183602589		2142	4197	6339	SO:0001583	missense	55486	exon1			CCCACGCCTGGCC	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.46G>T	chr3.hg19:g.183602589C>A	ENSP00000325421:p.Ala16Ser	29.0	0.0	.	1985	29.0	5.0	.	NM_018622	Q96CQ4|Q9BTJ6|Q9P1E3	Missense_Mutation	SNP	ENST00000317096.4	hg19	CCDS3248.1	.	.	.	.	.	.	.	.	.	.	C	4.654	0.121534	0.08881	.	.	ENSG00000175193	ENST00000317096;ENST00000311101;ENST00000435888	T;T;T	0.74947	-0.89;-0.89;-0.89	4.72	2.9	0.33743	.	0.347388	0.23680	N	0.045621	T	0.53786	0.1818	N	0.12182	0.205	0.26225	N	0.979108	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.002	T	0.50039	-0.8874	10	0.66056	D	0.02	-4.6318	7.7714	0.29010	0.0:0.8057:0.0:0.1943	.	16;16	Q9H300-2;Q9H300	.;PARL_HUMAN	S	16	ENSP00000325421:A16S;ENSP00000310676:A16S;ENSP00000402137:A16S	ENSP00000310676:A16S	A	-	1	0	PARL	185085283	0.667000	0.27484	0.913000	0.36048	0.025000	0.11179	0.254000	0.18314	0.693000	0.31634	0.655000	0.94253	GCG	.	.	.	none		0.711	PARL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346465.1	NM_018622		A	183602589	C	A	183602589	3	1	39	1	0	0	0	0	1	0	0	0	11458	739	26	4	1133	4	PARL	3	183602589	Missense_Mutation	SNP	C	TCGA-5P-A9KE-01A-11D-A42J-10	126907632	183602589	14419841	24	2804											
SLC2A9	56606	hgsc.bcm.edu	37	chr4	10022970	10022970	+	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	tccagcagtgccctccctggCcctggaggcccggcgtggct	3	7	14	17	2	0	0	0	0	0	0	2	1	2	1	5	5	2	2	5	5	0	0			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr4:10022970C>T	ENST00000264784.3	-	1	137	c.84G>A	c.(82-84)ggG>ggA	p.G28G	SLC2A9_ENST00000309065.3_Intron|SLC2A9_ENST00000506583.1_Intron	NM_020041.2	NP_064425.2	Q9NRM0	GTR9_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 9	28					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)	CCCTCCCTGGCCCTGGAGGCC	0.587																																					p.G28G		Atlas-SNP	.											.	SLC2A9	158	.	0			c.G84A						PASS	.						126	136	133					4																	10022970		2203	4300	6503	SO:0001819	synonymous_variant	56606	exon1			CCCTGGCCCTGGA	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.84G>A	chr4.hg19:g.10022970C>T		88.0	0.0	.		67.0	32.0	.	NM_020041	Q0VGC4|Q4W5D1|Q8WV30|Q96P00	Silent	SNP	ENST00000264784.3	hg19	CCDS3407.1																																																																																			.	.	.	none		0.587	SLC2A9-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207055.1			T	10022970	C	T	10022970	2	4	39	1	0	0	0	0	0	0	0	1	14565	726	26	2		2	SLC2A9	4	10022970	Silent	SNP	C	TCGA-5P-A9KE-01A-11D-A42J-10		10022970	181131306	25	2805											
FAT4	79633	hgsc.bcm.edu	37	chr4	126372770	126372770	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgatgacccttcagtccacTgaccctgatctccctccaaa	9	10	6	16	0	2	4	1	4	1	0	5	4	4	4	5	0	0	0	5	0	1	1			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr4:126372770T>C	ENST00000394329.3	+	9	10612	c.10599T>C	c.(10597-10599)acT>acC	p.T3533T	FAT4_ENST00000335110.5_Silent_p.T1831T	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3533	Cadherin 34. {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						TTCAGTCCACTGACCCTGATC	0.483																																					p.T3533T		Atlas-SNP	.											.	FAT4	1752	.	0			c.T10599C						PASS	.						120	119	120					4																	126372770		2203	4300	6503	SO:0001819	synonymous_variant	79633	exon9			GTCCACTGACCCT	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.10599T>C	chr4.hg19:g.126372770T>C		90.0	0.0	.		93.0	19.0	.	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	hg19	CCDS3732.3																																																																																			.	.	.	none		0.483	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		C	126372770	T	C	126372770	2	2	39	1	0	0	0	0	0	0	0	1	5699	1567	55	3		3	FAT4	4	126372770	Silent	SNP	T	TCGA-5P-A9KE-01A-11D-A42J-10	116349800	126372770	64781506	26	2806											
CDH9	1007	hgsc.bcm.edu	37	chr5	26890623	26890623	+	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	tgaaaatagaaccattttctGagtgaataccaaaaatacgg	18	10	7	6	1	1	4	0	3	1	1	1	4	1	4	2	1	3	0	2	1	9	5			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr5:26890623G>A	ENST00000231021.4	-	8	1476	c.1304C>T	c.(1303-1305)tCa>tTa	p.S435L		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	435	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						ACCATTTTCTGAGTGAATACC	0.403																																					p.S435L	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.C1304T						PASS	.						102	102	102					5																	26890623		2203	4300	6503	SO:0001583	missense	1007	exon8			TTTTCTGAGTGAA	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.1304C>T	chr5.hg19:g.26890623G>A	ENSP00000231021:p.Ser435Leu	112.0	0.0	.		88.0	26.0	.	NM_016279	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	hg19	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	G	17.33	3.362967	0.61403	.	.	ENSG00000113100	ENST00000231021	T	0.53206	0.63	5.09	5.09	0.68999	Cadherin (4);Cadherin-like (1);	0.301425	0.32736	N	0.005707	T	0.66257	0.2771	M	0.90595	3.13	0.53688	D	0.999978	B;B	0.26041	0.14;0.092	B;B	0.41174	0.219;0.349	T	0.67601	-0.5629	9	.	.	.	.	17.0519	0.86521	0.0:0.0:1.0:0.0	.	28;435	B4DFP0;Q9ULB4	.;CADH9_HUMAN	L	435	ENSP00000231021:S435L	.	S	-	2	0	CDH9	26926380	1.000000	0.71417	0.716000	0.30569	0.693000	0.40251	9.825000	0.99386	2.385000	0.81259	0.453000	0.30009	TCA	.	.	.	none		0.403	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		A	26890623	G	A	26890623	3	1	39	1	0	0	0	0	1	0	0	0	3119	1294	45	2	1085	2	CDH9	5	26890623	Missense_Mutation	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10		26890623	154024637	27	2807											
HMGCS1	3157	hgsc.bcm.edu	37	chr5	43294862	43294863	+	Frame_Shift_Ins	INS	-	-	GT																															tccattttgatttgatacaaINSgtaaagatgcctttgttttc																										TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr5:43294862_43294863insGT	ENST00000325110.6	-	7	1212_1213	c.1006_1007insAC	c.(1006-1008)cttfs	p.L336fs	HMGCS1_ENST00000433297.2_Frame_Shift_Ins_p.L336fs	NM_001098272.2	NP_001091742.1	Q01581	HMCS1_HUMAN	3-hydroxy-3-methylglutaryl-CoA synthase 1 (soluble)	336					brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|lipid metabolic process (GO:0006629)|liver development (GO:0001889)|male gonad development (GO:0008584)|response to acid chemical (GO:0001101)|response to drug (GO:0042493)|response to lipoprotein particle (GO:0055094)|response to low light intensity stimulus (GO:0009645)|response to purine-containing compound (GO:0014074)|response to tellurium ion (GO:0046690)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hydroxymethylglutaryl-CoA synthase activity (GO:0004421)|isomerase activity (GO:0016853)|organic acid binding (GO:0043177)			NS(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|stomach(1)|urinary_tract(1)	15						ATTTGATACAAGTAAAGATGCC	0.356																																					p.L336fs		Atlas-Indel,Pindel	.											.	HMGCS1	33	.	0			c.1007_1008insAC						PASS	.																																			SO:0001589	frameshift_variant	3157	exon6			.		CCDS34154.1	5p14-p13	2012-10-02	2010-04-30			ENSG00000112972	2.3.3.10		5007	protein-coding gene	gene with protein product	"3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) synthase"	142940	"3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble)"	HMGCS			Standard	NM_001098272		Approved		uc003jnq.5	Q01581		ENST00000325110.6:c.1005_1006dupAC	chr5.hg19:g.43294863_43294864dupGT	ENSP00000322706:p.Leu336fs	50.0	0.0	0		53.0	19.0	0.358491	NM_002130	B2RDL8	Frame_Shift_Ins	INS	ENST00000325110.6	hg19	CCDS34154.1																																																																																			.	.	.	none		0.356	HMGCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368022.1			GT	43294863	-	GT	43294862	7	5	39	1	0	1	1	0	0	0	0	0	7239	72	3	0	575	0	HMGCS1	5	43294862	Frame_Shift_Ins	INS	-	TCGA-5P-A9KE-01A-11D-A42J-10	16404239	43294862	137620398	28	2808											
C5orf35	133383	hgsc.bcm.edu	37	chr5	56207069	56207069	+	Missense_Mutation	SNP	A	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	atgtcctaggaacattactgAaagttttccaggctctattc	11	14	7	9	0	1	1	0	1	1	0	4	2	3	2	2	2	2	2	2	2	5	6			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr5:56207069A>C	ENST00000285947.2	+	2	558	c.172A>C	c.(172-174)Aaa>Caa	p.K58Q	SETD9_ENST00000541720.1_Missense_Mutation_p.K58Q|SETD9_ENST00000475908.1_Intron|AC008937.3_ENST00000453721.1_RNA	NM_153706.3	NP_714917.2	Q8NE22	SETD9_HUMAN	SET domain containing 9	58							methyltransferase activity (GO:0008168)										AACATTACTGAAAGTTTTCCA	0.358																																					p.K58Q		Atlas-SNP	.											.	.	.	.	0			c.A172C						PASS	.						41	43	42					5																	56207069		2202	4300	6502	SO:0001583	missense	133383	exon2			TTACTGAAAGTTT	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.172A>C	chr5.hg19:g.56207069A>C	ENSP00000285947:p.Lys58Gln	135.0	0.0	.		135.0	32.0	.	NM_153706	F5H713	Missense_Mutation	SNP	ENST00000285947.2	hg19	CCDS3972.1	.	.	.	.	.	.	.	.	.	.	A	11.05	1.525967	0.27299	.	.	ENSG00000155542	ENST00000285947;ENST00000541720;ENST00000423328	T;T	0.32023	1.48;1.47	5.3	1.52	0.23074	.	0.646198	0.16385	N	0.216710	T	0.23611	0.0571	L	0.50333	1.59	0.24433	N	0.994567	B	0.11235	0.004	B	0.06405	0.002	T	0.21211	-1.0252	10	0.27785	T	0.31	-11.5557	6.4957	0.22140	0.7288:0.1316:0.1396:0.0	.	58	Q8NE22	CE035_HUMAN	Q	58;58;32	ENSP00000285947:K58Q;ENSP00000442886:K58Q	ENSP00000285947:K58Q	K	+	1	0	C5orf35	56242826	0.995000	0.38212	0.994000	0.49952	0.992000	0.81027	0.899000	0.28417	0.026000	0.15269	0.533000	0.62120	AAA	.	.	.	none		0.358	SETD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132304.2	NM_153706		C	56207069	A	C	56207069	3	2	39	1	0	0	0	0	1	0	0	0	2296	247	9	5	178	5	C5orf35	5	56207069	Missense_Mutation	SNP	A	TCGA-5P-A9KE-01A-11D-A42J-10	12912207	56207069	124708191	29	2809											
POU5F2	134187	hgsc.bcm.edu	37	chr5	93076952	93076952	+	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	aacttcggaatgctccgcagGgcaatgtagggccccgggag	9	6	15	11	3	0	0	0	0	0	0	2	2	1	2	3	4	2	4	3	4	4	2			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr5:93076952G>C	ENST00000510627.4	-	1	391	c.318C>G	c.(316-318)gcC>gcG	p.A106A	FAM172A_ENST00000509163.1_Intron|FAM172A_ENST00000509739.1_Intron|RP11-185E12.2_ENST00000606528.1_RNA|FAM172A_ENST00000395965.3_Intron|FAM172A_ENST00000505869.1_Intron|POU5F2_ENST00000606183.1_5'Flank	NM_153216.1	NP_694948.1	Q8N7G0	PO5F2_HUMAN	POU domain class 5, transcription factor 2	106					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)						all_cancers(142;3.87e-05)|all_epithelial(76;4.59e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0415)|all cancers(79;2.03e-19)		TGCTCCGCAGGGCAATGTAGG	0.637																																					p.A106A		Atlas-SNP	.											.	POU5F2	10	.	0			c.C318G						PASS	.						52	51	51					5																	93076952		1903	4113	6016	SO:0001819	synonymous_variant	134187	exon1			CCGCAGGGCAATG		CCDS59489.1	5q15	2011-06-20				ENSG00000248483		"Homeoboxes / POU class"	26367	protein-coding gene	gene with protein product						7908264	Standard	NM_153216		Approved	SPRM-1, FLJ25680	uc003kkl.1	Q8N7G0		ENST00000510627.4:c.318C>G	chr5.hg19:g.93076952G>C		57.0	0.0	.		45.0	11.0	.	NM_153216	Q15169|Q6MZL7|Q8N748	Silent	SNP	ENST00000510627.4	hg19	CCDS59489.1																																																																																			.	.	.	none		0.637	POU5F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369873.5	NM_153216		C	93076952	G	C	93076952	2	2	39	1	0	0	0	0	0	0	0	1	12290	1219	43	4		4	POU5F2	5	93076952	Silent	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10	36869883	93076952	87838308	30	2810											
C5orf13	9315	hgsc.bcm.edu	37	chr5	111312420	111312420	+	Intron	SNP	T	T	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	cacataccaaagcagaataaTtccaaactcctttcattcca	16	10	2	13	0	1	1	1	0	0	1	4	1	4	1	4	0	3	1	4	0	5	5			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr5:111312420T>A	ENST00000450761.2	-	1	141				NREP-AS1_ENST00000503242.1_RNA|NREP_ENST00000395634.3_Missense_Mutation_p.N6I|NREP-AS1_ENST00000507222.1_RNA			Q16612	NREP_HUMAN	neuronal regeneration related protein						axon regeneration (GO:0031103)|regulation of neuron differentiation (GO:0045664)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											AGCAGAATAATTCCAAACTCC	0.398																																					p.N6I		Atlas-SNP	.											.	.	.	.	0			c.A17T						PASS	.						196	165	175					5																	111312420		692	1591	2283	SO:0001627	intron_variant	9315	exon1			GAATAATTCCAAA	AF119859	CCDS4105.1, CCDS47255.1	5q22.1	2012-12-07	2012-12-07	2012-01-23	ENSG00000134986	ENSG00000134986			16834	protein-coding gene	gene with protein product	"neuronal protein 3.1"	607332	"chromosome 5 open reading frame 13", "neuronal regeneration related protein homolog (rat)"	C5orf13		8261136, 10981724, 15485502	Standard	NM_004772		Approved	P311, D4S114, PRO1873, PTZ17, SEZ17	uc011cvr.2	Q16612	OTTHUMG00000128795	ENST00000450761.2:c.57+20600A>T	chr5.hg19:g.111312420T>A		133.0	0.0	.		100.0	21.0	.	NM_001142475	B2RDN8|B7Z5D2|D3DSZ8	Missense_Mutation	SNP	ENST00000450761.2	hg19	CCDS4105.1	.	.	.	.	.	.	.	.	.	.	T	7.833	0.720334	0.15372	.	.	ENSG00000134986	ENST00000395634	T	0.51325	0.71	4.17	-5.73	0.02398	.	.	.	.	.	T	0.30039	0.0752	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.31308	-0.9948	8	0.87932	D	0	.	5.377	0.16170	0.266:0.4746:0.0:0.2595	.	6	B7Z5D2	.	I	6	ENSP00000378996:N6I	ENSP00000378996:N6I	N	-	2	0	C5orf13	111340319	0.000000	0.05858	0.000000	0.03702	0.578000	0.36192	-0.626000	0.05527	-1.222000	0.02587	-0.301000	0.09380	AAT	.	.	.	none		0.398	NREP-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370888.1	NM_004772		A	111312420	T	A	111312420	1	1	39	0	1	0	0	0	0	0	0	0	2284	1493	52	5		5	C5orf13	5	111312420	Intron	SNP	T	TCGA-5P-A9KE-01A-11D-A42J-10	18235468	111312420	69602840	31	2811											
CEP120	153241	hgsc.bcm.edu	37	chr5	122713195	122713195	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcttgcaggttccgctgaCgttctgattgcagttccttt	4	17	10	10	2	2	2	0	2	2	0	4	2	4	2	2	1	2	7	2	1	0	7	rs376401743		TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr5:122713195C>T	ENST00000306467.5	-	16	2535	c.2231G>A	c.(2230-2232)cGt>cAt	p.R744H	CEP120_ENST00000328236.5_Missense_Mutation_p.R744H|CEP120_ENST00000306481.6_Missense_Mutation_p.R718H			Q8N960	CE120_HUMAN	centrosomal protein 120kDa	744					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						GTTCCGCTGACGTTCTGATTG	0.398													C|||	1	0.000199681	8e-04	0	5008	,	,		16908	0		0	False		,,,				2504	0				p.R744H		Atlas-SNP	.											.	CEP120	72	.	0			c.G2231A						PASS	.						182	167	172					5																	122713195		2203	4300	6503	SO:0001583	missense	153241	exon17			CGCTGACGTTCTG	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.2231G>A	chr5.hg19:g.122713195C>T	ENSP00000303058:p.Arg744His	63.0	0.0	.		50.0	12.0	.	NM_153223	Q6AI52|Q6AW89|Q8IWB5|Q8N9Y0|Q8NDE8	Missense_Mutation	SNP	ENST00000306467.5	hg19	CCDS4134.2	.	.	.	.	.	.	.	.	.	.	C	10.91	1.485237	0.26598	.	.	ENSG00000168944	ENST00000306467;ENST00000328236;ENST00000306481;ENST00000508442	T;T;T;T	0.46063	0.88;0.88;0.88;0.88	5.82	4.84	0.62591	.	0.362557	0.31922	N	0.006848	T	0.09468	0.0233	N	0.00210	-1.845	0.80722	D	1	B	0.09022	0.002	B	0.04013	0.001	T	0.33189	-0.9878	10	0.11182	T	0.66	-14.0862	7.0171	0.24895	0.0:0.8097:0.0:0.1903	.	744	Q8N960	CE120_HUMAN	H	744;744;718;718	ENSP00000303058:R744H;ENSP00000327504:R744H;ENSP00000307419:R718H;ENSP00000421620:R718H	ENSP00000303058:R744H	R	-	2	0	CEP120	122741094	1.000000	0.71417	1.000000	0.80357	0.734000	0.41952	3.469000	0.53093	2.767000	0.95098	0.655000	0.94253	CGT	.	.	.	weak		0.398	CEP120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250899.2	NM_153223		T	122713195	C	T	122713195	3	4	39	1	0	0	0	0	1	0	0	0	3248	536	19	1	749	1	CEP120	5	122713195	Missense_Mutation	SNP	C	TCGA-5P-A9KE-01A-11D-A42J-10	11400775	122713195	58202065	32	2812											
NPM1	4869	hgsc.bcm.edu	37	chr5	170814986	170814986	+	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	tggacatggacatgagccccCtgaggccccagaactatctt	10	8	10	13	0	1	3	0	2	1	1	1	5	1	5	4	3	2	0	4	3	2	2			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr5:170814986C>A	ENST00000296930.5	+	1	335	c.34C>A	c.(34-36)Ctg>Atg	p.L12M	NPM1_ENST00000351986.6_Missense_Mutation_p.L12M|NPM1_ENST00000517671.1_Missense_Mutation_p.L12M|NPM1_ENST00000393820.2_Missense_Mutation_p.L12M|MIR3912_ENST00000577566.1_RNA	NM_002520.6	NP_002511.1	P06748	NPM_HUMAN	nucleophosmin (nucleolar phosphoprotein B23, numatrin)	12	Necessary for interaction with APEX1.|Required for interaction with SENP3.				cell aging (GO:0007569)|CENP-A containing nucleosome assembly (GO:0034080)|centrosome cycle (GO:0007098)|DNA repair (GO:0006281)|intracellular protein transport (GO:0006886)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of centrosome duplication (GO:0010826)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|nucleocytoplasmic transport (GO:0006913)|nucleosome assembly (GO:0006334)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of translation (GO:0045727)|protein localization (GO:0008104)|protein oligomerization (GO:0051259)|regulation of centriole replication (GO:0046599)|regulation of eIF2 alpha phosphorylation by dsRNA (GO:0060735)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of endoribonuclease activity (GO:0060699)|response to stress (GO:0006950)|ribosome assembly (GO:0042255)|signal transduction (GO:0007165)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle pole centrosome (GO:0031616)	histone binding (GO:0042393)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|unfolded protein binding (GO:0051082)		NPM1/ALK(632)	central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4261)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	4269	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CATGAGCCCCCTGAGGCCCCA	0.622			"T, F "	"ALK, RARA, MLF1"	"NHL, APL, AML"																																p.L12M		Atlas-SNP	.		Dom	yes		5	5q35	4869	"nucleophosmin (nucleolar phosphoprotein B23, numatrin)"		L	.	NPM1	5003	.	0			c.C34A						PASS	.						23	27	26					5																	170814986		2203	4296	6499	SO:0001583	missense	4869	exon1			AGCCCCCTGAGGC	M26697	CCDS4376.1, CCDS4377.1, CCDS43399.1	5q35.1	2014-09-17			ENSG00000181163	ENSG00000181163			7910	protein-coding gene	gene with protein product	"nucleolar phosphoprotein B23", "numatrin", "nucleophosmin/nucleoplasmin family, member 1"	164040				8471164, 8122112	Standard	NM_002520		Approved	B23, NPM	uc003mbi.3	P06748	OTTHUMG00000130465	ENST00000296930.5:c.34C>A	chr5.hg19:g.170814986C>A	ENSP00000296930:p.Leu12Met	84.0	0.0	.		89.0	25.0	.	NM_199185	A8K3N7|B5BU00|D3DQL6|P08693|Q12826|Q13440|Q13441|Q14115|Q5EU94|Q5EU95|Q5EU96|Q5EU97|Q5EU98|Q5EU99|Q6V962|Q8WTW5|Q96AT6|Q96DC4|Q96EA5|Q9BYG9|Q9UDJ7	Missense_Mutation	SNP	ENST00000296930.5	hg19	CCDS4376.1	.	.	.	.	.	.	.	.	.	.	c	17.74	3.464060	0.63513	.	.	ENSG00000181163	ENST00000517671;ENST00000296930;ENST00000351986;ENST00000393820;ENST00000523622	T;T;T;T	0.50001	0.76;0.76;0.76;0.76	4.27	2.47	0.30058	Nucleoplasmin core (2);	0.179442	0.34802	U	0.003663	T	0.55369	0.1916	L	0.56199	1.76	0.26244	N	0.978822	P;P;D	0.56746	0.619;0.94;0.977	B;P;D	0.64687	0.132;0.481;0.928	T	0.44221	-0.9342	10	0.31617	T	0.26	.	8.1166	0.30946	0.0:0.8033:0.0:0.1967	.	12;12;12	P06748-2;P06748;Q9BYG9	.;NPM_HUMAN;.	M	12	ENSP00000428755:L12M;ENSP00000296930:L12M;ENSP00000341168:L12M;ENSP00000377408:L12M	ENSP00000296930:L12M	L	+	1	2	NPM1	170747591	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.062000	0.30555	0.372000	0.24591	0.472000	0.43445	CTG	.	.	.	none		0.622	NPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252858.2	NM_002520		A	170814986	C	A	170814986	3	1	39	1	0	0	0	0	1	0	0	0	10594	680	24	4	36	4	NPM1	5	170814986	Missense_Mutation	SNP	C	TCGA-5P-A9KE-01A-11D-A42J-10	48101791	170814986	10100274	33	2813											
ABCF1	23	hgsc.bcm.edu	37	chr6	30558445	30558445	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgggaggtgttggaggccctGggtgaagtcatggtcagccg	6	8	19	8	2	2	1	2	1	0	0	2	3	2	3	2	6	1	1	2	6	1	1			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr6:30558445G>A	ENST00000326195.8	+	25	2617	c.2505G>A	c.(2503-2505)ctG>ctA	p.L835L	ABCF1_ENST00000396515.4_Silent_p.L228L|ABCF1_ENST00000376545.3_Silent_p.L797L	NM_001025091.1	NP_001020262.1	Q8NE71	ABCF1_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 1	835	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				inflammatory response (GO:0006954)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)|ribosome (GO:0005840)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|translation activator activity (GO:0008494)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|skin(2)	21						TGGAGGCCCTGGGTGAAGTCA	0.552																																					p.L835L		Atlas-SNP	.											.	ABCF1	61	.	0			c.G2505A						PASS	.						161	178	172					6																	30558445		1510	2708	4218	SO:0001819	synonymous_variant	23	exon25			GGCCCTGGGTGAA	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.2505G>A	chr6.hg19:g.30558445G>A		152.0	0.0	.		122.0	34.0	.	NM_001025091	A2BF75|O14897|Q69YP6	Silent	SNP	ENST00000326195.8	hg19	CCDS34380.1																																																																																			.	.	.	none		0.552	ABCF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076137.3			A	30558445	G	A	30558445	2	1	39	1	0	0	0	0	0	0	0	1	65	1335	47	2		2	ABCF1	6	30558445	Silent	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10		30558445	140556622	34	2814											
RPL10A	4736	hgsc.bcm.edu	37	chr6	35437954	35437954	+	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	aatggcttcctctctctatcAgccaagaagtatgatgcgtt	10	13	8	10	1	3	2	1	1	2	1	5	2	4	2	2	1	2	3	2	1	5	4			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr6:35437954A>G	ENST00000322203.6	+	5	337		c.e5-1		RPL10A_ENST00000467020.1_Splice_Site	NM_007104.4	NP_009035.3	P62906	RL10A_HUMAN	ribosomal protein L10a						anatomical structure morphogenesis (GO:0009653)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|large_intestine(2)|ovary(1)	4						TCTCTCTATCAGCCAAGAAGT	0.483																																					.		Atlas-SNP	.											.	RPL10A	13	.	0			c.311-2A>G						PASS	.						93	85	88					6																	35437954		2203	4300	6503	SO:0001630	splice_region_variant	4736	exon5			TCTATCAGCCAAG	U12404	CCDS4806.1	6p21.31	2011-04-06			ENSG00000198755	ENSG00000198755		"L ribosomal proteins"	10299	protein-coding gene	gene with protein product		615660		NEDD6		7609734, 9647638	Standard	NM_007104		Approved	Csa-19, L10A	uc003okp.1	P62906	OTTHUMG00000014566	ENST00000322203.6:c.311-1A>G	chr6.hg19:g.35437954A>G		33.0	0.0	.		41.0	14.0	.	NM_007104	B2R801|P52859|P53025|Q5TZT6|Q8J013	Splice_Site	SNP	ENST00000322203.6	hg19	CCDS4806.1	.	.	.	.	.	.	.	.	.	.	A	8.257	0.810319	0.16537	.	.	ENSG00000198755	ENST00000322203	.	.	.	3.94	3.94	0.45596	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.0737	0.48019	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RPL10A	35545932	1.000000	0.71417	0.929000	0.37066	0.230000	0.25150	5.893000	0.69798	1.788000	0.52465	0.460000	0.39030	.	.	.	.	none		0.483	RPL10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040283.1	NM_007104	Intron	G	35437954	A	G	35437954	5	3	39	1	0	0	0	0	0	0	1	0	13568	202	7	3	327	3	RPL10A	6	35437954	Splice_Site	SNP	A	TCGA-5P-A9KE-01A-11D-A42J-10	4879509	35437954	135677113	35	2815											
C6orf64	55776	hgsc.bcm.edu	37	chr6	39082699	39082699	+	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	cccgggcactcgcgggcctaGgtttccataccaggaaccgc	7	6	12	16	4	0	0	0	0	0	0	2	1	1	1	5	4	2	2	5	4	3	3			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr6:39082699G>C	ENST00000229903.4	-	1	266	c.167C>G	c.(166-168)cCt>cGt	p.P56R	SAYSD1_ENST00000481599.1_5'UTR	NM_018322.1	NP_060792.1	Q9NPB0	SMDC1_HUMAN	SAYSVFN motif domain containing 1	56						cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)											CGCGGGCCTAGGTTTCCATAC	0.657																																					p.P56R		Atlas-SNP	.											.	.	.	.	0			c.C167G						PASS	.						36	43	41					6																	39082699		2203	4300	6503	SO:0001583	missense	55776	exon1			GGCCTAGGTTTCC	BC022007	CCDS4840.1	6p21.1	2011-12-13	2011-12-13	2011-12-13	ENSG00000112167	ENSG00000112167			21025	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 64"	C6orf64			Standard	XM_005249222		Approved	FLJ11101	uc003ook.1	Q9NPB0	OTTHUMG00000014641	ENST00000229903.4:c.167C>G	chr6.hg19:g.39082699G>C	ENSP00000229903:p.Pro56Arg	59.0	0.0	.		49.0	13.0	.	NM_018322	Q9H0D8	Missense_Mutation	SNP	ENST00000229903.4	hg19	CCDS4840.1	.	.	.	.	.	.	.	.	.	.	G	12.92	2.082573	0.36758	.	.	ENSG00000112167	ENST00000229903	.	.	.	5.15	0.0579	0.14325	.	0.551296	0.18522	N	0.138727	T	0.20210	0.0486	M	0.66939	2.045	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.24297	-1.0164	9	0.51188	T	0.08	-11.0707	4.3846	0.11311	0.3584:0.1591:0.4825:0.0	.	56	Q9NPB0	CF064_HUMAN	R	56	.	ENSP00000229903:P56R	P	-	2	0	C6orf64	39190677	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.087000	0.14958	0.144000	0.18951	-0.140000	0.14226	CCT	.	.	.	none		0.657	SAYSD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040448.1	NM_018322		C	39082699	G	C	39082699	3	2	39	1	0	0	0	0	1	0	0	0	2371	1000	35	4	392	4	C6orf64	6	39082699	Missense_Mutation	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10	3644745	39082699	132032368	36	2816											
SLC29A1	2030	hgsc.bcm.edu	37	chr6	44201182	44201182	+	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	agccagctgaggcagagaccGcaggagccatcatggccttc	10	5	13	13	1	1	2	1	1	0	1	2	4	1	3	4	3	3	3	4	3	0	1	rs74750454		TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr6:44201182G>C	ENST00000393841.1	+	14	1779	c.1288G>C	c.(1288-1290)Gca>Cca	p.A430P	SLC29A1_ENST00000371724.1_Missense_Mutation_p.A430P|SLC29A1_ENST00000371708.1_Missense_Mutation_p.A430P|SLC29A1_ENST00000371713.1_Missense_Mutation_p.A430P|SLC29A1_ENST00000393844.1_Missense_Mutation_p.A430P|SLC29A1_ENST00000371740.5_Missense_Mutation_p.A430P|SLC29A1_ENST00000371755.3_Missense_Mutation_p.A430P|SLC29A1_ENST00000427851.2_Missense_Mutation_p.A430P|SLC29A1_ENST00000313248.7_Missense_Mutation_p.A509P|SLC29A1_ENST00000371731.1_Missense_Mutation_p.A430P	NM_001078177.1	NP_001071645.1	Q99808	S29A1_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 1	430					cellular response to glucose stimulus (GO:0071333)|cellular response to hypoxia (GO:0071456)|lactation (GO:0007595)|nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|sleep (GO:0030431)|transmembrane transport (GO:0055085)|uridine transport (GO:0015862)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside transmembrane transporter activity (GO:0005337)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(2)	17	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)		Cytarabine(DB00987)|Didanosine(DB00900)|Fludarabine(DB01073)|Fluorouracil(DB00544)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Pemetrexed(DB00642)|Ribavirin(DB00811)|Zalcitabine(DB00943)	GGCAGAGACCGCAGGAGCCAT	0.577																																					p.A430P		Atlas-SNP	.											.	SLC29A1	45	.	0			c.G1288C						PASS	.						161	151	155					6																	44201182		2203	4300	6503	SO:0001583	missense	2030	exon13			GAGACCGCAGGAG	U81375	CCDS4908.1	6p21.1	2013-07-17	2013-07-17		ENSG00000112759	ENSG00000112759		"Solute carriers"	11003	protein-coding gene	gene with protein product		602193	"solute carrier family 29 (nucleoside transporters), member 1"	ENT1		8986748, 9344680	Standard	NM_004955		Approved		uc003owy.2	Q99808	OTTHUMG00000014759	ENST00000393841.1:c.1288G>C	chr6.hg19:g.44201182G>C	ENSP00000377424:p.Ala430Pro	56.0	0.0	.		60.0	10.0	.	NM_004955	B3KQV7|B3KQY5|Q5T9W9|Q9UJY2	Missense_Mutation	SNP	ENST00000393841.1	hg19	CCDS4908.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.729616	0.89390	.	.	ENSG00000112759	ENST00000393844;ENST00000313248;ENST00000427851;ENST00000371755;ENST00000371740;ENST00000371731;ENST00000393841;ENST00000371724;ENST00000371713;ENST00000371708	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	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	D	0.92701	0.7680	H	0.95679	3.705	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94086	0.7348	10	0.87932	D	0	-13.2332	19.2711	0.94010	0.0:0.0:1.0:0.0	.	509;430	B3KQV7;Q99808	.;S29A1_HUMAN	P	430;509;430;430;430;430;430;430;430;430	ENSP00000377427:A430P;ENSP00000319152:A509P;ENSP00000392668:A430P;ENSP00000360820:A430P;ENSP00000360805:A430P;ENSP00000360796:A430P;ENSP00000377424:A430P;ENSP00000360789:A430P;ENSP00000360778:A430P;ENSP00000360773:A430P	ENSP00000319152:A509P	A	+	1	0	SLC29A1	44309160	1.000000	0.71417	0.076000	0.20297	0.725000	0.41563	8.890000	0.92477	2.789000	0.95967	0.655000	0.94253	GCA	.	G|0.999;A|0.001	.	alt		0.577	SLC29A1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040721.1			C	44201182	G	C	44201182	3	2	39	1	0	0	0	0	1	0	0	0	14547	1087	38	4	1334	4	SLC29A1	6	44201182	Missense_Mutation	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10	5118483	44201182	126913885	37	2817											
GPRC6A	222545	hgsc.bcm.edu	37	chr6	117121778	117121778	+	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	tgaactcattttttgtttccTgatctgggatgatgaagaca	10	16	9	6	0	2	5	1	4	1	1	3	6	3	6	1	1	1	1	1	1	2	4			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr6:117121778T>A	ENST00000310357.3	-	4	1538	c.1517A>T	c.(1516-1518)cAg>cTg	p.Q506L	GPRC6A_ENST00000530250.1_Missense_Mutation_p.Q331L|GPRC6A_ENST00000368549.3_Intron	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	506					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)		TTTTGTTTCCTGATCTGGGAT	0.423																																					p.Q506L		Atlas-SNP	.											.	GPRC6A	152	.	0			c.A1517T						PASS	.						191	166	175					6																	117121778		2203	4300	6503	SO:0001583	missense	222545	exon4			GTTTCCTGATCTG	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.1517A>T	chr6.hg19:g.117121778T>A	ENSP00000309493:p.Gln506Leu	111.0	0.0	.		83.0	12.0	.	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Missense_Mutation	SNP	ENST00000310357.3	hg19	CCDS5112.1	.	.	.	.	.	.	.	.	.	.	T	7.166	0.586705	0.13749	.	.	ENSG00000173612	ENST00000310357;ENST00000530250	D;D	0.90955	-2.52;-2.76	5.13	3.93	0.45458	.	0.408254	0.20735	N	0.086659	T	0.66356	0.2781	N	0.08118	0	0.25789	N	0.984637	B;B	0.21309	0.014;0.054	B;B	0.17433	0.018;0.008	T	0.59220	-0.7495	10	0.52906	T	0.07	.	7.3059	0.26447	0.0:0.0751:0.1437:0.7812	.	331;506	Q5T6X5-2;Q5T6X5	.;GPC6A_HUMAN	L	506;331	ENSP00000309493:Q506L;ENSP00000433465:Q331L	ENSP00000309493:Q506L	Q	-	2	0	GPRC6A	117228471	0.988000	0.35896	0.966000	0.40874	0.067000	0.16453	3.221000	0.51215	2.159000	0.67721	0.477000	0.44152	CAG	.	.	.	none		0.423	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2			A	117121778	T	A	117121778	3	1	39	1	0	0	0	0	1	0	0	0	6735	1580	55	5	1275	5	GPRC6A	6	117121778	Missense_Mutation	SNP	T	TCGA-5P-A9KE-01A-11D-A42J-10	72920596	117121778	53993289	38	2818											
DNAJC30	84277	hgsc.bcm.edu	37	chr7	73097483	73097483	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcctgggagatgcgcgtgaAgcgctcggcggcctccgcgc	4	5	18	14	7	0	2	0	1	0	1	2	3	1	2	3	4	2	1	3	4	1	0			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr7:73097483A>G	ENST00000395176.2	-	1	300	c.271T>C	c.(271-273)Ttc>Ctc	p.F91L	WBSCR22_ENST00000423497.1_5'Flank|WBSCR22_ENST00000423166.2_5'Flank|WBSCR22_ENST00000265758.2_5'Flank|WBSCR22_ENST00000464615.1_3'UTR	NM_032317.2	NP_115693.2	Q96LL9	DJC30_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 30	91	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.					mitochondrion (GO:0005739)				kidney(1)|large_intestine(2)|lung(1)	4						ATGCGCGTGAAGCGCTCGGCG	0.667																																					p.F91L		Atlas-SNP	.											.	DNAJC30	12	.	0			c.T271C						PASS	.						51	60	57					7																	73097483		2201	4297	6498	SO:0001583	missense	84277	exon1			GCGTGAAGCGCTC	AF412025	CCDS5556.1	7q11.23	2011-09-02	2008-06-17	2008-06-17	ENSG00000176410	ENSG00000176410		"Heat shock proteins / DNAJ (HSP40)"	16410	protein-coding gene	gene with protein product			"Williams Beuren syndrome chromosome region 18"	WBSCR18		12073013	Standard	NM_032317		Approved		uc003tys.1	Q96LL9	OTTHUMG00000023290	ENST00000395176.2:c.271T>C	chr7.hg19:g.73097483A>G	ENSP00000378605:p.Phe91Leu	64.0	0.0	.		98.0	17.0	.	NM_032317	Q9BSG8	Missense_Mutation	SNP	ENST00000395176.2	hg19	CCDS5556.1	.	.	.	.	.	.	.	.	.	.	A	36	5.928610	0.97116	.	.	ENSG00000176410	ENST00000395176;ENST00000539255	T	0.46063	0.88	5.15	5.15	0.70609	Heat shock protein DnaJ, N-terminal (5);	0.000000	0.85682	D	0.000000	T	0.62744	0.2453	M	0.72118	2.19	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.66732	-0.5849	10	0.87932	D	0	-8.5361	12.9762	0.58538	1.0:0.0:0.0:0.0	.	91	Q96LL9	DJC30_HUMAN	L	91;88	ENSP00000378605:F91L	ENSP00000378605:F91L	F	-	1	0	DNAJC30	72735419	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.811000	0.86092	2.160000	0.67779	0.528000	0.53228	TTC	.	.	.	none		0.667	DNAJC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252304.2			G	73097483	A	G	73097483	3	3	39	1	0	0	0	0	1	0	0	0	4650	72	3	3	413	3	DNAJC30	7	73097483	Missense_Mutation	SNP	A	TCGA-5P-A9KE-01A-11D-A42J-10		73097483	86041180	39	2819											
COPS6	10980	hgsc.bcm.edu	37	chr7	99686979	99686979	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgctctccatccccttgtcaTtctcaacatctcagaccact	8	12	3	18	1	4	1	3	0	3	1	8	1	5	1	4	0	1	1	4	0	1	2			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr7:99686979T>C	ENST00000303904.3	+	2	180	c.143T>C	c.(142-144)aTt>aCt	p.I48T	COPS6_ENST00000418625.1_Missense_Mutation_p.I47T	NM_006833.4	NP_006824.2	Q7L5N1	CSN6_HUMAN	COP9 signalosome subunit 6	48	MPN.				cullin deneddylation (GO:0010388)|viral process (GO:0016032)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|stomach(1)	12	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			CCCCTTGTCATTCTCAACATC	0.587																																					p.I48T		Atlas-SNP	.											.	COPS6	31	.	0			c.T143C						PASS	.						150	139	143					7																	99686979		2203	4300	6503	SO:0001583	missense	10980	exon2			TTGTCATTCTCAA	BC002520	CCDS5682.1	7q22.1	2013-03-14	2013-03-14		ENSG00000168090	ENSG00000168090			21749	protein-coding gene	gene with protein product	"COP9 subunit 6 (MOV34 homolog, 34 kD)"	614729	"COP9 constitutive photomorphogenic homolog subunit 6 (Arabidopsis)"			12477932	Standard	NM_006833		Approved	MOV34-34KD, CSN6	uc003usu.3	Q7L5N1	OTTHUMG00000154632	ENST00000303904.3:c.143T>C	chr7.hg19:g.99686979T>C	ENSP00000304102:p.Ile48Thr	49.0	0.0	.		60.0	13.0	.	NM_006833	A4D2A3|O15387	Missense_Mutation	SNP	ENST00000303904.3	hg19	CCDS5682.1	.	.	.	.	.	.	.	.	.	.	T	31	5.072932	0.93950	.	.	ENSG00000168090	ENST00000303904;ENST00000419210;ENST00000418625	T;T	0.55413	0.52;0.52	5.65	4.5	0.54988	.	0.060020	0.64402	N	0.000004	T	0.74574	0.3734	M	0.90542	3.125	0.80722	D	1	D;D	0.89917	1.0;0.992	D;D	0.79784	0.993;0.961	T	0.78048	-0.2356	10	0.87932	D	0	-12.4631	9.559	0.39357	0.0:0.0815:0.0:0.9185	.	48;48	B4DHR8;Q7L5N1	.;CSN6_HUMAN	T	48;18;47	ENSP00000304102:I48T;ENSP00000400617:I47T	ENSP00000304102:I48T	I	+	2	0	COPS6	99524915	1.000000	0.71417	0.992000	0.48379	0.987000	0.75469	7.150000	0.77403	1.160000	0.42584	0.533000	0.62120	ATT	.	.	.	none		0.587	COPS6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336412.3	NM_006833		C	99686979	T	C	99686979	3	2	39	1	0	0	0	0	1	0	0	0	3739	1493	52	3	149	3	COPS6	7	99686979	Missense_Mutation	SNP	T	TCGA-5P-A9KE-01A-11D-A42J-10	26589496	99686979	59451684	40	2820											
DUS4L	11062	hgsc.bcm.edu	37	chr7	107217029	107217029	+	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	aaatgtgtggcggattactgGgacagatggtaagaaataag	15	9	14	3	1	0	2	0	0	0	2	0	4	0	4	0	4	1	1	0	4	5	3			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr7:107217029G>T	ENST00000265720.3	+	7	1060	c.698G>T	c.(697-699)gGg>gTg	p.G233V	RP4-593H12.1_ENST00000610269.1_RNA|DUS4L_ENST00000402620.1_Missense_Mutation_p.G112V	NM_001270419.1|NM_181581.2	NP_001257348.1|NP_853559.1	O95620	DUS4L_HUMAN	dihydrouridine synthase 4-like (S. cerevisiae)	233							flavin adenine dinucleotide binding (GO:0050660)|tRNA dihydrouridine synthase activity (GO:0017150)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	8						CGGATTACTGGGACAGATGGT	0.343																																					p.G233V		Atlas-SNP	.											.	DUS4L	27	.	0			c.G698T						PASS	.						48	49	49					7																	107217029		2203	4300	6503	SO:0001583	missense	11062	exon7			TTACTGGGACAGA	U62767	CCDS5745.1	7q22-q31	2007-12-04			ENSG00000105865	ENSG00000105865			21517	protein-coding gene	gene with protein product	"protein similar to E.coli yhdg and R. capsulatus nifR3"						Standard	NM_181581		Approved	PP35, DUS4	uc031syv.1	O95620	OTTHUMG00000154763	ENST00000265720.3:c.698G>T	chr7.hg19:g.107217029G>T	ENSP00000265720:p.Gly233Val	117.0	0.0	.		127.0	20.0	.	NM_001270419	B4DLX0|Q2NKK1	Missense_Mutation	SNP	ENST00000265720.3	hg19	CCDS5745.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.383852	0.82792	.	.	ENSG00000105865	ENST00000265720;ENST00000402620	T;T	0.57752	0.38;0.38	6.01	6.01	0.97437	Aldolase-type TIM barrel (1);	0.000000	0.85682	D	0.000000	D	0.82323	0.5012	H	0.98048	4.135	0.80722	D	1	D;D	0.54397	0.966;0.966	D;D	0.66979	0.948;0.948	D	0.87908	0.2695	10	0.87932	D	0	.	15.5789	0.76418	0.0672:0.0:0.9328:0.0	.	233;233	A4D0R5;O95620	.;DUS4L_HUMAN	V	233;112	ENSP00000265720:G233V;ENSP00000385274:G112V	ENSP00000265720:G233V	G	+	2	0	DUS4L	107004265	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.156000	0.64905	2.861000	0.98227	0.650000	0.86243	GGG	.	.	.	none		0.343	DUS4L-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336967.2	NM_181581		T	107217029	G	T	107217029	3	4	39	1	0	0	0	0	1	0	0	0	4810	1232	43	4	716	4	DUS4L	7	107217029	Missense_Mutation	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10	7530050	107217029	51921634	41	2821											
C8orf86	389649	hgsc.bcm.edu	37	chr8	38369906	38369906	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgttctcggccagtggttctTaaacttcagcacacaccaga	10	11	8	12	1	3	1	1	0	2	1	4	1	3	1	2	2	2	3	2	2	2	4			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr8:38369906T>C	ENST00000358138.1	-	3	695	c.671A>G	c.(670-672)tAa>tGa	p.*224*	C8orf86_ENST00000437935.2_3'UTR	NM_207412.1	NP_997295.1	Q6ZUL3	CH086_HUMAN	chromosome 8 open reading frame 86	0										breast(1)|endometrium(1)|large_intestine(1)|lung(1)|prostate(1)	5						cagtggttcttaaacttcagc	0.547																																					p.X224X		Atlas-SNP	.											.	C8orf86	17	.	0			c.A671G						PASS	.						34	35	35					8																	38369906		2203	4300	6503	SO:0001819	synonymous_variant	389649	exon3			GGTTCTTAAACTT	BC137511	CCDS6108.1	8p12-p11.23	2009-03-03			ENSG00000196166	ENSG00000196166			33774	protein-coding gene	gene with protein product							Standard	NM_207412		Approved	FLJ43582	uc003xlx.1	Q6ZUL3	OTTHUMG00000163992	ENST00000358138.1:c.671A>G	chr8.hg19:g.38369906T>C		99.0	0.0	.		94.0	28.0	.	NM_207412	A4QPB7	Silent	SNP	ENST00000358138.1	hg19	CCDS6108.1																																																																																			.	.	.	none		0.547	C8orf86-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376668.1	NM_207412		C	38369906	T	C	38369906	2	2	39	1	0	0	0	0	0	0	0	1	2444	1761	61	3		3	C8orf86	8	38369906	Silent	SNP	T	TCGA-5P-A9KE-01A-11D-A42J-10		38369906	107994116	42	2822											
CYHR1	50626	hgsc.bcm.edu	37	chr8	145689559	145689559	+	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	gggcccggcagtaagcccagCtgcctacagccaaggcccag	9	3	13	16	1	0	0	0	0	0	0	0	0	0	0	5	3	5	3	5	3	3	2			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr8:145689559C>T	ENST00000438911.2	-	2	380				KIFC2_ENST00000301332.2_5'Flank|CYHR1_ENST00000403000.2_Missense_Mutation_p.S177N|CYHR1_ENST00000424149.2_Missense_Mutation_p.S177N|CYHR1_ENST00000530374.1_5'Flank|CTD-2517M22.16_ENST00000525461.1_RNA|CYHR1_ENST00000306145.5_Missense_Mutation_p.S177N	NM_138496.1	NP_612505.1	Q6ZMK1	CYHR1_HUMAN	cysteine/histidine-rich 1							cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)	zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|lung(3)|ovary(2)	7	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)			GTAAGCCCAGCTGCCTACAGC	0.642											OREG0019056	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S177N		Atlas-SNP	.											.	CYHR1	39	.	0			c.G530A						PASS	.						51	56	55					8																	145689559		2203	4300	6503	SO:0001627	intron_variant	50626	exon3			GCCCAGCTGCCTA	AB007965	CCDS6426.1, CCDS47943.1	8q24	2004-12-07	2005-07-24		ENSG00000187954	ENSG00000187954			17806	protein-coding gene	gene with protein product			"cysteine and histidine rich 1"			10745073	Standard	NM_138496		Approved	CHRP, KIAA0496, MGC13010	uc003zcv.2	Q6ZMK1	OTTHUMG00000165171	ENST00000438911.2:c.246+283G>A	chr8.hg19:g.145689559C>T		78.0	0.0	.	1696	76.0	24.0	.	NM_032687	B3KSX0|D3DWM3|Q9BSF6|Q9BSU6	Missense_Mutation	SNP	ENST00000438911.2	hg19	CCDS47943.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.158532	0.78114	.	.	ENSG00000187954	ENST00000403000;ENST00000424149;ENST00000306145	T;T;T	0.55052	0.54;0.54;0.54	4.79	3.91	0.45181	.	0.155120	0.40469	N	0.001087	T	0.37892	0.1020	.	.	.	0.20196	N	0.999922	B	0.09022	0.002	B	0.12837	0.008	T	0.22243	-1.0222	9	0.35671	T	0.21	.	8.9929	0.36035	0.0:0.8958:0.0:0.1042	.	177	Q6ZMK1-3	.	N	177	ENSP00000385962:S177N;ENSP00000414647:S177N;ENSP00000304826:S177N	ENSP00000304826:S177N	S	-	2	0	CYHR1	145660367	0.978000	0.34361	0.981000	0.43875	0.946000	0.59487	0.811000	0.27198	1.014000	0.39417	0.462000	0.41574	AGC	.	.	.	none		0.642	CYHR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000382438.1	NM_032687		T	145689559	C	T	145689559	1	4	39	0	1	0	0	0	0	0	0	0	4142	797	28	2		2	CYHR1	8	145689559	Intron	SNP	C	TCGA-5P-A9KE-01A-11D-A42J-10	107319653	145689559	674463	43	2823											
TSC1	7248	hgsc.bcm.edu	37	chr9	135781381	135781381	+	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	ggctcagggttcacgctggcGccctgagaactggaggctgc	6	7	16	12	2	2	1	2	1	0	1	2	3	2	2	1	5	2	4	1	5	1	1	rs149439187		TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr9:135781381G>A	ENST00000298552.3	-	15	1805	c.1584C>T	c.(1582-1584)ggC>ggT	p.G528G	TSC1_ENST00000440111.2_Silent_p.G528G|TSC1_ENST00000545250.1_Silent_p.G477G	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	528					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.A529S(1)|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)		TCACGCTGGCGCCCTGAGAAC	0.592			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.G528G		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"E, O"	.	TSC1	167	.	2	Substitution - Missense(1)|Unknown(1)	lung(1)|bone(1)	c.C1584T						PASS	.	G	,,	0,4406		0,0,2203	62	61	61		1584,1581,1431	-3.3	0	9	dbSNP_134	61	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	TSC1	NM_000368.4,NM_001162426.1,NM_001162427.1	,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,	528/1165,527/1164,477/1114	135781381	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	7248	exon15	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	GCTGGCGCCCTGA	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.1584C>T	chr9.hg19:g.135781381G>A		117.0	0.0	.		118.0	30.0	.	NM_000368	B7Z897|Q5VVN5	Silent	SNP	ENST00000298552.3	hg19	CCDS6956.1																																																																																			.	G|1.000;A|0.000	0.000	weak		0.592	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1			A	135781381	G	A	135781381	2	1	39	1	0	0	0	0	0	0	0	1	16617	1074	38	1		1	TSC1	9	135781381	Silent	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10		135781381	5432050	44	2824											
SVIL	6840	hgsc.bcm.edu	37	chr10	29821690	29821690	+	Frame_Shift_Del	DEL	C	C	-																															cttgcgctttttcgaggcttCcctgttgtgaccagttggtt																										TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr10:29821690delC	ENST00000355867.4	-	8	2358	c.1606delG	c.(1606-1608)gaafs	p.E536fs	SVIL_ENST00000375400.3_Intron|SVIL_ENST00000375398.2_Frame_Shift_Del_p.E536fs	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	536					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)				TTCGAGGCTTCCCTGTTGTGA	0.567																																					p.E536fs		Atlas-Indel,Pindel	.											.	SVIL	226	.	0			c.1607delA						PASS	.						213	205	208					10																	29821690		2203	4300	6503	SO:0001589	frameshift_variant	6840	exon8			.	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"archvillin"	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.1606delG	chr10.hg19:g.29821690delC	ENSP00000348128:p.Glu536fs	85.0	0.0	0		71.0	21.0	0.295775	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Frame_Shift_Del	DEL	ENST00000355867.4	hg19	CCDS7164.1																																																																																			.	.	.	none		0.567	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			-	29821690	C	-	29821690	7	5	39	1	0	1	0	1	0	0	0	0	15433	864	30	0	5162	0	SVIL	10	29821690	Frame_Shift_Del	DEL	C	TCGA-5P-A9KE-01A-11D-A42J-10		29821690	105713057	45	2825											
STOX1	219736	hgsc.bcm.edu	37	chr10	70644560	70644560	+	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	cacagcagtttctctgctcaGttcccacctgaagaatggcc	9	10	8	14	0	2	2	1	1	1	1	4	2	3	2	3	1	2	4	3	1	2	2			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr10:70644560G>T	ENST00000298596.6	+	3	1091	c.1008G>T	c.(1006-1008)caG>caT	p.Q336H	STOX1_ENST00000399169.4_Missense_Mutation_p.Q336H|STOX1_ENST00000399162.2_Intron|STOX1_ENST00000399165.4_Intron|STOX1_ENST00000421961.2_Missense_Mutation_p.Q226H	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	336						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						TCTCTGCTCAGTTCCCACCTG	0.423																																					p.Q336H		Atlas-SNP	.											.	STOX1	75	.	0			c.G1008T						PASS	.						103	101	102					10																	70644560		1904	4122	6026	SO:0001583	missense	219736	exon3			TGCTCAGTTCCCA	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.1008G>T	chr10.hg19:g.70644560G>T	ENSP00000298596:p.Gln336His	160.0	0.0	.		93.0	30.0	.	NM_152709	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Missense_Mutation	SNP	ENST00000298596.6	hg19	CCDS41535.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.971544	0.74246	.	.	ENSG00000165730	ENST00000399169;ENST00000298596;ENST00000421961	D;D;D	0.92911	-3.13;-3.13;-2.64	6.08	6.08	0.98989	.	0.000000	0.64402	U	0.000001	D	0.96034	0.8708	M	0.82323	2.585	0.51012	D	0.999903	D	0.89917	1.0	D	0.87578	0.998	D	0.95942	0.8947	10	0.87932	D	0	.	13.8168	0.63297	0.0695:0.0:0.9305:0.0	.	336	Q6ZVD7	STOX1_HUMAN	H	336;336;226	ENSP00000382121:Q336H;ENSP00000298596:Q336H;ENSP00000394509:Q226H	ENSP00000298596:Q336H	Q	+	3	2	STOX1	70314566	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.634000	0.67833	2.894000	0.99253	0.591000	0.81541	CAG	.	.	.	none		0.423	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709		T	70644560	G	T	70644560	3	4	39	1	0	0	0	0	1	0	0	0	15331	1020	36	4	1018	4	STOX1	10	70644560	Missense_Mutation	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10	40822870	70644560	64890187	46	2826											
BMPR1A	657	hgsc.bcm.edu	37	chr10	88678972	88678972	+	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	ggtacaggttcctggactcaGctctatttgattactgatta	9	15	9	8	0	2	2	1	2	1	0	3	3	3	3	1	3	3	3	1	3	4	6			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr10:88678972G>C	ENST00000372037.3	+	10	1449	c.912G>C	c.(910-912)caG>caC	p.Q304H		NM_004329.2	NP_004320.2	P36894	BMR1A_HUMAN	bone morphogenetic protein receptor, type IA	304	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|developmental growth (GO:0048589)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic digit morphogenesis (GO:0042733)|embryonic organ development (GO:0048568)|endocardial cushion formation (GO:0003272)|heart formation (GO:0060914)|hindlimb morphogenesis (GO:0035137)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lateral mesoderm development (GO:0048368)|lung development (GO:0030324)|mesendoderm development (GO:0048382)|mesoderm formation (GO:0001707)|Mullerian duct regression (GO:0001880)|negative regulation of neurogenesis (GO:0050768)|neural crest cell development (GO:0014032)|neural plate mediolateral regionalization (GO:0021998)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|paraxial mesoderm structural organization (GO:0048352)|pituitary gland development (GO:0021983)|positive regulation of bone mineralization (GO:0030501)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of lateral mesodermal cell fate specification (GO:0048378)|somitogenesis (GO:0001756)|stem cell maintenance (GO:0019827)|transforming growth factor beta receptor signaling pathway (GO:0007179)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|skin(1)|stomach(1)	24						CCTGGACTCAGCTCTATTTGA	0.418			"Mis, N, F"			gastrointestinal polyps			Juvenile Polyposis;Hereditary Mixed Polyposis syndrome type 2																												p.Q304H	Ovarian(190;603 2086 22044 30335 47971)	Atlas-SNP	.	yes	Rec		Juvenile polyposis	10	10q22.3	657	"bone morphogenetic protein receptor, type IA"		E	.	BMPR1A	118	.	0			c.G912C						PASS	.						106	106	106					10																	88678972		2203	4300	6503	SO:0001583	missense	657	exon10	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HMPS2	GACTCAGCTCTAT	BC028383	CCDS7378.1	10q22.3	2014-09-17			ENSG00000107779	ENSG00000107779		"CD molecules"	1076	protein-coding gene	gene with protein product		601299		ACVRLK3		8397373, 9730621	Standard	NM_004329		Approved	ALK3, CD292	uc001kdy.3	P36894	OTTHUMG00000018657	ENST00000372037.3:c.912G>C	chr10.hg19:g.88678972G>C	ENSP00000361107:p.Gln304His	112.0	0.0	.		86.0	20.0	.	NM_004329	A8K6U9|Q8NEN8	Missense_Mutation	SNP	ENST00000372037.3	hg19	CCDS7378.1	.	.	.	.	.	.	.	.	.	.	G	17.56	3.419851	0.62622	.	.	ENSG00000107779	ENST00000224764;ENST00000372037	T	0.64438	-0.1	4.95	0.902	0.19290	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	0.46112	0.1376	L	0.39326	1.205	0.58432	D	0.999999	P	0.36110	0.537	B	0.34824	0.19	T	0.29822	-0.9999	10	0.72032	D	0.01	.	5.0205	0.14358	0.357:0.0:0.5133:0.1296	.	304	P36894	BMR1A_HUMAN	H	304	ENSP00000361107:Q304H	ENSP00000224764:Q304H	Q	+	3	2	BMPR1A	88668952	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	1.412000	0.34714	-0.028000	0.13850	0.467000	0.42956	CAG	.	.	.	none		0.418	BMPR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049170.3	NM_004329		C	88678972	G	C	88678972	3	2	39	1	0	0	0	0	1	0	0	0	1469	962	34	4	942	4	BMPR1A	10	88678972	Missense_Mutation	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10	18034412	88678972	46855775	47	2827											
MICAL2	9645	hgsc.bcm.edu	37	chr11	12263967	12263967	+	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	cggctgcagcaagtggaggaAaagattctccaggtgagaga	13	6	15	7	1	1	3	0	1	1	2	2	6	1	5	1	4	2	3	1	4	3	1			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr11:12263967A>T	ENST00000256194.4	+	19	2832	c.2544A>T	c.(2542-2544)gaA>gaT	p.E848D	MICAL2_ENST00000527546.1_Intron|MICAL2_ENST00000342902.5_Missense_Mutation_p.E848D|MICAL2_ENST00000537344.1_Intron|MICAL2_ENST00000379612.3_Intron	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	848					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)		AAGTGGAGGAAAAGATTCTCC	0.597																																					p.E848D		Atlas-SNP	.											.	MICAL2	114	.	0			c.A2544T						PASS	.						35	29	31					11																	12263967		2201	4294	6495	SO:0001583	missense	9645	exon19			GGAGGAAAAGATT	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.2544A>T	chr11.hg19:g.12263967A>T	ENSP00000256194:p.Glu848Asp	71.0	0.0	.		63.0	18.0	.	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Missense_Mutation	SNP	ENST00000256194.4	hg19	CCDS7809.1	.	.	.	.	.	.	.	.	.	.	A	14.40	2.525074	0.44969	.	.	ENSG00000133816	ENST00000256194;ENST00000342902	T;T	0.63580	-0.04;-0.05	5.79	-2.48	0.06423	.	0.173691	0.33753	N	0.004600	T	0.35913	0.0948	N	0.17082	0.46	0.80722	D	1	B;B	0.12013	0.005;0.001	B;B	0.11329	0.006;0.001	T	0.05354	-1.0890	10	0.16420	T	0.52	.	8.1203	0.30967	0.5788:0.1194:0.3018:0.0	.	848;848	G3XAC8;O94851	.;MICA2_HUMAN	D	848	ENSP00000256194:E848D;ENSP00000344894:E848D	ENSP00000256194:E848D	E	+	3	2	MICAL2	12220543	0.976000	0.34144	0.964000	0.40570	0.988000	0.76386	0.136000	0.15974	-0.336000	0.08438	0.460000	0.39030	GAA	.	.	.	none		0.597	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632		T	12263967	A	T	12263967	3	4	39	1	0	0	0	0	1	0	0	0	9577	11	1	5	2610	5	MICAL2	11	12263967	Missense_Mutation	SNP	A	TCGA-5P-A9KE-01A-11D-A42J-10		12263967	122742549	48	2828											
PIK3C2A	5286	hgsc.bcm.edu	37	chr11	17124355	17124355	+	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	gctacacagcatccagcacaGgaatagataaagttctctga	15	8	8	10	0	1	2	0	1	1	1	3	3	2	3	1	1	3	4	1	1	5	4			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr11:17124355G>T	ENST00000265970.7	-	23	3704	c.3705C>A	c.(3703-3705)tcC>tcA	p.S1235S	PIK3C2A_ENST00000531428.1_Intron|PIK3C2A_ENST00000540361.1_Silent_p.S855S	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	1235	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				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						ATCCAGCACAGGAATAGATAA	0.333																																					p.S1235S		Atlas-SNP	.											.	PIK3C2A	148	.	0			c.C3705A						PASS	.						67	60	63					11																	17124355		2200	4293	6493	SO:0001819	synonymous_variant	5286	exon23			AGCACAGGAATAG	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.3705C>A	chr11.hg19:g.17124355G>T		57.0	0.0	.		54.0	4.0	.	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Silent	SNP	ENST00000265970.7	hg19	CCDS7824.1																																																																																			.	.	.	none		0.333	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		T	17124355	G	T	17124355	2	4	39	1	0	0	0	0	0	0	0	1	11916	987	35	4		4	PIK3C2A	11	17124355	Silent	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10	4860388	17124355	117882161	49	2829											
PHLDB1	23187	hgsc.bcm.edu	37	chr11	118498570	118498570	+	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	tactgtcttggcggaggcccGgagagccactgagagccccc	7	6	14	14	2	1	2	0	1	1	2	1	5	1	3	4	4	3	0	4	4	1	2			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr11:118498570G>C	ENST00000361417.2	+	7	1442	c.1031G>C	c.(1030-1032)cGg>cCg	p.R344P	PHLDB1_ENST00000356063.5_Missense_Mutation_p.R344P	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	344										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)		GCGGAGGCCCGGAGAGCCACT	0.667																																					p.R344P		Atlas-SNP	.											.	PHLDB1	103	.	0			c.G1031C						PASS	.						20	23	22					11																	118498570		2199	4288	6487	SO:0001583	missense	23187	exon6			AGGCCCGGAGAGC		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.1031G>C	chr11.hg19:g.118498570G>C	ENSP00000354498:p.Arg344Pro	30.0	0.0	.		33.0	8.0	.	NM_001144758	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Missense_Mutation	SNP	ENST00000361417.2	hg19	CCDS8401.1	.	.	.	.	.	.	.	.	.	.	G	14.76	2.631475	0.46944	.	.	ENSG00000019144	ENST00000361417;ENST00000361465;ENST00000543207;ENST00000356063	T;T	0.32515	1.46;1.45	5.13	4.22	0.49857	.	0.644418	0.16313	N	0.219911	T	0.40645	0.1125	L	0.36672	1.1	0.80722	D	1	B;B;P;D	0.67145	0.254;0.009;0.943;0.996	B;B;P;D	0.72982	0.113;0.011;0.681;0.979	T	0.16247	-1.0409	10	0.48119	T	0.1	-8.6545	7.1746	0.25736	0.0904:0.1718:0.7379:0.0	.	343;344;344;344	B4DIX4;Q86UU1-3;Q86UU1-2;Q86UU1	.;.;.;PHLB1_HUMAN	P	344;103;343;344	ENSP00000354498:R344P;ENSP00000348359:R344P	ENSP00000348359:R344P	R	+	2	0	PHLDB1	118003780	0.698000	0.27777	1.000000	0.80357	0.994000	0.84299	1.948000	0.40303	1.392000	0.46585	0.563000	0.77884	CGG	.	.	.	none		0.667	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157		C	118498570	G	C	118498570	3	2	39	1	0	0	0	0	1	0	0	0	11858	1116	39	4	1049	4	PHLDB1	11	118498570	Missense_Mutation	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10	101374215	118498570	16507946	50	2830											
AEBP2	121536	hgsc.bcm.edu	37	chr12	19615597	19615597	+	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	caggcttgcttcaactctagCccagatctggcagatcacat	10	10	8	13	0	4	2	2	0	2	2	4	2	4	2	1	2	3	3	1	2	2	3			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr12:19615597C>T	ENST00000398864.3	+	2	851	c.825C>T	c.(823-825)agC>agT	p.S275S	AEBP2_ENST00000360995.4_Silent_p.S59S|AEBP2_ENST00000266508.9_Silent_p.S275S|AEBP2_ENST00000541908.1_Silent_p.S46S	NM_001114176.1	NP_001107648.1	Q6ZN18	AEBP2_HUMAN	AE binding protein 2	275	Interaction with RBBP4.				chromatin modification (GO:0016568)	ESC/E(Z) complex (GO:0035098)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription corepressor activity (GO:0003714)			ovary(1)	1	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)|Esophageal squamous(101;0.143)					TCAACTCTAGCCCAGATCTGG	0.443																																					p.S275S		Atlas-SNP	.											.	AEBP2	21	.	0			c.C825T						PASS	.						135	129	130					12																	19615597		1945	4140	6085	SO:0001819	synonymous_variant	121536	exon2			CTCTAGCCCAGAT		CCDS44841.1, CCDS44842.1, CCDS58215.1	12p12.3	2012-10-02			ENSG00000139154	ENSG00000139154			24051	protein-coding gene	gene with protein product						10329662	Standard	NM_153207		Approved	MGC17922	uc001ref.2	Q6ZN18	OTTHUMG00000168906	ENST00000398864.3:c.825C>T	chr12.hg19:g.19615597C>T		78.0	0.0	.		70.0	11.0	.	NM_001114176	Q59FS5|Q6ZN62|Q96BG3	Silent	SNP	ENST00000398864.3	hg19	CCDS44841.1																																																																																			.	.	.	none		0.443	AEBP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401575.1	NM_153207		T	19615597	C	T	19615597	2	4	39	1	0	0	0	0	0	0	0	1	350	738	26	2		2	AEBP2	12	19615597	Silent	SNP	C	TCGA-5P-A9KE-01A-11D-A42J-10		19615597	114236298	51	2831											
KRT73	319101	hgsc.bcm.edu	37	chr12	53011930	53011930	+	Missense_Mutation	SNP	T	T	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	ccgctcctgggcacgcacttTctggatttcagggtccagct	5	11	11	14	2	2	0	1	0	1	0	4	1	4	1	3	3	1	4	3	3	0	2			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr12:53011930T>G	ENST00000305748.3	-	1	413	c.379A>C	c.(379-381)Aaa>Caa	p.K127Q	RP11-641A6.2_ENST00000552364.1_RNA	NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	127	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)		GCACGCACTTTCTGGATTTCA	0.577																																					p.K127Q		Atlas-SNP	.											.	KRT73	101	.	0			c.A379C						PASS	.						132	132	132					12																	53011930		2203	4300	6503	SO:0001583	missense	319101	exon1			GCACTTTCTGGAT	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.379A>C	chr12.hg19:g.53011930T>G	ENSP00000307014:p.Lys127Gln	87.0	0.0	.		92.0	18.0	.	NM_175068	Q32MB2	Missense_Mutation	SNP	ENST00000305748.3	hg19	CCDS8834.1	.	.	.	.	.	.	.	.	.	.	T	13.80	2.344058	0.41498	.	.	ENSG00000186049	ENST00000305748	T	0.75367	-0.93	4.4	3.21	0.36854	.	0.000000	0.52532	D	0.000073	T	0.74809	0.3765	L	0.45744	1.44	0.25981	N	0.982374	D	0.62365	0.991	P	0.58721	0.844	T	0.63906	-0.6531	10	0.33940	T	0.23	.	7.536	0.27710	0.1468:0.0:0.1346:0.7185	.	127	Q86Y46	K2C73_HUMAN	Q	127	ENSP00000307014:K127Q	ENSP00000307014:K127Q	K	-	1	0	KRT73	51298197	0.000000	0.05858	0.998000	0.56505	0.817000	0.46193	-0.029000	0.12329	0.763000	0.33175	0.533000	0.62120	AAA	.	.	.	none		0.577	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068		G	53011930	T	G	53011930	3	3	39	1	0	0	0	0	1	0	0	0	8493	1792	62	5	1279	5	KRT73	12	53011930	Missense_Mutation	SNP	T	TCGA-5P-A9KE-01A-11D-A42J-10	33396333	53011930	80839965	52	2832											
MON2	23041	hgsc.bcm.edu	37	chr12	62892784	62892784	+	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	tacagtgcgacaagttgttaCtgttgtttttgagaggatgg	9	15	13	4	1	0	1	0	1	0	1	0	4	0	2	0	2	3	4	0	2	3	6			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr12:62892784C>G	ENST00000393632.2	+	5	912	c.521C>G	c.(520-522)aCt>aGt	p.T174S	MON2_ENST00000552115.1_Missense_Mutation_p.T174S|MON2_ENST00000393630.3_Missense_Mutation_p.T174S|MON2_ENST00000549378.1_3'UTR|MON2_ENST00000552738.1_Missense_Mutation_p.T174S|MON2_ENST00000393629.2_Missense_Mutation_p.T174S|MON2_ENST00000280379.6_Missense_Mutation_p.T174S|MON2_ENST00000546600.1_Missense_Mutation_p.T174S	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	174					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)		CAAGTTGTTACTGTTGTTTTT	0.368																																					p.T174S		Atlas-SNP	.											.	MON2	160	.	0			c.C521G						PASS	.						241	230	234					12																	62892784		2203	4300	6503	SO:0001583	missense	23041	exon5			TTGTTACTGTTGT		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.521C>G	chr12.hg19:g.62892784C>G	ENSP00000377252:p.Thr174Ser	107.0	0.0	.		78.0	16.0	.	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	ENST00000393632.2	hg19	CCDS31849.1	.	.	.	.	.	.	.	.	.	.	C	10.07	1.249102	0.22880	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000261188;ENST00000552738;ENST00000393629;ENST00000552115	T;T;T;T;T;T;T	0.65178	0.7;-0.14;-0.14;0.71;0.71;-0.14;0.71	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.39937	0.1097	N	0.03050	-0.425	0.80722	D	1	B;B;B;B;B	0.22346	0.068;0.037;0.041;0.066;0.039	B;B;B;B;B	0.22386	0.018;0.032;0.032;0.039;0.018	T	0.33574	-0.9863	9	.	.	.	-16.895	19.173	0.93588	0.0:1.0:0.0:0.0	.	174;174;174;174;174	B9EGP5;F8VWA6;F8W1Z6;Q7Z3U7-4;Q7Z3U7	.;.;.;.;MON2_HUMAN	S	174;174;174;174;102;174;174;174	ENSP00000377252:T174S;ENSP00000377250:T174S;ENSP00000280379:T174S;ENSP00000447407:T174S;ENSP00000449215:T174S;ENSP00000377249:T174S;ENSP00000446635:T174S	.	T	+	2	0	MON2	61179051	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.818000	0.86416	2.553000	0.86117	0.491000	0.48974	ACT	.	.	.	none		0.368	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		G	62892784	C	G	62892784	3	3	39	1	0	0	0	0	1	0	0	0	9707	565	20	4	539	4	MON2	12	62892784	Missense_Mutation	SNP	C	TCGA-5P-A9KE-01A-11D-A42J-10	9880854	62892784	70959111	53	2833											
RNFT2	84900	hgsc.bcm.edu	37	chr12	117178872	117178872	+	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	gatgcagagacgccacagcaGcaacacggataacattccac	15	4	9	13	2	0	1	0	0	0	1	1	4	1	2	2	1	5	3	2	1	2	2			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr12:117178872G>C	ENST00000257575.4	+	3	289	c.56G>C	c.(55-57)aGc>aCc	p.S19T	RNFT2_ENST00000392549.2_Missense_Mutation_p.S19T|C12orf49_ENST00000536380.1_5'Flank|RNFT2_ENST00000319176.7_Missense_Mutation_p.S19T|RNFT2_ENST00000407967.3_Missense_Mutation_p.S19T			Q96EX2	RNFT2_HUMAN	ring finger protein, transmembrane 2	19						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(1)|urinary_tract(1)	6	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.034)		CGCCACAGCAGCAACACGGAT	0.527																																					p.S19T		Atlas-SNP	.											.	RNFT2	28	.	0			c.G56C						PASS	.						100	107	105					12																	117178872		2197	4296	6493	SO:0001583	missense	84900	exon3			ACAGCAGCAACAC	AK027533	CCDS9180.2, CCDS44987.1	12q24.22	2013-01-09	2008-02-26	2008-02-26	ENSG00000135119	ENSG00000135119		"RING-type (C3HC4) zinc fingers"	25905	protein-coding gene	gene with protein product			"transmembrane protein 118"	TMEM118		12477932	Standard	NM_032814		Approved	FLJ14627	uc009zwn.3	Q96EX2	OTTHUMG00000150882	ENST00000257575.4:c.56G>C	chr12.hg19:g.117178872G>C	ENSP00000257575:p.Ser19Thr	61.0	0.0	.		47.0	9.0	.	NM_001109903	E9PAM7|Q96SU5	Missense_Mutation	SNP	ENST00000257575.4	hg19	CCDS44987.1	.	.	.	.	.	.	.	.	.	.	G	15.33	2.800522	0.50315	.	.	ENSG00000135119	ENST00000257575;ENST00000407967;ENST00000392549;ENST00000319176	T;T	0.58506	0.33;0.33	4.49	4.49	0.54785	.	.	.	.	.	T	0.69815	0.3153	L	0.43152	1.355	0.54753	D	0.999981	P;D	0.67145	0.956;0.996	D;D	0.76071	0.931;0.987	T	0.73849	-0.3853	9	0.87932	D	0	-3.2449	17.4248	0.87524	0.0:0.0:1.0:0.0	.	19;19	Q96EX2;E9PAM7	RNFT2_HUMAN;.	T	19	ENSP00000257575:S19T;ENSP00000376332:S19T	ENSP00000257575:S19T	S	+	2	0	RNFT2	115663255	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.055000	0.93873	2.347000	0.79759	0.555000	0.69702	AGC	.	.	.	none		0.527	RNFT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320417.1	NM_032814		C	117178872	G	C	117178872	3	2	39	1	0	0	0	0	1	0	0	0	13515	971	34	4	62	4	RNFT2	12	117178872	Missense_Mutation	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10	54286088	117178872	16673023	54	2834											
HIP1R	9026	hgsc.bcm.edu	37	chr12	123340130	123340131	+	Frame_Shift_Ins	INS	-	-	C																															tcttcgatcagacgtttggaINSccccccaatgggtctgtgaa																										TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr12:123340130_123340131insC	ENST00000253083.4	+	12	1151_1152	c.1026_1027insC	c.(1027-1029)cccfs	p.P343fs		NM_003959.1	NP_003950.1	O75146	HIP1R_HUMAN	huntingtin interacting protein 1 related	343					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)		AGACGTTTGGACCCCCCAATGG	0.634																																					p.G342fs		Atlas-Indel,Pindel	.											.	HIP1R	68	.	0			c.1026_1027insC						PASS	.																																			SO:0001589	frameshift_variant	9026	exon12			.	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.1032dupC	chr12.hg19:g.123340136_123340136dupC	ENSP00000253083:p.Pro343fs	46.0	0.0	0		41.0	13.0	0.317073	NM_003959	A6NHQ6|Q6NXG8|Q9UED9	Frame_Shift_Ins	INS	ENST00000253083.4	hg19	CCDS31922.1																																																																																			.	.	.	none		0.634	HIP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400935.1	NM_003959		C	123340131	-	C	123340130	7	5	39	1	0	1	1	0	0	0	0	0	7122	262	10	0	1072	0	HIP1R	12	123340130	Frame_Shift_Ins	INS	-	TCGA-5P-A9KE-01A-11D-A42J-10	6161258	123340130	10511765	55	2835											
SACS	26278	hgsc.bcm.edu	37	chr13	23929405	23929405	+	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	tttcctcaccaggtggtaaaGgaaggaaacaaaatgctttt	14	11	9	7	0	1	0	1	0	0	0	2	2	2	2	2	4	2	2	2	4	6	4			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr13:23929405G>C	ENST00000382292.3	-	7	1619	c.1346C>G	c.(1345-1347)cCt>cGt	p.P449R	SACS_ENST00000382298.3_Missense_Mutation_p.P449R|SACS_ENST00000476776.1_5'Flank|SACS_ENST00000402364.1_5'UTR			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	449					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)		AGGTGGTAAAGGAAGGAAACA	0.458																																					p.P449R		Atlas-SNP	.											.	SACS	871	.	0			c.C1346G						PASS	.						81	72	75					13																	23929405		2203	4300	6503	SO:0001583	missense	26278	exon8			GGTAAAGGAAGGA	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.1346C>G	chr13.hg19:g.23929405G>C	ENSP00000371729:p.Pro449Arg	64.0	0.0	.		41.0	9.0	.	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	hg19	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	G	18.71	3.681299	0.68042	.	.	ENSG00000151835	ENST00000382292;ENST00000382298;ENST00000423156	T;T;T	0.18338	2.22;2.22;2.22	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.52191	0.1719	M	0.88450	2.955	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	1.0;1.0;0.99	T	0.58103	-0.7695	10	0.87932	D	0	.	20.2406	0.98372	0.0:0.0:1.0:0.0	.	348;236;449	B2REB1;E9PAL4;Q9NZJ4	.;.;SACS_HUMAN	R	449;449;73	ENSP00000371729:P449R;ENSP00000371735:P449R;ENSP00000390925:P73R	ENSP00000371729:P449R	P	-	2	0	SACS	22827405	1.000000	0.71417	0.847000	0.33407	0.377000	0.30045	9.798000	0.99111	2.857000	0.98124	0.650000	0.86243	CCT	.	.	.	none		0.458	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		C	23929405	G	C	23929405	3	2	39	1	0	0	0	0	1	0	0	0	13817	1000	35	4	12405	4	SACS	13	23929405	Missense_Mutation	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10		23929405	91240473	56	2836											
RNF17	56163	hgsc.bcm.edu	37	chr13	25373622	25373622	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caatagagggtagaaataccAgaaaaccttgtagtccaacc	17	7	8	9	0	0	3	0	0	0	3	1	3	1	3	4	1	3	2	4	1	9	5			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr13:25373622A>G	ENST00000255324.5	+	12	1541	c.1489A>G	c.(1489-1491)Aga>Gga	p.R497G	RNF17_ENST00000381921.1_Missense_Mutation_p.R497G|RNF17_ENST00000255325.6_Missense_Mutation_p.R497G	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	497					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)		TAGAAATACCAGAAAACCTTG	0.348																																					p.R497G		Atlas-SNP	.											.	RNF17	259	.	0			c.A1489G						PASS	.						106	112	110					13																	25373622		2203	4298	6501	SO:0001583	missense	56163	exon12			AATACCAGAAAAC	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.1489A>G	chr13.hg19:g.25373622A>G	ENSP00000255324:p.Arg497Gly	101.0	0.0	.		65.0	21.0	.	NM_001184993	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Missense_Mutation	SNP	ENST00000255324.5	hg19	CCDS9308.2	.	.	.	.	.	.	.	.	.	.	A	9.146	1.015011	0.19355	.	.	ENSG00000132972	ENST00000255324;ENST00000381921;ENST00000429047;ENST00000255325	T;T;T	0.17370	3.51;3.51;2.28	5.41	2.99	0.34606	Maternal tudor protein (1);	0.222829	0.33916	N	0.004431	T	0.07188	0.0182	N	0.08118	0	0.80722	D	1	B;B	0.12013	0.001;0.005	B;B	0.14578	0.005;0.011	T	0.24621	-1.0155	10	0.26408	T	0.33	.	5.2251	0.15389	0.6627:0.0:0.3373:0.0	.	497;497	B7Z7S1;Q9BXT8	.;RNF17_HUMAN	G	497;497;356;498	ENSP00000255324:R497G;ENSP00000371346:R497G;ENSP00000255325:R498G	ENSP00000255324:R497G	R	+	1	2	RNF17	24271622	0.908000	0.30866	0.777000	0.31699	0.600000	0.36913	1.532000	0.36029	1.059000	0.40554	0.455000	0.32223	AGA	.	.	.	none		0.348	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994		G	25373622	A	G	25373622	3	3	39	1	0	0	0	0	1	0	0	0	13474	180	7	3	1535	3	RNF17	13	25373622	Missense_Mutation	SNP	A	TCGA-5P-A9KE-01A-11D-A42J-10	1444217	25373622	89796256	57	2837											
GPR12	2835	hgsc.bcm.edu	37	chr13	27333950	27333950	+	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	agcccgcttaaattgaccttCaggtcttcattcattttaac	10	15	5	11	1	4	1	3	1	1	0	4	1	4	1	2	1	2	1	2	1	3	7			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr13:27333950C>T	ENST00000381436.2	-	1	477	c.15G>A	c.(13-15)ctG>ctA	p.L5L	GPR12_ENST00000405846.3_Silent_p.L5L			P47775	GPR12_HUMAN	G protein-coupled receptor 12	5					cellular calcium ion homeostasis (GO:0006874)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|phosphatidylcholine binding (GO:0031210)			endometrium(7)|kidney(2)|large_intestine(6)|lung(14)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33	Colorectal(5;5.77e-05)	Breast(139;0.198)		Epithelial(112;9.37e-07)|OV - Ovarian serous cystadenocarcinoma(117;1.16e-06)|all cancers(112;8.31e-06)|GBM - Glioblastoma multiforme(144;0.00121)|Lung(94;0.111)|LUSC - Lung squamous cell carcinoma(192;0.184)		AATTGACCTTCAGGTCTTCAT	0.478																																					p.L5L		Atlas-SNP	.											.	GPR12	67	.	0			c.G15A						PASS	.						32	37	35					13																	27333950		2199	4300	6499	SO:0001819	synonymous_variant	2835	exon2			GACCTTCAGGTCT	U18548	CCDS9319.1	13q12	2014-06-12			ENSG00000132975	ENSG00000132975		"GPCR / Class A : Orphans"	4466	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 84"	600752				8262253, 8530049	Standard	NM_005288		Approved	GPCR21, PPP1R84	uc010aal.3	P47775	OTTHUMG00000016620	ENST00000381436.2:c.15G>A	chr13.hg19:g.27333950C>T		64.0	0.0	.		45.0	12.0	.	NM_005288	Q5T8P3	Silent	SNP	ENST00000381436.2	hg19	CCDS9319.1																																																																																			.	.	.	none		0.478	GPR12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044257.2			T	27333950	C	T	27333950	2	4	39	1	0	0	0	0	0	0	0	1	6642	813	29	2		2	GPR12	13	27333950	Silent	SNP	C	TCGA-5P-A9KE-01A-11D-A42J-10	1960328	27333950	87835928	58	2838											
MYH7	4625	hgsc.bcm.edu	37	chr14	23893155	23893155	+	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	ttctccttctccactttggcCagtgtcagctccagatcatc	6	14	6	15	0	4	1	2	0	2	1	8	1	5	1	4	1	1	1	4	1	0	3			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr14:23893155C>A	ENST00000355349.3	-	23	3045	c.2883G>T	c.(2881-2883)ctG>ctT	p.L961L		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	961					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		CCACTTTGGCCAGTGTCAGCT	0.532																																					p.L961L		Atlas-SNP	.											.	MYH7	349	.	0			c.G2883T						PASS	.						186	169	175					14																	23893155		2203	4300	6503	SO:0001819	synonymous_variant	4625	exon23			TTTGGCCAGTGTC	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.2883G>T	chr14.hg19:g.23893155C>A		35.0	0.0	.		38.0	11.0	.	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Silent	SNP	ENST00000355349.3	hg19	CCDS9601.1																																																																																			.	.	.	none		0.532	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		A	23893155	C	A	23893155	2	1	39	1	0	0	0	0	0	0	0	1	10046	581	21	4		4	MYH7	14	23893155	Silent	SNP	C	TCGA-5P-A9KE-01A-11D-A42J-10		23893155	83456385	59	2839											
ALDH6A1	4329	hgsc.bcm.edu	37	chr14	74531541	74531541	+	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	ttacctgtttgccatagaaaTtggtgtctcccctgaaggag	9	13	10	9	0	1	2	0	1	1	1	2	3	1	3	4	2	2	1	4	2	4	4			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr14:74531541T>A	ENST00000553458.1	-	11	1585	c.1487A>T	c.(1486-1488)aAt>aTt	p.N496I	AC005484.5_ENST00000492026.1_RNA|ALDH6A1_ENST00000555126.1_Missense_Mutation_p.N213I|CCDC176_ENST00000394009.3_3'UTR|ALDH6A1_ENST00000350259.4_Missense_Mutation_p.N483I|CCDC176_ENST00000553773.1_Intron	NM_001278593.1|NM_005589.2	NP_001265522.1|NP_005580.1	Q02252	MMSA_HUMAN	aldehyde dehydrogenase 6 family, member A1	496					branched-chain amino acid catabolic process (GO:0009083)|brown fat cell differentiation (GO:0050873)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|thymine catabolic process (GO:0006210)|thymine metabolic process (GO:0019859)|valine catabolic process (GO:0006574)|valine metabolic process (GO:0006573)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	fatty-acyl-CoA binding (GO:0000062)|malonate-semialdehyde dehydrogenase (acetylating) activity (GO:0018478)|methylmalonate-semialdehyde dehydrogenase (acylating) activity (GO:0004491)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(3)|skin(3)	21				BRCA - Breast invasive adenocarcinoma(234;0.00354)		GCCATAGAAATTGGTGTCTCC	0.413																																					p.N496I		Atlas-SNP	.											.	ALDH6A1	42	.	0			c.A1487T						PASS	.						49	49	49					14																	74531541		2203	4300	6503	SO:0001583	missense	4329	exon11			TAGAAATTGGTGT	M93405	CCDS9826.1, CCDS61501.1	14q24.3	2014-02-03			ENSG00000119711	ENSG00000119711	1.2.1.27	"Aldehyde dehydrogenases"	7179	protein-coding gene	gene with protein product		603178		MMSDH		1527093	Standard	NM_005589		Approved		uc001xpo.3	Q02252	OTTHUMG00000171203	ENST00000553458.1:c.1487A>T	chr14.hg19:g.74531541T>A	ENSP00000450436:p.Asn496Ile	221.0	0.0	.		204.0	51.0	.	NM_005589	B2R609|B4DFS8|J3KNU8|Q9UKM8	Missense_Mutation	SNP	ENST00000553458.1	hg19	CCDS9826.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.818862	0.90873	.	.	ENSG00000119711	ENST00000553458;ENST00000350259;ENST00000555126	T;T;T	0.76186	-1.0;-1.0;-1.0	6.17	6.17	0.99709	Aldehyde dehydrogenase domain (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.85682	D	0.000000	D	0.87208	0.6120	M	0.87038	2.855	0.80722	D	1	P;D	0.52996	0.924;0.957	P;P	0.61397	0.888;0.888	D	0.89098	0.3487	10	0.87932	D	0	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	483;496	B4DFS8;Q02252	.;MMSA_HUMAN	I	496;483;213	ENSP00000450436:N496I;ENSP00000342564:N483I;ENSP00000452081:N213I	ENSP00000342564:N496I	N	-	2	0	ALDH6A1	73601294	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.040000	0.89188	2.371000	0.80710	0.533000	0.62120	AAT	.	.	.	none		0.413	ALDH6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412309.1			A	74531541	T	A	74531541	3	1	39	1	0	0	0	0	1	0	0	0	503	1493	52	5	128	5	ALDH6A1	14	74531541	Missense_Mutation	SNP	T	TCGA-5P-A9KE-01A-11D-A42J-10	50638386	74531541	32817999	60	2840											
RYR3	6263	hgsc.bcm.edu	37	chr15	33941289	33941290	+	Missense_Mutation	DNP	TC	TC	AT																															acagcagtgctactacgccaTccgcatctttgctggacagg																										TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr15:33941289_33941290TC>AT	ENST00000389232.4	+	31	4065_4066	c.3995_3996TC>AT	c.(3994-3996)aTC>aAT	p.I1332N	RYR3_ENST00000415757.3_Missense_Mutation_p.I1332N	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	1332	4 X approximate repeats.|B30.2/SPRY 3. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TACTACGCCATCCGCATCTTTG	0.53																																					p.I1332N|p.I1332I		Atlas-SNP	.											.	RYR3	760	.	0			c.T3995A|c.C3996T						PASS	.																																			SO:0001583	missense	6263	exon31			ACGCCATCCGCAT|CGCCATCCGCATC		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		Exception_encountered	chr15.hg19:g.33941289_33941290delinsAT	ENSP00000373884:p.Ile1332Asn	49.0	0.0	.		50.0|52.0	14.0|16.0	.	NM_001243996	O15175|Q15412	Missense_Mutation|Silent	SNP	ENST00000389232.4	hg19	CCDS45210.1																																																																																			.	.	.	none		0.53	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			AT	33941290	TC	AT	33941289	3	1	39	1	0	0	0	0	1	0	0	0	13783	1435	50	5	4117	5	RYR3	15	33941289	Missense_Mutation	DNP	TC	TCGA-5P-A9KE-01A-11D-A42J-10		33941289	68590103	61	2841											
EIF2AK4	440275	hgsc.bcm.edu	37	chr15	40268924	40268924	+	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	ccatcctcagcagctcggtgGagtggagcacttcgggcgag	7	7	15	12	3	1	0	1	0	0	0	4	3	2	2	2	4	3	3	2	4	0	1			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr15:40268924G>A	ENST00000263791.5	+	12	2171	c.2128G>A	c.(2128-2130)Gag>Aag	p.E710K	EIF2AK4_ENST00000382727.2_Missense_Mutation_p.E710K	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	710	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to starvation (GO:0009267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of translation (GO:0017148)|protein phosphorylation (GO:0006468)|regulation of translational initiation (GO:0006446)|regulation of translational initiation in response to stress (GO:0043558)	cytosolic ribosome (GO:0022626)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		CAGCTCGGTGGAGTGGAGCAC	0.721																																					p.E710K		Atlas-SNP	.											.	EIF2AK4	107	.	0			c.G2128A						PASS	.						22	25	24					15																	40268924		1774	3885	5659	SO:0001583	missense	440275	exon12			TCGGTGGAGTGGA	AB037759	CCDS42016.1	15q13.3	2008-08-18				ENSG00000128829			19687	protein-coding gene	gene with protein product		609280				10504407	Standard	XM_005254392		Approved	GCN2, KIAA1338	uc001zkm.1	Q9P2K8		ENST00000263791.5:c.2128G>A	chr15.hg19:g.40268924G>A	ENSP00000263791:p.Glu710Lys	71.0	0.0	.		63.0	12.0	.	NM_001013703	C9JEC4|Q69YL7|Q6DC97|Q96GN6|Q9H5K1|Q9NSQ3|Q9NSZ5|Q9UJ56	Missense_Mutation	SNP	ENST00000263791.5	hg19	CCDS42016.1	.	.	.	.	.	.	.	.	.	.	G	37	6.303692	0.97458	.	.	ENSG00000128829	ENST00000263791;ENST00000382727	T;T	0.71103	-0.54;-0.5	5.34	5.34	0.76211	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.79203	0.4406	L	0.41356	1.27	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.75266	-0.3378	10	0.29301	T	0.29	-25.8872	19.4115	0.94675	0.0:0.0:1.0:0.0	.	710	Q9P2K8	E2AK4_HUMAN	K	710	ENSP00000263791:E710K;ENSP00000372174:E710K	ENSP00000263791:E710K	E	+	1	0	EIF2AK4	38056216	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.700000	0.98707	2.651000	0.90000	0.585000	0.79938	GAG	.	.	.	none		0.721	EIF2AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418395.1			A	40268924	G	A	40268924	3	1	39	1	0	0	0	0	1	0	0	0	5001	1175	41	2	2174	2	EIF2AK4	15	40268924	Missense_Mutation	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10	6327635	40268924	62262468	62	2842											
LRRC57	255252	hgsc.bcm.edu	37	chr15	42839565	42839565	+	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	tcacatccaggtgccgtaggCtacaaagttggggaggtaat	11	9	13	8	1	1	0	1	0	0	0	2	1	2	1	2	5	2	4	2	5	4	4			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr15:42839565C>A	ENST00000323443.2	-	3	753	c.386G>T	c.(385-387)aGc>aTc	p.S129I	HAUS2_ENST00000568876.1_5'Flank|HAUS2_ENST00000568846.2_5'Flank|LRRC57_ENST00000397130.3_Missense_Mutation_p.S129I|HAUS2_ENST00000260372.3_5'Flank|LRRC57_ENST00000563454.1_Missense_Mutation_p.S129I			Q8N9N7	LRC57_HUMAN	leucine rich repeat containing 57	129						extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|lung(5)|prostate(1)	8		all_cancers(109;1.99e-12)|all_epithelial(112;5.11e-11)|Lung NSC(122;4.53e-07)|all_lung(180;1.64e-06)|Melanoma(134;0.0262)		GBM - Glioblastoma multiforme(94;6.87e-07)		GTGCCGTAGGCTACAAAGTTG	0.527																																					p.S129I		Atlas-SNP	.											.	LRRC57	20	.	0			c.G386T						PASS	.						96	83	87					15																	42839565		2203	4299	6502	SO:0001583	missense	255252	exon4			CGTAGGCTACAAA	AK094891	CCDS10089.1	15q15.1	2006-02-13			ENSG00000180979	ENSG00000180979			26719	protein-coding gene	gene with protein product							Standard	NM_153260		Approved	FLJ36812	uc001zqc.3	Q8N9N7	OTTHUMG00000130679	ENST00000323443.2:c.386G>T	chr15.hg19:g.42839565C>A	ENSP00000326817:p.Ser129Ile	71.0	0.0	.		72.0	23.0	.	NM_153260	Q7Z2Z6|Q8N1T6	Missense_Mutation	SNP	ENST00000323443.2	hg19	CCDS10089.1	.	.	.	.	.	.	.	.	.	.	C	11.67	1.707022	0.30232	.	.	ENSG00000180979	ENST00000323443;ENST00000397130	T;T	0.58940	0.3;0.3	5.41	0.293	0.15742	.	0.471361	0.27749	N	0.018005	T	0.49966	0.1588	M	0.70275	2.135	0.28209	N	0.927029	B	0.27192	0.171	B	0.28465	0.09	T	0.44847	-0.9301	10	0.42905	T	0.14	.	5.8582	0.18732	0.0:0.5396:0.1234:0.337	.	129	Q8N9N7	LRC57_HUMAN	I	129	ENSP00000326817:S129I;ENSP00000380319:S129I	ENSP00000326817:S129I	S	-	2	0	LRRC57	40626857	1.000000	0.71417	0.970000	0.41538	0.620000	0.37586	0.915000	0.28638	0.092000	0.17331	-0.818000	0.03119	AGC	.	.	.	none		0.527	LRRC57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253174.1	NM_153260		A	42839565	C	A	42839565	3	1	39	1	0	0	0	0	1	0	0	0	9020	797	28	4	345	4	LRRC57	15	42839565	Missense_Mutation	SNP	C	TCGA-5P-A9KE-01A-11D-A42J-10	2570641	42839565	59691827	63	2843											
DMXL2	23312	hgsc.bcm.edu	37	chr15	51758502	51758502	+	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	accactatcagacaaaggaaGaaatggctgcaataaaaggt	19	6	9	7	0	1	2	1	0	0	2	1	3	1	3	1	3	1	2	1	3	7	2			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr15:51758502G>A	ENST00000251076.5	-	30	7683	c.7396C>T	c.(7396-7398)Ctt>Ttt	p.L2466F	DMXL2_ENST00000543779.2_Missense_Mutation_p.L2467F|RP11-707P17.1_ENST00000561007.1_RNA|DMXL2_ENST00000449909.3_Missense_Mutation_p.L1830F	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	2466						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		GACAAAGGAAGAAATGGCTGC	0.239																																					p.L2467F		Atlas-SNP	.											DMXL2,bladder,carcinoma,0,1	DMXL2	262	.	0			c.C7399T						PASS	.						62	61	62					15																	51758502		2195	4290	6485	SO:0001583	missense	23312	exon30			AAGGAAGAAATGG	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.7396C>T	chr15.hg19:g.51758502G>A	ENSP00000251076:p.Leu2466Phe	142.0	1.0	.		123.0	43.0	.	NM_001174116	B2RTR3|B7ZMH3|F5GWF1|O94938	Missense_Mutation	SNP	ENST00000251076.5	hg19	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.522339	0.85600	.	.	ENSG00000104093	ENST00000251076;ENST00000543779;ENST00000449909;ENST00000436119	T;T;T	0.27557	1.8;1.79;1.66	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.55705	0.1937	M	0.69358	2.11	0.80722	D	1	D;D;D;P	0.76494	0.998;0.998;0.999;0.597	D;D;D;B	0.80764	0.943;0.986;0.994;0.293	T	0.55366	-0.8152	10	0.54805	T	0.06	.	18.8489	0.92218	0.0:0.0:1.0:0.0	.	2467;1830;2466;2467	F5GWF1;B2RTR3;Q8TDJ6;B7ZMH3	.;.;DMXL2_HUMAN;.	F	2466;2467;1830;11	ENSP00000251076:L2466F;ENSP00000441858:L2467F;ENSP00000400855:L1830F	ENSP00000251076:L2466F	L	-	1	0	DMXL2	49545794	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.154000	0.77437	2.697000	0.92050	0.556000	0.70494	CTT	.	.	.	none		0.239	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		A	51758502	G	A	51758502	3	1	39	1	0	0	0	0	1	0	0	0	4597	942	33	2	1770	2	DMXL2	15	51758502	Missense_Mutation	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10	8918937	51758502	50772890	64	2844											
ZSCAN10	84891	hgsc.bcm.edu	37	chr16	3141821	3141821	+	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	ctctggccatggtgaggggcCctggggacctgacggcattg	5	8	17	11	1	1	2	0	2	1	0	1	3	1	3	3	7	0	1	3	7	0	1			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr16:3141821C>T	ENST00000252463.2	-	3	595	c.508G>A	c.(508-510)Ggc>Agc	p.G170S	ZSCAN10_ENST00000575108.1_5'UTR|ZSCAN10_ENST00000538082.2_Missense_Mutation_p.G88S|ZSCAN10_ENST00000572548.1_Silent_p.R35R	NM_032805.1	NP_116194.1	Q96SZ4	ZSC10_HUMAN	zinc finger and SCAN domain containing 10	170	Pro-rich.				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						GGTGAGGGGCCCTGGGGACCT	0.647																																					p.G170S		Atlas-SNP	.											.	ZSCAN10	63	.	0			c.G508A						PASS	.						14	13	14					16																	3141821		2189	4291	6480	SO:0001583	missense	84891	exon3			AGGGGCCCTGGGG	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.508G>A	chr16.hg19:g.3141821C>T	ENSP00000252463:p.Gly170Ser	90.0	0.0	.		101.0	18.0	.	NM_032805	B3KQD3|H0YFS6|Q1WWM2	Missense_Mutation	SNP	ENST00000252463.2	hg19	CCDS10493.1	.	.	.	.	.	.	.	.	.	.	C	18.93	3.727505	0.69074	.	.	ENSG00000130182	ENST00000538082;ENST00000252463	T	0.06068	3.35	4.64	4.64	0.57946	.	0.377632	0.19741	N	0.107124	T	0.05044	0.0135	N	0.08118	0	0.80722	D	1	D;D	0.54047	0.964;0.964	P;P	0.47673	0.554;0.554	T	0.58306	-0.7659	10	0.18710	T	0.47	-25.2064	13.0179	0.58768	0.0:1.0:0.0:0.0	.	103;170	Q1WWM2;Q96SZ4	.;ZSC10_HUMAN	S	103;170	ENSP00000252463:G170S	ENSP00000252463:G170S	G	-	1	0	ZSCAN10	3081822	0.088000	0.21588	0.987000	0.45799	0.590000	0.36582	0.394000	0.20834	2.150000	0.67090	0.561000	0.74099	GGC	.	.	.	none		0.647	ZSCAN10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437124.2	NM_032805		T	3141821	C	T	3141821	3	4	39	1	0	0	0	0	1	0	0	0	18239	623	22	2	1681	2	ZSCAN10	16	3141821	Missense_Mutation	SNP	C	TCGA-5P-A9KE-01A-11D-A42J-10		3141821	87212932	65	2845											
VWA3A	146177	hgsc.bcm.edu	37	chr16	22130234	22130234	+	Frame_Shift_Del	DEL	C	C	-																															caccctcagcactacaccagCcgggacatggatgagctcct																										TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr16:22130234delC	ENST00000389398.5	+	12	1098	c.1002delC	c.(1000-1002)agcfs	p.S334fs	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	334						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)		ACTACACCAGCCGGGACATGG	0.607																																					p.S334fs		Atlas-Indel,Pindel	.											.	VWA3A	115	.	0			c.1001delG						PASS	.						53	57	56					16																	22130234		2107	4232	6339	SO:0001589	frameshift_variant	146177	exon12			.	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.1002delC	chr16.hg19:g.22130234delC	ENSP00000374049:p.Ser334fs	140.0	0.0	0		152.0	25.0	0.164474	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Frame_Shift_Del	DEL	ENST00000389398.5	hg19	CCDS45441.1																																																																																			.	.	.	none		0.607	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1			-	22130234	C	-	22130234	7	5	39	1	0	1	0	1	0	0	0	0	17252	738	26	0	1048	0	VWA3A	16	22130234	Frame_Shift_Del	DEL	C	TCGA-5P-A9KE-01A-11D-A42J-10	18988413	22130234	68224519	66	2846											
HSF4	3299	hgsc.bcm.edu	37	chr16	67199508	67199508	+	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	ttcaagcatagcaacatggcGagcttcgtgcgccaactcaa	12	8	9	12	3	2	0	2	0	0	0	3	1	2	0	1	1	6	3	1	1	5	3			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr16:67199508G>T	ENST00000521374.1	+	2	207	c.207G>T	c.(205-207)gcG>gcT	p.A69A	HSF4_ENST00000264009.8_Silent_p.A69A|RP11-5A19.5_ENST00000518227.1_3'UTR|HSF4_ENST00000584272.1_Silent_p.A69A|HSF4_ENST00000421453.1_Silent_p.A69A			Q9ULV5	HSF4_HUMAN	heat shock transcription factor 4	69					camera-type eye development (GO:0043010)|cell development (GO:0048468)|histone H3-K9 demethylation (GO:0033169)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotrimerization (GO:0070207)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	12		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.0335)|all cancers(182;0.184)		GCAACATGGCGAGCTTCGTGC	0.647																																					p.A69A		Atlas-SNP	.											.	HSF4	33	.	0			c.G207T						PASS	.						52	58	56					16																	67199508		2154	4289	6443	SO:0001819	synonymous_variant	3299	exon4			CATGGCGAGCTTC	D87673	CCDS42175.1, CCDS45510.1	16q21	2013-01-22			ENSG00000102878	ENSG00000102878			5227	protein-coding gene	gene with protein product		602438	"cataract, Marner"	CTM		8972228, 10488131, 12089525	Standard	NM_001538		Approved		uc002erl.2	Q9ULV5	OTTHUMG00000178325	ENST00000521374.1:c.207G>T	chr16.hg19:g.67199508G>T		87.0	0.0	.		97.0	21.0	.	NM_001538	Q99472|Q9ULV6	Silent	SNP	ENST00000521374.1	hg19	CCDS42175.1																																																																																			.	.	.	none		0.647	HSF4-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375080.1	NM_001538		T	67199508	G	T	67199508	2	4	39	1	0	0	0	0	0	0	0	1	7405	1045	37	4		4	HSF4	16	67199508	Silent	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10	45069274	67199508	23155245	67	2847											
MINK1	50488	hgsc.bcm.edu	37	chr17	4788851	4788851	+	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	ttcattgggactccctactgGatggctccagaggtcatcgc	7	11	11	12	1	2	1	2	0	0	1	5	3	4	3	2	4	1	1	2	4	1	3			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr17:4788851G>A	ENST00000355280.6	+	7	778	c.582G>A	c.(580-582)tgG>tgA	p.W194*	MINK1_ENST00000347992.7_Nonsense_Mutation_p.W194*|RN7SL784P_ENST00000577319.1_RNA|MINK1_ENST00000453408.3_Nonsense_Mutation_p.W194*	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						CTCCCTACTGGATGGCTCCAG	0.577																																					p.W194X		Atlas-SNP	.											.	MINK1	110	.	0			c.G582A						PASS	.						97	102	100					17																	4788851		2062	4183	6245	SO:0001587	stop_gained	50488	exon7			CTACTGGATGGCT	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.582G>A	chr17.hg19:g.4788851G>A	ENSP00000347427:p.Trp194*	70.0	0.0	.		73.0	21.0	.	NM_170663		Nonsense_Mutation	SNP	ENST00000355280.6	hg19	CCDS45588.1	.	.	.	.	.	.	.	.	.	.	G	38	6.985257	0.97983	.	.	ENSG00000141503	ENST00000355280;ENST00000453408;ENST00000347992	.	.	.	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.0271	0.86450	0.0:0.0:1.0:0.0	.	.	.	.	X	194	.	ENSP00000269296:W194X	W	+	3	0	MINK1	4729634	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.657000	0.98554	2.884000	0.98904	0.655000	0.94253	TGG	.	.	.	none		0.577	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439801.1	NM_015716		A	4788851	G	A	4788851	4	1	39	1	0	0	0	0	0	1	0	0	9594	1183	41	2	347	2	MINK1	17	4788851	Nonsense_Mutation	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10		4788851	76406359	68	2848											
SLC2A4	6517	hgsc.bcm.edu	37	chr17	7187813	7187813	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccttctccaggtctgaagcGcctgacaggctgggccgatg	6	8	13	14	2	2	2	0	2	2	0	3	3	2	2	4	3	1	1	4	3	1	1			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr17:7187813G>A	ENST00000317370.8	+	7	1005	c.737G>A	c.(736-738)cGc>cAc	p.R246H	RP1-4G17.2_ENST00000576271.1_RNA|SLC2A4_ENST00000571308.1_Missense_Mutation_p.R246H|SLC2A4_ENST00000424875.2_Missense_Mutation_p.R236H	NM_001042.2	NP_001033.1	P14672	GTR4_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 4	246					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)	p.R246H(1)		breast(1)|endometrium(3)|large_intestine(7)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17						GGTCTGAAGCGCCTGACAGGC	0.637																																					p.R246H		Atlas-SNP	.											SLC2A4,colon,carcinoma,0,1	SLC2A4	44	.	1	Substitution - Missense(1)	large_intestine(1)	c.G737A						PASS	.						42	44	43					17																	7187813		2203	4300	6503	SO:0001583	missense	6517	exon7			TGAAGCGCCTGAC	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.737G>A	chr17.hg19:g.7187813G>A	ENSP00000320935:p.Arg246His	114.0	0.0	.		143.0	29.0	.	NM_001042	Q05BQ3|Q14CX2	Missense_Mutation	SNP	ENST00000317370.8	hg19	CCDS11097.1	.	.	.	.	.	.	.	.	.	.	G	15.29	2.789231	0.49997	.	.	ENSG00000181856	ENST00000317370;ENST00000424875	T;T	0.76448	-1.02;-1.02	4.88	3.84	0.44239	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.124816	0.51477	D	0.000087	T	0.75744	0.3891	M	0.90650	3.135	0.48040	D	0.999573	P;P	0.51933	0.484;0.949	B;B	0.37989	0.15;0.262	T	0.79642	-0.1718	10	0.59425	D	0.04	.	5.782	0.18312	0.2087:0.0:0.7913:0.0	.	246;236	P14672;F5H081	GTR4_HUMAN;.	H	246;236	ENSP00000320935:R246H;ENSP00000396887:R236H	ENSP00000320935:R246H	R	+	2	0	SLC2A4	7128537	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	3.296000	0.51802	2.535000	0.85469	0.655000	0.94253	CGC	.	.	.	none		0.637	SLC2A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220031.3			A	7187813	G	A	7187813	3	1	39	1	0	0	0	0	1	0	0	0	14559	1087	38	1	763	1	SLC2A4	17	7187813	Missense_Mutation	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10	2398962	7187813	74007397	69	2849											
SHMT1	6470	hgsc.bcm.edu	37	chr17	18232685	18232685	+	Missense_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	cagccgcagtccactgggccGcagagcgcttctgtcaccta	7	7	11	16	3	2	1	1	0	1	1	3	1	3	1	4	1	2	3	4	1	1	2	rs140862126		TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr17:18232685G>A	ENST00000316694.3	-	11	1323	c.1189C>T	c.(1189-1191)Cgg>Tgg	p.R397W	SHMT1_ENST00000539052.1_Missense_Mutation_p.R259W|SHMT1_ENST00000352886.6_Missense_Mutation_p.R317W|SHMT1_ENST00000354098.3_Missense_Mutation_p.R358W	NM_004169.3	NP_004160.3	P34896	GLYC_HUMAN	serine hydroxymethyltransferase 1 (soluble)	397					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)	CCACTGGGCCGCAGAGCGCTT	0.517																																					p.R397W		Atlas-SNP	.											.	SHMT1	36	.	0			c.C1189T						PASS	.	G	TRP/ARG,TRP/ARG	0,4406		0,0,2203	37	39	38		1189,1072	3.4	1	17	dbSNP_134	38	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	SHMT1	NM_004169.3,NM_148918.1	101,101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	397/484,358/445	18232685	1,13005	2203	4300	6503	SO:0001583	missense	6470	exon11			TGGGCCGCAGAGC		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.1189C>T	chr17.hg19:g.18232685G>A	ENSP00000318868:p.Arg397Trp	46.0	0.0	.		48.0	9.0	.	NM_004169	B4DPM9|D3DXD0|Q96HY0|Q9UMD1|Q9UMD2	Missense_Mutation	SNP	ENST00000316694.3	hg19	CCDS11196.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.044222	0.75732	0.0	1.16E-4	ENSG00000176974	ENST00000316694;ENST00000395684;ENST00000352886;ENST00000539052;ENST00000354098	T;T;T;T	0.43294	0.95;1.54;0.95;1.54	5.52	3.36	0.38483	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.051991	0.85682	D	0.000000	T	0.56077	0.1961	L	0.56124	1.755	0.80722	D	1	D;D	0.89917	1.0;0.999	D;P	0.66497	0.944;0.839	T	0.56613	-0.7950	10	0.37606	T	0.19	-17.6168	15.0169	0.71594	0.0:0.0:0.7428:0.2572	.	358;397	P34896-2;P34896	.;GLYC_HUMAN	W	397;172;317;259;358	ENSP00000318868:R397W;ENSP00000345881:R317W;ENSP00000440089:R259W;ENSP00000318805:R358W	ENSP00000318868:R397W	R	-	1	2	SHMT1	18173410	1.000000	0.71417	0.965000	0.40720	0.794000	0.44872	4.977000	0.63792	1.429000	0.47314	0.655000	0.94253	CGG	.	G|1.000;A|0.000	0.000	weak		0.517	SHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130831.2	NM_004169		A	18232685	G	A	18232685	3	1	39	1	0	0	0	0	1	0	0	0	14298	1086	38	1	270	1	SHMT1	17	18232685	Missense_Mutation	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10	11044872	18232685	62962525	70	2850											
EFCAB5	374786	hgsc.bcm.edu	37	chr17	28380417	28380417	+	Missense_Mutation	SNP	G	G	A																															tcatgctagcaaaacccaaaGtaaattattagaaagtccag																										TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr17:28380417G>A	ENST00000394835.3	+	10	1637	c.1445G>A	c.(1444-1446)aGt>aAt	p.S482N	EFCAB5_ENST00000394832.2_Missense_Mutation_p.S482N|EFCAB5_ENST00000536908.2_Missense_Mutation_p.S426N|EFCAB5_ENST00000320856.5_Missense_Mutation_p.S482N|EFCAB5_ENST00000541045.1_Missense_Mutation_p.S139N|EFCAB5_ENST00000378738.3_Missense_Mutation_p.S482N	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	482							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						AAAACCCAAAGTAAATTATTA	0.388																																					p.S482N		Atlas-SNP	.											.	EFCAB5	122	.	0			c.G1445A						PASS	.						135	135	135					17																	28380417		1894	4113	6007	SO:0001583	missense	374786	exon10			CCCAAAGTAAATT	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.1445G>A	chr17.hg19:g.28380417G>A	ENSP00000378312:p.Ser482Asn	179.0	0.0	.		170.0	31.0	.	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Missense_Mutation	SNP	ENST00000394835.3	hg19	CCDS11254.2	.	.	.	.	.	.	.	.	.	.	G	19.02	3.746070	0.69418	.	.	ENSG00000176927	ENST00000536908;ENST00000534836;ENST00000541045;ENST00000394835;ENST00000320856;ENST00000394832;ENST00000378738;ENST00000423598;ENST00000419434	T;T;T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83;0.83;0.83	4.92	0.725	0.18242	.	0.461885	0.20171	N	0.097728	T	0.49864	0.1582	L	0.54323	1.7	0.09310	N	1	D;D;P;B;B;P	0.59767	0.976;0.986;0.949;0.004;0.011;0.949	P;P;P;B;B;P	0.58520	0.696;0.84;0.57;0.009;0.015;0.57	T	0.41592	-0.9500	10	0.19590	T	0.45	-1.5963	7.0606	0.25123	0.3652:0.0:0.6348:0.0	.	426;426;482;482;482;482	B4DS75;F5GYL2;A8MSY9;B5MEA3;E7EVS9;A4FU69	.;.;.;.;.;EFCB5_HUMAN	N	426;225;139;482;482;482;482;426;288	ENSP00000440619:S426N;ENSP00000445575:S139N;ENSP00000378312:S482N;ENSP00000322003:S482N;ENSP00000378309:S482N;ENSP00000368012:S482N;ENSP00000417009:S288N	ENSP00000322003:S482N	S	+	2	0	EFCAB5	25404543	0.000000	0.05858	0.000000	0.03702	0.750000	0.42670	-0.383000	0.07398	0.091000	0.17302	0.655000	0.94253	AGT	.	.	.	none		0.388	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529		A	28380417	G	A	28380417	3	1	39	1	0	0	0	0	1	0	0	0	4940	1029	36	2	1483	2	EFCAB5	17	28380417	Missense_Mutation	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10	10147732	28380417	52814793	71	2851	36	2									
EFCAB5	374786	hgsc.bcm.edu	37	chr17	28380419	28380419	+	Nonsense_Mutation	SNP	A	A	T																															atgctagcaaaacccaaagtAaattattagaaagtccagat																										TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr17:28380419A>T	ENST00000394835.3	+	10	1639	c.1447A>T	c.(1447-1449)Aaa>Taa	p.K483*	EFCAB5_ENST00000394832.2_Nonsense_Mutation_p.K483*|EFCAB5_ENST00000536908.2_Nonsense_Mutation_p.K427*|EFCAB5_ENST00000320856.5_Nonsense_Mutation_p.K483*|EFCAB5_ENST00000541045.1_Nonsense_Mutation_p.K140*|EFCAB5_ENST00000378738.3_Nonsense_Mutation_p.K483*	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	483							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						AACCCAAAGTAAATTATTAGA	0.383																																					p.K483X		Atlas-SNP	.											.	EFCAB5	122	.	0			c.A1447T						PASS	.						135	135	135					17																	28380419		1892	4115	6007	SO:0001587	stop_gained	374786	exon10			CAAAGTAAATTAT	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.1447A>T	chr17.hg19:g.28380419A>T	ENSP00000378312:p.Lys483*	180.0	0.0	.		168.0	30.0	.	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Nonsense_Mutation	SNP	ENST00000394835.3	hg19	CCDS11254.2	.	.	.	.	.	.	.	.	.	.	A	18.64	3.667002	0.67814	.	.	ENSG00000176927	ENST00000536908;ENST00000534836;ENST00000541045;ENST00000394835;ENST00000320856;ENST00000394832;ENST00000378738;ENST00000423598;ENST00000419434	.	.	.	4.92	1.33	0.21861	.	0.764210	0.11787	N	0.529575	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05525	T	0.97	-9.109	5.3513	0.16038	0.5721:0.3355:0.0924:0.0	.	.	.	.	X	427;226;140;483;483;483;483;427;289	.	ENSP00000322003:K483X	K	+	1	0	EFCAB5	25404545	0.000000	0.05858	0.000000	0.03702	0.791000	0.44710	0.097000	0.15168	0.083000	0.17047	0.533000	0.62120	AAA	.	.	.	none		0.383	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529		T	28380419	A	T	28380419	4	4	39	1	0	0	0	0	0	1	0	0	4940	363	13	5	1485	5	EFCAB5	17	28380419	Nonsense_Mutation	SNP	A	TCGA-5P-A9KE-01A-11D-A42J-10	2	28380419	52814791	72	2852	36	2									
MLLT6	4302	hgsc.bcm.edu	37	chr17	36880963	36880991	+	Frame_Shift_Del	DEL	CCCATGGCCAGCCTGCTGGCAGGAAGCTC	CCCATGGCCAGCCTGCTGGCAGGAAGCTC	-																															tggctgggggctcccagctgCccatggccagcctgctggca																								rs150877733|rs528335314		TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	CCCATGGCCAGCCTGCTGGCAGGAAGCTC	CCCATGGCCAGCCTGCTGGCAGGAAGCTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr17:36880963_36880991delCCCATGGCCAGCCTGCTGGCAGGAAGCTC	ENST00000325718.7	+	19	3065_3093	c.2974_3002delCCCATGGCCAGCCTGCTGGCAGGAAGCTC	c.(2974-3003)cccatggccagcctgctggcaggaagctccfs	p.PMASLLAGSS992fs		NM_005937.3	NP_005928	P55198	AF17_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6	992					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)					CTCCCAGCTGCCCATGGCCAGCCTGCTGGCAGGAAGCTCCACCCCGCTG	0.664			T	MLL	AL																																p.991_1001del		Atlas-Indel,Pindel	.		Dom	yes		17	17q21	4302	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6 (AF17)"		L	.	MLLT6	80	.	0			c.2973_3001del						PASS	.																																			SO:0001589	frameshift_variant	4302	exon19			.		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.2974_3002delCCCATGGCCAGCCTGCTGGCAGGAAGCTC	chr17.hg19:g.36880963_36880991delCCCATGGCCAGCCTGCTGGCAGGAAGCTC	ENSP00000316426:p.Pro992fs	74.0	0.0	0		78.0	23.0	0.294872	NM_005937	Q59F28|Q96IU3|Q9H5F6|Q9UF49	Frame_Shift_Del	DEL	ENST00000325718.7	hg19	CCDS11327.1																																																																																			.	.	.	none		0.664	MLLT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256799.1	NM_005937		-	36880991	CCCATGGCCAGCCTGCTGGCAGGAAGCTC	-	36880963	7	5	39	1	0	1	0	1	0	0	0	0	9637	739	26	0	3048	0	MLLT6	17	36880963	Frame_Shift_Del	DEL	CCCATGGCCAGCCTGCTGGCAGGAAGCTC	TCGA-5P-A9KE-01A-11D-A42J-10	8500544	36880963	44314247	73	2853											
STAT3	6774	hgsc.bcm.edu	37	chr17	40481785	40481786	+	Missense_Mutation	DNP	CC	CC	TA																															cctctgagagctgcaacgtcCccagagtctctgtaagaaca																										TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr17:40481785_40481786CC>TA	ENST00000264657.5	-	12	1430_1431	c.1118_1119GG>TA	c.(1117-1119)gGG>gTA	p.G373V	STAT3_ENST00000404395.3_Missense_Mutation_p.G373V|STAT3_ENST00000585517.1_Missense_Mutation_p.G373V|STAT3_ENST00000389272.3_Missense_Mutation_p.G275V|STAT3_ENST00000588969.1_Missense_Mutation_p.G373V	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)	373					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)		CTGCAACGTCCCCAGAGTCTCT	0.421									Hyperimmunoglobulin E Recurrent Infection Syndrome																												p.G373G|p.G373V		Atlas-SNP	.											.	STAT3	268	.	0			c.G1119A|c.G1118T						PASS	.																																			SO:0001583	missense	6774	exon12	Familial Cancer Database	HIES, Hyper IgE syndrome, autosomal dominant (Job syndrome) / recessive	AACGTCCCCAGAG|ACGTCCCCAGAGT	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.1118_1119delinsTA	chr17.hg19:g.40481785_40481786delinsTA	ENSP00000264657:p.Gly373Val	113.0	0.0	.		120.0	37.0|36.0	.	NM_003150	A8K7B8|K7ENL3|O14916|Q9BW54	Silent|Missense_Mutation	SNP	ENST00000264657.5	hg19	CCDS32656.1																																																																																			.	.	.	none		0.421	STAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319353.3	NM_139276, NM_003150		TA	40481786	CC	TA	40481785	3	4	39	1	0	0	0	0	1	0	0	0	15278	610	22	2	1245	2	STAT3	17	40481785	Missense_Mutation	DNP	CC	TCGA-5P-A9KE-01A-11D-A42J-10	3600822	40481785	40713425	74	2854											
EFTUD2	9343	hgsc.bcm.edu	37	chr17	42949881	42949881	+	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	atgctgtactgggagctggaGaagcagacgttacccaggag	11	7	15	8	1	0	2	0	0	0	2	0	5	0	4	1	3	5	5	1	3	3	2			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr17:42949881G>A	ENST00000426333.2	-	11	1224	c.927C>T	c.(925-927)ttC>ttT	p.F309F	EFTUD2_ENST00000592576.1_Silent_p.F299F|EFTUD2_ENST00000591382.1_Silent_p.F309F|EFTUD2_ENST00000402521.3_Silent_p.F274F	NM_001142605.1|NM_001258354.1|NM_004247.3	NP_001136077.1|NP_001245283.1|NP_004238.3	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain containing 2	309	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	32		Prostate(33;0.109)				GGGAGCTGGAGAAGCAGACGT	0.547																																					p.F309F	Ovarian(10;65 485 10258 29980 30707)	Atlas-SNP	.											.	EFTUD2	85	.	0			c.C927T						PASS	.						187	166	174					17																	42949881		2203	4300	6503	SO:0001819	synonymous_variant	9343	exon11			GCTGGAGAAGCAG	D21163	CCDS11489.1, CCDS45707.1, CCDS59295.1	17q21.31	2014-08-12			ENSG00000108883	ENSG00000108883			30858	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 116 kD"	603892				9233818	Standard	NM_004247		Approved	U5-116KD, Snrp116, Snu114, SNRNP116	uc002ihn.2	Q15029	OTTHUMG00000179865	ENST00000426333.2:c.927C>T	chr17.hg19:g.42949881G>A		102.0	0.0	.		162.0	73.0	.	NM_004247	B4DK30|B4DMC0|D3DX58|K7EJ81|Q9BUR0	Silent	SNP	ENST00000426333.2	hg19	CCDS11489.1																																																																																			.	.	.	none		0.547	EFTUD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448672.1	NM_004247		A	42949881	G	A	42949881	2	1	39	1	0	0	0	0	0	0	0	1	4963	933	33	2		2	EFTUD2	17	42949881	Silent	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10	2468096	42949881	38245329	75	2855											
NFE2L1	4779	hgsc.bcm.edu	37	chr17	46128721	46128721	+	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	tggacaattacttcactgccCggcggctcctcagtcaggtg	7	10	11	13	2	3	0	3	0	0	0	4	1	4	1	2	4	2	1	2	4	2	2			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr17:46128721C>A	ENST00000362042.3	+	2	857	c.241C>A	c.(241-243)Cgg>Agg	p.R81R	NFE2L1_ENST00000361665.3_Silent_p.R81R|NFE2L1_ENST00000585291.1_Silent_p.R81R|NFE2L1_ENST00000357480.5_Silent_p.R81R	NM_003204.2	NP_003195.1	Q14494	NF2L1_HUMAN	nuclear factor, erythroid 2-like 1	81					anatomical structure morphogenesis (GO:0009653)|erythrocyte differentiation (GO:0030218)|heme biosynthetic process (GO:0006783)|inflammatory response (GO:0006954)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)			cervix(1)|endometrium(3)|kidney(9)|large_intestine(7)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						CTTCACTGCCCGGCGGCTCCT	0.562																																					p.R81R		Atlas-SNP	.											.	NFE2L1	60	.	0			c.C241A						PASS	.						81	83	82					17																	46128721		2203	4300	6503	SO:0001819	synonymous_variant	4779	exon2			ACTGCCCGGCGGC	AK090459	CCDS11524.1	17q21.3	2013-08-23	2013-08-23			ENSG00000082641		"basic leucine zipper proteins"	7781	protein-coding gene	gene with protein product		163260	"nuclear factor (erythroid-derived 2)-like 1"	TCF11		8248256, 9501099	Standard	NM_003204		Approved	NRF1, LCR-F1, FLJ00380	uc002imz.4	Q14494		ENST00000362042.3:c.241C>A	chr17.hg19:g.46128721C>A		76.0	0.0	.		83.0	32.0	.	NM_003204	D3DTU3|D3DTU5|Q12877|Q96FN6	Silent	SNP	ENST00000362042.3	hg19	CCDS11524.1																																																																																			.	.	.	none		0.562	NFE2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443019.1	NM_003204		A	46128721	C	A	46128721	2	1	39	1	0	0	0	0	0	0	0	1	10374	643	23	4		4	NFE2L1	17	46128721	Silent	SNP	C	TCGA-5P-A9KE-01A-11D-A42J-10	3178840	46128721	35066489	76	2856											
CLTC	1213	hgsc.bcm.edu	37	chr17	57754372	57754372	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgagggctgtgaggagccTgctactcacaatgccttagc	9	9	12	11	0	1	2	1	2	0	0	1	3	1	3	2	2	5	2	2	2	3	2			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr17:57754372T>C	ENST00000269122.3	+	17	2893	c.2619T>C	c.(2617-2619)ccT>ccC	p.P873P	CLTC_ENST00000393043.1_Silent_p.P873P|CLTC_ENST00000579815.1_3'UTR|CLTC_ENST00000579456.1_Intron	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	873	Heavy chain arm.|Proximal segment.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					GTGAGGAGCCTGCTACTCACA	0.428			T	"ALK, TFE3"	"ALCL, renal "																																p.P873P		Atlas-SNP	.		Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	.	CLTC	124	.	0			c.T2619C						PASS	.						59	64	62					17																	57754372		2203	4300	6503	SO:0001819	synonymous_variant	1213	exon17			GGAGCCTGCTACT	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.2619T>C	chr17.hg19:g.57754372T>C		95.0	0.0	.		91.0	34.0	.	NM_004859	D3DU00|Q6N0A0|Q86TF2	Silent	SNP	ENST00000269122.3	hg19	CCDS32696.1																																																																																			.	.	.	none		0.428	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859		C	57754372	T	C	57754372	2	2	39	1	0	0	0	0	0	0	0	1	3568	1567	55	3		3	CLTC	17	57754372	Silent	SNP	T	TCGA-5P-A9KE-01A-11D-A42J-10	11625651	57754372	23440838	77	2857											
ABCA10	10349	hgsc.bcm.edu	37	chr17	67170897	67170897	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggccagaggcctgaaatccAtaactgggattgaacatttt	13	10	10	8	0	0	3	0	2	0	1	1	4	1	4	3	3	2	0	3	3	3	4	rs368716488		TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr17:67170897A>G	ENST00000269081.4	-	25	3808	c.2899T>C	c.(2899-2901)Tgg>Cgg	p.W967R	ABCA10_ENST00000519732.1_Intron|ABCA10_ENST00000416101.2_3'UTR	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	967					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)					CCTGAAATCCATAACTGGGAT	0.348																																					p.W967R		Atlas-SNP	.											.	ABCA10	209	.	0			c.T2899C						PASS	.	A	ARG/TRP	0,4402		0,0,2201	64	70	68		2899	-0.4	0.1	17		68	1,8595		0,1,4297	no	missense	ABCA10	NM_080282.3	101	0,1,6498	GG,GA,AA		0.0116,0.0,0.0077	benign	967/1544	67170897	1,12997	2201	4298	6499	SO:0001583	missense	10349	exon25			AAATCCATAACTG	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.2899T>C	chr17.hg19:g.67170897A>G	ENSP00000269081:p.Trp967Arg	187.0	0.0	.		236.0	57.0	.	NM_080282	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Missense_Mutation	SNP	ENST00000269081.4	hg19	CCDS11684.1	.	.	.	.	.	.	.	.	.	.	A	0.006	-2.075060	0.00379	0.0	1.16E-4	ENSG00000154263	ENST00000269081	T	0.80738	-1.41	3.3	-0.428	0.12306	.	.	.	.	.	T	0.50411	0.1614	N	0.03608	-0.345	0.24933	N	0.99191	B	0.10296	0.003	B	0.15484	0.013	T	0.39333	-0.9619	9	0.07030	T	0.85	.	3.54	0.07807	0.2691:0.0:0.2278:0.5031	.	967	Q8WWZ4	ABCAA_HUMAN	R	967	ENSP00000269081:W967R	ENSP00000269081:W967R	W	-	1	0	ABCA10	64682492	0.000000	0.05858	0.063000	0.19743	0.677000	0.39632	-1.398000	0.02509	-0.357000	0.08175	0.334000	0.21626	TGG	.	.	.	weak		0.348	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282		G	67170897	A	G	67170897	3	3	39	1	0	0	0	0	1	0	0	0	29	217	8	3	1796	3	ABCA10	17	67170897	Missense_Mutation	SNP	A	TCGA-5P-A9KE-01A-11D-A42J-10	9416525	67170897	14024313	78	2858											
DCC	1630	hgsc.bcm.edu	37	chr18	50432459	50432459	+	Missense_Mutation	SNP	T	T	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	agaatctgtcacagccttcaTgggagacacagtgctactca	12	9	9	11	0	4	2	3	0	1	2	4	3	4	2	1	1	3	1	1	1	2	2			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr18:50432459T>G	ENST00000442544.2	+	3	1074	c.458T>G	c.(457-459)aTg>aGg	p.M153R	DCC_ENST00000412726.1_Start_Codon_SNP_p.M1R	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	153	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)		ACAGCCTTCATGGGAGACACA	0.463																																					p.M153R		Atlas-SNP	.											.	DCC	360	.	0			c.T458G						PASS	.						95	89	91					18																	50432459		2203	4300	6503	SO:0001583	missense	1630	exon3			CCTTCATGGGAGA	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.458T>G	chr18.hg19:g.50432459T>G	ENSP00000389140:p.Met153Arg	74.0	0.0	.		46.0	13.0	.	NM_005215		Missense_Mutation	SNP	ENST00000442544.2	hg19	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	T	15.71	2.912913	0.52439	.	.	ENSG00000187323	ENST00000442544;ENST00000304775;ENST00000412726	T;T	0.55760	1.16;0.5	5.71	5.71	0.89125	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.064022	0.64402	D	0.000003	T	0.26593	0.0650	N	0.04387	-0.21	0.80722	D	1	B;B	0.18968	0.032;0.001	B;B	0.15052	0.012;0.001	T	0.19549	-1.0302	10	0.10111	T	0.7	.	9.9749	0.41777	0.0:0.0792:0.0:0.9208	.	1;153	E7EQM8;P43146	.;DCC_HUMAN	R	153;86;1	ENSP00000389140:M153R;ENSP00000397322:M1R	ENSP00000304146:M86R	M	+	2	0	DCC	48686457	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.352000	0.59404	2.171000	0.68590	0.533000	0.62120	ATG	.	.	.	none		0.463	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		G	50432459	T	G	50432459	3	3	39	1	0	0	0	0	1	0	0	0	4284	1464	51	5	468	5	DCC	18	50432459	Missense_Mutation	SNP	T	TCGA-5P-A9KE-01A-11D-A42J-10		50432459	27644789	79	2859											
TNFRSF11A	8792	hgsc.bcm.edu	37	chr18	60017119	60017119	+	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	gtggcccggatgaatacttgGatagctggaatgaagaagat	13	9	14	5	1	0	4	0	2	0	2	0	7	0	7	1	4	2	1	1	4	6	3			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr18:60017119G>C	ENST00000586569.1	+	3	270	c.232G>C	c.(232-234)Gat>Cat	p.D78H	TNFRSF11A_ENST00000269485.7_Missense_Mutation_p.D78H	NM_001270949.1|NM_003839.3	NP_001257878.1|NP_003830.1	Q9Y6Q6	TNR11_HUMAN	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	78					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)				TGAATACTTGGATAGCTGGAA	0.438																																					p.D78H		Atlas-SNP	.											.	TNFRSF11A	51	.	0			c.G232C						PASS	.						195	184	188					18																	60017119		2203	4300	6503	SO:0001583	missense	8792	exon3			TACTTGGATAGCT	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.232G>C	chr18.hg19:g.60017119G>C	ENSP00000465500:p.Asp78His	45.0	0.0	.		56.0	21.0	.	NM_001270951	I4EC36|I4EC38|I4EC39|I7JE63|N0GVH0|Q59EP9	Missense_Mutation	SNP	ENST00000586569.1	hg19	CCDS11980.1	.	.	.	.	.	.	.	.	.	.	G	12.81	2.048412	0.36181	.	.	ENSG00000141655	ENST00000382790;ENST00000269485	T	0.72051	-0.62	5.33	4.4	0.53042	TNFR/CD27/30/40/95 cysteine-rich region (1);	0.160278	0.56097	D	0.000040	T	0.63022	0.2476	L	0.55103	1.725	0.34410	D	0.696278	B;B	0.31752	0.338;0.272	B;B	0.26864	0.065;0.074	T	0.70332	-0.4901	9	.	.	.	-22.1742	13.9329	0.64007	0.0:0.1522:0.8478:0.0	.	100;78	Q59EP9;Q9Y6Q6	.;TNR11_HUMAN	H	100;78	ENSP00000269485:D78H	.	D	+	1	0	TNFRSF11A	58168099	1.000000	0.71417	1.000000	0.80357	0.684000	0.39900	3.139000	0.50577	2.646000	0.89796	0.462000	0.41574	GAT	.	.	.	none		0.438	TNFRSF11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256186.2			C	60017119	G	C	60017119	3	2	39	1	0	0	0	0	1	0	0	0	16296	1174	41	4	242	4	TNFRSF11A	18	60017119	Missense_Mutation	SNP	G	TCGA-5P-A9KE-01A-11D-A42J-10	9584660	60017119	18060129	80	2860											
ZNF557	79230	hgsc.bcm.edu	37	chr19	7083714	7083714	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatccttcacaagtaactccTacctttctgtgcatacgaga	12	12	5	12	1	2	1	1	0	1	1	4	2	4	1	3	0	4	2	3	0	5	5			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr19:7083714T>C	ENST00000439035.2	+	8	1471	c.1231T>C	c.(1231-1233)Tac>Cac	p.Y411H	ZNF557_ENST00000414706.1_Missense_Mutation_p.Y418H|ZNF557_ENST00000252840.6_Missense_Mutation_p.Y418H			Q8N988	ZN557_HUMAN	zinc finger protein 557	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(6)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17				Lung(535;0.179)		AAGTAACTCCTACCTTTCTGT	0.368																																					p.Y418H		Atlas-SNP	.											.	ZNF557	40	.	0			c.T1252C						PASS	.						90	92	91					19																	7083714		2174	4284	6458	SO:0001583	missense	79230	exon8			AACTCCTACCTTT	AK095524	CCDS42485.1, CCDS45945.1	19p13.2	2013-09-20			ENSG00000130544	ENSG00000130544		"Zinc fingers, C2H2-type", "-"	28632	protein-coding gene	gene with protein product						12477932	Standard	NM_024341		Approved	MGC4054	uc002mgc.3	Q8N988	OTTHUMG00000181977	ENST00000439035.2:c.1231T>C	chr19.hg19:g.7083714T>C	ENSP00000398965:p.Tyr411His	214.0	0.0	.		171.0	37.0	.	NM_001044387	Q6PEJ3|Q9BTZ1	Missense_Mutation	SNP	ENST00000439035.2	hg19	CCDS45945.1	.	.	.	.	.	.	.	.	.	.	T	5.054	0.195550	0.09599	.	.	ENSG00000130544	ENST00000252840;ENST00000414706;ENST00000439035	T;T;T	0.07444	3.19;3.19;3.19	0.994	-0.105	0.13601	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03608	0.0103	N	0.16790	0.44	0.09310	N	1	B;B	0.15473	0.007;0.013	B;B	0.09377	0.002;0.004	T	0.46803	-0.9165	9	0.10377	T	0.69	.	2.0833	0.03640	0.2944:0.0:0.2971:0.4085	.	411;418	Q8N988;Q8N988-2	ZN557_HUMAN;.	H	418;418;411	ENSP00000252840:Y418H;ENSP00000404065:Y418H;ENSP00000398965:Y411H	ENSP00000252840:Y418H	Y	+	1	0	ZNF557	7034714	0.000000	0.05858	0.064000	0.19789	0.002000	0.02628	-3.017000	0.00644	-0.106000	0.12110	-0.991000	0.02546	TAC	.	.	.	none		0.368	ZNF557-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458502.1	NM_024341		C	7083714	T	C	7083714	3	2	39	1	0	0	0	0	1	0	0	0	18000	1522	53	3	1274	3	ZNF557	19	7083714	Missense_Mutation	SNP	T	TCGA-5P-A9KE-01A-11D-A42J-10		7083714	52045269	81	2861											
KEAP1	9817	hgsc.bcm.edu	37	chr19	10602767	10602767	+	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	cgtcaacgagtggcagcgcaCggcccgcagcagcgcctgga	8	3	15	15	6	1	0	1	0	0	0	1	2	1	1	2	3	4	4	2	3	1	0			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr19:10602767C>A	ENST00000171111.5	-	3	1358	c.811G>T	c.(811-813)Gtg>Ttg	p.V271L	CTC-429L19.3_ENST00000592671.1_RNA|KEAP1_ENST00000588024.1_5'UTR|KEAP1_ENST00000393623.2_Missense_Mutation_p.V271L	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	271	BACK.				cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	TGGCAGCGCACGGCCCGCAGC	0.617																																					p.V271L		Atlas-SNP	.											KEAP1,right_upper_lobe,carcinoma,0,1	KEAP1	182	.	0			c.G811T						PASS	.						57	57	57					19																	10602767		2203	4300	6503	SO:0001583	missense	9817	exon3			AGCGCACGGCCCG	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"Kelch-like", "BTB/POZ domain containing"	23177	protein-coding gene	gene with protein product	"kelch-like family member 19"	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.811G>T	chr19.hg19:g.10602767C>A	ENSP00000171111:p.Val271Leu	53.0	0.0	.		47.0	12.0	.	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Missense_Mutation	SNP	ENST00000171111.5	hg19	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	C	33	5.208480	0.95069	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	T;T	0.76316	-1.01;-1.01	5.61	5.61	0.85477	BTB/Kelch-associated (2);	0.056422	0.64402	N	0.000001	D	0.84897	0.5574	M	0.82630	2.6	0.80722	D	1	P	0.52170	0.951	P	0.50270	0.636	D	0.87391	0.2363	10	0.87932	D	0	.	17.1459	0.86766	0.0:1.0:0.0:0.0	.	271	Q14145	KEAP1_HUMAN	L	271	ENSP00000171111:V271L;ENSP00000377245:V271L	ENSP00000171111:V271L	V	-	1	0	KEAP1	10463767	1.000000	0.71417	0.997000	0.53966	0.942000	0.58702	5.874000	0.69652	2.656000	0.90262	0.561000	0.74099	GTG	.	.	.	none		0.617	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		A	10602767	C	A	10602767	3	1	39	1	0	0	0	0	1	0	0	0	8148	536	19	4	1079	4	KEAP1	19	10602767	Missense_Mutation	SNP	C	TCGA-5P-A9KE-01A-11D-A42J-10	3519053	10602767	48526216	82	2862											
IL17RA	23765	hgsc.bcm.edu	37	chr22	17590035	17590035	+	Missense_Mutation	SNP	A	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	gacccgctggtcggggaggaAggaggagcagcagtggcaaa	11	3	19	8	2	0	0	0	0	0	0	1	5	0	4	1	7	2	4	1	7	2	0			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr22:17590035A>C	ENST00000319363.6	+	13	2059	c.1926A>C	c.(1924-1926)gaA>gaC	p.E642D		NM_014339.5	NP_055154.3	Q96F46	I17RA_HUMAN	interleukin 17 receptor A	642					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)		TCGGGGAGGAAGGAGGAGCAG	0.721																																					p.E642D		Atlas-SNP	.											.	IL17RA	62	.	0			c.A1926C						PASS	.						4	4	4					22																	17590035		2040	4043	6083	SO:0001583	missense	23765	exon13			GGAGGAAGGAGGA	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.1926A>C	chr22.hg19:g.17590035A>C	ENSP00000320936:p.Glu642Asp	404.0	1.0	.		423.0	106.0	.	NM_014339	O43844|Q20WK1	Missense_Mutation	SNP	ENST00000319363.6	hg19	CCDS13739.1	.	.	.	.	.	.	.	.	.	.	A	15.77	2.932763	0.52866	.	.	ENSG00000177663	ENST00000425985;ENST00000319363	T	0.07800	3.16	4.89	1.27	0.21489	.	0.945953	0.08934	N	0.872522	T	0.10380	0.0254	M	0.70595	2.14	0.09310	N	1	P;P	0.47106	0.651;0.89	B;B	0.42625	0.115;0.393	T	0.27872	-1.0061	10	0.46703	T	0.11	-3.6798	1.3359	0.02145	0.4246:0.2756:0.0927:0.2071	.	590;642	D3YTB4;Q96F46	.;I17RA_HUMAN	D	590;642	ENSP00000320936:E642D	ENSP00000320936:E642D	E	+	3	2	IL17RA	15970035	0.024000	0.19004	0.004000	0.12327	0.011000	0.07611	0.018000	0.13422	0.301000	0.22738	0.459000	0.35465	GAA	.	.	.	none		0.721	IL17RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315820.1	NM_014339		C	17590035	A	C	17590035	3	2	39	1	0	0	0	0	1	0	0	0	7646	69	3	5	1976	5	IL17RA	22	17590035	Missense_Mutation	SNP	A	TCGA-5P-A9KE-01A-11D-A42J-10		17590035	33714531	83	2863											
MICAL3	57553	hgsc.bcm.edu	37	chr22	18300493	18300493	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtgggggagtcaggccggCgctccttgccctgggagggt	3	8	20	10	2	1	0	1	0	0	0	2	2	2	2	3	6	1	1	3	6	0	1	rs369106641		TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr22:18300493C>T	ENST00000441493.2	-	26	5286	c.4934G>A	c.(4933-4935)cGc>cAc	p.R1645H	MICAL3_ENST00000580469.1_5'Flank	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	1645					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)		GTCAGGCCGGCGCTCCTTGCC	0.711																																					p.R1645H		Atlas-SNP	.											.	MICAL3	53	.	0			c.G4934A						PASS	.	C	HIS/ARG	0,3844		0,0,1922	15	19	18		4934	-3.4	0	22		18	1,8197		0,1,4098	no	missense	MICAL3	NM_015241.2	29	0,1,6020	TT,TC,CC		0.0122,0.0,0.0083	benign	1645/2003	18300493	1,12041	1922	4099	6021	SO:0001583	missense	57553	exon26			GGCCGGCGCTCCT	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.4934G>A	chr22.hg19:g.18300493C>T	ENSP00000416015:p.Arg1645His	32.0	0.0	.		40.0	7.0	.	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Missense_Mutation	SNP	ENST00000441493.2	hg19	CCDS46659.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	4.047|4.047	0.006384|0.006384	0.07866|0.07866	0.0|0.0	1.22E-4|1.22E-4	ENSG00000093100|ENSG00000093100	ENST00000252134|ENST00000441493	.|T	.|0.62232	.|0.04	4.65|4.65	-3.39|-3.39	0.04868|0.04868	.|.	.|2.091240	.|0.02041	.|N	.|0.049305	T|T	0.37652|0.37652	0.1011|0.1011	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.13045|0.13045	-1.0524|-1.0524	5|10	.|0.44086	.|T	.|0.13	.|.	2.5643|2.5643	0.04779|0.04779	0.2761:0.3993:0.2159:0.1087|0.2761:0.3993:0.2159:0.1087	.|.	.|1645	.|Q7RTP6	.|MICA3_HUMAN	T|H	627|1645	.|ENSP00000416015:R1645H	.|ENSP00000416015:R1645H	A|R	-|-	1|2	0|0	XXbac-B461K10.4|XXbac-B461K10.4	16680493|16680493	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.055000|0.055000	0.15305|0.15305	0.227000|0.227000	0.17795|0.17795	-0.871000|-0.871000	0.04042|0.04042	-0.291000|-0.291000	0.09656|0.09656	GCC|CGC	.	.	.	weak		0.711	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			T	18300493	C	T	18300493	3	4	39	1	0	0	0	0	1	0	0	0	9578	768	27	1	1102	1	MICAL3	22	18300493	Missense_Mutation	SNP	C	TCGA-5P-A9KE-01A-11D-A42J-10	710458	18300493	33004073	84	2864											
PPIL2	23759	hgsc.bcm.edu	37	chr22	22024222	22024222	+	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	gtacattacctgtgctgaatAcactcacttttatggtggca	10	14	8	9	0	1	1	1	1	0	0	1	1	1	1	1	2	4	3	1	2	5	5			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr22:22024222A>T	ENST00000335025.8	+	2	144	c.53A>T	c.(52-54)tAc>tTc	p.Y18F	PPIL2_ENST00000406385.1_Missense_Mutation_p.Y18F|PPIL2_ENST00000398831.3_Missense_Mutation_p.Y18F|PPIL2_ENST00000492445.2_Missense_Mutation_p.Y18F|PPIL2_ENST00000412327.1_Missense_Mutation_p.Y18F|PPIL2_ENST00000456792.2_Missense_Mutation_p.Y18F					peptidylprolyl isomerase (cyclophilin)-like 2											endometrium(4)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	17	Colorectal(54;0.105)					TGTGCTGAATACACTCACTTT	0.448																																					p.Y18F		Atlas-SNP	.											.	PPIL2	38	.	0			c.A53T						PASS	.						199	161	174					22																	22024222		2203	4300	6503	SO:0001583	missense	23759	exon2			CTGAATACACTCA		CCDS13793.1	22q11.21	2013-01-29			ENSG00000100023	ENSG00000100023		"U-box domain containing"	9261	protein-coding gene	gene with protein product	"U-box domain containing 7"	607588				10591208	Standard	NM_014337		Approved	UBOX7, CYC4, Cyp-60	uc002zvh.4	Q13356	OTTHUMG00000030174	ENST00000335025.8:c.53A>T	chr22.hg19:g.22024222A>T	ENSP00000334553:p.Tyr18Phe	73.0	0.0	.		82.0	4.0	.	NM_014337		Missense_Mutation	SNP	ENST00000335025.8	hg19	CCDS13793.1	.	.	.	.	.	.	.	.	.	.	A	17.87	3.494928	0.64186	.	.	ENSG00000100023	ENST00000412327;ENST00000335025;ENST00000398831;ENST00000492445;ENST00000458567;ENST00000406385;ENST00000456792	T;T;T;T;T;T	0.28454	1.66;1.7;1.7;1.7;1.7;1.61	4.39	4.39	0.52855	.	0.071138	0.64402	D	0.000017	T	0.34890	0.0913	L	0.59436	1.845	0.50632	D	0.999883	P;P;P	0.47409	0.61;0.868;0.895	B;P;B	0.46299	0.219;0.511;0.313	T	0.22591	-1.0212	10	0.87932	D	0	.	10.2502	0.43364	1.0:0.0:0.0:0.0	.	18;18;18	E7EW80;Q13356-2;Q13356	.;.;PPIL2_HUMAN	F	18;18;18;18;49;18;18	ENSP00000390427:Y18F;ENSP00000334553:Y18F;ENSP00000381812:Y18F;ENSP00000445312:Y18F;ENSP00000384299:Y18F;ENSP00000396228:Y18F	ENSP00000334553:Y18F	Y	+	2	0	PPIL2	20354222	1.000000	0.71417	0.999000	0.59377	0.975000	0.68041	4.011000	0.57124	1.974000	0.57490	0.456000	0.33151	TAC	.	.	.	none		0.448	PPIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075028.4			T	22024222	A	T	22024222	3	4	39	1	0	0	0	0	1	0	0	0	12337	391	14	5	59	5	PPIL2	22	22024222	Missense_Mutation	SNP	A	TCGA-5P-A9KE-01A-11D-A42J-10	3723729	22024222	29280344	85	2865											
MN1	4330	hgsc.bcm.edu	37	chr22	28193956	28193956	+	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	cggtctcgttctggctcagtTtcctcttgccctctggcggg	1	14	12	14	3	5	0	1	0	4	0	7	0	6	0	2	4	1	3	2	4	0	3			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr22:28193956T>A	ENST00000302326.4	-	1	3530	c.2576A>T	c.(2575-2577)aAa>aTa	p.K859I		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	859					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						CTGGCTCAGTTTCCTCTTGCC	0.662			T	ETV6	"AML, meningioma"																																p.K859I		Atlas-SNP	.		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"L, O"	.	MN1	122	.	0			c.A2576T						PASS	.						68	74	72					22																	28193956		1884	4092	5976	SO:0001583	missense	4330	exon1			CTCAGTTTCCTCT	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.2576A>T	chr22.hg19:g.28193956T>A	ENSP00000304956:p.Lys859Ile	35.0	0.0	.		34.0	11.0	.	NM_002430	A9Z1V9	Missense_Mutation	SNP	ENST00000302326.4	hg19	CCDS42998.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.966868	0.74131	.	.	ENSG00000169184	ENST00000302326	T	0.60920	0.15	3.74	3.74	0.42951	.	0.064498	0.64402	D	0.000019	T	0.61912	0.2385	L	0.29908	0.895	0.47862	D	0.99953	D	0.76494	0.999	D	0.87578	0.998	T	0.59306	-0.7479	10	0.33141	T	0.24	0.0091	11.4387	0.50083	0.0:0.0:0.0:1.0	.	859	Q10571	MN1_HUMAN	I	859	ENSP00000304956:K859I	ENSP00000304956:K859I	K	-	2	0	MN1	26523956	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.044000	0.64214	1.567000	0.49668	0.379000	0.24179	AAA	.	.	.	none		0.662	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430		A	28193956	T	A	28193956	3	1	39	1	0	0	0	0	1	0	0	0	9680	1841	64	5	1394	5	MN1	22	28193956	Missense_Mutation	SNP	T	TCGA-5P-A9KE-01A-11D-A42J-10	6169734	28193956	23110610	86	2866											
EMID1	129080	hgsc.bcm.edu	37	chr22	29628294	29628294	+	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	cgggctggagctgtgggcacCcctggagagaggggacctcc	6	5	18	12	1	0	1	0	0	0	1	1	5	1	4	4	6	1	3	4	6	0	0			TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chr22:29628294C>A	ENST00000404820.3	+	8	853	c.726C>A	c.(724-726)acC>acA	p.T242T	EMID1_ENST00000484039.1_3'UTR|EMID1_ENST00000334018.6_Silent_p.T242T|EMID1_ENST00000404755.3_Silent_p.T242T			Q96A84	EMID1_HUMAN	EMI domain containing 1	240	Collagen-like.					collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(2)|skin(3)	12						CTGTGGGCACCCCTGGAGAGA	0.697																																					p.T242T		Atlas-SNP	.											.	EMID1	33	.	0			c.C726A						PASS	.						16	20	19					22																	29628294		2181	4257	6438	SO:0001819	synonymous_variant	129080	exon8			GGGCACCCCTGGA	AJ416090	CCDS33630.1	22q12.2	2009-08-04			ENSG00000186998	ENSG00000186998		"EMI domain containing"	18036	protein-coding gene	gene with protein product	"emilin and multimerin-domain containing protein 1", "putative emu1"	608926				12221002	Standard	NM_001267895		Approved	EMU1, hEmu1, EMI5	uc003aem.4	Q96A84	OTTHUMG00000151013	ENST00000404820.3:c.726C>A	chr22.hg19:g.29628294C>A		160.0	0.0	.		158.0	56.0	.	NM_133455	B0QYK6|Q6ICG1|Q86SS7	Silent	SNP	ENST00000404820.3	hg19		.	.	.	.	.	.	.	.	.	.	C	6.566	0.472782	0.12461	.	.	ENSG00000186998	ENST00000433143	.	.	.	4.12	0.833	0.18875	.	.	.	.	.	T	0.51635	0.1686	.	.	.	0.52501	D	0.999958	.	.	.	.	.	.	T	0.40831	-0.9542	4	.	.	.	-0.3746	5.7145	0.17952	0.0:0.6496:0.0:0.3504	.	.	.	.	H	105	.	.	P	+	2	0	EMID1	27958294	0.171000	0.23029	0.523000	0.27875	0.749000	0.42624	0.362000	0.20284	0.466000	0.27193	0.555000	0.69702	CCC	.	.	.	none		0.697	EMID1-002	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321075.1	NM_133455		A	29628294	C	A	29628294	2	1	39	1	0	0	0	0	0	0	0	1	5093	610	22	4		4	EMID1	22	29628294	Silent	SNP	C	TCGA-5P-A9KE-01A-11D-A42J-10	1434338	29628294	21676272	87	2867											
KDM6A	7403	hgsc.bcm.edu	37	chrX	44929004	44929005	+	Frame_Shift_Ins	INS	-	-	A																															tctcaatcacctctcctctcINSacactgctacctcaggtgga																										TCGA-5P-A9KE-01A-11D-A42J-10	TCGA-5P-A9KE-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bbd6f0f2-a322-4772-8c98-3594288fbf8d	f4097292-72af-4234-b9af-3cdcbb8333b2	g.chrX:44929004_44929005insA	ENST00000377967.4	+	17	2145_2146	c.2104_2105insA	c.(2104-2106)cacfs	p.H702fs	KDM6A_ENST00000382899.4_Frame_Shift_Ins_p.H709fs|KDM6A_ENST00000536777.1_Frame_Shift_Ins_p.H657fs|KDM6A_ENST00000543216.1_Frame_Shift_Ins_p.H623fs	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	702	Interaction with SUPT6H. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0?(6)|p.H702fs*28(1)		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						CCTCTCCTCTCACACTGCTACC	0.515			"D, N, F, S"		"renal, oesophageal SCC, MM"																																p.H702fs	Colon(129;1273 1667 15230 27352 52914)	Atlas-Indel,Pindel	.		Rec	yes		X	Xp11.2	7403	"lysine (K)-specific demethylase 6A, UTX"		"E, L"	.	KDM6A	274	.	7	Whole gene deletion(6)|Insertion - Frameshift(1)	oesophagus(2)|breast(2)|pancreas(2)|urinary_tract(1)	c.2104_2105insA						PASS	.																																			SO:0001589	frameshift_variant	7403	exon17			.	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.2105dupA	chrX.hg19:g.44929005_44929005dupA	ENSP00000367203:p.His702fs	98.0	0.0	0		81.0	49.0	0.604938	NM_021140	Q52LL9|Q5JVQ7	Frame_Shift_Ins	INS	ENST00000377967.4	hg19	CCDS14265.1																																																																																			.	.	.	none		0.515	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140		A	44929005	-	A	44929004	7	5	39	1	0	1	1	0	0	0	0	0	8144	826	29	0	2170	0	KDM6A	23	44929004	Frame_Shift_Ins	INS	-	TCGA-5P-A9KE-01A-11D-A42J-10		44929004	110341556	88	2868											
HMCN1	83872	hgsc.bcm.edu	37	chr1	186114982	186114982	+	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	cggctgtgcgaccatcctgtGccagttaaaggtggccgtcc	6	9	13	13	3	0	0	0	0	0	0	2	1	2	0	5	3	2	2	5	3	2	1			TCGA-5P-A9KH-01A-11D-A42J-10	TCGA-5P-A9KH-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d91e36f3-e4a2-4af3-802a-3148b09be900	ccc45b0a-b066-47dd-934b-6f892b6c61a4	g.chr1:186114982G>T	ENST00000271588.4	+	93	14764	c.14535G>T	c.(14533-14535)gtG>gtT	p.V4845V	HMCN1_ENST00000367492.2_Silent_p.V4845V	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4845	TSP type-1 6. {ECO:0000255|PROSITE- ProRule:PRU00210}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						ACCATCCTGTGCCAGTTAAAG	0.547																																					p.V4845V		Atlas-SNP	.											.	HMCN1	797	.	0			c.G14535T						PASS	.						82	71	75					1																	186114982		2203	4300	6503	SO:0001819	synonymous_variant	83872	exon93			TCCTGTGCCAGTT	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.14535G>T	chr1.hg19:g.186114982G>T		112.0	0.0	.		88.0	63.0	.	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.	.	none		0.547	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		T	186114982	G	T	186114982	2	4	40	1	0	0	0	0	0	0	0	1	7227	1306	46	4		4	HMCN1	1	186114982	Silent	SNP	G	TCGA-5P-A9KH-01A-11D-A42J-10		186114982	63135639	1	2869											
CCDC74A	90557	hgsc.bcm.edu	37	chr2	132289289	132289289	+	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	aagcaagattcaaaagctgaCgtctcccagaaggcggacct	14	6	10	11	2	2	3	1	1	1	2	3	4	2	4	2	2	2	2	2	2	5	1			TCGA-5P-A9KH-01A-11D-A42J-10	TCGA-5P-A9KH-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d91e36f3-e4a2-4af3-802a-3148b09be900	ccc45b0a-b066-47dd-934b-6f892b6c61a4	g.chr2:132289289C>T	ENST00000295171.6	+	4	735	c.597C>T	c.(595-597)gaC>gaT	p.D199D	CCDC74A_ENST00000467992.2_Silent_p.D301D|CCDC74A_ENST00000409856.3_Silent_p.D133D	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	199										endometrium(4)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						CAAAAGCTGACGTCTCCCAGA	0.587																																					p.D241D		Atlas-SNP	.											.	CCDC74A	44	.	0			c.C723T						PASS	.						54	94	81					2																	132289289		1850	4189	6039	SO:0001819	synonymous_variant	90557	exon4			AGCTGACGTCTCC		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.597C>T	chr2.hg19:g.132289289C>T		113.0	0.0	.		69.0	42.0	.	NM_001258304	Q6P4I5	Silent	SNP	ENST00000295171.6	hg19	CCDS2167.1																																																																																			.	.	.	none		0.587	CCDC74A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254570.2	NM_138770		T	132289289	C	T	132289289	2	4	40	1	0	0	0	0	0	0	0	1	2849	535	19	1		1	CCDC74A	2	132289289	Silent	SNP	C	TCGA-5P-A9KH-01A-11D-A42J-10		132289289	110910084	2	2870											
SEL1L3	23231	hgsc.bcm.edu	37	chr4	25834646	25834646	+	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	gttaaaagagatatccagtcGaaaccactccttcaaaggta	16	9	7	9	1	1	1	1	0	0	1	4	3	3	1	3	1	1	2	3	1	6	4			TCGA-5P-A9KH-01A-11D-A42J-10	TCGA-5P-A9KH-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d91e36f3-e4a2-4af3-802a-3148b09be900	ccc45b0a-b066-47dd-934b-6f892b6c61a4	g.chr4:25834646G>A	ENST00000399878.3	-	5	1191	c.1069C>T	c.(1069-1071)Cga>Tga	p.R357*	SEL1L3_ENST00000502949.1_Nonsense_Mutation_p.R204*|SEL1L3_ENST00000264868.5_Nonsense_Mutation_p.R322*|SEL1L3_ENST00000513364.1_5'Flank	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	357						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						ATATCCAGTCGAAACCACTCC	0.393																																					p.R357X		Atlas-SNP	.											.	SEL1L3	62	.	0			c.C1069T						PASS	.						106	105	106					4																	25834646		1926	4139	6065	SO:0001587	stop_gained	23231	exon5			CCAGTCGAAACCA	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.1069C>T	chr4.hg19:g.25834646G>A	ENSP00000382767:p.Arg357*	51.0	0.0	.		91.0	39.0	.	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Nonsense_Mutation	SNP	ENST00000399878.3	hg19	CCDS47037.1	.	.	.	.	.	.	.	.	.	.	G	36	5.924911	0.97110	.	.	ENSG00000091490	ENST00000399878;ENST00000264868;ENST00000502949	.	.	.	6.03	3.32	0.38043	.	0.057213	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.4793	7.9475	0.29995	0.0738:0.0:0.6407:0.2855	.	.	.	.	X	357;322;204	.	ENSP00000264868:R322X	R	-	1	2	SEL1L3	25443744	1.000000	0.71417	0.635000	0.29338	0.929000	0.56500	2.981000	0.49329	0.404000	0.25506	0.655000	0.94253	CGA	.	.	.	none		0.393	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187		A	25834646	G	A	25834646	4	1	40	1	0	0	0	0	0	1	0	0	14025	1066	37	1	2409	1	SEL1L3	4	25834646	Nonsense_Mutation	SNP	G	TCGA-5P-A9KH-01A-11D-A42J-10		25834646	165319630	3	2871											
GABRB2	2561	hgsc.bcm.edu	37	chr5	160973398	160973398	+	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	accgtctctttaaccagcgaCatattactagggtcattgac	11	12	7	11	2	2	1	1	1	1	0	3	2	2	1	2	1	3	0	2	1	4	6			TCGA-5P-A9KH-01A-11D-A42J-10	TCGA-5P-A9KH-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d91e36f3-e4a2-4af3-802a-3148b09be900	ccc45b0a-b066-47dd-934b-6f892b6c61a4	g.chr5:160973398C>T	ENST00000393959.1	-	2	98	c.99G>A	c.(97-99)atG>atA	p.M33I	GABRB2_ENST00000520240.1_Missense_Mutation_p.M33I|GABRB2_ENST00000523730.1_5'Flank|GABRB2_ENST00000353437.6_Missense_Mutation_p.M33I|GABRB2_ENST00000517547.1_Intron|GABRB2_ENST00000517901.1_Intron|GABRB2_ENST00000274547.2_Missense_Mutation_p.M33I			P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 2	33					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|GABA-A receptor activity (GO:0004890)|inhibitory extracellular ligand-gated ion channel activity (GO:0005237)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(9)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	26	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TAACCAGCGACATATTACTAG	0.433																																					p.M33I		Atlas-SNP	.											.	GABRB2	161	.	0			c.G99A						PASS	.						84	77	80					5																	160973398		2203	4300	6503	SO:0001583	missense	2561	exon3			CAGCGACATATTA		CCDS4354.1, CCDS4355.1	5q34	2012-06-22			ENSG00000145864	ENSG00000145864		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4082	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 2"	600232				7851879	Standard	NM_000813		Approved		uc003lys.1	P47870	OTTHUMG00000130349	ENST00000393959.1:c.99G>A	chr5.hg19:g.160973398C>T	ENSP00000377531:p.Met33Ile	104.0	0.0	.		137.0	19.0	.	NM_021911	A8K115|A8K1A0|D1LYT0|D1LYT1|Q16323|Q4FZB2	Missense_Mutation	SNP	ENST00000393959.1	hg19	CCDS4355.1	.	.	.	.	.	.	.	.	.	.	C	17.20	3.329800	0.60743	.	.	ENSG00000145864	ENST00000393959;ENST00000274547;ENST00000353437;ENST00000520240	T;T;T;T	0.79247	-1.24;-1.24;-1.25;-1.25	5.63	5.63	0.86233	.	0.037933	0.85682	D	0.000000	T	0.66665	0.2812	N	0.19112	0.55	0.80722	D	1	B;P;B	0.37985	0.007;0.613;0.003	B;B;B	0.38264	0.013;0.269;0.03	T	0.63756	-0.6565	10	0.10902	T	0.67	.	19.6807	0.95962	0.0:1.0:0.0:0.0	.	33;33;33	B7Z4P0;P47870;P47870-1	.;GBRB2_HUMAN;.	I	33	ENSP00000377531:M33I;ENSP00000274547:M33I;ENSP00000274546:M33I;ENSP00000429320:M33I	ENSP00000274547:M33I	M	-	3	0	GABRB2	160905976	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.726000	0.84824	2.653000	0.90120	0.650000	0.86243	ATG	.	.	.	none		0.433	GABRB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252704.1			T	160973398	C	T	160973398	3	4	40	1	0	0	0	0	1	0	0	0	6174	478	17	2	1475	2	GABRB2	5	160973398	Missense_Mutation	SNP	C	TCGA-5P-A9KH-01A-11D-A42J-10		160973398	19941862	4	2872											
FAM46A	55603	hgsc.bcm.edu	37	chr6	82461742	82461742	+	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	ccgccaccgccgaagtcgccGccgccgaagtcgccgccgcc	5	2	12	22	10	0	0	0	0	0	0	2	2	0	0	10	0	0	0	10	0	2	0			TCGA-5P-A9KH-01A-11D-A42J-10	TCGA-5P-A9KH-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d91e36f3-e4a2-4af3-802a-3148b09be900	ccc45b0a-b066-47dd-934b-6f892b6c61a4	g.chr6:82461742G>A	ENST00000320172.6	-	2	431	c.117C>T	c.(115-117)ggC>ggT	p.G39G	FAM46A_ENST00000369756.3_Silent_p.G120G|FAM46A_ENST00000369754.3_Silent_p.G58G	NM_017633.2	NP_060103.2	Q96IP4	FA46A_HUMAN	family with sequence similarity 46, member A	39			Missing. {ECO:0000269|PubMed:12054608, ECO:0000269|PubMed:16545789}.		regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)		poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	12		all_cancers(76;6.74e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000282)|all_epithelial(107;0.0104)		BRCA - Breast invasive adenocarcinoma(397;0.0428)		cgaagtcgccgccgccgaagt	0.667																																					p.G39G		Atlas-SNP	.											.	FAM46A	37	.	0			c.C117T						PASS	.						7	8	8					6																	82461742		1601	3424	5025	SO:0001819	synonymous_variant	55603	exon2			GTCGCCGCCGCCG	AF350451	CCDS34489.1	6q14	2008-07-03	2004-08-19	2004-08-26	ENSG00000112773	ENSG00000112773			18345	protein-coding gene	gene with protein product		611357	"chromosome 6 open reading frame 37"	C6orf37		12054608, 17803723	Standard	NM_017633		Approved	FLJ20037	uc003pjg.3	Q96IP4	OTTHUMG00000015097	ENST00000320172.6:c.117C>T	chr6.hg19:g.82461742G>A		38.0	0.0	.		30.0	5.0	.	NM_017633	A8K7U4|Q5TF86|Q8NFZ9|Q9BW32|Q9NXV5	Silent	SNP	ENST00000320172.6	hg19	CCDS34489.1																																																																																			.	.	.	none		0.667	FAM46A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041331.1			A	82461742	G	A	82461742	2	1	40	1	0	0	0	0	0	0	0	1	5572	1074	38	1		1	FAM46A	6	82461742	Silent	SNP	G	TCGA-5P-A9KH-01A-11D-A42J-10		82461742	88653325	5	2873											
GRM3	2913	hgsc.bcm.edu	37	chr7	86394802	86394802	+	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	gcaatcactggagtttgtcaGggcatctttgacaaaagtgg	11	11	12	7	0	3	1	2	1	1	0	3	2	3	2	0	3	0	3	0	3	3	2			TCGA-5P-A9KH-01A-11D-A42J-10	TCGA-5P-A9KH-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d91e36f3-e4a2-4af3-802a-3148b09be900	ccc45b0a-b066-47dd-934b-6f892b6c61a4	g.chr7:86394802G>A	ENST00000361669.2	+	2	1440	c.341G>A	c.(340-342)aGg>aAg	p.R114K	GRM3_ENST00000546348.1_Intron|GRM3_ENST00000394720.2_Missense_Mutation_p.R112K|GRM3_ENST00000536043.1_Intron|GRM3_ENST00000439827.1_Missense_Mutation_p.R114K	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3	114					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)					GAGTTTGTCAGGGCATCTTTG	0.428																																					p.R114K	GBM(52;969 1098 3139 52280)	Atlas-SNP	.											.	GRM3	237	.	0			c.G341A						PASS	.						182	166	172					7																	86394802		2203	4300	6503	SO:0001583	missense	2913	exon2			TTGTCAGGGCATC		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.341G>A	chr7.hg19:g.86394802G>A	ENSP00000355316:p.Arg114Lys	99.0	0.0	.		157.0	15.0	.	NM_000840	Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Missense_Mutation	SNP	ENST00000361669.2	hg19	CCDS5600.1	.	.	.	.	.	.	.	.	.	.	G	17.70	3.454649	0.63290	.	.	ENSG00000198822	ENST00000361669;ENST00000439827;ENST00000394720	T;T;T	0.52754	0.65;0.65;0.65	5.24	5.24	0.73138	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	T	0.48572	0.1507	L	0.53617	1.68	0.80722	D	1	B;B	0.22146	0.065;0.026	B;B	0.28784	0.067;0.094	T	0.41538	-0.9503	10	0.41790	T	0.15	.	17.9854	0.89154	0.0:0.0:1.0:0.0	.	114;114	G5E9K2;Q14832	.;GRM3_HUMAN	K	114;114;112	ENSP00000355316:R114K;ENSP00000398767:R114K;ENSP00000378209:R112K	ENSP00000355316:R114K	R	+	2	0	GRM3	86232738	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.580000	0.74040	2.732000	0.93576	0.655000	0.94253	AGG	.	.	.	none		0.428	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253362.2			A	86394802	G	A	86394802	3	1	40	1	0	0	0	0	1	0	0	0	6805	1000	35	2	343	2	GRM3	7	86394802	Missense_Mutation	SNP	G	TCGA-5P-A9KH-01A-11D-A42J-10		86394802	72743861	6	2874											
EPHB4	2050	hgsc.bcm.edu	37	chr7	100410509	100410509	+	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	ggaggcctcgctcagaaactCacgccgctgccgctccgtgt	6	7	12	16	5	2	1	2	0	0	1	4	2	3	2	4	2	2	3	4	2	1	0			TCGA-5P-A9KH-01A-11D-A42J-10	TCGA-5P-A9KH-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d91e36f3-e4a2-4af3-802a-3148b09be900	ccc45b0a-b066-47dd-934b-6f892b6c61a4	g.chr7:100410509C>A	ENST00000358173.3	-	12	2446	c.1978G>T	c.(1978-1980)Gag>Tag	p.E660*	EPHB4_ENST00000477446.1_5'Flank|EPHB4_ENST00000360620.3_Nonsense_Mutation_p.E660*	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	660	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)					CTCAGAAACTCACGCCGCTGC	0.627																																					p.E660X	GBM(200;2113 3072 25865 52728)	Atlas-SNP	.											.	EPHB4	106	.	0			c.G1978T						PASS	.						103	102	103					7																	100410509		2203	4300	6503	SO:0001587	stop_gained	2050	exon12			GAAACTCACGCCG	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.1978G>T	chr7.hg19:g.100410509C>A	ENSP00000350896:p.Glu660*	74.0	0.0	.		75.0	34.0	.	NM_004444	B5A970|B5A971|B5A972|Q7Z635|Q9BTA5|Q9BXP0	Nonsense_Mutation	SNP	ENST00000358173.3	hg19	CCDS5706.1	.	.	.	.	.	.	.	.	.	.	C	41	9.119006	0.99071	.	.	ENSG00000196411	ENST00000360620;ENST00000358173	.	.	.	4.79	4.79	0.61399	.	0.000000	0.56097	D	0.000040	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	15.6721	0.77286	0.0:1.0:0.0:0.0	.	.	.	.	X	660	.	ENSP00000350896:E660X	E	-	1	0	EPHB4	100248445	1.000000	0.71417	0.955000	0.39395	0.173000	0.22820	7.705000	0.84606	2.368000	0.80403	0.650000	0.86243	GAG	.	.	.	none		0.627	EPHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347222.1	NM_004444		A	100410509	C	A	100410509	4	1	40	1	0	0	0	0	0	1	0	0	5179	835	29	4	1009	4	EPHB4	7	100410509	Nonsense_Mutation	SNP	C	TCGA-5P-A9KH-01A-11D-A42J-10	14015707	100410509	58728154	7	2875											
SLC4A2	6522	hgsc.bcm.edu	37	chr7	150771197	150771197	+	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	gtggacggcggtgagaacatGacatgggccggggcaagacc	10	4	18	9	3	0	3	0	2	0	2	0	5	0	4	2	6	1	1	2	6	2	0			TCGA-5P-A9KH-01A-11D-A42J-10	TCGA-5P-A9KH-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d91e36f3-e4a2-4af3-802a-3148b09be900	ccc45b0a-b066-47dd-934b-6f892b6c61a4	g.chr7:150771197G>A	ENST00000485713.1	+	17	3647	c.2607G>A	c.(2605-2607)atG>atA	p.M869I	SLC4A2_ENST00000461735.1_Missense_Mutation_p.M855I|SLC4A2_ENST00000413384.2_Missense_Mutation_p.M869I|SLC4A2_ENST00000310317.5_Missense_Mutation_p.M787I|SLC4A2_ENST00000392826.2_Missense_Mutation_p.M860I|RP11-148K1.12_ENST00000485974.1_RNA|FASTK_ENST00000489884.1_5'Flank	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	869	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)		GTGAGAACATGACATGGGCCG	0.687																																					p.M869I		Atlas-SNP	.											.	SLC4A2	98	.	0			c.G2607A						PASS	.						34	40	38					7																	150771197		2202	4300	6502	SO:0001583	missense	6522	exon17			GAACATGACATGG		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.2607G>A	chr7.hg19:g.150771197G>A	ENSP00000419412:p.Met869Ile	186.0	0.0	.		213.0	71.0	.	NM_003040	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Missense_Mutation	SNP	ENST00000485713.1	hg19	CCDS5917.1	.	.	.	.	.	.	.	.	.	.	G	1.317	-0.600662	0.03744	.	.	ENSG00000164889	ENST00000485713;ENST00000413384;ENST00000310317;ENST00000392826;ENST00000461735	T;T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18;-1.18	5.54	-1.43	0.08884	Bicarbonate transporter, C-terminal (1);	2.629030	0.00927	N	0.002677	T	0.59252	0.2180	N	0.08118	0	0.19300	N	0.999979	B;B;B	0.11235	0.0;0.001;0.004	B;B;B	0.06405	0.0;0.001;0.002	T	0.49447	-0.8939	10	0.37606	T	0.19	.	6.7854	0.23670	0.422:0.2891:0.2888:0.0	.	860;855;869	F8W682;P04920-2;P04920	.;.;B3A2_HUMAN	I	869;869;787;860;855	ENSP00000419412:M869I;ENSP00000405600:M869I;ENSP00000311402:M787I;ENSP00000376571:M860I;ENSP00000419164:M855I	ENSP00000311402:M787I	M	+	3	0	SLC4A2	150402130	0.000000	0.05858	0.003000	0.11579	0.007000	0.05969	-0.508000	0.06344	-0.176000	0.10707	-0.258000	0.10820	ATG	.	.	.	none		0.687	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040		A	150771197	G	A	150771197	3	1	40	1	0	0	0	0	1	0	0	0	14667	1290	45	2	2669	2	SLC4A2	7	150771197	Missense_Mutation	SNP	G	TCGA-5P-A9KH-01A-11D-A42J-10	50360688	150771197	8367466	8	2876											
MYOM2	9172	hgsc.bcm.edu	37	chr8	2037960	2037960	+	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	tgctgtcagcaaaccggcatGgcctgagcgaaccttcggag	9	7	13	12	3	1	1	1	1	0	0	2	3	1	2	3	3	5	3	3	3	2	1			TCGA-5P-A9KH-01A-11D-A42J-10	TCGA-5P-A9KH-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d91e36f3-e4a2-4af3-802a-3148b09be900	ccc45b0a-b066-47dd-934b-6f892b6c61a4	g.chr8:2037960G>T	ENST00000262113.4	+	15	1915	c.1774G>T	c.(1774-1776)Ggc>Tgc	p.G592C	MYOM2_ENST00000523438.1_Missense_Mutation_p.G17C	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	592	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		AAACCGGCATGGCCTGAGCGA	0.572																																					p.G592C		Atlas-SNP	.											.	MYOM2	251	.	0			c.G1774T						PASS	.						134	104	114					8																	2037960		2203	4300	6503	SO:0001583	missense	9172	exon15			CGGCATGGCCTGA		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.1774G>T	chr8.hg19:g.2037960G>T	ENSP00000262113:p.Gly592Cys	63.0	0.0	.		65.0	33.0	.	NM_003970	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	hg19	CCDS5957.1	.	.	.	.	.	.	.	.	.	.	G	18.87	3.716094	0.68844	.	.	ENSG00000036448	ENST00000262113;ENST00000523438	T;T	0.65178	-0.14;-0.14	5.6	5.6	0.85130	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.88607	0.6482	H	0.98918	4.37	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92947	0.6377	10	0.87932	D	0	.	19.6185	0.95645	0.0:0.0:1.0:0.0	.	592	P54296	MYOM2_HUMAN	C	592;17	ENSP00000262113:G592C;ENSP00000428396:G17C	ENSP00000262113:G592C	G	+	1	0	MYOM2	2025367	1.000000	0.71417	0.982000	0.44146	0.074000	0.17049	9.480000	0.97931	2.641000	0.89580	0.462000	0.41574	GGC	.	.	.	none		0.572	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970		T	2037960	G	T	2037960	3	4	40	1	0	0	0	0	1	0	0	0	10099	1348	47	4	1828	4	MYOM2	8	2037960	Missense_Mutation	SNP	G	TCGA-5P-A9KH-01A-11D-A42J-10		2037960	144326062	9	2877											
UBXN2B	137886	hgsc.bcm.edu	37	chr8	59343157	59343158	+	In_Frame_Ins	INS	-	-	AAG																															aattgtgaatgaacttttcaINSaagaggcaagggaacatggg																										TCGA-5P-A9KH-01A-11D-A42J-10	TCGA-5P-A9KH-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d91e36f3-e4a2-4af3-802a-3148b09be900	ccc45b0a-b066-47dd-934b-6f892b6c61a4	g.chr8:59343157_59343158insAAG	ENST00000399598.2	+	3	390_391	c.268_269insAAG	c.(268-270)aaa>aAAGaa	p.91_92insE	UBXN2B_ENST00000522978.1_3'UTR	NM_001077619.1	NP_001071087.1	Q14CS0	UBX2B_HUMAN	UBX domain protein 2B	91						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						TGAACTTTTCAAAGAGGCAAGG	0.361																																					p.K90delinsKE		Atlas-Indel,Pindel	.											.	UBXN2B	36	.	0			c.268_269insAAG						PASS	.																																			SO:0001652	inframe_insertion	137886	exon3			.	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.269_271dupAAG	chr8.hg19:g.59343158_59343160dupAAG	ENSP00000382507:p.Glu91_Glu91dup	319.0	0.0	0		453.0	54.0	0.119205	NM_001077619	B3KWZ3	In_Frame_Ins	INS	ENST00000399598.2	hg19	CCDS43741.1																																																																																			.	.	.	none		0.361	UBXN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378184.1	NM_001077619		AAG	59343158	-	AAG	59343157	7	5	40	1	0	1	1	0	0	0	0	0	16927	131	5	0	278	0	UBXN2B	8	59343157	In_Frame_Ins	INS	-	TCGA-5P-A9KH-01A-11D-A42J-10	57305197	59343157	87020865	10	2878											
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79465477	79465477	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggaatatgtggaatgattcGgaaatatttagctcttctaa	13	14	9	5	2	2	1	0	1	2	0	3	4	2	4	0	3	1	1	0	3	7	7			TCGA-5P-A9KH-01A-11D-A42J-10	TCGA-5P-A9KH-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d91e36f3-e4a2-4af3-802a-3148b09be900	ccc45b0a-b066-47dd-934b-6f892b6c61a4	g.chr9:79465477G>A	ENST00000376718.3	-	3	369	c.246C>T	c.(244-246)tcC>tcT	p.S82S	PRUNE2_ENST00000376713.3_Silent_p.S82S|PRUNE2_ENST00000428286.1_5'UTR	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	82					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						GGAATGATTCGGAAATATTTA	0.428																																					p.S82S		Atlas-SNP	.											.	PRUNE2	331	.	0			c.C246T						PASS	.						157	162	160					9																	79465477		2203	4300	6503	SO:0001819	synonymous_variant	158471	exon3			TGATTCGGAAATA	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.246C>T	chr9.hg19:g.79465477G>A		151.0	0.0	.		196.0	76.0	.	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Silent	SNP	ENST00000376718.3	hg19	CCDS47982.1																																																																																			.	.	.	none		0.428	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		A	79465477	G	A	79465477	2	1	40	1	0	0	0	0	0	0	0	1	12651	1103	39	1		1	PRUNE2	9	79465477	Silent	SNP	G	TCGA-5P-A9KH-01A-11D-A42J-10		79465477	61747954	11	2879											
TRIM22	10346	hgsc.bcm.edu	37	chr11	5730402	5730402	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caaatccatgtgatttttctGcttttggtgtcttcggctgc	5	18	9	9	1	2	1	0	1	2	0	4	1	3	1	1	2	2	2	1	2	1	5	rs199987600		TCGA-5P-A9KH-01A-11D-A42J-10	TCGA-5P-A9KH-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d91e36f3-e4a2-4af3-802a-3148b09be900	ccc45b0a-b066-47dd-934b-6f892b6c61a4	g.chr11:5730402G>A	ENST00000379965.3	+	8	1298	c.1021G>A	c.(1021-1023)Gct>Act	p.A341T	TRIM5_ENST00000380027.1_Intron	NM_001199573.1|NM_006074.4	NP_001186502.1|NP_006065.2	Q8IYM9	TRI22_HUMAN	tripartite motif containing 22	341	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)		TGATTTTTCTGCTTTTGGTGT	0.433																																					p.A341T	GBM(104;491 2336 5222)	Atlas-SNP	.											TRIM22,NS,carcinoma,0,1	TRIM22	66	.	0			c.G1021A						PASS	.						156	143	147					11																	5730402		1861	4103	5964	SO:0001583	missense	10346	exon8			TTTTCTGCTTTTG	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.1021G>A	chr11.hg19:g.5730402G>A	ENSP00000369299:p.Ala341Thr	126.0	0.0	.		127.0	44.0	.	NM_006074	Q05CQ0|Q15521	Missense_Mutation	SNP	ENST00000379965.3	hg19	CCDS41612.1	.	.	.	.	.	.	.	.	.	.	G	7.371	0.626808	0.14257	.	.	ENSG00000132274	ENST00000379965;ENST00000545338;ENST00000455293	T	0.04862	3.54	2.99	-0.531	0.11894	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.02929	0.0087	N	0.13098	0.295	0.09310	N	1	B;B;B	0.23377	0.084;0.001;0.001	B;B;B	0.17722	0.019;0.007;0.004	T	0.46665	-0.9175	9	0.22109	T	0.4	.	2.2684	0.04085	0.3013:0.0:0.4546:0.2442	.	263;337;341	F8WAP8;Q8IYM9-2;Q8IYM9	.;.;TRI22_HUMAN	T	341;152;263	ENSP00000369299:A341T	ENSP00000369299:A341T	A	+	1	0	TRIM22	5686978	0.000000	0.05858	0.000000	0.03702	0.243000	0.25628	-1.073000	0.03430	0.109000	0.17891	-0.384000	0.06662	GCT	.	G|0.999;A|0.001	0.001	weak		0.433	TRIM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143387.2	NM_006074		A	5730402	G	A	5730402	3	1	40	1	0	0	0	0	1	0	0	0	16508	1319	46	2	1047	2	TRIM22	11	5730402	Missense_Mutation	SNP	G	TCGA-5P-A9KH-01A-11D-A42J-10		5730402	129276114	12	2880											
SMPD1	6609	hgsc.bcm.edu	37	chr11	6411970	6411970	+	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	tggcgctggcgctggcgctgGctctgtctgactctcgggtt	1	12	16	12	4	3	1	0	1	3	0	4	1	3	1	0	5	0	5	0	5	0	1			TCGA-5P-A9KH-01A-11D-A42J-10	TCGA-5P-A9KH-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d91e36f3-e4a2-4af3-802a-3148b09be900	ccc45b0a-b066-47dd-934b-6f892b6c61a4	g.chr11:6411970G>T	ENST00000342245.4	+	1	310	c.142G>T	c.(142-144)Gct>Tct	p.A48S	SMPD1_ENST00000527275.1_Missense_Mutation_p.A48S|SMPD1_ENST00000356761.2_Missense_Mutation_p.A48S|SMPD1_ENST00000299397.3_Missense_Mutation_p.A48S|SMPD1_ENST00000533196.1_3'UTR	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	47					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)	gctggcgctggcTCTGTCTGA	0.697																																					p.A48S		Atlas-SNP	.											.	SMPD1	108	.	0			c.G142T						PASS	.						24	27	26					11																	6411970		2201	4296	6497	SO:0001583	missense	6609	exon1			GCGCTGGCTCTGT	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.142G>T	chr11.hg19:g.6411970G>T	ENSP00000340409:p.Ala48Ser	90.0	0.0	.		119.0	6.0	.	NM_000543	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Missense_Mutation	SNP	ENST00000342245.4	hg19	CCDS44531.1	.	.	.	.	.	.	.	.	.	.	G	11.04	1.521946	0.27211	.	.	ENSG00000166311	ENST00000299397;ENST00000356761;ENST00000342245;ENST00000527275	T;T;T;T	0.10382	2.88;2.88;2.89;2.89	.	.	.	.	0.196334	0.29861	N	0.011014	T	0.07143	0.0181	L	0.40543	1.245	0.09310	N	1	B;P;P	0.40476	0.442;0.718;0.629	B;B;B	0.35607	0.11;0.206;0.163	T	0.24728	-1.0152	9	0.56958	D	0.05	-36.845	5.0357	0.14432	0.0:0.0:1.0:0.0	.	48;48;46	E9PKS3;G3XAB5;P17405	.;.;ASM_HUMAN	S	48	ENSP00000299397:A48S;ENSP00000349203:A48S;ENSP00000340409:A48S;ENSP00000435350:A48S	ENSP00000299397:A48S	A	+	1	0	SMPD1	6368546	0.045000	0.20229	0.241000	0.24154	0.101000	0.19017	0.462000	0.21956	-0.000000	0.14550	0.000000	0.15137	GCT	.	.	.	none		0.697	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543		T	6411970	G	T	6411970	3	4	40	1	0	0	0	0	1	0	0	0	14817	1203	42	4	144	4	SMPD1	11	6411970	Missense_Mutation	SNP	G	TCGA-5P-A9KH-01A-11D-A42J-10	681568	6411970	128594546	13	2881											
MLL2	8085	hgsc.bcm.edu	37	chr12	49438022	49438022	+	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	cccactcaacacctccgcctGtgcagcaggcccctttttcg	6	9	7	19	2	1	0	1	0	0	0	3	0	2	0	6	1	3	2	6	1	1	2			TCGA-5P-A9KH-01A-11D-A42J-10	TCGA-5P-A9KH-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d91e36f3-e4a2-4af3-802a-3148b09be900	ccc45b0a-b066-47dd-934b-6f892b6c61a4	g.chr12:49438022G>T	ENST00000301067.7	-	21	5148	c.5149C>A	c.(5149-5151)Cag>Aag	p.Q1717K		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1717					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)										ACCTCCGCCTGTGCAGCAGGC	0.617											OREG0021780	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q1717K		Atlas-SNP	.											.	MLL2	1173	.	0			c.C5149A						PASS	.						48	55	53					12																	49438022		2119	4237	6356	SO:0001583	missense	8085	exon21			CCGCCTGTGCAGC	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.5149C>A	chr12.hg19:g.49438022G>T	ENSP00000301067:p.Gln1717Lys	49.0	0.0	.	962	96.0	43.0	.	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	12.88	2.070431	0.36566	.	.	ENSG00000167548	ENST00000301067	T	0.78707	-1.2	4.82	3.9	0.45041	.	0.000000	0.33457	N	0.004900	T	0.57533	0.2060	N	0.22421	0.69	0.24145	N	0.995719	B	0.34061	0.436	B	0.26202	0.067	T	0.55444	-0.8140	10	0.87932	D	0	.	4.7551	0.13080	0.1743:0.0:0.6471:0.1787	.	1717	O14686	MLL2_HUMAN	K	1717	ENSP00000301067:Q1717K	ENSP00000301067:Q1717K	Q	-	1	0	MLL2	47724289	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.428000	0.44749	2.498000	0.84270	0.563000	0.77884	CAG	.	.	.	none		0.617	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			T	49438022	G	T	49438022	3	4	40	1	0	0	0	0	1	0	0	0	9628	1386	48	4	11600	4	MLL2	12	49438022	Missense_Mutation	SNP	G	TCGA-5P-A9KH-01A-11D-A42J-10		49438022	84413873	14	2882											
GRASP	160622	hgsc.bcm.edu	37	chr12	52408635	52408635	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgacgggccaggggcgacgcCgacgacgccgtctaccacac	8	2	14	17	8	1	0	0	0	1	0	1	4	1	0	4	3	1	0	4	3	1	1			TCGA-5P-A9KH-01A-11D-A42J-10	TCGA-5P-A9KH-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d91e36f3-e4a2-4af3-802a-3148b09be900	ccc45b0a-b066-47dd-934b-6f892b6c61a4	g.chr12:52408635C>T	ENST00000293662.4	+	8	920	c.840C>T	c.(838-840)gcC>gcT	p.A280A	GRASP_ENST00000552963.1_3'UTR|GRASP_ENST00000380039.2_Silent_p.A137A|GRASP_ENST00000552049.1_Silent_p.A137A	NM_181711.2	NP_859062.1	Q7Z6J2	GRASP_HUMAN	GRP1 (general receptor for phosphoinositides 1)-associated scaffold protein	280					protein localization (GO:0008104)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				central_nervous_system(1)|large_intestine(1)|lung(1)|skin(2)	5				BRCA - Breast invasive adenocarcinoma(357;0.0967)		GGGGCGACGCCGACGACGCCG	0.821																																					p.A280A		Atlas-SNP	.											.	GRASP	23	.	0			c.C840T						PASS	.						1	1	1					12																	52408635		646	1615	2261	SO:0001819	synonymous_variant	160622	exon8			CGACGCCGACGAC	AC019244	CCDS8817.1, CCDS61124.1	12q13.13	2011-09-02			ENSG00000161835	ENSG00000161835			18707	protein-coding gene	gene with protein product		612027				10828067	Standard	NM_001271856		Approved		uc001rzo.2	Q7Z6J2	OTTHUMG00000169595	ENST00000293662.4:c.840C>T	chr12.hg19:g.52408635C>T		7.0	0.0	.		10.0	6.0	.	NM_181711	Q6PIF8|Q7Z741	Silent	SNP	ENST00000293662.4	hg19	CCDS8817.1																																																																																			.	.	.	none		0.821	GRASP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404972.1			T	52408635	C	T	52408635	2	4	40	1	0	0	0	0	0	0	0	1	6762	639	23	1		1	GRASP	12	52408635	Silent	SNP	C	TCGA-5P-A9KH-01A-11D-A42J-10	2970613	52408635	81443260	15	2883											
GPR137C	283554	hgsc.bcm.edu	37	chr14	53101695	53101695	+	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	ttgggctggtatggcaccatGactgggtgtggcagcagcag	7	9	17	8	0	0	1	0	1	0	0	0	1	0	1	1	5	2	6	1	5	1	2			TCGA-5P-A9KH-01A-11D-A42J-10	TCGA-5P-A9KH-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d91e36f3-e4a2-4af3-802a-3148b09be900	ccc45b0a-b066-47dd-934b-6f892b6c61a4	g.chr14:53101695G>T	ENST00000321662.6	+	7	1152	c.1152G>T	c.(1150-1152)atG>atT	p.M384I		NM_001099652.1	NP_001093122.1	Q8N3F9	G137C_HUMAN	G protein-coupled receptor 137C	384						integral component of membrane (GO:0016021)				NS(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	8	Breast(41;0.0716)					ATGGCACCATGACTGGGTGTG	0.418																																					p.M384I		Atlas-SNP	.											.	GPR137C	24	.	0			c.G1152T						PASS	.						116	114	115					14																	53101695		1940	4138	6078	SO:0001583	missense	283554	exon7			CACCATGACTGGG	BX647179	CCDS45106.1	14q22.1	2012-08-10				ENSG00000180998			25445	protein-coding gene	gene with protein product							Standard	NM_001099652		Approved	DKFZp762F0713, TM7SF1L2	uc001wzu.4	Q8N3F9		ENST00000321662.6:c.1152G>T	chr14.hg19:g.53101695G>T	ENSP00000315106:p.Met384Ile	103.0	0.0	.		156.0	58.0	.	NM_001099652	Q86SM2	Missense_Mutation	SNP	ENST00000321662.6	hg19	CCDS45106.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	1.724|1.724	-0.495942|-0.495942	0.04291|0.04291	.|.	.|.	ENSG00000180998|ENSG00000180998	ENST00000542169|ENST00000321662	.|T	.|0.37584	.|1.19	5.92|5.92	2.35|2.35	0.29111|0.29111	.|.	.|0.114776	.|0.64402	.|N	.|0.000010	T|T	0.08268|0.08268	0.0206|0.0206	N|N	0.00413|0.00413	-1.525|-1.525	0.33382|0.33382	D|D	0.575044|0.575044	.|B;B	.|0.06786	.|0.0;0.001	.|B;B	.|0.06405	.|0.001;0.002	T|T	0.10291|0.10291	-1.0636|-1.0636	5|10	.|0.21014	.|T	.|0.42	-19.4003|-19.4003	4.6484|4.6484	0.12584|0.12584	0.1073:0.1726:0.5872:0.133|0.1073:0.1726:0.5872:0.133	.|.	.|384;213	.|Q8N3F9;B3KW22	.|G137C_HUMAN;.	Y|I	354|384	.|ENSP00000315106:M384I	.|ENSP00000315106:M384I	D|M	+|+	1|3	0|0	GPR137C|GPR137C	52171445|52171445	0.974000|0.974000	0.33945|0.33945	0.993000|0.993000	0.49108|0.49108	0.780000|0.780000	0.44128|0.44128	0.995000|0.995000	0.29706|0.29706	1.393000|1.393000	0.46605|0.46605	0.655000|0.655000	0.94253|0.94253	GAC|ATG	.	.	.	none		0.418	GPR137C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411685.1	XM_290615		T	53101695	G	T	53101695	3	4	40	1	0	0	0	0	1	0	0	0	6654	1290	45	4	1178	4	GPR137C	14	53101695	Missense_Mutation	SNP	G	TCGA-5P-A9KH-01A-11D-A42J-10		53101695	54247845	16	2884											
DUOXA1	90527	hgsc.bcm.edu	37	chr15	45415103	45415103	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggcaggatgacgatgaacGtggccagtgcagtcagaaag	13	5	15	8	2	1	3	1	2	0	1	1	5	1	4	1	3	2	2	1	3	2	0	rs374411208		TCGA-5P-A9KH-01A-11D-A42J-10	TCGA-5P-A9KH-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d91e36f3-e4a2-4af3-802a-3148b09be900	ccc45b0a-b066-47dd-934b-6f892b6c61a4	g.chr15:45415103G>A	ENST00000560572.1	-	1	115	c.110C>T	c.(109-111)aCg>aTg	p.T37M	DUOXA1_ENST00000558422.1_Missense_Mutation_p.T37M|DUOXA1_ENST00000558996.1_Missense_Mutation_p.T37M|DUOXA1_ENST00000559014.1_Missense_Mutation_p.T37M|DUOXA1_ENST00000430224.2_Missense_Mutation_p.T37M|DUOXA1_ENST00000267803.4_Missense_Mutation_p.T37M	NM_001276266.1	NP_001263195.1	Q1HG43	DOXA1_HUMAN	dual oxidase maturation factor 1	37					hydrogen peroxide metabolic process (GO:0042743)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein transport (GO:0015031)|regulation of inflammatory response (GO:0050727)|regulation of thyroid hormone generation (GO:2000609)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	16		all_cancers(109;6.02e-08)|all_epithelial(112;1.83e-06)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.82e-18)|GBM - Glioblastoma multiforme(94;4.39e-07)|COAD - Colon adenocarcinoma(120;0.0676)|Colorectal(133;0.0686)		GACGATGAACGTGGCCAGTGC	0.572																																					p.T37M		Atlas-SNP	.											.	DUOXA1	32	.	0			c.C110T						PASS	.	G	MET/THR	0,4396		0,0,2198	144	120	128		110	3.5	1	15		128	1,8595	1.2+/-3.3	0,1,4297	no	missense	DUOXA1	NM_144565.2	81	0,1,6495	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	37/484	45415103	1,12991	2198	4298	6496	SO:0001583	missense	90527	exon4			ATGAACGTGGCCA	BC029819	CCDS10119.1, CCDS61619.1, CCDS61620.1, CCDS61621.1	15q21.1	2006-11-29	2006-01-23	2006-07-25	ENSG00000140254	ENSG00000140254			26507	protein-coding gene	gene with protein product		612771				16651268	Standard	NM_144565		Approved	FLJ32334, NUMBIP, NIP, mol	uc010bec.4	Q1HG43	OTTHUMG00000131352	ENST00000560572.1:c.110C>T	chr15.hg19:g.45415103G>A	ENSP00000454084:p.Thr37Met	142.0	0.0	.		174.0	75.0	.	NM_144565	Q8N6K9|Q96MI4	Missense_Mutation	SNP	ENST00000560572.1	hg19		.	.	.	.	.	.	.	.	.	.	G	16.64	3.179690	0.57800	0.0	1.16E-4	ENSG00000140254	ENST00000267803;ENST00000430224	T;T	0.57595	0.39;0.39	5.4	3.54	0.40534	.	0.105523	0.64402	D	0.000004	T	0.67552	0.2905	M	0.68317	2.08	0.35847	D	0.826508	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.78314	0.98;0.987;0.99;0.991	T	0.75436	-0.3318	10	0.87932	D	0	-20.3562	10.7497	0.46203	0.154:0.0:0.846:0.0	.	37;37;37;37	B5M0C0;B5M0B8;Q1HG43;A8K9Q6	.;.;DOXA1_HUMAN;.	M	37	ENSP00000267803:T37M;ENSP00000415512:T37M	ENSP00000267803:T37M	T	-	2	0	DUOXA1	43202395	0.978000	0.34361	0.998000	0.56505	0.535000	0.34838	1.451000	0.35145	0.863000	0.35553	0.655000	0.94253	ACG	.	.	.	weak		0.572	DUOXA1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000416242.1	NM_144565		A	45415103	G	A	45415103	3	1	40	1	0	0	0	0	1	0	0	0	4804	1145	40	1	1373	1	DUOXA1	15	45415103	Missense_Mutation	SNP	G	TCGA-5P-A9KH-01A-11D-A42J-10		45415103	57116289	17	2885											
MCTP2	55784	hgsc.bcm.edu	37	chr15	95001475	95001477	+	Splice_Site	DEL	AGT	AGT	-																															ttttggagaaaggattaagaAgtaagttctaaatttgtgtt																										TCGA-5P-A9KH-01A-11D-A42J-10	TCGA-5P-A9KH-10A-01D-A42M-10	AGT	AGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d91e36f3-e4a2-4af3-802a-3148b09be900	ccc45b0a-b066-47dd-934b-6f892b6c61a4	g.chr15:95001475_95001477delAGT	ENST00000357742.4	+	19	2360	c.2360delAGT	c.(2359-2361)aag>ag	p.K787del	MCTP2_ENST00000451018.3_Splice_Site_p.K732del	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	787					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)			AGGATTAAGAAGTAAGTTCTAAA	0.399																																					p.787_787del		Atlas-Indel,Pindel	.											.	MCTP2	122	.	0			c.2359_2360del						PASS	.																																			SO:0001630	splice_region_variant	55784	exon19			.	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.2360+1AGT>-	chr15.hg19:g.95001475_95001477delAGT		93.0	0.0	0		129.0	32.0	0.248062	NM_018349	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Frame_Shift_Del	DEL	ENST00000357742.4	hg19	CCDS32338.1																																																																																			.	.	.	none		0.399	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349	In_Frame_Del	-	95001477	AGT	-	95001475	8	5	40	1	0	1	0	1	0	0	1	0	9408	86	3	0	2510	0	MCTP2	15	95001475	Splice_Site	DEL	AGT	TCGA-5P-A9KH-01A-11D-A42J-10	49586372	95001475	7529917	18	2886											
SLC13A5	284111	hgsc.bcm.edu	37	chr17	6594200	6594200	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagatcaaggtgatggctgcCgggggcactgcgtgcaaggg	9	6	18	8	2	1	2	1	1	0	1	1	2	1	2	1	5	3	3	1	5	3	0	rs138802643		TCGA-5P-A9KH-01A-11D-A42J-10	TCGA-5P-A9KH-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d91e36f3-e4a2-4af3-802a-3148b09be900	ccc45b0a-b066-47dd-934b-6f892b6c61a4	g.chr17:6594200C>T	ENST00000433363.2	-	10	1568	c.1335G>A	c.(1333-1335)ccG>ccA	p.P445P	SLC13A5_ENST00000293800.6_Silent_p.P428P|SLC13A5_ENST00000573648.1_Silent_p.P445P|SLC13A5_ENST00000381074.4_Silent_p.P402P	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	445					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						TGATGGCTGCCGGGGGCACTG	0.622																																					p.P445P		Atlas-SNP	.											.	SLC13A5	57	.	0			c.G1335A						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	181	160	167		1335,1335	-10.1	0	17	dbSNP_134	167	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SLC13A5	NM_001143838.1,NM_177550.3	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	445/523,445/569	6594200	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	284111	exon10			GGCTGCCGGGGGC	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.1335G>A	chr17.hg19:g.6594200C>T		51.0	0.0	.		47.0	38.0	.	NM_001143838	B3KXR0|B7Z4P2|B7ZLB4|F8W7N2|Q6ZMG1	Silent	SNP	ENST00000433363.2	hg19	CCDS11079.1																																																																																			.	C|1.000;T|0.000	0.000	weak		0.622	SLC13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219853.2	NM_177550		T	6594200	C	T	6594200	2	4	40	1	0	0	0	0	0	0	0	1	14408	639	23	1		1	SLC13A5	17	6594200	Silent	SNP	C	TCGA-5P-A9KH-01A-11D-A42J-10		6594200	74601010	19	2887											
TP53	7157	hgsc.bcm.edu	37	chr17	7577515	7577517	+	In_Frame_Del	DEL	TGA	TGA	-																															tgacctggagtcttccagtgTgatgatggtgaggatgggcc																								rs587781433		TCGA-5P-A9KH-01A-11D-A42J-10	TCGA-5P-A9KH-10A-01D-A42M-10	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d91e36f3-e4a2-4af3-802a-3148b09be900	ccc45b0a-b066-47dd-934b-6f892b6c61a4	g.chr17:7577515_7577517delTGA	ENST00000269305.4	-	7	953_955	c.764_766delTCA	c.(763-768)atcaca>aca	p.I255del	TP53_ENST00000455263.2_In_Frame_Del_p.I255del|TP53_ENST00000420246.2_In_Frame_Del_p.I255del|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_In_Frame_Del_p.I255del|TP53_ENST00000359597.4_In_Frame_Del_p.I255del|TP53_ENST00000445888.2_In_Frame_Del_p.I255del	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	255	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		I -> F (in sporadic cancers; somatic mutation).|I -> M (in sporadic cancers; somatic mutation).|I -> N (in sporadic cancers; somatic mutation).|I -> S (in sporadic cancers; somatic mutation).|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.I255S(10)|p.0?(8)|p.I255N(7)|p.I255del(7)|p.I255T(7)|p.T256A(3)|p.T256fs*89(3)|p.T256fs*8(2)|p.T256S(2)|p.I255I(2)|p.I255fs*8(1)|p.?(1)|p.I254fs*7(1)|p.I255M(1)|p.T256fs*90(1)|p.T256P(1)|p.T256del(1)|p.R249_T256delRPILTIIT(1)|p.T256fs*87(1)|p.T256fs*17(1)|p.I254_T256del(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)	TCTTCCAGTGTGATGATGGTGAG	0.586		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.255_256del	Pancreas(47;798 1329 9957 10801)	Atlas-Indel,Pindel	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000413465,NS,carcinoma,0,1	TP53	33396	.	62	Substitution - Missense(31)|Deletion - In frame(10)|Whole gene deletion(8)|Deletion - Frameshift(6)|Insertion - Frameshift(4)|Substitution - coding silent(2)|Unknown(1)	breast(15)|ovary(7)|pancreas(6)|central_nervous_system(5)|bone(5)|upper_aerodigestive_tract(4)|large_intestine(3)|haematopoietic_and_lymphoid_tissue(3)|urinary_tract(3)|oesophagus(3)|lung(3)|thyroid(1)|stomach(1)|liver(1)|endometrium(1)|skin(1)	c.765_767del						PASS	.																																			SO:0001651	inframe_deletion	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.764_766delTCA	chr17.hg19:g.7577518_7577520delTGA	ENSP00000269305:p.Ile255del	88.0	0.0	0		70.0	18.0	0.257143	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	In_Frame_Del	DEL	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.	.	none		0.586	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		-	7577517	TGA	-	7577515	7	5	40	1	0	1	0	1	0	0	0	0	16393	1696	59	0	524	0	TP53	17	7577515	In_Frame_Del	DEL	TGA	TCGA-5P-A9KH-01A-11D-A42J-10	983315	7577515	73617695	20	2888											
TAC4	255061	hgsc.bcm.edu	37	chr17	47921450	47921450	+	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	cactcgcttccccatcagccCaaagaactggcttgccttgc	8	9	7	17	1	1	1	1	0	0	1	3	1	2	1	4	1	4	2	4	1	2	3			TCGA-5P-A9KH-01A-11D-A42J-10	TCGA-5P-A9KH-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d91e36f3-e4a2-4af3-802a-3148b09be900	ccc45b0a-b066-47dd-934b-6f892b6c61a4	g.chr17:47921450C>A	ENST00000334568.4	-	2	192	c.193G>T	c.(193-195)Ggg>Tgg	p.G65W	TAC4_ENST00000326219.5_Missense_Mutation_p.G59W|TAC4_ENST00000352793.2_Missense_Mutation_p.G59W|TAC4_ENST00000398154.1_Missense_Mutation_p.G59W|RP11-304F15.3_ENST00000376609.1_RNA|TAC4_ENST00000436235.1_Missense_Mutation_p.G59W	NM_170685.2	NP_733786.2			tachykinin 4 (hemokinin)											breast(1)|large_intestine(1)|lung(3)	5						CCCATCAGCCCAAAGAACTGG	0.557																																					p.G65W		Atlas-SNP	.											.	TAC4	6	.	0			c.G193T						PASS	.						182	187	185					17																	47921450		1998	4184	6182	SO:0001583	missense	255061	exon2			TCAGCCCAAAGAA	AF521560	CCDS42357.1, CCDS42358.1, CCDS42359.1, CCDS42360.1, CCDS45727.1	17q21.33	2014-01-30			ENSG00000176358	ENSG00000176358		"Endogenous ligands"	16641	protein-coding gene	gene with protein product		607833				11062498, 12383518	Standard	NM_170685		Approved	HK-1, Pptc, PPT-C	uc002ipp.1	Q86UU9	OTTHUMG00000161830	ENST00000334568.4:c.193G>T	chr17.hg19:g.47921450C>A	ENSP00000334042:p.Gly65Trp	67.0	0.0	.		55.0	40.0	.	NM_170685		Missense_Mutation	SNP	ENST00000334568.4	hg19	CCDS42357.1	.	.	.	.	.	.	.	.	.	.	C	19.54	3.847466	0.71603	.	.	ENSG00000176358	ENST00000352793;ENST00000334568;ENST00000398154;ENST00000436235;ENST00000326219	.	.	.	4.9	3.91	0.45181	Tachykinin/Neurokinin-like, conserved site (1);	0.286836	0.25366	N	0.031192	T	0.65375	0.2685	L	0.36672	1.1	0.38235	D	0.941162	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;0.999	T	0.70594	-0.4829	9	0.87932	D	0	-13.9808	11.3861	0.49787	0.0:0.8175:0.1825:0.0	.	59;59;59;59;65	Q86UU9-4;Q86UU9-2;Q86UU9-3;Q86UU9-5;Q86UU9	.;.;.;.;TKN4_HUMAN	W	59;65;59;59;59	.	ENSP00000325286:G59W	G	-	1	0	TAC4	45276449	0.997000	0.39634	0.999000	0.59377	0.986000	0.74619	1.991000	0.40727	1.398000	0.46701	0.650000	0.86243	GGG	.	.	.	none		0.557	TAC4-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000366198.1	NM_170685		A	47921450	C	A	47921450	3	1	40	1	0	0	0	0	1	0	0	0	15512	594	21	4	164	4	TAC4	17	47921450	Missense_Mutation	SNP	C	TCGA-5P-A9KH-01A-11D-A42J-10	40343935	47921450	33273760	21	2889											
MEGF8	1954	hgsc.bcm.edu	37	chr19	42866746	42866746	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacgcggcagttcaagaggAcaggtgagcagtgggcctag	10	5	18	8	2	1	2	1	1	0	1	1	4	1	4	1	5	1	3	1	5	2	2			TCGA-5P-A9KH-01A-11D-A42J-10	TCGA-5P-A9KH-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d91e36f3-e4a2-4af3-802a-3148b09be900	ccc45b0a-b066-47dd-934b-6f892b6c61a4	g.chr19:42866746A>G	ENST00000251268.6	+	34	6055	c.6055A>G	c.(6055-6057)Aca>Gca	p.T2019A	MEGF8_ENST00000334370.4_Missense_Mutation_p.T1952A	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	2019					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)				GTTCAAGAGGACAGGTGAGCA	0.667																																					p.T2019A		Atlas-SNP	.											.	MEGF8	358	.	0			c.A6055G						PASS	.						56	56	56					19																	42866746		2202	4300	6502	SO:0001583	missense	1954	exon34			AAGAGGACAGGTG	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.6055A>G	chr19.hg19:g.42866746A>G	ENSP00000251268:p.Thr2019Ala	38.0	0.0	.		43.0	11.0	.	NM_001271938	A8KAY0|O75097	Missense_Mutation	SNP	ENST00000251268.6	hg19		.	.	.	.	.	.	.	.	.	.	A	12.54	1.969158	0.34754	.	.	ENSG00000105429	ENST00000334370;ENST00000251268	T;T	0.21361	2.01;2.01	5.17	4.14	0.48551	.	0.000000	0.64402	D	0.000002	T	0.28665	0.0710	L	0.43152	1.355	0.80722	D	1	P;D	0.54964	0.944;0.969	B;P	0.56648	0.437;0.803	T	0.01363	-1.1374	10	0.27082	T	0.32	-8.6728	10.4224	0.44359	0.8534:0.0:0.0:0.1466	.	2019;1952	Q7Z7M0;Q7Z7M0-2	MEGF8_HUMAN;.	A	1952;2019	ENSP00000334219:T1952A;ENSP00000251268:T2019A	ENSP00000251268:T2019A	T	+	1	0	MEGF8	47558586	1.000000	0.71417	0.973000	0.42090	0.118000	0.20060	8.653000	0.91088	0.796000	0.33947	-0.490000	0.04691	ACA	.	.	.	none		0.667	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		G	42866746	A	G	42866746	3	3	40	1	0	0	0	0	1	0	0	0	9470	275	10	3	5984	3	MEGF8	19	42866746	Missense_Mutation	SNP	A	TCGA-5P-A9KH-01A-11D-A42J-10		42866746	16262237	22	2890											
KCNG1	3755	hgsc.bcm.edu	37	chr20	49626294	49626294	+	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	tcggccgggccctcgctgtcGcggccctcgctgtccagcgc	1	7	14	19	7	0	0	0	0	0	0	5	0	1	0	4	3	1	2	4	3	0	0			TCGA-5P-A9KH-01A-11D-A42J-10	TCGA-5P-A9KH-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d91e36f3-e4a2-4af3-802a-3148b09be900	ccc45b0a-b066-47dd-934b-6f892b6c61a4	g.chr20:49626294G>A	ENST00000371571.4	-	2	867	c.582C>T	c.(580-582)cgC>cgT	p.R194R	RP5-955M13.4_ENST00000424566.1_RNA|KCNG1_ENST00000396017.3_Silent_p.R194R|KCNG1_ENST00000506387.1_5'Flank	NM_002237.3	NP_002228.2	Q9UIX4	KCNG1_HUMAN	potassium voltage-gated channel, subfamily G, member 1	194					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						CCTCGCTGTCGCGGCCCTCGC	0.716																																					p.R194R		Atlas-SNP	.											.	KCNG1	86	.	0			c.C582T						PASS	.						18	20	19					20																	49626294		2199	4282	6481	SO:0001819	synonymous_variant	3755	exon2			GCTGTCGCGGCCC	AF033383	CCDS13436.1	20q13	2011-07-05			ENSG00000026559	ENSG00000026559		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6248	protein-coding gene	gene with protein product		603788		KCNG		9434767, 16382104	Standard	NM_002237		Approved	Kv6.1, kH2, K13	uc002xwa.4	Q9UIX4	OTTHUMG00000032745	ENST00000371571.4:c.582C>T	chr20.hg19:g.49626294G>A		35.0	0.0	.		53.0	15.0	.	NM_002237	A8K3S4|O43528|Q5JXL5|Q9BRC1	Silent	SNP	ENST00000371571.4	hg19	CCDS13436.1																																																																																			.	.	.	none		0.716	KCNG1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079726.4	NM_002237		A	49626294	G	A	49626294	2	1	40	1	0	0	0	0	0	0	0	1	8034	1074	38	1		1	KCNG1	20	49626294	Silent	SNP	G	TCGA-5P-A9KH-01A-11D-A42J-10		49626294	13399226	23	2891											
NCOA1	8648	hgsc.bcm.edu	37	chr2	24991159	24991159	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtaggcggggacccttacCtgaaccagcctggtccactg	7	8	13	13	1	0	1	0	1	0	0	1	2	1	2	5	5	3	1	5	5	3	2			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr2:24991159C>T	ENST00000406961.1	+	23	4877	c.4225C>T	c.(4225-4227)Ctg>Ttg	p.L1409L	NCOA1_ENST00000405141.1_3'UTR|NCOA1_ENST00000348332.3_Silent_p.L1409L|NCOA1_ENST00000288599.5_3'UTR|NCOA1_ENST00000538539.1_3'UTR|NCOA1_ENST00000407230.1_3'UTR|NCOA1_ENST00000395856.3_Silent_p.L1408L			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	1409					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)					GGACCCTTACCTGAACCAGCC	0.532			T	PAX3	alveolar rhadomyosarcoma																																p.L1409L		Atlas-SNP	.		Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	NCOA1	210	.	0			c.C4225T						PASS	.						89	90	90					2																	24991159		2203	4300	6503	SO:0001819	synonymous_variant	8648	exon21			CCTTACCTGAACC	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.4225C>T	chr2.hg19:g.24991159C>T		159.0	0.0	.		141.0	27.0	.	NM_003743	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Silent	SNP	ENST00000406961.1	hg19	CCDS1712.1																																																																																			.	.	.	none		0.532	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223		T	24991159	C	T	24991159	2	4	41	1	0	0	0	0	0	0	0	1	10235	680	24	2		2	NCOA1	2	24991159	Silent	SNP	C	TCGA-A4-7286-01A-11D-2136-08		24991159	218208214	1	2892											
CCDC75	253635	hgsc.bcm.edu	37	chr2	37319335	37319336	+	Missense_Mutation	DNP	AA	AA	CT																															cttaaaaataagcaagatgaAatgaagctagaaggagatct																										TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr2:37319335_37319336AA>CT	ENST00000608836.1	+	6	610_611	c.465_466AA>CT	c.(463-468)gaAAtg>gaCTtg	p.155_156EM>DL	GPATCH11_ENST00000281932.5_Missense_Mutation_p.52_53EM>DL|GPATCH11_ENST00000409774.1_Missense_Mutation_p.181_182EM>DL	NM_174931.2	NP_777591.3	Q8N954	GPT11_HUMAN	G patch domain containing 11	155							nucleic acid binding (GO:0003676)										AGCAAGATGAAATGAAGCTAGA	0.361																																					p.E155D|p.M156L		Atlas-SNP	.											.	.	.	.	0			c.A465C|c.A466T						PASS	.																																			SO:0001583	missense	253635	exon6			AGATGAAATGAAG|GATGAAATGAAGC	AK095667	CCDS1785.2, CCDS62891.1, CCDS1785.3	2p22.2	2013-11-05	2013-01-28	2013-01-28	ENSG00000152133	ENSG00000152133		"G patch domain containing"	26768	protein-coding gene	gene with protein product	"centromere protein Y"		"coiled-coil domain containing 75"	CCDC75			Standard	NM_001278505		Approved	FLJ38348, CENPY, CENP-Y	uc010ezz.3	Q8N954	OTTHUMG00000128469	Exception_encountered	chr2.hg19:g.37319335_37319336delinsCT	ENSP00000476383:p.E155_M156delinsDL	29.0|28.0	0.0	.		27.0|28.0	9.0	.	NM_174931	A8K0D9|B7Z2G4|B8ZZ44	Missense_Mutation	SNP	ENST00000608836.1	hg19	CCDS1785.2																																																																																			.	.	.	none		0.361	GPATCH11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_174931		CT	37319336	AA	CT	37319335	3	2	41	1	0	0	0	0	1	0	0	0	2851	11	1	5	483	5	CCDC75	2	37319335	Missense_Mutation	DNP	AA	TCGA-A4-7286-01A-11D-2136-08	12328176	37319335	205880038	2	2893											
RTKN	6242	hgsc.bcm.edu	37	chr2	74657398	74657398	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caagagcacattgctctgaaAggagatgtctgtgagggtcc	11	9	13	8	0	2	4	0	2	2	2	3	5	3	4	1	2	2	2	1	2	2	1			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr2:74657398A>G	ENST00000233330.6	-	5	693	c.376T>C	c.(376-378)Ttt>Ctt	p.F126L	RTKN_ENST00000484453.1_5'Flank|RTKN_ENST00000272430.5_Missense_Mutation_p.F176L|RTKN_ENST00000305557.5_Missense_Mutation_p.F163L	NM_001015056.1	NP_001015056.1			rhotekin											endometrium(3)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	16						TTGCTCTGAAAGGAGATGTCT	0.562																																					p.F176L		Atlas-SNP	.											.	RTKN	80	.	0			c.T526C						PASS	.						101	89	93					2																	74657398		2203	4300	6503	SO:0001583	missense	6242	exon5			TCTGAAAGGAGAT	AF049227	CCDS1941.1, CCDS33226.1, CCDS42699.1	2p13.1	2013-01-10			ENSG00000114993	ENSG00000114993		"Pleckstrin homology (PH) domain containing"	10466	protein-coding gene	gene with protein product		602288				9073523, 10940294	Standard	XM_005264478		Approved	B5	uc002sle.3	Q9BST9	OTTHUMG00000129955	ENST00000233330.6:c.376T>C	chr2.hg19:g.74657398A>G	ENSP00000233330:p.Phe126Leu	49.0	0.0	.		44.0	8.0	.	NM_001015055		Missense_Mutation	SNP	ENST00000233330.6	hg19	CCDS42699.1	.	.	.	.	.	.	.	.	.	.	A	29.8	5.037389	0.93630	.	.	ENSG00000114993	ENST00000305557;ENST00000272430;ENST00000233330	T;T;T	0.53857	0.6;0.6;0.6	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.72104	0.3419	M	0.81112	2.525	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.74494	-0.3647	10	0.48119	T	0.1	.	12.7658	0.57391	1.0:0.0:0.0:0.0	.	176;163	Q9BST9;Q9BST9-2	RTKN_HUMAN;.	L	163;176;126	ENSP00000305298:F163L;ENSP00000272430:F176L;ENSP00000233330:F126L	ENSP00000233330:F126L	F	-	1	0	RTKN	74510906	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.671000	0.91174	2.111000	0.64477	0.460000	0.39030	TTT	.	.	.	none		0.562	RTKN-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000328236.3	NM_001015055		G	74657398	A	G	74657398	3	3	41	1	0	0	0	0	1	0	0	0	13735	72	3	3	1197	3	RTKN	2	74657398	Missense_Mutation	SNP	A	TCGA-A4-7286-01A-11D-2136-08	37338063	74657398	168541975	3	2894											
SPOPL	339745	hgsc.bcm.edu	37	chr2	139308572	139308572	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaaaagtgaagttcgagcAaaattcaaattttcccttct	14	12	5	10	1	2	1	1	1	1	0	4	2	3	1	2	0	1	2	2	0	6	5			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr2:139308572A>G	ENST00000280098.4	+	4	679	c.300A>G	c.(298-300)gcA>gcG	p.A100A		NM_001001664.2	NP_001001664.1	Q6IQ16	SPOPL_HUMAN	speckle-type POZ protein-like	100	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				negative regulation of protein ubiquitination (GO:0031397)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nucleus (GO:0005634)				breast(2)|cervix(2)|endometrium(2)|large_intestine(2)|lung(11)|skin(2)	21				BRCA - Breast invasive adenocarcinoma(221;0.0296)		AAGTTCGAGCAAAATTCAAAT	0.368																																					p.A100A		Atlas-SNP	.											.	SPOPL	54	.	0			c.A300G						PASS	.						69	73	72					2																	139308572		2203	4299	6502	SO:0001819	synonymous_variant	339745	exon4			TCGAGCAAAATTC		CCDS33298.1	2q22.1	2013-01-09			ENSG00000144228	ENSG00000144228		"BTB/POZ domain containing"	27934	protein-coding gene	gene with protein product	"HIB homolog 2", "roadkill homolog 2"						Standard	NM_001001664		Approved	BTBD33	uc002tvh.3	Q6IQ16	OTTHUMG00000153635	ENST00000280098.4:c.300A>G	chr2.hg19:g.139308572A>G		103.0	0.0	.		119.0	32.0	.	NM_001001664		Silent	SNP	ENST00000280098.4	hg19	CCDS33298.1																																																																																			.	.	.	none		0.368	SPOPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331897.1			G	139308572	A	G	139308572	2	3	41	1	0	0	0	0	0	0	0	1	15097	117	5	3		3	SPOPL	2	139308572	Silent	SNP	A	TCGA-A4-7286-01A-11D-2136-08	64651174	139308572	103890801	4	2895											
KYNU	8942	hgsc.bcm.edu	37	chr2	143718222	143718222	+	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	accttaagaatagaggatatCcttgaagtaattgagaagga	17	10	10	4	0	0	4	0	2	0	3	1	7	1	6	2	2	0	1	2	2	7	6			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr2:143718222C>G	ENST00000264170.4	+	8	870	c.612C>G	c.(610-612)atC>atG	p.I204M	KYNU_ENST00000375773.2_Missense_Mutation_p.I204M|KYNU_ENST00000409512.1_Missense_Mutation_p.I204M	NM_003937.2	NP_003928.1			kynureninase											large_intestine(10)|liver(1)|lung(18)|prostate(3)|skin(4)	36				BRCA - Breast invasive adenocarcinoma(221;0.072)		TAGAGGATATCCTTGAAGTAA	0.368																																					p.I204M		Atlas-SNP	.											.	KYNU	110	.	0			c.C612G						PASS	.						105	106	106					2																	143718222		2203	4300	6503	SO:0001583	missense	8942	exon9			GGATATCCTTGAA	U57721	CCDS2183.1, CCDS33299.1	2q22.2	2010-11-23	2010-11-23		ENSG00000115919	ENSG00000115919	3.7.1.3		6469	protein-coding gene	gene with protein product	"L-kynurenine hydrolase"	605197	"kynureninase (L-kynurenine hydrolase)"			8706755, 9180257	Standard	NM_001199241		Approved		uc002tvl.3	Q16719	OTTHUMG00000131829	ENST00000264170.4:c.612C>G	chr2.hg19:g.143718222C>G	ENSP00000264170:p.Ile204Met	87.0	0.0	.		93.0	15.0	.	NM_001199241		Missense_Mutation	SNP	ENST00000264170.4	hg19	CCDS2183.1	.	.	.	.	.	.	.	.	.	.	C	15.87	2.960574	0.53400	.	.	ENSG00000115919	ENST00000264170;ENST00000375773;ENST00000409512	T;T;T	0.58797	0.31;0.31;0.31	5.35	-0.683	0.11335	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.000000	0.85682	D	0.000000	T	0.76176	0.3951	M	0.93898	3.47	0.80722	D	1	D;D	0.76494	0.975;0.999	D;D	0.85130	0.927;0.997	T	0.72567	-0.4254	10	0.72032	D	0.01	.	6.1677	0.20400	0.123:0.4133:0.0:0.4637	.	204;204	Q16719;Q9BVW3	KYNU_HUMAN;.	M	204	ENSP00000264170:I204M;ENSP00000364928:I204M;ENSP00000386731:I204M	ENSP00000264170:I204M	I	+	3	3	KYNU	143434692	0.998000	0.40836	0.989000	0.46669	0.991000	0.79684	0.528000	0.23002	-0.374000	0.07967	-0.147000	0.13772	ATC	.	.	.	none		0.368	KYNU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254772.1	NM_001032998		G	143718222	C	G	143718222	3	3	41	1	0	0	0	0	1	0	0	0	8594	845	30	4	638	4	KYNU	2	143718222	Missense_Mutation	SNP	C	TCGA-A4-7286-01A-11D-2136-08	4409650	143718222	99481151	5	2896											
LY75	4065	hgsc.bcm.edu	37	chr2	160665004	160665004	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccaaactctcatggtaatgTtattattttccctcatcagt	10	16	5	10	0	3	0	3	0	1	0	5	0	4	0	2	1	1	2	2	1	4	5			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr2:160665004T>C	ENST00000263636.4	-	33	4805	c.4778A>G	c.(4777-4779)aAc>aGc	p.N1593S	LY75_ENST00000554112.1_Missense_Mutation_p.N1593S|LY75_ENST00000553424.1_Missense_Mutation_p.N1593S|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.N1593S|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.N1593S	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1593	C-type lectin 10. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		CATGGTAATGTTATTATTTTC	0.338																																					p.N1593S		Atlas-SNP	.											.	LY75	151	.	0			c.A4778G						PASS	.						224	217	219					2																	160665004		2202	4299	6501	SO:0001583	missense	4065	exon33			GTAATGTTATTAT	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.4778A>G	chr2.hg19:g.160665004T>C	ENSP00000263636:p.Asn1593Ser	80.0	0.0	.		82.0	21.0	.	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	hg19	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	T	10.94	1.491766	0.26774	.	.	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.06849	3.25;3.25;3.25;3.25;3.25	5.55	5.55	0.83447	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.242632	0.21380	U	0.075495	T	0.09818	0.0241	L	0.33710	1.025	0.26761	N	0.969999	B;P;D	0.53619	0.082;0.912;0.961	B;P;P	0.52066	0.087;0.574;0.689	T	0.09422	-1.0675	10	0.08381	T	0.77	-17.923	9.2003	0.37254	0.2708:0.0:0.0:0.7292	.	1593;1593;1593	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	S	1593	ENSP00000451511:N1593S;ENSP00000451446:N1593S;ENSP00000263636:N1593S;ENSP00000423463:N1593S;ENSP00000421035:N1593S	ENSP00000423463:N1593S	N	-	2	0	LY75;LY75-CD302	160373250	0.999000	0.42202	0.998000	0.56505	0.984000	0.73092	2.859000	0.48364	2.105000	0.64084	0.402000	0.26972	AAC	.	.	.	none		0.338	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1			C	160665004	T	C	160665004	3	2	41	1	0	0	0	0	1	0	0	0	9106	1725	60	3	402	3	LY75	2	160665004	Missense_Mutation	SNP	T	TCGA-A4-7286-01A-11D-2136-08	16946782	160665004	82534369	6	2897											
CCNG2	901	hgsc.bcm.edu	37	chr4	78082688	78082688	+	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	agctgaaagcttgcaactgcCgactcatcttttcaaaagca	13	10	7	11	1	3	1	2	1	1	0	3	2	3	1	1	0	6	4	1	0	4	3			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr4:78082688C>T	ENST00000316355.5	+	5	939	c.583C>T	c.(583-585)Cga>Tga	p.R195*	CCNG2_ENST00000354403.5_Nonsense_Mutation_p.R195*|CCNG2_ENST00000502280.1_Nonsense_Mutation_p.R195*|CCNG2_ENST00000509972.1_Nonsense_Mutation_p.R195*|CCNG2_ENST00000497512.1_3'UTR|CCNG2_ENST00000395640.1_Nonsense_Mutation_p.R195*	NM_004354.2	NP_004345.1	Q16589	CCNG2_HUMAN	cyclin G2	195					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						TTGCAACTGCCGACTCATCTT	0.294																																					p.R195X		Atlas-SNP	.											.	CCNG2	27	.	0			c.C583T						PASS	.						52	59	57					4																	78082688		2202	4300	6502	SO:0001587	stop_gained	901	exon5			AACTGCCGACTCA	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.583C>T	chr4.hg19:g.78082688C>T	ENSP00000315743:p.Arg195*	64.0	0.0	.		57.0	9.0	.	NM_004354	B4DF25|Q6FGA7|Q6FGC6	Nonsense_Mutation	SNP	ENST00000316355.5	hg19	CCDS3581.1	.	.	.	.	.	.	.	.	.	.	C	38	6.688916	0.97764	.	.	ENSG00000138764	ENST00000316355;ENST00000354403;ENST00000502280;ENST00000395640;ENST00000509972	.	.	.	5.52	4.68	0.58851	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.4327	15.8563	0.78979	0.1366:0.8634:0.0:0.0	.	.	.	.	X	195	.	ENSP00000315743:R195X	R	+	1	2	CCNG2	78301712	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.923000	0.48868	1.331000	0.45412	-0.152000	0.13540	CGA	.	.	.	none		0.294	CCNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252404.3	NM_004354		T	78082688	C	T	78082688	4	4	41	1	0	0	0	0	0	1	0	0	2926	644	23	1	597	1	CCNG2	4	78082688	Nonsense_Mutation	SNP	C	TCGA-A4-7286-01A-11D-2136-08		78082688	113071588	7	2898											
SYNPO2	171024	hgsc.bcm.edu	37	chr4	119952706	119952706	+	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	cacctcctcctgtggcctatAatcctatccactcgccgtct	6	12	5	18	2	1	0	0	0	1	0	6	0	5	0	7	1	0	0	7	1	3	3			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr4:119952706A>T	ENST00000429713.2	+	4	2958	c.2776A>T	c.(2776-2778)Aat>Tat	p.N926Y	SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000307142.4_Missense_Mutation_p.N926Y|SYNPO2_ENST00000434046.2_Missense_Mutation_p.N926Y	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	926						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						TGTGGCCTATAATCCTATCCA	0.572																																					p.N926Y		Atlas-SNP	.											.	SYNPO2	353	.	0			c.A2776T						PASS	.						87	82	84					4																	119952706		2203	4300	6503	SO:0001583	missense	171024	exon4			GCCTATAATCCTA	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.2776A>T	chr4.hg19:g.119952706A>T	ENSP00000395143:p.Asn926Tyr	128.0	0.0	.		108.0	30.0	.	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	hg19	CCDS47129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.3|20.3	3.960913|3.960913	0.74016|0.74016	.|.	.|.	ENSG00000172403|ENSG00000172403	ENST00000307142;ENST00000429713;ENST00000434046|ENST00000504178	T;T;T|.	0.15017|.	2.46;2.58;2.46|.	5.66|5.66	5.66|5.66	0.87406|0.87406	.|.	0.000000|.	0.64402|.	D|.	0.000002|.	T|.	0.77239|.	0.4101|.	M|M	0.80982|0.80982	2.52|2.52	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;0.997|.	D;D;D;D|.	0.91635|.	0.998;0.999;0.997;0.991|.	T|.	0.78874|.	-0.2032|.	9|.	.|.	.|.	.|.	-24.3416|-24.3416	15.8861|15.8861	0.79251|0.79251	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	926;926;926;926|.	B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6|.	.;.;.;SYNP2_HUMAN|.	Y|L	926|877	ENSP00000306015:N926Y;ENSP00000395143:N926Y;ENSP00000390965:N926Y|.	.|.	N|X	+|+	1|2	0|2	SYNPO2|SYNPO2	120172154|120172154	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.913000|0.913000	0.54294|0.54294	9.339000|9.339000	0.96797|0.96797	2.156000|2.156000	0.67533|0.67533	0.533000|0.533000	0.62120|0.62120	AAT|TAA	.	.	.	none		0.572	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1			T	119952706	A	T	119952706	3	4	41	1	0	0	0	0	1	0	0	0	15469	362	13	5	2790	5	SYNPO2	4	119952706	Missense_Mutation	SNP	A	TCGA-A4-7286-01A-11D-2136-08	41870018	119952706	71201570	8	2899											
FTMT	94033	hgsc.bcm.edu	37	chr5	121188229	121188229	+	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	aaggtgacccccatttgtgcGatttcctggaaacctactac	10	11	8	12	1	0	1	0	1	0	0	1	3	1	2	4	2	4	0	4	2	4	4			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr5:121188229G>A	ENST00000321339.1	+	1	580	c.571G>A	c.(571-573)Gat>Aat	p.D191N		NM_177478.1	NP_803431.1	Q8N4E7	FTMT_HUMAN	ferritin mitochondrial	191	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)		CCATTTGTGCGATTTCCTGGA	0.507																																					p.D191N		Atlas-SNP	.											.	FTMT	71	.	0			c.G571A						PASS	.						133	130	131					5																	121188229		2203	4300	6503	SO:0001583	missense	94033	exon1			TTGTGCGATTTCC	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.571G>A	chr5.hg19:g.121188229G>A	ENSP00000313691:p.Asp191Asn	237.0	0.0	.		217.0	55.0	.	NM_177478		Missense_Mutation	SNP	ENST00000321339.1	hg19	CCDS4128.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.316794	0.81469	.	.	ENSG00000181867	ENST00000321339	T	0.70516	-0.49	3.39	3.39	0.38822	Ferritin/ribonucleotide reductase-like (1);Ferritin, conserved site (1);Ferritin-related (1);Ferritin/DPS protein domain (1);Ferritin-like (1);	0.000000	0.85682	D	0.000000	T	0.78253	0.4254	M	0.67700	2.07	0.58432	D	0.999999	P	0.52577	0.954	P	0.57548	0.823	T	0.81355	-0.0970	10	0.72032	D	0.01	.	13.0805	0.59112	0.0:0.0:1.0:0.0	.	191	Q8N4E7	FTMT_HUMAN	N	191	ENSP00000313691:D191N	ENSP00000313691:D191N	D	+	1	0	FTMT	121216128	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	8.967000	0.93402	2.185000	0.69588	0.609000	0.83330	GAT	.	.	.	none		0.507	FTMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250884.1	NM_177478		A	121188229	G	A	121188229	3	1	41	1	0	0	0	0	1	0	0	0	6092	1058	37	1	573	1	FTMT	5	121188229	Missense_Mutation	SNP	G	TCGA-A4-7286-01A-11D-2136-08		121188229	59727031	9	2900											
TRIM52	84851	hgsc.bcm.edu	37	chr5	180687083	180687083	+	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	tctcggcacaccacacagatGgcctctttgtccacctcaca	9	9	6	17	1	3	1	1	0	2	1	5	1	4	1	4	2	0	1	4	2	0	1			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr5:180687083G>T	ENST00000327767.4	-	1	1036	c.732C>A	c.(730-732)gcC>gcA	p.A244A	TRIM52-AS1_ENST00000507434.1_RNA|CTC-338M12.4_ENST00000505151.1_RNA|TRIM52-AS1_ENST00000509252.1_RNA|CTC-338M12.4_ENST00000417281.2_RNA|TRIM52_ENST00000514805.1_5'UTR|CTC-338M12.4_ENST00000506340.1_RNA|TRIM52-AS1_ENST00000514146.1_RNA|CTC-338M12.4_ENST00000511331.1_RNA	NM_032765.2	NP_116154.1	Q96A61	TRI52_HUMAN	tripartite motif containing 52	244					positive regulation of NF-kappaB transcription factor activity (GO:0051092)	intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	8	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;0.0106)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.0588)|all_lung(500;0.149)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.232)		CCACACAGATGGCCTCTTTGT	0.537																																					p.A244A		Atlas-SNP	.											.	TRIM52	20	.	0			c.C732A						PASS	.						135	129	131					5																	180687083		2203	4300	6503	SO:0001819	synonymous_variant	84851	exon1			ACAGATGGCCTCT		CCDS4467.1	5q35.3	2013-01-09	2011-01-25		ENSG00000183718	ENSG00000183718		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19024	protein-coding gene	gene with protein product			"tripartite motif-containing 52"				Standard	NM_032765		Approved	RNF102	uc003mnp.3	Q96A61	OTTHUMG00000130964	ENST00000327767.4:c.732C>A	chr5.hg19:g.180687083G>T		257.0	0.0	.		155.0	39.0	.	NM_032765		Silent	SNP	ENST00000327767.4	hg19	CCDS4467.1																																																																																			.	.	.	none		0.537	TRIM52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253572.3	NM_032765		T	180687083	G	T	180687083	2	4	41	1	0	0	0	0	0	0	0	1	16539	1335	47	4		4	TRIM52	5	180687083	Silent	SNP	G	TCGA-A4-7286-01A-11D-2136-08	59498854	180687083	228177	10	2901											
BCLAF1	9774	hgsc.bcm.edu	37	chr6	136596669	136596669	+	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	tactaaacatactaagcataCctttaacatgatgaaccaag	18	10	4	9	0	0	2	0	2	0	0	0	2	0	2	2	0	7	1	2	0	9	7			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr6:136596669C>T	ENST00000531224.1	-	6	2105		c.e6+1		BCLAF1_ENST00000527536.1_Splice_Site|BCLAF1_ENST00000530767.1_Splice_Site|BCLAF1_ENST00000392348.2_Splice_Site|BCLAF1_ENST00000353331.4_Splice_Site|BCLAF1_ENST00000527759.1_Splice_Site	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1						apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		ACTAAGCATACCTTTAACATG	0.358																																					.	Colon(142;1534 1789 5427 7063 28491)	Atlas-SNP	.											.	BCLAF1	203	.	0			c.1852+1G>A						PASS	.						146	131	136					6																	136596669		2203	4300	6503	SO:0001630	splice_region_variant	9774	exon7			AGCATACCTTTAA	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.1852+1G>A	chr6.hg19:g.136596669C>T		108.0	0.0	.		112.0	8.0	.	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Splice_Site	SNP	ENST00000531224.1	hg19	CCDS5177.1	.	.	.	.	.	.	.	.	.	.	C	16.19	3.053045	0.55218	.	.	ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000530767;ENST00000527759;ENST00000392348;ENST00000529826	.	.	.	5.14	5.14	0.70334	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.9665	0.86287	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	BCLAF1	136638362	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	6.683000	0.74533	2.661000	0.90470	0.460000	0.39030	.	.	.	.	none		0.358	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739	Intron	T	136596669	C	T	136596669	5	4	41	1	0	0	0	0	0	0	1	0	1383	521	18	2	941	2	BCLAF1	6	136596669	Splice_Site	SNP	C	TCGA-A4-7286-01A-11D-2136-08		136596669	34518398	11	2902											
MEOX2	4223	hgsc.bcm.edu	37	chr7	15725809	15725809	+	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	tggtggtgatggtggtggtgGtggtggtggtggtggtgccc	1	13	24	3	0	0	1	0	1	0	0	0	1	0	1	1	11	1	0	1	11	0	0			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr7:15725809G>A	ENST00000262041.5	-	1	628	c.219C>T	c.(217-219)caC>caT	p.H73H	AC005550.5_ENST00000438923.1_lincRNA|AC005550.4_ENST00000442176.1_lincRNA	NM_005924.4	NP_005915.2	P50222	MEOX2_HUMAN	mesenchyme homeobox 2	73	Poly-His.				angiogenesis (GO:0001525)|blood circulation (GO:0008015)|limb development (GO:0060173)|multicellular organismal development (GO:0007275)|neuron death (GO:0070997)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle tissue development (GO:0007519)|somite specification (GO:0001757)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding (GO:0043565)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (126;0.0822)		ggtggtggtggtggtggtggt	0.597																																					p.H73H	Esophageal Squamous(140;197 1769 16409 18257 29929)	Atlas-SNP	.											MEOX2,caecum,carcinoma,0,1	MEOX2	68	.	0			c.C219T						PASS	.						22	23	23					7																	15725809		2203	4299	6502	SO:0001819	synonymous_variant	4223	exon1			GTGGTGGTGGTGG		CCDS34605.1	7p22.1-p21.3	2014-07-15	2005-12-22		ENSG00000106511	ENSG00000106511		"Homeoboxes / ANTP class : HOXL subclass"	7014	protein-coding gene	gene with protein product	"growth arrest-specific homeobox"	600535	"mesenchyme homeo box 2 (growth arrest-specific homeo box)", "mesenchyme homeobox 2 (growth arrest-specific homeo box)"	GAX		7713505	Standard	NM_005924		Approved	MOX2	uc003stc.3	P50222	OTTHUMG00000152390	ENST00000262041.5:c.219C>T	chr7.hg19:g.15725809G>A		16.0	2.0	.		17.0	8.0	.	NM_005924	B2R8I7|O75263|Q9UPL6	Silent	SNP	ENST00000262041.5	hg19	CCDS34605.1																																																																																			.	.	.	none		0.597	MEOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326058.2	NM_005924		A	15725809	G	A	15725809	2	1	41	1	0	0	0	0	0	0	0	1	9481	1252	44	2		2	MEOX2	7	15725809	Silent	SNP	G	TCGA-A4-7286-01A-11D-2136-08		15725809	143412854	12	2903											
FKBP9	11328	hgsc.bcm.edu	37	chr7	33014881	33014881	+	Frame_Shift_Del	DEL	C	C	-																															agaccaggttcagattcacaCctatttcaagcccccgagtt																										TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr7:33014881delC	ENST00000242209.4	+	3	624	c.455delC	c.(454-456)accfs	p.T152fs	FKBP9_ENST00000538336.1_Frame_Shift_Del_p.T205fs|FKBP9_ENST00000538443.1_Frame_Shift_Del_p.T14fs|AVL9_ENST00000404479.1_Intron	NM_001284343.1|NM_007270.3	NP_001271272.1|NP_009201.2	O95302	FKBP9_HUMAN	FK506 binding protein 9, 63 kDa	152					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)			CAGATTCACACCTATTTCAAG	0.468																																					p.T152fs		Atlas-INDEL	.											.	FKBP9	335	.	0			c.454delA						PASS	.						114	103	107					7																	33014881		2203	4300	6503	SO:0001589	frameshift_variant	11328	exon3			.	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.455delC	chr7.hg19:g.33014881delC	ENSP00000242209:p.Thr152fs	111.0	0.0	0		95.0	17.0	0.178947	NM_007270	B3KY35|B7Z1G9|B7Z6H3|Q2M2A1|Q3MIR7|Q6IN76|Q6P2N1|Q96EX5|Q96IJ9	Frame_Shift_Del	DEL	ENST00000242209.4	hg19	CCDS5439.1																																																																																			.	.	.	none		0.468	FKBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215137.1	NM_007270		-	33014881	C	-	33014881	7	5	41	1	0	1	0	1	0	0	0	0	5922	507	18	0	465	0	FKBP9	7	33014881	Frame_Shift_Del	DEL	C	TCGA-A4-7286-01A-11D-2136-08	17289072	33014881	126123782	13	2904											
DDX56	54606	hgsc.bcm.edu	37	chr7	44607797	44607797	+	Missense_Mutation	SNP	T	T	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	catgccgcagcagctggaggTccctagggttgtcttcaaag	8	9	13	11	1	2	0	1	0	1	0	3	1	3	1	2	3	3	4	2	3	2	3			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr7:44607797T>G	ENST00000258772.5	-	12	1515	c.1409A>C	c.(1408-1410)gAc>gCc	p.D470A	DDX56_ENST00000485367.1_5'UTR|DDX56_ENST00000431640.1_Missense_Mutation_p.D430A	NM_001257189.1|NM_019082.3	NP_001244118.1|NP_061955.1	Q9NY93	DDX56_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 56	470					ATP catabolic process (GO:0006200)|rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(5)|upper_aerodigestive_tract(1)	16						CAGCTGGAGGTCCCTAGGGTT	0.567																																					p.D470A		Atlas-SNP	.											.	DDX56	36	.	0			c.A1409C						PASS	.						80	76	77					7																	44607797		2203	4300	6503	SO:0001583	missense	54606	exon12			TGGAGGTCCCTAG	AJ131712	CCDS5492.1, CCDS59053.1	7p13	2012-02-23	2012-02-23		ENSG00000136271	ENSG00000136271		"DEAD-boxes"	18193	protein-coding gene	gene with protein product	"nucleolar helicase of 61 kDa"	608023	"DEAD (Asp-Glu-Ala-Asp) box polypeptide 56"			10749921	Standard	NM_019082		Approved	NOH61	uc003tlg.4	Q9NY93	OTTHUMG00000129211	ENST00000258772.5:c.1409A>C	chr7.hg19:g.44607797T>G	ENSP00000258772:p.Asp470Ala	57.0	0.0	.		53.0	9.0	.	NM_019082	A4D2K9|C9JV95|Q6IAE2|Q9H9I8	Missense_Mutation	SNP	ENST00000258772.5	hg19	CCDS5492.1	.	.	.	.	.	.	.	.	.	.	.	27.7	4.856346	0.91355	.	.	ENSG00000136271	ENST00000258772;ENST00000431640;ENST00000448192	T;T	0.07908	3.19;3.15	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.34658	0.0905	M	0.88570	2.965	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.26608	-1.0098	10	0.62326	D	0.03	-35.5767	13.7285	0.62771	0.0:0.0:0.0:1.0	.	430;470	C9JV95;Q9NY93	.;DDX56_HUMAN	A	470;430;75	ENSP00000258772:D470A;ENSP00000393488:D430A	ENSP00000258772:D470A	D	-	2	0	DDX56	44574322	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	6.924000	0.75823	2.137000	0.66172	0.533000	0.62120	GAC	.	.	.	none		0.567	DDX56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251291.1	NM_019082		G	44607797	T	G	44607797	3	3	41	1	0	0	0	0	1	0	0	0	4376	1667	58	5	246	5	DDX56	7	44607797	Missense_Mutation	SNP	T	TCGA-A4-7286-01A-11D-2136-08	11592916	44607797	114530866	14	2905											
RELN	5649	hgsc.bcm.edu	37	chr7	103234873	103234873	+	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	tagtcctcccctgagaacacGggctgccaccagcggaacct	9	6	10	16	2	0	1	0	1	0	1	2	3	2	2	6	2	4	1	6	2	3	1			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr7:103234873G>C	ENST00000428762.1	-	26	3765	c.3606C>G	c.(3604-3606)ccC>ccG	p.P1202P	RELN_ENST00000424685.2_Silent_p.P1202P|RELN_ENST00000343529.5_Silent_p.P1202P	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1202					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)		CTGAGAACACGGGCTGCCACC	0.488																																					p.P1202P	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.C3606G						PASS	.						182	181	181					7																	103234873		2203	4300	6503	SO:0001819	synonymous_variant	5649	exon26			GAACACGGGCTGC		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.3606C>G	chr7.hg19:g.103234873G>C		334.0	0.0	.		341.0	22.0	.	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	hg19	CCDS47680.1																																																																																			.	.	.	none		0.488	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		C	103234873	G	C	103234873	2	2	41	1	0	0	0	0	0	0	0	1	13233	1103	39	4		4	RELN	7	103234873	Silent	SNP	G	TCGA-A4-7286-01A-11D-2136-08	58627076	103234873	55903790	15	2906											
PRSS55	203074	hgsc.bcm.edu	37	chr8	10388999	10388999	+	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	catctgcctccccacgcagcCcggccctgccacatggcgcg	5	5	10	21	4	1	0	0	0	1	0	2	0	2	0	6	2	3	1	6	2	0	0			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr8:10388999C>G	ENST00000328655.3	+	3	582	c.542C>G	c.(541-543)cCc>cGc	p.P181R	PRSS55_ENST00000522210.1_Missense_Mutation_p.P181R|PRSS51_ENST00000523024.1_RNA	NM_198464.3	NP_940866.2	Q6UWB4	PRS55_HUMAN	protease, serine, 55	181	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)	31						CCCACGCAGCCCGGCCCTGCC	0.587																																					p.P181R		Atlas-SNP	.											.	PRSS55	67	.	0			c.C542G						PASS	.						70	64	66					8																	10388999		2203	4300	6503	SO:0001583	missense	203074	exon3			CGCAGCCCGGCCC	AY358867	CCDS5976.1, CCDS56523.1	8p23.1	2014-01-21			ENSG00000184647	ENSG00000184647		"Serine peptidases / Serine peptidases"	30824	protein-coding gene	gene with protein product		615144				12975309, 18844450	Standard	NM_198464		Approved	T-SP1, UNQ9391, CT153	uc003wta.3	Q6UWB4	OTTHUMG00000129345	ENST00000328655.3:c.542C>G	chr8.hg19:g.10388999C>G	ENSP00000333003:p.Pro181Arg	110.0	0.0	.		102.0	11.0	.	NM_001197020	E5RJX5	Missense_Mutation	SNP	ENST00000328655.3	hg19	CCDS5976.1	.	.	.	.	.	.	.	.	.	.	C	5.554	0.287080	0.10513	.	.	ENSG00000184647	ENST00000328655;ENST00000522210	D;D	0.88509	-2.39;-2.39	4.79	-3.88	0.04205	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.401620	0.05168	N	0.499078	T	0.71256	0.3318	N	0.11427	0.14	0.09310	N	1	B	0.31256	0.316	B	0.28553	0.091	T	0.62210	-0.6902	10	0.16896	T	0.51	.	1.6522	0.02774	0.3222:0.3223:0.2083:0.1472	.	181	Q6UWB4	PRS55_HUMAN	R	181	ENSP00000333003:P181R;ENSP00000430459:P181R	ENSP00000333003:P181R	P	+	2	0	PRSS55	10426409	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.518000	0.06267	-0.898000	0.03906	-2.547000	0.00178	CCC	.	.	.	none		0.587	PRSS55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251493.3	NM_198464		G	10388999	C	G	10388999	3	3	41	1	0	0	0	0	1	0	0	0	12644	623	22	4	552	4	PRSS55	8	10388999	Missense_Mutation	SNP	C	TCGA-A4-7286-01A-11D-2136-08		10388999	135975023	16	2907											
COL22A1	169044	hgsc.bcm.edu	37	chr8	139790649	139790649	+	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	tccaggtggtccttggggccCctgcagaagagcatttacag	8	9	13	11	0	0	2	0	0	0	2	2	2	2	2	4	4	3	2	4	4	2	3			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr8:139790649C>T	ENST00000303045.6	-	15	2151	c.1705G>A	c.(1705-1707)Ggg>Agg	p.G569R	COL22A1_ENST00000435777.1_Splice_Site_p.G569R	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	569	Collagen-like 3.|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)			CCTTGGGGCCCCTGCAGAAGA	0.572										HNSCC(7;0.00092)																											p.G569R		Atlas-SNP	.											COL22A1,NS,malignant_melanoma,0,1	COL22A1	390	.	0			c.G1705A						PASS	.						41	46	44					8																	139790649		2203	4300	6503	SO:0001630	splice_region_variant	169044	exon15			GGGGCCCCTGCAG	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.1705-1G>A	chr8.hg19:g.139790649C>T		55.0	0.0	.		59.0	21.0	.	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	hg19	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	C	5.522	0.281168	0.10458	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000522546	D;D;D	0.99488	-5.77;-3.26;-6.0	4.97	3.15	0.36227	.	0.000000	0.48286	U	0.000185	D	0.99127	0.9699	H	0.96633	3.855	0.44966	D	0.997988	B	0.20052	0.041	B	0.26202	0.067	D	0.99679	1.0998	10	0.72032	D	0.01	.	6.7777	0.23628	0.0:0.7264:0.1791:0.0945	.	569	Q8NFW1	COMA1_HUMAN	R	569;569;19	ENSP00000303153:G569R;ENSP00000387655:G569R;ENSP00000428244:G19R	ENSP00000303153:G569R	G	-	1	0	COL22A1	139859831	1.000000	0.71417	0.962000	0.40283	0.102000	0.19082	3.260000	0.51523	0.791000	0.33826	-0.176000	0.13171	GGG	.	.	.	none		0.572	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	Missense_Mutation	T	139790649	C	T	139790649	5	4	41	1	0	0	0	0	0	0	1	0	3683	637	22	2	3379	2	COL22A1	8	139790649	Splice_Site	SNP	C	TCGA-A4-7286-01A-11D-2136-08	129401650	139790649	6573373	17	2908											
ANKS6	203286	hgsc.bcm.edu	37	chr9	101533259	101533259	+	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	tgaatgaggcgagtggttgaAgtttccagaattggcagaag	12	10	15	4	1	0	5	0	3	0	2	1	6	1	5	1	3	0	3	1	3	4	3			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr9:101533259A>T	ENST00000353234.4	-	10	1938	c.1891T>A	c.(1891-1893)Ttc>Atc	p.F631I	ANKS6_ENST00000375019.2_Missense_Mutation_p.F330I|ANKS6_ENST00000375018.1_Missense_Mutation_p.F631I|ANKS6_ENST00000540940.1_Missense_Mutation_p.F436I			Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain containing 6	631	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)				GAGTGGTTGAAGTTTCCAGAA	0.582																																					p.F631I		Atlas-SNP	.											.	ANKS6	59	.	0			c.T1891A						PASS	.						51	57	55					9																	101533259		1872	4107	5979	SO:0001583	missense	203286	exon10			GGTTGAAGTTTCC	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.1891T>A	chr9.hg19:g.101533259A>T	ENSP00000297837:p.Phe631Ile	56.0	0.0	.		56.0	13.0	.	NM_173551	A0SE62|Q5VSL0|Q5VSL2|Q5VSL3|Q5VSL4|Q68DB8|Q6P2R2|Q8N9L6|Q96D62	Missense_Mutation	SNP	ENST00000353234.4	hg19	CCDS43856.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.4|20.4	3.990515|3.990515	0.74589|0.74589	.|.	.|.	ENSG00000165138|ENSG00000165138	ENST00000375019;ENST00000375018;ENST00000353234;ENST00000540940|ENST00000444472	T;T;T;T|.	0.70045|.	1.72;-0.45;-0.45;1.97|.	5.76|5.76	4.61|4.61	0.57282|0.57282	.|.	0.212682|.	0.51477|.	D|.	0.000093|.	T|T	0.62380|0.62380	0.2423|0.2423	L|L	0.56769|0.56769	1.78|1.78	0.43617|0.43617	D|D	0.995998|0.995998	D;D|.	0.89917|.	1.0;0.999|.	D;D|.	0.83275|.	0.996;0.991|.	T|T	0.59215|0.59215	-0.7496|-0.7496	10|5	0.36615|.	T|.	0.2|.	-12.8842|-12.8842	11.2813|11.2813	0.49197|0.49197	0.8468:0.1532:0.0:0.0|0.8468:0.1532:0.0:0.0	.|.	631;631|.	Q68DC2-4;Q68DC2|.	.;ANKS6_HUMAN|.	I|H	330;631;631;436|99	ENSP00000364159:F330I;ENSP00000364158:F631I;ENSP00000297837:F631I;ENSP00000442189:F436I|.	ENSP00000297837:F631I|.	F|L	-|-	1|2	0|0	ANKS6|ANKS6	100573080|100573080	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.549000|0.549000	0.35272|0.35272	5.521000|5.521000	0.67086|0.67086	0.994000|0.994000	0.38892|0.38892	-0.648000|-0.648000	0.03929|0.03929	TTC|CTT	.	.	.	none		0.582	ANKS6-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277053.1	NM_173551		T	101533259	A	T	101533259	3	4	41	1	0	0	0	0	1	0	0	0	692	72	3	5	748	5	ANKS6	9	101533259	Missense_Mutation	SNP	A	TCGA-A4-7286-01A-11D-2136-08		101533259	39680172	18	2909											
ALG2	85365	hgsc.bcm.edu	37	chr9	101980774	101980774	+	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	ttcttcctttcgtatctgttGatggagagcagcaggaattt	8	16	10	7	1	2	2	0	1	2	1	4	4	3	3	1	2	2	4	1	2	2	6			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr9:101980774G>A	ENST00000476832.1	-	2	754	c.693C>T	c.(691-693)atC>atT	p.I231I	ALG2_ENST00000319033.6_Silent_p.I138I	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)				CGTATCTGTTGATGGAGAGCA	0.463																																					p.I231I		Atlas-SNP	.											.	ALG2	37	.	0			c.C693T						PASS	.						124	124	124					9																	101980774		2203	4300	6503	SO:0001819	synonymous_variant	85365	exon2			TCTGTTGATGGAG	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.693C>T	chr9.hg19:g.101980774G>A		127.0	0.0	.		98.0	25.0	.	NM_033087	B2RD16|E7ESR3|Q2YDC2|Q5TZS0	Silent	SNP	ENST00000476832.1	hg19	CCDS6739.1																																																																																			.	.	.	none		0.463	ALG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215080.1	NM_033087		A	101980774	G	A	101980774	2	1	41	1	0	0	0	0	0	0	0	1	519	1280	45	2		2	ALG2	9	101980774	Silent	SNP	G	TCGA-A4-7286-01A-11D-2136-08	447515	101980774	39232657	19	2910											
CCKBR	887	hgsc.bcm.edu	37	chr11	6281226	6281226	+	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	gccgggggcttccctgtgccGcccgggggcgcctctcctca	1	7	15	18	4	2	0	1	0	1	0	4	0	3	0	6	4	1	1	6	4	0	1			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr11:6281226G>C	ENST00000334619.2	+	1	261	c.68G>C	c.(67-69)cGc>cCc	p.R23P	CCKBR_ENST00000525462.1_Missense_Mutation_p.R23P|CCKBR_ENST00000531712.1_Missense_Mutation_p.R23P|CCKBR_ENST00000532715.1_Missense_Mutation_p.R23P|CCKBR_ENST00000525014.1_Missense_Mutation_p.R23P	NM_176875.3	NP_795344.1	P32239	GASR_HUMAN	cholecystokinin B receptor	23					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)	TCCCTGTGCCGCCCGGGGGCG	0.716																																					p.R23P		Atlas-SNP	.											.	CCKBR	232	.	0			c.G68C						PASS	.						9	13	12					11																	6281226		2165	4246	6411	SO:0001583	missense	887	exon1			TGTGCCGCCCGGG	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.68G>C	chr11.hg19:g.6281226G>C	ENSP00000335544:p.Arg23Pro	23.0	0.0	.		26.0	7.0	.	NM_176875	A8K7P9|O75824|Q16144|Q92492|Q96LC6|Q9NYK7|Q9UBV1	Missense_Mutation	SNP	ENST00000334619.2	hg19	CCDS7761.1	.	.	.	.	.	.	.	.	.	.	g	8.885	0.952549	0.18431	.	.	ENSG00000110148	ENST00000334619;ENST00000532715;ENST00000525014;ENST00000525462;ENST00000531712	T;T;T;T;T	0.77098	0.34;-1.07;-0.06;0.35;0.15	2.75	2.75	0.32379	.	0.513554	0.16331	U	0.219138	T	0.78027	0.4219	L	0.47716	1.5	0.31075	N	0.712597	D;B	0.61080	0.989;0.337	P;B	0.56865	0.808;0.11	T	0.74156	-0.3756	10	0.31617	T	0.26	.	9.2026	0.37268	0.0:0.0:1.0:0.0	.	23;23	P32239-2;P32239	.;GASR_HUMAN	P	23	ENSP00000335544:R23P;ENSP00000432079:R23P;ENSP00000437001:R23P;ENSP00000435534:R23P;ENSP00000435675:R23P	ENSP00000335544:R23P	R	+	2	0	CCKBR	6237802	1.000000	0.71417	0.996000	0.52242	0.042000	0.13812	1.757000	0.38400	1.859000	0.53934	0.580000	0.79431	CGC	.	.	.	none		0.716	CCKBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257230.2	NM_176875		C	6281226	G	C	6281226	3	2	41	1	0	0	0	0	1	0	0	0	2883	1087	38	4	70	4	CCKBR	11	6281226	Missense_Mutation	SNP	G	TCGA-A4-7286-01A-11D-2136-08		6281226	128725290	20	2911											
SLC17A6	57084	hgsc.bcm.edu	37	chr11	22363111	22363112	+	Frame_Shift_Del	DEL	GA	GA	-																															aagacaccggggagacaatcGagctgacggaggatgggaag																										TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	GA	GA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr11:22363111_22363112delGA	ENST00000263160.3	+	2	561_562	c.124_125delGA	c.(124-126)gagfs	p.E42fs		NM_020346.2	NP_065079.1	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 6	42					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						GGAGACAATCGAGCTGACGGAG	0.649																																					p.41_42del		Atlas-INDEL	.											.	SLC17A6	135	.	0			c.123_124del						PASS	.																																			SO:0001589	frameshift_variant	57084	exon2			.	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.124_125delGA	chr11.hg19:g.22363111_22363112delGA	ENSP00000263160:p.Glu42fs	113.0	0.0	0		112.0	17.0	0.151786	NM_020346	A6NKS2	Frame_Shift_Del	DEL	ENST00000263160.3	hg19	CCDS7856.1																																																																																			.	.	.	none		0.649	SLC17A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387671.1	NM_020346		-	22363112	GA	-	22363111	7	5	41	1	0	1	0	1	0	0	0	0	14434	1059	37	0	130	0	SLC17A6	11	22363111	Frame_Shift_Del	DEL	GA	TCGA-A4-7286-01A-11D-2136-08	16081885	22363111	112643405	21	2912											
RIMKLB	57494	hgsc.bcm.edu	37	chr12	8906507	8906507	+	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	taaagctgttttcttggctcGagataagcaccatttggctg	9	14	10	8	1	1	1	0	0	1	1	2	2	1	1	1	2	2	5	1	2	3	6	rs369058701		TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr12:8906507G>T	ENST00000538135.1	+	5	1340	c.515G>T	c.(514-516)cGa>cTa	p.R172L	RIMKLB_ENST00000299673.5_3'UTR|RIMKLB_ENST00000357529.3_Missense_Mutation_p.R172L|RIMKLB_ENST00000535829.1_Missense_Mutation_p.R172L			Q9ULI2	RIMKB_HUMAN	ribosomal modification protein rimK-like family member B	172	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						TTCTTGGCTCGAGATAAGCAC	0.388																																					p.R172L		Atlas-SNP	.											.	RIMKLB	47	.	0			c.G515T						PASS	.						94	82	86					12																	8906507		1884	4110	5994	SO:0001583	missense	57494	exon6			TGGCTCGAGATAA	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.515G>T	chr12.hg19:g.8906507G>T	ENSP00000440943:p.Arg172Leu	95.0	0.0	.		95.0	5.0	.	NM_020734	B7Z834|D3DUV2|Q8N4P4|Q8WTW6	Missense_Mutation	SNP	ENST00000538135.1	hg19	CCDS41748.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.750151	0.89753	.	.	ENSG00000166532	ENST00000535829;ENST00000357529;ENST00000538135	.	.	.	4.83	4.83	0.62350	ATP-grasp fold (1);ATP-grasp fold, RimK-type (1);ATP-grasp fold, subdomain 1 (1);	0.000000	0.64402	U	0.000004	T	0.54062	0.1835	L	0.31065	0.9	0.80722	D	1	B;B	0.33448	0.412;0.339	B;B	0.40901	0.232;0.343	T	0.60541	-0.7243	9	0.87932	D	0	.	16.8371	0.85959	0.0:0.0:1.0:0.0	.	172;172	Q9ULI2-2;Q9ULI2	.;RIMKB_HUMAN	L	172	.	ENSP00000350136:R172L	R	+	2	0	RIMKLB	8797774	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.835000	0.92100	2.379000	0.81126	0.591000	0.81541	CGA	.	.	.	alt		0.388	RIMKLB-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398874.1	NM_020734		T	8906507	G	T	8906507	3	4	41	1	0	0	0	0	1	0	0	0	13379	1058	37	4	529	4	RIMKLB	12	8906507	Missense_Mutation	SNP	G	TCGA-A4-7286-01A-11D-2136-08		8906507	124945388	22	2913											
EPS8	2059	hgsc.bcm.edu	37	chr12	15784493	15784493	+	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	ctttgacacaggaacaggtgCtggagtggaagggggaaggg	11	6	19	5	0	0	1	0	1	0	0	0	5	0	5	0	7	2	1	0	7	3	1			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr12:15784493C>A	ENST00000281172.5	-	18	2363	c.1927G>T	c.(1927-1929)Gca>Tca	p.A643S	EPS8_ENST00000540613.1_Missense_Mutation_p.A383S|EPS8_ENST00000543523.1_Missense_Mutation_p.A643S|EPS8_ENST00000543612.1_Missense_Mutation_p.A643S|EPS8_ENST00000542903.1_Missense_Mutation_p.A383S	NM_004447.5	NP_004438.3	Q12929	EPS8_HUMAN	epidermal growth factor receptor pathway substrate 8	643	Pro-rich.				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)		GGAACAGGTGCTGGAGTGGAA	0.547																																					p.A643S		Atlas-SNP	.											.	EPS8	70	.	0			c.G1927T						PASS	.						152	128	136					12																	15784493		2203	4300	6503	SO:0001583	missense	2059	exon18			CAGGTGCTGGAGT	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.1927G>T	chr12.hg19:g.15784493C>A	ENSP00000281172:p.Ala643Ser	150.0	0.0	.		173.0	28.0	.	NM_004447	A6NMC3|A8K6W2|A8KA66|B4DX66|Q8N6J0	Missense_Mutation	SNP	ENST00000281172.5	hg19	CCDS31753.1	.	.	.	.	.	.	.	.	.	.	C	16.23	3.064340	0.55432	.	.	ENSG00000151491	ENST00000543523;ENST00000281172;ENST00000543612;ENST00000540613;ENST00000542903;ENST00000543223	T;T;T;T;T	0.08546	3.21;3.21;3.21;3.08;3.08	5.75	5.75	0.90469	.	0.131007	0.51477	D	0.000098	T	0.19846	0.0477	L	0.38531	1.155	0.44104	D	0.996874	D	0.63880	0.993	D	0.72625	0.978	T	0.02654	-1.1128	10	0.20519	T	0.43	-4.529	18.1274	0.89590	0.0:1.0:0.0:0.0	.	643	Q12929	EPS8_HUMAN	S	643;643;643;383;383;643	ENSP00000441867:A643S;ENSP00000281172:A643S;ENSP00000442388:A643S;ENSP00000441888:A383S;ENSP00000437806:A383S	ENSP00000281172:A643S	A	-	1	0	EPS8	15675760	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	2.997000	0.49457	2.714000	0.92807	0.650000	0.86243	GCA	.	.	.	none		0.547	EPS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401093.1			A	15784493	C	A	15784493	3	1	41	1	0	0	0	0	1	0	0	0	5196	797	28	4	557	4	EPS8	12	15784493	Missense_Mutation	SNP	C	TCGA-A4-7286-01A-11D-2136-08	6877986	15784493	118067402	23	2914											
SFRS2IP	9169	hgsc.bcm.edu	37	chr12	46320210	46320210	+	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	ttgccaccgattttcattctGatctttataggcaaaactac	11	15	5	10	1	3	1	1	1	2	0	3	2	3	1	2	1	3	1	2	1	5	8			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr12:46320210G>T	ENST00000369367.3	-	11	3507	c.3274C>A	c.(3274-3276)Cag>Aag	p.Q1092K	SCAF11_ENST00000549162.1_Missense_Mutation_p.Q900K|SCAF11_ENST00000550629.1_5'Flank|SCAF11_ENST00000465950.1_Missense_Mutation_p.Q777K|SCAF11_ENST00000419565.2_Missense_Mutation_p.Q1092K	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	1092					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						TTTTCATTCTGATCTTTATAG	0.433																																					p.Q1092K		Atlas-SNP	.											.	SCAF11	145	.	0			c.C3274A						PASS	.						68	73	71					12																	46320210		2203	4300	6503	SO:0001583	missense	9169	exon11			CATTCTGATCTTT	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.3274C>A	chr12.hg19:g.46320210G>T	ENSP00000358374:p.Gln1092Lys	133.0	0.0	.		145.0	23.0	.	NM_004719	A6NEU9|A6NLW5|Q8IW59	Missense_Mutation	SNP	ENST00000369367.3	hg19	CCDS8748.2	.	.	.	.	.	.	.	.	.	.	G	18.09	3.546855	0.65198	.	.	ENSG00000139218	ENST00000465950;ENST00000369367;ENST00000549162;ENST00000419565	T;T;T;T	0.49720	0.77;0.77;0.77;0.77	5.85	5.85	0.93711	.	0.089021	0.49916	D	0.000137	T	0.64294	0.2585	M	0.62723	1.935	0.28696	N	0.904354	D;D	0.71674	0.998;0.988	D;P	0.65684	0.937;0.788	T	0.58578	-0.7612	10	0.12766	T	0.61	-12.0691	20.1563	0.98114	0.0:0.0:1.0:0.0	.	900;1092	F8VXG7;Q99590	.;SCAFB_HUMAN	K	777;1092;900;1092	ENSP00000449812:Q777K;ENSP00000358374:Q1092K;ENSP00000448864:Q900K;ENSP00000413036:Q1092K	ENSP00000358374:Q1092K	Q	-	1	0	SCAF11	44606477	1.000000	0.71417	0.980000	0.43619	0.815000	0.46073	5.535000	0.67173	2.775000	0.95449	0.655000	0.94253	CAG	.	.	.	none		0.433	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719		T	46320210	G	T	46320210	3	4	41	1	0	0	0	0	1	0	0	0	14190	1299	45	4	1137	4	SFRS2IP	12	46320210	Missense_Mutation	SNP	G	TCGA-A4-7286-01A-11D-2136-08	30535717	46320210	87531685	24	2915											
INHBC	3626	hgsc.bcm.edu	37	chr12	57828750	57828750	+	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	agagctggcggtcagtgtccAgcatgtggggggcccacctt	6	8	16	11	1	1	1	1	0	0	1	2	1	2	1	3	5	2	2	3	5	0	1			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr12:57828750A>C	ENST00000309668.2	+	1	208	c.81A>C	c.(79-81)ccA>ccC	p.P27P	RP11-756H6.1_ENST00000547552.1_lincRNA	NM_005538.2	NP_005529.1	P55103	INHBC_HUMAN	inhibin, beta C	27					growth (GO:0040007)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	transforming growth factor beta receptor binding (GO:0005160)			breast(2)|endometrium(1)|large_intestine(6)|liver(2)|lung(4)|prostate(1)	16						GTCAGTGTCCAGCATGTGGGG	0.607																																					p.P27P		Atlas-SNP	.											.	INHBC	28	.	0			c.A81C						PASS	.						41	41	41					12																	57828750		2203	4300	6503	SO:0001819	synonymous_variant	3626	exon1			GTGTCCAGCATGT		CCDS8938.1	12q13	2008-02-05				ENSG00000175189			6068	protein-coding gene	gene with protein product		601233				7826378	Standard	NM_005538		Approved		uc001snv.1	P55103	OTTHUMG00000169994	ENST00000309668.2:c.81A>C	chr12.hg19:g.57828750A>C		67.0	0.0	.		97.0	15.0	.	NM_005538	A1L3Y2	Silent	SNP	ENST00000309668.2	hg19	CCDS8938.1																																																																																			.	.	.	none		0.607	INHBC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406770.1	NM_005538		C	57828750	A	C	57828750	2	2	41	1	0	0	0	0	0	0	0	1	7750	175	7	5		5	INHBC	12	57828750	Silent	SNP	A	TCGA-A4-7286-01A-11D-2136-08	11508540	57828750	76023145	25	2916											
ALDH1L2	160428	hgsc.bcm.edu	37	chr12	105428135	105428135	+	Missense_Mutation	SNP	A	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	acgaacaaccgcccagcagcAatacagttctctcctttgtt	11	10	6	14	2	1	0	0	0	1	0	3	1	2	0	3	0	5	4	3	0	4	4			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr12:105428135A>C	ENST00000258494.9	-	19	2327	c.2187T>G	c.(2185-2187)atT>atG	p.I729M	C12orf45_ENST00000548583.1_Intron	NM_001034173.3	NP_001029345.2	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2	729	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|prostate(2)|skin(3)|stomach(2)	35						GCCCAGCAGCAATACAGTTCT	0.418																																					p.I729M		Atlas-SNP	.											.	ALDH1L2	71	.	0			c.T2187G						PASS	.						107	90	96					12																	105428135		2203	4300	6503	SO:0001583	missense	160428	exon19			AGCAGCAATACAG	AK095827	CCDS31891.1	12q23.3	2014-09-11			ENSG00000136010	ENSG00000136010	1.5.1.6	"Aldehyde dehydrogenases"	26777	protein-coding gene	gene with protein product	"mitochondrial 10-formyltetrahydrofolate dehydrogenase"	613584				20498374	Standard	NM_001034173		Approved	FLJ38508, mtFDH	uc001tlc.3	Q3SY69	OTTHUMG00000169823	ENST00000258494.9:c.2187T>G	chr12.hg19:g.105428135A>C	ENSP00000258494:p.Ile729Met	95.0	0.0	.		91.0	18.0	.	NM_001034173	Q3SY68|Q68D62|Q6AI55|Q8N922	Missense_Mutation	SNP	ENST00000258494.9	hg19	CCDS31891.1	.	.	.	.	.	.	.	.	.	.	A	18.79	3.699315	0.68501	.	.	ENSG00000136010	ENST00000258494	T	0.76839	-1.05	5.46	-0.924	0.10462	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);Aldehyde dehydrogenase, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.76442	0.3988	N	0.20574	0.59	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75227	-0.3392	10	0.87932	D	0	.	11.4475	0.50131	0.6024:0.0:0.3976:0.0	.	729	Q3SY69	AL1L2_HUMAN	M	729	ENSP00000258494:I729M	ENSP00000258494:I729M	I	-	3	3	ALDH1L2	103952265	1.000000	0.71417	0.991000	0.47740	0.968000	0.65278	1.140000	0.31516	-0.085000	0.12573	-0.388000	0.06559	ATT	.	.	.	none		0.418	ALDH1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406098.1	XM_090294		C	105428135	A	C	105428135	3	2	41	1	0	0	0	0	1	0	0	0	495	126	5	5	604	5	ALDH1L2	12	105428135	Missense_Mutation	SNP	A	TCGA-A4-7286-01A-11D-2136-08	47599385	105428135	28423760	26	2917											
MORN3	283385	hgsc.bcm.edu	37	chr12	122107353	122107353	+	Frame_Shift_Del	DEL	G	G	-																															ccggtcccaccccttccacaGggactccgacttttttgggc																										TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr12:122107353delG	ENST00000355329.3	-	1	207	c.37delC	c.(37-39)ctgfs	p.L13fs		NM_173855.4	NP_776254.3	Q6PF18	MORN3_HUMAN	MORN repeat containing 3	13						nucleus (GO:0005634)				breast(2)|large_intestine(1)|lung(4)|skin(1)|stomach(1)	9	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000409)|Epithelial(86;0.00145)		CCCTTCCACAGGGACTCCGAC	0.602																																					p.L13fs		Atlas-INDEL	.											.	MORN3	20	.	0			c.38delT						PASS	.						126	115	119					12																	122107353		2203	4300	6503	SO:0001589	frameshift_variant	283385	exon1			.	BC057760	CCDS31917.1	12q24.31	2006-01-17			ENSG00000139714	ENSG00000139714			29807	protein-coding gene	gene with protein product							Standard	NM_173855		Approved		uc001uax.3	Q6PF18	OTTHUMG00000169075	ENST00000355329.3:c.37delC	chr12.hg19:g.122107353delG	ENSP00000347486:p.Leu13fs	203.0	0.0	0		236.0	42.0	0.177966	NM_173855	Q86YQ9	Frame_Shift_Del	DEL	ENST00000355329.3	hg19	CCDS31917.1																																																																																			.	.	.	none		0.602	MORN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402154.1	NM_173855		-	122107353	G	-	122107353	7	5	41	1	0	1	0	1	0	0	0	0	9716	991	35	0	705	0	MORN3	12	122107353	Frame_Shift_Del	DEL	G	TCGA-A4-7286-01A-11D-2136-08	16679218	122107353	11744542	27	2918											
RNF6	6049	hgsc.bcm.edu	37	chr13	26788332	26788332	+	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	cctgccacccctactgtcacTgtttcgagtatgaggctggg	6	11	11	13	1	1	1	1	1	0	0	2	2	1	1	4	2	2	3	4	2	2	3			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr13:26788332T>A	ENST00000381588.4	-	5	2439	c.1687A>T	c.(1687-1689)Agt>Tgt	p.S563C	RNF6_ENST00000381570.3_Missense_Mutation_p.S563C|RNF6_ENST00000468480.1_Intron|RNF6_ENST00000399762.2_Missense_Mutation_p.S207C|RNF6_ENST00000346166.3_Missense_Mutation_p.S563C	NM_005977.3	NP_005968.1	Q9Y252	RNF6_HUMAN	ring finger protein (C3H2C3 type) 6	563					negative regulation of axon extension (GO:0030517)|positive regulation of transcription, DNA-templated (GO:0045893)|protein K27-linked ubiquitination (GO:0044314)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	axon (GO:0030424)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|PML body (GO:0016605)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(3)|ovary(2)|prostate(2)|skin(2)	23	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.00893)|Epithelial(112;0.0481)|OV - Ovarian serous cystadenocarcinoma(117;0.148)|GBM - Glioblastoma multiforme(144;0.23)|Lung(94;0.245)		CTACTGTCACTGTTTCGAGTA	0.483																																					p.S563C		Atlas-SNP	.											.	RNF6	68	.	0			c.A1687T						PASS	.						152	148	149					13																	26788332		2203	4300	6503	SO:0001583	missense	6049	exon5			TGTCACTGTTTCG	AJ010346	CCDS9316.1	13q12.2	2013-01-09			ENSG00000127870	ENSG00000127870		"RING-type (C3HC4) zinc fingers"	10069	protein-coding gene	gene with protein product	"RING-H2 protein RNF-6"	604242				10331950	Standard	NM_005977		Approved	DKFZp686P0776	uc001uqq.3	Q9Y252	OTTHUMG00000016614	ENST00000381588.4:c.1687A>T	chr13.hg19:g.26788332T>A	ENSP00000371000:p.Ser563Cys	198.0	0.0	.		185.0	50.0	.	NM_183043	B4DDP0|Q5W0H0|Q9BZP5|Q9UF41	Missense_Mutation	SNP	ENST00000381588.4	hg19	CCDS9316.1	.	.	.	.	.	.	.	.	.	.	T	5.021	0.189542	0.09547	.	.	ENSG00000127870	ENST00000346166;ENST00000381588;ENST00000381570;ENST00000399762	T;T;T;T	0.15834	2.97;2.97;2.97;2.39	4.87	0.818	0.18778	.	0.588235	0.19777	N	0.106316	T	0.18215	0.0437	L	0.43152	1.355	0.09310	N	1	D;P	0.56287	0.975;0.948	P;B	0.49047	0.599;0.41	T	0.08371	-1.0725	10	0.59425	D	0.04	-0.6579	8.2879	0.31939	0.0:0.069:0.3791:0.552	.	207;563	B4DDP0;Q9Y252	.;RNF6_HUMAN	C	563;563;563;207	ENSP00000342121:S563C;ENSP00000371000:S563C;ENSP00000370982:S563C;ENSP00000382665:S207C	ENSP00000342121:S563C	S	-	1	0	RNF6	25686332	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.774000	0.26675	0.069000	0.16605	0.460000	0.39030	AGT	.	.	.	none		0.483	RNF6-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044246.2	NM_005977		A	26788332	T	A	26788332	3	1	41	1	0	0	0	0	1	0	0	0	13511	1580	55	5	374	5	RNF6	13	26788332	Missense_Mutation	SNP	T	TCGA-A4-7286-01A-11D-2136-08		26788332	88381546	28	2919											
TEP1	7011	hgsc.bcm.edu	37	chr14	20857434	20857434	+	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	acagcctgagagtgtcacatCattgggattcaaatctgttg	11	12	10	8	0	4	1	3	1	1	1	4	3	4	2	1	1	1	1	1	1	1	3			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr14:20857434C>T	ENST00000262715.5	-	17	2528	c.2488G>A	c.(2488-2490)Gat>Aat	p.D830N	TEP1_ENST00000556935.1_Missense_Mutation_p.D722N	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	830					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)		AGTGTCACATCATTGGGATTC	0.418																																					p.D830N		Atlas-SNP	.											.	TEP1	224	.	0			c.G2488A						PASS	.						170	144	153					14																	20857434		2203	4300	6503	SO:0001583	missense	7011	exon17			TCACATCATTGGG		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.2488G>A	chr14.hg19:g.20857434C>T	ENSP00000262715:p.Asp830Asn	141.0	0.0	.		77.0	17.0	.	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	hg19	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	C	14.91	2.675408	0.47781	.	.	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935	T;T	0.51817	0.7;0.69	5.14	5.14	0.70334	.	0.398706	0.30219	N	0.010131	T	0.55481	0.1923	L	0.41824	1.3	0.80722	D	1	D;B;D	0.57257	0.979;0.005;0.964	P;B;P	0.59703	0.862;0.01;0.732	T	0.55483	-0.8134	10	0.51188	T	0.08	-3.8703	14.0724	0.64868	0.0:1.0:0.0:0.0	.	722;180;830	G3V5X7;G3V2A4;Q99973	.;.;TEP1_HUMAN	N	830;830;722	ENSP00000262715:D830N;ENSP00000452574:D722N	ENSP00000262715:D830N	D	-	1	0	TEP1	19927274	0.981000	0.34729	0.998000	0.56505	0.734000	0.41952	0.854000	0.27791	2.392000	0.81423	0.561000	0.74099	GAT	.	.	.	none		0.418	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		T	20857434	C	T	20857434	3	4	41	1	0	0	0	0	1	0	0	0	15771	826	29	2	5551	2	TEP1	14	20857434	Missense_Mutation	SNP	C	TCGA-A4-7286-01A-11D-2136-08		20857434	86492106	29	2920											
ATP10A	57194	hgsc.bcm.edu	37	chr15	25959389	25959389	+	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	agctcaaacctcaccctcacCtgcaagagaaatggtcagaa	15	6	7	13	0	4	2	4	0	0	2	4	3	4	2	3	1	3	2	3	1	4	0			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr15:25959389C>G	ENST00000356865.6	-	10	1888		c.e10-1			NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A						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)		TCACCCTCACCTGCAAGAGAA	0.582																																					.		Atlas-SNP	.											.	ATP10A	270	.	0			c.1777-1G>C						PASS	.						26	30	29					15																	25959389		2188	4268	6456	SO:0001630	splice_region_variant	57194	exon11			CCTCACCTGCAAG	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.1777-1G>C	chr15.hg19:g.25959389C>G		79.0	0.0	.		43.0	5.0	.	NM_024490	Q4G0S9|Q969I4	Splice_Site	SNP	ENST00000356865.6	hg19	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.018554	0.75275	.	.	ENSG00000206190	ENST00000356865	.	.	.	4.62	4.62	0.57501	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.6469	0.88151	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ATP10A	23510482	1.000000	0.71417	0.996000	0.52242	0.877000	0.50540	6.761000	0.74945	2.412000	0.81896	0.655000	0.94253	.	.	.	.	none		0.582	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	Intron	G	25959389	C	G	25959389	5	3	41	1	0	0	0	0	0	0	1	0	1116	695	24	4	2771	4	ATP10A	15	25959389	Splice_Site	SNP	C	TCGA-A4-7286-01A-11D-2136-08		25959389	76572003	30	2921											
ALDH3A2	224	hgsc.bcm.edu	37	chr17	19575183	19575183	+	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	caaaggtggattggggaaaaTtttttctcttgaaacggttc	11	14	11	5	1	1	1	0	1	1	0	3	3	1	3	0	5	1	1	0	5	4	6			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr17:19575183T>A	ENST00000176643.6	+	9	1803	c.1357T>A	c.(1357-1359)Ttt>Att	p.F453I	ALDH3A2_ENST00000579855.1_Missense_Mutation_p.F453I|ALDH3A2_ENST00000571163.1_Intron|ALDH3A2_ENST00000395575.2_Missense_Mutation_p.F453I|ALDH3A2_ENST00000581518.1_Missense_Mutation_p.F453I|ALDH3A2_ENST00000339618.4_Missense_Mutation_p.F453I			P51648	AL3A2_HUMAN	aldehyde dehydrogenase 3 family, member A2	453					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)					TTGGGGAAAATTTTTTCTCTT	0.423																																					p.F453I		Atlas-SNP	.											.	ALDH3A2	41	.	0			c.T1357A						PASS	.						129	143	138					17																	19575183		2203	4300	6503	SO:0001583	missense	224	exon9			GGAAAATTTTTTC	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.1357T>A	chr17.hg19:g.19575183T>A	ENSP00000176643:p.Phe453Ile	236.0	0.0	.		298.0	65.0	.	NM_001031806	Q6I9T3|Q93011|Q96J37	Missense_Mutation	SNP	ENST00000176643.6	hg19	CCDS11210.1	.	.	.	.	.	.	.	.	.	.	T	13.13	2.144131	0.37825	.	.	ENSG00000072210	ENST00000176643;ENST00000395575;ENST00000339618	T;T;T	0.80909	-1.42;-1.42;-1.43	6.07	3.72	0.42706	.	0.133335	0.64402	D	0.000001	T	0.66703	0.2816	N	0.24115	0.695	0.22656	N	0.998887	B;P	0.37061	0.444;0.58	B;B	0.39068	0.133;0.289	T	0.55237	-0.8172	10	0.22706	T	0.39	-18.8603	8.3131	0.32084	0.0:0.0691:0.1325:0.7984	.	453;453	P51648;P51648-2	AL3A2_HUMAN;.	I	453	ENSP00000176643:F453I;ENSP00000378942:F453I;ENSP00000345774:F453I	ENSP00000176643:F453I	F	+	1	0	ALDH3A2	19515775	0.922000	0.31269	0.032000	0.17829	0.671000	0.39405	1.408000	0.34668	1.093000	0.41377	0.533000	0.62120	TTT	.	.	.	none		0.423	ALDH3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132268.1			A	19575183	T	A	19575183	3	1	41	1	0	0	0	0	1	0	0	0	498	1493	52	5	1391	5	ALDH3A2	17	19575183	Missense_Mutation	SNP	T	TCGA-A4-7286-01A-11D-2136-08		19575183	61620027	31	2922											
PROCA1	83871	hgsc.bcm.edu	37	chr17	27038593	27038593	+	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	0	0	0	0	0	0	0	0	0	0	ccccgcccctcttaccgcggCatctgctctcatcccacgag	5	8	7	21	4	3	0	1	0	3	0	5	1	4	0	6	1	2	2	6	1	1	1			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr17:27038593C>T	ENST00000395245.3	-	0	1736				PROCA1_ENST00000439862.3_5'Flank|PROCA1_ENST00000581289.1_Missense_Mutation_p.C29Y|PROCA1_ENST00000579650.1_5'Flank|PROCA1_ENST00000301039.2_Missense_Mutation_p.C29Y	NM_001256281.1|NM_031934.5	NP_001243210.1|NP_114140.4	Q9BZG1	RAB34_HUMAN	RAB34, member RAS oncogene family						antigen processing and presentation (GO:0019882)|Golgi to plasma membrane protein transport (GO:0043001)|lysosome localization (GO:0032418)|phagosome maturation (GO:0090382)|phagosome-lysosome fusion (GO:0090385)|protein localization to plasma membrane (GO:0072659)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|Golgi stack (GO:0005795)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|vesicle (GO:0031982)	GTP binding (GO:0005525)			endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(8)|skin(2)	14	Lung NSC(42;0.00431)					CTTACCGCGGCATCTGCTCTC	0.682																																					p.C29Y	Pancreas(175;216 2049 29940 32498 41589)	Atlas-SNP	.											.	PROCA1	28	.	0			c.G86A						PASS	.						78	68	72					17																	27038593		2203	4300	6503	SO:0001628	intergenic_variant	147011	exon1			CCGCGGCATCTGC	AF322067	CCDS11240.1, CCDS45636.1, CCDS54101.1, CCDS58536.1	17q11.2	2008-07-18			ENSG00000109113	ENSG00000109113		"RAB, member RAS oncogene"	16519	protein-coding gene	gene with protein product		610917				12446704	Standard	NM_031934		Approved	RAB39, RAH	uc010was.1	P0DI83	OTTHUMG00000132680		chr17.hg19:g.27038593C>T		87.0	0.0	.		86.0	13.0	.	NM_152465	B4E3A0|E9PEJ9|Q5BJE6|Q8NCJ8|Q96AR4	Missense_Mutation	SNP	ENST00000395245.3	hg19	CCDS11240.1	.	.	.	.	.	.	.	.	.	.	C	8.048	0.765458	0.15914	.	.	ENSG00000167525	ENST00000301039	T	0.29917	1.55	2.0	2.0	0.26442	.	0.967617	0.08473	U	0.940674	T	0.16642	0.0400	N	0.08118	0	0.27121	N	0.962131	B	0.11235	0.004	B	0.14023	0.01	T	0.16748	-1.0392	10	0.56958	D	0.05	.	7.523	0.27639	0.0:1.0:0.0:0.0	.	29	Q8NCQ7-2	.	Y	29	ENSP00000301039:C29Y	ENSP00000301039:C29Y	C	-	2	0	PROCA1	24062720	0.026000	0.19158	0.014000	0.15608	0.004000	0.04260	0.601000	0.24119	1.414000	0.47017	0.514000	0.50259	TGC	.	.	.	none		0.682	RAB34-018	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345906.1	NM_031934		T	27038593	C	T	27038593	1	4	41	0	1	0	0	0	0	0	0	0	12556	710	25	2		2	PROCA1	17	27038593	IGR	SNP	C	TCGA-A4-7286-01A-11D-2136-08	7463410	27038593	54156617	32	2923											
ENGASE	64772	hgsc.bcm.edu	37	chr17	77079593	77079593	+	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	ccgactggagcgttatctgcCcacacatagcatctgctcct	8	10	8	15	2	2	0	0	0	2	0	3	2	3	1	3	1	4	3	3	1	2	2			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr17:77079593C>G	ENST00000579016.1	+	9	1172	c.1172C>G	c.(1171-1173)cCc>cGc	p.P391R	ENGASE_ENST00000584568.1_3'UTR	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	391						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						CGTTATCTGCCCACACATAGC	0.617																																					p.P391R		Atlas-SNP	.											.	ENGASE	55	.	0			c.C1172G						PASS	.						111	118	116					17																	77079593		2136	4241	6377	SO:0001583	missense	64772	exon9			ATCTGCCCACACA	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.1172C>G	chr17.hg19:g.77079593C>G	ENSP00000462333:p.Pro391Arg	52.0	0.0	.		78.0	11.0	.	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Missense_Mutation	SNP	ENST00000579016.1	hg19	CCDS42394.1	.	.	.	.	.	.	.	.	.	.	C	12.60	1.987187	0.35036	.	.	ENSG00000167280	ENST00000545583	.	.	.	5.47	5.47	0.80525	Glycoside hydrolase, family 85 (1);	0.309415	0.36778	N	0.002406	T	0.61173	0.2326	M	0.69823	2.125	0.80722	D	1	P	0.45240	0.854	P	0.46144	0.505	T	0.59685	-0.7408	9	0.28530	T	0.3	-4.1388	12.6473	0.56742	0.0:0.9243:0.0:0.0757	.	391	Q8NFI3	ENASE_HUMAN	R	391	.	ENSP00000438577:P391R	P	+	2	0	ENGASE	74591188	1.000000	0.71417	1.000000	0.80357	0.393000	0.30537	2.094000	0.41719	2.563000	0.86464	0.561000	0.74099	CCC	.	.	.	none		0.617	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759		G	77079593	C	G	77079593	3	3	41	1	0	0	0	0	1	0	0	0	5120	623	22	4	1206	4	ENGASE	17	77079593	Missense_Mutation	SNP	C	TCGA-A4-7286-01A-11D-2136-08	50041000	77079593	4115617	33	2924											
AATK	9625	hgsc.bcm.edu	37	chr17	79094952	79094952	+	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	agcgctcgcggctgccctccAgaggggccagtggccgacgg	5	4	17	15	5	0	1	0	0	0	1	2	2	1	1	4	5	2	2	4	5	0	0			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr17:79094952A>T	ENST00000326724.4	-	11	2808	c.2784T>A	c.(2782-2784)tcT>tcA	p.S928S	AATK_ENST00000417379.1_Silent_p.S825S	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	928					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)			GCTGCCCTCCAGAGGGGCCAG	0.647																																					p.S928S		Atlas-SNP	.											.	AATK	102	.	0			c.T2784A						PASS	.						10	12	11					17																	79094952		1972	4143	6115	SO:0001819	synonymous_variant	9625	exon11			CCCTCCAGAGGGG	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.2784T>A	chr17.hg19:g.79094952A>T		29.0	0.0	.		27.0	7.0	.	NM_001080395	O75136|Q6ZN31|Q86X28	Silent	SNP	ENST00000326724.4	hg19	CCDS45807.1	.	.	.	.	.	.	.	.	.	.	A	0.866	-0.733743	0.03111	.	.	ENSG00000181409	ENST00000417379	.	.	.	3.95	-2.58	0.06228	.	.	.	.	.	T	0.43188	0.1236	.	.	.	0.37603	D	0.920626	.	.	.	.	.	.	T	0.43048	-0.9415	4	.	.	.	.	5.1955	0.15233	0.3603:0.1879:0.4518:0.0	.	.	.	.	Q	881	.	.	L	-	2	0	AATK	76709547	0.166000	0.22962	0.006000	0.13384	0.142000	0.21351	0.558000	0.23469	-0.121000	0.11787	-0.464000	0.05259	CTG	.	.	.	none		0.647	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920		T	79094952	A	T	79094952	2	4	41	1	0	0	0	0	0	0	0	1	26	175	7	5		5	AATK	17	79094952	Silent	SNP	A	TCGA-A4-7286-01A-11D-2136-08	2015359	79094952	2100258	34	2925											
CSRP2BP	57325	hgsc.bcm.edu	37	chr20	18142850	18142850	+	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	tttcagaagcagatctgattCcagatgtgatgcccccacaa	12	10	8	11	0	2	5	1	2	1	3	3	5	3	5	3	0	2	1	3	0	2	2			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr20:18142850C>G	ENST00000435364.3	+	5	1410	c.1069C>G	c.(1069-1071)Cca>Gca	p.P357A	CSRP2BP_ENST00000489634.2_Missense_Mutation_p.P229A|CSRP2BP_ENST00000377681.3_Missense_Mutation_p.P356A	NM_020536.4	NP_065397	Q9H8E8	CSR2B_HUMAN	CSRP2 binding protein	357					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						AGATCTGATTCCAGATGTGAT	0.458																																					p.P357A		Atlas-SNP	.											.	CSRP2BP	80	.	0			c.C1069G						PASS	.						216	229	224					20																	18142850		2203	4300	6503	SO:0001583	missense	57325	exon5			CTGATTCCAGATG	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.1069C>G	chr20.hg19:g.18142850C>G	ENSP00000392318:p.Pro357Ala	596.0	0.0	.		629.0	129.0	.	NM_020536	A2A2I5|Q96GW6|Q96IH3|Q9HBF0|Q9UIY5	Missense_Mutation	SNP	ENST00000435364.3	hg19	CCDS13133.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.555785	0.86231	.	.	ENSG00000149474	ENST00000278816;ENST00000377681;ENST00000435364;ENST00000489634	T;T;T;T	0.43294	0.95;0.95;0.95;0.99	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.55955	0.1953	L	0.27053	0.805	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.994	T	0.57004	-0.7885	10	0.72032	D	0.01	-20.8382	20.5666	0.99351	0.0:1.0:0.0:0.0	.	229;357	Q9H8E8-2;Q9H8E8	.;CSR2B_HUMAN	A	357;356;357;229	ENSP00000278816:P357A;ENSP00000366909:P356A;ENSP00000392318:P357A;ENSP00000425909:P229A	ENSP00000278816:P357A	P	+	1	0	CSRP2BP	18090850	1.000000	0.71417	0.993000	0.49108	0.996000	0.88848	7.364000	0.79526	2.854000	0.98071	0.655000	0.94253	CCA	.	.	.	none		0.458	CSRP2BP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078152.5	NM_020536		G	18142850	C	G	18142850	3	3	41	1	0	0	0	0	1	0	0	0	3970	855	30	4	1087	4	CSRP2BP	20	18142850	Missense_Mutation	SNP	C	TCGA-A4-7286-01A-11D-2136-08		18142850	44882670	35	2926											
HM13	81502	hgsc.bcm.edu	37	chr20	30137040	30137040	+	Missense_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	ccaacaacctttttggcctgGccttctcccttaatggagta	8	13	7	13	0	1	0	0	0	1	0	2	1	1	1	5	3	2	1	5	3	4	5			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr20:30137040G>A	ENST00000340852.5	+	6	695	c.571G>A	c.(571-573)Gcc>Acc	p.A191T	HM13_ENST00000335574.5_Missense_Mutation_p.A191T|HM13_ENST00000492709.1_3'UTR|HM13_ENST00000398174.3_Missense_Mutation_p.A191T|HM13_ENST00000376127.3_Intron	NM_030789.2	NP_110416.1	Q8TCT9	HM13_HUMAN	histocompatibility (minor) 13	191					membrane protein proteolysis (GO:0033619)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	aspartic endopeptidase activity, intramembrane cleaving (GO:0042500)|peptidase activity (GO:0008233)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	12	all_cancers(5;3.44e-05)|Lung NSC(7;4.38e-06)|all_lung(7;7.65e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		all cancers(5;0.000479)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264)			TTTTGGCCTGGCCTTCTCCCT	0.567																																					p.A191T		Atlas-SNP	.											.	HM13	52	.	0			c.G571A						PASS	.						216	199	205					20																	30137040		2203	4300	6503	SO:0001583	missense	81502	exon6			GGCCTGGCCTTCT	AL110115	CCDS13182.1, CCDS13183.1, CCDS42861.1	20q11.21	2012-02-21			ENSG00000101294	ENSG00000101294			16435	protein-coding gene	gene with protein product	"signal peptide peptidase beta", "presenilin-like protein 3", "intramembrane protease", "signal peptide peptidase like 1"	607106				12077416, 14704149	Standard	NM_030789		Approved	H13, dJ324O17.1, SPP, PSL3, IMP1, IMPAS, PSENL3, SPPL1	uc002wwc.3	Q8TCT9	OTTHUMG00000032175	ENST00000340852.5:c.571G>A	chr20.hg19:g.30137040G>A	ENSP00000343032:p.Ala191Thr	326.0	0.0	.		349.0	63.0	.	NM_178581	B2RAY5|E1P5L3|Q15K36|Q540H8|Q5JWP2|Q5JWP3|Q5JWP4|Q5JWP5|Q7Z4F2|Q86Y35|Q95H87|Q9H110|Q9H111	Missense_Mutation	SNP	ENST00000340852.5	hg19	CCDS13182.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.315948	0.81469	.	.	ENSG00000101294	ENST00000335574;ENST00000340852;ENST00000398174	T;T;T	0.21361	2.01;2.01;2.01	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.42359	0.1199	M	0.73962	2.25	0.80722	D	1	P;P;B	0.43519	0.809;0.802;0.338	P;P;B	0.54210	0.745;0.607;0.281	T	0.21314	-1.0249	10	0.48119	T	0.1	-2.7651	17.5166	0.87776	0.0:0.0:1.0:0.0	.	191;191;191	Q8TCT9;Q8TCT9-4;Q8TCT9-2	HM13_HUMAN;.;.	T	191	ENSP00000335294:A191T;ENSP00000343032:A191T;ENSP00000381237:A191T	ENSP00000335294:A191T	A	+	1	0	HM13	29600701	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.992000	0.93519	2.604000	0.88044	0.650000	0.86243	GCC	.	.	.	none		0.567	HM13-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078527.2	NM_178580		A	30137040	G	A	30137040	3	1	41	1	0	0	0	0	1	0	0	0	7224	1203	42	2	660	2	HM13	20	30137040	Missense_Mutation	SNP	G	TCGA-A4-7286-01A-11D-2136-08	11994190	30137040	32888480	36	2927											
CHD6	84181	hgsc.bcm.edu	37	chr20	40080522	40080522	+	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	tggtaggtgtgatcagttccCaaatgaaactcttgatcttc	10	14	9	8	0	3	3	1	3	2	0	5	3	4	3	1	2	1	2	1	2	3	4			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr20:40080522C>G	ENST00000373233.3	-	22	3644	c.3467G>C	c.(3466-3468)tGg>tCg	p.W1156S	CHD6_ENST00000309279.7_Missense_Mutation_p.W639S	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1156					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)				GATCAGTTCCCAAATGAAACT	0.522																																					p.W1156S		Atlas-SNP	.											.	CHD6	312	.	0			c.G3467C						PASS	.						259	206	224					20																	40080522		2203	4300	6503	SO:0001583	missense	84181	exon22			AGTTCCCAAATGA	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.3467G>C	chr20.hg19:g.40080522C>G	ENSP00000362330:p.Trp1156Ser	213.0	0.0	.		279.0	45.0	.	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	hg19	CCDS13317.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.2|28.2	4.899700|4.899700	0.91962|0.91962	.|.	.|.	ENSG00000124177|ENSG00000124177	ENST00000440697|ENST00000373233;ENST00000309279	.|D;D	.|0.98060	.|-4.69;-4.69	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	.|0.000000	.|0.56097	.|D	.|0.000033	D|D	0.98801|0.98801	0.9596|0.9596	M|M	0.84326|0.84326	2.69|2.69	0.80722|0.80722	D|D	1|1	.|D	.|0.69078	.|0.997	.|D	.|0.72982	.|0.979	D|D	0.99651|0.99651	1.0991|1.0991	5|10	.|0.87932	.|D	.|0	-10.1751|-10.1751	20.0435|20.0435	0.97601|0.97601	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1156	.|Q8TD26	.|CHD6_HUMAN	R|S	342|1156;639	.|ENSP00000362330:W1156S;ENSP00000308684:W639S	.|ENSP00000308684:W639S	G|W	-|-	1|2	0|0	CHD6|CHD6	39513936|39513936	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.776000|7.776000	0.85560|0.85560	2.731000|2.731000	0.93534|0.93534	0.650000|0.650000	0.86243|0.86243	GGG|TGG	.	.	.	none		0.522	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			G	40080522	C	G	40080522	3	3	41	1	0	0	0	0	1	0	0	0	3331	595	21	4	4744	4	CHD6	20	40080522	Missense_Mutation	SNP	C	TCGA-A4-7286-01A-11D-2136-08	9943482	40080522	22944998	37	2928											
PARD6B	84612	hgsc.bcm.edu	37	chr20	49367023	49367023	+	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	atggaacaatcataacattaTgaaaccgtggtttgaatgtt	15	13	8	5	1	1	2	1	2	0	0	1	3	1	3	1	2	3	2	1	2	6	4			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr20:49367023T>C	ENST00000371610.2	+	3	1360	c.1117T>C	c.(1117-1119)Tga>Cga	p.*373R	PARD6B_ENST00000396039.1_Intron	NM_032521.2	NP_115910.1	Q9BYG5	PAR6B_HUMAN	par-6 family cell polarity regulator beta	0					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						CATAACATTATGAAACCGTGG	0.398																																					p.X373R		Atlas-SNP	.											.	PARD6B	31	.	0			c.T1117C						PASS	.						35	34	34					20																	49367023		2202	4298	6500	SO:0001578	stop_lost	84612	exon3			ACATTATGAAACC	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.1117T>C	chr20.hg19:g.49367023T>C	ENSP00000360672:p.*373Argext*13	59.0	0.0	.		62.0	11.0	.	NM_032521	A2A2A7|Q9Y510	Missense_Mutation	SNP	ENST00000371610.2	hg19	CCDS33485.1	.	.	.	.	.	.	.	.	.	.	T	11.63	1.695570	0.30052	.	.	ENSG00000124171	ENST00000371610	.	.	.	5.46	5.46	0.80206	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5383	0.76021	0.0:0.0:0.0:1.0	.	.	.	.	R	373	.	.	X	+	1	0	PARD6B	48800430	1.000000	0.71417	0.503000	0.27626	0.446000	0.32137	6.377000	0.73145	2.073000	0.62155	0.482000	0.46254	TGA	.	.	.	none		0.398	PARD6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079697.2	NM_032521		C	49367023	T	C	49367023	4	2	41	1	0	0	0	0	0	0	0	0	11453	1477	51	3	1127	3	PARD6B	20	49367023	Nonstop_Mutation	SNP	T	TCGA-A4-7286-01A-11D-2136-08	9286501	49367023	13658497	38	2929											
ZNRF3	84133	hgsc.bcm.edu	37	chr22	29445639	29445639	+	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	gggcagtccccacctagcctCgcaccccggggcccggcccg	4	3	13	21	4	0	0	0	0	0	0	2	0	1	0	8	4	1	2	8	4	1	1			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chr22:29445639C>A	ENST00000544604.2	+	8	1645	c.1470C>A	c.(1468-1470)ctC>ctA	p.L490L	ZNRF3_ENST00000332811.4_Silent_p.L390L|ZNRF3_ENST00000406323.3_Silent_p.L390L|ZNRF3_ENST00000402174.1_Silent_p.L390L	NM_001206998.1	NP_001193927.1	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	490					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)	p.L390L(1)		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						CACCTAGCCTCGCACCCCGGG	0.682																																					p.L490L		Atlas-SNP	.											ZNRF3,NS,carcinoma,0,1	ZNRF3	75	.	1	Substitution - coding silent(1)	lung(1)	c.C1470A						PASS	.						23	27	25					22																	29445639		2081	4180	6261	SO:0001819	synonymous_variant	84133	exon8			TAGCCTCGCACCC	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.1470C>A	chr22.hg19:g.29445639C>A		35.0	0.0	.		25.0	2.0	.	NM_001206998	B3KU18|Q6ICH1|Q6NTF8|Q8WU18	Silent	SNP	ENST00000544604.2	hg19	CCDS56225.1																																																																																			.	.	.	none		0.682	ZNRF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320943.2	XM_290972		A	29445639	C	A	29445639	2	1	41	1	0	0	0	0	0	0	0	1	18225	871	31	4		4	ZNRF3	22	29445639	Silent	SNP	C	TCGA-A4-7286-01A-11D-2136-08		29445639	21858927	39	2930											
BHLHB9	80823	hgsc.bcm.edu	37	chrX	102004858	102004858	+	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	tgggattaagccatttgcttGtccttgcaaaatggaatgct	10	14	10	7	0	0	0	0	0	0	0	1	2	1	2	2	2	4	3	2	2	4	4			TCGA-A4-7286-01A-11D-2136-08	TCGA-A4-7286-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ab0f9d3-99a7-4bcc-9b8e-643a30a9979c	08ec176f-4bd6-4128-97b3-ea6aa610eeb9	g.chrX:102004858G>C	ENST00000372735.1	+	4	1520	c.935G>C	c.(934-936)tGt>tCt	p.C312S	BHLHB9_ENST00000448867.1_Missense_Mutation_p.C312S|BHLHB9_ENST00000361229.4_Missense_Mutation_p.C312S|BHLHB9_ENST00000447531.1_Missense_Mutation_p.C312S|BHLHB9_ENST00000457056.1_Missense_Mutation_p.C312S			Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class B, 9	312					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						CCATTTGCTTGTCCTTGCAAA	0.398																																					p.C312S		Atlas-SNP	.											.	BHLHB9	60	.	0			c.G935C						PASS	.						93	85	88					X																	102004858		2203	4300	6503	SO:0001583	missense	80823	exon2			TTGCTTGTCCTTG	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.935G>C	chrX.hg19:g.102004858G>C	ENSP00000361820:p.Cys312Ser	67.0	0.0	.		62.0	19.0	.	NM_001142530	Q9C0G2	Missense_Mutation	SNP	ENST00000372735.1	hg19	CCDS14502.1	.	.	.	.	.	.	.	.	.	.	G	16.30	3.084883	0.55861	.	.	ENSG00000198908	ENST00000457056;ENST00000361229;ENST00000447531;ENST00000448867;ENST00000372735	T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52	4.68	4.68	0.58851	Armadillo-type fold (1);	0.000000	0.51477	D	0.000090	T	0.47857	0.1468	L	0.52905	1.665	0.33452	D	0.583863	D	0.89917	1.0	D	0.91635	0.999	T	0.57118	-0.7866	9	.	.	.	-17.5444	11.7841	0.52032	0.0:0.0:1.0:0.0	.	312	Q6PI77	BHLH9_HUMAN	S	312	ENSP00000403226:C312S;ENSP00000354675:C312S;ENSP00000405893:C312S;ENSP00000391722:C312S;ENSP00000361820:C312S	.	C	+	2	0	BHLHB9	101891514	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.642000	0.54367	2.557000	0.86248	0.594000	0.82650	TGT	.	.	.	none		0.398	BHLHB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057630.1	NM_030639		C	102004858	G	C	102004858	3	2	41	1	0	0	0	0	1	0	0	0	1420	1377	48	4	937	4	BHLHB9	23	102004858	Missense_Mutation	SNP	G	TCGA-A4-7286-01A-11D-2136-08		102004858	53265702	40	2931											
PLA2G2D	26279	hgsc.bcm.edu	37	chr1	20440719	20440719	+	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	ccacctccttgtcacaggcaCacagctgctgctcacaccag	9	7	7	18	0	2	0	2	0	0	0	3	0	3	0	4	1	3	4	4	1	0	1			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:20440719C>T	ENST00000375105.3	-	4	384	c.326G>A	c.(325-327)tGt>tAt	p.C109Y		NM_012400.2	NP_036532.1	Q9UNK4	PA2GD_HUMAN	phospholipase A2, group IID	109					glycerophospholipid biosynthetic process (GO:0046474)|inflammatory response (GO:0006954)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			endometrium(1)|lung(2)	3		Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.000175)|GBM - Glioblastoma multiforme(114;0.000798)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GTCACAGGCACACAGCTGCTG	0.597										Multiple Myeloma(11;0.12)																											p.C109Y	Melanoma(60;742 1548 31762 39240)	Atlas-SNP	.											.	PLA2G2D	7	.	0			c.G326A						PASS	.						63	60	61					1																	20440719		2203	4300	6503	SO:0001583	missense	26279	exon4			CAGGCACACAGCT	AF112982	CCDS203.1, CCDS72721.1	1p36.12	2008-09-19			ENSG00000117215	ENSG00000117215	3.1.1.4		9033	protein-coding gene	gene with protein product		605630				10455175	Standard	NM_012400		Approved	sPLA2S	uc001bcz.4	Q9UNK4	OTTHUMG00000002701	ENST00000375105.3:c.326G>A	chr1.hg19:g.20440719C>T	ENSP00000364246:p.Cys109Tyr	76.0	0.0	.		61.0	15.0	.	NM_012400	A8K2Z1|B1AEL9|Q9UK01	Missense_Mutation	SNP	ENST00000375105.3	hg19	CCDS203.1	.	.	.	.	.	.	.	.	.	.	C	19.68	3.873650	0.72180	.	.	ENSG00000117215	ENST00000375105	D	0.86097	-2.07	5.2	5.2	0.72013	Phospholipase A2 (3);	0.000000	0.53938	D	0.000050	D	0.94443	0.8212	H	0.95365	3.66	0.47949	D	0.999553	D	0.89917	1.0	D	0.97110	1.0	D	0.95704	0.8752	10	0.87932	D	0	-24.7657	14.2445	0.65978	0.0:1.0:0.0:0.0	.	109	Q9UNK4	PA2GD_HUMAN	Y	109	ENSP00000364246:C109Y	ENSP00000364246:C109Y	C	-	2	0	PLA2G2D	20313306	0.996000	0.38824	0.998000	0.56505	0.910000	0.53928	4.132000	0.57977	2.443000	0.82685	0.462000	0.41574	TGT	.	.	.	none		0.597	PLA2G2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007683.1			T	20440719	C	T	20440719	3	4	42	1	0	0	0	0	1	0	0	0	12004	478	17	2	115	2	PLA2G2D	1	20440719	Missense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08		20440719	228809902	1	2932											
AGL	178	hgsc.bcm.edu	37	chr1	100327977	100327977	+	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	acttagggttgcaaaagaatCaggtaatgtcagcttgcttt	12	13	10	6	0	2	1	2	0	0	1	2	1	2	1	0	2	3	5	0	2	5	5			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:100327977C>G	ENST00000294724.4	+	4	936	c.458C>G	c.(457-459)tCa>tGa	p.S153*	AGL_ENST00000361302.3_Nonsense_Mutation_p.S137*|AGL_ENST00000370163.3_Nonsense_Mutation_p.S153*|AGL_ENST00000370161.2_Nonsense_Mutation_p.S137*|AGL_ENST00000361915.3_Nonsense_Mutation_p.S153*|AGL_ENST00000370165.3_Nonsense_Mutation_p.S153*|AGL_ENST00000361522.4_Nonsense_Mutation_p.S136*	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	153					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)		GCAAAAGAATCAGGTAATGTC	0.338																																					p.S153X		Atlas-SNP	.											.	AGL	137	.	0			c.C458G						PASS	.						159	150	153					1																	100327977		2203	4300	6503	SO:0001587	stop_gained	178	exon4			AAGAATCAGGTAA	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.458C>G	chr1.hg19:g.100327977C>G	ENSP00000294724:p.Ser153*	111.0	0.0	.		102.0	23.0	.	NM_000644	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Nonsense_Mutation	SNP	ENST00000294724.4	hg19	CCDS759.1	.	.	.	.	.	.	.	.	.	.	C	39	7.619744	0.98393	.	.	ENSG00000162688	ENST00000361915;ENST00000370165;ENST00000370163;ENST00000294724;ENST00000361302;ENST00000370161;ENST00000361522	.	.	.	5.53	5.53	0.82687	.	0.435109	0.23914	N	0.043307	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	.	19.4571	0.94897	0.0:1.0:0.0:0.0	.	.	.	.	X	153;153;153;153;137;137;136	.	ENSP00000294724:S153X	S	+	2	0	AGL	100100565	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	7.764000	0.85297	2.599000	0.87857	0.655000	0.94253	TCA	.	.	.	none		0.338	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028		G	100327977	C	G	100327977	4	3	42	1	0	0	0	0	0	1	0	0	384	838	29	4	537	4	AGL	1	100327977	Nonsense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08	79887258	100327977	148922644	2	2933											
NTRK1	4914	hgsc.bcm.edu	37	chr1	156843561	156843561	+	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	aatgagaccagcttcatcttCactgagttcctggagccggc	9	10	10	12	1	3	2	2	2	1	1	4	4	4	3	3	2	2	2	3	2	1	3			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:156843561C>T	ENST00000524377.1	+	8	1028	c.987C>T	c.(985-987)ttC>ttT	p.F329F	NTRK1_ENST00000368196.3_Silent_p.F329F|NTRK1_ENST00000392302.2_Silent_p.F299F|NTRK1_ENST00000358660.3_Silent_p.F329F	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	329	Ig-like C2-type 2.				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)	GCTTCATCTTCACTGAGTTCC	0.617			T	"TPM3, TPR, TFG"	papillary thyroid					TSP Lung(10;0.080)																											p.F329F		Atlas-SNP	.		Dom	yes		1	1q21-q22	4914	"neurotrophic tyrosine kinase, receptor, type 1"		E	.	NTRK1	287	.	0			c.C987T						PASS	.						44	36	39					1																	156843561		2203	4299	6502	SO:0001819	synonymous_variant	4914	exon8			CATCTTCACTGAG	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.987C>T	chr1.hg19:g.156843561C>T		41.0	0.0	.		25.0	8.0	.	NM_001012331	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Silent	SNP	ENST00000524377.1	hg19	CCDS1161.1																																																																																			.	.	.	none		0.617	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1	NM_002529		T	156843561	C	T	156843561	2	4	42	1	0	0	0	0	0	0	0	1	10713	825	29	2		2	NTRK1	1	156843561	Silent	SNP	C	TCGA-A4-7287-01A-11D-2136-08	56515584	156843561	92407060	3	2934											
GORAB	92344	hgsc.bcm.edu	37	chr1	170501324	170501324	+	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	agtgttggcagtcgcggctgCgagatttgggcacttttggg	5	12	17	7	3	0	1	0	0	0	1	1	2	0	1	0	4	1	4	0	4	0	4			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:170501324C>T	ENST00000367763.3	+	1	55	c.35C>T	c.(34-36)gCg>gTg	p.A12V	RP11-576I22.2_ENST00000456083.1_RNA|GORAB_ENST00000367762.1_Missense_Mutation_p.A12V|RP11-576I22.2_ENST00000421020.1_RNA	NM_152281.2	NP_689494.2	Q5T7V8	GORAB_HUMAN	golgin, RAB6-interacting	12						cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)				endometrium(2)|large_intestine(3)|liver(2)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	17						GTCGCGGCTGCGAGATTTGGG	0.622																																					p.A12V		Atlas-SNP	.											.	GORAB	41	.	0			c.C35T						PASS	.						51	62	58					1																	170501324		2203	4300	6503	SO:0001583	missense	92344	exon1			CGGCTGCGAGATT	AK021814	CCDS1289.1, CCDS53428.1	1q24.2	2009-02-13	2009-02-13	2009-02-13	ENSG00000120370	ENSG00000120370			25676	protein-coding gene	gene with protein product	"gerodermia osteodysplastica"	607983	"SCY1-like 1 binding protein 1"	SCYL1BP1		12783284, 15781263, 18997784	Standard	NM_152281		Approved	FLJ11752, NTKL-BP1, GO	uc001gha.2	Q5T7V8	OTTHUMG00000035228	ENST00000367763.3:c.35C>T	chr1.hg19:g.170501324C>T	ENSP00000356737:p.Ala12Val	113.0	0.0	.		95.0	16.0	.	NM_152281	Q49A22|Q6P1P9|Q9HAE6|Q9Y350	Missense_Mutation	SNP	ENST00000367763.3	hg19	CCDS1289.1	.	.	.	.	.	.	.	.	.	.	C	12.10	1.836253	0.32421	.	.	ENSG00000120370	ENST00000367763;ENST00000367762	T;T	0.79247	-0.28;-1.25	5.24	-10.5	0.00291	.	3.953700	0.00937	N	0.002796	T	0.28167	0.0695	N	0.08118	0	0.09310	N	1	B;B	0.17268	0.021;0.021	B;B	0.14023	0.005;0.01	T	0.36986	-0.9725	10	0.37606	T	0.19	.	7.2128	0.25943	0.1379:0.6439:0.1383:0.0799	.	12;12	Q5T7V8-2;Q5T7V8	.;GORAB_HUMAN	V	12	ENSP00000356737:A12V;ENSP00000356736:A12V	ENSP00000356736:A12V	A	+	2	0	GORAB	168767948	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-4.322000	0.00253	-3.663000	0.00124	-1.000000	0.02509	GCG	.	.	.	none		0.622	GORAB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085226.1	NM_152281		T	170501324	C	T	170501324	3	4	42	1	0	0	0	0	1	0	0	0	6581	768	27	1	37	1	GORAB	1	170501324	Missense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08	13657763	170501324	78749297	4	2935											
RGS21	431704	hgsc.bcm.edu	37	chr1	192321246	192321246	+	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	aaatgttgagttctggcttgCctgtgaagactttaagaaaa	13	13	10	5	0	1	4	0	2	1	2	1	4	1	4	1	1	1	3	1	1	5	5			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:192321246C>A	ENST00000417209.2	+	4	332	c.158C>A	c.(157-159)gCc>gAc	p.A53D		NM_001039152.3	NP_001034241.1	Q2M5E4	RGS21_HUMAN	regulator of G-protein signaling 21	53	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			NS(1)|endometrium(3)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	15						TTCTGGCTTGCCTGTGAAGAC	0.328																																					p.A53D		Atlas-SNP	.											.	RGS21	32	.	0			c.C158A						PASS	.						68	66	66					1																	192321246		1836	4106	5942	SO:0001583	missense	431704	exon4			GGCTTGCCTGTGA	AY643711	CCDS41448.1	1q31.2	2013-09-24	2007-08-14		ENSG00000253148	ENSG00000253148		"Regulators of G-protein signaling"	26839	protein-coding gene	gene with protein product		612407	"regulator of G-protein signalling 21"			15066150	Standard	NM_001039152		Approved		uc001gsh.3	Q2M5E4	OTTHUMG00000035594	ENST00000417209.2:c.158C>A	chr1.hg19:g.192321246C>A	ENSP00000428343:p.Ala53Asp	57.0	0.0	.		51.0	11.0	.	NM_001039152		Missense_Mutation	SNP	ENST00000417209.2	hg19	CCDS41448.1	.	.	.	.	.	.	.	.	.	.	C	32	5.159165	0.94686	.	.	ENSG00000253148	ENST00000417209	T	0.02015	4.5	5.77	5.77	0.91146	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);	0.000000	0.33691	U	0.004656	T	0.14313	0.0346	M	0.77486	2.375	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.00016	-1.2383	10	0.87932	D	0	.	18.5418	0.91031	0.0:1.0:0.0:0.0	.	53	Q2M5E4	RGS21_HUMAN	D	53	ENSP00000428343:A53D	ENSP00000428343:A53D	A	+	2	0	RGS21	190587869	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.747000	0.85070	2.733000	0.93635	0.557000	0.71058	GCC	.	.	.	none		0.328	RGS21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086387.2			A	192321246	C	A	192321246	3	1	42	1	0	0	0	0	1	0	0	0	13317	739	26	4	168	4	RGS21	1	192321246	Missense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08	21819922	192321246	56929375	5	2936											
CDC73	79577	hgsc.bcm.edu	37	chr1	193099338	193099338	+	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	tgtggttagaagacctgatcGaaaagatctacttggatatc	13	12	10	6	1	1	4	0	1	1	3	3	6	1	5	1	2	1	1	1	2	6	4			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:193099338G>A	ENST00000367435.3	+	3	456	c.272G>A	c.(271-273)cGa>cAa	p.R91Q		NM_024529.4	NP_078805.3	Q6P1J9	CDC73_HUMAN	cell division cycle 73	91			R -> P (found in a patient with isolated hyperparathyroidism and parathyroid adenomas). {ECO:0000269|PubMed:17639062}.		cell cycle (GO:0007049)|cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|protein destabilization (GO:0031648)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleus (GO:0005634)	RNA polymerase II core binding (GO:0000993)	p.R91Q(1)		breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(14)|ovary(1)|pancreas(1)|parathyroid(51)|skin(1)|upper_aerodigestive_tract(1)	87						AGACCTGATCGAAAAGATCTA	0.294																																					p.R91Q		Atlas-SNP	.											CDC73,caecum,carcinoma,0,1	CDC73	163	.	1	Substitution - Missense(1)	large_intestine(1)	c.G272A	GRCh37	CM072926	CDC73	M		PASS	.						140	144	143					1																	193099338		2203	4300	6503	SO:0001583	missense	79577	exon3			CTGATCGAAAAGA	AF312865	CCDS1382.1	1q25	2014-09-17	2013-01-17	2005-07-20	ENSG00000134371	ENSG00000134371			16783	protein-coding gene	gene with protein product	"Paf1/RNA polymerase II complex component"	607393	"chromosome 1 open reading frame 28", "hyperparathyroidism 2 (with jaw tumor)", "cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)", "hyperparathyroidism 1"	C1orf28, HRPT2, HRPT1		11318611, 15632063, 18755853	Standard	NM_024529		Approved	parafibromin, FIHP	uc001gtb.3	Q6P1J9	OTTHUMG00000035676	ENST00000367435.3:c.272G>A	chr1.hg19:g.193099338G>A	ENSP00000356405:p.Arg91Gln	68.0	0.0	.		61.0	7.0	.	NM_024529	A6NLZ8|B2RBR2|Q6PK51|Q96A07|Q9H245|Q9H5L7	Missense_Mutation	SNP	ENST00000367435.3	hg19	CCDS1382.1	.	.	.	.	.	.	.	.	.	.	G	34	5.351125	0.95830	.	.	ENSG00000134371	ENST00000367435;ENST00000445394	D	0.91407	-2.84	5.62	4.71	0.59529	.	0.000000	0.85682	D	0.000000	D	0.95648	0.8585	M	0.87682	2.9	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96226	0.9164	10	0.87932	D	0	-10.3544	14.535	0.67953	0.0704:0.0:0.9296:0.0	.	91	Q6P1J9	CDC73_HUMAN	Q	91	ENSP00000356405:R91Q	ENSP00000356405:R91Q	R	+	2	0	CDC73	191365961	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	9.743000	0.98849	1.377000	0.46286	0.561000	0.74099	CGA	.	.	.	none		0.294	CDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086696.2	NM_024529		A	193099338	G	A	193099338	3	1	42	1	0	0	0	0	1	0	0	0	3087	1058	37	1	282	1	CDC73	1	193099338	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08	778092	193099338	56151283	6	2937											
SNRPE	6635	hgsc.bcm.edu	37	chr1	203832834	203832834	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctatgagcaagtgaatatgcGgatagaaggctgtatcattg	13	11	12	5	1	1	3	1	2	0	1	1	4	1	4	0	2	2	3	0	2	7	5			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:203832834G>A	ENST00000414487.2	+	3	170	c.125G>A	c.(124-126)cGg>cAg	p.R42Q	SNRPE_ENST00000367208.1_Missense_Mutation_p.R2Q|SNRPE_ENST00000483099.1_3'UTR	NM_003094.2	NP_003085.1	P62304	RUXE_HUMAN	small nuclear ribonucleoprotein polypeptide E	42					gene expression (GO:0010467)|hair cycle (GO:0042633)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|methylosome (GO:0034709)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pICln-Sm protein complex (GO:0034715)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN-Sm protein complex (GO:0034719)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)|U12-type spliceosomal complex (GO:0005689)|U4 snRNP (GO:0005687)|U7 snRNP (GO:0005683)	RNA binding (GO:0003723)			breast(1)|large_intestine(2)|lung(1)|skin(1)	5	all_cancers(21;0.103)		BRCA - Breast invasive adenocarcinoma(75;0.109)			GTGAATATGCGGATAGAAGGC	0.428																																					p.R42Q	Ovarian(83;324 1318 17952 32395 39614)	Atlas-SNP	.											.	SNRPE	8	.	0			c.G125A						PASS	.						128	129	128					1																	203832834		2203	4300	6503	SO:0001583	missense	6635	exon3			ATATGCGGATAGA	M37716	CCDS30979.1	1q32	2011-10-11			ENSG00000182004	ENSG00000182004			11161	protein-coding gene	gene with protein product		128260				1835977, 2143747	Standard	NM_003094		Approved	Sm-E	uc001hai.3	P62304	OTTHUMG00000035985	ENST00000414487.2:c.125G>A	chr1.hg19:g.203832834G>A	ENSP00000400591:p.Arg42Gln	238.0	0.0	.		245.0	87.0	.	NM_003094	B2R5B9|P08578|Q15498|Q5BKT2	Missense_Mutation	SNP	ENST00000414487.2	hg19	CCDS30979.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.058902	0.76074	.	.	ENSG00000182004	ENST00000414487;ENST00000367208	T;T	0.40756	1.02;1.02	5.35	5.35	0.76521	Like-Sm ribonucleoprotein (LSM) domain, eukaryotic/archaea-type (1);Like-Sm ribonucleoprotein (LSM) domain (1);Like-Sm ribonucleoprotein (LSM)-related domain (1);	0.060085	0.64402	D	0.000002	T	0.40570	0.1122	.	.	.	0.80722	D	1	B	0.13594	0.008	B	0.15052	0.012	T	0.20940	-1.0260	9	0.54805	T	0.06	.	18.6824	0.91551	0.0:0.0:1.0:0.0	.	42	P62304	RUXE_HUMAN	Q	42;2	ENSP00000400591:R42Q;ENSP00000356176:R2Q	ENSP00000356176:R2Q	R	+	2	0	SNRPE	202099457	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.937000	0.87672	2.503000	0.84419	0.650000	0.86243	CGG	.	.	.	none		0.428	SNRPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087703.1	NM_003094		A	203832834	G	A	203832834	3	1	42	1	0	0	0	0	1	0	0	0	14880	1116	39	1	135	1	SNRPE	1	203832834	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08	10733496	203832834	45417787	7	2938											
LBR	3930	hgsc.bcm.edu	37	chr1	225599084	225599084	+	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	tcacaaaagtatttgagatcAaaagtaccaattcgagggtt	16	11	8	6	1	2	1	2	1	0	1	3	3	2	1	1	1	1	3	1	1	7	5			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:225599084A>T	ENST00000338179.2	-	9	1268	c.1143T>A	c.(1141-1143)ttT>ttA	p.F381L	AC092811.1_ENST00000366845.2_5'Flank|LBR_ENST00000272163.4_Missense_Mutation_p.F381L	NM_194442.2	NP_919424.1	Q14739	LBR_HUMAN	lamin B receptor	381					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)		ATTTGAGATCAAAAGTACCAA	0.373																																					p.F381L		Atlas-SNP	.											.	LBR	54	.	0			c.T1143A						PASS	.						122	130	127					1																	225599084		2203	4300	6503	SO:0001583	missense	3930	exon9			GAGATCAAAAGTA	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.1143T>A	chr1.hg19:g.225599084A>T	ENSP00000339883:p.Phe381Leu	147.0	0.0	.		153.0	28.0	.	NM_194442	B2R5P3|Q14740|Q53GU7|Q59FE6	Missense_Mutation	SNP	ENST00000338179.2	hg19	CCDS1545.1	.	.	.	.	.	.	.	.	.	.	A	16.15	3.040696	0.55003	.	.	ENSG00000143815	ENST00000272163;ENST00000338179;ENST00000424022	D;D;D	0.96885	-4.16;-4.16;-4.16	6.16	2.64	0.31445	.	0.045876	0.85682	D	0.000000	D	0.93135	0.7814	L	0.33710	1.025	0.48288	D	0.99962	P	0.39782	0.688	P	0.46685	0.524	D	0.87185	0.2230	10	0.13853	T	0.58	-33.8453	9.3222	0.37971	0.796:0.0:0.204:0.0	.	381	Q14739	LBR_HUMAN	L	381;381;12	ENSP00000272163:F381L;ENSP00000339883:F381L;ENSP00000397817:F12L	ENSP00000272163:F381L	F	-	3	2	LBR	223665707	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.577000	0.53885	0.212000	0.20703	0.528000	0.53228	TTT	.	.	.	none		0.373	LBR-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091398.1	NM_002296		T	225599084	A	T	225599084	3	4	42	1	0	0	0	0	1	0	0	0	8659	127	5	5	728	5	LBR	1	225599084	Missense_Mutation	SNP	A	TCGA-A4-7287-01A-11D-2136-08	21766250	225599084	23651537	8	2939											
HYAL1	3373	hgsc.bcm.edu	37	chr3	50340364	50340364	+	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	aaggtcaggaagagggcgcaGatgggaagcaggtgggctgc	11	4	20	6	1	1	2	1	0	0	2	1	4	1	4	0	6	2	3	0	6	3	0	rs370239620		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr3:50340364G>C	ENST00000266031.4	-	1	639	c.24C>G	c.(22-24)atC>atG	p.I8M	HYAL1_ENST00000457214.2_Intron|HYAL1_ENST00000320295.8_Missense_Mutation_p.I8M|HYAL1_ENST00000447605.2_Intron|HYAL1_ENST00000395144.2_Missense_Mutation_p.I8M|HYAL1_ENST00000395143.2_Missense_Mutation_p.I8M			Q12794	HYAL1_HUMAN	hyaluronoglucosaminidase 1	8					carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to interleukin-1 (GO:0071347)|cellular response to pH (GO:0071467)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to UV-B (GO:0071493)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal joint morphogenesis (GO:0060272)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|inflammatory response (GO:0006954)|negative regulation of cell growth (GO:0030308)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of growth (GO:0045927)|positive regulation of hyaluranon cable assembly (GO:1900106)|response to antibiotic (GO:0046677)|response to reactive oxygen species (GO:0000302)|response to virus (GO:0009615)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|hyaluranon cable (GO:0036117)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	hyaluronan synthase activity (GO:0050501)|hyalurononglucosaminidase activity (GO:0004415)|transcription factor binding (GO:0008134)			cervix(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		AGAGGGCGCAGATGGGAAGCA	0.607																																					p.I8M		Atlas-SNP	.											.	HYAL1	28	.	0			c.C24G						PASS	.						35	38	37					3																	50340364		2203	4300	6503	SO:0001583	missense	3373	exon2			GGCGCAGATGGGA	U90094	CCDS2816.1, CCDS2817.1, CCDS46832.1, CCDS46833.1	3p21.31	2014-07-17			ENSG00000114378	ENSG00000114378	3.2.1.35		5320	protein-coding gene	gene with protein product		607071				9223416, 9409739	Standard	NM_153281		Approved	LUCA1, HYAL-1, FUS2, NAT6	uc003czp.4	Q12794	OTTHUMG00000156941	ENST00000266031.4:c.24C>G	chr3.hg19:g.50340364G>C	ENSP00000266031:p.Ile8Met	60.0	0.0	.		46.0	6.0	.	NM_033159	Q6FH23|Q6PIZ6|Q7KYU2|Q7LE34|Q8NFK5|Q8NFK6|Q8NFK7|Q8NFK8|Q8NFK9|Q93013|Q9UKD5|Q9UNI8	Missense_Mutation	SNP	ENST00000266031.4	hg19	CCDS2816.1	.	.	.	.	.	.	.	.	.	.	G	15.26	2.780578	0.49891	.	.	ENSG00000114378	ENST00000395144;ENST00000266031;ENST00000320295;ENST00000395143;ENST00000418723;ENST00000452672	T;T;T;T;T;T	0.48522	2.16;2.16;2.16;1.83;0.81;0.81	5.3	1.26	0.21427	.	3.721710	0.00447	N	0.000080	T	0.49236	0.1545	L	0.50333	1.59	0.24266	N	0.99527	P;P;P	0.37636	0.603;0.603;0.468	B;B;B	0.42386	0.386;0.295;0.293	T	0.34179	-0.9839	10	0.46703	T	0.11	-3.0796	6.6937	0.23187	0.2193:0.0:0.6565:0.1242	.	8;8;8	Q12794-7;Q12794-2;Q12794	.;.;HYAL1_HUMAN	M	8	ENSP00000378576:I8M;ENSP00000266031:I8M;ENSP00000346068:I8M;ENSP00000378575:I8M;ENSP00000394526:I8M;ENSP00000391666:I8M	ENSP00000266031:I8M	I	-	3	3	HYAL1	50315368	0.761000	0.28439	0.005000	0.12908	0.266000	0.26442	1.468000	0.35332	0.324000	0.23333	0.655000	0.94253	ATC	.	.	.	alt		0.607	HYAL1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346703.1			C	50340364	G	C	50340364	3	2	42	1	0	0	0	0	1	0	0	0	7470	932	33	4	1295	4	HYAL1	3	50340364	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08		50340364	147682066	9	2940											
LMLN	89782	hgsc.bcm.edu	37	chr3	197687277	197687277	+	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	cgtctccttgggcagttcccCtccctgccggcaccacgtcc	3	9	9	20	3	1	0	0	0	1	0	5	0	4	0	7	2	1	3	7	2	0	2			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr3:197687277C>A	ENST00000330198.4	+	1	207	c.185C>A	c.(184-186)cCt>cAt	p.P62H	LMLN_ENST00000420910.2_Missense_Mutation_p.P62H|IQCG_ENST00000480302.1_5'Flank|IQCG_ENST00000265239.6_5'Flank|LMLN_ENST00000332636.5_Intron|LMLN_ENST00000482695.1_Intron	NM_033029.3	NP_149018.2	Q96KR4	LMLN_HUMAN	leishmanolysin-like (metallopeptidase M8 family)	62					cell adhesion (GO:0007155)|mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)		GGCAGTTCCCCTCCCTGCCGG	0.662																																					p.P62H		Atlas-SNP	.											.	LMLN	53	.	0			c.C185A						PASS	.						43	47	46					3																	197687277		2203	4300	6503	SO:0001583	missense	89782	exon1			GTTCCCCTCCCTG	AJ312398	CCDS3332.1, CCDS46988.1	3q29	2008-02-04			ENSG00000185621	ENSG00000185621	3.4.24.36		15991	protein-coding gene	gene with protein product		609380					Standard	NM_033029		Approved	Gp63, Msp	uc010iar.3	Q96KR4	OTTHUMG00000155375	ENST00000330198.4:c.185C>A	chr3.hg19:g.197687277C>A	ENSP00000328829:p.Pro62His	172.0	0.0	.		133.0	6.0	.	NM_001136049	B3LDG9|B3LDH0|C9J796|F8WB28|Q96KR5	Missense_Mutation	SNP	ENST00000330198.4	hg19	CCDS3332.1	.	.	.	.	.	.	.	.	.	.	C	15.98	2.992122	0.54041	.	.	ENSG00000185621	ENST00000330198;ENST00000420910	T;T	0.41758	0.99;0.99	4.22	1.34	0.21922	.	0.647122	0.14803	N	0.297489	T	0.22003	0.0530	N	0.02011	-0.69	0.18873	N	0.999987	B;P	0.36249	0.003;0.545	B;P	0.47376	0.01;0.545	T	0.31364	-0.9946	10	0.16896	T	0.51	-1.1491	6.4356	0.21821	0.0:0.5507:0.349:0.1003	.	62;62	Q96KR4;F8WB28	LMLN_HUMAN;.	H	62	ENSP00000328829:P62H;ENSP00000410926:P62H	ENSP00000328829:P62H	P	+	2	0	LMLN	199171674	0.000000	0.05858	0.290000	0.24890	0.995000	0.86356	0.090000	0.15025	0.161000	0.19458	0.456000	0.33151	CCT	.	.	.	none		0.662	LMLN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339701.1	NM_033029		A	197687277	C	A	197687277	3	1	42	1	0	0	0	0	1	0	0	0	8854	681	24	4	187	4	LMLN	3	197687277	Missense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08	147346913	197687277	335153	10	2941											
DCK	1633	hgsc.bcm.edu	37	chr4	71892401	71892401	+	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	gaaccaacttcgattatcttCaagaggtgcctatcttaaca	13	12	6	10	1	3	1	1	0	2	1	4	3	3	1	2	1	4	0	2	1	6	5			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr4:71892401C>A	ENST00000286648.5	+	6	1082	c.685C>A	c.(685-687)Caa>Aaa	p.Q229K	DCK_ENST00000504730.1_Nonsense_Mutation_p.S190*|DCK_ENST00000504952.1_Missense_Mutation_p.Q229K	NM_000788.2	NP_000779.1	P27707	DCK_HUMAN	deoxycytidine kinase	229					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)	CGATTATCTTCAAGAGGTGCC	0.284																																					p.Q229K		Atlas-SNP	.											.	DCK	23	.	0			c.C685A						PASS	.						43	45	44					4																	71892401		2202	4288	6490	SO:0001583	missense	1633	exon6			TATCTTCAAGAGG	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.685C>A	chr4.hg19:g.71892401C>A	ENSP00000286648:p.Gln229Lys	70.0	0.0	.		39.0	13.0	.	NM_000788	B2R8V6|Q5TZY7|Q6FI11	Missense_Mutation	SNP	ENST00000286648.5	hg19	CCDS3548.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.0|27.0	4.787431|4.787431	0.90367|0.90367	.|.	.|.	ENSG00000156136|ENSG00000156136	ENST00000286648;ENST00000504952|ENST00000504730	D;D|.	0.97870|.	-4.58;-4.58|.	5.78|5.78	4.92|4.92	0.64577|0.64577	.|.	0.274194|.	0.41194|.	D|.	0.000924|.	T|.	0.49864|.	0.1582|.	N|N	0.16233|0.16233	0.39|0.39	0.45272|0.45272	D|D	0.998276|0.998276	B|.	0.09022|.	0.002|.	B|.	0.09377|.	0.004|.	T|.	0.44483|.	-0.9325|.	10|.	0.05351|.	T|.	0.99|.	.|.	16.6255|16.6255	0.84969|0.84969	0.0:0.8699:0.1301:0.0|0.0:0.8699:0.1301:0.0	.|.	229|.	P27707|.	DCK_HUMAN|.	K|X	229|190	ENSP00000286648:Q229K;ENSP00000421508:Q229K|.	ENSP00000286648:Q229K|.	Q|S	+|+	1|2	0|0	DCK|DCK	72111265|72111265	0.983000|0.983000	0.35010|0.35010	0.987000|0.987000	0.45799|0.45799	0.467000|0.467000	0.32768|0.32768	3.040000|3.040000	0.49799|0.49799	1.391000|1.391000	0.46566|0.46566	0.591000|0.591000	0.81541|0.81541	CAA|TCA	.	.	.	none		0.284	DCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252159.2			A	71892401	C	A	71892401	3	1	42	1	0	0	0	0	1	0	0	0	4292	827	29	4	707	4	DCK	4	71892401	Missense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08		71892401	119261875	11	2942											
FAT4	79633	hgsc.bcm.edu	37	chr4	126371574	126371574	+	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	tttcttcaggaaatgaagaaGgcatttttgcaatcaattct	13	15	7	6	0	4	2	2	1	2	1	4	3	4	3	0	2	1	2	0	2	5	5			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr4:126371574G>A	ENST00000394329.3	+	9	9416	c.9403G>A	c.(9403-9405)Ggc>Agc	p.G3135S	FAT4_ENST00000335110.5_Missense_Mutation_p.G1433S	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3135	Cadherin 30. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						AAATGAAGAAGGCATTTTTGC	0.388																																					p.G3135S		Atlas-SNP	.											.	FAT4	1752	.	0			c.G9403A						PASS	.						67	68	68					4																	126371574		2203	4300	6503	SO:0001583	missense	79633	exon9			GAAGAAGGCATTT	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.9403G>A	chr4.hg19:g.126371574G>A	ENSP00000377862:p.Gly3135Ser	89.0	0.0	.		37.0	15.0	.	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	14.20	2.464553	0.43736	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.61859	0.07;0.07	5.63	4.79	0.61399	Cadherin (4);Cadherin-like (1);	0.000000	0.35067	U	0.003472	T	0.60650	0.2285	N	0.25647	0.755	0.80722	D	1	P;D;D	0.89917	0.839;1.0;1.0	B;D;D	0.97110	0.287;0.997;1.0	T	0.54951	-0.8216	10	0.08599	T	0.76	.	14.512	0.67794	0.0698:0.0:0.9302:0.0	.	1433;3135;3135	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	S	3135;1433	ENSP00000377862:G3135S;ENSP00000335169:G1433S	ENSP00000335169:G1433S	G	+	1	0	FAT4	126591024	1.000000	0.71417	0.835000	0.33067	0.669000	0.39330	7.835000	0.86780	1.389000	0.46526	0.655000	0.94253	GGC	.	.	.	none		0.388	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126371574	G	A	126371574	3	1	42	1	0	0	0	0	1	0	0	0	5699	1000	35	2	9437	2	FAT4	4	126371574	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08	54479173	126371574	64782702	12	2943											
HIST1H4C	8364	hgsc.bcm.edu	37	chr6	26104205	26104205	+	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	cgcggcaaaggcggaaaaggCttggggaagggtggtgctaa	11	5	19	6	3	0	0	0	0	0	0	0	2	0	2	0	8	1	3	0	8	5	2	rs139978722	byFrequency	TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:26104205C>G	ENST00000377803.2	+	1	102	c.30C>G	c.(28-30)ggC>ggG	p.G10G		NM_003542.3	NP_003533.1	P62805	H4_HUMAN	histone cluster 1, H4c	10					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						GCGGAAAAGGCTTGGGGAAGG	0.532																																					p.G10G		Atlas-SNP	.											.	HIST1H4C	14	.	0			c.C30G						PASS	.						57	58	58					6																	26104205		2203	4300	6503	SO:0001819	synonymous_variant	8364	exon1			AAAAGGCTTGGGG	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.30C>G	chr6.hg19:g.26104205C>G		115.0	0.0	.		88.0	21.0	.	NM_003542	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000377803.2	hg19	CCDS4583.1																																																																																			.	C|0.999;T|0.001	.	alt		0.532	HIST1H4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040092.2	NM_003542		G	26104205	C	G	26104205	2	3	42	1	0	0	0	0	0	0	0	1	7174	784	28	4		4	HIST1H4C	6	26104205	Silent	SNP	C	TCGA-A4-7287-01A-11D-2136-08		26104205	145010862	13	2944											
ZNF192	7745	hgsc.bcm.edu	37	chr6	28116192	28116192	+	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	cttttcaggctctaatggctGaagaatcaagaaagccttca	13	11	8	9	0	4	3	3	1	1	2	4	3	4	3	1	2	1	2	1	2	5	4			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:28116192G>A	ENST00000330236.6	+	2	191	c.7G>A	c.(7-9)Gaa>Aaa	p.E3K	ZKSCAN8_ENST00000457389.2_Missense_Mutation_p.E3K	NM_001278119.1|NM_001278121.1|NM_001278122.1|NM_006298.2	NP_001265048.1|NP_001265050.1|NP_001265051.1|NP_006289.2	Q15776	ZKSC8_HUMAN	zinc finger with KRAB and SCAN domains 8	3					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TCTAATGGCTGAAGAATCAAG	0.473																																					p.E3K		Atlas-SNP	.											.	.	.	.	0			c.G7A						PASS	.						50	48	49					6																	28116192		2203	4300	6503	SO:0001583	missense	7745	exon2			ATGGCTGAAGAAT		CCDS4645.1	6p21	2013-01-09	2013-01-09	2013-01-09	ENSG00000198315	ENSG00000198315		"Zinc fingers, C2H2-type", "-", "-", "-"	12983	protein-coding gene	gene with protein product		602240	"zinc finger protein 192"	ZNF192			Standard	NM_001278119		Approved	LD5-1, ZSCAN40	uc003nkn.2	Q15776	OTTHUMG00000014510	ENST00000330236.6:c.7G>A	chr6.hg19:g.28116192G>A	ENSP00000332750:p.Glu3Lys	67.0	0.0	.		35.0	12.0	.	NM_006298	A1L3D4|B4DYF1|Q4VAR1|Q4VAR2|Q4VAR3|Q9H4T1	Missense_Mutation	SNP	ENST00000330236.6	hg19	CCDS4645.1	.	.	.	.	.	.	.	.	.	.	G	14.70	2.614734	0.46631	.	.	ENSG00000198315	ENST00000330236;ENST00000457389;ENST00000536028	T;T;T	0.05580	3.42;3.42;3.99	5.2	-0.593	0.11667	.	1.155400	0.06424	N	0.722860	T	0.01189	0.0039	N	0.19112	0.55	0.22827	N	0.998682	B	0.02656	0.0	B	0.01281	0.0	T	0.48592	-0.9022	10	0.42905	T	0.14	.	3.6279	0.08120	0.2558:0.0:0.4473:0.2969	.	3	Q15776	ZN192_HUMAN	K	3	ENSP00000332750:E3K;ENSP00000402948:E3K;ENSP00000439117:E3K	ENSP00000332750:E3K	E	+	1	0	ZNF192	28224171	0.141000	0.22595	0.921000	0.36526	0.930000	0.56654	0.165000	0.16564	-0.225000	0.09913	0.563000	0.77884	GAA	.	.	.	none		0.473	ZKSCAN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040178.2			A	28116192	G	A	28116192	3	1	42	1	0	0	0	0	1	0	0	0	17768	1291	45	2	9	2	ZNF192	6	28116192	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08	2011987	28116192	142998875	14	2945											
CRISP3	10321	hgsc.bcm.edu	37	chr6	49696475	49696475	+	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	gtttgaacaattgcaggaggCcttgcaactgtccctgacca	10	10	10	11	0	0	2	0	2	0	0	1	3	1	3	3	2	4	3	3	2	3	3			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:49696475C>T	ENST00000393666.1	-	7	712	c.706G>A	c.(706-708)Gcc>Acc	p.A236T	CRISP3_ENST00000423399.2_Missense_Mutation_p.A146T|CRISP3_ENST00000433368.2_Missense_Mutation_p.A259T|CRISP3_ENST00000371159.4_Missense_Mutation_p.A267T|CRISP3_ENST00000263045.4_Missense_Mutation_p.A249T			P54108	CRIS3_HUMAN	cysteine-rich secretory protein 3	236	ShKT. {ECO:0000255|PROSITE- ProRule:PRU01005}.				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)			TTGCAGGAGGCCTTGCAACTG	0.403																																					p.A259T		Atlas-SNP	.											.	CRISP3	67	.	0			c.G775A						PASS	.						188	169	175					6																	49696475		2203	4300	6503	SO:0001583	missense	10321	exon8			AGGAGGCCTTGCA	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.706G>A	chr6.hg19:g.49696475C>T	ENSP00000377274:p.Ala236Thr	150.0	0.0	.		120.0	38.0	.	NM_001190986	A8K9S1|B2R8I8|Q15512|Q3MJ82|Q53FA9|Q5JW83|Q9H108	Missense_Mutation	SNP	ENST00000393666.1	hg19		.	.	.	.	.	.	.	.	.	.	C	17.52	3.410104	0.62399	.	.	ENSG00000096006	ENST00000263045;ENST00000433368;ENST00000393666;ENST00000423399;ENST00000371159	T;T;T;T;T	0.16073	2.88;2.87;2.9;2.37;2.87	4.55	4.55	0.56014	Cysteine-rich secretory protein (1);	0.089556	0.44285	U	0.000474	T	0.21921	0.0528	M	0.83483	2.645	0.30644	N	0.756123	D	0.60575	0.988	P	0.50590	0.645	T	0.06180	-1.0841	10	0.72032	D	0.01	.	13.1387	0.59423	0.0:1.0:0.0:0.0	.	236	P54108	CRIS3_HUMAN	T	249;259;236;146;267	ENSP00000263045:A249T;ENSP00000389026:A259T;ENSP00000377274:A236T;ENSP00000410469:A146T;ENSP00000360201:A267T	ENSP00000263045:A249T	A	-	1	0	CRISP3	49804434	0.287000	0.24315	0.827000	0.32855	0.121000	0.20230	1.129000	0.31381	2.236000	0.73375	0.609000	0.83330	GCC	.	.	.	none		0.403	CRISP3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_006061		T	49696475	C	T	49696475	3	4	42	1	0	0	0	0	1	0	0	0	3883	739	26	2	35	2	CRISP3	6	49696475	Missense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08	21580283	49696475	121418592	15	2946											
COL9A1	1297	hgsc.bcm.edu	37	chr6	70990561	70990561	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctggagctcctggctttcccGgttcacctgcaggaccctga	5	10	11	15	1	1	1	1	1	0	0	3	3	3	3	4	4	2	4	4	4	0	2			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:70990561G>A	ENST00000357250.6	-	10	1087	c.929C>T	c.(928-930)cCg>cTg	p.P310L	COL9A1_ENST00000370499.4_Missense_Mutation_p.P67L|COL9A1_ENST00000370496.3_Missense_Mutation_p.P310L|COL9A1_ENST00000489611.1_5'Flank|COL9A1_ENST00000320755.7_Missense_Mutation_p.P67L	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	310	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						TGGCTTTCCCGGTTCACCTGC	0.627																																					p.P310L		Atlas-SNP	.											.	COL9A1	228	.	0			c.C929T						PASS	.						18	19	19					6																	70990561		2203	4300	6503	SO:0001583	missense	1297	exon10			TTTCCCGGTTCAC		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.929C>T	chr6.hg19:g.70990561G>A	ENSP00000349790:p.Pro310Leu	33.0	0.0	.		28.0	9.0	.	NM_001851	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Missense_Mutation	SNP	ENST00000357250.6	hg19	CCDS4971.1	.	.	.	.	.	.	.	.	.	.	G	10.65	1.410959	0.25465	.	.	ENSG00000112280	ENST00000357250;ENST00000320755;ENST00000370499;ENST00000370496	D;D;D;D	0.94000	-3.33;-3.33;-3.33;-3.28	5.6	4.72	0.59763	.	0.325795	0.37012	N	0.002296	D	0.90435	0.7005	M	0.84846	2.72	0.46981	D	0.999279	P;P	0.44429	0.835;0.516	B;B	0.38327	0.271;0.135	D	0.89481	0.3750	10	0.30854	T	0.27	.	15.4859	0.75569	0.0:0.139:0.861:0.0	.	310;67	P20849;P20849-2	CO9A1_HUMAN;.	L	310;67;67;310	ENSP00000349790:P310L;ENSP00000315252:P67L;ENSP00000359530:P67L;ENSP00000359527:P310L	ENSP00000315252:P67L	P	-	2	0	COL9A1	71047282	0.999000	0.42202	0.747000	0.31113	0.002000	0.02628	4.673000	0.61604	1.347000	0.45714	0.563000	0.77884	CCG	.	.	.	none		0.627	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2			A	70990561	G	A	70990561	3	1	42	1	0	0	0	0	1	0	0	0	3709	1116	39	1	1952	1	COL9A1	6	70990561	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08	21294086	70990561	100124506	16	2947											
IMPG1	3617	hgsc.bcm.edu	37	chr6	76660465	76660465	+	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	acaggagtggtatcctccaaGaaatgatctgggacagaaac	15	7	11	8	0	1	3	0	1	1	2	3	5	3	5	2	3	1	1	2	3	4	1			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:76660465G>C	ENST00000369950.3	-	13	1827	c.1638C>G	c.(1636-1638)ttC>ttG	p.F546L	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)				TATCCTCCAAGAAATGATCTG	0.483																																					p.F546L	Pancreas(37;839 1141 2599 26037)	Atlas-SNP	.											.	IMPG1	143	.	0			c.C1638G						PASS	.						93	79	84					6																	76660465		2203	4300	6503	SO:0001583	missense	3617	exon13			CTCCAAGAAATGA	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.1638C>G	chr6.hg19:g.76660465G>C	ENSP00000358966:p.Phe546Leu	87.0	0.0	.		63.0	15.0	.	NM_001563		Missense_Mutation	SNP	ENST00000369950.3	hg19	CCDS4985.1	.	.	.	.	.	.	.	.	.	.	G	9.188	1.025421	0.19512	.	.	ENSG00000112706	ENST00000369950	T	0.19532	2.14	5.67	0.817	0.18773	.	0.942898	0.08930	N	0.873167	T	0.08223	0.0205	M	0.73598	2.24	0.09310	N	1	B	0.26258	0.145	B	0.20955	0.032	T	0.42292	-0.9460	10	0.15066	T	0.55	.	8.972	0.35912	0.39:0.0:0.61:0.0	.	546	Q17R60	IMPG1_HUMAN	L	546	ENSP00000358966:F546L	ENSP00000358966:F546L	F	-	3	2	IMPG1	76717185	0.000000	0.05858	0.026000	0.17262	0.005000	0.04900	-0.651000	0.05372	0.055000	0.16094	-0.142000	0.14014	TTC	.	.	.	none		0.483	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563		C	76660465	G	C	76660465	3	2	42	1	0	0	0	0	1	0	0	0	7735	933	33	4	775	4	IMPG1	6	76660465	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08	5669904	76660465	94454602	17	2948			1	7		4	3	172	N	G	2.306594e-08
IMPG1	3617	hgsc.bcm.edu	37	chr6	76660529	76660529	+	Missense_Mutation	SNP	G	G	A																															cagatggggcaggagtgtcaGacagatccatttcatctagg																										TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:76660529G>A	ENST00000369950.3	-	13	1763	c.1574C>T	c.(1573-1575)tCt>tTt	p.S525F	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)				AGGAGTGTCAGACAGATCCAT	0.488																																					p.S525F	Pancreas(37;839 1141 2599 26037)	Atlas-SNP	.											.	IMPG1	143	.	0			c.C1574T						PASS	.						97	80	86					6																	76660529		2203	4300	6503	SO:0001583	missense	3617	exon13			GTGTCAGACAGAT	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.1574C>T	chr6.hg19:g.76660529G>A	ENSP00000358966:p.Ser525Phe	54.0	0.0	.		40.0	9.0	.	NM_001563		Missense_Mutation	SNP	ENST00000369950.3	hg19	CCDS4985.1	.	.	.	.	.	.	.	.	.	.	G	13.33	2.206277	0.39003	.	.	ENSG00000112706	ENST00000369950	T	0.21031	2.03	4.94	2.19	0.27852	.	1.695600	0.02971	N	0.144359	T	0.07954	0.0199	L	0.38175	1.15	0.09310	N	0.999999	P	0.46706	0.883	B	0.44044	0.439	T	0.13361	-1.0512	10	0.39692	T	0.17	.	4.5254	0.11980	0.435:0.0:0.4185:0.1465	.	525	Q17R60	IMPG1_HUMAN	F	525	ENSP00000358966:S525F	ENSP00000358966:S525F	S	-	2	0	IMPG1	76717249	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.632000	0.24583	0.339000	0.23719	0.650000	0.86243	TCT	.	.	.	none		0.488	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563		A	76660529	G	A	76660529	3	1	42	1	0	0	0	0	1	0	0	0	7735	942	33	2	839	2	IMPG1	6	76660529	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08	64	76660529	94454538	18	2949	37	2	1	7		4	3	172	N	G	2.306594e-08
IMPG1	3617	hgsc.bcm.edu	37	chr6	76660533	76660533	+	Silent	SNP	G	G	A																															tggggcaggagtgtcagacaGatccatttcatctaggtgtc																										TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:76660533G>A	ENST00000369950.3	-	13	1759	c.1570C>T	c.(1570-1572)Ctg>Ttg	p.L524L	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)				GTGTCAGACAGATCCATTTCA	0.493																																					p.L524L	Pancreas(37;839 1141 2599 26037)	Atlas-SNP	.											.	IMPG1	143	.	0			c.C1570T						PASS	.						99	82	88					6																	76660533		2203	4300	6503	SO:0001819	synonymous_variant	3617	exon13			CAGACAGATCCAT	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.1570C>T	chr6.hg19:g.76660533G>A		52.0	0.0	.		39.0	10.0	.	NM_001563		Silent	SNP	ENST00000369950.3	hg19	CCDS4985.1																																																																																			.	.	.	none		0.493	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563		A	76660533	G	A	76660533	2	1	42	1	0	0	0	0	0	0	0	1	7735	933	33	2		2	IMPG1	6	76660533	Silent	SNP	G	TCGA-A4-7287-01A-11D-2136-08	4	76660533	94454534	19	2950	37	2	1	7		4	3	172	N	G	2.306594e-08
IMPG1	3617	hgsc.bcm.edu	37	chr6	76660636	76660636	+	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	attcccagagccagttggctGattgcagaataatcactggt	11	11	10	9	0	1	3	1	1	0	2	2	3	2	3	2	2	2	3	2	2	2	4			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:76660636G>A	ENST00000369950.3	-	13	1656	c.1467C>T	c.(1465-1467)atC>atT	p.I489I	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)				CCAGTTGGCTGATTGCAGAAT	0.498																																					p.I489I	Pancreas(37;839 1141 2599 26037)	Atlas-SNP	.											.	IMPG1	143	.	0			c.C1467T						PASS	.						159	151	153					6																	76660636		2203	4300	6503	SO:0001819	synonymous_variant	3617	exon13			TTGGCTGATTGCA	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.1467C>T	chr6.hg19:g.76660636G>A		104.0	0.0	.		78.0	20.0	.	NM_001563		Silent	SNP	ENST00000369950.3	hg19	CCDS4985.1																																																																																			.	.	.	none		0.498	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563		A	76660636	G	A	76660636	2	1	42	1	0	0	0	0	0	0	0	1	7735	1280	45	2		2	IMPG1	6	76660636	Silent	SNP	G	TCGA-A4-7287-01A-11D-2136-08	103	76660636	94454431	20	2951			1	7		4	3	172	N	G	2.306594e-08
LAMA4	3910	hgsc.bcm.edu	37	chr6	112454683	112454683	+	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	tctaggggaaggtgtgctctGagggccctggaaaagaaagt	11	8	16	6	0	2	2	0	1	2	1	2	4	2	4	1	5	1	1	1	5	5	1			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:112454683G>C	ENST00000230538.7	-	27	3961	c.3564C>G	c.(3562-3564)ctC>ctG	p.L1188L	LAMA4_ENST00000389463.4_Silent_p.L1181L|LAMA4_ENST00000424408.2_Silent_p.L1181L|LAMA4_ENST00000522006.1_Silent_p.L1181L	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	1188	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		GGTGTGCTCTGAGGGCCCTGG	0.438																																					p.L1188L		Atlas-SNP	.											.	LAMA4	227	.	0			c.C3564G						PASS	.						101	96	97					6																	112454683		2203	4300	6503	SO:0001819	synonymous_variant	3910	exon27			TGCTCTGAGGGCC		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.3564C>G	chr6.hg19:g.112454683G>C		154.0	0.0	.		119.0	29.0	.	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Silent	SNP	ENST00000230538.7	hg19	CCDS43491.1																																																																																			.	.	.	none		0.438	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206		C	112454683	G	C	112454683	2	2	42	1	0	0	0	0	0	0	0	1	8615	1277	45	4		4	LAMA4	6	112454683	Silent	SNP	G	TCGA-A4-7287-01A-11D-2136-08	35794047	112454683	58660384	21	2952											
MSRA	4482	hgsc.bcm.edu	37	chr8	9912062	9912062	+	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	cggagggcttgccagctcctCctcctccacagcctctttcc	4	10	8	19	1	1	0	0	0	1	0	6	1	6	1	7	2	3	2	7	2	0	2			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr8:9912062C>T	ENST00000317173.4	+	1	285	c.36C>T	c.(34-36)ctC>ctT	p.L12L	MSRA_ENST00000441698.2_Silent_p.L12L|RP11-1E4.1_ENST00000562143.1_RNA|MSRA_ENST00000518255.1_Silent_p.L12L	NM_012331.3	NP_036463.1	Q9UJ68	MSRA_HUMAN	methionine sulfoxide reductase A	12				Missing (in Ref. 6; AAG09689). {ECO:0000305}.	cellular protein modification process (GO:0006464)|methionine metabolic process (GO:0006555)|protein repair (GO:0030091)|response to oxidative stress (GO:0006979)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	peptide-methionine (S)-S-oxide reductase activity (GO:0008113)			central_nervous_system(1)|endometrium(2)|kidney(1)|lung(4)	8		Myeloproliferative disorder(644;0.178)			L-Methionine(DB00134)	GCCAGCTCCTCCTCCTCCACA	0.716																																					p.L12L	NSCLC(88;1378 1469 30580 49103 52286)	Atlas-SNP	.											.	MSRA	21	.	0			c.C36T						PASS	.						36	35	36					8																	9912062		2203	4300	6503	SO:0001819	synonymous_variant	4482	exon1			GCTCCTCCTCCTC	BC054033	CCDS5975.1, CCDS47798.1, CCDS47799.1, CCDS56522.1	8p23.1	2009-07-10			ENSG00000175806	ENSG00000175806	1.8.4.11		7377	protein-coding gene	gene with protein product		601250				10452521	Standard	NM_012331		Approved		uc003wsx.3	Q9UJ68	OTTHUMG00000090517	ENST00000317173.4:c.36C>T	chr8.hg19:g.9912062C>T		67.0	0.0	.		43.0	16.0	.	NM_012331	E9PAS8|Q52TC4|Q549N4|Q66MI7	Silent	SNP	ENST00000317173.4	hg19	CCDS5975.1																																																																																			.	.	.	none		0.716	MSRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207005.1	NM_012331		T	9912062	C	T	9912062	2	4	42	1	0	0	0	0	0	0	0	1	9894	842	30	2		2	MSRA	8	9912062	Silent	SNP	C	TCGA-A4-7287-01A-11D-2136-08		9912062	136451960	22	2953			2	8		2	2	42	C		5.165137e-05
MSRA	4482	hgsc.bcm.edu	37	chr8	9912103	9912103	+	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	cgtcccgaggatgggcaactCggcctcgaacatcgtcagcc	8	6	12	15	5	1	0	1	0	0	0	5	3	2	1	3	3	3	1	3	3	2	0			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr8:9912103C>T	ENST00000317173.4	+	1	326	c.77C>T	c.(76-78)tCg>tTg	p.S26L	MSRA_ENST00000441698.2_Missense_Mutation_p.S26L|RP11-1E4.1_ENST00000562143.1_RNA|MSRA_ENST00000518255.1_Missense_Mutation_p.S26L	NM_012331.3	NP_036463.1	Q9UJ68	MSRA_HUMAN	methionine sulfoxide reductase A	26					cellular protein modification process (GO:0006464)|methionine metabolic process (GO:0006555)|protein repair (GO:0030091)|response to oxidative stress (GO:0006979)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	peptide-methionine (S)-S-oxide reductase activity (GO:0008113)			central_nervous_system(1)|endometrium(2)|kidney(1)|lung(4)	8		Myeloproliferative disorder(644;0.178)			L-Methionine(DB00134)	ATGGGCAACTCGGCCTCGAAC	0.697																																					p.S26L	NSCLC(88;1378 1469 30580 49103 52286)	Atlas-SNP	.											.	MSRA	21	.	0			c.C77T						PASS	.						38	37	37					8																	9912103		2203	4300	6503	SO:0001583	missense	4482	exon1			GCAACTCGGCCTC	BC054033	CCDS5975.1, CCDS47798.1, CCDS47799.1, CCDS56522.1	8p23.1	2009-07-10			ENSG00000175806	ENSG00000175806	1.8.4.11		7377	protein-coding gene	gene with protein product		601250				10452521	Standard	NM_012331		Approved		uc003wsx.3	Q9UJ68	OTTHUMG00000090517	ENST00000317173.4:c.77C>T	chr8.hg19:g.9912103C>T	ENSP00000313921:p.Ser26Leu	69.0	0.0	.		51.0	15.0	.	NM_012331	E9PAS8|Q52TC4|Q549N4|Q66MI7	Missense_Mutation	SNP	ENST00000317173.4	hg19	CCDS5975.1	.	.	.	.	.	.	.	.	.	.	C	11.38	1.622922	0.28889	.	.	ENSG00000175806	ENST00000317173;ENST00000441698;ENST00000518255	.	.	.	4.84	3.94	0.45596	.	0.300238	0.32015	N	0.006711	T	0.34629	0.0904	L	0.42245	1.32	0.34862	D	0.74275	D;B	0.53885	0.963;0.249	B;B	0.37601	0.254;0.036	T	0.50039	-0.8874	8	.	.	.	0.3672	10.6214	0.45483	0.1922:0.8078:0.0:0.0	.	26;26	Q9UJ68-4;Q9UJ68	.;MSRA_HUMAN	L	26	.	.	S	+	2	0	MSRA	9949513	0.147000	0.22687	0.178000	0.23040	0.019000	0.09904	1.820000	0.39032	1.113000	0.41760	0.313000	0.20887	TCG	.	.	.	none		0.697	MSRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207005.1	NM_012331		T	9912103	C	T	9912103	3	4	42	1	0	0	0	0	1	0	0	0	9894	893	31	1	79	1	MSRA	8	9912103	Missense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08	41	9912103	136451919	23	2954			2	8		2	2	42	C		5.165137e-05
RAB11FIP1	80223	hgsc.bcm.edu	37	chr8	37730588	37730589	+	Frame_Shift_Ins	INS	-	-	G																															gcaccatgtcccaattcagaINSggggacagatgcctggccag																										TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr8:37730588_37730589insG	ENST00000330843.4	-	4	1743_1744	c.1731_1732insC	c.(1729-1734)ccctctfs	p.S578fs	RAB11FIP1_ENST00000522727.1_Intron|RAB11FIP1_ENST00000523182.1_5'UTR|RAB11FIP1_ENST00000524118.1_Intron|RAB11FIP1_ENST00000287263.4_Intron	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	578	Ser-rich.				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)			CCCAATTCAGAGGGGACAGATG	0.559																																					p.S578fs		Atlas-INDEL	.											.	RAB11FIP1	105	.	0			c.1732_1733insC						PASS	.																																			SO:0001589	frameshift_variant	80223	exon4			.	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.1732dupC	chr8.hg19:g.37730592_37730592dupG	ENSP00000331342:p.Ser578fs	115.0	0.0	0		77.0	26.0	0.337662	NM_001002814	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Frame_Shift_Ins	INS	ENST00000330843.4	hg19	CCDS34882.1																																																																																			.	.	.	none		0.559	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151		G	37730589	-	G	37730588	7	5	42	1	0	1	1	0	0	0	0	0	12906	304	11	0	2131	0	RAB11FIP1	8	37730588	Frame_Shift_Ins	INS	-	TCGA-A4-7287-01A-11D-2136-08	27818485	37730588	108633434	24	2955											
ZNF189	7743	hgsc.bcm.edu	37	chr9	104170234	104170234	+	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	ttttgaacagagataaggatGaggagccaactgtaaaacaa	18	8	10	5	0	0	3	0	2	0	1	0	6	0	5	1	2	4	1	1	2	6	4			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr9:104170234G>C	ENST00000339664.2	+	3	313	c.184G>C	c.(184-186)Gag>Cag	p.E62Q	ZNF189_ENST00000374861.3_Missense_Mutation_p.E48Q|ZNF189_ENST00000259395.4_Missense_Mutation_p.E20Q	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	62	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)				AGATAAGGATGAGGAGCCAAC	0.368																																					p.E62Q		Atlas-SNP	.											.	ZNF189	79	.	0			c.G184C						PASS	.						58	60	60					9																	104170234		2202	4300	6502	SO:0001583	missense	7743	exon3			AAGGATGAGGAGC	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.184G>C	chr9.hg19:g.104170234G>C	ENSP00000342019:p.Glu62Gln	29.0	0.0	.		17.0	5.0	.	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Missense_Mutation	SNP	ENST00000339664.2	hg19	CCDS6754.1	.	.	.	.	.	.	.	.	.	.	G	5.540	0.284544	0.10513	.	.	ENSG00000136870	ENST00000374861;ENST00000339664;ENST00000259395	T;T;T	0.05580	5.66;5.66;3.42	4.79	4.79	0.61399	Krueppel-associated box (3);	0.000000	0.49916	D	0.000140	T	0.03220	0.0094	N	0.16201	0.385	0.34306	D	0.684889	B;B;B	0.33073	0.396;0.396;0.006	B;B;B	0.26864	0.074;0.074;0.011	T	0.43261	-0.9402	10	0.14252	T	0.57	.	9.2106	0.37316	0.0942:0.0:0.9058:0.0	.	47;48;62	B7ZLK9;Q5T7D8;O75820	.;.;ZN189_HUMAN	Q	48;62;20	ENSP00000363995:E48Q;ENSP00000342019:E62Q;ENSP00000259395:E20Q	ENSP00000259395:E20Q	E	+	1	0	ZNF189	103210055	0.191000	0.23288	1.000000	0.80357	0.895000	0.52256	0.622000	0.24433	2.941000	0.99782	0.655000	0.94253	GAG	.	.	.	none		0.368	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452		C	104170234	G	C	104170234	3	2	42	1	0	0	0	0	1	0	0	0	17766	1291	45	4	194	4	ZNF189	9	104170234	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08		104170234	37043197	25	2956											
OR10Q1	219960	hgsc.bcm.edu	37	chr11	57996225	57996225	+	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	gctgtgttgccacagaggatCatcaagtagaggaggaggaa	13	7	15	6	0	2	2	2	0	0	2	2	6	2	6	1	4	1	3	1	4	3	2			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr11:57996225C>T	ENST00000316770.2	-	1	165	c.123G>A	c.(121-123)atG>atA	p.M41I		NM_001004471.2	NP_001004471.1	Q8NGQ4	O10Q1_HUMAN	olfactory receptor, family 10, subfamily Q, member 1	41						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)	35		Breast(21;0.0589)				CACAGAGGATCATCAAGTAGA	0.527																																					p.M41I		Atlas-SNP	.											.	OR10Q1	79	.	0			c.G123A						PASS	.						114	122	119					11																	57996225		2200	4294	6494	SO:0001583	missense	219960	exon1			GAGGATCATCAAG	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.123G>A	chr11.hg19:g.57996225C>T	ENSP00000314324:p.Met41Ile	129.0	0.0	.		106.0	28.0	.	NM_001004471	Q6IFG4	Missense_Mutation	SNP	ENST00000316770.2	hg19	CCDS31547.1	.	.	.	.	.	.	.	.	.	.	C	8.116	0.779975	0.16120	.	.	ENSG00000180475	ENST00000316770	T	0.00392	7.58	5.28	2.25	0.28309	.	0.123417	0.36555	N	0.002525	T	0.00178	0.0005	N	0.13168	0.305	0.09310	N	1	B	0.34181	0.44	B	0.30646	0.118	T	0.31558	-0.9939	10	0.10377	T	0.69	.	11.4267	0.50015	0.136:0.3334:0.5306:0.0	.	41	Q8NGQ4	O10Q1_HUMAN	I	41	ENSP00000314324:M41I	ENSP00000314324:M41I	M	-	3	0	OR10Q1	57752801	0.000000	0.05858	0.013000	0.15412	0.626000	0.37791	-0.168000	0.09925	0.305000	0.22832	0.650000	0.86243	ATG	.	.	.	none		0.527	OR10Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394706.1	NM_001004471		T	57996225	C	T	57996225	3	4	42	1	0	0	0	0	1	0	0	0	10923	826	29	2	840	2	OR10Q1	11	57996225	Missense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08		57996225	77010291	26	2957											
ZNF385A	25946	hgsc.bcm.edu	37	chr12	54764720	54764720	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttagacccacctgtttcagTtggacctccgagttgacctt	7	13	8	13	1	1	2	1	1	0	1	2	4	2	3	5	1	0	3	5	1	1	5			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr12:54764720T>C	ENST00000338010.5	-	6	878	c.825A>G	c.(823-825)caA>caG	p.Q275Q	ZNF385A_ENST00000551109.1_Silent_p.Q255Q|ZNF385A_ENST00000551771.1_Silent_p.Q174Q|RP11-753H16.5_ENST00000552785.1_RNA|RP11-753H16.3_ENST00000550474.1_RNA|ZNF385A_ENST00000546970.1_Silent_p.Q255Q|ZNF385A_ENST00000552382.1_5'UTR|ZNF385A_ENST00000352268.6_Silent_p.Q194Q|ZNF385A_ENST00000394313.2_Silent_p.Q255Q	NM_001130967.1	NP_001124439.1	Q96PM9	Z385A_HUMAN	zinc finger protein 385A	275	Necessary for binding to ITPR1, CEBPA and p53/TP53 mRNAs. {ECO:0000250}.				apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|hemostasis (GO:0007599)|learning or memory (GO:0007611)|locomotory behavior (GO:0007626)|megakaryocyte development (GO:0035855)|mRNA localization resulting in posttranscriptional regulation of gene expression (GO:0010609)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)|positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:1902164)|positive regulation of fat cell differentiation (GO:0045600)|regulation of cytoplasmic translation (GO:2000765)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA 3'-UTR binding (GO:0003730)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|urinary_tract(1)	15						CCTGTTTCAGTTGGACCTCCG	0.597											OREG0021894	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q275Q		Atlas-SNP	.											.	ZNF385A	45	.	0			c.A825G						PASS	.						89	96	94					12																	54764720		2203	4300	6503	SO:0001819	synonymous_variant	25946	exon6			TTTCAGTTGGACC	AF304052	CCDS8879.1, CCDS44910.1, CCDS44911.1	12q13.13	2012-10-05	2007-12-06	2007-12-06		ENSG00000161642			17521	protein-coding gene	gene with protein product		609124	"zinc finger protein 385"	ZNF385			Standard	XM_005268785		Approved	DKFZp586G1122, Hzf, ZFP385	uc001sfy.3	Q96PM9	OTTHUMG00000169840	ENST00000338010.5:c.825A>G	chr12.hg19:g.54764720T>C		217.0	0.0	.	1002	122.0	34.0	.	NM_001130967	B2RDN5|B4DKH2|F1T0F1|J3KNS3|Q5VH53|Q9H7R6|Q9UFU3	Silent	SNP	ENST00000338010.5	hg19	CCDS44911.1																																																																																			.	.	.	none		0.597	ZNF385A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406162.1	NM_015481		C	54764720	T	C	54764720	2	2	42	1	0	0	0	0	0	0	0	1	17888	1722	60	3		3	ZNF385A	12	54764720	Silent	SNP	T	TCGA-A4-7287-01A-11D-2136-08		54764720	79087175	27	2958											
C12orf74	338809	hgsc.bcm.edu	37	chr12	93100691	93100691	+	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	gccaggaagcccaaaggattCttcacacttgctgtcaccct	10	9	8	14	0	3	0	2	0	1	0	3	2	3	2	3	2	2	1	3	2	2	3			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr12:93100691C>G	ENST00000397833.3	+	2	735	c.284C>G	c.(283-285)tCt>tGt	p.S95C	C12orf74_ENST00000544406.2_Missense_Mutation_p.S95C	NM_001037671.3|NM_001178097.2	NP_001032760.1|NP_001171568.1	Q32Q52	CL074_HUMAN	chromosome 12 open reading frame 74	95										kidney(1)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(2)	10						CCAAAGGATTCTTCACACTTG	0.582																																					p.S95C		Atlas-SNP	.											.	C12orf74	17	.	0			c.C284G						PASS	.						55	59	58					12																	93100691		1914	4126	6040	SO:0001583	missense	338809	exon2			AGGATTCTTCACA	BC043363	CCDS41819.1, CCDS53818.1	12q22	2012-08-16			ENSG00000214215	ENSG00000214215			27887	protein-coding gene	gene with protein product						12477932	Standard	NM_001037671		Approved		uc001tch.2	Q32Q52	OTTHUMG00000170105	ENST00000397833.3:c.284C>G	chr12.hg19:g.93100691C>G	ENSP00000380933:p.Ser95Cys	138.0	0.0	.		87.0	23.0	.	NM_001037671	F5H4P0	Missense_Mutation	SNP	ENST00000397833.3	hg19	CCDS41819.1	.	.	.	.	.	.	.	.	.	.	C	11.05	1.525193	0.27299	.	.	ENSG00000214215	ENST00000397833;ENST00000544406	.	.	.	4.98	0.507	0.16967	.	.	.	.	.	T	0.24314	0.0589	N	0.24115	0.695	0.09310	N	1	B;B	0.20261	0.043;0.043	B;B	0.21546	0.035;0.035	T	0.20940	-1.0260	8	0.37606	T	0.19	.	3.0572	0.06188	0.175:0.401:0.327:0.097	.	95;95	F5H4P0;Q32Q52	.;CL074_HUMAN	C	95	.	ENSP00000380933:S95C	S	+	2	0	C12orf74	91624822	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.457000	0.06745	0.212000	0.20703	0.462000	0.41574	TCT	.	.	.	none		0.582	C12orf74-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407285.1	NM_001037671		G	93100691	C	G	93100691	3	3	42	1	0	0	0	0	1	0	0	0	1716	913	32	4	286	4	C12orf74	12	93100691	Missense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08	38335971	93100691	40751204	28	2959											
COASY	80347	hgsc.bcm.edu	37	chr17	40717244	40717244	+	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	gccctctgttcccctccccaGaagcagctgaagatactcac	9	8	7	17	0	2	3	1	1	1	2	4	3	4	3	5	0	3	3	5	0	3	2			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr17:40717244G>T	ENST00000393818.2	+	6	1758		c.e6-1		COASY_ENST00000421097.2_Splice_Site|COASY_ENST00000420359.1_Splice_Site|MLX_ENST00000246912.4_5'Flank|COASY_ENST00000590958.1_Splice_Site|MLX_ENST00000435881.2_5'Flank|COASY_ENST00000449624.1_Splice_Site|MLX_ENST00000346833.4_5'Flank	NM_025233.6	NP_079509.5	Q13057	COASY_HUMAN	CoA synthase						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)		CCCCTCCCCAGAAGCAGCTGA	0.562																																					.		Atlas-SNP	.											.	COASY	45	.	0			c.1303-1G>T						PASS	.						135	138	137					17																	40717244		2203	4300	6503	SO:0001630	splice_region_variant	80347	exon7			TCCCCAGAAGCAG	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.1303-1G>T	chr17.hg19:g.40717244G>T		307.0	0.0	.		219.0	45.0	.	NM_001042529	B2RA78|B4DLU0|Q6GS23|Q8NBM7|Q8NEW1|Q8WXD4|Q9NRM3	Splice_Site	SNP	ENST00000393818.2	hg19	CCDS11429.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.197183	0.79015	.	.	ENSG00000068120	ENST00000421097;ENST00000449624;ENST00000420359;ENST00000393818	.	.	.	5.56	5.56	0.83823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.7387	0.85454	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	COASY	37970770	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	8.174000	0.89682	2.649000	0.89929	0.556000	0.70494	.	.	.	.	none		0.562	COASY-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450409.1	NM_025233	Intron	T	40717244	G	T	40717244	5	4	42	1	0	0	0	0	0	0	1	0	3654	956	33	4	1415	4	COASY	17	40717244	Splice_Site	SNP	G	TCGA-A4-7287-01A-11D-2136-08		40717244	40477966	29	2960											
AOC2	314	hgsc.bcm.edu	37	chr17	40997487	40997487	+	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	ttaagtctggccggttggaaGtggttagagtccctctacct	7	13	12	9	1	2	1	0	0	2	1	3	2	3	2	3	4	1	2	3	4	4	4			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr17:40997487G>C	ENST00000253799.3	+	1	871	c.844G>C	c.(844-846)Gtg>Ctg	p.V282L	AOC2_ENST00000452774.2_Missense_Mutation_p.V282L	NM_009590.2	NP_033720.2	O75106	AOC2_HUMAN	amine oxidase, copper containing 2 (retina-specific)	282					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)		CCGGTTGGAAGTGGTTAGAGT	0.572																																					p.V282L		Atlas-SNP	.											.	AOC2	61	.	0			c.G844C						PASS	.						85	85	85					17																	40997487		2203	4300	6503	SO:0001583	missense	314	exon1			TTGGAAGTGGTTA	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.844G>C	chr17.hg19:g.40997487G>C	ENSP00000253799:p.Val282Leu	116.0	0.0	.		102.0	23.0	.	NM_009590	A5PKW2|O00120|O75105|Q4TTW5|Q9UNY0	Missense_Mutation	SNP	ENST00000253799.3	hg19	CCDS11443.1	.	.	.	.	.	.	.	.	.	.	G	12.32	1.902404	0.33628	.	.	ENSG00000131480	ENST00000253799;ENST00000452774	T;T	0.22945	1.93;1.93	5.75	5.75	0.90469	Copper amine oxidase, N2/N3-terminal (1);Copper amine oxidase, N-terminal (1);	0.267133	0.37219	N	0.002188	T	0.18087	0.0434	N	0.08118	0	0.19945	N	0.99994	P;P	0.50617	0.533;0.937	B;P	0.49561	0.069;0.615	T	0.16424	-1.0403	10	0.10902	T	0.67	-33.3282	14.1397	0.65311	0.0717:0.0:0.9283:0.0	.	282;282	O75106;O75106-2	AOC2_HUMAN;.	L	282	ENSP00000253799:V282L;ENSP00000406134:V282L	ENSP00000253799:V282L	V	+	1	0	AOC2	38251013	0.986000	0.35501	0.707000	0.30419	0.755000	0.42902	2.284000	0.43478	2.720000	0.93068	0.561000	0.74099	GTG	.	.	.	none		0.572	AOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452442.1	NM_009590, NM_001158		C	40997487	G	C	40997487	3	2	42	1	0	0	0	0	1	0	0	0	727	1029	36	4	846	4	AOC2	17	40997487	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08	280243	40997487	40197723	30	2961											
MAPT	4137	hgsc.bcm.edu	37	chr17	44101444	44101444	+	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	ccacggcatctcagcaatgtCtcctccaccggcagcatcga	9	7	8	17	3	2	0	1	0	2	0	6	1	3	0	4	2	2	4	4	2	1	0			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr17:44101444C>G	ENST00000571987.1	+	13	2184	c.2184C>G	c.(2182-2184)gtC>gtG	p.V728V	MAPT_ENST00000535772.1_Silent_p.V380V|MAPT_ENST00000344290.5_Silent_p.V746V|MAPT_ENST00000576518.1_Silent_p.V311V|MAPT_ENST00000420682.2_Silent_p.V382V|MAPT_ENST00000340799.5_Silent_p.V382V|MAPT_ENST00000415613.2_Silent_p.V746V|MAPT_ENST00000574436.1_Silent_p.V411V|MAPT_ENST00000446361.3_Silent_p.V353V|MAPT_ENST00000262410.5_Silent_p.V728V|MAPT_ENST00000334239.8_Silent_p.V322V|MAPT_ENST00000351559.5_Silent_p.V411V|MAPT_ENST00000431008.3_Silent_p.V380V|MAPT_ENST00000347967.5_Silent_p.V286V			P10636	TAU_HUMAN	microtubule-associated protein tau	728					adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	TCAGCAATGTCTCCTCCACCG	0.622																																					p.V746V		Atlas-SNP	.											.	MAPT	135	.	0			c.C2238G						PASS	.						124	105	112					17																	44101444		2203	4300	6503	SO:0001819	synonymous_variant	4137	exon15			CAATGTCTCCTCC	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"G protein beta1/gamma2 subunit-interacting factor 1", "microtubule-associated protein tau, isoform 4", "protein phosphatase 1, regulatory subunit 103"	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.2184C>G	chr17.hg19:g.44101444C>G		186.0	0.0	.		155.0	10.0	.	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Silent	SNP	ENST00000571987.1	hg19	CCDS11501.1																																																																																			.	.	.	none		0.622	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835		G	44101444	C	G	44101444	2	3	42	1	0	0	0	0	0	0	0	1	9304	900	32	4		4	MAPT	17	44101444	Silent	SNP	C	TCGA-A4-7287-01A-11D-2136-08	3103957	44101444	37093766	31	2962											
NDC80	10403	hgsc.bcm.edu	37	chr18	2616466	2616466	+	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	aggagcagattgctaaagttGatagagaatatgaagaatgc	17	9	12	3	0	0	5	0	2	0	3	0	7	0	6	0	1	3	3	0	1	7	5			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr18:2616466G>C	ENST00000261597.4	+	17	2004	c.1822G>C	c.(1822-1824)Gat>Cat	p.D608H		NM_006101.2	NP_006092.1	O14777	NDC80_HUMAN	NDC80 kinetochore complex component	608	Interaction with NEK2 and ZWINT.|Interaction with the C-terminus of CDCA1 and the SPBC24-SPBC25 subcomplex.				attachment of spindle microtubules to kinetochore (GO:0008608)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				NS(1)|biliary_tract(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)|urinary_tract(2)	22						TGCTAAAGTTGATAGAGAATA	0.269																																					p.D608H		Atlas-SNP	.											.	NDC80	62	.	0			c.G1822C						PASS	.						44	47	46					18																	2616466		2200	4284	6484	SO:0001583	missense	10403	exon17			AAAGTTGATAGAG	AF017790	CCDS11827.1	18p11.31	2013-01-17	2013-01-17	2007-03-02	ENSG00000080986	ENSG00000080986			16909	protein-coding gene	gene with protein product		607272	"highly expressed in cancer, rich in leucine heptad repeats (yeast)", "kinetochore associated 2", "NDC80 kinetochore complex component homolog (S. cerevisiae)"	KNTC2		9315664, 12351790	Standard	NM_006101		Approved	HEC, HEC1, hsNDC80, TID3	uc002kli.3	O14777	OTTHUMG00000131483	ENST00000261597.4:c.1822G>C	chr18.hg19:g.2616466G>C	ENSP00000261597:p.Asp608His	58.0	0.0	.		60.0	17.0	.	NM_006101	Q6PJX2	Missense_Mutation	SNP	ENST00000261597.4	hg19	CCDS11827.1	.	.	.	.	.	.	.	.	.	.	G	8.778	0.927542	0.18056	.	.	ENSG00000080986	ENST00000261597	T	0.51325	0.71	5.32	3.48	0.39840	.	0.281499	0.39834	N	0.001252	T	0.43942	0.1270	M	0.62723	1.935	0.38915	D	0.957602	P	0.39216	0.664	B	0.38655	0.278	T	0.42498	-0.9448	10	0.46703	T	0.11	-22.92	9.4287	0.38597	0.0766:0.0:0.7799:0.1435	.	608	O14777	NDC80_HUMAN	H	608	ENSP00000261597:D608H	ENSP00000261597:D608H	D	+	1	0	NDC80	2606466	0.973000	0.33851	0.655000	0.29622	0.368000	0.29767	1.715000	0.37971	0.699000	0.31761	-0.266000	0.10368	GAT	.	.	.	none		0.269	NDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254327.1	NM_006101		C	2616466	G	C	2616466	3	2	42	1	0	0	0	0	1	0	0	0	10249	1290	45	4	1884	4	NDC80	18	2616466	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08		2616466	75460782	32	2963			3	9		2	2	52	G		6.424886e-05
NDC80	10403	hgsc.bcm.edu	37	chr18	2616517	2616517	+	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	atctctcggaaaatattaaaGagattagagataagtatgag	18	11	9	3	1	1	3	0	1	1	2	3	6	1	4	0	1	0	1	0	1	8	5			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr18:2616517G>C	ENST00000261597.4	+	17	2055	c.1873G>C	c.(1873-1875)Gag>Cag	p.E625Q		NM_006101.2	NP_006092.1	O14777	NDC80_HUMAN	NDC80 kinetochore complex component	625	Interaction with the C-terminus of CDCA1 and the SPBC24-SPBC25 subcomplex.				attachment of spindle microtubules to kinetochore (GO:0008608)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				NS(1)|biliary_tract(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)|urinary_tract(2)	22						AAATATTAAAGAGATTAGAGA	0.299																																					p.E625Q		Atlas-SNP	.											.	NDC80	62	.	0			c.G1873C						PASS	.						40	43	42					18																	2616517		2199	4282	6481	SO:0001583	missense	10403	exon17			ATTAAAGAGATTA	AF017790	CCDS11827.1	18p11.31	2013-01-17	2013-01-17	2007-03-02	ENSG00000080986	ENSG00000080986			16909	protein-coding gene	gene with protein product		607272	"highly expressed in cancer, rich in leucine heptad repeats (yeast)", "kinetochore associated 2", "NDC80 kinetochore complex component homolog (S. cerevisiae)"	KNTC2		9315664, 12351790	Standard	NM_006101		Approved	HEC, HEC1, hsNDC80, TID3	uc002kli.3	O14777	OTTHUMG00000131483	ENST00000261597.4:c.1873G>C	chr18.hg19:g.2616517G>C	ENSP00000261597:p.Glu625Gln	38.0	0.0	.		37.0	10.0	.	NM_006101	Q6PJX2	Missense_Mutation	SNP	ENST00000261597.4	hg19	CCDS11827.1	.	.	.	.	.	.	.	.	.	.	G	7.891	0.732376	0.15507	.	.	ENSG00000080986	ENST00000261597	T	0.49432	0.78	5.47	4.59	0.56863	.	0.333418	0.34245	N	0.004123	T	0.34948	0.0915	L	0.47716	1.5	0.28039	N	0.933831	P	0.39216	0.664	B	0.34242	0.178	T	0.18871	-1.0323	10	0.15066	T	0.55	-4.8199	10.1561	0.42823	0.0768:0.137:0.7862:0.0	.	625	O14777	NDC80_HUMAN	Q	625	ENSP00000261597:E625Q	ENSP00000261597:E625Q	E	+	1	0	NDC80	2606517	1.000000	0.71417	0.991000	0.47740	0.167000	0.22549	2.210000	0.42816	1.407000	0.46875	0.555000	0.69702	GAG	.	.	.	none		0.299	NDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254327.1	NM_006101		C	2616517	G	C	2616517	3	2	42	1	0	0	0	0	1	0	0	0	10249	943	33	4	1935	4	NDC80	18	2616517	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08	51	2616517	75460731	33	2964			3	9		2	2	52	G		6.424886e-05
FBXW9	84261	hgsc.bcm.edu	37	chr19	12800616	12800616	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttgcggttggcgaagacgtGcagcaggccctggttgtcac	6	9	16	10	3	1	1	1	0	0	1	1	2	1	1	1	4	3	5	1	4	1	3			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr19:12800616G>A	ENST00000380339.3	-	7	1231	c.1195C>T	c.(1195-1197)Cac>Tac	p.H399Y	FBXW9_ENST00000544494.1_Missense_Mutation_p.H107Y|CTD-2192J16.26_ENST00000593554.1_lincRNA|CTD-2659N19.2_ENST00000585742.1_RNA|FBXW9_ENST00000587955.1_Missense_Mutation_p.H389Y|FBXW9_ENST00000393261.3_Missense_Mutation_p.H369Y			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	399					SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						GCGAAGACGTGCAGCAGGCCC	0.647																																					p.H369Y		Atlas-SNP	.											.	FBXW9	30	.	0			c.C1105T						PASS	.						63	62	62					19																	12800616		2203	4300	6503	SO:0001583	missense	84261	exon7			AGACGTGCAGCAG	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.1195C>T	chr19.hg19:g.12800616G>A	ENSP00000369696:p.His399Tyr	180.0	0.0	.		98.0	22.0	.	NM_032301	B3KVP7|Q9BT89	Missense_Mutation	SNP	ENST00000380339.3	hg19		.	.	.	.	.	.	.	.	.	.	G	11.70	1.716443	0.30413	.	.	ENSG00000132004	ENST00000544494;ENST00000393261;ENST00000380339	T;T;T	0.75367	-0.93;-0.93;-0.93	4.62	3.5	0.40072	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.191473	0.45361	N	0.000365	T	0.48390	0.1497	N	0.11106	0.095	0.42212	D	0.991813	B;B;B	0.28880	0.226;0.011;0.002	B;B;B	0.22386	0.039;0.023;0.006	T	0.51356	-0.8716	10	0.51188	T	0.08	-14.7405	3.666	0.08255	0.3848:0.0:0.6152:0.0	.	389;399;369	Q5XUX1-2;Q5XUX1;Q5XUX1-3	.;FBXW9_HUMAN;.	Y	107;369;399	ENSP00000442714:H107Y;ENSP00000376945:H369Y;ENSP00000369696:H399Y	ENSP00000369696:H399Y	H	-	1	0	FBXW9	12661616	1.000000	0.71417	1.000000	0.80357	0.522000	0.34438	3.310000	0.51911	2.129000	0.65627	0.484000	0.47621	CAC	.	.	.	none		0.647	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301		A	12800616	G	A	12800616	3	1	42	1	0	0	0	0	1	0	0	0	5778	1319	46	2	287	2	FBXW9	19	12800616	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08		12800616	46328367	34	2965											
LYPD3	27076	hgsc.bcm.edu	37	chr19	43967294	43967300	+	Frame_Shift_Del	DEL	GTTGCCG	GTTGCCG	-																															tcacctgccgtcaaggtgacGttgccgtcgaagcagccctt																										TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	GTTGCCG	GTTGCCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr19:43967294_43967300delGTTGCCG	ENST00000244333.3	-	4	610_616	c.522_528delCGGCAAC	c.(520-528)gacggcaacfs	p.DGN174fs		NM_014400.2	NP_055215.2	O95274	LYPD3_HUMAN	LY6/PLAUR domain containing 3	174	UPAR/Ly6 2.				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)				TCAAGGTGACGTTGCCGTCGAAGCAGC	0.647																																					p.175_177del		Atlas-INDEL	.											.	LYPD3	24	.	0			c.523_529del						PASS	.																																			SO:0001589	frameshift_variant	27076	exon4			.	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.522_528delCGGCAAC	chr19.hg19:g.43967294_43967300delGTTGCCG	ENSP00000244333:p.Asp174fs	171.0	0.0	0		98.0	20.0	0.204082	NM_014400	Q9UJ74	Frame_Shift_Del	DEL	ENST00000244333.3	hg19	CCDS12620.1																																																																																			.	.	.	none		0.647	LYPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463177.1	NM_014400		-	43967300	GTTGCCG	-	43967294	7	5	42	1	0	1	0	1	0	0	0	0	9118	1136	40	0	520	0	LYPD3	19	43967294	Frame_Shift_Del	DEL	GTTGCCG	TCGA-A4-7287-01A-11D-2136-08	31166678	43967294	15161689	35	2966											
SIRPG	55423	hgsc.bcm.edu	37	chr20	1615980	1615980	+	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	agggcaaggcgtttgctgacCgccagctgcccatcatgctt	7	9	12	13	2	1	1	1	1	0	0	1	1	1	1	3	2	4	5	3	2	1	2	rs147655438		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr20:1615980C>A	ENST00000303415.3	-	4	1078	c.1014G>T	c.(1012-1014)gcG>gcT	p.A338A	SIRPG_ENST00000381580.1_Silent_p.A305A|RP11-77C3.3_ENST00000437384.1_RNA|SIRPG_ENST00000344103.4_Intron|SIRPG_ENST00000381583.2_Intron|SIRPG_ENST00000216927.4_Intron|RP11-77C3.3_ENST00000456177.1_RNA	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	338	Ig-like C1-type 2.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						GTTTGCTGACCGCCAGCTGCC	0.502																																					p.A338A		Atlas-SNP	.											SIRPG,NS,carcinoma,0,1	SIRPG	61	.	0			c.G1014T						PASS	.						116	94	101					20																	1615980		2203	4300	6503	SO:0001819	synonymous_variant	55423	exon4			GCTGACCGCCAGC	AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"Signal-regulatory proteins", "CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C1-set domain containing"	15757	protein-coding gene	gene with protein product		605466	"signal-regulatory protein beta 2"	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.1014G>T	chr20.hg19:g.1615980C>A		131.0	0.0	.		90.0	24.0	.	NM_018556	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Silent	SNP	ENST00000303415.3	hg19	CCDS13020.2																																																																																			.	C|1.000;T|0.000	.	alt		0.502	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2	NM_018556		A	1615980	C	A	1615980	2	1	42	1	0	0	0	0	0	0	0	1	14349	639	23	4		4	SIRPG	20	1615980	Silent	SNP	C	TCGA-A4-7287-01A-11D-2136-08		1615980	61409540	36	2967											
FTCD	10841	hgsc.bcm.edu	37	chr21	47571511	47571511	+	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	tgctcccgcaggttgagcgcGatgcggtgggcttgctcctt	3	11	15	12	4	0	1	0	1	0	0	2	2	2	1	2	3	4	5	2	3	0	3			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr21:47571511G>T	ENST00000291670.5	-	5	640	c.597C>A	c.(595-597)atC>atA	p.I199I	FTCD_ENST00000498355.2_5'UTR|FTCD-AS1_ENST00000446649.1_RNA|FTCD_ENST00000397748.1_Silent_p.I199I|FTCD_ENST00000397746.3_Silent_p.I199I|FTCD_ENST00000397743.1_Silent_p.I199I|FTCD_ENST00000355384.2_Silent_p.I199I|FTCD_ENST00000359679.2_Silent_p.I199I	NM_006657.2	NP_006648.1	O95954	FTCD_HUMAN	formimidoyltransferase cyclodeaminase	199	Formiminotransferase C-subdomain. {ECO:0000250}.				cellular nitrogen compound metabolic process (GO:0034641)|cytoskeleton organization (GO:0007010)|folic acid-containing compound metabolic process (GO:0006760)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	folic acid binding (GO:0005542)|formimidoyltetrahydrofolate cyclodeaminase activity (GO:0030412)|glutamate formimidoyltransferase activity (GO:0030409)			endometrium(1)|large_intestine(2)|lung(9)|pancreas(1)|prostate(3)|skin(3)	19	Breast(49;0.214)			Colorectal(79;0.235)	Tetrahydrofolic acid(DB00116)	GGTTGAGCGCGATGCGGTGGG	0.647																																					p.I199I		Atlas-SNP	.											.	FTCD	59	.	0			c.C597A						PASS	.						67	71	69					21																	47571511		2203	4300	6503	SO:0001819	synonymous_variant	10841	exon5			GAGCGCGATGCGG	U91541	CCDS13731.1	21q22.3	2013-06-10	2013-06-10		ENSG00000160282	ENSG00000160282	2.1.2.5, 4.3.1.4		3974	protein-coding gene	gene with protein product		606806	"formiminotransferase cyclodeaminase"			10029623, 10773664	Standard	NM_006657		Approved		uc002zif.3	O95954	OTTHUMG00000090488	ENST00000291670.5:c.597C>A	chr21.hg19:g.47571511G>T		157.0	0.0	.		97.0	27.0	.	NM_206965	B9EGD0|Q86V03|Q9HCT4|Q9HCT5|Q9HCT6|Q9UHJ2	Silent	SNP	ENST00000291670.5	hg19	CCDS13731.1																																																																																			.	.	.	none		0.647	FTCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206962.1	NM_006657		T	47571511	G	T	47571511	2	4	42	1	0	0	0	0	0	0	0	1	6088	1048	37	4		4	FTCD	21	47571511	Silent	SNP	G	TCGA-A4-7287-01A-11D-2136-08		47571511	558384	37	2968											
MSN	4478	hgsc.bcm.edu	37	chrX	64936758	64936758	+	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	ccaccgggaagcagctatttGaccaggtaaggcggagactc	11	6	13	11	2	0	2	0	1	0	1	1	4	0	3	3	4	2	3	3	4	3	3			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chrX:64936758G>C	ENST00000360270.5	+	2	263	c.91G>C	c.(91-93)Gac>Cac	p.D31H		NM_002444.2	NP_002435.1	P26038	MOES_HUMAN	moesin	31	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						GCAGCTATTTGACCAGGTAAG	0.507			T	ALK	ALCL																																p.D31H		Atlas-SNP	.		Dom	yes		X	Xq11.2-q12	4478	moesin		L	.	MSN	89	.	0			c.G91C						PASS	.						132	99	111					X																	64936758		2203	4300	6503	SO:0001583	missense	4478	exon2			CTATTTGACCAGG	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.91G>C	chrX.hg19:g.64936758G>C	ENSP00000353408:p.Asp31His	105.0	0.0	.		77.0	13.0	.	NM_002444		Missense_Mutation	SNP	ENST00000360270.5	hg19	CCDS14382.1	.	.	.	.	.	.	.	.	.	.	g	17.67	3.446489	0.63178	.	.	ENSG00000147065	ENST00000360270	T	0.80304	-1.36	5.73	5.73	0.89815	FERM, N-terminal (1);Band 4.1 domain (1);FERM domain (1);	0.000000	0.85682	D	0.000000	D	0.90892	0.7138	H	0.98155	4.16	0.80722	D	1	P	0.43542	0.81	P	0.47891	0.56	D	0.93688	0.7004	10	0.87932	D	0	.	16.1334	0.81461	0.0:0.0:1.0:0.0	.	31	P26038	MOES_HUMAN	H	31	ENSP00000353408:D31H	ENSP00000353408:D31H	D	+	1	0	MSN	64853483	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	8.899000	0.92544	2.412000	0.81896	0.597000	0.82753	GAC	.	.	.	none		0.507	MSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056981.1	NM_002444		C	64936758	G	C	64936758	3	2	42	1	0	0	0	0	1	0	0	0	9892	1290	45	4	97	4	MSN	23	64936758	Missense_Mutation	SNP	G	TCGA-A4-7287-01A-11D-2136-08		64936758	90333802	38	2969											
OGT	8473	hgsc.bcm.edu	37	chrX	70782731	70782731	+	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	ataccctgggacgagtggtgCgcttttcatggattatatta	9	14	11	7	2	1	0	1	0	0	0	1	3	1	2	1	3	2	1	1	3	4	6			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chrX:70782731C>T	ENST00000373719.3	+	16	2229	c.2012C>T	c.(2011-2013)gCg>gTg	p.A671V	OGT_ENST00000373701.3_Missense_Mutation_p.A661V	NM_181672.2|NM_181673.2	NP_858058.1|NP_858059.1	O15294	OGT1_HUMAN	O-linked N-acetylglucosamine (GlcNAc) transferase	671					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)					ACGAGTGGTGCGCTTTTCATG	0.393																																					p.A671V		Atlas-SNP	.											.	OGT	207	.	0			c.C2012T						PASS	.						129	115	120					X																	70782731		2203	4300	6503	SO:0001583	missense	8473	exon16			GTGGTGCGCTTTT	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.2012C>T	chrX.hg19:g.70782731C>T	ENSP00000362824:p.Ala671Val	123.0	0.0	.		132.0	31.0	.	NM_181672	Q7Z3K0|Q8WWM8|Q96CC1|Q9UG57	Missense_Mutation	SNP	ENST00000373719.3	hg19	CCDS14414.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.612830	0.87258	.	.	ENSG00000147162	ENST00000373719;ENST00000373701	T;T	0.18338	2.22;2.22	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.42063	0.1186	M	0.74258	2.255	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.78314	0.991;0.99;0.989	T	0.15435	-1.0437	10	0.23302	T	0.38	.	17.876	0.88825	0.0:1.0:0.0:0.0	.	545;661;671	Q548W1;O15294-3;O15294	.;.;OGT1_HUMAN	V	671;661	ENSP00000362824:A671V;ENSP00000362805:A661V	ENSP00000362805:A661V	A	+	2	0	OGT	70699456	1.000000	0.71417	0.922000	0.36590	0.793000	0.44817	7.626000	0.83164	2.410000	0.81850	0.594000	0.82650	GCG	.	.	.	none		0.393	OGT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000081829.3	NM_003605, NM_181672		T	70782731	C	T	70782731	3	4	42	1	0	0	0	0	1	0	0	0	10854	768	27	1	2074	1	OGT	23	70782731	Missense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08	5845973	70782731	84487829	39	2970											
STAG2	10735	hgsc.bcm.edu	37	chrX	123197834	123197834	+	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	cttcaacagagtagatatttCaagaagtcaactgatagatg	16	11	8	6	0	3	5	3	1	0	4	3	5	3	5	0	0	2	1	0	0	7	5			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chrX:123197834C>A	ENST00000371160.1	+	20	2248	c.1958C>A	c.(1957-1959)tCa>tAa	p.S653*	STAG2_ENST00000371145.3_Nonsense_Mutation_p.S653*|STAG2_ENST00000354548.5_Nonsense_Mutation_p.S584*|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Nonsense_Mutation_p.S653*|STAG2_ENST00000371157.3_Nonsense_Mutation_p.S653*|STAG2_ENST00000371144.3_Nonsense_Mutation_p.S653*	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	653					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						GTAGATATTTCAAGAAGTCAA	0.333																																					p.S653X		Atlas-SNP	.											.	STAG2	309	.	0			c.C1958A						PASS	.						64	56	59					X																	123197834		2203	4300	6503	SO:0001587	stop_gained	10735	exon20			ATATTTCAAGAAG	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.1958C>A	chrX.hg19:g.123197834C>A	ENSP00000360202:p.Ser653*	55.0	0.0	.		61.0	15.0	.	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Nonsense_Mutation	SNP	ENST00000371160.1	hg19	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	C	40	8.002701	0.98605	.	.	ENSG00000101972	ENST00000218089;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	.	.	.	5.28	5.28	0.74379	.	0.124104	0.53938	D	0.000049	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	-19.1078	18.0751	0.89424	0.0:1.0:0.0:0.0	.	.	.	.	X	653;584;653;653;653;653	.	ENSP00000218089:S653X	S	+	2	0	STAG2	123025515	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.759000	0.85235	2.203000	0.70933	0.600000	0.82982	TCA	.	.	.	none		0.333	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		A	123197834	C	A	123197834	4	1	42	1	0	0	0	0	0	1	0	0	15255	838	29	4	2028	4	STAG2	23	123197834	Nonsense_Mutation	SNP	C	TCGA-A4-7287-01A-11D-2136-08	52415103	123197834	32072726	40	2971											
DDI2	84301	hgsc.bcm.edu	37	chr1	15957021	15957021	+	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	cttgctgaaggaacgcaatcCacccctggcagaagctctgc	10	7	10	14	1	1	2	0	1	1	1	2	3	2	3	3	2	4	4	3	2	4	1			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr1:15957021C>T	ENST00000480945.1	+	3	641	c.470C>T	c.(469-471)cCa>cTa	p.P157L		NM_032341.4	NP_115717.3	Q5TDH0	DDI2_HUMAN	DNA-damage inducible 1 homolog 2 (S. cerevisiae)	157							aspartic-type endopeptidase activity (GO:0004190)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|stomach(1)	17		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00327)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.03e-07)|COAD - Colon adenocarcinoma(227;4.48e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)		GAACGCAATCCACCCCTGGCA	0.502																																					p.P157L		Atlas-SNP	.											.	DDI2	38	.	0			c.C470T						PASS	.						90	85	86					1																	15957021		2203	4300	6503	SO:0001583	missense	84301	exon3			GCAATCCACCCCT		CCDS30607.1	1p36.13	2010-05-04	2010-05-04		ENSG00000197312	ENSG00000197312			24578	protein-coding gene	gene with protein product			"DDI1, DNA-damage inducible 1, homolog 2 (S. cerevisiae)"				Standard	NM_032341		Approved	MGC14844	uc001awx.2	Q5TDH0	OTTHUMG00000002381	ENST00000480945.1:c.470C>T	chr1.hg19:g.15957021C>T	ENSP00000417748:p.Pro157Leu	138.0	0.0	.		92.0	33.0	.	NM_032341	A8KAE1|Q7RTZ0|Q9BRT1	Missense_Mutation	SNP	ENST00000480945.1	hg19	CCDS30607.1	.	.	.	.	.	.	.	.	.	.	C	31	5.082015	0.94050	.	.	ENSG00000197312	ENST00000480945	T	0.43294	0.95	5.67	5.67	0.87782	.	0.000000	0.85682	U	0.000000	T	0.73674	0.3617	M	0.91038	3.17	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.79492	-0.1781	10	0.87932	D	0	-24.5775	19.3867	0.94560	0.0:1.0:0.0:0.0	.	157	Q5TDH0	DDI2_HUMAN	L	157	ENSP00000417748:P157L	ENSP00000449475:P42L	P	+	2	0	DDI2	15829608	1.000000	0.71417	0.998000	0.56505	0.950000	0.60333	7.323000	0.79105	2.684000	0.91462	0.650000	0.86243	CCA	.	.	.	none		0.502	DDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006826.1	NM_032341		T	15957021	C	T	15957021	3	4	43	1	0	0	0	0	1	0	0	0	4331	594	21	2	480	2	DDI2	1	15957021	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08		15957021	233293600	1	2972											
GALE	11313	hgsc.bcm.edu	37	chr1	24124297	24124297	+	IGR	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	catcaaggggcaggtactggGggttcccgtacacagtggct	8	8	15	10	1	1	0	1	0	0	0	2	0	2	0	1	6	2	5	1	6	3	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr1:24124297G>T	ENST00000374514.3	+	0	1810				GALE_ENST00000374497.3_Missense_Mutation_p.P139H|GALE_ENST00000470383.1_5'Flank	NM_007260.2	NP_009191.1	O95372	LYPA2_HUMAN	lysophospholipase II						fatty acid metabolic process (GO:0006631)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	hydrolase activity (GO:0016787)			endometrium(3)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|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;1.79e-24)|Colorectal(126;4.8e-08)|COAD - Colon adenocarcinoma(152;2.83e-06)|GBM - Glioblastoma multiforme(114;4.22e-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)		CAGGTACTGGGGGTTCCCGTA	0.587																																					p.P139H		Atlas-SNP	.											.	GALE	22	.	0			c.C416A						PASS	.																																			SO:0001628	intergenic_variant	2582	exon6			TACTGGGGGTTCC	AF098668	CCDS241.1	1p36.11	2008-08-08			ENSG00000011009	ENSG00000011009	3.1.1.5		6738	protein-coding gene	gene with protein product							Standard	NM_007260		Approved	APT-2	uc001bht.3	O95372	OTTHUMG00000002961		chr1.hg19:g.24124297G>T		93.0	0.0	.		57.0	29.0	.	NM_000403	Q7Z4Z2	Missense_Mutation	SNP	ENST00000374514.3	hg19	CCDS241.1	.	.	.	.	.	.	.	.	.	.	G	16.71	3.199561	0.58126	.	.	ENSG00000117308	ENST00000374498;ENST00000374497;ENST00000429356;ENST00000418277;ENST00000425913;ENST00000445705	D;D;D;D;D	0.93307	-3.2;-3.2;-3.2;-3.2;-3.2	4.72	3.81	0.43845	NAD-dependent epimerase/dehydratase (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.97349	0.9133	H	0.94183	3.505	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.97877	1.0289	10	0.87932	D	0	-12.5969	12.5955	0.56468	0.0812:0.0:0.9188:0.0	.	65;75;139;139	B3KQ39;E9PH43;Q38G75;Q14376	.;.;.;GALE_HUMAN	H	75;139;75;75;139;139	ENSP00000363621:P139H;ENSP00000398585:P75H;ENSP00000414719:P75H;ENSP00000393359:P139H;ENSP00000398257:P139H	ENSP00000363621:P139H	P	-	2	0	GALE	23996884	1.000000	0.71417	1.000000	0.80357	0.406000	0.30931	9.191000	0.94940	1.224000	0.43551	-0.136000	0.14681	CCC	.	.	.	none		0.587	LYPLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008245.1			T	24124297	G	T	24124297	1	4	43	0	1	0	0	0	0	0	0	0	6209	1232	43	4		4	GALE	1	24124297	IGR	SNP	G	TCGA-A4-7288-01A-11D-2136-08	8167276	24124297	225126324	2	2973											
NUDC	10726	hgsc.bcm.edu	37	chr1	27250638	27250638	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agactttttcattggaggagAagaagggatggcagagaagg	14	8	16	3	0	1	4	1	0	0	4	1	8	1	6	0	5	0	1	0	5	3	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr1:27250638A>G	ENST00000321265.5	+	2	263	c.140A>G	c.(139-141)gAa>gGa	p.E47G		NM_006600.3	NP_006591.1	Q9Y266	NUDC_HUMAN	nudC nuclear distribution protein	47					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)		ATTGGAGGAGAAGAAGGGATG	0.458																																					p.E47G		Atlas-SNP	.											.	NUDC	15	.	0			c.A140G						PASS	.						90	87	88					1																	27250638		2203	4300	6503	SO:0001583	missense	10726	exon2			GAGGAGAAGAAGG		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.140A>G	chr1.hg19:g.27250638A>G	ENSP00000319664:p.Glu47Gly	71.0	0.0	.		74.0	31.0	.	NM_006600	Q5QP31|Q5QP35|Q9H0N2|Q9Y2B6	Missense_Mutation	SNP	ENST00000321265.5	hg19	CCDS292.1	.	.	.	.	.	.	.	.	.	.	A	13.28	2.191460	0.38707	.	.	ENSG00000090273	ENST00000435827;ENST00000321265	D	0.81908	-1.55	5.49	5.49	0.81192	.	0.143063	0.64402	D	0.000008	T	0.70798	0.3265	N	0.16790	0.44	0.54753	D	0.999987	B	0.06786	0.001	B	0.13407	0.009	T	0.65475	-0.6159	10	0.18710	T	0.47	-0.1195	14.4801	0.67576	1.0:0.0:0.0:0.0	.	47	Q9Y266	NUDC_HUMAN	G	51;47	ENSP00000319664:E47G	ENSP00000319664:E47G	E	+	2	0	NUDC	27123225	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.005000	0.88553	2.222000	0.72286	0.533000	0.62120	GAA	.	.	.	none		0.458	NUDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012172.2			G	27250638	A	G	27250638	3	3	43	1	0	0	0	0	1	0	0	0	10728	246	9	3	146	3	NUDC	1	27250638	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	3126341	27250638	221999983	3	2974											
PARS2	25973	hgsc.bcm.edu	37	chr1	55224237	55224237	+	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	catgtaaaactctcggccacGgagaagaccaaagcggggcc	13	4	12	12	3	1	2	0	0	1	2	2	3	1	2	3	4	2	1	3	4	4	1			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr1:55224237G>T	ENST00000371279.3	-	2	680	c.598C>A	c.(598-600)Cgt>Agt	p.R200S		NM_152268.3	NP_689481.2	Q7L3T8	SYPM_HUMAN	prolyl-tRNA synthetase 2, mitochondrial (putative)	200					gene expression (GO:0010467)|prolyl-tRNA aminoacylation (GO:0006433)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|proline-tRNA ligase activity (GO:0004827)			breast(1)|endometrium(3)|kidney(2)|lung(4)|ovary(2)|prostate(2)|skin(1)	15					L-Proline(DB00172)	TCTCGGCCACGGAGAAGACCA	0.552																																					p.R200S		Atlas-SNP	.											.	PARS2	29	.	0			c.C598A						PASS	.						78	80	80					1																	55224237		2203	4300	6503	SO:0001583	missense	25973	exon2			GGCCACGGAGAAG	AK025585	CCDS597.1	1p32.2	2011-07-01	2007-02-23		ENSG00000162396	ENSG00000162396	6.1.1.15	"Aminoacyl tRNA synthetases / Class II"	30563	protein-coding gene	gene with protein product	"proline tRNA ligase 2, mitochondrial (putative)"	612036				15779907	Standard	NM_152268		Approved	DKFZp727A071	uc001cxy.3	Q7L3T8	OTTHUMG00000009915	ENST00000371279.3:c.598C>A	chr1.hg19:g.55224237G>T	ENSP00000360327:p.Arg200Ser	127.0	0.0	.		98.0	4.0	.	NM_152268	A8K0W4|Q9H6S5|Q9UFT1	Missense_Mutation	SNP	ENST00000371279.3	hg19	CCDS597.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.364441	0.82463	.	.	ENSG00000162396	ENST00000371279	D	0.96830	-4.14	5.2	5.2	0.72013	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (G/ H/ P/ S), conserved domain (1);	0.000000	0.85682	D	0.000000	D	0.98927	0.9636	H	0.97659	4.05	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99509	1.0955	10	0.87932	D	0	-13.0894	18.7683	0.91881	0.0:0.0:1.0:0.0	.	200	Q7L3T8	SYPM_HUMAN	S	200	ENSP00000360327:R200S	ENSP00000360327:R200S	R	-	1	0	PARS2	54996825	1.000000	0.71417	0.964000	0.40570	0.890000	0.51754	9.614000	0.98353	2.419000	0.82065	0.557000	0.71058	CGT	.	.	.	none		0.552	PARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027436.1	NM_152268		T	55224237	G	T	55224237	3	4	43	1	0	0	0	0	1	0	0	0	11474	1116	39	4	833	4	PARS2	1	55224237	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08	27973599	55224237	194026384	4	2975											
DOCK7	85440	hgsc.bcm.edu	37	chr1	63119666	63119666	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctccttacctttcttcaggTacagctgaaacaagagttct	10	14	6	11	0	4	2	1	1	3	1	5	2	4	2	2	1	4	3	2	1	4	5			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr1:63119666T>C	ENST00000340370.5	-	3	326	c.309A>G	c.(307-309)gtA>gtG	p.V103V	DOCK7_ENST00000404627.2_Silent_p.V103V|DOCK7_ENST00000251157.5_Silent_p.V103V	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	103					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						TTTCTTCAGGTACAGCTGAAA	0.388																																					p.V103V		Atlas-SNP	.											.	DOCK7	184	.	0			c.A309G						PASS	.						56	57	57					1																	63119666		2203	4300	6503	SO:0001819	synonymous_variant	85440	exon3			TTCAGGTACAGCT		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.309A>G	chr1.hg19:g.63119666T>C		69.0	0.0	.		56.0	4.0	.	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Silent	SNP	ENST00000340370.5	hg19	CCDS30734.1																																																																																			.	.	.	none		0.388	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		C	63119666	T	C	63119666	2	2	43	1	0	0	0	0	0	0	0	1	4694	1625	57	3		3	DOCK7	1	63119666	Silent	SNP	T	TCGA-A4-7288-01A-11D-2136-08	7895429	63119666	186130955	5	2976											
CTH	1491	hgsc.bcm.edu	37	chr1	70877247	70877247	+	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	gtccaccacgttcaagcaagGggcgcctggccagcactcgg	8	5	13	15	3	1	0	1	0	0	0	3	0	2	0	4	4	2	3	4	4	2	1			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr1:70877247G>C	ENST00000370938.3	+	1	293	c.149G>C	c.(148-150)gGg>gCg	p.G50A	CTH_ENST00000346806.2_Missense_Mutation_p.G50A|CTH_ENST00000411986.2_Missense_Mutation_p.G50A|CTH_ENST00000464926.1_3'UTR	NM_001902.5	NP_001893.2	Q96IQ7	VSIG2_HUMAN	cystathionine gamma-lyase	0	Ig-like V-type.					integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						TTCAAGCAAGGGGCGCCTGGC	0.572																																					p.G50A		Atlas-SNP	.											.	CTH	48	.	0			c.G149C						PASS	.						51	50	50					1																	70877247		2203	4300	6503	SO:0001583	missense	1491	exon1			AGCAAGGGGCGCC	BC015807	CCDS650.1, CCDS651.1, CCDS53333.1	1p31.1	2014-06-24	2014-06-24		ENSG00000116761	ENSG00000116761	4.4.1.1		2501	protein-coding gene	gene with protein product		607657	"cystathionase (cystathionine gamma-lyase)"			1339280	Standard	NM_001902		Approved		uc001dfd.3	P32929	OTTHUMG00000009352	ENST00000370938.3:c.149G>C	chr1.hg19:g.70877247G>C	ENSP00000359976:p.Gly50Ala	98.0	0.0	.		83.0	29.0	.	NM_153742	O95791|Q9NX42	Missense_Mutation	SNP	ENST00000370938.3	hg19	CCDS650.1	.	.	.	.	.	.	.	.	.	.	G	0.025	-1.375323	0.01214	.	.	ENSG00000116761	ENST00000411986;ENST00000370938;ENST00000346806	D;D;D	0.83673	-1.75;-1.55;-1.75	5.18	-8.32	0.00996	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	1.452490	0.03681	N	0.245551	T	0.29882	0.0747	N	0.03115	-0.41	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.14023	0.01;0.002;0.001	T	0.35822	-0.9773	10	0.20519	T	0.43	-5.4518	1.6154	0.02702	0.3741:0.2347:0.2428:0.1485	.	50;50;50	E9PDV0;P32929-2;P32929	.;.;CGL_HUMAN	A	50	ENSP00000413407:G50A;ENSP00000359976:G50A;ENSP00000311554:G50A	ENSP00000311554:G50A	G	+	2	0	CTH	70649835	0.000000	0.05858	0.000000	0.03702	0.237000	0.25408	-0.581000	0.05820	-1.909000	0.01085	-2.768000	0.00120	GGG	.	.	.	none		0.572	CTH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025918.1	NM_001902		C	70877247	G	C	70877247	3	2	43	1	0	0	0	0	1	0	0	0	4011	1232	43	4	151	4	CTH	1	70877247	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08	7757581	70877247	178373374	6	2977											
DNTTIP2	30836	hgsc.bcm.edu	37	chr1	94337674	94337674	+	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	tatcatttttcttgtaaaatCttttcgggtccatgctggct	7	19	7	8	1	3	0	1	0	2	0	5	0	4	0	1	2	1	3	1	2	3	7			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr1:94337674C>A	ENST00000436063.2	-	5	2078	c.2021G>T	c.(2020-2022)aGa>aTa	p.R674I		NM_014597.4	NP_055412.2	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 2	674					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	38		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		CTTGTAAAATCTTTTCGGGTC	0.408																																					p.R674I		Atlas-SNP	.											.	DNTTIP2	59	.	0			c.G2021T						PASS	.						265	258	260					1																	94337674		1860	4107	5967	SO:0001583	missense	30836	exon5			TAAAATCTTTTCG	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.2021G>T	chr1.hg19:g.94337674C>A	ENSP00000411010:p.Arg674Ile	338.0	1.0	.		302.0	135.0	.	NM_014597	Q12987|Q53H59|Q5TFJ4|Q6TLI0|Q76MJ8|Q86WX9	Missense_Mutation	SNP	ENST00000436063.2	hg19	CCDS44174.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.550698	0.86127	.	.	ENSG00000067334	ENST00000436063	T	0.51817	0.69	6.02	5.1	0.69264	Fcf2 pre-rRNA processing (1);	0.159613	0.50627	D	0.000114	T	0.66607	0.2806	M	0.91920	3.255	0.58432	D	0.999999	D	0.89917	1.0	D	0.81914	0.995	T	0.75502	-0.3295	10	0.87932	D	0	.	11.1086	0.48218	0.0:0.7959:0.1307:0.0734	.	674	Q5QJE6	TDIF2_HUMAN	I	674	ENSP00000411010:R674I	ENSP00000411010:R674I	R	-	2	0	DNTTIP2	94110262	1.000000	0.71417	0.974000	0.42286	0.972000	0.66771	4.733000	0.62036	1.539000	0.49286	0.650000	0.86243	AGA	.	.	.	none		0.408	DNTTIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028317.2	NM_014597		A	94337674	C	A	94337674	3	1	43	1	0	0	0	0	1	0	0	0	4684	913	32	4	261	4	DNTTIP2	1	94337674	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	23460427	94337674	154912947	7	2978											
SETDB1	9869	hgsc.bcm.edu	37	chr1	150936790	150936790	+	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	tgggcagtgtggaaggcaagGagctactctgttgctgtggg	7	10	18	6	0	1	0	0	0	1	0	1	2	1	2	0	5	3	5	0	5	3	2			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr1:150936790G>A	ENST00000271640.5	+	22	4016	c.3826G>A	c.(3826-3828)Gag>Aag	p.E1276K	CERS2_ENST00000561294.1_3'UTR|RP11-316M1.12_ENST00000561111.1_RNA|SETDB1_ENST00000368969.4_Missense_Mutation_p.E1275K|CERS2_ENST00000345896.4_5'Flank|RP11-316M1.12_ENST00000560481.1_RNA	NM_001145415.1|NM_012432.3	NP_001138887.1|NP_036564.3	Q15047	SETB1_HUMAN	SET domain, bifurcated 1	1276	Post-SET. {ECO:0000255|PROSITE- ProRule:PRU00155}.				bone development (GO:0060348)|histone H3-K9 trimethylation (GO:0036124)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)			GGAAGGCAAGGAGCTACTCTG	0.507																																					p.E1276K		Atlas-SNP	.											.	SETDB1	204	.	0			c.G3826A						PASS	.						183	141	155					1																	150936790		2203	4300	6503	SO:0001583	missense	9869	exon22			GGCAAGGAGCTAC	D31891	CCDS972.1, CCDS44217.1, CCDS58026.1	1q21	2013-01-23			ENSG00000143379	ENSG00000143379		"Chromatin-modifying enzymes / K-methyltransferases", "Tudor domain containing"	10761	protein-coding gene	gene with protein product	"tudor domain containing 21"	604396				10343109	Standard	NM_001145415		Approved	KG1T, KIAA0067, ESET, KMT1E, TDRD21	uc001evu.2	Q15047	OTTHUMG00000035003	ENST00000271640.5:c.3826G>A	chr1.hg19:g.150936790G>A	ENSP00000271640:p.Glu1276Lys	88.0	0.0	.		63.0	16.0	.	NM_001145415	A6NEW2|Q5SZD8|Q5SZD9|Q5SZE0|Q5SZE7|Q96GM9	Missense_Mutation	SNP	ENST00000271640.5	hg19	CCDS44217.1	.	.	.	.	.	.	.	.	.	.	G	8.523	0.869314	0.17322	.	.	ENSG00000143379	ENST00000271640;ENST00000368969	D;D	0.87029	-2.2;-2.2	4.81	4.81	0.61882	Post-SET domain (2);	0.167783	0.50627	D	0.000103	T	0.51483	0.1677	N	0.04090	-0.28	0.80722	D	1	B;B	0.19445	0.036;0.02	B;B	0.17979	0.02;0.007	T	0.55373	-0.8151	10	0.02654	T	1	.	11.2196	0.48846	0.0851:0.0:0.9149:0.0	.	1275;1276	Q15047-3;Q15047	.;SETB1_HUMAN	K	1276;1275	ENSP00000271640:E1276K;ENSP00000357965:E1275K	ENSP00000271640:E1276K	E	+	1	0	SETDB1	149203414	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	7.694000	0.84235	2.493000	0.84123	0.462000	0.41574	GAG	.	.	.	none		0.507	SETDB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084717.2			A	150936790	G	A	150936790	3	1	43	1	0	0	0	0	1	0	0	0	14151	1175	41	2	3908	2	SETDB1	1	150936790	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08	56599116	150936790	98313831	8	2979											
SLC27A3	11000	hgsc.bcm.edu	37	chr1	153752431	153752431	+	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	taggtgcctacctgcccctcAcaactgcccggtacagcgcc	7	7	9	18	2	1	0	1	0	0	0	1	0	1	0	6	2	7	1	6	2	4	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr1:153752431A>T	ENST00000368661.3	+	10	2211	c.2146A>T	c.(2146-2148)Aca>Tca	p.T716S	SLC27A3_ENST00000484014.1_3'UTR|SLC27A3_ENST00000271857.2_Missense_Mutation_p.T797S	NM_024330.1	NP_077306.1	Q5K4L6	S27A3_HUMAN	solute carrier family 27 (fatty acid transporter), member 3	716					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)			CCTGCCCCTCACAACTGCCCG	0.597																																					p.T716S		Atlas-SNP	.											.	SLC27A3	42	.	0			c.A2146T						PASS	.						79	59	66					1																	153752431		2203	4300	6503	SO:0001583	missense	11000	exon10			CCCCTCACAACTG	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.2146A>T	chr1.hg19:g.153752431A>T	ENSP00000357650:p.Thr716Ser	56.0	0.0	.		40.0	18.0	.	NM_024330	Q5VUQ7|Q5VUQ8|Q5VUR3|Q6ZV16|Q8N2X7|Q8TEJ0|Q96SW5|Q9BTJ5|Q9BTY5	Missense_Mutation	SNP	ENST00000368661.3	hg19	CCDS1053.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.033819	0.75504	.	.	ENSG00000143554	ENST00000271857;ENST00000368661	T;T	0.58797	0.31;0.33	4.36	4.36	0.52297	.	0.131608	0.49916	D	0.000131	T	0.47710	0.1460	L	0.49513	1.565	0.35861	D	0.827484	P	0.47545	0.897	P	0.51945	0.685	T	0.49331	-0.8951	10	0.33940	T	0.23	-10.5075	10.175	0.42933	1.0:0.0:0.0:0.0	.	716	Q5K4L6	S27A3_HUMAN	S	797;716	ENSP00000271857:T797S;ENSP00000357650:T716S	ENSP00000271857:T797S	T	+	1	0	SLC27A3	152019055	1.000000	0.71417	0.999000	0.59377	0.431000	0.31685	6.078000	0.71282	1.976000	0.57569	0.477000	0.44152	ACA	.	.	.	none		0.597	SLC27A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_024330		T	153752431	A	T	153752431	3	4	43	1	0	0	0	0	1	0	0	0	14540	159	6	5	2184	5	SLC27A3	1	153752431	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	2815641	153752431	95498190	9	2980											
SLC4A5	57835	hgsc.bcm.edu	37	chr2	74458396	74458396	+	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	gccaggaagacagagattccCgtcaggatgaagacgatgat	14	6	13	8	2	1	5	1	2	0	3	2	9	2	7	2	2	0	0	2	2	2	1			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr2:74458396C>A	ENST00000423644.1	-	24	3032	c.2635G>T	c.(2635-2637)Ggg>Tgg	p.G879W	SLC4A5_ENST00000346834.4_Silent_p.T938T|SLC4A5_ENST00000394019.2_Silent_p.T938T|SLC4A5_ENST00000357822.5_Silent_p.T938T|SLC4A5_ENST00000359484.4_Silent_p.T836T|SLC4A5_ENST00000377634.4_Silent_p.T938T|RP11-287D1.3_ENST00000451608.2_3'UTR|SLC4A5_ENST00000377632.1_Silent_p.T938T|SLC4A5_ENST00000483195.1_5'UTR|SLC4A5_ENST00000358683.4_Silent_p.T836T					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						CAGAGATTCCCGTCAGGATGA	0.562																																					p.T938T		Atlas-SNP	.											.	SLC4A5	215	.	0			c.G2814T						PASS	.						179	146	157					2																	74458396		2203	4300	6503	SO:0001583	missense	57835	exon20			GATTCCCGTCAGG	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	ENST00000423644.1:c.2635G>T	chr2.hg19:g.74458396C>A	ENSP00000395804:p.Gly879Trp	131.0	0.0	.		103.0	5.0	.	NM_021196		Silent	SNP	ENST00000423644.1	hg19		.	.	.	.	.	.	.	.	.	.	C	5.936	0.356646	0.11239	.	.	ENSG00000188687	ENST00000423644;ENST00000425249	T;T	0.74315	-0.83;-0.47	4.47	-8.36	0.00980	.	.	.	.	.	T	0.52996	0.1769	.	.	.	0.19575	N	0.999969	B	0.11235	0.004	B	0.09377	0.004	T	0.41070	-0.9529	8	0.59425	D	0.04	.	1.6798	0.02830	0.3015:0.1537:0.0994:0.4453	.	841	E7EQT3	.	W	879;841	ENSP00000395804:G879W;ENSP00000405678:G841W	ENSP00000395804:G879W	G	-	1	0	SLC4A5	74311904	0.000000	0.05858	0.373000	0.26003	0.924000	0.55760	-4.346000	0.00249	-2.458000	0.00538	-2.805000	0.00112	GGG	.	.	.	none		0.562	SLC4A5-204	KNOWN	basic	protein_coding	protein_coding				A	74458396	C	A	74458396	3	1	43	1	0	0	0	0	1	0	0	0	14670	639	23	4	627	4	SLC4A5	2	74458396	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08		74458396	168740977	10	2981											
RANBP2	5903	hgsc.bcm.edu	37	chr2	109383218	109383218	+	Missense_Mutation	SNP	A	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	atggcaaactaagaatgctgAtgcgaagagaacaagtacta	18	7	10	6	1	0	3	0	1	0	2	0	5	0	3	0	1	5	3	0	1	8	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr2:109383218A>C	ENST00000283195.6	+	20	6349	c.6223A>C	c.(6223-6225)Atg>Ctg	p.M2075L		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	2075	RanBD1 2. {ECO:0000255|PROSITE- ProRule:PRU00164}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						AAGAATGCTGATGCGAAGAGA	0.408																																					p.M2075L		Atlas-SNP	.											.	RANBP2	488	.	0			c.A6223C						PASS	.						190	209	202					2																	109383218		2202	4285	6487	SO:0001583	missense	5903	exon20			ATGCTGATGCGAA	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.6223A>C	chr2.hg19:g.109383218A>C	ENSP00000283195:p.Met2075Leu	697.0	0.0	.		566.0	257.0	.	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	hg19	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.065716	0.76187	.	.	ENSG00000153201	ENST00000409491;ENST00000283195	T	0.50548	0.74	5.65	5.65	0.86999	Pleckstrin homology-type (1);Ran binding protein 1 (3);	.	.	.	.	T	0.69269	0.3092	M	0.73962	2.25	0.42261	D	0.992016	D	0.76494	0.999	D	0.83275	0.996	T	0.73603	-0.3930	9	0.72032	D	0.01	-23.7784	15.8694	0.79101	1.0:0.0:0.0:0.0	.	2075	P49792	RBP2_HUMAN	L	1099;2075	ENSP00000283195:M2075L	ENSP00000283195:M2075L	M	+	1	0	RANBP2	108749650	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.143000	0.66587	0.455000	0.32223	ATG	.	.	.	none		0.408	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		C	109383218	A	C	109383218	3	2	43	1	0	0	0	0	1	0	0	0	13041	333	12	5	6301	5	RANBP2	2	109383218	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	34924822	109383218	133816155	11	2982											
ZNF804A	91752	hgsc.bcm.edu	37	chr2	185802128	185802128	+	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	cagaatccatatccttaagtGacaatgaagaaatgtgtaaa	18	10	7	6	0	0	4	0	2	0	2	2	4	2	4	2	0	0	1	2	0	8	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr2:185802128G>C	ENST00000302277.6	+	4	2599	c.2005G>C	c.(2005-2007)Gac>Cac	p.D669H		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	669							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						ATCCTTAAGTGACAATGAAGA	0.323																																					p.D669H		Atlas-SNP	.											.	ZNF804A	322	.	0			c.G2005C						PASS	.						83	86	85					2																	185802128		2203	4297	6500	SO:0001583	missense	91752	exon4			TTAAGTGACAATG	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.2005G>C	chr2.hg19:g.185802128G>C	ENSP00000303252:p.Asp669His	126.0	0.0	.		112.0	44.0	.	NM_194250	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	hg19	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	G	15.42	2.829378	0.50845	.	.	ENSG00000170396	ENST00000302277	T	0.05996	3.36	5.54	4.47	0.54385	.	0.381496	0.22235	N	0.062766	T	0.03608	0.0103	N	0.08118	0	0.09310	N	1	B	0.33448	0.412	B	0.31191	0.125	T	0.41680	-0.9495	10	0.46703	T	0.11	-15.3768	10.7923	0.46440	0.0812:0.0:0.7837:0.1351	.	669	Q7Z570	Z804A_HUMAN	H	669	ENSP00000303252:D669H	ENSP00000303252:D669H	D	+	1	0	ZNF804A	185510373	0.943000	0.32029	0.885000	0.34714	0.589000	0.36550	1.746000	0.38288	2.609000	0.88269	0.655000	0.94253	GAC	.	.	.	none		0.323	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		C	185802128	G	C	185802128	3	2	43	1	0	0	0	0	1	0	0	0	18182	1290	45	4	2019	4	ZNF804A	2	185802128	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08	76418910	185802128	57397245	12	2983											
ANKRD44	91526	hgsc.bcm.edu	37	chr2	198001337	198001337	+	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	tcacttctggaagcaacagcCcggtgcagtggagtcagcca	10	7	12	12	1	3	0	2	0	1	0	3	2	3	2	2	3	5	2	2	3	2	1			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr2:198001337C>A	ENST00000328737.2	-	4	241	c.165G>T	c.(163-165)cgG>cgT	p.R55R	ANKRD44_ENST00000282272.8_Silent_p.R72R|ANKRD44_ENST00000450567.1_Silent_p.R55R|ANKRD44_ENST00000539527.1_Silent_p.R8R|ANKRD44_ENST00000409919.1_Silent_p.R80R|ANKRD44_ENST00000409153.1_Silent_p.R80R|ANKRD44_ENST00000337207.5_Silent_p.R55R			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	80										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)			AAGCAACAGCCCGGTGCAGTG	0.443																																					p.R80R		Atlas-SNP	.											.	ANKRD44	281	.	0			c.G240T						PASS	.						86	86	86					2																	198001337		2203	4300	6503	SO:0001819	synonymous_variant	91526	exon4			AACAGCCCGGTGC	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.165G>T	chr2.hg19:g.198001337C>A		86.0	0.0	.		67.0	30.0	.	NM_153697	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Silent	SNP	ENST00000328737.2	hg19																																																																																				.	.	.	none		0.443	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697		A	198001337	C	A	198001337	2	1	43	1	0	0	0	0	0	0	0	1	672	610	22	4		4	ANKRD44	2	198001337	Silent	SNP	C	TCGA-A4-7288-01A-11D-2136-08	12199209	198001337	45198036	13	2984											
DCP1A	55802	hgsc.bcm.edu	37	chr3	53376261	53376261	+	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	tagattgtgcatatttagtcGattcacaatggtaaaaccat	14	14	7	6	1	1	1	1	0	0	1	2	2	1	1	1	1	2	2	1	1	6	7			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr3:53376261G>T	ENST00000607628.1	-	3	323	c.214C>A	c.(214-216)Cga>Aga	p.R72R	DCP1A_ENST00000294241.6_Silent_p.R72R|DCP1A_ENST00000480258.1_5'UTR|DCP1A_ENST00000606822.1_Silent_p.R72R	NM_018403.5	NP_060873.4	Q9NPI6	DCP1A_HUMAN	decapping mRNA 1A	72					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.000164)|KIRC - Kidney renal clear cell carcinoma(197;0.00525)|Kidney(197;0.00579)|OV - Ovarian serous cystadenocarcinoma(275;0.0647)		ATATTTAGTCGATTCACAATG	0.318																																					p.R72R		Atlas-SNP	.											.	DCP1A	30	.	0			c.C214A						PASS	.						55	54	55					3																	53376261		1826	4080	5906	SO:0001819	synonymous_variant	55802	exon3			TTAGTCGATTCAC	AJ275986	CCDS74946.1	3p21.1	2013-05-02	2013-05-02		ENSG00000162290	ENSG00000272886			18714	protein-coding gene	gene with protein product		607010	"DCP1 decapping enzyme homolog A (S. cerevisiae)"				Standard	XM_005278360		Approved	HSA275986, SMIF, SMAD4IP1	uc021wzi.1	Q9NPI6	OTTHUMG00000158193	ENST00000607628.1:c.214C>A	chr3.hg19:g.53376261G>T		22.0	0.0	.		17.0	11.0	.	NM_018403	B4DHN9|U3KQM8	Silent	SNP	ENST00000607628.1	hg19																																																																																				.	.	.	none		0.318	DCP1A-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_018403		T	53376261	G	T	53376261	2	4	43	1	0	0	0	0	0	0	0	1	4300	1066	37	4		4	DCP1A	3	53376261	Silent	SNP	G	TCGA-A4-7288-01A-11D-2136-08		53376261	144646169	14	2985											
MORC1	27136	hgsc.bcm.edu	37	chr3	108703606	108703606	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcttcttttcattgctagaaCatcattgcacagctcctgtt	8	16	6	11	0	3	1	2	0	1	1	4	1	4	1	1	0	4	5	1	0	2	7			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr3:108703606C>T	ENST00000483760.1	-	22	2261	c.2218G>A	c.(2218-2220)Gtt>Att	p.V740I	MORC1_ENST00000232603.5_Missense_Mutation_p.V761I					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						ATTGCTAGAACATCATTGCAC	0.363																																					p.V761I		Atlas-SNP	.											.	MORC1	211	.	0			c.G2281A						PASS	.						105	94	98					3																	108703606		2203	4299	6502	SO:0001583	missense	27136	exon23			CTAGAACATCATT	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.2218G>A	chr3.hg19:g.108703606C>T	ENSP00000417282:p.Val740Ile	47.0	0.0	.		33.0	12.0	.	NM_014429		Missense_Mutation	SNP	ENST00000483760.1	hg19		.	.	.	.	.	.	.	.	.	.	C	1.485	-0.556108	0.03967	.	.	ENSG00000114487	ENST00000232603;ENST00000483760	T;T	0.05580	3.44;3.42	5.49	-3.41	0.04839	.	1.888090	0.02334	N	0.074205	T	0.04092	0.0114	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	0.41378	-0.9512	10	0.25751	T	0.34	3.2721	11.5425	0.50675	0.0:0.5909:0.0:0.4091	.	740;761	E7ERX1;Q86VD1	.;MORC1_HUMAN	I	761;740	ENSP00000232603:V761I;ENSP00000417282:V740I	ENSP00000232603:V761I	V	-	1	0	MORC1	110186296	0.000000	0.05858	0.000000	0.03702	0.067000	0.16453	-1.274000	0.02820	-0.729000	0.04875	0.655000	0.94253	GTT	.	.	.	none		0.363	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1			T	108703606	C	T	108703606	3	4	43	1	0	0	0	0	1	0	0	0	9708	478	17	2	697	2	MORC1	3	108703606	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	55327345	108703606	89318824	15	2986											
PLOD2	5352	hgsc.bcm.edu	37	chr3	145803003	145803003	+	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	gtccttggatttgtcaaaacAacatctgcatccacactaaa	14	11	5	11	0	2	0	1	0	1	0	4	1	4	1	2	1	3	1	2	1	5	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr3:145803003A>T	ENST00000360060.3	-	11	1362	c.1185T>A	c.(1183-1185)gtT>gtA	p.V395V	PLOD2_ENST00000461497.1_Silent_p.V55V|PLOD2_ENST00000282903.5_Silent_p.V395V|PLOD2_ENST00000494950.1_Silent_p.V340V|RP11-274H2.2_ENST00000480247.1_RNA	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	395					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)	TTGTCAAAACAACATCTGCAT	0.284																																					p.V395V		Atlas-SNP	.											.	PLOD2	81	.	0			c.T1185A						PASS	.						70	70	70					3																	145803003		2203	4297	6500	SO:0001819	synonymous_variant	5352	exon11			CAAAACAACATCT	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.1185T>A	chr3.hg19:g.145803003A>T		83.0	0.0	.		54.0	21.0	.	NM_182943	B3KWS3|Q59ED2|Q8N170	Silent	SNP	ENST00000360060.3	hg19	CCDS3131.1																																																																																			.	.	.	none		0.284	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935		T	145803003	A	T	145803003	2	4	43	1	0	0	0	0	0	0	0	1	12109	117	5	5		5	PLOD2	3	145803003	Silent	SNP	A	TCGA-A4-7288-01A-11D-2136-08	37099397	145803003	52219427	16	2987											
TBL1XR1	79718	hgsc.bcm.edu	37	chr3	176767825	176767825	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catccttgttgcttggaacaTcttgccctccttctcgtata	6	16	6	13	1	2	0	0	0	2	0	5	1	4	1	3	1	3	3	3	1	3	7			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr3:176767825T>C	ENST00000430069.1	-	7	921	c.662A>G	c.(661-663)gAt>gGt	p.D221G	TBL1XR1_ENST00000457928.2_Missense_Mutation_p.D221G|TBL1XR1-AS1_ENST00000454723.2_RNA			Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1	221					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)			GCTTGGAACATCTTGCCCTCC	0.413																																					p.D221G		Atlas-SNP	.											.	TBL1XR1	87	.	0			c.A662G						PASS	.						167	157	160					3																	176767825		2000	4151	6151	SO:0001583	missense	79718	exon7			GGAACATCTTGCC	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.662A>G	chr3.hg19:g.176767825T>C	ENSP00000405574:p.Asp221Gly	54.0	0.0	.		50.0	27.0	.	NM_024665	D3DNQ9|Q14DC3|Q9H2I1|Q9H9A1	Missense_Mutation	SNP	ENST00000430069.1	hg19	CCDS46961.1	.	.	.	.	.	.	.	.	.	.	T	17.84	3.486855	0.63962	.	.	ENSG00000177565	ENST00000430069;ENST00000457928;ENST00000536758	T;T	0.54279	0.58;0.58	5.23	5.23	0.72850	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	0.44350	0.1289	L	0.39514	1.22	0.80722	D	1	B	0.28933	0.228	B	0.29077	0.098	T	0.32508	-0.9904	10	0.23302	T	0.38	-8.7332	14.6231	0.68599	0.0:0.0:0.0:1.0	.	221	Q9BZK7	TBL1R_HUMAN	G	221;221;83	ENSP00000405574:D221G;ENSP00000413251:D221G	ENSP00000405574:D221G	D	-	2	0	TBL1XR1	178250519	1.000000	0.71417	0.971000	0.41717	0.936000	0.57629	8.031000	0.88826	2.100000	0.63781	0.533000	0.62120	GAT	.	.	.	none		0.413	TBL1XR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347587.3	NM_024665		C	176767825	T	C	176767825	3	2	43	1	0	0	0	0	1	0	0	0	15652	1435	50	3	922	3	TBL1XR1	3	176767825	Missense_Mutation	SNP	T	TCGA-A4-7288-01A-11D-2136-08	30964822	176767825	21254605	17	2988											
MAP3K13	9175	hgsc.bcm.edu	37	chr3	185191375	185191375	+	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	ccctctgctgagccagtgggGaggagccctgacctttccaa	7	8	12	14	0	1	2	0	2	1	0	2	4	2	4	5	3	3	1	5	3	1	1			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr3:185191375G>A	ENST00000265026.3	+	11	2590	c.2256G>A	c.(2254-2256)ggG>ggA	p.G752G	MAP3K13_ENST00000446828.1_Silent_p.G545G|MAP3K13_ENST00000443863.1_Silent_p.G608G|MAP3K13_ENST00000535426.1_Silent_p.G608G|MAP3K13_ENST00000424227.1_Silent_p.G752G	NM_004721.4	NP_004712.1			mitogen-activated protein kinase kinase kinase 13											NS(1)|biliary_tract(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(13)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			AGCCAGTGGGGAGGAGCCCTG	0.542																																					p.G752G		Atlas-SNP	.											.	MAP3K13	209	.	0			c.G2256A						PASS	.						97	100	99					3																	185191375		2203	4300	6503	SO:0001819	synonymous_variant	9175	exon11			AGTGGGGAGGAGC	BC031677	CCDS3270.1, CCDS56298.1	3q27	2011-06-09			ENSG00000073803	ENSG00000073803		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6852	protein-coding gene	gene with protein product	"leucine zipper-bearing kinase"	604915				9353328	Standard	NM_004721		Approved	LZK, MEKK13	uc003fpi.3	O43283	OTTHUMG00000156673	ENST00000265026.3:c.2256G>A	chr3.hg19:g.185191375G>A		219.0	0.0	.		185.0	10.0	.	NM_004721		Silent	SNP	ENST00000265026.3	hg19	CCDS3270.1																																																																																			.	.	.	none		0.542	MAP3K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345268.1	NM_004721		A	185191375	G	A	185191375	2	1	43	1	0	0	0	0	0	0	0	1	9254	1161	41	2		2	MAP3K13	3	185191375	Silent	SNP	G	TCGA-A4-7288-01A-11D-2136-08	8423550	185191375	12831055	18	2989											
AHSG	197	hgsc.bcm.edu	37	chr3	186335047	186335047	+	Missense_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	cgctgaacgacaccagggtgGtgcacgccgcgaaagctgcc	9	4	14	14	5	0	1	0	1	0	0	0	3	0	1	3	2	4	3	3	2	2	0			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr3:186335047G>A	ENST00000273784.5	+	4	560	c.484G>A	c.(484-486)Gtg>Atg	p.V162M	AHSG_ENST00000411641.2_Missense_Mutation_p.V161M	NM_001622.2	NP_001613.2	P02765	FETUA_HUMAN	alpha-2-HS-glycoprotein	161	Cystatin fetuin-A-type 2. {ECO:0000255|PROSITE-ProRule:PRU00861}.			PLLAPLNDTRVVHAAKAALAAFNAQNNGSNFQL -> MVGW QEGANHKNGAGRSQKQEMAEKMVPEVASG (in Ref. 12; AAF69649). {ECO:0000305}.	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)		CACCAGGGTGGTGCACGCCGC	0.612											OREG0015968	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V161M		Atlas-SNP	.											.	AHSG	40	.	0			c.G481A						PASS	.						71	68	69					3																	186335047		2203	4300	6503	SO:0001583	missense	197	exon4			AGGGTGGTGCACG	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.484G>A	chr3.hg19:g.186335047G>A	ENSP00000273784:p.Val162Met	164.0	0.0	.	2006	120.0	63.0	.	NM_001622	A8K9N6|B2R7G1|O14961|O14962|Q9P152	Missense_Mutation	SNP	ENST00000273784.5	hg19		.	.	.	.	.	.	.	.	.	.	g	16.33	3.091941	0.55968	.	.	ENSG00000145192	ENST00000411641;ENST00000541510;ENST00000273784	T;T	0.27720	1.65;1.65	5.61	2.7	0.31948	Proteinase inhibitor I25, cystatin (2);	0.536617	0.18379	N	0.143005	T	0.51398	0.1672	M	0.82323	2.585	0.30380	N	0.782048	D;D;D;D	0.76494	0.999;0.999;0.974;0.997	D;D;P;D	0.79108	0.983;0.992;0.842;0.985	T	0.52653	-0.8547	10	0.87932	D	0	-14.4644	4.9244	0.13885	0.1851:0.1755:0.6394:0.0	.	227;161;162;161	F5H0Q5;P02765;C9JV77;B7Z556	.;FETUA_HUMAN;.;.	M	161;227;162	ENSP00000393887:V161M;ENSP00000273784:V162M	ENSP00000273784:V162M	V	+	1	0	AHSG	187817741	0.998000	0.40836	1.000000	0.80357	0.460000	0.32559	0.737000	0.26144	1.513000	0.48852	0.561000	0.74099	GTG	.	.	.	none		0.612	AHSG-002	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000344762.1	NM_001622		A	186335047	G	A	186335047	3	1	43	1	0	0	0	0	1	0	0	0	420	1261	44	2	495	2	AHSG	3	186335047	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08	1143672	186335047	11687383	19	2990											
WHSC2	7469	hgsc.bcm.edu	37	chr4	1985129	1985129	+	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	catctcaaacactgtgtccaCcagcatggttgtgctaccct	9	11	7	14	0	1	0	1	0	1	0	3	0	2	0	3	1	4	3	3	1	2	2			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr4:1985129C>T	ENST00000411638.2	-	11	1519	c.1504G>A	c.(1504-1506)Gtg>Atg	p.V502M	NELFA_ENST00000542778.1_Missense_Mutation_p.V367M|MIR943_ENST00000401286.1_RNA|NELFA_ENST00000382882.3_Missense_Mutation_p.V513M	NM_005663.4	NP_005654.3	Q9H3P2	NELFA_HUMAN	negative elongation factor complex member A	502					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)										ACTGTGTCCACCAGCATGGTT	0.592																																					p.V513M		Atlas-SNP	.											.	.	.	.	0			c.G1537A						PASS	.						223	192	203					4																	1985129		2203	4300	6503	SO:0001583	missense	7469	exon11			TGTCCACCAGCAT	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.1504G>A	chr4.hg19:g.1985129C>T	ENSP00000399165:p.Val502Met	255.0	0.0	.		180.0	81.0	.	NM_005663	A2A2T1|O95392	Missense_Mutation	SNP	ENST00000411638.2	hg19		.	.	.	.	.	.	.	.	.	.	C	31	5.095651	0.94197	.	.	ENSG00000185049	ENST00000382882;ENST00000416258;ENST00000542778;ENST00000411638	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.74696	0.3750	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.78193	-0.2299	10	0.87932	D	0	-33.4962	18.8462	0.92208	0.0:1.0:0.0:0.0	.	502	Q9H3P2	NELFA_HUMAN	M	513;506;367;502	ENSP00000372335:V513M;ENSP00000387647:V506M;ENSP00000445757:V367M;ENSP00000399165:V502M	ENSP00000372335:V513M	V	-	1	0	WHSC2	1954927	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.720000	0.84759	2.466000	0.83321	0.462000	0.41574	GTG	.	.	.	none		0.592	NELFA-015	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000473007.1	NM_005663		T	1985129	C	T	1985129	3	4	43	1	0	0	0	0	1	0	0	0	17376	507	18	2	86	2	WHSC2	4	1985129	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08		1985129	189169147	20	2991											
COMMD8	54951	hgsc.bcm.edu	37	chr4	47462160	47462160	+	Splice_Site	DEL	C	C	-																															agaaatgtgcagagaagttaCctcttcatcaggtaagtttt																										TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr4:47462160delC	ENST00000381571.4	-	2	290		c.e2+1			NM_017845.3	NP_060315.1	Q9NX08	COMD8_HUMAN	COMM domain containing 8											large_intestine(2)|lung(5)|prostate(1)	8						AGAGAAGTTACCTCTTCATCA	0.338																																					.		Atlas-INDEL	.											.	COMMD8	15	.	0			c.222+2G>-						PASS	.						93	97	96					4																	47462160		2203	4300	6503	SO:0001630	splice_region_variant	54951	exon3			.	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.222+1G>-	chr4.hg19:g.47462160delC		129.0	0.0	0		72.0	33.0	0.458333	NM_017845	Q8WUR4|Q9HC15	Splice_Site	DEL	ENST00000381571.4	hg19	CCDS3475.1																																																																																			.	.	.	none		0.338	COMMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216898.2	NM_017845	Intron	-	47462160	C	-	47462160	8	5	43	1	0	1	0	1	0	0	1	0	3724	521	18	0	344	0	COMMD8	4	47462160	Splice_Site	DEL	C	TCGA-A4-7288-01A-11D-2136-08	45477031	47462160	143692116	21	2992	38	2									
COMMD8	54951	hgsc.bcm.edu	37	chr4	47462163	47462163	+	Missense_Mutation	SNP	C	C	T																															aatgtgcagagaagttacctCttcatcaggtaagtttttac																								rs550666373		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr4:47462163C>T	ENST00000381571.4	-	2	287	c.220G>A	c.(220-222)Gag>Aag	p.E74K		NM_017845.3	NP_060315.1	Q9NX08	COMD8_HUMAN	COMM domain containing 8	74										large_intestine(2)|lung(5)|prostate(1)	8						GAAGTTACCTCTTCATCAGGT	0.338													C|||	1	0.000199681	0	0	5008	,	,		16976	0		0	False		,,,				2504	0.001				p.E74K		Atlas-SNP	.											.	COMMD8	15	.	0			c.G220A						PASS	.						94	98	97					4																	47462163		2203	4300	6503	SO:0001583	missense	54951	exon2			TTACCTCTTCATC	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.220G>A	chr4.hg19:g.47462163C>T	ENSP00000370984:p.Glu74Lys	132.0	0.0	.		76.0	36.0	.	NM_017845	Q8WUR4|Q9HC15	Missense_Mutation	SNP	ENST00000381571.4	hg19	CCDS3475.1	.	.	.	.	.	.	.	.	.	.	C	15.44	2.835702	0.50951	.	.	ENSG00000169019	ENST00000381571	T	0.10382	2.88	5.48	4.45	0.53987	.	0.093678	0.64402	D	0.000001	T	0.12475	0.0303	L	0.54908	1.71	0.53688	D	0.999977	B	0.21688	0.059	B	0.21917	0.037	T	0.05305	-1.0893	10	0.26408	T	0.33	-13.9433	14.0881	0.64971	0.0:0.9117:0.0:0.0883	.	74	Q9NX08	COMD8_HUMAN	K	74	ENSP00000370984:E74K	ENSP00000370984:E74K	E	-	1	0	COMMD8	47156920	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	3.167000	0.50793	2.574000	0.86865	0.591000	0.81541	GAG	.	.	.	none		0.338	COMMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216898.2	NM_017845		T	47462163	C	T	47462163	3	4	43	1	0	0	0	0	1	0	0	0	3724	922	32	2	347	2	COMMD8	4	47462163	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	3	47462163	143692113	22	2993	38	2									
CEP135	9662	hgsc.bcm.edu	37	chr4	56847415	56847423	+	In_Frame_Del	DEL	TAAGAAAGG	TAAGAAAGG	-																															tcaggaagaattatctgcccTaagaaaggaatccacccaaa																										TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	TAAGAAAGG	TAAGAAAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr4:56847415_56847423delTAAGAAAGG	ENST00000257287.4	+	13	1773_1781	c.1649_1657delTAAGAAAGG	c.(1648-1659)ctaagaaaggaa>caa	p.550_553LRKE>Q		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	550					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)					TTATCTGCCCTAAGAAAGGAATCCACCCA	0.321																																					p.550_552del		Atlas-INDEL	.											.	CEP135	115	.	0			c.1648_1656del						PASS	.																																			SO:0001651	inframe_deletion	9662	exon13			.	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.1649_1657delTAAGAAAGG	chr4.hg19:g.56847415_56847423delTAAGAAAGG	ENSP00000257287:p.Leu550_Glu553delinsGln	103.0	0.0	0		56.0	19.0	0.339286	NM_025009	B2RMY0|O75130|Q58F25|Q9H8H7	In_Frame_Del	DEL	ENST00000257287.4	hg19	CCDS33986.1																																																																																			.	.	.	none		0.321	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009		-	56847423	TAAGAAAGG	-	56847415	7	5	43	1	0	1	0	1	0	0	0	0	3249	1522	53	0	1695	0	CEP135	4	56847415	In_Frame_Del	DEL	TAAGAAAGG	TCGA-A4-7288-01A-11D-2136-08	9385252	56847415	134306861	23	2994											
AASDH	132949	hgsc.bcm.edu	37	chr4	57204741	57204741	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacactttcccatcagtagAtgctgctgccagcaacattt	10	11	6	14	0	1	1	1	0	0	1	2	1	2	1	3	0	5	4	3	0	2	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr4:57204741A>G	ENST00000205214.6	-	15	3304	c.3124T>C	c.(3124-3126)Tct>Cct	p.S1042P	AASDH_ENST00000451613.1_3'UTR|AASDH_ENST00000434343.2_Missense_Mutation_p.S557P|AASDH_ENST00000513376.1_Missense_Mutation_p.S942P	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	1042					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				CCATCAGTAGATGCTGCTGCC	0.443																																					p.S1042P		Atlas-SNP	.											.	AASDH	101	.	0			c.T3124C						PASS	.						83	78	80					4																	57204741		2203	4300	6503	SO:0001583	missense	132949	exon15			CAGTAGATGCTGC	AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"Acyl-CoA synthetase family"	23993	protein-coding gene	gene with protein product	"acyl-CoA synthetase family member 4"	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.3124T>C	chr4.hg19:g.57204741A>G	ENSP00000205214:p.Ser1042Pro	95.0	0.0	.		66.0	29.0	.	NM_181806	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Missense_Mutation	SNP	ENST00000205214.6	hg19	CCDS3504.1	.	.	.	.	.	.	.	.	.	.	A	31	5.102080	0.94245	.	.	ENSG00000157426	ENST00000205214;ENST00000513376;ENST00000434343	T;T;T	0.58797	0.31;0.31;0.31	6.04	6.04	0.98038	Quinonprotein alcohol dehydrogenase-like (2);	0.000000	0.85682	D	0.000000	T	0.81592	0.4855	M	0.91196	3.185	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.85713	0.1320	10	0.87932	D	0	-12.0294	16.6275	0.84975	1.0:0.0:0.0:0.0	.	1042	Q4L235	ACSF4_HUMAN	P	1042;942;557	ENSP00000205214:S1042P;ENSP00000423760:S942P;ENSP00000392158:S557P	ENSP00000205214:S1042P	S	-	1	0	AASDH	56899498	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	7.532000	0.81985	2.330000	0.79161	0.529000	0.55759	TCT	.	.	.	none		0.443	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806		G	57204741	A	G	57204741	3	3	43	1	0	0	0	0	1	0	0	0	22	333	12	3	176	3	AASDH	4	57204741	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	357326	57204741	133949535	24	2995											
RG9MTD2	93587	hgsc.bcm.edu	37	chr4	100470297	100470297	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtgattttccttatcctgcTtttcttcatgtggtgaatct	5	21	7	8	0	3	2	1	2	2	0	5	2	5	2	2	1	1	1	2	1	2	6			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr4:100470297T>C	ENST00000273962.3	-	8	1280	c.968A>G	c.(967-969)aAg>aGg	p.K323R	TRMT10A_ENST00000394877.3_Missense_Mutation_p.K323R|TRMT10A_ENST00000394876.2_Missense_Mutation_p.K323R	NM_152292.4	NP_689505.1	Q8TBZ6	TM10A_HUMAN	tRNA methyltransferase 10 homolog A (S. cerevisiae)	323					magnesium ion homeostasis (GO:0010960)	extracellular vesicular exosome (GO:0070062)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)										CTTATCCTGCTTTTCTTCATG	0.408																																					p.K323R		Atlas-SNP	.											.	.	.	.	0			c.A968G						PASS	.						229	204	212					4																	100470297		2203	4300	6503	SO:0001583	missense	93587	exon8			TCCTGCTTTTCTT	BC028373	CCDS3650.1	4q23	2012-06-28	2012-06-28	2012-06-28	ENSG00000145331	ENSG00000145331			28403	protein-coding gene	gene with protein product			"RNA (guanine-9-) methyltransferase domain containing 2"	RG9MTD2		12477932	Standard	NM_152292		Approved	MGC27034, TRM10	uc003hva.4	Q8TBZ6	OTTHUMG00000131025	ENST00000273962.3:c.968A>G	chr4.hg19:g.100470297T>C	ENSP00000273962:p.Lys323Arg	171.0	0.0	.		154.0	83.0	.	NM_001134666	B2R8X7|Q9Y2T9	Missense_Mutation	SNP	ENST00000273962.3	hg19	CCDS3650.1	.	.	.	.	.	.	.	.	.	.	T	11.16	1.557204	0.27827	.	.	ENSG00000145331	ENST00000394877;ENST00000273962;ENST00000394876	T;T;T	0.18338	2.22;2.22;2.22	5.77	3.27	0.37495	.	2.001830	0.01754	N	0.030106	T	0.11024	0.0269	N	0.14661	0.345	0.09310	N	1	B	0.28713	0.22	B	0.21708	0.036	T	0.25779	-1.0122	10	0.16896	T	0.51	-3.9397	7.5405	0.27735	0.0:0.0782:0.1452:0.7766	.	323	Q8TBZ6	RG9D2_HUMAN	R	323	ENSP00000378343:K323R;ENSP00000273962:K323R;ENSP00000378342:K323R	ENSP00000273962:K323R	K	-	2	0	RG9MTD2	100689320	0.014000	0.17966	0.146000	0.22360	0.546000	0.35178	1.895000	0.39778	1.082000	0.41137	0.533000	0.62120	AAG	.	.	.	none		0.408	TRMT10A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253668.1	NM_152292		C	100470297	T	C	100470297	3	2	43	1	0	0	0	0	1	0	0	0	13285	1609	56	3	55	3	RG9MTD2	4	100470297	Missense_Mutation	SNP	T	TCGA-A4-7288-01A-11D-2136-08	43265556	100470297	90683979	25	2996											
TET2	54790	hgsc.bcm.edu	37	chr4	106156045	106156045	+	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	caatgctaaatacctgttccTttcagaaaccagaacaacta	16	10	4	11	0	1	2	1	0	0	2	2	2	2	2	3	0	5	2	3	0	8	5			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr4:106156045T>A	ENST00000540549.1	+	3	1806	c.946T>A	c.(946-948)Ttt>Att	p.F316I	TET2_ENST00000545826.1_Missense_Mutation_p.F316I|TET2_ENST00000394764.1_Missense_Mutation_p.F316I|TET2_ENST00000305737.2_Missense_Mutation_p.F316I|TET2_ENST00000380013.4_Missense_Mutation_p.F316I|TET2_ENST00000513237.1_Missense_Mutation_p.F337I|TET2_ENST00000413648.2_Missense_Mutation_p.F316I			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	316					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)		TACCTGTTCCTTTCAGAAACC	0.453			"Mis N, F"		MDS																																p.F316I		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	0			c.T946A						PASS	.						85	82	83					4																	106156045		2203	4300	6503	SO:0001583	missense	54790	exon3			TGTTCCTTTCAGA	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.946T>A	chr4.hg19:g.106156045T>A	ENSP00000442788:p.Phe316Ile	92.0	0.0	.		60.0	36.0	.	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Missense_Mutation	SNP	ENST00000540549.1	hg19	CCDS47120.1	.	.	.	.	.	.	.	.	.	.	T	12.75	2.030078	0.35797	.	.	ENSG00000168769	ENST00000305737;ENST00000540549;ENST00000545826;ENST00000513237;ENST00000380013;ENST00000394764;ENST00000413648;ENST00000535110	T;T;T;T;T;T;T	0.04970	3.53;4.27;3.52;4.26;4.27;3.53;3.55	4.98	-0.249	0.13011	.	2.314700	0.02876	U	0.132326	T	0.06005	0.0156	L	0.29908	0.895	0.24527	N	0.994132	B;B;B	0.11235	0.002;0.002;0.004	B;B;B	0.12156	0.002;0.002;0.007	T	0.41538	-0.9503	10	0.66056	D	0.02	.	4.0271	0.09692	0.2106:0.5083:0.0:0.2811	.	337;316;316	E7EQS8;Q6N021;Q6N021-2	.;TET2_HUMAN;.	I	316;316;316;337;316;316;316;316	ENSP00000306705:F316I;ENSP00000442788:F316I;ENSP00000442867:F316I;ENSP00000425443:F337I;ENSP00000369351:F316I;ENSP00000378245:F316I;ENSP00000391448:F316I	ENSP00000265149:F316I	F	+	1	0	TET2	106375494	0.211000	0.23529	0.867000	0.34043	0.171000	0.22731	0.357000	0.20199	-0.016000	0.14127	0.533000	0.62120	TTT	.	.	.	none		0.453	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		A	106156045	T	A	106156045	3	1	43	1	0	0	0	0	1	0	0	0	15782	1609	56	5	948	5	TET2	4	106156045	Missense_Mutation	SNP	T	TCGA-A4-7288-01A-11D-2136-08	5685748	106156045	84998231	26	2997											
SLC12A7	10723	hgsc.bcm.edu	37	chr5	1064225	1064225	+	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	tggcgcagcaggaagggcagCagcatgagcatgccgccgtc	9	4	16	12	3	0	1	0	1	0	0	1	2	0	2	2	3	5	6	2	3	1	0			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr5:1064225C>G	ENST00000264930.5	-	19	2623	c.2580G>C	c.(2578-2580)ctG>ctC	p.L860L	MIR4635_ENST00000583759.1_RNA	NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	860					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)	GGAAGGGCAGCAGCATGAGCA	0.697																																					p.L860L		Atlas-SNP	.											.	SLC12A7	97	.	0			c.G2580C						PASS	.						43	38	39					5																	1064225		2200	4296	6496	SO:0001819	synonymous_variant	10723	exon19			GGGCAGCAGCATG	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.2580G>C	chr5.hg19:g.1064225C>G		32.0	0.0	.		40.0	19.0	.	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Silent	SNP	ENST00000264930.5	hg19	CCDS34129.1	.	.	.	.	.	.	.	.	.	.	C	7.240	0.601120	0.13939	.	.	ENSG00000113504	ENST00000513223	.	.	.	4.26	3.35	0.38373	.	.	.	.	.	T	0.54415	0.1857	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47761	-0.9092	4	.	.	.	.	5.8497	0.18685	0.2009:0.696:0.0:0.1031	.	.	.	.	P	218	.	.	A	-	1	0	SLC12A7	1117225	1.000000	0.71417	1.000000	0.80357	0.678000	0.39670	1.547000	0.36190	0.716000	0.32124	0.313000	0.20887	GCT	.	.	.	none		0.697	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598		G	1064225	C	G	1064225	2	3	43	1	0	0	0	0	0	0	0	1	14401	697	25	4		4	SLC12A7	5	1064225	Silent	SNP	C	TCGA-A4-7288-01A-11D-2136-08		1064225	179851035	27	2998											
TNPO1	3842	hgsc.bcm.edu	37	chr5	72192301	72192301	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctagctgatttcatgccaatAttgggaaccaacctaaatcc	13	11	6	11	0	1	1	1	1	0	0	2	2	2	2	4	1	4	1	4	1	7	5			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr5:72192301A>G	ENST00000337273.5	+	19	2586	c.2160A>G	c.(2158-2160)atA>atG	p.I720M	TNPO1_ENST00000506351.2_Missense_Mutation_p.I712M|TNPO1_ENST00000523768.1_Missense_Mutation_p.I670M|TNPO1_ENST00000454282.1_Missense_Mutation_p.I670M	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1	720					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)		TCATGCCAATATTGGGAACCA	0.338																																					p.I720M		Atlas-SNP	.											.	TNPO1	90	.	0			c.A2160G						PASS	.						62	61	62					5																	72192301		2203	4300	6503	SO:0001583	missense	3842	exon19			GCCAATATTGGGA	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.2160A>G	chr5.hg19:g.72192301A>G	ENSP00000336712:p.Ile720Met	99.0	0.0	.		60.0	22.0	.	NM_002270	B4DVC6|Q92957|Q92975	Missense_Mutation	SNP	ENST00000337273.5	hg19	CCDS43329.1	.	.	.	.	.	.	.	.	.	.	A	12.55	1.971943	0.34754	.	.	ENSG00000083312	ENST00000337273;ENST00000454282;ENST00000523768;ENST00000506351;ENST00000519220	T;T;T;T	0.34859	1.34;1.34;1.34;1.34	5.66	1.57	0.23409	Armadillo-like helical (1);Armadillo-type fold (1);	0.084050	0.85682	D	0.000000	T	0.40145	0.1105	M	0.84773	2.715	0.80722	D	1	B;B	0.21225	0.053;0.011	B;B	0.28232	0.087;0.029	T	0.29058	-1.0024	10	0.52906	T	0.07	-14.1628	6.2257	0.20706	0.3859:0.1164:0.0:0.4977	.	670;720	Q92973-3;Q92973	.;TNPO1_HUMAN	M	720;670;670;712;231	ENSP00000336712:I720M;ENSP00000398524:I670M;ENSP00000428899:I670M;ENSP00000425118:I712M	ENSP00000336712:I720M	I	+	3	3	TNPO1	72228057	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.854000	0.27791	0.371000	0.24564	-0.316000	0.08728	ATA	.	.	.	none		0.338	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	NM_002270		G	72192301	A	G	72192301	3	3	43	1	0	0	0	0	1	0	0	0	16347	439	16	3	2234	3	TNPO1	5	72192301	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	71128076	72192301	108722959	28	2999											
TRAF3IP2	10758	hgsc.bcm.edu	37	chr6	111912700	111912700	+	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	ggggctgggaatcatatcccGtgtctatggttggcagatcc	7	11	14	9	1	2	1	1	0	1	1	4	2	4	2	2	5	0	3	2	5	3	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr6:111912700G>T	ENST00000340026.6	-	3	1211	c.617C>A	c.(616-618)aCg>aAg	p.T206K	TRAF3IP2-AS1_ENST00000532353.1_RNA|TRAF3IP2_ENST00000359831.4_Missense_Mutation_p.T197K|TRAF3IP2_ENST00000368761.5_Missense_Mutation_p.T197K|TRAF3IP2_ENST00000392556.4_5'UTR			O43734	CIKS_HUMAN	TRAF3 interacting protein 2	206	Mediates interaction with TRAF6.				B cell apoptotic process (GO:0001783)|humoral immune response (GO:0006959)|immunoglobulin secretion (GO:0048305)|intracellular signal transduction (GO:0035556)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)					central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	18		all_cancers(87;7.87e-06)|Acute lymphoblastic leukemia(125;3.61e-09)|all_hematologic(75;2.63e-07)|all_epithelial(87;0.0024)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.033)|all cancers(137;0.0412)|Epithelial(106;0.0732)		ATCATATCCCGTGTCTATGGT	0.627																																					p.T197K		Atlas-SNP	.											.	TRAF3IP2	35	.	0			c.C590A						PASS	.						61	62	62					6																	111912700		2203	4300	6503	SO:0001583	missense	10758	exon2			TATCCCGTGTCTA	AF136405	CCDS5093.1, CCDS55049.1, CCDS55050.1	6q21	2008-09-05	2002-06-20	2005-04-13	ENSG00000056972	ENSG00000056972			1343	protein-coding gene	gene with protein product		607043	"chromosome 6 open reading frame 5", "chromosome 6 open reading frame 2"	C6orf4, C6orf5, C6orf6, C6orf2		10962033, 10962024	Standard	NR_028338		Approved	DKFZP586G0522, ACT1, CIKS	uc003pvf.4	O43734	OTTHUMG00000015379	ENST00000340026.6:c.617C>A	chr6.hg19:g.111912700G>T	ENSP00000345984:p.Thr206Lys	145.0	0.0	.		107.0	12.0	.	NM_147686	B2RAY9|E1P555|Q5R3A3|Q7Z6Q1|Q7Z6Q2|Q7Z6Q3|Q9H5W2|Q9H6Y3|Q9NS14|Q9UG72	Missense_Mutation	SNP	ENST00000340026.6	hg19		.	.	.	.	.	.	.	.	.	.	G	18.22	3.576782	0.65878	.	.	ENSG00000056972	ENST00000392555;ENST00000368761;ENST00000340026;ENST00000359831	T;T;T	0.37584	1.2;1.2;1.19	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.49201	0.1543	M	0.68952	2.095	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.76071	0.97;0.987;0.97	T	0.52011	-0.8632	10	0.87932	D	0	-10.0022	12.3995	0.55404	0.0771:0.0:0.9229:0.0	.	206;197;197	O43734;O43734-2;Q7Z6Q1	CIKS_HUMAN;.;.	K	206;197;206;197	ENSP00000357750:T197K;ENSP00000345984:T206K;ENSP00000352889:T197K	ENSP00000345984:T206K	T	-	2	0	TRAF3IP2	112019393	1.000000	0.71417	0.988000	0.46212	0.642000	0.38348	3.685000	0.54678	2.702000	0.92279	0.555000	0.69702	ACG	.	.	.	none		0.627	TRAF3IP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000041841.2			T	111912700	G	T	111912700	3	4	43	1	0	0	0	0	1	0	0	0	16453	1145	40	4	1139	4	TRAF3IP2	6	111912700	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08		111912700	59202367	29	3000											
LPL	4023	hgsc.bcm.edu	37	chr8	19816813	19816813	+	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	tcatttttctgggactgagaGtgaaacccataccaatcagg	12	11	9	9	0	3	2	2	2	1	1	3	4	3	3	2	2	2	0	2	2	3	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr8:19816813G>C	ENST00000311322.8	+	7	1531	c.1061G>C	c.(1060-1062)aGt>aCt	p.S354T		NM_000237.2	NP_000228.1	P06858	LIPL_HUMAN	lipoprotein lipase	354	Heparin-binding. {ECO:0000250}.|PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				chylomicron remodeling (GO:0034371)|fatty acid biosynthetic process (GO:0006633)|lipoprotein metabolic process (GO:0042157)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of sequestering of triglyceride (GO:0010890)|response to cold (GO:0009409)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|triglyceride metabolic process (GO:0006641)|very-low-density lipoprotein particle remodeling (GO:0034372)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|lipoprotein lipase activity (GO:0004465)|phospholipase activity (GO:0004620)|receptor binding (GO:0005102)|triglyceride binding (GO:0017129)|triglyceride lipase activity (GO:0004806)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	36				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	AST-120(DB05269)|Tyloxapol(DB06439)	GGGACTGAGAGTGAAACCCAT	0.453																																					p.S354T		Atlas-SNP	.											.	LPL	78	.	0			c.G1061C						PASS	.						111	99	103					8																	19816813		2203	4300	6503	SO:0001583	missense	4023	exon7			CTGAGAGTGAAAC		CCDS6012.1	8p22	2012-10-02			ENSG00000175445	ENSG00000175445	3.1.1.34		6677	protein-coding gene	gene with protein product		609708		LIPD			Standard	NM_000237		Approved		uc003wzk.4	P06858	OTTHUMG00000036645	ENST00000311322.8:c.1061G>C	chr8.hg19:g.19816813G>C	ENSP00000309757:p.Ser354Thr	62.0	0.0	.		61.0	26.0	.	NM_000237	B2R5T9|Q16282|Q16283|Q96FC4	Missense_Mutation	SNP	ENST00000311322.8	hg19	CCDS6012.1	.	.	.	.	.	.	.	.	.	.	G	0.380	-0.928995	0.02359	.	.	ENSG00000175445	ENST00000311322;ENST00000535763	T	0.62364	0.03	5.93	0.818	0.18778	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	6.232250	0.00166	N	0.000000	T	0.45776	0.1359	N	0.19112	0.55	0.21675	N	0.999596	B	0.02656	0.0	B	0.08055	0.003	T	0.13980	-1.0489	8	.	.	.	-1.2704	4.6754	0.12710	0.3185:0.2811:0.4004:0.0	.	354	P06858	LIPL_HUMAN	T	354;340	ENSP00000309757:S354T	.	S	+	2	0	LPL	19861093	0.007000	0.16637	0.000000	0.03702	0.149000	0.21700	0.725000	0.25970	-0.125000	0.11703	0.643000	0.83706	AGT	.	.	.	none		0.453	LPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089113.3			C	19816813	G	C	19816813	3	2	43	1	0	0	0	0	1	0	0	0	8928	1029	36	4	1087	4	LPL	8	19816813	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08		19816813	126547209	30	3001											
RP1	6101	hgsc.bcm.edu	37	chr8	55540098	55540099	+	Frame_Shift_Ins	INS	-	-	T																															tccacggtcaacattcagagINStgttcctaagtgcagtgaaa																								rs139588212|rs145115379		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr8:55540098_55540099insT	ENST00000220676.1	+	4	3804_3805	c.3656_3657insT	c.(3655-3660)agtgttfs	p.V1220fs		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1220					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)			AACATTCAGAGTGTTCCTAAGT	0.446																																					p.S1219fs	Colon(91;1014 1389 7634 14542 40420)	Atlas-INDEL	.											.	RP1	429	.	0			c.3656_3657insT						PASS	.																																			SO:0001589	frameshift_variant	6101	exon4			.	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.3657dupT	chr8.hg19:g.55540099_55540099dupT	ENSP00000220676:p.Val1220fs	139.0	0.0	0		123.0	58.0	0.471545	NM_006269		Frame_Shift_Ins	INS	ENST00000220676.1	hg19	CCDS6160.1																																																																																			.	.	.	none		0.446	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		T	55540099	-	T	55540098	7	5	43	1	0	1	1	0	0	0	0	0	13545	1029	36	0	3666	0	RP1	8	55540098	Frame_Shift_Ins	INS	-	TCGA-A4-7288-01A-11D-2136-08	35723285	55540098	90823924	31	3002											
TTC35	9694	hgsc.bcm.edu	37	chr8	109462083	109462083	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaatgagaaaatggagagaAgaaaactcaagaaatagtga	24	5	10	2	0	1	5	1	2	0	4	1	8	1	6	0	1	1	0	0	1	10	1			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr8:109462083A>G	ENST00000220853.3	+	2	107	c.72A>G	c.(70-72)gaA>gaG	p.E24E		NM_014673.3	NP_055488.1	Q15006	EMC2_HUMAN	ER membrane protein complex subunit 2	24						cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|ER membrane protein complex (GO:0072546)|mitochondrion (GO:0005739)|nucleus (GO:0005634)											AATGGAGAGAAGAAAACTCAA	0.318																																					p.E24E		Atlas-SNP	.											.	.	.	.	0			c.A72G						PASS	.						97	112	107					8																	109462083		2203	4298	6501	SO:0001819	synonymous_variant	9694	exon2			GAGAGAAGAAAAC	BC021667	CCDS6309.1	8q23.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000104412	ENSG00000104412			28963	protein-coding gene	gene with protein product		607722	"tetratricopeptide repeat domain 35"	KIAA0103, TTC35		7788527, 22119785	Standard	NM_014673		Approved		uc003ymw.1	Q15006	OTTHUMG00000164873	ENST00000220853.3:c.72A>G	chr8.hg19:g.109462083A>G		119.0	0.0	.		82.0	36.0	.	NM_014673	Q8WUE1	Silent	SNP	ENST00000220853.3	hg19	CCDS6309.1																																																																																			.	.	.	none		0.318	EMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380717.1	NM_014673		G	109462083	A	G	109462083	2	3	43	1	0	0	0	0	0	0	0	1	16715	69	3	3		3	TTC35	8	109462083	Silent	SNP	A	TCGA-A4-7288-01A-11D-2136-08	53921985	109462083	36901939	32	3003											
AQP7	364	hgsc.bcm.edu	37	chr9	33385805	33385805	+	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	tctgttcctggcagtgctggGttgttctcctggtccgtgat	2	16	13	10	1	2	1	0	1	2	0	5	1	4	1	3	3	1	5	3	3	0	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr9:33385805G>T	ENST00000537089.1	-	6	627	c.309C>A	c.(307-309)aaC>aaA	p.N103K	AQP7_ENST00000377425.4_Missense_Mutation_p.N138K|AQP7_ENST00000541274.1_Missense_Mutation_p.P64T|AQP7_ENST00000539936.1_Missense_Mutation_p.N195K			O14520	AQP7_HUMAN	aquaporin 7	195					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)		GCAGTGCTGGGTTGTTCTCCT	0.617																																					p.N195K		Atlas-SNP	.											.	AQP7	58	.	0			c.C585A						PASS	.						121	106	111					9																	33385805		2203	4300	6503	SO:0001583	missense	364	exon7			TGCTGGGTTGTTC	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.309C>A	chr9.hg19:g.33385805G>T	ENSP00000441619:p.Asn103Lys	198.0	0.0	.		130.0	39.0	.	NM_001170	Q08E94|Q5T5L9|Q8NHM3	Missense_Mutation	SNP	ENST00000537089.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	0.022|0.022	-1.416408|-1.416408	0.01136|0.01136	.|.	.|.	ENSG00000165269|ENSG00000165269	ENST00000537089;ENST00000379507;ENST00000447660;ENST00000297988;ENST00000377425;ENST00000439678;ENST00000379506;ENST00000539936;ENST00000379503|ENST00000541274	D;D;D;D;D;D;D;D;D|T	0.84660|0.48836	-1.88;-1.88;-1.88;-1.88;-1.88;-1.88;-1.88;-1.88;-1.88|0.8	4.77|4.77	0.809|0.809	0.18725|0.18725	Aquaporin-like (2);|.	0.423208|.	0.29383|.	N|.	0.012320|.	T|T	0.37758|0.37758	0.1015|0.1015	L|L	0.48642|0.48642	1.525|1.525	0.09310|0.09310	N|N	1|1	B;B;B;B|B	0.25007|0.27286	0.022;0.049;0.022;0.116|0.174	B;B;B;B|B	0.25987|0.26310	0.038;0.063;0.038;0.065|0.068	T|T	0.24584|0.24584	-1.0156|-1.0156	10|9	0.16896|0.38643	T|T	0.51|0.18	-15.7477|-15.7477	7.845|7.845	0.29421|0.29421	0.3724:0.0:0.6276:0.0|0.3724:0.0:0.6276:0.0	.|.	194;195;138;195|64	Q5T5M0;B7Z4U2;Q6P5T0;O14520|B7Z7F6	.;.;.;AQP7_HUMAN|.	K|T	103;194;63;195;138;103;194;195;131|64	ENSP00000441619:N103K;ENSP00000368821:N194K;ENSP00000412868:N63K;ENSP00000297988:N195K;ENSP00000396111:N138K;ENSP00000410138:N103K;ENSP00000368820:N194K;ENSP00000439534:N195K;ENSP00000368817:N131K|ENSP00000438860:P64T	ENSP00000297988:N195K|ENSP00000438860:P64T	N|P	-|-	3|1	2|0	AQP7|AQP7	33375805|33375805	0.000000|0.000000	0.05858|0.05858	0.060000|0.060000	0.19600|0.19600	0.083000|0.083000	0.17756|0.17756	-0.334000|-0.334000	0.07883|0.07883	-0.018000|-0.018000	0.14079|0.14079	0.454000|0.454000	0.30748|0.30748	AAC|CCC	.	.	.	none		0.617	AQP7-202	KNOWN	basic	protein_coding	protein_coding		NM_001170		T	33385805	G	T	33385805	3	4	43	1	0	0	0	0	1	0	0	0	831	1252	44	4	451	4	AQP7	9	33385805	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08		33385805	107827626	33	3004											
C10orf71	118461	hgsc.bcm.edu	37	chr10	50530974	50530974	+	Frame_Shift_Del	DEL	G	G	-																															gtccagaggagactggaggtGccagtttccggcctaaggag																										TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr10:50530974delG	ENST00000374144.3	+	3	672	c.384delG	c.(382-384)gtgfs	p.V128fs	C10orf71_ENST00000323868.4_Frame_Shift_Del_p.V128fs			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	128										endometrium(1)	1						GACTGGAGGTGCCAGTTTCCG	0.547																																					p.V128fs		Atlas-INDEL	.											.	C10orf71	179	.	0			c.383delT						PASS	.						81	95	91					10																	50530974		1948	4145	6093	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.384delG	chr10.hg19:g.50530974delG	ENSP00000363259:p.Val128fs	165.0	0.0	0		122.0	44.0	0.360656	NM_001135196	A0AVL8	Frame_Shift_Del	DEL	ENST00000374144.3	hg19	CCDS44387.1																																																																																			.	.	.	none		0.547	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459		-	50530974	G	-	50530974	7	5	43	1	0	1	0	1	0	0	0	0	1616	1306	46	0	386	0	C10orf71	10	50530974	Frame_Shift_Del	DEL	G	TCGA-A4-7288-01A-11D-2136-08		50530974	85003773	34	3005											
MUC2	4583	hgsc.bcm.edu	37	chr11	1075662	1075662	+	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	ctccctcagagggcagaaccCgaaaccacggccacaacgtc	12	3	9	17	3	1	2	1	0	0	2	3	3	2	2	4	2	3	1	4	2	3	0			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr11:1075662C>G	ENST00000441003.2	+	2	115	c.88C>G	c.(88-90)Cga>Gga	p.R30G	MUC2_ENST00000359061.5_Missense_Mutation_p.R30G	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	30					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)	GGGCAGAACCCGAAACCACGG	0.632																																					p.R30G		Atlas-SNP	.											.	MUC2	614	.	0			c.C88G						PASS	.						30	35	33					11																	1075662		2128	4223	6351	SO:0001583	missense	4583	exon2			AGAACCCGAAACC	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.88C>G	chr11.hg19:g.1075662C>G	ENSP00000415183:p.Arg30Gly	47.0	0.0	.		38.0	11.0	.	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	C	8.980	0.975205	0.18736	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.12672	2.69;2.66	3.78	2.81	0.32909	.	0.537890	0.13893	U	0.355461	T	0.10637	0.0260	L	0.27053	0.805	0.09310	N	1	P	0.40398	0.716	P	0.44477	0.451	T	0.15694	-1.0428	10	0.08837	T	0.75	.	8.7802	0.34787	0.1808:0.6671:0.1521:0.0	.	30	E7EUV1	.	G	30	ENSP00000415183:R30G;ENSP00000351956:R30G	ENSP00000351956:R30G	R	+	1	2	MUC2	1065662	0.009000	0.17119	0.001000	0.08648	0.150000	0.21749	2.439000	0.44846	0.525000	0.28522	0.491000	0.48974	CGA	.	.	.	none		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		G	1075662	C	G	1075662	3	3	43	1	0	0	0	0	1	0	0	0	9982	644	23	4	94	4	MUC2	11	1075662	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08		1075662	133930854	35	3006											
SLC5A12	159963	hgsc.bcm.edu	37	chr11	26725402	26725402	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acattgtggaatcccccagcAtgagttgatccttgaatgag	11	11	10	9	0	0	4	0	4	0	0	2	5	2	5	3	1	1	2	3	1	2	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr11:26725402A>G	ENST00000396005.3	-	5	927	c.618T>C	c.(616-618)caT>caC	p.H206H	SLC5A12_ENST00000280467.6_Silent_p.H206H	NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	206					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						ATCCCCCAGCATGAGTTGATC	0.388																																					p.H206H		Atlas-SNP	.											.	SLC5A12	134	.	0			c.T618C						PASS	.						233	218	223					11																	26725402		2203	4299	6502	SO:0001819	synonymous_variant	159963	exon5			CCCAGCATGAGTT	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.618T>C	chr11.hg19:g.26725402A>G		287.0	0.0	.		225.0	91.0	.	NM_178498	Q86UC7	Silent	SNP	ENST00000396005.3	hg19	CCDS7860.2																																																																																			.	.	.	none		0.388	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498		G	26725402	A	G	26725402	2	3	43	1	0	0	0	0	0	0	0	1	14677	214	8	3		3	SLC5A12	11	26725402	Silent	SNP	A	TCGA-A4-7288-01A-11D-2136-08	25649740	26725402	108281114	36	3007											
TCP11L1	55346	hgsc.bcm.edu	37	chr11	33083137	33083137	+	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	gaggaccttatgactcagaaGtataaacacgccctgccagt	13	8	9	11	1	1	2	1	1	0	1	1	4	1	3	3	1	2	1	3	1	5	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr11:33083137G>C	ENST00000334274.4	+	7	1237	c.837G>C	c.(835-837)aaG>aaC	p.K279N	TCP11L1_ENST00000324357.9_Missense_Mutation_p.K58N|TCP11L1_ENST00000432887.1_Missense_Mutation_p.K279N|TCP11L1_ENST00000531632.2_Missense_Mutation_p.K279N	NM_018393.3	NP_060863.3	Q9NUJ3	T11L1_HUMAN	t-complex 11, testis-specific-like 1	279						microtubule (GO:0005874)				kidney(1)|liver(2)|lung(2)|skin(1)	6						TGACTCAGAAGTATAAACACG	0.527																																					p.K279N		Atlas-SNP	.											.	TCP11L1	40	.	0			c.G837C						PASS	.						57	57	57					11																	33083137		2202	4298	6500	SO:0001583	missense	55346	exon7			TCAGAAGTATAAA	BC041696	CCDS7882.1	11p13	2014-08-12	2012-09-20		ENSG00000176148	ENSG00000176148			25655	protein-coding gene	gene with protein product			"t-complex 11 (mouse) like 1"				Standard	NM_001145541		Approved	FLJ11336	uc010rei.2	Q9NUJ3	OTTHUMG00000165303	ENST00000334274.4:c.837G>C	chr11.hg19:g.33083137G>C	ENSP00000335595:p.Lys279Asn	59.0	0.0	.		55.0	22.0	.	NM_001145541	D3DR01|Q8IVX4	Missense_Mutation	SNP	ENST00000334274.4	hg19	CCDS7882.1	.	.	.	.	.	.	.	.	.	.	G	11.86	1.764820	0.31228	.	.	ENSG00000176148	ENST00000334274;ENST00000531632;ENST00000432887;ENST00000324357	T;T;T;T	0.11495	2.77;2.77;2.77;2.77	5.01	5.01	0.66863	.	0.702810	0.14718	N	0.302495	T	0.08582	0.0213	L	0.29908	0.895	0.09310	N	1	B	0.25007	0.116	B	0.22152	0.038	T	0.27331	-1.0077	10	0.21540	T	0.41	-10.0501	10.8411	0.46715	0.0965:0.0:0.9035:0.0	.	279	Q9NUJ3	T11L1_HUMAN	N	279;279;279;58	ENSP00000335595:K279N;ENSP00000433067:K279N;ENSP00000395070:K279N;ENSP00000316279:K58N	ENSP00000316279:K58N	K	+	3	2	TCP11L1	33039713	0.874000	0.30092	0.537000	0.28052	0.762000	0.43233	1.682000	0.37628	2.320000	0.78422	0.555000	0.69702	AAG	.	.	.	none		0.527	TCP11L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383377.4	NM_018393		C	33083137	G	C	33083137	3	2	43	1	0	0	0	0	1	0	0	0	15726	1020	36	4	859	4	TCP11L1	11	33083137	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08	6357735	33083137	101923379	37	3008											
NDUFS3	4722	hgsc.bcm.edu	37	chr11	47605943	47605943	+	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	gagttccgcaaatttgacctGaacagcccctgggaggcttt	9	10	11	11	1	0	2	0	2	0	0	1	4	1	3	4	2	2	3	4	2	2	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr11:47605943G>A	ENST00000263774.4	+	7	787	c.705G>A	c.(703-705)ctG>ctA	p.L235L	FAM180B_ENST00000538490.1_5'Flank|FAM180B_ENST00000356737.2_5'Flank|NDUFS3_ENST00000533507.1_3'UTR	NM_004551.2	NP_004542.1	O75489	NDUS3_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 3, 30kDa (NADH-coenzyme Q reductase)	235					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|negative regulation of cell growth (GO:0030308)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)	9					Doxorubicin(DB00997)	AATTTGACCTGAACAGCCCCT	0.557																																					p.L235L	Pancreas(15;551 601 22438 23457 52512)	Atlas-SNP	.											.	NDUFS3	19	.	0			c.G705A						PASS	.						137	141	140					11																	47605943		2201	4298	6499	SO:0001819	synonymous_variant	4722	exon7			TGACCTGAACAGC	AF067139	CCDS7941.1	11p11.11	2011-08-03	2002-08-29		ENSG00000213619	ENSG00000213619	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7710	protein-coding gene	gene with protein product	"complex I 30kDa subunit", "NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial"	603846	"NADH dehydrogenase (ubiquinone) Fe-S protein 3 (30kD) (NADH-coenzyme Q reductase)"			9763677	Standard	NM_004551		Approved	CI-30	uc001nga.2	O75489	OTTHUMG00000166893	ENST00000263774.4:c.705G>A	chr11.hg19:g.47605943G>A		305.0	0.0	.		205.0	85.0	.	NM_004551	B2R9J1|B4DFM8|Q9UNQ8	Silent	SNP	ENST00000263774.4	hg19	CCDS7941.1																																																																																			.	.	.	none		0.557	NDUFS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391749.1	NM_004551		A	47605943	G	A	47605943	2	1	43	1	0	0	0	0	0	0	0	1	10300	1277	45	2		2	NDUFS3	11	47605943	Silent	SNP	G	TCGA-A4-7288-01A-11D-2136-08	14522806	47605943	87400573	38	3009											
ATL3	25923	hgsc.bcm.edu	37	chr11	63403801	63403802	+	Frame_Shift_Ins	INS	-	-	A																															tgctctttgaattcaccagcINSaatatctgttcacaggacga																										TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr11:63403801_63403802insA	ENST00000398868.3	-	9	1131_1132	c.855_856insT	c.(853-858)attgctfs	p.A286fs	ATL3_ENST00000332645.4_Frame_Shift_Ins_p.A313fs|RP11-697H9.2_ENST00000540307.1_RNA|ATL3_ENST00000538786.1_Frame_Shift_Ins_p.A268fs	NM_015459.3	NP_056274.3	Q6DD88	ATLA3_HUMAN	atlastin GTPase 3	286	GB1/RHD3-type G.				endoplasmic reticulum organization (GO:0007029)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	11						AATTCACCAGCAATATCTGTTC	0.416											OREG0021036	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A286fs		Atlas-INDEL	.											.	ATL3	31	.	0			c.856_857insT						PASS	.																																			SO:0001589	frameshift_variant	25923	exon9			.		CCDS41663.1, CCDS73309.1	11q13.1	2008-09-17			ENSG00000184743	ENSG00000184743			24526	protein-coding gene	gene with protein product		609369				18270207	Standard	XM_005273891		Approved	DKFZP564J0863	uc001nxk.1	Q6DD88	OTTHUMG00000167854	ENST00000398868.3:c.856dupT	chr11.hg19:g.63403803_63403803dupA	ENSP00000381844:p.Ala286fs	135.0	0.0	0	1068	110.0	44.0	0.4	NM_015459	Q8N7W5|Q9H8Q5|Q9UFL1	Frame_Shift_Ins	INS	ENST00000398868.3	hg19	CCDS41663.1																																																																																			.	.	.	none		0.416	ATL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396637.1	NM_015459		A	63403802	-	A	63403801	7	5	43	1	0	1	1	0	0	0	0	0	1108	710	25	0	789	0	ATL3	11	63403801	Frame_Shift_Ins	INS	-	TCGA-A4-7288-01A-11D-2136-08	15797858	63403801	71602715	39	3010											
ATP5L	10632	hgsc.bcm.edu	37	chr11	118272388	118272388	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccattccagaaccatggcccAatttgtccgtaaccttgtgg	9	11	8	13	1	0	1	0	0	0	1	2	1	2	1	6	2	2	1	6	2	3	4			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr11:118272388A>G	ENST00000300688.3	+	1	520	c.8A>G	c.(7-9)cAa>cGa	p.Q3R	ATP5L_ENST00000529770.1_3'UTR|ATP5L_ENST00000524422.1_Missense_Mutation_p.Q3R|RP11-770J1.5_ENST00000534438.1_5'UTR|RP11-770J1.5_ENST00000531742.1_5'Flank	NM_006476.4	NP_006467.4	O75964	ATP5L_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit G	3					ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) (GO:0000276)|mitochondrion (GO:0005739)	hydrogen ion transmembrane transporter activity (GO:0015078)|transmembrane transporter activity (GO:0022857)			breast(1)|endometrium(1)|large_intestine(2)|lung(3)	7	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;3.07e-05)		ACCATGGCCCAATTTGTCCGT	0.667																																					p.Q3R		Atlas-SNP	.											.	ATP5L	11	.	0			c.A8G						PASS	.						45	40	42					11																	118272388		2200	4296	6496	SO:0001583	missense	10632	exon1			TGGCCCAATTTGT	AF092124	CCDS8397.1	11q23.3	2012-10-12	2010-06-11		ENSG00000167283	ENSG00000167283		"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	14247	protein-coding gene	gene with protein product			"ATP synthase, H+ transporting, mitochondrial F0 complex, subunit g", "ATP synthase, H+ transporting, mitochondrial F0 complex, subunit G"			11230166, 11042152	Standard	NR_033759		Approved	ATP5JG	uc001psx.3	O75964		ENST00000300688.3:c.8A>G	chr11.hg19:g.118272388A>G	ENSP00000300688:p.Gln3Arg	60.0	0.0	.		49.0	20.0	.	NM_006476	A8K0K3|Q96BV6|Q9UBZ7	Missense_Mutation	SNP	ENST00000300688.3	hg19	CCDS8397.1	.	.	.	.	.	.	.	.	.	.	A	15.60	2.880213	0.51801	.	.	ENSG00000167283	ENST00000300688;ENST00000524422	.	.	.	6.17	5.05	0.67936	.	0.166760	0.56097	D	0.000039	T	0.56804	0.2010	L	0.61387	1.9	0.39789	D	0.972403	B	0.06786	0.001	B	0.09377	0.004	T	0.54403	-0.8299	9	0.36615	T	0.2	-2.3772	9.3868	0.38347	0.9198:0.0:0.0802:0.0	.	3	O75964	ATP5L_HUMAN	R	3	.	ENSP00000300688:Q3R	Q	+	2	0	ATP5L	117777598	1.000000	0.71417	1.000000	0.80357	0.653000	0.38743	3.233000	0.51311	1.142000	0.42291	0.533000	0.62120	CAA	.	.	.	none		0.667	ATP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389220.1	NM_006476		G	118272388	A	G	118272388	3	3	43	1	0	0	0	0	1	0	0	0	1160	130	5	3	10	3	ATP5L	11	118272388	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	54868587	118272388	16734128	40	3011											
TMEM45B	120224	hgsc.bcm.edu	37	chr11	129724698	129724698	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agactggttatggctgtggcAgtattcatggaaggtaattt	10	14	13	4	0	1	1	1	0	0	1	1	2	1	2	0	5	0	5	0	5	4	5			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr11:129724698A>G	ENST00000524567.1	+	3	653	c.372A>G	c.(370-372)gcA>gcG	p.A124A	TMEM45B_ENST00000281441.3_Silent_p.A124A			Q96B21	TM45B_HUMAN	transmembrane protein 45B	124						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)		TGGCTGTGGCAGTATTCATGG	0.453																																					p.A124A		Atlas-SNP	.											.	TMEM45B	25	.	0			c.A372G						PASS	.						138	125	129					11																	129724698		2201	4297	6498	SO:0001819	synonymous_variant	120224	exon3			TGTGGCAGTATTC	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.372A>G	chr11.hg19:g.129724698A>G		151.0	0.0	.		103.0	39.0	.	NM_138788	A8K2L8	Silent	SNP	ENST00000524567.1	hg19	CCDS8482.1																																																																																			.	.	.	none		0.453	TMEM45B-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386062.1	NM_138788		G	129724698	A	G	129724698	2	3	43	1	0	0	0	0	0	0	0	1	16182	175	7	3		3	TMEM45B	11	129724698	Silent	SNP	A	TCGA-A4-7288-01A-11D-2136-08	11452310	129724698	5281818	41	3012											
IFFO1	25900	hgsc.bcm.edu	37	chr12	6649694	6649694	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatcgcgatcggagtcctcAgcctcgcttggcggcggcgg	5	7	15	14	7	1	0	1	0	0	0	5	2	2	1	2	5	1	1	2	5	0	1			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr12:6649694A>G	ENST00000396840.2	-	9	1676	c.1635T>C	c.(1633-1635)gcT>gcC	p.A545A	IFFO1_ENST00000465801.1_Silent_p.A241A|IFFO1_ENST00000436152.2_Silent_p.A242A|IFFO1_ENST00000336604.4_Silent_p.A548A|RP5-940J5.9_ENST00000602946.1_RNA|RP5-940J5.8_ENST00000499202.2_RNA|IFFO1_ENST00000356896.4_Silent_p.A549A			Q0D2I5	IFFO1_HUMAN	intermediate filament family orphan 1	545						intermediate filament (GO:0005882)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	20						CGGAGTCCTCAGCCTCGCTTG	0.617																																					p.A557A		Atlas-SNP	.											.	IFFO1	55	.	0			c.T1671C						PASS	.						53	54	54					12																	6649694		2203	4300	6503	SO:0001819	synonymous_variant	25900	exon10			GTCCTCAGCCTCG	AF124432	CCDS8550.1, CCDS41741.1, CCDS8550.2, CCDS73425.1	12p13.31	2013-01-16	2008-09-11	2008-09-11	ENSG00000010295	ENSG00000010295		"Intermediate filament family orphans"	24970	protein-coding gene	gene with protein product		610495	"intermediate filament family orphan"	IFFO		8771189, 3052284	Standard	NM_001193457		Approved	HOM-TES-103	uc010sfe.2	Q0D2I5	OTTHUMG00000141264	ENST00000396840.2:c.1635T>C	chr12.hg19:g.6649694A>G		137.0	0.0	.		89.0	83.0	.	NM_001193457	Q24JT6|Q7L5J9|Q7Z5X4|Q9BQ46	Silent	SNP	ENST00000396840.2	hg19		.	.	.	.	.	.	.	.	.	.	A	12.53	1.964511	0.34659	.	.	ENSG00000010295	ENST00000416019;ENST00000423501	.	.	.	4.84	1.14	0.20703	.	.	.	.	.	T	0.30727	0.0774	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.07966	-1.0745	6	.	.	.	0.8566	4.8721	0.13639	0.4992:0.2689:0.2318:0.0	.	240	Q6P593	.	P	279;185	.	.	L	-	2	0	IFFO1	6519955	0.938000	0.31826	1.000000	0.80357	0.982000	0.71751	-0.065000	0.11617	0.887000	0.36136	0.459000	0.35465	CTG	.	.	.	none		0.617	IFFO1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000280428.1	NM_080730		G	6649694	A	G	6649694	2	3	43	1	0	0	0	0	0	0	0	1	7517	175	7	3		3	IFFO1	12	6649694	Silent	SNP	A	TCGA-A4-7288-01A-11D-2136-08		6649694	127202201	42	3013											
TAS2R50	259296	hgsc.bcm.edu	37	chr12	11139402	11139402	+	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	gaagccattggcaaagtttcCgagaacaaataaaaccatta	18	8	7	8	1	0	1	0	0	0	1	1	3	1	1	3	1	3	2	3	1	7	4			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr12:11139402C>A	ENST00000506868.1	-	1	109	c.58G>T	c.(58-60)Gga>Tga	p.G20*	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176890.2	NP_795371.2	P59544	T2R50_HUMAN	taste receptor, type 2, member 50	20					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)	p.G20*(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(4)|ovary(2)|pancreas(1)	17						GCAAAGTTTCCGAGAACAAAT	0.348																																					p.G20X		Atlas-SNP	.											TAS2R50,NS,carcinoma,0,1	TAS2R50	37	.	1	Substitution - Nonsense(1)	lung(1)	c.G58T						PASS	.						45	52	50					12																	11139402		2201	4297	6498	SO:0001587	stop_gained	259296	exon1			AGTTTCCGAGAAC	AF494235	CCDS8638.1	12p13.2	2012-08-22			ENSG00000212126	ENSG00000212126		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18882	protein-coding gene	gene with protein product		609627				12379855, 12584440, 16175505	Standard	NM_176890		Approved	T2R51	uc001qzl.2	P59544	OTTHUMG00000162719	ENST00000506868.1:c.58G>T	chr12.hg19:g.11139402C>A	ENSP00000424040:p.Gly20*	75.0	0.0	.		68.0	4.0	.	NM_176890	P59545|Q2M255|Q645Y0	Nonsense_Mutation	SNP	ENST00000506868.1	hg19	CCDS8638.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.735938	0.49045	.	.	ENSG00000212126	ENST00000506868	.	.	.	2.19	1.23	0.21249	.	0.204251	0.31199	U	0.008071	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	6.9195	0.24380	0.0:0.8404:0.0:0.1596	.	.	.	.	X	20	.	ENSP00000424040:G20X	G	-	1	0	TAS2R50	11030669	0.162000	0.22906	0.008000	0.14137	0.132000	0.20833	1.423000	0.34837	0.218000	0.20820	0.313000	0.20887	GGA	.	.	.	none		0.348	TAS2R50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370192.2	NM_176890		A	11139402	C	A	11139402	4	1	43	1	0	0	0	0	0	1	0	0	15596	661	23	4	845	4	TAS2R50	12	11139402	Nonsense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	4489708	11139402	122712493	43	3014											
ARID2	196528	hgsc.bcm.edu	37	chr12	46285793	46285793	+	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	tgcttcctcttcctcaaaaaGgataagcactgttcaaagga	13	11	7	10	0	3	0	2	0	1	0	5	2	5	2	2	2	2	3	2	2	4	4			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr12:46285793G>A	ENST00000334344.6	+	18	5233		c.e18-1		ARID2_ENST00000457135.1_Splice_Site|ARID2_ENST00000479608.1_Splice_Site|ARID2_ENST00000422737.1_Splice_Site|ARID2_ENST00000444670.1_Splice_Site	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)						chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		TCCTCAAAAAGGATAAGCACT	0.388			"N, S, F"		hepatocellular carcinoma																																.		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.5062-1G>A						PASS	.						117	109	112					12																	46285793		2203	4300	6503	SO:0001630	splice_region_variant	196528	exon18			CAAAAAGGATAAG		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.5062-1G>A	chr12.hg19:g.46285793G>A		64.0	0.0	.		59.0	54.0	.	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Splice_Site	SNP	ENST00000334344.6	hg19	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.730640	0.48939	.	.	ENSG00000189079	ENST00000334344;ENST00000549153;ENST00000338636;ENST00000422737;ENST00000444670;ENST00000457135	.	.	.	4.89	4.89	0.63831	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.6022	0.91253	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARID2	44572060	1.000000	0.71417	1.000000	0.80357	0.654000	0.38779	9.070000	0.93974	2.690000	0.91761	0.655000	0.94253	.	.	.	.	none		0.388	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875	Intron	A	46285793	G	A	46285793	5	1	43	1	0	0	0	0	0	0	1	0	915	1014	35	2	5131	2	ARID2	12	46285793	Splice_Site	SNP	G	TCGA-A4-7288-01A-11D-2136-08	35146391	46285793	87566102	44	3015											
ESPL1	9700	hgsc.bcm.edu	37	chr12	53685605	53685605	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacgtctacagggcctgacAgtaccaagcaatagccacct	12	6	10	13	1	1	1	0	1	1	0	1	2	1	2	4	2	4	2	4	2	5	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr12:53685605A>G	ENST00000257934.4	+	26	5743	c.5652A>G	c.(5650-5652)acA>acG	p.T1884T	ESPL1_ENST00000552462.1_Silent_p.T1884T	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	1884					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						AGGGCCTGACAGTACCAAGCA	0.587																																					p.T1884T	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											.	ESPL1	158	.	0			c.A5652G						PASS	.						130	115	120					12																	53685605		2203	4300	6503	SO:0001819	synonymous_variant	9700	exon26			CCTGACAGTACCA	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.5652A>G	chr12.hg19:g.53685605A>G		189.0	0.0	.		140.0	126.0	.	NM_012291		Silent	SNP	ENST00000257934.4	hg19	CCDS8852.1																																																																																			.	.	.	none		0.587	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291		G	53685605	A	G	53685605	2	3	43	1	0	0	0	0	0	0	0	1	5255	175	7	3		3	ESPL1	12	53685605	Silent	SNP	A	TCGA-A4-7288-01A-11D-2136-08	7399812	53685605	80166290	45	3016											
HNRNPC	3183	hgsc.bcm.edu	37	chr14	21679712	21679713	+	Frame_Shift_Del	DEL	AT	AT	-																															tgctcctcttctgacttatcAttcttcatctctactgcgga																										TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr14:21679712_21679713delAT	ENST00000320084.7	-	7	928_929	c.689_690delAT	c.(688-690)aatfs	p.N230fs	HNRNPC_ENST00000554969.1_Frame_Shift_Del_p.N217fs|HNRNPC_ENST00000556142.1_Intron|HNRNPC_ENST00000556897.1_Frame_Shift_Del_p.N217fs|HNRNPC_ENST00000553300.1_Frame_Shift_Del_p.N217fs|HNRNPC_ENST00000556513.1_Intron|HNRNPC_ENST00000553753.1_Frame_Shift_Del_p.N217fs|HNRNPC_ENST00000557201.1_Frame_Shift_Del_p.N230fs|HNRNPC_ENST00000420743.2_Frame_Shift_Del_p.N230fs|HNRNPC_ENST00000554455.1_Frame_Shift_Del_p.N230fs|HNRNPC_ENST00000555914.1_Frame_Shift_Del_p.N216fs|HNRNPC_ENST00000336053.6_Frame_Shift_Del_p.N217fs|HNRNPC_ENST00000555883.1_Frame_Shift_Del_p.N174fs|HNRNPC_ENST00000449098.1_Frame_Shift_Del_p.N217fs|HNRNPC_ENST00000555309.1_Frame_Shift_Del_p.N229fs|HNRNPC_ENST00000556628.1_Frame_Shift_Del_p.N150fs|HNRNPC_ENST00000430246.2_Frame_Shift_Del_p.N217fs	NM_001077442.1	NP_001070910.1	P07910	HNRPC_HUMAN	heterogeneous nuclear ribonucleoprotein C (C1/C2)	230	Asp/Glu-rich (acidic).				3'-UTR-mediated mRNA stabilization (GO:0070935)|ATP-dependent chromatin remodeling (GO:0043044)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|spliceosomal complex (GO:0005681)	identical protein binding (GO:0042802)|mRNA 3'-UTR binding (GO:0003730)|nucleosomal DNA binding (GO:0031492)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)			breast(1)|liver(1)|lung(6)|skin(1)	9	all_cancers(95;0.00176)		Epithelial(56;1.08e-06)|all cancers(55;8.95e-06)	GBM - Glioblastoma multiforme(265;0.00783)		CTGACTTATCATTCTTCATCTC	0.505																																					p.230_231del	NSCLC(108;607 2244 12726 38757)	Atlas-INDEL	.											.	HNRNPC	31	.	0			c.690_691del						PASS	.																																			SO:0001589	frameshift_variant	3183	exon8			.		CCDS41915.1, CCDS45079.1	14q11.2	2013-06-12		2007-08-16	ENSG00000092199	ENSG00000092199		"RNA binding motif (RRM) containing"	5035	protein-coding gene	gene with protein product		164020		HNRPC		3457372	Standard	NM_031314		Approved	hnRNPC	uc001waa.3	P07910	OTTHUMG00000170757	ENST00000320084.7:c.689_690delAT	chr14.hg19:g.21679712_21679713delAT	ENSP00000319690:p.Asn230fs	22.0	0.0	0		31.0	16.0	0.516129	NM_031314	D3DS19|D3DS22|P22628|Q53EX2|Q59FD3|Q5FWE8|Q86SF8|Q86U45|Q96HK7|Q96HM4|Q96IY5|Q9BTS3	Frame_Shift_Del	DEL	ENST00000320084.7	hg19	CCDS41915.1																																																																																			.	.	.	none		0.505	HNRNPC-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410235.1			-	21679713	AT	-	21679712	7	5	43	1	0	1	0	1	0	0	0	0	7269	214	8	0	238	0	HNRNPC	14	21679712	Frame_Shift_Del	DEL	AT	TCGA-A4-7288-01A-11D-2136-08		21679712	85669828	46	3017											
RAB2B	84932	hgsc.bcm.edu	37	chr14	21931921	21931921	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcacatccctgcgggactctAggtcactgcaagagattaat	11	10	9	11	1	3	1	2	0	1	1	4	3	4	2	1	2	2	1	1	2	3	2			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr14:21931921A>G	ENST00000397762.1	-	6	468	c.368T>C	c.(367-369)cTa>cCa	p.L123P	RAB2B_ENST00000461909.1_5'UTR	NM_001163380.1|NM_032846.3	NP_001156852.1|NP_116235.2	Q8WUD1	RAB2B_HUMAN	RAB2B, member RAS oncogene family	123					positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			NS(1)|central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)	6	all_cancers(95;0.000858)		Epithelial(56;1.53e-06)|all cancers(55;1.44e-05)	GBM - Glioblastoma multiforme(265;0.00391)		GCGGGACTCTAGGTCACTGCA	0.408																																					p.L123P	Melanoma(131;1007 1750 28652 34486 42672)	Atlas-SNP	.											.	RAB2B	19	.	0			c.T368C						PASS	.						86	80	82					14																	21931921		2203	4300	6503	SO:0001583	missense	84932	exon6			GACTCTAGGTCAC	AK027730	CCDS9570.1	14q11.1	2006-12-18			ENSG00000129472	ENSG00000129472		"RAB, member RAS oncogene"	20246	protein-coding gene	gene with protein product		607466				12376746	Standard	NM_032846		Approved	FLJ14824	uc010tlt.2	Q8WUD1	OTTHUMG00000029693	ENST00000397762.1:c.368T>C	chr14.hg19:g.21931921A>G	ENSP00000380869:p.Leu123Pro	113.0	0.0	.		85.0	37.0	.	NM_032846	B2RD03|D3DS24|Q6NZ33	Missense_Mutation	SNP	ENST00000397762.1	hg19	CCDS9570.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.416717	0.83449	.	.	ENSG00000129472	ENST00000397762;ENST00000304034	D	0.85013	-1.93	5.62	5.62	0.85841	Small GTP-binding protein domain (1);	0.000000	0.52532	D	0.000080	D	0.96137	0.8741	H	0.99712	4.72	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.996;0.99;0.998	D	0.97978	1.0347	10	0.87932	D	0	.	14.8111	0.69996	1.0:0.0:0.0:0.0	.	123;77;58	Q8WUD1;B4DUD4;Q6NZ33	RAB2B_HUMAN;.;.	P	123	ENSP00000380869:L123P	ENSP00000302005:L123P	L	-	2	0	RAB2B	21001761	1.000000	0.71417	0.984000	0.44739	0.958000	0.62258	6.854000	0.75440	2.145000	0.66743	0.533000	0.62120	CTA	.	.	.	none		0.408	RAB2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074053.4			G	21931921	A	G	21931921	3	3	43	1	0	0	0	0	1	0	0	0	12931	420	15	3	294	3	RAB2B	14	21931921	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	252209	21931921	85417619	47	3018											
PCK2	5106	hgsc.bcm.edu	37	chr14	24568928	24568928	+	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	tggatgaggtttgacagtgaAggtgagggactctcagatca	11	10	15	5	0	2	5	2	4	1	1	3	7	2	7	0	4	0	1	0	4	1	1			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr14:24568928A>C	ENST00000216780.4	+	6	1282	c.1014A>C	c.(1012-1014)gaA>gaC	p.E338D	PCK2_ENST00000561286.1_Splice_Site_p.E204D|PCK2_ENST00000559250.1_Splice_Site_p.E350D|PCK2_ENST00000396973.4_Splice_Site_p.E338D|NRL_ENST00000561028.1_Intron|PCK2_ENST00000558096.1_Splice_Site_p.E204D|PCK2_ENST00000545054.2_Splice_Site_p.E204D	NM_004563.2	NP_004554.2	Q16822	PCKGM_HUMAN	phosphoenolpyruvate carboxykinase 2 (mitochondrial)	338					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)		TTGACAGTGAAGGTGAGGGAC	0.517																																					p.E338D		Atlas-SNP	.											PCK2_ENST00000396973,NS,carcinoma,0,2	PCK2	66	.	0			c.A1014C						PASS	.						209	179	189					14																	24568928		2203	4300	6503	SO:0001630	splice_region_variant	5106	exon6			CAGTGAAGGTGAG	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.1015+1A>C	chr14.hg19:g.24568928A>C		183.0	0.0	.		118.0	29.0	.	NM_001018073	O43253|Q86U01|Q9BV62	Missense_Mutation	SNP	ENST00000216780.4	hg19	CCDS9609.1	.	.	.	.	.	.	.	.	.	.	A	8.481	0.859731	0.17178	.	.	ENSG00000100889	ENST00000216780;ENST00000396973;ENST00000545054	T;T;T	0.06849	3.25;3.25;3.25	5.5	-8.34	0.00988	Phosphoenolpyruvate carboxykinase, C-terminal (1);	0.280145	0.45606	N	0.000341	T	0.01695	0.0054	N	0.02120	-0.675	0.43088	D	0.99475	B;B;B;B	0.09022	0.001;0.0;0.002;0.0	B;B;B;B	0.15052	0.012;0.012;0.007;0.006	T	0.43245	-0.9403	10	0.02654	T	1	-4.464	9.0824	0.36561	0.2559:0.5071:0.0:0.237	.	204;338;338;338	B4DW73;Q16822;Q16822-2;Q6IB91	.;PCKGM_HUMAN;.;.	D	338;338;204	ENSP00000216780:E338D;ENSP00000380171:E338D;ENSP00000441826:E204D	ENSP00000216780:E338D	E	+	3	2	PCK2	23638768	0.996000	0.38824	0.953000	0.39169	0.948000	0.59901	0.536000	0.23129	-0.926000	0.03770	0.459000	0.35465	GAA	.	.	.	none		0.517	PCK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071900.3	NM_001018073	Missense_Mutation	C	24568928	A	C	24568928	5	2	43	1	0	0	0	0	0	0	1	0	11589	86	3	5	1036	5	PCK2	14	24568928	Splice_Site	SNP	A	TCGA-A4-7288-01A-11D-2136-08	2637007	24568928	82780612	48	3019											
NID2	22795	hgsc.bcm.edu	37	chr14	52494036	52494036	+	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	acaggtatgactgccatcctCacaggggttggcaggtgggg	8	8	16	9	0	1	1	1	1	0	0	2	1	2	1	2	7	1	3	2	7	1	2			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr14:52494036C>T	ENST00000216286.5	-	12	2556	c.2557G>A	c.(2557-2559)Gag>Aag	p.E853K	NID2_ENST00000541773.1_Intron	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	853	EGF-like 4. {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)					CTGCCATCCTCACAGGGGTTG	0.572																																					p.E853K		Atlas-SNP	.											.	NID2	201	.	0			c.G2557A						PASS	.						37	36	36					14																	52494036		2203	4300	6503	SO:0001583	missense	22795	exon12			CATCCTCACAGGG	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.2557G>A	chr14.hg19:g.52494036C>T	ENSP00000216286:p.Glu853Lys	55.0	0.0	.		37.0	15.0	.	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	hg19	CCDS9706.1	.	.	.	.	.	.	.	.	.	.	C	14.97	2.692957	0.48202	.	.	ENSG00000087303	ENST00000216286;ENST00000316204;ENST00000395707	D	0.87334	-2.24	5.76	4.86	0.63082	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.479683	0.23171	N	0.051140	T	0.81894	0.4919	L	0.42008	1.315	0.80722	D	1	B;P;B	0.35411	0.04;0.5;0.417	B;B;B	0.35278	0.017;0.09;0.199	T	0.77705	-0.2488	10	0.11182	T	0.66	.	15.3665	0.74526	0.0:0.8547:0.1453:0.0	.	447;855;853	E7EPP3;Q5CZI2;Q14112	.;.;NID2_HUMAN	K	853;447;855	ENSP00000216286:E853K	ENSP00000216286:E853K	E	-	1	0	NID2	51563786	0.975000	0.34042	0.998000	0.56505	0.694000	0.40290	1.623000	0.37008	1.397000	0.46682	0.563000	0.77884	GAG	.	.	.	none		0.572	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			T	52494036	C	T	52494036	3	4	43	1	0	0	0	0	1	0	0	0	10422	835	29	2	1614	2	NID2	14	52494036	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	27925108	52494036	54855504	49	3020											
PPM1A	5494	hgsc.bcm.edu	37	chr14	60750192	60750192	+	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	tgtgattttgtaagatccagActtgaagtcactgatgacct	11	14	9	7	0	1	6	1	4	0	2	2	6	2	6	2	0	0	1	2	0	2	4			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr14:60750192A>T	ENST00000395076.4	+	2	1201	c.771A>T	c.(769-771)agA>agT	p.R257S	PPM1A_ENST00000325642.3_Missense_Mutation_p.R330S|PPM1A_ENST00000529574.1_Missense_Mutation_p.R257S|PPM1A_ENST00000325658.3_Missense_Mutation_p.R257S	NM_021003.4	NP_066283.1	P35813	PPM1A_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1A	257					cell cycle arrest (GO:0007050)|dephosphorylation (GO:0016311)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|N-terminal protein myristoylation (GO:0006499)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|protein dephosphorylation (GO:0006470)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|voltage-gated calcium channel complex (GO:0005891)	calmodulin-dependent protein phosphatase activity (GO:0033192)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)|R-SMAD binding (GO:0070412)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(1)|large_intestine(8)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(108;0.046)		TAAGATCCAGACTTGAAGTCA	0.348																																					p.R330S		Atlas-SNP	.											.	PPM1A	72	.	0			c.A990T						PASS	.						153	150	151					14																	60750192		2203	4300	6503	SO:0001583	missense	5494	exon2			ATCCAGACTTGAA	S87759	CCDS9744.1, CCDS9745.1, CCDS45120.1	14q23.1	2013-01-24	2010-03-05		ENSG00000100614	ENSG00000100614	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9275	protein-coding gene	gene with protein product	"phosphatase 2C alpha", "protein phosphatase 2C, alpha isoform"	606108	"protein phosphatase 1A (formerly 2C), magnesium-dependent, alpha isoform"			1311954	Standard	NM_177952		Approved	MGC9201, PP2Calpha, PP2CA	uc001xew.4	P35813	OTTHUMG00000140333	ENST00000395076.4:c.771A>T	chr14.hg19:g.60750192A>T	ENSP00000378514:p.Arg257Ser	329.0	1.0	.		232.0	94.0	.	NM_177952	B5BU11|J3KNM0|O75551	Missense_Mutation	SNP	ENST00000395076.4	hg19	CCDS9744.1	.	.	.	.	.	.	.	.	.	.	A	17.45	3.391550	0.62066	.	.	ENSG00000100614	ENST00000325642;ENST00000529574;ENST00000395076;ENST00000325658	T;T;T;T	0.17213	2.29;2.29;2.29;2.29	5.69	0.8	0.18672	Protein phosphatase 2C-like (5);	0.000000	0.85682	D	0.000000	T	0.37732	0.1014	M	0.80982	2.52	0.80722	D	1	D;D;D	0.71674	0.985;0.998;0.985	D;D;D	0.70716	0.909;0.97;0.909	T	0.14090	-1.0485	10	0.66056	D	0.02	-4.9401	9.4876	0.38940	0.6003:0.0:0.3997:0.0	.	257;257;257	P35813;P35813-2;B2R8E4	PPM1A_HUMAN;.;.	S	330;257;257;257	ENSP00000327255:R330S;ENSP00000432966:R257S;ENSP00000378514:R257S;ENSP00000314850:R257S	ENSP00000327255:R330S	R	+	3	2	PPM1A	59819945	0.994000	0.37717	1.000000	0.80357	0.997000	0.91878	0.406000	0.21032	0.109000	0.17891	0.477000	0.44152	AGA	.	.	.	none		0.348	PPM1A-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276949.2	NM_021003		T	60750192	A	T	60750192	3	4	43	1	0	0	0	0	1	0	0	0	12345	272	10	5	996	5	PPM1A	14	60750192	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	8256156	60750192	46599348	50	3021											
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94079328	94079328	+	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	cggtcaagcgacacctgtacGtcttactcggctatgaccag	9	9	10	13	4	2	1	1	1	1	0	3	2	2	1	2	2	3	2	2	2	4	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr14:94079328G>T	ENST00000393151.2	+	27	3940	c.3940G>T	c.(3940-3942)Gtc>Ttc	p.V1314F	UNC79_ENST00000555664.1_Missense_Mutation_p.V1314F|UNC79_ENST00000553484.1_Missense_Mutation_p.V1336F|UNC79_ENST00000256339.4_Missense_Mutation_p.V1137F			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1314					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						ACACCTGTACGTCTTACTCGG	0.483																																					p.V1137F		Atlas-SNP	.											UNC79,colon,carcinoma,0,2	UNC79	366	.	0			c.G3409T						PASS	.						137	114	122					14																	94079328		2203	4300	6503	SO:0001583	missense	57578	exon27			CTGTACGTCTTAC	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.3940G>T	chr14.hg19:g.94079328G>T	ENSP00000376858:p.Val1314Phe	79.0	0.0	.		93.0	4.0	.	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	hg19		.	.	.	.	.	.	.	.	.	.	G	22.6	4.309029	0.81247	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.20332	2.12;2.09;2.08;2.12	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.36771	0.0979	N	0.25647	0.755	0.48135	D	0.99959	D	0.76494	0.999	D	0.81914	0.995	T	0.16188	-1.0411	10	0.72032	D	0.01	-20.0599	19.5316	0.95231	0.0:0.0:1.0:0.0	.	1336	C9JQL1	.	F	1137;1314;1336;1314;1336	ENSP00000256339:V1137F;ENSP00000450868:V1314F;ENSP00000451360:V1336F;ENSP00000376858:V1314F	ENSP00000256339:V1137F	V	+	1	0	KIAA1409	93149081	1.000000	0.71417	0.963000	0.40424	0.994000	0.84299	7.818000	0.86416	2.617000	0.88574	0.650000	0.86243	GTC	.	.	.	none		0.483	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		T	94079328	G	T	94079328	3	4	43	1	0	0	0	0	1	0	0	0	8237	1145	40	4	3503	4	KIAA1409	14	94079328	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08	33329136	94079328	13270212	51	3022											
UBR1	197131	hgsc.bcm.edu	37	chr15	43299483	43299483	+	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	agtcactgactgctggggtgCtaccaaaagaaatgatcaga	14	8	11	8	0	2	4	2	2	0	2	2	4	2	4	1	2	3	2	1	2	4	1			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr15:43299483C>A	ENST00000290650.4	-	30	3288		c.e30-1		UBR1_ENST00000568782.1_Splice_Site|UBR1_ENST00000382177.2_Splice_Site	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1						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)		TGCTGGGGTGCTACCAAAAGA	0.403																																					.		Atlas-SNP	.											.	UBR1	124	.	0			c.3210-1G>T						PASS	.						48	44	45					15																	43299483		2203	4299	6502	SO:0001630	splice_region_variant	197131	exon31			GGGGTGCTACCAA		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.3210-1G>T	chr15.hg19:g.43299483C>A		41.0	0.0	.		19.0	8.0	.	NM_174916	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Splice_Site	SNP	ENST00000290650.4	hg19	CCDS10091.1	.	.	.	.	.	.	.	.	.	.	C	18.11	3.550046	0.65311	.	.	ENSG00000159459	ENST00000290650	.	.	.	4.87	4.87	0.63330	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.1988	0.89831	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	UBR1	41086775	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.935000	0.56560	2.534000	0.85438	0.655000	0.94253	.	.	.	.	none		0.403	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916	Intron	A	43299483	C	A	43299483	5	1	43	1	0	0	0	0	0	0	1	0	16913	811	28	4	2112	4	UBR1	15	43299483	Splice_Site	SNP	C	TCGA-A4-7288-01A-11D-2136-08		43299483	59231909	52	3023											
PARP6	56965	hgsc.bcm.edu	37	chr15	72556908	72556908	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttcttactttttcaactgaAgacccagcccaaatccttcc	10	13	4	14	0	2	2	1	1	1	1	4	2	4	2	4	0	3	1	4	0	4	5			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr15:72556908A>G	ENST00000569795.1	-	8	1070	c.383T>C	c.(382-384)cTt>cCt	p.L128P	PARP6_ENST00000260376.7_Missense_Mutation_p.L128P|PARP6_ENST00000413097.2_5'UTR|PARP6_ENST00000287196.9_Missense_Mutation_p.L128P			Q2NL67	PARP6_HUMAN	poly (ADP-ribose) polymerase family, member 6	128							NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(8)|skin(1)|urinary_tract(1)	18						TTTCAACTGAAGACCCAGCCC	0.428																																					p.L128P		Atlas-SNP	.											.	PARP6	44	.	0			c.T383C						PASS	.						122	115	117					15																	72556908		1851	4081	5932	SO:0001583	missense	56965	exon7			AACTGAAGACCCA	AL390093	CCDS10241.2	15q22	2010-02-16			ENSG00000137817	ENSG00000137817		"Poly (ADP-ribose) polymerases"	26921	protein-coding gene	gene with protein product						15273990	Standard	XM_005254557		Approved	pART17	uc002auc.3	Q2NL67	OTTHUMG00000133443	ENST00000569795.1:c.383T>C	chr15.hg19:g.72556908A>G	ENSP00000456348:p.Leu128Pro	121.0	0.0	.		112.0	5.0	.	NM_020214	Q9H7C5|Q9H9X6|Q9HAF3|Q9NPS6|Q9UFG4	Missense_Mutation	SNP	ENST00000569795.1	hg19	CCDS10241.2	.	.	.	.	.	.	.	.	.	.	A	22.2	4.259245	0.80246	.	.	ENSG00000137817	ENST00000419739;ENST00000287196;ENST00000260376;ENST00000336471	.	.	.	5.5	5.5	0.81552	.	0.061156	0.64402	D	0.000002	T	0.40272	0.1110	N	0.14661	0.345	0.80722	D	1	P;P	0.47409	0.694;0.895	B;B	0.44278	0.346;0.445	T	0.30416	-0.9979	9	0.32370	T	0.25	-0.6581	14.7832	0.69781	1.0:0.0:0.0:0.0	.	128;128	Q0VDG0;Q2NL67	.;PARP6_HUMAN	P	128	.	ENSP00000260376:L128P	L	-	2	0	PARP6	70343962	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.265000	0.95647	2.087000	0.62958	0.460000	0.39030	CTT	.	.	.	none		0.428	PARP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257315.2	NM_020214		G	72556908	A	G	72556908	3	3	43	1	0	0	0	0	1	0	0	0	11471	72	3	3	1577	3	PARP6	15	72556908	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	29257425	72556908	29974484	53	3024											
IDH2	3418	hgsc.bcm.edu	37	chr15	90634783	90634783	+	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	ccacttcaggagggggcactAccttctccttgatgaactgc	8	10	10	13	0	2	2	1	2	1	0	3	3	2	3	3	3	3	1	3	3	2	4			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr15:90634783A>G	ENST00000330062.3	-	2	321		c.e2+1		IDH2_ENST00000539790.1_Intron|IDH2_ENST00000559482.1_Splice_Site|IDH2_ENST00000540499.2_Splice_Site	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+), mitochondrial						2-oxoglutarate metabolic process (GO:0006103)|carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)			biliary_tract(11)|bone(19)|central_nervous_system(107)|endometrium(1)|haematopoietic_and_lymphoid_tissue(953)|large_intestine(8)|lung(5)|skin(5)	1109	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)			AGGGGGCACTACCTTCTCCTT	0.577			M		GBM																																.		Atlas-SNP	.		Dom	yes		15	15q26.1	3418	"socitrate dehydrogenase 2 (NADP+), mitochondrial "		M	.	IDH2	1372	.	0			c.207+2T>C						PASS	.						169	135	146					15																	90634783		2200	4298	6498	SO:0001630	splice_region_variant	3418	exon3			GGCACTACCTTCT		CCDS10359.1	15q26.1	2014-09-17			ENSG00000182054	ENSG00000182054	1.1.1.42		5383	protein-coding gene	gene with protein product		147650					Standard	NM_001289910		Approved		uc002box.3	P48735	OTTHUMG00000149815	ENST00000330062.3:c.207+1T>C	chr15.hg19:g.90634783A>G		127.0	0.0	.		95.0	12.0	.	NM_002168	B2R6L6|B4DFL2|Q96GT3	Splice_Site	SNP	ENST00000330062.3	hg19	CCDS10359.1	.	.	.	.	.	.	.	.	.	.	A	16.24	3.066137	0.55539	.	.	ENSG00000182054	ENST00000330062;ENST00000540499	.	.	.	5.19	5.19	0.71726	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.0239	0.58804	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	IDH2	88435787	1.000000	0.71417	0.925000	0.36789	0.501000	0.33797	9.290000	0.96065	1.965000	0.57142	0.459000	0.35465	.	.	.	.	none		0.577	IDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313426.1		Intron	G	90634783	A	G	90634783	5	3	43	1	0	0	0	0	0	0	1	0	7502	405	14	3	1189	3	IDH2	15	90634783	Splice_Site	SNP	A	TCGA-A4-7288-01A-11D-2136-08	18077875	90634783	11896609	54	3025											
RAB40C	57799	hgsc.bcm.edu	37	chr16	677608	677608	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaactgctcgcggagtaacTgcaagatctcctagcgggga	11	7	13	10	3	1	2	0	0	1	2	3	4	1	4	1	3	5	3	1	3	4	2			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr16:677608T>C	ENST00000248139.3	+	6	1035	c.832T>C	c.(832-834)Tgc>Cgc	p.C278R	RAB40C_ENST00000539661.1_Missense_Mutation_p.C278R|RAB40C_ENST00000535977.1_Missense_Mutation_p.C278R|RAB40C_ENST00000538492.1_Missense_Mutation_p.C278R	NM_021168.4	NP_066991.3	Q96S21	RB40C_HUMAN	RAB40C, member RAS oncogene family	278					protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)			NS(1)|endometrium(2)|large_intestine(1)|lung(1)|prostate(1)	6		Hepatocellular(780;0.0218)				GCGGAGTAACTGCAAGATCTC	0.697																																					p.C278R	Melanoma(123;1631 1690 28262 44104 44957)	Atlas-SNP	.											.	RAB40C	32	.	0			c.T832C						PASS	.						47	51	49					16																	677608		2201	4300	6501	SO:0001583	missense	57799	exon6			AGTAACTGCAAGA	Z84779	CCDS10413.1	16p13.3	2008-07-28	2003-10-14		ENSG00000197562	ENSG00000197562		"RAB, member RAS oncogene"	18285	protein-coding gene	gene with protein product			"RAS-like, family 8, member C"	RASL8C		11697911, 18485483	Standard	NM_021168		Approved	RARL	uc021szv.1	Q96S21	OTTHUMG00000047854	ENST00000248139.3:c.832T>C	chr16.hg19:g.677608T>C	ENSP00000248139:p.Cys278Arg	111.0	0.0	.		104.0	59.0	.	NM_021168	A2IDE2|D3DU54|O60795|Q4TT41|Q5PXE8|Q6PIU5	Missense_Mutation	SNP	ENST00000248139.3	hg19	CCDS10413.1	.	.	.	.	.	.	.	.	.	.	T	19.77	3.889349	0.72524	.	.	ENSG00000197562	ENST00000535977;ENST00000539661;ENST00000538492;ENST00000248139	T;T;T;T	0.73469	-0.75;-0.75;-0.75;-0.75	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.81725	0.4883	L	0.47190	1.495	0.80722	D	1	D;D	0.89917	1.0;0.995	D;P	0.87578	0.998;0.814	D	0.83701	0.0182	10	0.87932	D	0	.	13.6194	0.62128	0.0:0.0:0.0:1.0	.	278;259	Q96S21;Q5PXE8	RB40C_HUMAN;.	R	278	ENSP00000438492:C278R;ENSP00000445050:C278R;ENSP00000438382:C278R;ENSP00000248139:C278R	ENSP00000248139:C278R	C	+	1	0	RAB40C	617609	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.918000	0.87506	1.808000	0.52836	0.459000	0.35465	TGC	.	.	.	none		0.697	RAB40C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109079.4	NM_021168		C	677608	T	C	677608	3	2	43	1	0	0	0	0	1	0	0	0	12955	1580	55	3	854	3	RAB40C	16	677608	Missense_Mutation	SNP	T	TCGA-A4-7288-01A-11D-2136-08		677608	89677145	55	3026											
HS3ST2	9956	hgsc.bcm.edu	37	chr16	22926750	22926750	+	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	agaatcgagcctcctgcctcGatgcttgggcaaatcaaaag	12	8	10	11	2	1	1	1	0	0	1	4	3	2	1	3	1	3	2	3	1	4	1			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr16:22926750G>A	ENST00000261374.3	+	2	1405	c.971G>A	c.(970-972)cGa>cAa	p.R324Q		NM_006043.1	NP_006034.1	Q9Y278	HS3S2_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 2	324					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)		CTCCTGCCTCGATGCTTGGGC	0.403																																					p.R324Q		Atlas-SNP	.											HS3ST2,brain,glioma,0,1	HS3ST2	59	.	0			c.G971A						PASS	.						135	148	143					16																	22926750		2197	4300	6497	SO:0001583	missense	9956	exon2			TGCCTCGATGCTT	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.971G>A	chr16.hg19:g.22926750G>A	ENSP00000261374:p.Arg324Gln	264.0	0.0	.		328.0	17.0	.	NM_006043	Q52LZ1	Missense_Mutation	SNP	ENST00000261374.3	hg19	CCDS10606.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.382090	0.82792	.	.	ENSG00000122254	ENST00000261374	D	0.83755	-1.76	5.11	5.11	0.69529	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	D	0.89860	0.6837	M	0.79805	2.47	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	D	0.89491	0.3757	10	0.44086	T	0.13	.	11.0723	0.48010	0.0843:0.0:0.9157:0.0	.	324	Q9Y278	HS3S2_HUMAN	Q	324	ENSP00000261374:R324Q	ENSP00000261374:R324Q	R	+	2	0	HS3ST2	22834251	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.872000	0.75536	2.375000	0.81037	0.561000	0.74099	CGA	.	.	.	none		0.403	HS3ST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211598.1	NM_006043		A	22926750	G	A	22926750	3	1	43	1	0	0	0	0	1	0	0	0	7371	1058	37	1	977	1	HS3ST2	16	22926750	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08	22249142	22926750	67428003	56	3027											
ABCC11	85320	hgsc.bcm.edu	37	chr16	48249161	48249161	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtacattttaatcagcttaAtgcaagtgagaacttcactg	13	14	7	7	0	2	1	2	1	0	1	2	2	2	1	0	0	4	3	0	0	5	5			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr16:48249161A>G	ENST00000394747.1	-	7	1395	c.1046T>C	c.(1045-1047)aTt>aCt	p.I349T	ABCC11_ENST00000537808.1_Missense_Mutation_p.I349T|ABCC11_ENST00000394748.1_Missense_Mutation_p.I349T|ABCC11_ENST00000356608.2_Missense_Mutation_p.I349T|ABCC11_ENST00000353782.5_Missense_Mutation_p.I349T	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	349	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)	AATCAGCTTAATGCAAGTGAG	0.453																																					p.I349T		Atlas-SNP	.											.	ABCC11	177	.	0			c.T1046C						PASS	.						148	144	145					16																	48249161		2201	4300	6501	SO:0001583	missense	85320	exon7			AGCTTAATGCAAG	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.1046T>C	chr16.hg19:g.48249161A>G	ENSP00000378230:p.Ile349Thr	136.0	0.0	.		139.0	42.0	.	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Missense_Mutation	SNP	ENST00000394747.1	hg19	CCDS10732.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.099866	0.76983	.	.	ENSG00000121270	ENST00000353782;ENST00000356608;ENST00000394748;ENST00000394747;ENST00000537808	D;D;D;D;D	0.92805	-3.11;-3.11;-3.11;-3.11;-3.11	5.23	5.23	0.72850	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.125360	0.53938	D	0.000060	D	0.95642	0.8583	M	0.80982	2.52	0.48632	D	0.999682	D;D	0.62365	0.979;0.991	P;D	0.72625	0.801;0.978	D	0.96028	0.9014	10	0.87932	D	0	-4.6607	12.6309	0.56657	1.0:0.0:0.0:0.0	.	349;349	Q96J66-2;Q96J66	.;ABCCB_HUMAN	T	349	ENSP00000311326:I349T;ENSP00000349017:I349T;ENSP00000378231:I349T;ENSP00000378230:I349T;ENSP00000438530:I349T	ENSP00000311326:I349T	I	-	2	0	ABCC11	46806662	1.000000	0.71417	0.599000	0.28851	0.926000	0.56050	6.131000	0.71670	1.978000	0.57642	0.528000	0.53228	ATT	.	.	.	none		0.453	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583		G	48249161	A	G	48249161	3	3	43	1	0	0	0	0	1	0	0	0	51	101	4	3	3194	3	ABCC11	16	48249161	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	25322411	48249161	42105592	57	3028											
INPP5K	51763	hgsc.bcm.edu	37	chr17	1400005	1400005	+	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	gggctgctggggaagtccgaGgttgaagagtagctgaccat	9	8	17	7	1	0	3	0	2	0	1	1	5	1	4	2	4	2	5	2	4	3	2			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr17:1400005G>C	ENST00000421807.2	-	9	1444	c.1056C>G	c.(1054-1056)acC>acG	p.T352T	INPP5K_ENST00000542125.1_Silent_p.T256T|INPP5K_ENST00000406424.4_Silent_p.T276T|INPP5K_ENST00000397335.3_Silent_p.T260T|INPP5K_ENST00000320345.6_Silent_p.T276T	NM_016532.3	NP_057616.2	Q9BT40	INP5K_HUMAN	inositol polyphosphate-5-phosphatase K	352	Required for ruffle localization.				actin cytoskeleton organization (GO:0030036)|cellular response to cAMP (GO:0071320)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hormone stimulus (GO:0032870)|cellular response to insulin stimulus (GO:0032869)|cellular response to tumor necrosis factor (GO:0071356)|dephosphorylation (GO:0016311)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inositol phosphate dephosphorylation (GO:0046855)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of dephosphorylation (GO:0035305)|negative regulation of glucose transport (GO:0010829)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of stress fiber assembly (GO:0051497)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of renal water transport (GO:2001153)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urine volume (GO:0035810)|protein targeting to plasma membrane (GO:0072661)|regulation of glycogen biosynthetic process (GO:0005979)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	inositol bisphosphate phosphatase activity (GO:0016312)|inositol trisphosphate phosphatase activity (GO:0046030)|inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|lipid phosphatase activity (GO:0042577)|phosphatidylinositol phosphate 5-phosphatase activity (GO:0034595)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:0034485)|vasopressin receptor activity (GO:0005000)			endometrium(1)|large_intestine(7)|lung(3)|skin(1)	12						GGAAGTCCGAGGTTGAAGAGT	0.567																																					p.T352T		Atlas-SNP	.											.	INPP5K	30	.	0			c.C1056G						PASS	.						141	113	123					17																	1400005		2203	4300	6503	SO:0001819	synonymous_variant	51763	exon9			GTCCGAGGTTGAA		CCDS11004.1, CCDS11005.1	17p13.3	2008-09-09			ENSG00000132376	ENSG00000132376			33882	protein-coding gene	gene with protein product	"skeletal muscle and kidney enriched inositol phosphatase"	607875				10753883, 12536145	Standard	NM_016532		Approved	SKIP	uc002fsr.3	Q9BT40	OTTHUMG00000150648	ENST00000421807.2:c.1056C>G	chr17.hg19:g.1400005G>C		135.0	0.0	.		124.0	68.0	.	NM_016532	B2R6I2|B2R750|D3DTH8|Q15733|Q9NPJ5|Q9P2R5	Silent	SNP	ENST00000421807.2	hg19	CCDS11004.1																																																																																			.	.	.	none		0.567	INPP5K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319381.4			C	1400005	G	C	1400005	2	2	43	1	0	0	0	0	0	0	0	1	7767	987	35	4		4	INPP5K	17	1400005	Silent	SNP	G	TCGA-A4-7288-01A-11D-2136-08		1400005	79795205	58	3029											
LHX1	3975	hgsc.bcm.edu	37	chr17	35297717	35297717	+	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	gtaacaagcagctctccactGgcgaggaactctacatcatc	12	8	8	13	1	3	0	1	0	2	0	5	2	3	1	1	2	5	3	1	2	4	2			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr17:35297717G>T	ENST00000254457.5	+	2	1712	c.301G>T	c.(301-303)Ggc>Tgc	p.G101C	RP11-445F12.2_ENST00000607336.1_RNA	NM_005568.3	NP_005559.2	P48742	LHX1_HUMAN	LIM homeobox 1	101	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell-cell signaling (GO:0007267)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation (GO:0021937)|cerebellum development (GO:0021549)|cervix development (GO:0060067)|comma-shaped body morphogenesis (GO:0072049)|dorsal/ventral pattern formation (GO:0009953)|ectoderm formation (GO:0001705)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|embryonic viscerocranium morphogenesis (GO:0048703)|endoderm formation (GO:0001706)|epithelium development (GO:0060429)|forebrain regionalization (GO:0021871)|gastrulation with mouth forming second (GO:0001702)|head development (GO:0060322)|horizontal cell localization (GO:0035852)|kidney development (GO:0001822)|lateral motor column neuron migration (GO:0097477)|mesonephric duct development (GO:0072177)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerulus development (GO:0072224)|metanephric part of ureteric bud development (GO:0035502)|metanephric renal vesicle morphogenesis (GO:0072283)|metanephric S-shaped body morphogenesis (GO:0072284)|motor neuron axon guidance (GO:0008045)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct elongation (GO:0035849)|nephric duct morphogenesis (GO:0072178)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|oviduct development (GO:0060066)|oviduct epithelium development (GO:0035846)|paramesonephric duct development (GO:0061205)|pattern specification process (GO:0007389)|positive regulation of anterior head development (GO:2000744)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|primitive streak formation (GO:0090009)|pronephros development (GO:0048793)|regulation of gene expression (GO:0010468)|renal vesicle morphogenesis (GO:0072077)|retina layer formation (GO:0010842)|S-shaped body morphogenesis (GO:0072050)|somite rostral/caudal axis specification (GO:0032525)|spinal cord association neuron differentiation (GO:0021527)|telencephalon development (GO:0021537)|transcription from RNA polymerase II promoter (GO:0006366)|ureteric bud development (GO:0001657)|urogenital system development (GO:0001655)|uterine epithelium development (GO:0035847)|uterus development (GO:0060065)|vagina development (GO:0060068)|ventral spinal cord development (GO:0021517)	nucleus (GO:0005634)|protein complex (GO:0043234)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	16		Breast(25;0.00607)				GCTCTCCACTGGCGAGGAACT	0.517																																					p.G101C		Atlas-SNP	.											.	LHX1	48	.	0			c.G301T						PASS	.						89	75	79					17																	35297717		2203	4300	6503	SO:0001583	missense	3975	exon2			TCCACTGGCGAGG	U14755	CCDS11316.1	17q12	2014-04-11			ENSG00000132130	ENSG00000273706		"Homeoboxes / LIM class"	6593	protein-coding gene	gene with protein product		601999				9212161	Standard	NM_005568		Approved	LIM-1, LIM1	uc002hnh.2	P48742	OTTHUMG00000188456	ENST00000254457.5:c.301G>T	chr17.hg19:g.35297717G>T	ENSP00000254457:p.Gly101Cys	60.0	0.0	.		68.0	16.0	.	NM_005568	Q3MIW0	Missense_Mutation	SNP	ENST00000254457.5	hg19	CCDS11316.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.719232	0.89205	.	.	ENSG00000132130	ENST00000254457	D	0.88664	-2.41	4.05	4.05	0.47172	Zinc finger, LIM-type (4);	0.000000	0.85682	D	0.000000	D	0.96312	0.8797	H	0.96430	3.82	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97620	1.0135	10	0.87932	D	0	.	17.5157	0.87772	0.0:0.0:1.0:0.0	.	101;101	B4DPA6;P48742	.;LHX1_HUMAN	C	101	ENSP00000254457:G101C	ENSP00000254457:G101C	G	+	1	0	LHX1	32371830	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.573000	0.98181	2.553000	0.86117	0.561000	0.74099	GGC	.	.	.	none		0.517	LHX1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256704.3	NM_005568		T	35297717	G	T	35297717	3	4	43	1	0	0	0	0	1	0	0	0	8777	1348	47	4	307	4	LHX1	17	35297717	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08	33897712	35297717	45897493	59	3030											
ACLY	47	hgsc.bcm.edu	37	chr17	40048661	40048661	+	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	ttgaagacagggatcaggatCtctttgtgcccccagtaaaa	12	10	10	9	0	2	2	1	1	1	1	3	4	2	4	2	2	1	1	2	2	3	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr17:40048661C>A	ENST00000352035.2	-	16	1771	c.1641G>T	c.(1639-1641)gaG>gaT	p.E547D	ACLY_ENST00000353196.1_Missense_Mutation_p.E537D|ACLY_ENST00000537919.1_Missense_Mutation_p.E276D|ACLY_ENST00000590151.1_Missense_Mutation_p.E547D|ACLY_ENST00000393896.2_Missense_Mutation_p.E537D	NM_001096.2	NP_001087.2	P53396	ACLY_HUMAN	ATP citrate lyase	547					ATP catabolic process (GO:0006200)|cellular carbohydrate metabolic process (GO:0044262)|cellular lipid metabolic process (GO:0044255)|citrate metabolic process (GO:0006101)|coenzyme A metabolic process (GO:0015936)|energy reserve metabolic process (GO:0006112)|lipid biosynthetic process (GO:0008610)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	citrate lyase complex (GO:0009346)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)		NTN1/ACLY(2)	breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	28		Breast(137;0.000143)				GGATCAGGATCTCTTTGTGCC	0.493																																					p.E547D	Colon(64;807 1396 15971 30971)	Atlas-SNP	.											.	ACLY	85	.	0			c.G1641T						PASS	.						128	113	118					17																	40048661		2203	4300	6503	SO:0001583	missense	47	exon16			CAGGATCTCTTTG	X64330	CCDS11412.1, CCDS11413.1	17q21.2	2010-04-27			ENSG00000131473	ENSG00000131473	2.3.3.8		115	protein-coding gene	gene with protein product	"ATP citrate synthase"	108728				1371749, 8088842	Standard	NM_001096		Approved	ATPCL, CLATP, ACL	uc002hyg.3	P53396	OTTHUMG00000133507	ENST00000352035.2:c.1641G>T	chr17.hg19:g.40048661C>A	ENSP00000253792:p.Glu547Asp	112.0	0.0	.		180.0	68.0	.	NM_001096	B4DIM0|B4E3P0|Q13037|Q9BRL0	Missense_Mutation	SNP	ENST00000352035.2	hg19	CCDS11412.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.447728	0.84101	.	.	ENSG00000131473	ENST00000352035;ENST00000401700;ENST00000353196;ENST00000537919;ENST00000393896	D;D;D;D	0.89939	-1.61;-1.62;-2.59;-1.62	5.49	4.52	0.55395	CoA-binding (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.95373	0.8498	H	0.95328	3.655	0.80722	D	1	P;D;D;D;P	0.57899	0.92;0.981;0.981;0.973;0.92	D;P;P;D;D	0.66084	0.922;0.805;0.805;0.941;0.922	D	0.95675	0.8727	10	0.72032	D	0.01	.	10.7053	0.45952	0.0:0.8307:0.0:0.1693	.	276;591;601;537;547	B4E3P0;B4DIM0;E7ENH9;G3XAI4;P53396	.;.;.;.;ACLY_HUMAN	D	547;601;537;276;537	ENSP00000253792:E547D;ENSP00000345398:E537D;ENSP00000445349:E276D;ENSP00000377474:E537D	ENSP00000253792:E547D	E	-	3	2	ACLY	37302187	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	1.474000	0.35398	1.430000	0.47334	0.561000	0.74099	GAG	.	.	.	none		0.493	ACLY-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257465.1	NM_001096		A	40048661	C	A	40048661	3	1	43	1	0	0	0	0	1	0	0	0	143	912	32	4	1720	4	ACLY	17	40048661	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	4750944	40048661	41146549	60	3031											
HDAC5	10014	hgsc.bcm.edu	37	chr17	42158172	42158172	+	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	tggaaagaagttcccgttgtCatagcgatgcagagagatgt	12	10	13	6	2	1	3	1	0	0	3	2	6	2	4	1	1	2	3	1	1	3	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr17:42158172C>A	ENST00000393622.2	-	21	3017	c.2686G>T	c.(2686-2688)Gac>Tac	p.D896Y	HDAC5_ENST00000586802.1_Missense_Mutation_p.D896Y|HDAC5_ENST00000336057.5_Missense_Mutation_p.D811Y|HDAC5_ENST00000225983.6_Missense_Mutation_p.D897Y	NM_001015053.1|NM_005474.4	NP_001015053.1|NP_005465.2	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5	896	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|chromatin silencing (GO:0006342)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|inflammatory response (GO:0006954)|multicellular organismal response to stress (GO:0033555)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|osteoblast development (GO:0002076)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression, epigenetic (GO:0040029)|regulation of myotube differentiation (GO:0010830)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|histone deacetylase complex (GO:0000118)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	21		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		TTCCCGTTGTCATAGCGATGC	0.562																																					p.D897Y		Atlas-SNP	.											.	HDAC5	67	.	0			c.G2689T						PASS	.						117	103	108					17																	42158172		2203	4300	6503	SO:0001583	missense	10014	exon21			CGTTGTCATAGCG	AF249731	CCDS32663.1, CCDS45696.1	17q21	2008-07-18					3.5.1.98		14068	protein-coding gene	gene with protein product		605315				10220385, 9610721	Standard	XM_005256905		Approved	KIAA0600, NY-CO-9, FLJ90614	uc002iff.1	Q9UQL6		ENST00000393622.2:c.2686G>T	chr17.hg19:g.42158172C>A	ENSP00000377244:p.Asp896Tyr	98.0	0.0	.		119.0	44.0	.	NM_001015053	C9JFV9|O60340|O60528|Q96DY4	Missense_Mutation	SNP	ENST00000393622.2	hg19	CCDS45696.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.376869	0.82682	.	.	ENSG00000108840	ENST00000225983;ENST00000393622;ENST00000336057	T;T;T	0.55234	0.53;0.53;0.64	4.63	4.63	0.57726	Histone deacetylase domain (2);	0.000000	0.85682	D	0.000000	T	0.80138	0.4568	H	0.94886	3.595	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.989;1.0	D	0.86300	0.1679	10	0.87932	D	0	-22.7715	16.4039	0.83651	0.0:1.0:0.0:0.0	.	811;897;896	Q9UQL6-2;Q9UQL6-3;Q9UQL6	.;.;HDAC5_HUMAN	Y	897;896;811	ENSP00000225983:D897Y;ENSP00000377244:D896Y;ENSP00000337290:D811Y	ENSP00000225983:D897Y	D	-	1	0	HDAC5	39513698	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.630000	0.83225	2.411000	0.81874	0.563000	0.77884	GAC	.	.	.	none		0.562	HDAC5-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457686.1	NM_001015053		A	42158172	C	A	42158172	3	1	43	1	0	0	0	0	1	0	0	0	7017	826	29	4	710	4	HDAC5	17	42158172	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	2109511	42158172	39037038	61	3032											
IMP5	162540	hgsc.bcm.edu	37	chr17	43922606	43922611	+	In_Frame_Del	DEL	GGCCAA	GGCCAA	-																															cgaaaggctggctggctcagGgccaaggtgcccacgggctg																										TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	GGCCAA	GGCCAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr17:43922606_43922611delGGCCAA	ENST00000329196.5	+	1	351_356	c.334_339delGGCCAA	c.(334-339)ggccaadel	p.GQ112del	MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000579244.1_RNA|MAPT-AS1_ENST00000581125.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	112	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)										GCTGGCTCAGGGCCAAGGTGCCCACG	0.68																																					p.111_113del		Atlas-INDEL	.											.	.	.	.	0			c.333_338del						PASS	.																																			SO:0001651	inframe_deletion	162540	exon1			.		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.334_339delGGCCAA	chr17.hg19:g.43922606_43922611delGGCCAA	ENSP00000332488:p.Gly112_Gln113del	105.0	0.0	0		95.0	10.0	0.105263	NM_175882	Q8TC67|Q8WVZ6	In_Frame_Del	DEL	ENST00000329196.5	hg19	CCDS32673.1																																																																																			.	.	.	none		0.68	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882		-	43922611	GGCCAA	-	43922606	7	5	43	1	0	1	0	1	0	0	0	0	7728	1232	43	0	336	0	IMP5	17	43922606	In_Frame_Del	DEL	GGCCAA	TCGA-A4-7288-01A-11D-2136-08	1764434	43922606	37272604	62	3033											
AFG3L2	10939	hgsc.bcm.edu	37	chr18	12358734	12358734	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagaaattcacaaattccaTgatctctagcttggcctcct	12	12	5	12	0	2	2	1	1	1	1	5	2	4	2	3	1	1	1	3	1	4	4			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr18:12358734T>C	ENST00000269143.3	-	8	1192	c.961A>G	c.(961-963)Atg>Gtg	p.M321V		NM_006796.2	NP_006787.2	Q9Y4W6	AFG32_HUMAN	AFG3-like AAA ATPase 2	321					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)	ACAAATTCCATGATCTCTAGC	0.383																																					p.M321V		Atlas-SNP	.											.	AFG3L2	60	.	0			c.A961G						PASS	.						86	78	80					18																	12358734		2203	4300	6503	SO:0001583	missense	10939	exon8			ATTCCATGATCTC	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.961A>G	chr18.hg19:g.12358734T>C	ENSP00000269143:p.Met321Val	74.0	0.0	.		67.0	27.0	.	NM_006796	Q6P1L0	Missense_Mutation	SNP	ENST00000269143.3	hg19	CCDS11859.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.163727	0.78226	.	.	ENSG00000141385	ENST00000269143;ENST00000537174	T	0.39787	1.06	5.76	5.76	0.90799	Peptidase M41, FtsH (2);	0.000000	0.85682	D	0.000000	T	0.45796	0.1360	L	0.42744	1.35	0.80722	D	1	P	0.45986	0.87	P	0.47251	0.542	T	0.45469	-0.9259	10	0.66056	D	0.02	.	16.0735	0.80951	0.0:0.0:0.0:1.0	.	321	Q9Y4W6	AFG32_HUMAN	V	321;336	ENSP00000269143:M321V	ENSP00000269143:M321V	M	-	1	0	AFG3L2	12348734	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.912000	0.69948	2.195000	0.70347	0.533000	0.62120	ATG	.	.	.	none		0.383	AFG3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254603.2	NM_006796		C	12358734	T	C	12358734	3	2	43	1	0	0	0	0	1	0	0	0	360	1464	51	3	1472	3	AFG3L2	18	12358734	Missense_Mutation	SNP	T	TCGA-A4-7288-01A-11D-2136-08		12358734	65718514	63	3034											
APC2	10297	hgsc.bcm.edu	37	chr19	1468067	1468067	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagctccctcagcgagccCgagccctcggagccgccggc	5	3	13	20	5	1	0	1	0	0	0	3	3	2	1	6	2	5	1	6	2	0	0			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr19:1468067C>T	ENST00000535453.1	+	14	6480	c.4767C>T	c.(4765-4767)ccC>ccT	p.P1589P	APC2_ENST00000233607.2_Silent_p.P1589P|APC2_ENST00000238483.4_Silent_p.P1315P|C19orf25_ENST00000588427.1_Intron			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)		TCAGCGAGCCCGAGCCCTCGG	0.766																																					p.P1589P		Atlas-SNP	.											.	APC2	50	.	0			c.C4767T						PASS	.						4	4	4					19																	1468067		1704	3627	5331	SO:0001819	synonymous_variant	10297	exon15			CGAGCCCGAGCCC		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.4767C>T	chr19.hg19:g.1468067C>T		20.0	0.0	.		20.0	9.0	.	NM_005883	C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	Silent	SNP	ENST00000535453.1	hg19	CCDS12068.1																																																																																			.	.	.	none		0.766	APC2-004	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449539.2	NM_005883		T	1468067	C	T	1468067	2	4	43	1	0	0	0	0	0	0	0	1	764	639	23	1		1	APC2	19	1468067	Silent	SNP	C	TCGA-A4-7288-01A-11D-2136-08		1468067	57660916	64	3035											
SF4	57794	hgsc.bcm.edu	37	chr19	19420931	19420931	+	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	ctggtctgtgccttctgcaaCttcagaaactgctgcaagaa	10	11	9	11	0	3	2	1	0	2	2	3	2	3	2	1	1	6	3	1	1	4	2			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr19:19420931C>T	ENST00000247001.5	-	3	632	c.285G>A	c.(283-285)aaG>aaA	p.K95K	SUGP1_ENST00000334782.5_Silent_p.K95K|SUGP1_ENST00000585763.1_5'UTR	NM_172231.3	NP_757386.2	Q8IWZ8	SUGP1_HUMAN	SURP and G patch domain containing 1	95					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						CCTTCTGCAACTTCAGAAACT	0.512																																					p.K95K		Atlas-SNP	.											.	SUGP1	63	.	0			c.G285A						PASS	.						149	120	130					19																	19420931		2203	4300	6503	SO:0001819	synonymous_variant	57794	exon3			CTGCAACTTCAGA	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.285G>A	chr19.hg19:g.19420931C>T		103.0	0.0	.		84.0	36.0	.	NM_172231	O60378|Q6P3X9|Q8TCQ4|Q8WWT4|Q8WWT5|Q9NTG3	Silent	SNP	ENST00000247001.5	hg19	CCDS12399.1																																																																																			.	.	.	none		0.512	SUGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460128.4	NM_021164		T	19420931	C	T	19420931	2	4	43	1	0	0	0	0	0	0	0	1	14168	564	20	2		2	SF4	19	19420931	Silent	SNP	C	TCGA-A4-7288-01A-11D-2136-08	17952864	19420931	39708052	65	3036											
ZNF347	84671	hgsc.bcm.edu	37	chr19	53643807	53643807	+	Silent	SNP	A	A	G																															taaggtttctctccagtatgAattccccgatgtcttgcaag																										TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr19:53643807A>G	ENST00000334197.7	-	5	2342	c.2274T>C	c.(2272-2274)atT>atC	p.I758I	ZNF347_ENST00000452676.2_Silent_p.I759I|ZNF347_ENST00000601469.2_Silent_p.I759I|ZNF347_ENST00000601804.1_Intron	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	758					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		CTCCAGTATGAATTCCCCGAT	0.423																																					p.I759I	Melanoma(64;205 1597 17324 45721)	Atlas-SNP	.											.	ZNF347	87	.	0			c.T2277C						PASS	.						157	152	154					19																	53643807		2203	4300	6503	SO:0001819	synonymous_variant	84671	exon5			AGTATGAATTCCC	AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"Zinc fingers, C2H2-type", "-"	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.2274T>C	chr19.hg19:g.53643807A>G		226.0	0.0	.		265.0	24.0	.	NM_001172675	B3KU77|B9EG59|G5E9N4|Q8TCN1	Silent	SNP	ENST00000334197.7	hg19	CCDS33097.1																																																																																			.	.	.	none		0.423	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		G	53643807	A	G	53643807	2	3	43	1	0	0	0	0	0	0	0	1	17873	242	9	3		3	ZNF347	19	53643807	Silent	SNP	A	TCGA-A4-7288-01A-11D-2136-08	34222876	53643807	5485176	66	3037	39	2									
ZNF347	84671	hgsc.bcm.edu	37	chr19	53643811	53643811	+	Missense_Mutation	SNP	C	C	G																															gtttctctccagtatgaattCcccgatgtcttgcaaggtgt																										TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr19:53643811C>G	ENST00000334197.7	-	5	2338	c.2270G>C	c.(2269-2271)gGa>gCa	p.G757A	ZNF347_ENST00000452676.2_Missense_Mutation_p.G758A|ZNF347_ENST00000601469.2_Missense_Mutation_p.G758A|ZNF347_ENST00000601804.1_Intron	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	757					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		AGTATGAATTCCCCGATGTCT	0.423																																					p.G758A	Melanoma(64;205 1597 17324 45721)	Atlas-SNP	.											.	ZNF347	87	.	0			c.G2273C						PASS	.						159	153	155					19																	53643811		2203	4300	6503	SO:0001583	missense	84671	exon5			TGAATTCCCCGAT	AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"Zinc fingers, C2H2-type", "-"	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.2270G>C	chr19.hg19:g.53643811C>G	ENSP00000334146:p.Gly757Ala	226.0	0.0	.		267.0	28.0	.	NM_001172675	B3KU77|B9EG59|G5E9N4|Q8TCN1	Missense_Mutation	SNP	ENST00000334197.7	hg19	CCDS33097.1	.	.	.	.	.	.	.	.	.	.	C	5.602	0.295791	0.10622	.	.	ENSG00000197937	ENST00000334197;ENST00000452676	T;T	0.16897	2.31;2.31	3.15	2.07	0.26955	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09862	0.0242	N	0.04063	-0.285	0.23739	N	0.996976	B;B	0.27068	0.167;0.0	B;B	0.32864	0.154;0.0	T	0.36138	-0.9760	9	0.72032	D	0.01	.	10.7968	0.46466	0.0:0.6301:0.3699:0.0	.	758;757	G5E9N4;Q96SE7	.;ZN347_HUMAN	A	757;758	ENSP00000334146:G757A;ENSP00000405218:G758A	ENSP00000334146:G757A	G	-	2	0	ZNF347	58335623	0.000000	0.05858	0.005000	0.12908	0.016000	0.09150	-3.284000	0.00527	0.642000	0.30620	0.650000	0.86243	GGA	.	.	.	none		0.423	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		G	53643811	C	G	53643811	3	3	43	1	0	0	0	0	1	0	0	0	17873	855	30	4	253	4	ZNF347	19	53643811	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	4	53643811	5485172	67	3038	39	2									
RBBP9	10741	hgsc.bcm.edu	37	chr20	18471080	18471080	+	Missense_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	cccccaagtctgatgtgtacGcagacactaatacaatagca	14	8	7	12	1	1	2	0	1	1	1	1	2	1	2	2	0	3	3	2	0	6	4			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr20:18471080G>A	ENST00000337227.4	-	4	368	c.293C>T	c.(292-294)gCg>gTg	p.A98V	RBBP9_ENST00000493184.1_Intron	NM_006606.2	NP_006597.2	O75884	RBBP9_HUMAN	retinoblastoma binding protein 9	98					regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|prostate(1)	9						TGATGTGTACGCAGACACTAA	0.408																																					p.A98V		Atlas-SNP	.											.	RBBP9	17	.	0			c.C293T						PASS	.						158	140	146					20																	18471080		2203	4300	6503	SO:0001583	missense	10741	exon4			GTGTACGCAGACA	AF039564	CCDS13136.1	20p11.2	2008-08-01	2001-11-28		ENSG00000089050	ENSG00000089050			9892	protein-coding gene	gene with protein product		602908	"retinoblastoma-binding protein 9"			9697699, 10449909	Standard	NM_006606		Approved	Bog	uc002wqy.3	O75884	OTTHUMG00000031972	ENST00000337227.4:c.293C>T	chr20.hg19:g.18471080G>A	ENSP00000336866:p.Ala98Val	135.0	0.0	.		111.0	39.0	.	NM_006606	D3DW31|Q5JPH9|Q9H1D8	Missense_Mutation	SNP	ENST00000337227.4	hg19	CCDS13136.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.350862	0.82132	.	.	ENSG00000089050	ENST00000337227;ENST00000339848	.	.	.	5.26	4.32	0.51571	.	0.000000	0.64402	D	0.000001	T	0.76615	0.4012	M	0.79614	2.46	0.45676	D	0.998592	D	0.89917	1.0	D	0.72625	0.978	T	0.77032	-0.2738	9	0.41790	T	0.15	-9.6629	11.6719	0.51406	0.0851:0.0:0.9149:0.0	.	98	O75884	RBBP9_HUMAN	V	98	.	ENSP00000336866:A98V	A	-	2	0	RBBP9	18419080	1.000000	0.71417	0.983000	0.44433	0.986000	0.74619	6.413000	0.73308	1.455000	0.47813	0.655000	0.94253	GCG	.	.	.	none		0.408	RBBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078175.1	NM_006606		A	18471080	G	A	18471080	3	1	43	1	0	0	0	0	1	0	0	0	13119	1087	38	1	275	1	RBBP9	20	18471080	Missense_Mutation	SNP	G	TCGA-A4-7288-01A-11D-2136-08		18471080	44554440	68	3039											
ENTPD6	955	hgsc.bcm.edu	37	chr20	25201971	25201971	+	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	gtttcagggcagaaagcaggTacggggagggttgctgcctg	8	8	18	7	1	1	1	1	0	0	1	1	2	1	2	1	5	4	6	1	5	2	3			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr20:25201971T>A	ENST00000376652.4	+	11	1208		c.e11+2		ENTPD6_ENST00000360031.2_Splice_Site|ENTPD6_ENST00000433259.2_Intron|ENTPD6_ENST00000354989.5_Splice_Site			O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6 (putative)						response to calcium ion (GO:0051592)|response to magnesium ion (GO:0032026)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity (GO:0008894)|nucleoside-triphosphatase activity (GO:0017111)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|prostate(1)|skin(1)	27						AGAAAGCAGGTACGGGGAGGG	0.582																																					.		Atlas-SNP	.											.	ENTPD6	57	.	0			c.1045+2T>A						PASS	.						87	75	79					20																	25201971		2203	4300	6503	SO:0001630	splice_region_variant	955	exon11			AGCAGGTACGGGG	AF039916	CCDS13170.1, CCDS46586.1	20p11.21	2010-06-24	2010-06-24		ENSG00000197586	ENSG00000197586			3368	protein-coding gene	gene with protein product		603160	"interleukin 6 signal transducer-2"	CD39L2, IL6ST2		9676430	Standard	NM_001247		Approved	NTPDase-6, dJ738P15.3	uc002wuj.2	O75354	OTTHUMG00000032116	ENST00000376652.4:c.1045+2T>A	chr20.hg19:g.25201971T>A		52.0	0.0	.		41.0	21.0	.	NM_001247	A6NCX6|D3DW49|Q5QPJ2|Q5QPJ5|Q7Z5B5|Q8N3H3|Q8TAS7|Q9UJD1	Splice_Site	SNP	ENST00000376652.4	hg19	CCDS13170.1	.	.	.	.	.	.	.	.	.	.	T	11.07	1.531860	0.27387	.	.	ENSG00000197586	ENST00000354989;ENST00000360031;ENST00000525986;ENST00000376641;ENST00000376652;ENST00000433417;ENST00000376666	.	.	.	5.27	5.27	0.74061	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.8578	0.57894	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ENTPD6	25149971	1.000000	0.71417	0.919000	0.36401	0.014000	0.08584	6.084000	0.71335	2.124000	0.65301	0.459000	0.35465	.	.	.	.	none		0.582	ENTPD6-020	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078414.2		Intron	A	25201971	T	A	25201971	5	1	43	1	0	0	0	0	0	0	1	0	5145	1652	57	5	1092	5	ENTPD6	20	25201971	Splice_Site	SNP	T	TCGA-A4-7288-01A-11D-2136-08	6730891	25201971	37823549	69	3040											
SGK2	10110	hgsc.bcm.edu	37	chr20	42208647	42208647	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catgtattcttcagccccatAaactgggatgacctgtacca	11	11	7	12	0	2	1	1	1	1	0	2	2	2	2	4	1	3	2	4	1	4	5			TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr20:42208647A>G	ENST00000341458.4	+	11	1284	c.1065A>G	c.(1063-1065)atA>atG	p.I355M	SGK2_ENST00000373077.1_Missense_Mutation_p.I294M|SGK2_ENST00000423407.3_Missense_Mutation_p.I295M|SGK2_ENST00000373100.1_Missense_Mutation_p.I295M|SGK2_ENST00000426287.1_Missense_Mutation_p.I321M|SGK2_ENST00000373092.3_Missense_Mutation_p.I295M	NM_016276.3	NP_057360.2	Q9HBY8	SGK2_HUMAN	serum/glucocorticoid regulated kinase 2	355	AGC-kinase C-terminal.				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)			TCAGCCCCATAAACTGGGATG	0.502																																					p.I355M		Atlas-SNP	.											.	SGK2	50	.	0			c.A1065G						PASS	.						133	118	123					20																	42208647		2203	4300	6503	SO:0001583	missense	10110	exon11			CCCCATAAACTGG	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.1065A>G	chr20.hg19:g.42208647A>G	ENSP00000340608:p.Ile355Met	131.0	0.0	.		107.0	51.0	.	NM_016276	Q52PK5|Q5H8Y6|Q5H8Z1|Q5TZR3|Q9UKG6	Missense_Mutation	SNP	ENST00000341458.4	hg19	CCDS13320.1	.	.	.	.	.	.	.	.	.	.	A	16.64	3.178740	0.57692	.	.	ENSG00000101049	ENST00000373100;ENST00000373092;ENST00000373077;ENST00000423407;ENST00000341458;ENST00000426287	T;T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;0.55;0.55	4.62	2.2	0.27929	AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.68751	0.3035	M	0.82823	2.61	0.52501	D	0.999953	D;D;D	0.89917	0.998;0.995;1.0	D;D;D	0.77557	0.986;0.972;0.99	T	0.66524	-0.5902	10	0.87932	D	0	.	6.32	0.21213	0.5364:0.3128:0.0:0.1508	.	321;355;295	Q9HBY8-3;Q9HBY8;Q9HBY8-2	.;SGK2_HUMAN;.	M	295;295;294;295;355;321	ENSP00000362192:I295M;ENSP00000362184:I295M;ENSP00000362168:I294M;ENSP00000392795:I295M;ENSP00000340608:I355M;ENSP00000412214:I321M	ENSP00000340608:I355M	I	+	3	3	SGK2	41642061	0.996000	0.38824	1.000000	0.80357	0.967000	0.64934	0.539000	0.23175	0.183000	0.20059	0.460000	0.39030	ATA	.	.	.	none		0.502	SGK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080383.1			G	42208647	A	G	42208647	3	3	43	1	0	0	0	0	1	0	0	0	14222	352	13	3	1107	3	SGK2	20	42208647	Missense_Mutation	SNP	A	TCGA-A4-7288-01A-11D-2136-08	17006676	42208647	20816873	70	3041											
LIMK2	3985	hgsc.bcm.edu	37	chr22	31655910	31655910	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaggtggtgctggcacccaTgtttgagagactctccacag	8	10	13	10	0	1	3	0	2	1	1	2	4	1	3	2	3	1	3	2	3	0	1	rs377628882		TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr22:31655910T>C	ENST00000331728.4	+	5	512	c.398T>C	c.(397-399)aTg>aCg	p.M133T	LIMK2_ENST00000340552.4_Missense_Mutation_p.M112T|LIMK2_ENST00000333611.4_Missense_Mutation_p.M112T|LIMK2_ENST00000406516.1_Missense_Mutation_p.M55T|LIMK2_ENST00000444929.2_Intron	NM_005569.3	NP_005560.1	P53671	LIMK2_HUMAN	LIM domain kinase 2	133					phosphorylation (GO:0016310)|spermatogenesis (GO:0007283)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			endometrium(7)|kidney(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(4)|skin(1)	29						CTGGCACCCATGTTTGAGAGA	0.602																																					p.M133T		Atlas-SNP	.											.	LIMK2	101	.	0			c.T398C						PASS	.	T	THR/MET,THR/MET,THR/MET	1,4405	2.1+/-5.4	0,1,2202	55	50	52		335,398,335	5.6	1	22		52	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	LIMK2	NM_001031801.1,NM_005569.3,NM_016733.2	81,81,81	0,2,6501	CC,CT,TT		0.0116,0.0227,0.0154	benign,benign,benign	112/687,133/639,112/618	31655910	2,13004	2203	4300	6503	SO:0001583	missense	3985	exon5			CACCCATGTTTGA	D45906	CCDS13891.1, CCDS13892.1, CCDS33637.1	22q12	2005-01-21			ENSG00000182541	ENSG00000182541			6614	protein-coding gene	gene with protein product		601988				8537403, 10591208	Standard	NM_005569		Approved		uc003akh.3	P53671	OTTHUMG00000151251	ENST00000331728.4:c.398T>C	chr22.hg19:g.31655910T>C	ENSP00000332687:p.Met133Thr	95.0	0.0	.		38.0	32.0	.	NM_005569	A8K6H5|Q7KZ80|Q7L3H5|Q96E10|Q99464|Q9UFU0	Missense_Mutation	SNP	ENST00000331728.4	hg19	CCDS13891.1	.	.	.	.	.	.	.	.	.	.	T	13.43	2.234384	0.39498	2.27E-4	1.16E-4	ENSG00000182541	ENST00000406516;ENST00000331728;ENST00000436394;ENST00000333611;ENST00000340552	T;T;T;T	0.73575	-0.76;-0.59;-0.64;-0.71	5.63	5.63	0.86233	.	0.039543	0.85682	D	0.000000	T	0.61862	0.2381	L	0.36672	1.1	0.80722	D	1	B;B;B;P	0.35328	0.01;0.017;0.002;0.495	B;B;B;B	0.33750	0.018;0.008;0.004;0.169	T	0.59397	-0.7462	10	0.20519	T	0.43	-31.4981	10.2918	0.43601	0.1471:0.0:0.0:0.8529	.	165;112;133;55	F5GY29;Q7L3H5;P53671;B5MC51	.;.;LIMK2_HUMAN;.	T	55;133;165;112;112	ENSP00000384602:M55T;ENSP00000332687:M133T;ENSP00000330470:M112T;ENSP00000339916:M112T	ENSP00000332687:M133T	M	+	2	0	LIMK2	29985910	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.829000	0.69316	2.144000	0.66660	0.459000	0.35465	ATG	.	.	.	weak		0.602	LIMK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321911.1	NM_016733		C	31655910	T	C	31655910	3	2	43	1	0	0	0	0	1	0	0	0	8809	1464	51	3	473	3	LIMK2	22	31655910	Missense_Mutation	SNP	T	TCGA-A4-7288-01A-11D-2136-08		31655910	19648656	71	3042											
BAIAP2L2	80115	hgsc.bcm.edu	37	chr22	38482355	38482355	+	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	ttggcacccggcttggggtgCgggagcgggactggccatcc	4	7	18	12	3	0	0	0	0	0	0	1	2	1	2	3	7	2	2	3	7	0	2	rs371997714|rs113792005|rs66500630	byFrequency	TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr22:38482355C>G	ENST00000381669.3	-	12	1505	c.1361G>C	c.(1360-1362)cGc>cCc	p.R454P	SLC16A8_ENST00000469516.1_5'Flank	NM_025045.4	NP_079321.3	Q6UXY1	BI2L2_HUMAN	BAI1-associated protein 2-like 2	454					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)			large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	8	Melanoma(58;0.045)					GCTTGGGGTGCGGGAGCGGGA	0.697																																					p.R454P		Atlas-SNP	.											.,1	BAIAP2L2	39	.	0			c.G1361C						PASS	.						17	19	18					22																	38482355		2066	3890	5956	SO:0001583	missense	80115	exon12			GGGGTGCGGGAGC	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.1361G>C	chr22.hg19:g.38482355C>G	ENSP00000371085:p.Arg454Pro	0.0	0.0	.		2.0	2.0	.	NM_025045	B0QYE2|Q96BG7	Missense_Mutation	SNP	ENST00000381669.3	hg19	CCDS43018.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.52|15.52	2.857588|2.857588	0.51376|0.51376	.|.	.|.	ENSG00000128298|ENSG00000128298	ENST00000402500|ENST00000381669;ENST00000428572	.|T	.|0.49139	.|0.79	4.42|4.42	2.26|2.26	0.28386|0.28386	.|.	.|1.035940	.|0.07692	.|U	.|0.938938	.|T	.|0.36026	.|0.0952	L|L	0.38531|0.38531	1.155|1.155	0.19300|0.19300	N|N	0.999976|0.999976	.|P	.|0.43578	.|0.811	.|B	.|0.36719	.|0.231	.|T	.|0.18650	.|-1.0330	.|10	.|0.42905	.|T	.|0.14	.|-8.7443	8.9998|8.9998	0.36074|0.36074	0.0:0.8207:0.0:0.1793|0.0:0.8207:0.0:0.1793	.|.	.|454	.|Q6UXY1	.|BI2L2_HUMAN	.|P	-1|454;145	.|ENSP00000410074:R145P	.|ENSP00000371085:R454P	.|R	-|-	.|2	.|0	BAIAP2L2|BAIAP2L2	36812301|36812301	0.028000|0.028000	0.19301|0.19301	0.834000|0.834000	0.33040|0.33040	0.620000|0.620000	0.37586|0.37586	0.644000|0.644000	0.24766|0.24766	0.846000|0.846000	0.35142|0.35142	0.462000|0.462000	0.41574|0.41574	.|CGC	.	.	.	weak		0.697	BAIAP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321727.1	NM_025045		G	38482355	C	G	38482355	3	3	43	1	0	0	0	0	1	0	0	0	1303	768	27	4	240	4	BAIAP2L2	22	38482355	Missense_Mutation	SNP	C	TCGA-A4-7288-01A-11D-2136-08	6826445	38482355	12822211	72	3043											
PLA2G6	8398	hgsc.bcm.edu	37	chr22	38536176	38536176	+	Splice_Site	DEL	G	G	-																															cactgcgttccttccaaggaGctgatgaaagaggaagggaa																										TCGA-A4-7288-01A-11D-2136-08	TCGA-A4-7288-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e5b1d55b-d7a2-4f48-bf14-67df3cf49d98	b8c7c479-4d3e-45ee-9f6c-8f3d1c372965	g.chr22:38536176delG	ENST00000332509.3	-	5	793	c.610delC	c.(610-612)ctc>tc	p.L205fs	PLA2G6_ENST00000436218.1_Splice_Site_p.S143fs|PLA2G6_ENST00000402064.1_Splice_Site_p.L205fs|PLA2G6_ENST00000335539.3_Splice_Site_p.L205fs	NM_003560.2	NP_003551.2	O60733	PLPL9_HUMAN	phospholipase A2, group VI (cytosolic, calcium-independent)	205					cardiolipin acyl-chain remodeling (GO:0035965)|cardiolipin biosynthetic process (GO:0032049)|cell death (GO:0008219)|chemotaxis (GO:0006935)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phospholipid metabolic process (GO:0006644)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of exocytosis (GO:0045921)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of vasodilation (GO:0045909)|regulation of store-operated calcium channel activity (GO:1901339)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|urinary bladder smooth muscle contraction (GO:0014832)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipase A2 activity (GO:0004623)			breast(2)|endometrium(6)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	24	Melanoma(58;0.045)				Quinacrine(DB01103)	CTTCCAAGGAGCTGATGAAAG	0.567																																					p.L204fs		Atlas-INDEL	.											.	PLA2G6	54	.	0			c.611delT						PASS	.						45	43	44					22																	38536176		2203	4300	6503	SO:0001630	splice_region_variant	8398	exon5			.	AF064594	CCDS13967.1, CCDS33645.1	22q13.1	2013-01-10			ENSG00000184381	ENSG00000184381	3.1.1.4	"Patatin-like phospholipase domain containing", "Parkinson disease", "Ankyrin repeat domain containing"	9039	protein-coding gene	gene with protein product	"neurodegeneration with brain iron accumulation 2"	603604				9417066, 16799181, 19029121	Standard	NM_001199562		Approved	iPLA2, PNPLA9, PARK14, iPLA2beta, NBIA2	uc003aux.1	O60733	OTTHUMG00000151246	ENST00000332509.3:c.610-1C>-	chr22.hg19:g.38536176delG		83.0	0.0	0		37.0	30.0	0.810811	NM_001004426	A8K597|B0QYE8|O75645|Q8N452|Q9UG29|Q9UIT0|Q9Y671	Frame_Shift_Del	DEL	ENST00000332509.3	hg19	CCDS13967.1																																																																																			.	.	.	none		0.567	PLA2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321860.1	NM_001004426	Frame_Shift_Del	-	38536176	G	-	38536176	8	5	43	1	0	1	0	1	0	0	1	0	12015	985	34	0	1862	0	PLA2G6	22	38536176	Splice_Site	DEL	G	TCGA-A4-7288-01A-11D-2136-08	53821	38536176	12768390	73	3044											
CLCA2	9635	hgsc.bcm.edu	37	chr1	86890015	86890015	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	taagttcagaactcccattcCtgggagctggagtacagctt	10	11	10	10	0	1	1	1	0	0	1	3	3	3	3	2	2	4	4	2	2	3	5			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr1:86890015C>T	ENST00000370565.4	+	1	247	c.85C>T	c.(85-87)Ctg>Ttg	p.L29L		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	29					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)		ACTCCCATTCCTGGGAGCTGG	0.443																																					p.L29L	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.C85T						PASS	.						113	103	106					1																	86890015		2203	4300	6503	SO:0001819	synonymous_variant	9635	exon1			CCATTCCTGGGAG		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.85C>T	chr1.hg19:g.86890015C>T		47.0	0.0	.		55.0	35.0	.	NM_006536	A8K2T3|Q9Y6N2	Silent	SNP	ENST00000370565.4	hg19	CCDS708.1																																																																																			.	.	.	none		0.443	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536		T	86890015	C	T	86890015	2	4	44	1	0	0	0	0	0	0	0	1	3460	680	24	2		2	CLCA2	1	86890015	Silent	SNP	C	TCGA-A4-7583-01A-11D-2136-08		86890015	162360606	1	3045											
ADAR	103	hgsc.bcm.edu	37	chr1	154574741	154574741	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttcctggaaatgtgaggaaAggcaatcaacacctctctgt	12	10	10	9	0	2	1	1	1	1	0	4	3	3	3	2	3	1	2	2	3	4	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr1:154574741A>G	ENST00000368474.4	-	2	576	c.377T>C	c.(376-378)cTt>cCt	p.L126P	ADAR_ENST00000471068.1_5'UTR|ADAR_ENST00000292205.5_Missense_Mutation_p.L169P|ADAR_ENST00000368471.3_5'UTR	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	126					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)		ATGTGAGGAAAGGCAATCAAC	0.537																																					p.L126P		Atlas-SNP	.											.	ADAR	113	.	0			c.T377C						PASS	.						63	65	64					1																	154574741		2203	4300	6503	SO:0001583	missense	103	exon2			GAGGAAAGGCAAT	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.377T>C	chr1.hg19:g.154574741A>G	ENSP00000357459:p.Leu126Pro	94.0	0.0	.		41.0	24.0	.	NM_015840	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Missense_Mutation	SNP	ENST00000368474.4	hg19	CCDS1071.1	.	.	.	.	.	.	.	.	.	.	A	14.52	2.559114	0.45590	.	.	ENSG00000160710	ENST00000292205;ENST00000368474;ENST00000529168	T;T;T	0.79749	-1.3;-1.3;-1.3	4.47	4.47	0.54385	.	0.972834	0.08506	N	0.935700	D	0.86167	0.5868	M	0.63843	1.955	0.54753	D	0.999983	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.85130	0.991;0.991;0.997	T	0.82985	-0.0185	10	0.87932	D	0	-16.02	13.8697	0.63610	1.0:0.0:0.0:0.0	.	126;126;126	P55265-3;P55265-2;P55265	.;.;DSRAD_HUMAN	P	169;126;121	ENSP00000292205:L169P;ENSP00000357459:L126P;ENSP00000431794:L121P	ENSP00000292205:L169P	L	-	2	0	ADAR	152841365	0.992000	0.36948	0.866000	0.34008	0.393000	0.30537	5.187000	0.65087	1.992000	0.58205	0.402000	0.26972	CTT	.	.	.	none		0.537	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111		G	154574741	A	G	154574741	3	3	44	1	0	0	0	0	1	0	0	0	281	72	3	3	3359	3	ADAR	1	154574741	Missense_Mutation	SNP	A	TCGA-A4-7583-01A-11D-2136-08	67684726	154574741	94675880	2	3046											
HDGF	3068	hgsc.bcm.edu	37	chr1	156715103	156715104	+	Frame_Shift_Ins	INS	-	-	A																															ctcacgtctcgtgggtcccgINSaaaaaaaagacttggtattt																										TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr1:156715103_156715104insA	ENST00000357325.5	-	2	463_464	c.149_150insT	c.(148-150)ttcfs	p.F50fs	HDGF_ENST00000368209.5_Frame_Shift_Ins_p.F43fs|HDGF_ENST00000537739.1_Frame_Shift_Ins_p.F50fs|HDGF_ENST00000465180.1_5'UTR|HDGF_ENST00000416666.2_Frame_Shift_Ins_p.F18fs|HDGF_ENST00000368206.5_Frame_Shift_Ins_p.F66fs	NM_004494.2	NP_004485.1	P51858	HDGF_HUMAN	hepatoma-derived growth factor	50	PWWP. {ECO:0000255|PROSITE- ProRule:PRU00162}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription corepressor binding (GO:0001222)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9	all_hematologic(923;0.088)|Hepatocellular(266;0.158)	Breast(1374;0.198)		Colorectal(1306;0.018)		CGTGGGTCCCGAAAAAAAAGAC	0.564																																					p.F66fs		Atlas-INDEL	.											.,2	HDGF	60	.	0			c.198_199insT						PASS	.																																			SO:0001589	frameshift_variant	3068	exon2			.	D16431	CCDS1156.1, CCDS44247.1, CCDS44248.1	1q23.1	2013-10-14	2010-03-19		ENSG00000143321	ENSG00000143321			4856	protein-coding gene	gene with protein product	"high-mobility group protein 1-like"	600339	"hepatoma-derived growth factor (high-mobility group protein 1-like)"			8833162	Standard	NM_004494		Approved	HMG1L2	uc001fpy.4	P51858	OTTHUMG00000041295	ENST00000357325.5:c.150dupT	chr1.hg19:g.156715111_156715111dupA	ENSP00000349878:p.Phe50fs	42.0	0.0	0		21.0	13.0	0.619048	NM_001126050	B3KU21|D3DVC9|Q5SZ07|Q5SZ08|Q5SZ09	Frame_Shift_Ins	INS	ENST00000357325.5	hg19	CCDS1156.1																																																																																			.	.	.	none		0.564	HDGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098946.1	NM_004494		A	156715104	-	A	156715103	7	5	44	1	0	1	1	0	0	0	0	0	7025	1049	37	0	592	0	HDGF	1	156715103	Frame_Shift_Ins	INS	-	TCGA-A4-7583-01A-11D-2136-08	2140362	156715103	92535518	3	3047											
MIA3	375056	hgsc.bcm.edu	37	chr1	222838735	222838735	+	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	ggacctgcctctccaccctcGgggatttttacctggacacg	6	10	10	15	2	1	0	0	0	1	0	3	3	1	3	5	4	2	0	5	4	1	3			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr1:222838735G>T	ENST00000344922.5	+	28	5523	c.5498G>T	c.(5497-5499)cGg>cTg	p.R1833L	MIA3_ENST00000340535.7_Missense_Mutation_p.R711L|MIA3_ENST00000344441.6_Missense_Mutation_p.R1833L|AIDA_ENST00000474863.1_5'Flank|MIA3_ENST00000344507.1_Intron	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	1833	Pro-rich.				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)		p.R1833L(1)		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)		CTCCACCCTCGGGGATTTTTA	0.517																																					p.R1833L		Atlas-SNP	.											.	MIA3	167	.	1	Substitution - Missense(1)	lung(1)	c.G5498T						PASS	.						205	206	206					1																	222838735		1896	4114	6010	SO:0001583	missense	375056	exon28			ACCCTCGGGGATT		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.5498G>T	chr1.hg19:g.222838735G>T	ENSP00000340900:p.Arg1833Leu	315.0	0.0	.		185.0	9.0	.	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Missense_Mutation	SNP	ENST00000344922.5	hg19	CCDS41470.1	.	.	.	.	.	.	.	.	.	.	G	17.85	3.489698	0.64074	.	.	ENSG00000154305	ENST00000344922;ENST00000344441;ENST00000320831;ENST00000340535;ENST00000284471	T;T;T	0.09630	3.47;3.47;2.96	5.89	5.89	0.94794	.	.	.	.	.	T	0.30324	0.0761	M	0.71581	2.175	0.44234	D	0.997072	D;D	0.57257	0.979;0.972	P;P	0.56343	0.796;0.707	T	0.00411	-1.1756	9	0.72032	D	0.01	.	19.817	0.96573	0.0:0.0:1.0:0.0	.	711;1833	Q5JRA6-4;Q5JRA6	.;MIA3_HUMAN	L	1833;1833;1774;711;711	ENSP00000340900:R1833L;ENSP00000340587:R1833L;ENSP00000345866:R711L	ENSP00000284471:R711L	R	+	2	0	MIA3	220905358	1.000000	0.71417	0.917000	0.36280	0.179000	0.23085	6.055000	0.71103	2.786000	0.95864	0.591000	0.81541	CGG	.	.	.	none		0.517	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551		T	222838735	G	T	222838735	3	4	44	1	0	0	0	0	1	0	0	0	9572	1116	39	4	5608	4	MIA3	1	222838735	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08	66123632	222838735	26411886	4	3048											
CCT7	10574	hgsc.bcm.edu	37	chr2	73471795	73471795	+	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	atgatgctcgatgatttgctGcagcttaaaatgattggaat	12	14	10	5	1	0	3	0	3	0	0	1	5	0	4	0	1	4	4	0	1	3	3			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr2:73471795G>T	ENST00000258091.5	+	6	711	c.570G>T	c.(568-570)ctG>ctT	p.L190L	CCT7_ENST00000473786.1_3'UTR|CCT7_ENST00000540468.1_Silent_p.L103L|CCT7_ENST00000398422.2_Intron|CCT7_ENST00000538797.1_Silent_p.L62L|CCT7_ENST00000537131.1_Silent_p.L90L|CCT7_ENST00000539919.1_Silent_p.L146L	NM_006429.3	NP_006420.1	Q99832	TCPH_HUMAN	chaperonin containing TCP1, subunit 7 (eta)	190					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			breast(1)|cervix(1)|endometrium(1)|lung(3)|stomach(1)	7						ATGATTTGCTGCAGCTTAAAA	0.498																																					p.L190L		Atlas-SNP	.											.	CCT7	60	.	0			c.G570T						PASS	.						64	63	63					2																	73471795		2046	4197	6243	SO:0001819	synonymous_variant	10574	exon6			TTTGCTGCAGCTT	AF026292	CCDS42696.1, CCDS46336.1, CCDS54366.1, CCDS54367.1	2p13.2	2011-09-02			ENSG00000135624	ENSG00000135624		"Heat Shock Proteins / Chaperonins"	1622	protein-coding gene	gene with protein product		605140				9819444	Standard	NM_006429		Approved	Ccth, Nip7-1	uc002siz.3	Q99832	OTTHUMG00000152765	ENST00000258091.5:c.570G>T	chr2.hg19:g.73471795G>T		39.0	0.0	.		38.0	12.0	.	NM_006429	A8K7E6|A8MWI8|B7WNW9|B7Z4T9|B7Z4Z7|O14871|Q6FI26	Silent	SNP	ENST00000258091.5	hg19	CCDS46336.1																																																																																			.	.	.	none		0.498	CCT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327714.2			T	73471795	G	T	73471795	2	4	44	1	0	0	0	0	0	0	0	1	2961	1306	46	4		4	CCT7	2	73471795	Silent	SNP	G	TCGA-A4-7583-01A-11D-2136-08		73471795	169727578	5	3049											
GORASP2	26003	hgsc.bcm.edu	37	chr2	171806790	171806790	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tataattggagcagatacagTcatgaatgaggtaattcgtg	14	12	11	4	1	1	3	1	2	0	1	2	4	1	4	0	2	2	2	0	2	5	6			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr2:171806790T>C	ENST00000234160.4	+	4	1240	c.425T>C	c.(424-426)gTc>gCc	p.V142A	GORASP2_ENST00000452526.2_Missense_Mutation_p.V154A|GORASP2_ENST00000493692.1_3'UTR	NM_001201428.1|NM_015530.4	NP_001188357.1|NP_056345.3	Q9H8Y8	GORS2_HUMAN	golgi reassembly stacking protein 2, 55kDa	142					mitotic cell cycle (GO:0000278)|organelle organization (GO:0006996)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	14						GCAGATACAGTCATGAATGAG	0.368																																					p.V142A		Atlas-SNP	.											.	GORASP2	40	.	0			c.T425C						PASS	.						72	73	73					2																	171806790		2203	4300	6503	SO:0001583	missense	26003	exon4			ATACAGTCATGAA		CCDS33325.1	2q31.1	2012-09-20	2002-08-29		ENSG00000115806	ENSG00000115806			17500	protein-coding gene	gene with protein product		608693	"golgi reassembly stacking protein 2, 55 kDa"			10487747	Standard	NM_015530		Approved	GRASP55, GRS2, GOLPH6	uc002ugj.3	Q9H8Y8	OTTHUMG00000154072	ENST00000234160.4:c.425T>C	chr2.hg19:g.171806790T>C	ENSP00000234160:p.Val142Ala	29.0	0.0	.		76.0	32.0	.	NM_015530	B4DKT0|Q53TE3|Q96I74|Q96K84|Q9H946|Q9UFW4	Missense_Mutation	SNP	ENST00000234160.4	hg19	CCDS33325.1	.	.	.	.	.	.	.	.	.	.	T	18.25	3.583219	0.65992	.	.	ENSG00000115806	ENST00000234160;ENST00000452526	T;T	0.31247	1.5;1.5	5.95	5.95	0.96441	PDZ/DHR/GLGF (1);	0.116778	0.64402	D	0.000018	T	0.44201	0.1282	M	0.73753	2.245	0.58432	D	0.999992	B;B;B	0.23591	0.045;0.088;0.035	B;B;B	0.36845	0.107;0.168;0.234	T	0.35201	-0.9798	10	0.45353	T	0.12	-6.4014	16.4069	0.83677	0.0:0.0:0.0:1.0	.	98;154;142	B4DNR1;B4DKT0;Q9H8Y8	.;.;GORS2_HUMAN	A	142;154	ENSP00000234160:V142A;ENSP00000410208:V154A	ENSP00000234160:V142A	V	+	2	0	GORASP2	171515036	1.000000	0.71417	0.995000	0.50966	0.997000	0.91878	4.174000	0.58256	2.272000	0.75746	0.460000	0.39030	GTC	.	.	.	none		0.368	GORASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333719.2			C	171806790	T	C	171806790	3	2	44	1	0	0	0	0	1	0	0	0	6583	1667	58	3	439	3	GORASP2	2	171806790	Missense_Mutation	SNP	T	TCGA-A4-7583-01A-11D-2136-08	98334995	171806790	71392583	6	3050											
TTN	7273	hgsc.bcm.edu	37	chr2	179411556	179411556	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccacaaccttgctgcctccAtcatacgctggggcagacca	9	7	8	17	1	1	1	1	0	0	1	2	1	2	1	5	2	4	3	5	2	2	2			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr2:179411556A>G	ENST00000591111.1	-	291	89900	c.89676T>C	c.(89674-89676)gaT>gaC	p.D29892D	TTN_ENST00000342175.6_Silent_p.D22660D|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.D22593D|TTN_ENST00000460472.2_Silent_p.D22468D|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000589042.1_Silent_p.D31533D|TTN_ENST00000342992.6_Silent_p.D28965D|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590807.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA			Q8WZ42	TITIN_HUMAN	titin	29892	Fibronectin type-III 118. {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)			TGCTGCCTCCATCATACGCTG	0.498																																					p.D31533D		Atlas-SNP	.											.	TTN	18412	.	0			c.T94599C						PASS	.						60	61	61					2																	179411556		2069	4216	6285	SO:0001819	synonymous_variant	7273	exon341			GCCTCCATCATAC	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.89676T>C	chr2.hg19:g.179411556A>G		17.0	0.0	.		44.0	22.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.	.	none		0.498	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179411556	A	G	179411556	2	3	44	1	0	0	0	0	0	0	0	1	16747	214	8	3		3	TTN	2	179411556	Silent	SNP	A	TCGA-A4-7583-01A-11D-2136-08	7604766	179411556	63787817	7	3051											
SF3B1	23451	hgsc.bcm.edu	37	chr2	198269882	198269882	+	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	tttgctcttctggactaagtGttgattcatcaacatcaacc	10	15	6	10	0	5	1	3	1	2	0	5	2	5	2	1	1	3	2	1	1	3	5			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr2:198269882G>C	ENST00000335508.6	-	11	1548	c.1457C>G	c.(1456-1458)aCa>aGa	p.T486R	SF3B1_ENST00000462613.1_5'Flank|SNORA4_ENST00000365564.1_RNA	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	486	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)			TGGACTAAGTGTTGATTCATC	0.289			Mis		myelodysplastic syndrome																																p.T486R		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1	1038	.	0			c.C1457G						PASS	.						51	54	53					2																	198269882		2201	4295	6496	SO:0001583	missense	23451	exon11			CTAAGTGTTGATT	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.1457C>G	chr2.hg19:g.198269882G>C	ENSP00000335321:p.Thr486Arg	29.0	0.0	.		42.0	4.0	.	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	hg19	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	G	15.77	2.931911	0.52866	.	.	ENSG00000115524	ENST00000335508	.	.	.	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.53334	0.1790	L	0.27053	0.805	0.80722	D	1	B	0.23806	0.091	B	0.23275	0.045	T	0.44817	-0.9303	9	0.35671	T	0.21	.	19.9254	0.97100	0.0:0.0:1.0:0.0	.	486	O75533	SF3B1_HUMAN	R	486	.	ENSP00000335321:T486R	T	-	2	0	SF3B1	197978127	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.721000	0.98766	2.710000	0.92621	0.655000	0.94253	ACA	.	.	.	none		0.289	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			C	198269882	G	C	198269882	3	2	44	1	0	0	0	0	1	0	0	0	14162	1377	48	4	2517	4	SF3B1	2	198269882	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08	18858326	198269882	44929491	8	3052											
SATB2	23314	hgsc.bcm.edu	37	chr2	200193570	200193570	+	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	ctgcatggccctcaggtttaCtagaagagactgagaggctg	10	9	13	9	0	1	3	1	1	0	3	1	5	1	3	1	3	2	3	1	3	3	3			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr2:200193570C>A	ENST00000417098.1	-	8	2053	c.1237G>T	c.(1237-1239)Gta>Tta	p.V413L	RP11-486F17.1_ENST00000489557.2_RNA|SATB2_ENST00000428695.1_Missense_Mutation_p.V295L|SATB2_ENST00000443023.1_Missense_Mutation_p.V354L|SATB2_ENST00000260926.5_Missense_Mutation_p.V413L|SATB2_ENST00000457245.1_Missense_Mutation_p.V413L	NM_001172509.1	NP_001165980.1	Q9UPW6	SATB2_HUMAN	SATB homeobox 2	413					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						CTCAGGTTTACTAGAAGAGAC	0.488																																					p.V413L	Colon(30;262 767 11040 24421 36230)	Atlas-SNP	.											.	SATB2	134	.	0			c.G1237T						PASS	.						93	87	89					2																	200193570		2203	4300	6503	SO:0001583	missense	23314	exon9			GGTTTACTAGAAG	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.1237G>T	chr2.hg19:g.200193570C>A	ENSP00000401112:p.Val413Leu	16.0	0.0	.		46.0	11.0	.	NM_015265	A8K5Z8|Q3ZB87|Q4V763	Missense_Mutation	SNP	ENST00000417098.1	hg19	CCDS2327.1	.	.	.	.	.	.	.	.	.	.	C	31	5.081487	0.94050	.	.	ENSG00000119042	ENST00000417098;ENST00000443023;ENST00000260926;ENST00000428695;ENST00000457245	T;T;T;T;T	0.54675	0.58;0.59;0.58;0.56;0.58	4.98	4.98	0.66077	Homeodomain protein CUT (2);Lambda repressor-like, DNA-binding (2);	0.000000	0.85682	D	0.000000	T	0.71273	0.3320	M	0.63428	1.95	0.80722	D	1	D;D	0.69078	0.997;0.996	D;D	0.87578	0.992;0.998	T	0.73030	-0.4111	10	0.66056	D	0.02	-10.9637	18.8143	0.92071	0.0:1.0:0.0:0.0	.	295;413	Q3ZB87;Q9UPW6	.;SATB2_HUMAN	L	413;354;413;295;413	ENSP00000401112:V413L;ENSP00000388764:V354L;ENSP00000260926:V413L;ENSP00000388581:V295L;ENSP00000405420:V413L	ENSP00000260926:V413L	V	-	1	0	SATB2	199901815	1.000000	0.71417	0.995000	0.50966	0.983000	0.72400	7.609000	0.82925	2.747000	0.94245	0.650000	0.86243	GTA	.	.	.	none		0.488	SATB2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256140.1	NM_015265		A	200193570	C	A	200193570	3	1	44	1	0	0	0	0	1	0	0	0	13867	565	20	4	980	4	SATB2	2	200193570	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08	1923688	200193570	43005803	9	3053											
NOP58	51602	hgsc.bcm.edu	37	chr2	203155146	203155146	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttaggaaaaattatttcagaTaatttaacatactgcaagtg	17	14	6	4	0	1	1	1	0	0	1	1	2	1	2	0	1	3	1	0	1	8	7			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr2:203155146T>C	ENST00000264279.5	+	7	826	c.600T>C	c.(598-600)gaT>gaC	p.D200D	SNORD11_ENST00000459124.1_RNA|SNORD11B_ENST00000607707.1_RNA	NM_015934.3	NP_057018.1	Q9Y2X3	NOP58_HUMAN	NOP58 ribonucleoprotein	200					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)			breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|lung(4)|prostate(2)	16						TTATTTCAGATAATTTAACAT	0.323																																					p.D200D		Atlas-SNP	.											.	NOP58	41	.	0			c.T600C						PASS	.						92	98	96					2																	203155146		2203	4299	6502	SO:0001819	synonymous_variant	51602	exon7			TTCAGATAATTTA		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.600T>C	chr2.hg19:g.203155146T>C		58.0	0.0	.		76.0	31.0	.	NM_015934	Q53SA4|Q6PK08|Q9P036|Q9UFN3	Silent	SNP	ENST00000264279.5	hg19	CCDS2353.1																																																																																			.	.	.	none		0.323	NOP58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256313.2	NM_015934		C	203155146	T	C	203155146	2	2	44	1	0	0	0	0	0	0	0	1	10547	1403	49	3		3	NOP58	2	203155146	Silent	SNP	T	TCGA-A4-7583-01A-11D-2136-08	2961576	203155146	40044227	10	3054											
CYP27A1	1593	hgsc.bcm.edu	37	chr2	219677361	219677361	+	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	tgaccttcgtcagatccatcGggttaatgttccagaactca	10	12	8	11	2	2	3	2	1	0	2	6	3	4	3	3	1	1	2	3	1	2	3			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr2:219677361G>T	ENST00000258415.4	+	4	1160	c.733G>T	c.(733-735)Ggg>Tgg	p.G245W		NM_000784.3	NP_000775.1	Q02318	CP27A_HUMAN	cytochrome P450, family 27, subfamily A, polypeptide 1	245					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)	CAGATCCATCGGGTTAATGTT	0.542																																					p.G245W		Atlas-SNP	.											CYP27A1,NS,malignant_melanoma,-1,1	CYP27A1	52	.	0			c.G733T						PASS	.						293	279	283					2																	219677361		2203	4300	6503	SO:0001583	missense	1593	exon4			TCCATCGGGTTAA	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.733G>T	chr2.hg19:g.219677361G>T	ENSP00000258415:p.Gly245Trp	528.0	1.0	.		328.0	15.0	.	NM_000784	A8K303|Q6LDB4|Q86YQ6	Missense_Mutation	SNP	ENST00000258415.4	hg19	CCDS2423.1	.	.	.	.	.	.	.	.	.	.	G	12.80	2.046552	0.36085	.	.	ENSG00000135929	ENST00000258415;ENST00000411688	T;T	0.68624	-0.34;-0.34	6.15	5.26	0.73747	.	0.687740	0.15167	N	0.276843	T	0.80747	0.4682	M	0.80616	2.505	0.09310	N	1	D	0.76494	0.999	D	0.73708	0.981	T	0.71686	-0.4518	10	0.59425	D	0.04	-13.3933	9.5132	0.39089	0.0802:0.1812:0.7386:0.0	.	245	Q02318	CP27A_HUMAN	W	245;151	ENSP00000258415:G245W;ENSP00000392671:G151W	ENSP00000258415:G245W	G	+	1	0	CYP27A1	219385605	0.163000	0.22920	0.017000	0.16124	0.140000	0.21249	2.817000	0.48034	1.510000	0.48803	0.643000	0.83706	GGG	.	.	.	none		0.542	CYP27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109734.4			T	219677361	G	T	219677361	3	4	44	1	0	0	0	0	1	0	0	0	4160	1116	39	4	747	4	CYP27A1	2	219677361	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08	16522215	219677361	23522012	11	3055											
MLH1	4292	hgsc.bcm.edu	37	chr3	37067255	37067255	+	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	gatggttcgtacagattcccGggaacagaagcttgatgcat	11	10	12	8	2	0	3	0	1	0	2	2	5	1	4	1	2	4	4	1	2	3	4	rs63750361	byFrequency	TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr3:37067255G>T	ENST00000231790.2	+	12	1382	c.1166G>T	c.(1165-1167)cGg>cTg	p.R389L	MLH1_ENST00000458205.2_Missense_Mutation_p.R148L|MLH1_ENST00000455445.2_Missense_Mutation_p.R148L|MLH1_ENST00000539477.1_Missense_Mutation_p.R148L|MLH1_ENST00000536378.1_Missense_Mutation_p.R148L|MLH1_ENST00000435176.1_Missense_Mutation_p.R291L	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	389					ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.0?(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						ACAGATTCCCGGGAACAGAAG	0.493		1	"D, Mis, N, F, S"		"colorectal, endometrial, ovarian, CNS"	"colorectal, endometrial, ovarian, CNS"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.R389L		Atlas-SNP	.	yes	Rec	yes	"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	3	3p21.3	4292	E.coli MutL homolog gene		"E, O"	.	MLH1	226	.	1	Whole gene deletion(1)	ovary(1)	c.G1166T	GRCh37	CM076299	MLH1	M	rs63750361	PASS	.						108	108	108					3																	37067255		2203	4300	6503	SO:0001583	missense	4292	exon12	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	ATTCCCGGGAACA	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.1166G>T	chr3.hg19:g.37067255G>T	ENSP00000231790:p.Arg389Leu	206.0	0.0	.		186.0	12.0	.	NM_000249	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	hg19	CCDS2663.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.26|19.26	3.792596|3.792596	0.70452|0.70452	.|.	.|.	ENSG00000076242|ENSG00000076242	ENST00000456676|ENST00000231790;ENST00000383761;ENST00000458205;ENST00000539477;ENST00000455445;ENST00000435176;ENST00000536378	.|D;D;D;D;D;D	.|0.90133	.|-2.62;-2.62;-2.62;-2.62;-2.62;-2.62	5.67|5.67	5.67|5.67	0.87782|0.87782	.|.	.|0.066158	.|0.64402	.|D	.|0.000013	D|D	0.89227|0.89227	0.6655|0.6655	L|L	0.49350|0.49350	1.555|1.555	0.80722|0.80722	D|D	1|1	.|B;B;P;P;B;B	.|0.38565	.|0.114;0.065;0.511;0.637;0.052;0.052	.|B;B;B;B;B;B	.|0.38020	.|0.046;0.068;0.254;0.263;0.04;0.04	D|D	0.88671|0.88671	0.3195|0.3195	5|10	.|0.46703	.|T	.|0.11	-17.9936|-17.9936	19.7664|19.7664	0.96346|0.96346	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|291;291;148;148;389;389	.|E9PCU2;B4DQ11;B7Z821;B4DI13;Q53GX1;P40692	.|.;.;.;.;.;MLH1_HUMAN	W|L	381|389;253;148;148;148;291;148	.|ENSP00000231790:R389L;ENSP00000402667:R148L;ENSP00000443665:R148L;ENSP00000398272:R148L;ENSP00000402564:R291L;ENSP00000444286:R148L	.|ENSP00000231790:R389L	G|R	+|+	1|2	0|0	MLH1|MLH1	37042259|37042259	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.985000|0.985000	0.73830|0.73830	7.058000|7.058000	0.76676|0.76676	2.671000|2.671000	0.90904|0.90904	0.557000|0.557000	0.71058|0.71058	GGG|CGG	.	G|1.000;A|0.000	.	alt		0.493	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249		T	37067255	G	T	37067255	3	4	44	1	0	0	0	0	1	0	0	0	9624	1116	39	4	1212	4	MLH1	3	37067255	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08		37067255	160955175	12	3056											
PBRM1	55193	hgsc.bcm.edu	37	chr3	52588791	52588791	+	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	acctggcggaagatggtgggGtggaggccccccagggtgaa	8	5	19	9	1	0	2	0	1	0	1	0	4	0	4	4	8	0	0	4	8	2	0			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr3:52588791G>T	ENST00000296302.7	-	27	4559	c.4558C>A	c.(4558-4560)Ccc>Acc	p.P1520T	PBRM1_ENST00000410007.1_Missense_Mutation_p.P1440T|SMIM4_ENST00000476842.1_Intron|PBRM1_ENST00000356770.4_Missense_Mutation_p.P1433T|PBRM1_ENST00000409114.3_Intron|RNU6-856P_ENST00000516959.1_RNA|PBRM1_ENST00000337303.4_Intron|PBRM1_ENST00000409767.1_Intron|PBRM1_ENST00000409057.1_Missense_Mutation_p.P1465T|PBRM1_ENST00000394830.3_Missense_Mutation_p.P1413T			Q86U86	PB1_HUMAN	polybromo 1	1520	Pro-rich.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		AGATGGTGGGGTGGAGGCCCC	0.582			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.P1413T		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.C4237A						PASS	.						46	46	46					3																	52588791		2203	4300	6503	SO:0001583	missense	55193	exon27			GGTGGGGTGGAGG	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.4558C>A	chr3.hg19:g.52588791G>T	ENSP00000296302:p.Pro1520Thr	47.0	0.0	.		39.0	19.0	.	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Missense_Mutation	SNP	ENST00000296302.7	hg19		.	.	.	.	.	.	.	.	.	.	G	15.23	2.771379	0.49680	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000409057;ENST00000410007	T;T;T;T;T	0.34859	1.35;1.34;1.39;1.35;1.35	5.75	5.75	0.90469	.	0.192124	0.47455	D	0.000227	T	0.21761	0.0524	N	0.08118	0	0.80722	D	1	B;B;B;B;B	0.32829	0.386;0.386;0.386;0.267;0.386	B;B;B;B;B	0.31101	0.124;0.124;0.124;0.058;0.086	T	0.08411	-1.0723	10	0.22706	T	0.39	-8.6684	18.1254	0.89584	0.0:0.0:1.0:0.0	.	1440;1413;1465;1520;1433	Q86U86-9;Q86U86-4;Q86U86-2;Q86U86;Q86U86-3	.;.;.;PB1_HUMAN;.	T	1433;1413;1520;1465;1440	ENSP00000349213:P1433T;ENSP00000378307:P1413T;ENSP00000296302:P1520T;ENSP00000386593:P1465T;ENSP00000386529:P1440T	ENSP00000296302:P1520T	P	-	1	0	PBRM1	52563831	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.959000	0.63666	2.696000	0.92011	0.655000	0.94253	CCC	.	.	.	none		0.582	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		T	52588791	G	T	52588791	3	4	44	1	0	0	0	0	1	0	0	0	11498	1261	44	4	527	4	PBRM1	3	52588791	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08	15521536	52588791	145433639	13	3057											
CLDN18	51208	hgsc.bcm.edu	37	chr3	137742626	137742626	+	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	ggaggactctgccaaagccaAcatgacactgacctccggga	12	5	11	13	1	1	2	0	2	1	0	2	5	2	5	4	3	3	0	4	3	2	0			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr3:137742626A>T	ENST00000183605.5	+	2	573	c.347A>T	c.(346-348)aAc>aTc	p.N116I	CLDN18_ENST00000343735.4_Missense_Mutation_p.N116I	NM_016369.3	NP_057453.1	P56856	CLD18_HUMAN	claudin 18	116					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(1)|large_intestine(2)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	6						GCCAAAGCCAACATGACACTG	0.502																																					p.N116I		Atlas-SNP	.											.	CLDN18	33	.	0			c.A347T						PASS	.						105	85	92					3																	137742626		2203	4300	6503	SO:0001583	missense	51208	exon2			AAGCCAACATGAC	AF221069, AY102073	CCDS3095.1, CCDS33862.1	3q	2008-08-27			ENSG00000066405	ENSG00000066405		"Claudins"	2039	protein-coding gene	gene with protein product		609210	"surfactant associated protein J"	SFTPJ			Standard	NM_001002026		Approved		uc003ero.1	P56856	OTTHUMG00000159762	ENST00000183605.5:c.347A>T	chr3.hg19:g.137742626A>T	ENSP00000183605:p.Asn116Ile	89.0	0.0	.		68.0	22.0	.	NM_016369	A5PL21|Q96PH4	Missense_Mutation	SNP	ENST00000183605.5	hg19	CCDS3095.1	.	.	.	.	.	.	.	.	.	.	A	15.24	2.774666	0.49786	.	.	ENSG00000066405	ENST00000343735;ENST00000183605;ENST00000536138	D;D	0.85773	-1.98;-2.03	5.43	4.25	0.50352	.	0.400442	0.26013	N	0.026870	T	0.79684	0.4488	L	0.31065	0.9	0.36035	D	0.839645	P;P	0.38250	0.487;0.624	B;B	0.41332	0.285;0.354	T	0.81972	-0.0688	10	0.48119	T	0.1	.	12.5759	0.56363	0.861:0.139:0.0:0.0	.	116;116	P56856;P56856-2	CLD18_HUMAN;.	I	116;116;105	ENSP00000340939:N116I;ENSP00000183605:N116I	ENSP00000183605:N116I	N	+	2	0	CLDN18	139225316	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.836000	0.55813	0.878000	0.35920	0.528000	0.53228	AAC	.	.	.	none		0.502	CLDN18-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357199.2	NM_001002026		T	137742626	A	T	137742626	3	4	44	1	0	0	0	0	1	0	0	0	3481	43	2	5	577	5	CLDN18	3	137742626	Missense_Mutation	SNP	A	TCGA-A4-7583-01A-11D-2136-08	85153835	137742626	60279804	14	3058											
FNDC3B	64778	hgsc.bcm.edu	37	chr3	171965496	171965496	+	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	gcttactacccacctgttacCggacctggagatatgccgcc	8	9	9	15	2	0	1	0	0	0	1	0	3	0	2	6	2	4	2	6	2	4	4	rs139712731		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr3:171965496C>A	ENST00000336824.4	+	5	537	c.438C>A	c.(436-438)acC>acA	p.T146T	FNDC3B_ENST00000416957.1_Silent_p.T146T|FNDC3B_ENST00000415807.2_Silent_p.T146T	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	146					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)		CACCTGTTACCGGACCTGGAG	0.502																																					p.T146T		Atlas-SNP	.											.	FNDC3B	118	.	0			c.C438A						PASS	.						208	182	191					3																	171965496		2203	4300	6503	SO:0001819	synonymous_variant	64778	exon5			TGTTACCGGACCT	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.438C>A	chr3.hg19:g.171965496C>A		168.0	0.0	.		145.0	8.0	.	NM_001135095	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Silent	SNP	ENST00000336824.4	hg19	CCDS3217.1																																																																																			.	C|0.999;T|0.001	.	alt		0.502	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763		A	171965496	C	A	171965496	2	1	44	1	0	0	0	0	0	0	0	1	5977	639	23	4		4	FNDC3B	3	171965496	Silent	SNP	C	TCGA-A4-7583-01A-11D-2136-08	34222870	171965496	26056934	15	3059											
TMEM41A	90407	hgsc.bcm.edu	37	chr3	185209397	185209397	+	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	tgcagatgtttctgactaaaTtttttaatgagggttccagg	10	16	10	5	0	1	3	0	2	1	1	2	3	2	3	1	2	1	3	1	2	3	6			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr3:185209397T>A	ENST00000421852.1	-	5	818	c.723A>T	c.(721-723)aaA>aaT	p.K241N	TMEM41A_ENST00000475480.1_Intron|TMEM41A_ENST00000296254.3_3'UTR	NM_080652.3	NP_542383.1	Q96HV5	TM41A_HUMAN	transmembrane protein 41A	241						integral component of membrane (GO:0016021)				large_intestine(1)|lung(2)|skin(1)	4	all_cancers(143;7.78e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			TCTGACTAAATTTTTTAATGA	0.408																																					p.K241N		Atlas-SNP	.											.,1	TMEM41A	18	.	0			c.A723T						PASS	.						115	114	115					3																	185209397		2203	4300	6503	SO:0001583	missense	90407	exon5			ACTAAATTTTTTA	BC019884	CCDS3271.1	3q27.2	2006-04-12			ENSG00000163900	ENSG00000163900			30544	protein-coding gene	gene with protein product						12975309	Standard	NM_080652		Approved	MGC15397	uc003fpj.2	Q96HV5	OTTHUMG00000156660	ENST00000421852.1:c.723A>T	chr3.hg19:g.185209397T>A	ENSP00000406885:p.Lys241Asn	75.0	0.0	.		95.0	41.0	.	NM_080652	A8K4B3|D3DNU2|Q6ZMJ0	Missense_Mutation	SNP	ENST00000421852.1	hg19	CCDS3271.1	.	.	.	.	.	.	.	.	.	.	T	14.08	2.427515	0.43122	.	.	ENSG00000163900	ENST00000421852	.	.	.	6.08	-4.0	0.04057	.	0.341077	0.31772	N	0.007083	T	0.54078	0.1836	M	0.76574	2.34	0.80722	D	1	B	0.14805	0.011	B	0.17433	0.018	T	0.42916	-0.9423	9	0.29301	T	0.29	-18.9262	10.7523	0.46216	0.0:0.4413:0.0938:0.4649	.	241	Q96HV5	TM41A_HUMAN	N	241	.	ENSP00000406885:K241N	K	-	3	2	TMEM41A	186692091	0.000000	0.05858	0.846000	0.33378	0.988000	0.76386	-1.837000	0.01689	-0.284000	0.09102	0.533000	0.62120	AAA	.	.	.	none		0.408	TMEM41A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345174.1	NM_080652		A	185209397	T	A	185209397	3	1	44	1	0	0	0	0	1	0	0	0	16176	1490	52	5	75	5	TMEM41A	3	185209397	Missense_Mutation	SNP	T	TCGA-A4-7583-01A-11D-2136-08	13243901	185209397	12813033	16	3060											
FGFR3	2261	hgsc.bcm.edu	37	chr4	1806088	1806088	+	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	ctggtggaggctgacgaggcGggcagtgtgtatgcaggcat	7	8	19	7	2	0	1	0	1	0	0	0	3	0	2	0	6	1	5	0	6	1	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr4:1806088G>T	ENST00000260795.2	+	8	1209	c.1107G>T	c.(1105-1107)gcG>gcT	p.A369A	FGFR3_ENST00000340107.4_Silent_p.A371A|FGFR3_ENST00000481110.2_Silent_p.A369A|FGFR3_ENST00000440486.2_Silent_p.A369A|FGFR3_ENST00000352904.1_Intron|FGFR3_ENST00000412135.2_Intron			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	369					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)	p.A369A(6)|p.A369_G370>VC(1)		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)	CTGACGAGGCGGGCAGTGTGT	0.692		1	"Mis, T"	"IGH@, ETV6"	"bladder, MM, T-cell lymphoma"		"Hypochondroplasia, Thanatophoric dysplasia"		Saethre-Chotzen syndrome;Muenke syndrome																												p.A371A		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"L, E"	FGFR3,bladder,carcinoma,0,6	FGFR3	3320	.	7	Substitution - coding silent(6)|Complex - compound substitution(1)	urinary_tract(7)	c.G1113T						PASS	.						129	125	126					4																	1806088		2203	4300	6503	SO:0001819	synonymous_variant	2261	exon9	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	CGAGGCGGGCAGT	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.1107G>T	chr4.hg19:g.1806088G>T		289.0	0.0	.		166.0	8.0	.	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Silent	SNP	ENST00000260795.2	hg19	CCDS3353.1																																																																																			.	.	.	none		0.692	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142		T	1806088	G	T	1806088	2	4	44	1	0	0	0	0	0	0	0	1	5874	1103	39	4		4	FGFR3	4	1806088	Silent	SNP	G	TCGA-A4-7583-01A-11D-2136-08		1806088	189348188	17	3061											
PROM1	8842	hgsc.bcm.edu	37	chr4	15989284	15989287	+	Splice_Site	DEL	ACCA	ACCA	-																															agaaaacaaagtaaacccttAccaacaatccattccctgtg																										TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	ACCA	ACCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr4:15989284_15989287delACCA	ENST00000510224.1	-	20	2377_2379	c.2129_2131delTGGT	c.(2128-2133)ttggta>tta	p.V711fs	PROM1_ENST00000508167.1_Splice_Site_p.V702fs|PROM1_ENST00000543373.1_Splice_Site_p.V702fs|PROM1_ENST00000539194.1_Splice_Site_p.V711fs|PROM1_ENST00000505450.1_Splice_Site_p.V702fs|PROM1_ENST00000447510.2_Splice_Site_p.V711fs|PROM1_ENST00000540805.1_Splice_Site_p.V711fs			O43490	PROM1_HUMAN	prominin 1	711					camera-type eye photoreceptor cell differentiation (GO:0060219)|glomerular parietal epithelial cell differentiation (GO:0072139)|glomerular visceral epithelial cell differentiation (GO:0072112)|photoreceptor cell maintenance (GO:0045494)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|retina layer formation (GO:0010842)|retina morphogenesis in camera-type eye (GO:0060042)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actinin binding (GO:0042805)|cadherin binding (GO:0045296)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2)	35						GTAAACCCTTACCAACAATCCATT	0.343																																					p.710_710del		Atlas-INDEL	.											.	PROM1	91	.	0			c.2130_2130del						PASS	.																																			SO:0001630	splice_region_variant	8842	exon19			.	AF027208	CCDS47029.1, CCDS54746.1, CCDS54747.1, CCDS54748.1	4p15	2013-06-06	2001-11-28	2003-03-28	ENSG00000007062	ENSG00000007062		"CD molecules"	9454	protein-coding gene	gene with protein product		604365	"prominin (mouse)-like 1", "macular dystrophy, retinal 2", "Stargardt disease 4 (autosomal dominant)"	PROML1, MCDR2, STGD4		11467842	Standard	NM_006017		Approved	AC133, CD133, RP41, CORD12	uc003goo.2	O43490	OTTHUMG00000160180	ENST00000510224.1:c.2130+1TGGT>-	chr4.hg19:g.15989284_15989287delACCA		228.0	0.0	0		233.0	69.0	0.296137	NM_001145850	Q6SV49|Q6SV50|Q6SV51|Q6SV52|Q6SV53|Q96EN6	Frame_Shift_Del	DEL	ENST00000510224.1	hg19	CCDS47029.1																																																																																			.	.	.	none		0.343	PROM1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359595.2	NM_006017	Frame_Shift_Del	-	15989287	ACCA	-	15989284	8	5	44	1	0	1	0	1	0	0	1	0	12565	405	14	0	497	0	PROM1	4	15989284	Splice_Site	DEL	ACCA	TCGA-A4-7583-01A-11D-2136-08	14183196	15989284	175164992	18	3062											
SLC10A6	345274	hgsc.bcm.edu	37	chr4	87749228	87749228	+	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	aaagatgaaactgatggtcaGaagggtgatgtctgaattcc	14	10	12	5	0	2	6	1	4	1	2	3	6	3	6	1	2	1	0	1	2	4	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr4:87749228G>C	ENST00000273905.6	-	4	826	c.679C>G	c.(679-681)Ctg>Gtg	p.L227V	SLC10A6_ENST00000505535.1_Intron	NM_197965.2	NP_932069.1	Q3KNW5	SOAT_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 6	227					sodium-dependent organic anion transport (GO:0043251)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid:sodium symporter activity (GO:0008508)|sodium-dependent organic anion transmembrane transporter activity (GO:0043250)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)	9		Acute lymphoblastic leukemia(40;0.244)|all_hematologic(202;0.248)		OV - Ovarian serous cystadenocarcinoma(123;0.00099)		CTGATGGTCAGAAGGGTGATG	0.498																																					p.L227V		Atlas-SNP	.											.	SLC10A6	40	.	0			c.C679G						PASS	.						89	81	84					4																	87749228		2203	4300	6503	SO:0001583	missense	345274	exon4			TGGTCAGAAGGGT	AJ583502	CCDS3614.1	4q22.1	2013-07-18	2013-07-18		ENSG00000145283	ENSG00000145283		"Solute carriers"	30603	protein-coding gene	gene with protein product		613366				15020217, 17491011	Standard	NM_197965		Approved	SOAT	uc003hqd.2	Q3KNW5	OTTHUMG00000130596	ENST00000273905.6:c.679C>G	chr4.hg19:g.87749228G>C	ENSP00000273905:p.Leu227Val	55.0	0.0	.		45.0	16.0	.	NM_197965	Q70EX7	Missense_Mutation	SNP	ENST00000273905.6	hg19	CCDS3614.1	.	.	.	.	.	.	.	.	.	.	G	12.68	2.010693	0.35511	.	.	ENSG00000145283	ENST00000273905	T	0.78816	-1.21	5.28	3.48	0.39840	.	0.167902	0.30320	N	0.009895	T	0.67477	0.2897	L	0.54323	1.7	0.28830	N	0.897216	P	0.42357	0.777	B	0.39339	0.297	T	0.66118	-0.6003	10	0.49607	T	0.09	-15.0839	4.1624	0.10291	0.1683:0.0:0.6333:0.1984	.	227	Q3KNW5	SOAT_HUMAN	V	227	ENSP00000273905:L227V	ENSP00000273905:L227V	L	-	1	2	SLC10A6	87968252	0.998000	0.40836	0.998000	0.56505	0.705000	0.40729	1.536000	0.36072	2.736000	0.93811	0.655000	0.94253	CTG	.	.	.	none		0.498	SLC10A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253043.2	NM_197965		C	87749228	G	C	87749228	3	2	44	1	0	0	0	0	1	0	0	0	14391	933	33	4	466	4	SLC10A6	4	87749228	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08	71759944	87749228	103405048	19	3063											
CAMK2D	817	hgsc.bcm.edu	37	chr4	114434488	114434488	+	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	ttcccaatgcatgtacctgaGaaattccttgtagccagcat	11	12	7	11	0	0	1	0	1	0	1	2	2	2	1	4	0	4	4	4	0	4	5			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr4:114434488G>A	ENST00000342666.5	-	12	941	c.942C>T	c.(940-942)ttC>ttT	p.F314F	CAMK2D_ENST00000418639.2_Silent_p.F314F|CAMK2D_ENST00000505990.1_Silent_p.F314F|CAMK2D_ENST00000429180.1_Silent_p.F314F|CAMK2D_ENST00000511664.1_Silent_p.F314F|CAMK2D_ENST00000514328.1_Silent_p.F314F|CAMK2D_ENST00000394524.3_Silent_p.F314F|CAMK2D_ENST00000296402.5_Silent_p.F314F|CAMK2D_ENST00000508738.1_Silent_p.F314F|CAMK2D_ENST00000454265.2_Silent_p.F314F|CAMK2D_ENST00000379773.2_Silent_p.F314F|CAMK2D_ENST00000394522.3_Silent_p.F314F|CAMK2D_ENST00000394526.2_Silent_p.F314F|CAMK2D_ENST00000515496.1_Silent_p.F314F			Q13557	KCC2D_HUMAN	calcium/calmodulin-dependent protein kinase II delta	314					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)		ATGTACCTGAGAAATTCCTTG	0.358																																					p.F314F		Atlas-SNP	.											.	CAMK2D	55	.	0			c.C942T						PASS	.						94	93	93					4																	114434488		2203	4300	6503	SO:0001819	synonymous_variant	817	exon12			ACCTGAGAAATTC	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.942C>T	chr4.hg19:g.114434488G>A		84.0	0.0	.		113.0	42.0	.	NM_172128	A8MVS8|Q52PK4|Q59G21|Q8N553|Q9UGH6|Q9UQE9	Silent	SNP	ENST00000342666.5	hg19	CCDS3703.1	.	.	.	.	.	.	.	.	.	.	G	7.680	0.688715	0.14973	.	.	ENSG00000145349	ENST00000513132	.	.	.	5.36	-2.88	0.05682	.	.	.	.	.	T	0.51839	0.1698	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48031	-0.9070	4	.	.	.	.	8.2973	0.31993	0.2489:0.0:0.6045:0.1466	.	.	.	.	F	18	.	.	L	-	1	0	CAMK2D	114653937	1.000000	0.71417	0.988000	0.46212	0.671000	0.39405	2.348000	0.44045	-0.497000	0.06641	-1.284000	0.01376	CTC	.	.	.	none		0.358	CAMK2D-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256420.2			A	114434488	G	A	114434488	2	1	44	1	0	0	0	0	0	0	0	1	2603	933	33	2		2	CAMK2D	4	114434488	Silent	SNP	G	TCGA-A4-7583-01A-11D-2136-08	26685260	114434488	76719788	20	3064											
NPY1R	4886	hgsc.bcm.edu	37	chr4	164246582	164246582	+	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	ttgtttcataatcatcatccCgagaccggaaatcacaaaag	15	10	6	10	2	4	1	4	0	0	1	5	3	5	2	2	1	0	1	2	1	4	3			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr4:164246582C>A	ENST00000296533.2	-	3	1559	c.1028G>T	c.(1027-1029)cGg>cTg	p.R343L	NPY1R_ENST00000509586.1_Missense_Mutation_p.R100L	NM_000909.5	NP_000900.1	P25929	NPY1R_HUMAN	neuropeptide Y receptor Y1	343					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose metabolic process (GO:0006006)|locomotory behavior (GO:0007626)|neuropeptide signaling pathway (GO:0007218)|outflow tract morphogenesis (GO:0003151)|regulation of blood pressure (GO:0008217)|regulation of multicellular organism growth (GO:0040014)|sensory perception of pain (GO:0019233)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)|pancreatic polypeptide receptor activity (GO:0001602)|peptide YY receptor activity (GO:0001601)	p.R343L(1)		breast(1)|cervix(1)|large_intestine(4)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)	30	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				ATCATCATCCCGAGACCGGAA	0.398																																					p.R343L		Atlas-SNP	.											.	NPY1R	72	.	1	Substitution - Missense(1)	lung(1)	c.G1028T						PASS	.						140	147	144					4																	164246582		2203	4300	6503	SO:0001583	missense	4886	exon3			TCATCCCGAGACC		CCDS34089.1	4q31.3-q32	2012-08-08				ENSG00000164128		"GPCR / Class A : Neuropeptide receptors : Y"	7956	protein-coding gene	gene with protein product		162641		NPYR		8095935	Standard	NM_000909		Approved		uc003iqm.2	P25929		ENST00000296533.2:c.1028G>T	chr4.hg19:g.164246582C>A	ENSP00000354652:p.Arg343Leu	113.0	0.0	.		188.0	8.0	.	NM_000909	B2R6H5	Missense_Mutation	SNP	ENST00000296533.2	hg19	CCDS34089.1	.	.	.	.	.	.	.	.	.	.	C	9.774	1.173580	0.21704	.	.	ENSG00000164128	ENST00000296533;ENST00000509586	T;T	0.36878	1.23;1.23	5.48	4.64	0.57946	.	0.258733	0.30859	N	0.008736	T	0.27798	0.0684	L	0.31926	0.97	0.46774	D	0.99919	B	0.27229	0.172	B	0.19391	0.025	T	0.03555	-1.1025	10	0.28530	T	0.3	.	14.4236	0.67200	0.0:0.9289:0.0:0.0711	.	343	P25929	NPY1R_HUMAN	L	343;100	ENSP00000354652:R343L;ENSP00000427284:R100L	ENSP00000354652:R343L	R	-	2	0	NPY1R	164466032	0.986000	0.35501	1.000000	0.80357	0.998000	0.95712	2.261000	0.43276	1.309000	0.44985	0.655000	0.94253	CGG	.	.	.	none		0.398	NPY1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364685.1			A	164246582	C	A	164246582	3	1	44	1	0	0	0	0	1	0	0	0	10615	652	23	4	130	4	NPY1R	4	164246582	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08	49812094	164246582	26907694	21	3065											
TLR3	7098	hgsc.bcm.edu	37	chr4	187004092	187004092	+	Missense_Mutation	SNP	A	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	tactcaacctaaccaagaatAaaatctcaaaaatagagagt	21	8	4	8	0	2	2	2	0	1	2	3	3	2	2	2	0	3	0	2	0	10	4			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr4:187004092A>C	ENST00000296795.3	+	4	1356	c.1252A>C	c.(1252-1254)Aaa>Caa	p.K418Q	TLR3_ENST00000504367.1_Missense_Mutation_p.K141Q	NM_003265.2	NP_003256.1	O15455	TLR3_HUMAN	toll-like receptor 3	418					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)		AACCAAGAATAAAATCTCAAA	0.403																																					p.K418Q		Atlas-SNP	.											.	TLR3	83	.	0			c.A1252C						PASS	.						60	56	57					4																	187004092		2203	4299	6502	SO:0001583	missense	7098	exon4			AAGAATAAAATCT	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.1252A>C	chr4.hg19:g.187004092A>C	ENSP00000296795:p.Lys418Gln	62.0	0.0	.		79.0	26.0	.	NM_003265	B2RAI7|B7Z7K0|E6Y0F0|E6Y0F1|E9PGH4|Q4VAL2|Q504W0	Missense_Mutation	SNP	ENST00000296795.3	hg19	CCDS3846.1	.	.	.	.	.	.	.	.	.	.	A	12.05	1.822070	0.32237	.	.	ENSG00000164342	ENST00000296795;ENST00000542020;ENST00000504367	T;T	0.59083	0.29;0.29	5.78	4.59	0.56863	.	0.253731	0.46145	D	0.000313	T	0.42539	0.1207	L	0.31207	0.915	0.25382	N	0.988604	B	0.24823	0.112	B	0.29176	0.099	T	0.31998	-0.9923	10	0.37606	T	0.19	.	5.6089	0.17394	0.7025:0.1541:0.1434:0.0	.	418	O15455	TLR3_HUMAN	Q	418;418;141	ENSP00000296795:K418Q;ENSP00000423684:K141Q	ENSP00000296795:K418Q	K	+	1	0	TLR3	187241086	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.225000	0.58600	0.999000	0.39023	0.455000	0.32223	AAA	.	.	.	none		0.403	TLR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360313.4			C	187004092	A	C	187004092	3	2	44	1	0	0	0	0	1	0	0	0	15964	363	13	5	1262	5	TLR3	4	187004092	Missense_Mutation	SNP	A	TCGA-A4-7583-01A-11D-2136-08	22757510	187004092	4150184	22	3066											
ZFR	51663	hgsc.bcm.edu	37	chr5	32403408	32403408	+	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	aaggagaggcagtcggctttGaagcagatacagctgttgaa	13	8	14	6	1	0	4	0	2	0	2	1	5	0	4	0	3	3	5	0	3	4	3			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr5:32403408G>A	ENST00000265069.8	-	8	1421	c.1319C>T	c.(1318-1320)tCa>tTa	p.S440L		NM_016107.3	NP_057191.2	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein	440					multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|upper_aerodigestive_tract(2)	32				STAD - Stomach adenocarcinoma(35;0.19)		AGTCGGCTTTGAAGCAGATAC	0.418																																					p.S440L		Atlas-SNP	.											.	ZFR	98	.	0			c.C1319T						PASS	.						188	171	177					5																	32403408		2203	4300	6503	SO:0001583	missense	51663	exon8			GGCTTTGAAGCAG	AF100742	CCDS34139.1	5p15.2	2014-03-03			ENSG00000056097	ENSG00000056097			17277	protein-coding gene	gene with protein product		615635				11574164, 24482476	Standard	NM_016107		Approved	ZFR1, SPG71	uc003jhr.1	Q96KR1	OTTHUMG00000161979	ENST00000265069.8:c.1319C>T	chr5.hg19:g.32403408G>A	ENSP00000265069:p.Ser440Leu	102.0	0.0	.		160.0	70.0	.	NM_016107	B2RNR5|Q05C08|Q3B7X5|Q6P5A3|Q86UA0|Q9H6V4|Q9NTI1|Q9Y687	Missense_Mutation	SNP	ENST00000265069.8	hg19	CCDS34139.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.934133	0.73442	.	.	ENSG00000056097	ENST00000265069;ENST00000382126	T	0.05925	3.37	5.95	5.95	0.96441	.	0.316034	0.39210	N	0.001439	T	0.09555	0.0235	L	0.43152	1.355	0.58432	D	0.999997	B	0.26935	0.164	B	0.21917	0.037	T	0.08207	-1.0733	10	0.72032	D	0.01	.	20.3719	0.98893	0.0:0.0:1.0:0.0	.	440	Q96KR1	ZFR_HUMAN	L	440;418	ENSP00000265069:S440L	ENSP00000265069:S440L	S	-	2	0	ZFR	32439165	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.494000	0.81503	2.826000	0.97356	0.491000	0.48974	TCA	.	.	.	none		0.418	ZFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366586.1			A	32403408	G	A	32403408	3	1	44	1	0	0	0	0	1	0	0	0	17671	1294	45	2	1957	2	ZFR	5	32403408	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08		32403408	148511852	23	3067											
PIK3R1	5295	hgsc.bcm.edu	37	chr5	67576767	67576767	+	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	tcttacagctctgataatacTgaaaacctcataaaagttat	16	13	4	8	0	3	2	1	2	2	0	3	2	3	2	1	0	4	2	1	0	8	5			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr5:67576767T>G	ENST00000521381.1	+	7	1465	c.849T>G	c.(847-849)acT>acG	p.T283T	PIK3R1_ENST00000274335.5_Silent_p.T283T|PIK3R1_ENST00000521657.1_Silent_p.T283T|PIK3R1_ENST00000396611.1_Silent_p.T283T	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	283	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.0?(1)|p.?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	CTGATAATACTGAAAACCTCA	0.328			"Mis, F, O"		"gliobastoma, ovarian, colorectal"					TCGA GBM(4;<1E-08)																											p.T283T		Atlas-SNP	.		Rec	yes		5	5q13.1	5295	"phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"		"E, O"	.	PIK3R1	869	.	2	Whole gene deletion(1)|Unknown(1)	large_intestine(1)|lung(1)	c.T849G						PASS	.						53	58	57					5																	67576767		2203	4299	6502	SO:0001819	synonymous_variant	5295	exon7			TAATACTGAAAAC	M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"SH2 domain containing"	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.849T>G	chr5.hg19:g.67576767T>G		41.0	0.0	.		61.0	18.0	.	NM_181523	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Silent	SNP	ENST00000521381.1	hg19	CCDS3993.1																																																																																			.	.	.	none		0.328	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		G	67576767	T	G	67576767	2	3	44	1	0	0	0	0	0	0	0	1	11925	1567	55	5		5	PIK3R1	5	67576767	Silent	SNP	T	TCGA-A4-7583-01A-11D-2136-08	35173359	67576767	113338493	24	3068											
PAPD4	167153	hgsc.bcm.edu	37	chr5	78975410	78975410	+	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	ttcttcttatagctggaataGtcaaatgatttcagttcgtg	10	17	8	6	1	4	1	2	1	2	0	5	2	4	2	0	1	1	2	0	1	5	7			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr5:78975410G>C	ENST00000296783.3	+	14	1516	c.1217G>C	c.(1216-1218)aGt>aCt	p.S406T	PAPD4_ENST00000428308.2_Missense_Mutation_p.S406T|PAPD4_ENST00000453514.1_Missense_Mutation_p.S406T|PAPD4_ENST00000504233.1_Missense_Mutation_p.S363T|PAPD4_ENST00000423041.2_Missense_Mutation_p.S402T			Q6PIY7	GLD2_HUMAN	PAP associated domain containing 4	406	PAP-associated.				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)		AGCTGGAATAGTCAAATGATT	0.323																																					p.S406T		Atlas-SNP	.											.	PAPD4	51	.	0			c.G1217C						PASS	.						106	99	102					5																	78975410		2203	4300	6503	SO:0001583	missense	167153	exon14			GGAATAGTCAAAT	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.1217G>C	chr5.hg19:g.78975410G>C	ENSP00000296783:p.Ser406Thr	57.0	0.0	.		73.0	33.0	.	NM_173797	Q86WZ2|Q8N927	Missense_Mutation	SNP	ENST00000296783.3	hg19	CCDS4048.1	.	.	.	.	.	.	.	.	.	.	G	11.49	1.653395	0.29425	.	.	ENSG00000164329	ENST00000453514;ENST00000423041;ENST00000504233;ENST00000428308;ENST00000296783	T;T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97;-0.97	6.06	4.2	0.49525	PAP/25A-associated (1);	0.512215	0.23215	N	0.050628	T	0.50701	0.1631	N	0.08118	0	0.22982	N	0.998471	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.06405	0.001;0.001;0.002	T	0.33954	-0.9848	10	0.30854	T	0.27	-6.8279	7.1177	0.25427	0.1866:0.1805:0.6329:0.0	.	406;402;363	Q6PIY7;Q6PIY7-2;D6RAF2	GLD2_HUMAN;.;.	T	406;402;363;406;406	ENSP00000397563:S406T;ENSP00000393412:S402T;ENSP00000421966:S363T;ENSP00000396861:S406T;ENSP00000296783:S406T	ENSP00000296783:S406T	S	+	2	0	PAPD4	79011166	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	1.626000	0.37039	1.428000	0.47296	0.655000	0.94253	AGT	.	.	.	none		0.323	PAPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226967.1	NM_173797		C	78975410	G	C	78975410	3	2	44	1	0	0	0	0	1	0	0	0	11431	1029	36	4	1263	4	PAPD4	5	78975410	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08	11398643	78975410	101939850	25	3069											
RDBP	7936	hgsc.bcm.edu	37	chr6	31922209	31922209	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggctcgccgttcagggaaTgaatccgaccctttgggagc	7	8	15	11	3	1	1	1	1	0	0	3	4	2	3	3	4	1	2	3	4	2	2			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr6:31922209T>C	ENST00000375429.3	-	8	979	c.753A>G	c.(751-753)tcA>tcG	p.S251S	NELFE_ENST00000375425.5_Silent_p.S258S|MIR1236_ENST00000408340.1_RNA|NELFE_ENST00000444811.2_Silent_p.S221S	NM_002904.5	NP_002895.3	P18615	NELFE_HUMAN	negative elongation factor complex member E	251					gene expression (GO:0010467)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)										GTTCAGGGAATGAATCCGACC	0.483																																					p.S251S		Atlas-SNP	.											.	.	.	.	0			c.A753G						PASS	.						96	90	92					6																	31922209		2203	4300	6503	SO:0001819	synonymous_variant	7936	exon8			AGGGAATGAATCC	M33230	CCDS4730.1	6p21.3	2013-02-12	2013-01-31	2013-01-31	ENSG00000204356	ENSG00000204356		"RNA binding motif (RRM) containing"	13974	protein-coding gene	gene with protein product		154040	"RD RNA-binding protein", "RD RNA binding protein"	RDBP			Standard	XM_006715205		Approved	RD, D6S45, NELF-E, RDP	uc003nyk.3	P18615	OTTHUMG00000031046	ENST00000375429.3:c.753A>G	chr6.hg19:g.31922209T>C		109.0	0.0	.		88.0	30.0	.	NM_002904	A2BE08|B4DUN1|B4DYX9|Q5JP74|Q5JP75|Q96F56|Q9NPK2	Silent	SNP	ENST00000375429.3	hg19	CCDS4730.1																																																																																			.	.	.	none		0.483	NELFE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076047.4			C	31922209	T	C	31922209	2	2	44	1	0	0	0	0	0	0	0	1	13201	1451	51	3		3	RDBP	6	31922209	Silent	SNP	T	TCGA-A4-7583-01A-11D-2136-08		31922209	139192858	26	3070											
EYS	346007	hgsc.bcm.edu	37	chr6	66204808	66204808	+	Missense_Mutation	SNP	T	T	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	ctgctgtttcactgtcacatTtagtcgaagtcccagtggac	8	13	9	11	1	2	0	2	0	0	0	4	2	3	1	1	1	1	2	1	1	2	3			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr6:66204808T>G	ENST00000370621.3	-	4	1022	c.496A>C	c.(496-498)Aat>Cat	p.N166H	EYS_ENST00000503581.1_Missense_Mutation_p.N166H|EYS_ENST00000393380.2_Missense_Mutation_p.N166H|EYS_ENST00000342421.5_Missense_Mutation_p.N166H|EYS_ENST00000370616.2_Missense_Mutation_p.N166H|EYS_ENST00000370618.3_Missense_Mutation_p.N166H			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	166					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						ACTGTCACATTTAGTCGAAGT	0.423																																					p.N166H		Atlas-SNP	.											.	EYS	527	.	0			c.A496C						PASS	.						72	64	66					6																	66204808		2203	4300	6503	SO:0001583	missense	346007	exon4			TCACATTTAGTCG		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.496A>C	chr6.hg19:g.66204808T>G	ENSP00000359655:p.Asn166His	54.0	0.0	.		97.0	32.0	.	NM_001142801	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	T	16.65	3.181420	0.57800	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616;ENST00000393380;ENST00000342421;ENST00000370618	D;D;D;D;D;D	0.88277	-2.36;-2.36;-2.36;-2.36;-2.36;-2.36	4.54	3.34	0.38264	.	.	.	.	.	T	0.69824	0.3154	N	0.08118	0	0.21020	N	0.99981	P;P;P	0.49862	0.844;0.929;0.884	B;P;P	0.48030	0.383;0.564;0.51	T	0.64588	-0.6372	9	0.45353	T	0.12	.	9.2337	0.37453	0.0:0.0:0.1827:0.8173	.	166;166;166	Q5T1H1-1;Q5T1H1-2;Q5SZM4	.;.;.	H	166	ENSP00000424243:N166H;ENSP00000359655:N166H;ENSP00000359650:N166H;ENSP00000377042:N166H;ENSP00000341818:N166H;ENSP00000359652:N166H	ENSP00000341818:N166H	N	-	1	0	EYS	66261529	0.997000	0.39634	0.962000	0.40283	0.996000	0.88848	2.828000	0.48120	0.667000	0.31107	0.482000	0.46254	AAT	.	.	.	none		0.423	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		G	66204808	T	G	66204808	3	3	44	1	0	0	0	0	1	0	0	0	5334	1841	64	5	9060	5	EYS	6	66204808	Missense_Mutation	SNP	T	TCGA-A4-7583-01A-11D-2136-08	34282599	66204808	104910259	27	3071											
ETV1	2115	hgsc.bcm.edu	37	chr7	13971323	13971323	+	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	ggacgtccttcccttggcatCgtcggcaaaggaggaaagga	10	7	14	10	3	0	0	0	0	0	0	4	4	2	4	2	6	0	2	2	6	2	2	rs531769320	byFrequency	TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr7:13971323C>G	ENST00000430479.1	-	9	1273	c.606G>C	c.(604-606)acG>acC	p.T202T	ETV1_ENST00000403685.1_Silent_p.T184T|ETV1_ENST00000420159.2_Silent_p.T144T|ETV1_ENST00000405358.4_Silent_p.T216T|ETV1_ENST00000405218.2_Silent_p.T202T|ETV1_ENST00000405192.2_Silent_p.T202T|ETV1_ENST00000403527.1_Silent_p.T162T|ETV1_ENST00000399357.3_Silent_p.T99T|ETV1_ENST00000476720.2_5'UTR|ETV1_ENST00000242066.5_Silent_p.T184T|ETV1_ENST00000343495.5_Silent_p.T184T	NM_004956.4	NP_004947.2	P50549	ETV1_HUMAN	ets variant 1	202					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						CCCTTGGCATCGTCGGCAAAG	0.502			T	"EWSR1, TMPRSS2, SLC45A3, C15orf21, HNRNPA2B1. ACSL3"	"Ewing sarcoma, prostate"																																p.T202T		Atlas-SNP	.		Dom	yes		7	7p22	2115	ets variant gene 1		"M, E"	.	ETV1	138	.	0			c.G606C						PASS	.						116	112	113					7																	13971323		2010	4169	6179	SO:0001819	synonymous_variant	2115	exon9			TGGCATCGTCGGC		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.606G>C	chr7.hg19:g.13971323C>G		46.0	0.0	.		45.0	17.0	.	NM_004956	A4D118|B2R768|B7Z2I4|B7Z618|B7Z9P2|C9JT37|E9PHB1|F5GXR2|O75849|Q4KMQ6|Q59GA7|Q6AI30|Q9UQ71|Q9Y636	Silent	SNP	ENST00000430479.1	hg19	CCDS55088.1																																																																																			.	.	.	none		0.502	ETV1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326111.1	NM_004956		G	13971323	C	G	13971323	2	3	44	1	0	0	0	0	0	0	0	1	5279	871	31	4		4	ETV1	7	13971323	Silent	SNP	C	TCGA-A4-7583-01A-11D-2136-08		13971323	145167340	28	3072											
SUN3	256979	hgsc.bcm.edu	37	chr7	48035693	48035693	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cccatgccagtacaattttgCtttattatttttataacttt	10	20	3	8	0	0	0	0	0	0	0	0	0	0	0	2	0	4	2	2	0	6	11			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr7:48035693C>T	ENST00000297325.4	-	7	787	c.628G>A	c.(628-630)Gca>Aca	p.A210T	SUN3_ENST00000453192.2_Missense_Mutation_p.A198T|SUN3_ENST00000412142.1_Missense_Mutation_p.A110T|SUN3_ENST00000395572.2_Missense_Mutation_p.A210T|SUN3_ENST00000473723.1_5'UTR	NM_001030019.1	NP_001025190.1	Q8TAQ9	SUN3_HUMAN	Sad1 and UNC84 domain containing 3	210	SUN. {ECO:0000255|PROSITE- ProRule:PRU00802}.					integral component of membrane (GO:0016021)|SUN-KASH complex (GO:0034993)				central_nervous_system(1)|endometrium(3)|large_intestine(8)|liver(1)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TACAATTTTGCTTTATTATTT	0.299																																					p.A210T		Atlas-SNP	.											.	SUN3	52	.	0			c.G628A						PASS	.						82	87	85					7																	48035693		2203	4288	6491	SO:0001583	missense	256979	exon8			ATTTTGCTTTATT	AF429967	CCDS34636.1, CCDS64647.1	7p12.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164744	ENSG00000164744			22429	protein-coding gene	gene with protein product			"Sad1 and UNC84 domain containing 1"	SUNC1			Standard	NM_001284350		Approved	MGC33329	uc003tof.3	Q8TAQ9	OTTHUMG00000155646	ENST00000297325.4:c.628G>A	chr7.hg19:g.48035693C>T	ENSP00000297325:p.Ala210Thr	115.0	0.0	.		126.0	40.0	.	NM_152782	A4D2F3|B4DXK1|D3DVM3|E7EWC8|Q4F965|Q7Z4U8	Missense_Mutation	SNP	ENST00000297325.4	hg19	CCDS34636.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.484372	0.44147	.	.	ENSG00000164744	ENST00000297325;ENST00000412371;ENST00000412142;ENST00000395572;ENST00000453192;ENST00000438771	T;T;T;T;T;T	0.46063	1.83;0.88;1.84;1.83;2.42;1.84	5.25	4.37	0.52481	Sad1/UNC-like, C-terminal (1);	0.236128	0.42548	N	0.000694	T	0.35537	0.0935	L	0.49350	1.555	0.34170	D	0.669671	B;B;B	0.31503	0.047;0.326;0.192	B;B;B	0.28465	0.019;0.09;0.065	T	0.52873	-0.8517	10	0.87932	D	0	.	9.6842	0.40089	0.0:0.9039:0.0:0.0961	.	198;110;210	E7EWC8;Q8TAQ9-2;Q8TAQ9	.;.;SUN3_HUMAN	T	210;32;110;210;198;110	ENSP00000297325:A210T;ENSP00000406887:A32T;ENSP00000410204:A110T;ENSP00000378939:A210T;ENSP00000387525:A198T;ENSP00000409077:A110T	ENSP00000297325:A210T	A	-	1	0	SUN3	48002218	0.937000	0.31787	0.973000	0.42090	0.803000	0.45373	1.417000	0.34770	1.244000	0.43870	0.650000	0.86243	GCA	.	.	.	none		0.299	SUN3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340962.1	NM_152782		T	48035693	C	T	48035693	3	4	44	1	0	0	0	0	1	0	0	0	15405	797	28	2	461	2	SUN3	7	48035693	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08	34064370	48035693	111102970	29	3073											
PEX1	5189	hgsc.bcm.edu	37	chr7	92151473	92151473	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtctgttaatttcagccacAttttcaccttgatcactaaa	11	16	4	10	0	4	1	3	1	1	0	4	1	4	1	2	0	1	1	2	0	3	6			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr7:92151473A>G	ENST00000248633.4	-	2	311	c.216T>C	c.(214-216)aaT>aaC	p.N72N	PEX1_ENST00000428214.1_Silent_p.N72N|PEX1_ENST00000438045.1_Silent_p.N72N	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	72					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)			TTTCAGCCACATTTTCACCTT	0.408																																					p.N72N		Atlas-SNP	.											.	PEX1	102	.	0			c.T216C						PASS	.						130	121	124					7																	92151473		2203	4300	6503	SO:0001819	synonymous_variant	5189	exon2			AGCCACATTTTCA	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.216T>C	chr7.hg19:g.92151473A>G		90.0	0.0	.		130.0	55.0	.	NM_000466	A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Silent	SNP	ENST00000248633.4	hg19	CCDS5627.1																																																																																			.	.	.	none		0.408	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466		G	92151473	A	G	92151473	2	3	44	1	0	0	0	0	0	0	0	1	11742	214	8	3		3	PEX1	7	92151473	Silent	SNP	A	TCGA-A4-7583-01A-11D-2136-08	44115780	92151473	66987190	30	3074											
TUSC3	7991	hgsc.bcm.edu	37	chr8	15508312	15508312	+	Missense_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	actatgatgaggggacagacGtttttcagcaggtaaagagt	13	10	13	5	1	1	4	1	2	0	2	1	5	1	5	0	3	1	3	0	3	3	4	rs371225890		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr8:15508312G>A	ENST00000503731.1	+	3	563	c.415G>A	c.(415-417)Gtt>Att	p.V139I	TUSC3_ENST00000506802.1_Missense_Mutation_p.V139I|TUSC3_ENST00000503191.1_Intron|TUSC3_ENST00000382020.4_Missense_Mutation_p.V139I|TUSC3_ENST00000509380.1_Missense_Mutation_p.V139I	NM_006765.3	NP_006756.2	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3	139	Thioredoxin.				cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|magnesium ion transport (GO:0015693)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|oligosaccharyltransferase complex (GO:0008250)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(10)|ovary(2)	28				Colorectal(111;0.113)		GGGGACAGACGTTTTTCAGCA	0.343																																					p.V139I		Atlas-SNP	.											.	TUSC3	98	.	0			c.G415A						PASS	.	G	ILE/VAL,ILE/VAL	0,4406		0,0,2203	239	237	238		415,415	3.7	1	8		238	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	TUSC3	NM_006765.3,NM_178234.2	29,29	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign,benign	139/349,139/348	15508312	2,13004	2203	4300	6503	SO:0001583	missense	7991	exon3			ACAGACGTTTTTC	AK026149	CCDS5993.1, CCDS5994.1	8p22	2010-10-22			ENSG00000104723	ENSG00000104723			30242	protein-coding gene	gene with protein product	"oligosaccharyltransferase 3 homolog A (S. cerevisiae)"	601385				8661104, 10097140	Standard	NM_178234		Approved	MGC13453, N33, OST3A, MRT7	uc003wwt.3	Q13454	OTTHUMG00000094803	ENST00000503731.1:c.415G>A	chr8.hg19:g.15508312G>A	ENSP00000424544:p.Val139Ile	163.0	0.0	.		222.0	96.0	.	NM_178234	A8MSM0|D3DSP2|Q14911|Q14912|Q96FW0	Missense_Mutation	SNP	ENST00000503731.1	hg19	CCDS5994.1	.	.	.	.	.	.	.	.	.	.	G	19.34	3.809796	0.70797	0.0	2.33E-4	ENSG00000104723	ENST00000382020;ENST00000506802;ENST00000509380;ENST00000503731	T;T;T;T	0.38722	1.12;1.12;1.12;1.12	5.47	3.67	0.42095	Thioredoxin domain (1);Thioredoxin-like fold (2);	0.162707	0.53938	N	0.000046	T	0.55893	0.1949	M	0.66297	2.02	0.44323	D	0.997205	D;D;D;D;D;B	0.65815	0.971;0.995;0.981;0.977;0.995;0.004	P;P;D;P;P;B	0.65010	0.838;0.771;0.931;0.613;0.784;0.007	T	0.51411	-0.8709	10	0.27082	T	0.32	-11.5841	10.6624	0.45710	0.0719:0.1325:0.7956:0.0	.	139;139;139;139;139;139	D6RDV0;D6RIY7;Q13454-2;Q13454;D6RA37;A8MSM0	.;.;.;TUSC3_HUMAN;.;.	I	139	ENSP00000371450:V139I;ENSP00000425777:V139I;ENSP00000423426:V139I;ENSP00000424544:V139I	ENSP00000221167:V139I	V	+	1	0	TUSC3	15552683	1.000000	0.71417	0.993000	0.49108	0.970000	0.65996	7.654000	0.83653	0.780000	0.33566	0.563000	0.77884	GTT	.	.	.	weak		0.343	TUSC3-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365367.1	NM_006765		A	15508312	G	A	15508312	3	1	44	1	0	0	0	0	1	0	0	0	16790	1145	40	1	425	1	TUSC3	8	15508312	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08		15508312	130855710	31	3075											
PSD3	23362	hgsc.bcm.edu	37	chr8	18430149	18430149	+	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	acagctgccacacaattgatTttgtttatccacccttgcat	10	14	5	12	0	0	1	0	1	0	0	1	1	1	1	3	0	3	3	3	0	2	6			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr8:18430149T>A	ENST00000327040.8	-	14	2775	c.2673A>T	c.(2671-2673)aaA>aaT	p.K891N	PSD3_ENST00000523619.1_Missense_Mutation_p.K826N|PSD3_ENST00000428502.2_Missense_Mutation_p.K220N|PSD3_ENST00000286485.8_Missense_Mutation_p.K357N|PSD3_ENST00000440756.2_Missense_Mutation_p.K893N	NM_015310.3	NP_056125.3	Q9NYI0	PSD3_HUMAN	pleckstrin and Sec7 domain containing 3	892	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)		CACAATTGATTTTGTTTATCC	0.433																																					p.K891N		Atlas-SNP	.											.	PSD3	142	.	0			c.A2673T						PASS	.						167	173	171					8																	18430149		2203	4300	6503	SO:0001583	missense	23362	exon14			ATTGATTTTGTTT	AF243495	CCDS34854.1, CCDS43720.1	8p21.3	2013-01-10			ENSG00000156011	ENSG00000156011		"Pleckstrin homology (PH) domain containing"	19093	protein-coding gene	gene with protein product		614440					Standard	NM_206909		Approved	KIAA0942, HCA67, EFA6R, DKFZp761K1423	uc003wza.3	Q9NYI0	OTTHUMG00000163711	ENST00000327040.8:c.2673A>T	chr8.hg19:g.18430149T>A	ENSP00000324127:p.Lys891Asn	115.0	0.0	.		225.0	73.0	.	NM_015310	A6NFQ4|E9KL50|Q6B003|Q9Y2F1	Missense_Mutation	SNP	ENST00000327040.8	hg19	CCDS43720.1	.	.	.	.	.	.	.	.	.	.	T	17.96	3.516949	0.64634	.	.	ENSG00000156011	ENST00000327040;ENST00000440756;ENST00000286485;ENST00000428502;ENST00000523619	T;T;T;T;T	0.79352	-1.26;-1.26;-1.26;-1.26;-1.26	5.71	2.04	0.26737	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.683311	0.11566	U	0.551222	T	0.74711	0.3752	L	0.48174	1.505	0.39428	D	0.967023	B;B;B;P	0.37688	0.423;0.423;0.048;0.605	P;P;B;B	0.45946	0.498;0.498;0.061;0.388	T	0.69647	-0.5089	10	0.72032	D	0.01	.	4.8511	0.13537	0.0:0.2364:0.1485:0.615	.	891;892;357;220	E9KL50;Q9NYI0;Q9NYI0-3;B4DKF8	.;PSD3_HUMAN;.;.	N	891;893;357;220;826	ENSP00000324127:K891N;ENSP00000401704:K893N;ENSP00000286485:K357N;ENSP00000393228:K220N;ENSP00000430640:K826N	ENSP00000286485:K357N	K	-	3	2	PSD3	18474429	0.972000	0.33761	0.998000	0.56505	0.918000	0.54935	0.105000	0.15333	0.177000	0.19895	-0.297000	0.09499	AAA	.	.	.	none		0.433	PSD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000374867.1	NM_015310		A	18430149	T	A	18430149	3	1	44	1	0	0	0	0	1	0	0	0	12658	1838	64	5	482	5	PSD3	8	18430149	Missense_Mutation	SNP	T	TCGA-A4-7583-01A-11D-2136-08	2921837	18430149	127933873	32	3076											
ZNF395	55893	hgsc.bcm.edu	37	chr8	28206721	28206721	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctggctgctggggctcgcTgaagcttagcgaccggctcc	4	9	15	13	3	0	1	0	1	0	0	2	2	1	1	2	4	4	7	2	4	2	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr8:28206721T>C	ENST00000344423.5	-	9	1482	c.1351A>G	c.(1351-1353)Agc>Ggc	p.S451G	ZNF395_ENST00000523202.1_Missense_Mutation_p.S451G|ZNF395_ENST00000523095.1_Missense_Mutation_p.S451G	NM_018660.2	NP_061130.1	Q9H8N7	ZN395_HUMAN	zinc finger protein 395	451					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(5)|large_intestine(6)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.102)|Kidney(114;0.123)|Colorectal(74;0.142)		TGGGGCTCGCTGAAGCTTAGC	0.617																																					p.S451G		Atlas-SNP	.											.	ZNF395	54	.	0			c.A1351G						PASS	.						75	79	78					8																	28206721		2203	4300	6503	SO:0001583	missense	55893	exon9			GCTCGCTGAAGCT	AB044750	CCDS6067.1	8p21	2008-05-02			ENSG00000186918	ENSG00000186918		"Zinc fingers, C2H2-type"	18737	protein-coding gene	gene with protein product		609494				14625278	Standard	NM_018660		Approved	PRF-1, HDBP2, PBF, DKFZp434K1210	uc003xgr.3	Q9H8N7	OTTHUMG00000102137	ENST00000344423.5:c.1351A>G	chr8.hg19:g.28206721T>C	ENSP00000340494:p.Ser451Gly	110.0	0.0	.		70.0	22.0	.	NM_018660	B3KUY7|D3DST4|Q6F6H2|Q9BY72|Q9NPB2|Q9NS57|Q9NS58|Q9NS59	Missense_Mutation	SNP	ENST00000344423.5	hg19	CCDS6067.1	.	.	.	.	.	.	.	.	.	.	T	11.12	1.544128	0.27563	.	.	ENSG00000186918	ENST00000344423;ENST00000523202;ENST00000523095	T;T;T	0.46063	0.88;0.88;0.88	5.5	4.27	0.50696	.	0.318422	0.40908	D	0.001000	T	0.19046	0.0457	N	0.05487	-0.04	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.09335	-1.0679	10	0.09338	T	0.73	-15.6215	8.8687	0.35303	0.0:0.0:0.189:0.811	.	451	Q9H8N7	ZN395_HUMAN	G	451	ENSP00000340494:S451G;ENSP00000429640:S451G;ENSP00000428452:S451G	ENSP00000340494:S451G	S	-	1	0	ZNF395	28262640	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.178000	0.50879	2.099000	0.63709	0.459000	0.35465	AGC	.	.	.	none		0.617	ZNF395-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219976.1			C	28206721	T	C	28206721	3	2	44	1	0	0	0	0	1	0	0	0	17893	1580	55	3	198	3	ZNF395	8	28206721	Missense_Mutation	SNP	T	TCGA-A4-7583-01A-11D-2136-08	9776572	28206721	118157301	33	3077											
ARID3C	138715	hgsc.bcm.edu	37	chr9	34622092	34622092	+	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	gcctgccagattaagaggccCatccagccgctcttctgtcc	7	9	9	16	1	2	2	0	0	2	2	4	2	4	2	6	1	2	1	6	1	1	2			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr9:34622092C>T	ENST00000378909.2	-	6	1155	c.1063G>A	c.(1063-1065)Ggg>Agg	p.G355R	DCTN3_ENST00000378916.4_5'Flank|DCTN3_ENST00000477738.2_5'Flank|DCTN3_ENST00000341694.2_5'Flank|DCTN3_ENST00000259632.7_5'Flank|DCTN3_ENST00000378913.2_5'Flank|DCTN3_ENST00000447983.2_5'Flank	NM_001017363.1	NP_001017363.1	A6NKF2	ARI3C_HUMAN	AT rich interactive domain 3C (BRIGHT-like)	355	Pro-rich.|REKLES. {ECO:0000255|PROSITE- ProRule:PRU00819}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane raft (GO:0045121)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)	14	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.175)		TTAAGAGGCCCATCCAGCCGC	0.517																																					p.G355R		Atlas-SNP	.											.	ARID3C	33	.	0			c.G1063A						PASS	.						91	84	87					9																	34622092		2203	4300	6503	SO:0001583	missense	138715	exon6			GAGGCCCATCCAG		CCDS35006.1	9p13.2	2013-02-07	2006-11-08		ENSG00000205143	ENSG00000205143		"-"	21209	protein-coding gene	gene with protein product			"AT rich interactive domain 3C (BRIGHT- like)"				Standard	NM_001017363		Approved		uc011lon.2	A6NKF2	OTTHUMG00000000445	ENST00000378909.2:c.1063G>A	chr9.hg19:g.34622092C>T	ENSP00000368189:p.Gly355Arg	184.0	0.0	.		130.0	44.0	.	NM_001017363		Missense_Mutation	SNP	ENST00000378909.2	hg19	CCDS35006.1	.	.	.	.	.	.	.	.	.	.	C	13.77	2.335039	0.41398	.	.	ENSG00000205143	ENST00000378909	T	0.41065	1.01	5.03	5.03	0.67393	REKLES domain (1);	0.000000	0.47093	D	0.000254	T	0.35856	0.0946	L	0.51422	1.61	0.29866	N	0.827257	P	0.39831	0.69	B	0.35727	0.209	T	0.32481	-0.9905	10	0.17369	T	0.5	-15.5988	15.9067	0.79436	0.0:1.0:0.0:0.0	.	355	A6NKF2	ARI3C_HUMAN	R	355	ENSP00000368189:G355R	ENSP00000368189:G355R	G	-	1	0	ARID3C	34612092	0.960000	0.32886	1.000000	0.80357	0.988000	0.76386	1.491000	0.35583	2.612000	0.88384	0.549000	0.68633	GGG	.	.	.	none		0.517	ARID3C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348265.1	XM_071061		T	34622092	C	T	34622092	3	4	44	1	0	0	0	0	1	0	0	0	918	594	21	2	182	2	ARID3C	9	34622092	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08		34622092	106591339	34	3078											
RUSC2	9853	hgsc.bcm.edu	37	chr9	35547391	35547391	+	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	agcaccctctacaacaagatGcatggcaccccccgtgccaa	12	5	7	17	1	1	1	0	0	1	1	1	1	1	1	5	1	5	3	5	1	4	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr9:35547391G>C	ENST00000455600.1	+	2	1442	c.873G>C	c.(871-873)atG>atC	p.M291I		NM_001135999.1	NP_001129471	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	291						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)	Rab GTPase binding (GO:0017137)			NS(1)|breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(4)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)			ACAACAAGATGCATGGCACCC	0.582																																					p.M291I		Atlas-SNP	.											.	RUSC2	88	.	0			c.G873C						PASS	.						79	70	73					9																	35547391		2203	4300	6503	SO:0001583	missense	9853	exon2			CAAGATGCATGGC	AB002373	CCDS35008.1	9p13.2	2003-12-02			ENSG00000198853	ENSG00000198853			23625	protein-coding gene	gene with protein product		611053				9205841	Standard	NM_001135999		Approved	KIAA0375	uc003zww.3	Q8N2Y8	OTTHUMG00000019861	ENST00000455600.1:c.873G>C	chr9.hg19:g.35547391G>C	ENSP00000393922:p.Met291Ile	150.0	0.0	.		93.0	31.0	.	NM_014806	A2RU62|A7E2A9|O15080|Q5W134|Q641Q6|Q6P1W7	Missense_Mutation	SNP	ENST00000455600.1	hg19	CCDS35008.1	.	.	.	.	.	.	.	.	.	.	G	13.78	2.339018	0.41398	.	.	ENSG00000198853	ENST00000361226;ENST00000455600;ENST00000543478	T;T	0.28069	1.63;1.63	5.61	5.61	0.85477	.	0.089636	0.85682	D	0.000000	T	0.28167	0.0695	L	0.29908	0.895	0.42729	D	0.993703	B	0.24258	0.1	B	0.24541	0.054	T	0.05338	-1.0891	10	0.62326	D	0.03	-8.6538	18.6114	0.91286	0.0:0.0:1.0:0.0	.	291	Q8N2Y8	RUSC2_HUMAN	I	291	ENSP00000355177:M291I;ENSP00000393922:M291I	ENSP00000355177:M291I	M	+	3	0	RUSC2	35537391	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.341000	0.79300	2.649000	0.89929	0.561000	0.74099	ATG	.	.	.	none		0.582	RUSC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052309.1	XM_048462		C	35547391	G	C	35547391	3	2	44	1	0	0	0	0	1	0	0	0	13764	1319	46	4	875	4	RUSC2	9	35547391	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08	925299	35547391	105666040	35	3079											
NANS	54187	hgsc.bcm.edu	37	chr9	100840514	100840514	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtgggatgcagtcaatggAcaccatgaagcaagtttatc	13	9	11	8	0	1	1	1	1	0	0	2	3	1	3	1	2	2	3	1	2	4	2			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr9:100840514A>G	ENST00000210444.5	+	4	558	c.488A>G	c.(487-489)gAc>gGc	p.D163G	TRIM14_ENST00000375098.3_Intron|NANS_ENST00000461452.1_3'UTR|TRIM14_ENST00000478530.1_5'Flank	NM_018946.3	NP_061819.2	Q9NR45	SIAS_HUMAN	N-acetylneuraminic acid synthase	163					lipopolysaccharide biosynthetic process (GO:0009103)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	N-acetylneuraminate synthase activity (GO:0050462)|N-acylneuraminate cytidylyltransferase activity (GO:0008781)|N-acylneuraminate-9-phosphate synthase activity (GO:0047444)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	11		Acute lymphoblastic leukemia(62;0.0559)				CAGTCAATGGACACCATGAAG	0.522																																					p.D163G		Atlas-SNP	.											.	NANS	24	.	0			c.A488G						PASS	.						229	181	197					9																	100840514		2203	4300	6503	SO:0001583	missense	54187	exon4			CAATGGACACCAT	AF161387	CCDS6733.1	9p24.1-p23	2008-07-31	2008-07-31		ENSG00000095380	ENSG00000095380			19237	protein-coding gene	gene with protein product	"sialic acid synthase"	605202				10749855	Standard	NM_018946		Approved	SAS	uc004ayc.3	Q9NR45	OTTHUMG00000020341	ENST00000210444.5:c.488A>G	chr9.hg19:g.100840514A>G	ENSP00000210444:p.Asp163Gly	167.0	0.0	.		127.0	47.0	.	NM_018946	B2RE98|Q8WUV9|Q9BWS6|Q9NVD4	Missense_Mutation	SNP	ENST00000210444.5	hg19	CCDS6733.1	.	.	.	.	.	.	.	.	.	.	A	10.92	1.487927	0.26686	.	.	ENSG00000095380	ENST00000210444;ENST00000415280	T;T	0.42900	0.96;0.96	5.32	1.49	0.22878	Aldolase-type TIM barrel (1);N-acetylneuraminic acid synthase, N-terminal (1);	0.346769	0.36167	N	0.002757	T	0.16896	0.0406	N	0.02103	-0.685	0.80722	D	1	B	0.06786	0.001	B	0.10450	0.005	T	0.05370	-1.0889	10	0.24483	T	0.36	-13.5844	11.9513	0.52956	0.5778:0.4222:0.0:0.0	.	163	Q9NR45	SIAS_HUMAN	G	163;22	ENSP00000210444:D163G;ENSP00000404107:D22G	ENSP00000210444:D163G	D	+	2	0	NANS	99880335	1.000000	0.71417	0.993000	0.49108	0.969000	0.65631	2.784000	0.47774	0.070000	0.16634	-1.293000	0.01348	GAC	.	.	.	none		0.522	NANS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053359.1	NM_018946		G	100840514	A	G	100840514	3	3	44	1	0	0	0	0	1	0	0	0	10162	275	10	3	502	3	NANS	9	100840514	Missense_Mutation	SNP	A	TCGA-A4-7583-01A-11D-2136-08	65293123	100840514	40372917	36	3080											
NR6A1	2649	hgsc.bcm.edu	37	chr9	127316717	127316717	+	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	cacgactgcatcgatataccCgtttgttgcaaatgctccgc	9	11	8	13	4	0	0	0	0	0	0	2	2	1	0	2	0	4	5	2	0	3	4			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr9:127316717C>A	ENST00000487099.2	-	3	432	c.275G>T	c.(274-276)cGg>cTg	p.R92L	NR6A1_ENST00000373584.3_Missense_Mutation_p.R88L|NR6A1_ENST00000344523.4_Missense_Mutation_p.R92L|NR6A1_ENST00000416460.2_Missense_Mutation_p.R88L	NM_001278546.1	NP_001265475.1	Q15406	NR6A1_HUMAN	nuclear receptor subfamily 6, group A, member 1	92					cell proliferation (GO:0008283)|gamete generation (GO:0007276)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(1)	17						TCGATATACCCGTTTGTTGCA	0.532																																					p.R92L	Esophageal Squamous(192;272 2884 6208 20560)	Atlas-SNP	.											.	NR6A1	38	.	0			c.G275T						PASS	.						158	135	143					9																	127316717		2203	4300	6503	SO:0001583	missense	2649	exon3			TATACCCGTTTGT	U64876	CCDS35137.1, CCDS55340.1, CCDS65127.1	9q33.3	2014-01-21			ENSG00000148200	ENSG00000148200		"Nuclear hormone receptors"	7985	protein-coding gene	gene with protein product		602778		GCNF		9134503, 8982251	Standard	NM_001489		Approved	GCNF1, RTR, CT150	uc004bor.1	Q15406	OTTHUMG00000020661	ENST00000487099.2:c.275G>T	chr9.hg19:g.127316717C>A	ENSP00000420267:p.Arg92Leu	107.0	0.0	.		135.0	7.0	.	NM_033334	O00551|O00603|Q5T6F4|Q8NHQ0|Q92898|Q99802	Missense_Mutation	SNP	ENST00000487099.2	hg19	CCDS35137.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.295326	0.81025	.	.	ENSG00000148200	ENST00000487099;ENST00000373584;ENST00000416460;ENST00000344523;ENST00000475178	D;D;D;D;D	0.95918	-3.85;-3.85;-3.85;-3.85;-3.85	5.66	5.66	0.87406	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (3);	0.000000	0.85682	D	0.000000	D	0.94588	0.8256	N	0.12887	0.27	0.80722	D	1	D;D;D	0.89917	1.0;0.986;1.0	D;D;D	0.97110	1.0;0.96;0.998	D	0.92193	0.5761	10	0.13108	T	0.6	.	18.751	0.91814	0.0:1.0:0.0:0.0	.	88;92;88	F1DAM1;Q15406;Q15406-5	.;NR6A1_HUMAN;.	L	92;88;88;92;50	ENSP00000420267:R92L;ENSP00000362686:R88L;ENSP00000413701:R88L;ENSP00000341135:R92L;ENSP00000420587:R50L	ENSP00000341135:R92L	R	-	2	0	NR6A1	126356538	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.802000	0.62539	2.653000	0.90120	0.563000	0.77884	CGG	.	.	.	none		0.532	NR6A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054043.4			A	127316717	C	A	127316717	3	1	44	1	0	0	0	0	1	0	0	0	10644	652	23	4	1199	4	NR6A1	9	127316717	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08	26476203	127316717	13896714	37	3081											
DOLK	22845	hgsc.bcm.edu	37	chr9	131708944	131708945	+	Frame_Shift_Ins	INS	-	-	G																															cctgactttccaccagtgtcINSagagagcgcttgatgagctg																										TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr9:131708944_131708945insG	ENST00000372586.3	-	1	953_954	c.638_639insC	c.(637-639)ctgfs	p.L213fs	RP11-101E3.5_ENST00000482796.1_Intron|NUP188_ENST00000372577.2_5'Flank	NM_014908.3	NP_055723.1	Q9UPQ8	DOLK_HUMAN	dolichol kinase	213					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						CCACCAGTGTCAGAGAGCGCTT	0.55																																					p.L213fs		Atlas-INDEL	.											.	DOLK	39	.	0			c.639_640insC						PASS	.																																			SO:0001589	frameshift_variant	22845	exon1			.	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.638_639insC	chr9.hg19:g.131708944_131708945insG	ENSP00000361667:p.Leu213fs	146.0	0.0	0		105.0	36.0	0.342857	NM_014908	Q5SRE6	Frame_Shift_Ins	INS	ENST00000372586.3	hg19	CCDS6915.1																																																																																			.	.	.	none		0.55	DOLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054515.1	NM_014908		G	131708945	-	G	131708944	7	5	44	1	0	1	1	0	0	0	0	0	4705	813	29	0	981	0	DOLK	9	131708944	Frame_Shift_Ins	INS	-	TCGA-A4-7583-01A-11D-2136-08	4392227	131708944	9504487	38	3082											
USP6NL	9712	hgsc.bcm.edu	37	chr10	11523768	11523768	+	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	aagtattggggtaattcttaCcaggttctggaaggtctaac	11	13	11	6	0	3	0	0	0	3	0	3	1	3	1	1	5	2	3	1	5	6	7			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr10:11523768C>G	ENST00000609104.1	-	14	1473		c.e14+1		USP6NL_ENST00000379237.2_Splice_Site|USP6NL_ENST00000277575.5_Splice_Site	NM_014688.2	NP_055503.1	Q92738	US6NL_HUMAN	USP6 N-terminal like						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						GTAATTCTTACCAGGTTCTGG	0.368																																					.		Atlas-SNP	.											USP6NL,NS,carcinoma,0,1	USP6NL	57	.	0			c.1078+1G>C						PASS	.						62	60	60					10																	11523768		1820	4075	5895	SO:0001630	splice_region_variant	9712	exon15			TTCTTACCAGGTT	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.1078+1G>C	chr10.hg19:g.11523768C>G		41.0	0.0	.		50.0	2.0	.	NM_014688	A8KA79|Q15400|Q5VV10|Q7L0K9	Splice_Site	SNP	ENST00000609104.1	hg19	CCDS53492.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.280472	0.80692	.	.	ENSG00000148429	ENST00000535316;ENST00000277575;ENST00000379237	.	.	.	5.84	4.92	0.64577	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.8921	0.86090	0.0:0.8719:0.1281:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	USP6NL	11563774	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.140000	0.77322	1.431000	0.47355	0.655000	0.94253	.	.	.	.	none		0.368	USP6NL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046764.3	NM_014688	Intron	G	11523768	C	G	11523768	5	3	44	1	0	0	0	0	0	0	1	0	17099	521	18	4	1415	4	USP6NL	10	11523768	Splice_Site	SNP	C	TCGA-A4-7583-01A-11D-2136-08		11523768	124010979	39	3083											
THNSL1	79896	hgsc.bcm.edu	37	chr10	25312238	25312238	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgttaaaacggataaacatgCacagcgatttctttcaagaa	16	11	7	7	2	2	1	1	0	1	1	2	3	2	2	0	1	4	2	0	1	6	4			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr10:25312238C>T	ENST00000524413.1	+	3	433	c.86C>T	c.(85-87)gCa>gTa	p.A29V	THNSL1_ENST00000376356.4_Missense_Mutation_p.A29V			Q8IYQ7	THNS1_HUMAN	threonine synthase-like 1 (S. cerevisiae)	29						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)	GATAAACATGCACAGCGATTT	0.363																																					p.A29V		Atlas-SNP	.											.	THNSL1	70	.	0			c.C86T						PASS	.						97	99	98					10																	25312238		2203	4300	6503	SO:0001583	missense	79896	exon3			AACATGCACAGCG	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.86C>T	chr10.hg19:g.25312238C>T	ENSP00000434887:p.Ala29Val	80.0	0.0	.		118.0	48.0	.	NM_024838	B3KWL1|D3DRV3|Q5VV21	Missense_Mutation	SNP	ENST00000524413.1	hg19	CCDS7147.1	.	.	.	.	.	.	.	.	.	.	C	1.381	-0.583490	0.03827	.	.	ENSG00000185875	ENST00000524413;ENST00000376356	T;T	0.07444	3.19;3.19	5.87	1.3	0.21679	.	1.328470	0.05152	N	0.496208	T	0.03263	0.0095	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.37596	-0.9699	10	0.02654	T	1	-32.9386	0.8315	0.01132	0.1692:0.23:0.1664:0.4344	.	29	Q8IYQ7	THNS1_HUMAN	V	29	ENSP00000434887:A29V;ENSP00000365534:A29V	ENSP00000365534:A29V	A	+	2	0	THNSL1	25352244	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.012000	0.13287	-0.006000	0.14370	0.557000	0.71058	GCA	.	.	.	none		0.363	THNSL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394913.1	NM_024838		T	25312238	C	T	25312238	3	4	44	1	0	0	0	0	1	0	0	0	15874	710	25	2	88	2	THNSL1	10	25312238	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08	13788470	25312238	110222509	40	3084											
TULP3	7289	hgsc.bcm.edu	37	chr12	3048537	3048537	+	Missense_Mutation	SNP	A	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	cgtgttcacactggattacaActacccactttgtgcagtac	10	12	7	12	1	1	0	1	0	0	0	1	1	1	1	1	1	5	3	1	1	4	5			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr12:3048537A>C	ENST00000448120.2	+	11	1307	c.1256A>C	c.(1255-1257)aAc>aCc	p.N419T	TULP3_ENST00000397132.2_Missense_Mutation_p.N419T	NM_003324.4	NP_003315.2	O75386	TULP3_HUMAN	tubby like protein 3	419					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)			CTGGATTACAACTACCCACTT	0.443																																					p.N419T		Atlas-SNP	.											.,1	TULP3	45	.	0			c.A1256C						PASS	.						313	257	276					12																	3048537		2203	4300	6503	SO:0001583	missense	7289	exon11			ATTACAACTACCC	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.1256A>C	chr12.hg19:g.3048537A>C	ENSP00000410051:p.Asn419Thr	170.0	0.0	.		165.0	48.0	.	NM_003324	B3KNB7|B7Z6A2|D3DUQ4|F8WBZ9|Q8N5B0	Missense_Mutation	SNP	ENST00000448120.2	hg19	CCDS8519.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.02|12.02	1.811439|1.811439	0.32053|0.32053	.|.	.|.	ENSG00000078246|ENSG00000078246	ENST00000228245;ENST00000542730;ENST00000448120;ENST00000397132|ENST00000541678;ENST00000538704	D;D|.	0.85088|.	-1.94;-1.94|.	5.64|5.64	1.97|1.97	0.26223|0.26223	Tubby, C-terminal (3);|.	0.134805|.	0.64402|.	D|.	0.000003|.	T|T	0.52661|0.52661	0.1748|0.1748	L|L	0.42487|0.42487	1.325|1.325	0.47214|0.47214	D|D	0.999359|0.999359	B;B;B|.	0.34161|.	0.051;0.078;0.439|.	B;B;B|.	0.40982|.	0.14;0.345;0.332|.	T|T	0.36138|0.36138	-0.9760|-0.9760	9|5	.|.	.|.	.|.	1.337|1.337	8.4366|8.4366	0.32791|0.32791	0.7077:0.0:0.2923:0.0|0.7077:0.0:0.2923:0.0	.|.	243;419;419|.	B7Z1E7;O75386;F8WBZ9|.	.;TULP3_HUMAN;.|.	T|H	419;243;419;419|95;84	ENSP00000410051:N419T;ENSP00000380321:N419T|.	.|.	N|Q	+|+	2|3	0|2	TULP3|TULP3	2918798|2918798	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.640000|0.640000	0.38277|0.38277	1.203000|1.203000	0.32284|0.32284	0.089000|0.089000	0.17243|0.17243	-0.589000|-0.589000	0.04120|0.04120	AAC|CAA	.	.	.	none		0.443	TULP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398468.1	NM_003324		C	3048537	A	C	3048537	3	2	44	1	0	0	0	0	1	0	0	0	16787	43	2	5	1298	5	TULP3	12	3048537	Missense_Mutation	SNP	A	TCGA-A4-7583-01A-11D-2136-08		3048537	130803358	41	3085											
HEBP1	50865	hgsc.bcm.edu	37	chr12	13142261	13142261	+	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	cgaccttgggcattgcttccCgtagagcctcatccacaggc	7	9	10	15	2	1	1	1	0	0	1	3	2	3	1	4	2	2	3	4	2	1	4			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr12:13142261C>A	ENST00000014930.4	-	2	325	c.167G>T	c.(166-168)cGg>cTg	p.R56L	HEBP1_ENST00000536942.1_Missense_Mutation_p.R56L	NM_015987.4	NP_057071.2	Q9NRV9	HEBP1_HUMAN	heme binding protein 1	56					circadian rhythm (GO:0007623)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	heme binding (GO:0020037)			breast(1)|endometrium(1)|large_intestine(3)|lung(1)|urinary_tract(1)	7		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.153)		CATTGCTTCCCGTAGAGCCTC	0.542																																					p.R56L		Atlas-SNP	.											.	HEBP1	16	.	0			c.G167T						PASS	.						203	153	170					12																	13142261		2203	4300	6503	SO:0001583	missense	50865	exon2			GCTTCCCGTAGAG	AF117615	CCDS31749.1	12p13.2	2014-01-30			ENSG00000013583	ENSG00000013583		"Endogenous ligands"	17176	protein-coding gene	gene with protein product		605826				10640688	Standard	NM_015987		Approved	HEBP, HBP	uc001rbd.3	Q9NRV9	OTTHUMG00000168771	ENST00000014930.4:c.167G>T	chr12.hg19:g.13142261C>A	ENSP00000014930:p.Arg56Leu	118.0	0.0	.		138.0	7.0	.	NM_015987	A8K1G2|Q9Y5Z5	Missense_Mutation	SNP	ENST00000014930.4	hg19	CCDS31749.1	.	.	.	.	.	.	.	.	.	.	C	13.94	2.385915	0.42308	.	.	ENSG00000013583	ENST00000014930;ENST00000536942	T;T	0.22743	1.94;1.94	6.02	3.89	0.44902	Regulatory factor, effector, bacterial (1);	0.389996	0.27749	N	0.018006	T	0.21307	0.0513	M	0.62723	1.935	0.20926	N	0.999824	B	0.28850	0.225	B	0.34242	0.178	T	0.13710	-1.0499	10	0.22706	T	0.39	-10.7345	7.1904	0.25822	0.0:0.676:0.0:0.324	.	56	Q9NRV9	HEBP1_HUMAN	L	56	ENSP00000014930:R56L;ENSP00000441678:R56L	ENSP00000014930:R56L	R	-	2	0	HEBP1	13033528	0.760000	0.28428	0.984000	0.44739	0.971000	0.66376	2.083000	0.41615	1.554000	0.49487	0.650000	0.86243	CGG	.	.	.	none		0.542	HEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401001.1			A	13142261	C	A	13142261	3	1	44	1	0	0	0	0	1	0	0	0	7043	652	23	4	414	4	HEBP1	12	13142261	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08	10093724	13142261	120709634	42	3086											
HOXC11	3227	hgsc.bcm.edu	37	chr12	54367330	54367330	+	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	ggccgacgagcttatgcaccGggagtgcctgcctccttcca	6	8	12	15	3	0	0	0	0	0	0	2	3	2	1	6	2	4	2	6	2	1	2			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr12:54367330G>T	ENST00000546378.1	+	1	421	c.305G>T	c.(304-306)cGg>cTg	p.R102L	HOTAIR_ENST00000424518.1_RNA|HOTAIR_ENST00000455246.1_RNA|HOXC11_ENST00000243082.4_Missense_Mutation_p.R102L			O43248	HXC11_HUMAN	homeobox C11	102					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						CTTATGCACCGGGAGTGCCTG	0.672			T	NUP98	AML																																p.R102L		Atlas-SNP	.		Dom	yes		12	12q13.3	3227	homeo box C11		L	HOXC11_ENST00000546378,bladder,carcinoma,0,1	HOXC11	32	.	0			c.G305T						PASS	.						94	106	102					12																	54367330		2203	4300	6503	SO:0001583	missense	3227	exon1			TGCACCGGGAGTG		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.305G>T	chr12.hg19:g.54367330G>T	ENSP00000446680:p.Arg102Leu	258.0	1.0	.		192.0	9.0	.	NM_014212	A8K7D1|Q96DH2	Missense_Mutation	SNP	ENST00000546378.1	hg19	CCDS8867.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.280254	0.80692	.	.	ENSG00000123388	ENST00000546378;ENST00000243082	T;T	0.59083	0.29;0.29	4.31	4.31	0.51392	Domain of unknown function DUF3528, homeobox protein, eukaryotic (1);	0.000000	0.85682	D	0.000000	T	0.77412	0.4126	M	0.83483	2.645	0.58432	D	0.999996	D	0.76494	0.999	D	0.79108	0.992	T	0.81922	-0.0711	10	0.87932	D	0	.	16.0846	0.81031	0.0:0.0:1.0:0.0	.	102	O43248	HXC11_HUMAN	L	102	ENSP00000446680:R102L;ENSP00000243082:R102L	ENSP00000243082:R102L	R	+	2	0	HOXC11	52653597	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	9.221000	0.95188	2.386000	0.81285	0.555000	0.69702	CGG	.	.	.	none		0.672	HOXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358869.2			T	54367330	G	T	54367330	3	4	44	1	0	0	0	0	1	0	0	0	7317	1116	39	4	307	4	HOXC11	12	54367330	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08	41225069	54367330	79484565	43	3087											
ACAD10	80724	hgsc.bcm.edu	37	chr12	112183962	112183962	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgataggagaaagccaaagcTgaaggactttggaacctttt	14	10	11	6	0	0	3	0	2	0	1	0	6	0	5	2	3	3	1	2	3	5	4			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr12:112183962T>C	ENST00000313698.4	+	14	2285	c.2130T>C	c.(2128-2130)gcT>gcC	p.A710A	ACAD10_ENST00000392636.2_Silent_p.A312A|ACAD10_ENST00000455480.2_Silent_p.A741A|ACAD10_ENST00000413681.3_3'UTR	NM_025247.5	NP_079523.3	Q6JQN1	ACD10_HUMAN	acyl-CoA dehydrogenase family, member 10	710						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						AAGCCAAAGCTGAAGGACTTT	0.433																																					p.A741A		Atlas-SNP	.											.	ACAD10	93	.	0			c.T2223C						PASS	.						88	88	88					12																	112183962		2203	4300	6503	SO:0001819	synonymous_variant	80724	exon15			CAAAGCTGAAGGA	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.2130T>C	chr12.hg19:g.112183962T>C		132.0	0.0	.		101.0	34.0	.	NM_001136538	G3XAJ0|Q8N828|Q8NAP2|Q96BX5	Silent	SNP	ENST00000313698.4	hg19	CCDS31903.1																																																																																			.	.	.	none		0.433	ACAD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368307.1	NM_025247		C	112183962	T	C	112183962	2	2	44	1	0	0	0	0	0	0	0	1	108	1567	55	3		3	ACAD10	12	112183962	Silent	SNP	T	TCGA-A4-7583-01A-11D-2136-08	57816632	112183962	21667933	44	3088											
GAS6	2621	hgsc.bcm.edu	37	chr13	114523928	114523928	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccaggtccagcagcctccggTtgacctccagtgtcatgcag	7	8	11	15	1	1	1	1	1	0	0	4	1	4	1	6	2	3	3	6	2	0	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr13:114523928T>C	ENST00000327773.6	-	15	2092	c.1946A>G	c.(1945-1947)aAc>aGc	p.N649S	GAS6_ENST00000450766.1_Missense_Mutation_p.N376S|GAS6_ENST00000357389.3_Missense_Mutation_p.N692S|GAS6_ENST00000418959.3_Missense_Mutation_p.N350S|GAS6_ENST00000355761.4_Missense_Mutation_p.N595S|GAS6-AS1_ENST00000458001.1_RNA	NM_000820.2	NP_000811.1	Q14393	GAS6_HUMAN	growth arrest-specific 6	692	Laminin G-like 2. {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)				CAGCCTCCGGTTGACCTCCAG	0.662																																					p.N649S		Atlas-SNP	.											.	GAS6	75	.	0			c.A1946G						PASS	.						51	45	47					13																	114523928		2202	4299	6501	SO:0001583	missense	2621	exon15			CTCCGGTTGACCT		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.1946A>G	chr13.hg19:g.114523928T>C	ENSP00000331831:p.Asn649Ser	69.0	0.0	.		52.0	23.0	.	NM_000820	B3KRQ7|B3KVL4|E9PBL7|Q6IMN1|Q7Z7N3	Missense_Mutation	SNP	ENST00000327773.6	hg19	CCDS45072.1	.	.	.	.	.	.	.	.	.	.	T	12.32	1.901729	0.33535	.	.	ENSG00000183087	ENST00000357389;ENST00000355761;ENST00000450766;ENST00000418959;ENST00000327773	D;D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68;-1.68	4.72	3.54	0.40534	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	T	0.79924	0.4530	M	0.83223	2.63	0.44547	D	0.997504	P;B;B	0.41214	0.742;0.015;0.1	B;B;B	0.32864	0.154;0.026;0.01	T	0.78204	-0.2295	9	0.62326	D	0.03	-27.6441	8.071	0.30689	0.0:0.1832:0.0:0.8168	.	692;376;649	Q14393;B3KVL4;Q14393-2	GAS6_HUMAN;.;.	S	692;595;376;350;649	ENSP00000349962:N692S;ENSP00000348003:N595S;ENSP00000416498:N376S;ENSP00000400117:N350S;ENSP00000331831:N649S	ENSP00000331831:N649S	N	-	2	0	GAS6	113590015	0.993000	0.37304	0.858000	0.33744	0.120000	0.20174	2.505000	0.45424	0.664000	0.31047	0.379000	0.24179	AAC	.	.	.	none		0.662	GAS6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045946.2	NM_000820		C	114523928	T	C	114523928	3	2	44	1	0	0	0	0	1	0	0	0	6256	1725	60	3	94	3	GAS6	13	114523928	Missense_Mutation	SNP	T	TCGA-A4-7583-01A-11D-2136-08		114523928	645950	45	3089											
RBM23	55147	hgsc.bcm.edu	37	chr14	23374814	23374814	+	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	cagtgttcattatcaacccaCctgactgggctcttctctct	7	14	6	14	0	5	1	2	1	3	0	6	1	5	1	2	1	1	2	2	1	2	3			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr14:23374814C>G	ENST00000359890.3	-	6	651		c.e6+1		RBM23_ENST00000399922.2_Splice_Site|RBM23_ENST00000542016.2_Splice_Site|RBM23_ENST00000556984.1_5'Flank|RBM23_ENST00000555209.1_Intron|RBM23_ENST00000346528.5_Intron	NM_001077351.1	NP_001070819.1	Q86U06	RBM23_HUMAN	RNA binding motif protein 23						mRNA processing (GO:0006397)	membrane (GO:0016020)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(3)|kidney(2)|lung(3)|prostate(1)|skin(1)	10	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.0128)		TATCAACCCACCTGACTGGGC	0.378																																					.		Atlas-SNP	.											.	RBM23	44	.	0			c.407+1G>C						PASS	.						90	80	83					14																	23374814		1844	4103	5947	SO:0001630	splice_region_variant	55147	exon6			AACCCACCTGACT	AF275678	CCDS41919.1, CCDS41920.1, CCDS41921.1	14q11.1	2014-07-03	2004-04-23	2004-04-23		ENSG00000100461		"RNA binding motif (RRM) containing"	20155	protein-coding gene	gene with protein product	"coactivator of activating protein-1 and estrogen recep- tors beta"		"RNA-binding region (RNP1, RRM) containing 4"	RNPC4		15694343	Standard	NM_018107		Approved	FLJ10482, CAPERbeta	uc001whg.3	Q86U06		ENST00000359890.3:c.455+1G>C	chr14.hg19:g.23374814C>G		99.0	0.0	.		40.0	26.0	.	NM_018107	D3DS32|Q8ND16|Q8TB88|Q8WY40|Q9BUJ1|Q9NVV7	Splice_Site	SNP	ENST00000359890.3	hg19	CCDS41921.1	.	.	.	.	.	.	.	.	.	.	C	16.23	3.065110	0.55432	.	.	ENSG00000100461	ENST00000359890;ENST00000338980;ENST00000399922	.	.	.	4.88	3.99	0.46301	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2615	0.54652	0.0:0.9161:0.0:0.0839	.	.	.	.	.	-1	.	.	.	-	.	.	RBM23	22444654	1.000000	0.71417	0.998000	0.56505	0.851000	0.48451	3.163000	0.50763	1.422000	0.47177	0.655000	0.94253	.	.	.	.	none		0.378	RBM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000413545.3		Intron	G	23374814	C	G	23374814	5	3	44	1	0	0	0	0	0	0	1	0	13136	521	18	4	899	4	RBM23	14	23374814	Splice_Site	SNP	C	TCGA-A4-7583-01A-11D-2136-08		23374814	83974726	46	3090											
SMG1	23049	hgsc.bcm.edu	37	chr16	18840922	18840922	+	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	tccgagggcttggttgggtaGccctatcaagagctgcctca	7	10	13	11	1	2	1	2	0	0	1	3	2	3	1	3	3	3	4	3	3	3	4			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr16:18840922G>T	ENST00000446231.2	-	54	9701	c.9289C>A	c.(9289-9291)Cta>Ata	p.L3097I	SMG1_ENST00000389467.3_Missense_Mutation_p.L3097I			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	3097					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						TGGTTGGGTAGCCCTATCAAG	0.468																																					p.L3097I		Atlas-SNP	.											.	SMG1	401	.	0			c.C9289A						PASS	.						58	57	57					16																	18840922		1905	4128	6033	SO:0001583	missense	23049	exon54			TGGGTAGCCCTAT	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.9289C>A	chr16.hg19:g.18840922G>T	ENSP00000402515:p.Leu3097Ile	38.0	0.0	.		70.0	40.0	.	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	hg19	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	G	14.36	2.510741	0.44660	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.01005	5.45;5.45	6.07	5.11	0.69529	.	0.000000	0.53938	D	0.000041	T	0.00875	0.0029	N	0.12182	0.205	0.41248	D	0.986699	B	0.13145	0.007	B	0.15484	0.013	T	0.67565	-0.5638	10	0.20519	T	0.43	.	16.7418	0.85461	0.0:0.0:0.8697:0.1303	.	3097	Q96Q15	SMG1_HUMAN	I	3097	ENSP00000402515:L3097I;ENSP00000374118:L3097I	ENSP00000374118:L3097I	L	-	1	2	SMG1	18748423	1.000000	0.71417	0.831000	0.32960	0.967000	0.64934	6.417000	0.73337	1.558000	0.49541	0.585000	0.79938	CTA	.	.	.	none		0.468	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		T	18840922	G	T	18840922	3	4	44	1	0	0	0	0	1	0	0	0	14808	962	34	4	1736	4	SMG1	16	18840922	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08		18840922	71513831	47	3091											
FTSJD1	55783	hgsc.bcm.edu	37	chr16	71317552	71317552	+	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	gttgataatttcttctctctCtctttgaataatgaaatgca	11	18	5	7	0	4	3	0	3	4	0	6	3	4	3	0	0	1	2	0	0	4	6			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr16:71317552C>T	ENST00000338099.5	-	3	2608	c.2272G>A	c.(2272-2274)Gag>Aag	p.E758K	CMTR2_ENST00000434935.2_Missense_Mutation_p.E758K			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	758					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)										TCTTCTCTCTCTCTTTGAATA	0.373																																					p.E758K		Atlas-SNP	.											.	FTSJD1	70	.	0			c.G2272A						PASS	.						38	42	41					16																	71317552		2198	4300	6498	SO:0001583	missense	55783	exon3			CTCTCTCTCTTTG	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.2272G>A	chr16.hg19:g.71317552C>T	ENSP00000337512:p.Glu758Lys	31.0	0.0	.		67.0	17.0	.	NM_018348	B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Missense_Mutation	SNP	ENST00000338099.5	hg19	CCDS10898.1	.	.	.	.	.	.	.	.	.	.	C	14.34	2.507361	0.44558	.	.	ENSG00000180917	ENST00000338099;ENST00000434935	T;T	0.15603	2.41;2.41	5.8	4.8	0.61643	.	0.225081	0.35677	N	0.003053	T	0.09555	0.0235	N	0.17082	0.46	0.32079	N	0.593443	B	0.21071	0.051	B	0.17979	0.02	T	0.07214	-1.0784	10	0.27785	T	0.31	-35.113	7.8477	0.29435	0.0:0.6486:0.2684:0.083	.	758	Q8IYT2	FTSJ1_HUMAN	K	758	ENSP00000337512:E758K;ENSP00000411148:E758K	ENSP00000337512:E758K	E	-	1	0	FTSJD1	69875053	0.991000	0.36638	1.000000	0.80357	0.802000	0.45316	1.495000	0.35627	2.741000	0.93983	0.585000	0.79938	GAG	.	.	.	none		0.373	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348		T	71317552	C	T	71317552	3	4	44	1	0	0	0	0	1	0	0	0	6097	922	32	2	44	2	FTSJD1	16	71317552	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08	52476630	71317552	19037201	48	3092											
PLCG2	5336	hgsc.bcm.edu	37	chr16	81990321	81990321	+	Missense_Mutation	SNP	T	T	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	agagcgaagaggaactttacTcctcctgtcgccagctgagg	10	8	12	11	2	0	3	0	1	0	2	3	5	2	4	3	2	4	1	3	2	3	2			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr16:81990321T>G	ENST00000359376.3	+	32	3806	c.3592T>G	c.(3592-3594)Tcc>Gcc	p.S1198A		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	1198					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						GGAACTTTACTCCTCCTGTCG	0.527																																					p.S1198A		Atlas-SNP	.											.	PLCG2	276	.	0			c.T3592G						PASS	.						59	61	61					16																	81990321		1979	4160	6139	SO:0001583	missense	5336	exon32			CTTTACTCCTCCT		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.3592T>G	chr16.hg19:g.81990321T>G	ENSP00000352336:p.Ser1198Ala	67.0	0.0	.		77.0	28.0	.	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	hg19	CCDS42204.1	.	.	.	.	.	.	.	.	.	.	T	9.506	1.104525	0.20632	.	.	ENSG00000197943	ENST00000359376	T	0.65732	-0.17	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.53658	0.1810	L	0.52573	1.65	0.45205	D	0.998216	B	0.16166	0.016	B	0.12156	0.007	T	0.50224	-0.8853	10	0.10111	T	0.7	.	13.9529	0.64129	0.0:0.0:0.0:1.0	.	1198	P16885	PLCG2_HUMAN	A	1198	ENSP00000352336:S1198A	ENSP00000352336:S1198A	S	+	1	0	PLCG2	80547822	0.988000	0.35896	0.980000	0.43619	0.866000	0.49608	2.961000	0.49168	2.106000	0.64143	0.454000	0.30748	TCC	.	.	.	none		0.527	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1			G	81990321	T	G	81990321	3	3	44	1	0	0	0	0	1	0	0	0	12043	1551	54	5	3714	5	PLCG2	16	81990321	Missense_Mutation	SNP	T	TCGA-A4-7583-01A-11D-2136-08	10672769	81990321	8364432	49	3093											
CRLF3	51379	hgsc.bcm.edu	37	chr17	29119514	29119514	+	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	gctctggagtagagaacaccCgatgattcagaatcgttccg	11	9	11	10	3	2	3	1	1	1	2	4	6	3	4	2	1	1	3	2	1	3	3			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr17:29119514C>A	ENST00000324238.6	-	6	1027	c.903G>T	c.(901-903)tcG>tcT	p.S301S	CRLF3_ENST00000577725.1_Intron|CTD-2349P21.9_ENST00000580085.1_lincRNA|CRLF3_ENST00000544695.1_Silent_p.S185S	NM_015986.3	NP_057070.3	Q8IUI8	CRLF3_HUMAN	cytokine receptor-like factor 3	301					G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of cell growth (GO:0030308)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)		p.S301S(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	17		all_hematologic(16;0.014)|Acute lymphoblastic leukemia(14;0.0236)|Myeloproliferative disorder(56;0.0255)				AGAGAACACCCGATGATTCAG	0.433																																					p.S301S	Pancreas(30;346 881 29244 33464 41299)	Atlas-SNP	.											.	CRLF3	36	.	1	Substitution - coding silent(1)	lung(1)	c.G903T						PASS	.						153	147	149					17																	29119514		2203	4300	6503	SO:0001819	synonymous_variant	51379	exon6			AACACCCGATGAT	AF120151	CCDS32607.1	17q11.2	2008-05-02				ENSG00000176390			17177	protein-coding gene	gene with protein product		614853					Standard	NM_015986		Approved	CREME9, CYTOR4	uc002hfr.4	Q8IUI8		ENST00000324238.6:c.903G>T	chr17.hg19:g.29119514C>A		205.0	0.0	.		189.0	11.0	.	NM_015986	A6NJF3|B2R8C3|Q2MLY7|Q9UNI3|Q9Y6M8	Silent	SNP	ENST00000324238.6	hg19	CCDS32607.1																																																																																			.	.	.	none		0.433	CRLF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444354.1			A	29119514	C	A	29119514	2	1	44	1	0	0	0	0	0	0	0	1	3890	639	23	4		4	CRLF3	17	29119514	Silent	SNP	C	TCGA-A4-7583-01A-11D-2136-08		29119514	52075696	50	3094											
ZNHIT3	9326	hgsc.bcm.edu	37	chr17	34849806	34849806	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgattttctcaatagtgAtgaggaagaagacagagttt	14	12	11	4	0	1	6	1	3	1	3	2	7	1	7	0	1	1	2	0	1	4	4			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr17:34849806A>G	ENST00000225410.4	+	4	307	c.242A>G	c.(241-243)gAt>gGt	p.D81G	ZNHIT3_ENST00000592616.1_Missense_Mutation_p.D81G|ZNHIT3_ENST00000490126.2_5'UTR|RNA5SP439_ENST00000517103.1_RNA|ZNHIT3_ENST00000590858.1_Intron|ZNHIT3_ENST00000588253.1_5'UTR	NM_004773.2	NP_004764.1	Q15649	ZNHI3_HUMAN	zinc finger, HIT-type containing 3	81					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			lung(1)|pancreas(1)|prostate(1)	3		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0188)		CTCAATAGTGATGAGGAAGAA	0.373																																					p.D81G	Pancreas(89;112 2361 26810)	Atlas-SNP	.											.	ZNHIT3	14	.	0			c.A242G						PASS	.						152	148	149					17																	34849806		2203	4300	6503	SO:0001583	missense	9326	exon4			ATAGTGATGAGGA	L40410	CCDS11312.1, CCDS62156.1	17q21.1	2014-04-10	2010-09-15	2005-09-08	ENSG00000108278	ENSG00000273611		"Zinc fingers, HIT-type"	12309	protein-coding gene	gene with protein product		604500	"thyroid hormone receptor interactor 3", "zinc finger, HIT type 3"	TRIP3		7776974	Standard	NM_004773		Approved		uc002hms.1	Q15649	OTTHUMG00000188436	ENST00000225410.4:c.242A>G	chr17.hg19:g.34849806A>G	ENSP00000225410:p.Asp81Gly	128.0	0.0	.		162.0	65.0	.	NM_004773	A8K493|K7EQP1|Q8WVJ3	Missense_Mutation	SNP	ENST00000225410.4	hg19	CCDS11312.1	.	.	.	.	.	.	.	.	.	.	A	11.65	1.700781	0.30142	.	.	ENSG00000108278	ENST00000225410	.	.	.	6.02	4.94	0.65067	.	0.084595	0.85682	D	0.000000	T	0.69584	0.3127	M	0.72353	2.195	0.80722	D	1	D	0.76494	0.999	D	0.64144	0.922	T	0.68387	-0.5422	9	0.37606	T	0.19	-14.422	9.5969	0.39580	0.8443:0.0:0.0:0.1557	.	81	Q15649	ZNHI3_HUMAN	G	81	.	ENSP00000225410:D81G	D	+	2	0	ZNHIT3	31923919	1.000000	0.71417	1.000000	0.80357	0.398000	0.30690	5.963000	0.70372	1.084000	0.41184	-0.327000	0.08410	GAT	.	.	.	none		0.373	ZNHIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256697.1	NM_004773		G	34849806	A	G	34849806	3	3	44	1	0	0	0	0	1	0	0	0	18220	333	12	3	256	3	ZNHIT3	17	34849806	Missense_Mutation	SNP	A	TCGA-A4-7583-01A-11D-2136-08	5730292	34849806	46345404	51	3095											
DLX3	1747	hgsc.bcm.edu	37	chr17	48072053	48072053	+	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	ctcacctgggtcctgggctgGcagcggctgctcccgatacg	4	8	14	15	3	1	0	1	0	0	0	3	1	3	0	3	4	3	4	3	4	1	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr17:48072053G>C	ENST00000434704.2	-	1	535	c.310C>G	c.(310-312)Cca>Gca	p.P104A	RP11-1094H24.3_ENST00000511867.1_lincRNA|DLX3_ENST00000512495.2_5'Flank	NM_005220.2	NP_005211.1	O60479	DLX3_HUMAN	distal-less homeobox 3	104					blood vessel development (GO:0001568)|odontoblast differentiation (GO:0071895)|odontogenesis of dentin-containing tooth (GO:0042475)|placenta development (GO:0001890)	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	12						TCCTGGGCTGGCAGCGGCTGC	0.622																																					p.P104A		Atlas-SNP	.											.	DLX3	28	.	0			c.C310G						PASS	.						22	28	26					17																	48072053		2195	4295	6490	SO:0001583	missense	1747	exon1			GGGCTGGCAGCGG		CCDS11556.1	17q21.33	2011-06-20	2005-12-22			ENSG00000064195		"Homeoboxes / ANTP class : NKL subclass"	2916	protein-coding gene	gene with protein product		600525	"distal-less homeo box 3"			7613049	Standard	NM_005220		Approved		uc002ipy.3	O60479		ENST00000434704.2:c.310C>G	chr17.hg19:g.48072053G>C	ENSP00000389870:p.Pro104Ala	69.0	0.0	.		51.0	25.0	.	NM_005220	B3KQL6	Missense_Mutation	SNP	ENST00000434704.2	hg19	CCDS11556.1	.	.	.	.	.	.	.	.	.	.	G	13.39	2.222006	0.39300	.	.	ENSG00000064195	ENST00000434704	D	0.91945	-2.94	5.01	5.01	0.66863	Homeodomain-like (1);	0.078892	0.53938	D	0.000057	D	0.86029	0.5835	N	0.21240	0.645	0.80722	D	1	B	0.11235	0.004	B	0.24006	0.05	T	0.80538	-0.1338	10	0.24483	T	0.36	-29.5674	13.6755	0.62451	0.0:0.0:1.0:0.0	.	104	O60479	DLX3_HUMAN	A	104	ENSP00000389870:P104A	ENSP00000389870:P104A	P	-	1	0	DLX3	45427052	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	4.079000	0.57613	2.617000	0.88574	0.491000	0.48974	CCA	.	.	.	none		0.622	DLX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366307.1			C	48072053	G	C	48072053	3	2	44	1	0	0	0	0	1	0	0	0	4574	1203	42	4	565	4	DLX3	17	48072053	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08	13222247	48072053	33123157	52	3096											
TBCD	6904	hgsc.bcm.edu	37	chr17	80885835	80885835	+	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	ctgacacttctgctggctcgGagccagcctgagctgatcga	7	9	12	13	2	1	3	0	3	1	0	3	5	1	4	2	2	4	3	2	2	0	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr17:80885835G>C	ENST00000355528.4	+	30	2794	c.2664G>C	c.(2662-2664)cgG>cgC	p.R888R	TBCD_ENST00000539345.2_Silent_p.R888R	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	888					'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)			TGCTGGCTCGGAGCCAGCCTG	0.642																																					p.R888R		Atlas-SNP	.											.	TBCD	94	.	0			c.G2664C						PASS	.						57	60	59					17																	80885835		2056	4211	6267	SO:0001819	synonymous_variant	6904	exon30			GGCTCGGAGCCAG	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.2664G>C	chr17.hg19:g.80885835G>C		108.0	0.0	.		97.0	33.0	.	NM_005993	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Silent	SNP	ENST00000355528.4	hg19	CCDS45818.1																																																																																			.	.	.	none		0.642	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993		C	80885835	G	C	80885835	2	2	44	1	0	0	0	0	0	0	0	1	15645	1161	41	4		4	TBCD	17	80885835	Silent	SNP	G	TCGA-A4-7583-01A-11D-2136-08	32813782	80885835	309375	53	3097											
NPC1	4864	hgsc.bcm.edu	37	chr18	21128030	21128030	+	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	cattatagtaattattgacaGggaaggtaatcacaagggca	16	10	10	5	0	1	1	1	1	0	0	1	2	1	2	0	3	0	3	0	3	7	6			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr18:21128030G>T	ENST00000269228.5	-	11	2251	c.1697C>A	c.(1696-1698)cCt>cAt	p.P566H	NPC1_ENST00000540608.1_5'UTR|NPC1_ENST00000412552.2_Intron	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	566					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)					ATTATTGACAGGGAAGGTAAT	0.423																																					p.P566H		Atlas-SNP	.											.	NPC1	114	.	0			c.C1697A						PASS	.						153	147	149					18																	21128030		2203	4300	6503	SO:0001583	missense	4864	exon11			TTGACAGGGAAGG	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.1697C>A	chr18.hg19:g.21128030G>T	ENSP00000269228:p.Pro566His	207.0	0.0	.		184.0	72.0	.	NM_000271	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	hg19	CCDS11878.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.682504	0.88542	.	.	ENSG00000141458	ENST00000269228;ENST00000540608	D	0.93811	-3.29	5.72	4.85	0.62838	.	0.000000	0.85682	D	0.000000	D	0.95906	0.8667	M	0.81942	2.565	0.80722	D	1	D	0.63880	0.993	P	0.58928	0.848	D	0.96104	0.9071	10	0.66056	D	0.02	-8.8197	14.813	0.70010	0.0692:0.0:0.9308:0.0	.	566	O15118	NPC1_HUMAN	H	566;411	ENSP00000269228:P566H	ENSP00000269228:P566H	P	-	2	0	NPC1	19382028	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.865000	0.87049	1.417000	0.47077	0.563000	0.77884	CCT	.	.	.	none		0.423	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271		T	21128030	G	T	21128030	3	4	44	1	0	0	0	0	1	0	0	0	10577	1000	35	4	2199	4	NPC1	18	21128030	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08		21128030	56949218	54	3098											
RNF165	494470	hgsc.bcm.edu	37	chr18	44013351	44013353	+	In_Frame_Del	DEL	CCC	CCC	-																															gtcgctgaccccgctgcccaCcctgcagttccaggacgtca																										TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	CCC	CCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr18:44013351_44013353delCCC	ENST00000269439.7	+	2	311_313	c.260_262delCCC	c.(259-264)accctg>atg	p.87_88TL>M	RNF165_ENST00000543885.1_Intron	NM_152470.2	NP_689683.2	Q6ZSG1	RN165_HUMAN	ring finger protein 165	87							zinc ion binding (GO:0008270)			NS(1)|large_intestine(4)|lung(6)	11				READ - Rectum adenocarcinoma(1;0.0873)		CCGCTGCCCACCCTGCAGTTCCA	0.7																																					p.87_87del		Atlas-INDEL	.											.	RNF165	34	.	0			c.259_261del						PASS	.																																			SO:0001651	inframe_deletion	494470	exon2			.	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.260_262delCCC	chr18.hg19:g.44013351_44013353delCCC	ENSP00000269439:p.Thr87_Leu88delinsMet	51.0	0.0	0		49.0	15.0	0.306122	NM_152470	B3KVD1	In_Frame_Del	DEL	ENST00000269439.7	hg19	CCDS32823.1																																																																																			.	.	.	none		0.7	RNF165-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445358.1	NM_152470		-	44013353	CCC	-	44013351	7	5	44	1	0	1	0	1	0	0	0	0	13469	507	18	0	266	0	RNF165	18	44013351	In_Frame_Del	DEL	CCC	TCGA-A4-7583-01A-11D-2136-08	22885321	44013351	34063897	55	3099	40	2									
RNF165	494470	hgsc.bcm.edu	37	chr18	44013357	44013357	+	Missense_Mutation	SNP	A	A	G																															gaccccgctgcccaccctgcAgttccaggacgtcacaggtc																										TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr18:44013357A>G	ENST00000269439.7	+	2	317	c.266A>G	c.(265-267)cAg>cGg	p.Q89R	RNF165_ENST00000543885.1_Intron	NM_152470.2	NP_689683.2	Q6ZSG1	RN165_HUMAN	ring finger protein 165	89							zinc ion binding (GO:0008270)			NS(1)|large_intestine(4)|lung(6)	11				READ - Rectum adenocarcinoma(1;0.0873)		CCCACCCTGCAGTTCCAGGAC	0.697																																					p.Q89R		Atlas-SNP	.											.	RNF165	34	.	0			c.A266G						PASS	.						35	34	34					18																	44013357		2203	4300	6503	SO:0001583	missense	494470	exon2			CCCTGCAGTTCCA	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.266A>G	chr18.hg19:g.44013357A>G	ENSP00000269439:p.Gln89Arg	58.0	0.0	.		58.0	16.0	.	NM_152470	B3KVD1	Missense_Mutation	SNP	ENST00000269439.7	hg19	CCDS32823.1	.	.	.	.	.	.	.	.	.	.	A	9.420	1.082835	0.20309	.	.	ENSG00000141622	ENST00000269439	T	0.18657	2.2	5.48	4.27	0.50696	.	0.146503	0.47093	D	0.000241	T	0.18676	0.0448	L	0.47716	1.5	0.80722	D	1	B	0.26445	0.149	B	0.28784	0.094	T	0.03717	-1.1010	10	0.12766	T	0.61	-5.9439	13.0518	0.58958	0.8124:0.1876:0.0:0.0	.	89	Q6ZSG1	RN165_HUMAN	R	89	ENSP00000269439:Q89R	ENSP00000269439:Q89R	Q	+	2	0	RNF165	42267355	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.579000	0.46059	2.086000	0.62901	0.455000	0.32223	CAG	.	.	.	none		0.697	RNF165-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445358.1	NM_152470		G	44013357	A	G	44013357	3	3	44	1	0	0	0	0	1	0	0	0	13469	188	7	3	272	3	RNF165	18	44013357	Missense_Mutation	SNP	A	TCGA-A4-7583-01A-11D-2136-08	6	44013357	34063891	56	3100	40	2									
ABCA7	10347	hgsc.bcm.edu	37	chr19	1062293	1062293	+	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	tgcgcgcctgcgcggtgtccCggaggcccaggttgcccagg	3	6	17	15	5	0	0	0	0	0	0	1	1	1	1	4	5	3	1	4	5	0	1	rs144378856		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr19:1062293C>A	ENST00000263094.6	+	42	5924	c.5693C>A	c.(5692-5694)cCg>cAg	p.P1898Q	ABCA7_ENST00000433129.1_Missense_Mutation_p.P1898Q|ABCA7_ENST00000435683.2_Missense_Mutation_p.P1760Q	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1898	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)		CGCGGTGTCCCGGAGGCCCAG	0.677																																					p.P1898Q		Atlas-SNP	.											.	ABCA7	174	.	0			c.C5693A						PASS	.						78	86	83					19																	1062293		2203	4296	6499	SO:0001583	missense	10347	exon42			GTGTCCCGGAGGC	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.5693C>A	chr19.hg19:g.1062293C>A	ENSP00000263094:p.Pro1898Gln	244.0	0.0	.		128.0	8.0	.	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	hg19	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	C	12.49	1.952395	0.34471	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.96396	-4.0;-4.0	3.4	2.34	0.29019	ATPase, AAA+ type, core (1);ABC transporter-like (2);	.	.	.	.	D	0.96827	0.8964	L	0.56280	1.765	0.33986	D	0.648578	D;P	0.89917	1.0;0.941	D;P	0.83275	0.996;0.787	D	0.96923	0.9675	9	0.87932	D	0	.	9.6915	0.40131	0.0:0.8916:0.0:0.1084	.	1023;1898	D6W5Y0;Q8IZY2	.;ABCA7_HUMAN	Q	1898	ENSP00000263094:P1898Q;ENSP00000414062:P1898Q	ENSP00000263094:P1898Q	P	+	2	0	ABCA7	1013293	0.620000	0.27068	0.034000	0.17996	0.151000	0.21798	2.777000	0.47717	0.628000	0.30357	0.555000	0.69702	CCG	.	C|1.000;T|0.000	.	alt		0.677	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		A	1062293	C	A	1062293	3	1	44	1	0	0	0	0	1	0	0	0	37	652	23	4	5855	4	ABCA7	19	1062293	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08		1062293	58066690	57	3101											
MUC16	94025	hgsc.bcm.edu	37	chr19	9061598	9061598	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggtgctgctcaaatttggAggtgaactggtttcaggttc	8	13	14	6	0	2	1	2	1	0	0	3	3	2	2	0	5	3	4	0	5	2	3			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr19:9061598A>G	ENST00000397910.4	-	3	26051	c.25848T>C	c.(25846-25848)ccT>ccC	p.P8616P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	8618	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						TCAAATTTGGAGGTGAACTGG	0.483																																					p.P8616P		Atlas-SNP	.											.	MUC16	4315	.	0			c.T25848C						PASS	.						143	133	136					19																	9061598		2004	4163	6167	SO:0001819	synonymous_variant	94025	exon3			ATTTGGAGGTGAA	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.25848T>C	chr19.hg19:g.9061598A>G		66.0	0.0	.		100.0	4.0	.	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.	.	none		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9061598	A	G	9061598	2	3	44	1	0	0	0	0	0	0	0	1	9980	291	11	3		3	MUC16	19	9061598	Silent	SNP	A	TCGA-A4-7583-01A-11D-2136-08	7999305	9061598	50067385	58	3102											
LDLR	3949	hgsc.bcm.edu	37	chr19	11216253	11216253	+	Missense_Mutation	SNP	A	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	tggtggccccgactgcaaggAcaaatctgacgaggaaaact	13	6	12	10	2	1	1	0	1	1	0	1	5	1	3	2	4	2	1	2	4	4	0			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr19:11216253A>C	ENST00000558518.1	+	4	858	c.671A>C	c.(670-672)gAc>gCc	p.D224A	LDLR_ENST00000455727.2_Intron|LDLR_ENST00000545707.1_Intron|LDLR_ENST00000558013.1_Missense_Mutation_p.D224A|LDLR_ENST00000535915.1_Missense_Mutation_p.D183A|LDLR_ENST00000557933.1_Missense_Mutation_p.D224A	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor	224	LDL-receptor class A 5. {ECO:0000255|PROSITE-ProRule:PRU00124}.		D -> G (in Italy-2).|D -> N (in Portugal).|D -> V (in FH; Cologne patient). {ECO:0000269|PubMed:7649546}.		cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|intestinal cholesterol absorption (GO:0030299)|lipid metabolic process (GO:0006629)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|phototransduction, visible light (GO:0007603)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol homeostasis (GO:2000188)|regulation of phosphatidylcholine catabolic process (GO:0010899)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.?(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Porfimer(DB00707)	GACTGCAAGGACAAATCTGAC	0.647																																					p.D224A	GBM(18;201 575 7820 21545)	Atlas-SNP	.											.	LDLR	72	.	1	Unknown(1)	lung(1)	c.A671C	GRCh37	CM920421|CM950756|CM994425	LDLR	M		PASS	.						31	36	34					19																	11216253		2202	4299	6501	SO:0001583	missense	3949	exon4			GCAAGGACAAATC	AY114155	CCDS12254.1, CCDS56083.1, CCDS56084.1, CCDS56085.1, CCDS58651.1	19p13.2	2014-09-17	2008-08-01		ENSG00000130164	ENSG00000130164		"Low density lipoprotein receptors"	6547	protein-coding gene	gene with protein product	"familial hypercholesterolemia"	606945					Standard	NM_000527		Approved	LDLCQ2	uc002mqk.4	P01130		ENST00000558518.1:c.671A>C	chr19.hg19:g.11216253A>C	ENSP00000454071:p.Asp224Ala	74.0	0.0	.		66.0	28.0	.	NM_001195798	B4DII3|B4DJZ8|B4DR00|B4DTQ3|C0JYY8|H0YLU8|H0YNT7|Q53ZD9|Q59FQ1|Q9UDH7	Missense_Mutation	SNP	ENST00000558518.1	hg19	CCDS12254.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.301164	0.81136	.	.	ENSG00000130164	ENST00000252444;ENST00000535915	D;D	0.99220	-5.58;-4.44	5.6	5.6	0.85130	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.64402	D	0.000010	D	0.99677	0.9879	H	0.98407	4.225	0.80722	D	1	P;D;D;D	0.71674	0.917;0.998;0.996;0.998	D;D;D;D	0.83275	0.92;0.996;0.99;0.99	D	0.97323	0.9945	10	0.87932	D	0	.	14.7566	0.69569	1.0:0.0:0.0:0.0	.	103;183;236;224	B4DII3;B4DTQ3;Q59FQ1;P01130	.;.;.;LDLR_HUMAN	A	224;183	ENSP00000252444:D224A;ENSP00000440520:D183A	ENSP00000252444:D224A	D	+	2	0	LDLR	11077253	1.000000	0.71417	1.000000	0.80357	0.511000	0.34104	9.228000	0.95250	2.139000	0.66308	0.482000	0.46254	GAC	.	.	.	none		0.647	LDLR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415973.2			C	11216253	A	C	11216253	3	2	44	1	0	0	0	0	1	0	0	0	8711	275	10	5	685	5	LDLR	19	11216253	Missense_Mutation	SNP	A	TCGA-A4-7583-01A-11D-2136-08	2154655	11216253	47912730	59	3103											
AP1M1	8907	hgsc.bcm.edu	37	chr19	16339616	16339616	+	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	aagcggcggtcaacagccaaCaacgtggagatccacattcc	13	5	10	13	3	1	1	1	0	0	1	3	2	3	1	3	3	5	0	3	3	4	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr19:16339616C>G	ENST00000291439.3	+	9	1373	c.924C>G	c.(922-924)aaC>aaG	p.N308K	AP1M1_ENST00000429941.2_Intron|AP1M1_ENST00000444449.2_Missense_Mutation_p.N320K|AP1M1_ENST00000541844.1_Missense_Mutation_p.N236K|AP1M1_ENST00000590756.1_Missense_Mutation_p.N236K	NM_032493.3	NP_115882.1	Q9BXS5	AP1M1_HUMAN	adaptor-related protein complex 1, mu 1 subunit	308	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|trans-Golgi network membrane (GO:0032588)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(3)|prostate(2)	21						CAACAGCCAACAACGTGGAGA	0.617																																					p.N320K		Atlas-SNP	.											.	AP1M1	48	.	0			c.C960G						PASS	.						173	116	135					19																	16339616		2203	4300	6503	SO:0001583	missense	8907	exon10			AGCCAACAACGTG		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.924C>G	chr19.hg19:g.16339616C>G	ENSP00000291439:p.Asn308Lys	78.0	0.0	.		56.0	19.0	.	NM_001130524	Q4TTY5	Missense_Mutation	SNP	ENST00000291439.3	hg19	CCDS12342.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.429106	0.83667	.	.	ENSG00000072958	ENST00000444449;ENST00000291439;ENST00000541844	T;T;T	0.18502	2.21;2.21;2.21	3.64	3.64	0.41730	Clathrin adaptor, mu subunit, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.40347	0.1113	M	0.70787	2.145	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.39901	-0.9591	10	0.62326	D	0.03	-49.532	14.4911	0.67651	0.0:1.0:0.0:0.0	.	320;308	Q4TTY5;Q9BXS5	.;AP1M1_HUMAN	K	320;308;236	ENSP00000388996:N320K;ENSP00000291439:N308K;ENSP00000445682:N236K	ENSP00000291439:N308K	N	+	3	2	AP1M1	16200616	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.764000	0.55264	1.871000	0.54225	0.561000	0.74099	AAC	.	.	.	none		0.617	AP1M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460492.1	NM_032493		G	16339616	C	G	16339616	3	3	44	1	0	0	0	0	1	0	0	0	734	477	17	4	998	4	AP1M1	19	16339616	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08	5123363	16339616	42789367	60	3104											
ZNF737	100129842	hgsc.bcm.edu	37	chr19	20728254	20728254	+	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	atttgtagggtttctctccaCtatgaattatcttatgtgca	9	18	7	7	0	2	1	0	1	2	0	4	1	3	1	1	1	1	3	1	1	5	6			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr19:20728254C>G	ENST00000427401.4	-	4	849	c.755G>C	c.(754-756)aGt>aCt	p.S252T		NM_001159293.1	NP_001152765.1	O75373	ZN737_HUMAN	zinc finger protein 737	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)			breast(2)|kidney(1)|lung(7)|ovary(1)|stomach(1)|urinary_tract(1)	13						TTTCTCTCCACTATGAATTAT	0.403																																					p.S252T		Atlas-SNP	.											ZNF737,NS,carcinoma,0,1	ZNF737	50	.	0			c.G755C						PASS	.						34	34	34					19																	20728254		692	1591	2283	SO:0001583	missense	100129842	exon4			TCTCCACTATGAA	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.755G>C	chr19.hg19:g.20728254C>G	ENSP00000395733:p.Ser252Thr	22.0	0.0	.		33.0	2.0	.	NM_001159293	C9JHM3	Missense_Mutation	SNP	ENST00000427401.4	hg19	CCDS54238.1	.	.	.	.	.	.	.	.	.	.	-	0	-2.857622	0.00065	.	.	ENSG00000237440	ENST00000427401	T	0.12879	2.64	0.1	-0.2	0.13216	.	.	.	.	.	T	0.03871	0.0109	N	0.03050	-0.425	0.24703	N	0.993244	B	0.02656	0.0	B	0.06405	0.002	T	0.41413	-0.9510	9	0.02654	T	1	.	5.4374	0.16488	0.0:0.645:0.355:0.0	.	252	C9JHM3	.	T	252	ENSP00000395733:S252T	ENSP00000395733:S252T	S	-	2	0	ZNF737	20520094	0.066000	0.20996	0.041000	0.18516	0.041000	0.13682	0.057000	0.14279	-1.260000	0.02465	-1.278000	0.01390	AGT	.	.	.	none		0.403	ZNF737-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447844.2	NM_145289		G	20728254	C	G	20728254	3	3	44	1	0	0	0	0	1	0	0	0	18138	565	20	4	859	4	ZNF737	19	20728254	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08	4388638	20728254	38400729	61	3105											
ZNF430	80264	hgsc.bcm.edu	37	chr19	21240182	21240182	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtggcaaagcttttaaccaAtcctcaacccttactacaca	13	11	4	13	0	1	0	1	0	0	0	2	0	2	0	3	1	5	2	3	1	6	4			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr19:21240182A>G	ENST00000261560.5	+	5	1249	c.1068A>G	c.(1066-1068)caA>caG	p.Q356Q	AC012627.1_ENST00000578233.1_RNA	NM_001172671.1|NM_025189.3	NP_001166142.1|NP_079465.3	Q9H8G1	ZN430_HUMAN	zinc finger protein 430	356					regulation of transcription, DNA-templated (GO:0006355)|substantia nigra development (GO:0021762)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q356Q(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23						CTTTTAACCAATCCTCAACCC	0.383																																					p.Q356Q		Atlas-SNP	.											ZNF430,NS,carcinoma,0,1	ZNF430	59	.	1	Substitution - coding silent(1)	lung(1)	c.A1068G						PASS	.						53	57	56					19																	21240182		2201	4290	6491	SO:0001819	synonymous_variant	80264	exon5			TAACCAATCCTCA	AK023721	CCDS32978.1	19p12	2013-01-08				ENSG00000118620		"Zinc fingers, C2H2-type", "-"	20808	protein-coding gene	gene with protein product							Standard	NM_025189		Approved	FLJ13659	uc002npj.3	Q9H8G1		ENST00000261560.5:c.1068A>G	chr19.hg19:g.21240182A>G		69.0	1.0	.		94.0	4.0	.	NM_025189	Q86V70	Silent	SNP	ENST00000261560.5	hg19	CCDS32978.1																																																																																			.	.	.	none		0.383	ZNF430-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463539.1	NM_025189		G	21240182	A	G	21240182	2	3	44	1	0	0	0	0	0	0	0	1	17916	98	4	3		3	ZNF430	19	21240182	Silent	SNP	A	TCGA-A4-7583-01A-11D-2136-08	511928	21240182	37888801	62	3106											
SAMD4B	55095	hgsc.bcm.edu	37	chr19	39868382	39868391	+	Frame_Shift_Del	DEL	TCCCACTGAT	TCCCACTGAT	-																															ccacctccaccagctccagcTcccactgatggcagtgagcc																								rs149585231		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	TCCCACTGAT	TCCCACTGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr19:39868382_39868391delTCCCACTGAT	ENST00000314471.6	+	10	2397_2406	c.1362_1371delTCCCACTGAT	c.(1360-1371)gctcccactgatfs	p.APTD454fs	SAMD4B_ENST00000598913.1_Frame_Shift_Del_p.APTD454fs|SAMD4B_ENST00000596368.1_Intron	NM_018028.2	NP_060498.2	Q5PRF9	SMAG2_HUMAN	sterile alpha motif domain containing 4B	454					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)			CAGCTCCAGCTCCCACTGATGGCAGTGAGC	0.648																																					p.454_457del		Atlas-INDEL	.											.	SAMD4B	48	.	0			c.1361_1370del						PASS	.																																			SO:0001589	frameshift_variant	55095	exon10			.		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.1362_1371delTCCCACTGAT	chr19.hg19:g.39868382_39868391delTCCCACTGAT	ENSP00000317224:p.Ala454fs	110.0	0.0	0		61.0	10.0	0.163934	NM_018028	A5Z0M6|Q6P194	Frame_Shift_Del	DEL	ENST00000314471.6	hg19	CCDS33020.1																																																																																			.	.	.	none		0.648	SAMD4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464467.1	NM_018028		-	39868391	TCCCACTGAT	-	39868382	7	5	44	1	0	1	0	1	0	0	0	0	13835	1538	54	0	1384	0	SAMD4B	19	39868382	Frame_Shift_Del	DEL	TCCCACTGAT	TCGA-A4-7583-01A-11D-2136-08	18628200	39868382	19260601	63	3107											
FCGBP	8857	hgsc.bcm.edu	37	chr19	40362919	40362919	+	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	ctgggggttccggagctgccCgcaggcctcgttgctctcat	3	10	14	14	3	1	0	1	0	1	0	4	1	2	1	3	4	3	5	3	4	0	2			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr19:40362919C>A	ENST00000221347.6	-	32	15158	c.15151G>T	c.(15151-15153)Ggg>Tgg	p.G5051W		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	5051	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)			CGGAGCTGCCCGCAGGCCTCG	0.672																																					p.G5051W		Atlas-SNP	.											.	FCGBP	416	.	0			c.G15151T						PASS	.						46	53	50					19																	40362919		2203	4299	6502	SO:0001583	missense	8857	exon32			GCTGCCCGCAGGC	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.15151G>T	chr19.hg19:g.40362919C>A	ENSP00000221347:p.Gly5051Trp	148.0	0.0	.		82.0	8.0	.	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	hg19	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	14.84	2.656182	0.47467	.	.	ENSG00000090920	ENST00000221347	T	0.78003	-1.14	4.84	4.84	0.62591	von Willebrand factor, type D domain (1);Uncharacterised domain, cysteine-rich (2);	0.000000	0.64402	U	0.000001	D	0.90359	0.6983	M	0.92649	3.33	0.40754	D	0.982949	D	0.89917	1.0	D	0.97110	1.0	D	0.92815	0.6267	10	0.87932	D	0	.	14.9744	0.71261	0.0:1.0:0.0:0.0	.	5051	Q9Y6R7	FCGBP_HUMAN	W	5051	ENSP00000221347:G5051W	ENSP00000221347:G5051W	G	-	1	0	FCGBP	45054759	0.047000	0.20315	0.851000	0.33527	0.103000	0.19146	1.926000	0.40084	2.521000	0.84997	0.462000	0.41574	GGG	.	.	.	none		0.672	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		A	40362919	C	A	40362919	3	1	44	1	0	0	0	0	1	0	0	0	5785	652	23	4	1086	4	FCGBP	19	40362919	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08	494537	40362919	18766064	64	3108											
ZNF577	84765	hgsc.bcm.edu	37	chr19	52376753	52376753	+	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	tttcctggagaaggctctccCgcacacactgcattcatgtg	8	11	9	13	1	2	1	1	0	1	1	4	2	3	1	2	2	1	3	2	2	1	2	rs200063901		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr19:52376753C>A	ENST00000301399.5	-	7	855	c.490G>T	c.(490-492)Ggg>Tgg	p.G164W	ZNF577_ENST00000412216.1_Intron|ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000420592.1_Missense_Mutation_p.G105W|ZNF577_ENST00000451628.2_Missense_Mutation_p.G105W	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	164					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|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)		AAGGCTCTCCCGCACACACTG	0.443																																					p.G164W		Atlas-SNP	.											.	ZNF577	63	.	0			c.G490T						PASS	.						135	130	132					19																	52376753		2203	4300	6503	SO:0001583	missense	84765	exon7			CTCTCCCGCACAC	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.490G>T	chr19.hg19:g.52376753C>A	ENSP00000301399:p.Gly164Trp	158.0	0.0	.		159.0	7.0	.	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Missense_Mutation	SNP	ENST00000301399.5	hg19	CCDS12842.2	.	.	.	.	.	.	.	.	.	.	.	10.17	1.275338	0.23307	.	.	ENSG00000161551	ENST00000301399;ENST00000420592;ENST00000451628;ENST00000458390	T;T;T;T	0.60040	0.22;0.22;0.22;0.22	3.1	2.04	0.26737	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.83142	0.5190	H	0.98507	4.25	0.27641	N	0.947716	D;D	0.89917	1.0;0.996	D;P	0.87578	0.998;0.784	T	0.73902	-0.3836	9	0.87932	D	0	.	9.3367	0.38054	0.0:0.8873:0.0:0.1127	.	164;105	Q9BSK1;Q9BSK1-2	ZN577_HUMAN;.	W	164;105;105;164	ENSP00000301399:G164W;ENSP00000413476:G105W;ENSP00000389652:G105W;ENSP00000404509:G164W	ENSP00000301399:G164W	G	-	1	0	ZNF577	57068565	0.001000	0.12720	0.027000	0.17364	0.014000	0.08584	1.074000	0.30703	0.611000	0.30052	0.655000	0.94253	GGG	.	C|1.000;T|0.000	.	alt		0.443	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679		A	52376753	C	A	52376753	3	1	44	1	0	0	0	0	1	0	0	0	18021	652	23	4	971	4	ZNF577	19	52376753	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08	12013834	52376753	6752230	65	3109											
UBOX5	22888	hgsc.bcm.edu	37	chr20	3102965	3102965	+	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	cctccttgtctgggacagatGgctcagctgggcccagggtc	5	9	14	13	0	2	1	1	0	1	1	4	2	3	2	3	4	1	2	3	4	0	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr20:3102965G>A	ENST00000217173.2	-	3	791	c.320C>T	c.(319-321)cCa>cTa	p.P107L	UBOX5-AS1_ENST00000446537.1_RNA|UBOX5_ENST00000348031.2_Missense_Mutation_p.P107L	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						TGGGACAGATGGCTCAGCTGG	0.567																																					p.P107L		Atlas-SNP	.											.	UBOX5	47	.	0			c.C320T						PASS	.						59	59	59					20																	3102965		2203	4300	6503	SO:0001583	missense	22888	exon3			ACAGATGGCTCAG	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.320C>T	chr20.hg19:g.3102965G>A	ENSP00000217173:p.Pro107Leu	116.0	0.0	.		73.0	23.0	.	NM_014948		Missense_Mutation	SNP	ENST00000217173.2	hg19	CCDS13046.1	.	.	.	.	.	.	.	.	.	.	G	9.568	1.120384	0.20877	.	.	ENSG00000185019	ENST00000217173;ENST00000348031	T;T	0.29397	1.57;1.57	4.8	2.74	0.32292	.	0.705996	0.12704	U	0.446080	T	0.22859	0.0552	L	0.44542	1.39	0.29757	N	0.835874	B;B;B	0.13145	0.004;0.003;0.007	B;B;B	0.08055	0.003;0.002;0.003	T	0.13176	-1.0519	10	0.38643	T	0.18	-0.4251	5.1325	0.14917	0.1731:0.0:0.5509:0.276	.	107;107;107	Q53GQ5;Q86X87;O94941	.;.;RNF37_HUMAN	L	107	ENSP00000217173:P107L;ENSP00000311726:P107L	ENSP00000217173:P107L	P	-	2	0	UBOX5	3050965	0.241000	0.23857	0.305000	0.25099	0.964000	0.63967	0.662000	0.25038	1.232000	0.43678	0.563000	0.77884	CCA	.	.	.	none		0.567	UBOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077706.2	NM_014948		A	3102965	G	A	3102965	3	1	44	1	0	0	0	0	1	0	0	0	16906	1348	47	2	1317	2	UBOX5	20	3102965	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08		3102965	59922555	66	3110											
HAO1	54363	hgsc.bcm.edu	37	chr20	7886831	7886832	+	In_Frame_Ins	INS	-	-	TTT																															ccctttgcaacaattggcaaINStgatgtcagtcttctcagcc																										TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr20:7886831_7886832insTTT	ENST00000378789.3	-	4	741_742	c.690_691insAAA	c.(688-693)tcattg>tcaAAAttg	p.230_231SL>SKL		NM_017545.2	NP_060015.1	Q9UJM8	HAOX1_HUMAN	hydroxyacid oxidase (glycolate oxidase) 1	230	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						ACAATTGGCAATGATGTCAGTC	0.386																																					p.L231delinsKL		Atlas-INDEL	.											.	HAO1	71	.	0			c.691_692insAAA						PASS	.																																			SO:0001652	inframe_insertion	54363	exon4			.	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.690_691insAAA	chr20.hg19:g.7886831_7886832insTTT	ENSP00000368066:p.Ser230_Leu231insLys	120.0	0.0	0		183.0	51.0	0.278689	NM_017545	Q14CQ0|Q9UPZ0|Q9Y3I7	In_Frame_Ins	INS	ENST00000378789.3	hg19	CCDS13100.1																																																																																			.	.	.	none		0.386	HAO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077926.2			TTT	7886832	-	TTT	7886831	7	5	44	1	0	1	1	0	0	0	0	0	6958	98	4	0	441	0	HAO1	20	7886831	In_Frame_Ins	INS	-	TCGA-A4-7583-01A-11D-2136-08	4783866	7886831	55138689	67	3111											
PLAGL2	5326	hgsc.bcm.edu	37	chr20	30784822	30784822	+	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	accagggagtgtggcacgccCgtgctgggcatggtagggat	7	7	18	9	2	0	0	0	0	0	0	0	2	0	2	2	5	1	4	2	5	1	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr20:30784822C>A	ENST00000246229.4	-	3	1188	c.924G>T	c.(922-924)acG>acT	p.T308T		NM_002657.3	NP_002648.1	Q9UPG8	PLAL2_HUMAN	pleiomorphic adenoma gene-like 2	308					chylomicron assembly (GO:0034378)|lipid metabolic process (GO:0006629)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|post-embryonic development (GO:0009791)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|liver(1)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	21			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			GTGGCACGCCCGTGCTGGGCA	0.597																																					p.T308T	Colon(163;15 1893 11280 16306 47518)	Atlas-SNP	.											PLAGL2,NS,carcinoma,-1,1	PLAGL2	56	.	0			c.G924T						PASS	.						99	100	100					20																	30784822		2202	4300	6502	SO:0001819	synonymous_variant	5326	exon3			CACGCCCGTGCTG		CCDS13197.1	20q11.21	2013-01-08			ENSG00000126003	ENSG00000126003		"Zinc fingers, C2H2-type"	9047	protein-coding gene	gene with protein product	"C2H2-type zinc finger protein"	604866				15585652, 17950244	Standard	NM_002657		Approved	ZNF900	uc002wxn.2	Q9UPG8	OTTHUMG00000032210	ENST00000246229.4:c.924G>T	chr20.hg19:g.30784822C>A		177.0	1.0	.		146.0	8.0	.	NM_002657	A8K8T5|E1P5M3|Q92584	Silent	SNP	ENST00000246229.4	hg19	CCDS13197.1																																																																																			.	.	.	none		0.597	PLAGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078615.2	NM_002657		A	30784822	C	A	30784822	2	1	44	1	0	0	0	0	0	0	0	1	12027	639	23	4		4	PLAGL2	20	30784822	Silent	SNP	C	TCGA-A4-7583-01A-11D-2136-08	22897991	30784822	32240698	68	3112											
BPIL1	80341	hgsc.bcm.edu	37	chr20	31604905	31604906	+	Frame_Shift_Ins	INS	-	-	T																															tgtccacctgggcaccttaaINSttggtaagatctgggagcca																										TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr20:31604905_31604906insT	ENST00000170150.3	+	7	769_770	c.574_575insT	c.(574-576)attfs	p.I192fs		NM_025227.1	NP_079503.1	Q8N4F0	BPIB2_HUMAN	BPI fold containing family B, member 2	192						extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										GGGCACCTTAATTGGTAAGATC	0.619																																					p.I192fs		Atlas-INDEL	.											.	.	.	.	0			c.574_575insT						PASS	.																																			SO:0001589	frameshift_variant	80341	exon7			.	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.576dupT	chr20.hg19:g.31604907_31604907dupT	ENSP00000170150:p.Ile192fs	143.0	0.0	0		111.0	35.0	0.315315	NM_025227	Q6UWN3|Q6ZME0|Q8NFQ7	Frame_Shift_Ins	INS	ENST00000170150.3	hg19	CCDS13210.1																																																																																			.	.	.	none		0.619	BPIFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078652.2	NM_025227		T	31604906	-	T	31604905	7	5	44	1	0	1	1	0	0	0	0	0	1493	101	4	0	596	0	BPIL1	20	31604905	Frame_Shift_Ins	INS	-	TCGA-A4-7583-01A-11D-2136-08	820083	31604905	31420615	69	3113											
SETD4	54093	hgsc.bcm.edu	37	chr21	37418117	37418117	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaactcctgcacgtgggcTctctgctcttcagcctttgc	6	12	9	14	1	3	1	1	0	2	1	5	1	4	1	2	1	5	3	2	1	2	2			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr21:37418117T>C	ENST00000399215.1	-	5	1861	c.489A>G	c.(487-489)agA>agG	p.R163R	SETD4_ENST00000399212.1_Silent_p.R139R|SETD4_ENST00000399201.1_Silent_p.R139R|SETD4_ENST00000399207.1_Silent_p.R163R|SETD4_ENST00000399208.2_Silent_p.R163R|SETD4_ENST00000332131.4_Silent_p.R163R|SETD4_ENST00000399205.1_Silent_p.R139R|SETD4_ENST00000481477.1_5'UTR			Q9NVD3	SETD4_HUMAN	SET domain containing 4	163	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						GCACGTGGGCTCTCTGCTCTT	0.502																																					p.R163R		Atlas-SNP	.											.	SETD4	37	.	0			c.A489G						PASS	.						99	112	107					21																	37418117		2203	4300	6503	SO:0001819	synonymous_variant	54093	exon6			GTGGGCTCTCTGC	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.489A>G	chr21.hg19:g.37418117T>C		200.0	0.0	.		204.0	90.0	.	NM_001007259	B4DT14|D3DSG2|D3DSG4|Q8NE19|Q9BU46	Silent	SNP	ENST00000399215.1	hg19	CCDS13640.1																																																																																			.	.	.	none		0.502	SETD4-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194456.1	NM_017438		C	37418117	T	C	37418117	2	2	44	1	0	0	0	0	0	0	0	1	14146	1548	54	3		3	SETD4	21	37418117	Silent	SNP	T	TCGA-A4-7583-01A-11D-2136-08		37418117	10711778	70	3114											
SIK1	150094	hgsc.bcm.edu	37	chr21	44841223	44841223	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggacagaggctctcctgacTtgtagaaattcccaaatcca	12	10	8	11	0	1	3	0	1	1	2	4	4	3	4	3	2	0	2	3	2	3	3			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr21:44841223T>C	ENST00000270162.6	-	6	656	c.524A>G	c.(523-525)aAg>aGg	p.K175R		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	175	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle cell differentiation (GO:0055007)|cell cycle (GO:0007049)|entrainment of circadian clock by photoperiod (GO:0043153)|intracellular signal transduction (GO:0035556)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of triglyceride biosynthetic process (GO:0010868)|positive regulation of anoikis (GO:2000210)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell differentiation (GO:0045595)|regulation of mitotic cell cycle (GO:0007346)|regulation of myotube differentiation (GO:0010830)|regulation of sodium ion transport (GO:0002028)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|cAMP response element binding protein binding (GO:0008140)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21					Dabrafenib(DB08912)	CTCTCCTGACTTGTAGAAATT	0.567																																					p.K175R		Atlas-SNP	.											.	SIK1	65	.	0			c.A524G						PASS	.						51	61	58					21																	44841223		2203	4299	6502	SO:0001583	missense	150094	exon6			CCTGACTTGTAGA	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.524A>G	chr21.hg19:g.44841223T>C	ENSP00000270162:p.Lys175Arg	168.0	0.0	.		119.0	46.0	.	NM_173354	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Missense_Mutation	SNP	ENST00000270162.6	hg19	CCDS33575.1	.	.	.	.	.	.	.	.	.	.	T	17.40	3.379901	0.61845	.	.	ENSG00000142178	ENST00000270162	T	0.66280	-0.2	5.08	5.08	0.68730	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.208643	0.49916	D	0.000136	T	0.45677	0.1354	N	0.12182	0.205	0.45150	D	0.998166	B	0.24721	0.11	B	0.25759	0.063	T	0.40664	-0.9551	10	0.37606	T	0.19	.	14.8612	0.70382	0.0:0.0:0.0:1.0	.	175	P57059	SIK1_HUMAN	R	175	ENSP00000270162:K175R	ENSP00000270162:K175R	K	-	2	0	SIK1	43665651	1.000000	0.71417	0.886000	0.34754	0.944000	0.59088	5.865000	0.69583	1.909000	0.55274	0.459000	0.35465	AAG	.	.	.	none		0.567	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354		C	44841223	T	C	44841223	3	2	44	1	0	0	0	0	1	0	0	0	14330	1609	56	3	1863	3	SIK1	21	44841223	Missense_Mutation	SNP	T	TCGA-A4-7583-01A-11D-2136-08	7423106	44841223	3288672	71	3115											
COL18A1	80781	hgsc.bcm.edu	37	chr21	46911142	46911143	+	Missense_Mutation	DNP	GA	GA	AT																															gtggcctcctcttccagggaGatccagggaaggacggagtc																										TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr21:46911142_46911143GA>AT	ENST00000359759.4	+	21	3337_3338	c.3316_3317GA>AT	c.(3316-3318)GAt>ATt	p.D1106I	COL18A1_ENST00000355480.5_Missense_Mutation_p.D871I|COL18A1_ENST00000400337.2_Missense_Mutation_p.D691I			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1106	Triple-helical region 4 (COL4).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		CTTCCAGGGAGATCCAGGGAAG	0.698																																					p.D871N|p.D871V		Atlas-SNP	.											.	COL18A1	129	.	0			c.G2611A|c.A2612T						PASS	.																																			SO:0001583	missense	80781	exon21			CAGGGAGATCCAG|AGGGAGATCCAGG		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	Exception_encountered	chr21.hg19:g.46911142_46911143delinsAT	ENSP00000352798:p.Asp1106Ile	65.0	0.0	.		52.0|51.0	19.0|18.0	.	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	hg19																																																																																				.	.	.	none		0.698	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			AT	46911143	GA	AT	46911142	3	1	44	1	0	0	0	0	1	0	0	0	3677	942	33	2	3512	2	COL18A1	21	46911142	Missense_Mutation	DNP	GA	TCGA-A4-7583-01A-11D-2136-08	2069919	46911142	1218753	72	3116											
PHF21B	112885	hgsc.bcm.edu	37	chr22	45312440	45312440	+	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	tggccttctggaatgttgggGgctgcttgggtggccggtcc	2	12	18	9	1	1	0	0	0	1	0	2	1	2	1	3	7	1	3	3	7	1	3			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chr22:45312440G>T	ENST00000313237.5	-	4	434	c.284C>A	c.(283-285)cCc>cAc	p.P95H	PHF21B_ENST00000403565.1_5'UTR|PHF21B_ENST00000396103.3_Missense_Mutation_p.P95H|PHF21B_ENST00000447824.3_Missense_Mutation_p.P83H|PHF21B_ENST00000404079.2_Missense_Mutation_p.P83H	NM_138415.4	NP_612424.1	Q96EK2	PF21B_HUMAN	PHD finger protein 21B	95							zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(14)|ovary(2)|prostate(1)|skin(2)	25		all_neural(38;0.00802)|Glioma(61;0.0353)|Ovarian(80;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0203)		GAATGTTGGGGGCTGCTTGGG	0.647																																					p.P95H		Atlas-SNP	.											.	PHF21B	61	.	0			c.C284A						PASS	.						43	48	46					22																	45312440		2202	4300	6502	SO:0001583	missense	112885	exon4			GTTGGGGGCTGCT	AK091480	CCDS14061.1, CCDS56234.1, CCDS63504.1	22q13.31	2013-01-28			ENSG00000056487	ENSG00000056487		"Zinc fingers, PHD-type"	25161	protein-coding gene	gene with protein product			"PHD finger protein 4"	PHF4		12477932	Standard	NM_138415		Approved	BHC80L, FLJ34161	uc011aql.2	Q96EK2	OTTHUMG00000151199	ENST00000313237.5:c.284C>A	chr22.hg19:g.45312440G>T	ENSP00000324403:p.Pro95His	134.0	0.0	.		85.0	30.0	.	NM_138415	B0QYW3|B0QYW4|B3KRU4|B7Z4F8|Q5TFL2|Q6ICC0	Missense_Mutation	SNP	ENST00000313237.5	hg19	CCDS14061.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.671013	0.88348	.	.	ENSG00000056487	ENST00000313237;ENST00000396103;ENST00000404079;ENST00000447824;ENST00000420689	T;T;T;T;T	0.24538	1.85;1.85;1.85;1.85;1.85	5.06	5.06	0.68205	.	0.076937	0.51477	D	0.000089	T	0.47619	0.1455	L	0.54323	1.7	0.47065	D	0.999309	D;D;D;D	0.89917	0.999;0.999;1.0;0.999	D;D;D;P	0.68621	0.919;0.959;0.943;0.885	T	0.48636	-0.9018	10	0.87932	D	0	0.0639	18.4696	0.90767	0.0:0.0:1.0:0.0	.	83;95;83;95	B7Z657;Q96EK2-3;B7Z4F8;Q96EK2	.;.;.;PF21B_HUMAN	H	95;95;83;83;83	ENSP00000324403:P95H;ENSP00000379410:P95H;ENSP00000385105:P83H;ENSP00000388619:P83H;ENSP00000401294:P83H	ENSP00000324403:P95H	P	-	2	0	PHF21B	43691104	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.530000	0.90606	2.346000	0.79739	0.655000	0.94253	CCC	.	.	.	none		0.647	PHF21B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321731.2	NM_138415		T	45312440	G	T	45312440	3	4	44	1	0	0	0	0	1	0	0	0	11841	1232	43	4	1351	4	PHF21B	22	45312440	Missense_Mutation	SNP	G	TCGA-A4-7583-01A-11D-2136-08		45312440	5992126	73	3117											
KLHL4	56062	hgsc.bcm.edu	37	chrX	86773063	86773063	+	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	gggcaggttgaagagccactCtcgggacagaaacggactga	12	5	15	9	2	1	4	0	2	1	2	2	6	1	6	1	4	2	2	1	4	2	1			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chrX:86773063C>G	ENST00000373119.4	+	1	312	c.167C>G	c.(166-168)tCt>tGt	p.S56C	KLHL4_ENST00000373114.4_Missense_Mutation_p.S56C	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	56						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(29)|ovary(2)|prostate(1)|skin(1)	67						AAGAGCCACTCTCGGGACAGA	0.547																																					p.S56C		Atlas-SNP	.											.	KLHL4	263	.	0			c.C167G						PASS	.						77	65	69					X																	86773063		2203	4300	6503	SO:0001583	missense	56062	exon1			GCCACTCTCGGGA	AF284765	CCDS14456.1, CCDS14457.1	Xq21.3	2013-01-30	2013-01-30		ENSG00000102271	ENSG00000102271		"Kelch-like", "BTB/POZ domain containing"	6355	protein-coding gene	gene with protein product		300348	"kelch (Drosophila)-like 4", "kelch-like 4 (Drosophila)"			11401425	Standard	NM_019117		Approved	KIAA1687, DKELCHL, KHL4	uc004efa.2	Q9C0H6	OTTHUMG00000021946	ENST00000373119.4:c.167C>G	chrX.hg19:g.86773063C>G	ENSP00000362211:p.Ser56Cys	16.0	0.0	.		31.0	26.0	.	NM_019117	B2RTW2|Q9Y3J5	Missense_Mutation	SNP	ENST00000373119.4	hg19	CCDS14457.1	.	.	.	.	.	.	.	.	.	.	C	19.05	3.752200	0.69533	.	.	ENSG00000102271	ENST00000373119;ENST00000373114	T;T	0.76448	-1.02;-0.99	5.05	5.05	0.67936	.	2.035340	0.02405	N	0.081043	D	0.85894	0.5803	L	0.57536	1.79	0.58432	D	0.999993	B;P	0.42973	0.384;0.796	B;P	0.51415	0.345;0.669	T	0.71341	-0.4622	10	0.72032	D	0.01	.	16.3817	0.83467	0.0:1.0:0.0:0.0	.	56;56	Q9C0H6;Q9C0H6-2	KLHL4_HUMAN;.	C	56	ENSP00000362211:S56C;ENSP00000362206:S56C	ENSP00000362206:S56C	S	+	2	0	KLHL4	86659719	1.000000	0.71417	0.968000	0.41197	0.845000	0.48019	6.820000	0.75267	2.327000	0.79052	0.513000	0.50165	TCT	.	.	.	none		0.547	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1			G	86773063	C	G	86773063	3	3	44	1	0	0	0	0	1	0	0	0	8398	913	32	4	169	4	KLHL4	23	86773063	Missense_Mutation	SNP	C	TCGA-A4-7583-01A-11D-2136-08		86773063	68497497	74	3118											
GAB3	139716	hgsc.bcm.edu	37	chrX	153928305	153928305	+	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	caaactaagccgcttgtctcGgtgtcttaaggattggcctt	8	13	10	10	2	2	0	0	0	2	0	3	1	2	1	2	3	2	1	2	3	3	5			TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	g.chrX:153928305G>T	ENST00000369575.3	-	5	1127	c.1096C>A	c.(1096-1098)Cga>Aga	p.R366R	GAB3_ENST00000496390.1_5'UTR|GAB3_ENST00000424127.2_Silent_p.R367R	NM_001081573.1|NM_080612.2	NP_001075042.1|NP_542179.1	Q8WWW8	GAB3_HUMAN	GRB2-associated binding protein 3	366					macrophage differentiation (GO:0030225)			p.R366*(1)		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)					CGCTTGTCTCGGTGTCTTAAG	0.393																																					p.R367R		Atlas-SNP	.											.	GAB3	73	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1099A						PASS	.						159	142	148					X																	153928305		2203	4300	6503	SO:0001819	synonymous_variant	139716	exon5			TGTCTCGGTGTCT	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.1096C>A	chrX.hg19:g.153928305G>T		84.0	0.0	.		137.0	7.0	.	NM_001081573	A6NHF8|E9PB44	Silent	SNP	ENST00000369575.3	hg19	CCDS14760.1																																																																																			.	.	.	none		0.393	GAB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061192.2	NM_001081573		T	153928305	G	T	153928305	2	4	44	1	0	0	0	0	0	0	0	1	6157	1124	39	4		4	GAB3	23	153928305	Silent	SNP	G	TCGA-A4-7583-01A-11D-2136-08	67155242	153928305	1342255	75	3119											
CPSF3L	54973	hgsc.bcm.edu	37	chr1	1248497	1248497	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcacgcagtagccgggcAtgatgacctgggggcaggca	8	5	16	12	2	0	2	0	2	0	0	0	2	0	2	3	4	2	6	3	4	1	1			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:1248497A>G	ENST00000435064.1	-	11	1131	c.1049T>C	c.(1048-1050)aTg>aCg	p.M350T	CPSF3L_ENST00000421495.2_Missense_Mutation_p.M92T|CPSF3L_ENST00000540437.1_Missense_Mutation_p.M356T|CPSF3L_ENST00000419704.1_Missense_Mutation_p.M249T|CPSF3L_ENST00000450926.2_Missense_Mutation_p.M328T|CPSF3L_ENST00000411962.1_Missense_Mutation_p.M252T|CPSF3L_ENST00000545578.1_Missense_Mutation_p.M321T|CPSF3L_ENST00000462432.1_5'UTR	NM_001256460.1|NM_017871.5	NP_001243389.1|NP_060341.2	Q5TA45	INT11_HUMAN	cleavage and polyadenylation specific factor 3-like	350					snRNA processing (GO:0016180)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|integrator complex (GO:0032039)	hydrolase activity (GO:0016787)			endometrium(4)|kidney(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(3)	13	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(86;4.35e-21)|Colorectal(212;0.000166)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.00235)|BRCA - Breast invasive adenocarcinoma(365;0.00255)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0349)|Lung(427;0.201)		GTAGCCGGGCATGATGACCTG	0.677																																					p.M356T		Atlas-SNP	.											.	CPSF3L	33	.	0			c.T1067C						PASS	.						22	21	21					1																	1248497		2196	4288	6484	SO:0001583	missense	54973	exon13			CCGGGCATGATGA	AL136813	CCDS21.1, CCDS57959.1, CCDS57960.1, CCDS57961.1, CCDS72678.1	1p36.33	2008-02-05			ENSG00000127054	ENSG00000127054			26052	protein-coding gene	gene with protein product	"integrator complex subunit 11"	611354				15684398, 16239144	Standard	NM_001256456		Approved	FLJ20542, RC-68, CPSF73L, INT11, INTS11	uc001aee.2	Q5TA45	OTTHUMG00000003330	ENST00000435064.1:c.1049T>C	chr1.hg19:g.1248497A>G	ENSP00000413493:p.Met350Thr	37.0	0.0	.		31.0	12.0	.	NM_001256456	A8K5S2|B3KPR3|B4DM87|G3V1S5|Q5TA46|Q5TA48|Q5TA52|Q5TA53|Q5TA54|Q7L3D7|Q96HY1|Q9BW36|Q9H0F9|Q9H8R5|Q9HAA6|Q9NWX9	Missense_Mutation	SNP	ENST00000435064.1	hg19	CCDS21.1	.	.	.	.	.	.	.	.	.	.	A	17.07	3.295485	0.60086	.	.	ENSG00000127054	ENST00000435064;ENST00000411962;ENST00000294579;ENST00000419704;ENST00000540437;ENST00000450926;ENST00000545578	T;T;T;T;T	0.46451	0.95;0.95;0.95;0.95;0.87	5.48	5.48	0.80851	Beta-Casp domain (1);	0.000000	0.85682	D	0.000000	T	0.62085	0.2399	M	0.78049	2.395	0.80722	D	1	P;P;P;P;P;P	0.51933	0.696;0.741;0.949;0.936;0.837;0.741	P;P;P;P;P;P	0.57960	0.535;0.665;0.83;0.738;0.617;0.665	T	0.67632	-0.5621	10	0.87932	D	0	-54.7181	15.5355	0.75998	1.0:0.0:0.0:0.0	.	328;321;252;249;356;350	Q5TA45-3;B4DM87;C9IYS7;Q5TA45-2;G3V1S5;Q5TA45	.;.;.;.;.;INT11_HUMAN	T	350;252;243;249;356;328;321	ENSP00000413493:M350T;ENSP00000404886:M249T;ENSP00000445001:M356T;ENSP00000392848:M328T;ENSP00000444672:M321T	ENSP00000294579:M243T	M	-	2	0	CPSF3L	1238360	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	8.568000	0.90741	2.077000	0.62373	0.460000	0.39030	ATG	.	.	.	none		0.677	CPSF3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009360.2	NM_017871		G	1248497	A	G	1248497	3	3	45	1	0	0	0	0	1	0	0	0	3829	217	8	3	781	3	CPSF3L	1	1248497	Missense_Mutation	SNP	A	TCGA-A4-7584-01A-11D-2136-08		1248497	248002124	1	3120											
PLCH2	9651	hgsc.bcm.edu	37	chr1	2430213	2430213	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctttgtggaggtggagatcAttgggctccctgtggactgc	5	12	15	9	0	1	1	1	0	0	1	2	4	2	3	2	5	1	1	2	5	0	2			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:2430213A>G	ENST00000419816.2	+	18	2654	c.2380A>G	c.(2380-2382)Att>Gtt	p.I794V	PLCH2_ENST00000449969.1_Missense_Mutation_p.I767V|PLCH2_ENST00000378486.3_Missense_Mutation_p.I794V|PLCH2_ENST00000288766.5_Missense_Mutation_p.I82V|PLCH2_ENST00000378488.3_Missense_Mutation_p.I758V			O75038	PLCH2_HUMAN	phospholipase C, eta 2	794	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				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)		GGTGGAGATCATTGGGCTCCC	0.657																																					p.I794V		Atlas-SNP	.											.	PLCH2	131	.	0			c.A2380G						PASS	.						28	32	31					1																	2430213		2068	4190	6258	SO:0001583	missense	9651	exon18			GAGATCATTGGGC	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.2380A>G	chr1.hg19:g.2430213A>G	ENSP00000389803:p.Ile794Val	39.0	0.0	.		31.0	14.0	.	NM_014638	A2VCM3|B9DI80|Q3LUA8|Q86XJ2|Q86XU1|Q86YU7|Q8TEH5|Q8WUS6	Missense_Mutation	SNP	ENST00000419816.2	hg19		.	.	.	.	.	.	.	.	.	.	A	21.1	4.104041	0.76983	.	.	ENSG00000149527	ENST00000449969;ENST00000378486;ENST00000378488;ENST00000288766;ENST00000378483;ENST00000343889;ENST00000278878	T;T;T;T	0.13538	2.58;2.58;2.58;2.58	4.93	4.93	0.64822	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	0.25005	0.0607	L	0.28400	0.85	0.48632	D	0.999685	P;P;D;P	0.69078	0.938;0.938;0.997;0.938	P;P;D;P	0.77557	0.679;0.842;0.99;0.842	T	0.01661	-1.1301	10	0.52906	T	0.07	.	13.39	0.60818	1.0:0.0:0.0:0.0	.	641;546;767;794	B9DI81;B9DI82;O75038-2;O75038	.;.;.;PLCH2_HUMAN	V	767;794;758;82;80;641;546	ENSP00000397289:I767V;ENSP00000367747:I794V;ENSP00000367749:I758V;ENSP00000288766:I82V	ENSP00000278878:I546V	I	+	1	0	PLCH2	2420073	1.000000	0.71417	0.993000	0.49108	0.499000	0.33736	5.860000	0.69546	1.845000	0.53610	0.459000	0.35465	ATT	.	.	.	none		0.657	PLCH2-009	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467514.1	NM_014638		G	2430213	A	G	2430213	3	3	45	1	0	0	0	0	1	0	0	0	12045	217	8	3	2450	3	PLCH2	1	2430213	Missense_Mutation	SNP	A	TCGA-A4-7584-01A-11D-2136-08	1181716	2430213	246820408	2	3121											
HMGB4	127540	hgsc.bcm.edu	37	chr1	34329977	34329977	+	Missense_Mutation	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	tgaaaaggccaaatatgaagCcctggccaaactcgacaaag	17	5	9	10	1	0	2	0	2	0	0	1	3	0	2	3	2	2	0	3	2	7	1			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:34329977C>T	ENST00000522796.1	+	4	2090	c.185C>T	c.(184-186)gCc>gTc	p.A62V	CSMD2_ENST00000373381.4_Intron|HMGB4_ENST00000519684.1_Missense_Mutation_p.A62V|HMGB4_ENST00000425537.1_3'UTR			Q8WW32	HMGB4_HUMAN	high mobility group box 4	62						chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				AAATATGAAGCCCTGGCCAAA	0.463																																					p.A62V		Atlas-SNP	.											.	HMGB4	27	.	0			c.C185T						PASS	.						120	135	130					1																	34329977		2203	4300	6503	SO:0001583	missense	127540	exon2			ATGAAGCCCTGGC		CCDS30668.1	1p35.1	2011-07-01	2011-04-05		ENSG00000176256	ENSG00000176256		"High-mobility group / Canonical"	24954	protein-coding gene	gene with protein product			"high-mobility group box 4"				Standard	NR_033264		Approved	FLJ40388	uc001bxp.3	Q8WW32	OTTHUMG00000013143	ENST00000522796.1:c.185C>T	chr1.hg19:g.34329977C>T	ENSP00000430919:p.Ala62Val	189.0	0.0	.		133.0	55.0	.	NM_145205	B2R4X7|Q0QWA4	Missense_Mutation	SNP	ENST00000522796.1	hg19	CCDS30668.1	.	.	.	.	.	.	.	.	.	.	C	18.07	3.542128	0.65198	.	.	ENSG00000176256	ENST00000519684;ENST00000522796	T;T	0.14144	2.53;2.53	5.58	0.467	0.16721	.	0.232725	0.37053	N	0.002268	T	0.18002	0.0432	M	0.68317	2.08	0.31177	N	0.702474	P	0.40931	0.733	P	0.46758	0.526	T	0.09662	-1.0664	10	0.87932	D	0	.	4.817	0.13372	0.4359:0.4072:0.0:0.1569	.	62	B2R4X7	.	V	62	ENSP00000429214:A62V;ENSP00000430919:A62V	ENSP00000429214:A62V	A	+	2	0	HMGB4	34102564	0.991000	0.36638	0.082000	0.20525	0.854000	0.48673	2.434000	0.44802	-0.049000	0.13379	-0.192000	0.12808	GCC	.	.	.	none		0.463	HMGB4-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375773.1	NM_145205		T	34329977	C	T	34329977	3	4	45	1	0	0	0	0	1	0	0	0	7235	739	26	2	187	2	HMGB4	1	34329977	Missense_Mutation	SNP	C	TCGA-A4-7584-01A-11D-2136-08	31899764	34329977	214920644	3	3122											
SSBP3	23648	hgsc.bcm.edu	37	chr1	54870254	54870254	+	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	atcacacaaacttaccaccaCcacgagtgcaaaaacccagg	17	4	5	15	1	1	0	1	0	0	0	1	1	1	0	4	1	4	1	4	1	4	1			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:54870254C>T	ENST00000371320.3	-	3	596	c.186G>A	c.(184-186)tgG>tgA	p.W62*	SSBP3_ENST00000371319.3_Nonsense_Mutation_p.W62*|SSBP3_ENST00000357475.4_Nonsense_Mutation_p.W62*|SSBP3_ENST00000417664.2_De_novo_Start_OutOfFrame	NM_145716.2	NP_663768.1	Q9BWW4	SSBP3_HUMAN	single stranded DNA binding protein 3	62					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						CTTACCACCACCACGAGTGCA	0.507																																					p.W62X		Atlas-SNP	.											.	SSBP3	65	.	0			c.G186A						PASS	.						88	76	80					1																	54870254		2203	4300	6503	SO:0001587	stop_gained	23648	exon3			CCACCACCACGAG		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.186G>A	chr1.hg19:g.54870254C>T	ENSP00000360371:p.Trp62*	149.0	0.0	.		68.0	19.0	.	NM_145716	A8K0A9|Q5T860|Q5T861|Q9BTM0|Q9BWW3	Nonsense_Mutation	SNP	ENST00000371320.3	hg19	CCDS591.1	.	.	.	.	.	.	.	.	.	.	C	43	10.209365	0.99360	.	.	ENSG00000157216	ENST00000371320;ENST00000371319;ENST00000357475	.	.	.	5.03	5.03	0.67393	.	0.000000	0.64402	U	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.2803	18.3392	0.90299	0.0:1.0:0.0:0.0	.	.	.	.	X	62	.	ENSP00000350067:W62X	W	-	3	0	SSBP3	54642842	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.556000	0.82233	2.502000	0.84385	0.561000	0.74099	TGG	.	.	.	none		0.507	SSBP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022721.1	NM_018070		T	54870254	C	T	54870254	4	4	45	1	0	0	0	0	0	1	0	0	15193	508	18	2	1044	2	SSBP3	1	54870254	Nonsense_Mutation	SNP	C	TCGA-A4-7584-01A-11D-2136-08	20540277	54870254	194380367	4	3123											
LIX1L	128077	hgsc.bcm.edu	37	chr1	145497429	145497430	+	Frame_Shift_Ins	INS	-	-	T																															tgacaacccaaatacagggaINSttggtgccttccgattcatg																										TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:145497429_145497430insT	ENST00000369308.3	+	4	708_709	c.634_635insT	c.(634-636)attfs	p.I212fs	RP11-315I20.1_ENST00000595518.1_RNA|RP11-315I20.1_ENST00000599147.1_RNA|RP11-315I20.1_ENST00000600340.1_RNA|RP11-315I20.1_ENST00000597144.1_RNA|RP11-315I20.1_ENST00000598354.1_RNA|RP11-315I20.1_ENST00000437797.1_RNA|RP11-315I20.1_ENST00000448561.1_RNA|RP11-315I20.1_ENST00000421764.1_RNA|RP11-315I20.1_ENST00000599469.1_RNA|RP11-315I20.1_ENST00000595494.1_RNA|RP11-315I20.1_ENST00000601726.1_RNA|RP11-315I20.1_ENST00000412239.1_RNA|RP11-315I20.1_ENST00000598103.1_RNA|RP11-315I20.1_ENST00000599626.1_RNA	NM_153713.1	NP_714924.1	Q8IVB5	LIX1L_HUMAN	Lix1 homolog (chicken) like	212										large_intestine(4)|lung(6)|ovary(2)|skin(1)	13	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					AAATACAGGGATTGGTGCCTTC	0.45																																					p.I212fs		Atlas-INDEL	.											.	LIX1L	28	.	0			c.634_635insT						PASS	.																																			SO:0001589	frameshift_variant	128077	exon4			.	AK128733	CCDS72873.1	1q21.1	2014-07-15	2014-07-15		ENSG00000152022	ENSG00000271601			28715	protein-coding gene	gene with protein product			"Lix1 homolog (mouse) like", "Lix1 homolog (chicken)-like"			12477932	Standard	NM_153713		Approved	MGC46719	uc001enr.3	Q8IVB5	OTTHUMG00000013741	ENST00000369308.3:c.636dupT	chr1.hg19:g.145497431_145497431dupT	ENSP00000358314:p.Ile212fs	58.0	0.0	0		44.0	15.0	0.340909	NM_153713	Q6AI36	Frame_Shift_Ins	INS	ENST00000369308.3	hg19	CCDS915.1																																																																																			.	.	.	none		0.45	LIX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038513.1	NM_153713		T	145497430	-	T	145497429	7	5	45	1	0	1	1	0	0	0	0	0	8839	333	12	0	648	0	LIX1L	1	145497429	Frame_Shift_Ins	INS	-	TCGA-A4-7584-01A-11D-2136-08	90627175	145497429	103753192	5	3124											
GLT25D2	23127	hgsc.bcm.edu	37	chr1	183944269	183944269	+	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	tttttccctcgcagttcgaaGggctgcctgtcgtagtttca	5	15	10	11	3	1	0	1	0	0	0	5	1	2	0	2	1	1	5	2	1	2	5			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:183944269G>C	ENST00000361927.4	-	3	825	c.454C>G	c.(454-456)Ctt>Gtt	p.L152V	COLGALT2_ENST00000546159.1_Missense_Mutation_p.L152V	NM_015101.2	NP_055916.1	Q8IYK4	GT252_HUMAN	collagen beta(1-O)galactosyltransferase 2	152					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)	procollagen galactosyltransferase activity (GO:0050211)										GCAGTTCGAAGGGCTGCCTGT	0.438																																					p.L152V		Atlas-SNP	.											.	.	.	.	0			c.C454G						PASS	.						119	113	115					1																	183944269		2203	4300	6503	SO:0001583	missense	23127	exon3			TTCGAAGGGCTGC	AF288389	CCDS1360.1	1q25	2013-02-27	2013-02-27	2013-02-27	ENSG00000198756	ENSG00000198756			16790	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 17", "glycosyltransferase 25 domain containing 2"	C1orf17, GLT25D2		19075007	Standard	XM_005245008		Approved	KIAA0584	uc001gqr.3	Q8IYK4	OTTHUMG00000035460	ENST00000361927.4:c.454C>G	chr1.hg19:g.183944269G>C	ENSP00000354960:p.Leu152Val	150.0	0.0	.		99.0	35.0	.	NM_015101	O60327|Q9BZR0	Missense_Mutation	SNP	ENST00000361927.4	hg19	CCDS1360.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.519102	0.85495	.	.	ENSG00000198756	ENST00000546159;ENST00000361927	T;T	0.62364	0.03;0.03	5.2	5.2	0.72013	.	0.000000	0.64402	D	0.000001	T	0.80889	0.4710	M	0.89840	3.065	0.80722	D	1	D;D	0.67145	0.993;0.996	P;D	0.67725	0.873;0.953	D	0.84426	0.0574	10	0.87932	D	0	.	12.479	0.55831	0.0768:0.0:0.9232:0.0	.	152;152	F5H3T5;Q8IYK4	.;GT252_HUMAN	V	152	ENSP00000439112:L152V;ENSP00000354960:L152V	ENSP00000354960:L152V	L	-	1	0	GLT25D2	182210892	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.705000	0.84606	2.583000	0.87209	0.650000	0.86243	CTT	.	.	.	none		0.438	COLGALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086128.1	NM_015101		C	183944269	G	C	183944269	3	2	45	1	0	0	0	0	1	0	0	0	6474	1000	35	4	1466	4	GLT25D2	1	183944269	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08	38446840	183944269	65306352	6	3125											
HMCN1	83872	hgsc.bcm.edu	37	chr1	186083139	186083139	+	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	aacataaaggggggcccccaGagccttgtaattcttttaaa	13	10	9	9	0	1	1	0	0	1	1	1	1	1	1	3	3	2	1	3	3	6	6			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr1:186083139G>A	ENST00000271588.4	+	73	11389	c.11160G>A	c.(11158-11160)caG>caA	p.Q3720Q	HMCN1_ENST00000367492.2_Silent_p.Q3720Q	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3720	Ig-like C2-type 36.				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						GGGGCCCCCAGAGCCTTGTAA	0.423																																					p.Q3720Q		Atlas-SNP	.											.	HMCN1	797	.	0			c.G11160A						PASS	.						114	133	127					1																	186083139		2203	4300	6503	SO:0001819	synonymous_variant	83872	exon73			CCCCCAGAGCCTT	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.11160G>A	chr1.hg19:g.186083139G>A		278.0	0.0	.		208.0	69.0	.	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.	.	none		0.423	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186083139	G	A	186083139	2	1	45	1	0	0	0	0	0	0	0	1	7227	933	33	2		2	HMCN1	1	186083139	Silent	SNP	G	TCGA-A4-7584-01A-11D-2136-08	2138870	186083139	63167482	7	3126											
GCC2	9648	hgsc.bcm.edu	37	chr2	109109239	109109239	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcttaagaatgaaccgacCacaagaagtatgtatgtaca	17	8	8	8	1	0	3	0	1	0	2	0	4	0	3	2	0	3	4	2	0	8	4			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr2:109109239C>T	ENST00000309863.6	+	19	5154	c.4440C>T	c.(4438-4440)acC>acT	p.T1480T		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	1480					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						ATGAACCGACCACAAGAAGTA	0.373																																					p.T1480T		Atlas-SNP	.											.	GCC2	129	.	0			c.C4440T						PASS	.						85	85	85					2																	109109239		2203	4300	6503	SO:0001819	synonymous_variant	9648	exon19			ACCGACCACAAGA	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.4440C>T	chr2.hg19:g.109109239C>T		73.0	0.0	.		45.0	21.0	.	NM_181453	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Silent	SNP	ENST00000309863.6	hg19	CCDS33268.1																																																																																			.	.	.	none		0.373	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635		T	109109239	C	T	109109239	2	4	45	1	0	0	0	0	0	0	0	1	6293	581	21	2		2	GCC2	2	109109239	Silent	SNP	C	TCGA-A4-7584-01A-11D-2136-08		109109239	134090134	8	3127											
TTN	7273	hgsc.bcm.edu	37	chr2	179611391	179611391	+	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	ctctcccccttctcctttttGaatgttagaaatttccagtg	7	17	5	12	0	2	2	0	1	2	1	5	2	3	2	4	0	0	1	4	0	3	5			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr2:179611391G>C	ENST00000591111.1	-	46	10585				TTN_ENST00000342992.6_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000360870.5_Missense_Mutation_p.Q5246E|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000578746.1_RNA|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)			TCTCCTTTTTGAATGTTAGAA	0.388																																					p.Q5246E		Atlas-SNP	.											.	TTN	18412	.	0			c.C15736G						PASS	.						136	129	131					2																	179611391		2203	4300	6503	SO:0001627	intron_variant	7273	exon46			CTTTTTGAATGTT	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.10361-4743C>G	chr2.hg19:g.179611391G>C		63.0	0.0	.		92.0	40.0	.	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	3.110	-0.182790	0.06340	.	.	ENSG00000155657	ENST00000360870;ENST00000306136	T	0.65916	-0.18	5.95	5.95	0.96441	.	.	.	.	.	T	0.48352	0.1495	L	0.49778	1.585	0.80722	D	1	P	0.39282	0.666	B	0.28916	0.096	T	0.53063	-0.8491	9	0.02654	T	1	.	15.7227	0.77724	0.0:0.0:0.802:0.198	.	5246	Q8WZ42-6	.	E	5246;527	ENSP00000354117:Q5246E	ENSP00000304714:Q527E	Q	-	1	0	TTN	179319636	0.997000	0.39634	0.984000	0.44739	0.974000	0.67602	2.850000	0.48294	2.825000	0.97269	0.655000	0.94253	CAA	.	.	.	none		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179611391	G	C	179611391	1	2	45	0	1	0	0	0	0	0	0	0	16747	1299	45	4		4	TTN	2	179611391	Intron	SNP	G	TCGA-A4-7584-01A-11D-2136-08	70502152	179611391	63587982	9	3128											
GPR1	2825	hgsc.bcm.edu	37	chr2	207040930	207040930	+	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	agctgtttccaggagacacaGattcttggtttctgagttcc	8	14	10	9	0	2	3	0	1	2	2	4	4	4	3	2	2	1	4	2	2	0	5			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr2:207040930G>A	ENST00000407325.2	-	3	1404	c.1042C>T	c.(1042-1044)Ctg>Ttg	p.L348L	GPR1_ENST00000437420.1_Silent_p.L348L	NM_001098199.1|NM_001261452.1|NM_001261453.1|NM_001261454.1|NM_001261455.1|NM_005279.3	NP_001091669.1|NP_001248381.1|NP_001248382.1|NP_001248383.1|NP_001248384.1|NP_005270.2	P46091	GPR1_HUMAN	G protein-coupled receptor 1	348					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	18		Lung NSC(271;7.93e-06)|Renal(323;0.000147)|Hepatocellular(293;0.000888)		UCEC - Uterine corpus endometrioid carcinoma (47;0.000241)|Epithelial(149;1.91e-37)|STAD - Stomach adenocarcinoma(1183;0.00178)|Lung(261;0.111)|LUSC - Lung squamous cell carcinoma(261;0.184)		AGGAGACACAGATTCTTGGTT	0.428																																					p.L348L		Atlas-SNP	.											GPR1,NS,carcinoma,0,1	GPR1	38	.	0			c.C1042T						PASS	.						64	61	62					2																	207040930		2203	4300	6503	SO:0001819	synonymous_variant	2825	exon3			GACACAGATTCTT		CCDS2368.1	2q33.3	2014-01-30			ENSG00000183671	ENSG00000183671		"GPCR / Class A : Orphans"	4463	protein-coding gene	gene with protein product		600239				7851889	Standard	NM_005279		Approved		uc031rqv.1	P46091	OTTHUMG00000132894	ENST00000407325.2:c.1042C>T	chr2.hg19:g.207040930G>A		63.0	0.0	.		46.0	17.0	.	NM_001098199	A5JUU6|A8K4L1|Q53TR9|Q6NVX4	Silent	SNP	ENST00000407325.2	hg19	CCDS2368.1																																																																																			.	.	.	none		0.428	GPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256394.2	NM_001098199		A	207040930	G	A	207040930	2	1	45	1	0	0	0	0	0	0	0	1	6628	933	33	2		2	GPR1	2	207040930	Silent	SNP	G	TCGA-A4-7584-01A-11D-2136-08	27429539	207040930	36158443	10	3129											
RBM44	375316	hgsc.bcm.edu	37	chr2	238722326	238722326	+	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	tggaggcaacctccaaaaagGtaagggtctagtccacttac	13	8	10	10	0	1	0	0	0	1	0	3	1	3	1	3	4	2	2	3	4	6	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr2:238722326G>T	ENST00000444524.2	+	2	201		c.e2+1		RBM44_ENST00000409864.1_Splice_Site|RBM44_ENST00000316997.4_Splice_Site			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44							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)		CTCCAAAAAGGTAAGGGTCTA	0.448																																					.		Atlas-SNP	.											.	RBM44	167	.	0			c.76+1G>T						PASS	.						55	57	57					2																	238722326		1917	4134	6051	SO:0001630	splice_region_variant	375316	exon2			AAAAAGGTAAGGG	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	ENST00000444524.2:c.201+1G>T	chr2.hg19:g.238722326G>T		51.0	0.0	.		31.0	16.0	.	NM_001080504	A0AUW3	Splice_Site	SNP	ENST00000444524.2	hg19		.	.	.	.	.	.	.	.	.	.	G	10.22	1.289839	0.23478	.	.	ENSG00000177483	ENST00000316997;ENST00000409864	.	.	.	4.25	4.25	0.50352	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4628	0.55741	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RBM44	238387065	1.000000	0.71417	0.956000	0.39512	0.166000	0.22503	3.694000	0.54742	2.660000	0.90430	0.655000	0.94253	.	.	.	.	none		0.448	RBM44-003	PUTATIVE	basic|exp_conf	processed_transcript	protein_coding	OTTHUMT00000400909.1	NM_001080504	Intron	T	238722326	G	T	238722326	5	4	45	1	0	0	0	0	0	0	1	0	13151	1275	44	4	79	4	RBM44	2	238722326	Splice_Site	SNP	G	TCGA-A4-7584-01A-11D-2136-08	31681396	238722326	4477047	11	3130											
RAD54L2	23132	hgsc.bcm.edu	37	chr3	51697207	51697207	+	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	attctcacagccactcctgtCcgagccgaggatgtttgcgc	7	10	10	14	3	1	0	1	0	1	0	4	3	3	1	4	1	3	1	4	1	0	2			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr3:51697207C>G	ENST00000409535.2	+	22	4300	c.4175C>G	c.(4174-4176)tCc>tGc	p.S1392C	RAD54L2_ENST00000296477.3_Missense_Mutation_p.S1086C	NM_015106.2	NP_055921.2	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2 (S. cerevisiae)	1392						nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|transcription cofactor activity (GO:0003712)			NS(2)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|liver(2)|lung(9)|ovary(4)|skin(2)	31				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)		CCACTCCTGTCCGAGCCGAGG	0.567																																					p.S1392C		Atlas-SNP	.											.	RAD54L2	94	.	0			c.C4175G						PASS	.						153	132	139					3																	51697207		2203	4300	6503	SO:0001583	missense	23132	exon22			TCCTGTCCGAGCC	AB018352	CCDS33765.2	3p21.2	2006-01-17			ENSG00000164080	ENSG00000164080			29123	protein-coding gene	gene with protein product						9872452	Standard	NM_015106		Approved	KIAA0809, SRISNF2L	uc011bdt.2	Q9Y4B4	OTTHUMG00000152936	ENST00000409535.2:c.4175C>G	chr3.hg19:g.51697207C>G	ENSP00000386520:p.Ser1392Cys	183.0	0.0	.		123.0	48.0	.	NM_015106	Q8TB57|Q9BV54	Missense_Mutation	SNP	ENST00000409535.2	hg19	CCDS33765.2	.	.	.	.	.	.	.	.	.	.	C	17.44	3.390512	0.62066	.	.	ENSG00000164080	ENST00000409535;ENST00000296477	D;D	0.94092	-3.24;-3.35	5.56	5.56	0.83823	.	0.324591	0.28927	N	0.013698	D	0.85643	0.5744	N	0.08118	0	0.80722	D	1	P;P	0.46327	0.661;0.876	B;B	0.36289	0.221;0.221	D	0.88801	0.3285	10	0.72032	D	0.01	-4.0774	18.5281	0.90980	0.0:1.0:0.0:0.0	.	1392;981	Q9Y4B4;B3KV54	ARIP4_HUMAN;.	C	1392;1086	ENSP00000386520:S1392C;ENSP00000296477:S1086C	ENSP00000296477:S1086C	S	+	2	0	RAD54L2	51672247	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.158000	0.58150	2.609000	0.88269	0.655000	0.94253	TCC	.	.	.	none		0.567	RAD54L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328700.2	NM_015106		G	51697207	C	G	51697207	3	3	45	1	0	0	0	0	1	0	0	0	13007	855	30	4	4257	4	RAD54L2	3	51697207	Missense_Mutation	SNP	C	TCGA-A4-7584-01A-11D-2136-08		51697207	146325223	12	3131											
MITF	4286	hgsc.bcm.edu	37	chr3	69928532	69928532	+	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	aggtgccgatggaagtccttAaggtacgtgagtgttgctct	8	12	14	7	2	1	1	0	1	1	0	2	3	2	2	2	3	3	3	2	3	3	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr3:69928532A>T	ENST00000448226.2	+	2	479	c.352A>T	c.(352-354)Aag>Tag	p.K118*	MITF_ENST00000314589.5_Nonsense_Mutation_p.K102*|MITF_ENST00000352241.4_Nonsense_Mutation_p.K118*|MITF_ENST00000394355.2_Nonsense_Mutation_p.K93*|MITF_ENST00000328528.6_Nonsense_Mutation_p.K117*|MITF_ENST00000472437.1_Nonsense_Mutation_p.K66*			O75030	MITF_HUMAN	microphthalmia-associated transcription factor	118					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)		GGAAGTCCTTAAGGTACGTGA	0.478			A		melanoma		"Waardenburg syndrome type 2, Tietz syndrome"																														p.K118X	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.A352T						PASS	.						53	59	57					3																	69928532		2104	4227	6331	SO:0001587	stop_gained	4286	exon2			GTCCTTAAGGTAC		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.352A>T	chr3.hg19:g.69928532A>T	ENSP00000391803:p.Lys118*	35.0	0.0	.		35.0	19.0	.	NM_198159	B4DJL2|D3K197|E9PFN0|Q14841|Q9P2V0|Q9P2V1|Q9P2V2|Q9P2Y8	Nonsense_Mutation	SNP	ENST00000448226.2	hg19		.	.	.	.	.	.	.	.	.	.	A	33	5.248140	0.95305	.	.	ENSG00000187098	ENST00000352241;ENST00000448226;ENST00000429090;ENST00000433517;ENST00000472437;ENST00000457080;ENST00000328528;ENST00000451708;ENST00000314589;ENST00000394355	.	.	.	6.02	6.02	0.97574	.	0.088619	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5446	0.84426	1.0:0.0:0.0:0.0	.	.	.	.	X	118;118;66;66;66;117;117;102;102;93	.	.	K	+	1	0	MITF	70011222	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	8.923000	0.92808	2.311000	0.77944	0.533000	0.62120	AAG	.	.	.	none		0.478	MITF-007	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000313947.1	NM_198159		T	69928532	A	T	69928532	4	4	45	1	0	0	0	0	0	1	0	0	9603	363	13	5	523	5	MITF	3	69928532	Nonsense_Mutation	SNP	A	TCGA-A4-7584-01A-11D-2136-08	18231325	69928532	128093898	13	3132											
FAM55C	91775	hgsc.bcm.edu	37	chr3	101520832	101520832	+	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	cagagagtgctttcttccagAggtatgtactgctttttctt	7	17	9	8	0	2	2	0	0	2	2	3	3	3	2	1	1	3	4	1	1	2	7			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr3:101520832A>T	ENST00000491511.2	+	5	1803	c.847A>T	c.(847-849)Agt>Tgt	p.S283C	NXPE3_ENST00000273347.5_Splice_Site_p.S283C|NXPE3_ENST00000422132.1_Splice_Site_p.S283C|NXPE3_ENST00000477909.1_Splice_Site_p.S283C	NM_001134456.1	NP_001127928.1	Q969Y0	NXPE3_HUMAN	neurexophilin and PC-esterase domain family, member 3	283						extracellular region (GO:0005576)											TTTCTTCCAGAGGTATGTACT	0.443																																					p.S283C		Atlas-SNP	.											.	.	.	.	0			c.A847T						PASS	.						92	98	96					3																	101520832		2177	4287	6464	SO:0001630	splice_region_variant	91775	exon5			TTCCAGAGGTATG	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.848+1A>T	chr3.hg19:g.101520832A>T		233.0	0.0	.		174.0	65.0	.	NM_145037	A8K0X4|D3DN53|Q7Z2S8	Missense_Mutation	SNP	ENST00000491511.2	hg19	CCDS2945.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.677582	0.88445	.	.	ENSG00000144815	ENST00000273347;ENST00000491511;ENST00000477909;ENST00000422132	T;T;T;T	0.13420	2.59;2.59;2.59;2.59	5.8	5.8	0.92144	.	0.197973	0.64402	D	0.000006	T	0.37461	0.1004	M	0.69823	2.125	0.58432	D	0.999999	D	0.76494	0.999	D	0.71656	0.974	T	0.10941	-1.0608	10	0.66056	D	0.02	-3.0682	16.1475	0.81580	1.0:0.0:0.0:0.0	.	283	Q969Y0	FA55C_HUMAN	C	283	ENSP00000273347:S283C;ENSP00000417485:S283C;ENSP00000418369:S283C;ENSP00000396421:S283C	ENSP00000273347:S283C	S	+	1	0	FAM55C	103003522	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	9.300000	0.96151	2.213000	0.71641	0.528000	0.53228	AGT	.	.	.	none		0.443	NXPE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353711.2	NM_145037	Missense_Mutation	T	101520832	A	T	101520832	5	4	45	1	0	0	0	0	0	0	1	0	5593	318	11	5	853	5	FAM55C	3	101520832	Splice_Site	SNP	A	TCGA-A4-7584-01A-11D-2136-08	31592300	101520832	96501598	14	3133											
AP2M1	1173	hgsc.bcm.edu	37	chr3	183898969	183898969	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgggatgaatgacaagattgTtattgaaaagcagggcaaag	16	9	13	3	0	0	4	0	3	0	1	0	5	0	5	0	2	1	3	0	2	6	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr3:183898969T>C	ENST00000292807.5	+	7	810	c.662T>C	c.(661-663)gTt>gCt	p.V221A	AP2M1_ENST00000439647.1_Missense_Mutation_p.V219A|EIF2B5_ENST00000444495.1_Intron|AP2M1_ENST00000382456.3_Missense_Mutation_p.V219A|AP2M1_ENST00000411763.2_Missense_Mutation_p.V246A|AP2M1_ENST00000461733.1_3'UTR	NM_004068.3	NP_004059.2	Q96CW1	AP2M1_HUMAN	adaptor-related protein complex 2, mu 1 subunit	221	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of protein localization to plasma membrane (GO:1903077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	18	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.92e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GACAAGATTGTTATTGAAAAG	0.562																																					p.V219A		Atlas-SNP	.											.	AP2M1	35	.	0			c.T656C						PASS	.						145	153	151					3																	183898969		2060	4205	6265	SO:0001583	missense	1173	exon6			AGATTGTTATTGA	U36188	CCDS43177.1, CCDS43178.1	3q28	2008-07-18			ENSG00000161203	ENSG00000161203			564	protein-coding gene	gene with protein product	"clathrin-associated/assembly/adaptor protein, medium 1", "plasma membrane adaptor AP-2 50kDA protein", "clathrin coat adaptor protein AP50", "clathrin adaptor complex AP2, mu subunit", "HA2 50 kDA subunit", "clathrin assembly protein complex 2 medium chain", "AP-2 mu 2 chain"	601024		CLAPM1		8595912	Standard	NM_004068		Approved	AP50, mu2	uc003fmw.3	Q96CW1	OTTHUMG00000156822	ENST00000292807.5:c.662T>C	chr3.hg19:g.183898969T>C	ENSP00000292807:p.Val221Ala	257.0	0.0	.		197.0	87.0	.	NM_001025205	A6NE12|D3DNT1|P20172|P53679	Missense_Mutation	SNP	ENST00000292807.5	hg19	CCDS43177.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.963122	0.53507	.	.	ENSG00000161203	ENST00000382456;ENST00000411763;ENST00000292807;ENST00000540821;ENST00000539646;ENST00000439647	T;T;T;T	0.18657	2.2;2.2;2.2;2.2	6.07	4.91	0.64330	Clathrin adaptor, mu subunit, C-terminal (3);	0.164876	0.53938	D	0.000053	T	0.33059	0.0850	M	0.67569	2.06	0.58432	D	0.999999	B;B;B;B	0.26602	0.003;0.076;0.154;0.127	B;B;B;B	0.41174	0.039;0.349;0.198;0.125	T	0.09122	-1.0689	10	0.46703	T	0.11	.	12.1758	0.54184	0.0:0.0663:0.0:0.9337	.	111;91;221;219	B7Z4N2;B4DTI4;Q96CW1;Q96CW1-2	.;.;AP2M1_HUMAN;.	A	219;246;221;161;206;219	ENSP00000371894:V219A;ENSP00000403362:V246A;ENSP00000292807:V221A;ENSP00000409081:V219A	ENSP00000292807:V221A	V	+	2	0	AP2M1	185381663	1.000000	0.71417	0.993000	0.49108	0.920000	0.55202	7.375000	0.79646	1.119000	0.41883	-0.256000	0.11100	GTT	.	.	.	none		0.562	AP2M1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346013.1	NM_004068		C	183898969	T	C	183898969	3	2	45	1	0	0	0	0	1	0	0	0	742	1725	60	3	681	3	AP2M1	3	183898969	Missense_Mutation	SNP	T	TCGA-A4-7584-01A-11D-2136-08	82378137	183898969	14123461	15	3134											
FIP1L1	81608	hgsc.bcm.edu	37	chr4	54266007	54266007	+	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	actgggcttccaccgagcagGttagttacatagttataact	11	12	9	9	1	0	0	0	0	0	0	1	1	1	0	2	2	3	5	2	2	5	6			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr4:54266007G>C	ENST00000337488.6	+	10	1009		c.e10+1		FIP1L1_ENST00000306932.6_Splice_Site|FIP1L1_ENST00000507922.1_Splice_Site|FIP1L1_ENST00000507166.1_Splice_Site|FIP1L1_ENST00000358575.5_Splice_Site	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1						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)			CACCGAGCAGGTTAGTTACAT	0.363			T	PDGFRA	idiopathic hypereosinophilic syndrome																																.		Atlas-SNP	.		Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	.	FIP1L1	60	.	0			c.701+1G>C						PASS	.						132	128	129					4																	54266007		2203	4300	6503	SO:0001630	splice_region_variant	81608	exon8			GAGCAGGTTAGTT	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.815+1G>C	chr4.hg19:g.54266007G>C		142.0	0.0	.		76.0	31.0	.	NM_001134938	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Splice_Site	SNP	ENST00000337488.6	hg19	CCDS3491.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.122802	0.56613	.	.	ENSG00000145216	ENST00000337488;ENST00000358575;ENST00000507922;ENST00000306932;ENST00000507166	.	.	.	5.38	5.38	0.77491	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.5077	0.95125	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FIP1L1	53960764	1.000000	0.71417	1.000000	0.80357	0.625000	0.37756	7.864000	0.87037	2.683000	0.91414	0.655000	0.94253	.	.	.	.	none		0.363	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250602.1	NM_030917	Intron	C	54266007	G	C	54266007	5	2	45	1	0	0	0	0	0	0	1	0	5903	1275	44	4	854	4	FIP1L1	4	54266007	Splice_Site	SNP	G	TCGA-A4-7584-01A-11D-2136-08		54266007	136888269	16	3135											
PLRG1	5356	hgsc.bcm.edu	37	chr4	155465648	155465648	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggttttggcattgtaggggcTtttttagccatcagtgcaga	7	15	13	6	0	1	1	1	0	0	1	1	1	1	1	1	4	2	5	1	4	2	7			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr4:155465648T>C	ENST00000499023.2	-	7	669	c.543A>G	c.(541-543)aaA>aaG	p.K181K	PLRG1_ENST00000302078.5_Silent_p.K172K|PLRG1_ENST00000393905.2_Silent_p.K181K|RNU6-1285P_ENST00000363480.1_RNA	NM_001201564.1|NM_002669.3	NP_001188493.1|NP_002660.1	O43660	PLRG1_HUMAN	pleiotropic regulator 1	181					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|protein localization to nucleus (GO:0034504)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|skin(1)|urinary_tract(1)	22	all_hematologic(180;0.215)	Renal(120;0.0854)				TTGTAGGGGCTTTTTTAGCCA	0.408																																					p.K181K		Atlas-SNP	.											.,1	PLRG1	43	.	0			c.A543G						PASS	.						139	140	139					4																	155465648		2203	4300	6503	SO:0001819	synonymous_variant	5356	exon7			AGGGGCTTTTTTA	AF044333	CCDS34083.1, CCDS56341.1	4q31.2-q32.1	2013-01-10	2011-05-19		ENSG00000171566	ENSG00000171566		"WD repeat domain containing"	9089	protein-coding gene	gene with protein product	"transport and golgi organization 4 homolog (Drosophila)"	605961	"pleiotropic regulator 1 (PRL1, Arabidopsis homolog)", "pleiotropic regulator 1 (PRL1 homolog, Arabidopsis)"				Standard	NM_002669		Approved	PRL1, Prp46, PRPF46, Cwc1, TANGO4	uc003iny.3	O43660	OTTHUMG00000161411	ENST00000499023.2:c.543A>G	chr4.hg19:g.155465648T>C		97.0	0.0	.		66.0	25.0	.	NM_002669	B3KMK4|Q3KQY5|Q8WUD8	Silent	SNP	ENST00000499023.2	hg19	CCDS34083.1																																																																																			.	.	.	none		0.408	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364824.1	NM_002669		C	155465648	T	C	155465648	2	2	45	1	0	0	0	0	0	0	0	1	12113	1606	56	3		3	PLRG1	4	155465648	Silent	SNP	T	TCGA-A4-7584-01A-11D-2136-08	101199641	155465648	35688628	17	3136											
PCSK1	5122	hgsc.bcm.edu	37	chr5	95761622	95761622	+	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	ttctttttcatactgttgttCagcccatatcacctacaagg	9	16	5	11	0	4	0	3	0	1	0	4	0	4	0	2	1	3	2	2	1	4	8			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr5:95761622C>G	ENST00000311106.3	-	3	535	c.298G>C	c.(298-300)Gaa>Caa	p.E100Q	CTD-2337A12.1_ENST00000502645.2_RNA|PCSK1_ENST00000508626.1_Missense_Mutation_p.E53Q	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	100					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)"	TACTGTTGTTCAGCCCATATC	0.383																																					p.E100Q		Atlas-SNP	.											.	PCSK1	93	.	0			c.G298C						PASS	.						141	129	133					5																	95761622		2203	4300	6503	SO:0001583	missense	5122	exon3			GTTGTTCAGCCCA		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.298G>C	chr5.hg19:g.95761622C>G	ENSP00000308024:p.Glu100Gln	50.0	0.0	.		40.0	16.0	.	NM_000439	B7Z8T7|E9PHA1|P78478|Q92532	Missense_Mutation	SNP	ENST00000311106.3	hg19	CCDS4081.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.305017	0.81247	.	.	ENSG00000175426	ENST00000311106;ENST00000508626;ENST00000509190	T;T;T	0.33216	1.42;1.42;2.19	5.63	5.63	0.86233	Proteinase inhibitor, propeptide (1);	0.000000	0.85682	D	0.000000	T	0.35740	0.0942	L	0.39633	1.23	0.58432	D	0.999997	D	0.53312	0.959	P	0.49887	0.625	T	0.01613	-1.1312	10	0.15066	T	0.55	-30.1455	19.6351	0.95728	0.0:1.0:0.0:0.0	.	100	P29120	NEC1_HUMAN	Q	100;53;100	ENSP00000308024:E100Q;ENSP00000421600:E53Q;ENSP00000427294:E100Q	ENSP00000308024:E100Q	E	-	1	0	PCSK1	95787378	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.393000	0.79851	2.805000	0.96524	0.655000	0.94253	GAA	.	.	.	none		0.383	PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1	NM_000439		G	95761622	C	G	95761622	3	3	45	1	0	0	0	0	1	0	0	0	11607	835	29	4	2011	4	PCSK1	5	95761622	Missense_Mutation	SNP	C	TCGA-A4-7584-01A-11D-2136-08		95761622	85153638	18	3137											
FAM71B	153745	hgsc.bcm.edu	37	chr5	156590018	156590018	+	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	attccagacttcagcactggGctgggaaactttctggcttc	8	12	10	11	0	2	1	1	0	1	1	4	2	3	2	1	3	2	3	1	3	1	4			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr5:156590018G>C	ENST00000302938.4	-	2	1353	c.1258C>G	c.(1258-1260)Ccc>Gcc	p.P420A		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	420						nucleus (GO:0005634)				NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TCAGCACTGGGCTGGGAAACT	0.488																																					p.P420A		Atlas-SNP	.											.	FAM71B	145	.	0			c.C1258G						PASS	.						102	103	102					5																	156590018		2203	4300	6503	SO:0001583	missense	153745	exon2			CACTGGGCTGGGA		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.1258C>G	chr5.hg19:g.156590018G>C	ENSP00000305596:p.Pro420Ala	137.0	0.0	.		113.0	54.0	.	NM_130899	Q1EDD9|Q8TC64|Q96LY8	Missense_Mutation	SNP	ENST00000302938.4	hg19	CCDS4335.1	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.631608	0.00813	.	.	ENSG00000170613	ENST00000302938	T	0.17528	2.27	4.4	-1.91	0.07641	.	0.847983	0.09952	N	0.734546	T	0.10035	0.0246	L	0.48877	1.53	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.42849	-0.9427	10	0.07482	T	0.82	-0.6432	2.0469	0.03562	0.1:0.2599:0.2424:0.3977	.	420	Q8TC56	FA71B_HUMAN	A	420	ENSP00000305596:P420A	ENSP00000305596:P420A	P	-	1	0	FAM71B	156522596	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.057000	0.11768	-0.177000	0.10690	-0.291000	0.09656	CCC	.	.	.	none		0.488	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899		C	156590018	G	C	156590018	3	2	45	1	0	0	0	0	1	0	0	0	5615	1203	42	4	563	4	FAM71B	5	156590018	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08	60828396	156590018	24325242	19	3138											
BAI3	577	hgsc.bcm.edu	37	chr6	69666026	69666027	+	Frame_Shift_Ins	INS	-	-	A																															agctgcccatggaggctccgINSaatgcagagggccatgggca																								rs141698131		TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr6:69666026_69666027insA	ENST00000370598.1	+	7	2127_2128	c.1306_1307insA	c.(1306-1308)gaafs	p.E436fs		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	436	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	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)				TGGAGGCTCCGAATGCAGAGGG	0.554																																					p.E436fs		Atlas-INDEL	.											.	BAI3	451	.	0			c.1306_1307insA						PASS	.																																			SO:0001589	frameshift_variant	577	exon7			.	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.1308dupA	chr6.hg19:g.69666028_69666028dupA	ENSP00000359630:p.Glu436fs	37.0	0.0	0		53.0	22.0	0.415094	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Frame_Shift_Ins	INS	ENST00000370598.1	hg19	CCDS4968.1																																																																																			.	.	.	none		0.554	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			A	69666027	-	A	69666026	7	5	45	1	0	1	1	0	0	0	0	0	1300	1059	37	0	1324	0	BAI3	6	69666026	Frame_Shift_Ins	INS	-	TCGA-A4-7584-01A-11D-2136-08		69666026	101449041	20	3139											
DDO	8528	hgsc.bcm.edu	37	chr6	110734538	110734538	+	Missense_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	ttccggctgccacatcactgGtggtatctggagtaaacttg	8	12	11	10	1	2	0	1	0	1	0	3	1	3	1	2	4	2	3	2	4	3	4			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr6:110734538G>A	ENST00000368924.3	-	2	227	c.212C>T	c.(211-213)aCc>aTc	p.T71I	DDO_ENST00000368923.3_Missense_Mutation_p.T71I	NM_003649.2	NP_003640.2	Q99489	OXDD_HUMAN	D-aspartate oxidase	43					aspartate catabolic process (GO:0006533)|aspartate metabolic process (GO:0006531)|D-amino acid catabolic process (GO:0019478)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insemination (GO:0007320)|oxidation-reduction process (GO:0055114)	peroxisome (GO:0005777)	cofactor binding (GO:0048037)|D-aspartate oxidase activity (GO:0008445)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|pancreas(1)|skin(3)	24		all_cancers(87;3.47e-21)|all_epithelial(87;9.03e-20)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_lung(197;2.98e-05)|Lung NSC(302;3.25e-05)|Colorectal(196;3.46e-05)|Ovarian(999;0.00327)		all cancers(137;2.54e-48)|Epithelial(106;3.11e-44)|OV - Ovarian serous cystadenocarcinoma(136;2.08e-24)|BRCA - Breast invasive adenocarcinoma(108;0.000141)|GBM - Glioblastoma multiforme(226;0.00046)		CACATCACTGGTGGTATCTGG	0.493																																					p.T71I		Atlas-SNP	.											.	DDO	51	.	0			c.C212T						PASS	.						133	116	122					6																	110734538		2203	4300	6503	SO:0001583	missense	8528	exon2			TCACTGGTGGTAT	D89858	CCDS5082.1, CCDS5083.1	6q22.1	2008-02-05			ENSG00000203797	ENSG00000203797	1.4.3.1		2727	protein-coding gene	gene with protein product		124450				9163533	Standard	NM_003649		Approved		uc003puc.3	Q99489	OTTHUMG00000015360	ENST00000368924.3:c.212C>T	chr6.hg19:g.110734538G>A	ENSP00000357920:p.Thr71Ile	207.0	0.0	.		125.0	53.0	.	NM_004032	A8KAG4|Q5JXM4|Q5JXM5|Q5JXM6|Q8N552	Missense_Mutation	SNP	ENST00000368924.3	hg19	CCDS5082.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.287509	0.80803	.	.	ENSG00000203797	ENST00000368924;ENST00000368923;ENST00000368925	D;D;D	0.83250	-1.7;-1.7;-1.7	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	D	0.94221	0.8145	H	0.96777	3.88	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.95581	0.8646	10	0.72032	D	0.01	-21.4422	19.187	0.93648	0.0:0.0:1.0:0.0	.	71;71	Q99489-4;Q99489-3	.;.	I	71;71;43	ENSP00000357920:T71I;ENSP00000357919:T71I;ENSP00000357921:T43I	ENSP00000357919:T71I	T	-	2	0	DDO	110841231	1.000000	0.71417	0.997000	0.53966	0.546000	0.35178	7.120000	0.77153	2.614000	0.88457	0.655000	0.94253	ACC	.	.	.	none		0.493	DDO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041796.1			A	110734538	G	A	110734538	3	1	45	1	0	0	0	0	1	0	0	0	4336	1261	44	2	913	2	DDO	6	110734538	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08	41068512	110734538	60380529	21	3140											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152631610	152631610	+	Missense_Mutation	SNP	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	ttgcctgggcttgctccaagGcagcttgtaactttttcaac	7	14	9	11	0	1	0	1	0	0	0	2	0	2	0	2	2	5	5	2	2	3	6			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr6:152631610G>A	ENST00000367255.5	-	89	17541	c.16940C>T	c.(16939-16941)gCc>gTc	p.A5647V	SYNE1_ENST00000423061.1_Missense_Mutation_p.A5576V|SYNE1_ENST00000356820.4_Missense_Mutation_p.A171V|SYNE1_ENST00000265368.4_Missense_Mutation_p.A5647V|SYNE1_ENST00000341594.5_Missense_Mutation_p.A5259V|SYNE1_ENST00000448038.1_Missense_Mutation_p.A5576V	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5647					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.A5647V(2)		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)		TTGCTCCAAGGCAGCTTGTAA	0.433										HNSCC(10;0.0054)																											p.A5647V		Atlas-SNP	.											SYNE1_ENST00000265368,caecum,carcinoma,0,2	SYNE1	3227	.	2	Substitution - Missense(2)	large_intestine(2)	c.C16940T						PASS	.						104	103	103					6																	152631610		2203	4300	6503	SO:0001583	missense	23345	exon89			TCCAAGGCAGCTT	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.16940C>T	chr6.hg19:g.152631610G>A	ENSP00000356224:p.Ala5647Val	86.0	0.0	.		50.0	19.0	.	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	22.7	4.327610	0.81690	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820	T;T;T;T;T;T	0.50548	1.38;1.38;1.38;1.38;0.74;1.38	6.06	6.06	0.98353	.	0.000000	0.64402	D	0.000009	T	0.64136	0.2571	M	0.72118	2.19	0.53688	D	0.99997	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.74348	0.961;0.961;0.983	T	0.57963	-0.7720	10	0.39692	T	0.17	.	20.6208	0.99490	0.0:0.0:1.0:0.0	.	5647;5647;5576	Q8NF91;E7EQI5;Q8NF91-4	SYNE1_HUMAN;.;.	V	5647;5576;5647;5576;5259;171	ENSP00000356224:A5647V;ENSP00000396024:A5576V;ENSP00000265368:A5647V;ENSP00000390975:A5576V;ENSP00000341887:A5259V;ENSP00000349276:A171V	ENSP00000265368:A5647V	A	-	2	0	SYNE1	152673303	1.000000	0.71417	0.811000	0.32455	0.720000	0.41350	7.876000	0.87215	2.882000	0.98803	0.655000	0.94253	GCC	.	.	.	none		0.433	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152631610	G	A	152631610	3	1	45	1	0	0	0	0	1	0	0	0	15457	1203	42	2	9758	2	SYNE1	6	152631610	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08	41897072	152631610	18483457	22	3141											
ACTB	60	hgsc.bcm.edu	37	chr7	5568977	5568977	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgaggatgcctctcttgcTctgggcctcgtcgcccacat	4	11	12	14	2	2	1	0	1	2	0	5	2	2	2	3	3	2	1	3	3	0	1			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr7:5568977T>C	ENST00000331789.5	-	3	369	c.178A>G	c.(178-180)Agc>Ggc	p.S60G	ACTB_ENST00000464611.1_5'Flank|AC006483.1_ENST00000579427.1_RNA	NM_001101.3	NP_001092.1	P63261	ACTG_HUMAN	actin, beta	60					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)		CCTCTCTTGCTCTGGGCCTCG	0.587																																					p.S60G		Atlas-SNP	.											.	ACTB	45	.	0			c.A178G						PASS	.						71	73	73					7																	5568977		2203	4298	6501	SO:0001583	missense	60	exon3			TCTTGCTCTGGGC	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.178A>G	chr7.hg19:g.5568977T>C	ENSP00000349960:p.Ser60Gly	181.0	0.0	.		178.0	97.0	.	NM_001101	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000331789.5	hg19	CCDS5341.1	.	.	.	.	.	.	.	.	.	.	T	15.56	2.870663	0.51695	.	.	ENSG00000075624	ENST00000331789;ENST00000445914;ENST00000432588;ENST00000443528;ENST00000417101;ENST00000414620	D;D;D;D;D	0.90732	-2.72;-2.72;-2.72;-2.72;-2.72	4.91	4.91	0.64330	Actin, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.92704	0.7681	M	0.81497	2.545	0.45594	D	0.998536	P	0.35033	0.481	P	0.45195	0.473	D	0.93247	0.6631	10	0.87932	D	0	.	12.5141	0.56021	0.0:0.0:0.0:1.0	.	60	P60709	ACTB_HUMAN	G	60;60;60;60;63;60	ENSP00000349960:S60G;ENSP00000407473:S60G;ENSP00000393951:S60G;ENSP00000399487:S63G;ENSP00000401032:S60G	ENSP00000349960:S60G	S	-	1	0	ACTB	5535503	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.816000	0.86201	1.837000	0.53436	0.460000	0.39030	AGC	.	.	.	none		0.587	ACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059589.4	NM_001101		C	5568977	T	C	5568977	3	2	45	1	0	0	0	0	1	0	0	0	193	1551	54	3	965	3	ACTB	7	5568977	Missense_Mutation	SNP	T	TCGA-A4-7584-01A-11D-2136-08		5568977	153569686	23	3142											
ANKMY2	57037	hgsc.bcm.edu	37	chr7	16650259	16650260	+	Missense_Mutation	DNP	TC	TC	CT																															acagcttatgtaatgcatctTcatagccaatacttcattca																										TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr7:16650259_16650260TC>CT	ENST00000306999.2	-	6	903_904	c.660_661GA>AG	c.(658-663)atGAag>atAGag	p.220_221MK>IE		NM_020319.2	NP_064715.1	Q8IV38	ANKY2_HUMAN	ankyrin repeat and MYND domain containing 2	220						cilium (GO:0005929)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	23	Lung NSC(10;0.103)|all_lung(11;0.204)			UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		TAATGCATCTTCATAGCCAATA	0.351																																					p.K221E|p.M220I		Atlas-SNP	.											.	ANKMY2	46	.	0			c.A661G|c.G660A						PASS	.																																			SO:0001583	missense	57037	exon6			GCATCTTCATAGC|CATCTTCATAGCC	AK001740	CCDS5361.1	7p21	2013-01-10			ENSG00000106524	ENSG00000106524		"Zinc fingers, MYND-type", "Ankyrin repeat domain containing"	25370	protein-coding gene	gene with protein product						12477932	Standard	NM_020319		Approved	DKFZP564O043, ZMYND20	uc003sti.3	Q8IV38	OTTHUMG00000090806	ENST00000306999.2:c.660_661delinsCT	chr7.hg19:g.16650259_16650260delinsCT	ENSP00000303570:p.M220_K221delinsIE	94.0|96.0	0.0	.		74.0|73.0	35.0|34.0	.	NM_020319	A4D124|Q659G1|Q96BL3	Missense_Mutation	SNP	ENST00000306999.2	hg19	CCDS5361.1																																																																																			.	.	.	none		0.351	ANKMY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207600.2	NM_020319		CT	16650260	TC	CT	16650259	3	2	45	1	0	0	0	0	1	0	0	0	635	1792	62	3	684	3	ANKMY2	7	16650259	Missense_Mutation	DNP	TC	TCGA-A4-7584-01A-11D-2136-08	11081282	16650259	142488404	24	3143											
PCLO	27445	hgsc.bcm.edu	37	chr7	82584714	82584714	+	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	attcagaacaagaagatctaTggagctcctccatttctgca	13	11	7	10	0	3	3	1	0	2	3	5	4	5	4	2	1	3	2	2	1	4	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr7:82584714T>A	ENST00000333891.9	-	5	5892	c.5555A>T	c.(5554-5556)cAt>cTt	p.H1852L	PCLO_ENST00000423517.2_Missense_Mutation_p.H1852L	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						AGAAGATCTATGGAGCTCCTC	0.408																																					p.H1852L		Atlas-SNP	.											.	PCLO	1506	.	0			c.A5555T						PASS	.						178	163	168					7																	82584714		1858	4097	5955	SO:0001583	missense	27445	exon5			GATCTATGGAGCT	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.5555A>T	chr7.hg19:g.82584714T>A	ENSP00000334319:p.His1852Leu	159.0	0.0	.		202.0	67.0	.	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	10.58	1.390651	0.25118	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.19938	2.11;2.12	5.57	5.57	0.84162	.	.	.	.	.	T	0.16727	0.0402	N	0.19112	0.55	0.80722	D	1	P;P	0.41848	0.763;0.763	B;B	0.39185	0.293;0.293	T	0.02860	-1.1101	9	0.87932	D	0	.	15.7247	0.77747	0.0:0.0:0.0:1.0	.	1852;1852	Q9Y6V0-5;Q9Y6V0-6	.;.	L	1783;1852;1852	ENSP00000334319:H1852L;ENSP00000388393:H1852L	ENSP00000334319:H1852L	H	-	2	0	PCLO	82422650	0.995000	0.38212	0.924000	0.36721	0.989000	0.77384	2.626000	0.46460	2.116000	0.64780	0.533000	0.62120	CAT	.	.	.	none		0.408	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82584714	T	A	82584714	3	1	45	1	0	0	0	0	1	0	0	0	11590	1464	51	5	9974	5	PCLO	7	82584714	Missense_Mutation	SNP	T	TCGA-A4-7584-01A-11D-2136-08	65934455	82584714	76553949	25	3144											
WDR91	29062	hgsc.bcm.edu	37	chr7	134871027	134871027	+	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	caggggctcggtggccacctAggctcaagcagctctccaga	8	6	13	14	1	2	1	1	0	1	1	4	1	2	1	3	5	2	4	3	5	2	1			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr7:134871027A>T	ENST00000354475.4	-	15	2151	c.2120T>A	c.(2119-2121)cTa>cAa	p.L707Q	WDR91_ENST00000423565.1_Missense_Mutation_p.L672Q|WDR91_ENST00000344400.5_3'UTR	NM_014149.3	NP_054868.3	A4D1P6	WDR91_HUMAN	WD repeat domain 91	707										breast(3)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	40						GTGGCCACCTAGGCTCAAGCA	0.587																																					p.L707Q		Atlas-SNP	.											.	WDR91	82	.	0			c.T2120A						PASS	.						73	60	65					7																	134871027		2203	4300	6503	SO:0001583	missense	29062	exon15			CCACCTAGGCTCA	AF161534	CCDS34758.1	7q33	2013-01-09			ENSG00000105875	ENSG00000105875		"WD repeat domain containing"	24997	protein-coding gene	gene with protein product						11042152, 11230166	Standard	NM_014149		Approved	HSPC049	uc003vsp.2	A4D1P6	OTTHUMG00000155414	ENST00000354475.4:c.2120T>A	chr7.hg19:g.134871027A>T	ENSP00000346466:p.Leu707Gln	50.0	0.0	.		69.0	36.0	.	NM_014149	A6NK54|C9JMI4|Q6FI65|Q6MZQ1|Q6P4I1|Q96AE5|Q96G63|Q9H062|Q9H9B6|Q9NVG7|Q9NZY6	Missense_Mutation	SNP	ENST00000354475.4	hg19	CCDS34758.1	.	.	.	.	.	.	.	.	.	.	A	31	5.060981	0.93846	.	.	ENSG00000105875	ENST00000354475;ENST00000423565	T;T	0.68479	-0.33;-0.33	5.54	5.54	0.83059	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.80008	0.4545	L	0.61218	1.895	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82174	-0.0588	10	0.87932	D	0	-16.5822	15.6802	0.77360	1.0:0.0:0.0:0.0	.	707	A4D1P6	WDR91_HUMAN	Q	707;672	ENSP00000346466:L707Q;ENSP00000392555:L672Q	ENSP00000346466:L707Q	L	-	2	0	WDR91	134521567	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	2.103000	0.63969	0.533000	0.62120	CTA	.	.	.	none		0.587	WDR91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340019.1	NM_014149		T	134871027	A	T	134871027	3	4	45	1	0	0	0	0	1	0	0	0	17350	420	15	5	127	5	WDR91	7	134871027	Missense_Mutation	SNP	A	TCGA-A4-7584-01A-11D-2136-08	52286313	134871027	24267636	26	3145											
FAM164A	51101	hgsc.bcm.edu	37	chr8	79578395	79578395	+	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	ggtggcgcgatggagggactGgaaggtgaggcgatgaaggg	9	5	23	4	3	0	2	0	2	0	0	0	7	0	5	0	8	0	0	0	8	2	0			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr8:79578395G>C	ENST00000263849.4	+	1	114	c.12G>C	c.(10-12)ctG>ctC	p.L4L	ZC2HC1A_ENST00000521176.1_3'UTR	NM_016010.2	NP_057094.2	Q96GY0	ZC21A_HUMAN	zinc finger, C2HC-type containing 1A	4							metal ion binding (GO:0046872)										TGGAGGGACTGGAAGGTGAGG	0.672																																					p.L4L		Atlas-SNP	.											.	.	.	.	0			c.G12C						PASS	.						112	84	93					8																	79578395		2187	4279	6466	SO:0001819	synonymous_variant	51101	exon1			GGGACTGGAAGGT		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.12G>C	chr8.hg19:g.79578395G>C		2.0	0.0	.		10.0	6.0	.	NM_016010	Q9Y372	Silent	SNP	ENST00000263849.4	hg19	CCDS6223.1																																																																																			.	.	.	none		0.672	ZC2HC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379423.2	NM_016010		C	79578395	G	C	79578395	2	2	45	1	0	0	0	0	0	0	0	1	5482	1335	47	4		4	FAM164A	8	79578395	Silent	SNP	G	TCGA-A4-7584-01A-11D-2136-08		79578395	66785627	27	3146											
EFR3A	23167	hgsc.bcm.edu	37	chr8	132968018	132968018	+	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	ttctcgttcctttttagtcgCataggccctccttcttctcc	3	18	5	15	2	3	0	0	0	3	0	8	0	5	0	4	1	0	2	4	1	2	8			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr8:132968018C>T	ENST00000254624.5	+	7	867	c.642C>T	c.(640-642)cgC>cgT	p.R214R	EFR3A_ENST00000519656.1_Silent_p.R178R|EFR3A_ENST00000334503.4_Silent_p.R214R	NM_015137.4	NP_055952.2	Q14156	EFR3A_HUMAN	EFR3 homolog A (S. cerevisiae)	214						extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|skin(1)|stomach(2)	35	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)			TTTTTAGTCGCATAGGCCCTC	0.358																																					p.R214R		Atlas-SNP	.											.	EFR3A	96	.	0			c.C642T						PASS	.						108	111	110					8																	132968018		2203	4300	6503	SO:0001819	synonymous_variant	23167	exon7			TAGTCGCATAGGC	D63477	CCDS34942.2	8q24.22	2008-10-23			ENSG00000132294	ENSG00000132294			28970	protein-coding gene	gene with protein product		611798				15363888	Standard	NM_015137		Approved	KIAA0143	uc003yte.3	Q14156	OTTHUMG00000150552	ENST00000254624.5:c.642C>T	chr8.hg19:g.132968018C>T		112.0	0.0	.		86.0	26.0	.	NM_015137	A7MD19|Q2VPK2|Q63HL7|Q68DX1|Q6IQ18	Silent	SNP	ENST00000254624.5	hg19	CCDS34942.2																																																																																			.	.	.	none		0.358	EFR3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318886.1	NM_015137		T	132968018	C	T	132968018	2	4	45	1	0	0	0	0	0	0	0	1	4960	697	25	2		2	EFR3A	8	132968018	Silent	SNP	C	TCGA-A4-7584-01A-11D-2136-08	53389623	132968018	13396004	28	3147											
USP20	10868	hgsc.bcm.edu	37	chr9	132623219	132623219	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgggtctttaacacaggacTccccgccaccctcccaccct	7	9	6	19	1	1	0	0	0	1	0	3	1	3	1	6	2	1	0	6	2	1	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr9:132623219T>C	ENST00000315480.4	+	7	492	c.334T>C	c.(334-336)Tcc>Ccc	p.S112P	USP20_ENST00000372429.3_Missense_Mutation_p.S112P|USP20_ENST00000358355.1_Missense_Mutation_p.S112P			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	112					endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				AACACAGGACTCCCCGCCACC	0.567																																					p.S112P		Atlas-SNP	.											.	USP20	186	.	0			c.T334C						PASS	.						146	150	149					9																	132623219		1918	4121	6039	SO:0001583	missense	10868	exon7			CAGGACTCCCCGC	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"Ubiquitin-specific peptidases"	12619	protein-coding gene	gene with protein product		615143	"ubiquitin specific protease 20"			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.334T>C	chr9.hg19:g.132623219T>C	ENSP00000313811:p.Ser112Pro	394.0	1.0	.		219.0	72.0	.	NM_001008563	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Missense_Mutation	SNP	ENST00000315480.4	hg19	CCDS43892.1	.	.	.	.	.	.	.	.	.	.	T	11.93	1.787014	0.31593	.	.	ENSG00000136878	ENST00000372429;ENST00000315480;ENST00000358355	T;T;T	0.20463	2.07;2.07;2.07	5.66	1.8	0.24995	.	0.866856	0.10550	N	0.661611	T	0.16342	0.0393	L	0.46157	1.445	0.38108	D	0.937486	B	0.02656	0.0	B	0.04013	0.001	T	0.10337	-1.0634	10	0.30078	T	0.28	.	4.2306	0.10601	0.1241:0.0686:0.1298:0.6776	.	112	Q9Y2K6	UBP20_HUMAN	P	112	ENSP00000361506:S112P;ENSP00000313811:S112P;ENSP00000351122:S112P	ENSP00000313811:S112P	S	+	1	0	USP20	131663040	0.020000	0.18652	0.710000	0.30468	0.947000	0.59692	1.028000	0.30128	0.407000	0.25591	0.459000	0.35465	TCC	.	.	.	none		0.567	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2			C	132623219	T	C	132623219	3	2	45	1	0	0	0	0	1	0	0	0	17064	1551	54	3	352	3	USP20	9	132623219	Missense_Mutation	SNP	T	TCGA-A4-7584-01A-11D-2136-08		132623219	8590212	29	3148											
AKR1C3	8644	hgsc.bcm.edu	37	chr10	5139704	5139704	+	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	agaaagctcaattggactatGttgacctctatcttattcat	12	15	6	8	0	4	2	2	1	2	1	4	3	4	3	1	1	1	2	1	1	5	6			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr10:5139704G>C	ENST00000380554.3	+	3	983	c.331G>C	c.(331-333)Gtt>Ctt	p.V111L	AKR1C3_ENST00000439082.2_5'UTR|AKR1C3_ENST00000605149.1_Missense_Mutation_p.V88L|AKR1C3_ENST00000470862.2_3'UTR	NM_001253908.1|NM_003739.5	NP_001240837.1|NP_003730.4	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3	111					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)	ATTGGACTATGTTGACCTCTA	0.403																																					p.V111L		Atlas-SNP	.											.	AKR1C3	21	.	0			c.G331C						PASS	.						146	138	141					10																	5139704		2203	4300	6503	SO:0001583	missense	8644	exon3			GACTATGTTGACC	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.331G>C	chr10.hg19:g.5139704G>C	ENSP00000369927:p.Val111Leu	96.0	0.0	.		89.0	40.0	.	NM_001253908	A8K2V0|B4DL37|Q5T2L1|Q96DJ1|Q96KI8|Q99530|Q9UCX1|Q9UII3|Q9UKL9	Missense_Mutation	SNP	ENST00000380554.3	hg19	CCDS7063.1	.	.	.	.	.	.	.	.	.	.	G	0.014	-1.596157	0.00857	.	.	ENSG00000196139	ENST00000380554	T	0.47528	0.84	1.62	0.671	0.17929	NADP-dependent oxidoreductase domain (3);	0.237158	0.29558	N	0.011809	T	0.23410	0.0566	N	0.17564	0.495	0.80722	D	1	B;B;B	0.23249	0.082;0.005;0.005	B;B;B	0.30251	0.113;0.046;0.046	T	0.06972	-1.0797	10	0.07325	T	0.83	.	4.0982	0.10002	0.3926:0.0:0.6074:0.0	.	111;111;111	B4DKT3;P42330;Q2XPP3	.;AK1C3_HUMAN;.	L	111	ENSP00000369927:V111L	ENSP00000369927:V111L	V	+	1	0	AKR1C3	5129704	1.000000	0.71417	0.072000	0.20136	0.187000	0.23431	2.141000	0.42168	0.234000	0.21139	0.305000	0.20034	GTT	.	.	.	none		0.403	AKR1C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046533.2	NM_003739		C	5139704	G	C	5139704	3	2	45	1	0	0	0	0	1	0	0	0	471	1377	48	4	341	4	AKR1C3	10	5139704	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08		5139704	130395043	30	3149											
TACR2	6865	hgsc.bcm.edu	37	chr10	71175766	71175766	+	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	agaggttctggaagtagcagAaggcacggccaaagtaccag	14	5	14	8	1	1	2	0	0	1	2	1	3	1	3	2	4	2	5	2	4	5	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr10:71175766A>T	ENST00000373306.4	-	1	857	c.314T>A	c.(313-315)tTc>tAc	p.F105Y		NM_001057.2	NP_001048.2	P21452	NK2R_HUMAN	tachykinin receptor 2	105					excretion (GO:0007588)|intestine smooth muscle contraction (GO:0014827)|muscle contraction (GO:0006936)|negative regulation of luteinizing hormone secretion (GO:0033685)|operant conditioning (GO:0035106)|positive regulation of acetylcholine secretion, neurotransmission (GO:0014057)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vascular permeability (GO:0043117)|prolactin secretion (GO:0070459)|tachykinin receptor signaling pathway (GO:0007217)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	substance K receptor activity (GO:0016497)|tachykinin receptor activity (GO:0004995)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	11						GAAGTAGCAGAAGGCACGGCC	0.552																																					p.F105Y		Atlas-SNP	.											.	TACR2	37	.	0			c.T314A						PASS	.						92	81	85					10																	71175766		2203	4300	6503	SO:0001583	missense	6865	exon1			TAGCAGAAGGCAC		CCDS7293.1	10q22.1	2012-09-20			ENSG00000075073	ENSG00000075073		"GPCR / Class A : Tachykinin receptors"	11527	protein-coding gene	gene with protein product		162321		TAC2R, NKNAR			Standard	NM_001057		Approved	SKR, NK2R	uc001jpn.2	P21452	OTTHUMG00000018377	ENST00000373306.4:c.314T>A	chr10.hg19:g.71175766A>T	ENSP00000362403:p.Phe105Tyr	53.0	0.0	.		43.0	19.0	.	NM_001057	A8K7I1|Q4QRI5|Q8NGQ8|Q9UDE6|Q9UDE7	Missense_Mutation	SNP	ENST00000373306.4	hg19	CCDS7293.1	.	.	.	.	.	.	.	.	.	.	A	7.919	0.738168	0.15574	.	.	ENSG00000075073	ENST00000373306	T	0.38240	1.15	5.18	5.18	0.71444	GPCR, rhodopsin-like superfamily (1);	0.063724	0.64402	D	0.000003	T	0.11922	0.0290	N	0.01493	-0.835	0.42246	D	0.99195	B	0.22146	0.065	B	0.20577	0.03	T	0.20140	-1.0284	10	0.02654	T	1	.	10.5582	0.45129	0.8559:0.0:0.0:0.1441	.	105	P21452	NK2R_HUMAN	Y	105	ENSP00000362403:F105Y	ENSP00000362403:F105Y	F	-	2	0	TACR2	70845772	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.205000	0.51090	2.093000	0.63338	0.460000	0.39030	TTC	.	.	.	none		0.552	TACR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048411.1			T	71175766	A	T	71175766	3	4	45	1	0	0	0	0	1	0	0	0	15518	246	9	5	902	5	TACR2	10	71175766	Missense_Mutation	SNP	A	TCGA-A4-7584-01A-11D-2136-08	66036062	71175766	64358981	31	3150											
MRPL17	63875	hgsc.bcm.edu	37	chr11	6703594	6703594	+	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	agtttgatctttgtaccgagGggccagtacttgaaacagct	10	12	11	8	1	1	2	0	2	1	0	1	3	1	2	2	2	4	4	2	2	3	5			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr11:6703594G>A	ENST00000288937.6	-	3	387	c.283C>T	c.(283-285)Cct>Tct	p.P95S	MRPL17_ENST00000532676.1_5'UTR	NM_022061.3	NP_071344.1	Q9NRX2	RM17_HUMAN	mitochondrial ribosomal protein L17	95					translation (GO:0006412)	mitochondrial inner membrane (GO:0005743)|ribosome (GO:0005840)	protein domain specific binding (GO:0019904)|structural constituent of ribosome (GO:0003735)			lung(4)	4		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TTGTACCGAGGGGCCAGTACT	0.473																																					p.P95S		Atlas-SNP	.											.	MRPL17	11	.	0			c.C283T						PASS	.						115	114	114					11																	6703594		2201	4296	6497	SO:0001583	missense	63875	exon3			ACCGAGGGGCCAG	AB051620	CCDS31412.1	11p15.5-p15.4	2012-09-13				ENSG00000158042		"Mitochondrial ribosomal proteins / large subunits"	14053	protein-coding gene	gene with protein product		611830					Standard	NM_022061		Approved	RPML26, MRP-L26	uc001men.2	Q9NRX2		ENST00000288937.6:c.283C>T	chr11.hg19:g.6703594G>A	ENSP00000288937:p.Pro95Ser	197.0	0.0	.		141.0	48.0	.	NM_022061	D3DQU3|Q6IAH8|Q96Q53|Q9C066	Missense_Mutation	SNP	ENST00000288937.6	hg19	CCDS31412.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.970737	0.74246	.	.	ENSG00000158042	ENST00000288937;ENST00000532203	.	.	.	5.73	5.73	0.89815	.	0.051442	0.85682	D	0.000000	D	0.83275	0.5219	M	0.85041	2.73	0.58432	D	0.999999	P	0.52061	0.95	D	0.65010	0.931	D	0.85197	0.1013	9	0.72032	D	0.01	-5.0434	17.4724	0.87649	0.0:0.0:1.0:0.0	.	95	Q9NRX2	RM17_HUMAN	S	95;72	.	ENSP00000288937:P95S	P	-	1	0	MRPL17	6660170	1.000000	0.71417	0.999000	0.59377	0.565000	0.35776	6.015000	0.70791	2.720000	0.93068	0.555000	0.69702	CCT	.	.	.	none		0.473	MRPL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384544.1	NM_022061		A	6703594	G	A	6703594	3	1	45	1	0	0	0	0	1	0	0	0	9789	1232	43	2	248	2	MRPL17	11	6703594	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08		6703594	128302922	32	3151											
FDXACB1	91893	hgsc.bcm.edu	37	chr11	111749725	111749725	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agattctcccaggccagtggAtcccgagccaactcggccgg	8	6	12	15	3	1	1	0	0	1	1	4	3	2	2	5	4	2	0	5	4	1	1			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr11:111749725A>G	ENST00000260257.4	-	1	179	c.132T>C	c.(130-132)gaT>gaC	p.D44D	C11orf1_ENST00000529270.1_5'Flank|C11orf1_ENST00000528125.1_5'UTR|C11orf1_ENST00000530214.1_5'Flank|ALG9_ENST00000524880.1_Silent_p.D44D|C11orf1_ENST00000260276.3_5'Flank|ALG9_ENST00000527377.1_5'Flank|FDXACB1_ENST00000542429.1_5'UTR	NM_138378.2	NP_612387.1	Q9BRP7	FDXA1_HUMAN	ferredoxin-fold anticodon binding domain containing 1	44					phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA processing (GO:0008033)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|tRNA binding (GO:0000049)			endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(3)	19						AGGCCAGTGGATCCCGAGCCA	0.667											OREG0021330	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D44D		Atlas-SNP	.											.	FDXACB1	74	.	0			c.T132C						PASS	.						16	22	20					11																	111749725		1936	4151	6087	SO:0001819	synonymous_variant	91893	exon1			CAGTGGATCCCGA		CCDS44729.1	11q23.1	2011-04-15			ENSG00000255561	ENSG00000255561			25110	protein-coding gene	gene with protein product	"hypothetical protein BC006136"						Standard	NR_038364		Approved	LOC91893, hCG_2033039	uc001pmc.4	Q9BRP7	OTTHUMG00000166795	ENST00000260257.4:c.132T>C	chr11.hg19:g.111749725A>G		28.0	0.0	.	1437	25.0	11.0	.	NM_138378	A0PJW7|B4DUU2	Silent	SNP	ENST00000260257.4	hg19	CCDS44729.1																																																																																			.	.	.	none		0.667	FDXACB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391497.1	NM_138378		G	111749725	A	G	111749725	2	3	45	1	0	0	0	0	0	0	0	1	5813	330	12	3		3	FDXACB1	11	111749725	Silent	SNP	A	TCGA-A4-7584-01A-11D-2136-08	105046131	111749725	23256791	33	3152											
MANSC1	54682	hgsc.bcm.edu	37	chr12	12483592	12483592	+	Frame_Shift_Del	DEL	T	T	-																															tagctgggagcgcactcacaTtttcaggcagcagatgagct																										TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr12:12483592delT	ENST00000535902.1	-	4	1228	c.665delA	c.(664-666)aatfs	p.N222fs	MANSC1_ENST00000545735.1_Frame_Shift_Del_p.N141fs|MANSC1_ENST00000396349.3_Frame_Shift_Del_p.N188fs			Q9H8J5	MANS1_HUMAN	MANSC domain containing 1	222						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|skin(1)|stomach(4)	23		Prostate(47;0.0865)		BRCA - Breast invasive adenocarcinoma(232;0.185)		CGCACTCACATTTTCAGGCAG	0.502																																					p.N222fs		Atlas-INDEL	.											.	MANSC1	38	.	0			c.666delT						PASS	.						101	106	104					12																	12483592		2203	4300	6503	SO:0001589	frameshift_variant	54682	exon4			.	AK001160	CCDS8648.1	12p13.2	2006-04-12				ENSG00000111261			25505	protein-coding gene	gene with protein product						12975309	Standard	NM_018050		Approved	FLJ10298, LOH12CR3	uc001rai.1	Q9H8J5		ENST00000535902.1:c.665delA	chr12.hg19:g.12483592delT	ENSP00000438205:p.Asn222fs	107.0	0.0	0		109.0	37.0	0.33945	NM_018050	Q8NEC1|Q9NW60	Frame_Shift_Del	DEL	ENST00000535902.1	hg19	CCDS8648.1																																																																																			.	.	.	none		0.502	MANSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400144.1	NM_018050		-	12483592	T	-	12483592	7	5	45	1	0	1	0	1	0	0	0	0	9231	1493	52	0	634	0	MANSC1	12	12483592	Frame_Shift_Del	DEL	T	TCGA-A4-7584-01A-11D-2136-08		12483592	121368303	34	3153											
GUCY2C	2984	hgsc.bcm.edu	37	chr12	14772233	14772233	+	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	ttgattcccacaactccagcAgcacagggacctgaaatgaa	14	7	8	12	0	0	3	0	3	0	0	2	4	2	4	3	1	3	2	3	1	3	2			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr12:14772233A>C	ENST00000261170.3	-	24	2923	c.2787T>G	c.(2785-2787)gcT>gcG	p.A929A	RP11-695J4.2_ENST00000545424.1_RNA|RP11-695J4.2_ENST00000542401.1_RNA	NM_004963.3	NP_004954.2	P25092	GUC2C_HUMAN	guanylate cyclase 2C (heat stable enterotoxin receptor)	929	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.				intracellular signal transduction (GO:0035556)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of cell proliferation (GO:0042127)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|toxic substance binding (GO:0015643)			breast(3)|endometrium(7)|kidney(3)|large_intestine(9)|lung(17)|ovary(4)|skin(7)|urinary_tract(1)	51					Linaclotide(DB08890)	CAACTCCAGCAGCACAGGGAC	0.483																																					p.A929A		Atlas-SNP	.											.	GUCY2C	126	.	0			c.T2787G						PASS	.						95	93	93					12																	14772233		2203	4300	6503	SO:0001819	synonymous_variant	2984	exon24			TCCAGCAGCACAG		CCDS8664.1	12p12	2008-08-18			ENSG00000070019	ENSG00000070019			4688	protein-coding gene	gene with protein product		601330		GUC2C		8661067	Standard	NM_004963		Approved	STAR	uc001rcd.3	P25092	OTTHUMG00000168732	ENST00000261170.3:c.2787T>G	chr12.hg19:g.14772233A>C		82.0	0.0	.		91.0	29.0	.	NM_004963	B2RMY6	Silent	SNP	ENST00000261170.3	hg19	CCDS8664.1																																																																																			.	.	.	none		0.483	GUCY2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400835.1			C	14772233	A	C	14772233	2	2	45	1	0	0	0	0	0	0	0	1	6903	175	7	5		5	GUCY2C	12	14772233	Silent	SNP	A	TCGA-A4-7584-01A-11D-2136-08	2288641	14772233	119079662	35	3154											
CNTN1	1272	hgsc.bcm.edu	37	chr12	41316146	41316146	+	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	ttatcaacaaccctgacaaaCagaaagatgctggaatatac	18	8	6	9	0	1	3	1	1	0	2	1	4	1	4	1	1	5	1	1	1	8	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr12:41316146C>T	ENST00000551295.2	+	5	433	c.316C>T	c.(316-318)Cag>Tag	p.Q106*	CNTN1_ENST00000360099.3_Nonsense_Mutation_p.Q106*|CNTN1_ENST00000348761.2_Nonsense_Mutation_p.Q95*|CNTN1_ENST00000347616.1_Nonsense_Mutation_p.Q106*|CNTN1_ENST00000547702.1_Nonsense_Mutation_p.Q106*|CNTN1_ENST00000547849.1_Nonsense_Mutation_p.Q106*	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	106	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)				CCCTGACAAACAGAAAGATGC	0.398																																					p.Q106X		Atlas-SNP	.											CNTN1,NS,carcinoma,0,1	CNTN1	207	.	0			c.C316T						PASS	.						138	123	128					12																	41316146		2203	4300	6503	SO:0001587	stop_gained	1272	exon5			GACAAACAGAAAG	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.316C>T	chr12.hg19:g.41316146C>T	ENSP00000447006:p.Gln106*	69.0	0.0	.		84.0	38.0	.	NM_001256063	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Nonsense_Mutation	SNP	ENST00000551295.2	hg19	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.063249	0.76187	.	.	ENSG00000018236	ENST00000547702;ENST00000551295;ENST00000547849;ENST00000347616;ENST00000360099;ENST00000348761	.	.	.	5.65	4.74	0.60224	.	0.687302	0.15218	N	0.274073	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	.	7.1246	0.25465	0.0:0.7637:0.0:0.2363	.	.	.	.	X	106;106;106;106;106;95	.	ENSP00000325660:Q106X	Q	+	1	0	CNTN1	39602413	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	1.250000	0.32850	2.833000	0.97629	0.585000	0.79938	CAG	.	.	.	none		0.398	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		T	41316146	C	T	41316146	4	4	45	1	0	0	0	0	0	1	0	0	3642	479	17	2	330	2	CNTN1	12	41316146	Nonsense_Mutation	SNP	C	TCGA-A4-7584-01A-11D-2136-08	26543913	41316146	92535749	36	3155											
KIF5A	3798	hgsc.bcm.edu	37	chr12	57975209	57975209	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttattgcagccaaacccgtcCggcctggccactacccagca	9	7	8	17	2	0	0	0	0	0	0	1	0	1	0	6	2	5	2	6	2	3	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr12:57975209C>T	ENST00000455537.2	+	25	3041	c.2767C>T	c.(2767-2769)Cgg>Tgg	p.R923W	KIF5A_ENST00000286452.5_Missense_Mutation_p.R834W	NM_004984.2	NP_004975.2	Q12840	KIF5A_HUMAN	kinesin family member 5A	923	Globular.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein localization (GO:0008104)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(32)|ovary(2)|prostate(2)|skin(2)	62						CAAACCCGTCCGGCCTGGCCA	0.547																																					p.R923W		Atlas-SNP	.											.	KIF5A	143	.	0			c.C2767T						PASS	.						74	75	75					12																	57975209		2203	4300	6503	SO:0001583	missense	3798	exon25			CCCGTCCGGCCTG	U06698	CCDS8945.1	12q13.13	2011-07-15	2004-02-13			ENSG00000155980		"Kinesins"	6323	protein-coding gene	gene with protein product		602821	"spastic paraplegia 10 (autosomal dominant)"	SPG10		9858832, 10441583, 16489470	Standard	NM_004984		Approved	D12S1889, NKHC, MY050	uc001sor.1	Q12840	OTTHUMG00000170143	ENST00000455537.2:c.2767C>T	chr12.hg19:g.57975209C>T	ENSP00000408979:p.Arg923Trp	150.0	0.0	.		125.0	50.0	.	NM_004984	A6H8M5|Q4LE26	Missense_Mutation	SNP	ENST00000455537.2	hg19	CCDS8945.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.159251	0.78226	.	.	ENSG00000155980	ENST00000455537;ENST00000286452;ENST00000547989	T;T	0.81078	-1.38;-1.45	4.52	3.59	0.41128	.	0.201593	0.32343	N	0.006224	D	0.86715	0.5999	M	0.64404	1.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.71184	0.972;0.972	D	0.87757	0.2596	10	0.87932	D	0	.	12.7339	0.57212	0.1717:0.8283:0.0:0.0	.	834;923	B7Z2M7;Q12840	.;KIF5A_HUMAN	W	923;834;17	ENSP00000408979:R923W;ENSP00000286452:R834W	ENSP00000286452:R834W	R	+	1	2	KIF5A	56261476	1.000000	0.71417	0.989000	0.46669	0.881000	0.50899	5.716000	0.68437	1.212000	0.43366	0.561000	0.74099	CGG	.	.	.	none		0.547	KIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407634.1	NM_004984		T	57975209	C	T	57975209	3	4	45	1	0	0	0	0	1	0	0	0	8312	643	23	1	2865	1	KIF5A	12	57975209	Missense_Mutation	SNP	C	TCGA-A4-7584-01A-11D-2136-08	16659063	57975209	75876686	37	3156											
NAV3	89795	hgsc.bcm.edu	37	chr12	78604234	78604234	+	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	tactcgagcacacaaagctgCgacagcgaaagcaccagcca	15	3	9	14	3	0	0	0	0	0	0	1	3	0	0	2	0	7	3	2	0	3	1			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr12:78604234C>T	ENST00000397909.2	+	40	7268	c.7095C>T	c.(7093-7095)tgC>tgT	p.C2365C	NAV3_ENST00000266692.7_Silent_p.C2166C|NAV3_ENST00000536525.2_Silent_p.C2343C|NAV3_ENST00000228327.6_Silent_p.C2343C|NAV3_ENST00000541270.1_Silent_p.C195C			Q8IVL0	NAV3_HUMAN	neuron navigator 3	2365						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						CACAAAGCTGCGACAGCGAAA	0.403										HNSCC(70;0.22)																											p.C2343C		Atlas-SNP	.											.	NAV3	506	.	0			c.C7029T						PASS	.						55	58	57					12																	78604234		1952	4172	6124	SO:0001819	synonymous_variant	89795	exon39			AAGCTGCGACAGC	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.7095C>T	chr12.hg19:g.78604234C>T		59.0	0.0	.		71.0	26.0	.	NM_014903	Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	hg19		.	.	.	.	.	.	.	.	.	.	C	0.069	-1.207030	0.01568	.	.	ENSG00000067798	ENST00000552895;ENST00000551162	.	.	.	5.35	-7.82	0.01205	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-2.2288	19.8674	0.96824	0.0:0.1434:0.0:0.8566	.	.	.	.	X	1238;233	.	.	R	+	1	2	NAV3	77128365	0.348000	0.24861	0.594000	0.28785	0.129000	0.20672	-0.324000	0.07986	-1.610000	0.01583	-2.173000	0.00322	CGA	.	.	.	none		0.403	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		T	78604234	C	T	78604234	2	4	45	1	0	0	0	0	0	0	0	1	10192	776	27	1		1	NAV3	12	78604234	Silent	SNP	C	TCGA-A4-7584-01A-11D-2136-08	20629025	78604234	55247661	38	3157											
TBX5	6910	hgsc.bcm.edu	37	chr12	114793542	114793542	+	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	ggtgctggaacattccctctCccagctgtggggagccatgg	6	9	14	12	0	1	0	0	0	1	0	3	2	2	2	3	5	4	2	3	5	1	1			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr12:114793542C>G	ENST00000310346.4	-	9	2018	c.1352G>C	c.(1351-1353)gGa>gCa	p.G451A	TBX5_ENST00000405440.2_Missense_Mutation_p.G451A|TBX5_ENST00000349716.5_Missense_Mutation_p.G401A	NM_000192.3	NP_000183.2	Q99593	TBX5_HUMAN	T-box 5	451				MDRLPYQHFSAHFTSGPLVPRLAGMANHGSPQLGEGMFQHQ TS -> WTGYPTSTSPLTSPRGPWSLGWLAWQPWLPTAGRG NVPSTRPP (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)	p.G451V(1)		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)		CATTCCCTCTCCCAGCTGTGG	0.662																																					p.G451A	NSCLC(152;1358 1980 4050 23898 40356)	Atlas-SNP	.											TBX5,NS,carcinoma,0,1	TBX5	188	.	1	Substitution - Missense(1)	lung(1)	c.G1352C						PASS	.						27	29	28					12																	114793542		2203	4300	6503	SO:0001583	missense	6910	exon9			CCCTCTCCCAGCT	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.1352G>C	chr12.hg19:g.114793542C>G	ENSP00000309913:p.Gly451Ala	41.0	0.0	.		43.0	2.0	.	NM_000192	A6ND77|O15301|Q96TB0|Q9Y4I2	Missense_Mutation	SNP	ENST00000310346.4	hg19	CCDS9173.1	.	.	.	.	.	.	.	.	.	.	C	15.38	2.817720	0.50633	.	.	ENSG00000089225	ENST00000349716;ENST00000310346;ENST00000448888;ENST00000405440	T;T;T	0.54279	0.58;0.58;0.58	5.27	5.27	0.74061	.	0.682044	0.14424	N	0.320472	T	0.45538	0.1347	L	0.32530	0.975	0.80722	D	1	B	0.12013	0.005	B	0.12837	0.008	T	0.28902	-1.0029	10	0.42905	T	0.14	.	15.949	0.79817	0.0:0.8652:0.1348:0.0	.	451	Q99593	TBX5_HUMAN	A	401;451;348;451	ENSP00000337723:G401A;ENSP00000309913:G451A;ENSP00000384152:G451A	ENSP00000309913:G451A	G	-	2	0	TBX5	113277925	0.959000	0.32827	0.383000	0.26132	0.922000	0.55478	2.879000	0.48522	2.463000	0.83235	0.655000	0.94253	GGA	.	.	.	none		0.662	TBX5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388297.1	NM_080717		G	114793542	C	G	114793542	3	3	45	1	0	0	0	0	1	0	0	0	15673	855	30	4	208	4	TBX5	12	114793542	Missense_Mutation	SNP	C	TCGA-A4-7584-01A-11D-2136-08	36189308	114793542	19058353	39	3158											
ABCB9	23457	hgsc.bcm.edu	37	chr12	123429030	123429030	+	Frame_Shift_Del	DEL	A	A	-																															gatgacaaggtggcccccgtAgtagaggatgctgacctgga																										TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr12:123429030delA	ENST00000542678.1	-	7	4126	c.1288delT	c.(1288-1290)tacfs	p.Y430fs	ABCB9_ENST00000392439.3_Frame_Shift_Del_p.Y430fs|ABCB9_ENST00000280560.8_Frame_Shift_Del_p.Y430fs|ABCB9_ENST00000540285.1_Frame_Shift_Del_p.Y430fs|ABCB9_ENST00000442833.2_Frame_Shift_Del_p.Y430fs|ABCB9_ENST00000541983.1_5'UTR|ABCB9_ENST00000442028.2_Frame_Shift_Del_p.Y430fs|ABCB9_ENST00000344275.7_Frame_Shift_Del_p.Y430fs|ABCB9_ENST00000346530.5_Intron			Q9NP78	ABCB9_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 9	430	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				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)		TGGCCCCCGTAGTAGAGGATG	0.592																																					p.Y430fs	Ovarian(49;786 1333 9175 38236)	Atlas-INDEL	.											.	ABCB9	50	.	0			c.1289delA						PASS	.						139	120	127					12																	123429030		2203	4300	6503	SO:0001589	frameshift_variant	23457	exon7			.	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.1288delT	chr12.hg19:g.123429030delA	ENSP00000440288:p.Tyr430fs	210.0	0.0	0		180.0	58.0	0.322222	NM_001243014	B4E2J0|Q5W9G7|Q769F3|Q769F4|Q96AB1|Q9P208	Frame_Shift_Del	DEL	ENST00000542678.1	hg19	CCDS9241.1																																																																																			.	.	.	none		0.592	ABCB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400956.1	NM_019624		-	123429030	A	-	123429030	7	5	45	1	0	1	0	1	0	0	0	0	48	420	15	0	1036	0	ABCB9	12	123429030	Frame_Shift_Del	DEL	A	TCGA-A4-7584-01A-11D-2136-08	8635488	123429030	10422865	40	3159											
KCTD4	386618	hgsc.bcm.edu	37	chr13	45768535	45768535	+	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	actataccttcaaggaaagtGtctgggtacttggtcagtgt	10	13	11	7	0	3	0	2	0	1	0	3	1	3	1	1	3	2	1	1	3	5	5			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr13:45768535G>A	ENST00000379108.1	-	1	317	c.168C>T	c.(166-168)gaC>gaT	p.D56D	GTF2F2_ENST00000340473.6_Intron|KCTD4_ENST00000405872.1_Silent_p.D56D			Q8WVF5	KCTD4_HUMAN	potassium channel tetramerization domain containing 4	56	BTB.				protein homooligomerization (GO:0051260)					breast(1)|endometrium(1)|large_intestine(2)|lung(4)	8		Lung NSC(96;6.55e-05)|Breast(139;0.00378)|Prostate(109;0.00438)|Lung SC(185;0.0262)|Hepatocellular(98;0.0524)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000249)|BRCA - Breast invasive adenocarcinoma(63;0.207)		CAAGGAAAGTGTCTGGGTACT	0.413																																					p.D56D		Atlas-SNP	.											.	KCTD4	18	.	0			c.C168T						PASS	.						266	265	265					13																	45768535		2203	4300	6503	SO:0001819	synonymous_variant	386618	exon2			GAAAGTGTCTGGG	BC018063	CCDS9396.1	13q14.12-q14.13	2013-06-20	2013-06-20		ENSG00000180332	ENSG00000180332			23227	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 4"				Standard	NM_198404		Approved	bA321C24.3	uc001uzx.4	Q8WVF5	OTTHUMG00000016844	ENST00000379108.1:c.168C>T	chr13.hg19:g.45768535G>A		288.0	0.0	.		182.0	55.0	.	NM_198404	Q5W0P9	Silent	SNP	ENST00000379108.1	hg19	CCDS9396.1																																																																																			.	.	.	none		0.413	KCTD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044757.1			A	45768535	G	A	45768535	2	1	45	1	0	0	0	0	0	0	0	1	8118	1368	48	2		2	KCTD4	13	45768535	Silent	SNP	G	TCGA-A4-7584-01A-11D-2136-08		45768535	69401343	41	3160											
SDCCAG1	9147	hgsc.bcm.edu	37	chr14	50256253	50256253	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agttcacggtcttcttcatcCtggtctttgtatttttcttt	4	22	6	9	1	6	0	2	0	4	0	7	0	7	0	1	2	0	2	1	2	1	8			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr14:50256253C>T	ENST00000298310.5	-	27	3107	c.2658G>A	c.(2656-2658)caG>caA	p.Q886Q	NEMF_ENST00000546046.1_Silent_p.Q865Q|NEMF_ENST00000545773.1_Silent_p.Q844Q|NEMF_ENST00000556925.1_5'UTR|NEMF_ENST00000382135.2_Silent_p.Q86Q			O60524	NEMF_HUMAN	nuclear export mediator factor	886					nuclear export (GO:0051168)	nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(13)|liver(1)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	36						CTTCTTCATCCTGGTCTTTGT	0.328																																					p.Q886Q		Atlas-SNP	.											.	NEMF	79	.	0			c.G2658A						PASS	.						130	123	125					14																	50256253		2203	4300	6503	SO:0001819	synonymous_variant	9147	exon27			TTCATCCTGGTCT	AF039687	CCDS9694.1	14q21.3	2012-11-19	2011-01-31	2011-01-31	ENSG00000165525	ENSG00000165525			10663	protein-coding gene	gene with protein product		608378	"serologically defined colon cancer antigen 1"	SDCCAG1		9610721, 10575219	Standard	XR_429334		Approved	NY-CO-1, FLJ10051	uc001wxc.3	O60524	OTTHUMG00000170857	ENST00000298310.5:c.2658G>A	chr14.hg19:g.50256253C>T		89.0	0.0	.		63.0	17.0	.	NM_004713	A0JLQ3|B3KSK1|B4DDL3|B4DHA9|B4E3F3|Q32Q66|Q8WW70|Q9NWG1	Silent	SNP	ENST00000298310.5	hg19	CCDS9694.1																																																																																			.	.	.	none		0.328	NEMF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410798.1	NM_004713		T	50256253	C	T	50256253	2	4	45	1	0	0	0	0	0	0	0	1	13970	680	24	2		2	SDCCAG1	14	50256253	Silent	SNP	C	TCGA-A4-7584-01A-11D-2136-08		50256253	57093287	42	3161											
VRK1	7443	hgsc.bcm.edu	37	chr14	97321567	97321567	+	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	ttggaaatttataggtgtacTtggtagattatggccttgct	9	17	11	4	0	0	1	0	0	0	1	0	2	0	2	1	4	2	3	1	4	6	9			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr14:97321567T>A	ENST00000216639.3	+	8	732	c.583T>A	c.(583-585)Ttg>Atg	p.L195M		NM_003384.2	NP_003375.1	Q99986	VRK1_HUMAN	vaccinia related kinase 1	195	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				Golgi disassembly (GO:0090166)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-T3 phosphorylation (GO:0072355)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi stack (GO:0005795)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H3-S10 specific) (GO:0035175)|histone kinase activity (H3-T3 specific) (GO:0072354)|nucleosomal histone binding (GO:0031493)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|endometrium(1)|large_intestine(5)|lung(3)|skin(1)|stomach(1)	12		Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.234)		ATAGGTGTACTTGGTAGATTA	0.388																																					p.L195M		Atlas-SNP	.											.	VRK1	34	.	0			c.T583A						PASS	.						199	195	196					14																	97321567		2203	4300	6503	SO:0001583	missense	7443	exon8			GTGTACTTGGTAG	AB000449	CCDS9947.1	14q32.2	2012-07-05			ENSG00000100749	ENSG00000100749			12718	protein-coding gene	gene with protein product		602168				9344656	Standard	XM_006720247		Approved		uc001yft.3	Q99986	OTTHUMG00000171459	ENST00000216639.3:c.583T>A	chr14.hg19:g.97321567T>A	ENSP00000216639:p.Leu195Met	134.0	0.0	.		105.0	46.0	.	NM_003384	Q3SYL2	Missense_Mutation	SNP	ENST00000216639.3	hg19	CCDS9947.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.34|19.34	3.808500|3.808500	0.70797|0.70797	.|.	.|.	ENSG00000100749|ENSG00000100749	ENST00000557222|ENST00000216639	.|T	.|0.72835	.|-0.69	5.95|5.95	1.04|1.04	0.20106|0.20106	.|Serine/threonine-protein kinase-like domain (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	T|T	0.81024|0.81024	0.4737|0.4737	M|M	0.76938|0.76938	2.355|2.355	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	T|T	0.78823|0.78823	-0.2052|-0.2052	6|10	.|0.66056	.|D	.|0.02	-11.377|-11.377	9.4931|9.4931	0.38971|0.38971	0.0:0.2599:0.0:0.7401|0.0:0.2599:0.0:0.7401	.|.	.|195	.|Q99986	.|VRK1_HUMAN	H|M	51|195	.|ENSP00000216639:L195M	.|ENSP00000216639:L195M	L|L	+|+	2|1	0|2	VRK1|VRK1	96391320|96391320	0.992000|0.992000	0.36948|0.36948	0.995000|0.995000	0.50966|0.50966	0.985000|0.985000	0.73830|0.73830	0.976000|0.976000	0.29462|0.29462	-0.050000|-0.050000	0.13356|0.13356	0.533000|0.533000	0.62120|0.62120	CTT|TTG	.	.	.	none		0.388	VRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413520.1	NM_003384		A	97321567	T	A	97321567	3	1	45	1	0	0	0	0	1	0	0	0	17231	1606	56	5	609	5	VRK1	14	97321567	Missense_Mutation	SNP	T	TCGA-A4-7584-01A-11D-2136-08	47065314	97321567	10027973	43	3162											
FAM82A2	55177	hgsc.bcm.edu	37	chr15	41037304	41037305	+	Frame_Shift_Ins	INS	-	-	GCACT																															aggaacctccagcctccaggINSgcactggaggcacctgaagc																										TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr15:41037304_41037305insGCACT	ENST00000260385.6	-	4	1744_1745	c.677_678insAGTGC	c.(676-678)gccfs	p.-226fs	RMDN3_ENST00000338376.3_Frame_Shift_Ins_p.-226fs|RMDN3_ENST00000558560.1_Intron			Q96TC7	RMD3_HUMAN	regulator of microtubule dynamics 3						apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|cellular calcium ion homeostasis (GO:0006874)	integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)											CAGCCTCCAGGGCACTGGAGGC	0.599																																					p.A226fs		Atlas-INDEL	.											.	.	.	.	0			c.678_679insAGTGC						PASS	.																																			SO:0001589	frameshift_variant	55177	exon5			.	AK001441	CCDS10063.1	15q15.1	2013-01-11	2013-01-11	2013-01-11	ENSG00000137824	ENSG00000137824			25550	protein-coding gene	gene with protein product		611873	"family with sequence similarity 82, member A2"	FAM82C, FAM82A2		12975309	Standard	XM_005254531		Approved	FLJ10579, PTPIP51, RMD3	uc001zmp.1	Q96TC7	OTTHUMG00000130066	ENST00000260385.6:c.673_677dupAGTGC	chr15.hg19:g.41037305_41037309dupGCACT	ENSP00000260385:p.Ala226fs	114.0	0.0	0		61.0	16.0	0.262295	NM_018145	A9UMZ9|B3KRR3|Q6ZWE9|Q96H23|Q96SD6|Q9H6G1|Q9NVQ6	Frame_Shift_Ins	INS	ENST00000260385.6	hg19	CCDS10063.1																																																																																			.	.	.	none		0.599	RMDN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252357.1	NM_018145		GCACT	41037305	-	GCACT	41037304	7	5	45	1	0	1	1	0	0	0	0	0	5638	1219	43	0	770	0	FAM82A2	15	41037304	Frame_Shift_Ins	INS	-	TCGA-A4-7584-01A-11D-2136-08		41037304	61494088	44	3163											
DUOX1	53905	hgsc.bcm.edu	37	chr15	45453182	45453182	+	Frame_Shift_Del	DEL	C	C	-																															tggtgaaggcggagctgctgCcctcaggtaccagcctggca																										TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr15:45453182delC	ENST00000321429.4	+	30	4257	c.3850delC	c.(3850-3852)cccfs	p.P1284fs	DUOX1_ENST00000561166.1_Frame_Shift_Del_p.P930fs|DUOX1_ENST00000389037.3_Frame_Shift_Del_p.P1284fs|CTD-2651B20.1_ENST00000558039.1_lincRNA	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	1284	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				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)		GGAGCTGCTGCCCTCAGGTAC	0.617																																					p.L1283fs		Atlas-INDEL	.											.	DUOX1	125	.	0			c.3849delG						PASS	.						81	65	71					15																	45453182		2198	4298	6496	SO:0001589	frameshift_variant	53905	exon29			.	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.3850delC	chr15.hg19:g.45453182delC	ENSP00000317997:p.Pro1284fs	67.0	0.0	0		61.0	22.0	0.360656	NM_175940	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Frame_Shift_Del	DEL	ENST00000321429.4	hg19	CCDS32221.1																																																																																			.	.	.	none		0.617	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434		-	45453182	C	-	45453182	7	5	45	1	0	1	0	1	0	0	0	0	4802	739	26	0	3960	0	DUOX1	15	45453182	Frame_Shift_Del	DEL	C	TCGA-A4-7584-01A-11D-2136-08	4415878	45453182	57078210	45	3164											
DUOX1	53905	hgsc.bcm.edu	37	chr15	45456067	45456068	+	Missense_Mutation	DNP	GT	GT	TA																															ctccatcacccactttggccGtcccccctttgagcccttct																										TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G|T	G|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr15:45456067_45456068GT>TA	ENST00000321429.4	+	34	4891_4892	c.4484_4485GT>TA	c.(4483-4485)cGT>cTA	p.R1495L	DUOX1_ENST00000561166.1_Missense_Mutation_p.R1141L|DUOX1_ENST00000389037.3_Missense_Mutation_p.R1495L|CTD-2651B20.1_ENST00000558039.1_lincRNA	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	1495					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)		CACTTTGGCCGTCCCCCCTTTG	0.55																																					p.R1495L|p.R1495R		Atlas-SNP	.											.	DUOX1	125	.	0			c.G4484T|c.T4485A						PASS	.																																			SO:0001583	missense	53905	exon34			TTGGCCGTCCCCC|TGGCCGTCCCCCC	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		Exception_encountered	chr15.hg19:g.45456067_45456068delinsTA	ENSP00000317997:p.Arg1495Leu	212.0|213.0	0.0	.		132.0|134.0	56.0|58.0	.	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Missense_Mutation|Silent	SNP	ENST00000321429.4	hg19	CCDS32221.1																																																																																			.	.	.	none		0.55	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434		TA	45456068	GT	TA	45456067	3	4	45	1	0	0	0	0	1	0	0	0	4802	1145	40	4	4610	4	DUOX1	15	45456067	Missense_Mutation	DNP	GT	TCGA-A4-7584-01A-11D-2136-08	2885	45456067	57075325	46	3165											
ZNF609	23060	hgsc.bcm.edu	37	chr15	64791991	64791991	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaagaggtgcaggggcgcTcaggagatggtgccaatgct	11	6	17	7	1	1	3	1	0	0	3	1	4	1	3	1	5	3	3	1	5	2	0			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr15:64791991T>C	ENST00000326648.3	+	1	501	c.373T>C	c.(373-375)Tca>Cca	p.S125P	ZNF609_ENST00000416172.1_Missense_Mutation_p.S125P	NM_015042.1	NP_055857.1	O15014	ZN609_HUMAN	zinc finger protein 609	125						nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GCAGGGGCGCTCAGGAGATGG	0.567																																					p.S125P		Atlas-SNP	.											.	ZNF609	106	.	0			c.T373C						PASS	.						44	48	46					15																	64791991		2203	4300	6503	SO:0001583	missense	23060	exon1			GGGCGCTCAGGAG	BC014251	CCDS32270.1	15q22.1	2008-05-02				ENSG00000180357		"Zinc fingers, C2H2-type"	29003	protein-coding gene	gene with protein product						9205841	Standard	NM_015042		Approved	KIAA0295	uc002ann.3	O15014		ENST00000326648.3:c.373T>C	chr15.hg19:g.64791991T>C	ENSP00000316527:p.Ser125Pro	54.0	0.0	.		62.0	18.0	.	NM_015042	Q0D2I2	Missense_Mutation	SNP	ENST00000326648.3	hg19	CCDS32270.1	.	.	.	.	.	.	.	.	.	.	.	5.590	0.293619	0.10567	.	.	ENSG00000180357	ENST00000416172;ENST00000326648	T	0.42513	0.97	5.5	3.1	0.35709	.	0.722344	0.13093	N	0.414351	T	0.24699	0.0599	N	0.16368	0.405	0.40301	D	0.97861	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.05241	-1.0897	10	0.21540	T	0.41	-18.1137	8.0215	0.30412	0.0:0.0671:0.2567:0.6762	.	125;125	E7ERY8;O15014	.;ZN609_HUMAN	P	125	ENSP00000316527:S125P	ENSP00000316527:S125P	S	+	1	0	ZNF609	62579044	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	1.673000	0.37534	0.419000	0.25927	-0.322000	0.08575	TCA	.	.	.	none		0.567	ZNF609-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418130.1	XM_042833		C	64791991	T	C	64791991	3	2	45	1	0	0	0	0	1	0	0	0	18047	1551	54	3	375	3	ZNF609	15	64791991	Missense_Mutation	SNP	T	TCGA-A4-7584-01A-11D-2136-08	19335924	64791991	37739401	47	3166											
CLCN7	1186	hgsc.bcm.edu	37	chr16	1505793	1505793	+	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	cctccaagctgaacaggaccCcacctggaaggcaggcggcc	10	3	12	16	1	0	1	0	1	0	0	1	3	1	3	6	5	2	2	6	5	3	0			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr16:1505793C>T	ENST00000382745.4	-	11	1525	c.920G>A	c.(919-921)gGg>gAg	p.G307E	CLCN7_ENST00000448525.1_Missense_Mutation_p.G283E|CLCN7_ENST00000262318.8_Missense_Mutation_p.G283E	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	307					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)				GAACAGGACCCCACCTGGAAG	0.642																																					p.G307E		Atlas-SNP	.											.	CLCN7	53	.	0			c.G920A						PASS	.						89	74	79					16																	1505793		2199	4300	6499	SO:0001583	missense	1186	exon11			AGGACCCCACCTG	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.920G>A	chr16.hg19:g.1505793C>T	ENSP00000372193:p.Gly307Glu	63.0	0.0	.		73.0	43.0	.	NM_001287	A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	Missense_Mutation	SNP	ENST00000382745.4	hg19	CCDS32361.1	.	.	.	.	.	.	.	.	.	.	C	19.58	3.854384	0.71719	.	.	ENSG00000103249	ENST00000448525;ENST00000262318;ENST00000382745;ENST00000428756	D;D	0.98701	-5.08;-5.08	5.13	5.13	0.70059	Chloride channel, core (2);	0.000000	0.85682	D	0.000000	D	0.99530	0.9832	H	0.98426	4.23	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97845	1.0271	10	0.87932	D	0	-37.9855	17.1357	0.86739	0.0:1.0:0.0:0.0	.	283;307	E9PDB9;P51798	.;CLCN7_HUMAN	E	283;260;307;249	ENSP00000410907:G283E;ENSP00000372193:G307E	ENSP00000262318:G260E	G	-	2	0	CLCN7	1445794	1.000000	0.71417	0.996000	0.52242	0.531000	0.34715	7.468000	0.80943	2.387000	0.81309	0.313000	0.20887	GGG	.	.	.	none		0.642	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287		T	1505793	C	T	1505793	3	4	45	1	0	0	0	0	1	0	0	0	3470	623	22	2	1557	2	CLCN7	16	1505793	Missense_Mutation	SNP	C	TCGA-A4-7584-01A-11D-2136-08		1505793	88848960	48	3167											
HEATR3	55027	hgsc.bcm.edu	37	chr16	50112741	50112741	+	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	1	0	0	0	0	0	0	0	0	agatcttatctgaagttttgGgaatggatgctggtgaaatg	11	14	13	3	0	2	3	0	2	2	1	2	5	2	5	0	3	1	2	0	3	4	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr16:50112741G>T	ENST00000299192.7	+	7	1044	c.853G>T	c.(853-855)Gga>Tga	p.G285*	HEATR3_ENST00000285767.4_Nonsense_Mutation_p.G199*	NM_182922.2	NP_891552.1	Q7Z4Q2	HEAT3_HUMAN	HEAT repeat containing 3	285										cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						TGAAGTTTTGGGAATGGATGC	0.373																																					p.G285X		Atlas-SNP	.											.	HEATR3	59	.	0			c.G853T						PASS	.						79	78	78					16																	50112741		2198	4300	6498	SO:0001587	stop_gained	55027	exon7			GTTTTGGGAATGG	BC018730	CCDS10739.1	16q12.1	2008-02-05			ENSG00000155393	ENSG00000155393			26087	protein-coding gene	gene with protein product		614951				12477932	Standard	XM_005256013		Approved	FLJ20718	uc002efw.3	Q7Z4Q2	OTTHUMG00000133174	ENST00000299192.7:c.853G>T	chr16.hg19:g.50112741G>T	ENSP00000299192:p.Gly285*	75.0	0.0	.		91.0	5.0	.	NM_182922	A8K1N4|Q8N525|Q8WV56|Q96CC9|Q9NWN7	Nonsense_Mutation	SNP	ENST00000299192.7	hg19	CCDS10739.1	.	.	.	.	.	.	.	.	.	.	G	39	7.589360	0.98374	.	.	ENSG00000155393	ENST00000285767;ENST00000299192	.	.	.	5.61	4.66	0.58398	.	0.526535	0.23112	N	0.051781	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	.	10.9314	0.47220	0.1434:0.0:0.8566:0.0	.	.	.	.	X	199;285	.	ENSP00000285767:G199X	G	+	1	0	HEATR3	48670242	1.000000	0.71417	0.826000	0.32828	0.973000	0.67179	5.765000	0.68834	1.516000	0.48900	-0.277000	0.10078	GGA	.	.	.	none		0.373	HEATR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256880.2	NM_182922		T	50112741	G	T	50112741	4	4	45	1	0	0	0	0	0	1	0	0	7036	1233	43	4	879	4	HEATR3	16	50112741	Nonsense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08	48606948	50112741	40242012	49	3168											
CIAPIN1	57019	hgsc.bcm.edu	37	chr16	57463170	57463170	+	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	ggtaggggcagctggcacagCggaaggcatcgcccaggtag	9	4	18	10	2	0	0	0	0	0	0	1	1	0	1	1	7	2	6	1	7	3	2			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr16:57463170C>T	ENST00000569979.1	-	6	699	c.653G>A	c.(652-654)cGc>cAc	p.R218H	CIAPIN1_ENST00000567518.1_Missense_Mutation_p.R271H|CIAPIN1_ENST00000568940.1_Silent_p.P245P|CIAPIN1_ENST00000569370.1_Silent_p.P245P|CIAPIN1_ENST00000569246.1_5'Flank|CIAPIN1_ENST00000394391.4_Missense_Mutation_p.R284H|CIAPIN1_ENST00000565961.1_Silent_p.P218P					cytokine induced apoptosis inhibitor 1											cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	10						GCTGGCACAGCGGAAGGCATC	0.532																																					p.R284H		Atlas-SNP	.											.	CIAPIN1	17	.	0			c.G851A						PASS	.						56	57	57					16																	57463170		2015	4178	6193	SO:0001583	missense	57019	exon9			GCACAGCGGAAGG	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.653G>A	chr16.hg19:g.57463170C>T	ENSP00000458000:p.Arg218His	83.0	0.0	.		73.0	38.0	.	NM_020313		Missense_Mutation	SNP	ENST00000569979.1	hg19		.	.	.	.	.	.	.	.	.	.	C	34	5.381122	0.95945	.	.	ENSG00000005194	ENST00000394391	T	0.68181	-0.31	4.73	4.73	0.59995	.	0.000000	0.85682	D	0.000000	D	0.87184	0.6114	H	0.95539	3.685	0.53688	D	0.99997	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.91214	0.5001	10	0.72032	D	0.01	-16.045	17.0668	0.86561	0.0:1.0:0.0:0.0	.	271;284	Q6FI81-3;Q6FI81	.;CPIN1_HUMAN	H	284	ENSP00000377914:R284H	ENSP00000377914:R284H	R	-	2	0	CIAPIN1	56020671	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.141000	0.77330	2.347000	0.79759	0.561000	0.74099	CGC	.	.	.	none		0.532	CIAPIN1-010	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432580.1	NM_020313		T	57463170	C	T	57463170	3	4	45	1	0	0	0	0	1	0	0	0	3421	768	27	1	91	1	CIAPIN1	16	57463170	Missense_Mutation	SNP	C	TCGA-A4-7584-01A-11D-2136-08	7350429	57463170	32891583	50	3169											
DNAH2	146754	hgsc.bcm.edu	37	chr17	7727461	7727461	+	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	gctggaggattcaaccccacGatccccactcgtgttcatcc	8	9	8	16	2	2	0	2	0	0	0	5	3	4	2	5	2	1	2	5	2	1	2	rs368019673		TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr17:7727461G>A	ENST00000572933.1	+	76	12961	c.11501G>A	c.(11500-11502)cGa>cAa	p.R3834Q	DNAH2_ENST00000389173.2_Missense_Mutation_p.R3834Q			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	3834	AAA 6. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|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)				TCAACCCCACGATCCCCACTC	0.597																																					p.R3834Q		Atlas-SNP	.											.	DNAH2	498	.	0			c.G11501A						PASS	.	G	GLN/ARG	0,4406		0,0,2203	103	87	93		11501	4.1	0.2	17		93	1,8599	1.2+/-3.3	0,1,4299	no	missense	DNAH2	NM_020877.2	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	3834/4428	7727461	1,13005	2203	4300	6503	SO:0001583	missense	146754	exon75			CCCCACGATCCCC	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.11501G>A	chr17.hg19:g.7727461G>A	ENSP00000458355:p.Arg3834Gln	180.0	0.0	.		205.0	26.0	.	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	G	11.61	1.690038	0.29962	0.0	1.16E-4	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.08193	3.12	5.03	4.06	0.47325	Dynein heavy chain (1);	0.102365	0.48286	D	0.000190	T	0.04227	0.0117	N	0.25201	0.72	0.44985	D	0.998	B;B	0.32829	0.227;0.386	B;B	0.22753	0.024;0.041	T	0.42396	-0.9454	10	0.10111	T	0.7	.	8.878	0.35356	0.1665:0.0:0.8335:0.0	.	3795;3834	Q9P225-2;Q9P225	.;DYH2_HUMAN	Q	3795;3834	ENSP00000373825:R3834Q	ENSP00000353818:R3795Q	R	+	2	0	DNAH2	7668186	0.186000	0.23225	0.167000	0.22817	0.981000	0.71138	2.589000	0.46145	2.350000	0.79820	0.511000	0.50034	CGA	.	.	.	weak		0.597	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		A	7727461	G	A	7727461	3	1	45	1	0	0	0	0	1	0	0	0	4604	1058	37	1	11799	1	DNAH2	17	7727461	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08		7727461	73467749	51	3170											
EFCAB5	374786	hgsc.bcm.edu	37	chr17	28407885	28407885	+	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	gattataatggttcattcctGgctctgcctcttcaagatgc	8	15	8	10	0	4	1	2	0	2	1	5	2	5	1	2	2	2	2	2	2	3	5			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr17:28407885G>C	ENST00000394835.3	+	17	3504	c.3312G>C	c.(3310-3312)ctG>ctC	p.L1104L	EFCAB5_ENST00000394832.2_Intron|EFCAB5_ENST00000320856.5_Silent_p.L980L	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	1104							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						GTTCATTCCTGGCTCTGCCTC	0.438																																					p.L1104L		Atlas-SNP	.											.	EFCAB5	122	.	0			c.G3312C						PASS	.						91	88	89					17																	28407885		1881	4112	5993	SO:0001819	synonymous_variant	374786	exon17			ATTCCTGGCTCTG	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.3312G>C	chr17.hg19:g.28407885G>C		82.0	0.0	.		63.0	24.0	.	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Silent	SNP	ENST00000394835.3	hg19	CCDS11254.2																																																																																			.	.	.	none		0.438	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529		C	28407885	G	C	28407885	2	2	45	1	0	0	0	0	0	0	0	1	4940	1335	47	4		4	EFCAB5	17	28407885	Silent	SNP	G	TCGA-A4-7584-01A-11D-2136-08	20680424	28407885	52787325	52	3171											
KRT32	3882	hgsc.bcm.edu	37	chr17	39622089	39622090	+	Frame_Shift_Ins	INS	-	-	C																															ctcaacctgggcctccaggtINScagccttgcacagagtgaga																										TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr17:39622089_39622090insC	ENST00000225899.3	-	3	746_747	c.643_644insG	c.(643-645)gacfs	p.D215fs	RNU2-32P_ENST00000411193.1_RNA	NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	215	Coil 1B.|Rod.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				GGCCTCCAGGTCAGCCTTGCAC	0.604																																					p.D215fs		Atlas-INDEL	.											.	KRT32	57	.	0			c.644_645insG						PASS	.																																			SO:0001589	frameshift_variant	3882	exon3			.	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.644dupG	chr17.hg19:g.39622090_39622090dupC	ENSP00000225899:p.Asp215fs	120.0	0.0	0		146.0	85.0	0.582192	NM_002278		Frame_Shift_Ins	INS	ENST00000225899.3	hg19	CCDS11393.1																																																																																			.	.	.	none		0.604	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278		C	39622090	-	C	39622089	7	5	45	1	0	1	1	0	0	0	0	0	8475	1667	58	0	722	0	KRT32	17	39622089	Frame_Shift_Ins	INS	-	TCGA-A4-7584-01A-11D-2136-08	11214204	39622089	41573121	53	3172											
HELZ	9931	hgsc.bcm.edu	37	chr17	65214853	65214853	+	Missense_Mutation	SNP	T	T	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	tgcagtgcttgagggccattTcatagtcctgcctcttaagt	7	14	10	10	0	2	1	1	1	1	0	3	1	3	1	3	1	3	2	3	1	2	4			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr17:65214853T>G	ENST00000358691.5	-	4	234	c.68A>C	c.(67-69)gAa>gCa	p.E23A	HELZ_ENST00000580168.1_Missense_Mutation_p.E23A|HELZ_ENST00000580662.1_5'UTR	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	23						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)					GAGGGCCATTTCATAGTCCTG	0.473																																					p.E23A		Atlas-SNP	.											.	HELZ	160	.	0			c.A68C						PASS	.						127	119	121					17																	65214853		1892	4130	6022	SO:0001583	missense	9931	exon4			GCCATTTCATAGT	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.68A>C	chr17.hg19:g.65214853T>G	ENSP00000351524:p.Glu23Ala	120.0	0.0	.		142.0	34.0	.	NM_014877	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	hg19	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	t	15.08	2.728346	0.48833	.	.	ENSG00000198265	ENST00000358691;ENST00000417253	T;T	0.75589	-0.95;-0.95	5.27	5.27	0.74061	.	0.046820	0.85682	D	0.000000	T	0.70692	0.3253	L	0.29908	0.895	0.58432	D	0.999999	B;P;B	0.48503	0.247;0.911;0.247	B;P;B	0.47941	0.078;0.562;0.078	T	0.75019	-0.3465	10	0.66056	D	0.02	-4.8435	15.1782	0.72931	0.0:0.0:0.0:1.0	.	23;23;23	B7ZLW2;F8WBX6;P42694	.;.;HELZ_HUMAN	A	23	ENSP00000351524:E23A;ENSP00000411144:E23A	ENSP00000351524:E23A	E	-	2	0	HELZ	62645315	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	7.414000	0.80117	1.980000	0.57719	0.455000	0.32223	GAA	.	.	.	none		0.473	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		G	65214853	T	G	65214853	3	3	45	1	0	0	0	0	1	0	0	0	7056	1783	62	5	5880	5	HELZ	17	65214853	Missense_Mutation	SNP	T	TCGA-A4-7584-01A-11D-2136-08	25592764	65214853	15980357	54	3173											
COG1	9382	hgsc.bcm.edu	37	chr17	71199203	71199203	+	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	tggctcagttctggccacagCcaccagctgggatgagctag	8	8	13	12	0	2	1	1	1	1	0	2	2	2	2	3	3	3	4	3	3	1	2			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr17:71199203C>A	ENST00000299886.4	+	8	2218	c.2138C>A	c.(2137-2139)gCc>gAc	p.A713D		NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	713					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)			CTGGCCACAGCCACCAGCTGG	0.512																																					p.A713D		Atlas-SNP	.											.	COG1	46	.	0			c.C2138A						PASS	.						80	74	76					17																	71199203		2203	4300	6503	SO:0001583	missense	9382	exon8			CCACAGCCACCAG		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.2138C>A	chr17.hg19:g.71199203C>A	ENSP00000299886:p.Ala713Asp	83.0	0.0	.		87.0	58.0	.	NM_018714	Q9NPV9|Q9P2G6	Missense_Mutation	SNP	ENST00000299886.4	hg19	CCDS11692.1	.	.	.	.	.	.	.	.	.	.	C	18.47	3.632096	0.67015	.	.	ENSG00000166685	ENST00000438720;ENST00000299886	T;T	0.25414	1.8;1.81	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.54581	0.1867	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	0.999;1.0;0.999	T	0.37572	-0.9700	10	0.35671	T	0.21	-30.898	20.8794	0.99867	0.0:1.0:0.0:0.0	.	713;713;713	E9PBL8;Q8WTW3;Q4G0L8	.;COG1_HUMAN;.	D	713	ENSP00000400111:A713D;ENSP00000299886:A713D	ENSP00000299886:A713D	A	+	2	0	COG1	68710798	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.456000	0.80751	2.941000	0.99782	0.655000	0.94253	GCC	.	.	.	none		0.512	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441638.1			A	71199203	C	A	71199203	3	1	45	1	0	0	0	0	1	0	0	0	3659	739	26	4	2168	4	COG1	17	71199203	Missense_Mutation	SNP	C	TCGA-A4-7584-01A-11D-2136-08	5984350	71199203	9996007	55	3174											
FDXR	2232	hgsc.bcm.edu	37	chr17	72861043	72861043	+	Missense_Mutation	SNP	A	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	cacccagggctgccttcgtgAtgtccgttctctggcacaaa	7	10	10	14	2	1	1	0	1	1	0	4	1	2	1	3	2	1	3	3	2	1	2			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr17:72861043A>C	ENST00000293195.5	-	7	698	c.620T>G	c.(619-621)aTc>aGc	p.I207S	FDXR_ENST00000581969.1_5'Flank|FDXR_ENST00000420580.2_Missense_Mutation_p.I167S|FDXR_ENST00000583917.1_Missense_Mutation_p.I208S|FDXR_ENST00000582944.1_Missense_Mutation_p.I199S|FDXR_ENST00000455107.2_Missense_Mutation_p.I163S|FDXR_ENST00000544854.1_Missense_Mutation_p.I155S|FDXR_ENST00000413947.2_Missense_Mutation_p.I238S|FDXR_ENST00000581530.1_Missense_Mutation_p.I213S|FDXR_ENST00000442102.2_Missense_Mutation_p.I250S	NM_001258014.1|NM_004110.3|NM_024417.2	NP_001244943.1|NP_004101.2|NP_077728.2	P22570	ADRO_HUMAN	ferredoxin reductase	207					cholesterol metabolic process (GO:0008203)|generation of precursor metabolites and energy (GO:0006091)|NADPH oxidation (GO:0070995)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ferredoxin-NADP+ reductase activity (GO:0004324)|NADPH binding (GO:0070402)|NADPH-adrenodoxin reductase activity (GO:0015039)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16	all_lung(278;0.172)|Lung NSC(278;0.207)				Flavin adenine dinucleotide(DB03147)	TGCCTTCGTGATGTCCGTTCT	0.592											OREG0024720	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I250S		Atlas-SNP	.											.	FDXR	68	.	0			c.T749G						PASS	.						96	80	86					17																	72861043		2203	4300	6503	SO:0001583	missense	2232	exon7			TTCGTGATGTCCG	J03826	CCDS11707.1, CCDS58591.1, CCDS58592.1, CCDS58593.1, CCDS58594.1, CCDS58595.1, CCDS58596.1	17q25.1	2013-06-18			ENSG00000161513	ENSG00000161513	1.18.1.6		3642	protein-coding gene	gene with protein product	"adrenodoxin-NADP(+) reductase", "adrenodoxin reductase"	103270		ADXR		2969697	Standard	NM_001258014		Approved		uc010wrl.2	P22570	OTTHUMG00000179026	ENST00000293195.5:c.620T>G	chr17.hg19:g.72861043A>C	ENSP00000293195:p.Ile207Ser	80.0	0.0	.	1140	102.0	54.0	.	NM_001258012	B4DDI7|B4DHX5|B4DQQ4|B4DX24|B7Z7G2|E7EQC1|Q13716|Q4PJI0|Q9BU12	Missense_Mutation	SNP	ENST00000293195.5	hg19	CCDS58593.1	.	.	.	.	.	.	.	.	.	.	a	15.15	2.747032	0.49257	.	.	ENSG00000161513	ENST00000420580;ENST00000544854;ENST00000293195;ENST00000455107;ENST00000442102;ENST00000413947	T;T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83;-0.83	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.89931	0.6858	H	0.94345	3.525	0.80722	D	1	D;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;1.0	D;D;D;D;D;D;D;D;D;D	0.97110	0.992;0.983;0.984;1.0;0.996;0.984;0.978;1.0;0.978;0.996	D	0.92675	0.6153	10	0.87932	D	0	-11.7911	15.4798	0.75517	1.0:0.0:0.0:0.0	.	167;250;238;205;155;238;207;199;207;213	B4DQQ4;B4DHX5;E7EQC1;B4DDI9;B7Z7G2;B4DDI7;Q6GSK2;B4DX24;P22570;P22570-2	.;.;.;.;.;.;.;.;ADRO_HUMAN;.	S	167;155;213;163;250;238	ENSP00000414172:I167S;ENSP00000445432:I155S;ENSP00000390875:I163S;ENSP00000416515:I250S;ENSP00000408595:I238S	ENSP00000293195:I213S	I	-	2	0	FDXR	70372638	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	5.738000	0.68613	2.145000	0.66743	0.454000	0.30748	ATC	.	.	.	none		0.592	FDXR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000444449.1	NM_004110		C	72861043	A	C	72861043	3	2	45	1	0	0	0	0	1	0	0	0	5814	333	12	5	879	5	FDXR	17	72861043	Missense_Mutation	SNP	A	TCGA-A4-7584-01A-11D-2136-08	1661840	72861043	8334167	56	3175											
ITGB4	3691	hgsc.bcm.edu	37	chr17	73752854	73752855	+	In_Frame_Ins	INS	-	-	GCTGCA																															actgccctgagcccagactcINSgctgcagctgagctgggagc																								rs370378040		TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr17:73752854_73752855insGCTGCA	ENST00000200181.3	+	37	5154_5155	c.4967_4968insGCTGCA	c.(4966-4971)tcgctg>tcGCTGCAgctg	p.1659_1660insQL	ITGB4_ENST00000449880.2_In_Frame_Ins_p.1642_1643insQL|ITGB4_ENST00000579662.1_In_Frame_Ins_p.1589_1590insQL|GALK1_ENST00000225614.2_Intron|ITGB4_ENST00000339591.3_In_Frame_Ins_p.1642_1643insQL|ITGB4_ENST00000450894.3_In_Frame_Ins_p.1589_1590insQL	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	1659	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			AGCCCAGACTCGCTGCAGCTGA	0.658																																					p.S1656delinsSLQ		Atlas-INDEL	.											.	ITGB4	165	.	0			c.4967_4968insGCTGCA						PASS	.																																			SO:0001652	inframe_insertion	3691	exon37			.		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.4968_4973dupGCTGCA	chr17.hg19:g.73752855_73752860dupGCTGCA	ENSP00000200181:p.Gln1658_Leu1659dup	166.0	0.0	0		137.0	35.0	0.255474	NM_000213	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	In_Frame_Ins	INS	ENST00000200181.3	hg19	CCDS11727.1																																																																																			.	.	.	none		0.658	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			GCTGCA	73752855	-	GCTGCA	73752854	7	5	45	1	0	1	1	0	0	0	0	0	7904	893	31	0	5272	0	ITGB4	17	73752854	In_Frame_Ins	INS	-	TCGA-A4-7584-01A-11D-2136-08	891811	73752854	7442356	57	3176											
SLC26A11	6448	hgsc.bcm.edu	37	chr17	78197109	78197109	+	5'Flank	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	ggcttcacctctgctgctgcCgtcaccatcggctttggaca	5	11	10	15	2	3	0	2	0	1	0	4	1	3	1	3	3	3	4	3	3	0	2			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr17:78197109C>G	ENST00000326317.6	-	0	0				SGSH_ENST00000570923.1_5'Flank|SGSH_ENST00000572208.1_5'Flank|SLC26A11_ENST00000361193.3_Silent_p.A162A|SLC26A11_ENST00000546047.2_Silent_p.A162A|SLC26A11_ENST00000411502.3_Silent_p.A162A|SLC26A11_ENST00000572725.1_Silent_p.A162A|SGSH_ENST00000534910.1_5'Flank	NM_000199.3	NP_000190.1	P51688	SPHM_HUMAN	N-sulfoglucosamine sulfohydrolase						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)			CTGCTGCTGCCGTCACCATCG	0.622																																					p.A162A		Atlas-SNP	.											.	SLC26A11	60	.	0			c.C486G						PASS	.						95	67	76					17																	78197109		2203	4300	6503	SO:0001631	upstream_gene_variant	284129	exon5			TGCTGCCGTCACC	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			chr17.hg19:g.78197109C>G	Exception_encountered	84.0	0.0	.		82.0	4.0	.	NM_173626	A8K5E2	Silent	SNP	ENST00000326317.6	hg19	CCDS11770.1																																																																																			.	.	.	none		0.622	SGSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437695.1	NM_000199		G	78197109	C	G	78197109	1	3	45	0	1	0	0	0	0	0	0	0	14529	639	23	4		4	SLC26A11	17	78197109	5'Flank	SNP	C	TCGA-A4-7584-01A-11D-2136-08	4444255	78197109	2998101	58	3177											
EMILIN2	84034	hgsc.bcm.edu	37	chr18	2913257	2913257	+	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	gcatacctgcgggggcccggGggcattccacctcatcgtgc	5	7	14	15	3	1	0	1	0	0	0	3	0	2	0	4	4	3	2	4	4	1	2			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr18:2913257G>T	ENST00000254528.3	+	8	3176	c.3017G>T	c.(3016-3018)gGg>gTg	p.G1006V	EMILIN2_ENST00000308080.5_3'UTR	NM_032048.2	NP_114437.2	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	1006	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				cell adhesion (GO:0007155)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)			breast(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(4)	48				READ - Rectum adenocarcinoma(2;0.1)		GGGGGCCCGGGGGCATTCCAC	0.607																																					p.G1006V		Atlas-SNP	.											.	EMILIN2	97	.	0			c.G3017T						PASS	.						41	43	43					18																	2913257		2203	4300	6503	SO:0001583	missense	84034	exon8			GCCCGGGGGCATT	AF270513	CCDS11828.1	18p11.3	2008-02-05			ENSG00000132205	ENSG00000132205		"EMI domain containing"	19881	protein-coding gene	gene with protein product		608928					Standard	NM_032048		Approved	FLJ33200, FOAP-10	uc002kln.3	Q9BXX0	OTTHUMG00000128525	ENST00000254528.3:c.3017G>T	chr18.hg19:g.2913257G>T	ENSP00000254528:p.Gly1006Val	76.0	0.0	.		49.0	13.0	.	NM_032048	B2RMY3|Q8NBH3|Q96JQ4	Missense_Mutation	SNP	ENST00000254528.3	hg19	CCDS11828.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.989478	0.53934	.	.	ENSG00000132205	ENST00000254528;ENST00000308080	T	0.74842	-0.88	5.61	5.61	0.85477	Tumour necrosis factor-like (2);Complement C1q protein (2);	0.000000	0.85682	D	0.000000	D	0.83087	0.5178	L	0.48174	1.505	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.79771	-0.1663	10	0.33940	T	0.23	-34.4219	20.0086	0.97443	0.0:0.0:1.0:0.0	.	1006	Q9BXX0	EMIL2_HUMAN	V	1006;283	ENSP00000254528:G1006V	ENSP00000254528:G1006V	G	+	2	0	EMILIN2	2903257	1.000000	0.71417	0.301000	0.25044	0.022000	0.10575	5.618000	0.67722	2.808000	0.96608	0.655000	0.94253	GGG	.	.	.	none		0.607	EMILIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250337.2	NM_032048		T	2913257	G	T	2913257	3	4	45	1	0	0	0	0	1	0	0	0	5096	1232	43	4	3047	4	EMILIN2	18	2913257	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08		2913257	75163991	59	3178											
C18orf34	374864	hgsc.bcm.edu	37	chr18	30926327	30926327	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttaatgagacgaatggccTctgagagcaatgtttccatt	11	14	9	7	1	1	2	0	2	1	2	2	5	2	2	2	1	1	2	2	1	3	4			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr18:30926327T>C	ENST00000383096.3	-	9	688	c.506A>G	c.(505-507)gAg>gGg	p.E169G	CCDC178_ENST00000403303.1_Missense_Mutation_p.E169G|CCDC178_ENST00000406524.2_Missense_Mutation_p.E169G|CCDC178_ENST00000402325.1_Missense_Mutation_p.E169G|CCDC178_ENST00000300227.8_Missense_Mutation_p.E169G|CCDC178_ENST00000579916.1_Intron|CCDC178_ENST00000583930.1_Missense_Mutation_p.E169G|CCDC178_ENST00000579947.1_Missense_Mutation_p.E169G			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	169																	ACGAATGGCCTCTGAGAGCAA	0.343																																					p.E169G		Atlas-SNP	.											.	.	.	.	0			c.A506G						PASS	.						93	88	90					18																	30926327		2203	4300	6503	SO:0001583	missense	374864	exon8			ATGGCCTCTGAGA	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.506A>G	chr18.hg19:g.30926327T>C	ENSP00000372576:p.Glu169Gly	79.0	0.0	.		83.0	26.0	.	NM_001105528	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Missense_Mutation	SNP	ENST00000383096.3	hg19	CCDS42424.1	.	.	.	.	.	.	.	.	.	.	T	9.274	1.046438	0.19748	.	.	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524;ENST00000402325;ENST00000399177	T;T;T;T;T;T	0.57107	1.82;1.82;1.83;1.82;1.83;0.42	5.59	4.36	0.52297	.	.	.	.	.	T	0.65133	0.2662	L	0.54323	1.7	0.31006	N	0.719736	D;D;D;D	0.89917	1.0;0.996;0.996;0.996	D;D;D;D	0.74674	0.984;0.944;0.944;0.944	T	0.65520	-0.6148	9	0.59425	D	0.04	-20.3796	10.1932	0.43039	0.0:0.0:0.1668:0.8332	.	169;169;169;169	F8W7A7;B5MD75;Q5BJE1-2;Q5BJE1	.;.;.;CR034_HUMAN	G	169	ENSP00000385591:E169G;ENSP00000372576:E169G;ENSP00000300227:E169G;ENSP00000385867:E169G;ENSP00000385234:E169G;ENSP00000382130:E169G	ENSP00000300227:E169G	E	-	2	0	C18orf34	29180325	1.000000	0.71417	0.996000	0.52242	0.418000	0.31294	3.210000	0.51129	2.129000	0.65627	0.455000	0.32223	GAG	.	.	.	none		0.343	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995		C	30926327	T	C	30926327	3	2	45	1	0	0	0	0	1	0	0	0	1904	1551	54	3	2157	3	C18orf34	18	30926327	Missense_Mutation	SNP	T	TCGA-A4-7584-01A-11D-2136-08	28013070	30926327	47150921	60	3179											
MUC16	94025	hgsc.bcm.edu	37	chr19	9059472	9059472	+	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	atgttctgctagaagagatgGcttctgtcctggagacctca	9	12	11	9	0	3	3	1	0	2	3	4	5	4	3	2	2	1	3	2	2	2	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr19:9059472G>T	ENST00000397910.4	-	3	28177	c.27974C>A	c.(27973-27975)gCc>gAc	p.A9325D		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9327	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						AGAAGAGATGGCTTCTGTCCT	0.507																																					p.A9325D		Atlas-SNP	.											.	MUC16	4315	.	0			c.C27974A						PASS	.						162	157	158					19																	9059472		1993	4179	6172	SO:0001583	missense	94025	exon3			GAGATGGCTTCTG	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.27974C>A	chr19.hg19:g.9059472G>T	ENSP00000381008:p.Ala9325Asp	199.0	0.0	.		143.0	69.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	5.093	0.202874	0.09704	.	.	ENSG00000181143	ENST00000397910	T	0.02812	4.15	2.43	-4.86	0.03132	.	.	.	.	.	T	0.02727	0.0082	N	0.19112	0.55	.	.	.	P	0.52316	0.952	P	0.50049	0.629	T	0.26677	-1.0096	8	0.87932	D	0	.	4.6628	0.12650	0.5463:0.176:0.2777:0.0	.	9325	B5ME49	.	D	9325	ENSP00000381008:A9325D	ENSP00000381008:A9325D	A	-	2	0	MUC16	8920472	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-1.962000	0.01514	-1.169000	0.02772	-0.382000	0.06688	GCC	.	.	.	none		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9059472	G	T	9059472	3	4	45	1	0	0	0	0	1	0	0	0	9980	1203	42	4	15877	4	MUC16	19	9059472	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08		9059472	50069511	61	3180											
ZNF317	57693	hgsc.bcm.edu	37	chr19	9271676	9271676	+	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	atacgggtgcgatctctgcgGgaaagctttcagcgcgagtt	8	10	14	9	5	2	0	1	0	1	0	3	3	2	1	0	2	5	2	0	2	2	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr19:9271676G>A	ENST00000247956.6	+	7	1660	c.1355G>A	c.(1354-1356)gGg>gAg	p.G452E	ZNF317_ENST00000360385.3_Missense_Mutation_p.G420E	NM_020933.4	NP_065984.3	Q96PQ6	ZN317_HUMAN	zinc finger protein 317	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	27						GATCTCTGCGGGAAAGCTTTC	0.547																																					p.G452E		Atlas-SNP	.											.	ZNF317	61	.	0			c.G1355A						PASS	.						62	59	60					19																	9271676		2203	4300	6503	SO:0001583	missense	57693	exon7			TCTGCGGGAAAGC	AF275255	CCDS12210.1, CCDS54213.1	19p13	2013-01-08				ENSG00000130803		"Zinc fingers, C2H2-type", "-"	13507	protein-coding gene	gene with protein product		613864				10997877, 11688974	Standard	NM_020933		Approved		uc002mku.3	Q96PQ6		ENST00000247956.6:c.1355G>A	chr19.hg19:g.9271676G>A	ENSP00000247956:p.Gly452Glu	67.0	0.0	.		58.0	20.0	.	NM_020933	Q6DCA9|Q96PM0|Q96PM1|Q96PT2|Q9HCI4	Missense_Mutation	SNP	ENST00000247956.6	hg19	CCDS12210.1	.	.	.	.	.	.	.	.	.	.	G	19.27	3.795593	0.70452	.	.	ENSG00000130803	ENST00000247956;ENST00000360385	T;T	0.07114	3.22;3.22	3.04	3.04	0.35103	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.43260	D	0.000600	T	0.22627	0.0546	L	0.59436	1.845	0.47009	D	0.999286	D;D	0.89917	1.0;0.994	D;D	0.83275	0.996;0.924	T	0.01013	-1.1481	10	0.59425	D	0.04	-30.6663	12.2796	0.54757	0.0:0.0:1.0:0.0	.	420;452	Q96PQ6-2;Q96PQ6	.;ZN317_HUMAN	E	452;420	ENSP00000247956:G452E;ENSP00000353554:G420E	ENSP00000247956:G452E	G	+	2	0	ZNF317	9132676	0.999000	0.42202	0.881000	0.34555	0.542000	0.35054	3.149000	0.50655	2.031000	0.59945	0.491000	0.48974	GGG	.	.	.	none		0.547	ZNF317-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448995.1	NM_020933		A	9271676	G	A	9271676	3	1	45	1	0	0	0	0	1	0	0	0	17847	1232	43	2	1377	2	ZNF317	19	9271676	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08	212204	9271676	49857307	62	3181											
C19orf57	79173	hgsc.bcm.edu	37	chr19	13996869	13996869	+	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	ttgttccccgaaggaaagagCtggaaagagagcacaaggtg	14	6	14	7	1	0	2	0	0	0	2	1	6	1	4	2	3	2	3	2	3	4	2			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr19:13996869C>G	ENST00000586783.1	-	6	1668		c.e6-1		C19orf57_ENST00000591586.1_Splice_Site|C19orf57_ENST00000454313.1_Splice_Site|C19orf57_ENST00000346736.2_Splice_Site			Q0VDD7	CS057_HUMAN	chromosome 19 open reading frame 57						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)			AAGGAAAGAGCTGGAAAGAGA	0.632																																					.		Atlas-SNP	.											.	C19orf57	34	.	0			c.1669-1G>C						PASS	.						33	34	34					19																	13996869		2203	4300	6503	SO:0001630	splice_region_variant	79173	exon8			AAAGAGCTGGAAA	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.1669-1G>C	chr19.hg19:g.13996869C>G		58.0	0.0	.		58.0	21.0	.	NM_024323	Q13411|Q8N825|Q96D63|Q9BU49	Splice_Site	SNP	ENST00000586783.1	hg19		.	.	.	.	.	.	.	.	.	.	C	9.061	0.994432	0.19043	.	.	ENSG00000132016	ENST00000454313;ENST00000346736	.	.	.	3.01	3.01	0.34805	.	.	.	.	.	.	.	.	.	.	.	0.45762	D	0.998659	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.7555	0.40500	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C19orf57	13857869	0.176000	0.23096	0.016000	0.15963	0.050000	0.14768	2.605000	0.46283	2.000000	0.58554	0.563000	0.77884	.	.	.	.	none		0.632	C19orf57-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000457947.1	NM_024323	Intron	G	13996869	C	G	13996869	5	3	45	1	0	0	0	0	0	0	1	0	1941	811	28	4	253	4	C19orf57	19	13996869	Splice_Site	SNP	C	TCGA-A4-7584-01A-11D-2136-08	4725193	13996869	45132114	63	3182											
CD22	933	hgsc.bcm.edu	37	chr19	35828752	35828752	+	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	tgcgaggtcagcagcagcaaCccggagtacacgacggtatc	11	5	13	12	4	1	0	1	0	0	0	2	3	1	1	1	3	6	5	1	3	3	2			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr19:35828752C>T	ENST00000085219.5	+	5	879	c.813C>T	c.(811-813)aaC>aaT	p.N271N	CD22_ENST00000341773.6_Intron|CD22_ENST00000594250.1_Intron|CD22_ENST00000419549.2_Silent_p.N99N|CD22_ENST00000536635.2_Silent_p.N271N|CD22_ENST00000544992.2_Silent_p.N271N|CD22_ENST00000270311.6_Silent_p.N151N	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule	271	Ig-like C2-type 2.				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)			GCAGCAGCAACCCGGAGTACA	0.567																																					p.N271N	Ovarian(42;1009 1133 23674 26041)	Atlas-SNP	.											.	CD22	129	.	0			c.C813T						PASS	.						90	75	80					19																	35828752		2203	4300	6503	SO:0001819	synonymous_variant	933	exon5			CAGCAACCCGGAG	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.813C>T	chr19.hg19:g.35828752C>T		107.0	0.0	.		77.0	32.0	.	NM_001185100	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Silent	SNP	ENST00000085219.5	hg19	CCDS12457.1																																																																																			.	.	.	none		0.567	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771		T	35828752	C	T	35828752	2	4	45	1	0	0	0	0	0	0	0	1	2987	506	18	2		2	CD22	19	35828752	Silent	SNP	C	TCGA-A4-7584-01A-11D-2136-08	21831883	35828752	23300231	64	3183											
EXOC3L2	90332	hgsc.bcm.edu	37	chr19	45720794	45720794	+	Frame_Shift_Del	DEL	G	G	-																															cccgacactgaccagccgccGgaacagcctctgcagttgcg																										TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr19:45720794delG	ENST00000252482.3	-	7	838	c.811delC	c.(811-813)cggfs	p.R272fs	EXOC3L2_ENST00000413988.1_Frame_Shift_Del_p.R272fs			Q2M3D2	EX3L2_HUMAN	exocyst complex component 3-like 2	272					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)		ACCAGCCGCCGGAACAGCCTC	0.701																																					p.R271fs		Atlas-INDEL	.											.	EXOC3L2	30	.	0			c.812delG						PASS	.						9	12	11					19																	45720794		2147	4221	6368	SO:0001589	frameshift_variant	90332	exon8			.	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.811delC	chr19.hg19:g.45720794delG	ENSP00000252482:p.Arg272fs	28.0	0.0	0		19.0	10.0	0.526316	NM_138568	Q8N9W2|Q96GV2	Frame_Shift_Del	DEL	ENST00000252482.3	hg19	CCDS12657.1																																																																																			.	.	.	none		0.701	EXOC3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338073.1	NM_138568		-	45720794	G	-	45720794	7	5	45	1	0	1	0	1	0	0	0	0	5307	1115	39	0	430	0	EXOC3L2	19	45720794	Frame_Shift_Del	DEL	G	TCGA-A4-7584-01A-11D-2136-08	9892042	45720794	13408189	65	3184											
SCAF1	58506	hgsc.bcm.edu	37	chr19	50161552	50161552	+	Missense_Mutation	SNP	A	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	agcgctaccgctacttccgcAagcacggtcgcaagccaggg	9	5	12	15	5	0	0	0	0	0	0	2	0	1	0	3	2	5	5	3	2	4	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr19:50161552A>C	ENST00000360565.3	+	11	3959	c.3835A>C	c.(3835-3837)Aag>Cag	p.K1279Q	IRF3_ENST00000599680.1_5'Flank	NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	1279	Necessary for interaction with the CTD domain of POLR2A.				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)		CTACTTCCGCAAGCACGGTCG	0.701																																					p.K1279Q		Atlas-SNP	.											.	SCAF1	78	.	0			c.A3835C						PASS	.						20	18	19					19																	50161552		2196	4296	6492	SO:0001583	missense	58506	exon11			TTCCGCAAGCACG	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.3835A>C	chr19.hg19:g.50161552A>C	ENSP00000353769:p.Lys1279Gln	28.0	0.0	.		20.0	10.0	.	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Missense_Mutation	SNP	ENST00000360565.3	hg19	CCDS33074.1	.	.	.	.	.	.	.	.	.	.	A	19.04	3.749503	0.69533	.	.	ENSG00000126461	ENST00000360565	T	0.50548	0.74	4.94	4.94	0.65067	.	0.000000	0.41001	D	0.000978	T	0.62575	0.2439	L	0.52905	1.665	0.45076	D	0.998095	D	0.76494	0.999	D	0.71656	0.974	T	0.65800	-0.6080	10	0.72032	D	0.01	-23.9463	13.702	0.62616	1.0:0.0:0.0:0.0	.	1279	Q9H7N4	SFR19_HUMAN	Q	1279	ENSP00000353769:K1279Q	ENSP00000353769:K1279Q	K	+	1	0	SCAF1	54853364	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.499000	0.90494	2.064000	0.61679	0.533000	0.62120	AAG	.	.	.	none		0.701	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228		C	50161552	A	C	50161552	3	2	45	1	0	0	0	0	1	0	0	0	13881	131	5	5	3873	5	SCAF1	19	50161552	Missense_Mutation	SNP	A	TCGA-A4-7584-01A-11D-2136-08	4440758	50161552	8967431	66	3185											
LILRB1	10859	hgsc.bcm.edu	37	chr19	55144006	55144006	+	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	cagtgtggctctgatgctggCtacaacagatttgttctgta	8	14	11	8	0	2	2	0	1	2	1	2	2	2	2	0	2	3	5	0	2	3	4			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr19:55144006C>A	ENST00000396331.1	+	7	1110	c.753C>A	c.(751-753)ggC>ggA	p.G251G	LILRB1_ENST00000396317.1_Silent_p.G251G|LILRB1_ENST00000396321.2_Silent_p.G251G|LILRB1_ENST00000418536.2_Silent_p.G251G|LILRB1_ENST00000324602.7_Silent_p.G251G|LILRB1_ENST00000396327.3_Silent_p.G251G|LILRB1_ENST00000427581.2_Silent_p.G287G|LILRB1_ENST00000396315.1_Silent_p.G251G|LILRB1_ENST00000448689.1_Silent_p.G251G|LILRB1_ENST00000396332.4_Silent_p.G251G|LILRB1_ENST00000434867.2_Silent_p.G251G	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	251	Ig-like C2-type 3.				cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		CTGATGCTGGCTACAACAGAT	0.572										HNSCC(37;0.09)																											p.G251G		Atlas-SNP	.											.	LILRB1	140	.	0			c.C753A						PASS	.						100	105	103					19																	55144006		2203	4300	6503	SO:0001819	synonymous_variant	10859	exon6			TGCTGGCTACAAC	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.753C>A	chr19.hg19:g.55144006C>A		173.0	0.0	.		110.0	44.0	.	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Silent	SNP	ENST00000396331.1	hg19	CCDS42617.1																																																																																			.	.	.	none		0.572	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4			A	55144006	C	A	55144006	2	1	45	1	0	0	0	0	0	0	0	1	8797	784	28	4		4	LILRB1	19	55144006	Silent	SNP	C	TCGA-A4-7584-01A-11D-2136-08	4982454	55144006	3984977	67	3186											
ZNF543	125919	hgsc.bcm.edu	37	chr19	57839968	57839968	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaaaagctttttgcgagagtGcagacctcattcaacactac	13	10	8	10	1	2	2	2	0	0	2	2	4	2	2	1	0	5	2	1	0	4	4			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr19:57839968G>A	ENST00000321545.4	+	4	1483	c.1138G>A	c.(1138-1140)Gca>Aca	p.A380T		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	380					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)		TTGCGAGAGTGCAGACCTCAT	0.512																																					p.A380T		Atlas-SNP	.											.	ZNF543	61	.	0			c.G1138A						PASS	.						84	73	76					19																	57839968		2203	4300	6503	SO:0001583	missense	125919	exon4			GAGAGTGCAGACC	AL834534	CCDS33130.1	19q13.43	2013-01-08				ENSG00000178229		"Zinc fingers, C2H2-type", "-"	25281	protein-coding gene	gene with protein product							Standard	NM_213598		Approved	DKFZp434H055	uc002qoi.2	Q08ER8		ENST00000321545.4:c.1138G>A	chr19.hg19:g.57839968G>A	ENSP00000322545:p.Ala380Thr	119.0	0.0	.		83.0	35.0	.	NM_213598	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	Missense_Mutation	SNP	ENST00000321545.4	hg19	CCDS33130.1	.	.	.	.	.	.	.	.	.	.	G	2.550	-0.304214	0.05495	.	.	ENSG00000178229	ENST00000321545	T	0.15139	2.45	3.14	-2.57	0.06248	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10337	0.0253	N	0.25825	0.765	0.09310	N	1	B	0.21071	0.051	B	0.14023	0.01	T	0.32188	-0.9916	9	0.42905	T	0.14	.	7.5755	0.27933	0.138:0.0:0.7015:0.1605	.	380	Q08ER8	ZN543_HUMAN	T	380	ENSP00000322545:A380T	ENSP00000322545:A380T	A	+	1	0	ZNF543	62531780	0.000000	0.05858	0.000000	0.03702	0.661000	0.39034	-1.477000	0.02331	-0.214000	0.10078	0.561000	0.74099	GCA	.	.	.	none		0.512	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865		A	57839968	G	A	57839968	3	1	45	1	0	0	0	0	1	0	0	0	17988	1319	46	2	1152	2	ZNF543	19	57839968	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08	2695962	57839968	1289015	68	3187											
ZNF335	63925	hgsc.bcm.edu	37	chr20	44578919	44578919	+	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	atggtctgggttggggtctgGgtaggggcccgggctgtagg	3	10	22	6	1	2	0	0	0	2	0	2	0	2	0	1	9	0	4	1	9	2	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr20:44578919G>C	ENST00000322927.2	-	22	3526	c.3426C>G	c.(3424-3426)acC>acG	p.T1142T	ZNF335_ENST00000426788.1_Silent_p.T987T	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	1142					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				TTGGGGTCTGGGTAGGGGCCC	0.612																																					p.T1142T		Atlas-SNP	.											.	ZNF335	115	.	0			c.C3426G						PASS	.						90	93	92					20																	44578919		2203	4300	6503	SO:0001819	synonymous_variant	63925	exon22			GGTCTGGGTAGGG	AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"Zinc fingers, C2H2-type"	15807	protein-coding gene	gene with protein product	"NRC-interacting factor 1"	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.3426C>G	chr20.hg19:g.44578919G>C		133.0	0.0	.		97.0	30.0	.	NM_022095	B4DLG7|Q548D0|Q9H684	Silent	SNP	ENST00000322927.2	hg19	CCDS13389.1																																																																																			.	.	.	none		0.612	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095		C	44578919	G	C	44578919	2	2	45	1	0	0	0	0	0	0	0	1	17864	1219	43	4		4	ZNF335	20	44578919	Silent	SNP	G	TCGA-A4-7584-01A-11D-2136-08		44578919	18446601	69	3188											
PARD6B	84612	hgsc.bcm.edu	37	chr20	49366295	49366295	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaccatagaaaaaagccacAtatagtcattagtatgcccc	17	8	5	11	0	1	1	1	0	0	1	1	1	1	1	4	0	3	1	4	0	9	5			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr20:49366295A>G	ENST00000371610.2	+	3	632	c.389A>G	c.(388-390)cAt>cGt	p.H130R	PARD6B_ENST00000396039.1_Intron	NM_032521.2	NP_115910.1	Q9BYG5	PAR6B_HUMAN	par-6 family cell polarity regulator beta	130	Interaction with PARD3 and CDC42. {ECO:0000250}.				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)		p.H130R(1)		NS(1)|breast(1)|endometrium(1)|kidney(4)|lung(3)|urinary_tract(1)	11						AAAAAGCCACATATAGTCATT	0.403																																					p.H130R		Atlas-SNP	.											PARD6B,NS,carcinoma,0,1	PARD6B	31	.	1	Substitution - Missense(1)	kidney(1)	c.A389G						PASS	.						76	74	75					20																	49366295		2203	4300	6503	SO:0001583	missense	84612	exon3			AGCCACATATAGT	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.389A>G	chr20.hg19:g.49366295A>G	ENSP00000360672:p.His130Arg	77.0	0.0	.		48.0	16.0	.	NM_032521	A2A2A7|Q9Y510	Missense_Mutation	SNP	ENST00000371610.2	hg19	CCDS33485.1	.	.	.	.	.	.	.	.	.	.	A	11.30	1.597328	0.28445	.	.	ENSG00000124171	ENST00000371610	T	0.41400	1.0	5.6	5.6	0.85130	.	0.151580	0.64402	D	0.000014	T	0.36991	0.0987	L	0.43152	1.355	0.80722	D	1	B	0.06786	0.001	B	0.09377	0.004	T	0.11421	-1.0588	10	0.25106	T	0.35	-32.4385	15.7847	0.78294	1.0:0.0:0.0:0.0	.	130	Q9BYG5	PAR6B_HUMAN	R	130	ENSP00000360672:H130R	ENSP00000360672:H130R	H	+	2	0	PARD6B	48799702	0.992000	0.36948	0.650000	0.29550	0.857000	0.48899	3.467000	0.53078	2.135000	0.66039	0.533000	0.62120	CAT	.	.	.	none		0.403	PARD6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079697.2	NM_032521		G	49366295	A	G	49366295	3	3	45	1	0	0	0	0	1	0	0	0	11453	217	8	3	399	3	PARD6B	20	49366295	Missense_Mutation	SNP	A	TCGA-A4-7584-01A-11D-2136-08	4787376	49366295	13659225	70	3189											
GAL3ST1	9514	hgsc.bcm.edu	37	chr22	30951203	30951203	+	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	ggtccgcatgcgctcgttggCatggcgcagggcggccacct	4	7	16	14	5	0	0	0	0	0	0	2	0	1	0	3	5	1	5	3	5	0	1			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr22:30951203C>G	ENST00000402321.1	-	3	1326	c.1009G>C	c.(1009-1011)Gcc>Ccc	p.A337P	GAL3ST1_ENST00000338911.5_Missense_Mutation_p.A337P|GAL3ST1_ENST00000406955.1_Missense_Mutation_p.A337P|GAL3ST1_ENST00000402369.1_Missense_Mutation_p.A337P|GAL3ST1_ENST00000406361.1_Missense_Mutation_p.A337P|GAL3ST1_ENST00000443111.2_Missense_Mutation_p.A337P|GAL3ST1_ENST00000401975.1_Missense_Mutation_p.A337P			Q99999	G3ST1_HUMAN	galactose-3-O-sulfotransferase 1	337					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						CGCTCGTTGGCATGGCGCAGG	0.721																																					p.A337P		Atlas-SNP	.											.	GAL3ST1	44	.	0			c.G1009C						PASS	.						20	22	21					22																	30951203		2199	4288	6487	SO:0001583	missense	9514	exon4			CGTTGGCATGGCG	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.1009G>C	chr22.hg19:g.30951203C>G	ENSP00000385735:p.Ala337Pro	23.0	0.0	.		25.0	13.0	.	NM_004861	Q96C63	Missense_Mutation	SNP	ENST00000402321.1	hg19	CCDS13879.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.017684	0.75161	.	.	ENSG00000128242	ENST00000406955;ENST00000402321;ENST00000402369;ENST00000401975;ENST00000338911;ENST00000406361;ENST00000443111	T;T;T;T;T;T;T	0.17691	2.26;2.26;2.26;2.26;2.26;2.26;2.26	5.55	5.55	0.83447	.	0.225320	0.47455	D	0.000227	T	0.24547	0.0595	L	0.55990	1.75	0.80722	D	1	P	0.43938	0.822	P	0.48425	0.577	T	0.00557	-1.1672	10	0.30854	T	0.27	-13.5376	12.4548	0.55697	0.0:0.9221:0.0:0.0779	.	337	Q99999	G3ST1_HUMAN	P	337	ENSP00000385825:A337P;ENSP00000385735:A337P;ENSP00000384122:A337P;ENSP00000384388:A337P;ENSP00000343234:A337P;ENSP00000385207:A337P;ENSP00000402587:A337P	ENSP00000343234:A337P	A	-	1	0	GAL3ST1	29281203	0.970000	0.33590	0.958000	0.39756	0.894000	0.52154	2.095000	0.41729	2.615000	0.88500	0.561000	0.74099	GCC	.	.	.	none		0.721	GAL3ST1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321745.1	NM_004861		G	30951203	C	G	30951203	3	3	45	1	0	0	0	0	1	0	0	0	6204	710	25	4	266	4	GAL3ST1	22	30951203	Missense_Mutation	SNP	C	TCGA-A4-7584-01A-11D-2136-08		30951203	20353363	71	3190											
CARD10	29775	hgsc.bcm.edu	37	chr22	37914027	37914027	+	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	tcctggcccgtgagcagcgtGaagtgttcggggtagtagaa	8	9	16	8	3	0	3	0	2	0	1	2	3	1	3	2	3	2	4	2	3	4	3			TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chr22:37914027G>C	ENST00000403299.1	-	3	540	c.324C>G	c.(322-324)ttC>ttG	p.F108L	CARD10_ENST00000251973.5_Missense_Mutation_p.F108L			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	108	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				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)					TGAGCAGCGTGAAGTGTTCGG	0.622																																					p.F108L		Atlas-SNP	.											.	CARD10	55	.	0			c.C324G						PASS	.						94	80	85					22																	37914027		2203	4300	6503	SO:0001583	missense	29775	exon2			CAGCGTGAAGTGT	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.324C>G	chr22.hg19:g.37914027G>C	ENSP00000384570:p.Phe108Leu	93.0	0.0	.		60.0	13.0	.	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Missense_Mutation	SNP	ENST00000403299.1	hg19	CCDS13948.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.694688	0.88830	.	.	ENSG00000100065	ENST00000403299;ENST00000251973	T;T	0.20069	2.1;2.1	4.67	3.64	0.41730	DEATH-like (2);Caspase Recruitment (2);	0.151059	0.46442	D	0.000290	T	0.20007	0.0481	L	0.47716	1.5	0.46774	D	0.99919	P	0.40000	0.698	B	0.38683	0.279	T	0.02713	-1.1120	10	0.66056	D	0.02	-23.0196	11.2943	0.49269	0.0863:0.0:0.9137:0.0	.	108	Q9BWT7	CAR10_HUMAN	L	108	ENSP00000384570:F108L;ENSP00000251973:F108L	ENSP00000251973:F108L	F	-	3	2	CARD10	36243973	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	4.159000	0.58157	1.061000	0.40601	0.462000	0.41574	TTC	.	.	.	none		0.622	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550		C	37914027	G	C	37914027	3	2	45	1	0	0	0	0	1	0	0	0	2646	1281	45	4	2850	4	CARD10	22	37914027	Missense_Mutation	SNP	G	TCGA-A4-7584-01A-11D-2136-08	6962824	37914027	13390539	72	3191											
KDM6A	7403	hgsc.bcm.edu	37	chrX	44870257	44870257	+	Frame_Shift_Del	DEL	T	T	-																															tctacttccattataatgcaTttcagtggtaagttgacata																										TCGA-A4-7584-01A-11D-2136-08	TCGA-A4-7584-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a4f7bf60-293b-44c8-a121-1d8b2c590f78	969e0233-3df2-44b1-a37c-f056f8c5ba97	g.chrX:44870257delT	ENST00000377967.4	+	5	477	c.436delT	c.(436-438)tttfs	p.F146fs	KDM6A_ENST00000536777.1_Frame_Shift_Del_p.F146fs|KDM6A_ENST00000543216.1_Frame_Shift_Del_p.F146fs|KDM6A_ENST00000382899.4_Frame_Shift_Del_p.F146fs	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	146	Interaction with SUPT6H. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0(12)|p.0?(6)|p.?(1)		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						TTATAATGCATTTCAGTGGTA	0.323			"D, N, F, S"		"renal, oesophageal SCC, MM"																																p.A145fs	Colon(129;1273 1667 15230 27352 52914)	Atlas-INDEL	.		Rec	yes		X	Xp11.2	7403	"lysine (K)-specific demethylase 6A, UTX"		"E, L"	.	KDM6A	274	.	19	No detectable mRNA/protein(12)|Whole gene deletion(6)|Unknown(1)	haematopoietic_and_lymphoid_tissue(11)|oesophagus(4)|breast(2)|pancreas(2)	c.435delA						PASS	.						117	99	105					X																	44870257		2203	4297	6500	SO:0001589	frameshift_variant	7403	exon5			.	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.436delT	chrX.hg19:g.44870257delT	ENSP00000367203:p.Phe146fs	35.0	0.0	0		20.0	13.0	0.65	NM_021140	Q52LL9|Q5JVQ7	Frame_Shift_Del	DEL	ENST00000377967.4	hg19	CCDS14265.1																																																																																			.	.	.	none		0.323	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140		-	44870257	T	-	44870257	7	5	45	1	0	1	0	1	0	0	0	0	8144	1493	52	0	454	0	KDM6A	23	44870257	Frame_Shift_Del	DEL	T	TCGA-A4-7584-01A-11D-2136-08		44870257	110400303	73	3192											
BAI2	576	hgsc.bcm.edu	37	chr1	32207416	32207416	+	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	agtacctggacacctcttctCactacaaggcttcacctcct	9	11	5	16	0	3	0	2	0	2	0	5	1	4	1	4	2	2	2	4	2	3	4			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr1:32207416C>A	ENST00000373658.3	-	9	1911	c.1570G>T	c.(1570-1572)Gag>Tag	p.E524*	BAI2_ENST00000398542.1_Nonsense_Mutation_p.E457*|BAI2_ENST00000398538.1_Nonsense_Mutation_p.E512*|BAI2_ENST00000527361.1_Nonsense_Mutation_p.E524*|BAI2_ENST00000257070.4_Nonsense_Mutation_p.E524*|BAI2_ENST00000440175.2_Nonsense_Mutation_p.E166*|BAI2_ENST00000373655.2_Nonsense_Mutation_p.E524*|BAI2_ENST00000398547.1_Nonsense_Mutation_p.E457*|BAI2_ENST00000398556.3_Nonsense_Mutation_p.E472*	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	524	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			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)		CACCTCTTCTCACTACAAGGC	0.652																																					p.E524X		Atlas-SNP	.											.	BAI2	128	.	0			c.G1570T						PASS	.						95	100	98					1																	32207416		2203	4299	6502	SO:0001587	stop_gained	576	exon9			TCTTCTCACTACA	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.1570G>T	chr1.hg19:g.32207416C>A	ENSP00000362762:p.Glu524*	109.0	0.0	.		110.0	17.0	.	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Nonsense_Mutation	SNP	ENST00000373658.3	hg19	CCDS346.2	.	.	.	.	.	.	.	.	.	.	C	36	5.737223	0.96865	.	.	ENSG00000121753	ENST00000398556;ENST00000398547;ENST00000373658;ENST00000373655;ENST00000398542;ENST00000257070;ENST00000527361;ENST00000440175;ENST00000398538;ENST00000420125;ENST00000533175	.	.	.	4.95	4.95	0.65309	.	0.000000	0.39985	N	0.001213	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	.	17.3262	0.87248	0.0:1.0:0.0:0.0	.	.	.	.	X	472;457;524;524;457;524;524;166;512;462;503	.	ENSP00000257070:E524X	E	-	1	0	BAI2	31980003	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	5.765000	0.68834	2.457000	0.83068	0.561000	0.74099	GAG	.	.	.	none		0.652	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703		A	32207416	C	A	32207416	4	1	46	1	0	0	0	0	0	1	0	0	1299	835	29	4	3287	4	BAI2	1	32207416	Nonsense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08		32207416	217043205	1	3193											
TOE1	114034	hgsc.bcm.edu	37	chr1	45808095	45808095	+	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	agtcagtacggaccctattcCtggagctaatccgagcccgc	9	8	10	14	3	1	0	1	0	0	0	3	3	3	2	4	2	3	2	4	2	3	4			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr1:45808095C>G	ENST00000372090.5	+	6	1115	c.532C>G	c.(532-534)Ctg>Gtg	p.L178V	MUTYH_ENST00000531105.1_5'Flank|MUTYH_ENST00000372115.3_5'Flank|TOE1_ENST00000495703.1_3'UTR|MUTYH_ENST00000456914.2_5'Flank|MUTYH_ENST00000372110.3_5'Flank|MUTYH_ENST00000488731.2_5'Flank|MUTYH_ENST00000372100.5_5'Flank|MUTYH_ENST00000372098.3_5'Flank|MUTYH_ENST00000354383.6_5'Flank|TESK2_ENST00000486676.1_5'Flank|MUTYH_ENST00000528013.2_5'Flank|MUTYH_ENST00000450313.1_5'Flank|MUTYH_ENST00000448481.1_5'Flank|MUTYH_ENST00000355498.2_5'Flank|TOE1_ENST00000539779.1_Missense_Mutation_p.L98V|MUTYH_ENST00000529984.1_5'Flank|MUTYH_ENST00000372104.1_5'Flank|MUTYH_ENST00000528332.2_5'Flank	NM_025077.3	NP_079353.3	Q96GM8	TOE1_HUMAN	target of EGR1, member 1 (nuclear)	178						nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	11	Acute lymphoblastic leukemia(166;0.155)					GACCCTATTCCTGGAGCTAAT	0.552																																					p.L178V		Atlas-SNP	.											.	TOE1	27	.	0			c.C532G						PASS	.						97	100	99					1																	45808095		2203	4300	6503	SO:0001583	missense	114034	exon6			CTATTCCTGGAGC		CCDS521.1	1p33	2011-02-03			ENSG00000132773	ENSG00000132773			15954	protein-coding gene	gene with protein product		613931				12562764	Standard	NM_025077		Approved		uc009vxq.3	Q96GM8	OTTHUMG00000007678	ENST00000372090.5:c.532C>G	chr1.hg19:g.45808095C>G	ENSP00000361162:p.Leu178Val	168.0	0.0	.		168.0	29.0	.	NM_025077	B4DEM6|Q6IA35|Q8IWN5|Q9H846	Missense_Mutation	SNP	ENST00000372090.5	hg19	CCDS521.1	.	.	.	.	.	.	.	.	.	.	C	9.622	1.133977	0.21123	.	.	ENSG00000132773	ENST00000372090;ENST00000539779	T;T	0.23552	1.9;1.9	5.79	4.88	0.63580	Ribonuclease H-like (1);	0.129811	0.53938	D	0.000050	T	0.24661	0.0598	L	0.36672	1.1	0.41103	D	0.985687	B;P;P	0.40398	0.164;0.716;0.716	B;B;B	0.42245	0.077;0.381;0.194	T	0.02358	-1.1171	10	0.27785	T	0.31	-8.8608	14.7036	0.69171	0.0:0.9309:0.0:0.0691	.	184;98;178	B4DP23;B4DEM6;Q96GM8	.;.;TOE1_HUMAN	V	178;98	ENSP00000361162:L178V;ENSP00000438900:L98V	ENSP00000361162:L178V	L	+	1	2	TOE1	45580682	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	2.049000	0.41288	1.455000	0.47813	0.655000	0.94253	CTG	.	.	.	none		0.552	TOE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020517.1	NM_025077		G	45808095	C	G	45808095	3	3	46	1	0	0	0	0	1	0	0	0	16361	680	24	4	554	4	TOE1	1	45808095	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	13600679	45808095	203442526	2	3194											
LPHN2	23266	hgsc.bcm.edu	37	chr1	82456455	82456455	+	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	ctcagcggactcactcccttCtgtaccaaccccagaagaaa	12	7	6	16	1	3	2	2	0	1	2	4	3	4	3	4	1	3	1	4	1	4	2			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr1:82456455C>G	ENST00000370728.1	+	25	4651	c.4006C>G	c.(4006-4008)Ctg>Gtg	p.L1336V	LPHN2_ENST00000370717.2_Missense_Mutation_p.L1351V|LPHN2_ENST00000370725.1_Missense_Mutation_p.L1351V|LPHN2_ENST00000394879.1_Missense_Mutation_p.L1338V|LPHN2_ENST00000370721.1_Missense_Mutation_p.L1261V|LPHN2_ENST00000469377.2_3'UTR|LPHN2_ENST00000370723.1_Missense_Mutation_p.L1338V|LPHN2_ENST00000319517.6_Missense_Mutation_p.L1280V|LPHN2_ENST00000370730.1_Missense_Mutation_p.L1293V|LPHN2_ENST00000271029.4_Missense_Mutation_p.L1308V|LPHN2_ENST00000370715.1_3'UTR|LPHN2_ENST00000359929.3_Missense_Mutation_p.L1280V|LPHN2_ENST00000370727.1_Missense_Mutation_p.L1308V|LPHN2_ENST00000370713.1_3'UTR|LPHN2_ENST00000335786.5_Missense_Mutation_p.L1293V			O95490	LPHN2_HUMAN	latrophilin 2	1336					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)		TCACTCCCTTCTGTACCAACC	0.527																																					p.L1280V		Atlas-SNP	.											.	LPHN2	464	.	0			c.C3838G						PASS	.						84	87	86					1																	82456455		2203	4300	6503	SO:0001583	missense	23266	exon20			TCCCTTCTGTACC	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.4006C>G	chr1.hg19:g.82456455C>G	ENSP00000359763:p.Leu1336Val	142.0	0.0	.		165.0	44.0	.	NM_012302	A5XEI2|B1ALT8|B1ALT9|B1ALU0|B1ALU2|B1ALU4|B1ALU5|B1ALU6|O94882|Q5VX76|Q9UKY5|Q9UKY6	Missense_Mutation	SNP	ENST00000370728.1	hg19		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	13.57|13.57|13.57	2.275917|2.275917|2.275917	0.40294|0.40294|0.40294	.|.|.	.|.|.	ENSG00000117114|ENSG00000117114|ENSG00000117114	ENST00000449420|ENST00000370721;ENST00000370728;ENST00000370730;ENST00000370727;ENST00000370725;ENST00000370723;ENST00000359929;ENST00000319517;ENST00000370717;ENST00000394879;ENST00000271029;ENST00000335786|ENST00000402328	.|T;T;T;T;T;T;T;T;T;T;T;T|.	.|0.72835|.	.|-0.52;-0.53;-0.69;-0.63;-0.47;-0.43;-0.63;-0.63;-0.47;-0.43;-0.63;-0.69|.	5.67|5.67|5.67	5.67|5.67|5.67	0.87782|0.87782|0.87782	.|.|.	.|0.000000|.	.|0.64402|.	.|D|.	.|0.000011|.	T|T|T	0.68375|0.68375|0.68375	0.2994|0.2994|0.2994	M|M|M	0.62723|0.62723|0.62723	1.935|1.935|1.935	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|P;D|.	.|0.69078|.	.|0.663;0.997|.	.|B;D|.	.|0.76071|.	.|0.395;0.987|.	T|T|T	0.64841|0.64841|0.64841	-0.6312|-0.6312|-0.6312	5|10|5	.|0.59425|.	.|D|.	.|0.04|.	.|.|.	19.773|19.773|19.773	0.96379|0.96379|0.96379	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	.|1280;260|.	.|O95490-2;B3KVU1|.	.|.;.|.	L|V|C	1227|1261;1336;1293;1308;1351;1338;1280;1280;1351;1338;1308;1293|347	.|ENSP00000359756:L1261V;ENSP00000359763:L1336V;ENSP00000359765:L1293V;ENSP00000359762:L1308V;ENSP00000359760:L1351V;ENSP00000359758:L1338V;ENSP00000353006:L1280V;ENSP00000322270:L1280V;ENSP00000359752:L1351V;ENSP00000378344:L1338V;ENSP00000271029:L1308V;ENSP00000337306:L1293V|.	.|ENSP00000271029:L1308V|.	F|L|S	+|+|+	3|1|2	2|2|0	LPHN2|LPHN2|LPHN2	82229043|82229043|82229043	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.988000|0.988000|0.988000	0.76386|0.76386|0.76386	5.773000|5.773000|5.773000	0.68898|0.68898|0.68898	2.677000|2.677000|2.677000	0.91161|0.91161|0.91161	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	TTC|CTG|TCT	.	.	.	none		0.527	LPHN2-007	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000027188.1	NM_012302		G	82456455	C	G	82456455	3	3	46	1	0	0	0	0	1	0	0	0	8923	912	32	4	3912	4	LPHN2	1	82456455	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	36648360	82456455	166794166	3	3195											
C1orf51	148523	hgsc.bcm.edu	37	chr1	150259000	150259000	+	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	ctcacctggatccacaccacTccaatttgcaacccccctct	9	9	3	20	0	2	0	1	0	1	0	4	1	4	1	7	1	2	1	7	1	2	1			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr1:150259000T>A	ENST00000290363.5	+	5	1241	c.792T>A	c.(790-792)acT>acA	p.T264T	C1orf51_ENST00000369094.1_Silent_p.T176T|C1orf51_ENST00000369095.1_Silent_p.T264T	NM_144697.2	NP_653298.1	Q8N365	CIART_HUMAN		264					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)			TCCACACCACTCCAATTTGCA	0.522																																					p.T264T		Atlas-SNP	.											.	C1orf51	35	.	0			c.T792A						PASS	.						243	190	208					1																	150259000		2203	4300	6503	SO:0001819	synonymous_variant	148523	exon5			CACCACTCCAATT																												ENST00000290363.5:c.792T>A	chr1.hg19:g.150259000T>A		161.0	0.0	.		183.0	35.0	.	NM_144697	B2RD43|D3DV01|Q8N795|Q96MG6	Silent	SNP	ENST00000290363.5	hg19	CCDS949.1																																																																																			.	.	.	none		0.522	C1orf51-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035058.1			A	150259000	T	A	150259000	2	1	46	1	0	0	0	0	0	0	0	1	2045	1538	54	5		5	C1orf51	1	150259000	Silent	SNP	T	TCGA-A4-7585-01A-11D-2136-08	67802545	150259000	98991621	4	3196											
CRTC2	200186	hgsc.bcm.edu	37	chr1	153924520	153924520	+	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	catcatagcctgggcccaggCccatgcccctgctgatgccc	6	7	10	18	0	1	1	1	1	0	0	1	1	1	1	6	2	4	1	6	2	1	1			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr1:153924520C>A	ENST00000368633.1	-	10	1098	c.971G>T	c.(970-972)gGc>gTc	p.G324V	CRTC2_ENST00000368630.3_Intron|CRTC2_ENST00000476883.1_5'Flank	NM_181715.2	NP_859066.1	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2	324				MGL -> HGP (in Ref. 1; AAQ98857). {ECO:0000305}.	gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|histone H3-K9 acetylation (GO:0043970)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cAMP response element binding protein binding (GO:0008140)			NS(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	27	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			TGGGCCCAGGCCCATGCCCCT	0.607																																					p.G324V		Atlas-SNP	.											.	CRTC2	58	.	0			c.G971T						PASS	.						58	57	57					1																	153924520		2203	4300	6503	SO:0001583	missense	200186	exon10			CCCAGGCCCATGC	AY360172	CCDS30875.1	1q21.3	2008-02-05			ENSG00000160741	ENSG00000160741			27301	protein-coding gene	gene with protein product		608972				14506290, 14536081	Standard	NM_181715		Approved	TORC2	uc021pab.1	Q53ET0	OTTHUMG00000037156	ENST00000368633.1:c.971G>T	chr1.hg19:g.153924520C>A	ENSP00000357622:p.Gly324Val	95.0	0.0	.		108.0	14.0	.	NM_181715	Q6UUV8|Q7Z3X7|Q8N332	Missense_Mutation	SNP	ENST00000368633.1	hg19	CCDS30875.1	.	.	.	.	.	.	.	.	.	.	c	6.593	0.477845	0.12521	.	.	ENSG00000160741	ENST00000368633	T	0.12774	2.65	4.84	3.92	0.45320	.	0.625789	0.15810	N	0.243526	T	0.05502	0.0145	L	0.36672	1.1	0.48830	D	0.999715	B	0.23249	0.082	B	0.21708	0.036	T	0.09185	-1.0686	10	0.66056	D	0.02	-3.8662	11.1372	0.48381	0.0:0.813:0.187:0.0	.	324	Q53ET0	CRTC2_HUMAN	V	324	ENSP00000357622:G324V	ENSP00000357622:G324V	G	-	2	0	CRTC2	152191144	0.420000	0.25457	0.997000	0.53966	0.095000	0.18619	0.767000	0.26575	1.028000	0.39785	0.450000	0.29827	GGC	.	.	.	none		0.607	CRTC2-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090272.3	NM_181715		A	153924520	C	A	153924520	3	1	46	1	0	0	0	0	1	0	0	0	3902	739	26	4	1130	4	CRTC2	1	153924520	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	3665520	153924520	95326101	5	3197											
FAM5C	339479	hgsc.bcm.edu	37	chr1	190067269	190067269	+	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	gcttgagtctatgacgaagcAagcaagagaaaagatctaga	17	7	11	6	1	2	5	0	2	2	3	2	7	2	5	0	0	2	3	0	0	7	3			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr1:190067269A>T	ENST00000367462.3	-	8	2411	c.2180T>A	c.(2179-2181)tTg>tAg	p.L727*	BRINP3_ENST00000534846.1_Nonsense_Mutation_p.L625*	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	727					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)											ATGACGAAGCAAGCAAGAGAA	0.463																																					p.L727X		Atlas-SNP	.											.	FAM5C	343	.	0			c.T2180A						PASS	.						115	111	112					1																	190067269		2203	4300	6503	SO:0001587	stop_gained	339479	exon8			CGAAGCAAGCAAG	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.2180T>A	chr1.hg19:g.190067269A>T	ENSP00000356432:p.Leu727*	146.0	0.0	.		129.0	14.0	.	NM_199051	B3KVP1|B7Z260|O95726|Q2M330	Nonsense_Mutation	SNP	ENST00000367462.3	hg19	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	A	37	6.250241	0.97412	.	.	ENSG00000162670	ENST00000367462;ENST00000534846	.	.	.	5.72	4.6	0.57074	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.7499	0.40470	0.9186:0.0:0.0814:0.0	.	.	.	.	X	727;625	.	ENSP00000356432:L727X	L	-	2	0	FAM5C	188333892	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.237000	0.95368	1.005000	0.39183	0.528000	0.53228	TTG	.	.	.	none		0.463	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		T	190067269	A	T	190067269	4	4	46	1	0	0	0	0	0	1	0	0	5601	131	5	5	124	5	FAM5C	1	190067269	Nonsense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	36142749	190067269	59183352	6	3198											
TAF1B	9014	hgsc.bcm.edu	37	chr2	10016047	10016047	+	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	ttgaatactcacaacgaaagGagaagggaatcgtgaagatg	17	7	12	5	2	1	4	1	2	0	2	2	7	1	5	0	2	2	0	0	2	7	2			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr2:10016047G>C	ENST00000263663.5	+	7	795	c.607G>C	c.(607-609)Gag>Cag	p.E203Q	TAF1B_ENST00000396242.3_Intron	NM_005680.2	NP_005671	Q53T94	TAF1B_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa	203	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)					ACAACGAAAGGAGAAGGGAAT	0.408																																					p.E203Q		Atlas-SNP	.											.	TAF1B	62	.	0			c.G607C						PASS	.						223	193	203					2																	10016047		2203	4300	6503	SO:0001583	missense	9014	exon7			CGAAAGGAGAAGG	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.607G>C	chr2.hg19:g.10016047G>C	ENSP00000263663:p.Glu203Gln	210.0	0.0	.		200.0	40.0	.	NM_005680	B4DI42|F8WD72|Q15574|Q8WVC3	Missense_Mutation	SNP	ENST00000263663.5	hg19	CCDS33143.1	.	.	.	.	.	.	.	.	.	.	G	9.995	1.231767	0.22626	.	.	ENSG00000115750	ENST00000263663	T	0.01902	4.57	5.82	4.0	0.46444	.	0.254066	0.44285	D	0.000476	T	0.02807	0.0084	L	0.41236	1.265	0.80722	D	1	B;P	0.52316	0.172;0.952	B;P	0.46659	0.025;0.523	T	0.60419	-0.7267	9	.	.	.	-14.0229	5.6394	0.17554	0.1472:0.178:0.6747:0.0	.	203;203	Q53T94;Q53T94-2	TAF1B_HUMAN;.	Q	203	ENSP00000263663:E203Q	.	E	+	1	0	TAF1B	9933498	1.000000	0.71417	0.994000	0.49952	0.941000	0.58515	1.150000	0.31639	1.442000	0.47568	0.655000	0.94253	GAG	.	.	.	none		0.408	TAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323426.2	NM_005680		C	10016047	G	C	10016047	3	2	46	1	0	0	0	0	1	0	0	0	15532	1175	41	4	633	4	TAF1B	2	10016047	Missense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08		10016047	233183326	7	3199											
CAD	790	hgsc.bcm.edu	37	chr2	27460276	27460276	+	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	atgtccatgtgcacctgcggGaaccaggtgggacacataag	11	7	13	10	1	0	0	0	0	0	0	1	2	1	2	3	3	3	1	3	3	2	1			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr2:27460276G>A	ENST00000403525.1	+	27	4381	c.4237G>A	c.(4237-4239)Gaa>Aaa	p.E1413K	CAD_ENST00000264705.4_Missense_Mutation_p.E1476K			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)					GCACCTGCGGGAACCAGGTGG	0.552																																					p.E1476K		Atlas-SNP	.											.	CAD	199	.	0			c.G4426A						PASS	.						87	84	85					2																	27460276		2203	4300	6503	SO:0001583	missense	790	exon28			CTGCGGGAACCAG	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.4237G>A	chr2.hg19:g.27460276G>A	ENSP00000384510:p.Glu1413Lys	119.0	0.0	.		120.0	20.0	.	NM_004341	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Missense_Mutation	SNP	ENST00000403525.1	hg19		.	.	.	.	.	.	.	.	.	.	G	28.5	4.927886	0.92389	.	.	ENSG00000084774	ENST00000264705;ENST00000403525	T;T	0.46063	0.88;0.88	4.91	4.01	0.46588	Dihydroorotase, conserved site (1);Amidohydrolase 1 (1);	0.167071	0.52532	D	0.000062	T	0.73249	0.3563	H	0.98111	4.15	0.80722	D	1	P;D	0.65815	0.941;0.995	P;P	0.62885	0.66;0.908	T	0.80306	-0.1438	10	0.33141	T	0.24	-0.4186	13.2019	0.59774	0.0:0.0:0.8392:0.1608	.	1413;1476	F8VPD4;P27708	.;PYR1_HUMAN	K	1476;1413	ENSP00000264705:E1476K;ENSP00000384510:E1413K	ENSP00000264705:E1476K	E	+	1	0	CAD	27313780	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.360000	0.97119	1.030000	0.39839	0.561000	0.74099	GAA	.	.	.	none		0.552	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1			A	27460276	G	A	27460276	3	1	46	1	0	0	0	0	1	0	0	0	2567	1175	41	2	4536	2	CAD	2	27460276	Missense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08	17444229	27460276	215739097	8	3200											
TSGA10	80705	hgsc.bcm.edu	37	chr2	99720473	99720473	+	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	ttgtctgccaagttcactttCggtatccattgcctttcttg	5	18	7	11	1	3	0	1	0	2	0	5	0	4	0	3	1	2	2	3	1	2	7	rs545440386	byFrequency	TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr2:99720473C>A	ENST00000393483.3	-	10	1412	c.568G>T	c.(568-570)Gaa>Taa	p.E190*	TSGA10_ENST00000410001.1_Nonsense_Mutation_p.E190*|TSGA10_ENST00000355053.4_Nonsense_Mutation_p.E190*|TSGA10_ENST00000542655.1_Nonsense_Mutation_p.E190*|TSGA10_ENST00000478090.1_5'UTR|TSGA10_ENST00000539964.1_Nonsense_Mutation_p.E190*	NM_025244.2	NP_079520.1	Q9BZW7	TSG10_HUMAN	testis specific, 10	190					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						AGTTCACTTTCGGTATCCATT	0.348																																					p.E190X		Atlas-SNP	.											.	TSGA10	81	.	0			c.G568T						PASS	.						240	212	222					2																	99720473		2202	4299	6501	SO:0001587	stop_gained	80705	exon9			CACTTTCGGTATC	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.568G>T	chr2.hg19:g.99720473C>A	ENSP00000377123:p.Glu190*	86.0	0.0	.		113.0	12.0	.	NM_182911	B7Z925|D3DVH7|Q8NEP0|Q9BWX0	Nonsense_Mutation	SNP	ENST00000393483.3	hg19	CCDS2037.1	.	.	.	.	.	.	.	.	.	.	C	42	9.602630	0.99217	.	.	ENSG00000135951	ENST00000393483;ENST00000410001;ENST00000355053;ENST00000539964;ENST00000409564;ENST00000393482;ENST00000542655	.	.	.	5.36	5.36	0.76844	.	0.000000	0.64402	D	0.000017	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	-16.4617	16.7002	0.85348	0.0:1.0:0.0:0.0	.	.	.	.	X	190	.	ENSP00000347161:E190X	E	-	1	0	TSGA10	99086905	0.986000	0.35501	0.969000	0.41365	0.988000	0.76386	2.774000	0.47694	2.801000	0.96364	0.650000	0.86243	GAA	.	.	.	none		0.348	TSGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253125.1	NM_182911		A	99720473	C	A	99720473	4	1	46	1	0	0	0	0	0	1	0	0	16629	893	31	4	1576	4	TSGA10	2	99720473	Nonsense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	72260197	99720473	143478900	9	3201											
LCT	3938	hgsc.bcm.edu	37	chr2	136566494	136566494	+	Frame_Shift_Del	DEL	T	T	-																															tgcagcattcggtcagcggcTtccacatctctggggacccc																										TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr2:136566494delT	ENST00000264162.2	-	8	3433	c.3423delA	c.(3421-3423)gaafs	p.E1141fs	Y_RNA_ENST00000363794.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	1141	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)	GGTCAGCGGCTTCCACATCTC	0.552																																					p.A1142fs		Atlas-INDEL	.											.	LCT	309	.	0			c.3424delG						PASS	.						71	75	74					2																	136566494		2203	4300	6503	SO:0001589	frameshift_variant	3938	exon8			.	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.3423delA	chr2.hg19:g.136566494delT	ENSP00000264162:p.Glu1141fs	128.0	0.0	0		159.0	21.0	0.132075	NM_002299	Q4ZG58	Frame_Shift_Del	DEL	ENST00000264162.2	hg19	CCDS2178.1																																																																																			.	.	.	none		0.552	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		-	136566494	T	-	136566494	7	5	46	1	0	1	0	1	0	0	0	0	8700	1606	56	0	2400	0	LCT	2	136566494	Frame_Shift_Del	DEL	T	TCGA-A4-7585-01A-11D-2136-08	36846021	136566494	106632879	10	3202											
DARS	1615	hgsc.bcm.edu	37	chr2	136736937	136736937	+	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	aacccgaaccaaaactcgatCtgtaataacagtaaacgatt	18	8	5	10	3	1	0	0	0	1	0	2	3	1	0	2	0	5	2	2	0	8	4			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr2:136736937C>A	ENST00000264161.4	-	3	340		c.e3-1		DARS_ENST00000463008.1_Splice_Site|DARS_ENST00000537273.1_Splice_Site	NM_001349.2	NP_001340.2	P14868	SYDC_HUMAN	aspartyl-tRNA synthetase						aspartyl-tRNA aminoacylation (GO:0006422)|gene expression (GO:0010467)|protein complex assembly (GO:0006461)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacylase activity (GO:0004046)|aspartate-tRNA ligase activity (GO:0004815)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(2)	15				BRCA - Breast invasive adenocarcinoma(221;0.168)	L-Aspartic Acid(DB00128)	AAAACTCGATCTGTAATAACA	0.318																																					.		Atlas-SNP	.											.	DARS	44	.	0			c.125-1G>T						PASS	.						105	108	107					2																	136736937		2203	4300	6503	SO:0001630	splice_region_variant	1615	exon4			CTCGATCTGTAAT	J05032	CCDS2180.1	2q21.3	2011-07-01			ENSG00000115866	ENSG00000115866	6.1.1.12	"Aminoacyl tRNA synthetases / Class II"	2678	protein-coding gene	gene with protein product	"aspartate tRNA ligase 1, cytoplasmic"	603084				2674137	Standard	NM_001349		Approved		uc002tux.1	P14868	OTTHUMG00000131741	ENST00000264161.4:c.125-1G>T	chr2.hg19:g.136736937C>A		93.0	0.0	.		124.0	25.0	.	NM_001349	A8K3J2|D3DP77|Q2TNI3|Q32Q69|Q53HV4|Q53YC5|Q68CR9|Q9BW52	Splice_Site	SNP	ENST00000264161.4	hg19	CCDS2180.1	.	.	.	.	.	.	.	.	.	.	C	11.16	1.558088	0.27827	.	.	ENSG00000115866	ENST00000264161;ENST00000441323;ENST00000456565;ENST00000449218	.	.	.	5.34	5.34	0.76211	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3312	0.83015	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DARS	136453407	1.000000	0.71417	1.000000	0.80357	0.161000	0.22273	5.328000	0.65887	2.655000	0.90218	0.462000	0.41574	.	.	.	.	none		0.318	DARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254660.5	NM_001349	Intron	A	136736937	C	A	136736937	5	1	46	1	0	0	0	0	0	0	1	0	4243	927	32	4	1437	4	DARS	2	136736937	Splice_Site	SNP	C	TCGA-A4-7585-01A-11D-2136-08	170443	136736937	106462436	11	3203											
KIF5C	3800	hgsc.bcm.edu	37	chr2	149835496	149835496	+	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	tgaagcaacagatgttggatCaggatgaggtaaagaatgca	16	8	13	4	0	1	4	1	2	0	2	1	6	1	6	0	3	3	4	0	3	5	2			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr2:149835496C>T	ENST00000435030.1	+	13	1722	c.1354C>T	c.(1354-1356)Cag>Tag	p.Q452*	KIF5C_ENST00000464066.1_3'UTR|KIF5C_ENST00000414838.2_Nonsense_Mutation_p.Q357*|KIF5C_ENST00000397413.1_Nonsense_Mutation_p.Q220*			O60282	KIF5C_HUMAN	kinesin family member 5C	452					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)		GATGTTGGATCAGGATGAGGT	0.353																																					p.Q452X		Atlas-SNP	.											.	KIF5C	166	.	0			c.C1354T						PASS	.						78	78	78					2																	149835496		1852	4105	5957	SO:0001587	stop_gained	3800	exon13			TTGGATCAGGATG	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.1354C>T	chr2.hg19:g.149835496C>T	ENSP00000393379:p.Gln452*	44.0	0.0	.		61.0	17.0	.	NM_004522	O95079|Q2YDC5	Nonsense_Mutation	SNP	ENST00000435030.1	hg19		.	.	.	.	.	.	.	.	.	.	C	39	7.391751	0.98255	.	.	ENSG00000168280	ENST00000435030;ENST00000414838;ENST00000334436;ENST00000397413	.	.	.	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	.	19.9142	0.97043	0.0:1.0:0.0:0.0	.	.	.	.	X	452;357;355;220	.	ENSP00000334176:Q355X	Q	+	1	0	KIF5C	149543742	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.627000	0.83176	2.941000	0.99782	0.655000	0.94253	CAG	.	.	.	none		0.353	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522		T	149835496	C	T	149835496	4	4	46	1	0	0	0	0	0	1	0	0	8314	827	29	2	1326	2	KIF5C	2	149835496	Nonsense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	13098559	149835496	93363877	12	3204											
USP37	57695	hgsc.bcm.edu	37	chr2	219328058	219328058	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaactcggtagctcttttgAggtcatcatcttctttctgt	6	19	7	9	1	6	1	2	1	4	0	7	1	6	1	0	2	2	2	0	2	2	6			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr2:219328058A>G	ENST00000258399.3	-	22	2910	c.2498T>C	c.(2497-2499)cTc>cCc	p.L833P	USP37_ENST00000418019.1_Missense_Mutation_p.L833P|USP37_ENST00000415516.1_Missense_Mutation_p.L739P|USP37_ENST00000454775.1_Missense_Mutation_p.L833P	NM_020935.2	NP_065986	Q86T82	UBP37_HUMAN	ubiquitin specific peptidase 37	833	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)		AGCTCTTTTGAGGTCATCATC	0.318																																					p.L833P		Atlas-SNP	.											.	USP37	76	.	0			c.T2498C						PASS	.						107	106	106					2																	219328058		2203	4300	6503	SO:0001583	missense	57695	exon22			CTTTTGAGGTCAT	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.2498T>C	chr2.hg19:g.219328058A>G	ENSP00000258399:p.Leu833Pro	99.0	0.0	.		87.0	5.0	.	NM_020935	A2RUQ8|B7ZM38|B7ZM41|E9PHL3|Q2KHT2|Q53S10|Q7Z3A5|Q9HCH8	Missense_Mutation	SNP	ENST00000258399.3	hg19	CCDS2418.1	.	.	.	.	.	.	.	.	.	.	A	16.55	3.154173	0.57259	.	.	ENSG00000135913	ENST00000258399;ENST00000454775;ENST00000415516;ENST00000418019	T;T;T;T	0.55588	0.55;0.55;0.51;0.55	4.77	4.77	0.60923	Ubiquitin interacting motif (3);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.127314	0.53938	D	0.000041	T	0.65678	0.2714	L	0.59436	1.845	0.80722	D	1	D;D	0.62365	0.989;0.991	P;P	0.61658	0.892;0.881	T	0.68401	-0.5418	10	0.56958	D	0.05	-2.9498	14.7551	0.69557	1.0:0.0:0.0:0.0	.	739;833	Q86T82-2;Q86T82	.;UBP37_HUMAN	P	833;833;739;833	ENSP00000258399:L833P;ENSP00000393662:L833P;ENSP00000400902:L739P;ENSP00000396585:L833P	ENSP00000258399:L833P	L	-	2	0	USP37	219036302	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.305000	0.89960	2.127000	0.65507	0.477000	0.44152	CTC	.	.	.	none		0.318	USP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256779.3	NM_020935		G	219328058	A	G	219328058	3	3	46	1	0	0	0	0	1	0	0	0	17080	304	11	3	461	3	USP37	2	219328058	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	69492562	219328058	23871315	13	3205											
PTPRN	5798	hgsc.bcm.edu	37	chr2	220161767	220161767	+	Missense_Mutation	SNP	A	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	ctccccctgcgcggtggcacAggtgtttggctctgcttggt	2	12	14	13	2	1	0	0	0	1	0	2	0	2	0	2	5	2	4	2	5	0	2			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr2:220161767A>C	ENST00000295718.2	-	15	2416	c.2176T>G	c.(2176-2178)Tgt>Ggt	p.C726G	PTPRN_ENST00000423636.2_Missense_Mutation_p.C636G|PTPRN_ENST00000497977.1_5'Flank|PTPRN_ENST00000409251.3_Missense_Mutation_p.C697G|MIR153-1_ENST00000384914.1_RNA|AC114803.3_ENST00000417355.1_RNA	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	726	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		GCGGTGGCACAGGTGTTTGGC	0.637																																					p.C726G		Atlas-SNP	.											.	PTPRN	138	.	0			c.T2176G						PASS	.						95	99	98					2																	220161767		2203	4300	6503	SO:0001583	missense	5798	exon15			TGGCACAGGTGTT		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.2176T>G	chr2.hg19:g.220161767A>C	ENSP00000295718:p.Cys726Gly	80.0	0.0	.		75.0	21.0	.	NM_002846	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Missense_Mutation	SNP	ENST00000295718.2	hg19	CCDS2440.1	.	.	.	.	.	.	.	.	.	.	A	12.22	1.872163	0.33069	.	.	ENSG00000054356	ENST00000409251;ENST00000295718;ENST00000539342;ENST00000537666	T;T;T	0.14516	2.5;2.5;2.5	4.31	4.31	0.51392	Protein-tyrosine phosphatase, receptor/non-receptor type (2);	0.250911	0.35179	N	0.003398	T	0.24044	0.0582	M	0.67397	2.05	0.39123	D	0.961697	D;B	0.60160	0.987;0.081	P;B	0.51385	0.668;0.078	T	0.06409	-1.0828	10	0.33940	T	0.23	.	13.3146	0.60399	1.0:0.0:0.0:0.0	.	697;726	Q6NSL1;Q16849	.;PTPRN_HUMAN	G	697;726;697;636	ENSP00000386638:C697G;ENSP00000295718:C726G;ENSP00000444244:C636G	ENSP00000295718:C726G	C	-	1	0	PTPRN	219870011	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.355000	0.52262	1.806000	0.52798	0.379000	0.24179	TGT	.	.	.	none		0.637	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2			C	220161767	A	C	220161767	3	2	46	1	0	0	0	0	1	0	0	0	12820	188	7	5	799	5	PTPRN	2	220161767	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	833709	220161767	23037606	14	3206											
COL6A3	1293	hgsc.bcm.edu	37	chr2	238275884	238275884	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaaactgtccctcctgaagTtgatggaaccatccaacagg	12	8	10	11	0	0	2	0	2	0	0	3	4	3	4	4	3	3	1	4	3	4	1			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr2:238275884T>C	ENST00000295550.4	-	11	5398	c.4946A>G	c.(4945-4947)aAc>aGc	p.N1649S	COL6A3_ENST00000346358.4_Missense_Mutation_p.N1449S|COL6A3_ENST00000347401.3_Missense_Mutation_p.N1448S|COL6A3_ENST00000353578.4_Missense_Mutation_p.N1443S|COL6A3_ENST00000472056.1_Missense_Mutation_p.N1042S|COL6A3_ENST00000409809.1_Missense_Mutation_p.N1443S	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1649	Nonhelical region.|VWFA 9. {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)		CCTCCTGAAGTTGATGGAACC	0.438																																					p.N1649S		Atlas-SNP	.											.	COL6A3	608	.	0			c.A4946G						PASS	.						73	64	67					2																	238275884		2203	4300	6503	SO:0001583	missense	1293	exon11			CTGAAGTTGATGG	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.4946A>G	chr2.hg19:g.238275884T>C	ENSP00000295550:p.Asn1649Ser	60.0	0.0	.		52.0	9.0	.	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	T	13.60	2.285417	0.40394	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	T;T;T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.66;-0.66;-0.66	5.5	5.5	0.81552	von Willebrand factor, type A (3);	0.000000	0.64402	D	0.000018	T	0.65217	0.2670	N	0.05031	-0.125	0.46654	D	0.999143	D;D;D	0.76494	0.999;0.999;0.998	D;D;D	0.87578	0.998;0.998;0.953	T	0.62469	-0.6848	10	0.02654	T	1	.	15.5966	0.76587	0.0:0.0:0.0:1.0	.	1042;1443;1649	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	S	1649;1448;1443;1042;1443;1449	ENSP00000295550:N1649S;ENSP00000315609:N1448S;ENSP00000315873:N1443S;ENSP00000418285:N1042S;ENSP00000386844:N1443S;ENSP00000295546:N1449S	ENSP00000295550:N1649S	N	-	2	0	COL6A3	237940623	1.000000	0.71417	0.994000	0.49952	0.786000	0.44442	4.105000	0.57797	2.080000	0.62538	0.533000	0.62120	AAC	.	.	.	none		0.438	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		C	238275884	T	C	238275884	3	2	46	1	0	0	0	0	1	0	0	0	3703	1725	60	3	4723	3	COL6A3	2	238275884	Missense_Mutation	SNP	T	TCGA-A4-7585-01A-11D-2136-08	18114117	238275884	4923489	15	3207											
SETD5	55209	hgsc.bcm.edu	37	chr3	9512542	9512542	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagacctctctcgtggatccTtgtcacctggtggtgaaagg	8	11	12	10	1	2	2	1	1	1	1	5	3	3	3	3	4	0	0	3	4	2	1			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr3:9512542T>C	ENST00000406341.1	+	18	3314	c.3124T>C	c.(3124-3126)Ttg>Ctg	p.L1042L	SETD5_ENST00000302463.6_Silent_p.L944L|SETD5_ENST00000407969.1_Silent_p.L1061L|SETD5_ENST00000402466.1_Silent_p.L944L|SETD5_ENST00000402198.1_Silent_p.L1042L			Q9C0A6	SETD5_HUMAN	SET domain containing 5	1042										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)		TCGTGGATCCTTGTCACCTGG	0.478																																					p.L1042L		Atlas-SNP	.											.	SETD5	210	.	0			c.T3124C						PASS	.						24	23	23					3																	9512542		1861	4094	5955	SO:0001819	synonymous_variant	55209	exon19			GGATCCTTGTCAC	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.3124T>C	chr3.hg19:g.9512542T>C		24.0	0.0	.		25.0	4.0	.	NM_001080517	Q6AI17|Q8WUB6|Q9H3X4|Q9H6V7|Q9H7S3|Q9NVI9	Silent	SNP	ENST00000406341.1	hg19	CCDS46741.1	.	.	.	.	.	.	.	.	.	.	T	8.531	0.871085	0.17322	.	.	ENSG00000168137	ENST00000399686;ENST00000421188	.	.	.	5.51	-0.229	0.13094	.	0.261170	0.47093	D	0.000242	T	0.54367	0.1854	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45673	-0.9245	5	.	.	.	-3.3658	8.5026	0.33168	0.5133:0.3613:0.0:0.1253	.	.	.	.	P	709;372	.	.	L	+	2	0	SETD5	9487542	1.000000	0.71417	0.999000	0.59377	0.979000	0.70002	1.768000	0.38511	0.028000	0.15324	-0.649000	0.03915	CTT	.	.	.	none		0.478	SETD5-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318425.1	XM_371614		C	9512542	T	C	9512542	2	2	46	1	0	0	0	0	0	0	0	1	14147	1606	56	3		3	SETD5	3	9512542	Silent	SNP	T	TCGA-A4-7585-01A-11D-2136-08		9512542	188509888	16	3208											
CAPN7	23473	hgsc.bcm.edu	37	chr3	15262464	15262464	+	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	tgcacaaggacagagatacaCagcagaagaaatagaagtac	20	4	10	7	0	0	4	0	0	0	4	0	6	0	5	0	1	4	3	0	1	7	3			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr3:15262464C>T	ENST00000253693.2	+	5	867	c.614C>T	c.(613-615)aCa>aTa	p.T205I		NM_014296.2	NP_055111.1	Q9Y6W3	CAN7_HUMAN	calpain 7	205					positive regulation of epithelial cell migration (GO:0010634)|self proteolysis (GO:0097264)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|endopeptidase activity (GO:0004175)|MIT domain binding (GO:0090541)			breast(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|skin(2)	22						CAGAGATACACAGCAGAAGAA	0.363																																					p.T205I		Atlas-SNP	.											.	CAPN7	63	.	0			c.C614T						PASS	.						59	59	59					3																	15262464		2203	4300	6503	SO:0001583	missense	23473	exon5			GATACACAGCAGA	AB028639	CCDS2624.1	3p24	2008-07-18			ENSG00000131375	ENSG00000131375			1484	protein-coding gene	gene with protein product	"calpain like protease", "homolog of Aspergillus Nidulans PALB"	606400				8163008, 10051333	Standard	NM_014296		Approved	PalBH	uc003bzn.3	Q9Y6W3	OTTHUMG00000129863	ENST00000253693.2:c.614C>T	chr3.hg19:g.15262464C>T	ENSP00000253693:p.Thr205Ile	51.0	0.0	.		65.0	16.0	.	NM_014296		Missense_Mutation	SNP	ENST00000253693.2	hg19	CCDS2624.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.640356	0.87859	.	.	ENSG00000131375	ENST00000253693	T	0.43294	0.95	5.79	4.92	0.64577	.	0.109635	0.64402	D	0.000008	T	0.59959	0.2232	M	0.81802	2.56	0.58432	D	0.999998	D	0.62365	0.991	P	0.56823	0.807	T	0.65092	-0.6252	10	0.54805	T	0.06	-9.0239	12.9819	0.58568	0.0:0.9247:0.0:0.0753	.	205	Q9Y6W3	CAN7_HUMAN	I	205	ENSP00000253693:T205I	ENSP00000253693:T205I	T	+	2	0	CAPN7	15237468	1.000000	0.71417	0.555000	0.28281	0.997000	0.91878	7.223000	0.78033	1.465000	0.48006	0.555000	0.69702	ACA	.	.	.	none		0.363	CAPN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252105.2	NM_014296		T	15262464	C	T	15262464	3	4	46	1	0	0	0	0	1	0	0	0	2633	478	17	2	632	2	CAPN7	3	15262464	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	5749922	15262464	182759966	17	3209											
EXOSC7	23016	hgsc.bcm.edu	37	chr3	45048921	45048921	+	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	tgcctttgcagattggctatCggcatgtggtggatgctact	6	14	13	8	1	0	1	0	0	0	1	1	2	0	2	1	4	4	4	1	4	2	4			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr3:45048921C>T	ENST00000265564.7	+	7	673	c.625C>T	c.(625-627)Cgg>Tgg	p.R209W	CLEC3B_ENST00000490386.1_Intron|EXOSC7_ENST00000461361.1_3'UTR	NM_015004.3	NP_055819.2	Q15024	EXOS7_HUMAN	exosome component 7	209					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 catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|RNA binding (GO:0003723)			endometrium(3)|large_intestine(1)|lung(3)	7				BRCA - Breast invasive adenocarcinoma(193;0.00911)|KIRC - Kidney renal clear cell carcinoma(197;0.0509)|Kidney(197;0.064)		GATTGGCTATCGGCATGTGGT	0.612																																					p.R209W		Atlas-SNP	.											.	EXOSC7	19	.	0			c.C625T						PASS	.						62	53	56					3																	45048921		2203	4300	6503	SO:0001583	missense	23016	exon7			GGCTATCGGCATG	BC012831	CCDS2725.1	3p21.32	2010-05-07			ENSG00000075914	ENSG00000075914	3.1.13.-		28112	protein-coding gene	gene with protein product		606488				11719186, 11812149	Standard	NR_023353		Approved	hRrp42p, Rrp42p, RRP42, EAP1, KIAA0116, p8	uc003coi.2	Q15024	OTTHUMG00000133095	ENST00000265564.7:c.625C>T	chr3.hg19:g.45048921C>T	ENSP00000265564:p.Arg209Trp	57.0	0.0	.		31.0	10.0	.	NM_015004	Q96E72	Missense_Mutation	SNP	ENST00000265564.7	hg19	CCDS2725.1	.	.	.	.	.	.	.	.	.	.	C	19.72	3.879280	0.72294	.	.	ENSG00000075914	ENST00000265564	T	0.44482	0.92	5.77	4.82	0.62117	Exoribonuclease, phosphorolytic domain 2 (1);	0.000000	0.85682	D	0.000000	T	0.62974	0.2472	M	0.81802	2.56	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.66716	0.946;0.946	T	0.62525	-0.6836	10	0.38643	T	0.18	-14.1235	13.4903	0.61390	0.2342:0.7658:0.0:0.0	.	209;209	B2RDZ9;Q15024	.;EXOS7_HUMAN	W	209	ENSP00000265564:R209W	ENSP00000265564:R209W	R	+	1	2	EXOSC7	45023925	0.964000	0.33143	0.994000	0.49952	0.991000	0.79684	2.331000	0.43894	2.723000	0.93209	0.655000	0.94253	CGG	.	.	.	none		0.612	EXOSC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256754.2	NM_015004		T	45048921	C	T	45048921	3	4	46	1	0	0	0	0	1	0	0	0	5321	875	31	1	651	1	EXOSC7	3	45048921	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	29786457	45048921	152973509	18	3210											
TREX1	11277	hgsc.bcm.edu	37	chr3	48508760	48508760	+	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	tcaggcccatgtatggggtcAcagcctctgctaggaccaag	9	8	12	12	0	3	0	2	0	1	0	3	1	3	1	3	4	2	2	3	4	3	2			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr3:48508760A>T	ENST00000422277.2	+	1	1532	c.871A>T	c.(871-873)Aca>Tca	p.T291S	SHISA5_ENST00000465449.1_5'Flank|TREX1_ENST00000492235.1_3'UTR|TREX1_ENST00000444177.1_Missense_Mutation_p.T226S|TREX1_ENST00000456089.1_Missense_Mutation_p.T97S|TREX1_ENST00000433541.1_Missense_Mutation_p.T97S|TREX1_ENST00000436480.2_Missense_Mutation_p.T236S|TREX1_ENST00000296443.9_Missense_Mutation_p.T236S	NM_016381.4	NP_057465.1	Q9NSU2	TREX1_HUMAN	three prime repair exonuclease 1	291	Necessary for endoplasmic reticulum localization. {ECO:0000250}.				cell death (GO:0008219)|cellular response to interferon-beta (GO:0035458)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|innate immune response (GO:0045087)|mismatch repair (GO:0006298)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	endoplasmic reticulum membrane (GO:0005789)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|3'-5'-exodeoxyribonuclease activity (GO:0008296)|adenyl deoxyribonucleotide binding (GO:0032558)|double-stranded DNA binding (GO:0003690)|exodeoxyribonuclease III activity (GO:0008853)|metal ion binding (GO:0046872)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein homodimerization activity (GO:0042803)|single-stranded DNA binding (GO:0003697)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|skin(3)	9				BRCA - Breast invasive adenocarcinoma(193;0.000286)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		GTATGGGGTCACAGCCTCTGC	0.617																																					p.T291S		Atlas-SNP	.											.	TREX1	17	.	0			c.A871T	GRCh37	CI075712	TREX1	I		PASS	.						97	83	88					3																	48508760		2203	4300	6503	SO:0001583	missense	11277	exon1			GGGGTCACAGCCT	AF151105	CCDS2769.1, CCDS59451.1	3p21.31	2014-09-17			ENSG00000213689	ENSG00000213689			12269	protein-coding gene	gene with protein product		606609	"Aicardi-Goutieres syndrome 1"	AGS1		10391904, 10393201, 16845398	Standard	NM_033629		Approved	DRN3	uc010hka.4	Q9NSU2	OTTHUMG00000156205	ENST00000422277.2:c.871A>T	chr3.hg19:g.48508760A>T	ENSP00000390478:p.Thr291Ser	101.0	0.0	.		93.0	12.0	.	NM_016381	B2RCN9|Q8TEU2|Q9BPW1|Q9Y4X2	Missense_Mutation	SNP	ENST00000422277.2	hg19	CCDS43086.1	.	.	.	.	.	.	.	.	.	.	A	19.05	3.752702	0.69533	.	.	ENSG00000213689	ENST00000296443;ENST00000433541;ENST00000436480;ENST00000422277;ENST00000444177;ENST00000456089	T;T;T;T;T;T	0.47528	1.49;0.84;1.49;1.44;1.49;0.84	5.1	-6.21	0.02065	.	.	.	.	.	T	0.32010	0.0815	L	0.54323	1.7	0.09310	N	1	B	0.24426	0.103	B	0.19391	0.025	T	0.34304	-0.9834	9	0.10902	T	0.67	.	6.7824	0.23654	0.2855:0.3313:0.3832:0.0	.	291	Q9NSU2	TREX1_HUMAN	S	236;97;236;291;226;97	ENSP00000296443:T236S;ENSP00000412404:T97S;ENSP00000392569:T236S;ENSP00000390478:T291S;ENSP00000415972:T226S;ENSP00000411331:T97S	ENSP00000296443:T236S	T	+	1	0	TREX1	48483764	0.000000	0.05858	0.000000	0.03702	0.852000	0.48524	-0.417000	0.07088	-1.057000	0.03201	0.459000	0.35465	ACA	.	.	.	none		0.617	TREX1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_016381		T	48508760	A	T	48508760	3	4	46	1	0	0	0	0	1	0	0	0	16488	159	6	5	873	5	TREX1	3	48508760	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	3459839	48508760	149513670	19	3211											
VPS8	23355	hgsc.bcm.edu	37	chr3	184700420	184700420	+	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	tgtccagttcagccattcctCatctacactctgaaggtaag	10	12	7	12	0	4	1	2	1	2	0	6	1	6	1	3	1	2	2	3	1	3	4			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr3:184700420C>T	ENST00000437079.3	+	41	3658	c.3487C>T	c.(3487-3489)Cat>Tat	p.H1163Y	VPS8_ENST00000436792.2_Missense_Mutation_p.H1161Y|VPS8_ENST00000446204.2_Missense_Mutation_p.H1071Y|VPS8_ENST00000287546.4_Missense_Mutation_p.H1163Y	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	1163							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)			AGCCATTCCTCATCTACACTC	0.393																																					p.H1163Y		Atlas-SNP	.											.	VPS8	109	.	0			c.C3487T						PASS	.						81	71	75					3																	184700420		1894	4126	6020	SO:0001583	missense	23355	exon40			ATTCCTCATCTAC	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.3487C>T	chr3.hg19:g.184700420C>T	ENSP00000397879:p.His1163Tyr	65.0	0.0	.		71.0	13.0	.	NM_001009921	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Missense_Mutation	SNP	ENST00000437079.3	hg19	CCDS46971.1	.	.	.	.	.	.	.	.	.	.	C	0.295	-0.977536	0.02197	.	.	ENSG00000156931	ENST00000287546;ENST00000437079;ENST00000436792;ENST00000446204	T;T;T;T	0.17854	2.25;2.25;2.25;2.25	6.05	6.05	0.98169	.	0.769709	0.13007	N	0.421217	T	0.17789	0.0427	L	0.38175	1.15	0.24222	N	0.995432	B;B;B	0.13145	0.0;0.007;0.0	B;B;B	0.19391	0.0;0.025;0.001	T	0.09684	-1.0663	10	0.62326	D	0.03	-11.998	13.6828	0.62496	0.0:0.8456:0.1544:0.0	.	1163;1071;1161	Q8N3P4;Q8N3P4-2;Q8N3P4-3	VPS8_HUMAN;.;.	Y	1163;1163;1161;1071	ENSP00000287546:H1163Y;ENSP00000397879:H1163Y;ENSP00000404704:H1161Y;ENSP00000405483:H1071Y	ENSP00000287546:H1163Y	H	+	1	0	VPS8	186183114	0.126000	0.22350	0.812000	0.32479	0.520000	0.34377	1.477000	0.35431	2.878000	0.98634	0.650000	0.86243	CAT	.	.	.	none		0.393	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015303		T	184700420	C	T	184700420	3	4	46	1	0	0	0	0	1	0	0	0	17230	826	29	2	3641	2	VPS8	3	184700420	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	136191660	184700420	13322010	20	3212											
ABCG2	9429	hgsc.bcm.edu	37	chr4	89042889	89042889	+	Missense_Mutation	SNP	A	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	cagtgataagctccattcctAtactagtcctttttctttct	8	18	4	11	0	2	1	0	1	2	0	5	1	5	1	3	0	2	1	3	0	4	8			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr4:89042889A>C	ENST00000237612.3	-	6	1132	c.587T>G	c.(586-588)aTa>aGa	p.I196R	ABCG2_ENST00000515655.1_Missense_Mutation_p.I196R	NM_004827.2	NP_004818.2	Q9UNQ0	ABCG2_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 2 (Junior blood group)	196	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular iron ion homeostasis (GO:0006879)|drug export (GO:0046618)|drug transmembrane transport (GO:0006855)|embryonic process involved in female pregnancy (GO:0060136)|heme transport (GO:0015886)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(13)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Afatinib(DB08916)|Apixaban(DB06605)|Buprenorphine(DB00921)|Cabazitaxel(DB06772)|Carboplatin(DB00958)|Cisplatin(DB00515)|Cladribine(DB00242)|Clofarabine(DB00631)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gefitinib(DB00317)|Glyburide(DB01016)|Hesperetin(DB01094)|Hydrocortisone(DB00741)|Imatinib(DB00619)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Methotrexate(DB00563)|Mitoxantrone(DB01204)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Nilotinib(DB04868)|Nitrofurantoin(DB00698)|Novobiocin(DB01051)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Prazosin(DB00457)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Teniposide(DB00444)|Teriflunomide(DB08880)|Testosterone(DB00624)|Topotecan(DB01030)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vincristine(DB00541)|Vismodegib(DB08828)|Zafirlukast(DB00549)|Zidovudine(DB00495)	CTCCATTCCTATACTAGTCCT	0.398																																					p.I196R		Atlas-SNP	.											.	ABCG2	151	.	0			c.T587G						PASS	.						154	147	149					4																	89042889		2203	4300	6503	SO:0001583	missense	9429	exon6			ATTCCTATACTAG	AF103796	CCDS3628.1, CCDS58910.1	4q22.1	2014-08-27	2014-08-27		ENSG00000118777	ENSG00000118777		"CD molecules", "ATP binding cassette transporters / subfamily G"	74	protein-coding gene	gene with protein product		603756	"ATP-binding cassette, sub-family G (WHITE), member 2"			8894702, 9861027	Standard	NM_001257386		Approved	EST157481, MXR, BCRP, ABCP, CD338	uc003hrg.3	Q9UNQ0	OTTHUMG00000130601	ENST00000237612.3:c.587T>G	chr4.hg19:g.89042889A>C	ENSP00000237612:p.Ile196Arg	70.0	0.0	.		75.0	13.0	.	NM_004827	A0A1W3|A8K1T5|O95374|Q4W5I3|Q53ZQ1|Q569L4|Q5YLG4|Q86V64|Q8IX16|Q96LD6|Q96TA8|Q9BY73|Q9NUS0	Missense_Mutation	SNP	ENST00000237612.3	hg19	CCDS3628.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.478150	0.84747	.	.	ENSG00000118777	ENST00000515655;ENST00000237612	D;D	0.96168	-3.93;-3.93	5.55	5.55	0.83447	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.98601	0.9532	H	0.97240	3.965	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	0.99755	1.1019	10	0.87932	D	0	-42.7755	15.3809	0.74654	1.0:0.0:0.0:0.0	.	196;196;196	Q9UNQ0-2;Q9UNQ0;Q4W5I3	.;ABCG2_HUMAN;.	R	196	ENSP00000426917:I196R;ENSP00000237612:I196R	ENSP00000237612:I196R	I	-	2	0	ABCG2	89261913	1.000000	0.71417	0.984000	0.44739	0.893000	0.52053	8.948000	0.93006	2.117000	0.64856	0.533000	0.62120	ATA	.	.	.	none		0.398	ABCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253051.1	NM_004827		C	89042889	A	C	89042889	3	2	46	1	0	0	0	0	1	0	0	0	69	449	16	5	1424	5	ABCG2	4	89042889	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08		89042889	102111387	21	3213											
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123156097	123156097	+	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	cattttcaagcacaagtgcaGagtctgatatgtattatgga	13	13	9	6	0	2	2	1	1	1	1	2	3	2	3	0	1	2	3	0	1	5	5			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr4:123156097G>T	ENST00000264501.4	+	27	3866	c.3493G>T	c.(3493-3495)Gag>Tag	p.E1165*	KIAA1109_ENST00000455637.1_Nonsense_Mutation_p.E1165*|KIAA1109_ENST00000388738.3_Nonsense_Mutation_p.E1165*|KIAA1109_ENST00000495260.1_3'UTR			Q2LD37	K1109_HUMAN	KIAA1109	1165					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CACAAGTGCAGAGTCTGATAT	0.393																																					p.E1165X		Atlas-SNP	.											.	KIAA1109	424	.	0			c.G3493T						PASS	.						109	106	107					4																	123156097		1863	4108	5971	SO:0001587	stop_gained	84162	exon25			AGTGCAGAGTCTG	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.3493G>T	chr4.hg19:g.123156097G>T	ENSP00000264501:p.Glu1165*	102.0	0.0	.		107.0	25.0	.	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Nonsense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	39|39	7.713265|7.713265	0.98447|0.98447	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637|ENST00000424425	.|.	.|.	.|.	5.14|5.14	5.14|5.14	0.70334|0.70334	.|.	0.138537|.	0.28067|.	U|.	0.016735|.	.|T	.|0.74612	.|0.3739	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73956	.|-0.3819	.|3	0.14656|.	T|.	0.56|.	.|.	18.61|18.61	0.91281|0.91281	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|I	1165|996	.|.	ENSP00000264501:E1165X|.	E|R	+|+	1|2	0|0	KIAA1109|KIAA1109	123375547|123375547	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.981000|0.981000	0.71138|0.71138	9.147000|9.147000	0.94646|0.94646	2.391000|2.391000	0.81399|0.81399	0.563000|0.563000	0.77884|0.77884	GAG|AGA	.	.	.	none		0.393	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		T	123156097	G	T	123156097	4	4	46	1	0	0	0	0	0	1	0	0	8215	943	33	4	3591	4	KIAA1109	4	123156097	Nonsense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08	34113208	123156097	67998179	22	3214											
PCDH18	54510	hgsc.bcm.edu	37	chr4	138452043	138452043	+	Frame_Shift_Del	DEL	A	A	-																															agtttaaagtgaccatgtccAtgaagcttacaaactatttc																										TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr4:138452043delA	ENST00000344876.4	-	1	1586	c.1200delT	c.(1198-1200)catfs	p.H400fs	PCDH18_ENST00000507846.1_Frame_Shift_Del_p.H180fs|PCDH18_ENST00000412923.2_Frame_Shift_Del_p.H400fs|PCDH18_ENST00000510305.1_Intron|PCDH18_ENST00000511115.1_Intron	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	400	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					GACCATGTCCATGAAGCTTAC	0.348																																					p.G401fs		Atlas-INDEL	.											.	PCDH18	229	.	0			c.1201delG						PASS	.						100	106	104					4																	138452043		2203	4300	6503	SO:0001589	frameshift_variant	54510	exon1			.	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.1200delT	chr4.hg19:g.138452043delA	ENSP00000355082:p.His400fs	80.0	0.0	0		88.0	13.0	0.147727	NM_019035	A8K7K3|B7ZKT1|Q52LS2	Frame_Shift_Del	DEL	ENST00000344876.4	hg19	CCDS34064.1																																																																																			.	.	.	none		0.348	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		-	138452043	A	-	138452043	7	5	46	1	0	1	0	1	0	0	0	0	11520	214	8	0	2223	0	PCDH18	4	138452043	Frame_Shift_Del	DEL	A	TCGA-A4-7585-01A-11D-2136-08	15295946	138452043	52702233	23	3215											
FASTKD3	79072	hgsc.bcm.edu	37	chr5	7867621	7867621	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcagcaacaggctactttgAggatccacatgcaacagaat	14	9	8	10	0	1	2	1	1	0	1	2	3	2	3	1	2	5	3	1	2	4	3			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr5:7867621A>G	ENST00000264669.5	-	2	712	c.576T>C	c.(574-576)ccT>ccC	p.P192P	MTRR_ENST00000440940.2_5'Flank|MTRR_ENST00000502509.1_Intron|MTRR_ENST00000264668.2_5'Flank|FASTKD3_ENST00000513658.1_Intron|MTRR_ENST00000341013.6_5'Flank	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	192					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						GGCTACTTTGAGGATCCACAT	0.443																																					p.P192P		Atlas-SNP	.											.	FASTKD3	88	.	0			c.T576C						PASS	.						90	90	90					5																	7867621		2203	4300	6503	SO:0001819	synonymous_variant	79072	exon2			ACTTTGAGGATCC	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.576T>C	chr5.hg19:g.7867621A>G		130.0	0.0	.		180.0	23.0	.	NM_024091	Q9BVD3	Silent	SNP	ENST00000264669.5	hg19	CCDS3873.1																																																																																			.	.	.	none		0.443	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091		G	7867621	A	G	7867621	2	3	46	1	0	0	0	0	0	0	0	1	5694	291	11	3		3	FASTKD3	5	7867621	Silent	SNP	A	TCGA-A4-7585-01A-11D-2136-08		7867621	173047639	24	3216											
ADAMTS6	11174	hgsc.bcm.edu	37	chr5	64537954	64537954	+	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	1	0	0	0	0	0	0	cagtatagggtttccagttaTaatactttcctcggaaaggc	11	13	9	8	1	0	0	0	0	0	0	3	1	2	1	2	3	1	3	2	3	6	7			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr5:64537954T>G								ADAMTS6 (43362 upstream) : ADAMTS6 (55080 downstream)																							TTTCCAGTTATAATACTTTCC	0.358																																					p.Y637S		Atlas-SNP	.											.	ADAMTS6	174	.	0			c.A1910C						PASS	.						97	101	100					5																	64537954		2203	4300	6503	SO:0001628	intergenic_variant	11174	exon15			CAGTTATAATACT																													chr5.hg19:g.64537954T>G		67.0	0.0	.		79.0	4.0	.	NM_197941		Missense_Mutation	SNP		hg19		.	.	.	.	.	.	.	.	.	.	T	16.74	3.205533	0.58234	.	.	ENSG00000049192	ENST00000381055;ENST00000261306;ENST00000464680	T;T	0.06608	3.28;7.39	5.62	5.62	0.85841	.	0.054793	0.85682	D	0.000000	T	0.12305	0.0299	M	0.71871	2.18	0.80722	D	1	B;B	0.22346	0.068;0.008	B;B	0.24848	0.056;0.034	T	0.01349	-1.1378	10	0.72032	D	0.01	.	15.8202	0.78633	0.0:0.0:0.0:1.0	.	637;637	D6R9L6;Q9UKP5	.;ATS6_HUMAN	S	637;587;637	ENSP00000370443:Y637S;ENSP00000423551:Y637S	ENSP00000261306:Y587S	Y	-	2	0	ADAMTS6	64573710	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.581000	0.82535	2.139000	0.66308	0.460000	0.39030	TAT	.	.	.	none	0	0.358									G	64537954	T	G	64537954	1	3	46	0	1	0	0	0	0	0	0	0	270	1406	49	5		5	ADAMTS6	5	64537954	IGR	SNP	T	TCGA-A4-7585-01A-11D-2136-08	56670333	64537954	116377306	25	3217											
SPATA9	83890	hgsc.bcm.edu	37	chr5	94994451	94994451	+	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	ctggcttctccggcaatgacCtataaggttttgctttgatt	7	16	9	9	1	1	2	0	2	1	0	2	2	1	2	2	3	1	4	2	3	3	7			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr5:94994451C>G	ENST00000274432.8	-	5	782	c.641G>C	c.(640-642)aGg>aCg	p.R214T	RFESD_ENST00000508206.1_Intron|SPATA9_ENST00000477047.2_Intron	NM_031952.3	NP_114158.2	Q9BWV2	SPAT9_HUMAN	spermatogenesis associated 9	214					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)		CGGCAATGACCTATAAGGTTT	0.403																																					p.R214T		Atlas-SNP	.											.	SPATA9	17	.	0			c.G641C						PASS	.						102	98	99					5																	94994451		2203	4299	6502	SO:0001583	missense	83890	exon5			AATGACCTATAAG	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.641G>C	chr5.hg19:g.94994451C>G	ENSP00000274432:p.Arg214Thr	51.0	0.0	.		62.0	10.0	.	NM_031952	A8K8H3|Q4G122|Q86X33|Q8NA28	Missense_Mutation	SNP	ENST00000274432.8	hg19	CCDS4076.1	.	.	.	.	.	.	.	.	.	.	C	10.93	1.491277	0.26774	.	.	ENSG00000145757	ENST00000274432	T	0.31510	1.49	5.37	5.37	0.77165	.	0.173364	0.39985	N	0.001210	T	0.31857	0.0810	L	0.27053	0.805	0.80722	D	1	P	0.51351	0.944	P	0.49999	0.628	T	0.02214	-1.1194	10	0.54805	T	0.06	-9.9082	14.4904	0.67647	0.0:1.0:0.0:0.0	.	214	Q9BWV2	SPAT9_HUMAN	T	214	ENSP00000274432:R214T	ENSP00000274432:R214T	R	-	2	0	SPATA9	95020207	1.000000	0.71417	1.000000	0.80357	0.026000	0.11368	2.187000	0.42602	2.808000	0.96608	0.650000	0.86243	AGG	.	.	.	none		0.403	SPATA9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304036.1	NM_031952		G	94994451	C	G	94994451	3	3	46	1	0	0	0	0	1	0	0	0	15028	681	24	4	127	4	SPATA9	5	94994451	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	30456497	94994451	85920809	26	3218											
SEC24A	10802	hgsc.bcm.edu	37	chr5	133997149	133997160	+	In_Frame_Del	DEL	CTCACAAACAAA	CTCACAAACAAA	-																															tataactatccatccacagcCtcacaaacaaaccattgtcc																										TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	CTCACAAACAAA	CTCACAAACAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr5:133997149_133997160delCTCACAAACAAA	ENST00000398844.2	+	2	726_737	c.438_449delCTCACAAACAAA	c.(436-450)gcctcacaaacaaac>gcc	p.SQTN147del	SEC24A_ENST00000322887.4_In_Frame_Del_p.SQTN147del	NM_021982.2	NP_068817.1	O95486	SC24A_HUMAN	SEC24 family member A	147	Pro-rich.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of protein secretion (GO:0050714)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045714)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	36			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CATCCACAGCCTCACAAACAAACCATTGTCCT	0.415																																					p.146_150del		Atlas-INDEL	.											.	SEC24A	77	.	0			c.437_448del						PASS	.																																			SO:0001651	inframe_deletion	10802	exon2			.	AJ131244	CCDS43363.1, CCDS58967.1	5q31.1	2013-10-21	2013-10-21		ENSG00000113615	ENSG00000113615			10703	protein-coding gene	gene with protein product		607183	"SEC24 (S. cerevisiae) related gene family, member A", "SEC24 family, member A (S. cerevisiae)"			10075675, 10329445	Standard	NM_021982		Approved		uc003kzs.3	O95486	OTTHUMG00000163064	ENST00000398844.2:c.438_449delCTCACAAACAAA	chr5.hg19:g.133997149_133997160delCTCACAAACAAA	ENSP00000381823:p.Ser147_Asn150del	108.0	0.0	0		104.0	12.0	0.115385	NM_021982	A8MVW3|Q8WUV2|Q96GP7	In_Frame_Del	DEL	ENST00000398844.2	hg19	CCDS43363.1																																																																																			.	.	.	none		0.415	SEC24A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371563.1			-	133997160	CTCACAAACAAA	-	133997149	7	5	46	1	0	1	0	1	0	0	0	0	14007	668	24	0	444	0	SEC24A	5	133997149	In_Frame_Del	DEL	CTCACAAACAAA	TCGA-A4-7585-01A-11D-2136-08	39002698	133997149	46918111	27	3219											
SLC36A2	153201	hgsc.bcm.edu	37	chr5	150701645	150701645	+	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	cgaggcgaatggacagatccAgaggcagtgcccagcgtgtt	10	6	15	10	3	0	2	0	0	0	2	1	5	1	3	2	3	2	2	2	3	1	1			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr5:150701645A>T	ENST00000335244.4	-	9	1271	c.1142T>A	c.(1141-1143)cTg>cAg	p.L381Q	SLC36A2_ENST00000450886.1_Missense_Mutation_p.L105Q|SLC36A2_ENST00000521967.1_Missense_Mutation_p.L381Q	NM_181776.2	NP_861441.2	Q495M3	S36A2_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 2	381					amino acid transport (GO:0006865)|ion transport (GO:0006811)|proline transmembrane transport (GO:0035524)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine transmembrane transporter activity (GO:0015187)|hydrogen:amino acid symporter activity (GO:0005280)|L-alanine transmembrane transporter activity (GO:0015180)|L-proline transmembrane transporter activity (GO:0015193)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(14)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Cycloserine(DB00260)	GGACAGATCCAGAGGCAGTGC	0.542																																					p.L381Q		Atlas-SNP	.											.	SLC36A2	71	.	0			c.T1142A						PASS	.						138	127	131					5																	150701645		2203	4300	6503	SO:0001583	missense	153201	exon9			AGATCCAGAGGCA	AY162214	CCDS4315.1	5q33.1	2013-05-22			ENSG00000186335	ENSG00000186335		"Solute carriers"	18762	protein-coding gene	gene with protein product		608331				11959859	Standard	NM_181776		Approved	PAT2, tramdorin, TRAMD1	uc003lty.3	Q495M3	OTTHUMG00000130129	ENST00000335244.4:c.1142T>A	chr5.hg19:g.150701645A>T	ENSP00000334223:p.Leu381Gln	130.0	0.0	.		147.0	31.0	.	NM_181776	Q495M4|Q495M6|Q6ZWK5|Q7Z6B5	Missense_Mutation	SNP	ENST00000335244.4	hg19	CCDS4315.1	.	.	.	.	.	.	.	.	.	.	A	13.87	2.366710	0.41902	.	.	ENSG00000186335	ENST00000335244;ENST00000450886;ENST00000521967	T;T;T	0.11495	4.19;4.19;2.77	4.76	2.4	0.29515	.	0.920881	0.09207	N	0.833849	T	0.18383	0.0441	L	0.57536	1.79	0.31863	N	0.620713	P;B	0.45531	0.86;0.132	P;B	0.50314	0.637;0.158	T	0.16897	-1.0387	10	0.28530	T	0.3	-0.0361	8.697	0.34303	0.8453:0.0:0.1547:0.0	.	381;381	E5RJJ5;Q495M3	.;S36A2_HUMAN	Q	381;105;381	ENSP00000334223:L381Q;ENSP00000399479:L105Q;ENSP00000430535:L381Q	ENSP00000334223:L381Q	L	-	2	0	SLC36A2	150681838	0.997000	0.39634	0.549000	0.28204	0.633000	0.38033	4.784000	0.62411	0.426000	0.26116	0.460000	0.39030	CTG	.	.	.	none		0.542	SLC36A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252437.1			T	150701645	A	T	150701645	3	4	46	1	0	0	0	0	1	0	0	0	14607	188	7	5	317	5	SLC36A2	5	150701645	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	16704496	150701645	30213615	28	3220											
DOCK2	1794	hgsc.bcm.edu	37	chr5	169463529	169463529	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccctacctagaatttctacaAagataacaacagggaggaga	17	7	8	9	0	1	3	0	0	1	3	1	5	1	4	2	2	4	0	2	2	7	5			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr5:169463529A>G	ENST00000256935.8	+	36	3715	c.3635A>G	c.(3634-3636)aAa>aGa	p.K1212R	DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000540750.1_Missense_Mutation_p.K273R|DOCK2_ENST00000520908.1_Missense_Mutation_p.K704R	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1212	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)			AATTTCTACAAAGATAACAAC	0.423																																					p.K1212R		Atlas-SNP	.											.	DOCK2	389	.	0			c.A3635G						PASS	.						135	132	133					5																	169463529		2203	4300	6503	SO:0001583	missense	1794	exon36			TCTACAAAGATAA	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.3635A>G	chr5.hg19:g.169463529A>G	ENSP00000256935:p.Lys1212Arg	74.0	0.0	.		85.0	23.0	.	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	A	19.91	3.914002	0.72983	.	.	ENSG00000134516	ENST00000256935;ENST00000520908;ENST00000540750	T;T;T	0.55930	0.49;0.49;0.49	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.53174	0.1780	M	0.69463	2.115	0.41312	D	0.987117	P;P	0.46859	0.885;0.468	B;B	0.41299	0.353;0.074	T	0.57510	-0.7799	10	0.38643	T	0.18	.	15.5299	0.75952	1.0:0.0:0.0:0.0	.	704;1212	E7ERW7;Q92608	.;DOCK2_HUMAN	R	1212;704;273	ENSP00000256935:K1212R;ENSP00000429283:K704R;ENSP00000438827:K273R	ENSP00000256935:K1212R	K	+	2	0	DOCK2	169396107	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.358000	0.90090	2.147000	0.66899	0.533000	0.62120	AAA	.	.	.	none		0.423	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		G	169463529	A	G	169463529	3	3	46	1	0	0	0	0	1	0	0	0	4689	14	1	3	3777	3	DOCK2	5	169463529	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	18761884	169463529	11451731	29	3221											
NSD1	64324	hgsc.bcm.edu	37	chr5	176696648	176696648	+	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	cctcgagctgttccttccaaCattgataagatgagacatga	12	11	8	10	1	0	4	0	3	0	2	3	6	2	4	3	0	2	2	3	0	2	4			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr5:176696648C>T	ENST00000439151.2	+	16	5394	c.5349C>T	c.(5347-5349)aaC>aaT	p.N1783N	NSD1_ENST00000361032.4_Silent_p.N1680N|NSD1_ENST00000347982.4_Silent_p.N1514N|NSD1_ENST00000354179.4_Silent_p.N1514N	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	1783	PWWP 2. {ECO:0000255|PROSITE- ProRule:PRU00162}.				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)		TTCCTTCCAACATTGATAAGA	0.488			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.N1783N		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.C5349T	GRCh37	CD052485	NSD1	D		PASS	.						107	101	103					5																	176696648		2203	4300	6503	SO:0001819	synonymous_variant	64324	exon16	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	TTCCAACATTGAT	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.5349C>T	chr5.hg19:g.176696648C>T		73.0	0.0	.		89.0	14.0	.	NM_022455	Q96PD8|Q96RN7	Silent	SNP	ENST00000439151.2	hg19	CCDS4412.1																																																																																			.	.	.	none		0.488	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		T	176696648	C	T	176696648	2	4	46	1	0	0	0	0	0	0	0	1	10676	477	17	2		2	NSD1	5	176696648	Silent	SNP	C	TCGA-A4-7585-01A-11D-2136-08	7233119	176696648	4218612	30	3222											
CLPS	1208	hgsc.bcm.edu	37	chr6	35765001	35765001	+	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	ccaggttgataatgatccccCgggggccaggagctgcatag	9	7	14	11	1	0	2	0	2	0	0	1	3	1	3	4	4	2	3	4	4	2	3	rs140966197	byFrequency	TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr6:35765001C>G	ENST00000259938.2	-	1	87	c.65G>C	c.(64-66)cGg>cCg	p.R22P		NM_001832.3	NP_001823.1	P04118	COL_HUMAN	colipase, pancreatic	22					lipid catabolic process (GO:0016042)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	enzyme activator activity (GO:0008047)			large_intestine(2)|lung(2)|prostate(1)	5						AATGATCCCCCGGGGGCCAGG	0.587																																					p.R22P	Melanoma(167;2962 3494 37796)	Atlas-SNP	.											CLPS,NS,carcinoma,+1,1	CLPS	15	.	0			c.G65C						PASS	.						84	81	82					6																	35765001		2203	4300	6503	SO:0001583	missense	1208	exon1			ATCCCCCGGGGGC		CCDS4811.1, CCDS75437.1, CCDS75438.1	6p21.31	2012-02-06			ENSG00000137392	ENSG00000137392			2085	protein-coding gene	gene with protein product		120105				2045105	Standard	NM_001832		Approved		uc003ole.2	P04118	OTTHUMG00000014578	ENST00000259938.2:c.65G>C	chr6.hg19:g.35765001C>G	ENSP00000259938:p.Arg22Pro	118.0	0.0	.		153.0	13.0	.	NM_001252598	Q5T9G7|Q5U809	Missense_Mutation	SNP	ENST00000259938.2	hg19	CCDS4811.1	.	.	.	.	.	.	.	.	.	.	C	9.579	1.123120	0.20959	.	.	ENSG00000137392	ENST00000259938;ENST00000541088	T	0.36878	1.23	4.74	4.74	0.60224	Colipase, N-terminal (1);	0.240709	0.29486	N	0.012016	T	0.52468	0.1736	M	0.73962	2.25	0.42641	D	0.993411	D;B	0.89917	1.0;0.22	D;B	0.85130	0.997;0.117	T	0.56763	-0.7925	10	0.66056	D	0.02	-16.1424	14.5722	0.68218	0.0:1.0:0.0:0.0	.	22;22	G3V1M8;P04118	.;COL_HUMAN	P	22	ENSP00000259938:R22P	ENSP00000259938:R22P	R	-	2	0	CLPS	35872979	0.958000	0.32768	0.993000	0.49108	0.025000	0.11179	3.128000	0.50492	2.462000	0.83206	0.655000	0.94253	CGG	.	C|0.999;T|0.001	.	alt		0.587	CLPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040312.1	NM_001832		G	35765001	C	G	35765001	3	3	46	1	0	0	0	0	1	0	0	0	3555	652	23	4	285	4	CLPS	6	35765001	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08		35765001	135350066	31	3223											
KIAA0240	23506	hgsc.bcm.edu	37	chr6	42796705	42796705	+	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	gtcagattagtggttctggtCaaatacagttaattgggtca	11	14	11	5	0	4	1	3	0	1	1	4	1	4	1	0	3	1	2	0	3	4	5			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr6:42796705C>G	ENST00000314073.5	+	6	810	c.634C>G	c.(634-636)Caa>Gaa	p.Q212E	GLTSCR1L_ENST00000394168.1_Missense_Mutation_p.Q212E			Q6AI39	GSC1L_HUMAN	GLTSCR1-like	212								p.Q212*(1)									TGGTTCTGGTCAAATACAGTT	0.418																																					p.Q212E		Atlas-SNP	.											KIAA0240,NS,carcinoma,0,1	.	.	.	1	Substitution - Nonsense(1)	lung(1)	c.C634G						PASS	.						149	143	145					6																	42796705		2203	4300	6503	SO:0001583	missense	23506	exon5			TCTGGTCAAATAC	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.634C>G	chr6.hg19:g.42796705C>G	ENSP00000313933:p.Gln212Glu	215.0	0.0	.		221.0	35.0	.	NM_015349	A1L3W2|Q5TFZ3|Q92514	Missense_Mutation	SNP	ENST00000314073.5	hg19	CCDS34451.1	.	.	.	.	.	.	.	.	.	.	C	17.94	3.510409	0.64522	.	.	ENSG00000112624	ENST00000394167;ENST00000536004;ENST00000314073;ENST00000394168	T;T	0.35973	1.28;1.28	5.49	5.49	0.81192	.	0.000000	0.64402	D	0.000005	T	0.50599	0.1625	M	0.61703	1.905	0.58432	D	0.999998	P;D;D	0.61697	0.954;0.99;0.99	D;P;P	0.67900	0.954;0.848;0.848	T	0.36768	-0.9734	10	0.40728	T	0.16	-10.2526	19.7507	0.96267	0.0:1.0:0.0:0.0	.	212;212;212	F5H616;Q6AI39;B7Z2G7	.;K0240_HUMAN;.	E	212	ENSP00000313933:Q212E;ENSP00000377723:Q212E	ENSP00000313933:Q212E	Q	+	1	0	KIAA0240	42904683	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.946000	0.75953	2.722000	0.93159	0.655000	0.94253	CAA	.	.	.	none		0.418	GLTSCR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040562.3	NM_015349		G	42796705	C	G	42796705	3	3	46	1	0	0	0	0	1	0	0	0	8171	827	29	4	648	4	KIAA0240	6	42796705	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	7031704	42796705	128318362	32	3224											
MRPL2	51069	hgsc.bcm.edu	37	chr6	43023646	43023646	+	Missense_Mutation	SNP	A	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	tccccatacctgcagctcggAtatattgggcaccccggcct	7	9	9	16	2	0	0	0	0	0	0	2	1	1	1	6	3	3	3	6	3	3	4			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr6:43023646A>C	ENST00000388752.3	-	5	1044	c.620T>G	c.(619-621)aTc>aGc	p.I207S	MRPL2_ENST00000230413.5_Missense_Mutation_p.I207S|MRPL2_ENST00000489623.1_Intron|CUL7_ENST00000535468.1_5'Flank|CUL7_ENST00000265348.3_5'Flank	NM_015950.3	NP_057034.2	Q5T653	RM02_HUMAN	mitochondrial ribosomal protein L2	207					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(2)	9		Ovarian(999;0.0014)	Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00708)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)	BRCA - Breast invasive adenocarcinoma(397;0.0026)		TGCAGCTCGGATATATTGGGC	0.567																																					p.I207S		Atlas-SNP	.											.	MRPL2	30	.	0			c.T620G						PASS	.						44	39	40					6																	43023646		2203	4300	6503	SO:0001583	missense	51069	exon5			GCTCGGATATATT	AB051617	CCDS34454.1, CCDS75458.1	6p21.3	2012-09-13			ENSG00000112651	ENSG00000112651		"Mitochondrial ribosomal proteins / large subunits"	14056	protein-coding gene	gene with protein product		611822					Standard	XM_005249161		Approved	MRP-L14, RPML14, CGI-22	uc003ots.1	Q5T653	OTTHUMG00000014719	ENST00000388752.3:c.620T>G	chr6.hg19:g.43023646A>C	ENSP00000373404:p.Ile207Ser	44.0	0.0	.		41.0	10.0	.	NM_015950	B2RC56|Q8WUL1|Q96Q56|Q9Y311	Missense_Mutation	SNP	ENST00000388752.3	hg19	CCDS34454.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.589723	0.86851	.	.	ENSG00000112651	ENST00000388752;ENST00000230413	T;T	0.44482	0.92;0.92	5.94	5.94	0.96194	Translation protein SH3-like (1);Translation protein SH3-like, subgroup (1);Ribosomal protein L2, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.47135	0.1429	L	0.49571	1.57	0.80722	D	1	D	0.63880	0.993	D	0.67382	0.951	T	0.37197	-0.9716	10	0.33141	T	0.24	-18.6054	14.9662	0.71196	1.0:0.0:0.0:0.0	.	207	Q5T653	RM02_HUMAN	S	207	ENSP00000373404:I207S;ENSP00000230413:I207S	ENSP00000230413:I207S	I	-	2	0	MRPL2	43131624	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.952000	0.93031	2.272000	0.75746	0.460000	0.39030	ATC	.	.	.	none		0.567	MRPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040577.2			C	43023646	A	C	43023646	3	2	46	1	0	0	0	0	1	0	0	0	9792	333	12	5	309	5	MRPL2	6	43023646	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	226941	43023646	128091421	33	3225											
SENP6	26054	hgsc.bcm.edu	37	chr6	76412443	76412443	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcctcattaccatgaaaatGctgtcatacagaaatgttca	15	12	5	9	0	3	2	3	1	0	1	4	2	4	2	2	0	3	2	2	0	5	3			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr6:76412443G>A	ENST00000447266.2	+	19	2849	c.2371G>A	c.(2371-2373)Gct>Act	p.A791T	SENP6_ENST00000370010.2_Missense_Mutation_p.A784T|SENP6_ENST00000370014.3_Missense_Mutation_p.A791T|SENP6_ENST00000541192.1_Intron	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	791	Protease.				protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				CCATGAAAATGCTGTCATACA	0.383																																					p.A791T		Atlas-SNP	.											.	SENP6	189	.	0			c.G2371A						PASS	.						59	55	56					6																	76412443		1832	4093	5925	SO:0001583	missense	26054	exon19			GAAAATGCTGTCA		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.2371G>A	chr6.hg19:g.76412443G>A	ENSP00000402527:p.Ala791Thr	58.0	0.0	.		62.0	11.0	.	NM_015571	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Missense_Mutation	SNP	ENST00000447266.2	hg19	CCDS47454.1	.	.	.	.	.	.	.	.	.	.	G	11.12	1.545641	0.27652	.	.	ENSG00000112701	ENST00000370010;ENST00000370014;ENST00000447266	T;T;T	0.12255	2.7;2.7;2.7	5.74	3.51	0.40186	.	0.723156	0.13837	N	0.359285	T	0.02494	0.0076	L	0.33485	1.01	0.24879	N	0.992236	B;B	0.06786	0.001;0.001	B;B	0.11329	0.004;0.006	T	0.41698	-0.9494	10	0.25751	T	0.34	-0.6313	0.5061	0.00588	0.197:0.1755:0.2906:0.3369	.	784;791	Q9GZR1-2;Q9GZR1	.;SENP6_HUMAN	T	784;791;791	ENSP00000359027:A784T;ENSP00000359031:A791T;ENSP00000402527:A791T	ENSP00000359027:A784T	A	+	1	0	SENP6	76469163	0.954000	0.32549	0.998000	0.56505	0.939000	0.58152	0.671000	0.25172	1.214000	0.43395	0.579000	0.79373	GCT	.	.	.	none		0.383	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571		A	76412443	G	A	76412443	3	1	46	1	0	0	0	0	1	0	0	0	14063	1319	46	2	2445	2	SENP6	6	76412443	Missense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08	33388797	76412443	94702624	34	3226											
SHPRH	257218	hgsc.bcm.edu	37	chr6	146234630	146234630	+	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	ttacctgttttcctagctgtCgagcacagattgggcaaggt	8	13	11	9	1	0	1	0	0	0	1	2	2	1	1	2	2	3	4	2	2	3	5			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr6:146234630C>G	ENST00000367505.2	-	24	4574	c.4310G>C	c.(4309-4311)cGa>cCa	p.R1437P	SHPRH_ENST00000438092.2_Missense_Mutation_p.R1441P|SHPRH_ENST00000275233.7_Missense_Mutation_p.R1437P|SHPRH_ENST00000367503.3_Missense_Mutation_p.R1441P			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	1437					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)		TCCTAGCTGTCGAGCACAGAT	0.308																																					p.R1441P		Atlas-SNP	.											.	SHPRH	169	.	0			c.G4322C						PASS	.						123	123	123					6																	146234630		1803	4069	5872	SO:0001583	missense	257218	exon24			AGCTGTCGAGCAC	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.4310G>C	chr6.hg19:g.146234630C>G	ENSP00000356475:p.Arg1437Pro	80.0	0.0	.		95.0	18.0	.	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	hg19	CCDS43513.2	.	.	.	.	.	.	.	.	.	.	C	23.4	4.415831	0.83449	.	.	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233	D;D;D;D	0.84730	-1.89;-1.89;-1.89;-1.89	5.52	4.65	0.58169	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);	0.088147	0.47455	D	0.000232	D	0.88514	0.6457	M	0.61703	1.905	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.89205	0.3560	10	0.51188	T	0.08	-9.0526	14.3892	0.66965	0.0:0.9287:0.0:0.0713	.	1437;1441	Q149N8;Q149N8-4	SHPRH_HUMAN;.	P	1437;1441;1441;1437	ENSP00000356475:R1437P;ENSP00000356473:R1441P;ENSP00000412797:R1441P;ENSP00000275233:R1437P	ENSP00000275233:R1437P	R	-	2	0	SHPRH	146276323	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	4.749000	0.62155	1.469000	0.48083	0.591000	0.81541	CGA	.	.	.	none		0.308	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082		G	146234630	C	G	146234630	3	3	46	1	0	0	0	0	1	0	0	0	14304	884	31	4	786	4	SHPRH	6	146234630	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	69822187	146234630	24880437	35	3227											
LPA	4018	hgsc.bcm.edu	37	chr6	161027563	161027563	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtaatagttggaggcgcgaCggcagtcccttctgcgtctg	6	10	15	10	4	2	0	0	0	2	0	3	2	3	1	1	4	1	3	1	4	2	4			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr6:161027563C>T	ENST00000316300.5	-	17	2775	c.2731G>A	c.(2731-2733)Gtc>Atc	p.V911I	LPA_ENST00000447678.1_Missense_Mutation_p.V911I			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3419	Kringle 8. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	GGAGGCGCGACGGCAGTCCCT	0.547																																					p.V911I		Atlas-SNP	.											LPA,colon,carcinoma,0,1	LPA	237	.	0			c.G2731A						PASS	.						105	110	108					6																	161027563		2068	4257	6325	SO:0001583	missense	4018	exon18			GCGCGACGGCAGT	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.2731G>A	chr6.hg19:g.161027563C>T	ENSP00000321334:p.Val911Ile	214.0	0.0	.		197.0	8.0	.	NM_005577	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	hg19	CCDS43523.1	.	.	.	.	.	.	.	.	.	.	c	11.74	1.727367	0.30593	.	.	ENSG00000198670	ENST00000316300;ENST00000447678	T;T	0.62232	0.04;0.04	2.18	-2.62	0.06152	Kringle (1);Kringle-like fold (1);	.	.	.	.	T	0.21267	0.0512	L	0.38838	1.175	0.09310	N	1	P	0.50943	0.94	P	0.48089	0.566	T	0.26985	-1.0087	9	0.02654	T	1	.	0.3677	0.00374	0.2413:0.3112:0.2389:0.2086	.	3419	P08519	APOA_HUMAN	I	911	ENSP00000321334:V911I;ENSP00000395608:V911I	ENSP00000321334:V911I	V	-	1	0	LPA	160947553	0.000000	0.05858	0.000000	0.03702	0.108000	0.19459	-2.331000	0.01110	-0.260000	0.09418	0.184000	0.17185	GTC	.	.	.	none		0.547	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		T	161027563	C	T	161027563	3	4	46	1	0	0	0	0	1	0	0	0	8910	536	19	1	3483	1	LPA	6	161027563	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	14792933	161027563	10087504	36	3228											
KIAA0895	23366	hgsc.bcm.edu	37	chr7	36396613	36396613	+	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	ttgtaggtatagtcagatttGaagaatctcagtttttcttt	10	19	8	4	0	3	3	2	1	2	2	4	3	3	3	0	1	0	3	0	1	5	8			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr7:36396613G>A	ENST00000297063.6	-	3	815	c.765C>T	c.(763-765)ttC>ttT	p.F255F	KIAA0895_ENST00000436884.1_Silent_p.F104F|KIAA0895_ENST00000440378.1_Silent_p.F204F|KIAA0895_ENST00000317020.6_Silent_p.F204F|KIAA0895_ENST00000338533.5_Silent_p.F242F|KIAA0895_ENST00000453212.1_Intron|KIAA0895_ENST00000415803.2_Silent_p.F242F|KIAA0895_ENST00000480192.1_Intron	NM_001100425.1	NP_001093895.1	Q8NCT3	K0895_HUMAN	KIAA0895	255										breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						AGTCAGATTTGAAGAATCTCA	0.393																																					p.F255F		Atlas-SNP	.											.	KIAA0895	89	.	0			c.C765T						PASS	.						103	95	97					7																	36396613		1840	4095	5935	SO:0001819	synonymous_variant	23366	exon3			AGATTTGAAGAAT	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.765C>T	chr7.hg19:g.36396613G>A		85.0	0.0	.		79.0	11.0	.	NM_001100425	B4DF35|B7ZLT4|B9EGB9|O94969|Q0VGC1|Q7Z4L2	Silent	SNP	ENST00000297063.6	hg19	CCDS43570.1																																																																																			.	.	.	none		0.393	KIAA0895-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337717.1	NM_015314		A	36396613	G	A	36396613	2	1	46	1	0	0	0	0	0	0	0	1	8204	1281	45	2		2	KIAA0895	7	36396613	Silent	SNP	G	TCGA-A4-7585-01A-11D-2136-08		36396613	122742050	37	3229											
URGCP	55665	hgsc.bcm.edu	37	chr7	43918082	43918082	+	Missense_Mutation	SNP	A	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	aggccacaggttctgggaaaAtgtccaagtcctcccttccg	9	9	10	13	1	1	0	0	0	1	0	5	1	5	1	5	3	0	1	5	3	3	2			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr7:43918082A>C	ENST00000453200.1	-	6	1473	c.980T>G	c.(979-981)aTt>aGt	p.I327S	URGCP_ENST00000443736.1_Missense_Mutation_p.I284S|URGCP_ENST00000447717.3_Missense_Mutation_p.I284S|URGCP_ENST00000223341.7_Missense_Mutation_p.I284S|URGCP_ENST00000497914.1_5'UTR|URGCP_ENST00000336086.6_Missense_Mutation_p.I284S|URGCP-MRPS24_ENST00000603700.1_Intron|URGCP_ENST00000402306.3_Missense_Mutation_p.I318S			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	327					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						TTCTGGGAAAATGTCCAAGTC	0.512																																					p.I327S		Atlas-SNP	.											.	URGCP	170	.	0			c.T980G						PASS	.						69	70	70					7																	43918082		1897	4129	6026	SO:0001583	missense	55665	exon6			GGGAAAATGTCCA		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.980T>G	chr7.hg19:g.43918082A>C	ENSP00000396918:p.Ile327Ser	76.0	0.0	.		109.0	24.0	.	NM_001077663	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Missense_Mutation	SNP	ENST00000453200.1	hg19	CCDS47578.1	.	.	.	.	.	.	.	.	.	.	A	11.05	1.526247	0.27299	.	.	ENSG00000106608	ENST00000223341;ENST00000336086;ENST00000402306;ENST00000443736;ENST00000453200;ENST00000447717	T;T;T;T;T;T	0.09630	2.96;2.96;2.96;2.96;2.96;2.96	5.66	5.66	0.87406	.	0.567596	0.17461	N	0.173449	T	0.10981	0.0268	L	0.47716	1.5	0.09310	N	1	B;B	0.30973	0.302;0.302	B;B	0.29942	0.109;0.109	T	0.20207	-1.0282	10	0.49607	T	0.09	-6.1339	8.3974	0.32566	0.913:0.0:0.087:0.0	.	318;327	Q8TCY9-2;Q8TCY9	.;URGCP_HUMAN	S	284;284;318;284;327;284	ENSP00000223341:I284S;ENSP00000336872:I284S;ENSP00000384955:I318S;ENSP00000392136:I284S;ENSP00000396918:I327S;ENSP00000402803:I284S	ENSP00000223341:I284S	I	-	2	0	URGCP	43884607	0.050000	0.20438	0.044000	0.18714	0.845000	0.48019	3.327000	0.52045	2.158000	0.67659	0.482000	0.46254	ATT	.	.	.	none		0.512	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664		C	43918082	A	C	43918082	3	2	46	1	0	0	0	0	1	0	0	0	17038	101	4	5	1819	5	URGCP	7	43918082	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	7521469	43918082	115220581	38	3230											
RELN	5649	hgsc.bcm.edu	37	chr7	103629656	103629656	+	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	gagcacctcgccctgctcccCatccccttccagctccccgt	4	8	6	23	2	0	0	0	0	0	0	5	1	4	0	9	0	3	3	9	0	0	1			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr7:103629656C>T	ENST00000428762.1	-	1	307	c.148G>A	c.(148-150)Ggg>Agg	p.G50R	RELN_ENST00000424685.2_Missense_Mutation_p.G50R|RELN_ENST00000343529.5_Missense_Mutation_p.G50R	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	50	Reelin. {ECO:0000255|PROSITE- ProRule:PRU00363}.				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)		CCCTGCTCCCCATCCCCTTCC	0.642																																					p.G50R	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.G148A						PASS	.						52	53	53					7																	103629656		2203	4300	6503	SO:0001583	missense	5649	exon1			GCTCCCCATCCCC		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.148G>A	chr7.hg19:g.103629656C>T	ENSP00000392423:p.Gly50Arg	90.0	0.0	.		112.0	20.0	.	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	hg19	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.301758	0.81136	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.21361	2.01;2.01;2.01	4.63	4.63	0.57726	Reeler domain (1);	0.000000	0.64402	U	0.000010	T	0.32645	0.0836	N	0.19112	0.55	0.58432	D	0.999997	D;D	0.89917	0.999;1.0	D;D	0.75484	0.976;0.986	T	0.19095	-1.0316	10	0.52906	T	0.07	.	17.6802	0.88240	0.0:1.0:0.0:0.0	.	50;50	P78509-2;P78509	.;RELN_HUMAN	R	50	ENSP00000392423:G50R;ENSP00000345694:G50R;ENSP00000388446:G50R	ENSP00000345694:G50R	G	-	1	0	RELN	103416892	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.718000	0.74713	2.386000	0.81285	0.563000	0.77884	GGG	.	.	.	none		0.642	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		T	103629656	C	T	103629656	3	4	46	1	0	0	0	0	1	0	0	0	13233	594	21	2	10494	2	RELN	7	103629656	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	59711574	103629656	55509007	39	3231											
HAS2	3037	hgsc.bcm.edu	37	chr8	122641473	122641473	+	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	tagtaattatccgtttggatAaactggtagccaacaatata	15	13	7	6	1	0	0	0	0	0	0	1	1	1	1	2	2	3	3	2	2	10	8			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr8:122641473A>T	ENST00000303924.4	-	2	645	c.108T>A	c.(106-108)ttT>ttA	p.F36L		NM_005328.2	NP_005319.1	Q92819	HYAS2_HUMAN	hyaluronan synthase 2	36					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)			CCGTTTGGATAAACTGGTAGC	0.423																																					p.F36L		Atlas-SNP	.											.	HAS2	87	.	0			c.T108A						PASS	.						88	85	86					8																	122641473		2203	4300	6503	SO:0001583	missense	3037	exon2			TTGGATAAACTGG	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.108T>A	chr8.hg19:g.122641473A>T	ENSP00000306991:p.Phe36Leu	95.0	0.0	.		90.0	16.0	.	NM_005328	Q32MM3	Missense_Mutation	SNP	ENST00000303924.4	hg19	CCDS6335.1	.	.	.	.	.	.	.	.	.	.	A	8.872	0.949410	0.18356	.	.	ENSG00000170961	ENST00000303924;ENST00000443194	T	0.37584	1.19	6.17	3.85	0.44370	.	0.042814	0.85682	D	0.000000	T	0.22166	0.0534	L	0.28192	0.835	0.53688	D	0.999978	B	0.09022	0.002	B	0.06405	0.002	T	0.05178	-1.0901	10	0.12430	T	0.62	-24.2374	9.8975	0.41327	0.809:0.0:0.191:0.0	.	36	Q92819	HAS2_HUMAN	L	36	ENSP00000306991:F36L	ENSP00000306991:F36L	F	-	3	2	HAS2	122710654	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	1.132000	0.31418	1.161000	0.42604	-0.250000	0.11733	TTT	.	.	.	none		0.423	HAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381150.2	NM_005328		T	122641473	A	T	122641473	3	4	46	1	0	0	0	0	1	0	0	0	6969	359	13	5	1562	5	HAS2	8	122641473	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08		122641473	23722549	40	3232											
COL5A1	1289	hgsc.bcm.edu	37	chr9	137734002	137734002	+	Splice_Site	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	atctgtctccctcttccccaGaccaagaaaggctaccagaa	12	8	6	15	0	3	3	0	0	3	3	5	3	4	3	5	1	1	1	5	1	4	2			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr9:137734002G>C	ENST00000371817.3	+	66	5784		c.e66-1			NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1						axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CTCTTCCCCAGACCAAGAAAG	0.547																																					.		Atlas-SNP	.											.	COL5A1	323	.	0			c.5371-1G>C						PASS	.						89	81	83					9																	137734002		2203	4300	6503	SO:0001630	splice_region_variant	1289	exon66			TCCCCAGACCAAG	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.5371-1G>C	chr9.hg19:g.137734002G>C		82.0	0.0	.		100.0	12.0	.	NM_000093	Q15094|Q5SUX4	Splice_Site	SNP	ENST00000371817.3	hg19	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.985830	0.74589	.	.	ENSG00000130635	ENST00000371817;ENST00000355306	.	.	.	4.42	4.42	0.53409	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.3629	0.87356	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	COL5A1	136873823	1.000000	0.71417	0.075000	0.20258	0.907000	0.53573	9.541000	0.98083	2.174000	0.68829	0.563000	0.77884	.	.	.	.	none		0.547	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	Intron	C	137734002	G	C	137734002	5	2	46	1	0	0	0	0	0	0	1	0	3698	956	33	4	5632	4	COL5A1	9	137734002	Splice_Site	SNP	G	TCGA-A4-7585-01A-11D-2136-08		137734002	3479429	41	3233											
PPRC1	23082	hgsc.bcm.edu	37	chr10	103898442	103898442	+	Frame_Shift_Del	DEL	A	A	-																															ctctgacggagatcttggacAatgcagattctgagaacctt																										TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr10:103898442delA	ENST00000278070.2	+	3	448	c.409delA	c.(409-411)aatfs	p.N137fs	PPRC1_ENST00000370012.1_5'Flank|PPRC1_ENST00000413464.2_Frame_Shift_Del_p.N137fs	NM_015062.3	NP_055877.3	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator-related 1	137					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(10)|lung(19)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		GATCTTGGACAATGCAGATTC	0.532																																					p.D136fs		Atlas-INDEL	.											.	PPRC1	151	.	0			c.408delC						PASS	.						120	108	112					10																	103898442		2203	4300	6503	SO:0001589	frameshift_variant	23082	exon3			.	AF325193	CCDS7529.1, CCDS73186.1	10q24.32	2013-02-12	2006-10-17		ENSG00000148840	ENSG00000148840		"RNA binding motif (RRM) containing"	30025	protein-coding gene	gene with protein product			"peroxisome proliferative activated receptor, gamma, coactivator-related 1"			9628581, 11340167	Standard	XM_005269656		Approved	PRC, KIAA0595, MGC74642	uc001kum.3	Q5VV67	OTTHUMG00000018948	ENST00000278070.2:c.409delA	chr10.hg19:g.103898442delA	ENSP00000278070:p.Asn137fs	87.0	0.0	0		90.0	15.0	0.166667	NM_015062	Q5VV66|Q6P3U5|Q6P3W1|Q76N31|Q9BUJ3|Q9BZE5|Q9Y4E0	Frame_Shift_Del	DEL	ENST00000278070.2	hg19	CCDS7529.1																																																																																			.	.	.	none		0.532	PPRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050021.1	NM_015062		-	103898442	A	-	103898442	7	5	46	1	0	1	0	1	0	0	0	0	12420	130	5	0	419	0	PPRC1	10	103898442	Frame_Shift_Del	DEL	A	TCGA-A4-7585-01A-11D-2136-08		103898442	31636305	42	3234											
HTRA1	5654	hgsc.bcm.edu	37	chr10	124273843	124273843	+	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	ggggtaatgaagatatcatgAtcacagtgattcccgaagaa	15	9	11	6	1	2	5	2	3	0	2	3	6	3	5	1	2	0	1	1	2	5	3			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr10:124273843A>T	ENST00000368984.3	+	9	1539	c.1411A>T	c.(1411-1413)Atc>Ttc	p.I471F		NM_002775.4	NP_002766.1	Q92743	HTRA1_HUMAN	HtrA serine peptidase 1	471					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)				AGATATCATGATCACAGTGAT	0.507																																					p.I471F		Atlas-SNP	.											.	HTRA1	40	.	0			c.A1411T						PASS	.						155	138	144					10																	124273843		2203	4300	6503	SO:0001583	missense	5654	exon9			ATCATGATCACAG	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.1411A>T	chr10.hg19:g.124273843A>T	ENSP00000357980:p.Ile471Phe	100.0	0.0	.		99.0	20.0	.	NM_002775	D3DRE4|Q9UNS5	Missense_Mutation	SNP	ENST00000368984.3	hg19	CCDS7630.1	.	.	.	.	.	.	.	.	.	.	A	1.382	-0.583027	0.03827	.	.	ENSG00000166033	ENST00000368984;ENST00000435263;ENST00000420892	D;D	0.82893	-1.66;-1.66	5.48	1.75	0.24633	PDZ/DHR/GLGF (1);	0.119403	0.56097	D	0.000029	T	0.67636	0.2914	L	0.31371	0.925	0.51767	D	0.999938	B	0.06786	0.001	B	0.06405	0.002	T	0.51601	-0.8685	10	0.28530	T	0.3	-8.1432	3.9311	0.09285	0.4669:0.3415:0.0687:0.1228	.	471	Q92743	HTRA1_HUMAN	F	471;438;212	ENSP00000357980:I471F;ENSP00000412676:I212F	ENSP00000357980:I471F	I	+	1	0	HTRA1	124263833	0.991000	0.36638	0.304000	0.25085	0.093000	0.18481	0.396000	0.20867	0.043000	0.15746	-0.313000	0.08912	ATC	.	.	.	none		0.507	HTRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128327.1	NM_002775		T	124273843	A	T	124273843	3	4	46	1	0	0	0	0	1	0	0	0	7460	333	12	5	1445	5	HTRA1	10	124273843	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08	20375401	124273843	11260904	43	3235											
TECTA	7007	hgsc.bcm.edu	37	chr11	120980039	120980039	+	Frame_Shift_Del	DEL	A	A	-																															tgggcagatgtgcacaatggAattcgaggcgagatctatta																										TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr11:120980039delA	ENST00000392793.1	+	4	589	c.318delA	c.(316-318)ggafs	p.G106fs	TECTA_ENST00000264037.2_Frame_Shift_Del_p.G106fs			O75443	TECTA_HUMAN	tectorin alpha	106	NIDO. {ECO:0000255|PROSITE- ProRule:PRU00570}.				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)		TGCACAATGGAATTCGAGGCG	0.498																																					p.G106fs		Atlas-INDEL	.											.	TECTA	329	.	0			c.317delG						PASS	.						105	97	100					11																	120980039		2203	4299	6502	SO:0001589	frameshift_variant	7007	exon3			.	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.318delA	chr11.hg19:g.120980039delA	ENSP00000376543:p.Gly106fs	72.0	0.0	0		76.0	19.0	0.25	NM_005422		Frame_Shift_Del	DEL	ENST00000392793.1	hg19	CCDS8434.1																																																																																			.	.	.	none		0.498	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		-	120980039	A	-	120980039	7	5	46	1	0	1	0	1	0	0	0	0	15759	233	9	0	328	0	TECTA	11	120980039	Frame_Shift_Del	DEL	A	TCGA-A4-7585-01A-11D-2136-08		120980039	14026477	44	3236											
CNTN1	1272	hgsc.bcm.edu	37	chr12	41327590	41327590	+	Missense_Mutation	SNP	A	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	gggctgttcttaagatcttcAatattcagctagaagatgaa	13	13	9	6	0	4	4	2	1	2	3	4	4	4	4	0	1	1	3	0	1	6	6			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr12:41327590A>C	ENST00000551295.2	+	9	1012	c.895A>C	c.(895-897)Aat>Cat	p.N299H	CNTN1_ENST00000347616.1_Missense_Mutation_p.N299H|CNTN1_ENST00000547702.1_Missense_Mutation_p.N299H|CNTN1_ENST00000547849.1_Missense_Mutation_p.N299H|CNTN1_ENST00000360099.3_Missense_Mutation_p.N299H|CNTN1_ENST00000348761.2_Missense_Mutation_p.N288H	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	299	Ig-like C2-type 3.				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)				TAAGATCTTCAATATTCAGCT	0.408																																					p.N299H		Atlas-SNP	.											.	CNTN1	207	.	0			c.A895C						PASS	.						85	87	87					12																	41327590		2203	4299	6502	SO:0001583	missense	1272	exon9			ATCTTCAATATTC	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.895A>C	chr12.hg19:g.41327590A>C	ENSP00000447006:p.Asn299His	84.0	0.0	.		76.0	14.0	.	NM_001256063	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Missense_Mutation	SNP	ENST00000551295.2	hg19	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.293171	0.80914	.	.	ENSG00000018236	ENST00000547702;ENST00000551295;ENST00000547849;ENST00000347616;ENST00000360099;ENST00000348761	T;T;T;T;T;T	0.34472	1.36;1.36;1.36;1.36;1.36;1.36	5.24	5.24	0.73138	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.55033	0.1895	L	0.56124	1.755	0.54753	D	0.999986	D;D;D	0.89917	1.0;0.997;0.998	D;D;D	0.75484	0.986;0.968;0.981	T	0.54309	-0.8313	10	0.46703	T	0.11	.	15.4433	0.75204	1.0:0.0:0.0:0.0	.	299;288;299	Q12860-3;Q12860-2;Q12860	.;.;CNTN1_HUMAN	H	299;299;299;299;299;288	ENSP00000448004:N299H;ENSP00000447006:N299H;ENSP00000448653:N299H;ENSP00000325660:N299H;ENSP00000353213:N299H;ENSP00000261160:N288H	ENSP00000325660:N299H	N	+	1	0	CNTN1	39613857	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.730000	0.91510	2.130000	0.65690	0.528000	0.53228	AAT	.	.	.	none		0.408	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		C	41327590	A	C	41327590	3	2	46	1	0	0	0	0	1	0	0	0	3642	130	5	5	925	5	CNTN1	12	41327590	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08		41327590	92524305	45	3237											
KRT77	374454	hgsc.bcm.edu	37	chr12	53097170	53097170	+	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	agagctggtactataaacccGcctgctcattgaactaaacg	13	9	8	11	2	1	2	1	1	0	1	1	2	1	2	2	1	6	3	2	1	7	5	rs375217197		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr12:53097170G>T	ENST00000341809.3	-	1	77	c.49C>A	c.(49-51)Cgg>Agg	p.R17R	KRT77_ENST00000537195.1_5'UTR	NM_175078.2	NP_778253.2	Q7Z794	K2C1B_HUMAN	keratin 77	17	Head.					cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(2)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						CTATAAACCCGCCTGCTCATT	0.542																																					p.R17R		Atlas-SNP	.											.	KRT77	58	.	0			c.C49A						PASS	.						64	70	68					12																	53097170		2203	4300	6503	SO:0001819	synonymous_variant	374454	exon1			AAACCCGCCTGCT	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.49C>A	chr12.hg19:g.53097170G>T		78.0	0.0	.		70.0	19.0	.	NM_175078	Q7RTS8	Silent	SNP	ENST00000341809.3	hg19	CCDS8837.1																																																																																			.	.	.	alt		0.542	KRT77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404111.1	NM_175078		T	53097170	G	T	53097170	2	4	46	1	0	0	0	0	0	0	0	1	8497	1086	38	4		4	KRT77	12	53097170	Silent	SNP	G	TCGA-A4-7585-01A-11D-2136-08	11769580	53097170	80754725	46	3238											
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120599294	120599294	+	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	aagtgcctccgtgtactcacCtccttcagctccagctcgat	7	11	7	16	2	2	0	2	0	0	0	6	1	5	0	5	0	4	3	5	0	2	2			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr12:120599294C>T	ENST00000300648.6	-	22	2448	c.2436G>A	c.(2434-2436)gaG>gaA	p.E812E		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	812					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)					GTGTACTCACCTCCTTCAGCT	0.512																																					p.E812E		Atlas-SNP	.											.	GCN1L1	207	.	0			c.G2436A						PASS	.						166	169	168					12																	120599294		2172	4262	6434	SO:0001630	splice_region_variant	10985	exon22			ACTCACCTCCTTC	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.2436+1G>A	chr12.hg19:g.120599294C>T		120.0	0.0	.		119.0	10.0	.	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Silent	SNP	ENST00000300648.6	hg19	CCDS41847.1																																																																																			.	.	.	none		0.512	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1		Silent	T	120599294	C	T	120599294	5	4	46	1	0	0	0	0	0	0	1	0	6306	695	24	2	5727	2	GCN1L1	12	120599294	Splice_Site	SNP	C	TCGA-A4-7585-01A-11D-2136-08	67502124	120599294	13252601	47	3239											
NFKBIA	4792	hgsc.bcm.edu	37	chr14	35871629	35871629	+	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	tgtgaactccgtgaactctgActctgtgtcatagctctcct	7	14	8	12	1	4	3	1	3	3	0	6	3	5	3	2	0	3	1	2	0	3	1			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr14:35871629A>T	ENST00000216797.5	-	5	978	c.877T>A	c.(877-879)Tca>Aca	p.S293T	NFKBIA_ENST00000557100.1_5'Flank|NFKBIA_ENST00000557389.1_Missense_Mutation_p.S203T|NFKBIA_ENST00000557140.1_Missense_Mutation_p.S250T	NM_020529.2	NP_065390.1	P25963	IKBA_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha	293					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)	GTGAACTCTGACTCTGTGTCA	0.562																																					p.S293T		Atlas-SNP	.											.	NFKBIA	28	.	0			c.T877A						PASS	.						88	94	92					14																	35871629		2203	4300	6503	SO:0001583	missense	4792	exon5			ACTCTGACTCTGT		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.877T>A	chr14.hg19:g.35871629A>T	ENSP00000216797:p.Ser293Thr	144.0	0.0	.		145.0	24.0	.	NM_020529	B2R8L6	Missense_Mutation	SNP	ENST00000216797.5	hg19	CCDS9656.1	.	.	.	.	.	.	.	.	.	.	A	15.19	2.759198	0.49468	.	.	ENSG00000100906	ENST00000216797;ENST00000557140;ENST00000557389	T;T;T	0.46063	0.88;0.89;1.06	5.9	4.73	0.59995	Ankyrin repeat-containing domain (1);	.	.	.	.	T	0.28400	0.0702	L	0.29908	0.895	0.34457	D	0.701352	B;B	0.32467	0.372;0.145	B;B	0.30316	0.114;0.034	T	0.36915	-0.9728	9	0.35671	T	0.21	0.4354	7.8624	0.29517	0.7845:0.1395:0.0759:0.0	.	250;293	G3V3I4;P25963	.;IKBA_HUMAN	T	293;250;203	ENSP00000216797:S293T;ENSP00000451257:S250T;ENSP00000450514:S203T	ENSP00000216797:S293T	S	-	1	0	NFKBIA	34941380	1.000000	0.71417	0.820000	0.32676	0.916000	0.54674	3.478000	0.53158	1.015000	0.39444	0.533000	0.62120	TCA	.	.	.	none		0.562	NFKBIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276683.1	NM_020529		T	35871629	A	T	35871629	3	4	46	1	0	0	0	0	1	0	0	0	10384	275	10	5	84	5	NFKBIA	14	35871629	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08		35871629	71477911	48	3240											
SLC39A9	55334	hgsc.bcm.edu	37	chr14	69866098	69866098	+	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	gagggcagaatggatgatttCatctccattagcctgctgtc	9	12	11	9	0	2	2	1	1	1	1	4	4	2	3	2	2	2	2	2	2	2	2			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr14:69866098C>T	ENST00000336643.5	+	1	690	c.12C>T	c.(10-12)ttC>ttT	p.F4F	ERH_ENST00000555373.1_5'Flank|SLC39A9_ENST00000031146.4_Silent_p.F4F|SLC39A9_ENST00000555245.1_Intron|ERH_ENST00000216520.6_5'Flank|SLC39A9_ENST00000556605.1_Silent_p.F4F|ERH_ENST00000557016.1_5'Flank|SLC39A9_ENST00000557046.1_Silent_p.F4F	NM_018375.4	NP_060845.2	Q9NUM3	S39A9_HUMAN	solute carrier family 39, member 9	4					zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)	p.F4F(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|skin(1)|stomach(1)	14				all cancers(60;0.00299)|BRCA - Breast invasive adenocarcinoma(234;0.0145)|OV - Ovarian serous cystadenocarcinoma(108;0.0373)		TGGATGATTTCATCTCCATTA	0.438																																					p.F4F		Atlas-SNP	.											SLC39A9,NS,carcinoma,0,1	SLC39A9	27	.	1	Substitution - coding silent(1)	endometrium(1)	c.C12T						PASS	.						224	200	208					14																	69866098		2203	4300	6503	SO:0001819	synonymous_variant	55334	exon1			TGATTTCATCTCC		CCDS9795.1, CCDS58327.1, CCDS58328.1	14q24.1	2013-07-17	2013-07-17			ENSG00000029364		"Solute carriers"	20182	protein-coding gene	gene with protein product							Standard	NM_018375		Approved	FLJ11274	uc001xle.3	Q9NUM3		ENST00000336643.5:c.12C>T	chr14.hg19:g.69866098C>T		39.0	0.0	.		47.0	13.0	.	NM_001252150	G3V5J8|Q53HN3|Q5MJQ0|Q6P2Q1|Q86WY2	Silent	SNP	ENST00000336643.5	hg19	CCDS9795.1																																																																																			.	.	.	none		0.438	SLC39A9-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412446.1	NM_018375		T	69866098	C	T	69866098	2	4	46	1	0	0	0	0	0	0	0	1	14638	825	29	2		2	SLC39A9	14	69866098	Silent	SNP	C	TCGA-A4-7585-01A-11D-2136-08	33994469	69866098	37483442	49	3241											
SLC28A2	9153	hgsc.bcm.edu	37	chr15	45561728	45561728	+	Missense_Mutation	SNP	A	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	ttgagggagagaaacagtggAtttctgtaagtgacaatcca	14	10	12	5	0	1	3	0	2	1	1	2	6	2	5	1	2	1	1	1	2	3	3			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr15:45561728A>C	ENST00000347644.3	+	14	1626	c.1561A>C	c.(1561-1563)Att>Ctt	p.I521L	CTD-2651B20.3_ENST00000561404.1_RNA|CTD-2651B20.3_ENST00000560344.1_RNA	NM_004212.3	NP_004203.2	O43868	S28A2_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 2	521					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)	GAAACAGTGGATTTCTGTAAG	0.433																																					p.I521L	NSCLC(92;493 1501 26361 28917 47116)	Atlas-SNP	.											.	SLC28A2	64	.	0			c.A1561C						PASS	.						96	90	92					15																	45561728		2198	4298	6496	SO:0001583	missense	9153	exon14			CAGTGGATTTCTG	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.1561A>C	chr15.hg19:g.45561728A>C	ENSP00000315006:p.Ile521Leu	38.0	0.0	.		37.0	6.0	.	NM_004212	A8K7F9|O43239|Q52LZ0	Missense_Mutation	SNP	ENST00000347644.3	hg19	CCDS10121.1	.	.	.	.	.	.	.	.	.	.	A	17.79	3.475336	0.63737	.	.	ENSG00000137860	ENST00000347644	T	0.04454	3.62	6.17	3.87	0.44632	Na dependent nucleoside transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.05318	0.0141	N	0.20445	0.575	0.58432	D	0.999999	P	0.39551	0.678	P	0.46339	0.513	T	0.50381	-0.8835	10	0.48119	T	0.1	-12.9596	7.5865	0.27995	0.7845:0.1422:0.0733:0.0	.	521	O43868	S28A2_HUMAN	L	521	ENSP00000315006:I521L	ENSP00000315006:I521L	I	+	1	0	SLC28A2	43349020	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.369000	0.52365	0.559000	0.29153	0.533000	0.62120	ATT	.	.	.	none		0.433	SLC28A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254219.2	NM_004212		C	45561728	A	C	45561728	3	2	46	1	0	0	0	0	1	0	0	0	14545	333	12	5	1611	5	SLC28A2	15	45561728	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08		45561728	56969664	50	3242											
MTFMT	123263	hgsc.bcm.edu	37	chr15	65295424	65295424	+	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	tcaatgcattgttgcatagcAacagtttttttctgcttctt	8	19	6	8	0	3	0	1	0	2	0	3	0	3	0	0	0	5	6	0	0	3	8			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr15:65295424A>C	ENST00000220058.4	-	9	1159	c.1146T>G	c.(1144-1146)gtT>gtG	p.V382V		NM_139242.3	NP_640335.2	Q96DP5	FMT_HUMAN	mitochondrial methionyl-tRNA formyltransferase	382						mitochondrion (GO:0005739)	methionyl-tRNA formyltransferase activity (GO:0004479)			endometrium(1)|large_intestine(3)|lung(3)|ovary(3)	10					Tetrahydrofolic acid(DB00116)	GTTGCATAGCAACAGTTTTTT	0.348																																					p.V382V		Atlas-SNP	.											.	MTFMT	28	.	0			c.T1146G						PASS	.						111	98	102					15																	65295424		1825	4084	5909	SO:0001819	synonymous_variant	123263	exon9			CATAGCAACAGTT	AK055688	CCDS45280.1	15q22.31	2006-11-29		2005-08-09		ENSG00000103707			29666	protein-coding gene	gene with protein product		611766				9614118	Standard	NM_139242		Approved	FMT1	uc002aof.4	Q96DP5		ENST00000220058.4:c.1146T>G	chr15.hg19:g.65295424A>C		38.0	0.0	.		56.0	9.0	.	NM_139242	B7Z734	Silent	SNP	ENST00000220058.4	hg19	CCDS45280.1																																																																																			.	.	.	none		0.348	MTFMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418155.1	NM_139242		C	65295424	A	C	65295424	2	2	46	1	0	0	0	0	0	0	0	1	9931	117	5	5		5	MTFMT	15	65295424	Silent	SNP	A	TCGA-A4-7585-01A-11D-2136-08	19733696	65295424	37235968	51	3243											
C15orf27	123591	hgsc.bcm.edu	37	chr15	76484312	76484312	+	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	cccgtctccctccgcagtttGagatccggcagctgcgcgcg	4	8	12	17	6	1	1	0	1	1	1	4	2	3	1	4	1	2	4	4	1	0	1			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr15:76484312G>A	ENST00000388942.3	+	9	1048	c.772G>A	c.(772-774)Gag>Aag	p.E258K		NM_152335.2	NP_689548.2	Q2M3C6	CO027_HUMAN	chromosome 15 open reading frame 27	258					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						TCCGCAGTTTGAGATCCGGCA	0.741																																					p.E258K		Atlas-SNP	.											.	C15orf27	32	.	0			c.G772A						PASS	.						8	10	9					15																	76484312		2045	4020	6065	SO:0001583	missense	123591	exon9			CAGTTTGAGATCC	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.772G>A	chr15.hg19:g.76484312G>A	ENSP00000373594:p.Glu258Lys	43.0	0.0	.		49.0	9.0	.	NM_152335	Q8N993|Q96LL5	Missense_Mutation	SNP	ENST00000388942.3	hg19	CCDS10289.2	.	.	.	.	.	.	.	.	.	.	G	19.39	3.818369	0.71028	.	.	ENSG00000169758	ENST00000388942	T	0.47869	0.83	4.58	4.58	0.56647	.	0.123666	0.56097	D	0.000027	T	0.67392	0.2888	M	0.73962	2.25	0.58432	D	0.999999	D;D	0.71674	0.998;0.996	D;D	0.80764	0.994;0.99	T	0.70590	-0.4830	10	0.52906	T	0.07	-5.2743	14.5154	0.67816	0.0:0.0:1.0:0.0	.	222;258	Q2M3C6-2;Q2M3C6	.;CO027_HUMAN	K	258	ENSP00000373594:E258K	ENSP00000373594:E258K	E	+	1	0	C15orf27	74271367	1.000000	0.71417	1.000000	0.80357	0.669000	0.39330	8.737000	0.91562	2.097000	0.63578	0.491000	0.48974	GAG	.	.	.	none		0.741	C15orf27-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286637.2	NM_152335		A	76484312	G	A	76484312	3	1	46	1	0	0	0	0	1	0	0	0	1790	1291	45	2	802	2	C15orf27	15	76484312	Missense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08	11188888	76484312	26047080	52	3244											
CIITA	4261	hgsc.bcm.edu	37	chr16	10992818	10992818	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagtgatcggtgagagtaTggagatgccagcagaagttg	12	9	16	4	1	0	5	0	3	0	3	1	7	0	5	1	2	2	3	1	2	3	2			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr16:10992818T>C	ENST00000324288.8	+	5	528	c.395T>C	c.(394-396)aTg>aCg	p.M132T	CIITA_ENST00000381835.5_Missense_Mutation_p.M132T|CIITA_ENST00000537380.1_3'UTR	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	132	Asp/Glu-rich (acidic).|Required for acetyltransferase activity.				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						GGTGAGAGTATGGAGATGCCA	0.483			T	"FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"	"PMBL, Hodgkin Lymphona, "																																p.M132T		Atlas-SNP	.		Dom	yes		16	16p13	4261	"class II, major histocompatibility complex, transactivator"		L	.	CIITA	92	.	0			c.T395C						PASS	.						183	172	176					16																	10992818		2197	4300	6497	SO:0001583	missense	4261	exon5			AGAGTATGGAGAT	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.395T>C	chr16.hg19:g.10992818T>C	ENSP00000316328:p.Met132Thr	141.0	0.0	.		137.0	15.0	.	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Missense_Mutation	SNP	ENST00000324288.8	hg19	CCDS10544.1	.	.	.	.	.	.	.	.	.	.	T	5.450	0.268042	0.10349	.	.	ENSG00000179583	ENST00000324288;ENST00000381835;ENST00000388910;ENST00000537380	T;T	0.70749	-0.51;1.78	3.81	2.68	0.31781	.	1.431470	0.05038	N	0.475874	T	0.52224	0.1721	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B;B	0.30824	0.296;0.01;0.017;0.017;0.052;0.109	B;B;B;B;B;B	0.28849	0.095;0.005;0.014;0.014;0.047;0.021	T	0.44283	-0.9338	10	0.30078	T	0.28	.	5.0256	0.14383	0.0:0.1558:0.0:0.8442	.	132;132;132;132;133;132	F5H2J4;E9PFE0;A0N0N9;P33076;F2Z2G8;Q96KL4	.;.;.;C2TA_HUMAN;.;.	T	132;132;133;132	ENSP00000316328:M132T;ENSP00000371257:M132T	ENSP00000316328:M132T	M	+	2	0	CIITA	10900319	0.615000	0.27026	0.024000	0.17045	0.006000	0.05464	1.060000	0.30530	0.628000	0.30357	0.455000	0.32223	ATG	.	.	.	none		0.483	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246		C	10992818	T	C	10992818	3	2	46	1	0	0	0	0	1	0	0	0	3430	1464	51	3	413	3	CIITA	16	10992818	Missense_Mutation	SNP	T	TCGA-A4-7585-01A-11D-2136-08		10992818	79361935	53	3245											
GAN	8139	hgsc.bcm.edu	37	chr16	81411103	81411103	+	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	cactccttccatccgaccttCgccgtacaggatgtgcagcc	7	9	8	17	3	0	0	0	0	0	0	4	2	3	1	6	1	3	2	6	1	1	3	rs368372086		TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr16:81411103C>T	ENST00000568107.2	+	11	1858	c.1696C>T	c.(1696-1698)Cgc>Tgc	p.R566C		NM_022041.3	NP_071324.1	Q9H2C0	GAN_HUMAN	gigaxonin	566					cell death (GO:0008219)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)	25		Colorectal(91;0.153)				ATCCGACCTTCGCCGTACAGG	0.493																																					p.R566C	GBM(106;1239 1507 7582 9741 33976)	Atlas-SNP	.											.	GAN	59	.	0			c.C1696T						PASS	.	C	CYS/ARG	1,4401	2.1+/-5.4	0,1,2200	237	206	216		1696	5.6	0.9	16		216	0,8600		0,0,4300	no	missense	GAN	NM_022041.3	180	0,1,6500	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	566/598	81411103	1,13001	2201	4300	6501	SO:0001583	missense	8139	exon11			GACCTTCGCCGTA	AF291673	CCDS10935.1	16q24.1	2014-09-17	2008-08-01		ENSG00000261609	ENSG00000261609		"Kelch-like", "BTB/POZ domain containing"	4137	protein-coding gene	gene with protein product	"kelch-like family member 16"	605379	"giant axonal neuropathy (gigaxonin)"			9450783, 11062483	Standard	NM_022041		Approved	GAN1, KLHL16	uc002fgo.3	Q9H2C0	OTTHUMG00000137627	ENST00000568107.2:c.1696C>T	chr16.hg19:g.81411103C>T	ENSP00000476795:p.Arg566Cys	261.0	0.0	.		359.0	54.0	.	NM_022041		Missense_Mutation	SNP	ENST00000568107.2	hg19	CCDS10935.1	.	.	.	.	.	.	.	.	.	.	C	17.99	3.524137	0.64747	2.27E-4	0.0	ENSG00000127688	ENST00000248272	T	0.76448	-1.02	5.58	5.58	0.84498	.	0.183579	0.47852	D	0.000209	T	0.70064	0.3181	N	0.14661	0.345	0.80722	D	1	D	0.69078	0.997	P	0.47470	0.548	T	0.70103	-0.4964	10	0.29301	T	0.29	.	19.5747	0.95438	0.0:1.0:0.0:0.0	.	566	Q9H2C0	GAN_HUMAN	C	566	ENSP00000248272:R566C	ENSP00000248272:R566C	R	+	1	0	GAN	79968604	1.000000	0.71417	0.950000	0.38849	0.726000	0.41606	4.573000	0.60893	2.631000	0.89168	0.467000	0.42956	CGC	.	.	.	weak		0.493	GAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269050.3			T	81411103	C	T	81411103	3	4	46	1	0	0	0	0	1	0	0	0	6239	884	31	1	1738	1	GAN	16	81411103	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	70418285	81411103	8943650	54	3246											
KRT9	3857	hgsc.bcm.edu	37	chr17	39726126	39726126	+	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	cctacctccttatgattcttCttgagggccatcagctcctc	6	14	6	15	0	3	2	1	2	2	0	6	2	5	2	5	1	2	1	5	1	2	5			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr17:39726126C>A	ENST00000246662.4	-	3	932	c.867G>T	c.(865-867)aaG>aaT	p.K289N	KRT9_ENST00000588431.1_Missense_Mutation_p.K56N	NM_000226.3	NP_000217.2	P35527	K1C9_HUMAN	keratin 9	289	Coil 1B.|Rod.				epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)	p.K289N(1)		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)				TATGATTCTTCTTGAGGGCCA	0.537																																					p.K289N		Atlas-SNP	.											KRT9,NS,carcinoma,0,1	KRT9	78	.	1	Substitution - Missense(1)	lung(1)	c.G867T						PASS	.						100	101	101					17																	39726126		2200	4295	6495	SO:0001583	missense	3857	exon3			ATTCTTCTTGAGG		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.867G>T	chr17.hg19:g.39726126C>A	ENSP00000246662:p.Lys289Asn	264.0	0.0	.		277.0	60.0	.	NM_000226	O00109|Q0IJ47|Q14665	Missense_Mutation	SNP	ENST00000246662.4	hg19	CCDS32654.1	.	.	.	.	.	.	.	.	.	.	C	15.92	2.974370	0.53720	.	.	ENSG00000171403	ENST00000246662	D	0.93547	-3.24	4.86	2.84	0.33178	Filament (1);	0.249082	0.20923	N	0.083245	D	0.95940	0.8678	M	0.86805	2.84	0.29942	N	0.821017	D	0.58268	0.982	P	0.59825	0.864	D	0.92785	0.6243	10	0.87932	D	0	.	11.0067	0.47637	0.0:0.8453:0.0:0.1547	.	289	P35527	K1C9_HUMAN	N	289	ENSP00000246662:K289N	ENSP00000246662:K289N	K	-	3	2	KRT9	36979652	1.000000	0.71417	0.925000	0.36789	0.365000	0.29674	1.620000	0.36976	0.452000	0.26830	0.491000	0.48974	AAG	.	.	.	none		0.537	KRT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257707.1	NM_000226		A	39726126	C	A	39726126	3	1	46	1	0	0	0	0	1	0	0	0	8508	912	32	4	1024	4	KRT9	17	39726126	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08		39726126	41469084	55	3247											
CACNA1G	8913	hgsc.bcm.edu	37	chr17	48692731	48692732	+	Frame_Shift_Del	DEL	GC	GC	-																															tgccccatcagaagcccagtGcaaaccttactactccgact																										TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr17:48692731_48692732delGC	ENST00000359106.5	+	27	4769_4770	c.4769_4770delGC	c.(4768-4770)tgcfs	p.C1590fs	CACNA1G_ENST00000515765.1_Frame_Shift_Del_p.C1579fs|CACNA1G_ENST00000360761.4_Frame_Shift_Del_p.C1567fs|CACNA1G_ENST00000515165.1_Frame_Shift_Del_p.C1590fs|CACNA1G_ENST00000358244.5_Frame_Shift_Del_p.C1556fs|CACNA1G_ENST00000510366.1_Frame_Shift_Del_p.C1538fs|CACNA1G_ENST00000354983.4_Frame_Shift_Del_p.C1556fs|CACNA1G_ENST00000429973.2_Frame_Shift_Del_p.C1572fs|CACNA1G_ENST00000507896.1_Frame_Shift_Del_p.C1579fs|CACNA1G_ENST00000352832.5_Frame_Shift_Del_p.C1556fs|CACNA1G_ENST00000514181.1_Frame_Shift_Del_p.C1572fs|CACNA1G_ENST00000442258.2_Frame_Shift_Del_p.C1549fs|CACNA1G_ENST00000505165.1_Frame_Shift_Del_p.C1590fs|CACNA1G_ENST00000515411.1_Frame_Shift_Del_p.C1572fs|CACNA1G_ENST00000514717.1_Frame_Shift_Del_p.C1533fs|CACNA1G_ENST00000507510.2_Frame_Shift_Del_p.C1590fs|CACNA1G_ENST00000502264.1_Frame_Shift_Del_p.C1567fs|CACNA1G_ENST00000514079.1_Frame_Shift_Del_p.C1597fs|CACNA1G_ENST00000512389.1_Frame_Shift_Del_p.C1579fs|CACNA1G_ENST00000513964.1_Frame_Shift_Del_p.C1545fs|CACNA1G_ENST00000507609.1_Frame_Shift_Del_p.C1590fs|CACNA1G_ENST00000513689.2_Frame_Shift_Del_p.C1545fs|CACNA1G_ENST00000503485.1_Frame_Shift_Del_p.C1556fs|CACNA1G_ENST00000507336.1_Frame_Shift_Del_p.C1579fs|CACNA1G_ENST00000510115.1_Frame_Shift_Del_p.C1556fs	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	1590					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)	GAAGCCCAGTGCAAACCTTACT	0.629																																					p.1597_1597del		Atlas-INDEL	.											.	CACNA1G	659	.	0			c.4789_4790del						PASS	.																																			SO:0001589	frameshift_variant	8913	exon27			.	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.4769_4770delGC	chr17.hg19:g.48692731_48692732delGC	ENSP00000352011:p.Cys1590fs	50.0	0.0	0		75.0	13.0	0.173333	NM_001256325	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Frame_Shift_Del	DEL	ENST00000359106.5	hg19	CCDS45730.1																																																																																			.	.	.	none		0.629	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		-	48692732	GC	-	48692731	7	5	46	1	0	1	0	1	0	0	0	0	2546	1319	46	0	5142	0	CACNA1G	17	48692731	Frame_Shift_Del	DEL	GC	TCGA-A4-7585-01A-11D-2136-08	8966605	48692731	32502479	56	3248											
PPM1D	8493	hgsc.bcm.edu	37	chr17	58740446	58740446	+	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	ccttctcagagaattttttaGaggtttcagctgagatagct	10	15	9	7	0	2	3	2	1	1	3	3	5	2	3	1	1	2	3	1	1	3	6			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr17:58740446G>T	ENST00000305921.3	+	6	1583	c.1351G>T	c.(1351-1353)Gag>Tag	p.E451*	RNU6-623P_ENST00000363143.1_RNA	NM_003620.3	NP_003611.1	O15297	PPM1D_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1D	451					G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of cell proliferation (GO:0008285)|peptidyl-threonine dephosphorylation (GO:0035970)|protein dephosphorylation (GO:0006470)|response to bacterium (GO:0009617)|response to radiation (GO:0009314)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	15	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;6.75e-12)|all cancers(12;1.96e-10)			GAATTTTTTAGAGGTTTCAGC	0.443											OREG0031485	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.E451X		Atlas-SNP	.											.	PPM1D	50	.	0			c.G1351T						PASS	.						100	99	100					17																	58740446		2203	4300	6503	SO:0001587	stop_gained	8493	exon6			TTTTTAGAGGTTT	U78305	CCDS11625.1	17q23.3	2014-09-17	2010-03-05		ENSG00000170836	ENSG00000170836		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9277	protein-coding gene	gene with protein product	"wild-type p53-induced phosphatase 1", "protein phosphatase 2C, delta isoform"	605100	"protein phosphatase 1D magnesium-dependent, delta isoform"			9177166	Standard	NM_003620		Approved	Wip1, PP2C-DELTA	uc002iyt.2	O15297		ENST00000305921.3:c.1351G>T	chr17.hg19:g.58740446G>T	ENSP00000306682:p.Glu451*	101.0	0.0	.	1033	142.0	42.0	.	NM_003620	Q53XP4|Q6P991|Q8IVR6	Nonsense_Mutation	SNP	ENST00000305921.3	hg19	CCDS11625.1	.	.	.	.	.	.	.	.	.	.	G	39	7.470853	0.98306	.	.	ENSG00000170836	ENST00000305921	.	.	.	6.08	6.08	0.98989	.	0.064947	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	-21.5774	13.8168	0.63297	0.0695:0.0:0.9305:0.0	.	.	.	.	X	451	.	ENSP00000306682:E451X	E	+	1	0	PPM1D	56095228	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	5.119000	0.64679	2.894000	0.99253	0.591000	0.81541	GAG	.	.	.	none		0.443	PPM1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449474.1	NM_003620		T	58740446	G	T	58740446	4	4	46	1	0	0	0	0	0	1	0	0	12347	943	33	4	1373	4	PPM1D	17	58740446	Nonsense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08	10047715	58740446	22454764	57	3249											
TANC2	26115	hgsc.bcm.edu	37	chr17	61490920	61490920	+	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	acaggtccagccacatgggcGatggccacctccaagccaga	11	4	11	15	1	0	1	0	0	0	1	2	2	2	1	6	3	2	0	6	3	1	0			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr17:61490920G>T	ENST00000424789.2	+	22	3697	c.3693G>T	c.(3691-3693)gcG>gcT	p.A1231A	RP11-269G24.3_ENST00000583552.1_RNA|TANC2_ENST00000389520.4_Silent_p.A1241A|AC015923.1_ENST00000431604.1_RNA	NM_025185.3	NP_079461.2	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	1231					in utero embryonic development (GO:0001701)					breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|upper_aerodigestive_tract(3)	44						CCACATGGGCGATGGCCACCT	0.488																																					p.A1231A		Atlas-SNP	.											TANC2_ENST00000389520,NS,carcinoma,0,2	TANC2	266	.	0			c.G3693T						PASS	.						42	41	41					17																	61490920		2039	4205	6244	SO:0001819	synonymous_variant	26115	exon22			ATGGGCGATGGCC	AB032974	CCDS45754.1	17q23.3	2013-01-11				ENSG00000170921		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30212	protein-coding gene	gene with protein product	"rolling pebbles homolog B (Drosophila)"	615047					Standard	NM_025185		Approved	DKFZP564D166, FLJ10215, FLJ11824, KIAA1148, KIAA1636, rols, ROLSA	uc002jal.4	Q9HCD6		ENST00000424789.2:c.3693G>T	chr17.hg19:g.61490920G>T		14.0	0.0	.		28.0	4.0	.	NM_025185	Q9HAC3|Q9NW88|Q9NXY9|Q9ULS2	Silent	SNP	ENST00000424789.2	hg19	CCDS45754.1																																																																																			.	.	.	none		0.488	TANC2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444765.1			T	61490920	G	T	61490920	2	4	46	1	0	0	0	0	0	0	0	1	15557	1045	37	4		4	TANC2	17	61490920	Silent	SNP	G	TCGA-A4-7585-01A-11D-2136-08	2750474	61490920	19704290	58	3250											
ABCA8	10351	hgsc.bcm.edu	37	chr17	66928478	66928478	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtcatcaaggccttcatccTtttcctctctcttgtgacat	6	17	5	13	0	5	1	3	1	2	0	8	1	7	1	3	1	0	0	3	1	1	4	rs149928780	byFrequency	TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr17:66928478T>C	ENST00000269080.2	-	6	885	c.748A>G	c.(748-750)Agg>Ggg	p.R250G	ABCA8_ENST00000430352.2_Missense_Mutation_p.R250G|ABCA8_ENST00000586539.1_Missense_Mutation_p.R250G	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	250					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)					GCCTTCATCCTTTTCCTCTCT	0.393													T|||	2	0.000399361	0.0015	0	5008	,	,		20503	0		0	False		,,,				2504	0				p.R250G		Atlas-SNP	.											.	ABCA8	213	.	0			c.A748G						PASS	.	T	GLY/ARG	1,4405	2.1+/-5.4	0,1,2202	89	82	84		748	1.2	0	17	dbSNP_134	84	0,8600		0,0,4300	no	missense	ABCA8	NM_007168.2	125	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign	250/1582	66928478	1,13005	2203	4300	6503	SO:0001583	missense	10351	exon6			TCATCCTTTTCCT	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.748A>G	chr17.hg19:g.66928478T>C	ENSP00000269080:p.Arg250Gly	47.0	0.0	.		76.0	5.0	.	NM_007168	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	hg19	CCDS11680.1	.	.	.	.	.	.	.	.	.	.	T	7.800	0.713528	0.15306	2.27E-4	0.0	ENSG00000141338	ENST00000269080;ENST00000430352;ENST00000541225;ENST00000428549	D;D	0.84070	-1.8;-1.8	4.86	1.22	0.21188	.	0.865701	0.09871	N	0.744923	T	0.76550	0.4003	L	0.55481	1.735	0.09310	N	1	B;B;B;B;B	0.27951	0.195;0.157;0.044;0.109;0.034	B;B;B;B;B	0.29524	0.089;0.103;0.038;0.098;0.044	T	0.65253	-0.6213	10	0.56958	D	0.05	.	3.7768	0.08663	0.3317:0.0923:0.0:0.576	.	189;250;250;250;250	F5H6Z4;A1L3U3;B4DJ11;C9JQE6;O94911	.;.;.;.;ABCA8_HUMAN	G	250;250;189;250	ENSP00000269080:R250G;ENSP00000402814:R250G	ENSP00000269080:R250G	R	-	1	2	ABCA8	64440073	0.000000	0.05858	0.002000	0.10522	0.197000	0.23852	0.098000	0.15189	0.065000	0.16485	0.460000	0.39030	AGG	.	T|1.000;C|0.000	0.000	weak		0.393	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		C	66928478	T	C	66928478	3	2	46	1	0	0	0	0	1	0	0	0	38	1608	56	3	4129	3	ABCA8	17	66928478	Missense_Mutation	SNP	T	TCGA-A4-7585-01A-11D-2136-08	5437558	66928478	14266732	59	3251											
ABCA5	23461	hgsc.bcm.edu	37	chr17	67304486	67304486	+	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	tgaggaccagtactgagcagCctcacatgattttgaacagc	12	9	10	10	0	1	4	1	4	0	0	1	5	1	5	2	1	5	2	2	1	2	3			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr17:67304486C>G	ENST00000392676.3	-	5	557	c.493G>C	c.(493-495)Gct>Cct	p.A165P	ABCA5_ENST00000588877.1_Missense_Mutation_p.A165P|ABCA5_ENST00000392677.2_Missense_Mutation_p.A165P			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	165					cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	TACTGAGCAGCCTCACATGAT	0.378																																					p.A165P		Atlas-SNP	.											.	ABCA5	162	.	0			c.G493C						PASS	.						98	103	101					17																	67304486		2203	4300	6503	SO:0001583	missense	23461	exon4			GAGCAGCCTCACA	U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"ATP binding cassette transporters / subfamily A"	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.493G>C	chr17.hg19:g.67304486C>G	ENSP00000376443:p.Ala165Pro	170.0	0.0	.		174.0	23.0	.	NM_018672	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Missense_Mutation	SNP	ENST00000392676.3	hg19	CCDS11685.1	.	.	.	.	.	.	.	.	.	.	C	15.02	2.710325	0.48517	.	.	ENSG00000154265	ENST00000392677;ENST00000392676	T;T	0.39229	1.09;1.09	4.96	4.96	0.65561	.	0.108387	0.40908	D	0.000993	T	0.54727	0.1876	L	0.47190	1.495	0.49483	D	0.999799	D;D	0.63880	0.984;0.993	P;D	0.67725	0.877;0.953	T	0.51276	-0.8726	9	.	.	.	.	13.9115	0.63869	0.1528:0.8472:0.0:0.0	.	165;165	Q8WWZ7-2;Q8WWZ7	.;ABCA5_HUMAN	P	165	ENSP00000376444:A165P;ENSP00000376443:A165P	.	A	-	1	0	ABCA5	64816081	0.993000	0.37304	0.999000	0.59377	0.987000	0.75469	2.955000	0.49121	2.293000	0.77203	0.585000	0.79938	GCT	.	.	.	none		0.378	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672		G	67304486	C	G	67304486	3	3	46	1	0	0	0	0	1	0	0	0	35	739	26	4	4575	4	ABCA5	17	67304486	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08	376008	67304486	13890724	60	3252											
GAA	2548	hgsc.bcm.edu	37	chr17	78085893	78085894	+	Frame_Shift_Del	DEL	CC	CC	-																															cctgaccgaagccatcgcctCccacaggtgagggccacgtc																										TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	CC	CC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr17:78085893_78085894delCC	ENST00000302262.3	+	12	1967_1968	c.1748_1749delCC	c.(1747-1749)tccfs	p.S583fs	GAA_ENST00000390015.3_Frame_Shift_Del_p.S583fs	NM_000152.3	NP_000143.2	P10253	LYAG_HUMAN	glucosidase, alpha; acid	583					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)	GCCATCGCCTCCCACAGGTGAG	0.649																																					p.583_583del		Atlas-INDEL	.											.	GAA	66	.	0			c.1747_1748del	GRCh37	CM082761	GAA	M		PASS	.																																			SO:0001589	frameshift_variant	2548	exon13			.		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.1748_1749delCC	chr17.hg19:g.78085893_78085894delCC	ENSP00000305692:p.Ser583fs	108.0	0.0	0		107.0	20.0	0.186916	NM_001079803	Q09GN4|Q14351|Q16302|Q8IWE7	Frame_Shift_Del	DEL	ENST00000302262.3	hg19	CCDS32760.1																																																																																			.	.	.	none		0.649	GAA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437441.1			-	78085894	CC	-	78085893	7	5	46	1	0	1	0	1	0	0	0	0	6154	855	30	0	1790	0	GAA	17	78085893	Frame_Shift_Del	DEL	CC	TCGA-A4-7585-01A-11D-2136-08	10781407	78085893	3109317	61	3253											
ZNF681	148213	hgsc.bcm.edu	37	chr19	23926507	23926507	+	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	cttttaggtttgtagagtttCtcaccagtatgaattttctt	8	20	7	6	0	2	2	1	1	2	1	3	2	2	2	1	1	0	4	1	1	4	9			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr19:23926507C>G	ENST00000402377.3	-	4	1986	c.1845G>C	c.(1843-1845)gaG>gaC	p.E615D	ZNF681_ENST00000395385.3_Missense_Mutation_p.E546D	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	615					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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)				TGTAGAGTTTCTCACCAGTAT	0.333																																					p.E615D		Atlas-SNP	.											ZNF681,colon,carcinoma,0,2	ZNF681	76	.	0			c.G1845C						PASS	.						60	61	61					19																	23926507		2202	4300	6502	SO:0001583	missense	148213	exon4			GAGTTTCTCACCA	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.1845G>C	chr19.hg19:g.23926507C>G	ENSP00000384000:p.Glu615Asp	16.0	0.0	.		27.0	4.0	.	NM_138286	B3KVF7	Missense_Mutation	SNP	ENST00000402377.3	hg19	CCDS12414.2	.	.	.	.	.	.	.	.	.	.	.	8.238	0.806253	0.16467	.	.	ENSG00000196172	ENST00000402377;ENST00000395385	T;T	0.34472	1.36;1.36	1.44	1.44	0.22558	Zinc finger, C2H2 (1);	.	.	.	.	T	0.31327	0.0793	L	0.49350	1.555	0.25356	N	0.988829	B	0.18013	0.025	B	0.17979	0.02	T	0.31447	-0.9943	9	0.62326	D	0.03	.	8.329	0.32175	0.0:1.0:0.0:0.0	.	615	Q96N22	ZN681_HUMAN	D	615;546	ENSP00000384000:E615D;ENSP00000378783:E546D	ENSP00000378783:E546D	E	-	3	2	ZNF681	23718347	0.416000	0.25424	0.017000	0.16124	0.114000	0.19823	0.067000	0.14510	0.754000	0.32968	0.205000	0.17691	GAG	.	.	.	none		0.333	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286		G	23926507	C	G	23926507	3	3	46	1	0	0	0	0	1	0	0	0	18100	912	32	4	96	4	ZNF681	19	23926507	Missense_Mutation	SNP	C	TCGA-A4-7585-01A-11D-2136-08		23926507	35202476	62	3254											
SLC23A2	9962	hgsc.bcm.edu	37	chr20	4855238	4855238	+	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	tcacagggaacattttgaacAgctgtaacttgtacgcagtc	12	11	9	9	1	1	1	1	1	0	0	2	2	1	2	0	1	5	4	0	1	4	5			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr20:4855238A>T	ENST00000379333.1	-	10	1321	c.929T>A	c.(928-930)cTg>cAg	p.L310Q	SLC23A2_ENST00000338244.1_Missense_Mutation_p.L310Q|SLC23A2_ENST00000468355.1_5'UTR|SLC23A2_ENST00000424750.2_Missense_Mutation_p.L196Q	NM_203327.1	NP_976072.1	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 2	310					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						CATTTTGAACAGCTGTAACTT	0.383																																					p.L310Q		Atlas-SNP	.											.	SLC23A2	62	.	0			c.T929A						PASS	.						195	187	190					20																	4855238		2203	4300	6503	SO:0001583	missense	9962	exon10			TTGAACAGCTGTA	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.929T>A	chr20.hg19:g.4855238A>T	ENSP00000368637:p.Leu310Gln	213.0	0.0	.		181.0	28.0	.	NM_203327	B4DJZ1|Q8WWR4|Q92512|Q96D54|Q9UNU1|Q9UP85	Missense_Mutation	SNP	ENST00000379333.1	hg19	CCDS13085.1	.	.	.	.	.	.	.	.	.	.	A	12.02	1.811425	0.32053	.	.	ENSG00000089057	ENST00000379333;ENST00000338244;ENST00000424750	T;T;T	0.21543	2.0;2.0;2.0	5.44	5.44	0.79542	.	0.062992	0.64402	D	0.000005	T	0.40694	0.1127	M	0.62088	1.915	0.58432	D	0.999999	D;D;D	0.59767	0.986;0.976;0.976	P;P;P	0.60789	0.876;0.879;0.879	T	0.28996	-1.0026	10	0.87932	D	0	-14.7288	14.3204	0.66482	1.0:0.0:0.0:0.0	.	196;310;310	B4DJZ1;A0MSJ5;Q9UGH3	.;.;S23A2_HUMAN	Q	310;310;196	ENSP00000368637:L310Q;ENSP00000344322:L310Q;ENSP00000406601:L196Q	ENSP00000344322:L310Q	L	-	2	0	SLC23A2	4803238	1.000000	0.71417	0.998000	0.56505	0.004000	0.04260	9.339000	0.96797	2.063000	0.61619	0.533000	0.62120	CTG	.	.	.	none		0.383	SLC23A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077832.1			T	4855238	A	T	4855238	3	4	46	1	0	0	0	0	1	0	0	0	14476	188	7	5	1055	5	SLC23A2	20	4855238	Missense_Mutation	SNP	A	TCGA-A4-7585-01A-11D-2136-08		4855238	58170282	63	3255											
MYO18B	84700	hgsc.bcm.edu	37	chr22	26423002	26423002	+	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	ttcagttcctgcgagtccctCttagaatccagaccgagcat	9	11	8	13	2	2	2	1	0	1	2	5	4	5	2	4	0	2	2	4	0	2	3			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr22:26423002C>G	ENST00000407587.2	+	43	7234	c.7065C>G	c.(7063-7065)ctC>ctG	p.L2355L	MYO18B_ENST00000335473.7_Silent_p.L2354L|MYO18B_ENST00000536101.1_Silent_p.L2354L			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2354						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						GCGAGTCCCTCTTAGAATCCA	0.572																																					p.L2354L		Atlas-SNP	.											MYO18B,right_upper_lobe,carcinoma,0,1	MYO18B	322	.	0			c.C7062G						PASS	.						86	94	91					22																	26423002		1936	4137	6073	SO:0001819	synonymous_variant	84700	exon43			GTCCCTCTTAGAA	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.7065C>G	chr22.hg19:g.26423002C>G		185.0	0.0	.		200.0	48.0	.	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	hg19		.	.	.	.	.	.	.	.	.	.	C	3.671	-0.067510	0.07273	.	.	ENSG00000133454	ENST00000543971	.	.	.	4.89	-0.276	0.12902	.	.	.	.	.	T	0.40222	0.1108	.	.	.	0.31595	N	0.653425	.	.	.	.	.	.	T	0.47100	-0.9143	4	.	.	.	.	8.3531	0.32314	0.0:0.4167:0.4883:0.095	.	.	.	.	C	304	.	.	S	+	2	0	MYO18B	24753002	0.045000	0.20229	0.019000	0.16419	0.647000	0.38526	-0.357000	0.07651	-0.215000	0.10063	0.462000	0.41574	TCT	.	.	.	none		0.572	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		G	26423002	C	G	26423002	2	3	46	1	0	0	0	0	0	0	0	1	10073	900	32	4		4	MYO18B	22	26423002	Silent	SNP	C	TCGA-A4-7585-01A-11D-2136-08		26423002	24881564	64	3256											
PKDREJ	10343	hgsc.bcm.edu	37	chr22	46653660	46653660	+	Missense_Mutation	SNP	T	T	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	aggcttataagtaaatccatTggtactctcatctatagcct	12	14	6	9	0	2	0	1	0	2	0	4	0	3	0	2	2	2	3	2	2	7	7			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr22:46653660T>G	ENST00000253255.5	-	1	5559	c.5560A>C	c.(5560-5562)Aat>Cat	p.N1854H		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	1854					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)		GTAAATCCATTGGTACTCTCA	0.383																																					p.N1854H		Atlas-SNP	.											.	PKDREJ	195	.	0			c.A5560C						PASS	.						133	136	135					22																	46653660		2203	4300	6503	SO:0001583	missense	10343	exon1			ATCCATTGGTACT	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.5560A>C	chr22.hg19:g.46653660T>G	ENSP00000253255:p.Asn1854His	134.0	0.0	.		137.0	34.0	.	NM_006071	B1AJY3|O95850	Missense_Mutation	SNP	ENST00000253255.5	hg19	CCDS14073.1	.	.	.	.	.	.	.	.	.	.	T	4.903	0.167837	0.09339	.	.	ENSG00000130943	ENST00000253255	T	0.70045	-0.45	4.51	-2.95	0.05564	Polycystin cation channel, PKD1/PKD2 (1);	1.774300	0.02687	N	0.110187	T	0.44371	0.1290	N	0.11560	0.145	0.09310	N	1	B	0.12013	0.005	B	0.15052	0.012	T	0.20940	-1.0260	10	0.30078	T	0.28	-0.4113	5.5709	0.17196	0.0:0.3289:0.2649:0.4062	.	1854	Q9NTG1	PKDRE_HUMAN	H	1854	ENSP00000253255:N1854H	ENSP00000253255:N1854H	N	-	1	0	PKDREJ	45032324	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-0.516000	0.06282	-0.535000	0.06307	0.374000	0.22700	AAT	.	.	.	none		0.383	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		G	46653660	T	G	46653660	3	3	46	1	0	0	0	0	1	0	0	0	11977	1812	63	5	1205	5	PKDREJ	22	46653660	Missense_Mutation	SNP	T	TCGA-A4-7585-01A-11D-2136-08	20230658	46653660	4650906	65	3257											
SAPS2	9701	hgsc.bcm.edu	37	chr22	50878437	50878437	+	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	tccggtggacacagaatgcaGccatgctgagggcagccgga	10	5	15	11	2	0	2	0	1	0	1	1	4	1	4	3	4	4	3	3	4	1	0			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chr22:50878437G>T	ENST00000216061.5	+	22	2703	c.2333G>T	c.(2332-2334)aGc>aTc	p.S778I	PPP6R2_ENST00000395744.3_Missense_Mutation_p.S751I|PPP6R2_ENST00000395741.3_Missense_Mutation_p.S752I|PPP6R2_ENST00000359139.3_Missense_Mutation_p.S752I			O75170	PP6R2_HUMAN	protein phosphatase 6, regulatory subunit 2	778						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						ACAGAATGCAGCCATGCTGAG	0.642																																					p.S778I		Atlas-SNP	.											.	PPP6R2	71	.	0			c.G2333T						PASS	.						42	42	42					22																	50878437		2203	4300	6503	SO:0001583	missense	9701	exon21			AATGCAGCCATGC	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.2333G>T	chr22.hg19:g.50878437G>T	ENSP00000216061:p.Ser778Ile	86.0	0.0	.		69.0	13.0	.	NM_001242898	A6PVG3|B7Z7T3|Q5U5P3|Q7Z2L2|Q7Z5G5|Q7Z731|Q9UGB9	Missense_Mutation	SNP	ENST00000216061.5	hg19		.	.	.	.	.	.	.	.	.	.	G	16.34	3.095777	0.56075	.	.	ENSG00000100239	ENST00000359139;ENST00000395741;ENST00000395744;ENST00000216061	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	4.84	2.68	0.31781	.	0.269718	0.36628	N	0.002493	T	0.63153	0.2487	M	0.70275	2.135	0.09310	N	1	D;D;D;D;D;D	0.71674	0.993;0.992;0.986;0.998;0.996;0.998	P;D;P;D;D;D	0.70716	0.877;0.917;0.828;0.956;0.917;0.97	T	0.55296	-0.8163	10	0.72032	D	0.01	-11.7634	10.2693	0.43473	0.0:0.1469:0.7006:0.1524	.	311;778;778;752;751;752	F2Z3M7;O75170-5;O75170;O75170-3;O75170-4;O75170-2	.;.;PP6R2_HUMAN;.;.;.	I	752;752;751;778	ENSP00000352051:S752I;ENSP00000379090:S752I;ENSP00000379093:S751I;ENSP00000216061:S778I	ENSP00000216061:S778I	S	+	2	0	PPP6R2	49225303	0.020000	0.18652	0.001000	0.08648	0.015000	0.08874	1.601000	0.36773	0.523000	0.28482	0.561000	0.74099	AGC	.	.	.	none		0.642	PPP6R2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316809.1	NM_014678		T	50878437	G	T	50878437	3	4	46	1	0	0	0	0	1	0	0	0	13850	971	34	4	2322	4	SAPS2	22	50878437	Missense_Mutation	SNP	G	TCGA-A4-7585-01A-11D-2136-08	4224777	50878437	426129	66	3258											
PTCHD1	139411	hgsc.bcm.edu	37	chrX	23411958	23411959	+	Frame_Shift_Ins	INS	-	-	G																															tgctccaatgttatccacatINSttgttctgggcaaggatttc																										TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chrX:23411958_23411959insG	ENST00000379361.4	+	3	3183_3184	c.2323_2324insG	c.(2323-2325)tttfs	p.F775fs		NM_173495.2	NP_775766.2	Q96NR3	PTHD1_HUMAN	patched domain containing 1	775					cognition (GO:0050890)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(4)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(4)|skin(2)|urinary_tract(2)	42						GTTATCCACATTTGTTCTGGGC	0.371																																					p.F775fs		Atlas-INDEL	.											.	PTCHD1	213	.	0			c.2323_2324insG						PASS	.																																			SO:0001589	frameshift_variant	139411	exon3			.	AK054858	CCDS35215.2	Xp22.13	2008-02-05			ENSG00000165186	ENSG00000165186			26392	protein-coding gene	gene with protein product		300828					Standard	NM_173495		Approved	FLJ30296	uc004dal.4	Q96NR3	OTTHUMG00000021251	Exception_encountered	chrX.hg19:g.23411958_23411959insG	ENSP00000368666:p.Phe775fs	55.0	0.0	0		44.0	19.0	0.431818	NM_173495	B4DQH0|Q0IJ60|Q6P6B8	Frame_Shift_Ins	INS	ENST00000379361.4	hg19	CCDS35215.2																																																																																			.	.	.	none		0.371	PTCHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056047.2	NM_173495		G	23411959	-	G	23411958	7	5	46	1	0	1	1	0	0	0	0	0	12742	1493	52	0	2333	0	PTCHD1	23	23411958	Frame_Shift_Ins	INS	-	TCGA-A4-7585-01A-11D-2136-08		23411958	131858602	67	3259											
FMR1	2332	hgsc.bcm.edu	37	chrX	147011651	147011651	+	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	aatttaaatcatttagtccaTcaatgaagtcacctcaaagc	16	12	4	9	0	4	1	4	1	0	0	5	1	5	1	2	0	1	0	2	0	7	4			TCGA-A4-7585-01A-11D-2136-08	TCGA-A4-7585-11A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62550e91-8d87-4feb-a763-bedc2e84cebe	2e2066d9-8dd8-4483-8bd9-67b26cbedc59	g.chrX:147011651T>A	ENST00000370475.4	+	7	646	c.518T>A	c.(517-519)aTc>aAc	p.I173N	FMR1_ENST00000334557.6_Missense_Mutation_p.I173N|FMR1_ENST00000218200.8_Missense_Mutation_p.I173N|FMR1_ENST00000440235.2_5'Flank|FMR1_ENST00000439526.2_Missense_Mutation_p.I173N|FMR1_ENST00000370471.3_Missense_Mutation_p.I173N|FMR1_ENST00000370470.1_Missense_Mutation_p.I173N|FMR1_ENST00000370477.1_Missense_Mutation_p.I173N	NM_002024.5	NP_002015.1	Q06787	FMR1_HUMAN	fragile X mental retardation 1	173					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)					ATTTAGTCCATCAATGAAGTC	0.353									Fragile X syndrome																												p.I173N		Atlas-SNP	.											.	FMR1	93	.	0			c.T518A						PASS	.						116	99	105					X																	147011651		2203	4300	6503	SO:0001583	missense	2332	exon7	Familial Cancer Database	Martin-Bell syndrome, FRAXA syndrome	AGTCCATCAATGA	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.518T>A	chrX.hg19:g.147011651T>A	ENSP00000359506:p.Ile173Asn	69.0	0.0	.		47.0	4.0	.	NM_002024	A6NNH4|D3DWT0|D3DWT1|D3DWT2|G8JL90|Q16578|Q5PQZ6|Q99054	Missense_Mutation	SNP	ENST00000370475.4	hg19	CCDS14682.1	.	.	.	.	.	.	.	.	.	.	T	7.528	0.658159	0.14645	.	.	ENSG00000102081	ENST00000218200;ENST00000370471;ENST00000370477;ENST00000370475;ENST00000334557;ENST00000439526;ENST00000370470	T;T;T;T;T;T;T	0.56103	1.25;0.48;1.26;1.26;1.56;1.27;1.28	5.12	5.12	0.69794	.	0.053956	0.85682	D	0.000000	T	0.40119	0.1104	N	0.02011	-0.69	0.80722	D	1	B;P;B;D;D	0.62365	0.0;0.88;0.007;0.991;0.98	B;B;B;P;P	0.59889	0.001;0.296;0.008;0.865;0.805	T	0.45760	-0.9239	10	0.17832	T	0.49	-24.9991	13.3209	0.60432	0.0:0.0:0.0:1.0	.	173;173;89;173;173	Q8IXW7;Q06787;Q59GC1;Q06787-8;G3V0J0	.;FMR1_HUMAN;.;.;.	N	173	ENSP00000218200:I173N;ENSP00000359502:I173N;ENSP00000359508:I173N;ENSP00000359506:I173N;ENSP00000355115:I173N;ENSP00000395923:I173N;ENSP00000359501:I173N	ENSP00000218200:I173N	I	+	2	0	FMR1	146819343	1.000000	0.71417	0.999000	0.59377	0.830000	0.47004	6.149000	0.71795	1.808000	0.52836	0.430000	0.28490	ATC	.	.	.	none		0.353	FMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058655.1	NM_002024		A	147011651	T	A	147011651	3	1	46	1	0	0	0	0	1	0	0	0	5967	1435	50	5	544	5	FMR1	23	147011651	Missense_Mutation	SNP	T	TCGA-A4-7585-01A-11D-2136-08	123599693	147011651	8258909	68	3260											
TMEM200B	399474	hgsc.bcm.edu	37	chr1	29447533	29447533	+	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	ccgagctgctggggccccaaGgaggagctccccaaggccca	8	3	14	16	1	0	0	0	0	0	0	1	3	1	2	6	5	3	3	6	5	2	0			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr1:29447533G>A	ENST00000420504.2	-	2	965	c.808C>T	c.(808-810)Ctt>Ttt	p.L270F	TMEM200B_ENST00000521452.1_Missense_Mutation_p.L270F	NM_001171868.1	NP_001165339.1	Q69YZ2	T200B_HUMAN	transmembrane protein 200B	270						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)		GGGGCCCCAAGGAGGAGCTCC	0.622																																					p.L270F		Atlas-SNP	.											.	TMEM200B	9	.	0			c.C808T						PASS	.						23	25	25					1																	29447533		2202	4300	6502	SO:0001583	missense	399474	exon2			CCCCAAGGAGGAG		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.808C>T	chr1.hg19:g.29447533G>A	ENSP00000428544:p.Leu270Phe	72.0	0.0	.		34.0	14.0	.	NM_001171868	Q6P2G8|Q6P2Q5	Missense_Mutation	SNP	ENST00000420504.2	hg19	CCDS30658.1	.	.	.	.	.	.	.	.	.	.	G	18.17	3.565457	0.65651	.	.	ENSG00000253304	ENST00000521452;ENST00000420504	.	.	.	4.15	4.15	0.48705	.	0.000000	0.35903	U	0.002907	T	0.64681	0.2620	L	0.27053	0.805	0.35733	D	0.818101	D	0.89917	1.0	D	0.80764	0.994	T	0.75133	-0.3425	9	0.87932	D	0	.	15.9517	0.79843	0.0:0.0:1.0:0.0	.	270	Q69YZ2	T200B_HUMAN	F	270	.	ENSP00000428544:L270F	L	-	1	0	TMEM200B	29320120	0.952000	0.32445	1.000000	0.80357	0.996000	0.88848	2.717000	0.47227	2.288000	0.76882	0.655000	0.94253	CTT	.	.	.	none		0.622	TMEM200B-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010377.2	NM_001003682		A	29447533	G	A	29447533	3	1	47	1	0	0	0	0	1	0	0	0	16136	1000	35	2	119	2	TMEM200B	1	29447533	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08		29447533	219803088	1	3261											
ABCA4	24	hgsc.bcm.edu	37	chr1	94548962	94548962	+	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	cctccccaagatctcagattGataccttgagaacggctgtc	10	10	8	13	1	1	4	1	2	1	3	4	5	2	4	4	1	2	1	4	1	3	3			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr1:94548962G>A	ENST00000370225.3	-	7	890	c.804C>T	c.(802-804)atC>atT	p.I268I	ABCA4_ENST00000535735.1_Silent_p.I268I	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	268					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)		ATCTCAGATTGATACCTTGAG	0.348																																					p.I268I		Atlas-SNP	.											.	ABCA4	275	.	0			c.C804T						PASS	.						188	206	200					1																	94548962		2203	4300	6503	SO:0001819	synonymous_variant	24	exon7			CAGATTGATACCT	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.804C>T	chr1.hg19:g.94548962G>A		393.0	1.0	.		257.0	119.0	.	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	hg19	CCDS747.1																																																																																			.	.	.	none		0.348	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		A	94548962	G	A	94548962	2	1	47	1	0	0	0	0	0	0	0	1	34	1280	45	2		2	ABCA4	1	94548962	Silent	SNP	G	TCGA-A4-7732-01A-11D-2136-08	65101429	94548962	154701659	2	3262											
PTPN22	26191	hgsc.bcm.edu	37	chr1	114402065	114402065	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgtctgccttgtacttggtAgattgccttttcagcttctg	4	19	9	9	0	3	1	1	0	2	1	3	1	3	1	2	1	4	3	2	1	2	9			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr1:114402065A>G	ENST00000359785.5	-	2	240	c.105T>C	c.(103-105)tcT>tcC	p.S35S	PTPN22_ENST00000528414.1_Silent_p.S35S|PTPN22_ENST00000525799.1_Silent_p.S35S|PTPN22_ENST00000420377.2_Silent_p.S35S|AP4B1-AS1_ENST00000419536.1_RNA|PTPN22_ENST00000460620.1_Silent_p.S35S|PTPN22_ENST00000534519.1_5'UTR|PTPN22_ENST00000538253.1_5'UTR	NM_001193431.1|NM_015967.5	NP_001180360.1|NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	35	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of T cell activation (GO:0050868)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphoanandamide dephosphorylation (GO:0035644)|protein dephosphorylation (GO:0006470)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of innate immune response (GO:0045088)|regulation of natural killer cell proliferation (GO:0032817)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	kinase binding (GO:0019900)|protein tyrosine phosphatase activity (GO:0004725)|SH3 domain binding (GO:0017124)			NS(1)|breast(1)|kidney(3)|large_intestine(4)|lung(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGTACTTGGTAGATTGCCTTT	0.373																																					p.S35S		Atlas-SNP	.											.	PTPN22	90	.	0			c.T105C						PASS	.						151	151	151					1																	114402065		2203	4300	6503	SO:0001819	synonymous_variant	26191	exon2			CTTGGTAGATTGC	AF001846	CCDS863.1, CCDS864.1, CCDS864.2	1p13.2	2011-06-09	2005-02-02		ENSG00000134242	ENSG00000134242		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9652	protein-coding gene	gene with protein product		600716	"protein tyrosine phosphatase, non-receptor type 8"	PTPN8		10068674, 1373816	Standard	NM_015967		Approved	Lyp, Lyp1, Lyp2	uc001eds.3	Q9Y2R2	OTTHUMG00000011936	ENST00000359785.5:c.105T>C	chr1.hg19:g.114402065A>G		151.0	0.0	.		97.0	46.0	.	NM_015967	A0N0K6|B1ALC8|D4NZ71|E9PLD8|E9PPI1|O95063|O95064|Q6IPX8|Q8WVM1	Silent	SNP	ENST00000359785.5	hg19	CCDS863.1																																																																																			.	.	.	none		0.373	PTPN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033015.1	NM_015967		G	114402065	A	G	114402065	2	3	47	1	0	0	0	0	0	0	0	1	12800	407	15	3		3	PTPN22	1	114402065	Silent	SNP	A	TCGA-A4-7732-01A-11D-2136-08	19853103	114402065	134848556	3	3263											
CRNN	49860	hgsc.bcm.edu	37	chr1	152382377	152382391	+	In_Frame_Del	DEL	TCAGGGTTGCTCACT	TCAGGGTTGCTCACT	-																															ccggtactgtctctcctgccTcagggttgctcacttgcatc																										TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	TCAGGGTTGCTCACT	TCAGGGTTGCTCACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr1:152382377_152382391delTCAGGGTTGCTCACT	ENST00000271835.3	-	3	1229_1243	c.1167_1181delAGTGAGCAACCCTGA	c.(1165-1182)caagtgagcaaccctgag>cag	p.VSNPE390del	RP1-91G5.3_ENST00000411804.1_RNA	NM_016190.2	NP_057274.1	Q9UBG3	CRNN_HUMAN	cornulin	390					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)			CTCTCCTGCCTCAGGGTTGCTCACTTGCATCCATC	0.595																																					p.390_394del		Atlas-INDEL	.											.	CRNN	78	.	0			c.1168_1182del						PASS	.																																			SO:0001651	inframe_deletion	49860	exon3			.	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.1167_1181delAGTGAGCAACCCTGA	chr1.hg19:g.152382377_152382391delTCAGGGTTGCTCACT	ENSP00000271835:p.Val390_Glu394del	149.0	0.0	0		73.0	23.0	0.315068	NM_016190	B2RE60|Q8N613	In_Frame_Del	DEL	ENST00000271835.3	hg19	CCDS1010.1																																																																																			.	.	.	none		0.595	CRNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034503.1	NM_016190		-	152382391	TCAGGGTTGCTCACT	-	152382377	7	5	47	1	0	1	0	1	0	0	0	0	3894	1551	54	0	310	0	CRNN	1	152382377	In_Frame_Del	DEL	TCAGGGTTGCTCACT	TCGA-A4-7732-01A-11D-2136-08	37980312	152382377	96868244	4	3264											
CABC1	56997	hgsc.bcm.edu	37	chr1	227174187	227174187	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccacttggatgccatcctcAtcctgggggaggccttcgcc	5	9	11	16	1	1	0	1	0	0	0	4	2	3	2	6	4	1	0	6	4	0	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr1:227174187A>G	ENST00000366779.1	+	20	4464	c.1693A>G	c.(1693-1695)Atc>Gtc	p.I565V	ADCK3_ENST00000366778.1_Missense_Mutation_p.I513V|ADCK3_ENST00000433743.2_Missense_Mutation_p.I239V|ADCK3_ENST00000366777.3_Missense_Mutation_p.I565V|ADCK3_ENST00000458507.2_Missense_Mutation_p.I286V|ADCK3_ENST00000478406.1_3'UTR			Q8NI60	ADCK3_HUMAN	aarF domain containing kinase 3	565					cell death (GO:0008219)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|kidney(2)|large_intestine(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	9						TGCCATCCTCATCCTGGGGGA	0.592																																					p.I565V		Atlas-SNP	.											.	ADCK3	77	.	0			c.A1693G						PASS	.						89	90	90					1																	227174187		2203	4300	6503	SO:0001583	missense	56997	exon15			ATCCTCATCCTGG	AJ278126	CCDS1557.1	1q42.11	2011-05-03	2010-10-01	2010-10-01	ENSG00000163050	ENSG00000163050			16812	protein-coding gene	gene with protein product	"coenzyme Q8 homolog (yeast)"	606980	"chaperone-ABC1 (activity of bc1 complex, S.pombe)-like", "chaperone, ABC1 activity of bc1 complex like (S. pombe)", "chaperone, ABC1 activity of bc1 complex homolog (S. pombe)"	CABC1			Standard	NM_020247		Approved	COQ8, SCAR9	uc001hqn.1	Q8NI60	OTTHUMG00000037621	ENST00000366779.1:c.1693A>G	chr1.hg19:g.227174187A>G	ENSP00000355741:p.Ile565Val	134.0	0.0	.		97.0	45.0	.	NM_020247	Q5T7A5|Q63HK0|Q8NCJ6|Q9HBQ1|Q9NQ67	Missense_Mutation	SNP	ENST00000366779.1	hg19	CCDS1557.1	.	.	.	.	.	.	.	.	.	.	A	16.71	3.198951	0.58126	.	.	ENSG00000163050	ENST00000366779;ENST00000366778;ENST00000366777;ENST00000366776;ENST00000458507;ENST00000366775;ENST00000405743;ENST00000433743	T;T;T;T;T;T;T	0.74737	-0.76;-0.73;-0.76;-0.87;-0.43;-0.83;-0.71	5.87	5.87	0.94306	.	0.044860	0.85682	D	0.000000	T	0.71117	0.3302	L	0.60012	1.86	0.80722	D	1	B;B	0.20550	0.001;0.046	B;B	0.19148	0.01;0.024	T	0.66101	-0.6007	10	0.24483	T	0.36	-21.7545	16.2688	0.82603	1.0:0.0:0.0:0.0	.	239;565	E7EVZ8;Q8NI60	.;ADCK3_HUMAN	V	565;513;565;490;286;410;516;239	ENSP00000355741:I565V;ENSP00000355740:I513V;ENSP00000355739:I565V;ENSP00000355738:I490V;ENSP00000403704:I286V;ENSP00000355737:I410V;ENSP00000404550:I239V	ENSP00000355737:I410V	I	+	1	0	ADCK3	225240810	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.289000	0.96061	2.244000	0.73946	0.533000	0.62120	ATC	.	.	.	none		0.592	ADCK3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091712.1	NM_020247		G	227174187	A	G	227174187	3	3	47	1	0	0	0	0	1	0	0	0	2529	217	8	3	1747	3	CABC1	1	227174187	Missense_Mutation	SNP	A	TCGA-A4-7732-01A-11D-2136-08	74791810	227174187	22076434	5	3265											
PCNXL2	80003	hgsc.bcm.edu	37	chr1	233134020	233134020	+	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	ttctctgtgtcccttcacagGatgacaccccgtgctgagca	7	11	9	14	1	2	2	1	2	1	0	4	3	3	3	3	1	2	2	3	1	0	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr1:233134020G>A	ENST00000258229.9	-	32	6002	c.5768C>T	c.(5767-5769)tCc>tTc	p.S1923F	PCNXL2_ENST00000344698.2_Missense_Mutation_p.S575F	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	1923						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				CCCTTCACAGGATGACACCCC	0.592																																					p.S1923F		Atlas-SNP	.											.	PCNXL2	204	.	0			c.C5768T						PASS	.						43	46	45					1																	233134020		2040	4195	6235	SO:0001583	missense	80003	exon32			TCACAGGATGACA	AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"pecanex (Drosophila)-like 2"			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.5768C>T	chr1.hg19:g.233134020G>A	ENSP00000258229:p.Ser1923Phe	28.0	0.0	.		18.0	9.0	.	NM_014801	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	ENST00000258229.9	hg19	CCDS44335.1	.	.	.	.	.	.	.	.	.	.	G	11.91	1.779932	0.31502	.	.	ENSG00000135749	ENST00000344698;ENST00000258229	T;T	0.24723	1.84;3.01	4.86	4.86	0.63082	.	1.450940	0.04437	N	0.370187	T	0.23410	0.0566	L	0.36672	1.1	0.25414	N	0.988333	P;B	0.40266	0.71;0.302	B;B	0.26614	0.071;0.047	T	0.43491	-0.9388	10	0.72032	D	0.01	.	15.136	0.72566	0.0:0.0:1.0:0.0	.	1923;575	A6NKB5;A6NKB5-3	PCX2_HUMAN;.	F	575;1923	ENSP00000340759:S575F;ENSP00000258229:S1923F	ENSP00000258229:S1923F	S	-	2	0	PCNXL2	231200643	0.023000	0.18921	0.320000	0.25306	0.131000	0.20780	2.059000	0.41384	2.255000	0.74692	0.563000	0.77884	TCC	.	.	.	none		0.592	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801		A	233134020	G	A	233134020	3	1	47	1	0	0	0	0	1	0	0	0	11599	1174	41	2	657	2	PCNXL2	1	233134020	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	5959833	233134020	16116601	6	3266											
C2orf3	6936	hgsc.bcm.edu	37	chr2	75929399	75929399	+	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	ttctcttttcatggtcatcaGgctcactctcagggtcatct	6	16	7	12	0	8	0	6	0	3	0	10	0	8	0	0	3	0	1	0	3	0	3			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr2:75929399G>T	ENST00000321027.3	-	3	678	c.545C>A	c.(544-546)cCt>cAt	p.P182H	GCFC2_ENST00000470503.1_Missense_Mutation_p.P182H|GCFC2_ENST00000409857.3_Intron|GCFC2_ENST00000541687.1_Missense_Mutation_p.P182H	NM_001201334.1|NM_003203.4	NP_001188263.1|NP_003194.3	P16383	GCFC2_HUMAN	GC-rich sequence DNA-binding factor 2	182					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)|U2-type post-mRNA release spliceosomal complex (GO:0071008)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)										ATGGTCATCAGGCTCACTCTC	0.418																																					p.P182H		Atlas-SNP	.											.	.	.	.	0			c.C545A						PASS	.						196	185	189					2																	75929399		2203	4300	6503	SO:0001583	missense	6936	exon3			TCATCAGGCTCAC	AB026911	CCDS1961.1, CCDS62943.1	2p12	2014-01-17	2011-11-24	2011-11-24	ENSG00000005436	ENSG00000005436			1317	protein-coding gene	gene with protein product	"GC binding factor"	189901	"transcription factor 9 (binds GC-rich sequences)", "chromosome 2 open reading frame 3"	TCF9, C2orf3		1370479, 2556218, 17309879, 24304693	Standard	NM_003203		Approved	DNABF, GCF	uc002sno.3	P16383	OTTHUMG00000129989	ENST00000321027.3:c.545C>A	chr2.hg19:g.75929399G>T	ENSP00000318690:p.Pro182His	202.0	0.0	.		135.0	59.0	.	NM_001201335	A4UHQ8|O95032|Q53TY0|Q6P2F2	Missense_Mutation	SNP	ENST00000321027.3	hg19	CCDS1961.1	.	.	.	.	.	.	.	.	.	.	G	17.92	3.505961	0.64410	.	.	ENSG00000005436	ENST00000321027;ENST00000541687	T;T	0.34072	2.49;1.38	4.85	4.85	0.62838	.	0.455607	0.22605	N	0.057903	T	0.54822	0.1882	M	0.66939	2.045	0.27164	N	0.961081	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.987	T	0.49031	-0.8981	10	0.56958	D	0.05	-15.8005	9.7929	0.40717	0.0967:0.0:0.9033:0.0	.	182;182	A4UHQ8;P16383	.;GCF_HUMAN	H	182	ENSP00000318690:P182H;ENSP00000437767:P182H	ENSP00000318690:P182H	P	-	2	0	C2orf3	75782907	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.496000	0.53288	2.620000	0.88729	0.591000	0.81541	CCT	.	.	.	none		0.418	GCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252255.2	NM_003203		T	75929399	G	T	75929399	3	4	47	1	0	0	0	0	1	0	0	0	2164	1000	35	4	1860	4	C2orf3	2	75929399	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08		75929399	167269974	7	3267											
NCAPH	23397	hgsc.bcm.edu	37	chr2	97017659	97017669	+	Frame_Shift_Del	DEL	AGAAGTGAACT	AGAAGTGAACT	-																															ctctccactgccaggactacAgaagtgaactgctgtttccc																										TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	AGAAGTGAACT	AGAAGTGAACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr2:97017659_97017669delAGAAGTGAACT	ENST00000240423.4	+	7	854_864	c.811_821delAGAAGTGAACT	c.(811-822)agaagtgaactgfs	p.RSEL271fs	NCAPH_ENST00000455200.1_Frame_Shift_Del_p.RSEL260fs|NCAPH_ENST00000427946.1_Frame_Shift_Del_p.RSEL135fs	NM_001281710.1|NM_001281711.1|NM_015341.3	NP_001268639.1|NP_001268640.1|NP_056156.2	Q15003	CND2_HUMAN	non-SMC condensin I complex, subunit H	271					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(717;0.0221)				CCAGGACTACAGAAGTGAACTGCTGTTTCCC	0.479																																					p.270_274del		Atlas-INDEL	.											.	NCAPH	67	.	0			c.810_820del						PASS	.																																			SO:0001589	frameshift_variant	23397	exon7			.	BC024211	CCDS2021.1, CCDS62960.1	2q11.2	2008-02-05	2006-09-04	2006-09-04	ENSG00000121152	ENSG00000121152			1112	protein-coding gene	gene with protein product		602332	"barren (Drosophila) homolog", "barren homolog (Drosophila)", "barren homolog 1 (Drosophila)"	BRRN1		9417923	Standard	NM_015341		Approved	CAP-H, hCAP-H	uc002svz.1	Q15003	OTTHUMG00000130451	ENST00000240423.4:c.811_821delAGAAGTGAACT	chr2.hg19:g.97017659_97017669delAGAAGTGAACT	ENSP00000240423:p.Arg271fs	112.0	0.0	0		55.0	17.0	0.309091	NM_015341	B4E189|Q8TB87	Frame_Shift_Del	DEL	ENST00000240423.4	hg19	CCDS2021.1																																																																																			.	.	.	none		0.479	NCAPH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252842.2	NM_015341		-	97017669	AGAAGTGAACT	-	97017659	7	5	47	1	0	1	0	1	0	0	0	0	10216	180	7	0	837	0	NCAPH	2	97017659	Frame_Shift_Del	DEL	AGAAGTGAACT	TCGA-A4-7732-01A-11D-2136-08	21088260	97017659	146181714	8	3268											
IL1R1	3554	hgsc.bcm.edu	37	chr2	102792833	102792833	+	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	acattgttgaggtcattaatGaaaacgtaaagaaaagcaga	19	9	9	4	1	1	4	1	2	0	2	1	4	1	4	0	1	2	3	0	1	7	4			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr2:102792833G>C	ENST00000410023.1	+	12	1642	c.1324G>C	c.(1324-1326)Gaa>Caa	p.E442Q	IL1R1_ENST00000409589.1_Intron|AC007271.3_ENST00000428188.1_RNA|IL1R1_ENST00000424272.1_3'UTR|IL1R1_ENST00000409929.1_Missense_Mutation_p.E411Q|IL1R1_ENST00000233946.3_Missense_Mutation_p.E442Q			P14778	IL1R1_HUMAN	interleukin 1 receptor, type I	442	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|interleukin-1-mediated signaling pathway (GO:0070498)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)|platelet-derived growth factor receptor binding (GO:0005161)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|prostate(2)|skin(3)	19					Anakinra(DB00026)	GGTCATTAATGAAAACGTAAA	0.373																																					p.E442Q		Atlas-SNP	.											IL1R1,NS,malignant_melanoma,0,2	IL1R1	52	.	0			c.G1324C						PASS	.						49	51	50					2																	102792833		2203	4300	6503	SO:0001583	missense	3554	exon11			ATTAATGAAAACG	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.1324G>C	chr2.hg19:g.102792833G>C	ENSP00000386380:p.Glu442Gln	52.0	0.0	.		36.0	2.0	.	NM_000877	Q587I7	Missense_Mutation	SNP	ENST00000410023.1	hg19	CCDS2055.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.154988	0.78114	.	.	ENSG00000115594	ENST00000409929;ENST00000428279;ENST00000410023;ENST00000233946	T;T;T;T	0.09538	2.97;2.97;2.97;2.97	5.61	4.73	0.59995	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.465576	0.25450	N	0.030588	T	0.33556	0.0867	M	0.77313	2.365	0.37504	D	0.916883	D;D	0.89917	1.0;0.998	D;D	0.85130	0.997;0.983	T	0.18808	-1.0325	10	0.62326	D	0.03	.	13.9351	0.64021	0.0726:0.0:0.9274:0.0	.	411;442	B8ZZW4;P14778	.;IL1R1_HUMAN	Q	411;298;442;442	ENSP00000386776:E411Q;ENSP00000410461:E298Q;ENSP00000386380:E442Q;ENSP00000233946:E442Q	ENSP00000233946:E442Q	E	+	1	0	IL1R1	102159265	1.000000	0.71417	0.947000	0.38551	0.951000	0.60555	4.341000	0.59335	2.646000	0.89796	0.563000	0.77884	GAA	.	.	.	none		0.373	IL1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253299.1			C	102792833	G	C	102792833	3	2	47	1	0	0	0	0	1	0	0	0	7665	1291	45	4	1362	4	IL1R1	2	102792833	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	5775174	102792833	140406540	9	3269											
SCN2A	6326	hgsc.bcm.edu	37	chr2	166210795	166210795	+	Missense_Mutation	SNP	A	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	acgaaatgaataatctccagAttgctgtgggaaggatgcag	14	9	12	6	1	1	2	0	1	1	1	2	5	1	4	1	2	2	2	1	2	4	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr2:166210795A>C	ENST00000375437.2	+	17	3303	c.3013A>C	c.(3013-3015)Att>Ctt	p.I1005L	SCN2A_ENST00000283256.6_Missense_Mutation_p.I1005L|SCN2A_ENST00000375427.2_Missense_Mutation_p.I1005L|SCN2A_ENST00000357398.3_Missense_Mutation_p.I1005L	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	1005					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)	TAATCTCCAGATTGCTGTGGG	0.383																																					p.I1005L		Atlas-SNP	.											.	SCN2A	589	.	0			c.A3013C						PASS	.						146	151	149					2																	166210795		2203	4300	6503	SO:0001583	missense	6326	exon16			CTCCAGATTGCTG	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.3013A>C	chr2.hg19:g.166210795A>C	ENSP00000364586:p.Ile1005Leu	219.0	0.0	.		154.0	66.0	.	NM_001040143	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	hg19	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	A	13.51	2.257989	0.39896	.	.	ENSG00000136531	ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D	0.84589	-1.87;-1.87;-1.87;-1.87	5.6	5.6	0.85130	Sodium ion transport-associated (1);	0.080914	0.52532	D	0.000063	D	0.83101	0.5181	L	0.53671	1.685	0.49915	D	0.999837	B;B	0.17268	0.021;0.005	B;B	0.25291	0.059;0.042	T	0.78513	-0.2175	10	0.30854	T	0.27	.	15.7718	0.78176	1.0:0.0:0.0:0.0	.	1005;1005	Q99250-2;Q99250	.;SCN2A_HUMAN	L	1005	ENSP00000364586:I1005L;ENSP00000349973:I1005L;ENSP00000283256:I1005L;ENSP00000364576:I1005L	ENSP00000283256:I1005L	I	+	1	0	SCN2A	165919041	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.572000	0.82409	2.110000	0.64415	0.482000	0.46254	ATT	.	.	.	none		0.383	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		C	166210795	A	C	166210795	3	2	47	1	0	0	0	0	1	0	0	0	13929	333	12	5	3171	5	SCN2A	2	166210795	Missense_Mutation	SNP	A	TCGA-A4-7732-01A-11D-2136-08	63417962	166210795	76988578	10	3270											
PDE11A	50940	hgsc.bcm.edu	37	chr2	178936278	178936278	+	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	aggcatcaggaatgttgaccGtttctccatgctccccgaca	9	10	9	13	2	2	1	1	1	1	0	4	3	3	2	4	2	1	4	4	2	1	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr2:178936278G>T	ENST00000286063.6	-	1	1204	c.887C>A	c.(886-888)aCg>aAg	p.T296K	PDE11A_ENST00000358450.4_Intron	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	296	GAF 1.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	AATGTTGACCGTTTCTCCATG	0.537									Primary Pigmented Nodular Adrenocortical Disease, Familial																												p.T296K		Atlas-SNP	.											PDE11A,NS,carcinoma,0,1	PDE11A	283	.	0			c.C887A						PASS	.						153	132	139					2																	178936278		2203	4300	6503	SO:0001583	missense	50940	exon1	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	TTGACCGTTTCTC	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.887C>A	chr2.hg19:g.178936278G>T	ENSP00000286063:p.Thr296Lys	169.0	0.0	.		100.0	52.0	.	NM_016953	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Missense_Mutation	SNP	ENST00000286063.6	hg19	CCDS33334.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.521048	0.85495	.	.	ENSG00000128655	ENST00000286063	T	0.68181	-0.31	5.63	5.63	0.86233	GAF (2);	0.042243	0.85682	D	0.000000	D	0.82559	0.5063	M	0.82716	2.605	0.80722	D	1	D	0.64830	0.994	D	0.65140	0.932	T	0.82643	-0.0356	10	0.44086	T	0.13	.	18.6717	0.91514	0.0:0.0:1.0:0.0	.	296	Q9HCR9	PDE11_HUMAN	K	296	ENSP00000286063:T296K	ENSP00000286063:T296K	T	-	2	0	PDE11A	178644524	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	9.379000	0.97198	2.650000	0.89964	0.655000	0.94253	ACG	.	.	.	none		0.537	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2			T	178936278	G	T	178936278	3	4	47	1	0	0	0	0	1	0	0	0	11638	1145	40	4	1994	4	PDE11A	2	178936278	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	12725483	178936278	64263095	11	3271											
KIAA0226	9711	hgsc.bcm.edu	37	chr3	197427622	197427622	+	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	ggacagctggctctccccacCtccttcctggtcccctaagg	5	9	9	18	0	1	0	0	0	1	0	5	1	4	1	7	4	1	2	7	4	1	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr3:197427622C>G	ENST00000296343.5	-	7	1122	c.1123G>C	c.(1123-1125)Ggt>Cgt	p.G375R	KIAA0226_ENST00000449205.1_Missense_Mutation_p.G375R|KIAA0226_ENST00000273582.5_Missense_Mutation_p.G315R|KIAA0226_ENST00000467303.1_5'Flank|KIAA0226_ENST00000389665.5_Missense_Mutation_p.G375R	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	375	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)		CTCTCCCCACCTCCTTCCTGG	0.577																																					p.G375R	Esophageal Squamous(3;167 355 3763 15924)	Atlas-SNP	.											.	KIAA0226	136	.	0			c.G1123C						PASS	.						57	61	60					3																	197427622		2021	4184	6205	SO:0001583	missense	9711	exon7			CCCCACCTCCTTC	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.1123G>C	chr3.hg19:g.197427622C>G	ENSP00000296343:p.Gly375Arg	76.0	0.0	.		36.0	11.0	.	NM_014687	Q96CK5	Missense_Mutation	SNP	ENST00000296343.5	hg19	CCDS43195.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	1.899|1.899|1.899	-0.453623|-0.453623|-0.453623	0.04540|0.04540|0.04540	.|.|.	.|.|.	ENSG00000145016|ENSG00000145016|ENSG00000145016	ENST00000415452|ENST00000273582;ENST00000296343;ENST00000389665;ENST00000447048;ENST00000449205|ENST00000413360	.|.|.	.|.|.	.|.|.	5.85|5.85|5.85	2.98|2.98|2.98	0.34508|0.34508|0.34508	.|.|.	.|0.954594|.	.|0.08839|.	.|N|.	.|0.886108|.	T|T|T	0.23886|0.23886|0.23886	0.0578|0.0578|0.0578	N|N|N	0.19112|0.19112|0.19112	0.55|0.55|0.55	0.09310|0.09310|0.09310	N|N|N	1|1|1	.|P;P;P;P;B|.	.|0.52577|.	.|0.954;0.785;0.704;0.905;0.282|.	.|P;P;B;B;B|.	.|0.50192|.	.|0.634;0.49;0.299;0.394;0.051|.	T|T|T	0.20538|0.20538|0.20538	-1.0272|-1.0272|-1.0272	5|9|5	.|0.16896|.	.|T|.	.|0.51|.	.|.|.	7.6388|7.6388|7.6388	0.28282|0.28282|0.28282	0.0:0.5923:0.0:0.4077|0.0:0.5923:0.0:0.4077|0.0:0.5923:0.0:0.4077	.|.|.	.|375;208;375;315;375|.	.|E9PEM3;Q5HYI6;Q92622-3;Q92622-2;Q92622|.	.|.;.;.;.;RUBIC_HUMAN|.	D|R|T	133|315;375;375;7;375|353	.|.|.	.|ENSP00000273582:G315R|.	E|G|R	-|-|-	3|1|2	2|0|0	KIAA0226|KIAA0226|KIAA0226	198912019|198912019|198912019	0.000000|0.000000|0.000000	0.05858|0.05858|0.05858	0.010000|0.010000|0.010000	0.14722|0.14722|0.14722	0.364000|0.364000|0.364000	0.29643|0.29643|0.29643	0.779000|0.779000|0.779000	0.26746|0.26746|0.26746	0.756000|0.756000|0.756000	0.33013|0.33013|0.33013	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GAG|GGT|AGG	.	.	.	none		0.577	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901		G	197427622	C	G	197427622	3	3	47	1	0	0	0	0	1	0	0	0	8169	681	24	4	1900	4	KIAA0226	3	197427622	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08		197427622	594808	12	3272											
TRIO	7204	hgsc.bcm.edu	37	chr5	14387672	14387672	+	Frame_Shift_Del	DEL	T	T	-																															aagaggtacagagatttctcTctgcggatggagaagtacag																										TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr5:14387672delT	ENST00000344204.4	+	22	3720	c.3696delT	c.(3694-3696)tctfs	p.S1232fs	TRIO_ENST00000537187.1_Frame_Shift_Del_p.S1232fs|TRIO_ENST00000509967.2_Frame_Shift_Del_p.S1183fs	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	1232					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)					GAGATTTCTCTCTGCGGATGG	0.433																																					p.S1232fs		Atlas-INDEL	.											.	TRIO	305	.	0			c.3695delC						PASS	.						118	132	127					5																	14387672		2203	4300	6503	SO:0001589	frameshift_variant	7204	exon22			.	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.3696delT	chr5.hg19:g.14387672delT	ENSP00000339299:p.Ser1232fs	193.0	0.0	0		94.0	38.0	0.404255	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Frame_Shift_Del	DEL	ENST00000344204.4	hg19	CCDS3883.1																																																																																			.	.	.	none		0.433	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		-	14387672	T	-	14387672	7	5	47	1	0	1	0	1	0	0	0	0	16564	1538	54	0	3782	0	TRIO	5	14387672	Frame_Shift_Del	DEL	T	TCGA-A4-7732-01A-11D-2136-08		14387672	166527588	13	3273											
PCDHGB7	56099	hgsc.bcm.edu	37	chr5	140798373	140798373	+	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	tgaagaagtagaaagatataCgataaacatagaagcaaaag	23	6	9	3	1	0	5	0	1	0	4	0	6	0	5	0	0	3	2	0	0	12	5	rs200530054		TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr5:140798373C>G	ENST00000398594.2	+	1	947	c.947C>G	c.(946-948)aCg>aGg	p.T316R	PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000398587.2_5'Flank|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA11_ENST00000518882.1_5'Flank	NM_018927.3	NP_061750.1	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7	316	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(13)|lung(15)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(3)	56			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAAAGATATACGATAAACATA	0.408																																					p.T316R		Atlas-SNP	.											.	PCDHGB7	117	.	0			c.C947G						PASS	.						66	62	63					5																	140798373		1868	4100	5968	SO:0001583	missense	56099	exon1			GATATACGATAAA	AF152523	CCDS47293.1, CCDS75344.1	5q31	2010-01-26			ENSG00000254122	ENSG00000254122		"Cadherins / Protocadherins : Clustered"	8714	other	protocadherin	"cadherin ME6"	606304				10380929	Standard	NM_032101		Approved	ME6, PCDH-GAMMA-B7		Q9Y5F8	OTTHUMG00000164054	ENST00000398594.2:c.947C>G	chr5.hg19:g.140798373C>G	ENSP00000381594:p.Thr316Arg	27.0	0.0	.		24.0	4.0	.	NM_018927	Q9UN63	Missense_Mutation	SNP	ENST00000398594.2	hg19	CCDS47293.1	.	.	.	.	.	.	.	.	.	.	c	11.77	1.736942	0.30774	.	.	ENSG00000254122	ENST00000398594	T	0.51325	0.71	5.7	3.93	0.45458	Cadherin (5);Cadherin-like (1);	1.919090	0.04837	U	0.439841	T	0.56615	0.1997	L	0.49350	1.555	0.09310	N	1	D;D	0.54397	0.966;0.958	P;P	0.57204	0.815;0.795	T	0.26916	-1.0089	10	0.54805	T	0.06	.	4.1608	0.10282	0.1578:0.5582:0.0:0.284	.	316;316	Q9Y5F8;Q9Y5F8-2	PCDGJ_HUMAN;.	R	316	ENSP00000381594:T316R	ENSP00000381594:T316R	T	+	2	0	PCDHGB7	140778557	0.000000	0.05858	0.048000	0.18961	0.684000	0.39900	0.516000	0.22817	0.776000	0.33473	0.561000	0.74099	ACG	.	C|1.000;T|0.000	.	alt		0.408	PCDHGB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376973.1	NM_018927		G	140798373	C	G	140798373	3	3	47	1	0	0	0	0	1	0	0	0	11575	536	19	4	949	4	PCDHGB7	5	140798373	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08	126410701	140798373	40116887	14	3274											
ARHGEF37	389337	hgsc.bcm.edu	37	chr5	149006787	149006787	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatcgtggccatccttcaaaAcaaggacaccaaaggcaaca	17	5	7	12	1	1	0	1	0	0	0	3	1	2	1	3	3	2	1	3	3	6	1			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr5:149006787A>G	ENST00000333677.6	+	11	1776	c.1613A>G	c.(1612-1614)aAc>aGc	p.N538S		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	538	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						ATCCTTCAAAACAAGGACACC	0.597																																					p.N538S		Atlas-SNP	.											.	ARHGEF37	45	.	0			c.A1613G						PASS	.						82	94	90					5																	149006787		2091	4214	6305	SO:0001583	missense	389337	exon11			TTCAAAACAAGGA	BC041325	CCDS43385.1	5q33.1	2012-07-24			ENSG00000183111	ENSG00000183111		"Rho guanine nucleotide exchange factors"	34430	protein-coding gene	gene with protein product							Standard	XM_005268448		Approved	FLJ41603	uc003lra.1	A1IGU5	OTTHUMG00000163491	ENST00000333677.6:c.1613A>G	chr5.hg19:g.149006787A>G	ENSP00000328083:p.Asn538Ser	251.0	0.0	.		116.0	43.0	.	NM_001001669	Q6ZW51	Missense_Mutation	SNP	ENST00000333677.6	hg19	CCDS43385.1	.	.	.	.	.	.	.	.	.	.	A	11.15	1.553479	0.27739	.	.	ENSG00000183111	ENST00000333677	T	0.41065	1.01	5.11	3.94	0.45596	Src homology-3 domain (2);Variant SH3 (1);	0.646786	0.17386	N	0.176119	T	0.23965	0.0580	N	0.16478	0.41	0.28347	N	0.921071	B	0.23249	0.082	B	0.21151	0.033	T	0.19745	-1.0296	10	0.14656	T	0.56	.	8.9935	0.36039	0.8446:0.0:0.1554:0.0	.	538	A1IGU5	ARH37_HUMAN	S	538	ENSP00000328083:N538S	ENSP00000328083:N538S	N	+	2	0	ARHGEF37	148986980	0.615000	0.27026	1.000000	0.80357	0.932000	0.56968	3.659000	0.54489	0.785000	0.33685	-0.441000	0.05720	AAC	.	.	.	none		0.597	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1	NM_001001669		G	149006787	A	G	149006787	3	3	47	1	0	0	0	0	1	0	0	0	906	43	2	3	1651	3	ARHGEF37	5	149006787	Missense_Mutation	SNP	A	TCGA-A4-7732-01A-11D-2136-08	8208414	149006787	31908473	15	3275											
PRSS16	10279	hgsc.bcm.edu	37	chr6	27222771	27222771	+	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	tcctttctttccaggggacaCagacccctggcatgtgctaa	8	11	9	13	0	1	1	0	0	1	1	3	2	3	2	4	3	1	2	4	3	1	3			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr6:27222771C>T	ENST00000230582.3	+	11	1352	c.1337C>T	c.(1336-1338)aCa>aTa	p.T446I	PRSS16_ENST00000377456.2_3'UTR|PRSS16_ENST00000421826.2_Missense_Mutation_p.T189I	NM_005865.3	NP_005856.1	Q9NQE7	TSSP_HUMAN	protease, serine, 16 (thymus)	446					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						CCAGGGGACACAGACCCCTGG	0.547																																					p.T446I	NSCLC(178;1118 2105 17078 23587 44429)	Atlas-SNP	.											.	PRSS16	66	.	0			c.C1337T						PASS	.						123	127	126					6																	27222771		2203	4300	6503	SO:0001583	missense	10279	exon11			GGGACACAGACCC	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.1337C>T	chr6.hg19:g.27222771C>T	ENSP00000230582:p.Thr446Ile	266.0	0.0	.		184.0	83.0	.	NM_005865	O75416	Missense_Mutation	SNP	ENST00000230582.3	hg19	CCDS4623.1	.	.	.	.	.	.	.	.	.	.	C	0.210	-1.036976	0.02013	.	.	ENSG00000112812	ENST00000421826;ENST00000230582	T;T	0.12039	2.72;2.72	4.64	-1.58	0.08479	.	0.476548	0.23981	N	0.042674	T	0.01222	0.0040	N	0.02011	-0.69	0.09310	N	1	B;B	0.15930	0.015;0.002	B;B	0.10450	0.005;0.001	T	0.46005	-0.9222	10	0.23302	T	0.38	0.0031	9.7619	0.40537	0.0:0.3092:0.0:0.6908	.	189;446	F2Z2N5;Q9NQE7	.;TSSP_HUMAN	I	189;446	ENSP00000404349:T189I;ENSP00000230582:T446I	ENSP00000230582:T446I	T	+	2	0	PRSS16	27330750	0.007000	0.16637	0.571000	0.28486	0.927000	0.56198	-0.021000	0.12504	-0.193000	0.10415	-0.267000	0.10333	ACA	.	.	.	none		0.547	PRSS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043418.2			T	27222771	C	T	27222771	3	4	47	1	0	0	0	0	1	0	0	0	12626	478	17	2	1379	2	PRSS16	6	27222771	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08		27222771	143892296	16	3276											
HSPA1L	3305	hgsc.bcm.edu	37	chr6	31779708	31779708	+	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	cccacacaggagtaggtggtGcccaggtcgatgcctatggc	8	7	14	12	1	0	0	0	0	0	0	1	2	0	1	3	5	2	1	3	5	2	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr6:31779708G>A	ENST00000375654.4	-	2	231	c.42C>T	c.(40-42)ggC>ggT	p.G14G	HSPA1L_ENST00000417199.3_Silent_p.G14G	NM_005527.3	NP_005518.3	P34931	HS71L_HUMAN	heat shock 70kDa protein 1-like	14					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						AGTAGGTGGTGCCCAGGTCGA	0.557																																					p.G14G		Atlas-SNP	.											.	HSPA1L	185	.	0			c.C42T						PASS	.						71	60	64					6																	31779708		2203	4300	6503	SO:0001819	synonymous_variant	3305	exon2			GGTGGTGCCCAGG	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.42C>T	chr6.hg19:g.31779708G>A		85.0	0.0	.		36.0	16.0	.	NM_005527	A6NNB0|B0UXW8|O75634|Q2HXR3|Q8NE72|Q96QC9|Q9UQM1	Silent	SNP	ENST00000375654.4	hg19	CCDS34413.1																																																																																			.	.	.	none		0.557	HSPA1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076416.2			A	31779708	G	A	31779708	2	1	47	1	0	0	0	0	0	0	0	1	7417	1306	46	2		2	HSPA1L	6	31779708	Silent	SNP	G	TCGA-A4-7732-01A-11D-2136-08	4556937	31779708	139335359	17	3277											
SLC26A5	375611	hgsc.bcm.edu	37	chr7	103029857	103029857	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcaggttgacaatcacaatGgccgacagcacagcctgaaa	14	7	9	11	1	2	2	2	2	0	0	2	3	2	2	2	2	2	2	2	2	3	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr7:103029857G>A	ENST00000306312.3	-	13	1587	c.1326C>T	c.(1324-1326)gcC>gcT	p.A442A	SLC26A5_ENST00000354356.4_5'UTR|SLC26A5_ENST00000393723.1_Intron|SLC26A5_ENST00000393730.1_Intron|SLC26A5_ENST00000393729.1_Silent_p.A405A|SLC26A5_ENST00000432958.2_Intron|SLC26A5_ENST00000339444.6_Silent_p.A442A|SLC26A5_ENST00000393735.2_Silent_p.A442A|SLC26A5_ENST00000393727.1_Silent_p.A442A|SLC26A5_ENST00000356767.4_Intron	NM_198999.2	NP_945350.1	P58743	S26A5_HUMAN	solute carrier family 26 (anion exchanger), member 5	442					regulation of cell shape (GO:0008360)|regulation of membrane potential (GO:0042391)|sensory perception of sound (GO:0007605)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)	secondary active sulfate transmembrane transporter activity (GO:0008271)			endometrium(5)|kidney(2)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)	43						CAATCACAATGGCCGACAGCA	0.498																																					p.A442A		Atlas-SNP	.											.	SLC26A5	231	.	0			c.C1326T						PASS	.						145	124	131					7																	103029857		2203	4300	6503	SO:0001819	synonymous_variant	375611	exon13			CACAATGGCCGAC	AC005064	CCDS5733.1, CCDS43630.1, CCDS55150.1, CCDS5732.1, CCDS43629.1	7q22	2013-07-18	2013-07-18	2005-09-13	ENSG00000170615	ENSG00000170615		"Solute carriers"	9359	protein-coding gene	gene with protein product	"deafness, neurosensory, autosomal recessive, 61"	604943	"prestin (motor protein)"	PRES		10821263	Standard	NM_206883		Approved	DFNB61	uc003vbz.3	P58743	OTTHUMG00000149911	ENST00000306312.3:c.1326C>T	chr7.hg19:g.103029857G>A		78.0	0.0	.		78.0	30.0	.	NM_206883	Q496J2|Q7Z7F3|Q86UF8|Q86UF9|Q86UG0	Silent	SNP	ENST00000306312.3	hg19	CCDS5733.1																																																																																			.	.	.	none		0.498	SLC26A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313860.1	NM_198999		A	103029857	G	A	103029857	2	1	47	1	0	0	0	0	0	0	0	1	14533	1335	47	2		2	SLC26A5	7	103029857	Silent	SNP	G	TCGA-A4-7732-01A-11D-2136-08		103029857	56108806	18	3278											
MAPK15	225689	hgsc.bcm.edu	37	chr8	144801161	144801161	+	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	tcagcctgcctcctctctgcAgccgtccaatgtgctcctgg	4	11	9	17	1	2	0	1	0	1	0	6	0	5	0	6	1	5	2	6	1	1	0			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr8:144801161A>T	ENST00000338033.4	+	6	536		c.e6-1		RP11-429J17.5_ENST00000527908.1_RNA|MAPK15_ENST00000395107.4_Splice_Site|MAPK15_ENST00000395108.2_Splice_Site	NM_139021.2	NP_620590.2	Q8TD08	MK15_HUMAN	mitogen-activated protein kinase 15						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)			TCCTCTCTGCAGCCGTCCAAT	0.711																																					.		Atlas-SNP	.											.	MAPK15	32	.	0			c.418-2A>T						PASS	.						21	19	20					8																	144801161		2202	4299	6501	SO:0001630	splice_region_variant	225689	exon6			CTCTGCAGCCGTC	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.418-1A>T	chr8.hg19:g.144801161A>T		26.0	0.0	.		12.0	7.0	.	NM_139021	Q2TCF9|Q8N362	Splice_Site	SNP	ENST00000338033.4	hg19	CCDS6409.2	.	.	.	.	.	.	.	.	.	.	A	16.20	3.054752	0.55325	.	.	ENSG00000181085	ENST00000338033;ENST00000395107;ENST00000395108	.	.	.	4.02	4.02	0.46733	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.9881	0.24739	0.8928:0.0:0.1072:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MAPK15	144873149	1.000000	0.71417	0.912000	0.35992	0.794000	0.44872	4.544000	0.60691	1.680000	0.50976	0.157000	0.16456	.	.	.	.	none		0.711	MAPK15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000300348.1	NM_139021	Intron	T	144801161	A	T	144801161	5	4	47	1	0	0	0	0	0	0	1	0	9284	202	7	5	438	5	MAPK15	8	144801161	Splice_Site	SNP	A	TCGA-A4-7732-01A-11D-2136-08		144801161	1562861	19	3279											
SLC1A1	6505	hgsc.bcm.edu	37	chr9	4585458	4585458	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgccttggaatccacaatccTtgacaacgaagactcagaca	14	8	7	12	1	1	3	1	1	0	2	3	5	3	4	3	1	2	0	3	1	4	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr9:4585458T>C	ENST00000262352.3	+	12	1711	c.1475T>C	c.(1474-1476)cTt>cCt	p.L492P		NM_004170.5	NP_004161.4	P43005	EAA3_HUMAN	solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	492					D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|pancreas(1)|skin(1)	15		Acute lymphoblastic leukemia(2;0.0359)|Breast(48;0.0457)		GBM - Glioblastoma multiforme(50;0.0124)|Lung(218;0.183)	L-Aspartic Acid(DB00128)|Pregabalin(DB00230)	TCCACAATCCTTGACAACGAA	0.463																																					p.L492P		Atlas-SNP	.											.	SLC1A1	43	.	0			c.T1475C						PASS	.						134	109	118					9																	4585458		2203	4300	6503	SO:0001583	missense	6505	exon12			CAATCCTTGACAA		CCDS6452.1	9p24	2013-05-22			ENSG00000106688	ENSG00000106688		"Solute carriers"	10939	protein-coding gene	gene with protein product		133550				8020993	Standard	NM_004170		Approved	EAAC1, EAAT3	uc003zij.2	P43005	OTTHUMG00000019468	ENST00000262352.3:c.1475T>C	chr9.hg19:g.4585458T>C	ENSP00000262352:p.Leu492Pro	84.0	0.0	.		56.0	27.0	.	NM_004170	O75587|Q5VZ24|Q8N199|Q9UEW2	Missense_Mutation	SNP	ENST00000262352.3	hg19	CCDS6452.1	.	.	.	.	.	.	.	.	.	.	T	3.609	-0.079875	0.07141	.	.	ENSG00000106688	ENST00000262352	T	0.57752	0.38	5.71	3.33	0.38152	.	0.566440	0.18485	N	0.139812	T	0.28200	0.0696	N	0.08118	0	0.21878	N	0.999492	B	0.12013	0.005	B	0.11329	0.006	T	0.14420	-1.0473	10	0.35671	T	0.21	.	5.5545	0.17109	0.1284:0.1394:0.0:0.7322	.	492	P43005	EAA3_HUMAN	P	492	ENSP00000262352:L492P	ENSP00000262352:L492P	L	+	2	0	SLC1A1	4575458	0.890000	0.30428	0.013000	0.15412	0.092000	0.18411	3.193000	0.50997	0.417000	0.25871	0.460000	0.39030	CTT	.	.	.	none		0.463	SLC1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051571.1			C	4585458	T	C	4585458	3	2	47	1	0	0	0	0	1	0	0	0	14444	1609	56	3	1521	3	SLC1A1	9	4585458	Missense_Mutation	SNP	T	TCGA-A4-7732-01A-11D-2136-08		4585458	136627973	20	3280											
APTX	54840	hgsc.bcm.edu	37	chr9	32988092	32988092	+	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	tacacctacctgctttacctTgacatatcccttgttacact	9	15	3	14	0	0	1	0	1	0	0	1	1	1	1	4	0	5	2	4	0	5	8			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr9:32988092T>A	ENST00000379819.1	-	3	210	c.211A>T	c.(211-213)Aag>Tag	p.K71*	APTX_ENST00000468275.1_Nonsense_Mutation_p.K57*|APTX_ENST00000379817.2_Nonsense_Mutation_p.K57*|APTX_ENST00000476858.1_Intron|APTX_ENST00000309615.3_Nonsense_Mutation_p.K71*|APTX_ENST00000379813.3_Nonsense_Mutation_p.K57*|APTX_ENST00000397172.3_Nonsense_Mutation_p.K71*|APTX_ENST00000436040.2_Nonsense_Mutation_p.K57*|APTX_ENST00000463596.1_Nonsense_Mutation_p.K57*|APTX_ENST00000379825.2_Nonsense_Mutation_p.K71*			Q7Z2E3	APTX_HUMAN	aprataxin	71	FHA-like.|Interactions with ADPRT and NCL.				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)		TGCTTTACCTTGACATATCCC	0.388								Editing and processing nucleases																													p.K71X		Atlas-SNP	.											.	APTX	44	.	0			c.A211T						PASS	.						136	132	134					9																	32988092		2203	4300	6503	SO:0001587	stop_gained	54840	exon3			TTACCTTGACATA	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.211A>T	chr9.hg19:g.32988092T>A	ENSP00000369147:p.Lys71*	132.0	0.0	.		76.0	25.0	.	NM_001195252	A8MTN4|D3DRK9|D3DRL0|Q0P662|Q5T781|Q5T782|Q5T784|Q6JV81|Q6JV82|Q6JV85|Q7Z2F3|Q7Z336|Q7Z5R5|Q7Z6V7|Q7Z6V8|Q9NXM5	Nonsense_Mutation	SNP	ENST00000379819.1	hg19		.	.	.	.	.	.	.	.	.	.	T	36	5.750052	0.96890	.	.	ENSG00000137074	ENST00000379825;ENST00000309615;ENST00000397172;ENST00000379817;ENST00000436040;ENST00000379819;ENST00000468275;ENST00000463596;ENST00000344355;ENST00000379813;ENST00000379812	.	.	.	5.16	5.16	0.70880	.	0.326514	0.35805	N	0.002978	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.792	12.9503	0.58397	0.0:0.0:0.0:1.0	.	.	.	.	X	71;71;71;57;57;71;57;57;71;57;71	.	ENSP00000311547:K71X	K	-	1	0	APTX	32978092	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.233000	0.58651	1.957000	0.56846	0.455000	0.32223	AAG	.	.	.	none		0.388	APTX-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000052028.2	NM_017692		A	32988092	T	A	32988092	4	1	47	1	0	0	0	0	0	1	0	0	820	1821	63	5	892	5	APTX	9	32988092	Nonsense_Mutation	SNP	T	TCGA-A4-7732-01A-11D-2136-08	28402634	32988092	108225339	21	3281											
PTCH1	5727	hgsc.bcm.edu	37	chr9	98268787	98268787	+	Missense_Mutation	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	ggcccacaaccaagaacttgCcgcagtttttttgaatgtaa	12	11	8	10	1	0	2	0	1	0	1	0	2	0	2	3	1	3	3	3	1	5	5			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr9:98268787C>T	ENST00000331920.6	-	2	595	c.296G>A	c.(295-297)gGc>gAc	p.G99D	PTCH1_ENST00000437951.1_Missense_Mutation_p.G33D|PTCH1_ENST00000430669.2_Missense_Mutation_p.G33D|PTCH1_ENST00000418258.1_5'UTR|RP11-435O5.5_ENST00000604104.1_RNA|PTCH1_ENST00000375274.2_Missense_Mutation_p.G98D|PTCH1_ENST00000429896.2_5'UTR|PTCH1_ENST00000421141.1_5'UTR|PTCH1_ENST00000468211.2_Missense_Mutation_p.G33D	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	99					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)	p.C98fs*13(1)		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)				CAAGAACTTGCCGCAGTTTTT	0.537																																					p.G99D		Atlas-SNP	.											.	PTCH1	1850	.	1	Deletion - Frameshift(1)	skin(1)	c.G296A						PASS	.						67	69	68					9																	98268787		2203	4300	6503	SO:0001583	missense	5727	exon2			AACTTGCCGCAGT	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.296G>A	chr9.hg19:g.98268787C>T	ENSP00000332353:p.Gly99Asp	77.0	0.0	.		36.0	17.0	.	NM_000264	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000331920.6	hg19	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.593802	0.86953	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000430669;ENST00000375274;ENST00000544247;ENST00000468211	D;D;D;D;D	0.89123	-2.47;-2.47;-2.47;-2.47;-2.47	4.49	4.49	0.54785	.	0.000000	0.85682	D	0.000000	D	0.94056	0.8095	M	0.78916	2.43	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.998	D	0.93805	0.7104	10	0.40728	T	0.16	-11.9121	16.7843	0.85570	0.0:1.0:0.0:0.0	.	33;98;99	Q13635-3;Q13635-2;Q13635	.;.;PTC1_HUMAN	D	99;33;33;98;33;33	ENSP00000332353:G99D;ENSP00000389744:G33D;ENSP00000410287:G33D;ENSP00000364423:G98D;ENSP00000449745:G33D	ENSP00000332353:G99D	G	-	2	0	PTCH1	97308608	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.168000	0.77570	2.033000	0.60031	0.561000	0.74099	GGC	.	.	.	none		0.537	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		T	98268787	C	T	98268787	3	4	47	1	0	0	0	0	1	0	0	0	12740	739	26	2	4135	2	PTCH1	9	98268787	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08	65280695	98268787	42944644	22	3282											
ZMYND11	10771	hgsc.bcm.edu	37	chr10	287963	287963	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaacatttaatttccagatAcctaatcatgagctggtttg	14	14	6	7	0	1	2	1	1	0	1	2	2	2	2	2	1	3	2	2	1	5	6			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr10:287963A>G	ENST00000397962.3	+	10	1262	c.834A>G	c.(832-834)atA>atG	p.I278M	ZMYND11_ENST00000602682.1_Missense_Mutation_p.I193M|ZMYND11_ENST00000402736.1_Missense_Mutation_p.I247M|ZMYND11_ENST00000381604.4_Missense_Mutation_p.I238M|ZMYND11_ENST00000381602.4_Missense_Mutation_p.I238M|ZMYND11_ENST00000509513.2_Missense_Mutation_p.I277M|ZMYND11_ENST00000381607.4_Missense_Mutation_p.I184M|ZMYND11_ENST00000403354.1_Missense_Mutation_p.I198M|ZMYND11_ENST00000397959.3_Missense_Mutation_p.I193M|ZMYND11_ENST00000545619.1_Missense_Mutation_p.I158M|ZMYND11_ENST00000381584.1_Missense_Mutation_p.I261M|ZMYND11_ENST00000381591.1_Missense_Mutation_p.I278M|ZMYND11_ENST00000558098.2_Missense_Mutation_p.I278M|ZMYND11_ENST00000309776.4_Missense_Mutation_p.I238M|ZMYND11_ENST00000535374.1_Missense_Mutation_p.I73M			Q15326	ZMY11_HUMAN	zinc finger, MYND-type containing 11	278					cell cycle (GO:0007049)|cell proliferation (GO:0008283)|chromatin modification (GO:0016568)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription elongation from RNA polymerase II promoter (GO:0034243)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	24		all_cancers(4;1.32e-05)|all_lung(4;3.67e-05)|Lung NSC(4;0.000301)|all_epithelial(10;0.000416)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.132)	Epithelial(11;0.00289)|all cancers(11;0.0108)|Lung(33;0.0689)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		ATTTCCAGATACCTAATCATG	0.328																																					p.I278M		Atlas-SNP	.											.	ZMYND11	72	.	0			c.A834G						PASS	.						111	110	111					10																	287963		2203	4300	6503	SO:0001583	missense	10771	exon10			CCAGATACCTAAT	X86098	CCDS7052.1, CCDS7053.1, CCDS7052.2, CCDS55696.1, CCDS55697.1, CCDS7053.2, CCDS73060.1, CCDS73061.1	10p14	2011-01-26	2011-01-26		ENSG00000015171	ENSG00000015171		"Zinc fingers, MYND-type"	16966	protein-coding gene	gene with protein product		608668	"zinc finger, MYND domain containing 11"			7621829, 10734313	Standard	NM_006624		Approved	BS69	uc010pzx.2	Q15326	OTTHUMG00000017526	ENST00000397962.3:c.834A>G	chr10.hg19:g.287963A>G	ENSP00000381053:p.Ile278Met	76.0	0.0	.		46.0	17.0	.	NM_006624	B2R6G8|B7Z293|F6UH50|Q2LD45|Q2LD46|Q2LD47|Q2LD48|Q5VUI1|Q8N4B3	Missense_Mutation	SNP	ENST00000397962.3	hg19	CCDS7052.2	.	.	.	.	.	.	.	.	.	.	A	16.71	3.199641	0.58126	.	.	ENSG00000015171	ENST00000397962;ENST00000309776;ENST00000381602;ENST00000509513;ENST00000397959;ENST00000381591;ENST00000403354;ENST00000381607;ENST00000402736;ENST00000381604;ENST00000381584;ENST00000545619;ENST00000535374	T;T;T;T;T;T;T;T;T;T;T;T	0.70282	-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47	6.17	5.03	0.67393	PWWP (2);	0.248837	0.46758	D	0.000271	T	0.59088	0.2168	N	0.08118	0	0.30416	N	0.778601	P;P;P;P;D;P;P;P;P;D	0.55800	0.918;0.921;0.727;0.727;0.973;0.832;0.918;0.882;0.927;0.973	P;P;P;P;P;P;P;B;B;P	0.49752	0.49;0.587;0.56;0.56;0.592;0.621;0.49;0.397;0.402;0.592	T	0.70839	-0.4763	9	0.46703	T	0.11	-28.5082	12.919	0.58222	0.8782:0.0:0.0:0.1218	.	238;278;193;223;278;198;207;224;224;247	Q15326;Q2LD45;B7Z293;B7Z2J6;Q2LD48;B0QZE2;B0QZE3;Q2LD46;Q2LD47;E7ENI9	ZMY11_HUMAN;.;.;.;.;.;.;.;.;.	M	278;238;238;278;193;278;198;184;247;238;261;158;73	ENSP00000381053:I278M;ENSP00000309992:I238M;ENSP00000371015:I238M;ENSP00000381050:I193M;ENSP00000371003:I278M;ENSP00000385484:I198M;ENSP00000371020:I184M;ENSP00000386010:I247M;ENSP00000371017:I238M;ENSP00000370996:I261M;ENSP00000438461:I158M;ENSP00000439587:I73M	ENSP00000309992:I238M	I	+	3	3	ZMYND11	277963	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.942000	0.40243	1.134000	0.42165	0.533000	0.62120	ATA	.	.	.	none		0.328	ZMYND11-206	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046382.4	NM_006624		G	287963	A	G	287963	3	3	47	1	0	0	0	0	1	0	0	0	17718	381	14	3	868	3	ZMYND11	10	287963	Missense_Mutation	SNP	A	TCGA-A4-7732-01A-11D-2136-08		287963	135246784	23	3283											
PPRC1	23082	hgsc.bcm.edu	37	chr10	103900396	103900396	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcagcaccccagctcctcGtggagtcagagtccttggac	7	9	11	14	1	2	1	2	0	0	1	5	3	4	3	4	2	2	3	4	2	0	2	rs17847386		TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr10:103900396G>A	ENST00000278070.2	+	5	2170	c.2131G>A	c.(2131-2133)Gtg>Atg	p.V711M	PPRC1_ENST00000370012.1_5'Flank|PPRC1_ENST00000413464.2_Missense_Mutation_p.V711M	NM_015062.3	NP_055877.3	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator-related 1	711					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(10)|lung(19)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		CCAGCTCCTCGTGGAGTCAGA	0.532																																					p.V711M		Atlas-SNP	.											PPRC1,colon,carcinoma,0,1	PPRC1	151	.	0			c.G2131A						PASS	.						79	75	76					10																	103900396		2203	4300	6503	SO:0001583	missense	23082	exon5			CTCCTCGTGGAGT	AF325193	CCDS7529.1, CCDS73186.1	10q24.32	2013-02-12	2006-10-17		ENSG00000148840	ENSG00000148840		"RNA binding motif (RRM) containing"	30025	protein-coding gene	gene with protein product			"peroxisome proliferative activated receptor, gamma, coactivator-related 1"			9628581, 11340167	Standard	XM_005269656		Approved	PRC, KIAA0595, MGC74642	uc001kum.3	Q5VV67	OTTHUMG00000018948	ENST00000278070.2:c.2131G>A	chr10.hg19:g.103900396G>A	ENSP00000278070:p.Val711Met	101.0	0.0	.		64.0	6.0	.	NM_015062	Q5VV66|Q6P3U5|Q6P3W1|Q76N31|Q9BUJ3|Q9BZE5|Q9Y4E0	Missense_Mutation	SNP	ENST00000278070.2	hg19	CCDS7529.1	.	.	.	.	.	.	.	.	.	.	g	8.673	0.903227	0.17760	.	.	ENSG00000148840	ENST00000278070;ENST00000413464	T;T	0.24151	1.88;1.87	3.89	-0.341	0.12639	.	0.355194	0.16037	N	0.232573	T	0.08670	0.0215	N	0.08118	0	0.09310	N	1	B;P;B	0.41345	0.191;0.746;0.191	B;B;B	0.31191	0.036;0.125;0.036	T	0.22765	-1.0207	10	0.46703	T	0.11	.	5.7647	0.18219	0.0:0.3035:0.4867:0.2099	rs17847386	711;591;711	E7EVG6;Q5VV67-2;Q5VV67	.;.;PPRC1_HUMAN	M	711	ENSP00000278070:V711M;ENSP00000399743:V711M	ENSP00000278070:V711M	V	+	1	0	PPRC1	103890386	0.000000	0.05858	0.006000	0.13384	0.068000	0.16541	-0.952000	0.03881	-0.046000	0.13446	-1.200000	0.01667	GTG	.	G|0.999;T|0.001	.	weak		0.532	PPRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050021.1	NM_015062		A	103900396	G	A	103900396	3	1	47	1	0	0	0	0	1	0	0	0	12420	1145	40	1	2149	1	PPRC1	10	103900396	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	103612433	103900396	31634351	24	3284											
SLC43A3	29015	hgsc.bcm.edu	37	chr11	57177469	57177469	+	Missense_Mutation	SNP	T	T	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	gcggctgatcacttgcaggaTgaaggtgaggtactggagag	10	8	17	6	1	1	4	1	3	0	1	1	6	1	5	0	5	2	3	0	5	2	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr11:57177469T>G	ENST00000395123.2	-	12	1490	c.1186A>C	c.(1186-1188)Atc>Ctc	p.I396L	SLC43A3_ENST00000352187.1_Missense_Mutation_p.I396L|SLC43A3_ENST00000395124.1_Missense_Mutation_p.I396L|SLC43A3_ENST00000533524.1_Missense_Mutation_p.I409L|RP11-872D17.8_ENST00000529411.1_Missense_Mutation_p.I40L|SLC43A3_ENST00000529554.1_Missense_Mutation_p.I396L	NM_001278201.1|NM_014096.2	NP_001265130.1|NP_054815.2	Q8NBI5	S43A3_HUMAN	solute carrier family 43, member 3	396					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	27						ACTTGCAGGATGAAGGTGAGG	0.632																																					p.I396L		Atlas-SNP	.											.	SLC43A3	54	.	0			c.A1186C						PASS	.						93	72	79					11																	57177469		2201	4296	6497	SO:0001583	missense	29015	exon12			GCAGGATGAAGGT	AL157431	CCDS7956.1, CCDS60784.1	11q11	2013-05-22			ENSG00000134802	ENSG00000134802		"Solute carriers"	17466	protein-coding gene	gene with protein product	"likely ortholog of mouse embryonic epithelial gene 1"					7531438, 11704567	Standard	NM_017611		Approved	SEEEG-1, Eeg1, DKFZp762A227, FOAP-13, PRO1659	uc001nki.3	Q8NBI5	OTTHUMG00000167113	ENST00000395123.2:c.1186A>C	chr11.hg19:g.57177469T>G	ENSP00000378555:p.Ile396Leu	47.0	0.0	.		24.0	7.0	.	NM_017611	B4DNR8|E7EQD2|Q9NSS4	Missense_Mutation	SNP	ENST00000395123.2	hg19	CCDS7956.1	.	.	.	.	.	.	.	.	.	.	T	18.85	3.711618	0.68730	.	.	ENSG00000254979;ENSG00000134802;ENSG00000134802;ENSG00000134802;ENSG00000134802;ENSG00000134802	ENST00000529411;ENST00000395123;ENST00000395124;ENST00000352187;ENST00000529554;ENST00000533524	T;T;T;T;T;T	0.80123	-1.34;0.43;0.43;0.43;0.43;0.43	5.65	0.744	0.18353	Major facilitator superfamily domain, general substrate transporter (1);	0.373532	0.30235	N	0.010082	T	0.73218	0.3559	M	0.64997	1.995	0.35492	D	0.799026	B;B	0.22276	0.031;0.067	B;B	0.25614	0.062;0.062	T	0.64343	-0.6430	10	0.23891	T	0.37	-18.2579	8.0046	0.30317	0.0:0.353:0.0:0.647	.	409;396	E7EQD2;Q8NBI5	.;S43A3_HUMAN	L	40;396;396;396;396;409	ENSP00000431536:I40L;ENSP00000378555:I396L;ENSP00000378556:I396L;ENSP00000337561:I396L;ENSP00000436254:I396L;ENSP00000434515:I409L	ENSP00000431536:I40L	I	-	1	0	RP11-872D17.8;SLC43A3	56934045	0.962000	0.33011	0.995000	0.50966	0.953000	0.61014	-0.028000	0.12350	-0.110000	0.12022	0.533000	0.62120	ATC	.	.	.	none		0.632	SLC43A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393057.1	NM_017611		G	57177469	T	G	57177469	3	3	47	1	0	0	0	0	1	0	0	0	14647	1464	51	5	301	5	SLC43A3	11	57177469	Missense_Mutation	SNP	T	TCGA-A4-7732-01A-11D-2136-08		57177469	77829047	25	3285											
USP28	57646	hgsc.bcm.edu	37	chr11	113705056	113705056	+	Splice_Site	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	attcaggcaattgaaagagaGactgaaataaagaaagaaag	22	6	10	3	0	1	6	1	2	0	4	1	7	1	6	0	1	0	1	0	1	7	3			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr11:113705056G>C	ENST00000003302.4	-	6	604	c.536C>G	c.(535-537)tCt>tGt	p.S179C	USP28_ENST00000545540.1_Splice_Site_p.S54C|USP28_ENST00000537706.1_Splice_Site_p.S179C|USP28_ENST00000260188.5_Splice_Site_p.S179C|USP28_ENST00000542033.1_5'UTR	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN	ubiquitin specific peptidase 28	179	USP.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		TTGAAAGAGAGACTGAAATAA	0.313																																					p.S179C	Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)	Atlas-SNP	.											.	USP28	135	.	0			c.C536G						PASS	.						83	78	80					11																	113705056		2201	4296	6497	SO:0001630	splice_region_variant	57646	exon6			AAGAGAGACTGAA	AB040948	CCDS31680.1, CCDS73394.1	11q23	2008-04-11	2005-08-08		ENSG00000048028	ENSG00000048028		"Ubiquitin-specific peptidases"	12625	protein-coding gene	gene with protein product		610748	"ubiquitin specific protease 28"			12838346, 11597335	Standard	XM_005271630		Approved	KIAA1515	uc001poh.3	Q96RU2	OTTHUMG00000168205	ENST00000003302.4:c.535-1C>G	chr11.hg19:g.113705056G>C		47.0	0.0	.		34.0	18.0	.	NM_020886	B0YJC0|B0YJC1|Q9P213	Missense_Mutation	SNP	ENST00000003302.4	hg19	CCDS31680.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.470732	0.84533	.	.	ENSG00000048028	ENST00000003302;ENST00000260188;ENST00000545540;ENST00000537706	T;T;T;T	0.29142	1.58;1.58;1.58;1.58	5.08	5.08	0.68730	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.52533	0.1740	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	0.994;1.0;0.997;0.999	T	0.55147	-0.8186	10	0.87932	D	0	-14.6997	17.4468	0.87580	0.0:0.0:1.0:0.0	.	179;54;179;179	B4E2Q2;B4E3L3;Q6NZX9;Q96RU2	.;.;.;UBP28_HUMAN	C	179;179;54;179	ENSP00000003302:S179C;ENSP00000260188:S179C;ENSP00000444991:S54C;ENSP00000445743:S179C	ENSP00000003302:S179C	S	-	2	0	USP28	113210266	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.444000	0.97578	2.357000	0.79964	0.460000	0.39030	TCT	.	.	.	none		0.313	USP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398789.1		Missense_Mutation	C	113705056	G	C	113705056	5	2	47	1	0	0	0	0	0	0	1	0	17070	956	33	4	2777	4	USP28	11	113705056	Splice_Site	SNP	G	TCGA-A4-7732-01A-11D-2136-08	56527587	113705056	21301460	26	3286											
DPAGT1	1798	hgsc.bcm.edu	37	chr11	118969112	118969112	+	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	cttatccacaggcctacttaCcagttgtggtagagcaatcc	10	11	8	12	0	0	1	0	0	0	1	2	1	2	1	4	2	3	3	4	2	5	5			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr11:118969112C>T	ENST00000409993.2	-	7	2280		c.e7+1		DPAGT1_ENST00000432443.2_Splice_Site|DPAGT1_ENST00000445653.1_5'Flank|H2AFX_ENST00000530167.1_5'Flank|DPAGT1_ENST00000354202.4_Splice_Site			Q9H3H5	GPT_HUMAN	dolichyl-phosphate (UDP-N-acetylglucosamine) N-acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)						cellular protein metabolic process (GO:0044267)|dolichol biosynthetic process (GO:0019408)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|protein oligomerization (GO:0051259)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	phospho-N-acetylmuramoyl-pentapeptide-transferase activity (GO:0008963)|transferase activity, transferring glycosyl groups (GO:0016757)|UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity (GO:0003975)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2)	17	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.55e-05)		GGCCTACTTACCAGTTGTGGT	0.463																																					.		Atlas-SNP	.											DPAGT1,NS,malignant_melanoma,0,1	DPAGT1	43	.	0			c.728+1G>A						PASS	.						194	173	180					11																	118969112		2200	4295	6495	SO:0001630	splice_region_variant	1798	exon6			TACTTACCAGTTG	Z82022	CCDS8411.1	11q23.3	2007-12-14			ENSG00000172269	ENSG00000172269	2.7.8.15		2995	protein-coding gene	gene with protein product		191350		DPAGT2, DPAGT		8244387	Standard	NM_001382		Approved	GPT, D11S366, DGPT, ALG7, CDG-Ij	uc001pvi.3	Q9H3H5	OTTHUMG00000153533	ENST00000409993.2:c.728+1G>A	chr11.hg19:g.118969112C>T		175.0	0.0	.		101.0	50.0	.	NM_001382	O15216|Q86WV9|Q9BWE6	Splice_Site	SNP	ENST00000409993.2	hg19	CCDS8411.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.476893	0.84640	.	.	ENSG00000172269	ENST00000409993;ENST00000354202;ENST00000432443	.	.	.	5.37	5.37	0.77165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.2906	0.90129	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DPAGT1	118474322	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.570000	0.82390	2.788000	0.95919	0.650000	0.86243	.	.	.	.	none		0.463	DPAGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331527.2	NM_001382	Intron	T	118969112	C	T	118969112	5	4	47	1	0	0	0	0	0	0	1	0	4712	521	18	2	517	2	DPAGT1	11	118969112	Splice_Site	SNP	C	TCGA-A4-7732-01A-11D-2136-08	5264056	118969112	16037404	27	3287											
TFCP2	7024	hgsc.bcm.edu	37	chr12	51495806	51495806	+	Missense_Mutation	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	agttaatttcaataaatctgCccctggaataaatataagaa	18	12	5	6	0	2	1	1	0	1	1	2	2	2	2	2	1	1	1	2	1	10	6			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr12:51495806C>T	ENST00000257915.5	-	11	1521	c.1063G>A	c.(1063-1065)Gca>Aca	p.A355T	TFCP2_ENST00000548115.1_Missense_Mutation_p.A304T|TFCP2_ENST00000307660.4_Missense_Mutation_p.A304T|TFCP2_ENST00000549867.1_Intron	NM_001173452.1|NM_005653.4	NP_001166923.1|NP_005644.2	Q12800	TFCP2_HUMAN	transcription factor CP2	355	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						AATAAATCTGCCCCTGGAATA	0.343																																					p.A355T		Atlas-SNP	.											.	TFCP2	49	.	0			c.G1063A						PASS	.						51	53	52					12																	51495806		2202	4300	6502	SO:0001583	missense	7024	exon11			AATCTGCCCCTGG	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.1063G>A	chr12.hg19:g.51495806C>T	ENSP00000257915:p.Ala355Thr	93.0	0.0	.		65.0	15.0	.	NM_001173452	A8K5E9|Q12801|Q9UD75|Q9UD77	Missense_Mutation	SNP	ENST00000257915.5	hg19	CCDS8808.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.089945	0.76756	.	.	ENSG00000135457	ENST00000257915;ENST00000307660;ENST00000548115;ENST00000548108	T;T;T;T	0.51325	2.11;0.71;0.74;2.09	5.19	4.31	0.51392	Sterile alpha motif/pointed domain (1);	0.000000	0.85682	D	0.000000	T	0.61689	0.2367	L	0.53729	1.69	0.58432	D	0.999995	D;B;B	0.67145	0.996;0.059;0.182	D;B;B	0.79784	0.993;0.059;0.177	T	0.61564	-0.7037	10	0.42905	T	0.14	-20.1909	12.9675	0.58492	0.0:0.9209:0.0:0.0791	.	304;355;355	Q12800-2;Q12800;Q12800-4	.;TFCP2_HUMAN;.	T	355;304;304;257	ENSP00000257915:A355T;ENSP00000304411:A304T;ENSP00000447991:A304T;ENSP00000449280:A257T	ENSP00000257915:A355T	A	-	1	0	TFCP2	49782073	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.576000	0.60915	1.574000	0.49760	0.563000	0.77884	GCA	.	.	.	none		0.343	TFCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405119.1	NM_005653		T	51495806	C	T	51495806	3	4	47	1	0	0	0	0	1	0	0	0	15807	739	26	2	465	2	TFCP2	12	51495806	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08		51495806	82356089	28	3288											
SLC39A5	283375	hgsc.bcm.edu	37	chr12	56626598	56626598	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagccccctcgggcctggAcctccttcacaggcttctgt	4	9	10	18	1	2	0	1	0	1	0	4	1	3	1	6	3	1	1	6	3	0	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr12:56626598A>G	ENST00000266980.4	+	3	706	c.413A>G	c.(412-414)gAc>gGc	p.D138G	SLC39A5_ENST00000454355.2_Missense_Mutation_p.D138G	NM_001135195.1	NP_001128667.1	Q6ZMH5	S39A5_HUMAN	solute carrier family 39 (zinc transporter), member 5	138					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						TCGGGCCTGGACCTCCTTCAC	0.612																																					p.D138G		Atlas-SNP	.											.	SLC39A5	52	.	0			c.A413G						PASS	.						51	52	52					12																	56626598		2203	4300	6503	SO:0001583	missense	283375	exon5			GCCTGGACCTCCT		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.413A>G	chr12.hg19:g.56626598A>G	ENSP00000266980:p.Asp138Gly	86.0	0.0	.		83.0	32.0	.	NM_173596	B2R808|Q8N6Y3	Missense_Mutation	SNP	ENST00000266980.4	hg19	CCDS8912.2	.	.	.	.	.	.	.	.	.	.	A	10.38	1.334275	0.24253	.	.	ENSG00000139540	ENST00000419753;ENST00000454355;ENST00000436633;ENST00000266980	T;T;T;T	0.22945	1.93;1.93;1.93;1.93	5.43	-4.08	0.03963	.	0.862131	0.10182	N	0.705702	T	0.15739	0.0379	N	0.25647	0.755	0.23473	N	0.997603	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.31668	-0.9935	9	.	.	.	-2.6848	13.1574	0.59524	0.4593:0.0:0.5407:0.0	.	138;29	Q6ZMH5;B4DPG8	S39A5_HUMAN;.	G	138;138;109;138	ENSP00000402891:D138G;ENSP00000405360:D138G;ENSP00000391711:D109G;ENSP00000266980:D138G	.	D	+	2	0	SLC39A5	54912865	0.782000	0.28689	0.322000	0.25334	0.858000	0.48976	-0.215000	0.09279	-0.637000	0.05516	-0.269000	0.10298	GAC	.	.	.	none		0.612	SLC39A5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346834.1	NM_173596		G	56626598	A	G	56626598	3	3	47	1	0	0	0	0	1	0	0	0	14634	275	10	3	419	3	SLC39A5	12	56626598	Missense_Mutation	SNP	A	TCGA-A4-7732-01A-11D-2136-08	5130792	56626598	77225297	29	3289											
GLI1	2735	hgsc.bcm.edu	37	chr12	57864354	57864354	+	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	ctgcagcatccagcctggatCggataggtggtcttcccatg	7	10	12	12	1	1	0	0	0	1	0	4	2	3	2	3	4	3	2	3	4	1	2	rs368078339		TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr12:57864354C>T	ENST00000228682.2	+	12	1922	c.1831C>T	c.(1831-1833)Cgg>Tgg	p.R611W	GLI1_ENST00000543426.1_Missense_Mutation_p.R483W|GLI1_ENST00000546141.1_Missense_Mutation_p.R570W	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	611					cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			CAGCCTGGATCGGATAGGTGG	0.617																																					p.R611W	Pancreas(157;841 1936 10503 41495 50368)	Atlas-SNP	.											.	GLI1	141	.	0			c.C1831T						PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG	1,4405		0,1,2202	55	47	49		1447,1708,1831	3.9	1	12		49	0,8600		0,0,4300	no	missense,missense,missense	GLI1	NM_001160045.1,NM_001167609.1,NM_005269.2	101,101,101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging	483/979,570/1066,611/1107	57864354	1,13005	2203	4300	6503	SO:0001583	missense	2735	exon12			CTGGATCGGATAG		CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"Zinc fingers, C2H2-type"	4317	protein-coding gene	gene with protein product		165220	"glioma-associated oncogene homolog 1 (zinc finger protein)", "glioma-associated oncogene family zinc finger 1"	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.1831C>T	chr12.hg19:g.57864354C>T	ENSP00000228682:p.Arg611Trp	77.0	0.0	.		57.0	21.0	.	NM_005269	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Missense_Mutation	SNP	ENST00000228682.2	hg19	CCDS8940.1	.	.	.	.	.	.	.	.	.	.	C	11.13	1.547626	0.27652	2.27E-4	0.0	ENSG00000111087	ENST00000543426;ENST00000228682;ENST00000546141;ENST00000528467	T;T;T;T	0.22336	2.12;1.96;2.06;2.06	3.86	3.86	0.44501	.	0.172694	0.28166	N	0.016347	T	0.21761	0.0524	M	0.64997	1.995	0.37842	D	0.929105	B	0.09022	0.002	B	0.04013	0.001	T	0.14839	-1.0458	10	0.87932	D	0	.	9.2479	0.37539	0.328:0.672:0.0:0.0	.	611	P08151	GLI1_HUMAN	W	483;611;570;570	ENSP00000437607:R483W;ENSP00000228682:R611W;ENSP00000441006:R570W;ENSP00000434408:R570W	ENSP00000228682:R611W	R	+	1	2	GLI1	56150621	0.021000	0.18746	0.995000	0.50966	0.883000	0.51084	0.653000	0.24902	2.436000	0.82500	0.491000	0.48974	CGG	.	.	.	weak		0.617	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269		T	57864354	C	T	57864354	3	4	47	1	0	0	0	0	1	0	0	0	6444	875	31	1	1873	1	GLI1	12	57864354	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08	1237756	57864354	75987541	30	3290											
NAA16	79612	hgsc.bcm.edu	37	chr13	41894809	41894809	+	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	ccttaacttaataggttggcAtgtatatggactcttgcagc	10	14	9	8	0	1	0	0	0	1	0	1	1	1	1	1	3	3	4	1	3	5	7			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr13:41894809A>T	ENST00000379406.3	+	4	575	c.251A>T	c.(250-252)cAt>cTt	p.H84L	NAA16_ENST00000379367.3_Missense_Mutation_p.H84L|NAA16_ENST00000403412.3_Missense_Mutation_p.H84L	NM_024561.4	NP_078837.3	Q6N069	NAA16_HUMAN	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	84					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						ATAGGTTGGCATGTATATGGA	0.299																																					p.H84L		Atlas-SNP	.											.	NAA16	74	.	0			c.A251T						PASS	.						76	79	78					13																	41894809		2203	4300	6503	SO:0001583	missense	79612	exon4			GTTGGCATGTATA	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.251A>T	chr13.hg19:g.41894809A>T	ENSP00000368716:p.His84Leu	72.0	0.0	.		58.0	4.0	.	NM_001110798	B0QZ59|Q5VSP9|Q6P2D5|Q8N5J3|Q8N870	Missense_Mutation	SNP	ENST00000379406.3	hg19	CCDS9379.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.530845	0.85706	.	.	ENSG00000172766	ENST00000379367;ENST00000379406;ENST00000403412	T;T;T	0.58060	0.36;0.36;0.36	4.9	4.9	0.64082	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.64402	D	0.000001	T	0.80265	0.4591	H	0.95816	3.725	0.80722	D	1	D;P;D	0.76494	0.999;0.754;0.985	D;P;D	0.85130	0.997;0.673;0.943	D	0.86393	0.1737	10	0.72032	D	0.01	-17.5873	14.6766	0.68983	1.0:0.0:0.0:0.0	.	84;84;84	Q6N069;Q6N069-4;Q6N069-5	NAA16_HUMAN;.;.	L	84	ENSP00000368674:H84L;ENSP00000368716:H84L;ENSP00000386103:H84L	ENSP00000368674:H84L	H	+	2	0	NAA16	40792809	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.523000	0.90576	2.048000	0.60808	0.533000	0.62120	CAT	.	.	.	none		0.299	NAA16-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044672.2	NM_018527		T	41894809	A	T	41894809	3	4	47	1	0	0	0	0	1	0	0	0	10126	217	8	5	265	5	NAA16	13	41894809	Missense_Mutation	SNP	A	TCGA-A4-7732-01A-11D-2136-08		41894809	73275069	31	3291											
MDGA2	161357	hgsc.bcm.edu	37	chr14	47351354	47351354	+	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	ttagctctgtcaagttatatGtaattaattctcccttttga	10	19	5	7	0	3	1	1	1	2	0	4	1	3	1	1	0	1	3	1	0	6	8	rs369029916		TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr14:47351354G>T	ENST00000399232.2	-	11	2466	c.2102C>A	c.(2101-2103)aCa>aAa	p.T701K	MDGA2_ENST00000426342.1_Missense_Mutation_p.T472K|MDGA2_ENST00000357362.3_Missense_Mutation_p.T472K|MDGA2_ENST00000399222.3_5'UTR|MDGA2_ENST00000439988.3_Missense_Mutation_p.T770K	NM_001113498.2	NP_001106970.3	Q7Z553	MDGA2_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 2	701	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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						CAAGTTATATGTAATTAATTC	0.368																																					p.T770K		Atlas-SNP	.											.	MDGA2	470	.	0			c.C2309A						PASS	.						65	62	63					14																	47351354		1827	4086	5913	SO:0001583	missense	161357	exon11			TTATATGTAATTA	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.2102C>A	chr14.hg19:g.47351354G>T	ENSP00000382178:p.Thr701Lys	25.0	0.0	.		29.0	7.0	.	NM_001113498	F6W3S7|J3KPX6	Missense_Mutation	SNP	ENST00000399232.2	hg19		.	.	.	.	.	.	.	.	.	.	G	15.69	2.907198	0.52333	.	.	ENSG00000139915	ENST00000439988;ENST00000426342;ENST00000399232;ENST00000357362	T;T;T;T	0.54866	0.55;0.55;0.55;0.55	5.1	5.1	0.69264	Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.000000	0.52532	U	0.000066	T	0.49098	0.1537	L	0.36672	1.1	0.80722	D	1	P;B	0.35139	0.486;0.227	B;B	0.38755	0.281;0.146	T	0.52388	-0.8582	10	0.54805	T	0.06	.	17.4396	0.87562	0.0:0.0:1.0:0.0	.	472;701	F6W3S7;Q7Z553	.;MDGA2_HUMAN	K	701;472;770;472	ENSP00000400011:T701K;ENSP00000405456:T472K;ENSP00000382178:T770K;ENSP00000349925:T472K	ENSP00000349925:T472K	T	-	2	0	MDGA2	46421104	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.258000	0.72487	2.547000	0.85894	0.467000	0.42956	ACA	.	.	.	alt		0.368	MDGA2-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000073352.5	NM_182830		T	47351354	G	T	47351354	3	4	47	1	0	0	0	0	1	0	0	0	9414	1377	48	4	796	4	MDGA2	14	47351354	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08		47351354	59998186	32	3292											
KCNK13	56659	hgsc.bcm.edu	37	chr14	90528673	90528673	+	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	ccgccgtcttctccgcgctgGagctggcgcacgagcgccag	4	6	14	17	7	2	0	0	0	2	0	3	2	2	1	4	2	2	3	4	2	0	1			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr14:90528673G>A	ENST00000282146.4	+	1	565	c.124G>A	c.(124-126)Gag>Aag	p.E42K		NM_022054.2	NP_071337.2	Q9HB14	KCNKD_HUMAN	potassium channel, subfamily K, member 13	42					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)				CTCCGCGCTGGAGCTGGCGCA	0.721																																					p.E42K		Atlas-SNP	.											.	KCNK13	76	.	0			c.G124A						PASS	.						4	5	4					14																	90528673		1987	3967	5954	SO:0001583	missense	56659	exon1			GCGCTGGAGCTGG	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.124G>A	chr14.hg19:g.90528673G>A	ENSP00000282146:p.Glu42Lys	12.0	0.0	.		7.0	4.0	.	NM_022054	B5TJL8|Q96E79	Missense_Mutation	SNP	ENST00000282146.4	hg19	CCDS9889.1	.	.	.	.	.	.	.	.	.	.	G	35	5.521378	0.96416	.	.	ENSG00000152315	ENST00000282146	T	0.39787	1.06	4.0	4.0	0.46444	.	0.000000	0.32753	N	0.005686	T	0.71492	0.3346	M	0.90977	3.165	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80843	-0.1201	10	0.87932	D	0	.	16.446	0.83932	0.0:0.0:1.0:0.0	.	42	Q9HB14	KCNKD_HUMAN	K	42	ENSP00000282146:E42K	ENSP00000282146:E42K	E	+	1	0	KCNK13	89598426	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	9.054000	0.93866	1.946000	0.56461	0.313000	0.20887	GAG	.	.	.	none		0.721	KCNK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411251.1	NM_022054		A	90528673	G	A	90528673	3	1	47	1	0	0	0	0	1	0	0	0	8068	1175	41	2	126	2	KCNK13	14	90528673	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	43177319	90528673	16820867	33	3293											
RRN3	54700	hgsc.bcm.edu	37	chr16	15159184	15159184	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgactggcagcatctggcgaTtgttcctctcaatgatggtg	7	13	12	9	1	2	2	1	2	2	0	4	3	3	2	1	3	1	3	1	3	1	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr16:15159184T>C	ENST00000198767.6	-	16	1681	c.1598A>G	c.(1597-1599)aAt>aGt	p.N533S	RRN3_ENST00000429751.2_Missense_Mutation_p.N503S|PDXDC1_ENST00000535621.2_Intron|RRN3_ENST00000327307.7_Missense_Mutation_p.N500S|RRN3_ENST00000563559.1_Missense_Mutation_p.N533S|RRN3_ENST00000540462.1_Missense_Mutation_p.N351S	NM_018427.3	NP_060897.3	Q9NYV6	RRN3_HUMAN	RRN3 RNA polymerase I transcription factor homolog (S. cerevisiae)	533	Interaction with TWISTNB.				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						CATCTGGCGATTGTTCCTCTC	0.502																																					p.N533S		Atlas-SNP	.											.	RRN3	36	.	0			c.A1598G						PASS	.						95	80	85					16																	15159184		2197	4300	6497	SO:0001583	missense	54700	exon16			TGGCGATTGTTCC	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.1598A>G	chr16.hg19:g.15159184T>C	ENSP00000198767:p.Asn533Ser	105.0	0.0	.		77.0	13.0	.	NM_018427	A2RTY9|B4E0J7|B4E3T2|Q3MHU9|Q6IPL4|Q9H4F0	Missense_Mutation	SNP	ENST00000198767.6	hg19	CCDS10559.1	.	.	.	.	.	.	.	.	.	.	.	8.281	0.815443	0.16607	.	.	ENSG00000085721	ENST00000198767;ENST00000429751;ENST00000327307;ENST00000540462	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	5.39	3.07	0.35406	.	0.056806	0.64402	D	0.000003	T	0.35038	0.0918	L	0.48642	1.525	0.47123	D	0.999324	B;B;B	0.17038	0.004;0.02;0.01	B;B;B	0.27500	0.009;0.08;0.022	T	0.07849	-1.0751	10	0.23891	T	0.37	.	9.8617	0.41118	0.0:0.127:0.0:0.873	.	503;434;533	F5H148;B4DZL9;Q9NYV6	.;.;RRN3_HUMAN	S	533;503;500;351	ENSP00000198767:N533S;ENSP00000402027:N503S;ENSP00000318484:N500S;ENSP00000437963:N351S	ENSP00000198767:N533S	N	-	2	0	RRN3	15066685	1.000000	0.71417	0.993000	0.49108	0.185000	0.23345	3.207000	0.51106	0.410000	0.25675	0.482000	0.46254	AAT	.	.	.	none		0.502	RRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252087.2	NM_018427		C	15159184	T	C	15159184	3	2	47	1	0	0	0	0	1	0	0	0	13697	1493	52	3	369	3	RRN3	16	15159184	Missense_Mutation	SNP	T	TCGA-A4-7732-01A-11D-2136-08		15159184	75195569	34	3294											
TMCO7	79613	hgsc.bcm.edu	37	chr16	68909060	68909060	+	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	tctctccattgtgccagcggGagcagctggtggaagtgatg	7	10	15	9	1	1	1	0	1	1	0	3	3	2	3	2	3	4	2	2	3	1	1			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr16:68909060G>T	ENST00000261778.1	+	5	1010	c.998G>T	c.(997-999)gGa>gTa	p.G333V		NM_024562.1	NP_078838.1	Q9C0B7	TNG6_HUMAN	transport and golgi organization 6 homolog (Drosophila)	333						integral component of membrane (GO:0016021)											GTGCCAGCGGGAGCAGCTGGT	0.473																																					p.G333V		Atlas-SNP	.											.	.	.	.	0			c.G998T						PASS	.						78	88	85					16																	68909060		2134	4251	6385	SO:0001583	missense	79613	exon5			CAGCGGGAGCAGC		CCDS45516.1	16q22.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000103047	ENSG00000103047			25749	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 7"	TMCO7		11214970	Standard	NM_024562		Approved	FLJ12688, KIAA1746	uc002ewi.4	Q9C0B7	OTTHUMG00000176743	ENST00000261778.1:c.998G>T	chr16.hg19:g.68909060G>T	ENSP00000261778:p.Gly333Val	97.0	0.0	.		37.0	17.0	.	NM_024562	Q569F9|Q9H9K1	Missense_Mutation	SNP	ENST00000261778.1	hg19	CCDS45516.1	.	.	.	.	.	.	.	.	.	.	G	15.03	2.713100	0.48517	.	.	ENSG00000103047	ENST00000261778	T	0.69175	-0.38	4.94	4.94	0.65067	.	.	.	.	.	T	0.81138	0.4760	M	0.77820	2.39	0.80722	D	1	D	0.69078	0.997	D	0.64687	0.928	D	0.83369	0.0006	9	0.59425	D	0.04	-8.1136	17.3079	0.87200	0.0:0.0:1.0:0.0	.	333	Q9C0B7	TMCO7_HUMAN	V	333	ENSP00000261778:G333V	ENSP00000261778:G333V	G	+	2	0	TMCO7	67466561	1.000000	0.71417	0.969000	0.41365	0.107000	0.19398	5.015000	0.64035	2.437000	0.82529	0.591000	0.81541	GGA	.	.	.	none		0.473	TANGO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433471.2	XM_928235.2		T	68909060	G	T	68909060	3	4	47	1	0	0	0	0	1	0	0	0	16013	1174	41	4	1016	4	TMCO7	16	68909060	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	53749876	68909060	21445693	35	3295											
KIAA0664	23277	hgsc.bcm.edu	37	chr17	2601454	2601454	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggtgccgcaggatcttgAggggccgactcgtgcgctcc	4	8	15	14	4	1	1	0	1	1	0	3	3	2	2	4	4	2	2	4	4	0	1			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr17:2601454A>G	ENST00000570628.2	-	10	1688	c.1583T>C	c.(1582-1584)cTc>cCc	p.L528P	CLUH_ENST00000538975.1_Missense_Mutation_p.L528P|CLUH_ENST00000435359.1_Missense_Mutation_p.L528P			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	528					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)											CAGGATCTTGAGGGGCCGACT	0.647																																					p.L528P		Atlas-SNP	.											.	.	.	.	0			c.T1583C						PASS	.						37	48	44					17																	2601454		2169	4256	6425	SO:0001583	missense	23277	exon10			ATCTTGAGGGGCC	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.1583T>C	chr17.hg19:g.2601454A>G	ENSP00000458986:p.Leu528Pro	9.0	0.0	.		9.0	7.0	.	NM_015229	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Missense_Mutation	SNP	ENST00000570628.2	hg19	CCDS45572.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.819136	0.90873	.	.	ENSG00000132361	ENST00000435359;ENST00000322335;ENST00000538975	D;D	0.87412	-2.25;-2.25	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.95098	0.8412	M	0.93507	3.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.96211	0.9153	10	0.87932	D	0	.	15.0034	0.71492	1.0:0.0:0.0:0.0	.	528;528	O75153;C9J6D7	K0664_HUMAN;.	P	528	ENSP00000388872:L528P;ENSP00000439628:L528P	ENSP00000320468:L528P	L	-	2	0	KIAA0664	2548204	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.144000	0.66660	0.533000	0.62120	CTC	.	.	.	none		0.647	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229		G	2601454	A	G	2601454	3	3	47	1	0	0	0	0	1	0	0	0	8196	304	11	3	2414	3	KIAA0664	17	2601454	Missense_Mutation	SNP	A	TCGA-A4-7732-01A-11D-2136-08		2601454	78593756	36	3296											
DNAH9	1770	hgsc.bcm.edu	37	chr17	11772554	11772554	+	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	agtgaccgcagtcaccatctCccttgccaaccgcctggtga	8	8	9	16	2	2	2	1	2	1	0	3	2	2	2	6	1	2	1	6	1	1	1			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr17:11772554C>T	ENST00000262442.4	+	51	10105	c.10037C>T	c.(10036-10038)tCc>tTc	p.S3346F	DNAH9_ENST00000454412.2_Missense_Mutation_p.S3346F	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3346					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)		GTCACCATCTCCCTTGCCAAC	0.498																																					p.S3346F		Atlas-SNP	.											.	DNAH9	695	.	0			c.C10037T						PASS	.						93	83	87					17																	11772554		2203	4300	6503	SO:0001583	missense	1770	exon51			CCATCTCCCTTGC	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.10037C>T	chr17.hg19:g.11772554C>T	ENSP00000262442:p.Ser3346Phe	118.0	0.0	.		91.0	28.0	.	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	C	16.32	3.091444	0.55968	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.75589	-0.95;-0.95	4.54	4.54	0.55810	Dynein heavy chain, coiled coil stalk (1);	0.361482	0.29246	N	0.012706	D	0.84238	0.5428	M	0.87682	2.9	0.80722	D	1	P	0.44195	0.828	P	0.52554	0.702	D	0.87047	0.2144	10	0.66056	D	0.02	.	15.0338	0.71728	0.0:0.8577:0.1423:0.0	.	3346	Q9NYC9	DYH9_HUMAN	F	3346;3346;1928	ENSP00000262442:S3346F;ENSP00000414874:S3346F	ENSP00000262442:S3346F	S	+	2	0	DNAH9	11713279	0.799000	0.28903	1.000000	0.80357	0.588000	0.36517	1.816000	0.38992	2.510000	0.84645	0.643000	0.83706	TCC	.	.	.	none		0.498	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11772554	C	T	11772554	3	4	47	1	0	0	0	0	1	0	0	0	4610	855	30	2	10239	2	DNAH9	17	11772554	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08	9171100	11772554	69422656	37	3297											
ZNF207	7756	hgsc.bcm.edu	37	chr17	30692444	30692444	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttaatagaccacctgcaccaAcagcaactgtacctgcccca	13	7	5	16	0	0	1	0	0	0	1	0	1	0	1	6	0	6	3	6	0	5	3			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr17:30692444A>G	ENST00000321233.6	+	7	872	c.718A>G	c.(718-720)Aca>Gca	p.T240A	ZNF207_ENST00000394670.4_Missense_Mutation_p.T256A|ZNF207_ENST00000341711.6_Missense_Mutation_p.T157A|ZNF207_ENST00000342555.6_Missense_Mutation_p.T259A|ZNF207_ENST00000577908.1_Missense_Mutation_p.T256A|ZNF207_ENST00000394673.2_Missense_Mutation_p.T256A	NM_003457.3	NP_003448.1	O43670	ZN207_HUMAN	zinc finger protein 207	240					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)			ACCTGCACCAACAGCAACTGT	0.502																																					p.T256A		Atlas-SNP	.											.	ZNF207	32	.	0			c.A766G						PASS	.						70	60	63					17																	30692444		2203	4300	6503	SO:0001583	missense	7756	exon8			GCACCAACAGCAA	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.718A>G	chr17.hg19:g.30692444A>G	ENSP00000322777:p.Thr240Ala	62.0	0.0	.		82.0	4.0	.	NM_001098507	A8K6Y6|E1P660|E1P661|E1P662|Q53XS9|Q96HW5|Q9BUQ7	Missense_Mutation	SNP	ENST00000321233.6	hg19	CCDS11271.1	.	.	.	.	.	.	.	.	.	.	A	11.34	1.611008	0.28712	.	.	ENSG00000010244	ENST00000394670;ENST00000394673;ENST00000394679;ENST00000321233;ENST00000341711;ENST00000342555	T;T	0.41065	1.01;1.04	5.87	2.05	0.26809	.	0.483859	0.24044	N	0.042070	T	0.20495	0.0493	N	0.14661	0.345	0.24350	N	0.99493	B;B;B;B;B	0.16396	0.0;0.0;0.0;0.0;0.017	B;B;B;B;B	0.20767	0.0;0.0;0.0;0.0;0.031	T	0.25950	-1.0117	10	0.07644	T	0.81	.	8.3666	0.32391	0.6656:0.0:0.3344:0.0	.	240;259;256;256;240	A8MTG3;Q59G94;E1P660;O43670-2;O43670	.;.;.;.;ZN207_HUMAN	A	256;240;259;256;157;240	ENSP00000378165:T256A;ENSP00000344913:T157A	ENSP00000322777:T256A	T	+	1	0	ZNF207	27716557	0.786000	0.28738	1.000000	0.80357	0.998000	0.95712	0.603000	0.24149	0.492000	0.27815	0.477000	0.44152	ACA	.	.	.	none		0.502	ZNF207-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256251.2			G	30692444	A	G	30692444	3	3	47	1	0	0	0	0	1	0	0	0	17777	43	2	3	796	3	ZNF207	17	30692444	Missense_Mutation	SNP	A	TCGA-A4-7732-01A-11D-2136-08	18919890	30692444	50502766	38	3298											
KRTAP4-5	85289	hgsc.bcm.edu	37	chr17	39305911	39305911	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggcttgcagcagctggggcGgcagcaggtggtcctgcagc	5	6	19	11	1	0	0	0	0	0	0	1	0	1	0	1	6	6	7	1	6	0	1	rs557154279|rs141058010	byFrequency	TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr17:39305911G>A	ENST00000343246.4	-	1	143	c.109C>T	c.(109-111)Cgc>Tgc	p.R37C		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	37	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)			CAGCTGGGGCGGCAGCAGGTG	0.657																																					p.R37C		Atlas-SNP	.											KRTAP4-5,NS,carcinoma,0,1	KRTAP4-5	34	.	0			c.C109T						PASS	.						25	29	27					17																	39305911		2176	4272	6448	SO:0001583	missense	85289	exon1			TGGGGCGGCAGCA	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.109C>T	chr17.hg19:g.39305911G>A	ENSP00000340546:p.Arg37Cys	86.0	1.0	.		78.0	7.0	.	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	hg19	CCDS32650.1	.	.	.	.	.	.	.	.	.	.	.	12.13	1.844454	0.32606	.	.	ENSG00000198271	ENST00000343246	T	0.01455	4.87	3.22	-1.8	0.07907	.	2.080600	0.03668	U	0.243553	T	0.02767	0.0083	L	0.57536	1.79	0.18873	N	0.999989	B	0.18461	0.028	B	0.12837	0.008	T	0.47045	-0.9147	10	0.56958	D	0.05	.	5.7249	0.18008	0.1011:0.0:0.4232:0.4757	.	37	Q9BYR2	KRA45_HUMAN	C	37	ENSP00000340546:R37C	ENSP00000340546:R37C	R	-	1	0	KRTAP4-5	36559437	0.000000	0.05858	0.674000	0.29902	0.928000	0.56348	-0.202000	0.09451	-0.272000	0.09259	0.556000	0.70494	CGC	.	.	.	weak		0.657	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1			A	39305911	G	A	39305911	3	1	47	1	0	0	0	0	1	0	0	0	8561	1116	39	1	440	1	KRTAP4-5	17	39305911	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	8613467	39305911	41889299	39	3299											
SLC16A5	9121	hgsc.bcm.edu	37	chr17	73096278	73096278	+	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	gctggaggggtaccttccttGtcttcggcgggatctttctc	3	14	13	11	2	3	0	0	0	3	0	6	2	4	2	2	5	1	2	2	5	1	5			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr17:73096278G>T	ENST00000450736.2	+	4	935	c.520G>T	c.(520-522)Gtc>Ttc	p.V174F	SLC16A5_ENST00000538213.2_Missense_Mutation_p.V214F|SLC16A5_ENST00000580123.1_Missense_Mutation_p.V174F|SLC16A5_ENST00000329783.4_Missense_Mutation_p.V174F			O15375	MOT6_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 5	174					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)	TACCTTCCTTGTCTTCGGCGG	0.642																																					p.V174F		Atlas-SNP	.											.	SLC16A5	80	.	0			c.G520T						PASS	.						49	49	49					17																	73096278		2203	4300	6503	SO:0001583	missense	9121	exon5			TTCCTTGTCTTCG	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.520G>T	chr17.hg19:g.73096278G>T	ENSP00000390564:p.Val174Phe	77.0	0.0	.		49.0	4.0	.	NM_001271765	B4E288	Missense_Mutation	SNP	ENST00000450736.2	hg19	CCDS11713.1	.	.	.	.	.	.	.	.	.	.	G	8.724	0.915027	0.17907	.	.	ENSG00000170190	ENST00000329783;ENST00000450736;ENST00000538213	T;T;T	0.59772	0.24;0.24;0.24	4.58	-5.33	0.02713	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.457119	0.24674	N	0.036522	T	0.53899	0.1825	L	0.39692	1.235	0.21740	N	0.99956	D;D	0.56287	0.975;0.975	P;P	0.58391	0.791;0.838	T	0.55933	-0.8062	10	0.66056	D	0.02	.	8.4103	0.32640	0.444:0.112:0.444:0.0	.	214;174	B4E288;O15375	.;MOT6_HUMAN	F	174;174;214	ENSP00000330141:V174F;ENSP00000390564:V174F;ENSP00000440212:V214F	ENSP00000330141:V174F	V	+	1	0	SLC16A5	70607873	0.006000	0.16342	0.067000	0.19924	0.636000	0.38137	0.220000	0.17660	-1.012000	0.03387	0.561000	0.74099	GTC	.	.	.	none		0.642	SLC16A5-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445547.1	NM_004695		T	73096278	G	T	73096278	3	4	47	1	0	0	0	0	1	0	0	0	14424	1377	48	4	530	4	SLC16A5	17	73096278	Missense_Mutation	SNP	G	TCGA-A4-7732-01A-11D-2136-08	33790367	73096278	8098932	40	3300											
ZNF439	90594	hgsc.bcm.edu	37	chr19	11978986	11978986	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggcttttattctgccaagTcatttcaaagacatgaaaaa	16	12	6	7	0	3	2	2	1	1	1	3	2	3	2	1	1	1	1	1	1	6	4			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr19:11978986T>C	ENST00000304030.2	+	3	1302	c.1102T>C	c.(1102-1104)Tca>Cca	p.S368P	ZNF439_ENST00000455282.1_Missense_Mutation_p.S232P|ZNF439_ENST00000592534.1_Intron	NM_152262.2	NP_689475.1	Q8NDP4	ZN439_HUMAN	zinc finger protein 439	368					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(7)|pancreas(1)|skin(2)	27						TTCTGCCAAGTCATTTCAAAG	0.383																																					p.S368P		Atlas-SNP	.											.	ZNF439	67	.	0			c.T1102C						PASS	.						65	66	66					19																	11978986		2203	4300	6503	SO:0001583	missense	90594	exon3			GCCAAGTCATTTC	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.1102T>C	chr19.hg19:g.11978986T>C	ENSP00000305077:p.Ser368Pro	109.0	0.0	.		60.0	4.0	.	NM_152262	Q8IYZ7|Q96SU1	Missense_Mutation	SNP	ENST00000304030.2	hg19	CCDS12268.1	.	.	.	.	.	.	.	.	.	.	t	11.77	1.736704	0.30774	.	.	ENSG00000171291	ENST00000455282;ENST00000304030	T;T	0.07908	3.15;3.15	0.575	0.575	0.17374	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.24392	0.0591	M	0.84082	2.675	0.09310	N	1	P	0.49961	0.93	P	0.62885	0.908	T	0.03863	-1.0997	9	0.54805	T	0.06	.	6.7827	0.23654	0.0:0.0:0.0:1.0	.	368	Q8NDP4	ZN439_HUMAN	P	232;368	ENSP00000395632:S232P;ENSP00000305077:S368P	ENSP00000305077:S368P	S	+	1	0	ZNF439	11839986	0.000000	0.05858	0.002000	0.10522	0.010000	0.07245	-1.393000	0.02521	0.485000	0.27652	0.163000	0.16589	TCA	.	.	.	none		0.383	ZNF439-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344513.1			C	11978986	T	C	11978986	3	2	47	1	0	0	0	0	1	0	0	0	17923	1667	58	3	1112	3	ZNF439	19	11978986	Missense_Mutation	SNP	T	TCGA-A4-7732-01A-11D-2136-08		11978986	47149997	41	3301											
ZNF226	7769	hgsc.bcm.edu	37	chr19	44680650	44680650	+	Frame_Shift_Del	DEL	T	T	-																															tcttcaatcccatcaaagagTtcatacaggagagaaaccat																										TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr19:44680650delT	ENST00000590089.1	+	7	1602	c.1235delT	c.(1234-1236)gttfs	p.V412fs	ZNF226_ENST00000337433.5_Frame_Shift_Del_p.V412fs|ZNF226_ENST00000588883.1_3'UTR|ZNF226_ENST00000454662.2_Frame_Shift_Del_p.V412fs			Q9NYT6	ZN226_HUMAN	zinc finger protein 226	412					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)						Prostate(69;0.0352)|all_neural(266;0.202)				CATCAAAGAGTTCATACAGGA	0.433																																					p.V412fs	Pancreas(115;581 1665 13228 19278 50070)	Atlas-INDEL	.											.	.	.	.	0			c.1234delG						PASS	.						62	66	65					19																	44680650		2197	4300	6497	SO:0001589	frameshift_variant	7769	exon6			.	AF024707	CCDS46102.1, CCDS46103.1	19q13.31	2013-01-08	2012-09-11	2012-09-11	ENSG00000167380	ENSG00000167380		"Zinc fingers, C2H2-type", "-"	13019	protein-coding gene	gene with protein product							Standard	NM_001146220		Approved		uc002oyp.3	Q9NYT6		ENST00000590089.1:c.1235delT	chr19.hg19:g.44680650delT	ENSP00000465121:p.Val412fs	68.0	0.0	0		46.0	19.0	0.413043	NM_001032372	Q8WWE6|Q96TE6|Q9NS44	Frame_Shift_Del	DEL	ENST00000590089.1	hg19	CCDS46102.1																																																																																			.	.	.	none		0.433	ZNF226-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460712.1			-	44680650	T	-	44680650	7	5	47	1	0	1	0	1	0	0	0	0	17792	1725	60	0	1303	0	ZNF226	19	44680650	Frame_Shift_Del	DEL	T	TCGA-A4-7732-01A-11D-2136-08	32701664	44680650	14448333	42	3302											
KPTN	11133	hgsc.bcm.edu	37	chr19	47987312	47987312	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcagctccccgcgcccgcCggcgccgcctgccagcccgt	3	3	12	23	7	0	0	0	0	0	0	1	0	1	0	8	1	4	2	8	1	0	0			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr19:47987312C>T	ENST00000338134.3	-	1	213	c.106G>A	c.(106-108)Ggc>Agc	p.G36S	NAPA-AS1_ENST00000594367.1_RNA|KPTN_ENST00000536339.1_5'UTR|NAPA-AS1_ENST00000593284.1_RNA|KPTN_ENST00000595484.1_5'UTR	NM_007059.2	NP_008990.2	Q9Y664	KPTN_HUMAN	kaptin (actin binding protein)	36					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)		ccgcgcccgccggcgccgccT	0.697											OREG0025593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G36S		Atlas-SNP	.											.	KPTN	34	.	0			c.G106A						PASS	.						16	20	19					19																	47987312		1778	3946	5724	SO:0001583	missense	11133	exon1			GCCCGCCGGCGCC	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.106G>A	chr19.hg19:g.47987312C>T	ENSP00000337850:p.Gly36Ser	64.0	0.0	.	951	43.0	17.0	.	NM_007059	B3KN86|B4DQ76|Q96GT1	Missense_Mutation	SNP	ENST00000338134.3	hg19	CCDS42583.1	.	.	.	.	.	.	.	.	.	.	C	5.953	0.359822	0.11296	.	.	ENSG00000118162	ENST00000338134	.	.	.	4.59	1.01	0.19927	.	0.822214	0.11218	N	0.586992	T	0.16041	0.0386	N	0.10874	0.06	0.22968	N	0.998498	B	0.12013	0.005	B	0.10450	0.005	T	0.30060	-0.9991	9	0.15952	T	0.53	-4.8928	5.1034	0.14772	0.0:0.5015:0.17:0.3285	.	36	Q9Y664	KPTN_HUMAN	S	36	.	ENSP00000337850:G36S	G	-	1	0	KPTN	52679124	0.103000	0.21917	0.979000	0.43373	0.439000	0.31926	1.690000	0.37711	0.509000	0.28195	0.313000	0.20887	GGC	.	.	.	none		0.697	KPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466672.2			T	47987312	C	T	47987312	3	4	47	1	0	0	0	0	1	0	0	0	8444	652	23	1	1252	1	KPTN	19	47987312	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08	3306662	47987312	11141671	43	3303											
MKKS	8195	hgsc.bcm.edu	37	chr20	10385928	10385928	+	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	tcaataacatatgaaagatcCaaaatcaaattggctgtctc	17	11	5	8	0	3	2	2	1	1	1	5	2	4	2	1	1	1	1	1	1	7	3			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chr20:10385928C>A	ENST00000347364.3	-	6	2442	c.1680G>T	c.(1678-1680)ttG>ttT	p.L560F	MKKS_ENST00000399054.2_Missense_Mutation_p.L560F	NM_170784.2	NP_740754.1	Q9NPJ1	MKKS_HUMAN	McKusick-Kaufman syndrome	560					artery smooth muscle contraction (GO:0014824)|brain morphogenesis (GO:0048854)|cartilage development (GO:0051216)|cerebral cortex development (GO:0021987)|chaperone-mediated protein complex assembly (GO:0051131)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|determination of left/right symmetry (GO:0007368)|fat cell differentiation (GO:0045444)|gonad development (GO:0008406)|heart development (GO:0007507)|heart looping (GO:0001947)|hippocampus development (GO:0021766)|intracellular transport (GO:0046907)|melanosome transport (GO:0032402)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of multicellular organism growth (GO:0040018)|protein folding (GO:0006457)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|sensory perception of smell (GO:0007608)|social behavior (GO:0035176)|spermatid development (GO:0007286)|striatum development (GO:0021756)|vasodilation (GO:0042311)|visual perception (GO:0007601)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|motile cilium (GO:0031514)	ATP binding (GO:0005524)|RNA polymerase II repressing transcription factor binding (GO:0001103)|unfolded protein binding (GO:0051082)			kidney(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)|stomach(2)	16						ATGAAAGATCCAAAATCAAAT	0.393																																					p.L560F	Melanoma(79;1979 2212 6640)	Atlas-SNP	.											.	MKKS	35	.	0			c.G1680T						PASS	.						32	31	31					20																	10385928		2203	4300	6503	SO:0001583	missense	8195	exon6			AAGATCCAAAATC	AF221993	CCDS13111.1	20p12	2013-01-08			ENSG00000125863	ENSG00000125863		"Heat Shock Proteins / Chaperonins"	7108	protein-coding gene	gene with protein product		604896		BBS6		9467007	Standard	NR_072977		Approved		uc002wnu.2	Q9NPJ1	OTTHUMG00000031868	ENST00000347364.3:c.1680G>T	chr20.hg19:g.10385928C>A	ENSP00000246062:p.Leu560Phe	44.0	0.0	.		32.0	9.0	.	NM_170784	A8K7B0|D3DW18	Missense_Mutation	SNP	ENST00000347364.3	hg19	CCDS13111.1	.	.	.	.	.	.	.	.	.	.	C	19.52	3.843811	0.71488	.	.	ENSG00000125863	ENST00000347364;ENST00000399054	D;D	0.87966	-2.32;-2.32	6.07	2.82	0.32997	.	0.000000	0.64402	D	0.000001	D	0.91791	0.7403	M	0.77616	2.38	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	D	0.90008	0.4119	10	0.87932	D	0	-8.0737	8.1919	0.31374	0.0:0.6163:0.0:0.3837	.	560	Q9NPJ1	MKKS_HUMAN	F	560	ENSP00000246062:L560F;ENSP00000382008:L560F	ENSP00000246062:L560F	L	-	3	2	MKKS	10333928	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	0.884000	0.28214	0.279000	0.22186	0.655000	0.94253	TTG	.	.	.	none		0.393	MKKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077991.3			A	10385928	C	A	10385928	3	1	47	1	0	0	0	0	1	0	0	0	9607	593	21	4	36	4	MKKS	20	10385928	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08		10385928	52639592	44	3304											
GYG2	8908	hgsc.bcm.edu	37	chrX	2772026	2772026	+	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	acatgtctgttccagggtcaTcctctcgaaggtgttcgatg	7	13	11	10	2	3	0	1	0	2	0	7	2	5	0	2	2	0	2	2	2	1	2			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chrX:2772026T>A	ENST00000381163.3	+	5	530	c.248T>A	c.(247-249)aTc>aAc	p.I83N	GYG2_ENST00000542787.1_Missense_Mutation_p.I83N|GYG2-AS1_ENST00000445107.1_RNA|GYG2_ENST00000338623.5_Missense_Mutation_p.I83N|GYG2_ENST00000398806.3_Missense_Mutation_p.I52N|GYG2_ENST00000381161.1_3'UTR	NM_001079855.1|NM_001184702.1|NM_003918.2	NP_001073324.1|NP_001171631.1|NP_003909.2	O15488	GLYG2_HUMAN	glycogenin 2	83					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)	glycogenin glucosyltransferase activity (GO:0008466)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)	13		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)				TCCAGGGTCATCCTCTCGAAG	0.507																																					p.I83N		Atlas-SNP	.											.	GYG2	39	.	0			c.T248A						PASS	.						126	99	108					X																	2772026		2203	4298	6501	SO:0001583	missense	8908	exon5			GGGTCATCCTCTC	U94361	CCDS14121.1, CCDS48074.1	Xp22.3	2013-02-22			ENSG00000056998	ENSG00000056998	2.4.1.186	"Glycosyltransferase family 8 domain containing"	4700	protein-coding gene	gene with protein product	"glycogenin glucosyltransferase"	300198				9857012	Standard	NM_001079855		Approved	GN-2	uc004cqs.1	O15488	OTTHUMG00000021079	ENST00000381163.3:c.248T>A	chrX.hg19:g.2772026T>A	ENSP00000370555:p.Ile83Asn	47.0	0.0	.		47.0	43.0	.	NM_003918	B7WNN6|O15485|O15486|O15487|O15489|O15490	Missense_Mutation	SNP	ENST00000381163.3	hg19	CCDS14121.1	.	.	.	.	.	.	.	.	.	.	T	11.25	1.584140	0.28268	.	.	ENSG00000056998	ENST00000398806;ENST00000381163;ENST00000338623;ENST00000542787;ENST00000520904	T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97	3.59	2.41	0.29592	.	0.614533	0.14619	N	0.308517	T	0.37999	0.1024	L	0.39898	1.24	0.25836	N	0.984116	P;D;P;B;P	0.54964	0.731;0.969;0.847;0.378;0.489	P;P;P;B;P	0.49887	0.477;0.558;0.625;0.3;0.522	T	0.12016	-1.0564	10	0.41790	T	0.15	.	6.5	0.22164	0.0:0.2109:0.0:0.7891	.	83;43;52;52;83	O15488-4;O15488-3;A8K8Y1;O15488-2;O15488	.;.;.;.;GLYG2_HUMAN	N	52;83;83;83;52	ENSP00000381786:I52N;ENSP00000370555:I83N;ENSP00000341273:I83N;ENSP00000446092:I83N;ENSP00000430764:I52N	ENSP00000341273:I83N	I	+	2	0	GYG2	2782026	0.959000	0.32827	0.051000	0.19133	0.019000	0.09904	1.290000	0.33319	1.271000	0.44313	0.481000	0.45027	ATC	.	.	.	none		0.507	GYG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055645.1	NM_003918		A	2772026	T	A	2772026	3	1	47	1	0	0	0	0	1	0	0	0	6913	1435	50	5	262	5	GYG2	23	2772026	Missense_Mutation	SNP	T	TCGA-A4-7732-01A-11D-2136-08		2772026	152498534	45	3305											
SYP	6855	hgsc.bcm.edu	37	chrX	49050637	49050638	+	Frame_Shift_Del	DEL	TG	TG	-																															actcaccagcatgggcccttTgttattctctcggtacttgt																										TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chrX:49050637_49050638delTG	ENST00000263233.4	-	4	480_481	c.408_409delCA	c.(406-411)aacaaafs	p.N136fs	SYP_ENST00000479808.1_Frame_Shift_Del_p.N136fs|SYP_ENST00000538567.1_Frame_Shift_Del_p.N18fs	NM_003179.2	NP_003170.1	P08247	SYPH_HUMAN	synaptophysin	136	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				cellular response to organic substance (GO:0071310)|endocytosis (GO:0006897)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of opioid receptor signaling pathway (GO:2000474)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|synaptic vesicle maturation (GO:0016188)|synaptic vesicle membrane organization (GO:0048499)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|integral component of synaptic vesicle membrane (GO:0030285)|neuron projection (GO:0043005)|neuron projection terminus (GO:0044306)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	cholesterol binding (GO:0015485)|protein self-association (GO:0043621)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)	15		all_lung(315;0.00016)				ATGGGCCCTTTGTTATTCTCTC	0.564																																					p.137_137del		Atlas-INDEL	.											.	SYP	71	.	0			c.409_410del						PASS	.																																			SO:0001589	frameshift_variant	6855	exon4			.	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.408_409delCA	chrX.hg19:g.49050637_49050638delTG	ENSP00000263233:p.Asn136fs	51.0	0.0	0		27.0	20.0	0.740741	NM_003179	B2R7L6|B7Z359|Q6P2F7	Frame_Shift_Del	DEL	ENST00000263233.4	hg19	CCDS14321.1																																																																																			.	.	.	none		0.564	SYP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083625.2	NM_003179		-	49050638	TG	-	49050637	7	5	47	1	0	1	0	1	0	0	0	0	15473	1821	63	0	544	0	SYP	23	49050637	Frame_Shift_Del	DEL	TG	TCGA-A4-7732-01A-11D-2136-08	46278611	49050637	106219923	46	3306											
PHKA1	5255	hgsc.bcm.edu	37	chrX	71829514	71829514	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggttctggaggaagtcctaCtgtcaaatgtttctggtggg	8	13	14	6	0	3	0	1	0	2	0	4	2	4	2	1	5	1	2	1	5	3	3			TCGA-A4-7732-01A-11D-2136-08	TCGA-A4-7732-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f779f68-566c-4996-8aab-4ca7af95061c	b7fc117a-dadb-4f07-8dce-04bf472d7559	g.chrX:71829514C>T	ENST00000373542.4	-	23	2725	c.2566G>A	c.(2566-2568)Gta>Ata	p.V856I	PHKA1_ENST00000541944.1_Missense_Mutation_p.V797I|PHKA1_ENST00000373545.3_Missense_Mutation_p.V797I|PHKA1_ENST00000339490.3_Missense_Mutation_p.V856I|PHKA1_ENST00000373539.3_Missense_Mutation_p.V856I	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	856					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)					GGAAGTCCTACTGTCAAATGT	0.453																																					p.V856I		Atlas-SNP	.											.	PHKA1	129	.	0			c.G2566A						PASS	.						226	193	204					X																	71829514		2203	4300	6503	SO:0001583	missense	5255	exon23			GTCCTACTGTCAA		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.2566G>A	chrX.hg19:g.71829514C>T	ENSP00000362643:p.Val856Ile	80.0	0.0	.		53.0	47.0	.	NM_002637	B7ZL05|B7ZL07|Q2M3D7	Missense_Mutation	SNP	ENST00000373542.4	hg19	CCDS14421.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.271260	0.80469	.	.	ENSG00000067177	ENST00000373545;ENST00000373542;ENST00000541944;ENST00000339490;ENST00000373539	D;D;D;D;D	0.92149	-2.98;-2.98;-2.98;-2.98;-2.98	5.65	5.65	0.86999	Glycoside hydrolase 15-related (1);	0.000000	0.85682	D	0.000000	D	0.95172	0.8435	M	0.84082	2.675	0.54753	D	0.999987	B;B;B	0.33637	0.118;0.389;0.42	B;P;B	0.48627	0.21;0.584;0.421	D	0.94813	0.7980	10	0.52906	T	0.07	-4.9016	15.893	0.79315	0.0:1.0:0.0:0.0	.	797;856;856	B7ZL07;P46020-2;P46020	.;.;KPB1_HUMAN	I	797;856;797;856;856	ENSP00000362646:V797I;ENSP00000362643:V856I;ENSP00000441251:V797I;ENSP00000342469:V856I;ENSP00000362640:V856I	ENSP00000342469:V856I	V	-	1	0	PHKA1	71746239	0.999000	0.42202	0.998000	0.56505	0.964000	0.63967	4.396000	0.59684	2.353000	0.79882	0.544000	0.68410	GTA	.	.	.	none		0.453	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1			T	71829514	C	T	71829514	3	4	47	1	0	0	0	0	1	0	0	0	11850	565	20	2	1145	2	PHKA1	23	71829514	Missense_Mutation	SNP	C	TCGA-A4-7732-01A-11D-2136-08	22778877	71829514	83441046	47	3307											
ZNF644	84146	hgsc.bcm.edu	37	chr1	91406116	91406116	+	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	ttagtcataagaaattgaatGaactctttttggggatccca	13	14	8	6	0	2	3	1	2	1	1	3	4	3	4	1	2	1	0	1	2	5	5			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr1:91406116G>A	ENST00000370440.1	-	3	1012	c.795C>T	c.(793-795)ttC>ttT	p.F265F	ZNF644_ENST00000347275.5_Intron|ZNF644_ENST00000337393.5_Silent_p.F265F|ZNF644_ENST00000467231.1_Intron|ZNF644_ENST00000361321.5_Intron			Q9H582	ZN644_HUMAN	zinc finger protein 644	265					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(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)		GAAATTGAATGAACTCTTTTT	0.353																																					p.F265F		Atlas-SNP	.											.	ZNF644	120	.	0			c.C795T						PASS	.						106	105	105					1																	91406116		2202	4300	6502	SO:0001819	synonymous_variant	84146	exon3			TTGAATGAACTCT	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.795C>T	chr1.hg19:g.91406116G>A		102.0	0.0	.		144.0	57.0	.	NM_201269	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Silent	SNP	ENST00000370440.1	hg19	CCDS731.1																																																																																			.	.	.	none		0.353	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186		A	91406116	G	A	91406116	2	1	48	1	0	0	0	0	0	0	0	1	18072	1281	45	2		2	ZNF644	1	91406116	Silent	SNP	G	TCGA-A4-7734-01A-11D-2136-08		91406116	157844505	1	3308											
KCND3	3752	hgsc.bcm.edu	37	chr1	112524716	112524716	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacggcagctccttgctgccCgggaccgtgccgcacggcac	5	5	13	18	5	0	0	0	0	0	0	1	1	1	1	4	3	4	5	4	3	0	1	rs35131566	byFrequency	TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr1:112524716C>T	ENST00000315987.2	-	2	1112	c.633G>A	c.(631-633)ccG>ccA	p.P211P	KCND3_ENST00000302127.4_Silent_p.P211P|KCND3_ENST00000369697.1_Silent_p.P211P	NM_004980.4	NP_004971.2	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 3	211					cell death (GO:0008219)|membrane repolarization (GO:0086009)|potassium ion export (GO:0071435)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	49		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)	Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	CCTTGCTGCCCGGGACCGTGC	0.647																																					p.P211P		Atlas-SNP	.											.	KCND3	150	.	0			c.G633A						PASS	.						27	28	28					1																	112524716		2203	4300	6503	SO:0001819	synonymous_variant	3752	exon2			GCTGCCCGGGACC	AF048713	CCDS843.1, CCDS844.1	1p13.2	2014-09-17			ENSG00000171385	ENSG00000171385		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6239	protein-coding gene	gene with protein product		605411	"spinocerebellar ataxia 22", "spinocerebellar ataxia 19"	SCA22, SCA19		10942109, 16382104, 23280837	Standard	NM_172198		Approved	Kv4.3, KSHIVB	uc001ebu.1	Q9UK17	OTTHUMG00000011989	ENST00000315987.2:c.633G>A	chr1.hg19:g.112524716C>T		60.0	0.0	.		34.0	13.0	.	NM_004980	O60576|O60577|Q14D71|Q5T0M0|Q9UH85|Q9UH86|Q9UK16	Silent	SNP	ENST00000315987.2	hg19	CCDS843.1																																																																																			.	C|0.999;A|0.001	.	alt		0.647	KCND3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000033144.1	NM_172198		T	112524716	C	T	112524716	2	4	48	1	0	0	0	0	0	0	0	1	8027	639	23	1		1	KCND3	1	112524716	Silent	SNP	C	TCGA-A4-7734-01A-11D-2136-08	21118600	112524716	136725905	2	3309											
YY1AP1	55249	hgsc.bcm.edu	37	chr1	155638446	155638446	+	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	tgttgtcaggagctctgttcAtgttgaggttcttgattctc	5	18	11	7	0	5	2	2	2	3	0	6	3	5	3	0	2	1	5	0	2	0	6			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr1:155638446A>T	ENST00000295566.4	-	9	1012	c.989T>A	c.(988-990)aTg>aAg	p.M330K	YY1AP1_ENST00000405763.3_Missense_Mutation_p.M422K|MSTO1_ENST00000452804.2_Intron|MSTO1_ENST00000538143.1_Intron|YY1AP1_ENST00000476093.1_5'Flank|YY1AP1_ENST00000368340.5_Missense_Mutation_p.M402K|YY1AP1_ENST00000359205.5_Missense_Mutation_p.M273K|YY1AP1_ENST00000535662.1_Missense_Mutation_p.M130K|YY1AP1_ENST00000368339.5_Missense_Mutation_p.M422K|YY1AP1_ENST00000347088.5_Missense_Mutation_p.M284K|YY1AP1_ENST00000368330.2_Missense_Mutation_p.M284K|YY1AP1_ENST00000407221.1_Missense_Mutation_p.M253K|YY1AP1_ENST00000355499.4_Missense_Mutation_p.M284K|YY1AP1_ENST00000311573.5_Missense_Mutation_p.M253K|YY1AP1_ENST00000361831.5_Missense_Mutation_p.M273K|YY1AP1_ENST00000404643.1_Missense_Mutation_p.M264K	NM_001198906.1|NM_139118.2	NP_001185835.1|NP_620829.1	Q9H869	YYAP1_HUMAN	YY1 associated protein 1	330					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)					AGCTCTGTTCATGTTGAGGTT	0.433																																					p.M422K		Atlas-SNP	.											.	YY1AP1	104	.	0			c.T1265A						PASS	.						307	257	274					1																	155638446		2203	4300	6503	SO:0001583	missense	55249	exon8			CTGTTCATGTTGA	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.989T>A	chr1.hg19:g.155638446A>T	ENSP00000295566:p.Met330Lys	197.0	0.0	.		149.0	46.0	.	NM_001198903	B0QZ54|B4DMP2|B4E0I0|D3DV96|D3DV98|H7BY62|Q5VYZ1|Q5VYZ4|Q5VYZ7|Q7L4C3|Q7L5E2|Q8IXA6|Q8TEW5|Q8TF04|Q96HB6|Q9BQ64|Q9NV84	Missense_Mutation	SNP	ENST00000295566.4	hg19	CCDS1115.1	.	.	.	.	.	.	.	.	.	.	A	14.05	2.419504	0.42918	.	.	ENSG00000163374	ENST00000359205;ENST00000355499;ENST00000311573;ENST00000347088;ENST00000361831;ENST00000368340;ENST00000295566;ENST00000368330;ENST00000407221;ENST00000404643;ENST00000368339;ENST00000535662;ENST00000405763	T;T;T;T;T;T;T;T;T;T;T;T	0.24151	1.9;1.9;1.92;1.9;1.9;1.9;1.91;1.9;1.92;1.93;1.87;1.93	3.4	-0.935	0.10423	.	0.476592	0.21278	N	0.077194	T	0.07999	0.0200	L	0.53249	1.67	0.80722	D	1	B;B;B;B;B;P;B	0.40211	0.12;0.103;0.169;0.297;0.034;0.707;0.088	B;B;B;B;B;B;B	0.36845	0.098;0.025;0.079;0.175;0.017;0.234;0.046	T	0.14671	-1.0464	10	0.32370	T	0.25	.	4.6279	0.12488	0.6197:0.0:0.0911:0.2892	.	350;422;264;422;330;284;402	B4DQQ0;B4DMP2;Q9H869-4;B0QZ55;Q9H869;Q9H869-2;Q5VYZ1	.;.;.;.;YYAP1_HUMAN;.;.	K	273;284;253;284;273;402;330;284;253;264;422;130;422	ENSP00000352134:M273K;ENSP00000347686:M284K;ENSP00000311138:M253K;ENSP00000316079:M284K;ENSP00000355298:M273K;ENSP00000357324:M402K;ENSP00000295566:M330K;ENSP00000357314:M284K;ENSP00000385791:M253K;ENSP00000385390:M264K;ENSP00000357323:M422K;ENSP00000437926:M130K	ENSP00000295566:M330K	M	-	2	0	YY1AP1	153905070	0.275000	0.24201	0.971000	0.41717	0.982000	0.71751	0.942000	0.29017	0.038000	0.15604	0.379000	0.24179	ATG	.	.	.	none		0.433	YY1AP1-043	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000086027.1	NM_139118		T	155638446	A	T	155638446	3	4	48	1	0	0	0	0	1	0	0	0	17520	217	8	5	1413	5	YY1AP1	1	155638446	Missense_Mutation	SNP	A	TCGA-A4-7734-01A-11D-2136-08	43113730	155638446	93612175	3	3310											
APOB	338	hgsc.bcm.edu	37	chr2	21251317	21251317	+	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	aattttgttaatatctgcctGtgaaggactcctcatcaaca	12	14	6	9	0	3	1	2	1	1	0	4	2	4	2	2	1	2	1	2	1	5	4			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr2:21251317G>A	ENST00000233242.1	-	13	1838	c.1711C>T	c.(1711-1713)Cag>Tag	p.Q571*	APOB_ENST00000399256.4_Nonsense_Mutation_p.Q571*	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	571	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)					ATATCTGCCTGTGAAGGACTC	0.438																																					p.Q571X		Atlas-SNP	.											.	APOB	761	.	0			c.C1711T						PASS	.						131	133	132					2																	21251317		2203	4300	6503	SO:0001587	stop_gained	338	exon13			CTGCCTGTGAAGG	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.1711C>T	chr2.hg19:g.21251317G>A	ENSP00000233242:p.Gln571*	179.0	0.0	.		144.0	55.0	.	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Nonsense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	37	6.513092	0.97629	.	.	ENSG00000084674	ENST00000233242;ENST00000535079;ENST00000399256	.	.	.	5.69	3.47	0.39725	.	0.330090	0.28688	N	0.014472	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	.	5.0861	0.14682	0.0975:0.133:0.632:0.1375	.	.	.	.	X	571	.	ENSP00000233242:Q571X	Q	-	1	0	APOB	21104822	0.134000	0.22483	0.496000	0.27539	0.194000	0.23727	0.571000	0.23669	0.602000	0.29896	0.655000	0.94253	CAG	.	.	.	none		0.438	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21251317	G	A	21251317	4	1	48	1	0	0	0	0	0	1	0	0	785	1386	48	2	12048	2	APOB	2	21251317	Nonsense_Mutation	SNP	G	TCGA-A4-7734-01A-11D-2136-08		21251317	221948056	4	3311											
ITGA6	3655	hgsc.bcm.edu	37	chr2	173352903	173352903	+	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	gaggtacagttgttggcgagCaagctatgaaatctgaagat	13	10	13	5	1	1	3	0	2	1	1	1	5	1	3	0	2	3	5	0	2	5	4			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr2:173352903C>A	ENST00000264106.6	+	20	2772	c.2569C>A	c.(2569-2571)Caa>Aaa	p.Q857K	AC093818.1_ENST00000442417.1_RNA|ITGA6_ENST00000264107.7_Missense_Mutation_p.Q818K|ITGA6_ENST00000409532.1_Missense_Mutation_p.Q699K|ITGA6_ENST00000343713.4_Missense_Mutation_p.Q813K|ITGA6_ENST00000409080.1_Missense_Mutation_p.Q818K|ITGA6_ENST00000375221.2_Missense_Mutation_p.Q857K			P23229	ITA6_HUMAN	integrin, alpha 6	857					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)			TGTTGGCGAGCAAGCTATGAA	0.368																																					p.Q818K		Atlas-SNP	.											.	ITGA6	171	.	0			c.C2452A						PASS	.						152	153	153					2																	173352903		2203	4300	6503	SO:0001583	missense	3655	exon19			GGCGAGCAAGCTA		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.2569C>A	chr2.hg19:g.173352903C>A	ENSP00000264106:p.Gln857Lys	159.0	0.0	.		115.0	46.0	.	NM_000210	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Missense_Mutation	SNP	ENST00000264106.6	hg19		.	.	.	.	.	.	.	.	.	.	C	14.43	2.532122	0.45073	.	.	ENSG00000091409	ENST00000409532;ENST00000264107;ENST00000264106;ENST00000375221;ENST00000343713;ENST00000409080;ENST00000442250;ENST00000458358;ENST00000416789	T;T;T;T;T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86	5.76	3.78	0.43462	.	0.192038	0.56097	D	0.000033	T	0.33904	0.0879	N	0.22421	0.69	0.31631	N	0.648993	B;B;B;B	0.16802	0.007;0.008;0.019;0.019	B;B;B;B	0.19666	0.015;0.026;0.026;0.016	T	0.36065	-0.9763	10	0.42905	T	0.14	.	12.9758	0.58537	0.3451:0.6549:0.0:0.0	.	813;857;818;818	P23229-4;P23229-9;G5E9H1;P23229-2	.;.;.;.	K	699;818;857;857;813;818;857;813;43	ENSP00000386614:Q699K;ENSP00000264107:Q818K;ENSP00000264106:Q857K;ENSP00000364369:Q857K;ENSP00000341078:Q813K;ENSP00000386896:Q818K;ENSP00000406694:Q857K;ENSP00000394169:Q813K;ENSP00000388435:Q43K	ENSP00000264106:Q857K	Q	+	1	0	ITGA6	173061149	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	4.932000	0.63476	2.725000	0.93324	0.585000	0.79938	CAA	.	.	.	none		0.368	ITGA6-201	KNOWN	basic	protein_coding	protein_coding				A	173352903	C	A	173352903	3	1	48	1	0	0	0	0	1	0	0	0	7887	711	25	4	2526	4	ITGA6	2	173352903	Missense_Mutation	SNP	C	TCGA-A4-7734-01A-11D-2136-08	152101586	173352903	69846470	5	3312											
ZNF385B	151126	hgsc.bcm.edu	37	chr2	180310448	180310448	+	Frame_Shift_Del	DEL	T	T	-																															gcttcaaccatggtcttgtgTttagatcctaagacagaaag																										TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr2:180310448delT	ENST00000410066.1	-	8	1527	c.924delA	c.(922-924)aaafs	p.K308fs	ZNF385B_ENST00000409343.1_Frame_Shift_Del_p.K232fs|ZNF385B_ENST00000336917.5_Frame_Shift_Del_p.K206fs|ZNF385B_ENST00000409692.1_Frame_Shift_Del_p.K206fs|ZNF385B_ENST00000466398.1_5'UTR	NM_152520.4	NP_689733.3	Q569K4	Z385B_HUMAN	zinc finger protein 385B	308	Interaction with p53/TP53.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|p53 binding (GO:0002039)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	26			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)			TGGTCTTGTGTTTAGATCCTA	0.388																																					p.H309fs	Colon(155;204 2491 32774 51842)	Atlas-INDEL	.											.	ZNF385B	68	.	0			c.925delC						PASS	.						103	95	98					2																	180310448		2203	4300	6503	SO:0001589	frameshift_variant	151126	exon8			.	AK057999	CCDS33339.1, CCDS46463.1, CCDS46464.1	2q31.3-q32.1	2012-10-05	2007-12-06	2007-12-06	ENSG00000144331	ENSG00000144331			26332	protein-coding gene	gene with protein product		612344	"zinc finger protein 533"	ZNF533		12477932	Standard	NM_152520		Approved	FLJ25270	uc002unn.4	Q569K4	OTTHUMG00000154559	ENST00000410066.1:c.924delA	chr2.hg19:g.180310448delT	ENSP00000386845:p.Lys308fs	81.0	0.0	0		91.0	30.0	0.32967	NM_152520	Q49A04|Q6ZMZ7|Q8IY01|Q8N8H2|Q96DK4	Frame_Shift_Del	DEL	ENST00000410066.1	hg19	CCDS33339.1																																																																																			.	.	.	none		0.388	ZNF385B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335972.1	NM_152520		-	180310448	T	-	180310448	7	5	48	1	0	1	0	1	0	0	0	0	17889	1722	60	0	503	0	ZNF385B	2	180310448	Frame_Shift_Del	DEL	T	TCGA-A4-7734-01A-11D-2136-08	6957545	180310448	62888925	6	3313											
NEK10	152110	hgsc.bcm.edu	37	chr3	27297798	27297798	+	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	tgtccttaccaagaatacagGattgttccaaccacagaggt	13	10	8	10	0	0	2	0	0	0	2	2	3	2	3	4	2	3	1	4	2	5	4			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr3:27297798G>A	ENST00000429845.2	-	24	2441	c.2079C>T	c.(2077-2079)atC>atT	p.I693I	NEK10_ENST00000357467.2_Silent_p.I90I|NEK10_ENST00000341435.5_Silent_p.I693I			Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10	693	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein autophosphorylation (GO:0031954)|protein phosphorylation (GO:0006468)|regulation of cell cycle G2/M phase transition (GO:1902749)|regulation of ERK1 and ERK2 cascade (GO:0070372)	protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						AAGAATACAGGATTGTTCCAA	0.343																																					p.I693I		Atlas-SNP	.											.	NEK10	271	.	0			c.C2079T						PASS	.						122	116	118					3																	27297798		2201	4300	6501	SO:0001819	synonymous_variant	152110	exon24			ATACAGGATTGTT	AK123061, AK057247	CCDS46781.1	3p24.1	2012-11-15	2012-11-15		ENSG00000163491	ENSG00000163491			18592	protein-coding gene	gene with protein product			"NIMA (never in mitosis gene a)- related kinase 10"			15289607	Standard	NM_199347		Approved	FLJ32685	uc003cdt.2	Q6ZWH5	OTTHUMG00000130571	ENST00000429845.2:c.2079C>T	chr3.hg19:g.27297798G>A		39.0	0.0	.		27.0	9.0	.	NM_199347	A8MWG1|B9ZVR0|Q45VJ4|Q6ZR11|Q7Z671|Q86XB1|Q96MB3	Silent	SNP	ENST00000429845.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.197|9.197	1.027478|1.027478	0.19512|0.19512	.|.	.|.	ENSG00000163491|ENSG00000163491	ENST00000435584|ENST00000424275	.|.	.|.	.|.	4.96|4.96	1.54|1.54	0.23209|0.23209	.|.	.|.	.|.	.|.	.|.	T|T	0.51873|0.51873	0.1700|0.1700	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.41233|0.41233	-0.9520|-0.9520	4|4	.|.	.|.	.|.	.|.	5.416|5.416	0.16374|0.16374	0.5096:0.0:0.4904:0.0|0.5096:0.0:0.4904:0.0	.|.	.|.	.|.	.|.	S|F	150|180	.|.	.|.	P|S	-|-	1|2	0|0	NEK10|NEK10	27272802|27272802	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.998000|0.998000	0.95712|0.95712	1.244000|1.244000	0.32778|0.32778	0.568000|0.568000	0.29311|0.29311	0.591000|0.591000	0.81541|0.81541	CCT|TCC	.	.	.	none		0.343	NEK10-016	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000438156.1	NM_152534		A	27297798	G	A	27297798	2	1	48	1	0	0	0	0	0	0	0	1	10329	1164	41	2		2	NEK10	3	27297798	Silent	SNP	G	TCGA-A4-7734-01A-11D-2136-08		27297798	170724632	7	3314											
KBTBD5	131377	hgsc.bcm.edu	37	chr3	42727131	42727131	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atggcgctgggcttggagcaGgcggaggagcagcggttgta	7	7	20	7	3	0	0	0	0	0	0	0	3	0	3	0	7	3	6	0	7	1	3			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr3:42727131G>A	ENST00000287777.4	+	1	121	c.21G>A	c.(19-21)caG>caA	p.Q7Q		NM_152393.2	NP_689606.2	Q2TBA0	KLH40_HUMAN	kelch-like family member 40	7					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)											GCTTGGAGCAGGCGGAGGAGC	0.647																																					p.Q7Q		Atlas-SNP	.											.	.	.	.	0			c.G21A						PASS	.						29	23	25					3																	42727131		2198	4298	6496	SO:0001819	synonymous_variant	131377	exon1			GGAGCAGGCGGAG	AK056577	CCDS2703.1	3p21.33	2013-07-30	2013-02-22	2013-01-08	ENSG00000157119	ENSG00000157119		"Kelch-like", "BTB/POZ domain containing"	30372	protein-coding gene	gene with protein product	"sarcosynapsin", "nemaline myopathy type 8"	615340	"kelch repeat and BTB (POZ) domain containing 5", "kelch-like 40 (Drosophila)"	KBTBD5		23746549	Standard	NM_152393		Approved	SRYP, NEM8	uc003clv.1	Q2TBA0	OTTHUMG00000133045	ENST00000287777.4:c.21G>A	chr3.hg19:g.42727131G>A		22.0	0.0	.		16.0	8.0	.	NM_152393	Q86SI1|Q96MR2	Silent	SNP	ENST00000287777.4	hg19	CCDS2703.1																																																																																			.	.	.	none		0.647	KLHL40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256651.1	NM_152393		A	42727131	G	A	42727131	2	1	48	1	0	0	0	0	0	0	0	1	8003	991	35	2		2	KBTBD5	3	42727131	Silent	SNP	G	TCGA-A4-7734-01A-11D-2136-08	15429333	42727131	155295299	8	3315											
HERC5	51191	hgsc.bcm.edu	37	chr4	89410409	89410409	+	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	cccacgtttgatctaacagtCagaaggaatcacttgattga	13	11	8	9	1	3	4	2	3	1	1	3	5	3	5	1	1	1	1	1	1	3	4	rs141289100	byFrequency	TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr4:89410409C>G	ENST00000264350.3	+	16	2208	c.2055C>G	c.(2053-2055)gtC>gtG	p.V685V	HERC5_ENST00000508159.1_Silent_p.V323V	NM_016323.3	NP_057407.2	Q9UII4	HERC5_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 5	685					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)		ATCTAACAGTCAGAAGGAATC	0.383																																					p.V685V	Esophageal Squamous(39;887 1012 34045 50514)	Atlas-SNP	.											.	HERC5	114	.	0			c.C2055G						PASS	.						177	183	181					4																	89410409		2203	4300	6503	SO:0001819	synonymous_variant	51191	exon16			AACAGTCAGAAGG	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.2055C>G	chr4.hg19:g.89410409C>G		259.0	0.0	.		220.0	98.0	.	NM_016323	B2RTQ1|Q69G20	Silent	SNP	ENST00000264350.3	hg19	CCDS3630.1																																																																																			.	C|1.000;T|0.000	.	alt		0.383	HERC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253554.2	NM_016323		G	89410409	C	G	89410409	2	3	48	1	0	0	0	0	0	0	0	1	7068	813	29	4		4	HERC5	4	89410409	Silent	SNP	C	TCGA-A4-7734-01A-11D-2136-08		89410409	101743867	9	3316											
FAT4	79633	hgsc.bcm.edu	37	chr4	126411930	126411930	+	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	cacacaccaaaattttcaatCcagaggcacagtcccctagg	14	7	6	14	0	1	1	1	0	0	1	3	1	3	1	4	2	0	1	4	2	4	3			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr4:126411930C>A	ENST00000394329.3	+	17	13966	c.13953C>A	c.(13951-13953)atC>atA	p.I4651I	FAT4_ENST00000335110.5_Silent_p.I2892I	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4651					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						AATTTTCAATCCAGAGGCACA	0.502																																					p.I4651I		Atlas-SNP	.											.	FAT4	1752	.	0			c.C13953A						PASS	.						75	70	72					4																	126411930		2203	4300	6503	SO:0001819	synonymous_variant	79633	exon17			TTCAATCCAGAGG	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.13953C>A	chr4.hg19:g.126411930C>A		85.0	0.0	.		73.0	32.0	.	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	hg19	CCDS3732.3																																																																																			.	.	.	none		0.502	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126411930	C	A	126411930	2	1	48	1	0	0	0	0	0	0	0	1	5699	845	30	4		4	FAT4	4	126411930	Silent	SNP	C	TCGA-A4-7734-01A-11D-2136-08	37001521	126411930	64742346	10	3317											
NSUN2	54888	hgsc.bcm.edu	37	chr5	6620336	6620336	+	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	tgaccaccatgatgcaggggCtgctcagcctcttggcttga	7	10	12	12	0	2	3	1	3	1	0	2	3	2	3	3	3	3	4	3	3	0	2			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr5:6620336C>T	ENST00000264670.6	-	7	1009	c.698G>A	c.(697-699)aGc>aAc	p.S233N	NSUN2_ENST00000539938.1_5'UTR|NSUN2_ENST00000506139.1_Missense_Mutation_p.S198N|NSUN2_ENST00000505264.1_5'UTR	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	233					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						GATGCAGGGGCTGCTCAGCCT	0.502																																					p.S233N		Atlas-SNP	.											.	NSUN2	82	.	0			c.G698A						PASS	.						99	99	99					5																	6620336		2203	4300	6503	SO:0001583	missense	54888	exon7			CAGGGGCTGCTCA	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.698G>A	chr5.hg19:g.6620336C>T	ENSP00000264670:p.Ser233Asn	151.0	0.0	.		144.0	9.0	.	NM_017755	A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Missense_Mutation	SNP	ENST00000264670.6	hg19	CCDS3869.1	.	.	.	.	.	.	.	.	.	.	C	36	5.656410	0.96724	.	.	ENSG00000037474	ENST00000264670;ENST00000506139	T;T	0.41065	1.01;1.04	6.02	6.02	0.97574	.	0.070917	0.85682	D	0.000000	T	0.67813	0.2933	M	0.76170	2.325	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.66571	-0.5890	10	0.56958	D	0.05	-41.3851	20.5407	0.99260	0.0:1.0:0.0:0.0	.	198;233	B4DQW2;Q08J23	.;NSUN2_HUMAN	N	233;198	ENSP00000264670:S233N;ENSP00000420957:S198N	ENSP00000264670:S233N	S	-	2	0	NSUN2	6673336	1.000000	0.71417	0.994000	0.49952	0.961000	0.63080	7.366000	0.79548	2.865000	0.98341	0.655000	0.94253	AGC	.	.	.	none		0.502	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755		T	6620336	C	T	6620336	3	4	48	1	0	0	0	0	1	0	0	0	10685	797	28	2	1657	2	NSUN2	5	6620336	Missense_Mutation	SNP	C	TCGA-A4-7734-01A-11D-2136-08		6620336	174294924	11	3318											
FCHO2	115548	hgsc.bcm.edu	37	chr5	72378596	72378596	+	Missense_Mutation	SNP	A	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	ttcttattgcaggaatgcagAacaaatgaaagccttttgga	14	12	9	6	0	1	2	0	1	1	1	1	4	1	4	1	2	4	2	1	2	5	5			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr5:72378596A>C	ENST00000430046.2	+	24	2305	c.2189A>C	c.(2188-2190)gAa>gCa	p.E730A	FCHO2_ENST00000341845.6_Missense_Mutation_p.E730A|FCHO2_ENST00000512348.1_Missense_Mutation_p.E697A	NM_001146032.1|NM_138782.2	NP_001139504.1|NP_620137.2	Q0JRZ9	FCHO2_HUMAN	FCH domain only 2	730	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.|Mediates interaction with DAB2, EPS15, EPS15R and ITSN1.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|membrane invagination (GO:0010324)|protein localization to plasma membrane (GO:0072659)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	17		Lung NSC(167;0.0465)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;4.6e-53)		AGGAATGCAGAACAAATGAAA	0.308																																					p.E730A		Atlas-SNP	.											.	FCHO2	96	.	0			c.A2189C						PASS	.						67	66	66					5																	72378596		1810	4076	5886	SO:0001583	missense	115548	exon24			ATGCAGAACAAAT	AL831971	CCDS47230.1, CCDS54868.1	5q13.2	2005-08-15			ENSG00000157107	ENSG00000157107			25180	protein-coding gene	gene with protein product		613438				15254787	Standard	NM_138782		Approved		uc003kcl.3	Q0JRZ9	OTTHUMG00000162413	ENST00000430046.2:c.2189A>C	chr5.hg19:g.72378596A>C	ENSP00000393776:p.Glu730Ala	25.0	0.0	.		14.0	9.0	.	NM_138782	A8K6W7|B2RNQ9|B4DHK0|E9PG79|Q0JTJ3|Q96CF5	Missense_Mutation	SNP	ENST00000430046.2	hg19	CCDS47230.1	.	.	.	.	.	.	.	.	.	.	A	17.13	3.309909	0.60414	.	.	ENSG00000157107	ENST00000430046;ENST00000341845;ENST00000512348	T;T;T	0.54071	0.59;0.59;0.59	5.31	5.31	0.75309	Muniscin C-terminal mu homology domain (1);	0.172570	0.49305	D	0.000142	T	0.49081	0.1536	L	0.52364	1.645	0.58432	D	0.999996	B;B	0.10296	0.003;0.003	B;B	0.21151	0.01;0.033	T	0.43572	-0.9383	10	0.40728	T	0.16	-23.3471	14.6045	0.68466	1.0:0.0:0.0:0.0	.	697;730	E9PG79;Q0JRZ9	.;FCHO2_HUMAN	A	730;730;697	ENSP00000393776:E730A;ENSP00000344034:E730A;ENSP00000427296:E697A	ENSP00000344034:E730A	E	+	2	0	FCHO2	72414352	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.460000	0.90369	2.231000	0.72958	0.533000	0.62120	GAA	.	.	.	none		0.308	FCHO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368795.3	XM_291142		C	72378596	A	C	72378596	3	2	48	1	0	0	0	0	1	0	0	0	5795	246	9	5	2283	5	FCHO2	5	72378596	Missense_Mutation	SNP	A	TCGA-A4-7734-01A-11D-2136-08	65758260	72378596	108536664	12	3319											
SLC12A2	6558	hgsc.bcm.edu	37	chr5	127419881	127419881	+	Missense_Mutation	SNP	A	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	tggggcccaccccgagccagAgccgtttccaggtggacctg	6	6	14	15	2	0	1	0	0	0	1	1	3	1	2	7	4	2	1	7	4	0	1	rs557916029		TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr5:127419881A>C	ENST00000262461.2	+	1	424	c.235A>C	c.(235-237)Agc>Cgc	p.S79R	SLC12A2_ENST00000343225.4_Missense_Mutation_p.S79R|CTC-228N24.3_ENST00000501702.2_lincRNA	NM_001046.2	NP_001037.1	P55011	S12A2_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 2	79					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|branching involved in mammary gland duct morphogenesis (GO:0060444)|chloride transmembrane transport (GO:1902476)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|gamma-aminobutyric acid signaling pathway (GO:0007214)|hyperosmotic response (GO:0006972)|ion transport (GO:0006811)|mammary duct terminal end bud growth (GO:0060763)|multicellular organism growth (GO:0035264)|positive regulation of cell volume (GO:0045795)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transepithelial ammonium transport (GO:0070634)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ammonium transmembrane transporter activity (GO:0008519)|sodium:potassium:chloride symporter activity (GO:0008511)			breast(3)|endometrium(5)|kidney(5)|large_intestine(12)|lung(16)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)|Quinethazone(DB01325)	CCCGAGCCAGAGCCGTTTCCA	0.816													A|||	1	0.000199681	0	0	5008	,	,		6545	0		0.001	False		,,,				2504	0				p.S79R		Atlas-SNP	.											.	SLC12A2	119	.	0			c.A235C						PASS	.						1	2	1					5																	127419881		861	2057	2918	SO:0001583	missense	6558	exon1			AGCCAGAGCCGTT		CCDS4144.1, CCDS58965.1	5q23.3	2014-06-13	2013-07-18		ENSG00000064651	ENSG00000064651		"Solute carriers"	10911	protein-coding gene	gene with protein product	"bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1", "basolateral Na-K-Cl symporter", "protein phosphatase 1, regulatory subunit 141"	600840				7629105	Standard	NM_001256461		Approved	NKCC1, BSC, BSC2, PPP1R141	uc003kus.3	P55011	OTTHUMG00000128983	ENST00000262461.2:c.235A>C	chr5.hg19:g.127419881A>C	ENSP00000262461:p.Ser79Arg	8.0	0.0	.		7.0	5.0	.	NM_001046	Q8N713|Q8WWH7	Missense_Mutation	SNP	ENST00000262461.2	hg19	CCDS4144.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.467578	0.84533	.	.	ENSG00000064651	ENST00000262461;ENST00000343225	D;D	0.86865	-2.16;-2.18	4.11	2.95	0.34219	.	0.128217	0.50627	D	0.000110	D	0.89280	0.6670	L	0.47190	1.495	0.58432	D	0.99999	D;D	0.76494	0.999;0.998	D;D	0.80764	0.994;0.986	D	0.88787	0.3275	10	0.72032	D	0.01	.	8.7601	0.34669	0.9077:0.0:0.0923:0.0	.	79;79	P55011-3;P55011	.;S12A2_HUMAN	R	79	ENSP00000262461:S79R;ENSP00000340878:S79R	ENSP00000262461:S79R	S	+	1	0	SLC12A2	127447780	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	4.501000	0.60393	1.474000	0.48178	0.260000	0.18958	AGC	.	.	.	none		0.816	SLC12A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250972.1	NM_001046		C	127419881	A	C	127419881	3	2	48	1	0	0	0	0	1	0	0	0	14396	304	11	5	237	5	SLC12A2	5	127419881	Missense_Mutation	SNP	A	TCGA-A4-7734-01A-11D-2136-08	55041285	127419881	53495379	13	3320											
CAMK2A	815	hgsc.bcm.edu	37	chr5	149644564	149644564	+	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	gcagatgcgggcttcacgctCcagcttctgatggtctgaaa	8	10	12	11	2	3	3	1	2	2	1	4	3	4	3	1	2	2	4	1	2	1	2			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr5:149644564C>G	ENST00000348628.6	-	3	837	c.172G>C	c.(172-174)Gag>Cag	p.E58Q	CAMK2A_ENST00000398376.3_Missense_Mutation_p.E58Q	NM_015981.3|NM_171825.2	NP_057065.2|NP_741960.1	Q9UQM7	KCC2A_HUMAN	calcium/calmodulin-dependent protein kinase II alpha	58	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				calcium ion transport (GO:0006816)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|kinase activity (GO:0016301)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|skin(1)|stomach(1)	15		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCTTCACGCTCCAGCTTCTGA	0.607																																					p.E58Q		Atlas-SNP	.											.	CAMK2A	42	.	0			c.G172C						PASS	.						44	49	47					5																	149644564		2002	4186	6188	SO:0001583	missense	815	exon3			CACGCTCCAGCTT	AB023185	CCDS43386.1, CCDS43387.1	5q32	2013-09-20	2008-10-30		ENSG00000070808	ENSG00000070808	2.7.11.17		1460	protein-coding gene	gene with protein product	"CaM-kinase II alpha chain", "calcium/calmodulin-dependent protein kinase II alpha-B subunit", "CaM kinase II alpha subunit", "CaMK-II alpha subunit", "calcium/calmodulin-dependent protein kinase type II alpha chain"	114078	"calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha"	CAMKA		10231032, 3475713	Standard	NM_015981		Approved	KIAA0968, CaMKIINalpha	uc003lrt.2	Q9UQM7	OTTHUMG00000134281	ENST00000348628.6:c.172G>C	chr5.hg19:g.149644564C>G	ENSP00000261793:p.Glu58Gln	98.0	0.0	.		68.0	20.0	.	NM_171825	Q9UL21|Q9Y2H4|Q9Y352	Missense_Mutation	SNP	ENST00000348628.6	hg19	CCDS43386.1	.	.	.	.	.	.	.	.	.	.	c	17.93	3.509651	0.64522	.	.	ENSG00000070808	ENST00000348628;ENST00000398376;ENST00000510347	T;T;T	0.24538	1.85;1.85;1.85	4.6	4.6	0.57074	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.067804	0.64402	U	0.000020	T	0.28863	0.0716	N	0.21448	0.665	0.58432	D	0.999997	B;B	0.29552	0.248;0.248	B;P	0.45099	0.307;0.469	T	0.27905	-1.0060	10	0.87932	D	0	.	13.2562	0.60081	0.0:1.0:0.0:0.0	.	58;58	Q9UQM7;A8K161	KCC2A_HUMAN;.	Q	58	ENSP00000261793:E58Q;ENSP00000381412:E58Q;ENSP00000426607:E58Q	ENSP00000261793:E58Q	E	-	1	0	CAMK2A	149624757	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.110000	0.71535	2.281000	0.76405	0.306000	0.20318	GAG	.	.	.	none		0.607	CAMK2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258869.2	NM_015981		G	149644564	C	G	149644564	3	3	48	1	0	0	0	0	1	0	0	0	2601	864	30	4	1365	4	CAMK2A	5	149644564	Missense_Mutation	SNP	C	TCGA-A4-7734-01A-11D-2136-08	22224683	149644564	31270696	14	3321											
KIF13A	63971	hgsc.bcm.edu	37	chr6	17796913	17796913	+	Missense_Mutation	SNP	T	T	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	tacaaacctgtcatgcagtgTtcttgtcttagcatgaagag	11	13	9	8	0	3	2	1	1	2	1	3	2	3	2	1	0	4	3	1	0	4	4			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr6:17796913T>G	ENST00000259711.6	-	23	3034	c.2929A>C	c.(2929-2931)Aca>Cca	p.T977P	KIF13A_ENST00000378843.2_Missense_Mutation_p.T977P|KIF13A_ENST00000378814.5_Missense_Mutation_p.T977P|KIF13A_ENST00000378816.5_Missense_Mutation_p.T977P|KIF13A_ENST00000378826.2_Missense_Mutation_p.T977P	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	977					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)			TCATGCAGTGTTCTTGTCTTA	0.507																																					p.T977P		Atlas-SNP	.											.	KIF13A	276	.	0			c.A2929C						PASS	.						149	142	144					6																	17796913		1924	4131	6055	SO:0001583	missense	63971	exon23			GCAGTGTTCTTGT	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.2929A>C	chr6.hg19:g.17796913T>G	ENSP00000259711:p.Thr977Pro	248.0	0.0	.		175.0	75.0	.	NM_001105567	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Missense_Mutation	SNP	ENST00000259711.6	hg19	CCDS47381.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.3|24.3	4.513415|4.513415	0.85389|0.85389	.|.	.|.	ENSG00000137177|ENSG00000137177	ENST00000358380|ENST00000378814;ENST00000259711;ENST00000378826;ENST00000378843;ENST00000378816;ENST00000506044	.|T;T;T;T;T	.|0.72505	.|-0.62;-0.66;-0.62;-0.63;-0.62	5.05|5.05	5.05|5.05	0.67936|0.67936	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.75939|0.75939	0.3918|0.3918	L|L	0.55481|0.55481	1.735|1.735	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.76494	.|0.997;0.999;0.994;0.999	.|D;D;D;D	.|0.71184	.|0.947;0.962;0.922;0.972	T|T	0.79892|0.79892	-0.1611|-0.1611	5|10	.|0.87932	.|D	.|0	.|.	15.0983|15.0983	0.72253|0.72253	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|977;977;977;977	.|Q9H1H9-4;Q9H1H9-2;Q9H1H9;Q9H1H9-3	.|.;.;KI13A_HUMAN;.	D|P	370|977;977;977;977;977;37	.|ENSP00000368091:T977P;ENSP00000259711:T977P;ENSP00000368103:T977P;ENSP00000368120:T977P;ENSP00000368093:T977P	.|ENSP00000259711:T977P	E|T	-|-	3|1	2|0	KIF13A|KIF13A	17904892|17904892	1.000000|1.000000	0.71417|0.71417	0.959000|0.959000	0.39883|0.39883	0.984000|0.984000	0.73092|0.73092	5.938000|5.938000	0.70170|0.70170	2.019000|2.019000	0.59389|0.59389	0.460000|0.460000	0.39030|0.39030	GAA|ACA	.	.	.	none		0.507	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4			G	17796913	T	G	17796913	3	3	48	1	0	0	0	0	1	0	0	0	8281	1725	60	5	2581	5	KIF13A	6	17796913	Missense_Mutation	SNP	T	TCGA-A4-7734-01A-11D-2136-08		17796913	153318154	15	3322											
DST	667	hgsc.bcm.edu	37	chr6	56463337	56463337	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctcctttttagactgttcTgcttttaaattaagctgttc	8	19	6	8	0	1	1	0	0	1	1	3	1	2	1	1	0	3	5	1	0	4	8			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr6:56463337T>C	ENST00000361203.3	-	42	11239	c.11232A>G	c.(11230-11232)gcA>gcG	p.A3744A	DST_ENST00000312431.6_Silent_p.A3744A|DST_ENST00000421834.2_Silent_p.A1658A|DST_ENST00000244364.6_Silent_p.A1332A|DST_ENST00000370788.2_Silent_p.A1658A|DST_ENST00000370769.4_Silent_p.A3746A|DST_ENST00000370754.5_Silent_p.A3924A|DST_ENST00000446842.2_Silent_p.A3420A			Q03001	DYST_HUMAN	dystonin	3744					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)			TAGACTGTTCTGCTTTTAAAT	0.353																																					p.A1332A		Atlas-SNP	.											.	DST	1427	.	0			c.A3996G						PASS	.						159	143	148					6																	56463337		1845	4078	5923	SO:0001819	synonymous_variant	667	exon27			CTGTTCTGCTTTT	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.11232A>G	chr6.hg19:g.56463337T>C		28.0	0.0	.		34.0	13.0	.	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	hg19																																																																																				.	.	.	none		0.353	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		C	56463337	T	C	56463337	2	2	48	1	0	0	0	0	0	0	0	1	4785	1567	55	3		3	DST	6	56463337	Silent	SNP	T	TCGA-A4-7734-01A-11D-2136-08	38666424	56463337	114651730	16	3323											
TYW1	55253	hgsc.bcm.edu	37	chr7	66514966	66514966	+	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	aacagcaggaagagaagtctGgtttgttcaggaacatgggg	13	8	15	5	0	2	1	1	0	1	1	2	4	2	3	0	5	3	3	0	5	4	2			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr7:66514966G>T	ENST00000359626.5	+	8	1179	c.1015G>T	c.(1015-1017)Ggt>Tgt	p.G339C		NM_018264.2	NP_060734.2	Q9NV66	TYW1_HUMAN	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	339					tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(8)|kidney(10)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(3)|stomach(2)|urinary_tract(2)	46		Lung NSC(55;0.0846)|all_lung(88;0.183)				AGAGAAGTCTGGTTTGTTCAG	0.383																																					p.G339C		Atlas-SNP	.											.	TYW1	71	.	0			c.G1015T						PASS	.						45	47	47					7																	66514966		2203	4298	6501	SO:0001583	missense	55253	exon8			AAGTCTGGTTTGT	AK001762	CCDS5538.1	7q11.21	2007-11-29	2007-11-29	2007-11-29	ENSG00000198874	ENSG00000198874			25598	protein-coding gene	gene with protein product	"tRNA-yW synthesizing protein 1 homolog A (S. cerevisiae)"	611243	"radical S-adenosyl methionine and flavodoxin domains 1"	RSAFD1		16162496, 17150819	Standard	NM_018264		Approved	FLJ10900, MGC23001, MGC60291, YPL207W, TYW1A	uc003tvn.4	Q9NV66	OTTHUMG00000129723	ENST00000359626.5:c.1015G>T	chr7.hg19:g.66514966G>T	ENSP00000352645:p.Gly339Cys	70.0	0.0	.		92.0	18.0	.	NM_018264	Q6PJG8|Q75MG8|Q75MN3|Q86V12|Q8IVS7|Q9H9C4	Missense_Mutation	SNP	ENST00000359626.5	hg19	CCDS5538.1	.	.	.	.	.	.	.	.	.	.	G	6.950	0.545036	0.13312	.	.	ENSG00000198874	ENST00000359626	T	0.17854	2.25	3.59	-7.17	0.01511	.	1.038170	0.07760	U	0.949947	T	0.14700	0.0355	L	0.39898	1.24	0.09310	N	1	P	0.39376	0.67	B	0.42112	0.376	T	0.31336	-0.9947	10	0.72032	D	0.01	.	9.461	0.38785	0.2223:0.1477:0.6299:0.0	.	339	Q9NV66	TYW1_HUMAN	C	339	ENSP00000352645:G339C	ENSP00000352645:G339C	G	+	1	0	TYW1	66152401	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-2.640000	0.00865	-1.521000	0.01771	-1.012000	0.02466	GGT	.	.	.	none		0.383	TYW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251932.2	NM_018264		T	66514966	G	T	66514966	3	4	48	1	0	0	0	0	1	0	0	0	16830	1348	47	4	1045	4	TYW1	7	66514966	Missense_Mutation	SNP	G	TCGA-A4-7734-01A-11D-2136-08		66514966	92623697	17	3324											
MET	4233	hgsc.bcm.edu	37	chr7	116423433	116423433	+	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	tatgataaagaatactatagTgtacacaacaaaacaggtgc	19	9	7	6	0	0	2	0	1	0	1	0	2	0	2	0	1	5	1	0	1	11	6			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr7:116423433T>A	ENST00000318493.6	+	19	3949	c.3762T>A	c.(3760-3762)agT>agA	p.S1254R	MET_ENST00000397752.3_Missense_Mutation_p.S1236R|MET_ENST00000539704.1_Missense_Mutation_p.S106R			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)			AATACTATAGTGTACACAACA	0.383			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.S1254R		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.T3762A						PASS	.						99	95	96					7																	116423433		1861	4097	5958	SO:0001583	missense	4233	exon19	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	CTATAGTGTACAC	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.3762T>A	chr7.hg19:g.116423433T>A	ENSP00000317272:p.Ser1254Arg	74.0	0.0	.		105.0	62.0	.	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	T	13.28	2.189759	0.38707	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000539704	T;T;T	0.34072	1.38;1.38;1.38	5.46	-2.57	0.06248	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	0.30696	0.0773	N	0.03304	-0.355	0.54753	D	0.999982	P;D	0.89917	0.924;1.0	P;D	0.85130	0.574;0.997	T	0.26326	-1.0106	10	0.87932	D	0	.	11.8823	0.52581	0.0:0.4505:0.0:0.5495	.	1254;1236	P08581-2;P08581	.;MET_HUMAN	R	1236;1254;106	ENSP00000380860:S1236R;ENSP00000317272:S1254R;ENSP00000445020:S106R	ENSP00000317272:S1254R	S	+	3	2	MET	116210669	0.936000	0.31750	0.978000	0.43139	0.978000	0.69477	0.045000	0.14013	-0.366000	0.08064	0.460000	0.39030	AGT	.	.	.	none		0.383	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			A	116423433	T	A	116423433	3	1	48	1	0	0	0	0	1	0	0	0	9492	1693	59	5	3832	5	MET	7	116423433	Missense_Mutation	SNP	T	TCGA-A4-7734-01A-11D-2136-08	49908467	116423433	42715230	18	3325											
SPAM1	6677	hgsc.bcm.edu	37	chr7	123599995	123599995	+	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	cattgttagtattttgtttcTtatcatttcttctgtagcga	7	22	6	6	1	4	0	1	0	3	0	4	1	4	0	0	0	1	4	0	0	4	10			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr7:123599995T>A	ENST00000439500.1	+	6	2115	c.1502T>A	c.(1501-1503)cTt>cAt	p.L501H	SPAM1_ENST00000460182.1_Missense_Mutation_p.L501H|SPAM1_ENST00000340011.5_Intron|SPAM1_ENST00000402183.2_Missense_Mutation_p.L501H|SPAM1_ENST00000223028.7_Missense_Mutation_p.L501H	NM_001174045.1|NM_001174046.1	NP_001167516.1|NP_001167517.1	P38567	HYALP_HUMAN	sperm adhesion molecule 1 (PH-20 hyaluronidase, zona pellucida binding)	501					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	hyalurononglucosaminidase activity (GO:0004415)			breast(1)|cervix(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(23)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						ATTTTGTTTCTTATCATTTCT	0.353																																					p.L501H		Atlas-SNP	.											.	SPAM1	195	.	0			c.T1502A						PASS	.						87	83	84					7																	123599995		2203	4300	6503	SO:0001583	missense	6677	exon5			TGTTTCTTATCAT	L13781	CCDS5790.1, CCDS5791.1	7q31	2008-05-02			ENSG00000106304	ENSG00000106304			11217	protein-coding gene	gene with protein product		600930				8282124, 8575780	Standard	NM_153189		Approved	HYAL5, PH-20, SPAG15	uc003vle.3	P38567	OTTHUMG00000157284	ENST00000439500.1:c.1502T>A	chr7.hg19:g.123599995T>A	ENSP00000402123:p.Leu501His	50.0	0.0	.		97.0	54.0	.	NM_153189	Q8TC30	Missense_Mutation	SNP	ENST00000439500.1	hg19	CCDS5791.1	.	.	.	.	.	.	.	.	.	.	T	9.524	1.109145	0.20714	.	.	ENSG00000106304	ENST00000402183;ENST00000460182;ENST00000439500;ENST00000223028	T;T;T;T	0.16743	2.32;2.32;2.32;2.32	2.06	2.06	0.26882	.	.	.	.	.	T	0.05960	0.0155	N	0.08118	0	0.09310	N	1	P	0.49862	0.929	B	0.30316	0.114	T	0.22836	-1.0205	9	0.72032	D	0.01	.	6.1126	0.20110	0.0:0.0:0.0:1.0	.	501	P38567	HYALP_HUMAN	H	501	ENSP00000386028:L501H;ENSP00000417934:L501H;ENSP00000402123:L501H;ENSP00000223028:L501H	ENSP00000223028:L501H	L	+	2	0	SPAM1	123387231	0.016000	0.18221	0.004000	0.12327	0.009000	0.06853	2.479000	0.45197	1.210000	0.43336	0.528000	0.53228	CTT	.	.	.	none		0.353	SPAM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348309.1			A	123599995	T	A	123599995	3	1	48	1	0	0	0	0	1	0	0	0	14999	1609	56	5	1512	5	SPAM1	7	123599995	Missense_Mutation	SNP	T	TCGA-A4-7734-01A-11D-2136-08	7176562	123599995	35538668	19	3326											
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110420393	110420393	+	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	ttcacactgaattgggatggGatcgcttctaagccactcac	10	11	9	11	1	3	1	2	1	1	0	4	3	3	3	1	2	1	1	1	2	2	4			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr8:110420393G>C	ENST00000378402.5	+	18	2033	c.1929G>C	c.(1927-1929)ggG>ggC	p.G643G		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	643					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)			ATTGGGATGGGATCGCTTCTA	0.428										HNSCC(38;0.096)																											p.G643G		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.G1929C						PASS	.						121	121	121					8																	110420393		1946	4145	6091	SO:0001819	synonymous_variant	93035	exon18			GGATGGGATCGCT	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.1929G>C	chr8.hg19:g.110420393G>C		60.0	0.0	.		58.0	12.0	.	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	hg19	CCDS47911.1																																																																																			.	.	.	none		0.428	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		C	110420393	G	C	110420393	2	2	48	1	0	0	0	0	0	0	0	1	11979	1161	41	4		4	PKHD1L1	8	110420393	Silent	SNP	G	TCGA-A4-7734-01A-11D-2136-08		110420393	35943629	20	3327											
VPS28	51160	hgsc.bcm.edu	37	chr8	145651588	145651588	+	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	acagctccggcttgttcccaGgggctgcaagagaaggcaga	10	6	14	11	1	0	2	0	0	0	2	2	3	2	2	2	4	2	6	2	4	2	2			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr8:145651588G>T	ENST00000526054.1	-	2	78	c.41C>A	c.(40-42)cCt>cAt	p.P14H	VPS28_ENST00000377348.2_Missense_Mutation_p.P14H|VPS28_ENST00000292510.4_Missense_Mutation_p.P14H|VPS28_ENST00000526734.1_5'UTR|VPS28_ENST00000529182.1_Missense_Mutation_p.P14H			Q9UK41	VPS28_HUMAN	vacuolar protein sorting 28 homolog (S. cerevisiae)	14	VPS28 N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00645}.				endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|negative regulation of protein ubiquitination (GO:0031397)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(1)|lung(4)|prostate(1)	7	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			CTTGTTCCCAGGGGCTGCAAG	0.632																																					p.P14H		Atlas-SNP	.											.	VPS28	23	.	0			c.C41A						PASS	.						20	19	20					8																	145651588		2194	4296	6490	SO:0001583	missense	51160	exon3			TTCCCAGGGGCTG	AF316887	CCDS6425.1, CCDS34967.1	8q24.3	2014-08-12	2006-04-04		ENSG00000160948	ENSG00000160948			18178	protein-coding gene	gene with protein product		611952	"vacuolar protein sorting 28 (yeast)"				Standard	NM_183057		Approved		uc003zct.1	Q9UK41	OTTHUMG00000165209	ENST00000526054.1:c.41C>A	chr8.hg19:g.145651588G>T	ENSP00000434064:p.Pro14His	27.0	0.0	.		13.0	8.0	.	NM_016208	Q86VK0	Missense_Mutation	SNP	ENST00000526054.1	hg19	CCDS6425.1	.	.	.	.	.	.	.	.	.	.	g	19.57	3.851936	0.71719	.	.	ENSG00000160948	ENST00000529182;ENST00000526054;ENST00000292510;ENST00000377348;ENST00000533806;ENST00000531032;ENST00000530790	.	.	.	5.09	5.09	0.68999	Vacuolar protein sorting-associated, VPS28, N-terminal (1);	0.051939	0.85682	D	0.000000	T	0.52948	0.1766	N	0.08118	0	0.51482	D	0.999924	D;D	0.76494	0.999;0.986	D;P	0.66979	0.948;0.575	T	0.63120	-0.6708	9	0.62326	D	0.03	.	16.3554	0.83234	0.0:0.0:1.0:0.0	.	14;14	Q9UK41-2;Q9UK41	.;VPS28_HUMAN	H	14	.	ENSP00000292510:P14H	P	-	2	0	VPS28	145622396	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.858000	0.69532	2.515000	0.84797	0.650000	0.86243	CCT	.	.	.	none		0.632	VPS28-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382694.1			T	145651588	G	T	145651588	3	4	48	1	0	0	0	0	1	0	0	0	17211	1000	35	4	770	4	VPS28	8	145651588	Missense_Mutation	SNP	G	TCGA-A4-7734-01A-11D-2136-08	35231195	145651588	712434	21	3328											
KIAA1797	54914	hgsc.bcm.edu	37	chr9	20990148	20990148	+	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	gacttcttcttgctgatattTgcaaccgcagtggttgcatg	7	15	10	9	1	2	1	0	1	2	0	2	2	2	1	1	1	4	5	1	1	2	6			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr9:20990148T>A	ENST00000380249.1	+	44	5395	c.5031T>A	c.(5029-5031)ttT>ttA	p.F1677L	FOCAD_ENST00000338382.6_Missense_Mutation_p.F1677L|FOCAD_ENST00000605086.1_Missense_Mutation_p.F1113L	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	1677						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											TGCTGATATTTGCAACCGCAG	0.488																																					p.F1677L		Atlas-SNP	.											.	.	.	.	0			c.T5031A						PASS	.						89	79	82					9																	20990148		2203	4300	6503	SO:0001583	missense	54914	exon44			GATATTTGCAACC	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.5031T>A	chr9.hg19:g.20990148T>A	ENSP00000369599:p.Phe1677Leu	93.0	0.0	.		89.0	39.0	.	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	hg19	CCDS34993.1	.	.	.	.	.	.	.	.	.	.	T	16.08	3.022456	0.54683	.	.	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.22945	1.93;1.93	6.06	3.75	0.43078	.	0.052794	0.85682	D	0.000000	T	0.27489	0.0675	L	0.57536	1.79	0.54753	D	0.999988	P	0.42296	0.775	B	0.42738	0.396	T	0.01574	-1.1321	10	0.33141	T	0.24	-19.4576	10.2953	0.43620	0.0:0.1318:0.0:0.8682	.	1677	Q5VW36	K1797_HUMAN	L	1677	ENSP00000369599:F1677L;ENSP00000344307:F1677L	ENSP00000344307:F1677L	F	+	3	2	KIAA1797	20980148	1.000000	0.71417	0.998000	0.56505	0.834000	0.47266	1.862000	0.39448	0.543000	0.28864	0.533000	0.62120	TTT	.	.	.	none		0.488	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		A	20990148	T	A	20990148	3	1	48	1	0	0	0	0	1	0	0	0	8265	1809	63	5	5193	5	KIAA1797	9	20990148	Missense_Mutation	SNP	T	TCGA-A4-7734-01A-11D-2136-08		20990148	120223283	22	3329											
SMC5	23137	hgsc.bcm.edu	37	chr9	72913102	72913102	+	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	aggcgaaataattgataagcGaagagagagggaaactctag	18	6	13	4	2	1	3	0	1	1	2	1	7	1	4	0	2	2	0	0	2	6	4			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr9:72913102G>C	ENST00000361138.5	+	9	1332	c.1274G>C	c.(1273-1275)cGa>cCa	p.R425P		NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	425					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						ATTGATAAGCGAAGAGAGAGG	0.358																																					p.R425P		Atlas-SNP	.											.	SMC5	96	.	0			c.G1274C						PASS	.						90	86	87					9																	72913102		2203	4300	6503	SO:0001583	missense	23137	exon9			ATAAGCGAAGAGA	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.1274G>C	chr9.hg19:g.72913102G>C	ENSP00000354957:p.Arg425Pro	81.0	0.0	.		89.0	31.0	.	NM_015110	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Missense_Mutation	SNP	ENST00000361138.5	hg19	CCDS6632.1	.	.	.	.	.	.	.	.	.	.	G	14.40	2.524798	0.44969	.	.	ENSG00000198887	ENST00000361138	T	0.19669	2.13	5.72	-2.63	0.06133	RecF/RecN/SMC (1);	0.559219	0.18103	N	0.151640	T	0.17109	0.0411	L	0.46157	1.445	0.09310	N	1	P	0.48694	0.914	P	0.48840	0.592	T	0.11446	-1.0587	10	0.32370	T	0.25	-0.2642	2.2335	0.04002	0.3745:0.0877:0.3454:0.1924	.	425	Q8IY18	SMC5_HUMAN	P	425	ENSP00000354957:R425P	ENSP00000354957:R425P	R	+	2	0	SMC5	72102922	0.591000	0.26824	0.162000	0.22713	0.993000	0.82548	0.529000	0.23019	-0.132000	0.11557	0.591000	0.81541	CGA	.	.	.	none		0.358	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110		C	72913102	G	C	72913102	3	2	48	1	0	0	0	0	1	0	0	0	14799	1058	37	4	1308	4	SMC5	9	72913102	Missense_Mutation	SNP	G	TCGA-A4-7734-01A-11D-2136-08	51922954	72913102	68300329	23	3330											
VPS13A	23230	hgsc.bcm.edu	37	chr9	79981712	79981712	+	Missense_Mutation	SNP	A	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	caaaacaaaatggaggactgAttccagttcattctttaaat	16	12	6	7	0	2	1	1	1	1	0	3	3	3	3	1	2	1	1	1	2	6	5	rs566242673		TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr9:79981712A>C	ENST00000360280.3	+	61	8655	c.8395A>C	c.(8395-8397)Att>Ctt	p.I2799L	VPS13A_ENST00000357409.5_Missense_Mutation_p.I2799L|VPS13A_ENST00000376634.4_Missense_Mutation_p.I2799L|VPS13A_ENST00000376636.3_Missense_Mutation_p.I2760L	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	2799					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						TGGAGGACTGATTCCAGTTCA	0.313																																					p.I2799L		Atlas-SNP	.											.	VPS13A	735	.	0			c.A8395C						PASS	.						66	69	68					9																	79981712		2203	4299	6502	SO:0001583	missense	23230	exon61			GGACTGATTCCAG	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.8395A>C	chr9.hg19:g.79981712A>C	ENSP00000353422:p.Ile2799Leu	39.0	0.0	.		42.0	20.0	.	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	hg19	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	A	14.18	2.457324	0.43634	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14	5.56	0.396	0.16309	.	0.303860	0.34178	N	0.004187	T	0.64757	0.2627	L	0.54323	1.7	0.80722	D	1	B;B;B;B	0.14438	0.001;0.002;0.01;0.004	B;B;B;B	0.15870	0.007;0.006;0.014;0.014	T	0.47005	-0.9150	9	.	.	.	.	3.193	0.06624	0.643:0.1183:0.1256:0.1131	.	2760;2799;2799;2799	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	L	2799;2760;2799;2799	ENSP00000365821:I2799L;ENSP00000365823:I2760L;ENSP00000353422:I2799L;ENSP00000349985:I2799L	.	I	+	1	0	VPS13A	79171532	1.000000	0.71417	0.083000	0.20561	0.958000	0.62258	3.532000	0.53553	-0.167000	0.10871	-0.376000	0.06991	ATT	.	.	.	none		0.313	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		C	79981712	A	C	79981712	3	2	48	1	0	0	0	0	1	0	0	0	17201	333	12	5	8637	5	VPS13A	9	79981712	Missense_Mutation	SNP	A	TCGA-A4-7734-01A-11D-2136-08	7068610	79981712	61231719	24	3331											
PDCL	5082	hgsc.bcm.edu	37	chr9	125582792	125582792	+	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	actggagatctcaaaaacctGcttgaattggggccccttgt	10	11	10	10	0	1	2	1	1	1	1	2	3	1	2	3	3	2	1	3	3	3	3			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr9:125582792G>A	ENST00000259467.4	-	4	643	c.478C>T	c.(478-480)Cag>Tag	p.Q160*		NM_005388.4	NP_005379.3	Q13371	PHLP_HUMAN	phosducin-like	160					heterotrimeric G-protein complex assembly (GO:1902605)|intracellular signal transduction (GO:0035556)|negative regulation of protein refolding (GO:0061084)|protein folding (GO:0006457)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|visual perception (GO:0007601)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)			endometrium(1)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	10						TCAAAAACCTGCTTGAATTGG	0.443																																					p.Q160X		Atlas-SNP	.											.	PDCL	24	.	0			c.C478T						PASS	.						104	102	102					9																	125582792		2203	4300	6503	SO:0001587	stop_gained	5082	exon4			AAACCTGCTTGAA	AF083325	CCDS6845.1	9q12-q13	2008-07-21			ENSG00000136940	ENSG00000136940			8770	protein-coding gene	gene with protein product		604421				10095058	Standard	NM_005388		Approved	PhLP, DKFZp564M1863	uc004bmz.2	Q13371	OTTHUMG00000020624	ENST00000259467.4:c.478C>T	chr9.hg19:g.125582792G>A	ENSP00000259467:p.Gln160*	232.0	0.0	.		162.0	56.0	.	NM_005388	Q4VXB6|Q96AF1|Q9UEW7|Q9UFL0|Q9UNX1|Q9UNX2	Nonsense_Mutation	SNP	ENST00000259467.4	hg19	CCDS6845.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.440900	0.83993	.	.	ENSG00000136940	ENST00000259467	.	.	.	5.58	4.67	0.58626	.	0.160604	0.56097	D	0.000026	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.79	12.8162	0.57667	0.0:0.0:0.7031:0.2969	.	.	.	.	X	160	.	ENSP00000259467:Q160X	Q	-	1	0	PDCL	124622613	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.527000	0.45615	1.349000	0.45751	0.655000	0.94253	CAG	.	.	.	none		0.443	PDCL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053956.1	NM_005388		A	125582792	G	A	125582792	4	1	48	1	0	0	0	0	0	1	0	0	11633	1328	46	2	431	2	PDCL	9	125582792	Nonsense_Mutation	SNP	G	TCGA-A4-7734-01A-11D-2136-08	45601080	125582792	15630639	25	3332											
SLC2A8	29988	hgsc.bcm.edu	37	chr9	130167105	130167105	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccgcctgcaggtgtggtcAtggtgttcagcacgagtgcc	5	10	14	12	2	2	0	2	0	0	0	3	1	3	0	3	3	3	3	3	3	0	1			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr9:130167105A>G	ENST00000373371.3	+	8	1074	c.985A>G	c.(985-987)Atg>Gtg	p.M329V	SLC2A8_ENST00000485806.1_3'UTR|SLC2A8_ENST00000373360.3_Missense_Mutation_p.M329V|SLC2A8_ENST00000373352.1_Missense_Mutation_p.M66V	NM_001271712.1|NM_014580.3	NP_001258641.1|NP_055395.2	Q9NY64	GTR8_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 8	329					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						AGGTGTGGTCATGGTGTTCAG	0.697																																					p.M329V		Atlas-SNP	.											.	SLC2A8	27	.	0			c.A985G						PASS	.						50	45	47					9																	130167105		2203	4297	6500	SO:0001583	missense	29988	exon8			GTGGTCATGGTGT	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.985A>G	chr9.hg19:g.130167105A>G	ENSP00000362469:p.Met329Val	98.0	0.0	.		64.0	14.0	.	NM_014580	Q8WUZ9|Q9NSC4	Missense_Mutation	SNP	ENST00000373371.3	hg19	CCDS6870.1	.	.	.	.	.	.	.	.	.	.	A	16.44	3.122981	0.56613	.	.	ENSG00000136856	ENST00000373371;ENST00000451404;ENST00000373352;ENST00000373360;ENST00000439597;ENST00000423934;ENST00000373350;ENST00000430147	T;T;T;T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14;-1.14;-1.14;-1.14	5.16	5.16	0.70880	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.071263	0.85682	D	0.000000	D	0.86585	0.5968	M	0.71036	2.16	0.80722	D	1	D;D	0.69078	0.997;0.994	D;D	0.80764	0.994;0.992	D	0.87560	0.2471	10	0.56958	D	0.05	.	14.2805	0.66208	1.0:0.0:0.0:0.0	.	329;329	Q5VVV9;Q9NY64	.;GTR8_HUMAN	V	329;166;66;329;168;194;194;168	ENSP00000362469:M329V;ENSP00000392434:M166V;ENSP00000362450:M66V;ENSP00000362458:M329V;ENSP00000404893:M168V;ENSP00000389070:M194V;ENSP00000391213:M168V	ENSP00000362448:M194V	M	+	1	0	SLC2A8	129206926	1.000000	0.71417	1.000000	0.80357	0.120000	0.20174	6.771000	0.74996	2.073000	0.62155	0.533000	0.62120	ATG	.	.	.	none		0.697	SLC2A8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054177.1	NM_014580		G	130167105	A	G	130167105	3	3	48	1	0	0	0	0	1	0	0	0	14564	217	8	3	1015	3	SLC2A8	9	130167105	Missense_Mutation	SNP	A	TCGA-A4-7734-01A-11D-2136-08	4584313	130167105	11046326	26	3333											
ARID5B	84159	hgsc.bcm.edu	37	chr10	63852307	63852307	+	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	tgattgcagggaaaaaggccCgggcagtgtctcccttagac	10	8	13	10	1	1	2	0	1	1	1	2	3	1	3	2	3	1	2	2	3	3	2			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr10:63852307C>A	ENST00000279873.7	+	10	3495	c.3085C>A	c.(3085-3087)Cgg>Agg	p.R1029R	ARID5B_ENST00000309334.5_Silent_p.R786R	NM_032199.2	NP_115575.1	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	1029					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)	p.R1029W(1)		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)					GAAAAAGGCCCGGGCAGTGTC	0.597																																					p.R1029R		Atlas-SNP	.											ARID5B,colon,carcinoma,0,1	ARID5B	125	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3085A						PASS	.						62	70	67					10																	63852307		2203	4300	6503	SO:0001819	synonymous_variant	84159	exon10			AAGGCCCGGGCAG	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.3085C>A	chr10.hg19:g.63852307C>A		184.0	0.0	.		131.0	44.0	.	NM_032199	B4DLB3|Q05DG6|Q32Q59|Q5VST4|Q6NZ42|Q7Z3M4|Q8N421|Q9H786	Silent	SNP	ENST00000279873.7	hg19	CCDS31208.1																																																																																			.	.	.	none		0.597	ARID5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048233.1	XM_084482		A	63852307	C	A	63852307	2	1	48	1	0	0	0	0	0	0	0	1	922	643	23	4		4	ARID5B	10	63852307	Silent	SNP	C	TCGA-A4-7734-01A-11D-2136-08		63852307	71682440	27	3334											
PTPRJ	5795	hgsc.bcm.edu	37	chr11	48181586	48181586	+	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	ccggaatggaccatcagagaTttcacagtgaaaaatgtaag	16	8	10	7	1	2	2	2	1	0	1	2	5	2	4	2	2	0	1	2	2	4	2			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr11:48181586T>A	ENST00000418331.2	+	22	3895	c.3543T>A	c.(3541-3543)gaT>gaA	p.D1181E		NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	1181	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				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						CCATCAGAGATTTCACAGTGA	0.393																																					p.D1181E		Atlas-SNP	.											.	PTPRJ	225	.	0			c.T3543A						PASS	.						109	99	102					11																	48181586		2201	4298	6499	SO:0001583	missense	5795	exon22			CAGAGATTTCACA	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.3543T>A	chr11.hg19:g.48181586T>A	ENSP00000400010:p.Asp1181Glu	160.0	0.0	.		145.0	56.0	.	NM_002843	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	hg19	CCDS7945.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.277957	0.80692	.	.	ENSG00000149177	ENST00000418331	D	0.82526	-1.62	5.53	4.46	0.54185	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	.	.	.	.	T	0.59542	0.2201	N	0.02658	-0.545	0.80722	D	1	P	0.41131	0.739	B	0.44133	0.442	T	0.59537	-0.7436	9	0.07813	T	0.8	.	4.5662	0.12187	0.0:0.3223:0.0:0.6777	.	1181	Q12913	PTPRJ_HUMAN	E	1181	ENSP00000400010:D1181E	ENSP00000400010:D1181E	D	+	3	2	PTPRJ	48138162	0.990000	0.36364	1.000000	0.80357	0.994000	0.84299	0.202000	0.17295	1.076000	0.40961	0.529000	0.55759	GAT	.	.	.	none		0.393	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1			A	48181586	T	A	48181586	3	1	48	1	0	0	0	0	1	0	0	0	12817	1490	52	5	3638	5	PTPRJ	11	48181586	Missense_Mutation	SNP	T	TCGA-A4-7734-01A-11D-2136-08		48181586	86824930	28	3335											
CAPN1	823	hgsc.bcm.edu	37	chr11	64974118	64974118	+	Missense_Mutation	SNP	T	T	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	gggcgacttcgtgctgcgctTcttctcagagaagagtgctg	6	11	14	10	3	2	2	1	0	2	2	4	4	2	2	0	1	3	3	0	1	1	3			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr11:64974118T>G	ENST00000527323.1	+	12	1778	c.1538T>G	c.(1537-1539)tTc>tGc	p.F513C	CAPN1_ENST00000533129.1_Missense_Mutation_p.F513C|CAPN1_ENST00000524773.1_Missense_Mutation_p.F513C|CAPN1_ENST00000533820.1_Missense_Mutation_p.F513C|CAPN1_ENST00000279247.6_Missense_Mutation_p.F513C			P07384	CAN1_HUMAN	calpain 1, (mu/I) large subunit	513	Domain III.				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)		GTGCTGCGCTTCTTCTCAGAG	0.652																																					p.F513C		Atlas-SNP	.											.	CAPN1	44	.	0			c.T1538G						PASS	.						30	34	33					11																	64974118		2089	4209	6298	SO:0001583	missense	823	exon13			TGCGCTTCTTCTC	X04366	CCDS44644.1	11q13	2013-01-10			ENSG00000014216	ENSG00000014216	3.4.22.52	"EF-hand domain containing"	1476	protein-coding gene	gene with protein product		114220				3017764, 2209092	Standard	NM_005186		Approved	muCANP, muCL, CANP, CANPL1	uc009yqd.2	P07384	OTTHUMG00000165614	ENST00000527323.1:c.1538T>G	chr11.hg19:g.64974118T>G	ENSP00000431984:p.Phe513Cys	57.0	0.0	.		53.0	12.0	.	NM_001198869	Q2TTR0|Q6DHV4	Missense_Mutation	SNP	ENST00000527323.1	hg19	CCDS44644.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.227125	0.79576	.	.	ENSG00000014216	ENST00000533820;ENST00000533129;ENST00000524773;ENST00000279247;ENST00000259755;ENST00000527323	D;D;D;D;D	0.87103	-2.21;-2.21;-2.21;-2.21;-2.21	5.06	5.06	0.68205	Peptidase C2, calpain, large subunit, domain III (2);Peptidase C2, calpain, domain III (1);	0.209169	0.43416	D	0.000576	D	0.88171	0.6365	L	0.33753	1.03	0.46774	D	0.999196	P	0.48350	0.909	P	0.59115	0.852	D	0.89382	0.3682	10	0.87932	D	0	.	12.7595	0.57356	0.0:0.0:0.0:1.0	.	513	P07384	CAN1_HUMAN	C	513;513;513;513;459;513	ENSP00000435272:F513C;ENSP00000431686:F513C;ENSP00000434176:F513C;ENSP00000279247:F513C;ENSP00000431984:F513C	ENSP00000259755:F459C	F	+	2	0	CAPN1	64730694	1.000000	0.71417	1.000000	0.80357	0.669000	0.39330	7.950000	0.87804	1.897000	0.54924	0.379000	0.24179	TTC	.	.	.	none		0.652	CAPN1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385325.1			G	64974118	T	G	64974118	3	3	48	1	0	0	0	0	1	0	0	0	2624	1783	62	5	1584	5	CAPN1	11	64974118	Missense_Mutation	SNP	T	TCGA-A4-7734-01A-11D-2136-08	16792532	64974118	70032398	29	3336											
RNF26	79102	hgsc.bcm.edu	37	chr11	119206410	119206410	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttcctagcccacatttccaGcagtgctgtggccatggcca	7	10	9	15	0	0	0	0	0	0	0	2	0	2	0	5	2	3	2	5	2	1	3	rs200033048		TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr11:119206410G>A	ENST00000311413.4	+	1	1174	c.578G>A	c.(577-579)aGc>aAc	p.S193N	RP11-334E6.10_ENST00000501918.2_RNA	NM_032015.4	NP_114404.1	Q9BY78	RNF26_HUMAN	ring finger protein 26	193						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)		CACATTTCCAGCAGTGCTGTG	0.622																																					p.S193N		Atlas-SNP	.											.	RNF26	23	.	0			c.G578A						PASS	.	G	ASN/SER	0,4398		0,0,2199	115	95	102		578	5.1	1	11		102	1,8589	1.2+/-3.3	0,1,4294	no	missense	RNF26	NM_032015.3	46	0,1,6493	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	193/434	119206410	1,12987	2199	4295	6494	SO:0001583	missense	79102	exon1			TTTCCAGCAGTGC	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.578G>A	chr11.hg19:g.119206410G>A	ENSP00000312439:p.Ser193Asn	72.0	0.0	.		69.0	28.0	.	NM_032015	Q542Y8	Missense_Mutation	SNP	ENST00000311413.4	hg19	CCDS8419.1	.	.	.	.	.	.	.	.	.	.	G	16.69	3.192453	0.58017	0.0	1.16E-4	ENSG00000173456	ENST00000311413	T	0.79653	-1.29	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.73613	0.3609	L	0.32530	0.975	0.47659	D	0.999484	D	0.53312	0.959	P	0.46940	0.532	T	0.71024	-0.4712	10	0.26408	T	0.33	-16.3913	11.0828	0.48070	0.0844:0.0:0.9156:0.0	.	193	Q9BY78	RNF26_HUMAN	N	193	ENSP00000312439:S193N	ENSP00000312439:S193N	S	+	2	0	RNF26	118711620	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.210000	0.65214	2.393000	0.81446	0.561000	0.74099	AGC	.	G|0.999;A|0.001	0.001	weak		0.622	RNF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388220.1	NM_032015		A	119206410	G	A	119206410	3	1	48	1	0	0	0	0	1	0	0	0	13499	971	34	2	580	2	RNF26	11	119206410	Missense_Mutation	SNP	G	TCGA-A4-7734-01A-11D-2136-08	54232292	119206410	15800106	30	3337											
H2AFJ	55766	hgsc.bcm.edu	37	chr12	14927594	14927594	+	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	agtaccttacggcggagatcCtggagctggctggcaacgcc	8	7	14	12	3	0	1	0	0	0	1	1	3	1	2	3	5	4	4	3	5	3	2			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr12:14927594C>G	ENST00000544848.1	+	1	325	c.190C>G	c.(190-192)Ctg>Gtg	p.L64V		NM_177925.2	NP_808760.1	Q9BTM1	H2AJ_HUMAN	H2A histone family, member J	64						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|kidney(1)|ovary(1)|skin(1)	5						GGCGGAGATCCTGGAGCTGGC	0.632																																					p.L64V		Atlas-SNP	.											.	H2AFJ	14	.	0			c.C190G						PASS	.						49	56	54					12																	14927594		2203	4300	6503	SO:0001583	missense	55766	exon1			GAGATCCTGGAGC	AK001765	CCDS31752.1	12p12.3	2012-09-11			ENSG00000246705	ENSG00000246705		"Histones / Replication-independent"	14456	protein-coding gene	gene with protein product							Standard	NM_177925		Approved	FLJ10903, MGC921	uc009zia.3	Q9BTM1	OTTHUMG00000168736	ENST00000544848.1:c.190C>G	chr12.hg19:g.14927594C>G	ENSP00000438553:p.Leu64Val	139.0	0.0	.		105.0	36.0	.	NM_177925	Q9NV63	Missense_Mutation	SNP	ENST00000544848.1	hg19	CCDS31752.1	.	.	.	.	.	.	.	.	.	.	C	13.94	2.387309	0.42308	.	.	ENSG00000246705	ENST00000544848;ENST00000228929	T;T	0.72282	-0.64;-0.64	4.67	3.78	0.43462	Histone-fold (2);Histone core (1);Histone H2A (2);	.	.	.	.	T	0.81489	0.4833	H	0.97158	3.95	0.45139	D	0.998151	B	0.22800	0.075	B	0.30251	0.113	D	0.84014	0.0350	9	0.87932	D	0	.	13.3675	0.60694	0.0:0.8405:0.1594:0.0	.	64	Q9BTM1	H2AJ_HUMAN	V	64	ENSP00000438553:L64V;ENSP00000228929:L64V	ENSP00000228929:L64V	L	+	1	2	H2AFJ	14818861	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.833000	0.55790	1.571000	0.49722	-0.156000	0.13503	CTG	.	.	.	none		0.632	H2AFJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400845.1	NM_177925		G	14927594	C	G	14927594	3	3	48	1	0	0	0	0	1	0	0	0	6933	680	24	4	192	4	H2AFJ	12	14927594	Missense_Mutation	SNP	C	TCGA-A4-7734-01A-11D-2136-08		14927594	118924301	31	3338											
CPM	1368	hgsc.bcm.edu	37	chr12	69326479	69326479	+	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	tttcacagatttcccaatacTgtgtaagtgagtgacagaac	13	12	8	8	0	1	4	1	2	0	2	2	4	2	4	1	0	2	1	1	0	4	4			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr12:69326479T>A	ENST00000551568.1	-	2	199	c.139A>T	c.(139-141)Agt>Tgt	p.S47C	CPM_ENST00000338356.3_Missense_Mutation_p.S47C|CPM_ENST00000546373.1_Missense_Mutation_p.S47C	NM_001005502.2|NM_198320.3	NP_001005502.1|NP_938079.1	P14384	CBPM_HUMAN	carboxypeptidase M	47					anatomical structure morphogenesis (GO:0009653)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(6)|prostate(2)	9	all_epithelial(5;1.09e-35)|Lung NSC(4;1.47e-33)|all_lung(4;1.02e-31)|Breast(13;1.59e-06)		all cancers(2;2.69e-50)|GBM - Glioblastoma multiforme(2;7.34e-41)|BRCA - Breast invasive adenocarcinoma(5;5.38e-10)|Lung(24;4.61e-05)|LUAD - Lung adenocarcinoma(15;0.000376)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			TTCCCAATACTGTGTAAGTGA	0.473																																					p.S47C		Atlas-SNP	.											.	CPM	30	.	0			c.A139T						PASS	.						117	109	112					12																	69326479		2203	4300	6503	SO:0001583	missense	1368	exon2			CAATACTGTGTAA	AF368463	CCDS8987.1	12q15	2012-02-10			ENSG00000135678	ENSG00000135678	3.4.17.12		2311	protein-coding gene	gene with protein product	"renal carboxypeptidase", "urinary carboxypeptidase B"	114860				8586455	Standard	NM_001874		Approved		uc001suq.3	P14384	OTTHUMG00000169300	ENST00000551568.1:c.139A>T	chr12.hg19:g.69326479T>A	ENSP00000448517:p.Ser47Cys	108.0	0.0	.		104.0	53.0	.	NM_001005502	B2R800|Q9H2K9	Missense_Mutation	SNP	ENST00000551568.1	hg19	CCDS8987.1	.	.	.	.	.	.	.	.	.	.	T	15.94	2.981836	0.53827	.	.	ENSG00000135678	ENST00000551568;ENST00000338356;ENST00000546373;ENST00000548954;ENST00000548262;ENST00000549781	T;T;T;T;T;T	0.12984	2.63;2.63;2.63;2.63;2.63;3.2	4.24	4.24	0.50183	Peptidase M14, carboxypeptidase A (2);	0.000000	0.85682	D	0.000000	T	0.29850	0.0746	H	0.94183	3.505	0.58432	D	0.999997	B	0.28324	0.207	B	0.34418	0.182	T	0.18650	-1.0330	9	.	.	.	-17.8592	11.2744	0.49157	0.0:0.0:0.0:1.0	.	47	P14384	CBPM_HUMAN	C	47	ENSP00000448517:S47C;ENSP00000339157:S47C;ENSP00000447255:S47C;ENSP00000446799:S47C;ENSP00000449911:S47C;ENSP00000448078:S47C	.	S	-	1	0	CPM	67612746	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.980000	0.49321	1.899000	0.54978	0.460000	0.39030	AGT	.	.	.	none		0.473	CPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403355.1	NM_198320		A	69326479	T	A	69326479	3	1	48	1	0	0	0	0	1	0	0	0	3810	1580	55	5	1224	5	CPM	12	69326479	Missense_Mutation	SNP	T	TCGA-A4-7734-01A-11D-2136-08	54398885	69326479	64525416	32	3339											
DUSP6	1848	hgsc.bcm.edu	37	chr12	89744677	89744677	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agactcgatgtccgaggaagAgtcagagctgatccgcaggc	11	6	14	10	3	1	4	1	1	0	3	4	7	3	5	2	2	1	2	2	2	1	0			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr12:89744677A>G	ENST00000279488.7	-	2	1757	c.526T>C	c.(526-528)Tct>Cct	p.S176P	DUSP6_ENST00000547291.1_Missense_Mutation_p.S51P|DUSP6_ENST00000308385.6_Intron|DUSP6_ENST00000547140.1_5'UTR	NM_001946.2	NP_001937.2	Q16828	DUS6_HUMAN	dual specificity phosphatase 6	176					cell differentiation (GO:0030154)|dorsal/ventral pattern formation (GO:0009953)|inactivation of MAPK activity (GO:0000188)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of apoptotic process (GO:0043065)|regulation of endodermal cell fate specification (GO:0042663)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of heart growth (GO:0060420)|response to drug (GO:0042493)|response to nitrosative stress (GO:0051409)|response to organic cyclic compound (GO:0014070)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)			large_intestine(5)|lung(8)|skin(2)|urinary_tract(1)	16						TCCGAGGAAGAGTCAGAGCTG	0.607																																					p.S176P	Colon(132;3456 5224)	Atlas-SNP	.											.	DUSP6	30	.	0			c.T526C						PASS	.						53	48	50					12																	89744677		2203	4300	6503	SO:0001583	missense	1848	exon2			AGGAAGAGTCAGA	BC037236	CCDS9033.1, CCDS9034.1	12q22-q23	2011-06-09				ENSG00000139318		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3072	protein-coding gene	gene with protein product		602748				8626780, 9205128	Standard	NM_001946		Approved	MKP-3, PYST1	uc001tay.3	Q16828		ENST00000279488.7:c.526T>C	chr12.hg19:g.89744677A>G	ENSP00000279488:p.Ser176Pro	72.0	0.0	.		63.0	28.0	.	NM_001946	O75109|Q53Y75|Q9BSH6	Missense_Mutation	SNP	ENST00000279488.7	hg19	CCDS9033.1	.	.	.	.	.	.	.	.	.	.	A	17.70	3.455071	0.63290	.	.	ENSG00000139318	ENST00000279488;ENST00000547291	T;T	0.03035	4.28;4.07	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.05090	0.0136	L	0.44542	1.39	0.80722	D	1	B	0.10296	0.003	B	0.06405	0.002	T	0.43940	-0.9360	10	0.22706	T	0.39	.	16.0353	0.80625	1.0:0.0:0.0:0.0	.	176	Q16828	DUS6_HUMAN	P	176;51	ENSP00000279488:S176P;ENSP00000449838:S51P	ENSP00000279488:S176P	S	-	1	0	DUSP6	88268808	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	4.624000	0.61254	2.178000	0.69098	0.533000	0.62120	TCT	.	.	.	none		0.607	DUSP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406534.2	NM_001946, NM_022652		G	89744677	A	G	89744677	3	3	48	1	0	0	0	0	1	0	0	0	4831	304	11	3	627	3	DUSP6	12	89744677	Missense_Mutation	SNP	A	TCGA-A4-7734-01A-11D-2136-08	20418198	89744677	44107218	33	3340											
ABCD4	5826	hgsc.bcm.edu	37	chr14	74756774	74756774	+	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	gaagaatggcttttgtggcaGgaatagcaccccatggggcc	10	8	14	9	0	0	1	0	0	0	1	0	3	0	2	3	5	1	3	3	5	4	3			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr14:74756774G>T	ENST00000356924.4	-	13	1518	c.1375C>A	c.(1375-1377)Ctg>Atg	p.L459M	ABCD4_ENST00000557554.1_5'Flank|ABCD4_ENST00000298816.7_Missense_Mutation_p.L355M|AC005519.4_ENST00000554532.2_RNA	NM_005050.3	NP_005041.1	O14678	ABCD4_HUMAN	ATP-binding cassette, sub-family D (ALD), member 4	459	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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)		TTTTGTGGCAGGAATAGCACC	0.592											OREG0022800	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L459M		Atlas-SNP	.											.	ABCD4	54	.	0			c.C1375A						PASS	.						80	82	82					14																	74756774		2203	4300	6503	SO:0001583	missense	5826	exon13			GTGGCAGGAATAG	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.1375C>A	chr14.hg19:g.74756774G>T	ENSP00000349396:p.Leu459Met	147.0	0.0	.	1155	105.0	36.0	.	NM_005050	A8K5L7|Q6IAQ0|Q96E75	Missense_Mutation	SNP	ENST00000356924.4	hg19	CCDS9828.1	.	.	.	.	.	.	.	.	.	.	G	19.52	3.843870	0.71488	.	.	ENSG00000119688	ENST00000356924;ENST00000298816	D;D	0.95035	-2.78;-3.59	5.76	4.87	0.63330	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.64402	D	0.000001	D	0.96367	0.8815	M	0.66560	2.04	0.58432	D	0.999996	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.996;0.998;0.998	D	0.96434	0.9321	10	0.72032	D	0.01	.	11.9671	0.53042	0.1395:0.0:0.8605:0.0	.	355;459;459	F8W7M4;A8K5L7;O14678	.;.;ABCD4_HUMAN	M	459;355	ENSP00000349396:L459M;ENSP00000298816:L355M	ENSP00000298816:L355M	L	-	1	2	ABCD4	73826527	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	4.539000	0.60657	1.443000	0.47586	0.462000	0.41574	CTG	.	.	.	none		0.592	ABCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314382.1	NM_005050		T	74756774	G	T	74756774	3	4	48	1	0	0	0	0	1	0	0	0	63	991	35	4	473	4	ABCD4	14	74756774	Missense_Mutation	SNP	G	TCGA-A4-7734-01A-11D-2136-08		74756774	32592766	34	3341											
NEDD4	4734	hgsc.bcm.edu	37	chr15	56208931	56208934	+	Frame_Shift_Del	DEL	CATG	CATG	-																															cgtgttggtcttttgaagcaCatgtgaacatggctatccaa																								rs1912403	byFrequency	TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	CATG	CATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr15:56208931_56208934delCATG	ENST00000508342.1	-	1	395_398	c.96_99delCATG	c.(94-99)cacatgfs	p.HM32fs	NEDD4_ENST00000506154.1_Frame_Shift_Del_p.HM32fs|NEDD4_ENST00000338963.2_Frame_Shift_Del_p.HM32fs|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	32					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)		TTTTGAAGCACATGTGAACATGGC	0.436																																					p.33_34del		Atlas-INDEL	.											.	NEDD4	167	.	0			c.97_100del						PASS	.																																			SO:0001589	frameshift_variant	4734	exon1			.	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.96_99delCATG	chr15.hg19:g.56208931_56208934delCATG	ENSP00000424827:p.His32fs	225.0	0.0	0		214.0	67.0	0.313084	NM_198400	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Frame_Shift_Del	DEL	ENST00000508342.1	hg19																																																																																				.	.	.	none		0.436	NEDD4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000359817.1	NM_198400		-	56208934	CATG	-	56208931	7	5	48	1	0	1	0	1	0	0	0	0	10317	478	17	0	3960	0	NEDD4	15	56208931	Frame_Shift_Del	DEL	CATG	TCGA-A4-7734-01A-11D-2136-08		56208931	46322461	35	3342	41	2									
NEDD4	4734	hgsc.bcm.edu	37	chr15	56208934	56208934	+	Silent	SNP	G	G	A																															gttggtcttttgaagcacatGtgaacatggctatccaagtc																										TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr15:56208934G>A	ENST00000508342.1	-	1	395	c.96C>T	c.(94-96)caC>caT	p.H32H	NEDD4_ENST00000506154.1_Silent_p.H32H|NEDD4_ENST00000338963.2_Silent_p.H32H|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	32					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)		TGAAGCACATGTGAACATGGC	0.438																																					p.H32H		Atlas-SNP	.											.	NEDD4	167	.	0			c.C96T						PASS	.						184	172	176					15																	56208934		2193	4291	6484	SO:0001819	synonymous_variant	4734	exon1			GCACATGTGAACA	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.96C>T	chr15.hg19:g.56208934G>A		231.0	0.0	.		162.0	7.0	.	NM_198400	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Silent	SNP	ENST00000508342.1	hg19																																																																																				.	.	.	none		0.438	NEDD4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000359817.1	NM_198400		A	56208934	G	A	56208934	2	1	48	1	0	0	0	0	0	0	0	1	10317	1368	48	2		2	NEDD4	15	56208934	Silent	SNP	G	TCGA-A4-7734-01A-11D-2136-08	3	56208934	46322458	36	3343	41	2									
PPIB	5479	hgsc.bcm.edu	37	chr15	64454355	64454355	+	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	ttcgtaggtcaaaatacaccTgaggaaagagaccatttcca	15	9	8	9	1	1	2	1	1	0	1	3	4	2	3	3	2	1	1	3	2	5	4			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr15:64454355T>C	ENST00000300026.3	-	2	354		c.e2-2		PPIB_ENST00000558492.1_Intron	NM_000942.4	NP_000933.1	P23284	PPIB_HUMAN	peptidylprolyl isomerase B (cyclophilin B)						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)	AAAATACACCTGAGGAAAGAG	0.463																																					.	GBM(105;399 1481 32889 33051 36637)	Atlas-SNP	.											.	PPIB	20	.	0			c.136-2A>G						PASS	.						132	141	138					15																	64454355		2203	4300	6503	SO:0001630	splice_region_variant	5479	exon3			TACACCTGAGGAA		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.136-2A>G	chr15.hg19:g.64454355T>C		220.0	0.0	.		187.0	80.0	.	NM_000942	A8K534|Q6IBH5|Q9BVK5	Splice_Site	SNP	ENST00000300026.3	hg19	CCDS10191.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.086591	0.76642	.	.	ENSG00000166794	ENST00000300026	.	.	.	5.57	5.57	0.84162	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3959	0.74794	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PPIB	62241408	1.000000	0.71417	0.976000	0.42696	0.823000	0.46562	7.490000	0.81461	2.121000	0.65114	0.374000	0.22700	.	.	.	.	none		0.463	PPIB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256604.1		Intron	C	64454355	T	C	64454355	5	2	48	1	0	0	0	0	0	0	1	0	12329	1594	55	3	532	3	PPIB	15	64454355	Splice_Site	SNP	T	TCGA-A4-7734-01A-11D-2136-08	8245421	64454355	38077037	37	3344											
CORO1A	11151	hgsc.bcm.edu	37	chr16	30198546	30198547	+	Splice_Site	INS	-	-	GA																															aaaggcactgtcgtagctgtINSgagtcgccatctaccctgac																										TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr16:30198546_30198547insGA	ENST00000219150.5	+	5	941		c.e5+2		CORO1A_ENST00000570045.1_Splice_Site|RP11-455F5.5_ENST00000567153.1_RNA|CORO1A_ENST00000565497.1_Splice_Site|RP11-455F5.5_ENST00000568506.1_RNA|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						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						GTCGTAGCTGTGAGTCGCCATC	0.589																																					.		Atlas-INDEL	.											.	CORO1A	36	.	0			c.636+2->GA						PASS	.																																			SO:0001630	splice_region_variant	11151	exon5			.	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.636+2->GA	chr16.hg19:g.30198547_30198548dupGA		102.0	0.0	0		74.0	21.0	0.283784	NM_007074	B2RBL1|Q2YD73	Splice_Site	INS	ENST00000219150.5	hg19	CCDS10673.1																																																																																			.	.	.	none		0.589	CORO1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255195.2	NM_007074	Intron	GA	30198547	-	GA	30198546	8	5	48	1	0	1	1	0	0	0	1	0	3755	1710	59	0	652	0	CORO1A	16	30198546	Splice_Site	INS	-	TCGA-A4-7734-01A-11D-2136-08		30198546	60156207	38	3345											
GPR97	222487	hgsc.bcm.edu	37	chr16	57719830	57719830	+	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	catctttgcacttttcaactCcttgcaaggtgaggcccctg	7	13	8	13	0	2	1	1	1	1	0	3	1	3	1	3	2	3	2	3	2	2	4			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr16:57719830C>T	ENST00000333493.4	+	11	1693	c.1532C>T	c.(1531-1533)tCc>tTc	p.S511F	GPR97_ENST00000450388.3_Missense_Mutation_p.S391F|GPR97_ENST00000327655.6_Missense_Mutation_p.S301F|RP11-405F3.4_ENST00000563062.1_RNA	NM_170776.4	NP_740746.4	Q86Y34	GPR97_HUMAN	G protein-coupled receptor 97	511					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CTTTTCAACTCCTTGCAAGGT	0.597																																					p.S511F		Atlas-SNP	.											.	GPR97	74	.	0			c.C1532T						PASS	.						88	82	84					16																	57719830		2198	4300	6498	SO:0001583	missense	222487	exon11			TCAACTCCTTGCA	AY140959	CCDS10786.1	16q13	2014-08-08			ENSG00000182885	ENSG00000182885		"-", "GPCR / Class B : Orphans"	13728	protein-coding gene	gene with protein product						12435584, 222487	Standard	NM_170776		Approved	Pb99, PGR26	uc002emh.3	Q86Y34	OTTHUMG00000133458	ENST00000333493.4:c.1532C>T	chr16.hg19:g.57719830C>T	ENSP00000332900:p.Ser511Phe	187.0	0.0	.		120.0	52.0	.	NM_170776	Q6ZMF4|Q86SL9|Q8IZF1	Missense_Mutation	SNP	ENST00000333493.4	hg19	CCDS10786.1	.	.	.	.	.	.	.	.	.	.	C	19.05	3.752027	0.69533	.	.	ENSG00000182885	ENST00000333493;ENST00000327655;ENST00000450388	T;T;T	0.56611	0.45;0.45;0.45	5.62	5.62	0.85841	GPCR, family 2-like (1);	0.000000	0.56097	D	0.000025	T	0.80737	0.4680	M	0.93939	3.475	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85478	0.1177	10	0.87932	D	0	.	18.6332	0.91368	0.0:1.0:0.0:0.0	.	511	Q86Y34	GPR97_HUMAN	F	511;301;391	ENSP00000332900:S511F;ENSP00000331199:S301F;ENSP00000404803:S391F	ENSP00000331199:S301F	S	+	2	0	GPR97	56277331	1.000000	0.71417	0.998000	0.56505	0.375000	0.29983	4.512000	0.60469	2.647000	0.89833	0.655000	0.94253	TCC	.	.	.	none		0.597	GPR97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257333.2	NM_170776		T	57719830	C	T	57719830	3	4	48	1	0	0	0	0	1	0	0	0	6727	855	30	2	1574	2	GPR97	16	57719830	Missense_Mutation	SNP	C	TCGA-A4-7734-01A-11D-2136-08	27521284	57719830	32634923	39	3346											
KIFC3	3801	hgsc.bcm.edu	37	chr16	57806198	57806198	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcttctccttcaggtgttcTacctgtgggcacagagtcag	7	12	11	11	0	4	1	2	0	2	1	5	1	4	1	2	2	2	3	2	2	1	4			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr16:57806198T>C	ENST00000379655.4	-	4	575	c.318A>G	c.(316-318)gtA>gtG	p.V106V	KIFC3_ENST00000543930.1_5'UTR|KIFC3_ENST00000562903.1_5'UTR|KIFC3_ENST00000445690.2_Silent_p.V106V|KIFC3_ENST00000465878.2_5'UTR|KIFC3_ENST00000539578.1_Silent_p.V48V|KIFC3_ENST00000541240.1_Silent_p.V128V|KIFC3_ENST00000566975.1_5'UTR|KIFC3_ENST00000421376.2_5'UTR|KIFC3_ENST00000540079.2_Silent_p.V4V	NM_005550.3	NP_005541.3	Q9BVG8	KIFC3_HUMAN	kinesin family member C3	106					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)				TCAGGTGTTCTACCTGTGGGC	0.617																																					p.V106V		Atlas-SNP	.											.	KIFC3	55	.	0			c.A318G						PASS	.						117	92	101					16																	57806198		2198	4300	6498	SO:0001819	synonymous_variant	3801	exon4			GTGTTCTACCTGT	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.318A>G	chr16.hg19:g.57806198T>C		99.0	0.0	.		79.0	31.0	.	NM_001130100	A8K6S2|B7Z484|O75299|Q49A29|Q49AQ0|Q59G19|Q8IUT3|Q96HW6	Silent	SNP	ENST00000379655.4	hg19	CCDS10789.2																																																																																			.	.	.	none		0.617	KIFC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257329.2	NM_005550		C	57806198	T	C	57806198	2	2	48	1	0	0	0	0	0	0	0	1	8321	1509	53	3		3	KIFC3	16	57806198	Silent	SNP	T	TCGA-A4-7734-01A-11D-2136-08	86368	57806198	32548555	40	3347											
MYO1C	4641	hgsc.bcm.edu	37	chr17	1370772	1370772	+	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	ccgggggccgcccgcgcctcAcctgccctggttgatgttga	3	8	14	16	4	1	2	1	2	0	0	1	2	1	2	6	3	1	2	6	3	0	2			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr17:1370772A>C	ENST00000575158.1	-	30	3137		c.e30+1		MYO1C_ENST00000438665.2_Splice_Site|MYO1C_ENST00000361007.2_Splice_Site|MYO1C_ENST00000359786.5_Splice_Site|MYO1C_ENST00000545534.2_Splice_Site			Q12965	MYO1E_HUMAN	myosin IC						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)		CCCGCGCCTCACCTGCCCTGG	0.677																																					.		Atlas-SNP	.											.	MYO1C	57	.	0			c.2960+2T>G						PASS	.						64	58	60					17																	1370772		2203	4299	6502	SO:0001630	splice_region_variant	4641	exon31			CGCCTCACCTGCC	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.2960+1T>G	chr17.hg19:g.1370772A>C		81.0	0.0	.		82.0	36.0	.	NM_033375	Q14778	Splice_Site	SNP	ENST00000575158.1	hg19	CCDS11003.1	.	.	.	.	.	.	.	.	.	.	a	23.7	4.448047	0.84101	.	.	ENSG00000197879	ENST00000359786;ENST00000438665;ENST00000535856;ENST00000361007;ENST00000545534	.	.	.	5.31	5.31	0.75309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5923	0.68373	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MYO1C	1317522	1.000000	0.71417	0.994000	0.49952	0.936000	0.57629	9.119000	0.94362	2.231000	0.72958	0.456000	0.33151	.	.	.	.	none		0.677	MYO1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438694.2		Intron	C	1370772	A	C	1370772	5	2	48	1	0	0	0	0	0	0	1	0	10077	173	6	5	136	5	MYO1C	17	1370772	Splice_Site	SNP	A	TCGA-A4-7734-01A-11D-2136-08		1370772	79824438	41	3348											
LUC7L3	51747	hgsc.bcm.edu	37	chr17	48818486	48818486	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagaagagctctcgtttcaTgaaagttggctatgagagag	12	11	13	5	1	2	5	1	3	1	3	3	7	2	5	0	1	1	4	0	1	3	3			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr17:48818486T>C	ENST00000505658.1	+	4	419	c.230T>C	c.(229-231)aTg>aCg	p.M77T	LUC7L3_ENST00000544170.1_Start_Codon_SNP_p.M1T|LUC7L3_ENST00000240304.1_Missense_Mutation_p.M77T|LUC7L3_ENST00000393227.2_Missense_Mutation_p.M77T			O95232	LC7L3_HUMAN	LUC7-like 3 (S. cerevisiae)	77					mRNA splice site selection (GO:0006376)|RNA splicing (GO:0008380)	focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|U1 snRNP (GO:0005685)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	12						TCTCGTTTCATGAAAGTTGGC	0.383																																					p.M77T		Atlas-SNP	.											.	LUC7L3	32	.	0			c.T230C						PASS	.						180	182	181					17																	48818486		2203	4300	6503	SO:0001583	missense	51747	exon4			GTTTCATGAAAGT		CCDS11573.1	17q21.33	2010-02-17			ENSG00000108848	ENSG00000108848			24309	protein-coding gene	gene with protein product	"cisplatin resistance associated overexpressed protein", "CRE-associated protein"	609434				10631324, 12565863	Standard	NM_016424		Approved	LUC7A, CROP, OA48-18, CREAP-1, FLJ11063, CRA, hLuc7A	uc002iss.3	O95232	OTTHUMG00000162257	ENST00000505658.1:c.230T>C	chr17.hg19:g.48818486T>C	ENSP00000425092:p.Met77Thr	306.0	0.0	.		310.0	87.0	.	NM_006107	B3KN54|D3DTY1|Q6PHR9|Q9NUY0|Q9P2S7	Missense_Mutation	SNP	ENST00000505658.1	hg19	CCDS11573.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.064693	0.76187	.	.	ENSG00000108848	ENST00000505658;ENST00000393227;ENST00000240304;ENST00000542316;ENST00000505619;ENST00000544170;ENST00000510984	T;T;T;T;T	0.47528	1.31;1.31;1.31;1.03;0.84	5.95	4.83	0.62350	.	0.071512	0.85682	D	0.000000	T	0.39036	0.1063	L	0.31065	0.9	0.80722	D	1	D;B;B	0.53885	0.963;0.369;0.369	P;B;B	0.47786	0.557;0.171;0.237	T	0.11275	-1.0594	10	0.09338	T	0.73	-10.5258	13.4049	0.60906	0.0:0.0:0.1306:0.8694	.	1;77;77	B4DJ96;O95232;A8K3C5	.;LC7L3_HUMAN;.	T	77;77;77;77;126;1;1	ENSP00000425092:M77T;ENSP00000376919:M77T;ENSP00000240304:M77T;ENSP00000420933:M126T;ENSP00000444253:M1T	ENSP00000240304:M77T	M	+	2	0	LUC7L3	46173485	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.043000	0.64208	2.272000	0.75746	0.460000	0.39030	ATG	.	.	.	none		0.383	LUC7L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368205.2	NM_016424		C	48818486	T	C	48818486	3	2	48	1	0	0	0	0	1	0	0	0	9091	1464	51	3	244	3	LUC7L3	17	48818486	Missense_Mutation	SNP	T	TCGA-A4-7734-01A-11D-2136-08	47447714	48818486	32376724	42	3349											
CLTC	1213	hgsc.bcm.edu	37	chr17	57724783	57724783	+	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	gaaaactcttcagatttttaAcattgaaatgaaaagtaaaa	20	12	5	4	0	2	3	1	2	1	1	2	4	2	3	0	0	2	1	0	0	8	6			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr17:57724783A>T	ENST00000269122.3	+	3	549	c.275A>T	c.(274-276)aAc>aTc	p.N92I	CLTC_ENST00000579456.1_Missense_Mutation_p.N92I|CLTC_ENST00000393043.1_Missense_Mutation_p.N92I	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	92	Globular terminal domain.|WD40-like repeat 2.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					CAGATTTTTAACATTGAAATG	0.318			T	"ALK, TFE3"	"ALCL, renal "																																p.N92I		Atlas-SNP	.		Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	.	CLTC	124	.	0			c.A275T						PASS	.						73	71	72					17																	57724783		2203	4300	6503	SO:0001583	missense	1213	exon3			TTTTTAACATTGA	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.275A>T	chr17.hg19:g.57724783A>T	ENSP00000269122:p.Asn92Ile	87.0	0.0	.		91.0	28.0	.	NM_004859	D3DU00|Q6N0A0|Q86TF2	Missense_Mutation	SNP	ENST00000269122.3	hg19	CCDS32696.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.244879	0.79912	.	.	ENSG00000141367	ENST00000269122;ENST00000393043	T;T	0.27256	1.68;1.68	5.79	5.79	0.91817	Clathrin, heavy chain, propeller, N-terminal (1);Clathrin, heavy chain, linker/propeller domain (1);	0.043886	0.85682	D	0.000000	T	0.63390	0.2507	H	0.94222	3.51	0.31520	N	0.662492	D;D	0.76494	0.994;0.999	D;D	0.79784	0.993;0.993	T	0.77419	-0.2595	10	0.87932	D	0	.	16.1376	0.81497	1.0:0.0:0.0:0.0	.	92;92	Q00610;Q00610-2	CLH1_HUMAN;.	I	92	ENSP00000269122:N92I;ENSP00000376763:N92I	ENSP00000269122:N92I	N	+	2	0	CLTC	55079565	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.339000	0.96797	2.212000	0.71576	0.533000	0.62120	AAC	.	.	.	none		0.318	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859		T	57724783	A	T	57724783	3	4	48	1	0	0	0	0	1	0	0	0	3568	43	2	5	285	5	CLTC	17	57724783	Missense_Mutation	SNP	A	TCGA-A4-7734-01A-11D-2136-08	8906297	57724783	23470427	43	3350											
MUC16	94025	hgsc.bcm.edu	37	chr19	9064319	9064319	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggaaggggagagggggggatAtgtgctaggaatgtggtgga	10	7	23	1	0	0	1	0	0	0	1	0	6	0	5	0	9	1	1	0	9	4	2			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr19:9064319A>G	ENST00000397910.4	-	3	23330	c.23127T>C	c.(23125-23127)caT>caC	p.H7709H		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7711	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						AGGGGGGGATATGTGCTAGGA	0.547																																					p.H7709H		Atlas-SNP	.											.	MUC16	4315	.	0			c.T23127C						PASS	.						102	105	104					19																	9064319		2045	4180	6225	SO:0001819	synonymous_variant	94025	exon3			GGGGATATGTGCT	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.23127T>C	chr19.hg19:g.9064319A>G		115.0	0.0	.		92.0	4.0	.	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.	.	none		0.547	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9064319	A	G	9064319	2	3	48	1	0	0	0	0	0	0	0	1	9980	446	16	3		3	MUC16	19	9064319	Silent	SNP	A	TCGA-A4-7734-01A-11D-2136-08		9064319	50064664	44	3351											
TBCB	1155	hgsc.bcm.edu	37	chr19	36606528	36606528	+	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	agcagctccctcaacaccttCcgctccgagaagcgatacag	11	6	8	16	3	1	1	1	0	0	1	4	3	4	1	4	0	5	3	4	0	3	2			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr19:36606528C>G	ENST00000221855.3	+	1	641	c.66C>G	c.(64-66)ttC>ttG	p.F22L	POLR2I_ENST00000221859.4_5'Flank|TBCB_ENST00000392178.4_3'UTR|TBCB_ENST00000586868.1_5'Flank|TBCB_ENST00000589996.1_Missense_Mutation_p.F22L|TBCB_ENST00000585746.1_5'Flank	NM_001281.2	NP_001272.2	Q99426	TBCB_HUMAN	tubulin folding cofactor B	22					'de novo' posttranslational protein folding (GO:0051084)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	5	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			TCAACACCTTCCGCTCCGAGA	0.667																																					p.F22L		Atlas-SNP	.											.	TBCB	13	.	0			c.C66G						PASS	.						35	25	28					19																	36606528		2202	4298	6500	SO:0001583	missense	1155	exon1			CACCTTCCGCTCC	AF013488	CCDS12488.1, CCDS74344.1	19q13.11-q13.12	2008-02-05	2006-11-22	2006-11-22	ENSG00000105254	ENSG00000105254			1989	protein-coding gene	gene with protein product		601303	"cytoskeleton-associated protein 1", "cytoskeleton associated protein 1"	CKAP1		8978778	Standard	NM_001281		Approved	CG22, CKAPI	uc002odg.1	Q99426	OTTHUMG00000048143	ENST00000221855.3:c.66C>G	chr19.hg19:g.36606528C>G	ENSP00000221855:p.Phe22Leu	43.0	0.0	.		28.0	10.0	.	NM_001281	O00111|O00674|O14728|Q6FGY5	Missense_Mutation	SNP	ENST00000221855.3	hg19	CCDS12488.1	.	.	.	.	.	.	.	.	.	.	C	17.44	3.391016	0.62066	.	.	ENSG00000105254	ENST00000221855;ENST00000392178	D	0.91068	-2.78	5.33	1.7	0.24286	.	0.000000	0.85682	D	0.000000	D	0.86916	0.6048	M	0.65498	2.005	0.80722	D	1	B	0.15473	0.013	B	0.20955	0.032	T	0.77035	-0.2737	10	0.28530	T	0.3	-21.5313	8.0558	0.30604	0.0:0.7565:0.0:0.2435	.	22	Q99426	TBCB_HUMAN	L	22	ENSP00000221855:F22L	ENSP00000221855:F22L	F	+	3	2	TBCB	41298368	1.000000	0.71417	0.999000	0.59377	0.866000	0.49608	1.041000	0.30291	0.088000	0.17205	0.484000	0.47621	TTC	.	.	.	none		0.667	TBCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156291.2	NM_001281		G	36606528	C	G	36606528	3	3	48	1	0	0	0	0	1	0	0	0	15642	854	30	4	68	4	TBCB	19	36606528	Missense_Mutation	SNP	C	TCGA-A4-7734-01A-11D-2136-08	27542209	36606528	22522455	45	3352											
CIC	23152	hgsc.bcm.edu	37	chr19	42795453	42795453	+	Missense_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	tggcacctgccccagcaccaGcccctgggaccaaggcagcg	8	3	12	18	1	0	0	0	0	0	0	0	1	0	1	7	3	4	3	7	3	1	0			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr19:42795453G>A	ENST00000575354.2	+	10	2573	c.2533G>A	c.(2533-2535)Gcc>Acc	p.A845T	CIC_ENST00000572681.2_Missense_Mutation_p.A1754T|CIC_ENST00000160740.3_Missense_Mutation_p.A845T	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	845	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)				CCCAGCACCAGCCCCTGGGAC	0.677			"Mis, F, S"		oligodendroglioma																																p.A845T		Atlas-SNP	.		Rec	yes		19	19q13.2	23152	capicua homolog		O	.	CIC	249	.	0			c.G2533A						PASS	.						16	17	17					19																	42795453		2165	4211	6376	SO:0001583	missense	23152	exon10			GCACCAGCCCCTG	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.2533G>A	chr19.hg19:g.42795453G>A	ENSP00000458663:p.Ala845Thr	64.0	0.0	.		45.0	19.0	.	NM_015125	Q7LGI1|Q9UEG5|Q9Y6T1	Missense_Mutation	SNP	ENST00000575354.2	hg19	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	G	14.48	2.547541	0.45383	.	.	ENSG00000079432	ENST00000160740	.	.	.	4.44	1.07	0.20283	.	.	.	.	.	T	0.20901	0.0503	N	0.08118	0	0.30059	N	0.811071	B	0.11235	0.004	B	0.04013	0.001	T	0.17319	-1.0373	8	0.87932	D	0	-7.4144	5.5731	0.17208	0.1937:0.1695:0.6368:0.0	.	845	Q96RK0	CIC_HUMAN	T	845	.	ENSP00000160740:A845T	A	+	1	0	CIC	47487293	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.094000	0.41719	0.553000	0.29044	0.561000	0.74099	GCC	.	.	.	none		0.677	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			A	42795453	G	A	42795453	3	1	48	1	0	0	0	0	1	0	0	0	3426	971	34	2	2571	2	CIC	19	42795453	Missense_Mutation	SNP	G	TCGA-A4-7734-01A-11D-2136-08	6188925	42795453	16333530	46	3353											
TUBB1	81027	hgsc.bcm.edu	37	chr20	57597910	57597910	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctttcagttctgggagaTgattggtgaggaacacggga	9	11	15	6	1	2	3	1	2	1	1	2	6	2	5	0	4	2	2	0	4	1	3	rs374942824		TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr20:57597910T>C	ENST00000217133.1	+	2	337	c.68T>C	c.(67-69)aTg>aCg	p.M23T		NM_030773.3	NP_110400.1	Q9H4B7	TBB1_HUMAN	tubulin, beta 1 class VI	23					'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)	TTCTGGGAGATGATTGGTGAG	0.547																																					p.M23T		Atlas-SNP	.											.	TUBB1	42	.	0			c.T68C						PASS	.	T	THR/MET	1,4405	2.1+/-5.4	0,1,2202	67	63	65		68	4.4	1	20		65	0,8600		0,0,4300	no	missense	TUBB1	NM_030773.3	81	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign	23/452	57597910	1,13005	2203	4300	6503	SO:0001583	missense	81027	exon2			GGGAGATGATTGG	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.68T>C	chr20.hg19:g.57597910T>C	ENSP00000217133:p.Met23Thr	82.0	0.0	.		88.0	51.0	.	NM_030773		Missense_Mutation	SNP	ENST00000217133.1	hg19	CCDS13475.1	.	.	.	.	.	.	.	.	.	.	T	12.98	2.099754	0.37048	2.27E-4	0.0	ENSG00000101162	ENST00000217133	T	0.68903	-0.36	4.36	4.36	0.52297	Tubulin/FtsZ, GTPase domain (3);	0.121035	0.56097	D	0.000037	T	0.31888	0.0811	N	0.00277	-1.72	0.37932	D	0.932041	B	0.02656	0.0	B	0.04013	0.001	T	0.41413	-0.9510	10	0.87932	D	0	.	13.0037	0.58692	0.0:0.0:0.0:1.0	.	23	Q9H4B7	TBB1_HUMAN	T	23	ENSP00000217133:M23T	ENSP00000217133:M23T	M	+	2	0	TUBB1	57031305	1.000000	0.71417	0.989000	0.46669	0.464000	0.32679	7.967000	0.87967	1.727000	0.51537	0.528000	0.53228	ATG	.	.	.	weak		0.547	TUBB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079903.1	NM_030773		C	57597910	T	C	57597910	3	2	48	1	0	0	0	0	1	0	0	0	16765	1464	51	3	74	3	TUBB1	20	57597910	Missense_Mutation	SNP	T	TCGA-A4-7734-01A-11D-2136-08		57597910	5427610	47	3354											
SON	6651	hgsc.bcm.edu	37	chr21	34927198	34927198	+	Frame_Shift_Del	DEL	A	A	-																															agaggaagaagatctgtatcAaaagagaagcgcaaaagatc																										TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr21:34927198delA	ENST00000356577.4	+	3	6136	c.5661delA	c.(5659-5661)tcafs	p.S1887fs	SON_ENST00000290239.6_Frame_Shift_Del_p.S1887fs|SON_ENST00000381692.2_Intron|SON_ENST00000381679.4_Frame_Shift_Del_p.S1887fs|SON_ENST00000300278.4_Frame_Shift_Del_p.S1887fs	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	1887					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						GATCTGTATCAAAAGAGAAGC	0.453																																					p.S1887X		Atlas-INDEL	.											.	SON	343	.	0			c.5660delC						PASS	.						52	50	51					21																	34927198		2203	4300	6503	SO:0001589	frameshift_variant	6651	exon3			.	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.5661delA	chr21.hg19:g.34927198delA	ENSP00000348984:p.Ser1887fs	38.0	0.0	0		42.0	15.0	0.357143	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Frame_Shift_Del	DEL	ENST00000356577.4	hg19	CCDS13629.1																																																																																			.	.	.	none		0.453	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		-	34927198	A	-	34927198	7	5	48	1	0	1	0	1	0	0	0	0	14939	117	5	0	5671	0	SON	21	34927198	Frame_Shift_Del	DEL	A	TCGA-A4-7734-01A-11D-2136-08		34927198	13202697	48	3355											
SLC37A1	54020	hgsc.bcm.edu	37	chr21	43963563	43963563	+	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	caggagaggtttgattatggGggtctggaactcccacacct	9	10	13	9	0	1	2	0	1	1	1	2	4	2	3	2	5	1	1	2	5	2	2			TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chr21:43963563G>A	ENST00000352133.2	+	8	1563	c.581G>A	c.(580-582)gGg>gAg	p.G194E	SLC37A1_ENST00000398341.3_Missense_Mutation_p.G194E			P57057	GLPT_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 1	194					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						TTGATTATGGGGGTCTGGAAC	0.572																																					p.G194E		Atlas-SNP	.											.	SLC37A1	48	.	0			c.G581A						PASS	.						165	155	158					21																	43963563		2203	4300	6503	SO:0001583	missense	54020	exon9			TTATGGGGGTCTG	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.581G>A	chr21.hg19:g.43963563G>A	ENSP00000344648:p.Gly194Glu	320.0	0.0	.		243.0	75.0	.	NM_018964	D3DSJ7|Q9HAQ1	Missense_Mutation	SNP	ENST00000352133.2	hg19	CCDS13689.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.732737	0.89482	.	.	ENSG00000160190	ENST00000398341;ENST00000352133	T;T	0.66099	-0.19;-0.19	4.99	4.99	0.66335	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.177957	0.49916	D	0.000125	D	0.85292	0.5663	H	0.94542	3.55	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89875	0.4026	10	0.87932	D	0	-14.7963	18.3114	0.90201	0.0:0.0:1.0:0.0	.	194	P57057	GLPT_HUMAN	E	194	ENSP00000381383:G194E;ENSP00000344648:G194E	ENSP00000344648:G194E	G	+	2	0	SLC37A1	42836632	1.000000	0.71417	0.995000	0.50966	0.986000	0.74619	9.423000	0.97461	2.324000	0.78689	0.650000	0.86243	GGG	.	.	.	none		0.572	SLC37A1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195377.1			A	43963563	G	A	43963563	3	1	48	1	0	0	0	0	1	0	0	0	14610	1232	43	2	607	2	SLC37A1	21	43963563	Missense_Mutation	SNP	G	TCGA-A4-7734-01A-11D-2136-08	9036365	43963563	4166332	49	3356											
GPR174	84636	hgsc.bcm.edu	37	chrX	78427128	78427128	+	Frame_Shift_Del	DEL	G	G	-																															ctatattgtacctggaagacGgttttatcactgcaagataa																										TCGA-A4-7734-01A-11D-2136-08	TCGA-A4-7734-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	397b1104-cfd3-4d68-9e37-7ce13f64d5ea	9436630f-ab20-427a-9f0d-a8c636844aa8	g.chrX:78427128delG	ENST00000276077.1	+	1	660	c.624delG	c.(622-624)acgfs	p.T208fs		NM_032553.1	NP_115942.1	Q9BXC1	GP174_HUMAN	G protein-coupled receptor 174	208						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	38						CCTGGAAGACGGTTTTATCAC	0.438										HNSCC(63;0.18)																											p.T208fs		Atlas-INDEL	.											.	GPR174	79	.	0			c.623delC						PASS	.						97	93	94					X																	78427128		2203	4300	6503	SO:0001589	frameshift_variant	84636	exon1			.	AF345567	CCDS14443.1	Xq13.3	2012-08-21			ENSG00000147138	ENSG00000147138		"GPCR / Class A : Orphans"	30245	protein-coding gene	gene with protein product		300903					Standard	NM_032553		Approved	FKSG79	uc004edg.1	Q9BXC1	OTTHUMG00000021898	ENST00000276077.1:c.624delG	chrX.hg19:g.78427128delG	ENSP00000276077:p.Thr208fs	101.0	0.0	0		151.0	60.0	0.397351	NM_032553	Q2M3F7	Frame_Shift_Del	DEL	ENST00000276077.1	hg19	CCDS14443.1																																																																																			.	.	.	none		0.438	GPR174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057327.1	NM_032553		-	78427128	G	-	78427128	7	5	48	1	0	1	0	1	0	0	0	0	6679	1103	39	0	626	0	GPR174	23	78427128	Frame_Shift_Del	DEL	G	TCGA-A4-7734-01A-11D-2136-08		78427128	76843432	50	3357											
MTOR	2475	hgsc.bcm.edu	37	chr1	11184573	11184573	+	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	acctgaggtttttccgaagaGatgttgggtcattggccaga	9	12	13	7	1	1	3	1	1	0	2	2	5	2	3	3	3	0	2	3	3	1	4	rs587777894		TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr1:11184573G>T	ENST00000361445.4	-	47	6720	c.6644C>A	c.(6643-6645)tCt>tAt	p.S2215Y	MTOR_ENST00000376838.1_Missense_Mutation_p.S420Y	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	2215	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		S -> Y (in a colorectal adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)	p.S2215Y(4)		breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	TTTCCGAAGAGATGTTGGGTC	0.438																																					p.S2215Y		Atlas-SNP	.											MTOR,NS,malignant_melanoma,0,5	MTOR	327	.	4	Substitution - Missense(4)	large_intestine(2)|kidney(1)|endometrium(1)	c.C6644A						PASS	.						101	98	99					1																	11184573		2203	4300	6503	SO:0001583	missense	2475	exon47			CGAAGAGATGTTG	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"FK506 binding protein 12-rapamycin associated protein 2", "rapamycin target protein", "FKBP12-rapamycin complex-associated protein 1", "FKBP-rapamycin associated protein", "rapamycin associated protein FRAP2", "dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)", "rapamycin and FKBP12 target 1", "mammalian target of rapamycin"	601231	"FK506 binding protein 12-rapamycin associated protein 1"	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.6644C>A	chr1.hg19:g.11184573G>T	ENSP00000354558:p.Ser2215Tyr	83.0	0.0	.		71.0	24.0	.	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	hg19	CCDS127.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.903707	0.92035	.	.	ENSG00000198793	ENST00000361445;ENST00000376838	T;T	0.78364	-1.17;-1.17	5.8	5.8	0.92144	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	D	0.88862	0.6552	M	0.86651	2.83	0.80722	D	1	D	0.58970	0.984	P	0.60541	0.876	D	0.90182	0.4243	10	0.87932	D	0	-14.2436	18.2956	0.90145	0.0:0.0:1.0:0.0	.	2215	P42345	MTOR_HUMAN	Y	2215;420	ENSP00000354558:S2215Y;ENSP00000366034:S420Y	ENSP00000354558:S2215Y	S	-	2	0	MTOR	11107160	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	9.362000	0.97126	2.761000	0.94854	0.650000	0.86243	TCT	.	.	.	none		0.438	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		T	11184573	G	T	11184573	3	4	49	1	0	0	0	0	1	0	0	0	9961	942	33	4	1053	4	MTOR	1	11184573	Missense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08		11184573	238066048	1	3358											
C1orf175	374977	hgsc.bcm.edu	37	chr1	55118778	55118778	+	Missense_Mutation	SNP	A	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	tggcttggctctcgttccagAtcttaatgattctttgagtc	6	17	9	9	1	3	3	0	2	3	1	6	3	4	3	1	2	0	3	1	2	1	5			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr1:55118778A>C	ENST00000421030.2	+	3	464	c.179A>C	c.(178-180)gAt>gCt	p.D60A	MROH7_ENST00000545244.1_Intron|MROH7_ENST00000454855.2_Intron|MROH7-TTC4_ENST00000414150.2_Missense_Mutation_p.D60A|MROH7_ENST00000395690.2_Missense_Mutation_p.D60A|MROH7_ENST00000472987.1_3'UTR|MROH7_ENST00000409996.1_Intron|MROH7_ENST00000339553.5_Missense_Mutation_p.D60A	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	60						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											CTCGTTCCAGATCTTAATGAT	0.567																																					p.D60A		Atlas-SNP	.											.	.	.	.	0			c.A179C						PASS	.						77	78	77					1																	55118778		1918	4127	6045	SO:0001583	missense	374977	exon3			TTCCAGATCTTAA	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.179A>C	chr1.hg19:g.55118778A>C	ENSP00000396622:p.Asp60Ala	144.0	0.0	.		148.0	46.0	.	NM_001039464	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Missense_Mutation	SNP	ENST00000421030.2	hg19	CCDS41342.2	.	.	.	.	.	.	.	.	.	.	A	6.762	0.509542	0.12883	.	.	ENSG00000184313	ENST00000421030;ENST00000414867;ENST00000339553;ENST00000395690	T;T;T	0.02974	4.62;4.09;4.11	3.58	1.19	0.21007	.	.	.	.	.	T	0.02012	0.0063	N	0.17082	0.46	0.09310	N	0.999998	B;B;P	0.46142	0.154;0.015;0.873	B;B;B	0.42495	0.053;0.018;0.389	T	0.47724	-0.9095	9	0.33141	T	0.24	.	3.5678	0.07907	0.6251:0.247:0.1279:0.0	.	60;60;60	F8W8P2;Q68CQ1;Q68CQ1-4	.;HEAT8_HUMAN;.	A	60	ENSP00000396622:D60A;ENSP00000343211:D60A;ENSP00000379044:D60A	ENSP00000343211:D60A	D	+	2	0	HEATR8	54891366	0.027000	0.19231	0.058000	0.19502	0.109000	0.19521	0.013000	0.13310	0.238000	0.21222	0.459000	0.35465	GAT	.	.	.	none		0.567	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547		C	55118778	A	C	55118778	3	2	49	1	0	0	0	0	1	0	0	0	2018	333	12	5	181	5	C1orf175	1	55118778	Missense_Mutation	SNP	A	TCGA-A4-7828-01A-11D-2136-08	43934205	55118778	194131843	2	3359											
TRIM33	51592	hgsc.bcm.edu	37	chr1	114948195	114948195	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tccaatccttgccgacctgtGcatgaggcttcgaattgggg	7	11	12	11	2	0	1	0	1	0	0	3	3	2	1	4	3	2	2	4	3	2	3			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr1:114948195G>A	ENST00000358465.2	-	15	2688	c.2605C>T	c.(2605-2607)Cac>Tac	p.H869Y	TRIM33_ENST00000476908.1_5'UTR|TRIM33_ENST00000450349.2_Missense_Mutation_p.H501Y|TRIM33_ENST00000369543.2_Missense_Mutation_p.H869Y	NM_015906.3	NP_056990.3	Q9UPN9	TRI33_HUMAN	tripartite motif containing 33	869					gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	48	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GCCGACCTGTGCATGAGGCTT	0.468			T	RET	papillary thyroid																																p.H869Y		Atlas-SNP	.		Dom	yes		1	1p13	51592	" tripartite motif-containing 33 (PTC7,TIF1G)"		E	TRIM33,NS,carcinoma,0,1	TRIM33	115	.	0			c.C2605T						PASS	.						218	196	203					1																	114948195		2203	4300	6503	SO:0001583	missense	51592	exon15			ACCTGTGCATGAG	AF220136	CCDS872.1, CCDS873.1	1p13.1	2014-02-17	2011-01-25		ENSG00000197323	ENSG00000197323		"Tripartite motif containing / Tripartite motif containing", "Zinc fingers, PHD-type", "RING-type (C3HC4) zinc fingers"	16290	protein-coding gene	gene with protein product	"transcriptional intermediary factor 1 gamma", "ret-fused gene 7"	605769	"tripartite motif-containing 33"			11331580, 10022127	Standard	XM_005270936		Approved	TIF1GAMMA, FLJ11429, KIAA1113, TIFGAMMA, RFG7, TF1G, TIF1G, PTC7	uc001eew.3	Q9UPN9	OTTHUMG00000011891	ENST00000358465.2:c.2605C>T	chr1.hg19:g.114948195G>A	ENSP00000351250:p.His869Tyr	243.0	0.0	.		243.0	65.0	.	NM_033020	O95855|Q5TG72|Q5TG73|Q5TG74|Q9C017|Q9UJ79	Missense_Mutation	SNP	ENST00000358465.2	hg19	CCDS872.1	.	.	.	.	.	.	.	.	.	.	G	19.80	3.895312	0.72639	.	.	ENSG00000197323	ENST00000358465;ENST00000369543;ENST00000450349	T;T;T	0.75589	-0.81;-0.71;-0.95	5.29	5.29	0.74685	Zinc finger, FYVE/PHD-type (1);	0.224309	0.50627	D	0.000108	T	0.66944	0.2841	N	0.19112	0.55	0.53688	D	0.999974	D;D;P;P;P	0.54601	0.967;0.957;0.952;0.952;0.92	P;B;B;P;B	0.53102	0.718;0.402;0.446;0.548;0.346	T	0.72261	-0.4345	10	0.59425	D	0.04	-10.5094	19.2948	0.94118	0.0:0.0:1.0:0.0	.	501;501;64;869;869	E7EN20;B3KN30;Q9HAL0;Q9UPN9-2;Q9UPN9	.;.;.;.;TRI33_HUMAN	Y	869;869;501	ENSP00000351250:H869Y;ENSP00000358556:H869Y;ENSP00000412077:H501Y	ENSP00000351250:H869Y	H	-	1	0	TRIM33	114749718	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	6.388000	0.73195	2.636000	0.89361	0.491000	0.48974	CAC	.	.	.	none		0.468	TRIM33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032854.1	NM_015906		A	114948195	G	A	114948195	3	1	49	1	0	0	0	0	1	0	0	0	16519	1319	46	2	802	2	TRIM33	1	114948195	Missense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08	59829417	114948195	134302426	3	3360											
ADAMTSL4	54507	hgsc.bcm.edu	37	chr1	150525534	150525534	+	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	ccctacagtgcagctccaccCgagtctgcccctccctcccc	5	7	6	23	1	1	0	0	0	1	0	4	1	4	0	8	0	4	2	8	0	1	1	rs146377111		TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr1:150525534C>A	ENST00000369038.2	+	3	440	c.239C>A	c.(238-240)cCg>cAg	p.P80Q	MIR4257_ENST00000581735.1_RNA|ADAMTSL4_ENST00000271643.4_Missense_Mutation_p.P80Q|ADAMTSL4_ENST00000369041.5_Missense_Mutation_p.P80Q|ADAMTSL4_ENST00000369039.5_Missense_Mutation_p.P80Q|RP11-54A4.2_ENST00000442435.2_RNA			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	80	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|positive regulation of apoptotic process (GO:0043065)	interstitial matrix (GO:0005614)	metalloendopeptidase activity (GO:0004222)|protease binding (GO:0002020)			breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			CAGCTCCACCCGAGTCTGCCC	0.692																																					p.P80Q		Atlas-SNP	.											ADAMTSL4,NS,carcinoma,0,2	ADAMTSL4	101	.	0			c.C239A						PASS	.						23	26	25					1																	150525534		2202	4295	6497	SO:0001583	missense	54507	exon5			TCCACCCGAGTCT	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.239C>A	chr1.hg19:g.150525534C>A	ENSP00000358034:p.Pro80Gln	64.0	0.0	.		71.0	3.0	.	NM_019032	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Missense_Mutation	SNP	ENST00000369038.2	hg19	CCDS955.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.732956	0.00687	.	.	ENSG00000143382	ENST00000369041;ENST00000271643;ENST00000369039;ENST00000369038	T;T;T;T	0.65549	-0.05;-0.16;0.15;-0.16	4.35	-7.79	0.01218	.	.	.	.	.	T	0.08714	0.0216	N	0.03608	-0.345	0.09310	N	1	B;B;B;B	0.15473	0.001;0.002;0.003;0.013	B;B;B;B	0.12837	0.003;0.005;0.006;0.008	T	0.15925	-1.0420	9	0.21540	T	0.41	.	0.0314	0.00006	0.3189:0.1828:0.2132:0.2851	.	80;80;80;80	B7ZMJ3;F8WAD0;Q6UY14;Q6UY14-2	.;.;ATL4_HUMAN;.	Q	80	ENSP00000358037:P80Q;ENSP00000271643:P80Q;ENSP00000358035:P80Q;ENSP00000358034:P80Q	ENSP00000271643:P80Q	P	+	2	0	ADAMTSL4	148792158	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.846000	0.04336	-1.557000	0.01692	-2.375000	0.00234	CCG	.	C|1.000;T|0.000	.	alt		0.692	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032		A	150525534	C	A	150525534	3	1	49	1	0	0	0	0	1	0	0	0	277	652	23	4	249	4	ADAMTSL4	1	150525534	Missense_Mutation	SNP	C	TCGA-A4-7828-01A-11D-2136-08	35577339	150525534	98725087	4	3361											
APOB	338	hgsc.bcm.edu	37	chr2	21224920	21224921	+	Frame_Shift_Ins	INS	-	-	G																															tctctttcccttttccatctINSggatcggtaaggatgctaag																										TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr2:21224920_21224921insG	ENST00000233242.1	-	29	13500_13501	c.13373_13374insC	c.(13372-13374)ccafs	p.P4458fs	RP11-116D2.1_ENST00000567376.2_lincRNA	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	4458					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)					CTTTTCCATCTGGATCGGTAAG	0.396																																					p.P4458fs		Atlas-INDEL	.											.	APOB	761	.	0			c.13374_13375insC						PASS	.																																			SO:0001589	frameshift_variant	338	exon29			.	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"Apolipoproteins"	603	protein-coding gene	gene with protein product		107730	"apolipoprotein B (including Ag(x) antigen)"				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.13374dupC	chr2.hg19:g.21224922_21224922dupG	ENSP00000233242:p.Pro4458fs	87.0	0.0	0		117.0	33.0	0.282051	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Ins	INS	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.	.	none		0.396	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			G	21224921	-	G	21224920	7	5	49	1	0	1	1	0	0	0	0	0	785	1567	55	0	321	0	APOB	2	21224920	Frame_Shift_Ins	INS	-	TCGA-A4-7828-01A-11D-2136-08		21224920	221974453	5	3362											
DHRS9	10170	hgsc.bcm.edu	37	chr2	169938176	169938176	+	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	taaagattgaagacatcactGataagtacatttttatcact	16	14	5	6	0	2	4	2	2	0	2	2	4	2	4	0	0	1	1	0	0	6	7			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr2:169938176G>A	ENST00000327239.4	+	5	1589	c.85G>A	c.(85-87)Gat>Aat	p.D29N	DHRS9_ENST00000432060.2_Missense_Mutation_p.D89N|DHRS9_ENST00000357546.2_Missense_Mutation_p.D29N|DHRS9_ENST00000412271.1_Missense_Mutation_p.D29N|DHRS9_ENST00000428522.1_Missense_Mutation_p.D29N|DHRS9_ENST00000421653.1_5'UTR|DHRS9_ENST00000602501.1_Missense_Mutation_p.D29N|DHRS9_ENST00000436483.2_Missense_Mutation_p.D29N	NM_005771.4	NP_005762.2	Q9BPW9	DHRS9_HUMAN	dehydrogenase/reductase (SDR family) member 9	29					9-cis-retinoic acid biosynthetic process (GO:0042904)|androgen metabolic process (GO:0008209)|epithelial cell differentiation (GO:0030855)|progesterone metabolic process (GO:0042448)|retinol metabolic process (GO:0042572)	integral component of endoplasmic reticulum membrane (GO:0030176)	alcohol dehydrogenase (NAD) activity (GO:0004022)|racemase and epimerase activity (GO:0016854)|retinol dehydrogenase activity (GO:0004745)|testosterone dehydrogenase (NAD+) activity (GO:0047035)			breast(1)|endometrium(3)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	13						AGACATCACTGATAAGTACAT	0.428																																					p.D29N		Atlas-SNP	.											.	DHRS9	29	.	0			c.G85A						PASS	.						118	117	117					2																	169938176		2203	4300	6503	SO:0001583	missense	10170	exon5			ATCACTGATAAGT	AF067174	CCDS2231.1, CCDS74600.1	2q31.1	2011-09-14			ENSG00000073737	ENSG00000073737		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	16888	protein-coding gene	gene with protein product	"NADP-dependent retinol dehydrogenase/reductase", "3-alpha hydroxysteroid dehydrogenase", "retinol dehydrogenase homolog", "short chain dehydrogenase/reductase family 9C, member 4"	612131				11304534, 11294878, 19027726	Standard	NM_001142270		Approved	RDHL, 3alpha-HSD, RETSDR8, RDH15, SDR9C4	uc010zde.2	Q9BPW9	OTTHUMG00000132180	ENST00000327239.4:c.85G>A	chr2.hg19:g.169938176G>A	ENSP00000316670:p.Asp29Asn	121.0	0.0	.		134.0	7.0	.	NM_005771	B7Z416|D3DPC1|Q5RKX1|Q9NRA9|Q9NRB0	Missense_Mutation	SNP	ENST00000327239.4	hg19	CCDS2231.1	.	.	.	.	.	.	.	.	.	.	G	16.35	3.099956	0.56183	.	.	ENSG00000073737	ENST00000327239;ENST00000357546;ENST00000432060;ENST00000428522;ENST00000450153;ENST00000436483;ENST00000412271	D;D;D;D;T;D;D	0.89552	-2.53;-2.53;-2.53;-2.53;0.73;-2.53;-2.53	5.88	2.98	0.34508	NAD(P)-binding domain (1);	0.501056	0.24625	N	0.036936	T	0.77624	0.4158	N	0.11756	0.17	0.34824	D	0.738968	B;B	0.17268	0.021;0.013	B;B	0.19666	0.026;0.018	T	0.73550	-0.3947	10	0.30854	T	0.27	.	10.261	0.43427	0.228:0.0:0.772:0.0	.	89;29	B7Z416;Q9BPW9	.;DHRS9_HUMAN	N	29;29;89;29;29;29;29	ENSP00000316670:D29N;ENSP00000350154:D29N;ENSP00000389241:D89N;ENSP00000388564:D29N;ENSP00000391214:D29N;ENSP00000407167:D29N;ENSP00000407747:D29N	ENSP00000316670:D29N	D	+	1	0	DHRS9	169646422	0.316000	0.24580	0.753000	0.31225	0.908000	0.53690	0.839000	0.27586	0.752000	0.32923	0.655000	0.94253	GAT	.	.	.	none		0.428	DHRS9-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333612.3	NM_005771		A	169938176	G	A	169938176	3	1	49	1	0	0	0	0	1	0	0	0	4500	1290	45	2	87	2	DHRS9	2	169938176	Missense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08	148713256	169938176	73261197	6	3363											
ICA1L	130026	hgsc.bcm.edu	37	chr2	203680713	203680713	+	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	tcattcgagctgttttcttcCagaatccaagcagtgttctc	8	15	7	11	1	3	1	1	0	2	1	7	2	5	1	2	0	2	4	2	0	2	5			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr2:203680713C>A	ENST00000392237.2	-	8	861	c.704G>T	c.(703-705)tGg>tTg	p.W235L	ICA1L_ENST00000358299.2_Missense_Mutation_p.W235L	NM_138468.4	NP_612477.3	Q8NDH6	ICA1L_HUMAN	islet cell autoantigen 1,69kDa-like	235	AH. {ECO:0000255|PROSITE- ProRule:PRU00294}.									breast(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TGTTTTCTTCCAGAATCCAAG	0.388																																					p.W235L		Atlas-SNP	.											.	ICA1L	33	.	0			c.G704T						PASS	.						100	97	98					2																	203680713		2203	4300	6503	SO:0001583	missense	130026	exon8			TTCTTCCAGAATC	AB053317	CCDS2354.1, CCDS74632.1	2q33	2008-02-05	2006-05-26	2006-05-26	ENSG00000163596	ENSG00000163596			14442	protein-coding gene	gene with protein product			"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 15", "amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 14"	ALS2CR15, ALS2CR14		11586298	Standard	NM_138468		Approved		uc002uzh.1	Q8NDH6	OTTHUMG00000132856	ENST00000392237.2:c.704G>T	chr2.hg19:g.203680713C>A	ENSP00000376070:p.Trp235Leu	59.0	0.0	.		84.0	4.0	.	NM_138468	B3KRW6|Q53P45|Q53QZ4|Q53T97|Q96N47|Q96Q32|Q9BVQ2	Missense_Mutation	SNP	ENST00000392237.2	hg19	CCDS2354.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.293325	0.80914	.	.	ENSG00000163596	ENST00000392237;ENST00000358299	T;T	0.76186	-1.0;-1.0	5.77	4.87	0.63330	Arfaptin-like (3);	0.058720	0.64402	N	0.000001	T	0.79143	0.4396	M	0.65975	2.015	0.80722	D	1	P	0.45011	0.848	P	0.50825	0.651	T	0.78575	-0.2151	10	0.39692	T	0.17	.	13.7616	0.62971	0.1549:0.8451:0.0:0.0	.	235	Q8NDH6	ICA1L_HUMAN	L	235	ENSP00000376070:W235L;ENSP00000351047:W235L	ENSP00000351047:W235L	W	-	2	0	ICA1L	203388958	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.358000	0.66064	1.399000	0.46721	0.655000	0.94253	TGG	.	.	.	none		0.388	ICA1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256330.1	NM_138468		A	203680713	C	A	203680713	3	1	49	1	0	0	0	0	1	0	0	0	7485	595	21	4	772	4	ICA1L	2	203680713	Missense_Mutation	SNP	C	TCGA-A4-7828-01A-11D-2136-08	33742537	203680713	39518660	7	3364											
CLCN2	1181	hgsc.bcm.edu	37	chr3	184075764	184075764	+	Missense_Mutation	SNP	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	agttacctctttgccaagcgGcatcccgctgcctagggcgc	6	9	11	15	3	1	0	0	0	1	0	2	0	2	0	4	2	4	3	4	2	3	3			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr3:184075764G>A	ENST00000265593.4	-	5	772	c.601C>T	c.(601-603)Ccg>Tcg	p.P201S	CLCN2_ENST00000344937.7_Missense_Mutation_p.P201S|CLCN2_ENST00000423355.2_5'UTR|CLCN2_ENST00000457512.1_Missense_Mutation_p.P201S|EIF2B5_ENST00000444495.1_Intron|CLCN2_ENST00000434054.2_Missense_Mutation_p.P157S|CLCN2_ENST00000475279.1_5'Flank	NM_004366.5	NP_004357.3	P51788	CLCN2_HUMAN	chloride channel, voltage-sensitive 2	201					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)	TTGCCAAGCGGCATCCCGCTG	0.597																																					p.P201S		Atlas-SNP	.											.	CLCN2	74	.	0			c.C601T						PASS	.						57	55	56					3																	184075764		2203	4300	6503	SO:0001583	missense	1181	exon5			CAAGCGGCATCCC	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.601C>T	chr3.hg19:g.184075764G>A	ENSP00000265593:p.Pro201Ser	119.0	0.0	.		100.0	5.0	.	NM_001171087	B4DQT9|B4DZ58|E9PBD9|E9PCD2|O14864|Q6IPA9|Q8WU13	Missense_Mutation	SNP	ENST00000265593.4	hg19	CCDS3263.1	.	.	.	.	.	.	.	.	.	.	g	21.3	4.123267	0.77436	.	.	ENSG00000114859	ENST00000265593;ENST00000344937;ENST00000434054;ENST00000457512	D;D;D;D	0.91577	-2.87;-2.87;-2.87;-2.87	4.58	4.58	0.56647	Chloride channel, core (2);	0.000000	0.85682	D	0.000000	D	0.92450	0.7603	L	0.31926	0.97	0.80722	D	1	D;D;P;D;D	0.89917	0.999;1.0;0.915;0.976;0.992	D;D;P;P;D	0.97110	0.994;1.0;0.851;0.9;0.932	D	0.93567	0.6900	10	0.87932	D	0	-17.2281	16.3077	0.82855	0.0:0.0:1.0:0.0	.	201;157;201;201;201	B4DYE3;E9PBD9;E9PCD2;P51788-3;P51788	.;.;.;.;CLCN2_HUMAN	S	201;201;157;201	ENSP00000265593:P201S;ENSP00000345056:P201S;ENSP00000400425:P157S;ENSP00000391928:P201S	ENSP00000265593:P201S	P	-	1	0	CLCN2	185558458	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	9.595000	0.98260	2.378000	0.81104	0.561000	0.74099	CCG	.	.	.	none		0.597	CLCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345571.1			A	184075764	G	A	184075764	3	1	49	1	0	0	0	0	1	0	0	0	3465	1203	42	2	2175	2	CLCN2	3	184075764	Missense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08		184075764	13946666	8	3365											
POLR2B	5431	hgsc.bcm.edu	37	chr4	57888371	57888373	+	In_Frame_Del	DEL	AAG	AAG	-																															gtctaaaaaaggatttgatcAagaagaagtttttgagaagc																										TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr4:57888371_57888373delAAG	ENST00000381227.1	+	19	2887_2889	c.2474_2476delAAG	c.(2473-2478)caagaa>caa	p.E827del	POLR2B_ENST00000431623.2_In_Frame_Del_p.E752del|POLR2B_ENST00000314595.5_In_Frame_Del_p.E827del|POLR2B_ENST00000441246.2_In_Frame_Del_p.E820del			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	827					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					GGATTTGATCAAGAAGAAGTTTT	0.34																																					p.825_825del		Atlas-INDEL	.											.	POLR2B	108	.	0			c.2473_2475del						PASS	.																																			SO:0001651	inframe_deletion	5431	exon18			.		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.2474_2476delAAG	chr4.hg19:g.57888377_57888379delAAG	ENSP00000370625:p.Glu827del	62.0	0.0	0		81.0	13.0	0.160494	NM_000938	A8K1A8|Q8IZ61	In_Frame_Del	DEL	ENST00000381227.1	hg19	CCDS3511.1																																																																																			.	.	.	none		0.34	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938		-	57888373	AAG	-	57888371	7	5	49	1	0	1	0	1	0	0	0	0	12222	130	5	0	2544	0	POLR2B	4	57888371	In_Frame_Del	DEL	AAG	TCGA-A4-7828-01A-11D-2136-08		57888371	133265905	9	3366											
ITGA2	3673	hgsc.bcm.edu	37	chr5	52366069	52366069	+	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	aatcaagcacagagttgcccCgagcacatcatttatataca	15	9	6	11	1	2	1	2	0	0	1	2	2	2	1	2	0	4	3	2	0	5	5	rs142557473		TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr5:52366069C>G	ENST00000296585.5	+	17	2357	c.2214C>G	c.(2212-2214)ccC>ccG	p.P738P		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	738					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)				AGAGTTGCCCCGAGCACATCA	0.398																																					p.P738P		Atlas-SNP	.											.	ITGA2	211	.	0			c.C2214G						PASS	.						72	71	71					5																	52366069		2203	4300	6503	SO:0001819	synonymous_variant	3673	exon17			TTGCCCCGAGCAC		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.2214C>G	chr5.hg19:g.52366069C>G		57.0	0.0	.		114.0	34.0	.	NM_002203	Q14595	Silent	SNP	ENST00000296585.5	hg19	CCDS3957.1																																																																																			.	C|1.000;T|0.000	.	alt		0.398	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203		G	52366069	C	G	52366069	2	3	49	1	0	0	0	0	0	0	0	1	7882	639	23	4		4	ITGA2	5	52366069	Silent	SNP	C	TCGA-A4-7828-01A-11D-2136-08		52366069	128549191	10	3367											
CMYA5	202333	hgsc.bcm.edu	37	chr5	79034426	79034426	+	Frame_Shift_Del	DEL	G	G	-																															accaaccgatagctgcagaaGgggaaatttggggaaagttt																										TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr5:79034426delG	ENST00000446378.2	+	2	9869	c.9838delG	c.(9838-9840)gggfs	p.G3280fs		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	3280					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)		AGCTGCAGAAGGGGAAATTTG	0.453																																					p.E3279fs		Atlas-INDEL	.											.	CMYA5	643	.	0			c.9837delA						PASS	.						104	100	101					5																	79034426		1865	4114	5979	SO:0001589	frameshift_variant	202333	exon2			.	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"Tripartite motif containing / Tripartite motif containing", "A-kinase anchor proteins", "Fibronectin type III domain containing"	14305	protein-coding gene	gene with protein product	"genethonin-3", "tripartite motif-containing 76"	612193	"chromosome 5 open reading frame 10"	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.9838delG	chr5.hg19:g.79034426delG	ENSP00000394770:p.Gly3280fs	110.0	0.0	0		144.0	25.0	0.173611	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Frame_Shift_Del	DEL	ENST00000446378.2	hg19	CCDS47238.1																																																																																			.	.	.	none		0.453	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		-	79034426	G	-	79034426	7	5	49	1	0	1	0	1	0	0	0	0	3592	1000	35	0	9844	0	CMYA5	5	79034426	Frame_Shift_Del	DEL	G	TCGA-A4-7828-01A-11D-2136-08	26668357	79034426	101880834	11	3368											
PCDHAC1	56135	hgsc.bcm.edu	37	chr5	140307713	140307713	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagcagatcagtgaataccaAgtcctgatcacggcctcaga	13	7	10	11	1	3	4	3	2	0	2	4	5	4	4	3	1	2	1	3	1	3	1			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr5:140307713A>G	ENST00000253807.2	+	1	1236	c.1236A>G	c.(1234-1236)caA>caG	p.Q412Q	PCDHA1_ENST00000394633.3_Intron|PCDHAC1_ENST00000409700.3_Silent_p.Q412Q|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	412	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|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)			GTGAATACCAAGTCCTGATCA	0.517																																					p.Q412Q		Atlas-SNP	.											.	PCDHAC1	141	.	0			c.A1236G						PASS	.						81	79	80					5																	140307713		2203	4300	6503	SO:0001819	synonymous_variant	56135	exon1			ATACCAAGTCCTG	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.1236A>G	chr5.hg19:g.140307713A>G		90.0	0.0	.		99.0	22.0	.	NM_031882	Q9Y5F5|Q9Y5I5	Silent	SNP	ENST00000253807.2	hg19	CCDS4241.1																																																																																			.	.	.	none		0.517	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898		G	140307713	A	G	140307713	2	3	49	1	0	0	0	0	0	0	0	1	11539	69	3	3		3	PCDHAC1	5	140307713	Silent	SNP	A	TCGA-A4-7828-01A-11D-2136-08	61273287	140307713	40607547	12	3369											
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47944905	47944905	+	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	tgtggcaaacacagttccatTtgtgtagacagagacggctg	11	10	12	8	1	0	2	0	0	0	2	1	3	1	2	1	2	1	4	1	2	2	3			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr7:47944905T>A	ENST00000289672.2	-	11	1590	c.1540A>T	c.(1540-1542)Aat>Tat	p.N514Y		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	514	PKD 1. {ECO:0000255|PROSITE- ProRule:PRU00151}.				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						ACAGTTCCATTTGTGTAGACA	0.443																																					p.N514Y		Atlas-SNP	.											.	PKD1L1	328	.	0			c.A1540T						PASS	.						139	128	132					7																	47944905		2203	4300	6503	SO:0001583	missense	168507	exon11			TTCCATTTGTGTA	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.1540A>T	chr7.hg19:g.47944905T>A	ENSP00000289672:p.Asn514Tyr	221.0	0.0	.		174.0	37.0	.	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	hg19	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	T	17.97	3.518459	0.64634	.	.	ENSG00000158683	ENST00000289672	T	0.69435	-0.4	5.38	5.38	0.77491	PKD/Chitinase domain (1);	0.178382	0.36519	N	0.002559	T	0.72260	0.3438	L	0.29908	0.895	0.32501	N	0.53884	D	0.89917	1.0	D	0.75484	0.986	T	0.78435	-0.2205	10	0.59425	D	0.04	-24.3676	13.6779	0.62465	0.0:0.0:0.0:1.0	.	514	Q8TDX9	PK1L1_HUMAN	Y	514	ENSP00000289672:N514Y	ENSP00000289672:N514Y	N	-	1	0	PKD1L1	47911430	0.998000	0.40836	0.991000	0.47740	0.970000	0.65996	2.029000	0.41098	2.185000	0.69588	0.529000	0.55759	AAT	.	.	.	none		0.443	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		A	47944905	T	A	47944905	3	1	49	1	0	0	0	0	1	0	0	0	11971	1841	64	5	7197	5	PKD1L1	7	47944905	Missense_Mutation	SNP	T	TCGA-A4-7828-01A-11D-2136-08		47944905	111193758	13	3370											
ZKSCAN5	23660	hgsc.bcm.edu	37	chr7	99129235	99129235	+	Missense_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	tcagcatcagagcgtgcacaGtggggagagacccttcaagt	11	7	13	10	1	3	2	3	0	0	2	3	4	3	3	1	2	3	2	1	2	1	1			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr7:99129235G>A	ENST00000394170.2	+	7	2134	c.1883G>A	c.(1882-1884)aGt>aAt	p.S628N	ZKSCAN5_ENST00000326775.5_Missense_Mutation_p.S628N|ZKSCAN5_ENST00000451158.1_Missense_Mutation_p.S628N	NM_014569.3	NP_055384.1	Q9Y2L8	ZKSC5_HUMAN	zinc finger with KRAB and SCAN domains 5	628					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)					AGCGTGCACAGTGGGGAGAGA	0.557																																					p.S628N		Atlas-SNP	.											.	ZKSCAN5	63	.	0			c.G1883A						PASS	.						80	70	74					7																	99129235		2203	4300	6503	SO:0001583	missense	23660	exon7			TGCACAGTGGGGA	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.1883G>A	chr7.hg19:g.99129235G>A	ENSP00000377725:p.Ser628Asn	84.0	0.0	.		85.0	5.0	.	NM_145102	A4D280|D6W5S9	Missense_Mutation	SNP	ENST00000394170.2	hg19	CCDS5667.1	.	.	.	.	.	.	.	.	.	.	G	19.57	3.852959	0.71719	.	.	ENSG00000196652	ENST00000537357;ENST00000326775;ENST00000451158;ENST00000394170	T;T;T	0.19394	2.15;2.15;2.15	5.23	4.29	0.51040	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.091827	0.48767	D	0.000175	T	0.29389	0.0732	L	0.46885	1.475	0.35690	D	0.814761	P;P	0.49185	0.92;0.92	P;P	0.53313	0.598;0.723	T	0.14090	-1.0485	10	0.52906	T	0.07	.	11.8173	0.52218	0.0:0.2653:0.7347:0.0	.	628;628	Q8N718;Q9Y2L8	.;ZKSC5_HUMAN	N	628	ENSP00000322872:S628N;ENSP00000392104:S628N;ENSP00000377725:S628N	ENSP00000322872:S628N	S	+	2	0	ZKSCAN5	98967171	0.999000	0.42202	0.986000	0.45419	0.987000	0.75469	3.694000	0.54742	2.894000	0.99253	0.591000	0.81541	AGT	.	.	.	none		0.557	ZKSCAN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345597.1	NM_014569		A	99129235	G	A	99129235	3	1	49	1	0	0	0	0	1	0	0	0	17702	1029	36	2	1905	2	ZKSCAN5	7	99129235	Missense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08	51184330	99129235	60009428	14	3371											
VGF	7425	hgsc.bcm.edu	37	chr7	100806695	100806695	+	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	tcttccgcttccgcttctccTccacctcctcgatgatgctg	3	14	6	18	3	2	1	0	1	2	0	8	2	6	1	6	0	1	3	6	0	0	3			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr7:100806695T>A	ENST00000249330.2	-	2	1669	c.1430A>T	c.(1429-1431)gAg>gTg	p.E477V	VGF_ENST00000445482.2_Missense_Mutation_p.E477V	NM_003378.3	NP_003369.2	O15240	VGF_HUMAN	VGF nerve growth factor inducible	477					defense response to bacterium (GO:0042742)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|ovarian follicle development (GO:0001541)|response to cAMP (GO:0051591)|response to cold (GO:0009409)|response to dietary excess (GO:0002021)|response to insulin (GO:0032868)|sexual reproduction (GO:0019953)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)				cervix(1)|large_intestine(1)|lung(4)|prostate(2)|skin(1)	9	Lung NSC(181;0.168)|all_lung(186;0.215)					CCGCTTCTCCTCCACCTCCTC	0.697																																					p.E477V		Atlas-SNP	.											.	VGF	29	.	0			c.A1430T						PASS	.						58	61	60					7																	100806695		2203	4300	6503	SO:0001583	missense	7425	exon2			TTCTCCTCCACCT	Y12661	CCDS5712.1	7q22	2008-07-18			ENSG00000128564	ENSG00000128564			12684	protein-coding gene	gene with protein product	"neuro-endocrine specific protein VGF"	602186				9344675	Standard	NM_003378		Approved		uc003uxx.4	O15240	OTTHUMG00000157109	ENST00000249330.2:c.1430A>T	chr7.hg19:g.100806695T>A	ENSP00000249330:p.Glu477Val	73.0	0.0	.		56.0	15.0	.	NM_003378	Q9UDW8	Missense_Mutation	SNP	ENST00000249330.2	hg19	CCDS5712.1	.	.	.	.	.	.	.	.	.	.	T	17.42	3.386102	0.61956	.	.	ENSG00000128564	ENST00000249330;ENST00000445482	.	.	.	4.41	4.41	0.53225	.	0.000000	0.48286	U	0.000186	T	0.56307	0.1976	N	0.24115	0.695	0.40841	D	0.983675	D	0.76494	0.999	D	0.80764	0.994	T	0.61720	-0.7005	9	0.87932	D	0	-7.6164	10.0532	0.42228	0.0:0.0:0.0:1.0	.	477	O15240	VGF_HUMAN	V	477	.	ENSP00000249330:E477V	E	-	2	0	VGF	100593415	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.280000	0.51677	1.650000	0.50662	0.449000	0.29647	GAG	.	.	.	none		0.697	VGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347462.1	NM_003378		A	100806695	T	A	100806695	3	1	49	1	0	0	0	0	1	0	0	0	17169	1551	54	5	421	5	VGF	7	100806695	Missense_Mutation	SNP	T	TCGA-A4-7828-01A-11D-2136-08	1677460	100806695	58331968	15	3372											
TBXAS1	6916	hgsc.bcm.edu	37	chr7	139719838	139719838	+	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	attttaggtaccgctgcagcTagaatccaaatctgccctag	11	11	8	11	1	1	1	0	0	1	1	2	1	2	1	3	1	4	4	3	1	6	5			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr7:139719838T>C	ENST00000411653.1	+	12	1505	c.1378T>C	c.(1378-1380)Tag>Cag	p.*460Q	TBXAS1_ENST00000425687.1_Missense_Mutation_p.L447P|TBXAS1_ENST00000416849.2_Missense_Mutation_p.L561P|TBXAS1_ENST00000436047.2_Missense_Mutation_p.L515P|TBXAS1_ENST00000336425.5_Missense_Mutation_p.L514P|TBXAS1_ENST00000263552.6_Missense_Mutation_p.L515P|TBXAS1_ENST00000414508.2_Nonstop_Mutation_p.*461Q|TBXAS1_ENST00000448866.1_Missense_Mutation_p.L514P|TBXAS1_ENST00000458722.1_Missense_Mutation_p.L560P			P24557	THAS_HUMAN	thromboxane A synthase 1 (platelet)	0					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)	CCGCTGCAGCTAGAATCCAAA	0.453																																					p.X461Q		Atlas-SNP	.											.	TBXAS1	121	.	0			c.T1381C						PASS	.						86	87	86					7																	139719838		2203	4300	6503	SO:0001578	stop_lost	6916	exon12			TGCAGCTAGAATC	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	ENST00000411653.1:c.1378T>C	chr7.hg19:g.139719838T>C	ENSP00000411326:p.*460Glnext*6	100.0	0.0	.		79.0	4.0	.	NM_030984	B4DJG6|E7EMU9|E7EP08|E7ESB5|O14987|Q16843|Q16844|Q8IUN1|Q96CN2|Q9GZW4|Q9HD77|Q9HD78|Q9HD79|Q9HD80|Q9HD81|Q9HD82|Q9HD83|Q9HD84	Missense_Mutation	SNP	ENST00000411653.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.44|16.44	3.125072|3.125072	0.56721|0.56721	.|.	.|.	ENSG00000059377|ENSG00000059377	ENST00000425687;ENST00000263552;ENST00000336425;ENST00000416849;ENST00000436047;ENST00000448866;ENST00000458722|ENST00000414508;ENST00000411653	T;T;T;T;T;T;T|.	0.68331|.	-0.32;-0.32;-0.32;-0.32;-0.32;-0.32;-0.32|.	5.42|5.42	5.42|5.42	0.78866|0.78866	.|.	0.000000|.	0.64402|.	D|.	0.000002|.	T|.	0.70657|.	0.3249|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D|.	0.97110|.	0.999;1.0;1.0;0.996;0.996|.	T|.	0.69914|.	-0.5016|.	9|.	0.87932|.	D|.	0|.	.|.	14.324|14.324	0.66507|0.66507	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	495;561;447;515;514|.	B4DVP1;E7EP08;E7ESB5;Q53F23;P24557|.	.;.;.;.;THAS_HUMAN|.	P|Q	447;515;514;561;515;514;560|461;460	ENSP00000388736:L447P;ENSP00000263552:L515P;ENSP00000338087:L514P;ENSP00000389414:L561P;ENSP00000392361:L515P;ENSP00000402536:L514P;ENSP00000411274:L560P|.	ENSP00000263552:L515P|.	L|X	+|+	2|1	0|0	TBXAS1|TBXAS1	139366307|139366307	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.872000|0.872000	0.50106|0.50106	5.929000|5.929000	0.70096|0.70096	2.187000|2.187000	0.69744|0.69744	0.459000|0.459000	0.35465|0.35465	CTA|TAG	.	.	.	none		0.453	TBXAS1-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348377.1			C	139719838	T	C	139719838	4	2	49	1	0	0	0	0	0	0	0	0	15676	1535	53	3	1736	3	TBXAS1	7	139719838	Nonstop_Mutation	SNP	T	TCGA-A4-7828-01A-11D-2136-08	38913143	139719838	19418825	16	3373											
CPA6	57094	hgsc.bcm.edu	37	chr8	68397000	68397000	+	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	caacatttttctcatggctgGgtcactcttatatgttagaa	10	16	7	8	0	3	1	2	0	2	1	4	1	3	1	0	2	1	2	0	2	5	5			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr8:68397000G>A	ENST00000297770.4	-	7	876	c.661C>T	c.(661-663)Cca>Tca	p.P221S	CPA6_ENST00000518549.1_Missense_Mutation_p.P221S|CPA6_ENST00000297769.4_Missense_Mutation_p.P73S	NM_020361.4	NP_065094.3	Q8N4T0	CBPA6_HUMAN	carboxypeptidase A6	221						proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(5)	26			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)			CTCATGGCTGGGTCACTCTTA	0.353																																					p.P221S		Atlas-SNP	.											.	CPA6	69	.	0			c.C661T						PASS	.						92	81	84					8																	68397000		2203	4300	6503	SO:0001583	missense	57094	exon7			TGGCTGGGTCACT	AF221594	CCDS6200.1	8q12.3	2012-02-10			ENSG00000165078	ENSG00000165078			17245	protein-coding gene	gene with protein product		609562				11836249	Standard	NM_020361		Approved	CPAH	uc003xxq.4	Q8N4T0	OTTHUMG00000164575	ENST00000297770.4:c.661C>T	chr8.hg19:g.68397000G>A	ENSP00000297770:p.Pro221Ser	74.0	0.0	.		85.0	21.0	.	NM_020361	Q8NEX8|Q8TDE8|Q9NRI9	Missense_Mutation	SNP	ENST00000297770.4	hg19	CCDS6200.1	.	.	.	.	.	.	.	.	.	.	G	11.61	1.689277	0.29962	.	.	ENSG00000165078	ENST00000297769;ENST00000297770;ENST00000518549	T;T;T	0.10860	2.83;2.83;2.83	5.25	4.36	0.52297	Peptidase M14, carboxypeptidase A (2);	0.112178	0.64402	D	0.000006	T	0.08980	0.0222	L	0.28115	0.83	0.44587	D	0.997554	P;P;B	0.48230	0.907;0.537;0.003	B;B;B	0.41691	0.364;0.203;0.013	T	0.26573	-1.0099	10	0.32370	T	0.25	.	13.3643	0.60674	0.0:0.1588:0.8412:0.0	.	221;73;221	Q8N4T0-2;Q8N4T0-3;Q8N4T0	.;.;CBPA6_HUMAN	S	73;221;221	ENSP00000297769:P73S;ENSP00000297770:P221S;ENSP00000431112:P221S	ENSP00000297769:P73S	P	-	1	0	CPA6	68559554	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.498000	0.66931	1.306000	0.44926	0.643000	0.83706	CCA	.	.	.	none		0.353	CPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379296.2	NM_020361		A	68397000	G	A	68397000	3	1	49	1	0	0	0	0	1	0	0	0	3796	1232	43	2	672	2	CPA6	8	68397000	Missense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08		68397000	77967022	17	3374											
HEATR7A	727957	hgsc.bcm.edu	37	chr8	145267981	145267981	+	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	ctgccctgcacgtgctgctcCgcagcctgctgatctaacgg	5	9	11	16	3	1	1	0	1	1	0	2	1	2	1	3	1	7	5	3	1	1	1			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr8:145267981C>T	ENST00000528919.1	+	12	1262				MROH1_ENST00000423230.2_Missense_Mutation_p.P409L|MROH1_ENST00000527071.1_Intron|MROH1_ENST00000534366.1_Intron|MROH1_ENST00000398656.4_Intron|MROH1_ENST00000326134.5_Intron	NM_032450.2	NP_115826	Q8NDA8	MROH1_HUMAN	maestro heat-like repeat family member 1																		CGTGCTGCTCCGCAGCCTGCT	0.557																																					p.P409L		Atlas-SNP	.											.	.	.	.	0			c.C1226T						PASS	.						93	104	100					8																	145267981		2144	4245	6389	SO:0001627	intron_variant	727957	exon13			CTGCTCCGCAGCC		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.1142-7522C>T	chr8.hg19:g.145267981C>T		134.0	0.0	.		118.0	21.0	.	NM_001099280	C9JWM5|D3DWL5|Q0P612|Q569G6|Q6NVW4|Q8N230|Q8NAD1|Q8ND95|Q96JJ4	Missense_Mutation	SNP	ENST00000528919.1	hg19	CCDS47938.1	.	.	.	.	.	.	.	.	.	.	C	2.586	-0.296322	0.05532	.	.	ENSG00000179832	ENST00000423230	T	0.15718	2.4	0.818	-1.64	0.08318	.	.	.	.	.	T	0.06371	0.0164	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40627	-0.9553	8	0.13470	T	0.59	.	1.5793	0.02631	0.3347:0.385:0.0:0.2803	.	409	Q8NDA8-4	.	L	409	ENSP00000388174:P409L	ENSP00000388174:P409L	P	+	2	0	HEATR7A	145339969	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	0.583000	0.23849	-0.788000	0.04504	0.460000	0.39030	CCG	.	.	.	none		0.557	MROH1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386183.1	NM_032450		T	145267981	C	T	145267981	1	4	49	0	1	0	0	0	0	0	0	0	7041	652	23	1		1	HEATR7A	8	145267981	Intron	SNP	C	TCGA-A4-7828-01A-11D-2136-08	76870981	145267981	1096041	18	3375											
C10orf137	26098	hgsc.bcm.edu	37	chr10	127442312	127442312	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgatgcttctcctagtctcaAtcgagaagaagtgatgaaac	13	11	9	8	1	2	5	1	3	2	2	5	6	2	5	1	0	2	1	1	0	5	2	rs199695348		TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr10:127442312A>G	ENST00000356792.4	+	24	3675	c.3443A>G	c.(3442-3444)aAt>aGt	p.N1148S	RP11-383C5.7_ENST00000602030.1_RNA|RP11-383C5.7_ENST00000594025.1_RNA|C10orf137_ENST00000337623.3_Missense_Mutation_p.N1114S|RP11-383C5.7_ENST00000593871.1_RNA|RP11-383C5.7_ENST00000601363.1_RNA	NM_001202438.1	NP_001189367.1	Q3B7T1	EDRF1_HUMAN		1148					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)				CCTAGTCTCAATCGAGAAGAA	0.393																																					p.N1148S		Atlas-SNP	.											.	C10orf137	153	.	0			c.A3443G						PASS	.						153	143	146					10																	127442312		2203	4300	6503	SO:0001583	missense	26098	exon24			GTCTCAATCGAGA																												ENST00000356792.4:c.3443A>G	chr10.hg19:g.127442312A>G	ENSP00000349244:p.Asn1148Ser	132.0	0.0	.		120.0	42.0	.	NM_001202438	B2RC65|Q3KR40|Q4G190|Q5VZQ4|Q8IZ74|Q9Y3W4	Missense_Mutation	SNP	ENST00000356792.4	hg19	CCDS55733.1	.	.	.	.	.	.	.	.	.	.	A	8.698	0.908981	0.17833	.	.	ENSG00000107938	ENST00000356792;ENST00000337623	T;T	0.42131	0.98;0.98	4.89	-2.12	0.07165	.	0.274294	0.39020	N	0.001485	T	0.14313	0.0346	N	0.04508	-0.205	0.09310	N	1	B;B;B	0.18310	0.027;0.013;0.0	B;B;B	0.14578	0.009;0.011;0.003	T	0.26018	-1.0115	10	0.13470	T	0.59	.	6.4393	0.21841	0.5191:0.1277:0.3532:0.0	.	1148;495;1114	Q3B7T1;Q5VZQ1;Q3B7T1-5	EDRF1_HUMAN;.;.	S	1148;1114	ENSP00000349244:N1148S;ENSP00000336727:N1114S	ENSP00000336727:N1114S	N	+	2	0	C10orf137	127432302	0.081000	0.21417	0.000000	0.03702	0.099000	0.18886	1.651000	0.37302	-0.178000	0.10672	-0.274000	0.10170	AAT	.	A|0.999;G|0.001	0.001	weak		0.393	C10orf137-007	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388539.1			G	127442312	A	G	127442312	3	3	49	1	0	0	0	0	1	0	0	0	1596	101	4	3	3431	3	C10orf137	10	127442312	Missense_Mutation	SNP	A	TCGA-A4-7828-01A-11D-2136-08		127442312	8092435	19	3376											
SLCO2B1	11309	hgsc.bcm.edu	37	chr11	74883496	74883496	+	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	gggtttcctcatcgctgccgGtgcagtggccctggctgcca	3	10	14	14	2	1	0	1	0	0	0	3	0	2	0	4	4	3	4	4	4	0	1			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr11:74883496G>C	ENST00000289575.5	+	7	1249	c.854G>C	c.(853-855)gGt>gCt	p.G285A	SLCO2B1_ENST00000428359.2_Missense_Mutation_p.G263A|SLCO2B1_ENST00000341411.4_Missense_Mutation_p.G58A|SLCO2B1_ENST00000526660.1_3'UTR|SLCO2B1_ENST00000525650.1_Missense_Mutation_p.G141A|SLCO2B1_ENST00000454962.2_Missense_Mutation_p.G58A|SLCO2B1_ENST00000531756.1_Missense_Mutation_p.G30A|SLCO2B1_ENST00000532236.1_Missense_Mutation_p.G169A	NM_007256.4	NP_009187	O94956	SO2B1_HUMAN	solute carrier organic anion transporter family, member 2B1	285					liver development (GO:0001889)|sodium-independent icosanoid transport (GO:0071718)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid transmembrane transporter activity (GO:0015125)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(2)|endometrium(1)|large_intestine(7)|lung(20)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	39					Acetic acid(DB03166)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Digoxin(DB00390)|Dinoprostone(DB00917)|Ergoloid mesylate(DB01049)|Estradiol(DB00783)|Estrone(DB00655)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Glyburide(DB01016)|Ibuprofen(DB01050)|Iloprost(DB01088)|Latanoprost(DB00654)|Montelukast(DB00471)|Niacin(DB00627)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Tolbutamide(DB01124)	ATCGCTGCCGGTGCAGTGGCC	0.557																																					p.G285A		Atlas-SNP	.											.	SLCO2B1	84	.	0			c.G854C						PASS	.						93	81	85					11																	74883496		2200	4293	6493	SO:0001583	missense	11309	exon7			CTGCCGGTGCAGT	AB026256	CCDS8235.1, CCDS44683.1, CCDS53679.1	11q13	2013-05-22	2003-11-25	2003-11-26				"Solute carriers"	10962	protein-coding gene	gene with protein product		604988	"solute carrier family 21 (organic anion transporter), member 9"	SLC21A9			Standard	NM_007256		Approved	OATP-B, OATP2B1	uc001owb.3	O94956		ENST00000289575.5:c.854G>C	chr11.hg19:g.74883496G>C	ENSP00000289575:p.Gly285Ala	84.0	0.0	.		103.0	30.0	.	NM_007256	A8K2G9|B4DGA9|B4DTB0|E7ERN5|E9PPU8|Q9H2Z0|Q9UFU1	Missense_Mutation	SNP	ENST00000289575.5	hg19	CCDS8235.1	.	.	.	.	.	.	.	.	.	.	G	5.226	0.227121	0.09916	.	.	ENSG00000137491	ENST00000289575;ENST00000341411;ENST00000532236;ENST00000531756;ENST00000525650;ENST00000454962;ENST00000428359	T;T;T;T;T;T;T	0.80033	0.41;-1.33;-1.33;-1.33;-1.33;-1.33;0.41	5.65	3.76	0.43208	Major facilitator superfamily domain, general substrate transporter (1);	0.406164	0.30347	N	0.009837	T	0.67979	0.2951	N	0.26092	0.79	0.19945	N	0.999945	B;B;B;B	0.19935	0.019;0.04;0.016;0.008	B;B;B;B	0.26969	0.034;0.075;0.02;0.015	T	0.51545	-0.8692	10	0.16896	T	0.51	.	10.9072	0.47086	0.0:0.1411:0.7122:0.1467	.	141;30;58;285	E9PPU8;E9PPJ4;O94956-2;O94956	.;.;.;SO2B1_HUMAN	A	285;58;169;30;141;58;263	ENSP00000289575:G285A;ENSP00000341286:G58A;ENSP00000434112:G169A;ENSP00000432650:G30A;ENSP00000436324:G141A;ENSP00000389653:G58A;ENSP00000388912:G263A	ENSP00000289575:G285A	G	+	2	0	SLCO2B1	74561144	0.897000	0.30589	0.001000	0.08648	0.003000	0.03518	3.898000	0.56281	0.903000	0.36546	0.655000	0.94253	GGT	.	.	.	none		0.557	SLCO2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383933.1	NM_007256		C	74883496	G	C	74883496	3	2	49	1	0	0	0	0	1	0	0	0	14740	1261	44	4	880	4	SLCO2B1	11	74883496	Missense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08		74883496	60123020	20	3377											
GTSF1	121355	hgsc.bcm.edu	37	chr12	54857070	54857070	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagccaatttgcttgcaacAtcaggatgattctgtggaac	11	12	10	8	0	2	1	1	1	1	0	2	3	2	3	1	2	5	3	1	2	4	4			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr12:54857070A>G	ENST00000552397.1	-	4	1025	c.129T>C	c.(127-129)gaT>gaC	p.D43D	GTSF1_ENST00000552395.1_5'UTR|RP11-753H16.5_ENST00000552785.1_RNA|RP11-753H16.3_ENST00000550474.1_RNA|GTSF1_ENST00000305879.5_Silent_p.D43D			Q8WW33	GTSF1_HUMAN	gametocyte specific factor 1	43						cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5		Myeloproliferative disorder(1001;0.00452)				TGCTTGCAACATCAGGATGAT	0.433																																					p.D43D		Atlas-SNP	.											.	GTSF1	15	.	0			c.T129C						PASS	.						125	113	117					12																	54857070		2203	4300	6503	SO:0001819	synonymous_variant	121355	exon4			TGCAACATCAGGA	AK098819	CCDS8881.1	12q13.2	2008-02-04	2007-11-27	2007-11-27		ENSG00000170627			26565	protein-coding gene	gene with protein product			"family with sequence similarity 112, member B"	FAM112B		12477932	Standard	NM_144594		Approved	FLJ32942	uc001sgb.3	Q8WW33		ENST00000552397.1:c.129T>C	chr12.hg19:g.54857070A>G		85.0	0.0	.		93.0	27.0	.	NM_144594	B3KQ60|Q0VGM4|Q8N778	Silent	SNP	ENST00000552397.1	hg19	CCDS8881.1																																																																																			.	.	.	none		0.433	GTSF1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406187.1	NM_144594		G	54857070	A	G	54857070	2	3	49	1	0	0	0	0	0	0	0	1	6893	214	8	3		3	GTSF1	12	54857070	Silent	SNP	A	TCGA-A4-7828-01A-11D-2136-08		54857070	78994825	21	3378											
COCH	1690	hgsc.bcm.edu	37	chr14	31353851	31353851	+	Missense_Mutation	SNP	A	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	agtaggtttcagagggggtaAttccaatacaggtaagtaga	14	10	13	4	0	1	2	1	0	0	2	2	2	2	2	1	4	1	5	1	4	6	7			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr14:31353851A>C	ENST00000396618.3	+	9	778	c.722A>C	c.(721-723)aAt>aCt	p.N241T	COCH_ENST00000216361.4_Missense_Mutation_p.N241T|COCH_ENST00000475087.1_Missense_Mutation_p.N241T|RP11-829H16.3_ENST00000468444.2_RNA|RP11-829H16.3_ENST00000555421.1_RNA|COCH_ENST00000460581.2_Missense_Mutation_p.N129T|RP11-829H16.3_ENST00000556786.1_RNA|COCH_ENST00000382493.4_Missense_Mutation_p.N48T|RP11-829H16.3_ENST00000555108.1_RNA	NM_004086.2	NP_004077.1	O43405	COCH_HUMAN	cochlin	241	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				defense response to bacterium (GO:0042742)|positive regulation of innate immune response (GO:0045089)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|pancreas(1)|skin(3)	19	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.00645)		AGAGGGGGTAATTCCAATACA	0.358																																					p.N241T		Atlas-SNP	.											.	COCH	54	.	0			c.A722C						PASS	.						69	72	71					14																	31353851		2203	4299	6502	SO:0001583	missense	1690	exon9			GGGGTAATTCCAA		CCDS9640.1	14q11.2-q13	2013-05-01	2013-05-01		ENSG00000100473	ENSG00000100473			2180	protein-coding gene	gene with protein product		603196	"coagulation factor C (Limulus polyphemus homolog); cochlin", "coagulation factor C homolog, cochlin (Limulus polyphemus)"	DFNA31, DFNA9		9806553	Standard	NM_004086		Approved	COCH-5B2	uc001wqp.2	O43405	OTTHUMG00000029432	ENST00000396618.3:c.722A>C	chr14.hg19:g.31353851A>C	ENSP00000379862:p.Asn241Thr	64.0	0.0	.		71.0	18.0	.	NM_004086	A8K9K9|D3DS84|Q96IU6	Missense_Mutation	SNP	ENST00000396618.3	hg19	CCDS9640.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.1|23.1	4.373608|4.373608	0.82573|0.82573	.|.	.|.	ENSG00000100473|ENSG00000100473	ENST00000468826|ENST00000216361;ENST00000396618;ENST00000475087;ENST00000555881;ENST00000460581;ENST00000542225;ENST00000382493	.|D;D;D;D;D;D	.|0.83075	.|-1.68;-1.68;-1.68;-1.68;-1.68;-1.68	5.78|5.78	5.78|5.78	0.91487|0.91487	.|von Willebrand factor, type A (3);	.|0.040966	.|0.85682	.|D	.|0.000000	D|D	0.89114|0.89114	0.6623|0.6623	M|M	0.64676|0.64676	1.99|1.99	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.64830	.|0.994;0.992;0.975	.|D;P;P	.|0.67231	.|0.95;0.87;0.819	D|D	0.88337|0.88337	0.2972|0.2972	5|10	.|0.39692	.|T	.|0.17	-22.9226|-22.9226	16.1145|16.1145	0.81295|0.81295	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|48;241;241	.|E7EN67;Q96IU6;O43405	.|.;.;COCH_HUMAN	L|T	81|241;241;241;123;129;129;48	.|ENSP00000216361:N241T;ENSP00000379862:N241T;ENSP00000451528:N241T;ENSP00000452569:N123T;ENSP00000451713:N129T;ENSP00000371933:N48T	.|ENSP00000216361:N241T	I|N	+|+	1|2	0|0	COCH|COCH	30423602|30423602	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	8.474000|8.474000	0.90413|0.90413	2.205000|2.205000	0.71048|0.71048	0.454000|0.454000	0.30748|0.30748	ATT|AAT	.	.	.	none		0.358	COCH-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276608.1	NM_004086		C	31353851	A	C	31353851	3	2	49	1	0	0	0	0	1	0	0	0	3658	101	4	5	752	5	COCH	14	31353851	Missense_Mutation	SNP	A	TCGA-A4-7828-01A-11D-2136-08		31353851	75995689	22	3379											
CCDC57	284001	hgsc.bcm.edu	37	chr17	80129603	80129603	+	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	tctctgtcgaggtgcggacgCtgggctgagactcagcatga	7	9	15	10	3	2	2	1	2	1	1	4	5	2	3	0	3	2	3	0	3	0	0			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr17:80129603C>G	ENST00000389641.4	-	12	1892	c.1856G>C	c.(1855-1857)aGc>aCc	p.S619T	CCDC57_ENST00000392347.1_Missense_Mutation_p.S619T|CCDC57_ENST00000327026.3_5'UTR|CCDC57_ENST00000392343.3_Missense_Mutation_p.S619T			Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	619										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)			GGTGCGGACGCTGGGCTGAGA	0.478																																					p.S619T		Atlas-SNP	.											.	CCDC57	102	.	0			c.G1856C						PASS	.						95	99	98					17																	80129603		1929	4143	6072	SO:0001583	missense	284001	exon12			CGGACGCTGGGCT	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.1856G>C	chr17.hg19:g.80129603C>G	ENSP00000374292:p.Ser619Thr	79.0	0.0	.		90.0	15.0	.	NM_198082	A6NP51|A8MQC7|Q8IWG2|Q8TER3	Missense_Mutation	SNP	ENST00000389641.4	hg19		.	.	.	.	.	.	.	.	.	.	C	10.52	1.371836	0.24857	.	.	ENSG00000176155	ENST00000389641;ENST00000392347;ENST00000327026;ENST00000392343	T;T;T	0.24538	3.02;3.02;1.85	2.92	-1.57	0.08506	.	2.029070	0.02447	N	0.085210	T	0.23846	0.0577	L	0.57536	1.79	0.09310	N	0.999995	P;P	0.44816	0.844;0.572	B;B	0.41088	0.347;0.122	T	0.19257	-1.0311	10	0.22109	T	0.4	5.4141	3.303	0.06989	0.0:0.3889:0.2116:0.3995	.	619;619	Q2TAC2-2;Q2TAC2	.;CCD57_HUMAN	T	619;619;127;619	ENSP00000374292:S619T;ENSP00000376158:S619T;ENSP00000376154:S619T	ENSP00000315967:S127T	S	-	2	0	CCDC57	77722892	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.431000	0.06965	-0.298000	0.08921	0.561000	0.74099	AGC	.	.	.	none		0.478	CCDC57-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000277182.3	NM_198082		G	80129603	C	G	80129603	3	3	49	1	0	0	0	0	1	0	0	0	2829	797	28	4	915	4	CCDC57	17	80129603	Missense_Mutation	SNP	C	TCGA-A4-7828-01A-11D-2136-08		80129603	1065607	23	3380											
EPB41L3	23136	hgsc.bcm.edu	37	chr18	5416056	5416056	+	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	gaggttggtttcagaaaggtTggggaaagagaggtatccat	12	10	16	3	0	1	2	1	0	0	2	2	5	2	3	1	6	0	4	1	6	3	4			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr18:5416056T>A	ENST00000341928.2	-	13	2168	c.1828A>T	c.(1828-1830)Aac>Tac	p.N610Y	EPB41L3_ENST00000540638.2_Intron|EPB41L3_ENST00000544123.1_Intron|EPB41L3_ENST00000427684.2_Intron|EPB41L3_ENST00000542146.1_Intron|EPB41L3_ENST00000400111.3_Intron|EPB41L3_ENST00000542652.2_Intron|EPB41L3_ENST00000342933.3_Missense_Mutation_p.N610Y	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	610	Spectrin--actin-binding. {ECO:0000255}.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			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						TCAGAAAGGTTGGGGAAAGAG	0.532																																					p.N610Y		Atlas-SNP	.											.	EPB41L3	222	.	0			c.A1828T						PASS	.						157	126	136					18																	5416056		2203	4300	6503	SO:0001583	missense	23136	exon13			AAAGGTTGGGGAA	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.1828A>T	chr18.hg19:g.5416056T>A	ENSP00000343158:p.Asn610Tyr	137.0	0.0	.		138.0	37.0	.	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	hg19	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	T	14.51	2.558267	0.45590	.	.	ENSG00000082397	ENST00000341928;ENST00000342933	T;T	0.81415	-1.49;-1.49	5.74	4.55	0.56014	.	0.102804	0.64402	D	0.000003	T	0.77377	0.4121	L	0.57536	1.79	0.80722	D	1	P	0.49447	0.924	B	0.41088	0.347	T	0.78593	-0.2144	10	0.72032	D	0.01	.	12.8348	0.57767	0.0:0.0:0.1364:0.8636	.	610	Q9Y2J2	E41L3_HUMAN	Y	610	ENSP00000343158:N610Y;ENSP00000341138:N610Y	ENSP00000343158:N610Y	N	-	1	0	EPB41L3	5406056	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.743000	0.62110	0.958000	0.37956	0.460000	0.39030	AAC	.	.	.	none		0.532	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		A	5416056	T	A	5416056	3	1	49	1	0	0	0	0	1	0	0	0	5156	1812	63	5	1475	5	EPB41L3	18	5416056	Missense_Mutation	SNP	T	TCGA-A4-7828-01A-11D-2136-08		5416056	72661192	24	3381											
TMEM205	374882	hgsc.bcm.edu	37	chr19	11453637	11453637	+	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	ggggtccttctctcgcagctGgcggtagggatcgggaccct	4	9	16	12	3	1	0	0	0	1	0	5	2	2	2	2	6	1	3	2	6	1	2			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr19:11453637G>T	ENST00000354882.5	-	3	850	c.424C>A	c.(424-426)Cag>Aag	p.Q142K	TMEM205_ENST00000586218.1_Missense_Mutation_p.Q81K|TMEM205_ENST00000586956.1_Missense_Mutation_p.Q142K|TMEM205_ENST00000589555.1_Missense_Mutation_p.Q142K|RAB3D_ENST00000589655.1_Intron|TMEM205_ENST00000588560.1_Missense_Mutation_p.Q142K|CCDC159_ENST00000588790.1_5'Flank|TMEM205_ENST00000586590.1_Missense_Mutation_p.Q142K|TMEM205_ENST00000593256.2_Missense_Mutation_p.Q142K|TMEM205_ENST00000447337.1_Missense_Mutation_p.Q142K|TMEM205_ENST00000587948.1_Missense_Mutation_p.Q142K			Q6UW68	TM205_HUMAN	transmembrane protein 205	142						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				endometrium(1)|lung(1)	2						TCTCGCAGCTGGCGGTAGGGA	0.627																																					p.Q142K		Atlas-SNP	.											.	TMEM205	14	.	0			c.C424A						PASS	.						94	85	88					19																	11453637		2203	4300	6503	SO:0001583	missense	374882	exon4			GCAGCTGGCGGTA	AK127147	CCDS32909.1	19p13.2	2008-01-09				ENSG00000105518			29631	protein-coding gene	gene with protein product		613771				12975309	Standard	NM_198536		Approved	UNQ501, MBC3205	uc002mrb.2	Q6UW68		ENST00000354882.5:c.424C>A	chr19.hg19:g.11453637G>T	ENSP00000346954:p.Gln142Lys	111.0	0.0	.		149.0	48.0	.	NM_033408		Missense_Mutation	SNP	ENST00000354882.5	hg19	CCDS32909.1	.	.	.	.	.	.	.	.	.	.	G	6.199	0.404917	0.11754	.	.	ENSG00000105518	ENST00000354882;ENST00000447337	.	.	.	4.96	3.9	0.45041	.	0.240493	0.34245	U	0.004140	T	0.34250	0.0891	L	0.36672	1.1	0.30403	N	0.779844	B	0.12013	0.005	B	0.09377	0.004	T	0.26224	-1.0109	9	0.06365	T	0.9	-4.5936	14.6711	0.68945	0.0:0.1463:0.8537:0.0	.	142	Q6UW68	TM205_HUMAN	K	142	.	ENSP00000346954:Q142K	Q	-	1	0	TMEM205	11314637	1.000000	0.71417	1.000000	0.80357	0.765000	0.43378	3.726000	0.54977	1.193000	0.43086	0.655000	0.94253	CAG	.	.	.	none		0.627	TMEM205-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458743.1	NM_198536		T	11453637	G	T	11453637	3	4	49	1	0	0	0	0	1	0	0	0	16142	1357	47	4	149	4	TMEM205	19	11453637	Missense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08		11453637	47675346	25	3382											
ZNF813	126017	hgsc.bcm.edu	37	chr19	53995130	53995130	+	Missense_Mutation	SNP	T	T	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	catagacttcatactggagaTaaaccttacaagtgtaatga	16	11	7	7	0	1	3	1	1	0	2	1	4	1	3	1	1	3	1	1	1	7	6			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr19:53995130T>G	ENST00000396403.4	+	4	1772	c.1644T>G	c.(1642-1644)gaT>gaG	p.D548E	ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	548					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		ATACTGGAGATAAACCTTACA	0.378																																					p.D548E		Atlas-SNP	.											ZNF813_ENST00000396403,NS,carcinoma,0,1	ZNF813	81	.	0			c.T1644G						PASS	.						48	51	50					19																	53995130		2198	4297	6495	SO:0001583	missense	126017	exon4			TGGAGATAAACCT	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.1644T>G	chr19.hg19:g.53995130T>G	ENSP00000379684:p.Asp548Glu	47.0	0.0	.		49.0	2.0	.	NM_001004301		Missense_Mutation	SNP	ENST00000396403.4	hg19	CCDS46172.1	.	.	.	.	.	.	.	.	.	.	t	0.013	-1.629910	0.00813	.	.	ENSG00000198346	ENST00000396403	T	0.11063	2.81	1.32	-2.63	0.06133	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02418	0.0074	N	0.01277	-0.915	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.49943	-0.8885	9	0.02654	T	1	.	7.8524	0.29462	0.0:0.0:0.5868:0.4132	.	548	Q6ZN06	ZN813_HUMAN	E	548	ENSP00000379684:D548E	ENSP00000379684:D548E	D	+	3	2	ZNF813	58686942	0.288000	0.24324	0.030000	0.17652	0.043000	0.13939	0.064000	0.14437	-1.341000	0.02225	-1.294000	0.01345	GAT	.	.	.	none		0.378	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301		G	53995130	T	G	53995130	3	3	49	1	0	0	0	0	1	0	0	0	18187	1403	49	5	1654	5	ZNF813	19	53995130	Missense_Mutation	SNP	T	TCGA-A4-7828-01A-11D-2136-08	42541493	53995130	5133853	26	3383											
ISOC2	79763	hgsc.bcm.edu	37	chr19	55966664	55966664	+	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	gtccaccaccacatggacctGcagcccccggtctaggaggt	8	6	11	16	1	1	0	0	0	1	0	2	2	2	2	6	4	2	1	6	4	1	1			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr19:55966664G>A	ENST00000425675.2	-	4	442	c.382C>T	c.(382-384)Cag>Tag	p.Q128*	ISOC2_ENST00000438389.2_Nonsense_Mutation_p.Q58*|ISOC2_ENST00000085068.3_Nonsense_Mutation_p.Q144*			Q96AB3	ISOC2_HUMAN	isochorismatase domain containing 2	128					protein destabilization (GO:0031648)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			endometrium(1)|lung(4)|ovary(1)|stomach(1)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0535)		ACATGGACCTGCAGCCCCCGG	0.662																																					p.Q144X		Atlas-SNP	.											.	ISOC2	16	.	0			c.C430T						PASS	.						32	34	33					19																	55966664		2203	4300	6503	SO:0001587	stop_gained	79763	exon4			GGACCTGCAGCCC	AK027122	CCDS12925.1, CCDS46194.1, CCDS46195.1	19q13.42	2011-07-14			ENSG00000063241	ENSG00000063241			26278	protein-coding gene	gene with protein product		612928				17658461	Standard	NM_024710		Approved	FLJ23469	uc002qla.3	Q96AB3		ENST00000425675.2:c.382C>T	chr19.hg19:g.55966664G>A	ENSP00000401726:p.Gln128*	29.0	0.0	.		28.0	5.0	.	NM_024710	Q6ZN91|Q9H5G0	Nonsense_Mutation	SNP	ENST00000425675.2	hg19	CCDS46195.1	.	.	.	.	.	.	.	.	.	.	G	34	5.324290	0.95708	.	.	ENSG00000063241	ENST00000085068;ENST00000425675;ENST00000438389	.	.	.	3.62	2.44	0.29823	.	0.212717	0.38436	N	0.001695	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-16.1072	10.4505	0.44520	0.0:0.2009:0.7991:0.0	.	.	.	.	X	144;128;58	.	ENSP00000085068:Q144X	Q	-	1	0	ISOC2	60658476	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.156000	0.50708	1.977000	0.57605	0.486000	0.48141	CAG	.	.	.	none		0.662	ISOC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453179.1	NM_024710		A	55966664	G	A	55966664	4	1	49	1	0	0	0	0	0	1	0	0	7870	1328	46	2	247	2	ISOC2	19	55966664	Nonsense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08	1971534	55966664	3162319	27	3384											
PTPRT	11122	hgsc.bcm.edu	37	chr20	41306544	41306544	+	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	tggtgaggggaggccctggcGgtcccgtacccccctcacct	4	7	14	16	2	1	1	1	1	0	0	2	2	2	2	6	6	1	1	6	6	1	1			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chr20:41306544G>T	ENST00000373187.1	-	7	1114	c.1115C>A	c.(1114-1116)cCg>cAg	p.P372Q	PTPRT_ENST00000373193.3_Missense_Mutation_p.P372Q|PTPRT_ENST00000373198.4_Missense_Mutation_p.P372Q|PTPRT_ENST00000373184.1_Missense_Mutation_p.P372Q|PTPRT_ENST00000373190.1_Missense_Mutation_p.P372Q|PTPRT_ENST00000373201.1_Missense_Mutation_p.P372Q|PTPRT_ENST00000356100.2_Missense_Mutation_p.P372Q			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	372	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				AGGCCCTGGCGGTCCCGTACC	0.542																																					p.P372Q		Atlas-SNP	.											.	PTPRT	372	.	0			c.C1115A						PASS	.						87	87	87					20																	41306544		1919	4125	6044	SO:0001583	missense	11122	exon7			CCTGGCGGTCCCG	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.1115C>A	chr20.hg19:g.41306544G>T	ENSP00000362283:p.Pro372Gln	124.0	0.0	.		150.0	42.0	.	NM_007050	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	ENST00000373187.1	hg19	CCDS42874.1	.	.	.	.	.	.	.	.	.	.	G	15.12	2.737618	0.49045	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	T;T;T;T;T;T;T	0.80909	-1.43;-1.43;-1.43;-1.43;-1.43;-1.43;-1.43	5.42	5.42	0.78866	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.81346	0.4803	L	0.29908	0.895	0.58432	D	0.999991	D;D	0.56746	0.971;0.977	P;P	0.55391	0.775;0.772	T	0.78523	-0.2171	10	0.28530	T	0.3	.	19.1814	0.93625	0.0:0.0:1.0:0.0	.	372;372	O14522-1;O14522	.;PTPRT_HUMAN	Q	372	ENSP00000362286:P372Q;ENSP00000362283:P372Q;ENSP00000362289:P372Q;ENSP00000348408:P372Q;ENSP00000362294:P372Q;ENSP00000362280:P372Q;ENSP00000362297:P372Q	ENSP00000348408:P372Q	P	-	2	0	PTPRT	40739958	1.000000	0.71417	0.973000	0.42090	0.948000	0.59901	5.469000	0.66749	2.705000	0.92388	0.655000	0.94253	CCG	.	.	.	none		0.542	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			T	41306544	G	T	41306544	3	4	49	1	0	0	0	0	1	0	0	0	12825	1116	39	4	3371	4	PTPRT	20	41306544	Missense_Mutation	SNP	G	TCGA-A4-7828-01A-11D-2136-08		41306544	21718976	28	3385											
RGAG1	57529	hgsc.bcm.edu	37	chrX	109695056	109695056	+	Frame_Shift_Del	DEL	G	G	-																															gatgtctgcaccaccagtaaGagctttagattctggagcaa																										TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chrX:109695056delG	ENST00000465301.2	+	3	1457	c.1211delG	c.(1210-1212)agafs	p.R404fs	RGAG1_ENST00000540313.1_Frame_Shift_Del_p.R404fs	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	404										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						CCACCAGTAAGAGCTTTAGAT	0.502																																					p.R404fs		Atlas-INDEL	.											.	RGAG1	168	.	0			c.1210delA						PASS	.						195	202	200					X																	109695056		2203	4300	6503	SO:0001589	frameshift_variant	57529	exon3			.	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.1211delG	chrX.hg19:g.109695056delG	ENSP00000419786:p.Arg404fs	585.0	0.0	0		661.0	185.0	0.279879	NM_020769	Q9P2M8	Frame_Shift_Del	DEL	ENST00000465301.2	hg19	CCDS14552.1																																																																																			.	.	.	none		0.502	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		-	109695056	G	-	109695056	7	5	49	1	0	1	0	1	0	0	0	0	13287	942	33	0	1213	0	RGAG1	23	109695056	Frame_Shift_Del	DEL	G	TCGA-A4-7828-01A-11D-2136-08		109695056	45575504	29	3386											
MBNL3	55796	hgsc.bcm.edu	37	chrX	131540269	131540269	+	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	gacttacaagtgatgacattTgagcgttttggagcataagc	12	12	11	6	1	0	3	0	3	0	0	0	5	0	4	0	1	4	2	0	1	3	5			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chrX:131540269T>A	ENST00000370853.3	-	2	407	c.329A>T	c.(328-330)cAa>cTa	p.Q110L	MBNL3_ENST00000370849.3_Missense_Mutation_p.Q60L|MBNL3_ENST00000370844.1_Missense_Mutation_p.Q14L|MBNL3_ENST00000394311.2_Missense_Mutation_p.Q14L|RAP2C-AS1_ENST00000441399.2_RNA|MBNL3_ENST00000370839.3_Missense_Mutation_p.Q110L|RAP2C-AS1_ENST00000421483.2_RNA|MBNL3_ENST00000370857.3_Missense_Mutation_p.Q110L|MBNL3_ENST00000538204.1_Missense_Mutation_p.Q60L|MBNL3_ENST00000473364.1_5'UTR	NM_018388.3	NP_060858.2	Q9NUK0	MBNL3_HUMAN	muscleblind-like splicing regulator 3	110					mRNA processing (GO:0006397)|multicellular organismal development (GO:0007275)|negative regulation of myoblast differentiation (GO:0045662)|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)			NS(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|prostate(2)	16	Acute lymphoblastic leukemia(192;0.000127)					TGATGACATTTGAGCGTTTTG	0.453																																					p.Q110L		Atlas-SNP	.											.	MBNL3	62	.	0			c.A329T						PASS	.						144	116	125					X																	131540269		2203	4300	6503	SO:0001583	missense	55796	exon2			GACATTTGAGCGT	AF491305	CCDS14633.1, CCDS14634.1, CCDS55492.1, CCDS55493.1, CCDS55494.1	Xq26.2	2013-01-18	2012-02-23		ENSG00000076770	ENSG00000076770		"Zinc fingers, CCCH-type domain containing"	20564	protein-coding gene	gene with protein product		300413	"muscleblind-like 3 (Drosophila)"			12297108, 10970838	Standard	NM_018388		Approved	CHCR, FLJ11316, MBLX39, MBXL	uc004ewv.4	Q9NUK0	OTTHUMG00000022426	ENST00000370853.3:c.329A>T	chrX.hg19:g.131540269T>A	ENSP00000359890:p.Gln110Leu	180.0	0.0	.		183.0	62.0	.	NM_018388	Q5JXN8|Q5JXN9|Q5JXP4|Q6UDQ1|Q8IUR4|Q8TAD9|Q8TAF4|Q9H0Z7|Q9UF37	Missense_Mutation	SNP	ENST00000370853.3	hg19	CCDS14633.1	.	.	.	.	.	.	.	.	.	.	T	11.08	1.534641	0.27475	.	.	ENSG00000076770	ENST00000394311;ENST00000538204;ENST00000370857;ENST00000370853;ENST00000370849;ENST00000370839;ENST00000370844;ENST00000436215;ENST00000421707	T;T;T;T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96	5.57	5.57	0.84162	.	0.086244	0.49916	D	0.000138	T	0.46328	0.1387	M	0.66939	2.045	0.49483	D	0.999793	B;B;B;P;P	0.35272	0.404;0.246;0.246;0.454;0.493	B;B;B;B;B	0.42771	0.287;0.346;0.286;0.397;0.157	T	0.38373	-0.9664	10	0.07644	T	0.81	-4.1668	14.7499	0.69516	0.0:0.0:0.0:1.0	.	60;110;110;60;14	Q9NUK0-4;Q9NUK0;Q9NUK0-2;Q9NUK0-3;Q8IUR4	.;MBNL3_HUMAN;.;.;.	L	14;60;110;110;60;110;14;14;14	ENSP00000377848:Q14L;ENSP00000439618:Q60L;ENSP00000359894:Q110L;ENSP00000359890:Q110L;ENSP00000359886:Q60L;ENSP00000359876:Q110L;ENSP00000359881:Q14L;ENSP00000406014:Q14L;ENSP00000402128:Q14L	ENSP00000359876:Q110L	Q	-	2	0	MBNL3	131367950	1.000000	0.71417	0.905000	0.35620	0.731000	0.41821	4.662000	0.61525	1.864000	0.54056	0.486000	0.48141	CAA	.	.	.	none		0.453	MBNL3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058319.1	NM_018388		A	131540269	T	A	131540269	3	1	49	1	0	0	0	0	1	0	0	0	9362	1812	63	5	824	5	MBNL3	23	131540269	Missense_Mutation	SNP	T	TCGA-A4-7828-01A-11D-2136-08	21845213	131540269	23730291	30	3387											
ATP6AP1	537	hgsc.bcm.edu	37	chrX	153657422	153657422	+	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	gggctcctgcggccgacactCatgaaggccacatcaccagc	9	5	11	16	2	2	1	2	1	0	0	3	2	3	1	4	3	2	1	4	3	1	0			TCGA-A4-7828-01A-11D-2136-08	TCGA-A4-7828-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	89b510b4-b46f-44f1-b973-0e7b01c3afd1	df0c98a4-c394-4d62-ac84-e6893a743883	g.chrX:153657422C>A	ENST00000369762.2	+	2	251	c.190C>A	c.(190-192)Cat>Aat	p.H64N		NM_001183.4	NP_001174.2	Q15904	VAS1_HUMAN	ATPase, H+ transporting, lysosomal accessory protein 1	64					ATP hydrolysis coupled proton transport (GO:0015991)|establishment of organelle localization (GO:0051656)|pH reduction (GO:0045851)|positive regulation of bone resorption (GO:0045780)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoclast development (GO:2001206)|proton transport (GO:0015992)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|vacuole (GO:0005773)	ATP binding (GO:0005524)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)			breast(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(5)	14	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GGCCGACACTCATGAAGGCCA	0.617																																					p.H64N		Atlas-SNP	.											.	ATP6AP1	46	.	0			c.C190A						PASS	.						87	75	79					X																	153657422		2203	4300	6503	SO:0001583	missense	537	exon2			GACACTCATGAAG	D16469	CCDS35451.1	Xq28	2010-03-10	2003-08-28	2003-08-29	ENSG00000071553	ENSG00000071553			868	protein-coding gene	gene with protein product		300197	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), subunit 1"	ATP6S1, ATP6IP1		8733135, 8281148	Standard	NM_001183		Approved	ORF, XAP-3, VATPS1, 16A, Ac45, XAP3, CF2	uc004flf.1	Q15904	OTTHUMG00000033291	ENST00000369762.2:c.190C>A	chrX.hg19:g.153657422C>A	ENSP00000358777:p.His64Asn	137.0	0.0	.		130.0	33.0	.	NM_001183	A6ZKI4|Q8NBT4|Q9H0C7	Missense_Mutation	SNP	ENST00000369762.2	hg19	CCDS35451.1	.	.	.	.	.	.	.	.	.	.	C	15.18	2.756732	0.49362	.	.	ENSG00000071553	ENST00000369762;ENST00000422890;ENST00000449556	.	.	.	4.74	4.74	0.60224	.	0.240499	0.42420	D	0.000718	T	0.49133	0.1539	M	0.70275	2.135	0.09310	N	0.999994	B;B	0.30439	0.279;0.178	B;B	0.35813	0.18;0.211	T	0.43491	-0.9388	9	0.28530	T	0.3	-20.593	12.2641	0.54668	0.0:1.0:0.0:0.0	.	24;64	B3KR70;Q15904	.;VAS1_HUMAN	N	64	.	ENSP00000358777:H64N	H	+	1	0	ATP6AP1	153310616	0.775000	0.28604	0.966000	0.40874	0.457000	0.32468	1.869000	0.39519	1.939000	0.56221	0.529000	0.55759	CAT	.	.	.	none		0.617	ATP6AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081639.4	NM_001183		A	153657422	C	A	153657422	3	1	49	1	0	0	0	0	1	0	0	0	1165	826	29	4	196	4	ATP6AP1	23	153657422	Missense_Mutation	SNP	C	TCGA-A4-7828-01A-11D-2136-08	22117153	153657422	1613138	31	3388											
PRDM16	63976	hgsc.bcm.edu	37	chr1	3342300	3342300	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacctcaagaagcacgagcAcgagaacgcaccaggtgggc	13	2	13	13	3	1	2	1	0	0	2	1	4	1	2	2	2	3	4	2	2	3	0			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr1:3342300A>G	ENST00000270722.5	+	13	3144	c.3095A>G	c.(3094-3096)cAc>cGc	p.H1032R	PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000378391.2_Missense_Mutation_p.H1032R|PRDM16_ENST00000442529.2_Missense_Mutation_p.H1031R|PRDM16_ENST00000511072.1_Missense_Mutation_p.H1033R|PRDM16_ENST00000514189.1_Missense_Mutation_p.H1032R|PRDM16_ENST00000441472.2_Missense_Mutation_p.H1031R|PRDM16_ENST00000378398.3_Missense_Mutation_p.H1032R			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	1032	Interaction with CTBP1 and CTBP2. {ECO:0000250}.|Mediates interaction with SKI and regulation of TGF-beta signaling.				brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		AAGCACGAGCACGAGAACGCA	0.667			T	EVI1	"MDS, AML"																																p.H1032R		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.A3095G						PASS	.						60	69	66					1																	3342300		2112	4203	6315	SO:0001583	missense	63976	exon13			ACGAGCACGAGAA	AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"Zinc fingers, C2H2-type"	14000	protein-coding gene	gene with protein product	"MDS1/EVI1-like", "PR-domain zinc finger protein 16", "transcription factor MEL1"	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.3095A>G	chr1.hg19:g.3342300A>G	ENSP00000270722:p.His1032Arg	137.0	0.0	.		123.0	24.0	.	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Missense_Mutation	SNP	ENST00000270722.5	hg19	CCDS41236.2	.	.	.	.	.	.	.	.	.	.	A	15.68	2.904180	0.52333	.	.	ENSG00000142611	ENST00000511072;ENST00000378398;ENST00000441472;ENST00000442529;ENST00000378391;ENST00000514189;ENST00000270722;ENST00000512462;ENST00000408992;ENST00000509860	T;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;2.53	4.02	4.02	0.46733	Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.50627	U	0.000113	T	0.33702	0.0872	M	0.68317	2.08	0.51012	D	0.999906	D;D;B;D	0.60575	0.973;0.988;0.369;0.979	D;D;B;D	0.72982	0.921;0.979;0.364;0.953	T	0.08659	-1.0711	10	0.66056	D	0.02	.	12.9149	0.58200	1.0:0.0:0.0:0.0	.	1032;1032;1031;1031	Q9HAZ2;Q9HAZ2-2;F8WEV3;D3YTA5	PRD16_HUMAN;.;.;.	R	1033;1032;1031;1031;1032;1032;1032;848;848;840	ENSP00000426975:H1033R;ENSP00000367651:H1032R;ENSP00000407968:H1031R;ENSP00000405253:H1031R;ENSP00000367643:H1032R;ENSP00000421400:H1032R;ENSP00000270722:H1032R;ENSP00000422504:H848R;ENSP00000425796:H840R	ENSP00000270722:H1032R	H	+	2	0	PRDM16	3332160	1.000000	0.71417	0.998000	0.56505	0.946000	0.59487	7.051000	0.76627	1.451000	0.47736	0.379000	0.24179	CAC	.	.	.	none		0.667	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114		G	3342300	A	G	3342300	3	3	50	1	0	0	0	0	1	0	0	0	12467	159	6	3	3145	3	PRDM16	1	3342300	Missense_Mutation	SNP	A	TCGA-A4-7915-01A-11D-2201-08		3342300	245908321	1	3389											
TAS1R1	80835	hgsc.bcm.edu	37	chr1	6639491	6639491	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaagtacctgcctgcggcCaacatgatggctgggctgag	8	7	15	11	1	0	2	0	2	0	0	0	2	0	2	3	4	4	4	3	4	3	1			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr1:6639491C>T	ENST00000333172.6	+	6	2566	c.2373C>T	c.(2371-2373)gcC>gcT	p.A791A	TAS1R1_ENST00000351136.3_Silent_p.A537A|TAS1R1_ENST00000328191.4_3'UTR|ZBTB48_ENST00000377674.4_5'Flank	NM_138697.3	NP_619642.2	Q7RTX1	TS1R1_HUMAN	taste receptor, type 1, member 1	791					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)		TGCCTGCGGCCAACATGATGG	0.587																																					p.A791A		Atlas-SNP	.											.	TAS1R1	76	.	0			c.C2373T						PASS	.						97	86	90					1																	6639491		2203	4300	6503	SO:0001819	synonymous_variant	80835	exon6			TGCGGCCAACATG		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.2373C>T	chr1.hg19:g.6639491C>T		105.0	0.0	.		114.0	46.0	.	NM_138697	B2RMX0|Q5SY22|Q5SY24|Q8NGZ7|Q8TDJ7|Q8TDJ8|Q8TDJ9|Q8TDK0	Silent	SNP	ENST00000333172.6	hg19	CCDS81.1																																																																																			.	.	.	none		0.587	TAS1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004211.1			T	6639491	C	T	6639491	2	4	50	1	0	0	0	0	0	0	0	1	15574	594	21	2		2	TAS1R1	1	6639491	Silent	SNP	C	TCGA-A4-7915-01A-11D-2201-08	3297191	6639491	242611130	2	3390											
COL8A2	1296	hgsc.bcm.edu	37	chr1	36564488	36564488	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgggcccacagctcctggcTcccccctggggcctggaact	4	8	12	17	0	0	0	0	0	0	0	2	1	2	1	6	5	2	2	6	5	1	1			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr1:36564488T>C	ENST00000397799.1	-	4	1018	c.794A>G	c.(793-795)gAg>gGg	p.E265G	COL8A2_ENST00000303143.4_Missense_Mutation_p.E265G|COL8A2_ENST00000481785.1_Missense_Mutation_p.E200G			P25067	CO8A2_HUMAN	collagen, type VIII, alpha 2	265	Triple-helical region.				angiogenesis (GO:0001525)|camera-type eye morphogenesis (GO:0048593)|collagen catabolic process (GO:0030574)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			NS(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				AGCTCCTGGCTCCCCCCTGGG	0.657																																					p.E265G		Atlas-SNP	.											.	COL8A2	41	.	0			c.A794G						PASS	.						14	17	16					1																	36564488		2193	4289	6482	SO:0001583	missense	1296	exon2			CCTGGCTCCCCCC	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.794A>G	chr1.hg19:g.36564488T>C	ENSP00000380901:p.Glu265Gly	61.0	0.0	.		65.0	4.0	.	NM_005202	Q5JV31|Q8TEJ5	Missense_Mutation	SNP	ENST00000397799.1	hg19	CCDS403.1	.	.	.	.	.	.	.	.	.	.	T	6.827	0.521652	0.13005	.	.	ENSG00000171812	ENST00000303143;ENST00000397799;ENST00000481785	D;D;D	0.93906	-3.31;-3.31;-3.31	3.91	3.91	0.45181	.	0.198447	0.43747	D	0.000533	D	0.88742	0.6519	L	0.52206	1.635	0.46298	D	0.998977	P	0.44877	0.845	B	0.40329	0.326	D	0.84976	0.0885	10	0.18276	T	0.48	.	8.5265	0.33309	0.1725:0.0:0.0:0.8275	.	265	P25067	CO8A2_HUMAN	G	265;265;200	ENSP00000305913:E265G;ENSP00000380901:E265G;ENSP00000436433:E200G	ENSP00000305913:E265G	E	-	2	0	COL8A2	36337075	1.000000	0.71417	1.000000	0.80357	0.465000	0.32709	3.987000	0.56944	1.639000	0.50556	0.334000	0.21626	GAG	.	.	.	none		0.657	COL8A2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313674.1	NM_005202		C	36564488	T	C	36564488	3	2	50	1	0	0	0	0	1	0	0	0	3708	1551	54	3	1321	3	COL8A2	1	36564488	Missense_Mutation	SNP	T	TCGA-A4-7915-01A-11D-2201-08	29924997	36564488	212686133	3	3391											
MCOLN2	255231	hgsc.bcm.edu	37	chr1	85431299	85431299	+	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	acggaatctggcgtctggctCggtatttttcacaagggctc	7	12	12	10	3	3	0	1	0	2	0	5	1	3	1	0	5	0	3	0	5	3	3	rs527268491		TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr1:85431299C>A	ENST00000370608.3	-	2	237	c.170G>T	c.(169-171)cGa>cTa	p.R57L	MCOLN2_ENST00000284027.5_Missense_Mutation_p.R29L|MCOLN2_ENST00000531325.1_5'UTR	NM_153259.2	NP_694991.2	Q8IZK6	MCLN2_HUMAN	mucolipin 2	57					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	18				all cancers(265;0.0111)|Epithelial(280;0.0263)|OV - Ovarian serous cystadenocarcinoma(397;0.217)		GCGTCTGGCTCGGTATTTTTC	0.418																																					p.R57L		Atlas-SNP	.											.	MCOLN2	60	.	0			c.G170T						PASS	.						102	102	102					1																	85431299		2203	4300	6503	SO:0001583	missense	255231	exon2			CTGGCTCGGTATT	AK094010	CCDS30762.1	1p22	2011-12-16			ENSG00000153898	ENSG00000153898		"Voltage-gated ion channels / Transient receptor potential cation channels"	13357	protein-coding gene	gene with protein product		607399				16382100	Standard	XM_005270719		Approved	TRPML2, FLJ36691, TRP-ML2	uc001dkm.3	Q8IZK6	OTTHUMG00000009954	ENST00000370608.3:c.170G>T	chr1.hg19:g.85431299C>A	ENSP00000359640:p.Arg57Leu	111.0	0.0	.		109.0	5.0	.	NM_153259	A6NI99|Q2M3I6|Q5TAG5|Q8N9R3	Missense_Mutation	SNP	ENST00000370608.3	hg19	CCDS30762.1	.	.	.	.	.	.	.	.	.	.	C	33	5.264250	0.95399	.	.	ENSG00000153898	ENST00000370608;ENST00000284027	T;T	0.57107	0.42;0.42	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.67924	0.2945	M	0.72894	2.215	0.58432	D	0.999994	D	0.89917	1.0	D	0.65987	0.94	T	0.66212	-0.5980	10	0.54805	T	0.06	-39.7485	20.5827	0.99408	0.0:1.0:0.0:0.0	.	57	Q8IZK6	MCLN2_HUMAN	L	57;29	ENSP00000359640:R57L;ENSP00000284027:R29L	ENSP00000284027:R29L	R	-	2	0	MCOLN2	85203887	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.568000	0.60857	2.941000	0.99782	0.655000	0.94253	CGA	.	.	.	none		0.418	MCOLN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027567.2	NM_153259		A	85431299	C	A	85431299	3	1	50	1	0	0	0	0	1	0	0	0	9403	884	31	4	1582	4	MCOLN2	1	85431299	Missense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08	48866811	85431299	163819322	4	3392											
PAPPA2	60676	hgsc.bcm.edu	37	chr1	176809321	176809321	+	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	ccctacagcccttccaagcaGatggttggtgtgacactatc	9	10	9	13	0	0	2	0	1	0	1	2	2	1	2	3	2	3	2	3	2	3	4			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr1:176809321G>A	ENST00000367662.3	+	22	6379	c.5215G>A	c.(5215-5217)Gat>Aat	p.D1739N		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	1739				D -> N (in Ref. 6; CAC11134). {ECO:0000305}.	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						CTTCCAAGCAGATGGTTGGTG	0.507																																					p.D1739N		Atlas-SNP	.											.	PAPPA2	665	.	0			c.G5215A						PASS	.						155	155	155					1																	176809321		2032	4183	6215	SO:0001583	missense	60676	exon22			CAAGCAGATGGTT	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.5215G>A	chr1.hg19:g.176809321G>A	ENSP00000356634:p.Asp1739Asn	277.0	0.0	.		310.0	90.0	.	NM_020318	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	ENST00000367662.3	hg19	CCDS41438.1	.	.	.	.	.	.	.	.	.	.	G	35	5.437435	0.96168	.	.	ENSG00000116183	ENST00000367662	D	0.91894	-2.93	5.44	5.44	0.79542	Notch domain (2);	0.000000	0.85682	D	0.000000	D	0.95674	0.8593	M	0.67700	2.07	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95767	0.8805	10	0.66056	D	0.02	-17.6405	18.8699	0.92309	0.0:0.0:1.0:0.0	.	1739	Q9BXP8	PAPP2_HUMAN	N	1739	ENSP00000356634:D1739N	ENSP00000356634:D1739N	D	+	1	0	PAPPA2	175075944	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	8.729000	0.91490	2.544000	0.85801	0.655000	0.94253	GAT	.	.	.	none		0.507	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			A	176809321	G	A	176809321	3	1	50	1	0	0	0	0	1	0	0	0	11440	942	33	2	5350	2	PAPPA2	1	176809321	Missense_Mutation	SNP	G	TCGA-A4-7915-01A-11D-2201-08	91378022	176809321	72441300	5	3393											
GREB1	9687	hgsc.bcm.edu	37	chr2	11716612	11716612	+	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	aagtattacctggtccgtaaTgcacaagggactctaaccaa	14	9	8	10	1	1	0	0	0	1	0	2	1	2	1	3	2	3	3	3	2	7	4			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr2:11716612T>A	ENST00000381486.2	+	5	888	c.588T>A	c.(586-588)aaT>aaA	p.N196K	GREB1_ENST00000234142.5_Missense_Mutation_p.N196K|GREB1_ENST00000263834.5_Missense_Mutation_p.N196K|GREB1_ENST00000389825.3_Missense_Mutation_p.N86K|GREB1_ENST00000381483.2_Missense_Mutation_p.N196K	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	196						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)		TGGTCCGTAATGCACAAGGGA	0.478																																					p.N196K	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.T588A						PASS	.						126	120	122					2																	11716612		2203	4300	6503	SO:0001583	missense	9687	exon5			CCGTAATGCACAA		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.588T>A	chr2.hg19:g.11716612T>A	ENSP00000370896:p.Asn196Lys	168.0	0.0	.		192.0	8.0	.	NM_148903	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	hg19	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	T	17.98	3.520760	0.64747	.	.	ENSG00000196208	ENST00000381486;ENST00000263834;ENST00000389825;ENST00000381483;ENST00000234142	T;D;D;D;T	0.82167	3.02;-1.58;-1.58;-1.58;3.02	5.08	-3.82	0.04281	.	0.000000	0.85682	D	0.000000	D	0.84428	0.5470	M	0.66939	2.045	0.58432	D	0.99999	P;D;P;D	0.54772	0.94;0.968;0.897;0.959	P;P;P;P	0.54889	0.625;0.763;0.465;0.526	T	0.82952	-0.0202	10	0.72032	D	0.01	-8.2171	13.0658	0.59032	0.0:0.4458:0.0:0.5542	.	196;86;196;196	Q4ZG55-2;F8W6E5;Q4ZG55-3;Q4ZG55	.;.;.;GREB1_HUMAN	K	196;196;86;196;196	ENSP00000370896:N196K;ENSP00000263834:N196K;ENSP00000374475:N86K;ENSP00000370892:N196K;ENSP00000234142:N196K	ENSP00000234142:N196K	N	+	3	2	GREB1	11634063	0.667000	0.27484	0.014000	0.15608	0.860000	0.49131	-0.199000	0.09491	-1.399000	0.02063	-1.139000	0.01908	AAT	.	.	.	none		0.478	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		A	11716612	T	A	11716612	3	1	50	1	0	0	0	0	1	0	0	0	6767	1461	51	5	602	5	GREB1	2	11716612	Missense_Mutation	SNP	T	TCGA-A4-7915-01A-11D-2201-08		11716612	231482761	6	3394											
GRM2	2912	hgsc.bcm.edu	37	chr3	51750001	51750001	+	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	cgctggcctacaatgtgctcCtcatcgcgctctgcacgctt	5	11	9	16	4	2	0	1	0	1	0	4	0	3	0	2	1	3	5	2	1	2	2			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr3:51750001C>T	ENST00000395052.3	+	4	2446	c.2212C>T	c.(2212-2214)Ctc>Ttc	p.L738F	GRM2_ENST00000475478.1_3'UTR|GRM2_ENST00000442933.2_Intron	NM_000839.3	NP_000830.2	Q14416	GRM2_HUMAN	glutamate receptor, metabotropic 2	738					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)		CAATGTGCTCCTCATCGCGCT	0.577																																					p.L738F		Atlas-SNP	.											.	GRM2	91	.	0			c.C2212T						PASS	.						120	94	103					3																	51750001		2203	4300	6503	SO:0001583	missense	2912	exon4			GTGCTCCTCATCG	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.2212C>T	chr3.hg19:g.51750001C>T	ENSP00000378492:p.Leu738Phe	133.0	0.0	.		104.0	31.0	.	NM_000839	B0M0K7|Q14CU5|Q52MC6|Q9H3N6	Missense_Mutation	SNP	ENST00000395052.3	hg19	CCDS2834.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.937162	0.73557	.	.	ENSG00000164082	ENST00000395052	D	0.96365	-3.99	5.14	5.14	0.70334	GPCR, family 3, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.98604	0.9533	H	0.96604	3.85	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98917	1.0782	10	0.87932	D	0	.	10.6161	0.45451	0.0:0.8753:0.0:0.1247	.	738	Q14416	GRM2_HUMAN	F	738	ENSP00000378492:L738F	ENSP00000378492:L738F	L	+	1	0	GRM2	51725041	1.000000	0.71417	0.998000	0.56505	0.864000	0.49448	5.989000	0.70587	2.567000	0.86603	0.549000	0.68633	CTC	.	.	.	none		0.577	GRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346542.1			T	51750001	C	T	51750001	3	4	50	1	0	0	0	0	1	0	0	0	6804	681	24	2	2222	2	GRM2	3	51750001	Missense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08		51750001	146272429	7	3395											
CADPS	8618	hgsc.bcm.edu	37	chr3	62477094	62477096	+	In_Frame_Del	DEL	AAC	AAC	-																															tccatcagatccacatatctAacaacaagtggggcaaacag																										TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr3:62477094_62477096delAAC	ENST00000383710.4	-	21	3293_3295	c.2944_2946delGTT	c.(2944-2946)gttdel	p.V982del	CADPS_ENST00000283269.9_In_Frame_Del_p.V992del|CADPS_ENST00000357948.3_In_Frame_Del_p.V952del	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	982	Interaction with DRD2.|MHD1. {ECO:0000255|PROSITE- ProRule:PRU00587}.				catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		CCACATATCTAACAACAAGTGGG	0.419																																					p.992_993del		Atlas-INDEL	.											.	CADPS	387	.	0			c.2975_2977del						PASS	.																																			SO:0001651	inframe_deletion	8618	exon20			.	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.2944_2946delGTT	chr3.hg19:g.62477097_62477099delAAC	ENSP00000373215:p.Val982del	203.0	0.0	0		191.0	53.0	0.277487	NM_183394	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	In_Frame_Del	DEL	ENST00000383710.4	hg19	CCDS46858.1																																																																																			.	.	.	none		0.419	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394		-	62477096	AAC	-	62477094	7	5	50	1	0	1	0	1	0	0	0	0	2572	349	13	0	1155	0	CADPS	3	62477094	In_Frame_Del	DEL	AAC	TCGA-A4-7915-01A-11D-2201-08	10727093	62477094	135545336	8	3396											
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113376859	113376859	+	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	agttgaatcctgtaaagatgCatttgatgttttaattccta	12	17	7	5	0	0	3	0	2	0	1	2	3	2	3	2	0	1	4	2	0	5	7			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr3:113376859C>A	ENST00000478658.1	-	5	3687	c.3670G>T	c.(3670-3672)Gca>Tca	p.A1224S	KIAA2018_ENST00000316407.4_Missense_Mutation_p.A1224S|KIAA2018_ENST00000491165.1_Intron			Q68DE3	K2018_HUMAN	KIAA2018	1224						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						TGTAAAGATGCATTTGATGTT	0.418																																					p.A1224S		Atlas-SNP	.											.	KIAA2018	180	.	0			c.G3670T						PASS	.						86	83	84					3																	113376859		1945	4164	6109	SO:0001583	missense	205717	exon7			AAGATGCATTTGA	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.3670G>T	chr3.hg19:g.113376859C>A	ENSP00000420721:p.Ala1224Ser	97.0	0.0	.		101.0	29.0	.	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Missense_Mutation	SNP	ENST00000478658.1	hg19	CCDS43133.1	.	.	.	.	.	.	.	.	.	.	C	3.356	-0.131444	0.06753	.	.	ENSG00000176542	ENST00000316407;ENST00000478658	T;T	0.14022	2.54;2.54	5.67	3.84	0.44239	.	0.282276	0.34386	N	0.004013	T	0.05547	0.0146	N	0.14661	0.345	0.28041	N	0.933755	B	0.15141	0.012	B	0.12156	0.007	T	0.38950	-0.9637	10	0.07030	T	0.85	-2.1301	2.9175	0.05757	0.3149:0.4409:0.1391:0.1051	.	1224	Q68DE3	K2018_HUMAN	S	1224	ENSP00000320794:A1224S;ENSP00000420721:A1224S	ENSP00000320794:A1224S	A	-	1	0	KIAA2018	114859549	0.971000	0.33674	0.911000	0.35937	0.515000	0.34225	0.248000	0.18198	0.701000	0.31803	0.561000	0.74099	GCA	.	.	.	none		0.418	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		A	113376859	C	A	113376859	3	1	50	1	0	0	0	0	1	0	0	0	8275	710	25	4	3071	4	KIAA2018	3	113376859	Missense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08	50899765	113376859	84645571	9	3397											
ADAD1	132612	hgsc.bcm.edu	37	chr4	123305047	123305047	+	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	aaataaaaaggagtctagatCcaatgcagcaaaattagctc	19	8	7	7	0	1	1	0	0	1	1	3	2	2	2	1	1	3	3	1	1	9	3			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr4:123305047C>G	ENST00000296513.2	+	5	640	c.455C>G	c.(454-456)tCc>tGc	p.S152C	ADAD1_ENST00000388724.2_Missense_Mutation_p.S152C|ADAD1_ENST00000492454.1_3'UTR|ADAD1_ENST00000388725.2_Missense_Mutation_p.S134C	NM_139243.3	NP_640336.1	Q96M93	ADAD1_HUMAN	adenosine deaminase domain containing 1 (testis-specific)	152	DRBM. {ECO:0000255|PROSITE- ProRule:PRU00266}.				multicellular organismal development (GO:0007275)|RNA processing (GO:0006396)|spermatid development (GO:0007286)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	35						GAGTCTAGATCCAATGCAGCA	0.368																																					p.S152C		Atlas-SNP	.											.	ADAD1	94	.	0			c.C455G						PASS	.						123	120	121					4																	123305047		2203	4300	6503	SO:0001583	missense	132612	exon5			CTAGATCCAATGC	AK057303	CCDS34058.1, CCDS54800.1, CCDS54801.1	4q27	2007-05-31			ENSG00000164113	ENSG00000164113			30713	protein-coding gene	gene with protein product		614130				7543294, 9541871	Standard	NM_139243		Approved	Tenr	uc003iep.3	Q96M93	OTTHUMG00000150128	ENST00000296513.2:c.455C>G	chr4.hg19:g.123305047C>G	ENSP00000296513:p.Ser152Cys	99.0	0.0	.		115.0	29.0	.	NM_139243	A6NKN4|B7WPB0|D3DNX2|Q8IWG6|Q8NA06	Missense_Mutation	SNP	ENST00000296513.2	hg19	CCDS34058.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.993627	0.74703	.	.	ENSG00000164113	ENST00000446706;ENST00000296513;ENST00000439307;ENST00000388724;ENST00000388725	T;T;T;T;T	0.77620	-1.11;-1.11;-1.11;-1.11;-1.11	5.84	5.84	0.93424	Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1);	0.354445	0.30455	N	0.009587	T	0.82181	0.4981	L	0.29908	0.895	0.33397	D	0.576823	D;D	0.69078	0.996;0.997	D;D	0.66351	0.936;0.943	D	0.85408	0.1135	10	0.54805	T	0.06	-7.2127	18.912	0.92489	0.0:1.0:0.0:0.0	.	152;152	Q96M93-2;Q96M93	.;ADAD1_HUMAN	C	152;152;152;152;134	ENSP00000390510:S152C;ENSP00000296513:S152C;ENSP00000397254:S152C;ENSP00000373376:S152C;ENSP00000373377:S134C	ENSP00000296513:S152C	S	+	2	0	ADAD1	123524497	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.447000	0.35101	2.768000	0.95171	0.579000	0.79373	TCC	.	.	.	none		0.368	ADAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316452.1	NM_139243		G	123305047	C	G	123305047	3	3	50	1	0	0	0	0	1	0	0	0	231	855	30	4	465	4	ADAD1	4	123305047	Missense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08		123305047	67849229	10	3398											
C5orf40	408263	hgsc.bcm.edu	37	chr5	156769880	156769880	+	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	ctccccactctcattccccaCaatgaggcagtatagcgggt	9	9	8	15	1	1	1	1	1	1	0	4	1	3	1	4	2	1	2	4	2	3	3			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr5:156769880C>A	ENST00000312349.4	-	2	852	c.665G>T	c.(664-666)tGt>tTt	p.C222F	CYFIP2_ENST00000522463.1_Intron|CYFIP2_ENST00000442283.2_Intron|CYFIP2_ENST00000318218.6_Intron|CYFIP2_ENST00000347377.6_Intron|CYFIP2_ENST00000377576.3_Intron|CYFIP2_ENST00000435847.2_Intron|CYFIP2_ENST00000521420.1_Intron|CYFIP2_ENST00000541131.1_Intron	NM_001001343.3	NP_001001343.2	Q8TBE3	FNDC9_HUMAN	fibronectin type III domain containing 9	222						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	9						TCATTCCCCACAATGAGGCAG	0.547											OREG0016977	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C222F		Atlas-SNP	.											.	FNDC9	22	.	0			c.G665T						PASS	.						32	33	33					5																	156769880		2203	4300	6503	SO:0001583	missense	408263	exon2			TCCCCACAATGAG	BC022570	CCDS4337.1	5q33.3	2013-02-11	2011-01-25	2011-01-25	ENSG00000172568	ENSG00000172568		"Fibronectin type III domain containing"	33547	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 40"	C5orf40			Standard	NM_001001343		Approved	MGC27121	uc003lwu.2	Q8TBE3	OTTHUMG00000130248	ENST00000312349.4:c.665G>T	chr5.hg19:g.156769880C>A	ENSP00000310594:p.Cys222Phe	98.0	0.0	.	1781	94.0	4.0	.	NM_001001343	A8K0Y6	Missense_Mutation	SNP	ENST00000312349.4	hg19	CCDS4337.1	.	.	.	.	.	.	.	.	.	.	C	1.582	-0.531287	0.04112	.	.	ENSG00000172568	ENST00000312349	T	0.22134	1.97	5.08	-2.29	0.06805	.	1.364320	0.05031	N	0.474544	T	0.08626	0.0214	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30650	-0.9971	10	0.10111	T	0.7	-9.222	4.6072	0.12383	0.4398:0.2011:0.0:0.3591	.	222	Q8TBE3	FNDC9_HUMAN	F	222	ENSP00000310594:C222F	ENSP00000310594:C222F	C	-	2	0	FNDC9	156702458	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-1.134000	0.03228	-0.447000	0.07138	-0.339000	0.08088	TGT	.	.	.	none		0.547	FNDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252573.2	NM_001001343		A	156769880	C	A	156769880	3	1	50	1	0	0	0	0	1	0	0	0	2301	478	17	4	13	4	C5orf40	5	156769880	Missense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08		156769880	24145380	11	3399											
SLC35D3	340146	hgsc.bcm.edu	37	chr6	137245376	137245376	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggtgtggtgaagagcatcGccaccatcacggtgggcatg	8	8	16	9	2	1	2	1	1	0	1	2	2	1	2	2	4	1	2	2	4	1	0			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr6:137245376G>A	ENST00000331858.4	+	2	958	c.793G>A	c.(793-795)Gcc>Acc	p.A265T		NM_001008783.1	NP_001008783.1	Q5M8T2	S35D3_HUMAN	solute carrier family 35, member D3	265					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)		GAAGAGCATCGCCACCATCAC	0.592																																					p.A265T		Atlas-SNP	.											.	SLC35D3	33	.	0			c.G793A						PASS	.						77	64	68					6																	137245376		2203	4300	6503	SO:0001583	missense	340146	exon2			AGCATCGCCACCA		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.793G>A	chr6.hg19:g.137245376G>A	ENSP00000333591:p.Ala265Thr	72.0	0.0	.		76.0	12.0	.	NM_001008783	B4DI58|Q5QNZ6|Q6NX71	Missense_Mutation	SNP	ENST00000331858.4	hg19	CCDS34544.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.354459	0.82243	.	.	ENSG00000182747	ENST00000331858	T	0.64085	-0.08	5.68	5.68	0.88126	Domain of unknown function DUF250 (1);	0.056787	0.64402	D	0.000001	T	0.63034	0.2477	L	0.36672	1.1	0.58432	D	0.999995	D	0.67145	0.996	P	0.60682	0.878	T	0.58713	-0.7588	10	0.34782	T	0.22	-25.1818	19.7951	0.96477	0.0:0.0:1.0:0.0	.	265	Q5M8T2	S35D3_HUMAN	T	265	ENSP00000333591:A265T	ENSP00000333591:A265T	A	+	1	0	SLC35D3	137287069	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.777000	0.85628	2.698000	0.92095	0.561000	0.74099	GCC	.	.	.	none		0.592	SLC35D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042389.2	XM_294017		A	137245376	G	A	137245376	3	1	50	1	0	0	0	0	1	0	0	0	14596	1087	38	1	799	1	SLC35D3	6	137245376	Missense_Mutation	SNP	G	TCGA-A4-7915-01A-11D-2201-08		137245376	33869691	12	3400											
IFNGR1	3459	hgsc.bcm.edu	37	chr6	137519461	137519461	+	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	ggagtgatacgagtttaaagCgatgctgccaggttcagact	11	10	13	7	2	1	2	1	1	0	1	1	5	1	3	1	2	4	3	1	2	3	4			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr6:137519461C>A	ENST00000367739.4	-	7	1298	c.1177G>T	c.(1177-1179)Gct>Tct	p.A393S	IFNGR1_ENST00000543628.1_Missense_Mutation_p.A365S	NM_000416.2	NP_000407.1	P15260	INGR1_HUMAN	interferon gamma receptor 1	393					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)	GAGTTTAAAGCGATGCTGCCA	0.443																																					p.A393S		Atlas-SNP	.											.	IFNGR1	46	.	0			c.G1177T						PASS	.						88	88	88					6																	137519461		2203	4300	6503	SO:0001583	missense	3459	exon7			TTAAAGCGATGCT		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.1177G>T	chr6.hg19:g.137519461C>A	ENSP00000356713:p.Ala393Ser	125.0	0.0	.		103.0	5.0	.	NM_000416	B4DFT7|E1P587|Q53Y96	Missense_Mutation	SNP	ENST00000367739.4	hg19	CCDS5185.1	.	.	.	.	.	.	.	.	.	.	C	11.90	1.776120	0.31411	.	.	ENSG00000027697	ENST00000367739;ENST00000543628	T;T	0.72394	-0.65;-0.49	6.06	-12.1	0.00011	.	2.161120	0.01880	N	0.037820	T	0.20577	0.0495	N	0.12182	0.205	0.09310	N	1	B;B	0.20164	0.031;0.042	B;B	0.22601	0.04;0.03	T	0.10917	-1.0609	10	0.27082	T	0.32	-0.1572	5.4548	0.16584	0.1953:0.5294:0.0993:0.176	.	365;393	F5H5M7;P15260	.;INGR1_HUMAN	S	393;365	ENSP00000356713:A393S;ENSP00000443282:A365S	ENSP00000356713:A393S	A	-	1	0	IFNGR1	137561154	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-1.897000	0.01603	-2.423000	0.00562	-1.202000	0.01658	GCT	.	.	.	none		0.443	IFNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042401.1			A	137519461	C	A	137519461	3	1	50	1	0	0	0	0	1	0	0	0	7556	768	27	4	296	4	IFNGR1	6	137519461	Missense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08	274085	137519461	33595606	13	3401											
LAMB1	3912	hgsc.bcm.edu	37	chr7	107572810	107572810	+	Missense_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	ggaacaggaggcccctggggGtgttccacaggtctgcaaca	9	6	15	11	0	1	0	0	0	1	0	2	2	2	2	3	6	3	2	3	6	2	1			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr7:107572810G>A	ENST00000222399.6	-	28	4431	c.4201C>T	c.(4201-4203)Ccc>Tcc	p.P1401S	LAMB1_ENST00000474380.1_5'UTR|LAMB1_ENST00000393561.1_Missense_Mutation_p.P1425S	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	1401	Domain alpha.				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.P1401T(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						GCCCCTGGGGGTGTTCCACAG	0.592																																					p.P1401S		Atlas-SNP	.											LAMB1,NS,carcinoma,0,1	LAMB1	185	.	1	Substitution - Missense(1)	lung(1)	c.C4201T						PASS	.						67	64	65					7																	107572810		2203	4300	6503	SO:0001583	missense	3912	exon28			CTGGGGGTGTTCC	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.4201C>T	chr7.hg19:g.107572810G>A	ENSP00000222399:p.Pro1401Ser	132.0	1.0	.		152.0	45.0	.	NM_002291	Q14D91	Missense_Mutation	SNP	ENST00000222399.6	hg19	CCDS5750.1	.	.	.	.	.	.	.	.	.	.	G	12.37	1.918956	0.33908	.	.	ENSG00000091136	ENST00000393561;ENST00000222399	T;T	0.29917	1.55;1.55	5.28	5.28	0.74379	.	.	.	.	.	T	0.24890	0.0604	L	0.37850	1.14	0.33891	D	0.637353	B;B	0.17667	0.023;0.014	B;B	0.17098	0.017;0.016	T	0.20042	-1.0287	9	0.45353	T	0.12	.	9.8304	0.40939	0.0744:0.1405:0.7851:0.0	.	1401;1425	P07942;G3XAI2	LAMB1_HUMAN;.	S	1425;1401	ENSP00000377191:P1425S;ENSP00000222399:P1401S	ENSP00000222399:P1401S	P	-	1	0	LAMB1	107360046	0.999000	0.42202	0.979000	0.43373	0.967000	0.64934	4.639000	0.61361	2.627000	0.88993	0.655000	0.94253	CCC	.	.	.	none		0.592	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291		A	107572810	G	A	107572810	3	1	50	1	0	0	0	0	1	0	0	0	8617	1261	44	2	1187	2	LAMB1	7	107572810	Missense_Mutation	SNP	G	TCGA-A4-7915-01A-11D-2201-08		107572810	51565853	14	3402											
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121653581	121653581	+	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	cacaagtgtatcctcagacaGtcaaactggtatggacagaa	15	8	9	9	0	2	2	2	0	0	2	3	3	3	3	1	2	1	2	1	2	5	2			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr7:121653581G>T	ENST00000393386.2	+	12	4892	c.4481G>T	c.(4480-4482)aGt>aTt	p.S1494I	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	1494					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						TCCTCAGACAGTCAAACTGGT	0.398																																					p.S1494I		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.G4481T						PASS	.						88	85	86					7																	121653581		2203	4300	6503	SO:0001583	missense	5803	exon12			CAGACAGTCAAAC	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.4481G>T	chr7.hg19:g.121653581G>T	ENSP00000377047:p.Ser1494Ile	78.0	0.0	.		91.0	29.0	.	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	hg19	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.756857	0.49362	.	.	ENSG00000106278	ENST00000393386	T	0.54071	0.59	4.95	4.07	0.47477	.	0.299113	0.33057	N	0.005339	T	0.43456	0.1248	L	0.44542	1.39	0.80722	D	1	B	0.33379	0.41	B	0.35550	0.205	T	0.33394	-0.9870	10	0.37606	T	0.19	.	9.1534	0.36978	0.1675:0.0:0.8325:0.0	.	1494	P23471	PTPRZ_HUMAN	I	1494	ENSP00000377047:S1494I	ENSP00000377047:S1494I	S	+	2	0	PTPRZ1	121440817	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	1.448000	0.35112	1.215000	0.43411	0.555000	0.69702	AGT	.	.	.	none		0.398	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		T	121653581	G	T	121653581	3	4	50	1	0	0	0	0	1	0	0	0	12827	1029	36	4	4527	4	PTPRZ1	7	121653581	Missense_Mutation	SNP	G	TCGA-A4-7915-01A-11D-2201-08	14080771	121653581	37485082	15	3403											
SCARA5	286133	hgsc.bcm.edu	37	chr8	27737097	27737097	+	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	gcgccttaccttgcccgaatCgagctgtgcggtacacctcc	6	9	10	16	4	0	0	0	0	0	0	2	2	1	0	5	1	5	2	5	1	3	3			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr8:27737097C>T	ENST00000354914.3	-	8	1825	c.1340G>A	c.(1339-1341)cGa>cAa	p.R447Q	SCARA5_ENST00000380385.2_Missense_Mutation_p.R222Q	NM_173833.5	NP_776194.2	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5	447	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				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)	p.R447P(1)		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)		TTGCCCGAATCGAGCTGTGCG	0.622																																					p.R447Q		Atlas-SNP	.											SCARA5,NS,carcinoma,0,1	SCARA5	53	.	1	Substitution - Missense(1)	lung(1)	c.G1340A						PASS	.						142	110	121					8																	27737097		2203	4300	6503	SO:0001583	missense	286133	exon8			CCGAATCGAGCTG	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.1340G>A	chr8.hg19:g.27737097C>T	ENSP00000346990:p.Arg447Gln	171.0	0.0	.		187.0	49.0	.	NM_173833	Q6UXZ1|Q7Z4A1|Q8N4Z7	Missense_Mutation	SNP	ENST00000354914.3	hg19	CCDS6064.1	.	.	.	.	.	.	.	.	.	.	C	14.29	2.491434	0.44249	.	.	ENSG00000168079	ENST00000354914;ENST00000380385	T;T	0.44482	0.92;0.92	4.87	1.96	0.26148	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.165261	0.40554	N	0.001077	T	0.28732	0.0712	L	0.38649	1.16	0.80722	D	1	B;B	0.22851	0.003;0.076	B;B	0.15870	0.003;0.014	T	0.07501	-1.0769	10	0.46703	T	0.11	.	7.6192	0.28175	0.0:0.6991:0.0:0.3009	.	222;447	Q6ZMJ2-4;Q6ZMJ2	.;SCAR5_HUMAN	Q	447;222	ENSP00000346990:R447Q;ENSP00000369746:R222Q	ENSP00000346990:R447Q	R	-	2	0	SCARA5	27793016	0.174000	0.23070	0.360000	0.25837	0.505000	0.33919	1.411000	0.34702	0.536000	0.28733	0.591000	0.81541	CGA	.	.	.	none		0.622	SCARA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255223.2	NM_173833		T	27737097	C	T	27737097	3	4	50	1	0	0	0	0	1	0	0	0	13893	884	31	1	155	1	SCARA5	8	27737097	Missense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08		27737097	118626925	16	3404											
RAD21	5885	hgsc.bcm.edu	37	chr8	117862960	117862960	+	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	agatatttggaggttcttctGggggaagctctacaggtggt	8	13	15	5	0	3	1	0	0	3	1	3	3	3	3	0	6	2	2	0	6	3	5			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr8:117862960G>A	ENST00000297338.2	-	12	1804	c.1517C>T	c.(1516-1518)cCa>cTa	p.P506L	RAD21_ENST00000523986.1_Missense_Mutation_p.P10L|RAD21_ENST00000518055.1_Missense_Mutation_p.P51L|RAD21_ENST00000517749.1_5'Flank	NM_006265.2	NP_006256.1	O60216	RAD21_HUMAN	RAD21 homolog (S. pombe)	506	Pro-rich.				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)					AGGTTCTTCTGGGGGAAGCTC	0.378																																					p.P506L		Atlas-SNP	.											.	RAD21	95	.	0			c.C1517T						PASS	.						131	130	130					8																	117862960		2203	4300	6503	SO:0001583	missense	5885	exon12			TCTTCTGGGGGAA	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.1517C>T	chr8.hg19:g.117862960G>A	ENSP00000297338:p.Pro506Leu	150.0	0.0	.		173.0	7.0	.	NM_006265	A8K0E0|Q15001|Q99568	Missense_Mutation	SNP	ENST00000297338.2	hg19	CCDS6321.1	.	.	.	.	.	.	.	.	.	.	G	16.75	3.208572	0.58343	.	.	ENSG00000164754	ENST00000297338;ENST00000523986;ENST00000518055	T;T;T	0.80123	0.64;-1.34;-0.19	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.77585	0.4152	L	0.60455	1.87	0.80722	D	1	B	0.31318	0.319	B	0.27608	0.081	T	0.74262	-0.3722	10	0.22109	T	0.4	-6.1488	19.0827	0.93188	0.0:0.0:1.0:0.0	.	506	O60216	RAD21_HUMAN	L	506;10;51	ENSP00000297338:P506L;ENSP00000428513:P10L;ENSP00000428003:P51L	ENSP00000297338:P506L	P	-	2	0	RAD21	117932141	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	7.869000	0.87170	2.477000	0.83638	0.460000	0.39030	CCA	.	.	.	none		0.378	RAD21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381184.1	NM_006265		A	117862960	G	A	117862960	3	1	50	1	0	0	0	0	1	0	0	0	12994	1348	47	2	390	2	RAD21	8	117862960	Missense_Mutation	SNP	G	TCGA-A4-7915-01A-11D-2201-08	90125863	117862960	28501062	17	3405											
CCIN	881	hgsc.bcm.edu	37	chr9	36170395	36170395	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gttcaatgatggagtgtttgCttatatcatccaggagaacc	11	13	10	7	0	2	2	2	1	0	1	3	4	3	3	2	2	2	3	2	2	4	4			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr9:36170395C>T	ENST00000335119.2	+	1	1007	c.896C>T	c.(895-897)gCt>gTt	p.A299V		NM_005893.2	NP_005884.2	Q13939	CALI_HUMAN	calicin	299					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				breast(3)|endometrium(2)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(4)	21			STAD - Stomach adenocarcinoma(86;0.228)			GGAGTGTTTGCTTATATCATC	0.557																																					p.A299V		Atlas-SNP	.											.	CCIN	56	.	0			c.C896T						PASS	.						79	75	76					9																	36170395		2203	4300	6503	SO:0001583	missense	881	exon1			TGTTTGCTTATAT	Z46967	CCDS6599.1	9p13.1	2013-10-02			ENSG00000185972	ENSG00000185972		"BTB/POZ domain containing"	1568	protein-coding gene	gene with protein product		603960				7641791	Standard	NM_005893		Approved	KBTBD14, BTBD20	uc003zzb.4	Q13939	OTTHUMG00000019901	ENST00000335119.2:c.896C>T	chr9.hg19:g.36170395C>T	ENSP00000334996:p.Ala299Val	169.0	0.0	.		135.0	8.0	.	NM_005893	Q9BXG7	Missense_Mutation	SNP	ENST00000335119.2	hg19	CCDS6599.1	.	.	.	.	.	.	.	.	.	.	C	17.90	3.502198	0.64298	.	.	ENSG00000185972	ENST00000335119	T	0.65732	-0.17	5.97	5.97	0.96955	Kelch-type beta propeller (1);	0.000000	0.56097	D	0.000024	T	0.66577	0.2803	L	0.29908	0.895	0.39812	D	0.972727	D	0.63880	0.993	D	0.68192	0.956	T	0.59386	-0.7464	10	0.12766	T	0.61	.	15.9243	0.79603	0.0:1.0:0.0:0.0	.	299	Q13939	CALI_HUMAN	V	299	ENSP00000334996:A299V	ENSP00000334996:A299V	A	+	2	0	CCIN	36160395	0.997000	0.39634	1.000000	0.80357	0.954000	0.61252	4.483000	0.60264	2.839000	0.97877	0.655000	0.94253	GCT	.	.	.	none		0.557	CCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052418.1	NM_005893		T	36170395	C	T	36170395	3	4	50	1	0	0	0	0	1	0	0	0	2880	797	28	2	898	2	CCIN	9	36170395	Missense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08		36170395	105043036	18	3406											
ANO5	203859	hgsc.bcm.edu	37	chr11	22294380	22294380	+	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	tggcctcttttcctttggctCctcttcttgctctcataaat	4	19	5	13	0	4	0	1	0	4	0	7	0	6	0	3	2	1	2	3	2	2	6			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr11:22294380C>A	ENST00000324559.8	+	19	2397	c.2080C>A	c.(2080-2082)Cct>Act	p.P694T	ANO5_ENST00000532043.1_3'UTR	NM_001142649.1|NM_213599.2	NP_001136121.1|NP_998764.1	Q75V66	ANO5_HUMAN	anoctamin 5	694					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)	p.P694fs*7(1)		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						TCCTTTGGCTCCTCTTCTTGC	0.378																																					p.P694T		Atlas-SNP	.											.,1	ANO5	162	.	1	Deletion - Frameshift(1)	breast(1)	c.C2080A						PASS	.						150	131	138					11																	22294380		2203	4300	6503	SO:0001583	missense	203859	exon19			TTGGCTCCTCTTC	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.2080C>A	chr11.hg19:g.22294380C>A	ENSP00000315371:p.Pro694Thr	98.0	1.0	.		98.0	29.0	.	NM_213599		Missense_Mutation	SNP	ENST00000324559.8	hg19	CCDS31444.1	.	.	.	.	.	.	.	.	.	.	c	21.0	4.087948	0.76642	.	.	ENSG00000171714	ENST00000324559	T	0.68025	-0.3	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	D	0.84606	0.5509	H	0.96748	3.875	0.80722	D	1	B	0.22276	0.067	B	0.39771	0.309	D	0.85101	0.0957	10	0.87932	D	0	.	19.9071	0.97012	0.0:1.0:0.0:0.0	.	694	Q75V66	ANO5_HUMAN	T	694	ENSP00000315371:P694T	ENSP00000315371:P694T	P	+	1	0	ANO5	22250956	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.767000	0.85331	2.776000	0.95493	0.651000	0.88453	CCT	.	.	.	none		0.378	ANO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387615.1	NM_213599		A	22294380	C	A	22294380	3	1	50	1	0	0	0	0	1	0	0	0	700	855	30	4	2154	4	ANO5	11	22294380	Missense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08		22294380	112712136	19	3407											
RCOR2	283248	hgsc.bcm.edu	37	chr11	63679913	63679913	+	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	cctccagattgaagcggcgcCggtagctcacaaagaaagtc	12	6	11	12	3	1	3	1	1	0	2	3	3	2	3	3	2	2	2	3	2	4	2			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr11:63679913C>A	ENST00000301459.4	-	11	1508	c.1121G>T	c.(1120-1122)cGg>cTg	p.R374L	RCOR2_ENST00000473926.2_5'Flank	NM_173587.3	NP_775858.2	Q8IZ40	RCOR2_HUMAN	REST corepressor 2	374	SANT 2. {ECO:0000255|PROSITE- ProRule:PRU00624}.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	17						GAAGCGGCGCCGGTAGCTCAC	0.587																																					p.R374L		Atlas-SNP	.											.	RCOR2	43	.	0			c.G1121T						PASS	.						64	76	72					11																	63679913		2201	4297	6498	SO:0001583	missense	283248	exon11			CGGCGCCGGTAGC	BC010608	CCDS8052.1	11q13.1	2008-02-05			ENSG00000167771	ENSG00000167771			27455	protein-coding gene	gene with protein product						12477932	Standard	NM_173587		Approved		uc001nyc.3	Q8IZ40	OTTHUMG00000150472	ENST00000301459.4:c.1121G>T	chr11.hg19:g.63679913C>A	ENSP00000301459:p.Arg374Leu	188.0	0.0	.		180.0	55.0	.	NM_173587	Q96FP3	Missense_Mutation	SNP	ENST00000301459.4	hg19	CCDS8052.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.040706	0.93685	.	.	ENSG00000167771	ENST00000301459	T	0.37411	1.2	4.55	4.55	0.56014	Myb, DNA-binding (1);SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);SANT, eukarya (1);	0.000000	0.85682	D	0.000000	T	0.66237	0.2769	M	0.89287	3.02	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.74237	-0.3730	10	0.87932	D	0	.	16.6282	0.84992	0.0:1.0:0.0:0.0	.	374	Q8IZ40	RCOR2_HUMAN	L	374	ENSP00000301459:R374L	ENSP00000301459:R374L	R	-	2	0	RCOR2	63436489	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.314000	0.78988	2.536000	0.85505	0.561000	0.74099	CGG	.	.	.	none		0.587	RCOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318233.1	NM_173587		A	63679913	C	A	63679913	3	1	50	1	0	0	0	0	1	0	0	0	13196	652	23	4	458	4	RCOR2	11	63679913	Missense_Mutation	SNP	C	TCGA-A4-7915-01A-11D-2201-08	41385533	63679913	71326603	20	3408											
RBM4B	83759	hgsc.bcm.edu	37	chr11	66444485	66444485	+	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	agcaccttcccatactgctcGaagagtgagcgaatctcctg	10	9	9	13	2	1	2	0	1	1	1	4	4	2	2	3	0	4	2	3	0	3	2			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr11:66444485G>A	ENST00000525754.1	-	1	734	c.66C>T	c.(64-66)ttC>ttT	p.F22F	RBM4B_ENST00000524637.1_Silent_p.F22F|RBM4B_ENST00000531969.1_Silent_p.F22F|RBM4B_ENST00000531036.2_Silent_p.F22F|RBM4B_ENST00000310046.4_Silent_p.F22F			Q9BQ04	RBM4B_HUMAN	RNA binding motif protein 4B	22	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|entrainment of circadian clock by photoperiod (GO:0043153)|mRNA processing (GO:0006397)|positive regulation of gene expression (GO:0010628)|regulation of translation (GO:0006417)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(4)|lung(1)|urinary_tract(2)	10						CATACTGCTCGAAGAGTGAGC	0.512																																					p.F22F		Atlas-SNP	.											.	RBM4B	27	.	0			c.C66T						PASS	.						91	91	91					11																	66444485		2200	4295	6495	SO:0001819	synonymous_variant	83759	exon2			CTGCTCGAAGAGT	AK095158	CCDS8149.1, CCDS66144.1	11q13	2013-02-12	2006-01-25	2006-01-25				"Zinc fingers, CCHC domain containing", "RNA binding motif (RRM) containing"	28842	protein-coding gene	gene with protein product			"RNA binding motif protein 30"	RBM30		12477932	Standard	XR_247213		Approved	MGC10871, ZCCHC15, RBM4L, ZCRB3B, ZCCHC21B	uc001ojb.3	Q9BQ04		ENST00000525754.1:c.66C>T	chr11.hg19:g.66444485G>A		259.0	0.0	.		235.0	52.0	.	NM_031492	B3KT83	Silent	SNP	ENST00000525754.1	hg19	CCDS8149.1																																																																																			.	.	.	none		0.512	RBM4B-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393851.1	NM_031492		A	66444485	G	A	66444485	2	1	50	1	0	0	0	0	0	0	0	1	13155	1049	37	1		1	RBM4B	11	66444485	Silent	SNP	G	TCGA-A4-7915-01A-11D-2201-08	2764572	66444485	68562031	21	3409											
SLC36A4	120103	hgsc.bcm.edu	37	chr11	92917687	92917687	+	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	gcataagagtttgtacaaatCtgaaaagtaaaagttgtaag	18	11	9	3	0	1	2	0	1	1	1	1	2	1	2	0	0	1	6	0	0	8	6			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr11:92917687C>A	ENST00000326402.4	-	3	310		c.e3-1		SLC36A4_ENST00000529184.1_Splice_Site	NM_152313.2	NP_689526.2	Q6YBV0	S36A4_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 4						L-alanine transport (GO:0015808)|proline transport (GO:0015824)|tryptophan transport (GO:0015827)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	25		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TTGTACAAATCTGAAAAGTAA	0.313																																					.		Atlas-SNP	.											.	SLC36A4	61	.	0			c.180-1G>T						PASS	.						99	105	103					11																	92917687		2201	4297	6498	SO:0001630	splice_region_variant	120103	exon4			ACAAATCTGAAAA	AY162216	CCDS8291.1, CCDS66202.1	11q21	2013-05-22			ENSG00000180773	ENSG00000180773		"Solute carriers"	19660	protein-coding gene	gene with protein product		613760					Standard	XM_005273758		Approved	PAT4, FLJ38932	uc001pdn.3	Q6YBV0	OTTHUMG00000167368	ENST00000326402.4:c.180-1G>T	chr11.hg19:g.92917687C>A		135.0	0.0	.		135.0	50.0	.	NM_152313	Q86X30|Q8IVM5|Q8N8S6	Splice_Site	SNP	ENST00000326402.4	hg19	CCDS8291.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.172159	0.78452	.	.	ENSG00000180773	ENST00000326402	.	.	.	6.07	6.07	0.98685	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.2544	0.98414	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC36A4	92557335	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.132000	0.71676	2.885000	0.99019	0.655000	0.94253	.	.	.	.	none		0.313	SLC36A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394329.2		Intron	A	92917687	C	A	92917687	5	1	50	1	0	0	0	0	0	0	1	0	14609	927	32	4	1371	4	SLC36A4	11	92917687	Splice_Site	SNP	C	TCGA-A4-7915-01A-11D-2201-08	26473202	92917687	42088829	22	3410											
ITGAL	3683	hgsc.bcm.edu	37	chr16	30490672	30490672	+	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	aatgtatcaagggcaacgtaGacctggtatttctgtttgat	11	14	10	6	1	2	2	1	1	1	1	2	2	2	2	1	2	1	5	1	2	6	5			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr16:30490672G>A	ENST00000356798.6	+	6	646	c.466G>A	c.(466-468)Gac>Aac	p.D156N	ITGAL_ENST00000433423.2_Intron|ITGAL_ENST00000358164.5_Intron|ITGAL_ENST00000454514.2_Intron|RP11-297C4.3_ENST00000562525.1_RNA|RP11-297C4.2_ENST00000569459.1_RNA	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	156	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell proliferation (GO:0042102)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(10)|kidney(4)|large_intestine(12)|lung(32)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	76					Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227)	GGGCAACGTAGACCTGGTATT	0.478																																					p.D156N	NSCLC(110;1462 1641 3311 33990 49495)	Atlas-SNP	.											.	ITGAL	149	.	0			c.G466A						PASS	.						120	108	112					16																	30490672		2197	4300	6497	SO:0001583	missense	3683	exon6			AACGTAGACCTGG		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.466G>A	chr16.hg19:g.30490672G>A	ENSP00000349252:p.Asp156Asn	104.0	0.0	.		101.0	43.0	.	NM_002209	O43746|Q45H73|Q96HB1|Q9UBC8	Missense_Mutation	SNP	ENST00000356798.6	hg19	CCDS32433.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.796940	0.90453	.	.	ENSG00000005844	ENST00000356798	D	0.92149	-2.98	5.98	5.98	0.97165	von Willebrand factor, type A (3);	0.000000	0.56097	D	0.000021	D	0.94434	0.8209	M	0.73430	2.235	0.80722	D	1	P	0.44006	0.824	P	0.51193	0.662	D	0.94464	0.7679	10	0.72032	D	0.01	.	17.3632	0.87357	0.0:0.0:1.0:0.0	.	156	P20701	ITAL_HUMAN	N	156	ENSP00000349252:D156N	ENSP00000349252:D156N	D	+	1	0	ITGAL	30398173	1.000000	0.71417	0.978000	0.43139	0.941000	0.58515	4.655000	0.61476	2.838000	0.97847	0.514000	0.50259	GAC	.	.	.	none		0.478	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2			A	30490672	G	A	30490672	3	1	50	1	0	0	0	0	1	0	0	0	7893	942	33	2	488	2	ITGAL	16	30490672	Missense_Mutation	SNP	G	TCGA-A4-7915-01A-11D-2201-08		30490672	59864081	23	3411											
DNAJA2	10294	hgsc.bcm.edu	37	chr16	47005807	47005807	+	Splice_Site	DEL	C	C	-																															aaaaaggtgcaaataacttaCtttgtctcctgcatttggat																										TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr16:47005807delC	ENST00000317089.5	-	2	354		c.e2+1		RP11-169E6.1_ENST00000562536.1_RNA	NM_005880.3	NP_005871.1	O60884	DNJA2_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 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)				AAATAACTTACTTTGTCTCCT	0.343																																					.		Atlas-INDEL	.											.	DNAJA2	28	.	0			c.138+2G>-						PASS	.						127	126	126					16																	47005807		2203	4300	6503	SO:0001630	splice_region_variant	10294	exon3			.	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.138+1G>-	chr16.hg19:g.47005807delC		179.0	0.0	0		155.0	47.0	0.303226	NM_005880	B2R7L7|O14711	Splice_Site	DEL	ENST00000317089.5	hg19	CCDS10726.1																																																																																			.	.	.	none		0.343	DNAJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256769.2		Intron	-	47005807	C	-	47005807	8	5	50	1	0	1	0	1	0	0	1	0	4614	579	20	0	1131	0	DNAJA2	16	47005807	Splice_Site	DEL	C	TCGA-A4-7915-01A-11D-2201-08	16515135	47005807	43348946	24	3412											
SHD	56961	hgsc.bcm.edu	37	chr19	4290585	4290585	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccactgccggtgcagggtgcCgagcatctggctctgctgta	5	9	14	13	2	2	0	0	0	2	0	2	1	2	0	3	3	5	5	3	3	1	1	rs111268424		TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr19:4290585C>T	ENST00000543264.2	+	6	2441	c.978C>T	c.(976-978)gcC>gcT	p.A326A	SHD_ENST00000599689.1_Silent_p.A286A	NM_020209.3	NP_064594.3	Q96IW2	SHD_HUMAN	Src homology 2 domain containing transforming protein D	326	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.									breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|stomach(1)	14				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0337)|STAD - Stomach adenocarcinoma(1328;0.18)		TGCAGGGTGCCGAGCATCTGG	0.657																																					p.A326A		Atlas-SNP	.											.	SHD	33	.	0			c.C978T						PASS	.						59	53	55					19																	4290585		2203	4300	6503	SO:0001819	synonymous_variant	56961	exon6			GGGTGCCGAGCAT	BC007206	CCDS12125.1	19p13.3	2013-02-14				ENSG00000105251		"SH2 domain containing"	30633	protein-coding gene	gene with protein product		610481				9315092	Standard	NM_020209		Approved		uc002lzw.2	Q96IW2		ENST00000543264.2:c.978C>T	chr19.hg19:g.4290585C>T		105.0	0.0	.		107.0	42.0	.	NM_020209	Q96NC2	Silent	SNP	ENST00000543264.2	hg19	CCDS12125.1																																																																																			.	C|0.500;T|0.500	0.500	weak		0.657	SHD-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458082.1	NM_020209		T	4290585	C	T	4290585	2	4	50	1	0	0	0	0	0	0	0	1	14288	639	23	1		1	SHD	19	4290585	Silent	SNP	C	TCGA-A4-7915-01A-11D-2201-08		4290585	54838398	25	3413											
ARHGAP35	2909	hgsc.bcm.edu	37	chr19	47422875	47422875	+	Frame_Shift_Del	DEL	C	C	-																															atgtctacctggaagggactCagaaagccaagaagctgttt																										TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr19:47422875delC	ENST00000404338.3	+	1	943	c.943delC	c.(943-945)cagfs	p.Q315fs		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	315	FF 1.				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)										GGAAGGGACTCAGAAAGCCAA	0.507																																					p.T314fs		Atlas-INDEL	.											.	.	.	.	0			c.942delT						PASS	.						32	32	32					19																	47422875		1979	4167	6146	SO:0001589	frameshift_variant	2909	exon1			.	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.943delC	chr19.hg19:g.47422875delC	ENSP00000385720:p.Gln315fs	55.0	0.0	0		46.0	13.0	0.282609	NM_004491	A7E2A4|Q14452|Q9C0E1	Frame_Shift_Del	DEL	ENST00000404338.3	hg19	CCDS46127.1																																																																																			.	.	.	none		0.507	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491		-	47422875	C	-	47422875	7	5	50	1	0	1	0	1	0	0	0	0	6802	827	29	0	945	0	ARHGAP35	19	47422875	Frame_Shift_Del	DEL	C	TCGA-A4-7915-01A-11D-2201-08	43132290	47422875	11706108	26	3414											
TP53RK	112858	hgsc.bcm.edu	37	chr20	45315804	45315804	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcgaacagtcactgagcctTcaatttcttccatatataag	12	13	5	11	1	3	1	2	1	1	0	5	2	4	1	2	0	2	0	2	0	5	6			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr20:45315804T>C	ENST00000372102.3	-	2	380	c.355A>G	c.(355-357)Aag>Gag	p.K119E	RP1-28H20.3_ENST00000606362.1_lincRNA			Q96S44	PRPK_HUMAN	TP53 regulating kinase	0	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				lipopolysaccharide biosynthetic process (GO:0009103)|protein phosphorylation (GO:0006468)|tRNA processing (GO:0008033)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|hydrolase activity (GO:0016787)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|large_intestine(1)|lung(4)|skin(1)	7		Myeloproliferative disorder(115;0.0122)				CACTGAGCCTTCAATTTCTTC	0.418																																					p.E117G		Atlas-SNP	.											.	TP53RK	13	.	0			c.A350G						PASS	.						151	172	165					20																	45315804		2202	4300	6502	SO:0001583	missense	112858	exon2			GAGCCTTCAATTT		CCDS13401.1	20q13.2	2014-05-14	2004-05-10	2004-05-12	ENSG00000172315	ENSG00000172315			16197	protein-coding gene	gene with protein product		608679	"chromosome 20 open reading frame 64"	C20orf64		11546806, 12914926	Standard	NM_033550		Approved	dJ101A2.2, prpk, Nori-2p, BUD32	uc002xsk.3	Q96S44	OTTHUMG00000085887	ENST00000372102.3:c.355A>G	chr20.hg19:g.45315804T>C	ENSP00000361174:p.Lys119Glu	408.0	1.0	.		360.0	116.0	.	NM_033550	B3KU44|Q3T977|Q5JZ01|Q6NZ60|Q96FM7|Q9NQE6	Missense_Mutation	SNP	ENST00000372102.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.74|11.74	1.727453|1.727453	0.30593|0.30593	.|.	.|.	ENSG00000172315|ENSG00000172315	ENST00000372114|ENST00000372102	T|T	0.12361|0.47869	2.69|0.83	5.38|5.38	3.04|3.04	0.35103|0.35103	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.167964|.	0.52532|.	D|.	0.000073|.	T|T	0.33731|0.33731	0.0873|0.0873	L|L	0.39898|0.39898	1.24|1.24	0.23677|0.23677	N|N	0.997139|0.997139	P|B	0.49961|0.31548	0.93|0.328	P|B	0.53224|0.34242	0.721|0.178	T|T	0.25641|0.25641	-1.0126|-1.0126	10|9	0.42905|0.07644	T|T	0.14|0.81	-10.1094|-10.1094	6.7483|6.7483	0.23474|0.23474	0.1725:0.0:0.2393:0.5882|0.1725:0.0:0.2393:0.5882	.|.	117|119	Q96S44|Q5JZ02	PRPK_HUMAN|.	G|E	117|119	ENSP00000361186:E117G|ENSP00000361174:K119E	ENSP00000361186:E117G|ENSP00000361174:K119E	E|K	-|-	2|1	0|0	TP53RK|TP53RK	44749211|44749211	0.999000|0.999000	0.42202|0.42202	0.971000|0.971000	0.41717|0.41717	0.502000|0.502000	0.33828|0.33828	1.944000|1.944000	0.40263|0.40263	0.449000|0.449000	0.26747|0.26747	-0.313000|-0.313000	0.08912|0.08912	GAA|AAG	.	.	.	none		0.418	TP53RK-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000193688.1	NM_033550		C	45315804	T	C	45315804	3	2	50	1	0	0	0	0	1	0	0	0	16402	1783	62	3	415	3	TP53RK	20	45315804	Missense_Mutation	SNP	T	TCGA-A4-7915-01A-11D-2201-08		45315804	17709716	27	3415											
KDELR3	11015	hgsc.bcm.edu	37	chr22	38877225	38877225	+	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	tctttggctcagatcctctgGactttctctatctatctgga	6	17	7	11	0	6	1	1	0	5	1	8	3	7	3	1	3	0	1	1	3	2	4			TCGA-A4-7915-01A-11D-2201-08	TCGA-A4-7915-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	42528857-7966-471e-a0fe-27a109429871	e6538442-84f0-47d1-aee6-60a032d2d9d0	g.chr22:38877225G>A	ENST00000216014.4	+	4	532	c.360G>A	c.(358-360)tgG>tgA	p.W120*	KDELR3_ENST00000471268.1_3'UTR|KDELR3_ENST00000409006.3_Nonsense_Mutation_p.W120*	NM_006855.2	NP_006846.1	O43731	ERD23_HUMAN	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3	120					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein retention in ER lumen (GO:0006621)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ER retention sequence binding (GO:0046923)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)	13	Melanoma(58;0.0286)					AGATCCTCTGGACTTTCTCTA	0.448																																					p.W120X	Ovarian(11;103 529 24120 28493 32980)	Atlas-SNP	.											.	KDELR3	39	.	0			c.G360A						PASS	.						173	182	179					22																	38877225		2203	4300	6503	SO:0001587	stop_gained	11015	exon4			CCTCTGGACTTTC	AL035081	CCDS13972.1, CCDS46705.1	22q13	2008-05-02			ENSG00000100196	ENSG00000100196			6306	protein-coding gene	gene with protein product							Standard	NM_006855		Approved		uc003avu.3	O43731	OTTHUMG00000153520	ENST00000216014.4:c.360G>A	chr22.hg19:g.38877225G>A	ENSP00000216014:p.Trp120*	285.0	0.0	.		282.0	79.0	.	NM_016657	A8K7T7|B8ZZ26|O95557|Q4V750|Q4V767|Q53FP4|Q53GK1	Nonsense_Mutation	SNP	ENST00000216014.4	hg19	CCDS13972.1	.	.	.	.	.	.	.	.	.	.	G	35	5.560833	0.96527	.	.	ENSG00000100196	ENST00000216014;ENST00000409006	.	.	.	4.97	4.97	0.65823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.4255	0.90607	0.0:0.0:1.0:0.0	.	.	.	.	X	120	.	ENSP00000216014:W120X	W	+	3	0	KDELR3	37207171	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.657000	0.98554	2.595000	0.87683	0.650000	0.86243	TGG	.	.	.	none		0.448	KDELR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331474.1			A	38877225	G	A	38877225	4	1	50	1	0	0	0	0	0	1	0	0	8128	1183	41	2	374	2	KDELR3	22	38877225	Nonsense_Mutation	SNP	G	TCGA-A4-7915-01A-11D-2201-08		38877225	12427341	28	3416											
RERE	473	hgsc.bcm.edu	37	chr1	8674682	8674682	+	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	ctgtgatgccaccggcagagAgcatgctggggggtcacaca	9	6	15	11	1	1	2	1	1	0	1	1	3	1	2	2	4	3	3	2	4	0	0			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr1:8674682A>T	ENST00000337907.3	-	5	1094	c.460T>A	c.(460-462)Tct>Act	p.S154T	RERE_ENST00000400907.2_Missense_Mutation_p.S154T|RERE_ENST00000400908.2_Missense_Mutation_p.S154T	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	154	BAH. {ECO:0000255|PROSITE- ProRule:PRU00370}.				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)		ACCGGCAGAGAGCATGCTGGG	0.498																																					p.S154T		Atlas-SNP	.											.	RERE	129	.	0			c.T460A						PASS	.						77	86	83					1																	8674682		2203	4300	6503	SO:0001583	missense	473	exon5			GCAGAGAGCATGC	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.460T>A	chr1.hg19:g.8674682A>T	ENSP00000338629:p.Ser154Thr	217.0	0.0	.		183.0	57.0	.	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Missense_Mutation	SNP	ENST00000337907.3	hg19	CCDS95.1	.	.	.	.	.	.	.	.	.	.	A	14.55	2.568378	0.45798	.	.	ENSG00000142599	ENST00000337907;ENST00000400907;ENST00000400908	T;T	0.43294	0.95;0.95	5.33	5.33	0.75918	Bromo adjacent homology (BAH) domain (3);	.	.	.	.	T	0.42314	0.1197	N	0.17631	0.505	0.80722	D	1	D	0.53885	0.963	D	0.67231	0.95	T	0.21827	-1.0234	9	0.07644	T	0.81	-16.2545	11.6091	0.51049	1.0:0.0:0.0:0.0	.	154	Q9P2R6	RERE_HUMAN	T	154	ENSP00000338629:S154T;ENSP00000383700:S154T	ENSP00000338629:S154T	S	-	1	0	RERE	8597269	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.525000	0.22956	2.234000	0.73211	0.533000	0.62120	TCT	.	.	.	none		0.498	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1			T	8674682	A	T	8674682	3	4	51	1	0	0	0	0	1	0	0	0	13244	304	11	5	4320	5	RERE	1	8674682	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08		8674682	240575939	1	3417											
TNFRSF1B	7133	hgsc.bcm.edu	37	chr1	12266986	12266986	+	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	ggaggaatgtgcctttcggtCacagctggagacgccagaga	10	7	15	9	2	1	2	1	0	0	2	2	6	1	4	2	4	2	1	2	4	1	1			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr1:12266986C>T	ENST00000376259.3	+	10	1384	c.1295C>T	c.(1294-1296)tCa>tTa	p.S432L	TNFRSF1B_ENST00000492361.1_3'UTR	NM_001066.2	NP_001057.1	P20333	TNR1B_HUMAN	tumor necrosis factor receptor superfamily, member 1B	432					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)	GCCTTTCGGTCACAGCTGGAG	0.622																																					p.S432L		Atlas-SNP	.											.	TNFRSF1B	28	.	0			c.C1295T						PASS	.						100	96	98					1																	12266986		2203	4300	6503	SO:0001583	missense	7133	exon10			TTCGGTCACAGCT	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.1295C>T	chr1.hg19:g.12266986C>T	ENSP00000365435:p.Ser432Leu	137.0	0.0	.		116.0	34.0	.	NM_001066	B1AJZ3|Q16042|Q6YI29|Q9UIH1	Missense_Mutation	SNP	ENST00000376259.3	hg19	CCDS145.1	.	.	.	.	.	.	.	.	.	.	C	8.806	0.934041	0.18206	.	.	ENSG00000028137	ENST00000376259	D	0.86865	-2.18	4.93	3.01	0.34805	.	3.844360	0.01082	N	0.005008	D	0.85366	0.5680	L	0.57536	1.79	0.09310	N	0.999998	B	0.30068	0.267	B	0.28139	0.086	T	0.66901	-0.5806	10	0.44086	T	0.13	-20.2744	6.4642	0.21973	0.1787:0.7264:0.0:0.0949	.	432	P20333	TNR1B_HUMAN	L	432	ENSP00000365435:S432L	ENSP00000365435:S432L	S	+	2	0	TNFRSF1B	12189573	0.043000	0.20138	0.045000	0.18777	0.005000	0.04900	2.194000	0.42668	0.564000	0.29238	0.561000	0.74099	TCA	.	.	.	none		0.622	TNFRSF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005133.1	NM_001066		T	12266986	C	T	12266986	3	4	51	1	0	0	0	0	1	0	0	0	16306	838	29	2	1333	2	TNFRSF1B	1	12266986	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	3592304	12266986	236983635	2	3418											
AGMAT	79814	hgsc.bcm.edu	37	chr1	15909721	15909721	+	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	aatacagccagctgctacaaTtttctcataggcctcttgaa	12	12	6	11	0	2	1	1	1	2	0	3	1	2	1	2	1	5	2	2	1	6	6			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr1:15909721T>A	ENST00000375826.3	-	2	584	c.442A>T	c.(442-444)Att>Ttt	p.I148F	DNAJC16_ENST00000483270.1_Intron|RP4-680D5.2_ENST00000428945.1_RNA	NM_024758.4	NP_079034.3	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase)	148					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)		GCTGCTACAATTTTCTCATAG	0.502																																					p.I148F	NSCLC(126;1678 1780 25805 43508 49531)	Atlas-SNP	.											.	AGMAT	25	.	0			c.A442T						PASS	.						60	62	61					1																	15909721		2203	4300	6503	SO:0001583	missense	79814	exon2			CTACAATTTTCTC	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.442A>T	chr1.hg19:g.15909721T>A	ENSP00000364986:p.Ile148Phe	74.0	0.0	.		59.0	24.0	.	NM_024758	Q5TDH1|Q9H5J3	Missense_Mutation	SNP	ENST00000375826.3	hg19	CCDS160.1	.	.	.	.	.	.	.	.	.	.	T	13.60	2.284549	0.40394	.	.	ENSG00000116771	ENST00000375826	D	0.86097	-2.07	5.17	4.0	0.46444	Ureohydrolase domain (1);	0.051325	0.85682	D	0.000000	D	0.85864	0.5796	M	0.88241	2.94	0.49483	D	0.99979	B	0.30914	0.3	B	0.28553	0.091	D	0.83786	0.0228	10	0.62326	D	0.03	-10.0798	10.1512	0.42794	0.0:0.0812:0.0:0.9188	.	148	Q9BSE5	SPEB_HUMAN	F	148	ENSP00000364986:I148F	ENSP00000364986:I148F	I	-	1	0	AGMAT	15782308	1.000000	0.71417	0.015000	0.15790	0.482000	0.33219	3.489000	0.53237	0.768000	0.33290	0.460000	0.39030	ATT	.	.	.	none		0.502	AGMAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006763.1	NM_024758		A	15909721	T	A	15909721	3	1	51	1	0	0	0	0	1	0	0	0	385	1493	52	5	640	5	AGMAT	1	15909721	Missense_Mutation	SNP	T	TCGA-A4-7996-01A-11D-2201-08	3642735	15909721	233340900	3	3419											
SLC5A9	200010	hgsc.bcm.edu	37	chr1	48713171	48713171	+	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	tctgcaacatcaatgctgtcCttttgctggccatcaacatc	9	13	6	13	0	3	0	2	0	1	0	5	0	4	0	2	1	5	3	2	1	3	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr1:48713171C>T	ENST00000438567.2	+	14	2054	c.2002C>T	c.(2002-2004)Ctt>Ttt	p.L668F	SLC5A9_ENST00000236495.5_Missense_Mutation_p.L693F|SLC5A9_ENST00000533824.1_Missense_Mutation_p.L689F|SLC5A9_ENST00000471020.1_3'UTR	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	668					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						CAATGCTGTCCTTTTGCTGGC	0.527																																					p.L693F		Atlas-SNP	.											.	SLC5A9	82	.	0			c.C2077T						PASS	.						118	109	112					1																	48713171		2203	4300	6503	SO:0001583	missense	200010	exon15			GCTGTCCTTTTGC	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.2002C>T	chr1.hg19:g.48713171C>T	ENSP00000401730:p.Leu668Phe	143.0	0.0	.		131.0	36.0	.	NM_001135181	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Missense_Mutation	SNP	ENST00000438567.2	hg19	CCDS30709.2	.	.	.	.	.	.	.	.	.	.	C	14.77	2.633803	0.47049	.	.	ENSG00000117834	ENST00000533824;ENST00000438567;ENST00000236495	D;D;D	0.89485	-2.46;-2.45;-2.52	4.91	-2.59	0.06209	.	0.427982	0.25433	N	0.030704	D	0.85208	0.5644	L	0.43646	1.37	0.80722	D	1	P;P;P	0.52577	0.883;0.954;0.954	P;P;P	0.50617	0.459;0.526;0.646	T	0.80341	-0.1423	10	0.28530	T	0.3	.	10.552	0.45095	0.6789:0.2512:0.0:0.0699	.	689;668;693	E9PJ08;Q2M3M2;E9PAK4	.;SC5A9_HUMAN;.	F	689;668;693	ENSP00000431900:L689F;ENSP00000401730:L668F;ENSP00000236495:L693F	ENSP00000236495:L693F	L	+	1	0	SLC5A9	48485758	0.564000	0.26602	0.314000	0.25224	0.881000	0.50899	-0.070000	0.11523	-0.340000	0.08388	0.561000	0.74099	CTT	.	.	.	none		0.527	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174		T	48713171	C	T	48713171	3	4	51	1	0	0	0	0	1	0	0	0	14685	681	24	2	2135	2	SLC5A9	1	48713171	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	32803450	48713171	200537450	4	3420											
ZYG11B	79699	hgsc.bcm.edu	37	chr1	53287171	53287171	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcagcatttatacaacatcaAagatcatgaacatactgatc	17	10	5	9	0	2	3	2	2	0	1	3	3	2	3	0	0	5	2	0	0	6	4			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr1:53287171A>G	ENST00000294353.6	+	14	2250	c.2105A>G	c.(2104-2106)aAa>aGa	p.K702R	ZYG11B_ENST00000443756.2_Missense_Mutation_p.K632R	NM_024646.2	NP_078922.1	Q9C0D3	ZY11B_HUMAN	zyg-11 family member B, cell cycle regulator	702										breast(1)|endometrium(1)|kidney(6)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	30						TACAACATCAAAGATCATGAA	0.418																																					p.K702R		Atlas-SNP	.											.	ZYG11B	61	.	0			c.A2105G						PASS	.						98	85	89					1																	53287171		2203	4300	6503	SO:0001583	missense	79699	exon14			ACATCAAAGATCA	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.2105A>G	chr1.hg19:g.53287171A>G	ENSP00000294353:p.Lys702Arg	83.0	0.0	.		84.0	18.0	.	NM_024646	Q8N2X3|Q9H8L8	Missense_Mutation	SNP	ENST00000294353.6	hg19	CCDS30717.1	.	.	.	.	.	.	.	.	.	.	A	10.83	1.462431	0.26248	.	.	ENSG00000162378	ENST00000443756;ENST00000294353	T;T	0.48836	0.8;0.8	5.36	5.36	0.76844	Armadillo-like helical (1);Armadillo-type fold (1);	0.155352	0.56097	D	0.000023	T	0.25791	0.0628	N	0.08118	0	0.80722	D	1	B;B	0.16802	0.019;0.001	B;B	0.22753	0.041;0.001	T	0.13415	-1.0510	10	0.14656	T	0.56	.	9.8251	0.40908	0.9231:0.0:0.0769:0.0	.	632;702	B4DK95;Q9C0D3	.;ZY11B_HUMAN	R	632;702	ENSP00000400522:K632R;ENSP00000294353:K702R	ENSP00000294353:K702R	K	+	2	0	ZYG11B	53059759	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.218000	0.51192	2.019000	0.59389	0.482000	0.46254	AAA	.	.	.	none		0.418	ZYG11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024749.1	NM_024646		G	53287171	A	G	53287171	3	3	51	1	0	0	0	0	1	0	0	0	18265	14	1	3	2159	3	ZYG11B	1	53287171	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08	4574000	53287171	195963450	5	3421											
USP24	23358	hgsc.bcm.edu	37	chr1	55612677	55612677	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggcacgattccagcccagAtacagagtagcttcttgcaa	11	10	9	11	1	1	2	0	0	1	2	2	3	2	2	2	1	4	4	2	1	3	6			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr1:55612677A>G	ENST00000294383.6	-	19	2174	c.2175T>C	c.(2173-2175)taT>taC	p.Y725Y	USP24_ENST00000407756.1_Silent_p.Y565Y	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	725					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						TCCAGCCCAGATACAGAGTAG	0.393																																					p.Y725Y		Atlas-SNP	.											.	USP24	323	.	0			c.T2175C						PASS	.						104	99	101					1																	55612677		1852	4098	5950	SO:0001819	synonymous_variant	23358	exon19			GCCCAGATACAGA	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.2175T>C	chr1.hg19:g.55612677A>G		55.0	0.0	.		54.0	20.0	.	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Silent	SNP	ENST00000294383.6	hg19	CCDS44154.2																																																																																			.	.	.	none		0.393	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			G	55612677	A	G	55612677	2	3	51	1	0	0	0	0	0	0	0	1	17067	340	12	3		3	USP24	1	55612677	Silent	SNP	A	TCGA-A4-7996-01A-11D-2201-08	2325506	55612677	193637944	6	3422											
INADL	10207	hgsc.bcm.edu	37	chr1	62365295	62365295	+	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	aaggcgaaggagaagaaactCcaaattttagccactggggt	15	7	12	7	1	0	2	0	0	0	2	1	4	1	2	2	4	2	0	2	4	6	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr1:62365295C>T	ENST00000371158.2	+	23	3286	c.3172C>T	c.(3172-3174)Cca>Tca	p.P1058S	INADL_ENST00000316485.6_Missense_Mutation_p.P1058S	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1058					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						AGAAGAAACTCCAAATTTTAG	0.398																																					p.P1058S		Atlas-SNP	.											.	INADL	179	.	0			c.C3172T						PASS	.						179	177	178					1																	62365295		2203	4300	6503	SO:0001583	missense	10207	exon23			GAAACTCCAAATT	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.3172C>T	chr1.hg19:g.62365295C>T	ENSP00000360200:p.Pro1058Ser	263.0	0.0	.		256.0	78.0	.	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	hg19	CCDS617.2	.	.	.	.	.	.	.	.	.	.	C	25.3	4.626785	0.87560	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000255202	T;T	0.13307	2.74;2.6	5.26	5.26	0.73747	PDZ/DHR/GLGF (1);	0.000000	0.64402	D	0.000001	T	0.39655	0.1086	M	0.73598	2.24	0.80722	D	1	D;D;D	0.89917	0.991;0.999;1.0	D;D;D	0.85130	0.98;0.997;0.994	T	0.04915	-1.0918	10	0.34782	T	0.22	.	19.2911	0.94100	0.0:1.0:0.0:0.0	.	1058;1058;1058	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	S	1058	ENSP00000360200:P1058S;ENSP00000326199:P1058S	ENSP00000255202:P1058S	P	+	1	0	INADL	62137883	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.990000	0.63876	2.636000	0.89361	0.579000	0.79373	CCA	.	.	.	none		0.398	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		T	62365295	C	T	62365295	3	4	51	1	0	0	0	0	1	0	0	0	7738	855	30	2	3258	2	INADL	1	62365295	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	6752618	62365295	186885326	7	3423											
TCHH	7062	hgsc.bcm.edu	37	chr1	152082279	152082279	+	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	tcctcttcctcccgatattgCctctccagctcctggcgcct	3	13	6	19	2	2	0	0	0	2	0	7	1	6	0	7	1	2	1	7	1	1	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr1:152082279C>T	ENST00000368804.1	-	2	3413	c.3414G>A	c.(3412-3414)agG>agA	p.R1138R		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1138	10 X 30 AA 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)			cccgatattgcctctccagct	0.612																																					p.R1138R		Atlas-SNP	.											.	TCHH	275	.	0			c.G3414A						PASS	.						91	90	90					1																	152082279		2000	4154	6154	SO:0001819	synonymous_variant	7062	exon3			ATATTGCCTCTCC	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.3414G>A	chr1.hg19:g.152082279C>T		175.0	0.0	.		139.0	39.0	.	NM_007113	Q5VUI3	Silent	SNP	ENST00000368804.1	hg19	CCDS41396.1																																																																																			.	.	.	none		0.612	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		T	152082279	C	T	152082279	2	4	51	1	0	0	0	0	0	0	0	1	15712	738	26	2		2	TCHH	1	152082279	Silent	SNP	C	TCGA-A4-7996-01A-11D-2201-08	89716984	152082279	97168342	8	3424											
KCNN3	3782	hgsc.bcm.edu	37	chr1	154841688	154841688	+	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	gctttggggaaggtggtgctGctggcggtggtgccggcatg	3	10	21	7	2	0	0	0	0	0	0	0	1	0	1	1	8	3	4	1	8	1	1			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr1:154841688G>A	ENST00000271915.4	-	1	1068	c.753C>T	c.(751-753)agC>agT	p.S251S	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	256					potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	AGGTGGTGCTGCTGGCGGTGG	0.567																																					p.S251S		Atlas-SNP	.											.	KCNN3	141	.	0			c.C753T						PASS	.						109	104	106					1																	154841688		2203	4300	6503	SO:0001819	synonymous_variant	3782	exon1			GGTGCTGCTGGCG	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.753C>T	chr1.hg19:g.154841688G>A		161.0	0.0	.		113.0	41.0	.	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Silent	SNP	ENST00000271915.4	hg19	CCDS30880.1																																																																																			.	.	.	none		0.567	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		A	154841688	G	A	154841688	2	1	51	1	0	0	0	0	0	0	0	1	8087	1310	46	2		2	KCNN3	1	154841688	Silent	SNP	G	TCGA-A4-7996-01A-11D-2201-08	2759409	154841688	94408933	9	3425											
EFNA1	1942	hgsc.bcm.edu	37	chr1	155104075	155104075	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacacctttcaccctgggcaAggagttcaaagaaggacaca	14	6	9	12	0	2	1	2	0	0	1	2	3	2	3	2	3	0	2	2	3	3	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr1:155104075A>G	ENST00000368407.3	+	2	871	c.353A>G	c.(352-354)aAg>aGg	p.K118R	EFNA1_ENST00000469878.1_3'UTR|EFNA1_ENST00000368406.2_Missense_Mutation_p.K118R	NM_004428.2	NP_004419.2	P20827	EFNA1_HUMAN	ephrin-A1	118	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|aortic valve morphogenesis (GO:0003180)|axon guidance (GO:0007411)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|endocardial cushion to mesenchymal transition involved in heart valve formation (GO:0003199)|ephrin receptor signaling pathway (GO:0048013)|mitral valve morphogenesis (GO:0003183)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|notochord formation (GO:0014028)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of angiogenesis (GO:0045765)|regulation of axonogenesis (GO:0050770)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|substrate adhesion-dependent cell spreading (GO:0034446)	anchored component of plasma membrane (GO:0046658)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ephrin receptor binding (GO:0046875)|receptor binding (GO:0005102)			breast(1)|endometrium(1)|kidney(1)|lung(1)|skin(1)	5	all_epithelial(22;4.71e-30)|all_lung(78;3.15e-27)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;2.28e-10)|all cancers(21;6.16e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000395)|LUSC - Lung squamous cell carcinoma(543;0.193)			ACCCTGGGCAAGGAGTTCAAA	0.527																																					p.K118R		Atlas-SNP	.											.	EFNA1	10	.	0			c.A353G						PASS	.						53	47	49					1																	155104075		2203	4300	6503	SO:0001583	missense	1942	exon2			TGGGCAAGGAGTT		CCDS1091.1, CCDS1092.1	1q21-q22	2011-03-09			ENSG00000169242	ENSG00000169242		"Ephrins"	3221	protein-coding gene	gene with protein product		191164		TNFAIP4, EPLG1		2233719, 8660976	Standard	NM_182685		Approved	LERK1, ECKLG	uc001fhh.3	P20827	OTTHUMG00000035312	ENST00000368407.3:c.353A>G	chr1.hg19:g.155104075A>G	ENSP00000357392:p.Lys118Arg	65.0	0.0	.		47.0	10.0	.	NM_182685	D3DV86|Q5SR60|Q5SR61|Q6I9T9|Q8N578	Missense_Mutation	SNP	ENST00000368407.3	hg19	CCDS1091.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.554194	0.86231	.	.	ENSG00000169242	ENST00000368407;ENST00000368406	T;T	0.43294	0.95;0.95	5.22	5.22	0.72569	Ephrin, conserved site (1);Cupredoxin (2);	0.045262	0.85682	D	0.000000	T	0.51500	0.1678	M	0.71581	2.175	0.53688	D	0.999973	D;D	0.76494	0.997;0.999	P;D	0.71184	0.9;0.972	T	0.51124	-0.8745	10	0.33940	T	0.23	-2.5539	13.3345	0.60509	1.0:0.0:0.0:0.0	.	118;118	P20827-2;P20827	.;EFNA1_HUMAN	R	118	ENSP00000357392:K118R;ENSP00000357391:K118R	ENSP00000357391:K118R	K	+	2	0	EFNA1	153370699	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.204000	0.51082	2.097000	0.63578	0.533000	0.62120	AAG	.	.	.	none		0.527	EFNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085428.1	NM_004428		G	155104075	A	G	155104075	3	3	51	1	0	0	0	0	1	0	0	0	4952	72	3	3	359	3	EFNA1	1	155104075	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08	262387	155104075	94146546	10	3426											
FAM72A	729533	hgsc.bcm.edu	37	chr1	206139310	206139310	+	Frame_Shift_Del	DEL	T	T	-																															ccttcctgcgacgccatgtcTaccaacatttgtagtttcaa																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr1:206139310delT	ENST00000367128.3	+	1	854	c.6delT	c.(4-6)tctfs	p.S2fs	FAM72A_ENST00000367129.2_Intron|FAM72A_ENST00000341209.5_Frame_Shift_Del_p.S2fs|FAM72A_ENST00000470041.1_Intron|RP11-312O7.2_ENST00000606644.1_RNA|FAM72A_ENST00000607379.1_Frame_Shift_Del_p.S2fs|RP11-312O7.2_ENST00000429210.1_RNA			Q5TYM5	FA72A_HUMAN	family with sequence similarity 72, member A	2						mitochondrion (GO:0005739)				endometrium(2)	2						ACGCCATGTCTACCAACATTT	0.438																																					p.S2fs		Atlas-INDEL	.											.	FAM72A	9	.	0			c.5delC						PASS	.						1	1	1					1																	206139310		212	579	791	SO:0001589	frameshift_variant	729533	exon1			.	CR407567	CCDS73016.1	1q32.1	2008-03-26			ENSG00000196550	ENSG00000196550			24044	protein-coding gene	gene with protein product		614710				12477932	Standard	NM_001123168		Approved	MGC57827, RP11-312O7.1	uc001hdr.4	Q5TYM5	OTTHUMG00000042552	ENST00000367128.3:c.6delT	chr1.hg19:g.206139310delT	ENSP00000356096:p.Ser2fs	401.0	0.0	0		359.0	47.0	0.130919	NM_001123168	B2RV15|Q5TYM4	Frame_Shift_Del	DEL	ENST00000367128.3	hg19	CCDS41458.1																																																																																			.	.	.	none		0.438	FAM72A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100825.1			-	206139310	T	-	206139310	7	5	51	1	0	1	0	1	0	0	0	0	5621	1509	53	0	8	0	FAM72A	1	206139310	Frame_Shift_Del	DEL	T	TCGA-A4-7996-01A-11D-2201-08	51035235	206139310	43111311	11	3427											
LRPPRC	10128	hgsc.bcm.edu	37	chr2	44139638	44139638	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taatttaatgagattgctgtAggtttcagcattaaacacaa	15	14	7	5	0	1	1	1	1	0	1	1	2	1	1	0	1	3	4	0	1	6	7			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr2:44139638A>G	ENST00000260665.7	-	30	3265	c.3208T>C	c.(3208-3210)Tac>Cac	p.Y1070H		NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	1070					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)				AGATTGCTGTAGGTTTCAGCA	0.313																																					p.Y1070H		Atlas-SNP	.											.	LRPPRC	105	.	0			c.T3208C						PASS	.						112	107	109					2																	44139638		2202	4297	6499	SO:0001583	missense	10128	exon30			TGCTGTAGGTTTC	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.3208T>C	chr2.hg19:g.44139638A>G	ENSP00000260665:p.Tyr1070His	58.0	0.0	.		86.0	33.0	.	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Missense_Mutation	SNP	ENST00000260665.7	hg19	CCDS33189.1	.	.	.	.	.	.	.	.	.	.	A	18.53	3.643279	0.67244	.	.	ENSG00000138095	ENST00000465633;ENST00000260665	T	0.13420	2.59	5.78	5.78	0.91487	.	0.065106	0.64402	D	0.000006	T	0.40272	0.1110	M	0.78637	2.42	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.994;0.998	T	0.27773	-1.0064	10	0.66056	D	0.02	-5.0562	15.7709	0.78167	1.0:0.0:0.0:0.0	.	970;1070	F5H4J6;P42704	.;LPPRC_HUMAN	H	970;1070	ENSP00000260665:Y1070H	ENSP00000260665:Y1070H	Y	-	1	0	LRPPRC	43993142	1.000000	0.71417	0.283000	0.24790	0.010000	0.07245	7.018000	0.76406	2.205000	0.71048	0.533000	0.62120	TAC	.	.	.	none		0.313	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259		G	44139638	A	G	44139638	3	3	51	1	0	0	0	0	1	0	0	0	8972	420	15	3	1012	3	LRPPRC	2	44139638	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08		44139638	199059735	12	3428											
MTHFD2	10797	hgsc.bcm.edu	37	chr2	74441208	74441208	+	Missense_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	tgtcttgtttctatgtaggaGtcagacaaaaagctgggtat	11	14	11	5	0	3	1	1	0	2	1	3	2	3	2	0	2	1	4	0	2	5	5			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr2:74441208G>A	ENST00000394053.2	+	8	972	c.892G>A	c.(892-894)Gtc>Atc	p.V298I	MTHFD2_ENST00000409804.1_Missense_Mutation_p.V170I|SLC4A5_ENST00000483195.1_5'Flank|MTHFD2_ENST00000264090.4_Missense_Mutation_p.V196I|MTHFD2_ENST00000409601.1_Missense_Mutation_p.V215I|RP11-287D1.3_ENST00000451608.2_Intron|MTHFD2_ENST00000394050.3_Missense_Mutation_p.V134I	NM_006636.3	NP_006627.2	P13995	MTDC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase	298					folic acid-containing compound biosynthetic process (GO:0009396)|one-carbon metabolic process (GO:0006730)|tetrahydrofolate metabolic process (GO:0046653)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	magnesium ion binding (GO:0000287)|methenyltetrahydrofolate cyclohydrolase activity (GO:0004477)|methylenetetrahydrofolate dehydrogenase (NAD+) activity (GO:0004487)|methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488)|phosphate ion binding (GO:0042301)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6					Tetrahydrofolic acid(DB00116)	CTATGTAGGAGTCAGACAAAA	0.398																																					p.V298I		Atlas-SNP	.											.	MTHFD2	43	.	0			c.G892A						PASS	.						110	119	116					2																	74441208		2029	4215	6244	SO:0001583	missense	10797	exon8			GTAGGAGTCAGAC	X16396	CCDS1935.2	2p13.1	2008-05-02			ENSG00000065911	ENSG00000065911			7434	protein-coding gene	gene with protein product		604887				2587219, 8218174	Standard	NR_027405		Approved		uc002skk.3	P13995	OTTHUMG00000129814	ENST00000394053.2:c.892G>A	chr2.hg19:g.74441208G>A	ENSP00000377617:p.Val298Ile	274.0	0.0	.		244.0	71.0	.	NM_006636	Q53G90|Q53GV5|Q53S36|Q7Z650	Missense_Mutation	SNP	ENST00000394053.2	hg19	CCDS1935.2	.	.	.	.	.	.	.	.	.	.	G	24.5	4.540151	0.85917	.	.	ENSG00000065911	ENST00000394053;ENST00000409804;ENST00000264090;ENST00000394050;ENST00000409601	T;T;T;T;T	0.60797	0.16;0.16;0.16;0.16;0.37	5.58	5.58	0.84498	Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain (1);NAD(P)-binding domain (1);	0.114477	0.64402	D	0.000017	T	0.78291	0.4260	M	0.82323	2.585	0.80722	D	1	D;D	0.71674	0.988;0.998	D;D	0.74023	0.919;0.982	T	0.80569	-0.1324	10	0.72032	D	0.01	.	17.4533	0.87599	0.0:0.0:1.0:0.0	.	215;298	B8ZZU9;P13995	.;MTDC_HUMAN	I	298;170;196;134;215	ENSP00000377617:V298I;ENSP00000386536:V170I;ENSP00000264090:V196I;ENSP00000377614:V134I;ENSP00000386542:V215I	ENSP00000264090:V196I	V	+	1	0	MTHFD2	74294716	1.000000	0.71417	0.821000	0.32701	0.724000	0.41520	9.415000	0.97375	2.813000	0.96785	0.655000	0.94253	GTC	.	.	.	none		0.398	MTHFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252045.2			A	74441208	G	A	74441208	3	1	51	1	0	0	0	0	1	0	0	0	9936	1029	36	2	922	2	MTHFD2	2	74441208	Missense_Mutation	SNP	G	TCGA-A4-7996-01A-11D-2201-08	30301570	74441208	168758165	13	3429											
IL1RL2	8808	hgsc.bcm.edu	37	chr2	102849533	102849533	+	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	tgcccgaggtgttggagagaCaatgtggatataagttgttt	10	13	14	4	1	0	1	0	0	0	1	0	5	0	3	1	3	1	3	1	3	3	5			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr2:102849533C>T	ENST00000264257.2	+	10	1372	c.1246C>T	c.(1246-1248)Caa>Taa	p.Q416*	IL1RL2_ENST00000441515.2_Nonsense_Mutation_p.Q298*|IL1RL2_ENST00000481806.1_3'UTR|IL1RL2_ENST00000539491.1_Nonsense_Mutation_p.Q416*	NM_003854.2	NP_003845.2	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2	416	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						GTTGGAGAGACAATGTGGATA	0.453																																					p.Q416X		Atlas-SNP	.											.	IL1RL2	118	.	0			c.C1246T						PASS	.						116	111	113					2																	102849533		2203	4300	6503	SO:0001587	stop_gained	8808	exon10			GAGAGACAATGTG	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.1246C>T	chr2.hg19:g.102849533C>T	ENSP00000264257:p.Gln416*	127.0	0.0	.		128.0	38.0	.	NM_003854	A4FU63|Q13525|Q45H74|Q53TU8|Q587I8	Nonsense_Mutation	SNP	ENST00000264257.2	hg19	CCDS2056.1	.	.	.	.	.	.	.	.	.	.	C	36	5.844802	0.97016	.	.	ENSG00000115598	ENST00000264257;ENST00000441515;ENST00000539491	.	.	.	6.07	6.07	0.98685	.	0.205036	0.43919	D	0.000507	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16420	T	0.52	.	20.6593	0.99626	0.0:1.0:0.0:0.0	.	.	.	.	X	416;298;416	.	ENSP00000264257:Q416X	Q	+	1	0	IL1RL2	102215965	0.985000	0.35326	1.000000	0.80357	0.447000	0.32167	2.970000	0.49240	2.885000	0.99019	0.655000	0.94253	CAA	.	.	.	none		0.453	IL1RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253290.1	NM_003854		T	102849533	C	T	102849533	4	4	51	1	0	0	0	0	0	1	0	0	7671	479	17	2	1280	2	IL1RL2	2	102849533	Nonsense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	28408325	102849533	140349840	14	3430											
RGPD5	84220	hgsc.bcm.edu	37	chr2	110582512	110582512	+	Frame_Shift_Del	DEL	A	A	-																															gctctgcttgtacattgggcAaaataccttcagaaaacggt																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr2:110582512delA	ENST00000016946.3	+	12	1898	c.1740delA	c.(1738-1740)gcafs	p.A580fs	RGPD5_ENST00000393283.1_Frame_Shift_Del_p.A580fs|RGPD5_ENST00000272454.6_Frame_Shift_Del_p.A580fs	NM_005054.2	NP_005045.2	Q99666	RGPD5_HUMAN	RANBP2-like and GRIP domain containing 5	580					protein targeting to Golgi (GO:0000042)	cytoplasm (GO:0005737)				central_nervous_system(1)	1						TACATTGGGCAAAATACCTTC	0.323																																					p.A580fs		Atlas-INDEL	.											.	RGPD5	1	.	0			c.1739delC						PASS	.						1	1	1					2																	110582512		1	3	4	SO:0001589	frameshift_variant	84220	exon13			.	U64675	CCDS2082.1, CCDS2083.1	2q13	2013-01-10			ENSG00000015568	ENSG00000015568		"Tetratricopeptide (TTC) repeat domain containing"	32418	protein-coding gene	gene with protein product		612708				15710750, 15815621	Standard	NM_032260		Approved	RGP5, BS-63, DKFZp686I1842		Q99666	OTTHUMG00000130985	ENST00000016946.3:c.1740delA	chr2.hg19:g.110582512delA	ENSP00000016946:p.Ala580fs	396.0	0.0	0		362.0	26.0	0.0718232	NM_032260	Q53QN2|Q53T03|Q59GM7|Q9H0B2	Frame_Shift_Del	DEL	ENST00000016946.3	hg19	CCDS2082.1																																																																																			.	.	.	none		0.323	RGPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253599.3	NM_005054		-	110582512	A	-	110582512	7	5	51	1	0	1	0	1	0	0	0	0	13302	117	5	0	1786	0	RGPD5	2	110582512	Frame_Shift_Del	DEL	A	TCGA-A4-7996-01A-11D-2201-08	7732979	110582512	132616861	15	3431											
RGPD5	729540	hgsc.bcm.edu	37	chr2	111304146	111304146	+	Frame_Shift_Del	DEL	T	T	-																															ctcaccgttttctgaaggtaTtttgcccaatgtacaagcag																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr2:111304146delT	ENST00000329516.3	-	12	1819	c.1743delA	c.(1741-1743)aaafs	p.K581fs	RGPD6_ENST00000330331.5_Frame_Shift_Del_p.K581fs	NM_001123363.3	NP_001116835.1	Q99666	RGPD5_HUMAN	RANBP2-like and GRIP domain containing 6	581					protein targeting to Golgi (GO:0000042)	cytoplasm (GO:0005737)											TCTGAAGGTATTTTGCCCAAT	0.323																																					p.Y582fs		Atlas-INDEL	.											.	RGPD5	1	.	0			c.1744delT						PASS	.																																			SO:0001589	frameshift_variant	84220	exon13			.	AK056675	CCDS46388.1, CCDS42729.1	2q13	2013-01-10			ENSG00000183054	ENSG00000183054		"Tetratricopeptide (TTC) repeat domain containing"	32419	protein-coding gene	gene with protein product		612709				15710750, 15815621, 9480752	Standard	NM_001037866		Approved	RGP6	uc021vly.1	Q99666	OTTHUMG00000153196	ENST00000329516.3:c.1743delA	chr2.hg19:g.111304146delT	ENSP00000330842:p.Lys581fs	366.0	0.0	0		376.0	27.0	0.0718085	NM_032260	Q53QN2|Q53T03|Q59GM7|Q9H0B2	Frame_Shift_Del	DEL	ENST00000329516.3	hg19	CCDS46388.1																																																																																			.	.	.	none		0.323	RGPD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330029.5	NM_001123363		-	111304146	T	-	111304146	7	5	51	1	0	1	0	1	0	0	0	0	13302	1490	52	0	9226	0	RGPD5	2	111304146	Frame_Shift_Del	DEL	T	TCGA-A4-7996-01A-11D-2201-08	721634	111304146	131895227	16	3432											
RGPD5	727851	hgsc.bcm.edu	37	chr2	113158709	113158709	+	Frame_Shift_Del	DEL	T	T	-																															ctcaccgttttctgaaggtaTtttgcccaatgtacaagcag																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr2:113158709delT	ENST00000302558.3	-	12	1934	c.1743delA	c.(1741-1743)aaafs	p.K581fs	RGPD8_ENST00000330575.5_Frame_Shift_Del_p.K581fs|RGPD8_ENST00000409750.1_Frame_Shift_Del_p.K441fs	NM_001164463.1	NP_001157935.1	O14715	RGPD8_HUMAN	RANBP2-like and GRIP domain containing 8	581					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						TCTGAAGGTATTTTGCCCAAT	0.323																																					p.Y582fs		Atlas-INDEL	.											.	RGPD8	81	.	0			c.1744delT						PASS	.																																			SO:0001589	frameshift_variant	727851	exon12			.	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.1743delA	chr2.hg19:g.113158709delT	ENSP00000306637:p.Lys581fs	360.0	0.0	0		379.0	26.0	0.0686016	NM_001164463	Q5CZA8	Frame_Shift_Del	DEL	ENST00000302558.3	hg19	CCDS46394.1																																																																																			.	.	.	none		0.323	RGPD8-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375951.1	XM_001722279		-	113158709	T	-	113158709	7	5	51	1	0	1	0	1	0	0	0	0	13302	1490	52	0	14616	0	RGPD5	2	113158709	Frame_Shift_Del	DEL	T	TCGA-A4-7996-01A-11D-2201-08	1854563	113158709	130040664	17	3433											
PSMD14	10213	hgsc.bcm.edu	37	chr2	162227815	162227815	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagtggttgtggatcccatTcagagtgtaaaaggaaaggt	12	10	14	5	0	1	1	1	0	0	1	2	3	2	3	1	4	0	3	1	4	3	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr2:162227815T>C	ENST00000409682.3	+	7	1148	c.444T>C	c.(442-444)atT>atC	p.I148I		NM_005805.5	NP_005796.1	O00487	PSDE_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 14	148					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of endopeptidase activity (GO:0010950)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K63-linked deubiquitination (GO:0070536)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle, lid subcomplex (GO:0008541)	endopeptidase activator activity (GO:0061133)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|proteasome binding (GO:0070628)|ubiquitin thiolesterase activity (GO:0004221)			breast(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(2)	12						TGGATCCCATTCAGAGTGTAA	0.408																																					p.I148I		Atlas-SNP	.											.	PSMD14	22	.	0			c.T444C						PASS	.						121	120	121					2																	162227815		1930	4131	6061	SO:0001819	synonymous_variant	10213	exon7			TCCCATTCAGAGT	U86782	CCDS46437.1	2q14.3	2008-05-22			ENSG00000115233	ENSG00000115233		"Proteasome (prosome, macropain) subunits"	16889	protein-coding gene	gene with protein product		607173				9374539	Standard	NM_005805		Approved	POH1, pad1, Rpn11	uc002ubu.3	O00487	OTTHUMG00000153882	ENST00000409682.3:c.444T>C	chr2.hg19:g.162227815T>C		25.0	0.0	.		20.0	4.0	.	NM_005805	B3KNW2|O00176	Silent	SNP	ENST00000409682.3	hg19	CCDS46437.1																																																																																			.	.	.	none		0.408	PSMD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332833.1	NM_005805		C	162227815	T	C	162227815	2	2	51	1	0	0	0	0	0	0	0	1	12707	1771	62	3		3	PSMD14	2	162227815	Silent	SNP	T	TCGA-A4-7996-01A-11D-2201-08	49069106	162227815	80971558	18	3434											
COL5A2	1290	hgsc.bcm.edu	37	chr2	189898818	189898819	+	Frame_Shift_Ins	INS	-	-	TT																															cacaaaacaaactggcccaaINStttcaacgccgaattcctgg																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr2:189898818_189898819insTT	ENST00000374866.3	-	54	4751_4752	c.4477_4478insAA	c.(4477-4479)attfs	p.I1493fs		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	1493	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			AACTGGCCCAATTTCAACGCCG	0.46																																					p.I1493fs		Atlas-INDEL	.											.	COL5A2	230	.	0			c.4478_4479insAA						PASS	.																																			SO:0001589	frameshift_variant	1290	exon54			.	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.4476_4477dupAA	chr2.hg19:g.189898819_189898820dupTT	ENSP00000364000:p.Ile1493fs	66.0	0.0	0		68.0	15.0	0.220588	NM_000393	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Frame_Shift_Ins	INS	ENST00000374866.3	hg19	CCDS33350.1																																																																																			.	.	.	none		0.46	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393		TT	189898819	-	TT	189898818	7	5	51	1	0	1	1	0	0	0	0	0	3699	101	4	0	25	0	COL5A2	2	189898818	Frame_Shift_Ins	INS	-	TCGA-A4-7996-01A-11D-2201-08	27671003	189898818	53300555	19	3435											
NBEAL1	65065	hgsc.bcm.edu	37	chr2	204039877	204039877	+	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	tttttccccacagatatgaaAattttgaggatcctatggga	12	14	8	7	0	0	3	0	2	0	1	2	5	2	5	3	2	0	0	3	2	4	6			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr2:204039877A>T	ENST00000449802.1	+	41	6577	c.6244A>T	c.(6244-6246)Aat>Tat	p.N2082Y		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	2082	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.									NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						CAGATATGAAAATTTTGAGGA	0.333																																					p.N2082Y		Atlas-SNP	.											.	NBEAL1	266	.	0			c.A6244T						PASS	.						66	66	66					2																	204039877		1802	4060	5862	SO:0001583	missense	65065	exon41			TATGAAAATTTTG	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.6244A>T	chr2.hg19:g.204039877A>T	ENSP00000399903:p.Asn2082Tyr	93.0	0.0	.		83.0	27.0	.	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	hg19	CCDS46495.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.547864	0.86022	.	.	ENSG00000144426	ENST00000449802;ENST00000340268;ENST00000414576	T;T	0.80304	-1.36;-1.36	5.92	5.92	0.95590	BEACH domain (4);	0.091060	0.85682	D	0.000000	D	0.82300	0.5007	L	0.28649	0.875	0.54753	D	0.999985	P;P	0.48016	0.904;0.904	P;P	0.57371	0.819;0.748	T	0.82971	-0.0192	10	0.48119	T	0.1	.	16.0292	0.80564	1.0:0.0:0.0:0.0	.	2082;2071	Q6ZS30;C9JGK5	NBEL1_HUMAN;.	Y	2082;2082;97	ENSP00000399903:N2082Y;ENSP00000388466:N97Y	ENSP00000344985:N2082Y	N	+	1	0	NBEAL1	203748122	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	9.287000	0.95975	2.254000	0.74563	0.528000	0.53228	AAT	.	.	.	none		0.333	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4			T	204039877	A	T	204039877	3	4	51	1	0	0	0	0	1	0	0	0	10195	14	1	5	6402	5	NBEAL1	2	204039877	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08	14141059	204039877	39159496	20	3436											
ANKZF1	55139	hgsc.bcm.edu	37	chr2	220099806	220099806	+	Frame_Shift_Del	DEL	C	C	-																															tttgctggatgaggccaaagCccctggtcagccagagctct																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr2:220099806delC	ENST00000323348.5	+	10	1637	c.1463delC	c.(1462-1464)gccfs	p.A488fs	GLB1L_ENST00000497855.1_5'Flank|ANKZF1_ENST00000410034.3_Frame_Shift_Del_p.A488fs|ANKZF1_ENST00000409849.1_Frame_Shift_Del_p.A278fs	NM_018089.2	NP_060559.2	Q9H8Y5	ANKZ1_HUMAN	ankyrin repeat and zinc finger domain containing 1	488						membrane (GO:0016020)	metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	23		Renal(207;0.0474)		Epithelial(149;1.2e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GAGGCCAAAGCCCCTGGTCAG	0.587																																					p.A488fs		Atlas-INDEL	.											.	ANKZF1	45	.	0			c.1462delG						PASS	.						49	53	51					2																	220099806		1987	4163	6150	SO:0001589	frameshift_variant	55139	exon10			.	AF364318	CCDS42821.1, CCDS63129.1	2q35	2013-01-10			ENSG00000163516	ENSG00000163516		"Zinc fingers, C2H2-type", "Ankyrin repeat domain containing"	25527	protein-coding gene	gene with protein product						12477932	Standard	NM_018089		Approved	FLJ10415, ZNF744	uc002vkg.3	Q9H8Y5	OTTHUMG00000154533	ENST00000323348.5:c.1463delC	chr2.hg19:g.220099806delC	ENSP00000321617:p.Ala488fs	83.0	0.0	0		70.0	20.0	0.285714	NM_018089	Q9NVZ4	Frame_Shift_Del	DEL	ENST00000323348.5	hg19	CCDS42821.1																																																																																			.	.	.	none		0.587	ANKZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335790.1	NM_018089		-	220099806	C	-	220099806	7	5	51	1	0	1	0	1	0	0	0	0	693	739	26	0	1497	0	ANKZF1	2	220099806	Frame_Shift_Del	DEL	C	TCGA-A4-7996-01A-11D-2201-08	16059929	220099806	23099567	21	3437											
GIGYF2	26058	hgsc.bcm.edu	37	chr2	233660917	233660917	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggtattacaaagatcctcAgggagaaattcaaggcaagt	15	9	11	6	0	2	2	2	0	0	2	3	3	3	2	1	3	1	2	1	3	6	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr2:233660917A>G	ENST00000409547.1	+	16	1936	c.1625A>G	c.(1624-1626)cAg>cGg	p.Q542R	GIGYF2_ENST00000409480.1_Missense_Mutation_p.Q564R|GIGYF2_ENST00000452341.2_Missense_Mutation_p.Q373R|GIGYF2_ENST00000409451.3_Missense_Mutation_p.Q563R|GIGYF2_ENST00000409196.3_Missense_Mutation_p.Q536R|GIGYF2_ENST00000373566.3_Missense_Mutation_p.Q564R|GIGYF2_ENST00000373563.4_Missense_Mutation_p.Q542R	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	542	GYF. {ECO:0000255|PROSITE- ProRule:PRU00101}.				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)		AAAGATCCTCAGGGAGAAATT	0.378																																					p.Q563R		Atlas-SNP	.											.,2	GIGYF2	288	.	0			c.A1688G						PASS	.						121	117	118					2																	233660917		2203	4300	6503	SO:0001583	missense	26058	exon16			ATCCTCAGGGAGA	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.1625A>G	chr2.hg19:g.233660917A>G	ENSP00000386537:p.Gln542Arg	117.0	0.0	.		136.0	33.0	.	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	hg19	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.654738	0.88056	.	.	ENSG00000204120	ENST00000373566;ENST00000414511;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000535418;ENST00000423659;ENST00000409196;ENST00000409451;ENST00000440945;ENST00000452341	T;T;T;T;D;T;T;T;T	0.81579	-1.35;-1.33;-1.35;-1.33;-1.51;-1.32;-1.35;-1.45;-1.27	5.68	5.68	0.88126	GYF (4);	0.000000	0.85682	D	0.000000	D	0.91529	0.7325	M	0.89658	3.05	0.80722	D	1	D;D;D;D	0.71674	0.994;0.998;0.997;0.969	D;D;D;D	0.83275	0.986;0.996;0.992;0.968	D	0.93157	0.6554	10	0.87932	D	0	-17.6236	16.2119	0.82168	1.0:0.0:0.0:0.0	.	373;563;542;536	E9PC50;A6H8W4;Q6Y7W6;E9PBB0	.;.;PERQ2_HUMAN;.	R	564;485;542;564;542;542;485;536;563;536;373	ENSP00000362667:Q564R;ENSP00000362664:Q542R;ENSP00000386765:Q564R;ENSP00000386537:Q542R;ENSP00000404195:Q485R;ENSP00000387070:Q536R;ENSP00000387170:Q563R;ENSP00000410297:Q536R;ENSP00000411505:Q373R	ENSP00000362664:Q542R	Q	+	2	0	GIGYF2	233369161	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.287000	0.95975	2.288000	0.76882	0.482000	0.46254	CAG	.	.	.	none		0.378	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		G	233660917	A	G	233660917	3	3	51	1	0	0	0	0	1	0	0	0	6385	188	7	3	1741	3	GIGYF2	2	233660917	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08	13561111	233660917	9538456	22	3438											
CCR3	1232	hgsc.bcm.edu	37	chr3	46307340	46307340	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaacgctgctgaggtgccccAgtaaaaaaaagtacaaggcc	16	5	10	10	1	0	1	0	1	0	0	0	1	0	1	3	2	4	4	3	2	7	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr3:46307340A>G	ENST00000357422.2	+	4	1234	c.691A>G	c.(691-693)Agt>Ggt	p.S231G	CCR3_ENST00000541018.1_Missense_Mutation_p.S231G|CCR3_ENST00000395942.2_Missense_Mutation_p.S231G|CCR3_ENST00000545097.1_Missense_Mutation_p.S252G|CCR3_ENST00000395940.2_Missense_Mutation_p.S231G			P51677	CCR3_HUMAN	chemokine (C-C motif) receptor 3	231					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)		GAGGTGCCCCAGTAAAAAAAA	0.463																																					p.S252G		Atlas-SNP	.											.	CCR3	52	.	0			c.A754G						PASS	.						73	72	72					3																	46307340		2203	4300	6503	SO:0001583	missense	1232	exon3			TGCCCCAGTAAAA	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.691A>G	chr3.hg19:g.46307340A>G	ENSP00000350003:p.Ser231Gly	101.0	0.0	.		62.0	28.0	.	NM_178328	B3KVQ1|F5GWL6|Q15748|Q2YDB9|Q86WD2|Q8TDP6|Q9ULY8	Missense_Mutation	SNP	ENST00000357422.2	hg19	CCDS2738.1	.	.	.	.	.	.	.	.	.	.	A	11.68	1.712194	0.30322	.	.	ENSG00000183625	ENST00000357422;ENST00000545097;ENST00000541018;ENST00000395940;ENST00000395942	T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82	5.96	2.3	0.28687	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.34424	0.0897	N	0.21448	0.665	0.09310	N	1	B;B	0.14805	0.009;0.011	B;B	0.23150	0.036;0.044	T	0.31166	-0.9953	9	0.66056	D	0.02	.	9.5513	0.39313	0.8017:0.0:0.1983:0.0	.	252;231	F5GWL6;P51677	.;CCR3_HUMAN	G	231;252;231;231;231	ENSP00000350003:S231G;ENSP00000441600:S252G;ENSP00000440097:S231G;ENSP00000379271:S231G;ENSP00000379273:S231G	ENSP00000350003:S231G	S	+	1	0	CCR3	46282344	0.001000	0.12720	0.041000	0.18516	0.744000	0.42396	1.757000	0.38400	0.158000	0.19367	0.533000	0.62120	AGT	.	.	.	none		0.463	CCR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257380.2			G	46307340	A	G	46307340	3	3	51	1	0	0	0	0	1	0	0	0	2944	188	7	3	760	3	CCR3	3	46307340	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08		46307340	151715090	23	3439											
GNAI2	2771	hgsc.bcm.edu	37	chr3	50294280	50294280	+	Missense_Mutation	SNP	A	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	ggtgctagctgaggacgaggAgatggtgagaggatgagaga	12	6	20	3	1	0	5	0	3	0	3	0	11	0	7	0	5	2	2	0	5	1	1			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr3:50294280A>C	ENST00000313601.6	+	6	1103	c.719A>C	c.(718-720)gAg>gCg	p.E240A	GNAI2_ENST00000440628.1_Missense_Mutation_p.E188A|GNAI2_ENST00000266027.5_Missense_Mutation_p.E224A|GNAI2_ENST00000536647.1_Missense_Mutation_p.E159A|GNAI2_ENST00000491100.1_3'UTR|GNAI2_ENST00000422163.1_Missense_Mutation_p.E224A|GNAI2_ENST00000451956.1_Missense_Mutation_p.E203A	NM_002070.2	NP_002061.1	P04899	GNAI2_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 2	240					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)		GAGGACGAGGAGATGGTGAGA	0.577																																					p.E240A		Atlas-SNP	.											.	GNAI2	42	.	0			c.A719C						PASS	.						113	107	109					3																	50294280		2203	4300	6503	SO:0001583	missense	2771	exon6			ACGAGGAGATGGT	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.719A>C	chr3.hg19:g.50294280A>C	ENSP00000312999:p.Glu240Ala	105.0	0.0	.		87.0	35.0	.	NM_002070	B3KTZ0|B4DYA0|B4E2X5|Q6B6N3|Q8IZ71	Missense_Mutation	SNP	ENST00000313601.6	hg19	CCDS2813.1	.	.	.	.	.	.	.	.	.	.	A	18.81	3.703847	0.68501	.	.	ENSG00000114353	ENST00000422163;ENST00000313601;ENST00000536647;ENST00000540560;ENST00000440628;ENST00000451956;ENST00000266027	T;T;T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39;-0.39;-0.39	4.62	4.62	0.57501	.	0.117678	0.64402	D	0.000009	T	0.67924	0.2945	M	0.77103	2.36	0.80722	D	1	B;B;B;B	0.17852	0.002;0.007;0.024;0.019	B;B;B;B	0.23852	0.049;0.049;0.049;0.029	T	0.69928	-0.5012	10	0.72032	D	0.01	.	12.3095	0.54920	1.0:0.0:0.0:0.0	.	203;240;224;224	B4DYA0;P04899;B3KTZ0;P04899-2	.;GNAI2_HUMAN;.;.	A	224;240;159;240;188;203;224	ENSP00000406871:E224A;ENSP00000312999:E240A;ENSP00000444360:E159A;ENSP00000395736:E188A;ENSP00000406369:E203A;ENSP00000266027:E224A	ENSP00000266027:E224A	E	+	2	0	GNAI2	50269284	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.285000	0.78660	2.088000	0.63022	0.459000	0.35465	GAG	.	.	.	none		0.577	GNAI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346688.1	NM_002070		C	50294280	A	C	50294280	3	2	51	1	0	0	0	0	1	0	0	0	6512	304	11	5	752	5	GNAI2	3	50294280	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08	3986940	50294280	147728150	24	3440											
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-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	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	.	0			c.G4416A						PASS	.						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	chr3.hg19:g.113376113C>T		42.0	2.0	.		46.0	7.0	.	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	hg19	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	51	1	0	0	0	0	0	0	0	1	8275	796	28	2		2	KIAA2018	3	113376113	Silent	SNP	C	TCGA-A4-7996-01A-11D-2201-08	63081833	113376113	84646317	25	3441											
ZXDC	79364	hgsc.bcm.edu	37	chr3	126194470	126194470	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcgccgccgtgcggcactTccagcagcaccaagaaagag	11	3	12	15	4	0	2	0	0	0	2	1	2	1	2	4	1	4	3	4	1	2	1			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr3:126194470T>C	ENST00000389709.3	-	1	292	c.239A>G	c.(238-240)gAa>gGa	p.E80G	ZXDC_ENST00000336332.5_Missense_Mutation_p.E80G	NM_025112.4	NP_079388.3	Q2QGD7	ZXDC_HUMAN	ZXD family zinc finger C	80					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|LRR domain binding (GO:0030275)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(1)	17				GBM - Glioblastoma multiforme(114;0.155)		GTGCGGCACTTCCAGCAGCAC	0.766																																					p.E80G		Atlas-SNP	.											.	ZXDC	87	.	0			c.A239G						PASS	.						10	11	10					3																	126194470		1178	2759	3937	SO:0001583	missense	79364	exon1			GGCACTTCCAGCA	AK023923	CCDS43145.1, CCDS43146.1	3q21.3	2014-02-12			ENSG00000070476	ENSG00000070476		"Zinc fingers, C2H2-type"	28160	protein-coding gene	gene with protein product		615746				8619474, 9110174	Standard	XM_005247757		Approved	MGC11349, FLJ13861	uc003eiv.3	Q2QGD7	OTTHUMG00000162754	ENST00000389709.3:c.239A>G	chr3.hg19:g.126194470T>C	ENSP00000374359:p.Glu80Gly	40.0	0.0	.		18.0	11.0	.	NM_025112	C5J0H9|Q6DKI8|Q7L3L1|Q8NAU2	Missense_Mutation	SNP	ENST00000389709.3	hg19	CCDS43145.1	.	.	.	.	.	.	.	.	.	.	T	7.919	0.738083	0.15574	.	.	ENSG00000070476	ENST00000389709;ENST00000336332	T;T	0.29142	1.58;1.58	3.22	1.97	0.26223	.	3.885840	0.01408	U	0.013872	T	0.25269	0.0614	L	0.40543	1.245	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.04013	0.001;0.001	T	0.10800	-1.0614	10	0.23891	T	0.37	-0.3189	3.4994	0.07668	0.0:0.1312:0.2352:0.6336	.	80;80	Q2QGD7-2;Q2QGD7	.;ZXDC_HUMAN	G	80	ENSP00000374359:E80G;ENSP00000337694:E80G	ENSP00000337694:E80G	E	-	2	0	ZXDC	127677160	0.000000	0.05858	0.272000	0.24630	0.077000	0.17291	0.070000	0.14573	0.233000	0.21120	0.358000	0.22013	GAA	.	.	.	none		0.766	ZXDC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370327.2	NM_025112		C	126194470	T	C	126194470	3	2	51	1	0	0	0	0	1	0	0	0	18264	1783	62	3	2383	3	ZXDC	3	126194470	Missense_Mutation	SNP	T	TCGA-A4-7996-01A-11D-2201-08	12818357	126194470	71827960	26	3442											
C4orf36	132989	hgsc.bcm.edu	37	chr4	87809274	87809274	+	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	gcagaacttaaggaacttacAttctgcagaagggagcagtc	14	8	11	8	0	1	2	0	0	1	2	2	4	1	4	0	2	5	3	0	2	5	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr4:87809274A>T	ENST00000473559.1	-	6	883	c.220T>A	c.(220-222)Tct>Act	p.S74T	C4orf36_ENST00000503001.1_5'Flank|C4orf36_ENST00000295898.3_Splice_Site_p.S74T			Q96KX1	CD036_HUMAN	chromosome 4 open reading frame 36	74										breast(1)|kidney(1)|lung(1)|prostate(1)	4		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00141)		AGGAACTTACATTCTGCAGAA	0.363																																					p.S74T		Atlas-SNP	.											.	C4orf36	10	.	0			c.T220A						PASS	.						65	66	66					4																	87809274		2203	4300	6503	SO:0001630	splice_region_variant	132989	exon3			ACTTACATTCTGC	BC016746	CCDS3615.1	4q21.3	2008-02-05			ENSG00000163633	ENSG00000163633			28386	protein-coding gene	gene with protein product						12477932	Standard	NM_144645		Approved	MGC26744	uc003hqe.4	Q96KX1	OTTHUMG00000130597	ENST00000473559.1:c.220+1T>A	chr4.hg19:g.87809274A>T		101.0	0.0	.		89.0	25.0	.	NM_144645		Missense_Mutation	SNP	ENST00000473559.1	hg19	CCDS3615.1	.	.	.	.	.	.	.	.	.	.	A	7.943	0.743153	0.15642	.	.	ENSG00000163633	ENST00000295898;ENST00000473559;ENST00000506308;ENST00000504008	T;T;T;T	0.38887	1.11;1.11;1.11;1.11	5.13	-6.29	0.02013	.	1.537520	0.03676	N	0.244784	T	0.22003	0.0530	N	0.17082	0.46	0.23249	N	0.99805	B	0.06786	0.001	B	0.08055	0.003	T	0.13764	-1.0497	9	.	.	.	0.0079	6.0792	0.19933	0.2272:0.2261:0.0:0.5468	.	74	Q96KX1	CD036_HUMAN	T	74	ENSP00000295898:S74T;ENSP00000420949:S74T;ENSP00000421141:S74T;ENSP00000422720:S74T	.	S	-	1	0	C4orf36	88028298	0.908000	0.30866	0.122000	0.21767	0.240000	0.25518	-0.311000	0.08124	-0.602000	0.05775	0.482000	0.46254	TCT	.	.	.	none		0.363	C4orf36-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253045.2	NM_144645	Missense_Mutation	T	87809274	A	T	87809274	5	4	51	1	0	0	0	0	0	0	1	0	2268	231	8	5	141	5	C4orf36	4	87809274	Splice_Site	SNP	A	TCGA-A4-7996-01A-11D-2201-08		87809274	103345002	27	3443											
PLK4	10733	hgsc.bcm.edu	37	chr4	128812805	128812805	+	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	ccaccctcacctactgacaaCatcagtaggtacagctttga	12	9	6	14	0	2	2	2	2	0	0	2	2	2	2	3	1	4	3	3	1	4	4			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr4:128812805C>A	ENST00000270861.5	+	9	2281	c.2007C>A	c.(2005-2007)aaC>aaA	p.N669K	PLK4_ENST00000515069.1_Missense_Mutation_p.N591K|RNU6-583P_ENST00000516012.1_RNA|PLK4_ENST00000514379.1_Missense_Mutation_p.N628K|PLK4_ENST00000507249.1_Missense_Mutation_p.N608K|PLK4_ENST00000513090.1_Missense_Mutation_p.N637K	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	669					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						CTACTGACAACATCAGTAGGT	0.318																																					p.N669K	Colon(135;508 1718 19061 31832 42879)	Atlas-SNP	.											.	PLK4	65	.	0			c.C2007A						PASS	.						89	97	94					4																	128812805		2203	4300	6503	SO:0001583	missense	10733	exon9			TGACAACATCAGT	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.2007C>A	chr4.hg19:g.128812805C>A	ENSP00000270861:p.Asn669Lys	162.0	0.0	.		176.0	59.0	.	NM_014264	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Missense_Mutation	SNP	ENST00000270861.5	hg19	CCDS3735.1	.	.	.	.	.	.	.	.	.	.	C	16.62	3.175146	0.57692	.	.	ENSG00000142731	ENST00000270861;ENST00000515069;ENST00000513090;ENST00000507249;ENST00000514379	T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51	5.07	2.4	0.29515	.	0.153463	0.56097	D	0.000021	T	0.32255	0.0823	L	0.51422	1.61	0.35092	D	0.764371	P;P	0.47762	0.9;0.839	P;B	0.48400	0.576;0.372	T	0.41360	-0.9513	10	0.59425	D	0.04	-4.1709	7.6088	0.28118	0.1342:0.724:0.0:0.1418	.	637;669	O00444-2;O00444	.;PLK4_HUMAN	K	669;591;637;608;628	ENSP00000270861:N669K;ENSP00000421774:N591K;ENSP00000427554:N637K;ENSP00000423412:N608K;ENSP00000423582:N628K	ENSP00000270861:N669K	N	+	3	2	PLK4	129032255	0.963000	0.33076	0.983000	0.44433	0.892000	0.51952	0.033000	0.13754	0.309000	0.22966	0.467000	0.42956	AAC	.	.	.	none		0.318	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3			A	128812805	C	A	128812805	3	1	51	1	0	0	0	0	1	0	0	0	12105	477	17	4	2041	4	PLK4	4	128812805	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	41003531	128812805	62341471	28	3444											
FHDC1	85462	hgsc.bcm.edu	37	chr4	153896859	153896859	+	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	aggaaggcggggaaggggatGgctccatgtcctctggggtt	7	8	19	7	1	1	0	0	0	1	0	3	3	3	3	2	9	0	2	2	9	2	1			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr4:153896859G>A	ENST00000511601.1	+	12	2604	c.2416G>A	c.(2416-2418)Ggc>Agc	p.G806S	FHDC1_ENST00000260008.3_Missense_Mutation_p.G806S			Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	806									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)					GGAAGGGGATGGCTCCATGTC	0.652																																					p.G806S		Atlas-SNP	.											.	FHDC1	102	.	0			c.G2416A						PASS	.						51	61	58					4																	153896859		2203	4300	6503	SO:0001583	missense	85462	exon11			GGGGATGGCTCCA	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.2416G>A	chr4.hg19:g.153896859G>A	ENSP00000427567:p.Gly806Ser	151.0	0.0	.		139.0	52.0	.	NM_033393		Missense_Mutation	SNP	ENST00000511601.1	hg19	CCDS34081.1	.	.	.	.	.	.	.	.	.	.	G	5.523	0.281358	0.10458	.	.	ENSG00000137460	ENST00000511601;ENST00000260008	T;T	0.29917	1.55;1.55	4.95	3.16	0.36331	.	0.771246	0.12008	N	0.508193	T	0.16811	0.0404	L	0.29908	0.895	0.09310	N	1	P	0.39282	0.666	B	0.33339	0.162	T	0.07947	-1.0746	10	0.02654	T	1	.	10.0533	0.42230	0.0:0.1495:0.695:0.1555	.	806	Q9C0D6	FHDC1_HUMAN	S	806	ENSP00000427567:G806S;ENSP00000260008:G806S	ENSP00000260008:G806S	G	+	1	0	FHDC1	154116309	0.062000	0.20869	0.002000	0.10522	0.222000	0.24845	2.052000	0.41316	0.455000	0.26910	0.563000	0.77884	GGC	.	.	.	none		0.652	FHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364981.2	NM_033393		A	153896859	G	A	153896859	3	1	51	1	0	0	0	0	1	0	0	0	5883	1348	47	2	2458	2	FHDC1	4	153896859	Missense_Mutation	SNP	G	TCGA-A4-7996-01A-11D-2201-08	25084054	153896859	37257417	29	3445											
SLC12A7	10723	hgsc.bcm.edu	37	chr5	1074691	1074691	+	Missense_Mutation	SNP	T	T	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	gcggtgctcacctccagttcTtggtgtgggggggaccgtgc	3	10	17	11	2	2	0	1	0	1	0	3	1	3	1	3	5	2	2	3	5	0	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr5:1074691T>G	ENST00000264930.5	-	16	2106	c.2063A>C	c.(2062-2064)aAg>aCg	p.K688T		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	688					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)	CCTCCAGTTCTTGGTGTGGGG	0.657																																					p.K688T		Atlas-SNP	.											.	SLC12A7	97	.	0			c.A2063C						PASS	.						54	51	52					5																	1074691		2201	4299	6500	SO:0001583	missense	10723	exon16			CAGTTCTTGGTGT	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.2063A>C	chr5.hg19:g.1074691T>G	ENSP00000264930:p.Lys688Thr	103.0	0.0	.		100.0	31.0	.	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Missense_Mutation	SNP	ENST00000264930.5	hg19	CCDS34129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	17.74|17.74	3.464117|3.464117	0.63513|0.63513	.|.	.|.	ENSG00000113504|ENSG00000113504	ENST00000264930|ENST00000513223	D|.	0.99186|.	-5.53|.	3.81|3.81	3.81|3.81	0.43845|0.43845	Amino acid permease domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.86682|0.86682	0.5991|0.5991	H|H	0.97707|0.97707	4.06|4.06	0.58432|0.58432	D|D	0.999998|0.999998	P|.	0.46912|.	0.886|.	P|.	0.46339|.	0.513|.	D|D	0.89599|0.89599	0.3833|0.3833	10|5	0.87932|.	D|.	0|.	.|.	10.8081|10.8081	0.46529|0.46529	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	688|.	Q9Y666|.	S12A7_HUMAN|.	T|H	688|45	ENSP00000264930:K688T|.	ENSP00000264930:K688T|.	K|Q	-|-	2|3	0|2	SLC12A7|SLC12A7	1127691|1127691	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.335000|0.335000	0.28730|0.28730	7.076000|7.076000	0.76806|0.76806	1.501000|1.501000	0.48654|0.48654	0.260000|0.260000	0.18958|0.18958	AAG|CAA	.	.	.	none		0.657	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598		G	1074691	T	G	1074691	3	3	51	1	0	0	0	0	1	0	0	0	14401	1609	56	5	1224	5	SLC12A7	5	1074691	Missense_Mutation	SNP	T	TCGA-A4-7996-01A-11D-2201-08		1074691	179840569	30	3446											
MAT2B	27430	hgsc.bcm.edu	37	chr5	162940576	162940577	+	Frame_Shift_Ins	INS	-	-	A																															ctagccccatgttatagtacINSattgtgcagcagagagaaga																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr5:162940576_162940577insA	ENST00000321757.6	+	3	413_414	c.274_275insA	c.(274-276)catfs	p.H92fs	MAT2B_ENST00000280969.5_Frame_Shift_Ins_p.H81fs|MAT2B_ENST00000518095.1_Frame_Shift_Ins_p.H92fs	NM_013283.3	NP_037415.1	Q9NZL9	MAT2B_HUMAN	methionine adenosyltransferase II, beta	92					cellular nitrogen compound metabolic process (GO:0034641)|extracellular polysaccharide biosynthetic process (GO:0045226)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|regulation of catalytic activity (GO:0050790)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|methionine adenosyltransferase complex (GO:0048269)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dTDP-4-dehydrorhamnose reductase activity (GO:0008831)|enzyme binding (GO:0019899)|methionine adenosyltransferase regulator activity (GO:0048270)			endometrium(3)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)	14	Renal(175;0.000281)	Medulloblastoma(196;0.0208)|all_neural(177;0.0765)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.027)|OV - Ovarian serous cystadenocarcinoma(192;0.0406)|Epithelial(171;0.0797)	L-Methionine(DB00134)	TGTTATAGTACATTGTGCAGCA	0.371																																					p.H92fs		Atlas-INDEL	.											.	MAT2B	42	.	0			c.274_275insA						PASS	.																																			SO:0001589	frameshift_variant	27430	exon3			.	AF182814	CCDS4364.1, CCDS4365.1	5q34-q35	2011-09-14			ENSG00000038274	ENSG00000038274		"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	6905	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 23E, member 1"	605527				9055605, 10644686, 19027726	Standard	NM_182796		Approved	MATIIbeta, SDR23E1	uc003lzk.4	Q9NZL9	OTTHUMG00000130379	ENST00000321757.6:c.275dupA	chr5.hg19:g.162940577_162940577dupA	ENSP00000325425:p.His92fs	155.0	0.0	0		104.0	37.0	0.355769	NM_013283	B2R5Y6|Q1WAI7|Q27J92|Q3LIE8|Q567T7|Q6NYC7|Q9BS89|Q9H3E1|Q9UJ54	Frame_Shift_Ins	INS	ENST00000321757.6	hg19	CCDS4365.1																																																																																			.	.	.	none		0.371	MAT2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252749.2	NM_013283		A	162940577	-	A	162940576	7	5	51	1	0	1	1	0	0	0	0	0	9338	478	17	0	318	0	MAT2B	5	162940576	Frame_Shift_Ins	INS	-	TCGA-A4-7996-01A-11D-2201-08	161865885	162940576	17974684	31	3447											
CLTB	1212	hgsc.bcm.edu	37	chr5	175843340	175843342	+	In_Frame_Del	DEL	AGA	AGA	-																															ggcaccgctctccgacgacgAgaagaagccaaagtcatcag																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr5:175843340_175843342delAGA	ENST00000310418.4	-	1	228_230	c.23_25delTCT	c.(22-27)ttctcg>tcg	p.F8del	CLTB_ENST00000345807.2_In_Frame_Del_p.F8del	NM_007097.3	NP_009028.1	P09497	CLCB_HUMAN	clathrin, light chain B	8					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)		TCCGACGACGAGAAGAAGCCAAA	0.724																																					p.8_9del		Atlas-INDEL	.											.	CLTB	17	.	0			c.24_26del						PASS	.																																			SO:0001651	inframe_deletion	1212	exon1			.	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.23_25delTCT	chr5.hg19:g.175843343_175843345delAGA	ENSP00000309415:p.Phe8del	71.0	0.0	0		36.0	15.0	0.416667	NM_007097	Q53Y37|Q6FHW1	In_Frame_Del	DEL	ENST00000310418.4	hg19	CCDS4403.1																																																																																			.	.	.	none		0.724	CLTB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253153.1			-	175843342	AGA	-	175843340	7	5	51	1	0	1	0	1	0	0	0	0	3567	304	11	0	688	0	CLTB	5	175843340	In_Frame_Del	DEL	AGA	TCGA-A4-7996-01A-11D-2201-08	12902764	175843340	5071920	32	3448											
F12	2161	hgsc.bcm.edu	37	chr5	176831350	176831350	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcactgtgccaggtcgcagtActcccagctcagccggtcgc	6	7	12	16	3	1	0	1	0	0	0	4	0	2	0	3	2	4	4	3	2	1	1			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr5:176831350A>G	ENST00000253496.3	-	9	913	c.865T>C	c.(865-867)Tac>Cac	p.Y289H	F12_ENST00000514943.1_5'Flank	NM_000505.3	NP_000496.2	P00748	FA12_HUMAN	coagulation factor XII (Hageman factor)	289	Kringle. {ECO:0000255|PROSITE- ProRule:PRU00121}.				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)	AGGTCGCAGTACTCCCAGCTC	0.697									Hereditary Angioedema		OREG0017088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y289H		Atlas-SNP	.											.	F12	35	.	0			c.T865C						PASS	.						16	20	19					5																	176831350		2200	4296	6496	SO:0001583	missense	2161	exon9	Familial Cancer Database	HAE, type I-III, Hereditary Angioneurotic Edema, HANE,	CGCAGTACTCCCA	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.865T>C	chr5.hg19:g.176831350A>G	ENSP00000253496:p.Tyr289His	33.0	0.0	.	1934	36.0	15.0	.	NM_000505	P78339	Missense_Mutation	SNP	ENST00000253496.3	hg19	CCDS34302.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.074641	0.76415	.	.	ENSG00000131187	ENST00000253496	T	0.66460	-0.21	5.45	5.45	0.79879	Kringle (5);Kringle-like fold (1);	0.000000	0.42682	D	0.000679	T	0.73497	0.3594	M	0.75150	2.29	0.80722	D	1	P	0.51537	0.946	P	0.54210	0.745	T	0.74548	-0.3629	10	0.41790	T	0.15	.	9.0885	0.36596	0.9168:0.0:0.0832:0.0	.	289	P00748	FA12_HUMAN	H	289	ENSP00000253496:Y289H	ENSP00000253496:Y289H	Y	-	1	0	F12	176763956	0.924000	0.31332	0.575000	0.28536	0.770000	0.43624	2.546000	0.45778	2.080000	0.62538	0.459000	0.35465	TAC	.	.	.	none		0.697	F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373217.1			G	176831350	A	G	176831350	3	3	51	1	0	0	0	0	1	0	0	0	5341	391	14	3	1006	3	F12	5	176831350	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08	988010	176831350	4083910	33	3449											
SKIV2L	6499	hgsc.bcm.edu	37	chr6	31927082	31927082	+	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	ctttccccgtagtgctacccCctccagatcccctggaccta	6	10	6	19	1	0	1	0	0	0	1	3	2	3	2	8	1	2	2	8	1	3	4	rs563036739	byFrequency	TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr6:31927082C>A	ENST00000375394.2	+	2	144	c.31C>A	c.(31-33)Cct>Act	p.P11T	NELFE_ENST00000375429.3_5'Flank|NELFE_ENST00000444811.2_5'Flank|MIR1236_ENST00000408340.1_RNA|SKIV2L_ENST00000488648.1_3'UTR|NELFE_ENST00000375425.5_5'Flank|SKIV2L_ENST00000544581.1_5'UTR	NM_006929.4	NP_008860.4	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like (S. cerevisiae)	11					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						AGTGCTACCCCCTCCAGATCC	0.602																																					p.P11T		Atlas-SNP	.											.	SKIV2L	97	.	0			c.C31A						PASS	.						221	230	227					6																	31927082		2203	4299	6502	SO:0001583	missense	6499	exon2			CTACCCCCTCCAG		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.31C>A	chr6.hg19:g.31927082C>A	ENSP00000364543:p.Pro11Thr	587.0	1.0	.		457.0	133.0	.	NM_006929	O15005|Q12902|Q15476|Q5ST66	Missense_Mutation	SNP	ENST00000375394.2	hg19	CCDS4731.1	.	.	.	.	.	.	.	.	.	.	C	9.522	1.108545	0.20714	.	.	ENSG00000204351	ENST00000375394	T	0.45276	0.9	5.18	3.42	0.39159	.	0.176723	0.50627	D	0.000113	T	0.18130	0.0435	L	0.47716	1.5	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.04900	-1.0919	10	0.40728	T	0.16	-13.5646	9.0377	0.36298	0.0:0.8274:0.0:0.1726	.	11	Q15477	SKIV2_HUMAN	T	11	ENSP00000364543:P11T	ENSP00000364543:P11T	P	+	1	0	SKIV2L	32035061	1.000000	0.71417	0.993000	0.49108	0.481000	0.33189	1.932000	0.40143	0.781000	0.33589	0.655000	0.94253	CCT	.	.	.	none		0.602	SKIV2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076264.3			A	31927082	C	A	31927082	3	1	51	1	0	0	0	0	1	0	0	0	14372	623	22	4	37	4	SKIV2L	6	31927082	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08		31927082	139187985	34	3450											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51930865	51930865	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcccagtttctggaaacacAgataatatttctgcaagagt	13	12	7	9	0	2	2	0	0	2	2	3	3	3	3	1	1	2	2	1	1	4	4			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr6:51930865A>G	ENST00000371117.3	-	12	1064	c.789T>C	c.(787-789)tcT>tcC	p.S263S	PKHD1_ENST00000340994.4_Silent_p.S263S	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	263	IPT/TIG 3.				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)					CTGGAAACACAGATAATATTT	0.328																																					p.S263S		Atlas-SNP	.											.	PKHD1	927	.	0			c.T789C						PASS	.						67	66	66					6																	51930865		2203	4300	6503	SO:0001819	synonymous_variant	5314	exon12			AAACACAGATAAT	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.789T>C	chr6.hg19:g.51930865A>G		66.0	0.0	.		53.0	15.0	.	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	hg19	CCDS4935.1																																																																																			.	.	.	none		0.328	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		G	51930865	A	G	51930865	2	3	51	1	0	0	0	0	0	0	0	1	11978	175	7	3		3	PKHD1	6	51930865	Silent	SNP	A	TCGA-A4-7996-01A-11D-2201-08	20003783	51930865	119184202	35	3451											
MPP6	51678	hgsc.bcm.edu	37	chr7	24727063	24727075	+	Frame_Shift_Del	DEL	GACTTGAAGAAAA	GACTTGAAGAAAA	-																															aaactcttcaacaggactctGacttgaagaaaacagtggat																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	GACTTGAAGAAAA	GACTTGAAGAAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr7:24727063_24727075delGACTTGAAGAAAA	ENST00000222644.5	+	12	1703_1715	c.1453_1465delGACTTGAAGAAAA	c.(1453-1467)gacttgaagaaaacafs	p.DLKKT485fs	MPP6_ENST00000409761.1_Frame_Shift_Del_p.DLKKT373fs|MPP6_ENST00000396475.2_Frame_Shift_Del_p.DLKKT485fs			Q99547	MPH6_HUMAN	membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)	0					maturation of 5.8S rRNA (GO:0000460)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|skin(2)	20						ACAGGACTCTGACTTGAAGAAAACAGTGGATGA	0.324																																					p.484_488del		Atlas-INDEL	.											.	MPP6	62	.	0			c.1452_1464del						PASS	.																																			SO:0001589	frameshift_variant	51678	exon13			.	AF162130	CCDS5388.1	7p15	2007-08-01			ENSG00000105926	ENSG00000105926			18167	protein-coding gene	gene with protein product		606959				10753959, 11311936	Standard	NM_016447		Approved	PALS2, VAM-1, p55T	uc003swx.3	Q9NZW5	OTTHUMG00000023507	ENST00000222644.5:c.1453_1465delGACTTGAAGAAAA	chr7.hg19:g.24727063_24727075delGACTTGAAGAAAA	ENSP00000222644:p.Asp485fs	130.0	0.0	0		142.0	50.0	0.352113	NM_016447	B2RAF0	Frame_Shift_Del	DEL	ENST00000222644.5	hg19	CCDS5388.1																																																																																			.	.	.	none		0.324	MPP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250272.4			-	24727075	GACTTGAAGAAAA	-	24727063	7	5	51	1	0	1	0	1	0	0	0	0	9745	1290	45	0	1495	0	MPP6	7	24727063	Frame_Shift_Del	DEL	GACTTGAAGAAAA	TCGA-A4-7996-01A-11D-2201-08		24727063	134411600	36	3452											
ZMIZ2	83637	hgsc.bcm.edu	37	chr7	44807159	44807159	+	Frame_Shift_Del	DEL	G	G	-																															gatgagctactgtcctacttGggcccacccgacctccctac																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr7:44807159delG	ENST00000309315.4	+	19	2823	c.2700delG	c.(2698-2700)ttgfs	p.L900fs	ZMIZ2_ENST00000413916.1_Frame_Shift_Del_p.L842fs|ZMIZ2_ENST00000441627.1_Frame_Shift_Del_p.L900fs|ZMIZ2_ENST00000463931.1_3'UTR|ZMIZ2_ENST00000265346.7_Frame_Shift_Del_p.L874fs|ZMIZ2_ENST00000433667.1_Frame_Shift_Del_p.L868fs	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2	900	Pro-rich.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						TGTCCTACTTGGGCCCACCCG	0.552																																					p.L900fs	NSCLC(20;604 852 1948 16908 50522)	Atlas-INDEL	.											.	ZMIZ2	82	.	0			c.2699delT						PASS	.						145	159	155					7																	44807159		2045	4190	6235	SO:0001589	frameshift_variant	83637	exon19			.	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.2700delG	chr7.hg19:g.44807159delG	ENSP00000311778:p.Leu900fs	118.0	0.0	0		122.0	24.0	0.196721	NM_031449	A4D2K7|D3DVL1|O94790|Q0VGB4|Q659A8|Q6JKL5|Q8WTX8|Q96Q01|Q9BQH7	Frame_Shift_Del	DEL	ENST00000309315.4	hg19	CCDS43576.1																																																																																			.	.	.	none		0.552	ZMIZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341790.1	NM_031449		-	44807159	G	-	44807159	7	5	51	1	0	1	0	1	0	0	0	0	17709	1339	47	0	2770	0	ZMIZ2	7	44807159	Frame_Shift_Del	DEL	G	TCGA-A4-7996-01A-11D-2201-08	20080096	44807159	114331504	37	3453											
DOCK4	9732	hgsc.bcm.edu	37	chr7	111555869	111555869	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttgaaaatcccagcttccttGttatggatactccatgagaa	12	13	7	9	0	0	2	0	2	0	1	3	4	3	3	3	1	2	2	3	1	5	5			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr7:111555869G>A	ENST00000437633.1	-	13	1413	c.1157C>T	c.(1156-1158)aCa>aTa	p.T386I	DOCK4_ENST00000428084.1_Missense_Mutation_p.T386I|DOCK4_ENST00000476846.1_5'UTR	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	386					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)				CAGCTTCCTTGTTATGGATAC	0.368																																					p.T386I		Atlas-SNP	.											.	DOCK4	365	.	0			c.C1157T						PASS	.						57	53	54					7																	111555869		1820	4078	5898	SO:0001583	missense	9732	exon13			TTCCTTGTTATGG		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.1157C>T	chr7.hg19:g.111555869G>A	ENSP00000404179:p.Thr386Ile	35.0	0.0	.		48.0	13.0	.	NM_014705	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	hg19	CCDS47688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.3|27.3	4.816438|4.816438	0.90790|0.90790	.|.	.|.	ENSG00000128512|ENSG00000128512	ENST00000445943|ENST00000352877;ENST00000428084;ENST00000437633;ENST00000342288;ENST00000544250	.|T;T	.|0.03580	.|3.88;3.88	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.19167	.|0.0460	M|M	0.74467|0.74467	2.265|2.265	0.80722|0.80722	D|D	1|1	.|D;D	.|0.69078	.|0.997;0.997	.|D;D	.|0.67103	.|0.949;0.949	.|T	.|0.00003	.|-1.2602	.|10	.|0.87932	.|D	.|0	.|.	19.3311|19.3311	0.94288|0.94288	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|386;386	.|Q149N5;Q8N1I0	.|.;DOCK4_HUMAN	X|I	374|374;386;386;374;385	.|ENSP00000410746:T386I;ENSP00000404179:T386I	.|ENSP00000345432:T374I	Q|T	-|-	1|2	0|0	DOCK4|DOCK4	111343105|111343105	1.000000|1.000000	0.71417|0.71417	0.974000|0.974000	0.42286|0.42286	0.960000|0.960000	0.62799|0.62799	8.322000|8.322000	0.90000|0.90000	2.868000|2.868000	0.98415|0.98415	0.555000|0.555000	0.69702|0.69702	CAA|ACA	.	.	.	none		0.368	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705		A	111555869	G	A	111555869	3	1	51	1	0	0	0	0	1	0	0	0	4691	1377	48	2	4903	2	DOCK4	7	111555869	Missense_Mutation	SNP	G	TCGA-A4-7996-01A-11D-2201-08	66748710	111555869	47582794	38	3454											
KIF13B	23303	hgsc.bcm.edu	37	chr8	28991695	28991695	+	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	aacacaaagtgggacagatgCtgtggcaacccagtagcttg	13	7	12	9	0	0	1	0	0	0	1	0	2	0	2	1	2	4	4	1	2	4	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr8:28991695C>G	ENST00000524189.1	-	22	2684	c.2646G>C	c.(2644-2646)caG>caC	p.Q882H	CTD-2647L4.1_ENST00000523661.1_RNA	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	882					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)		GGGACAGATGCTGTGGCAACC	0.488																																					p.Q882H		Atlas-SNP	.											.	KIF13B	192	.	0			c.G2646C						PASS	.						81	81	81					8																	28991695		1901	4128	6029	SO:0001583	missense	23303	exon22			CAGATGCTGTGGC	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.2646G>C	chr8.hg19:g.28991695C>G	ENSP00000427900:p.Gln882His	119.0	0.0	.		122.0	45.0	.	NM_015254	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Missense_Mutation	SNP	ENST00000524189.1	hg19	CCDS55217.1	.	.	.	.	.	.	.	.	.	.	C	16.84	3.235189	0.58886	.	.	ENSG00000197892	ENST00000524189	T	0.10382	2.88	5.28	2.49	0.30216	.	0.057734	0.64402	D	0.000001	T	0.23094	0.0558	M	0.68317	2.08	0.80722	D	1	D	0.60575	0.988	P	0.59221	0.854	T	0.00992	-1.1488	10	0.45353	T	0.12	.	10.5748	0.45221	0.0:0.7286:0.0:0.2714	.	882	F8VPJ2	.	H	882	ENSP00000427900:Q882H	ENSP00000427900:Q882H	Q	-	3	2	KIF13B	29047614	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	0.458000	0.21892	0.810000	0.34279	0.650000	0.86243	CAG	.	.	.	none		0.488	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1			G	28991695	C	G	28991695	3	3	51	1	0	0	0	0	1	0	0	0	8282	796	28	4	2910	4	KIF13B	8	28991695	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08		28991695	117372327	39	3455											
C8orf46	254778	hgsc.bcm.edu	37	chr8	67405943	67405943	+	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	gaagttttcaccaccgtgatTccttccaagggtgagtgaaa	11	11	10	9	1	1	3	1	3	0	0	3	4	3	3	4	1	0	1	4	1	3	4	rs139160272	byFrequency	TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr8:67405943T>A	ENST00000305454.3	+	1	501	c.60T>A	c.(58-60)atT>atA	p.I20I	C8orf46_ENST00000521495.1_Silent_p.I20I|C8orf46_ENST00000480005.1_Silent_p.I20I|C8orf46_ENST00000522977.1_Silent_p.I20I|C8orf46_ENST00000482608.2_Intron	NM_152765.3	NP_689978.2	Q8TAG6	CH046_HUMAN	chromosome 8 open reading frame 46	20										endometrium(1)|large_intestine(1)|lung(1)|prostate(1)|skin(2)	6			Epithelial(68;0.0224)|BRCA - Breast invasive adenocarcinoma(89;0.0508)|all cancers(69;0.0558)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			CCACCGTGATTCCTTCCAAGG	0.502																																					p.I20I		Atlas-SNP	.											.	C8orf46	22	.	0			c.T60A						PASS	.						124	98	107					8																	67405943		2203	4300	6503	SO:0001819	synonymous_variant	254778	exon1			CGTGATTCCTTCC	BC028400	CCDS6191.2	8q13.1	2005-08-09			ENSG00000169085	ENSG00000169085			28498	protein-coding gene	gene with protein product						12477932	Standard	NM_152765		Approved	MGC33510	uc003xwg.3	Q8TAG6	OTTHUMG00000156998	ENST00000305454.3:c.60T>A	chr8.hg19:g.67405943T>A		71.0	0.0	.		76.0	22.0	.	NM_152765	B2RDC3|B4DFU4|C9J814|C9JCS3	Silent	SNP	ENST00000305454.3	hg19	CCDS6191.2																																																																																			.	T|0.999;C|0.001	.	alt		0.502	C8orf46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347010.1	NM_152765		A	67405943	T	A	67405943	2	1	51	1	0	0	0	0	0	0	0	1	2433	1771	62	5		5	C8orf46	8	67405943	Silent	SNP	T	TCGA-A4-7996-01A-11D-2201-08	38414248	67405943	78958079	40	3456											
TRAPPC9	83696	hgsc.bcm.edu	37	chr8	141449171	141449172	+	Frame_Shift_Del	DEL	TT	TT	-																															ctccaagccacagaaagtcaTtcacagaacgcagcagctcc																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr8:141449171_141449172delTT	ENST00000438773.2	-	3	842_843	c.709_710delAA	c.(709-711)aatfs	p.N237fs	TRAPPC9_ENST00000389327.3_Frame_Shift_Del_p.N237fs|TRAPPC9_ENST00000389328.4_Frame_Shift_Del_p.N335fs	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	237					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						CAGAAAGTCATTCACAGAACGC	0.525																																					p.335_335del		Atlas-INDEL	.											.	TRAPPC9	114	.	0			c.1004_1005del						PASS	.																																			SO:0001589	frameshift_variant	83696	exon3			.	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.709_710delAA	chr8.hg19:g.141449171_141449172delTT	ENSP00000405060:p.Asn237fs	174.0	0.0	0		160.0	72.0	0.45	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Frame_Shift_Del	DEL	ENST00000438773.2	hg19	CCDS55278.1																																																																																			.	.	.	none		0.525	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466		-	141449172	TT	-	141449171	7	5	51	1	0	1	0	1	0	0	0	0	16477	1493	52	0	2820	0	TRAPPC9	8	141449171	Frame_Shift_Del	DEL	TT	TCGA-A4-7996-01A-11D-2201-08	74043228	141449171	4914851	41	3457											
KCNV2	169522	hgsc.bcm.edu	37	chr9	2718279	2718279	+	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	gacgggctgtgtccgcgccgCttcctggaggagctgggcta	4	8	17	12	4	0	0	0	0	0	0	2	3	2	2	3	4	1	4	3	4	1	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr9:2718279C>T	ENST00000382082.3	+	1	778	c.540C>T	c.(538-540)cgC>cgT	p.R180R		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	180					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)		GTCCGCGCCGCTTCCTGGAGG	0.657																																					p.R180R		Atlas-SNP	.											.	KCNV2	72	.	0			c.C540T						PASS	.						19	17	18					9																	2718279		2200	4292	6492	SO:0001819	synonymous_variant	169522	exon1			GCGCCGCTTCCTG	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.540C>T	chr9.hg19:g.2718279C>T		34.0	0.0	.		17.0	6.0	.	NM_133497	Q5T6X0	Silent	SNP	ENST00000382082.3	hg19	CCDS6447.1																																																																																			.	.	.	none		0.657	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497		T	2718279	C	T	2718279	2	4	51	1	0	0	0	0	0	0	0	1	8102	784	28	2		2	KCNV2	9	2718279	Silent	SNP	C	TCGA-A4-7996-01A-11D-2201-08		2718279	138495152	42	3458											
TLN1	7094	hgsc.bcm.edu	37	chr9	35699405	35699405	+	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	gtgacggaaccagccacacgCtttgaatgtcctgtcaactg	10	9	10	12	2	1	2	1	2	0	0	2	3	2	3	3	1	3	1	3	1	3	1			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr9:35699405C>A	ENST00000314888.9	-	51	7175	c.6822G>T	c.(6820-6822)aaG>aaT	p.K2274N	TLN1_ENST00000540444.1_Missense_Mutation_p.K2162N	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	2274					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)			CAGCCACACGCTTTGAATGTC	0.562																																					p.K2274N		Atlas-SNP	.											.	TLN1	185	.	0			c.G6822T						PASS	.						158	127	137					9																	35699405		2203	4300	6503	SO:0001583	missense	7094	exon51			CACACGCTTTGAA	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.6822G>T	chr9.hg19:g.35699405C>A	ENSP00000316029:p.Lys2274Asn	97.0	0.0	.		99.0	32.0	.	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	hg19	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	c	18.95	3.732220	0.69189	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.69926	-0.44;-0.44	5.79	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.79028	0.4377	M	0.81239	2.535	0.58432	D	0.999996	D	0.67145	0.996	P	0.61397	0.888	T	0.81519	-0.0896	10	0.72032	D	0.01	-23.9158	10.9276	0.47199	0.0:0.8574:0.0:0.1426	.	2274	Q9Y490	TLN1_HUMAN	N	2274;2162	ENSP00000316029:K2274N;ENSP00000442981:K2162N	ENSP00000316029:K2274N	K	-	3	2	TLN1	35689405	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.766000	0.38491	1.472000	0.48140	0.651000	0.88453	AAG	.	.	.	none		0.562	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		A	35699405	C	A	35699405	3	1	51	1	0	0	0	0	1	0	0	0	15959	796	28	4	831	4	TLN1	9	35699405	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	32981126	35699405	105514026	43	3459											
OLFML2A	169611	hgsc.bcm.edu	37	chr9	127572163	127572163	+	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	gtgtaccagggcgccttctaCtacaaccgcgccttcaccaa	9	8	8	16	3	2	0	1	0	1	0	2	0	2	0	5	1	4	1	5	1	5	5			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr9:127572163C>T	ENST00000373580.3	+	8	1431	c.1431C>T	c.(1429-1431)taC>taT	p.Y477Y	OLFML2A_ENST00000288815.5_Silent_p.Y263Y	NM_182487.2	NP_872293.2	Q68BL7	OLM2A_HUMAN	olfactomedin-like 2A	477	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)			endometrium(5)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	25						GCGCCTTCTACTACAACCGCG	0.602																																					p.Y477Y		Atlas-SNP	.											.	OLFML2A	61	.	0			c.C1431T						PASS	.						124	99	108					9																	127572163		2203	4300	6503	SO:0001819	synonymous_variant	169611	exon8			CTTCTACTACAAC	AK092255	CCDS6857.2, CCDS65129.1	9q34.11	2008-02-05			ENSG00000185585	ENSG00000185585			27270	protein-coding gene	gene with protein product		615899				12477932	Standard	NM_001282715		Approved	FLJ00237	uc004bov.3	Q68BL7	OTTHUMG00000020663	ENST00000373580.3:c.1431C>T	chr9.hg19:g.127572163C>T		114.0	0.0	.		96.0	32.0	.	NM_182487	Q5JTM5|Q5JTM6|Q6UXW1|Q7Z5V3	Silent	SNP	ENST00000373580.3	hg19	CCDS6857.2																																																																																			.	.	.	none		0.602	OLFML2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054046.2	NM_182487		T	127572163	C	T	127572163	2	4	51	1	0	0	0	0	0	0	0	1	10864	576	20	2		2	OLFML2A	9	127572163	Silent	SNP	C	TCGA-A4-7996-01A-11D-2201-08	91872758	127572163	13641268	44	3460											
CCBL1	883	hgsc.bcm.edu	37	chr9	131607633	131607633	+	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	cccagcccagctggctcaccAggggttgtagtcgatcccgt	6	8	12	15	2	1	0	1	0	0	0	3	1	2	0	4	3	2	4	4	3	1	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr9:131607633A>T	ENST00000302586.3	-	2	214	c.52T>A	c.(52-54)Tgg>Agg	p.W18R	CCBL1_ENST00000320665.6_Splice_Site_p.W18R|CCBL1_ENST00000483599.1_5'UTR|CCBL1_ENST00000436267.2_Splice_Site_p.W112R	NM_001122671.1|NM_004059.4	NP_001116143.1|NP_004050.3	Q16773	KAT1_HUMAN	cysteine conjugate-beta lyase, cytoplasmic	18					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)	CTGGCTCACCAGGGGTTGTAG	0.602																																					p.W18R		Atlas-SNP	.											.	CCBL1	36	.	0			c.T52A						PASS	.						53	62	59					9																	131607633		2053	4192	6245	SO:0001630	splice_region_variant	883	exon2			CTCACCAGGGGTT	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.53+1T>A	chr9.hg19:g.131607633A>T		88.0	0.0	.		48.0	8.0	.	NM_001122672	Q5T275|Q8N191	Missense_Mutation	SNP	ENST00000302586.3	hg19	CCDS43884.1	.	.	.	.	.	.	.	.	.	.	A	17.72	3.458148	0.63401	.	.	ENSG00000171097	ENST00000302586;ENST00000372610;ENST00000320665;ENST00000436267;ENST00000451800;ENST00000416084;ENST00000427720	T;D;T;T;T	0.83075	-0.95;-1.68;-1.0;-0.87;0.85	5.28	5.28	0.74379	Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	T	0.81917	0.4924	M	0.66378	2.025	0.80722	D	1	B;B;B;B;B	0.26081	0.141;0.047;0.018;0.047;0.019	B;B;B;B;B	0.24974	0.046;0.02;0.057;0.02;0.02	T	0.81256	-0.1015	10	0.72032	D	0.01	-3.8485	14.326	0.66521	1.0:0.0:0.0:0.0	.	112;18;18;18;18	B7Z4W5;A8K563;Q16773-2;Q16773;Q5T278	.;.;.;KAT1_HUMAN;.	R	18;19;18;112;18;18;19	ENSP00000302227:W18R;ENSP00000317342:W18R;ENSP00000399415:W112R;ENSP00000390377:W18R;ENSP00000412402:W18R	ENSP00000302227:W18R	W	-	1	0	CCBL1	130647454	0.996000	0.38824	0.998000	0.56505	0.955000	0.61496	3.509000	0.53386	2.120000	0.65058	0.460000	0.39030	TGG	.	.	.	none		0.602	CCBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054521.2		Missense_Mutation	T	131607633	A	T	131607633	5	4	51	1	0	0	0	0	0	0	1	0	2734	202	7	5	1264	5	CCBL1	9	131607633	Splice_Site	SNP	A	TCGA-A4-7996-01A-11D-2201-08	4035470	131607633	9605798	45	3461											
PTCHD3	374308	hgsc.bcm.edu	37	chr10	27687708	27687708	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatgtacaaaacatatataaAgactacaaaatacttggact	20	10	5	6	0	0	1	0	0	0	1	0	3	0	2	0	1	4	1	0	1	11	7			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr10:27687708A>G	ENST00000438700.3	-	4	1936	c.1819T>C	c.(1819-1821)Ttt>Ctt	p.F607L		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	607					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						ACATATATAAAGACTACAAAA	0.383																																					p.F607L		Atlas-SNP	.											.	PTCHD3	140	.	0			c.T1819C						PASS	.						64	65	64					10																	27687708		2203	4300	6503	SO:0001583	missense	374308	exon4			ATATAAAGACTAC	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.1819T>C	chr10.hg19:g.27687708A>G	ENSP00000417658:p.Phe607Leu	92.0	0.0	.		95.0	63.0	.	NM_001034842	I3L499|Q6ZU28	Missense_Mutation	SNP	ENST00000438700.3	hg19	CCDS31173.1	.	.	.	.	.	.	.	.	.	.	A	0.001	-2.996644	0.00044	.	.	ENSG00000182077	ENST00000438700	D	0.83914	-1.78	4.05	-0.446	0.12238	.	0.493132	0.20919	N	0.083307	T	0.41650	0.1168	N	0.00707	-1.245	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.48410	-0.9038	10	0.02654	T	1	-5.7246	0.1591	0.00101	0.2673:0.2583:0.2122:0.2622	.	607	Q3KNS1	PTHD3_HUMAN	L	607	ENSP00000417658:F607L	ENSP00000417658:F607L	F	-	1	0	PTCHD3	27727714	0.012000	0.17670	0.007000	0.13788	0.009000	0.06853	-0.796000	0.04575	-0.287000	0.09064	-0.425000	0.05940	TTT	.	.	.	none		0.383	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541		G	27687708	A	G	27687708	3	3	51	1	0	0	0	0	1	0	0	0	12744	72	3	3	488	3	PTCHD3	10	27687708	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08		27687708	107847039	46	3462											
NCOA4	8031	hgsc.bcm.edu	37	chr10	51585156	51585156	+	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	gctttgcagagtgtgtgtgtGatgagaattgtgagaaggag	10	12	17	2	0	0	4	0	3	0	3	0	7	0	5	0	1	1	2	0	1	2	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr10:51585156G>T	ENST00000443446.1	+	8	1484	c.1255G>T	c.(1255-1257)Gat>Tat	p.D419Y	NCOA4_ENST00000430396.2_Missense_Mutation_p.D319Y|NCOA4_ENST00000414907.2_Missense_Mutation_p.D253Y|NCOA4_ENST00000452682.1_Missense_Mutation_p.D435Y|NCOA4_ENST00000374082.1_Missense_Mutation_p.D419Y|NCOA4_ENST00000344348.6_Missense_Mutation_p.D419Y|NCOA4_ENST00000438493.1_Missense_Mutation_p.D435Y|NCOA4_ENST00000374087.4_Missense_Mutation_p.D419Y	NM_001145262.1	NP_001138734.1	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4	419					androgen receptor signaling pathway (GO:0030521)|male gonad development (GO:0008584)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|skin(1)	5						GTGTGTGTGTGATGAGAATTG	0.483			T	RET	papillary thyroid																																p.D435Y		Atlas-SNP	.		Dom	yes		10	10q11.2	8031	nuclear receptor coactivator 4 - PTC3 (ELE1)		E	.	NCOA4	58	.	0			c.G1303T						PASS	.						71	74	73					10																	51585156		2203	4300	6503	SO:0001583	missense	8031	exon9			GTGTGTGATGAGA	L49399	CCDS73092.1, CCDS73093.1, CCDS73094.1	10q11.2	2014-04-10			ENSG00000138293	ENSG00000266412			7671	protein-coding gene	gene with protein product	"RET-activating gene ELE1"	601984				8290261, 8643607, 24695223	Standard	NM_001145260		Approved	ARA70, RFG, ELE1, PTC3, DKFZp762E1112	uc009xon.3	Q13772	OTTHUMG00000188314	ENST00000443446.1:c.1255G>T	chr10.hg19:g.51585156G>T	ENSP00000390713:p.Asp419Tyr	99.0	0.0	.		104.0	69.0	.	NM_001145261	A8K8W5|B4E260|E9PAV7|J3KQN8|Q14239	Missense_Mutation	SNP	ENST00000443446.1	hg19	CCDS7237.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.878324	0.91740	.	.	ENSG00000138293	ENST00000438493;ENST00000452682;ENST00000430396;ENST00000374087;ENST00000414907;ENST00000344348;ENST00000374082;ENST00000443446	T;T;T;T;T;T;T;T	0.30981	1.99;2.0;1.7;2.0;1.51;2.0;1.7;2.0	5.6	5.6	0.85130	.	0.334273	0.35805	N	0.002979	T	0.54983	0.1892	M	0.70275	2.135	0.80722	D	1	D;D;D;D	0.76494	0.999;0.994;0.994;0.997	D;P;P;P	0.63488	0.915;0.87;0.87;0.819	T	0.51593	-0.8686	9	.	.	.	-20.3172	19.608	0.95587	0.0:0.0:1.0:0.0	.	319;435;435;419	B4DF87;B4E260;E9PAV7;Q13772	.;.;.;NCOA4_HUMAN	Y	435;435;319;419;253;419;419;419	ENSP00000405146:D435Y;ENSP00000395465:D435Y;ENSP00000393053:D319Y;ENSP00000363200:D419Y;ENSP00000411018:D253Y;ENSP00000344552:D419Y;ENSP00000363195:D419Y;ENSP00000390713:D419Y	.	D	+	1	0	NCOA4	51255162	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.392000	0.97252	2.647000	0.89833	0.650000	0.86243	GAT	.	.	.	none		0.483	NCOA4-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048052.1	NM_005437		T	51585156	G	T	51585156	3	4	51	1	0	0	0	0	1	0	0	0	10238	1290	45	4	1333	4	NCOA4	10	51585156	Missense_Mutation	SNP	G	TCGA-A4-7996-01A-11D-2201-08	23897448	51585156	83949591	47	3463											
WAPAL	23063	hgsc.bcm.edu	37	chr10	88259986	88259986	+	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	ccacaacttacaccccctttCtttgcctgattcaggccatc	8	12	4	17	0	2	1	1	1	1	0	3	1	2	1	5	1	3	0	5	1	2	4			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr10:88259986C>A	ENST00000298767.5	-	3	1486	c.1014G>T	c.(1012-1014)aaG>aaT	p.K338N		NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	338	Mediates interaction with the cohesin complex.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)				breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						CACCCCCTTTCTTTGCCTGAT	0.448																																					p.K338N		Atlas-SNP	.											.	WAPAL	81	.	0			c.G1014T						PASS	.						182	152	162					10																	88259986		2203	4300	6503	SO:0001583	missense	23063	exon3			CCCTTTCTTTGCC	AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"friend of EBNA2"	610754	"KIAA0261"	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.1014G>T	chr10.hg19:g.88259986C>A	ENSP00000298767:p.Lys338Asn	190.0	0.0	.		166.0	117.0	.	NM_015045	A7E2B5|Q5VSK5|Q8IX10|Q92549	Missense_Mutation	SNP	ENST00000298767.5	hg19	CCDS7375.1	.	.	.	.	.	.	.	.	.	.	C	11.49	1.653403	0.29425	.	.	ENSG00000062650	ENST00000342368;ENST00000298767;ENST00000372076	T	0.29397	1.57	5.77	0.75	0.18387	.	0.497401	0.21168	N	0.079024	T	0.20901	0.0503	L	0.36672	1.1	0.80722	D	1	B;B;B	0.26809	0.099;0.099;0.16	B;B;B	0.28232	0.017;0.027;0.087	T	0.04708	-1.0932	10	0.52906	T	0.07	.	5.8006	0.18412	0.126:0.4044:0.0:0.4696	.	338;338;381	B2RTX8;Q7Z5K2;Q7Z5K2-2	.;WAPL_HUMAN;.	N	423;338;423	ENSP00000298767:K338N	ENSP00000298767:K338N	K	-	3	2	WAPAL	88249966	0.994000	0.37717	0.998000	0.56505	0.897000	0.52465	0.251000	0.18257	0.097000	0.17492	-0.145000	0.13849	AAG	.	.	.	none		0.448	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045		A	88259986	C	A	88259986	3	1	51	1	0	0	0	0	1	0	0	0	17260	912	32	4	2626	4	WAPAL	10	88259986	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	36674830	88259986	47274761	48	3464											
PAPSS2	9060	hgsc.bcm.edu	37	chr10	89503313	89503313	+	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	gcggatgaagcagcacgcggCtgtgctcgaggaaggggtcc	8	5	18	10	4	0	1	0	1	0	0	2	4	1	3	1	5	3	4	1	5	2	0			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr10:89503313C>T	ENST00000361175.4	+	10	1760	c.1391C>T	c.(1390-1392)gCt>gTt	p.A464V	PAPSS2_ENST00000456849.1_Missense_Mutation_p.A469V|PAPSS2_ENST00000427144.2_Missense_Mutation_p.A468V	NM_004670.3	NP_004661.2	O95340	PAPS2_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 2	464					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|blood coagulation (GO:0007596)|bone development (GO:0060348)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	adenylylsulfate kinase activity (GO:0004020)|ATP binding (GO:0005524)|nucleotidyltransferase activity (GO:0016779)|sulfate adenylyltransferase (ATP) activity (GO:0004781)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|stomach(1)	20		Melanoma(5;0.019)|Colorectal(252;0.123)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00164)|Colorectal(12;0.000323)|COAD - Colon adenocarcinoma(12;0.00124)		CAGCACGCGGCTGTGCTCGAG	0.587																																					p.A469V		Atlas-SNP	.											.	PAPSS2	46	.	0			c.C1406T						PASS	.						105	91	96					10																	89503313		2203	4300	6503	SO:0001583	missense	9060	exon11			ACGCGGCTGTGCT	AF091242	CCDS7385.1, CCDS44453.1	10q24	2008-02-07			ENSG00000198682	ENSG00000198682	2.7.7.4, 2.7.1.25		8604	protein-coding gene	gene with protein product		603005				9771708	Standard	NM_004670		Approved	ATPSK2	uc001kex.3	O95340	OTTHUMG00000018683	ENST00000361175.4:c.1391C>T	chr10.hg19:g.89503313C>T	ENSP00000354436:p.Ala464Val	108.0	0.0	.		91.0	47.0	.	NM_001015880	Q9BZL2|Q9P0G6|Q9UHM1|Q9UKD3|Q9UP30	Missense_Mutation	SNP	ENST00000361175.4	hg19	CCDS7385.1	.	.	.	.	.	.	.	.	.	.	C	31	5.099439	0.94197	.	.	ENSG00000198682	ENST00000361175;ENST00000456849;ENST00000427144;ENST00000371981	T;T;T	0.34472	1.36;1.36;1.36	5.33	5.33	0.75918	Sulphate adenylyltransferase (2);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.047627	0.85682	D	0.000000	T	0.56441	0.1985	M	0.62154	1.92	0.80722	D	1	D;D	0.63880	0.991;0.993	P;P	0.61201	0.885;0.773	T	0.54043	-0.8352	10	0.49607	T	0.09	-17.1332	19.2123	0.93760	0.0:1.0:0.0:0.0	.	464;469	O95340;O95340-2	PAPS2_HUMAN;.	V	464;469;468;468	ENSP00000354436:A464V;ENSP00000406157:A469V;ENSP00000397123:A468V	ENSP00000354436:A464V	A	+	2	0	PAPSS2	89493293	1.000000	0.71417	0.889000	0.34880	0.628000	0.37860	7.315000	0.78998	2.771000	0.95319	0.561000	0.74099	GCT	.	.	.	none		0.587	PAPSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049229.1			T	89503313	C	T	89503313	3	4	51	1	0	0	0	0	1	0	0	0	11442	797	28	2	1448	2	PAPSS2	10	89503313	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	1243327	89503313	46031434	49	3465											
PTEN	5728	hgsc.bcm.edu	37	chr10	89717645	89717646	+	Frame_Shift_Del	DEL	AT	AT	-																															tctgccagctaaaggtgaagAtatattcctccaattcagga																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr10:89717645_89717646delAT	ENST00000371953.3	+	7	2027_2028	c.670_671delAT	c.(670-672)atafs	p.I224fs	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	224	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.?(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)		AAAGGTGAAGATATATTCCTCC	0.421		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.223_224del		Atlas-INDEL	.	yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	.	PTEN	3652	.	48	Whole gene deletion(37)|Deletion - Frameshift(9)|Deletion - In frame(1)|Unknown(1)	prostate(16)|central_nervous_system(10)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)	c.669_670del						PASS	.																																			SO:0001589	frameshift_variant	5728	exon7	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.670_671delAT	chr10.hg19:g.89717649_89717650delAT	ENSP00000361021:p.Ile224fs	162.0	0.0	0		150.0	84.0	0.56	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Frame_Shift_Del	DEL	ENST00000371953.3	hg19	CCDS31238.1																																																																																			.	.	.	none		0.421	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		-	89717646	AT	-	89717645	7	5	51	1	0	1	0	1	0	0	0	0	12748	333	12	0	696	0	PTEN	10	89717645	Frame_Shift_Del	DEL	AT	TCGA-A4-7996-01A-11D-2201-08	214332	89717645	45817102	50	3466											
ABCC2	1244	hgsc.bcm.edu	37	chr10	101606844	101606844	+	Frame_Shift_Del	DEL	G	G	-																															ttgtggccagcctgcaacttGggttatcccacgaagtgaca																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr10:101606844delG	ENST00000370449.4	+	30	4386	c.4273delG	c.(4273-4275)gggfs	p.G1425fs		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	1425	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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)	p.G1425W(1)		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)	CCTGCAACTTGGGTTATCCCA	0.537																																					p.L1424fs		Atlas-INDEL	.											.	ABCC2	160	.	1	Substitution - Missense(1)	lung(1)	c.4272delT						PASS	.						104	97	99					10																	101606844		2203	4300	6503	SO:0001589	frameshift_variant	1244	exon30			.	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.4273delG	chr10.hg19:g.101606844delG	ENSP00000359478:p.Gly1425fs	197.0	0.0	0		150.0	101.0	0.673333	NM_000392	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Frame_Shift_Del	DEL	ENST00000370449.4	hg19	CCDS7484.1																																																																																			.	.	.	none		0.537	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392		-	101606844	G	-	101606844	7	5	51	1	0	1	0	1	0	0	0	0	53	1348	47	0	4391	0	ABCC2	10	101606844	Frame_Shift_Del	DEL	G	TCGA-A4-7996-01A-11D-2201-08	11889199	101606844	33927903	51	3467											
MMP21	118856	hgsc.bcm.edu	37	chr10	127455343	127455343	+	Frame_Shift_Del	DEL	T	T	-																															aggaattctgttgtttgtccTtgtcattaactaccttccag																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr10:127455343delT	ENST00000368808.3	-	7	1597	c.1598delA	c.(1597-1599)aagfs	p.K533fs		NM_147191.1	NP_671724.1	Q8N119	MMP21_HUMAN	matrix metallopeptidase 21	533					hematopoietic progenitor cell differentiation (GO:0002244)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	16		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)			Marimastat(DB00786)	TTGTTTGTCCTTGTCATTAAC	0.363																																					p.K533fs		Atlas-INDEL	.											.	MMP21	46	.	0			c.1599delG						PASS	.						131	131	131					10																	127455343		2203	4300	6503	SO:0001589	frameshift_variant	118856	exon7			.	AF331526	CCDS7647.1	10q26.3	2008-07-28	2005-08-08		ENSG00000154485	ENSG00000154485			14357	protein-coding gene	gene with protein product		608416	"matrix metalloproteinase 21"			11255011	Standard	NM_147191		Approved		uc001liu.3	Q8N119	OTTHUMG00000019235	ENST00000368808.3:c.1598delA	chr10.hg19:g.127455343delT	ENSP00000357798:p.Lys533fs	138.0	0.0	0		119.0	63.0	0.529412	NM_147191	Q5VZP9|Q8NG02	Frame_Shift_Del	DEL	ENST00000368808.3	hg19	CCDS7647.1																																																																																			.	.	.	none		0.363	MMP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050928.1			-	127455343	T	-	127455343	7	5	51	1	0	1	0	1	0	0	0	0	9667	1609	56	0	115	0	MMP21	10	127455343	Frame_Shift_Del	DEL	T	TCGA-A4-7996-01A-11D-2201-08	25848499	127455343	8079404	52	3468											
OR52K1	390036	hgsc.bcm.edu	37	chr11	4510932	4510932	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtcatgcaccgtgtagccCgccatgctgcccctcgtgtc	5	9	10	17	3	1	0	1	0	0	0	3	0	1	0	5	0	4	3	5	0	1	1			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr11:4510932C>T	ENST00000307632.3	+	1	824	c.802C>T	c.(802-804)Cgc>Tgc	p.R268C		NM_001005171.2	NP_001005171.2	Q8NGK4	O52K1_HUMAN	olfactory receptor, family 52, subfamily K, member 1	268						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R268S(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(18)|skin(2)|stomach(1)	32		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;1.76e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0836)|LUSC - Lung squamous cell carcinoma(625;0.192)		CCGTGTAGCCCGCCATGCTGC	0.507																																					p.R268C		Atlas-SNP	.											.	OR52K1	70	.	1	Substitution - Missense(1)	lung(1)	c.C802T						PASS	.						213	192	199					11																	4510932		2201	4298	6499	SO:0001583	missense	390036	exon1			GTAGCCCGCCATG	AB065790	CCDS31352.1	11p15.4	2012-08-09			ENSG00000196778	ENSG00000196778		"GPCR / Class A : Olfactory receptors"	15222	protein-coding gene	gene with protein product							Standard	NM_001005171		Approved		uc001lza.2	Q8NGK4	OTTHUMG00000165705	ENST00000307632.3:c.802C>T	chr11.hg19:g.4510932C>T	ENSP00000302422:p.Arg268Cys	300.0	0.0	.		230.0	66.0	.	NM_001005171	B9EH54|Q6IFK5	Missense_Mutation	SNP	ENST00000307632.3	hg19	CCDS31352.1	.	.	.	.	.	.	.	.	.	.	C	3.130	-0.178651	0.06380	.	.	ENSG00000196778	ENST00000307632	T	0.37411	1.2	4.5	3.59	0.41128	GPCR, rhodopsin-like superfamily (1);	0.429234	0.17846	N	0.160035	T	0.28896	0.0717	L	0.42529	1.33	0.09310	N	1	B	0.11235	0.004	B	0.16289	0.015	T	0.25328	-1.0135	10	0.87932	D	0	.	6.8973	0.24262	0.1728:0.7359:0.0:0.0912	.	268	Q8NGK4	O52K1_HUMAN	C	268	ENSP00000302422:R268C	ENSP00000302422:R268C	R	+	1	0	OR52K1	4467508	0.000000	0.05858	0.723000	0.30687	0.076000	0.17211	-0.593000	0.05740	1.235000	0.43724	0.411000	0.27672	CGC	.	.	.	none		0.507	OR52K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385846.1	NM_001005171		T	4510932	C	T	4510932	3	4	51	1	0	0	0	0	1	0	0	0	11130	652	23	1	804	1	OR52K1	11	4510932	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08		4510932	130495584	53	3469											
DENND5A	23258	hgsc.bcm.edu	37	chr11	9173965	9173965	+	Frame_Shift_Del	DEL	G	G	-																															gttgtcctgataatgtaacaGgtgggaccataaggctgatt																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr11:9173965delG	ENST00000328194.3	-	13	2781	c.2461delC	c.(2461-2463)ctgfs	p.L822fs	DENND5A_ENST00000527700.1_Frame_Shift_Del_p.L165fs|DENND5A_ENST00000530044.1_Frame_Shift_Del_p.L822fs	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A	822	RUN 1. {ECO:0000255|PROSITE- ProRule:PRU00178}.				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						TAATGTAACAGGTGGGACCAT	0.473																																					p.L821fs		Atlas-INDEL	.											.	DENND5A	84	.	0			c.2462delT						PASS	.						268	217	234					11																	9173965		2201	4296	6497	SO:0001589	frameshift_variant	23258	exon13			.	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.2461delC	chr11.hg19:g.9173965delG	ENSP00000328524:p.Leu822fs	169.0	0.0	0		188.0	58.0	0.308511	NM_001243254	B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	Frame_Shift_Del	DEL	ENST00000328194.3	hg19	CCDS31423.1																																																																																			.	.	.	none		0.473	DENND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385910.2	NM_015213		-	9173965	G	-	9173965	7	5	51	1	0	1	0	1	0	0	0	0	4438	991	35	0	1446	0	DENND5A	11	9173965	Frame_Shift_Del	DEL	G	TCGA-A4-7996-01A-11D-2201-08	4663033	9173965	125832551	54	3470											
SLC25A45	283130	hgsc.bcm.edu	37	chr11	65144060	65144060	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcagtccatccatctgcaTccgggacttgatcatgtcta	8	13	7	13	1	4	1	2	1	3	0	8	2	7	2	3	1	1	1	3	1	1	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr11:65144060T>C	ENST00000527174.1	-	6	740	c.685A>G	c.(685-687)Atg>Gtg	p.M229V	SLC25A45_ENST00000526432.1_Missense_Mutation_p.M167V|SLC25A45_ENST00000360662.3_Missense_Mutation_p.M205V|SLC25A45_ENST00000294187.6_Missense_Mutation_p.M187V|SLC25A45_ENST00000534028.1_Missense_Mutation_p.M205V|SLC25A45_ENST00000417511.2_Missense_Mutation_p.M187V|RP11-867O8.5_ENST00000533886.1_RNA|SLC25A45_ENST00000398802.1_Missense_Mutation_p.M229V|SLC25A45_ENST00000377152.2_Missense_Mutation_p.M125V			Q8N413	S2545_HUMAN	solute carrier family 25, member 45	229					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						TCCATCTGCATCCGGGACTTG	0.617																																					p.M229V		Atlas-SNP	.											.	SLC25A45	23	.	0			c.A685G						PASS	.						92	97	95					11																	65144060		2158	4257	6415	SO:0001583	missense	283130	exon7			TCTGCATCCGGGA	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.685A>G	chr11.hg19:g.65144060T>C	ENSP00000435489:p.Met229Val	150.0	0.0	.		121.0	33.0	.	NM_182556	Q6PL49|Q8IW29	Missense_Mutation	SNP	ENST00000527174.1	hg19	CCDS41670.1	.	.	.	.	.	.	.	.	.	.	T	17.61	3.433016	0.62844	.	.	ENSG00000162241	ENST00000527174;ENST00000534028;ENST00000398802;ENST00000360662;ENST00000377152;ENST00000294187;ENST00000417511;ENST00000526432	T;T;T;T;T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32;-1.32;-1.32;-1.32;-1.32	4.58	3.41	0.39046	Mitochondrial carrier domain (2);	.	.	.	.	T	0.72566	0.3476	L	0.37630	1.12	0.37087	D	0.899261	B;B;B	0.31256	0.316;0.056;0.122	B;B;B	0.35470	0.203;0.139;0.156	T	0.73943	-0.3823	9	0.72032	D	0.01	-0.0527	8.8454	0.35168	0.0:0.0:0.3728:0.6272	.	167;205;229	E9PJQ3;Q8N413-4;Q8N413	.;.;S2545_HUMAN	V	229;205;229;205;125;187;187;167	ENSP00000435489:M229V;ENSP00000431769:M205V;ENSP00000381782:M229V;ENSP00000353879:M205V;ENSP00000366357:M125V;ENSP00000294187:M187V;ENSP00000407530:M187V;ENSP00000435547:M167V	ENSP00000294187:M187V	M	-	1	0	SLC25A45	64900636	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	2.144000	0.42197	0.866000	0.35629	0.459000	0.35465	ATG	.	.	.	none		0.617	SLC25A45-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388744.3	NM_182556		C	65144060	T	C	65144060	3	2	51	1	0	0	0	0	1	0	0	0	14523	1435	50	3	185	3	SLC25A45	11	65144060	Missense_Mutation	SNP	T	TCGA-A4-7996-01A-11D-2201-08	55970095	65144060	69862456	55	3471											
RELA	5970	hgsc.bcm.edu	37	chr11	65423175	65423175	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttacctggcttggggacagaAgctgagctgcgggaaggcac	9	7	16	9	1	0	2	0	1	0	1	0	4	0	4	1	5	4	4	1	5	3	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr11:65423175A>G	ENST00000406246.3	-	10	1278	c.1017T>C	c.(1015-1017)gcT>gcC	p.A339A	RELA_ENST00000525693.1_Silent_p.A339A|RELA_ENST00000308639.9_Silent_p.A336A	NM_001243984.1|NM_001243985.1|NM_021975.3	NP_001230913.1|NP_001230914.1|NP_068810.3	Q04206	TF65_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog A	339					acetaldehyde metabolic process (GO:0006117)|aging (GO:0007568)|cellular defense response (GO:0006968)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|Fc-epsilon receptor signaling pathway (GO:0038095)|hair follicle development (GO:0001942)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|liver development (GO:0001889)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of Schwann cell differentiation (GO:0014040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to amino acid (GO:0043200)|response to cAMP (GO:0051591)|response to cobalamin (GO:0033590)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to interleukin-1 (GO:0070555)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to muramyl dipeptide (GO:0032495)|response to organic substance (GO:0010033)|response to progesterone (GO:0032570)|response to UV-B (GO:0010224)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phosphate ion binding (GO:0042301)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|repressing transcription factor binding (GO:0070491)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(11)|ovary(1)|urinary_tract(1)	19						TGGGGACAGAAGCTGAGCTGC	0.607																																					p.A339A		Atlas-SNP	.											.	RELA	44	.	0			c.T1017C						PASS	.						79	75	77					11																	65423175		2201	4297	6498	SO:0001819	synonymous_variant	5970	exon10			GACAGAAGCTGAG	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.1017T>C	chr11.hg19:g.65423175A>G		74.0	0.0	.		67.0	16.0	.	NM_021975	Q6GTV1|Q6SLK1	Silent	SNP	ENST00000406246.3	hg19	CCDS31609.1	.	.	.	.	.	.	.	.	.	.	A	1.229	-0.624695	0.03636	.	.	ENSG00000173039	ENST00000426617	.	.	.	4.46	0.645	0.17782	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.817	0.18497	0.5244:0.0:0.4756:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RELA	65179751	0.675000	0.27558	0.008000	0.14137	0.234000	0.25298	0.116000	0.15561	0.141000	0.18875	0.454000	0.30748	.	.	.	.	none		0.607	RELA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390457.2	NM_021975		G	65423175	A	G	65423175	2	3	51	1	0	0	0	0	0	0	0	1	13229	59	3	3		3	RELA	11	65423175	Silent	SNP	A	TCGA-A4-7996-01A-11D-2201-08	279115	65423175	69583341	56	3472											
ANO1	55107	hgsc.bcm.edu	37	chr11	69951883	69951883	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctttttcgacagcaaaaccCggagcacgattgtaagtatc	12	10	8	11	3	0	0	0	0	0	0	2	3	0	1	2	1	3	4	2	1	4	5			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr11:69951883C>T	ENST00000355303.5	+	5	1041	c.736C>T	c.(736-738)Cgg>Tgg	p.R246W	ANO1_ENST00000531349.1_5'Flank|ANO1_ENST00000538023.1_Missense_Mutation_p.R246W|ANO1_ENST00000530676.1_Missense_Mutation_p.R130W|ANO1_ENST00000316296.5_Missense_Mutation_p.R218W|ANO1_ENST00000398543.2_Missense_Mutation_p.R130W	NM_018043.5	NP_060513.5	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	246					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)	CAGCAAAACCCGGAGCACGAT	0.488																																					p.R246W		Atlas-SNP	.											ANO1_ENST00000355303,colon,carcinoma,0,2	ANO1	156	.	0			c.C736T						PASS	.						91	90	91					11																	69951883		1928	4129	6057	SO:0001583	missense	55107	exon5			AAAACCCGGAGCA	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.736C>T	chr11.hg19:g.69951883C>T	ENSP00000347454:p.Arg246Trp	94.0	0.0	.		47.0	15.0	.	NM_018043	A8KAM3|Q8IYY8|Q8N7V3	Missense_Mutation	SNP	ENST00000355303.5	hg19	CCDS44663.1	.	.	.	.	.	.	.	.	.	.	C	14.73	2.621448	0.46736	.	.	ENSG00000131620	ENST00000355303;ENST00000538023;ENST00000398543;ENST00000546327;ENST00000531604;ENST00000316296;ENST00000530676	T;T;T;T;T;T	0.71222	-0.55;-0.55;-0.55;-0.55;-0.55;-0.55	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	D	0.86965	0.6060	M	0.93720	3.45	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.89503	0.3765	9	.	.	.	.	11.6143	0.51080	0.2839:0.7161:0.0:0.0	.	218;246	Q5XXA6-3;Q5XXA6	.;ANO1_HUMAN	W	246;246;130;30;213;218;130	ENSP00000347454:R246W;ENSP00000444689:R246W;ENSP00000381551:R130W;ENSP00000436392:R213W;ENSP00000319477:R218W;ENSP00000435797:R130W	.	R	+	1	2	ANO1	69629531	0.996000	0.38824	1.000000	0.80357	0.109000	0.19521	3.489000	0.53237	2.437000	0.82529	0.650000	0.86243	CGG	.	.	.	none		0.488	ANO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393685.1	NM_018043		T	69951883	C	T	69951883	3	4	51	1	0	0	0	0	1	0	0	0	695	643	23	1	754	1	ANO1	11	69951883	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	4528708	69951883	65054633	57	3473											
ZC3H12C	85463	hgsc.bcm.edu	37	chr11	110007683	110007683	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtcagaacaattgggtagcaTttcagtagagccaggcttga	12	10	12	7	0	2	3	2	1	0	2	2	3	2	3	1	2	3	4	1	2	4	5			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr11:110007683T>C	ENST00000278590.3	+	2	368	c.317T>C	c.(316-318)aTt>aCt	p.I106T	ZC3H12C_ENST00000528673.1_Missense_Mutation_p.I107T|ZC3H12C_ENST00000453089.2_Missense_Mutation_p.I75T	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	106							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)		TTGGGTAGCATTTCAGTAGAG	0.448																																					p.I106T		Atlas-SNP	.											.	ZC3H12C	83	.	0			c.T317C						PASS	.						42	41	41					11																	110007683		1893	4130	6023	SO:0001583	missense	85463	exon2			GTAGCATTTCAGT		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.317T>C	chr11.hg19:g.110007683T>C	ENSP00000278590:p.Ile106Thr	33.0	0.0	.		27.0	15.0	.	NM_033390	B4DI65|B4DR47	Missense_Mutation	SNP	ENST00000278590.3	hg19	CCDS44727.1	.	.	.	.	.	.	.	.	.	.	t	0.015	-1.546583	0.00926	.	.	ENSG00000149289	ENST00000278590;ENST00000528673;ENST00000453089	T;T;T	0.29917	1.55;1.55;1.56	5.42	4.29	0.51040	.	.	.	.	.	T	0.18759	0.0450	N	0.25647	0.755	0.09310	N	1	B;B;B	0.10296	0.001;0.003;0.003	B;B;B	0.11329	0.005;0.006;0.006	T	0.31475	-0.9942	9	0.13853	T	0.58	-1.7133	6.4988	0.22158	0.0:0.1421:0.1326:0.7254	.	107;106;106	B4DR47;B4DI65;Q9C0D7	.;.;ZC12C_HUMAN	T	106;107;75	ENSP00000278590:I106T;ENSP00000431821:I107T;ENSP00000413094:I75T	ENSP00000278590:I106T	I	+	2	0	ZC3H12C	109512893	0.003000	0.15002	0.297000	0.24988	0.069000	0.16628	0.578000	0.23773	0.902000	0.36520	0.528000	0.53228	ATT	.	.	.	none		0.448	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390		C	110007683	T	C	110007683	3	2	51	1	0	0	0	0	1	0	0	0	17575	1493	52	3	323	3	ZC3H12C	11	110007683	Missense_Mutation	SNP	T	TCGA-A4-7996-01A-11D-2201-08	40055800	110007683	24998833	58	3474											
DRD2	1813	hgsc.bcm.edu	37	chr11	113295344	113295344	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctgcctctccagatcatcAtcataccaggacagattcag	11	11	6	13	0	6	2	4	0	2	2	7	3	6	3	3	1	2	0	3	1	1	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr11:113295344A>G	ENST00000362072.3	-	2	374	c.30T>C	c.(28-30)gaT>gaC	p.D10D	DRD2_ENST00000538967.1_Silent_p.D10D|DRD2_ENST00000542968.1_Silent_p.D10D|DRD2_ENST00000355319.2_Silent_p.D10D|DRD2_ENST00000346454.3_Silent_p.D10D|DRD2_ENST00000535984.1_5'Flank|DRD2_ENST00000544518.1_Silent_p.D10D	NM_000795.3	NP_000786.1	P14416	DRD2_HUMAN	dopamine receptor D2	10					activation of protein kinase activity (GO:0032147)|adenohypophysis development (GO:0021984)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adult walking behavior (GO:0007628)|arachidonic acid secretion (GO:0050482)|associative learning (GO:0008306)|auditory behavior (GO:0031223)|axonogenesis (GO:0007409)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|branching morphogenesis of a nerve (GO:0048755)|cellular calcium ion homeostasis (GO:0006874)|cerebral cortex GABAergic interneuron migration (GO:0021853)|circadian regulation of gene expression (GO:0032922)|dopamine metabolic process (GO:0042417)|feeding behavior (GO:0007631)|G-protein coupled receptor internalization (GO:0002031)|grooming behavior (GO:0007625)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|long-term memory (GO:0007616)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of circadian sleep/wake cycle, sleep (GO:0042321)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of insulin secretion (GO:0046676)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein secretion (GO:0050709)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|neuron-neuron synaptic transmission (GO:0007270)|orbitofrontal cortex development (GO:0021769)|peristalsis (GO:0030432)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|pigmentation (GO:0043473)|positive regulation of cytokinesis (GO:0032467)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of dopamine uptake involved in synaptic transmission (GO:0051586)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of receptor internalization (GO:0002092)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of urine volume (GO:0035810)|prepulse inhibition (GO:0060134)|protein localization (GO:0008104)|regulation of cAMP metabolic process (GO:0030814)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of heart rate (GO:0002027)|regulation of locomotion involved in locomotory behavior (GO:0090325)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of potassium ion transport (GO:0043266)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, GABAergic (GO:0032228)|release of sequestered calcium ion into cytosol (GO:0051209)|response to amphetamine (GO:0001975)|response to axon injury (GO:0048678)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to histamine (GO:0034776)|response to hypoxia (GO:0001666)|response to inactivity (GO:0014854)|response to iron ion (GO:0010039)|response to light stimulus (GO:0009416)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to toxic substance (GO:0009636)|sensory perception of smell (GO:0007608)|striatum development (GO:0021756)|synapse assembly (GO:0007416)|synaptic transmission, dopaminergic (GO:0001963)|temperature homeostasis (GO:0001659)|visual learning (GO:0008542)|Wnt signaling pathway (GO:0016055)	acrosomal vesicle (GO:0001669)|axon (GO:0030424)|axon terminus (GO:0043679)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|sperm flagellum (GO:0036126)|synaptic vesicle membrane (GO:0030672)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity, coupled via Gi/Go (GO:0001591)|drug binding (GO:0008144)|identical protein binding (GO:0042802)|potassium channel regulator activity (GO:0015459)			endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(18)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	39		all_cancers(61;3.91e-16)|all_epithelial(67;2.95e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000977)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0494)		BRCA - Breast invasive adenocarcinoma(274;5.77e-06)|Epithelial(105;6.66e-05)|all cancers(92;0.000307)|OV - Ovarian serous cystadenocarcinoma(223;0.216)	Acepromazine(DB01614)|Acetophenazine(DB01063)|Alizapride(DB01425)|Amantadine(DB00915)|Amisulpride(DB06288)|Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Desipramine(DB01151)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Droperidol(DB00450)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Memantine(DB01043)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Metoclopramide(DB01233)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sertindole(DB06144)|Sulpiride(DB00391)|Tetrabenazine(DB04844)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	CCAGATCATCATCATACCAGG	0.587																																					p.D10D		Atlas-SNP	.											.	DRD2	98	.	0			c.T30C						PASS	.						116	103	107					11																	113295344		2201	4296	6497	SO:0001819	synonymous_variant	1813	exon2			ATCATCATCATAC	M29066	CCDS8361.1, CCDS8362.1	11q22-q23	2012-08-08						"GPCR / Class A : Dopamine receptors"	3023	protein-coding gene	gene with protein product		126450					Standard	NM_000795		Approved		uc001poa.4	P14416		ENST00000362072.3:c.30T>C	chr11.hg19:g.113295344A>G		132.0	0.0	.		107.0	27.0	.	NM_016574	Q9NZR3|Q9UPA9	Silent	SNP	ENST00000362072.3	hg19	CCDS8361.1																																																																																			.	.	.	none		0.587	DRD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395834.1	NM_000795		G	113295344	A	G	113295344	2	3	51	1	0	0	0	0	0	0	0	1	4759	214	8	3		3	DRD2	11	113295344	Silent	SNP	A	TCGA-A4-7996-01A-11D-2201-08	3287661	113295344	21711172	59	3475											
FAM113B	91523	hgsc.bcm.edu	37	chr12	47628909	47628909	+	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	aataagttcgtggtcatcctGggggactctgtgcatagggc	8	11	14	8	1	2	0	1	0	1	0	4	1	3	1	1	4	1	2	1	4	3	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr12:47628909G>T	ENST00000546455.1	+	4	794	c.63G>T	c.(61-63)ctG>ctT	p.L21L	PCED1B_ENST00000432328.1_Silent_p.L21L|RP11-493L12.3_ENST00000547748.1_RNA			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B	21							hydrolase activity (GO:0016787)										TGGTCATCCTGGGGGACTCTG	0.602																																					p.L21L		Atlas-SNP	.											.	.	.	.	0			c.G63T						PASS	.						73	71	72					12																	47628909		2203	4300	6503	SO:0001819	synonymous_variant	91523	exon2			CATCCTGGGGGAC	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.63G>T	chr12.hg19:g.47628909G>T		89.0	0.0	.		74.0	24.0	.	NM_138371	Q96B20	Silent	SNP	ENST00000546455.1	hg19	CCDS8752.1																																																																																			.	.	.	none		0.602	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371		T	47628909	G	T	47628909	2	4	51	1	0	0	0	0	0	0	0	1	5406	1335	47	4		4	FAM113B	12	47628909	Silent	SNP	G	TCGA-A4-7996-01A-11D-2201-08		47628909	86222986	60	3476											
TMEM120B	144404	hgsc.bcm.edu	37	chr12	122190050	122190050	+	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	gcaggttcgcctacaaggacGaatatgagaagttcaagctc	13	8	11	9	2	1	1	1	1	0	1	3	4	1	2	1	2	2	4	1	2	6	4			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr12:122190050G>A	ENST00000449592.2	+	5	483	c.382G>A	c.(382-384)Gaa>Aaa	p.E128K	TMEM120B_ENST00000540377.1_5'UTR	NM_001080825.2	NP_001074294.2	A0PK00	T120B_HUMAN	transmembrane protein 120B	128						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(6)	11	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;5.75e-05)|Epithelial(86;0.000128)|BRCA - Breast invasive adenocarcinoma(302;0.238)		CTACAAGGACGAATATGAGAA	0.577																																					p.E128K		Atlas-SNP	.											.	TMEM120B	43	.	0			c.G382A						PASS	.						111	130	124					12																	122190050		2155	4240	6395	SO:0001583	missense	144404	exon5			AAGGACGAATATG	BC127768	CCDS41852.1	12q24.31	2007-08-01			ENSG00000188735	ENSG00000188735			32008	protein-coding gene	gene with protein product							Standard	NM_001080825		Approved		uc001ubc.4	A0PK00	OTTHUMG00000169076	ENST00000449592.2:c.382G>A	chr12.hg19:g.122190050G>A	ENSP00000404991:p.Glu128Lys	129.0	0.0	.		120.0	40.0	.	NM_001080825	A0PK01|B3KX33	Missense_Mutation	SNP	ENST00000449592.2	hg19	CCDS41852.1	.	.	.	.	.	.	.	.	.	.	G	32	5.129163	0.94473	.	.	ENSG00000188735	ENST00000449592;ENST00000541467	T;T	0.42513	0.97;0.97	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	T	0.73133	0.3548	M	0.94021	3.485	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.81391	-0.0954	10	0.87932	D	0	-29.3312	15.8383	0.78818	0.0:0.0:1.0:0.0	.	128	A0PK00	T120B_HUMAN	K	128;107	ENSP00000404991:E128K;ENSP00000442105:E107K	ENSP00000345152:E128K	E	+	1	0	TMEM120B	120674433	1.000000	0.71417	0.995000	0.50966	0.953000	0.61014	9.405000	0.97313	2.387000	0.81309	0.491000	0.48974	GAA	.	.	.	none		0.577	TMEM120B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402158.1	NM_001080825		A	122190050	G	A	122190050	3	1	51	1	0	0	0	0	1	0	0	0	16046	1059	37	1	400	1	TMEM120B	12	122190050	Missense_Mutation	SNP	G	TCGA-A4-7996-01A-11D-2201-08	74561141	122190050	11661845	61	3477											
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102500785	102500785	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatcatgctgaaacgattcAataggtatgagctcgggtgc	11	10	11	9	2	2	2	2	2	0	0	3	3	2	2	1	2	4	3	1	2	4	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr14:102500785A>G	ENST00000360184.4	+	56	10914	c.10750A>G	c.(10750-10752)Aat>Gat	p.N3584D	DYNC1H1_ENST00000556791.1_3'UTR|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	3584	AAA 5. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						GAAACGATTCAATAGGTATGA	0.473																																					p.N3584D		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.A10750G						PASS	.						94	85	88					14																	102500785		2203	4300	6503	SO:0001583	missense	1778	exon56			CGATTCAATAGGT	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.10750A>G	chr14.hg19:g.102500785A>G	ENSP00000348965:p.Asn3584Asp	186.0	0.0	.		137.0	39.0	.	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	hg19	CCDS9966.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.89|14.89	2.671516|2.671516	0.47781|0.47781	.|.	.|.	ENSG00000197102|ENSG00000197102	ENST00000360184|ENST00000553423	T|.	0.52057|.	0.68|.	5.17|5.17	5.17|5.17	0.71159|0.71159	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72358|0.72358	0.3450|0.3450	M|M	0.68728|0.68728	2.09|2.09	0.80722|0.80722	D|D	1|1	D|.	0.60160|.	0.987|.	D|.	0.63488|.	0.915|.	T|T	0.72491|0.72491	-0.4277|-0.4277	10|5	0.41790|.	T|.	0.15|.	.|.	15.2984|15.2984	0.73928|0.73928	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	3584|.	Q14204|.	DYHC1_HUMAN|.	D|R	3584|59	ENSP00000348965:N3584D|.	ENSP00000348965:N3584D|.	N|Q	+|+	1|2	0|0	DYNC1H1|DYNC1H1	101570538|101570538	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.411000|0.411000	0.31082|0.31082	7.417000|7.417000	0.80156|0.80156	2.090000|2.090000	0.63153|0.63153	0.482000|0.482000	0.46254|0.46254	AAT|CAA	.	.	.	none		0.473	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		G	102500785	A	G	102500785	3	3	51	1	0	0	0	0	1	0	0	0	4843	130	5	3	10972	3	DYNC1H1	14	102500785	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08		102500785	4848755	62	3478											
NTRK3	4916	hgsc.bcm.edu	37	chr15	88679229	88679229	+	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	ctcactcgtcacattcaccaGcgtcaagttgatggcatgaa	11	10	8	12	2	4	2	4	2	0	0	5	2	4	2	1	1	1	2	1	1	2	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr15:88679229G>C	ENST00000360948.2	-	8	969	c.808C>G	c.(808-810)Ctg>Gtg	p.L270V	NTRK3_ENST00000317501.3_Missense_Mutation_p.L270V|NTRK3_ENST00000557856.1_Missense_Mutation_p.L270V|NTRK3_ENST00000355254.2_Missense_Mutation_p.L270V|NTRK3_ENST00000542733.2_Missense_Mutation_p.L172V|NTRK3_ENST00000540489.2_Missense_Mutation_p.L270V|NTRK3_ENST00000558676.1_Missense_Mutation_p.L270V|NTRK3_ENST00000394480.2_Missense_Mutation_p.L270V|NTRK3_ENST00000357724.2_Missense_Mutation_p.L270V	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	270	Ig-like C2-type 1.				activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.L270M(1)	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)			ACATTCACCAGCGTCAAGTTG	0.478			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)																											p.L270V		Atlas-SNP	.		Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	NTRK3_ENST00000360948,caecum,carcinoma,+2,1	NTRK3	587	.	1	Substitution - Missense(1)	lung(1)	c.C808G						PASS	.						241	164	190					15																	88679229		2201	4299	6500	SO:0001583	missense	4916	exon9			TCACCAGCGTCAA	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.808C>G	chr15.hg19:g.88679229G>C	ENSP00000354207:p.Leu270Val	164.0	0.0	.		136.0	42.0	.	NM_001243101	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	hg19	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	G	17.57	3.422428	0.62622	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254;ENST00000542733;ENST00000540489;ENST00000317501	T;T;T;T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25;-0.25;-0.25;-0.25	5.51	4.6	0.57074	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.072619	0.56097	D	0.000024	T	0.75982	0.3924	L	0.57536	1.79	0.47819	D	0.999528	D;D;P;D;D;P	0.71674	0.967;0.969;0.87;0.998;0.969;0.87	P;P;P;D;P;P	0.69824	0.808;0.645;0.777;0.966;0.594;0.718	T	0.76515	-0.2931	10	0.54805	T	0.06	.	10.3176	0.43747	0.1599:0.0:0.8401:0.0	.	172;270;270;270;270;270	B7Z7U4;E9PG56;B7Z4C5;Q96CY4;Q16288-3;Q16288	.;.;.;.;.;NTRK3_HUMAN	V	270;270;270;270;172;270;270	ENSP00000377990:L270V;ENSP00000354207:L270V;ENSP00000350356:L270V;ENSP00000347397:L270V;ENSP00000437773:L172V;ENSP00000444673:L270V;ENSP00000318328:L270V	ENSP00000318328:L270V	L	-	1	2	NTRK3	86480233	1.000000	0.71417	0.940000	0.37924	0.891000	0.51852	4.245000	0.58734	1.336000	0.45506	-0.253000	0.11424	CTG	.	.	.	none		0.478	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				C	88679229	G	C	88679229	3	2	51	1	0	0	0	0	1	0	0	0	10715	962	34	4	2021	4	NTRK3	15	88679229	Missense_Mutation	SNP	G	TCGA-A4-7996-01A-11D-2201-08		88679229	13852163	63	3479											
ACAN	176	hgsc.bcm.edu	37	chr15	89398462	89398462	+	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	gtttcaggacaccttgacttCagtgggcagctgtcagggga	8	10	14	9	0	3	1	3	1	0	0	3	3	3	3	1	4	1	3	1	4	0	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr15:89398462C>T	ENST00000561243.1	+	11	2646	c.2646C>T	c.(2644-2646)ttC>ttT	p.F882F	ACAN_ENST00000559004.1_Silent_p.F882F|ACAN_ENST00000439576.2_Silent_p.F882F|ACAN_ENST00000352105.7_Silent_p.F882F			P16112	PGCA_HUMAN	aggrecan	881	CS-1.				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)			ACCTTGACTTCAGTGGGCAGC	0.597																																					p.F882F		Atlas-SNP	.											.	ACAN	220	.	0			c.C2646T						PASS	.						59	65	63					15																	89398462		2009	4185	6194	SO:0001819	synonymous_variant	176	exon12			TGACTTCAGTGGG	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.2646C>T	chr15.hg19:g.89398462C>T		101.0	0.0	.		74.0	22.0	.	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Silent	SNP	ENST00000561243.1	hg19	CCDS53970.1																																																																																			.	.	.	none		0.597	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		T	89398462	C	T	89398462	2	4	51	1	0	0	0	0	0	0	0	1	117	825	29	2		2	ACAN	15	89398462	Silent	SNP	C	TCGA-A4-7996-01A-11D-2201-08	719233	89398462	13132930	64	3480											
RHCG	51458	hgsc.bcm.edu	37	chr15	90026327	90026327	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttaaggagaatgaactcatTcacagcgaagagggtcactt	14	9	11	7	1	3	3	3	1	0	2	3	5	3	3	0	2	2	1	0	2	4	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr15:90026327T>C	ENST00000268122.4	-	3	561	c.493A>G	c.(493-495)Aat>Gat	p.N165D	RHCG_ENST00000544600.1_Missense_Mutation_p.N165D	NM_016321.1	NP_057405.1	Q9UBD6	RHCG_HUMAN	Rh family, C glycoprotein	165					amine transport (GO:0015837)|ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|cellular ion homeostasis (GO:0006873)|epithelial cell differentiation (GO:0030855)|homeostatic process (GO:0042592)|regulation of pH (GO:0006885)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Lung NSC(78;0.0237)|all_lung(78;0.0478)					ATGAACTCATTCACAGCGAAG	0.537																																					p.N165D		Atlas-SNP	.											.	RHCG	49	.	0			c.A493G						PASS	.						68	51	57					15																	90026327		2200	4299	6499	SO:0001583	missense	51458	exon3			ACTCATTCACAGC	AF081497	CCDS10351.1	15q25	2013-05-22	2006-02-23		ENSG00000140519	ENSG00000140519		"Solute carriers"	18140	protein-coding gene	gene with protein product		605381	"chromosome 15 open reading frame 6", "Rhesus blood group, C glycoprotein"	C15orf6		10852913	Standard	NM_016321		Approved	RHGK, PDRC2, SLC42A3	uc002bnz.2	Q9UBD6	OTTHUMG00000149647	ENST00000268122.4:c.493A>G	chr15.hg19:g.90026327T>C	ENSP00000268122:p.Asn165Asp	67.0	0.0	.		78.0	29.0	.	NM_016321	A8K4D4|Q6X3Y4	Missense_Mutation	SNP	ENST00000268122.4	hg19	CCDS10351.1	.	.	.	.	.	.	.	.	.	.	T	19.35	3.811144	0.70797	.	.	ENSG00000140519	ENST00000544600;ENST00000268122;ENST00000536247	T;T	0.23147	1.92;1.92	5.47	5.47	0.80525	Ammonium transporter AmtB-like (3);	0.089021	0.85682	D	0.000000	T	0.63570	0.2522	H	0.95611	3.695	0.58432	D	0.999999	D;D	0.69078	0.997;0.997	D;D	0.72075	0.976;0.976	T	0.76181	-0.3053	9	.	.	.	-18.2072	15.5452	0.76093	0.0:0.0:0.0:1.0	.	165;165	A8K4D4;Q9UBD6	.;RHCG_HUMAN	D	165;165;156	ENSP00000438123:N165D;ENSP00000268122:N165D	.	N	-	1	0	RHCG	87827331	1.000000	0.71417	0.940000	0.37924	0.612000	0.37316	5.740000	0.68629	2.076000	0.62316	0.533000	0.62120	AAT	.	.	.	none		0.537	RHCG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000312855.2	NM_016321		C	90026327	T	C	90026327	3	2	51	1	0	0	0	0	1	0	0	0	13339	1783	62	3	978	3	RHCG	15	90026327	Missense_Mutation	SNP	T	TCGA-A4-7996-01A-11D-2201-08	627865	90026327	12505065	65	3481											
BAIAP3	8938	hgsc.bcm.edu	37	chr16	1398015	1398021	+	Splice_Site	DEL	ACTTGTG	ACTTGTG	-																															tgtatacgacgaactcttctActtgtgagtgtcctaagccc																								rs112608838		TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	ACTTGTG	ACTTGTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr16:1398015_1398021delACTTGTG	ENST00000324385.5	+	32	3409_3412	c.3251_3254delACTTGTG	c.(3250-3255)tacttg>tg	p.YL1084fs	BAIAP3_ENST00000426824.3_Splice_Site_p.YL1049fs|BAIAP3_ENST00000397489.1_Splice_Site_p.YL1066fs|BAIAP3_ENST00000421665.2_Splice_Site_p.YL1013fs|BAIAP3_ENST00000562208.1_Splice_Site_p.YL1026fs|BAIAP3_ENST00000568887.1_Splice_Site_p.YL1021fs|BAIAP3_ENST00000397488.2_Splice_Site_p.YL1066fs	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	1084	C2 2. {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)				GAACTCTTCTACTTGTGAGTGTCCTAa	0.657																																					p.1084_1085del		Atlas-INDEL	.											.	BAIAP3	88	.	0			c.3250_3254del						PASS	.																																			SO:0001630	splice_region_variant	8938	exon32			.	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.3254+1ACTTGTG>-	chr16.hg19:g.1398015_1398021delACTTGTG		120.0	0.0	0		115.0	43.0	0.373913	NM_003933	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Frame_Shift_Del	DEL	ENST00000324385.5	hg19	CCDS10434.1																																																																																			.	.	.	none		0.657	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3		Frame_Shift_Del	-	1398021	ACTTGTG	-	1398015	8	5	51	1	0	1	0	1	0	0	1	0	1304	391	14	0	3377	0	BAIAP3	16	1398015	Splice_Site	DEL	ACTTGTG	TCGA-A4-7996-01A-11D-2201-08		1398015	88956738	66	3482	42	2									
BAIAP3	8938	hgsc.bcm.edu	37	chr16	1398016	1398016	+	Nonsense_Mutation	SNP	C	C	G																															gtatacgacgaactcttctaCttgtgagtgtcctaagcccc																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr16:1398016C>G	ENST00000324385.5	+	32	3410	c.3252C>G	c.(3250-3252)taC>taG	p.Y1084*	BAIAP3_ENST00000426824.3_Nonsense_Mutation_p.Y1049*|BAIAP3_ENST00000397489.1_Nonsense_Mutation_p.Y1066*|BAIAP3_ENST00000421665.2_Nonsense_Mutation_p.Y1013*|BAIAP3_ENST00000562208.1_Nonsense_Mutation_p.Y1026*|BAIAP3_ENST00000568887.1_Nonsense_Mutation_p.Y1021*|BAIAP3_ENST00000397488.2_Nonsense_Mutation_p.Y1066*	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	1084	C2 2. {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)				AACTCTTCTACTTGTGAGTGT	0.652																																					p.Y1084X		Atlas-SNP	.											.	BAIAP3	88	.	0			c.C3252G						PASS	.						50	50	50					16																	1398016		2198	4300	6498	SO:0001587	stop_gained	8938	exon32			CTTCTACTTGTGA	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.3252C>G	chr16.hg19:g.1398016C>G	ENSP00000324510:p.Tyr1084*	115.0	0.0	.		66.0	6.0	.	NM_003933	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Nonsense_Mutation	SNP	ENST00000324385.5	hg19	CCDS10434.1	.	.	.	.	.	.	.	.	.	.	C	38	6.826251	0.97865	.	.	ENSG00000007516	ENST00000426824;ENST00000397488;ENST00000324385;ENST00000397489;ENST00000421665	.	.	.	4.65	1.6	0.23607	.	0.402932	0.24625	N	0.036938	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-19.1567	6.7323	0.23390	0.0:0.6052:0.0:0.3948	.	.	.	.	X	1049;1066;1084;1066;1013	.	ENSP00000324510:Y1084X	Y	+	3	2	BAIAP3	1338017	0.998000	0.40836	0.998000	0.56505	0.087000	0.18053	0.792000	0.26929	0.068000	0.16574	-0.258000	0.10820	TAC	.	.	.	none		0.652	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3			G	1398016	C	G	1398016	4	3	51	1	0	0	0	0	0	1	0	0	1304	576	20	4	3378	4	BAIAP3	16	1398016	Nonsense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	1	1398016	88956737	67	3483	42	2									
PRSS22	64063	hgsc.bcm.edu	37	chr16	2905588	2905589	+	Missense_Mutation	DNP	GC	GC	AT																															gccgcacctccatcttggatGctcccccagcctgagatcca																								rs556704172		TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr16:2905588_2905589GC>AT	ENST00000161006.3	-	4	610_611	c.545_546GC>AT	c.(544-546)aGC>aAT	p.S182N	LA16c-325D7.1_ENST00000577140.1_RNA|PRSS22_ENST00000571228.1_Intron|PRSS22_ENST00000574768.1_5'Flank	NM_022119.3	NP_071402.1	Q9GZN4	BSSP4_HUMAN	protease, serine, 22	182	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(2)|skin(2)	10						CATCTTGGATGCTCCCCCAGCC	0.589																																					p.S182S|p.S182N		Atlas-SNP	.											.	PRSS22	23	.	0			c.C546T|c.G545A						PASS	.																																			SO:0001583	missense	64063	exon4			TTGGATGCTCCCC|TGGATGCTCCCCC	AF321182	CCDS10481.1	16p13.3	2010-05-07			ENSG00000005001	ENSG00000005001		"Serine peptidases / Serine peptidases"	14368	protein-coding gene	gene with protein product	"brain-specific serine protease 4"	609343				11602603, 15701722	Standard	XM_005255473		Approved	hBSSP-4, BSSP-4, SP001LA	uc002cry.1	Q9GZN4	OTTHUMG00000128961	ENST00000161006.3:c.545_546delinsAT	chr16.hg19:g.2905588_2905589delinsAT	ENSP00000161006:p.Ser182Asn	111.0|113.0	0.0	.		121.0	63.0|62.0	.	NM_022119	O43342|Q6UXE0	Silent|Missense_Mutation	SNP	ENST00000161006.3	hg19	CCDS10481.1																																																																																			.	.	.	none		0.589	PRSS22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250943.1	NM_022119		AT	2905589	GC	AT	2905588	3	1	51	1	0	0	0	0	1	0	0	0	12629	1310	46	2	419	2	PRSS22	16	2905588	Missense_Mutation	DNP	GC	TCGA-A4-7996-01A-11D-2201-08	1507572	2905588	87449165	68	3484											
ZNF200	7752	hgsc.bcm.edu	37	chr16	3274128	3274128	+	Frame_Shift_Del	DEL	G	G	-																															actccgatgagaattctgacGgaagttttttccacactgag																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr16:3274128delG	ENST00000431561.3	-	5	1564	c.952delC	c.(952-954)cgtfs	p.R318fs	ZNF200_ENST00000396871.4_Frame_Shift_Del_p.R317fs|ZNF200_ENST00000396870.4_Frame_Shift_Del_p.R317fs|AJ003147.9_ENST00000576468.1_RNA|ZNF200_ENST00000575948.1_Frame_Shift_Del_p.R317fs|ZNF200_ENST00000396868.3_Frame_Shift_Del_p.R317fs|ZNF200_ENST00000414144.2_Frame_Shift_Del_p.R318fs	NM_001145447.1|NM_003454.3	NP_001138919.1|NP_003445.2	P98182	ZN200_HUMAN	zinc finger protein 200	318					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						GAATTCTGACGGAAGTTTTTT	0.393																																					p.R318fs		Atlas-INDEL	.											.	ZNF200	36	.	0			c.953delG						PASS	.						110	110	110					16																	3274128		2197	4300	6497	SO:0001589	frameshift_variant	7752	exon5			.	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.952delC	chr16.hg19:g.3274128delG	ENSP00000395723:p.Arg318fs	186.0	0.0	0		233.0	109.0	0.467811	NM_003454	D3DUB7|D3DUB8|O15361|Q5XKM5|Q7Z5V1	Frame_Shift_Del	DEL	ENST00000431561.3	hg19	CCDS10497.1																																																																																			.	.	.	none		0.393	ZNF200-005	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000437545.1			-	3274128	G	-	3274128	7	5	51	1	0	1	0	1	0	0	0	0	17774	1116	39	0	239	0	ZNF200	16	3274128	Frame_Shift_Del	DEL	G	TCGA-A4-7996-01A-11D-2201-08	368540	3274128	87080625	69	3485											
PSMB10	5699	hgsc.bcm.edu	37	chr16	67970649	67970649	+	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	gggctccagggctggcttcaGcatcttggggcaggcagagg	6	7	18	10	0	2	1	1	0	1	1	3	1	3	1	1	7	1	6	1	7	0	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr16:67970649G>C	ENST00000358514.4	-	1	341	c.4C>G	c.(4-6)Ctg>Gtg	p.L2V	CTC-479C5.12_ENST00000573493.1_5'Flank	NM_002801.3	NP_002792.1	P40306	PSB10_HUMAN	proteasome (prosome, macropain) subunit, beta type, 10	2					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cell morphogenesis (GO:0000902)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|humoral immune response (GO:0006959)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|T cell proliferation (GO:0042098)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)			NS(2)|endometrium(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00415)|Epithelial(162;0.0182)|all cancers(182;0.119)	Carfilzomib(DB08889)	GCTGGCTTCAGCATCTTGGGG	0.657																																					p.L2V		Atlas-SNP	.											.	PSMB10	19	.	0			c.C4G						PASS	.						6	9	8					16																	67970649		2068	4126	6194	SO:0001583	missense	5699	exon1			GCTTCAGCATCTT	Y13640	CCDS10853.1	16q22.1	2008-02-05			ENSG00000205220	ENSG00000205220		"Proteasome (prosome, macropain) subunits"	9538	protein-coding gene	gene with protein product		176847		MECL1		8268911	Standard	NM_002801		Approved	LMP10, MGC1665, beta2i	uc002eux.2	P40306	OTTHUMG00000137553	ENST00000358514.4:c.4C>G	chr16.hg19:g.67970649G>C	ENSP00000351314:p.Leu2Val	2.0	0.0	.		11.0	6.0	.	NM_002801	B2R5J4|Q5U098	Missense_Mutation	SNP	ENST00000358514.4	hg19	CCDS10853.1	.	.	.	.	.	.	.	.	.	.	G	17.35	3.368139	0.61513	.	.	ENSG00000205220	ENST00000358514	T	0.29917	1.55	5.44	3.45	0.39498	.	0.789141	0.11429	N	0.564987	T	0.22322	0.0538	L	0.34521	1.04	0.31055	N	0.714774	B	0.21225	0.053	B	0.17722	0.019	T	0.14783	-1.0460	10	0.33940	T	0.23	-0.1279	7.6089	0.28118	0.1898:0.0:0.8102:0.0	.	2	P40306	PSB10_HUMAN	V	2	ENSP00000351314:L2V	ENSP00000351314:L2V	L	-	1	2	PSMB10	66528150	0.741000	0.28217	0.993000	0.49108	0.082000	0.17680	0.926000	0.28804	1.422000	0.47177	0.549000	0.68633	CTG	.	.	.	none		0.657	PSMB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268887.1	NM_002801		C	67970649	G	C	67970649	3	2	51	1	0	0	0	0	1	0	0	0	12685	962	34	4	849	4	PSMB10	16	67970649	Missense_Mutation	SNP	G	TCGA-A4-7996-01A-11D-2201-08	64696521	67970649	22384104	70	3486											
TRAF4	9618	hgsc.bcm.edu	37	chr17	27074242	27074243	+	Frame_Shift_Ins	INS	-	-	C																															catttcagtgaaggagtcttINScaagtgccctgaggaccagc																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr17:27074242_27074243insC	ENST00000262395.5	+	2	284_285	c.155_156insC	c.(154-159)ttcaagfs	p.K53fs	TRAF4_ENST00000262396.6_Frame_Shift_Ins_p.K53fs|AC010761.10_ENST00000579468.1_RNA|TRAF4_ENST00000444415.3_Frame_Shift_Ins_p.K53fs|AC010761.9_ENST00000577325.1_RNA	NM_004295.3	NP_004286.2	Q9BUZ4	TRAF4_HUMAN	TNF receptor-associated factor 4	53					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of protein kinase activity (GO:0045860)|regulation of apoptotic process (GO:0042981)|respiratory gaseous exchange (GO:0007585)|respiratory tube development (GO:0030323)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	DNA binding (GO:0003677)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|WW domain binding (GO:0050699)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	10	Lung NSC(42;0.01)		Epithelial(11;3.26e-05)|all cancers(11;0.000272)|OV - Ovarian serous cystadenocarcinoma(11;0.235)			GAAGGAGTCTTCAAGTGCCCTG	0.594																																					p.F52fs		Atlas-INDEL	.											.	TRAF4	20	.	0			c.155_156insC						PASS	.																																			SO:0001589	frameshift_variant	9618	exon2			.	X80200	CCDS11243.1	17q11-q21.3	2013-01-09			ENSG00000076604	ENSG00000076604		"RING-type (C3HC4) zinc fingers"	12034	protein-coding gene	gene with protein product		602464				7592751, 7490069	Standard	NM_004295		Approved	CART1, MLN62, RNF83	uc002hcs.3	Q9BUZ4	OTTHUMG00000132677	ENST00000262395.5:c.156dupC	chr17.hg19:g.27074243_27074243dupC	ENSP00000262395:p.Lys53fs	184.0	0.0	0		158.0	82.0	0.518987	NM_004295	O75615|Q14848|Q2KJU4|Q2PJN8	Frame_Shift_Ins	INS	ENST00000262395.5	hg19	CCDS11243.1																																																																																			.	.	.	none		0.594	TRAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255944.2	NM_145751		C	27074243	-	C	27074242	7	5	51	1	0	1	1	0	0	0	0	0	16455	1783	62	0	161	0	TRAF4	17	27074242	Frame_Shift_Ins	INS	-	TCGA-A4-7996-01A-11D-2201-08		27074242	54120968	71	3487											
SSH2	85464	hgsc.bcm.edu	37	chr17	27975326	27975326	+	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	gaggctgagcgactcaccccCattttgcagtgcacaaggca	10	7	11	13	1	1	1	1	1	0	0	1	3	1	1	2	2	3	4	2	2	1	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr17:27975326C>A	ENST00000269033.3	-	13	1333	c.1182G>T	c.(1180-1182)atG>atT	p.M394I	SSH2_ENST00000540801.1_Missense_Mutation_p.M421I|RP11-68I3.2_ENST00000581474.1_RNA|RP11-68I3.11_ENST00000582881.1_RNA	NM_001282129.1|NM_033389.2	NP_001269058.1|NP_203747.2	Q76I76	SSH2_HUMAN	slingshot protein phosphatase 2	394	Tyrosine-protein phosphatase.				actin cytoskeleton organization (GO:0030036)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)		SSH2/SUZ12(2)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GACTCACCCCCATTTTGCAGT	0.443																																					p.M394I		Atlas-SNP	.											.	SSH2	107	.	0			c.G1182T						PASS	.						89	78	82					17																	27975326		2203	4300	6503	SO:0001583	missense	85464	exon13			CACCCCCATTTTG	AB072359	CCDS11253.1, CCDS74024.1	17q11.2	2013-03-05	2013-03-05		ENSG00000141298	ENSG00000141298		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"	30580	protein-coding gene	gene with protein product		606779	"slingshot homolog 2 (Drosophila)"			11832213, 11214970	Standard	XM_005258059		Approved	KIAA1725	uc002heo.1	Q76I76	OTTHUMG00000132752	ENST00000269033.3:c.1182G>T	chr17.hg19:g.27975326C>A	ENSP00000269033:p.Met394Ile	60.0	0.0	.		85.0	46.0	.	NM_033389	Q8TDB5|Q8WYL1|Q8WYL2|Q96F40|Q96H36|Q9C0D8	Missense_Mutation	SNP	ENST00000269033.3	hg19	CCDS11253.1	.	.	.	.	.	.	.	.	.	.	C	36	5.803091	0.96960	.	.	ENSG00000141298	ENST00000269033;ENST00000540801;ENST00000394848	D;D	0.85411	-1.98;-1.98	5.95	5.95	0.96441	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.000000	0.85682	D	0.000000	D	0.94611	0.8263	M	0.94101	3.495	0.80722	D	1	P;P;P	0.50710	0.526;0.895;0.938	P;P;D	0.65233	0.701;0.647;0.933	D	0.94987	0.8131	10	0.87932	D	0	-16.2523	20.3932	0.98965	0.0:1.0:0.0:0.0	.	421;394;394	F5H527;Q76I76-4;Q76I76	.;.;SSH2_HUMAN	I	394;421;394	ENSP00000269033:M394I;ENSP00000444743:M421I	ENSP00000269033:M394I	M	-	3	0	SSH2	24999452	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.824000	0.97209	0.655000	0.94253	ATG	.	.	.	none		0.443	SSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256116.1	NM_033389		A	27975326	C	A	27975326	3	1	51	1	0	0	0	0	1	0	0	0	15197	594	21	4	3101	4	SSH2	17	27975326	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	901084	27975326	53219884	72	3488											
WIPF2	147179	hgsc.bcm.edu	37	chr17	38416825	38416825	+	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	aagctgagtagagatgagcaGcggggtcgaggcgccctctt	9	7	16	9	3	1	3	0	2	1	1	2	5	1	3	1	3	3	3	1	3	2	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr17:38416825G>A	ENST00000323571.4	+	3	342	c.102G>A	c.(100-102)caG>caA	p.Q34Q	WIPF2_ENST00000585043.1_Silent_p.Q34Q|WIPF2_ENST00000394103.3_Silent_p.Q34Q|WIPF2_ENST00000583130.1_Silent_p.Q34Q|WIPF2_ENST00000536600.1_Silent_p.Q34Q|WIPF2_ENST00000494757.1_3'UTR	NM_133264.4	NP_573571.1	Q8TF74	WIPF2_HUMAN	WAS/WASL interacting protein family, member 2	34					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	30						GAGATGAGCAGCGGGGTCGAG	0.522										HNSCC(43;0.11)																											p.Q34Q		Atlas-SNP	.											.	WIPF2	55	.	0			c.G102A						PASS	.						101	89	93					17																	38416825		2203	4300	6503	SO:0001819	synonymous_variant	147179	exon3			TGAGCAGCGGGGT	BC025965	CCDS11364.1	17q21.2	2006-10-12			ENSG00000171475	ENSG00000171475			30923	protein-coding gene	gene with protein product		609692				12213210, 11829459	Standard	XM_005257083		Approved	WICH, WIRE	uc002hug.1	Q8TF74	OTTHUMG00000133331	ENST00000323571.4:c.102G>A	chr17.hg19:g.38416825G>A		158.0	0.0	.		161.0	38.0	.	NM_133264	A8K0L3|Q658J8|Q71RE1|Q8TE44	Silent	SNP	ENST00000323571.4	hg19	CCDS11364.1																																																																																			.	.	.	none		0.522	WIPF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257157.2	NM_133264		A	38416825	G	A	38416825	2	1	51	1	0	0	0	0	0	0	0	1	17380	962	34	2		2	WIPF2	17	38416825	Silent	SNP	G	TCGA-A4-7996-01A-11D-2201-08	10441499	38416825	42778385	73	3489											
FAM59A	64762	hgsc.bcm.edu	37	chr18	29867256	29867256	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attcttcactagcttctgggAaaaggtagtcgctcccacta	10	12	8	11	1	3	0	1	0	2	0	5	1	4	1	1	2	1	3	1	2	5	6			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr18:29867256A>G	ENST00000269209.6	-	4	1307	c.1304T>C	c.(1303-1305)tTc>tCc	p.F435S	RP11-344B2.2_ENST00000579580.1_RNA|GAREM_ENST00000578619.1_5'Flank|GAREM_ENST00000399218.4_Missense_Mutation_p.F435S			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	435					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)										AGCTTCTGGGAAAAGGTAGTC	0.557																																					p.F435S		Atlas-SNP	.											.	.	.	.	0			c.T1304C						PASS	.						103	109	107					18																	29867256		2203	4300	6503	SO:0001583	missense	64762	exon4			TCTGGGAAAAGGT	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.1304T>C	chr18.hg19:g.29867256A>G	ENSP00000269209:p.Phe435Ser	211.0	0.0	.		210.0	69.0	.	NM_022751	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	Missense_Mutation	SNP	ENST00000269209.6	hg19	CCDS56057.1	.	.	.	.	.	.	.	.	.	.	A	0.031	-1.336778	0.01287	.	.	ENSG00000141441	ENST00000399218;ENST00000269209	T;T	0.13538	2.58;2.58	5.65	5.65	0.86999	.	0.136032	0.64402	D	0.000002	T	0.09468	0.0233	N	0.12182	0.205	0.58432	D	0.99999	B;B	0.17852	0.024;0.012	B;B	0.20577	0.03;0.019	T	0.28839	-1.0031	10	0.22109	T	0.4	-29.2932	16.1512	0.81624	1.0:0.0:0.0:0.0	.	435;435	Q9H706;Q9H706-3	FA59A_HUMAN;.	S	435	ENSP00000382165:F435S;ENSP00000269209:F435S	ENSP00000269209:F435S	F	-	2	0	FAM59A	28121254	1.000000	0.71417	1.000000	0.80357	0.104000	0.19210	7.042000	0.76565	2.275000	0.75901	0.459000	0.35465	TTC	.	.	.	none		0.557	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255365.1	NM_022751		G	29867256	A	G	29867256	3	3	51	1	0	0	0	0	1	0	0	0	5599	246	9	3	1335	3	FAM59A	18	29867256	Missense_Mutation	SNP	A	TCGA-A4-7996-01A-11D-2201-08		29867256	48209992	74	3490											
ZNF516	9658	hgsc.bcm.edu	37	chr18	74154041	74154041	+	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	gccggcgacgatcacctcctCctggaccacgttgttgatgg	6	9	12	14	4	1	1	1	1	0	0	3	4	3	2	5	3	0	2	5	3	0	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr18:74154041C>T	ENST00000443185.2	-	3	1287	c.970G>A	c.(970-972)Gag>Aag	p.E324K	ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	324					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)		ATCACCTCCTCCTGGACCACG	0.602																																					p.E324K		Atlas-SNP	.											.	ZNF516	102	.	0			c.G970A						PASS	.						64	73	70					18																	74154041		2178	4264	6442	SO:0001583	missense	9658	exon3			CCTCCTCCTGGAC	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.970G>A	chr18.hg19:g.74154041C>T	ENSP00000394757:p.Glu324Lys	98.0	0.0	.		87.0	24.0	.	NM_014643		Missense_Mutation	SNP	ENST00000443185.2	hg19		.	.	.	.	.	.	.	.	.	.	C	25.9	4.681412	0.88542	.	.	ENSG00000101493	ENST00000443185	T	0.11495	2.77	4.97	4.97	0.65823	.	0.095344	0.49916	D	0.000140	T	0.36138	0.0956	.	.	.	0.54753	D	0.999984	D	0.76494	0.999	D	0.80764	0.994	T	0.12604	-1.0541	9	0.62326	D	0.03	-3.4552	18.4275	0.90614	0.0:1.0:0.0:0.0	.	324	Q92618	ZN516_HUMAN	K	324	ENSP00000394757:E324K	ENSP00000394757:E324K	E	-	1	0	ZNF516	72283029	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.572000	0.67411	2.578000	0.87016	0.655000	0.94253	GAG	.	.	.	none		0.602	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643		T	74154041	C	T	74154041	3	4	51	1	0	0	0	0	1	0	0	0	17972	864	30	2	2542	2	ZNF516	18	74154041	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	44286785	74154041	3923207	75	3491											
PTPRS	5802	hgsc.bcm.edu	37	chr19	5208061	5208061	+	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	gaagacgcccgtcctgcccaCgccggcactggtggcagtaa	8	5	13	15	4	0	1	0	0	0	1	1	2	1	1	4	3	1	3	4	3	2	1			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr19:5208061C>A	ENST00000587303.1	-	36	5749	c.5650G>T	c.(5650-5652)Gtg>Ttg	p.V1884L	PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000262963.6_Missense_Mutation_p.V1864L|PTPRS_ENST00000588012.1_Missense_Mutation_p.V1846L|PTPRS_ENST00000592099.1_Missense_Mutation_p.V1437L|PTPRS_ENST00000348075.2_Missense_Mutation_p.V1846L|PTPRS_ENST00000353284.2_Missense_Mutation_p.V1437L|PTPRS_ENST00000357368.4_Missense_Mutation_p.V1884L|PTPRS_ENST00000372412.4_Missense_Mutation_p.V1885L			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	1884	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				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)	GTCCTGCCCACGCCGGCACTG	0.602																																					p.V1884L		Atlas-SNP	.											PTPRS,colon,carcinoma,0,2	PTPRS	169	.	0			c.G5650T						PASS	.						53	41	45					19																	5208061		2203	4300	6503	SO:0001583	missense	5802	exon37			TGCCCACGCCGGC	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.5650G>T	chr19.hg19:g.5208061C>A	ENSP00000467537:p.Val1884Leu	32.0	0.0	.		38.0	2.0	.	NM_002850	O75255|O75870|Q15718|Q16341|Q2M3R7	Missense_Mutation	SNP	ENST00000587303.1	hg19	CCDS45930.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.070068	0.76301	.	.	ENSG00000105426	ENST00000536396;ENST00000372412;ENST00000357368;ENST00000355005;ENST00000356037;ENST00000262963;ENST00000348075;ENST00000355322;ENST00000544524;ENST00000353284	D;D;D;D;D	0.84660	-1.88;-1.88;-1.88;-1.88;-1.88	2.78	2.78	0.32641	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.56097	U	0.000021	D	0.91365	0.7276	M	0.79011	2.435	0.80722	D	1	D;D;D;D;D;D	0.67145	0.978;0.97;0.996;0.992;0.994;0.993	D;P;D;D;D;D	0.85130	0.927;0.877;0.995;0.97;0.997;0.997	D	0.92491	0.6000	10	0.87932	D	0	.	13.6312	0.62196	0.0:1.0:0.0:0.0	.	1466;1437;1441;1846;1884;1479	F8W800;Q13332-7;F5H2T4;Q13332-6;Q13332;Q59FX6	.;.;.;.;PTPRS_HUMAN;.	L	1479;1885;1884;1884;1875;1864;1846;1466;1441;1437	ENSP00000361489:V1885L;ENSP00000349932:V1884L;ENSP00000262963:V1864L;ENSP00000269907:V1846L;ENSP00000327313:V1437L	ENSP00000262963:V1864L	V	-	1	0	PTPRS	5159061	1.000000	0.71417	0.990000	0.47175	0.547000	0.35210	7.562000	0.82300	1.397000	0.46682	0.471000	0.43371	GTG	.	.	.	none		0.602	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2			A	5208061	C	A	5208061	3	1	51	1	0	0	0	0	1	0	0	0	12824	536	19	4	204	4	PTPRS	19	5208061	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08		5208061	53920922	76	3492											
CD209	30835	hgsc.bcm.edu	37	chr19	7810714	7810714	+	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	agccaggtcagctcctggtaGatctcctgcagcttagattt	8	12	10	11	0	2	2	1	0	1	2	4	2	3	2	3	2	4	4	3	2	2	3			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr19:7810714G>A	ENST00000315599.7	-	4	460	c.438C>T	c.(436-438)atC>atT	p.I146I	CD209_ENST00000315591.8_Silent_p.I122I|CD209_ENST00000601256.1_Silent_p.I122I|CD209_ENST00000301357.8_Intron|CD209_ENST00000204801.8_Silent_p.I102I|CD209_ENST00000394173.4_Intron|CD209_ENST00000593821.1_Silent_p.I102I|CD209_ENST00000593660.1_Silent_p.I122I|CD209_ENST00000602261.1_Silent_p.I146I|CD209_ENST00000394161.5_Intron|CD209_ENST00000354397.6_Silent_p.I146I|CD209_ENST00000601951.1_Silent_p.I122I	NM_001144895.1|NM_001144897.1|NM_021155.3	NP_001138367.1|NP_001138369.1|NP_066978.1	Q9NNX6	CD209_HUMAN	CD209 molecule	146	7 X approximate tandem repeats.				antigen processing and presentation (GO:0019882)|cell-cell recognition (GO:0009988)|endocytosis (GO:0006897)|heterophilic cell-cell adhesion (GO:0007157)|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 T cell proliferation (GO:0042129)|viral genome replication (GO:0019079)|virion attachment to host cell (GO:0019062)	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)	carbohydrate binding (GO:0030246)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)|peptide antigen binding (GO:0042605)|virion binding (GO:0046790)			endometrium(7)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						GCTCCTGGTAGATCTCCTGCA	0.547																																					p.I146I		Atlas-SNP	.											.	CD209	166	.	0			c.C438T						PASS	.						106	105	105					19																	7810714		2197	4299	6496	SO:0001819	synonymous_variant	30835	exon4			CTGGTAGATCTCC	M98457	CCDS12186.1, CCDS45949.1, CCDS45950.1, CCDS45951.1, CCDS45952.1, CCDS59344.1, CCDS59345.1	19p13	2011-08-30	2006-03-28			ENSG00000090659		"C-type lectin domain containing", "CD molecules"	1641	protein-coding gene	gene with protein product		604672	"CD209 antigen"			1518869	Standard	NM_021155		Approved	DC-SIGN, CDSIGN, DC-SIGN1, CLEC4L	uc002mht.2	Q9NNX6		ENST00000315599.7:c.438C>T	chr19.hg19:g.7810714G>A		367.0	0.0	.		237.0	73.0	.	NM_021155	A8KAM4|A8MVQ9|G5E9C4|Q2TB19|Q96QP7|Q96QP8|Q96QP9|Q96QQ0|Q96QQ1|Q96QQ2|Q96QQ3|Q96QQ4|Q96QQ5|Q96QQ6|Q96QQ7|Q96QQ8	Silent	SNP	ENST00000315599.7	hg19	CCDS12186.1																																																																																			.	.	.	none		0.547	CD209-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462241.1	NM_021155		A	7810714	G	A	7810714	2	1	51	1	0	0	0	0	0	0	0	1	2986	932	33	2		2	CD209	19	7810714	Silent	SNP	G	TCGA-A4-7996-01A-11D-2201-08	2602653	7810714	51318269	77	3493											
BRD4	23476	hgsc.bcm.edu	37	chr19	15350519	15350519	+	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	ctctccgggtgcttggggggCtccggccgcagcgaggggct	2	7	19	13	4	1	0	0	0	1	0	3	1	2	0	3	7	2	4	3	7	0	1			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr19:15350519C>T	ENST00000263377.2	-	16	3617	c.3396G>A	c.(3394-3396)gaG>gaA	p.E1132E		NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	1132	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)			GCTTGGGGGGCTCCGGCCGCA	0.711			T	C15orf55	lethal midline carcinoma of young people																																p.E1132E		Atlas-SNP	.		Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	.	BRD4	172	.	0			c.G3396A						PASS	.						19	26	24					19																	15350519		2159	4231	6390	SO:0001819	synonymous_variant	23476	exon16			GGGGGGCTCCGGC	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.3396G>A	chr19.hg19:g.15350519C>T		88.0	0.0	.		69.0	27.0	.	NM_058243	O60433|Q4G0X8|Q86YS8|Q96PD3	Silent	SNP	ENST00000263377.2	hg19	CCDS12328.1																																																																																			.	.	.	none		0.711	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243		T	15350519	C	T	15350519	2	4	51	1	0	0	0	0	0	0	0	1	1506	796	28	2		2	BRD4	19	15350519	Silent	SNP	C	TCGA-A4-7996-01A-11D-2201-08	7539805	15350519	43778464	78	3494											
FCGBP	8857	hgsc.bcm.edu	37	chr19	40419757	40419757	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccctgggggtccagcttgctAtggcactcccggaagggccc	5	7	14	15	1	0	0	0	0	0	0	2	1	2	1	4	5	2	3	4	5	2	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr19:40419757A>G	ENST00000221347.6	-	6	3244	c.3237T>C	c.(3235-3237)caT>caC	p.H1079H		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1079	VWFD 2. {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)			CCAGCTTGCTATGGCACTCCC	0.642																																					p.H1079H		Atlas-SNP	.											.	FCGBP	416	.	0			c.T3237C						PASS	.						70	65	67					19																	40419757		2203	4300	6503	SO:0001819	synonymous_variant	8857	exon6			CTTGCTATGGCAC	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.3237T>C	chr19.hg19:g.40419757A>G		181.0	0.0	.		162.0	44.0	.	NM_003890	O95784	Silent	SNP	ENST00000221347.6	hg19	CCDS12546.1																																																																																			.	.	.	none		0.642	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		G	40419757	A	G	40419757	2	3	51	1	0	0	0	0	0	0	0	1	5785	446	16	3		3	FCGBP	19	40419757	Silent	SNP	A	TCGA-A4-7996-01A-11D-2201-08	25069238	40419757	18709226	79	3495											
HRC	3270	hgsc.bcm.edu	37	chr19	49658077	49658077	+	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	agctgagtcttccgtgtcttCactcccgtggcctctgtgcc	3	13	10	15	2	4	1	1	1	3	0	6	1	6	1	4	1	2	1	4	1	0	2			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr19:49658077C>G	ENST00000252825.4	-	1	604	c.418G>C	c.(418-420)Gaa>Caa	p.E140Q	TRPM4_ENST00000427978.2_5'Flank|HRC_ENST00000595625.1_Missense_Mutation_p.E140Q|TRPM4_ENST00000252826.5_5'Flank	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	140	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)		TCCGTGTCTTCACTCCCGTGG	0.597																																					p.E140Q	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.G418C						PASS	.						176	128	144					19																	49658077		2203	4300	6503	SO:0001583	missense	3270	exon1			TGTCTTCACTCCC		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.418G>C	chr19.hg19:g.49658077C>G	ENSP00000252825:p.Glu140Gln	152.0	0.0	.		113.0	34.0	.	NM_002152	Q504Y6	Missense_Mutation	SNP	ENST00000252825.4	hg19	CCDS12759.1	.	.	.	.	.	.	.	.	.	.	C	16.95	3.264155	0.59431	.	.	ENSG00000130528	ENST00000252825;ENST00000434964	T	0.06933	3.24	2.6	2.6	0.31112	.	.	.	.	.	T	0.24624	0.0597	M	0.73217	2.22	0.23923	N	0.996455	D	0.89917	1.0	D	0.79108	0.992	T	0.03000	-1.1084	9	0.35671	T	0.21	-0.6964	11.3389	0.49520	0.0:1.0:0.0:0.0	.	140	P23327	SRCH_HUMAN	Q	140;110	ENSP00000252825:E140Q	ENSP00000252825:E140Q	E	-	1	0	HRC	54349889	0.062000	0.20869	0.037000	0.18230	0.019000	0.09904	1.982000	0.40638	1.775000	0.52247	0.462000	0.41574	GAA	.	.	.	none		0.597	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		G	49658077	C	G	49658077	3	3	51	1	0	0	0	0	1	0	0	0	7359	835	29	4	1705	4	HRC	19	49658077	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	9238320	49658077	9470906	80	3496											
VN1R2	317701	hgsc.bcm.edu	37	chr19	53762787	53762787	+	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	tctgctgcagaagaaatagaCgattctttcatgatttcagg	12	13	9	7	1	4	4	2	1	2	3	4	5	4	4	0	1	2	2	0	1	3	4	rs374706531		TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr19:53762787C>T	ENST00000341702.3	+	1	1243	c.1159C>T	c.(1159-1161)Cga>Tga	p.R387*	VN1R2_ENST00000598458.1_Intron	NM_173856.2	NP_776255.2	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	387					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)		AAGAAATAGACGATTCTTTCA	0.433																																					p.R387X		Atlas-SNP	.											VN1R2,colon,carcinoma,-1,1	VN1R2	71	.	0			c.C1159T						PASS	.						105	103	104					19																	53762787		2203	4300	6503	SO:0001587	stop_gained	317701	exon1			AATAGACGATTCT	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.1159C>T	chr19.hg19:g.53762787C>T	ENSP00000351244:p.Arg387*	165.0	0.0	.		139.0	35.0	.	NM_173856	A1L411|Q8TDU4	Nonsense_Mutation	SNP	ENST00000341702.3	hg19	CCDS12862.1	.	.	.	.	.	.	.	.	.	.	C	12.73	2.024586	0.35701	.	.	ENSG00000196131	ENST00000341702	.	.	.	2.92	-5.84	0.02318	.	.	.	.	.	.	.	.	.	.	.	0.20764	N	0.999858	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	2.3458	0.04271	0.3322:0.4169:0.1115:0.1395	.	.	.	.	X	387	.	ENSP00000351244:R387X	R	+	1	2	VN1R2	58454599	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.676000	0.00396	-3.923000	0.00091	-0.582000	0.04134	CGA	.	.	.	weak		0.433	VN1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464285.1	NM_173856		T	53762787	C	T	53762787	4	4	51	1	0	0	0	0	0	1	0	0	17191	528	19	1	1161	1	VN1R2	19	53762787	Nonsense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08	4104710	53762787	5366196	81	3497											
SLC24A3	57419	hgsc.bcm.edu	37	chr20	19679325	19679325	+	Splice_Site	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	ctgtggattacggatcctacGtaagtggttttctccaggac	8	13	11	9	2	1	0	0	0	1	0	3	3	2	3	2	4	2	2	2	4	3	5	rs201062990		TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr20:19679325G>C	ENST00000328041.6	+	15	1916		c.e15+1		RP4-718D20.3_ENST00000600889.1_RNA|RP4-718D20.3_ENST00000435992.2_RNA|RP4-718D20.3_ENST00000598694.1_RNA|RP4-718D20.3_ENST00000609846.1_RNA|RP4-718D20.3_ENST00000593770.1_RNA	NM_020689.3	NP_065740.2	Q9HC58	NCKX3_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 3						ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						CGGATCCTACGTAAGTGGTTT	0.542																																					.		Atlas-SNP	.											.	SLC24A3	92	.	0			c.1719+1G>C						PASS	.						79	63	68					20																	19679325		2203	4299	6502	SO:0001630	splice_region_variant	57419	exon15			TCCTACGTAAGTG	AF169257	CCDS13140.1	20p13	2013-05-22			ENSG00000185052	ENSG00000185052		"Solute carriers"	10977	protein-coding gene	gene with protein product		609839					Standard	NM_020689		Approved		uc002wrl.3	Q9HC58	OTTHUMG00000031993	ENST00000328041.6:c.1719+1G>C	chr20.hg19:g.19679325G>C		14.0	0.0	.		19.0	9.0	.	NM_020689	B1AKV7|Q9BQJ9|Q9BQL7|Q9BQY3|Q9H519	Splice_Site	SNP	ENST00000328041.6	hg19	CCDS13140.1	.	.	.	.	.	.	.	.	.	.	G	32	5.120039	0.94385	.	.	ENSG00000185052	ENST00000328041	.	.	.	5.8	5.8	0.92144	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.8252	0.92115	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC24A3	19627325	1.000000	0.71417	0.994000	0.49952	0.964000	0.63967	9.869000	0.99810	2.758000	0.94735	0.561000	0.74099	.	.	G|1.000;A|0.000	.	alt		0.542	SLC24A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078207.4	NM_020689	Intron	C	19679325	G	C	19679325	5	2	51	1	0	0	0	0	0	0	1	0	14480	1159	40	4	1778	4	SLC24A3	20	19679325	Splice_Site	SNP	G	TCGA-A4-7996-01A-11D-2201-08		19679325	43346195	82	3498											
MOCS3	8813	hgsc.bcm.edu	37	chr20	49576203	49576203	+	5'Flank	SNP	T	T	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	cccctcttacagtggcagctTgttgctctttgatgccctga	5	14	9	13	0	2	2	0	2	2	0	2	2	2	2	3	1	4	4	3	1	1	4			TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr20:49576203T>G	ENST00000371588.5	-	0	0				DPM1_ENST00000371582.4_5'Flank|MOCS3_ENST00000244051.1_Missense_Mutation_p.L275W|DPM1_ENST00000466152.1_5'Flank|DPM1_ENST00000371583.5_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						AGTGGCAGCTTGTTGCTCTTT	0.632																																					p.L275W		Atlas-SNP	.											.	MOCS3	44	.	0			c.T824G						PASS	.						46	51	50					20																	49576203		2203	4300	6503	SO:0001631	upstream_gene_variant	27304	exon1			GCAGCTTGTTGCT	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		chr20.hg19:g.49576203T>G	Exception_encountered	104.0	0.0	.		120.0	63.0	.	NM_014484	O15157|Q6IB78|Q96HK0	Missense_Mutation	SNP	ENST00000371588.5	hg19	CCDS13434.1	.	.	.	.	.	.	.	.	.	.	T	16.87	3.243077	0.58995	.	.	ENSG00000124217	ENST00000244051	T	0.37058	1.22	5.27	5.27	0.74061	Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);MoeZ/MoeB (1);	0.229560	0.37483	N	0.002066	T	0.75824	0.3902	H	0.98965	4.385	0.58432	D	0.999998	D	0.89917	1.0	D	0.87578	0.998	D	0.86356	0.1714	9	.	.	.	-5.0901	15.1888	0.73025	0.0:0.0:0.0:1.0	.	275	O95396	MOCS3_HUMAN	W	275	ENSP00000244051:L275W	.	L	+	2	0	MOCS3	49009610	1.000000	0.71417	0.918000	0.36340	0.234000	0.25298	5.437000	0.66544	1.992000	0.58205	0.459000	0.35465	TTG	.	.	.	none		0.632	DPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079716.1	NM_003859		G	49576203	T	G	49576203	1	3	51	0	1	0	0	0	0	0	0	0	9699	1821	63	5		5	MOCS3	20	49576203	5'Flank	SNP	T	TCGA-A4-7996-01A-11D-2201-08	29896878	49576203	13449317	83	3499											
ARVCF	421	hgsc.bcm.edu	37	chr22	19965495	19965495	+	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	gcccaccttgttgtcagtgtCcttccggcccacagccgact	5	10	9	17	2	1	0	1	0	0	0	3	1	3	0	6	1	1	1	6	1	0	3	rs373958610		TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr22:19965495C>G	ENST00000263207.3	-	8	1975	c.1684G>C	c.(1684-1686)Gac>Cac	p.D562H	ARVCF_ENST00000406522.1_Missense_Mutation_p.D499H|ARVCF_ENST00000406259.1_Missense_Mutation_p.D562H|ARVCF_ENST00000344269.3_Missense_Mutation_p.D499H|ARVCF_ENST00000401994.1_Missense_Mutation_p.D499H	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	562					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)					TTGTCAGTGTCCTTCCGGCCC	0.652																																					p.D562H		Atlas-SNP	.											.	ARVCF	54	.	0			c.G1684C						PASS	.						61	50	54					22																	19965495		2203	4300	6503	SO:0001583	missense	421	exon8			CAGTGTCCTTCCG		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.1684G>C	chr22.hg19:g.19965495C>G	ENSP00000263207:p.Asp562His	77.0	0.0	.		58.0	16.0	.	NM_001670	B7WNV2	Missense_Mutation	SNP	ENST00000263207.3	hg19	CCDS13771.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.145373	0.77888	.	.	ENSG00000099889	ENST00000263207;ENST00000344269;ENST00000401994;ENST00000406522;ENST00000406259	D;D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54;-1.54	4.03	4.03	0.46877	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.88912	0.6566	M	0.73598	2.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.973;0.999	D	0.89030	0.3441	9	.	.	.	-17.2062	17.0615	0.86548	0.0:1.0:0.0:0.0	.	562;84	O00192;E7EV58	ARVC_HUMAN;.	H	562;499;499;499;562	ENSP00000263207:D562H;ENSP00000342042:D499H;ENSP00000384341:D499H;ENSP00000384732:D499H;ENSP00000385444:D562H	.	D	-	1	0	ARVCF	18345495	1.000000	0.71417	1.000000	0.80357	0.670000	0.39368	5.569000	0.67391	2.541000	0.85698	0.655000	0.94253	GAC	.	.	.	alt		0.652	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670		G	19965495	C	G	19965495	3	3	51	1	0	0	0	0	1	0	0	0	1003	855	30	4	1252	4	ARVCF	22	19965495	Missense_Mutation	SNP	C	TCGA-A4-7996-01A-11D-2201-08		19965495	31339071	84	3500											
PKDREJ	10343	hgsc.bcm.edu	37	chr22	46655720	46655720	+	Frame_Shift_Del	DEL	G	G	-																															accgtagatccacaggattaGggatcacaatcaccttggcc																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chr22:46655720delG	ENST00000253255.5	-	1	3499	c.3500delC	c.(3499-3501)cctfs	p.P1167fs		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	1167					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)		CACAGGATTAGGGATCACAAT	0.493																																					p.P1167fs		Atlas-INDEL	.											.	PKDREJ	195	.	0			c.3501delT						PASS	.						160	152	155					22																	46655720		2203	4300	6503	SO:0001589	frameshift_variant	10343	exon1			.	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.3500delC	chr22.hg19:g.46655720delG	ENSP00000253255:p.Pro1167fs	208.0	0.0	0		205.0	50.0	0.243902	NM_006071	B1AJY3|O95850	Frame_Shift_Del	DEL	ENST00000253255.5	hg19	CCDS14073.1																																																																																			.	.	.	none		0.493	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		-	46655720	G	-	46655720	7	5	51	1	0	1	0	1	0	0	0	0	11977	1000	35	0	3265	0	PKDREJ	22	46655720	Frame_Shift_Del	DEL	G	TCGA-A4-7996-01A-11D-2201-08	26690225	46655720	4648846	85	3501											
RLIM	51132	hgsc.bcm.edu	37	chrX	73815805	73815805	+	Frame_Shift_Del	DEL	T	T	-																															ctttgtcattggaatctgagTtttccatattgatgaacaag																										TCGA-A4-7996-01A-11D-2201-08	TCGA-A4-7996-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8cf8d4b0-1532-48a1-ac95-242f1fc0a867	5b059d3b-661d-4e07-b668-c140b421ade8	g.chrX:73815805delT	ENST00000332687.6	-	2	226	c.8delA	c.(7-9)aacfs	p.N3fs	RLIM_ENST00000349225.2_Frame_Shift_Del_p.N3fs	NM_016120.3	NP_057204.2	Q9NVW2	RNF12_HUMAN	ring finger protein, LIM domain interacting	3					negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|random inactivation of X chromosome (GO:0060816)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GGAATCTGAGTTTTCCATATT	0.358																																					p.N3fs	Esophageal Squamous(169;1899 1923 14997 18818 32118)	Atlas-INDEL	.											.	RLIM	90	.	0			c.9delC						PASS	.						53	49	50					X																	73815805		2203	4300	6503	SO:0001589	frameshift_variant	51132	exon3			.	AF155109	CCDS14427.1	Xq13-q21	2013-01-09	2009-02-17	2009-02-17	ENSG00000131263	ENSG00000131263		"RING-type (C3HC4) zinc fingers"	13429	protein-coding gene	gene with protein product	"ring zinc finger protein NY-REN-43antigen", "LIM domain interacting ring finger protein"	300379	"ring finger protein 12"	RNF12		10508479	Standard	NM_016120		Approved	NY-REN-43, MGC15161	uc004ebw.3	Q9NVW2	OTTHUMG00000021859	ENST00000332687.6:c.8delA	chrX.hg19:g.73815805delT	ENSP00000328059:p.Asn3fs	87.0	0.0	0		69.0	31.0	0.449275	NM_183353	B2RBQ1|D3DTE0|Q96D38|Q9Y598	Frame_Shift_Del	DEL	ENST00000332687.6	hg19	CCDS14427.1																																																																																			.	.	.	none		0.358	RLIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057268.1	NM_016120		-	73815805	T	-	73815805	7	5	51	1	0	1	0	1	0	0	0	0	13403	1725	60	0	1878	0	RLIM	23	73815805	Frame_Shift_Del	DEL	T	TCGA-A4-7996-01A-11D-2201-08		73815805	81454755	86	3502											
RERE	473	hgsc.bcm.edu	37	chr1	8422892	8422892	+	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	ctgcttcttccgaccactgcGtagtgtcgacatctgcccac	6	11	8	16	3	2	0	0	0	2	0	4	2	3	0	3	0	3	2	3	0	1	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr1:8422892G>T	ENST00000337907.3	-	17	2387	c.1753C>A	c.(1753-1755)Cgc>Agc	p.R585S	RERE_ENST00000377464.1_Missense_Mutation_p.R317S|RERE_ENST00000476556.1_Missense_Mutation_p.R31S|RERE_ENST00000400908.2_Missense_Mutation_p.R585S|RERE_ENST00000400907.2_Intron	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	585					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)		CGACCACTGCGTAGTGTCGAC	0.617																																					p.R585S		Atlas-SNP	.											.	RERE	129	.	0			c.C1753A						PASS	.						95	83	87					1																	8422892		2203	4300	6503	SO:0001583	missense	473	exon17			CACTGCGTAGTGT	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.1753C>A	chr1.hg19:g.8422892G>T	ENSP00000338629:p.Arg585Ser	120.0	0.0	.		92.0	29.0	.	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Missense_Mutation	SNP	ENST00000337907.3	hg19	CCDS95.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.444981	0.83993	.	.	ENSG00000142599	ENST00000337907;ENST00000377464;ENST00000476556;ENST00000400908;ENST00000505225	T;T;T;T	0.05025	3.51;3.51;3.51;3.51	5.8	5.8	0.92144	.	.	.	.	.	T	0.21509	0.0518	M	0.67953	2.075	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.85130	0.997;0.997	T	0.07481	-1.0770	9	0.06891	T	0.86	-30.1132	19.0501	0.93039	0.0:0.0:1.0:0.0	.	317;585	B1AKN3;Q9P2R6	.;RERE_HUMAN	S	585;317;31;585;5	ENSP00000338629:R585S;ENSP00000366684:R317S;ENSP00000422246:R31S;ENSP00000383700:R585S	ENSP00000338629:R585S	R	-	1	0	RERE	8345479	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.407000	0.97325	2.730000	0.93505	0.563000	0.77884	CGC	.	.	.	none		0.617	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1			T	8422892	G	T	8422892	3	4	52	1	0	0	0	0	1	0	0	0	13244	1145	40	4	2979	4	RERE	1	8422892	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08		8422892	240827729	1	3503											
MAST2	23139	hgsc.bcm.edu	37	chr1	46290209	46290209	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcgacaactgagtcaggaTgattgtaagttatggagagg	13	9	14	5	1	1	3	1	2	0	1	1	6	1	4	0	3	2	2	0	3	3	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr1:46290209T>C	ENST00000361297.2	+	2	565	c.282T>C	c.(280-282)gaT>gaC	p.D94D	MAST2_ENST00000372009.2_Silent_p.D94D	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)					TGAGTCAGGATGATTGTAAGT	0.398																																					p.D94D		Atlas-SNP	.											.	MAST2	136	.	0			c.T282C						PASS	.						166	149	154					1																	46290209		1856	4094	5950	SO:0001819	synonymous_variant	23139	exon2			TCAGGATGATTGT	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.282T>C	chr1.hg19:g.46290209T>C		282.0	0.0	.		265.0	88.0	.	NM_015112		Silent	SNP	ENST00000361297.2	hg19	CCDS41326.1																																																																																			.	.	.	none		0.398	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112		C	46290209	T	C	46290209	2	2	52	1	0	0	0	0	0	0	0	1	9332	1461	51	3		3	MAST2	1	46290209	Silent	SNP	T	TCGA-A4-7997-01A-11D-2201-08	37867317	46290209	202960412	2	3504											
WDR3	10885	hgsc.bcm.edu	37	chr1	118502024	118502024	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tagccacttggaagagaagaAgaggaagaggaaaaagaggg	19	3	16	3	0	0	5	0	0	0	5	0	9	0	8	1	4	1	0	1	4	7	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr1:118502024A>G	ENST00000349139.5	+	27	2833	c.2786A>G	c.(2785-2787)aAg>aGg	p.K929R	SPAG17_ENST00000336338.5_Intron	NM_006784.2	NP_006775.1	Q9UNX4	WDR3_HUMAN	WD repeat domain 3	929						nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(9)|liver(2)|lung(22)|prostate(2)|upper_aerodigestive_tract(1)	49	Esophageal squamous(2;0.162)	all_cancers(81;2.72e-05)|Acute lymphoblastic leukemia(138;1e-08)|all_epithelial(167;4.4e-07)|all_lung(203;1.7e-06)|Lung NSC(69;1.98e-05)|Prostate(1639;0.00955)|Breast(1374;0.244)		OV - Ovarian serous cystadenocarcinoma(397;1.39e-08)|Epithelial(280;1.82e-07)|all cancers(265;2.04e-05)|Lung(183;0.0525)|BRCA - Breast invasive adenocarcinoma(282;0.0695)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.185)		GAAGagaagaagaggaagagg	0.378																																					p.K929R		Atlas-SNP	.											.	WDR3	81	.	0			c.A2786G						PASS	.						70	77	74					1																	118502024		2203	4300	6503	SO:0001583	missense	10885	exon27			AGAAGAAGAGGAA	AF083217	CCDS898.1	1p12	2013-01-09			ENSG00000065183	ENSG00000065183		"WD repeat domain containing"	12755	protein-coding gene	gene with protein product		604737				10395803	Standard	NM_006784		Approved	FLJ12796, UTP12, DIP2	uc010oxe.1	Q9UNX4	OTTHUMG00000012197	ENST00000349139.5:c.2786A>G	chr1.hg19:g.118502024A>G	ENSP00000308179:p.Lys929Arg	50.0	0.0	.		66.0	24.0	.	NM_006784		Missense_Mutation	SNP	ENST00000349139.5	hg19	CCDS898.1	.	.	.	.	.	.	.	.	.	.	A	14.33	2.502821	0.44558	.	.	ENSG00000065183	ENST00000349139	T	0.54479	0.57	5.47	4.35	0.52113	.	0.188191	0.56097	D	0.000032	T	0.15782	0.0380	N	0.08118	0	0.80722	D	1	B	0.12013	0.005	B	0.12156	0.007	T	0.06734	-1.0810	10	0.28530	T	0.3	-11.5094	10.512	0.44868	0.9233:0.0:0.0767:0.0	.	929	Q9UNX4	WDR3_HUMAN	R	929	ENSP00000308179:K929R	ENSP00000308179:K929R	K	+	2	0	WDR3	118303547	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.417000	0.44653	2.091000	0.63221	0.496000	0.49642	AAG	.	.	.	none		0.378	WDR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033720.2	NM_006784		G	118502024	A	G	118502024	3	3	52	1	0	0	0	0	1	0	0	0	17297	72	3	3	2888	3	WDR3	1	118502024	Missense_Mutation	SNP	A	TCGA-A4-7997-01A-11D-2201-08	72211815	118502024	130748597	3	3505											
ASH1L	55870	hgsc.bcm.edu	37	chr1	155491175	155491175	+	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	ccgtttgcgaaggtcctcttCctcctttgtgtttttttcta	3	20	7	11	2	2	0	0	0	2	0	5	1	5	0	4	1	1	2	4	1	2	7			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr1:155491175C>T	ENST00000368346.3	-	2	775	c.136G>A	c.(136-138)Gaa>Aaa	p.E46K	ASH1L_ENST00000548830.1_Missense_Mutation_p.E46K|ASH1L_ENST00000392403.3_Missense_Mutation_p.E46K			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	46					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)			AGGTCCTCTTCCTCCTTTGTG	0.418																																					p.E46K		Atlas-SNP	.											.	ASH1L	279	.	0			c.G136A						PASS	.						302	301	301					1																	155491175		2203	4300	6503	SO:0001583	missense	55870	exon2			CCTCTTCCTCCTT	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.136G>A	chr1.hg19:g.155491175C>T	ENSP00000357330:p.Glu46Lys	518.0	0.0	.		495.0	164.0	.	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	hg19		.	.	.	.	.	.	.	.	.	.	C	36	5.771812	0.96922	.	.	ENSG00000116539	ENST00000368346;ENST00000392403;ENST00000548830	D;D	0.89875	-2.58;-2.58	5.51	5.51	0.81932	.	0.134693	0.48286	N	0.000192	T	0.73776	0.3630	N	0.08118	0	0.46874	D	0.999234	B;B	0.30281	0.18;0.275	B;B	0.28232	0.04;0.087	T	0.76487	-0.2941	10	0.72032	D	0.01	.	19.2027	0.93717	0.0:1.0:0.0:0.0	.	46;46	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	K	46	ENSP00000357330:E46K;ENSP00000376204:E46K	ENSP00000357330:E46K	E	-	1	0	ASH1L	153757799	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	7.059000	0.76684	2.868000	0.98415	0.557000	0.71058	GAA	.	.	.	none		0.418	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		T	155491175	C	T	155491175	3	4	52	1	0	0	0	0	1	0	0	0	1041	864	30	2	8866	2	ASH1L	1	155491175	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	36989151	155491175	93759446	4	3506											
SLC41A1	254428	hgsc.bcm.edu	37	chr1	205770146	205770146	+	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	gagccccagcagcgcaggcaCtaggatgaagacctctgtca	11	5	12	13	1	2	2	1	1	1	1	2	4	2	3	3	2	3	3	3	2	2	1			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr1:205770146C>T	ENST00000367137.3	-	3	1429	c.415G>A	c.(415-417)Gtg>Atg	p.V139M	SLC41A1_ENST00000468057.1_5'UTR	NM_173854.4	NP_776253.3	Q8IVJ1	S41A1_HUMAN	solute carrier family 41 (magnesium transporter), member 1	139					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)			AGCGCAGGCACTAGGATGAAG	0.562																																					p.V139M		Atlas-SNP	.											.	SLC41A1	46	.	0			c.G415A						PASS	.						109	105	106					1																	205770146		2203	4300	6503	SO:0001583	missense	254428	exon3			CAGGCACTAGGAT	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.415G>A	chr1.hg19:g.205770146C>T	ENSP00000356105:p.Val139Met	151.0	0.0	.		133.0	39.0	.	NM_173854	Q63HJ4|Q658Z5|Q659A4|Q6MZK2	Missense_Mutation	SNP	ENST00000367137.3	hg19	CCDS30988.1	.	.	.	.	.	.	.	.	.	.	C	32	5.182269	0.94885	.	.	ENSG00000133065	ENST00000367137	T	0.29917	1.55	5.78	5.78	0.91487	MgtE magnesium transporter, integral membrane (1);	0.000000	0.85682	D	0.000000	T	0.68091	0.2963	M	0.93638	3.44	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.73538	-0.3951	10	0.51188	T	0.08	-13.616	19.9618	0.97254	0.0:1.0:0.0:0.0	.	139	Q8IVJ1	S41A1_HUMAN	M	139	ENSP00000356105:V139M	ENSP00000356105:V139M	V	-	1	0	SLC41A1	204036769	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.768000	0.85345	2.894000	0.99253	0.655000	0.94253	GTG	.	.	.	none		0.562	SLC41A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087731.1			T	205770146	C	T	205770146	3	4	52	1	0	0	0	0	1	0	0	0	14642	565	20	2	1162	2	SLC41A1	1	205770146	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	50278971	205770146	43480475	5	3507											
PIGR	5284	hgsc.bcm.edu	37	chr1	207109097	207109097	+	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	tttccttacggttgtaggggCagagcacggccacagagcct	8	9	13	11	2	0	2	0	0	0	2	1	2	1	2	3	4	3	4	3	4	2	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr1:207109097C>T	ENST00000356495.4	-	5	1295	c.1112G>A	c.(1111-1113)tGc>tAc	p.C371Y		NM_002644.3	NP_002635.2	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor	371	Ig-like V-type 4.				detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc receptor signaling pathway (GO:0038093)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|receptor clustering (GO:0043113)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	polymeric immunoglobulin receptor activity (GO:0001792)			central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						GTTGTAGGGGCAGAGCACGGC	0.622											OREG0014186	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C371Y		Atlas-SNP	.											.	PIGR	98	.	0			c.G1112A						PASS	.						33	37	36					1																	207109097		2203	4300	6503	SO:0001583	missense	5284	exon5			TAGGGGCAGAGCA		CCDS1474.1	1q31-q41	2013-01-11			ENSG00000162896	ENSG00000162896		"Immunoglobulin superfamily / V-set domain containing"	8968	protein-coding gene	gene with protein product		173880					Standard	NM_002644		Approved		uc001hez.3	P01833	OTTHUMG00000036581	ENST00000356495.4:c.1112G>A	chr1.hg19:g.207109097C>T	ENSP00000348888:p.Cys371Tyr	41.0	0.0	.	2165	43.0	17.0	.	NM_002644	Q68D81|Q8IZY7	Missense_Mutation	SNP	ENST00000356495.4	hg19	CCDS1474.1	.	.	.	.	.	.	.	.	.	.	C	15.86	2.956538	0.53293	.	.	ENSG00000162896	ENST00000356495	T	0.40476	1.03	5.55	5.55	0.83447	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	T	0.75882	0.3910	H	0.96518	3.835	0.53005	D	0.999964	D	0.89917	1.0	D	0.97110	1.0	D	0.83757	0.0212	10	0.87932	D	0	-23.806	16.2203	0.82255	0.0:1.0:0.0:0.0	.	371	P01833	PIGR_HUMAN	Y	371	ENSP00000348888:C371Y	ENSP00000348888:C371Y	C	-	2	0	PIGR	205175720	1.000000	0.71417	0.930000	0.37139	0.097000	0.18754	4.383000	0.59600	2.614000	0.88457	0.655000	0.94253	TGC	.	.	.	none		0.622	PIGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088975.1	NM_002644		T	207109097	C	T	207109097	3	4	52	1	0	0	0	0	1	0	0	0	11904	710	25	2	1210	2	PIGR	1	207109097	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	1338951	207109097	42141524	6	3508											
IRF6	3664	hgsc.bcm.edu	37	chr1	209974723	209974723	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccacctgggccaccagccaGggctttagccggactctgcg	6	7	12	16	2	1	0	0	0	1	0	2	1	2	1	6	3	3	1	6	3	1	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr1:209974723G>A	ENST00000367021.3	-	3	208	c.36C>T	c.(34-36)ccC>ccT	p.P12P	IRF6_ENST00000542854.1_Intron	NM_006147.3	NP_006138.1	O14896	IRF6_HUMAN	interferon regulatory factor 6	12					cell cycle arrest (GO:0007050)|cell development (GO:0048468)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell proliferation (GO:0008285)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|large_intestine(4)|lung(12)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	28				OV - Ovarian serous cystadenocarcinoma(81;0.0351)		CCACCAGCCAGGGCTTTAGCC	0.607										HNSCC(57;0.16)																											p.P12P		Atlas-SNP	.											.	IRF6	65	.	0			c.C36T						PASS	.						55	63	60					1																	209974723		2202	4300	6502	SO:0001819	synonymous_variant	3664	exon3			CAGCCAGGGCTTT	AL022398	CCDS1492.1, CCDS55681.1	1q32.2-q32.3	2011-02-10			ENSG00000117595	ENSG00000117595			6121	protein-coding gene	gene with protein product		607199	"Van der Woude syndrome"	VWS, LPS		12219090	Standard	NM_006147		Approved	OFC6, VWS1	uc001hhq.2	O14896	OTTHUMG00000036521	ENST00000367021.3:c.36C>T	chr1.hg19:g.209974723G>A		161.0	0.0	.		151.0	46.0	.	NM_006147	B4DLE2|D3DT90|F5GWX8|G0ZTL0	Silent	SNP	ENST00000367021.3	hg19	CCDS1492.1																																																																																			.	.	.	none		0.607	IRF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088827.1	NM_006147		A	209974723	G	A	209974723	2	1	52	1	0	0	0	0	0	0	0	1	7841	987	35	2		2	IRF6	1	209974723	Silent	SNP	G	TCGA-A4-7997-01A-11D-2201-08	2865626	209974723	39275898	7	3509											
EXOC8	149371	hgsc.bcm.edu	37	chr1	231472205	231472205	+	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	gccctgtttctcaaaaatagCtcacaggccttcgtgcactg	9	11	8	13	1	2	0	2	0	1	0	4	0	2	0	2	1	2	3	2	1	3	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr1:231472205C>A	ENST00000360394.2	-	1	1373	c.1287G>T	c.(1285-1287)gaG>gaT	p.E429D	SPRTN_ENST00000008440.9_5'Flank|SPRTN_ENST00000391858.4_5'Flank|SPRTN_ENST00000295050.7_5'Flank|EXOC8_ENST00000366645.1_Missense_Mutation_p.E425D	NM_175876.3	NP_787072.2	Q8IYI6	EXOC8_HUMAN	exocyst complex component 8	429					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)				TCAAAAATAGCTCACAGGCCT	0.527																																					p.E429D		Atlas-SNP	.											.	EXOC8	42	.	0			c.G1287T						PASS	.						48	49	49					1																	231472205		2203	4300	6503	SO:0001583	missense	149371	exon1			AAATAGCTCACAG	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.1287G>T	chr1.hg19:g.231472205C>A	ENSP00000353564:p.Glu429Asp	95.0	0.0	.		86.0	18.0	.	NM_175876	B3KU33|Q5TE82	Missense_Mutation	SNP	ENST00000360394.2	hg19	CCDS1593.1	.	.	.	.	.	.	.	.	.	.	C	11.50	1.657151	0.29425	.	.	ENSG00000116903	ENST00000360394;ENST00000366645	T;T	0.77098	-1.07;-1.07	5.97	5.05	0.67936	Cullin repeat-like-containing domain (1);	0.052227	0.85682	D	0.000000	T	0.67297	0.2878	L	0.31526	0.94	0.58432	D	0.999998	P	0.45957	0.869	B	0.43754	0.43	T	0.62431	-0.6856	10	0.15066	T	0.55	-29.5152	12.807	0.57619	0.0:0.8715:0.0:0.1285	.	429	Q8IYI6	EXOC8_HUMAN	D	429;425	ENSP00000353564:E429D;ENSP00000355605:E425D	ENSP00000353564:E429D	E	-	3	2	EXOC8	229538828	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	3.827000	0.55745	2.837000	0.97791	0.655000	0.94253	GAG	.	.	.	none		0.527	EXOC8-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_175876		A	231472205	C	A	231472205	3	1	52	1	0	0	0	0	1	0	0	0	5313	796	28	4	894	4	EXOC8	1	231472205	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	21497482	231472205	17778416	8	3510											
IRF2BP2	359948	hgsc.bcm.edu	37	chr1	234744251	234744251	+	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	aacaacctgcctgcagtcagGgccggctccttcttaaactt	9	10	8	14	1	2	0	1	0	1	0	3	0	3	0	4	2	5	2	4	2	4	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr1:234744251G>T	ENST00000366609.3	-	1	1020	c.990C>A	c.(988-990)gcC>gcA	p.A330A	IRF2BP2_ENST00000491430.1_5'Flank|IRF2BP2_ENST00000366610.3_Silent_p.A330A|RP4-781K5.2_ENST00000436039.1_RNA	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)			CTGCAGTCAGGGCCGGCTCCT	0.637																																					p.A330A		Atlas-SNP	.											.	IRF2BP2	37	.	0			c.C990A						PASS	.						22	21	21					1																	234744251		2201	4300	6501	SO:0001819	synonymous_variant	359948	exon1			AGTCAGGGCCGGC	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.990C>A	chr1.hg19:g.234744251G>T		36.0	0.0	.		39.0	15.0	.	NM_182972	B1AM35|B1AM36|Q6P083|Q7Z5L8|Q8N351|Q8WUH8	Silent	SNP	ENST00000366609.3	hg19	CCDS1602.1																																																																																			.	.	.	none		0.637	IRF2BP2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000092705.1	NM_182972		T	234744251	G	T	234744251	2	4	52	1	0	0	0	0	0	0	0	1	7837	1219	43	4		4	IRF2BP2	1	234744251	Silent	SNP	G	TCGA-A4-7997-01A-11D-2201-08	3272046	234744251	14506370	9	3511											
GPR113	165082	hgsc.bcm.edu	37	chr2	26533773	26533773	+	Frame_Shift_Del	DEL	C	C	-																															atggccatggctagtaccagCccattcacgcctatgatggc																										TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr2:26533773delC	ENST00000311519.1	-	11	2822	c.2823delG	c.(2821-2823)gggfs	p.G941fs	GPR113_ENST00000459892.1_5'UTR|GPR113_ENST00000333478.6_Frame_Shift_Del_p.G742fs|GPR113_ENST00000541401.1_Frame_Shift_Del_p.G544fs|GPR113_ENST00000421160.2_Frame_Shift_Del_p.G872fs	NM_001145168.1	NP_001138640.1	Q8IZF5	GP113_HUMAN	G protein-coupled receptor 113	941					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)					CTAGTACCAGCCCATTCACGC	0.597																																					p.L942fs		Atlas-INDEL	.											.	GPR113	134	.	0			c.2824delC						PASS	.						58	51	53					2																	26533773		2203	4300	6503	SO:0001589	frameshift_variant	165082	exon11			.	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.2823delG	chr2.hg19:g.26533773delC	ENSP00000307831:p.Gly941fs	36.0	0.0	0		39.0	18.0	0.461538	NM_001145168	B4DF15|E9PEV1|Q53TA5|Q6UXT7|Q6UXX3|Q86SL7|Q8IXD8|Q8TDT3	Frame_Shift_Del	DEL	ENST00000311519.1	hg19	CCDS46239.1																																																																																			.	.	.	none		0.597	GPR113-004	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316892.1	NM_153835		-	26533773	C	-	26533773	7	5	52	1	0	1	0	1	0	0	0	0	6637	726	26	0	517	0	GPR113	2	26533773	Frame_Shift_Del	DEL	C	TCGA-A4-7997-01A-11D-2201-08		26533773	216665600	10	3512											
OTOF	9381	hgsc.bcm.edu	37	chr2	26700635	26700635	+	Intron	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	ttcctgtgaatcaggagtgtGggtgatgctgggccacagcc	7	10	15	9	0	1	2	1	2	0	0	2	3	2	3	3	3	2	1	3	3	1	1			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr2:26700635G>C	ENST00000272371.2	-	19	2341				OTOF_ENST00000403946.3_Intron|OTOF_ENST00000338581.6_Intron|OTOF_ENST00000339598.3_Intron|OTOF_ENST00000402415.3_Missense_Mutation_p.H43D	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin						membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCAGGAGTGTGGGTGATGCTG	0.602																																					p.H43D	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.C127G						PASS	.						53	41	45					2																	26700635		2194	4294	6488	SO:0001627	intron_variant	9381	exon1			GAGTGTGGGTGAT	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.2215-18C>G	chr2.hg19:g.26700635G>C		43.0	0.0	.		36.0	16.0	.	NM_194322	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	hg19	CCDS1725.1	.	.	.	.	.	.	.	.	.	.	G	7.354	0.623380	0.14193	.	.	ENSG00000115155	ENST00000402415	T	0.76709	-1.04	3.28	-1.12	0.09808	.	.	.	.	.	T	0.59307	0.2184	.	.	.	0.09310	N	1	B	0.15473	0.013	B	0.16289	0.015	T	0.36138	-0.9760	7	.	.	.	.	6.8786	0.24160	0.2752:0.1313:0.5935:0.0	.	43	Q9HC10-3	.	D	43	ENSP00000383906:H43D	.	H	-	1	0	OTOF	26554139	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.033000	0.13754	-0.801000	0.04427	-1.268000	0.01426	CAC	.	.	.	none		0.602	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3			C	26700635	G	C	26700635	1	2	52	0	1	0	0	0	0	0	0	0	11310	1348	47	4		4	OTOF	2	26700635	Intron	SNP	G	TCGA-A4-7997-01A-11D-2201-08	166862	26700635	216498738	11	3513											
C2orf73	129852	hgsc.bcm.edu	37	chr2	54587528	54587528	+	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	caacaaaattctcaggagctGttagagcctaaaactcactt	15	10	6	10	0	2	1	2	0	1	1	3	2	2	2	1	1	4	2	1	1	6	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr2:54587528G>T	ENST00000398634.2	+	5	735	c.693G>T	c.(691-693)ctG>ctT	p.L231L	C2orf73_ENST00000405749.1_Intron|C2orf73_ENST00000491538.1_Intron	NM_001100396.1	NP_001093866.1	Q8N5S3	CB073_HUMAN	chromosome 2 open reading frame 73	231										breast(2)	2						CTCAGGAGCTGTTAGAGCCTA	0.493																																					p.L231L		Atlas-SNP	.											.	C2orf73	17	.	0			c.G693T						PASS	.						35	34	35					2																	54587528		1907	4128	6035	SO:0001819	synonymous_variant	129852	exon5			GGAGCTGTTAGAG	BC031669, AK097617	CCDS46285.1	2p16.2	2008-07-07			ENSG00000177994	ENSG00000177994			26861	protein-coding gene	gene with protein product						14702039	Standard	NM_001100396		Approved	FLJ40298	uc002rxt.1	Q8N5S3	OTTHUMG00000151826	ENST00000398634.2:c.693G>T	chr2.hg19:g.54587528G>T		19.0	0.0	.		31.0	8.0	.	NM_001100396	A0AV79|A0AV81|Q8N7V4	Silent	SNP	ENST00000398634.2	hg19	CCDS46285.1																																																																																			.	.	.	none		0.493	C2orf73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324075.2	NM_001100396		T	54587528	G	T	54587528	2	4	52	1	0	0	0	0	0	0	0	1	2194	1364	48	4		4	C2orf73	2	54587528	Silent	SNP	G	TCGA-A4-7997-01A-11D-2201-08	27886893	54587528	188611845	12	3514											
ZAP70	7535	hgsc.bcm.edu	37	chr2	98341626	98341626	+	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	ctcattgctacgacggcccaCgagcggatgccctggtacca	8	7	11	15	4	1	0	1	0	0	0	1	3	1	1	3	3	5	2	3	3	2	3	rs56404668	byFrequency	TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr2:98341626C>A	ENST00000264972.5	+	4	689	c.474C>A	c.(472-474)caC>caA	p.H158Q	ZAP70_ENST00000463643.1_3'UTR|ZAP70_ENST00000442208.1_Missense_Mutation_p.H32Q	NM_001079.3	NP_001070.2	P43403	ZAP70_HUMAN	zeta-chain (TCR) associated protein kinase 70kDa	158	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						CGACGGCCCACGAGCGGATGC	0.637																																					p.H158Q		Atlas-SNP	.											.	ZAP70	77	.	0			c.C474A						PASS	.						48	43	45					2																	98341626		2203	4300	6503	SO:0001583	missense	7535	exon4			GGCCCACGAGCGG	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.474C>A	chr2.hg19:g.98341626C>A	ENSP00000264972:p.His158Gln	82.0	0.0	.		75.0	36.0	.	NM_001079	A6NFP4|Q6PIA4|Q8IXD6|Q9UBS6	Missense_Mutation	SNP	ENST00000264972.5	hg19	CCDS33254.1	.	.	.	.	.	.	.	.	.	.	C	18.52	3.642553	0.67244	.	.	ENSG00000115085	ENST00000264972;ENST00000442208	D;D	0.92858	-3.12;-3.12	5.37	1.01	0.19927	SH2 motif (1);	0.000000	0.50627	D	0.000112	D	0.93262	0.7853	L	0.58810	1.83	0.51012	D	0.999903	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;1.0;0.999	D	0.90788	0.4684	10	0.62326	D	0.03	.	6.7946	0.23719	0.0:0.491:0.0:0.509	.	158;32;158	B4E0E2;P43403-3;P43403	.;.;ZAP70_HUMAN	Q	158;32	ENSP00000264972:H158Q;ENSP00000411141:H32Q	ENSP00000264972:H158Q	H	+	3	2	ZAP70	97708058	0.004000	0.15560	1.000000	0.80357	0.763000	0.43281	-1.323000	0.02692	0.354000	0.24105	-0.216000	0.12614	CAC	.	C|0.998;T|0.002	.	alt		0.637	ZAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329278.1			A	98341626	C	A	98341626	3	1	52	1	0	0	0	0	1	0	0	0	17526	535	19	4	480	4	ZAP70	2	98341626	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	43754098	98341626	144857747	13	3515											
SUMF1	285362	hgsc.bcm.edu	37	chr3	4490972	4490972	+	Missense_Mutation	SNP	A	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	cctgttgaatattggtcttcActtgctcactcaacatgcct	8	15	6	12	0	4	1	3	1	1	0	4	1	4	1	2	1	3	2	2	1	3	5			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr3:4490972A>C	ENST00000272902.5	-	3	532	c.497T>G	c.(496-498)gTg>gGg	p.V166G	SUMF1_ENST00000405420.2_Missense_Mutation_p.V166G|SUMF1_ENST00000458465.2_Intron|SUMF1_ENST00000383843.5_Intron|SUMF1_ENST00000534863.1_Missense_Mutation_p.V166G	NM_182760.3	NP_877437.2	Q8NBK3	SUMF1_HUMAN	sulfatase modifying factor 1	166					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)		ATTGGTCTTCACTTGCTCACT	0.393																																					p.V166G		Atlas-SNP	.											.	SUMF1	23	.	0			c.T497G						PASS	.						172	171	171					3																	4490972		2203	4300	6503	SO:0001583	missense	285362	exon3			GTCTTCACTTGCT	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.497T>G	chr3.hg19:g.4490972A>C	ENSP00000272902:p.Val166Gly	235.0	0.0	.		260.0	84.0	.	NM_001164675	B4DXK5|B7XD05|E9PGL0|G5E9B0|Q0VAC6|Q0VAC7|Q2NL78|Q53ZE4|Q6UY39|Q96AK5|Q96DK8	Missense_Mutation	SNP	ENST00000272902.5	hg19	CCDS2564.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.002331	0.74932	.	.	ENSG00000144455	ENST00000534982;ENST00000534863;ENST00000272902;ENST00000405420	D;D;D	0.97553	-4.43;-4.43;-4.43	5.53	5.53	0.82687	C-type lectin fold (1);Formylglycine-generating sulphatase enzyme domain (2);	0.000000	0.85682	D	0.000000	D	0.97002	0.9021	L	0.41824	1.3	0.80722	D	1	D;P	0.67145	0.996;0.541	D;P	0.65684	0.937;0.566	D	0.96392	0.9290	10	0.32370	T	0.25	-14.8274	14.671	0.68945	1.0:0.0:0.0:0.0	.	166;166	E9PGL0;Q8NBK3	.;SUMF1_HUMAN	G	166	ENSP00000440421:V166G;ENSP00000272902:V166G;ENSP00000384977:V166G	ENSP00000272902:V166G	V	-	2	0	SUMF1	4465972	1.000000	0.71417	0.989000	0.46669	0.926000	0.56050	7.392000	0.79840	2.100000	0.63781	0.533000	0.62120	GTG	.	.	.	none		0.393	SUMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206591.2	NM_182760		C	4490972	A	C	4490972	3	2	52	1	0	0	0	0	1	0	0	0	15397	159	6	5	655	5	SUMF1	3	4490972	Missense_Mutation	SNP	A	TCGA-A4-7997-01A-11D-2201-08		4490972	193531458	14	3516											
ANO10	55129	hgsc.bcm.edu	37	chr3	43618738	43618738	+	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	gagcaattgtttccccaaagTagccacgaatactgtctata	13	11	7	10	1	1	0	0	0	1	0	2	2	2	0	3	0	3	3	3	0	7	6			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr3:43618738T>A	ENST00000292246.3	-	6	778	c.608A>T	c.(607-609)tAc>tTc	p.Y203F	ANO10_ENST00000396091.3_Missense_Mutation_p.Y137F|ANO10_ENST00000414522.2_Missense_Mutation_p.Y203F|ANO10_ENST00000350459.4_Intron|ANO10_ENST00000451430.2_Missense_Mutation_p.Y92F	NM_018075.3	NP_060545.3	Q9NW15	ANO10_HUMAN	anoctamin 10	203					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell death (GO:0008219)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(3)|skin(3)	29						TTCCCCAAAGTAGCCACGAAT	0.343																																					p.Y203F		Atlas-SNP	.											.	ANO10	70	.	0			c.A608T						PASS	.						20	22	21					3																	43618738		2189	4296	6485	SO:0001583	missense	55129	exon6			CCAAAGTAGCCAC	AL832508	CCDS2710.2, CCDS56247.1, CCDS56248.1, CCDS56249.1, CCDS56250.1	3p22.1-p21.33	2014-04-09	2008-08-28	2008-08-28	ENSG00000160746	ENSG00000160746		"Ion channels / Chloride channels : Calcium activated : Anoctamins"	25519	protein-coding gene	gene with protein product		613726	"transmembrane protein 16K"	TMEM16K		12477932, 24692353	Standard	NM_001204831		Approved	FLJ10375, MGC47890, SCAR10	uc003cmv.3	Q9NW15	OTTHUMG00000133044	ENST00000292246.3:c.608A>T	chr3.hg19:g.43618738T>A	ENSP00000292246:p.Tyr203Phe	42.0	0.0	.		51.0	18.0	.	NM_018075	A8K8K3|A8MV74|B3KTZ1|B3KY93|B4DJ83|B4DNK2|B7WP12|C9JHS1|Q8IXX9	Missense_Mutation	SNP	ENST00000292246.3	hg19	CCDS2710.2	.	.	.	.	.	.	.	.	.	.	T	24.3	4.511689	0.85389	.	.	ENSG00000160746	ENST00000292246;ENST00000396091;ENST00000414522;ENST00000451430;ENST00000428472	T;T;T;T;T	0.72167	-0.63;-0.63;-0.63;-0.63;-0.63	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	D	0.87577	0.6212	M	0.91354	3.2	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;1.0;1.0	D	0.90259	0.4299	10	0.87932	D	0	.	16.3127	0.82898	0.0:0.0:0.0:1.0	.	92;203;137;203	Q9NW15-4;C9JHS1;Q9NW15-3;Q9NW15	.;.;.;ANO10_HUMAN	F	203;137;203;92;92	ENSP00000292246:Y203F;ENSP00000379398:Y137F;ENSP00000396990:Y203F;ENSP00000394119:Y92F;ENSP00000416266:Y92F	ENSP00000292246:Y203F	Y	-	2	0	ANO10	43593742	1.000000	0.71417	1.000000	0.80357	0.715000	0.41141	8.040000	0.89188	2.246000	0.74042	0.533000	0.62120	TAC	.	.	.	none		0.343	ANO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256649.2	NM_018075		A	43618738	T	A	43618738	3	1	52	1	0	0	0	0	1	0	0	0	696	1638	57	5	1406	5	ANO10	3	43618738	Missense_Mutation	SNP	T	TCGA-A4-7997-01A-11D-2201-08	39127766	43618738	154403692	15	3517											
ARHGEF3	50650	hgsc.bcm.edu	37	chr3	56787577	56787577	+	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	atcaagtcttcttctccttgGgaaagctcaaagatcgcctg	10	12	8	11	1	5	1	2	0	3	1	7	2	5	2	2	1	1	1	2	1	3	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr3:56787577G>C	ENST00000296315.3	-	4	561	c.393C>G	c.(391-393)tcC>tcG	p.S131S	ARHGEF3_ENST00000498517.1_5'UTR|ARHGEF3_ENST00000413728.2_Silent_p.S137S|ARHGEF3_ENST00000338458.4_Silent_p.S163S|ARHGEF3_ENST00000496106.1_Silent_p.S137S|ARHGEF3_ENST00000497267.1_Silent_p.S102S|ARHGEF3_ENST00000495373.1_Silent_p.S131S	NM_019555.2	NP_062455.1	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor (GEF) 3	131	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of 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)		CTTCTCCTTGGGAAAGCTCAA	0.363																																					p.S163S		Atlas-SNP	.											.	ARHGEF3	128	.	0			c.C489G						PASS	.						116	120	118					3																	56787577		2203	4300	6503	SO:0001819	synonymous_variant	50650	exon7			TCCTTGGGAAAGC	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.393C>G	chr3.hg19:g.56787577G>C		137.0	0.0	.		93.0	20.0	.	NM_001128615	A8K5U7|Q4FZB6|Q4QQI5|Q4QQQ0|Q59F00|Q6NUN3|Q7Z4U2|Q7Z5T2|Q9H7T4	Silent	SNP	ENST00000296315.3	hg19	CCDS2878.1																																																																																			.	.	.	none		0.363	ARHGEF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352431.2	NM_019555		C	56787577	G	C	56787577	2	2	52	1	0	0	0	0	0	0	0	1	904	1219	43	4		4	ARHGEF3	3	56787577	Silent	SNP	G	TCGA-A4-7997-01A-11D-2201-08	13168839	56787577	141234853	16	3518											
TMF1	7110	hgsc.bcm.edu	37	chr3	69096768	69096770	+	In_Frame_Del	DEL	GAA	GAA	-																															ctgttttagactttggagttGaagaattaactataataggc																										TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr3:69096768_69096770delGAA	ENST00000398559.2	-	2	1302_1304	c.1086_1088delTTC	c.(1084-1089)tcttca>tca	p.362_363SS>S	MIR3136_ENST00000583498.1_RNA|CTD-2013N24.2_ENST00000596732.1_RNA|CTD-2013N24.2_ENST00000597950.1_RNA|CTD-2013N24.2_ENST00000601735.1_RNA|TMF1_ENST00000543976.1_In_Frame_Del_p.362_363SS>S|CTD-2013N24.2_ENST00000598783.1_RNA|CTD-2013N24.2_ENST00000482368.2_RNA|CTD-2013N24.2_ENST00000596523.1_RNA|CTD-2013N24.2_ENST00000595925.1_RNA|CTD-2013N24.2_ENST00000596274.1_RNA			P82094	TMF1_HUMAN	TATA element modulatory factor 1	362					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)		CTTTGGAGTTGAAGAATTAACTA	0.355																																					p.363_363del		Atlas-INDEL	.											.	TMF1	77	.	0			c.1087_1089del						PASS	.																																			SO:0001651	inframe_deletion	7110	exon2			.		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.1086_1088delTTC	chr3.hg19:g.69096771_69096773delGAA	ENSP00000381567:p.Ser363del	88.0	0.0	0		98.0	27.0	0.27551	NM_007114	B7ZLJ2|Q17R87|Q59GK0	In_Frame_Del	DEL	ENST00000398559.2	hg19	CCDS43105.1																																																																																			.	.	.	none		0.355	TMF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352106.1	NM_007114		-	69096770	GAA	-	69096768	7	5	52	1	0	1	0	1	0	0	0	0	16240	1294	45	0	2257	0	TMF1	3	69096768	In_Frame_Del	DEL	GAA	TCGA-A4-7997-01A-11D-2201-08	12309191	69096768	128925662	17	3519											
EAF2	55840	hgsc.bcm.edu	37	chr3	121591418	121591418	+	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	gctagtctaatggaccagatGagtagttgtgatagttcatc	11	13	11	6	0	2	3	1	2	1	1	3	4	2	4	1	1	0	4	1	1	4	6			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr3:121591418G>A	ENST00000273668.2	+	5	590	c.519G>A	c.(517-519)atG>atA	p.M173I	EAF2_ENST00000451944.2_Missense_Mutation_p.M173I	NM_018456.4	NP_060926.2	Q96CJ1	EAF2_HUMAN	ELL associated factor 2	173					apoptotic process (GO:0006915)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	ELL-EAF complex (GO:0032783)|transcription elongation factor complex (GO:0008023)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)	9				GBM - Glioblastoma multiforme(114;0.0972)		TGGACCAGATGAGTAGTTGTG	0.313																																					p.M173I	Esophageal Squamous(194;1942 2097 24663 29345 31866)	Atlas-SNP	.											.	EAF2	26	.	0			c.G519A						PASS	.						120	123	122					3																	121591418		2203	4300	6503	SO:0001583	missense	55840	exon5			CCAGATGAGTAGT	AF517829	CCDS3006.1	3q21.1	2007-08-01			ENSG00000145088	ENSG00000145088			23115	protein-coding gene	gene with protein product		607659				12446457, 12907652	Standard	NM_018456		Approved	BM040, TRAITS, U19	uc003een.3	Q96CJ1	OTTHUMG00000159424	ENST00000273668.2:c.519G>A	chr3.hg19:g.121591418G>A	ENSP00000273668:p.Met173Ile	184.0	0.0	.		288.0	154.0	.	NM_018456	Q9NZ82	Missense_Mutation	SNP	ENST00000273668.2	hg19	CCDS3006.1	.	.	.	.	.	.	.	.	.	.	G	16.45	3.127060	0.56721	.	.	ENSG00000145088	ENST00000273668;ENST00000451944	.	.	.	4.74	4.74	0.60224	.	0.135191	0.64402	D	0.000004	T	0.62258	0.2413	M	0.77820	2.39	0.47862	D	0.999539	B	0.30406	0.278	B	0.27887	0.084	T	0.62243	-0.6895	9	0.29301	T	0.29	-9.0448	15.2478	0.73521	0.0:0.0:1.0:0.0	.	173	Q96CJ1	EAF2_HUMAN	I	173	.	ENSP00000273668:M173I	M	+	3	0	EAF2	123074108	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.397000	0.79903	2.456000	0.83038	0.305000	0.20034	ATG	.	.	.	none		0.313	EAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355247.1	NM_018456		A	121591418	G	A	121591418	3	1	52	1	0	0	0	0	1	0	0	0	4878	1290	45	2	537	2	EAF2	3	121591418	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	52494650	121591418	76431012	18	3520											
COL6A6	131873	hgsc.bcm.edu	37	chr3	130287032	130287032	+	Missense_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	accagatcgggtgcaaattgGtgtagtccagttcagcgaca	11	9	12	9	2	1	1	1	0	0	1	3	2	2	1	2	2	2	3	2	2	2	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr3:130287032G>A	ENST00000358511.6	+	5	2016	c.1985G>A	c.(1984-1986)gGt>gAt	p.G662D	COL6A6_ENST00000453409.2_Missense_Mutation_p.G662D	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	662	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						GTGCAAATTGGTGTAGTCCAG	0.408																																					p.G662D		Atlas-SNP	.											.	COL6A6	497	.	0			c.G1985A						PASS	.						176	171	173					3																	130287032		1915	4119	6034	SO:0001583	missense	131873	exon5			AAATTGGTGTAGT	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.1985G>A	chr3.hg19:g.130287032G>A	ENSP00000351310:p.Gly662Asp	184.0	0.0	.		297.0	79.0	.	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	hg19	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	G	14.84	2.654369	0.47467	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	D;D	0.82711	-1.64;-1.64	5.53	5.53	0.82687	von Willebrand factor, type A (3);	0.000000	0.64402	D	0.000018	D	0.93350	0.7880	H	0.94886	3.595	0.54753	D	0.999986	D	0.89917	1.0	D	0.87578	0.998	D	0.94709	0.7890	10	0.87932	D	0	.	14.6487	0.68780	0.0:0.1454:0.8546:0.0	.	662	A6NMZ7	CO6A6_HUMAN	D	662	ENSP00000351310:G662D;ENSP00000399236:G662D	ENSP00000351310:G662D	G	+	2	0	COL6A6	131769722	1.000000	0.71417	0.353000	0.25747	0.014000	0.08584	5.227000	0.65305	2.616000	0.88540	0.655000	0.94253	GGT	.	.	.	none		0.408	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		A	130287032	G	A	130287032	3	1	52	1	0	0	0	0	1	0	0	0	3705	1261	44	2	2003	2	COL6A6	3	130287032	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	8695614	130287032	67735398	19	3521											
CP	1356	hgsc.bcm.edu	37	chr3	148930432	148930432	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaagataaagggccttcttaTatagtctcccaattctatct	12	14	6	9	0	4	1	0	0	4	1	5	2	4	1	2	1	0	0	2	1	8	7	rs141532762		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr3:148930432T>C	ENST00000264613.6	-	2	462	c.200A>G	c.(199-201)tAt>tGt	p.Y67C		NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	67	F5/8 type A 1.|Plastocyanin-like 1.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	GGCCTTCTTATATAGTCTCCC	0.388																																					p.Y67C		Atlas-SNP	.											.	CP	112	.	0			c.A200G						PASS	.	T	CYS/TYR	1,4405	2.1+/-5.4	0,1,2202	74	73	73		200	5.4	0.5	3	dbSNP_134	73	0,8600		0,0,4300	no	missense	CP	NM_000096.3	194	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	probably-damaging	67/1066	148930432	1,13005	2203	4300	6503	SO:0001583	missense	1356	exon2			TTCTTATATAGTC	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.200A>G	chr3.hg19:g.148930432T>C	ENSP00000264613:p.Tyr67Cys	56.0	0.0	.		66.0	29.0	.	NM_000096	Q14063|Q2PP18|Q9UKS4	Missense_Mutation	SNP	ENST00000264613.6	hg19	CCDS3141.1	.	.	.	.	.	.	.	.	.	.	T	18.49	3.636271	0.67130	2.27E-4	0.0	ENSG00000047457	ENST00000264613;ENST00000455472	D;D	0.99277	-5.67;-5.67	5.42	5.42	0.78866	Cupredoxin (2);	0.000000	0.85682	D	0.000000	D	0.99530	0.9832	M	0.92784	3.345	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.984;0.993	D	0.98194	1.0464	10	0.87932	D	0	-24.6173	15.6278	0.76874	0.0:0.0:0.0:1.0	.	67;67	A8K5A4;P00450	.;CERU_HUMAN	C	67;107	ENSP00000264613:Y67C;ENSP00000426888:Y107C	ENSP00000264613:Y67C	Y	-	2	0	CP	150413122	1.000000	0.71417	0.500000	0.27589	0.701000	0.40568	7.525000	0.81892	2.280000	0.76307	0.460000	0.39030	TAT	.	T|1.000;C|0.000	0.000	weak		0.388	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096		C	148930432	T	C	148930432	3	2	52	1	0	0	0	0	1	0	0	0	3789	1406	49	3	3069	3	CP	3	148930432	Missense_Mutation	SNP	T	TCGA-A4-7997-01A-11D-2201-08	18643400	148930432	49091998	20	3522											
HTT	3064	hgsc.bcm.edu	37	chr4	3156098	3156098	+	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	aggagaaagaaccaggagaaCaagcatctgtaccgttgagt	16	6	12	7	1	1	4	0	1	1	3	1	6	1	4	2	2	4	3	2	2	5	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr4:3156098C>A	ENST00000355072.5	+	27	3722	c.3577C>A	c.(3577-3579)Caa>Aaa	p.Q1193K		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	1193					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)		ACCAGGAGAACAAGCATCTGT	0.498																																					p.Q1193K		Atlas-SNP	.											.	HTT	221	.	0			c.C3577A						PASS	.						55	53	54					4																	3156098		2049	4207	6256	SO:0001583	missense	3064	exon27			GGAGAACAAGCAT	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.3577C>A	chr4.hg19:g.3156098C>A	ENSP00000347184:p.Gln1193Lys	43.0	0.0	.		33.0	9.0	.	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	C	12.85	2.061554	0.36373	.	.	ENSG00000197386	ENST00000355072	T	0.05081	3.5	5.2	5.2	0.72013	.	0.378699	0.27906	N	0.017370	T	0.07683	0.0193	L	0.43152	1.355	0.27971	N	0.936396	B	0.20887	0.049	B	0.19148	0.024	T	0.21143	-1.0254	10	0.17832	T	0.49	.	16.9201	0.86162	0.0:1.0:0.0:0.0	.	1193	P42858	HD_HUMAN	K	1193	ENSP00000347184:Q1193K	ENSP00000347184:Q1193K	Q	+	1	0	HTT	3125896	0.989000	0.36119	0.644000	0.29465	0.961000	0.63080	3.195000	0.51013	2.430000	0.82344	0.557000	0.71058	CAA	.	.	.	none		0.498	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		A	3156098	C	A	3156098	3	1	52	1	0	0	0	0	1	0	0	0	7464	479	17	4	3683	4	HTT	4	3156098	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08		3156098	187998178	21	3523											
TECRL	253017	hgsc.bcm.edu	37	chr4	65180367	65180367	+	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	gtgtgtgtgtatcacttactGtaccactgggtggcgtaatc	7	14	12	8	1	1	0	1	0	0	0	2	0	1	0	1	2	2	3	1	2	4	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr4:65180367G>A	ENST00000381210.3	-	5	660	c.550C>T	c.(550-552)Cac>Tac	p.H184Y	TECRL_ENST00000513125.1_5'UTR|TECRL_ENST00000507440.1_Splice_Site_p.H184Y	NM_001010874.4	NP_001010874.2	Q5HYJ1	TECRL_HUMAN	trans-2,3-enoyl-CoA reductase-like	184					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						ATCACTTACTGTACCACTGGG	0.428																																					p.H184Y		Atlas-SNP	.											.	TECRL	106	.	0			c.C550T						PASS	.						83	76	78					4																	65180367		2203	4300	6503	SO:0001630	splice_region_variant	253017	exon5			CTTACTGTACCAC	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.551+1C>T	chr4.hg19:g.65180367G>A		51.0	0.0	.		33.0	10.0	.	NM_001010874		Missense_Mutation	SNP	ENST00000381210.3	hg19	CCDS33990.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.191677	0.78902	.	.	ENSG00000205678	ENST00000507440;ENST00000381210	T;T	0.42900	0.96;0.96	5.7	5.7	0.88788	.	0.124523	0.52532	D	0.000077	T	0.64832	0.2634	M	0.85777	2.775	0.80722	D	1	D;D	0.67145	0.996;0.993	D;P	0.78314	0.991;0.866	T	0.63537	-0.6615	10	0.07644	T	0.81	-12.79	16.5536	0.84479	0.0:0.0:1.0:0.0	.	184;184	Q6IN47;Q5HYJ1	.;TECRL_HUMAN	Y	184	ENSP00000426043:H184Y;ENSP00000370607:H184Y	ENSP00000370607:H184Y	H	-	1	0	TECRL	64862962	1.000000	0.71417	1.000000	0.80357	0.736000	0.42039	4.899000	0.63245	2.689000	0.91719	0.591000	0.81541	CAC	.	.	.	none		0.428	TECRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361705.4	NM_001010874	Missense_Mutation	A	65180367	G	A	65180367	5	1	52	1	0	0	0	0	0	0	1	0	15758	1391	48	2	573	2	TECRL	4	65180367	Splice_Site	SNP	G	TCGA-A4-7997-01A-11D-2201-08	62024269	65180367	125973909	22	3524											
SEPT11	55752	hgsc.bcm.edu	37	chr4	77941678	77941678	+	Missense_Mutation	SNP	T	T	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	agaatgaaaatcattgcgatTttgtgaaacttcgagagatg	15	12	10	4	2	1	4	1	2	0	2	2	7	1	4	0	0	2	0	0	0	4	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr4:77941678T>G	ENST00000264893.6	+	7	1009	c.808T>G	c.(808-810)Ttt>Gtt	p.F270V	SEPT11_ENST00000512575.1_Intron|SEPT11_ENST00000510515.1_Missense_Mutation_p.F280V|SEPT11_ENST00000502584.1_Missense_Mutation_p.F270V|SEPT11_ENST00000541121.1_Missense_Mutation_p.F280V|SEPT11_ENST00000505788.1_Missense_Mutation_p.F270V	NM_018243.2	NP_060713.1	Q9NVA2	SEP11_HUMAN	septin 11	270	Septin-type G.				cell cycle (GO:0007049)|cell division (GO:0051301)|protein heterooligomerization (GO:0051291)	cell junction (GO:0030054)|cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|septin complex (GO:0031105)|stress fiber (GO:0001725)|synapse (GO:0045202)	GTP binding (GO:0005525)			endometrium(2)|kidney(3)|large_intestine(3)|lung(1)|skin(1)|stomach(1)	11						TCATTGCGATTTTGTGAAACT	0.468																																					p.F270V		Atlas-SNP	.											.	SEPT11	31	.	0			c.T808G						PASS	.						96	93	94					4																	77941678		2203	4300	6503	SO:0001583	missense	55752	exon7			TGCGATTTTGTGA	AK001711	CCDS34018.1	4q21.1	2013-01-21			ENSG00000138758	ENSG00000138758		"Septins"	25589	protein-coding gene	gene with protein product		612887				14999297, 15140406	Standard	NM_018243		Approved	FLJ10849	uc003hkj.3	Q9NVA2	OTTHUMG00000160854	ENST00000264893.6:c.808T>G	chr4.hg19:g.77941678T>G	ENSP00000264893:p.Phe270Val	127.0	0.0	.		157.0	52.0	.	NM_018243	B7Z7Z6|E9KL32|Q4W5G1|Q7L4N1|Q96SP1|Q9UFY9	Missense_Mutation	SNP	ENST00000264893.6	hg19	CCDS34018.1	.	.	.	.	.	.	.	.	.	.	T	29.5	5.015347	0.93404	.	.	ENSG00000138758	ENST00000264893;ENST00000502584;ENST00000510641;ENST00000505788;ENST00000510515;ENST00000541121	T;T;T;T;T;T	0.68765	-0.35;-0.35;-0.35;-0.35;-0.35;-0.35	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	D	0.88724	0.6514	H	0.98388	4.22	0.58432	D	0.999996	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.80764	0.99;0.989;0.994	D	0.93076	0.6487	10	0.87932	D	0	.	15.1435	0.72630	0.0:0.0:0.0:1.0	.	280;262;270	Q9NVA2-2;D6RDU5;Q9NVA2	.;.;SEP11_HUMAN	V	270;270;262;270;280;280	ENSP00000264893:F270V;ENSP00000426344:F270V;ENSP00000420839:F262V;ENSP00000424925:F270V;ENSP00000422896:F280V;ENSP00000443701:F280V	ENSP00000264893:F270V	F	+	1	0	SEPT11	78160702	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.698000	0.84413	1.975000	0.57531	0.482000	0.46254	TTT	.	.	.	none		0.468	SEPT11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362676.1	NM_018243		G	77941678	T	G	77941678	3	3	52	1	0	0	0	0	1	0	0	0	14074	1841	64	5	834	5	SEPT11	4	77941678	Missense_Mutation	SNP	T	TCGA-A4-7997-01A-11D-2201-08	12761311	77941678	113212598	23	3525											
SKP2	6502	hgsc.bcm.edu	37	chr5	36163851	36163851	+	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	gtgtttgtaagaggtggtatCgcctagcgtaagtatttttc	8	16	12	5	2	0	1	0	0	0	1	2	1	0	1	1	2	1	5	1	2	5	8			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr5:36163851C>A	ENST00000274255.6	+	3	581	c.385C>A	c.(385-387)Cgc>Agc	p.R129S	SKP2_ENST00000274254.5_Missense_Mutation_p.R129S|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	129	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)			GAGGTGGTATCGCCTAGCGTA	0.468																																					p.R129S		Atlas-SNP	.											.	SKP2	70	.	0			c.C385A						PASS	.						139	119	126					5																	36163851		2203	4300	6503	SO:0001583	missense	6502	exon3			TGGTATCGCCTAG	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.385C>A	chr5.hg19:g.36163851C>A	ENSP00000274255:p.Arg129Ser	82.0	0.0	.		82.0	5.0	.	NM_032637	A8K5E0|B4DJT4|Q8TDZ0|Q8TDZ1|Q9BV69	Missense_Mutation	SNP	ENST00000274255.6	hg19	CCDS3916.1	.	.	.	.	.	.	.	.	.	.	C	13.87	2.365916	0.41902	.	.	ENSG00000145604	ENST00000274254;ENST00000274255;ENST00000308927;ENST00000513151	T;T;T	0.42513	0.97;0.97;0.97	4.92	0.0927	0.14474	F-box domain, cyclin-like (2);F-box domain, Skp2-like (1);	0.302114	0.42548	N	0.000698	T	0.29288	0.0729	L	0.48362	1.52	0.80722	D	1	B;B	0.23249	0.082;0.077	B;B	0.25291	0.021;0.059	T	0.04090	-1.0978	10	0.29301	T	0.29	-0.2876	5.0024	0.14271	0.1582:0.6121:0.0:0.2297	.	129;129	Q13309-2;Q13309	.;SKP2_HUMAN	S	129;129;95;129	ENSP00000274254:R129S;ENSP00000274255:R129S;ENSP00000423188:R129S	ENSP00000274254:R129S	R	+	1	0	SKP2	36199608	0.912000	0.30974	0.985000	0.45067	0.998000	0.95712	0.041000	0.13927	-0.102000	0.12197	0.650000	0.86243	CGC	.	.	.	none		0.468	SKP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253769.2	NM_005983		A	36163851	C	A	36163851	3	1	52	1	0	0	0	0	1	0	0	0	14375	884	31	4	395	4	SKP2	5	36163851	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08		36163851	144751409	24	3526											
NIPBL	25836	hgsc.bcm.edu	37	chr5	36984988	36984988	+	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	ctccataaaaaagcctgaagAaatcaaacaatgtaatgatg	20	8	6	7	0	1	3	1	2	0	1	2	3	2	3	2	0	2	1	2	0	8	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr5:36984988A>T	ENST00000282516.8	+	10	2205	c.1706A>T	c.(1705-1707)gAa>gTa	p.E569V	NIPBL_ENST00000448238.2_Missense_Mutation_p.E569V|NIPBL_ENST00000504430.1_3'UTR	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	569					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)			AAGCCTGAAGAAATCAAACAA	0.393																																					p.E569V		Atlas-SNP	.											.	NIPBL	513	.	0			c.A1706T						PASS	.						92	96	94					5																	36984988		2203	4300	6503	SO:0001583	missense	25836	exon10			CTGAAGAAATCAA	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.1706A>T	chr5.hg19:g.36984988A>T	ENSP00000282516:p.Glu569Val	143.0	0.0	.		179.0	72.0	.	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	ENST00000282516.8	hg19	CCDS3920.1	.	.	.	.	.	.	.	.	.	.	A	12.56	1.974280	0.34848	.	.	ENSG00000164190	ENST00000282516;ENST00000448238	D;D	0.94417	-3.41;-3.42	5.98	5.98	0.97165	.	0.120361	0.64402	D	0.000018	D	0.90933	0.7150	N	0.19112	0.55	0.42318	D	0.992241	P;P	0.48503	0.856;0.911	B;P	0.44561	0.266;0.453	D	0.91908	0.5537	10	0.49607	T	0.09	.	16.4781	0.84144	1.0:0.0:0.0:0.0	.	569;569	Q6KC79;Q6KC79-2	NIPBL_HUMAN;.	V	569	ENSP00000282516:E569V;ENSP00000406266:E569V	ENSP00000282516:E569V	E	+	2	0	NIPBL	37020745	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.883000	0.69721	2.288000	0.76882	0.528000	0.53228	GAA	.	.	.	none		0.393	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		T	36984988	A	T	36984988	3	4	52	1	0	0	0	0	1	0	0	0	10435	246	9	5	1740	5	NIPBL	5	36984988	Missense_Mutation	SNP	A	TCGA-A4-7997-01A-11D-2201-08	821137	36984988	143930272	25	3527											
ARHGAP26	23092	hgsc.bcm.edu	37	chr5	142416823	142416823	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatccatgctgtggaaaccAgaggtaaagtagtttaacag	14	9	11	7	0	0	1	0	0	0	1	1	2	1	2	2	2	3	5	2	2	5	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr5:142416823A>G	ENST00000274498.4	+	13	1585	c.1207A>G	c.(1207-1209)Aga>Gga	p.R403G	ARHGAP26_ENST00000378004.3_Missense_Mutation_p.R403G	NM_015071.4	NP_055886.1	Q9UNA1	RHG26_HUMAN	Rho GTPase activating protein 26	403	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				actin cytoskeleton organization (GO:0030036)|filopodium assembly (GO:0046847)|nervous system development (GO:0007399)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(7)|ovary(1)	25		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGTGGAAACCAGAGGTAAAGT	0.468																																					p.R403G		Atlas-SNP	.											.	ARHGAP26	57	.	0			c.A1207G						PASS	.						127	106	113					5																	142416823		2203	4300	6503	SO:0001583	missense	23092	exon13			GAAACCAGAGGTA	AB014521	CCDS4277.1, CCDS47297.1	5q31	2011-06-29			ENSG00000145819	ENSG00000145819		"Rho GTPase activating proteins"	17073	protein-coding gene	gene with protein product	"GTPase regulator associated with the focal adhesion kinase pp125"	605370				9858476, 8649427	Standard	NM_001135608		Approved	GRAF, KIAA0621, OPHN1L, OPHN1L1	uc011dbj.2	Q9UNA1	OTTHUMG00000059705	ENST00000274498.4:c.1207A>G	chr5.hg19:g.142416823A>G	ENSP00000274498:p.Arg403Gly	59.0	0.0	.		81.0	41.0	.	NM_015071	O75117|Q5D035|Q9BYS6|Q9BYS7|Q9UJ00	Missense_Mutation	SNP	ENST00000274498.4	hg19	CCDS4277.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.144516	0.77888	.	.	ENSG00000145819	ENST00000274498;ENST00000378004	T;T	0.21031	2.03;2.03	5.84	4.64	0.57946	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.42268	0.1195	M	0.85945	2.785	0.58432	D	0.999996	P;D	0.53619	0.924;0.961	P;P	0.54590	0.508;0.756	T	0.42241	-0.9463	10	0.49607	T	0.09	.	12.0971	0.53761	0.856:0.144:0.0:0.0	.	403;403	Q9UNA1;Q9UNA1-2	RHG26_HUMAN;.	G	403	ENSP00000274498:R403G;ENSP00000367243:R403G	ENSP00000274498:R403G	R	+	1	2	ARHGAP26	142397016	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.389000	0.52516	0.988000	0.38734	0.455000	0.32223	AGA	.	.	.	none		0.468	ARHGAP26-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132744.3	NM_015071		G	142416823	A	G	142416823	3	3	52	1	0	0	0	0	1	0	0	0	875	180	7	3	1257	3	ARHGAP26	5	142416823	Missense_Mutation	SNP	A	TCGA-A4-7997-01A-11D-2201-08	105431835	142416823	38498437	26	3528											
JAKMIP2	9832	hgsc.bcm.edu	37	chr5	147000262	147000262	+	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	tcaagagcttgttttctgtaGtctagttcttcctccagata	8	17	7	9	0	4	2	1	0	3	2	6	2	6	2	2	0	1	4	2	0	4	8			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr5:147000262G>T	ENST00000265272.5	-	18	2576	c.2109C>A	c.(2107-2109)gaC>gaA	p.D703E	JAKMIP2_ENST00000333010.6_Missense_Mutation_p.D661E|JAKMIP2_ENST00000507386.1_Missense_Mutation_p.D682E	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2	703						Golgi apparatus (GO:0005794)				NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTTTTCTGTAGTCTAGTTCTT	0.388																																					p.D703E		Atlas-SNP	.											.	JAKMIP2	154	.	0			c.C2109A						PASS	.						308	258	275					5																	147000262		2203	4300	6503	SO:0001583	missense	9832	exon18			TCTGTAGTCTAGT	AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049			29067	protein-coding gene	gene with protein product		611197				9628581	Standard	NM_001270941		Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.2109C>A	chr5.hg19:g.147000262G>T	ENSP00000265272:p.Asp703Glu	105.0	0.0	.		176.0	85.0	.	NM_001270941	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Missense_Mutation	SNP	ENST00000265272.5	hg19	CCDS4285.1	.	.	.	.	.	.	.	.	.	.	G	17.04	3.287394	0.59976	.	.	ENSG00000176049	ENST00000507386;ENST00000265272;ENST00000333010;ENST00000539401	T;T;T	0.25912	1.8;1.77;1.78	5.66	3.82	0.43975	.	0.000000	0.85682	D	0.000000	T	0.41558	0.1164	M	0.64404	1.975	0.49389	D	0.999788	D;D;D;D	0.61697	0.99;0.99;0.99;0.99	D;D;D;D	0.70935	0.971;0.971;0.971;0.971	T	0.22347	-1.0219	10	0.15952	T	0.53	.	10.5305	0.44973	0.1413:0.0:0.8587:0.0	.	661;703;682;703	B4DSG0;Q96AA8-3;G5E9Y0;Q96AA8	.;.;.;JKIP2_HUMAN	E	682;703;661;682	ENSP00000421398:D682E;ENSP00000265272:D703E;ENSP00000328989:D661E	ENSP00000265272:D703E	D	-	3	2	JAKMIP2	146980455	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.966000	0.40481	0.817000	0.34445	0.591000	0.81541	GAC	.	.	.	none		0.388	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790		T	147000262	G	T	147000262	3	4	52	1	0	0	0	0	1	0	0	0	7948	1020	36	4	339	4	JAKMIP2	5	147000262	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	4583439	147000262	33914998	27	3529											
C5orf41	153222	hgsc.bcm.edu	37	chr5	172518026	172518026	+	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	agaaaaaagggatggagcctCttcaaggtcatgccactccc	13	7	10	11	0	3	1	2	0	1	1	4	3	4	3	3	3	2	0	3	3	4	1			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr5:172518026C>G	ENST00000296953.2	+	4	1163	c.844C>G	c.(844-846)Ctt>Gtt	p.L282V	CREBRF_ENST00000540014.1_Missense_Mutation_p.L282V|CREBRF_ENST00000520420.1_Missense_Mutation_p.L282V|CREBRF_ENST00000522692.1_Missense_Mutation_p.L282V	NM_153607.2	NP_705835.2	Q8IUR6	CRERF_HUMAN	CREB3 regulatory factor	282					negative regulation of endoplasmic reticulum unfolded protein response (GO:1900102)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of intracellular transport (GO:0032388)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein transport (GO:0051222)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GATGGAGCCTCTTCAAGGTCA	0.522																																					p.L282V		Atlas-SNP	.											.	.	.	.	0			c.C844G						PASS	.						60	61	60					5																	172518026		2203	4300	6503	SO:0001583	missense	153222	exon4			GAGCCTCTTCAAG	AY139008	CCDS34293.1, CCDS54948.1	5q35.2	2012-03-06	2012-03-06	2012-03-06	ENSG00000164463	ENSG00000164463			24050	protein-coding gene	gene with protein product	"luman/CREB3 recruitment factor"		"chromosome 5 open reading frame 41"	C5orf41		18391022	Standard	NM_153607		Approved	LRF	uc003mch.3	Q8IUR6	OTTHUMG00000163322	ENST00000296953.2:c.844C>G	chr5.hg19:g.172518026C>G	ENSP00000296953:p.Leu282Val	91.0	0.0	.		96.0	26.0	.	NM_153607	B3DFH2|B3KW49|D3DQM2|F5GXN3|Q5HYG4|Q5HYK0|Q86YR3|Q8IZG1	Missense_Mutation	SNP	ENST00000296953.2	hg19	CCDS34293.1	.	.	.	.	.	.	.	.	.	.	C	3.060	-0.193550	0.06259	.	.	ENSG00000164463	ENST00000522692;ENST00000296953;ENST00000540014;ENST00000520420;ENST00000538538;ENST00000393776	T;T	0.43294	0.95;0.95	5.29	2.49	0.30216	.	0.733387	0.13308	N	0.397700	T	0.23766	0.0575	N	0.24115	0.695	0.09310	N	1	B;B	0.25609	0.039;0.13	B;B	0.24269	0.052;0.043	T	0.27191	-1.0081	10	0.07482	T	0.82	.	8.0149	0.30374	0.1291:0.7322:0.0:0.1387	.	282;282	Q8IUR6;Q8IUR6-2	CE041_HUMAN;.	V	282	ENSP00000296953:L282V;ENSP00000440075:L282V	ENSP00000296953:L282V	L	+	1	0	C5orf41	172450632	0.996000	0.38824	0.050000	0.19076	0.931000	0.56810	3.394000	0.52551	0.215000	0.20761	0.563000	0.77884	CTT	.	.	.	none		0.522	CREBRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372667.1	NM_153607		G	172518026	C	G	172518026	3	3	52	1	0	0	0	0	1	0	0	0	2302	913	32	4	854	4	C5orf41	5	172518026	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	25517764	172518026	8397234	28	3530											
SPDEF	25803	hgsc.bcm.edu	37	chr6	34512076	34512076	+	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	gtagaaggcggacaggccctGctcgggcgtggcgggtggac	6	5	20	10	4	0	1	0	0	0	1	1	3	0	3	1	7	1	2	1	7	2	1			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr6:34512076G>T	ENST00000374037.3	-	2	571	c.157C>A	c.(157-159)Cag>Aag	p.Q53K	SPDEF_ENST00000544425.1_Missense_Mutation_p.Q53K	NM_012391.2	NP_036523.1	O95238	SPDEF_HUMAN	SAM pointed domain containing ETS transcription factor	53					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						GACAGGCCCTGCTCGGGCGTG	0.687																																					p.Q53K		Atlas-SNP	.											.	SPDEF	34	.	0			c.C157A						PASS	.						35	40	38					6																	34512076		2203	4300	6503	SO:0001583	missense	25803	exon2			GGCCCTGCTCGGG	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.157C>A	chr6.hg19:g.34512076G>T	ENSP00000363149:p.Gln53Lys	87.0	0.0	.		79.0	18.0	.	NM_001252294	B4DWH8|F5H778	Missense_Mutation	SNP	ENST00000374037.3	hg19	CCDS4794.1	.	.	.	.	.	.	.	.	.	.	G	14.43	2.534021	0.45073	.	.	ENSG00000124664	ENST00000374037;ENST00000544425	T;T	0.14022	2.54;2.73	4.97	4.97	0.65823	.	0.498805	0.17278	N	0.180107	T	0.04452	0.0122	L	0.27053	0.805	0.28482	N	0.914903	B;B	0.25904	0.137;0.085	B;B	0.25140	0.058;0.026	T	0.26121	-1.0112	10	0.35671	T	0.21	.	13.5867	0.61935	0.0:0.1561:0.8439:0.0	.	53;53	F5H778;O95238	.;SPDEF_HUMAN	K	53	ENSP00000363149:Q53K;ENSP00000442715:Q53K	ENSP00000363149:Q53K	Q	-	1	0	SPDEF	34620054	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	4.798000	0.62510	2.286000	0.76751	0.591000	0.81541	CAG	.	.	.	none		0.687	SPDEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040246.1	NM_012391		T	34512076	G	T	34512076	3	4	52	1	0	0	0	0	1	0	0	0	15038	1328	46	4	870	4	SPDEF	6	34512076	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08		34512076	136602991	29	3531											
SNX9	51429	hgsc.bcm.edu	37	chr6	158288583	158288583	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctccactcctgataggctcGggttatgtatgattttgctg	6	16	10	9	1	1	2	0	2	1	0	4	2	2	2	2	2	1	4	2	2	3	5			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr6:158288583G>A	ENST00000392185.3	+	2	188	c.17G>A	c.(16-18)cGg>cAg	p.R6Q		NM_016224.3	NP_057308.1	Q9Y5X1	SNX9_HUMAN	sorting nexin 9	6	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|lipid tube assembly (GO:0060988)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein oligomerization (GO:0032461)|receptor-mediated endocytosis (GO:0006898)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle membrane (GO:0030659)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	1-phosphatidylinositol binding (GO:0005545)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	20		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)		TGATAGGCTCGGGTTATGTAT	0.393																																					p.R6Q		Atlas-SNP	.											.	SNX9	43	.	0			c.G17A						PASS	.						171	140	150					6																	158288583		2203	4300	6503	SO:0001583	missense	51429	exon2			AGGCTCGGGTTAT	AF121859	CCDS5253.1	6q25.1-q26	2008-05-22			ENSG00000130340	ENSG00000130340		"Sorting nexins"	14973	protein-coding gene	gene with protein product		605952				10531379, 17609109	Standard	NM_016224		Approved	SH3PX1, SDP1, SH3PXD3A	uc003qqv.1	Q9Y5X1	OTTHUMG00000015903	ENST00000392185.3:c.17G>A	chr6.hg19:g.158288583G>A	ENSP00000376024:p.Arg6Gln	99.0	0.0	.		72.0	23.0	.	NM_016224	Q9BSI7|Q9BVM1|Q9UJH6|Q9UP20	Missense_Mutation	SNP	ENST00000392185.3	hg19	CCDS5253.1	.	.	.	.	.	.	.	.	.	.	G	15.69	2.908097	0.52333	.	.	ENSG00000130340	ENST00000539592;ENST00000392185	T	0.24350	1.86	5.22	4.33	0.51752	Src homology-3 domain (3);	0.434714	0.25546	N	0.029934	T	0.11281	0.0275	L	0.42686	1.345	0.80722	D	1	B	0.29936	0.262	B	0.26770	0.073	T	0.03514	-1.1029	10	0.45353	T	0.12	-7.1352	12.8925	0.58080	0.0:0.164:0.836:0.0	.	6	Q9Y5X1	SNX9_HUMAN	Q	6	ENSP00000376024:R6Q	ENSP00000376024:R6Q	R	+	2	0	SNX9	158208571	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	4.078000	0.57606	1.204000	0.43247	0.655000	0.94253	CGG	.	.	.	none		0.393	SNX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042856.1			A	158288583	G	A	158288583	3	1	52	1	0	0	0	0	1	0	0	0	14922	1116	39	1	23	1	SNX9	6	158288583	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	123776507	158288583	12826484	30	3532											
MET	4233	hgsc.bcm.edu	37	chr7	116417463	116417463	+	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	ggcattttggttgtgtatatCatgggactttgttggacaat	8	17	12	4	0	1	0	1	0	0	0	1	2	1	2	0	4	0	4	0	4	3	7	rs121913244		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr7:116417463C>T	ENST00000318493.6	+	16	3521	c.3334C>T	c.(3334-3336)Cat>Tat	p.H1112Y	MET_ENST00000397752.3_Missense_Mutation_p.H1094Y|MET_ENST00000539704.1_5'UTR			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.H1112Y(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)			TTGTGTATATCATGGGACTTT	0.343			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.H1112Y		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,colon,carcinoma,0,2	MET	412	.	1	Substitution - Missense(1)	kidney(1)	c.C3334T	GRCh37	CM993668	MET	M	rs121913244	PASS	.						188	175	179					7																	116417463		1832	4086	5918	SO:0001583	missense	4233	exon16	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	GTATATCATGGGA	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.3334C>T	chr7.hg19:g.116417463C>T	ENSP00000317272:p.His1112Tyr	199.0	0.0	.		276.0	144.0	.	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.615896	0.87359	.	.	ENSG00000105976	ENST00000397752;ENST00000318493	T;T	0.33654	1.4;1.4	5.29	5.29	0.74685	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	0.43919	0.1269	N	0.11364	0.135	0.80722	D	1	P;D	0.89917	0.937;1.0	P;D	0.91635	0.854;0.999	T	0.52711	-0.8539	10	0.51188	T	0.08	-16.8984	19.2953	0.94119	0.0:1.0:0.0:0.0	.	1112;1094	P08581-2;P08581	.;MET_HUMAN	Y	1094;1112	ENSP00000380860:H1094Y;ENSP00000317272:H1112Y	ENSP00000317272:H1112Y	H	+	1	0	MET	116204699	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.776000	0.85560	2.628000	0.89032	0.655000	0.94253	CAT	.	.	.	weak		0.343	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			T	116417463	C	T	116417463	3	4	52	1	0	0	0	0	1	0	0	0	9492	826	29	2	3392	2	MET	7	116417463	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08		116417463	42721200	31	3533											
CTTNBP2	83992	hgsc.bcm.edu	37	chr7	117365303	117365303	+	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	tgacgccattccacagcttaGacatccacctagcaggagag	12	7	9	13	1	0	3	0	1	0	2	2	4	2	3	4	1	2	2	4	1	2	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr7:117365303G>C	ENST00000160373.3	-	18	4155	c.4064C>G	c.(4063-4065)tCt>tGt	p.S1355C		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1355					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)		CCACAGCTTAGACATCCACCT	0.468																																					p.S1355C		Atlas-SNP	.											.	CTTNBP2	200	.	0			c.C4064G						PASS	.						138	134	135					7																	117365303		2203	4300	6503	SO:0001583	missense	83992	exon18			AGCTTAGACATCC		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.4064C>G	chr7.hg19:g.117365303G>C	ENSP00000160373:p.Ser1355Cys	192.0	0.0	.		326.0	72.0	.	NM_033427	O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	hg19	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	G	15.54	2.864762	0.51482	.	.	ENSG00000077063	ENST00000160373	D	0.91068	-2.78	5.72	5.72	0.89469	.	0.267144	0.43416	D	0.000578	D	0.87557	0.6207	L	0.41824	1.3	0.80722	D	1	B	0.14012	0.009	B	0.15484	0.013	T	0.81274	-0.1007	10	0.23891	T	0.37	9.6033	20.244	0.98389	0.0:0.0:1.0:0.0	.	1355	Q8WZ74	CTTB2_HUMAN	C	1355	ENSP00000160373:S1355C	ENSP00000160373:S1355C	S	-	2	0	CTTNBP2	117152539	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.149000	0.71795	2.865000	0.98341	0.655000	0.94253	TCT	.	.	.	none		0.468	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		C	117365303	G	C	117365303	3	2	52	1	0	0	0	0	1	0	0	0	4047	942	33	4	951	4	CTTNBP2	7	117365303	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	947840	117365303	41773360	32	3534											
MLL3	58508	hgsc.bcm.edu	37	chr7	151917756	151917756	+	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	ggaactgtaactgtgaggctCtgtaactgagtcatccctga	10	11	11	9	0	2	3	1	3	1	0	3	4	3	4	1	2	3	3	1	2	3	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr7:151917756C>A	ENST00000262189.6	-	23	3782	c.3564G>T	c.(3562-3564)caG>caT	p.Q1188H	KMT2C_ENST00000355193.2_Missense_Mutation_p.Q1188H	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1188					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)										CTGTGAGGCTCTGTAACTGAG	0.408																																					p.Q1188H		Atlas-SNP	.											.	MLL3	1564	.	0			c.G3564T						PASS	.						72	69	70					7																	151917756		2203	4298	6501	SO:0001583	missense	58508	exon23			GAGGCTCTGTAAC	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.3564G>T	chr7.hg19:g.151917756C>A	ENSP00000262189:p.Gln1188His	118.0	0.0	.		163.0	71.0	.	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	15.83	2.948672	0.53186	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.85171	-1.95;-1.95	4.44	3.56	0.40772	.	0.000000	0.41605	U	0.000856	D	0.89763	0.6809	L	0.56769	1.78	0.80722	D	1	D;D	0.76494	0.996;0.999	D;D	0.75484	0.986;0.971	D	0.89849	0.4008	10	0.66056	D	0.02	.	12.545	0.56195	0.0:0.9173:0.0:0.0827	.	1188;249	Q8NEZ4;Q8NEZ4-2	MLL3_HUMAN;.	H	1188	ENSP00000262189:Q1188H;ENSP00000347325:Q1188H	ENSP00000262189:Q1188H	Q	-	3	2	MLL3	151548689	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.614000	0.61183	0.976000	0.38417	0.484000	0.47621	CAG	.	.	.	none		0.408	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			A	151917756	C	A	151917756	3	1	52	1	0	0	0	0	1	0	0	0	9629	912	32	4	11319	4	MLL3	7	151917756	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	34552453	151917756	7220907	33	3535											
CDH17	1015	hgsc.bcm.edu	37	chr8	95201459	95201459	+	Missense_Mutation	SNP	A	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	ttggccttcataaatagaaaAtgtcatgggtttcaggggtc	11	13	11	6	0	3	1	3	0	0	1	4	1	3	1	1	4	0	1	1	4	5	5			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr8:95201459A>C	ENST00000027335.3	-	3	230	c.106T>G	c.(106-108)Ttt>Gtt	p.F36V	CDH17_ENST00000450165.2_Missense_Mutation_p.F36V|CDH17_ENST00000441892.2_Missense_Mutation_p.F36V	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	36	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)			NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			TAAATAGAAAATGTCATGGGT	0.403																																					p.F36V		Atlas-SNP	.											.	CDH17	119	.	0			c.T106G						PASS	.						118	120	119					8																	95201459		2203	4300	6503	SO:0001583	missense	1015	exon3			TAGAAAATGTCAT	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"Cadherins / Major cadherins"	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.106T>G	chr8.hg19:g.95201459A>C	ENSP00000027335:p.Phe36Val	102.0	0.0	.		97.0	76.0	.	NM_004063	Q15336|Q2M2E0	Missense_Mutation	SNP	ENST00000027335.3	hg19	CCDS6260.1	.	.	.	.	.	.	.	.	.	.	A	9.966	1.224134	0.22457	.	.	ENSG00000079112	ENST00000027335;ENST00000441892;ENST00000450165;ENST00000521491	T;T;T;T	0.60040	0.26;0.26;0.26;0.22	5.43	5.43	0.79202	Cadherin (1);Cadherin-like (1);	0.000000	0.49305	D	0.000150	T	0.59959	0.2232	L	0.39514	1.22	0.47374	D	0.999407	D;D	0.62365	0.979;0.991	P;P	0.56042	0.622;0.79	T	0.57365	-0.7824	10	0.30854	T	0.27	-19.528	11.8845	0.52594	1.0:0.0:0.0:0.0	.	36;36	E7EN24;Q12864	.;CAD17_HUMAN	V	36	ENSP00000027335:F36V;ENSP00000392811:F36V;ENSP00000401468:F36V;ENSP00000428189:F36V	ENSP00000027335:F36V	F	-	1	0	CDH17	95270635	0.957000	0.32711	0.996000	0.52242	0.606000	0.37113	2.732000	0.47352	2.057000	0.61298	0.482000	0.46254	TTT	.	.	.	none		0.403	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063		C	95201459	A	C	95201459	3	2	52	1	0	0	0	0	1	0	0	0	3104	101	4	5	2456	5	CDH17	8	95201459	Missense_Mutation	SNP	A	TCGA-A4-7997-01A-11D-2201-08		95201459	51162563	34	3536											
BNC2	54796	hgsc.bcm.edu	37	chr9	16419221	16419221	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacaagctgctgaacataagAgatcctgaaacttcagcccc	14	7	8	12	0	1	3	1	2	0	1	2	5	2	3	3	0	5	2	3	0	4	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr9:16419221A>G	ENST00000380672.4	-	7	3123	c.3066T>C	c.(3064-3066)tcT>tcC	p.S1022S	BNC2_ENST00000545497.1_Silent_p.S927S|BNC2_ENST00000380667.2_Silent_p.S955S	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)		TGAACATAAGAGATCCTGAAA	0.547																																					p.S1022S		Atlas-SNP	.											.	BNC2	166	.	0			c.T3066C						PASS	.						81	72	75					9																	16419221		2203	4300	6503	SO:0001819	synonymous_variant	54796	exon7			CATAAGAGATCCT	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.3066T>C	chr9.hg19:g.16419221A>G		100.0	0.0	.		96.0	29.0	.	NM_017637		Silent	SNP	ENST00000380672.4	hg19	CCDS6482.2																																																																																			.	.	.	none		0.547	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637		G	16419221	A	G	16419221	2	3	52	1	0	0	0	0	0	0	0	1	1475	291	11	3		3	BNC2	9	16419221	Silent	SNP	A	TCGA-A4-7997-01A-11D-2201-08		16419221	124794210	35	3537											
GRIN3A	116443	hgsc.bcm.edu	37	chr9	104449145	104449145	+	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	gaagttcagggggcatgaccCcaaactgggttgtaatttcg	10	10	13	8	1	1	1	1	1	0	0	2	2	1	1	2	3	1	4	2	3	3	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr9:104449145C>G	ENST00000361820.3	-	2	1637	c.1037G>C	c.(1036-1038)gGg>gCg	p.G346A		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	346					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)	GGGCATGACCCCAAACTGGGT	0.507																																					p.G346A		Atlas-SNP	.											.	GRIN3A	186	.	0			c.G1037C						PASS	.						66	64	65					9																	104449145		2203	4300	6503	SO:0001583	missense	116443	exon2			ATGACCCCAAACT		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.1037G>C	chr9.hg19:g.104449145C>G	ENSP00000355155:p.Gly346Ala	54.0	0.0	.		68.0	33.0	.	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	hg19	CCDS6758.1	.	.	.	.	.	.	.	.	.	.	C	14.98	2.696202	0.48202	.	.	ENSG00000198785	ENST00000361820	D	0.90732	-2.72	5.83	4.92	0.64577	.	0.942080	0.09021	N	0.860194	D	0.90017	0.6883	L	0.59436	1.845	0.58432	D	0.999992	B	0.28419	0.211	B	0.26864	0.074	D	0.83443	0.0044	10	0.66056	D	0.02	.	15.7632	0.78103	0.1471:0.8529:0.0:0.0	.	346	Q8TCU5	NMD3A_HUMAN	A	346	ENSP00000355155:G346A	ENSP00000355155:G346A	G	-	2	0	GRIN3A	103488966	1.000000	0.71417	0.885000	0.34714	0.653000	0.38743	4.782000	0.62396	1.403000	0.46800	0.563000	0.77884	GGG	.	.	.	none		0.507	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1			G	104449145	C	G	104449145	3	3	52	1	0	0	0	0	1	0	0	0	6790	623	22	4	2342	4	GRIN3A	9	104449145	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	88029924	104449145	36764286	36	3538											
MASTL	84930	hgsc.bcm.edu	37	chr10	27459483	27459483	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accaatgatagcaaaaaaccTtatgtgtgaactcgatgaag	17	9	8	7	1	0	3	0	3	0	0	1	4	0	3	2	0	3	1	2	0	8	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr10:27459483T>C	ENST00000375940.4	+	8	1652	c.1595T>C	c.(1594-1596)cTt>cCt	p.L532P	MASTL_ENST00000375946.4_Missense_Mutation_p.L532P|MASTL_ENST00000477034.1_3'UTR|MASTL_ENST00000342386.6_Missense_Mutation_p.L532P			Q96GX5	GWL_HUMAN	microtubule associated serine/threonine kinase-like	532	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						GCAAAAAACCTTATGTGTGAA	0.313																																					p.L532P		Atlas-SNP	.											.	MASTL	81	.	0			c.T1595C						PASS	.						89	92	91					10																	27459483		2203	4300	6503	SO:0001583	missense	84930	exon8			AAAACCTTATGTG	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.1595T>C	chr10.hg19:g.27459483T>C	ENSP00000365107:p.Leu532Pro	122.0	0.0	.		132.0	46.0	.	NM_032844	Q5T8D5|Q5T8D7|Q8NCD6|Q96SJ5	Missense_Mutation	SNP	ENST00000375940.4	hg19	CCDS53502.1	.	.	.	.	.	.	.	.	.	.	T	15.96	2.985988	0.53934	.	.	ENSG00000120539	ENST00000375946;ENST00000342386;ENST00000375940	T;T;T	0.33654	1.4;1.4;1.4	5.67	5.67	0.87782	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.61590	0.2359	M	0.75264	2.295	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.65957	-0.6042	10	0.87932	D	0	-17.4573	15.9272	0.79628	0.0:0.0:0.0:1.0	.	532;532;532	Q96GX5-2;Q96GX5;Q96GX5-3	.;GWL_HUMAN;.	P	532	ENSP00000365113:L532P;ENSP00000343446:L532P;ENSP00000365107:L532P	ENSP00000343446:L532P	L	+	2	0	MASTL	27499489	1.000000	0.71417	0.861000	0.33841	0.432000	0.31715	6.170000	0.71920	2.153000	0.67306	0.533000	0.62120	CTT	.	.	.	none		0.313	MASTL-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047320.1	NM_032844		C	27459483	T	C	27459483	3	2	52	1	0	0	0	0	1	0	0	0	9335	1609	56	3	1625	3	MASTL	10	27459483	Missense_Mutation	SNP	T	TCGA-A4-7997-01A-11D-2201-08		27459483	108075264	37	3539											
UNC5B	219699	hgsc.bcm.edu	37	chr10	73055666	73055666	+	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	cacaacctgcgcctctccctCcatgacctcccccatgccca	7	7	4	23	1	1	1	0	1	1	0	4	1	3	1	8	0	3	0	8	0	1	0			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr10:73055666C>T	ENST00000335350.6	+	14	2690	c.2274C>T	c.(2272-2274)ctC>ctT	p.L758L	UNC5B_ENST00000373192.4_Silent_p.L747L	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	758	UPA domain. {ECO:0000250}.				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						GCCTCTCCCTCCATGACCTCC	0.612																																					p.L758L		Atlas-SNP	.											.	UNC5B	123	.	0			c.C2274T						PASS	.						133	105	115					10																	73055666		2203	4300	6503	SO:0001819	synonymous_variant	219699	exon14			CTCCCTCCATGAC	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.2274C>T	chr10.hg19:g.73055666C>T		116.0	0.0	.		116.0	46.0	.	NM_170744	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Silent	SNP	ENST00000335350.6	hg19	CCDS7309.1																																																																																			.	.	.	none		0.612	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744		T	73055666	C	T	73055666	2	4	52	1	0	0	0	0	0	0	0	1	17004	842	30	2		2	UNC5B	10	73055666	Silent	SNP	C	TCGA-A4-7997-01A-11D-2201-08	45596183	73055666	62479081	38	3540											
PIK3C2A	5286	hgsc.bcm.edu	37	chr11	17124313	17124313	+	Missense_Mutation	SNP	A	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	atattgtcattgtgtcgatcAcagatgcctaaaacataggt	13	13	8	7	1	2	1	2	0	0	1	3	2	2	1	1	1	2	0	1	1	4	5			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr11:17124313A>C	ENST00000265970.7	-	23	3746	c.3747T>G	c.(3745-3747)tgT>tgG	p.C1249W	PIK3C2A_ENST00000531428.1_Intron|PIK3C2A_ENST00000540361.1_Missense_Mutation_p.C869W	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	1249	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				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						TGTGTCGATCACAGATGCCTA	0.383																																					p.C1249W		Atlas-SNP	.											.	PIK3C2A	148	.	0			c.T3747G						PASS	.						102	88	93					11																	17124313		2200	4293	6493	SO:0001583	missense	5286	exon23			TCGATCACAGATG	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.3747T>G	chr11.hg19:g.17124313A>C	ENSP00000265970:p.Cys1249Trp	110.0	0.0	.		103.0	37.0	.	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	hg19	CCDS7824.1	.	.	.	.	.	.	.	.	.	.	A	17.56	3.420006	0.62622	.	.	ENSG00000011405	ENST00000265970;ENST00000540361	T;T	0.80909	-1.43;-1.43	5.45	4.32	0.51571	Protein kinase-like domain (1);Phosphatidylinositol 3/4-kinase, conserved site (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.000000	0.85682	D	0.000000	D	0.89199	0.6647	M	0.82517	2.595	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89599	0.3833	10	0.72032	D	0.01	-12.9025	11.3328	0.49485	0.9285:0.0:0.0715:0.0	.	1249	O00443	P3C2A_HUMAN	W	1249;869	ENSP00000265970:C1249W;ENSP00000438687:C869W	ENSP00000265970:C1249W	C	-	3	2	PIK3C2A	17080889	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.320000	0.51991	1.021000	0.39600	0.533000	0.62120	TGT	.	.	.	none		0.383	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		C	17124313	A	C	17124313	3	2	52	1	0	0	0	0	1	0	0	0	11916	157	6	5	1353	5	PIK3C2A	11	17124313	Missense_Mutation	SNP	A	TCGA-A4-7997-01A-11D-2201-08		17124313	117882203	39	3541											
ENDOD1	23052	hgsc.bcm.edu	37	chr11	94823276	94823276	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgtcagcgcgcggagggtgCtgagcgcttcgccaccctct	4	8	14	15	5	2	1	1	1	1	0	3	2	2	2	2	2	3	2	2	2	0	1			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr11:94823276C>T	ENST00000278505.4	+	1	303	c.185C>T	c.(184-186)gCt>gTt	p.A62V		NM_015036.2	NP_055851.1	O94919	ENDD1_HUMAN	endonuclease domain containing 1	62						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)				GCGGAGGGTGCTGAGCGCTTC	0.716																																					p.A62V		Atlas-SNP	.											.	ENDOD1	26	.	0			c.C185T						PASS	.						12	17	15					11																	94823276		1882	4102	5984	SO:0001583	missense	23052	exon1			AGGGTGCTGAGCG	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.185C>T	chr11.hg19:g.94823276C>T	ENSP00000278505:p.Ala62Val	15.0	0.0	.		17.0	7.0	.	NM_015036	A8K6K8|Q6GQY5|Q8TAQ8	Missense_Mutation	SNP	ENST00000278505.4	hg19	CCDS41699.1	.	.	.	.	.	.	.	.	.	.	C	13.98	2.399463	0.42512	.	.	ENSG00000149218	ENST00000278505	T	0.69306	-0.39	4.43	1.23	0.21249	DNA/RNA non-specific endonuclease (1);Extracellular Endonuclease, subunit A (2);	1.135320	0.06834	N	0.794557	T	0.55800	0.1943	L	0.36672	1.1	0.09310	N	0.999999	B	0.33413	0.411	B	0.40165	0.321	T	0.50206	-0.8855	10	0.28530	T	0.3	-13.357	2.0739	0.03619	0.3599:0.396:0.1335:0.1106	.	62	O94919	ENDD1_HUMAN	V	62	ENSP00000278505:A62V	ENSP00000278505:A62V	A	+	2	0	ENDOD1	94462924	0.076000	0.21285	0.977000	0.42913	0.495000	0.33615	0.653000	0.24902	0.848000	0.35191	0.585000	0.79938	GCT	.	.	.	none		0.716	ENDOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396545.1	NM_015036		T	94823276	C	T	94823276	3	4	52	1	0	0	0	0	1	0	0	0	5116	797	28	2	187	2	ENDOD1	11	94823276	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	77698963	94823276	40183240	40	3542											
ATM	472	hgsc.bcm.edu	37	chr11	108155202	108155202	+	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	aaacttattgggaaaacaggTatggcttcaatttttatgta	14	15	8	4	0	1	0	1	0	0	0	1	1	1	1	0	3	2	3	0	3	8	8			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr11:108155202T>C	ENST00000452508.2	+	27	4182		c.e27+2		ATM_ENST00000278616.4_Splice_Site			Q13315	ATM_HUMAN	ATM serine/threonine kinase						brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	GGAAAACAGGTATGGCTTCAA	0.348			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																											.		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	ATM_ENST00000278616,colon,carcinoma,0,2	ATM	1657	.	0			c.3993+2T>C						PASS	.						93	90	91					11																	108155202		2201	4298	6499	SO:0001630	splice_region_variant	472	exon26	Familial Cancer Database	AT, Louis-Bar syndrome	AACAGGTATGGCT	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.3993+2T>C	chr11.hg19:g.108155202T>C		107.0	0.0	.		96.0	34.0	.	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Splice_Site	SNP	ENST00000452508.2	hg19	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	T	17.13	3.311730	0.60414	.	.	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508;ENST00000531525	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4694	0.75429	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ATM	107660412	1.000000	0.71417	0.998000	0.56505	0.827000	0.46813	7.450000	0.80656	2.070000	0.61991	0.455000	0.32223	.	.	.	.	none		0.348	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	Intron	C	108155202	T	C	108155202	5	2	52	1	0	0	0	0	0	0	1	0	1109	1652	57	3	4093	3	ATM	11	108155202	Splice_Site	SNP	T	TCGA-A4-7997-01A-11D-2201-08	13331926	108155202	26851314	41	3543											
VWF	7450	hgsc.bcm.edu	37	chr12	6138619	6138619	+	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	ccagactccaccacctcaaaGtgagtctcatccttcatggg	10	9	7	15	0	3	2	3	1	1	1	6	2	5	2	5	1	0	0	5	1	1	1			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr12:6138619G>A	ENST00000261405.5	-	22	3110	c.2856C>T	c.(2854-2856)caC>caT	p.H952H		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	952	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)	CCACCTCAAAGTGAGTCTCAT	0.572																																					p.H952H		Atlas-SNP	.											.	VWF	338	.	0			c.C2856T						PASS	.						108	95	99					12																	6138619		2203	4300	6503	SO:0001819	synonymous_variant	7450	exon22			CTCAAAGTGAGTC		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.2856C>T	chr12.hg19:g.6138619G>A		108.0	0.0	.		126.0	76.0	.	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	hg19	CCDS8539.1																																																																																			.	.	.	none		0.572	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		A	6138619	G	A	6138619	2	1	52	1	0	0	0	0	0	0	0	1	17258	1020	36	2		2	VWF	12	6138619	Silent	SNP	G	TCGA-A4-7997-01A-11D-2201-08		6138619	127713276	42	3544											
LRRC23	10233	hgsc.bcm.edu	37	chr12	7014840	7014840	+	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	aagactctgagccagaccagGatgattctgagaaagaagag	16	6	12	7	0	2	7	0	3	2	5	2	9	2	8	2	1	1	0	2	1	3	1			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr12:7014840G>C	ENST00000007969.8	+	2	263	c.43G>C	c.(43-45)Gat>Cat	p.D15H	LRRC23_ENST00000433346.1_Missense_Mutation_p.D15H|LRRC23_ENST00000449039.1_3'UTR|LRRC23_ENST00000443597.2_Missense_Mutation_p.D15H|LRRC23_ENST00000436789.1_Missense_Mutation_p.D15H|LRRC23_ENST00000429740.1_Missense_Mutation_p.D15H|LRRC23_ENST00000323702.5_Missense_Mutation_p.D15H	NM_001135217.1|NM_201650.2	NP_001128689.1|NP_964013.1	Q53EV4	LRC23_HUMAN	leucine rich repeat containing 23	15										NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|stomach(1)	13						GCCAGACCAGGATGATTCTga	0.498																																					p.D15H		Atlas-SNP	.											.	LRRC23	46	.	0			c.G43C						PASS	.						70	74	73					12																	7014840		2203	4300	6503	SO:0001583	missense	10233	exon2			GACCAGGATGATT	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.43G>C	chr12.hg19:g.7014840G>C	ENSP00000007969:p.Asp15His	120.0	0.0	.		148.0	43.0	.	NM_001135217	A8K8C6|D3DUT1|Q8N6K6|Q92977|Q99620	Missense_Mutation	SNP	ENST00000007969.8	hg19	CCDS8569.1	.	.	.	.	.	.	.	.	.	.	G	12.33	1.906459	0.33628	.	.	ENSG00000010626	ENST00000433346;ENST00000007969;ENST00000323702;ENST00000443597;ENST00000415834;ENST00000436789;ENST00000429740	T;T;T;T;T;T;T	0.71461	1.55;-0.26;-0.57;-0.26;0.55;1.6;1.19	4.74	4.74	0.60224	.	.	.	.	.	T	0.79088	0.4387	L	0.60455	1.87	0.47698	D	0.999497	D;D;D;D	0.69078	0.997;0.997;0.984;0.991	D;P;P;P	0.63877	0.919;0.884;0.769;0.769	T	0.80533	-0.1340	9	0.62326	D	0.03	-12.2314	13.0943	0.59182	0.0:0.0:1.0:0.0	.	15;15;15;15	E9PDZ4;Q53EV4-2;Q53EV4;C9JKE8	.;.;LRC23_HUMAN;.	H	15	ENSP00000402554:D15H;ENSP00000007969:D15H;ENSP00000317464:D15H;ENSP00000390932:D15H;ENSP00000408066:D15H;ENSP00000396049:D15H;ENSP00000397192:D15H	ENSP00000007969:D15H	D	+	1	0	LRRC23	6885101	0.995000	0.38212	0.960000	0.40013	0.183000	0.23260	2.632000	0.46511	2.452000	0.82932	0.561000	0.74099	GAT	.	.	.	none		0.498	LRRC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345214.1	NM_006992		C	7014840	G	C	7014840	3	2	52	1	0	0	0	0	1	0	0	0	8985	1174	41	4	45	4	LRRC23	12	7014840	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	876221	7014840	126837055	43	3545											
MLL2	8085	hgsc.bcm.edu	37	chr12	49416134	49416134	+	Missense_Mutation	SNP	A	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	cggaacatgtagatgcctcgAttctagaaaggcagaggttg	12	9	13	7	2	1	3	0	0	1	3	2	5	1	4	1	3	2	3	1	3	4	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr12:49416134A>C	ENST00000301067.7	-	52	16340	c.16341T>G	c.(16339-16341)aaT>aaG	p.N5447K		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	5447	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)										AGATGCCTCGATTCTAGAAAG	0.512																																					p.N5447K		Atlas-SNP	.											.	MLL2	1173	.	0			c.T16341G						PASS	.						45	44	44					12																	49416134		2076	4217	6293	SO:0001583	missense	8085	exon52			GCCTCGATTCTAG	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.16341T>G	chr12.hg19:g.49416134A>C	ENSP00000301067:p.Asn5447Lys	21.0	0.0	.		26.0	14.0	.	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	A	13.01	2.109690	0.37242	.	.	ENSG00000167548	ENST00000301067;ENST00000526209	T;T	0.80824	-1.42;-1.42	5.11	0.159	0.14968	SET domain (3);	0.000000	0.38326	N	0.001723	D	0.85013	0.5600	L	0.60067	1.865	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.82888	-0.0234	10	0.87932	D	0	.	10.057	0.42250	0.4781:0.0:0.5219:0.0	.	5447	O14686	MLL2_HUMAN	K	5447;128	ENSP00000301067:N5447K;ENSP00000435714:N128K	ENSP00000301067:N5447K	N	-	3	2	MLL2	47702401	1.000000	0.71417	0.997000	0.53966	0.985000	0.73830	1.117000	0.31234	-0.129000	0.11620	-0.256000	0.11100	AAT	.	.	.	none		0.512	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			C	49416134	A	C	49416134	3	2	52	1	0	0	0	0	1	0	0	0	9628	330	12	5	284	5	MLL2	12	49416134	Missense_Mutation	SNP	A	TCGA-A4-7997-01A-11D-2201-08	42401294	49416134	84435761	44	3546											
ULK1	8408	hgsc.bcm.edu	37	chr12	132405713	132405713	+	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	gtcccacgctaccacaaggcCctgctgctcctggaggggct	6	7	12	16	1	0	0	0	0	0	0	2	1	2	1	4	4	3	4	4	4	2	1			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr12:132405713C>G	ENST00000321867.4	+	27	3381	c.3030C>G	c.(3028-3030)gcC>gcG	p.A1010A	ULK1_ENST00000540647.1_Silent_p.A255A	NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	1010					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)		ACCACAAGGCCCTGCTGCTCC	0.677																																					p.A1010A		Atlas-SNP	.											.	ULK1	92	.	0			c.C3030G						PASS	.						54	52	53					12																	132405713		2203	4299	6502	SO:0001819	synonymous_variant	8408	exon27			CAAGGCCCTGCTG	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.3030C>G	chr12.hg19:g.132405713C>G		89.0	0.0	.		96.0	53.0	.	NM_003565	Q9UQ28	Silent	SNP	ENST00000321867.4	hg19	CCDS9274.1																																																																																			.	.	.	none		0.677	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3			G	132405713	C	G	132405713	2	3	52	1	0	0	0	0	0	0	0	1	16987	610	22	4		4	ULK1	12	132405713	Silent	SNP	C	TCGA-A4-7997-01A-11D-2201-08	82989579	132405713	1446182	45	3547											
SSTR1	6751	hgsc.bcm.edu	37	chr14	38678657	38678657	+	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	agccccagcccgggcagctgCggcgaaggcggcggcagcag	7	1	18	15	5	0	0	0	0	0	0	0	1	0	0	3	5	5	4	3	5	1	0			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr14:38678657C>G	ENST00000267377.2	+	3	680	c.63C>G	c.(61-63)tgC>tgG	p.C21W		NM_001049.2	NP_001040.1	P30872	SSR1_HUMAN	somatostatin receptor 1	21					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)	p.C21C(1)		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)	CGGGCAGCTGCGGCGAAGGCG	0.736																																					p.C21W		Atlas-SNP	.											SSTR1,brain,glioma,0,1	SSTR1	66	.	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C63G						PASS	.						12	13	13					14																	38678657		2183	4234	6417	SO:0001583	missense	6751	exon3			CAGCTGCGGCGAA		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.63C>G	chr14.hg19:g.38678657C>G	ENSP00000267377:p.Cys21Trp	28.0	0.0	.		13.0	2.0	.	NM_001049		Missense_Mutation	SNP	ENST00000267377.2	hg19	CCDS9666.1	.	.	.	.	.	.	.	.	.	.	C	11.34	1.608924	0.28623	.	.	ENSG00000139874	ENST00000267377	T	0.70045	-0.45	5.17	1.05	0.20165	.	0.310059	0.23375	N	0.048870	T	0.36496	0.0969	N	0.08118	0	0.39683	D	0.970939	P	0.35700	0.516	B	0.24541	0.054	T	0.12528	-1.0544	10	0.37606	T	0.19	.	8.1652	0.31222	0.0:0.6547:0.0:0.3453	.	21	P30872	SSR1_HUMAN	W	21	ENSP00000267377:C21W	ENSP00000267377:C21W	C	+	3	2	SSTR1	37748408	0.002000	0.14202	0.877000	0.34402	0.931000	0.56810	0.205000	0.17356	0.016000	0.14998	0.563000	0.77884	TGC	.	.	.	none		0.736	SSTR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409930.2			G	38678657	C	G	38678657	3	3	52	1	0	0	0	0	1	0	0	0	15209	776	27	4	65	4	SSTR1	14	38678657	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08		38678657	68670883	46	3548											
ARID4A	5926	hgsc.bcm.edu	37	chr14	58827680	58827680	+	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	gaggcagaagtcaaaacgggGacgacctcctttaaaatcaa	16	6	10	9	2	2	1	2	0	0	1	3	4	3	2	2	3	1	1	2	3	6	2	rs145426502		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr14:58827680G>C	ENST00000355431.3	+	19	2373	c.2000G>C	c.(1999-2001)gGa>gCa	p.G667A	ARID4A_ENST00000348476.3_Missense_Mutation_p.G667A|ARID4A_ENST00000395168.3_Missense_Mutation_p.G667A|ARID4A_ENST00000431317.2_Missense_Mutation_p.G667A	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	667					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						TCAAAACGGGGACGACCTCCT	0.443																																					p.G667A		Atlas-SNP	.											.	ARID4A	222	.	0			c.G2000C						PASS	.						172	159	163					14																	58827680		2203	4300	6503	SO:0001583	missense	5926	exon19			AACGGGGACGACC	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.2000G>C	chr14.hg19:g.58827680G>C	ENSP00000347602:p.Gly667Ala	105.0	0.0	.		99.0	14.0	.	NM_002892	Q15991|Q15992|Q15993	Missense_Mutation	SNP	ENST00000355431.3	hg19	CCDS9732.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.723941	0.89298	.	.	ENSG00000032219	ENST00000355431;ENST00000348476;ENST00000395168;ENST00000431317;ENST00000417477	T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96	5.71	5.71	0.89125	Chromo domain-like (1);	0.105040	0.64402	D	0.000004	T	0.56124	0.1964	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	0.999;0.998;0.999	T	0.49790	-0.8902	10	0.35671	T	0.21	-26.8249	19.8505	0.96738	0.0:0.0:1.0:0.0	.	667;667;667	P29374-3;P29374;P29374-2	.;ARI4A_HUMAN;.	A	667;667;667;667;345	ENSP00000347602:G667A;ENSP00000344556:G667A;ENSP00000378597:G667A;ENSP00000397368:G667A;ENSP00000416053:G345A	ENSP00000344556:G667A	G	+	2	0	ARID4A	57897433	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.225000	0.78051	2.688000	0.91661	0.655000	0.94253	GGA	.	G|1.000;A|0.000	.	alt		0.443	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001		C	58827680	G	C	58827680	3	2	52	1	0	0	0	0	1	0	0	0	919	1174	41	4	2070	4	ARID4A	14	58827680	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	20149023	58827680	48521860	47	3549											
CDAN1	146059	hgsc.bcm.edu	37	chr15	43023981	43023981	+	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	actcaacacatctggggcctCgcccaagacggtgcccccag	9	5	10	17	2	2	1	1	0	1	1	3	1	2	1	4	3	2	0	4	3	2	0			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr15:43023981C>T	ENST00000356231.3	-	11	1599	c.1576G>A	c.(1576-1578)Gag>Aag	p.E526K		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	526					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)		TCTGGGGCCTCGCCCAAGACG	0.587																																					p.E526K		Atlas-SNP	.											.	CDAN1	70	.	0			c.G1576A						PASS	.						38	42	41					15																	43023981		2203	4299	6502	SO:0001583	missense	146059	exon11			GGGCCTCGCCCAA	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.1576G>A	chr15.hg19:g.43023981C>T	ENSP00000348564:p.Glu526Lys	102.0	0.0	.		103.0	35.0	.	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Missense_Mutation	SNP	ENST00000356231.3	hg19	CCDS32209.1	.	.	.	.	.	.	.	.	.	.	c	21.0	4.074758	0.76415	.	.	ENSG00000140326	ENST00000356231;ENST00000267892	D	0.90324	-2.65	5.9	4.99	0.66335	.	0.297879	0.39020	N	0.001487	D	0.92708	0.7682	M	0.65975	2.015	0.44432	D	0.997352	D	0.71674	0.998	P	0.54312	0.748	D	0.93041	0.6457	10	0.59425	D	0.04	-19.189	15.0277	0.71682	0.0:0.9321:0.0:0.0679	.	526	Q8IWY9	CDAN1_HUMAN	K	526;524	ENSP00000348564:E526K	ENSP00000267892:E524K	E	-	1	0	CDAN1	40811273	1.000000	0.71417	0.246000	0.24233	0.217000	0.24651	7.039000	0.76544	1.511000	0.48818	0.651000	0.88453	GAG	.	.	.	none		0.587	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300		T	43023981	C	T	43023981	3	4	52	1	0	0	0	0	1	0	0	0	3056	893	31	1	2179	1	CDAN1	15	43023981	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08		43023981	59507411	48	3550											
GNB5	10681	hgsc.bcm.edu	37	chr15	52446239	52446239	+	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	ctggtcttcatgacaaactgCcccagggcctccacccgctc	7	8	8	18	1	2	1	1	1	1	0	4	1	3	1	5	2	2	1	5	2	1	1			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr15:52446239C>T	ENST00000261837.7	-	4	338	c.273G>A	c.(271-273)ggG>ggA	p.G91G	GNB5_ENST00000560116.1_Silent_p.G49G|GNB5_ENST00000396335.4_Silent_p.G49G|GNB5_ENST00000358784.7_Silent_p.G49G	NM_016194.3	NP_057278.2	O14775	GBB5_HUMAN	guanine nucleotide binding protein (G protein), beta 5	91					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)		TGACAAACTGCCCCAGGGCCT	0.572																																					p.G91G		Atlas-SNP	.											.	GNB5	28	.	0			c.G273A						PASS	.						115	95	102					15																	52446239		2195	4293	6488	SO:0001819	synonymous_variant	10681	exon4			AAACTGCCCCAGG	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.273G>A	chr15.hg19:g.52446239C>T		80.0	0.0	.		57.0	17.0	.	NM_016194	B2RBR5|Q9HAU9|Q9UFT3	Silent	SNP	ENST00000261837.7	hg19	CCDS10149.1																																																																																			.	.	.	none		0.572	GNB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254842.1			T	52446239	C	T	52446239	2	4	52	1	0	0	0	0	0	0	0	1	6528	726	26	2		2	GNB5	15	52446239	Silent	SNP	C	TCGA-A4-7997-01A-11D-2201-08	9422258	52446239	50085153	49	3551											
HERC1	8925	hgsc.bcm.edu	37	chr15	64021464	64021464	+	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	tttctccaacactgccattcCaaggactttctttgagcaaa	11	13	5	12	0	2	1	0	1	2	0	4	2	3	2	3	1	3	1	3	1	3	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr15:64021464C>T	ENST00000443617.2	-	16	3212	c.3125G>A	c.(3124-3126)tGg>tAg	p.W1042*		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	1042					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						ACTGCCATTCCAAGGACTTTC	0.363																																					p.W1042X		Atlas-SNP	.											.	HERC1	624	.	0			c.G3125A						PASS	.						43	40	41					15																	64021464		1833	4095	5928	SO:0001587	stop_gained	8925	exon16			CCATTCCAAGGAC	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.3125G>A	chr15.hg19:g.64021464C>T	ENSP00000390158:p.Trp1042*	40.0	0.0	.		25.0	4.0	.	NM_003922	Q8IW65	Nonsense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	C	41	8.909842	0.99000	.	.	ENSG00000103657	ENST00000443617	.	.	.	5.6	5.6	0.85130	.	0.000000	0.64402	U	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	.	19.6131	0.95618	0.0:1.0:0.0:0.0	.	.	.	.	X	1042	.	ENSP00000390158:W1042X	W	-	2	0	HERC1	61808517	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.840000	0.69402	2.652000	0.90054	0.561000	0.74099	TGG	.	.	.	none		0.363	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		T	64021464	C	T	64021464	4	4	52	1	0	0	0	0	0	1	0	0	7064	595	21	2	11712	2	HERC1	15	64021464	Nonsense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	11575225	64021464	38509928	50	3552											
AXIN1	8312	hgsc.bcm.edu	37	chr16	396884	396884	+	Missense_Mutation	SNP	T	T	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	acctttaatgccaacaccttTcccggagcagaaactgtagc	12	9	7	13	1	0	1	0	0	0	1	1	2	1	2	4	1	5	2	4	1	4	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr16:396884T>G	ENST00000262320.3	-	2	513	c.142A>C	c.(142-144)Aaa>Caa	p.K48Q	AXIN1_ENST00000354866.3_Missense_Mutation_p.K48Q|AXIN1_ENST00000481769.1_Intron	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	48					activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				CCAACACCTTTCCCGGAGCAG	0.627											OREG0003698	type=REGULATORY REGION|Gene=AXIN1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.K48Q		Atlas-SNP	.											.	AXIN1	290	.	0			c.A142C						PASS	.						44	44	44					16																	396884		2202	4300	6502	SO:0001583	missense	8312	exon2			CACCTTTCCCGGA	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.142A>C	chr16.hg19:g.396884T>G	ENSP00000262320:p.Lys48Gln	59.0	0.0	.	588	70.0	39.0	.	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Missense_Mutation	SNP	ENST00000262320.3	hg19	CCDS10405.1	.	.	.	.	.	.	.	.	.	.	T	17.68	3.449477	0.63178	.	.	ENSG00000103126	ENST00000262320;ENST00000354866	T;T	0.61980	0.06;0.07	5.34	5.34	0.76211	.	0.138741	0.64402	D	0.000005	T	0.77143	0.4087	M	0.74258	2.255	0.58432	D	0.999991	D;D	0.69078	0.997;0.996	D;P	0.63703	0.917;0.894	T	0.80051	-0.1544	10	0.62326	D	0.03	-17.2364	15.3197	0.74112	0.0:0.0:0.0:1.0	.	48;48	O15169-2;O15169	.;AXIN1_HUMAN	Q	48	ENSP00000262320:K48Q;ENSP00000346935:K48Q	ENSP00000262320:K48Q	K	-	1	0	AXIN1	336885	1.000000	0.71417	0.998000	0.56505	0.388000	0.30384	5.889000	0.69766	2.039000	0.60335	0.533000	0.62120	AAA	.	.	.	none		0.627	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			G	396884	T	G	396884	3	3	52	1	0	0	0	0	1	0	0	0	1236	1792	62	5	2486	5	AXIN1	16	396884	Missense_Mutation	SNP	T	TCGA-A4-7997-01A-11D-2201-08		396884	89957869	51	3553											
HAGH	3029	hgsc.bcm.edu	37	chr16	1869997	1869997	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagcttgaccagtttctcAttcccgccagcatggtccct	6	12	7	16	1	1	1	1	1	1	0	5	1	4	1	5	1	2	3	5	1	0	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr16:1869997A>G	ENST00000397356.3	-	4	739	c.333T>C	c.(331-333)aaT>aaC	p.N111N	HAGH_ENST00000455446.2_Silent_p.N111N|HAGH_ENST00000397353.2_Silent_p.N63N|HAGH_ENST00000566709.1_Silent_p.N63N	NM_005326.4	NP_005317.2	Q16775	GLO2_HUMAN	hydroxyacylglutathione hydrolase	111					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)	CCAGTTTCTCATTCCCGCCAG	0.617																																					p.N111N	Pancreas(55;1048 1176 25227 40124 41333)	Atlas-SNP	.											.	HAGH	20	.	0			c.T333C						PASS	.						95	78	83					16																	1869997		2199	4300	6499	SO:0001819	synonymous_variant	3029	exon4			TTTCTCATTCCCG	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.333T>C	chr16.hg19:g.1869997A>G		122.0	0.0	.		135.0	26.0	.	NM_005326	A8K290|B4DP33|B4DRA7|E7EN93	Silent	SNP	ENST00000397356.3	hg19	CCDS10447.2																																																																																			.	.	.	none		0.617	HAGH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250548.2	NM_005326		G	1869997	A	G	1869997	2	3	52	1	0	0	0	0	0	0	0	1	6952	214	8	3		3	HAGH	16	1869997	Silent	SNP	A	TCGA-A4-7997-01A-11D-2201-08	1473113	1869997	88484756	52	3554											
CREBBP	1387	hgsc.bcm.edu	37	chr16	3807907	3807907	+	Missense_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	aaaacttatagactcgggatGtcttgcgattatagagccag	13	11	10	7	2	1	2	0	0	1	2	2	4	1	3	1	1	3	0	1	1	6	5			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr16:3807907G>A	ENST00000262367.5	-	18	4321	c.3512C>T	c.(3511-3513)aCa>aTa	p.T1171I	CREBBP_ENST00000382070.3_Missense_Mutation_p.T1133I	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1171	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.|Interaction with ASF1A. {ECO:0000269|PubMed:24616510}.				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)		GACTCGGGATGTCTTGCGATT	0.502			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.T1171I		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.C3512T	GRCh37	CI084721	CREBBP	I		PASS	.						148	125	133					16																	3807907		2197	4300	6497	SO:0001583	missense	1387	exon18			CGGGATGTCTTGC	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.3512C>T	chr16.hg19:g.3807907G>A	ENSP00000262367:p.Thr1171Ile	111.0	0.0	.		147.0	39.0	.	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	hg19	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	G	17.01	3.279568	0.59758	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	T;T	0.19669	2.13;2.13	5.59	5.59	0.84812	Bromodomain (6);	0.000000	0.85682	D	0.000000	T	0.45236	0.1332	L	0.56199	1.76	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.83275	0.996;0.996	T	0.26608	-1.0098	10	0.62326	D	0.03	-14.9891	19.5896	0.95503	0.0:0.0:1.0:0.0	.	1201;1171	Q4LE28;Q92793	.;CBP_HUMAN	I	1171;1201;1133	ENSP00000262367:T1171I;ENSP00000371502:T1133I	ENSP00000262367:T1171I	T	-	2	0	CREBBP	3747908	1.000000	0.71417	0.993000	0.49108	0.989000	0.77384	9.731000	0.98807	2.632000	0.89209	0.585000	0.79938	ACA	.	.	.	none		0.502	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		A	3807907	G	A	3807907	3	1	52	1	0	0	0	0	1	0	0	0	3863	1377	48	2	3872	2	CREBBP	16	3807907	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	1937910	3807907	86546846	53	3555											
GLYR1	84656	hgsc.bcm.edu	37	chr16	4895118	4895118	+	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	cacaaagaagcatttctttcCgcgaggtttcttcaagtcct	10	13	7	11	2	3	1	1	0	2	1	5	2	5	1	2	1	1	2	2	1	3	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr16:4895118C>G	ENST00000321919.9	-	3	188	c.112G>C	c.(112-114)Gga>Cga	p.G38R	UBN1_ENST00000262376.6_5'Flank|GLYR1_ENST00000436648.5_Missense_Mutation_p.G38R|UBN1_ENST00000545171.1_5'Flank|GLYR1_ENST00000381983.3_Missense_Mutation_p.G38R|GLYR1_ENST00000591451.1_Missense_Mutation_p.G38R	NM_032569.3	NP_115958	Q49A26	GLYR1_HUMAN	glyoxylate reductase 1 homolog (Arabidopsis)	38	PWWP. {ECO:0000255|PROSITE- ProRule:PRU00162}.				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						CATTTCTTTCCGCGAGGTTTC	0.463																																					p.G38R		Atlas-SNP	.											.	GLYR1	49	.	0			c.G112C						PASS	.						107	118	115					16																	4895118		2197	4300	6497	SO:0001583	missense	84656	exon3			TCTTTCCGCGAGG	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.112G>C	chr16.hg19:g.4895118C>G	ENSP00000322716:p.Gly38Arg	235.0	0.0	.		241.0	118.0	.	NM_032569	B4DL47|C9JJ40|C9JJ60|Q5U632|Q6P1Q2|Q6V3W7|Q9BTI1|Q9BXK2	Missense_Mutation	SNP	ENST00000321919.9	hg19	CCDS10524.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.062788	0.76187	.	.	ENSG00000140632	ENST00000321919;ENST00000381983;ENST00000436648	T;T;T	0.70045	-0.45;-0.45;-0.45	5.25	5.25	0.73442	PWWP (2);	0.000000	0.85682	D	0.000000	T	0.72787	0.3504	N	0.25647	0.755	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	0.72424	-0.4298	10	0.37606	T	0.19	-9.014	17.6028	0.88030	0.0:1.0:0.0:0.0	.	38;38;38	Q49A26-5;Q49A26-3;Q49A26	.;.;GLYR1_HUMAN	R	38	ENSP00000322716:G38R;ENSP00000371413:G38R;ENSP00000390276:G38R	ENSP00000322716:G38R	G	-	1	0	GLYR1	4835119	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	5.931000	0.70113	2.451000	0.82905	0.491000	0.48974	GGA	.	.	.	none		0.463	GLYR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251717.2	NM_032569		G	4895118	C	G	4895118	3	3	52	1	0	0	0	0	1	0	0	0	6490	661	23	4	1605	4	GLYR1	16	4895118	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	1087211	4895118	85459635	54	3556											
PALB2	79728	hgsc.bcm.edu	37	chr16	23646368	23646368	+	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	cttgggcaactgccttcctaGacaagtcattatcttcagtg	9	13	8	11	0	3	1	2	0	1	1	4	1	4	1	2	1	2	1	2	1	4	5			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr16:23646368G>A	ENST00000261584.4	-	4	1651	c.1499C>T	c.(1498-1500)tCt>tTt	p.S500F		NM_024675.3	NP_078951.2	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2	500	DNA-binding (with the preference D loop > dsDNA > ssDNA).				DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|inner cell mass cell proliferation (GO:0001833)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|post-anal tail morphogenesis (GO:0036342)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(3)	55				GBM - Glioblastoma multiforme(48;0.0167)		TGCCTTCCTAGACAAGTCATT	0.473			"F, N, Mis"			"Wilms tumor, medulloblastoma, AML ,breast"		Involved in tolerance or repair of DNA crosslinks																													p.S500F		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.C1499T						PASS	.						146	143	144					16																	23646368		2197	4300	6497	SO:0001583	missense	79728	exon4			TTCCTAGACAAGT		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.1499C>T	chr16.hg19:g.23646368G>A	ENSP00000261584:p.Ser500Phe	194.0	0.0	.		242.0	64.0	.	NM_024675	A6NIE1|Q8N7Y6|Q8ND31|Q9H6W1	Missense_Mutation	SNP	ENST00000261584.4	hg19	CCDS32406.1	.	.	.	.	.	.	.	.	.	.	g	17.98	3.521575	0.64747	.	.	ENSG00000083093	ENST00000261584	T	0.17691	2.26	5.27	1.12	0.20585	.	0.782893	0.11510	N	0.556845	T	0.15955	0.0384	L	0.57536	1.79	0.09310	N	1	B	0.11235	0.004	B	0.12156	0.007	T	0.27606	-1.0069	10	0.46703	T	0.11	-0.048	4.9673	0.14096	0.2567:0.1532:0.5902:0.0	.	500	Q86YC2	PALB2_HUMAN	F	500	ENSP00000261584:S500F	ENSP00000261584:S500F	S	-	2	0	PALB2	23553869	0.000000	0.05858	0.000000	0.03702	0.614000	0.37383	0.098000	0.15189	0.057000	0.16193	-0.121000	0.15023	TCT	.	.	.	none		0.473	PALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435287.2	NM_024675		A	23646368	G	A	23646368	3	1	52	1	0	0	0	0	1	0	0	0	11413	942	33	2	2101	2	PALB2	16	23646368	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	18751250	23646368	66708385	55	3557											
CENPT	80152	hgsc.bcm.edu	37	chr16	67863889	67863889	+	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	catcgtgtaagggctctactTcatcttctccagagacacca	10	11	7	13	1	4	1	1	0	3	1	6	2	4	1	2	1	1	2	2	1	2	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr16:67863889T>A	ENST00000562787.1	-	12	1513	c.965A>T	c.(964-966)gAa>gTa	p.E322V	CENPT_ENST00000440851.2_Missense_Mutation_p.E322V|CENPT_ENST00000219172.3_Missense_Mutation_p.E322V|CENPT_ENST00000562947.1_5'Flank|CENPT_ENST00000564817.1_Missense_Mutation_p.E322V	NM_025082.3	NP_079358.3	Q96BT3	CENPT_HUMAN	centromere protein T	322	Flexible stalk domain. {ECO:0000250}.				chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|lung(6)|urinary_tract(1)	10		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00429)|Epithelial(162;0.019)|all cancers(182;0.124)		GGGCTCTACTTCATCTTCTCC	0.532																																					p.E322V		Atlas-SNP	.											.	CENPT	26	.	0			c.A965T						PASS	.						189	187	188					16																	67863889		2040	4195	6235	SO:0001583	missense	80152	exon12			TCTACTTCATCTT	AK056097	CCDS42182.1	16q22.1	2013-11-05	2006-06-15	2006-06-15		ENSG00000102901			25787	protein-coding gene	gene with protein product		611510	"chromosome 16 open reading frame 56"	C16orf56		16622420, 16622419	Standard	NM_025082		Approved	FLJ13111, CENP-T	uc002eun.4	Q96BT3		ENST00000562787.1:c.965A>T	chr16.hg19:g.67863889T>A	ENSP00000457810:p.Glu322Val	290.0	0.0	.		314.0	79.0	.	NM_025082	Q96I29|Q96IC6|Q96NK9|Q9H901	Missense_Mutation	SNP	ENST00000562787.1	hg19	CCDS42182.1	.	.	.	.	.	.	.	.	.	.	T	10.97	1.502660	0.26949	.	.	ENSG00000102901	ENST00000440851;ENST00000436104;ENST00000219172	T;T	0.43294	0.95;0.95	4.08	-1.05	0.10036	.	0.294496	0.23852	N	0.043925	T	0.23249	0.0562	L	0.29908	0.895	0.26493	N	0.974919	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.09377	0.004;0.002;0.001	T	0.07635	-1.0762	10	0.42905	T	0.14	.	3.7971	0.08744	0.1696:0.5023:0.0:0.3281	.	80;322;322	F5H5A6;Q96BT3;B3KPB2	.;CENPT_HUMAN;.	V	322;80;322	ENSP00000400140:E322V;ENSP00000219172:E322V	ENSP00000219172:E322V	E	-	2	0	CENPT	66421390	0.000000	0.05858	0.023000	0.16930	0.019000	0.09904	-1.893000	0.01609	0.003000	0.14656	-0.313000	0.08912	GAA	.	.	.	none		0.532	CENPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422020.1	NM_025082		A	67863889	T	A	67863889	3	1	52	1	0	0	0	0	1	0	0	0	3244	1783	62	5	740	5	CENPT	16	67863889	Missense_Mutation	SNP	T	TCGA-A4-7997-01A-11D-2201-08	44217521	67863889	22490864	56	3558											
KDM6B	23135	hgsc.bcm.edu	37	chr17	7755333	7755333	+	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	ggcccaggcgactgcgagtgGttcgcggtgcacgagcacta	7	6	16	12	5	0	0	0	0	0	0	1	3	0	0	1	4	3	3	1	4	1	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr17:7755333G>C	ENST00000448097.2	+	18	4561	c.4230G>C	c.(4228-4230)tgG>tgC	p.W1410C	KDM6B_ENST00000254846.5_Missense_Mutation_p.W1410C			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	1410	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				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						ACTGCGAGTGGTTCGCGGTGC	0.627											OREG0024145	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.W1410C		Atlas-SNP	.											.	KDM6B	95	.	0			c.G4230C						PASS	.						93	80	84					17																	7755333		2203	4300	6503	SO:0001583	missense	23135	exon18			CGAGTGGTTCGCG	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.4230G>C	chr17.hg19:g.7755333G>C	ENSP00000412513:p.Trp1410Cys	86.0	0.0	.	644	71.0	14.0	.	NM_001080424	C9IZ40|Q96G33	Missense_Mutation	SNP	ENST00000448097.2	hg19		.	.	.	.	.	.	.	.	.	.	G	14.04	2.416033	0.42817	.	.	ENSG00000132510	ENST00000254846;ENST00000448097	D;D	0.86230	-2.09;-2.09	4.99	3.95	0.45737	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.062767	0.64402	D	0.000002	D	0.95194	0.8442	H	0.95780	3.72	0.80722	D	1	D;B	0.89917	1.0;0.058	D;B	0.97110	1.0;0.064	D	0.95975	0.8973	10	0.87932	D	0	-8.7797	15.1416	0.72615	0.0:0.1428:0.8572:0.0	.	1410;1410	O15054;O15054-1	KDM6B_HUMAN;.	C	1410	ENSP00000254846:W1410C;ENSP00000412513:W1410C	ENSP00000254846:W1410C	W	+	3	0	KDM6B	7696058	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	7.404000	0.79996	2.769000	0.95229	0.561000	0.74099	TGG	.	.	.	none		0.627	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272		C	7755333	G	C	7755333	3	2	52	1	0	0	0	0	1	0	0	0	8145	1270	44	4	4288	4	KDM6B	17	7755333	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08		7755333	73439877	57	3559											
KRT33A	3883	hgsc.bcm.edu	37	chr17	39505660	39505660	+	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	tgcaccacaagcctggcattCtcagacttgctgcacaggat	10	9	9	13	0	1	1	1	0	1	1	2	2	1	2	2	2	4	4	2	2	1	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr17:39505660C>G	ENST00000007735.3	-	2	413	c.369G>C	c.(367-369)gaG>gaC	p.E123D		NM_004138.3	NP_004129.2	O76009	KT33A_HUMAN	keratin 33A	123	Coil 1B.|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)				GCCTGGCATTCTCAGACTTGC	0.478																																					p.E123D		Atlas-SNP	.											.	KRT33A	53	.	0			c.G369C						PASS	.						110	100	104					17																	39505660		2203	4300	6503	SO:0001583	missense	3883	exon2			GGCATTCTCAGAC	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.369G>C	chr17.hg19:g.39505660C>G	ENSP00000007735:p.Glu123Asp	70.0	0.0	.		74.0	32.0	.	NM_004138	B2RA87|Q6NTB9|Q6ZZB9	Missense_Mutation	SNP	ENST00000007735.3	hg19	CCDS11388.1	.	.	.	.	.	.	.	.	.	.	C	12.38	1.920429	0.33908	.	.	ENSG00000006059	ENST00000007735	D	0.89617	-2.54	4.8	4.8	0.61643	Filament (1);	0.000000	0.64402	D	0.000019	D	0.84750	0.5541	L	0.42744	1.35	0.31832	N	0.624605	B	0.22211	0.066	B	0.34385	0.181	T	0.80443	-0.1380	10	0.27082	T	0.32	.	8.7524	0.34626	0.1523:0.572:0.2757:0.0	.	123	O76009	KT33A_HUMAN	D	123	ENSP00000007735:E123D	ENSP00000007735:E123D	E	-	3	2	KRT33A	36759186	0.937000	0.31787	1.000000	0.80357	0.994000	0.84299	0.006000	0.13152	2.643000	0.89663	0.655000	0.94253	GAG	.	.	.	none		0.478	KRT33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257295.1	NM_004138		G	39505660	C	G	39505660	3	3	52	1	0	0	0	0	1	0	0	0	8476	912	32	4	869	4	KRT33A	17	39505660	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	31750327	39505660	41689550	58	3560											
SCRN2	90507	hgsc.bcm.edu	37	chr17	45916322	45916322	+	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	ccgcagctccgggtgttgggCcgagatgtccgtgccaatgc	5	8	15	13	4	0	1	0	0	0	1	2	2	2	1	5	2	3	3	5	2	1	1			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr17:45916322C>A	ENST00000290216.9	-	5	732	c.607G>T	c.(607-609)Gcc>Tcc	p.A203S	SCRN2_ENST00000584123.1_Missense_Mutation_p.A211S|SCRN2_ENST00000407215.3_Missense_Mutation_p.A203S	NM_001145023.1|NM_138355.3	NP_001138495.1|NP_612364.2	Q96FV2	SCRN2_HUMAN	secernin 2	203						extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)			cervix(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	14						GGGTGTTGGGCCGAGATGTCC	0.592																																					p.A203S		Atlas-SNP	.											.	SCRN2	35	.	0			c.G607T						PASS	.						85	89	88					17																	45916322		2203	4300	6503	SO:0001583	missense	90507	exon5			GTTGGGCCGAGAT	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.607G>T	chr17.hg19:g.45916322C>A	ENSP00000290216:p.Ala203Ser	219.0	0.0	.		177.0	57.0	.	NM_138355	A8K3N1|B7Z8S7|E9PBV5|Q96AC3|Q9BU04	Missense_Mutation	SNP	ENST00000290216.9	hg19	CCDS11519.1	.	.	.	.	.	.	.	.	.	.	C	1.216	-0.628224	0.03610	.	.	ENSG00000141295	ENST00000290216;ENST00000407215	T;T	0.20881	2.04;2.04	5.52	5.52	0.82312	.	0.215480	0.47455	D	0.000225	T	0.15392	0.0371	L	0.37630	1.12	0.09310	N	1	B;B;B	0.25850	0.051;0.136;0.051	B;B;B	0.27608	0.081;0.081;0.081	T	0.25606	-1.0127	10	0.07482	T	0.82	-11.1584	11.6628	0.51356	0.0:0.9174:0.0:0.0825	.	203;203;203	E9PBV5;Q96FV2;B7Z8S7	.;SCRN2_HUMAN;.	S	203	ENSP00000290216:A203S;ENSP00000383935:A203S	ENSP00000290216:A203S	A	-	1	0	SCRN2	43271321	0.000000	0.05858	0.026000	0.17262	0.066000	0.16364	0.485000	0.22324	2.588000	0.87417	0.655000	0.94253	GCC	.	.	.	none		0.592	SCRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441383.1	NM_138355		A	45916322	C	A	45916322	3	1	52	1	0	0	0	0	1	0	0	0	13952	739	26	4	704	4	SCRN2	17	45916322	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	6410662	45916322	35278888	59	3561											
NARF	26502	hgsc.bcm.edu	37	chr17	80443450	80443450	+	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	tgctgcagcctatggctttcGaaacatccagaacatgatcc	11	10	8	12	1	0	2	0	1	0	1	3	3	2	2	3	1	5	3	3	1	3	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr17:80443450G>A	ENST00000309794.11	+	10	1247	c.1049G>A	c.(1048-1050)cGa>cAa	p.R350Q	NARF-IT1_ENST00000584012.1_RNA|NARF_ENST00000457415.3_Missense_Mutation_p.R396Q|NARF_ENST00000345415.7_Missense_Mutation_p.R302Q|NARF_ENST00000390006.4_Missense_Mutation_p.R291Q	NM_012336.3|NM_031968.2	NP_036468.1|NP_114174.1	Q9UHQ1	NARF_HUMAN	nuclear prelamin A recognition factor	350						lamin filament (GO:0005638)|nuclear lamina (GO:0005652)|nuclear lumen (GO:0031981)|nucleus (GO:0005634)	lamin binding (GO:0005521)			endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			TATGGCTTTCGAAACATCCAG	0.493																																					p.R350Q		Atlas-SNP	.											.	NARF	51	.	0			c.G1049A						PASS	.						151	133	139					17																	80443450		2203	4300	6503	SO:0001583	missense	26502	exon10			GCTTTCGAAACAT	BC000438	CCDS32777.1, CCDS42403.1, CCDS42404.1	17q25.3	2011-12-19			ENSG00000141562	ENSG00000141562			29916	protein-coding gene	gene with protein product	"iron-only hydrogenase-like protein 2"	605349				10514485, 15667261	Standard	NM_031968		Approved	FLJ10067, DKFZp434G0420, IOP2	uc002kfg.4	Q9UHQ1		ENST00000309794.11:c.1049G>A	chr17.hg19:g.80443450G>A	ENSP00000309899:p.Arg350Gln	156.0	0.0	.		142.0	18.0	.	NM_012336	A6NCJ3|B3KPX2|K4DI98|Q96AY9|Q9BWC6	Missense_Mutation	SNP	ENST00000309794.11	hg19	CCDS32777.1	.	.	.	.	.	.	.	.	.	.	.	16.94	3.261532	0.59431	.	.	ENSG00000141562	ENST00000390006;ENST00000374611;ENST00000309794;ENST00000345415	T;T;T	0.47177	0.85;0.85;0.85	5.32	5.32	0.75619	Iron hydrogenase, large subunit, C-terminal (1);Iron hydrogenase (1);	0.000000	0.85682	D	0.000000	T	0.63355	0.2504	M	0.77406	2.37	0.80722	D	1	D;D;D;P	0.55605	0.972;0.972;0.961;0.895	P;P;P;P	0.54140	0.743;0.743;0.727;0.473	T	0.63332	-0.6661	10	0.33940	T	0.23	-19.4724	17.9724	0.89117	0.0:0.0:1.0:0.0	.	396;302;397;350	Q9UHQ1-2;Q9UHQ1-3;E9PH27;Q9UHQ1	.;.;.;NARF_HUMAN	Q	291;397;350;302	ENSP00000374656:R291Q;ENSP00000309899:R350Q;ENSP00000283996:R302Q	ENSP00000309899:R350Q	R	+	2	0	NARF	78036739	1.000000	0.71417	0.941000	0.38009	0.854000	0.48673	9.273000	0.95719	2.480000	0.83734	0.561000	0.74099	CGA	.	.	.	none		0.493	NARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443573.2	NM_031968		A	80443450	G	A	80443450	3	1	52	1	0	0	0	0	1	0	0	0	10174	1058	37	1	1229	1	NARF	17	80443450	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	34527128	80443450	751760	60	3562											
EPB41L3	23136	hgsc.bcm.edu	37	chr18	5394764	5394764	+	Missense_Mutation	SNP	T	T	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	acatgtcagggtgctgctctTtggcctctttaattgcctga	6	15	10	10	0	3	1	1	1	2	0	3	1	3	1	2	2	3	2	2	2	1	4			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr18:5394764T>G	ENST00000341928.2	-	22	3522	c.3182A>C	c.(3181-3183)aAa>aCa	p.K1061T	EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000540638.2_Missense_Mutation_p.K839T|EPB41L3_ENST00000544123.1_Intron|EPB41L3_ENST00000427684.2_Missense_Mutation_p.K358T|EPB41L3_ENST00000400111.3_Missense_Mutation_p.K839T|EPB41L3_ENST00000542146.1_Missense_Mutation_p.K366T|EPB41L3_ENST00000342933.3_Missense_Mutation_p.K1061T	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	1061	C-terminal (CTD).				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						GTGCTGCTCTTTGGCCTCTTT	0.498																																					p.K1061T		Atlas-SNP	.											.	EPB41L3	222	.	0			c.A3182C						PASS	.						208	171	184					18																	5394764		2203	4300	6503	SO:0001583	missense	23136	exon22			TGCTCTTTGGCCT	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.3182A>C	chr18.hg19:g.5394764T>G	ENSP00000343158:p.Lys1061Thr	133.0	0.0	.		125.0	46.0	.	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	hg19	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.858556	0.91433	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000545076;ENST00000427684;ENST00000542146;ENST00000342933;ENST00000400111	T;D;T;T;T;T	0.85339	-1.48;-1.97;-1.48;-1.48;-1.48;-1.48	5.82	5.82	0.92795	Band 4.1, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.89996	0.6877	L	0.49126	1.545	0.80722	D	1	D;D;D;D;P;D;P	0.89917	1.0;1.0;1.0;1.0;0.66;1.0;0.887	D;D;D;D;B;D;P	0.91635	0.996;0.99;0.994;0.998;0.376;0.999;0.809	D	0.88953	0.3388	10	0.36615	T	0.2	.	16.1814	0.81903	0.0:0.0:0.0:1.0	.	358;366;453;730;839;1061;296	E7EUF8;F5H7W5;B7Z8M8;A8K968;Q9Y2J2-2;Q9Y2J2;B3KT50	.;.;.;.;.;E41L3_HUMAN;.	T	1061;730;730;358;366;1061;839	ENSP00000343158:K1061T;ENSP00000442091:K730T;ENSP00000392195:K358T;ENSP00000442233:K366T;ENSP00000341138:K1061T;ENSP00000382981:K839T	ENSP00000343158:K1061T	K	-	2	0	EPB41L3	5384764	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.991000	0.88244	2.234000	0.73211	0.533000	0.62120	AAA	.	.	.	none		0.498	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		G	5394764	T	G	5394764	3	3	52	1	0	0	0	0	1	0	0	0	5156	1841	64	5	85	5	EPB41L3	18	5394764	Missense_Mutation	SNP	T	TCGA-A4-7997-01A-11D-2201-08		5394764	72682484	61	3563											
STK11	6794	hgsc.bcm.edu	37	chr19	1223168	1223168	+	Missense_Mutation	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	acactcaggacttcacggtgCccggtgagtctggcgggggc	6	7	16	12	3	3	1	2	1	1	0	3	2	3	2	1	6	1	0	1	6	0	1			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr19:1223168C>T	ENST00000326873.7	+	8	2278	c.1105C>T	c.(1105-1107)Ccc>Tcc	p.P369S		NM_000455.4	NP_000446.1	Q15831	STK11_HUMAN	serine/threonine kinase 11	369					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)		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)		CTTCACGGTGCCCGGTGAGTC	0.642		14	"D, Mis, N, F, S"		"NSCLC, pancreatic"	"jejunal harmartoma, ovarian, testicular, pancreatic"			Peutz-Jeghers syndrome	TSP Lung(3;<1E-08)																											p.P369S		Atlas-SNP	.	yes	Rec	yes	Peutz-Jeghers syndrome	19	19p13.3	6794	serine/threonine kinase 11 gene (LKB1)		"E, M, O"	.	STK11	410	.	20	Whole gene deletion(20)	cervix(14)|lung(2)|oesophagus(1)|ovary(1)|kidney(1)|pancreas(1)	c.C1105T						PASS	.						36	45	42					19																	1223168		2094	4215	6309	SO:0001583	missense	6794	exon8	Familial Cancer Database	PJS, Hamartous Intestinal Polyposis	ACGGTGCCCGGTG	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.1105C>T	chr19.hg19:g.1223168C>T	ENSP00000324856:p.Pro369Ser	26.0	0.0	.		23.0	10.0	.	NM_000455	B2RBX7|E7EW76	Missense_Mutation	SNP	ENST00000326873.7	hg19	CCDS45896.1	.	.	.	.	.	.	.	.	.	.	.	15.23	2.770635	0.49680	.	.	ENSG00000118046	ENST00000326873;ENST00000405031	T	0.68181	-0.31	3.66	3.66	0.41972	.	0.115197	0.64402	N	0.000011	T	0.62889	0.2465	M	0.71581	2.175	0.80722	D	1	P	0.40398	0.716	B	0.39339	0.297	T	0.62728	-0.6793	10	0.10636	T	0.68	-19.522	14.5402	0.67987	0.0:1.0:0.0:0.0	.	369	Q15831	STK11_HUMAN	S	369	ENSP00000324856:P369S	ENSP00000324856:P369S	P	+	1	0	STK11	1174168	1.000000	0.71417	1.000000	0.80357	0.216000	0.24613	7.025000	0.76449	1.884000	0.54569	0.313000	0.20887	CCC	.	.	.	none		0.642	STK11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449839.3	NM_000455		T	1223168	C	T	1223168	3	4	52	1	0	0	0	0	1	0	0	0	15299	739	26	2	1135	2	STK11	19	1223168	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08		1223168	57905815	62	3564											
ZNF433	163059	hgsc.bcm.edu	37	chr19	12126384	12126384	+	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	gtgtttgaaggagtgaggcaGatctgaaggctttcccacat	10	11	13	7	0	1	4	0	3	1	1	2	5	2	5	1	3	0	3	1	3	2	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr19:12126384G>T	ENST00000344980.6	-	4	1468	c.1298C>A	c.(1297-1299)tCt>tAt	p.S433Y	CTD-2006C1.2_ENST00000406892.2_RNA|CTD-2006C1.2_ENST00000495324.1_RNA|ZNF433_ENST00000419886.2_Missense_Mutation_p.S398Y|CTD-2006C1.2_ENST00000476474.1_RNA	NM_001080411.1	NP_001073880.1	Q8N7K0	ZN433_HUMAN	zinc finger protein 433	433					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						GAGTGAGGCAGATCTGAAGGC	0.418																																					p.S433Y		Atlas-SNP	.											.	ZNF433	49	.	0			c.C1298A						PASS	.						93	97	96					19																	12126384		2202	4300	6502	SO:0001583	missense	163059	exon4			GAGGCAGATCTGA	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.1298C>A	chr19.hg19:g.12126384G>T	ENSP00000339767:p.Ser433Tyr	128.0	0.0	.		118.0	34.0	.	NM_001080411	Q86VX3	Missense_Mutation	SNP	ENST00000344980.6	hg19	CCDS45983.1	.	.	.	.	.	.	.	.	.	.	G	1.694	-0.503274	0.04261	.	.	ENSG00000197647	ENST00000419886;ENST00000344980	T;T	0.06608	3.28;3.28	1.18	-2.37	0.06643	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06462	0.0166	L	0.45744	1.44	0.09310	N	1	D	0.56746	0.977	P	0.53224	0.721	T	0.16217	-1.0410	9	0.02654	T	1	.	0.9392	0.01351	0.1557:0.2904:0.2991:0.2549	.	433	Q8N7K0	ZN433_HUMAN	Y	398;433	ENSP00000393416:S398Y;ENSP00000339767:S433Y	ENSP00000339767:S433Y	S	-	2	0	ZNF433	11987384	0.000000	0.05858	0.000000	0.03702	0.881000	0.50899	-3.866000	0.00347	-1.541000	0.01727	0.298000	0.19748	TCT	.	.	.	none		0.418	ZNF433-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403716.1	NM_152602		T	12126384	G	T	12126384	3	4	52	1	0	0	0	0	1	0	0	0	17919	942	33	4	727	4	ZNF433	19	12126384	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	10903216	12126384	47002599	63	3565											
KIAA1683	80726	hgsc.bcm.edu	37	chr19	18368726	18368726	+	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	gcgccaggtagccacggacgCccgcctggatagtgatcact	8	6	13	14	4	1	1	1	1	0	0	1	3	1	3	4	3	1	1	4	3	2	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr19:18368726C>G	ENST00000600328.3	-	4	3000	c.2807G>C	c.(2806-2808)gGc>gCc	p.G936A	PDE4C_ENST00000596647.1_5'Flank|KIAA1683_ENST00000392413.4_Missense_Mutation_p.G1123A|KIAA1683_ENST00000600359.3_Missense_Mutation_p.G890A|PDE4C_ENST00000355502.3_5'Flank			Q9H0B3	K1683_HUMAN	KIAA1683	936	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						GCCACGGACGCCCGCCTGGAT	0.672																																					p.G1123A		Atlas-SNP	.											.	KIAA1683	190	.	0			c.G3368C						PASS	.						51	53	52					19																	18368726		2201	4295	6496	SO:0001583	missense	80726	exon4			CGGACGCCCGCCT	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.2807G>C	chr19.hg19:g.18368726C>G	ENSP00000470780:p.Gly936Ala	121.0	0.0	.		127.0	41.0	.	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	hg19	CCDS32958.1	.	.	.	.	.	.	.	.	.	.	C	8.574	0.880834	0.17467	.	.	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634;ENST00000392412;ENST00000411671	T;T;T	0.21932	1.98;1.98;1.98	4.33	-0.667	0.11395	.	0.473857	0.15866	N	0.240773	T	0.09992	0.0245	N	0.10972	0.075	0.09310	N	1	B;P	0.38148	0.101;0.62	B;P	0.45610	0.073;0.487	T	0.16988	-1.0384	10	0.16896	T	0.51	-0.3503	0.5212	0.00612	0.1866:0.3422:0.2124:0.2589	.	1123;936	E9PDE0;Q9H0B3	.;K1683_HUMAN	A	1123;936;890;200;550	ENSP00000376213:G1123A;ENSP00000352774:G936A;ENSP00000404501:G890A	ENSP00000352774:G936A	G	-	2	0	KIAA1683	18229726	0.000000	0.05858	0.002000	0.10522	0.074000	0.17049	0.457000	0.21875	0.249000	0.21456	0.313000	0.20887	GGC	.	.	.	none		0.672	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3			G	18368726	C	G	18368726	3	3	52	1	0	0	0	0	1	0	0	0	8258	739	26	4	739	4	KIAA1683	19	18368726	Missense_Mutation	SNP	C	TCGA-A4-7997-01A-11D-2201-08	6242342	18368726	40760257	64	3566											
ZNF681	148213	hgsc.bcm.edu	37	chr19	23927146	23927146	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggtgtgaggacttgttaaaAgctttgccacattcttcaca	11	13	9	8	0	2	1	1	1	1	0	2	2	2	2	1	2	2	2	1	2	2	5			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr19:23927146A>G	ENST00000402377.3	-	4	1347	c.1206T>C	c.(1204-1206)gcT>gcC	p.A402A	ZNF681_ENST00000395385.3_Silent_p.A333A	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	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)|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)				ACTTGTTAAAAGCTTTGCCAC	0.398																																					p.A402A		Atlas-SNP	.											ZNF681,bladder,carcinoma,0,8	ZNF681	76	.	0			c.T1206C						PASS	.						69	74	72					19																	23927146		2203	4300	6503	SO:0001819	synonymous_variant	148213	exon4			GTTAAAAGCTTTG	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.1206T>C	chr19.hg19:g.23927146A>G		72.0	2.0	.		74.0	3.0	.	NM_138286	B3KVF7	Silent	SNP	ENST00000402377.3	hg19	CCDS12414.2																																																																																			.	.	.	none		0.398	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286		G	23927146	A	G	23927146	2	3	52	1	0	0	0	0	0	0	0	1	18100	59	3	3		3	ZNF681	19	23927146	Silent	SNP	A	TCGA-A4-7997-01A-11D-2201-08	5558420	23927146	35201837	65	3567											
U2AF2	11338	hgsc.bcm.edu	37	chr19	56180114	56180114	+	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	gtgccacggggctctccaagGgctacgccttctgtgagtac	6	9	13	13	2	2	1	0	1	2	0	3	1	2	1	3	3	3	3	3	3	3	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr19:56180114G>A	ENST00000308924.4	+	9	941	c.901G>A	c.(901-903)Ggc>Agc	p.G301S	CTD-2537I9.13_ENST00000592252.1_RNA|U2AF2_ENST00000590551.1_Missense_Mutation_p.G137S|U2AF2_ENST00000450554.2_Missense_Mutation_p.G301S|CTD-2537I9.12_ENST00000589456.1_RNA|CTD-2537I9.12_ENST00000585940.1_RNA			P26368	U2AF2_HUMAN	U2 small nuclear RNA auxiliary factor 2	301	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA 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)		GCTCTCCAAGGGCTACGCCTT	0.617																																					p.G301S		Atlas-SNP	.											.	U2AF2	62	.	0			c.G901A						PASS	.						68	65	66					19																	56180114		2203	4300	6503	SO:0001583	missense	11338	exon9			TCCAAGGGCTACG	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.901G>A	chr19.hg19:g.56180114G>A	ENSP00000307863:p.Gly301Ser	148.0	0.0	.		91.0	30.0	.	NM_001012478	Q96HC5	Missense_Mutation	SNP	ENST00000308924.4	hg19	CCDS12933.1	.	.	.	.	.	.	.	.	.	.	G	35	5.448539	0.96205	.	.	ENSG00000063244	ENST00000308924;ENST00000450554	D;T	0.83419	-1.72;0.1	4.4	4.4	0.53042	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	D	0.94683	0.8285	H	0.98646	4.29	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96949	0.9693	10	0.87932	D	0	-32.268	16.1527	0.81634	0.0:0.0:1.0:0.0	.	301;301	P26368;P26368-2	U2AF2_HUMAN;.	S	301	ENSP00000307863:G301S;ENSP00000388475:G301S	ENSP00000307863:G301S	G	+	1	0	U2AF2	60871926	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.145000	0.94634	2.184000	0.69523	0.655000	0.94253	GGC	.	.	.	none		0.617	U2AF2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453599.1	NM_007279		A	56180114	G	A	56180114	3	1	52	1	0	0	0	0	1	0	0	0	16835	1232	43	2	935	2	U2AF2	19	56180114	Missense_Mutation	SNP	G	TCGA-A4-7997-01A-11D-2201-08	32252968	56180114	2948869	66	3568											
TBC1D20	128637	hgsc.bcm.edu	37	chr20	419913	419913	+	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	atgtcacagtcacagtccagGacttcctgctcgcgatacaa	11	9	8	13	2	2	0	2	0	0	0	5	2	4	1	2	1	2	1	2	1	2	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr20:419913G>T	ENST00000354200.4	-	7	942	c.795C>A	c.(793-795)gtC>gtA	p.V265V	TBC1D20_ENST00000461188.1_5'UTR	NM_144628.2	NP_653229.1	Q96BZ9	TBC20_HUMAN	TBC1 domain family, member 20	265					acrosome assembly (GO:0001675)|cargo loading into COPII-coated vesicle (GO:0090110)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|lens fiber cell morphogenesis (GO:0070309)|lipid particle organization (GO:0034389)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|seminiferous tubule development (GO:0072520)|virion assembly (GO:0019068)	endoplasmic reticulum membrane (GO:0005789)|integral component of Golgi membrane (GO:0030173)|nuclear membrane (GO:0031965)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	12		all_epithelial(17;0.228)|Breast(17;0.231)				CACAGTCCAGGACTTCCTGCT	0.562																																					p.V265V		Atlas-SNP	.											.	TBC1D20	34	.	0			c.C795A						PASS	.						137	118	124					20																	419913		2203	4300	6503	SO:0001819	synonymous_variant	128637	exon7			GTCCAGGACTTCC	AK055573	CCDS13002.1	20p13	2013-07-10	2005-01-05	2005-01-05	ENSG00000125875	ENSG00000125875			16133	protein-coding gene	gene with protein product		611663	"chromosome 20 open reading frame 140"	C20orf140		17901050	Standard	XM_005260661		Approved	dJ852M4.2	uc002wds.3	Q96BZ9	OTTHUMG00000031637	ENST00000354200.4:c.795C>A	chr20.hg19:g.419913G>T		82.0	0.0	.		81.0	48.0	.	NM_144628	A8K6I3|B9A6M1|Q5JWQ7|Q6ZSY8|Q96NE1|Q9BYM7|Q9H140	Silent	SNP	ENST00000354200.4	hg19	CCDS13002.1																																																																																			.	.	.	none		0.562	TBC1D20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251397.2	NM_144628		T	419913	G	T	419913	2	4	52	1	0	0	0	0	0	0	0	1	15621	1161	41	4		4	TBC1D20	20	419913	Silent	SNP	G	TCGA-A4-7997-01A-11D-2201-08		419913	62605607	67	3569											
FAM65C	140876	hgsc.bcm.edu	37	chr20	49219116	49219116	+	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	tcgctgtcagacaggtagctGaggatggaggtggcccttgg	7	9	17	8	1	1	2	1	1	0	1	2	4	1	4	1	6	1	3	1	6	1	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr20:49219116G>A	ENST00000327979.2	-	13	1551	c.1140C>T	c.(1138-1140)ctC>ctT	p.L380L	FAM65C_ENST00000535356.1_Silent_p.L384L|FAM65C_ENST00000045083.2_Silent_p.L380L			Q96MK2	FA65C_HUMAN	family with sequence similarity 65, member C	380										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(1)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						ACAGGTAGCTGAGGATGGAGG	0.637																																					p.L380L		Atlas-SNP	.											.	FAM65C	87	.	0			c.C1140T						PASS	.						26	28	27					20																	49219116		2061	4109	6170	SO:0001819	synonymous_variant	140876	exon13			GTAGCTGAGGATG	AL133230	CCDS13431.2	20q13.13	2011-11-24	2008-06-13	2008-06-13	ENSG00000042062	ENSG00000042062			16168	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 175", "chromosome 20 open reading frame 176"	C20orf175, C20orf176			Standard	XM_005260294		Approved	dJ530I15.2, dJ530I15.3	uc002xvm.3	Q96MK2	OTTHUMG00000032724	ENST00000327979.2:c.1140C>T	chr20.hg19:g.49219116G>A		90.0	0.0	.		115.0	24.0	.	NM_080829	Q5QPB6|Q9NQQ2	Silent	SNP	ENST00000327979.2	hg19	CCDS13431.2																																																																																			.	.	.	none		0.637	FAM65C-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257962.1			A	49219116	G	A	49219116	2	1	52	1	0	0	0	0	0	0	0	1	5608	1277	45	2		2	FAM65C	20	49219116	Silent	SNP	G	TCGA-A4-7997-01A-11D-2201-08	48799203	49219116	13806404	68	3570											
CYP24A1	1591	hgsc.bcm.edu	37	chr20	52773943	52773943	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttacccaacaaagagccaaaTgcagttgaagctctgctaat	15	9	7	10	0	1	2	0	1	1	1	1	2	1	2	2	0	6	4	2	0	6	3			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr20:52773943T>C	ENST00000216862.3	-	10	1811	c.1418A>G	c.(1417-1419)cAt>cGt	p.H473R	CYP24A1_ENST00000395955.3_Intron|CYP24A1_ENST00000460643.1_5'Flank|CYP24A1_ENST00000395954.3_Missense_Mutation_p.H331R	NM_000782.4	NP_000773.2	Q07973	CP24A_HUMAN	cytochrome P450, family 24, subfamily A, polypeptide 1	473					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)	AAGAGCCAAATGCAGTTGAAG	0.423																																					p.H473R		Atlas-SNP	.											.	CYP24A1	75	.	0			c.A1418G						PASS	.						81	76	78					20																	52773943		2203	4300	6503	SO:0001583	missense	1591	exon10			GCCAAATGCAGTT	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.1418A>G	chr20.hg19:g.52773943T>C	ENSP00000216862:p.His473Arg	74.0	0.0	.		85.0	42.0	.	NM_000782	Q15807|Q32ML3|Q5I2W7	Missense_Mutation	SNP	ENST00000216862.3	hg19	CCDS33491.1	.	.	.	.	.	.	.	.	.	.	t	15.34	2.805491	0.50315	.	.	ENSG00000019186	ENST00000216862;ENST00000395954	T;T	0.67345	-0.26;-0.26	5.2	4.06	0.47325	.	0.101356	0.64402	D	0.000001	T	0.63698	0.2533	N	0.25992	0.78	0.41376	D	0.987529	D;P	0.54964	0.969;0.934	P;B	0.55161	0.77;0.424	T	0.60979	-0.7155	10	0.33141	T	0.24	-19.4807	11.563	0.50788	0.0:0.0:0.1498:0.8502	.	473;331	Q07973;Q5I2W7	CP24A_HUMAN;.	R	473;331	ENSP00000216862:H473R;ENSP00000379284:H331R	ENSP00000216862:H473R	H	-	2	0	CYP24A1	52207350	1.000000	0.71417	0.969000	0.41365	0.303000	0.27691	4.744000	0.62118	0.884000	0.36064	0.451000	0.29950	CAT	.	.	.	none		0.423	CYP24A1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079769.2			C	52773943	T	C	52773943	3	2	52	1	0	0	0	0	1	0	0	0	4156	1464	51	3	134	3	CYP24A1	20	52773943	Missense_Mutation	SNP	T	TCGA-A4-7997-01A-11D-2201-08	3554827	52773943	10251577	69	3571											
APP	351	hgsc.bcm.edu	37	chr21	27348294	27348294	+	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	actgccttcttatcagctttAggcaagttctttgcttgacg	7	16	8	10	1	3	1	1	1	2	0	3	1	3	1	1	1	3	4	1	1	3	7			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chr21:27348294A>C	ENST00000346798.3	-	10	1305	c.1272T>G	c.(1270-1272)ccT>ccG	p.P424P	APP_ENST00000359726.3_Silent_p.P368P|APP_ENST00000357903.3_Silent_p.P405P|APP_ENST00000440126.3_Silent_p.P400P|APP_ENST00000439274.2_Silent_p.P368P|APP_ENST00000348990.5_Silent_p.P349P|APP_ENST00000358918.3_Silent_p.P424P|APP_ENST00000448388.2_Silent_p.P314P|APP_ENST00000354192.3_Silent_p.P293P	NM_000484.3	NP_000475.1	P05067	A4_HUMAN	amyloid beta (A4) precursor protein	424					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)				TATCAGCTTTAGGCAAGTTCT	0.383																																					p.P424P		Atlas-SNP	.											.	APP	90	.	0			c.T1272G						PASS	.						249	199	216					21																	27348294		2203	4300	6503	SO:0001819	synonymous_variant	351	exon10			AGCTTTAGGCAAG	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.1272T>G	chr21.hg19:g.27348294A>C		94.0	0.0	.		96.0	28.0	.	NM_000484	B2R5V1|B4DII8|D3DSD1|D3DSD2|D3DSD3|P09000|P78438|Q13764|Q13778|Q13793|Q16011|Q16014|Q16019|Q16020|Q6GSC0|Q8WZ99|Q9BT38|Q9UC33|Q9UCA9|Q9UCB6|Q9UCC8|Q9UCD1|Q9UQ58	Silent	SNP	ENST00000346798.3	hg19	CCDS13576.1	.	.	.	.	.	.	.	.	.	.	A	10.87	1.472507	0.26423	.	.	ENSG00000142192	ENST00000448850;ENST00000415997	.	.	.	5.11	-5.12	0.02893	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-6.1356	2.2262	0.03985	0.1134:0.1931:0.3431:0.3504	.	.	.	.	E	327;159	.	.	X	-	1	0	APP	26270165	0.085000	0.21516	0.973000	0.42090	0.999000	0.98932	-0.688000	0.05150	-0.726000	0.04895	0.529000	0.55759	TAA	.	.	.	none		0.383	APP-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171340.1	NM_000484		C	27348294	A	C	27348294	2	2	52	1	0	0	0	0	0	0	0	1	815	407	15	5		5	APP	21	27348294	Silent	SNP	A	TCGA-A4-7997-01A-11D-2201-08		27348294	20781601	70	3572											
WNK3	65267	hgsc.bcm.edu	37	chrX	54259340	54259340	+	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	gacgtggtgatgcaggtggcAaaggaatctcagtagattgg	11	9	16	5	1	1	2	1	1	1	1	2	4	1	3	0	5	1	3	0	5	3	2			TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	g.chrX:54259340A>T	ENST00000375159.2	-	20	4741	c.4742T>A	c.(4741-4743)tTg>tAg	p.L1581*	WNK3_ENST00000375169.3_Nonsense_Mutation_p.L1534*|WNK3_ENST00000354646.2_Nonsense_Mutation_p.L1581*			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	1581					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						TGCAGGTGGCAAAGGAATCTC	0.473																																					p.L1581X		Atlas-SNP	.											.	WNK3	218	.	0			c.T4742A						PASS	.						161	143	149					X																	54259340		2203	4300	6503	SO:0001587	stop_gained	65267	exon21			GGTGGCAAAGGAA	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.4742T>A	chrX.hg19:g.54259340A>T	ENSP00000364301:p.Leu1581*	91.0	0.0	.		99.0	4.0	.	NM_020922	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Nonsense_Mutation	SNP	ENST00000375159.2	hg19	CCDS14357.1	.	.	.	.	.	.	.	.	.	.	A	44	10.908169	0.99487	.	.	ENSG00000196632	ENST00000375169;ENST00000354646;ENST00000375159	.	.	.	5.69	3.25	0.37280	.	0.330632	0.21916	N	0.067229	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.0621	4.1221	0.10109	0.6809:0.0:0.1657:0.1534	.	.	.	.	X	1534;1581;1581	.	ENSP00000346667:L1581X	L	-	2	0	WNK3	54276065	0.522000	0.26266	0.845000	0.33349	0.967000	0.64934	1.485000	0.35519	0.262000	0.21774	0.481000	0.45027	TTG	.	.	.	none		0.473	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922		T	54259340	A	T	54259340	4	4	52	1	0	0	0	0	0	1	0	0	17391	131	5	5	676	5	WNK3	23	54259340	Nonsense_Mutation	SNP	A	TCGA-A4-7997-01A-11D-2201-08		54259340	101011220	71	3573											
ITGA10	8515	hgsc.bcm.edu	37	chr1	145532515	145532515	+	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	ctctttcctgagagaaattaGaactattgccagtgatccag	12	12	8	9	0	1	4	0	2	1	2	3	5	3	4	3	0	2	0	3	0	4	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:145532515G>A	ENST00000369304.3	+	9	1143	c.968G>A	c.(967-969)aGa>aAa	p.R323K	ITGA10_ENST00000538811.1_Missense_Mutation_p.R192K|ITGA10_ENST00000539363.1_Missense_Mutation_p.R180K|ITGA10_ENST00000481236.1_3'UTR	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	323	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					AGAGAAATTAGAACTATTGCC	0.473																																					p.R323K		Atlas-SNP	.											.	ITGA10	131	.	0			c.G968A						PASS	.						144	138	140					1																	145532515		2203	4300	6503	SO:0001583	missense	8515	exon9			AAATTAGAACTAT	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.968G>A	chr1.hg19:g.145532515G>A	ENSP00000358310:p.Arg323Lys	143.0	0.0	.		170.0	66.0	.	NM_003637	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Missense_Mutation	SNP	ENST00000369304.3	hg19	CCDS918.1	.	.	.	.	.	.	.	.	.	.	G	7.649	0.682583	0.14907	.	.	ENSG00000143127	ENST00000369304;ENST00000543043;ENST00000539363;ENST00000538811	D;D;D	0.83914	-1.78;-1.78;-1.78	5.27	4.34	0.51931	von Willebrand factor, type A (3);	0.060779	0.64402	D	0.000004	T	0.34600	0.0903	N	0.01771	-0.73	0.35261	D	0.779612	B;B;B;B	0.18741	0.024;0.024;0.024;0.03	B;B;B;B	0.23150	0.021;0.021;0.044;0.036	T	0.39292	-0.9621	10	0.02654	T	1	.	7.3767	0.26833	0.1809:0.0:0.8191:0.0	.	289;192;180;323	F5H3T9;F5GY13;B2RTV5;O75578	.;.;.;ITA10_HUMAN	K	323;289;180;192	ENSP00000358310:R323K;ENSP00000439894:R180K;ENSP00000440011:R192K	ENSP00000358310:R323K	R	+	2	0	ITGA10	144243872	1.000000	0.71417	0.974000	0.42286	0.966000	0.64601	5.786000	0.69006	2.653000	0.90120	0.561000	0.74099	AGA	.	.	.	none		0.473	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637		A	145532515	G	A	145532515	3	1	53	1	0	0	0	0	1	0	0	0	7880	942	33	2	1002	2	ITGA10	1	145532515	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08		145532515	103718106	1	3574											
SEMA6C	10500	hgsc.bcm.edu	37	chr1	151109386	151109386	+	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	gcagagcggccatgcaggttCacaggcccagtcaaggcctg	9	5	14	13	1	2	1	2	0	0	1	2	1	2	1	3	4	2	3	3	4	1	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:151109386C>T	ENST00000341697.3	-	11	2612	c.921G>A	c.(919-921)gtG>gtA	p.V307V				Q9H3T2	SEM6C_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	307	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	28	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CATGCAGGTTCACAGGCCCAG	0.542																																					p.V307V		Atlas-SNP	.											.	SEMA6C	70	.	0			c.G921A						PASS	.						101	108	106					1																	151109386		2203	4300	6503	SO:0001819	synonymous_variant	10500	exon11			CAGGTTCACAGGC	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.921G>A	chr1.hg19:g.151109386C>T		184.0	0.0	.		165.0	47.0	.	NM_001178061	D3DV15|Q5JR71|Q5JR72|Q5JR73|Q8WXT8|Q8WXT9|Q8WXU0|Q96JF8	Silent	SNP	ENST00000341697.3	hg19	CCDS984.1																																																																																			.	.	.	none		0.542	SEMA6C-004	KNOWN	alternative_5_UTR|mRNA_start_NF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034074.1	NM_030913		T	151109386	C	T	151109386	2	4	53	1	0	0	0	0	0	0	0	1	14054	813	29	2		2	SEMA6C	1	151109386	Silent	SNP	C	TCGA-A4-8098-01A-11D-2396-08	5576871	151109386	98141235	2	3575											
PEAR1	375033	hgsc.bcm.edu	37	chr1	156877993	156877993	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgactgcgccccggacgccCgttgcttcccggccaacggc	4	5	13	19	7	0	0	0	0	0	0	1	2	1	1	5	3	3	2	5	3	1	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:156877993C>T	ENST00000338302.3	+	10	1201	c.976C>T	c.(976-978)Cgt>Tgt	p.R326C	PEAR1_ENST00000292357.7_Missense_Mutation_p.R326C			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	326	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CCCGGACGCCCGTTGCTTCCC	0.692																																					p.R326C		Atlas-SNP	.											.	PEAR1	118	.	0			c.C976T						PASS	.						21	26	24					1																	156877993		2202	4296	6498	SO:0001583	missense	375033	exon9			GACGCCCGTTGCT	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.976C>T	chr1.hg19:g.156877993C>T	ENSP00000344465:p.Arg326Cys	31.0	0.0	.		22.0	11.0	.	NM_001080471	Q8TEK2	Missense_Mutation	SNP	ENST00000338302.3	hg19	CCDS30892.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.373658	0.82573	.	.	ENSG00000187800	ENST00000338302;ENST00000292357	T;T	0.18016	2.24;2.24	4.33	4.33	0.51752	EGF-like, laminin (2);Epidermal growth factor-like, type 3 (1);	0.152429	0.30920	N	0.008604	T	0.30603	0.0770	M	0.72479	2.2	0.58432	D	0.999999	D;D	0.76494	0.998;0.999	D;D	0.70016	0.953;0.967	T	0.05582	-1.0876	10	0.62326	D	0.03	.	14.3643	0.66795	0.0:1.0:0.0:0.0	.	127;326	Q8N780;Q5VY43	.;PEAR1_HUMAN	C	326	ENSP00000344465:R326C;ENSP00000292357:R326C	ENSP00000292357:R326C	R	+	1	0	PEAR1	155144617	0.978000	0.34361	1.000000	0.80357	0.896000	0.52359	2.495000	0.45337	2.230000	0.72887	0.561000	0.74099	CGT	.	.	.	none		0.692	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471		T	156877993	C	T	156877993	3	4	53	1	0	0	0	0	1	0	0	0	11719	652	23	1	1006	1	PEAR1	1	156877993	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	5768607	156877993	92372628	3	3576											
DUSP27	92235	hgsc.bcm.edu	37	chr1	167096129	167096129	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctccgacgtcagcctgacAgcctaccaggcctggaagct	8	6	10	17	2	1	1	1	1	0	0	2	3	2	2	6	2	4	1	6	2	2	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:167096129A>G	ENST00000361200.2	+	6	1927	c.1761A>G	c.(1759-1761)acA>acG	p.T587T	DUSP27_ENST00000271385.5_Silent_p.T587T|DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000443333.1_Silent_p.T587T			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	587					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						TCAGCCTGACAGCCTACCAGG	0.597																																					p.T587T		Atlas-SNP	.											.	DUSP27	235	.	0			c.A1761G						PASS	.						45	45	45					1																	167096129		2203	4300	6503	SO:0001819	synonymous_variant	92235	exon5			CCTGACAGCCTAC	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.1761A>G	chr1.hg19:g.167096129A>G		68.0	0.0	.		63.0	29.0	.	NM_001080426	A0AUM4|Q9C074	Silent	SNP	ENST00000361200.2	hg19	CCDS30932.1																																																																																			.	.	.	none		0.597	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		G	167096129	A	G	167096129	2	3	53	1	0	0	0	0	0	0	0	1	4826	175	7	3		3	DUSP27	1	167096129	Silent	SNP	A	TCGA-A4-8098-01A-11D-2396-08	10218136	167096129	82154492	4	3577											
ATP1B1	481	hgsc.bcm.edu	37	chr1	169100749	169100768	+	Frame_Shift_Del	DEL	CGTTTTCAGGGACGTTTTGA	CGTTTTCAGGGACGTTTTGA	-																															ttgggtacagtgagaaagacCgttttcagggacgttttgat																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	CGTTTTCAGGGACGTTTTGA	CGTTTTCAGGGACGTTTTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:169100749_169100768delCGTTTTCAGGGACGTTTTGA	ENST00000367816.1	+	7	1397_1416	c.868_887delCGTTTTCAGGGACGTTTTGA	c.(868-888)cgttttcagggacgttttgatfs	p.RFQGRFD290fs	ATP1B1_ENST00000367815.4_Frame_Shift_Del_p.RFQGRFD290fs|ATP1B1_ENST00000367813.3_Frame_Shift_Del_p.RFQGRFD282fs|ATP1B1_ENST00000499679.3_Frame_Shift_Del_p.RFQGRFD234fs			P05026	AT1B1_HUMAN	ATPase, Na+/K+ transporting, beta 1 polypeptide	290	immunoglobulin-like.				blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular potassium ion homeostasis (GO:0030007)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|leukocyte migration (GO:0050900)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|positive regulation of ATP catabolic process (GO:1903291)|positive regulation of ATPase activity (GO:0032781)|positive regulation of calcium:sodium antiporter activity (GO:1903281)|positive regulation of potassium ion import (GO:1903288)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of sodium ion export from cell (GO:1903278)|potassium ion import (GO:0010107)|protein localization to plasma membrane (GO:0072659)|protein stabilization (GO:0050821)|protein transport into plasma membrane raft (GO:0044861)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression (GO:0010468)|relaxation of cardiac muscle (GO:0055119)|response to hypoxia (GO:0001666)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|vesicle (GO:0031982)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|MHC class II protein complex binding (GO:0023026)|sodium:potassium-exchanging ATPase activity (GO:0005391)	p.R290S(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	14	all_hematologic(923;0.208)					TGAGAAAGACCGTTTTCAGGGACGTTTTGATGTAAAAATT	0.4																																					p.289_296del		Atlas-INDEL	.											.	ATP1B1	29	.	1	Substitution - Missense(1)	lung(1)	c.867_886del						PASS	.																																			SO:0001589	frameshift_variant	481	exon6			.	U16799	CCDS1276.1	1q24.2	2012-10-22			ENSG00000143153	ENSG00000143153		"ATPases / P-type"	804	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit beta-1", "sodium pump subunit beta-1", "sodium-potassium ATPase subunit beta 1 (non-catalytic)"	182330		ATP1B			Standard	NM_001677		Approved		uc001gfr.1	P05026	OTTHUMG00000034590	ENST00000367816.1:c.868_887delCGTTTTCAGGGACGTTTTGA	chr1.hg19:g.169100749_169100768delCGTTTTCAGGGACGTTTTGA	ENSP00000356790:p.Arg290fs	113.0	0.0	0		79.0	26.0	0.329114	NM_001677	Q5TGZ3	Frame_Shift_Del	DEL	ENST00000367816.1	hg19	CCDS1276.1																																																																																			.	.	.	none		0.4	ATP1B1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083696.1			-	169100768	CGTTTTCAGGGACGTTTTGA	-	169100749	7	5	53	1	0	1	0	1	0	0	0	0	1132	652	23	0	890	0	ATP1B1	1	169100749	Frame_Shift_Del	DEL	CGTTTTCAGGGACGTTTTGA	TCGA-A4-8098-01A-11D-2396-08	2004620	169100749	80149872	5	3578											
C1orf112	55732	hgsc.bcm.edu	37	chr1	169806133	169806133	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctctgtggcaacatatttcCttccaggcgttacctcctga	7	13	7	14	1	1	1	0	1	1	0	4	1	4	1	5	2	2	2	5	2	3	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:169806133C>T	ENST00000286031.6	+	17	2305	c.1605C>T	c.(1603-1605)tcC>tcT	p.S535S	C1orf112_ENST00000359326.4_Silent_p.S535S|C1orf112_ENST00000498289.1_3'UTR	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	535										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)					AACATATTTCCTTCCAGGCGT	0.438																																					p.S535S		Atlas-SNP	.											.	C1orf112	74	.	0			c.C1605T						PASS	.						73	69	71					1																	169806133		2203	4300	6503	SO:0001819	synonymous_variant	55732	exon17			TATTTCCTTCCAG	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.1605C>T	chr1.hg19:g.169806133C>T		63.0	0.0	.		65.0	23.0	.	NM_018186	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Silent	SNP	ENST00000286031.6	hg19	CCDS1285.1																																																																																			.	.	.	none		0.438	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186		T	169806133	C	T	169806133	2	4	53	1	0	0	0	0	0	0	0	1	1987	668	24	2		2	C1orf112	1	169806133	Silent	SNP	C	TCGA-A4-8098-01A-11D-2396-08	705384	169806133	79444488	6	3579											
PPFIA4	8497	hgsc.bcm.edu	37	chr1	203025587	203025587	+	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	cttcctcacccaggacgctgCggctagagaagcttggccac	8	7	11	15	2	1	1	1	0	0	1	2	3	2	2	3	3	2	3	3	3	2	3	rs549873910		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr1:203025587C>A	ENST00000447715.2	+	23	2566	c.2125C>A	c.(2125-2127)Cgg>Agg	p.R709R	PPFIA4_ENST00000295706.4_Silent_p.R225R|PPFIA4_ENST00000414050.2_Silent_p.R438R|PPFIA4_ENST00000367240.2_Silent_p.R710R|PPFIA4_ENST00000599966.1_Silent_p.R225R|PPFIA4_ENST00000272198.6_Silent_p.R225R			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	709					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)		p.R856W(1)		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						CAGGACGCTGCGGCTAGAGAA	0.567																																					p.R225R		Atlas-SNP	.											PPFIA4_ENST00000272198,colon,carcinoma,0,3	PPFIA4	139	.	1	Substitution - Missense(1)	large_intestine(1)	c.C673A						PASS	.						37	43	41					1																	203025587		2040	4173	6213	SO:0001819	synonymous_variant	8497	exon5			ACGCTGCGGCTAG	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.2125C>A	chr1.hg19:g.203025587C>A		51.0	0.0	.		47.0	3.0	.	NM_015053	A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Silent	SNP	ENST00000447715.2	hg19																																																																																				.	.	.	none		0.567	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053		A	203025587	C	A	203025587	2	1	53	1	0	0	0	0	0	0	0	1	12319	759	27	4		4	PPFIA4	1	203025587	Silent	SNP	C	TCGA-A4-8098-01A-11D-2396-08	33219454	203025587	46225034	7	3580											
EMILIN1	11117	hgsc.bcm.edu	37	chr2	27306240	27306240	+	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	gccttcgggatggtgtggagCgctgctcctgccccctgttg	2	11	15	13	2	0	0	0	0	0	0	2	2	1	2	4	3	3	3	4	3	0	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:27306240C>A	ENST00000380320.4	+	4	2300	c.1801C>A	c.(1801-1803)Cgc>Agc	p.R601S		NM_007046.3	NP_008977	Q9Y6C2	EMIL1_HUMAN	elastin microfibril interfacer 1	601					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)			breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(1)|lung(14)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	26	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGGTGTGGAGCGCTGCTCCTG	0.697																																					p.R601S		Atlas-SNP	.											.	EMILIN1	75	.	0			c.C1801A						PASS	.						31	38	36					2																	27306240		2181	4280	6461	SO:0001583	missense	11117	exon4			GTGGAGCGCTGCT	AF088916	CCDS1733.1	2p23.3-p23.2	2008-02-05			ENSG00000138080	ENSG00000138080		"EMI domain containing"	19880	protein-coding gene	gene with protein product		130660					Standard	NM_007046		Approved	DKFZp586M121, gp115	uc002rii.4	Q9Y6C2	OTTHUMG00000097069	ENST00000380320.4:c.1801C>A	chr2.hg19:g.27306240C>A	ENSP00000369677:p.Arg601Ser	98.0	0.0	.		88.0	4.0	.	NM_007046	A5PL03|H0Y7A0|Q53SY9|Q96G58|Q96IH6|Q9UG76	Missense_Mutation	SNP	ENST00000380320.4	hg19	CCDS1733.1	.	.	.	.	.	.	.	.	.	.	C	14.33	2.504285	0.44558	.	.	ENSG00000138080	ENST00000380320	T	0.62364	0.03	4.73	4.73	0.59995	.	0.252874	0.30859	N	0.008737	T	0.40322	0.1112	N	0.08118	0	0.31742	N	0.635692	B	0.29646	0.253	B	0.31290	0.127	T	0.43556	-0.9384	10	0.15066	T	0.55	-16.6262	13.0709	0.59061	0.0:1.0:0.0:0.0	.	601	Q9Y6C2	EMIL1_HUMAN	S	601	ENSP00000369677:R601S	ENSP00000369677:R601S	R	+	1	0	EMILIN1	27159744	0.997000	0.39634	1.000000	0.80357	0.998000	0.95712	1.045000	0.30341	2.456000	0.83038	0.561000	0.74099	CGC	.	.	.	none		0.697	EMILIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214185.1	NM_007046		A	27306240	C	A	27306240	3	1	53	1	0	0	0	0	1	0	0	0	5095	768	27	4	1815	4	EMILIN1	2	27306240	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08		27306240	215893133	8	3581											
EIF2AK2	5610	hgsc.bcm.edu	37	chr2	37365711	37365711	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtagtagcaaaagaaccagaGgacaggtagtcagatttctg	15	8	12	6	0	2	3	1	0	1	3	2	4	2	4	1	2	2	4	1	2	6	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:37365711G>A	ENST00000233057.4	-	7	856	c.534C>T	c.(532-534)tcC>tcT	p.S178S	EIF2AK2_ENST00000405334.1_Silent_p.S178S|EIF2AK2_ENST00000395127.2_Silent_p.S178S	NM_001135651.2	NP_001129123.1	P19525	E2AK2_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 2	178					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)				AAGAACCAGAGGACAGGTAGT	0.363																																					p.S178S		Atlas-SNP	.											.	EIF2AK2	54	.	0			c.C534T						PASS	.						90	93	92					2																	37365711		2203	4300	6503	SO:0001819	synonymous_variant	5610	exon5			ACCAGAGGACAGG	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.534C>T	chr2.hg19:g.37365711G>A		75.0	0.0	.		71.0	32.0	.	NM_001135652	A8K3P0|D6W584|E9PC80|Q52M43|Q7Z6F6|Q9UIR4	Silent	SNP	ENST00000233057.4	hg19	CCDS1786.1																																																																																			.	.	.	none		0.363	EIF2AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218571.2	NM_002759		A	37365711	G	A	37365711	2	1	53	1	0	0	0	0	0	0	0	1	4999	987	35	2		2	EIF2AK2	2	37365711	Silent	SNP	G	TCGA-A4-8098-01A-11D-2396-08	10059471	37365711	205833662	9	3582											
KIAA1841	84542	hgsc.bcm.edu	37	chr2	61310382	61310382	+	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	ttaatgcaaatcttctcacaCgtatagctgatctgttctca	11	15	5	10	1	4	1	2	1	4	0	6	1	4	1	0	0	2	4	0	0	4	5	rs140620846	byFrequency	TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:61310382C>A	ENST00000402291.1	+	8	1064	c.823C>A	c.(823-825)Cgt>Agt	p.R275S	KIAA1841_ENST00000356719.2_Missense_Mutation_p.R275S|KIAA1841_ENST00000295031.5_Missense_Mutation_p.R275S|KIAA1841_ENST00000482513.1_3'UTR|KIAA1841_ENST00000453873.1_Missense_Mutation_p.R275S	NM_001129993.1	NP_001123465.1	Q6NSI8	K1841_HUMAN	KIAA1841	275										breast(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	25			Epithelial(17;0.193)			TCTTCTCACACGTATAGCTGA	0.303																																					p.R275S		Atlas-SNP	.											KIAA1841_ENST00000402291,colon,carcinoma,0,2	KIAA1841	95	.	0			c.C823A						PASS	.						104	88	94					2																	61310382		2203	4299	6502	SO:0001583	missense	84542	exon8			CTCACACGTATAG	BC070104	CCDS1867.1, CCDS46296.1	2p15	2010-06-22			ENSG00000162929	ENSG00000162929			29387	protein-coding gene	gene with protein product						11347906	Standard	NM_032506		Approved		uc002saw.4	Q6NSI8	OTTHUMG00000129421	ENST00000402291.1:c.823C>A	chr2.hg19:g.61310382C>A	ENSP00000385579:p.Arg275Ser	48.0	0.0	.		45.0	2.0	.	NM_032506	Q49AF0|Q6ZND0|Q96JI6	Missense_Mutation	SNP	ENST00000402291.1	hg19	CCDS46296.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.975234	0.74360	.	.	ENSG00000162929	ENST00000402291;ENST00000295031;ENST00000356719;ENST00000453873	.	.	.	5.48	-0.618	0.11576	.	0.109289	0.64402	D	0.000006	T	0.63674	0.2531	M	0.83223	2.63	0.43936	D	0.99659	D;P;D	0.57571	0.963;0.902;0.98	P;P;P	0.52881	0.677;0.637;0.712	T	0.62445	-0.6853	9	0.87932	D	0	-4.9877	6.0162	0.19605	0.1151:0.5612:0.0:0.3237	.	275;275;275	Q6NSI8-2;Q6NSI8;Q6NSI8-4	.;K1841_HUMAN;.	S	275	.	ENSP00000295031:R275S	R	+	1	0	KIAA1841	61163886	0.999000	0.42202	0.895000	0.35142	0.966000	0.64601	3.890000	0.56220	-0.342000	0.08363	-0.119000	0.15052	CGT	.	C|0.999;T|0.001	.	alt		0.303	KIAA1841-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325477.1	NM_032506		A	61310382	C	A	61310382	3	1	53	1	0	0	0	0	1	0	0	0	8268	536	19	4	845	4	KIAA1841	2	61310382	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	23944671	61310382	181888991	10	3583											
GPAT2	150763	hgsc.bcm.edu	37	chr2	96687959	96687959	+	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	ctagtttttcctgattgtccAggctggcaaaagtaggggac	9	12	12	8	0	0	1	0	1	0	0	2	2	2	2	2	4	0	4	2	4	4	5			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:96687959A>T	ENST00000434632.1	-	23	2795	c.2336T>A	c.(2335-2337)cTg>cAg	p.L779Q	GPAT2_ENST00000359548.4_Missense_Mutation_p.L779Q|FAHD2CP_ENST00000607780.1_RNA|GPAT2_ENST00000453542.1_Missense_Mutation_p.L708Q|GPAT2_ENST00000377137.3_3'UTR			Q6NUI2	GPAT2_HUMAN	glycerol-3-phosphate acyltransferase 2, mitochondrial	779					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)	p.L779Q(2)		NS(1)|breast(1)|cervix(1)|endometrium(4)|large_intestine(1)|lung(5)|skin(3)	16						CTGATTGTCCAGGCTGGCAAA	0.567																																					p.L779Q		Atlas-SNP	.											GPAT2,trunk,malignant_melanoma,0,2	GPAT2	46	.	2	Substitution - Missense(2)	skin(2)	c.T2336A						PASS	.						30	30	30					2																	96687959		1847	4102	5949	SO:0001583	missense	150763	exon22			TTGTCCAGGCTGG	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.2336T>A	chr2.hg19:g.96687959A>T	ENSP00000389395:p.Leu779Gln	34.0	0.0	.		35.0	2.0	.	NM_207328	Q6P2E4|Q6ZNI3|Q6ZNI5|Q6ZWJ4	Missense_Mutation	SNP	ENST00000434632.1	hg19	CCDS42714.1	.	.	.	.	.	.	.	.	.	.	t	0.005	-2.199373	0.00299	.	.	ENSG00000186281	ENST00000359548;ENST00000434632;ENST00000453542	T;T;T	0.74526	-0.85;-0.85;0.16	4.97	-1.85	0.07784	.	.	.	.	.	T	0.31857	0.0810	N	0.00483	-1.445	0.09310	N	0.999997	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	0.39187	-0.9626	9	0.02654	T	1	-26.1951	5.7343	0.18057	0.1497:0.2636:0.0:0.5866	.	708;785;779;708	E9PE95;Q6NUI2-4;Q6NUI2;B4DNZ9	.;.;GPAT2_HUMAN;.	Q	779;779;708	ENSP00000352547:L779Q;ENSP00000389395:L779Q;ENSP00000393770:L708Q	ENSP00000352547:L779Q	L	-	2	0	GPAT2	96051686	0.001000	0.12720	0.375000	0.26029	0.081000	0.17604	-0.019000	0.12546	-0.483000	0.06772	-0.751000	0.03497	CTG	.	.	.	none		0.567	GPAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338786.1	NM_207328		T	96687959	A	T	96687959	3	4	53	1	0	0	0	0	1	0	0	0	6596	188	7	5	55	5	GPAT2	2	96687959	Missense_Mutation	SNP	A	TCGA-A4-8098-01A-11D-2396-08	35377577	96687959	146511414	11	3584											
CNNM4	26504	hgsc.bcm.edu	37	chr2	97428127	97428127	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttggatgccatgctggaggAgttcaagaagggtaaggcca	11	8	16	6	0	1	1	1	0	0	1	1	4	1	4	2	5	2	4	2	5	3	3			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:97428127A>G	ENST00000377075.2	+	1	1489	c.1391A>G	c.(1390-1392)gAg>gGg	p.E464G		NM_020184.3	NP_064569.3	Q6P4Q7	CNNM4_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 4	464	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.				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						ATGCTGGAGGAGTTCAAGAAG	0.517																																					p.E464G		Atlas-SNP	.											.	CNNM4	48	.	0			c.A1391G						PASS	.						87	83	85					2																	97428127		2203	4300	6503	SO:0001583	missense	26504	exon1			TGGAGGAGTTCAA	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.1391A>G	chr2.hg19:g.97428127A>G	ENSP00000366275:p.Glu464Gly	82.0	0.0	.		81.0	36.0	.	NM_020184	B7Z1U0|C7SQM3|C7SQM4|C7SQM5|Q53RE5|Q9H9G3|Q9HCI0|Q9NRN1	Missense_Mutation	SNP	ENST00000377075.2	hg19	CCDS2024.2	.	.	.	.	.	.	.	.	.	.	A	20.1	3.937929	0.73557	.	.	ENSG00000158158	ENST00000377075	D	0.93712	-3.27	5.26	5.26	0.73747	Cystathionine beta-synthase, core (2);	0.000000	0.85682	D	0.000000	D	0.96623	0.8898	M	0.83774	2.66	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97084	0.9786	10	0.66056	D	0.02	-1.1101	14.1805	0.65572	1.0:0.0:0.0:0.0	.	464	Q6P4Q7	CNNM4_HUMAN	G	464	ENSP00000366275:E464G	ENSP00000366275:E464G	E	+	2	0	CNNM4	96791854	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.281000	0.95811	1.996000	0.58369	0.533000	0.62120	GAG	.	.	.	none		0.517	CNNM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252954.1	NM_020184		G	97428127	A	G	97428127	3	3	53	1	0	0	0	0	1	0	0	0	3617	304	11	3	1393	3	CNNM4	2	97428127	Missense_Mutation	SNP	A	TCGA-A4-8098-01A-11D-2396-08	740168	97428127	145771246	12	3585											
TMEM131	23505	hgsc.bcm.edu	37	chr2	98413329	98413329	+	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	tctgtacaatcttttaacaaTgcttccgtgattttaaagcg	11	16	6	8	2	2	1	0	1	2	0	3	1	3	1	1	0	4	2	1	0	6	6			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:98413329T>A	ENST00000186436.5	-	27	3219	c.2991A>T	c.(2989-2991)gcA>gcT	p.A997A		NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131	997						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						CTTTTAACAATGCTTCCGTGA	0.393																																					p.A997A		Atlas-SNP	.											.	TMEM131	258	.	0			c.A2991T						PASS	.						109	108	109					2																	98413329		1899	4122	6021	SO:0001819	synonymous_variant	23505	exon27			TAACAATGCTTCC	AK025852	CCDS46368.1	2q11.2	2006-04-12			ENSG00000075568	ENSG00000075568			30366	protein-coding gene	gene with protein product		615659				9039502, 10996388	Standard	NM_015348		Approved	CC28, YR-23, RW1, KIAA0257, PRO1048	uc002syh.4	Q92545	OTTHUMG00000153061	ENST00000186436.5:c.2991A>T	chr2.hg19:g.98413329T>A		59.0	0.0	.		65.0	23.0	.	NM_015348		Silent	SNP	ENST00000186436.5	hg19	CCDS46368.1																																																																																			.	.	.	none		0.393	TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329285.2	XM_371542		A	98413329	T	A	98413329	2	1	53	1	0	0	0	0	0	0	0	1	16056	1451	51	5		5	TMEM131	2	98413329	Silent	SNP	T	TCGA-A4-8098-01A-11D-2396-08	985202	98413329	144786044	13	3586											
GALNT5	11227	hgsc.bcm.edu	37	chr2	158115698	158115699	+	Frame_Shift_Ins	INS	-	-	T																															atagaagtgagatgtcttccINStcttcacttgctccacatag																								rs141648249		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:158115698_158115699insT	ENST00000259056.4	+	1	1589_1590	c.1104_1105insT	c.(1105-1107)tctfs	p.S369fs		NM_014568.1	NP_055383.1	Q7Z7M9	GALT5_HUMAN	polypeptide N-acetylgalactosaminyltransferase 5	369					cellular protein metabolic process (GO:0044267)|glycosaminoglycan biosynthetic process (GO:0006024)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(4)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	56						AGATGTCTTCCTCTTCACTTGC	0.416																																					p.S368fs		Atlas-INDEL	.											.	GALNT5	112	.	0			c.1104_1105insT						PASS	.																																			SO:0001589	frameshift_variant	11227	exon1			.	AJ245539	CCDS2203.1	2q24.1	2014-03-13	2014-03-13		ENSG00000136542	ENSG00000136542	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4127	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 5"	615129	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5 (GalNAc-T5)"			10545594	Standard	NM_014568		Approved	GalNAc-T5	uc002tzg.3	Q7Z7M9	OTTHUMG00000131965	ENST00000259056.4:c.1105dupT	chr2.hg19:g.158115699_158115699dupT	ENSP00000259056:p.Ser369fs	186.0	0.0	0		147.0	49.0	0.333333	NM_014568	A5PKZ1|Q9UGK7|Q9UHL6	Frame_Shift_Ins	INS	ENST00000259056.4	hg19	CCDS2203.1																																																																																			.	.	.	none		0.416	GALNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254925.2	NM_014568		T	158115699	-	T	158115698	7	5	53	1	0	1	1	0	0	0	0	0	6223	668	24	0	1106	0	GALNT5	2	158115698	Frame_Shift_Ins	INS	-	TCGA-A4-8098-01A-11D-2396-08	59702369	158115698	85083675	14	3587											
COL6A3	1293	hgsc.bcm.edu	37	chr2	238280361	238280361	+	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	gctccaaggagaacctccgaCgcccccatctcacctggagg	9	5	10	17	2	1	1	1	0	1	1	4	4	3	2	6	3	1	1	6	3	2	0	rs373893821		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr2:238280361C>T	ENST00000295550.4	-	9	4738				COL6A3_ENST00000346358.4_Intron|COL6A3_ENST00000392003.2_Silent_p.A1026A|COL6A3_ENST00000347401.3_Intron|COL6A3_ENST00000409809.1_Intron|COL6A3_ENST00000353578.4_Intron|COL6A3_ENST00000392004.3_Silent_p.A1227A|COL6A3_ENST00000472056.1_Intron	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3						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.A1227A(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)		GAACCTCCGACGCCCCCATCT	0.473																																					p.A1227A		Atlas-SNP	.											.	COL6A3	608	.	1	Substitution - coding silent(1)	lung(1)	c.G3681A						PASS	.	C	,,,,	1,4405	2.1+/-5.4	0,1,2202	69	78	75		,3078,3681,,	-1.3	0	2		75	0,8600		0,0,4300	no	intron,coding-synonymous,coding-synonymous,intron,intron	COL6A3	NM_004369.3,NM_057164.4,NM_057165.4,NM_057166.4,NM_057167.3	,,,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,,,	,1026/1037,1227/1238,,	238280361	1,13005	2203	4300	6503	SO:0001627	intron_variant	1293	exon8			CTCCGACGCCCCC	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.4285+13G>A	chr2.hg19:g.238280361C>T		147.0	0.0	.		171.0	54.0	.	NM_057165	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	hg19	CCDS33412.1																																																																																			.	.	.	weak		0.473	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238280361	C	T	238280361	1	4	53	0	1	0	0	0	0	0	0	0	3703	523	19	1		1	COL6A3	2	238280361	Intron	SNP	C	TCGA-A4-8098-01A-11D-2396-08	80164663	238280361	4919012	15	3588											
CAPN7	23473	hgsc.bcm.edu	37	chr3	15288921	15288921	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	accccatctaccaattccatAtagaaaagactgggccgtta	14	9	6	12	1	1	2	0	0	1	2	2	2	2	2	5	1	1	1	5	1	7	5			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr3:15288921A>G	ENST00000253693.2	+	19	2414	c.2161A>G	c.(2161-2163)Ata>Gta	p.I721V		NM_014296.2	NP_055111.1	Q9Y6W3	CAN7_HUMAN	calpain 7	721	Domain N.				positive regulation of epithelial cell migration (GO:0010634)|self proteolysis (GO:0097264)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|endopeptidase activity (GO:0004175)|MIT domain binding (GO:0090541)			breast(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|skin(2)	22						CCAATTCCATATAGAAAAGAC	0.363																																					p.I721V		Atlas-SNP	.											.	CAPN7	63	.	0			c.A2161G						PASS	.						84	84	84					3																	15288921		2203	4300	6503	SO:0001583	missense	23473	exon19			TTCCATATAGAAA	AB028639	CCDS2624.1	3p24	2008-07-18			ENSG00000131375	ENSG00000131375			1484	protein-coding gene	gene with protein product	"calpain like protease", "homolog of Aspergillus Nidulans PALB"	606400				8163008, 10051333	Standard	NM_014296		Approved	PalBH	uc003bzn.3	Q9Y6W3	OTTHUMG00000129863	ENST00000253693.2:c.2161A>G	chr3.hg19:g.15288921A>G	ENSP00000253693:p.Ile721Val	121.0	0.0	.		116.0	46.0	.	NM_014296		Missense_Mutation	SNP	ENST00000253693.2	hg19	CCDS2624.1	.	.	.	.	.	.	.	.	.	.	A	7.495	0.651423	0.14516	.	.	ENSG00000131375	ENST00000253693	D	0.85629	-2.01	5.57	-3.39	0.04868	Peptidase C2, calpain, large subunit, domain III (2);Peptidase C2, calpain, domain III (1);	0.669254	0.16098	N	0.229700	T	0.62816	0.2459	N	0.16266	0.395	0.21105	N	0.999789	B	0.02656	0.0	B	0.12837	0.008	T	0.49244	-0.8960	10	0.15066	T	0.55	-2.6499	1.3262	0.02126	0.3616:0.1918:0.2926:0.154	.	721	Q9Y6W3	CAN7_HUMAN	V	721	ENSP00000253693:I721V	ENSP00000253693:I721V	I	+	1	0	CAPN7	15263925	0.062000	0.20869	0.564000	0.28396	0.978000	0.69477	-0.068000	0.11561	-0.127000	0.11661	0.533000	0.62120	ATA	.	.	.	none		0.363	CAPN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252105.2	NM_014296		G	15288921	A	G	15288921	3	3	53	1	0	0	0	0	1	0	0	0	2633	449	16	3	2235	3	CAPN7	3	15288921	Missense_Mutation	SNP	A	TCGA-A4-8098-01A-11D-2396-08		15288921	182733509	16	3589											
ACAA1	30	hgsc.bcm.edu	37	chr3	38168151	38168151	+	Missense_Mutation	SNP	T	T	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	cgtggtggtcacaggcacaaTctcagcttggaaacagccct	10	8	11	12	1	2	0	2	0	1	0	3	1	2	1	1	4	3	2	1	4	2	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr3:38168151T>G	ENST00000333167.8	-	8	839	c.667A>C	c.(667-669)Att>Ctt	p.I223L	ACAA1_ENST00000444607.2_3'UTR|ACAA1_ENST00000301810.7_Missense_Mutation_p.I190L|ACAA1_ENST00000544624.1_Missense_Mutation_p.I71L|ACAA1_ENST00000480865.1_5'UTR|ACAA1_ENST00000450296.1_Missense_Mutation_p.I182L|Y_RNA_ENST00000365095.1_RNA	NM_001607.3	NP_001598.1	P09110	THIK_HUMAN	acetyl-CoA acyltransferase 1	223					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)		ACAGGCACAATCTCAGCTTGG	0.612																																					p.I223L		Atlas-SNP	.											.	ACAA1	32	.	0			c.A667C						PASS	.						146	120	129					3																	38168151		2203	4300	6503	SO:0001583	missense	30	exon8			GCACAATCTCAGC	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.667A>C	chr3.hg19:g.38168151T>G	ENSP00000333664:p.Ile223Leu	117.0	0.0	.		125.0	54.0	.	NM_001607	G5E935|Q96CA6	Missense_Mutation	SNP	ENST00000333167.8	hg19	CCDS2673.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	32|32	5.183188|5.183188	0.94885|0.94885	.|.	.|.	ENSG00000060971|ENSG00000060971	ENST00000333167;ENST00000301810;ENST00000450296;ENST00000358122;ENST00000544624|ENST00000452171;ENST00000421218	D;D;D;D|.	0.93547|.	-3.11;-3.11;-3.24;-3.24|.	5.46|5.46	5.46|5.46	0.80206|0.80206	Thiolase-like, subgroup (1);Thiolase, N-terminal (1);Thiolase-like (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.78892|0.78892	0.4355|0.4355	M|M	0.84585|0.84585	2.705|2.705	0.80722|0.80722	D|D	1|1	P;D;D;D|.	0.71674|.	0.911;0.997;0.998;0.993|.	D;D;D;D|.	0.85130|.	0.926;0.914;0.997;0.956|.	T|T	0.81484|0.81484	-0.0912|-0.0912	10|5	0.87932|.	D|.	0|.	-10.3475|-10.3475	15.5417|15.5417	0.76057|0.76057	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	155;182;190;223|.	F5GXL8;C9JDE9;G5E935;P09110|.	.;.;.;THIK_HUMAN|.	L|S	223;190;182;155;71|95;112	ENSP00000333664:I223L;ENSP00000301810:I190L;ENSP00000395183:I182L;ENSP00000445710:I71L|.	ENSP00000301810:I190L|.	I|R	-|-	1|3	0|2	ACAA1|ACAA1	38143155|38143155	1.000000|1.000000	0.71417|0.71417	0.988000|0.988000	0.46212|0.46212	0.998000|0.998000	0.95712|0.95712	6.148000|6.148000	0.71788|0.71788	2.072000|2.072000	0.62099|0.62099	0.533000|0.533000	0.62120|0.62120	ATT|AGA	.	.	.	none		0.612	ACAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342980.1	NM_001607		G	38168151	T	G	38168151	3	3	53	1	0	0	0	0	1	0	0	0	104	1435	50	5	627	5	ACAA1	3	38168151	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08	22879230	38168151	159854279	17	3590											
TGM4	7047	hgsc.bcm.edu	37	chr3	44926858	44926858	+	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	acttcttgaatcaggacaacGccgtttctcaccacacatgg	11	10	7	13	2	3	1	2	1	2	0	4	2	3	2	2	2	1	1	2	2	2	3			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr3:44926858G>T	ENST00000296125.4	+	2	129	c.61G>T	c.(61-63)Gcc>Tcc	p.A21S		NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	21					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)	TCAGGACAACGCCGTTTCTCA	0.522																																					p.A21S		Atlas-SNP	.											.	TGM4	82	.	0			c.G61T						PASS	.						102	93	96					3																	44926858		2203	4300	6503	SO:0001583	missense	7047	exon2			GACAACGCCGTTT	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.61G>T	chr3.hg19:g.44926858G>T	ENSP00000296125:p.Ala21Ser	48.0	0.0	.		44.0	13.0	.	NM_003241	Q16707|Q96QN4	Missense_Mutation	SNP	ENST00000296125.4	hg19	CCDS2723.1	.	.	.	.	.	.	.	.	.	.	G	9.481	1.098065	0.20552	.	.	ENSG00000163810	ENST00000296125	D	0.84873	-1.91	2.77	-1.63	0.08345	Immunoglobulin E-set (1);Transglutaminase, N-terminal (1);Immunoglobulin-like fold (1);	0.329666	0.20233	U	0.096458	T	0.70850	0.3271	L	0.33245	0.995	0.09310	N	1	B;P	0.36027	0.448;0.533	B;B	0.37047	0.24;0.1	T	0.62296	-0.6884	10	0.10902	T	0.67	.	6.6582	0.22998	0.4424:0.0:0.5576:0.0	.	21;21	P49221;B4YUQ1	TGM4_HUMAN;.	S	21	ENSP00000296125:A21S	ENSP00000296125:A21S	A	+	1	0	TGM4	44901862	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.711000	0.05019	-0.425000	0.07371	0.467000	0.42956	GCC	.	.	.	none		0.522	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241		T	44926858	G	T	44926858	3	4	53	1	0	0	0	0	1	0	0	0	15844	1087	38	4	67	4	TGM4	3	44926858	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	6758707	44926858	153095572	18	3591											
SETD2	29072	hgsc.bcm.edu	37	chr3	47127778	47127778	+	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	ccatgacgttccagaaaggaCttcaggcaggactgtgagtg	11	8	13	9	1	1	3	1	2	0	1	2	5	2	5	2	3	0	2	2	3	1	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr3:47127778C>A	ENST00000409792.3	-	11	5346	c.5304G>T	c.(5302-5304)aaG>aaT	p.K1768N	SETD2_ENST00000492397.1_5'Flank|snoU13_ENST00000516129.1_RNA	NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1768					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CCAGAAAGGACTTCAGGCAGG	0.512			"N, F, S, Mis"		clear cell renal carcinoma																																p.K1768N		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.G5304T						PASS	.						127	110	116					3																	47127778		2203	4300	6503	SO:0001583	missense	29072	exon11			AAAGGACTTCAGG	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.5304G>T	chr3.hg19:g.47127778C>A	ENSP00000386759:p.Lys1768Asn	72.0	0.0	.		57.0	22.0	.	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	C	20.4	3.988848	0.74589	.	.	ENSG00000181555	ENST00000451092;ENST00000409792	D	0.90504	-2.68	5.47	4.52	0.55395	.	0.000000	0.56097	D	0.000025	D	0.93220	0.7840	M	0.62723	1.935	0.58432	D	0.999992	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.91914	0.5542	10	0.42905	T	0.14	.	9.269	0.37659	0.0:0.8236:0.0:0.1764	.	1768;1768	F2Z317;Q9BYW2	.;SETD2_HUMAN	N	1768	ENSP00000386759:K1768N	ENSP00000386759:K1768N	K	-	3	2	SETD2	47102782	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.865000	0.39479	1.167000	0.42706	0.650000	0.86243	AAG	.	.	.	none		0.512	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		A	47127778	C	A	47127778	3	1	53	1	0	0	0	0	1	0	0	0	14144	564	20	4	2434	4	SETD2	3	47127778	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	2200920	47127778	150894652	19	3592											
TMEM175	84286	hgsc.bcm.edu	37	chr4	947053	947053	+	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	agcgctctgcccacagggctCtgtaccgacgacacgtcctg	7	7	11	16	4	2	0	0	0	2	0	3	2	3	0	3	1	3	3	3	1	1	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr4:947053C>G	ENST00000264771.4	+	8	723	c.538C>G	c.(538-540)Ctg>Gtg	p.L180V	TMEM175_ENST00000515740.1_Missense_Mutation_p.L64V|TMEM175_ENST00000508204.1_Missense_Mutation_p.L98V|TMEM175_ENST00000504180.1_3'UTR	NM_032326.2	NP_115702.1	Q9BSA9	TM175_HUMAN	transmembrane protein 175	180						integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				NS(1)|endometrium(1)|large_intestine(2)|lung(6)|pancreas(1)|upper_aerodigestive_tract(3)	14			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			CCACAGGGCTCTGTACCGACG	0.617																																					p.L180V		Atlas-SNP	.											.	TMEM175	44	.	0			c.C538G						PASS	.						120	100	107					4																	947053		2203	4300	6503	SO:0001583	missense	84286	exon8			AGGGCTCTGTACC	BC005158	CCDS3341.1, CCDS75087.1, CCDS75088.1	4p16.3	2008-02-05			ENSG00000127419	ENSG00000127419			28709	protein-coding gene	gene with protein product						12477932	Standard	XM_005272301		Approved	MGC4618	uc003gbq.3	Q9BSA9	OTTHUMG00000118996	ENST00000264771.4:c.538C>G	chr4.hg19:g.947053C>G	ENSP00000264771:p.Leu180Val	52.0	0.0	.		65.0	33.0	.	NM_032326	D3DVN4|Q8ND13	Missense_Mutation	SNP	ENST00000264771.4	hg19	CCDS3341.1	.	.	.	.	.	.	.	.	.	.	c	0.044	-1.272845	0.01421	.	.	ENSG00000127419	ENST00000264771;ENST00000514453;ENST00000515492;ENST00000359768;ENST00000509508;ENST00000515740;ENST00000508204;ENST00000510493	T;T;T;T	0.46819	1.44;0.94;1.49;0.86	4.71	-0.169	0.13339	.	0.217286	0.39083	N	0.001461	T	0.31263	0.0791	L	0.54323	1.7	0.09310	N	1	B;B;B	0.20887	0.001;0.049;0.031	B;B;B	0.19666	0.001;0.026;0.005	T	0.11251	-1.0595	10	0.15499	T	0.54	-27.4926	1.8457	0.03158	0.1956:0.2847:0.3858:0.1339	.	98;180;98	D6RBE5;Q9BSA9;B3KR27	.;TM175_HUMAN;.	V	180;167;98;98;86;64;98;98	ENSP00000264771:L180V;ENSP00000425181:L167V;ENSP00000427039:L64V;ENSP00000423669:L98V	ENSP00000264771:L180V	L	+	1	2	TMEM175	937053	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.647000	0.24812	0.040000	0.15660	-0.322000	0.08575	CTG	.	.	.	none		0.617	TMEM175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239193.2	NM_032326		G	947053	C	G	947053	3	3	53	1	0	0	0	0	1	0	0	0	16103	912	32	4	564	4	TMEM175	4	947053	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08		947053	190207223	20	3593											
FGFR3	2261	hgsc.bcm.edu	37	chr4	1805487	1805487	+	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	cacaacgtcacctttgaggaCgccggggagtacacctgcct	9	7	11	14	3	1	1	1	1	0	0	1	3	1	3	4	3	3	1	4	3	2	2	rs370530264		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr4:1805487C>T	ENST00000260795.2	+	7	1101	c.999C>T	c.(997-999)gaC>gaT	p.D333D	FGFR3_ENST00000352904.1_Intron|FGFR3_ENST00000340107.4_Intron|FGFR3_ENST00000481110.2_Silent_p.D333D|FGFR3_ENST00000440486.2_Silent_p.D333D|FGFR3_ENST00000412135.2_Intron			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	333	Ig-like C2-type 3.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)			NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	CCTTTGAGGACGCCGGGGAGT	0.592		1	"Mis, T"	"IGH@, ETV6"	"bladder, MM, T-cell lymphoma"		"Hypochondroplasia, Thanatophoric dysplasia"		Saethre-Chotzen syndrome;Muenke syndrome																												p.D333D		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"L, E"	FGFR3,colon,carcinoma,0,1	FGFR3	3320	.	0			c.C999T						PASS	.	C	,,	0,4406		0,0,2203	101	99	100		999,,	-1.1	1	4		100	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,intron,intron	FGFR3	NM_000142.4,NM_001163213.1,NM_022965.3	,,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,,	333/807,,	1805487	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	2261	exon8	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	TGAGGACGCCGGG	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.999C>T	chr4.hg19:g.1805487C>T		65.0	0.0	.		70.0	3.0	.	NM_000142	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Silent	SNP	ENST00000260795.2	hg19	CCDS3353.1																																																																																			.	.	.	weak		0.592	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142		T	1805487	C	T	1805487	2	4	53	1	0	0	0	0	0	0	0	1	5874	535	19	1		1	FGFR3	4	1805487	Silent	SNP	C	TCGA-A4-8098-01A-11D-2396-08	858434	1805487	189348789	21	3594											
HGFAC	3083	hgsc.bcm.edu	37	chr4	3443800	3443800	+	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	0	0	0	0	0	0	0	0	0	cccttcctcctcctcctcctGctgctgctgctgctgccacg	1	12	7	21	1	0	0	0	0	0	0	5	0	5	0	7	0	6	5	7	0	0	1	rs372137428		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr4:3443800G>C	ENST00000382774.3	+	1	187	c.72G>C	c.(70-72)ctG>ctC	p.L24L	HGFAC_ENST00000511533.1_Silent_p.L24L	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	24					proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		TCCTCCTCCTGCTGCTGCTGC	0.716													G|||	1	0.000199681	8e-04	0	5008	,	,		13355	0		0	False		,,,				2504	0				p.L24L		Atlas-SNP	.											.	HGFAC	69	.	0			c.G72C						PASS	.	G		5,3433		0,5,1714	13	16	15		72	0.1	1	4		15	0,7164		0,0,3582	no	coding-synonymous	HGFAC	NM_001528.2		0,5,5296	CC,CG,GG		0.0,0.1454,0.0472		24/656	3443800	5,10597	1719	3582	5301	SO:0001819	synonymous_variant	3083	exon1			CCTCCTGCTGCTG	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.72G>C	chr4.hg19:g.3443800G>C		39.0	0.0	.		55.0	5.0	.	NM_001528	Q14726|Q2M1W7|Q53X47	Silent	SNP	ENST00000382774.3	hg19	CCDS3369.1																																																																																			.	.	.	weak		0.716	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3			C	3443800	G	C	3443800	2	2	53	1	0	0	0	0	0	0	0	1	7093	1306	46	4		4	HGFAC	4	3443800	Silent	SNP	G	TCGA-A4-8098-01A-11D-2396-08	1638313	3443800	187710476	22	3595											
DRD5	1816	hgsc.bcm.edu	37	chr4	9784197	9784197	+	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	cggtccagctcaactggcacAgggaccaggcggcctcttgg	7	6	14	14	2	2	0	1	0	1	0	3	1	3	1	3	6	2	2	3	6	1	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr4:9784197A>T	ENST00000304374.2	+	1	940	c.544A>T	c.(544-546)Agg>Tgg	p.R182W		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	182					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|associative learning (GO:0008306)|cellular calcium ion homeostasis (GO:0006874)|cellular response to catecholamine stimulus (GO:0071870)|long term synaptic depression (GO:0060292)|negative regulation of blood pressure (GO:0045776)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|reactive oxygen species metabolic process (GO:0072593)|regulation of female receptivity (GO:0045924)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|sensitization (GO:0046960)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)|transmission of nerve impulse (GO:0019226)|wound healing (GO:0042060)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)			NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57					Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinnarizine(DB00568)|Dopamine(DB00988)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Ropinirole(DB00268)|Rotigotine(DB05271)|Trimipramine(DB00726)|Ziprasidone(DB00246)	CAACTGGCACAGGGACCAGGC	0.617																																					p.R182W		Atlas-SNP	.											.	DRD5	119	.	0			c.A544T						PASS	.						35	36	35					4																	9784197		2203	4299	6502	SO:0001583	missense	1816	exon1			TGGCACAGGGACC	X58454	CCDS3405.1	4p16.1	2012-08-08			ENSG00000169676	ENSG00000169676		"GPCR / Class A : Dopamine receptors"	3026	protein-coding gene	gene with protein product		126453		DRD1L2		1774076	Standard	NM_000798		Approved	DRD1B	uc003gmb.4	P21918	OTTHUMG00000128489	ENST00000304374.2:c.544A>T	chr4.hg19:g.9784197A>T	ENSP00000306129:p.Arg182Trp	92.0	0.0	.		84.0	33.0	.	NM_000798	B2R9S3|Q8NEQ8	Missense_Mutation	SNP	ENST00000304374.2	hg19	CCDS3405.1	.	.	.	.	.	.	.	.	.	.	a	16.35	3.098148	0.56183	.	.	ENSG00000169676	ENST00000304374	T	0.73047	-0.71	4.53	-6.0	0.02206	GPCR, rhodopsin-like superfamily (1);	0.214762	0.44483	D	0.000455	T	0.80088	0.4559	M	0.74881	2.28	0.37769	D	0.926595	D	0.71674	0.998	D	0.70935	0.971	T	0.82639	-0.0358	10	0.87932	D	0	.	17.6446	0.88145	0.2761:0.7239:0.0:0.0	.	182	P21918	DRD5_HUMAN	W	182	ENSP00000306129:R182W	ENSP00000306129:R182W	R	+	1	2	DRD5	9393295	1.000000	0.71417	0.162000	0.22713	0.673000	0.39480	3.173000	0.50839	-1.286000	0.02384	-0.973000	0.02599	AGG	.	.	.	none		0.617	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1			T	9784197	A	T	9784197	3	4	53	1	0	0	0	0	1	0	0	0	4762	179	7	5	546	5	DRD5	4	9784197	Missense_Mutation	SNP	A	TCGA-A4-8098-01A-11D-2396-08	6340397	9784197	181370079	23	3596											
ANK2	287	hgsc.bcm.edu	37	chr4	114232517	114232517	+	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	cagttcctggatggtatgaaTtacctgcgatacagcttgga	10	12	11	8	1	0	1	0	1	0	0	1	4	1	3	2	3	4	3	2	3	4	5			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr4:114232517T>A	ENST00000357077.4	+	24	2708	c.2655T>A	c.(2653-2655)aaT>aaA	p.N885K	ANK2_ENST00000264366.6_Missense_Mutation_p.N885K|ANK2_ENST00000394537.3_Missense_Mutation_p.N885K|ANK2_ENST00000509550.1_Missense_Mutation_p.N94K|ANK2_ENST00000506722.1_Missense_Mutation_p.N864K	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	885					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)		ATGGTATGAATTACCTGCGAT	0.438																																					p.N885K		Atlas-SNP	.											.	ANK2	576	.	0			c.T2655A						PASS	.						163	134	144					4																	114232517		2203	4300	6503	SO:0001583	missense	287	exon24			TATGAATTACCTG	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.2655T>A	chr4.hg19:g.114232517T>A	ENSP00000349588:p.Asn885Lys	95.0	0.0	.		73.0	39.0	.	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	hg19	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	T	11.00	1.511662	0.27036	.	.	ENSG00000145362	ENST00000503271;ENST00000503423;ENST00000506722;ENST00000504454;ENST00000394537;ENST00000357077;ENST00000264366;ENST00000343056;ENST00000509550	T;T;T;T;T;T;T;T	0.75154	-0.04;0.07;-0.13;-0.04;-0.12;-0.17;-0.2;-0.91	5.15	-2.52	0.06346	.	0.000000	0.53938	D	0.000056	T	0.53932	0.1827	L	0.27053	0.805	0.80722	D	1	B;P;B;P;B;B	0.44627	0.0;0.839;0.372;0.835;0.026;0.288	B;B;B;B;B;B	0.36719	0.001;0.231;0.058;0.228;0.029;0.081	T	0.51810	-0.8658	10	0.21014	T	0.42	.	14.3697	0.66830	0.0:0.6687:0.0:0.3313	.	94;885;885;885;864;864	E9PCH6;Q01484;Q01484-2;Q01484-4;Q01484-5;F8WEF9	.;ANK2_HUMAN;.;.;.;.	K	864;831;864;900;885;885;885;864;94	ENSP00000423799:N864K;ENSP00000421011:N831K;ENSP00000421067:N864K;ENSP00000424722:N900K;ENSP00000378044:N885K;ENSP00000349588:N885K;ENSP00000264366:N885K;ENSP00000426944:N94K	ENSP00000264366:N885K	N	+	3	2	ANK2	114451966	0.711000	0.27906	0.990000	0.47175	0.999000	0.98932	-0.123000	0.10611	-0.397000	0.07691	0.533000	0.62120	AAT	.	.	.	none		0.438	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		A	114232517	T	A	114232517	3	1	53	1	0	0	0	0	1	0	0	0	621	1490	52	5	2774	5	ANK2	4	114232517	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08	104448320	114232517	76921759	24	3597											
TRPC3	7222	hgsc.bcm.edu	37	chr4	122825594	122825594	+	Missense_Mutation	SNP	A	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	atattttctatgaatttgtgAtcatatttgagcacaacgga	13	16	7	5	1	2	3	1	3	1	0	2	4	2	4	0	1	2	1	0	1	5	7			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr4:122825594A>C	ENST00000379645.3	-	8	2209	c.2136T>G	c.(2134-2136)gaT>gaG	p.D712E	TRPC3_ENST00000264811.5_Missense_Mutation_p.D639E|TRPC3_ENST00000513531.1_Missense_Mutation_p.D584E	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	627					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						TGAATTTGTGATCATATTTGA	0.308																																					p.D712E		Atlas-SNP	.											.	TRPC3	201	.	0			c.T2136G						PASS	.						89	86	87					4																	122825594		2203	4298	6501	SO:0001583	missense	7222	exon8			TTTGTGATCATAT	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.2136T>G	chr4.hg19:g.122825594A>C	ENSP00000368966:p.Asp712Glu	74.0	0.0	.		52.0	20.0	.	NM_001130698	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Missense_Mutation	SNP	ENST00000379645.3	hg19	CCDS47130.1	.	.	.	.	.	.	.	.	.	.	A	15.95	2.982982	0.53827	.	.	ENSG00000138741	ENST00000264811;ENST00000379645;ENST00000513531	T;T;T	0.75938	-0.76;-0.98;-0.92	5.77	0.478	0.16789	Ion transport (1);	0.000000	0.85682	D	0.000000	T	0.59622	0.2207	L	0.35487	1.065	0.43187	D	0.995017	B;B;B	0.19935	0.002;0.018;0.04	B;B;B	0.30716	0.057;0.057;0.119	T	0.39121	-0.9629	10	0.10111	T	0.7	-24.2756	9.899	0.41335	0.7445:0.0:0.2555:0.0	.	627;584;712	Q13507;E9PCJ9;Q5G1L5	TRPC3_HUMAN;.;.	E	639;712;584	ENSP00000264811:D639E;ENSP00000368966:D712E;ENSP00000426899:D584E	ENSP00000264811:D639E	D	-	3	2	TRPC3	123045044	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	1.041000	0.30291	-0.050000	0.13356	0.533000	0.62120	GAT	.	.	.	none		0.308	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305		C	122825594	A	C	122825594	3	2	53	1	0	0	0	0	1	0	0	0	16591	330	12	5	649	5	TRPC3	4	122825594	Missense_Mutation	SNP	A	TCGA-A4-8098-01A-11D-2396-08	8593077	122825594	68328682	25	3598											
ADAM29	11086	hgsc.bcm.edu	37	chr4	175898831	175898832	+	Frame_Shift_Ins	INS	-	-	A																															tccatctgcaaaagaagaggINSaaaaaattcagcgtcgacct																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr4:175898831_175898832insA	ENST00000359240.3	+	5	2825_2826	c.2155_2156insA	c.(2155-2157)gaafs	p.E719fs	ADAM29_ENST00000514159.1_Frame_Shift_Ins_p.E719fs|ADAM29_ENST00000404450.4_Frame_Shift_Ins_p.E719fs|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000445694.1_Frame_Shift_Ins_p.E719fs	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	719					spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.E719K(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)		AAAAGAAGAGGAAAAAATTCAG	0.406																																					p.E719fs	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-INDEL	.											ADAM29,NS,malignant_melanoma,0,1	ADAM29	262	.	1	Substitution - Missense(1)	NS(1)	c.2155_2156insA						PASS	.																																			SO:0001589	frameshift_variant	11086	exon5			.	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.2161dupA	chr4.hg19:g.175898837_175898837dupA	ENSP00000352177:p.Glu719fs	101.0	0.0	0		73.0	46.0	0.630137	NM_014269	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Frame_Shift_Ins	INS	ENST00000359240.3	hg19	CCDS3823.1																																																																																			.	.	.	none		0.406	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding				A	175898832	-	A	175898831	7	5	53	1	0	1	1	0	0	0	0	0	247	1175	41	0	2157	0	ADAM29	4	175898831	Frame_Shift_Ins	INS	-	TCGA-A4-8098-01A-11D-2396-08	53073237	175898831	15255445	26	3599											
CENPH	64946	hgsc.bcm.edu	37	chr5	68505552	68505552	+	Frame_Shift_Del	DEL	A	A	-																															agaaccttattttggggagtAaagtcaattgggcagaggat																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr5:68505552delA	ENST00000283006.2	+	9	757	c.670delA	c.(670-672)aaafs	p.K224fs	CENPH_ENST00000515001.1_Frame_Shift_Del_p.K205fs	NM_022909.3	NP_075060.1			centromere protein H											kidney(15)|large_intestine(2)|lung(3)	20		Lung NSC(167;5.51e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.41e-56)|Epithelial(20;1.29e-52)|all cancers(19;3.15e-48)|Lung(70;0.0178)		TTTGGGGAGTAAAGTCAATTG	0.289																																					p.S223fs		Atlas-INDEL	.											.	CENPH	28	.	0			c.669delT						PASS	.						78	78	78					5																	68505552		2203	4300	6503	SO:0001589	frameshift_variant	64946	exon9			.	AB035124	CCDS3998.1	5p15.2	2013-11-05			ENSG00000153044	ENSG00000153044			17268	protein-coding gene	gene with protein product		605607				11092768, 15502821	Standard	NM_022909		Approved		uc003jvp.3	Q9H3R5	OTTHUMG00000097816	ENST00000283006.2:c.670delA	chr5.hg19:g.68505552delA	ENSP00000283006:p.Lys224fs	57.0	0.0	0		57.0	31.0	0.54386	NM_022909		Frame_Shift_Del	DEL	ENST00000283006.2	hg19	CCDS3998.1																																																																																			.	.	.	none		0.289	CENPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215083.1			-	68505552	A	-	68505552	7	5	53	1	0	1	0	1	0	0	0	0	3234	363	13	0	704	0	CENPH	5	68505552	Frame_Shift_Del	DEL	A	TCGA-A4-8098-01A-11D-2396-08		68505552	112409708	27	3600											
GFM2	84340	hgsc.bcm.edu	37	chr5	74026107	74026107	+	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	gtggcacgaactgagtttagGatggtctctcgatatgccac	9	11	12	9	2	1	1	0	1	1	0	3	4	1	2	1	3	2	2	1	3	3	3			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr5:74026107G>T	ENST00000296805.3	-	17	2161	c.1704C>A	c.(1702-1704)atC>atA	p.I568I	GFM2_ENST00000509430.1_Silent_p.I568I|GFM2_ENST00000345239.2_Silent_p.I521I|GFM2_ENST00000515125.1_Intron	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)		CTGAGTTTAGGATGGTCTCTC	0.413																																					p.I568I		Atlas-SNP	.											.	GFM2	38	.	0			c.C1704A						PASS	.						106	100	102					5																	74026107		2203	4300	6503	SO:0001819	synonymous_variant	84340	exon17			GTTTAGGATGGTC	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.1704C>A	chr5.hg19:g.74026107G>T		69.0	0.0	.		114.0	32.0	.	NM_032380		Silent	SNP	ENST00000296805.3	hg19	CCDS4023.1																																																																																			.	.	.	none		0.413	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380		T	74026107	G	T	74026107	2	4	53	1	0	0	0	0	0	0	0	1	6349	1164	41	4		4	GFM2	5	74026107	Silent	SNP	G	TCGA-A4-8098-01A-11D-2396-08	5520555	74026107	106889153	28	3601											
POC5	134359	hgsc.bcm.edu	37	chr5	74981182	74981182	+	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	cctccgacggcggctggtggGgatggcagcagtggtgatgt	5	8	19	9	3	0	1	0	1	0	0	1	3	1	2	2	7	1	3	2	7	0	0			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr5:74981182G>C	ENST00000428202.2	-	10	1446	c.1257C>G	c.(1255-1257)tcC>tcG	p.S419S	POC5_ENST00000510798.1_Silent_p.S302S|POC5_ENST00000514838.2_Silent_p.S391S|POC5_ENST00000380475.2_Silent_p.S302S|POC5_ENST00000446329.2_Silent_p.S394S	NM_001099271.1	NP_001092741.1	Q8NA72	POC5_HUMAN	POC5 centriolar protein	419					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						CGGCTGGTGGGGATGGCAGCA	0.557																																					p.S419S		Atlas-SNP	.											.	POC5	82	.	0			c.C1257G						PASS	.						100	118	112					5																	74981182		2058	4209	6267	SO:0001819	synonymous_variant	134359	exon10			TGGTGGGGATGGC	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.1257C>G	chr5.hg19:g.74981182G>C		120.0	0.0	.		199.0	47.0	.	NM_001099271	B4DJG7|Q494X7|Q494X9|Q6P085	Silent	SNP	ENST00000428202.2	hg19	CCDS47236.1																																																																																			.	.	.	none		0.557	POC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369124.1	NM_152408		C	74981182	G	C	74981182	2	2	53	1	0	0	0	0	0	0	0	1	12184	1219	43	4		4	POC5	5	74981182	Silent	SNP	G	TCGA-A4-8098-01A-11D-2396-08	955075	74981182	105934078	29	3602											
MSH3	4437	hgsc.bcm.edu	37	chr5	80160742	80160743	+	Frame_Shift_Ins	INS	-	-	GAAA																															gattcttggtcagtgaggatINSgaaagcaaactggatccagg																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr5:80160742_80160743insGAAA	ENST00000265081.6	+	22	3191_3192	c.3111_3112insGAAA	c.(3112-3114)gaafs	p.-1038fs		NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3						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)		TCAGTGAGGATGAAAGCAAACT	0.396								Mismatch excision repair (MMR)																													p.D1037fs	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-INDEL	.											.	MSH3	129	.	0			c.3111_3112insGAAA						PASS	.																																			SO:0001589	frameshift_variant	4437	exon22			.	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.3112_3115dupGAAA	chr5.hg19:g.80160743_80160746dupGAAA	ENSP00000265081:p.Glu1038fs	143.0	0.0	0		171.0	38.0	0.222222	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Frame_Shift_Ins	INS	ENST00000265081.6	hg19	CCDS34195.1																																																																																			.	.	.	none		0.396	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		GAAA	80160743	-	GAAA	80160742	7	5	53	1	0	1	1	0	0	0	0	0	9878	1461	51	0	3197	0	MSH3	5	80160742	Frame_Shift_Ins	INS	-	TCGA-A4-8098-01A-11D-2396-08	5179560	80160742	100754518	30	3603											
CHD1	1105	hgsc.bcm.edu	37	chr5	98195710	98195710	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gttttttaatagcatgcttaTataatttatgtaattttctt	11	23	4	3	0	1	0	0	0	1	0	1	0	1	0	0	0	2	4	0	0	7	13			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr5:98195710T>C	ENST00000284049.3	-	32	4639	c.4490A>G	c.(4489-4491)tAt>tGt	p.Y1497C		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	1497					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)	AGCATGCTTATATAATTTATG	0.274																																					p.Y1497C		Atlas-SNP	.											.	CHD1	137	.	0			c.A4490G						PASS	.						37	42	40					5																	98195710		2193	4275	6468	SO:0001583	missense	1105	exon32			TGCTTATATAATT	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.4490A>G	chr5.hg19:g.98195710T>C	ENSP00000284049:p.Tyr1497Cys	62.0	0.0	.		67.0	42.0	.	NM_001270	Q17RZ3	Missense_Mutation	SNP	ENST00000284049.3	hg19	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.048523	0.75846	.	.	ENSG00000153922	ENST00000422663;ENST00000284049	D	0.97041	-4.22	5.09	5.09	0.68999	.	0.000000	0.31233	U	0.008011	D	0.98378	0.9461	M	0.83384	2.64	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.99620	1.0983	10	0.87932	D	0	.	15.1564	0.72746	0.0:0.0:0.0:1.0	.	1497	O14646	CHD1_HUMAN	C	87;1497	ENSP00000284049:Y1497C	ENSP00000284049:Y1497C	Y	-	2	0	CHD1	98223610	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.671000	0.83941	2.036000	0.60181	0.533000	0.62120	TAT	.	.	.	none		0.274	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270		C	98195710	T	C	98195710	3	2	53	1	0	0	0	0	1	0	0	0	3325	1406	49	3	658	3	CHD1	5	98195710	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08	18034968	98195710	82719550	31	3604											
PCDHGA3	56112	hgsc.bcm.edu	37	chr5	140724210	140724210	+	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	agcgggccctggaccgtgagAaaaaagaaattcaccagctt	14	6	11	10	2	1	2	1	1	0	2	1	4	1	3	3	2	2	1	3	2	4	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr5:140724210A>T	ENST00000253812.6	+	1	610	c.610A>T	c.(610-612)Aaa>Taa	p.K204*	PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	204	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGACCGTGAGAAAAAAGAAAT	0.537																																					p.K204X		Atlas-SNP	.											.	PCDHGA3	246	.	0			c.A610T						PASS	.						48	51	50					5																	140724210		2151	4270	6421	SO:0001587	stop_gained	56112	exon1			CGTGAGAAAAAAG	AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"Cadherins / Protocadherins : Clustered"	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.610A>T	chr5.hg19:g.140724210A>T	ENSP00000253812:p.Lys204*	111.0	0.0	.		136.0	39.0	.	NM_032011	Q9Y5D4	Nonsense_Mutation	SNP	ENST00000253812.6	hg19	CCDS47290.1	.	.	.	.	.	.	.	.	.	.	.	16.89	3.246840	0.59103	.	.	ENSG00000254245	ENST00000253812	.	.	.	5.65	1.35	0.21983	.	0.498029	0.14302	U	0.328230	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	5.4155	0.16372	0.3545:0.1525:0.4931:0.0	.	.	.	.	X	204	.	ENSP00000253812:K204X	K	+	1	0	PCDHGA3	140704394	0.000000	0.05858	0.941000	0.38009	0.356000	0.29392	0.140000	0.16056	0.282000	0.22254	0.533000	0.62120	AAA	.	.	.	none		0.537	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916		T	140724210	A	T	140724210	4	4	53	1	0	0	0	0	0	1	0	0	11562	247	9	5	612	5	PCDHGA3	5	140724210	Nonsense_Mutation	SNP	A	TCGA-A4-8098-01A-11D-2396-08	42528500	140724210	40191050	32	3605											
PCDH1	5097	hgsc.bcm.edu	37	chr5	141233788	141233788	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggggccgttttggtgttcCggtcttccggggggctgggg	0	11	21	9	4	1	0	0	0	1	0	3	0	3	0	3	9	0	3	3	9	0	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr5:141233788C>T	ENST00000287008.3	-	5	3680	c.3533G>A	c.(3532-3534)cGg>cAg	p.R1178Q	PCDH1_ENST00000503492.1_3'UTR	NM_032420.2	NP_115796.2	Q08174	PCDH1_HUMAN	protocadherin 1	0					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)		TTTGGTGTTCCGGTCTTCCGG	0.652																																					p.R1178Q	Ovarian(132;1609 1739 4190 14731 45037)	Atlas-SNP	.											PCDH1,NS,carcinoma,0,1	PCDH1	119	.	0			c.G3533A						PASS	.						20	22	21					5																	141233788		2202	4299	6501	SO:0001583	missense	5097	exon5			GTGTTCCGGTCTT	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	ENST00000287008.3:c.3533G>A	chr5.hg19:g.141233788C>T	ENSP00000287008:p.Arg1178Gln	18.0	0.0	.		39.0	3.0	.	NM_032420	Q8IUP2	Missense_Mutation	SNP	ENST00000287008.3	hg19	CCDS4267.1	.	.	.	.	.	.	.	.	.	.	C	14.29	2.490764	0.44249	.	.	ENSG00000156453	ENST00000287008	T	0.53423	0.62	4.78	3.9	0.45041	.	1.032420	0.07798	U	0.956009	T	0.40886	0.1135	L	0.40543	1.245	0.80722	D	1	P	0.50443	0.935	B	0.38755	0.281	T	0.20472	-1.0274	10	0.41790	T	0.15	.	13.0535	0.58967	0.0:0.8367:0.1633:0.0	.	1178	Q08174-2	.	Q	1178	ENSP00000287008:R1178Q	ENSP00000287008:R1178Q	R	-	2	0	PCDH1	141213972	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.887000	0.48586	1.131000	0.42111	0.448000	0.29417	CGG	.	.	.	none		0.652	PCDH1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320587.2	NM_032420		T	141233788	C	T	141233788	3	4	53	1	0	0	0	0	1	0	0	0	11513	652	23	1	184	1	PCDH1	5	141233788	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	509578	141233788	39681472	33	3606											
SLC26A8	116369	hgsc.bcm.edu	37	chr6	35923086	35923086	+	Frame_Shift_Del	DEL	T	T	-																															caggcagtcctggtgagctgTttcttgatgagttattagga																								rs200648238		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr6:35923086delT	ENST00000490799.1	-	17	2428	c.2075delA	c.(2074-2076)aacfs	p.N692fs	SLC26A8_ENST00000394602.2_Frame_Shift_Del_p.N587fs|SLC26A8_ENST00000355574.2_Frame_Shift_Del_p.N692fs	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						TGGTGAGCTGTTTCTTGATGA	0.507																																					p.N692fs		Atlas-INDEL	.											.	SLC26A8	95	.	0			c.2076delC						PASS	.						194	187	190					6																	35923086		2203	4300	6503	SO:0001589	frameshift_variant	116369	exon17			.	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.2075delA	chr6.hg19:g.35923086delT	ENSP00000417638:p.Asn692fs	122.0	0.0	0		108.0	45.0	0.416667	NM_001193476		Frame_Shift_Del	DEL	ENST00000490799.1	hg19	CCDS4813.1																																																																																			.	.	.	none		0.507	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2			-	35923086	T	-	35923086	7	5	53	1	0	1	0	1	0	0	0	0	14536	1725	60	0	853	0	SLC26A8	6	35923086	Frame_Shift_Del	DEL	T	TCGA-A4-8098-01A-11D-2396-08		35923086	135191981	34	3607											
SLC22A7	10864	hgsc.bcm.edu	37	chr6	43266249	43266249	+	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	cctgcccaccgatgtgccctGccgggtgcccctgccaactt	4	8	10	19	2	0	0	0	0	0	0	0	1	0	0	8	1	6	0	8	1	1	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr6:43266249G>A	ENST00000372585.5	+	1	248	c.153G>A	c.(151-153)ctG>ctA	p.L51L	SLC22A7_ENST00000372574.3_Silent_p.L51L|SLC22A7_ENST00000372589.3_Silent_p.L51L|SLC22A7_ENST00000487175.1_Intron	NM_153320.2	NP_696961.2	Q9Y694	S22A7_HUMAN	solute carrier family 22 (organic anion transporter), member 7	51					organic anion transport (GO:0015711)|response to stilbenoid (GO:0035634)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			NS(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(3)	26			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)		Acetylsalicylic acid(DB00945)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Cimetidine(DB00501)|Clarithromycin(DB01211)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Docetaxel(DB01248)|Enalapril(DB00584)|Erythromycin(DB00199)|Fluorouracil(DB00544)|Ganciclovir(DB01004)|Glyburide(DB01016)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Oxtriphylline(DB01303)|Oxytetracycline(DB00595)|Pravastatin(DB00175)|Probenecid(DB01032)|Rifampicin(DB01045)|Salicylic acid(DB00936)|Testosterone(DB00624)|Tetracycline(DB00759)|Theophylline(DB00277)|Valproic Acid(DB00313)|Zalcitabine(DB00943)|Zidovudine(DB00495)	GATGTGCCCTGCCGGGTGCCC	0.662																																					p.L51L		Atlas-SNP	.											SLC22A7,NS,carcinoma,0,1	SLC22A7	69	.	0			c.G153A						PASS	.						51	51	51					6																	43266249		2203	4300	6503	SO:0001819	synonymous_variant	10864	exon1			TGCCCTGCCGGGT	AF097518	CCDS4892.1, CCDS4893.2	6p21.1	2013-05-22			ENSG00000137204	ENSG00000137204		"Solute carriers"	10971	protein-coding gene	gene with protein product		604995				9650585, 10773670	Standard	XM_006714970		Approved	NLT, OAT2	uc003out.3	Q9Y694	OTTHUMG00000014726	ENST00000372585.5:c.153G>A	chr6.hg19:g.43266249G>A		116.0	0.0	.		89.0	35.0	.	NM_006672	B2CZX6|Q5T046|Q5T048|Q5T050|Q9H2W5	Silent	SNP	ENST00000372585.5	hg19	CCDS4893.2																																																																																			.	.	.	none		0.662	SLC22A7-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040588.1			A	43266249	G	A	43266249	2	1	53	1	0	0	0	0	0	0	0	1	14472	1306	46	2		2	SLC22A7	6	43266249	Silent	SNP	G	TCGA-A4-8098-01A-11D-2396-08	7343163	43266249	127848818	35	3608											
LRRC1	55227	hgsc.bcm.edu	37	chr6	53660212	53660212	+	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	ccagctccgcgagctgcccgAggtaagggtccggcctcacc	6	5	13	17	4	1	0	1	0	0	0	3	2	3	0	6	3	3	3	6	3	1	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr6:53660212A>T	ENST00000370888.1	+	1	435	c.158A>T	c.(157-159)gAg>gTg	p.E53V	RP13-476E20.1_ENST00000429053.1_RNA|LRRC1_ENST00000370882.1_Splice_Site_p.E53V	NM_018214.4	NP_060684.4	Q9BTT6	LRRC1_HUMAN	leucine rich repeat containing 1	53						cytoplasm (GO:0005737)|membrane (GO:0016020)				cervix(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)		GAGCTGCCCGAGGTAAGGGTC	0.682																																					p.E53V		Atlas-SNP	.											.	LRRC1	59	.	0			c.A158T						PASS	.						28	28	28					6																	53660212		2203	4300	6503	SO:0001630	splice_region_variant	55227	exon1			TGCCCGAGGTAAG	AF332199	CCDS4953.2	6p12.2	2014-07-30	2003-11-19		ENSG00000137269	ENSG00000137269			14307	protein-coding gene	gene with protein product		608195	"leucine-rich repeat-containing 1"				Standard	NM_018214		Approved	dJ523E19.1, LANO, FLJ10775, FLJ11834	uc003pcd.1	Q9BTT6	OTTHUMG00000014885	ENST00000370888.1:c.159+1A>T	chr6.hg19:g.53660212A>T		26.0	0.0	.		31.0	9.0	.	NM_018214	Q5TGN3|Q9HAC0|Q9NVF1	Missense_Mutation	SNP	ENST00000370888.1	hg19	CCDS4953.2	.	.	.	.	.	.	.	.	.	.	A	18.98	3.737840	0.69304	.	.	ENSG00000137269	ENST00000370888;ENST00000370882	T;T	0.58797	0.31;0.31	4.88	3.68	0.42216	.	0.264852	0.37623	N	0.002013	T	0.35008	0.0917	N	0.25380	0.74	0.39279	D	0.96452	B	0.32467	0.372	B	0.42319	0.383	T	0.38373	-0.9664	10	0.87932	D	0	.	9.613	0.39674	0.914:0.0:0.086:0.0	.	53	Q9BTT6	LRRC1_HUMAN	V	53	ENSP00000359925:E53V;ENSP00000359919:E53V	ENSP00000359919:E53V	E	+	2	0	LRRC1	53768171	1.000000	0.71417	0.996000	0.52242	0.968000	0.65278	8.227000	0.89787	0.660000	0.30964	0.460000	0.39030	GAG	.	.	.	none		0.682	LRRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040970.2	NM_025168	Missense_Mutation	T	53660212	A	T	53660212	5	4	53	1	0	0	0	0	0	0	1	0	8973	318	11	5	160	5	LRRC1	6	53660212	Splice_Site	SNP	A	TCGA-A4-8098-01A-11D-2396-08	10393963	53660212	117454855	36	3609											
CD109	135228	hgsc.bcm.edu	37	chr6	74407130	74407130	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggaactctttaggcctcggTttctggtgacagccccaggg	6	10	14	11	1	2	1	0	1	2	0	3	2	2	2	3	5	2	1	3	5	2	3			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr6:74407130T>C	ENST00000287097.5	+	2	194	c.82T>C	c.(82-84)Ttt>Ctt	p.F28L	CD109_ENST00000437994.2_Missense_Mutation_p.F28L|RP11-553A21.3_ENST00000428865.2_RNA|CD109_ENST00000422508.2_Missense_Mutation_p.F28L			Q6YHK3	CD109_HUMAN	CD109 molecule	28					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						TAGGCCTCGGTTTCTGGTGAC	0.507																																					p.F28L		Atlas-SNP	.											.	CD109	170	.	0			c.T82C						PASS	.						103	101	102					6																	74407130		2203	4300	6503	SO:0001583	missense	135228	exon2			CCTCGGTTTCTGG	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.82T>C	chr6.hg19:g.74407130T>C	ENSP00000287097:p.Phe28Leu	113.0	0.0	.		118.0	49.0	.	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	hg19	CCDS4982.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.192857	0.78902	.	.	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.35421	1.86;1.31;1.86	5.31	5.31	0.75309	.	0.000000	0.64402	D	0.000004	T	0.29850	0.0746	N	0.19112	0.55	0.23555	N	0.997424	D;D;D;D	0.69078	0.965;0.997;0.986;0.985	P;D;P;P	0.66716	0.63;0.946;0.84;0.873	T	0.19516	-1.0303	10	0.72032	D	0.01	.	12.8889	0.58058	0.0:0.0:0.0:1.0	.	28;28;28;28	Q6YHK3-2;Q6YHK3-3;Q6YHK3-4;Q6YHK3	.;.;.;CD109_HUMAN	L	28	ENSP00000388062:F28L;ENSP00000404475:F28L;ENSP00000287097:F28L	ENSP00000287097:F28L	F	+	1	0	CD109	74463851	0.998000	0.40836	0.964000	0.40570	0.607000	0.37147	4.263000	0.58853	2.243000	0.73865	0.533000	0.62120	TTT	.	.	.	none		0.507	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493		C	74407130	T	C	74407130	3	2	53	1	0	0	0	0	1	0	0	0	2965	1725	60	3	88	3	CD109	6	74407130	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08	20746918	74407130	96707937	37	3610											
PHIP	55023	hgsc.bcm.edu	37	chr6	79724879	79724879	+	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	atcatgaccagcagaaaagaGaactctaggatcgaacgggt	16	6	11	8	2	2	3	1	1	1	2	3	6	2	4	1	2	3	1	1	2	5	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr6:79724879G>A	ENST00000275034.4	-	15	1611	c.1444C>T	c.(1444-1446)Ctc>Ttc	p.L482F		NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	482					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)		GCAGAAAAGAGAACTCTAGGA	0.358																																					p.L482F		Atlas-SNP	.											.	PHIP	177	.	0			c.C1444T						PASS	.						101	94	96					6																	79724879		2203	4300	6503	SO:0001583	missense	55023	exon15			AAAAGAGAACTCT	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.1444C>T	chr6.hg19:g.79724879G>A	ENSP00000275034:p.Leu482Phe	93.0	0.0	.		82.0	10.0	.	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	hg19	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.033289	0.75504	.	.	ENSG00000146247	ENST00000275034	T	0.68479	-0.33	5.23	5.23	0.72850	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.52532	D	0.000061	T	0.60586	0.2280	N	0.21194	0.64	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.998	T	0.61093	-0.7132	9	.	.	.	-5.5196	11.6141	0.51078	0.0821:0.0:0.9179:0.0	.	482;482	A7J992;Q8WWQ0	.;PHIP_HUMAN	F	482	ENSP00000275034:L482F	.	L	-	1	0	PHIP	79781598	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	3.663000	0.54518	2.586000	0.87340	0.460000	0.39030	CTC	.	.	.	none		0.358	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			A	79724879	G	A	79724879	3	1	53	1	0	0	0	0	1	0	0	0	11849	942	33	2	4125	2	PHIP	6	79724879	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	5317749	79724879	91390188	38	3611											
KIAA0776	23376	hgsc.bcm.edu	37	chr6	96996102	96996102	+	Frame_Shift_Del	DEL	C	C	-																															ttgaagattttttaagaaaaCacatacaagatgcccctgag																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr6:96996102delC	ENST00000369278.4	+	13	1531	c.1465delC	c.(1465-1467)cacfs	p.H489fs		NM_015323.4	NP_056138.1	O94874	UFL1_HUMAN	UFM1-specific ligase 1	489					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)										TTTAAGAAAACACATACAAGA	0.308																																					p.K488fs		Atlas-INDEL	.											.	.	.	.	0			c.1464delA						PASS	.						57	59	58					6																	96996102		2202	4300	6502	SO:0001589	frameshift_variant	23376	exon13			.	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.1465delC	chr6.hg19:g.96996102delC	ENSP00000358283:p.His489fs	45.0	0.0	0		35.0	17.0	0.485714	NM_015323	A0PJ53|B4DJ57|C0H5X5|Q8N765|Q9NTQ0	Frame_Shift_Del	DEL	ENST00000369278.4	hg19	CCDS5034.1																																																																																			.	.	.	none		0.308	UFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041557.1	NM_015323		-	96996102	C	-	96996102	7	5	53	1	0	1	0	1	0	0	0	0	8200	478	17	0	1515	0	KIAA0776	6	96996102	Frame_Shift_Del	DEL	C	TCGA-A4-8098-01A-11D-2396-08	17271223	96996102	74118965	39	3612											
GPNMB	10457	hgsc.bcm.edu	37	chr7	23306207	23306207	+	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	gccagattaacagatatggcCactttcaagccaccatcaca	14	8	6	13	0	2	2	2	0	0	2	2	2	2	2	4	1	2	0	4	1	3	3			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr7:23306207C>A	ENST00000381990.2	+	7	1287	c.1126C>A	c.(1126-1128)Cac>Aac	p.H376N	GPNMB_ENST00000453162.2_Missense_Mutation_p.H318N|GPNMB_ENST00000258733.4_Missense_Mutation_p.H364N|GPNMB_ENST00000539136.1_Missense_Mutation_p.H265N	NM_001005340.1|NM_002510.2	NP_001005340.1|NP_002501.1	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb	376					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)			CAGATATGGCCACTTTCAAGC	0.478																																					p.H376N		Atlas-SNP	.											.	GPNMB	88	.	0			c.C1126A						PASS	.						82	71	75					7																	23306207		2203	4300	6503	SO:0001583	missense	10457	exon7			TATGGCCACTTTC	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.1126C>A	chr7.hg19:g.23306207C>A	ENSP00000371420:p.His376Asn	52.0	0.0	.		52.0	19.0	.	NM_001005340	A4D155|Q6UVX1|Q8N1A1	Missense_Mutation	SNP	ENST00000381990.2	hg19	CCDS34610.1	.	.	.	.	.	.	.	.	.	.	C	6.226	0.409829	0.11812	.	.	ENSG00000136235	ENST00000258733;ENST00000435486;ENST00000381990;ENST00000425903;ENST00000539136;ENST00000453162	T;T;T;T	0.13657	2.58;2.58;2.57;2.58	5.89	-0.668	0.11392	PKD/Chitinase domain (1);	0.606085	0.16307	N	0.220182	T	0.12518	0.0304	L	0.47716	1.5	0.09310	N	0.999998	D;P;P;P	0.53745	0.962;0.82;0.913;0.744	B;B;B;B	0.43990	0.438;0.351;0.345;0.275	T	0.29212	-1.0019	10	0.22706	T	0.39	-12.8359	11.5467	0.50698	0.0:0.5539:0.0:0.4461	.	265;318;376;364	F6SKP1;F5GY20;Q14956;Q14956-2	.;.;GPNMB_HUMAN;.	N	364;411;376;259;265;318	ENSP00000258733:H364N;ENSP00000371420:H376N;ENSP00000445266:H265N;ENSP00000405586:H318N	ENSP00000258733:H364N	H	+	1	0	GPNMB	23272732	0.759000	0.28416	0.042000	0.18584	0.021000	0.10359	1.106000	0.31098	-0.061000	0.13110	-0.781000	0.03364	CAC	.	.	.	none		0.478	GPNMB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327152.1	NM_001005340		A	23306207	C	A	23306207	3	1	53	1	0	0	0	0	1	0	0	0	6627	594	21	4	1152	4	GPNMB	7	23306207	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08		23306207	135832456	40	3613											
GLI3	2737	hgsc.bcm.edu	37	chr7	42063171	42063171	+	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	tttgctttcatctttgtcccCttcctccttgacaagggttg	4	18	7	12	0	2	1	1	1	1	0	5	1	5	1	4	1	1	2	4	1	1	6	rs35488756	byFrequency	TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr7:42063171C>T	ENST00000395925.3	-	10	1477	c.1393G>A	c.(1393-1395)Ggg>Agg	p.G465R	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	465					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						TCTTTGTCCCCTTCCTCCTTG	0.542									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																												p.G465R		Atlas-SNP	.											.	GLI3	312	.	0			c.G1393A						PASS	.						152	118	129					7																	42063171		2203	4300	6503	SO:0001583	missense	2737	exon10	Familial Cancer Database	;	TGTCCCCTTCCTC		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.1393G>A	chr7.hg19:g.42063171C>T	ENSP00000379258:p.Gly465Arg	103.0	0.0	.		102.0	41.0	.	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	hg19	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	C	18.93	3.727028	0.69074	.	.	ENSG00000106571	ENST00000395925	T	0.69306	-0.39	5.81	5.81	0.92471	.	0.043845	0.85682	D	0.000000	T	0.66713	0.2817	L	0.57536	1.79	0.80722	D	1	B	0.16396	0.017	B	0.14023	0.01	T	0.60762	-0.7199	10	0.42905	T	0.14	.	20.0912	0.97820	0.0:1.0:0.0:0.0	.	465	P10071	GLI3_HUMAN	R	465	ENSP00000379258:G465R	ENSP00000379258:G465R	G	-	1	0	GLI3	42029696	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	5.975000	0.70475	2.746000	0.94184	0.591000	0.81541	GGG	.	C|0.997;G|0.003	.	alt		0.542	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		T	42063171	C	T	42063171	3	4	53	1	0	0	0	0	1	0	0	0	6446	681	24	2	3373	2	GLI3	7	42063171	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	18756964	42063171	117075492	41	3614											
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121651018	121651018	+	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	attcaacttcatcaggttcaGaagaatcactaaaggatcct	15	11	6	9	0	5	2	5	0	0	2	6	3	6	3	1	2	1	1	1	2	5	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr7:121651018G>C	ENST00000393386.2	+	12	2329	c.1918G>C	c.(1918-1920)Gaa>Caa	p.E640Q	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.E640Q	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	640					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						ATCAGGTTCAGAAGAATCACT	0.418																																					p.E640Q		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.G1918C						PASS	.						60	58	59					7																	121651018		2203	4300	6503	SO:0001583	missense	5803	exon12			GGTTCAGAAGAAT	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.1918G>C	chr7.hg19:g.121651018G>C	ENSP00000377047:p.Glu640Gln	113.0	0.0	.		105.0	45.0	.	NM_001206838	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	hg19	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	G	12.49	1.952906	0.34471	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	T;T	0.50548	0.8;0.74	5.87	5.87	0.94306	.	0.470308	0.21679	N	0.070741	T	0.61274	0.2334	M	0.67953	2.075	0.27751	N	0.944151	P;P;D	0.63880	0.779;0.671;0.993	B;B;P	0.55713	0.277;0.143;0.782	T	0.60182	-0.7313	10	0.59425	D	0.04	.	14.976	0.71273	0.0:0.0:0.8573:0.1427	.	640;640;640	P23471-2;C9JFM0;P23471	.;.;PTPRZ_HUMAN	Q	640	ENSP00000377047:E640Q;ENSP00000410000:E640Q	ENSP00000377047:E640Q	E	+	1	0	PTPRZ1	121438254	0.993000	0.37304	0.945000	0.38365	0.967000	0.64934	3.265000	0.51561	2.778000	0.95560	0.655000	0.94253	GAA	.	.	.	none		0.418	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		C	121651018	G	C	121651018	3	2	53	1	0	0	0	0	1	0	0	0	12827	943	33	4	1964	4	PTPRZ1	7	121651018	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	79587847	121651018	37487645	42	3615											
NCOA2	10499	hgsc.bcm.edu	37	chr8	71039066	71039067	+	Frame_Shift_Ins	INS	-	-	AAAC																															ccgtagtttggaggaaatggINSaaactgctgtgcatttgcct																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr8:71039066_71039067insAAAC	ENST00000452400.2	-	19	4078_4079	c.3897_3898insGTTT	c.(3895-3900)tttccafs	p.P1300fs	NCOA2_ENST00000267974.4_Frame_Shift_Ins_p.P388fs	NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	1300					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)			GGAGGAAATGGAAACTGCTGTG	0.53			T	"RUNXBP2, HEY1"	"AML, Chondrosarcoma"																																p.P1300fs		Atlas-INDEL	.		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	.	NCOA2	147	.	0			c.3898_3899insGTTT						PASS	.																																			SO:0001589	frameshift_variant	10499	exon19			.	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.3894_3897dupGTTT	chr8.hg19:g.71039067_71039070dupAAAC	ENSP00000399968:p.Pro1300fs	43.0	0.0	0		50.0	11.0	0.22	NM_006540	Q14CD2	Frame_Shift_Ins	INS	ENST00000452400.2	hg19	CCDS47872.1																																																																																			.	.	.	none		0.53	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1			AAAC	71039067	-	AAAC	71039066	7	5	53	1	0	1	1	0	0	0	0	0	10236	1174	41	0	516	0	NCOA2	8	71039066	Frame_Shift_Ins	INS	-	TCGA-A4-8098-01A-11D-2396-08		71039066	75324956	43	3616											
EPPK1	83481	hgsc.bcm.edu	37	chr8	144942527	144942527	+	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	aggtttctttcccgaacattCctgctttgaacgcctcctcc	6	14	6	15	2	1	1	0	1	1	0	5	2	5	1	5	1	3	2	5	1	2	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr8:144942527C>G	ENST00000525985.1	-	2	4966	c.4895G>C	c.(4894-4896)gGa>gCa	p.G1632A				P58107	EPIPL_HUMAN	epiplakin 1	1632						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)			CCCGAACATTCCTGCTTTGAA	0.627																																					p.G1632A		Atlas-SNP	.											.	EPPK1	199	.	0			c.G4895C						PASS	.						74	83	80					8																	144942527		2037	4184	6221	SO:0001583	missense	83481	exon1			AACATTCCTGCTT	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.4895G>C	chr8.hg19:g.144942527C>G	ENSP00000436337:p.Gly1632Ala	104.0	0.0	.		128.0	42.0	.	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.25	2.180920	0.38511	.	.	ENSG00000227184	ENST00000525985	D	0.85411	-1.98	4.41	4.41	0.53225	.	.	.	.	.	D	0.93798	0.8017	M	0.92317	3.295	0.09310	N	1	D	0.89917	1.0	D	0.72338	0.977	D	0.87143	0.2204	9	0.72032	D	0.01	.	14.5607	0.68133	0.0:1.0:0.0:0.0	.	1632	E9PPU0	.	A	1632	ENSP00000436337:G1632A	ENSP00000436337:G1632A	G	-	2	0	EPPK1	145014515	0.004000	0.15560	0.114000	0.21550	0.403000	0.30841	1.625000	0.37029	2.280000	0.76307	0.591000	0.81541	GGA	.	.	.	none		0.627	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		G	144942527	C	G	144942527	3	3	53	1	0	0	0	0	1	0	0	0	5192	855	30	4	2371	4	EPPK1	8	144942527	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	73903461	144942527	1421495	44	3617											
CEP110	11064	hgsc.bcm.edu	37	chr9	123900898	123900898	+	Missense_Mutation	SNP	T	T	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	atgcccttggaaaagcccagTtctcagaagaaaaggagcaa	16	6	10	9	0	1	2	1	0	1	2	2	4	1	4	2	2	3	2	2	2	6	2	rs566495778		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr9:123900898T>G	ENST00000373855.1	+	16	2538	c.2278T>G	c.(2278-2280)Ttc>Gtc	p.F760V	CNTRL_ENST00000373850.1_Missense_Mutation_p.F208V|CNTRL_ENST00000238341.5_Missense_Mutation_p.F760V|CNTRL_ENST00000373847.1_Missense_Mutation_p.F208V			Q7Z7A1	CNTRL_HUMAN	centriolin	760					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						AAAAGCCCAGTTCTCAGAAGA	0.418																																					p.F760V		Atlas-SNP	.											.	CNTRL	161	.	0			c.T2278G						PASS	.						97	98	98					9																	123900898		2203	4300	6503	SO:0001583	missense	11064	exon14			GCCCAGTTCTCAG	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.2278T>G	chr9.hg19:g.123900898T>G	ENSP00000362962:p.Phe760Val	93.0	0.0	.		101.0	42.0	.	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	hg19	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	T	13.48	2.248769	0.39797	.	.	ENSG00000119397	ENST00000373855;ENST00000238341;ENST00000454238;ENST00000373851;ENST00000373850;ENST00000373847	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	5.76	2.4	0.29515	.	.	.	.	.	T	0.24236	0.0587	N	0.14661	0.345	0.23731	N	0.996993	B;B;B	0.24483	0.049;0.082;0.104	B;B;B	0.21708	0.016;0.036;0.024	T	0.20338	-1.0278	9	0.27082	T	0.32	.	8.6368	0.33953	0.0:0.3003:0.0:0.6997	.	760;760;760	B2RP65;F5GZN0;Q7Z7A1	.;.;CNTRL_HUMAN	V	760;760;760;242;208;208	ENSP00000362962:F760V;ENSP00000238341:F760V;ENSP00000362956:F208V;ENSP00000362953:F208V	ENSP00000238341:F760V	F	+	1	0	CNTRL	122940719	0.982000	0.34865	0.996000	0.52242	0.970000	0.65996	0.049000	0.14099	0.269000	0.21961	0.533000	0.62120	TTC	.	.	.	none		0.418	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018		G	123900898	T	G	123900898	3	3	53	1	0	0	0	0	1	0	0	0	3247	1725	60	5	2332	5	CEP110	9	123900898	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08		123900898	17312533	45	3618											
ADAMTS13	11093	hgsc.bcm.edu	37	chr9	136305499	136305499	+	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	gggcgctatgtcgtggctggGaagatgagcatctcccctaa	8	9	14	10	2	1	2	0	1	1	1	3	3	1	3	2	3	1	3	2	3	3	2	rs371209152		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr9:136305499G>T	ENST00000371929.3	+	16	2265	c.1821G>T	c.(1819-1821)ggG>ggT	p.G607G	ADAMTS13_ENST00000536611.1_Silent_p.G279G|ADAMTS13_ENST00000485925.1_3'UTR|ADAMTS13_ENST00000356589.2_Silent_p.G576G|ADAMTS13_ENST00000371916.1_3'UTR|ADAMTS13_ENST00000355699.2_Silent_p.G607G	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	607	Spacer.				cell-matrix adhesion (GO:0007160)|glycoprotein metabolic process (GO:0009100)|integrin-mediated signaling pathway (GO:0007229)|peptide catabolic process (GO:0043171)|platelet activation (GO:0030168)|protein processing (GO:0016485)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to interleukin-4 (GO:0070670)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(4)	36				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		TCGTGGCTGGGAAGATGAGCA	0.642																																					p.G607G		Atlas-SNP	.											.	ADAMTS13	113	.	0			c.G1821T						PASS	.						138	98	111					9																	136305499		2203	4300	6503	SO:0001819	synonymous_variant	11093	exon16			GGCTGGGAAGATG	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.1821G>T	chr9.hg19:g.136305499G>T		107.0	0.0	.		103.0	32.0	.	NM_139027	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Silent	SNP	ENST00000371929.3	hg19	CCDS6970.1																																																																																			.	.	.	alt		0.642	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025		T	136305499	G	T	136305499	2	4	53	1	0	0	0	0	0	0	0	1	258	1161	41	4		4	ADAMTS13	9	136305499	Silent	SNP	G	TCGA-A4-8098-01A-11D-2396-08	12404601	136305499	4907932	46	3619											
C10orf18	54906	hgsc.bcm.edu	37	chr10	5790239	5790239	+	Frame_Shift_Del	DEL	T	T	-																															aaagcagtcagaaccatctcTttcccggtgatttgaaaaca																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr10:5790239delT	ENST00000328090.5	+	15	5480	c.4855delT	c.(4855-4857)tttfs	p.F1619fs		NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	1619																	GAACCATCTCTTTCCCGGTGA	0.453																																					p.L1618fs		Atlas-INDEL	.											.	.	.	.	0			c.4854delC						PASS	.						65	65	65					10																	5790239		1964	4151	6115	SO:0001589	frameshift_variant	54906	exon15			.	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.4855delT	chr10.hg19:g.5790239delT	ENSP00000328426:p.Phe1619fs	91.0	0.0	0		133.0	29.0	0.218045	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Frame_Shift_Del	DEL	ENST00000328090.5	hg19	CCDS41485.1																																																																																			.	.	.	none		0.453	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782		-	5790239	T	-	5790239	7	5	53	1	0	1	0	1	0	0	0	0	1598	1609	56	0	4901	0	C10orf18	10	5790239	Frame_Shift_Del	DEL	T	TCGA-A4-8098-01A-11D-2396-08		5790239	129744508	47	3620											
SLC18A3	6572	hgsc.bcm.edu	37	chr10	50819621	50819621	+	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	ctcgggccaacctgccagtgGgcactcccatccaccgcctc	6	6	9	20	2	0	0	0	0	0	0	4	0	2	0	7	2	2	1	7	2	1	0			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr10:50819621G>C	ENST00000374115.3	+	1	1275	c.835G>C	c.(835-837)Ggc>Cgc	p.G279R	CHAT_ENST00000339797.1_Intron|CHAT_ENST00000395562.2_5'Flank|CHAT_ENST00000337653.2_5'Flank|CHAT_ENST00000455728.2_5'Flank|CHAT_ENST00000351556.3_5'Flank|CHAT_ENST00000395559.2_5'Flank	NM_003055.2	NP_003046.2	Q16572	VACHT_HUMAN	solute carrier family 18 (vesicular acetylcholine transporter), member 3	279					acetylcholine transport (GO:0015870)|cation transmembrane transport (GO:0098655)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)	clathrin-sculpted acetylcholine transport vesicle membrane (GO:0060201)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	acetylcholine transmembrane transporter activity (GO:0005277)			endometrium(6)|kidney(2)|large_intestine(8)|liver(1)|lung(20)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	43						CCTGCCAGTGGGCACTCCCAT	0.647																																					p.G279R		Atlas-SNP	.											.	SLC18A3	100	.	0			c.G835C						PASS	.						45	42	43					10																	50819621		2202	4300	6502	SO:0001583	missense	6572	exon1			CCAGTGGGCACTC	BC007765	CCDS7231.1	10q11.2	2013-07-18	2013-07-18		ENSG00000187714	ENSG00000187714		"Solute carriers"	10936	protein-coding gene	gene with protein product		600336				8071310	Standard	NM_003055		Approved	VACHT	uc001jhw.3	Q16572	OTTHUMG00000018196	ENST00000374115.3:c.835G>C	chr10.hg19:g.50819621G>C	ENSP00000363229:p.Gly279Arg	120.0	0.0	.		126.0	31.0	.	NM_003055	B2R7S1	Missense_Mutation	SNP	ENST00000374115.3	hg19	CCDS7231.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.749750	0.89753	.	.	ENSG00000187714	ENST00000374115	T	0.80393	-1.37	5.42	5.42	0.78866	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.64402	U	0.000001	D	0.91408	0.7289	M	0.86420	2.815	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.92566	0.6062	10	0.87932	D	0	0.7852	19.2158	0.93778	0.0:0.0:1.0:0.0	.	279	Q16572	VACHT_HUMAN	R	279	ENSP00000363229:G279R	ENSP00000363229:G279R	G	+	1	0	SLC18A3	50489627	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.824000	0.99380	2.552000	0.86080	0.561000	0.74099	GGC	.	.	.	none		0.647	SLC18A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047995.1	NM_003055		C	50819621	G	C	50819621	3	2	53	1	0	0	0	0	1	0	0	0	14440	1232	43	4	837	4	SLC18A3	10	50819621	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	45029382	50819621	84715126	48	3621											
TET1	80312	hgsc.bcm.edu	37	chr10	70450862	70450862	+	Missense_Mutation	SNP	T	T	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	tgctgctgatggccctggcaTttcacagcttggcgaagtgg	6	11	14	10	1	1	1	1	1	0	0	1	2	1	1	1	4	3	4	1	4	1	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr10:70450862T>G	ENST00000373644.4	+	12	5911	c.5702T>G	c.(5701-5703)aTt>aGt	p.I1901S		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1901					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						GGCCCTGGCATTTCACAGCTT	0.572																																					p.I1901S		Atlas-SNP	.											.	TET1	255	.	0			c.T5702G						PASS	.						70	66	67					10																	70450862		2203	4300	6503	SO:0001583	missense	80312	exon12			CTGGCATTTCACA	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.5702T>G	chr10.hg19:g.70450862T>G	ENSP00000362748:p.Ile1901Ser	118.0	0.0	.		167.0	91.0	.	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	hg19	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	T	9.058	0.993658	0.19043	.	.	ENSG00000138336	ENST00000373644	T	0.06849	3.25	5.34	2.89	0.33648	Methylcytosine dioxygenase TET, double-stranded beta helix fold domain (1);	5.533840	0.00166	N	0.000001	T	0.11024	0.0269	L	0.41710	1.295	0.09310	N	1	P	0.38729	0.644	B	0.40329	0.326	T	0.22382	-1.0218	10	0.49607	T	0.09	.	5.5383	0.17023	0.0:0.152:0.1458:0.7022	.	1901	Q8NFU7	TET1_HUMAN	S	1901	ENSP00000362748:I1901S	ENSP00000362748:I1901S	I	+	2	0	TET1	70120868	0.002000	0.14202	0.006000	0.13384	0.050000	0.14768	0.124000	0.15728	0.300000	0.22699	0.533000	0.62120	ATT	.	.	.	none		0.572	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		G	70450862	T	G	70450862	3	3	53	1	0	0	0	0	1	0	0	0	15781	1493	52	5	5744	5	TET1	10	70450862	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08	19631241	70450862	65083885	49	3622											
H2AFY2	55506	hgsc.bcm.edu	37	chr10	71868875	71868875	+	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	gctccgacaaatgtgaagaaCagcttgaagagaccatcaaa	17	6	9	9	1	1	4	1	2	0	2	2	6	2	4	2	0	2	2	2	0	5	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr10:71868875C>A	ENST00000373255.4	+	8	1129	c.865C>A	c.(865-867)Cag>Aag	p.Q289K	AIFM2_ENST00000373248.1_Intron	NM_018649.2	NP_061119.1	Q9P0M6	H2AW_HUMAN	H2A histone family, member Y2	289	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				brain development (GO:0007420)|chromatin modification (GO:0016568)|dosage compensation (GO:0007549)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|nucleosome assembly (GO:0006334)	Barr body (GO:0001740)|extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|transcription regulatory region DNA binding (GO:0044212)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(4)|skin(1)	15						ATGTGAAGAACAGCTTGAAGA	0.557																																					p.Q289K		Atlas-SNP	.											.	H2AFY2	30	.	0			c.C865A						PASS	.						89	82	84					10																	71868875		2203	4300	6503	SO:0001583	missense	55506	exon8			GAAGAACAGCTTG	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.865C>A	chr10.hg19:g.71868875C>A	ENSP00000362352:p.Gln289Lys	92.0	0.0	.		167.0	24.0	.	NM_018649	Q5SQT2	Missense_Mutation	SNP	ENST00000373255.4	hg19	CCDS7296.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.119095	0.77323	.	.	ENSG00000099284	ENST00000373255;ENST00000395046;ENST00000455786	T;T	0.21031	2.03;2.03	6.03	6.03	0.97812	Appr-1-p processing (2);	0.000000	0.85682	D	0.000000	T	0.16769	0.0403	N	0.17723	0.515	0.80722	D	1	P	0.43231	0.801	B	0.38842	0.283	T	0.02553	-1.1142	10	0.25751	T	0.34	.	20.177	0.98182	0.0:1.0:0.0:0.0	.	289	Q9P0M6	H2AW_HUMAN	K	289;223;223	ENSP00000362352:Q289K;ENSP00000404584:Q223K	ENSP00000362352:Q289K	Q	+	1	0	H2AFY2	71538881	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.830000	0.62745	2.854000	0.98071	0.655000	0.94253	CAG	.	.	.	none		0.557	H2AFY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048480.2	NM_018649		A	71868875	C	A	71868875	3	1	53	1	0	0	0	0	1	0	0	0	6937	479	17	4	891	4	H2AFY2	10	71868875	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	1418013	71868875	63665872	50	3623											
TRIM8	81603	hgsc.bcm.edu	37	chr10	104415049	104415049	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagctgctctttgataagacGgaggatgtcagcttcatgaa	11	11	11	8	1	3	3	2	2	1	1	3	5	3	5	0	2	3	3	0	2	2	3			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr10:104415049G>A	ENST00000302424.7	+	3	1001	c.879G>A	c.(877-879)acG>acA	p.T293T	TRIM8_ENST00000487927.1_3'UTR	NM_030912.2	NP_112174.2	Q9BZR9	TRIM8_HUMAN	tripartite motif containing 8	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 ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|PML body (GO:0016605)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		TTGATAAGACGGAGGATGTCA	0.597																																					p.T293T		Atlas-SNP	.											.	TRIM8	35	.	0			c.G879A						PASS	.						31	34	33					10																	104415049		2202	4300	6502	SO:0001819	synonymous_variant	81603	exon3			TAAGACGGAGGAT	AF281046	CCDS31274.1	10q24.3	2013-01-09	2011-01-25	2002-06-14	ENSG00000171206	ENSG00000171206		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	15579	protein-coding gene	gene with protein product	"glioblastoma expressed ring finger protein"	606125	"ring finger protein 27", "tripartite motif-containing 8"	RNF27		11118312, 12163497	Standard	NM_030912		Approved	GERP	uc001kvz.2	Q9BZR9	OTTHUMG00000018964	ENST00000302424.7:c.879G>A	chr10.hg19:g.104415049G>A		74.0	0.0	.		92.0	8.0	.	NM_030912	A6NI31|Q9C028	Silent	SNP	ENST00000302424.7	hg19	CCDS31274.1																																																																																			.	.	.	none		0.597	TRIM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050084.3	NM_030912		A	104415049	G	A	104415049	2	1	53	1	0	0	0	0	0	0	0	1	16560	1103	39	1		1	TRIM8	10	104415049	Silent	SNP	G	TCGA-A4-8098-01A-11D-2396-08	32546174	104415049	31119698	51	3624											
NRAP	4892	hgsc.bcm.edu	37	chr10	115372127	115372127	+	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	cttcttggcatgcaccagggCggccatgtccaacggcagat	8	8	12	13	2	1	1	0	0	1	1	2	1	2	1	3	4	2	3	3	4	1	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr10:115372127C>G	ENST00000359988.3	-	30	3608	c.3364G>C	c.(3364-3366)Gcc>Ccc	p.A1122P	NRAP_ENST00000369358.4_Missense_Mutation_p.A1130P|NRAP_ENST00000360478.3_Missense_Mutation_p.A1087P|NRAP_ENST00000369360.3_Missense_Mutation_p.A1095P	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein									p.A1122T(1)		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)		TGCACCAGGGCGGCCATGTCC	0.532																																					p.A1122P		Atlas-SNP	.											NRAP,caecum,carcinoma,0,1	NRAP	208	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3364C						PASS	.						106	93	97					10																	115372127		2203	4300	6503	SO:0001583	missense	4892	exon30			CCAGGGCGGCCAT		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.3364G>C	chr10.hg19:g.115372127C>G	ENSP00000353078:p.Ala1122Pro	99.0	0.0	.		157.0	44.0	.	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	hg19	CCDS7579.1	.	.	.	.	.	.	.	.	.	.	C	10.85	1.467717	0.26335	.	.	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	T;T;T;T	0.32988	1.43;1.43;1.43;1.43	5.62	4.42	0.53409	.	0.222981	0.47852	D	0.000215	T	0.18923	0.0454	L	0.27053	0.805	0.19775	N	0.999954	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.08055	0.001;0.003;0.001	T	0.16335	-1.0406	10	0.30078	T	0.28	.	6.6353	0.22879	0.0:0.0846:0.2726:0.6428	.	1122;1087;1122	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	P	1130;1095;1122;1087	ENSP00000358365:A1130P;ENSP00000358367:A1095P;ENSP00000353078:A1122P;ENSP00000353666:A1087P	ENSP00000353078:A1122P	A	-	1	0	NRAP	115362117	0.827000	0.29292	0.788000	0.31933	0.559000	0.35586	1.269000	0.33074	0.978000	0.38470	-0.345000	0.07892	GCC	.	.	.	none		0.532	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175		G	115372127	C	G	115372127	3	3	53	1	0	0	0	0	1	0	0	0	10645	768	27	4	1880	4	NRAP	10	115372127	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	10957078	115372127	20162620	52	3625											
UEVLD	55293	hgsc.bcm.edu	37	chr11	18568448	18568448	+	Frame_Shift_Del	DEL	G	G	-																															tggttgagatgcaacgagcaGgacactgtgttgactataat																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:18568448delG	ENST00000396197.3	-	8	893	c.865delC	c.(865-867)ctgfs	p.L290fs	UEVLD_ENST00000543987.1_Frame_Shift_Del_p.L290fs|UEVLD_ENST00000541984.1_Intron|UEVLD_ENST00000535484.1_Frame_Shift_Del_p.L252fs|UEVLD_ENST00000540666.1_5'UTR|UEVLD_ENST00000379387.4_Frame_Shift_Del_p.L268fs|UEVLD_ENST00000320750.6_Frame_Shift_Del_p.L268fs	NM_001040697.2|NM_001261384.1	NP_001035787.1|NP_001248313.1			UEV and lactate/malate dehyrogenase domains											endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						GCAACGAGCAGGACACTGTGT	0.403																																					p.L289fs		Atlas-INDEL	.											.	UEVLD	58	.	0			c.866delT						PASS	.						142	133	136					11																	18568448		2199	4293	6492	SO:0001589	frameshift_variant	55293	exon8			.	AF503350	CCDS7843.1, CCDS41624.1, CCDS58122.1, CCDS58123.1, CCDS58124.1, CCDS58125.1, CCDS73266.1	11p15.1	2006-07-14			ENSG00000151116	ENSG00000151116			30866	protein-coding gene	gene with protein product		610985				12427560	Standard	NM_001040697		Approved	Attp, UEV3	uc001mot.4	Q8IX04	OTTHUMG00000167729	ENST00000396197.3:c.865delC	chr11.hg19:g.18568448delG	ENSP00000379500:p.Leu290fs	125.0	0.0	0		98.0	35.0	0.357143	NM_018314		Frame_Shift_Del	DEL	ENST00000396197.3	hg19	CCDS41624.1																																																																																			.	.	.	none		0.403	UEVLD-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395923.2	NM_018314		-	18568448	G	-	18568448	7	5	53	1	0	1	0	1	0	0	0	0	16945	991	35	0	570	0	UEVLD	11	18568448	Frame_Shift_Del	DEL	G	TCGA-A4-8098-01A-11D-2396-08		18568448	116438068	53	3626											
NELL1	4745	hgsc.bcm.edu	37	chr11	21594920	21594920	+	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	ttagtggctcagtgtggacgAtggctggatctccctgcaca	7	11	13	10	1	2	0	1	0	1	0	3	3	2	2	1	4	1	3	1	4	1	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:21594920A>T	ENST00000357134.5	+	19	2499	c.2347A>T	c.(2347-2349)Atg>Ttg	p.M783L	NELL1_ENST00000298925.5_Missense_Mutation_p.M811L|NELL1_ENST00000532434.1_Missense_Mutation_p.M736L|NELL1_ENST00000529218.1_3'UTR|NELL1_ENST00000325319.5_Missense_Mutation_p.M726L	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	783					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						AGTGTGGACGATGGCTGGATC	0.488																																					p.M783L		Atlas-SNP	.											.	NELL1	179	.	0			c.A2347T						PASS	.						165	145	152					11																	21594920		2203	4300	6503	SO:0001583	missense	4745	exon19			TGGACGATGGCTG	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.2347A>T	chr11.hg19:g.21594920A>T	ENSP00000349654:p.Met783Leu	211.0	0.0	.		211.0	75.0	.	NM_006157	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Missense_Mutation	SNP	ENST00000357134.5	hg19	CCDS7855.1	.	.	.	.	.	.	.	.	.	.	A	5.365	0.252558	0.10185	.	.	ENSG00000165973	ENST00000298925;ENST00000357134;ENST00000325319;ENST00000532434	T;T;T;T	0.78481	-1.18;-1.15;-1.07;-1.06	5.73	4.59	0.56863	.	0.047962	0.85682	N	0.000000	T	0.66655	0.2811	L	0.46157	1.445	0.34190	D	0.671993	P;B;B;B;P	0.37370	0.592;0.0;0.001;0.001;0.457	B;B;B;B;B	0.33254	0.16;0.0;0.002;0.007;0.077	T	0.68561	-0.5376	10	0.10636	T	0.68	-16.3644	12.2052	0.54348	0.872:0.0:0.0:0.1279	.	726;811;328;736;783	F5H6I3;B3KXR2;Q8N9Z6;Q92832-2;Q92832	.;.;.;.;NELL1_HUMAN	L	811;783;726;736	ENSP00000298925:M811L;ENSP00000349654:M783L;ENSP00000317837:M726L;ENSP00000437170:M736L	ENSP00000298925:M811L	M	+	1	0	NELL1	21551496	1.000000	0.71417	0.995000	0.50966	0.203000	0.24098	5.967000	0.70403	0.983000	0.38602	0.454000	0.30748	ATG	.	.	.	none		0.488	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157		T	21594920	A	T	21594920	3	4	53	1	0	0	0	0	1	0	0	0	10340	333	12	5	2421	5	NELL1	11	21594920	Missense_Mutation	SNP	A	TCGA-A4-8098-01A-11D-2396-08	3026472	21594920	113411596	54	3627											
LGR4	55366	hgsc.bcm.edu	37	chr11	27412675	27412676	+	In_Frame_Ins	INS	-	-	AAG																															ctcagccctcgaatggcttcINSactgggtactgttttcaact																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:27412675_27412676insAAG	ENST00000379214.4	-	4	809_810	c.366_367insCTT	c.(364-369)agtgaa>agtCTTgaa	p.122_123SE>SLE	LGR4_ENST00000480977.2_Intron|LGR4_ENST00000389858.4_In_Frame_Ins_p.98_99SE>SLE	NM_018490.2	NP_060960.2	Q9BXB1	LGR4_HUMAN	leucine-rich repeat containing G protein-coupled receptor 4	122					bone mineralization (GO:0030282)|bone remodeling (GO:0046849)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cell differentiation involved in metanephros development (GO:0072202)|epithelial cell proliferation (GO:0050673)|innate immune response (GO:0045087)|male genitalia development (GO:0030539)|metanephric glomerulus development (GO:0072224)|metanephric nephron tubule morphogenesis (GO:0072282)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(10)|ovary(1)	32						CGAATGGCTTCACTGGGTACTG	0.366																																					p.E123delinsLE		Atlas-INDEL	.											LGR4,NS,carcinoma,0,1	LGR4	87	.	0			c.367_368insCTT						PASS	.																																			SO:0001652	inframe_insertion	55366	exon4			.	AF257182	CCDS31449.1	11p14-p13	2012-08-21	2011-01-25	2004-11-12	ENSG00000205213	ENSG00000205213		"GPCR / Class A : Orphans"	13299	protein-coding gene	gene with protein product		606666	"G protein-coupled receptor 48", "leucine-rich repeat-containing G protein-coupled receptor 4"	GPR48		10894923	Standard	NM_018490		Approved		uc001mrj.4	Q9BXB1	OTTHUMG00000133508	ENST00000379214.4:c.366_367insCTT	chr11.hg19:g.27412675_27412676insAAG	ENSP00000368516:p.Ser122_Glu123insLeu	85.0	0.0	0		83.0	21.0	0.253012	NM_018490	A6NCH3|G5E9B3|Q8N537|Q9NYD1	In_Frame_Ins	INS	ENST00000379214.4	hg19	CCDS31449.1																																																																																			.	.	.	none		0.366	LGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257467.1	NM_018490		AAG	27412676	-	AAG	27412675	7	5	53	1	0	1	1	0	0	0	0	0	8763	835	29	0	2548	0	LGR4	11	27412675	In_Frame_Ins	INS	-	TCGA-A4-8098-01A-11D-2396-08	5817755	27412675	107593841	55	3628											
IMMP1L	196294	hgsc.bcm.edu	37	chr11	31482191	31482191	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctttggataccataaaaaTgtcgactaagattttctgca	14	13	6	8	1	1	1	0	0	1	1	2	3	1	2	2	1	2	1	2	1	5	6			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:31482191T>C	ENST00000278200.1	-	4	371	c.176A>G	c.(175-177)cAt>cGt	p.H59R	IMMP1L_ENST00000532287.1_Missense_Mutation_p.H59R|IMMP1L_ENST00000526776.1_Intron|IMMP1L_ENST00000534812.1_Intron|IMMP1L_ENST00000528161.1_Intron|IMMP1L_ENST00000533642.1_Intron	NM_144981.1	NP_659418.1	Q96LU5	IMP1L_HUMAN	IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae)	59					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)					ACCATAAAAATGTCGACTAAG	0.318																																					p.H59R		Atlas-SNP	.											.	IMMP1L	16	.	0			c.A176G						PASS	.						67	69	68					11																	31482191		2202	4295	6497	SO:0001583	missense	196294	exon4			TAAAAATGTCGAC		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.176A>G	chr11.hg19:g.31482191T>C	ENSP00000278200:p.His59Arg	59.0	0.0	.		36.0	11.0	.	NM_144981	D3DQZ7|Q96SH9	Missense_Mutation	SNP	ENST00000278200.1	hg19	CCDS7874.1	.	.	.	.	.	.	.	.	.	.	T	8.728	0.915998	0.17907	.	.	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);	0.046287	0.85682	D	0.000000	T	0.32102	0.0818	N	0.02403	-0.565	0.80722	D	1	P;B	0.38300	0.626;0.0	P;B	0.45232	0.474;0.006	T	0.36187	-0.9758	9	0.02654	T	1	-14.2458	16.0334	0.80603	0.0:0.0:0.0:1.0	.	59;59	E9PIG6;Q96LU5	.;IMP1L_HUMAN	R	59	.	ENSP00000278200:H59R	H	-	2	0	IMMP1L	31438767	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.245000	0.65405	2.243000	0.73865	0.533000	0.62120	CAT	.	.	.	none		0.318	IMMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388496.1	NM_144981		C	31482191	T	C	31482191	3	2	53	1	0	0	0	0	1	0	0	0	7723	1464	51	3	340	3	IMMP1L	11	31482191	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08	4069516	31482191	103524325	56	3629											
CCDC73	493860	hgsc.bcm.edu	37	chr11	32676507	32676507	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttatcaagtctgaggctgcTttttttagttccttaataag	9	19	7	6	0	2	1	1	1	1	0	3	1	3	1	1	1	1	3	1	1	5	9			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:32676507T>C	ENST00000335185.5	-	10	700	c.657A>G	c.(655-657)aaA>aaG	p.K219K	CCDC73_ENST00000534415.1_5'UTR	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73	219										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)					CTGAGGCTGCTTTTTTTAGTT	0.303																																					p.D219E		Atlas-SNP	.											CCDC73,NS,carcinoma,-2,1	CCDC73	136	.	0			c.T657G						PASS	.						80	67	71					11																	32676507		1809	4051	5860	SO:0001819	synonymous_variant	493860	exon10			GGCTGCTTTTTTT	AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279	ENST00000335185.5:c.657A>G	chr11.hg19:g.32676507T>C		42.0	0.0	.		25.0	2.0	.	NM_001008391	Q6P5Q7|Q6ZMW0|Q86WE7	Missense_Mutation	SNP	ENST00000335185.5	hg19	CCDS41630.1																																																																																			.	.	.	none		0.303	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391		C	32676507	T	C	32676507	2	2	53	1	0	0	0	0	0	0	0	1	2848	1606	56	3		3	CCDC73	11	32676507	Silent	SNP	T	TCGA-A4-8098-01A-11D-2396-08	1194316	32676507	102330009	57	3630											
PRR5L	79899	hgsc.bcm.edu	37	chr11	36472765	36472765	+	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	tgttcattttccagagtgttCacgagcccacaggcccaagt	9	11	9	12	1	2	1	2	0	0	1	3	2	3	1	3	1	1	2	3	1	1	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:36472765C>T	ENST00000378867.3	+	9	947	c.592C>T	c.(592-594)Cac>Tac	p.H198Y	PRR5L_ENST00000311599.5_Missense_Mutation_p.H125Y|PRR5L_ENST00000527487.1_Intron|PRR5L_ENST00000530639.1_Missense_Mutation_p.H198Y|PRR5L_ENST00000389693.3_3'UTR	NM_024841.4	NP_079117.3	Q6MZQ0	PRR5L_HUMAN	proline rich 5 like	198					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of signal transduction (GO:0009968)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|regulation of fibroblast migration (GO:0010762)|TORC2 signaling (GO:0038203)	mitochondrion (GO:0005739)|TORC2 complex (GO:0031932)	ubiquitin protein ligase binding (GO:0031625)	p.H198Y(1)		breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(7)|ovary(1)	19						CCAGAGTGTTCACGAGCCCAC	0.502																																					p.H198Y		Atlas-SNP	.											PRR5L,NS,carcinoma,0,1	PRR5L	35	.	1	Substitution - Missense(1)	cervix(1)	c.C592T						PASS	.						170	157	162					11																	36472765		2202	4298	6500	SO:0001583	missense	79899	exon9			AGTGTTCACGAGC		CCDS31463.1, CCDS53617.1	11p13-p12	2009-07-09				ENSG00000135362			25878	protein-coding gene	gene with protein product	"protein observed with Rictor-2"	611728				17461779	Standard	NM_024841		Approved	FLJ14213, PROTOR-2	uc001mwp.3	Q6MZQ0		ENST00000378867.3:c.592C>T	chr11.hg19:g.36472765C>T	ENSP00000368144:p.His198Tyr	145.0	0.0	.		156.0	67.0	.	NM_024841	A4QN22|E9PKY1|Q96H46|Q9H7V4	Missense_Mutation	SNP	ENST00000378867.3	hg19	CCDS31463.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.049026	0.75846	.	.	ENSG00000135362	ENST00000530639;ENST00000311599;ENST00000378867	T;T;T	0.36157	1.27;1.5;1.27	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.63861	0.2547	M	0.80982	2.52	0.58432	D	0.999995	D;D	0.71674	0.989;0.998	D;D	0.77557	0.979;0.99	T	0.69815	-0.5043	10	0.87932	D	0	-17.9831	17.9793	0.89136	0.0:1.0:0.0:0.0	.	70;198	Q6MZQ0-3;Q6MZQ0	.;PRR5L_HUMAN	Y	198;125;198	ENSP00000435050:H198Y;ENSP00000310103:H125Y;ENSP00000368144:H198Y	ENSP00000310103:H125Y	H	+	1	0	PRR5L	36429341	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	5.758000	0.68776	2.345000	0.79718	0.313000	0.20887	CAC	.	.	.	none		0.502	PRR5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389209.1	NM_024841		T	36472765	C	T	36472765	3	4	53	1	0	0	0	0	1	0	0	0	12612	826	29	2	624	2	PRR5L	11	36472765	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	3796258	36472765	98533751	58	3631											
C11orf67	28971	hgsc.bcm.edu	37	chr11	77580812	77580812	+	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	gatgtgaaggaagttgttgaGaagggtgtacagactcttgt	11	12	15	3	0	1	3	0	2	1	2	1	6	1	4	0	2	1	3	0	2	4	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:77580812G>A	ENST00000526415.1	+	4	350	c.177G>A	c.(175-177)gaG>gaA	p.E59E	AAMDC_ENST00000532481.1_Silent_p.E59E|AAMDC_ENST00000304716.8_Silent_p.E59E|RP11-91P24.6_ENST00000530972.1_RNA|AAMDC_ENST00000393427.2_Silent_p.E59E|AAMDC_ENST00000533193.1_Silent_p.E105E|AAMDC_ENST00000527134.1_Silent_p.E59E|AAMDC_ENST00000525409.1_Intron|AAMDC_ENST00000525034.1_Silent_p.E78E|RP11-91P24.7_ENST00000525594.1_RNA			Q9H7C9	AAMDC_HUMAN	adipogenesis associated, Mth938 domain containing	59	MTH138-like domain. {ECO:0000250}.				negative regulation of apoptotic process (GO:0043066)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)											AAGTTGTTGAGAAGGGTGTAC	0.493																																					p.E59E		Atlas-SNP	.											.	.	.	.	0			c.G177A						PASS	.						349	322	331					11																	77580812		2200	4292	6492	SO:0001819	synonymous_variant	28971	exon3			TGTTGAGAAGGGT	BC016854	CCDS8254.1	11q14.1	2012-10-08	2012-10-08	2012-10-08	ENSG00000087884	ENSG00000087884			30205	protein-coding gene	gene with protein product			"chromosome 11 open reading frame 67"	C11orf67		12477932	Standard	NM_024684		Approved	PTD015, FLJ21035, CK067	uc001oyq.3	Q9H7C9	OTTHUMG00000166651	ENST00000526415.1:c.177G>A	chr11.hg19:g.77580812G>A		338.0	0.0	.		264.0	91.0	.	NM_024684	Q96AQ4|Q9Y6B1	Silent	SNP	ENST00000526415.1	hg19	CCDS8254.1																																																																																			.	.	.	none		0.493	AAMDC-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390976.1	NM_024684		A	77580812	G	A	77580812	2	1	53	1	0	0	0	0	0	0	0	1	1659	933	33	2		2	C11orf67	11	77580812	Silent	SNP	G	TCGA-A4-8098-01A-11D-2396-08	41108047	77580812	57425704	59	3632											
PCF11	51585	hgsc.bcm.edu	37	chr11	82877724	82877724	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaagttccaagtctgccaaAagatggaaatctggttggga	14	9	11	7	0	2	1	0	0	2	1	3	3	3	3	2	3	1	2	2	3	5	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:82877724A>G	ENST00000298281.4	+	5	2237	c.1785A>G	c.(1783-1785)aaA>aaG	p.K595K		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	595					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						AGTCTGCCAAAAGATGGAAAT	0.348																																					p.K595K		Atlas-SNP	.											.	PCF11	220	.	0			c.A1785G						PASS	.						73	75	74					11																	82877724		1755	3856	5611	SO:0001819	synonymous_variant	51585	exon5			TGCCAAAAGATGG	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.1785A>G	chr11.hg19:g.82877724A>G		142.0	0.0	.		125.0	55.0	.	NM_015885	A6H8W7|O43671|Q6P0X8	Silent	SNP	ENST00000298281.4	hg19	CCDS44689.1																																																																																			.	.	.	none		0.348	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		G	82877724	A	G	82877724	2	3	53	1	0	0	0	0	0	0	0	1	11580	11	1	3		3	PCF11	11	82877724	Silent	SNP	A	TCGA-A4-8098-01A-11D-2396-08	5296912	82877724	52128792	60	3633											
ARHGAP32	9743	hgsc.bcm.edu	37	chr11	128840894	128840894	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaggtgcagcagcgggaccCgggcaccgtcccgcactttc	6	5	14	16	4	0	0	0	0	0	0	2	1	1	1	3	3	3	5	3	3	0	1	rs530219324		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr11:128840894C>T	ENST00000310343.9	-	22	4171	c.4172G>A	c.(4171-4173)cGg>cAg	p.R1391Q	ARHGAP32_ENST00000527272.1_Missense_Mutation_p.R1042Q|ARHGAP32_ENST00000392657.3_Missense_Mutation_p.R1042Q|ARHGAP32_ENST00000524655.1_3'UTR	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	1391	Interaction with GAB2.				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						CAGCGGGACCCGGGCACCGTC	0.632													C|||	1	0.000199681	0	0	5008	,	,		17039	0		0.001	False		,,,				2504	0				p.R1391Q		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.G4172A						PASS	.						45	47	47					11																	128840894		2201	4297	6498	SO:0001583	missense	9743	exon22			GGGACCCGGGCAC	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.4172G>A	chr11.hg19:g.128840894C>T	ENSP00000310561:p.Arg1391Gln	58.0	0.0	.		61.0	25.0	.	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Missense_Mutation	SNP	ENST00000310343.9	hg19	CCDS44769.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.168938	0.78339	.	.	ENSG00000134909	ENST00000310343;ENST00000392657;ENST00000527272	T;T;T	0.11712	2.77;2.75;2.75	5.71	5.71	0.89125	.	0.112572	0.56097	D	0.000024	T	0.19805	0.0476	M	0.69823	2.125	0.32214	N	0.576128	D	0.58620	0.983	P	0.44422	0.449	T	0.09207	-1.0685	10	0.37606	T	0.19	.	19.8599	0.96779	0.0:1.0:0.0:0.0	.	1391	A7KAX9	RHG32_HUMAN	Q	1391;1042;1042	ENSP00000310561:R1391Q;ENSP00000376425:R1042Q;ENSP00000432862:R1042Q	ENSP00000310561:R1391Q	R	-	2	0	ARHGAP32	128346104	0.998000	0.40836	0.932000	0.37286	0.291000	0.27294	3.773000	0.55333	2.710000	0.92621	0.655000	0.94253	CGG	.	.	.	none		0.632	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		T	128840894	C	T	128840894	3	4	53	1	0	0	0	0	1	0	0	0	881	652	23	1	2095	1	ARHGAP32	11	128840894	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	45963170	128840894	6165622	61	3634											
AKAP3	10566	hgsc.bcm.edu	37	chr12	4737430	4737430	+	Missense_Mutation	SNP	T	T	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	tcttcaaagtggacttgtatTtcaaatttgggggactttgt	9	17	10	5	0	3	0	2	0	1	0	3	2	3	2	0	3	0	1	0	3	3	6			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr12:4737430T>G	ENST00000545990.2	-	5	1162	c.638A>C	c.(637-639)aAa>aCa	p.K213T	AKAP3_ENST00000228850.1_Missense_Mutation_p.K213T|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	213					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						GGACTTGTATTTCAAATTTGG	0.468																																					p.K213T		Atlas-SNP	.											.	AKAP3	212	.	0			c.A638C						PASS	.						99	99	99					12																	4737430		2203	4300	6503	SO:0001583	missense	10566	exon4			TTGTATTTCAAAT	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.638A>C	chr12.hg19:g.4737430T>G	ENSP00000440994:p.Lys213Thr	173.0	0.0	.		202.0	121.0	.	NM_006422	O75945|Q86X01|Q9UM61	Missense_Mutation	SNP	ENST00000545990.2	hg19	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	T	13.40	2.224438	0.39300	.	.	ENSG00000111254	ENST00000228850;ENST00000545990	T;T	0.09255	3.0;3.0	4.87	1.27	0.21489	A-kinase anchor 110kDa, C-terminal (1);	0.332965	0.25968	N	0.027150	T	0.20861	0.0502	M	0.63428	1.95	0.09310	N	1	D	0.63046	0.992	P	0.60415	0.874	T	0.03651	-1.1016	10	0.87932	D	0	-14.2358	6.9349	0.24461	0.0:0.2845:0.0:0.7155	.	213	O75969	AKAP3_HUMAN	T	213	ENSP00000228850:K213T;ENSP00000440994:K213T	ENSP00000228850:K213T	K	-	2	0	AKAP3	4607691	0.949000	0.32298	0.109000	0.21407	0.693000	0.40251	1.094000	0.30951	0.121000	0.18284	0.528000	0.53228	AAA	.	.	.	none		0.468	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422		G	4737430	T	G	4737430	3	3	53	1	0	0	0	0	1	0	0	0	452	1841	64	5	1931	5	AKAP3	12	4737430	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08		4737430	129114465	62	3635											
GTSF1	121355	hgsc.bcm.edu	37	chr12	54856511	54856511	+	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	aggctcctggtttggttgacTgcaagacaataaagattgga	12	11	12	6	0	0	3	0	1	0	2	1	4	1	4	1	4	1	4	1	4	4	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr12:54856511T>A	ENST00000552397.1	-	5	1141		c.e5-2		RP11-753H16.3_ENST00000550474.1_RNA|GTSF1_ENST00000552395.1_Splice_Site|GTSF1_ENST00000305879.5_Splice_Site|RP11-753H16.5_ENST00000552785.1_RNA			Q8WW33	GTSF1_HUMAN	gametocyte specific factor 1							cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5		Myeloproliferative disorder(1001;0.00452)				TTTGGTTGACTGCAAGACAAT	0.483																																					.		Atlas-SNP	.											.	GTSF1	15	.	0			c.245-2A>T						PASS	.						92	91	92					12																	54856511		2203	4300	6503	SO:0001630	splice_region_variant	121355	exon6			GTTGACTGCAAGA	AK098819	CCDS8881.1	12q13.2	2008-02-04	2007-11-27	2007-11-27		ENSG00000170627			26565	protein-coding gene	gene with protein product			"family with sequence similarity 112, member B"	FAM112B		12477932	Standard	NM_144594		Approved	FLJ32942	uc001sgb.3	Q8WW33		ENST00000552397.1:c.245-2A>T	chr12.hg19:g.54856511T>A		93.0	0.0	.		168.0	46.0	.	NM_144594	B3KQ60|Q0VGM4|Q8N778	Splice_Site	SNP	ENST00000552397.1	hg19	CCDS8881.1	.	.	.	.	.	.	.	.	.	.	T	9.953	1.220561	0.22457	.	.	ENSG00000170627	ENST00000552397;ENST00000305879	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.3935	0.55373	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	GTSF1	53142778	1.000000	0.71417	0.971000	0.41717	0.231000	0.25187	4.551000	0.60740	2.183000	0.69458	0.533000	0.62120	.	.	.	.	none		0.483	GTSF1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406187.1	NM_144594	Intron	A	54856511	T	A	54856511	5	1	53	1	0	0	0	0	0	0	1	0	6893	1594	55	5	276	5	GTSF1	12	54856511	Splice_Site	SNP	T	TCGA-A4-8098-01A-11D-2396-08	50119081	54856511	78995384	63	3636											
WIF1	11197	hgsc.bcm.edu	37	chr12	65460514	65460514	+	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	catacatcgtggggtacaaaGggcttatagggagagagaac	14	7	14	6	1	0	2	0	0	0	2	1	4	0	2	0	4	3	2	0	4	6	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr12:65460514G>T	ENST00000286574.4	-	6	1011	c.637C>A	c.(637-639)Ctt>Att	p.L213I		NM_007191.4	NP_009122.2	Q9Y5W5	WIF1_HUMAN	WNT inhibitory factor 1	213	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				multicellular organismal development (GO:0007275)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)				cervix(1)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	21			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0231)		GGGGTACAAAGGGCTTATAGG	0.433			T	HMGA2	pleomorphic salivary gland adenoma																																p.L213I	Esophageal Squamous(148;1595 1816 48559 49439 49664)	Atlas-SNP	.		Dom	yes		12	12q14.3	11197	WNT inhibitory factor 1		E	.	WIF1	96	.	0			c.C637A						PASS	.						75	72	73					12																	65460514		2203	4300	6503	SO:0001583	missense	11197	exon6			TACAAAGGGCTTA	AF122922	CCDS8971.1	12q14.2	2008-04-11			ENSG00000156076	ENSG00000156076			18081	protein-coding gene	gene with protein product		605186				10201374	Standard	NM_007191		Approved		uc001ssk.3	Q9Y5W5	OTTHUMG00000168832	ENST00000286574.4:c.637C>A	chr12.hg19:g.65460514G>T	ENSP00000286574:p.Leu213Ile	44.0	0.0	.		54.0	14.0	.	NM_007191	Q6UXI1|Q8WVG4	Missense_Mutation	SNP	ENST00000286574.4	hg19	CCDS8971.1	.	.	.	.	.	.	.	.	.	.	G	14.56	2.572822	0.45798	.	.	ENSG00000156076	ENST00000286574	T	0.03035	4.07	5.23	4.34	0.51931	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.068823	0.64402	D	0.000016	T	0.02455	0.0075	N	0.05306	-0.075	0.53688	D	0.999978	B	0.19935	0.04	B	0.25291	0.059	T	0.54675	-0.8258	9	.	.	.	.	14.326	0.66521	0.0722:0.0:0.9278:0.0	.	213	Q9Y5W5	WIF1_HUMAN	I	213	ENSP00000286574:L213I	.	L	-	1	0	WIF1	63746781	1.000000	0.71417	0.998000	0.56505	0.123000	0.20343	4.824000	0.62701	1.530000	0.49136	0.655000	0.94253	CTT	.	.	.	none		0.433	WIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401258.2			T	65460514	G	T	65460514	3	4	53	1	0	0	0	0	1	0	0	0	17378	1000	35	4	522	4	WIF1	12	65460514	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	10604003	65460514	68391381	64	3637											
PARP4	143	hgsc.bcm.edu	37	chr13	25029240	25029240	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttgcttggcttgcaagaaTgtcacaccctccatggaact	10	12	8	11	0	1	1	1	0	0	1	2	2	2	2	2	2	3	3	2	2	3	3			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr13:25029240T>C	ENST00000381989.3	-	22	2778	c.2673A>G	c.(2671-2673)acA>acG	p.T891T	PARP4_ENST00000480576.1_5'Flank	NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	891	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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)		CTTGCAAGAATGTCACACCCT	0.502																																					p.T891T		Atlas-SNP	.											.	PARP4	142	.	0			c.A2673G						PASS	.						261	222	235					13																	25029240		2203	4300	6503	SO:0001819	synonymous_variant	143	exon22			CAAGAATGTCACA	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.2673A>G	chr13.hg19:g.25029240T>C		257.0	0.0	.		286.0	104.0	.	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	hg19	CCDS9307.1																																																																																			.	.	.	none		0.502	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437		C	25029240	T	C	25029240	2	2	53	1	0	0	0	0	0	0	0	1	11470	1451	51	3		3	PARP4	13	25029240	Silent	SNP	T	TCGA-A4-8098-01A-11D-2396-08		25029240	90140638	65	3638											
CPB2	1361	hgsc.bcm.edu	37	chr13	46658419	46658419	+	Missense_Mutation	SNP	A	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	acatcagatgcatttacaaaAaaatggacttgttttttctt	14	16	5	6	0	2	1	1	0	1	1	2	2	2	2	0	1	2	2	0	1	4	7			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr13:46658419A>C	ENST00000181383.4	-	3	226	c.210T>G	c.(208-210)ttT>ttG	p.F70L	CPB2-AS1_ENST00000606351.1_RNA|CPB2_ENST00000439329.3_Missense_Mutation_p.F70L|CPB2-AS1_ENST00000415033.2_RNA|CPB2-AS1_ENST00000606991.1_RNA|CPB2-AS1_ENST00000606243.1_RNA	NM_001872.3	NP_001863.3	Q96IY4	CBPB2_HUMAN	carboxypeptidase B2 (plasma)	70					blood coagulation (GO:0007596)|cellular response to glucose stimulus (GO:0071333)|fibrinolysis (GO:0042730)|liver regeneration (GO:0097421)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of plasminogen activation (GO:0010757)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to heat (GO:0009408)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|large_intestine(3)|liver(1)|lung(9)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Lung NSC(96;4.21e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|all_neural(104;0.235)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.44e-05)		CATTTACAAAAAAATGGACTT	0.368																																					p.F70L		Atlas-SNP	.											.	CPB2	60	.	0			c.T210G						PASS	.						151	139	143					13																	46658419		2203	4300	6503	SO:0001583	missense	1361	exon3			TACAAAAAAATGG	M75106	CCDS9401.1, CCDS73568.1	13q14.11	2012-02-10	2007-02-21		ENSG00000080618	ENSG00000080618			2300	protein-coding gene	gene with protein product	"thrombin-activatable fibrinolysis inhibitor", "carboxypeptidase U", "plasma carboxypeptidase B", "carboxypeptidase R"	603101	"carboxypeptidase B2 (plasma, carboxypeptidase U)"			1939207, 1427879	Standard	NM_001278541		Approved	CPU, PCPB, TAFI	uc001vaw.3	Q96IY4	OTTHUMG00000016867	ENST00000181383.4:c.210T>G	chr13.hg19:g.46658419A>C	ENSP00000181383:p.Phe70Leu	166.0	0.0	.		171.0	74.0	.	NM_001872	A8K464|Q15114|Q5T9K1|Q5T9K2|Q9P2Y6	Missense_Mutation	SNP	ENST00000181383.4	hg19	CCDS9401.1	.	.	.	.	.	.	.	.	.	.	A	15.13	2.740893	0.49151	.	.	ENSG00000080618	ENST00000181383;ENST00000439329	T;T	0.13538	2.58;2.58	5.41	-2.81	0.05805	Proteinase inhibitor, propeptide (1);Proteinase inhibitor, carboxypeptidase propeptide (2);	0.050842	0.85682	D	0.000000	T	0.12646	0.0307	L	0.42245	1.32	0.40335	D	0.978972	B;P	0.49253	0.337;0.921	B;P	0.46320	0.162;0.512	T	0.03875	-1.0996	10	0.44086	T	0.13	.	10.4812	0.44695	0.4897:0.0:0.5103:0.0	.	70;70	Q96IY4-2;Q96IY4	.;CBPB2_HUMAN	L	70	ENSP00000181383:F70L;ENSP00000400714:F70L	ENSP00000181383:F70L	F	-	3	2	CPB2	45556420	0.999000	0.42202	0.991000	0.47740	0.819000	0.46315	0.355000	0.20163	-0.389000	0.07786	-0.263000	0.10527	TTT	.	.	.	none		0.368	CPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044803.2	NM_001872		C	46658419	A	C	46658419	3	2	53	1	0	0	0	0	1	0	0	0	3799	11	1	5	1097	5	CPB2	13	46658419	Missense_Mutation	SNP	A	TCGA-A4-8098-01A-11D-2396-08	21629179	46658419	68511459	66	3639											
AP1G2	8906	hgsc.bcm.edu	37	chr14	24032848	24032848	+	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	agcgtttggttggagcaaacCtaggggatatatggctcatc	10	11	13	7	1	1	0	1	0	0	0	2	2	1	2	1	5	3	4	1	5	4	5			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr14:24032848C>T	ENST00000308724.5	-	12	1988		c.e12-1		RP11-66N24.3_ENST00000555968.1_RNA|RP11-66N24.4_ENST00000553985.1_RNA|AP1G2_ENST00000556277.1_5'Flank|AP1G2_ENST00000397120.3_Splice_Site	NM_003917.2	NP_003908.1	O75843	AP1G2_HUMAN	adaptor-related protein complex 1, gamma 2 subunit						intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	AP-1 adaptor complex (GO:0030121)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|membrane (GO:0016020)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	28	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00672)		TGGAGCAAACCTAGGGGATAT	0.567											OREG0022605	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-SNP	.											.	AP1G2	75	.	0			c.1233-1G>A						PASS	.						138	109	119					14																	24032848		2203	4300	6503	SO:0001630	splice_region_variant	8906	exon14			GCAAACCTAGGGG	AB015318	CCDS9602.1	14q11.2	2008-07-03			ENSG00000213983	ENSG00000213983			556	protein-coding gene	gene with protein product		603534				9733768, 9762922	Standard	XM_005268167		Approved	G2AD	uc001wkl.2	O75843	OTTHUMG00000028760	ENST00000308724.5:c.1233-1G>A	chr14.hg19:g.24032848C>T		103.0	0.0	.	768	68.0	46.0	.	NM_003917	D3DS51|O75504	Splice_Site	SNP	ENST00000308724.5	hg19	CCDS9602.1	.	.	.	.	.	.	.	.	.	.	C	14.96	2.691409	0.48097	.	.	ENSG00000213983	ENST00000308724;ENST00000397120;ENST00000545295;ENST00000535852	.	.	.	4.5	4.5	0.54988	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7542	0.69552	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	AP1G2	23102688	1.000000	0.71417	0.997000	0.53966	0.613000	0.37349	4.964000	0.63701	2.314000	0.78098	0.557000	0.71058	.	.	.	.	none		0.567	AP1G2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071812.4	NM_003917	Intron	T	24032848	C	T	24032848	5	4	53	1	0	0	0	0	0	0	1	0	733	695	24	2	1165	2	AP1G2	14	24032848	Splice_Site	SNP	C	TCGA-A4-8098-01A-11D-2396-08		24032848	83316692	67	3640											
C14orf106	55320	hgsc.bcm.edu	37	chr14	45711249	45711249	+	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	tttcccacctgattttttttAagtccatttgtaacagtttg	8	20	5	8	0	0	1	0	1	0	0	2	1	2	1	3	0	1	2	3	0	2	8			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr14:45711249A>C	ENST00000310806.4	-	4	1589	c.1131T>G	c.(1129-1131)ctT>ctG	p.L377L	MIS18BP1_ENST00000492652.1_5'UTR	NM_018353.4	NP_060823.3	Q6P0N0	M18BP_HUMAN	MIS18 binding protein 1	377					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						GATTTTTTTTAAGTCCATTTG	0.308																																					p.L377L		Atlas-SNP	.											.	MIS18BP1	92	.	0			c.T1131G						PASS	.						57	66	63					14																	45711249		2202	4294	6496	SO:0001819	synonymous_variant	55320	exon4			TTTTTTAAGTCCA	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.1131T>G	chr14.hg19:g.45711249A>C		110.0	0.0	.		47.0	30.0	.	NM_018353	D3DSA7|Q86V14|Q96PY4|Q9NUR5|Q9Y4X9	Silent	SNP	ENST00000310806.4	hg19	CCDS9684.1																																																																																			.	.	.	none		0.308	MIS18BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276795.2			C	45711249	A	C	45711249	2	2	53	1	0	0	0	0	0	0	0	1	1740	349	13	5		5	C14orf106	14	45711249	Silent	SNP	A	TCGA-A4-8098-01A-11D-2396-08	21678401	45711249	61638291	68	3641											
LRRK1	79705	hgsc.bcm.edu	37	chr15	101529603	101529603	+	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	agcagttatccgggaaaaacAgtgagtagtcactgcctgtg	12	9	12	8	1	1	1	1	1	0	0	2	2	2	2	2	1	3	3	2	1	4	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr15:101529603A>G	ENST00000388948.3	+	6	1121	c.762A>G	c.(760-762)acA>acG	p.T254T	LRRK1_ENST00000532029.2_Silent_p.T254T|LRRK1_ENST00000284395.5_Splice_Site_p.T251T	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)			CGGGAAAAACAGTGAGTAGTC	0.433																																					p.T254T		Atlas-SNP	.											.	LRRK1	310	.	0			c.A762G						PASS	.						80	79	79					15																	101529603		1890	4124	6014	SO:0001630	splice_region_variant	79705	exon6			AAAAACAGTGAGT	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.762+1A>G	chr15.hg19:g.101529603A>G		59.0	0.0	.		64.0	30.0	.	NM_024652		Silent	SNP	ENST00000388948.3	hg19	CCDS42086.1																																																																																			.	.	.	none		0.433	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652	Silent	G	101529603	A	G	101529603	5	3	53	1	0	0	0	0	0	0	1	0	9039	202	7	3	780	3	LRRK1	15	101529603	Splice_Site	SNP	A	TCGA-A4-8098-01A-11D-2396-08		101529603	1001789	69	3642											
RAB11FIP3	9727	hgsc.bcm.edu	37	chr16	570232	570232	+	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	ctgcaggagtaccacagccgCgcccgggagagcgagctgga	9	3	16	13	4	0	1	0	0	0	1	0	5	0	3	3	3	5	3	3	3	1	1			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr16:570232C>T	ENST00000262305.4	+	12	2359	c.1971C>T	c.(1969-1971)cgC>cgT	p.R657R	RAB11FIP3_ENST00000457159.1_Silent_p.R702R|RAB11FIP3_ENST00000450428.1_Silent_p.R361R	NM_014700.3	NP_055515.1	O75154	RFIP3_HUMAN	RAB11 family interacting protein 3 (class II)	657					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)				ACCACAGCCGCGCCCGGGAGA	0.682																																					p.R657R	Melanoma(160;2366 2595 4474 8099)	Atlas-SNP	.											.	RAB11FIP3	31	.	0			c.C1971T						PASS	.						5	9	8					16																	570232		2086	4138	6224	SO:0001819	synonymous_variant	9727	exon12			CAGCCGCGCCCGG	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.1971C>T	chr16.hg19:g.570232C>T		8.0	0.0	.		11.0	6.0	.	NM_014700	B0QYI8|B0QYT8|B1AHQ0|B4DEI7|B4DZR6|Q4VXV7|Q7Z5E9|Q9H155|Q9H1G0|Q9NUI0	Silent	SNP	ENST00000262305.4	hg19	CCDS32351.1																																																																																			.	.	.	none		0.682	RAB11FIP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109066.4	NM_014700		T	570232	C	T	570232	2	4	53	1	0	0	0	0	0	0	0	1	12908	755	27	1		1	RAB11FIP3	16	570232	Silent	SNP	C	TCGA-A4-8098-01A-11D-2396-08		570232	89784521	70	3643											
ARL6IP1	23204	hgsc.bcm.edu	37	chr16	18810023	18810023	+	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	taatctaatagctcacttacAgaaacaccaaagaaaccaca	20	7	3	11	0	2	2	1	0	1	2	2	2	2	2	2	0	4	1	2	0	7	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr16:18810023A>G	ENST00000304414.7	-	2	381	c.170T>C	c.(169-171)cTg>cCg	p.L57P	ARL6IP1_ENST00000546206.2_Splice_Site_p.L28P|RP11-1035H13.3_ENST00000567078.2_Splice_Site_p.L57P|ARL6IP1_ENST00000562819.1_Intron	NM_015161.1	NP_055976.1	Q15041	AR6P1_HUMAN	ADP-ribosylation factor-like 6 interacting protein 1	57					cell death (GO:0008219)|cotranslational protein targeting to membrane (GO:0006613)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|Sec61 translocon complex (GO:0005784)				breast(1)|large_intestine(2)|lung(6)|pancreas(1)|prostate(1)	11						GCTCACTTACAGAAACACCAA	0.413																																					p.L57P		Atlas-SNP	.											.	ARL6IP1	23	.	0			c.T170C						PASS	.						132	115	121					16																	18810023		2197	4300	6497	SO:0001630	splice_region_variant	23204	exon2			ACTTACAGAAACA	BC010281	CCDS10572.1	16p12-p11.2	2014-03-12	2006-09-26	2006-09-26	ENSG00000170540	ENSG00000170540			697	protein-coding gene	gene with protein product		607669	"ADP-ribosylation factor-like 6 interacting protein"	ARL6IP		24482476	Standard	NM_015161		Approved	AIP1, ARMER, KIAA0069, SPG61	uc002dfl.1	Q15041	OTTHUMG00000131367	ENST00000304414.7:c.170+1T>C	chr16.hg19:g.18810023A>G		147.0	0.0	.		168.0	63.0	.	NM_015161		Missense_Mutation	SNP	ENST00000304414.7	hg19	CCDS10572.1	.	.	.	.	.	.	.	.	.	.	a	23.3	4.394667	0.83011	.	.	ENSG00000170540	ENST00000304414;ENST00000545430;ENST00000546206	T;T	0.52754	0.65;0.65	5.07	5.07	0.68467	.	0.320357	0.30930	N	0.008581	T	0.64182	0.2575	M	0.65498	2.005	0.80722	D	1	D	0.58970	0.984	D	0.64237	0.923	T	0.64841	-0.6312	9	.	.	.	-0.7325	14.7838	0.69787	1.0:0.0:0.0:0.0	.	57	Q15041	AR6P1_HUMAN	P	57;9;28	ENSP00000306788:L57P;ENSP00000440048:L28P	.	L	-	2	0	ARL6IP1	18717524	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.476000	0.81055	2.016000	0.59253	0.533000	0.62120	CTG	.	.	.	none		0.413	ARL6IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254156.2	NM_015161	Missense_Mutation	G	18810023	A	G	18810023	5	3	53	1	0	0	0	0	0	0	1	0	942	202	7	3	461	3	ARL6IP1	16	18810023	Splice_Site	SNP	A	TCGA-A4-8098-01A-11D-2396-08	18239791	18810023	71544730	71	3644											
PRSS53	339105	hgsc.bcm.edu	37	chr16	31098021	31098021	+	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	aaggggaagcgatgggcgggCtggggcaggcagaggggtgt	8	4	24	5	2	0	1	0	0	0	1	0	3	0	2	0	9	1	3	0	9	2	0			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr16:31098021C>T	ENST00000280606.6	-	4	594	c.441G>A	c.(439-441)caG>caA	p.Q147Q		NM_001039503.2	NP_001034592.1	Q2L4Q9	PRS53_HUMAN	protease, serine, 53	147	Peptidase S1 1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			large_intestine(1)|lung(3)	4						GATGGGCGGGCTGGGGCAGGC	0.657																																					p.Q147Q		Atlas-SNP	.											.	PRSS53	29	.	0			c.G441A						PASS	.						30	38	35					16																	31098021		1927	4114	6041	SO:0001819	synonymous_variant	339105	exon4			GGCGGGCTGGGGC		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.441G>A	chr16.hg19:g.31098021C>T		78.0	0.0	.		94.0	44.0	.	NM_001039503		Silent	SNP	ENST00000280606.6	hg19	CCDS42153.1																																																																																			.	.	.	none		0.657	PRSS53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108580.4	NM_001081268		T	31098021	C	T	31098021	2	4	53	1	0	0	0	0	0	0	0	1	12642	796	28	2		2	PRSS53	16	31098021	Silent	SNP	C	TCGA-A4-8098-01A-11D-2396-08	12287998	31098021	59256732	72	3645											
DDX19B	11269	hgsc.bcm.edu	37	chr16	70346536	70346536	+	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	gcaacttgcatcttaaggaaGagaaaatcaaaccagatacc	18	7	7	9	0	2	2	1	0	1	2	2	4	2	3	2	1	4	2	2	1	7	3			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr16:70346536G>C	ENST00000288071.6	+	2	327	c.82G>C	c.(82-84)Gag>Cag	p.E28Q	DDX19B_ENST00000451014.3_Missense_Mutation_p.E33Q|RP11-529K1.3_ENST00000567706.1_Missense_Mutation_p.E28Q|DDX19B_ENST00000393657.2_Intron|DDX19B_ENST00000568625.1_Intron|DDX19B_ENST00000563392.1_Intron|DDX19B_ENST00000563206.1_Missense_Mutation_p.E33Q|DDX19B_ENST00000570055.1_3'UTR|DDX19B_ENST00000355992.3_Missense_Mutation_p.E28Q	NM_007242.5	NP_009173.1	Q9UMR2	DD19B_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 19B	28	N-terminal lobe.				mRNA export from nucleus (GO:0006406)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|prostate(1)	9		Ovarian(137;0.0694)				TCTTAAGGAAGAGAAAATCAA	0.378																																					p.E33Q	Esophageal Squamous(26;382 757 1343 9728 15939)	Atlas-SNP	.											RP11-529K1.3,NS,carcinoma,0,2	DDX19B	31	.	0			c.G97C						PASS	.						100	94	96					16																	70346536		2198	4300	6498	SO:0001583	missense	11269	exon2			AAGGAAGAGAAAA	AJ237946	CCDS10888.1, CCDS32475.1, CCDS42187.1, CCDS58478.1	16q22.3	2012-02-23	2012-02-23	2005-07-13	ENSG00000157349	ENSG00000157349		"DEAD-boxes"	2742	protein-coding gene	gene with protein product		605812	"DEAD (Asp-Glu-Ala-As) box polypeptide 19", "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 19 (Dbp5, yeast, homolog)"	DDX19		10428971	Standard	NM_007242		Approved	DBP5	uc002eyo.4	Q9UMR2	OTTHUMG00000137577	ENST00000288071.6:c.82G>C	chr16.hg19:g.70346536G>C	ENSP00000288071:p.Glu28Gln	55.0	0.0	.		35.0	2.0	.	NM_001257172	B3KNE9|B4DXS6|E7EMK4|Q6FIB7|Q6IAE0|Q96KE7|Q9H0U0	Missense_Mutation	SNP	ENST00000288071.6	hg19	CCDS10888.1	.	.	.	.	.	.	.	.	.	.	G	15.04	2.714638	0.48622	.	.	ENSG00000157349	ENST00000451014;ENST00000355992;ENST00000288071	T;T;T	0.62639	3.73;0.01;0.01	5.24	5.24	0.73138	.	0.047526	0.85682	D	0.000000	T	0.50360	0.1611	L	0.31845	0.965	0.43000	D	0.994511	B;B;P;B	0.36535	0.085;0.259;0.557;0.006	B;B;B;B	0.33620	0.015;0.11;0.167;0.01	T	0.53436	-0.8439	10	0.42905	T	0.14	.	14.1874	0.65614	0.0:0.0:1.0:0.0	.	33;28;28;28	E7EMK4;Q7Z4W5;Q9UMR2-2;Q9UMR2	.;.;.;DD19B_HUMAN	Q	33;28;28	ENSP00000392639:E33Q;ENSP00000348271:E28Q;ENSP00000288071:E28Q	ENSP00000288071:E28Q	E	+	1	0	DDX19B	68904037	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.261000	0.65496	2.732000	0.93576	0.655000	0.94253	GAG	.	.	.	none		0.378	DDX19B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268965.3	NM_007242		C	70346536	G	C	70346536	3	2	53	1	0	0	0	0	1	0	0	0	4349	943	33	4	88	4	DDX19B	16	70346536	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	39248515	70346536	20008217	73	3646											
TXNL4B	54957	hgsc.bcm.edu	37	chr16	72120699	72120699	+	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	caaacttagtgtgatctggaGatctagacagcatagaagag	15	9	11	6	0	2	5	0	1	2	4	2	6	2	5	0	1	2	1	0	1	5	3			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr16:72120699G>T	ENST00000268483.3	-	4	608	c.287C>A	c.(286-288)tCt>tAt	p.S96Y	RP11-384M15.3_ENST00000561827.1_RNA|TXNL4B_ENST00000423037.1_Missense_Mutation_p.S96Y|TXNL4B_ENST00000426362.2_Missense_Mutation_p.S96Y	NM_001142318.1|NM_017853.2	NP_001135790.1|NP_060323.1	Q9NX01	TXN4B_HUMAN	thioredoxin-like 4B	96					mitotic nuclear division (GO:0007067)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	spliceosomal complex (GO:0005681)				cervix(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(2)	8						GTGATCTGGAGATCTAGACAG	0.358																																					p.S96Y		Atlas-SNP	.											.	TXNL4B	17	.	0			c.C287A						PASS	.						68	65	66					16																	72120699		2198	4300	6498	SO:0001583	missense	54957	exon4			TCTGGAGATCTAG	BC009646	CCDS10906.1	16q22.2	2012-11-19			ENSG00000140830	ENSG00000140830			26041	protein-coding gene	gene with protein product						15161931	Standard	NM_017853		Approved	FLJ20511, DLP, Dim2	uc010vmn.2	Q9NX01	OTTHUMG00000173453	ENST00000268483.3:c.287C>A	chr16.hg19:g.72120699G>T	ENSP00000268483:p.Ser96Tyr	68.0	0.0	.		61.0	26.0	.	NM_001142318	D3DWS6	Missense_Mutation	SNP	ENST00000268483.3	hg19	CCDS10906.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.824185	0.90955	.	.	ENSG00000140830	ENST00000268483;ENST00000426362;ENST00000423037	.	.	.	5.87	5.87	0.94306	Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	T	0.65365	0.2684	L	0.34521	1.04	0.80722	D	1	D	0.69078	0.997	P	0.60345	0.873	T	0.66594	-0.5884	9	0.87932	D	0	.	18.0718	0.89410	0.0:0.0:1.0:0.0	.	96	Q9NX01	TXN4B_HUMAN	Y	96	.	ENSP00000268483:S96Y	S	-	2	0	TXNL4B	70678200	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	9.813000	0.99286	2.941000	0.99782	0.655000	0.94253	TCT	.	.	.	none		0.358	TXNL4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269007.2	NM_017853		T	72120699	G	T	72120699	3	4	53	1	0	0	0	0	1	0	0	0	16818	942	33	4	166	4	TXNL4B	16	72120699	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	1774163	72120699	18234054	74	3647											
SLC2A4	6517	hgsc.bcm.edu	37	chr17	7189210	7189210	+	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	gcaacttcatcattggcatgGgtttccagtatgttgcggta	8	14	11	8	1	2	0	2	0	0	0	3	0	3	0	1	3	2	6	1	3	3	6			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:7189210G>C	ENST00000317370.8	+	10	1577	c.1309G>C	c.(1309-1311)Ggt>Cgt	p.G437R	SLC2A4_ENST00000571308.1_Missense_Mutation_p.G437R|SLC2A4_ENST00000424875.2_Missense_Mutation_p.G427R|RP1-4G17.2_ENST00000576271.1_RNA	NM_001042.2	NP_001033.1	P14672	GTR4_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 4	437					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						CATTGGCATGGGTTTCCAGTA	0.627																																					p.G437R		Atlas-SNP	.											.	SLC2A4	44	.	0			c.G1309C						PASS	.						88	72	77					17																	7189210		2203	4300	6503	SO:0001583	missense	6517	exon10			GGCATGGGTTTCC	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.1309G>C	chr17.hg19:g.7189210G>C	ENSP00000320935:p.Gly437Arg	62.0	0.0	.		71.0	24.0	.	NM_001042	Q05BQ3|Q14CX2	Missense_Mutation	SNP	ENST00000317370.8	hg19	CCDS11097.1	.	.	.	.	.	.	.	.	.	.	G	15.50	2.851854	0.51270	.	.	ENSG00000181856	ENST00000317370;ENST00000424875	T;T	0.74002	-0.8;-0.8	5.09	1.72	0.24424	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.256239	0.39834	N	0.001255	T	0.72162	0.3426	M	0.67569	2.06	0.46654	D	0.999149	P;P	0.40144	0.539;0.704	P;B	0.48488	0.579;0.443	T	0.65463	-0.6162	10	0.30854	T	0.27	.	3.2542	0.06826	0.2014:0.0:0.4319:0.3667	.	437;427	P14672;F5H081	GTR4_HUMAN;.	R	437;427	ENSP00000320935:G437R;ENSP00000396887:G427R	ENSP00000320935:G437R	G	+	1	0	SLC2A4	7129934	0.224000	0.23674	0.998000	0.56505	0.998000	0.95712	-0.437000	0.06914	0.677000	0.31305	0.563000	0.77884	GGT	.	.	.	none		0.627	SLC2A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220031.3			C	7189210	G	C	7189210	3	2	53	1	0	0	0	0	1	0	0	0	14559	1232	43	4	1347	4	SLC2A4	17	7189210	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08		7189210	74006000	75	3648											
POLR2A	5430	hgsc.bcm.edu	37	chr17	7399344	7399344	+	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	agcttggggggctgatggacCcgaggcagggggtgattgag	7	7	21	6	1	0	3	0	3	0	0	0	5	0	4	1	7	1	3	1	7	0	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:7399344C>G	ENST00000322644.6	+	2	577	c.178C>G	c.(178-180)Ccg>Gcg	p.P60A	POLR2A_ENST00000572844.1_Missense_Mutation_p.P60A	NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	60					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)				GCTGATGGACCCGAGGCAGGG	0.612																																					p.P60A		Atlas-SNP	.											.	POLR2A	157	.	0			c.C178G						PASS	.						42	48	46					17																	7399344		2202	4299	6501	SO:0001583	missense	5430	exon2			ATGGACCCGAGGC			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.178C>G	chr17.hg19:g.7399344C>G	ENSP00000314949:p.Pro60Ala	79.0	0.0	.		100.0	36.0	.	NM_000937	A6NN93|B9EH88|Q6NX41	Missense_Mutation	SNP	ENST00000322644.6	hg19	CCDS32548.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.134164	0.77662	.	.	ENSG00000181222	ENST00000322644	T	0.21734	1.99	5.33	5.33	0.75918	RNA polymerase Rpb1, domain 1 (1);	0.000000	0.85682	D	0.000000	T	0.48077	0.1480	M	0.71206	2.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.99;0.999	T	0.48927	-0.8991	10	0.87932	D	0	.	17.783	0.88529	0.0:1.0:0.0:0.0	.	60;60	P24928;Q6NX41	RPB1_HUMAN;.	A	60	ENSP00000314949:P60A	ENSP00000314949:P60A	P	+	1	0	SLC35G6	7340068	1.000000	0.71417	0.995000	0.50966	0.853000	0.48598	7.142000	0.77339	2.499000	0.84300	0.467000	0.42956	CCG	.	.	.	none		0.612	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937		G	7399344	C	G	7399344	3	3	53	1	0	0	0	0	1	0	0	0	12221	623	22	4	184	4	POLR2A	17	7399344	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	210134	7399344	73795866	76	3649											
TAF15	8148	hgsc.bcm.edu	37	chr17	34172014	34172014	+	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	ggggctacggaggagaccgaGgtggctatggaggcaaaatg	11	5	19	6	2	0	1	0	0	0	1	0	5	0	3	1	8	1	3	1	8	4	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:34172014G>T	ENST00000588240.1	+	15	1826	c.1711G>T	c.(1711-1713)Ggt>Tgt	p.G571C	TAF15_ENST00000311979.3_Missense_Mutation_p.G568C|TAF15_ENST00000592237.1_Missense_Mutation_p.E375D	NM_003487.3|NM_139215.2	NP_003478.1|NP_631961.1	Q16514	TAF12_HUMAN	TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa	0					chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of RNA biosynthetic process (GO:2001141)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)		TAF15/NR4A3(33)	lung(1)|ovary(1)|skin(2)|stomach(1)	5		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		AGGAGACCGAGGTGGCTATGG	0.527			T	"TEC, CHN1, ZNF384"	"extraskeletal myxoid chondrosarcomas, ALL"																																p.G571C		Atlas-SNP	.		Dom	yes		17	17q11.1-q11.2	8148	"TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa"		"L, M"	.	TAF15	46	.	0			c.G1711T						PASS	.						76	89	85					17																	34172014		2203	4300	6503	SO:0001583	missense	8148	exon15			GACCGAGGTGGCT	U51334	CCDS32623.1, CCDS59279.1	17q11.1-q11.2	2013-02-12	2002-08-29	2001-12-07		ENSG00000270647		"RNA binding motif (RRM) containing"	11547	protein-coding gene	gene with protein product		601574	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, N, 68kD (RNA-binding protein 56)"	TAF2N		8954779, 9795213	Standard	NM_003487		Approved	hTAFII68, RBP56, Npl3	uc002hkd.4	Q92804		ENST00000588240.1:c.1711G>T	chr17.hg19:g.34172014G>T	ENSP00000466950:p.Gly571Cys	168.0	0.0	.		165.0	55.0	.	NM_139215	D3DPM5|Q15775|Q5T077	Missense_Mutation	SNP	ENST00000588240.1	hg19	CCDS32623.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.911288	0.52439	.	.	ENSG00000172660	ENST00000311979;ENST00000536077	D	0.94862	-3.54	5.07	4.09	0.47781	.	.	.	.	.	D	0.94424	0.8206	L	0.34521	1.04	0.39114	D	0.961521	D;D	0.89917	1.0;1.0	D;D	0.69479	0.92;0.964	D	0.94444	0.7661	9	0.87932	D	0	-3.2622	10.8882	0.46978	0.0922:0.0:0.9078:0.0	.	571;568	Q92804;Q92804-2	RBP56_HUMAN;.	C	571;374	ENSP00000309558:G571C	ENSP00000309558:G571C	G	+	1	0	TAF15	31196127	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.652000	0.61454	2.520000	0.84964	0.591000	0.81541	GGT	.	.	.	none		0.527	TAF15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449134.1	NM_139215		T	34172014	G	T	34172014	3	4	53	1	0	0	0	0	1	0	0	0	15530	1000	35	4	1769	4	TAF15	17	34172014	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	26772670	34172014	47023196	77	3650											
ACACA	31	hgsc.bcm.edu	37	chr17	35567392	35567392	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atacggtacctgtttagcgtAgggatgttccctctgtaatt	8	15	10	8	2	1	0	0	0	1	0	2	1	2	1	2	2	3	5	2	2	5	8			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:35567392A>G	ENST00000394406.2	-	30	3775	c.3585T>C	c.(3583-3585)ccT>ccC	p.P1195P	ACACA_ENST00000353139.5_Silent_p.P1232P|ACACA_ENST00000360679.3_Silent_p.P1137P|ACACA_ENST00000335166.5_Silent_p.P1117P	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	1195					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)	TGTTTAGCGTAGGGATGTTCC	0.343																																					p.P1232P	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-SNP	.											.	ACACA	395	.	0			c.T3696C						PASS	.						94	95	95					17																	35567392		2203	4300	6503	SO:0001819	synonymous_variant	31	exon30			TAGCGTAGGGATG	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.3585T>C	chr17.hg19:g.35567392A>G		104.0	0.0	.		97.0	4.0	.	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Silent	SNP	ENST00000394406.2	hg19	CCDS11317.1																																																																																			.	.	.	none		0.343	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		G	35567392	A	G	35567392	2	3	53	1	0	0	0	0	0	0	0	1	106	407	15	3		3	ACACA	17	35567392	Silent	SNP	A	TCGA-A4-8098-01A-11D-2396-08	1395378	35567392	45627818	78	3651											
LRRC46	90506	hgsc.bcm.edu	37	chr17	45914207	45914207	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacctgctgaggatggagatGcagcccaccctcaccgacct	9	6	10	16	1	1	2	1	1	0	1	1	5	1	3	5	2	3	2	5	2	0	0			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:45914207G>A	ENST00000269025.4	+	8	1050	c.687G>A	c.(685-687)atG>atA	p.M229I		NM_033413.3	NP_219481.1	Q96FV0	LRC46_HUMAN	leucine rich repeat containing 46	229										endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)	9						GGATGGAGATGCAGCCCACCC	0.667																																					p.M229I		Atlas-SNP	.											.	LRRC46	25	.	0			c.G687A						PASS	.						54	56	55					17																	45914207		2203	4300	6503	SO:0001583	missense	90506	exon8			GGAGATGCAGCCC		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.687G>A	chr17.hg19:g.45914207G>A	ENSP00000269025:p.Met229Ile	97.0	0.0	.		132.0	38.0	.	NM_033413	A8K9Q0	Missense_Mutation	SNP	ENST00000269025.4	hg19	CCDS11518.1	.	.	.	.	.	.	.	.	.	.	G	6.561	0.471736	0.12461	.	.	ENSG00000141294	ENST00000269025	T	0.72167	-0.63	5.53	-11.1	0.00147	.	1.132520	0.06682	N	0.768096	T	0.41558	0.1164	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	0.47623	-0.9103	10	0.37606	T	0.19	0.4736	6.5183	0.22260	0.1084:0.4274:0.3331:0.131	.	229;229	A8K9Q0;Q96FV0	.;LRC46_HUMAN	I	229	ENSP00000269025:M229I	ENSP00000269025:M229I	M	+	3	0	LRRC46	43269206	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-6.635000	0.00058	-4.674000	0.00036	-1.325000	0.01285	ATG	.	.	.	none		0.667	LRRC46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441377.1	NM_033413		A	45914207	G	A	45914207	3	1	53	1	0	0	0	0	1	0	0	0	9010	1319	46	2	717	2	LRRC46	17	45914207	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	10346815	45914207	35281003	79	3652											
ACSF2	80221	hgsc.bcm.edu	37	chr17	48549793	48549793	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggccatcctgtcccaggcccGgatcatgaacatggaggcag	9	6	13	13	1	1	1	1	1	0	0	3	3	3	3	4	5	1	1	4	5	1	0			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:48549793G>A	ENST00000300441.4	+	12	1432	c.1328G>A	c.(1327-1329)cGg>cAg	p.R443Q	ACSF2_ENST00000504392.1_Missense_Mutation_p.R400Q|ACSF2_ENST00000541920.1_Missense_Mutation_p.R283Q|ACSF2_ENST00000502667.1_Missense_Mutation_p.R430Q|ACSF2_ENST00000506085.1_Intron|ACSF2_ENST00000427954.2_Missense_Mutation_p.R468Q	NM_025149.4	NP_079425.3	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2	443					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ligase activity (GO:0016874)			endometrium(7)|kidney(3)|large_intestine(1)|lung(1)|stomach(1)	13	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			TCCCAGGCCCGGATCATGAAC	0.612																																					p.R443Q		Atlas-SNP	.											.	ACSF2	46	.	0			c.G1328A						PASS	.						50	48	49					17																	48549793		2203	4300	6503	SO:0001583	missense	80221	exon12			AGGCCCGGATCAT	AK024573, BC012053	CCDS11567.1, CCDS74103.1, CCDS74104.1, CCDS74105.1	17q21.33	2007-10-17			ENSG00000167107	ENSG00000167107		"Acyl-CoA synthetase family"	26101	protein-coding gene	gene with protein product		610465				17762044	Standard	NM_001288968		Approved	FLJ20920, ACSMW	uc002iqu.2	Q96CM8	OTTHUMG00000162128	ENST00000300441.4:c.1328G>A	chr17.hg19:g.48549793G>A	ENSP00000300441:p.Arg443Gln	34.0	0.0	.		53.0	31.0	.	NM_025149	B4DFQ6|B4DHT5|B4DUF5|Q9H7G2	Missense_Mutation	SNP	ENST00000300441.4	hg19	CCDS11567.1	.	.	.	.	.	.	.	.	.	.	G	12.15	1.851859	0.32699	.	.	ENSG00000167107	ENST00000300441;ENST00000541920;ENST00000504392;ENST00000427954;ENST00000502667	T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9	5.09	1.7	0.24286	AMP-dependent synthetase/ligase (1);	0.312695	0.37393	N	0.002103	T	0.26810	0.0656	L	0.28192	0.835	0.24361	N	0.994876	B;B;B;B	0.15930	0.003;0.015;0.003;0.003	B;B;B;B	0.12156	0.007;0.007;0.007;0.007	T	0.18085	-1.0348	10	0.52906	T	0.07	-5.2723	7.7408	0.28841	0.7438:0.0:0.2562:0.0	.	430;468;400;443	B4DHT5;B4DFQ6;E9PF16;Q96CM8	.;.;.;ACSF2_HUMAN	Q	443;283;400;468;430	ENSP00000300441:R443Q;ENSP00000437987:R283Q;ENSP00000425964:R400Q;ENSP00000401831:R468Q;ENSP00000421884:R430Q	ENSP00000300441:R443Q	R	+	2	0	ACSF2	45904792	1.000000	0.71417	0.994000	0.49952	0.237000	0.25408	4.324000	0.59228	0.295000	0.22570	-0.378000	0.06908	CGG	.	.	.	none		0.612	ACSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367423.3	NM_025149		A	48549793	G	A	48549793	3	1	53	1	0	0	0	0	1	0	0	0	175	1116	39	1	1374	1	ACSF2	17	48549793	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	2635586	48549793	32645417	80	3653											
PITPNC1	26207	hgsc.bcm.edu	37	chr17	65665781	65665781	+	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	ggaacaatttgtacacaaggTaagtggtccaacagcagttc	14	9	10	8	0	0	0	0	0	0	0	2	1	1	1	1	3	4	4	1	3	6	4			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:65665781T>C	ENST00000581322.1	+	7	618		c.e7+2		PITPNC1_ENST00000335257.6_Splice_Site|PITPNC1_ENST00000580974.1_Splice_Site|PITPNC1_ENST00000299954.9_Splice_Site			Q9UKF7	PITC1_HUMAN	phosphatidylinositol transfer protein, cytoplasmic 1						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)			GTACACAAGGTAAGTGGTCCA	0.468																																					.		Atlas-SNP	.											.	PITPNC1	47	.	0			c.618+2T>C						PASS	.						64	68	67					17																	65665781		1987	4159	6146	SO:0001630	splice_region_variant	26207	exon7			ACAAGGTAAGTGG	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.618+2T>C	chr17.hg19:g.65665781T>C		10.0	0.0	.		20.0	12.0	.	NM_181671	A8K473|J3QR20|Q96I07	Splice_Site	SNP	ENST00000581322.1	hg19	CCDS58588.1	.	.	.	.	.	.	.	.	.	.	T	18.84	3.709581	0.68730	.	.	ENSG00000154217	ENST00000335257;ENST00000299954	.	.	.	5.58	5.58	0.84498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0556	0.80801	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	PITPNC1	63096243	1.000000	0.71417	0.955000	0.39395	0.604000	0.37047	7.880000	0.87243	2.239000	0.73571	0.533000	0.62120	.	.	.	.	none		0.468	PITPNC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447194.1	NM_012417	Intron	C	65665781	T	C	65665781	5	2	53	1	0	0	0	0	0	0	1	0	11956	1652	57	3	646	3	PITPNC1	17	65665781	Splice_Site	SNP	T	TCGA-A4-8098-01A-11D-2396-08	17115988	65665781	15529429	81	3654											
DNAH17	8632	hgsc.bcm.edu	37	chr17	76491997	76491997	+	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	ctcaggcagctccgcgcgtcCggcgtacccagggttcatgg	5	7	14	15	5	2	0	2	0	0	0	4	0	4	0	3	4	2	4	3	4	1	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr17:76491997C>G	ENST00000585328.1	-	38	5972	c.5848G>C	c.(5848-5850)Gga>Cga	p.G1950R	RP11-559N14.5_ENST00000585969.1_RNA|DNAH17-AS1_ENST00000598378.1_5'Flank|DNAH17_ENST00000389840.5_Missense_Mutation_p.G1941R|RP11-559N14.5_ENST00000591373.1_RNA	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	1941	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)			TCCGCGCGTCCGGCGTACCCA	0.557																																					p.G1955R		Atlas-SNP	.											.	DNAH17	347	.	0			c.G5863C						PASS	.						93	94	94					17																	76491997		2059	4237	6296	SO:0001583	missense	8632	exon38			CGCGTCCGGCGTA	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.5848G>C	chr17.hg19:g.76491997C>G	ENSP00000465516:p.Gly1950Arg	77.0	0.0	.		82.0	20.0	.	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	hg19		.	.	.	.	.	.	.	.	.	.	c	16.89	3.247501	0.59103	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.17528	2.27	4.49	4.49	0.54785	.	.	.	.	.	T	0.57902	0.2085	H	0.96833	3.89	0.58432	D	0.999995	.	.	.	.	.	.	T	0.74910	-0.3503	7	0.87932	D	0	.	17.7846	0.88533	0.0:1.0:0.0:0.0	.	.	.	.	R	1950;1941	ENSP00000374490:G1941R	ENSP00000300671:G1950R	G	-	1	0	DNAH17	74003592	1.000000	0.71417	0.121000	0.21740	0.087000	0.18053	7.472000	0.80996	2.501000	0.84356	0.537000	0.68136	GGA	.	.	.	none		0.557	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		G	76491997	C	G	76491997	3	3	53	1	0	0	0	0	1	0	0	0	4603	661	23	4	7701	4	DNAH17	17	76491997	Missense_Mutation	SNP	C	TCGA-A4-8098-01A-11D-2396-08	10826216	76491997	4703213	82	3655											
PNPLA6	10908	hgsc.bcm.edu	37	chr19	7615223	7615223	+	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	agtgtggtgctgagtgcggcGcacacggtggcagccaggat	7	7	18	9	3	0	1	0	1	0	0	0	2	0	2	1	5	3	3	1	5	0	0			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr19:7615223G>A	ENST00000221249.6	+	18	2168	c.1737G>A	c.(1735-1737)gcG>gcA	p.A579A	PNPLA6_ENST00000545201.2_Silent_p.A553A|PNPLA6_ENST00000600737.1_Silent_p.A618A|PNPLA6_ENST00000450331.3_Silent_p.A579A|PNPLA6_ENST00000414982.3_Silent_p.A627A|PNPLA6_ENST00000594864.1_3'UTR	NM_006702.4	NP_006693.3	Q8IY17	PLPL6_HUMAN	patatin-like phospholipase domain containing 6	618					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						TGAGTGCGGCGCACACGGTGG	0.637																																					p.A627A		Atlas-SNP	.											.	PNPLA6	163	.	0			c.G1881A						PASS	.						61	58	59					19																	7615223		2202	4290	6492	SO:0001819	synonymous_variant	10908	exon17			TGCGGCGCACACG	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.1737G>A	chr19.hg19:g.7615223G>A		113.0	0.0	.		149.0	53.0	.	NM_001166111	A6NGQ0|B4DFB9|B7Z7T2|F5H5K9|J3KQS3|O60859|Q86W58|Q9UG58	Silent	SNP	ENST00000221249.6	hg19	CCDS32891.1																																																																																			.	.	.	none		0.637	PNPLA6-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459275.1	NM_006702		A	7615223	G	A	7615223	2	1	53	1	0	0	0	0	0	0	0	1	12176	1074	38	1		1	PNPLA6	19	7615223	Silent	SNP	G	TCGA-A4-8098-01A-11D-2396-08		7615223	51513760	83	3656											
JUNB	3726	hgsc.bcm.edu	37	chr19	12902787	12902787	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agggcggcggtggcggcagcTacttttctggtcagggctcg	4	9	18	10	4	2	0	1	0	1	0	3	0	2	0	0	7	2	3	0	7	1	3			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr19:12902787T>C	ENST00000302754.4	+	1	478	c.202T>C	c.(202-204)Tac>Cac	p.Y68H		NM_002229.2	NP_002220.1	P17275	JUNB_HUMAN	jun B proto-oncogene	68					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						TGGCGGCAGCTACTTTTCTGG	0.672																																					p.Y68H		Atlas-SNP	.											.	JUNB	14	.	0			c.T202C						PASS	.						12	13	13					19																	12902787		2200	4294	6494	SO:0001583	missense	3726	exon1			GGCAGCTACTTTT	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.202T>C	chr19.hg19:g.12902787T>C	ENSP00000303315:p.Tyr68His	15.0	0.0	.		31.0	13.0	.	NM_002229	Q96GH3	Missense_Mutation	SNP	ENST00000302754.4	hg19	CCDS12280.1	.	.	.	.	.	.	.	.	.	.	T	13.29	2.192125	0.38707	.	.	ENSG00000171223	ENST00000302754	T	0.29142	1.58	4.97	4.97	0.65823	Jun-like transcription factor (1);	1.243760	0.05788	U	0.609862	T	0.21103	0.0508	N	0.22421	0.69	0.34616	D	0.718126	B	0.18166	0.026	B	0.11329	0.006	T	0.28681	-1.0036	10	0.15499	T	0.54	-6.7954	6.385	0.21556	0.0:0.1805:0.0:0.8195	.	68	P17275	JUNB_HUMAN	H	68	ENSP00000303315:Y68H	ENSP00000303315:Y68H	Y	+	1	0	JUNB	12763787	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	1.617000	0.36943	1.865000	0.54081	0.448000	0.29417	TAC	.	.	.	none		0.672	JUNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451015.1	NM_002229		C	12902787	T	C	12902787	3	2	53	1	0	0	0	0	1	0	0	0	7977	1522	53	3	204	3	JUNB	19	12902787	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08	5287564	12902787	46226196	84	3657											
ZNF681	148213	hgsc.bcm.edu	37	chr19	23927146	23927146	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggtgtgaggacttgttaaaAgctttgccacattcttcaca	11	13	9	8	0	2	1	1	1	1	0	2	2	2	2	1	2	2	2	1	2	2	5			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr19:23927146A>G	ENST00000402377.3	-	4	1347	c.1206T>C	c.(1204-1206)gcT>gcC	p.A402A	ZNF681_ENST00000395385.3_Silent_p.A333A	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	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)|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)				ACTTGTTAAAAGCTTTGCCAC	0.398																																					p.A402A		Atlas-SNP	.											ZNF681,bladder,carcinoma,0,8	ZNF681	76	.	0			c.T1206C						PASS	.						69	74	72					19																	23927146		2203	4300	6503	SO:0001819	synonymous_variant	148213	exon4			GTTAAAAGCTTTG	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.1206T>C	chr19.hg19:g.23927146A>G		53.0	1.0	.		62.0	3.0	.	NM_138286	B3KVF7	Silent	SNP	ENST00000402377.3	hg19	CCDS12414.2																																																																																			.	.	.	none		0.398	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286		G	23927146	A	G	23927146	2	3	53	1	0	0	0	0	0	0	0	1	18100	59	3	3		3	ZNF681	19	23927146	Silent	SNP	A	TCGA-A4-8098-01A-11D-2396-08	11024359	23927146	35201837	85	3658											
LSM14A	26065	hgsc.bcm.edu	37	chr19	34712486	34712486	+	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	aatcccacttcgtccaaaccGtggccgtgggggatacagag	10	7	12	12	3	0	1	0	0	0	1	3	2	2	2	4	3	2	0	4	3	3	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr19:34712486G>T	ENST00000433627.5	+	9	1286	c.1211G>T	c.(1210-1212)cGt>cTt	p.R404L	LSM14A_ENST00000540746.2_Missense_Mutation_p.R363L|LSM14A_ENST00000544216.3_Missense_Mutation_p.R404L	NM_001114093.1	NP_001107565.1	Q8ND56	LS14A_HUMAN	LSM14A, SCD6 homolog A (S. cerevisiae)	404					cytoplasmic mRNA processing body assembly (GO:0033962)|multicellular organismal development (GO:0007275)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of translation (GO:0006417)|RIG-I signaling pathway (GO:0039529)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|intracellular membrane-bounded organelle (GO:0043231)	double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(7)|skin(1)	22	Esophageal squamous(110;0.162)					CGTCCAAACCGTGGCCGTGGG	0.507																																					p.R404L		Atlas-SNP	.											.	LSM14A	44	.	0			c.G1211T						PASS	.						96	71	79					19																	34712486		2203	4300	6503	SO:0001583	missense	26065	exon9			CAAACCGTGGCCG	AL834398	CCDS12435.1, CCDS46040.1	19q13.12	2010-01-27	2006-12-21	2006-01-24		ENSG00000257103			24489	protein-coding gene	gene with protein product		610677	"chromosome 19 open reading frame 13", "family with sequence similarity 61, member A", "LSM14 homolog A (SCD6, S. cerevisiae)"	C19orf13, FAM61A		12477932	Standard	NM_015578		Approved	DKFZP434D1335, RAP55A, RAP55	uc002nva.4	Q8ND56		ENST00000433627.5:c.1211G>T	chr19.hg19:g.34712486G>T	ENSP00000413964:p.Arg404Leu	87.0	0.0	.		63.0	20.0	.	NM_001114093	B4DTG6|Q76LX7|Q96AR3|Q96K73|Q96SN5|Q9UFR3	Missense_Mutation	SNP	ENST00000433627.5	hg19	CCDS46040.1	.	.	.	.	.	.	.	.	.	.	g	28.6	4.933243	0.92458	.	.	ENSG00000257103	ENST00000544216;ENST00000433627;ENST00000540746	T;T;T	0.18657	2.2;2.2;2.2	5.96	4.93	0.64822	.	0.104479	0.64402	D	0.000004	T	0.40297	0.1111	M	0.76002	2.32	0.80722	D	1	P;D;D	0.56287	0.889;0.958;0.975	B;P;P	0.55824	0.396;0.614;0.785	T	0.26503	-1.0101	10	0.37606	T	0.19	-9.5825	15.0274	0.71680	0.0679:0.0:0.9321:0.0	.	363;404;404	B4DTG6;Q8ND56;Q8ND56-2	.;LS14A_HUMAN;.	L	404;404;363	ENSP00000446271:R404L;ENSP00000413964:R404L;ENSP00000446451:R363L	ENSP00000314768:R404L	R	+	2	0	LSM14A	39404326	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.382000	0.97209	1.533000	0.49186	0.655000	0.94253	CGT	.	.	.	none		0.507	LSM14A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451576.3	NM_015578		T	34712486	G	T	34712486	3	4	53	1	0	0	0	0	1	0	0	0	9061	1145	40	4	1245	4	LSM14A	19	34712486	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	10785340	34712486	24416497	86	3659											
SIPA1L3	23094	hgsc.bcm.edu	37	chr19	38572702	38572702	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cggcagggccttcctcccccTtcggcaccgcagcagcagcg	5	5	12	19	4	0	0	0	0	0	0	3	0	2	0	5	3	3	5	5	3	0	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr19:38572702T>C	ENST00000222345.6	+	3	1006	c.497T>C	c.(496-498)cTt>cCt	p.L166P		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	166					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)			TTCCTCCCCCTTCGGCACCGC	0.711																																					p.L166P		Atlas-SNP	.											.	SIPA1L3	150	.	0			c.T497C						PASS	.						46	56	53					19																	38572702		2203	4299	6502	SO:0001583	missense	23094	exon3			TCCCCCTTCGGCA	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.497T>C	chr19.hg19:g.38572702T>C	ENSP00000222345:p.Leu166Pro	105.0	0.0	.		125.0	52.0	.	NM_015073	Q2TV87	Missense_Mutation	SNP	ENST00000222345.6	hg19	CCDS33007.1	.	.	.	.	.	.	.	.	.	.	T	18.67	3.672868	0.67928	.	.	ENSG00000105738	ENST00000222345	T	0.80994	-1.44	5.22	5.22	0.72569	.	0.000000	0.64402	D	0.000006	D	0.83737	0.5319	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	D	0.85925	0.1448	10	0.87932	D	0	-15.4086	14.0813	0.64925	0.0:0.0:0.0:1.0	.	166	O60292	SI1L3_HUMAN	P	166	ENSP00000222345:L166P	ENSP00000222345:L166P	L	+	2	0	SIPA1L3	43264542	0.433000	0.25562	0.937000	0.37676	0.960000	0.62799	3.929000	0.56514	1.971000	0.57363	0.460000	0.39030	CTT	.	.	.	none		0.711	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278		C	38572702	T	C	38572702	3	2	53	1	0	0	0	0	1	0	0	0	14344	1609	56	3	499	3	SIPA1L3	19	38572702	Missense_Mutation	SNP	T	TCGA-A4-8098-01A-11D-2396-08	3860216	38572702	20556281	87	3660											
MYL9	10398	hgsc.bcm.edu	37	chr20	35177592	35177592	+	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	cccattgataagaaaggcaaCttcaactacgtggagttcac	14	9	8	10	1	2	2	2	1	0	1	2	3	2	3	1	2	3	2	1	2	5	5			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr20:35177592C>T	ENST00000279022.2	+	4	563	c.459C>T	c.(457-459)aaC>aaT	p.N153N	RP5-977B1.11_ENST00000561134.1_RNA|RP5-977B1.7_ENST00000439595.1_RNA|RP5-977B1.7_ENST00000425233.1_RNA|MYL9_ENST00000346786.2_Silent_p.N99N	NM_006097.4	NP_006088.2	P24844	MYL9_HUMAN	myosin, light chain 9, regulatory	153	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				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)				AGAAAGGCAACTTCAACTACG	0.592																																					p.N153N		Atlas-SNP	.											.	MYL9	13	.	0			c.C459T						PASS	.						112	95	101					20																	35177592		2203	4300	6503	SO:0001819	synonymous_variant	10398	exon4			AGGCAACTTCAAC	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.459C>T	chr20.hg19:g.35177592C>T		49.0	0.0	.		69.0	20.0	.	NM_006097	E1P5T6|Q9BQL9|Q9BUF9|Q9H136	Silent	SNP	ENST00000279022.2	hg19	CCDS13276.1																																																																																			.	.	.	none		0.592	MYL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079015.2	NM_006097		T	35177592	C	T	35177592	2	4	53	1	0	0	0	0	0	0	0	1	10061	564	20	2		2	MYL9	20	35177592	Silent	SNP	C	TCGA-A4-8098-01A-11D-2396-08		35177592	27847928	88	3661											
TGIF2	60436	hgsc.bcm.edu	37	chr20	35219568	35219569	+	Frame_Shift_Ins	INS	-	-	A																															agcccctttcccacgtggggINSagctggagtctcccaagccc																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chr20:35219568_35219569insA	ENST00000373874.2	+	3	647_648	c.448_449insA	c.(448-450)gagfs	p.E150fs	TGIF2_ENST00000373872.4_Frame_Shift_Ins_p.E150fs|TGIF2-C20orf24_ENST00000558530.1_Intron|RP5-977B1.11_ENST00000561134.1_RNA	NM_001199514.1|NM_001199515.1	NP_001186443.1|NP_001186444.1	Q9GZN2	TGIF2_HUMAN	TGFB-induced factor homeobox 2	150	Repressive function.				gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nodal signaling pathway (GO:0038092)|positive regulation of neuron differentiation (GO:0045666)|regulation of gastrulation (GO:0010470)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(3)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	14	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)				CCCACGTGGGGAGCTGGAGTCT	0.629																																					p.E150fs		Atlas-INDEL	.											.	TGIF2	26	.	0			c.448_449insA						PASS	.																																			SO:0001589	frameshift_variant	60436	exon3			.	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.449dupA	chr20.hg19:g.35219569_35219569dupA	ENSP00000362981:p.Glu150fs	101.0	0.0	0		104.0	42.0	0.403846	NM_021809	B2R9U3|E1P5T9|H0YNI0	Frame_Shift_Ins	INS	ENST00000373874.2	hg19	CCDS13278.1																																																																																			.	.	.	none		0.629	TGIF2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079004.2	NM_021809		A	35219569	-	A	35219568	7	5	53	1	0	1	1	0	0	0	0	0	15838	1175	41	0	454	0	TGIF2	20	35219568	Frame_Shift_Ins	INS	-	TCGA-A4-8098-01A-11D-2396-08	41976	35219568	27805952	89	3662											
UBA1	7317	hgsc.bcm.edu	37	chrX	47069022	47069022	+	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	tctgtttgctctgtctgcagTgggctcgggatgagtttgaa	5	15	14	7	1	3	2	0	2	3	0	4	3	3	3	0	2	2	5	0	2	1	2			TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chrX:47069022T>G	ENST00000335972.6	+	17	2122	c.1939T>G	c.(1939-1941)Tgg>Ggg	p.W647G	UBA1_ENST00000377269.3_Missense_Mutation_p.W95G|UBA1_ENST00000377351.4_Splice_Site_p.W647G	NM_003334.3	NP_003325.2	P22314	UBA1_HUMAN	ubiquitin-like modifier activating enzyme 1	647					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						CTGTCTGCAGTGGGCTCGGGA	0.498																																					p.W647G		Atlas-SNP	.											.	UBA1	89	.	0			c.T1939G						PASS	.						122	93	103					X																	47069022		2203	4300	6503	SO:0001630	splice_region_variant	7317	exon17			CTGCAGTGGGCTC	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.1939-1T>G	chrX.hg19:g.47069022T>G		21.0	0.0	.		32.0	26.0	.	NM_153280	Q5JRR8|Q96E13	Missense_Mutation	SNP	ENST00000335972.6	hg19	CCDS14275.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.009850	0.75046	.	.	ENSG00000130985	ENST00000377351;ENST00000335972;ENST00000377269	T;T;T	0.51817	0.69;0.69;0.69	5.22	5.22	0.72569	Molybdenum cofactor biosynthesis, MoeB (1);Ubiquitin-activating enzyme (1);Ubiquitin-like 1 activating enzyme, catalytic cysteine domain (1);	0.111594	0.64402	D	0.000003	T	0.79782	0.4505	H	0.98577	4.27	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.86491	0.1797	10	0.87932	D	0	-10.8017	11.8816	0.52579	0.0:0.0:0.0:1.0	.	95;647	Q5JRR6;P22314	.;UBA1_HUMAN	G	647;647;95	ENSP00000366568:W647G;ENSP00000338413:W647G;ENSP00000366481:W95G	ENSP00000338413:W647G	W	+	1	0	UBA1	46953966	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.580000	0.82523	1.860000	0.53959	0.427000	0.28365	TGG	.	.	.	none		0.498	UBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056389.1	NM_003334	Missense_Mutation	G	47069022	T	G	47069022	5	3	53	1	0	0	0	0	0	0	1	0	16839	1710	59	5	2001	5	UBA1	23	47069022	Splice_Site	SNP	T	TCGA-A4-8098-01A-11D-2396-08		47069022	108201538	90	3663											
STAG2	10735	hgsc.bcm.edu	37	chrX	123211859	123211862	+	Frame_Shift_Del	DEL	AGAT	AGAT	-																															aacaatgagtaaaacaaggcAgatagacaaaattcagtgtg																										TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	AGAT	AGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chrX:123211859_123211862delAGAT	ENST00000371160.1	+	27	3016_3019	c.2726_2729delAGAT	c.(2725-2730)cagatafs	p.QI909fs	STAG2_ENST00000469481.1_Intron|STAG2_ENST00000371145.3_Frame_Shift_Del_p.QI909fs|STAG2_ENST00000218089.9_Frame_Shift_Del_p.QI909fs|STAG2_ENST00000371144.3_Frame_Shift_Del_p.QI909fs|STAG2_ENST00000354548.5_Frame_Shift_Del_p.QI840fs|STAG2_ENST00000371157.3_Frame_Shift_Del_p.QI909fs	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	909					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						AAAACAAGGCAGATAGACAAAATT	0.314																																					p.909_910del		Atlas-INDEL	.											.	STAG2	309	.	0			c.2725_2728del						PASS	.																																			SO:0001589	frameshift_variant	10735	exon27			.	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.2726_2729delAGAT	chrX.hg19:g.123211859_123211862delAGAT	ENSP00000360202:p.Gln909fs	69.0	0.0	0		58.0	45.0	0.775862	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Frame_Shift_Del	DEL	ENST00000371160.1	hg19	CCDS14607.1																																																																																			.	.	.	none		0.314	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		-	123211862	AGAT	-	123211859	7	5	53	1	0	1	0	1	0	0	0	0	15255	188	7	0	2824	0	STAG2	23	123211859	Frame_Shift_Del	DEL	AGAT	TCGA-A4-8098-01A-11D-2396-08	76142837	123211859	32058701	91	3664											
PLXNB3	5365	hgsc.bcm.edu	37	chrX	153037078	153037078	+	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	tgtgcccgccgggggctgtgGagctgctgtgtcctgcgccc	1	9	17	14	3	0	0	0	0	0	0	1	1	1	1	4	3	4	3	4	3	0	0	rs375202688		TCGA-A4-8098-01A-11D-2396-08	TCGA-A4-8098-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9c049bb8-3842-44e4-9961-ea59a3f347de	aea72058-4351-46a9-a314-5d54f681d649	g.chrX:153037078G>C	ENST00000361971.5	+	14	2599	c.2485G>C	c.(2485-2487)Gag>Cag	p.E829Q	PLXNB3_ENST00000538776.1_Missense_Mutation_p.E482Q|PLXNB3_ENST00000538966.1_Missense_Mutation_p.E852Q|PLXNB3_ENST00000538543.1_Intron|PLXNB3_ENST00000538282.1_Missense_Mutation_p.E439Q	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	829	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)					GGGGGCTGTGGAGCTGCTGTG	0.692																																					p.E852Q		Atlas-SNP	.											.	PLXNB3	208	.	0			c.G2554C						PASS	.						20	20	20					X																	153037078		2180	4292	6472	SO:0001583	missense	5365	exon15			GCTGTGGAGCTGC	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.2485G>C	chrX.hg19:g.153037078G>C	ENSP00000355378:p.Glu829Gln	14.0	0.0	.		12.0	12.0	.	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	hg19	CCDS14729.1	.	.	.	.	.	.	.	.	.	.	G	10.63	1.404697	0.25378	.	.	ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776;ENST00000538282	T;T;T;T	0.66460	5.33;5.29;4.71;-0.21	5.01	-0.321	0.12717	.	.	.	.	.	T	0.59945	0.2231	L	0.55103	1.725	0.09310	N	1	B;B;B;B	0.23128	0.001;0.08;0.009;0.003	B;B;B;B	0.17098	0.005;0.017;0.008;0.005	T	0.43718	-0.9374	9	0.12103	T	0.63	.	17.8542	0.88758	0.0:0.6872:0.3128:0.0	.	482;511;852;829	B7Z3H9;B7Z9A5;F5H773;Q9ULL4	.;.;.;PLXB3_HUMAN	Q	852;829;482;439	ENSP00000442736:E852Q;ENSP00000355378:E829Q;ENSP00000445569:E482Q;ENSP00000441919:E439Q	ENSP00000355378:E829Q	E	+	1	0	PLXNB3	152690272	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	0.736000	0.26130	-0.636000	0.05524	-0.347000	0.07816	GAG	.	.	.	weak		0.692	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1			C	153037078	G	C	153037078	3	2	53	1	0	0	0	0	1	0	0	0	12132	1175	41	4	2653	4	PLXNB3	23	153037078	Missense_Mutation	SNP	G	TCGA-A4-8098-01A-11D-2396-08	29825219	153037078	2233482	92	3665											
FBXO42	54455	hgsc.bcm.edu	37	chr1	16577319	16577320	+	Frame_Shift_Ins	INS	-	-	TATTAAA																															aggtccaaccacagaactgcINStattaaatactttccatttg																										TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr1:16577319_16577320insTATTAAA	ENST00000375592.3	-	10	2215_2216	c.1999_2000insTTTAATA	c.(1999-2001)agcfs	p.S667fs		NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	667										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)		CACAGAACTGCTATTAAATACT	0.475																																					p.S667_S668delinsIX		Atlas-INDEL	.											.	FBXO42	53	.	0			c.2000_2001insTTTAATA						PASS	.																																			SO:0001589	frameshift_variant	54455	exon10			.	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.1993_1999dupTTTAATA	chr1.hg19:g.16577320_16577326dupTATTAAA	ENSP00000364742:p.Ser667fs	261.0	0.0	0		217.0	30.0	0.138249	NM_018994	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	Frame_Shift_Ins	INS	ENST00000375592.3	hg19	CCDS30613.1																																																																																			.	.	.	none		0.475	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006285.1			TATTAAA	16577320	-	TATTAAA	16577319	7	5	54	1	0	1	1	0	0	0	0	0	5758	797	28	0	157	0	FBXO42	1	16577319	Frame_Shift_Ins	INS	-	TCGA-A4-8310-01A-11D-2396-08		16577319	232673302	1	3666											
ASAP3	55616	hgsc.bcm.edu	37	chr1	23779230	23779231	+	Frame_Shift_Ins	INS	-	-	GG																															ccccttcatcagactgtccaINSgggggaaagagacaatgttg																										TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr1:23779230_23779231insGG	ENST00000336689.3	-	4	426_427	c.382_383insCC	c.(382-384)ctgfs	p.L128fs	ASAP3_ENST00000437606.2_Frame_Shift_Ins_p.L128fs	NM_017707.3	NP_060177.2	Q8TDY4	ASAP3_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 3	128					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						CAGACTGTCCAGGGGGAAAGAG	0.559																																					p.L128fs		Atlas-INDEL	.											.	ASAP3	65	.	0			c.383_384insCC						PASS	.																																			SO:0001589	frameshift_variant	55616	exon4			.	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.381_382dupCC	chr1.hg19:g.23779233_23779234dupGG	ENSP00000338769:p.Leu128fs	233.0	0.0	0		214.0	80.0	0.373832	NM_001143778	B3KRW0|B4DHH4|Q6P9F4|Q86UY1|Q9NXK2	Frame_Shift_Ins	INS	ENST00000336689.3	hg19	CCDS235.1																																																																																			.	.	.	none		0.559	ASAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008916.2	NM_017707		GG	23779231	-	GG	23779230	7	5	54	1	0	1	1	0	0	0	0	0	1012	188	7	0	2439	0	ASAP3	1	23779230	Frame_Shift_Ins	INS	-	TCGA-A4-8310-01A-11D-2396-08	7201911	23779230	225471391	2	3667											
LDLRAP1	26119	hgsc.bcm.edu	37	chr1	25889193	25889193	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtcgcctttgagttttggcAggtgtccaaggaaggtgaga	9	11	15	6	1	0	2	0	2	0	1	2	4	1	3	2	4	0	2	2	4	2	3			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr1:25889193A>G	ENST00000374338.4	+	5	637	c.518A>G	c.(517-519)cAg>cGg	p.Q173R	LDLRAP1_ENST00000488127.1_3'UTR	NM_015627.2	NP_056442.2	Q5SW96	ARH_HUMAN	low density lipoprotein receptor adaptor protein 1	173	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				amyloid precursor protein metabolic process (GO:0042982)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|positive regulation of cholesterol metabolic process (GO:0090205)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of signal transduction (GO:0009967)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of protein binding (GO:0043393)|transport (GO:0006810)	axon (GO:0030424)|basal plasma membrane (GO:0009925)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|early endosome (GO:0005769)|neurofilament (GO:0005883)|recycling endosome (GO:0055037)	AP-2 adaptor complex binding (GO:0035612)|beta-amyloid binding (GO:0001540)|clathrin adaptor activity (GO:0035615)|clathrin binding (GO:0030276)|low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphotyrosine binding (GO:0001784)|receptor signaling complex scaffold activity (GO:0030159)|signaling adaptor activity (GO:0035591)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)|urinary_tract(1)	9		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;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.63e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000728)|STAD - Stomach adenocarcinoma(196;0.000766)|BRCA - Breast invasive adenocarcinoma(304;0.000969)|GBM - Glioblastoma multiforme(114;0.00914)|READ - Rectum adenocarcinoma(331;0.0649)		GAGTTTTGGCAGGTGTCCAAG	0.572																																					p.Q173R		Atlas-SNP	.											.	LDLRAP1	28	.	0			c.A518G						PASS	.						139	124	129					1																	25889193		2203	4300	6503	SO:0001583	missense	26119	exon5			TTTGGCAGGTGTC	BC029770	CCDS30639.1	1p36-p35	2014-09-17			ENSG00000157978	ENSG00000157978			18640	protein-coding gene	gene with protein product		605747					Standard	NM_015627		Approved	ARH, ARH2, FHCB1, FHCB2, MGC34705, DKFZp586D0624	uc001bkl.4	Q5SW96	OTTHUMG00000007386	ENST00000374338.4:c.518A>G	chr1.hg19:g.25889193A>G	ENSP00000363458:p.Gln173Arg	77.0	0.0	.		68.0	28.0	.	NM_015627	A2BHI5|Q6TQS9|Q8N2Y0|Q9UFI9	Missense_Mutation	SNP	ENST00000374338.4	hg19	CCDS30639.1	.	.	.	.	.	.	.	.	.	.	A	19.60	3.858315	0.71834	.	.	ENSG00000157978	ENST00000374338	T	0.64260	-0.09	5.56	5.56	0.83823	Phosphotyrosine interaction domain (1);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	T	0.65101	0.2659	L	0.49350	1.555	0.58432	D	0.999998	B	0.25105	0.118	B	0.39339	0.297	T	0.63950	-0.6521	10	0.45353	T	0.12	-17.9581	14.8888	0.70590	1.0:0.0:0.0:0.0	.	173	Q5SW96	ARH_HUMAN	R	173	ENSP00000363458:Q173R	ENSP00000363458:Q173R	Q	+	2	0	LDLRAP1	25761780	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.809000	0.91944	2.117000	0.64856	0.454000	0.30748	CAG	.	.	.	none		0.572	LDLRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019350.3	NM_015627		G	25889193	A	G	25889193	3	3	54	1	0	0	0	0	1	0	0	0	8715	188	7	3	536	3	LDLRAP1	1	25889193	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	2109963	25889193	223361428	3	3668											
GTF2B	2959	hgsc.bcm.edu	37	chr1	89325567	89325567	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acaaagctaaaaacttacctTtaaatgtcctaggaacccct	16	10	4	11	0	0	0	0	0	0	0	1	1	1	1	4	1	4	1	4	1	9	5			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr1:89325567T>C	ENST00000370500.5	-	5	651	c.533A>G	c.(532-534)aAa>aGa	p.K178R	GTF2B_ENST00000494819.1_5'UTR	NM_001514.5	NP_001505.1	Q00403	TF2B_HUMAN	general transcription factor IIB	178					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)	core promoter binding (GO:0001047)|thyroid hormone receptor binding (GO:0046966)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	10		Lung NSC(277;0.123)		all cancers(265;0.0131)|Epithelial(280;0.0255)		AAACTTACCTTTAAATGTCCT	0.418																																					p.K178R		Atlas-SNP	.											.	GTF2B	32	.	0			c.A533G						PASS	.						118	124	122					1																	89325567		2203	4300	6503	SO:0001583	missense	2959	exon5			TTACCTTTAAATG	M76766	CCDS715.1	1p22-p21	2010-03-23			ENSG00000137947	ENSG00000137947		"General transcription factors"	4648	protein-coding gene	gene with protein product		189963				1876184, 8162052	Standard	NM_001514		Approved	TFIIB	uc001dmo.4	Q00403	OTTHUMG00000010611	ENST00000370500.5:c.533A>G	chr1.hg19:g.89325567T>C	ENSP00000359531:p.Lys178Arg	121.0	0.0	.		101.0	46.0	.	NM_001514	A8K1A7|Q5JS30	Missense_Mutation	SNP	ENST00000370500.5	hg19	CCDS715.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.308867	0.81247	.	.	ENSG00000137947	ENST00000370500;ENST00000448623;ENST00000418217	T;T;T	0.51574	0.77;0.7;0.7	5.52	5.52	0.82312	Transcription factor TFIIB, cyclin-related (1);Cyclin-like (3);	0.000000	0.85682	D	0.000000	T	0.52933	0.1765	L	0.48174	1.505	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.50171	-0.8859	10	0.34782	T	0.22	-32.0439	15.9344	0.79691	0.0:0.0:0.0:1.0	.	178	Q00403	TF2B_HUMAN	R	178;177;173	ENSP00000359531:K178R;ENSP00000415741:K177R;ENSP00000402345:K173R	ENSP00000359531:K178R	K	-	2	0	GTF2B	89098155	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	7.587000	0.82613	2.214000	0.71695	0.482000	0.46254	AAA	.	.	.	none		0.418	GTF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029279.1	NM_001514		C	89325567	T	C	89325567	3	2	54	1	0	0	0	0	1	0	0	0	6862	1841	64	3	429	3	GTF2B	1	89325567	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08	63436374	89325567	159925054	4	3669											
CCDC18	343099	hgsc.bcm.edu	37	chr1	93680444	93680444	+	Frame_Shift_Del	DEL	C	C	-																															tgatttgaaggttaacatggCtcacagaactagtcagtttc																										TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr1:93680444delC	ENST00000343253.7	+	12	2139	c.1637delC	c.(1636-1638)gctfs	p.A546fs	CCDC18_ENST00000401026.3_Frame_Shift_Del_p.A547fs|CCDC18_ENST00000557479.1_Frame_Shift_Del_p.A665fs|CCDC18_ENST00000334652.5_5'UTR|CCDC18_ENST00000338949.4_Frame_Shift_Del_p.A346fs			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	546										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)		GTTAACATGGCTCACAGAACT	0.388																																					p.A547fs		Atlas-INDEL	.											CCDC18,rectum,carcinoma,0,2	CCDC18	93	.	0			c.1639delG						PASS	.						51	48	49					1																	93680444		1844	4098	5942	SO:0001589	frameshift_variant	343099	exon12			.			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.1637delC	chr1.hg19:g.93680444delC	ENSP00000343377:p.Ala546fs	21.0	0.0	0		33.0	11.0	0.333333	NM_206886	Q6ZU17	Frame_Shift_Del	DEL	ENST00000343253.7	hg19																																																																																				.	.	.	none		0.388	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886		-	93680444	C	-	93680444	7	5	54	1	0	1	0	1	0	0	0	0	2796	797	28	0	2040	0	CCDC18	1	93680444	Frame_Shift_Del	DEL	C	TCGA-A4-8310-01A-11D-2396-08	4354877	93680444	155570177	5	3670											
GOLPH3L	55204	hgsc.bcm.edu	37	chr1	150634375	150634375	+	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	gtttcatccagtaaaacatcAcctgttgggctgtctgactt	9	14	8	10	0	3	1	2	1	1	0	4	1	4	1	2	1	1	4	2	1	2	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr1:150634375A>T	ENST00000271732.3	-	4	389	c.345T>A	c.(343-345)ggT>ggA	p.G115G	GOLPH3L_ENST00000540514.1_Silent_p.G71G	NM_018178.5	NP_060648.2	Q9H4A5	GLP3L_HUMAN	golgi phosphoprotein 3-like	115					Golgi organization (GO:0007030)|positive regulation of protein secretion (GO:0050714)	Golgi membrane (GO:0000139)|trans-Golgi network membrane (GO:0032588)	phosphatidylinositol-4-phosphate binding (GO:0070273)			breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)	8	all_cancers(9;3.09e-52)|all_epithelial(9;4.47e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-31)|Breast(34;0.000615)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;1.2e-23)|all cancers(9;4.81e-23)|OV - Ovarian serous cystadenocarcinoma(6;1.93e-15)|BRCA - Breast invasive adenocarcinoma(12;0.000479)|LUSC - Lung squamous cell carcinoma(543;0.171)			GTAAAACATCACCTGTTGGGC	0.383																																					p.G115G		Atlas-SNP	.											.	GOLPH3L	20	.	0			c.T345A						PASS	.						167	160	162					1																	150634375		2203	4300	6503	SO:0001819	synonymous_variant	55204	exon4			AACATCACCTGTT	AJ296153	CCDS966.1	1q21	2008-02-05			ENSG00000143457	ENSG00000143457			24882	protein-coding gene	gene with protein product		612208					Standard	NM_018178		Approved	GPP34R	uc001evj.2	Q9H4A5	OTTHUMG00000035009	ENST00000271732.3:c.345T>A	chr1.hg19:g.150634375A>T		92.0	0.0	.		110.0	39.0	.	NM_018178	B1AN09|B7Z6N3|Q9NVK0	Silent	SNP	ENST00000271732.3	hg19	CCDS966.1																																																																																			.	.	.	none		0.383	GOLPH3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084734.1	NM_018178		T	150634375	A	T	150634375	2	4	54	1	0	0	0	0	0	0	0	1	6576	146	6	5		5	GOLPH3L	1	150634375	Silent	SNP	A	TCGA-A4-8310-01A-11D-2396-08	56953931	150634375	98616246	6	3671											
DENND4B	9909	hgsc.bcm.edu	37	chr1	153915526	153915526	+	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	gcccggggcctggaggggccAggtttgctgagtggctgtag	4	8	20	9	1	0	1	0	1	0	0	0	2	0	2	3	7	1	4	3	7	1	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr1:153915526A>T	ENST00000361217.4	-	3	816	c.398T>A	c.(397-399)cTg>cAg	p.L133Q		NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	133	MABP. {ECO:0000255|PROSITE- ProRule:PRU00831}.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			TGGAGGGGCCAGGTTTGCTGA	0.637																																					p.L133Q		Atlas-SNP	.											.	DENND4B	210	.	0			c.T398A						PASS	.						62	73	70					1																	153915526		1957	4140	6097	SO:0001583	missense	9909	exon3			GGGGCCAGGTTTG	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"DENN/MADD domain containing"	29044	protein-coding gene	gene with protein product			"KIAA0476"	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.398T>A	chr1.hg19:g.153915526A>T	ENSP00000354597:p.Leu133Gln	103.0	0.0	.		74.0	26.0	.	NM_014856	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	hg19	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.259272	0.80246	.	.	ENSG00000198837	ENST00000361217;ENST00000368646	T;T	0.24908	1.83;1.83	4.69	4.69	0.59074	MABP domain (1);	.	.	.	.	T	0.36690	0.0976	L	0.61218	1.895	0.58432	D	0.999992	D	0.76494	0.999	D	0.68765	0.96	T	0.28004	-1.0057	9	0.87932	D	0	-3.5699	13.2559	0.60079	1.0:0.0:0.0:0.0	.	133	O75064	DEN4B_HUMAN	Q	133;144	ENSP00000354597:L133Q;ENSP00000357635:L144Q	ENSP00000354597:L133Q	L	-	2	0	DENND4B	152182150	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.891000	0.92485	1.946000	0.56461	0.460000	0.39030	CTG	.	.	.	none		0.637	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806		T	153915526	A	T	153915526	3	4	54	1	0	0	0	0	1	0	0	0	4436	188	7	5	4196	5	DENND4B	1	153915526	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	3281151	153915526	95335095	7	3672											
FAM5C	339479	hgsc.bcm.edu	37	chr1	190068039	190068039	+	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	tcaggcttgcagagcccctgGctgagcatgtagccggtgtt	6	10	14	11	1	1	2	1	1	0	1	1	2	1	2	3	3	4	6	3	3	1	3			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr1:190068039G>C	ENST00000367462.3	-	8	1641	c.1410C>G	c.(1408-1410)agC>agG	p.S470R	BRINP3_ENST00000534846.1_Missense_Mutation_p.S368R	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	470					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)											AGAGCCCCTGGCTGAGCATGT	0.577																																					p.S470R		Atlas-SNP	.											.	FAM5C	343	.	0			c.C1410G						PASS	.						100	101	101					1																	190068039		2203	4300	6503	SO:0001583	missense	339479	exon8			CCCCTGGCTGAGC	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.1410C>G	chr1.hg19:g.190068039G>C	ENSP00000356432:p.Ser470Arg	244.0	0.0	.		170.0	40.0	.	NM_199051	B3KVP1|B7Z260|O95726|Q2M330	Missense_Mutation	SNP	ENST00000367462.3	hg19	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	G	9.011	0.982421	0.18889	.	.	ENSG00000162670	ENST00000367462;ENST00000534846	T;T	0.42131	0.98;0.98	5.75	3.56	0.40772	Epidermal growth factor-like (1);	0.146558	0.64402	D	0.000008	T	0.35219	0.0924	L	0.53249	1.67	0.45883	D	0.998734	P;P	0.43701	0.815;0.718	B;B	0.39258	0.295;0.154	T	0.12218	-1.0556	10	0.25751	T	0.34	-10.9852	11.0596	0.47940	0.177:0.0:0.823:0.0	.	368;470	B7Z260;Q76B58	.;FAM5C_HUMAN	R	470;368	ENSP00000356432:S470R;ENSP00000438022:S368R	ENSP00000356432:S470R	S	-	3	2	FAM5C	188334662	1.000000	0.71417	1.000000	0.80357	0.662000	0.39071	1.416000	0.34759	1.440000	0.47531	-0.229000	0.12294	AGC	.	.	.	none		0.577	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		C	190068039	G	C	190068039	3	2	54	1	0	0	0	0	1	0	0	0	5601	1194	42	4	894	4	FAM5C	1	190068039	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08	36152513	190068039	59182582	8	3673											
PCNXL2	80003	hgsc.bcm.edu	37	chr1	233190130	233190130	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcaatcgccagagctgtagTtgccccaacgtccaagaact	12	7	9	13	2	0	2	0	0	0	2	2	2	1	2	4	0	5	4	4	0	5	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr1:233190130T>C	ENST00000258229.9	-	25	4469	c.4235A>G	c.(4234-4236)aAc>aGc	p.N1412S	PCNXL2_ENST00000344698.2_Missense_Mutation_p.N64S	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	1412						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				AGAGCTGTAGTTGCCCCAACG	0.438																																					p.N1412S		Atlas-SNP	.											.	PCNXL2	204	.	0			c.A4235G						PASS	.						67	65	66					1																	233190130		1887	4122	6009	SO:0001583	missense	80003	exon25			CTGTAGTTGCCCC	AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"pecanex (Drosophila)-like 2"			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.4235A>G	chr1.hg19:g.233190130T>C	ENSP00000258229:p.Asn1412Ser	34.0	0.0	.		43.0	19.0	.	NM_014801	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	ENST00000258229.9	hg19	CCDS44335.1	.	.	.	.	.	.	.	.	.	.	T	17.63	3.437330	0.62955	.	.	ENSG00000135749	ENST00000344698;ENST00000258229	T;T	0.24151	1.87;3.01	4.97	2.65	0.31530	.	0.042018	0.85682	D	0.000000	T	0.23846	0.0577	L	0.42487	1.325	0.80722	D	1	B;P	0.52692	0.434;0.955	B;P	0.45449	0.263;0.481	T	0.02705	-1.1121	10	0.87932	D	0	.	8.878	0.35356	0.0:0.154:0.0:0.846	.	1412;64	A6NKB5;A6NKB5-3	PCX2_HUMAN;.	S	64;1412	ENSP00000340759:N64S;ENSP00000258229:N1412S	ENSP00000258229:N1412S	N	-	2	0	PCNXL2	231256753	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	4.826000	0.62715	0.862000	0.35528	0.533000	0.62120	AAC	.	.	.	none		0.438	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801		C	233190130	T	C	233190130	3	2	54	1	0	0	0	0	1	0	0	0	11599	1725	60	3	2218	3	PCNXL2	1	233190130	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08	43122091	233190130	16060491	9	3674											
NCKAP5	344148	hgsc.bcm.edu	37	chr2	133721438	133721438	+	Missense_Mutation	SNP	T	T	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	ttctctcttcctctgacagcTtttcctgaagcaagaaagaa	11	13	6	11	0	3	4	0	2	3	2	6	4	5	4	2	0	2	2	2	0	4	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr2:133721438T>G	ENST00000409261.1	-	8	807	c.434A>C	c.(433-435)aAg>aCg	p.K145T	NCKAP5_ENST00000409213.1_Missense_Mutation_p.K145T|NCKAP5_ENST00000317721.6_Missense_Mutation_p.K145T|NCKAP5_ENST00000405974.3_Missense_Mutation_p.K145T	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	145										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						CTCTGACAGCTTTTCCTGAAG	0.428																																					p.K145T		Atlas-SNP	.											.	NCKAP5	322	.	0			c.A434C						PASS	.						142	136	138					2																	133721438		1861	4093	5954	SO:0001583	missense	344148	exon8			GACAGCTTTTCCT	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.434A>C	chr2.hg19:g.133721438T>G	ENSP00000387128:p.Lys145Thr	94.0	0.0	.		105.0	38.0	.	NM_207481	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	hg19	CCDS46418.1	.	.	.	.	.	.	.	.	.	.	T	12.36	1.913961	0.33815	.	.	ENSG00000176771	ENST00000409261;ENST00000409213;ENST00000317721;ENST00000405974;ENST00000537661;ENST00000542834	T;T;T;T	0.48522	2.8;0.81;2.8;0.81	5.0	-0.271	0.12922	.	.	.	.	.	T	0.25717	0.0626	N	0.14661	0.345	0.09310	N	1	B;B;B	0.24823	0.0;0.001;0.112	B;B;B	0.24394	0.002;0.003;0.053	T	0.17440	-1.0369	9	0.38643	T	0.18	.	4.4156	0.11454	0.0:0.1923:0.3253:0.4823	.	120;145;145	O14513-3;O14513-2;O14513	.;.;NCKP5_HUMAN	T	145;145;145;145;145;120	ENSP00000387128:K145T;ENSP00000386952:K145T;ENSP00000380603:K145T;ENSP00000385692:K145T	ENSP00000380603:K145T	K	-	2	0	NCKAP5	133437908	0.968000	0.33430	0.029000	0.17559	0.554000	0.35429	1.269000	0.33074	-0.107000	0.12088	-0.321000	0.08615	AAG	.	.	.	none		0.428	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		G	133721438	T	G	133721438	3	3	54	1	0	0	0	0	1	0	0	0	10230	1609	56	5	5347	5	NCKAP5	2	133721438	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08		133721438	109477935	10	3675											
ACMSD	130013	hgsc.bcm.edu	37	chr2	135659397	135659398	+	Frame_Shift_Ins	INS	-	-	T																															aagccggcaatgccctggcaINStttttgggtcttgagagaaa																										TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr2:135659397_135659398insT	ENST00000356140.5	+	10	1114_1115	c.978_979insT	c.(979-981)tttfs	p.F327fs	AC016725.4_ENST00000428857.1_RNA|AC016725.4_ENST00000413962.1_RNA|ACMSD_ENST00000283054.4_Frame_Shift_Ins_p.F269fs|AC016725.4_ENST00000537615.1_RNA|ACMSD_ENST00000392928.1_Frame_Shift_Ins_p.F269fs|AC016725.4_ENST00000392929.2_RNA	NM_138326.2	NP_612199.2	Q8TDX5	ACMSD_HUMAN	aminocarboxymuconate semialdehyde decarboxylase	327					cellular nitrogen compound metabolic process (GO:0034641)|quinolinate metabolic process (GO:0046874)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aminocarboxymuconate-semialdehyde decarboxylase activity (GO:0001760)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(4)|lung(6)|skin(1)	14				BRCA - Breast invasive adenocarcinoma(221;0.115)		ATGCCCTGGCATTTTTGGGTCT	0.297																																					p.A326fs		Atlas-INDEL	.											.	ACMSD	43	.	0			c.978_979insT						PASS	.																																			SO:0001589	frameshift_variant	130013	exon10			.	AB071418	CCDS2173.2	2q21.3	2008-03-11			ENSG00000153086	ENSG00000153086	4.1.1.45		19288	protein-coding gene	gene with protein product		608889				12140278	Standard	NM_138326		Approved		uc002ttz.3	Q8TDX5	OTTHUMG00000131711	ENST00000356140.5:c.983dupT	chr2.hg19:g.135659402_135659402dupT	ENSP00000348459:p.Phe327fs	44.0	0.0	0		42.0	18.0	0.428571	NM_138326	Q3B7X3|Q53SR5|Q96KY2	Frame_Shift_Ins	INS	ENST00000356140.5	hg19	CCDS2173.2																																																																																			.	.	.	none		0.297	ACMSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254627.1			T	135659398	-	T	135659397	7	5	54	1	0	1	1	0	0	0	0	0	144	204	8	0	1016	0	ACMSD	2	135659397	Frame_Shift_Ins	INS	-	TCGA-A4-8310-01A-11D-2396-08	1937959	135659397	107539976	11	3676											
ACVR2A	92	hgsc.bcm.edu	37	chr2	148677893	148677893	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aatttgaggctggcaagtctGcaggcgatacccatggacag	11	8	13	9	1	1	1	0	1	1	0	1	3	1	2	1	4	2	3	1	4	3	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr2:148677893G>A	ENST00000241416.7	+	8	1693	c.1057G>A	c.(1057-1059)Gca>Aca	p.A353T	ACVR2A_ENST00000535787.1_Missense_Mutation_p.A245T|ACVR2A_ENST00000404590.1_Missense_Mutation_p.A353T	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	353	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		TGGCAAGTCTGCAGGCGATAC	0.383																																					p.A353T		Atlas-SNP	.											ACVR2A,NS,carcinoma,0,1	ACVR2A	125	.	0			c.G1057A						PASS	.						87	89	89					2																	148677893		2203	4300	6503	SO:0001583	missense	92	exon8			AAGTCTGCAGGCG		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.1057G>A	chr2.hg19:g.148677893G>A	ENSP00000241416:p.Ala353Thr	67.0	0.0	.		94.0	34.0	.	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Missense_Mutation	SNP	ENST00000241416.7	hg19	CCDS33301.1	.	.	.	.	.	.	.	.	.	.	G	16.14	3.039512	0.55003	.	.	ENSG00000121989	ENST00000241416;ENST00000535787;ENST00000404590	T;T;T	0.65732	-0.17;-0.17;-0.17	5.42	5.42	0.78866	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	0.38188	0.1031	N	0.02345	-0.59	0.80722	D	1	B	0.11235	0.004	B	0.13407	0.009	T	0.26849	-1.0091	10	0.34782	T	0.22	.	15.113	0.72375	0.0:0.1411:0.8589:0.0	.	353	P27037	AVR2A_HUMAN	T	353;245;353	ENSP00000241416:A353T;ENSP00000439988:A245T;ENSP00000384338:A353T	ENSP00000241416:A353T	A	+	1	0	ACVR2A	148394363	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.587000	0.67510	2.699000	0.92147	0.655000	0.94253	GCA	.	.	.	none		0.383	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616		A	148677893	G	A	148677893	3	1	54	1	0	0	0	0	1	0	0	0	223	1319	46	2	1087	2	ACVR2A	2	148677893	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08	13018496	148677893	94521480	12	3677											
NEB	4703	hgsc.bcm.edu	37	chr2	152482148	152482148	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtcccaggcttctgtgtatAagcgctgtgaaggataaaaa	12	11	11	7	1	1	1	0	1	1	0	2	2	2	2	1	2	1	3	1	2	6	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr2:152482148A>G	ENST00000172853.10	-	67	9770	c.9623T>C	c.(9622-9624)tTa>tCa	p.L3208S	NEB_ENST00000427231.2_Missense_Mutation_p.L3451S|NEB_ENST00000397345.3_Missense_Mutation_p.L3451S|NEB_ENST00000409198.1_Missense_Mutation_p.L3208S|NEB_ENST00000604864.1_Missense_Mutation_p.L3451S|NEB_ENST00000603639.1_Missense_Mutation_p.L3451S			P20929	NEBU_HUMAN	nebulin	3208					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)		TTCTGTGTATAAGCGCTGTGA	0.358																																					p.L3451S		Atlas-SNP	.											.	NEB	1697	.	0			c.T10352C						PASS	.						74	67	69					2																	152482148		1835	4090	5925	SO:0001583	missense	4703	exon71			GTGTATAAGCGCT	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.9623T>C	chr2.hg19:g.152482148A>G	ENSP00000172853:p.Leu3208Ser	11.0	0.0	.		28.0	10.0	.	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	hg19		.	.	.	.	.	.	.	.	.	.	A	18.62	3.662545	0.67700	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.53206	0.63;0.63;0.63;0.63	4.98	4.98	0.66077	.	0.086330	0.48286	D	0.000195	T	0.66366	0.2782	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.70285	-0.4914	10	0.72032	D	0.01	.	14.6222	0.68594	1.0:0.0:0.0:0.0	.	3208	P20929	NEBU_HUMAN	S	3208;3451;3451;3208	ENSP00000386259:L3208S;ENSP00000380505:L3451S;ENSP00000416578:L3451S;ENSP00000172853:L3208S	ENSP00000172853:L3208S	L	-	2	0	NEB	152190394	0.060000	0.20803	1.000000	0.80357	0.993000	0.82548	2.165000	0.42396	1.996000	0.58369	0.455000	0.32223	TTA	.	.	.	none		0.358	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		G	152482148	A	G	152482148	3	3	54	1	0	0	0	0	1	0	0	0	10309	372	13	3	15782	3	NEB	2	152482148	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	3804255	152482148	90717225	13	3678											
ICOS	29851	hgsc.bcm.edu	37	chr2	204822592	204822592	+	Missense_Mutation	SNP	A	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	agcagtgaacacagccaaaaAatctagactcacaggtatga	18	6	8	9	0	2	3	1	2	1	1	2	3	2	3	1	1	3	2	1	1	6	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr2:204822592A>C	ENST00000316386.6	+	4	639	c.572A>C	c.(571-573)aAa>aCa	p.K191T	ICOS_ENST00000435193.1_Intron	NM_012092.3	NP_036224.1	Q9Y6W8	ICOS_HUMAN	inducible T-cell co-stimulator	191					immune response (GO:0006955)|single organismal cell-cell adhesion (GO:0016337)|T cell costimulation (GO:0031295)|T cell tolerance induction (GO:0002517)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|large_intestine(1)|lung(4)	6						ACAGCCAAAAAATCTAGACTC	0.388																																					p.K191T		Atlas-SNP	.											.	ICOS	20	.	0			c.A572C						PASS	.						86	85	86					2																	204822592		2203	4300	6503	SO:0001583	missense	29851	exon4			CCAAAAAATCTAG	AB023135	CCDS2363.1	2q33	2014-09-17			ENSG00000163600	ENSG00000163600		"CD molecules"	5351	protein-coding gene	gene with protein product	"activation-inducible lymphocyte immunomediatory molecule"	604558				9930702, 10617205	Standard	NM_012092		Approved	AILIM, CD278	uc002vam.3	Q9Y6W8	OTTHUMG00000132880	ENST00000316386.6:c.572A>C	chr2.hg19:g.204822592A>C	ENSP00000319476:p.Lys191Thr	45.0	0.0	.		86.0	36.0	.	NM_012092	Q8N6W8	Missense_Mutation	SNP	ENST00000316386.6	hg19	CCDS2363.1	.	.	.	.	.	.	.	.	.	.	A	18.24	3.581135	0.65992	.	.	ENSG00000163600	ENST00000316386	.	.	.	5.73	3.24	0.37175	.	0.180516	0.37577	N	0.002037	T	0.41696	0.1170	M	0.72118	2.19	0.09310	N	0.999993	B;B	0.19583	0.037;0.037	B;B	0.17433	0.018;0.018	T	0.33979	-0.9847	9	0.30078	T	0.28	-32.144	5.7144	0.17952	0.6551:0.157:0.0:0.188	.	191;191	Q53QY6;Q9Y6W8	.;ICOS_HUMAN	T	191	.	ENSP00000319476:K191T	K	+	2	0	ICOS	204530837	0.794000	0.28838	0.002000	0.10522	0.508000	0.34012	1.387000	0.34430	0.383000	0.24910	0.383000	0.25322	AAA	.	.	.	none		0.388	ICOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256369.1	NM_012092		C	204822592	A	C	204822592	3	2	54	1	0	0	0	0	1	0	0	0	7493	14	1	5	586	5	ICOS	2	204822592	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	52340444	204822592	38376781	14	3679											
DNPEP	23549	hgsc.bcm.edu	37	chr2	220239739	220239739	+	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	ggggtgtcattccggaccatGagatcctagggagagcagga	10	7	16	8	1	1	2	1	1	0	2	3	6	3	4	3	5	1	1	3	5	1	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr2:220239739G>A	ENST00000273075.4	-	14	1465	c.1245C>T	c.(1243-1245)ctC>ctT	p.L415L	DNPEP_ENST00000523282.1_Silent_p.L423L|DNPEP_ENST00000373972.1_Silent_p.L340L|DNPEP_ENST00000490371.1_5'UTR	NM_012100.2	NP_036232	Q9ULA0	DNPEP_HUMAN	aspartyl aminopeptidase	405					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)		TCCGGACCATGAGATCCTAGG	0.582																																					p.L415L		Atlas-SNP	.											.	DNPEP	40	.	0			c.C1245T						PASS	.						54	57	56					2																	220239739		1995	4197	6192	SO:0001819	synonymous_variant	23549	exon14			GACCATGAGATCC		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.1245C>T	chr2.hg19:g.220239739G>A		56.0	0.0	.		60.0	23.0	.	NM_012100	Q9BW44|Q9NUV5	Silent	SNP	ENST00000273075.4	hg19	CCDS42823.1	.	.	.	.	.	.	.	.	.	.	G	9.087	1.000674	0.19121	.	.	ENSG00000123992	ENST00000337010	.	.	.	5.38	4.5	0.54988	.	.	.	.	.	T	0.72518	0.3470	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72830	-0.4174	4	.	.	.	-23.6962	16.3965	0.83607	0.0:0.1313:0.8686:0.0	.	.	.	.	L	415	.	.	S	-	2	0	DNPEP	219947983	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	3.609000	0.54117	1.492000	0.48499	0.655000	0.94253	TCA	.	.	.	none		0.582	DNPEP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000130212.1	NM_012100		A	220239739	G	A	220239739	2	1	54	1	0	0	0	0	0	0	0	1	4681	1277	45	2		2	DNPEP	2	220239739	Silent	SNP	G	TCGA-A4-8310-01A-11D-2396-08	15417147	220239739	22959634	15	3680											
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121433805	121433805	+	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	gaaattggctaatttctttgGatttttgctggagctgatct	8	18	10	5	0	2	1	0	1	2	0	2	4	2	3	0	3	2	3	0	3	2	6			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr3:121433805G>A	ENST00000340645.5	-	10	1417	c.1292C>T	c.(1291-1293)tCc>tTc	p.S431F	GOLGB1_ENST00000393667.3_Missense_Mutation_p.S436F	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	431					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)		AATTTCTTTGGATTTTTGCTG	0.328																																					p.S436F		Atlas-SNP	.											.	GOLGB1	319	.	0			c.C1307T						PASS	.						121	122	122					3																	121433805		2203	4300	6503	SO:0001583	missense	2804	exon10			TCTTTGGATTTTT	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.1292C>T	chr3.hg19:g.121433805G>A	ENSP00000341848:p.Ser431Phe	55.0	0.0	.		64.0	32.0	.	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	hg19	CCDS3004.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.900|8.900	0.956079|0.956079	0.18507|0.18507	.|.	.|.	ENSG00000173230|ENSG00000173230	ENST00000489400|ENST00000340645;ENST00000393667;ENST00000494517;ENST00000426235	.|T;T;T	.|0.25414	.|2.39;2.39;1.8	4.95|4.95	2.09|2.09	0.27110|0.27110	.|.	.|0.423391	.|0.20726	.|N	.|0.086819	T|T	0.43787|0.43787	0.1263|0.1263	M|M	0.68317|0.68317	2.08|2.08	0.25739|0.25739	N|N	0.985181|0.985181	.|D;D;D;D;D	.|0.89917	.|1.0;0.999;1.0;0.999;1.0	.|D;D;D;D;D	.|0.87578	.|0.998;0.996;0.998;0.996;0.998	T|T	0.18053|0.18053	-1.0349|-1.0349	5|10	.|0.51188	.|T	.|0.08	.|.	8.2496|8.2496	0.31708|0.31708	0.0:0.3271:0.5037:0.1692|0.0:0.3271:0.5037:0.1692	.|.	.|356;395;436;436;431	.|F1T0J2;E7EU81;E7EP74;B2ZZ91;Q14789	.|.;.;.;.;GOGB1_HUMAN	S|F	302|431;436;395;243	.|ENSP00000341848:S431F;ENSP00000377275:S436F;ENSP00000418231:S395F	.|ENSP00000341848:S431F	P|S	-|-	1|2	0|0	GOLGB1|GOLGB1	122916495|122916495	0.949000|0.949000	0.32298|0.32298	0.256000|0.256000	0.24389|0.24389	0.478000|0.478000	0.33099|0.33099	1.453000|1.453000	0.35167|0.35167	0.231000|0.231000	0.21079|0.21079	-0.188000|-0.188000	0.12872|0.12872	CCA|TCC	.	.	.	none		0.328	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		A	121433805	G	A	121433805	3	1	54	1	0	0	0	0	1	0	0	0	6572	1174	41	2	8539	2	GOLGB1	3	121433805	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08		121433805	76588625	16	3681											
TNIP2	79155	hgsc.bcm.edu	37	chr4	2746482	2746482	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgggccgtcctggaggccGccagctcctgcttcacttcg	3	8	12	18	4	1	0	1	0	0	0	4	1	3	1	6	3	2	2	6	3	0	2	rs150823075		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr4:2746482G>A	ENST00000315423.7	-	4	934	c.848C>T	c.(847-849)gCg>gTg	p.A283V	TNIP2_ENST00000503235.1_Intron|TNIP2_ENST00000510267.1_Missense_Mutation_p.A176V|TNIP2_ENST00000505186.1_5'UTR	NM_024309.3	NP_077285.3			TNFAIP3 interacting protein 2											breast(2)|central_nervous_system(1)|large_intestine(4)|lung(6)|prostate(1)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CCTGGAGGCCGCCAGCTCCTG	0.607																																					p.A283V		Atlas-SNP	.											.	TNIP2	28	.	0			c.C848T						PASS	.	G	VAL/ALA,VAL/ALA	0,4406		0,0,2203	44	50	48		527,848	2.7	0.6	4	dbSNP_134	48	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	TNIP2	NM_001161527.1,NM_024309.3	64,64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	176/323,283/430	2746482	1,13005	2203	4300	6503	SO:0001583	missense	79155	exon4			GAGGCCGCCAGCT	BC002740	CCDS3362.1, CCDS54714.1, CCDS75093.1	4p16.3	2008-08-01			ENSG00000168884	ENSG00000168884			19118	protein-coding gene	gene with protein product		610669				11390377, 12933576	Standard	NM_024309		Approved	ABIN-2, MGC4289, KLIP, FLIP1	uc003gfg.2	Q8NFZ5	OTTHUMG00000090267	ENST00000315423.7:c.848C>T	chr4.hg19:g.2746482G>A	ENSP00000321203:p.Ala283Val	124.0	0.0	.		107.0	46.0	.	NM_024309		Missense_Mutation	SNP	ENST00000315423.7	hg19	CCDS3362.1	.	.	.	.	.	.	.	.	.	.	G	11.55	1.671911	0.29693	0.0	1.16E-4	ENSG00000168884	ENST00000510267;ENST00000315423	T;T	0.46063	0.88;0.88	5.66	2.71	0.32032	.	0.165365	0.52532	D	0.000076	T	0.24928	0.0605	L	0.35723	1.085	0.80722	D	1	P	0.35155	0.487	B	0.19666	0.026	T	0.05435	-1.0885	10	0.42905	T	0.14	-8.1276	7.0861	0.25257	0.0878:0.0:0.3927:0.5195	.	283	Q8NFZ5	TNIP2_HUMAN	V	176;283	ENSP00000427613:A176V;ENSP00000321203:A283V	ENSP00000321203:A283V	A	-	2	0	TNIP2	2716280	0.729000	0.28090	0.600000	0.28864	0.114000	0.19823	1.029000	0.30140	0.754000	0.32968	0.555000	0.69702	GCG	.	G|1.000;A|0.000	0.000	weak		0.607	TNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206589.5	NM_024309		A	2746482	G	A	2746482	3	1	54	1	0	0	0	0	1	0	0	0	16327	1087	38	1	453	1	TNIP2	4	2746482	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08		2746482	188407794	17	3682											
DCUN1D4	23142	hgsc.bcm.edu	37	chr4	52765463	52765463	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acaacagaaaaactcagaaaTactttggattacttaagatc	19	10	5	7	0	1	3	1	0	0	3	2	4	1	4	0	1	4	0	0	1	7	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr4:52765463T>C	ENST00000334635.5	+	8	714	c.534T>C	c.(532-534)aaT>aaC	p.N178N	DCUN1D4_ENST00000381441.3_Silent_p.N178N|DCUN1D4_ENST00000451288.2_Silent_p.N222N|DCUN1D4_ENST00000381437.4_Silent_p.N118N	NM_001040402.1	NP_001035492.1	Q92564	DCNL4_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 4	178	DCUN1. {ECO:0000255|PROSITE- ProRule:PRU00574}.					nucleus (GO:0005634)				endometrium(2)|large_intestine(2)|lung(2)|ovary(2)|skin(1)	9			GBM - Glioblastoma multiforme(4;1.93e-11)|LUSC - Lung squamous cell carcinoma(32;0.00654)			AACTCAGAAATACTTTGGATT	0.299																																					p.N178N		Atlas-SNP	.											.	DCUN1D4	26	.	0			c.T534C						PASS	.						39	41	41					4																	52765463		2201	4297	6498	SO:0001819	synonymous_variant	23142	exon8			CAGAAATACTTTG	D87466	CCDS3487.2, CCDS33982.1, CCDS75123.1	4q11	2013-06-10	2013-06-10		ENSG00000109184	ENSG00000109184			28998	protein-coding gene	gene with protein product		612977	"DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)"			15988528	Standard	XM_005265731		Approved	KIAA0276	uc003gze.3	Q92564	OTTHUMG00000128700	ENST00000334635.5:c.534T>C	chr4.hg19:g.52765463T>C		17.0	0.0	.		25.0	10.0	.	NM_015115	B4DH25|Q7Z3F3|Q7Z6B8	Silent	SNP	ENST00000334635.5	hg19	CCDS33982.1																																																																																			.	.	.	none		0.299	DCUN1D4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250599.2	NM_015115		C	52765463	T	C	52765463	2	2	54	1	0	0	0	0	0	0	0	1	4318	1403	49	3		3	DCUN1D4	4	52765463	Silent	SNP	T	TCGA-A4-8310-01A-11D-2396-08	50018981	52765463	138388813	18	3683											
HMGB2	3148	hgsc.bcm.edu	37	chr4	174254247	174254247	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttaggagcattggggtccTttttcttccccttcttatca	5	19	7	10	0	3	0	1	0	2	0	5	1	5	1	3	3	1	1	3	3	2	8			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr4:174254247T>C	ENST00000296503.5	-	3	1142	c.269A>G	c.(268-270)aAg>aGg	p.K90R	HMGB2_ENST00000438704.2_Missense_Mutation_p.K90R|HMGB2_ENST00000446922.2_Missense_Mutation_p.K90R			P26583	HMGB2_HUMAN	high mobility group box 2	90					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)	p.K90R(1)		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)		ATTGGGGTCCTTTTTCTTCCC	0.398																																					p.K90R		Atlas-SNP	.											HMGB2,NS,carcinoma,0,1	HMGB2	24	.	1	Substitution - Missense(1)	endometrium(1)	c.A269G						PASS	.						222	233	229					4																	174254247		2203	4300	6503	SO:0001583	missense	3148	exon2			GGGTCCTTTTTCT		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.269A>G	chr4.hg19:g.174254247T>C	ENSP00000296503:p.Lys90Arg	226.0	0.0	.		276.0	104.0	.	NM_001130689	B2R4K8|D3DP37|Q5U072	Missense_Mutation	SNP	ENST00000296503.5	hg19	CCDS3816.1	.	.	.	.	.	.	.	.	.	.	T	14.16	2.451760	0.43531	.	.	ENSG00000164104	ENST00000296503;ENST00000446922;ENST00000438704;ENST00000506267	D;D;D;D	0.94687	-3.49;-3.49;-3.49;-3.49	5.06	5.06	0.68205	High mobility group, superfamily (1);	0.000000	0.64402	D	0.000001	D	0.96883	0.8982	M	0.81802	2.56	0.58432	D	0.99999	P	0.48350	0.909	D	0.65987	0.94	D	0.96930	0.9680	10	0.51188	T	0.08	.	14.1447	0.65344	0.0:0.0:0.0:1.0	.	90	P26583	HMGB2_HUMAN	R	90	ENSP00000296503:K90R;ENSP00000393448:K90R;ENSP00000404912:K90R;ENSP00000423001:K90R	ENSP00000296503:K90R	K	-	2	0	HMGB2	174490822	1.000000	0.71417	1.000000	0.80357	0.122000	0.20287	7.626000	0.83164	2.122000	0.65172	0.460000	0.39030	AAG	.	.	.	none		0.398	HMGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362362.1	NM_001130688		C	174254247	T	C	174254247	3	2	54	1	0	0	0	0	1	0	0	0	7233	1609	56	3	372	3	HMGB2	4	174254247	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08	121488784	174254247	16900029	19	3684											
SNX25	83891	hgsc.bcm.edu	37	chr4	186188140	186188140	+	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	tagtcttgaagccggtagtgGagttactgagtaatccagat	11	12	12	6	1	1	3	0	2	1	1	2	4	2	4	2	2	2	3	2	2	5	5			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr4:186188140G>A	ENST00000504273.1	+	5	724	c.430G>A	c.(430-432)Gag>Aag	p.E144K	SNX25_ENST00000264694.8_Missense_Mutation_p.E144K			Q9H3E2	SNX25_HUMAN	sorting nexin 25	144	PXA. {ECO:0000255|PROSITE- ProRule:PRU00147, ECO:0000255|PROSITE- ProRule:PRU00553}.				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)	p.E144Q(1)		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)		GCCGGTAGTGGAGTTACTGAG	0.423																																					p.E144K		Atlas-SNP	.											SNX25,NS,carcinoma,0,1	SNX25	100	.	1	Substitution - Missense(1)	lung(1)	c.G430A						PASS	.						78	72	74					4																	186188140		2203	4300	6503	SO:0001583	missense	83891	exon5			GTAGTGGAGTTAC	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.430G>A	chr4.hg19:g.186188140G>A	ENSP00000426255:p.Glu144Lys	74.0	0.0	.		95.0	39.0	.	NM_031953	Q3ZT30|Q8N6K3	Missense_Mutation	SNP	ENST00000504273.1	hg19	CCDS34116.1	.	.	.	.	.	.	.	.	.	.	G	15.53	2.860679	0.51482	.	.	ENSG00000109762	ENST00000504273;ENST00000264694	T;T	0.10192	2.9;2.9	5.16	4.32	0.51571	Phox-associated domain (2);	0.188926	0.44688	D	0.000437	T	0.14227	0.0344	L	0.53249	1.67	0.42561	D	0.993145	P	0.35493	0.505	B	0.38803	0.282	T	0.04140	-1.0974	10	0.36615	T	0.2	-5.5611	13.8858	0.63708	0.0734:0.0:0.9266:0.0	.	144	Q9H3E2	SNX25_HUMAN	K	144	ENSP00000426255:E144K;ENSP00000264694:E144K	ENSP00000264694:E144K	E	+	1	0	SNX25	186425134	1.000000	0.71417	0.427000	0.26684	0.993000	0.82548	7.437000	0.80417	1.402000	0.46780	0.591000	0.81541	GAG	.	.	.	none		0.423	SNX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360756.1	NM_031953		A	186188140	G	A	186188140	3	1	54	1	0	0	0	0	1	0	0	0	14909	1175	41	2	444	2	SNX25	4	186188140	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08	11933893	186188140	4966136	20	3685											
CLPTM1L	81037	hgsc.bcm.edu	37	chr5	1323010	1323010	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accgttgacgaagctgttgaTtaaccaggagtaccagctga	12	9	11	9	2	0	3	0	3	0	0	0	5	0	4	3	1	4	5	3	1	3	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr5:1323010T>C	ENST00000320895.5	-	13	1554	c.1297A>G	c.(1297-1299)Atc>Gtc	p.I433V	CLPTM1L_ENST00000506641.1_5'UTR|CLPTM1L_ENST00000507807.1_Missense_Mutation_p.I264V|CLPTM1L_ENST00000320927.6_Missense_Mutation_p.I397V	NM_030782.3	NP_110409.2	Q96KA5	CLP1L_HUMAN	CLPTM1-like	433					apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24	Lung NSC(6;5.78e-14)|all_lung(6;4.47e-13)|all_epithelial(6;4.47e-09)		Epithelial(17;0.00931)|OV - Ovarian serous cystadenocarcinoma(19;0.0116)|all cancers(22;0.0181)	KIRC - Kidney renal clear cell carcinoma(5;0.177)|Kidney(13;0.208)		AAGCTGTTGATTAACCAGGAG	0.388																																					p.I433V		Atlas-SNP	.											.	CLPTM1L	60	.	0			c.A1297G						PASS	.						152	150	151					5																	1323010		2203	4300	6503	SO:0001583	missense	81037	exon13			TGTTGATTAACCA	AK027306	CCDS3862.1	5p15.33	2008-02-05			ENSG00000049656	ENSG00000049656			24308	protein-coding gene	gene with protein product	"cisplatin resistance related protein"	612585				11162647	Standard	NM_030782		Approved	FLJ14400, CRR9	uc003jch.3	Q96KA5	OTTHUMG00000131015	ENST00000320895.5:c.1297A>G	chr5.hg19:g.1323010T>C	ENSP00000313854:p.Ile433Val	111.0	0.0	.		143.0	42.0	.	NM_030782	D3DTC1|Q658W6|Q7LG29|Q96AZ0|Q9H3N4	Missense_Mutation	SNP	ENST00000320895.5	hg19	CCDS3862.1	.	.	.	.	.	.	.	.	.	.	T	12.47	1.947015	0.34377	.	.	ENSG00000049656	ENST00000320895;ENST00000507807;ENST00000320927	T;T;T	0.51817	0.69;0.8;0.78	4.58	3.39	0.38822	.	0.047837	0.85682	D	0.000000	T	0.32556	0.0833	N	0.26042	0.785	0.54753	D	0.999983	B;B	0.06786	0.001;0.001	B;B	0.14023	0.005;0.01	T	0.07009	-1.0795	10	0.35671	T	0.21	-39.5635	9.5543	0.39328	0.0:0.087:0.0:0.913	.	433;264	Q96KA5;G5E9Z2	CLP1L_HUMAN;.	V	433;264;397	ENSP00000313854:I433V;ENSP00000423321:I264V;ENSP00000315196:I397V	ENSP00000313854:I433V	I	-	1	0	CLPTM1L	1376010	1.000000	0.71417	0.825000	0.32803	0.932000	0.56968	4.256000	0.58810	0.694000	0.31654	0.402000	0.26972	ATC	.	.	.	none		0.388	CLPTM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253649.2	NM_030782		C	1323010	T	C	1323010	3	2	54	1	0	0	0	0	1	0	0	0	3557	1493	52	3	339	3	CLPTM1L	5	1323010	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08		1323010	179592250	21	3686											
ADAMTS16	170690	hgsc.bcm.edu	37	chr5	5240027	5240027	+	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	ctggaccaaccaacgagacaCtgattgtggaggtaaagtcc	13	7	11	10	1	0	2	0	1	0	1	1	5	1	4	3	3	2	1	3	3	4	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr5:5240027C>G	ENST00000274181.7	+	16	2650	c.2512C>G	c.(2512-2514)Ctg>Gtg	p.L838V		NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	838	Spacer.				branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						CAACGAGACACTGATTGTGGA	0.478																																					p.L838V		Atlas-SNP	.											.	ADAMTS16	543	.	0			c.C2512G						PASS	.						86	83	84					5																	5240027		1878	4117	5995	SO:0001583	missense	170690	exon16			GAGACACTGATTG	AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536		"ADAM metallopeptidases with thrombospondin type 1 motif"	17108	protein-coding gene	gene with protein product		607510	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16"			11867212	Standard	NM_139056		Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.2512C>G	chr5.hg19:g.5240027C>G	ENSP00000274181:p.Leu838Val	127.0	0.0	.		135.0	15.0	.	NM_139056	C6G490|Q8IVE2	Missense_Mutation	SNP	ENST00000274181.7	hg19	CCDS43299.1	.	.	.	.	.	.	.	.	.	.	C	13.73	2.325582	0.41197	.	.	ENSG00000145536	ENST00000274181;ENST00000536857	T	0.61742	0.08	5.56	3.45	0.39498	ADAM-TS Spacer 1 (1);	0.000000	0.64402	D	0.000013	T	0.70325	0.3211	M	0.62266	1.93	0.48452	D	0.999658	D;D	0.89917	1.0;0.991	D;D	0.87578	0.998;0.919	T	0.69450	-0.5142	10	0.36615	T	0.2	.	12.5248	0.56079	0.0:0.8343:0.0:0.1657	.	838;838	Q8TE57;Q8TE57-2	ATS16_HUMAN;.	V	838	ENSP00000274181:L838V	ENSP00000274181:L838V	L	+	1	2	ADAMTS16	5293027	0.864000	0.29904	0.134000	0.22075	0.299000	0.27559	1.676000	0.37565	1.352000	0.45808	0.655000	0.94253	CTG	.	.	.	none		0.478	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056		G	5240027	C	G	5240027	3	3	54	1	0	0	0	0	1	0	0	0	261	564	20	4	2574	4	ADAMTS16	5	5240027	Missense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08	3917017	5240027	175675233	22	3687											
PDZD2	23037	hgsc.bcm.edu	37	chr5	32059458	32059458	+	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	tggccaagatggagagcaacCtgaggtttgttgtttgcctg	8	12	14	7	0	0	3	0	1	0	2	0	4	0	3	3	3	3	4	3	3	2	3			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr5:32059458C>A	ENST00000438447.1	+	13	2702	c.2314C>A	c.(2314-2316)Ctg>Atg	p.L772M	PDZD2_ENST00000282493.3_Missense_Mutation_p.L772M			O15018	PDZD2_HUMAN	PDZ domain containing 2	772	PDZ 4. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						GGAGAGCAACCTGAGGTTTGT	0.448																																					p.L772M		Atlas-SNP	.											.	PDZD2	306	.	0			c.C2314A						PASS	.						102	88	93					5																	32059458		2203	4300	6503	SO:0001583	missense	23037	exon12			AGCAACCTGAGGT	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.2314C>A	chr5.hg19:g.32059458C>A	ENSP00000402033:p.Leu772Met	50.0	0.0	.		53.0	20.0	.	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	hg19	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	C	20.0	3.930044	0.73327	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.50001	0.76;0.76	5.79	3.98	0.46160	PDZ/DHR/GLGF (4);	0.000000	0.36268	N	0.002696	T	0.71896	0.3394	M	0.91249	3.19	0.40854	D	0.983775	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.77292	-0.2642	10	0.72032	D	0.01	.	10.7091	0.45973	0.0:0.8633:0.0:0.1367	.	598;772	B4E3P2;O15018	.;PDZD2_HUMAN	M	772;591;772	ENSP00000402033:L772M;ENSP00000282493:L772M	ENSP00000282493:L772M	L	+	1	2	PDZD2	32095215	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	2.741000	0.47426	2.726000	0.93360	0.655000	0.94253	CTG	.	.	.	none		0.448	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			A	32059458	C	A	32059458	3	1	54	1	0	0	0	0	1	0	0	0	11708	680	24	4	2360	4	PDZD2	5	32059458	Missense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08	26819431	32059458	148855802	23	3688											
C5orf42	65250	hgsc.bcm.edu	37	chr5	37181023	37181023	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agttccacctggagttgctaCtgcaactgaaccgccagcat	10	9	9	13	1	0	1	0	1	0	0	1	2	1	2	4	1	6	5	4	1	3	3			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr5:37181023C>T	ENST00000508244.1	-	26	5599	c.5506G>A	c.(5506-5508)Gta>Ata	p.V1836I	C5orf42_ENST00000274258.7_Missense_Mutation_p.V717I|C5orf42_ENST00000425232.2_Missense_Mutation_p.V1836I			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	1836						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)			GGAGTTGCTACTGCAACTGAA	0.403																																					p.V1836I		Atlas-SNP	.											.	C5orf42	422	.	0			c.G5506A						PASS	.						72	67	69					5																	37181023		2203	4300	6503	SO:0001583	missense	65250	exon27			TTGCTACTGCAAC		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.5506G>A	chr5.hg19:g.37181023C>T	ENSP00000421690:p.Val1836Ile	55.0	0.0	.		65.0	24.0	.	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	hg19	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	C	12.91	2.078569	0.36662	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.20200	2.09;2.09;2.09;2.09	5.91	1.94	0.25998	.	2.430320	0.01888	N	0.038363	T	0.19604	0.0471	L	0.40543	1.245	0.09310	N	1	P;B	0.34724	0.465;0.386	B;B	0.31101	0.124;0.124	T	0.29119	-1.0022	10	0.26408	T	0.33	.	9.6655	0.39981	0.0:0.5185:0.4071:0.0744	.	1836;717	E9PH94;Q9H799	.;CE042_HUMAN	I	1836;1836;717;884;717	ENSP00000421690:V1836I;ENSP00000389014:V1836I;ENSP00000274258:V717I;ENSP00000424223:V884I	ENSP00000274258:V717I	V	-	1	0	C5orf42	37216780	0.021000	0.18746	0.000000	0.03702	0.019000	0.09904	0.036000	0.13819	0.067000	0.16545	0.655000	0.94253	GTA	.	.	.	none		0.403	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		T	37181023	C	T	37181023	3	4	54	1	0	0	0	0	1	0	0	0	2303	565	20	2	4191	2	C5orf42	5	37181023	Missense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08	5121565	37181023	143734237	24	3689											
DAB2	1601	hgsc.bcm.edu	37	chr5	39390645	39390645	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acatcacgggcaatgaaagaAatcttatttactggatgttc	14	12	8	7	1	2	2	1	1	1	1	3	3	2	3	0	2	1	2	0	2	5	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr5:39390645A>G	ENST00000320816.6	-	5	830	c.363T>C	c.(361-363)atT>atC	p.I121I	DAB2_ENST00000545653.1_Silent_p.I121I|DAB2_ENST00000512525.1_5'UTR|DAB2_ENST00000509337.1_Silent_p.I121I|DAB2_ENST00000339788.6_Silent_p.I121I	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	121	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				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)			CAATGAAAGAAATCTTATTTA	0.398																																					p.I121I		Atlas-SNP	.											.	DAB2	124	.	0			c.T363C						PASS	.						74	78	76					5																	39390645		2203	4300	6503	SO:0001819	synonymous_variant	1601	exon5			GAAAGAAATCTTA	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.363T>C	chr5.hg19:g.39390645A>G		62.0	0.0	.		78.0	34.0	.	NM_001343	A6NES5|Q13598|Q9BTY0|Q9UK04	Silent	SNP	ENST00000320816.6	hg19	CCDS34149.1																																																																																			.	.	.	none		0.398	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343		G	39390645	A	G	39390645	2	3	54	1	0	0	0	0	0	0	0	1	4220	10	1	3		3	DAB2	5	39390645	Silent	SNP	A	TCGA-A4-8310-01A-11D-2396-08	2209622	39390645	141524615	25	3690											
DAB2	1601	hgsc.bcm.edu	37	chr5	39394411	39394411	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttggttgcacttgtttctacTtcgttagacatggcaagaag	9	15	10	7	1	1	2	0	0	1	2	2	2	1	2	0	2	2	5	0	2	4	7			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr5:39394411T>C	ENST00000320816.6	-	2	479	c.12A>G	c.(10-12)gaA>gaG	p.E4E	DAB2_ENST00000545653.1_Silent_p.E4E|DAB2_ENST00000512525.1_5'Flank|DAB2_ENST00000509337.1_Silent_p.E4E|DAB2_ENST00000339788.6_Silent_p.E4E	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	4					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)			TTGTTTCTACTTCGTTAGACA	0.478																																					p.E4E		Atlas-SNP	.											.	DAB2	124	.	0			c.A12G						PASS	.						147	131	137					5																	39394411		2203	4300	6503	SO:0001819	synonymous_variant	1601	exon2			TTCTACTTCGTTA	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.12A>G	chr5.hg19:g.39394411T>C		66.0	0.0	.		81.0	32.0	.	NM_001343	A6NES5|Q13598|Q9BTY0|Q9UK04	Silent	SNP	ENST00000320816.6	hg19	CCDS34149.1																																																																																			.	.	.	none		0.478	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343		C	39394411	T	C	39394411	2	2	54	1	0	0	0	0	0	0	0	1	4220	1606	56	3		3	DAB2	5	39394411	Silent	SNP	T	TCGA-A4-8310-01A-11D-2396-08	3766	39394411	141520849	26	3691											
PLK2	10769	hgsc.bcm.edu	37	chr5	57753133	57753133	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggacggcattgtataccttgCttcccttatgcacctataag	9	13	8	11	1	0	0	0	0	0	0	1	1	1	1	3	2	3	4	3	2	5	8			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr5:57753133C>T	ENST00000274289.3	-	7	1183	c.883G>A	c.(883-885)Gca>Aca	p.A295T	PLK2_ENST00000502671.1_5'UTR	NM_001252226.1|NM_006622.3	NP_001239155.1|NP_006613.2	Q9NYY3	PLK2_HUMAN	polo-like kinase 2	295	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				G1/S transition of mitotic cell cycle (GO:0000082)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|mitotic cell cycle checkpoint (GO:0007093)|mitotic spindle organization (GO:0007052)|negative regulation of apoptotic process (GO:0043066)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|Rap protein signal transduction (GO:0032486)|Ras protein signal transduction (GO:0007265)|regulation of centriole replication (GO:0046599)|regulation of synaptic plasticity (GO:0048167)	centriole (GO:0005814)|centrosome (GO:0005813)|dendrite (GO:0030425)|intracellular (GO:0005622)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			endometrium(7)|large_intestine(7)|lung(5)|ovary(3)|prostate(2)|skin(2)	26		all_cancers(5;1.76e-12)|all_epithelial(5;2.09e-13)|all_lung(5;6.64e-05)|Lung NSC(5;0.000127)|Prostate(74;0.055)|Breast(144;0.0602)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;7.03e-37)		GTATACCTTGCTTCCCTTATG	0.433																																					p.A295T		Atlas-SNP	.											.	PLK2	71	.	0			c.G883A						PASS	.						79	76	77					5																	57753133		2203	4300	6503	SO:0001583	missense	10769	exon7			ACCTTGCTTCCCT		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.883G>A	chr5.hg19:g.57753133C>T	ENSP00000274289:p.Ala295Thr	40.0	0.0	.		48.0	14.0	.	NM_006622	O60679|Q96CV7|Q9UE61	Missense_Mutation	SNP	ENST00000274289.3	hg19	CCDS3974.1	.	.	.	.	.	.	.	.	.	.	C	35	5.479369	0.96307	.	.	ENSG00000145632	ENST00000274289;ENST00000537944;ENST00000442330	T	0.64618	-0.11	5.27	5.27	0.74061	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	0.70055	0.3180	L	0.33624	1.015	0.80722	D	1	D	0.64830	0.994	D	0.65140	0.932	T	0.69363	-0.5165	10	0.40728	T	0.16	-15.6861	18.9292	0.92558	0.0:1.0:0.0:0.0	.	295	Q9NYY3	PLK2_HUMAN	T	295;295;281	ENSP00000274289:A295T	ENSP00000274289:A295T	A	-	1	0	PLK2	57788890	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.388000	0.79795	2.461000	0.83175	0.655000	0.94253	GCA	.	.	.	none		0.433	PLK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214150.1	NM_006622		T	57753133	C	T	57753133	3	4	54	1	0	0	0	0	1	0	0	0	12103	797	28	2	1206	2	PLK2	5	57753133	Missense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08	18358722	57753133	123162127	27	3692											
FBN2	2201	hgsc.bcm.edu	37	chr5	127641530	127641530	+	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	attaccttcacaaaccaacaGcaggtcattgtaactgaatc	15	10	5	11	0	2	1	2	1	0	0	3	1	2	1	2	1	5	2	2	1	5	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr5:127641530G>C	ENST00000508053.1	-	49	6507	c.5533C>G	c.(5533-5535)Ctg>Gtg	p.L1845V	FBN2_ENST00000262464.4_Missense_Mutation_p.L1845V			P35556	FBN2_HUMAN	fibrillin 2	1845	EGF-like 29; 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)		CAAACCAACAGCAGGTCATTG	0.363																																					p.L1845V		Atlas-SNP	.											.	FBN2	858	.	0			c.C5533G						PASS	.						123	118	120					5																	127641530		2203	4300	6503	SO:0001583	missense	2201	exon43			CCAACAGCAGGTC	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.5533C>G	chr5.hg19:g.127641530G>C	ENSP00000424571:p.Leu1845Val	88.0	0.0	.		122.0	11.0	.	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	hg19	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.015309	0.75161	.	.	ENSG00000138829	ENST00000262464;ENST00000508053	D;D	0.95554	-3.74;-3.74	5.24	5.24	0.73138	EGF-like region, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.53938	D	0.000045	D	0.95548	0.8553	L	0.50333	1.59	0.35026	D	0.758342	D	0.55605	0.972	P	0.54346	0.749	D	0.94672	0.7857	10	0.16896	T	0.51	.	19.3745	0.94503	0.0:0.0:1.0:0.0	.	1845	P35556	FBN2_HUMAN	V	1845	ENSP00000262464:L1845V;ENSP00000424571:L1845V	ENSP00000262464:L1845V	L	-	1	2	FBN2	127669429	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	6.312000	0.72840	2.880000	0.98712	0.650000	0.86243	CTG	.	.	.	none		0.363	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		C	127641530	G	C	127641530	3	2	54	1	0	0	0	0	1	0	0	0	5710	962	34	4	3297	4	FBN2	5	127641530	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08	69888397	127641530	53273730	28	3693											
RUFY1	80230	hgsc.bcm.edu	37	chr5	178987050	178987050	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taagtgccagatgatggaggAgcgtgccaacctgatgcaca	12	7	13	9	1	0	3	0	2	0	1	0	5	0	5	3	2	5	1	3	2	2	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr5:178987050A>G	ENST00000319449.4	+	2	347	c.335A>G	c.(334-336)gAg>gGg	p.E112G	RUFY1_ENST00000377001.2_Missense_Mutation_p.E112G|RUFY1_ENST00000437570.2_Missense_Mutation_p.E4G|RUFY1_ENST00000393438.2_Missense_Mutation_p.E4G	NM_025158.4	NP_079434.3	Q96T51	RUFY1_HUMAN	RUN and FYVE domain containing 1	112					endocytosis (GO:0006897)|regulation of endocytosis (GO:0030100)	cytoplasm (GO:0005737)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	lipid binding (GO:0008289)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ATGATGGAGGAGCGTGCCAAC	0.597										HNSCC(44;0.11)																											p.E112G		Atlas-SNP	.											.	RUFY1	101	.	0			c.A335G						PASS	.						82	59	67					5																	178987050		2203	4300	6503	SO:0001583	missense	80230	exon2			TGGAGGAGCGTGC	AF361055	CCDS4445.2, CCDS34312.1	5q35.3	2008-02-05			ENSG00000176783	ENSG00000176783		"Zinc fingers, FYVE domain containing"	19760	protein-coding gene	gene with protein product		610327				11877430	Standard	NM_001040451		Approved	FLJ22251, ZFYVE12, RABIP4	uc003mka.2	Q96T51	OTTHUMG00000130913	ENST00000319449.4:c.335A>G	chr5.hg19:g.178987050A>G	ENSP00000325594:p.Glu112Gly	38.0	0.0	.		32.0	17.0	.	NM_025158	Q59FF3|Q71S93|Q9H6I3	Missense_Mutation	SNP	ENST00000319449.4	hg19	CCDS4445.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	34|34	5.405080|5.405080	0.96051|0.96051	.|.	.|.	ENSG00000176783|ENSG00000176783	ENST00000319449;ENST00000377001;ENST00000437570;ENST00000393438|ENST00000502984	T;T;T;T|.	0.12984|.	2.63;2.63;2.63;2.63|.	5.56|5.56	5.56|5.56	0.83823|0.83823	.|.	0.098275|.	0.64402|.	D|.	0.000002|.	T|T	0.77082|0.77082	0.4078|0.4078	M|M	0.80982|0.80982	2.52|2.52	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.87578|.	0.998|.	T|T	0.78663|0.78663	-0.2116|-0.2116	10|5	0.87932|.	D|.	0|.	-27.8219|-27.8219	15.7239|15.7239	0.77736|0.77736	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	112|.	Q96T51|.	RUFY1_HUMAN|.	G|G	112;112;4;4|70	ENSP00000325594:E112G;ENSP00000366200:E112G;ENSP00000390025:E4G;ENSP00000377087:E4G|.	ENSP00000325594:E112G|.	E|S	+|+	2|1	0|0	RUFY1|RUFY1	178919656|178919656	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.223000|7.223000	0.78033|0.78033	2.128000|2.128000	0.65567|0.65567	0.459000|0.459000	0.35465|0.35465	GAG|AGC	.	.	.	none		0.597	RUFY1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253505.2	NM_001040451		G	178987050	A	G	178987050	3	3	54	1	0	0	0	0	1	0	0	0	13751	304	11	3	341	3	RUFY1	5	178987050	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	51345520	178987050	1928210	29	3694											
DDAH2	23564	hgsc.bcm.edu	37	chr6	31696435	31696435	+	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	agcctcaccggtgaagagaaCgtcagtgccatccagcgtcg	10	6	12	13	4	2	2	2	1	0	1	4	3	3	2	4	1	4	0	4	1	2	0			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr6:31696435C>T	ENST00000375789.2	-	2	1015	c.385G>A	c.(385-387)Gtt>Att	p.V129I	DDAH2_ENST00000375792.3_Missense_Mutation_p.V129I|DDAH2_ENST00000375787.2_Missense_Mutation_p.V129I|DDAH2_ENST00000480913.1_5'UTR			O95865	DDAH2_HUMAN	dimethylarginine dimethylaminohydrolase 2	129					arginine catabolic process (GO:0006527)|citrulline metabolic process (GO:0000052)|negative regulation of apoptotic process (GO:0043066)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of nitric oxide biosynthetic process (GO:0045429)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|catalytic activity (GO:0003824)|dimethylargininase activity (GO:0016403)			endometrium(1)|large_intestine(3)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	11					L-Citrulline(DB00155)	GTGAAGAGAACGTCAGTGCCA	0.572																																					p.V129I		Atlas-SNP	.											.	DDAH2	15	.	0			c.G385A						PASS	.						71	55	61					6																	31696435		1511	2709	4220	SO:0001583	missense	23564	exon3			AGAGAACGTCAGT	AF070667	CCDS4718.1	6p21	2010-02-17			ENSG00000213722	ENSG00000213722	3.5.3.18		2716	protein-coding gene	gene with protein product		604744				10493931	Standard	XM_005248974		Approved		uc003nwq.3	O95865	OTTHUMG00000031212	ENST00000375789.2:c.385G>A	chr6.hg19:g.31696435C>T	ENSP00000364945:p.Val129Ile	53.0	0.0	.		44.0	18.0	.	NM_013974	A2BEZ7	Missense_Mutation	SNP	ENST00000375789.2	hg19	CCDS4718.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.08|13.08	2.130498|2.130498	0.37630|0.37630	.|.	.|.	ENSG00000213722|ENSG00000213722	ENST00000437288|ENST00000375789;ENST00000375787;ENST00000375792;ENST00000416410;ENST00000436437	.|.	.|.	.|.	4.99|4.99	4.99|4.99	0.66335|0.66335	.|.	.|0.130895	.|0.50627	.|D	.|0.000101	T|T	0.32041|0.32041	0.0816|0.0816	L|L	0.45051|0.45051	1.395|1.395	0.40188|0.40188	D|D	0.977377|0.977377	.|B	.|0.33477	.|0.413	.|B	.|0.31290	.|0.127	T|T	0.28808|0.28808	-1.0032|-1.0032	5|9	.|0.38643	.|T	.|0.18	-22.272|-22.272	9.2267|9.2267	0.37412|0.37412	0.0:0.9044:0.0:0.0956|0.0:0.9044:0.0:0.0956	.|.	.|129	.|O95865	.|DDAH2_HUMAN	H|I	34|129	.|.	.|ENSP00000364943:V129I	R|V	-|-	2|1	0|0	DDAH2|DDAH2	31804414|31804414	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.892000|0.892000	0.51952|0.51952	3.286000|3.286000	0.51724|0.51724	2.585000|2.585000	0.87301|0.87301	0.655000|0.655000	0.94253|0.94253	CGT|GTT	.	.	.	none		0.572	DDAH2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076432.2			T	31696435	C	T	31696435	3	4	54	1	0	0	0	0	1	0	0	0	4324	536	19	1	492	1	DDAH2	6	31696435	Missense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08		31696435	139418632	30	3695											
DAXX	1616	hgsc.bcm.edu	37	chr6	33287891	33287891	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaatctgtggcctcctcctcTtcttcttcctcctcctcctc	2	16	4	19	0	4	0	0	0	4	0	11	1	10	0	7	1	0	0	7	1	1	3			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr6:33287891T>C	ENST00000374542.5	-	5	1566	c.1362A>G	c.(1360-1362)gaA>gaG	p.E454E	ZBTB22_ENST00000418724.1_5'Flank|DAXX_ENST00000414083.2_Silent_p.E379E|DAXX_ENST00000266000.6_Silent_p.E454E|DAXX_ENST00000477162.1_5'UTR|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	454	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						cctcctcctcttcttcttcct	0.552			"Mis, F, N"		Pancreatic neuroendocrine tumors. Paediatric GBM																																p.E466E		Atlas-SNP	.		Rec	yes		6	6p21.3	1616	death-domain associated protein		E	DAXX,NS,malignant_melanoma,0,1	DAXX	111	.	0			c.A1398G						PASS	.						135	104	114					6																	33287891		2203	4300	6503	SO:0001819	synonymous_variant	1616	exon5			CTCCTCTTCTTCT	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.1362A>G	chr6.hg19:g.33287891T>C		41.0	0.0	.		41.0	2.0	.	NM_001141970	B4E1I3|F5H082|O14747|O15141|O15208|Q5STK9|Q9BWI3	Silent	SNP	ENST00000374542.5	hg19	CCDS4776.1																																																																																			.	.	.	none		0.552	DAXX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076403.1			C	33287891	T	C	33287891	2	2	54	1	0	0	0	0	0	0	0	1	4245	1606	56	3		3	DAXX	6	33287891	Silent	SNP	T	TCGA-A4-8310-01A-11D-2396-08	1591456	33287891	137827176	31	3696											
GSTA1	2938	hgsc.bcm.edu	37	chr6	52658943	52658943	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttttcaaaggcagggaagtAgcgattttttattttctctt	9	19	8	5	1	2	0	1	0	1	0	3	2	2	1	0	2	1	2	0	2	4	9			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr6:52658943A>G	ENST00000334575.5	-	5	549	c.394T>C	c.(394-396)Tac>Cac	p.Y132H	GSTA1_ENST00000493331.1_5'UTR	NM_145740.3	NP_665683.1	P08263	GSTA1_HUMAN	glutathione S-transferase alpha 1	132	GST C-terminal.				epithelial cell differentiation (GO:0030855)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|metabolic process (GO:0008152)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)			large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	12	Lung NSC(77;0.118)				Azathioprine(DB00993)|Busulfan(DB01008)|Glutathione(DB00143)	GCAGGGAAGTAGCGATTTTTT	0.433																																					p.Y132H		Atlas-SNP	.											.	GSTA1	40	.	0			c.T394C						PASS	.						249	246	247					6																	52658943		2203	4300	6503	SO:0001583	missense	2938	exon5			GGAAGTAGCGATT		CCDS4945.1	6p12.2	2012-06-21	2008-11-26		ENSG00000243955	ENSG00000243955	2.5.1.18	"Glutathione S-transferases / Soluble"	4626	protein-coding gene	gene with protein product		138359	"glutathione S-transferase A1"			9503014	Standard	NM_145740		Approved		uc003paz.3	P08263	OTTHUMG00000014861	ENST00000334575.5:c.394T>C	chr6.hg19:g.52658943A>G	ENSP00000335620:p.Tyr132His	263.0	0.0	.		342.0	114.0	.	NM_145740	Q14750|Q5GHF8|Q5SZC1	Missense_Mutation	SNP	ENST00000334575.5	hg19	CCDS4945.1	.	.	.	.	.	.	.	.	.	.	a	13.85	2.359274	0.41801	.	.	ENSG00000243955	ENST00000334575	T	0.02103	4.45	2.58	2.58	0.30949	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.157818	0.43579	D	0.000559	T	0.04679	0.0127	M	0.76727	2.345	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.12811	-1.0533	10	0.87932	D	0	.	9.4793	0.38891	1.0:0.0:0.0:0.0	.	132	P08263	GSTA1_HUMAN	H	132	ENSP00000335620:Y132H	ENSP00000335620:Y132H	Y	-	1	0	GSTA1	52766902	0.951000	0.32395	0.003000	0.11579	0.017000	0.09413	5.478000	0.66806	0.928000	0.37168	0.164000	0.16699	TAC	.	.	.	none		0.433	GSTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040922.1			G	52658943	A	G	52658943	3	3	54	1	0	0	0	0	1	0	0	0	6837	420	15	3	286	3	GSTA1	6	52658943	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	19371052	52658943	118456124	32	3697											
IBTK	25998	hgsc.bcm.edu	37	chr6	82904254	82904254	+	Missense_Mutation	SNP	T	T	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	atcaattctgttactgggaaTaggctgtggagcagatattt	11	14	11	5	0	2	1	1	0	1	1	2	3	2	3	0	3	2	3	0	3	5	5			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr6:82904254T>G	ENST00000306270.7	-	23	3829	c.3280A>C	c.(3280-3282)Att>Ctt	p.I1094L	IBTK_ENST00000503631.1_Missense_Mutation_p.I893L|IBTK_ENST00000510291.1_Missense_Mutation_p.I1079L	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	1094					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)			central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		TTACTGGGAATAGGCTGTGGA	0.368																																					p.I1094L		Atlas-SNP	.											.	IBTK	128	.	0			c.A3280C						PASS	.						92	95	94					6																	82904254		2203	4300	6503	SO:0001583	missense	25998	exon23			TGGGAATAGGCTG	AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	17853	protein-coding gene	gene with protein product		606457	"Bruton agammaglobulinemia tyrosine kinase inhibitor"	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.3280A>C	chr6.hg19:g.82904254T>G	ENSP00000305721:p.Ile1094Leu	42.0	0.0	.		49.0	21.0	.	NM_015525	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Missense_Mutation	SNP	ENST00000306270.7	hg19	CCDS34490.1	.	.	.	.	.	.	.	.	.	.	T	19.68	3.873221	0.72180	.	.	ENSG00000005700	ENST00000306270;ENST00000503631;ENST00000510291	T;T;T	0.38240	1.63;1.15;1.6	5.3	4.14	0.48551	.	0.226344	0.45126	D	0.000398	T	0.41511	0.1162	M	0.66939	2.045	0.45541	D	0.998499	P;P;D;D;P	0.69078	0.677;0.937;0.997;0.962;0.937	B;P;D;P;P	0.83275	0.243;0.506;0.996;0.701;0.506	T	0.30563	-0.9974	10	0.23302	T	0.38	-15.758	11.0232	0.47730	0.0:0.0732:0.0:0.9268	.	893;1079;45;1094;1094	E9PDR5;E7EPI0;B3KX60;Q9P2D0-2;Q9P2D0	.;.;.;.;IBTK_HUMAN	L	1094;893;1079	ENSP00000305721:I1094L;ENSP00000422762:I893L;ENSP00000426405:I1079L	ENSP00000305721:I1094L	I	-	1	0	IBTK	82960973	1.000000	0.71417	0.992000	0.48379	0.918000	0.54935	3.615000	0.54167	0.963000	0.38082	0.482000	0.46254	ATT	.	.	.	none		0.368	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525		G	82904254	T	G	82904254	3	3	54	1	0	0	0	0	1	0	0	0	7483	1406	49	5	809	5	IBTK	6	82904254	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08	30245311	82904254	88210813	33	3698											
KLHL32	114792	hgsc.bcm.edu	37	chr6	97562031	97562031	+	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	gtgagctggctcccatgcctGtgggaaggagccaccattgt	7	9	14	11	0	0	1	0	1	0	0	1	3	1	3	4	3	3	2	4	3	1	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr6:97562031G>T	ENST00000369261.4	+	7	1363	c.1000G>T	c.(1000-1002)Gtg>Ttg	p.V334L	KLHL32_ENST00000536676.1_Missense_Mutation_p.V298L|KLHL32_ENST00000539200.1_Missense_Mutation_p.V265L|KLHL32_ENST00000544166.1_Intron	NM_052904.3	NP_443136.2	Q96NJ5	KLH32_HUMAN	kelch-like family member 32	334										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)		TCCCATGCCTGTGGGAAGGAG	0.562																																					p.V334L		Atlas-SNP	.											.	KLHL32	85	.	0			c.G1000T						PASS	.						88	84	85					6																	97562031		2203	4300	6503	SO:0001583	missense	114792	exon7			ATGCCTGTGGGAA	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.1000G>T	chr6.hg19:g.97562031G>T	ENSP00000358265:p.Val334Leu	109.0	0.0	.		101.0	7.0	.	NM_052904	B7Z346|B7Z4E2|E1P528|Q5THT0|Q96PY7	Missense_Mutation	SNP	ENST00000369261.4	hg19	CCDS5038.1	.	.	.	.	.	.	.	.	.	.	G	15.16	2.750577	0.49257	.	.	ENSG00000186231	ENST00000369261;ENST00000536676;ENST00000539200	T;T;T	0.65916	-0.18;-0.18;-0.18	5.36	5.36	0.76844	Kelch-type beta propeller (1);	0.173711	0.52532	D	0.000077	T	0.48187	0.1486	M	0.64997	1.995	0.80722	D	1	B;B;B;B	0.11235	0.001;0.002;0.001;0.004	B;B;B;B	0.12156	0.001;0.003;0.004;0.007	T	0.48703	-0.9012	10	0.45353	T	0.12	.	14.5444	0.68017	0.0719:0.0:0.9281:0.0	.	265;298;334;334	B7Z4E2;B7Z346;Q96NJ5;Q6IQ08	.;.;KLH32_HUMAN;.	L	334;298;265	ENSP00000358265:V334L;ENSP00000440382:V298L;ENSP00000441527:V265L	ENSP00000358265:V334L	V	+	1	0	KLHL32	97668752	1.000000	0.71417	0.982000	0.44146	0.985000	0.73830	4.839000	0.62810	2.763000	0.94921	0.655000	0.94253	GTG	.	.	.	none		0.562	KLHL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041570.1	NM_052904		T	97562031	G	T	97562031	3	4	54	1	0	0	0	0	1	0	0	0	8393	1377	48	4	1022	4	KLHL32	6	97562031	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08	14657777	97562031	73553036	34	3699											
RGS17	26575	hgsc.bcm.edu	37	chr6	153332802	153332802	+	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	aaagaatctctgtgcattaaAgtatatatctgaagttgggc	14	13	9	5	0	2	2	0	1	2	1	3	2	2	2	0	1	1	3	0	1	8	5			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr6:153332802A>T	ENST00000367225.2	-	4	564	c.540T>A	c.(538-540)acT>acA	p.T180T	RGS17_ENST00000206262.1_Silent_p.T180T			Q9UGC6	RGS17_HUMAN	regulator of G-protein signaling 17	180	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			cervix(2)|endometrium(2)|large_intestine(4)|lung(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	14		Ovarian(120;0.126)		OV - Ovarian serous cystadenocarcinoma(155;1.09e-09)|BRCA - Breast invasive adenocarcinoma(81;0.0429)		TGTGCATTAAAGTATATATCT	0.353																																					p.T180T	Esophageal Squamous(78;500 1236 6775 24364 49058)	Atlas-SNP	.											.	RGS17	32	.	0			c.T540A						PASS	.						59	60	59					6																	153332802		2203	4300	6503	SO:0001819	synonymous_variant	26575	exon5			CATTAAAGTATAT	AF202257	CCDS5244.1	6q25-q26	2009-05-29	2007-08-14		ENSG00000091844	ENSG00000091844		"Regulators of G-protein signaling"	14088	protein-coding gene	gene with protein product		607191	"regulator of G-protein signalling 17"			10419452	Standard	NM_012419		Approved	RGSZ2, RGS-17	uc003qpm.3	Q9UGC6	OTTHUMG00000015858	ENST00000367225.2:c.540T>A	chr6.hg19:g.153332802A>T		38.0	0.0	.		44.0	10.0	.	NM_012419	Q5TF49|Q8TD61|Q9UJS8	Silent	SNP	ENST00000367225.2	hg19	CCDS5244.1																																																																																			.	.	.	none		0.353	RGS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042773.2			T	153332802	A	T	153332802	2	4	54	1	0	0	0	0	0	0	0	1	13312	59	3	5		5	RGS17	6	153332802	Silent	SNP	A	TCGA-A4-8310-01A-11D-2396-08	55770771	153332802	17782265	35	3700											
PPIA	5478	hgsc.bcm.edu	37	chr7	44839397	44839397	+	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	tcctaaagcatacgggtcctGgcatcttgtccatggcaaat	10	11	9	11	1	1	0	0	0	1	0	4	0	4	0	3	3	2	3	3	3	4	3			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr7:44839397G>T	ENST00000468812.1	+	4	331	c.286G>T	c.(286-288)Ggc>Tgc	p.G96C	PPIA_ENST00000355968.6_Missense_Mutation_p.G36C|PPIA_ENST00000480603.1_3'UTR|PPIA_ENST00000451562.1_Missense_Mutation_p.G96C|PPIA_ENST00000489459.1_Missense_Mutation_p.G36C	NM_021130.3	NP_066953.1	P62937	PPIA_HUMAN	peptidylprolyl isomerase A (cyclophilin A)	96	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				blood coagulation (GO:0007596)|entry into host cell (GO:0030260)|establishment of integrated proviral latency (GO:0075713)|leukocyte migration (GO:0050900)|lipid particle organization (GO:0034389)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of protein secretion (GO:0050714)|positive regulation of viral genome replication (GO:0045070)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|regulation of viral genome replication (GO:0045069)|RNA-dependent DNA replication (GO:0006278)|uncoating of virus (GO:0019061)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral release from host cell (GO:0019076)|virion assembly (GO:0019068)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	peptide binding (GO:0042277)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)|virion binding (GO:0046790)			breast(1)|endometrium(1)|lung(1)|urinary_tract(1)	4					Cyclosporine(DB00091)|L-Proline(DB00172)	TACGGGTCCTGGCATCTTGTC	0.483																																					p.G96C	Pancreas(95;605 727 734 1731 12572 23104 24406 38694 39103 44805)	Atlas-SNP	.											.	PPIA	10	.	0			c.G286T						PASS	.						85	81	82					7																	44839397		2203	4298	6501	SO:0001583	missense	5478	exon4			GGTCCTGGCATCT	X52851	CCDS5494.1, CCDS75592.1	7p13	2010-03-23			ENSG00000196262	ENSG00000196262	5.2.1.8		9253	protein-coding gene	gene with protein product		123840				1989998, 2197089	Standard	XM_005249791		Approved	CYPA	uc003tlw.3	P62937	OTTHUMG00000023687	ENST00000468812.1:c.286G>T	chr7.hg19:g.44839397G>T	ENSP00000419425:p.Gly96Cys	98.0	0.0	.		126.0	23.0	.	NM_021130	A8K220|P05092|Q3KQW3|Q567Q0|Q6IBU5|Q96IX3|Q9BRU4|Q9BTY9|Q9UC61	Missense_Mutation	SNP	ENST00000468812.1	hg19	CCDS5494.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.909500	0.92107	.	.	ENSG00000196262	ENST00000451562;ENST00000468812;ENST00000489459;ENST00000355968;ENST00000244636	T;T;T;T	0.50548	0.74;0.74;0.74;0.74	5.24	5.24	0.73138	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (4);Cyclophilin-like (1);	0.000000	0.85682	U	0.000000	D	0.83027	0.5165	H	0.99425	4.56	0.80722	D	1	D	0.67145	0.996	D	0.74348	0.983	D	0.90988	0.4833	10	0.87932	D	0	.	18.4613	0.90739	0.0:0.0:1.0:0.0	.	96	P62937	PPIA_HUMAN	C	96;96;36;36;36	ENSP00000405975:G96C;ENSP00000419425:G96C;ENSP00000427976:G36C;ENSP00000430817:G36C	ENSP00000442606:G36C	G	+	1	0	PPIA	44805922	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.601000	0.98297	2.449000	0.82847	0.563000	0.77884	GGC	.	.	.	none		0.483	PPIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251293.1	NM_021130		T	44839397	G	T	44839397	3	4	54	1	0	0	0	0	1	0	0	0	12323	1348	47	4	300	4	PPIA	7	44839397	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08		44839397	114299266	36	3701											
SLC7A2	6542	hgsc.bcm.edu	37	chr8	17419589	17419589	+	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	gttctcaccatctggaggcaGccccagaatcagcaaaaagt	13	7	9	12	0	3	1	2	0	2	1	4	2	3	2	3	2	2	3	3	2	3	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr8:17419589G>A	ENST00000494857.1	+	11	1859	c.1641G>A	c.(1639-1641)caG>caA	p.Q547Q	SLC7A2_ENST00000004531.10_Silent_p.Q587Q|SLC7A2_ENST00000522656.1_Silent_p.Q547Q|SLC7A2_ENST00000398090.3_Silent_p.Q586Q|SLC7A2_ENST00000470360.1_Silent_p.Q586Q	NM_001008539.3	NP_001008539.3	P52569	CTR2_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	547			Q -> L (in dbSNP:rs1981498).		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)	TCTGGAGGCAGCCCCAGAATC	0.468																																					p.Q587Q		Atlas-SNP	.											.	SLC7A2	157	.	0			c.G1761A						PASS	.						89	79	83					8																	17419589		2203	4300	6503	SO:0001819	synonymous_variant	6542	exon10			GAGGCAGCCCCAG	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.1641G>A	chr8.hg19:g.17419589G>A		76.0	0.0	.		67.0	32.0	.	NM_001164771	B7ZL54|O15291|O15292|Q14CQ6|Q6NSZ7|Q86TC6	Silent	SNP	ENST00000494857.1	hg19	CCDS34852.1																																																																																			.	.	.	none		0.468	SLC7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253367.3	NM_003046		A	17419589	G	A	17419589	2	1	54	1	0	0	0	0	0	0	0	1	14710	962	34	2		2	SLC7A2	8	17419589	Silent	SNP	G	TCGA-A4-8310-01A-11D-2396-08		17419589	128944433	37	3702											
KIAA0196	9897	hgsc.bcm.edu	37	chr8	126085409	126085409	+	Missense_Mutation	SNP	T	T	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	cattacctgagtctgctgtaTgaagcatcagccatcggatg	10	11	10	10	1	2	2	1	2	1	0	3	3	2	3	2	1	4	3	2	1	3	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr8:126085409T>G	ENST00000318410.7	-	9	1485	c.1136A>C	c.(1135-1137)cAt>cCt	p.H379P	KIAA0196_ENST00000517845.1_Missense_Mutation_p.H231P	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	379					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)			GTCTGCTGTATGAAGCATCAG	0.448																																					p.H379P		Atlas-SNP	.											.	KIAA0196	90	.	0			c.A1136C						PASS	.						117	101	106					8																	126085409		2203	4300	6503	SO:0001583	missense	9897	exon9			GCTGTATGAAGCA		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.1136A>C	chr8.hg19:g.126085409T>G	ENSP00000318016:p.His379Pro	82.0	0.0	.		90.0	39.0	.	NM_014846	A8K4R7|Q3KQX5|Q8TBQ2	Missense_Mutation	SNP	ENST00000318410.7	hg19	CCDS6355.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.178175	0.78564	.	.	ENSG00000164961	ENST00000318410;ENST00000517845	D;D	0.89552	-2.53;-2.53	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.95211	0.8447	M	0.87971	2.92	0.80722	D	1	D	0.67145	0.996	D	0.78314	0.991	D	0.95703	0.8751	10	0.87932	D	0	-28.8795	16.8222	0.85835	0.0:0.0:0.0:1.0	.	379	Q12768	STRUM_HUMAN	P	379;231	ENSP00000318016:H379P;ENSP00000429676:H231P	ENSP00000318016:H379P	H	-	2	0	KIAA0196	126154591	1.000000	0.71417	0.164000	0.22755	0.692000	0.40212	7.950000	0.87804	2.371000	0.80710	0.533000	0.62120	CAT	.	.	.	none		0.448	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846		G	126085409	T	G	126085409	3	3	54	1	0	0	0	0	1	0	0	0	8168	1464	51	5	2427	5	KIAA0196	8	126085409	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08	108665820	126085409	20278613	38	3703											
ADCY8	114	hgsc.bcm.edu	37	chr8	132052526	132052526	+	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	ccggccgggggcgtcgggtgGatggtgtagagttcctcgct	3	9	19	10	5	0	1	0	0	0	1	3	2	1	2	3	6	0	3	3	6	1	2	rs529228094	byFrequency	TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr8:132052526G>A	ENST00000286355.5	-	1	2146	c.54C>T	c.(52-54)atC>atT	p.I18I	ADCY8_ENST00000377928.3_Silent_p.I18I	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	18					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			GCGTCGGGTGGATGGTGTAGA	0.697										HNSCC(32;0.087)																											p.I18I		Atlas-SNP	.											.	ADCY8	291	.	0			c.C54T						PASS	.						5	6	5					8																	132052526		2067	4086	6153	SO:0001819	synonymous_variant	114	exon1			CGGGTGGATGGTG	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.54C>T	chr8.hg19:g.132052526G>A		10.0	0.0	.		7.0	4.0	.	NM_001115		Silent	SNP	ENST00000286355.5	hg19	CCDS6363.1																																																																																			.	.	.	none		0.697	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			A	132052526	G	A	132052526	2	1	54	1	0	0	0	0	0	0	0	1	300	1164	41	2		2	ADCY8	8	132052526	Silent	SNP	G	TCGA-A4-8310-01A-11D-2396-08	5967117	132052526	14311496	39	3704											
CYP11B1	1584	hgsc.bcm.edu	37	chr8	143957217	143957217	+	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	atgctggctgcggcggccagGctctcctggcgcagggcctg	3	7	17	14	3	1	0	0	0	1	0	2	0	1	0	3	6	2	4	3	6	0	0			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr8:143957217G>A	ENST00000292427.4	-	6	1064	c.1032C>T	c.(1030-1032)agC>agT	p.S344S	CYP11B1_ENST00000377675.3_Silent_p.S415S|CYP11B1_ENST00000517471.1_Silent_p.S344S	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1	344					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)	CGGCGGCCAGGCTCTCCTGGC	0.652									Familial Hyperaldosteronism type I																												p.S344S		Atlas-SNP	.											.	CYP11B1	128	.	0			c.C1032T						PASS	.						70	73	72					8																	143957217		2203	4300	6503	SO:0001819	synonymous_variant	1584	exon6	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	GGCCAGGCTCTCC	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.1032C>T	chr8.hg19:g.143957217G>A		267.0	0.0	.		169.0	70.0	.	NM_000497	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Silent	SNP	ENST00000292427.4	hg19	CCDS6392.1																																																																																			.	.	.	none		0.652	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379475.2			A	143957217	G	A	143957217	2	1	54	1	0	0	0	0	0	0	0	1	4147	1194	42	2		2	CYP11B1	8	143957217	Silent	SNP	G	TCGA-A4-8310-01A-11D-2396-08	11904691	143957217	2406805	40	3705											
NFX1	4799	hgsc.bcm.edu	37	chr9	33307212	33307212	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaaggtaaagaatcctgagTggagcagaaatgaaattcca	17	7	11	6	0	0	4	0	2	0	2	2	5	2	5	2	2	1	3	2	2	6	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr9:33307212T>C	ENST00000379540.3	+	5	1353	c.1291T>C	c.(1291-1293)Tgg>Cgg	p.W431R	NFX1_ENST00000379521.4_Missense_Mutation_p.W431R|NFX1_ENST00000318524.6_Missense_Mutation_p.W431R	NM_002504.4	NP_002495.2	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1	431					inflammatory response (GO:0006954)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)		GAATCCTGAGTGGAGCAGAAA	0.413																																					p.W431R		Atlas-SNP	.											.	NFX1	85	.	0			c.T1291C						PASS	.						148	147	147					9																	33307212		2203	4300	6503	SO:0001583	missense	4799	exon5			CCTGAGTGGAGCA	U19759	CCDS6538.1, CCDS6539.1, CCDS6540.1	9p12	2013-12-13			ENSG00000086102	ENSG00000086102			7803	protein-coding gene	gene with protein product		603255				7964459, 2511169	Standard	NM_002504		Approved	NFX2, MGC20369, Tex42, TEG-42	uc003zsq.3	Q12986	OTTHUMG00000019772	ENST00000379540.3:c.1291T>C	chr9.hg19:g.33307212T>C	ENSP00000368856:p.Trp431Arg	117.0	0.0	.		143.0	6.0	.	NM_147134	A8K6H8|Q5VXW6|Q96EL5|Q9BXI1	Missense_Mutation	SNP	ENST00000379540.3	hg19	CCDS6538.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.223848	0.79576	.	.	ENSG00000086102	ENST00000379540;ENST00000379521;ENST00000536210;ENST00000318524	T;T;T	0.12879	2.64;2.64;2.64	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.28532	0.0706	L	0.48642	1.525	0.58432	D	0.999999	D;D;P;D;B	0.76494	0.999;0.998;0.459;0.997;0.39	D;D;B;D;B	0.71414	0.973;0.926;0.218;0.966;0.176	T	0.00975	-1.1494	10	0.33940	T	0.23	-5.1452	13.5049	0.61479	0.0:0.0:0.0:1.0	.	431;315;431;431;431	F5GXD0;A0JLR2;Q12986;Q12986-2;Q12986-3	.;.;NFX1_HUMAN;.;.	R	431	ENSP00000368856:W431R;ENSP00000368836:W431R;ENSP00000317695:W431R	ENSP00000317695:W431R	W	+	1	0	NFX1	33297212	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.751000	0.85126	2.092000	0.63282	0.477000	0.44152	TGG	.	.	.	none		0.413	NFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052069.1			C	33307212	T	C	33307212	3	2	54	1	0	0	0	0	1	0	0	0	10394	1696	59	3	1309	3	NFX1	9	33307212	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08		33307212	107906219	41	3706											
HNRNPK	3190	hgsc.bcm.edu	37	chr9	86587099	86587099	+	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	ggctgtgcacgtcctttgatGggagactaaaaacagagatg	12	9	13	7	1	0	3	0	1	0	2	1	5	1	3	1	2	2	2	1	2	3	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr9:86587099G>T	ENST00000376264.2	-	11	909	c.651C>A	c.(649-651)ccC>ccA	p.P217P	HNRNPK_ENST00000376263.3_Silent_p.P217P|HNRNPK_ENST00000351839.3_Silent_p.P217P|HNRNPK_ENST00000376281.4_Silent_p.P217P|MIR7-1_ENST00000384871.1_RNA|HNRNPK_ENST00000360384.5_Silent_p.P217P|RP11-575L7.8_ENST00000448389.1_RNA	NM_002140.3|NM_031262.2	NP_002131.2|NP_112552.1	P61978	HNRPK_HUMAN	heterogeneous nuclear ribonucleoprotein K	217	2 X 22 AA approximate repeats.|5 X 4 AA repeats of G-X-G-G.|Interaction with ZIK1. {ECO:0000250}.|Necessary for interaction with DDX1.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter (GO:0072369)|regulation of low-density lipoprotein particle clearance (GO:0010988)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|single-stranded DNA binding (GO:0003697)			endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|stomach(1)	19						GTCCTTTGATGGGAGACTAAA	0.403																																					p.P217P		Atlas-SNP	.											.	HNRNPK	49	.	0			c.C651A						PASS	.						48	47	48					9																	86587099		2203	4300	6503	SO:0001819	synonymous_variant	3190	exon11			TTTGATGGGAGAC		CCDS6667.1, CCDS6668.1	9q21.32-q21.33	2011-10-24		2008-04-18	ENSG00000165119	ENSG00000165119			5044	protein-coding gene	gene with protein product	"transformation upregulated nuclear protein"	600712		HNRPK		8107114	Standard	NM_031263		Approved	CSBP, TUNP	uc004anf.4	P61978	OTTHUMG00000020107	ENST00000376264.2:c.651C>A	chr9.hg19:g.86587099G>T		60.0	0.0	.		75.0	35.0	.	NM_031262	Q07244|Q15671|Q59F98|Q5T6W4|Q60577|Q922Y7|Q96J62	Silent	SNP	ENST00000376264.2	hg19	CCDS6667.1																																																																																			.	.	.	none		0.403	HNRNPK-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052846.2			T	86587099	G	T	86587099	2	4	54	1	0	0	0	0	0	0	0	1	7276	1335	47	4		4	HNRNPK	9	86587099	Silent	SNP	G	TCGA-A4-8310-01A-11D-2396-08	53279887	86587099	54626332	42	3707											
CUBN	8029	hgsc.bcm.edu	37	chr10	17157562	17157562	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcgtcatatttggatgcacActggggtccgtacgtctcag	7	12	12	10	3	2	0	2	0	1	0	5	1	3	1	1	3	2	2	1	3	2	3			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr10:17157562A>G	ENST00000377833.4	-	7	693	c.628T>C	c.(628-630)Tgt>Cgt	p.C210R		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	210	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TTGGATGCACACTGGGGTCCG	0.542																																					p.C210R		Atlas-SNP	.											.	CUBN	515	.	0			c.T628C						PASS	.						147	123	131					10																	17157562		2203	4300	6503	SO:0001583	missense	8029	exon7			ATGCACACTGGGG	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.628T>C	chr10.hg19:g.17157562A>G	ENSP00000367064:p.Cys210Arg	92.0	0.0	.		110.0	37.0	.	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	A	16.02	3.003508	0.54254	.	.	ENSG00000107611	ENST00000377833	D	0.91521	-2.86	5.75	5.75	0.90469	EGF-like region, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.50627	D	0.000104	D	0.97362	0.9137	H	0.98276	4.19	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98939	1.0790	10	0.87932	D	0	.	15.7034	0.77558	1.0:0.0:0.0:0.0	.	210	O60494	CUBN_HUMAN	R	210	ENSP00000367064:C210R	ENSP00000367064:C210R	C	-	1	0	CUBN	17197568	1.000000	0.71417	1.000000	0.80357	0.059000	0.15707	7.574000	0.82434	2.197000	0.70478	0.533000	0.62120	TGT	.	.	.	none		0.542	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		G	17157562	A	G	17157562	3	3	54	1	0	0	0	0	1	0	0	0	4053	159	6	3	10487	3	CUBN	10	17157562	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08		17157562	118377185	43	3708											
HECTD2	143279	hgsc.bcm.edu	37	chr10	93252242	93252243	+	Splice_Site	INS	-	-	T																															atttttcatccagattatggINStaagtatgtaatctaatttt																										TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr10:93252242_93252243insT	ENST00000298068.5	+	13	1526		c.e13+1		HECTD2_ENST00000371667.1_Splice_Site|HECTD2_ENST00000536715.1_Splice_Site|HECTD2_ENST00000446394.1_Splice_Site	NM_182765.3	NP_877497	Q5U5R9	HECD2_HUMAN	HECT domain containing E3 ubiquitin protein ligase 2						protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|endometrium(2)|kidney(4)|large_intestine(10)|lung(7)|skin(1)|urinary_tract(1)	27						CCAGATTATGGTAAGTATGTAA	0.312																																					.	NSCLC(12;376 469 1699 39910 41417)	Atlas-INDEL	.											.	HECTD2	60	.	0			c.1432+1->T						PASS	.																																			SO:0001630	splice_region_variant	143279	exon13			.	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.1432+1->T	chr10.hg19:g.93252243_93252243dupT		33.0	0.0	0		38.0	14.0	0.368421	NM_182765	Q5VZ97|Q5VZ98|Q5VZ99|Q8N1X7|Q8TCP5	Splice_Site	INS	ENST00000298068.5	hg19	CCDS7414.1																																																																																			.	.	.	none		0.312	HECTD2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098620.1		Intron	T	93252243	-	T	93252242	8	5	54	1	0	1	1	0	0	0	1	0	7047	1275	44	0	1507	0	HECTD2	10	93252242	Splice_Site	INS	-	TCGA-A4-8310-01A-11D-2396-08	76094680	93252242	42282505	44	3709											
IDE	3416	hgsc.bcm.edu	37	chr10	94239044	94239044	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggtacttacatacatcccaTagatggtattttggagatca	12	13	9	7	0	1	2	1	0	0	2	2	3	2	2	1	3	3	2	1	3	5	7			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr10:94239044T>C	ENST00000265986.6	-	15	1930	c.1874A>G	c.(1873-1875)tAt>tGt	p.Y625C	IDE_ENST00000371581.5_Missense_Mutation_p.Y70C|IDE_ENST00000496903.1_Intron	NM_004969.3	NP_004960.2	P14735	IDE_HUMAN	insulin-degrading enzyme	625					beta-amyloid metabolic process (GO:0050435)|bradykinin catabolic process (GO:0010815)|determination of adult lifespan (GO:0008340)|hormone catabolic process (GO:0042447)|insulin catabolic process (GO:1901143)|insulin metabolic process (GO:1901142)|insulin receptor signaling pathway (GO:0008286)|negative regulation of proteolysis (GO:0045861)|positive regulation of protein oligomerization (GO:0032461)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|ubiquitin homeostasis (GO:0010992)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|beta-amyloid binding (GO:0001540)|beta-endorphin binding (GO:0031626)|glycoprotein binding (GO:0001948)|insulin binding (GO:0043559)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|urinary_tract(2)	33					"""Insulin(DB00071)|Bacitracin(DB00626)|Insulin Regular(DB00030)"	ATACATCCCATAGATGGTATT	0.408																																					p.Y625C		Atlas-SNP	.											.	IDE	77	.	0			c.A1874G						PASS	.						172	149	157					10																	94239044		2203	4300	6503	SO:0001583	missense	3416	exon15			ATCCCATAGATGG	M21188	CCDS7421.1, CCDS53554.1	10q23-q25	2007-03-27			ENSG00000119912	ENSG00000119912			5381	protein-coding gene	gene with protein product	"insulysin"	146680				2293021	Standard	NM_004969		Approved		uc001kia.3	P14735	OTTHUMG00000018759	ENST00000265986.6:c.1874A>G	chr10.hg19:g.94239044T>C	ENSP00000265986:p.Tyr625Cys	117.0	0.0	.		140.0	57.0	.	NM_004969	B2R721|B7ZAU2|D3DR35|Q5T5N2	Missense_Mutation	SNP	ENST00000265986.6	hg19	CCDS7421.1	.	.	.	.	.	.	.	.	.	.	T	14.39	2.522510	0.44866	.	.	ENSG00000119912	ENST00000265986;ENST00000371581	T;T	0.40756	1.02;1.02	5.64	5.64	0.86602	Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.140820	0.49305	D	0.000142	T	0.40956	0.1138	M	0.64170	1.965	0.80722	D	1	P	0.38370	0.628	B	0.33890	0.172	T	0.34601	-0.9822	10	0.38643	T	0.18	-12.9568	15.5248	0.75894	0.0:0.0:0.0:1.0	.	625	P14735	IDE_HUMAN	C	625;70	ENSP00000265986:Y625C;ENSP00000360637:Y70C	ENSP00000265986:Y625C	Y	-	2	0	IDE	94229024	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.152000	0.67230	0.533000	0.62120	TAT	.	.	.	none		0.408	IDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049393.1	NM_004969		C	94239044	T	C	94239044	3	2	54	1	0	0	0	0	1	0	0	0	7500	1406	49	3	1229	3	IDE	10	94239044	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08	986802	94239044	41295703	45	3710											
SLC22A8	9376	hgsc.bcm.edu	37	chr11	62782340	62782340	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcaggttgtggttggccaTgttgaggatcgggaggccca	7	9	17	8	1	0	1	0	1	0	0	1	3	0	3	2	6	1	4	2	6	0	3			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr11:62782340T>C	ENST00000336232.2	-	2	226	c.91A>G	c.(91-93)Atg>Gtg	p.M31V	SLC22A8_ENST00000535878.1_Intron|SLC22A8_ENST00000311438.8_Missense_Mutation_p.M31V|SLC22A8_ENST00000430500.2_Missense_Mutation_p.M31V|SLC22A8_ENST00000545207.1_Intron	NM_001184732.1|NM_001184736.1|NM_004254.3	NP_001171661.1|NP_001171665.1|NP_004245.2	Q8TCC7	S22A8_HUMAN	solute carrier family 22 (organic anion transporter), member 8	31					glutathione transport (GO:0034635)|response to methotrexate (GO:0031427)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|quaternary ammonium group transmembrane transporter activity (GO:0015651)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	28					Aciclovir(DB00787)|Adefovir Dipivoxil(DB00718)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Aspartame(DB00168)|Baclofen(DB00181)|Benzylpenicillin(DB01053)|Bumetanide(DB00887)|Cefacetrile(DB01414)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Ceftriaxone(DB01212)|Cephalexin(DB00567)|Cilastatin(DB01597)|Cimetidine(DB00501)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Enalapril(DB00584)|Estradiol(DB00783)|Famotidine(DB00927)|Furosemide(DB00695)|Ganciclovir(DB01004)|Guanidine(DB00536)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|L-Carnitine(DB00583)|Liothyronine(DB00279)|Liotrix(DB01583)|Melatonin(DB01065)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Methyltestosterone(DB06710)|Minocycline(DB01017)|Novobiocin(DB01051)|Oseltamivir(DB00198)|Ouabain(DB01092)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Ranitidine(DB00863)|Salicylic acid(DB00936)|Saxagliptin(DB06335)|Succinic acid(DB00139)|Tenofovir(DB00300)|Tenoxicam(DB00469)|Testosterone(DB00624)|Tetracycline(DB00759)|Valaciclovir(DB00577)|Valproic Acid(DB00313)|Zidovudine(DB00495)	TGGTTGGCCATGTTGAGGATC	0.617																																					p.M31V		Atlas-SNP	.											.	SLC22A8	60	.	0			c.A91G						PASS	.						183	179	181					11																	62782340		2201	4298	6499	SO:0001583	missense	9376	exon2			TGGCCATGTTGAG	AF097491, BC022387	CCDS8042.1, CCDS53643.1, CCDS53644.1	11q12.3	2013-05-22			ENSG00000149452	ENSG00000149452		"Solute carriers"	10972	protein-coding gene	gene with protein product		607581				10049739	Standard	NM_004254		Approved	OAT3	uc001nwo.3	Q8TCC7	OTTHUMG00000167768	ENST00000336232.2:c.91A>G	chr11.hg19:g.62782340T>C	ENSP00000337335:p.Met31Val	289.0	0.0	.		256.0	85.0	.	NM_001184732	B4DPH7|F5GWA8|F5H5J1|O95820|Q59EW9|Q96TC1	Missense_Mutation	SNP	ENST00000336232.2	hg19	CCDS8042.1	.	.	.	.	.	.	.	.	.	.	T	12.68	2.009360	0.35415	.	.	ENSG00000149452	ENST00000336232;ENST00000540631;ENST00000311438;ENST00000430500	T;T;T	0.53206	0.63;0.63;0.63	4.76	2.38	0.29361	.	0.446155	0.25666	N	0.029103	T	0.26484	0.0647	N	0.21282	0.65	0.24143	N	0.995726	B;B	0.18968	0.032;0.01	B;B	0.21917	0.037;0.016	T	0.23726	-1.0180	10	0.08381	T	0.77	.	6.2794	0.20999	0.153:0.0:0.1774:0.6696	.	31;31	Q8TCC7-2;Q8TCC7	.;S22A8_HUMAN	V	31	ENSP00000337335:M31V;ENSP00000311463:M31V;ENSP00000398548:M31V	ENSP00000311463:M31V	M	-	1	0	SLC22A8	62538916	0.007000	0.16637	0.736000	0.30914	0.989000	0.77384	0.313000	0.19415	0.303000	0.22785	0.533000	0.62120	ATG	.	.	.	none		0.617	SLC22A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396191.1	NM_004254		C	62782340	T	C	62782340	3	2	54	1	0	0	0	0	1	0	0	0	14473	1464	51	3	1577	3	SLC22A8	11	62782340	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08		62782340	72224176	46	3711											
PITPNM1	9600	hgsc.bcm.edu	37	chr11	67263727	67263727	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggcgatggcctggaactTcggggccagcaggggctcga	6	6	19	10	3	0	0	0	0	0	0	2	3	0	1	2	8	2	2	2	8	1	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr11:67263727T>C	ENST00000534749.1	-	14	2427	c.2239A>G	c.(2239-2241)Aag>Gag	p.K747E	PITPNM1_ENST00000526450.1_5'Flank|PITPNM1_ENST00000356404.3_Missense_Mutation_p.K747E|PITPNM1_ENST00000436757.2_Missense_Mutation_p.K746E			O00562	PITM1_HUMAN	phosphatidylinositol transfer protein, membrane-associated 1	747	DDHD. {ECO:0000255|PROSITE- ProRule:PRU00378}.				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						GCCTGGAACTTCGGGGCCAGC	0.642																																					p.K747E	GBM(28;144 709 4607 5525)	Atlas-SNP	.											.	PITPNM1	84	.	0			c.A2239G						PASS	.						41	42	42					11																	67263727		2200	4294	6494	SO:0001583	missense	9600	exon15			GGAACTTCGGGGC	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.2239A>G	chr11.hg19:g.67263727T>C	ENSP00000437286:p.Lys747Glu	110.0	0.0	.		73.0	36.0	.	NM_004910	A6NME4|Q6T7X3|Q8TBN3|Q9BZ73	Missense_Mutation	SNP	ENST00000534749.1	hg19	CCDS31620.1	.	.	.	.	.	.	.	.	.	.	T	11.84	1.758047	0.31137	.	.	ENSG00000110697	ENST00000534749;ENST00000436757;ENST00000356404	T;T;T	0.39787	1.06;1.06;1.06	4.43	3.29	0.37713	DDHD (2);	0.329601	0.26757	N	0.022648	T	0.26195	0.0639	N	0.13235	0.315	0.28852	N	0.896001	P;P	0.36712	0.51;0.566	B;B	0.40702	0.228;0.338	T	0.10086	-1.0645	10	0.46703	T	0.11	-28.7945	6.0013	0.19521	0.0:0.089:0.1682:0.7428	.	746;747	O00562-2;O00562	.;PITM1_HUMAN	E	747;746;747	ENSP00000437286:K747E;ENSP00000398787:K746E;ENSP00000348772:K747E	ENSP00000348772:K747E	K	-	1	0	PITPNM1	67020303	0.737000	0.28175	1.000000	0.80357	0.378000	0.30076	0.802000	0.27069	0.837000	0.34925	-0.429000	0.05907	AAG	.	.	.	none		0.642	PITPNM1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395520.1	NM_004910		C	67263727	T	C	67263727	3	2	54	1	0	0	0	0	1	0	0	0	11957	1792	62	3	1535	3	PITPNM1	11	67263727	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08	4481387	67263727	67742789	47	3712											
ALG9	79796	hgsc.bcm.edu	37	chr11	111715419	111715419	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgaaattcagaaatccattaAttaaatagaaataccagggt	19	11	6	5	0	1	3	1	1	0	2	2	3	2	3	2	1	1	0	2	1	8	5			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr11:111715419A>G	ENST00000531154.1	-	9	882	c.410T>C	c.(409-411)aTt>aCt	p.I137T	ALG9_ENST00000398006.2_Missense_Mutation_p.I137T|ALG9_ENST00000527228.1_5'UTR|ALG9_ENST00000524880.1_3'UTR	NM_024740.2	NP_079016.2	Q9H6U8	ALG9_HUMAN	ALG9, alpha-1,2-mannosyltransferase	308					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)		AAATCCATTAATTAAATAGAA	0.393																																					p.I308T		Atlas-SNP	.											.	ALG9	77	.	0			c.T923C						PASS	.						91	86	88					11																	111715419		1836	4091	5927	SO:0001583	missense	79796	exon10			CCATTAATTAAAT		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.410T>C	chr11.hg19:g.111715419A>G	ENSP00000435517:p.Ile137Thr	80.0	0.0	.		83.0	38.0	.	NM_001077690	Q6ZMD5|Q7Z4R4|Q96GS7|Q96PB9|Q9H068	Missense_Mutation	SNP	ENST00000531154.1	hg19	CCDS41714.1	.	.	.	.	.	.	.	.	.	.	A	16.28	3.077619	0.55753	.	.	ENSG00000086848	ENST00000531154;ENST00000398006;ENST00000428306	T;T	0.63417	-0.04;-0.04	5.69	5.69	0.88448	.	0.149147	0.64402	D	0.000012	T	0.67878	0.2940	L	0.60455	1.87	0.51767	D	0.999935	P;B;B;P	0.41080	0.549;0.068;0.055;0.737	B;B;B;P	0.49301	0.272;0.068;0.076;0.606	T	0.63782	-0.6559	10	0.22109	T	0.4	-13.3791	15.9548	0.79880	1.0:0.0:0.0:0.0	.	137;308;541;308	B4DQI3;Q9H6U8-3;B4DYW0;Q9H6U8	.;.;.;ALG9_HUMAN	T	137;137;541	ENSP00000435517:I137T;ENSP00000381090:I137T	ENSP00000381090:I137T	I	-	2	0	ALG9	111220629	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.161000	0.77505	2.171000	0.68590	0.528000	0.53228	ATT	.	.	.	none		0.393	ALG9-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000391485.1	NM_024740		G	111715419	A	G	111715419	3	3	54	1	0	0	0	0	1	0	0	0	524	101	4	3	961	3	ALG9	11	111715419	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	44451692	111715419	23291097	48	3713											
NCAPD2	9918	hgsc.bcm.edu	37	chr12	6638743	6638743	+	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	tggtggaaaagctgtgtcagCggttccgcacatcccggtat	8	10	13	10	3	1	0	1	0	0	0	3	1	3	1	2	4	2	4	2	4	3	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr12:6638743C>A	ENST00000315579.5	+	28	4436	c.3637C>A	c.(3637-3639)Cgg>Agg	p.R1213R	RP5-940J5.3_ENST00000537921.1_RNA|NCAPD2_ENST00000545962.1_Silent_p.R1168R	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	1213					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						GCTGTGTCAGCGGTTCCGCAC	0.602																																					p.R1213R		Atlas-SNP	.											.	NCAPD2	99	.	0			c.C3637A						PASS	.						95	82	86					12																	6638743		2203	4300	6503	SO:0001819	synonymous_variant	9918	exon28			TGTCAGCGGTTCC	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.3637C>A	chr12.hg19:g.6638743C>A		116.0	0.0	.		114.0	20.0	.	NM_014865	D3DUR4|Q8N6U3	Silent	SNP	ENST00000315579.5	hg19	CCDS8548.1																																																																																			.	.	.	none		0.602	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865		A	6638743	C	A	6638743	2	1	54	1	0	0	0	0	0	0	0	1	10212	759	27	4		4	NCAPD2	12	6638743	Silent	SNP	C	TCGA-A4-8310-01A-11D-2396-08		6638743	127213152	49	3714											
ESD	2098	hgsc.bcm.edu	37	chr13	47345616	47345616	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaggttgcaatgaagtagtAgctatgatcataaccctaga	16	10	9	6	0	1	3	1	2	0	1	1	3	1	3	1	1	3	5	1	1	8	6			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr13:47345616A>G	ENST00000378720.3	-	10	966	c.784T>C	c.(784-786)Tac>Cac	p.Y262H	ESD_ENST00000378697.1_Missense_Mutation_p.Y233H	NM_001984.1	NP_001975.1	P10768	ESTD_HUMAN	esterase D	262					formaldehyde catabolic process (GO:0046294)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carboxylic ester hydrolase activity (GO:0052689)|hydrolase activity, acting on ester bonds (GO:0016788)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)|S-formylglutathione hydrolase activity (GO:0018738)			endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)	9		all_lung(13;3.54e-08)|Lung NSC(96;9.1e-06)|Breast(56;0.000148)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)		GBM - Glioblastoma multiforme(144;2.66e-05)	Glutathione(DB00143)	ATGAAGTAGTAGCTATGATCA	0.328																																					p.Y262H		Atlas-SNP	.											.	ESD	23	.	0			c.T784C						PASS	.						152	154	153					13																	47345616		2203	4296	6499	SO:0001583	missense	2098	exon10			AGTAGTAGCTATG	M13450	CCDS9404.1	13q14.1-q14.2	2014-05-13	2010-05-07		ENSG00000139684	ENSG00000139684	3.1.2.12		3465	protein-coding gene	gene with protein product	"S-formylglutathione hydrolase"	133280	"esterase D/formylglutathione hydrolase"				Standard	NM_001984		Approved		uc001vbn.3	P10768	OTTHUMG00000016878	ENST00000378720.3:c.784T>C	chr13.hg19:g.47345616A>G	ENSP00000367992:p.Tyr262His	52.0	0.0	.		83.0	21.0	.	NM_001984	Q5TBU8|Q5TBV0|Q5TBV2|Q9BVJ2	Missense_Mutation	SNP	ENST00000378720.3	hg19	CCDS9404.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.686182	0.88639	.	.	ENSG00000139684	ENST00000378720;ENST00000378697	T;T	0.37584	1.19;1.19	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.72104	0.3419	H	0.95539	3.685	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81052	-0.1107	10	0.87932	D	0	-15.2421	16.0034	0.80327	1.0:0.0:0.0:0.0	.	262	P10768	ESTD_HUMAN	H	262;233	ENSP00000367992:Y262H;ENSP00000367969:Y233H	ENSP00000367969:Y233H	Y	-	1	0	ESD	46243617	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.060000	0.93907	2.371000	0.80710	0.533000	0.62120	TAC	.	.	.	none		0.328	ESD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044826.1			G	47345616	A	G	47345616	3	3	54	1	0	0	0	0	1	0	0	0	5252	420	15	3	68	3	ESD	13	47345616	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08		47345616	67824262	50	3715											
ATP7B	540	hgsc.bcm.edu	37	chr13	52511445	52511445	+	Missense_Mutation	SNP	T	T	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	tatcccaaccaggttataaaTcagtgccaggaccaggttga	13	9	9	10	0	1	1	1	1	0	0	2	2	2	2	4	3	2	2	4	3	5	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr13:52511445T>G	ENST00000242839.4	-	19	4144	c.3988A>C	c.(3988-3990)Att>Ctt	p.I1330L	ATP7B_ENST00000344297.5_Missense_Mutation_p.I1123L|ATP7B_ENST00000400366.3_Missense_Mutation_p.I1219L|ATP7B_ENST00000418097.2_Missense_Mutation_p.I1265L|ATP7B_ENST00000400370.3_Missense_Mutation_p.I900L|ATP7B_ENST00000417240.2_Missense_Mutation_p.I541L|ATP7B_ENST00000448424.2_Missense_Mutation_p.I1252L	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	1330					cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	AGGTTATAAATCAGTGCCAGG	0.532									Wilson disease																												p.I1330L		Atlas-SNP	.											.	ATP7B	123	.	0			c.A3988C						PASS	.						104	109	107					13																	52511445		2043	4195	6238	SO:0001583	missense	540	exon19	Familial Cancer Database		TATAAATCAGTGC	U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"ATPases / P-type"	870	protein-coding gene	gene with protein product	"Wilson disease", "copper pump 2", "copper-transporting ATPase 2"	606882	"ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.3988A>C	chr13.hg19:g.52511445T>G	ENSP00000242839:p.Ile1330Leu	83.0	0.0	.		76.0	33.0	.	NM_000053	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Missense_Mutation	SNP	ENST00000242839.4	hg19	CCDS41892.1	.	.	.	.	.	.	.	.	.	.	T	17.72	3.459608	0.63401	.	.	ENSG00000123191	ENST00000242839;ENST00000400366;ENST00000344297;ENST00000417240;ENST00000448424;ENST00000400370;ENST00000418097	D;D;D;D;D;D;D	0.99158	-5.5;-5.5;-5.5;-2.36;-5.5;-5.5;-5.5	5.34	5.34	0.76211	HAD-like domain (1);	0.000000	0.85682	D	0.000000	D	0.98689	0.9560	L	0.42008	1.315	0.80722	D	1	D;B;D;B;D;P;D;D	0.56521	0.974;0.191;0.976;0.447;0.976;0.678;0.976;0.974	D;B;P;B;P;P;P;P	0.66716	0.946;0.145;0.741;0.285;0.741;0.646;0.741;0.677	D	0.99474	1.0946	10	0.40728	T	0.16	-22.351	15.6255	0.76851	0.0:0.0:0.0:1.0	.	1252;1282;1265;541;900;1219;1123;1330	E7ET55;B7ZLR4;F5H748;E7EQQ2;F5H562;P35670-3;P35670-2;P35670	.;.;.;.;.;.;.;ATP7B_HUMAN	L	1330;1219;1123;541;1252;900;1265	ENSP00000242839:I1330L;ENSP00000383217:I1219L;ENSP00000342559:I1123L;ENSP00000390360:I541L;ENSP00000416738:I1252L;ENSP00000383221:I900L;ENSP00000393343:I1265L	ENSP00000242839:I1330L	I	-	1	0	ATP7B	51409446	1.000000	0.71417	0.983000	0.44433	0.966000	0.64601	6.243000	0.72384	2.144000	0.66660	0.533000	0.62120	ATT	.	.	.	none		0.532	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053		G	52511445	T	G	52511445	3	3	54	1	0	0	0	0	1	0	0	0	1191	1435	50	5	421	5	ATP7B	13	52511445	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08	5165829	52511445	62658433	51	3716											
STK24	8428	hgsc.bcm.edu	37	chr13	99114124	99114125	+	Frame_Shift_Ins	INS	-	-	C																															tccagtccccagaatcactgINSccccccgaggcttggccatc																										TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr13:99114124_99114125insC	ENST00000376547.3	-	8	1137_1138	c.992_993insG	c.(991-993)ggcfs	p.G331fs	STK24_ENST00000397517.2_Frame_Shift_Ins_p.G319fs|STK24_ENST00000539966.1_Frame_Shift_Ins_p.G300fs	NM_003576.3	NP_003567.2	Q9Y6E0	STK24_HUMAN	serine/threonine kinase 24	331					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of cell migration (GO:0030336)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of axon regeneration (GO:0048679)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	17	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			CAGAATCACTGCCCCCCGAGGC	0.535																																					p.G331fs		Atlas-INDEL	.											.,1	STK24	40	.	0			c.993_994insG						PASS	.																																			SO:0001589	frameshift_variant	8428	exon8			.	AF024636	CCDS9488.1, CCDS32001.1, CCDS66573.1	13q31.2-q32.3	2010-06-25	2010-06-25		ENSG00000102572	ENSG00000102572			11403	protein-coding gene	gene with protein product	"STE20-like kinase 3", "sterile 20-like kinase 3"	604984	"serine/threonine kinase 24 (Ste20, yeast homolog)"			9353338, 10644707	Standard	NM_003576		Approved	MST-3, MST3, MST3B, STK3, STE20	uc001vnn.1	Q9Y6E0	OTTHUMG00000017250	ENST00000376547.3:c.993dupG	chr13.hg19:g.99114130_99114130dupC	ENSP00000365730:p.Gly331fs	103.0	0.0	0		113.0	41.0	0.362832	NM_003576	O14840|Q5JV92	Frame_Shift_Ins	INS	ENST00000376547.3	hg19	CCDS9488.1																																																																																			.	.	.	none		0.535	STK24-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045549.2	NM_003576		C	99114125	-	C	99114124	7	5	54	1	0	1	1	0	0	0	0	0	15305	1306	46	0	354	0	STK24	13	99114124	Frame_Shift_Ins	INS	-	TCGA-A4-8310-01A-11D-2396-08	46602679	99114124	16055754	52	3717											
SERPINA10	51156	hgsc.bcm.edu	37	chr14	94756790	94756790	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctgctcatcttcctcttcCtccttgggagcctgcactac	4	14	6	17	0	3	0	1	0	2	0	7	1	7	1	5	1	4	2	5	1	1	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr14:94756790C>T	ENST00000393096.1	-	2	606	c.141G>A	c.(139-141)gaG>gaA	p.E47E	SERPINA10_ENST00000554723.1_Silent_p.E87E|SERPINA10_ENST00000554173.1_Silent_p.E47E|SERPINA10_ENST00000261994.4_Silent_p.E47E	NM_016186.2	NP_057270.1	Q9UK55	ZPI_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10	47					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)		CTTCCTCTTCCTCCTTGGGAG	0.622																																					p.E47E		Atlas-SNP	.											.	SERPINA10	83	.	0			c.G141A						PASS	.						39	38	38					14																	94756790		2203	4300	6503	SO:0001819	synonymous_variant	51156	exon2			CTCTTCCTCCTTG	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.141G>A	chr14.hg19:g.94756790C>T		54.0	0.0	.		33.0	13.0	.	NM_001100607	A5Z2A5|Q6UWX9|Q86U20	Silent	SNP	ENST00000393096.1	hg19	CCDS9923.1																																																																																			.	.	.	none		0.622	SERPINA10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413061.1	NM_016186		T	94756790	C	T	94756790	2	4	54	1	0	0	0	0	0	0	0	1	14100	680	24	2		2	SERPINA10	14	94756790	Silent	SNP	C	TCGA-A4-8310-01A-11D-2396-08		94756790	12592750	53	3718											
RORA	6095	hgsc.bcm.edu	37	chr15	60849084	60849084	+	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	cagtttgtacttccttatctTccttttgtgaatatggtggc	6	19	8	8	0	1	1	0	1	1	0	3	1	3	1	2	2	1	2	2	2	4	8			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr15:60849084T>C	ENST00000335670.6	-	3	297				RORA_ENST00000449337.2_Intron|RP11-219B17.1_ENST00000558235.1_RNA|RORA_ENST00000560004.1_Intron|RP11-219B17.1_ENST00000559824.1_RNA|RORA_ENST00000309157.4_Intron|RORA_ENST00000261523.5_Missense_Mutation_p.E88G	NM_134261.2	NP_599023.1	P35398	RORA_HUMAN	RAR-related orphan receptor A						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						TTCCTTATCTTCCTTTTGTGA	0.403																																					p.E88G		Atlas-SNP	.											.	RORA	114	.	0			c.A263G						PASS	.						325	278	294					15																	60849084		2203	4300	6503	SO:0001627	intron_variant	6095	exon3			TTATCTTCCTTTT	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.197-25034A>G	chr15.hg19:g.60849084T>C		129.0	0.0	.		169.0	83.0	.	NM_134260	P35397|P35399|P45445|Q495X4|Q96H83	Missense_Mutation	SNP	ENST00000335670.6	hg19	CCDS10177.1	.	.	.	.	.	.	.	.	.	.	T	11.19	1.566201	0.27915	.	.	ENSG00000069667	ENST00000261523	D	0.94457	-3.43	4.3	3.17	0.36434	.	2.259680	0.02344	N	0.075239	D	0.87815	0.6272	N	0.08118	0	0.09310	N	1	B	0.13594	0.008	B	0.14578	0.011	T	0.77749	-0.2471	10	0.22706	T	0.39	.	7.854	0.29472	0.0:0.0:0.2396:0.7604	.	88	P35398	RORA_HUMAN	G	88	ENSP00000261523:E88G	ENSP00000261523:E88G	E	-	2	0	RORA	58636376	0.028000	0.19301	0.012000	0.15200	0.033000	0.12548	0.610000	0.24253	0.985000	0.38656	0.533000	0.62120	GAA	.	.	.	none		0.403	RORA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256142.2			C	60849084	T	C	60849084	1	2	54	0	1	0	0	0	0	0	0	0	13541	1783	62	3		3	RORA	15	60849084	Intron	SNP	T	TCGA-A4-8310-01A-11D-2396-08		60849084	41682308	54	3719											
GFER	2671	hgsc.bcm.edu	37	chr16	2035934	2035934	+	Missense_Mutation	SNP	A	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	agtggctgtgccacctgcacAatgaagtgaaccgcaagctg	11	7	12	11	1	0	2	0	2	0	0	0	2	0	2	3	1	4	4	3	1	4	0			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr16:2035934A>C	ENST00000248114.6	+	3	529	c.523A>C	c.(523-525)Aat>Cat	p.N175H	AC005606.14_ENST00000564438.1_lincRNA|GFER_ENST00000569451.1_Missense_Mutation_p.Q109P|GFER_ENST00000567719.1_Missense_Mutation_p.N100H	NM_005262.2	NP_005253.3	P55789	ALR_HUMAN	growth factor, augmenter of liver regeneration	175	ERV/ALR sulfhydryl oxidase. {ECO:0000255|PROSITE-ProRule:PRU00654}.				cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|protein disulfide oxidoreductase activity (GO:0015035)|thiol oxidase activity (GO:0016972)			endometrium(1)|large_intestine(1)|lung(3)	5					Flavin adenine dinucleotide(DB03147)	CCACCTGCACAATGAAGTGAA	0.587																																					p.N175H		Atlas-SNP	.											.	GFER	8	.	0			c.A523C						PASS	.						95	91	92					16																	2035934		2198	4299	6497	SO:0001583	missense	2671	exon3			CTGCACAATGAAG	BC002429	CCDS32368.1	16p13.3-p13.12	2011-06-22	2008-08-01		ENSG00000127554	ENSG00000127554			4236	protein-coding gene	gene with protein product	"ERV1 homolog (S. cerevisiae)"	600924	"growth factor, erv1 (S. cerevisiae)-like (augmenter of liver regeneration)"			8575761	Standard	NM_005262		Approved	HSS, ERV1, ALR, HERV1, HPO1, HPO2	uc002cob.3	P55789		ENST00000248114.6:c.523A>C	chr16.hg19:g.2035934A>C	ENSP00000248114:p.Asn175His	185.0	0.0	.		201.0	121.0	.	NM_005262	Q53YM6|Q8TAH6|Q9H290|Q9UK40	Missense_Mutation	SNP	ENST00000248114.6	hg19	CCDS32368.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	19.71|19.71	3.878702|3.878702	0.72294|0.72294	.|.	.|.	ENSG00000127554|ENSG00000127554	ENST00000248114|ENST00000425414	T|.	0.79454|.	-1.27|.	4.43|4.43	4.43|4.43	0.53597|0.53597	Erv1/Alr (3);ERV/ALR sulphydryl oxidase (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.87799|0.87799	0.6268|0.6268	H|H	0.97852|0.97852	4.09|4.09	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	0.91675|0.91675	0.5353|0.5353	10|6	0.87932|0.72032	D|D	0|0.01	-22.5825|-22.5825	13.1409|13.1409	0.59434|0.59434	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	101;175|.	Q9UQK8;P55789|.	.;ALR_HUMAN|.	H|P	175|94	ENSP00000248114:N175H|.	ENSP00000248114:N175H|ENSP00000396950:Q94P	N|Q	+|+	1|2	0|0	GFER|GFER	1975935|1975935	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.444000|0.444000	0.32077|0.32077	6.743000|6.743000	0.74848|0.74848	1.763000|1.763000	0.52060|0.52060	0.418000|0.418000	0.28097|0.28097	AAT|CAA	.	.	.	none		0.587	GFER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434243.1	NM_005262		C	2035934	A	C	2035934	3	2	54	1	0	0	0	0	1	0	0	0	6345	130	5	5	533	5	GFER	16	2035934	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08		2035934	88318819	55	3720			1	10		2	2	34	N	T_A	7.994709e-05
GFER	2671	hgsc.bcm.edu	37	chr16	2035967	2035967	+	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	gcaagctgggcaagcctgacTtcgactgctcaaaagtggat	11	8	12	10	1	1	1	1	1	0	0	2	3	1	2	1	2	3	4	1	2	4	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr16:2035967T>A	ENST00000248114.6	+	3	562	c.556T>A	c.(556-558)Ttc>Atc	p.F186I	AC005606.14_ENST00000564438.1_lincRNA|GFER_ENST00000569451.1_3'UTR|GFER_ENST00000567719.1_Missense_Mutation_p.F111I	NM_005262.2	NP_005253.3	P55789	ALR_HUMAN	growth factor, augmenter of liver regeneration	186	ERV/ALR sulfhydryl oxidase. {ECO:0000255|PROSITE-ProRule:PRU00654}.				cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|protein disulfide oxidoreductase activity (GO:0015035)|thiol oxidase activity (GO:0016972)			endometrium(1)|large_intestine(1)|lung(3)	5					Flavin adenine dinucleotide(DB03147)	CAAGCCTGACTTCGACTGCTC	0.612																																					p.F186I		Atlas-SNP	.											.	GFER	8	.	0			c.T556A						PASS	.						93	87	89					16																	2035967		2198	4300	6498	SO:0001583	missense	2671	exon3			CCTGACTTCGACT	BC002429	CCDS32368.1	16p13.3-p13.12	2011-06-22	2008-08-01		ENSG00000127554	ENSG00000127554			4236	protein-coding gene	gene with protein product	"ERV1 homolog (S. cerevisiae)"	600924	"growth factor, erv1 (S. cerevisiae)-like (augmenter of liver regeneration)"			8575761	Standard	NM_005262		Approved	HSS, ERV1, ALR, HERV1, HPO1, HPO2	uc002cob.3	P55789		ENST00000248114.6:c.556T>A	chr16.hg19:g.2035967T>A	ENSP00000248114:p.Phe186Ile	182.0	1.0	.		171.0	101.0	.	NM_005262	Q53YM6|Q8TAH6|Q9H290|Q9UK40	Missense_Mutation	SNP	ENST00000248114.6	hg19	CCDS32368.1	.	.	.	.	.	.	.	.	.	.	t	33	5.218249	0.95104	.	.	ENSG00000127554	ENST00000248114	T	0.64803	-0.12	4.43	4.43	0.53597	Erv1/Alr (3);ERV/ALR sulphydryl oxidase (1);	0.000000	0.85682	D	0.000000	D	0.84951	0.5586	H	0.97077	3.935	0.80722	D	1	D;D	0.89917	0.985;1.0	D;D	0.81914	0.982;0.995	D	0.89667	0.3881	10	0.87932	D	0	-13.6696	13.1409	0.59434	0.0:0.0:0.0:1.0	.	112;186	Q9UQK8;P55789	.;ALR_HUMAN	I	186	ENSP00000248114:F186I	ENSP00000248114:F186I	F	+	1	0	GFER	1975968	1.000000	0.71417	0.993000	0.49108	0.876000	0.50452	7.301000	0.78850	1.763000	0.52060	0.418000	0.28097	TTC	.	.	.	none		0.612	GFER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434243.1	NM_005262		A	2035967	T	A	2035967	3	1	54	1	0	0	0	0	1	0	0	0	6345	1609	56	5	566	5	GFER	16	2035967	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08	33	2035967	88318786	56	3721			1	10		2	2	34	N	T_A	7.994709e-05
TSC2	7249	hgsc.bcm.edu	37	chr16	2134472	2134472	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagccctgaggttaaggccCggtcacagtcagggaccctg	8	7	14	12	1	2	2	2	2	0	0	2	3	2	3	3	4	1	1	3	4	1	1	rs137854296		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr16:2134472C>T	ENST00000219476.3	+	34	4879	c.4249C>T	c.(4249-4251)Cgg>Tgg	p.R1417W	TSC2_ENST00000568454.1_Missense_Mutation_p.R1361W|TSC2_ENST00000382538.6_Missense_Mutation_p.R1302W|TSC2_ENST00000401874.2_Missense_Mutation_p.R1350W|TSC2_ENST00000353929.4_Missense_Mutation_p.R1374W|TSC2_ENST00000350773.4_Missense_Mutation_p.R1394W|TSC2_ENST00000439673.2_Missense_Mutation_p.R1314W	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	1417					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)				GGTTAAGGCCCGGTCACAGTC	0.687			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.R1417W		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	.,5	TSC2	364	.	0			c.C4249T	GRCh37	CD052525	TSC2	D	rs137854055	PASS	.						20	21	21					16																	2134472		2177	4290	6467	SO:0001583	missense	7249	exon34	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	AAGGCCCGGTCAC	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.4249C>T	chr16.hg19:g.2134472C>T	ENSP00000219476:p.Arg1417Trp	47.0	0.0	.		41.0	2.0	.	NM_000548	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Missense_Mutation	SNP	ENST00000219476.3	hg19	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	C	13.77	2.337016	0.41398	.	.	ENSG00000103197	ENST00000219476;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000382538;ENST00000350773	D;D;D;D;D	0.89552	-2.44;-2.43;-2.53;-2.49;-2.45	5.03	4.01	0.46588	.	0.484865	0.20178	N	0.097594	D	0.87900	0.6294	N	0.19112	0.55	0.23254	N	0.998035	D;D;D;D;D;D;D	0.76494	0.998;0.999;0.999;0.999;0.999;0.999;0.995	P;D;D;D;D;D;P	0.67725	0.898;0.953;0.953;0.928;0.953;0.953;0.727	T	0.78730	-0.2090	10	0.66056	D	0.02	-16.5437	8.9464	0.35762	0.2272:0.6557:0.117:0.0	.	1302;1314;1394;192;1373;1350;1417	B4DIL8;P49815-6;P49815-4;B3KSR9;P49815-3;P49815-5;P49815	.;.;.;.;.;.;TSC2_HUMAN	W	1417;1351;1374;1314;1302;1394	ENSP00000219476:R1417W;ENSP00000248099:R1374W;ENSP00000399232:R1314W;ENSP00000371978:R1302W;ENSP00000344383:R1394W	ENSP00000219476:R1417W	R	+	1	2	TSC2	2074473	0.500000	0.26091	0.892000	0.35008	0.367000	0.29736	1.806000	0.38892	2.350000	0.79820	0.484000	0.47621	CGG	.	.	.	none		0.687	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		T	2134472	C	T	2134472	3	4	54	1	0	0	0	0	1	0	0	0	16618	643	23	1	4379	1	TSC2	16	2134472	Missense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08	98505	2134472	88220281	57	3722											
BFAR	51283	hgsc.bcm.edu	37	chr16	14755823	14755823	+	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	aggctgagtctgctctacctGtacctgtttgactacaccga	8	12	9	12	1	2	2	0	2	2	0	2	3	2	2	3	1	4	4	3	1	3	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr16:14755823G>T	ENST00000261658.2	+	6	1135	c.858G>T	c.(856-858)ctG>ctT	p.L286L	BFAR_ENST00000426842.2_Silent_p.L158L|BFAR_ENST00000563971.1_Silent_p.L161L	NM_016561.2	NP_057645.1	Q9NZS9	BFAR_HUMAN	bifunctional apoptosis regulator	286					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						TGCTCTACCTGTACCTGTTTG	0.567																																					p.L286L		Atlas-SNP	.											.	BFAR	38	.	0			c.G858T						PASS	.						237	201	213					16																	14755823		2197	4300	6497	SO:0001819	synonymous_variant	51283	exon6			CTACCTGTACCTG	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.858G>T	chr16.hg19:g.14755823G>T		211.0	0.0	.		280.0	161.0	.	NM_016561	A8K4Z9|B4DUT0|D3DUG8	Silent	SNP	ENST00000261658.2	hg19	CCDS10554.1																																																																																			.	.	.	none		0.567	BFAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252088.1	NM_016561		T	14755823	G	T	14755823	2	4	54	1	0	0	0	0	0	0	0	1	1414	1364	48	4		4	BFAR	16	14755823	Silent	SNP	G	TCGA-A4-8310-01A-11D-2396-08	12621351	14755823	75598930	58	3723											
XYLT1	64131	hgsc.bcm.edu	37	chr16	17202725	17202725	+	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	caacgagtccagccatccctCcagcgctgtgcccgtggagg	7	6	12	16	3	0	0	0	0	0	0	3	2	3	1	5	2	4	1	5	2	1	0			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr16:17202725C>A	ENST00000261381.6	-	12	2791	c.2707G>T	c.(2707-2709)Gag>Tag	p.E903*		NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	903					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)	p.E903Q(2)		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						AGCCATCCCTCCAGCGCTGTG	0.667																																					p.E903X		Atlas-SNP	.											XYLT1,NS,carcinoma,0,1	XYLT1	147	.	2	Substitution - Missense(2)	lung(2)	c.G2707T						PASS	.						71	63	66					16																	17202725		2197	4300	6497	SO:0001587	stop_gained	64131	exon12			ATCCCTCCAGCGC	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.2707G>T	chr16.hg19:g.17202725C>A	ENSP00000261381:p.Glu903*	98.0	0.0	.		125.0	9.0	.	NM_022166	Q9H1B6	Nonsense_Mutation	SNP	ENST00000261381.6	hg19	CCDS10569.1	.	.	.	.	.	.	.	.	.	.	C	40	8.341779	0.98769	.	.	ENSG00000103489	ENST00000261381	.	.	.	5.7	5.7	0.88788	.	0.042979	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-47.0445	18.8196	0.92090	0.0:1.0:0.0:0.0	.	.	.	.	X	903	.	ENSP00000261381:E903X	E	-	1	0	XYLT1	17110226	1.000000	0.71417	0.995000	0.50966	0.811000	0.45836	5.784000	0.68990	2.675000	0.91044	0.655000	0.94253	GAG	.	.	.	none		0.667	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166		A	17202725	C	A	17202725	4	1	54	1	0	0	0	0	0	1	0	0	17475	864	30	4	176	4	XYLT1	16	17202725	Nonsense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08	2446902	17202725	73152028	59	3724											
SLC12A4	6560	hgsc.bcm.edu	37	chr16	67982000	67982000	+	Missense_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	accggggccgccagttggggGtcctcaggagtgtctgcacc	5	7	16	13	2	2	0	1	0	1	0	3	1	3	1	5	5	1	2	5	5	0	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr16:67982000G>A	ENST00000316341.3	-	14	1951	c.1811C>T	c.(1810-1812)aCc>aTc	p.T604I	SLC12A4_ENST00000576616.1_Missense_Mutation_p.T604I|SLC12A4_ENST00000338335.3_Missense_Mutation_p.T604I|SLC12A4_ENST00000572037.1_Missense_Mutation_p.T556I|SLC12A4_ENST00000541864.2_Missense_Mutation_p.T573I|SLC12A4_ENST00000422611.2_Missense_Mutation_p.T606I|SLC12A4_ENST00000537830.2_Missense_Mutation_p.T598I	NM_001145961.1|NM_005072.4	NP_001139433.1|NP_005063.1	Q9UP95	S12A4_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 4	604					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|prostate(4)|skin(2)|urinary_tract(3)	29		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	CCAGTTGGGGGTCCTCAGGAG	0.617																																					p.T606I		Atlas-SNP	.											.	SLC12A4	81	.	0			c.C1817T						PASS	.						86	87	87					16																	67982000		2198	4300	6498	SO:0001583	missense	6560	exon13			TTGGGGGTCCTCA		CCDS10855.1, CCDS54030.1, CCDS54031.1, CCDS54032.1	16q22.1	2013-07-18	2013-07-18		ENSG00000124067	ENSG00000124067		"Solute carriers"	10913	protein-coding gene	gene with protein product		604119				8663127	Standard	NM_005072		Approved	KCC1	uc010ceu.2	Q9UP95	OTTHUMG00000137535	ENST00000316341.3:c.1811C>T	chr16.hg19:g.67982000G>A	ENSP00000318557:p.Thr604Ile	244.0	0.0	.		263.0	64.0	.	NM_001145962	B4DF69|B4DR04|B4DZ82|B7ZAV0|F5H066|F5H0S9|F5H3C0|O60632|O75893|Q13953|Q96LD5	Missense_Mutation	SNP	ENST00000316341.3	hg19	CCDS10855.1	.	.	.	.	.	.	.	.	.	.	G	35	5.548568	0.96488	.	.	ENSG00000124067	ENST00000422611;ENST00000541864;ENST00000537830;ENST00000338335;ENST00000316341	D;D;D;D;D	0.98531	-4.98;-4.98;-4.98;-4.98;-4.98	5.82	5.82	0.92795	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.98957	0.9645	M	0.79805	2.47	0.80722	D	1	B;P;D;P;P;P	0.69078	0.338;0.917;0.997;0.511;0.511;0.76	B;P;D;B;B;P	0.71184	0.373;0.783;0.972;0.373;0.281;0.507	D	0.99808	1.1039	10	0.87932	D	0	.	20.0953	0.97838	0.0:0.0:1.0:0.0	.	606;604;573;598;604;604	F5H3C0;B4DF30;F5H066;F5H0S9;Q9UP95-2;Q9UP95	.;.;.;.;.;S12A4_HUMAN	I	606;573;598;604;604	ENSP00000395983:T606I;ENSP00000438334:T573I;ENSP00000445962:T598I;ENSP00000343374:T604I;ENSP00000318557:T604I	ENSP00000318557:T604I	T	-	2	0	SLC12A4	66539501	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.807000	0.99171	2.767000	0.95098	0.655000	0.94253	ACC	.	.	.	none		0.617	SLC12A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268864.4	NM_005072		A	67982000	G	A	67982000	3	1	54	1	0	0	0	0	1	0	0	0	14398	1261	44	2	1490	2	SLC12A4	16	67982000	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08	50779275	67982000	22372753	60	3725											
KIAA0664	23277	hgsc.bcm.edu	37	chr17	2595388	2595388	+	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	tagactcgggcgacaaggtgGtggctgccgggaggcgcggc	6	5	20	10	5	0	1	0	0	0	1	1	3	0	2	1	7	1	1	1	7	2	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr17:2595388G>T	ENST00000570628.2	-	23	3552	c.3447C>A	c.(3445-3447)caC>caA	p.H1149Q	CLUH_ENST00000538975.1_Missense_Mutation_p.H1149Q|CLUH_ENST00000435359.1_Missense_Mutation_p.H1149Q			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	1149					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)											CGACAAGGTGGTGGCTGCCGG	0.687																																					p.H1149Q		Atlas-SNP	.											.	.	.	.	0			c.C3447A						PASS	.						9	10	10					17																	2595388		1998	4151	6149	SO:0001583	missense	23277	exon23			AAGGTGGTGGCTG	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.3447C>A	chr17.hg19:g.2595388G>T	ENSP00000458986:p.His1149Gln	19.0	0.0	.		13.0	9.0	.	NM_015229	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Missense_Mutation	SNP	ENST00000570628.2	hg19	CCDS45572.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.989729	0.74589	.	.	ENSG00000132361	ENST00000435359;ENST00000322335;ENST00000538975	D;D	0.93953	-3.32;-3.32	4.81	4.81	0.61882	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	D	0.94961	0.8370	L	0.49350	1.555	0.58432	D	0.999994	P;D	0.61697	0.629;0.99	P;D	0.66351	0.542;0.943	D	0.95039	0.8176	10	0.59425	D	0.04	.	15.1886	0.73025	0.0:0.0:1.0:0.0	.	1149;1150	O75153;C9J6D7	K0664_HUMAN;.	Q	1149;1150;1149	ENSP00000388872:H1149Q;ENSP00000439628:H1149Q	ENSP00000320468:H1150Q	H	-	3	2	KIAA0664	2542138	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	3.158000	0.50723	2.494000	0.84150	0.549000	0.68633	CAC	.	.	.	none		0.687	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229		T	2595388	G	T	2595388	3	4	54	1	0	0	0	0	1	0	0	0	8196	1252	44	4	498	4	KIAA0664	17	2595388	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08		2595388	78599822	61	3726											
NDEL1	81565	hgsc.bcm.edu	37	chr17	8350137	8350137	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgttagaagatgatttaagTcagactcgggccattaagga	13	11	12	5	1	1	4	1	1	0	3	2	5	1	5	1	2	0	1	1	2	4	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr17:8350137T>C	ENST00000334527.7	+	4	503	c.306T>C	c.(304-306)agT>agC	p.S102S	NDEL1_ENST00000585098.1_Intron|NDEL1_ENST00000299734.7_Silent_p.S102S|NDEL1_ENST00000402554.3_Silent_p.S102S|NDEL1_ENST00000380025.4_Silent_p.S102S	NM_030808.4	NP_110435.1	Q9GZM8	NDEL1_HUMAN	nudE neurodevelopment protein 1-like 1	102	Interaction with KATNB1. {ECO:0000250}.|Self-association. {ECO:0000250}.				activation of Cdc42 GTPase activity (GO:0032864)|central nervous system neuron axonogenesis (GO:0021955)|centrosome localization (GO:0051642)|cerebral cortex radially oriented cell migration (GO:0021799)|chromosome segregation (GO:0007059)|inner cell mass cell proliferation (GO:0001833)|mitotic cell cycle (GO:0000278)|mitotic centrosome separation (GO:0007100)|neurofilament cytoskeleton organization (GO:0060052)|neuron migration (GO:0001764)|neuron projection extension (GO:1990138)|nuclear envelope disassembly (GO:0051081)|positive regulation of axon extension (GO:0045773)|positive regulation of axon regeneration (GO:0048680)|retrograde axon cargo transport (GO:0008090)|vesicle transport along microtubule (GO:0047496)	axon hillock (GO:0043203)|cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|neurofilament cytoskeleton (GO:0060053)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)	oligopeptidase activity (GO:0070012)			large_intestine(6)|lung(4)|skin(3)	13						ATGATTTAAGTCAGACTCGGG	0.463																																					p.S102S		Atlas-SNP	.											.	NDEL1	47	.	0			c.T306C						PASS	.						114	104	107					17																	8350137		2203	4300	6503	SO:0001819	synonymous_variant	81565	exon4			TTTAAGTCAGACT	AF182078	CCDS11143.1, CCDS32564.1	17p13.1	2013-08-06	2013-08-06	2003-04-16	ENSG00000166579	ENSG00000166579			17620	protein-coding gene	gene with protein product		607538	"nudE nuclear distribution gene E homolog (A. nidulans)-like 1", "nudE nuclear distribution E homolog (A. nidulans)-like 1"			11163260, 11163259	Standard	NM_001025579		Approved	NUDEL, MITAP1, NDE1L1, NDE2	uc002glj.4	Q9GZM8	OTTHUMG00000108193	ENST00000334527.7:c.306T>C	chr17.hg19:g.8350137T>C		64.0	0.0	.		115.0	60.0	.	NM_001025579	B3KP93|D3DTS0|J3QT32|Q86T80|Q8TAR7|Q9UH50	Silent	SNP	ENST00000334527.7	hg19	CCDS11143.1																																																																																			.	.	.	none		0.463	NDEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226999.2	NM_030808		C	8350137	T	C	8350137	2	2	54	1	0	0	0	0	0	0	0	1	10251	1664	58	3		3	NDEL1	17	8350137	Silent	SNP	T	TCGA-A4-8310-01A-11D-2396-08	5754749	8350137	72845073	62	3727											
ACLY	47	hgsc.bcm.edu	37	chr17	40025023	40025023	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agggctccaatgtcaatataTtcatcagcttcctccctgca	10	12	6	13	0	3	0	3	0	0	0	6	0	6	0	3	1	2	3	3	1	4	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr17:40025023T>C	ENST00000352035.2	-	28	3280	c.3150A>G	c.(3148-3150)gaA>gaG	p.E1050E	ACLY_ENST00000537919.1_Silent_p.E779E|ACLY_ENST00000353196.1_Silent_p.E1040E|ACLY_ENST00000590151.1_Silent_p.E1050E|ACLY_ENST00000588779.1_5'UTR|ACLY_ENST00000393896.2_Silent_p.E1040E	NM_001096.2	NP_001087.2	P53396	ACLY_HUMAN	ATP citrate lyase	1050					ATP catabolic process (GO:0006200)|cellular carbohydrate metabolic process (GO:0044262)|cellular lipid metabolic process (GO:0044255)|citrate metabolic process (GO:0006101)|coenzyme A metabolic process (GO:0015936)|energy reserve metabolic process (GO:0006112)|lipid biosynthetic process (GO:0008610)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	citrate lyase complex (GO:0009346)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)		NTN1/ACLY(2)	breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	28		Breast(137;0.000143)				TGTCAATATATTCATCAGCTT	0.438																																					p.E1050E	Colon(64;807 1396 15971 30971)	Atlas-SNP	.											.	ACLY	85	.	0			c.A3150G						PASS	.						157	139	145					17																	40025023		2203	4300	6503	SO:0001819	synonymous_variant	47	exon28			AATATATTCATCA	X64330	CCDS11412.1, CCDS11413.1	17q21.2	2010-04-27			ENSG00000131473	ENSG00000131473	2.3.3.8		115	protein-coding gene	gene with protein product	"ATP citrate synthase"	108728				1371749, 8088842	Standard	NM_001096		Approved	ATPCL, CLATP, ACL	uc002hyg.3	P53396	OTTHUMG00000133507	ENST00000352035.2:c.3150A>G	chr17.hg19:g.40025023T>C		110.0	0.0	.		180.0	46.0	.	NM_001096	B4DIM0|B4E3P0|Q13037|Q9BRL0	Silent	SNP	ENST00000352035.2	hg19	CCDS11412.1																																																																																			.	.	.	none		0.438	ACLY-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257465.1	NM_001096		C	40025023	T	C	40025023	2	2	54	1	0	0	0	0	0	0	0	1	143	1490	52	3		3	ACLY	17	40025023	Silent	SNP	T	TCGA-A4-8310-01A-11D-2396-08	31674886	40025023	41170187	63	3728											
CSNK1D	1453	hgsc.bcm.edu	37	chr17	80202675	80202675	+	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	tctcatcggtgcacgacagaCtgaagaccactggaagccac	12	6	10	13	2	1	3	1	1	1	2	3	5	1	4	2	2	2	1	2	2	2	0			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr17:80202675C>T	ENST00000314028.6	-	9	1579	c.1230G>A	c.(1228-1230)caG>caA	p.Q410Q	CSNK1D_ENST00000398519.5_Intron|CSNK1D_ENST00000392334.2_3'UTR	NM_001893.4	NP_001884.2	P48730	KC1D_HUMAN	casein kinase 1, delta	410					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)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|signal transduction (GO:0007165)|spindle assembly (GO:0051225)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle (GO:0005819)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			breast(2)|large_intestine(2)|lung(7)	11	Breast(20;0.00136)|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;0.0155)			GCACGACAGACTGAAGACCAC	0.557											OREG0024822	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q410Q		Atlas-SNP	.											.	CSNK1D	118	.	0			c.G1230A						PASS	.						115	85	95					17																	80202675		2203	4300	6503	SO:0001819	synonymous_variant	1453	exon9			GACAGACTGAAGA		CCDS11805.1, CCDS11806.1	17q25	2013-01-17				ENSG00000141551			2452	protein-coding gene	gene with protein product		600864				7797465	Standard	NM_001893		Approved	HCKID, CKID, CKIdelta	uc002kej.3	P48730		ENST00000314028.6:c.1230G>A	chr17.hg19:g.80202675C>T		92.0	0.0	.	1196	98.0	47.0	.	NM_001893	A2I2P2|Q96KZ6|Q9BTN5	Silent	SNP	ENST00000314028.6	hg19	CCDS11805.1																																																																																			.	.	.	none		0.557	CSNK1D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442632.1	NM_139062		T	80202675	C	T	80202675	2	4	54	1	0	0	0	0	0	0	0	1	3954	564	20	2		2	CSNK1D	17	80202675	Silent	SNP	C	TCGA-A4-8310-01A-11D-2396-08	40177652	80202675	992535	64	3729											
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11132430	11132430	+	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	aagtacatgattgtggacgaAggtcaccgcatgaagaacca	15	7	11	8	2	1	3	1	2	0	1	1	5	1	4	2	2	2	2	2	2	5	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr19:11132430A>T	ENST00000429416.3	+	20	2927	c.2646A>T	c.(2644-2646)gaA>gaT	p.E882D	SMARCA4_ENST00000344626.4_Missense_Mutation_p.E882D|SMARCA4_ENST00000589677.1_Missense_Mutation_p.E882D|SMARCA4_ENST00000358026.2_Missense_Mutation_p.E882D|SMARCA4_ENST00000413806.3_Missense_Mutation_p.E882D|SMARCA4_ENST00000590574.1_Missense_Mutation_p.E882D|SMARCA4_ENST00000450717.3_Missense_Mutation_p.E882D|SMARCA4_ENST00000541122.2_Missense_Mutation_p.E882D|SMARCA4_ENST00000444061.3_Missense_Mutation_p.E882D	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	882	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				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)				TTGTGGACGAAGGTCACCGCA	0.632			"F, N, Mis"		NSCLC																																p.E882D		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.A2646T						PASS	.						77	61	67					19																	11132430		2202	4300	6502	SO:0001583	missense	6597	exon19			GGACGAAGGTCAC	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.2646A>T	chr19.hg19:g.11132430A>T	ENSP00000395654:p.Glu882Asp	55.0	0.0	.		34.0	11.0	.	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	A	19.43	3.825530	0.71143	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.99652	-6.3;-6.3;-6.3;-6.3;-6.3;-6.3;-6.3	4.66	-2.31	0.06765	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.99778	0.9908	H	0.99825	4.815	0.50313	D	0.999868	D;D;D;D;D;D;D;D	0.89917	0.999;0.999;0.999;0.999;0.999;1.0;0.999;0.999	D;D;D;D;D;D;D;D	0.97110	0.994;0.994;0.994;0.992;0.981;1.0;0.994;0.994	D	0.98030	1.0376	10	0.87932	D	0	-29.2033	10.9557	0.47356	0.5266:0.0:0.4734:0.0	.	882;882;882;882;882;102;882;882	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;A7E2E1;P51532	.;.;.;.;.;.;.;SMCA4_HUMAN	D	882;882;946;882;882;882;882;882	ENSP00000395654:E882D;ENSP00000350720:E882D;ENSP00000343896:E882D;ENSP00000445036:E882D;ENSP00000392837:E882D;ENSP00000397783:E882D;ENSP00000414727:E882D	ENSP00000343896:E882D	E	+	3	2	SMARCA4	10993430	0.554000	0.26522	0.953000	0.39169	0.784000	0.44337	-0.089000	0.11180	-0.861000	0.04094	-0.256000	0.11100	GAA	.	.	.	none		0.632	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		T	11132430	A	T	11132430	3	4	54	1	0	0	0	0	1	0	0	0	14783	69	3	5	2716	5	SMARCA4	19	11132430	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08		11132430	47996553	65	3730											
HRC	3270	hgsc.bcm.edu	37	chr19	49657889	49657889	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tactcagtggaggcctcctcTtcctcctcctcctcctcctc	3	13	5	20	0	2	0	1	0	1	0	10	1	9	1	8	2	1	0	8	2	1	2	rs57199624|rs147238387|rs551367394|rs542091249		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr19:49657889T>C	ENST00000252825.4	-	1	792	c.606A>G	c.(604-606)gaA>gaG	p.E202E	HRC_ENST00000595625.1_Silent_p.E202E	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	202	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Glu-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		AGGcctcctcttcctcctcct	0.567																																					p.E202E	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.,1	HRC	85	.	0			c.A606G						PASS	.						122	91	101					19																	49657889		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			CTCCTCTTCCTCC		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.606A>G	chr19.hg19:g.49657889T>C		59.0	0.0	.		46.0	2.0	.	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	hg19	CCDS12759.1																																																																																			.	.	.	none		0.567	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		C	49657889	T	C	49657889	2	2	54	1	0	0	0	0	0	0	0	1	7359	1606	56	3		3	HRC	19	49657889	Silent	SNP	T	TCGA-A4-8310-01A-11D-2396-08	38525459	49657889	9471094	66	3731											
SAPS1	22870	hgsc.bcm.edu	37	chr19	55752903	55752903	+	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	gccgcgggcgtagggcgtgcAaggcgcccacactggacaca	8	3	16	14	5	0	0	0	0	0	0	0	1	0	1	2	4	1	2	2	4	2	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr19:55752903A>T	ENST00000412770.2	-	8	1516	c.950T>A	c.(949-951)tTg>tAg	p.L317*	PPP6R1_ENST00000587283.1_Nonsense_Mutation_p.L317*	NM_014931.3	NP_055746.3	Q9UPN7	PP6R1_HUMAN	protein phosphatase 6, regulatory subunit 1	317	Interaction with PPP6C.				regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)	protein phosphatase binding (GO:0019903)			breast(1)	1						TAGGGCGTGCAAGGCGCCCAC	0.672																																					p.L317X		Atlas-SNP	.											.	PPP6R1	63	.	0			c.T950A						PASS	.						16	20	19					19																	55752903		2009	4156	6165	SO:0001587	stop_gained	22870	exon8			GCGTGCAAGGCGC	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.950T>A	chr19.hg19:g.55752903A>T	ENSP00000414202:p.Leu317*	20.0	0.0	.		15.0	4.0	.	NM_014931	Q2M2H3|Q504V2|Q6NVJ6|Q9BU97	Nonsense_Mutation	SNP	ENST00000412770.2	hg19	CCDS46186.1	.	.	.	.	.	.	.	.	.	.	A	36	5.920878	0.97105	.	.	ENSG00000105063	ENST00000412770	.	.	.	4.31	4.31	0.51392	.	0.000000	0.41938	D	0.000783	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.1454	11.7405	0.51790	1.0:0.0:0.0:0.0	.	.	.	.	X	317	.	ENSP00000414202:L317X	L	-	2	0	PPP6R1	60444715	1.000000	0.71417	0.898000	0.35279	0.236000	0.25371	4.122000	0.57910	1.937000	0.56155	0.379000	0.24179	TTG	.	.	.	none		0.672	PPP6R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452663.1	NM_014931		T	55752903	A	T	55752903	4	4	54	1	0	0	0	0	0	1	0	0	13849	131	5	5	1763	5	SAPS1	19	55752903	Nonsense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	6095014	55752903	3376080	67	3732											
DNMT3B	1789	hgsc.bcm.edu	37	chr20	31375212	31375212	+	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	caggggggcatggagtccccGcaggtggaggcagacagtgg	8	4	20	9	1	0	1	0	0	0	1	1	3	1	3	2	8	0	3	2	8	0	0	rs376501500		TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr20:31375212G>A	ENST00000328111.2	+	6	930	c.609G>A	c.(607-609)ccG>ccA	p.P203P	DNMT3B_ENST00000353855.2_Silent_p.P203P|DNMT3B_ENST00000344505.4_Silent_p.P203P|DNMT3B_ENST00000443239.3_Silent_p.P161P|DNMT3B_ENST00000456297.2_Silent_p.P127P|DNMT3B_ENST00000201963.3_Silent_p.P215P|DNMT3B_ENST00000348286.2_Silent_p.P203P|DNMT3B_ENST00000375623.4_Silent_p.P161P	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta	203	Interaction with DNMT1 and DNMT3A.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(16)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TGGAGTCCCCGCAGGTGGAGG	0.637																																					p.P215P		Atlas-SNP	.											.	DNMT3B	196	.	0			c.G645A						PASS	.	G	,,,,,	1,4405	2.1+/-5.4	0,1,2202	52	51	51		483,381,609,609,609,645	-7.6	0	20		51	1,8599	1.2+/-3.3	0,1,4299	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	,,,,,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,,,,,	161/729,127/695,203/854,203/834,203/771,215/846	31375212	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	1789	exon6			GTCCCCGCAGGTG		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.609G>A	chr20.hg19:g.31375212G>A		79.0	0.0	.		87.0	50.0	.	NM_175850	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Silent	SNP	ENST00000328111.2	hg19	CCDS13205.1																																																																																			.	.	.	weak		0.637	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892		A	31375212	G	A	31375212	2	1	54	1	0	0	0	0	0	0	0	1	4679	1074	38	1		1	DNMT3B	20	31375212	Silent	SNP	G	TCGA-A4-8310-01A-11D-2396-08		31375212	31650308	68	3733											
NCOA6	23054	hgsc.bcm.edu	37	chr20	33330861	33330861	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actctgttgcatgggcattcTctgggagtcggggttcaggg	5	12	16	8	1	3	0	1	0	2	0	5	1	3	1	0	5	1	4	0	5	0	3			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr20:33330861T>C	ENST00000374796.2	-	12	5769	c.3199A>G	c.(3199-3201)Aga>Gga	p.R1067G	NCOA6_ENST00000359003.2_Missense_Mutation_p.R1067G			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1067	NCOA1-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						ATGGGCATTCTCTGGGAGTCG	0.537																																					p.R1067G		Atlas-SNP	.											.	NCOA6	219	.	0			c.A3199G						PASS	.						112	117	115					20																	33330861		2203	4300	6503	SO:0001583	missense	23054	exon11			GCATTCTCTGGGA	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.3199A>G	chr20.hg19:g.33330861T>C	ENSP00000363929:p.Arg1067Gly	220.0	0.0	.		349.0	214.0	.	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	hg19	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	T	16.24	3.067284	0.55539	.	.	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.52526	0.66;0.66	5.82	5.82	0.92795	.	0.000000	0.64402	D	0.000001	T	0.56396	0.1982	L	0.32530	0.975	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.54827	-0.8235	10	0.38643	T	0.18	-10.3259	12.8878	0.58053	0.0:0.0:0.1444:0.8556	.	1067	Q14686	NCOA6_HUMAN	G	1067	ENSP00000363929:R1067G;ENSP00000351894:R1067G	ENSP00000351894:R1067G	R	-	1	2	NCOA6	32794522	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.049000	0.57397	2.225000	0.72522	0.460000	0.39030	AGA	.	.	.	none		0.537	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		C	33330861	T	C	33330861	3	2	54	1	0	0	0	0	1	0	0	0	10240	1559	54	3	3012	3	NCOA6	20	33330861	Missense_Mutation	SNP	T	TCGA-A4-8310-01A-11D-2396-08	1955649	33330861	29694659	69	3734											
ARFGEF2	10564	hgsc.bcm.edu	37	chr20	47628617	47628617	+	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	caaatacgtctctgagaggcCtcgggttcgtttttccccac	7	12	9	13	3	1	1	0	1	1	1	5	2	2	1	3	2	1	2	3	2	2	4			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr20:47628617C>A	ENST00000371917.4	+	28	3914	c.3914C>A	c.(3913-3915)cCt>cAt	p.P1305H		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	1305					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)			TCTGAGAGGCCTCGGGTTCGT	0.512																																					p.P1305H	Esophageal Squamous(176;1738 1974 26285 33069 35354)	Atlas-SNP	.											.	ARFGEF2	160	.	0			c.C3914A						PASS	.						93	88	90					20																	47628617		2203	4300	6503	SO:0001583	missense	10564	exon28			AGAGGCCTCGGGT	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.3914C>A	chr20.hg19:g.47628617C>A	ENSP00000360985:p.Pro1305His	95.0	0.0	.		215.0	55.0	.	NM_006420	Q5TFT9|Q9NTS1	Missense_Mutation	SNP	ENST00000371917.4	hg19	CCDS13411.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.767327	0.90020	.	.	ENSG00000124198	ENST00000371917	T	0.56611	0.45	5.46	5.46	0.80206	Armadillo-type fold (1);	0.050275	0.85682	D	0.000000	T	0.77246	0.4102	M	0.87827	2.91	0.80722	D	1	D	0.89917	1.0	D	0.70935	0.971	T	0.81337	-0.0978	10	0.87932	D	0	.	19.3208	0.94237	0.0:1.0:0.0:0.0	.	1305	Q9Y6D5	BIG2_HUMAN	H	1305	ENSP00000360985:P1305H	ENSP00000360985:P1305H	P	+	2	0	ARFGEF2	47062024	1.000000	0.71417	1.000000	0.80357	0.750000	0.42670	7.747000	0.85070	2.557000	0.86248	0.561000	0.74099	CCT	.	.	.	none		0.512	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420		A	47628617	C	A	47628617	3	1	54	1	0	0	0	0	1	0	0	0	853	681	24	4	4024	4	ARFGEF2	20	47628617	Missense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08	14297756	47628617	15396903	70	3735											
APOL6	80830	hgsc.bcm.edu	37	chr22	36055131	36055131	+	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	ctggaaagattatctataatCttagaaacaccttgaagtat	16	13	6	6	0	2	3	0	1	2	2	2	4	2	4	1	1	1	1	1	1	8	6			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chr22:36055131C>G	ENST00000409652.4	+	3	796	c.520C>G	c.(520-522)Ctt>Gtt	p.L174V		NM_030641.3	NP_085144.1	Q9BWW8	APOL6_HUMAN	apolipoprotein L, 6	174					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						TATCTATAATCTTAGAAACAC	0.493																																					p.L174V		Atlas-SNP	.											.	APOL6	26	.	0			c.C520G						PASS	.						61	63	62					22																	36055131		2203	4300	6503	SO:0001583	missense	80830	exon3			TATAATCTTAGAA	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.520C>G	chr22.hg19:g.36055131C>G	ENSP00000386280:p.Leu174Val	74.0	0.0	.		72.0	8.0	.	NM_030641	Q5R3S1|Q658J1|Q8IXX6|Q9UGG1	Missense_Mutation	SNP	ENST00000409652.4	hg19	CCDS13919.1	.	.	.	.	.	.	.	.	.	.	C	0.284	-0.984328	0.02180	.	.	ENSG00000221963	ENST00000409652	T	0.03124	4.04	4.05	-3.17	0.05202	.	1.542230	0.03383	N	0.200606	T	0.01489	0.0048	N	0.01482	-0.84	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46331	-0.9199	10	0.11182	T	0.66	-11.6376	7.5122	0.27579	0.0:0.1896:0.5669:0.2435	.	174	Q9BWW8	APOL6_HUMAN	V	174	ENSP00000386280:L174V	ENSP00000386280:L174V	L	+	1	0	APOL6	34385077	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.171000	0.09883	-0.392000	0.07751	-1.127000	0.01993	CTT	.	.	.	none		0.493	APOL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319081.2	NM_030641		G	36055131	C	G	36055131	3	3	54	1	0	0	0	0	1	0	0	0	810	913	32	4	526	4	APOL6	22	36055131	Missense_Mutation	SNP	C	TCGA-A4-8310-01A-11D-2396-08		36055131	15249435	71	3736											
BCOR	54880	hgsc.bcm.edu	37	chrX	39932880	39932880	+	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	ccatctgcattggcattgggGgcgggtgatgcggaggctgg	5	9	19	8	2	1	1	0	1	1	0	1	2	1	2	1	7	2	3	1	7	0	2			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chrX:39932880G>T	ENST00000378444.4	-	4	1947	c.1719C>A	c.(1717-1719)gcC>gcA	p.A573A	BCOR_ENST00000397354.3_Silent_p.A573A|BCOR_ENST00000378455.4_Silent_p.A573A|BCOR_ENST00000342274.4_Silent_p.A573A	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	573					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						TGGCATTGGGGGCGGGTGATG	0.617			"F, N, S, T"	RARA	"retinoblastoma, AML, APL(translocation)"		oculo-facio-cardio-dental genetic																														p.A573A		Atlas-SNP	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	0			c.C1719A						PASS	.						72	62	65					X																	39932880		2202	4300	6502	SO:0001819	synonymous_variant	54880	exon4			ATTGGGGGCGGGT	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.1719C>A	chrX.hg19:g.39932880G>T		70.0	0.0	.		38.0	32.0	.	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Silent	SNP	ENST00000378444.4	hg19	CCDS48093.1																																																																																			.	.	.	none		0.617	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		T	39932880	G	T	39932880	2	4	54	1	0	0	0	0	0	0	0	1	1386	1219	43	4		4	BCOR	23	39932880	Silent	SNP	G	TCGA-A4-8310-01A-11D-2396-08		39932880	115337680	72	3737											
CXorf38	159013	hgsc.bcm.edu	37	chrX	40506303	40506303	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggccagcggcccggccggcAgtttccccagtgcacatctc	5	6	13	17	3	1	0	0	0	1	0	3	0	2	0	5	4	2	3	5	4	0	1			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chrX:40506303A>G	ENST00000327877.5	-	2	333	c.307T>C	c.(307-309)Tgc>Cgc	p.C103R	CXorf38_ENST00000378426.1_5'UTR|CXorf38_ENST00000440784.2_Intron|CXorf38_ENST00000378418.2_Missense_Mutation_p.C103R|CXorf38_ENST00000378421.1_5'UTR	NM_144970.2	NP_659407.1	Q8TB03	CX038_HUMAN	chromosome X open reading frame 38	103										NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	12						CCCGGCCGGCAGTTTCCCCAG	0.622																																					p.C103R		Atlas-SNP	.											.	CXorf38	29	.	0			c.T307C						PASS	.						26	27	26					X																	40506303		2202	4300	6502	SO:0001583	missense	159013	exon2			GCCGGCAGTTTCC	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.307T>C	chrX.hg19:g.40506303A>G	ENSP00000330488:p.Cys103Arg	38.0	0.0	.		22.0	14.0	.	NM_144970	B3KW28|D3DWB5|Q5JPF5|Q8N941	Missense_Mutation	SNP	ENST00000327877.5	hg19	CCDS14253.1	.	.	.	.	.	.	.	.	.	.	a	22.0	4.230190	0.79688	.	.	ENSG00000185753	ENST00000327877;ENST00000378418	T;T	0.70516	-0.49;-0.49	5.26	4.06	0.47325	.	0.123229	0.56097	D	0.000040	T	0.79003	0.4373	M	0.66939	2.045	0.80722	D	1	D	0.55385	0.971	P	0.60473	0.875	T	0.78976	-0.1991	10	0.87932	D	0	-4.1854	10.4684	0.44622	0.8383:0.1617:0.0:0.0	.	103	Q8TB03	CX038_HUMAN	R	103	ENSP00000330488:C103R;ENSP00000367674:C103R	ENSP00000330488:C103R	C	-	1	0	CXorf38	40391247	1.000000	0.71417	0.995000	0.50966	0.997000	0.91878	7.258000	0.78371	0.627000	0.30340	0.483000	0.47432	TGC	.	.	.	none		0.622	CXorf38-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060685.3	NM_144970		G	40506303	A	G	40506303	3	3	54	1	0	0	0	0	1	0	0	0	4109	188	7	3	672	3	CXorf38	23	40506303	Missense_Mutation	SNP	A	TCGA-A4-8310-01A-11D-2396-08	573423	40506303	114764257	73	3738											
GJB1	2705	hgsc.bcm.edu	37	chrX	70444364	70444364	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcgccgcagccctggcacCggggctgggctggctgaaaa	6	5	16	14	3	0	1	0	1	0	0	0	1	0	1	3	5	2	5	3	5	2	0			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chrX:70444364C>T	ENST00000374022.3	+	2	902	c.807C>T	c.(805-807)acC>acT	p.T269T	GJB1_ENST00000361726.6_Silent_p.T269T|GJB1_ENST00000374029.1_Silent_p.T269T	NM_001097642.2	NP_001091111.1	P08034	CXB1_HUMAN	gap junction protein, beta 1, 32kDa	269					cell death (GO:0008219)|cell-cell signaling (GO:0007267)|gap junction assembly (GO:0016264)|membrane organization (GO:0061024)|nervous system development (GO:0007399)|protein oligomerization (GO:0051259)|purine ribonucleotide transport (GO:0015868)|transport (GO:0006810)	connexon complex (GO:0005922)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	gap junction channel activity (GO:0005243)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(1)	10	Renal(35;0.156)					GCCCTGGCACCGGGGCTGGGC	0.637																																					p.T269T		Atlas-SNP	.											.	GJB1	21	.	0			c.C807T						PASS	.						7	7	7					X																	70444364		2162	4203	6365	SO:0001819	synonymous_variant	2705	exon2			TGGCACCGGGGCT	X04325	CCDS14408.1	Xq13.1	2014-09-17	2007-01-16		ENSG00000169562	ENSG00000169562		"Ion channels / Gap junction proteins (connexins)"	4283	protein-coding gene	gene with protein product	"Charcot-Marie-Tooth neuropathy, X-linked", "connexin 32"	304040	"gap junction protein, beta 1, 32kD (connexin 32, Charcot-Marie-Tooth neuropathy, X-linked)", "gap junction protein, beta 1, 32kDa (connexin 32, Charcot-Marie-Tooth neuropathy, X-linked)", "gap junction protein, beta 1, 32kDa (connexin 32)"	CMTX1, CMTX		1319395	Standard	NM_000166		Approved	CX32	uc004dzf.3	P08034	OTTHUMG00000021797	ENST00000374022.3:c.807C>T	chrX.hg19:g.70444364C>T		19.0	0.0	.		10.0	7.0	.	NM_000166	B2R8R2|D3DVV2|Q5U0S4	Silent	SNP	ENST00000374022.3	hg19	CCDS14408.1																																																																																			.	.	.	none		0.637	GJB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057133.1	NM_000166		T	70444364	C	T	70444364	2	4	54	1	0	0	0	0	0	0	0	1	6414	639	23	1		1	GJB1	23	70444364	Silent	SNP	C	TCGA-A4-8310-01A-11D-2396-08	29938061	70444364	84826196	74	3739											
PASD1	139135	hgsc.bcm.edu	37	chrX	150828200	150828200	+	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	tacaggaccaaattgatattGcagaggttgagcagtatgga	14	10	12	5	0	0	3	0	2	0	1	0	5	0	5	1	3	3	4	1	3	4	6			TCGA-A4-8310-01A-11D-2396-08	TCGA-A4-8310-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6aaac72-5533-41b0-8bdb-8639f0339dd0	d8660b1d-6a91-4944-9e79-5911f80f873e	g.chrX:150828200G>T	ENST00000370357.4	+	10	978	c.733G>T	c.(733-735)Gca>Tca	p.A245S		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	245						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)					AATTGATATTGCAGAGGTTGA	0.373																																					p.A245S		Atlas-SNP	.											.	PASD1	286	.	0			c.G733T						PASS	.						200	160	173					X																	150828200		2203	4300	6503	SO:0001583	missense	139135	exon10			GATATTGCAGAGG	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.733G>T	chrX.hg19:g.150828200G>T	ENSP00000359382:p.Ala245Ser	32.0	0.0	.		40.0	4.0	.	NM_173493	Q3MNE0|Q69HD7|Q8N7X9	Missense_Mutation	SNP	ENST00000370357.4	hg19	CCDS35431.1	.	.	.	.	.	.	.	.	.	.	g	8.919	0.960719	0.18583	.	.	ENSG00000166049	ENST00000370357	T	0.70399	-0.48	3.46	-4.06	0.03986	.	.	.	.	.	T	0.44850	0.1313	N	0.14661	0.345	0.09310	N	1	B	0.26876	0.162	B	0.19666	0.026	T	0.16897	-1.0387	9	0.27082	T	0.32	-10.8623	5.9292	0.19130	0.6076:0.0:0.245:0.1474	.	245	Q8IV76	PASD1_HUMAN	S	245	ENSP00000359382:A245S	ENSP00000359382:A245S	A	+	1	0	PASD1	150578856	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.030000	0.03581	-1.424000	0.01999	-0.925000	0.02716	GCA	.	.	.	none		0.373	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493		T	150828200	G	T	150828200	3	4	54	1	0	0	0	0	1	0	0	0	11478	1319	46	4	767	4	PASD1	23	150828200	Missense_Mutation	SNP	G	TCGA-A4-8310-01A-11D-2396-08	80383836	150828200	4442360	75	3740											
PEX14	5195	hgsc.bcm.edu	37	chr1	10678475	10678475	+	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	gctttcaccagctctacaagGtgagtcacccccagcggctg	8	8	10	15	1	3	1	2	1	1	0	3	1	3	1	3	2	3	3	3	2	2	2			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr1:10678475G>A	ENST00000356607.4	+	5	464		c.e5+1		PEX14_ENST00000538836.1_Splice_Site|RN7SL614P_ENST00000461850.2_RNA	NM_004565.2	NP_004556.1	O75381	PEX14_HUMAN	peroxisomal biogenesis factor 14						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)		GCTCTACAAGGTGAGTCACCC	0.627																																					.		Atlas-SNP	.											.	PEX14	40	.	0			c.384+1G>A						PASS	.						70	62	64					1																	10678475		2203	4300	6503	SO:0001630	splice_region_variant	5195	exon5			TACAAGGTGAGTC	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.384+1G>A	chr1.hg19:g.10678475G>A		50.0	0.0	.		36.0	16.0	.	NM_004565	B2R7N1|B3KML6|B7Z1N2|Q8WX51	Splice_Site	SNP	ENST00000356607.4	hg19	CCDS30582.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.726384	0.89298	.	.	ENSG00000142655	ENST00000356607;ENST00000538836	.	.	.	4.79	4.79	0.61399	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.856	0.88762	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PEX14	10601062	1.000000	0.71417	0.999000	0.59377	0.952000	0.60782	9.430000	0.97488	2.195000	0.70347	0.655000	0.94253	.	.	.	.	none		0.627	PEX14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005414.1		Intron	A	10678475	G	A	10678475	5	1	55	1	0	0	0	0	0	0	1	0	11749	1275	44	2	403	2	PEX14	1	10678475	Splice_Site	SNP	G	TCGA-A4-8311-01A-11D-2396-08		10678475	238572146	1	3741											
ZCCHC11	23318	hgsc.bcm.edu	37	chr1	52961169	52961169	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atctagtcagagatgagccaTacaacctaagtgaacattct	15	10	7	9	0	3	3	1	2	2	1	3	4	3	3	2	0	4	0	2	0	5	4			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr1:52961169T>C	ENST00000371544.3	-	6	1458	c.1196A>G	c.(1195-1197)tAt>tGt	p.Y399C	ZCCHC11_ENST00000257177.4_Missense_Mutation_p.Y399C|ZCCHC11_ENST00000371541.1_5'UTR	NM_001009881.2|NM_015269.2	NP_001009881.1|NP_056084.1	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11	399					cytokine production (GO:0001816)|miRNA catabolic process (GO:0010587)|miRNA metabolic process (GO:0010586)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|pre-miRNA processing (GO:0031054)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|RNA 3'-end processing (GO:0031123)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(17)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	58						AGATGAGCCATACAACCTAAG	0.338																																					p.Y399C		Atlas-SNP	.											.	ZCCHC11	151	.	0			c.A1196G						PASS	.						56	58	57					1																	52961169		2203	4299	6502	SO:0001583	missense	23318	exon6			GAGCCATACAACC	D83776	CCDS30715.1, CCDS30716.1	1p32.3	2014-03-05			ENSG00000134744	ENSG00000134744		"Zinc fingers, CCHC domain containing"	28981	protein-coding gene	gene with protein product	"TUTase4"	613692				8724849, 12239557	Standard	NM_015269		Approved	KIAA0191, PAPD3, TUT4	uc001cty.2	Q5TAX3	OTTHUMG00000008200	ENST00000371544.3:c.1196A>G	chr1.hg19:g.52961169T>C	ENSP00000360599:p.Tyr399Cys	75.0	0.0	.		65.0	28.0	.	NM_015269	A2RRP0|B7Z8J5|D3DQ35|Q12764|Q5TAX2|Q5TAX4|Q86XZ3	Missense_Mutation	SNP	ENST00000371544.3	hg19	CCDS30716.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.180486	0.78677	.	.	ENSG00000134744	ENST00000257177;ENST00000371544;ENST00000528642;ENST00000484723	D;D;D;D	0.83992	-1.79;-1.79;-1.79;-1.79	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	D	0.90494	0.7022	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	0.994;0.999;0.998	D	0.91443	0.5175	10	0.87932	D	0	.	15.929	0.79646	0.0:0.0:0.0:1.0	.	158;399;399	E9PKX1;Q5TAX3-2;Q5TAX3	.;.;TUT4_HUMAN	C	399;399;399;158	ENSP00000257177:Y399C;ENSP00000360599:Y399C;ENSP00000433486:Y399C;ENSP00000435256:Y158C	ENSP00000257177:Y399C	Y	-	2	0	ZCCHC11	52733757	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.780000	0.62382	2.243000	0.73865	0.533000	0.62120	TAT	.	.	.	none		0.338	ZCCHC11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022462.1	XM_038288		C	52961169	T	C	52961169	3	2	55	1	0	0	0	0	1	0	0	0	17592	1406	49	3	3841	3	ZCCHC11	1	52961169	Missense_Mutation	SNP	T	TCGA-A4-8311-01A-11D-2396-08	42282694	52961169	196289452	2	3742											
KIDINS220	57498	hgsc.bcm.edu	37	chr2	8872073	8872073	+	Frame_Shift_Del	DEL	A	A	-																															ttcaatactggaatcctgggAattgagactcgaaagacttg																										TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr2:8872073delA	ENST00000256707.3	-	30	4274	c.4093delT	c.(4093-4095)tccfs	p.S1365fs	KIDINS220_ENST00000427284.1_Frame_Shift_Del_p.S1346fs|KIDINS220_ENST00000418530.1_Frame_Shift_Del_p.S1266fs|KIDINS220_ENST00000473731.1_Frame_Shift_Del_p.S1346fs	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	1365					activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234)	PDZ domain binding (GO:0030165)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GAATCCTGGGAATTGAGACTC	0.363																																					p.S1365fs		Atlas-INDEL	.											.	KIDINS220	136	.	0			c.4094delC						PASS	.						81	77	78					2																	8872073		1825	4096	5921	SO:0001589	frameshift_variant	57498	exon30			.	AK025528	CCDS42650.1	2p24	2013-01-10			ENSG00000134313	ENSG00000134313		"Ankyrin repeat domain containing"	29508	protein-coding gene	gene with protein product	"ankyrin repeat-rich membrane-spanning protein"	615759				10998417, 10574462	Standard	NM_020738		Approved	ARMS	uc002qzc.2	Q9ULH0	OTTHUMG00000151658	ENST00000256707.3:c.4093delT	chr2.hg19:g.8872073delA	ENSP00000256707:p.Ser1365fs	141.0	0.0	0		129.0	43.0	0.333333	NM_020738	A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Frame_Shift_Del	DEL	ENST00000256707.3	hg19	CCDS42650.1																																																																																			.	.	.	none		0.363	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738		-	8872073	A	-	8872073	7	5	55	1	0	1	0	1	0	0	0	0	8278	246	9	0	1226	0	KIDINS220	2	8872073	Frame_Shift_Del	DEL	A	TCGA-A4-8311-01A-11D-2396-08		8872073	234327300	3	3743											
SRBD1	55133	hgsc.bcm.edu	37	chr2	45616665	45616665	+	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	agagtggcattctcaactttGcctgtaagaactgtcccaat	11	12	8	10	0	1	2	1	0	1	2	3	2	2	2	2	1	3	2	2	1	4	3			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr2:45616665G>C	ENST00000263736.4	-	21	2834	c.2772C>G	c.(2770-2772)ggC>ggG	p.G924G	SRBD1_ENST00000490133.1_5'UTR|SRBD1_ENST00000535761.1_Silent_p.G443G	NM_018079.4	NP_060549.4	Q8N5C6	SRBD1_HUMAN	S1 RNA binding domain 1	924	S1 motif. {ECO:0000255|PROSITE- ProRule:PRU00180}.				nucleobase-containing compound metabolic process (GO:0006139)		hydrolase activity, acting on ester bonds (GO:0016788)|RNA binding (GO:0003723)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(13)|large_intestine(8)|lung(15)|skin(2)|stomach(1)|urinary_tract(1)	49		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)			TCTCAACTTTGCCTGTAAGAA	0.378																																					p.G924G		Atlas-SNP	.											.	SRBD1	107	.	0			c.C2772G						PASS	.						66	64	64					2																	45616665		2202	4300	6502	SO:0001819	synonymous_variant	55133	exon21			AACTTTGCCTGTA	AK056536	CCDS1823.1	2p21	2008-02-05			ENSG00000068784	ENSG00000068784			25521	protein-coding gene	gene with protein product						12477932	Standard	NM_018079		Approved	FLJ10379	uc002rus.3	Q8N5C6	OTTHUMG00000128814	ENST00000263736.4:c.2772C>G	chr2.hg19:g.45616665G>C		71.0	0.0	.		65.0	17.0	.	NM_018079	Q53T56|Q96TA4|Q9NW11	Silent	SNP	ENST00000263736.4	hg19	CCDS1823.1																																																																																			.	.	.	none		0.378	SRBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250747.3	NM_018079		C	45616665	G	C	45616665	2	2	55	1	0	0	0	0	0	0	0	1	15145	1306	46	4		4	SRBD1	2	45616665	Silent	SNP	G	TCGA-A4-8311-01A-11D-2396-08	36744592	45616665	197582708	4	3744											
ZNF514	84874	hgsc.bcm.edu	37	chr2	95815137	95815137	+	Missense_Mutation	SNP	A	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	gggtttctctccagtgtgaaAtctgtaatgttgagtgagag	9	14	13	5	0	2	3	0	3	2	1	4	4	3	3	1	1	0	3	1	1	2	3			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr2:95815137A>C	ENST00000295208.2	-	5	1555	c.1093T>G	c.(1093-1095)Ttt>Gtt	p.F365V	ZNF514_ENST00000411425.1_Missense_Mutation_p.F365V|MRPS5_ENST00000475040.1_5'UTR	NM_032788.1	NP_116177.1	Q96K75	ZN514_HUMAN	zinc finger protein 514	365					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(4)|lung(6)|urinary_tract(1)	11						CCAGTGTGAAATCTGTAATGT	0.398																																					p.F365V		Atlas-SNP	.											.	ZNF514	34	.	0			c.T1093G						PASS	.						78	72	74					2																	95815137		2203	4300	6503	SO:0001583	missense	84874	exon5			TGTGAAATCTGTA	AL832263	CCDS2011.1	2q11.2	2013-01-08			ENSG00000144026	ENSG00000144026		"Zinc fingers, C2H2-type", "-"	25894	protein-coding gene	gene with protein product							Standard	NM_032788		Approved	FLJ14457	uc002sue.1	Q96K75	OTTHUMG00000130391	ENST00000295208.2:c.1093T>G	chr2.hg19:g.95815137A>C	ENSP00000295208:p.Phe365Val	78.0	0.0	.		74.0	33.0	.	NM_032788	Q5JPJ3	Missense_Mutation	SNP	ENST00000295208.2	hg19	CCDS2011.1	.	.	.	.	.	.	.	.	.	.	A	12.19	1.864411	0.32977	.	.	ENSG00000144026	ENST00000295208;ENST00000411425	T;T	0.28454	1.61;1.61	2.74	1.57	0.23409	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08088	0.0202	N	0.00611	-1.325	0.23572	N	0.997388	B;B	0.14805	0.011;0.0	B;B	0.14578	0.011;0.002	T	0.26326	-1.0106	9	0.35671	T	0.21	.	2.3501	0.04281	0.6187:0.0:0.1395:0.2419	.	365;184	Q96K75;Q658L7	ZN514_HUMAN;.	V	365	ENSP00000295208:F365V;ENSP00000405509:F365V	ENSP00000295208:F365V	F	-	1	0	ZNF514	95178864	0.001000	0.12720	0.999000	0.59377	0.996000	0.88848	0.606000	0.24194	0.454000	0.26884	0.533000	0.62120	TTT	.	.	.	none		0.398	ZNF514-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252769.1	NM_032788		C	95815137	A	C	95815137	3	2	55	1	0	0	0	0	1	0	0	0	17971	101	4	5	113	5	ZNF514	2	95815137	Missense_Mutation	SNP	A	TCGA-A4-8311-01A-11D-2396-08	50198472	95815137	147384236	5	3745											
SF3B1	23451	hgsc.bcm.edu	37	chr2	198266726	198266726	+	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	tacctttcctctgtgttggcGgatacccttccataaaggct	7	14	8	12	1	1	0	0	0	1	0	3	1	3	1	4	3	2	2	4	3	4	6	rs78164940		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr2:198266726G>T	ENST00000335508.6	-	15	2297	c.2206C>A	c.(2206-2208)Cgc>Agc	p.R736S	SF3B1_ENST00000462613.1_5'Flank|SNORA4_ENST00000365564.1_RNA	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	736					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.R736C(1)		NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			CTGTGTTGGCGGATACCCTTC	0.373			Mis		myelodysplastic syndrome																																p.R736S		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	SF3B1,NS,carcinoma,0,1	SF3B1	1038	.	1	Substitution - Missense(1)	endometrium(1)	c.C2206A						PASS	.						92	88	89					2																	198266726		2203	4300	6503	SO:0001583	missense	23451	exon15			GTTGGCGGATACC	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.2206C>A	chr2.hg19:g.198266726G>T	ENSP00000335321:p.Arg736Ser	59.0	0.0	.		64.0	4.0	.	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	hg19	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	G	16.03	3.006500	0.54361	.	.	ENSG00000115524	ENST00000335508	T	0.63913	-0.07	5.47	5.47	0.80525	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.67496	0.2899	M	0.76574	2.34	0.80722	D	1	B	0.33857	0.429	B	0.36335	0.222	T	0.69525	-0.5122	10	0.52906	T	0.07	.	19.3674	0.94469	0.0:0.0:1.0:0.0	.	736	O75533	SF3B1_HUMAN	S	736	ENSP00000335321:R736S	ENSP00000335321:R736S	R	-	1	0	SF3B1	197974971	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.892000	0.56235	2.567000	0.86603	0.650000	0.86243	CGC	.	.	.	weak		0.373	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			T	198266726	G	T	198266726	3	4	55	1	0	0	0	0	1	0	0	0	14162	1116	39	4	1752	4	SF3B1	2	198266726	Missense_Mutation	SNP	G	TCGA-A4-8311-01A-11D-2396-08	102451589	198266726	44932647	6	3746											
UGT1A3	54659	hgsc.bcm.edu	37	chr2	234638329	234638329	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttagactttaagggcacacAgtgtccaaacccttcctcct	10	12	6	13	0	0	1	0	0	0	1	3	1	3	1	4	1	1	1	4	1	3	5			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr2:234638329A>G	ENST00000482026.1	+	1	576	c.557A>G	c.(556-558)cAg>cGg	p.Q186R	UGT1A5_ENST00000373414.3_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A1_ENST00000609767.1_Missense_Mutation_p.Q186R|UGT1A1_ENST00000373450.4_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000609637.1_Intron			P35503	UD13_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A3	186					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)	AAGGGCACACAGTGTCCAAAC	0.458																																					p.Q186R		Atlas-SNP	.											.	UGT1A3	91	.	0			c.A557G						PASS	.						184	182	183					2																	234638329		2203	4300	6503	SO:0001583	missense	54659	exon1			GCACACAGTGTCC	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.557A>G	chr2.hg19:g.234638329A>G	ENSP00000418532:p.Gln186Arg	234.0	0.0	.		254.0	122.0	.	NM_019093	B8K287	Missense_Mutation	SNP	ENST00000482026.1	hg19	CCDS2509.1	.	.	.	.	.	.	.	.	.	.	a	8.706	0.910893	0.17833	.	.	ENSG00000243135	ENST00000482026	T	0.61392	0.11	4.13	-0.128	0.13506	.	.	.	.	.	T	0.52403	0.1732	L	0.41961	1.31	0.26480	N	0.975128	P;P	0.38863	0.65;0.65	P;P	0.49140	0.601;0.601	T	0.46275	-0.9203	9	0.13108	T	0.6	.	6.8323	0.23917	0.6376:0.2835:0.0789:0.0	.	186;186	Q5DT01;P35503	.;UD13_HUMAN	R	186	ENSP00000418532:Q186R	ENSP00000418532:Q186R	Q	+	2	0	UGT1A3	234303068	0.618000	0.27051	0.013000	0.15412	0.284000	0.27059	2.244000	0.43124	-0.332000	0.08489	-0.359000	0.07587	CAG	.	.	.	none		0.458	UGT1A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130983.1	NM_019093		G	234638329	A	G	234638329	3	3	55	1	0	0	0	0	1	0	0	0	16958	188	7	3	559	3	UGT1A3	2	234638329	Missense_Mutation	SNP	A	TCGA-A4-8311-01A-11D-2396-08	36371603	234638329	8561044	7	3747											
SCLY	51540	hgsc.bcm.edu	37	chr2	238990470	238990470	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggccaacaatgagactggcaTtgtcatggtgagtcggcctt	9	10	13	9	1	1	2	1	2	0	1	2	3	1	2	2	4	1	1	2	4	2	2	rs548740545		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr2:238990470T>C	ENST00000555827.1	+	5	669	c.605T>C	c.(604-606)aTt>aCt	p.I202T	SCLY_ENST00000373332.3_Missense_Mutation_p.I120T|SCLY_ENST00000254663.6_Missense_Mutation_p.I210T|SCLY_ENST00000409736.2_Missense_Mutation_p.I202T|SCLY_ENST00000422984.2_Missense_Mutation_p.I108T|SCLY_ENST00000429612.2_Intron			Q96I15	SCLY_HUMAN	selenocysteine lyase	202					cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)	pyridoxal phosphate binding (GO:0030170)|selenocysteine lyase activity (GO:0009000)|transferase activity (GO:0016740)			endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	22		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)		GAGACTGGCATTGTCATGGTG	0.572													T|||	1	0.000199681	0	0	5008	,	,		19116	0		0	False		,,,				2504	0.001				p.I210T	Melanoma(24;424 891 11947 32582 36034)|Ovarian(46;648 1065 26199 32764 45893)	Atlas-SNP	.											.	SCLY	51	.	0			c.T629C						PASS	.						95	77	83					2																	238990470		2203	4300	6503	SO:0001583	missense	51540	exon5			CTGGCATTGTCAT	AF175767	CCDS2524.1, CCDS2524.2	2q37.3	2008-02-05			ENSG00000132330	ENSG00000132330			18161	protein-coding gene	gene with protein product	"putative selenocysteine lyase"	611056				10692412	Standard	NM_016510		Approved	SCL	uc010fyv.4	Q96I15	OTTHUMG00000133336	ENST00000555827.1:c.605T>C	chr2.hg19:g.238990470T>C	ENSP00000450613:p.Ile202Thr	62.0	0.0	.		50.0	19.0	.	NM_016510	B9A068|J3KN06|Q53SN1|Q53SN8|Q7L670|Q9NVT7|Q9NZR7	Missense_Mutation	SNP	ENST00000555827.1	hg19		.	.	.	.	.	.	.	.	.	.	T	5.647	0.303939	0.10678	.	.	ENSG00000132330	ENST00000254663;ENST00000555827;ENST00000373332;ENST00000413463;ENST00000409736;ENST00000422984;ENST00000450965	D;D;D;D;D;D;D	0.85339	-1.97;-1.97;-1.97;-1.97;-1.97;-1.97;-1.97	5.84	4.67	0.58626	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.126390	0.52532	D	0.000062	T	0.61874	0.2382	N	0.00996	-1.065	0.80722	D	1	B;B;B	0.24043	0.036;0.096;0.006	B;B;B	0.31751	0.132;0.135;0.016	T	0.61426	-0.7065	10	0.02654	T	1	-27.8716	12.3833	0.55320	0.0:0.0:0.1409:0.8591	.	108;202;202	E7ESG3;Q96I15;Q96I15-2	.;SCLY_HUMAN;.	T	210;202;120;116;202;108;32	ENSP00000254663:I210T;ENSP00000450613:I202T;ENSP00000362429:I120T;ENSP00000414165:I116T;ENSP00000387162:I202T;ENSP00000416865:I108T;ENSP00000414053:I32T	ENSP00000254663:I202T	I	+	2	0	SCLY	238655209	1.000000	0.71417	0.002000	0.10522	0.045000	0.14185	7.953000	0.87836	1.020000	0.39573	0.533000	0.62120	ATT	.	.	.	none		0.572	SCLY-204	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_016510		C	238990470	T	C	238990470	3	2	55	1	0	0	0	0	1	0	0	0	13920	1493	52	3	623	3	SCLY	2	238990470	Missense_Mutation	SNP	T	TCGA-A4-8311-01A-11D-2396-08	4352141	238990470	4208903	8	3748											
ANKRD28	23243	hgsc.bcm.edu	37	chr3	15751227	15751227	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accagtattcagcagaaggtTtaggcactccaaattcctat	13	11	7	10	0	1	1	1	0	0	1	3	1	3	1	3	2	1	4	3	2	5	6			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr3:15751227T>C	ENST00000399451.2	-	13	1631	c.1264A>G	c.(1264-1266)Aac>Gac	p.N422D	ANKRD28_ENST00000497037.1_5'UTR|ANKRD28_ENST00000383777.1_Missense_Mutation_p.N455D	NM_001195098.1|NM_001195099.1|NM_015199.3	NP_001182027.1|NP_001182028.1|NP_056014.2	O15084	ANR28_HUMAN	ankyrin repeat domain 28	422						nucleus (GO:0005634)				breast(2)|endometrium(1)|large_intestine(2)|prostate(1)	6						AGCAGAAGGTTTAGGCACTCC	0.323																																					p.N422D		Atlas-SNP	.											.	ANKRD28	121	.	0			c.A1264G						PASS	.						68	60	62					3																	15751227		1816	4070	5886	SO:0001583	missense	23243	exon13			GAAGGTTTAGGCA	AY367056	CCDS46769.1, CCDS74908.1	3p25.1	2013-01-10			ENSG00000206560	ENSG00000206560		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	29024	protein-coding gene	gene with protein product	"phosphatase interactor targeting K protein", "protein phosphatase 6 ankyrin repeat subunit A", "protein phosphatase 1, regulatory subunit 65"	611122				9205841	Standard	NM_015199		Approved	KIAA0379, PITK, PP6-ARS-A, PPP1R65	uc003caj.1	O15084	OTTHUMG00000155379	ENST00000399451.2:c.1264A>G	chr3.hg19:g.15751227T>C	ENSP00000382379:p.Asn422Asp	11.0	0.0	.		15.0	9.0	.	NM_015199	B4DES5|Q1WWL4|Q29RW6|Q3B857|Q6ULS0|Q6ZT57	Missense_Mutation	SNP	ENST00000399451.2	hg19	CCDS46769.1	.	.	.	.	.	.	.	.	.	.	T	15.98	2.992948	0.54041	.	.	ENSG00000206560	ENST00000399451;ENST00000383777;ENST00000412318	T;T;T	0.63744	-0.06;-0.06;-0.06	5.96	5.96	0.96718	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.44746	0.1308	N	0.05608	-0.01	0.80722	D	1	B;B;B	0.19817	0.039;0.019;0.003	B;B;B	0.20184	0.028;0.012;0.013	T	0.34950	-0.9808	10	0.32370	T	0.25	.	16.4311	0.83844	0.0:0.0:0.0:1.0	.	455;452;422	O15084-1;O15084-4;O15084	.;.;ANR28_HUMAN	D	422;455;422	ENSP00000382379:N422D;ENSP00000373287:N455D;ENSP00000397341:N422D	ENSP00000373287:N455D	N	-	1	0	ANKRD28	15726231	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.972000	0.88022	2.277000	0.76020	0.528000	0.53228	AAC	.	.	.	none		0.323	ANKRD28-003	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339758.1	NM_015199		C	15751227	T	C	15751227	3	2	55	1	0	0	0	0	1	0	0	0	656	1841	64	3	1961	3	ANKRD28	3	15751227	Missense_Mutation	SNP	T	TCGA-A4-8311-01A-11D-2396-08		15751227	182271203	9	3749											
SACM1L	22908	hgsc.bcm.edu	37	chr3	45780273	45780273	+	Splice_Site	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	tttcttcctttctgttctagGattccatagacttatttctt	6	22	4	9	0	4	1	0	0	4	1	6	2	6	2	2	1	0	1	2	1	3	10			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr3:45780273G>A	ENST00000389061.5	+	18	1681	c.1477G>A	c.(1477-1479)Gat>Aat	p.D493N	SACM1L_ENST00000418611.1_Splice_Site_p.D390N|SACM1L_ENST00000541314.1_Splice_Site_p.D432N	NM_014016.3	NP_054735.3	Q9NTJ5	SAC1_HUMAN	SAC1 suppressor of actin mutations 1-like (yeast)	493					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)	phosphatase activity (GO:0016791)|phosphatidylinositol bisphosphate phosphatase activity (GO:0034593)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)		TCTGTTCTAGGATTCCATAGA	0.363																																					p.D493N		Atlas-SNP	.											.	SACM1L	38	.	0			c.G1477A						PASS	.						145	139	141					3																	45780273		2203	4300	6503	SO:0001630	splice_region_variant	22908	exon18			TTCTAGGATTCCA	AB020658	CCDS33745.1	3p21.3	2010-03-11			ENSG00000211456	ENSG00000211456			17059	protein-coding gene	gene with protein product		606569				10048485, 11352561	Standard	NM_014016		Approved	SAC1, KIAA0851	uc003cos.2	Q9NTJ5	OTTHUMG00000156653	ENST00000389061.5:c.1477-1G>A	chr3.hg19:g.45780273G>A		47.0	0.0	.		55.0	31.0	.	NM_014016	A8K527|B4DK71|O94935|Q7LA14|Q7LA22|Q96AX7|Q9NQ46|Q9NQ57	Missense_Mutation	SNP	ENST00000389061.5	hg19	CCDS33745.1	.	.	.	.	.	.	.	.	.	.	G	33	5.226777	0.95173	.	.	ENSG00000211456	ENST00000418611;ENST00000389061;ENST00000541314;ENST00000433336	T;T;T;T	0.07327	3.2;3.2;3.2;3.2	6.05	6.05	0.98169	.	0.091827	0.85682	D	0.000000	T	0.27629	0.0679	M	0.72894	2.215	0.80722	D	1	D;D;D	0.89917	0.996;1.0;0.995	D;D;P	0.87578	0.918;0.998;0.831	T	0.00063	-1.2155	9	.	.	.	-4.7089	13.7549	0.62930	0.0698:0.0:0.9302:0.0	.	432;136;493	B4DK71;B3KX17;Q9NTJ5	.;.;SAC1_HUMAN	N	390;493;432;170	ENSP00000396387:D390N;ENSP00000373713:D493N;ENSP00000443373:D432N;ENSP00000412883:D170N	.	D	+	1	0	SACM1L	45755277	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.455000	0.80726	2.878000	0.98634	0.650000	0.86243	GAT	.	.	.	none		0.363	SACM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345065.2	NM_014016	Missense_Mutation	A	45780273	G	A	45780273	5	1	55	1	0	0	0	0	0	0	1	0	13816	1188	41	2	1547	2	SACM1L	3	45780273	Splice_Site	SNP	G	TCGA-A4-8311-01A-11D-2396-08	30029046	45780273	152242157	10	3750											
ACPL2	92370	hgsc.bcm.edu	37	chr3	140979087	140979087	+	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	tggcctttgtgagcctcagcCtgcagttctgtgagtagagc	6	12	13	10	0	2	3	1	2	1	1	2	3	2	3	3	1	4	3	3	1	1	3	rs367551091	byFrequency	TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr3:140979087C>A	ENST00000286353.4	+	2	207	c.70C>A	c.(70-72)Ctg>Atg	p.L24M	ACPL2_ENST00000393010.2_Missense_Mutation_p.L24M|ACPL2_ENST00000502783.1_5'UTR|ACPL2_ENST00000504264.1_5'Flank	NM_001037172.1|NM_001282728.1	NP_001032249.1|NP_001269657.1	Q8TE99	PXYP1_HUMAN		24						extracellular region (GO:0005576)	acid phosphatase activity (GO:0003993)			endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|prostate(2)|skin(2)	23						GAGCCTCAGCCTGCAGTTCTG	0.517																																					p.L24M		Atlas-SNP	.											.	ACPL2	50	.	0			c.C70A						PASS	.						49	56	53					3																	140979087		2203	4300	6503	SO:0001583	missense	92370	exon4			CTCAGCCTGCAGT																												ENST00000286353.4:c.70C>A	chr3.hg19:g.140979087C>A	ENSP00000286353:p.Leu24Met	47.0	0.0	.		46.0	22.0	.	NM_152282	D3DNF5|Q49AJ2|W0TR04	Missense_Mutation	SNP	ENST00000286353.4	hg19	CCDS3116.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.845120	0.51164	.	.	ENSG00000155893	ENST00000505013;ENST00000286353;ENST00000393010;ENST00000514680	T;T	0.25085	1.82;1.82	5.87	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.47021	0.1423	M	0.64997	1.995	0.80722	D	1	D	0.71674	0.998	D	0.80764	0.994	T	0.42832	-0.9428	10	0.49607	T	0.09	.	13.2927	0.60280	0.0:0.9233:0.0:0.0767	.	24	Q8TE99	ACPL2_HUMAN	M	24	ENSP00000286353:L24M;ENSP00000376733:L24M	ENSP00000286353:L24M	L	+	1	2	ACPL2	142461777	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.962000	0.63687	1.628000	0.50416	-0.150000	0.13652	CTG	.	.	.	alt		0.517	ACPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359533.2			A	140979087	C	A	140979087	3	1	55	1	0	0	0	0	1	0	0	0	166	680	24	4	72	4	ACPL2	3	140979087	Missense_Mutation	SNP	C	TCGA-A4-8311-01A-11D-2396-08	95198814	140979087	57043343	11	3751											
ZNF721	170960	hgsc.bcm.edu	37	chr4	437056	437056	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtgcagtaaggtttgttgaActattaaaggctttgccaca	11	14	10	6	0	0	1	0	1	0	0	0	1	0	1	1	2	3	5	1	2	5	6			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr4:437056A>G	ENST00000338977.5	-	2	1212	c.1164T>C	c.(1162-1164)agT>agC	p.S388S	ZNF721_ENST00000507078.1_Intron|ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000506646.1_Intron|ZNF721_ENST00000511833.2_Silent_p.S400S			Q8TF20	ZN721_HUMAN	zinc finger protein 721	388				NS -> VC (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						GGTTTGTTGAACTATTAAAGG	0.428																																					p.M400I		Atlas-SNP	.											.	ZNF721	205	.	0			c.G1200C						PASS	.						92	96	95					4																	437056		2109	4254	6363	SO:0001819	synonymous_variant	170960	exon3			TGTTGAACTATTA	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.1164T>C	chr4.hg19:g.437056A>G		59.0	0.0	.		56.0	24.0	.	NM_133474	Q69YG7	Missense_Mutation	SNP	ENST00000338977.5	hg19																																																																																				.	.	.	none		0.428	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474		G	437056	A	G	437056	2	3	55	1	0	0	0	0	0	0	0	1	18134	40	2	3		3	ZNF721	4	437056	Silent	SNP	A	TCGA-A4-8311-01A-11D-2396-08		437056	190717220	12	3752											
SLC26A1	10861	hgsc.bcm.edu	37	chr4	983983	983983	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcgcagcaggctcagccaTgtgaggaccaccatgccggg	8	4	14	15	3	1	1	1	1	0	0	1	2	1	2	5	3	3	3	5	3	0	0			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr4:983983T>C	ENST00000361661.2	-	4	1121	c.744A>G	c.(742-744)acA>acG	p.T248T	SLC26A1_ENST00000398520.2_Intron|IDUA_ENST00000453894.1_Intron|SLC26A1_ENST00000513138.1_5'Flank|SLC26A1_ENST00000398516.2_Silent_p.T248T|IDUA_ENST00000247933.4_Intron	NM_213613.2	NP_998778.1	Q9H2B4	S26A1_HUMAN	solute carrier family 26 (anion exchanger), member 1	248					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|chloride transport (GO:0006821)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|oxalate transport (GO:0019532)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|chloride transmembrane transporter activity (GO:0015108)|oxalate transmembrane transporter activity (GO:0019531)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(1)|endometrium(4)|pancreas(1)|prostate(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GGCTCAGCCATGTGAGGACCA	0.697																																					p.T248T		Atlas-SNP	.											.	SLC26A1	44	.	0			c.A744G						PASS	.						10	12	11					4																	983983		2134	4181	6315	SO:0001819	synonymous_variant	10861	exon3			CAGCCATGTGAGG	AF297659	CCDS33933.1, CCDS33934.1	4p16.3	2013-07-18	2013-07-18		ENSG00000145217	ENSG00000145217		"Solute carriers"	10993	protein-coding gene	gene with protein product		610130	"solute carrier family 26 (sulfate transporter), member 1"				Standard	NM_213613		Approved	SAT-1, EDM4	uc003gcc.3	Q9H2B4	OTTHUMG00000160003	ENST00000361661.2:c.744A>G	chr4.hg19:g.983983T>C		9.0	0.0	.		7.0	5.0	.	NM_022042	A8K9N2|Q7Z5R3|Q96BK0	Silent	SNP	ENST00000361661.2	hg19	CCDS33934.1																																																																																			.	.	.	none		0.697	SLC26A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358783.1	NM_022042, NM_134425		C	983983	T	C	983983	2	2	55	1	0	0	0	0	0	0	0	1	14527	1451	51	3		3	SLC26A1	4	983983	Silent	SNP	T	TCGA-A4-8311-01A-11D-2396-08	546927	983983	190170293	13	3753											
SH3BP2	6452	hgsc.bcm.edu	37	chr4	2824664	2824664	+	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	ccttgccacctcccacagggCccctgcgctttgtcatcatc	5	10	7	19	1	2	0	2	0	0	0	4	0	3	0	6	1	2	1	6	1	0	2			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr4:2824664C>T	ENST00000356331.5	+	3	400	c.139C>T	c.(139-141)Ccc>Tcc	p.P47S	SH3BP2_ENST00000452765.2_Missense_Mutation_p.P47S|SH3BP2_ENST00000442312.2_Missense_Mutation_p.P75S|SH3BP2_ENST00000511747.1_Missense_Mutation_p.P47S|SH3BP2_ENST00000503393.2_Missense_Mutation_p.P104S|SH3BP2_ENST00000435136.2_Missense_Mutation_p.P47S|SH3BP2_ENST00000389838.2_Missense_Mutation_p.P47S	NM_003023.4	NP_003014.3	P78314	3BP2_HUMAN	SH3-domain binding protein 2	47	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)		SH3/SH2 adaptor activity (GO:0005070)	p.P47S(1)		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)		TCCCACAGGGCCCCTGCGCTT	0.627									Cherubism																												p.P104S		Atlas-SNP	.											SH3BP2,NS,carcinoma,0,1	SH3BP2	43	.	1	Substitution - Missense(1)	prostate(1)	c.C310T						PASS	.						64	52	56					4																	2824664		2203	4300	6503	SO:0001583	missense	6452	exon3	Familial Cancer Database	Familial Benign Giant-cell Tumor of the Jaw, Familial Multilocular Cystic Disease	ACAGGGCCCCTGC	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.139C>T	chr4.hg19:g.2824664C>T	ENSP00000348685:p.Pro47Ser	22.0	0.0	.		33.0	14.0	.	NM_001145856	A6NNC2|B2R5R6|B4DT04|D3DVR0|D6R919|O00500|O15373|P78315	Missense_Mutation	SNP	ENST00000356331.5	hg19	CCDS33944.1	.	.	.	.	.	.	.	.	.	.	C	18.12	3.553572	0.65425	.	.	ENSG00000087266	ENST00000452765;ENST00000389838;ENST00000503219;ENST00000504294;ENST00000508385;ENST00000512014;ENST00000513095;ENST00000442312;ENST00000502260;ENST00000435136;ENST00000511747;ENST00000503393;ENST00000356331	T;T;T;T;T;T;T;T;T;T;T;T;T	0.11495	2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77	3.94	3.94	0.45596	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.20373	0.0490	L	0.31207	0.915	0.58432	D	0.999997	P;D;P;P	0.61080	0.863;0.989;0.939;0.939	P;D;P;P	0.64595	0.524;0.927;0.666;0.666	T	0.02877	-1.1099	10	0.52906	T	0.07	-4.9102	15.9158	0.79517	0.0:1.0:0.0:0.0	.	75;75;104;47	B4DT04;B7Z9B6;D6R919;P78314	.;.;.;3BP2_HUMAN	S	47;47;47;47;47;47;47;75;47;47;47;104;47	ENSP00000409746:P47S;ENSP00000374488:P47S;ENSP00000422796:P47S;ENSP00000423275:P47S;ENSP00000424917:P47S;ENSP00000424105:P47S;ENSP00000423823:P47S;ENSP00000388152:P75S;ENSP00000425537:P47S;ENSP00000403231:P47S;ENSP00000424846:P47S;ENSP00000422168:P104S;ENSP00000348685:P47S	ENSP00000348685:P47S	P	+	1	0	SH3BP2	2794462	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	6.870000	0.75526	1.927000	0.55829	0.491000	0.48974	CCC	.	.	.	none		0.627	SH3BP2-007	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362406.2	NM_003023		T	2824664	C	T	2824664	3	4	55	1	0	0	0	0	1	0	0	0	14258	739	26	2	404	2	SH3BP2	4	2824664	Missense_Mutation	SNP	C	TCGA-A4-8311-01A-11D-2396-08	1840681	2824664	188329612	14	3754											
MFSD10	10227	hgsc.bcm.edu	37	chr4	2934166	2934166	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagggcaaaccagggtgccAtttccaggggcagggaggct	9	5	17	10	0	0	0	0	0	0	0	1	1	1	1	3	6	2	4	3	6	1	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr4:2934166A>G	ENST00000329687.4	-	5	1139	c.605T>C	c.(604-606)aTg>aCg	p.M202T	MFSD10_ENST00000507555.1_Missense_Mutation_p.M202T|NOP14-AS1_ENST00000505731.1_RNA|NOP14-AS1_ENST00000507999.1_RNA|MFSD10_ENST00000508221.1_Missense_Mutation_p.M202T|MFSD10_ENST00000355443.4_Missense_Mutation_p.M202T|MFSD10_ENST00000514800.1_Missense_Mutation_p.M202T	NM_001120.4	NP_001111.3	Q14728	MFS10_HUMAN	major facilitator superfamily domain containing 10	202					apoptotic process (GO:0006915)|tetracycline transport (GO:0015904)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)	tetracycline transporter activity (GO:0008493)			breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		CCAGGGTGCCATTTCCAGGGG	0.632																																					p.M202T		Atlas-SNP	.											.	MFSD10	22	.	0			c.T605C						PASS	.						52	58	56					4																	2934166		2203	4300	6503	SO:0001583	missense	10227	exon5			GGTGCCATTTCCA	L11669	CCDS3365.1	4p16.3	2008-03-03			ENSG00000109736	ENSG00000109736			16894	protein-coding gene	gene with protein product	"tetracycline transporter like protein"	610977				8353488, 17362938	Standard	NM_001120		Approved	TETRAN, IT10C3	uc003gfz.3	Q14728	OTTHUMG00000122081	ENST00000329687.4:c.605T>C	chr4.hg19:g.2934166A>G	ENSP00000332646:p.Met202Thr	69.0	0.0	.		64.0	26.0	.	NM_001120	Q07706	Missense_Mutation	SNP	ENST00000329687.4	hg19	CCDS3365.1	.	.	.	.	.	.	.	.	.	.	A	0.137	-1.106537	0.01828	.	.	ENSG00000109736	ENST00000514800;ENST00000355443;ENST00000329687;ENST00000508221;ENST00000507555	T;T;T;T;T	0.56776	0.44;0.44;0.44;0.44;0.44	4.69	-2.4	0.06583	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.719668	0.14277	N	0.329747	T	0.14141	0.0342	N	0.00890	-1.11	0.09310	N	1	B;B;B;B	0.06786	0.0;0.001;0.001;0.0	B;B;B;B	0.04013	0.0;0.001;0.0;0.0	T	0.23762	-1.0179	10	0.15066	T	0.55	-26.4194	2.158	0.03818	0.4585:0.122:0.2967:0.1227	.	202;202;202;202	D6RIZ4;D6RE79;D6RA47;Q14728	.;.;.;MFS10_HUMAN	T	202	ENSP00000426907:M202T;ENSP00000347619:M202T;ENSP00000332646:M202T;ENSP00000425757:M202T;ENSP00000423402:M202T	ENSP00000332646:M202T	M	-	2	0	MFSD10	2903964	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-0.615000	0.05597	-0.477000	0.06832	-0.417000	0.06048	ATG	.	.	.	none		0.632	MFSD10-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358072.2	NM_001120		G	2934166	A	G	2934166	3	3	55	1	0	0	0	0	1	0	0	0	9535	217	8	3	794	3	MFSD10	4	2934166	Missense_Mutation	SNP	A	TCGA-A4-8311-01A-11D-2396-08	109502	2934166	188220110	15	3755											
COL25A1	84570	hgsc.bcm.edu	37	chr4	109817832	109817832	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaaactgtaccttttcgccTgtgtcacccttggggccgtt	6	13	9	13	2	1	0	1	0	0	0	2	0	1	0	4	2	2	2	4	2	3	5			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr4:109817832T>C	ENST00000399132.1	-	16	1427	c.897A>G	c.(895-897)acA>acG	p.T299T	COL25A1_ENST00000399126.1_Silent_p.T299T|COL25A1_ENST00000399127.1_Silent_p.T295T	NM_198721.2	NP_942014.1			collagen, type XXV, alpha 1											NS(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	49		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)		CCTTTTCGCCTGTGTCACCCT	0.418																																					p.T299T		Atlas-SNP	.											.	COL25A1	178	.	0			c.A897G						PASS	.						128	123	124					4																	109817832		1892	4115	6007	SO:0001819	synonymous_variant	84570	exon15			TTCGCCTGTGTCA	AF293340	CCDS43258.1, CCDS43259.1, CCDS58922.1	4q25	2013-01-16			ENSG00000188517	ENSG00000188517		"Collagens"	18603	protein-coding gene	gene with protein product		610004				11927537	Standard	NM_001256074		Approved		uc003hze.2	Q9BXS0	OTTHUMG00000150039	ENST00000399132.1:c.897A>G	chr4.hg19:g.109817832T>C		87.0	0.0	.		86.0	4.0	.	NM_198721		Silent	SNP	ENST00000399132.1	hg19	CCDS43258.1																																																																																			.	.	.	none		0.418	COL25A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315938.2	NM_032518		C	109817832	T	C	109817832	2	2	55	1	0	0	0	0	0	0	0	1	3686	1567	55	3		3	COL25A1	4	109817832	Silent	SNP	T	TCGA-A4-8311-01A-11D-2396-08	106883666	109817832	81336444	16	3756											
SLCO6A1	133482	hgsc.bcm.edu	37	chr5	101834204	101834204	+	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	ggctcaccttgacatatgagCaggatgcagtagaaaatcat	14	9	10	8	0	2	3	2	2	0	1	2	4	2	4	1	2	2	4	1	2	4	3			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr5:101834204C>A	ENST00000506729.1	-	1	516	c.345G>T	c.(343-345)ctG>ctT	p.L115L	SLCO6A1_ENST00000513675.1_Silent_p.L115L|SLCO6A1_ENST00000379807.3_Silent_p.L115L|SLCO6A1_ENST00000389019.3_Silent_p.L115L|RP11-58B2.1_ENST00000502494.1_RNA|SLCO6A1_ENST00000379810.1_Silent_p.L115L|SLCO6A1_ENST00000514551.1_5'UTR			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	115	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)		GACATATGAGCAGGATGCAGT	0.572																																					p.L115L		Atlas-SNP	.											.	SLCO6A1	153	.	0			c.G345T						PASS	.						59	60	60					5																	101834204		2203	4300	6503	SO:0001819	synonymous_variant	133482	exon1			TATGAGCAGGATG	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.345G>T	chr5.hg19:g.101834204C>A		73.0	0.0	.		73.0	35.0	.	NM_173488	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Silent	SNP	ENST00000506729.1	hg19	CCDS34206.1																																																																																			.	.	.	none		0.572	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488		A	101834204	C	A	101834204	2	1	55	1	0	0	0	0	0	0	0	1	14745	697	25	4		4	SLCO6A1	5	101834204	Silent	SNP	C	TCGA-A4-8311-01A-11D-2396-08		101834204	79081056	17	3757											
IL9	3578	hgsc.bcm.edu	37	chr5	135228124	135228124	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catcttttctttctggaaaaTttccagaagactcttcagaa	12	15	5	9	0	5	3	1	0	4	3	6	4	6	4	1	1	0	0	1	1	4	5			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr5:135228124T>C	ENST00000274520.1	-	5	401	c.391A>G	c.(391-393)Att>Gtt	p.I131V		NM_000590.1	NP_000581.1	P15248	IL9_HUMAN	interleukin 9	131					immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interleukin-5 biosynthetic process (GO:0045407)	extracellular space (GO:0005615)				large_intestine(3)|lung(2)|pancreas(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TTCTGGAAAATTTCCAGAAGA	0.368																																					p.I131V		Atlas-SNP	.											.	IL9	14	.	0			c.A391G						PASS	.						66	73	71					5																	135228124		2203	4300	6503	SO:0001583	missense	3578	exon5			GGAAAATTTCCAG	S63356	CCDS4189.1	5q31-q35	2008-07-18			ENSG00000145839	ENSG00000145839		"Interleukins and interleukin receptors"	6029	protein-coding gene	gene with protein product	"p40 T-cell and mast cell growth factor", "T-cell growth factor p40", "p40 cytokine", "homolog of mouse T cell and mast cell growth factor 40"	146931				8379467	Standard	NM_000590		Approved	IL-9, HP40, P40	uc003lbb.1	P15248	OTTHUMG00000129147	ENST00000274520.1:c.391A>G	chr5.hg19:g.135228124T>C	ENSP00000274520:p.Ile131Val	74.0	0.0	.		49.0	23.0	.	NM_000590		Missense_Mutation	SNP	ENST00000274520.1	hg19	CCDS4189.1	.	.	.	.	.	.	.	.	.	.	T	0.246	-1.010364	0.02095	.	.	ENSG00000145839	ENST00000274520	T	0.42131	0.98	5.48	-7.84	0.01196	.	1.696530	0.03303	N	0.189306	T	0.12944	0.0314	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.25916	-1.0118	10	0.08179	T	0.78	-2.0474	8.7041	0.34343	0.0:0.3821:0.1035:0.5144	.	131	P15248	IL9_HUMAN	V	131	ENSP00000274520:I131V	ENSP00000274520:I131V	I	-	1	0	IL9	135256023	0.000000	0.05858	0.000000	0.03702	0.112000	0.19704	-0.778000	0.04664	-1.878000	0.01128	-1.601000	0.00813	ATT	.	.	.	none		0.368	IL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251210.1	NM_000590		C	135228124	T	C	135228124	3	2	55	1	0	0	0	0	1	0	0	0	7714	1493	52	3	47	3	IL9	5	135228124	Missense_Mutation	SNP	T	TCGA-A4-8311-01A-11D-2396-08	33393920	135228124	45687136	18	3758											
SLC35A4	113829	hgsc.bcm.edu	37	chr5	139947279	139947279	+	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	cccagtccccctccagcagcTgctgccagccccatgcccct	5	6	7	23	0	0	0	0	0	0	0	2	0	2	0	9	0	6	3	9	0	0	0			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr5:139947279T>A	ENST00000514199.1	+	2	2211	c.525T>A	c.(523-525)gcT>gcA	p.A175A	APBB3_ENST00000507279.1_Intron|SLC35A4_ENST00000323146.3_Silent_p.A175A			Q96G79	S35A4_HUMAN	solute carrier family 35, member A4	175	Leu-rich.					Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sugar:proton symporter activity (GO:0005351)			endometrium(4)|kidney(2)|large_intestine(3)|lung(4)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCCAGCAGCTGCTGCCAGCC	0.622																																					p.A175A		Atlas-SNP	.											.	SLC35A4	25	.	0			c.T525A						PASS	.						59	57	58					5																	139947279		2203	4300	6503	SO:0001819	synonymous_variant	113829	exon3			AGCAGCTGCTGCC	AJ420598	CCDS4231.1	5q31.3	2013-05-22			ENSG00000176087	ENSG00000176087		"Solute carriers"	20753	protein-coding gene	gene with protein product							Standard	NM_080670		Approved		uc003lgg.1	Q96G79	OTTHUMG00000129495	ENST00000514199.1:c.525T>A	chr5.hg19:g.139947279T>A		89.0	0.0	.		73.0	35.0	.	NM_080670	A8K013	Silent	SNP	ENST00000514199.1	hg19	CCDS4231.1																																																																																			.	.	.	none		0.622	SLC35A4-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372815.1	NM_080670		A	139947279	T	A	139947279	2	1	55	1	0	0	0	0	0	0	0	1	14586	1567	55	5		5	SLC35A4	5	139947279	Silent	SNP	T	TCGA-A4-8311-01A-11D-2396-08	4719155	139947279	40967981	19	3759											
TREM2	54209	hgsc.bcm.edu	37	chr6	41129014	41129014	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cactcacctgccagcacctcCaccaggaccttcctgagggt	8	7	8	18	0	1	1	1	1	0	0	3	2	3	2	7	2	2	1	7	2	0	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr6:41129014C>T	ENST00000373113.3	-	2	471	c.378G>A	c.(376-378)gtG>gtA	p.V126V	TREM2_ENST00000338469.3_Silent_p.V126V|TREM2_ENST00000373122.4_Silent_p.V126V	NM_018965.2	NP_061838.1	Q9NZC2	TREM2_HUMAN	triggering receptor expressed on myeloid cells 2	126					axon guidance (GO:0007411)|dendritic cell differentiation (GO:0097028)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|positive regulation of antigen processing and presentation of peptide antigen via MHC class II (GO:0002588)|positive regulation of C-C chemokine receptor CCR7 signaling pathway (GO:1903082)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of CD40 signaling pathway (GO:2000350)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein localization to plasma membrane (GO:1903078)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			breast(1)|endometrium(2)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)	11	Ovarian(28;0.0418)|Colorectal(47;0.196)					CCAGCACCTCCACCAGGACCT	0.612																																					p.V126V		Atlas-SNP	.											.	TREM2	35	.	0			c.G378A						PASS	.						43	41	42					6																	41129014		2203	4300	6503	SO:0001819	synonymous_variant	54209	exon2			CACCTCCACCAGG	AF213457	CCDS4852.1, CCDS64422.1	6p21.1	2014-09-17	2002-08-15		ENSG00000095970	ENSG00000095970		"Immunoglobulin superfamily / V-set domain containing"	17761	protein-coding gene	gene with protein product		605086	"triggering receptor expressed on myeloid cells 2a"			10799849, 12080485	Standard	NM_001271821		Approved	TREM-2, Trem2a, Trem2b, Trem2c	uc003opy.3	Q9NZC2	OTTHUMG00000014671	ENST00000373113.3:c.378G>A	chr6.hg19:g.41129014C>T		45.0	0.0	.		42.0	13.0	.	NM_018965	Q8N5H8|Q8WYN6	Silent	SNP	ENST00000373113.3	hg19	CCDS4852.1																																																																																			.	.	.	none		0.612	TREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040499.1	NM_018965		T	41129014	C	T	41129014	2	4	55	1	0	0	0	0	0	0	0	1	16483	581	21	2		2	TREM2	6	41129014	Silent	SNP	C	TCGA-A4-8311-01A-11D-2396-08		41129014	129986053	20	3760											
TJAP1	93643	hgsc.bcm.edu	37	chr6	43466779	43466779	+	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	ctaagaaaccctaccgtaagGcaccaccagagcatcgggag	14	4	10	13	2	0	2	0	0	0	2	1	3	0	3	4	2	3	3	4	2	4	3			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr6:43466779G>C	ENST00000372445.5	+	4	416	c.40G>C	c.(40-42)Gca>Cca	p.A14P	TJAP1_ENST00000483640.1_3'UTR|TJAP1_ENST00000372452.1_Missense_Mutation_p.A14P|TJAP1_ENST00000372449.1_Missense_Mutation_p.A14P|TJAP1_ENST00000259751.1_Missense_Mutation_p.A14P|TJAP1_ENST00000438588.2_Missense_Mutation_p.A14P|TJAP1_ENST00000372444.2_Missense_Mutation_p.A14P|TJAP1_ENST00000436109.2_Missense_Mutation_p.A14P	NM_001146016.1	NP_001139488.1	Q5JTD0	TJAP1_HUMAN	tight junction associated protein 1 (peripheral)	14					Golgi organization (GO:0007030)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)|trans-Golgi network (GO:0005802)		p.A14S(1)		cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|urinary_tract(2)	21	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			CTACCGTAAGGCACCACCAGA	0.587																																					p.A14P		Atlas-SNP	.											TJAP1,NS,carcinoma,0,1	TJAP1	35	.	1	Substitution - Missense(1)	lung(1)	c.G40C						PASS	.						92	77	82					6																	43466779		2203	4300	6503	SO:0001583	missense	93643	exon4			CGTAAGGCACCAC	AK024269	CCDS4898.1, CCDS55004.1	6p21.1	2008-02-05	2005-07-05	2005-07-05	ENSG00000137221	ENSG00000137221			17949	protein-coding gene	gene with protein product		612658	"tight junction protein 4 (peripheral)"	TJP4		11602598	Standard	NM_001146016		Approved	PILT	uc011dvh.1	Q5JTD0	OTTHUMG00000014736	ENST00000372445.5:c.40G>C	chr6.hg19:g.43466779G>C	ENSP00000361522:p.Ala14Pro	51.0	0.0	.		51.0	4.0	.	NM_080604	Q05BH9|Q5JTD1|Q5JWW1|Q68DB2|Q6P2P3|Q9H7V7	Missense_Mutation	SNP	ENST00000372445.5	hg19	CCDS55004.1	.	.	.	.	.	.	.	.	.	.	G	34	5.300029	0.95574	.	.	ENSG00000137221	ENST00000372444;ENST00000372445;ENST00000436109;ENST00000442878;ENST00000259751;ENST00000372454;ENST00000372452;ENST00000372449;ENST00000438588	T;T;T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.56426	0.1984	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	0.998;0.999;0.999	T	0.60188	-0.7312	10	0.87932	D	0	-0.0171	17.1606	0.86802	0.0:0.0:1.0:0.0	.	14;14;14	E2QRK7;Q5JTD0;Q5JTD0-2	.;TJAP1_HUMAN;.	P	14	ENSP00000361521:A14P;ENSP00000361522:A14P;ENSP00000407080:A14P;ENSP00000390981:A14P;ENSP00000259751:A14P;ENSP00000361530:A14P;ENSP00000361527:A14P;ENSP00000408769:A14P	ENSP00000259751:A14P	A	+	1	0	TJAP1	43574757	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.903000	0.87398	2.495000	0.84180	0.655000	0.94253	GCA	.	.	.	none		0.587	TJAP1-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040629.1	NM_080604		C	43466779	G	C	43466779	3	2	55	1	0	0	0	0	1	0	0	0	15940	1203	42	4	42	4	TJAP1	6	43466779	Missense_Mutation	SNP	G	TCGA-A4-8311-01A-11D-2396-08	2337765	43466779	127648288	21	3761											
WDR91	29062	hgsc.bcm.edu	37	chr7	134873248	134873248	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaactccacagagtagacCtccccgtagtgggccctcca	9	7	9	16	1	0	3	0	1	0	2	3	3	3	3	6	1	1	2	6	1	3	2			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr7:134873248C>T	ENST00000354475.4	-	13	1849	c.1818G>A	c.(1816-1818)gaG>gaA	p.E606E	WDR91_ENST00000423565.1_Silent_p.E571E|WDR91_ENST00000344400.5_Intron	NM_014149.3	NP_054868.3	A4D1P6	WDR91_HUMAN	WD repeat domain 91	606										breast(3)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	40						CAGAGTAGACCTCCCCGTAGT	0.592																																					p.E606E		Atlas-SNP	.											.	WDR91	82	.	0			c.G1818A						PASS	.						177	161	167					7																	134873248		2203	4300	6503	SO:0001819	synonymous_variant	29062	exon13			GTAGACCTCCCCG	AF161534	CCDS34758.1	7q33	2013-01-09			ENSG00000105875	ENSG00000105875		"WD repeat domain containing"	24997	protein-coding gene	gene with protein product						11042152, 11230166	Standard	NM_014149		Approved	HSPC049	uc003vsp.2	A4D1P6	OTTHUMG00000155414	ENST00000354475.4:c.1818G>A	chr7.hg19:g.134873248C>T		217.0	0.0	.		304.0	64.0	.	NM_014149	A6NK54|C9JMI4|Q6FI65|Q6MZQ1|Q6P4I1|Q96AE5|Q96G63|Q9H062|Q9H9B6|Q9NVG7|Q9NZY6	Silent	SNP	ENST00000354475.4	hg19	CCDS34758.1																																																																																			.	.	.	none		0.592	WDR91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340019.1	NM_014149		T	134873248	C	T	134873248	2	4	55	1	0	0	0	0	0	0	0	1	17350	680	24	2		2	WDR91	7	134873248	Silent	SNP	C	TCGA-A4-8311-01A-11D-2396-08		134873248	24265415	22	3762											
VCPIP1	80124	hgsc.bcm.edu	37	chr8	67577113	67577113	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttttgttttctgtccagtaAgaataattttagttgggagc	9	19	9	4	0	1	1	0	0	1	1	2	2	2	2	1	1	1	3	1	1	4	9			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr8:67577113A>G	ENST00000310421.4	-	1	2339	c.2081T>C	c.(2080-2082)cTt>cCt	p.L694P	C8orf44_ENST00000519561.1_5'Flank|C8orf44_ENST00000521889.1_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	694					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)			CTGTCCAGTAAGAATAATTTT	0.373																																					p.L694P	NSCLC(179;265 2915 6144 43644)	Atlas-SNP	.											.	VCPIP1	110	.	0			c.T2081C						PASS	.						133	142	139					8																	67577113		2203	4300	6503	SO:0001583	missense	80124	exon1			CCAGTAAGAATAA	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.2081T>C	chr8.hg19:g.67577113A>G	ENSP00000309031:p.Leu694Pro	158.0	0.0	.		151.0	58.0	.	NM_025054	Q504T4|Q86T93|Q86W01|Q8N3A9|Q9H5R8	Missense_Mutation	SNP	ENST00000310421.4	hg19	CCDS6192.1	.	.	.	.	.	.	.	.	.	.	A	16.13	3.036462	0.54896	.	.	ENSG00000175073	ENST00000310421	T	0.46063	0.88	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.61160	0.2325	L	0.56769	1.78	0.80722	D	1	D	0.71674	0.998	D	0.81914	0.995	T	0.64778	-0.6327	10	0.87932	D	0	-11.0176	15.447	0.75238	1.0:0.0:0.0:0.0	.	694	Q96JH7	VCIP1_HUMAN	P	694	ENSP00000309031:L694P	ENSP00000309031:L694P	L	-	2	0	VCPIP1	67739667	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.244000	0.95423	2.091000	0.63221	0.533000	0.62120	CTT	.	.	.	none		0.373	VCPIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379227.1			G	67577113	A	G	67577113	3	3	55	1	0	0	0	0	1	0	0	0	17153	72	3	3	1599	3	VCPIP1	8	67577113	Missense_Mutation	SNP	A	TCGA-A4-8311-01A-11D-2396-08		67577113	78786909	23	3763											
TAF2	6873	hgsc.bcm.edu	37	chr8	120816142	120816142	+	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	tagaattttgatacccacaaGagaaaacatgagcacctctc	16	9	6	10	0	1	4	0	2	1	2	2	5	1	4	2	0	3	1	2	0	6	4			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr8:120816142G>A	ENST00000378164.2	-	5	834	c.536C>T	c.(535-537)tCt>tTt	p.S179F		NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	179					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)			ATACCCACAAGAGAAAACATG	0.333																																					p.S179F		Atlas-SNP	.											.	TAF2	204	.	0			c.C536T						PASS	.						138	140	139					8																	120816142		2203	4300	6503	SO:0001583	missense	6873	exon5			CCACAAGAGAAAA	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.536C>T	chr8.hg19:g.120816142G>A	ENSP00000367406:p.Ser179Phe	226.0	0.0	.		160.0	75.0	.	NM_003184	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Missense_Mutation	SNP	ENST00000378164.2	hg19	CCDS34937.1	.	.	.	.	.	.	.	.	.	.	G	33	5.198064	0.94997	.	.	ENSG00000064313	ENST00000378164	T	0.05855	3.38	5.89	5.89	0.94794	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.24431	0.0592	L	0.56769	1.78	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	T	0.00024	-1.2327	10	0.87932	D	0	-13.5961	20.2617	0.98447	0.0:0.0:1.0:0.0	.	179	Q6P1X5	TAF2_HUMAN	F	179	ENSP00000367406:S179F	ENSP00000367406:S179F	S	-	2	0	TAF2	120885323	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.814000	0.99346	2.793000	0.96121	0.655000	0.94253	TCT	.	.	.	none		0.333	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184		A	120816142	G	A	120816142	3	1	55	1	0	0	0	0	1	0	0	0	15536	942	33	2	3151	2	TAF2	8	120816142	Missense_Mutation	SNP	G	TCGA-A4-8311-01A-11D-2396-08	53239029	120816142	25547880	24	3764											
TNFSF15	9966	hgsc.bcm.edu	37	chr9	117552848	117552848	+	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	caaggagaacatggctccgaGgtagatgggctggaaccagt	12	6	15	8	1	0	2	0	0	0	2	1	5	1	3	2	5	2	3	2	5	4	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr9:117552848G>A	ENST00000374045.4	-	4	753	c.640C>T	c.(640-642)Ctc>Ttc	p.L214F	TNFSF15_ENST00000374044.1_Missense_Mutation_p.L137F|AL390240.1_ENST00000408807.1_RNA	NM_001204344.1|NM_005118.3	NP_001191273.1|NP_005109.2	O95150	TNF15_HUMAN	tumor necrosis factor (ligand) superfamily, member 15	214					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						ATGGCTCCGAGGTAGATGGGC	0.493																																					p.L214F		Atlas-SNP	.											.	TNFSF15	23	.	0			c.C640T						PASS	.						155	135	142					9																	117552848		2203	4300	6503	SO:0001583	missense	9966	exon4			CTCCGAGGTAGAT	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.640C>T	chr9.hg19:g.117552848G>A	ENSP00000363157:p.Leu214Phe	84.0	0.0	.		91.0	39.0	.	NM_005118	Q3SX69|Q5VJK8|Q5VWH1|Q8NFE9	Missense_Mutation	SNP	ENST00000374045.4	hg19	CCDS6809.1	.	.	.	.	.	.	.	.	.	.	G	17.09	3.299347	0.60195	.	.	ENSG00000181634	ENST00000374045;ENST00000374044	T;T	0.67523	-0.27;-0.27	6.03	4.2	0.49525	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	0.000000	0.64402	D	0.000009	T	0.77896	0.4199	M	0.73372	2.23	0.46203	D	0.998926	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.76539	-0.2922	10	0.48119	T	0.1	-26.8042	8.9914	0.36026	0.3322:0.0:0.6678:0.0	.	214;155	O95150;O95150-2	TNF15_HUMAN;.	F	214;137	ENSP00000363157:L214F;ENSP00000363156:L137F	ENSP00000363156:L137F	L	-	1	0	TNFSF15	116592669	0.994000	0.37717	0.997000	0.53966	0.967000	0.64934	0.902000	0.28459	0.885000	0.36088	0.655000	0.94253	CTC	.	.	.	none		0.493	TNFSF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055424.2	NM_005118		A	117552848	G	A	117552848	3	1	55	1	0	0	0	0	1	0	0	0	16320	1000	35	2	119	2	TNFSF15	9	117552848	Missense_Mutation	SNP	G	TCGA-A4-8311-01A-11D-2396-08		117552848	23660583	25	3765											
PIP5KL1	138429	hgsc.bcm.edu	37	chr9	130684238	130684238	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttccacaggtgctccagcCgcttgcggagcccgtagact	6	9	11	15	3	1	1	0	0	1	1	3	2	3	2	4	2	4	3	4	2	1	3			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr9:130684238C>T	ENST00000388747.4	-	10	1117	c.1073G>A	c.(1072-1074)cGg>cAg	p.R358Q	PIP5KL1_ENST00000300432.3_Missense_Mutation_p.R155Q	NM_001135219.1	NP_001128691.1	Q5T9C9	PI5L1_HUMAN	phosphatidylinositol-4-phosphate 5-kinase-like 1	358	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.					cell projection (GO:0042995)|cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)			endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|skin(1)	8						GTGCTCCAGCCGCTTGCGGAG	0.687											OREG0019512	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R358Q		Atlas-SNP	.											.	PIP5KL1	38	.	0			c.G1073A						PASS	.						21	21	21					9																	130684238		2183	4276	6459	SO:0001583	missense	138429	exon10			TCCAGCCGCTTGC	BC042184	CCDS6885.1, CCDS48030.1	9q34.13	2008-02-05			ENSG00000167103	ENSG00000167103			28711	protein-coding gene	gene with protein product		612865				12477932	Standard	NM_001135219		Approved	bA203J24.5, MGC46424	uc011mao.2	Q5T9C9	OTTHUMG00000020719	ENST00000388747.4:c.1073G>A	chr9.hg19:g.130684238C>T	ENSP00000373399:p.Arg358Gln	12.0	0.0	.	1582	5.0	4.0	.	NM_001135219	Q8IVS3	Missense_Mutation	SNP	ENST00000388747.4	hg19	CCDS48030.1	.	.	.	.	.	.	.	.	.	.	C	36	5.911299	0.97093	.	.	ENSG00000167103	ENST00000388747;ENST00000300432	T;T	0.35605	1.3;1.3	5.32	5.32	0.75619	Phosphatidylinositol-4-phosphate 5-kinase, core (2);	0.000000	0.85682	D	0.000000	T	0.54240	0.1846	L	0.48260	1.515	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.56013	-0.8049	10	0.87932	D	0	-38.4281	16.4798	0.84155	0.0:1.0:0.0:0.0	.	358	Q5T9C9	PI5L1_HUMAN	Q	358;155	ENSP00000373399:R358Q;ENSP00000300432:R155Q	ENSP00000300432:R155Q	R	-	2	0	PIP5KL1	129724059	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.211000	0.51137	2.473000	0.83533	0.555000	0.69702	CGG	.	.	.	none		0.687	PIP5KL1-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054289.2	NM_173492		T	130684238	C	T	130684238	3	4	55	1	0	0	0	0	1	0	0	0	11949	652	23	1	115	1	PIP5KL1	9	130684238	Missense_Mutation	SNP	C	TCGA-A4-8311-01A-11D-2396-08	13131390	130684238	10529193	26	3766											
C9orf69	90120	hgsc.bcm.edu	37	chr9	139008421	139008421	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgagcagctcgttcaccaggCggaagtccacgcgccggcgg	7	4	15	15	7	1	0	1	0	0	0	3	2	2	1	3	4	2	3	3	4	1	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr9:139008421C>T	ENST00000418388.1	-	2	828	c.326G>A	c.(325-327)cGc>cAc	p.R109H	C9orf69_ENST00000561457.1_Missense_Mutation_p.A134T			H0YL14	CI069_HUMAN	chromosome 9 open reading frame 69	109					cell cycle (GO:0007049)|positive regulation of cell proliferation (GO:0008284)|positive regulation of viral process (GO:0048524)|viral process (GO:0016032)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	GTP binding (GO:0005525)			endometrium(1)	1		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.58e-07)|Epithelial(140;6.42e-06)		GTTCACCAGGCGGAAGTCCAC	0.657																																					p.R109H		Atlas-SNP	.											.	C9orf69	10	.	0			c.G326A						PASS	.						13	18	16					9																	139008421		2159	4244	6403	SO:0001583	missense	90120	exon2			ACCAGGCGGAAGT		CCDS59155.1	9q34.3	2012-11-26	2012-07-05	2012-07-05	ENSG00000238227	ENSG00000238227			31009	protein-coding gene	gene with protein product						21667337	Standard	NM_152833		Approved	bA83N9.1	uc004cgx.5	H0YL14	OTTHUMG00000020922	ENST00000418388.1:c.326G>A	chr9.hg19:g.139008421C>T	ENSP00000453019:p.Arg109His	28.0	0.0	.		24.0	12.0	.	NM_152833		Missense_Mutation	SNP	ENST00000418388.1	hg19	CCDS59155.1																																																																																			.	.	.	none		0.657	C9orf69-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055043.3	NM_152833		T	139008421	C	T	139008421	3	4	55	1	0	0	0	0	1	0	0	0	2494	768	27	1	11	1	C9orf69	9	139008421	Missense_Mutation	SNP	C	TCGA-A4-8311-01A-11D-2396-08	8324183	139008421	2205010	27	3767											
TMEM72	643236	hgsc.bcm.edu	37	chr10	45429133	45429133	+	5'UTR	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	gtaagggagaaagcccactgGctgggctgcttccagaagtt	10	8	14	9	0	0	2	0	0	0	2	1	3	1	2	2	3	2	5	2	3	3	3			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr10:45429133G>C	ENST00000544540.1	+	0	388				TMEM72-AS1_ENST00000450287.2_RNA			A0PK05	TMM72_HUMAN	transmembrane protein 72							integral component of membrane (GO:0016021)				breast(2)|kidney(1)|large_intestine(2)|lung(10)	15						AAGCCCACTGGCTGGGCTGCT	0.602																																					p.W86C		Atlas-SNP	.											.	TMEM72	25	.	0			c.G258C						PASS	.						54	58	57					10																	45429133		1568	3582	5150	SO:0001623	5_prime_UTR_variant	643236	exon4			CCACTGGCTGGGC	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.-97G>C	chr10.hg19:g.45429133G>C		54.0	0.0	.		53.0	25.0	.	NM_001123376	A1L181|Q5T740	Missense_Mutation	SNP	ENST00000544540.1	hg19		.	.	.	.	.	.	.	.	.	.	G	17.68	3.448729	0.63178	.	.	ENSG00000187783	ENST00000389583	.	.	.	5.59	4.68	0.58851	.	0.407067	0.24354	N	0.039259	T	0.67439	0.2893	M	0.62723	1.935	0.80722	D	1	D	0.69078	0.997	D	0.63192	0.912	T	0.65512	-0.6150	9	0.42905	T	0.14	-9.242	9.7258	0.40330	0.0925:0.0:0.9075:0.0	.	86	A0PK05	TMM72_HUMAN	C	86	.	ENSP00000374234:W86C	W	+	3	0	TMEM72	44749139	0.995000	0.38212	1.000000	0.80357	0.867000	0.49689	0.969000	0.29370	2.793000	0.96121	0.655000	0.94253	TGG	.	.	.	none		0.602	TMEM72-201	KNOWN	basic	protein_coding	protein_coding		NM_001123376		C	45429133	G	C	45429133	1	2	55	0	1	0	0	0	0	0	0	0	16213	1212	42	4		4	TMEM72	10	45429133	5'UTR	SNP	G	TCGA-A4-8311-01A-11D-2396-08		45429133	90105614	28	3768											
GOLGA7B	401647	hgsc.bcm.edu	37	chr10	99619286	99619286	+	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	tttatccagagagactacagCgatgggaccatctgtcagtt	11	11	10	9	1	2	2	1	0	1	2	3	5	3	3	2	1	2	1	2	1	2	4			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr10:99619286C>A	ENST00000370602.1	+	2	149	c.84C>A	c.(82-84)agC>agA	p.S28R		NM_001010917.2	NP_001010917.1	Q2TAP0	GOG7B_HUMAN	golgin A7 family, member B	28						Golgi apparatus (GO:0005794)|membrane (GO:0016020)				endometrium(1)|large_intestine(3)|prostate(1)	5						GAGACTACAGCGATGGGACCA	0.577																																					p.S28R		Atlas-SNP	.											GOLGA7B,NS,carcinoma,0,1	GOLGA7B	11	.	0			c.C84A						PASS	.						84	78	80					10																	99619286		2203	4300	6503	SO:0001583	missense	401647	exon2			CTACAGCGATGGG	BC008047	CCDS31265.1	10q24.2	2011-10-25	2010-02-12	2008-10-03	ENSG00000155265	ENSG00000155265			31668	protein-coding gene	gene with protein product		614189	"chromosome 10 open reading frame 133", "chromosome 10 open reading frame 132", "golgi autoantigen, golgin subfamily a, 7B"	C10orf133, C10orf132			Standard	NM_001010917		Approved	bA459F3.4, bA451M19.3	uc001kos.3	Q2TAP0	OTTHUMG00000018869	ENST00000370602.1:c.84C>A	chr10.hg19:g.99619286C>A	ENSP00000359634:p.Ser28Arg	61.0	1.0	.		65.0	3.0	.	NM_001010917	Q5T4F5	Missense_Mutation	SNP	ENST00000370602.1	hg19	CCDS31265.1	.	.	.	.	.	.	.	.	.	.	C	17.36	3.369353	0.61624	.	.	ENSG00000155265	ENST00000370602	.	.	.	4.89	0.791	0.18619	Golgin subfamily A member 7/ERF4 (1);	0.000000	0.85682	D	0.000000	T	0.62708	0.2450	M	0.70903	2.155	0.53688	D	0.999974	D	0.54397	0.966	P	0.54026	0.74	T	0.60239	-0.7302	9	0.48119	T	0.1	-36.6947	8.5642	0.33530	0.0:0.3739:0.0:0.6261	.	28	Q2TAP0	GOG7B_HUMAN	R	28	.	ENSP00000359634:S28R	S	+	3	2	GOLGA7B	99609276	0.000000	0.05858	0.998000	0.56505	0.998000	0.95712	-2.574000	0.00911	-0.012000	0.14223	0.555000	0.69702	AGC	.	.	.	none		0.577	GOLGA7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049752.1	NM_001010917		A	99619286	C	A	99619286	3	1	55	1	0	0	0	0	1	0	0	0	6569	767	27	4	90	4	GOLGA7B	10	99619286	Missense_Mutation	SNP	C	TCGA-A4-8311-01A-11D-2396-08	54190153	99619286	35915461	29	3769											
PDZD8	118987	hgsc.bcm.edu	37	chr10	119049814	119049814	+	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	atcagttgactggacaagacGaagtgtaagtccaacacttt	14	10	9	8	1	1	2	1	1	0	1	2	4	2	3	1	1	1	2	1	1	4	3			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr10:119049814G>C	ENST00000334464.5	-	4	1383	c.1144C>G	c.(1144-1146)Cgt>Ggt	p.R382G	PDZD8_ENST00000482496.1_5'UTR	NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	382	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)		TGGACAAGACGAAGTGTAAGT	0.413																																					p.R382G		Atlas-SNP	.											PDZD8,colon,carcinoma,0,1	PDZD8	85	.	0			c.C1144G						PASS	.						110	99	103					10																	119049814		2203	4300	6503	SO:0001583	missense	118987	exon4			CAAGACGAAGTGT	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.1144C>G	chr10.hg19:g.119049814G>C	ENSP00000334642:p.Arg382Gly	59.0	0.0	.		43.0	0.0	.	NM_173791	Q86WE0|Q86WE5|Q9UFF1	Missense_Mutation	SNP	ENST00000334464.5	hg19	CCDS7600.1	.	.	.	.	.	.	.	.	.	.	G	18.09	3.547054	0.65198	.	.	ENSG00000165650	ENST00000334464	T	0.72051	-0.62	5.6	3.73	0.42828	PDZ/DHR/GLGF (4);	0.053775	0.64402	D	0.000001	T	0.57036	0.2026	L	0.27053	0.805	0.47584	D	0.999469	B	0.17038	0.02	B	0.21360	0.034	T	0.53830	-0.8383	10	0.72032	D	0.01	-3.528	9.9287	0.41507	0.0732:0.1379:0.7889:0.0	.	382	Q8NEN9	PDZD8_HUMAN	G	382	ENSP00000334642:R382G	ENSP00000334642:R382G	R	-	1	0	PDZD8	119039804	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.392000	0.59659	0.716000	0.32124	0.563000	0.77884	CGT	.	.	.	none		0.413	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791		C	119049814	G	C	119049814	3	2	55	1	0	0	0	0	1	0	0	0	11712	1058	37	4	2328	4	PDZD8	10	119049814	Missense_Mutation	SNP	G	TCGA-A4-8311-01A-11D-2396-08	19430528	119049814	16484933	30	3770											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1275533	1275533	+	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	agcatccactacaagtccatGgatatcgtcctcactgtcac	11	10	6	14	1	2	0	2	0	0	0	6	1	5	1	3	1	2	1	3	1	3	2			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr11:1275533G>C	ENST00000529681.1	+	34	15487	c.15429G>C	c.(15427-15429)atG>atC	p.M5143I	MUC5B_ENST00000447027.1_Missense_Mutation_p.M5146I	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5143	VWFD 4. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		ACAAGTCCATGGATATCGTCC	0.642																																					p.M5143I		Atlas-SNP	.											.	MUC5B	473	.	0			c.G15429C						PASS	.						34	41	39					11																	1275533		2164	4260	6424	SO:0001583	missense	727897	exon34			GTCCATGGATATC	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.15429G>C	chr11.hg19:g.1275533G>C	ENSP00000436812:p.Met5143Ile	47.0	0.0	.		53.0	21.0	.	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	hg19	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	G	11.94	1.789191	0.31685	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000546052;ENST00000406844	T;T	0.15952	2.38;2.58	4.31	-3.06	0.05379	.	.	.	.	.	T	0.09113	0.0225	L	0.29908	0.895	0.09310	N	1	P;P	0.34462	0.454;0.454	B;B	0.31191	0.125;0.125	T	0.29792	-1.0000	9	0.87932	D	0	.	2.4091	0.04420	0.4222:0.118:0.3402:0.1197	.	5480;5146	A7Y9J9;E9PBJ0	.;.	I	5143;5146;5087;42;4855	ENSP00000436812:M5143I;ENSP00000415793:M5146I	ENSP00000343037:M5087I	M	+	3	0	MUC5B	1232109	0.000000	0.05858	0.003000	0.11579	0.609000	0.37215	-0.057000	0.11768	-0.168000	0.10853	0.400000	0.26472	ATG	.	.	.	none		0.642	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		C	1275533	G	C	1275533	3	2	55	1	0	0	0	0	1	0	0	0	9986	1348	47	4	15572	4	MUC5B	11	1275533	Missense_Mutation	SNP	G	TCGA-A4-8311-01A-11D-2396-08		1275533	133730983	31	3771											
LGALS12	85329	hgsc.bcm.edu	37	chr11	63273900	63273900	+	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	gggggcagggctcctggaacGaggatctacagttggagttg	8	8	18	7	1	1	0	0	0	1	0	2	4	2	3	1	6	2	4	1	6	2	3			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr11:63273900G>C	ENST00000394618.3	+	1	327	c.36G>C	c.(34-36)acG>acC	p.T12T	LGALS12_ENST00000425950.2_5'Flank|LGALS12_ENST00000255684.5_Silent_p.T12T|LGALS12_ENST00000415491.2_5'Flank|LGALS12_ENST00000340246.5_Silent_p.T12T	NM_001142535.1|NM_033101.3	NP_001136007.1|NP_149092.2	Q96DT0	LEG12_HUMAN	lectin, galactoside-binding, soluble, 12	12					intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	16						CTCCTGGAACGAGGATCTACA	0.572																																					p.T12T		Atlas-SNP	.											LGALS12,bladder,carcinoma,+1,1	LGALS12	35	.	0			c.G36C						PASS	.						126	114	118					11																	63273900		2201	4298	6499	SO:0001819	synonymous_variant	85329	exon1			TGGAACGAGGATC	AF222695	CCDS8045.1, CCDS44633.1, CCDS44634.1, CCDS44635.1, CCDS53648.1	11q13	2011-08-04	2008-07-25		ENSG00000133317	ENSG00000133317		"Lectins, galactoside-binding"	15788	protein-coding gene	gene with protein product	"galectin 12"	606096				11283015, 11435439	Standard	NM_033101		Approved	GRIP1	uc001nxc.2	Q96DT0	OTTHUMG00000167807	ENST00000394618.3:c.36G>C	chr11.hg19:g.63273900G>C		103.0	0.0	.		86.0	5.0	.	NM_001142535	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Silent	SNP	ENST00000394618.3	hg19	CCDS8045.1																																																																																			.	.	.	none		0.572	LGALS12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396378.1	NM_033101		C	63273900	G	C	63273900	2	2	55	1	0	0	0	0	0	0	0	1	8746	1045	37	4		4	LGALS12	11	63273900	Silent	SNP	G	TCGA-A4-8311-01A-11D-2396-08	61998367	63273900	71732616	32	3772											
CATSPER1	117144	hgsc.bcm.edu	37	chr11	65788966	65788966	+	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	gtgggagccgtggccactgaCctgagcctccgcaggacccg	6	5	15	15	3	0	2	0	2	0	0	1	4	1	4	6	3	2	1	6	3	0	0			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr11:65788966C>T	ENST00000312106.5	-	4	1829		c.e4+1			NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1						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						TGGCCACTGACCTGAGCCTCC	0.627																																					.		Atlas-SNP	.											.	CATSPER1	101	.	0			c.1691+1G>A						PASS	.						41	45	44					11																	65788966		2201	4296	6497	SO:0001630	splice_region_variant	117144	exon5			CACTGACCTGAGC	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.1691+1G>A	chr11.hg19:g.65788966C>T		56.0	0.0	.		29.0	16.0	.	NM_053054	Q96P76	Splice_Site	SNP	ENST00000312106.5	hg19	CCDS8127.1	.	.	.	.	.	.	.	.	.	.	C	12.07	1.826703	0.32329	.	.	ENSG00000175294	ENST00000312106	.	.	.	4.84	4.84	0.62591	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.4667	0.61258	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CATSPER1	65545542	1.000000	0.71417	0.985000	0.45067	0.197000	0.23852	4.738000	0.62073	2.227000	0.72691	0.561000	0.74099	.	.	.	.	none		0.627	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054	Intron	T	65788966	C	T	65788966	5	4	55	1	0	0	0	0	0	0	1	0	2689	521	18	2	686	2	CATSPER1	11	65788966	Splice_Site	SNP	C	TCGA-A4-8311-01A-11D-2396-08	2515066	65788966	69217550	33	3773											
BCL9L	283149	hgsc.bcm.edu	37	chr11	118771983	118771983	+	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	cccatcacgccactgctgttCtgggcccgaacccgggccat	6	7	10	18	3	2	0	1	0	1	0	2	1	2	0	5	2	2	2	5	2	1	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr11:118771983C>T	ENST00000334801.3	-	6	3433	c.2469G>A	c.(2467-2469)caG>caA	p.Q823Q	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	823	Met-rich.				canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		CACTGCTGTTCTGGGCCCGAA	0.652																																					p.Q823Q		Atlas-SNP	.											.	BCL9L	254	.	0			c.G2469A						PASS	.						49	49	49					11																	118771983		2200	4295	6495	SO:0001819	synonymous_variant	283149	exon6			GCTGTTCTGGGCC	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.2469G>A	chr11.hg19:g.118771983C>T		78.0	0.0	.		92.0	38.0	.	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Silent	SNP	ENST00000334801.3	hg19	CCDS8403.1																																																																																			.	.	.	none		0.652	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557		T	118771983	C	T	118771983	2	4	55	1	0	0	0	0	0	0	0	1	1382	912	32	2		2	BCL9L	11	118771983	Silent	SNP	C	TCGA-A4-8311-01A-11D-2396-08	52983017	118771983	16234533	34	3774											
ARHGEF12	23365	hgsc.bcm.edu	37	chr11	120352127	120352127	+	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	agaatactcactccgatgggGcaatttcaccattcaccccc	11	9	6	15	1	3	1	3	0	0	1	4	2	4	1	4	2	1	1	4	2	3	3			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr11:120352127G>T	ENST00000397843.2	+	39	4562	c.4396G>T	c.(4396-4398)Gca>Tca	p.A1466S	ARHGEF12_ENST00000356641.3_Missense_Mutation_p.A1447S|ARHGEF12_ENST00000532993.1_Missense_Mutation_p.A1363S	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	1466					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)		CTCCGATGGGGCAATTTCACC	0.537			T	MLL	AML																																p.A1466S		Atlas-SNP	.		Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	ARHGEF12,NS,carcinoma,0,1	ARHGEF12	133	.	0			c.G4396T						PASS	.						91	92	92					11																	120352127		1937	4149	6086	SO:0001583	missense	23365	exon39			GATGGGGCAATTT	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.4396G>T	chr11.hg19:g.120352127G>T	ENSP00000380942:p.Ala1466Ser	94.0	0.0	.		83.0	28.0	.	NM_015313	O15086|Q6P526	Missense_Mutation	SNP	ENST00000397843.2	hg19	CCDS41727.1	.	.	.	.	.	.	.	.	.	.	G	12.05	1.820487	0.32145	.	.	ENSG00000196914	ENST00000397843;ENST00000356641;ENST00000532993	T;T;T	0.66099	-0.08;-0.19;-0.08	6.08	3.08	0.35506	.	0.599101	0.14093	N	0.341889	T	0.43233	0.1238	N	0.19112	0.55	0.18873	N	0.999987	B	0.23377	0.084	B	0.21708	0.036	T	0.22103	-1.0226	10	0.13108	T	0.6	-1.3411	10.087	0.42423	0.0683:0.2579:0.6738:0.0	.	1466	Q9NZN5	ARHGC_HUMAN	S	1466;1447;1363	ENSP00000380942:A1466S;ENSP00000349056:A1447S;ENSP00000432984:A1363S	ENSP00000349056:A1447S	A	+	1	0	ARHGEF12	119857337	1.000000	0.71417	0.695000	0.30226	0.341000	0.28922	3.420000	0.52735	0.398000	0.25338	0.655000	0.94253	GCA	.	.	.	none		0.537	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313		T	120352127	G	T	120352127	3	4	55	1	0	0	0	0	1	0	0	0	897	1203	42	4	4550	4	ARHGEF12	11	120352127	Missense_Mutation	SNP	G	TCGA-A4-8311-01A-11D-2396-08	1580144	120352127	14654389	35	3775											
LARP4	113251	hgsc.bcm.edu	37	chr12	50847454	50847454	+	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	accttactttgaaacaccacTggtaagtgagatccttacaa	14	11	6	10	0	0	2	0	2	0	1	1	3	1	2	3	1	3	1	3	1	5	4			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr12:50847454T>C	ENST00000398473.2	+	9	1128	c.1016T>C	c.(1015-1017)cTg>cCg	p.L339P	LARP4_ENST00000293618.8_Splice_Site_p.L339P|LARP4_ENST00000518444.1_Splice_Site_p.L338P|LARP4_ENST00000429001.3_Splice_Site_p.L345P|LARP4_ENST00000518561.1_Splice_Site_p.L269P|LARP4_ENST00000347328.5_Intron|LARP4_ENST00000522085.1_Splice_Site_p.L339P	NM_052879.4|NM_199188.2	NP_443111.4|NP_954658.2	Q71RC2	LARP4_HUMAN	La ribonucleoprotein domain family, member 4	339					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	23						GAAACACCACTGGTAAGTGAG	0.353																																					p.L339P		Atlas-SNP	.											.	LARP4	58	.	0			c.T1016C						PASS	.						143	119	126					12																	50847454		1844	4078	5922	SO:0001630	splice_region_variant	113251	exon9			CACCACTGGTAAG	AY004310	CCDS41782.1, CCDS44879.1, CCDS44880.1, CCDS44879.2, CCDS53789.1, CCDS53790.1	12q13.12	2005-08-09			ENSG00000161813	ENSG00000161813		"La ribonucleoprotein domain containing"	24320	protein-coding gene	gene with protein product						12477932	Standard	NM_052879		Approved	PP13296	uc001rwp.2	Q71RC2	OTTHUMG00000163724	ENST00000398473.2:c.1017+1T>C	chr12.hg19:g.50847454T>C		126.0	0.0	.		123.0	59.0	.	NM_001170808	A8K6T1|E9PDG5|G3XAA8|G5E976|Q5CZ97|Q6ZV14|Q96NF9	Missense_Mutation	SNP	ENST00000398473.2	hg19	CCDS41782.1	.	.	.	.	.	.	.	.	.	.	T	19.09	3.760444	0.69763	.	.	ENSG00000161813	ENST00000293618;ENST00000429001;ENST00000398473;ENST00000522085;ENST00000398464;ENST00000518444;ENST00000518561;ENST00000520064	T;T;T;T;T;T	0.34472	1.36;1.36;1.36;1.36;1.36;1.36	4.05	4.05	0.47172	.	0.000000	0.64402	D	0.000005	T	0.57784	0.2077	M	0.71581	2.175	0.80722	D	1	D;P;D;D;D	0.89917	1.0;0.911;1.0;1.0;1.0	D;P;D;D;D	0.91635	0.997;0.756;0.999;0.996;0.996	T	0.61739	-0.7001	10	0.54805	T	0.06	.	13.6919	0.62550	0.0:0.0:0.0:1.0	.	240;338;339;339;345	Q71RC2-2;Q71RC2-3;G3XAA8;Q71RC2;Q71RC2-4	.;.;.;LARP4_HUMAN;.	P	339;345;339;339;339;338;269;240	ENSP00000293618:L339P;ENSP00000415464:L345P;ENSP00000381490:L339P;ENSP00000429781:L339P;ENSP00000429077:L338P;ENSP00000430851:L269P	ENSP00000293618:L339P	L	+	2	0	LARP4	49133721	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.487000	0.81328	1.793000	0.52555	0.402000	0.26972	CTG	.	.	.	none		0.353	LARP4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374981.1	NM_052879	Missense_Mutation	C	50847454	T	C	50847454	5	2	55	1	0	0	0	0	0	0	1	0	8637	1594	55	3	1050	3	LARP4	12	50847454	Splice_Site	SNP	T	TCGA-A4-8311-01A-11D-2396-08		50847454	83004441	36	3776											
GRASP	160622	hgsc.bcm.edu	37	chr12	52401016	52401016	+	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	gccgagctgtaccgcgcgctCgccgtgtccgggggcaccct	3	6	15	17	7	0	0	0	0	0	0	2	1	1	0	5	2	2	4	5	2	1	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr12:52401016C>A	ENST00000293662.4	+	1	293	c.213C>A	c.(211-213)ctC>ctA	p.L71L		NM_181711.2	NP_859062.1	Q7Z6J2	GRASP_HUMAN	GRP1 (general receptor for phosphoinositides 1)-associated scaffold protein	71					protein localization (GO:0008104)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				central_nervous_system(1)|large_intestine(1)|lung(1)|skin(2)	5				BRCA - Breast invasive adenocarcinoma(357;0.0967)		ACCGCGCGCTCGCCGTGTCCG	0.741																																					p.L71L		Atlas-SNP	.											.	GRASP	23	.	0			c.C213A						PASS	.						8	9	9					12																	52401016		1938	4028	5966	SO:0001819	synonymous_variant	160622	exon1			CGCGCTCGCCGTG	AC019244	CCDS8817.1, CCDS61124.1	12q13.13	2011-09-02			ENSG00000161835	ENSG00000161835			18707	protein-coding gene	gene with protein product		612027				10828067	Standard	NM_001271856		Approved		uc001rzo.2	Q7Z6J2	OTTHUMG00000169595	ENST00000293662.4:c.213C>A	chr12.hg19:g.52401016C>A		22.0	0.0	.		25.0	14.0	.	NM_181711	Q6PIF8|Q7Z741	Silent	SNP	ENST00000293662.4	hg19	CCDS8817.1																																																																																			.	.	.	none		0.741	GRASP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404972.1			A	52401016	C	A	52401016	2	1	55	1	0	0	0	0	0	0	0	1	6762	871	31	4		4	GRASP	12	52401016	Silent	SNP	C	TCGA-A4-8311-01A-11D-2396-08	1553562	52401016	81450879	37	3777											
PCDH17	27253	hgsc.bcm.edu	37	chr13	58208351	58208351	+	Frame_Shift_Del	DEL	G	G	-																															aaggtgcttgctaaggactcGggggcgcccgcgcacttgga																										TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr13:58208351delG	ENST00000377918.3	+	1	1697	c.1671delG	c.(1669-1671)tcgfs	p.S557fs		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	557	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)		CTAAGGACTCGGGGGCGCCCG	0.592																																					p.S557fs	Melanoma(72;952 1291 1619 12849 33676)	Atlas-INDEL	.											.	PCDH17	304	.	0			c.1670delC						PASS	.						39	41	40					13																	58208351		2203	4300	6503	SO:0001589	frameshift_variant	27253	exon1			.	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.1671delG	chr13.hg19:g.58208351delG	ENSP00000367151:p.Ser557fs	78.0	0.0	0		93.0	21.0	0.225806	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Frame_Shift_Del	DEL	ENST00000377918.3	hg19	CCDS31986.1																																																																																			.	.	.	none		0.592	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		-	58208351	G	-	58208351	7	5	55	1	0	1	0	1	0	0	0	0	11519	1103	39	0	1673	0	PCDH17	13	58208351	Frame_Shift_Del	DEL	G	TCGA-A4-8311-01A-11D-2396-08		58208351	56961527	38	3778											
MTHFD1	4522	hgsc.bcm.edu	37	chr14	64914978	64914979	+	Frame_Shift_Del	DEL	AA	AA	-																															cttcagtaacttgaagaaacAaattgaaaatgccagaatgt																										TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr14:64914978_64914979delAA	ENST00000545908.1	+	23	2619_2620	c.2390_2391delAA	c.(2389-2391)caafs	p.Q797fs	MTHFD1_ENST00000216605.8_Frame_Shift_Del_p.Q741fs|CTD-2555O16.2_ENST00000556640.1_RNA			P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	741	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)	TTGAAGAAACAAATTGAAAATG	0.401																																					p.741_741del	Colon(18;220 581 13419 18191 31512)|GBM(126;343 1658 28700 44425 52519)	Atlas-INDEL	.											.	MTHFD1	61	.	0			c.2221_2222del						PASS	.																																			SO:0001589	frameshift_variant	4522	exon23			.	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.2390_2391delAA	chr14.hg19:g.64914978_64914979delAA	ENSP00000438588:p.Gln797fs	55.0	0.0	0		47.0	16.0	0.340426	NM_005956	B2R5Y2|G3V2B8|Q86VC9|Q9BVP5	Frame_Shift_Del	DEL	ENST00000545908.1	hg19																																																																																				.	.	.	none		0.401	MTHFD1-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000412167.1			-	64914979	AA	-	64914978	7	5	55	1	0	1	0	1	0	0	0	0	9934	130	5	0	2312	0	MTHFD1	14	64914978	Frame_Shift_Del	DEL	AA	TCGA-A4-8311-01A-11D-2396-08		64914978	42434562	39	3779											
MAPK6	5597	hgsc.bcm.edu	37	chr15	52338881	52338881	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tattagaagacttgaccatgAtaacattgtgaaagtgtttg	14	14	9	4	0	0	5	0	3	0	2	0	5	0	5	1	0	1	1	1	0	5	6			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr15:52338881A>G	ENST00000261845.5	+	2	1031	c.224A>G	c.(223-225)gAt>gGt	p.D75G		NM_002748.3	NP_002739.1	Q16659	MK06_HUMAN	mitogen-activated protein kinase 6	75	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	20				all cancers(107;0.0028)		CTTGACCATGATAACATTGTG	0.398																																					p.D75G		Atlas-SNP	.											.	MAPK6	70	.	0			c.A224G						PASS	.						95	94	94					15																	52338881		2195	4293	6488	SO:0001583	missense	5597	exon2			ACCATGATAACAT	L77964	CCDS10147.1	15q21	2011-06-10			ENSG00000069956	ENSG00000069956		"Mitogen-activated protein kinase cascade / Kinases"	6879	protein-coding gene	gene with protein product		602904		PRKM6		8875998	Standard	NM_002748		Approved	ERK3, p97MAPK, HsT17250	uc002abp.3	Q16659	OTTHUMG00000131891	ENST00000261845.5:c.224A>G	chr15.hg19:g.52338881A>G	ENSP00000261845:p.Asp75Gly	132.0	0.0	.		119.0	45.0	.	NM_002748	B2R945|B5BU65|Q68DH4|Q8IYN8	Missense_Mutation	SNP	ENST00000261845.5	hg19	CCDS10147.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.189988	0.78789	.	.	ENSG00000069956	ENST00000261845	T	0.43688	0.94	5.38	5.38	0.77491	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.60418	0.2267	L	0.56199	1.76	0.80722	D	1	D	0.60575	0.988	D	0.79784	0.993	T	0.63646	-0.6590	10	0.87932	D	0	-21.6017	15.4537	0.75297	1.0:0.0:0.0:0.0	.	75	Q16659	MK06_HUMAN	G	75	ENSP00000261845:D75G	ENSP00000261845:D75G	D	+	2	0	MAPK6	50126173	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.249000	0.95470	2.067000	0.61834	0.529000	0.55759	GAT	.	.	.	none		0.398	MAPK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254841.2	NM_002748		G	52338881	A	G	52338881	3	3	55	1	0	0	0	0	1	0	0	0	9288	333	12	3	226	3	MAPK6	15	52338881	Missense_Mutation	SNP	A	TCGA-A4-8311-01A-11D-2396-08		52338881	50192511	40	3780											
RAB11FIP3	9727	hgsc.bcm.edu	37	chr16	568988	568988	+	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	agtgaactccggtcctgcacGccctgtctgaaggccaacat	9	8	10	14	2	1	2	0	2	1	0	3	2	3	2	4	2	3	1	4	2	3	0			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr16:568988G>A	ENST00000262305.4	+	10	2074	c.1686G>A	c.(1684-1686)acG>acA	p.T562T	RAB11FIP3_ENST00000457159.1_Silent_p.T607T|RAB11FIP3_ENST00000450428.1_Silent_p.T266T	NM_014700.3	NP_055515.1	O75154	RFIP3_HUMAN	RAB11 family interacting protein 3 (class II)	562	ARF-binding domain (ABD).				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)				GGTCCTGCACGCCCTGTCTGA	0.612																																					p.T562T	Melanoma(160;2366 2595 4474 8099)	Atlas-SNP	.											.	RAB11FIP3	31	.	0			c.G1686A						PASS	.						142	124	130					16																	568988		2201	4300	6501	SO:0001819	synonymous_variant	9727	exon10			CTGCACGCCCTGT	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.1686G>A	chr16.hg19:g.568988G>A		130.0	0.0	.		129.0	34.0	.	NM_014700	B0QYI8|B0QYT8|B1AHQ0|B4DEI7|B4DZR6|Q4VXV7|Q7Z5E9|Q9H155|Q9H1G0|Q9NUI0	Silent	SNP	ENST00000262305.4	hg19	CCDS32351.1																																																																																			.	.	.	none		0.612	RAB11FIP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109066.4	NM_014700		A	568988	G	A	568988	2	1	55	1	0	0	0	0	0	0	0	1	12908	1074	38	1		1	RAB11FIP3	16	568988	Silent	SNP	G	TCGA-A4-8311-01A-11D-2396-08		568988	89785765	41	3781											
PKD1	5310	hgsc.bcm.edu	37	chr16	2155892	2155892	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagcacggtgaccagggccaAcgagtactcgatgacgtgct	10	6	13	12	4	0	2	0	2	0	0	1	4	0	2	2	2	4	3	2	2	2	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr16:2155892A>G	ENST00000262304.4	-	20	8045	c.7837T>C	c.(7837-7839)Ttg>Ctg	p.L2613L	PKD1_ENST00000561991.1_5'UTR|PKD1_ENST00000423118.1_Silent_p.L2613L	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	2613	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.		Missing (in PKD1; unknown pathological significance). {ECO:0000269|PubMed:11571556}.		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)	p.L2613L(1)		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						ACCAGGGCCAACGAGTACTCG	0.657																																					p.L2613L		Atlas-SNP	.											PKD1,NS,carcinoma,0,1	PKD1	184	.	1	Substitution - coding silent(1)	lung(1)	c.T7837C						PASS	.						46	45	45					16																	2155892		1400	2465	3865	SO:0001819	synonymous_variant	5310	exon20			GGGCCAACGAGTA	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.7837T>C	chr16.hg19:g.2155892A>G		51.0	0.0	.		65.0	3.0	.	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	hg19	CCDS32369.1																																																																																			.	.	.	none		0.657	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			G	2155892	A	G	2155892	2	3	55	1	0	0	0	0	0	0	0	1	11970	40	2	3		3	PKD1	16	2155892	Silent	SNP	A	TCGA-A4-8311-01A-11D-2396-08	1586904	2155892	88198861	42	3782											
ZNF263	10127	hgsc.bcm.edu	37	chr16	3339974	3339974	+	Frame_Shift_Del	DEL	T	T	-																															cgcacactggggagaagcccTacaagtgccctgagtgtggg																										TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr16:3339974delT	ENST00000219069.5	+	6	2344	c.1468delT	c.(1468-1470)tacfs	p.Y490fs	ZNF263_ENST00000538765.1_Frame_Shift_Del_p.Y138fs	NM_005741.4	NP_005732.2	O14978	ZN263_HUMAN	zinc finger protein 263	490					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|skin(4)|urinary_tract(3)	20						GGAGAAGCCCTACAAGTGCCC	0.537																																					p.P489fs		Atlas-INDEL	.											.	ZNF263	58	.	0			c.1467delC						PASS	.						69	67	68					16																	3339974		2197	4300	6497	SO:0001589	frameshift_variant	10127	exon6			.	AC004232	CCDS10499.1	16p13.3	2013-01-09			ENSG00000006194	ENSG00000006194		"Zinc fingers, C2H2-type", "-", "-", "-"	13056	protein-coding gene	gene with protein product		604191				9256059	Standard	NM_005741		Approved	FPM315, ZKSCAN12, ZSCAN44	uc002cuq.3	O14978	OTTHUMG00000129323	ENST00000219069.5:c.1468delT	chr16.hg19:g.3339974delT	ENSP00000219069:p.Tyr490fs	53.0	0.0	0		68.0	19.0	0.279412	NM_005741	B2R634|O43387|Q96H95	Frame_Shift_Del	DEL	ENST00000219069.5	hg19	CCDS10499.1																																																																																			.	.	.	none		0.537	ZNF263-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251463.2			-	3339974	T	-	3339974	7	5	55	1	0	1	0	1	0	0	0	0	17815	1522	53	0	1490	0	ZNF263	16	3339974	Frame_Shift_Del	DEL	T	TCGA-A4-8311-01A-11D-2396-08	1184082	3339974	87014779	43	3783											
ULK2	9706	hgsc.bcm.edu	37	chr17	19770705	19770705	+	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	ccacgagatccctcttgctgTactcgaagtcacccaccacc	9	8	6	18	2	2	1	1	0	1	1	4	3	3	1	5	0	2	2	5	0	2	2			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr17:19770705T>A	ENST00000395544.4	-	1	525	c.26A>T	c.(25-27)tAc>tTc	p.Y9F	ULK2_ENST00000361658.2_Missense_Mutation_p.Y9F	NM_014683.3	NP_055498.3	Q8IYT8	ULK2_HUMAN	unc-51 like autophagy activating kinase 2	9	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|negative regulation of collateral sprouting (GO:0048671)|protein autophosphorylation (GO:0046777)|regulation of autophagy (GO:0010506)|response to starvation (GO:0042594)|signal transduction (GO:0007165)	ATG1/UKL1 signaling complex (GO:0034273)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|pre-autophagosomal structure membrane (GO:0034045)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(1)|skin(4)|stomach(1)	6	all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186)					CCTCTTGCTGTACTCGAAGTC	0.771																																					p.Y9F		Atlas-SNP	.											.	ULK2	142	.	0			c.A26T						PASS	.						21	21	21					17																	19770705		2197	4295	6492	SO:0001583	missense	9706	exon1			TTGCTGTACTCGA	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.26A>T	chr17.hg19:g.19770705T>A	ENSP00000378914:p.Tyr9Phe	22.0	0.0	.		51.0	29.0	.	NM_001142610	A8MY69|O75119	Missense_Mutation	SNP	ENST00000395544.4	hg19	CCDS11213.1	.	.	.	.	.	.	.	.	.	.	T	13.25	2.181057	0.38511	.	.	ENSG00000083290	ENST00000361658;ENST00000395544	T;T	0.30981	1.51;1.51	4.71	3.61	0.41365	Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.067152	0.64402	D	0.000007	T	0.39860	0.1094	L	0.42744	1.35	0.49687	D	0.999814	D	0.76494	0.999	D	0.79108	0.992	T	0.21724	-1.0237	10	0.09590	T	0.72	-10.0083	9.917	0.41442	0.1526:0.0:0.0:0.8474	.	9	Q8IYT8	ULK2_HUMAN	F	9	ENSP00000354877:Y9F;ENSP00000378914:Y9F	ENSP00000354877:Y9F	Y	-	2	0	ULK2	19711297	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.963000	0.56773	0.633000	0.30452	0.472000	0.43445	TAC	.	.	.	none		0.771	ULK2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132375.2	NM_014683		A	19770705	T	A	19770705	3	1	55	1	0	0	0	0	1	0	0	0	16988	1638	57	5	3192	5	ULK2	17	19770705	Missense_Mutation	SNP	T	TCGA-A4-8311-01A-11D-2396-08		19770705	61424505	44	3784											
EVI2A	2123	hgsc.bcm.edu	37	chr17	29645740	29645740	+	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	aggactgttgctgacgacagAaggtatataaagctcctgtt	12	11	11	7	1	0	2	0	1	0	1	1	4	1	3	1	2	2	5	1	2	5	5			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr17:29645740A>T	ENST00000462804.2	-	2	691	c.292T>A	c.(292-294)Tct>Act	p.S98T	NF1_ENST00000356175.3_Intron|NF1_ENST00000581113.2_Intron|NF1_ENST00000358273.4_Intron|EVI2A_ENST00000247270.3_Missense_Mutation_p.S121T|EVI2A_ENST00000461237.1_Missense_Mutation_p.S98T|CTD-2370N5.3_ENST00000578584.1_Missense_Mutation_p.F37Y	NM_014210.3	NP_055025.2	P22794	EVI2A_HUMAN	ecotropic viral integration site 2A	98					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)	p.0?(8)|p.?(3)|p.S121P(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	14		all_cancers(10;6.97e-11)|all_epithelial(10;0.0051)|all_hematologic(16;0.0149)|Breast(31;0.0155)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|all_lung(9;0.0468)|Lung NSC(157;0.094)		UCEC - Uterine corpus endometrioid carcinoma (4;6.64e-05)|all cancers(4;5.94e-13)|Epithelial(4;7.98e-12)|OV - Ovarian serous cystadenocarcinoma(4;9.4e-12)|GBM - Glioblastoma multiforme(4;0.18)		CTGACGACAGAAGGTATATAA	0.368																																					p.S121T		Atlas-SNP	.											EVI2A,NS,carcinoma,0,1	EVI2A	27	.	12	Whole gene deletion(8)|Unknown(3)|Substitution - Missense(1)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)|liver(1)	c.T361A						PASS	.						153	153	153					17																	29645740		2203	4300	6503	SO:0001583	missense	2123	exon3			CGACAGAAGGTAT	M55267	CCDS32608.1, CCDS42293.1	17q11.2	2008-07-18			ENSG00000126860	ENSG00000126860			3499	protein-coding gene	gene with protein product		158380		EVI2		2117566	Standard	NM_014210		Approved	EVDA	uc002hgm.3	P22794	OTTHUMG00000159306	ENST00000462804.2:c.292T>A	chr17.hg19:g.29645740A>T	ENSP00000420557:p.Ser98Thr	122.0	0.0	.		196.0	116.0	.	NM_001003927	B2R5X2|B4DHX8	Missense_Mutation	SNP	ENST00000462804.2	hg19	CCDS42293.1	.	.	.	.	.	.	.	.	.	.	A	7.116	0.577064	0.13686	.	.	ENSG00000126860	ENST00000394755;ENST00000462804;ENST00000461237;ENST00000247270	.	.	.	4.67	-0.204	0.13200	.	1.194170	0.05806	N	0.613220	T	0.23249	0.0562	L	0.50333	1.59	0.19300	N	0.99998	B;B	0.33318	0.058;0.408	B;B	0.29785	0.091;0.107	T	0.12400	-1.0549	9	0.07175	T	0.84	.	0.9302	0.01333	0.421:0.1575:0.2688:0.1527	.	98;121	P22794;P22794-2	EVI2A_HUMAN;.	T	98;94;98;121	.	ENSP00000247270:S121T	S	-	1	0	EVI2A	26669866	0.000000	0.05858	0.002000	0.10522	0.601000	0.36947	0.005000	0.13129	-0.022000	0.13986	0.459000	0.35465	TCT	.	.	.	none		0.368	EVI2A-001	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354491.3	NM_014210		T	29645740	A	T	29645740	3	4	55	1	0	0	0	0	1	0	0	0	5289	246	9	5	422	5	EVI2A	17	29645740	Missense_Mutation	SNP	A	TCGA-A4-8311-01A-11D-2396-08	9875035	29645740	51549470	45	3785											
HNF1B	6928	hgsc.bcm.edu	37	chr17	36099582	36099582	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tccctctgggggatgttgtgTtgctgcatgtaacccttgat	5	15	12	9	0	1	1	0	1	1	0	2	2	2	2	2	2	3	5	2	2	1	4			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr17:36099582T>C	ENST00000225893.4	-	2	754	c.393A>G	c.(391-393)caA>caG	p.Q131Q	HNF1B_ENST00000561193.1_Silent_p.Q131Q|HNF1B_ENST00000427275.2_Silent_p.Q131Q|HNF1B_ENST00000560016.1_Silent_p.Q131Q	NM_000458.2|NM_001165923.1	NP_000449.1|NP_001159395.1	P35680	HNF1B_HUMAN	HNF1 homeobox B	131					anterior/posterior pattern specification (GO:0009952)|branching morphogenesis of an epithelial tube (GO:0048754)|embryonic digestive tract morphogenesis (GO:0048557)|endocrine pancreas development (GO:0031018)|endodermal cell fate specification (GO:0001714)|epithelial cell proliferation (GO:0050673)|genitalia development (GO:0048806)|hepatoblast differentiation (GO:0061017)|hindbrain development (GO:0030902)|inner cell mass cell differentiation (GO:0001826)|insulin secretion (GO:0030073)|kidney development (GO:0001822)|mesonephric duct formation (GO:0072181)|negative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis (GO:0061296)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric nephron tubule development (GO:0039020)|pronephros development (GO:0048793)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of endodermal cell fate specification (GO:0042663)|regulation of pronephros size (GO:0035565)|regulation of Wnt signaling pathway (GO:0030111)|response to glucose (GO:0009749)|ureteric bud elongation (GO:0060677)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(3)|large_intestine(2)|liver(1)|lung(3)|ovary(3)|prostate(1)|skin(2)	28		Breast(25;0.00765)|Ovarian(249;0.15)	STAD - Stomach adenocarcinoma(1;0.0142)			GGATGTTGTGTTGCTGCATGT	0.547																																					p.Q131Q	Colon(71;102 1179 9001 27917 43397)	Atlas-SNP	.											.	HNF1B	61	.	0			c.A393G						PASS	.						101	86	92					17																	36099582		2203	4300	6503	SO:0001819	synonymous_variant	6928	exon2			GTTGTGTTGCTGC	BC017714	CCDS11324.1, CCDS58538.1	17q12	2014-05-06	2007-08-24	2007-08-24	ENSG00000108753	ENSG00000275410		"Homeoboxes / HNF class"	11630	protein-coding gene	gene with protein product		189907	"transcription factor 2, hepatic; LF-B3; variant hepatic nuclear factor"	TCF2		1677179, 10484768	Standard	NM_000458		Approved	LFB3, VHNF1, HNF1beta, MODY5	uc002hok.4	P35680	OTTHUMG00000188478	ENST00000225893.4:c.393A>G	chr17.hg19:g.36099582T>C		46.0	0.0	.		68.0	42.0	.	NM_001165923	B4DKM3|E0YMJ9	Silent	SNP	ENST00000225893.4	hg19	CCDS11324.1																																																																																			.	.	.	none		0.547	HNF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256807.3	NM_000458		C	36099582	T	C	36099582	2	2	55	1	0	0	0	0	0	0	0	1	7259	1722	60	3		3	HNF1B	17	36099582	Silent	SNP	T	TCGA-A4-8311-01A-11D-2396-08	6453842	36099582	45095628	46	3786											
KRT26	353288	hgsc.bcm.edu	37	chr17	38926071	38926071	+	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	gcgttttaattcggtcagctCatttctggctgctgtggctg	4	16	12	9	2	3	0	2	0	1	0	4	0	3	0	0	3	2	5	0	3	1	4			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr17:38926071C>A	ENST00000335552.4	-	5	952	c.904G>T	c.(904-906)Gag>Tag	p.E302*		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)				TCGGTCAGCTCATTTCTGGCT	0.463																																					p.E302X		Atlas-SNP	.											.	KRT26	49	.	0			c.G904T						PASS	.						174	159	164					17																	38926071		2203	4300	6503	SO:0001587	stop_gained	353288	exon5			TCAGCTCATTTCT	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.904G>T	chr17.hg19:g.38926071C>A	ENSP00000334798:p.Glu302*	147.0	0.0	.		214.0	68.0	.	NM_181539		Nonsense_Mutation	SNP	ENST00000335552.4	hg19	CCDS11374.1	.	.	.	.	.	.	.	.	.	.	C	36	5.661653	0.96734	.	.	ENSG00000186393	ENST00000335552	.	.	.	5.24	4.24	0.50183	.	0.102432	0.42821	D	0.000643	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	15.7173	0.77677	0.0:0.7423:0.2577:0.0	.	.	.	.	X	302	.	ENSP00000334798:E302X	E	-	1	0	KRT26	36179597	0.424000	0.25490	1.000000	0.80357	0.917000	0.54804	1.023000	0.30065	1.292000	0.44672	0.655000	0.94253	GAG	.	.	.	none		0.463	KRT26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257215.1	NM_181539		A	38926071	C	A	38926071	4	1	55	1	0	0	0	0	0	1	0	0	8470	835	29	4	518	4	KRT26	17	38926071	Nonsense_Mutation	SNP	C	TCGA-A4-8311-01A-11D-2396-08	2826489	38926071	42269139	47	3787											
NARF	26502	hgsc.bcm.edu	37	chr17	80443514	80443514	+	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	ccattccactttgtggaggtCctcgcctgtgctggaggtga	5	12	13	11	1	0	1	0	1	0	0	3	3	2	3	4	4	1	1	4	4	0	2			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr17:80443514C>T	ENST00000309794.11	+	10	1311	c.1113C>T	c.(1111-1113)gtC>gtT	p.V371V	NARF_ENST00000457415.3_Silent_p.V417V|NARF_ENST00000390006.4_Silent_p.V312V|NARF-IT1_ENST00000584012.1_RNA|NARF_ENST00000345415.7_Silent_p.V323V	NM_012336.3|NM_031968.2	NP_036468.1|NP_114174.1	Q9UHQ1	NARF_HUMAN	nuclear prelamin A recognition factor	371						lamin filament (GO:0005638)|nuclear lamina (GO:0005652)|nuclear lumen (GO:0031981)|nucleus (GO:0005634)	lamin binding (GO:0005521)			endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			TTGTGGAGGTCCTCGCCTGTG	0.572																																					p.V371V		Atlas-SNP	.											.	NARF	51	.	0			c.C1113T						PASS	.						106	93	97					17																	80443514		2203	4300	6503	SO:0001819	synonymous_variant	26502	exon10			GGAGGTCCTCGCC	BC000438	CCDS32777.1, CCDS42403.1, CCDS42404.1	17q25.3	2011-12-19			ENSG00000141562	ENSG00000141562			29916	protein-coding gene	gene with protein product	"iron-only hydrogenase-like protein 2"	605349				10514485, 15667261	Standard	NM_031968		Approved	FLJ10067, DKFZp434G0420, IOP2	uc002kfg.4	Q9UHQ1		ENST00000309794.11:c.1113C>T	chr17.hg19:g.80443514C>T		85.0	0.0	.		123.0	86.0	.	NM_012336	A6NCJ3|B3KPX2|K4DI98|Q96AY9|Q9BWC6	Silent	SNP	ENST00000309794.11	hg19	CCDS32777.1																																																																																			.	.	.	none		0.572	NARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443573.2	NM_031968		T	80443514	C	T	80443514	2	4	55	1	0	0	0	0	0	0	0	1	10174	842	30	2		2	NARF	17	80443514	Silent	SNP	C	TCGA-A4-8311-01A-11D-2396-08	41517443	80443514	751696	48	3788											
MEP1B	4225	hgsc.bcm.edu	37	chr18	29788204	29788204	+	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	aggttcccagggggccagagAgtgatcactccaacatgggc	10	6	14	11	0	1	2	1	1	0	1	3	3	3	2	3	4	1	1	3	4	1	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr18:29788204A>T	ENST00000269202.6	+	9	936	c.889A>T	c.(889-891)Agt>Tgt	p.S297C	MEP1B_ENST00000581447.1_Missense_Mutation_p.S297C	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	297	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				digestion (GO:0007586)|inflammatory response (GO:0006954)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						GGGGCCAGAGAGTGATCACTC	0.478																																					p.S297C		Atlas-SNP	.											.	MEP1B	54	.	0			c.A889T						PASS	.						83	86	85					18																	29788204		1915	4116	6031	SO:0001583	missense	4225	exon9			CCAGAGAGTGATC	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.889A>T	chr18.hg19:g.29788204A>T	ENSP00000269202:p.Ser297Cys	69.0	0.0	.		83.0	36.0	.	NM_005925	B7ZM35|B9EGL6|Q670J1	Missense_Mutation	SNP	ENST00000269202.6	hg19	CCDS45846.1	.	.	.	.	.	.	.	.	.	.	A	16.37	3.103407	0.56291	.	.	ENSG00000141434	ENST00000269202	T	0.02369	4.32	5.48	4.33	0.51752	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.625246	0.18028	N	0.154004	T	0.11965	0.0291	M	0.77313	2.365	0.09310	N	1	P	0.51791	0.948	P	0.59948	0.866	T	0.02047	-1.1223	10	0.62326	D	0.03	-5.1783	10.7622	0.46272	0.9255:0.0:0.0745:0.0	.	297	Q16820	MEP1B_HUMAN	C	297	ENSP00000269202:S297C	ENSP00000269202:S297C	S	+	1	0	MEP1B	28042202	0.761000	0.28439	0.207000	0.23584	0.486000	0.33341	6.024000	0.70857	2.078000	0.62432	0.459000	0.35465	AGT	.	.	.	none		0.478	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925		T	29788204	A	T	29788204	3	4	55	1	0	0	0	0	1	0	0	0	9483	304	11	5	923	5	MEP1B	18	29788204	Missense_Mutation	SNP	A	TCGA-A4-8311-01A-11D-2396-08		29788204	48289044	49	3789											
PQLC1	80148	hgsc.bcm.edu	37	chr18	77679262	77679262	+	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	tggcttcggtcagcacagccAggaagcccagggtctccaca	9	6	12	14	1	2	0	1	0	1	0	4	1	2	1	3	4	3	2	3	4	1	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr18:77679262A>T	ENST00000397778.2	-	5	712	c.530T>A	c.(529-531)cTg>cAg	p.L177Q	PQLC1_ENST00000409073.1_Missense_Mutation_p.L94Q|PQLC1_ENST00000357575.4_Missense_Mutation_p.L159Q|PQLC1_ENST00000590381.1_Intron	NM_025078.4	NP_079354.2	Q8N2U9	PQLC1_HUMAN	PQ loop repeat containing 1	177						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)	9		Esophageal squamous(42;0.0212)|Melanoma(33;0.2)		OV - Ovarian serous cystadenocarcinoma(15;8.2e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0258)		CAGCACAGCCAGGAAGCCCAG	0.652																																					p.L177Q		Atlas-SNP	.											.	PQLC1	16	.	0			c.T530A						PASS	.						88	75	79					18																	77679262		2203	4300	6503	SO:0001583	missense	80148	exon5			ACAGCCAGGAAGC	AK123870	CCDS12020.1, CCDS54192.1, CCDS54193.1	18q23	2004-01-14			ENSG00000122490	ENSG00000122490			26188	protein-coding gene	gene with protein product						12477932	Standard	NM_025078		Approved	FLJ22378	uc002lnl.2	Q8N2U9	OTTHUMG00000132921	ENST00000397778.2:c.530T>A	chr18.hg19:g.77679262A>T	ENSP00000380880:p.Leu177Gln	58.0	0.0	.		50.0	18.0	.	NM_025078	B7Z7D9|G5E989|Q9H6D0	Missense_Mutation	SNP	ENST00000397778.2	hg19	CCDS12020.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.453736	0.84209	.	.	ENSG00000122490	ENST00000397778;ENST00000409073;ENST00000357575	D;D;D	0.98531	-4.98;-4.98;-4.98	5.1	3.95	0.45737	.	0.000000	0.64402	D	0.000002	D	0.98707	0.9566	M	0.85197	2.74	0.80722	D	1	D;P	0.89917	1.0;0.937	D;P	0.81914	0.995;0.71	D	0.98869	1.0765	10	0.56958	D	0.05	-19.803	10.2033	0.43099	0.9213:0.0:0.0786:0.0	.	177;159	Q8N2U9;G5E989	PQLC1_HUMAN;.	Q	177;94;159	ENSP00000380880:L177Q;ENSP00000387221:L94Q;ENSP00000350188:L159Q	ENSP00000350188:L159Q	L	-	2	0	PQLC1	75780250	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	6.181000	0.71988	1.917000	0.55516	0.533000	0.62120	CTG	.	.	.	none		0.652	PQLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256434.1	NM_025078		T	77679262	A	T	77679262	3	4	55	1	0	0	0	0	1	0	0	0	12428	188	7	5	293	5	PQLC1	18	77679262	Missense_Mutation	SNP	A	TCGA-A4-8311-01A-11D-2396-08	47891058	77679262	397986	50	3790											
ABCA7	10347	hgsc.bcm.edu	37	chr19	1046944	1046944	+	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	cgccatggggctcagccgcgCggtgctctggctaggctggt	3	8	17	13	4	2	0	1	0	1	0	2	0	2	0	2	6	2	4	2	6	1	1	rs144979723|rs142076058|rs375206158	byFrequency	TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr19:1046944C>G	ENST00000263094.6	+	14	1997	c.1766C>G	c.(1765-1767)gCg>gGg	p.A589G	ABCA7_ENST00000435683.2_Missense_Mutation_p.A451G|ABCA7_ENST00000533574.1_Intron|ABCA7_ENST00000433129.1_Missense_Mutation_p.A589G	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	589					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTCAGCCGCGCGGTGCTCTGG	0.692													C|||	5	0.000998403	0	0	5008	,	,		13253	0.002		0	False		,,,				2504	0.0031				p.A589G		Atlas-SNP	.											ABCA7,colon,carcinoma,0,1	ABCA7	174	.	0			c.C1766G						PASS	.						17	18	18					19																	1046944		2170	4265	6435	SO:0001583	missense	10347	exon14			GCCGCGCGGTGCT	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.1766C>G	chr19.hg19:g.1046944C>G	ENSP00000263094:p.Ala589Gly	8.0	1.0	.		10.0	3.0	.	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	hg19	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	c	0.005	-2.154384	0.00325	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	T;T	0.80909	-1.43;-1.43	4.68	0.595	0.17490	.	.	.	.	.	T	0.60183	0.2249	N	0.03948	-0.315	0.09310	N	1	B;B	0.14805	0.003;0.011	B;B	0.21546	0.015;0.035	T	0.30357	-0.9981	9	0.09590	T	0.72	.	16.2636	0.82563	0.0:0.5375:0.4625:0.0	.	451;589	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	G	589	ENSP00000263094:A589G;ENSP00000414062:A589G	ENSP00000263094:A589G	A	+	2	0	ABCA7	997944	0.806000	0.28996	0.000000	0.03702	0.012000	0.07955	1.386000	0.34419	0.054000	0.16065	-1.338000	0.01255	GCG	.	C|0.999;T|0.001	.	alt		0.692	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		G	1046944	C	G	1046944	3	3	55	1	0	0	0	0	1	0	0	0	37	768	27	4	1816	4	ABCA7	19	1046944	Missense_Mutation	SNP	C	TCGA-A4-8311-01A-11D-2396-08		1046944	58082039	51	3791											
MUC16	94025	hgsc.bcm.edu	37	chr19	9077786	9077786	+	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	gaatttctcacagtggacctGatctctgggctgatgctggg	7	12	13	9	0	2	2	1	2	2	0	4	4	2	3	1	3	1	2	1	3	1	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr19:9077786G>T	ENST00000397910.4	-	3	9863	c.9660C>A	c.(9658-9660)atC>atA	p.I3220I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3221	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						CAGTGGACCTGATCTCTGGGC	0.498																																					p.I3220I		Atlas-SNP	.											.	MUC16	4315	.	0			c.C9660A						PASS	.						142	140	140					19																	9077786		1965	4150	6115	SO:0001819	synonymous_variant	94025	exon3			GGACCTGATCTCT	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.9660C>A	chr19.hg19:g.9077786G>T		162.0	0.0	.		157.0	71.0	.	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.	.	none		0.498	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9077786	G	T	9077786	2	4	55	1	0	0	0	0	0	0	0	1	9980	1280	45	4		4	MUC16	19	9077786	Silent	SNP	G	TCGA-A4-8311-01A-11D-2396-08	8030842	9077786	50051197	52	3792											
RALGAPB	57148	hgsc.bcm.edu	37	chr20	37153507	37153507	+	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	cgttattctaaactctcctcCtttgttctgctgtgacttga	6	18	6	11	1	3	2	0	2	3	0	5	2	4	2	2	0	2	3	2	0	3	6			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr20:37153507C>A	ENST00000262879.6	+	11	1990	c.1706C>A	c.(1705-1707)cCt>cAt	p.P569H	RALGAPB_ENST00000397040.1_Missense_Mutation_p.P569H|RALGAPB_ENST00000397038.1_Missense_Mutation_p.P347H|RALGAPB_ENST00000397042.3_Missense_Mutation_p.P569H			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	569					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						AACTCTCCTCCTTTGTTCTGC	0.393																																					p.P569H		Atlas-SNP	.											.	RALGAPB	134	.	0			c.C1706A						PASS	.						301	273	283					20																	37153507		2203	4300	6503	SO:0001583	missense	57148	exon11			CTCCTCCTTTGTT	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.1706C>A	chr20.hg19:g.37153507C>A	ENSP00000262879:p.Pro569His	171.0	0.0	.		247.0	151.0	.	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Missense_Mutation	SNP	ENST00000262879.6	hg19	CCDS13305.1	.	.	.	.	.	.	.	.	.	.	C	16.90	3.249579	0.59212	.	.	ENSG00000170471	ENST00000262879;ENST00000397042;ENST00000304939;ENST00000397038;ENST00000397040;ENST00000438490	T;T	0.66280	-0.2;-0.2	5.51	4.54	0.55810	.	0.099219	0.64402	D	0.000001	T	0.49423	0.1556	N	0.22421	0.69	0.49299	D	0.999778	B;B;B;B	0.06786	0.0;0.001;0.001;0.001	B;B;B;B	0.06405	0.001;0.002;0.002;0.002	T	0.46707	-0.9172	10	0.48119	T	0.1	.	15.7457	0.77939	0.1369:0.8631:0.0:0.0	.	397;569;569;569	A2A2F0;Q86X10-4;A2A2E9;Q86X10	.;.;.;RLGPB_HUMAN	H	569;569;569;347;569;397	ENSP00000262879:P569H;ENSP00000380233:P569H	ENSP00000262879:P569H	P	+	2	0	RALGAPB	36586921	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.977000	0.70492	2.587000	0.87381	0.561000	0.74099	CCT	.	.	.	none		0.393	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336		A	37153507	C	A	37153507	3	1	55	1	0	0	0	0	1	0	0	0	13028	681	24	4	1744	4	RALGAPB	20	37153507	Missense_Mutation	SNP	C	TCGA-A4-8311-01A-11D-2396-08		37153507	25872013	53	3793											
SULF2	55959	hgsc.bcm.edu	37	chr20	46291842	46291842	+	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	ggtctgtgttgagatcaaagTactctaggaagccagttgca	11	11	12	7	0	3	1	1	1	2	1	3	3	3	2	1	2	3	4	1	2	4	4			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr20:46291842T>A	ENST00000359930.4	-	17	3193	c.2342A>T	c.(2341-2343)tAc>tTc	p.Y781F	SULF2_ENST00000467815.1_Missense_Mutation_p.Y781F|SULF2_ENST00000484875.1_Missense_Mutation_p.Y781F|SULF2_ENST00000361612.4_Missense_Mutation_p.Y781F	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	781					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						GAGATCAAAGTACTCTAGGAA	0.547											OREG0026005	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y781F		Atlas-SNP	.											.	SULF2	131	.	0			c.A2342T						PASS	.						155	142	147					20																	46291842		2203	4300	6503	SO:0001583	missense	55959	exon17			TCAAAGTACTCTA	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.2342A>T	chr20.hg19:g.46291842T>A	ENSP00000353007:p.Tyr781Phe	89.0	0.0	.	938	98.0	51.0	.	NM_001161841	E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Missense_Mutation	SNP	ENST00000359930.4	hg19	CCDS13408.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.42|19.42	3.824660|3.824660	0.71143|0.71143	.|.	.|.	ENSG00000196562|ENSG00000196562	ENST00000495544|ENST00000359930;ENST00000484875;ENST00000361612;ENST00000371978;ENST00000467815	.|D;D;D;D	.|0.96073	.|-3.9;-3.9;-3.9;-3.9	5.42|5.42	5.42|5.42	0.78866|0.78866	.|Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	.|0.054592	.|0.85682	.|D	.|0.000000	D|D	0.95956|0.95956	0.8683|0.8683	L|L	0.41356|0.41356	1.27|1.27	0.54753|0.54753	D|D	0.999982|0.999982	.|D;D	.|0.89917	.|1.0;0.998	.|D;D	.|0.87578	.|0.998;0.99	D|D	0.94418|0.94418	0.7638|0.7638	5|10	.|0.19147	.|T	.|0.46	-23.4617|-23.4617	15.4799|15.4799	0.75517|0.75517	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|781;781	.|Q8IWU5-2;Q8IWU5	.|.;SULF2_HUMAN	S|F	136|781;781;781;200;781	.|ENSP00000353007:Y781F;ENSP00000418290:Y781F;ENSP00000354662:Y781F;ENSP00000418442:Y781F	.|ENSP00000353007:Y781F	T|Y	-|-	1|2	0|0	SULF2|SULF2	45725249|45725249	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	8.040000|8.040000	0.89188|0.89188	2.068000|2.068000	0.61886|0.61886	0.454000|0.454000	0.30748|0.30748	ACT|TAC	.	.	.	none		0.547	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837		A	46291842	T	A	46291842	3	1	55	1	0	0	0	0	1	0	0	0	15383	1638	57	5	290	5	SULF2	20	46291842	Missense_Mutation	SNP	T	TCGA-A4-8311-01A-11D-2396-08	9138335	46291842	16733678	54	3794											
DDX27	55661	hgsc.bcm.edu	37	chr20	47835928	47835928	+	Missense_Mutation	SNP	A	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	agacgacgaggaggctgcgaAaagttaagggccggaccgca	13	3	16	9	5	0	1	0	0	0	1	0	6	0	3	2	4	1	3	2	4	3	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr20:47835928A>C	ENST00000371764.4	+	1	45	c.36A>C	c.(34-36)gaA>gaC	p.E12D	DDX27_ENST00000484427.1_3'UTR	NM_017895.7	NP_060365.7	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	12						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)			GAGGCTGCGAAAAGTTAAGGG	0.607																																					p.E12D		Atlas-SNP	.											.	DDX27	74	.	0			c.A36C						PASS	.						78	66	70					20																	47835928		2203	4300	6503	SO:0001583	missense	55661	exon1			CTGCGAAAAGTTA	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.36A>C	chr20.hg19:g.47835928A>C	ENSP00000360828:p.Glu12Asp	39.0	0.0	.		49.0	14.0	.	NM_017895	A0AVB6|B7ZLY1|Q5VXM7|Q8WYG4|Q969N7|Q96F57|Q96L97|Q9BWY9|Q9BXF0|Q9H990|Q9NWU3|Q9P0C2|Q9UGD6	Missense_Mutation	SNP	ENST00000371764.4	hg19	CCDS13416.1	.	.	.	.	.	.	.	.	.	.	A	8.891	0.954106	0.18431	.	.	ENSG00000124228	ENST00000535160;ENST00000371764	T	0.01446	4.88	5.04	-4.9E-5	0.14040	.	2.187840	0.02319	N	0.072815	T	0.01353	0.0044	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.46830	-0.9163	10	0.87932	D	0	4.3423	3.5735	0.07926	0.5451:0.0:0.2933:0.1616	.	12	Q96GQ7	DDX27_HUMAN	D	12	ENSP00000360828:E12D	ENSP00000360828:E12D	E	+	3	2	DDX27	47269335	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.050000	0.14120	-0.113000	0.11958	0.533000	0.62120	GAA	.	.	.	none		0.607	DDX27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080485.1			C	47835928	A	C	47835928	3	2	55	1	0	0	0	0	1	0	0	0	4356	11	1	5	38	5	DDX27	20	47835928	Missense_Mutation	SNP	A	TCGA-A4-8311-01A-11D-2396-08	1544086	47835928	15189592	55	3795											
CRYAA	1409	hgsc.bcm.edu	37	chr21	44589374	44589374	+	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	cgccagtccctcttccgcacCgtgctggactccggcatctc	4	9	9	19	4	2	0	0	0	2	0	6	1	5	1	5	2	1	3	5	2	0	1			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr21:44589374C>G	ENST00000291554.2	+	1	257	c.165C>G	c.(163-165)acC>acG	p.T55T	CRYAA_ENST00000398133.1_5'Flank|CRYAA_ENST00000398132.1_5'Flank|CRYAA_ENST00000482775.1_3'UTR	NM_000394.2	NP_000385.1	P02489	CRYAA_HUMAN	crystallin, alpha A	55					negative regulation of apoptotic process (GO:0043066)|negative regulation of intracellular transport (GO:0032387)|protein homooligomerization (GO:0051260)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural constituent of eye lens (GO:0005212)|unfolded protein binding (GO:0051082)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	11						TCTTCCGCACCGTGCTGGACT	0.622																																					p.T55T		Atlas-SNP	.											.	CRYAA	23	.	0			c.C165G						PASS	.						130	118	122					21																	44589374		2203	4300	6503	SO:0001819	synonymous_variant	1409	exon1			CCGCACCGTGCTG		CCDS13695.1	21q22.3	2011-09-05			ENSG00000160202	ENSG00000160202		"Heat shock proteins / HSPB"	2388	protein-coding gene	gene with protein product		123580		CRYA1			Standard	XM_005261093		Approved	HSPB4	uc002zdd.1	P02489	OTTHUMG00000086842	ENST00000291554.2:c.165C>G	chr21.hg19:g.44589374C>G		174.0	0.0	.		183.0	92.0	.	NM_000394	Q53X53	Silent	SNP	ENST00000291554.2	hg19	CCDS13695.1																																																																																			.	.	.	none		0.622	CRYAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195562.1			G	44589374	C	G	44589374	2	3	55	1	0	0	0	0	0	0	0	1	3907	639	23	4		4	CRYAA	21	44589374	Silent	SNP	C	TCGA-A4-8311-01A-11D-2396-08		44589374	3540521	56	3796											
MED15	51586	hgsc.bcm.edu	37	chr22	20920816	20920816	+	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	cagctccaacaacagcaacaGcagcagcagcagcagcagca	16	1	9	15	0	0	0	0	0	0	0	1	0	1	0	1	0	12	9	1	0	3	0	rs535773989	byFrequency	TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr22:20920816G>A	ENST00000263205.7	+	7	822	c.753G>A	c.(751-753)caG>caA	p.Q251Q	MED15_ENST00000542773.1_Silent_p.Q56Q|MED15_ENST00000425759.2_Silent_p.Q140Q|MED15_ENST00000541476.1_Silent_p.Q225Q|MED15_ENST00000292733.7_Silent_p.Q251Q|MED15_ENST00000382974.2_Silent_p.Q180Q|MED15_ENST00000406969.1_Silent_p.Q225Q|MED15_ENST00000478831.1_3'UTR	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)			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)			aacagcaacagcagcagcagc	0.592																																					p.Q251Q		Atlas-SNP	.											PCQAP,colon,carcinoma,0,2	MED15	68	.	0			c.G753A						PASS	.						19	25	23					22																	20920816		2129	4141	6270	SO:0001819	synonymous_variant	51586	exon7			GCAACAGCAGCAG	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.753G>A	chr22.hg19:g.20920816G>A		56.0	2.0	.		46.0	5.0	.	NM_015889	D3DX31|D3DX32|O15413|Q6IC31|Q8NF16|Q96CT0|Q96IH7|Q9P1T3	Silent	SNP	ENST00000263205.7	hg19	CCDS33602.1	.	.	.	.	.	.	.	.	.	.	G	3.627	-0.076441	0.07184	.	.	ENSG00000099917	ENST00000423862	.	.	.	0.998	0.998	0.19857	.	.	.	.	.	T	0.51839	0.1698	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39143	-0.9628	4	.	.	.	.	5.6489	0.17604	0.0:0.0:1.0:0.0	.	.	.	.	T	192	.	.	A	+	1	0	MED15	19250816	0.894000	0.30519	0.949000	0.38748	0.643000	0.38383	0.816000	0.27267	0.293000	0.22520	0.298000	0.19748	GCA	.	.	.	none		0.592	MED15-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320177.2	NM_015889		A	20920816	G	A	20920816	2	1	55	1	0	0	0	0	0	0	0	1	9440	962	34	2		2	MED15	22	20920816	Silent	SNP	G	TCGA-A4-8311-01A-11D-2396-08		20920816	30383750	57	3797											
UQCR10	29796	hgsc.bcm.edu	37	chr22	30163434	30163434	+	Missense_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	attgtactccctgctgttccGcaggacctccaccttcgccc	5	11	7	18	2	0	0	0	0	0	0	4	1	3	1	6	1	2	4	6	1	1	4			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr22:30163434G>A	ENST00000330029.6	+	1	77	c.47G>A	c.(46-48)cGc>cAc	p.R16H	UQCR10_ENST00000401406.3_Missense_Mutation_p.R16H|ZMAT5_ENST00000397781.3_5'Flank|ZMAT5_ENST00000344318.3_5'Flank	NM_001003684.1|NM_013387.3	NP_001003684.1|NP_037519.2	Q9UDW1	QCR9_HUMAN	ubiquinol-cytochrome c reductase, complex III subunit X	16					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)	ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)	5						CTGCTGTTCCGCAGGACCTCC	0.612																																					p.R16H		Atlas-SNP	.											.	UQCR10	10	.	0			c.G47A						PASS	.						54	62	59					22																	30163434		2053	4195	6248	SO:0001583	missense	29796	exon1			TGTTCCGCAGGAC	AB028598	CCDS46680.1, CCDS46681.1	22q12.2	2011-07-04			ENSG00000184076	ENSG00000184076		"Mitochondrial respiratory chain complex / Complex III"	30863	protein-coding gene	gene with protein product	"ubiquinol-cytochrome c reductase, complex III subunit X, 7.2kDa", "complex III subunit 9"	610843				11042152	Standard	NM_013387		Approved	HSPC051, UCRC, QCR9, UCCR7.2	uc003agq.1	Q9UDW1	OTTHUMG00000151283	ENST00000330029.6:c.47G>A	chr22.hg19:g.30163434G>A	ENSP00000332887:p.Arg16His	58.0	0.0	.		60.0	29.0	.	NM_001003684	B5MCM5|Q9T2V6	Missense_Mutation	SNP	ENST00000330029.6	hg19	CCDS46680.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.541323	0.85917	.	.	ENSG00000184076	ENST00000332801;ENST00000330029;ENST00000401406;ENST00000406782	T;T	0.61158	0.13;0.13	5.73	5.73	0.89815	.	0.000000	0.42821	D	0.000649	T	0.76485	0.3994	.	.	.	0.51482	D	0.999921	B;D	0.89917	0.403;1.0	B;D	0.85130	0.152;0.997	T	0.78137	-0.2321	9	0.62326	D	0.03	-4.8723	15.4576	0.75327	0.0:0.0:1.0:0.0	.	16;16	Q9UDW1;Q9UDW1-2	QCR9_HUMAN;.	H	16	ENSP00000332887:R16H;ENSP00000384962:R16H	ENSP00000332887:R16H	R	+	2	0	UQCR10	28493434	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.728000	0.62000	2.720000	0.93068	0.558000	0.71614	CGC	.	.	.	none		0.612	UQCR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322081.1	NM_013387		A	30163434	G	A	30163434	3	1	55	1	0	0	0	0	1	0	0	0	17028	1087	38	1	49	1	UQCR10	22	30163434	Missense_Mutation	SNP	G	TCGA-A4-8311-01A-11D-2396-08	9242618	30163434	21141132	58	3798											
SEC14L3	266629	hgsc.bcm.edu	37	chr22	30866522	30866522	+	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	cagcgtagaaggaaataatcAtcagggttgggcagggcagg	13	6	16	6	1	2	1	2	0	0	1	2	2	2	2	0	5	1	4	0	5	4	3			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr22:30866522A>T	ENST00000215812.4	-	2	192	c.102T>A	c.(100-102)gaT>gaA	p.D34E	SEC14L3_ENST00000403066.1_5'UTR|SEC14L3_ENST00000415957.2_5'UTR|SEC14L3_ENST00000401751.1_5'UTR|SEC14L3_ENST00000540910.1_5'UTR|SEC14L3_ENST00000539629.1_5'UTR|SEC14L3_ENST00000402286.1_5'UTR	NM_174975.4	NP_777635.1	Q9UDX4	S14L3_HUMAN	SEC14-like 3 (S. cerevisiae)	34						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)	GGAAATAATCATCAGGGTTGG	0.567																																					p.D34E	Esophageal Squamous(108;290 1516 3584 23771 37333)	Atlas-SNP	.											.	SEC14L3	46	.	0			c.T102A						PASS	.						131	111	118					22																	30866522		2203	4300	6503	SO:0001583	missense	266629	exon2			ATAATCATCAGGG	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.102T>A	chr22.hg19:g.30866522A>T	ENSP00000215812:p.Asp34Glu	61.0	0.0	.		63.0	31.0	.	NM_174975	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000215812.4	hg19	CCDS13877.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.81|17.81	3.481554|3.481554	0.63849|0.63849	.|.	.|.	ENSG00000100012|ENSG00000100012	ENST00000215812|ENST00000435069	D|.	0.87729|.	-2.29|.	5.39|5.39	0.515|0.515	0.17013|0.17013	Phosphatidylinositol transfer protein-like, N-terminal (1);Cellular retinaldehyde-binding/triple function, N-terminal (1);|.	0.223524|.	0.46145|.	D|.	0.000308|.	T|.	0.77890|.	0.4198|.	M|M	0.92367|0.92367	3.3|3.3	0.80722|0.80722	D|D	1|1	P|.	0.47253|.	0.892|.	P|.	0.58391|.	0.838|.	T|.	0.77958|.	-0.2392|.	10|.	0.59425|.	D|.	0.04|.	-19.4435|-19.4435	9.2711|9.2711	0.37673|0.37673	0.5993:0.0:0.4007:0.0|0.5993:0.0:0.4007:0.0	.|.	34|.	Q9UDX4|.	S14L3_HUMAN|.	E|R	34|15	ENSP00000215812:D34E|.	ENSP00000215812:D34E|.	D|X	-|-	3|1	2|0	SEC14L3|SEC14L3	29196522|29196522	0.999000|0.999000	0.42202|0.42202	0.999000|0.999000	0.59377|0.59377	0.890000|0.890000	0.51754|0.51754	0.735000|0.735000	0.26115|0.26115	0.058000|0.058000	0.16222|0.16222	0.528000|0.528000	0.53228|0.53228	GAT|TGA	.	.	.	none		0.567	SEC14L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321950.4	NM_174975		T	30866522	A	T	30866522	3	4	55	1	0	0	0	0	1	0	0	0	13996	214	8	5	1144	5	SEC14L3	22	30866522	Missense_Mutation	SNP	A	TCGA-A4-8311-01A-11D-2396-08	703088	30866522	20438044	59	3799											
SUN2	25777	hgsc.bcm.edu	37	chr22	39138452	39138452	+	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	agccccttgccgcagctccaGacgttccagccgcatggcct	6	7	10	18	3	0	1	0	0	0	1	2	1	2	1	7	1	4	4	7	1	0	2			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chr22:39138452G>A	ENST00000405510.1	-	10	1280	c.922C>T	c.(922-924)Ctg>Ttg	p.L308L	RP3-508I15.14_ENST00000416406.1_RNA|SUN2_ENST00000411587.2_Silent_p.L297L|SUN2_ENST00000216064.4_Silent_p.L308L|SUN2_ENST00000405018.1_Silent_p.L329L|SUN2_ENST00000406622.1_Silent_p.L308L|RP3-508I15.22_ENST00000607991.1_RNA|RP3-508I15.21_ENST00000609212.1_RNA	NM_001199580.1	NP_001186509.1	Q9UH99	SUN2_HUMAN	Sad1 and UNC84 domain containing 2	308					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|mitotic spindle organization (GO:0007052)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)	condensed nuclear chromosome (GO:0000794)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|SUN-KASH complex (GO:0034993)	identical protein binding (GO:0042802)|lamin binding (GO:0005521)|microtubule binding (GO:0008017)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)|stomach(1)	15						CGCAGCTCCAGACGTTCCAGC	0.647																																					p.L329L		Atlas-SNP	.											.	SUN2	59	.	0			c.C985T						PASS	.						30	30	30					22																	39138452		2203	4300	6503	SO:0001819	synonymous_variant	25777	exon9			GCTCCAGACGTTC	AF202723	CCDS13978.1, CCDS56231.1	22q12-q13	2010-05-18	2010-05-18	2010-01-27	ENSG00000100242	ENSG00000100242			14210	protein-coding gene	gene with protein product		613569	"unc-84 homolog B (C. elegans)"	UNC84B		10508607, 10375507	Standard	NM_015374		Approved		uc010gxq.2	Q9UH99	OTTHUMG00000151031	ENST00000405510.1:c.922C>T	chr22.hg19:g.39138452G>A		53.0	0.0	.		43.0	19.0	.	NM_001199579	B0QY62|O75156|Q2NKN8|Q2T9F7|Q504T5|Q6B4H1|Q7Z3E3	Silent	SNP	ENST00000405510.1	hg19	CCDS13978.1																																																																																			.	.	.	none		0.647	SUN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321057.1	XM_039332		A	39138452	G	A	39138452	2	1	55	1	0	0	0	0	0	0	0	1	15404	933	33	2		2	SUN2	22	39138452	Silent	SNP	G	TCGA-A4-8311-01A-11D-2396-08	8271930	39138452	12166114	60	3800											
TMEM27	57393	hgsc.bcm.edu	37	chrX	15682860	15682860	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggttgacagagttcagcAtgaatggcagtcaccagaaa	13	8	11	9	0	2	4	2	2	0	2	2	4	2	4	2	2	1	4	2	2	2	2			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chrX:15682860A>G	ENST00000380342.3	-	1	294	c.39T>C	c.(37-39)caT>caC	p.H13H		NM_020665.4	NP_065716.1	Q9HBJ8	TMM27_HUMAN	transmembrane protein 27	13					positive regulation of amino acid transport (GO:0051957)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of SNARE complex assembly (GO:0035543)	brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)			endometrium(3)|lung(4)|ovary(1)	8	Hepatocellular(33;0.183)					AGAGTTCAGCATGAATGGCAG	0.373																																					p.H13H		Atlas-SNP	.											.	TMEM27	21	.	0			c.T39C						PASS	.						58	53	55					X																	15682860		2203	4299	6502	SO:0001819	synonymous_variant	57393	exon1			TTCAGCATGAATG	AF229179	CCDS14170.1	Xp22	2012-04-13			ENSG00000147003	ENSG00000147003			29437	protein-coding gene	gene with protein product	"collectrin"	300631				11278314	Standard	NM_020665		Approved	NX17	uc004cxc.2	Q9HBJ8	OTTHUMG00000021181	ENST00000380342.3:c.39T>C	chrX.hg19:g.15682860A>G		34.0	0.0	.		34.0	26.0	.	NM_020665	B2R9M1|Q6UW07	Silent	SNP	ENST00000380342.3	hg19	CCDS14170.1																																																																																			.	.	.	none		0.373	TMEM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055879.1	NM_020665		G	15682860	A	G	15682860	2	3	55	1	0	0	0	0	0	0	0	1	16164	214	8	3		3	TMEM27	23	15682860	Silent	SNP	A	TCGA-A4-8311-01A-11D-2396-08		15682860	139587700	61	3801											
THOC2	57187	hgsc.bcm.edu	37	chrX	122756985	122756985	+	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	cagtactgctttcatccgatTtagatgcacttcctattgat	9	16	6	10	1	1	2	1	1	0	1	3	3	3	2	2	0	3	3	2	0	3	7			TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	g.chrX:122756985T>A	ENST00000245838.8	-	29	3684	c.3653A>T	c.(3652-3654)aAa>aTa	p.K1218I	THOC2_ENST00000497887.1_5'Flank|THOC2_ENST00000491737.1_Missense_Mutation_p.K1103I|THOC2_ENST00000355725.4_Missense_Mutation_p.K1218I	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	1218					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						TTCATCCGATTTAGATGCACT	0.403																																					p.K1218I		Atlas-SNP	.											.	THOC2	310	.	0			c.A3653T						PASS	.						100	89	93					X																	122756985		1868	4105	5973	SO:0001583	missense	57187	exon29			TCCGATTTAGATG	AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"THO complex subunits"	19073	protein-coding gene	gene with protein product		300395	"chromosome X open reading frame 3"	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.3653A>T	chrX.hg19:g.122756985T>A	ENSP00000245838:p.Lys1218Ile	73.0	0.0	.		67.0	60.0	.	NM_001081550	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Missense_Mutation	SNP	ENST00000245838.8	hg19	CCDS43988.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.82|15.82	2.945939|2.945939	0.53079|0.53079	.|.	.|.	ENSG00000125676|ENSG00000125676	ENST00000245838;ENST00000355725;ENST00000491737|ENST00000438358	T;T;T|.	0.48836|.	0.8;0.8;0.8|.	5.97|5.97	5.97|5.97	0.96955|0.96955	.|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|.	0.53850|.	0.1822|.	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.80764|.	0.994|.	T|.	0.52155|.	-0.8613|.	10|.	0.44086|.	T|.	0.13|.	-18.2877|-18.2877	11.3724|11.3724	0.49708|0.49708	0.0:0.0733:0.0:0.9266|0.0:0.0733:0.0:0.9266	.|.	1218|.	Q8NI27|.	THOC2_HUMAN|.	I|Y	1218;1218;1103|312	ENSP00000245838:K1218I;ENSP00000347959:K1218I;ENSP00000419795:K1103I|.	ENSP00000245838:K1218I|.	K|X	-|-	2|3	0|2	THOC2|THOC2	122584666|122584666	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.951000|0.951000	0.60555|0.60555	2.582000|2.582000	0.46085|0.46085	2.011000|2.011000	0.59026|0.59026	0.437000|0.437000	0.28790|0.28790	AAA|TAA	.	.	.	none		0.403	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3			A	122756985	T	A	122756985	3	1	55	1	0	0	0	0	1	0	0	0	15877	1841	64	5	1168	5	THOC2	23	122756985	Missense_Mutation	SNP	T	TCGA-A4-8311-01A-11D-2396-08	107074125	122756985	32513575	62	3802											
DUSP27	92235	hgsc.bcm.edu	37	chr1	167097085	167097085	+	Missense_Mutation	SNP	A	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	ttcccgcagtaattcccagaAacctgaaacagacacatgct	14	8	6	13	1	0	3	0	1	0	2	2	3	2	3	3	0	3	3	3	0	3	3	rs377480316		TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr1:167097085A>C	ENST00000361200.2	+	6	2883	c.2717A>C	c.(2716-2718)aAa>aCa	p.K906T	DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000443333.1_Missense_Mutation_p.K906T|DUSP27_ENST00000271385.5_Missense_Mutation_p.K906T			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	906	Ser-rich.				protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						AATTCCCAGAAACCTGAAACA	0.493																																					p.K906T		Atlas-SNP	.											.	DUSP27	235	.	0			c.A2717C						PASS	.	A	THR/LYS	0,4406		0,0,2203	87	77	81		2717	1.5	1	1		81	1,8599	1.2+/-3.3	0,1,4299	no	missense	DUSP27	NM_001080426.1	78	0,1,6502	CC,CA,AA		0.0116,0.0,0.0077	probably-damaging	906/1159	167097085	1,13005	2203	4300	6503	SO:0001583	missense	92235	exon5			CCCAGAAACCTGA	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.2717A>C	chr1.hg19:g.167097085A>C	ENSP00000354483:p.Lys906Thr	66.0	0.0	.		56.0	5.0	.	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	hg19	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	A	13.84	2.356232	0.41700	0.0	1.16E-4	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.04454	3.62;3.62;3.62	5.25	1.46	0.22682	.	0.874767	0.09948	N	0.735044	T	0.01905	0.0060	M	0.65975	2.015	0.09310	N	1	P	0.35433	0.501	B	0.27608	0.081	T	0.42899	-0.9424	10	0.87932	D	0	-19.6906	5.4857	0.16749	0.6201:0.1386:0.2413:0.0	.	906	Q5VZP5	DUS27_HUMAN	T	906	ENSP00000354483:K906T;ENSP00000271385:K906T;ENSP00000404874:K906T	ENSP00000271385:K906T	K	+	2	0	DUSP27	165363709	0.258000	0.24033	0.973000	0.42090	0.754000	0.42855	1.679000	0.37597	0.315000	0.23110	-0.269000	0.10298	AAA	.	.	.	none		0.493	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		C	167097085	A	C	167097085	3	2	56	1	0	0	0	0	1	0	0	0	4826	14	1	5	2735	5	DUSP27	1	167097085	Missense_Mutation	SNP	A	TCGA-A4-8312-01A-11D-2396-08		167097085	82153536	1	3803											
SMARCAL1	50485	hgsc.bcm.edu	37	chr2	217279802	217279802	+	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	ctcactggaatctctcctccCttggcacaaagtcctccaga	9	10	6	16	0	2	1	1	0	1	1	7	2	6	2	4	2	0	1	4	2	2	1			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr2:217279802C>G	ENST00000357276.4	+	3	705	c.375C>G	c.(373-375)ccC>ccG	p.P125P	AC098820.2_ENST00000457694.1_RNA|SMARCAL1_ENST00000358207.5_Silent_p.P125P	NM_014140.3	NP_054859.2	Q9NZC9	SMAL1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	125					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)		TCTCTCCTCCCTTGGCACAAA	0.507									Schimke Immuno-Osseous Dysplasia																												p.P125P		Atlas-SNP	.											.	SMARCAL1	93	.	0			c.C375G						PASS	.						88	80	82					2																	217279802		2203	4300	6503	SO:0001819	synonymous_variant	50485	exon3	Familial Cancer Database	SIOD	TCCTCCCTTGGCA	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.375C>G	chr2.hg19:g.217279802C>G		105.0	0.0	.		109.0	44.0	.	NM_014140	A6NEH0|Q53R00|Q96AY1|Q9NXQ5|Q9UFH3|Q9UI93	Silent	SNP	ENST00000357276.4	hg19	CCDS2403.1																																																																																			.	.	.	none		0.507	SMARCAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256671.2			G	217279802	C	G	217279802	2	3	56	1	0	0	0	0	0	0	0	1	14786	668	24	4		4	SMARCAL1	2	217279802	Silent	SNP	C	TCGA-A4-8312-01A-11D-2396-08		217279802	25919571	2	3804											
PARK2	5071	hgsc.bcm.edu	37	chr6	162206852	162206852	+	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	agggtcgtgaacaaactgccGatcattgagtcttgtcacac	11	10	10	10	2	3	2	2	2	1	0	4	3	3	2	1	1	3	0	1	1	2	2	rs34424986	byFrequency	TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr6:162206852G>C	ENST00000366898.1	-	7	925	c.823C>G	c.(823-825)Cgg>Ggg	p.R275G	PARK2_ENST00000338468.3_Missense_Mutation_p.R84G|PARK2_ENST00000366894.1_Missense_Mutation_p.R84G|PARK2_ENST00000366896.1_Missense_Mutation_p.R126G|PARK2_ENST00000366892.1_Missense_Mutation_p.R275G|PARK2_ENST00000366897.1_Missense_Mutation_p.R247G	NM_004562.2	NP_004553.2	O60260	PRKN2_HUMAN	parkin RBR E3 ubiquitin protein ligase	275	SYT11 binding 2.		R -> W (in PARK2 and PARK; at heterozygosity it is associated with late onset Parkinson disease; impairs the ability to ubiquitinate SNCAIP; abolishes p53/TP53 transcriptional repression; dbSNP:rs34424986). {ECO:0000269|PubMed:10072423, ECO:0000269|PubMed:10824074, ECO:0000269|PubMed:11179010, ECO:0000269|PubMed:11971093, ECO:0000269|PubMed:12114481, ECO:0000269|PubMed:12116199, ECO:0000269|PubMed:12730996, ECO:0000269|PubMed:22956510}.		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)		ACAAACTGCCGATCATTGAGT	0.478																																					p.R275G		Atlas-SNP	.											PARK2_ENST00000366892,NS,malignant_melanoma,0,2	PARK2	96	.	0			c.C823G	GRCh37	CM991007	PARK2	M	rs34424986	PASS	.						102	88	93					6																	162206852		2203	4300	6503	SO:0001583	missense	5071	exon7			ACTGCCGATCATT		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.823C>G	chr6.hg19:g.162206852G>C	ENSP00000355865:p.Arg275Gly	48.0	0.0	.		42.0	2.0	.	NM_004562	A3FG77|A8K975|D3JZW7|D3K2X0|Q5TFV8|Q5VVX4|Q6Q2I6|Q8NI41|Q8NI43|Q8NI44|Q8WW07	Missense_Mutation	SNP	ENST00000366898.1	hg19	CCDS5281.1	.	.	.	.	.	.	.	.	.	.	G	18.53	3.643036	0.67244	.	.	ENSG00000185345	ENST00000366898;ENST00000366897;ENST00000366896;ENST00000366894;ENST00000338468;ENST00000392134;ENST00000366892;ENST00000366895	D;D;D;D;D;D	0.90004	-2.6;-2.6;-2.6;-2.6;-2.6;-2.6	5.75	4.87	0.63330	.	0.000000	0.85682	D	0.000000	D	0.92322	0.7564	M	0.83483	2.645	0.36075	D	0.842404	D;D;D;D;D	0.89917	1.0;0.997;1.0;1.0;0.961	D;D;D;D;P	0.91635	0.999;0.987;0.999;0.999;0.666	D	0.91610	0.5302	10	0.25106	T	0.35	.	14.0915	0.64993	0.0:0.0:0.849:0.151	.	275;126;247;275;84	O60260-5;Q5VVX3;Q5VVX4;O60260;Q8NI42	.;.;.;PRKN2_HUMAN;.	G	275;247;126;84;84;84;275;196	ENSP00000355865:R275G;ENSP00000355863:R247G;ENSP00000355862:R126G;ENSP00000355860:R84G;ENSP00000343589:R84G;ENSP00000355858:R275G	ENSP00000343589:R84G	R	-	1	2	PARK2	162126842	0.982000	0.34865	0.751000	0.31187	0.863000	0.49368	1.685000	0.37659	1.406000	0.46857	0.650000	0.86243	CGG	.	G|0.998;A|0.002	.	alt		0.478	PARK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042995.1			C	162206852	G	C	162206852	3	2	56	1	0	0	0	0	1	0	0	0	11456	1057	37	4	598	4	PARK2	6	162206852	Missense_Mutation	SNP	G	TCGA-A4-8312-01A-11D-2396-08		162206852	8908215	3	3805											
TBP	6908	hgsc.bcm.edu	37	chr6	170871091	170871091	+	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	cagcagcagcagcagcagcaGcagcagcagcagcaacaggc	14	0	13	14	0	0	0	0	0	0	0	0	0	0	0	0	1	12	11	0	1	1	0			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr6:170871091G>A	ENST00000392092.2	+	3	546	c.267G>A	c.(265-267)caG>caA	p.Q89Q	TBP_ENST00000230354.6_Silent_p.Q89Q|TBP_ENST00000540980.1_Silent_p.Q69Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	89	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		agcagcagcagcagcagcagc	0.617																																					p.Q89Q		Atlas-SNP	.											TBP,NS,carcinoma,0,1	TBP	58	.	0			c.G267A						PASS	.						20	26	24					6																	170871091		1890	3708	5598	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAGCAG	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.267G>A	chr6.hg19:g.170871091G>A		60.0	0.0	.		71.0	3.0	.	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	hg19	CCDS5315.1																																																																																			.	.	.	none		0.617	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		A	170871091	G	A	170871091	2	1	56	1	0	0	0	0	0	0	0	1	15656	962	34	2		2	TBP	6	170871091	Silent	SNP	G	TCGA-A4-8312-01A-11D-2396-08	8664239	170871091	243976	4	3806											
FBXW2	26190	hgsc.bcm.edu	37	chr9	123527053	123527053	+	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	atgatgtacaggtagcggttGtcaaacagcagggcaaagat	14	8	13	6	1	1	2	1	1	0	1	1	2	1	2	0	3	4	5	0	3	4	3			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr9:123527053G>A	ENST00000608872.1	-	8	1336	c.1149C>T	c.(1147-1149)gaC>gaT	p.D383D	FBXW2_ENST00000493559.1_Intron|FBXW2_ENST00000340778.5_Silent_p.D318D	NM_012164.3	NP_036296.2	Q9UKT8	FBXW2_HUMAN	F-box and WD repeat domain containing 2	383					cellular protein modification process (GO:0006464)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)			ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	4						GGTAGCGGTTGTCAAACAGCA	0.502																																					p.D383D		Atlas-SNP	.											.	FBXW2	34	.	0			c.C1149T						PASS	.						92	90	91					9																	123527053		1949	4160	6109	SO:0001819	synonymous_variant	26190	exon8			GCGGTTGTCAAAC	AF129531	CCDS43872.1	9q34	2013-01-09	2007-02-08		ENSG00000119402	ENSG00000119402		"F-boxes / WD-40 domains", "WD repeat domain containing"	13608	protein-coding gene	gene with protein product		609071	"F-box and WD-40 domain protein 2"			10531035, 10828603	Standard	NM_012164		Approved	FBW2, Md6, Fwd2	uc004bkm.1	Q9UKT8	OTTHUMG00000020576	ENST00000608872.1:c.1149C>T	chr9.hg19:g.123527053G>A		139.0	0.0	.		125.0	11.0	.	NM_012164	B3KRL8|Q4VXH2|Q7Z4V6|Q8WV51|Q9HA09|Q9UKA3	Silent	SNP	ENST00000608872.1	hg19	CCDS43872.1																																																																																			.	.	.	none		0.502	FBXW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053834.2			A	123527053	G	A	123527053	2	1	56	1	0	0	0	0	0	0	0	1	5773	1368	48	2		2	FBXW2	9	123527053	Silent	SNP	G	TCGA-A4-8312-01A-11D-2396-08		123527053	17686378	5	3807											
MMP13	4322	hgsc.bcm.edu	37	chr11	102826393	102826393	+	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	ggcagggcccgacaatgagtCcagctcaagaagaggaaggc	13	3	15	10	1	1	3	1	1	0	2	2	5	2	4	2	4	1	2	2	4	4	0			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr11:102826393C>A	ENST00000260302.3	-	1	70	c.42G>T	c.(40-42)tgG>tgT	p.W14C	MMP13_ENST00000340273.4_Missense_Mutation_p.W14C	NM_002427.3	NP_002418.1	P45452	MMP13_HUMAN	matrix metallopeptidase 13 (collagenase 3)	14					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)	GACAATGAGTCCAGCTCAAGA	0.507																																					p.W14C		Atlas-SNP	.											.	MMP13	75	.	0			c.G42T						PASS	.						94	94	94					11																	102826393		2202	4299	6501	SO:0001583	missense	4322	exon1			ATGAGTCCAGCTC	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.42G>T	chr11.hg19:g.102826393C>A	ENSP00000260302:p.Trp14Cys	114.0	0.0	.		101.0	10.0	.	NM_002427	A8K846|B2RCZ3|Q6NWN6	Missense_Mutation	SNP	ENST00000260302.3	hg19	CCDS8324.1	.	.	.	.	.	.	.	.	.	.	C	6.549	0.469578	0.12461	.	.	ENSG00000137745	ENST00000260302;ENST00000546012;ENST00000340273	T;T	0.15139	2.64;2.45	5.87	5.87	0.94306	.	0.442712	0.26311	N	0.025120	T	0.11024	0.0269	N	0.14661	0.345	0.47994	D	0.999562	P	0.48640	0.913	B	0.40741	0.339	T	0.03306	-1.1050	10	0.45353	T	0.12	.	11.7621	0.51910	0.1372:0.7305:0.1323:0.0	.	14	P45452	MMP13_HUMAN	C	14	ENSP00000260302:W14C;ENSP00000339672:W14C	ENSP00000260302:W14C	W	-	3	0	MMP13	102331603	0.998000	0.40836	0.987000	0.45799	0.168000	0.22595	1.956000	0.40382	2.941000	0.99782	0.655000	0.94253	TGG	.	.	.	none		0.507	MMP13-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386648.1	NM_002427		A	102826393	C	A	102826393	3	1	56	1	0	0	0	0	1	0	0	0	9659	856	30	4	1413	4	MMP13	11	102826393	Missense_Mutation	SNP	C	TCGA-A4-8312-01A-11D-2396-08		102826393	32180123	6	3808											
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	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	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-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000556131.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.G12D	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	Atlas-SNP	.		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	KRAS_ENST00000256078,NS,adenocarcinoma,0,66	KRAS	30930	.	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	c.G35A						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>A	chr12.hg19:g.25398284C>T	ENSP00000256078:p.Gly12Asp	29.0	0.0	.		37.0	19.0	.	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT	.	.	.	weak		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398284	C	T	25398284	3	4	56	1	0	0	0	0	1	0	0	0	8445	507	18	2	671	2	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-A4-8312-01A-11D-2396-08		25398284	108453611	7	3809											
BICD1	636	hgsc.bcm.edu	37	chr12	32491723	32491724	+	Frame_Shift_Del	DEL	AT	AT	-																															cttggatctcctgcaagacaAttttcaccttccctttgtga																										TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr12:32491723_32491724delAT	ENST00000281474.5	+	8	2677_2678	c.2574_2575delAT	c.(2572-2577)caatttfs	p.QF858fs	BICD1_ENST00000548411.1_Intron	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	858					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)			CTGCAAGACAATTTTCACCTTC	0.406																																					p.858_858del		Atlas-INDEL	.											.	BICD1	89	.	0			c.2573_2574del						PASS	.																																			SO:0001589	frameshift_variant	636	exon8			.	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.2574_2575delAT	chr12.hg19:g.32491723_32491724delAT	ENSP00000281474:p.Gln858fs	200.0	0.0	0		182.0	62.0	0.340659	NM_001714	A8K2C3|F8W113|O43892|O43893	Frame_Shift_Del	DEL	ENST00000281474.5	hg19	CCDS8726.1																																																																																			.	.	.	none		0.406	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714		-	32491724	AT	-	32491723	7	5	56	1	0	1	0	1	0	0	0	0	1428	98	4	0	2604	0	BICD1	12	32491723	Frame_Shift_Del	DEL	AT	TCGA-A4-8312-01A-11D-2396-08	7093439	32491723	101360172	8	3810											
MTUS2	23281	hgsc.bcm.edu	37	chr13	29599704	29599704	+	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	tctgaatttgactttggcatCgaaggaaatcccaagtaaac	14	11	8	8	1	1	2	0	2	1	0	3	4	2	3	1	2	1	2	1	2	6	3			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr13:29599704C>T	ENST00000431530.3	+	1	957	c.899C>T	c.(898-900)tCg>tTg	p.S300L		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	290						cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)	p.S300L(2)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						ACTTTGGCATCGAAGGAAATC	0.507																																					p.S300L		Atlas-SNP	.											MTUS2_ENST00000431530,colon,carcinoma,-1,2	MTUS2	279	.	2	Substitution - Missense(2)	endometrium(1)|central_nervous_system(1)	c.C899T						PASS	.						40	40	40					13																	29599704		2007	4188	6195	SO:0001583	missense	23281	exon1			TGGCATCGAAGGA	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.899C>T	chr13.hg19:g.29599704C>T	ENSP00000392057:p.Ser300Leu	32.0	0.0	.		32.0	9.0	.	NM_001033602	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Missense_Mutation	SNP	ENST00000431530.3	hg19	CCDS45022.1	.	.	.	.	.	.	.	.	.	.	c	10.58	1.391325	0.25118	.	.	ENSG00000132938	ENST00000431530	T	0.13089	2.62	5.49	0.716	0.18191	.	0.981254	0.08305	N	0.966293	T	0.06096	0.0158	N	0.03115	-0.41	0.09310	N	1	B	0.21309	0.054	B	0.12156	0.007	T	0.44128	-0.9348	9	.	.	.	.	10.4835	0.44708	0.0:0.587:0.0:0.413	.	290	Q5JR59	MTUS2_HUMAN	L	300	ENSP00000392057:S300L	.	S	+	2	0	MTUS2	28497704	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	0.040000	0.13905	0.015000	0.14971	0.561000	0.74099	TCG	.	.	.	none		0.507	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270		T	29599704	C	T	29599704	3	4	56	1	0	0	0	0	1	0	0	0	9973	893	31	1	901	1	MTUS2	13	29599704	Missense_Mutation	SNP	C	TCGA-A4-8312-01A-11D-2396-08		29599704	85570174	9	3811											
SLC8A3	6547	hgsc.bcm.edu	37	chr14	70527578	70527578	+	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	attccacgttccatccatttCggttcaccaagggcaatgaa	11	11	7	12	2	1	1	1	1	0	0	5	1	4	1	4	2	0	3	4	2	3	4	rs376675749		TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr14:70527578C>T	ENST00000381269.2	-	3	2616	c.1863G>A	c.(1861-1863)ccG>ccA	p.P621P	SLC8A3_ENST00000216568.7_5'UTR|SLC8A3_ENST00000533541.1_Intron|SLC8A3_ENST00000528359.1_Intron|SLC8A3_ENST00000357887.3_Intron|SLC8A3_ENST00000394330.2_Intron|SLC8A3_ENST00000534137.1_Silent_p.P621P|SLC8A3_ENST00000356921.2_Silent_p.P621P|SLC8A3_ENST00000533899.1_5'UTR	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	621					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)		CCATCCATTTCGGTTCACCAA	0.343																																					p.P621P		Atlas-SNP	.											SLC8A3,caecum,carcinoma,0,1	SLC8A3	234	.	0			c.G1863A						PASS	.	C	,,,,,	2,4404	4.2+/-10.8	0,2,2201	167	144	152		,,1863,1863,,1863	5.9	1	14		152	0,8600		0,0,4300	no	utr-5,intron,coding-synonymous,coding-synonymous,intron,coding-synonymous	SLC8A3	NM_001130417.1,NM_033262.3,NM_058240.2,NM_182932.1,NM_182936.1,NM_183002.1	,,,,,	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	,,,,,	,,621/925,621/922,,621/928	70527578	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	6547	exon3			CCATTTCGGTTCA	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.1863G>A	chr14.hg19:g.70527578C>T		101.0	0.0	.		71.0	22.0	.	NM_183002	Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	Silent	SNP	ENST00000381269.2	hg19	CCDS35498.1																																																																																			.	.	.	weak		0.343	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390736.1			T	70527578	C	T	70527578	2	4	56	1	0	0	0	0	0	0	0	1	14721	871	31	1		1	SLC8A3	14	70527578	Silent	SNP	C	TCGA-A4-8312-01A-11D-2396-08		70527578	36821962	10	3812											
TRIP11	9321	hgsc.bcm.edu	37	chr14	92470654	92470654	+	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	atcacctgctgcttccactcTtccattttctttacttgctg	5	18	4	14	0	3	0	1	0	2	0	5	0	5	0	3	0	4	3	3	0	1	7			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr14:92470654T>A	ENST00000267622.4	-	11	4039	c.3666A>T	c.(3664-3666)gaA>gaT	p.E1222D		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	1222					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)		GCTTCCACTCTTCCATTTTCT	0.443			T	PDGFRB	AML																																p.E1222D	Ovarian(84;609 1888 9852 42686)	Atlas-SNP	.		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	.	TRIP11	184	.	0			c.A3666T						PASS	.						79	72	75					14																	92470654		2203	4300	6503	SO:0001583	missense	9321	exon11			CCACTCTTCCATT	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.3666A>T	chr14.hg19:g.92470654T>A	ENSP00000267622:p.Glu1222Asp	78.0	0.0	.		64.0	28.0	.	NM_004239	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	hg19	CCDS9899.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.88|11.88	1.771464|1.771464	0.31320|0.31320	.|.	.|.	ENSG00000100815|ENSG00000100815	ENST00000267622;ENST00000542257|ENST00000554357	T|.	0.05786|.	3.39|.	5.46|5.46	-4.33|-4.33	0.03677|0.03677	.|.	0.112824|.	0.64402|.	D|.	0.000015|.	T|.	0.44664|.	0.1304|.	L|L	0.32530|0.32530	0.975|0.975	0.41458|0.41458	D|D	0.988026|0.988026	D;D|.	0.89917|.	0.986;1.0|.	P;D|.	0.91635|.	0.78;0.999|.	T|.	0.32745|.	-0.9895|.	10|.	0.52906|.	T|.	0.07|.	.|.	8.2632|8.2632	0.31797|0.31797	0.119:0.4845:0.0:0.3964|0.119:0.4845:0.0:0.3964	.|.	958;1222|.	F5H1Z0;Q15643|.	.;TRIPB_HUMAN|.	D|X	1222;958|938	ENSP00000267622:E1222D|.	ENSP00000267622:E1222D|.	E|R	-|-	3|1	2|2	TRIP11|TRIP11	91540407|91540407	0.238000|0.238000	0.23825|0.23825	0.822000|0.822000	0.32727|0.32727	0.150000|0.150000	0.21749|0.21749	-0.435000|-0.435000	0.06931|0.06931	-1.215000|-1.215000	0.02610|0.02610	-0.624000|-0.624000	0.04008|0.04008	GAA|AGA	.	.	.	none		0.443	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1			A	92470654	T	A	92470654	3	1	56	1	0	0	0	0	1	0	0	0	16567	1606	56	5	2317	5	TRIP11	14	92470654	Missense_Mutation	SNP	T	TCGA-A4-8312-01A-11D-2396-08	21943076	92470654	14878886	11	3813											
ATP10A	57194	hgsc.bcm.edu	37	chr15	25972305	25972305	+	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	ggtgccaggtgcccgagcctAcctgcgtagatgacaatgcc	8	7	13	13	2	0	2	0	1	0	1	0	3	0	2	5	2	6	1	5	2	3	2			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr15:25972305A>T	ENST00000356865.6	-	4	959		c.e4+1			NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A						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)		GCCCGAGCCTACCTGCGTAGA	0.517																																					.		Atlas-SNP	.											.	ATP10A	270	.	0			c.847+2T>A						PASS	.						102	81	88					15																	25972305		2203	4300	6503	SO:0001630	splice_region_variant	57194	exon5			GAGCCTACCTGCG	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.847+1T>A	chr15.hg19:g.25972305A>T		86.0	0.0	.		81.0	36.0	.	NM_024490	Q4G0S9|Q969I4	Splice_Site	SNP	ENST00000356865.6	hg19	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.514606	0.85389	.	.	ENSG00000206190	ENST00000356865	.	.	.	5.34	5.34	0.76211	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3129	0.74048	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ATP10A	23523398	1.000000	0.71417	0.995000	0.50966	0.813000	0.45954	8.600000	0.90860	2.033000	0.60031	0.460000	0.39030	.	.	.	.	none		0.517	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	Intron	T	25972305	A	T	25972305	5	4	56	1	0	0	0	0	0	0	1	0	1116	405	14	5	3722	5	ATP10A	15	25972305	Splice_Site	SNP	A	TCGA-A4-8312-01A-11D-2396-08		25972305	76559087	12	3814											
SRCAP	10847	hgsc.bcm.edu	37	chr16	30718524	30718524	+	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	gaggccgagatcgagactcgGattgctgagctgcggaagga	10	6	17	8	4	0	3	0	1	0	2	2	9	0	6	1	4	3	2	1	4	1	1			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr16:30718524G>T	ENST00000262518.4	+	5	712	c.327G>T	c.(325-327)cgG>cgT	p.R109R	SRCAP_ENST00000344771.4_Silent_p.R109R|SRCAP_ENST00000395059.2_Silent_p.R109R	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	109					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)			TCGAGACTCGGATTGCTGAGC	0.547																																					p.R109R		Atlas-SNP	.											.	SRCAP	298	.	0			c.G327T						PASS	.						69	69	69					16																	30718524		1987	4166	6153	SO:0001819	synonymous_variant	10847	exon5			GACTCGGATTGCT	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.327G>T	chr16.hg19:g.30718524G>T		77.0	0.0	.		90.0	34.0	.	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Silent	SNP	ENST00000262518.4	hg19	CCDS10689.2																																																																																			.	.	.	none		0.547	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		T	30718524	G	T	30718524	2	4	56	1	0	0	0	0	0	0	0	1	15147	1161	41	4		4	SRCAP	16	30718524	Silent	SNP	G	TCGA-A4-8312-01A-11D-2396-08		30718524	59636229	13	3815											
SRCAP	10847	hgsc.bcm.edu	37	chr16	30727477	30727477	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgttatccgctgcaggctcTccaagcgtcaacgctgtctc	7	11	9	14	3	3	0	1	0	2	0	6	0	4	0	2	1	3	5	2	1	3	1			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr16:30727477T>C	ENST00000262518.4	+	17	2969	c.2584T>C	c.(2584-2586)Tcc>Ccc	p.S862P	SRCAP_ENST00000344771.4_Missense_Mutation_p.S862P|SRCAP_ENST00000395059.2_Missense_Mutation_p.S862P	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	862					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)			CTGCAGGCTCTCCAAGCGTCA	0.517																																					p.S862P		Atlas-SNP	.											.	SRCAP	298	.	0			c.T2584C						PASS	.						137	119	125					16																	30727477		2197	4300	6497	SO:0001583	missense	10847	exon17			AGGCTCTCCAAGC	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.2584T>C	chr16.hg19:g.30727477T>C	ENSP00000262518:p.Ser862Pro	105.0	0.0	.		117.0	5.0	.	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	hg19	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	T	18.97	3.735012	0.69189	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	T;T;T	0.79749	-1.3;-1.3;-1.3	5.25	5.25	0.73442	SNF2-related (1);	0.000000	0.53938	D	0.000054	D	0.89577	0.6755	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	0.999;0.998;0.999	D	0.90981	0.4827	10	0.87932	D	0	-15.3089	14.2776	0.66191	0.0:0.0:0.0:1.0	.	862;862;862	Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2	.;.;SRCAP_HUMAN	P	862	ENSP00000262518:S862P;ENSP00000378499:S862P;ENSP00000343042:S862P	ENSP00000262518:S862P	S	+	1	0	SRCAP	30634978	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.712000	0.84684	2.201000	0.70794	0.459000	0.35465	TCC	.	.	.	none		0.517	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		C	30727477	T	C	30727477	3	2	56	1	0	0	0	0	1	0	0	0	15147	1551	54	3	2642	3	SRCAP	16	30727477	Missense_Mutation	SNP	T	TCGA-A4-8312-01A-11D-2396-08	8953	30727477	59627276	14	3816											
LYZL6	57151	hgsc.bcm.edu	37	chr17	34261844	34261844	+	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	ccagtagaagagtggccggcCtgaacagtgcaacctccatt	11	7	11	12	1	0	3	0	1	0	2	1	3	1	3	5	2	3	2	5	2	4	2			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr17:34261844C>T	ENST00000585556.1	-	5	737	c.403G>A	c.(403-405)Ggc>Agc	p.G135S	LYZL6_ENST00000492340.2_5'Flank|LYZL6_ENST00000293274.4_Missense_Mutation_p.G135S|LYZL6_ENST00000394523.3_Missense_Mutation_p.G135S			O75951	LYZL6_HUMAN	lysozyme-like 6	135					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)			breast(1)|endometrium(1)|large_intestine(1)|lung(8)|stomach(1)	12				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		AGTGGCCGGCCTGAACAGTGC	0.542																																					p.G135S		Atlas-SNP	.											.	LYZL6	18	.	0			c.G403A						PASS	.						89	82	85					17																	34261844		2203	4300	6503	SO:0001583	missense	57151	exon4			GCCGGCCTGAACA	AF088219, AY742214	CCDS11302.1	17q11.2	2014-04-10			ENSG00000161572	ENSG00000275722			29614	protein-coding gene	gene with protein product		612751				10213461	Standard	NM_020426		Approved	LYC1, PRO1485, TKAL754	uc002hkj.2	O75951	OTTHUMG00000188400	ENST00000585556.1:c.403G>A	chr17.hg19:g.34261844C>T	ENSP00000468094:p.Gly135Ser	83.0	0.0	.		77.0	19.0	.	NM_020426	Q6UW30	Missense_Mutation	SNP	ENST00000585556.1	hg19	CCDS11302.1	.	.	.	.	.	.	.	.	.	.	C	17.52	3.410784	0.62399	.	.	ENSG00000161572	ENST00000293274;ENST00000394523	T;T	0.51325	0.71;0.71	4.65	4.65	0.58169	Lysozyme-like domain (1);	0.000000	0.64402	D	0.000004	T	0.66336	0.2779	M	0.87547	2.89	0.23988	N	0.996253	D	0.57257	0.979	P	0.56088	0.791	T	0.63844	-0.6545	10	0.62326	D	0.03	-0.303	13.7598	0.62959	0.0:1.0:0.0:0.0	.	135	O75951	LYZL6_HUMAN	S	135	ENSP00000293274:G135S;ENSP00000378031:G135S	ENSP00000293274:G135S	G	-	1	0	LYZL6	31285957	0.058000	0.20735	0.004000	0.12327	0.101000	0.19017	2.826000	0.48104	2.518000	0.84900	0.563000	0.77884	GGC	.	.	.	none		0.542	LYZL6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256578.2	NM_020426		T	34261844	C	T	34261844	3	4	56	1	0	0	0	0	1	0	0	0	9141	681	24	2	47	2	LYZL6	17	34261844	Missense_Mutation	SNP	C	TCGA-A4-8312-01A-11D-2396-08		34261844	46933366	15	3817											
MYCBPAP	84073	hgsc.bcm.edu	37	chr17	48600413	48600413	+	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	gccatttggtatgactggcgAcggcagcaccagccggacac	9	6	13	13	3	0	1	0	1	0	0	0	3	0	2	3	4	2	3	3	4	1	2			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr17:48600413A>T	ENST00000323776.5	+	11	1662	c.1500A>T	c.(1498-1500)cgA>cgT	p.R500R	MYCBPAP_ENST00000436259.2_Silent_p.R463R	NM_032133.4	NP_115509.4			MYCBP associated protein											breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(8)|ovary(4)|pancreas(1)|skin(2)|urinary_tract(2)	31	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			ATGACTGGCGACGGCAGCACC	0.507																																					p.R500R		Atlas-SNP	.											.	MYCBPAP	135	.	0			c.A1500T						PASS	.						108	105	106					17																	48600413		2203	4300	6503	SO:0001819	synonymous_variant	84073	exon11			CTGGCGACGGCAG	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.1500A>T	chr17.hg19:g.48600413A>T		165.0	0.0	.		144.0	54.0	.	NM_032133		Silent	SNP	ENST00000323776.5	hg19	CCDS32680.2																																																																																			.	.	.	none		0.507	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133		T	48600413	A	T	48600413	2	4	56	1	0	0	0	0	0	0	0	1	10026	262	10	5		5	MYCBPAP	17	48600413	Silent	SNP	A	TCGA-A4-8312-01A-11D-2396-08	14338569	48600413	32594797	16	3818											
ZNF626	199777	hgsc.bcm.edu	37	chr19	20807580	20807581	+	Missense_Mutation	DNP	GG	GG	AA																															cacattcttcacatttgtagGgtttctctccagtatgaatt																										TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr19:20807580_20807581GG>AA	ENST00000601440.1	-	4	1248_1249	c.1102_1103CC>TT	c.(1102-1104)CCc>TTc	p.P368F	CTC-513N18.7_ENST00000595094.1_lincRNA	NM_001076675.2	NP_001070143.1	Q68DY1	ZN626_HUMAN	zinc finger protein 626	368					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|lung(3)|skin(1)	6						ACATTTGTAGGGTTTCTCTCCA	0.396																																					p.P368L|p.P368S		Atlas-SNP	.											.	ZNF626	121	.	0			c.C1103T|c.C1102T						PASS	.																																			SO:0001583	missense	199777	exon4			TTGTAGGGTTTCT|TGTAGGGTTTCTC	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.1102_1103delinsAA	chr19.hg19:g.20807580_20807581delinsAA	ENSP00000469958:p.Pro368Phe	94.0|96.0	0.0	.		84.0	6.0	.	NM_001076675	Q8N8T4|Q96QM1	Missense_Mutation	SNP	ENST00000601440.1	hg19	CCDS42535.1																																																																																			.	.	.	none		0.396	ZNF626-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447845.2	NM_145297		AA	20807581	GG	AA	20807580	3	1	56	1	0	0	0	0	1	0	0	0	18062	1232	43	2	487	2	ZNF626	19	20807580	Missense_Mutation	DNP	GG	TCGA-A4-8312-01A-11D-2396-08		20807580	38321403	17	3819											
IL29	282618	hgsc.bcm.edu	37	chr19	39787490	39787490	+	Missense_Mutation	SNP	T	T	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	ggagttgcagctctcctgtcTtccccgggaattgggacctg	5	11	13	12	1	2	0	0	0	2	0	4	3	3	3	4	3	2	3	4	3	1	3			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr19:39787490T>G	ENST00000333625.2	+	2	314	c.217T>G	c.(217-219)Ttc>Gtc	p.F73V		NM_172140.1	NP_742152.1	Q8IU54	IFNL1_HUMAN	interferon, lambda 1	73					defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|negative regulation of cell proliferation (GO:0008285)|negative regulation of interleukin-13 production (GO:0032696)|negative regulation of interleukin-5 production (GO:0032714)|negative regulation of memory T cell differentiation (GO:0043381)|negative regulation of T cell differentiation (GO:0045581)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of immune response (GO:0050778)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-28 receptor complex (GO:0032002)	interleukin-28 receptor binding (GO:0032003)|receptor binding (GO:0005102)										CTCTCCTGTCTTCCCCGGGAA	0.572																																					p.F73V		Atlas-SNP	.											.	.	.	.	0			c.T217G						PASS	.						91	86	88					19																	39787490		2203	4300	6503	SO:0001583	missense	282618	exon2			CCTGTCTTCCCCG	AY129150	CCDS12531.1	19q13.13	2014-05-22	2012-11-26	2012-11-26	ENSG00000182393	ENSG00000182393		"Interferons"	18363	protein-coding gene	gene with protein product		607403	"interleukin 29", "interleukin 29 (interferon, lambda 1)"	IL29			Standard	NM_172140		Approved	IL-29	uc002okv.3	Q8IU54		ENST00000333625.2:c.217T>G	chr19.hg19:g.39787490T>G	ENSP00000329991:p.Phe73Val	99.0	0.0	.		120.0	5.0	.	NM_172140	A0AV25|Q17R34	Missense_Mutation	SNP	ENST00000333625.2	hg19	CCDS12531.1	.	.	.	.	.	.	.	.	.	.	T	17.77	3.470360	0.63625	.	.	ENSG00000182393	ENST00000333625	T	0.35421	1.31	3.69	3.69	0.42338	.	0.094954	0.46758	D	0.000269	T	0.59770	0.2218	M	0.84846	2.72	0.25011	N	0.991407	D	0.71674	0.998	D	0.71870	0.975	T	0.54098	-0.8344	10	0.66056	D	0.02	-28.5284	10.3642	0.44012	0.0:0.0:0.0:1.0	.	73	Q8IU54	IL29_HUMAN	V	73	ENSP00000329991:F73V	ENSP00000329991:F73V	F	+	1	0	IL29	44479330	0.956000	0.32656	0.939000	0.37840	0.068000	0.16541	1.113000	0.31184	1.553000	0.49476	0.374000	0.22700	TTC	.	.	.	none		0.572	IFNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463834.1	NM_172140		G	39787490	T	G	39787490	3	3	56	1	0	0	0	0	1	0	0	0	7692	1609	56	5	223	5	IL29	19	39787490	Missense_Mutation	SNP	T	TCGA-A4-8312-01A-11D-2396-08	18979910	39787490	19341493	18	3820											
C20orf160	140706	hgsc.bcm.edu	37	chr20	30617596	30617596	+	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	ccatccaggactattgcacaGgcctgctgaagctctacgga	10	8	10	13	1	1	1	0	1	1	0	2	3	2	3	3	3	4	3	3	3	3	3			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chr20:30617596G>T	ENST00000300415.8	+	9	1370	c.1357G>T	c.(1357-1359)Ggc>Tgc	p.G453C	CCM2L_ENST00000262659.8_Missense_Mutation_p.Q431H|RP1-310O13.7_ENST00000449519.1_RNA			Q9NUG4	CCM2L_HUMAN	cerebral cavernous malformation 2-like	453																	CTATTGCACAGGCCTGCTGAA	0.637																																					p.Q431H		Atlas-SNP	.											C20orf160_ENST00000300415,colon,carcinoma,0,2	.	.	.	0			c.G1293T						PASS	.						63	58	60					20																	30617596		2203	4300	6503	SO:0001583	missense	140706	exon8			TGCACAGGCCTGC	AL031658	CCDS13195.1	20q11.21	2012-10-30	2012-10-30	2012-10-30	ENSG00000101331	ENSG00000101331			16153	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 160"	C20orf160			Standard	NM_080625		Approved	dJ310O13.5	uc002wxf.2	Q9NUG4	OTTHUMG00000032197	ENST00000300415.8:c.1357G>T	chr20.hg19:g.30617596G>T	ENSP00000300415:p.Gly453Cys	105.0	0.0	.		122.0	6.0	.	NM_080625	Q5JYR9|Q8N5F1|Q8N6G8|Q96MD5	Missense_Mutation	SNP	ENST00000300415.8	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.66|15.66	2.898002|2.898002	0.52227|0.52227	.|.	.|.	ENSG00000101331|ENSG00000101331	ENST00000300415;ENST00000452892|ENST00000262659	T;T|T	0.37411|0.65916	1.2;1.2|-0.18	5.65|5.65	4.64|4.64	0.57946|0.57946	.|.	0.293408|.	0.36778|.	N|.	0.002419|.	T|T	0.58935|0.58935	0.2157|0.2157	.|.	.|.	.|.	0.28263|0.28263	N|N	0.924728|0.924728	D|B	0.63046|0.33512	0.992|0.415	P|B	0.56216|0.34301	0.794|0.179	T|T	0.60727|0.60727	-0.7206|-0.7206	9|8	0.62326|0.66056	D|D	0.03|0.02	-45.7996|-45.7996	17.3707|17.3707	0.87376|0.87376	0.0:0.1353:0.8647:0.0|0.0:0.1353:0.8647:0.0	.|.	453|431	Q9NUG4|Q9NUG4-2	CT160_HUMAN|.	C|H	453;206|431	ENSP00000300415:G453C;ENSP00000392448:G206C|ENSP00000262659:Q431H	ENSP00000300415:G453C|ENSP00000262659:Q431H	G|Q	+|+	1|3	0|2	C20orf160|C20orf160	30081257|30081257	1.000000|1.000000	0.71417|0.71417	0.960000|0.960000	0.40013|0.40013	0.898000|0.898000	0.52572|0.52572	3.363000|3.363000	0.52321|0.52321	2.648000|2.648000	0.89879|0.89879	0.563000|0.563000	0.77884|0.77884	GGC|CAG	.	.	.	none		0.637	CCM2L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_080625		T	30617596	G	T	30617596	3	4	56	1	0	0	0	0	1	0	0	0	2095	991	35	4	1323	4	C20orf160	20	30617596	Missense_Mutation	SNP	G	TCGA-A4-8312-01A-11D-2396-08		30617596	32407924	19	3821											
PHKA2	5256	hgsc.bcm.edu	37	chrX	18972370	18972370	+	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	tacagctgtcagtcactattAcctgctccagctcgtaggcc	8	11	8	14	1	2	0	2	0	0	0	4	0	3	0	3	1	5	4	3	1	4	4			TCGA-A4-8312-01A-11D-2396-08	TCGA-A4-8312-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f9961fbe-ca3b-4c52-b923-82430aef5a16	16e755f0-8784-4438-a9e3-0bc481bbaf86	g.chrX:18972370A>G	ENST00000379942.4	-	2	903		c.e2+1			NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)						carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61	Hepatocellular(33;0.183)					AGTCACTATTACCTGCTCCAG	0.537																																					.		Atlas-SNP	.											.	PHKA2	122	.	0			c.237+2T>C						PASS	.						138	107	117					X																	18972370		2203	4300	6503	SO:0001630	splice_region_variant	5256	exon3			ACTATTACCTGCT		CCDS14190.1	Xp22.2-p22.1	2009-07-10			ENSG00000044446	ENSG00000044446	2.7.11.19		8926	protein-coding gene	gene with protein product		300798		PHK, PYK		2387090	Standard	NM_000292		Approved		uc004cyv.4	P46019	OTTHUMG00000021222	ENST00000379942.4:c.237+1T>C	chrX.hg19:g.18972370A>G		73.0	0.0	.		95.0	4.0	.	NM_000292	A8K1T1|Q6LAJ5|Q7Z6W0|Q96CR3|Q9UDA1	Splice_Site	SNP	ENST00000379942.4	hg19	CCDS14190.1	.	.	.	.	.	.	.	.	.	.	A	16.96	3.266542	0.59540	.	.	ENSG00000044446	ENST00000379942	.	.	.	5.54	4.35	0.52113	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.0604	0.47944	0.8588:0.0:0.0:0.1412	.	.	.	.	.	-1	.	.	.	-	.	.	PHKA2	18882291	1.000000	0.71417	0.991000	0.47740	0.625000	0.37756	9.284000	0.95882	0.713000	0.32060	0.486000	0.48141	.	.	.	.	none		0.537	PHKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055960.1	NM_000292	Intron	G	18972370	A	G	18972370	5	3	56	1	0	0	0	0	0	0	1	0	11851	405	14	3	3596	3	PHKA2	23	18972370	Splice_Site	SNP	A	TCGA-A4-8312-01A-11D-2396-08		18972370	136298190	20	3822											
ARID1A	8289	hgsc.bcm.edu	37	chr1	27107195	27107195	+	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	ggtatcaccgttgatgaactCattggtttcacaagtcattt	10	15	8	8	1	4	2	4	2	0	0	4	2	4	2	1	2	1	3	1	2	3	5			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr1:27107195C>A	ENST00000324856.7	+	20	7177	c.6806C>A	c.(6805-6807)tCa>tAa	p.S2269*	ARID1A_ENST00000457599.2_Nonsense_Mutation_p.S2052*|ARID1A_ENST00000540690.1_Nonsense_Mutation_p.S597*|ARID1A_ENST00000374152.2_Nonsense_Mutation_p.S1886*	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	2269					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.S2269*(1)|p.S2269L(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)		TTGATGAACTCATTGGTTTCA	0.532			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.S2269X		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	ARID1A,NS,carcinoma,0,2	ARID1A	842	.	2	Substitution - Missense(1)|Substitution - Nonsense(1)	urinary_tract(1)|endometrium(1)	c.C6806A						PASS	.						126	99	109					1																	27107195		2203	4300	6503	SO:0001587	stop_gained	8289	exon20			TGAACTCATTGGT	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.6806C>A	chr1.hg19:g.27107195C>A	ENSP00000320485:p.Ser2269*	198.0	0.0	.		118.0	47.0	.	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Nonsense_Mutation	SNP	ENST00000324856.7	hg19	CCDS285.1	.	.	.	.	.	.	.	.	.	.	C	42	9.499439	0.99187	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152;ENST00000540690	.	.	.	4.6	4.6	0.57074	.	0.216209	0.40385	N	0.001101	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.9686	13.6859	0.62515	0.0:0.8453:0.1547:0.0	.	.	.	.	X	2269;2052;1886;597	.	ENSP00000320485:S2269X	S	+	2	0	ARID1A	26979782	1.000000	0.71417	0.998000	0.56505	0.977000	0.68977	5.627000	0.67784	2.552000	0.86080	0.591000	0.81541	TCA	.	.	.	none		0.532	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		A	27107195	C	A	27107195	4	1	57	1	0	0	0	0	0	1	0	0	913	838	29	4	6884	4	ARID1A	1	27107195	Nonsense_Mutation	SNP	C	TCGA-A4-8515-01A-11D-2396-08		27107195	222143426	1	3823											
AMY1A	276	hgsc.bcm.edu	37	chr1	104205519	104205520	+	Frame_Shift_Ins	INS	-	-	T																															gtttttaggaacatggttaaINStttccgcaatgtagtggatg																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr1:104205519_104205520insT	ENST00000370083.4	+	10	1452_1453	c.1232_1233insT	c.(1231-1236)aatttcfs	p.NF411fs	AMY1A_ENST00000494409.1_3'UTR	NM_001008221.1|NM_004038.3	NP_001008222.1|NP_004029.2	P04745	AMY1_HUMAN	amylase, alpha 1A (salivary)	411					carbohydrate metabolic process (GO:0005975)|digestion (GO:0007586)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|metal ion binding (GO:0046872)						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)		AACATGGTTAATTTCCGCAATG	0.356																																					p.N411fs	Pancreas(131;743 2392 43382 44986)	Atlas-INDEL	.											.	AMY1C	11	.	0			c.1232_1233insT						PASS	.																																			SO:0001589	frameshift_variant	278	exon10			.		CCDS30782.1	1p21	2012-10-02	2007-05-03		ENSG00000237763	ENSG00000237763	3.2.1.1		474	protein-coding gene	gene with protein product		104700	"amylase, alpha 1A; salivary"	AMY1			Standard	XM_005270755		Approved		uc001duv.3	P04745	OTTHUMG00000011020	ENST00000370083.4:c.1235dupT	chr1.hg19:g.104205522_104205522dupT	ENSP00000359100:p.Asn411fs	287.0	0.0	0		381.0	55.0	0.144357	NM_001008219	A6NJS5|A8K8H6|Q13763|Q5T083	Frame_Shift_Ins	INS	ENST00000370083.4	hg19	CCDS30782.1																																																																																			.	.	.	none		0.356	AMY1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030304.2	NM_001008221		T	104205520	-	T	104205519	7	5	57	1	0	1	1	0	0	0	0	0	591	101	4	0	1266	0	AMY1A	1	104205519	Frame_Shift_Ins	INS	-	TCGA-A4-8515-01A-11D-2396-08	77098324	104205519	145045102	2	3824											
AMY1A	277	hgsc.bcm.edu	37	chr1	104231690	104231691	+	Frame_Shift_Ins	INS	-	-	A																															ggccatccactacattgcggINSaaattaaccatgttcctaaa																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr1:104231690_104231691insA	ENST00000330330.5	-	10	1529_1530	c.1235_1236insT	c.(1234-1236)ttcfs	p.F412fs	AMY1B_ENST00000370080.3_Frame_Shift_Ins_p.F412fs	NM_001008218.1	NP_001008219.1	P04745	AMY1_HUMAN	amylase, alpha 1B (salivary)	412					carbohydrate metabolic process (GO:0005975)|digestion (GO:0007586)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|metal ion binding (GO:0046872)			large_intestine(1)|lung(1)	2		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)		CTACATTGCGGAAATTAACCAT	0.356																																					p.F412fs		Atlas-INDEL	.											.	AMY1C	11	.	0			c.1236_1237insT						PASS	.																																			SO:0001589	frameshift_variant	278	exon10			.		CCDS30783.1	1p21	2012-10-02	2007-05-03		ENSG00000174876	ENSG00000174876	3.2.1.1		475	protein-coding gene	gene with protein product		104701	"amylase, alpha 1B; salivary"	AMY1			Standard	XM_005270758		Approved			P04745	OTTHUMG00000011021	ENST00000330330.5:c.1236dupT	chr1.hg19:g.104231693_104231693dupA	ENSP00000330484:p.Phe412fs	315.0	0.0	0		357.0	54.0	0.151261	NM_001008219	A6NJS5|A8K8H6|Q13763|Q5T083	Frame_Shift_Ins	INS	ENST00000330330.5	hg19	CCDS30783.1																																																																																			.	.	.	none		0.356	AMY1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030309.1	NM_001008218		A	104231691	-	A	104231690	7	5	57	1	0	1	1	0	0	0	0	0	591	1165	41	0	1883	0	AMY1A	1	104231690	Frame_Shift_Ins	INS	-	TCGA-A4-8515-01A-11D-2396-08	26171	104231690	145018931	3	3825											
AMY1A	278	hgsc.bcm.edu	37	chr1	104299657	104299658	+	Frame_Shift_Ins	INS	-	-	T																															gtttttaggaacatggttaaINStttccgcaatgtagtggatg																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr1:104299657_104299658insT	ENST00000370079.3	+	9	1296_1297	c.1232_1233insT	c.(1231-1236)aatttcfs	p.NF411fs		NM_001008219.1	NP_001008220.1	P04745	AMY1_HUMAN	amylase, alpha 1C (salivary)	411					carbohydrate metabolic process (GO:0005975)|digestion (GO:0007586)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|metal ion binding (GO:0046872)			lung(5)|skin(3)	8		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)		AACATGGTTAATTTCCGCAATG	0.356																																					p.N411fs		Atlas-INDEL	.											.	AMY1C	11	.	0			c.1232_1233insT						PASS	.																																			SO:0001589	frameshift_variant	278	exon10			.		CCDS30784.1	1p21	2012-10-02	2007-05-03		ENSG00000187733	ENSG00000187733	3.2.1.1		476	protein-coding gene	gene with protein product		104702	"amylase, alpha 1C; salivary"	AMY1			Standard	XM_005270761		Approved			P04745	OTTHUMG00000011045	ENST00000370079.3:c.1235dupT	chr1.hg19:g.104299660_104299660dupT	ENSP00000359096:p.Asn411fs	332.0	0.0	0		398.0	43.0	0.10804	NM_001008219	A6NJS5|A8K8H6|Q13763|Q5T083	Frame_Shift_Ins	INS	ENST00000370079.3	hg19	CCDS30784.1																																																																																			.	.	.	none		0.356	AMY1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030375.1	NM_001008219		T	104299658	-	T	104299657	7	5	57	1	0	1	1	0	0	0	0	0	591	101	4	0	4418	0	AMY1A	1	104299657	Frame_Shift_Ins	INS	-	TCGA-A4-8515-01A-11D-2396-08	67967	104299657	144950964	4	3826											
C1orf194	127003	hgsc.bcm.edu	37	chr1	109649721	109649721	+	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	ttgtacaaggctgctaagcgGaagtccaggtcatcctttgg	9	11	12	9	1	1	0	1	0	0	0	3	1	3	1	2	4	3	3	2	4	4	4			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr1:109649721G>A	ENST00000369948.3	-	3	297	c.222C>T	c.(220-222)ttC>ttT	p.F74F	C1orf194_ENST00000369949.4_Silent_p.F62F|C1orf194_ENST00000369945.3_Silent_p.F35F			Q5T5A4	CA194_HUMAN	chromosome 1 open reading frame 194	74										large_intestine(2)|lung(2)|ovary(2)	6						CTGCTAAGCGGAAGTCCAGGT	0.483																																					p.F62F		Atlas-SNP	.											.	C1orf194	14	.	0			c.C186T						PASS	.						210	178	188					1																	109649721		1568	3582	5150	SO:0001819	synonymous_variant	127003	exon3			TAAGCGGAAGTCC		CCDS41364.1	1p13.3	2011-03-31			ENSG00000179902	ENSG00000179902			32331	protein-coding gene	gene with protein product							Standard	NM_001122961		Approved		uc009wew.3	Q5T5A4	OTTHUMG00000011735	ENST00000369948.3:c.222C>T	chr1.hg19:g.109649721G>A		183.0	0.0	.		217.0	93.0	.	NM_001122961	Q5T5A3	Silent	SNP	ENST00000369948.3	hg19																																																																																				.	.	.	none		0.483	C1orf194-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000032416.2	NM_001122961		A	109649721	G	A	109649721	2	1	57	1	0	0	0	0	0	0	0	1	2027	1165	41	2		2	C1orf194	1	109649721	Silent	SNP	G	TCGA-A4-8515-01A-11D-2396-08	5350064	109649721	139600900	5	3827											
RFX5	5993	hgsc.bcm.edu	37	chr1	151314667	151314667	+	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	ccccacagacctgtatcatgGgggtgttgcttttgggtctt	5	14	12	10	0	2	1	1	0	1	1	2	1	2	1	3	3	1	3	3	3	1	5			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr1:151314667G>T	ENST00000290524.4	-	11	2024	c.1846C>A	c.(1846-1848)Cca>Aca	p.P616T	RP11-126K1.8_ENST00000422153.1_RNA|RFX5_ENST00000452513.2_Missense_Mutation_p.P576T|RFX5_ENST00000368870.2_Missense_Mutation_p.P616T|RFX5_ENST00000452671.2_Missense_Mutation_p.P616T|RFX5_ENST00000478564.1_5'Flank	NM_000449.3|NM_001025603.1	NP_000440.1|NP_001020774.1	P48382	RFX5_HUMAN	regulatory factor X, 5 (influences HLA class II expression)	616					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)			CTGTATCATGGGGGTGTTGCT	0.453																																					p.P616T		Atlas-SNP	.											.	RFX5	69	.	0			c.C1846A						PASS	.						133	126	128					1																	151314667		2203	4300	6503	SO:0001583	missense	5993	exon11			ATCATGGGGGTGT		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.1846C>A	chr1.hg19:g.151314667G>T	ENSP00000290524:p.Pro616Thr	129.0	0.0	.		94.0	47.0	.	NM_000449	B7Z848|D3DV19|E9PFU4|Q5VWC3	Missense_Mutation	SNP	ENST00000290524.4	hg19	CCDS994.1	.	.	.	.	.	.	.	.	.	.	G	18.73	3.686722	0.68157	.	.	ENSG00000143390	ENST00000290524;ENST00000368870;ENST00000452671;ENST00000452513	T;T;T;T	0.74632	-0.68;-0.68;-0.68;-0.86	5.37	5.37	0.77165	.	0.000000	0.64402	D	0.000001	T	0.76111	0.3942	L	0.36672	1.1	0.35535	D	0.8026	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.941	T	0.79593	-0.1739	10	0.87932	D	0	.	14.4852	0.67611	0.0:0.0:1.0:0.0	.	576;616	B7Z848;P48382	.;RFX5_HUMAN	T	616;616;616;576	ENSP00000290524:P616T;ENSP00000357864:P616T;ENSP00000389130:P616T;ENSP00000398388:P576T	ENSP00000290524:P616T	P	-	1	0	RFX5	149581291	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	4.473000	0.60196	2.806000	0.96561	0.591000	0.81541	CCA	.	.	.	none		0.453	RFX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034892.6	NM_000449		T	151314667	G	T	151314667	3	4	57	1	0	0	0	0	1	0	0	0	13279	1232	43	4	8	4	RFX5	1	151314667	Missense_Mutation	SNP	G	TCGA-A4-8515-01A-11D-2396-08	41664946	151314667	97935954	6	3828											
USH2A	7399	hgsc.bcm.edu	37	chr1	216017693	216017693	+	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	agaataaacgacccaggcacAttcattccagtcttgtagag	14	9	8	10	1	2	2	1	0	1	2	3	3	3	2	2	1	1	2	2	1	4	5			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr1:216017693A>T	ENST00000307340.3	-	46	9587	c.9201T>A	c.(9199-9201)aaT>aaA	p.N3067K	USH2A_ENST00000366943.2_Missense_Mutation_p.N3067K	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3067	Fibronectin type-III 17. {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)		ACCCAGGCACATTCATTCCAG	0.393										HNSCC(13;0.011)																											p.N3067K		Atlas-SNP	.											.	USH2A	1168	.	0			c.T9201A						PASS	.						98	99	99					1																	216017693		2203	4300	6503	SO:0001583	missense	7399	exon46			AGGCACATTCATT	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.9201T>A	chr1.hg19:g.216017693A>T	ENSP00000305941:p.Asn3067Lys	75.0	0.0	.		77.0	24.0	.	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	A	8.287	0.816795	0.16607	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.53423	0.62;0.62	6.04	0.803	0.18691	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.298923	0.23197	N	0.050821	T	0.29749	0.0743	L	0.35723	1.085	0.19775	N	0.999957	B	0.13594	0.008	B	0.08055	0.003	T	0.15578	-1.0432	10	0.17832	T	0.49	.	6.0414	0.19736	0.4009:0.2965:0.3026:0.0	.	3067	O75445	USH2A_HUMAN	K	3067	ENSP00000305941:N3067K;ENSP00000355910:N3067K	ENSP00000305941:N3067K	N	-	3	2	USH2A	214084316	0.008000	0.16893	0.941000	0.38009	0.993000	0.82548	0.037000	0.13840	0.158000	0.19367	0.529000	0.55759	AAT	.	.	.	none		0.393	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216017693	A	T	216017693	3	4	57	1	0	0	0	0	1	0	0	0	17048	214	8	5	6515	5	USH2A	1	216017693	Missense_Mutation	SNP	A	TCGA-A4-8515-01A-11D-2396-08	64703026	216017693	33232928	7	3829											
SIPA1L2	57568	hgsc.bcm.edu	37	chr1	232650317	232650317	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ataatctaatcctgagatgcGgacaaattctcccctagaaa	15	10	6	10	1	2	2	0	1	2	2	4	4	3	3	3	1	1	0	3	1	5	4	rs371322486		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr1:232650317G>A	ENST00000366630.1	-	2	1127	c.769C>T	c.(769-771)Cgc>Tgc	p.R257C	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.R257C			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	257					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)				CCTGAGATGCGGACAAATTCT	0.502																																					p.R257C		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.C769T						PASS	.	G	CYS/ARG	1,3767		0,1,1883	68	67	67		769	5.4	1	1		67	0,8236		0,0,4118	no	missense	SIPA1L2	NM_020808.3	180	0,1,6001	AA,AG,GG		0.0,0.0265,0.0083	benign	257/1723	232650317	1,12003	1884	4118	6002	SO:0001583	missense	57568	exon1			AGATGCGGACAAA	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.769C>T	chr1.hg19:g.232650317G>A	ENSP00000355589:p.Arg257Cys	126.0	0.0	.		115.0	44.0	.	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	hg19	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	G	11.27	1.588865	0.28357	2.65E-4	0.0	ENSG00000116991	ENST00000366630;ENST00000262861	T;T	0.79749	-1.3;-1.3	5.44	5.44	0.79542	.	0.117092	0.56097	D	0.000023	T	0.69187	0.3083	N	0.25647	0.755	0.49483	D	0.999794	B	0.19935	0.04	B	0.12837	0.008	T	0.63963	-0.6518	10	0.37606	T	0.19	-23.1003	12.1037	0.53798	0.0:0.0:0.7162:0.2838	.	257	Q9P2F8	SI1L2_HUMAN	C	257	ENSP00000355589:R257C;ENSP00000262861:R257C	ENSP00000262861:R257C	R	-	1	0	SIPA1L2	230716940	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.388000	0.59633	2.834000	0.97654	0.650000	0.86243	CGC	.	.	.	none		0.502	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		A	232650317	G	A	232650317	3	1	57	1	0	0	0	0	1	0	0	0	14343	1116	39	1	4483	1	SIPA1L2	1	232650317	Missense_Mutation	SNP	G	TCGA-A4-8515-01A-11D-2396-08	16632624	232650317	16600304	8	3830											
C2orf71	388939	hgsc.bcm.edu	37	chr2	29297095	29297096	+	Frame_Shift_Ins	INS	-	-	A																															cactctttgcaacgctgtttINSacaaggtcactgtgtgaagg																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr2:29297095_29297096insA	ENST00000331664.5	-	1	31_32	c.32_33insT	c.(31-33)gtafs	p.V11fs		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	11					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						CAACGCTGTTTACAAGGTCACT	0.45																																					p.V11fs		Atlas-INDEL	.											.	C2orf71	146	.	0			c.33_34insT						PASS	.																																			SO:0001589	frameshift_variant	388939	exon1			.		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.33dupT	chr2.hg19:g.29297096_29297096dupA	ENSP00000332809:p.Val11fs	119.0	0.0	0		93.0	48.0	0.516129	NM_001029883		Frame_Shift_Ins	INS	ENST00000331664.5	hg19	CCDS42669.1																																																																																			.	.	.	none		0.45	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		A	29297096	-	A	29297095	7	5	57	1	0	1	1	0	0	0	0	0	2193	1741	61	0	3841	0	C2orf71	2	29297095	Frame_Shift_Ins	INS	-	TCGA-A4-8515-01A-11D-2396-08		29297095	213902278	9	3831											
PELI1	57162	hgsc.bcm.edu	37	chr2	64323347	64323347	+	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	ctctccatattccaggcttgGagtcttctgtgaacccattg	7	14	8	12	0	3	1	0	1	3	0	5	2	4	2	3	2	1	1	3	2	2	5			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr2:64323347G>A	ENST00000358912.4	-	6	1044	c.602C>T	c.(601-603)tCc>tTc	p.S201F		NM_020651.3	NP_065702.2	Q96FA3	PELI1_HUMAN	pellino E3 ubiquitin protein ligase 1	201					innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell proliferation (GO:0042130)|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 protein ubiquitination (GO:0031398)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|protein K48-linked ubiquitination (GO:0070936)|response to dsRNA (GO:0043331)|response to lipopolysaccharide (GO:0032496)|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)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.S201Y(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	19						TCCAGGCTTGGAGTCTTCTGT	0.453																																					p.S201F		Atlas-SNP	.											PELI1,NS,carcinoma,0,1	PELI1	34	.	1	Substitution - Missense(1)	lung(1)	c.C602T						PASS	.						166	151	156					2																	64323347		2203	4300	6503	SO:0001583	missense	57162	exon6			GGCTTGGAGTCTT		CCDS1876.1	2p13.3	2012-02-23	2012-02-23		ENSG00000197329	ENSG00000197329		"Pellino homologs"	8827	protein-coding gene	gene with protein product		614797	"pellino (Drosophila) homolog 1", "pellino homolog 1 (Drosophila)"			11306823, 16951688	Standard	NM_020651		Approved		uc002sct.4	Q96FA3	OTTHUMG00000129511	ENST00000358912.4:c.602C>T	chr2.hg19:g.64323347G>A	ENSP00000351789:p.Ser201Phe	121.0	0.0	.		124.0	45.0	.	NM_020651	Q96SM0|Q9GZY5|Q9HCX0	Missense_Mutation	SNP	ENST00000358912.4	hg19	CCDS1876.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.917014	0.92249	.	.	ENSG00000197329	ENST00000358912	T	0.53423	0.62	5.65	5.65	0.86999	.	0.096296	0.64402	D	0.000001	T	0.62720	0.2451	M	0.74881	2.28	0.80722	D	1	P	0.48911	0.917	P	0.50490	0.642	T	0.66044	-0.6021	10	0.72032	D	0.01	-12.6236	20.0965	0.97849	0.0:0.0:1.0:0.0	.	201	Q96FA3	PELI1_HUMAN	F	201	ENSP00000351789:S201F	ENSP00000351789:S201F	S	-	2	0	PELI1	64176851	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.813000	0.99286	2.824000	0.97209	0.655000	0.94253	TCC	.	.	.	none		0.453	PELI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251686.1	NM_020651		A	64323347	G	A	64323347	3	1	57	1	0	0	0	0	1	0	0	0	11728	1174	41	2	662	2	PELI1	2	64323347	Missense_Mutation	SNP	G	TCGA-A4-8515-01A-11D-2396-08	35026252	64323347	178876026	10	3832											
RAD18	56852	hgsc.bcm.edu	37	chr3	8955405	8955406	+	Splice_Site	INS	-	-	TG																															tctcgaactatttcagcagcINStgttaaaataagaaaataac																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr3:8955405_8955406insTG	ENST00000264926.2	-	8	1006		c.e8-1			NM_020165.3	NP_064550.3	Q9NS91	RAD18_HUMAN	RAD18 E3 ubiquitin protein ligase						DNA repair (GO:0006281)|negative regulation of DNA recombination (GO:0045910)|protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|spermatogenesis (GO:0007283)	chromatin (GO:0000785)|nucleus (GO:0005634)|replication fork (GO:0005657)|XY body (GO:0001741)	damaged DNA binding (GO:0003684)|ligase activity (GO:0016874)|polyubiquitin binding (GO:0031593)|ubiquitin protein ligase binding (GO:0031625)|Y-form DNA binding (GO:0000403)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)|skin(3)	15				OV - Ovarian serous cystadenocarcinoma(96;0.0552)		ATTTCAGCAGCTGTTAAAATAA	0.317								Rad6 pathway																													.		Atlas-INDEL	.											.	RAD18	52	.	0			c.890-1->CA						PASS	.																																			SO:0001630	splice_region_variant	56852	exon9			.		CCDS2571.1	3p25-p24	2014-08-04	2014-08-04		ENSG00000070950	ENSG00000070950		"RING-type (C3HC4) zinc fingers"	18278	protein-coding gene	gene with protein product		605256	"RAD18 homolog (S. cerevisiae)"			10884424, 10908344	Standard	NM_020165		Approved	RNF73	uc003brd.3	Q9NS91	OTTHUMG00000090545	ENST00000264926.2:c.890-1->CA	chr3.hg19:g.8955406_8955407dupTG		21.0	0.0	0		23.0	13.0	0.565217	NM_020165	Q58F55|Q9NRT6	Splice_Site	INS	ENST00000264926.2	hg19	CCDS2571.1																																																																																			.	.	.	none		0.317	RAD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207071.2	NM_020165	Intron	TG	8955406	-	TG	8955405	8	5	57	1	0	1	1	0	0	0	1	0	12993	811	28	0	622	0	RAD18	3	8955405	Splice_Site	INS	-	TCGA-A4-8515-01A-11D-2396-08		8955405	189067025	11	3833											
IQSEC1	9922	hgsc.bcm.edu	37	chr3	12957106	12957106	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacataccggctttttcccCacaatgagcttctccacctt	8	13	4	16	1	2	1	1	1	1	0	4	1	3	1	5	1	2	2	5	1	2	5			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr3:12957106C>T	ENST00000273221.4	-	7	2406	c.2190G>A	c.(2188-2190)gtG>gtA	p.V730V		NM_014869.5	NP_055684.3	Q6DN90	IQEC1_HUMAN	IQ motif and Sec7 domain 1	730					actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GCTTTTTCCCCACAATGAGCT	0.602																																					p.V730V		Atlas-SNP	.											.	IQSEC1	88	.	0			c.G2190A						PASS	.						187	140	156					3																	12957106		2203	4300	6503	SO:0001819	synonymous_variant	9922	exon7			TTTCCCCACAATG	BC010267	CCDS33703.1, CCDS74902.1	3p25.2	2011-09-23			ENSG00000144711	ENSG00000144711			29112	protein-coding gene	gene with protein product	"brefeldin A-resistant ARF-GEF2"	610166				9872452, 8619474	Standard	NM_001134382		Approved	KIAA0763, GEP100, BRAG2, ARF-GEP100	uc011auw.2	Q6DN90	OTTHUMG00000155398	ENST00000273221.4:c.2190G>A	chr3.hg19:g.12957106C>T		134.0	0.0	.		94.0	22.0	.	NM_014869	O94863|Q96D85	Silent	SNP	ENST00000273221.4	hg19	CCDS33703.1	.	.	.	.	.	.	.	.	.	.	C	8.705	0.910574	0.17833	.	.	ENSG00000144711	ENST00000450726	.	.	.	4.54	3.59	0.41128	.	.	.	.	.	T	0.46132	0.1377	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43393	-0.9394	4	.	.	.	.	3.2074	0.06671	0.1579:0.5539:0.1539:0.1342	.	.	.	.	R	731	.	.	G	-	1	0	IQSEC1	12932106	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	0.932000	0.28884	2.229000	0.72834	0.655000	0.94253	GGG	.	.	.	none		0.602	IQSEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339865.2	NM_014869		T	12957106	C	T	12957106	2	4	57	1	0	0	0	0	0	0	0	1	7824	581	21	2		2	IQSEC1	3	12957106	Silent	SNP	C	TCGA-A4-8515-01A-11D-2396-08	4001701	12957106	185065324	12	3834											
GOLGA4	2803	hgsc.bcm.edu	37	chr3	37369907	37369907	+	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	ggtacatttttattactcagAcaggagcaggaagatcttga	13	12	10	6	0	2	3	1	1	1	2	2	5	2	5	0	3	3	2	0	3	4	6			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr3:37369907A>G	ENST00000361924.2	+	15	6314	c.5940A>G	c.(5938-5940)aaA>aaG	p.K1980K	GOLGA4_ENST00000356847.4_Splice_Site_p.K2002K|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1980	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						TATTACTCAGACAGGAGCAGG	0.413																																					p.K2002K		Atlas-SNP	.											.	GOLGA4	173	.	0			c.A6006G						PASS	.						152	156	155					3																	37369907		2203	4300	6503	SO:0001630	splice_region_variant	2803	exon16			ACTCAGACAGGAG	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.5940-1A>G	chr3.hg19:g.37369907A>G		167.0	0.0	.		185.0	8.0	.	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Silent	SNP	ENST00000361924.2	hg19	CCDS2666.1																																																																																			.	.	.	none		0.413	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078	Silent	G	37369907	A	G	37369907	5	3	57	1	0	0	0	0	0	0	1	0	6562	289	10	3	6068	3	GOLGA4	3	37369907	Splice_Site	SNP	A	TCGA-A4-8515-01A-11D-2396-08	24412801	37369907	160652523	13	3835											
UGDH	7358	hgsc.bcm.edu	37	chr4	39515753	39515753	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcatcatcaatattggtagAaaaaaaaagattttttcctc	16	13	6	6	0	2	2	2	0	0	2	4	2	3	2	1	2	0	2	1	2	7	6			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr4:39515753A>G	ENST00000316423.6	-	3	556	c.214T>C	c.(214-216)Tct>Cct	p.S72P	UGDH_ENST00000515398.1_5'UTR|UGDH_ENST00000507089.1_5'UTR|UGDH_ENST00000506179.1_Missense_Mutation_p.S72P|UGDH_ENST00000501493.2_Missense_Mutation_p.S72P	NM_001184701.1|NM_003359.3	NP_001171630.1|NP_003350.1	O60701	UGDH_HUMAN	UDP-glucose 6-dehydrogenase	72					cellular glucuronidation (GO:0052695)|gastrulation with mouth forming second (GO:0001702)|glycosaminoglycan biosynthetic process (GO:0006024)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|NAD binding (GO:0051287)|UDP-glucose 6-dehydrogenase activity (GO:0003979)	p.S72fs*18(1)		breast(1)|central_nervous_system(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(2)	27						ATATTGGTAGAAAAAAAAAGA	0.299																																					p.S72P		Atlas-SNP	.											.,2	UGDH	52	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.T214C						PASS	.						64	75	72					4																	39515753		2201	4290	6491	SO:0001583	missense	7358	exon3			TGGTAGAAAAAAA	AF061016	CCDS3455.1, CCDS54757.1, CCDS54758.1	4p14	2011-11-16	2010-04-28		ENSG00000109814	ENSG00000109814	1.1.1.22		12525	protein-coding gene	gene with protein product		603370	"UDP-glucose dehydrogenase"			9737970, 10575217	Standard	NM_003359		Approved		uc003guk.2	O60701	OTTHUMG00000099371	ENST00000316423.6:c.214T>C	chr4.hg19:g.39515753A>G	ENSP00000319501:p.Ser72Pro	81.0	0.0	.		98.0	40.0	.	NM_003359	B3KUU2|B4DN25|O60589	Missense_Mutation	SNP	ENST00000316423.6	hg19	CCDS3455.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.642875	0.87859	.	.	ENSG00000109814	ENST00000316423;ENST00000501493;ENST00000506179;ENST00000515021;ENST00000514106;ENST00000509391;ENST00000505698	T;T;T;T;T;T;T	0.78003	-1.14;-1.13;-1.14;-1.14;-1.14;-1.14;-1.14	5.66	5.66	0.87406	UDP-glucose/GDP-mannose dehydrogenase, N-terminal (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.90700	0.7082	M	0.93197	3.39	0.80722	D	1	D;P	0.71674	0.998;0.752	D;B	0.73708	0.981;0.32	D	0.92839	0.6287	10	0.66056	D	0.02	-3.2805	15.077	0.72084	1.0:0.0:0.0:0.0	.	72;72	B3KUU2;O60701	.;UGDH_HUMAN	P	72;72;72;85;72;72;72	ENSP00000319501:S72P;ENSP00000422909:S72P;ENSP00000421757:S72P;ENSP00000421954:S85P;ENSP00000425834:S72P;ENSP00000422603:S72P;ENSP00000422565:S72P	ENSP00000319501:S72P	S	-	1	0	UGDH	39192148	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.263000	0.89864	2.148000	0.66965	0.454000	0.30748	TCT	.	.	.	none		0.299	UGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216818.3	NM_003359		G	39515753	A	G	39515753	3	3	57	1	0	0	0	0	1	0	0	0	16952	246	9	3	1310	3	UGDH	4	39515753	Missense_Mutation	SNP	A	TCGA-A4-8515-01A-11D-2396-08		39515753	151638523	14	3836											
SORBS2	8470	hgsc.bcm.edu	37	chr4	186545386	186545386	+	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	gacttgactttcgggtccggGaagctatcgcagtcgtcgtt	6	12	13	10	5	0	1	0	1	0	0	5	3	1	2	1	2	1	3	1	2	2	4			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr4:186545386G>T	ENST00000284776.7	-	13	1694	c.1185C>A	c.(1183-1185)ttC>ttA	p.F395L	SORBS2_ENST00000498125.1_Intron|SORBS2_ENST00000355634.5_Missense_Mutation_p.F495L|SORBS2_ENST00000431808.1_Missense_Mutation_p.F395L|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000418609.1_Missense_Mutation_p.F299L|SORBS2_ENST00000449407.2_Intron|SORBS2_ENST00000437304.2_Intron|SORBS2_ENST00000448662.2_Intron	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	395					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)		TCGGGTCCGGGAAGCTATCGC	0.577																																					p.F495L	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-SNP	.											.	SORBS2	300	.	0			c.C1485A						PASS	.						62	58	59					4																	186545386		2203	4300	6503	SO:0001583	missense	8470	exon16			GTCCGGGAAGCTA		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.1185C>A	chr4.hg19:g.186545386G>T	ENSP00000284776:p.Phe395Leu	96.0	0.0	.		70.0	30.0	.	NM_001270771	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Missense_Mutation	SNP	ENST00000284776.7	hg19	CCDS3845.1	.	.	.	.	.	.	.	.	.	.	G	1.601	-0.526481	0.04141	.	.	ENSG00000154556	ENST00000284776;ENST00000431808;ENST00000418609;ENST00000355634	T;T;T;T	0.35236	1.43;1.43;1.32;1.42	5.72	-0.19	0.13256	.	0.433914	0.25001	N	0.033913	T	0.23572	0.0570	L	0.50333	1.59	0.24909	N	0.992056	P;P;B	0.35612	0.512;0.512;0.329	B;B;B	0.35073	0.195;0.18;0.084	T	0.29822	-0.9999	10	0.10111	T	0.7	-15.4985	5.7099	0.17929	0.4632:0.2512:0.2856:0.0	.	299;495;395	B7Z3X6;B3KPQ7;O94875	.;.;SRBS2_HUMAN	L	395;395;299;495	ENSP00000284776:F395L;ENSP00000411764:F395L;ENSP00000397482:F299L;ENSP00000347852:F495L	ENSP00000284776:F395L	F	-	3	2	SORBS2	186782380	0.867000	0.29959	0.659000	0.29680	0.299000	0.27559	-0.021000	0.12504	-0.396000	0.07703	0.558000	0.71614	TTC	.	.	.	none		0.577	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603		T	186545386	G	T	186545386	3	4	57	1	0	0	0	0	1	0	0	0	14941	1165	41	4	2153	4	SORBS2	4	186545386	Missense_Mutation	SNP	G	TCGA-A4-8515-01A-11D-2396-08	147029633	186545386	4608890	15	3837											
MTRR	4552	hgsc.bcm.edu	37	chr5	7886796	7886796	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttttacctggtgtcttgaaAtccgagcaattcctaaaaag	12	14	7	8	1	1	1	0	1	1	0	3	2	3	1	3	1	2	1	3	1	6	6			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr5:7886796A>G	ENST00000264668.2	+	8	1237	c.1207A>G	c.(1207-1209)Atc>Gtc	p.I403V	MTRR_ENST00000341013.6_3'UTR|MTRR_ENST00000440940.2_Missense_Mutation_p.I376V	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	403	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)	GTGTCTTGAAATCCGAGCAAT	0.363																																					p.I403V		Atlas-SNP	.											.	MTRR	74	.	0			c.A1207G						PASS	.						129	124	126					5																	7886796		2203	4300	6503	SO:0001583	missense	4552	exon8			CTTGAAATCCGAG	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.1207A>G	chr5.hg19:g.7886796A>G	ENSP00000264668:p.Ile403Val	91.0	0.0	.		79.0	5.0	.	NM_024010	O60471|Q32MA9|Q7Z4M8	Missense_Mutation	SNP	ENST00000264668.2	hg19	CCDS3874.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.176144	0.78564	.	.	ENSG00000124275	ENST00000264668;ENST00000440940	T;T	0.42900	0.96;0.96	5.37	5.37	0.77165	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);	0.047649	0.85682	D	0.000000	T	0.59851	0.2224	M	0.72353	2.195	0.80722	D	1	D	0.64830	0.994	P	0.62649	0.905	T	0.62756	-0.6787	10	0.54805	T	0.06	-26.3682	12.5449	0.56193	0.8615:0.1384:0.0:0.0	.	403	Q9UBK8	MTRR_HUMAN	V	403;376	ENSP00000264668:I403V;ENSP00000402510:I376V	ENSP00000264668:I403V	I	+	1	0	MTRR	7939796	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	5.194000	0.65125	2.038000	0.60285	0.533000	0.62120	ATC	.	.	.	none		0.363	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1			G	7886796	A	G	7886796	3	3	57	1	0	0	0	0	1	0	0	0	9968	101	4	3	1237	3	MTRR	5	7886796	Missense_Mutation	SNP	A	TCGA-A4-8515-01A-11D-2396-08		7886796	173028464	16	3838											
HLA-B	3106	hgsc.bcm.edu	37	chr6	31323288	31323288	+	Frame_Shift_Del	DEL	G	G	-																															aggtcagtgtgatctccgcaGggtagaaacccagggcccag																								rs74428022		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr6:31323288delG	ENST00000412585.2	-	4	729	c.701delC	c.(700-702)cctfs	p.P234fs		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	234	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						GATCTCCGCAGGGTAGAAACC	0.587									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.P234fs		Atlas-INDEL	.											.	HLA-B	54	.	0			c.702delT						PASS	.						83	82	82					6																	31323288		2203	4298	6501	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.701delC	chr6.hg19:g.31323288delG	ENSP00000399168:p.Pro234fs	225.0	0.0	0		162.0	72.0	0.444444	NM_005514	Q29764	Frame_Shift_Del	DEL	ENST00000412585.2	hg19	CCDS34394.1																																																																																			.	.	.	none		0.587	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514		-	31323288	G	-	31323288	7	5	57	1	0	1	0	1	0	0	0	0	7203	1000	35	0	403	0	HLA-B	6	31323288	Frame_Shift_Del	DEL	G	TCGA-A4-8515-01A-11D-2396-08		31323288	139791779	17	3839											
FAM46A	55603	hgsc.bcm.edu	37	chr6	82461655	82461655	+	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	tccagccgctgcacttgctcCcagttcagcacattgcagtg	7	10	9	15	1	1	0	1	0	0	0	3	0	3	0	3	0	5	6	3	0	0	3			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr6:82461655C>A	ENST00000320172.6	-	2	518	c.204G>T	c.(202-204)tgG>tgT	p.W68C	FAM46A_ENST00000369756.3_Missense_Mutation_p.W149C|FAM46A_ENST00000369754.3_Missense_Mutation_p.W87C	NM_017633.2	NP_060103.2	Q96IP4	FA46A_HUMAN	family with sequence similarity 46, member A	68					regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)		poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	12		all_cancers(76;6.74e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000282)|all_epithelial(107;0.0104)		BRCA - Breast invasive adenocarcinoma(397;0.0428)		GCACTTGCTCCCAGTTCAGCA	0.647																																					p.W68C		Atlas-SNP	.											.	FAM46A	37	.	0			c.G204T						PASS	.						57	52	54					6																	82461655		2184	4283	6467	SO:0001583	missense	55603	exon2			TTGCTCCCAGTTC	AF350451	CCDS34489.1	6q14	2008-07-03	2004-08-19	2004-08-26	ENSG00000112773	ENSG00000112773			18345	protein-coding gene	gene with protein product		611357	"chromosome 6 open reading frame 37"	C6orf37		12054608, 17803723	Standard	NM_017633		Approved	FLJ20037	uc003pjg.3	Q96IP4	OTTHUMG00000015097	ENST00000320172.6:c.204G>T	chr6.hg19:g.82461655C>A	ENSP00000318298:p.Trp68Cys	197.0	0.0	.		124.0	61.0	.	NM_017633	A8K7U4|Q5TF86|Q8NFZ9|Q9BW32|Q9NXV5	Missense_Mutation	SNP	ENST00000320172.6	hg19	CCDS34489.1	.	.	.	.	.	.	.	.	.	.	C	17.50	3.404404	0.62288	.	.	ENSG00000112773	ENST00000369754;ENST00000320172;ENST00000369756	T;T;T	0.23147	1.92;1.92;1.92	5.44	5.44	0.79542	Domain of unknown function DUF1693 (1);	0.056200	0.85682	D	0.000000	T	0.47600	0.1454	M	0.76838	2.35	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.36114	-0.9761	9	.	.	.	-2.8137	19.0555	0.93062	0.0:1.0:0.0:0.0	.	68;87	Q96IP4;Q96IP4-2	FA46A_HUMAN;.	C	87;68;149	ENSP00000358769:W87C;ENSP00000318298:W68C;ENSP00000358771:W149C	.	W	-	3	0	FAM46A	82518374	1.000000	0.71417	1.000000	0.80357	0.183000	0.23260	5.897000	0.69831	2.837000	0.97791	0.655000	0.94253	TGG	.	.	.	none		0.647	FAM46A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041331.1			A	82461655	C	A	82461655	3	1	57	1	0	0	0	0	1	0	0	0	5572	624	22	4	1132	4	FAM46A	6	82461655	Missense_Mutation	SNP	C	TCGA-A4-8515-01A-11D-2396-08	51138367	82461655	88653412	18	3840											
MDN1	23195	hgsc.bcm.edu	37	chr6	90411386	90411386	+	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	gttctgagacagtctgaactTctttgtaatatctttaaagg	11	16	8	6	0	4	2	0	2	4	1	4	3	4	2	0	1	1	2	0	1	5	7			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr6:90411386T>A	ENST00000369393.3	-	55	8433	c.8318A>T	c.(8317-8319)gAa>gTa	p.E2773V	MDN1_ENST00000428876.1_Missense_Mutation_p.E2773V			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	2773					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		AGTCTGAACTTCTTTGTAATA	0.418																																					p.E2773V		Atlas-SNP	.											.	MDN1	478	.	0			c.A8318T						PASS	.						40	41	41					6																	90411386		2203	4300	6503	SO:0001583	missense	23195	exon55			TGAACTTCTTTGT	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.8318A>T	chr6.hg19:g.90411386T>A	ENSP00000358400:p.Glu2773Val	52.0	0.0	.		52.0	26.0	.	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	hg19	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	T	17.30	3.355386	0.61293	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03801	3.8;3.8	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.05686	0.0149	L	0.27053	0.805	0.53688	D	0.999978	D	0.71674	0.998	P	0.59115	0.852	T	0.49679	-0.8914	10	0.44086	T	0.13	.	16.1255	0.81392	0.0:0.0:0.0:1.0	.	2773	Q9NU22	MDN1_HUMAN	V	2773	ENSP00000358400:E2773V;ENSP00000413970:E2773V	ENSP00000358400:E2773V	E	-	2	0	MDN1	90468107	1.000000	0.71417	0.919000	0.36401	0.880000	0.50808	7.197000	0.77814	2.205000	0.71048	0.477000	0.44152	GAA	.	.	.	none		0.418	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			A	90411386	T	A	90411386	3	1	57	1	0	0	0	0	1	0	0	0	9422	1783	62	5	8664	5	MDN1	6	90411386	Missense_Mutation	SNP	T	TCGA-A4-8515-01A-11D-2396-08	7949731	90411386	80703681	19	3841											
ECHDC1	55862	hgsc.bcm.edu	37	chr6	127611395	127611395	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccatctctttgtggacgaaTctgatcttactctctggagt	7	15	8	11	1	4	1	0	1	4	0	6	4	4	3	1	2	1	0	1	2	2	2			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr6:127611395T>C	ENST00000531967.1	-	6	1046	c.543A>G	c.(541-543)agA>agG	p.R181R	ECHDC1_ENST00000368289.2_3'UTR|ECHDC1_ENST00000454859.3_Silent_p.R175R|ECHDC1_ENST00000430841.2_Silent_p.R175R|ECHDC1_ENST00000528402.1_3'UTR|ECHDC1_ENST00000474289.2_Silent_p.R175R|ECHDC1_ENST00000488087.1_5'UTR|ECHDC1_ENST00000454591.2_Silent_p.R100R|ECHDC1_ENST00000368291.2_3'UTR|ECHDC1_ENST00000309620.9_Silent_p.R158R	NM_001139510.1	NP_001132982.1	Q9NTX5	ECHD1_HUMAN	enoyl CoA hydratase domain containing 1	181						cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxy-lyase activity (GO:0016831)|methylmalonyl-CoA decarboxylase activity (GO:0004492)			large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	4				GBM - Glioblastoma multiforme(226;0.0423)|all cancers(137;0.156)		TGTGGACGAATCTGATCTTAC	0.408																																					p.R181R		Atlas-SNP	.											.	ECHDC1	41	.	0			c.A543G						PASS	.						65	58	60					6																	127611395		1869	4110	5979	SO:0001819	synonymous_variant	55862	exon6			GACGAATCTGATC	AK025796	CCDS34530.1, CCDS43504.1, CCDS47471.1, CCDS47472.1, CCDS55054.1	6q22.33	2011-12-12	2010-04-30		ENSG00000093144	ENSG00000093144			21489	protein-coding gene	gene with protein product		612136	"enoyl Coenzyme A hydratase domain containing 1"			22016388	Standard	NM_001002030		Approved	dJ351K20.2	uc003qax.3	Q9NTX5	OTTHUMG00000015523	ENST00000531967.1:c.543A>G	chr6.hg19:g.127611395T>C		80.0	0.0	.		93.0	37.0	.	NM_001139510	A6NFJ5|B7Z8S0|E9PEN7|E9PR31|F8W851|Q5TEF6|Q5TEF7|Q5TEG0|Q5TEG4|Q9NZ30|V9HW18	Silent	SNP	ENST00000531967.1	hg19	CCDS47471.1	.	.	.	.	.	.	.	.	.	.	T	10.72	1.430675	0.25726	.	.	ENSG00000093144	ENST00000436638;ENST00000460558	.	.	.	5.65	2.0	0.26442	.	.	.	.	.	T	0.44829	0.1312	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36578	-0.9742	4	.	.	.	.	9.6944	0.40147	0.0:0.2675:0.0:0.7325	.	.	.	.	G	189;54	.	.	D	-	2	0	ECHDC1	127653088	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.054000	0.30455	0.414000	0.25790	0.533000	0.62120	GAT	.	.	.	none		0.408	ECHDC1-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042131.2			C	127611395	T	C	127611395	2	2	57	1	0	0	0	0	0	0	0	1	4895	1432	50	3		3	ECHDC1	6	127611395	Silent	SNP	T	TCGA-A4-8515-01A-11D-2396-08	37200009	127611395	43503672	20	3842											
RSPH3	83861	hgsc.bcm.edu	37	chr6	159401839	159401839	+	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	atcataaaagtagccactatCcctgaggctgccaaaaacag	16	7	7	11	0	1	1	1	1	0	0	2	1	2	1	3	1	3	2	3	1	6	3			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr6:159401839C>T	ENST00000252655.1	-	6	1441	c.1252G>A	c.(1252-1254)Gat>Aat	p.D418N	RSPH3_ENST00000367069.2_Missense_Mutation_p.D276N|RSPH3_ENST00000449822.1_Missense_Mutation_p.D180N|RSPH3_ENST00000297262.3_Missense_Mutation_p.D322N	NM_031924.4	NP_114130.3	Q86UC2	RSPH3_HUMAN	radial spoke 3 homolog (Chlamydomonas)	418										endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|skin(1)|stomach(7)	23		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.36e-16)|BRCA - Breast invasive adenocarcinoma(81;5.92e-06)		TAGCCACTATCCCTGAGGCTG	0.408																																					p.D418N		Atlas-SNP	.											.	RSPH3	48	.	0			c.G1252A						PASS	.						126	104	111					6																	159401839		2203	4300	6503	SO:0001583	missense	83861	exon6			CACTATCCCTGAG	AF353618	CCDS5260.1	6q25.3	2014-05-16	2008-07-04	2007-06-26	ENSG00000130363	ENSG00000130363			21054	protein-coding gene	gene with protein product		615876	"radial spokehead-like 2"	RSHL2		12477932	Standard	NM_031924		Approved	dJ111C20.1, RSP3	uc003qrx.3	Q86UC2	OTTHUMG00000015924	ENST00000252655.1:c.1252G>A	chr6.hg19:g.159401839C>T	ENSP00000252655:p.Asp418Asn	60.0	0.0	.		44.0	18.0	.	NM_031924	Q96LQ5|Q96LX2|Q9BX75	Missense_Mutation	SNP	ENST00000252655.1	hg19	CCDS5260.1	.	.	.	.	.	.	.	.	.	.	C	15.71	2.914542	0.52546	.	.	ENSG00000130363	ENST00000367069;ENST00000449822;ENST00000252655;ENST00000297262	T;T;T;T	0.16743	2.32;2.32;2.32;2.32	5.81	4.94	0.65067	.	0.362264	0.33938	N	0.004405	T	0.05502	0.0145	L	0.38175	1.15	0.38862	D	0.9565	P;B	0.36010	0.532;0.091	B;B	0.30943	0.122;0.065	T	0.28586	-1.0039	10	0.23302	T	0.38	-23.6685	12.7512	0.57310	0.0:0.9196:0.0:0.0804	.	322;418	Q86UC2-2;Q86UC2	.;RSPH3_HUMAN	N	276;180;418;322	ENSP00000356036:D276N;ENSP00000393195:D180N;ENSP00000252655:D418N;ENSP00000297262:D322N	ENSP00000252655:D418N	D	-	1	0	RSPH3	159321827	1.000000	0.71417	0.838000	0.33150	0.987000	0.75469	3.471000	0.53107	1.431000	0.47355	0.591000	0.81541	GAT	.	.	.	none		0.408	RSPH3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031924		T	159401839	C	T	159401839	3	4	57	1	0	0	0	0	1	0	0	0	13718	855	30	2	442	2	RSPH3	6	159401839	Missense_Mutation	SNP	C	TCGA-A4-8515-01A-11D-2396-08	31790444	159401839	11713228	21	3843											
C7orf26	79034	hgsc.bcm.edu	37	chr7	6639468	6639468	+	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	ctttgtttgcagatgacctcAttccacctatggacttgctt	7	16	7	11	0	1	2	1	1	0	1	2	3	2	3	3	1	2	3	3	1	1	6			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr7:6639468A>T	ENST00000344417.5	+	4	856	c.589A>T	c.(589-591)Att>Ttt	p.I197F	C7orf26_ENST00000359073.5_Missense_Mutation_p.I178F|C7orf26_ENST00000472693.1_3'UTR	NM_024067.2	NP_076972.2	Q96N11	CG026_HUMAN	chromosome 7 open reading frame 26	197										endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	11		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)		AGATGACCTCATTCCACCTAT	0.498																																					p.I197F		Atlas-SNP	.											.	C7orf26	33	.	0			c.A589T						PASS	.						172	159	164					7																	6639468		2203	4300	6503	SO:0001583	missense	79034	exon4			GACCTCATTCCAC	BC005121	CCDS5353.1	7p22.1	2011-11-24			ENSG00000146576	ENSG00000146576			21702	protein-coding gene	gene with protein product							Standard	NM_024067		Approved	MGC2718	uc003sqo.1	Q96N11	OTTHUMG00000125517	ENST00000344417.5:c.589A>T	chr7.hg19:g.6639468A>T	ENSP00000340220:p.Ile197Phe	193.0	0.0	.		218.0	126.0	.	NM_024067	Q9BQ43	Missense_Mutation	SNP	ENST00000344417.5	hg19	CCDS5353.1	.	.	.	.	.	.	.	.	.	.	A	8.056	0.767095	0.15983	.	.	ENSG00000146576	ENST00000344417;ENST00000359073	T;T	0.42900	0.96;0.96	5.08	3.89	0.44902	.	0.136974	0.64402	D	0.000003	T	0.28764	0.0713	L	0.43152	1.355	0.40382	D	0.979454	B;B	0.32160	0.358;0.358	B;B	0.30495	0.116;0.116	T	0.06789	-1.0807	10	0.17369	T	0.5	-23.9783	5.9553	0.19269	0.7464:0.1654:0.0882:0.0	.	178;197	Q96N11-2;Q96N11	.;CG026_HUMAN	F	197;178	ENSP00000340220:I197F;ENSP00000351974:I178F	ENSP00000340220:I197F	I	+	1	0	C7orf26	6605993	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	4.865000	0.62998	0.995000	0.38917	0.454000	0.30748	ATT	.	.	.	none		0.498	C7orf26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246844.2	NM_024067		T	6639468	A	T	6639468	3	4	57	1	0	0	0	0	1	0	0	0	2383	217	8	5	603	5	C7orf26	7	6639468	Missense_Mutation	SNP	A	TCGA-A4-8515-01A-11D-2396-08		6639468	152499195	22	3844											
HERPUD2	64224	hgsc.bcm.edu	37	chr7	35707133	35707133	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcaatccttctgaggaagaAcccacagctaaagacaaggt	15	7	8	11	0	2	3	1	1	1	2	3	4	3	4	2	2	2	1	2	2	6	2			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr7:35707133A>G	ENST00000396081.1	-	4	1209	c.405T>C	c.(403-405)ggT>ggC	p.G135G	HERPUD2_ENST00000311350.3_Silent_p.G135G|HERPUD2_ENST00000426180.1_5'UTR	NM_022373.4	NP_071768.3	Q9BSE4	HERP2_HUMAN	HERPUD family member 2	135	Ser-rich.				response to unfolded protein (GO:0006986)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				kidney(3)|large_intestine(5)|lung(6)|ovary(3)|prostate(1)	18						CTGAGGAAGAACCCACAGCTA	0.398																																					p.G135G		Atlas-SNP	.											.	HERPUD2	47	.	0			c.T405C						PASS	.						143	130	134					7																	35707133		2203	4300	6503	SO:0001819	synonymous_variant	64224	exon5			GGAAGAACCCACA	BC020264	CCDS5446.1	7p14.2	2006-03-20	2006-03-20		ENSG00000122557	ENSG00000122557			21915	protein-coding gene	gene with protein product	"homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 2"						Standard	NM_022373		Approved	FLJ22313	uc003tes.4	Q9BSE4	OTTHUMG00000128687	ENST00000396081.1:c.405T>C	chr7.hg19:g.35707133A>G		133.0	0.0	.		179.0	111.0	.	NM_022373	A4D1Y8|Q9H6F9	Silent	SNP	ENST00000396081.1	hg19	CCDS5446.1																																																																																			.	.	.	none		0.398	HERPUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250584.1	NM_022373		G	35707133	A	G	35707133	2	3	57	1	0	0	0	0	0	0	0	1	7071	30	2	3		3	HERPUD2	7	35707133	Silent	SNP	A	TCGA-A4-8515-01A-11D-2396-08	29067665	35707133	123431530	23	3845											
EPHB4	2050	hgsc.bcm.edu	37	chr7	100404084	100404104	+	In_Frame_Del	DEL	CATCACCTCCCACATCACAAT	CATCACCTCCCACATCACAAT	-																															tacggcctctccccaaatgaCatcacctcccacatcacaat																								rs199910843		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	CATCACCTCCCACATCACAAT	CATCACCTCCCACATCACAAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr7:100404084_100404104delCATCACCTCCCACATCACAAT	ENST00000358173.3	-	14	2890_2910	c.2422_2442delATTGTGATGTGGGAGGTGATG	c.(2422-2442)attgtgatgtgggaggtgatgdel	p.IVMWEVM808del	EPHB4_ENST00000360620.3_In_Frame_Del_p.IVMWEVM808del	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	808	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)					CCCCAAATGACATCACCTCCCACATCACAATCCCGTAACTC	0.552																																					p.808_815del	GBM(200;2113 3072 25865 52728)	Atlas-INDEL	.											.	EPHB4	106	.	0			c.2423_2443del						PASS	.																																			SO:0001651	inframe_deletion	2050	exon14			.	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.2422_2442delATTGTGATGTGGGAGGTGATG	chr7.hg19:g.100404084_100404104delCATCACCTCCCACATCACAAT	ENSP00000350896:p.Ile808_Met814del	142.0	0.0	0		161.0	14.0	0.0869565	NM_004444	B5A970|B5A971|B5A972|Q7Z635|Q9BTA5|Q9BXP0	In_Frame_Del	DEL	ENST00000358173.3	hg19	CCDS5706.1																																																																																			.	.	.	none		0.552	EPHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347222.1	NM_004444		-	100404104	CATCACCTCCCACATCACAAT	-	100404084	7	5	57	1	0	1	0	1	0	0	0	0	5179	478	17	0	537	0	EPHB4	7	100404084	In_Frame_Del	DEL	CATCACCTCCCACATCACAAT	TCGA-A4-8515-01A-11D-2396-08	64696951	100404084	58734579	24	3846											
RUSC2	9853	hgsc.bcm.edu	37	chr9	35560975	35560975	+	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	aggctcccctcggactggctGagcctggacaagtccatgtt	7	9	12	13	1	0	1	0	1	0	0	3	3	2	3	4	4	1	3	4	4	1	1			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr9:35560975G>A	ENST00000455600.1	+	11	4799	c.4230G>A	c.(4228-4230)ctG>ctA	p.L1410L	FAM166B_ENST00000492890.1_5'Flank	NM_001135999.1	NP_001129471	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	1410						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)	Rab GTPase binding (GO:0017137)			NS(1)|breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(4)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)			CGGACTGGCTGAGCCTGGACA	0.662																																					p.L1410L		Atlas-SNP	.											.	RUSC2	88	.	0			c.G4230A						PASS	.						33	39	37					9																	35560975		2203	4300	6503	SO:0001819	synonymous_variant	9853	exon11			CTGGCTGAGCCTG	AB002373	CCDS35008.1	9p13.2	2003-12-02			ENSG00000198853	ENSG00000198853			23625	protein-coding gene	gene with protein product		611053				9205841	Standard	NM_001135999		Approved	KIAA0375	uc003zww.3	Q8N2Y8	OTTHUMG00000019861	ENST00000455600.1:c.4230G>A	chr9.hg19:g.35560975G>A		76.0	0.0	.		52.0	24.0	.	NM_014806	A2RU62|A7E2A9|O15080|Q5W134|Q641Q6|Q6P1W7	Silent	SNP	ENST00000455600.1	hg19	CCDS35008.1																																																																																			.	.	.	none		0.662	RUSC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052309.1	XM_048462		A	35560975	G	A	35560975	2	1	57	1	0	0	0	0	0	0	0	1	13764	1277	45	2		2	RUSC2	9	35560975	Silent	SNP	G	TCGA-A4-8515-01A-11D-2396-08		35560975	105652456	25	3847											
TRIM14	9830	hgsc.bcm.edu	37	chr9	100862406	100862406	+	Frame_Shift_Del	DEL	A	A	-																															gtagtaatctgagttcagtgAatttccccttcagccaggtt																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr9:100862406delA	ENST00000341469.2	-	3	353	c.344delT	c.(343-345)ttcfs	p.F115fs	TRIM14_ENST00000342043.3_Frame_Shift_Del_p.F115fs|TRIM14_ENST00000375098.3_Frame_Shift_Del_p.F115fs	NM_014788.2	NP_055603.2	Q14142	TRI14_HUMAN	tripartite motif containing 14	115					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)				GAGTTCAGTGAATTTCCCCTT	0.433																																					p.F115fs	Colon(14;460 597 13826 51781)	Atlas-INDEL	.											.	TRIM14	24	.	0			c.345delC						PASS	.						113	105	108					9																	100862406		2203	4300	6503	SO:0001589	frameshift_variant	9830	exon3			.	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.344delT	chr9.hg19:g.100862406delA	ENSP00000344208:p.Phe115fs	106.0	0.0	0		111.0	52.0	0.468468	NM_014788	A8K9W0|E7EQC4|F8W956|Q548W9|Q5TBQ8|Q6ZWL7|Q9BRD8|Q9C020	Frame_Shift_Del	DEL	ENST00000341469.2	hg19	CCDS6734.1																																																																																			.	.	.	none		0.433	TRIM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053350.1	NM_014788		-	100862406	A	-	100862406	7	5	57	1	0	1	0	1	0	0	0	0	16501	246	9	0	1000	0	TRIM14	9	100862406	Frame_Shift_Del	DEL	A	TCGA-A4-8515-01A-11D-2396-08	65301431	100862406	40351025	26	3848											
GAPVD1	26130	hgsc.bcm.edu	37	chr9	128117063	128117063	+	Missense_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	ccaatcgatactttaccactGtctgtgtgagattactgctt	9	15	7	10	1	1	1	0	1	1	1	2	3	1	1	2	0	4	1	2	0	4	5			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr9:128117063G>A	ENST00000495955.1	+	24	4044	c.3754G>A	c.(3754-3756)Gtc>Atc	p.V1252I	GAPVD1_ENST00000297933.6_Missense_Mutation_p.V1234I|GAPVD1_ENST00000394105.2_Missense_Mutation_p.V1261I|GAPVD1_ENST00000394083.2_Missense_Mutation_p.V1186I|GAPVD1_ENST00000312123.9_Missense_Mutation_p.V1213I|GAPVD1_ENST00000394104.2_Missense_Mutation_p.V1252I|GAPVD1_ENST00000265956.4_Missense_Mutation_p.V1226I|GAPVD1_ENST00000470056.1_Missense_Mutation_p.V1207I			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	1252					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						CTTTACCACTGTCTGTGTGAG	0.423																																					p.V1261I		Atlas-SNP	.											.	GAPVD1	124	.	0			c.G3781A						PASS	.						176	176	176					9																	128117063		2203	4300	6503	SO:0001583	missense	26130	exon23			ACCACTGTCTGTG		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.3754G>A	chr9.hg19:g.128117063G>A	ENSP00000419063:p.Val1252Ile	159.0	0.0	.		177.0	70.0	.	NM_015635	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Missense_Mutation	SNP	ENST00000495955.1	hg19		.	.	.	.	.	.	.	.	.	.	G	27.7	4.856083	0.91355	.	.	ENSG00000165219	ENST00000470056;ENST00000394105;ENST00000394104;ENST00000265956;ENST00000394083;ENST00000495955;ENST00000297933;ENST00000312123	.	.	.	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.63546	0.2520	L	0.47716	1.5	0.80722	D	1	P;P;P;P;P;P	0.39404	0.542;0.604;0.672;0.672;0.672;0.528	B;B;B;B;B;B	0.42282	0.213;0.205;0.382;0.382;0.382;0.382	T	0.62124	-0.6920	9	0.48119	T	0.1	.	19.6603	0.95864	0.0:0.0:1.0:0.0	.	1252;267;1207;1213;1234;1261	Q14C86;B3KTX2;Q14C86-3;Q14C86-4;Q14C86-2;Q14C86-6	GAPD1_HUMAN;.;.;.;.;.	I	1207;1261;1252;1226;1186;1252;1234;1213	.	ENSP00000265956:V1226I	V	+	1	0	GAPVD1	127156884	1.000000	0.71417	0.981000	0.43875	0.965000	0.64279	9.869000	0.99810	2.894000	0.99253	0.591000	0.81541	GTC	.	.	.	none		0.423	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1			A	128117063	G	A	128117063	3	1	57	1	0	0	0	0	1	0	0	0	6246	1377	48	2	3867	2	GAPVD1	9	128117063	Missense_Mutation	SNP	G	TCGA-A4-8515-01A-11D-2396-08	27254657	128117063	13096368	27	3849											
ARRDC1	92714	hgsc.bcm.edu	37	chr9	140508526	140508526	+	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	ccaagaagttctcctacaagCtggtgaagacgggcagcgtg	11	7	13	10	2	1	3	0	1	1	2	2	3	1	3	2	2	3	3	2	2	5	2			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr9:140508526C>A	ENST00000371421.4	+	5	542	c.478C>A	c.(478-480)Ctg>Atg	p.L160M	ARRDC1_ENST00000491911.1_3'UTR|C9orf37_ENST00000496793.1_5'Flank	NM_152285.2	NP_689498.1	Q8N5I2	ARRD1_HUMAN	arrestin domain containing 1	160						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(2)|lung(4)|prostate(1)|urinary_tract(1)	13	all_cancers(76;0.106)			OV - Ovarian serous cystadenocarcinoma(145;0.000273)|Epithelial(140;0.000464)		CTCCTACAAGCTGGTGAAGAC	0.637																																					p.L160M		Atlas-SNP	.											.	ARRDC1	24	.	0			c.C478A						PASS	.						99	95	96					9																	140508526		2203	4300	6503	SO:0001583	missense	92714	exon5			TACAAGCTGGTGA	AJ420420	CCDS7049.1	9q34.3	2013-10-11			ENSG00000197070	ENSG00000197070			28633	protein-coding gene	gene with protein product	"alpha-arrestin 1"					23886940	Standard	XM_005266119		Approved	MGC40555	uc004cns.3	Q8N5I2	OTTHUMG00000020993	ENST00000371421.4:c.478C>A	chr9.hg19:g.140508526C>A	ENSP00000360475:p.Leu160Met	225.0	0.0	.		183.0	61.0	.	NM_152285		Missense_Mutation	SNP	ENST00000371421.4	hg19	CCDS7049.1	.	.	.	.	.	.	.	.	.	.	c	19.88	3.909911	0.72983	.	.	ENSG00000197070	ENST00000371421;ENST00000431925	T;T	0.53206	3.16;0.63	5.47	4.38	0.52667	Immunoglobulin E-set (1);	0.141252	0.49305	D	0.000154	T	0.67411	0.2890	M	0.76838	2.35	0.51767	D	0.999938	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.66756	-0.5843	10	0.36615	T	0.2	-7.9494	14.2819	0.66219	0.0:0.9154:0.0:0.0846	.	49;177;160	Q59FD7;Q5T371;Q8N5I2	.;.;ARRD1_HUMAN	M	160;177	ENSP00000360475:L160M;ENSP00000406247:L177M	ENSP00000360475:L160M	L	+	1	2	ARRDC1	139628347	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.922000	0.40045	2.582000	0.87167	0.555000	0.69702	CTG	.	.	.	none		0.637	ARRDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055358.1	NM_152285		A	140508526	C	A	140508526	3	1	57	1	0	0	0	0	1	0	0	0	982	796	28	4	496	4	ARRDC1	9	140508526	Missense_Mutation	SNP	C	TCGA-A4-8515-01A-11D-2396-08	12391463	140508526	704905	28	3850											
FNBP4	23360	hgsc.bcm.edu	37	chr11	47745663	47745663	+	Missense_Mutation	SNP	G	G	T																															ccactgcagtgctaatttctGtagctttcctctttattcct																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr11:47745663G>T	ENST00000263773.5	-	14	2393	c.2381C>A	c.(2380-2382)aCa>aAa	p.T794K	Y_RNA_ENST00000363220.1_RNA	NM_015308.2	NP_056123.2	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	794			T -> A (in dbSNP:rs35040940).			nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	44						GCTAATTTCTGTAGCTTTCCT	0.428																																					p.T794K		Atlas-SNP	.											.	FNBP4	99	.	0			c.C2381A						PASS	.						132	133	133					11																	47745663		1886	4120	6006	SO:0001583	missense	23360	exon14			ATTTCTGTAGCTT	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.2381C>A	chr11.hg19:g.47745663G>T	ENSP00000263773:p.Thr794Lys	89.0	0.0	.		79.0	30.0	.	NM_015308	Q9H985|Q9NT81|Q9Y2L7	Missense_Mutation	SNP	ENST00000263773.5	hg19	CCDS41644.1	.	.	.	.	.	.	.	.	.	.	G	15.02	2.707845	0.48412	.	.	ENSG00000109920	ENST00000263773	T	0.50277	0.75	5.28	5.28	0.74379	.	0.468912	0.23563	N	0.046835	T	0.42337	0.1198	L	0.53249	1.67	0.28016	N	0.934697	B	0.31125	0.309	B	0.25140	0.058	T	0.47749	-0.9093	10	0.56958	D	0.05	-4.17	12.4896	0.55893	0.0803:0.0:0.9197:0.0	.	794	Q8N3X1	FNBP4_HUMAN	K	794	ENSP00000263773:T794K	ENSP00000263773:T794K	T	-	2	0	FNBP4	47702239	0.027000	0.19231	1.000000	0.80357	0.870000	0.49936	2.261000	0.43276	2.483000	0.83821	0.561000	0.74099	ACA	.	.	.	none		0.428	FNBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390237.3			T	47745663	G	T	47745663	3	4	57	1	0	0	0	0	1	0	0	0	5974	1377	48	4	688	4	FNBP4	11	47745663	Missense_Mutation	SNP	G	TCGA-A4-8515-01A-11D-2396-08		47745663	87260853	29	3851	43	2									
FNBP4	23360	hgsc.bcm.edu	37	chr11	47745665	47745665	+	Silent	SNP	A	A	G																															actgcagtgctaatttctgtAgctttcctctttattccttt																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr11:47745665A>G	ENST00000263773.5	-	14	2391	c.2379T>C	c.(2377-2379)gcT>gcC	p.A793A	Y_RNA_ENST00000363220.1_RNA	NM_015308.2	NP_056123.2	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	793						nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	44						TAATTTCTGTAGCTTTCCTCT	0.428																																					p.A793A		Atlas-SNP	.											.	FNBP4	99	.	0			c.T2379C						PASS	.						131	132	132					11																	47745665		1883	4121	6004	SO:0001819	synonymous_variant	23360	exon14			TTCTGTAGCTTTC	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.2379T>C	chr11.hg19:g.47745665A>G		90.0	0.0	.		75.0	29.0	.	NM_015308	Q9H985|Q9NT81|Q9Y2L7	Silent	SNP	ENST00000263773.5	hg19	CCDS41644.1																																																																																			.	.	.	none		0.428	FNBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390237.3			G	47745665	A	G	47745665	2	3	57	1	0	0	0	0	0	0	0	1	5974	407	15	3		3	FNBP4	11	47745665	Silent	SNP	A	TCGA-A4-8515-01A-11D-2396-08	2	47745665	87260851	30	3852	43	2									
PTPRJ	5795	hgsc.bcm.edu	37	chr11	48142761	48142761	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcatatgtattctccatcActccaggaataggcaatgag	12	12	7	10	0	3	1	2	1	1	0	5	2	4	2	2	2	0	2	2	2	5	5			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr11:48142761A>G	ENST00000418331.2	+	4	911	c.559A>G	c.(559-561)Act>Gct	p.T187A	PTPRJ_ENST00000440289.2_Missense_Mutation_p.T187A	NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	187	Fibronectin type-III 1. {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						ATTCTCCATCACTCCAGGAAT	0.428																																					p.T187A		Atlas-SNP	.											.	PTPRJ	225	.	0			c.A559G						PASS	.						129	120	123					11																	48142761		2201	4298	6499	SO:0001583	missense	5795	exon4			TCCATCACTCCAG	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.559A>G	chr11.hg19:g.48142761A>G	ENSP00000400010:p.Thr187Ala	102.0	0.0	.		69.0	20.0	.	NM_001098503	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	hg19	CCDS7945.1	.	.	.	.	.	.	.	.	.	.	A	12.23	1.875810	0.33162	.	.	ENSG00000149177	ENST00000278456;ENST00000418331;ENST00000440289;ENST00000534219	T;T;T	0.76448	0.49;0.49;-1.02	5.05	0.487	0.16842	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	T	0.70649	0.3248	L	0.44542	1.39	0.09310	N	1	B;P	0.36086	0.131;0.536	B;B	0.43623	0.068;0.425	T	0.57033	-0.7880	9	0.15066	T	0.55	.	8.4715	0.32988	0.4929:0.0:0.0:0.507	.	187;187	Q12913;Q6P4H4	PTPRJ_HUMAN;.	A	187;187;187;108	ENSP00000400010:T187A;ENSP00000409733:T187A;ENSP00000432686:T108A	ENSP00000278456:T187A	T	+	1	0	PTPRJ	48099337	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.045000	0.14013	0.206000	0.20587	0.482000	0.46254	ACT	.	.	.	none		0.428	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1			G	48142761	A	G	48142761	3	3	57	1	0	0	0	0	1	0	0	0	12817	159	6	3	573	3	PTPRJ	11	48142761	Missense_Mutation	SNP	A	TCGA-A4-8515-01A-11D-2396-08	397096	48142761	86863755	31	3853											
NCAM1	4684	hgsc.bcm.edu	37	chr11	113103986	113103986	+	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	cctcaaatacaaagctgagtGgagagcagttggtgaagaag	15	7	13	6	0	1	4	1	2	0	2	1	5	1	4	1	2	3	3	1	2	5	2			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr11:113103986G>T	ENST00000533760.1	+	12	1855	c.1256G>T	c.(1255-1257)tGg>tTg	p.W419L	NCAM1_ENST00000316851.7_Missense_Mutation_p.W537L|NCAM1_ENST00000397957.4_3'UTR|NCAM1_ENST00000401611.2_Missense_Mutation_p.W546L	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1	547	Ig-like C2-type 5.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		AAAGCTGAGTGGAGAGCAGTT	0.532																																					p.W573L		Atlas-SNP	.											.	NCAM1	372	.	0			c.G1718T						PASS	.						78	81	80					11																	113103986		2079	4205	6284	SO:0001583	missense	4684	exon15			CTGAGTGGAGAGC		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.1256G>T	chr11.hg19:g.113103986G>T	ENSP00000473281:p.Trp419Leu	45.0	0.0	.		42.0	16.0	.	NM_001242607	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Missense_Mutation	SNP	ENST00000533760.1	hg19		.	.	.	.	.	.	.	.	.	.	G	28.8	4.953276	0.92660	.	.	ENSG00000149294	ENST00000531044;ENST00000401611;ENST00000316851	T;T	0.56103	0.48;0.48	6.06	6.06	0.98353	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	U	0.000000	T	0.75459	0.3852	.	.	.	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	0.73808	-0.3866	9	0.49607	T	0.09	-34.0768	20.6208	0.99490	0.0:0.0:1.0:0.0	.	547;537;547;537	P13591-5;P13591-1;P13591;P13591-3	.;.;NCAM1_HUMAN;.	L	419;546;537	ENSP00000384055:W546L;ENSP00000318472:W537L	ENSP00000318472:W537L	W	+	2	0	NCAM1	112609196	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	9.476000	0.97823	2.882000	0.98803	0.655000	0.94253	TGG	.	.	.	none		0.532	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		T	113103986	G	T	113103986	3	4	57	1	0	0	0	0	1	0	0	0	10209	1357	47	4	1691	4	NCAM1	11	113103986	Missense_Mutation	SNP	G	TCGA-A4-8515-01A-11D-2396-08	64961225	113103986	21902530	32	3854											
PUS3	83480	hgsc.bcm.edu	37	chr11	125765906	125765922	+	Frame_Shift_Del	DEL	TCTCTTCAATGGTATTA	TCTCTTCAATGGTATTA	-																															ggttagagcttcaaacagttTctcttcaatggtattatttg																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	TCTCTTCAATGGTATTA	TCTCTTCAATGGTATTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr11:125765906_125765922delTCTCTTCAATGGTATTA	ENST00000530811.1	-	1	303_319	c.258_274delTAATACCATTGAAGAGA	c.(256-276)aataataccattgaagagaaafs	p.NNTIEE86fs	PUS3_ENST00000227474.3_Frame_Shift_Del_p.NNTIEE86fs|HYLS1_ENST00000526028.1_Intron|HYLS1_ENST00000356438.3_Intron|HYLS1_ENST00000425380.2_Intron			Q9BZE2	PUS3_HUMAN	pseudouridylate synthase 3	86					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)		TCAAACAGTTTCTCTTCAATGGTATTATTTGTGTTTT	0.447																																					p.87_92del		Atlas-INDEL	.											.	PUS3	33	.	0			c.259_275del						PASS	.																																			SO:0001589	frameshift_variant	83480	exon2			.	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.258_274delTAATACCATTGAAGAGA	chr11.hg19:g.125765906_125765922delTCTCTTCAATGGTATTA	ENSP00000432386:p.Asn86fs	236.0	0.0	0		194.0	60.0	0.309278	NM_031307	B2RAM0|Q96D17|Q96J23|Q96NB4	Frame_Shift_Del	DEL	ENST00000530811.1	hg19	CCDS8466.1																																																																																			.	.	.	none		0.447	PUS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386783.1	NM_031307		-	125765922	TCTCTTCAATGGTATTA	-	125765906	7	5	57	1	0	1	0	1	0	0	0	0	12845	1792	62	0	1183	0	PUS3	11	125765906	Frame_Shift_Del	DEL	TCTCTTCAATGGTATTA	TCGA-A4-8515-01A-11D-2396-08	12661920	125765906	9240610	33	3855											
LAG3	3902	hgsc.bcm.edu	37	chr12	6886460	6886460	+	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	atcctttgggtcacctggatCcctggggaagctgctttgtg	5	13	13	10	0	1	0	1	0	0	0	3	2	3	2	3	4	2	2	3	4	1	2			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr12:6886460C>G	ENST00000203629.2	+	6	1421	c.1088C>G	c.(1087-1089)tCc>tGc	p.S363C		NM_002286.5	NP_002277.4	P18627	LAG3_HUMAN	lymphocyte-activation gene 3	363	Ig-like C2-type 3.				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						TCACCTGGATCCCTGGGGAAG	0.517																																					p.S363C		Atlas-SNP	.											.	LAG3	35	.	0			c.C1088G						PASS	.						112	111	111					12																	6886460		2203	4300	6503	SO:0001583	missense	3902	exon6			CTGGATCCCTGGG		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.1088C>G	chr12.hg19:g.6886460C>G	ENSP00000203629:p.Ser363Cys	136.0	0.0	.		158.0	67.0	.	NM_002286	A8K7T9|Q7Z643	Missense_Mutation	SNP	ENST00000203629.2	hg19	CCDS8561.1	.	.	.	.	.	.	.	.	.	.	C	14.85	2.658513	0.47467	.	.	ENSG00000089692	ENST00000203629	T	0.15603	2.41	4.55	1.61	0.23674	.	0.653989	0.15030	N	0.284515	T	0.18509	0.0444	L	0.27053	0.805	0.19300	N	0.999976	D	0.71674	0.998	P	0.57371	0.819	T	0.10800	-1.0614	10	0.36615	T	0.2	-8.8465	6.2866	0.21037	0.2301:0.4544:0.3155:0.0	.	363	P18627	LAG3_HUMAN	C	363	ENSP00000203629:S363C	ENSP00000203629:S363C	S	+	2	0	LAG3	6756721	0.507000	0.26146	0.578000	0.28575	0.907000	0.53573	0.505000	0.22642	0.136000	0.18733	0.561000	0.74099	TCC	.	.	.	none		0.517	LAG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402846.1			G	6886460	C	G	6886460	3	3	57	1	0	0	0	0	1	0	0	0	8607	855	30	4	1110	4	LAG3	12	6886460	Missense_Mutation	SNP	C	TCGA-A4-8515-01A-11D-2396-08		6886460	126965435	34	3856											
PRB4	5545	hgsc.bcm.edu	37	chr12	11461501	11461501	+	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	ggggtggtctttctggctttCctggaggaggtgggggacgg	3	11	21	6	1	2	0	0	0	2	0	3	3	3	3	1	10	0	1	1	10	0	2			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr12:11461501C>A	ENST00000535904.1	-	3	449	c.416G>T	c.(415-417)gGa>gTa	p.G139V	PRB4_ENST00000445719.2_Intron|PRB4_ENST00000279575.1_Missense_Mutation_p.G139V			P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4	160	9.5 X 21 AA tandem repeats of K-P-[EQ]- [GR]-[PR]-[PR]-P-Q-G-G-N-Q-[PS]-[QH]- [RG]-[PT]-P-P-[PH]-P-G.		Missing (in allele M and allele S).			extracellular region (GO:0005576)				breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|skin(4)|upper_aerodigestive_tract(3)	30						TTCTGGCTTTCCTGGAGGAGG	0.602										HNSCC(22;0.051)																											p.G139V		Atlas-SNP	.											.	PRB4	59	.	0			c.G416T						PASS	.						176	197	190					12																	11461501		2202	4300	6502	SO:0001583	missense	5545	exon3			GGCTTTCCTGGAG		CCDS8641.1, CCDS58208.1	12p13.2	2012-10-02			ENSG00000230657	ENSG00000230657			9340	protein-coding gene	gene with protein product		180990					Standard	NM_002723		Approved		uc001qzt.4	P10163	OTTHUMG00000169116	ENST00000535904.1:c.416G>T	chr12.hg19:g.11461501C>A	ENSP00000442834:p.Gly139Val	531.0	0.0	.		566.0	232.0	.	NM_002723	A1L439|O00600|P02813|P10161|P10162|P81489	Missense_Mutation	SNP	ENST00000535904.1	hg19	CCDS8641.1	.	.	.	.	.	.	.	.	.	.	.	5.316	0.243693	0.10077	.	.	ENSG00000230657	ENST00000279575;ENST00000535904	T;T	0.08546	3.08;3.08	0.849	0.849	0.18972	.	.	.	.	.	T	0.22437	0.0541	M	0.78456	2.415	0.09310	N	0.999999	D	0.89917	1.0	D	0.66979	0.948	T	0.05178	-1.0901	9	0.87932	D	0	.	5.0427	0.14467	0.0:1.0:0.0:0.0	.	139	E9PAL0	.	V	139	ENSP00000279575:G139V;ENSP00000442834:G139V	ENSP00000279575:G139V	G	-	2	0	PRB4	11352768	0.002000	0.14202	0.003000	0.11579	0.004000	0.04260	0.087000	0.14958	0.744000	0.32741	0.502000	0.49764	GGA	.	.	.	none		0.602	PRB4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402308.1	NM_002723		A	11461501	C	A	11461501	3	1	57	1	0	0	0	0	1	0	0	0	12455	855	30	4	331	4	PRB4	12	11461501	Missense_Mutation	SNP	C	TCGA-A4-8515-01A-11D-2396-08	4575041	11461501	122390394	35	3857											
TMTC2	160335	hgsc.bcm.edu	37	chr12	83290130	83290130	+	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	acggagaacattgttgttctGtctttatctttgttaatcat	9	19	7	6	1	4	1	1	0	3	1	4	2	4	1	0	1	1	3	0	1	3	7			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr12:83290130G>A	ENST00000321196.3	+	3	1895	c.1188G>A	c.(1186-1188)ctG>ctA	p.L396L	TMTC2_ENST00000548305.1_Silent_p.L396L|TMTC2_ENST00000549919.1_Silent_p.L390L	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2	396					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						TTGTTGTTCTGTCTTTATCTT	0.393																																					p.L396L		Atlas-SNP	.											.	TMTC2	100	.	0			c.G1188A						PASS	.						191	193	192					12																	83290130		2203	4300	6503	SO:0001819	synonymous_variant	160335	exon3			TGTTCTGTCTTTA	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.1188G>A	chr12.hg19:g.83290130G>A		214.0	0.0	.		208.0	96.0	.	NM_152588	B2RCU7|Q8N2K8	Silent	SNP	ENST00000321196.3	hg19	CCDS9025.1																																																																																			.	.	.	none		0.393	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405663.1	NM_152588		A	83290130	G	A	83290130	2	1	57	1	0	0	0	0	0	0	0	1	16273	1364	48	2		2	TMTC2	12	83290130	Silent	SNP	G	TCGA-A4-8515-01A-11D-2396-08	71828629	83290130	50561765	36	3858											
BTG1	694	hgsc.bcm.edu	37	chr12	92537939	92537939	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccttacagctgattcggcTgtctaccatttgcacgttgg	6	14	9	12	2	1	1	0	1	1	0	3	1	2	1	2	2	4	4	2	2	2	5			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr12:92537939T>C	ENST00000256015.3	-	2	794	c.433A>G	c.(433-435)Agc>Ggc	p.S145G	C12orf79_ENST00000549802.1_5'Flank|C12orf79_ENST00000546975.1_5'Flank|RP11-796E2.4_ENST00000499685.2_RNA|C12orf79_ENST00000551843.1_5'Flank|C12orf79_ENST00000551563.2_5'Flank|RP11-796E2.4_ENST00000501008.2_RNA	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	145					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)				CTGATTCGGCTGTCTACCATT	0.473			T	MYC	BCLL						OREG0022024	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S145G		Atlas-SNP	.		Dom	yes		12	12q22	694	"B-cell translocation gene 1, anti-proliferative"		L	.	BTG1	30	.	0			c.A433G						PASS	.						109	92	98					12																	92537939		2203	4300	6503	SO:0001583	missense	694	exon2			TTCGGCTGTCTAC		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.433A>G	chr12.hg19:g.92537939T>C	ENSP00000256015:p.Ser145Gly	117.0	0.0	.	1291	116.0	56.0	.	NM_001731	P31607	Missense_Mutation	SNP	ENST00000256015.3	hg19	CCDS9043.1	.	.	.	.	.	.	.	.	.	.	T	6.001	0.368520	0.11352	.	.	ENSG00000133639	ENST00000256015;ENST00000552315	T;T	0.34275	1.79;1.37	5.8	5.8	0.92144	.	0.037276	0.85682	D	0.000000	T	0.31734	0.0806	L	0.36672	1.1	0.80722	D	1	B	0.12630	0.006	B	0.15484	0.013	T	0.04203	-1.0969	10	0.33141	T	0.24	-7.3735	16.1508	0.81622	0.0:0.0:0.0:1.0	.	145	P62324	BTG1_HUMAN	G	145;70	ENSP00000256015:S145G;ENSP00000447551:S70G	ENSP00000256015:S145G	S	-	1	0	BTG1	91062070	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.649000	0.83500	2.207000	0.71202	0.528000	0.53228	AGC	.	.	.	none		0.473	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1			C	92537939	T	C	92537939	3	2	57	1	0	0	0	0	1	0	0	0	1555	1580	55	3	86	3	BTG1	12	92537939	Missense_Mutation	SNP	T	TCGA-A4-8515-01A-11D-2396-08	9247809	92537939	41313956	37	3859											
TMCC3	57458	hgsc.bcm.edu	37	chr12	94976205	94976205	+	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	tgtctgcagtgagtttgaccTtgtggaagtccaggatgcca	8	12	13	8	0	1	2	0	2	1	0	2	4	2	4	3	2	2	2	3	2	1	2			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr12:94976205T>A	ENST00000261226.4	-	2	319	c.188A>T	c.(187-189)aAg>aTg	p.K63M	TMCC3_ENST00000551457.1_Missense_Mutation_p.K32M	NM_020698.2	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3	63						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	29						GAGTTTGACCTTGTGGAAGTC	0.483																																					p.K63M		Atlas-SNP	.											.	TMCC3	63	.	0			c.A188T						PASS	.						150	147	148					12																	94976205		2203	4300	6503	SO:0001583	missense	57458	exon2			TTGACCTTGTGGA	AB032971	CCDS31877.1, CCDS73506.1	12q22	2005-01-21	2005-07-13			ENSG00000057704		"Transmembrane and coiled-coil domain containing"	29199	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 3"			10574461	Standard	XM_005269039		Approved	KIAA1145	uc001tdj.2	Q9ULS5	OTTHUMG00000170225	ENST00000261226.4:c.188A>T	chr12.hg19:g.94976205T>A	ENSP00000261226:p.Lys63Met	166.0	0.0	.		146.0	62.0	.	NM_020698	Q8IWB2	Missense_Mutation	SNP	ENST00000261226.4	hg19	CCDS31877.1	.	.	.	.	.	.	.	.	.	.	T	17.71	3.457648	0.63401	.	.	ENSG00000057704	ENST00000261226;ENST00000551457;ENST00000548918	T;T	0.51574	1.34;0.7	5.91	5.91	0.95273	.	0.099394	0.64402	D	0.000002	T	0.67211	0.2869	M	0.61703	1.905	0.46203	D	0.998924	D	0.89917	1.0	D	0.91635	0.999	T	0.69555	-0.5114	10	0.72032	D	0.01	-45.39	16.3889	0.83525	0.0:0.0:0.0:1.0	.	63	Q9ULS5	TMCC3_HUMAN	M	63;32;32	ENSP00000261226:K63M;ENSP00000449888:K32M	ENSP00000261226:K63M	K	-	2	0	TMCC3	93500336	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	0.917000	0.28665	2.276000	0.75962	0.397000	0.26171	AAG	.	.	.	none		0.483	TMCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408113.1	NM_020698		A	94976205	T	A	94976205	3	1	57	1	0	0	0	0	1	0	0	0	16006	1609	56	5	1257	5	TMCC3	12	94976205	Missense_Mutation	SNP	T	TCGA-A4-8515-01A-11D-2396-08	2438266	94976205	38875690	38	3860											
ABCC4	10257	hgsc.bcm.edu	37	chr13	95886864	95886865	+	Splice_Site	DNP	CT	CT	AG																															taatgctgaatgtcacttacCttccgataaatcatatggca																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr13:95886864_95886865CT>AG	ENST00000376887.4	-	4	644_645	c.530_531AG>CT	c.(529-531)aAG>aCT	p.K177T	ABCC4_ENST00000536256.1_Intron|ABCC4_ENST00000431522.1_Splice_Site_p.K177T|ABCC4_ENST00000538287.1_3'UTR|ABCC4_ENST00000412704.1_Splice_Site_p.K177T	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	177	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				blood coagulation (GO:0007596)|oxidation-reduction process (GO:0055114)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of smooth muscle cell proliferation (GO:0048661)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cefazolin(DB01327)|Celecoxib(DB00482)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Leucovorin(DB00650)|Meloxicam(DB00814)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Probenecid(DB01032)|Rosuvastatin(DB01098)|Sildenafil(DB00203)|Sorafenib(DB00398)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tenofovir(DB00300)|Tioguanine(DB00352)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Zidovudine(DB00495)	TGTCACTTACCTTCCGATAAAT	0.391																																					p.K177N|p.K177T		Atlas-SNP	.											.	ABCC4	248	.	0			c.G531T|c.A530C						PASS	.																																			SO:0001630	splice_region_variant	10257	exon4			ACTTACCTTCCGA|CTTACCTTCCGAT	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.530_531delinsAG	chr13.hg19:g.95886864_95886865delinsAG		72.0|74.0	0.0	.		44.0|47.0	19.0|20.0	.	NM_005845	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Missense_Mutation	SNP	ENST00000376887.4	hg19	CCDS9474.1																																																																																			.	.	.	none		0.391	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845	Missense_Mutation	AG	95886865	CT	AG	95886864	5	1	57	1	0	0	0	0	0	0	1	0	55	695	24	4	3607	4	ABCC4	13	95886864	Splice_Site	DNP	CT	TCGA-A4-8515-01A-11D-2396-08		95886864	19283014	39	3861											
DENND4A	10260	hgsc.bcm.edu	37	chr15	66031104	66031104	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acaggcagagggtatttgctAtttgatggccaacattcaat	12	12	10	7	0	1	2	1	1	0	1	1	2	1	2	1	3	2	3	1	3	4	5			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr15:66031104A>G	ENST00000431932.2	-	6	949	c.741T>C	c.(739-741)aaT>aaC	p.N247N	DENND4A_ENST00000443035.3_Silent_p.N247N	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	247	UDENN.				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						GGTATTTGCTATTTGATGGCC	0.363																																					p.N247N		Atlas-SNP	.											.	DENND4A	217	.	0			c.T741C						PASS	.						117	113	114					15																	66031104		1819	4084	5903	SO:0001819	synonymous_variant	10260	exon6			TTTGCTATTTGAT	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.741T>C	chr15.hg19:g.66031104A>G		88.0	0.0	.		122.0	49.0	.	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Silent	SNP	ENST00000431932.2	hg19	CCDS45285.1																																																																																			.	.	.	none		0.363	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		G	66031104	A	G	66031104	2	3	57	1	0	0	0	0	0	0	0	1	4435	446	16	3		3	DENND4A	15	66031104	Silent	SNP	A	TCGA-A4-8515-01A-11D-2396-08		66031104	36500288	40	3862											
SENP8	123228	hgsc.bcm.edu	37	chr15	72432229	72432229	+	Frame_Shift_Del	DEL	G	G	-																															acaagagagttgtatttttaGccatcaatgataactccaac																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr15:72432229delG	ENST00000542035.2	+	2	598	c.265delG	c.(265-267)gccfs	p.A89fs	SENP8_ENST00000544171.1_Frame_Shift_Del_p.A89fs|RP11-2I17.4_ENST00000568984.1_RNA|SENP8_ENST00000340912.4_Frame_Shift_Del_p.A89fs|SENP8_ENST00000544411.1_Frame_Shift_Del_p.A89fs	NM_001166340.1	NP_001159812.1	Q96LD8	SENP8_HUMAN	SUMO/sentrin specific peptidase family member 8	89	Protease.						cysteine-type peptidase activity (GO:0008234)			breast(1)|kidney(2)|lung(1)|ovary(1)|skin(1)	6						TGTATTTTTAGCCATCAATGA	0.448																																					p.L88fs		Atlas-INDEL	.											.	SENP8	18	.	0			c.264delA						PASS	.						100	99	99					15																	72432229		2199	4297	6496	SO:0001589	frameshift_variant	123228	exon2			.	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.265delG	chr15.hg19:g.72432229delG	ENSP00000446057:p.Ala89fs	122.0	0.0	0		114.0	53.0	0.464912	NM_001166340	Q96QA4	Frame_Shift_Del	DEL	ENST00000542035.2	hg19	CCDS10240.1																																																																																			.	.	.	none		0.448	SENP8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420036.1	NM_145204		-	72432229	G	-	72432229	7	5	57	1	0	1	0	1	0	0	0	0	14065	971	34	0	267	0	SENP8	15	72432229	Frame_Shift_Del	DEL	G	TCGA-A4-8515-01A-11D-2396-08	6401125	72432229	30099163	41	3863											
C15orf59	388135	hgsc.bcm.edu	37	chr15	74032301	74032301	+	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	gtctagtggctgtgtagggcAgaaccgtctgcgtgctcttg	5	12	15	9	2	3	1	0	0	3	1	3	1	3	1	1	2	3	4	1	2	3	3			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr15:74032301A>T	ENST00000569673.1	-	3	2043	c.839T>A	c.(838-840)cTg>cAg	p.L280Q	C15orf59_ENST00000558834.1_5'UTR|C15orf59_ENST00000379822.4_Missense_Mutation_p.L280Q			Q2T9L4	CO059_HUMAN	chromosome 15 open reading frame 59	280										breast(1)|endometrium(2)|large_intestine(2)|lung(6)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						TGTGTAGGGCAGAACCGTCTG	0.572																																					p.L280Q		Atlas-SNP	.											.	C15orf59	38	.	0			c.T839A						PASS	.						92	99	97					15																	74032301		2198	4297	6495	SO:0001583	missense	388135	exon2			TAGGGCAGAACCG		CCDS32289.1	15q24.1	2012-09-27			ENSG00000205363	ENSG00000205363			33753	protein-coding gene	gene with protein product							Standard	XM_005254369		Approved	MGC131524, LOC388135	uc002avy.3	Q2T9L4	OTTHUMG00000172556	ENST00000569673.1:c.839T>A	chr15.hg19:g.74032301A>T	ENSP00000457205:p.Leu280Gln	250.0	0.0	.		163.0	72.0	.	NM_001039614		Missense_Mutation	SNP	ENST00000569673.1	hg19	CCDS32289.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.207083	0.79127	.	.	ENSG00000205363	ENST00000379822	T	0.57907	0.37	5.1	5.1	0.69264	.	0.000000	0.64402	D	0.000003	T	0.67933	0.2946	L	0.55481	1.735	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.71434	-0.4594	10	0.87932	D	0	.	14.5288	0.67909	1.0:0.0:0.0:0.0	.	280	Q2T9L4	CO059_HUMAN	Q	280	ENSP00000369150:L280Q	ENSP00000369150:L280Q	L	-	2	0	C15orf59	71819354	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	8.572000	0.90756	1.906000	0.55180	0.459000	0.35465	CTG	.	.	.	none		0.572	C15orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419077.2	NM_001039614		T	74032301	A	T	74032301	3	4	57	1	0	0	0	0	1	0	0	0	1809	188	7	5	46	5	C15orf59	15	74032301	Missense_Mutation	SNP	A	TCGA-A4-8515-01A-11D-2396-08	1600072	74032301	28499091	42	3864											
ACSM1	116285	hgsc.bcm.edu	37	chr16	20682868	20682868	+	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	cctaccttcctgggaaggagGgttgtaaggccaacccatgg	9	8	13	11	0	0	0	0	0	0	0	1	2	1	2	5	5	2	2	5	5	4	4			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr16:20682868G>T	ENST00000307493.4	-	4	804	c.737C>A	c.(736-738)cCc>cAc	p.P246H	ACSM1_ENST00000219151.4_5'UTR|ACSM1_ENST00000520010.1_Missense_Mutation_p.P246H	NM_052956.2	NP_443188.2	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member 1	246					benzoate metabolic process (GO:0018874)|butyrate metabolic process (GO:0019605)|cholesterol homeostasis (GO:0042632)|energy derivation by oxidation of organic compounds (GO:0015980)|fatty acid biosynthetic process (GO:0006633)|fatty acid oxidation (GO:0019395)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	blood microparticle (GO:0072562)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	acyl-CoA ligase activity (GO:0003996)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(23)|skin(3)|upper_aerodigestive_tract(2)	42						TGGGAAGGAGGGTTGTAAGGC	0.527																																					p.P246H		Atlas-SNP	.											.	ACSM1	118	.	0			c.C737A						PASS	.						99	83	89					16																	20682868		2201	4300	6501	SO:0001583	missense	116285	exon4			AAGGAGGGTTGTA	AB059429	CCDS10587.1	16p12.3	2008-02-05	2005-09-08	2005-09-08	ENSG00000166743	ENSG00000166743	6.2.1.2	"Acyl-CoA synthetase family"	18049	protein-coding gene	gene with protein product		614357	"butyryl Coenzyme A synthetase 1"	BUCS1		11470804, 12654705	Standard	NM_052956		Approved	MACS1	uc002dhm.1	Q08AH1	OTTHUMG00000131550	ENST00000307493.4:c.737C>A	chr16.hg19:g.20682868G>T	ENSP00000301956:p.Pro246His	61.0	0.0	.		111.0	36.0	.	NM_052956	Q08AH2|Q96A20	Missense_Mutation	SNP	ENST00000307493.4	hg19	CCDS10587.1	.	.	.	.	.	.	.	.	.	.	G	2.027	-0.423437	0.04734	.	.	ENSG00000166743	ENST00000307493;ENST00000520010	T;T	0.47177	0.85;0.85	4.95	1.81	0.25067	AMP-dependent synthetase/ligase (1);	1.028510	0.07746	N	0.947678	T	0.28300	0.0699	N	0.12471	0.22	0.09310	N	0.999995	B	0.06786	0.001	B	0.08055	0.003	T	0.22556	-1.0213	10	0.45353	T	0.12	.	5.2282	0.15406	0.0815:0.1431:0.6274:0.148	.	246	Q08AH1	ACSM1_HUMAN	H	246	ENSP00000301956:P246H;ENSP00000428047:P246H	ENSP00000301956:P246H	P	-	2	0	ACSM1	20590369	0.351000	0.24887	0.000000	0.03702	0.001000	0.01503	3.098000	0.50259	0.238000	0.21222	0.603000	0.83216	CCC	.	.	.	none		0.527	ACSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254412.1	NM_052956		T	20682868	G	T	20682868	3	4	57	1	0	0	0	0	1	0	0	0	182	1232	43	4	1036	4	ACSM1	16	20682868	Missense_Mutation	SNP	G	TCGA-A4-8515-01A-11D-2396-08		20682868	69671885	43	3865											
AP1G1	164	hgsc.bcm.edu	37	chr16	71768532	71768533	+	Frame_Shift_Ins	INS	-	-	A																															ttctgagggttcagaactttINSaatgacttgtgtgatggtcc																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr16:71768532_71768533insA	ENST00000299980.4	-	22	2787_2788	c.2346_2347insT	c.(2344-2349)attaaafs	p.K783fs	AP1G1_ENST00000564155.1_Frame_Shift_Ins_p.K208fs|AP1G1_ENST00000393512.3_Frame_Shift_Ins_p.K786fs|AP1G1_ENST00000569748.1_Frame_Shift_Ins_p.K783fs|AP1G1_ENST00000423132.2_Frame_Shift_Ins_p.K786fs|AP1G1_ENST00000433195.2_Frame_Shift_Ins_p.K806fs	NM_001128.5	NP_001119.3	O43747	AP1G1_HUMAN	adaptor-related protein complex 1, gamma 1 subunit	783	GAE. {ECO:0000255|PROSITE- ProRule:PRU00093}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|Golgi to lysosome transport (GO:0090160)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network membrane (GO:0032588)	GTP-dependent protein binding (GO:0030742)|kinesin binding (GO:0019894)|protein transporter activity (GO:0008565)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)			breast(1)|endometrium(8)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|urinary_tract(1)	28		Ovarian(137;0.125)				TTCAGAACTTTAATGACTTGTG	0.45																																					p.K786_V787delinsX		Atlas-INDEL	.											.	AP1G1	83	.	0			c.2356_2357insT						PASS	.																																			SO:0001589	frameshift_variant	164	exon23			.	Y12226	CCDS32480.1, CCDS45522.1	16q23	2009-08-03				ENSG00000166747			555	protein-coding gene	gene with protein product	"gamma1-adaptin"	603533		CLAPG1, ADTG		9653655, 9733768	Standard	NM_001128		Approved		uc010cgg.3	O43747		ENST00000299980.4:c.2347dupT	chr16.hg19:g.71768534_71768534dupA	ENSP00000299980:p.Lys783fs	376.0	0.0	0		657.0	369.0	0.561644	NM_001030007	O75709|O75842|Q9UG09|Q9Y3U4	Frame_Shift_Ins	INS	ENST00000299980.4	hg19	CCDS32480.1																																																																																			.	.	.	none		0.45	AP1G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434147.1			A	71768533	-	A	71768532	7	5	57	1	0	1	1	0	0	0	0	0	732	1763	61	0	129	0	AP1G1	16	71768532	Frame_Shift_Ins	INS	-	TCGA-A4-8515-01A-11D-2396-08	51085664	71768532	18586221	44	3866											
WDR81	124997	hgsc.bcm.edu	37	chr17	1633711	1633711	+	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	gtccgctggctgtctgccaaGctcggccccacagtggcctc	4	8	12	17	2	1	0	0	0	1	0	4	0	2	0	5	3	2	3	5	3	1	0			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr17:1633711G>A	ENST00000409644.1	+	2	3705	c.3705G>A	c.(3703-3705)aaG>aaA	p.K1235K	WDR81_ENST00000437219.2_Silent_p.K32K|WDR81_ENST00000419248.1_Silent_p.K8K|WDR81_ENST00000309182.5_Silent_p.K184K|WDR81_ENST00000446363.1_Intron|WDR81_ENST00000545662.1_5'Flank|RP11-961A15.1_ENST00000576540.1_RNA	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1235					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)		TGTCTGCCAAGCTCGGCCCCA	0.642																																					p.K1235K		Atlas-SNP	.											.	WDR81	180	.	0			c.G3705A						PASS	.						33	31	32					17																	1633711		2203	4299	6502	SO:0001819	synonymous_variant	124997	exon2			TGCCAAGCTCGGC	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.3705G>A	chr17.hg19:g.1633711G>A		67.0	0.0	.		69.0	15.0	.	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Silent	SNP	ENST00000409644.1	hg19	CCDS54062.1																																																																																			.	.	.	none		0.642	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348		A	1633711	G	A	1633711	2	1	57	1	0	0	0	0	0	0	0	1	17342	962	34	2		2	WDR81	17	1633711	Silent	SNP	G	TCGA-A4-8515-01A-11D-2396-08		1633711	79561499	45	3867											
ZZEF1	23140	hgsc.bcm.edu	37	chr17	3924472	3924472	+	Frame_Shift_Del	DEL	T	T	-																															ggccctcaagggggtccagcTttttctgctctgggtcgcca																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr17:3924472delT	ENST00000381638.2	-	45	7479	c.7355delA	c.(7354-7356)aagfs	p.K2452fs		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	2452							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						GGGGTCCAGCTTTTTCTGCTC	0.582																																					p.K2452fs		Atlas-INDEL	.											.	ZZEF1	195	.	0			c.7356delG						PASS	.						113	109	110					17																	3924472		2203	4300	6503	SO:0001589	frameshift_variant	23140	exon45			.	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.7355delA	chr17.hg19:g.3924472delT	ENSP00000371051:p.Lys2452fs	235.0	0.0	0		375.0	106.0	0.282667	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Frame_Shift_Del	DEL	ENST00000381638.2	hg19	CCDS11043.1																																																																																			.	.	.	none		0.582	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		-	3924472	T	-	3924472	7	5	57	1	0	1	0	1	0	0	0	0	18267	1609	56	0	1574	0	ZZEF1	17	3924472	Frame_Shift_Del	DEL	T	TCGA-A4-8515-01A-11D-2396-08	2290761	3924472	77270738	46	3868											
MYBBP1A	10514	hgsc.bcm.edu	37	chr17	4445915	4445915	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggccccaacactcaccgggTgccgggagaagaggctgagg	10	3	16	12	2	1	3	1	1	0	2	1	4	1	3	4	5	2	1	4	5	2	0			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr17:4445915T>C	ENST00000254718.4	-	21	3320	c.3014A>G	c.(3013-3015)cAc>cGc	p.H1005R	MYBBP1A_ENST00000381556.2_Missense_Mutation_p.H1005R			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	1005					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						ACTCACCGGGTGCCGGGAGAA	0.627																																					p.H1005R		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.A3014G						PASS	.						99	98	98					17																	4445915		2203	4300	6503	SO:0001583	missense	10514	exon21			ACCGGGTGCCGGG	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.3014A>G	chr17.hg19:g.4445915T>C	ENSP00000254718:p.His1005Arg	137.0	0.0	.		189.0	115.0	.	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Missense_Mutation	SNP	ENST00000254718.4	hg19	CCDS11046.1	.	.	.	.	.	.	.	.	.	.	T	18.01	3.527626	0.64860	.	.	ENSG00000132382	ENST00000381556;ENST00000254718	T;T	0.19532	2.14;2.14	5.53	4.44	0.53790	Armadillo-type fold (1);	0.481948	0.24846	N	0.035136	T	0.23965	0.0580	L	0.54323	1.7	0.25888	N	0.9835	P;P	0.47106	0.824;0.89	B;P	0.46796	0.327;0.527	T	0.07309	-1.0779	10	0.26408	T	0.33	-19.5303	8.7411	0.34558	0.1687:0.0:0.0:0.8313	.	1005;1005	Q9BQG0;Q9BQG0-2	MBB1A_HUMAN;.	R	1005	ENSP00000370968:H1005R;ENSP00000254718:H1005R	ENSP00000254718:H1005R	H	-	2	0	MYBBP1A	4392664	1.000000	0.71417	0.999000	0.59377	0.901000	0.52897	3.604000	0.54081	0.910000	0.36722	0.533000	0.62120	CAC	.	.	.	none		0.627	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520		C	4445915	T	C	4445915	3	2	57	1	0	0	0	0	1	0	0	0	10015	1696	59	3	1036	3	MYBBP1A	17	4445915	Missense_Mutation	SNP	T	TCGA-A4-8515-01A-11D-2396-08	521443	4445915	76749295	47	3869											
ALOX15B	247	hgsc.bcm.edu	37	chr17	7948982	7948982	+	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	ggctaccctgcgtcagctgcCccactgccaccctctcttca	5	9	7	20	1	3	0	2	0	1	0	4	0	3	0	5	1	5	2	5	1	1	2			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr17:7948982C>T	ENST00000380183.4	+	8	1317	c.1178C>T	c.(1177-1179)cCc>cTc	p.P393L	ALOX15B_ENST00000573359.1_Missense_Mutation_p.P393L|ALOX15B_ENST00000380173.2_Missense_Mutation_p.P393L|ALOX15B_ENST00000572022.1_Missense_Mutation_p.P393L	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	393	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						CGTCAGCTGCCCCACTGCCAC	0.612																																					p.P393L		Atlas-SNP	.											.	ALOX15B	66	.	0			c.C1178T						PASS	.						66	51	56					17																	7948982		2203	4300	6503	SO:0001583	missense	247	exon8			AGCTGCCCCACTG	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.1178C>T	chr17.hg19:g.7948982C>T	ENSP00000369530:p.Pro393Leu	45.0	0.0	.		78.0	38.0	.	NM_001141	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Missense_Mutation	SNP	ENST00000380183.4	hg19	CCDS11128.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.929812	0.92389	.	.	ENSG00000179593	ENST00000380173;ENST00000339694;ENST00000380183	D;D	0.91521	-2.86;-2.86	4.53	4.53	0.55603	Lipoxygenase, C-terminal (4);	0.000000	0.85682	D	0.000000	D	0.96062	0.8717	M	0.89658	3.05	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	0.97047	0.9761	10	0.87932	D	0	-23.6176	16.3899	0.83531	0.0:1.0:0.0:0.0	.	393;393;393;393	B4DNW8;O15296-2;O15296-4;O15296	.;.;.;LX15B_HUMAN	L	393	ENSP00000369520:P393L;ENSP00000369530:P393L	ENSP00000344337:P393L	P	+	2	0	ALOX15B	7889707	1.000000	0.71417	0.989000	0.46669	0.971000	0.66376	7.516000	0.81772	2.225000	0.72522	0.563000	0.77884	CCC	.	.	.	none		0.612	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2			T	7948982	C	T	7948982	3	4	57	1	0	0	0	0	1	0	0	0	539	623	22	2	1208	2	ALOX15B	17	7948982	Missense_Mutation	SNP	C	TCGA-A4-8515-01A-11D-2396-08	3503067	7948982	73246228	48	3870											
MYH2	4620	hgsc.bcm.edu	37	chr17	10433386	10433386	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctgcatcagccaagccttcGgcttccttaagttggaaaca	10	11	8	12	1	2	0	1	0	1	0	4	1	3	1	3	2	4	3	3	2	3	4			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr17:10433386G>A	ENST00000245503.5	-	23	3087	c.2703C>T	c.(2701-2703)gcC>gcT	p.A901A	MYH2_ENST00000397183.2_Silent_p.A901A|RP11-799N11.1_ENST00000581304.1_RNA|MYH2_ENST00000532183.2_Intron|RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	901					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						CCAAGCCTTCGGCTTCCTTAA	0.398																																					p.A901A		Atlas-SNP	.											.	MYH2	390	.	0			c.C2703T						PASS	.						124	121	122					17																	10433386		2203	4300	6503	SO:0001819	synonymous_variant	4620	exon23			GCCTTCGGCTTCC		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.2703C>T	chr17.hg19:g.10433386G>A		152.0	0.0	.		254.0	82.0	.	NM_017534	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Silent	SNP	ENST00000245503.5	hg19	CCDS11156.1																																																																																			.	.	.	none		0.398	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534		A	10433386	G	A	10433386	2	1	57	1	0	0	0	0	0	0	0	1	10042	1103	39	1		1	MYH2	17	10433386	Silent	SNP	G	TCGA-A4-8515-01A-11D-2396-08	2484404	10433386	70761824	49	3871											
TRIM37	4591	hgsc.bcm.edu	37	chr17	57078973	57078974	+	Frame_Shift_Del	DEL	TG	TG	-																															ctgcaccttcatccgggggcTgtgtcatgaccatgaaggag																										TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr17:57078973_57078974delTG	ENST00000262294.7	-	23	3056_3057	c.2797_2798delCA	c.(2797-2799)cagfs	p.Q933fs	TRIM37_ENST00000393065.2_Frame_Shift_Del_p.Q899fs|TRIM37_ENST00000376149.3_Intron|TRIM37_ENST00000393066.3_Frame_Shift_Del_p.Q933fs	NM_015294.3	NP_056109.1	O94972	TRI37_HUMAN	tripartite motif containing 37	933					aggresome assembly (GO:0070842)|negative regulation of centriole replication (GO:0046600)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autoubiquitination (GO:0051865)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisome (GO:0005777)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(13)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					ATCCGGGGGCTGTGTCATGACC	0.485									Mulibrey Nanism																												p.933_933del		Atlas-INDEL	.											.	TRIM37	105	.	0			c.2798_2799del						PASS	.																																			SO:0001589	frameshift_variant	4591	exon23	Familial Cancer Database	Perheentupa syndrome	.	AB020705	CCDS32694.1, CCDS45746.1	17q	2014-02-17	2011-01-25	2001-11-30		ENSG00000108395		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	7523	protein-coding gene	gene with protein product	"RING-B-box-coiled-coil protein"	605073	"tripartite motif-containing 37"	MUL		9106536, 10888877	Standard	NM_015294		Approved	KIAA0898, POB1, TEF3	uc002iwy.4	O94972		ENST00000262294.7:c.2797_2798delCA	chr17.hg19:g.57078975_57078976delTG	ENSP00000262294:p.Gln933fs	121.0	0.0	0		188.0	20.0	0.106383	NM_015294	Q7Z3E6|Q8IYF7|Q8WYF7	Frame_Shift_Del	DEL	ENST00000262294.7	hg19	CCDS32694.1																																																																																			.	.	.	none		0.485	TRIM37-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445930.1	NM_015294		-	57078974	TG	-	57078973	7	5	57	1	0	1	0	1	0	0	0	0	16523	1580	55	0	112	0	TRIM37	17	57078973	Frame_Shift_Del	DEL	TG	TCGA-A4-8515-01A-11D-2396-08	46645587	57078973	24116237	50	3872											
EPB41L3	23136	hgsc.bcm.edu	37	chr18	5406855	5406855	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgggggaggtggaaagcctcTtctcccattcattcgttacg	7	11	12	11	3	3	0	1	0	2	0	5	2	3	2	2	4	2	1	2	4	2	4			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr18:5406855T>C	ENST00000341928.2	-	16	2610	c.2270A>G	c.(2269-2271)aAg>aGg	p.K757R	EPB41L3_ENST00000427684.2_Missense_Mutation_p.K29R|EPB41L3_ENST00000400111.3_Missense_Mutation_p.K576R|EPB41L3_ENST00000544123.1_Missense_Mutation_p.K588R|EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000542146.1_Missense_Mutation_p.K29R|EPB41L3_ENST00000540638.2_Missense_Mutation_p.K576R|EPB41L3_ENST00000342933.3_Missense_Mutation_p.K757R	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	757	Spectrin--actin-binding. {ECO:0000255}.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			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						GGAAAGCCTCTTCTCCCATTC	0.512																																					p.K757R		Atlas-SNP	.											.	EPB41L3	222	.	0			c.A2270G						PASS	.						179	143	155					18																	5406855		2203	4300	6503	SO:0001583	missense	23136	exon16			AGCCTCTTCTCCC	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.2270A>G	chr18.hg19:g.5406855T>C	ENSP00000343158:p.Lys757Arg	162.0	0.0	.		116.0	49.0	.	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	hg19	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.245271	0.80024	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000427684;ENST00000542146;ENST00000342933;ENST00000400111	D;D;D;D;D;D	0.89875	-2.12;-2.58;-1.59;-1.5;-2.12;-2.37	5.78	5.78	0.91487	SAB (1);	0.043558	0.85682	D	0.000000	D	0.93360	0.7883	M	0.62266	1.93	0.58432	D	0.999999	D;D;D;D;D;D;D;D	0.89917	0.99;0.999;0.999;0.977;0.999;0.999;1.0;1.0	D;D;D;D;D;D;D;D	0.91635	0.979;0.996;0.996;0.98;0.995;0.97;0.999;0.998	D	0.93204	0.6594	10	0.48119	T	0.1	.	16.1138	0.81283	0.0:0.0:0.0:1.0	.	588;29;29;149;467;576;757;29	F5GX05;E7EUF8;F5H7W5;B7Z8M8;A8K968;Q9Y2J2-2;Q9Y2J2;B3KT50	.;.;.;.;.;.;E41L3_HUMAN;.	R	757;467;588;467;29;29;757;576	ENSP00000343158:K757R;ENSP00000441174:K588R;ENSP00000392195:K29R;ENSP00000442233:K29R;ENSP00000341138:K757R;ENSP00000382981:K576R	ENSP00000343158:K757R	K	-	2	0	EPB41L3	5396855	1.000000	0.71417	1.000000	0.80357	0.638000	0.38207	7.698000	0.84413	2.220000	0.72140	0.533000	0.62120	AAG	.	.	.	none		0.512	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		C	5406855	T	C	5406855	3	2	57	1	0	0	0	0	1	0	0	0	5156	1609	56	3	1021	3	EPB41L3	18	5406855	Missense_Mutation	SNP	T	TCGA-A4-8515-01A-11D-2396-08		5406855	72670393	51	3873											
DSC2	1824	hgsc.bcm.edu	37	chr18	28660278	28660278	+	Missense_Mutation	SNP	A	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	gagcttcattaactacaccaAtttgcaagatcatctgttgc	12	13	6	10	0	3	1	2	0	1	1	3	2	3	1	1	0	5	3	1	0	4	5			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr18:28660278A>C	ENST00000280904.6	-	10	1747	c.1304T>G	c.(1303-1305)aTt>aGt	p.I435S	DSC2_ENST00000251081.6_Missense_Mutation_p.I435S	NM_024422.3	NP_077740.1	Q02487	DSC2_HUMAN	desmocollin 2	435	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)			AACTACACCAATTTGCAAGAT	0.378																																					p.I435S		Atlas-SNP	.											.	DSC2	168	.	0			c.T1304G						PASS	.						159	138	145					18																	28660278		2203	4300	6503	SO:0001583	missense	1824	exon10			ACACCAATTTGCA	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.1304T>G	chr18.hg19:g.28660278A>C	ENSP00000280904:p.Ile435Ser	68.0	0.0	.		70.0	30.0	.	NM_024422		Missense_Mutation	SNP	ENST00000280904.6	hg19	CCDS11892.1	.	.	.	.	.	.	.	.	.	.	A	16.03	3.006051	0.54361	.	.	ENSG00000134755	ENST00000251081;ENST00000280904;ENST00000438199;ENST00000399347	T;T	0.48836	0.8;0.8	5.92	5.92	0.95590	Cadherin (5);Cadherin-like (1);	0.000000	0.32884	N	0.005536	T	0.78997	0.4372	H	0.97491	4.015	0.54753	D	0.999989	D;D	0.69078	0.997;0.996	D;D	0.65443	0.934;0.935	D	0.86616	0.1876	10	0.87932	D	0	.	15.3456	0.74334	1.0:0.0:0.0:0.0	.	435;435	Q02487;Q02487-2	DSC2_HUMAN;.	S	435;435;201;448	ENSP00000251081:I435S;ENSP00000280904:I435S	ENSP00000251081:I435S	I	-	2	0	DSC2	26914276	1.000000	0.71417	0.226000	0.23910	0.115000	0.19883	7.733000	0.84916	2.266000	0.75297	0.533000	0.62120	ATT	.	.	.	none		0.378	DSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254943.1	NM_004949		C	28660278	A	C	28660278	3	2	57	1	0	0	0	0	1	0	0	0	4768	101	4	5	1469	5	DSC2	18	28660278	Missense_Mutation	SNP	A	TCGA-A4-8515-01A-11D-2396-08	23253423	28660278	49416970	52	3874											
ICAM5	7087	hgsc.bcm.edu	37	chr19	10403449	10403449	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcagctaaatgccaccgagAacgacgacagacgcagcttc	13	6	9	13	4	1	2	1	0	0	2	2	5	1	2	2	0	4	3	2	0	3	3			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr19:10403449A>G	ENST00000221980.4	+	5	1186	c.1123A>G	c.(1123-1125)Aac>Gac	p.N375D		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	375	Ig-like C2-type 4.				phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			TGCCACCGAGAACGACGACAG	0.622																																					p.N375D		Atlas-SNP	.											.	ICAM5	53	.	0			c.A1123G						PASS	.						52	54	53					19																	10403449		2203	4300	6503	SO:0001583	missense	7087	exon5			ACCGAGAACGACG	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.1123A>G	chr19.hg19:g.10403449A>G	ENSP00000221980:p.Asn375Asp	99.0	0.0	.		56.0	8.0	.	NM_003259	Q9Y6F3	Missense_Mutation	SNP	ENST00000221980.4	hg19	CCDS12233.1	.	.	.	.	.	.	.	.	.	.	A	7.911	0.736583	0.15574	.	.	ENSG00000105376	ENST00000221980	T	0.05382	3.45	5.46	-10.9	0.00192	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	1.463300	0.03856	N	0.273164	T	0.02230	0.0069	N	0.04880	-0.145	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.34354	-0.9832	10	0.16420	T	0.52	-0.0897	4.6077	0.12385	0.1132:0.1885:0.5112:0.1871	.	375	Q9UMF0	ICAM5_HUMAN	D	375	ENSP00000221980:N375D	ENSP00000221980:N375D	N	+	1	0	ICAM5	10264449	0.000000	0.05858	0.000000	0.03702	0.137000	0.21094	-1.105000	0.03323	-3.113000	0.00241	-0.441000	0.05720	AAC	.	.	.	none		0.622	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259		G	10403449	A	G	10403449	3	3	57	1	0	0	0	0	1	0	0	0	7490	246	9	3	1141	3	ICAM5	19	10403449	Missense_Mutation	SNP	A	TCGA-A4-8515-01A-11D-2396-08		10403449	48725534	53	3875											
ROMO1	140823	hgsc.bcm.edu	37	chr20	34288799	34288799	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggcacctttggcacattcAtggccattgggatgggcatc	7	10	13	11	1	1	0	1	0	0	0	2	1	1	1	2	5	0	3	2	5	0	3			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr20:34288799A>G	ENST00000374078.1	+	3	391	c.211A>G	c.(211-213)Atg>Gtg	p.M71V	NFS1_ENST00000540053.1_5'Flank|ROMO1_ENST00000397416.1_Missense_Mutation_p.M71V|NFS1_ENST00000306750.3_5'Flank|ROMO1_ENST00000374072.1_3'UTR|NFS1_ENST00000541387.1_5'Flank|NFS1_ENST00000374092.4_5'Flank|ROMO1_ENST00000336695.4_Missense_Mutation_p.M71V|NFS1_ENST00000374085.1_5'Flank|NFS1_ENST00000397425.1_5'Flank|ROMO1_ENST00000374077.3_Missense_Mutation_p.M71V	NM_080748.2	NP_542786.1	P60602	ROMO1_HUMAN	reactive oxygen species modulator 1	71					cellular response to reactive oxygen species (GO:0034614)|defense response to bacterium (GO:0042742)|positive regulation of cell proliferation (GO:0008284)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|replicative cell aging (GO:0001302)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)				cervix(1)	1						TGGCACATTCATGGCCATTGG	0.517																																					p.M71V		Atlas-SNP	.											.	ROMO1	5	.	0			c.A211G						PASS	.						124	86	99					20																	34288799		2203	4300	6503	SO:0001583	missense	140823	exon3			ACATTCATGGCCA	AK000548	CCDS13264.1	20q11.22	2008-09-30	2008-09-30	2008-09-30	ENSG00000125995	ENSG00000125995			16185	protein-coding gene	gene with protein product	"mitochondrial targeting GXXXG protein"		"chromosome 20 open reading frame 52"	C20orf52		18313394, 17537404, 16842742	Standard	NM_080748		Approved	bA353C18.2, MTGMP	uc002xdy.3	P60602	OTTHUMG00000032360	ENST00000374078.1:c.211A>G	chr20.hg19:g.34288799A>G	ENSP00000363191:p.Met71Val	105.0	0.0	.		127.0	49.0	.	NM_080748	A7M872|E1P5R9|E9KL28|Q3MHD5|Q5QP16|Q9CQ98|Q9H1N2	Missense_Mutation	SNP	ENST00000374078.1	hg19	CCDS13264.1	.	.	.	.	.	.	.	.	.	.	A	17.65	3.442280	0.63067	.	.	ENSG00000125995	ENST00000374078;ENST00000374077;ENST00000397416;ENST00000336695	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	4.68	4.68	0.58851	.	0.039506	0.85682	D	0.000000	T	0.48059	0.1479	.	.	.	0.80722	D	1	B	0.25351	0.124	B	0.25506	0.061	T	0.52124	-0.8617	9	0.87932	D	0	.	14.3539	0.66722	1.0:0.0:0.0:0.0	.	71	P60602	ROMO1_HUMAN	V	71	ENSP00000363191:M71V;ENSP00000363190:M71V;ENSP00000380561:M71V;ENSP00000338293:M71V	ENSP00000338293:M71V	M	+	1	0	ROMO1	33752213	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.080000	0.94040	1.982000	0.57802	0.529000	0.55759	ATG	.	.	.	none		0.517	ROMO1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000126404.1	NM_080748		G	34288799	A	G	34288799	3	3	57	1	0	0	0	0	1	0	0	0	13535	217	8	3	217	3	ROMO1	20	34288799	Missense_Mutation	SNP	A	TCGA-A4-8515-01A-11D-2396-08		34288799	28736721	54	3876											
SON	6651	hgsc.bcm.edu	37	chr21	34948684	34948684	+	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	tgaataggtattgagaaatgGagcccttaccagacccaatt	14	10	9	8	0	0	3	0	2	0	2	0	5	0	4	3	2	2	1	3	2	6	5	rs397829693|rs34377180		TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chr21:34948684G>A	ENST00000356577.4	+	12	7710	c.7235G>A	c.(7234-7236)gGa>gAa	p.G2412E	DONSON_ENST00000303113.6_Intron|SON_ENST00000290239.6_3'UTR|AP000304.1_ENST00000595468.1_5'Flank|SON_ENST00000381692.2_Missense_Mutation_p.G440E|SON_ENST00000470533.1_Intron	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	2412	DRBM. {ECO:0000255|PROSITE- ProRule:PRU00266}.				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						TTGAGAAATGGAGCCCTTACC	0.338																																					p.G2412E		Atlas-SNP	.											.,1	SON	343	.	0			c.G7235A						PASS	.						55	55	55					21																	34948684		2201	4295	6496	SO:0001583	missense	6651	exon12			GAAATGGAGCCCT	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.7235G>A	chr21.hg19:g.34948684G>A	ENSP00000348984:p.Gly2412Glu	32.0	2.0	.		58.0	10.0	.	NM_138927	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	hg19	CCDS13629.1	.	.	.	.	.	.	.	.	.	.	G	14.10	2.434360	0.43224	.	.	ENSG00000159140	ENST00000356577;ENST00000381692	T;T	0.69306	-0.39;-0.39	5.42	5.42	0.78866	Double-stranded RNA-binding-like (1);	0.000000	0.51477	D	0.000097	T	0.71134	0.3304	M	0.69823	2.125	0.80722	D	1	D;P	0.59767	0.986;0.799	P;B	0.50970	0.655;0.435	T	0.75127	-0.3427	10	0.87932	D	0	.	9.3335	0.38036	0.0788:0.1457:0.7755:0.0	.	440;2412	Q6ZRV7;P18583	.;SON_HUMAN	E	2412;440	ENSP00000348984:G2412E;ENSP00000371111:G440E	ENSP00000348984:G2412E	G	+	2	0	SON	33870554	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.898000	0.48672	2.560000	0.86352	0.555000	0.69702	GGA	.	.	.	none		0.338	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		A	34948684	G	A	34948684	3	1	57	1	0	0	0	0	1	0	0	0	14939	1174	41	2	7540	2	SON	21	34948684	Missense_Mutation	SNP	G	TCGA-A4-8515-01A-11D-2396-08		34948684	13181211	55	3877											
FAM48B1	100130302	hgsc.bcm.edu	37	chrX	24381817	24381817	+	IGR	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	atgtggagaaacttgctaaaGggtatcagtccgtcacagct	12	10	11	8	1	2	1	2	0	0	1	3	2	3	1	1	2	3	3	1	2	4	3			TCGA-A4-8515-01A-11D-2396-08	TCGA-A4-8515-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0d3ff544-d2cb-4e64-8f22-6ff73447d5d8	af2ca6b1-94ef-4660-8a55-522a8022d5b2	g.chrX:24381817G>T								AC004552.1 (14794 upstream) : PDK3 (101520 downstream)																							ACTTGCTAAAGGGTATCAGTC	0.537																																					p.G314W		Atlas-SNP	.											.	.	.	.	0			c.G940T						PASS	.						141	117	125					X																	24381817		1568	3578	5146	SO:0001628	intergenic_variant	100130302	exon1			GCTAAAGGGTATC																													chrX.hg19:g.24381817G>T		185.0	0.0	.		181.0	119.0	.	NM_001136234		Missense_Mutation	SNP		hg19																																																																																				.	.	.	none	0	0.537									T	24381817	G	T	24381817	1	4	57	0	1	0	0	0	0	0	0	0	5580	1000	35	4		4	FAM48B1	23	24381817	IGR	SNP	G	TCGA-A4-8515-01A-11D-2396-08		24381817	130888743	56	3878											
SDC3	9672	hgsc.bcm.edu	37	chr1	31347253	31347253	+	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	gggcccgggcgggcacccttGggcagtgtcccaggtggaga	5	5	19	12	2	0	1	0	0	0	1	1	2	1	1	3	6	0	2	3	6	0	1			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr1:31347253G>T	ENST00000339394.6	-	4	1227	c.1053C>A	c.(1051-1053)ccC>ccA	p.P351P	SDC3_ENST00000336798.7_Silent_p.P293P|SDC3_ENST00000471567.1_5'Flank	NM_014654.3	NP_055469.3	O75056	SDC3_HUMAN	syndecan 3	351					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)		GGGCACCCTTGGGCAGTGTCC	0.632																																					p.P351P		Atlas-SNP	.											.	SDC3	45	.	0			c.C1053A						PASS	.						76	83	81					1																	31347253		2203	4300	6503	SO:0001819	synonymous_variant	9672	exon4			ACCCTTGGGCAGT	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.1053C>A	chr1.hg19:g.31347253G>T		85.0	0.0	.		96.0	31.0	.	NM_014654	Q5T1Z6|Q5T1Z7|Q96CT3|Q96PR8	Silent	SNP	ENST00000339394.6	hg19	CCDS30661.1																																																																																			.	.	.	none		0.632	SDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102017.1	NM_014654		T	31347253	G	T	31347253	2	4	58	1	0	0	0	0	0	0	0	1	13966	1335	47	4		4	SDC3	1	31347253	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08		31347253	217903368	1	3879											
PPIE	10450	hgsc.bcm.edu	37	chr1	40211152	40211152	+	Missense_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	agatgctcctgcgttctgatGtcgtgcccatgacagcaggt	7	11	12	11	2	1	3	0	2	1	1	3	3	2	3	2	1	4	3	2	1	0	1			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr1:40211152G>A	ENST00000324379.5	+	7	509	c.490G>A	c.(490-492)Gtc>Atc	p.V164I	PPIE_ENST00000372830.1_Missense_Mutation_p.V164I|PPIE_ENST00000470213.1_Intron|PPIE_ENST00000480169.1_3'UTR|PPIE_ENST00000356511.2_Missense_Mutation_p.V164I	NM_006112.3	NP_006103.1	Q9UNP9	PPIE_HUMAN	peptidylprolyl isomerase E (cyclophilin E)	164	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				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)			GCGTTCTGATGTCGTGCCCAT	0.572																																					p.V164I		Atlas-SNP	.											.	PPIE	33	.	0			c.G490A						PASS	.						67	55	59					1																	40211152		2203	4300	6503	SO:0001583	missense	10450	exon7			TCTGATGTCGTGC	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.490G>A	chr1.hg19:g.40211152G>A	ENSP00000312769:p.Val164Ile	49.0	0.0	.		36.0	20.0	.	NM_006112	B2R971|O43634|O43635|Q32Q72|Q3S611|Q5TGA0|Q5TGA2|Q5TGA3|Q9UIZ5	Missense_Mutation	SNP	ENST00000324379.5	hg19	CCDS443.1	.	.	.	.	.	.	.	.	.	.	G	12.11	1.839855	0.32513	.	.	ENSG00000084072	ENST00000324379;ENST00000356511;ENST00000497370;ENST00000372835;ENST00000372830	T;T;T;T;T	0.22134	1.97;1.97;1.97;1.97;1.97	5.0	0.793	0.18632	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (4);Cyclophilin-like (1);	0.135859	0.50627	D	0.000102	T	0.11750	0.0286	N	0.20357	0.565	0.47862	D	0.999531	B;B;B;B	0.17667	0.001;0.023;0.001;0.001	B;B;B;B	0.21917	0.01;0.037;0.005;0.009	T	0.13710	-1.0499	10	0.28530	T	0.3	-14.2927	8.5189	0.33264	0.4795:0.0:0.5205:0.0	.	85;164;164;164	B4E3F2;Q5TGA3;Q9UNP9-2;Q9UNP9	.;.;.;PPIE_HUMAN	I	164;164;98;113;164	ENSP00000312769:V164I;ENSP00000348904:V164I;ENSP00000433475:V98I;ENSP00000361925:V113I;ENSP00000361918:V164I	ENSP00000312769:V164I	V	+	1	0	PPIE	39983739	0.996000	0.38824	0.443000	0.26883	0.786000	0.44442	2.773000	0.47686	0.320000	0.23234	-0.251000	0.11542	GTC	.	.	.	none		0.572	PPIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025642.2	NM_006112		A	40211152	G	A	40211152	3	1	58	1	0	0	0	0	1	0	0	0	12332	1377	48	2	516	2	PPIE	1	40211152	Missense_Mutation	SNP	G	TCGA-A4-8517-01A-11D-2396-08	8863899	40211152	209039469	2	3880											
CAP1	5538	hgsc.bcm.edu	37	chr1	40536545	40536545	+	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	aaccatatccatcaacaaaaCagatggctgccatgcttacc	15	8	5	13	0	1	1	1	0	0	1	2	1	2	1	4	1	6	2	4	1	6	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr1:40536545C>T	ENST00000433473.3	-	0	2740				CAP1_ENST00000479759.1_3'UTR|CAP1_ENST00000372797.3_Missense_Mutation_p.T413I|CAP1_ENST00000372798.1_Missense_Mutation_p.T412I|CAP1_ENST00000340450.3_Missense_Mutation_p.T412I|PPT1_ENST00000372775.2_5'Flank|CAP1_ENST00000372805.3_Missense_Mutation_p.T413I|CAP1_ENST00000372792.2_Missense_Mutation_p.T413I|CAP1_ENST00000372802.1_Missense_Mutation_p.T412I	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)			ATCAACAAAACAGATGGCTGC	0.463																																					p.T413I		Atlas-SNP	.											.	CAP1	38	.	0			c.C1238T						PASS	.						138	126	130					1																	40536545		1891	4123	6014	SO:0001628	intergenic_variant	10487	exon12			ACAAAACAGATGG	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		chr1.hg19:g.40536545C>T		126.0	0.0	.		128.0	48.0	.	NM_006367	B4DY24|Q6FGQ4	Missense_Mutation	SNP	ENST00000433473.3	hg19	CCDS447.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.618558	0.87460	.	.	ENSG00000131236	ENST00000372797;ENST00000372802;ENST00000372792;ENST00000538246;ENST00000372798;ENST00000340450;ENST00000372805	T;T;T;T;T;T	0.10382	2.89;2.88;2.89;2.88;2.88;2.89	5.55	5.55	0.83447	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	0.37517	0.1006	M	0.79805	2.47	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.79784	0.993;0.989	T	0.04467	-1.0949	10	0.56958	D	0.05	-5.8536	18.6642	0.91483	0.0:1.0:0.0:0.0	.	360;413	E7ENY9;Q01518	.;CAP1_HUMAN	I	413;412;413;390;412;412;413	ENSP00000361883:T413I;ENSP00000361888:T412I;ENSP00000361878:T413I;ENSP00000361884:T412I;ENSP00000344832:T412I;ENSP00000361891:T413I	ENSP00000344832:T412I	T	+	2	0	CAP1	40309132	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.511000	0.81718	2.890000	0.99128	0.585000	0.79938	ACA	.	.	.	none		0.463	PPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013126.2	NM_000310		T	40536545	C	T	40536545	1	4	58	0	1	0	0	0	0	0	0	0	2621	478	17	2		2	CAP1	1	40536545	IGR	SNP	C	TCGA-A4-8517-01A-11D-2396-08	325393	40536545	208714076	3	3881											
ZNF642	339559	hgsc.bcm.edu	37	chr1	40961061	40961061	+	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	acctttcagatgtaaggaatGtggaagggcctttagtcaaa	13	11	11	6	0	2	1	2	0	0	1	2	3	2	3	2	3	0	1	2	3	5	4			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr1:40961061G>T	ENST00000372706.1	+	6	1917	c.911G>T	c.(910-912)tGt>tTt	p.C304F	RP11-656D10.3_ENST00000450713.1_RNA|ZFP69_ENST00000372705.3_Missense_Mutation_p.C304F			Q49AA0	ZFP69_HUMAN	ZFP69 zinc finger protein	304					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										TGTAAGGAATGTGGAAGGGCC	0.388																																					p.C304F		Atlas-SNP	.											.	.	.	.	0			c.G911T						PASS	.						60	58	59					1																	40961061		2203	4300	6503	SO:0001583	missense	339559	exon6			AGGAATGTGGAAG	AK122618	CCDS30686.1	1p34.2	2013-01-09	2012-11-27	2012-11-27	ENSG00000187815	ENSG00000187815		"Zinc fingers, C2H2-type", "-", "-", "-"	24708	protein-coding gene	gene with protein product	"ZFP69 zinc finger protein A"		"zinc finger protein 642"	ZNF642			Standard	XM_005270808		Approved	ZKSCAN23A, FLJ16030, ZFP69A, ZSCAN54A	uc001cfo.3	Q49AA0	OTTHUMG00000007303	ENST00000372706.1:c.911G>T	chr1.hg19:g.40961061G>T	ENSP00000361791:p.Cys304Phe	62.0	0.0	.		66.0	22.0	.	NM_198494	Q5SWM5|Q6ZWK8	Missense_Mutation	SNP	ENST00000372706.1	hg19	CCDS30686.1	.	.	.	.	.	.	.	.	.	.	G	19.32	3.804872	0.70682	.	.	ENSG00000187815	ENST00000372706;ENST00000372705	D;D	0.85861	-2.04;-2.04	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	0.47093	D	0.000241	D	0.95326	0.8483	H	0.98155	4.16	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96405	0.9300	10	0.87932	D	0	-9.3418	16.1533	0.81636	0.0:0.0:1.0:0.0	.	304	Q49AA0	ZN642_HUMAN	F	304	ENSP00000361791:C304F;ENSP00000361790:C304F	ENSP00000361790:C304F	C	+	2	0	ZNF642	40733648	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.601000	0.98297	2.941000	0.99782	0.655000	0.94253	TGT	.	.	.	none		0.388	ZFP69-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019082.1	NM_198494		T	40961061	G	T	40961061	3	4	58	1	0	0	0	0	1	0	0	0	18070	1377	48	4	929	4	ZNF642	1	40961061	Missense_Mutation	SNP	G	TCGA-A4-8517-01A-11D-2396-08	424516	40961061	208289560	4	3882											
NRD1	114883	hgsc.bcm.edu	37	chr1	52256297	52256297	+	IGR	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	aaggtgggtatcctcacactCcttcagcttgatgagagctg	9	11	11	10	0	2	2	2	2	0	1	4	3	4	2	2	2	2	3	2	2	2	3	rs147279713		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr1:52256297C>A	ENST00000428468.1	+	0	2893				NRD1_ENST00000354831.7_Nonsense_Mutation_p.E1094*|NRD1_ENST00000539524.1_Nonsense_Mutation_p.E962*|NRD1_ENST00000352171.7_Nonsense_Mutation_p.E1026*|NRD1_ENST00000485608.1_5'UTR			Q96SU4	OSBL9_HUMAN	oxysterol binding protein-like 9						lipid transport (GO:0006869)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(3)|pancreas(1)|prostate(3)|skin(1)	18						TCCTCACACTCCTTCAGCTTG	0.527																																					p.E1094X		Atlas-SNP	.											.	NRD1	89	.	0			c.G3280T						PASS	.						151	113	126					1																	52256297		2203	4300	6503	SO:0001628	intergenic_variant	4898	exon31			CACACTCCTTCAG	AF392445	CCDS558.1, CCDS41332.1, CCDS41333.1, CCDS41334.1, CCDS41332.2, CCDS41332.3, CCDS41333.2, CCDS44145.1, CCDS55598.1	1p32.3	2013-01-10			ENSG00000117859	ENSG00000117859		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16386	protein-coding gene	gene with protein product		606737					Standard	NM_148904		Approved		uc001csu.3	Q96SU4	OTTHUMG00000008234		chr1.hg19:g.52256297C>A		58.0	0.0	.		58.0	26.0	.	NM_002525	B1AKJ8|B3KPQ4|D3DQ31|Q5TFC0|Q6IA67|Q86YQ3|Q8NB17|Q8TAS8|Q96SK4|Q9H9X2	Nonsense_Mutation	SNP	ENST00000428468.1	hg19	CCDS41332.3	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	37|37	6.320771|6.320771	0.97471|0.97471	.|.	.|.	ENSG00000078618|ENSG00000078618	ENST00000352171;ENST00000354831;ENST00000539524;ENST00000371665;ENST00000546169|ENST00000440943	.|.	.|.	.|.	5.53|5.53	5.53|5.53	0.82687|0.82687	.|.	0.050156|.	0.85682|.	D|.	0.000000|.	.|T	.|0.75598	.|0.3871	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.72590	.|-0.4247	.|4	0.02654|.	T|.	1|.	-15.9931|-15.9931	19.6556|19.6556	0.95837|0.95837	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|V	1026;1094;962;428;1026|412	.|.	ENSP00000262679:E1026X|.	E|G	-|-	1|2	0|0	NRD1|NRD1	52028885|52028885	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	7.287000|7.287000	0.78681|0.78681	2.882000|2.882000	0.98803|0.98803	0.655000|0.655000	0.94253|0.94253	GAG|GGA	.	C|1.000;T|0.000	.	alt		0.527	OSBPL9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022584.4			A	52256297	C	A	52256297	1	1	58	0	1	0	0	0	0	0	0	0	10652	864	30	4		4	NRD1	1	52256297	IGR	SNP	C	TCGA-A4-8517-01A-11D-2396-08	11295236	52256297	196994324	5	3883											
PRMT6	55170	hgsc.bcm.edu	37	chr1	107600260	107600260	+	Frame_Shift_Del	DEL	C	C	-																															ggagaaacccctggtgctgtCcacctcgccttttcacccgg																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr1:107600260delC	ENST00000370078.1	+	1	960	c.923delC	c.(922-924)tccfs	p.S308fs	PRMT6_ENST00000361318.5_Frame_Shift_Del_p.S249fs			Q96LA8	ANM6_HUMAN	protein arginine methyltransferase 6	308	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				base-excision repair (GO:0006284)|histone H3-R2 methylation (GO:0034970)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	histone binding (GO:0042393)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H2A-R3 specific) (GO:0070612)|histone methyltransferase activity (H3-R2 specific) (GO:0070611)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)			biliary_tract(1)|breast(2)|kidney(1)|large_intestine(4)|lung(5)|urinary_tract(1)	14		all_epithelial(167;0.000429)|all_lung(203;0.00122)|Lung NSC(277;0.00185)		Lung(183;0.0305)|Epithelial(280;0.0765)|Colorectal(144;0.0998)|all cancers(265;0.14)|LUSC - Lung squamous cell carcinoma(189;0.173)|BRCA - Breast invasive adenocarcinoma(282;0.242)		CTGGTGCTGTCCACCTCGCCT	0.607																																					p.S308fs		Atlas-INDEL	.											.	PRMT6	55	.	0			c.922delT						PASS	.						44	48	47					1																	107600260		1973	4160	6133	SO:0001589	frameshift_variant	55170	exon1			.	AK001421	CCDS41360.1, CCDS41360.2	1p13.2	2008-02-05	2006-02-16	2006-02-16	ENSG00000198890	ENSG00000198890		"Protein arginine methyltransferases"	18241	protein-coding gene	gene with protein product		608274	"HMT1 hnRNP methyltransferase-like 6 (S. cerevisiae)"	HRMT1L6		11724789	Standard	NM_018137		Approved	FLJ10559	uc010ous.2	Q96LA8	OTTHUMG00000010964	ENST00000370078.1:c.923delC	chr1.hg19:g.107600260delC	ENSP00000359095:p.Ser308fs	93.0	0.0	0		83.0	37.0	0.445783	NM_018137	A3KME1|B4DID8|Q5T5Y5|Q6DKI4|Q9NVR8	Frame_Shift_Del	DEL	ENST00000370078.1	hg19	CCDS41360.2																																																																																			.	.	.	none		0.607	PRMT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030185.1	NM_018137		-	107600260	C	-	107600260	7	5	58	1	0	1	0	1	0	0	0	0	12550	855	30	0	925	0	PRMT6	1	107600260	Frame_Shift_Del	DEL	C	TCGA-A4-8517-01A-11D-2396-08	55343963	107600260	141650361	6	3884											
AHCYL1	10768	hgsc.bcm.edu	37	chr1	110561173	110561173	+	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	actgtgctttcttcctttcaGaccagcctccgcactccgga	6	12	7	16	2	2	1	1	0	1	1	5	2	5	2	5	1	2	2	5	1	0	3			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr1:110561173G>A	ENST00000369799.5	+	13	1585		c.e13-1		AHCYL1_ENST00000393614.4_Splice_Site|AHCYL1_ENST00000359172.3_Splice_Site	NM_001242673.1|NM_001242674.1|NM_006621.5	NP_001229602.1|NP_001229603.1|NP_006612.2	O43865	SAHH2_HUMAN	adenosylhomocysteinase-like 1						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)		CTTCCTTTCAGACCAGCCTCC	0.498																																					.		Atlas-SNP	.											.	AHCYL1	49	.	0			c.1219-1G>A						PASS	.						77	62	67					1																	110561173		2203	4300	6503	SO:0001630	splice_region_variant	10768	exon13			CTTTCAGACCAGC	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.1219-1G>A	chr1.hg19:g.110561173G>A		35.0	0.0	.		39.0	16.0	.	NM_006621	B4E168|Q2TAJ6|Q502W8|Q5VSM0|Q6P171|Q96PK4|Q9UG84	Splice_Site	SNP	ENST00000369799.5	hg19	CCDS818.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.444478	0.83993	.	.	ENSG00000168710	ENST00000369799;ENST00000359172;ENST00000393614	.	.	.	5.42	5.42	0.78866	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.2323	0.93845	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AHCYL1	110362696	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.869000	0.99810	2.541000	0.85698	0.655000	0.94253	.	.	.	.	none		0.498	AHCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032243.1		Intron	A	110561173	G	A	110561173	5	1	58	1	0	0	0	0	0	0	1	0	410	956	33	2	1268	2	AHCYL1	1	110561173	Splice_Site	SNP	G	TCGA-A4-8517-01A-11D-2396-08	2960913	110561173	138689448	7	3885											
POLR3C	10623	hgsc.bcm.edu	37	chr1	145592731	145592731	+	Frame_Shift_Del	DEL	G	G	-																															ctcaatgtaagactccagcaGgaagatggtttcgtccacct																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr1:145592731delG	ENST00000334163.3	-	15	1724	c.1564delC	c.(1564-1566)ctgfs	p.L523fs	POLR3C_ENST00000369294.1_3'UTR	NM_006468.6	NP_006459.3	Q9BUI4	RPC3_HUMAN	polymerase (RNA) III (DNA directed) polypeptide C (62kD)	523					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)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			breast(2)|endometrium(4)|kidney(1)|large_intestine(3)|liver(1)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)		Epithelial(2;7.55e-13)			GACTCCAGCAGGAAGATGGTT	0.438																																					p.L522fs		Atlas-INDEL	.											.	POLR3C	41	.	0			c.1565delT						PASS	.						124	107	113					1																	145592731		2203	4300	6503	SO:0001589	frameshift_variant	10623	exon15			.	AJ238234	CCDS72864.1	1q21	2013-01-21			ENSG00000186141	ENSG00000186141		"RNA polymerase subunits"	30076	protein-coding gene	gene with protein product						9171375, 12391170	Standard	NM_006468		Approved	RPC62, RPC3	uc001eoh.3	Q9BUI4	OTTHUMG00000013753	ENST00000334163.3:c.1564delC	chr1.hg19:g.145592731delG	ENSP00000334564:p.Leu523fs	96.0	0.0	0		83.0	30.0	0.361446	NM_006468	O15317|Q9Y3R6	Frame_Shift_Del	DEL	ENST00000334163.3	hg19	CCDS921.1																																																																																			.	.	.	none		0.438	POLR3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038542.1	NM_006468		-	145592731	G	-	145592731	7	5	58	1	0	1	0	1	0	0	0	0	12237	991	35	0	44	0	POLR3C	1	145592731	Frame_Shift_Del	DEL	G	TCGA-A4-8517-01A-11D-2396-08	35031558	145592731	103657890	8	3886											
COPA	1314	hgsc.bcm.edu	37	chr1	160305059	160305059	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaaacgtggtgcgaatataAtctaagtgcccaagcaatgt	16	9	9	7	2	1	0	0	0	1	0	1	1	1	0	1	1	4	1	1	1	8	3			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr1:160305059A>G	ENST00000241704.7	-	4	511	c.282T>C	c.(280-282)gaT>gaC	p.D94D	COPA_ENST00000368069.3_Silent_p.D94D	NM_001098398.1|NM_004371.3	NP_001091868.1|NP_004362.2	P53621	COPA_HUMAN	coatomer protein complex, subunit alpha	94					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)			TGCGAATATAATCTAAGTGCC	0.388																																					p.D94D		Atlas-SNP	.											.	COPA	181	.	0			c.T282C						PASS	.						65	58	61					1																	160305059		2203	4300	6503	SO:0001819	synonymous_variant	1314	exon4			AATATAATCTAAG	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.282T>C	chr1.hg19:g.160305059A>G		35.0	0.0	.		28.0	14.0	.	NM_001098398	Q5T201|Q8IXZ9	Silent	SNP	ENST00000241704.7	hg19	CCDS1202.1																																																																																			.	.	.	none		0.388	COPA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080638.1	NM_004371		G	160305059	A	G	160305059	2	3	58	1	0	0	0	0	0	0	0	1	3729	98	4	3		3	COPA	1	160305059	Silent	SNP	A	TCGA-A4-8517-01A-11D-2396-08	14712328	160305059	88945562	9	3887											
ASAP2	8853	hgsc.bcm.edu	37	chr2	9515054	9515054	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtggatcttacggaaaaaaTcccactggccaacggacatg	13	8	10	10	2	1	0	0	0	1	0	2	3	2	3	2	4	2	0	2	4	5	1			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr2:9515054T>C	ENST00000281419.3	+	17	2067	c.1727T>C	c.(1726-1728)aTc>aCc	p.I576T	ASAP2_ENST00000315273.4_Missense_Mutation_p.I576T	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	576					positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						ACGGAAAAAATCCCACTGGCC	0.473																																					p.I576T		Atlas-SNP	.											.	ASAP2	91	.	0			c.T1727C						PASS	.						86	87	86					2																	9515054		2203	4300	6503	SO:0001583	missense	8853	exon17			AAAAAATCCCACT	AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2721	protein-coding gene	gene with protein product	"centaurin, beta 3"	603817	"development and differentiation enhancing factor 2"	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.1727T>C	chr2.hg19:g.9515054T>C	ENSP00000281419:p.Ile576Thr	107.0	0.0	.		126.0	51.0	.	NM_001135191	D6W4Y8	Missense_Mutation	SNP	ENST00000281419.3	hg19	CCDS1661.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.279137	0.80692	.	.	ENSG00000151693	ENST00000281419;ENST00000315273	T;T	0.66099	-0.19;-0.19	5.4	5.4	0.78164	Ankyrin repeat-containing domain (1);	0.146210	0.64402	D	0.000013	T	0.73401	0.3582	L	0.47716	1.5	0.80722	D	1	D;D	0.65815	0.986;0.995	P;D	0.77004	0.904;0.989	T	0.74074	-0.3782	10	0.48119	T	0.1	.	15.4253	0.75045	0.0:0.0:0.0:1.0	.	576;576	O43150-2;O43150	.;ASAP2_HUMAN	T	576	ENSP00000281419:I576T;ENSP00000316404:I576T	ENSP00000281419:I576T	I	+	2	0	ASAP2	9432505	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.691000	0.84191	2.039000	0.60335	0.533000	0.62120	ATC	.	.	.	none		0.473	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887		C	9515054	T	C	9515054	3	2	58	1	0	0	0	0	1	0	0	0	1011	1435	50	3	1793	3	ASAP2	2	9515054	Missense_Mutation	SNP	T	TCGA-A4-8517-01A-11D-2396-08		9515054	233684319	10	3888											
TCF23	150921	hgsc.bcm.edu	37	chr2	27373231	27373231	+	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	tccgctacttgcaccctctcAaggtaagtcacaagccctgg	9	9	8	15	1	2	0	2	0	1	0	4	0	3	0	3	2	3	3	3	2	4	3			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr2:27373231A>T	ENST00000296096.5	+	2	593	c.463A>T	c.(463-465)Aag>Tag	p.K155*		NM_175769.2	NP_786951.1	Q7RTU1	TCF23_HUMAN	transcription factor 23	155					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	nucleus (GO:0005634)				large_intestine(2)|lung(11)|prostate(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCACCCTCTCAAGGTAAGTCA	0.622																																					p.K155X		Atlas-SNP	.											.	TCF23	28	.	0			c.A463T						PASS	.						100	109	106					2																	27373231		2203	4300	6503	SO:0001587	stop_gained	150921	exon2			CCTCTCAAGGTAA	AC013403	CCDS33163.1	2p23.3	2013-05-21			ENSG00000163792	ENSG00000163792		"Basic helix-loop-helix proteins"	18602	protein-coding gene	gene with protein product		609635				11701948, 10652346	Standard	NM_175769		Approved	OUT, bHLHa24	uc010ylg.2	Q7RTU1	OTTHUMG00000152031	ENST00000296096.5:c.463A>T	chr2.hg19:g.27373231A>T	ENSP00000296096:p.Lys155*	391.0	0.0	.		260.0	107.0	.	NM_175769	B2RNZ3	Nonsense_Mutation	SNP	ENST00000296096.5	hg19	CCDS33163.1	.	.	.	.	.	.	.	.	.	.	A	37	6.018528	0.97205	.	.	ENSG00000163792	ENST00000296096	.	.	.	5.66	5.66	0.87406	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-25.5975	13.8444	0.63459	1.0:0.0:0.0:0.0	.	.	.	.	X	155	.	ENSP00000296096:K155X	K	+	1	0	TCF23	27226735	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	8.489000	0.90461	2.164000	0.68074	0.459000	0.35465	AAG	.	.	.	none		0.622	TCF23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324980.1	NM_175769		T	27373231	A	T	27373231	4	4	58	1	0	0	0	0	0	1	0	0	15704	131	5	5	469	5	TCF23	2	27373231	Nonsense_Mutation	SNP	A	TCGA-A4-8517-01A-11D-2396-08	17858177	27373231	215826142	11	3889											
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54852000	54852000	+	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	ctggctttgcggaatgagctCataagacaggagaaactgga	13	8	13	7	1	1	3	1	1	0	2	1	6	1	5	0	4	3	2	0	4	3	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr2:54852000C>T	ENST00000356805.4	+	11	1523	c.1242C>T	c.(1240-1242)ctC>ctT	p.L414L	SPTBN1_ENST00000333896.5_Silent_p.L401L	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	414					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)			GGAATGAGCTCATAAGACAGG	0.493																																					p.L414L		Atlas-SNP	.											.	SPTBN1	378	.	0			c.C1242T						PASS	.						76	73	74					2																	54852000		2203	4300	6503	SO:0001819	synonymous_variant	6711	exon11			TGAGCTCATAAGA		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.1242C>T	chr2.hg19:g.54852000C>T		65.0	0.0	.		58.0	10.0	.	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Silent	SNP	ENST00000356805.4	hg19	CCDS33198.1																																																																																			.	.	.	none		0.493	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			T	54852000	C	T	54852000	2	4	58	1	0	0	0	0	0	0	0	1	15131	813	29	2		2	SPTBN1	2	54852000	Silent	SNP	C	TCGA-A4-8517-01A-11D-2396-08	27478769	54852000	188347373	12	3890											
RANBP2	5903	hgsc.bcm.edu	37	chr2	109380509	109380509	+	Missense_Mutation	SNP	T	T	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	atgatgatgacggtcctcacTttgagcctgtagtacctctt	8	14	9	10	1	2	4	1	4	1	0	3	4	3	4	3	1	2	2	3	1	2	4			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr2:109380509T>G	ENST00000283195.6	+	20	3640	c.3514T>G	c.(3514-3516)Ttt>Gtt	p.F1172V		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	1172	RanBD1 1. {ECO:0000255|PROSITE- ProRule:PRU00164}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						CGGTCCTCACTTTGAGCCTGT	0.428																																					p.F1172V		Atlas-SNP	.											.	RANBP2	488	.	0			c.T3514G						PASS	.						117	109	112					2																	109380509		2203	4299	6502	SO:0001583	missense	5903	exon20			CCTCACTTTGAGC	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.3514T>G	chr2.hg19:g.109380509T>G	ENSP00000283195:p.Phe1172Val	132.0	0.0	.		148.0	58.0	.	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	hg19	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	T	16.12	3.034233	0.54896	.	.	ENSG00000153201	ENST00000283195	T	0.39787	1.06	5.57	5.57	0.84162	Pleckstrin homology-type (1);Ran binding protein 1 (2);	.	.	.	.	T	0.64951	0.2645	M	0.74258	2.255	0.50039	D	0.999845	D	0.76494	0.999	D	0.79784	0.993	T	0.67684	-0.5607	9	0.54805	T	0.06	-23.4766	15.7401	0.77887	0.0:0.0:0.0:1.0	.	1172	P49792	RBP2_HUMAN	V	1172	ENSP00000283195:F1172V	ENSP00000283195:F1172V	F	+	1	0	RANBP2	108746941	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	8.040000	0.89188	2.107000	0.64212	0.528000	0.53228	TTT	.	.	.	none		0.428	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		G	109380509	T	G	109380509	3	3	58	1	0	0	0	0	1	0	0	0	13041	1609	56	5	3592	5	RANBP2	2	109380509	Missense_Mutation	SNP	T	TCGA-A4-8517-01A-11D-2396-08	54528509	109380509	133818864	13	3891											
LRP1B	53353	hgsc.bcm.edu	37	chr2	141816463	141816463	+	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	cccacttacctgttggttgaGttcttttttgataaattcgg	7	18	8	8	1	1	2	0	2	1	0	2	2	1	2	2	2	1	3	2	2	3	9			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr2:141816463G>C	ENST00000389484.3	-	9	2368	c.1397C>G	c.(1396-1398)aCt>aGt	p.T466S		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	466					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)		TGTTGGTTGAGTTCTTTTTTG	0.353										TSP Lung(27;0.18)																											p.T466S	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.C1397G						PASS	.						83	82	82					2																	141816463		2201	4298	6499	SO:0001583	missense	53353	exon9			GGTTGAGTTCTTT	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.1397C>G	chr2.hg19:g.141816463G>C	ENSP00000374135:p.Thr466Ser	28.0	0.0	.		31.0	14.0	.	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	G	7.474	0.647368	0.14516	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.97575	-4.44	5.45	2.69	0.31865	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.247105	0.32028	U	0.006685	D	0.93032	0.7782	L	0.33245	0.995	0.09310	N	1	B	0.17038	0.02	B	0.16722	0.016	D	0.84920	0.0853	10	0.40728	T	0.16	.	9.4538	0.38743	0.2856:0.0:0.7144:0.0	.	466	Q9NZR2	LRP1B_HUMAN	S	466;404	ENSP00000374135:T466S	ENSP00000374135:T466S	T	-	2	0	LRP1B	141532933	0.582000	0.26749	0.952000	0.39060	0.309000	0.27889	1.212000	0.32394	0.287000	0.22375	0.462000	0.41574	ACT	.	.	.	none		0.353	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		C	141816463	G	C	141816463	3	2	58	1	0	0	0	0	1	0	0	0	8962	1029	36	4	12734	4	LRP1B	2	141816463	Missense_Mutation	SNP	G	TCGA-A4-8517-01A-11D-2396-08	32435954	141816463	101382910	14	3892			1	11		2	2	14	N	G_A	3.317478e-05
LRP1B	53353	hgsc.bcm.edu	37	chr2	141816476	141816476	+	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	tggttgagttcttttttgatAaattcggattccccaagcat	9	17	8	7	1	1	2	0	2	1	0	3	3	2	3	2	2	1	3	2	2	3	8			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr2:141816476A>T	ENST00000389484.3	-	9	2355	c.1384T>A	c.(1384-1386)Tat>Aat	p.Y462N		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	462					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)		CTTTTTTGATAAATTCGGATT	0.343										TSP Lung(27;0.18)																											p.Y462N	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.T1384A						PASS	.						82	82	82					2																	141816476		2201	4297	6498	SO:0001583	missense	53353	exon9			TTTGATAAATTCG	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.1384T>A	chr2.hg19:g.141816476A>T	ENSP00000374135:p.Tyr462Asn	28.0	0.0	.		30.0	10.0	.	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	A	17.26	3.345446	0.61073	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.97404	-4.37	5.45	5.45	0.79879	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.000000	0.64402	U	0.000004	D	0.98588	0.9528	M	0.89095	3.005	0.58432	D	0.999994	D	0.76494	0.999	D	0.83275	0.996	D	0.99589	1.0975	10	0.62326	D	0.03	.	15.5201	0.75859	1.0:0.0:0.0:0.0	.	462	Q9NZR2	LRP1B_HUMAN	N	462;400	ENSP00000374135:Y462N	ENSP00000374135:Y462N	Y	-	1	0	LRP1B	141532946	1.000000	0.71417	0.974000	0.42286	0.256000	0.26092	8.865000	0.92300	2.080000	0.62538	0.379000	0.24179	TAT	.	.	.	none		0.343	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141816476	A	T	141816476	3	4	58	1	0	0	0	0	1	0	0	0	8962	362	13	5	12747	5	LRP1B	2	141816476	Missense_Mutation	SNP	A	TCGA-A4-8517-01A-11D-2396-08	13	141816476	101382897	15	3893			1	11		2	2	14	N	G_A	3.317478e-05
FBXO36	130888	hgsc.bcm.edu	37	chr2	230861514	230861516	+	In_Frame_Del	DEL	AAT	AAT	-																															gaatattagactatgtcatcAatttgtgcaaaggtaaattt																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr2:230861514_230861516delAAT	ENST00000283946.3	+	3	271_273	c.253_255delAAT	c.(253-255)aatdel	p.N85del	FBXO36_ENST00000373652.3_In_Frame_Del_p.N54del|FBXO36_ENST00000409992.1_Intron	NM_174899.4	NP_777559.3	Q8NEA4	FBX36_HUMAN	F-box protein 36	85										endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	7		Renal(207;0.0112)|all_lung(227;0.0179)|Lung NSC(271;0.0804)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;7.56e-14)|all cancers(144;7.74e-11)|Lung(119;0.00488)|LUSC - Lung squamous cell carcinoma(224;0.008)		CTATGTCATCAATTTGTGCAAAG	0.355																																					p.84_85del		Atlas-INDEL	.											.	FBXO36	22	.	0			c.252_254del						PASS	.																																			SO:0001651	inframe_deletion	130888	exon3			.	BC033935	CCDS2472.1	2q37.1	2008-02-05	2004-06-15		ENSG00000153832	ENSG00000153832		"F-boxes /  "other""	27020	protein-coding gene	gene with protein product		609105	"F-box only protein 36"			12477932	Standard	NM_174899		Approved	Fbx36, FLJ37592	uc002vqa.3	Q8NEA4	OTTHUMG00000133206	ENST00000283946.3:c.253_255delAAT	chr2.hg19:g.230861514_230861516delAAT	ENSP00000283946:p.Asn85del	152.0	0.0	0		115.0	47.0	0.408696	NM_174899	B3KVQ6|Q53TE6|Q8WWD4	In_Frame_Del	DEL	ENST00000283946.3	hg19	CCDS2472.1																																																																																			.	.	.	none		0.355	FBXO36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256919.2	NM_174899		-	230861516	AAT	-	230861514	7	5	58	1	0	1	0	1	0	0	0	0	5752	130	5	0	263	0	FBXO36	2	230861514	In_Frame_Del	DEL	AAT	TCGA-A4-8517-01A-11D-2396-08	89045038	230861514	12337859	16	3894											
HYAL2	8692	hgsc.bcm.edu	37	chr3	50357591	50357591	+	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	acacgtttctgcagcatcttCcggtgtgcccaaaggctgac	8	10	10	13	2	2	1	0	1	2	0	3	1	3	1	2	2	3	4	2	2	1	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr3:50357591C>T	ENST00000447092.1	-	1	2622	c.330G>A	c.(328-330)cgG>cgA	p.R110R	TUSC2_ENST00000462137.1_5'UTR|HYAL2_ENST00000357750.4_Silent_p.R110R|HYAL2_ENST00000395139.3_Silent_p.R110R|HYAL2_ENST00000442581.1_Silent_p.R110R			Q12891	HYAL2_HUMAN	hyaluronoglucosaminidase 2	110					carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to interleukin-1 (GO:0071347)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to UV-B (GO:0071493)|defense response to virus (GO:0051607)|fusion of virus membrane with host plasma membrane (GO:0019064)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hematopoietic progenitor cell differentiation (GO:0002244)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|kidney development (GO:0001822)|monocyte activation (GO:0042117)|multicellular organismal aging (GO:0010259)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of cell growth (GO:0030308)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of urine volume (GO:0035810)|renal water absorption (GO:0070295)|response to antibiotic (GO:0046677)|response to reactive oxygen species (GO:0000302)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)|transformation of host cell by virus (GO:0019087)|viral entry into host cell (GO:0046718)	anchored component of external side of plasma membrane (GO:0031362)|anchored component of plasma membrane (GO:0046658)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|lysosome (GO:0005764)|membrane raft (GO:0045121)|microvillus (GO:0005902)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|hyaluronic acid binding (GO:0005540)|hyaluronoglucuronidase activity (GO:0033906)|hyalurononglucosaminidase activity (GO:0004415)|receptor signaling protein tyrosine kinase inhibitor activity (GO:0030294)|receptor tyrosine kinase binding (GO:0030971)|transforming growth factor beta binding (GO:0050431)|virus receptor activity (GO:0001618)			breast(1)|endometrium(2)|kidney(1)|ovary(1)|prostate(1)|skin(1)	7				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		GCAGCATCTTCCGGTGTGCCC	0.597																																					p.R110R		Atlas-SNP	.											.	HYAL2	31	.	0			c.G330A						PASS	.						79	71	74					3																	50357591		2203	4300	6503	SO:0001819	synonymous_variant	8692	exon3			CATCTTCCGGTGT	AJ000099	CCDS2818.1	3p21.3	2008-07-18			ENSG00000068001	ENSG00000068001			5321	protein-coding gene	gene with protein product	"lysosomal hyaluronidase", "PH-20 homolog", "hyaluronidase 2"	603551				9712871, 9790770	Standard	NM_003773		Approved	LuCa-2, LUCA2	uc003czv.3	Q12891	OTTHUMG00000156876	ENST00000447092.1:c.330G>A	chr3.hg19:g.50357591C>T		105.0	0.0	.		87.0	30.0	.	NM_033158	B3KRZ2|O15177|Q9BW29	Silent	SNP	ENST00000447092.1	hg19	CCDS2818.1																																																																																			.	.	.	none		0.597	HYAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346391.1	NM_003773		T	50357591	C	T	50357591	2	4	58	1	0	0	0	0	0	0	0	1	7471	842	30	2		2	HYAL2	3	50357591	Silent	SNP	C	TCGA-A4-8517-01A-11D-2396-08		50357591	147664839	17	3895											
CEP63	80254	hgsc.bcm.edu	37	chr3	134267996	134267996	+	Frame_Shift_Del	DEL	A	A	-																															gatggaagcacataacaatgAatacaaagcagagattaaga																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr3:134267996delA	ENST00000337090.3	+	10	1333	c.1160delA	c.(1159-1161)gaafs	p.E387fs	CEP63_ENST00000332047.5_Frame_Shift_Del_p.E341fs|CEP63_ENST00000513612.2_Frame_Shift_Del_p.E387fs|CEP63_ENST00000606977.1_Frame_Shift_Del_p.E387fs|CEP63_ENST00000354446.3_Frame_Shift_Del_p.E341fs|CEP63_ENST00000383229.3_Frame_Shift_Del_p.E387fs			Q96MT8	CEP63_HUMAN	centrosomal protein 63kDa	387					centriole replication (GO:0007099)|DNA damage checkpoint (GO:0000077)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|signal transduction in response to DNA damage (GO:0042770)|spindle assembly (GO:0051225)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|spindle pole (GO:0000922)				kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						CATAACAATGAATACAAAGCA	0.373																																					p.E387fs		Atlas-INDEL	.											.	CEP63	56	.	0			c.1159delG						PASS	.						98	89	92					3																	134267996		2203	4300	6503	SO:0001589	frameshift_variant	80254	exon11			.	AK056465	CCDS3086.1, CCDS43152.1, CCDS43153.1, CCDS43154.1	3q22.1	2014-02-20			ENSG00000182923	ENSG00000182923			25815	protein-coding gene	gene with protein product		614724				14654843, 24240477	Standard	NM_001042383		Approved	FLJ13386	uc003eqo.1	Q96MT8	OTTHUMG00000159725	ENST00000337090.3:c.1160delA	chr3.hg19:g.134267996delA	ENSP00000336524:p.Glu387fs	38.0	0.0	0		52.0	16.0	0.307692	NM_025180	D3DND8|D3DND9|D3DNE0|Q96CR0|Q9H8F5|Q9H8N0	Frame_Shift_Del	DEL	ENST00000337090.3	hg19	CCDS3086.1																																																																																			.	.	.	none		0.373	CEP63-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000470139.1	NM_025180		-	134267996	A	-	134267996	7	5	58	1	0	1	0	1	0	0	0	0	3259	246	9	0	1194	0	CEP63	3	134267996	Frame_Shift_Del	DEL	A	TCGA-A4-8517-01A-11D-2396-08	83910405	134267996	63754434	18	3896											
MFN1	55669	hgsc.bcm.edu	37	chr3	179076735	179076735	+	Missense_Mutation	SNP	A	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	cctaagtgttgaaggaactgAtggagataaagcctatctta	14	11	10	6	0	1	3	0	2	1	1	1	5	1	4	2	2	2	1	2	2	7	5			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr3:179076735A>C	ENST00000471841.1	+	4	482	c.356A>C	c.(355-357)gAt>gCt	p.D119A	MFN1_ENST00000263969.5_Missense_Mutation_p.D119A|MFN1_ENST00000280653.7_Missense_Mutation_p.D119A	NM_033540.2	NP_284941	Q8IWA4	MFN1_HUMAN	mitofusin 1	119	Dynamin-type G.				mitochondrial fusion (GO:0008053)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(3)|prostate(1)|urinary_tract(1)	31	all_cancers(143;1.67e-16)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.00225)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			GAAGGAACTGATGGAGATAAA	0.378																																					p.D119A		Atlas-SNP	.											.	MFN1	72	.	0			c.A356C						PASS	.						150	139	143					3																	179076735		2203	4300	6503	SO:0001583	missense	55669	exon4			GAACTGATGGAGA	AF054986	CCDS3228.1	3q26.32	2006-12-13			ENSG00000171109	ENSG00000171109			18262	protein-coding gene	gene with protein product		608506				8358434, 11181170	Standard	NM_033540		Approved	FLJ20693	uc003fjs.3	Q8IWA4	OTTHUMG00000157385	ENST00000471841.1:c.356A>C	chr3.hg19:g.179076735A>C	ENSP00000420617:p.Asp119Ala	64.0	0.0	.		81.0	27.0	.	NM_033540	B2RAR1|D3DNR6|O15323|O60639|Q9BZB5|Q9NWQ2	Missense_Mutation	SNP	ENST00000471841.1	hg19	CCDS3228.1	.	.	.	.	.	.	.	.	.	.	A	19.42	3.824508	0.71143	.	.	ENSG00000171109	ENST00000471841;ENST00000280653;ENST00000539169;ENST00000467174;ENST00000263969	D;D;D;D	0.96830	-4.14;-4.14;-4.14;-4.14	5.86	5.86	0.93980	Dynamin, GTPase domain (1);	0.045333	0.85682	D	0.000000	D	0.97932	0.9320	M	0.80508	2.5	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.71656	0.974;0.964	D	0.97957	1.0335	10	0.42905	T	0.14	-26.3212	16.5602	0.84551	1.0:0.0:0.0:0.0	.	147;119	Q4AEJ4;Q8IWA4	.;MFN1_HUMAN	A	119	ENSP00000420617:D119A;ENSP00000280653:D119A;ENSP00000419134:D119A;ENSP00000263969:D119A	ENSP00000263969:D119A	D	+	2	0	MFN1	180559429	1.000000	0.71417	0.998000	0.56505	0.943000	0.58893	8.904000	0.92590	2.367000	0.80283	0.528000	0.53228	GAT	.	.	.	none		0.378	MFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348654.2	NM_017927		C	179076735	A	C	179076735	3	2	58	1	0	0	0	0	1	0	0	0	9530	333	12	5	366	5	MFN1	3	179076735	Missense_Mutation	SNP	A	TCGA-A4-8517-01A-11D-2396-08	44808739	179076735	18945695	19	3897											
USP13	8975	hgsc.bcm.edu	37	chr3	179426711	179426711	+	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	gacatgggctacccactagcCgtgaaactgggaaccatcac	12	6	10	13	1	1	1	1	1	0	0	1	3	1	2	3	2	4	1	3	2	4	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr3:179426711C>A	ENST00000263966.3	+	6	1242	c.771C>A	c.(769-771)gcC>gcA	p.A257A	USP13_ENST00000496897.1_Silent_p.A192A|USP13_ENST00000482333.1_3'UTR	NM_003940.2	NP_003931.2	Q92995	UBP13_HUMAN	ubiquitin specific peptidase 13 (isopeptidase T-3)	257					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)			ACCCACTAGCCGTGAAACTGG	0.547																																					p.A257A		Atlas-SNP	.											USP13,NS,malignant_melanoma,+1,1	USP13	117	.	0			c.C771A						PASS	.						75	70	71					3																	179426711		2203	4300	6503	SO:0001819	synonymous_variant	8975	exon6			ACTAGCCGTGAAA	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.771C>A	chr3.hg19:g.179426711C>A		92.0	0.0	.		73.0	33.0	.	NM_003940	A8K2S3|B4DYF3|D3DNS2|Q96B25	Silent	SNP	ENST00000263966.3	hg19	CCDS3235.1																																																																																			.	.	.	none		0.547	USP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349617.1			A	179426711	C	A	179426711	2	1	58	1	0	0	0	0	0	0	0	1	17056	639	23	4		4	USP13	3	179426711	Silent	SNP	C	TCGA-A4-8517-01A-11D-2396-08	349976	179426711	18595719	20	3898											
CPN2	1370	hgsc.bcm.edu	37	chr3	194062198	194062198	+	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	caggagccgatcggtgtactGctgcagccagttgaagaggt	9	8	15	9	2	0	2	0	1	0	1	1	4	0	3	2	3	5	4	2	3	2	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr3:194062198G>T	ENST00000323830.3	-	2	1323	c.1234C>A	c.(1234-1236)Cag>Aag	p.Q412K	CPN2_ENST00000429275.1_Missense_Mutation_p.Q412K	NM_001080513.2	NP_001073982	P22792	CPN2_HUMAN	carboxypeptidase N, polypeptide 2	412	LRRCT.				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)			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)		TCGGTGTACTGCTGCAGCCAG	0.602																																					p.Q412K		Atlas-SNP	.											.	CPN2	56	.	0			c.C1234A						PASS	.						62	64	63					3																	194062198		2203	4300	6503	SO:0001583	missense	1370	exon2			TGTACTGCTGCAG	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.1234C>A	chr3.hg19:g.194062198G>T	ENSP00000319464:p.Gln412Lys	84.0	0.0	.		76.0	28.0	.	NM_001080513	B2RPE7|Q86SU4|Q8N5V4	Missense_Mutation	SNP	ENST00000323830.3	hg19	CCDS33920.1	.	.	.	.	.	.	.	.	.	.	G	2.132	-0.398880	0.04865	.	.	ENSG00000178772	ENST00000323830;ENST00000429275	T;T	0.24151	1.87;1.87	5.56	1.46	0.22682	Cysteine-rich flanking region, C-terminal (1);	0.280456	0.19931	N	0.102851	T	0.10981	0.0268	N	0.25094	0.71	0.09310	N	1	B	0.21071	0.051	B	0.16722	0.016	T	0.32955	-0.9887	10	0.05436	T	0.98	.	4.2056	0.10486	0.0732:0.3827:0.2364:0.3077	.	412	P22792	CPN2_HUMAN	K	412	ENSP00000319464:Q412K;ENSP00000402232:Q412K	ENSP00000319464:Q412K	Q	-	1	0	CPN2	195543893	0.000000	0.05858	0.002000	0.10522	0.124000	0.20399	-0.469000	0.06648	0.787000	0.33731	-0.165000	0.13383	CAG	.	.	.	none		0.602	CPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342856.2	NM_001080513		T	194062198	G	T	194062198	3	4	58	1	0	0	0	0	1	0	0	0	3812	1328	46	4	407	4	CPN2	3	194062198	Missense_Mutation	SNP	G	TCGA-A4-8517-01A-11D-2396-08	14635487	194062198	3960232	21	3899											
ODAM	54959	hgsc.bcm.edu	37	chr4	71064324	71064324	+	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	ctatgtattctccttcaaaaTgcctcaagagcaaggacagg	13	10	8	10	0	3	1	2	0	1	1	4	2	3	2	2	2	2	2	2	2	6	4			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr4:71064324T>A	ENST00000396094.2	+	5	452	c.404T>A	c.(403-405)aTg>aAg	p.M135K		NM_017855.3	NP_060325.3	A1E959	ODAM_HUMAN	odontogenic, ameloblast asssociated	135	Gln-rich.				biomineral tissue development (GO:0031214)|odontogenesis of dentin-containing tooth (GO:0042475)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|fibril (GO:0043205)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(8)|ovary(3)|skin(2)	20						TCCTTCAAAATGCCTCAAGAG	0.378																																					p.M135K		Atlas-SNP	.											.	ODAM	38	.	0			c.T404A						PASS	.						120	116	118					4																	71064324		2203	4300	6503	SO:0001583	missense	54959	exon5			TCAAAATGCCTCA	AK000520	CCDS3536.2	4q13.3	2010-11-23			ENSG00000109205	ENSG00000109205			26043	protein-coding gene	gene with protein product		614843				14647039	Standard	NM_017855		Approved	APin, FLJ20513	uc003hfc.3	A1E959	OTTHUMG00000129406	ENST00000396094.2:c.404T>A	chr4.hg19:g.71064324T>A	ENSP00000379401:p.Met135Lys	73.0	0.0	.		91.0	6.0	.	NM_017855	Q8WWE5|Q9NWZ9	Missense_Mutation	SNP	ENST00000396094.2	hg19	CCDS3536.2	.	.	.	.	.	.	.	.	.	.	T	13.87	2.366377	0.41902	.	.	ENSG00000109205	ENST00000396094;ENST00000510709;ENST00000514097	T;T	0.48522	0.81;0.81	4.82	3.65	0.41850	.	0.949132	0.08736	N	0.901245	T	0.37972	0.1023	L	0.42245	1.32	0.22754	N	0.998773	P	0.38020	0.615	B	0.32805	0.153	T	0.30592	-0.9973	10	0.72032	D	0.01	-0.3936	7.1176	0.25424	0.0:0.101:0.0:0.899	.	135	A1E959	ODAM_HUMAN	K	135;121;88	ENSP00000379401:M135K;ENSP00000426106:M88K	ENSP00000379401:M135K	M	+	2	0	ODAM	71098913	0.773000	0.28580	0.893000	0.35052	0.676000	0.39594	0.800000	0.27042	0.987000	0.38709	0.374000	0.22700	ATG	.	.	.	none		0.378	ODAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251562.1	NM_017855		A	71064324	T	A	71064324	3	1	58	1	0	0	0	0	1	0	0	0	10831	1464	51	5	422	5	ODAM	4	71064324	Missense_Mutation	SNP	T	TCGA-A4-8517-01A-11D-2396-08		71064324	120089952	22	3900											
SLC4A4	8671	hgsc.bcm.edu	37	chr4	72429564	72429564	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaaaattccaatggacatcAtggaacagcaacctttccta	15	11	5	10	0	1	0	1	0	0	0	3	2	3	2	3	2	3	1	3	2	6	4			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr4:72429564A>G	ENST00000264485.5	+	24	3271	c.3154A>G	c.(3154-3156)Atg>Gtg	p.M1052V	SLC4A4_ENST00000351898.6_Missense_Mutation_p.M968V|SLC4A4_ENST00000340595.3_Missense_Mutation_p.M1008V|SLC4A4_ENST00000425175.1_Intron	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	1052					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)	p.M1008V(1)		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)	AATGGACATCATGGAACAGCA	0.358																																					p.M1052V		Atlas-SNP	.											SLC4A4,rectum,carcinoma,0,1	SLC4A4	269	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3154G						PASS	.						152	158	156					4																	72429564		2203	4300	6503	SO:0001583	missense	8671	exon24			GACATCATGGAAC	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.3154A>G	chr4.hg19:g.72429564A>G	ENSP00000264485:p.Met1052Val	112.0	0.0	.		122.0	45.0	.	NM_001098484	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	hg19	CCDS43236.1	.	.	.	.	.	.	.	.	.	.	A	7.750	0.703080	0.15172	.	.	ENSG00000080493	ENST00000264485;ENST00000351898;ENST00000340595	T;T;T	0.75154	-0.91;-0.58;-0.91	5.46	4.25	0.50352	.	0.037886	0.85682	D	0.000000	T	0.56572	0.1994	N	0.24115	0.695	0.80722	D	1	B;B;B	0.20164	0.012;0.042;0.025	B;B;B	0.21546	0.017;0.035;0.01	T	0.49643	-0.8918	10	0.02654	T	1	.	12.5178	0.56042	0.8603:0.1397:0.0:0.0	.	968;1008;1052	Q9Y6R1-4;Q9Y6R1-2;Q9Y6R1	.;.;S4A4_HUMAN	V	1052;968;1008	ENSP00000264485:M1052V;ENSP00000307349:M968V;ENSP00000344272:M1008V	ENSP00000264485:M1052V	M	+	1	0	SLC4A4	72648428	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.988000	0.76212	0.885000	0.36088	-0.619000	0.04042	ATG	.	.	.	none		0.358	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		G	72429564	A	G	72429564	3	3	58	1	0	0	0	0	1	0	0	0	14669	217	8	3	3365	3	SLC4A4	4	72429564	Missense_Mutation	SNP	A	TCGA-A4-8517-01A-11D-2396-08	1365240	72429564	118724712	23	3901											
SHROOM3	57619	hgsc.bcm.edu	37	chr4	77661360	77661360	+	Frame_Shift_Del	DEL	G	G	-																															ctgagaagacacagcagcctGgagctaggccggggaaccca																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr4:77661360delG	ENST00000296043.6	+	5	2987	c.2034delG	c.(2032-2034)ctgfs	p.L678fs		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	678					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)			ACAGCAGCCTGGAGCTAGGCC	0.602																																					p.L678fs		Atlas-INDEL	.											.	SHROOM3	134	.	0			c.2033delT						PASS	.						46	58	54					4																	77661360		2203	4300	6503	SO:0001589	frameshift_variant	57619	exon5			.	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.2034delG	chr4.hg19:g.77661360delG	ENSP00000296043:p.Leu678fs	156.0	0.0	0		165.0	83.0	0.50303	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Frame_Shift_Del	DEL	ENST00000296043.6	hg19	CCDS3579.2																																																																																			.	.	.	none		0.602	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859		-	77661360	G	-	77661360	7	5	58	1	0	1	0	1	0	0	0	0	14308	1335	47	0	2052	0	SHROOM3	4	77661360	Frame_Shift_Del	DEL	G	TCGA-A4-8517-01A-11D-2396-08	5231796	77661360	113492916	24	3902											
EXOSC9	5393	hgsc.bcm.edu	37	chr4	122724130	122724130	+	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	agatgtctaagaaattcgaaGtgtatagacactgagtctct	14	12	9	6	1	2	4	0	1	2	3	4	5	2	4	0	0	0	1	0	0	5	4			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr4:122724130G>A	ENST00000243498.5	+	4	450	c.342G>A	c.(340-342)aaG>aaA	p.K114K	EXOSC9_ENST00000512454.1_Silent_p.K98K|EXOSC9_ENST00000379663.3_Silent_p.K114K|EXOSC9_ENST00000509980.1_3'UTR	NM_005033.2	NP_005024.2	Q06265	EXOS9_HUMAN	exosome component 9	114	ARE binding.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|immune response (GO:0006955)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear-transcribed mRNA catabolic process (GO:0000956)|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)|intermediate filament cytoskeleton (GO:0045111)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|AU-rich element binding (GO:0017091)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|urinary_tract(1)	16						GAAATTCGAAGTGTATAGACA	0.393																																					p.K114K		Atlas-SNP	.											.	EXOSC9	51	.	0			c.G342A						PASS	.						126	118	121					4																	122724130		2203	4300	6503	SO:0001819	synonymous_variant	5393	exon4			TTCGAAGTGTATA	M58460	CCDS3722.2, CCDS34057.1	4q27	2010-05-07	2004-06-16	2004-06-18	ENSG00000123737	ENSG00000123737	3.1.13.-		9137	protein-coding gene	gene with protein product	"polymyositis/scleroderma autoantigen 1 (75kD)"	606180	"polymyositis/scleroderma autoantigen 1, 75kDa"	PMSCL1			Standard	XR_427545		Approved	PM/Scl-75, Rrp45p, RRP45, p5, p6	uc003idz.3	Q06265	OTTHUMG00000128783	ENST00000243498.5:c.342G>A	chr4.hg19:g.122724130G>A		74.0	0.0	.		69.0	32.0	.	NM_001034194	Q12883|Q4W5P5|Q86Y41|Q86Y48	Silent	SNP	ENST00000243498.5	hg19	CCDS3722.2																																																																																			.	.	.	none		0.393	EXOSC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250708.2	NM_005033		A	122724130	G	A	122724130	2	1	58	1	0	0	0	0	0	0	0	1	5323	1020	36	2		2	EXOSC9	4	122724130	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08	45062770	122724130	68430146	25	3903											
BDP1	55814	hgsc.bcm.edu	37	chr5	70813231	70813231	+	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	gtatgaaaatcaaagtcaggTggttcttgtagaaaaccttc	14	12	9	6	0	3	2	2	1	1	1	4	2	3	2	1	2	1	3	1	2	7	5			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr5:70813231T>A	ENST00000358731.4	+	22	5206	c.4943T>A	c.(4942-4944)gTg>gAg	p.V1648E	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	1648					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)		CAAAGTCAGGTGGTTCTTGTA	0.308																																					p.V1648E		Atlas-SNP	.											.	BDP1	204	.	0			c.T4943A						PASS	.						70	70	70					5																	70813231		1812	4074	5886	SO:0001583	missense	55814	exon22			GTCAGGTGGTTCT	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.4943T>A	chr5.hg19:g.70813231T>A	ENSP00000351575:p.Val1648Glu	43.0	0.0	.		76.0	32.0	.	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	hg19	CCDS43328.1	.	.	.	.	.	.	.	.	.	.	T	2.499	-0.315545	0.05422	.	.	ENSG00000145734	ENST00000358731;ENST00000451951	T	0.11495	2.77	3.38	-3.81	0.04294	.	1.408380	0.05200	N	0.504767	T	0.08846	0.0219	L	0.54323	1.7	0.09310	N	0.999996	B;B	0.25955	0.037;0.138	B;B	0.18561	0.008;0.022	T	0.41662	-0.9496	10	0.56958	D	0.05	.	0.473	0.00535	0.1852:0.283:0.1887:0.3431	.	1648;1648	A6H8Y1;A6H8Y1-2	BDP1_HUMAN;.	E	1648;1228	ENSP00000351575:V1648E	ENSP00000351575:V1648E	V	+	2	0	BDP1	70848987	0.000000	0.05858	0.004000	0.12327	0.069000	0.16628	-0.026000	0.12392	-0.363000	0.08101	0.383000	0.25322	GTG	.	.	.	none		0.308	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429		A	70813231	T	A	70813231	3	1	58	1	0	0	0	0	1	0	0	0	1395	1696	59	5	5029	5	BDP1	5	70813231	Missense_Mutation	SNP	T	TCGA-A4-8517-01A-11D-2396-08		70813231	110102029	26	3904											
VCAN	1462	hgsc.bcm.edu	37	chr5	82836395	82836395	+	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	gtagtttccaagaccgtttcAgggaattcgaggattccacc	10	11	10	10	2	1	1	1	0	0	1	4	4	3	3	4	2	0	3	4	2	3	5			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr5:82836395A>T	ENST00000265077.3	+	8	8138	c.7573A>T	c.(7573-7575)Agg>Tgg	p.R2525W	VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000343200.5_Missense_Mutation_p.R1538W|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR|VCAN-AS1_ENST00000513899.1_RNA	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2525	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)	AGACCGTTTCAGGGAATTCGA	0.403																																					p.R2525W		Atlas-SNP	.											.	VCAN	498	.	0			c.A7573T						PASS	.						53	54	54					5																	82836395		2203	4300	6503	SO:0001583	missense	1462	exon8			CGTTTCAGGGAAT	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.7573A>T	chr5.hg19:g.82836395A>T	ENSP00000265077:p.Arg2525Trp	56.0	0.0	.		56.0	21.0	.	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	hg19	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	A	10.51	1.370274	0.24771	.	.	ENSG00000038427	ENST00000265077;ENST00000343200	T;T	0.34072	1.38;1.38	6.17	-11.7	0.00046	.	1.888030	0.01961	N	0.043346	T	0.17577	0.0422	N	0.16478	0.41	0.09310	N	1	B;B	0.12630	0.006;0.004	B;B	0.11329	0.006;0.003	T	0.16808	-1.0390	10	0.54805	T	0.06	.	4.6375	0.12531	0.2227:0.3575:0.3326:0.0872	.	1538;2525	P13611-2;P13611	.;CSPG2_HUMAN	W	2525;1538	ENSP00000265077:R2525W;ENSP00000340062:R1538W	ENSP00000265077:R2525W	R	+	1	2	VCAN	82872151	0.000000	0.05858	0.000000	0.03702	0.260000	0.26232	-0.702000	0.05069	-2.549000	0.00480	0.533000	0.62120	AGG	.	.	.	none		0.403	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		T	82836395	A	T	82836395	3	4	58	1	0	0	0	0	1	0	0	0	17150	179	7	5	7599	5	VCAN	5	82836395	Missense_Mutation	SNP	A	TCGA-A4-8517-01A-11D-2396-08	12023164	82836395	98078865	27	3905											
PCDHGA3	56112	hgsc.bcm.edu	37	chr5	140724920	140724920	+	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	acagaaactcacatcaccctGcatgtgattgacatcaatga	15	9	6	11	0	3	4	3	3	0	1	3	4	3	4	1	0	2	1	1	0	2	1	rs567477411		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr5:140724920G>T	ENST00000253812.6	+	1	1320	c.1320G>T	c.(1318-1320)ctG>ctT	p.L440L	PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	440	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACATCACCCTGCATGTGATTG	0.502																																					p.L440L		Atlas-SNP	.											.	PCDHGA3	246	.	0			c.G1320T						PASS	.						103	114	110					5																	140724920		2107	4256	6363	SO:0001819	synonymous_variant	56112	exon1			CACCCTGCATGTG	AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"Cadherins / Protocadherins : Clustered"	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.1320G>T	chr5.hg19:g.140724920G>T		176.0	0.0	.		205.0	36.0	.	NM_032011	Q9Y5D4	Silent	SNP	ENST00000253812.6	hg19	CCDS47290.1																																																																																			.	.	.	none		0.502	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916		T	140724920	G	T	140724920	2	4	58	1	0	0	0	0	0	0	0	1	11562	1306	46	4		4	PCDHGA3	5	140724920	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08	57888525	140724920	40190340	28	3906											
TNIP1	10318	hgsc.bcm.edu	37	chr5	150444534	150444534	+	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	gctttacctaacatctttatCccttgcattttttccttcag	7	19	3	12	0	2	0	1	0	1	0	4	0	4	0	3	0	3	2	3	0	3	10			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr5:150444534C>G	ENST00000389378.2	-	2	711	c.123G>C	c.(121-123)ggG>ggC	p.G41G	TNIP1_ENST00000522226.1_Silent_p.G41G|TNIP1_ENST00000315050.7_Silent_p.G41G|TNIP1_ENST00000518977.1_Silent_p.G41G|TNIP1_ENST00000523338.1_Silent_p.G41G|TNIP1_ENST00000524280.1_Silent_p.G41G|TNIP1_ENST00000523200.1_Silent_p.G41G|TNIP1_ENST00000520931.1_Intron|TNIP1_ENST00000521591.1_Silent_p.G41G	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	41					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)			ACATCTTTATCCCTTGCATTT	0.567																																					p.G41G		Atlas-SNP	.											.	TNIP1	51	.	0			c.G123C						PASS	.						170	164	166					5																	150444534		2203	4300	6503	SO:0001819	synonymous_variant	10318	exon2			CTTTATCCCTTGC	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.123G>C	chr5.hg19:g.150444534C>G		151.0	0.0	.		128.0	45.0	.	NM_001252385	A4F1W8|A4F1W9|A4F1X2|A4F1X4|A4F1X5|A4F1X6|A4F1X7|A4F1X9|B7Z699|E7EPY1|E7ET96|O76008|Q05KP3|Q05KP4|Q6N077|Q96EL9|Q99833|Q9H1J3	Silent	SNP	ENST00000389378.2	hg19	CCDS34280.1																																																																																			.	.	.	none		0.567	TNIP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374914.1	NM_006058		G	150444534	C	G	150444534	2	3	58	1	0	0	0	0	0	0	0	1	16326	842	30	4		4	TNIP1	5	150444534	Silent	SNP	C	TCGA-A4-8517-01A-11D-2396-08	9719614	150444534	30470726	29	3907											
WWC1	23286	hgsc.bcm.edu	37	chr5	167833322	167833322	+	Missense_Mutation	SNP	A	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	tggggaaaaggaaaagcaagAtctcattaaggtatgcaagt	17	8	12	4	0	1	1	1	0	1	1	2	3	1	3	0	4	2	3	0	4	8	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr5:167833322A>C	ENST00000265293.4	+	6	1212	c.710A>C	c.(709-711)gAt>gCt	p.D237A	WWC1_ENST00000521089.1_Missense_Mutation_p.D237A	NM_001161661.1|NM_001161662.1|NM_015238.2	NP_001155133.1|NP_001155134.1|NP_056053.1	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	237					cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|hippo signaling (GO:0035329)|negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of MAPK cascade (GO:0043410)|regulation of hippo signaling (GO:0035330)|regulation of intracellular transport (GO:0032386)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(1)|skin(4)	43	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		GAAAAGCAAGATCTCATTAAG	0.458																																					p.D237A		Atlas-SNP	.											.	WWC1	98	.	0			c.A710C						PASS	.						189	179	182					5																	167833322		2203	4300	6503	SO:0001583	missense	23286	exon6			AGCAAGATCTCAT	AF506799	CCDS4366.1, CCDS54945.1	5q34	2014-06-13	2006-11-09		ENSG00000113645	ENSG00000113645		"WW, C2 and coiled-coil domain containing"	29435	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 168"	610533	"WW, C2 and coiled-coil domain containing 1"			10048485, 12559952	Standard	NM_001161661		Approved	KIBRA, KIAA0869, PPP1R168	uc011den.2	Q8IX03	OTTHUMG00000130408	ENST00000265293.4:c.710A>C	chr5.hg19:g.167833322A>C	ENSP00000265293:p.Asp237Ala	184.0	0.0	.		165.0	70.0	.	NM_015238	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Missense_Mutation	SNP	ENST00000265293.4	hg19	CCDS4366.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.2|24.2	4.503944|4.503944	0.85176|0.85176	.|.	.|.	ENSG00000113645|ENSG00000113645	ENST00000265293;ENST00000521089|ENST00000393895;ENST00000524228	T;T|.	0.07800|.	3.16;3.18|.	5.45|5.45	5.45|5.45	0.79879|0.79879	.|.	0.057843|.	0.64402|.	D|.	0.000002|.	T|T	0.75910|0.75910	0.3914|0.3914	M|M	0.78637|0.78637	2.42|2.42	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.60160|.	0.987;0.972;0.978;0.963|.	P;P;P;P|.	0.59012|.	0.85;0.737;0.796;0.63|.	T|T	0.77225|0.77225	-0.2666|-0.2666	10|5	0.52906|.	T|.	0.07|.	.|.	15.5264|15.5264	0.75910|0.75910	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	237;143;143;237|.	Q8IX03-2;F5H498;B3KX05;Q8IX03|.	.;.;.;KIBRA_HUMAN|.	A|S	237|198;13	ENSP00000265293:D237A;ENSP00000427772:D237A|.	ENSP00000265293:D237A|.	D|R	+|+	2|3	0|2	WWC1|WWC1	167765900|167765900	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	9.251000|9.251000	0.95483|0.95483	2.078000|2.078000	0.62432|0.62432	0.459000|0.459000	0.35465|0.35465	GAT|AGA	.	.	.	none		0.458	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238		C	167833322	A	C	167833322	3	2	58	1	0	0	0	0	1	0	0	0	17423	333	12	5	732	5	WWC1	5	167833322	Missense_Mutation	SNP	A	TCGA-A4-8517-01A-11D-2396-08	17388788	167833322	13081938	30	3908											
DDR1	780	hgsc.bcm.edu	37	chr6	30865203	30865203	+	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	catgtcgaggctcaaggaccCaaacatcattcggctgctgg	10	8	11	12	2	2	0	2	0	0	0	4	2	2	1	1	4	2	3	1	4	2	1	rs541302814		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr6:30865203C>A	ENST00000324771.8	+	17	2593	c.2045C>A	c.(2044-2046)cCa>cAa	p.P682Q	DDR1_ENST00000454612.2_Missense_Mutation_p.P645Q|DDR1_ENST00000376570.4_Missense_Mutation_p.P645Q|DDR1_ENST00000361741.4_Missense_Mutation_p.P349Q|DDR1_ENST00000376575.3_Missense_Mutation_p.P688Q|DDR1_ENST00000418800.2_Missense_Mutation_p.P645Q|DDR1_ENST00000446312.1_3'UTR|DDR1_ENST00000376568.3_Missense_Mutation_p.P682Q|DDR1_ENST00000376567.2_Missense_Mutation_p.P645Q|DDR1_ENST00000376569.3_Missense_Mutation_p.P645Q|DDR1_ENST00000513240.1_Missense_Mutation_p.P688Q|DDR1_ENST00000452441.1_Missense_Mutation_p.P682Q|DDR1_ENST00000508312.1_Missense_Mutation_p.P663Q			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	682	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	CTCAAGGACCCAAACATCATT	0.547																																					p.P688Q		Atlas-SNP	.											.	DDR1	213	.	0			c.C2063A						PASS	.						103	93	97					6																	30865203		2203	4300	6503	SO:0001583	missense	780	exon14			AGGACCCAAACAT	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.2045C>A	chr6.hg19:g.30865203C>A	ENSP00000318217:p.Pro682Gln	83.0	0.0	.		70.0	25.0	.	NM_013994	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Missense_Mutation	SNP	ENST00000324771.8	hg19	CCDS34385.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.6|28.6	4.933034|4.933034	0.92458|0.92458	.|.	.|.	ENSG00000204580|ENSG00000204580	ENST00000324771;ENST00000418800;ENST00000454612;ENST00000376569;ENST00000376575;ENST00000376570;ENST00000376568;ENST00000452441;ENST00000508312;ENST00000376567;ENST00000513240;ENST00000417521;ENST00000361741|ENST00000484556	D;D;D;D;D;D;D;D;D;D;D;D;D|.	0.91407|.	-2.84;-2.84;-2.84;-2.84;-2.84;-2.84;-2.84;-2.84;-2.84;-2.84;-2.84;-2.84;-2.84|.	5.39|5.39	5.39|5.39	0.77823|0.77823	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);|.	0.060949|.	0.64402|.	D|.	0.000003|.	T|T	0.65852|0.65852	0.2731|0.2731	M|M	0.64997|0.64997	1.995|1.995	0.80722|0.80722	D|D	1|1	D;P;D;D;D|.	0.89917|.	1.0;0.792;1.0;0.981;1.0|.	D;P;D;P;D|.	0.97110|.	0.999;0.643;0.999;0.888;1.0|.	T|T	0.64491|0.64491	-0.6395|-0.6395	10|5	0.56958|.	D|.	0.05|.	.|.	16.6419|16.6419	0.85128|0.85128	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	663;146;414;688;682|.	B7Z2K0;A2ABL4;A2ABM8;Q08345-5;Q08345|.	.;.;.;.;DDR1_HUMAN|.	Q|K	682;645;645;645;688;645;682;682;663;645;688;414;349|39	ENSP00000318217:P682Q;ENSP00000407699:P645Q;ENSP00000406091:P645Q;ENSP00000365753:P645Q;ENSP00000365759:P688Q;ENSP00000365754:P645Q;ENSP00000365752:P682Q;ENSP00000405039:P682Q;ENSP00000422442:P663Q;ENSP00000365751:P645Q;ENSP00000427552:P688Q;ENSP00000398682:P414Q;ENSP00000354844:P349Q|.	ENSP00000318217:P682Q|.	P|Q	+|+	2|1	0|0	DDR1|DDR1	30973182|30973182	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.974000|0.974000	0.67602|0.67602	5.959000|5.959000	0.70339|0.70339	2.525000|2.525000	0.85131|0.85131	0.462000|0.462000	0.41574|0.41574	CCA|CAA	.	.	.	none		0.547	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994		A	30865203	C	A	30865203	3	1	58	1	0	0	0	0	1	0	0	0	4338	594	21	4	2117	4	DDR1	6	30865203	Missense_Mutation	SNP	C	TCGA-A4-8517-01A-11D-2396-08		30865203	140249864	31	3909											
BAT4	7918	hgsc.bcm.edu	37	chr6	31632033	31632035	+	In_Frame_Del	DEL	TTC	TTC	-																															tgctgctggtgccttcattaTtcttcttttctttctctttc																								rs367920721		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr6:31632033_31632035delTTC	ENST00000375906.1	-	3	905_907	c.221_223delGAA	c.(220-225)agaata>ata	p.R74del	GPANK1_ENST00000375893.2_In_Frame_Del_p.R74del|GPANK1_ENST00000375896.4_In_Frame_Del_p.R74del|GPANK1_ENST00000375895.2_In_Frame_Del_p.R74del|Y_RNA_ENST00000364337.1_RNA|CSNK2B_ENST00000375866.2_5'Flank|CSNK2B-LY6G5B-1181_ENST00000375880.2_5'Flank|CSNK2B_ENST00000375865.2_5'Flank|GPANK1_ENST00000375900.4_In_Frame_Del_p.R74del|CSNK2B_ENST00000375885.4_5'Flank|CSNK2B_ENST00000375882.2_5'Flank	NM_001199237.1	NP_001186166.1	O95872	GPAN1_HUMAN	G patch domain and ankyrin repeats 1	74							nucleic acid binding (GO:0003676)			central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(7)	12						GCCTTCATTATTCTTCTTTTCTT	0.507																																					p.74_75del		Atlas-INDEL	.											.	GPANK1	19	.	0			c.222_224del						PASS	.		,,,,	3,4259		1,1,2129					,,,,	-2.1	0			84	2,8250		0,2,4124	no	coding,coding,coding,coding,coding	GPANK1	NM_033177.3,NM_001199240.1,NM_001199239.1,NM_001199238.1,NM_001199237.1	,,,,	1,3,6253	A1A1,A1R,RR		0.0242,0.0704,0.04	,,,,	,,,,		5,12509				SO:0001651	inframe_deletion	7918	exon3			.		CCDS4711.1	6p21.3	2013-01-28	2010-11-24	2010-11-24	ENSG00000204438	ENSG00000204438		"Ankyrin repeat domain containing", "G patch domain containing"	13920	protein-coding gene	gene with protein product	"G patch domain containing 10", "ankyrin repeat domain 59"	142610	"HLA-B associated transcript 4"	BAT4		2911734, 2813433	Standard	NM_001199237		Approved	G5, D6S54E, GPATCH10, ANKRD59	uc021yuu.1	O95872	OTTHUMG00000031174	ENST00000375906.1:c.221_223delGAA	chr6.hg19:g.31632036_31632038delTTC	ENSP00000365071:p.Arg74del	95.0	0.0	0		92.0	34.0	0.369565	NM_001199238	A6NG25|B0UXA2|Q5SQ49	In_Frame_Del	DEL	ENST00000375906.1	hg19	CCDS4711.1																																																																																			.	.	.	none		0.507	GPANK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144445.2	NM_033177		-	31632035	TTC	-	31632033	7	5	58	1	0	1	0	1	0	0	0	0	1323	1493	52	0	855	0	BAT4	6	31632033	In_Frame_Del	DEL	TTC	TCGA-A4-8517-01A-11D-2396-08	766830	31632033	139483034	32	3910											
KIFC1	3833	hgsc.bcm.edu	37	chr6	33365943	33365943	+	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	gatggcctggagcctgagaaGgtgagctgggcatggagagc	9	6	19	7	0	0	3	0	2	0	2	0	7	0	4	2	5	3	2	2	5	1	0			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr6:33365943G>T	ENST00000428849.2	+	2	600	c.150G>T	c.(148-150)aaG>aaT	p.K50N		NM_002263.3	NP_002254.2	Q9BW19	KIFC1_HUMAN	kinesin family member C1	50					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						AGCCTGAGAAGGTGAGCTGGG	0.542																																					p.K50N		Atlas-SNP	.											.	KIFC1	47	.	0			c.G150T						PASS	.						60	62	61					6																	33365943		2203	4300	6503	SO:0001630	splice_region_variant	3833	exon2			TGAGAAGGTGAGC	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.150+1G>T	chr6.hg19:g.33365943G>T		60.0	0.0	.		49.0	15.0	.	NM_002263	O60887|Q14834|Q4KMP0|Q5SU09|Q6GMS7|Q6P4A5|Q9UQP7	Missense_Mutation	SNP	ENST00000428849.2	hg19	CCDS34430.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.035950	0.75617	.	.	ENSG00000237649	ENST00000428849;ENST00000450504	T	0.75260	-0.92	4.78	4.78	0.61160	.	0.217099	0.39274	N	0.001409	T	0.54334	0.1852	L	0.34521	1.04	0.43010	D	0.994544	P;P	0.43094	0.799;0.799	B;B	0.40901	0.343;0.343	T	0.61865	-0.6975	10	0.46703	T	0.11	-16.7844	13.1674	0.59579	0.0:0.0:1.0:0.0	.	50;50	B4E063;Q9BW19	.;KIFC1_HUMAN	N	50	ENSP00000393963:K50N	ENSP00000393963:K50N	K	+	3	2	KIFC1	33473921	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	4.761000	0.62243	2.493000	0.84123	0.455000	0.32223	AAG	.	.	.	none		0.542	KIFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076417.1	NM_002263	Missense_Mutation	T	33365943	G	T	33365943	5	4	58	1	0	0	0	0	0	0	1	0	8319	1014	35	4	156	4	KIFC1	6	33365943	Splice_Site	SNP	G	TCGA-A4-8517-01A-11D-2396-08	1733910	33365943	137749124	33	3911											
CUL9	23113	hgsc.bcm.edu	37	chr6	43153712	43153713	+	Missense_Mutation	DNP	TC	TC	CT																															gatcccaggaaagctgctttTctccttggtgaagcgctacc																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr6:43153712_43153713TC>CT	ENST00000252050.4	+	4	854_855	c.770_771TC>CT	c.(769-771)tTC>tCT	p.F257S	CUL9_ENST00000354495.3_Missense_Mutation_p.F257S|CUL9_ENST00000372647.2_Missense_Mutation_p.F257S	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	257					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						AAGCTGCTTTTCTCCTTGGTGA	0.53																																					p.F257S|p.F257F		Atlas-SNP	.											.	CUL9	248	.	0			c.T770C|c.C771T						PASS	.																																			SO:0001583	missense	23113	exon4			TGCTTTTCTCCTT|GCTTTTCTCCTTG	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"parkin-like cytoplasmic p53 binding protein", "p53-associated parkin-like cytoplasmic protein"	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	Exception_encountered	chr6.hg19:g.43153712_43153713delinsCT	ENSP00000252050:p.Phe257Ser	66.0|67.0	0.0	.		69.0|71.0	28.0|30.0	.	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation|Silent	SNP	ENST00000252050.4	hg19	CCDS4890.1																																																																																			.	.	.	none		0.53	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		CT	43153713	TC	CT	43153712	3	2	58	1	0	0	0	0	1	0	0	0	4063	1783	62	3	780	3	CUL9	6	43153712	Missense_Mutation	DNP	TC	TCGA-A4-8517-01A-11D-2396-08	9787769	43153712	127961355	34	3912											
PLEKHG1	57480	hgsc.bcm.edu	37	chr6	151117019	151117019	+	Missense_Mutation	SNP	T	T	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	agttccacatttatacccagTattgcactaactatccaagg	13	12	5	11	0	0	0	0	0	0	0	2	0	2	0	3	1	3	3	3	1	6	8			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr6:151117019T>G	ENST00000358517.2	+	5	821	c.610T>G	c.(610-612)Tat>Gat	p.Y204D	PLEKHG1_ENST00000367328.1_Missense_Mutation_p.Y204D			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	204	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						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)		TTATACCCAGTATTGCACTAA	0.358																																					p.Y204D		Atlas-SNP	.											.	PLEKHG1	97	.	0			c.T610G						PASS	.						161	148	152					6																	151117019		2203	4300	6503	SO:0001583	missense	57480	exon6			ACCCAGTATTGCA	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.610T>G	chr6.hg19:g.151117019T>G	ENSP00000351318:p.Tyr204Asp	127.0	0.0	.		114.0	48.0	.	NM_001029884	Q5T1F2	Missense_Mutation	SNP	ENST00000358517.2	hg19	CCDS34552.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.310648	0.81358	.	.	ENSG00000120278	ENST00000367328;ENST00000535018;ENST00000358517	D;D	0.82255	-1.59;-1.59	5.58	5.58	0.84498	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	D	0.94503	0.8230	H	0.98818	4.34	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.96775	0.9571	10	0.87932	D	0	.	15.756	0.78025	0.0:0.0:0.0:1.0	.	11;204;204	Q5EBL9;Q5JYA6;Q9ULL1	.;.;PKHG1_HUMAN	D	204	ENSP00000356297:Y204D;ENSP00000351318:Y204D	ENSP00000351318:Y204D	Y	+	1	0	PLEKHG1	151158712	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.649000	0.83500	2.131000	0.65755	0.533000	0.62120	TAT	.	.	.	none		0.358	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1			G	151117019	T	G	151117019	3	3	58	1	0	0	0	0	1	0	0	0	12075	1638	57	5	624	5	PLEKHG1	6	151117019	Missense_Mutation	SNP	T	TCGA-A4-8517-01A-11D-2396-08	107963307	151117019	19998048	35	3913											
MLLT4	4301	hgsc.bcm.edu	37	chr6	168349109	168349109	+	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	ccagtggccaaattatgaggAaaagccacatatgcacacag	16	6	9	10	0	0	1	0	1	0	0	0	2	0	2	3	2	2	1	3	2	5	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr6:168349109A>T	ENST00000447894.2	+	28	3761	c.3761A>T	c.(3760-3762)gAa>gTa	p.E1254V	MLLT4_ENST00000366806.2_Missense_Mutation_p.E1254V|MLLT4_ENST00000400822.3_Missense_Mutation_p.E1253V|MLLT4_ENST00000392112.1_Missense_Mutation_p.E1237V|MLLT4_ENST00000351017.4_Missense_Mutation_p.E1261V|MLLT4_ENST00000344191.4_Missense_Mutation_p.E1254V|MLLT4_ENST00000392108.3_Missense_Mutation_p.E1254V			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	1254					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)		AATTATGAGGAAAAGCCACAT	0.448			T	MLL	AL																																p.E1254V		Atlas-SNP	.		Dom	yes		6	6q27	4301	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"		L	.,2	MLLT4	351	.	0			c.A3761T						PASS	.						90	84	86					6																	168349109		2203	4300	6503	SO:0001583	missense	4301	exon28			ATGAGGAAAAGCC	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.3761A>T	chr6.hg19:g.168349109A>T	ENSP00000404595:p.Glu1254Val	55.0	0.0	.		53.0	24.0	.	NM_001040000	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Missense_Mutation	SNP	ENST00000447894.2	hg19		.	.	.	.	.	.	.	.	.	.	A	17.88	3.496251	0.64186	.	.	ENSG00000130396	ENST00000344191;ENST00000351017;ENST00000392108;ENST00000366806;ENST00000392112;ENST00000341575;ENST00000400822;ENST00000447894	T;T;T;T;T;T;T	0.04970	3.73;3.62;3.72;3.72;3.52;3.62;3.62	5.52	5.52	0.82312	.	0.343079	0.30392	N	0.009726	T	0.05686	0.0149	L	0.57536	1.79	0.46954	D	0.999266	P;P;P;B	0.40376	0.556;0.683;0.715;0.305	B;B;B;B	0.40602	0.179;0.334;0.244;0.133	T	0.09164	-1.0687	10	0.62326	D	0.03	-23.1008	15.6454	0.77046	1.0:0.0:0.0:0.0	.	1254;1253;1254;1238	P55196;P55196-5;P55196-6;P55196-2	AFAD_HUMAN;.;.;.	V	1254;1261;1254;1254;1237;1254;1253;1254	ENSP00000341118:E1254V;ENSP00000252692:E1261V;ENSP00000375956:E1254V;ENSP00000355771:E1254V;ENSP00000375960:E1237V;ENSP00000383623:E1253V;ENSP00000404595:E1254V	ENSP00000345834:E1254V	E	+	2	0	MLLT4	168091958	1.000000	0.71417	0.894000	0.35097	0.875000	0.50365	5.595000	0.67563	2.084000	0.62774	0.533000	0.62120	GAA	.	.	.	none		0.448	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936		T	168349109	A	T	168349109	3	4	58	1	0	0	0	0	1	0	0	0	9636	246	9	5	3871	5	MLLT4	6	168349109	Missense_Mutation	SNP	A	TCGA-A4-8517-01A-11D-2396-08	17232090	168349109	2765958	36	3914											
OGDH	4967	hgsc.bcm.edu	37	chr7	44747234	44747234	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggtgcagaagtaccccaaTgctgagctggcctggtgcca	9	7	14	11	0	0	2	0	1	0	1	0	3	0	2	4	3	5	4	4	3	3	1			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr7:44747234T>C	ENST00000222673.5	+	22	2892	c.2850T>C	c.(2848-2850)aaT>aaC	p.N950N	OGDH_ENST00000449767.1_Silent_p.N946N|OGDH_ENST00000447398.1_Silent_p.N961N|OGDH_ENST00000444676.1_Silent_p.N965N|OGDH_ENST00000439616.2_Silent_p.N800N|OGDH_ENST00000543843.1_Silent_p.N901N	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	950					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)	AGTACCCCAATGCTGAGCTGG	0.567																																					p.N950N		Atlas-SNP	.											.	OGDH	145	.	0			c.T2850C						PASS	.						130	115	120					7																	44747234		2203	4300	6503	SO:0001819	synonymous_variant	4967	exon22			CCCCAATGCTGAG	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.2850T>C	chr7.hg19:g.44747234T>C		186.0	0.0	.		239.0	66.0	.	NM_002541	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Silent	SNP	ENST00000222673.5	hg19	CCDS34627.1																																																																																			.	.	.	none		0.567	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1			C	44747234	T	C	44747234	2	2	58	1	0	0	0	0	0	0	0	1	10846	1461	51	3		3	OGDH	7	44747234	Silent	SNP	T	TCGA-A4-8517-01A-11D-2396-08		44747234	114391429	37	3915											
SSPO	23145	hgsc.bcm.edu	37	chr7	149502569	149502569	+	RNA	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	tgccttgccccgggagggggCcctggctggcgcagtcgttc	2	8	17	14	3	0	0	0	0	0	0	2	1	0	1	4	5	2	3	4	5	0	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr7:149502569C>A	ENST00000378016.2	+	0	8382							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)			CGGGAGGGGGCCCTGGCTGGC	0.677																																					p.G2794G		Atlas-SNP	.											.	.	.	.	0			c.C8382A						PASS	.						35	41	39					7																	149502569		1903	4106	6009			23145	exon57			AGGGGGCCCTGGC	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149502569C>A		69.0	0.0	.		85.0	16.0	.	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	hg19																																																																																				.	.	.	none		0.677	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				A	149502569	C	A	149502569	1	1	58	0	1	0	0	0	0	0	0	0	15201	726	26	4		4	SSPO	7	149502569	RNA	SNP	C	TCGA-A4-8517-01A-11D-2396-08	104755335	149502569	9636094	38	3916											
UBE3C	9690	hgsc.bcm.edu	37	chr7	156963038	156963038	+	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	atttgatcgctgtgctacctTgtcacagtccgggggcgctt	5	13	12	11	3	1	1	1	1	0	0	3	1	2	1	2	2	2	3	2	2	1	4			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr7:156963038T>A	ENST00000348165.5	+	4	596	c.236T>A	c.(235-237)tTg>tAg	p.L79*	UBE3C_ENST00000389103.4_Nonsense_Mutation_p.L36*	NM_014671.2	NP_055486.2	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	79					protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(2)|endometrium(3)|kidney(16)|large_intestine(13)|lung(25)|ovary(2)|prostate(1)|urinary_tract(1)	63		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		TGTGCTACCTTGTCACAGTCC	0.393																																					p.L79X		Atlas-SNP	.											.	UBE3C	124	.	0			c.T236A						PASS	.						157	154	155					7																	156963038		2203	4300	6503	SO:0001587	stop_gained	9690	exon4			CTACCTTGTCACA	AK127280	CCDS34789.1	7q36.3	2004-05-04			ENSG00000009335	ENSG00000009335			16803	protein-coding gene	gene with protein product		614454				7584026, 11278995	Standard	NM_014671		Approved	KIAA0010, KIAA10	uc010lqs.3	Q15386	OTTHUMG00000157239	ENST00000348165.5:c.236T>A	chr7.hg19:g.156963038T>A	ENSP00000309198:p.Leu79*	97.0	0.0	.		158.0	43.0	.	NM_014671	A4D235|A6NCP3|Q8TC15|Q96CR4|Q9UDU3	Nonsense_Mutation	SNP	ENST00000348165.5	hg19	CCDS34789.1	.	.	.	.	.	.	.	.	.	.	T	8.672	0.903131	0.17760	.	.	ENSG00000009335	ENST00000348165;ENST00000389103	.	.	.	4.82	1.18	0.20946	.	0.609361	0.15952	N	0.236699	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	.	6.478	0.22047	0.0:0.3795:0.0:0.6205	.	.	.	.	X	79;36	.	ENSP00000309198:L79X	L	+	2	0	UBE3C	156655799	0.001000	0.12720	0.000000	0.03702	0.007000	0.05969	1.040000	0.30278	-0.027000	0.13873	0.528000	0.53228	TTG	.	.	.	none		0.393	UBE3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348108.1	NM_014671		A	156963038	T	A	156963038	4	1	58	1	0	0	0	0	0	1	0	0	16893	1821	63	5	250	5	UBE3C	7	156963038	Nonsense_Mutation	SNP	T	TCGA-A4-8517-01A-11D-2396-08	7460469	156963038	2175625	39	3917											
KIF13B	23303	hgsc.bcm.edu	37	chr8	28991587	28991587	+	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	tcaaagacaaccatgcagtgCggctccttgctgacggaaga	12	7	11	11	2	1	3	1	1	0	2	2	4	2	4	2	2	4	3	2	2	3	1			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr8:28991587C>T	ENST00000524189.1	-	22	2792	c.2754G>A	c.(2752-2754)ccG>ccA	p.P918P	CTD-2647L4.1_ENST00000523661.1_RNA	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	918					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)		CCATGCAGTGCGGCTCCTTGC	0.458																																					p.P918P		Atlas-SNP	.											.	KIF13B	192	.	0			c.G2754A						PASS	.						60	60	60					8																	28991587		1999	4166	6165	SO:0001819	synonymous_variant	23303	exon22			GCAGTGCGGCTCC	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.2754G>A	chr8.hg19:g.28991587C>T		37.0	0.0	.		52.0	19.0	.	NM_015254	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Silent	SNP	ENST00000524189.1	hg19	CCDS55217.1																																																																																			.	.	.	none		0.458	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1			T	28991587	C	T	28991587	2	4	58	1	0	0	0	0	0	0	0	1	8282	755	27	1		1	KIF13B	8	28991587	Silent	SNP	C	TCGA-A4-8517-01A-11D-2396-08		28991587	117372435	40	3918											
DDX58	23586	hgsc.bcm.edu	37	chr9	32467853	32467868	+	Frame_Shift_Del	DEL	AGGTGGCAATCAGAAT	AGGTGGCAATCAGAAT	-																															aatgccttcatcagcaactgAggtggcaatcagaatattgt																								rs61757209	byFrequency	TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	AGGTGGCAATCAGAAT	AGGTGGCAATCAGAAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr9:32467853_32467868delAGGTGGCAATCAGAAT	ENST00000379883.2	-	15	2234_2249	c.2077_2092delATTCTGATTGCCACCT	c.(2077-2094)attctgattgccacctcafs	p.ILIATS693fs	DDX58_ENST00000542096.1_Frame_Shift_Del_p.ILIATS622fs|DDX58_ENST00000379868.1_Frame_Shift_Del_p.ILIATS490fs|DDX58_ENST00000545044.1_Frame_Shift_Del_p.ILIATS490fs|DDX58_ENST00000379882.1_Frame_Shift_Del_p.ILIATS648fs	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	693	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.|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)		TCAGCAACTGAGGTGGCAATCAGAATATTGTGATCT	0.435																																					p.693_698del		Atlas-INDEL	.											.	DDX58	82	.	0			c.2078_2093del						PASS	.																																			SO:0001589	frameshift_variant	23586	exon15			.	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.2077_2092delATTCTGATTGCCACCT	chr9.hg19:g.32467853_32467868delAGGTGGCAATCAGAAT	ENSP00000369213:p.Ile693fs	79.0	0.0	0		56.0	17.0	0.303571	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Frame_Shift_Del	DEL	ENST00000379883.2	hg19	CCDS6526.1																																																																																			.	.	.	none		0.435	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314		-	32467868	AGGTGGCAATCAGAAT	-	32467853	7	5	58	1	0	1	0	1	0	0	0	0	4377	304	11	0	701	0	DDX58	9	32467853	Frame_Shift_Del	DEL	AGGTGGCAATCAGAAT	TCGA-A4-8517-01A-11D-2396-08		32467853	108745578	41	3919											
SPTLC1	10558	hgsc.bcm.edu	37	chr9	94821490	94821490	+	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	ttcgatctcttgttcttttaGtagtcgctcgaggtcagcca	6	16	9	10	3	3	0	1	0	2	0	7	2	3	0	1	1	1	3	1	1	2	6			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr9:94821490G>A	ENST00000262554.2	-	7	666	c.661C>T	c.(661-663)Cta>Tta	p.L221L	SPTLC1_ENST00000482632.1_5'UTR	NM_006415.2	NP_006406.1	O15269	SPTC1_HUMAN	serine palmitoyltransferase, long chain base subunit 1	221					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphinganine biosynthetic process (GO:0046511)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|serine C-palmitoyltransferase complex (GO:0017059)|SPOTS complex (GO:0035339)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			breast(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	14					L-Serine(DB00133)	TGTTCTTTTAGTAGTCGCTCG	0.353																																					p.L221L		Atlas-SNP	.											.	SPTLC1	42	.	0			c.C661T						PASS	.						82	76	78					9																	94821490		2203	4300	6503	SO:0001819	synonymous_variant	10558	exon7			CTTTTAGTAGTCG	Y08685	CCDS6692.1, CCDS6693.1	9q22.31	2014-09-17	2003-12-02		ENSG00000090054	ENSG00000090054	2.3.1.50		11277	protein-coding gene	gene with protein product		605712	"hereditary sensory neuropathy, type 1"	HSN1		9363775	Standard	NM_006415		Approved	LCB1, SPTI, HSAN1, hLCB1	uc004arl.1	O15269	OTTHUMG00000021047	ENST00000262554.2:c.661C>T	chr9.hg19:g.94821490G>A		20.0	0.0	.		25.0	10.0	.	NM_006415	A8K681|Q5VWB4|Q96IX6	Silent	SNP	ENST00000262554.2	hg19	CCDS6692.1																																																																																			.	.	.	none		0.353	SPTLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055553.1	NM_006415		A	94821490	G	A	94821490	2	1	58	1	0	0	0	0	0	0	0	1	15135	1020	36	2		2	SPTLC1	9	94821490	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08	62353637	94821490	46391941	42	3920											
OR1L8	138881	hgsc.bcm.edu	37	chr9	125330116	125330116	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtatataagagaaagcaatgCagagaaaacgagtcaccaaa	21	5	9	6	1	1	2	1	0	0	2	1	5	1	2	1	0	3	3	1	0	8	3	rs377120372		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr9:125330116C>T	ENST00000304865.2	-	1	722	c.641G>A	c.(640-642)tGc>tAc	p.C214Y		NM_001004454.1	NP_001004454.1	Q8NGR8	OR1L8_HUMAN	olfactory receptor, family 1, subfamily L, member 8	214						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						GAAAGCAATGCAGAGAAAACG	0.438																																					p.C214Y		Atlas-SNP	.											.	OR1L8	90	.	0			c.G641A						PASS	.						77	67	71					9																	125330116		2203	4300	6503	SO:0001583	missense	138881	exon1			GCAATGCAGAGAA		CCDS35124.1	9q33.2	2013-09-20			ENSG00000171496	ENSG00000171496		"GPCR / Class A : Olfactory receptors"	15110	protein-coding gene	gene with protein product							Standard	NM_001004454		Approved		uc004bmp.1	Q8NGR8	OTTHUMG00000020609	ENST00000304865.2:c.641G>A	chr9.hg19:g.125330116C>T	ENSP00000306607:p.Cys214Tyr	33.0	0.0	.		48.0	23.0	.	NM_001004454	A3KFM3|B9EIR6|Q6IF15|Q96R79	Missense_Mutation	SNP	ENST00000304865.2	hg19	CCDS35124.1	.	.	.	.	.	.	.	.	.	.	C	11.71	1.720346	0.30503	.	.	ENSG00000171496	ENST00000304865	T	0.37411	1.2	4.49	-1.53	0.08611	GPCR, rhodopsin-like superfamily (1);	0.418105	0.20181	N	0.097537	T	0.49745	0.1575	L	0.55213	1.73	0.28899	N	0.893404	P	0.38167	0.621	P	0.55871	0.786	T	0.58387	-0.7645	10	0.59425	D	0.04	-12.7197	15.5399	0.76035	0.7908:0.2092:0.0:0.0	.	214	Q8NGR8	OR1L8_HUMAN	Y	214	ENSP00000306607:C214Y	ENSP00000306607:C214Y	C	-	2	0	OR1L8	124369937	0.000000	0.05858	0.169000	0.22859	0.363000	0.29612	0.406000	0.21032	-0.042000	0.13535	0.449000	0.29647	TGC	.	.	.	alt		0.438	OR1L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053939.1			T	125330116	C	T	125330116	3	4	58	1	0	0	0	0	1	0	0	0	10974	710	25	2	292	2	OR1L8	9	125330116	Missense_Mutation	SNP	C	TCGA-A4-8517-01A-11D-2396-08	30508626	125330116	15883315	43	3921											
NUDT5	11164	hgsc.bcm.edu	37	chr10	12226925	12226925	+	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	atccatgtacgttgttttttCaagcttgacccattttcctt	7	19	5	10	1	1	1	1	1	0	0	3	1	3	1	3	0	2	4	3	0	2	9			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr10:12226925C>G	ENST00000491614.1	-	3	489	c.94G>C	c.(94-96)Gaa>Caa	p.E32Q	NUDT5_ENST00000378952.3_5'UTR|NUDT5_ENST00000378940.3_Missense_Mutation_p.E32Q|NUDT5_ENST00000378927.3_Missense_Mutation_p.E32Q|NUDT5_ENST00000537776.1_Missense_Mutation_p.E32Q|NUDT5_ENST00000378937.3_Missense_Mutation_p.E32Q			Q9UKK9	NUDT5_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 5	32					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)				GTTGTTTTTTCAAGCTTGACC	0.313																																					p.E32Q		Atlas-SNP	.											.	NUDT5	10	.	0			c.G94C						PASS	.						95	90	92					10																	12226925		2203	4299	6502	SO:0001583	missense	11164	exon3			TTTTTTCAAGCTT	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.94G>C	chr10.hg19:g.12226925C>G	ENSP00000419628:p.Glu32Gln	26.0	0.0	.		35.0	16.0	.	NM_014142	A8K516|Q6IAG0|Q9UH49	Missense_Mutation	SNP	ENST00000491614.1	hg19	CCDS7089.1	.	.	.	.	.	.	.	.	.	.	C	14.70	2.614095	0.46631	.	.	ENSG00000165609	ENST00000491614;ENST00000378929;ENST00000378937;ENST00000537776;ENST00000378940;ENST00000378927;ENST00000444732	T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92	5.87	5.87	0.94306	NUDIX hydrolase domain (1);NUDIX hydrolase domain-like (1);	0.044865	0.85682	D	0.000000	T	0.45377	0.1339	L	0.39514	1.22	0.45914	D	0.998752	D;D	0.65815	0.995;0.993	P;P	0.54889	0.763;0.647	T	0.08289	-1.0729	10	0.17832	T	0.49	-36.1269	13.3498	0.60595	0.0:0.9242:0.0:0.0758	.	32;32	A6NCQ0;Q9UKK9	.;NUDT5_HUMAN	Q	32	ENSP00000419628:E32Q;ENSP00000368219:E32Q;ENSP00000445116:E32Q;ENSP00000368222:E32Q;ENSP00000368209:E32Q	ENSP00000368209:E32Q	E	-	1	0	NUDT5	12266931	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.053000	0.57427	2.941000	0.99782	0.655000	0.94253	GAA	.	.	.	none		0.313	NUDT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046811.1			G	12226925	C	G	12226925	3	3	58	1	0	0	0	0	1	0	0	0	10749	835	29	4	597	4	NUDT5	10	12226925	Missense_Mutation	SNP	C	TCGA-A4-8517-01A-11D-2396-08		12226925	123307822	44	3922											
HSPA14	51182	hgsc.bcm.edu	37	chr10	14896200	14896200	+	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	gtgctgaagtagcgaaacatTctttgtcaaccttgggaagt	11	12	11	7	1	2	1	1	1	1	0	2	3	2	2	1	1	4	2	1	1	5	4			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr10:14896200T>A	ENST00000378372.3	+	9	1050	c.811T>A	c.(811-813)Tct>Act	p.S271T		NM_016299.2	NP_057383.2	Q0VDF9	HSP7E_HUMAN	heat shock 70kDa protein 14	271					'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						AGCGAAACATTCTTTGTCAAC	0.373																																					p.S271T		Atlas-SNP	.											.	HSPA14	42	.	0			c.T811A						PASS	.						154	147	149					10																	14896200		2203	4300	6503	SO:0001583	missense	51182	exon9			AAACATTCTTTGT	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.811T>A	chr10.hg19:g.14896200T>A	ENSP00000367623:p.Ser271Thr	98.0	0.0	.		91.0	12.0	.	NM_016299	A8K8F8|B0YIY9|Q9P0X2|Q9UI07	Missense_Mutation	SNP	ENST00000378372.3	hg19	CCDS7103.1	.	.	.	.	.	.	.	.	.	.	T	4.451	0.083454	0.08533	.	.	ENSG00000187522	ENST00000378372	T	0.00949	5.51	5.53	4.37	0.52481	.	0.173267	0.52532	D	0.000061	T	0.00468	0.0015	N	0.01515	-0.825	0.80722	D	1	B	0.14438	0.01	B	0.17433	0.018	T	0.46803	-0.9165	10	0.02654	T	1	-8.9176	11.4861	0.50354	0.0:0.0:0.2868:0.7132	.	271	Q0VDF9	HSP7E_HUMAN	T	271	ENSP00000367623:S271T	ENSP00000367623:S271T	S	+	1	0	HSPA14	14936206	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	2.499000	0.45372	0.916000	0.36871	0.533000	0.62120	TCT	.	.	.	none		0.373	HSPA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046910.1	NM_016299		A	14896200	T	A	14896200	3	1	58	1	0	0	0	0	1	0	0	0	7414	1783	62	5	845	5	HSPA14	10	14896200	Missense_Mutation	SNP	T	TCGA-A4-8517-01A-11D-2396-08	2669275	14896200	120638547	45	3923											
FAM13C	220965	hgsc.bcm.edu	37	chr10	61112192	61112192	+	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	ggcggcgcgtgctcttctacCagagcccctgcgtcggggta	4	8	15	14	5	2	1	0	0	2	1	3	1	2	1	3	4	4	2	3	4	2	3			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr10:61112192C>A	ENST00000373868.2	-	3	249	c.162G>T	c.(160-162)ctG>ctT	p.L54L	FAM13C_ENST00000373867.3_5'UTR|FAM13C_ENST00000435852.2_Silent_p.L54L|FAM13C_ENST00000277705.6_Silent_p.L54L|FAM13C_ENST00000419214.2_Silent_p.L54L|FAM13C_ENST00000422313.2_Silent_p.L54L|FAM13C_ENST00000468840.2_5'UTR|FAM13C_ENST00000442566.3_Silent_p.L54L	NM_198215.3	NP_937858.2	Q8NE31	FA13C_HUMAN	family with sequence similarity 13, member C	54										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						GCTCTTCTACCAGAGCCCCTG	0.502																																					p.L54L		Atlas-SNP	.											.	FAM13C	124	.	0			c.G162T						PASS	.						30	33	32					10																	61112192		2203	4300	6503	SO:0001819	synonymous_variant	220965	exon3			TTCTACCAGAGCC	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.162G>T	chr10.hg19:g.61112192C>A		26.0	0.0	.		37.0	13.0	.	NM_198215	B7ZB77|Q5T631|Q6P2M3|Q99787	Silent	SNP	ENST00000373868.2	hg19	CCDS7255.1																																																																																			.	.	.	none		0.502	FAM13C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048162.2			A	61112192	C	A	61112192	2	1	58	1	0	0	0	0	0	0	0	1	5458	581	21	4		4	FAM13C	10	61112192	Silent	SNP	C	TCGA-A4-8517-01A-11D-2396-08	46215992	61112192	74422555	46	3924											
CPEB3	22849	hgsc.bcm.edu	37	chr10	93999658	93999658	+	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	aggccgatctgcggggagaaAgtgcctccgaagactgggtt	9	7	16	9	3	1	2	0	0	1	2	2	5	2	2	3	4	2	1	3	4	2	1			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr10:93999658A>C	ENST00000265997.4	-	2	622	c.450T>G	c.(448-450)acT>acG	p.T150T	CPEB3_ENST00000412050.4_Silent_p.T150T	NM_014912.4	NP_055727.3	Q8NE35	CPEB3_HUMAN	cytoplasmic polyadenylation element binding protein 3	150	Pro-rich.				3'-UTR-mediated mRNA destabilization (GO:0061158)|cellular response to amino acid stimulus (GO:0071230)|long-term memory (GO:0007616)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation (GO:0017148)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of mRNA polyadenylation (GO:1900365)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|regulation of dendritic spine development (GO:0060998)|regulation of synaptic plasticity (GO:0048167)|translation (GO:0006412)	apical dendrite (GO:0097440)|CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuron projection (GO:0043005)|nucleus (GO:0005634)|synapse (GO:0045202)	mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|translation factor activity, nucleic acid binding (GO:0008135)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0869)				GCGGGGAGAAAGTGCCTCCGA	0.677																																					p.T150T		Atlas-SNP	.											.	CPEB3	43	.	0			c.T450G						PASS	.						39	36	37					10																	93999658		2203	4300	6503	SO:0001819	synonymous_variant	22849	exon2			GGAGAAAGTGCCT	AB023157	CCDS31246.1, CCDS53553.1	10q23.33	2013-02-12			ENSG00000107864	ENSG00000107864		"RNA binding motif (RRM) containing"	21746	protein-coding gene	gene with protein product		610606				10231032, 12672660	Standard	NM_014912		Approved	KIAA0940	uc001khw.2	Q8NE35	OTTHUMG00000018756	ENST00000265997.4:c.450T>G	chr10.hg19:g.93999658A>C		38.0	0.0	.		30.0	9.0	.	NM_014912	Q5T389|Q9NQJ7|Q9Y2E9	Silent	SNP	ENST00000265997.4	hg19	CCDS31246.1																																																																																			.	.	.	none		0.677	CPEB3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049387.2	NM_014912		C	93999658	A	C	93999658	2	2	58	1	0	0	0	0	0	0	0	1	3804	59	3	5		5	CPEB3	10	93999658	Silent	SNP	A	TCGA-A4-8517-01A-11D-2396-08	32887466	93999658	41535089	47	3925											
TLL2	7093	hgsc.bcm.edu	37	chr10	98145849	98145849	+	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	caaacacttcaaactgaaggGagatccggtactgagcgggg	13	6	13	9	2	1	3	1	2	0	1	2	4	2	3	1	4	4	1	1	4	4	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr10:98145849G>C	ENST00000357947.3	-	15	2201	c.1976C>G	c.(1975-1977)tCc>tGc	p.S659C		NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	659	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(15)|lung(22)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	58		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		AAACTGAAGGGAGATCCGGTA	0.517																																					p.S659C		Atlas-SNP	.											.	TLL2	122	.	0			c.C1976G						PASS	.						99	94	95					10																	98145849		2203	4300	6503	SO:0001583	missense	7093	exon15			TGAAGGGAGATCC	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.1976C>G	chr10.hg19:g.98145849G>C	ENSP00000350630:p.Ser659Cys	82.0	0.0	.		71.0	14.0	.	NM_012465	A6NDK0|Q2M1H1|Q6PJN5|Q9UQ00	Missense_Mutation	SNP	ENST00000357947.3	hg19	CCDS7449.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.617588	0.87359	.	.	ENSG00000095587	ENST00000357947	T	0.19669	2.13	4.77	4.77	0.60923	CUB (5);	0.000000	0.45126	D	0.000385	T	0.49406	0.1555	M	0.80332	2.49	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.48269	-0.9050	10	0.42905	T	0.14	.	17.3218	0.87238	0.0:0.0:1.0:0.0	.	659	Q9Y6L7	TLL2_HUMAN	C	659	ENSP00000350630:S659C	ENSP00000350630:S659C	S	-	2	0	TLL2	98135839	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.601000	0.98297	2.651000	0.90000	0.585000	0.79938	TCC	.	.	.	none		0.517	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049608.1			C	98145849	G	C	98145849	3	2	58	1	0	0	0	0	1	0	0	0	15958	1174	41	4	1099	4	TLL2	10	98145849	Missense_Mutation	SNP	G	TCGA-A4-8517-01A-11D-2396-08	4146191	98145849	37388898	48	3926											
GBF1	8729	hgsc.bcm.edu	37	chr10	104139057	104139057	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctagttgctagacctgatgcAcaccctgcacacgcgggcag	9	7	11	14	2	0	2	0	1	0	1	0	2	0	2	2	1	3	5	2	1	2	3			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr10:104139057A>G	ENST00000369983.3	+	34	4768	c.4508A>G	c.(4507-4509)cAc>cGc	p.H1503R		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	1503					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		GACCTGATGCACACCCTGCAC	0.587																																					p.H1503R		Atlas-SNP	.											.	GBF1	142	.	0			c.A4508G						PASS	.						71	64	66					10																	104139057		2203	4300	6503	SO:0001583	missense	8729	exon34			TGATGCACACCCT	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.4508A>G	chr10.hg19:g.104139057A>G	ENSP00000359000:p.His1503Arg	128.0	0.0	.		107.0	13.0	.	NM_004193	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	hg19	CCDS7533.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.132469	0.77662	.	.	ENSG00000107862	ENST00000369983	T	0.12039	2.72	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.36524	0.0970	M	0.71581	2.175	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.981	D;D;D	0.69824	0.959;0.961;0.966	T	0.12889	-1.0530	10	0.72032	D	0.01	-12.8919	15.3201	0.74115	1.0:0.0:0.0:0.0	.	1499;1499;1503	Q149P1;Q149P0;Q92538	.;.;GBF1_HUMAN	R	1503	ENSP00000359000:H1503R	ENSP00000359000:H1503R	H	+	2	0	GBF1	104129047	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.097000	0.94193	2.200000	0.70718	0.459000	0.35465	CAC	.	.	.	none		0.587	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			G	104139057	A	G	104139057	3	3	58	1	0	0	0	0	1	0	0	0	6278	159	6	3	4638	3	GBF1	10	104139057	Missense_Mutation	SNP	A	TCGA-A4-8517-01A-11D-2396-08	5993208	104139057	31395690	49	3927											
LRRC55	219527	hgsc.bcm.edu	37	chr11	56949791	56949792	+	Missense_Mutation	DNP	AA	AA	TC																															aggtgctggatttgcacaacAactccttaatggagctgccc																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr11:56949791_56949792AA>TC	ENST00000497933.1	+	1	571_572	c.424_425AA>TC	c.(424-426)AAc>TCc	p.N142S		NM_001005210.2	NP_001005210.1	Q6ZSA7	LRC55_HUMAN	leucine rich repeat containing 55	112					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						TTTGCACAACAACTCCTTAATG	0.584																																					p.N142Y|p.N142T		Atlas-SNP	.											.	LRRC55	52	.	0			c.A424T|c.A425C						PASS	.																																			SO:0001583	missense	219527	exon1			CACAACAACTCCT|ACAACAACTCCTT		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	Exception_encountered	chr11.hg19:g.56949791_56949792delinsTC	ENSP00000419542:p.Asn142Ser	51.0|50.0	0.0	.		42.0|41.0	16.0	.	NM_001005210	A7E2U7|B2RN81	Missense_Mutation	SNP	ENST00000497933.1	hg19	CCDS31539.1																																																																																			.	.	.	none		0.584	LRRC55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354503.2	NM_001005210		TC	56949792	AA	TC	56949791	3	4	58	1	0	0	0	0	1	0	0	0	9018	130	5	5	426	5	LRRC55	11	56949791	Missense_Mutation	DNP	AA	TCGA-A4-8517-01A-11D-2396-08		56949791	78056725	50	3928											
RAB38	23682	hgsc.bcm.edu	37	chr11	87908439	87908439	+	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	tccacgccgattgtggcccgGtagtgcgaagagaagttctg	8	9	14	10	4	1	1	0	0	1	1	2	4	2	1	3	2	1	2	3	2	3	3			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr11:87908439G>A	ENST00000243662.6	-	1	196	c.114C>T	c.(112-114)taC>taT	p.Y38Y	MIR3166_ENST00000577344.1_RNA	NM_022337.2	NP_071732.1	P57729	RAB38_HUMAN	RAB38, member RAS oncogene family	38					endosome to melanosome transport (GO:0035646)|GTP catabolic process (GO:0006184)|melanosome organization (GO:0032438)|phagosome acidification (GO:0090383)|platelet dense granule organization (GO:0060155)|protein localization to membrane (GO:0072657)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|early endosome (GO:0005769)|melanosome (GO:0042470)|membrane (GO:0016020)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	AP-1 adaptor complex binding (GO:0035650)|AP-3 adaptor complex binding (GO:0035651)|GTP binding (GO:0005525)|GTP-dependent protein binding (GO:0030742)|GTPase activity (GO:0003924)|protein complex binding (GO:0032403)			large_intestine(2)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TTGTGGCCCGGTAGTGCGAAG	0.612																																					p.Y38Y		Atlas-SNP	.											.	RAB38	20	.	0			c.C114T						PASS	.						109	78	88					11																	87908439		2201	4299	6500	SO:0001819	synonymous_variant	23682	exon1			GGCCCGGTAGTGC	AF235022	CCDS8281.1	11q14	2008-05-14			ENSG00000123892	ENSG00000123892		"RAB, member RAS oncogene"	9776	protein-coding gene	gene with protein product		606281				10910072	Standard	NM_022337		Approved	NY-MEL-1	uc001pcj.2	P57729	OTTHUMG00000167288	ENST00000243662.6:c.114C>T	chr11.hg19:g.87908439G>A		71.0	0.0	.		53.0	20.0	.	NM_022337	Q53XK7	Silent	SNP	ENST00000243662.6	hg19	CCDS8281.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.90|19.90	3.912749|3.912749	0.72983|0.72983	.|.	.|.	ENSG00000123892|ENSG00000123892	ENST00000531138|ENST00000526372	.|.	.|.	.|.	5.2|5.2	5.2|5.2	0.72013|0.72013	.|.	.|.	.|.	.|.	.|.	T|T	0.74846|0.74846	0.3770|0.3770	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.73173|0.73173	-0.4066|-0.4066	4|4	.|.	.|.	.|.	-2.7885|-2.7885	18.9316|18.9316	0.92568|0.92568	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	S|I	55|55	.|.	.|.	P|T	-|-	1|2	0|0	RAB38|RAB38	87548087|87548087	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	6.504000|6.504000	0.73704|0.73704	2.691000|2.691000	0.91804|0.91804	0.655000|0.655000	0.94253|0.94253	CCG|ACC	.	.	.	none		0.612	RAB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394015.2			A	87908439	G	A	87908439	2	1	58	1	0	0	0	0	0	0	0	1	12941	1256	44	2		2	RAB38	11	87908439	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08	30958648	87908439	47098077	51	3929											
FAM55D	54827	hgsc.bcm.edu	37	chr11	114450961	114450961	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcattttgactgtagccaaaCtacaggagacaggattccat	13	11	8	9	0	1	2	1	1	0	1	2	4	2	3	2	2	3	1	2	2	3	5			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr11:114450961C>T	ENST00000375478.3	-	5	1172	c.992G>A	c.(991-993)aGt>aAt	p.S331N	NXPE4_ENST00000424261.2_Missense_Mutation_p.S47N	NM_001077639.1	NP_001071107.1	Q6UWF7	NXPE4_HUMAN	neurexophilin and PC-esterase domain family, member 4	331						extracellular vesicular exosome (GO:0070062)											TGTAGCCAAACTACAGGAGAC	0.443																																					p.S331N		Atlas-SNP	.											.	.	.	.	0			c.G992A						PASS	.						187	175	179					11																	114450961		1880	4122	6002	SO:0001583	missense	54827	exon5			GCCAAACTACAGG	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.992G>A	chr11.hg19:g.114450961C>T	ENSP00000364627:p.Ser331Asn	123.0	0.0	.		134.0	54.0	.	NM_001077639	Q6QDB4|Q9NXP5	Missense_Mutation	SNP	ENST00000375478.3	hg19	CCDS41718.1	.	.	.	.	.	.	.	.	.	.	C	7.005	0.555720	0.13436	.	.	ENSG00000137634	ENST00000424261;ENST00000375478	T;T	0.13901	2.55;2.81	5.31	-0.797	0.10909	.	0.305202	0.31519	N	0.007506	T	0.07098	0.0180	L	0.40543	1.245	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.36553	-0.9743	10	0.09338	T	0.73	.	2.9753	0.05935	0.3243:0.2745:0.0:0.4012	.	331	Q6UWF7	FA55D_HUMAN	N	47;331	ENSP00000401503:S47N;ENSP00000364627:S331N	ENSP00000364627:S331N	S	-	2	0	FAM55D	113956171	0.159000	0.22864	0.003000	0.11579	0.936000	0.57629	0.469000	0.22067	0.168000	0.19655	0.655000	0.94253	AGT	.	.	.	none		0.443	NXPE4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399179.1	NM_017678		T	114450961	C	T	114450961	3	4	58	1	0	0	0	0	1	0	0	0	5594	565	20	2	650	2	FAM55D	11	114450961	Missense_Mutation	SNP	C	TCGA-A4-8517-01A-11D-2396-08	26542522	114450961	20555555	52	3930											
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117308640	117308640	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtcttggcctcgatgatcTcgctgatgcgcccagagccc	5	9	13	14	3	2	3	0	2	2	1	4	4	2	3	3	2	2	1	3	2	0	1			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr11:117308640T>C	ENST00000321322.6	-	25	4584	c.4583A>G	c.(4582-4584)gAg>gGg	p.E1528G	DSCAML1_ENST00000527706.1_Missense_Mutation_p.E1258G	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1468	Fibronectin type-III 6. {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)		CTCGATGATCTCGCTGATGCG	0.657																																					p.E1528G		Atlas-SNP	.											.	DSCAML1	286	.	0			c.A4583G						PASS	.						80	62	68					11																	117308640		2201	4296	6497	SO:0001583	missense	57453	exon25			ATGATCTCGCTGA		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.4583A>G	chr11.hg19:g.117308640T>C	ENSP00000315465:p.Glu1528Gly	39.0	0.0	.		28.0	12.0	.	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	hg19	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	T	17.75	3.465316	0.63513	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.56444	0.46;0.46	4.18	4.18	0.49190	Fibronectin, type III (2);Immunoglobulin-like fold (1);	.	.	.	.	T	0.60170	0.2248	M	0.86740	2.835	0.80722	D	1	B	0.18461	0.028	B	0.24394	0.053	T	0.65878	-0.6061	9	0.72032	D	0.01	.	13.7305	0.62785	0.0:0.0:0.0:1.0	.	1468	Q8TD84	DSCL1_HUMAN	G	1258;1528;1235	ENSP00000434335:E1258G;ENSP00000315465:E1528G	ENSP00000315465:E1528G	E	-	2	0	DSCAML1	116813850	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.785000	0.85724	1.878000	0.54408	0.454000	0.30748	GAG	.	.	.	none		0.657	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		C	117308640	T	C	117308640	3	2	58	1	0	0	0	0	1	0	0	0	4771	1551	54	3	1794	3	DSCAML1	11	117308640	Missense_Mutation	SNP	T	TCGA-A4-8517-01A-11D-2396-08	2857679	117308640	17697876	53	3931											
ARF3	377	hgsc.bcm.edu	37	chr12	49334777	49334777	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tccccgagtttcagcttgtaTaggatggtggtctttcctgc	5	15	11	10	1	2	0	1	0	1	0	4	2	4	1	3	3	2	3	3	3	2	5			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr12:49334777T>C	ENST00000256682.4	-	2	436	c.102A>G	c.(100-102)ctA>ctG	p.L34L	ARF3_ENST00000541959.1_Silent_p.L34L|AC073610.5_ENST00000537495.1_5'Flank|ARF3_ENST00000541967.1_5'Flank|RP11-302B13.5_ENST00000398092.4_Silent_p.L34L|ARF3_ENST00000447318.2_Silent_p.L34L	NM_001659.2	NP_001650.1	P61204	ARF3_HUMAN	ADP-ribosylation factor 3	34					GTP catabolic process (GO:0006184)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|lung(2)|skin(1)	4						TCAGCTTGTATAGGATGGTGG	0.552																																					p.L34L	Pancreas(189;1862 2134 4419 30933 49364)	Atlas-SNP	.											.	ARF3	11	.	0			c.A102G						PASS	.						246	205	219					12																	49334777		2203	4300	6503	SO:0001819	synonymous_variant	377	exon2			CTTGTATAGGATG	M74491	CCDS8774.1	12q13.12	2013-01-22			ENSG00000134287	ENSG00000134287		"ADP-ribosylation factors"	654	protein-coding gene	gene with protein product	"small GTP binding protein"	103190				8661066	Standard	NM_001659		Approved		uc001rsr.2	P61204	OTTHUMG00000168080	ENST00000256682.4:c.102A>G	chr12.hg19:g.49334777T>C		228.0	0.0	.		295.0	98.0	.	NM_001659	A8K6G8|B7ZB63|P16587	Silent	SNP	ENST00000256682.4	hg19	CCDS8774.1																																																																																			.	.	.	none		0.552	ARF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258242.2	NM_001659		C	49334777	T	C	49334777	2	2	58	1	0	0	0	0	0	0	0	1	845	1393	49	3		3	ARF3	12	49334777	Silent	SNP	T	TCGA-A4-8517-01A-11D-2396-08		49334777	84517118	54	3932											
CHD8	57680	hgsc.bcm.edu	37	chr14	21870158	21870158	+	Frame_Shift_Del	DEL	G	G	-																															ccttcagattcaatggtgatGgttgtagttcgtcttaacaa																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr14:21870158delG	ENST00000557364.1	-	20	4283	c.4020delC	c.(4018-4020)accfs	p.T1340fs	CHD8_ENST00000555962.1_5'UTR|CHD8_ENST00000430710.3_Frame_Shift_Del_p.T1061fs|CHD8_ENST00000399982.2_Frame_Shift_Del_p.T1340fs			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1340					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)		CAATGGTGATGGTTGTAGTTC	0.428																																					p.I1341fs		Atlas-INDEL	.											.	CHD8	339	.	0			c.4021delA						PASS	.						175	170	172					14																	21870158		2022	4216	6238	SO:0001589	frameshift_variant	57680	exon19			.	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.4020delC	chr14.hg19:g.21870158delG	ENSP00000451601:p.Thr1340fs	151.0	0.0	0		141.0	63.0	0.446809	NM_001170629	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Frame_Shift_Del	DEL	ENST00000557364.1	hg19	CCDS53885.1																																																																																			.	.	.	none		0.428	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920		-	21870158	G	-	21870158	7	5	58	1	0	1	0	1	0	0	0	0	3333	1335	47	0	3801	0	CHD8	14	21870158	Frame_Shift_Del	DEL	G	TCGA-A4-8517-01A-11D-2396-08		21870158	85479382	55	3933											
SYNE2	23224	hgsc.bcm.edu	37	chr14	64633956	64633956	+	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	attttttaaaaatagaatcaTgtgctggcactgacagccca	14	12	7	8	0	1	2	1	1	0	1	1	2	1	2	1	1	2	2	1	1	5	4			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr14:64633956T>A	ENST00000344113.4	+	91	16823	c.16611T>A	c.(16609-16611)caT>caA	p.H5537Q	SYNE2_ENST00000555002.1_Missense_Mutation_p.H2171Q|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000358025.3_Missense_Mutation_p.H5537Q|SYNE2_ENST00000357395.3_Missense_Mutation_p.H1922Q|SYNE2_ENST00000554584.1_Missense_Mutation_p.H5412Q|SYNE2_ENST00000394768.2_Missense_Mutation_p.H1922Q	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5537					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)		AATAGAATCATGTGCTGGCAC	0.378																																					p.H5537Q		Atlas-SNP	.											.	SYNE2	577	.	0			c.T16611A						PASS	.						46	47	46					14																	64633956		2203	4300	6503	SO:0001583	missense	23224	exon91			GAATCATGTGCTG	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.16611T>A	chr14.hg19:g.64633956T>A	ENSP00000341781:p.His5537Gln	29.0	0.0	.		51.0	14.0	.	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	T	3.587	-0.084487	0.07097	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	T;T;T;T;T;T	0.55234	0.84;4.13;0.83;0.53;4.19;4.13	5.78	-2.01	0.07410	.	0.246206	0.28241	N	0.016071	T	0.32224	0.0822	L	0.39245	1.2	0.58432	D	0.999999	B;B;B;B	0.25772	0.004;0.112;0.008;0.134	B;B;B;B	0.26864	0.007;0.032;0.011;0.074	T	0.04053	-1.0981	10	0.17369	T	0.5	.	3.6697	0.08269	0.1137:0.4232:0.1908:0.2723	.	1922;5412;5537;5537	Q8WXH0-7;G3V5X4;Q8WXH0;Q8WXH0-2	.;.;SYNE2_HUMAN;.	Q	5537;1922;5537;5412;5418;2171;1922	ENSP00000350719:H5537Q;ENSP00000349969:H1922Q;ENSP00000341781:H5537Q;ENSP00000452570:H5412Q;ENSP00000450831:H2171Q;ENSP00000378249:H1922Q	ENSP00000261678:H5418Q	H	+	3	2	SYNE2	63703709	0.000000	0.05858	0.820000	0.32676	0.932000	0.56968	-3.318000	0.00514	-0.265000	0.09352	0.533000	0.62120	CAT	.	.	.	none		0.378	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		A	64633956	T	A	64633956	3	1	58	1	0	0	0	0	1	0	0	0	15458	1461	51	5	16969	5	SYNE2	14	64633956	Missense_Mutation	SNP	T	TCGA-A4-8517-01A-11D-2396-08	42763798	64633956	42715584	56	3934											
FBLN5	10516	hgsc.bcm.edu	37	chr14	92349359	92349359	+	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	gggcaggagcagaagtatgtGccgggctggttcacacactc	9	7	15	10	1	1	1	1	0	0	1	2	2	1	2	1	4	2	5	1	4	2	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr14:92349359G>T	ENST00000342058.4	-	8	1394	c.801C>A	c.(799-801)ggC>ggA	p.G267G	FBLN5_ENST00000267620.10_Silent_p.G308G|FBLN5_ENST00000556154.1_Silent_p.G272G	NM_006329.3	NP_006320.2	Q9UBX5	FBLN5_HUMAN	fibulin 5	267	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell-matrix adhesion (GO:0007160)|elastic fiber assembly (GO:0048251)|extracellular matrix organization (GO:0030198)|protein localization to cell surface (GO:0034394)|regulation of cell growth (GO:0001558)|regulation of removal of superoxide radicals (GO:2000121)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	28		all_cancers(154;0.0722)				AGAAGTATGTGCCGGGCTGGT	0.562																																					p.G267G		Atlas-SNP	.											.	FBLN5	60	.	0			c.C801A						PASS	.						140	120	126					14																	92349359		2203	4300	6503	SO:0001819	synonymous_variant	10516	exon8			GTATGTGCCGGGC	AJ133490	CCDS9898.1	14q31	2014-09-17				ENSG00000140092		"Fibulins"	3602	protein-coding gene	gene with protein product		604580				10640802	Standard	NM_006329		Approved	EVEC, UP50, DANCE, ARMD3	uc001xzx.4	Q9UBX5		ENST00000342058.4:c.801C>A	chr14.hg19:g.92349359G>T		97.0	0.0	.		93.0	39.0	.	NM_006329	O75966|Q6IAL4|Q6UWA3	Silent	SNP	ENST00000342058.4	hg19	CCDS9898.1																																																																																			.	.	.	none		0.562	FBLN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411787.1			T	92349359	G	T	92349359	2	4	58	1	0	0	0	0	0	0	0	1	5707	1306	46	4		4	FBLN5	14	92349359	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08	27715403	92349359	15000181	57	3935											
VPS39	23339	hgsc.bcm.edu	37	chr15	42462024	42462024	+	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	aactgctttctgtagtctgtGggcagcaggtcagggtacag	8	11	14	8	0	3	0	1	0	2	0	3	0	3	0	0	3	4	5	0	3	3	3			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr15:42462024G>T	ENST00000348544.4	-	13	1163	c.1164C>A	c.(1162-1164)ccC>ccA	p.P388P	VPS39_ENST00000318006.5_Silent_p.P377P			Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39 homolog (S. cerevisiae)	388					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	endosome (GO:0005768)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	small GTPase regulator activity (GO:0005083)			breast(2)|kidney(5)|large_intestine(4)|lung(8)|ovary(1)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;3.05e-06)		TGTAGTCTGTGGGCAGCAGGT	0.493																																					p.P377P		Atlas-SNP	.											.	VPS39	53	.	0			c.C1131A						PASS	.						110	104	106					15																	42462024		2203	4299	6502	SO:0001819	synonymous_variant	23339	exon12			GTCTGTGGGCAGC	AF280814	CCDS10083.1, CCDS73710.1	15q14	2008-02-05	2006-12-19		ENSG00000166887	ENSG00000166887			20593	protein-coding gene	gene with protein product		612188	"vacuolar protein sorting 39 (yeast)"			11448994	Standard	XM_005254259		Approved	KIAA0770, VAM6	uc001zpc.3	Q96JC1	OTTHUMG00000130467	ENST00000348544.4:c.1164C>A	chr15.hg19:g.42462024G>T		89.0	0.0	.		73.0	33.0	.	NM_015289	O94869|Q71SQ6|Q7Z3V3|Q96B93|Q96RM0	Silent	SNP	ENST00000348544.4	hg19	CCDS10083.1																																																																																			.	.	.	none		0.493	VPS39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000420472.1	NM_015289		T	42462024	G	T	42462024	2	4	58	1	0	0	0	0	0	0	0	1	17221	1335	47	4		4	VPS39	15	42462024	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08		42462024	60069368	58	3936											
SCAPER	49855	hgsc.bcm.edu	37	chr15	76726602	76726603	+	Frame_Shift_Ins	INS	-	-	TA																															caagccttcaaaaacttgttINStatttgtatttctccccaaa																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr15:76726602_76726603insTA	ENST00000563290.1	-	26	3222_3223	c.3127_3128insTA	c.(3127-3129)aaafs	p.K1043fs	SCAPER_ENST00000538941.2_Frame_Shift_Ins_p.K797fs|SCAPER_ENST00000324767.7_Frame_Shift_Ins_p.K1043fs			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	1043						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						AAAAACTTGTTTATTTGTATTT	0.371																																					p.K1043fs		Atlas-INDEL	.											.	SCAPER	160	.	0			c.3128_3129insTA						PASS	.																																			SO:0001589	frameshift_variant	49855	exon25			.	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.3126_3127dupTA	chr15.hg19:g.76726603_76726604dupTA	ENSP00000454973:p.Lys1043fs	91.0	0.0	0		95.0	36.0	0.378947	NM_020843	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Frame_Shift_Ins	INS	ENST00000563290.1	hg19	CCDS53962.1																																																																																			.	.	.	none		0.371	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843		TA	76726603	-	TA	76726602	7	5	58	1	0	1	1	0	0	0	0	0	13891	1841	64	0	1102	0	SCAPER	15	76726602	Frame_Shift_Ins	INS	-	TCGA-A4-8517-01A-11D-2396-08	34264578	76726602	25804790	59	3937											
SMG1	23049	hgsc.bcm.edu	37	chr16	18856931	18856931	+	Frame_Shift_Del	DEL	C	C	-																															gcaaatacgatgggcttcatCaaagctgtgtgcttctccct																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr16:18856931delC	ENST00000446231.2	-	39	6451	c.6039delG	c.(6037-6039)ttgfs	p.L2013fs	SMG1_ENST00000389467.3_Frame_Shift_Del_p.L2013fs			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2013					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						TGGGCTTCATCAAAGCTGTGT	0.388																																					p.M2014X		Atlas-INDEL	.											.	SMG1	401	.	0			c.6040delA						PASS	.						130	120	123					16																	18856931		1903	4130	6033	SO:0001589	frameshift_variant	23049	exon39			.	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.6039delG	chr16.hg19:g.18856931delC	ENSP00000402515:p.Leu2013fs	99.0	0.0	0		140.0	84.0	0.6	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Frame_Shift_Del	DEL	ENST00000446231.2	hg19	CCDS45430.1																																																																																			.	.	.	none		0.388	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		-	18856931	C	-	18856931	7	5	58	1	0	1	0	1	0	0	0	0	14808	825	29	0	5046	0	SMG1	16	18856931	Frame_Shift_Del	DEL	C	TCGA-A4-8517-01A-11D-2396-08		18856931	71497822	60	3938											
NOL3	8996	hgsc.bcm.edu	37	chr16	67208730	67208730	+	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	cctctaaagaggctgaaccgGagccggagccagagccagag	12	3	14	12	2	1	4	0	1	1	3	1	6	1	6	5	3	4	1	5	3	3	1			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr16:67208730G>A	ENST00000568146.1	+	3	545	c.492G>A	c.(490-492)cgG>cgA	p.R164R	KIAA0895L_ENST00000563831.2_5'Flank|NOL3_ENST00000564053.1_Missense_Mutation_p.E230K|NOL3_ENST00000268605.7_Missense_Mutation_p.E168K|NOL3_ENST00000432069.2_Missense_Mutation_p.E168K			O60936	NOL3_HUMAN	nucleolar protein 3 (apoptosis repressor with CARD domain)	164					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)			ovary(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.0335)|all cancers(182;0.184)		GGctgaaccggagccggagcc	0.682																																					p.E230K		Atlas-SNP	.											.	NOL3	6	.	0			c.G688A						PASS	.						20	30	26					16																	67208730		2034	4211	6245	SO:0001819	synonymous_variant	8996	exon5			GAACCGGAGCCGG	AF043244	CCDS42176.1, CCDS58473.1, CCDS61960.1	16q22.1	2008-08-27				ENSG00000140939			7869	protein-coding gene	gene with protein product		605235				9560245	Standard	NM_001276312		Approved	ARC, NOP30, MYP, CARD2	uc010vjd.3	O60936		ENST00000568146.1:c.492G>A	chr16.hg19:g.67208730G>A		32.0	0.0	.		36.0	5.0	.	NM_001276319	B4DFL0|O60937	Missense_Mutation	SNP	ENST00000568146.1	hg19	CCDS58473.1	.	.	.	.	.	.	.	.	.	.	g	11.53	1.665514	0.29604	.	.	ENSG00000140939	ENST00000432069;ENST00000268605	T;T	0.72167	-0.63;-0.63	1.38	0.29	0.15728	.	2.201480	0.01451	N	0.015497	T	0.50205	0.1602	.	.	.	0.09310	N	1	B	0.23854	0.092	B	0.12837	0.008	T	0.29912	-0.9996	9	0.17369	T	0.5	-9.4969	4.2104	0.10509	0.2347:0.0:0.7653:0.0	.	230	B4DFL0	.	K	168	ENSP00000399831:E168K;ENSP00000268605:E168K	ENSP00000268605:E168K	E	+	1	0	NOL3	65766231	0.024000	0.19004	0.003000	0.11579	0.030000	0.12068	0.709000	0.25734	0.155000	0.19261	0.430000	0.28490	GAG	.	.	.	none		0.682	NOL3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422746.1			A	67208730	G	A	67208730	2	1	58	1	0	0	0	0	0	0	0	1	10530	1175	41	2		2	NOL3	16	67208730	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08	48351799	67208730	23146023	61	3939											
ADAD2	161931	hgsc.bcm.edu	37	chr16	84228709	84228709	+	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	catgagcagcgctgcgcagcGttggtgagcgccggctttga	6	8	16	11	5	0	3	0	3	0	0	0	3	0	3	1	2	5	5	1	2	0	2	rs369199969		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr16:84228709G>A	ENST00000315906.5	+	4	694	c.642G>A	c.(640-642)gcG>gcA	p.A214A	RP11-486L19.2_ENST00000565643.1_RNA|RP11-486L19.2_ENST00000561900.1_RNA|ADAD2_ENST00000268624.3_Silent_p.A286A|RP11-486L19.2_ENST00000536986.1_RNA|RP11-486L19.2_ENST00000569834.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	214					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						GCTGCGCAGCGTTGGTGAGCG	0.637																																					p.A286A		Atlas-SNP	.											.	ADAD2	46	.	0			c.G858A						PASS	.						45	47	46					16																	84228709		2200	4300	6500	SO:0001819	synonymous_variant	161931	exon5			CGCAGCGTTGGTG	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.642G>A	chr16.hg19:g.84228709G>A		77.0	0.0	.		86.0	21.0	.	NM_139174	B2RCL6|Q8NA94	Silent	SNP	ENST00000315906.5	hg19	CCDS45536.1																																																																																			.	.	.	weak		0.637	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174		A	84228709	G	A	84228709	2	1	58	1	0	0	0	0	0	0	0	1	232	1132	40	1		1	ADAD2	16	84228709	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08	17019979	84228709	6126044	62	3940											
PIP5K1C	23396	hgsc.bcm.edu	37	chr19	3653310	3653310	+	Frame_Shift_Del	DEL	T	T	-																															ggcagtcccgctgcagcgtcTtgaccagggcgctgaaggtg																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr19:3653310delT	ENST00000335312.3	-	7	987	c.899delA	c.(898-900)aagfs	p.K300fs	PIP5K1C_ENST00000587482.1_5'UTR|PIP5K1C_ENST00000589578.1_Frame_Shift_Del_p.K300fs|PIP5K1C_ENST00000537021.1_Frame_Shift_Del_p.K300fs|PIP5K1C_ENST00000539785.1_Frame_Shift_Del_p.K300fs	NM_001195733.1|NM_012398.2	NP_001182662.1|NP_036530.1	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, gamma	300	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				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)		CTGCAGCGTCTTGACCAGGGC	0.692																																					p.K300fs	Esophageal Squamous(135;99 1744 12852 27186 39851)	Atlas-INDEL	.											.	PIP5K1C	63	.	0			c.900delG						PASS	.						39	27	31					19																	3653310		2203	4297	6500	SO:0001589	frameshift_variant	23396	exon7			.	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.899delA	chr19.hg19:g.3653310delT	ENSP00000335333:p.Lys300fs	74.0	0.0	0		67.0	24.0	0.358209	NM_012398	B7Z9E7|C6GIJ7|C6GIJ8|Q7LE07	Frame_Shift_Del	DEL	ENST00000335312.3	hg19	CCDS32872.1																																																																																			.	.	.	none		0.692	PIP5K1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453432.2	NM_012398		-	3653310	T	-	3653310	7	5	58	1	0	1	0	1	0	0	0	0	11948	1609	56	0	1155	0	PIP5K1C	19	3653310	Frame_Shift_Del	DEL	T	TCGA-A4-8517-01A-11D-2396-08		3653310	55475673	63	3941											
ZNF709	163051	hgsc.bcm.edu	37	chr19	12576137	12576137	+	Missense_Mutation	SNP	T	T	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	aaatgaaggccttcccacatTccttacattcataaggtttc	12	13	5	11	0	1	1	1	1	0	0	4	1	3	1	3	2	1	1	3	2	4	6			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr19:12576137T>G	ENST00000397732.3	-	4	770	c.599A>C	c.(598-600)gAa>gCa	p.E200A	CTD-3105H18.18_ENST00000598753.1_Intron|ZNF709_ENST00000428311.1_Missense_Mutation_p.E200A	NM_152601.3	NP_689814.1	Q8N972	ZN709_HUMAN	zinc finger protein 709	200					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						CTTCCCACATTCCTTACATTC	0.413																																					p.E200A	GBM(33;565 669 12371 29134 51667)	Atlas-SNP	.											.	ZNF709	80	.	0			c.A599C						PASS	.						94	100	98					19																	12576137		2202	4300	6502	SO:0001583	missense	163051	exon4			CCACATTCCTTAC	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.599A>C	chr19.hg19:g.12576137T>G	ENSP00000380840:p.Glu200Ala	92.0	0.0	.		81.0	30.0	.	NM_152601	A8K4E6	Missense_Mutation	SNP	ENST00000397732.3	hg19	CCDS42504.1	.	.	.	.	.	.	.	.	.	.	T	17.48	3.399242	0.62177	.	.	ENSG00000242852;ENSG00000196826	ENST00000397732;ENST00000428311	T;T	0.06933	3.24;3.24	2.86	0.618	0.17624	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12305	0.0299	L	0.58354	1.805	0.09310	N	1	B	0.26002	0.139	B	0.40101	0.319	T	0.42378	-0.9455	9	0.59425	D	0.04	.	4.2166	0.10537	0.1786:0.1098:0.0:0.7115	.	200	Q8N972	ZN709_HUMAN	A	200	ENSP00000380840:E200A;ENSP00000404127:E200A	ENSP00000404127:E200A	E	-	2	0	ZNF709;CTD-2192J16.17	12437137	0.001000	0.12720	0.001000	0.08648	0.909000	0.53808	1.145000	0.31577	0.059000	0.16252	0.260000	0.18958	GAA	.	.	.	none		0.413	ZNF709-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344088.1	NM_152601		G	12576137	T	G	12576137	3	3	58	1	0	0	0	0	1	0	0	0	18125	1783	62	5	1330	5	ZNF709	19	12576137	Missense_Mutation	SNP	T	TCGA-A4-8517-01A-11D-2396-08	8922827	12576137	46552846	64	3942											
NOTCH3	4854	hgsc.bcm.edu	37	chr19	15303027	15303027	+	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	ggtgggcaggagcagaggaaGcgtccatcgggccccactga	9	4	17	11	2	0	2	0	1	0	1	2	4	1	4	3	5	2	2	3	5	1	0	rs116044239		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr19:15303027G>T	ENST00000263388.2	-	4	498	c.423C>A	c.(421-423)cgC>cgA	p.R141R		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	141	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.		R -> C (in CADASIL). {ECO:0000269|PubMed:10227618, ECO:0000269|PubMed:10371548, ECO:0000269|PubMed:10854111, ECO:0000269|PubMed:11102981, ECO:0000269|PubMed:11755616, ECO:0000269|PubMed:15229130, ECO:0000269|PubMed:15364702, ECO:0000269|PubMed:16009764, ECO:0000269|PubMed:9388399}.		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)			AGCAGAGGAAGCGTCCATCGG	0.701																																					p.R141R		Atlas-SNP	.											.	NOTCH3	340	.	0			c.C423A						PASS	.						20	22	22					19																	15303027		2201	4296	6497	SO:0001819	synonymous_variant	4854	exon4			GAGGAAGCGTCCA	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.423C>A	chr19.hg19:g.15303027G>T		34.0	0.0	.		28.0	10.0	.	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Silent	SNP	ENST00000263388.2	hg19	CCDS12326.1																																																																																			.	G|0.995;A|0.005	.	alt		0.701	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		T	15303027	G	T	15303027	2	4	58	1	0	0	0	0	0	0	0	1	10557	958	34	4		4	NOTCH3	19	15303027	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08	2726890	15303027	43825956	65	3943											
CLIP3	25999	hgsc.bcm.edu	37	chr19	36515358	36515358	+	Missense_Mutation	SNP	A	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	cccagtgcgctaagcatgagAttgcctgggacgttgtcata	9	10	12	10	2	1	1	1	1	0	1	1	3	1	2	2	1	3	3	2	1	2	4			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr19:36515358A>C	ENST00000360535.4	-	7	1085	c.858T>G	c.(856-858)aaT>aaG	p.N286K	AC002116.7_ENST00000586962.1_RNA|CLIP3_ENST00000593074.1_Missense_Mutation_p.N286K	NM_015526.2	NP_056341.1	Q96DZ5	CLIP3_HUMAN	CAP-GLY domain containing linker protein 3	286					chaperone-mediated protein transport (GO:0072321)|fat cell differentiation (GO:0045444)|membrane biogenesis (GO:0044091)|negative regulation of microtubule polymerization (GO:0031115)|peptidyl-L-cysteine S-palmitoylation (GO:0018230)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endocytosis (GO:0045807)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein phosphorylation (GO:0001934)	early endosome membrane (GO:0031901)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|trans-Golgi network (GO:0005802)|trans-Golgi network membrane (GO:0032588)	ganglioside binding (GO:0035594)|microtubule binding (GO:0008017)			cervix(1)|endometrium(6)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	23	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			TAAGCATGAGATTGCCTGGGA	0.617																																					p.N286K		Atlas-SNP	.											.	CLIP3	53	.	0			c.T858G						PASS	.						122	105	111					19																	36515358		2203	4300	6503	SO:0001583	missense	25999	exon6			CATGAGATTGCCT	AJ427922	CCDS12486.1	19q13.12	2014-08-12			ENSG00000105270	ENSG00000105270		"Ankyrin repeat domain containing"	24314	protein-coding gene	gene with protein product	"CLIP-170-related", "restin-like 1"	607382				11854307	Standard	NM_015526		Approved	CLIPR-59, RSNL1	uc002ocz.2	Q96DZ5	OTTHUMG00000181747	ENST00000360535.4:c.858T>G	chr19.hg19:g.36515358A>C	ENSP00000353732:p.Asn286Lys	122.0	0.0	.		70.0	30.0	.	NM_001199570	A8K0E4|Q8WWL1|Q96C99|Q9UFT7	Missense_Mutation	SNP	ENST00000360535.4	hg19	CCDS12486.1	.	.	.	.	.	.	.	.	.	.	A	8.190	0.795873	0.16327	.	.	ENSG00000105270	ENST00000360535;ENST00000544037;ENST00000534959	T	0.74842	-0.88	5.88	0.203	0.15195	Cytoskeleton-associated protein, Gly-rich domain (1);	0.000000	0.85682	D	0.000000	T	0.47173	0.1431	N	0.17082	0.46	0.52099	D	0.999948	B	0.32781	0.384	B	0.33196	0.159	T	0.46596	-0.9180	10	0.02654	T	1	-19.5733	5.4011	0.16297	0.3499:0.1781:0.472:0.0	.	286	Q96DZ5	CLIP3_HUMAN	K	286;168;262	ENSP00000353732:N286K	ENSP00000353732:N286K	N	-	3	2	CLIP3	41207198	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	0.954000	0.29175	-0.068000	0.12953	0.482000	0.46254	AAT	.	.	.	none		0.617	CLIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457426.1	NM_015526		C	36515358	A	C	36515358	3	2	58	1	0	0	0	0	1	0	0	0	3536	330	12	5	817	5	CLIP3	19	36515358	Missense_Mutation	SNP	A	TCGA-A4-8517-01A-11D-2396-08	21212331	36515358	22613625	66	3944											
CHMP2A	27243	hgsc.bcm.edu	37	chr19	59063432	59063433	+	Frame_Shift_Ins	INS	-	-	T																															tccccatacctctcctcttcINSatcttcctcatcacccatgg																										TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr19:59063432_59063433insT	ENST00000600118.1	-	3	893_894	c.468_469insA	c.(466-471)gatgaafs	p.E157fs	CHMP2A_ENST00000312547.2_Frame_Shift_Ins_p.E157fs|CHMP2A_ENST00000601220.1_Frame_Shift_Ins_p.E157fs			O43633	CHM2A_HUMAN	charged multivesicular body protein 2A	157	Interaction with VPS4B.				endosomal transport (GO:0016197)|establishment of protein localization (GO:0045184)|membrane organization (GO:0061024)|positive regulation of viral release from host cell (GO:1902188)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein domain specific binding (GO:0019904)			endometrium(1)|kidney(1)|large_intestine(3)|lung(2)	7		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		CTCTCCTCTTCATCTTCCTCAT	0.505																																					p.E157fs		Atlas-INDEL	.											.	CHMP2A	25	.	0			c.469_470insA						PASS	.																																			SO:0001589	frameshift_variant	27243	exon4			.	AF042384	CCDS12986.1	19q13.43	2014-09-04	2011-09-21		ENSG00000130724	ENSG00000130724		"Charged multivesicular body proteins"	30216	protein-coding gene	gene with protein product	"putative breast adenocarcinoma marker (32kD)", "VPS2 homolog A (S. cerevisiae)"	610893	"chromatin modifying protein 2A"			15173323, 11559748	Standard	XM_005258746		Approved	BC-2, CHMP2, VPS2, VPS2A	uc002qtk.3	O43633	OTTHUMG00000183547	ENST00000600118.1:c.468_469insA	chr19.hg19:g.59063432_59063433insT	ENSP00000469240:p.Glu157fs	281.0	0.0	0		216.0	80.0	0.37037	NM_198426	B2R4W6|Q3ZTT0	Frame_Shift_Ins	INS	ENST00000600118.1	hg19	CCDS12986.1																																																																																			.	.	.	none		0.505	CHMP2A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467088.1	NM_014453		T	59063433	-	T	59063432	7	5	58	1	0	1	1	0	0	0	0	0	3356	835	29	0	211	0	CHMP2A	19	59063432	Frame_Shift_Ins	INS	-	TCGA-A4-8517-01A-11D-2396-08	22548074	59063432	65551	67	3945											
PYGB	5834	hgsc.bcm.edu	37	chr20	25271238	25271238	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatcttcctggagaactaccGtgtgtccttggctgagaaag	9	11	12	9	1	1	2	0	1	1	2	3	5	3	2	3	2	2	1	3	2	3	3	rs139162483		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr20:25271238G>A	ENST00000216962.4	+	16	2059	c.1949G>A	c.(1948-1950)cGt>cAt	p.R650H		NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN	phosphorylase, glycogen; brain	650					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						GAGAACTACCGTGTGTCCTTG	0.552																																					p.R650H		Atlas-SNP	.											.	PYGB	84	.	0			c.G1949A						PASS	.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	225	198	207		1949	4.1	0.9	20	dbSNP_134	207	0,8600		0,0,4300	no	missense	PYGB	NM_002862.3	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	650/844	25271238	1,13005	2203	4300	6503	SO:0001583	missense	5834	exon16			ACTACCGTGTGTC		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.1949G>A	chr20.hg19:g.25271238G>A	ENSP00000216962:p.Arg650His	231.0	0.0	.		272.0	161.0	.	NM_002862	Q96AK1|Q9NPX8	Missense_Mutation	SNP	ENST00000216962.4	hg19	CCDS13171.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.5|28.5	4.923497|4.923497	0.92319|0.92319	2.27E-4|2.27E-4	0.0|0.0	ENSG00000100994|ENSG00000100994	ENST00000216962|ENST00000428458	D|.	0.93488|.	-3.23|.	4.1|4.1	4.1|4.1	0.47936|0.47936	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.86447|0.86447	0.5935|0.5935	H|H	0.94698|0.94698	3.57|3.57	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.68483|.	0.958|.	D|D	0.90808|0.90808	0.4699|0.4699	10|5	0.66056|.	D|.	0.02|.	-11.4783|-11.4783	16.4812|16.4812	0.84158|0.84158	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	650|.	P11216|.	PYGB_HUMAN|.	H|M	650|69	ENSP00000216962:R650H|.	ENSP00000216962:R650H|.	R|V	+|+	2|1	0|0	PYGB|PYGB	25219238|25219238	1.000000|1.000000	0.71417|0.71417	0.947000|0.947000	0.38551|0.38551	0.941000|0.941000	0.58515|0.58515	7.643000|7.643000	0.83403|0.83403	2.286000|2.286000	0.76751|0.76751	0.563000|0.563000	0.77884|0.77884	CGT|GTG	.	G|1.000;A|0.000	0.000	weak		0.552	PYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078415.2	NM_002862		A	25271238	G	A	25271238	3	1	58	1	0	0	0	0	1	0	0	0	12873	1145	40	1	2011	1	PYGB	20	25271238	Missense_Mutation	SNP	G	TCGA-A4-8517-01A-11D-2396-08		25271238	37754282	68	3946											
KIF3B	9371	hgsc.bcm.edu	37	chr20	30897803	30897803	+	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	agcagtttgaactgtacgatGagacgttccgaccacttgtt	10	12	10	9	3	0	2	0	2	0	1	1	5	1	2	2	0	3	5	2	0	2	5			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr20:30897803G>A	ENST00000375712.3	+	2	390	c.223G>A	c.(223-225)Gag>Aag	p.E75K	KIF3B_ENST00000418717.2_5'Flank	NM_004798.3	NP_004789.1	O15066	KIF3B_HUMAN	kinesin family member 3B	75	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterograde axon cargo transport (GO:0008089)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytoskeleton-dependent intracellular transport (GO:0030705)|determination of left/right symmetry (GO:0007368)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic centrosome separation (GO:0007100)|mitotic spindle organization (GO:0007052)|plus-end-directed vesicle transport along microtubule (GO:0072383)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intraciliary transport particle (GO:0030990)|kinesin II complex (GO:0016939)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|plus-end kinesin complex (GO:0005873)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|Rho GTPase binding (GO:0017048)			NS(2)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(5)|lung(9)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			ACTGTACGATGAGACGTTCCG	0.488																																					p.E75K		Atlas-SNP	.											.	KIF3B	75	.	0			c.G223A						PASS	.						157	136	143					20																	30897803		2203	4300	6503	SO:0001583	missense	9371	exon2			TACGATGAGACGT	AB002357	CCDS13200.1	20q11.21	2012-08-01			ENSG00000101350	ENSG00000101350		"Kinesins"	6320	protein-coding gene	gene with protein product		603754				9205841	Standard	NM_004798		Approved	KIAA0359, FLA8, KLP-11	uc002wxq.3	O15066	OTTHUMG00000032214	ENST00000375712.3:c.223G>A	chr20.hg19:g.30897803G>A	ENSP00000364864:p.Glu75Lys	100.0	0.0	.		149.0	84.0	.	NM_004798	B2RMP4|B4DSR5|E1P5M5	Missense_Mutation	SNP	ENST00000375712.3	hg19	CCDS13200.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.493801	0.84962	.	.	ENSG00000101350	ENST00000375712	T	0.74842	-0.88	4.76	4.76	0.60689	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	T	0.72471	0.3464	L	0.39692	1.235	0.80722	D	1	B;P	0.42620	0.02;0.785	B;P	0.44990	0.023;0.466	T	0.73464	-0.3974	10	0.42905	T	0.14	.	18.3265	0.90256	0.0:0.0:1.0:0.0	.	75;75	B4DYF2;O15066	.;KIF3B_HUMAN	K	75	ENSP00000364864:E75K	ENSP00000364864:E75K	E	+	1	0	KIF3B	30361464	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.601000	0.98297	2.630000	0.89119	0.561000	0.74099	GAG	.	.	.	none		0.488	KIF3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078619.1	NM_004798		A	30897803	G	A	30897803	3	1	58	1	0	0	0	0	1	0	0	0	8308	1291	45	2	225	2	KIF3B	20	30897803	Missense_Mutation	SNP	G	TCGA-A4-8517-01A-11D-2396-08	5626565	30897803	32127717	69	3947											
SDC4	6385	hgsc.bcm.edu	37	chr20	43959164	43959164	+	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	gttcggtggggacttggctcCcagaccctgccctctcaggg	4	9	14	14	1	1	1	1	0	1	1	4	2	2	2	3	5	1	2	3	5	0	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr20:43959164C>A	ENST00000372733.3	-	4	326	c.287G>T	c.(286-288)gGg>gTg	p.G96V	SDC4_ENST00000537976.1_Missense_Mutation_p.G24V	NM_002999.3	NP_002990.2	P31431	SDC4_HUMAN	syndecan 4	96					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)	p.G96E(1)	SDC4/ROS1(7)	NS(1)|breast(1)|endometrium(1)|large_intestine(2)	5		Myeloproliferative disorder(115;0.0122)				GACTTGGCTCCCAGACCCTGC	0.532			T	ROS1	NSCLC																																p.G96V		Atlas-SNP	.		Dom	yes		20	20q12	6385	syndecan 4		E	SDC4,NS,carcinoma,0,1	SDC4	16	.	1	Substitution - Missense(1)	endometrium(1)	c.G287T						PASS	.						86	73	77					20																	43959164		2203	4300	6503	SO:0001583	missense	6385	exon4			TGGCTCCCAGACC	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.287G>T	chr20.hg19:g.43959164C>A	ENSP00000361818:p.Gly96Val	52.0	0.0	.		66.0	17.0	.	NM_002999	O00773|Q16833|Q53FN9|Q6FGN3	Missense_Mutation	SNP	ENST00000372733.3	hg19	CCDS13350.1	.	.	.	.	.	.	.	.	.	.	C	1.625	-0.520393	0.04171	.	.	ENSG00000124145	ENST00000372733;ENST00000537976	T	0.29917	1.55	5.68	3.56	0.40772	.	0.486350	0.18834	N	0.129888	T	0.25457	0.0619	L	0.44542	1.39	0.25579	N	0.986817	B	0.10296	0.003	B	0.14023	0.01	T	0.13469	-1.0508	10	0.29301	T	0.29	-21.9327	11.2249	0.48877	0.143:0.7246:0.1323:0.0	.	96	P31431	SDC4_HUMAN	V	96;24	ENSP00000361818:G96V	ENSP00000361818:G96V	G	-	2	0	SDC4	43392578	0.042000	0.20092	0.902000	0.35471	0.284000	0.27059	0.780000	0.26760	1.334000	0.45468	0.561000	0.74099	GGG	.	.	.	none		0.532	SDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080515.1	NM_002999		A	43959164	C	A	43959164	3	1	58	1	0	0	0	0	1	0	0	0	13967	623	22	4	317	4	SDC4	20	43959164	Missense_Mutation	SNP	C	TCGA-A4-8517-01A-11D-2396-08	13061361	43959164	19066356	70	3948											
ARFGEF2	10564	hgsc.bcm.edu	37	chr20	47628619	47628619	+	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	aatacgtctctgagaggcctCgggttcgtttttccccacct	6	13	9	13	3	1	1	0	1	1	1	5	2	2	1	4	2	1	2	4	2	2	4	rs371146257		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr20:47628619C>A	ENST00000371917.4	+	28	3916	c.3916C>A	c.(3916-3918)Cgg>Agg	p.R1306R		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	1306					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)			TGAGAGGCCTCGGGTTCGTTT	0.512																																					p.R1306R	Esophageal Squamous(176;1738 1974 26285 33069 35354)	Atlas-SNP	.											.	ARFGEF2	160	.	0			c.C3916A						PASS	.						89	85	86					20																	47628619		2203	4300	6503	SO:0001819	synonymous_variant	10564	exon28			AGGCCTCGGGTTC	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.3916C>A	chr20.hg19:g.47628619C>A		97.0	0.0	.		109.0	61.0	.	NM_006420	Q5TFT9|Q9NTS1	Silent	SNP	ENST00000371917.4	hg19	CCDS13411.1																																																																																			.	.	.	alt		0.512	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420		A	47628619	C	A	47628619	2	1	58	1	0	0	0	0	0	0	0	1	853	875	31	4		4	ARFGEF2	20	47628619	Silent	SNP	C	TCGA-A4-8517-01A-11D-2396-08	3669455	47628619	15396901	71	3949											
CDH26	60437	hgsc.bcm.edu	37	chr20	58569544	58569544	+	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	ggaagttggggagaaattggGgtgagtttttgtattggtta	9	15	17	0	0	0	2	0	1	0	1	0	4	0	3	0	6	0	4	0	6	4	7			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr20:58569544G>C	ENST00000244047.5	+	11	1977	c.1666G>C	c.(1666-1668)Ggt>Cgt	p.G556R	CDH26_ENST00000497614.1_3'UTR|CDH26_ENST00000348616.4_Splice_Site_p.G556R|CDH26_ENST00000350849.6_5'Flank|CDH26_ENST00000244049.3_5'Flank			Q8IXH8	CAD26_HUMAN	cadherin 26	556					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)			GAGAAATTGGGGTGAGTTTTT	0.433																																					p.G556R		Atlas-SNP	.											.	CDH26	229	.	0			c.G1666C						PASS	.						34	33	33					20																	58569544		2203	4300	6503	SO:0001630	splice_region_variant	60437	exon11			AATTGGGGTGAGT	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.1666+1G>C	chr20.hg19:g.58569544G>C		62.0	0.0	.		74.0	24.0	.	NM_177980	A2A2M5|B3KNX3|Q6P5Y6|Q8TCH3|Q9BQN4|Q9NRU1	Missense_Mutation	SNP	ENST00000244047.5	hg19		.	.	.	.	.	.	.	.	.	.	G	16.64	3.180551	0.57800	.	.	ENSG00000124215	ENST00000244047;ENST00000348616	T;T	0.72835	-0.69;-0.69	4.35	4.35	0.52113	Cadherin-like (1);	0.391569	0.24463	N	0.038317	D	0.83436	0.5254	M	0.74258	2.255	0.49687	D	0.999815	D;D	0.89917	0.999;1.0	D;D	0.85130	0.973;0.997	D	0.86131	0.1575	10	0.87932	D	0	.	15.6637	0.77209	0.0:0.0:1.0:0.0	.	556;556	Q8IXH8;Q8IXH8-4	CAD26_HUMAN;.	R	556	ENSP00000244047:G556R;ENSP00000339390:G556R	ENSP00000244047:G556R	G	+	1	0	CDH26	58002939	1.000000	0.71417	0.388000	0.26195	0.582000	0.36321	5.190000	0.65104	1.954000	0.56735	0.655000	0.94253	GGT	.	.	.	none		0.433	CDH26-201	KNOWN	basic	protein_coding	protein_coding		NM_177980	Missense_Mutation	C	58569544	G	C	58569544	5	2	58	1	0	0	0	0	0	0	1	0	3112	1246	43	4	1708	4	CDH26	20	58569544	Splice_Site	SNP	G	TCGA-A4-8517-01A-11D-2396-08	10940925	58569544	4455976	72	3950											
NCAM2	4685	hgsc.bcm.edu	37	chr21	22849618	22849618	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tattgctttcacagaaagatAaggaagaccaatggctagag	16	9	10	6	0	1	4	1	0	0	4	1	5	1	5	1	2	1	2	1	2	6	5	rs201923816		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr21:22849618A>G	ENST00000400546.1	+	15	2152	c.1903A>G	c.(1903-1905)Aag>Gag	p.K635E	NCAM2_ENST00000284894.7_Missense_Mutation_p.K493E	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	635	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		ACAGAAAGATAAGGAAGACCA	0.338																																					p.K635E		Atlas-SNP	.											.	NCAM2	220	.	0			c.A1903G						PASS	.						80	74	76					21																	22849618		1822	4085	5907	SO:0001583	missense	4685	exon15			AAAGATAAGGAAG		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.1903A>G	chr21.hg19:g.22849618A>G	ENSP00000383392:p.Lys635Glu	45.0	0.0	.		36.0	12.0	.	NM_004540	A8MQ06|B7Z841|Q7Z7F2	Missense_Mutation	SNP	ENST00000400546.1	hg19	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.069133	0.76301	.	.	ENSG00000154654	ENST00000400546;ENST00000284894	T;T	0.51574	0.7;0.7	5.8	5.8	0.92144	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.52517	0.1739	N	0.15975	0.35	0.80722	D	1	D;D	0.62365	0.991;0.991	D;D	0.81914	0.995;0.995	T	0.58912	-0.7552	10	0.56958	D	0.05	-27.6898	14.9715	0.71238	1.0:0.0:0.0:0.0	.	493;635	B7Z5K2;O15394	.;NCAM2_HUMAN	E	635;493	ENSP00000383392:K635E;ENSP00000284894:K493E	ENSP00000284894:K493E	K	+	1	0	NCAM2	21771489	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	6.306000	0.72810	2.213000	0.71641	0.528000	0.53228	AAG	.	A|0.999;G|0.001	0.001	weak		0.338	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		G	22849618	A	G	22849618	3	3	58	1	0	0	0	0	1	0	0	0	10210	363	13	3	1961	3	NCAM2	21	22849618	Missense_Mutation	SNP	A	TCGA-A4-8517-01A-11D-2396-08		22849618	25280277	73	3951											
MRPL40	64976	hgsc.bcm.edu	37	chr22	19423455	19423455	+	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	aggtacaatgacatcaccaaGgtgtacacacaagtggagtt	15	8	10	8	0	1	1	1	1	0	0	1	2	1	2	1	3	2	3	1	3	5	3			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr22:19423455G>T	ENST00000333130.3	+	4	1244	c.591G>T	c.(589-591)aaG>aaT	p.K197N	MRPL40_ENST00000443660.1_3'UTR|HIRA_ENST00000541063.1_Intron|HIRA_ENST00000546308.1_Intron	NM_003776.2	NP_003767.2	Q9NQ50	RM40_HUMAN	mitochondrial ribosomal protein L40	197					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)					ACATCACCAAGGTGTACACAC	0.502																																					p.K197N		Atlas-SNP	.											.	MRPL40	13	.	0			c.G591T						PASS	.						116	106	109					22																	19423455		2203	4300	6503	SO:0001583	missense	64976	exon4			CACCAAGGTGTAC	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.591G>T	chr22.hg19:g.19423455G>T	ENSP00000333401:p.Lys197Asn	80.0	0.0	.		63.0	23.0	.	NM_003776	B3KVZ7|O95134	Missense_Mutation	SNP	ENST00000333130.3	hg19	CCDS13760.1	.	.	.	.	.	.	.	.	.	.	G	13.96	2.392258	0.42410	.	.	ENSG00000185608	ENST00000333130	T	0.52983	0.64	5.53	2.23	0.28157	.	0.102989	0.64402	D	0.000005	T	0.66247	0.2770	M	0.85542	2.76	0.45502	D	0.998462	D	0.76494	0.999	D	0.77557	0.99	T	0.67473	-0.5662	10	0.72032	D	0.01	-26.3156	7.4919	0.27466	0.4243:0.0:0.5757:0.0	.	197	Q9NQ50	RM40_HUMAN	N	197	ENSP00000333401:K197N	ENSP00000333401:K197N	K	+	3	2	MRPL40	17803455	1.000000	0.71417	1.000000	0.80357	0.113000	0.19764	1.675000	0.37555	0.898000	0.36418	0.655000	0.94253	AAG	.	.	.	none		0.502	MRPL40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316491.2	NM_003776		T	19423455	G	T	19423455	3	4	58	1	0	0	0	0	1	0	0	0	9811	991	35	4	605	4	MRPL40	22	19423455	Missense_Mutation	SNP	G	TCGA-A4-8517-01A-11D-2396-08		19423455	31881111	74	3952											
KLHL22	84861	hgsc.bcm.edu	37	chr22	20796432	20796432	+	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	tcagaggcaaagtccgggtcGgcctggctgcggtcaggggt	6	7	18	10	3	2	1	2	0	0	1	4	1	3	1	2	7	1	2	2	7	1	0	rs149300605		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr22:20796432G>C	ENST00000328879.4	-	7	1989	c.1833C>G	c.(1831-1833)gcC>gcG	p.A611A	KLHL22_ENST00000440659.2_Silent_p.A468A	NM_032775.3	NP_116164.2	Q53GT1	KLH22_HUMAN	kelch-like family member 22	611					cell division (GO:0051301)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|protein monoubiquitination (GO:0006513)	centrosome (GO:0005813)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|polar microtubule (GO:0005827)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|skin(2)|upper_aerodigestive_tract(1)	20	Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			AGTCCGGGTCGGCCTGGCTGC	0.647																																					p.A611A		Atlas-SNP	.											.	KLHL22	52	.	0			c.C1833G						PASS	.						29	30	30					22																	20796432		2203	4300	6503	SO:0001819	synonymous_variant	84861	exon7			CGGGTCGGCCTGG		CCDS13780.1	22q11.21	2013-01-30	2013-01-30		ENSG00000099910	ENSG00000099910		"Kelch-like", "BTB/POZ domain containing"	25888	protein-coding gene	gene with protein product			"kelch-like 22 (Drosophila)"			12477932	Standard	NM_032775		Approved	FLJ14360, KELCHL	uc002zsl.2	Q53GT1	OTTHUMG00000150778	ENST00000328879.4:c.1833C>G	chr22.hg19:g.20796432G>C		65.0	0.0	.		67.0	26.0	.	NM_032775	A8K3Q4|A8MTV3|B7Z2G1|D3DX30|Q96B68|Q96KC6	Silent	SNP	ENST00000328879.4	hg19	CCDS13780.1																																																																																			.	G|1.000;A|0.000	.	alt		0.647	KLHL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320045.2	NM_032775		C	20796432	G	C	20796432	2	2	58	1	0	0	0	0	0	0	0	1	8384	1103	39	4		4	KLHL22	22	20796432	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08	1372977	20796432	30508134	75	3953											
CELSR1	9620	hgsc.bcm.edu	37	chr22	46765598	46765598	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccacactcacgattataacAgctccgatgggccccgcaaa	12	6	7	16	3	1	0	1	0	0	0	2	2	2	0	4	1	2	2	4	1	3	2			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr22:46765598A>G	ENST00000262738.3	-	26	7862	c.7863T>C	c.(7861-7863)gcT>gcC	p.A2621A		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2621					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)		CGATTATAACAGCTCCGATGG	0.627																																					p.A2621A		Atlas-SNP	.											.	CELSR1	242	.	0			c.T7863C						PASS	.						55	54	54					22																	46765598		2203	4300	6503	SO:0001819	synonymous_variant	9620	exon26			TATAACAGCTCCG	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.7863T>C	chr22.hg19:g.46765598A>G		78.0	0.0	.		63.0	24.0	.	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	hg19	CCDS14076.1																																																																																			.	.	.	none		0.627	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		G	46765598	A	G	46765598	2	3	58	1	0	0	0	0	0	0	0	1	3223	175	7	3		3	CELSR1	22	46765598	Silent	SNP	A	TCGA-A4-8517-01A-11D-2396-08	25969166	46765598	4538968	76	3954											
MIOX	55586	hgsc.bcm.edu	37	chr22	50926723	50926723	+	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	gactggttccacctcgtcggGctcctgcacgacctggggaa	6	8	13	14	3	0	0	0	0	0	0	4	3	2	1	4	4	1	3	4	4	1	1			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chr22:50926723G>T	ENST00000216075.6	+	5	434	c.360G>T	c.(358-360)ggG>ggT	p.G120G	MIOX_ENST00000395732.3_Silent_p.G120G|MIOX_ENST00000395733.3_Missense_Mutation_p.G131V	NM_017584.5	NP_060054.4	Q9UGB7	MIOX_HUMAN	myo-inositol oxygenase	120					inositol catabolic process (GO:0019310)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)	aldo-keto reductase (NADP) activity (GO:0004033)|ferric iron binding (GO:0008199)|inositol oxygenase activity (GO:0050113)|NADP binding (GO:0050661)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen (GO:0016701)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	13		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		ACCTCGTCGGGCTCCTGCACG	0.652																																					p.G120G		Atlas-SNP	.											.	MIOX	21	.	0			c.G360T						PASS	.						57	55	56					22																	50926723		2203	4300	6503	SO:0001819	synonymous_variant	55586	exon5			CGTCGGGCTCCTG	AF197129	CCDS14092.1	22q13.3	2008-06-11	2005-06-15	2005-06-15	ENSG00000100253	ENSG00000100253			14522	protein-coding gene	gene with protein product	"kidney-specific protein 32"	606774	"aldehyde reductase (aldose reductase) like 6"	ALDRL6		10944187, 11716759	Standard	NM_017584		Approved		uc003bll.1	Q9UGB7	OTTHUMG00000150207	ENST00000216075.6:c.360G>T	chr22.hg19:g.50926723G>T		65.0	0.0	.		38.0	16.0	.	NM_017584	Q05DJ6|Q5S8C9|Q9BZZ1|Q9UHB8	Silent	SNP	ENST00000216075.6	hg19	CCDS14092.1	.	.	.	.	.	.	.	.	.	.	G	13.57	2.277251	0.40294	.	.	ENSG00000100253	ENST00000395733	.	.	.	4.4	2.3	0.28687	.	0.000000	0.85682	D	0.000000	T	0.42988	0.1227	.	.	.	0.80722	D	1	B	0.20671	0.047	B	0.17979	0.02	T	0.37150	-0.9718	8	0.87932	D	0	-5.0893	3.2524	0.06819	0.2255:0.0:0.5677:0.2069	.	131	Q9UGB7-2	.	V	131	.	ENSP00000379082:G131V	G	+	2	0	MIOX	49273589	0.998000	0.40836	0.980000	0.43619	0.906000	0.53458	0.593000	0.23999	0.468000	0.27243	0.436000	0.28706	GGC	.	.	.	none		0.652	MIOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316835.1	NM_017584		T	50926723	G	T	50926723	2	4	58	1	0	0	0	0	0	0	0	1	9597	1190	42	4		4	MIOX	22	50926723	Silent	SNP	G	TCGA-A4-8517-01A-11D-2396-08	4161125	50926723	377843	77	3955											
WWC3	55841	hgsc.bcm.edu	37	chrX	10094307	10094307	+	Frame_Shift_Del	DEL	C	C	-																															ctgaagtcacttcagttataCgtgtgttcagtgactccgca																								rs199701428		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chrX:10094307delC	ENST00000380861.4	+	15	2458	c.2067delC	c.(2065-2067)tacfs	p.Y689fs	WWC3_ENST00000454666.1_Frame_Shift_Del_p.Y689fs	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	689	C2.				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						TTCAGTTATACGTGTGTTCAG	0.572																																					p.Y689fs		Atlas-INDEL	.											.	WWC3	142	.	0			c.2066delA						PASS	.						114	95	101					X																	10094307		2203	4300	6503	SO:0001589	frameshift_variant	55841	exon15			.	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.2067delC	chrX.hg19:g.10094307delC	ENSP00000370242:p.Tyr689fs	85.0	0.0	0		78.0	11.0	0.141026	NM_015691	A8KA96|Q659C1|Q9BTQ1	Frame_Shift_Del	DEL	ENST00000380861.4	hg19	CCDS14136.1																																																																																			.	.	.	none		0.572	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691		-	10094307	C	-	10094307	7	5	58	1	0	1	0	1	0	0	0	0	17425	547	19	0	2121	0	WWC3	23	10094307	Frame_Shift_Del	DEL	C	TCGA-A4-8517-01A-11D-2396-08		10094307	145176253	78	3956											
THOC2	57187	hgsc.bcm.edu	37	chrX	122755201	122755201	+	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	ttggggacagtggtcttaaaTttctcatctttagctttttc	7	19	8	7	0	3	0	1	0	3	0	5	1	3	1	0	3	1	1	0	3	3	7			TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	g.chrX:122755201T>A	ENST00000245838.8	-	31	4054	c.4023A>T	c.(4021-4023)aaA>aaT	p.K1341N	THOC2_ENST00000497887.1_5'Flank|THOC2_ENST00000491737.1_Missense_Mutation_p.K1226N|THOC2_ENST00000355725.4_Missense_Mutation_p.K1341N	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	1341	Lys-rich.				mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						TGGTCTTAAATTTCTCATCTT	0.373																																					p.K1341N		Atlas-SNP	.											.	THOC2	310	.	0			c.A4023T						PASS	.						259	229	239					X																	122755201		1871	4088	5959	SO:0001583	missense	57187	exon31			CTTAAATTTCTCA	AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"THO complex subunits"	19073	protein-coding gene	gene with protein product		300395	"chromosome X open reading frame 3"	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.4023A>T	chrX.hg19:g.122755201T>A	ENSP00000245838:p.Lys1341Asn	74.0	0.0	.		68.0	56.0	.	NM_001081550	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Missense_Mutation	SNP	ENST00000245838.8	hg19	CCDS43988.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.36|12.36	1.915943|1.915943	0.33815|0.33815	.|.	.|.	ENSG00000125676|ENSG00000125676	ENST00000245838;ENST00000355725;ENST00000491737|ENST00000441692	T;T;T|.	0.22539|.	1.95;1.95;1.95|.	5.32|5.32	4.16|4.16	0.48862|0.48862	.|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.51126|0.51126	0.1656|0.1656	L|L	0.36672|0.36672	1.1|1.1	0.53688|0.53688	D|D	0.999974|0.999974	P|.	0.43094|.	0.799|.	B|.	0.42692|.	0.395|.	T|T	0.40194|0.40194	-0.9576|-0.9576	9|5	.|.	.|.	.|.	-12.8428|-12.8428	8.5327|8.5327	0.33344|0.33344	0.0:0.2225:0.0:0.7775|0.0:0.2225:0.0:0.7775	.|.	1341|.	Q8NI27|.	THOC2_HUMAN|.	N|I	1341;1341;1226|109	ENSP00000245838:K1341N;ENSP00000347959:K1341N;ENSP00000419795:K1226N|.	.|.	K|N	-|-	3|2	2|0	THOC2|THOC2	122582882|122582882	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.949000|0.949000	0.60115|0.60115	1.873000|1.873000	0.39558|0.39558	0.776000|0.776000	0.33473|0.33473	0.486000|0.486000	0.48141|0.48141	AAA|AAT	.	.	.	none		0.373	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3			A	122755201	T	A	122755201	3	1	58	1	0	0	0	0	1	0	0	0	15877	1490	52	5	790	5	THOC2	23	122755201	Missense_Mutation	SNP	T	TCGA-A4-8517-01A-11D-2396-08	112660894	122755201	32515359	79	3957											
KCNC4	3749	hgsc.bcm.edu	37	chr1	110774916	110774916	+	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	cctccaactgctgggactctGttcctgccacattgaggaag	8	10	10	13	0	1	1	0	1	1	0	3	3	3	3	4	2	3	2	4	2	2	2			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr1:110774916G>A	ENST00000369787.3	+	4	1920	c.1893G>A	c.(1891-1893)ctG>ctA	p.L631L	KCNC4_ENST00000438661.2_Intron|KCNC4_ENST00000412512.2_Intron|KCNC4_ENST00000413138.3_Intron	NM_004978.4	NP_004969.2	Q03721	KCNC4_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 4	631					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)		CTGGGACTCTGTTCCTGCCAC	0.562																																					p.L631L		Atlas-SNP	.											.	KCNC4	113	.	0			c.G1893A						PASS	.						74	54	61					1																	110774916		2203	4300	6503	SO:0001819	synonymous_variant	3749	exon4			GACTCTGTTCCTG	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.1893G>A	chr1.hg19:g.110774916G>A		25.0	0.0	.		32.0	10.0	.	NM_004978	Q3MIM4|Q5TBI6	Silent	SNP	ENST00000369787.3	hg19	CCDS821.1																																																																																			.	.	.	none		0.562	KCNC4-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052146.2	NM_001039574		A	110774916	G	A	110774916	2	1	59	1	0	0	0	0	0	0	0	1	8024	1364	48	2		2	KCNC4	1	110774916	Silent	SNP	G	TCGA-A4-8518-01A-11D-2396-08		110774916	138475705	1	3958											
NBPF14	25832	hgsc.bcm.edu	37	chr1	148015634	148015634	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaggtactcaccatccatgtTaacagccaagccaacacgct	14	7	6	14	1	1	0	1	0	0	0	2	0	2	0	4	1	5	3	4	1	5	2	rs200156420	byFrequency	TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr1:148015634T>C	ENST00000369219.1	-	8	1013	c.997A>G	c.(997-999)Aac>Gac	p.N333D				Q5TI25	NBPFE_HUMAN	neuroblastoma breakpoint family, member 14	333	NBPF 3. {ECO:0000255|PROSITE- ProRule:PRU00647}.			N -> D (in Ref. 3; AAO15399). {ECO:0000305}.		cytoplasm (GO:0005737)		p.N333D(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)					CCATCCATGTTAACAGCCAAG	0.463													-|||	445	0.0888578	0.146	0.0778	5008	,	,		13640	0.0675		0.0408	False		,,,				2504	0.091				p.N333D		Atlas-SNP	.											NBPF14_ENST00000310701,bladder,carcinoma,-1,2	NBPF14	107	.	1	Substitution - Missense(1)	skin(1)	c.A997G						PASS	.						4	3	4					1																	148015634		718	1612	2330	SO:0001583	missense	25832	exon8			CCATGTTAACAGC	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.997A>G	chr1.hg19:g.148015634T>C	ENSP00000358221:p.Asn333Asp	46.0	1.0	.		58.0	3.0	.	NM_015383	Q5TI23|Q8IX76|Q9UJI9	Missense_Mutation	SNP	ENST00000369219.1	hg19		.	.	.	.	.	.	.	.	.	.	-	0	-2.747081	0.00086	.	.	ENSG00000122497	ENST00000369219	T	0.04234	3.67	.	.	.	DUF1220 (2);	.	.	.	.	T	0.00210	0.0006	N	0.00028	-2.63	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43686	-0.9376	7	0.02654	T	1	.	.	.	.	.	333	Q5TI25	NBPFE_HUMAN	D	333	ENSP00000358221:N333D	ENSP00000358221:N333D	N	-	1	0	NBPF14	146482258	0.402000	0.25311	0.002000	0.10522	0.000000	0.00434	-1.348000	0.02629	0.357000	0.24183	0.000000	0.15137	AAC	.	.	.	weak		0.463	NBPF14-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_015383		C	148015634	T	C	148015634	3	2	59	1	0	0	0	0	1	0	0	0	10201	1754	61	3	1828	3	NBPF14	1	148015634	Missense_Mutation	SNP	T	TCGA-A4-8518-01A-11D-2396-08	37240718	148015634	101234987	2	3959											
LINGO4	339398	hgsc.bcm.edu	37	chr1	151774638	151774638	+	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	tccagggtgagggtgctcaaCttggctagccctgcaaaggc	8	8	14	11	0	1	1	1	1	0	0	2	1	2	1	2	4	4	3	2	4	3	2			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr1:151774638C>G	ENST00000368820.3	-	2	1480	c.543G>C	c.(541-543)aaG>aaC	p.K181N		NM_001004432.2	NP_001004432.1	Q6UY18	LIGO4_HUMAN	leucine rich repeat and Ig domain containing 4	181						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)			GGGTGCTCAACTTGGCTAGCC	0.612																																					p.K181N		Atlas-SNP	.											.	LINGO4	51	.	0			c.G543C						PASS	.						37	43	41					1																	151774638		2203	4299	6502	SO:0001583	missense	339398	exon2			GCTCAACTTGGCT		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.543G>C	chr1.hg19:g.151774638C>G	ENSP00000357810:p.Lys181Asn	115.0	0.0	.		101.0	6.0	.	NM_001004432		Missense_Mutation	SNP	ENST00000368820.3	hg19	CCDS30855.1	.	.	.	.	.	.	.	.	.	.	C	3.774	-0.047078	0.07407	.	.	ENSG00000213171	ENST00000368820	T	0.54071	0.59	5.13	2.23	0.28157	.	0.401034	0.21238	N	0.077871	T	0.09024	0.0223	N	0.05351	-0.065	0.20926	N	0.999823	B	0.06786	0.001	B	0.06405	0.002	T	0.39375	-0.9617	10	0.07482	T	0.82	.	8.7903	0.34845	0.0:0.748:0.0:0.252	.	181	Q6UY18	LIGO4_HUMAN	N	181	ENSP00000357810:K181N	ENSP00000357810:K181N	K	-	3	2	LINGO4	150041262	0.037000	0.19845	0.017000	0.16124	0.866000	0.49608	-0.213000	0.09305	0.328000	0.23435	0.462000	0.41574	AAG	.	.	.	none		0.612	LINGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036639.1	XM_291387		G	151774638	C	G	151774638	3	3	59	1	0	0	0	0	1	0	0	0	8824	564	20	4	1242	4	LINGO4	1	151774638	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	3759004	151774638	97475983	3	3960											
SLC16A14	151473	hgsc.bcm.edu	37	chr2	230910735	230910735	+	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	aagtcggctatgacgcccagGatcacttttccaaagatgtg	11	10	10	10	2	1	2	1	1	0	1	3	3	2	3	2	2	0	1	2	2	3	3			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr2:230910735G>A	ENST00000295190.4	-	4	1565	c.1107C>T	c.(1105-1107)atC>atT	p.I369I		NM_152527.4	NP_689740.2	Q7RTX9	MOT14_HUMAN	solute carrier family 16, member 14	369						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)	p.I369I(1)		NS(1)|cervix(1)|endometrium(7)|large_intestine(7)|lung(3)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.149)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;7.31e-13)|all cancers(144;5.1e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00948)		TGACGCCCAGGATCACTTTTC	0.433																																					p.I369I		Atlas-SNP	.											SLC16A14,NS,carcinoma,0,1	SLC16A14	75	.	1	Substitution - coding silent(1)	ovary(1)	c.C1107T						PASS	.						98	87	91					2																	230910735		2203	4300	6503	SO:0001819	synonymous_variant	151473	exon4			GCCCAGGATCACT	BN000146	CCDS2473.1	2q37.1	2013-07-18	2013-07-18		ENSG00000163053	ENSG00000163053		"Solute carriers"	26417	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 14"		"solute carrier family 16 (monocarboxylic acid transporters), member 14"				Standard	NM_152527		Approved	FLJ30794, MCT14	uc002vqd.2	Q7RTX9	OTTHUMG00000133205	ENST00000295190.4:c.1107C>T	chr2.hg19:g.230910735G>A		101.0	1.0	.		105.0	23.0	.	NM_152527	A8KA08|Q53R92|Q96NI7	Silent	SNP	ENST00000295190.4	hg19	CCDS2473.1																																																																																			.	.	.	none		0.433	SLC16A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256918.2	NM_152527		A	230910735	G	A	230910735	2	1	59	1	0	0	0	0	0	0	0	1	14420	1164	41	2		2	SLC16A14	2	230910735	Silent	SNP	G	TCGA-A4-8518-01A-11D-2396-08		230910735	12288638	4	3961											
USP19	10869	hgsc.bcm.edu	37	chr3	49148785	49148785	+	Frame_Shift_Del	DEL	C	C	-																															gcttcacttggatgctggtaCccaggcacagcagctgtgtg																										TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr3:49148785delC	ENST00000398888.2	-	21	3240	c.2922delG	c.(2920-2922)gggfs	p.G974fs	USP19_ENST00000398898.2_Frame_Shift_Del_p.G1014fs|USP19_ENST00000434032.2_Frame_Shift_Del_p.G1075fs|USP19_ENST00000453664.1_Frame_Shift_Del_p.G1065fs|USP19_ENST00000398896.1_Frame_Shift_Del_p.G782fs|USP19_ENST00000398892.3_Frame_Shift_Del_p.G1014fs|USP19_ENST00000417901.1_Frame_Shift_Del_p.G1077fs	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	974	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)		GATGCTGGTACCCAGGCACAG	0.532																																					p.Y1078fs		Atlas-INDEL	.											.	USP19	158	.	0			c.3232delT						PASS	.						101	106	105					3																	49148785		2047	4201	6248	SO:0001589	frameshift_variant	10869	exon22			.	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.2922delG	chr3.hg19:g.49148785delC	ENSP00000381863:p.Gly974fs	96.0	0.0	0		105.0	20.0	0.190476	NM_001199161	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Frame_Shift_Del	DEL	ENST00000398888.2	hg19	CCDS43090.1																																																																																			.	.	.	none		0.532	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677		-	49148785	C	-	49148785	7	5	59	1	0	1	0	1	0	0	0	0	17062	494	18	0	1058	0	USP19	3	49148785	Frame_Shift_Del	DEL	C	TCGA-A4-8518-01A-11D-2396-08		49148785	148873645	5	3962											
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-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	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	.	0			c.G4416A						PASS	.						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	chr3.hg19:g.113376113C>T		34.0	0.0	.		43.0	4.0	.	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	hg19	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	59	1	0	0	0	0	0	0	0	1	8275	796	28	2		2	KIAA2018	3	113376113	Silent	SNP	C	TCGA-A4-8518-01A-11D-2396-08	64227328	113376113	84646317	6	3963											
LMLN	89782	hgsc.bcm.edu	37	chr3	197687183	197687183	+	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	cgggccggagccggtggcgcTggagcgggtctgtgtgggtc	2	7	22	10	5	1	0	0	0	1	0	2	2	1	2	2	7	2	1	2	7	0	0	rs375365578		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr3:197687183T>A	ENST00000330198.4	+	1	113	c.91T>A	c.(91-93)Tgg>Agg	p.W31R	IQCG_ENST00000480302.1_5'Flank|IQCG_ENST00000265239.6_5'Flank|LMLN_ENST00000482695.1_Missense_Mutation_p.L19Q|LMLN_ENST00000332636.5_Missense_Mutation_p.L19Q|LMLN_ENST00000420910.2_Missense_Mutation_p.W31R	NM_033029.3	NP_149018.2	Q96KR4	LMLN_HUMAN	leishmanolysin-like (metallopeptidase M8 family)	31					cell adhesion (GO:0007155)|mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)		CCGGTGGCGCTGGAGCGGGTC	0.687																																					p.W31R		Atlas-SNP	.											.	LMLN	53	.	0			c.T91A						PASS	.	T	ARG/TRP,ARG/TRP	1,4405	2.1+/-5.4	0,1,2202	30	36	34		91,91	-0.9	0	3		34	0,8596		0,0,4298	no	missense,missense	LMLN	NM_033029.3,NM_001136049.2	101,101	0,1,6500	AA,AT,TT		0.0,0.0227,0.0077	benign,benign	31/656,31/693	197687183	1,13001	2203	4298	6501	SO:0001583	missense	89782	exon1			TGGCGCTGGAGCG	AJ312398	CCDS3332.1, CCDS46988.1	3q29	2008-02-04			ENSG00000185621	ENSG00000185621	3.4.24.36		15991	protein-coding gene	gene with protein product		609380					Standard	NM_033029		Approved	Gp63, Msp	uc010iar.3	Q96KR4	OTTHUMG00000155375	ENST00000330198.4:c.91T>A	chr3.hg19:g.197687183T>A	ENSP00000328829:p.Trp31Arg	136.0	0.0	.		97.0	19.0	.	NM_001136049	B3LDG9|B3LDH0|C9J796|F8WB28|Q96KR5	Missense_Mutation	SNP	ENST00000330198.4	hg19	CCDS3332.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.21|12.21	1.869215|1.869215	0.32977|0.32977	2.27E-4|2.27E-4	0.0|0.0	ENSG00000185621|ENSG00000185621	ENST00000482695;ENST00000332636|ENST00000330198;ENST00000420910	T;T|T;T	0.47528|0.41400	0.85;0.84|1.01;1.0	4.02|4.02	-0.95|-0.95	0.10372|0.10372	.|.	.|0.745603	.|0.11975	.|N	.|0.511342	T|T	0.22322|0.22322	0.0538|0.0538	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	B;B|B;B	0.24963|0.02656	0.115;0.115|0.0;0.0	B;B|B;B	0.28709|0.04013	0.093;0.093|0.0;0.001	T|T	0.24512|0.24512	-1.0158|-1.0158	9|10	0.13853|0.18276	T|T	0.58|0.48	-0.5349|-0.5349	7.0655|7.0655	0.25149|0.25149	0.0:0.4606:0.0:0.5394|0.0:0.4606:0.0:0.5394	.|.	19;19|31;31	F8WCE5;Q96KR4-2|Q96KR4;F8WB28	.;.|LMLN_HUMAN;.	Q|R	19|31	ENSP00000418324:L19Q;ENSP00000328611:L19Q|ENSP00000328829:W31R;ENSP00000410926:W31R	ENSP00000328611:L19Q|ENSP00000328829:W31R	L|W	+|+	2|1	0|0	LMLN|LMLN	199171580|199171580	0.031000|0.031000	0.19500|0.19500	0.003000|0.003000	0.11579|0.11579	0.735000|0.735000	0.41995|0.41995	0.079000|0.079000	0.14782|0.14782	-0.032000|-0.032000	0.13758|0.13758	0.374000|0.374000	0.22700|0.22700	CTG|TGG	.	.	.	weak		0.687	LMLN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339701.1	NM_033029		A	197687183	T	A	197687183	3	1	59	1	0	0	0	0	1	0	0	0	8854	1580	55	5	93	5	LMLN	3	197687183	Missense_Mutation	SNP	T	TCGA-A4-8518-01A-11D-2396-08	84311070	197687183	335247	7	3964											
TBC1D9B	23061	hgsc.bcm.edu	37	chr5	179320253	179320253	+	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	tgtggccggatgggcctaggCagggccttgtcctccaggaa	6	8	16	11	1	0	0	0	0	0	0	2	2	2	2	5	6	0	1	5	6	2	2			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr5:179320253C>G	ENST00000356834.3	-	5	829	c.792G>C	c.(790-792)ctG>ctC	p.L264L	TBC1D9B_ENST00000355235.3_Silent_p.L264L	NM_198868.2	NP_942568.2	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	264						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)			TGGGCCTAGGCAGGGCCTTGT	0.637																																					p.L264L		Atlas-SNP	.											TBC1D9B_ENST00000356834,right_upper_lobe,carcinoma,0,2	TBC1D9B	157	.	0			c.G792C						PASS	.						48	48	48					5																	179320253		2203	4300	6503	SO:0001819	synonymous_variant	23061	exon5			CCTAGGCAGGGCC	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.792G>C	chr5.hg19:g.179320253C>G		55.0	0.0	.		43.0	2.0	.	NM_198868	D3DWQ5|D3DWQ6|O75163|Q53EY0|Q6MZI2|Q96H49	Silent	SNP	ENST00000356834.3	hg19	CCDS43408.1																																																																																			.	.	.	none		0.637	TBC1D9B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253501.3	NM_015043		G	179320253	C	G	179320253	2	3	59	1	0	0	0	0	0	0	0	1	15640	697	25	4		4	TBC1D9B	5	179320253	Silent	SNP	C	TCGA-A4-8518-01A-11D-2396-08		179320253	1595007	8	3965											
KCNK5	8645	hgsc.bcm.edu	37	chr6	39161945	39161945	+	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	aggcagaggcagggactcacCggccacaaagtcaccgaagc	13	2	13	13	2	2	1	2	0	0	1	2	3	2	2	3	4	1	2	3	4	2	0			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr6:39161945C>T	ENST00000359534.3	-	4	972	c.634G>A	c.(634-636)Ggt>Agt	p.G212S		NM_003740.3	NP_003731.1	O95279	KCNK5_HUMAN	potassium channel, subfamily K, member 5	212					excretion (GO:0007588)|potassium ion transport (GO:0006813)	integral component of plasma membrane (GO:0005887)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(4)|skin(3)	19						AGGGACTCACCGGCCACAAAG	0.542																																					p.G212S		Atlas-SNP	.											.	KCNK5	57	.	0			c.G634A						PASS	.						92	79	84					6																	39161945		2203	4300	6503	SO:0001630	splice_region_variant	8645	exon4			ACTCACCGGCCAC	AF084830	CCDS4841.1	6p21	2012-03-07			ENSG00000164626	ENSG00000164626		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6280	protein-coding gene	gene with protein product		603493				9812978, 16382106	Standard	XM_005249456		Approved	K2p5.1, TASK-2	uc003oon.3	O95279	OTTHUMG00000014642	ENST00000359534.3:c.634+1G>A	chr6.hg19:g.39161945C>T		65.0	0.0	.		78.0	20.0	.	NM_003740	B2RAQ6|B5TJL2|Q5VV76	Missense_Mutation	SNP	ENST00000359534.3	hg19	CCDS4841.1	.	.	.	.	.	.	.	.	.	.	C	34	5.402436	0.96030	.	.	ENSG00000164626	ENST00000359534	T	0.30448	1.53	5.68	5.68	0.88126	Ion transport 2 (1);	0.101608	0.64402	D	0.000002	T	0.39911	0.1096	L	0.52759	1.655	0.80722	D	1	P	0.46512	0.879	P	0.58820	0.846	T	0.01909	-1.1249	9	.	.	.	.	19.7891	0.96450	0.0:1.0:0.0:0.0	.	212	O95279	KCNK5_HUMAN	S	212	ENSP00000352527:G212S	.	G	-	1	0	KCNK5	39269923	1.000000	0.71417	0.981000	0.43875	0.542000	0.35054	7.747000	0.85070	2.692000	0.91855	0.561000	0.74099	GGT	.	.	.	none		0.542	KCNK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040449.1	NM_003740	Missense_Mutation	T	39161945	C	T	39161945	5	4	59	1	0	0	0	0	0	0	1	0	8076	666	23	1	873	1	KCNK5	6	39161945	Splice_Site	SNP	C	TCGA-A4-8518-01A-11D-2396-08		39161945	131953122	9	3966											
TDRD6	221400	hgsc.bcm.edu	37	chr6	46658247	46658247	+	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	tggtgtcagctgaccaggaaCatacaaggacttaaaactct	14	9	9	9	0	2	1	1	1	1	0	2	3	2	3	1	3	4	1	1	3	5	2			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr6:46658247C>G	ENST00000316081.6	+	1	2382	c.2382C>G	c.(2380-2382)aaC>aaG	p.N794K	RP11-446F17.3_ENST00000422284.2_RNA|RP11-446F17.3_ENST00000434329.2_RNA|RP11-446F17.3_ENST00000571590.1_RNA|TDRD6_ENST00000544460.1_Missense_Mutation_p.N794K	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	794					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)			TGACCAGGAACATACAAGGAC	0.428																																					p.N794K		Atlas-SNP	.											.	TDRD6	205	.	0			c.C2382G						PASS	.						81	83	82					6																	46658247		2203	4300	6503	SO:0001583	missense	221400	exon1			CAGGAACATACAA	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.2382C>G	chr6.hg19:g.46658247C>G	ENSP00000346065:p.Asn794Lys	74.0	0.0	.		79.0	10.0	.	NM_001168359	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Missense_Mutation	SNP	ENST00000316081.6	hg19	CCDS34470.1	.	.	.	.	.	.	.	.	.	.	C	10.77	1.444596	0.25987	.	.	ENSG00000180113	ENST00000544460;ENST00000316081	T;T	0.12879	2.64;2.64	5.75	3.93	0.45458	Maternal tudor protein (1);	0.375482	0.34178	N	0.004185	T	0.07143	0.0181	L	0.41356	1.27	0.19575	N	0.999962	P;P	0.40834	0.548;0.73	B;P	0.51415	0.439;0.669	T	0.31024	-0.9958	10	0.24483	T	0.36	-13.6225	7.3207	0.26526	0.1058:0.6679:0.1027:0.1236	.	794;794	F5H5M3;O60522	.;TDRD6_HUMAN	K	794	ENSP00000443299:N794K;ENSP00000346065:N794K	ENSP00000346065:N794K	N	+	3	2	TDRD6	46766206	0.072000	0.21174	0.342000	0.25602	0.870000	0.49936	0.453000	0.21811	0.342000	0.23796	-0.797000	0.03246	AAC	.	.	.	none		0.428	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443		G	46658247	C	G	46658247	3	3	59	1	0	0	0	0	1	0	0	0	15746	477	17	4	2384	4	TDRD6	6	46658247	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	7496302	46658247	124456820	10	3967											
PREX2	80243	hgsc.bcm.edu	37	chr8	68995502	68995502	+	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	gcatggaagtcgggaaaaagAtttttgctattaatggtgac	13	12	12	4	1	0	2	0	1	0	1	1	4	0	4	0	3	1	2	0	3	5	4			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr8:68995502A>T	ENST00000288368.4	+	18	2183	c.1906A>T	c.(1906-1908)Att>Ttt	p.I636F	RP11-403D15.2_ENST00000526901.1_RNA|PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	636	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						CGGGAAAAAGATTTTTGCTAT	0.318																																					p.I636F		Atlas-SNP	.											.	PREX2	614	.	0			c.A1906T						PASS	.						93	94	93					8																	68995502		2203	4300	6503	SO:0001583	missense	80243	exon18			AAAAAGATTTTTG	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.1906A>T	chr8.hg19:g.68995502A>T	ENSP00000288368:p.Ile636Phe	58.0	0.0	.		78.0	6.0	.	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	hg19	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.358895	0.82353	.	.	ENSG00000046889	ENST00000288368;ENST00000396539;ENST00000354677	T	0.37235	1.21	5.77	5.77	0.91146	PDZ/DHR/GLGF (3);	0.144361	0.50627	D	0.000115	T	0.50718	0.1632	L	0.52573	1.65	0.54753	D	0.999989	P;P;P	0.52692	0.906;0.955;0.906	P;P;P	0.57101	0.578;0.781;0.813	T	0.51553	-0.8691	10	0.87932	D	0	.	16.3948	0.83586	1.0:0.0:0.0:0.0	.	636;636;636	Q70Z35-2;Q70Z35;Q70Z35-3	.;PREX2_HUMAN;.	F	636	ENSP00000288368:I636F	ENSP00000288368:I636F	I	+	1	0	PREX2	69158056	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.744000	0.55112	2.326000	0.78906	0.533000	0.62120	ATT	.	.	.	none		0.318	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		T	68995502	A	T	68995502	3	4	59	1	0	0	0	0	1	0	0	0	12487	333	12	5	1976	5	PREX2	8	68995502	Missense_Mutation	SNP	A	TCGA-A4-8518-01A-11D-2396-08		68995502	77368520	11	3968											
KDM4C	23081	hgsc.bcm.edu	37	chr9	7015904	7015904	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgatggatggctgtgtgcccGgtgcaaaagaaatgcgtgga	10	9	16	6	2	0	2	0	1	0	1	0	4	0	4	1	4	3	2	1	4	3	0			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr9:7015904G>A	ENST00000381309.3	+	15	2799	c.2234G>A	c.(2233-2235)cGg>cAg	p.R745Q	KDM4C_ENST00000442236.2_Missense_Mutation_p.R490Q|KDM4C_ENST00000428870.2_Missense_Mutation_p.R432Q|KDM4C_ENST00000381306.3_Missense_Mutation_p.R745Q|KDM4C_ENST00000535193.1_Missense_Mutation_p.R767Q|KDM4C_ENST00000543771.1_Missense_Mutation_p.R745Q|KDM4C_ENST00000536108.1_Missense_Mutation_p.R564Q	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	745					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						CTGTGTGCCCGGTGCAAAAGA	0.403																																					p.R767Q		Atlas-SNP	.											.	KDM4C	186	.	0			c.G2300A						PASS	.						210	199	203					9																	7015904		2203	4300	6503	SO:0001583	missense	23081	exon15			GTGCCCGGTGCAA	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.2234G>A	chr9.hg19:g.7015904G>A	ENSP00000370710:p.Arg745Gln	62.0	0.0	.		83.0	4.0	.	NM_001146696	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	hg19	CCDS6471.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.945619	0.73672	.	.	ENSG00000107077	ENST00000535193;ENST00000543771;ENST00000381309;ENST00000381306;ENST00000442236;ENST00000536108;ENST00000428870;ENST00000420847	T;T;T;T;T;T;T;D	0.98914	-0.04;-0.04;2.21;-0.04;-0.04;1.79;-0.04;-5.23	5.37	4.45	0.53987	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type (1);	0.122378	0.56097	D	0.000021	D	0.98785	0.9591	M	0.70595	2.14	0.58432	D	0.999998	D;D;D;P;D	0.89917	1.0;1.0;0.975;0.95;0.991	D;D;B;P;B	0.70227	0.968;0.966;0.424;0.496;0.446	D	0.98698	1.0699	10	0.72032	D	0.01	.	13.8091	0.63252	0.0743:0.0:0.9257:0.0	.	490;745;767;745;745	E7EV17;F5H347;F5H7P0;Q9H3R0;Q9H3R0-2	.;.;.;KDM4C_HUMAN;.	Q	767;745;745;745;490;564;432;89	ENSP00000442382:R767Q;ENSP00000445427:R745Q;ENSP00000370710:R745Q;ENSP00000370707:R745Q;ENSP00000409353:R490Q;ENSP00000440656:R564Q;ENSP00000405739:R432Q;ENSP00000400127:R89Q	ENSP00000370707:R745Q	R	+	2	0	KDM4C	7005904	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.606000	0.74159	2.654000	0.90174	0.591000	0.81541	CGG	.	.	.	none		0.403	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061		A	7015904	G	A	7015904	3	1	59	1	0	0	0	0	1	0	0	0	8137	1116	39	1	2358	1	KDM4C	9	7015904	Missense_Mutation	SNP	G	TCGA-A4-8518-01A-11D-2396-08		7015904	134197527	12	3969											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1258389	1258389	+	Missense_Mutation	SNP	T	T	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	ccaccttcgccgcctgccgcTcccaggtggggctctggtct	2	9	12	18	3	2	0	0	0	2	0	4	0	3	0	6	4	1	2	6	4	0	1			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr11:1258389T>G	ENST00000529681.1	+	25	3350	c.3292T>G	c.(3292-3294)Tcc>Gcc	p.S1098A	MUC5B_ENST00000447027.1_Missense_Mutation_p.S1101A	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1098	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)		CGCCTGCCGCTCCCAGGTGGG	0.682																																					p.S1098A		Atlas-SNP	.											MUC5B,NS,carcinoma,0,2	MUC5B	473	.	0			c.T3292G						PASS	.						10	15	13					11																	1258389		1897	4084	5981	SO:0001583	missense	727897	exon25			TGCCGCTCCCAGG	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.3292T>G	chr11.hg19:g.1258389T>G	ENSP00000436812:p.Ser1098Ala	43.0	0.0	.		24.0	2.0	.	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	hg19	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	T	5.715	0.316511	0.10845	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.76839	-1.05;-1.05	4.38	-4.2	0.03823	von Willebrand factor, type D domain (1);Uncharacterised domain, cysteine-rich (2);	.	.	.	.	T	0.59473	0.2196	N	0.10645	0.015	0.27479	N	0.952642	B;P;P	0.48089	0.026;0.905;0.905	B;P;P	0.47376	0.027;0.545;0.545	T	0.57613	-0.7781	9	0.87932	D	0	.	6.1245	0.20172	0.0:0.2029:0.3546:0.4425	.	1098;1791;1101	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	A	1098;1101;1099;1168	ENSP00000436812:S1098A;ENSP00000415793:S1101A	ENSP00000343037:S1099A	S	+	1	0	MUC5B	1214965	0.000000	0.05858	0.074000	0.20217	0.008000	0.06430	-0.169000	0.09911	-0.576000	0.05974	-0.648000	0.03929	TCC	.	.	.	none		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		G	1258389	T	G	1258389	3	3	59	1	0	0	0	0	1	0	0	0	9986	1551	54	5	3399	5	MUC5B	11	1258389	Missense_Mutation	SNP	T	TCGA-A4-8518-01A-11D-2396-08		1258389	133748127	13	3970											
MRVI1	10335	hgsc.bcm.edu	37	chr11	10626061	10626061	+	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	ccagagtgtagctgtcatttCtaaaggccaaggacagttgc	11	10	11	9	0	2	1	1	0	1	1	2	2	2	2	2	2	2	3	2	2	4	4	rs374023004		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr11:10626061C>G	ENST00000436272.1	-	12	1631	c.1553G>C	c.(1552-1554)aGa>aCa	p.R518T	MRVI1_ENST00000531107.1_Missense_Mutation_p.R537T|MRVI1_ENST00000534266.2_Missense_Mutation_p.R230T|MRVI1_ENST00000558540.1_Missense_Mutation_p.R230T|MRVI1_ENST00000423302.2_Missense_Mutation_p.R545T|MRVI1_ENST00000424001.1_Missense_Mutation_p.R230T|MRVI1_ENST00000527509.2_Missense_Mutation_p.R454T|MRVI1_ENST00000541483.1_Missense_Mutation_p.R339T|MRVI1_ENST00000545852.1_Missense_Mutation_p.R230T|MRVI1_ENST00000421747.1_Missense_Mutation_p.R536T|MRVI1_ENST00000552103.1_Missense_Mutation_p.R454T|MRVI1_ENST00000547195.1_Missense_Mutation_p.R454T|LYVE1_ENST00000531706.1_Intron			Q9Y6F6	MRVI1_HUMAN	murine retrovirus integration site 1 homolog	518	Interaction with ITPR1. {ECO:0000250}.				blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|relaxation of vascular smooth muscle (GO:0060087)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)	22				all cancers(16;2.68e-07)|Epithelial(150;3.04e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0723)		GCTGTCATTTCTAAAGGCCAA	0.488																																					p.R545T		Atlas-SNP	.											MRVI1_ENST00000547195,NS,carcinoma,0,2	MRVI1	113	.	0			c.G1634C						PASS	.						173	166	168					11																	10626061		1964	4161	6125	SO:0001583	missense	10335	exon13			TCATTTCTAAAGG	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.1553G>C	chr11.hg19:g.10626061C>G	ENSP00000412229:p.Arg518Thr	130.0	0.0	.		82.0	18.0	.	NM_130385	B7Z3T4|B7Z6I2|B7Z9A3|E9PQY6|F5H6A1|J3KQZ7|Q17S00|Q9UNY1	Missense_Mutation	SNP	ENST00000436272.1	hg19		.	.	.	.	.	.	.	.	.	.	C	27.5	4.839467	0.91117	.	.	ENSG00000072952	ENST00000421747;ENST00000308763;ENST00000436272;ENST00000547195;ENST00000552103;ENST00000545852;ENST00000424001;ENST00000423302;ENST00000541483;ENST00000531107;ENST00000527509	T;T;T;T;T;T;T;T;T;T	0.17528	2.27;2.27;2.27;2.27;2.27;2.27;2.27;2.27;2.27;2.27	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.40956	0.1138	L	0.57536	1.79	0.80722	D	1	D;D;D;D	0.89917	0.996;1.0;1.0;1.0	D;D;D;D	0.87578	0.99;0.998;0.998;0.997	T	0.13980	-1.0489	10	0.56958	D	0.05	-13.6185	19.0062	0.92852	0.0:1.0:0.0:0.0	.	339;518;537;536	F5H6A1;Q9Y6F6;E9PQY6;Q9Y6F6-4	.;MRVI1_HUMAN;.;.	T	536;519;518;454;454;230;230;545;339;537;454	ENSP00000414598:R536T;ENSP00000412229:R518T;ENSP00000448278:R454T;ENSP00000446764:R454T;ENSP00000441971:R230T;ENSP00000401205:R230T;ENSP00000412130:R545T;ENSP00000437784:R339T;ENSP00000432436:R537T;ENSP00000432067:R454T	ENSP00000307885:R519T	R	-	2	0	MRVI1	10582637	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.538000	0.67193	2.553000	0.86117	0.563000	0.77884	AGA	.	.	.	alt		0.488	MRVI1-203	KNOWN	basic	protein_coding	protein_coding		NM_001098579		G	10626061	C	G	10626061	3	3	59	1	0	0	0	0	1	0	0	0	9860	913	32	4	1140	4	MRVI1	11	10626061	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08	9367672	10626061	124380455	14	3971											
ANAPC7	51434	hgsc.bcm.edu	37	chr12	110813921	110813921	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcctgatactcattgacagcTacaaggaaatctcctaggat	13	11	7	10	0	2	2	1	2	1	0	4	4	3	4	2	2	3	1	2	2	5	4			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr12:110813921T>C	ENST00000455511.3	-	10	1560	c.1560A>G	c.(1558-1560)gtA>gtG	p.V520V	ANAPC7_ENST00000450008.2_Silent_p.V520V|ANAPC7_ENST00000481473.1_5'UTR	NM_016238.2	NP_057322.2	Q9UJX3	APC7_HUMAN	anaphase promoting complex subunit 7	520					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)			breast(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)	19						CATTGACAGCTACAAGGAAAT	0.498																																					p.V520V		Atlas-SNP	.											.	ANAPC7	68	.	0			c.A1560G						PASS	.						141	119	126					12																	110813921		2203	4300	6503	SO:0001819	synonymous_variant	51434	exon10			GACAGCTACAAGG	AF191340	CCDS9145.2, CCDS44971.1	12q13.12	2013-01-10			ENSG00000196510	ENSG00000196510		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	17380	protein-coding gene	gene with protein product		606949					Standard	NM_016238		Approved	APC7	uc001tqo.2	Q9UJX3	OTTHUMG00000157009	ENST00000455511.3:c.1560A>G	chr12.hg19:g.110813921T>C		76.0	0.0	.		75.0	14.0	.	NM_016238	Q96AC4|Q96GF4|Q9BU24|Q9NT16	Silent	SNP	ENST00000455511.3	hg19	CCDS9145.2	.	.	.	.	.	.	.	.	.	.	T	10.12	1.263642	0.23136	.	.	ENSG00000196510	ENST00000552087	.	.	.	5.55	2.43	0.29744	.	.	.	.	.	T	0.58337	0.2115	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50415	-0.8831	4	.	.	.	-22.9206	9.4319	0.38615	0.0:0.3125:0.0:0.6875	.	.	.	.	G	70	.	.	S	-	1	0	ANAPC7	109298304	0.916000	0.31088	1.000000	0.80357	0.998000	0.95712	-0.028000	0.12350	0.179000	0.19938	0.459000	0.35465	AGC	.	.	.	none		0.498	ANAPC7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347075.3	NM_016238		C	110813921	T	C	110813921	2	2	59	1	0	0	0	0	0	0	0	1	606	1509	53	3		3	ANAPC7	12	110813921	Silent	SNP	T	TCGA-A4-8518-01A-11D-2396-08		110813921	23037974	15	3972											
ITGB3	3690	hgsc.bcm.edu	37	chr17	45361999	45361999	+	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	ggcttcggggcatttgtggaCaagcctgtgtcaccatacat	8	11	12	10	1	1	0	1	0	0	0	2	1	1	1	2	4	2	2	2	4	2	3	rs202100960		TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr17:45361999C>A	ENST00000559488.1	+	4	568	c.552C>A	c.(550-552)gaC>gaA	p.D184E	ITGB3_ENST00000571680.1_Missense_Mutation_p.D184E|ITGB3_ENST00000560629.1_Missense_Mutation_p.Q173K|ITGB3_ENST00000435993.2_Missense_Mutation_p.D137E	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	184	VWFA.				activation of protein kinase activity (GO:0032147)|angiogenesis involved in wound healing (GO:0060055)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mesodermal cell differentiation (GO:0048333)|negative chemotaxis (GO:0050919)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein folding (GO:0006457)|regulation of bone resorption (GO:0045124)|smooth muscle cell migration (GO:0014909)|substrate adhesion-dependent cell spreading (GO:0034446)|tube development (GO:0035295)|viral entry into host cell (GO:0046718)|wound healing (GO:0042060)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|melanosome (GO:0042470)|microvillus membrane (GO:0031528)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|receptor complex (GO:0043235)|ruffle membrane (GO:0032587)	cell adhesion molecule binding (GO:0050839)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|identical protein binding (GO:0042802)|platelet-derived growth factor receptor binding (GO:0005161)|protease binding (GO:0002020)|protein disulfide isomerase activity (GO:0003756)|receptor activity (GO:0004872)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39					Abciximab(DB00054)|Antithymocyte globulin(DB00098)|Eptifibatide(DB00063)|Tirofiban(DB00775)	CATTTGTGGACAAGCCTGTGT	0.552																																					p.D184E		Atlas-SNP	.											.	ITGB3	157	.	0			c.C552A						PASS	.						128	134	132					17																	45361999		2203	4300	6503	SO:0001583	missense	3690	exon4			TGTGGACAAGCCT		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.552C>A	chr17.hg19:g.45361999C>A	ENSP00000452786:p.Asp184Glu	247.0	0.0	.		281.0	15.0	.	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Missense_Mutation	SNP	ENST00000559488.1	hg19	CCDS11511.1	.	.	.	.	.	.	.	.	.	.	C	13.93	2.385128	0.42308	.	.	ENSG00000178852	ENST00000262017;ENST00000435993	D	0.98400	-4.91	5.86	4.87	0.63330	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	0.000000	0.85682	D	0.000000	D	0.98043	0.9355	M	0.66560	2.04	0.80722	D	1	D;D	0.64830	0.994;0.962	D;D	0.76575	0.988;0.954	D	0.97929	1.0319	10	0.02654	T	1	.	11.3787	0.49743	0.0:0.9067:0.0:0.0933	.	184;184	P05106;Q2YFE1	ITB3_HUMAN;.	E	184;137	ENSP00000407801:D137E	ENSP00000262017:D184E	D	+	3	2	C17orf57	42716998	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	1.226000	0.32563	1.399000	0.46721	0.655000	0.94253	GAC	.	.	.	weak		0.552	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212		A	45361999	C	A	45361999	3	1	59	1	0	0	0	0	1	0	0	0	7902	477	17	4	566	4	ITGB3	17	45361999	Missense_Mutation	SNP	C	TCGA-A4-8518-01A-11D-2396-08		45361999	35833211	16	3973											
ZNF99	7652	hgsc.bcm.edu	37	chr19	22941316	22941316	+	Missense_Mutation	SNP	A	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	tcatgttttctaagggctgaAaaattgctaaaagctttgct	12	15	8	6	0	2	1	1	1	1	0	2	1	2	1	0	1	3	5	0	1	5	6			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chr19:22941316A>C	ENST00000596209.1	-	4	1485	c.1395T>G	c.(1393-1395)ttT>ttG	p.F465L	ZNF99_ENST00000397104.3_Missense_Mutation_p.F374L	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	465					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TAAGGGCTGAAAAATTGCTAA	0.358																																					p.F465L		Atlas-SNP	.											ZNF99,NS,carcinoma,0,1	ZNF99	273	.	0			c.T1395G						PASS	.																																			SO:0001583	missense	7652	exon4			GGCTGAAAAATTG	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"Zinc fingers, C2H2-type", "-"	13175	protein-coding gene	gene with protein product		603981	"zinc finger protein 99 (F8281)", "chromosome 19 open reading frame 9"	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1395T>G	chr19.hg19:g.22941316A>C	ENSP00000472969:p.Phe465Leu	45.0	0.0	.		50.0	2.0	.	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	hg19	CCDS59369.1	.	.	.	.	.	.	.	.	.	.	N	0.008	-1.908376	0.00508	.	.	ENSG00000213973	ENST00000397104	T	0.07021	3.23	1.28	-2.55	0.06288	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02649	0.0080	N	0.03115	-0.41	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.42749	-0.9433	9	0.11182	T	0.66	.	4.7313	0.12966	0.5088:0.3226:0.1686:0.0	.	374	A8MXY4	ZNF99_HUMAN	L	374	ENSP00000380293:F374L	ENSP00000380293:F374L	F	-	3	2	ZNF99	22733156	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.098000	0.01347	-1.992000	0.00975	-0.630000	0.03990	TTT	.	.	.	none		0.358	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124		C	22941316	A	C	22941316	3	2	59	1	0	0	0	0	1	0	0	0	18216	11	1	5	2002	5	ZNF99	19	22941316	Missense_Mutation	SNP	A	TCGA-A4-8518-01A-11D-2396-08		22941316	36187667	17	3974											
FATE1	89885	hgsc.bcm.edu	37	chrX	150891105	150891105	+	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	ttgactcctctgcagctgtaTgcagtcaaccggcgtctgcg	6	11	11	13	3	3	1	1	1	2	0	4	1	4	1	2	1	5	4	2	1	2	2			TCGA-A4-8518-01A-11D-2396-08	TCGA-A4-8518-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f18659a-ddbf-48b6-a0b7-a17bfa7e924c	b2d31124-b2e7-4487-864e-be8baf0a8289	g.chrX:150891105T>G	ENST00000370350.3	+	5	511	c.426T>G	c.(424-426)taT>taG	p.Y142*		NM_033085.2	NP_149076.1	Q969F0	FATE1_HUMAN	fetal and adult testis expressed 1	142						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(2)|lung(6)|ovary(1)	15	Acute lymphoblastic leukemia(192;6.56e-05)					TGCAGCTGTATGCAGTCAACC	0.612																																					p.Y142X		Atlas-SNP	.											.	FATE1	30	.	0			c.T426G						PASS	.						57	64	62					X																	150891105		2203	4298	6501	SO:0001587	stop_gained	89885	exon5			GCTGTATGCAGTC	AF249872	CCDS14700.1	Xq28	2009-03-25			ENSG00000147378	ENSG00000147378			24683	protein-coding gene	gene with protein product	"cancer/testis antigen 43"	300450				11694338	Standard	NM_033085		Approved	FATE, CT43	uc004fex.3	Q969F0	OTTHUMG00000024172	ENST00000370350.3:c.426T>G	chrX.hg19:g.150891105T>G	ENSP00000359375:p.Tyr142*	84.0	0.0	.		98.0	4.0	.	NM_033085		Nonsense_Mutation	SNP	ENST00000370350.3	hg19	CCDS14700.1	.	.	.	.	.	.	.	.	.	.	T	10.36	1.329167	0.24167	.	.	ENSG00000147378	ENST00000370350	.	.	.	4.55	-9.11	0.00711	.	2.770910	0.01081	N	0.004990	.	.	.	.	.	.	0.54753	D	0.99998	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	11.7727	2.708	0.05166	0.2388:0.3595:0.2921:0.1096	.	.	.	.	X	142	.	ENSP00000359375:Y142X	Y	+	3	2	FATE1	150641761	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.221000	0.00140	-4.843000	0.00030	-1.019000	0.02448	TAT	.	.	.	none		0.612	FATE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060885.1	NM_033085		G	150891105	T	G	150891105	4	3	59	1	0	0	0	0	0	1	0	0	5700	1471	51	5	444	5	FATE1	23	150891105	Nonsense_Mutation	SNP	T	TCGA-A4-8518-01A-11D-2396-08		150891105	4379455	18	3975											
SSU72	29101	hgsc.bcm.edu	37	chr1	1480325	1480325	+	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	cagttctggaatctttctggCcggggcttgattctcttatt	5	17	10	9	1	4	1	0	1	4	0	5	2	4	2	1	4	0	2	1	4	2	6	rs138912153		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr1:1480325C>T	ENST00000291386.3	-	3	593	c.282G>A	c.(280-282)cgG>cgA	p.R94R		NM_014188.2	NP_054907.1	Q9NP77	SSU72_HUMAN	SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae)	94					dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)|mRNA polyadenylation (GO:0006378)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)			large_intestine(2)|lung(5)	7	all_cancers(77;0.00125)|all_epithelial(69;0.000703)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.03e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;5.04e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.72e-23)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;0.000188)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|STAD - Stomach adenocarcinoma(132;0.00645)|BRCA - Breast invasive adenocarcinoma(365;0.00837)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)		ATCTTTCTGGCCGGGGCTTGA	0.478																																					p.R94R		Atlas-SNP	.											.	SSU72	15	.	0			c.G282A						PASS	.						183	192	189					1																	1480325		2203	4300	6503	SO:0001819	synonymous_variant	29101	exon3			TTCTGGCCGGGGC	AJ276409	CCDS32.1	1p36	2010-03-24	2006-04-04		ENSG00000160075	ENSG00000160075			25016	protein-coding gene	gene with protein product			"Ssu72 RNA polymerase II CTD phosphatase homolog (yeast)"			15125841, 15659578	Standard	NM_014188		Approved	HSPC182	uc001agd.3	Q9NP77	OTTHUMG00000000576	ENST00000291386.3:c.282G>A	chr1.hg19:g.1480325C>T		265.0	0.0	.		197.0	71.0	.	NM_014188	Q9BZS6|Q9H933	Silent	SNP	ENST00000291386.3	hg19	CCDS32.1																																																																																			.	C|1.000;A|0.000	.	alt		0.478	SSU72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001366.1	NM_014188		T	1480325	C	T	1480325	2	4	60	1	0	0	0	0	0	0	0	1	15214	726	26	2		2	SSU72	1	1480325	Silent	SNP	C	TCGA-A4-8630-01A-11D-2396-08		1480325	247770296	1	3976											
CELA3B	23436	hgsc.bcm.edu	37	chr1	22310247	22310247	+	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	ctgggagacgccgtccagctCgcctcactccctccggctgg	4	7	12	18	4	1	1	1	0	0	1	5	2	4	1	5	3	1	2	5	3	0	0			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr1:22310247C>T	ENST00000337107.6	+	5	442	c.423C>T	c.(421-423)ctC>ctT	p.L141L		NM_007352.2	NP_031378.1	P08861	CEL3B_HUMAN	chymotrypsin-like elastase family, member 3B	141	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cholesterol metabolic process (GO:0008203)|proteolysis (GO:0006508)		peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			breast(2)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	8						CCGTCCAGCTCGCCTCACTCC	0.632																																					p.L141L		Atlas-SNP	.											.	CELA3B	24	.	0			c.C423T						PASS	.						96	77	83					1																	22310247		2203	4300	6503	SO:0001819	synonymous_variant	23436	exon5			CCAGCTCGCCTCA	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.423C>T	chr1.hg19:g.22310247C>T		136.0	0.0	.		119.0	38.0	.	NM_007352	B2RE44|P11423|Q5VU28|Q5VU29|Q5VU30	Silent	SNP	ENST00000337107.6	hg19	CCDS219.1																																																																																			.	.	.	none		0.632	CELA3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007797.1	NM_007352		T	22310247	C	T	22310247	2	4	60	1	0	0	0	0	0	0	0	1	3216	871	31	1		1	CELA3B	1	22310247	Silent	SNP	C	TCGA-A4-8630-01A-11D-2396-08	20829922	22310247	226940374	2	3977											
ASAP3	55616	hgsc.bcm.edu	37	chr1	23759922	23759922	+	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	cagggctgggacccaccttcTcttcctcatcctcctcactg	5	11	7	18	0	3	0	2	0	1	0	7	1	6	1	5	2	0	1	5	2	0	2			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr1:23759922T>A	ENST00000336689.3	-	21	2167	c.2123A>T	c.(2122-2124)gAg>gTg	p.E708V	ASAP3_ENST00000437606.2_Missense_Mutation_p.E699V|ASAP3_ENST00000495646.1_Missense_Mutation_p.E212V	NM_017707.3	NP_060177.2	Q8TDY4	ASAP3_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 3	708					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						ACCCACCTTCTCTTCCTCATC	0.622																																					p.E708V		Atlas-SNP	.											.	ASAP3	65	.	0			c.A2123T						PASS	.						73	72	72					1																	23759922		2203	4300	6503	SO:0001583	missense	55616	exon21			ACCTTCTCTTCCT	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.2123A>T	chr1.hg19:g.23759922T>A	ENSP00000338769:p.Glu708Val	119.0	0.0	.		90.0	47.0	.	NM_017707	B3KRW0|B4DHH4|Q6P9F4|Q86UY1|Q9NXK2	Missense_Mutation	SNP	ENST00000336689.3	hg19	CCDS235.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.453556	0.84209	.	.	ENSG00000088280	ENST00000538685;ENST00000495646;ENST00000336689;ENST00000465372;ENST00000437606	T;T;T	0.56941	1.77;0.43;0.43	4.69	4.69	0.59074	.	3.712730	0.00567	N	0.000291	T	0.65228	0.2671	L	0.27053	0.805	0.58432	D	0.999999	D;D;D;D	0.76494	0.996;0.996;0.981;0.999	P;D;P;P	0.65874	0.892;0.939;0.77;0.905	T	0.50215	-0.8854	10	0.72032	D	0.01	.	13.4102	0.60938	0.0:0.0:0.0:1.0	.	699;577;231;708	Q8TDY4-3;B4DRP2;Q9NXH7;Q8TDY4	.;.;.;ASAP3_HUMAN	V	231;212;708;35;699	ENSP00000436150:E212V;ENSP00000338769:E708V;ENSP00000408826:E699V	ENSP00000338769:E708V	E	-	2	0	ASAP3	23632509	1.000000	0.71417	0.999000	0.59377	0.950000	0.60333	7.415000	0.80131	2.104000	0.64026	0.459000	0.35465	GAG	.	.	.	none		0.622	ASAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008916.2	NM_017707		A	23759922	T	A	23759922	3	1	60	1	0	0	0	0	1	0	0	0	1012	1551	54	5	608	5	ASAP3	1	23759922	Missense_Mutation	SNP	T	TCGA-A4-8630-01A-11D-2396-08	1449675	23759922	225490699	3	3978											
CSMD2	114784	hgsc.bcm.edu	37	chr1	33985175	33985175	+	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	gcctcgctggccatgatgtcTgtgggctggatgttgcggtc	3	12	16	10	2	1	1	0	1	1	0	3	2	1	2	2	4	1	3	2	4	0	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr1:33985175T>A	ENST00000373381.4	-	70	11015	c.10839A>T	c.(10837-10839)acA>acT	p.T3613T		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	3469						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)				CCATGATGTCTGTGGGCTGGA	0.592																																					p.T3469T		Atlas-SNP	.											.	CSMD2	946	.	0			c.A10407T						PASS	.						287	241	256					1																	33985175		2203	4300	6503	SO:0001819	synonymous_variant	114784	exon69			GATGTCTGTGGGC	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.10839A>T	chr1.hg19:g.33985175T>A		330.0	0.0	.		235.0	90.0	.	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Silent	SNP	ENST00000373381.4	hg19																																																																																				.	.	.	none		0.592	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		A	33985175	T	A	33985175	2	1	60	1	0	0	0	0	0	0	0	1	3947	1567	55	5		5	CSMD2	1	33985175	Silent	SNP	T	TCGA-A4-8630-01A-11D-2396-08	10225253	33985175	215265446	4	3979											
TTF2	8458	hgsc.bcm.edu	37	chr1	117618867	117618867	+	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	cagaagttgatcaaacaaatCcaggagctggaggaagtact	16	7	11	7	0	1	2	1	1	0	1	2	5	2	5	1	3	3	3	1	3	5	2			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr1:117618867C>G	ENST00000369466.4	+	6	1385	c.1341C>G	c.(1339-1341)atC>atG	p.I447M		NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	447					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)		TCAAACAAATCCAGGAGCTGG	0.478																																					p.I447M		Atlas-SNP	.											.	TTF2	92	.	0			c.C1341G						PASS	.						101	95	97					1																	117618867		2203	4300	6503	SO:0001583	missense	8458	exon6			ACAAATCCAGGAG	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.1341C>G	chr1.hg19:g.117618867C>G	ENSP00000358478:p.Ile447Met	75.0	0.0	.		48.0	19.0	.	NM_003594	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	Missense_Mutation	SNP	ENST00000369466.4	hg19	CCDS892.1	.	.	.	.	.	.	.	.	.	.	C	13.01	2.109329	0.37242	.	.	ENSG00000116830	ENST00000369466	D	0.88975	-2.45	5.41	-4.64	0.03349	.	0.000000	0.37906	N	0.001883	D	0.84379	0.5459	M	0.70595	2.14	0.34103	D	0.662138	D;D	0.67145	0.996;0.979	P;P	0.61800	0.894;0.857	T	0.77988	-0.2380	10	0.72032	D	0.01	-12.3789	1.4425	0.02357	0.2154:0.3707:0.1077:0.3062	.	447;447	Q9UNY4;Q9UNY4-2	TTF2_HUMAN;.	M	447	ENSP00000358478:I447M	ENSP00000358478:I447M	I	+	3	3	TTF2	117420390	0.918000	0.31147	0.794000	0.32065	0.071000	0.16799	-0.183000	0.09712	-0.727000	0.04888	0.561000	0.74099	ATC	.	.	.	none		0.478	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033277.3			G	117618867	C	G	117618867	3	3	60	1	0	0	0	0	1	0	0	0	16731	845	30	4	1363	4	TTF2	1	117618867	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08	83633692	117618867	131631754	5	3980											
SMG5	23381	hgsc.bcm.edu	37	chr1	156221203	156221203	+	Frame_Shift_Del	DEL	G	G	-																															taaaatgttaccaggcatctGcatcctgcctcttcagctta																										TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr1:156221203delG	ENST00000361813.5	-	20	2963	c.2819delC	c.(2818-2820)gcafs	p.A940fs	SMG5_ENST00000368267.5_Intron	NM_015327.2	NP_056142.2	Q9UPR3	SMG5_HUMAN	SMG5 nonsense mediated mRNA decay factor	940	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)					CCAGGCATCTGCATCCTGCCT	0.552																																					p.A940fs		Atlas-INDEL	.											.	SMG5	98	.	0			c.2820delA						PASS	.						224	214	217					1																	156221203		2203	4300	6503	SO:0001589	frameshift_variant	23381	exon20			.	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.2819delC	chr1.hg19:g.156221203delG	ENSP00000355261:p.Ala940fs	226.0	0.0	0		197.0	69.0	0.350254	NM_015327	D3DVB7|Q5QJE7|Q659C7|Q8IXC0|Q8IY09|Q96IJ7	Frame_Shift_Del	DEL	ENST00000361813.5	hg19	CCDS1137.1																																																																																			.	.	.	none		0.552	SMG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046308.1	NM_015327		-	156221203	G	-	156221203	7	5	60	1	0	1	0	1	0	0	0	0	14809	1319	46	0	243	0	SMG5	1	156221203	Frame_Shift_Del	DEL	G	TCGA-A4-8630-01A-11D-2396-08	38602336	156221203	93029418	6	3981											
C1orf66	51093	hgsc.bcm.edu	37	chr1	156706431	156706431	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctttctcccaggtttccaTgctgagctcctgcccatctt	4	14	6	17	0	2	1	0	1	2	0	5	1	4	1	5	1	3	3	5	1	0	3			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr1:156706431T>C	ENST00000368216.4	+	8	1944	c.1314T>C	c.(1312-1314)caT>caC	p.H438H	RRNAD1_ENST00000476229.1_Missense_Mutation_p.C154R|RRNAD1_ENST00000368218.4_Missense_Mutation_p.C277R|RRNAD1_ENST00000481920.1_Intron|MRPL24_ENST00000478899.1_5'Flank	NM_015997.3	NP_057081.3	Q96FB5	RRNAD_HUMAN	ribosomal RNA adenine dimethylase domain containing 1	438						integral component of membrane (GO:0016021)	rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(3)	9						CAGGTTTCCATGCTGAGCTCC	0.532																																					p.C277R		Atlas-SNP	.											RRNAD1,NS,carcinoma,0,1	RRNAD1	39	.	0			c.T829C						PASS	.						132	123	126					1																	156706431		2203	4300	6503	SO:0001819	synonymous_variant	51093	exon7			TTTCCATGCTGAG	BC011382	CCDS1154.1, CCDS44246.1	1q23.1	2011-01-28	2011-01-28	2011-01-28	ENSG00000143303	ENSG00000143303			24273	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 66"	C1orf66		10810093, 310876	Standard	NM_015997		Approved	CGI-41	uc001fpu.3	Q96FB5	OTTHUMG00000041302	ENST00000368216.4:c.1314T>C	chr1.hg19:g.156706431T>C		154.0	0.0	.		135.0	52.0	.	NM_001142560	D3DVC7|Q4VX71|Q5SZ03|Q9Y358	Missense_Mutation	SNP	ENST00000368216.4	hg19	CCDS1154.1	.	.	.	.	.	.	.	.	.	.	T	13.71	2.319855	0.41096	.	.	ENSG00000143303	ENST00000368218;ENST00000476229	.	.	.	5.87	0.792	0.18625	.	.	.	.	.	T	0.25232	0.0613	.	.	.	0.36802	D	0.885409	B	0.06786	0.001	B	0.01281	0.0	T	0.08638	-1.0712	7	0.87932	D	0	-4.8252	4.626	0.12479	0.0:0.2522:0.2302:0.5176	.	277	Q4VX71	.	R	277;154	.	ENSP00000357201:C277R	C	+	1	0	RRNAD1	154973055	0.996000	0.38824	1.000000	0.80357	0.386000	0.30323	0.158000	0.16422	0.158000	0.19367	0.533000	0.62120	TGC	.	.	.	none		0.532	RRNAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098973.1	NM_015997		C	156706431	T	C	156706431	2	2	60	1	0	0	0	0	0	0	0	1	2058	1464	51	3		3	C1orf66	1	156706431	Silent	SNP	T	TCGA-A4-8630-01A-11D-2396-08	485228	156706431	92544190	7	3982											
BAT2L2	23215	hgsc.bcm.edu	37	chr1	171482181	171482181	+	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	ttggaaaagtcggtatttcaCggcgtatgcctccacctgct	8	12	10	11	3	1	0	1	0	0	0	3	1	2	1	3	3	2	3	3	3	4	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr1:171482181C>G	ENST00000338920.4	+	3	391	c.154C>G	c.(154-156)Cgg>Ggg	p.R52G	PRRC2C_ENST00000367742.3_Missense_Mutation_p.R54G|PRRC2C_ENST00000476522.1_3'UTR|PRRC2C_ENST00000392078.3_Missense_Mutation_p.R54G|PRRC2C_ENST00000426496.2_Missense_Mutation_p.R52G	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	52					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										CGGTATTTCACGGCGTATGCC	0.403																																					p.R52G		Atlas-SNP	.											.	.	.	.	0			c.C154G						PASS	.						115	110	112					1																	171482181		2203	4300	6503	SO:0001583	missense	23215	exon3			ATTTCACGGCGTA	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.154C>G	chr1.hg19:g.171482181C>G	ENSP00000343629:p.Arg52Gly	65.0	0.0	.		56.0	20.0	.	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	hg19	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	C	12.62	1.993708	0.35131	.	.	ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920	T;T;T;T	0.51817	0.69;0.69;0.69;0.69	5.82	2.79	0.32731	BAT2, N-terminal (1);	0.000000	0.43579	D	0.000551	T	0.61110	0.2321	M	0.81341	2.54	0.54753	D	0.999983	D;D;D	0.89917	0.999;1.0;0.98	D;D;P	0.79108	0.943;0.992;0.749	T	0.69665	-0.5084	10	0.87932	D	0	.	15.4227	0.75025	0.5817:0.4183:0.0:0.0	.	52;54;52	Q9Y520-4;E7EPN9;Q9Y520	.;.;PRC2C_HUMAN	G	54;52;52;54;52	ENSP00000375928:R54G;ENSP00000410219:R52G;ENSP00000356716:R54G;ENSP00000343629:R52G	ENSP00000343629:R52G	R	+	1	2	PRRC2C	169748805	0.984000	0.35163	0.999000	0.59377	0.992000	0.81027	2.586000	0.46119	0.312000	0.23038	-0.169000	0.13324	CGG	.	.	.	none		0.403	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		G	171482181	C	G	171482181	3	3	60	1	0	0	0	0	1	0	0	0	1321	527	19	4	160	4	BAT2L2	1	171482181	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08	14775750	171482181	77768440	8	3983											
TRIM11	81559	hgsc.bcm.edu	37	chr1	228584695	228584695	+	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	gtcccgggaccctgcacacgGtcctcagctccataggcaca	8	6	10	17	2	1	0	1	0	0	0	4	1	4	1	4	3	2	3	4	3	1	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr1:228584695G>T	ENST00000284551.6	-	5	1090	c.812C>A	c.(811-813)aCc>aAc	p.T271N	RP11-245P10.8_ENST00000602963.1_RNA|TRIM11_ENST00000460651.1_5'UTR|TRIM11_ENST00000493030.2_Missense_Mutation_p.T146N|TRIM11_ENST00000366699.3_Missense_Mutation_p.T271N	NM_145214.2	NP_660215.1	Q96F44	TRI11_HUMAN	tripartite motif containing 11	271	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				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)				CCTGCACACGGTCCTCAGCTC	0.627																																					p.T271N		Atlas-SNP	.											.	TRIM11	38	.	0			c.C812A						PASS	.						85	85	85					1																	228584695		2203	4300	6503	SO:0001583	missense	81559	exon5			CACACGGTCCTCA	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.812C>A	chr1.hg19:g.228584695G>T	ENSP00000284551:p.Thr271Asn	101.0	0.0	.		80.0	35.0	.	NM_145214	A6NKE2|B2RB82|B3KUS3|B4DX88|Q5VSU1|Q8NCA6|Q9C022	Missense_Mutation	SNP	ENST00000284551.6	hg19	CCDS31048.1	.	.	.	.	.	.	.	.	.	.	G	18.10	3.549179	0.65311	.	.	ENSG00000154370	ENST00000284551;ENST00000366699	T;T	0.06768	3.26;3.26	4.97	4.97	0.65823	B30.2/SPRY domain (1);	0.000000	0.41605	D	0.000853	T	0.19127	0.0459	L	0.41079	1.255	0.34988	D	0.754698	D;D;P	0.89917	1.0;1.0;0.781	D;D;B	0.97110	1.0;1.0;0.248	T	0.11108	-1.0601	10	0.26408	T	0.33	.	14.103	0.65070	0.0:0.0:1.0:0.0	.	270;271;271	Q96F44-3;Q96F44-2;Q96F44	.;.;TRI11_HUMAN	N	271	ENSP00000284551:T271N;ENSP00000355660:T271N	ENSP00000284551:T271N	T	-	2	0	TRIM11	226651318	0.932000	0.31603	0.909000	0.35828	0.546000	0.35178	1.634000	0.37123	2.482000	0.83794	0.313000	0.20887	ACC	.	.	.	none		0.627	TRIM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095995.3	NM_145214		T	228584695	G	T	228584695	3	4	60	1	0	0	0	0	1	0	0	0	16499	1261	44	4	602	4	TRIM11	1	228584695	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08	57102514	228584695	20665926	9	3984											
SLC8A1	6546	hgsc.bcm.edu	37	chr2	40405590	40405590	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggaagaaggtcttgttttTctcatactcctcatcatcaa	12	14	6	9	0	5	1	4	0	2	1	7	2	6	2	1	2	1	1	1	2	5	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr2:40405590T>C	ENST00000403092.1	-	3	1885	c.1852A>G	c.(1852-1854)Aaa>Gaa	p.K618E	SLC8A1-AS1_ENST00000599956.1_RNA|SLC8A1_ENST00000408028.2_Intron|SLC8A1_ENST00000406785.2_Intron|SLC8A1_ENST00000406391.2_Intron|SLC8A1-AS1_ENST00000444629.1_RNA|SLC8A1-AS1_ENST00000599268.1_RNA|SLC8A1-AS1_ENST00000599740.1_RNA|SLC8A1_ENST00000542756.1_Missense_Mutation_p.K618E|SLC8A1_ENST00000405901.3_Missense_Mutation_p.K618E|SLC8A1-AS1_ENST00000593878.1_RNA|SLC8A1-AS1_ENST00000597385.1_RNA|SLC8A1_ENST00000542024.1_Intron|SLC8A1-AS1_ENST00000598247.1_RNA|SLC8A1-AS1_ENST00000596532.1_RNA|SLC8A1-AS1_ENST00000435515.1_RNA|SLC8A1_ENST00000405269.1_Intron|SLC8A1-AS1_ENST00000597170.1_RNA|SLC8A1-AS1_ENST00000601679.1_RNA|SLC8A1-AS1_ENST00000593848.1_RNA|SLC8A1_ENST00000332839.4_Missense_Mutation_p.K618E|SLC8A1_ENST00000402441.1_Intron			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1	618	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)	GTCTTGTTTTTCTCATACTCC	0.468																																					p.K618E		Atlas-SNP	.											SLC8A1,NS,carcinoma,0,1	SLC8A1	221	.	0			c.A1852G						PASS	.						239	235	237					2																	40405590		2203	4300	6503	SO:0001583	missense	6546	exon2			TGTTTTTCTCATA		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.1852A>G	chr2.hg19:g.40405590T>C	ENSP00000384763:p.Lys618Glu	270.0	0.0	.		241.0	108.0	.	NM_021097	A8K6N1|D6W595|O95849|Q4QQG6|Q587I6|Q59GN4|Q9UBL8|Q9UD55|Q9UDN1|Q9UDN2|Q9UKX6	Missense_Mutation	SNP	ENST00000403092.1	hg19	CCDS1806.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.338174	0.81911	.	.	ENSG00000183023	ENST00000378715;ENST00000542756;ENST00000403092;ENST00000405901;ENST00000332839	T;T;T;T	0.28069	1.63;1.63;1.63;1.63	5.39	5.39	0.77823	Na-Ca exchanger/integrin-beta4 (2);	0.000000	0.85682	D	0.000000	T	0.49423	0.1556	L	0.52011	1.625	0.80722	D	1	P;D	0.89917	0.917;1.0	P;D	0.91635	0.721;0.999	T	0.50800	-0.8785	10	0.87932	D	0	.	13.3557	0.60627	0.0:0.0:0.0:1.0	.	618;618	F6VPY9;P32418	.;NAC1_HUMAN	E	618	ENSP00000440727:K618E;ENSP00000384763:K618E;ENSP00000385678:K618E;ENSP00000332931:K618E	ENSP00000332931:K618E	K	-	1	0	SLC8A1	40259094	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.587000	0.82613	2.028000	0.59812	0.482000	0.46254	AAA	.	.	.	none		0.468	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	NM_021097		C	40405590	T	C	40405590	3	2	60	1	0	0	0	0	1	0	0	0	14719	1792	62	3	1213	3	SLC8A1	2	40405590	Missense_Mutation	SNP	T	TCGA-A4-8630-01A-11D-2396-08		40405590	202793783	10	3985											
FBXO11	80204	hgsc.bcm.edu	37	chr2	48049436	48049436	+	Missense_Mutation	SNP	A	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	tgatttccattaaatatagaAtttcccctataattatgcga	14	16	4	7	1	0	2	0	1	0	1	2	3	2	2	3	0	1	0	3	0	8	8			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr2:48049436A>C	ENST00000403359.3	-	13	1695	c.1623T>G	c.(1621-1623)aaT>aaG	p.N541K	FBXO11_ENST00000402508.1_Missense_Mutation_p.N457K|FBXO11_ENST00000316377.4_Missense_Mutation_p.N457K|FBXO11_ENST00000434523.2_5'UTR	NM_001190274.1	NP_001177203.1	Q86XK2	FBX11_HUMAN	F-box protein 11	541					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)			TAAATATAGAATTTCCCCTAT	0.343			"Mis, F, D"		DLBCL																																p.N541K		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.T1623G						PASS	.						51	51	51					2																	48049436		2202	4298	6500	SO:0001583	missense	80204	exon13			TATAGAATTTCCC	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.1623T>G	chr2.hg19:g.48049436A>C	ENSP00000384823:p.Asn541Lys	54.0	0.0	.		54.0	19.0	.	NM_001190274	A1L491|Q52ZP1|Q53EP7|Q53RT5|Q8IXG3|Q96E90|Q9H6V8|Q9H9L1|Q9NR14|Q9UFK1|Q9UHI1|Q9UKC2	Missense_Mutation	SNP	ENST00000403359.3	hg19	CCDS54357.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.6|20.6	4.023026|4.023026	0.75275|0.75275	.|.	.|.	ENSG00000138081|ENSG00000138081	ENST00000493962|ENST00000402508;ENST00000403359;ENST00000316377	.|D;D;D	.|0.89485	.|-2.52;-1.81;-2.52	5.42|5.42	5.42|5.42	0.78866|0.78866	.|Pectin lyase fold/virulence factor (1);Carbohydrate-binding/sugar hydrolysis domain (1);F-box domain, Skp2-like (1);Pectin lyase fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.93135|0.93135	0.7814|0.7814	M|M	0.92459|0.92459	3.31|3.31	0.80722|0.80722	D|D	1|1	.|B	.|0.26258	.|0.145	.|B	.|0.37304	.|0.246	D|D	0.92695|0.92695	0.6170|0.6170	5|10	.|0.66056	.|D	.|0.02	-16.8508|-16.8508	15.4471|15.4471	0.75238|0.75238	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|541	.|Q86XK2	.|FBX11_HUMAN	V|K	333|457;541;457	.|ENSP00000385398:N457K;ENSP00000384823:N541K;ENSP00000323822:N457K	.|ENSP00000323822:N457K	F|N	-|-	1|3	0|2	FBXO11|FBXO11	47902940|47902940	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	4.344000|4.344000	0.59354|0.59354	2.039000|2.039000	0.60335|0.60335	0.533000|0.533000	0.62120|0.62120	TTC|AAT	.	.	.	none		0.343	FBXO11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251181.3	NM_012167, NM_018693, NM_025133		C	48049436	A	C	48049436	3	2	60	1	0	0	0	0	1	0	0	0	5734	98	4	5	1294	5	FBXO11	2	48049436	Missense_Mutation	SNP	A	TCGA-A4-8630-01A-11D-2396-08	7643846	48049436	195149937	11	3986											
TTN	7273	hgsc.bcm.edu	37	chr2	179429832	179429834	+	In_Frame_Del	DEL	AAT	AAT	-																															gttgtatctcgcttctctacAatgtagttgcttatttggca																										TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr2:179429832_179429834delAAT	ENST00000591111.1	-	276	76326_76328	c.76102_76104delATT	c.(76102-76104)attdel	p.I25368del	TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000591332.1_RNA|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_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_In_Frame_Del_p.I18069del|TTN_ENST00000460472.2_In_Frame_Del_p.I17944del|TTN_ENST00000342992.6_In_Frame_Del_p.I24441del|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000589042.1_In_Frame_Del_p.I27009del|TTN_ENST00000342175.6_In_Frame_Del_p.I18136del			Q8WZ42	TITIN_HUMAN	titin	25368	Fibronectin type-III 84. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCTTCTCTACAATGTAGTTGCTT	0.443																																					p.27009_27010del		Atlas-INDEL	.											.	TTN	18412	.	0			c.81026_81028del						PASS	.																																			SO:0001651	inframe_deletion	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.76102_76104delATT	chr2.hg19:g.179429832_179429834delAAT	ENSP00000465570:p.Ile25368del	158.0	0.0	0		138.0	58.0	0.42029	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	In_Frame_Del	DEL	ENST00000591111.1	hg19																																																																																				.	.	.	none		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		-	179429834	AAT	-	179429832	7	5	60	1	0	1	0	1	0	0	0	0	16747	126	5	0	27100	0	TTN	2	179429832	In_Frame_Del	DEL	AAT	TCGA-A4-8630-01A-11D-2396-08	131380396	179429832	63769541	12	3987											
VGLL4	10533	hgsc.bcm.edu	37	chr3	11600049	11600049	+	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	ttcaggagaccacagaggggGagtgactgtggctgaccatg	10	7	16	8	0	1	4	1	2	0	2	1	6	1	5	2	4	0	1	2	4	0	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr3:11600049G>A	ENST00000354449.3	+	0	4959				VGLL4_ENST00000424529.2_Missense_Mutation_p.S201F|VGLL4_ENST00000404339.1_Missense_Mutation_p.S290F|VGLL4_ENST00000451674.2_Missense_Mutation_p.S205F|VGLL4_ENST00000273038.3_Missense_Mutation_p.S285F|VGLL4_ENST00000413604.1_Missense_Mutation_p.S226F|VGLL4_ENST00000430365.2_Missense_Mutation_p.S291F	NM_006395.2	NP_006386.1	O95352	ATG7_HUMAN	autophagy related 7						adult walking behavior (GO:0007628)|C-terminal protein lipidation (GO:0006501)|cardiac muscle cell development (GO:0055013)|cellular amino acid metabolic process (GO:0006520)|cellular protein modification process (GO:0006464)|cellular response to hyperoxia (GO:0071455)|cellular response to nitrogen starvation (GO:0006995)|cellular response to starvation (GO:0009267)|central nervous system neuron axonogenesis (GO:0021955)|cerebellar Purkinje cell layer development (GO:0021680)|cerebral cortex development (GO:0021987)|late nucleophagy (GO:0044805)|liver development (GO:0001889)|membrane fusion (GO:0061025)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of apoptotic process (GO:0043066)|negative stranded viral RNA replication (GO:0039689)|neurological system process (GO:0050877)|piecemeal microautophagy of nucleus (GO:0034727)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein modification process (GO:0031401)|post-embryonic development (GO:0009791)|protein catabolic process (GO:0030163)|protein lipidation (GO:0006497)|protein modification by small protein conjugation (GO:0032446)|protein transport (GO:0015031)|pyramidal neuron development (GO:0021860)|regulation of protein ubiquitination (GO:0031396)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|pre-autophagosomal structure (GO:0000407)	Atg12 activating enzyme activity (GO:0019778)|Atg8 activating enzyme (GO:0019779)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)|ubiquitin activating enzyme activity (GO:0004839)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(14)|prostate(1)|skin(2)|urinary_tract(1)	34						CACAGAGGGGGAGTGACTGTG	0.572																																					p.S291F		Atlas-SNP	.											.	VGLL4	47	.	0			c.C872T						PASS	.						43	49	47					3																	11600049		2203	4299	6502	SO:0001628	intergenic_variant	9686	exon5			GAGGGGGAGTGAC	AF094516	CCDS2605.1, CCDS46752.1, CCDS46753.1	3p25.3-p25.2	2014-02-18	2012-06-06	2005-09-11	ENSG00000197548	ENSG00000197548		"Ubiquitin-like modifier activating enzymes"	16935	protein-coding gene	gene with protein product	"ubiquitin-activating enzyme E1-like protein"	608760	"APG7 autophagy 7-like (S. cerevisiae)", "ATG7 autophagy related 7 homolog (S. cerevisiae)"	APG7L		10233149	Standard	NM_006395		Approved	GSA7, DKFZp434N0735	uc003bwc.3	O95352	OTTHUMG00000129740		chr3.hg19:g.11600049G>A		97.0	0.0	.		101.0	18.0	.	NM_001128219	B4E170|E9PB95|Q7L8L0|Q9BWP2|Q9UFH4	Missense_Mutation	SNP	ENST00000354449.3	hg19	CCDS2605.1	.	.	.	.	.	.	.	.	.	.	G	17.27	3.347047	0.61183	.	.	ENSG00000144560	ENST00000273038;ENST00000413604;ENST00000451674;ENST00000424529;ENST00000430365;ENST00000404339	T;T;T	0.60672	0.23;0.26;0.17	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	T	0.74696	0.3750	M	0.62723	1.935	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.998;0.998;0.998;0.998;0.998	T	0.77851	-0.2434	10	0.87932	D	0	-39.5652	18.3059	0.90180	0.0:0.0:1.0:0.0	.	291;205;201;290;285	G5E9M7;Q14135-6;Q14135-5;G5E9F4;Q14135	.;.;.;.;VGLL4_HUMAN	F	285;226;205;201;291;290	ENSP00000273038:S285F;ENSP00000404251:S291F;ENSP00000384705:S290F	ENSP00000273038:S285F	S	-	2	0	VGLL4	11575049	1.000000	0.71417	0.967000	0.41034	0.519000	0.34347	7.672000	0.83956	2.321000	0.78463	0.563000	0.77884	TCC	.	.	.	none		0.572	ATG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251951.3	NM_006395		A	11600049	G	A	11600049	1	1	60	0	1	0	0	0	0	0	0	0	17173	1174	41	2		2	VGLL4	3	11600049	IGR	SNP	G	TCGA-A4-8630-01A-11D-2396-08		11600049	186422381	13	3988											
B4GALT4	8702	hgsc.bcm.edu	37	chr3	118945881	118945881	+	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	ggtttgaaaatgagcttgctCtggcctcctacaatgaacat	11	12	9	9	0	1	3	0	3	1	0	2	3	2	3	2	2	4	3	2	2	5	3			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr3:118945881C>T	ENST00000483209.1	-	4	902	c.261G>A	c.(259-261)caG>caA	p.Q87Q	B4GALT4_ENST00000393765.2_Silent_p.Q87Q|B4GALT4_ENST00000460321.1_5'UTR|B4GALT4-AS1_ENST00000470790.1_RNA|B4GALT4_ENST00000471675.1_Silent_p.Q40Q|B4GALT4_ENST00000467604.1_Silent_p.Q87Q|B4GALT4_ENST00000359213.3_Silent_p.Q87Q			O60513	B4GT4_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 4	87					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)|membrane lipid metabolic process (GO:0006643)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)			breast(2)|endometrium(1)|large_intestine(1)|lung(6)|skin(2)|stomach(2)	14				GBM - Glioblastoma multiforme(114;0.222)	N-Acetyl-D-glucosamine(DB00141)	TGAGCTTGCTCTGGCCTCCTA	0.443																																					p.Q87Q		Atlas-SNP	.											.	B4GALT4	30	.	0			c.G261A						PASS	.						91	90	90					3																	118945881		2203	4300	6503	SO:0001819	synonymous_variant	8702	exon5			CTTGCTCTGGCCT	AF022367	CCDS2986.1	3q13.3	2013-02-19			ENSG00000121578	ENSG00000121578		"Beta 4-glycosyltransferases"	927	protein-coding gene	gene with protein product		604015				9597550	Standard	NM_003778		Approved	beta4Gal-T4	uc003eci.3	O60513	OTTHUMG00000159358	ENST00000483209.1:c.261G>A	chr3.hg19:g.118945881C>T		67.0	0.0	.		81.0	4.0	.	NM_212543	Q68D68|Q9BSW3|Q9C078	Silent	SNP	ENST00000483209.1	hg19	CCDS2986.1																																																																																			.	.	.	none		0.443	B4GALT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354925.2	NM_003778		T	118945881	C	T	118945881	2	4	60	1	0	0	0	0	0	0	0	1	1273	912	32	2		2	B4GALT4	3	118945881	Silent	SNP	C	TCGA-A4-8630-01A-11D-2396-08	107345832	118945881	79076549	14	3989											
ITGB5	3693	hgsc.bcm.edu	37	chr3	124487860	124487860	+	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	ggtggtggcagcacactcacCgatggtgtccacccatgtga	8	8	13	12	1	1	1	1	1	0	0	2	2	2	1	3	4	1	2	3	4	0	0	rs375122712		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr3:124487860C>T	ENST00000296181.4	-	12	2313	c.2017G>A	c.(2017-2019)Gtg>Atg	p.V673M	ITGB5_ENST00000461306.1_5'UTR	NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	673					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|epithelial cell-cell adhesion (GO:0090136)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alphav-beta5 complex (GO:0034684)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	30				GBM - Glioblastoma multiforme(114;0.163)		GCACACTCACCGATGGTGTCC	0.587																																					p.V673M		Atlas-SNP	.											.	ITGB5	66	.	0			c.G2017A						PASS	.	C	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	131	113	119		2017	4.3	1	3		119	0,8600		0,0,4300	no	missense-near-splice	ITGB5	NM_002213.3	21	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	673/800	124487860	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	3693	exon12			ACTCACCGATGGT	J05633	CCDS3030.1	3q21.2	2010-03-23			ENSG00000082781	ENSG00000082781		"Integrins"	6160	protein-coding gene	gene with protein product		147561				2211615	Standard	NM_002213		Approved		uc003eho.3	P18084	OTTHUMG00000159432	ENST00000296181.4:c.2017+1G>A	chr3.hg19:g.124487860C>T		71.0	0.0	.		101.0	29.0	.	NM_002213	B0LPF8|B2RD70	Missense_Mutation	SNP	ENST00000296181.4	hg19	CCDS3030.1	.	.	.	.	.	.	.	.	.	.	C	14.77	2.633900	0.47049	2.27E-4	0.0	ENSG00000082781	ENST00000296181	D	0.90261	-2.64	5.29	4.34	0.51931	Integrin beta subunit, tail (2);	0.762691	0.12573	N	0.457111	D	0.83151	0.5192	L	0.29908	0.895	0.38470	D	0.94744	B	0.20052	0.041	B	0.18561	0.022	T	0.76046	-0.3102	9	.	.	.	.	8.2832	0.31913	0.0:0.8282:0.0:0.1718	.	673	P18084	ITB5_HUMAN	M	673	ENSP00000296181:V673M	.	V	-	1	0	ITGB5	125970550	0.915000	0.31059	1.000000	0.80357	0.994000	0.84299	1.262000	0.32992	2.761000	0.94854	0.655000	0.94253	GTG	.	.	.	weak		0.587	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3	NM_002213	Missense_Mutation	T	124487860	C	T	124487860	5	4	60	1	0	0	0	0	0	0	1	0	7905	666	23	1	398	1	ITGB5	3	124487860	Splice_Site	SNP	C	TCGA-A4-8630-01A-11D-2396-08	5541979	124487860	73534570	15	3990											
FGFR3	2261	hgsc.bcm.edu	37	chr4	1807787	1807787	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccttccccagtgcatccacAgggacctggctgcccgcaat	7	7	9	18	1	0	0	0	0	0	0	2	1	2	1	6	2	2	3	6	2	1	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr4:1807787A>G	ENST00000260795.2	+	13	1948	c.1846A>G	c.(1846-1848)Agg>Ggg	p.R616G	FGFR3_ENST00000340107.4_Missense_Mutation_p.R618G|FGFR3_ENST00000481110.2_Missense_Mutation_p.R617G|FGFR3_ENST00000440486.2_Missense_Mutation_p.R616G|FGFR3_ENST00000412135.2_Missense_Mutation_p.R504G|FGFR3_ENST00000352904.1_Missense_Mutation_p.R504G			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	616	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)			NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	GTGCATCCACAGGGACCTGGC	0.642		1	"Mis, T"	"IGH@, ETV6"	"bladder, MM, T-cell lymphoma"		"Hypochondroplasia, Thanatophoric dysplasia"		Saethre-Chotzen syndrome;Muenke syndrome																												p.R618G		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"L, E"	.	FGFR3	3320	.	0			c.A1852G						PASS	.						39	39	39					4																	1807787		2202	4300	6502	SO:0001583	missense	2261	exon14	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	ATCCACAGGGACC	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.1846A>G	chr4.hg19:g.1807787A>G	ENSP00000260795:p.Arg616Gly	59.0	0.0	.		27.0	11.0	.	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Missense_Mutation	SNP	ENST00000260795.2	hg19	CCDS3353.1	.	.	.	.	.	.	.	.	.	.	a	13.53	2.264914	0.40095	.	.	ENSG00000068078	ENST00000481110;ENST00000340107;ENST00000440486;ENST00000412135;ENST00000260795;ENST00000352904	D;D;D;D;D;D	0.88354	-2.37;-2.37;-2.37;-2.37;-2.37;-2.37	4.18	1.28	0.21552	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	0.93559	0.7944	M	0.82433	2.59	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;0.998	D;D;D;D	0.97110	1.0;0.997;1.0;0.973	D	0.93158	0.6555	10	0.87932	D	0	.	11.472	0.50275	0.5856:0.4144:0.0:0.0	.	618;504;616;617	P22607-2;P22607-3;P22607;F8W9L4	.;.;FGFR3_HUMAN;.	G	617;618;616;504;616;504	ENSP00000420533:R617G;ENSP00000339824:R618G;ENSP00000414914:R616G;ENSP00000412903:R504G;ENSP00000260795:R616G;ENSP00000231803:R504G	ENSP00000260795:R616G	R	+	1	2	FGFR3	1777585	1.000000	0.71417	1.000000	0.80357	0.650000	0.38633	1.293000	0.33353	0.540000	0.28808	0.241000	0.17934	AGG	.	.	.	none		0.642	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142		G	1807787	A	G	1807787	3	3	60	1	0	0	0	0	1	0	0	0	5874	179	7	3	2051	3	FGFR3	4	1807787	Missense_Mutation	SNP	A	TCGA-A4-8630-01A-11D-2396-08		1807787	189346489	16	3991											
SLAIN2	57606	hgsc.bcm.edu	37	chr4	48384849	48384849	+	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	gggaatagaatatagtagagTgtccccacagcctatgatta	14	10	10	7	0	0	3	0	1	0	2	1	4	1	4	3	1	1	1	3	1	8	6			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr4:48384849T>A	ENST00000264313.6	+	5	1545	c.1127T>A	c.(1126-1128)gTg>gAg	p.V376E	SLAIN2_ENST00000512093.1_Missense_Mutation_p.V183E	NM_020846.1	NP_065897.1	Q9P270	SLAI2_HUMAN	SLAIN motif family, member 2	376					cytoplasmic microtubule organization (GO:0031122)|microtubule nucleation (GO:0007020)|positive regulation of microtubule polymerization (GO:0031116)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(1)	13						TATAGTAGAGTGTCCCCACAG	0.473																																					p.V376E		Atlas-SNP	.											.	SLAIN2	31	.	0			c.T1127A						PASS	.						89	89	89					4																	48384849		1998	4164	6162	SO:0001583	missense	57606	exon5			GTAGAGTGTCCCC	BC006139	CCDS47051.1	4p12	2008-02-05	2006-09-12	2006-09-12	ENSG00000109171	ENSG00000109171			29282	protein-coding gene	gene with protein product		610492	"KIAA1458"	KIAA1458		16546155	Standard	NM_020846		Approved	FLJ21611	uc003gya.4	Q9P270	OTTHUMG00000161701	ENST00000264313.6:c.1127T>A	chr4.hg19:g.48384849T>A	ENSP00000264313:p.Val376Glu	57.0	0.0	.		46.0	23.0	.	NM_020846	A8K4P1|Q8N5R3	Missense_Mutation	SNP	ENST00000264313.6	hg19	CCDS47051.1	.	.	.	.	.	.	.	.	.	.	T	4.898	0.166911	0.09339	.	.	ENSG00000109171	ENST00000264313;ENST00000512093	.	.	.	5.77	3.24	0.37175	.	0.222330	0.45867	D	0.000335	T	0.39306	0.1073	N	0.24115	0.695	0.43000	D	0.994515	B;B	0.25609	0.13;0.096	B;B	0.23574	0.047;0.026	T	0.24548	-1.0157	9	0.42905	T	0.14	-4.6941	7.659	0.28392	0.0:0.0736:0.141:0.7854	.	46;376	Q9H705;Q9P270	.;SLAI2_HUMAN	E	376;183	.	ENSP00000264313:V376E	V	+	2	0	SLAIN2	48079606	1.000000	0.71417	1.000000	0.80357	0.700000	0.40528	1.779000	0.38624	1.026000	0.39733	0.533000	0.62120	GTG	.	.	.	none		0.473	SLAIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365807.4	NM_020846		A	48384849	T	A	48384849	3	1	60	1	0	0	0	0	1	0	0	0	14379	1696	59	5	1145	5	SLAIN2	4	48384849	Missense_Mutation	SNP	T	TCGA-A4-8630-01A-11D-2396-08	46577062	48384849	142769427	17	3992											
TBCK	93627	hgsc.bcm.edu	37	chr4	106967781	106967781	+	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	gttggctttattttattaatGccaccatctagaatacagat	12	16	6	7	0	1	2	0	0	1	2	1	2	1	2	2	1	2	2	2	1	6	8			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr4:106967781G>A	ENST00000273980.5	-	27	3075	c.2628C>T	c.(2626-2628)ggC>ggT	p.G876G	TBCK_ENST00000394708.2_Silent_p.G876G|TBCK_ENST00000394706.3_Silent_p.G837G|TBCK_ENST00000432496.2_Silent_p.G876G|TBCK_ENST00000361687.4_Silent_p.G813G					TBC1 domain containing kinase											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						TTTTATTAATGCCACCATCTA	0.393																																					p.G876G		Atlas-SNP	.											.	TBCK	89	.	0			c.C2628T						PASS	.						120	116	117					4																	106967781		2203	4300	6503	SO:0001819	synonymous_variant	93627	exon26			ATTAATGCCACCA		CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.2628C>T	chr4.hg19:g.106967781G>A		66.0	0.0	.		50.0	15.0	.	NM_001163436		Silent	SNP	ENST00000273980.5	hg19	CCDS54788.1																																																																																			.	.	.	none		0.393	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115		A	106967781	G	A	106967781	2	1	60	1	0	0	0	0	0	0	0	1	15648	1306	46	2		2	TBCK	4	106967781	Silent	SNP	G	TCGA-A4-8630-01A-11D-2396-08	58582932	106967781	84186495	18	3993											
JMY	133746	hgsc.bcm.edu	37	chr5	78610483	78610483	+	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	tcctccccctcccccaccacCaccacctctgcctgttgcta	5	9	3	24	0	1	0	0	0	1	0	4	0	4	0	10	0	2	2	10	0	1	2			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr5:78610483C>T	ENST00000396137.4	+	9	2930	c.2468C>T	c.(2467-2469)cCa>cTa	p.P823L	JMY_ENST00000412001.1_Intron	NM_152405.4	NP_689618.4	Q8N9B5	JMY_HUMAN	junction mediating and regulatory protein, p53 cofactor	823	Pro-rich.				'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)		cccccaccaccaccacctcTG	0.547																																					p.P823L		Atlas-SNP	.											.	JMY	82	.	0			c.C2468T						PASS	.						17	17	17					5																	78610483		1826	4036	5862	SO:0001583	missense	133746	exon9			CACCACCACCACC	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.2468C>T	chr5.hg19:g.78610483C>T	ENSP00000379441:p.Pro823Leu	41.0	0.0	.		20.0	7.0	.	NM_152405	A1L4P5|B5MDS2|B5MDT0	Missense_Mutation	SNP	ENST00000396137.4	hg19	CCDS4047.3	.	.	.	.	.	.	.	.	.	.	C	13.78	2.340022	0.41398	.	.	ENSG00000152409	ENST00000282259;ENST00000396137	T	0.33654	1.4	4.69	3.8	0.43715	.	0.871791	0.09687	N	0.768999	T	0.55065	0.1897	L	0.54323	1.7	0.52099	D	0.999943	D	0.89917	1.0	D	0.91635	0.999	T	0.29458	-1.0011	10	0.25106	T	0.35	.	13.6524	0.62318	0.1565:0.8435:0.0:0.0	.	823	Q8N9B5	JMY_HUMAN	L	812;823	ENSP00000379441:P823L	ENSP00000282259:P812L	P	+	2	0	JMY	78646239	0.992000	0.36948	0.018000	0.16275	0.297000	0.27493	7.110000	0.77069	0.928000	0.37168	0.650000	0.86243	CCA	.	.	.	none		0.547	JMY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254070.4	NM_152405		T	78610483	C	T	78610483	3	4	60	1	0	0	0	0	1	0	0	0	7964	594	21	2	2502	2	JMY	5	78610483	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08		78610483	102304777	19	3994											
RAD50	10111	hgsc.bcm.edu	37	chr5	131953819	131953819	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaagaaatcataatttggcAttagggcgacagaaaggtta	18	9	10	4	1	1	2	1	0	0	2	1	3	1	2	0	3	0	2	0	3	7	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr5:131953819A>G	ENST00000265335.6	+	21	3609	c.3222A>G	c.(3220-3222)gcA>gcG	p.A1074A	RAD50_ENST00000378823.3_Silent_p.A935A			Q92878	RAD50_HUMAN	RAD50 homolog (S. cerevisiae)	1074					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)			ATAATTTGGCATTAGGGCGAC	0.318								Homologous recombination																													p.A1074A		Atlas-SNP	.											.	RAD50	246	.	0			c.A3222G						PASS	.						140	163	155					5																	131953819		2203	4299	6502	SO:0001819	synonymous_variant	10111	exon21			TTTGGCATTAGGG	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.3222A>G	chr5.hg19:g.131953819A>G		226.0	0.0	.		249.0	110.0	.	NM_005732	B9EGF5|O43254|Q6GMT7|Q6P5X3|Q9UP86	Silent	SNP	ENST00000265335.6	hg19	CCDS34233.1																																																																																			.	.	.	none		0.318	RAD50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132566.5	NM_005732		G	131953819	A	G	131953819	2	3	60	1	0	0	0	0	0	0	0	1	12997	204	8	3		3	RAD50	5	131953819	Silent	SNP	A	TCGA-A4-8630-01A-11D-2396-08	53343336	131953819	48961441	20	3995											
ZNF346	23567	hgsc.bcm.edu	37	chr5	176471535	176471535	+	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	gcagtccactaaggtggaagGtactggttttcctgagtagt	9	12	13	7	0	0	1	0	1	0	0	2	2	2	2	2	4	1	4	2	4	4	5			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr5:176471535G>C	ENST00000358149.3	+	4	560		c.e4+1		ZNF346_ENST00000506693.1_Intron|ZNF346_ENST00000512315.1_Intron|ZNF346_ENST00000503425.1_Splice_Site|ZNF346_ENST00000261948.4_Splice_Site|ZNF346_ENST00000511834.1_Splice_Site|ZNF346_ENST00000503039.1_Splice_Site	NM_012279.2	NP_036411.1	Q9UL40	ZN346_HUMAN	zinc finger protein 346						positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	14	all_cancers(89;6.3e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AAGGTGGAAGGTACTGGTTTT	0.552																																					.		Atlas-SNP	.											.	ZNF346	24	.	0			c.517+1G>C						PASS	.						117	109	112					5																	176471535		2203	4300	6503	SO:0001630	splice_region_variant	23567	exon4			TGGAAGGTACTGG	AF083340	CCDS4409.1	5q35.3	2012-10-05			ENSG00000113761	ENSG00000113761			16403	protein-coding gene	gene with protein product		605308				10488071	Standard	NM_012279		Approved	JAZ, Zfp346	uc003mfi.3	Q9UL40	OTTHUMG00000130848	ENST00000358149.3:c.517+1G>C	chr5.hg19:g.176471535G>C		81.0	0.0	.		80.0	28.0	.	NM_012279	B7Z367|Q68CV9|Q6ZMW1	Splice_Site	SNP	ENST00000358149.3	hg19	CCDS4409.1	.	.	.	.	.	.	.	.	.	.	G	5.228	0.227622	0.09916	.	.	ENSG00000113761	ENST00000358149;ENST00000503425;ENST00000261948;ENST00000511834;ENST00000503039	.	.	.	4.55	3.68	0.42216	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.8977	0.35474	0.1045:0.0:0.8955:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ZNF346	176404141	1.000000	0.71417	1.000000	0.80357	0.051000	0.14879	7.687000	0.84139	1.051000	0.40369	-0.160000	0.13428	.	.	.	.	none		0.552	ZNF346-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253415.2	NM_012279	Intron	C	176471535	G	C	176471535	5	2	60	1	0	0	0	0	0	0	1	0	17872	1275	44	4	532	4	ZNF346	5	176471535	Splice_Site	SNP	G	TCGA-A4-8630-01A-11D-2396-08	44517716	176471535	4443725	21	3996											
PECI	10455	hgsc.bcm.edu	37	chr6	4117677	4117677	+	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	ttctttccaaaaataagcatCtctgttgcctgaaatgaaaa	15	13	5	8	0	2	2	0	2	2	0	4	2	3	2	2	0	2	2	2	0	6	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr6:4117677C>G	ENST00000380118.3	-	9	930	c.894G>C	c.(892-894)gaG>gaC	p.E298D	ECI2_ENST00000465828.1_Missense_Mutation_p.E268D|ECI2_ENST00000361538.2_Missense_Mutation_p.E268D|C6orf201_ENST00000333388.5_Intron|C6orf201_ENST00000380175.4_Intron|C6orf201_ENST00000430835.2_Intron|ECI2_ENST00000413766.2_Missense_Mutation_p.E131D|ECI2_ENST00000380125.2_Missense_Mutation_p.E268D			O75521	ECI2_HUMAN	enoyl-CoA delta isomerase 2	298	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						AAATAAGCATCTCTGTTGCCT	0.393																																					p.E298D		Atlas-SNP	.											.	ECI2	59	.	0			c.G894C						PASS	.						86	90	89					6																	4117677		2203	4300	6503	SO:0001583	missense	10455	exon9			AAGCATCTCTGTT	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.894G>C	chr6.hg19:g.4117677C>G	ENSP00000369461:p.Glu298Asp	105.0	0.0	.		83.0	29.0	.	NM_206836	Q5JYK5|Q5JYK7|Q7L124|Q8N0X0|Q9BUE9|Q9H0T9|Q9NQH1|Q9NYH7|Q9UN55	Missense_Mutation	SNP	ENST00000380118.3	hg19	CCDS43420.2	.	.	.	.	.	.	.	.	.	.	C	21.3	4.129965	0.77549	.	.	ENSG00000198721	ENST00000380118;ENST00000380125;ENST00000413766;ENST00000361538;ENST00000465828	T;T;T;T;T	0.69806	-0.43;-0.43;-0.43;-0.43;-0.43	6.16	4.39	0.52855	Crotonase, core (1);	0.145207	0.64402	D	0.000008	T	0.63498	0.2516	M	0.74389	2.26	0.80722	D	1	P	0.41524	0.753	P	0.47705	0.555	T	0.68965	-0.5270	10	0.54805	T	0.06	.	11.2609	0.49083	0.0:0.8536:0.0:0.1464	.	298	O75521	ECI2_HUMAN	D	298;268;131;268;268	ENSP00000369461:E298D;ENSP00000369468:E268D;ENSP00000406969:E131D;ENSP00000354737:E268D;ENSP00000420309:E268D	ENSP00000354737:E268D	E	-	3	2	ECI2	4062676	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.699000	0.37804	1.627000	0.50400	0.650000	0.86243	GAG	.	.	.	none		0.393	ECI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039716.4	NM_006117		G	4117677	C	G	4117677	3	3	60	1	0	0	0	0	1	0	0	0	11723	912	32	4	298	4	PECI	6	4117677	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08		4117677	166997390	22	3997											
AMPH	273	hgsc.bcm.edu	37	chr7	38431574	38431574	+	Frame_Shift_Del	DEL	A	A	-																															tcgttttctccttcctcttcAtggttggaggcaggctctat																										TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr7:38431574delA	ENST00000356264.2	-	19	1868	c.1653delT	c.(1651-1653)catfs	p.H551fs	AMPH_ENST00000325590.5_Frame_Shift_Del_p.H509fs|AMPH_ENST00000471913.1_5'Flank|AMPH_ENST00000428293.2_Frame_Shift_Del_p.H509fs	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	551					endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						CTTCCTCTTCATGGTTGGAGG	0.587																																					p.E552fs		Atlas-INDEL	.											.	AMPH	157	.	0			c.1654delG						PASS	.						66	65	66					7																	38431574		2203	4300	6503	SO:0001589	frameshift_variant	273	exon19			.		CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)", "amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.1653delT	chr7.hg19:g.38431574delA	ENSP00000348602:p.His551fs	85.0	0.0	0		90.0	55.0	0.611111	NM_001635	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Frame_Shift_Del	DEL	ENST00000356264.2	hg19	CCDS5456.1																																																																																			.	.	.	none		0.587	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635		-	38431574	A	-	38431574	7	5	60	1	0	1	0	1	0	0	0	0	588	214	8	0	446	0	AMPH	7	38431574	Frame_Shift_Del	DEL	A	TCGA-A4-8630-01A-11D-2396-08		38431574	120707089	23	3998											
CCDC146	57639	hgsc.bcm.edu	37	chr7	76866323	76866323	+	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	gcgttaaaagccaagtatacCttgctgcatgacgccgtgat	11	10	10	10	3	0	2	0	2	0	0	0	2	0	2	3	0	4	4	3	0	5	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr7:76866323C>G	ENST00000285871.4	+	3	343	c.216C>G	c.(214-216)acC>acG	p.T72T	CCDC146_ENST00000431197.1_5'UTR	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	72										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)				CCAAGTATACCTTGCTGCATG	0.403																																					p.T72T		Atlas-SNP	.											.	CCDC146	87	.	0			c.C216G						PASS	.						194	144	161					7																	76866323		2203	4300	6503	SO:0001819	synonymous_variant	57639	exon3			GTATACCTTGCTG	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.216C>G	chr7.hg19:g.76866323C>G		54.0	0.0	.		98.0	4.0	.	NM_020879	A8K8X6|Q9P223	Silent	SNP	ENST00000285871.4	hg19	CCDS34671.1																																																																																			.	.	.	none		0.403	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879		G	76866323	C	G	76866323	2	3	60	1	0	0	0	0	0	0	0	1	2782	668	24	4		4	CCDC146	7	76866323	Silent	SNP	C	TCGA-A4-8630-01A-11D-2396-08	38434749	76866323	82272340	24	3999											
ASNS	440	hgsc.bcm.edu	37	chr7	97482647	97482647	+	Frame_Shift_Del	DEL	C	C	-																															ctcatttctggtggcagagaCaagtaataggaagaaaatcg																										TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr7:97482647delC	ENST00000394309.3	-	11	1761	c.1290delG	c.(1288-1290)ttgfs	p.L430fs	ASNS_ENST00000437628.1_Frame_Shift_Del_p.L347fs|ASNS_ENST00000444334.1_Frame_Shift_Del_p.L409fs|ASNS_ENST00000455086.1_Frame_Shift_Del_p.L347fs|ASNS_ENST00000394308.3_Frame_Shift_Del_p.L430fs|ASNS_ENST00000422745.1_Frame_Shift_Del_p.L409fs|ASNS_ENST00000175506.4_Frame_Shift_Del_p.L430fs	NM_133436.3	NP_597680.2	P08243	ASNS_HUMAN	asparagine synthetase (glutamine-hydrolyzing)	430	Asparagine synthetase.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|asparagine biosynthetic process (GO:0006529)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|cellular protein metabolic process (GO:0044267)|cellular response to glucose starvation (GO:0042149)|cellular response to hormone stimulus (GO:0032870)|endoplasmic reticulum unfolded protein response (GO:0030968)|glutamine metabolic process (GO:0006541)|L-asparagine biosynthetic process (GO:0070981)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|positive regulation of mitotic cell cycle (GO:0045931)|response to amino acid (GO:0043200)|response to follicle-stimulating hormone (GO:0032354)|response to light stimulus (GO:0009416)|response to mechanical stimulus (GO:0009612)|response to methotrexate (GO:0031427)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	asparagine synthase (glutamine-hydrolyzing) activity (GO:0004066)|ATP binding (GO:0005524)|cofactor binding (GO:0048037)			ovary(1)	1	all_cancers(62;6.64e-09)|all_epithelial(64;1.58e-09)|Esophageal squamous(72;0.00448)|Lung NSC(181;0.0342)|all_lung(186;0.0369)				Adenosine triphosphate(DB00171)|L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)|L-Glutamine(DB00130)	GTGGCAGAGACAAGTAATAGG	0.343																																					p.S431fs	Melanoma(70;6 1280 3108 3799 51123)|GBM(6;275 291 425 9929 27738)	Atlas-INDEL	.											.	ASNS	97	.	0			c.1291delT						PASS	.						73	75	75					7																	97482647		2203	4300	6503	SO:0001589	frameshift_variant	440	exon11			.	M27396	CCDS5652.1, CCDS55131.1, CCDS55132.1	7q21.3	2012-10-02	2010-05-07		ENSG00000070669	ENSG00000070669	6.3.5.4		753	protein-coding gene	gene with protein product		108370	"asparagine synthetase"				Standard	NM_001673		Approved		uc003uov.4	P08243	OTTHUMG00000022892	ENST00000394309.3:c.1290delG	chr7.hg19:g.97482647delC	ENSP00000377846:p.Leu430fs	72.0	0.0	0		109.0	25.0	0.229358	NM_001673	A4D1I8|B4DXZ1|B7ZAA9|D6W5R3|E9PCI3|E9PCX6|P08184|Q15666|Q549T9|Q96HD0	Frame_Shift_Del	DEL	ENST00000394309.3	hg19	CCDS5652.1																																																																																			.	.	.	none		0.343	ASNS-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333645.1	NM_001673, NM_183356		-	97482647	C	-	97482647	7	5	60	1	0	1	0	1	0	0	0	0	1048	477	17	0	407	0	ASNS	7	97482647	Frame_Shift_Del	DEL	C	TCGA-A4-8630-01A-11D-2396-08	20616324	97482647	61656016	25	4000											
ADAM7	8756	hgsc.bcm.edu	37	chr8	24339727	24339728	+	Frame_Shift_Ins	INS	-	-	TA																															acatgaagataaaatagaacINStatattcaaatatagaaact																										TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr8:24339727_24339728insTA	ENST00000175238.6	+	9	861_862	c.778_779insTA	c.(778-780)ctafs	p.L260fs	ADAM7_ENST00000380789.1_Frame_Shift_Ins_p.L260fs|RP11-624C23.1_ENST00000519689.1_RNA|ADAM7_ENST00000520720.1_Frame_Shift_Ins_p.L32fs|RP11-624C23.1_ENST00000523578.1_RNA	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	260	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)		TAAAATAGAACTATATTCAAAT	0.307																																					p.L260fs		Atlas-INDEL	.											.	ADAM7	165	.	0			c.778_779insTA						PASS	.																																			SO:0001589	frameshift_variant	8756	exon9			.	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.781_782dupTA	chr8.hg19:g.24339730_24339731dupTA	ENSP00000175238:p.Leu260fs	57.0	0.0	0		101.0	27.0	0.267327	NM_003817	A8K8X7|O75959|Q6PEJ6	Frame_Shift_Ins	INS	ENST00000175238.6	hg19	CCDS6045.1																																																																																			.	.	.	none		0.307	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817		TA	24339728	-	TA	24339727	7	5	60	1	0	1	1	0	0	0	0	0	251	564	20	0	812	0	ADAM7	8	24339727	Frame_Shift_Ins	INS	-	TCGA-A4-8630-01A-11D-2396-08		24339727	122024295	26	4001											
HSF1	3297	hgsc.bcm.edu	37	chr8	145535422	145535422	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcagctccagcctctacGcccctgatgctgtggccagc	7	7	10	17	1	1	1	0	1	1	0	2	1	2	1	5	1	6	3	5	1	1	1	rs201143946		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr8:145535422G>A	ENST00000528838.1	+	8	920	c.760G>A	c.(760-762)Gcc>Acc	p.A254T	GS1-393G12.12_ENST00000525023.1_RNA|HSF1_ENST00000400780.4_Missense_Mutation_p.A189T	NM_005526.2	NP_005517.1	Q00613	HSF1_HUMAN	heat shock transcription factor 1	254	Regulatory domain.				cellular response to heat (GO:0034605)|defense response (GO:0006952)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|female meiotic division (GO:0007143)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of tumor necrosis factor production (GO:0032720)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of spindle checkpoint (GO:0090231)|response to lipopolysaccharide (GO:0032496)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pronucleus (GO:0045120)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding (GO:0001162)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(1)|lung(3)|prostate(3)|skin(1)|urinary_tract(2)	11	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;1.12e-39)|all cancers(56;9.11e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0547)|Colorectal(110;0.055)			CAGCCTCTACGCCCCTGATGC	0.677																																					p.A254T		Atlas-SNP	.											.	HSF1	29	.	0			c.G760A						PASS	.	G	THR/ALA	0,4406		0,0,2203	40	41	41		760	-9.2	0	8		41	1,8591	1.2+/-3.3	0,1,4295	yes	missense	HSF1	NM_005526.2	58	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	benign	254/530	145535422	1,12997	2203	4296	6499	SO:0001583	missense	3297	exon8			CTCTACGCCCCTG	M64673	CCDS6419.1	8q24.3	2014-04-10			ENSG00000185122	ENSG00000185122			5224	protein-coding gene	gene with protein product		140580				1871105	Standard	NM_005526		Approved	HSTF1	uc003zbt.4	Q00613	OTTHUMG00000174604	ENST00000528838.1:c.760G>A	chr8.hg19:g.145535422G>A	ENSP00000431512:p.Ala254Thr	77.0	0.0	.		86.0	4.0	.	NM_005526	A8K4L0|A8MW26|Q53XT4	Missense_Mutation	SNP	ENST00000528838.1	hg19	CCDS6419.1	.	.	.	.	.	.	.	.	.	.	G	10.21	1.287380	0.23478	0.0	1.16E-4	ENSG00000185122	ENST00000528838;ENST00000400780	.	.	.	5.3	-9.22	0.00675	Vertebrate heat shock transcription factor (1);	0.615854	0.16090	N	0.230092	T	0.06462	0.0166	N	0.02539	-0.55	0.09310	N	0.999999	B	0.09022	0.002	B	0.06405	0.002	T	0.12218	-1.0556	9	0.25106	T	0.35	-20.7374	0.7851	0.01047	0.1584:0.2577:0.2439:0.34	.	254	Q00613	HSF1_HUMAN	T	254;189	.	ENSP00000383590:A189T	A	+	1	0	HSF1	145506230	0.003000	0.15002	0.004000	0.12327	0.095000	0.18619	-0.084000	0.11268	-1.940000	0.01043	-0.502000	0.04539	GCC	.	.	.	weak		0.677	HSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382053.1	NM_005526		A	145535422	G	A	145535422	3	1	60	1	0	0	0	0	1	0	0	0	7402	1087	38	1	790	1	HSF1	8	145535422	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08	121195695	145535422	828600	27	4002											
AGTPBP1	23287	hgsc.bcm.edu	37	chr9	88284416	88284416	+	Missense_Mutation	SNP	T	T	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	tcactttataagactggaatTcttcttactaaatggtccaa	13	15	5	8	0	3	1	1	0	2	1	4	2	4	2	1	2	1	0	1	2	7	7			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr9:88284416T>G	ENST00000357081.3	-	8	790	c.646A>C	c.(646-648)Aat>Cat	p.N216H	AGTPBP1_ENST00000376083.3_Missense_Mutation_p.N216H|AGTPBP1_ENST00000491784.1_5'UTR|AGTPBP1_ENST00000337006.4_Missense_Mutation_p.N158H|AGTPBP1_ENST00000432218.1_Missense_Mutation_p.N54H|AGTPBP1_ENST00000376080.1_Missense_Mutation_p.N158H|AGTPBP1_ENST00000376109.3_Missense_Mutation_p.N268H|AGTPBP1_ENST00000376081.4_Missense_Mutation_p.N216H			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	216					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						AGACTGGAATTCTTCTTACTA	0.368																																					p.N216H		Atlas-SNP	.											.	AGTPBP1	128	.	0			c.A646C						PASS	.						94	86	89					9																	88284416		2203	4298	6501	SO:0001583	missense	23287	exon8			TGGAATTCTTCTT	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.646A>C	chr9.hg19:g.88284416T>G	ENSP00000349592:p.Asn216His	63.0	0.0	.		65.0	26.0	.	NM_015239	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Missense_Mutation	SNP	ENST00000357081.3	hg19		.	.	.	.	.	.	.	.	.	.	T	12.67	2.007766	0.35415	.	.	ENSG00000135049	ENST00000337006;ENST00000357081;ENST00000376083;ENST00000376109;ENST00000432218;ENST00000376081;ENST00000376080	T;T;T;T;T;T;T	0.52754	1.94;1.94;0.65;0.65;1.94;1.94;1.94	5.76	5.76	0.90799	Armadillo-like helical (1);Armadillo-type fold (1);	0.081135	0.85682	D	0.000000	T	0.54886	0.1886	L	0.32530	0.975	0.54753	D	0.999983	D;D;D;B	0.89917	0.998;1.0;1.0;0.235	D;D;D;B	0.77004	0.949;0.962;0.989;0.102	T	0.46830	-0.9163	10	0.08837	T	0.75	-33.4404	16.087	0.81065	0.0:0.0:0.0:1.0	.	268;216;54;216	Q9UPW5-3;Q9UPW5;B4DHX2;Q9UPW5-2	.;CBPC1_HUMAN;.;.	H	158;216;216;268;54;216;158	ENSP00000338512:N158H;ENSP00000349592:N216H;ENSP00000365251:N216H;ENSP00000365277:N268H;ENSP00000402804:N54H;ENSP00000365249:N216H;ENSP00000365248:N158H	ENSP00000338512:N158H	N	-	1	0	AGTPBP1	87474236	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	7.376000	0.79658	2.202000	0.70862	0.533000	0.62120	AAT	.	.	.	none		0.368	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239		G	88284416	T	G	88284416	3	3	60	1	0	0	0	0	1	0	0	0	400	1783	62	5	2990	5	AGTPBP1	9	88284416	Missense_Mutation	SNP	T	TCGA-A4-8630-01A-11D-2396-08		88284416	52929015	28	4003											
CCBL1	883	hgsc.bcm.edu	37	chr9	131597888	131597888	+	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	cctgcgggaactgcacaaagTagctgctgggttggcggaag	9	7	16	9	2	0	0	0	0	0	0	0	2	0	2	1	4	5	5	1	4	4	2			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr9:131597888T>A	ENST00000302586.3	-	10	1076	c.914A>T	c.(913-915)tAc>tTc	p.Y305F	CCBL1_ENST00000436267.2_Missense_Mutation_p.Y399F|CCBL1_ENST00000320665.6_Missense_Mutation_p.Y255F|CCBL1_ENST00000483599.1_5'UTR	NM_001122671.1|NM_004059.4	NP_001116143.1|NP_004050.3	Q16773	KAT1_HUMAN	cysteine conjugate-beta lyase, cytoplasmic	305					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)	CTGCACAAAGTAGCTGCTGGG	0.597																																					p.Y305F		Atlas-SNP	.											.	CCBL1	36	.	0			c.A914T						PASS	.						56	58	57					9																	131597888		2103	4222	6325	SO:0001583	missense	883	exon10			ACAAAGTAGCTGC	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.914A>T	chr9.hg19:g.131597888T>A	ENSP00000302227:p.Tyr305Phe	63.0	0.0	.		57.0	23.0	.	NM_001122671	Q5T275|Q8N191	Missense_Mutation	SNP	ENST00000302586.3	hg19	CCDS43884.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.960807	0.74016	.	.	ENSG00000171097	ENST00000302586;ENST00000320665;ENST00000436267	D;D;D	0.90261	-2.64;-2.64;-2.64	5.3	5.3	0.74995	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.93304	0.7866	L	0.52364	1.645	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	0.92808	0.6262	10	0.40728	T	0.16	-2.7503	14.4079	0.67096	0.0:0.0:0.0:1.0	.	399;305;255;305	B7Z4W5;A8K563;Q16773-2;Q16773	.;.;.;KAT1_HUMAN	F	305;255;399	ENSP00000302227:Y305F;ENSP00000317342:Y255F;ENSP00000399415:Y399F	ENSP00000302227:Y305F	Y	-	2	0	CCBL1	130637709	1.000000	0.71417	1.000000	0.80357	0.429000	0.31625	7.196000	0.77805	1.997000	0.58415	0.358000	0.22013	TAC	.	.	.	none		0.597	CCBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054521.2			A	131597888	T	A	131597888	3	1	60	1	0	0	0	0	1	0	0	0	2734	1638	57	5	370	5	CCBL1	9	131597888	Missense_Mutation	SNP	T	TCGA-A4-8630-01A-11D-2396-08	43313472	131597888	9615543	29	4004											
NFKB2	4791	hgsc.bcm.edu	37	chr10	104158555	104158555	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccaccttctcccagcccttcGggggtggctcccacatgggt	4	9	11	17	1	1	0	0	0	1	0	4	0	2	0	5	4	1	1	5	4	0	2	rs45580031		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr10:104158555G>A	ENST00000369966.3	+	12	1301	c.1051G>A	c.(1051-1053)Ggg>Agg	p.G351R	NFKB2_ENST00000336486.5_3'UTR|NFKB2_ENST00000428099.1_Missense_Mutation_p.G351R|NFKB2_ENST00000189444.6_Missense_Mutation_p.G351R	NM_001077494.2	NP_001070962.1	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)	351	GRR.|Gly-rich.		G -> R (in dbSNP:rs45580031). {ECO:0000269|Ref.7}.		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)	CCAGCCCTTCGGGGGTGGCTC	0.627			T	IGH@	B-NHL																																p.G351R		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.G1051A						PASS	.						23	25	24					10																	104158555		1910	4115	6025	SO:0001583	missense	4791	exon12			CCCTTCGGGGGTG	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.1051G>A	chr10.hg19:g.104158555G>A	ENSP00000358983:p.Gly351Arg	54.0	0.0	.		35.0	16.0	.	NM_001077494	A8K9D9|D3DR83|Q04860|Q9BU75|Q9H471|Q9H472	Missense_Mutation	SNP	ENST00000369966.3	hg19	CCDS41564.1	.	.	.	.	.	.	.	.	.	.	G	14.96	2.691545	0.48097	.	.	ENSG00000077150	ENST00000428099;ENST00000369966;ENST00000336486;ENST00000189444	D;D;D	0.86164	-2.08;-2.08;-2.08	4.56	4.56	0.56223	Immunoglobulin E-set (1);	0.220426	0.45126	D	0.000387	D	0.90686	0.7078	L	0.42245	1.32	0.48341	D	0.999631	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.89788	0.3966	10	0.36615	T	0.2	.	17.5171	0.87777	0.0:0.0:1.0:0.0	.	351;351;351	D3DR86;Q00653;A8K9D9	.;NFKB2_HUMAN;.	R	351	ENSP00000410256:G351R;ENSP00000358983:G351R;ENSP00000189444:G351R	ENSP00000189444:G351R	G	+	1	0	NFKB2	104148545	1.000000	0.71417	0.993000	0.49108	0.956000	0.61745	4.681000	0.61663	2.387000	0.81309	0.561000	0.74099	GGG	.	G|0.993;C|0.007	.	alt		0.627	NFKB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050080.2			A	104158555	G	A	104158555	3	1	60	1	0	0	0	0	1	0	0	0	10383	1116	39	1	1093	1	NFKB2	10	104158555	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08		104158555	31376192	30	4005											
CTSC	1075	hgsc.bcm.edu	37	chr11	88045694	88045694	+	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	tcattgtctcgttgcagtaaGtggtcaccttgctgccctct	5	15	9	12	1	4	0	2	0	2	0	5	0	4	0	2	1	3	4	2	1	1	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr11:88045694G>C	ENST00000227266.5	-	3	461	c.347C>G	c.(346-348)aCt>aGt	p.T116S		NM_001814.4	NP_001805	P53634	CATC_HUMAN	cathepsin C	116					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)				GTTGCAGTAAGTGGTCACCTT	0.458																																					p.T116S		Atlas-SNP	.											.	CTSC	46	.	0			c.C347G						PASS	.						204	192	196					11																	88045694		2201	4299	6500	SO:0001583	missense	1075	exon3			CAGTAAGTGGTCA	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.347C>G	chr11.hg19:g.88045694G>C	ENSP00000227266:p.Thr116Ser	316.0	0.0	.		283.0	119.0	.	NM_001814	A8K7V2|B5MDD5|Q2HIY8|Q53G93|Q71E75|Q71E76|Q7M4N9|Q7Z3G7|Q7Z5U7|Q8WY99|Q8WYA7|Q8WYA8	Missense_Mutation	SNP	ENST00000227266.5	hg19	CCDS8282.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.162|0.162	-1.079798|-1.079798	0.01888|0.01888	.|.	.|.	ENSG00000109861|ENSG00000109861	ENST00000527018|ENST00000393302;ENST00000227266	.|D	.|0.84442	.|-1.85	5.97|5.97	4.11|4.11	0.48088|0.48088	.|Cathepsin C exclusion (1);	.|0.073747	.|0.85682	.|N	.|0.000000	T|T	0.48259|0.48259	0.1490|0.1490	N|N	0.00050|0.00050	-2.41|-2.41	0.80722|0.80722	D|D	1|1	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.54036|0.54036	-0.8353|-0.8353	5|9	.|.	.|.	.|.	.|.	12.6204|12.6204	0.56600|0.56600	0.1313:0.7414:0.1273:0.0|0.1313:0.7414:0.1273:0.0	.|.	.|116	.|P53634	.|CATC_HUMAN	V|S	73|99;116	.|ENSP00000227266:T116S	.|.	L|T	-|-	1|2	0|0	CTSC|CTSC	87685342|87685342	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.133000|0.133000	0.20885|0.20885	3.944000|3.944000	0.56629|0.56629	0.878000|0.878000	0.35920|0.35920	-0.783000|-0.783000	0.03347|0.03347	CTT|ACT	.	.	.	none		0.458	CTSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394019.2	NM_001814		C	88045694	G	C	88045694	3	2	60	1	0	0	0	0	1	0	0	0	4033	1029	36	4	1064	4	CTSC	11	88045694	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08		88045694	46960822	31	4006											
NELL2	4753	hgsc.bcm.edu	37	chr12	44915902	44915902	+	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	acattcagggcagcaaaaaaGatcaactgtgggattctcac	15	8	9	9	0	3	1	3	0	1	1	4	2	3	2	0	2	2	2	0	2	4	2			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr12:44915902G>C	ENST00000429094.2	-	18	2560	c.2056C>G	c.(2056-2058)Ctt>Gtt	p.L686V	NELL2_ENST00000551601.1_Missense_Mutation_p.L638V|NELL2_ENST00000549027.1_Missense_Mutation_p.L685V|NELL2_ENST00000437801.2_Missense_Mutation_p.L736V|NELL2_ENST00000395487.2_Missense_Mutation_p.L685V|NELL2_ENST00000452445.2_Missense_Mutation_p.L686V|NELL2_ENST00000333837.4_Missense_Mutation_p.L709V	NM_001145108.1	NP_001138580.1	Q99435	NELL2_HUMAN	NEL-like 2 (chicken)	686	VWFC 2. {ECO:0000255|PROSITE- ProRule:PRU00220}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.L686I(1)|p.L736I(1)		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)		CAGCAAAAAAGATCAACTGTG	0.428																																					p.L736V		Atlas-SNP	.											NELL2_ENST00000437801,rectum,carcinoma,0,2	NELL2	286	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2206G						PASS	.						122	111	115					12																	44915902		2203	4300	6503	SO:0001583	missense	4753	exon19			AAAAAAGATCAAC	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.2056C>G	chr12.hg19:g.44915902G>C	ENSP00000390680:p.Leu686Val	76.0	0.0	.		50.0	2.0	.	NM_001145107	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Missense_Mutation	SNP	ENST00000429094.2	hg19	CCDS8746.1	.	.	.	.	.	.	.	.	.	.	G	13.39	2.224335	0.39300	.	.	ENSG00000184613	ENST00000395487;ENST00000429094;ENST00000551601;ENST00000452445;ENST00000549027;ENST00000333837;ENST00000437801	D;D;T;D;D;T;D	0.82433	-1.56;-1.54;-1.24;-1.54;-1.56;-1.49;-1.61	5.7	5.7	0.88788	von Willebrand factor, type C (2);	0.063717	0.64402	D	0.000004	T	0.74619	0.3740	L	0.39020	1.185	0.51012	D	0.999902	B;P;B;B;B	0.36282	0.355;0.546;0.165;0.038;0.296	B;B;B;B;B	0.35312	0.1;0.2;0.069;0.018;0.125	T	0.71269	-0.4643	10	0.17369	T	0.5	-14.6968	14.0416	0.64678	0.0717:0.0:0.9283:0.0	.	709;736;638;686;685	B7Z2U7;B7Z9U3;F8VVB6;Q99435;Q96JS2	.;.;.;NELL2_HUMAN;.	V	685;686;638;686;685;709;736	ENSP00000378866:L685V;ENSP00000390680:L686V;ENSP00000449332:L638V;ENSP00000394612:L686V;ENSP00000447927:L685V;ENSP00000327988:L709V;ENSP00000416341:L736V	ENSP00000327988:L709V	L	-	1	0	NELL2	43202169	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.482000	0.66833	2.683000	0.91414	0.650000	0.86243	CTT	.	.	.	none		0.428	NELL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404180.1	NM_006159		C	44915902	G	C	44915902	3	2	60	1	0	0	0	0	1	0	0	0	10341	942	33	4	406	4	NELL2	12	44915902	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08		44915902	88935993	32	4007											
DIP2B	57609	hgsc.bcm.edu	37	chr12	51102296	51102296	+	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	ggtggttgcggaacaaagacCtgatgcttctgaggaagata	12	9	14	6	1	1	4	0	2	1	2	1	6	1	6	1	4	3	2	1	4	4	3			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr12:51102296C>A	ENST00000301180.5	+	22	2634	c.2600C>A	c.(2599-2601)cCt>cAt	p.P867H		NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	867						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						GAACAAAGACCTGATGCTTCT	0.502																																					p.P867H		Atlas-SNP	.											.	DIP2B	167	.	0			c.C2600A						PASS	.						262	192	215					12																	51102296		2203	4300	6503	SO:0001583	missense	57609	exon22			AAAGACCTGATGC	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.2600C>A	chr12.hg19:g.51102296C>A	ENSP00000301180:p.Pro867His	15.0	0.0	.		17.0	9.0	.	NM_173602	Q6B011|Q8N1L5|Q8NB38	Missense_Mutation	SNP	ENST00000301180.5	hg19	CCDS31799.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.337555	0.81911	.	.	ENSG00000066084	ENST00000301180	T	0.12465	2.68	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.44953	0.1318	M	0.87456	2.885	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.48581	-0.9023	10	0.66056	D	0.02	-15.6463	18.0462	0.89332	0.0:1.0:0.0:0.0	.	867	Q9P265	DIP2B_HUMAN	H	867	ENSP00000301180:P867H	ENSP00000301180:P867H	P	+	2	0	DIP2B	49388563	1.000000	0.71417	0.968000	0.41197	0.855000	0.48748	5.912000	0.69948	2.826000	0.97356	0.491000	0.48974	CCT	.	.	.	none		0.502	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602		A	51102296	C	A	51102296	3	1	60	1	0	0	0	0	1	0	0	0	4530	681	24	4	2686	4	DIP2B	12	51102296	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08	6186394	51102296	82749599	33	4008											
LETMD1	25875	hgsc.bcm.edu	37	chr12	51450186	51450186	+	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	tacctgcctcctcccttgttGagacatcgtttgaagactca	8	13	7	13	1	1	3	1	2	0	2	4	4	3	3	4	0	2	2	4	0	2	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr12:51450186G>A	ENST00000262055.4	+	7	855	c.816G>A	c.(814-816)ttG>ttA	p.L272L	LETMD1_ENST00000418425.2_Silent_p.L285L|LETMD1_ENST00000380123.2_3'UTR|LETMD1_ENST00000548516.1_3'UTR|LETMD1_ENST00000550929.1_Silent_p.L216L|LETMD1_ENST00000552739.1_Silent_p.L155L|LETMD1_ENST00000547008.1_Silent_p.L148L	NM_015416.4	NP_056231.3	Q6P1Q0	LTMD1_HUMAN	LETM1 domain containing 1	272	LETM1.					integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)				central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(3)	16						CTCCCTTGTTGAGACATCGTT	0.493																																					p.L285L		Atlas-SNP	.											.	LETMD1	33	.	0			c.G855A						PASS	.						174	148	156					12																	51450186		2203	4300	6503	SO:0001819	synonymous_variant	25875	exon7			CTTGTTGAGACAT	AF195651	CCDS8806.1, CCDS58231.1, CCDS73469.1	12q13.13	2006-04-12				ENSG00000050426			24241	protein-coding gene	gene with protein product	"cervical cancer 1 protooncogene"					12879013, 12061725	Standard	NM_015416		Approved	HCCR1	uc009zlw.3	Q6P1Q0	OTTHUMG00000169538	ENST00000262055.4:c.816G>A	chr12.hg19:g.51450186G>A		230.0	0.0	.		171.0	71.0	.	NM_001243689	A6NER7|B3KXK7|Q6X2E4|Q6X2E5|Q7L2G9|Q7L690|Q8WXW6|Q96PK7|Q9BY59|Q9Y3X3	Silent	SNP	ENST00000262055.4	hg19	CCDS8806.1	.	.	.	.	.	.	.	.	.	.	G	17.27	3.347756	0.61183	.	.	ENSG00000050426	ENST00000553043	.	.	.	5.49	3.69	0.42338	.	.	.	.	.	T	0.47192	0.1432	.	.	.	0.80722	D	1	B;B	0.14438	0.01;0.001	B;B	0.14578	0.011;0.004	T	0.44345	-0.9334	7	0.87932	D	0	-8.0385	7.6315	0.28243	0.3175:0.0:0.6825:0.0	.	110;110	B7Z9A7;F8W6J0	.;.	K	41	.	ENSP00000369478:E110K	E	+	1	0	LETMD1	49736453	1.000000	0.71417	0.675000	0.29917	0.599000	0.36880	1.036000	0.30228	0.822000	0.34565	-0.137000	0.14449	GAG	.	.	.	none		0.493	LETMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404710.1	NM_015416		A	51450186	G	A	51450186	2	1	60	1	0	0	0	0	0	0	0	1	8743	1281	45	2		2	LETMD1	12	51450186	Silent	SNP	G	TCGA-A4-8630-01A-11D-2396-08	347890	51450186	82401709	34	4009											
TDRD3	81550	hgsc.bcm.edu	37	chr13	61034625	61034625	+	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	tgcgattacagatgactgatGgtcatataagttgcacagca	13	11	10	7	1	1	3	1	2	0	1	1	4	1	3	0	1	4	3	0	1	3	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr13:61034625G>A	ENST00000196169.3	+	4	813	c.25G>A	c.(25-27)Ggt>Agt	p.G9S	TDRD3_ENST00000535286.1_Missense_Mutation_p.G102S|TDRD3_ENST00000377894.2_Missense_Mutation_p.G9S|TDRD3_ENST00000463109.1_3'UTR|TDRD3_ENST00000377881.2_Missense_Mutation_p.G9S	NM_001146071.1|NM_030794.2	NP_001139543.1|NP_110421.1	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3	9					chromatin modification (GO:0016568)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	40		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)		GATGACTGATGGTCATATAAG	0.358																																					p.G102S	Colon(36;164 906 35820 50723)	Atlas-SNP	.											.	TDRD3	123	.	0			c.G304A						PASS	.						123	111	115					13																	61034625		2203	4300	6503	SO:0001583	missense	81550	exon4			ACTGATGGTCATA	AK023578	CCDS9441.1, CCDS53872.1	13q14.3	2013-01-23			ENSG00000083544	ENSG00000083544		"Tudor domain containing"	20612	protein-coding gene	gene with protein product		614392					Standard	NM_030794		Approved	FLJ21007	uc010aeg.3	Q9H7E2	OTTHUMG00000017007	ENST00000196169.3:c.25G>A	chr13.hg19:g.61034625G>A	ENSP00000196169:p.Gly9Ser	89.0	0.0	.		111.0	23.0	.	NM_001146070	B2MWP9|Q53XA6|Q6P992	Missense_Mutation	SNP	ENST00000196169.3	hg19	CCDS9441.1	.	.	.	.	.	.	.	.	.	.	G	36	5.652402	0.96724	.	.	ENSG00000083544	ENST00000196169;ENST00000377881;ENST00000377894;ENST00000535286;ENST00000377882	D;D;D;D	0.99924	-7.4;-7.4;-7.4;-8.02	6.06	6.06	0.98353	.	0.048957	0.85682	N	0.000000	D	0.99937	0.9972	M	0.91920	3.255	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.96414	0.9306	10	0.87932	D	0	-15.3725	20.6397	0.99537	0.0:0.0:1.0:0.0	.	102;9;9	Q9H7E2-3;Q9H7E2-2;Q9H7E2	.;.;TDRD3_HUMAN	S	9;9;9;102;9	ENSP00000196169:G9S;ENSP00000367113:G9S;ENSP00000367126:G9S;ENSP00000440190:G102S	ENSP00000196169:G9S	G	+	1	0	TDRD3	59932626	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.476000	0.97823	2.880000	0.98712	0.650000	0.86243	GGT	.	.	.	none		0.358	TDRD3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045175.2	NM_030794		A	61034625	G	A	61034625	3	1	60	1	0	0	0	0	1	0	0	0	15744	1348	47	2	318	2	TDRD3	13	61034625	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08		61034625	54135253	35	4010											
SUPT16H	11198	hgsc.bcm.edu	37	chr14	21821646	21821648	+	Splice_Site	DEL	CCT	CCT	-																															aaacaacacatttttaaaaaCcttttcgggcttcttcctcc																										TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr14:21821646_21821648delCCT	ENST00000216297.2	-	25	3335_3337	c.2997_2999delAGG	c.(2995-3000)aaaggg>aag	p.G1000del		NM_007192.3	NP_009123.1	Q9Y5B9	SP16H_HUMAN	suppressor of Ty 16 homolog (S. cerevisiae)	1000	Glu-rich (acidic).				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)		TTTTTAAAAACCTTTTCGGGCTT	0.34																																					p.1000_1000del		Atlas-INDEL	.											.	SUPT16H	84	.	0			c.2998_2998del						PASS	.																																			SO:0001630	splice_region_variant	11198	exon25			.	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.2998+1AGG>-	chr14.hg19:g.21821646_21821648delCCT		109.0	0.0	0		62.0	24.0	0.387097	NM_007192	Q6GMT8|Q6P2F1|Q6PJM1|Q9NRX0	Frame_Shift_Del	DEL	ENST00000216297.2	hg19	CCDS9569.1																																																																																			.	.	.	none		0.34	SUPT16H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074025.2		In_Frame_Del	-	21821648	CCT	-	21821646	8	5	60	1	0	1	0	1	0	0	1	0	15408	521	18	0	152	0	SUPT16H	14	21821646	Splice_Site	DEL	CCT	TCGA-A4-8630-01A-11D-2396-08		21821646	85527894	36	4011											
RALGAPA1	253959	hgsc.bcm.edu	37	chr14	36104756	36104756	+	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	ttggagcagtgtctttagagGtaaggccatgatccagtcca	10	11	12	8	0	1	2	0	1	1	1	3	3	3	3	3	3	1	2	3	3	2	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr14:36104756G>C	ENST00000389698.3	-	31	4597	c.4207C>G	c.(4207-4209)Cct>Gct	p.P1403A	RALGAPA1_ENST00000382366.3_Missense_Mutation_p.P1416A|RALGAPA1_ENST00000258840.6_Missense_Mutation_p.P1450A|RALGAPA1_ENST00000307138.6_Missense_Mutation_p.P1403A	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	1403	Minimal domain that binds to TCF3/E12. {ECO:0000250}.				activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GTCTTTAGAGGTAAGGCCATG	0.363																																					p.P1403A		Atlas-SNP	.											.	RALGAPA1	289	.	0			c.C4207G						PASS	.						49	46	47					14																	36104756		2203	4296	6499	SO:0001583	missense	253959	exon31			TTAGAGGTAAGGC	AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"tuberin-like protein 1", "GAP-related interacting protein to E12"	608884	"GTPase activating RANGAP domain-like 1", "GTPase activating Rap/RanGAP domain-like 1"	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.4207C>G	chr14.hg19:g.36104756G>C	ENSP00000374348:p.Pro1403Ala	51.0	0.0	.		33.0	15.0	.	NM_194301	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Missense_Mutation	SNP	ENST00000389698.3	hg19	CCDS32065.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.520063	0.85495	.	.	ENSG00000174373	ENST00000389698;ENST00000307138;ENST00000335518;ENST00000258840;ENST00000554259;ENST00000382366;ENST00000553892	T;T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;1.52;-0.2;-0.2	5.41	5.41	0.78517	.	0.100260	0.64402	D	0.000001	T	0.81187	0.4770	M	0.81112	2.525	0.80722	D	1	D;D;D;P	0.89917	1.0;1.0;0.98;0.855	D;D;P;P	0.91635	0.999;0.999;0.885;0.667	T	0.81604	-0.0857	10	0.51188	T	0.08	-15.3316	19.5739	0.95434	0.0:0.0:1.0:0.0	.	1450;1416;1403;1403	Q6GYQ0-6;B9EK38;Q6GYQ0-2;Q6GYQ0	.;.;.;RGPA1_HUMAN	A	1403;1403;1403;1450;41;1416;1450	ENSP00000374348:P1403A;ENSP00000302647:P1403A;ENSP00000258840:P1450A;ENSP00000451133:P41A;ENSP00000371803:P1416A;ENSP00000451877:P1450A	ENSP00000258840:P1450A	P	-	1	0	RALGAPA1	35174507	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.934000	0.92915	2.691000	0.91804	0.563000	0.77884	CCT	.	.	.	none		0.363	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022		C	36104756	G	C	36104756	3	2	60	1	0	0	0	0	1	0	0	0	13026	1261	44	4	2096	4	RALGAPA1	14	36104756	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08	14283110	36104756	71244784	37	4012											
DUOXA2	405753	hgsc.bcm.edu	37	chr15	45410080	45410080	+	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	aagcaggccgctctcccagaCttaaaatgtatcaccactaa	14	8	6	13	1	2	1	1	0	1	1	3	1	2	1	3	1	1	3	3	1	5	3			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr15:45410080C>A	ENST00000323030.5	+	6	1221	c.936C>A	c.(934-936)gaC>gaA	p.D312E	DUOXA1_ENST00000558996.1_3'UTR|DUOXA1_ENST00000559014.1_Intron|DUOXA1_ENST00000430224.2_Intron|DUOXA1_ENST00000267803.4_Intron	NM_207581.3	NP_997464.2	Q1HG44	DOXA2_HUMAN	dual oxidase maturation factor 2	312					hydrogen peroxide metabolic process (GO:0042743)|protein transport (GO:0015031)|regulation of inflammatory response (GO:0050727)|regulation of thyroid hormone generation (GO:2000609)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)							all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;2.88e-18)|GBM - Glioblastoma multiforme(94;3.95e-07)|COAD - Colon adenocarcinoma(120;0.0652)|Colorectal(133;0.0659)		CTCTCCCAGACTTAAAATGTA	0.627											OREG0023102	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D312E		Atlas-SNP	.											.	DUOXA2	38	.	0			c.C936A						PASS	.						56	67	63					15																	45410080		2198	4298	6496	SO:0001583	missense	405753	exon6			CCCAGACTTAAAA	BX537581	CCDS10118.2	15q21.1	2008-10-30		2006-07-25	ENSG00000140274	ENSG00000140274			32698	protein-coding gene	gene with protein product		612772				16651268	Standard	NM_207581		Approved		uc001zuo.3	Q1HG44	OTTHUMG00000131354	ENST00000323030.5:c.936C>A	chr15.hg19:g.45410080C>A	ENSP00000319705:p.Asp312Glu	140.0	0.0	.	931	113.0	48.0	.	NM_207581	B2RPI9|H0YNQ6	Missense_Mutation	SNP	ENST00000323030.5	hg19	CCDS10118.2	.	.	.	.	.	.	.	.	.	.	C	11.80	1.747884	0.30955	.	.	ENSG00000140274	ENST00000323030	T	0.58060	0.36	4.74	1.8	0.24995	.	0.658067	0.14730	N	0.301826	T	0.27278	0.0669	N	0.08118	0	0.09310	N	0.999998	B	0.06786	0.001	B	0.08055	0.003	T	0.13737	-1.0498	10	0.44086	T	0.13	-18.3106	4.3109	0.10971	0.1793:0.6307:0.0:0.19	.	312	Q1HG44	DOXA2_HUMAN	E	312	ENSP00000319705:D312E	ENSP00000319705:D312E	D	+	3	2	DUOXA2	43197372	0.001000	0.12720	0.004000	0.12327	0.047000	0.14425	0.068000	0.14531	0.310000	0.22990	0.561000	0.74099	GAC	.	.	.	none		0.627	DUOXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254142.1	NM_207581		A	45410080	C	A	45410080	3	1	60	1	0	0	0	0	1	0	0	0	4805	564	20	4	958	4	DUOXA2	15	45410080	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08		45410080	57121312	38	4013											
MYO9A	4649	hgsc.bcm.edu	37	chr15	72172105	72172105	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagatattctgccgaaatTccttcagggcttttttaaat	11	16	7	7	1	2	2	1	1	1	1	3	3	3	2	2	1	1	1	2	1	5	7			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr15:72172105T>C	ENST00000356056.5	-	30	6168	c.5696A>G	c.(5695-5697)gAa>gGa	p.E1899G	MYO9A_ENST00000444904.1_Missense_Mutation_p.E1880G|MYO9A_ENST00000424560.1_Missense_Mutation_p.E1970G|MYO9A_ENST00000564571.1_Missense_Mutation_p.E1899G	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1899	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						CTGCCGAAATTCCTTCAGGGC	0.363																																					p.E1899G		Atlas-SNP	.											.	MYO9A	203	.	0			c.A5696G						PASS	.						108	106	107					15																	72172105		2199	4297	6496	SO:0001583	missense	4649	exon30			CGAAATTCCTTCA	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.5696A>G	chr15.hg19:g.72172105T>C	ENSP00000348349:p.Glu1899Gly	88.0	0.0	.		76.0	35.0	.	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	hg19	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.414821	0.83449	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	T;T;T	0.14893	2.47;2.47;2.47	4.73	4.73	0.59995	.	.	.	.	.	T	0.42899	0.1223	M	0.79258	2.445	0.58432	D	0.999997	D;D	0.89917	1.0;0.997	D;P	0.79108	0.992;0.848	T	0.43956	-0.9359	9	0.62326	D	0.03	.	14.5012	0.67722	0.0:0.0:0.0:1.0	.	1970;1899	B2RTY4-4;B2RTY4	.;MYO9A_HUMAN	G	1899;1970;1880	ENSP00000348349:E1899G;ENSP00000399162:E1970G;ENSP00000398250:E1880G	ENSP00000348349:E1899G	E	-	2	0	MYO9A	69959159	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.593000	0.82686	1.903000	0.55091	0.528000	0.53228	GAA	.	.	.	none		0.363	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		C	72172105	T	C	72172105	3	2	60	1	0	0	0	0	1	0	0	0	10091	1783	62	3	2002	3	MYO9A	15	72172105	Missense_Mutation	SNP	T	TCGA-A4-8630-01A-11D-2396-08	26762025	72172105	30359287	39	4014											
TMEM204	79652	hgsc.bcm.edu	37	chr16	1604905	1604905	+	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	cgctggcggcagccatgctcAtctggaacattctccacaag	9	8	10	14	2	3	0	1	0	2	0	4	1	3	1	2	3	3	3	2	3	2	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr16:1604905A>T	ENST00000566264.1	+	3	1262	c.559A>T	c.(559-561)Atc>Ttc	p.I187F	IFT140_ENST00000439987.2_Intron|TMEM204_ENST00000253934.5_Missense_Mutation_p.I187F|IFT140_ENST00000426508.2_Intron	NM_024600.5	NP_078876.2	Q9BSN7	TM204_HUMAN	transmembrane protein 204	187					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)				AGCCATGCTCATCTGGAACAT	0.597																																					p.I187F		Atlas-SNP	.											.	TMEM204	29	.	0			c.A559T						PASS	.						57	62	60					16																	1604905		2025	4177	6202	SO:0001583	missense	79652	exon3			ATGCTCATCTGGA		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.559A>T	chr16.hg19:g.1604905A>T	ENSP00000454945:p.Ile187Phe	74.0	0.0	.		85.0	23.0	.	NM_024600	D3DU76|Q3KRC1|Q9H7G5	Missense_Mutation	SNP	ENST00000566264.1	hg19	CCDS42098.1	.	.	.	.	.	.	.	.	.	.	a	19.43	3.826453	0.71143	.	.	ENSG00000131634	ENST00000253934	T	0.56275	0.47	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.63212	0.2492	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.66925	-0.5800	10	0.87932	D	0	-17.5451	16.269	0.82606	1.0:0.0:0.0:0.0	.	187	Q9BSN7	TM204_HUMAN	F	187	ENSP00000253934:I187F	ENSP00000253934:I187F	I	+	1	0	TMEM204	1544906	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.882000	0.92420	2.241000	0.73720	0.529000	0.55759	ATC	.	.	.	none		0.597	TMEM204-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432610.1	NM_024600		T	1604905	A	T	1604905	3	4	60	1	0	0	0	0	1	0	0	0	16141	217	8	5	569	5	TMEM204	16	1604905	Missense_Mutation	SNP	A	TCGA-A4-8630-01A-11D-2396-08		1604905	88749848	40	4015											
SCNN1B	6338	hgsc.bcm.edu	37	chr16	23387095	23387095	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttccaagaccacatgatcCgtaactgcaactgtggccac	11	8	8	14	1	0	2	0	1	0	1	2	2	2	2	4	1	3	3	4	1	3	2	rs372303239		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr16:23387095C>T	ENST00000343070.2	+	8	1365	c.1189C>T	c.(1189-1191)Cgt>Tgt	p.R397C	SCNN1B_ENST00000568085.1_Missense_Mutation_p.R361C|SCNN1B_ENST00000568923.1_Missense_Mutation_p.R370C|SCNN1B_ENST00000307331.5_Missense_Mutation_p.R442C	NM_000336.2	NP_000327.2	P51168	SCNNB_HUMAN	sodium channel, non-voltage-gated 1, beta subunit	397					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)	CCACATGATCCGTAACTGCAA	0.597																																					p.R397C		Atlas-SNP	.											.	SCNN1B	81	.	0			c.C1189T						PASS	.		CYS/ARG	1,4393	2.1+/-5.4	0,1,2196	191	152	165		1189	2.5	0.7	16		165	0,8600		0,0,4300	no	missense	SCNN1B	NM_000336.2	180	0,1,6496	TT,TC,CC		0.0,0.0228,0.0077	possibly-damaging	397/641	23387095	1,12993	2197	4300	6497	SO:0001583	missense	6338	exon8			ATGATCCGTAACT	X87159	CCDS10609.1	16p12.2-p12.1	2012-02-28	2012-02-28		ENSG00000168447	ENSG00000168447		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10600	protein-coding gene	gene with protein product	"Liddle syndrome"	600760	"sodium channel, nonvoltage-gated 1, beta", "sodium channel, non-voltage-gated 1, beta"				Standard	NM_000336		Approved	ENaCbeta	uc002dln.3	P51168	OTTHUMG00000131608	ENST00000343070.2:c.1189C>T	chr16.hg19:g.23387095C>T	ENSP00000345751:p.Arg397Cys	124.0	0.0	.		179.0	42.0	.	NM_000336	C5HTZ2|O60891|Q96KG2|Q9UJ32|Q9UMU5	Missense_Mutation	SNP	ENST00000343070.2	hg19	CCDS10609.1	.	.	.	.	.	.	.	.	.	.	c	11.77	1.739120	0.30774	2.28E-4	0.0	ENSG00000168447	ENST00000343070;ENST00000307331	T;T	0.64618	-0.11;-0.11	4.65	2.53	0.30540	Na+ channel, amiloride-sensitive, conserved site (1);	1.865040	0.02752	N	0.117609	T	0.67832	0.2935	L	0.48642	1.525	0.09310	N	1	P	0.36171	0.541	P	0.46275	0.51	T	0.58031	-0.7708	10	0.87932	D	0	-11.3583	9.6889	0.40116	0.0:0.7032:0.2048:0.0921	.	397	P51168	SCNNB_HUMAN	C	397;442	ENSP00000345751:R397C;ENSP00000302874:R442C	ENSP00000302874:R442C	R	+	1	0	SCNN1B	23294596	0.007000	0.16637	0.690000	0.30148	0.144000	0.21451	1.280000	0.33202	1.065000	0.40693	0.651000	0.88453	CGT	.	.	.	weak		0.597	SCNN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254495.2			T	23387095	C	T	23387095	3	4	60	1	0	0	0	0	1	0	0	0	13941	652	23	1	1215	1	SCNN1B	16	23387095	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08	21782190	23387095	66967658	41	4016											
ELMO3	79767	hgsc.bcm.edu	37	chr16	67236622	67236622	+	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	accaaggtgaatgcgctcacTtatggggaggtgctgcggct	8	9	15	9	2	1	1	1	1	0	0	1	2	1	2	1	5	3	3	1	5	3	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr16:67236622T>A	ENST00000360833.1	+	14	1656	c.1599T>A	c.(1597-1599)acT>acA	p.T533T	ELMO3_ENST00000477898.1_Silent_p.T384T|MIR328_ENST00000385213.1_RNA|ELMO3_ENST00000393997.2_Silent_p.T550T			Q96BJ8	ELMO3_HUMAN	engulfment and cell motility 3	497					apoptotic process (GO:0006915)|phagocytosis (GO:0006909)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				cervix(2)|kidney(4)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	18		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00067)|Epithelial(162;0.00442)|all cancers(182;0.0417)		ATGCGCTCACTTATGGGGAGG	0.647																																					p.T550T		Atlas-SNP	.											.	ELMO3	41	.	0			c.T1650A						PASS	.						42	49	46					16																	67236622		2076	4215	6291	SO:0001819	synonymous_variant	79767	exon15			GCTCACTTATGGG		CCDS10833.2	16q22.1	2010-03-18	2006-01-20		ENSG00000102890	ENSG00000102890		"Engulfment and cell motility proteins"	17289	protein-coding gene	gene with protein product		606422	"engulfment and cell motility 3 (ced-12 homolog, C. elegans)"			11595183	Standard	NM_024712		Approved	FLJ13824, CED12, ELMO-3, CED-12	uc002esa.3	Q96BJ8	OTTHUMG00000133570	ENST00000360833.1:c.1599T>A	chr16.hg19:g.67236622T>A		91.0	0.0	.		69.0	44.0	.	NM_024712	B4DV86|Q9H8A5	Silent	SNP	ENST00000360833.1	hg19																																																																																				.	.	.	none		0.647	ELMO3-001	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000257667.2	NM_024712		A	67236622	T	A	67236622	2	1	60	1	0	0	0	0	0	0	0	1	5069	1596	56	5		5	ELMO3	16	67236622	Silent	SNP	T	TCGA-A4-8630-01A-11D-2396-08	43849527	67236622	23118131	42	4017											
TEKT1	83659	hgsc.bcm.edu	37	chr17	6703554	6703554	+	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	gggctaaagtttccttcaatCtaggagaaagggaagaagag	15	8	13	5	0	2	3	1	0	1	3	3	5	3	4	1	3	0	2	1	3	7	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr17:6703554C>A	ENST00000338694.2	-	8	1179		c.e8-1		TEKT1_ENST00000535086.1_Splice_Site	NM_053285.1	NP_444515.1	Q969V4	TEKT1_HUMAN	tektin 1							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)				TTCCTTCAATCTAGGAGAAAG	0.463																																					.		Atlas-SNP	.											.	TEKT1	49	.	0			c.1050-1G>T						PASS	.						55	53	53					17																	6703554		2203	4300	6503	SO:0001630	splice_region_variant	83659	exon9			TTCAATCTAGGAG		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.1050-1G>T	chr17.hg19:g.6703554C>A		82.0	0.0	.		101.0	29.0	.	NM_053285	D3DTM7	Splice_Site	SNP	ENST00000338694.2	hg19	CCDS11083.1	.	.	.	.	.	.	.	.	.	.	C	14.52	2.558722	0.45590	.	.	ENSG00000167858	ENST00000338694;ENST00000535086	.	.	.	5.75	5.75	0.90469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.8163	0.88635	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TEKT1	6644278	1.000000	0.71417	0.148000	0.22405	0.065000	0.16274	5.783000	0.68982	2.885000	0.99019	0.655000	0.94253	.	.	.	.	none		0.463	TEKT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219867.2	NM_053285	Intron	A	6703554	C	A	6703554	5	1	60	1	0	0	0	0	0	0	1	0	15764	927	32	4	211	4	TEKT1	17	6703554	Splice_Site	SNP	C	TCGA-A4-8630-01A-11D-2396-08		6703554	74491656	43	4018											
RAI1	10743	hgsc.bcm.edu	37	chr17	17701717	17701717	+	Missense_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	cggcagagcccggcggggagGcccaggagcactgggtgcat	7	3	19	12	3	0	1	0	0	0	1	0	3	0	3	2	7	3	3	2	7	0	0			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr17:17701717G>A	ENST00000353383.1	+	3	5924	c.5455G>A	c.(5455-5457)Gcc>Acc	p.A1819T	RAI1_ENST00000261641.6_Intron	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	1819					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)		CGGCGGGGAGGCCCAGGAGCA	0.692																																					p.A1819T		Atlas-SNP	.											.	RAI1	121	.	0			c.G5455A						PASS	.						15	17	16					17																	17701717		2196	4296	6492	SO:0001583	missense	10743	exon3			GGGGAGGCCCAGG	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.5455G>A	chr17.hg19:g.17701717G>A	ENSP00000323074:p.Ala1819Thr	37.0	0.0	.		26.0	17.0	.	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Missense_Mutation	SNP	ENST00000353383.1	hg19	CCDS11188.1	.	.	.	.	.	.	.	.	.	.	G	3.249	-0.153699	0.06585	.	.	ENSG00000108557	ENST00000353383;ENST00000395776	T	0.65364	-0.15	4.42	0.819	0.18785	.	0.164676	0.41605	N	0.000849	T	0.24928	0.0605	N	0.01576	-0.805	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.04900	-1.0919	10	0.09843	T	0.71	.	5.4772	0.16702	0.6904:0.146:0.1635:0.0	.	1819	Q7Z5J4	RAI1_HUMAN	T	1819	ENSP00000323074:A1819T	ENSP00000323074:A1819T	A	+	1	0	RAI1	17642442	1.000000	0.71417	0.989000	0.46669	0.093000	0.18481	3.093000	0.50217	-0.047000	0.13423	-0.367000	0.07326	GCC	.	.	.	none		0.692	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665		A	17701717	G	A	17701717	3	1	60	1	0	0	0	0	1	0	0	0	13020	1203	42	2	5457	2	RAI1	17	17701717	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08	10998163	17701717	63493493	44	4019											
ALDH3A2	224	hgsc.bcm.edu	37	chr17	19566808	19566808	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttatgtattttcgcataaccAtaaggtaagctttagagaga	14	14	8	5	1	0	2	0	0	0	2	1	3	0	2	1	1	2	4	1	1	6	9			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr17:19566808A>G	ENST00000176643.6	+	7	1549	c.1103A>G	c.(1102-1104)cAt>cGt	p.H368R	SNORA31_ENST00000516540.1_RNA|ALDH3A2_ENST00000339618.4_Missense_Mutation_p.H368R|ALDH3A2_ENST00000581518.1_Missense_Mutation_p.H368R|ALDH3A2_ENST00000579855.1_Missense_Mutation_p.H368R|ALDH3A2_ENST00000395575.2_Missense_Mutation_p.H368R|ALDH3A2_ENST00000571163.1_Missense_Mutation_p.H41R			P51648	AL3A2_HUMAN	aldehyde dehydrogenase 3 family, member A2	368					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)					TCGCATAACCATAAGGTAAGC	0.358																																					p.H368R		Atlas-SNP	.											.	ALDH3A2	41	.	0			c.A1103G						PASS	.						77	76	76					17																	19566808		2203	4300	6503	SO:0001583	missense	224	exon7			ATAACCATAAGGT	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.1103A>G	chr17.hg19:g.19566808A>G	ENSP00000176643:p.His368Arg	78.0	0.0	.		82.0	37.0	.	NM_001031806	Q6I9T3|Q93011|Q96J37	Missense_Mutation	SNP	ENST00000176643.6	hg19	CCDS11210.1	.	.	.	.	.	.	.	.	.	.	A	6.134	0.392977	0.11638	.	.	ENSG00000072210	ENST00000176643;ENST00000395575;ENST00000339618	T;T;T	0.75367	-0.93;-0.93;-0.93	5.12	2.89	0.33648	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.561400	0.20786	N	0.085705	T	0.41581	0.1165	N	0.01003	-1.06	0.09310	N	0.99999	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.0	T	0.33163	-0.9879	10	0.33141	T	0.24	-1.3235	7.2008	0.25879	0.7763:0.147:0.0766:0.0	.	368;368	P51648;P51648-2	AL3A2_HUMAN;.	R	368	ENSP00000176643:H368R;ENSP00000378942:H368R;ENSP00000345774:H368R	ENSP00000176643:H368R	H	+	2	0	ALDH3A2	19507400	0.592000	0.26832	0.274000	0.24659	0.402000	0.30811	2.992000	0.49417	0.289000	0.22422	0.455000	0.32223	CAT	.	.	.	none		0.358	ALDH3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132268.1			G	19566808	A	G	19566808	3	3	60	1	0	0	0	0	1	0	0	0	498	217	8	3	1129	3	ALDH3A2	17	19566808	Missense_Mutation	SNP	A	TCGA-A4-8630-01A-11D-2396-08	1865091	19566808	61628402	45	4020											
TAF15	8148	hgsc.bcm.edu	37	chr17	34171754	34171754	+	Missense_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	tggctatggaggagatcgagGtggctatggaggagaccgag	10	7	19	5	2	0	2	0	0	0	2	1	8	0	4	1	7	0	2	1	7	2	2			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr17:34171754G>A	ENST00000588240.1	+	15	1566	c.1451G>A	c.(1450-1452)gGt>gAt	p.G484D	TAF15_ENST00000592237.1_Intron|TAF15_ENST00000311979.3_Missense_Mutation_p.G481D	NM_003487.3|NM_139215.2	NP_003478.1|NP_631961.1	Q16514	TAF12_HUMAN	TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa	0					chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of RNA biosynthetic process (GO:2001141)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)		TAF15/NR4A3(33)	lung(1)|ovary(1)|skin(2)|stomach(1)	5		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		ggagatcgaggtggctatgga	0.617			T	"TEC, CHN1, ZNF384"	"extraskeletal myxoid chondrosarcomas, ALL"																																p.G484D		Atlas-SNP	.		Dom	yes		17	17q11.1-q11.2	8148	"TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa"		"L, M"	.	TAF15	46	.	0			c.G1451A						PASS	.						69	59	62					17																	34171754		2203	4300	6503	SO:0001583	missense	8148	exon15			ATCGAGGTGGCTA	U51334	CCDS32623.1, CCDS59279.1	17q11.1-q11.2	2013-02-12	2002-08-29	2001-12-07		ENSG00000270647		"RNA binding motif (RRM) containing"	11547	protein-coding gene	gene with protein product		601574	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, N, 68kD (RNA-binding protein 56)"	TAF2N		8954779, 9795213	Standard	NM_003487		Approved	hTAFII68, RBP56, Npl3	uc002hkd.4	Q92804		ENST00000588240.1:c.1451G>A	chr17.hg19:g.34171754G>A	ENSP00000466950:p.Gly484Asp	21.0	0.0	.		36.0	17.0	.	NM_139215	D3DPM5|Q15775|Q5T077	Missense_Mutation	SNP	ENST00000588240.1	hg19	CCDS32623.1	.	.	.	.	.	.	.	.	.	.	G	14.70	2.613730	0.46631	.	.	ENSG00000172660	ENST00000311979;ENST00000536077	D	0.95171	-3.63	4.33	3.36	0.38483	.	.	.	.	.	D	0.88250	0.6386	N	0.22421	0.69	0.35491	D	0.798963	P;P	0.39282	0.536;0.666	B;B	0.35240	0.097;0.198	D	0.89286	0.3615	9	0.87932	D	0	.	9.8408	0.40998	0.1042:0.0:0.8958:0.0	.	484;481	Q92804;Q92804-2	RBP56_HUMAN;.	D	484;287	ENSP00000309558:G484D	ENSP00000309558:G484D	G	+	2	0	TAF15	31195867	0.956000	0.32656	0.753000	0.31225	0.954000	0.61252	3.509000	0.53386	0.943000	0.37553	0.467000	0.42956	GGT	.	.	.	none		0.617	TAF15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449134.1	NM_139215		A	34171754	G	A	34171754	3	1	60	1	0	0	0	0	1	0	0	0	15530	1261	44	2	1509	2	TAF15	17	34171754	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08	14604946	34171754	47023456	46	4021											
HELZ	9931	hgsc.bcm.edu	37	chr17	65074431	65074431	+	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	cctaggctcagttcctggaaGagagacagagggtcgctact	10	8	13	10	1	1	3	1	0	0	3	3	5	2	4	2	3	1	3	2	3	3	3			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr17:65074431G>A	ENST00000358691.5	-	33	5932	c.5766C>T	c.(5764-5766)ctC>ctT	p.L1922L	HELZ_ENST00000580168.1_Silent_p.L1923L	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	1922						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)					GTTCCTGGAAGAGAGACAGAG	0.522																																					p.L1922L		Atlas-SNP	.											.	HELZ	160	.	0			c.C5766T						PASS	.						44	46	45					17																	65074431		1860	4094	5954	SO:0001819	synonymous_variant	9931	exon33			CTGGAAGAGAGAC	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.5766C>T	chr17.hg19:g.65074431G>A		128.0	0.0	.		124.0	35.0	.	NM_014877	I6L9H4	Silent	SNP	ENST00000358691.5	hg19	CCDS42374.1																																																																																			.	.	.	none		0.522	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		A	65074431	G	A	65074431	2	1	60	1	0	0	0	0	0	0	0	1	7056	929	33	2		2	HELZ	17	65074431	Silent	SNP	G	TCGA-A4-8630-01A-11D-2396-08	30902677	65074431	16120779	47	4022											
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2718194	2718194	+	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	agattatttcgcatattagtCaacatggaggaaaatggcct	14	12	9	6	1	1	1	1	0	0	1	2	3	1	3	1	3	1	1	1	3	6	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr18:2718194C>T	ENST00000320876.6	+	18	2637	c.2299C>T	c.(2299-2301)Caa>Taa	p.Q767*	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Nonsense_Mutation_p.Q767*	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	767					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						GCATATTAGTCAACATGGAGG	0.284																																					p.Q767X		Atlas-SNP	.											.	SMCHD1	88	.	0			c.C2299T						PASS	.						91	85	87					18																	2718194		1809	4065	5874	SO:0001587	stop_gained	23347	exon18			ATTAGTCAACATG	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.2299C>T	chr18.hg19:g.2718194C>T	ENSP00000326603:p.Gln767*	46.0	0.0	.		46.0	19.0	.	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Nonsense_Mutation	SNP	ENST00000320876.6	hg19	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.313068	0.81358	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	.	.	.	5.62	5.62	0.85841	.	0.063495	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-12.072	19.6473	0.95784	0.0:1.0:0.0:0.0	.	.	.	.	X	767	.	ENSP00000261598:Q767X	Q	+	1	0	SMCHD1	2708194	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.933000	0.70130	2.650000	0.89964	0.591000	0.81541	CAA	.	.	.	none		0.284	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			T	2718194	C	T	2718194	4	4	60	1	0	0	0	0	0	1	0	0	14801	827	29	2	2369	2	SMCHD1	18	2718194	Nonsense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08		2718194	75359054	48	4023											
TCF4	6925	hgsc.bcm.edu	37	chr18	52921812	52921812	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctccattatgagaaggtccAatgattccatgcatgtcccc	10	11	8	12	0	0	2	0	2	0	1	4	3	4	2	5	1	1	2	5	1	3	2			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr18:52921812A>G	ENST00000356073.4	-	15	1877	c.1266T>C	c.(1264-1266)atT>atC	p.I422I	TCF4_ENST00000568673.1_Silent_p.I398I|TCF4_ENST00000570287.2_Silent_p.I262I|TCF4_ENST00000561831.3_Silent_p.I262I|TCF4_ENST00000566279.1_Silent_p.I362I|TCF4_ENST00000398339.1_Silent_p.I524I|TCF4_ENST00000537578.1_Silent_p.I398I|TCF4_ENST00000567880.1_Silent_p.I362I|TCF4_ENST00000457482.3_Silent_p.I262I|TCF4_ENST00000561992.1_Silent_p.I292I|TCF4_ENST00000564403.2_Silent_p.I428I|TCF4_ENST00000564999.1_Silent_p.I422I|TCF4_ENST00000565018.2_Silent_p.I422I|TCF4_ENST00000570177.2_Silent_p.I292I|TCF4_ENST00000544241.2_Silent_p.I351I|TCF4_ENST00000563760.1_5'UTR|TCF4_ENST00000564228.1_Silent_p.I351I|TCF4_ENST00000566286.1_Silent_p.I419I|TCF4_ENST00000568740.1_Silent_p.I397I|TCF4_ENST00000537856.3_Silent_p.I292I|TCF4_ENST00000540999.1_Silent_p.I398I|TCF4_ENST00000543082.1_Silent_p.I380I|TCF4_ENST00000354452.3_Silent_p.I422I	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4	422					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)		GAGAAGGTCCAATGATTCCAT	0.493																																					p.I524I		Atlas-SNP	.											.	TCF4	178	.	0			c.T1572C						PASS	.						118	106	110					18																	52921812		2203	4300	6503	SO:0001819	synonymous_variant	6925	exon16			AGGTCCAATGATT	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.1266T>C	chr18.hg19:g.52921812A>G		52.0	0.0	.		53.0	22.0	.	NM_001243226	B3KT62|B3KUC0|B4DT37|B4DUG3|B7Z5M6|B7Z6Y1|G0LNT9|G0LNU0|G0LNU1|G0LNU2|G0LNU4|G0LNU5|G0LNU8|G0LNU9|G0LNV0|G0LNV1|G0LNV2|H3BPQ1|Q08AP2|Q08AP3|Q15439|Q15440|Q15441	Silent	SNP	ENST00000356073.4	hg19	CCDS11960.1																																																																																			.	.	.	none		0.493	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	NM_003199		G	52921812	A	G	52921812	2	3	60	1	0	0	0	0	0	0	0	1	15707	126	5	3		3	TCF4	18	52921812	Silent	SNP	A	TCGA-A4-8630-01A-11D-2396-08	50203618	52921812	25155436	49	4024											
MUC16	94025	hgsc.bcm.edu	37	chr19	9056220	9056220	+	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	cttgataagcacttgtcactGttcccagctcaacgctctct	8	13	6	14	1	3	1	2	1	1	0	5	1	4	1	1	0	3	4	1	0	2	4			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr19:9056220G>C	ENST00000397910.4	-	3	31429	c.31226C>G	c.(31225-31227)aCa>aGa	p.T10409R		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10411	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						ACTTGTCACTGTTCCCAGCTC	0.473																																					p.T10409R		Atlas-SNP	.											.	MUC16	4315	.	0			c.C31226G						PASS	.						201	199	200					19																	9056220		2020	4181	6201	SO:0001583	missense	94025	exon3			GTCACTGTTCCCA	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.31226C>G	chr19.hg19:g.9056220G>C	ENSP00000381008:p.Thr10409Arg	268.0	0.0	.		246.0	94.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	7.773	0.707853	0.15239	.	.	ENSG00000181143	ENST00000397910	T	0.02525	4.26	3.94	-6.08	0.02151	.	.	.	.	.	T	0.01489	0.0048	N	0.19112	0.55	.	.	.	B	0.33044	0.395	B	0.27076	0.076	T	0.43798	-0.9369	8	0.87932	D	0	.	0.9223	0.01318	0.1739:0.2499:0.196:0.3802	.	10409	B5ME49	.	R	10409	ENSP00000381008:T10409R	ENSP00000381008:T10409R	T	-	2	0	MUC16	8917220	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.198000	0.01239	-1.038000	0.03279	-0.181000	0.13052	ACA	.	.	.	none		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9056220	G	C	9056220	3	2	60	1	0	0	0	0	1	0	0	0	9980	1377	48	4	12625	4	MUC16	19	9056220	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08		9056220	50072763	50	4025											
ZNF93	81931	hgsc.bcm.edu	37	chr19	20044771	20044771	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tacacataagagaattcataCtggagagaaaccatacaagt	19	8	7	7	0	1	2	1	0	0	2	1	5	1	3	1	1	4	0	1	1	7	5			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr19:20044771C>T	ENST00000343769.5	+	4	1035	c.1007C>T	c.(1006-1008)aCt>aTt	p.T336I	AC007204.2_ENST00000592245.1_lincRNA	NM_031218.3	NP_112495.2	P35789	ZNF93_HUMAN	zinc finger protein 93	336					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						AGAATTCATACTGGAGAGAAA	0.378																																					p.T336I		Atlas-SNP	.											.	ZNF93	81	.	0			c.C1007T						PASS	.						57	57	57					19																	20044771		2203	4300	6503	SO:0001583	missense	81931	exon4			TTCATACTGGAGA	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.1007C>T	chr19.hg19:g.20044771C>T	ENSP00000342002:p.Thr336Ile	53.0	0.0	.		53.0	21.0	.	NM_031218	A6NMY2|B9EGT2|Q8N8Q4|Q9H9X5|Q9Y2N8	Missense_Mutation	SNP	ENST00000343769.5	hg19	CCDS32973.1	.	.	.	.	.	.	.	.	.	.	c	17.57	3.422998	0.62733	.	.	ENSG00000184635	ENST00000343769;ENST00000427325	T	0.25749	1.78	0.85	0.85	0.18980	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.46521	0.1397	M	0.77103	2.36	0.28256	N	0.925036	D	0.71674	0.998	D	0.76575	0.988	T	0.30208	-0.9986	9	0.87932	D	0	.	6.9971	0.24789	0.0:1.0:0.0:0.0	.	336	P35789	ZNF93_HUMAN	I	336	ENSP00000342002:T336I	ENSP00000342002:T336I	T	+	2	0	ZNF93	19905771	0.931000	0.31567	0.796000	0.32109	0.795000	0.44927	1.895000	0.39778	0.192000	0.20272	0.195000	0.17529	ACT	.	.	.	none		0.378	ZNF93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460808.2	NM_031218		T	20044771	C	T	20044771	3	4	60	1	0	0	0	0	1	0	0	0	18214	565	20	2	1021	2	ZNF93	19	20044771	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08	10988551	20044771	39084212	51	4026											
ZNF585A	199704	hgsc.bcm.edu	37	chr19	37642653	37642653	+	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	cactcagcacacacgtaaggCttctctccagtgtgaattcg	10	10	8	13	2	2	1	1	1	1	0	5	1	3	1	1	1	1	3	1	1	2	3			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr19:37642653C>A	ENST00000356958.4	-	5	2406	c.2148G>T	c.(2146-2148)aaG>aaT	p.K716N	ZNF585A_ENST00000588723.1_Intron|ZNF585A_ENST00000392157.2_Missense_Mutation_p.K661N|ZNF585A_ENST00000355533.2_Missense_Mutation_p.K353N|ZNF585A_ENST00000292841.5_Missense_Mutation_p.K661N			Q6P3V2	Z585A_HUMAN	zinc finger protein 585A	716					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|central_nervous_system(1)|endometrium(2)|large_intestine(17)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ACACGTAAGGCTTCTCTCCAG	0.453																																					p.K661N		Atlas-SNP	.											.	ZNF585A	117	.	0			c.G1983T						PASS	.						120	99	106					19																	37642653		2203	4300	6503	SO:0001583	missense	199704	exon6			GTAAGGCTTCTCT	AK074345	CCDS12499.1, CCDS74353.1	19q13.13	2013-01-08				ENSG00000196967		"Zinc fingers, C2H2-type", "-"	26305	protein-coding gene	gene with protein product						12477932	Standard	NM_199126		Approved	FLJ23765	uc002ofn.1	Q6P3V2		ENST00000356958.4:c.2148G>T	chr19.hg19:g.37642653C>A	ENSP00000349440:p.Lys716Asn	153.0	0.0	.		106.0	46.0	.	NM_199126	Q8TE95|Q96MV3	Missense_Mutation	SNP	ENST00000356958.4	hg19		.	.	.	.	.	.	.	.	.	.	C	14.78	2.637787	0.47049	.	.	ENSG00000196967	ENST00000356958;ENST00000292841;ENST00000392157;ENST00000355533	T;T;T;T	0.26067	1.76;1.76;1.76;1.76	3.05	-1.58	0.08479	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.194401	0.25332	N	0.031425	T	0.42177	0.1191	.	.	.	0.34425	D	0.697868	D	0.61080	0.989	D	0.71184	0.972	T	0.52852	-0.8520	9	0.87932	D	0	.	7.5181	0.27612	0.0:0.29:0.0:0.71	.	716	Q6P3V2	Z585A_HUMAN	N	716;661;661;353	ENSP00000349440:K716N;ENSP00000292841:K661N;ENSP00000375998:K661N;ENSP00000347724:K353N	ENSP00000292841:K661N	K	-	3	2	ZNF585A	42334493	0.000000	0.05858	0.987000	0.45799	0.987000	0.75469	-2.016000	0.01446	-0.115000	0.11915	-0.136000	0.14681	AAG	.	.	.	none		0.453	ZNF585A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000457980.2	NM_152655		A	37642653	C	A	37642653	3	1	60	1	0	0	0	0	1	0	0	0	18029	796	28	4	165	4	ZNF585A	19	37642653	Missense_Mutation	SNP	C	TCGA-A4-8630-01A-11D-2396-08	17597882	37642653	21486330	52	4027											
SBF1	6305	hgsc.bcm.edu	37	chr22	50903300	50903300	+	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	cgtgacgcaggacacgctggGggtggttctcatccgcccgc	5	7	15	14	5	1	1	1	1	1	0	3	2	2	2	2	4	0	3	2	4	0	1			TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	g.chr22:50903300G>A	ENST00000390679.3	-	13	1563	c.1379C>T	c.(1378-1380)cCc>cTc	p.P460L	SBF1_ENST00000348911.6_Missense_Mutation_p.P461L|SBF1_ENST00000380817.3_Missense_Mutation_p.P460L			O95248	MTMR5_HUMAN	SET binding factor 1	460					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)		GACACGCTGGGGGTGGTTCTC	0.642																																					p.P460L		Atlas-SNP	.											.	SBF1	211	.	0			c.C1379T						PASS	.						46	51	49					22																	50903300		2127	4220	6347	SO:0001583	missense	6305	exon13			CGCTGGGGGTGGT	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.1379C>T	chr22.hg19:g.50903300G>A	ENSP00000375097:p.Pro460Leu	78.0	0.0	.		68.0	25.0	.	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Missense_Mutation	SNP	ENST00000390679.3	hg19		.	.	.	.	.	.	.	.	.	.	G	19.24	3.789727	0.70337	.	.	ENSG00000100241	ENST00000380817;ENST00000348911;ENST00000356279;ENST00000337034;ENST00000390679	D;D;D	0.86769	-2.16;-2.16;-2.17	4.17	4.17	0.49024	.	0.269330	0.29767	N	0.011248	D	0.87822	0.6274	L	0.49126	1.545	0.58432	D	0.999996	B;P;D	0.56746	0.021;0.873;0.977	B;P;P	0.55923	0.029;0.466;0.787	D	0.86760	0.1966	10	0.44086	T	0.13	.	9.8481	0.41039	0.0:0.0:0.6463:0.3537	.	460;461;460	O95248;G5E933;O95248-4	MTMR5_HUMAN;.;.	L	460;461;471;470;460	ENSP00000370196:P460L;ENSP00000252027:P461L;ENSP00000375097:P460L	ENSP00000336522:P470L	P	-	2	0	SBF1	49250166	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	3.603000	0.54074	2.156000	0.67533	0.591000	0.81541	CCC	.	.	.	none		0.642	SBF1-201	KNOWN	basic	protein_coding	protein_coding				A	50903300	G	A	50903300	3	1	60	1	0	0	0	0	1	0	0	0	13871	1232	43	2	4418	2	SBF1	22	50903300	Missense_Mutation	SNP	G	TCGA-A4-8630-01A-11D-2396-08		50903300	401266	53	4028											
H6PD	9563	hgsc.bcm.edu	37	chr1	9324818	9324818	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatgaagcgtgagatcaccAcgctggtgagccgggtgggc	8	6	18	9	3	1	3	1	3	0	1	1	5	1	4	2	4	2	1	2	4	1	0			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:9324818A>G	ENST00000377403.2	+	5	2568	c.2266A>G	c.(2266-2268)Acg>Gcg	p.T756A	H6PD_ENST00000602477.1_Missense_Mutation_p.T767A	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	756	6-phosphogluconolactonase.				pentose-phosphate shunt (GO:0006098)|response to alcohol (GO:0097305)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	6-phosphogluconolactonase activity (GO:0017057)|carbohydrate binding (GO:0030246)|glucose 1-dehydrogenase [NAD(P)] activity (GO:0047936)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	all_lung(157;0.23)	all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.88e-07)|COAD - Colon adenocarcinoma(227;7.47e-05)|Kidney(185;0.000244)|KIRC - Kidney renal clear cell carcinoma(229;0.000905)|STAD - Stomach adenocarcinoma(132;0.00176)|BRCA - Breast invasive adenocarcinoma(304;0.00183)|READ - Rectum adenocarcinoma(331;0.0419)		TGAGATCACCACGCTGGTGAG	0.637																																					p.T756A		Atlas-SNP	.											.	H6PD	71	.	0			c.A2266G						PASS	.						33	30	31					1																	9324818		2203	4297	6500	SO:0001583	missense	9563	exon5			ATCACCACGCTGG	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.2266A>G	chr1.hg19:g.9324818A>G	ENSP00000366620:p.Thr756Ala	183.0	0.0	.		259.0	61.0	.	NM_004285	Q4TT33|Q66I35|Q68DT3	Missense_Mutation	SNP	ENST00000377403.2	hg19	CCDS101.1	.	.	.	.	.	.	.	.	.	.	A	0.018	-1.467516	0.01053	.	.	ENSG00000049239	ENST00000377403	T	0.39406	1.08	5.45	-10.9	0.00192	Glucosamine/galactosamine-6-phosphate isomerase (1);6-phosphogluconolactonase, DevB-type (1);	0.671970	0.15660	N	0.250971	T	0.16257	0.0391	N	0.11560	0.145	0.09310	N	1	B	0.28128	0.201	B	0.28385	0.089	T	0.14896	-1.0456	10	0.35671	T	0.21	-7.8807	9.3226	0.37973	0.6541:0.1684:0.1206:0.057	.	756	O95479	G6PE_HUMAN	A	756	ENSP00000366620:T756A	ENSP00000366620:T756A	T	+	1	0	H6PD	9247405	0.002000	0.14202	0.001000	0.08648	0.225000	0.24961	0.628000	0.24522	-3.386000	0.00174	-2.411000	0.00221	ACG	.	.	.	none		0.637	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285		G	9324818	A	G	9324818	3	3	61	1	0	0	0	0	1	0	0	0	6943	159	6	3	2280	3	H6PD	1	9324818	Missense_Mutation	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10		9324818	239925803	1	4029											
SCP2	6342	hgsc.bcm.edu	37	chr1	53416459	53416459	+	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	gtgggcagagggctatctatCacagtttgggaatgactgga	10	10	15	6	0	2	2	1	1	1	1	2	4	2	4	0	4	0	3	0	4	3	3	rs371605573		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:53416459C>T	ENST00000371514.3	+	4	400	c.232C>T	c.(232-234)Cac>Tac	p.H78Y	SCP2_ENST00000407246.2_Missense_Mutation_p.H54Y|SCP2_ENST00000371513.5_Intron|SCP2_ENST00000371509.4_Intron|SCP2_ENST00000528311.1_5'UTR	NM_002979.4	NP_002970.2	Q9BX26	SYCP2_HUMAN	sterol carrier protein 2	0					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	15						GGCTATCTATCACAGTTTGGG	0.393																																					p.H78Y		Atlas-SNP	.											.	SCP2	44	.	0			c.C232T						PASS	.						164	155	158					1																	53416459		2203	4300	6503	SO:0001583	missense	6342	exon4			ATCTATCACAGTT	M75884	CCDS572.1, CCDS30719.1, CCDS41338.1, CCDS44149.1, CCDS44150.1, CCDS53317.1, CCDS53318.1, CCDS53319.1	1p32	2010-08-20			ENSG00000116171	ENSG00000116171			10606	protein-coding gene	gene with protein product		184755				1703300, 1718316	Standard	NM_001007098		Approved		uc001cur.2	P22307	OTTHUMG00000008936	ENST00000371514.3:c.232C>T	chr1.hg19:g.53416459C>T	ENSP00000360569:p.His78Tyr	110.0	0.0	.		118.0	25.0	.	NM_002979	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Missense_Mutation	SNP	ENST00000371514.3	hg19	CCDS572.1	.	.	.	.	.	.	.	.	.	.	C	16.66	3.184073	0.57800	.	.	ENSG00000116171	ENST00000371514;ENST00000407246	D;D	0.94138	-2.66;-3.36	5.09	5.09	0.68999	Thiolase-like, subgroup (1);Thiolase, N-terminal (1);Thiolase-like (1);	0.095236	0.64402	D	0.000001	D	0.96015	0.8702	M	0.76838	2.35	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.69307	0.96;0.963	D	0.94185	0.7435	10	0.17832	T	0.49	-12.7756	17.4125	0.87489	0.0:1.0:0.0:0.0	.	54;78	C9JC79;P22307	.;NLTP_HUMAN	Y	78;54	ENSP00000360569:H78Y;ENSP00000384569:H54Y	ENSP00000360569:H78Y	H	+	1	0	SCP2	53189047	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.914000	0.75764	2.629000	0.89072	0.563000	0.77884	CAC	.	.	.	none		0.393	SCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024740.2	NM_002979		T	53416459	C	T	53416459	3	4	61	1	0	0	0	0	1	0	0	0	13947	826	29	2	246	2	SCP2	1	53416459	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	44091641	53416459	195834162	2	4030											
PODN	127435	hgsc.bcm.edu	37	chr1	53535630	53535630	+	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	caggatttggccgaagtggcGgccacagcctgagccccgaa	9	5	14	13	3	0	1	0	1	0	0	0	4	0	2	5	4	2	0	5	4	2	1			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:53535630G>T	ENST00000312553.5	+	2	254	c.247G>T	c.(247-249)Ggc>Tgc	p.G83C	RP11-334A14.5_ENST00000447867.1_RNA|PODN_ENST00000395871.2_Missense_Mutation_p.G83C|PODN_ENST00000371500.3_Missense_Mutation_p.G64C	NM_001199081.1|NM_153703.4	NP_001186010.1|NP_714914.2	Q7Z5L7	PODN_HUMAN	podocan	35	LRRNT.				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						CCGAAGTGGCGGCCACAGCCT	0.697																																					p.G83C		Atlas-SNP	.											.	PODN	86	.	0			c.G247T						PASS	.						10	14	13					1																	53535630		2187	4283	6470	SO:0001583	missense	127435	exon2			AGTGGCGGCCACA	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.247G>T	chr1.hg19:g.53535630G>T	ENSP00000308315:p.Gly83Cys	28.0	0.0	.		50.0	23.0	.	NM_153703	B4DKN5|B4E373|Q5VVZ2|Q5VVZ3|Q6PIR3|Q6UXL8|Q8N641	Missense_Mutation	SNP	ENST00000312553.5	hg19	CCDS573.1	.	.	.	.	.	.	.	.	.	.	G	9.986	1.229555	0.22542	.	.	ENSG00000174348	ENST00000371500;ENST00000395871;ENST00000312553	T;T;T	0.59502	0.91;0.26;1.02	4.19	-3.33	0.04958	.	1.673490	0.03184	N	0.172477	T	0.54532	0.1864	N	0.08118	0	0.09310	N	1	D;P;P	0.65815	0.995;0.545;0.545	D;B;B	0.65010	0.931;0.209;0.306	T	0.53927	-0.8369	10	0.56958	D	0.05	.	10.02	0.42037	0.6741:0.0:0.3259:0.0	.	83;64;83	Q7Z5L7-4;Q7Z5L7-2;Q7Z5L7-3	.;.;.	C	64;83;83	ENSP00000360555:G64C;ENSP00000379212:G83C;ENSP00000308315:G83C	ENSP00000308315:G83C	G	+	1	0	PODN	53308218	0.000000	0.05858	0.001000	0.08648	0.042000	0.13812	-1.213000	0.02991	-0.646000	0.05452	-0.424000	0.05967	GGC	.	.	.	none		0.697	PODN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024735.1	NM_153703		T	53535630	G	T	53535630	3	4	61	1	0	0	0	0	1	0	0	0	12185	1116	39	4	253	4	PODN	1	53535630	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	119171	53535630	195714991	3	4031											
WLS	79971	hgsc.bcm.edu	37	chr1	68697907	68697910	+	Frame_Shift_Del	DEL	TTTG	TTTG	-																															tcccaccagaaaggcgatgaTttggaacacgagcagaatcc																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	TTTG	TTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:68697907_68697910delTTTG	ENST00000262348.4	-	1	326_329	c.73_76delCAAA	c.(73-78)caaatcfs	p.QI25fs	WLS_ENST00000354777.2_Frame_Shift_Del_p.QI25fs|WLS_ENST00000540432.1_Frame_Shift_Del_p.QI25fs|WLS_ENST00000370971.1_Frame_Shift_Del_p.QI25fs|WLS_ENST00000370976.3_Frame_Shift_Del_p.QI25fs	NM_024911.6	NP_079187.3	Q5T9L3	WLS_HUMAN	wntless Wnt ligand secretion mediator	25					anterior/posterior axis specification (GO:0009948)|mesoderm formation (GO:0001707)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|Wnt signaling pathway (GO:0016055)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(4)|prostate(3)|urinary_tract(1)	20						AAGGCGATGATTTGGAACACGAGC	0.505																																					p.25_26del		Atlas-Indel,Pindel	.											.	WLS	97	.	0			c.74_77del						PASS	.																																			SO:0001589	frameshift_variant	79971	exon1			.	BX538320	CCDS642.1, CCDS30750.1, CCDS53331.1	1p31.2	2013-10-03	2013-10-03	2010-03-02	ENSG00000116729	ENSG00000116729			30238	protein-coding gene	gene with protein product	"wntless homolog"	611514	"chromosome 1 open reading frame 139", "G protein-coupled receptor 177", "wntless homolog (Drosophila)"	C1orf139, GPR177		12761501	Standard	NM_024911		Approved	FLJ23091, MRP, wls, EVI, mig-14	uc001dee.3	Q5T9L3	OTTHUMG00000009153	ENST00000262348.4:c.73_76delCAAA	chr1.hg19:g.68697907_68697910delTTTG	ENSP00000262348:p.Gln25fs	135.0	0.0	0		131.0	34.0	0.259542	NM_001002292	B2RNT2|Q5JRS7|Q7Z2Z9|Q8NC43	Frame_Shift_Del	DEL	ENST00000262348.4	hg19	CCDS642.1																																																																																			.	.	.	none		0.505	WLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025368.1	NM_024911		-	68697910	TTTG	-	68697907	7	5	61	1	0	1	0	1	0	0	0	0	17388	1493	52	0	1723	0	WLS	1	68697907	Frame_Shift_Del	DEL	TTTG	TCGA-A4-A48D-01A-11D-A25F-10	15162277	68697907	180552714	4	4032											
NEXN	91624	hgsc.bcm.edu	37	chr1	78395127	78395127	+	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	atgaaaaaaggaaagcagaaGaagaagccagaaggagaata	24	2	12	3	0	0	6	0	1	0	5	0	8	0	7	1	2	2	1	1	2	10	1	rs533331740		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:78395127G>C	ENST00000334785.7	+	9	1175	c.991G>C	c.(991-993)Gaa>Caa	p.E331Q	NEXN_ENST00000330010.8_Missense_Mutation_p.E267Q|NEXN_ENST00000457030.1_Missense_Mutation_p.E317Q	NM_144573.3	NP_653174.3			nexilin (F actin binding protein)											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				Colorectal(170;0.114)		gaaagcagaagaagaagccag	0.388																																					p.E331Q		Atlas-SNP	.											.	NEXN	77	.	0			c.G991C						PASS	.						91	91	91					1																	78395127		1854	4094	5948	SO:0001583	missense	91624	exon9			GCAGAAGAAGAAG	AK057954	CCDS41351.1, CCDS53335.1	1p31.1	2014-09-17			ENSG00000162614	ENSG00000162614		"Immunoglobulin superfamily / I-set domain containing"	29557	protein-coding gene	gene with protein product		613121				12053183, 8227983	Standard	NM_144573		Approved	nexilin, NELIN	uc001dic.4	Q0ZGT2	OTTHUMG00000040533	ENST00000334785.7:c.991G>C	chr1.hg19:g.78395127G>C	ENSP00000333938:p.Glu331Gln	93.0	0.0	.		98.0	28.0	.	NM_144573		Missense_Mutation	SNP	ENST00000334785.7	hg19	CCDS41351.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.32|13.32	2.200748|2.200748	0.38905|0.38905	.|.	.|.	ENSG00000162614|ENSG00000162614	ENST00000401035;ENST00000457030;ENST00000330010;ENST00000334785;ENST00000440324|ENST00000342754	T;T;T;T;T|.	0.69175|.	-0.38;0.01;0.03;0.1;-0.33|.	4.98|4.98	4.05|4.05	0.47172|0.47172	.|.	0.289025|.	0.24238|.	N|.	0.040288|.	T|T	0.49029|0.49029	0.1533|0.1533	L|L	0.49455|0.49455	1.56|1.56	0.80722|0.80722	D|D	1|1	B;B;B;B|.	0.16603|.	0.006;0.018;0.011;0.006|.	B;B;B;B|.	0.18263|.	0.021;0.016;0.016;0.016|.	T|T	0.48375|0.48375	-0.9041|-0.9041	10|5	0.30078|.	T|.	0.28|.	-4.9227|-4.9227	13.6045|13.6045	0.62039|0.62039	0.0:0.156:0.844:0.0|0.0:0.156:0.844:0.0	.|.	267;317;331;267|.	D3DQ79;Q0ZGT2-2;Q0ZGT2;B4DPZ7|.	.;.;NEXN_HUMAN;.|.	Q|N	267;317;267;331;317|230	ENSP00000383814:E267Q;ENSP00000388048:E317Q;ENSP00000327363:E267Q;ENSP00000333938:E331Q;ENSP00000411902:E317Q|.	ENSP00000327363:E267Q|.	E|K	+|+	1|3	0|2	NEXN|NEXN	78167715|78167715	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.850000|0.850000	0.48378|0.48378	4.893000|4.893000	0.63199|0.63199	1.207000|1.207000	0.43291|0.43291	0.591000|0.591000	0.81541|0.81541	GAA|AAG	.	.	.	none		0.388	NEXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097549.1	NM_144573		C	78395127	G	C	78395127	3	2	61	1	0	0	0	0	1	0	0	0	10362	943	33	4	1021	4	NEXN	1	78395127	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	9697220	78395127	170855494	5	4033											
SLC6A17	388662	hgsc.bcm.edu	37	chr1	110734657	110734657	+	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	cccaggtcttctttgccttgGgcctgggctttggtggtgtc	1	15	14	11	0	2	0	0	0	2	0	3	0	2	0	3	5	1	1	3	5	0	4			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:110734657G>A	ENST00000331565.4	+	7	1413	c.928G>A	c.(928-930)Ggc>Agc	p.G310S		NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	310					alanine transport (GO:0032328)|glycine transport (GO:0015816)|leucine transport (GO:0015820)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		CTTTGCCTTGGGCCTGGGCTT	0.552																																					p.G310S		Atlas-SNP	.											.	SLC6A17	86	.	0			c.G928A						PASS	.						146	144	145					1																	110734657		2203	4300	6503	SO:0001583	missense	388662	exon7			GCCTTGGGCCTGG		CCDS30799.1	1p13.2	2013-07-19	2013-07-19		ENSG00000197106	ENSG00000197106		"Solute carriers"	31399	protein-coding gene	gene with protein product		610299	"solute carrier family 6 (neurotransmitter transporter), member 17", "solute carrier family 6, member 17"				Standard	NM_001010898		Approved		uc009wfq.3	Q9H1V8	OTTHUMG00000011761	ENST00000331565.4:c.928G>A	chr1.hg19:g.110734657G>A	ENSP00000330199:p.Gly310Ser	142.0	0.0	.		200.0	46.0	.	NM_001010898	A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Missense_Mutation	SNP	ENST00000331565.4	hg19	CCDS30799.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.205508	0.79127	.	.	ENSG00000197106	ENST00000331565;ENST00000450985	T	0.71579	-0.58	4.97	4.97	0.65823	.	0.000000	0.85682	D	0.000000	T	0.77280	0.4107	L	0.52823	1.66	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.75929	-0.3144	10	0.38643	T	0.18	.	18.2409	0.89967	0.0:0.0:1.0:0.0	.	310	Q9H1V8	S6A17_HUMAN	S	310	ENSP00000330199:G310S	ENSP00000330199:G310S	G	+	1	0	SLC6A17	110536180	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	9.414000	0.97362	2.298000	0.77334	0.650000	0.86243	GGC	.	.	.	none		0.552	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2	XM_371280		A	110734657	G	A	110734657	3	1	61	1	0	0	0	0	1	0	0	0	14693	1232	43	2	950	2	SLC6A17	1	110734657	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	32339530	110734657	138515964	6	4034											
SLC16A4	9122	hgsc.bcm.edu	37	chr1	110921516	110921516	+	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	aggcatccatgatgtcaatcCccagtgttttggctctggct	7	13	10	11	0	2	1	1	1	1	0	4	1	4	1	3	3	0	4	3	3	1	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:110921516C>A	ENST00000369779.4	-	6	1238	c.989G>T	c.(988-990)gGg>gTg	p.G330V	SLC16A4_ENST00000369781.4_Intron|SLC16A4_ENST00000497687.1_5'Flank|SLC16A4_ENST00000437429.2_Missense_Mutation_p.G220V|SLC16A4_ENST00000541986.1_Missense_Mutation_p.G268V|SLC16A4_ENST00000472422.2_Missense_Mutation_p.G282V	NM_001201547.1|NM_004696.2	NP_001188476.1|NP_004687.1	O15374	MOT5_HUMAN	solute carrier family 16, member 4	330					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)	GATGTCAATCCCCAGTGTTTT	0.418																																					p.G330V		Atlas-SNP	.											.	SLC16A4	47	.	0			c.G989T						PASS	.						108	105	106					1																	110921516		2203	4300	6503	SO:0001583	missense	9122	exon6			TCAATCCCCAGTG	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.989G>T	chr1.hg19:g.110921516C>A	ENSP00000358794:p.Gly330Val	163.0	0.0	.		157.0	47.0	.	NM_004696	A8K3V5|B2R9C9|B4DJ67|B4DPX7|E7EPY8|G3V175|Q5T612|Q8WU09	Missense_Mutation	SNP	ENST00000369779.4	hg19	CCDS823.1	.	.	.	.	.	.	.	.	.	.	c	19.00	3.741081	0.69304	.	.	ENSG00000168679	ENST00000369779;ENST00000472422;ENST00000437429;ENST00000541986;ENST00000467986	D;D;D;D;D	0.87179	-2.22;-2.22;-2.22;-2.22;-2.22	6.08	3.23	0.37069	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.367376	0.34156	N	0.004216	D	0.91005	0.7171	M	0.85197	2.74	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;0.997;0.999	D;D;D;D	0.79784	0.993;0.986;0.982;0.986	D	0.91070	0.4892	10	0.87932	D	0	.	10.0556	0.42244	0.0:0.7928:0.0:0.2072	.	220;268;282;330	E7EPY8;B4DJ67;G3V175;O15374	.;.;.;MOT5_HUMAN	V	330;282;220;268;97	ENSP00000358794:G330V;ENSP00000432495:G282V;ENSP00000394790:G220V;ENSP00000446087:G268V;ENSP00000435768:G97V	ENSP00000358794:G330V	G	-	2	0	SLC16A4	110723039	0.996000	0.38824	0.271000	0.24616	0.894000	0.52154	3.296000	0.51802	0.463000	0.27118	-0.156000	0.13503	GGG	.	.	.	none		0.418	SLC16A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000031115.3	NM_004696		A	110921516	C	A	110921516	3	1	61	1	0	0	0	0	1	0	0	0	14423	623	22	4	490	4	SLC16A4	1	110921516	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	186859	110921516	138329105	7	4035											
ZNF687	57592	hgsc.bcm.edu	37	chr1	151261140	151261140	+	Missense_Mutation	SNP	T	T	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	agccaattttcagacccatcTccgggaggcctgtctgcacg	8	9	10	14	2	3	1	1	0	2	1	4	2	3	2	4	2	2	1	4	2	1	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:151261140T>G	ENST00000368879.2	+	3	2350	c.2252T>G	c.(2251-2253)cTc>cGc	p.L751R		NM_020832.1	NP_065883.1	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	751					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	32	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CAGACCCATCTCCGGGAGGCC	0.582																																					p.L751R		Atlas-SNP	.											.	ZNF687	94	.	0			c.T2252G						PASS	.						124	110	115					1																	151261140		2203	4300	6503	SO:0001583	missense	57592	exon3			CCCATCTCCGGGA		CCDS992.1	1q21.2	2008-05-02			ENSG00000143373	ENSG00000143373			29277	protein-coding gene	gene with protein product		610568				10718198	Standard	NM_020832		Approved	KIAA1441	uc001exq.3	Q8N1G0	OTTHUMG00000012347	ENST00000368879.2:c.2252T>G	chr1.hg19:g.151261140T>G	ENSP00000357874:p.Leu751Arg	130.0	0.0	.		146.0	36.0	.	NM_020832	D3DV17|Q68DQ8|Q9H937|Q9P2A7	Missense_Mutation	SNP	ENST00000368879.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.3|25.3	4.623891|4.623891	0.87460|0.87460	.|.	.|.	ENSG00000143373|ENSG00000143373	ENST00000336715;ENST00000324048;ENST00000368879|ENST00000426871	T;T;T|.	0.02032|.	4.49;4.49;4.49|.	4.98|4.98	4.98|4.98	0.66077|0.66077	Zinc finger, C2H2-like (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);|.	0.000000|.	0.32068|.	N|.	0.006627|.	T|T	0.51126|0.51126	0.1656|0.1656	L|L	0.48986|0.48986	1.54|1.54	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;0.991|.	T|T	0.51084|0.51084	-0.8750|-0.8750	10|5	0.66056|.	D|.	0.02|.	.|.	13.7947|13.7947	0.63164|0.63164	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	751;751|.	Q8N1G0-2;Q8N1G0|.	.;ZN687_HUMAN|.	R|A	751|354	ENSP00000336620:L751R;ENSP00000319829:L751R;ENSP00000357874:L751R|.	ENSP00000319829:L751R|.	L|S	+|+	2|1	0|0	ZNF687|ZNF687	149527764|149527764	0.994000|0.994000	0.37717|0.37717	0.765000|0.765000	0.31456|0.31456	0.997000|0.997000	0.91878|0.91878	7.803000|7.803000	0.85983|0.85983	2.098000|2.098000	0.63641|0.63641	0.459000|0.459000	0.35465|0.35465	CTC|TCC	.	.	.	none		0.582	ZNF687-201	KNOWN	basic	protein_coding	protein_coding		NM_020832		G	151261140	T	G	151261140	3	3	61	1	0	0	0	0	1	0	0	0	18104	1551	54	5	2258	5	ZNF687	1	151261140	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	40339624	151261140	97989481	8	4036											
DCST1	149095	hgsc.bcm.edu	37	chr1	155015935	155015935	+	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	gcccggctggagtgggccctGgggctgctgcacgtgctgct	2	8	18	13	2	0	0	0	0	0	0	0	1	0	1	2	5	4	6	2	5	0	0			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:155015935G>T	ENST00000295542.1	+	10	1218	c.1122G>T	c.(1120-1122)ctG>ctT	p.L374L	DCST1_ENST00000392480.1_Silent_p.L374L|RP11-307C12.11_ENST00000452962.1_RNA|DCST1_ENST00000368419.2_Silent_p.L374L|DCST1_ENST00000423025.2_Silent_p.L349L	NM_152494.3	NP_689707.2	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1	374						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)			AGTGGGCCCTGGGGCTGCTGC	0.687																																					p.L374L		Atlas-SNP	.											.	DCST1	69	.	0			c.G1122T						PASS	.						51	52	52					1																	155015935		2203	4299	6502	SO:0001819	synonymous_variant	149095	exon10			GGCCCTGGGGCTG	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.1122G>T	chr1.hg19:g.155015935G>T		64.0	0.0	.		70.0	21.0	.	NM_152494	B4DXA0|E9PHV3|Q5T198|Q6P1W6|Q71S70|Q96M70	Silent	SNP	ENST00000295542.1	hg19	CCDS1083.1																																																																																			.	.	.	none		0.687	DCST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099006.1	NM_152494		T	155015935	G	T	155015935	2	4	61	1	0	0	0	0	0	0	0	1	4304	1335	47	4		4	DCST1	1	155015935	Silent	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	3754795	155015935	94234686	9	4037											
ADCY10	55811	hgsc.bcm.edu	37	chr1	167825476	167825476	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggagatgtcgttaggctgtaCtgcaccaatgacaatgtagg	11	10	13	7	1	0	2	0	1	0	1	1	3	0	2	1	3	2	5	1	3	5	3			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:167825476C>T	ENST00000367851.4	-	17	2282	c.2098G>A	c.(2098-2100)Gta>Ata	p.V700I	ADCY10_ENST00000545172.1_Missense_Mutation_p.V547I|ADCY10_ENST00000367848.1_Missense_Mutation_p.V608I	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	700					cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						TTAGGCTGTACTGCACCAATG	0.458																																					p.V700I		Atlas-SNP	.											.	ADCY10	175	.	0			c.G2098A						PASS	.						315	265	282					1																	167825476		2203	4300	6503	SO:0001583	missense	55811	exon17			GCTGTACTGCACC	AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	4.6.1.1	"Adenylate cyclases"	21285	protein-coding gene	gene with protein product	"soluble adenylyl cyclase", "Hypercalciuria, absorptive, 2"	605205					Standard	XM_006711449		Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.2098G>A	chr1.hg19:g.167825476C>T	ENSP00000356825:p.Val700Ile	240.0	0.0	.		284.0	89.0	.	NM_018417	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Missense_Mutation	SNP	ENST00000367851.4	hg19	CCDS1265.1	.	.	.	.	.	.	.	.	.	.	C	4.303	0.055518	0.08291	.	.	ENSG00000143199	ENST00000545172;ENST00000367851;ENST00000367848	T;T;T	0.26223	1.76;1.75;1.76	5.16	-9.58	0.00559	.	0.951722	0.08707	N	0.905544	T	0.03695	0.0105	N	0.13043	0.29	0.21527	N	0.999654	B;B;B	0.19583	0.037;0.018;0.006	B;B;B	0.16289	0.015;0.007;0.003	T	0.43032	-0.9416	9	0.54805	T	0.06	-0.402	8.8296	0.35076	0.0:0.1525:0.2062:0.6412	.	547;608;700	F5GWS5;Q96PN6-2;Q96PN6	.;.;ADCYA_HUMAN	I	547;700;608	ENSP00000441992:V547I;ENSP00000356825:V700I;ENSP00000356822:V608I	ENSP00000356822:V608I	V	-	1	0	ADCY10	166092100	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.529000	0.00945	-1.853000	0.01165	-0.440000	0.05779	GTA	.	.	.	none		0.458	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417		T	167825476	C	T	167825476	3	4	61	1	0	0	0	0	1	0	0	0	293	565	20	2	2802	2	ADCY10	1	167825476	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	12809541	167825476	81425145	10	4038											
KCNT2	343450	hgsc.bcm.edu	37	chr1	196227503	196227503	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccactgcatgctttttctcCgcagcaagggatggtccgac	7	10	10	14	2	1	0	0	0	1	0	3	2	2	1	3	2	3	4	3	2	1	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:196227503C>T	ENST00000294725.9	-	26	3947	c.3032G>A	c.(3031-3033)cGg>cAg	p.R1011Q	KCNT2_ENST00000498426.1_5'UTR|KCNT2_ENST00000451324.2_3'UTR|KCNT2_ENST00000609185.1_Missense_Mutation_p.R944Q|KCNT2_ENST00000367431.4_Missense_Mutation_p.R945Q|KCNT2_ENST00000367433.5_Missense_Mutation_p.R987Q			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	1011					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						GCTTTTTCTCCGCAGCAAGGG	0.517																																					p.R1011Q		Atlas-SNP	.											.	KCNT2	243	.	0			c.G3032A						PASS	.						169	140	150					1																	196227503		2203	4300	6503	SO:0001583	missense	343450	exon26			TTTCTCCGCAGCA	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.3032G>A	chr1.hg19:g.196227503C>T	ENSP00000294725:p.Arg1011Gln	168.0	0.0	.		165.0	8.0	.	NM_198503	Q3SY59|Q5VTN1|Q6ZMT3	Missense_Mutation	SNP	ENST00000294725.9	hg19	CCDS1384.1	.	.	.	.	.	.	.	.	.	.	C	17.92	3.507711	0.64410	.	.	ENSG00000162687	ENST00000367433;ENST00000367431;ENST00000294725	T;T;T	0.36699	1.37;1.24;1.88	5.74	4.83	0.62350	.	0.000000	0.53938	D	0.000058	T	0.61999	0.2392	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	0.81914	0.987;0.995;0.987;0.988	T	0.67799	-0.5577	10	0.66056	D	0.02	-9.2458	14.7148	0.69259	0.0:0.9307:0.0:0.0693	.	976;987;944;1011	Q6UVM3-4;Q6UVM3-2;Q6UVM3-3;Q6UVM3	.;.;.;KCNT2_HUMAN	Q	987;945;1011	ENSP00000356403:R987Q;ENSP00000356401:R945Q;ENSP00000294725:R1011Q	ENSP00000294725:R1011Q	R	-	2	0	KCNT2	194494126	1.000000	0.71417	0.995000	0.50966	0.305000	0.27757	7.487000	0.81328	1.437000	0.47472	-0.148000	0.13756	CGG	.	.	.	none		0.517	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503		T	196227503	C	T	196227503	3	4	61	1	0	0	0	0	1	0	0	0	8099	652	23	1	387	1	KCNT2	1	196227503	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	28402027	196227503	53023118	11	4039											
CHI3L1	1116	hgsc.bcm.edu	37	chr1	203151959	203151959	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttccctggctgggcttcctTtataaattcggccttcattt	5	18	7	11	1	1	0	1	0	0	0	4	0	3	0	3	3	0	2	3	3	3	8			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr1:203151959T>C	ENST00000255409.3	-	6	612	c.487A>G	c.(487-489)Aag>Gag	p.K163E		NM_001276.2	NP_001267.2	P36222	CH3L1_HUMAN	chitinase 3-like 1 (cartilage glycoprotein-39)	163					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)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|skin(1)	18						TGGGCTTCCTTTATAAATTCG	0.537																																					p.K163E		Atlas-SNP	.											.	CHI3L1	51	.	0			c.A487G						PASS	.						67	62	64					1																	203151959		2203	4300	6503	SO:0001583	missense	1116	exon6			CTTCCTTTATAAA	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.487A>G	chr1.hg19:g.203151959T>C	ENSP00000255409:p.Lys163Glu	82.0	0.0	.		108.0	29.0	.	NM_001276	B2R7B0|P30923|Q8IVA4|Q96HI7	Missense_Mutation	SNP	ENST00000255409.3	hg19	CCDS1435.1	.	.	.	.	.	.	.	.	.	.	T	4.508	0.094296	0.08632	.	.	ENSG00000133048	ENST00000255409	T	0.05996	3.36	5.51	-0.134	0.13481	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.813254	0.10863	N	0.625821	T	0.03959	0.0111	N	0.17723	0.515	0.09310	N	1	B	0.16802	0.019	B	0.19391	0.025	T	0.48547	-0.9026	10	0.12430	T	0.62	-9.5251	8.5461	0.33421	0.0:0.0823:0.5959:0.3217	.	163	P36222	CH3L1_HUMAN	E	163	ENSP00000255409:K163E	ENSP00000255409:K163E	K	-	1	0	CHI3L1	201418582	0.000000	0.05858	0.037000	0.18230	0.460000	0.32559	-0.071000	0.11505	0.013000	0.14918	0.459000	0.35465	AAG	.	.	.	none		0.537	CHI3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100265.1	NM_001276		C	203151959	T	C	203151959	3	2	61	1	0	0	0	0	1	0	0	0	3342	1850	64	3	684	3	CHI3L1	1	203151959	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	6924456	203151959	46098662	12	4040											
APOB	338	hgsc.bcm.edu	37	chr2	21227463	21227463	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catatttgccatcttcttcaTattctgcactgaagtcacgg	9	15	6	11	1	5	1	2	1	3	0	5	1	5	1	1	1	2	1	1	1	3	6			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr2:21227463T>C	ENST00000233242.1	-	27	12000	c.11873A>G	c.(11872-11874)tAt>tGt	p.Y3958C		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3958					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)					ATCTTCTTCATATTCTGCACT	0.363																																					p.Y3958C		Atlas-SNP	.											.	APOB	761	.	0			c.A11873G						PASS	.						155	147	150					2																	21227463		2203	4300	6503	SO:0001583	missense	338	exon27			TCTTCATATTCTG	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.11873A>G	chr2.hg19:g.21227463T>C	ENSP00000233242:p.Tyr3958Cys	138.0	0.0	.		159.0	39.0	.	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	T	13.44	2.236382	0.39498	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.20200	2.09	5.99	5.99	0.97316	.	0.000000	0.56097	D	0.000034	T	0.44623	0.1302	M	0.75447	2.3	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.45086	-0.9285	10	0.87932	D	0	.	10.0499	0.42210	0.0:0.0741:0.0:0.9259	.	3958	P04114	APOB_HUMAN	C	3958	ENSP00000233242:Y3958C	ENSP00000233242:Y3958C	Y	-	2	0	APOB	21080968	0.999000	0.42202	0.067000	0.19924	0.123000	0.20343	3.693000	0.54735	2.291000	0.77112	0.533000	0.62120	TAT	.	.	.	none		0.363	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			C	21227463	T	C	21227463	3	2	61	1	0	0	0	0	1	0	0	0	785	1406	49	3	1830	3	APOB	2	21227463	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10		21227463	221971910	13	4041											
C2orf71	388939	hgsc.bcm.edu	37	chr2	29295663	29295663	+	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	gtcttcctcctcctcctctgGgctgctgtcctcgctgtcac	1	14	8	18	1	3	0	1	0	2	0	9	0	8	0	5	1	1	3	5	1	0	1			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr2:29295663G>A	ENST00000331664.5	-	1	1464	c.1465C>T	c.(1465-1467)Cca>Tca	p.P489S		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	489					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						TCCTCCTCTGGGCTGCTGTCC	0.527																																					p.P489S		Atlas-SNP	.											.	C2orf71	146	.	0			c.C1465T						PASS	.						83	86	85					2																	29295663		2105	4227	6332	SO:0001583	missense	388939	exon1			CCTCTGGGCTGCT		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.1465C>T	chr2.hg19:g.29295663G>A	ENSP00000332809:p.Pro489Ser	208.0	0.0	.		254.0	80.0	.	NM_001029883		Missense_Mutation	SNP	ENST00000331664.5	hg19	CCDS42669.1	.	.	.	.	.	.	.	.	.	.	G	1.537	-0.542885	0.04053	.	.	ENSG00000179270	ENST00000331664	T	0.18016	2.24	5.3	-0.867	0.10655	.	0.860292	0.10501	N	0.667309	T	0.05227	0.0139	N	0.05199	-0.095	0.09310	N	1	B	0.10296	0.003	B	0.12156	0.007	T	0.40117	-0.9580	10	0.05525	T	0.97	-0.0051	2.483	0.04592	0.3929:0.1103:0.3836:0.1132	.	489	A6NGG8	CB071_HUMAN	S	489	ENSP00000332809:P489S	ENSP00000332809:P489S	P	-	1	0	C2orf71	29149167	0.015000	0.18098	0.442000	0.26870	0.446000	0.32137	0.072000	0.14617	-0.228000	0.09869	-1.036000	0.02392	CCA	.	.	.	none		0.527	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		A	29295663	G	A	29295663	3	1	61	1	0	0	0	0	1	0	0	0	2193	1232	43	2	2409	2	C2orf71	2	29295663	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	8068200	29295663	213903710	14	4042											
LRP2	4036	hgsc.bcm.edu	37	chr2	170012842	170012842	+	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	gacgtgaagccatcagcacaGacacactcataacttccttt	13	9	6	13	1	2	2	2	1	0	1	3	3	3	2	2	0	3	1	2	0	2	3			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr2:170012842G>T	ENST00000263816.3	-	65	12378	c.12093C>A	c.(12091-12093)gtC>gtA	p.V4031V		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	4031	EGF-like 15; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	CATCAGCACAGACACACTCAT	0.438																																					p.V4031V		Atlas-SNP	.											.	LRP2	751	.	0			c.C12093A						PASS	.						199	183	188					2																	170012842		2203	4300	6503	SO:0001819	synonymous_variant	4036	exon65			AGCACAGACACAC		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.12093C>A	chr2.hg19:g.170012842G>T		191.0	0.0	.		174.0	40.0	.	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	hg19	CCDS2232.1																																																																																			.	.	.	none		0.438	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		T	170012842	G	T	170012842	2	4	61	1	0	0	0	0	0	0	0	1	8963	929	33	4		4	LRP2	2	170012842	Silent	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	140717179	170012842	73186531	15	4043											
GIGYF2	26058	hgsc.bcm.edu	37	chr2	233676027	233676029	+	In_Frame_Del	DEL	CTT	CTT	-																															agcagcagcagcagttggcaCttcttcttcaacagtttcag																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr2:233676027_233676029delCTT	ENST00000409547.1	+	19	2283_2285	c.1972_1974delCTT	c.(1972-1974)cttdel	p.L660del	GIGYF2_ENST00000452341.2_In_Frame_Del_p.L491del|GIGYF2_ENST00000373563.4_In_Frame_Del_p.L660del|GIGYF2_ENST00000373566.3_In_Frame_Del_p.L682del|GIGYF2_ENST00000409196.3_In_Frame_Del_p.L654del|GIGYF2_ENST00000409480.1_In_Frame_Del_p.L682del|GIGYF2_ENST00000409451.3_In_Frame_Del_p.L681del	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	660	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)		GCAGTTGGCACTTCTTCTTCAAC	0.414																																					p.678_679del		Atlas-Indel,Pindel	.											.	GIGYF2	288	.	0			c.2034_2036del						PASS	.																																			SO:0001651	inframe_deletion	26058	exon19			.	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.1972_1974delCTT	chr2.hg19:g.233676033_233676035delCTT	ENSP00000386537:p.Leu660del	156.0	0.0	0		167.0	47.0	0.281437	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	In_Frame_Del	DEL	ENST00000409547.1	hg19	CCDS33401.1																																																																																			.	.	.	none		0.414	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		-	233676029	CTT	-	233676027	7	5	61	1	0	1	0	1	0	0	0	0	6385	565	20	0	2100	0	GIGYF2	2	233676027	In_Frame_Del	DEL	CTT	TCGA-A4-A48D-01A-11D-A25F-10	63663185	233676027	9523346	16	4044											
ITPR1	3708	hgsc.bcm.edu	37	chr3	4878618	4878618	+	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	gctgtcggaattaaaggatcAggtaaagaaagaaaatccca	18	7	10	6	1	1	2	1	0	0	2	3	4	2	4	1	3	0	2	1	3	8	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr3:4878618A>C	ENST00000443694.2	+	58	8144	c.8144A>C	c.(8143-8145)cAg>cCg	p.Q2715P	ITPR1_ENST00000302640.8_Splice_Site_p.Q2715P|ITPR1_ENST00000357086.4_Splice_Site_p.Q2682P|ITPR1_ENST00000456211.2_Splice_Site_p.Q2667P|ITPR1_ENST00000544951.1_Splice_Site_p.Q693P|AC018816.3_ENST00000449914.1_Intron|ITPR1_ENST00000423119.2_Splice_Site_p.Q2682P|AC018816.3_ENST00000441894.1_Intron|ITPR1_ENST00000463980.1_3'UTR|ITPR1_ENST00000354582.6_Splice_Site_p.Q2715P			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	2730					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)	TTAAAGGATCAGGTAAAGAAA	0.488																																					p.Q2715P		Atlas-SNP	.											.	ITPR1	659	.	0			c.A8144C						PASS	.						43	42	42					3																	4878618		1916	4131	6047	SO:0001630	splice_region_variant	3708	exon60			AGGATCAGGTAAA	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.8145+1A>C	chr3.hg19:g.4878618A>C		39.0	0.0	.		59.0	13.0	.	NM_001168272	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	hg19	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.802091	0.90538	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000426160;ENST00000357086;ENST00000456211;ENST00000544951;ENST00000443694	D;D;D;D;D;D;D	0.91996	-2.94;-2.95;-2.95;-2.95;-2.95;-1.79;-2.94	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.95928	0.8674	M	0.77486	2.375	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.999	D;P;D	0.78314	0.979;0.893;0.991	D	0.95864	0.8885	10	0.54805	T	0.06	.	16.6093	0.84858	1.0:0.0:0.0:0.0	.	693;2730;2682	B7ZMI3;Q14643;G5E9P1	.;ITPR1_HUMAN;.	P	2730;2715;2715;2682;1176;2682;2667;693;2715	ENSP00000306253:Q2715P;ENSP00000346595:Q2715P;ENSP00000405934:Q2682P;ENSP00000349597:Q2682P;ENSP00000397885:Q2667P;ENSP00000440564:Q693P;ENSP00000401671:Q2715P	ENSP00000306253:Q2715P	Q	+	2	0	ITPR1	4853618	1.000000	0.71417	1.000000	0.80357	0.825000	0.46686	9.243000	0.95416	2.324000	0.78689	0.533000	0.62120	CAG	.	.	.	none		0.488	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222	Missense_Mutation	C	4878618	A	C	4878618	5	2	61	1	0	0	0	0	0	0	1	0	7927	202	7	5	8423	5	ITPR1	3	4878618	Splice_Site	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10		4878618	193143812	17	4045											
SH3BP5	9467	hgsc.bcm.edu	37	chr3	15298471	15298471	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacagggctgggcagatccaGgctgccaggcctcacaaccg	9	4	13	15	1	1	1	1	0	0	1	2	1	2	1	4	4	2	3	4	4	1	0			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr3:15298471G>A	ENST00000383791.3	-	8	1259	c.1039C>T	c.(1039-1041)Ctg>Ttg	p.L347L	SH3BP5_ENST00000426925.1_Silent_p.L190L|SH3BP5_ENST00000408919.3_Silent_p.L190L|SH3BP5-AS1_ENST00000413977.1_RNA|SH3BP5-AS1_ENST00000420195.1_RNA|SH3BP5-AS1_ENST00000436602.1_RNA|SH3BP5_ENST00000253688.5_Silent_p.L190L	NM_004844.4	NP_004835.2	O60239	3BP5_HUMAN	SH3-domain binding protein 5 (BTK-associated)	347	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						GGCAGATCCAGGCTGCCAGGC	0.587																																					p.L347L		Atlas-SNP	.											.	SH3BP5	32	.	0			c.C1039T						PASS	.						73	63	67					3																	15298471		2203	4300	6503	SO:0001819	synonymous_variant	9467	exon8			GATCCAGGCTGCC	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.1039C>T	chr3.hg19:g.15298471G>A		150.0	0.0	.		221.0	46.0	.	NM_004844	B3KQW6|Q5JWV9	Silent	SNP	ENST00000383791.3	hg19	CCDS2625.2																																																																																			.	.	.	none		0.587	SH3BP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340740.2	NM_004844		A	15298471	G	A	15298471	2	1	61	1	0	0	0	0	0	0	0	1	14260	991	35	2		2	SH3BP5	3	15298471	Silent	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	10419853	15298471	182723959	18	4046											
ANKRD28	23243	hgsc.bcm.edu	37	chr3	15765925	15765925	+	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	agaaggtacttgactacgctGatcattccactagaggctgc	11	10	10	10	1	1	4	1	2	0	2	2	4	2	4	1	2	3	3	1	2	4	5			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr3:15765925G>A	ENST00000399451.2	-	7	1024	c.657C>T	c.(655-657)atC>atT	p.I219I	ANKRD28_ENST00000497037.1_5'UTR|ANKRD28_ENST00000383777.1_Silent_p.I252I	NM_001195098.1|NM_001195099.1|NM_015199.3	NP_001182027.1|NP_001182028.1|NP_056014.2	O15084	ANR28_HUMAN	ankyrin repeat domain 28	219						nucleus (GO:0005634)				breast(2)|endometrium(1)|large_intestine(2)|prostate(1)	6						TGACTACGCTGATCATTCCAC	0.363																																					p.I219I		Atlas-SNP	.											.	ANKRD28	121	.	0			c.C657T						PASS	.						56	53	54					3																	15765925		1940	4139	6079	SO:0001819	synonymous_variant	23243	exon7			TACGCTGATCATT	AY367056	CCDS46769.1, CCDS74908.1	3p25.1	2013-01-10			ENSG00000206560	ENSG00000206560		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits", "Ankyrin repeat domain containing"	29024	protein-coding gene	gene with protein product	"phosphatase interactor targeting K protein", "protein phosphatase 6 ankyrin repeat subunit A", "protein phosphatase 1, regulatory subunit 65"	611122				9205841	Standard	NM_015199		Approved	KIAA0379, PITK, PP6-ARS-A, PPP1R65	uc003caj.1	O15084	OTTHUMG00000155379	ENST00000399451.2:c.657C>T	chr3.hg19:g.15765925G>A		91.0	0.0	.		134.0	18.0	.	NM_015199	B4DES5|Q1WWL4|Q29RW6|Q3B857|Q6ULS0|Q6ZT57	Silent	SNP	ENST00000399451.2	hg19	CCDS46769.1																																																																																			.	.	.	none		0.363	ANKRD28-003	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339758.1	NM_015199		A	15765925	G	A	15765925	2	1	61	1	0	0	0	0	0	0	0	1	656	1280	45	2		2	ANKRD28	3	15765925	Silent	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	467454	15765925	182256505	19	4047											
SLC22A13	9390	hgsc.bcm.edu	37	chr3	38316203	38316203	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacatggccctgcgctttgcTgtggctactgccgtcgctgg	3	12	13	13	3	0	0	0	0	0	0	1	0	0	0	2	3	5	4	2	3	2	3			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr3:38316203T>C	ENST00000311856.4	+	3	640	c.591T>C	c.(589-591)gcT>gcC	p.A197A	SLC22A13_ENST00000450935.2_Intron	NM_004256.3	NP_004247.2	Q9Y226	S22AD_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 13	197					nicotinate transport (GO:2001142)|organic cation transport (GO:0015695)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	nicotinate transporter activity (GO:0090416)|organic cation transmembrane transporter activity (GO:0015101)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|urinary_tract(1)	20				KIRC - Kidney renal clear cell carcinoma(284;0.0533)|Kidney(284;0.067)		TGCGCTTTGCTGTGGCTACTG	0.617																																					p.A197A		Atlas-SNP	.											.	SLC22A13	42	.	0			c.T591C						PASS	.						72	68	69					3																	38316203		2203	4300	6503	SO:0001819	synonymous_variant	9390	exon3			CTTTGCTGTGGCT	AB010438	CCDS2676.1	3p22.2	2013-07-18	2013-07-18	2003-10-15	ENSG00000172940	ENSG00000172940		"Solute carriers"	8494	protein-coding gene	gene with protein product		604047	"organic cationic transporter-like 3", "solute carrier family 22 (organic anion transporter), member 13"	ORCTL3		10072596, 18411268	Standard	NM_004256		Approved	OCTL1, OCTL3, OAT10	uc003chz.3	Q9Y226	OTTHUMG00000131086	ENST00000311856.4:c.591T>C	chr3.hg19:g.38316203T>C		115.0	0.0	.		189.0	71.0	.	NM_004256	B2RCV9|Q8IYG1	Silent	SNP	ENST00000311856.4	hg19	CCDS2676.1																																																																																			.	.	.	none		0.617	SLC22A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253746.2	NM_004256		C	38316203	T	C	38316203	2	2	61	1	0	0	0	0	0	0	0	1	14457	1567	55	3		3	SLC22A13	3	38316203	Silent	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	22550278	38316203	159706227	20	4048											
VIPR1	7433	hgsc.bcm.edu	37	chr3	42577629	42577629	+	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	cggcgctggcacctgcagggCgtcctgggctggaaccccaa	6	5	15	15	3	0	0	0	0	0	0	1	1	1	1	4	5	2	4	4	5	2	0			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr3:42577629C>T	ENST00000325123.4	+	13	1343	c.1230C>T	c.(1228-1230)ggC>ggT	p.G410G	VIPR1_ENST00000438259.2_Silent_p.G200G|VIPR1_ENST00000543411.1_Silent_p.G362G|VIPR1-AS1_ENST00000452639.3_RNA|VIPR1_ENST00000433647.1_Silent_p.G369G|VIPR1-AS1_ENST00000610022.1_RNA|VIPR1-AS1_ENST00000608869.1_RNA	NM_001251885.1|NM_004624.3	NP_001238814.1|NP_004615.2	P32241	VIPR1_HUMAN	vasoactive intestinal peptide receptor 1	410					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)		ACCTGCAGGGCGTCCTGGGCT	0.682																																					p.G410G		Atlas-SNP	.											.	VIPR1	45	.	0			c.C1230T						PASS	.						14	17	16					3																	42577629		2190	4293	6483	SO:0001819	synonymous_variant	7433	exon13			GCAGGGCGTCCTG	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.1230C>T	chr3.hg19:g.42577629C>T		65.0	0.0	.		121.0	51.0	.	NM_004624	A5JUT9|B3KPV1|B4DEB5|B4DGI4|F5H1F5|G3V0I1|Q15871|Q6P2M6	Silent	SNP	ENST00000325123.4	hg19	CCDS2698.1																																																																																			.	.	.	none		0.682	VIPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254728.4	NM_004624		T	42577629	C	T	42577629	2	4	61	1	0	0	0	0	0	0	0	1	17181	755	27	1		1	VIPR1	3	42577629	Silent	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	4261426	42577629	155444801	21	4049											
ROPN1	54763	hgsc.bcm.edu	37	chr3	123695737	123695737	+	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	atgcaggatctttaacagctCaggtgttagctctgcccggt	8	12	11	10	1	3	0	1	0	2	0	3	1	3	1	1	3	5	4	1	3	2	3			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr3:123695737C>G	ENST00000184183.4	-	4	548	c.208G>C	c.(208-210)Gag>Cag	p.E70Q	ROPN1_ENST00000405845.3_Missense_Mutation_p.E70Q	NM_017578.2	NP_060048.2	Q9HAT0	ROP1A_HUMAN	rhophilin associated tail protein 1	70						cytoplasm (GO:0005737)|nucleus (GO:0005634)				lung(2)|ovary(1)|skin(1)	4				GBM - Glioblastoma multiforme(114;0.148)		TTTAACAGCTCAGGTGTTAGC	0.542																																					p.E70Q		Atlas-SNP	.											.	ROPN1	20	.	0			c.G208C						PASS	.						97	86	90					3																	123695737		2203	4300	6503	SO:0001583	missense	54763	exon4			ACAGCTCAGGTGT	AF231410	CCDS3026.1	3q21.1	2011-01-20	2011-01-20			ENSG00000065371			17692	protein-coding gene	gene with protein product	"cancer/testis antigen 91"	611757	"ropporin, rhophilin associated protein 1"			10591629	Standard	NM_017578		Approved	ODF6, ropporin, ROPN1A, CT91	uc003eha.3	Q9HAT0		ENST00000184183.4:c.208G>C	chr3.hg19:g.123695737C>G	ENSP00000184183:p.Glu70Gln	187.0	0.0	.		235.0	40.0	.	NM_017578	D3DN99|Q9UF38	Missense_Mutation	SNP	ENST00000184183.4	hg19	CCDS3026.1	.	.	.	.	.	.	.	.	.	.	C	14.65	2.599790	0.46318	.	.	ENSG00000065371	ENST00000184183;ENST00000405845;ENST00000467907;ENST00000460743;ENST00000495336;ENST00000496145	T;T;T;T	0.31247	1.99;1.99;1.99;1.5	4.37	4.37	0.52481	.	0.000000	0.56097	D	0.000025	T	0.22282	0.0537	N	0.22421	0.69	0.80722	D	1	P	0.41313	0.745	B	0.38803	0.282	T	0.04870	-1.0921	10	0.46703	T	0.11	-26.3117	14.1277	0.65233	0.0:1.0:0.0:0.0	.	70	Q9HAT0	ROP1A_HUMAN	Q	70	ENSP00000184183:E70Q;ENSP00000385919:E70Q;ENSP00000417067:E70Q;ENSP00000420310:E70Q	ENSP00000184183:E70Q	E	-	1	0	ROPN1	125178427	1.000000	0.71417	1.000000	0.80357	0.042000	0.13812	4.230000	0.58632	2.304000	0.77564	0.551000	0.68910	GAG	.	.	.	none		0.542	ROPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356188.2	NM_017578		G	123695737	C	G	123695737	3	3	61	1	0	0	0	0	1	0	0	0	13536	835	29	4	446	4	ROPN1	3	123695737	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	81118108	123695737	74326693	22	4050											
MME	4311	hgsc.bcm.edu	37	chr3	154855893	154855893	+	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	gctatttttttcttgcaggcTtgtacagcatatgtggattt	7	19	9	6	0	1	0	0	0	1	0	1	1	1	1	0	2	3	5	0	2	3	9			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr3:154855893T>A	ENST00000460393.1	+	9	843	c.723T>A	c.(721-723)gcT>gcA	p.A241A	MME_ENST00000360490.2_Silent_p.A241A|MME_ENST00000462745.1_Silent_p.A241A|MME_ENST00000492661.1_Silent_p.A241A|MME_ENST00000493237.1_Silent_p.A241A	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	241					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)	TCTTGCAGGCTTGTACAGCAT	0.323																																					p.A241A		Atlas-SNP	.											.	MME	133	.	0			c.T723A						PASS	.						153	163	160					3																	154855893		2203	4300	6503	SO:0001819	synonymous_variant	4311	exon9			GCAGGCTTGTACA		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.723T>A	chr3.hg19:g.154855893T>A		128.0	0.0	.		161.0	70.0	.	NM_007287	A8K6U6|D3DNJ9|Q3MIX4	Silent	SNP	ENST00000460393.1	hg19	CCDS3172.1																																																																																			.	.	.	none		0.323	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902		A	154855893	T	A	154855893	2	1	61	1	0	0	0	0	0	0	0	1	9652	1596	56	5		5	MME	3	154855893	Silent	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	31160156	154855893	43166537	23	4051											
GPR125	166647	hgsc.bcm.edu	37	chr4	22436990	22436990	+	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	tttttcaatcatttctgccaCaaatataacatccattttgt	12	18	2	9	0	3	0	2	0	1	0	4	0	4	0	2	0	2	0	2	0	4	7	rs146147575		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr4:22436990C>G	ENST00000334304.5	-	10	1656	c.1387G>C	c.(1387-1389)Gtg>Ctg	p.V463L	GPR125_ENST00000282943.5_5'UTR|GPR125_ENST00000502482.1_Missense_Mutation_p.V463L|GPR125_ENST00000508133.1_Missense_Mutation_p.V237L	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	463					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)				ATTTCTGCCACAAATATAACA	0.388																																					p.V463L		Atlas-SNP	.											.	GPR125	118	.	0			c.G1387C						PASS	.	C	LEU/VAL	1,4405	2.1+/-5.4	0,1,2202	81	80	80		1387	5.4	1	4	dbSNP_134	80	0,8600		0,0,4300	no	missense	GPR125	NM_145290.2	32	0,1,6502	GG,GC,CC		0.0,0.0227,0.0077	possibly-damaging	463/1322	22436990	1,13005	2203	4300	6503	SO:0001583	missense	166647	exon10			CTGCCACAAATAT	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.1387G>C	chr4.hg19:g.22436990C>G	ENSP00000334952:p.Val463Leu	148.0	0.0	.		203.0	47.0	.	NM_145290	Q6UXK9|Q86SQ5|Q8TC55	Missense_Mutation	SNP	ENST00000334304.5	hg19	CCDS33964.1	.	.	.	.	.	.	.	.	.	.	C	17.62	3.434578	0.62955	2.27E-4	0.0	ENSG00000152990	ENST00000334304;ENST00000508133;ENST00000502482	T;T;T	0.41400	1.0;1.0;1.0	5.42	5.42	0.78866	.	0.063133	0.64402	D	0.000006	T	0.45955	0.1368	L	0.38175	1.15	0.58432	D	0.999998	D;B;P;D	0.53312	0.957;0.448;0.851;0.959	P;B;P;P	0.49561	0.615;0.283;0.546;0.556	T	0.38243	-0.9670	10	0.48119	T	0.1	-35.6945	19.2098	0.93749	0.0:1.0:0.0:0.0	.	338;463;237;463	Q8IWK6-3;Q8IWK6-2;Q8IWK6-4;Q8IWK6	.;.;.;GP125_HUMAN	L	463;237;463	ENSP00000334952:V463L;ENSP00000422606:V237L;ENSP00000421006:V463L	ENSP00000334952:V463L	V	-	1	0	GPR125	22046088	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.377000	0.59562	2.528000	0.85240	0.563000	0.77884	GTG	.	C|1.000;G|0.000	0.000	weak		0.388	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3			G	22436990	C	G	22436990	3	3	61	1	0	0	0	0	1	0	0	0	6646	478	17	4	2618	4	GPR125	4	22436990	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10		22436990	168717286	24	4052											
TMEM156	80008	hgsc.bcm.edu	37	chr4	38988027	38988027	+	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	ttaagagaacagatgtaggtTtgtctctatgacctattccc	11	14	8	8	0	1	3	0	1	1	2	3	4	2	3	2	1	1	2	2	1	5	6			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr4:38988027T>A	ENST00000381938.3	-	5	859	c.752A>T	c.(751-753)aAa>aTa	p.K251I		NM_024943.1	NP_079219.1	Q8N614	TM156_HUMAN	transmembrane protein 156	251						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|stomach(1)	10						AGATGTAGGTTTGTCTCTATG	0.373																																					p.K251I		Atlas-SNP	.											.	TMEM156	31	.	0			c.A752T						PASS	.						97	87	90					4																	38988027		2203	4300	6503	SO:0001583	missense	80008	exon5			GTAGGTTTGTCTC	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.752A>T	chr4.hg19:g.38988027T>A	ENSP00000371364:p.Lys251Ile	71.0	0.0	.		53.0	10.0	.	NM_024943	Q9H5N9	Missense_Mutation	SNP	ENST00000381938.3	hg19	CCDS3448.1	.	.	.	.	.	.	.	.	.	.	T	9.849	1.193176	0.22037	.	.	ENSG00000121895	ENST00000381938	T	0.26660	1.72	5.08	-0.654	0.11443	.	0.927636	0.09222	N	0.831791	T	0.25457	0.0619	L	0.48642	1.525	0.09310	N	1	P	0.43701	0.815	P	0.46389	0.515	T	0.20874	-1.0262	10	0.54805	T	0.06	-3.0832	4.5798	0.12253	0.0:0.1723:0.3153:0.5124	.	251	Q8N614	TM156_HUMAN	I	251	ENSP00000371364:K251I	ENSP00000371364:K251I	K	-	2	0	TMEM156	38664422	0.000000	0.05858	0.001000	0.08648	0.027000	0.11550	0.171000	0.16685	-0.126000	0.11682	0.379000	0.24179	AAA	.	.	.	none		0.373	TMEM156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250435.3	NM_024943		A	38988027	T	A	38988027	3	1	61	1	0	0	0	0	1	0	0	0	16085	1841	64	5	146	5	TMEM156	4	38988027	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	16551037	38988027	152166249	25	4053											
HSPA4L	22824	hgsc.bcm.edu	37	chr4	128726257	128726266	+	Frame_Shift_Del	DEL	GAAATTGTAG	GAAATTGTAG	-																															gtgaagacattagtagtataGaaattgtaggaggagcaaca																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	GAAATTGTAG	GAAATTGTAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr4:128726257_128726266delGAAATTGTAG	ENST00000296464.4	+	9	1426_1435	c.1015_1024delGAAATTGTAG	c.(1015-1026)gaaattgtaggafs	p.EIVG339fs	HSPA4L_ENST00000508776.1_Frame_Shift_Del_p.EIVG339fs|HSPA4L_ENST00000505726.1_Frame_Shift_Del_p.EIVG313fs|HSPA4L_ENST00000439123.2_Frame_Shift_Del_p.EIVG370fs	NM_014278.2	NP_055093.2	O95757	HS74L_HUMAN	heat shock 70kDa protein 4-like	339					protein folding (GO:0006457)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)			central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						TAGTAGTATAGAAATTGTAGGAGGAGCAAC	0.333																																					p.338_341del		Pindel	.											.	HSPA4L	82	.	0			c.1014_1023del						PASS	.																																			SO:0001589	frameshift_variant	22824	exon9			.	AB023421	CCDS3734.1	4q28	2011-09-07			ENSG00000164070	ENSG00000164070		"Heat shock proteins / HSP70"	17041	protein-coding gene	gene with protein product						10524232	Standard	NM_014278		Approved	APG-1, Osp94, HSPH3	uc003ifm.3	O95757	OTTHUMG00000133302	ENST00000296464.4:c.1015_1024delGAAATTGTAG	chr4.hg19:g.128726257_128726266delGAAATTGTAG	ENSP00000296464:p.Glu339fs	175.0	0.0	.		134.0	14.0	0.104	NM_014278	A2ICT2|Q4W5M5|Q8IWA2	Frame_Shift_Del	DEL	ENST00000296464.4	hg19	CCDS3734.1																																																																																			.	.	.	none		0.333	HSPA4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257096.3	NM_014278		-	128726266	GAAATTGTAG	-	128726257	7	5	61	1	0	1	0	1	0	0	0	0	7420	943	33	0	1049	0	HSPA4L	4	128726257	Frame_Shift_Del	DEL	GAAATTGTAG	TCGA-A4-A48D-01A-11D-A25F-10	89738230	128726257	62428019	26	4054											
TIGD4	201798	hgsc.bcm.edu	37	chr4	153691183	153691183	+	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	gtcgatatttgattttaaggCttttaataacaccttgtttc	10	19	6	6	1	0	1	0	1	0	0	2	2	0	1	1	1	1	2	1	1	4	9			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr4:153691183C>T	ENST00000304337.2	-	2	1794	c.974G>A	c.(973-975)aGc>aAc	p.S325N		NM_145720.3	NP_663772.1	Q8IY51	TIGD4_HUMAN	tigger transposable element derived 4	325	DDE.					nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.093)					GATTTTAAGGCTTTTAATAAC	0.323																																					p.S325N		Atlas-SNP	.											.	TIGD4	53	.	0			c.G974A						PASS	.						75	78	77					4																	153691183		2203	4300	6503	SO:0001583	missense	201798	exon2			TTAAGGCTTTTAA	AK058054	CCDS34079.1	4q31.23	2008-02-05							18335	protein-coding gene	gene with protein product							Standard	NM_145720		Approved		uc003imy.3	Q8IY51		ENST00000304337.2:c.974G>A	chr4.hg19:g.153691183C>T	ENSP00000355162:p.Ser325Asn	130.0	0.0	.		140.0	32.0	.	NM_145720	Q96LP5	Missense_Mutation	SNP	ENST00000304337.2	hg19	CCDS34079.1	.	.	.	.	.	.	.	.	.	.	C	1.757	-0.487660	0.04352	.	.	ENSG00000169989	ENST00000304337	T	0.45276	0.9	6.03	4.22	0.49857	.	0.326215	0.26620	N	0.023365	T	0.25938	0.0632	N	0.21448	0.665	0.27351	N	0.956258	B	0.17268	0.021	B	0.16289	0.015	T	0.12863	-1.0531	10	0.21540	T	0.41	-2.7406	8.7415	0.34560	0.0:0.7308:0.1218:0.1475	.	325	Q8IY51	TIGD4_HUMAN	N	325	ENSP00000355162:S325N	ENSP00000355162:S325N	S	-	2	0	TIGD4	153910633	1.000000	0.71417	1.000000	0.80357	0.643000	0.38383	1.186000	0.32078	1.465000	0.48006	-0.345000	0.07892	AGC	.	.	.	none		0.323	TIGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365028.1	NM_145720		T	153691183	C	T	153691183	3	4	61	1	0	0	0	0	1	0	0	0	15910	797	28	2	568	2	TIGD4	4	153691183	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	24964926	153691183	37463093	27	4055											
NIPBL	25836	hgsc.bcm.edu	37	chr5	37017244	37017247	+	Frame_Shift_Del	DEL	ATAG	ATAG	-																															gcaaaatggatcaaggatctAtagaacgcattttaaaacag																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	ATAG	ATAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr5:37017244_37017247delATAG	ENST00000282516.8	+	24	5399_5402	c.4900_4903delATAG	c.(4900-4905)atagaafs	p.IE1634fs	NIPBL_ENST00000448238.2_Frame_Shift_Del_p.IE1634fs	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	1634					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)	p.E1635K(2)		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)			TCAAGGATCTATAGAACGCATTTT	0.333																																					p.1633_1634del		Atlas-Indel,Pindel	.											.	NIPBL	513	.	2	Substitution - Missense(2)	lung(2)	c.4899_4902del						PASS	.																																			SO:0001589	frameshift_variant	25836	exon24			.	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.4900_4903delATAG	chr5.hg19:g.37017244_37017247delATAG	ENSP00000282516:p.Ile1634fs	141.0	0.0	0		173.0	76.0	0.439306	NM_133433	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Frame_Shift_Del	DEL	ENST00000282516.8	hg19	CCDS3920.1																																																																																			.	.	.	none		0.333	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		-	37017247	ATAG	-	37017244	7	5	61	1	0	1	0	1	0	0	0	0	10435	449	16	0	4990	0	NIPBL	5	37017244	Frame_Shift_Del	DEL	ATAG	TCGA-A4-A48D-01A-11D-A25F-10		37017244	143898016	28	4056											
MAST4	375449	hgsc.bcm.edu	37	chr5	66449317	66449318	+	Missense_Mutation	DNP	CA	CA	AT																															aggaagtccggcatgccaggCaggactgaaggctggagatc																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr5:66449317_66449318CA>AT	ENST00000403625.2	+	26	3852_3853	c.3557_3558CA>AT	c.(3556-3558)gCA>gAT	p.A1186D	MAST4_ENST00000261569.7_Missense_Mutation_p.A992D|MAST4_ENST00000404260.3_Missense_Mutation_p.A1189D|MAST4_ENST00000405643.1_Missense_Mutation_p.A1007D|MAST4_ENST00000403666.1_Missense_Mutation_p.A997D	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	1189	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.					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)		GCATGCCAGGCAGGACTGAAGG	0.441																																					p.A1186E|p.A1186A		Atlas-SNP	.											.	MAST4	218	.	0			c.C3557A|c.A3558T						PASS	.																																			SO:0001583	missense	375449	exon26			GCCAGGCAGGACT|CCAGGCAGGACTG	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	Exception_encountered	chr5.hg19:g.66449317_66449318delinsAT	ENSP00000385727:p.Ala1186Asp	55.0|56.0	0.0	.		71.0|73.0	14.0	.	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation|Silent	SNP	ENST00000403625.2	hg19	CCDS54861.1																																																																																			.	.	.	none		0.441	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			AT	66449318	CA	AT	66449317	3	1	61	1	0	0	0	0	1	0	0	0	9334	710	25	4	3789	4	MAST4	5	66449317	Missense_Mutation	DNP	CA	TCGA-A4-A48D-01A-11D-A25F-10	29432073	66449317	114465943	29	4057											
VCAN	1462	hgsc.bcm.edu	37	chr5	82808191	82808191	+	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	gcttccctccccctgatagcAgatttgatgcctactgcttt	6	14	7	14	0	0	3	0	2	0	1	2	3	2	3	4	0	4	3	4	0	2	5	rs558902507		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr5:82808191A>C	ENST00000265077.3	+	6	1583	c.1018A>C	c.(1018-1020)Aga>Cga	p.R340R	VCAN_ENST00000343200.5_Silent_p.R340R|VCAN_ENST00000502527.2_Silent_p.R340R|VCAN_ENST00000342785.4_Silent_p.R340R|VCAN_ENST00000513984.1_Silent_p.R340R|VCAN_ENST00000512590.2_Silent_p.R292R	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	340	Link 2. {ECO:0000255|PROSITE- ProRule:PRU00323}.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	CCCTGATAGCAGATTTGATGC	0.448																																					p.R340R		Atlas-SNP	.											.	VCAN	498	.	0			c.A1018C						PASS	.						64	68	67					5																	82808191		2203	4300	6503	SO:0001819	synonymous_variant	1462	exon6			GATAGCAGATTTG	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.1018A>C	chr5.hg19:g.82808191A>C		114.0	0.0	.		109.0	34.0	.	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	hg19	CCDS4060.1																																																																																			.	.	.	none		0.448	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		C	82808191	A	C	82808191	2	2	61	1	0	0	0	0	0	0	0	1	17150	180	7	5		5	VCAN	5	82808191	Silent	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	16358874	82808191	98107069	30	4058											
TXNDC15	79770	hgsc.bcm.edu	37	chr5	134223683	134223688	+	In_Frame_Del	DEL	TGGCGC	TGGCGC	-																															gagagccttttctctctggaTggcgctggagcacacttccc																								rs144331590		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	TGGCGC	TGGCGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr5:134223683_134223688delTGGCGC	ENST00000358387.4	+	2	1027_1032	c.402_407delTGGCGC	c.(400-408)gatggcgct>gat	p.GA137del	TXNDC15_ENST00000546290.1_In_Frame_Del_p.GA114del	NM_024715.3	NP_078991.3	Q96J42	TXD15_HUMAN	thioredoxin domain containing 15	137					cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)		p.G135G(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TCTCTCTGGATGGCGCTGGAGCACAC	0.558																																					p.134_136del		Atlas-Indel,Pindel	.											.	TXNDC15	37	.	1	Substitution - coding silent(1)	endometrium(1)	c.401_406del						PASS	.																																			SO:0001651	inframe_deletion	79770	exon2			.	AK026278	CCDS4180.1	5q31.1	2008-02-05	2007-08-16	2007-08-16	ENSG00000113621	ENSG00000113621			20652	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 14"	C5orf14			Standard	NM_024715		Approved	2310047H23Rik, FLJ22625	uc003lac.1	Q96J42	OTTHUMG00000129115	ENST00000358387.4:c.402_407delTGGCGC	chr5.hg19:g.134223683_134223688delTGGCGC	ENSP00000351157:p.Gly137_Ala138del	112.0	0.0	0		184.0	27.0	0.146739	NM_024715	D3DQA9|Q96MT2|Q9H639	In_Frame_Del	DEL	ENST00000358387.4	hg19	CCDS4180.1																																																																																			.	.	.	none		0.558	TXNDC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251160.1	NM_024715		-	134223688	TGGCGC	-	134223683	7	5	61	1	0	1	0	1	0	0	0	0	16806	1461	51	0	408	0	TXNDC15	5	134223683	In_Frame_Del	DEL	TGGCGC	TCGA-A4-A48D-01A-11D-A25F-10	51415492	134223683	46691577	31	4059											
BRD8	10902	hgsc.bcm.edu	37	chr5	137506838	137506838	+	Frame_Shift_Del	DEL	C	C	-																															ccaccacttctcccttttcaCctcgtttccgtctgtggaaa																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr5:137506838delC	ENST00000254900.5	-	5	619	c.248delG	c.(247-249)ggtfs	p.G83fs	BRD8_ENST00000230901.5_Frame_Shift_Del_p.G83fs|BRD8_ENST00000402931.1_Frame_Shift_Del_p.G83fs|BRD8_ENST00000411594.2_Frame_Shift_Del_p.G83fs|BRD8_ENST00000455658.2_Frame_Shift_Del_p.G42fs	NM_139199.1	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8	83					cell surface receptor signaling pathway (GO:0007166)|chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|intracellular receptor signaling pathway (GO:0030522)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(3)|urinary_tract(1)	35			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TCCCTTTTCACCTCGTTTCCG	0.353																																					p.G83fs		Atlas-Indel,Pindel	.											.	BRD8	192	.	0			c.249delT						PASS	.						98	99	99					5																	137506838		2203	4300	6503	SO:0001589	frameshift_variant	10902	exon5			.	AF016270	CCDS4198.1, CCDS34241.1, CCDS54907.1	5q31	2008-02-05			ENSG00000112983	ENSG00000112983			19874	protein-coding gene	gene with protein product		602848				8611617, 9368056	Standard	NM_001164326		Approved	SMAP, p120	uc003lcf.1	Q9H0E9	OTTHUMG00000129204	ENST00000254900.5:c.248delG	chr5.hg19:g.137506838delC	ENSP00000254900:p.Gly83fs	114.0	0.0	0		134.0	19.0	0.141791	NM_139199	O43178|Q15355|Q58AB0|Q59GN0|Q969M9	Frame_Shift_Del	DEL	ENST00000254900.5	hg19	CCDS4198.1																																																																																			.	.	.	none		0.353	BRD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251282.3	NM_006696		-	137506838	C	-	137506838	7	5	61	1	0	1	0	1	0	0	0	0	1508	507	18	0	3838	0	BRD8	5	137506838	Frame_Shift_Del	DEL	C	TCGA-A4-A48D-01A-11D-A25F-10	3283155	137506838	43408422	32	4060											
HUS1B	135458	hgsc.bcm.edu	37	chr6	656335	656335	+	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	agggtttccaagatttttaaAataactttgaatggacacca	15	13	7	6	0	0	2	0	1	0	1	1	3	1	3	2	2	1	1	2	2	5	6			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr6:656335A>T	ENST00000380907.2	-	1	628	c.610T>A	c.(610-612)Ttt>Att	p.F204I	EXOC2_ENST00000230449.4_Intron|EXOC2_ENST00000448181.3_Intron	NM_148959.3	NP_683762.2	Q8NHY5	HUS1B_HUMAN	HUS1 checkpoint homolog b (S. pombe)	204					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)	checkpoint clamp complex (GO:0030896)|nucleolus (GO:0005730)				endometrium(3)|large_intestine(1)|lung(7)	11	Ovarian(93;0.0733)	Breast(5;0.00139)|all_lung(73;0.0691)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.041)|BRCA - Breast invasive adenocarcinoma(62;0.0965)		AGATTTTTAAAATAACTTTGA	0.532																																					p.F204I		Atlas-SNP	.											.	HUS1B	26	.	0			c.T610A						PASS	.						96	107	103					6																	656335		2203	4300	6503	SO:0001583	missense	135458	exon1			TTTTAAAATAACT	AF508547	CCDS4470.1	6p25.3	2008-08-08	2001-11-28		ENSG00000188996	ENSG00000188996			16485	protein-coding gene	gene with protein product		609713	"HUS1 (S. pombe) checkpoint homolog b"			11944979	Standard	NM_148959		Approved		uc003mtg.3	Q8NHY5	OTTHUMG00000090059	ENST00000380907.2:c.610T>A	chr6.hg19:g.656335A>T	ENSP00000370293:p.Phe204Ile	101.0	0.0	.		103.0	27.0	.	NM_148959	Q5T4Z2	Missense_Mutation	SNP	ENST00000380907.2	hg19	CCDS4470.1	.	.	.	.	.	.	.	.	.	.	A	17.01	3.279334	0.59758	.	.	ENSG00000188996	ENST00000380907	T	0.17854	2.25	3.61	2.42	0.29668	.	0.143577	0.46442	U	0.000298	T	0.21801	0.0525	M	0.79011	2.435	0.58432	D	0.999996	D	0.69078	0.997	D	0.63381	0.914	T	0.02104	-1.1213	10	0.59425	D	0.04	.	5.756	0.18172	0.871:0.0:0.129:0.0	.	204	Q8NHY5	HUS1B_HUMAN	I	204	ENSP00000370293:F204I	ENSP00000370293:F204I	F	-	1	0	HUS1B	601335	0.999000	0.42202	0.011000	0.14972	0.048000	0.14542	1.596000	0.36718	0.560000	0.29169	0.533000	0.62120	TTT	.	.	.	none		0.532	HUS1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205617.2	NM_148959		T	656335	A	T	656335	3	4	61	1	0	0	0	0	1	0	0	0	7467	14	1	5	230	5	HUS1B	6	656335	Missense_Mutation	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10		656335	170458732	33	4061											
RHAG	6005	hgsc.bcm.edu	37	chr6	49586991	49586991	+	Missense_Mutation	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	cagcaacgagtaggttgataCccacactgctgaagccatat	13	8	9	11	1	0	2	0	2	0	0	0	3	0	2	2	1	5	4	2	1	5	4			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr6:49586991C>T	ENST00000371175.4	-	2	268	c.242G>A	c.(241-243)gGt>gAt	p.G81D	RHAG_ENST00000229810.7_Missense_Mutation_p.G81D	NM_000324.2	NP_000315.2	Q02094	RHAG_HUMAN	Rh-associated glycoprotein	81					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|bicarbonate transport (GO:0015701)|carbon dioxide transport (GO:0015670)|cellular ion homeostasis (GO:0006873)|erythrocyte development (GO:0048821)|multicellular organismal iron ion homeostasis (GO:0060586)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			NS(1)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	39	Lung NSC(77;0.0255)					TAGGTTGATACCCACACTGCT	0.443																																					p.G81D	Ovarian(176;476 2003 7720 43408 44749)	Atlas-SNP	.											.	RHAG	85	.	0			c.G242A						PASS	.						112	95	101					6																	49586991		2203	4300	6503	SO:0001583	missense	6005	exon2			TTGATACCCACAC		CCDS4927.1	6p12.3	2014-07-19	2006-02-23		ENSG00000112077	ENSG00000112077		"CD molecules", "Blood group antigens", "Solute carriers"	10006	protein-coding gene	gene with protein product		180297	"Rhesus blood group-associated glycoprotein"			9479501	Standard	NM_000324		Approved	RH50A, CD241, SLC42A1	uc003ozk.4	Q02094	OTTHUMG00000016377	ENST00000371175.4:c.242G>A	chr6.hg19:g.49586991C>T	ENSP00000360217:p.Gly81Asp	98.0	0.0	.		130.0	30.0	.	NM_000324	B2R8T8|O43514|O43515|Q7L8L3|Q9H454	Missense_Mutation	SNP	ENST00000371175.4	hg19	CCDS4927.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.972877	0.74246	.	.	ENSG00000112077	ENST00000371175;ENST00000229810;ENST00000418071;ENST00000539403	T;T	0.24538	1.85;1.85	5.62	5.62	0.85841	Ammonium transporter AmtB-like (3);	0.043100	0.85682	D	0.000000	T	0.59211	0.2177	H	0.94658	3.565	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.76071	0.987;0.987;0.983	T	0.71497	-0.4575	10	0.87932	D	0	-11.5221	18.6546	0.91448	0.0:1.0:0.0:0.0	.	81;81;81	O43515;Q9UHG9;Q02094	.;.;RHAG_HUMAN	D	81	ENSP00000360217:G81D;ENSP00000229810:G81D	ENSP00000229810:G81D	G	-	2	0	RHAG	49694950	1.000000	0.71417	0.938000	0.37757	0.238000	0.25445	7.792000	0.85828	2.640000	0.89533	0.591000	0.81541	GGT	.	.	.	none		0.443	RHAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043806.1			T	49586991	C	T	49586991	3	4	61	1	0	0	0	0	1	0	0	0	13328	507	18	2	1023	2	RHAG	6	49586991	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	48930656	49586991	121528076	34	4062											
CD164	8763	hgsc.bcm.edu	37	chr6	109690201	109690201	+	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	acaggttgtgaggttggagtCacagtgttatttgttgtacc	8	15	13	5	0	1	1	1	1	0	0	1	2	1	2	1	3	1	5	1	3	2	6			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr6:109690201C>T	ENST00000310786.4	-	6	512	c.447G>A	c.(445-447)gtG>gtA	p.V149V	CD164_ENST00000324953.5_Silent_p.V130V|CD164_ENST00000275080.7_Silent_p.V136V|CD164_ENST00000413644.2_Silent_p.V149V|CD164_ENST00000368961.5_Silent_p.V117V|CD164_ENST00000504373.1_Silent_p.V115V|CD164_ENST00000512821.1_Intron|CD164_ENST00000506649.1_5'UTR	NM_001142404.1|NM_006016.4	NP_001135876.1|NP_006007.2	Q04900	MUC24_HUMAN	CD164 molecule, sialomucin	149	Thr-rich.				cell adhesion (GO:0007155)|hemopoiesis (GO:0030097)|heterophilic cell-cell adhesion (GO:0007157)|immune response (GO:0006955)|multicellular organismal development (GO:0007275)|muscle organ development (GO:0007517)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|plasma membrane (GO:0005886)				breast(1)|lung(2)	3		all_cancers(87;4.65e-22)|all_epithelial(87;2.54e-20)|all_lung(197;1.6e-05)|Lung NSC(302;2.92e-05)|Colorectal(196;3.46e-05)|Ovarian(999;0.0175)		Epithelial(106;7.83e-46)|all cancers(137;1.15e-45)|OV - Ovarian serous cystadenocarcinoma(136;2.89e-26)|BRCA - Breast invasive adenocarcinoma(108;0.00128)|GBM - Glioblastoma multiforme(226;0.16)		AGGTTGGAGTCACAGTGTTAT	0.408																																					p.V149V		Atlas-SNP	.											.	CD164	10	.	0			c.G447A						PASS	.						114	96	102					6																	109690201		2203	4300	6503	SO:0001819	synonymous_variant	8763	exon6			TGGAGTCACAGTG	AF106518	CCDS5073.1, CCDS47462.1, CCDS47463.1, CCDS47464.1, CCDS47465.1	6q21	2014-09-05	2006-03-28		ENSG00000135535	ENSG00000135535		"CD molecules"	1632	protein-coding gene	gene with protein product		603356	"CD164 antigen, sialomucin"			9680353, 9763543	Standard	NM_006016		Approved	MUC-24, MGC-24	uc003pte.3	Q04900	OTTHUMG00000015339	ENST00000310786.4:c.447G>A	chr6.hg19:g.109690201C>T		194.0	0.0	.		177.0	39.0	.	NM_006016	B4DQ85|E1P5E7|E1P5E8|E1P5E9|O95413|Q5JSU6|Q9BPV0|Q9NR26	Silent	SNP	ENST00000310786.4	hg19	CCDS5073.1																																																																																			.	.	.	none		0.408	CD164-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041742.1	NM_006016		T	109690201	C	T	109690201	2	4	61	1	0	0	0	0	0	0	0	1	2971	813	29	2		2	CD164	6	109690201	Silent	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	60103210	109690201	61424866	35	4063											
SNX9	51429	hgsc.bcm.edu	37	chr6	158330822	158330822	+	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	gaatatcagctaacacctacTgtaagtatccacgttatcaa	15	11	5	10	1	2	0	2	0	0	0	3	1	3	0	2	0	3	4	2	0	8	6			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr6:158330822T>G	ENST00000392185.3	+	8	1002	c.831T>G	c.(829-831)acT>acG	p.T277T		NM_016224.3	NP_057308.1	Q9Y5X1	SNX9_HUMAN	sorting nexin 9	277	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|lipid tube assembly (GO:0060988)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein oligomerization (GO:0032461)|receptor-mediated endocytosis (GO:0006898)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle membrane (GO:0030659)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	1-phosphatidylinositol binding (GO:0005545)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	20		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)		TAACACCTACTGTAAGTATCC	0.393																																					p.T277T		Atlas-SNP	.											.	SNX9	43	.	0			c.T831G						PASS	.						172	168	169					6																	158330822		2203	4300	6503	SO:0001630	splice_region_variant	51429	exon8			ACCTACTGTAAGT	AF121859	CCDS5253.1	6q25.1-q26	2008-05-22			ENSG00000130340	ENSG00000130340		"Sorting nexins"	14973	protein-coding gene	gene with protein product		605952				10531379, 17609109	Standard	NM_016224		Approved	SH3PX1, SDP1, SH3PXD3A	uc003qqv.1	Q9Y5X1	OTTHUMG00000015903	ENST00000392185.3:c.831+1T>G	chr6.hg19:g.158330822T>G		85.0	0.0	.		104.0	26.0	.	NM_016224	Q9BSI7|Q9BVM1|Q9UJH6|Q9UP20	Silent	SNP	ENST00000392185.3	hg19	CCDS5253.1																																																																																			.	.	.	none		0.393	SNX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042856.1		Silent	G	158330822	T	G	158330822	5	3	61	1	0	0	0	0	0	0	1	0	14922	1594	55	5	861	5	SNX9	6	158330822	Splice_Site	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	48640621	158330822	12784245	36	4064											
MICALL2	79778	hgsc.bcm.edu	37	chr7	1478499	1478499	+	Missense_Mutation	SNP	T	T	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	gtttgccctgaaggtgaggtTtcttctcctcctccttccag	4	15	9	13	0	2	2	0	2	2	0	6	2	5	2	5	2	1	2	5	2	1	4			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr7:1478499T>G	ENST00000297508.7	-	10	2274	c.2099A>C	c.(2098-2100)aAa>aCa	p.K700T	MICALL2_ENST00000405088.4_Missense_Mutation_p.K488T|MICALL2_ENST00000471899.1_5'UTR	NM_182924.3	NP_891554.1	Q8IY33	MILK2_HUMAN	MICAL-like 2	700	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)		AAGGTGAGGTTTCTTCTCCTC	0.632																																					p.K700T		Atlas-SNP	.											.	MICALL2	63	.	0			c.A2099C						PASS	.						80	79	79					7																	1478499		2203	4300	6503	SO:0001583	missense	79778	exon10			TGAGGTTTCTTCT	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.2099A>C	chr7.hg19:g.1478499T>G	ENSP00000297508:p.Lys700Thr	33.0	0.0	.		43.0	13.0	.	NM_182924	D3YTD2|Q7RTP4|Q7Z655|Q8TEQ4|Q9H5F9	Missense_Mutation	SNP	ENST00000297508.7	hg19	CCDS5324.1	.	.	.	.	.	.	.	.	.	.	T	7.035	0.561374	0.13498	.	.	ENSG00000164877	ENST00000405088;ENST00000297508	T;T	0.71698	2.33;-0.59	1.61	-2.18	0.07037	.	0.219361	0.22804	N	0.055427	T	0.42449	0.1203	N	0.24115	0.695	0.09310	N	1	B;P	0.42908	0.267;0.793	B;B	0.37601	0.039;0.254	T	0.41822	-0.9487	10	0.24483	T	0.36	.	1.4582	0.02390	0.3162:0.2383:0.0:0.4454	.	700;488	Q8IY33;D3YTD2	MILK2_HUMAN;.	T	488;700	ENSP00000385928:K488T;ENSP00000297508:K700T	ENSP00000297508:K700T	K	-	2	0	MICALL2	1445025	0.000000	0.05858	0.003000	0.11579	0.171000	0.22731	-0.124000	0.10595	-0.123000	0.11745	0.260000	0.18958	AAA	.	.	.	none		0.632	MICALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239223.2	NM_182924		G	1478499	T	G	1478499	3	3	61	1	0	0	0	0	1	0	0	0	9581	1841	64	5	647	5	MICALL2	7	1478499	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10		1478499	157660164	37	4065											
HIBADH	11112	hgsc.bcm.edu	37	chr7	27582616	27582616	+	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	ccaacagctccacagtacacCacgttggagcccatgcaccc	11	5	7	18	1	0	0	0	0	0	0	1	1	1	1	5	1	5	4	5	1	2	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr7:27582616C>G	ENST00000265395.2	-	5	794	c.588G>C	c.(586-588)gtG>gtC	p.V196V		NM_152740.3	NP_689953.1	P31937	3HIDH_HUMAN	3-hydroxyisobutyrate dehydrogenase	196					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)			CACAGTACACCACGTTGGAGC	0.468																																					p.V196V		Atlas-SNP	.											.	HIBADH	28	.	0			c.G588C						PASS	.						97	87	91					7																	27582616		2203	4300	6503	SO:0001819	synonymous_variant	11112	exon5			GTACACCACGTTG	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.588G>C	chr7.hg19:g.27582616C>G		118.0	0.0	.		142.0	34.0	.	NM_152740	Q546Z2|Q9UDN3	Silent	SNP	ENST00000265395.2	hg19	CCDS5414.1	.	.	.	.	.	.	.	.	.	.	C	7.289	0.610641	0.14066	.	.	ENSG00000106049	ENST00000425715	.	.	.	6.02	4.21	0.49690	.	.	.	.	.	T	0.58104	0.2099	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53760	-0.8393	4	.	.	.	-2.1097	7.8405	0.29395	0.1159:0.6925:0.0:0.1916	.	.	.	.	S	139	.	.	W	-	2	0	HIBADH	27549141	0.993000	0.37304	0.856000	0.33681	0.715000	0.41141	0.664000	0.25068	0.865000	0.35603	0.655000	0.94253	TGG	.	.	.	none		0.468	HIBADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214132.1	NM_152740		G	27582616	C	G	27582616	2	3	61	1	0	0	0	0	0	0	0	1	7106	581	21	4		4	HIBADH	7	27582616	Silent	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	26104117	27582616	131556047	38	4066											
HECW1	23072	hgsc.bcm.edu	37	chr7	43508701	43508701	+	Frame_Shift_Del	DEL	A	A	-																															atcaaaacggaccagcagggAaaggtgagtgtgacccacgt																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr7:43508701delA	ENST00000395891.2	+	16	3701	c.3096delA	c.(3094-3096)ggafs	p.G1032fs	HECW1_ENST00000453890.1_Frame_Shift_Del_p.G998fs	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1032	WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.				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						ACCAGCAGGGAAAGGTGAGTG	0.577																																					p.G1032fs		Atlas-Indel,Pindel	.											.	HECW1	540	.	0			c.3095delG						PASS	.						61	61	61					7																	43508701		1982	4167	6149	SO:0001589	frameshift_variant	23072	exon16			.	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.3096delA	chr7.hg19:g.43508701delA	ENSP00000379228:p.Gly1032fs	77.0	0.0	0		110.0	36.0	0.327273	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Frame_Shift_Del	DEL	ENST00000395891.2	hg19	CCDS5469.2																																																																																			.	.	.	none		0.577	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		-	43508701	A	-	43508701	7	5	61	1	0	1	0	1	0	0	0	0	7049	233	9	0	3150	0	HECW1	7	43508701	Frame_Shift_Del	DEL	A	TCGA-A4-A48D-01A-11D-A25F-10	15926085	43508701	115629962	39	4067											
CYP3A43	64816	hgsc.bcm.edu	37	chr7	99434139	99434139	+	Frame_Shift_Del	DEL	T	T	-																															cctgggccaacccctctgccTtttctgggaactattttgtt																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr7:99434139delT	ENST00000354829.2	+	2	238	c.135delT	c.(133-135)cctfs	p.P45fs	CYP3A43_ENST00000222382.5_Frame_Shift_Del_p.P45fs|CYP3A43_ENST00000342499.4_Intron|CYP3A43_ENST00000477658.1_Intron|CYP3A43_ENST00000417625.1_Frame_Shift_Del_p.P45fs|CYP3A43_ENST00000421837.2_Frame_Shift_Del_p.P45fs|CYP3A43_ENST00000415413.1_Frame_Shift_Del_p.P45fs|CYP3A43_ENST00000312017.5_Frame_Shift_Del_p.P45fs|CYP3A43_ENST00000444905.1_Intron	NM_022820.3|NM_057095.1	NP_073731.1|NP_476436.1	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 43	45			YGTHSHKLFKKLGIPGPTPLPFLGTILFYLRGLWNFDRECN EKYGEMWGLYEGQQPMLVIMDPD -> LGPIHINFLRSWEF LGQPLCLFWELFCSTLGVFGILTENVMKNTEKCGGCMRGNS PCWSSWIPT (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)	CCCCTCTGCCTTTTCTGGGAA	0.393																																					p.P45fs		Atlas-Indel,Pindel	.											.	CYP3A43	52	.	0			c.134delC						PASS	.						95	93	94					7																	99434139		2203	4300	6503	SO:0001589	frameshift_variant	64816	exon2			.	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.135delT	chr7.hg19:g.99434139delT	ENSP00000346887:p.Pro45fs	103.0	0.0	0		88.0	21.0	0.238636	NM_057095	Q495Y1|Q75MK2|Q75MK3|Q9HB52|Q9HB53|Q9HB54|Q9HB57	Frame_Shift_Del	DEL	ENST00000354829.2	hg19	CCDS5676.1																																																																																			.	.	.	none		0.393	CYP3A43-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000344379.1			-	99434139	T	-	99434139	7	5	61	1	0	1	0	1	0	0	0	0	4181	1596	56	0	141	0	CYP3A43	7	99434139	Frame_Shift_Del	DEL	T	TCGA-A4-A48D-01A-11D-A25F-10	55925438	99434139	59704524	40	4068											
PPP1R3A	5506	hgsc.bcm.edu	37	chr7	113519562	113519562	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttggaaattttttctttgttTttcattaacacctaaatata	12	21	3	5	0	2	0	1	0	1	0	2	1	2	1	1	1	1	1	1	1	6	11			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr7:113519562T>C	ENST00000284601.3	-	4	1653	c.1585A>G	c.(1585-1587)Aaa>Gaa	p.K529E		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	529					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						TTTCTTTGTTTTTCATTAACA	0.343																																					p.K529E		Atlas-SNP	.											.	PPP1R3A	317	.	0			c.A1585G						PASS	.						77	71	73					7																	113519562		2203	4300	6503	SO:0001583	missense	5506	exon4			TTTGTTTTTCATT	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.1585A>G	chr7.hg19:g.113519562T>C	ENSP00000284601:p.Lys529Glu	96.0	0.0	.		90.0	11.0	.	NM_002711	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Missense_Mutation	SNP	ENST00000284601.3	hg19	CCDS5759.1	.	.	.	.	.	.	.	.	.	.	T	10.63	1.404017	0.25291	.	.	ENSG00000154415	ENST00000284601	T	0.17054	2.3	6.02	4.81	0.61882	.	0.792728	0.11805	N	0.527776	T	0.14830	0.0358	M	0.63428	1.95	0.09310	N	1	P	0.44734	0.842	B	0.31442	0.13	T	0.30179	-0.9987	10	0.52906	T	0.07	-0.2155	6.933	0.24451	0.1335:0.0719:0.0:0.7946	.	529	Q16821	PPR3A_HUMAN	E	529	ENSP00000284601:K529E	ENSP00000284601:K529E	K	-	1	0	PPP1R3A	113306798	0.941000	0.31946	0.713000	0.30519	0.230000	0.25150	1.271000	0.33098	2.311000	0.77944	0.533000	0.62120	AAA	.	.	.	none		0.343	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		C	113519562	T	C	113519562	3	2	61	1	0	0	0	0	1	0	0	0	12381	1850	64	3	1787	3	PPP1R3A	7	113519562	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	14085423	113519562	45619101	41	4069											
DEFB136	613210	hgsc.bcm.edu	37	chr8	11831570	11831570	+	Missense_Mutation	SNP	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	gacacccgaagaaacatacgGctttctggctagtgcaggtg	11	8	12	10	2	1	1	0	0	1	1	1	3	1	1	1	3	3	3	1	3	4	3			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr8:11831570G>A	ENST00000382209.2	-	2	112	c.113C>T	c.(112-114)gCc>gTc	p.A38V		NM_001033018.2	NP_001028190.2	Q30KP8	DB136_HUMAN	defensin, beta 136	38					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)		GAAACATACGGCTTTCTGGCT	0.453																																					p.A38V		Atlas-SNP	.											.	DEFB136	16	.	0			c.C113T						PASS	.						162	168	166					8																	11831570		2014	4183	6197	SO:0001583	missense	613210	exon2			CATACGGCTTTCT	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.113C>T	chr8.hg19:g.11831570G>A	ENSP00000371644:p.Ala38Val	172.0	0.0	.		182.0	50.0	.	NM_001033018	Q4QY36	Missense_Mutation	SNP	ENST00000382209.2	hg19	CCDS43709.1	.	.	.	.	.	.	.	.	.	.	G	15.54	2.863779	0.51482	.	.	ENSG00000205884	ENST00000382209	T	0.18960	2.18	4.06	3.18	0.36537	.	0.135690	0.34435	N	0.003978	T	0.17066	0.0410	.	.	.	0.09310	N	1	P	0.35982	0.531	B	0.35353	0.201	T	0.14282	-1.0478	9	0.66056	D	0.02	-1.9327	9.761	0.40532	0.0:0.7758:0.2242:0.0	.	38	Q30KP8	DB136_HUMAN	V	38	ENSP00000371644:A38V	ENSP00000371644:A38V	A	-	2	0	DEFB136	11868979	0.022000	0.18835	0.045000	0.18777	0.001000	0.01503	1.228000	0.32588	1.290000	0.44636	-0.321000	0.08615	GCC	.	.	.	none		0.453	DEFB136-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351889.1	NM_001033018		A	11831570	G	A	11831570	3	1	61	1	0	0	0	0	1	0	0	0	4422	1203	42	2	125	2	DEFB136	8	11831570	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10		11831570	134532452	42	4070											
SCARA3	51435	hgsc.bcm.edu	37	chr8	27516084	27516084	+	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	ggccagagatccgaaaactgCaggaggagctggagggaatt	13	5	16	7	1	0	1	0	0	0	1	1	7	1	5	2	5	3	2	2	5	3	1			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr8:27516084C>T	ENST00000301904.3	+	5	417	c.397C>T	c.(397-399)Cag>Tag	p.Q133*	SCARA3_ENST00000337221.4_Nonsense_Mutation_p.Q133*	NM_016240.2	NP_057324.2	Q6AZY7	SCAR3_HUMAN	scavenger receptor class A, member 3	133					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)		CCGAAAACTGCAGGAGGAGCT	0.562																																					p.Q133X		Atlas-SNP	.											.	SCARA3	93	.	0			c.C397T						PASS	.						96	103	101					8																	27516084		2203	4300	6503	SO:0001587	stop_gained	51435	exon5			AAACTGCAGGAGG	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.397C>T	chr8.hg19:g.27516084C>T	ENSP00000301904:p.Gln133*	78.0	0.0	.		93.0	7.0	.	NM_182826	Q9UM15|Q9UM16	Nonsense_Mutation	SNP	ENST00000301904.3	hg19	CCDS34871.1	.	.	.	.	.	.	.	.	.	.	C	38	7.138755	0.98088	.	.	ENSG00000168077	ENST00000337221;ENST00000301904	.	.	.	6.04	6.04	0.98038	.	0.106561	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	-19.8686	18.073	0.89417	0.0:1.0:0.0:0.0	.	.	.	.	X	133	.	ENSP00000301904:Q133X	Q	+	1	0	SCARA3	27572003	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.363000	0.66104	2.873000	0.98535	0.561000	0.74099	CAG	.	.	.	none		0.562	SCARA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376258.2	NM_016240		T	27516084	C	T	27516084	4	4	61	1	0	0	0	0	0	1	0	0	13892	711	25	2	415	2	SCARA3	8	27516084	Nonsense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	15684514	27516084	118847938	43	4071											
RAB11FIP1	80223	hgsc.bcm.edu	37	chr8	37730035	37730036	+	Frame_Shift_Ins	INS	-	-	T																															agctgcatccctggctttgcINStctccacaagagacccagcc																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr8:37730035_37730036insT	ENST00000330843.4	-	4	2296_2297	c.2284_2285insA	c.(2284-2286)agcfs	p.S762fs	RAB11FIP1_ENST00000287263.4_Intron|RAB11FIP1_ENST00000523182.1_5'UTR|RAB11FIP1_ENST00000522727.1_Intron|RAB11FIP1_ENST00000524118.1_Intron	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	762					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)			CCTGGCTTTGCTCTCCACAAGA	0.569																																					p.S762fs		Atlas-Indel,Pindel	.											.	RAB11FIP1	105	.	0			c.2285_2286insA						PASS	.																																			SO:0001589	frameshift_variant	80223	exon4			.	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.2285dupA	chr8.hg19:g.37730036_37730036dupT	ENSP00000331342:p.Ser762fs	91.0	0.0	0		128.0	27.0	0.210938	NM_001002814	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Frame_Shift_Ins	INS	ENST00000330843.4	hg19	CCDS34882.1																																																																																			.	.	.	none		0.569	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151		T	37730036	-	T	37730035	7	5	61	1	0	1	1	0	0	0	0	0	12906	797	28	0	1578	0	RAB11FIP1	8	37730035	Frame_Shift_Ins	INS	-	TCGA-A4-A48D-01A-11D-A25F-10	10213951	37730035	108633987	44	4072											
HNF4G	3174	hgsc.bcm.edu	37	chr8	76463728	76463728	+	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	agctgaagttcggtctcgccAggtacctgtggcacggcagc	7	8	14	12	3	1	1	0	1	1	0	3	1	1	1	2	4	3	5	2	4	2	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr8:76463728A>G	ENST00000354370.1	+	5	617	c.347A>G	c.(346-348)cAg>cGg	p.Q116R	HNF4G_ENST00000396423.2_Splice_Site_p.Q153R			Q14541	HNF4G_HUMAN	hepatocyte nuclear factor 4, gamma	116					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)			CGGTCTCGCCAGGTACCTGTG	0.423																																					p.Q153R		Atlas-SNP	.											.	HNF4G	111	.	0			c.A458G						PASS	.						114	86	96					8																	76463728		2203	4300	6503	SO:0001630	splice_region_variant	3174	exon4			CTCGCCAGGTACC		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.348+1A>G	chr8.hg19:g.76463728A>G		65.0	0.0	.		67.0	10.0	.	NM_004133	Q7Z2V9|Q9UH81|Q9UIS6	Missense_Mutation	SNP	ENST00000354370.1	hg19		.	.	.	.	.	.	.	.	.	.	A	19.16	3.774742	0.70107	.	.	ENSG00000164749	ENST00000354370;ENST00000396423	D;D	0.94687	-3.49;-3.49	5.07	5.07	0.68467	Nuclear hormone receptor, ligand-binding (2);	0.485181	0.25587	N	0.029651	D	0.94853	0.8337	M	0.79258	2.445	0.80722	D	1	B;B	0.29571	0.249;0.249	B;B	0.38106	0.191;0.265	D	0.93931	0.7214	10	0.41790	T	0.15	.	15.1246	0.72472	1.0:0.0:0.0:0.0	.	153;116	F1D8Q4;Q14541	.;HNF4G_HUMAN	R	116;153	ENSP00000346339:Q116R;ENSP00000379701:Q153R	ENSP00000346339:Q116R	Q	+	2	0	HNF4G	76626283	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.152000	0.94680	2.026000	0.59711	0.528000	0.53228	CAG	.	.	.	none		0.423	HNF4G-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000313914.2	NM_004133	Missense_Mutation	G	76463728	A	G	76463728	5	3	61	1	0	0	0	0	0	0	1	0	7261	202	7	3	472	3	HNF4G	8	76463728	Splice_Site	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	38733693	76463728	69900294	45	4073											
CA1	759	hgsc.bcm.edu	37	chr8	86250502	86250502	+	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	tgatcggttatcgttgtcctCaaaatttacatggaaggaat	12	14	9	6	2	1	1	1	1	0	0	4	3	2	3	1	3	1	2	1	3	6	4			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr8:86250502C>T	ENST00000523953.1	-	4	1260	c.214G>A	c.(214-216)Gag>Aag	p.E72K	CA1_ENST00000256119.5_Missense_Mutation_p.E72K|CA1_ENST00000523022.1_Missense_Mutation_p.E72K|CA1_ENST00000518341.1_5'UTR|CA1_ENST00000432364.2_Missense_Mutation_p.E72K|CA1_ENST00000542576.1_Missense_Mutation_p.E72K|CA1_ENST00000522389.1_Intron|CA1_ENST00000431316.1_Missense_Mutation_p.E72K			P00915	CAH1_HUMAN	carbonic anhydrase I	72					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)	13		all_lung(136;4.89e-06)			Acetazolamide(DB00819)|Amlodipine(DB00381)|Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Brinzolamide(DB01194)|Chlorothiazide(DB00880)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Diclofenamide(DB01144)|Dorzolamide(DB00869)|Ethinamate(DB01031)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methazolamide(DB00703)|Methocarbamol(DB00423)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)|Zonisamide(DB00909)	TCGTTGTCCTCAAAATTTACA	0.388																																					p.E72K		Atlas-SNP	.											.	CA1	41	.	0			c.G214A						PASS	.						222	221	222					8																	86250502		2203	4300	6503	SO:0001583	missense	759	exon2			TGTCCTCAAAATT	M33987	CCDS6237.1	8q21.2	2006-03-10				ENSG00000133742	4.2.1.1	"Carbonic anhydrases"	1368	protein-coding gene	gene with protein product		114800				1916821	Standard	NM_001164830		Approved	Car1	uc003ydi.3	P00915		ENST00000523953.1:c.214G>A	chr8.hg19:g.86250502C>T	ENSP00000430656:p.Glu72Lys	120.0	0.0	.		100.0	8.0	.	NM_001164830		Missense_Mutation	SNP	ENST00000523953.1	hg19	CCDS6237.1	.	.	.	.	.	.	.	.	.	.	C	14.79	2.641247	0.47153	.	.	ENSG00000133742	ENST00000523953;ENST00000256119;ENST00000431316;ENST00000542576;ENST00000432364;ENST00000523022;ENST00000517618;ENST00000517590;ENST00000521846;ENST00000522579;ENST00000522814;ENST00000522662;ENST00000523858	T;T;T;T;T;T;T;T;T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3	5.53	3.74	0.42951	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.620194	0.17999	N	0.154974	T	0.60011	0.2236	L	0.42632	1.34	0.37858	D	0.929602	P	0.45715	0.865	B	0.42692	0.395	T	0.63323	-0.6663	10	0.59425	D	0.04	-2.5698	10.6538	0.45663	0.0:0.8437:0.0:0.1563	.	72	P00915	CAH1_HUMAN	K	72	ENSP00000430656:E72K;ENSP00000256119:E72K;ENSP00000392338:E72K;ENSP00000443517:E72K;ENSP00000401551:E72K;ENSP00000429798:E72K;ENSP00000430861:E72K;ENSP00000429843:E72K;ENSP00000430471:E72K;ENSP00000427852:E72K;ENSP00000430737:E72K;ENSP00000430372:E72K;ENSP00000430975:E72K	ENSP00000256119:E72K	E	-	1	0	CA1	86437754	0.998000	0.40836	0.108000	0.21378	0.434000	0.31775	2.575000	0.46025	0.706000	0.31912	0.591000	0.81541	GAG	.	.	.	none		0.388	CA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381067.1	NM_001738		T	86250502	C	T	86250502	3	4	61	1	0	0	0	0	1	0	0	0	2512	835	29	2	595	2	CA1	8	86250502	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	9786774	86250502	60113520	46	4074											
DECR1	1666	hgsc.bcm.edu	37	chr8	91029497	91029498	+	Frame_Shift_Ins	INS	-	-	A																															gggggaggtactggccttggINStaaaggaatgacaactcttc																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr8:91029497_91029498insA	ENST00000220764.2	+	2	303_304	c.215_216insA	c.(214-219)ggtaaafs	p.K73fs	DECR1_ENST00000522161.1_Frame_Shift_Ins_p.K64fs|DECR1_ENST00000519007.1_3'UTR	NM_001359.1	NP_001350.1	Q16698	DECR_HUMAN	2,4-dienoyl CoA reductase 1, mitochondrial	73					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	2,4-dienoyl-CoA reductase (NADPH) activity (GO:0008670)|NADPH binding (GO:0070402)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	15			BRCA - Breast invasive adenocarcinoma(11;0.00953)			ACTGGCCTTGGTAAAGGAATGA	0.45																																					p.G72fs		Atlas-Indel,Pindel	.											.	DECR1	37	.	0			c.215_216insA						PASS	.																																			SO:0001589	frameshift_variant	1666	exon2			.	L26050	CCDS6250.1	8q21.3	2011-09-14			ENSG00000104325	ENSG00000104325		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	2753	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 18C, member 1"	222745		DECR		7818482, 19027726	Standard	NM_001359		Approved	SDR18C1	uc003yek.1	Q16698	OTTHUMG00000163829	Exception_encountered	chr8.hg19:g.91029497_91029498insA	ENSP00000220764:p.Lys73fs	102.0	0.0	0		127.0	44.0	0.346457	NM_001359	B7Z6B8|Q2M304|Q93085	Frame_Shift_Ins	INS	ENST00000220764.2	hg19	CCDS6250.1																																																																																			.	.	.	none		0.45	DECR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375822.1			A	91029498	-	A	91029497	7	5	61	1	0	1	1	0	0	0	0	0	4384	1261	44	0	221	0	DECR1	8	91029497	Frame_Shift_Ins	INS	-	TCGA-A4-A48D-01A-11D-A25F-10	4778995	91029497	55334525	47	4075											
RGS22	26166	hgsc.bcm.edu	37	chr8	101076121	101076121	+	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	gtttcttttcaaggtatactCtcagaagagcttgagaagga	12	13	10	6	0	3	3	2	1	2	3	4	5	3	4	0	2	2	3	0	2	5	6			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr8:101076121C>G	ENST00000360863.6	-	8	1069	c.875G>C	c.(874-876)aGa>aCa	p.R292T	RGS22_ENST00000523287.1_Missense_Mutation_p.R111T|RGS22_ENST00000523437.1_Missense_Mutation_p.R280T	NM_015668.3	NP_056483.3	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	292					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)			AAGGTATACTCTCAGAAGAGC	0.343																																					p.R292T		Atlas-SNP	.											.	RGS22	319	.	0			c.G875C						PASS	.						79	79	79					8																	101076121		1823	4073	5896	SO:0001583	missense	26166	exon8			TATACTCTCAGAA	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.875G>C	chr8.hg19:g.101076121C>G	ENSP00000354109:p.Arg292Thr	64.0	0.0	.		62.0	7.0	.	NM_015668	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	Missense_Mutation	SNP	ENST00000360863.6	hg19	CCDS43758.1	.	.	.	.	.	.	.	.	.	.	C	16.86	3.240381	0.58995	.	.	ENSG00000132554	ENST00000360863;ENST00000427793;ENST00000523287;ENST00000523437	T;T;T	0.32988	1.44;1.43;1.44	5.86	4.98	0.66077	.	0.202669	0.37809	N	0.001934	T	0.25531	0.0621	M	0.64997	1.995	0.25094	N	0.990833	P;P;P	0.38597	0.506;0.506;0.639	B;B;B	0.30029	0.051;0.051;0.11	T	0.41215	-0.9521	10	0.66056	D	0.02	.	7.6392	0.28284	0.1248:0.6867:0.1208:0.0677	.	280;292;111	A8K944;Q8NE09;G3V112	.;RGS22_HUMAN;.	T	292;280;111;280	ENSP00000354109:R292T;ENSP00000429382:R111T;ENSP00000428212:R280T	ENSP00000354109:R292T	R	-	2	0	RGS22	101145297	0.590000	0.26815	0.978000	0.43139	0.698000	0.40448	1.435000	0.34969	2.937000	0.99478	0.650000	0.86243	AGA	.	.	.	none		0.343	RGS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380365.1	NM_015668		G	101076121	C	G	101076121	3	3	61	1	0	0	0	0	1	0	0	0	13318	913	32	4	2999	4	RGS22	8	101076121	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	10046624	101076121	45287901	48	4076											
ZNF572	137209	hgsc.bcm.edu	37	chr8	125988719	125988719	+	Missense_Mutation	SNP	A	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	taagcatgaggatgcaaaagAaatgccactgacatgggttc	15	8	11	7	0	0	3	0	2	0	1	1	4	0	4	1	2	3	3	1	2	4	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr8:125988719A>C	ENST00000319286.5	+	3	363	c.209A>C	c.(208-210)gAa>gCa	p.E70A		NM_152412.2	NP_689625.2	Q7Z3I7	ZN572_HUMAN	zinc finger protein 572	70					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)			GATGCAAAAGAAATGCCACTG	0.378										HNSCC(60;0.17)																											p.E70A		Atlas-SNP	.											.	ZNF572	82	.	0			c.A209C						PASS	.						91	89	90					8																	125988719		2203	4300	6503	SO:0001583	missense	137209	exon3			CAAAAGAAATGCC	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.209A>C	chr8.hg19:g.125988719A>C	ENSP00000319305:p.Glu70Ala	68.0	0.0	.		54.0	13.0	.	NM_152412	A1L4F1|Q8N1Q0	Missense_Mutation	SNP	ENST00000319286.5	hg19	CCDS6354.1	.	.	.	.	.	.	.	.	.	.	A	9.984	1.229005	0.22542	.	.	ENSG00000180938	ENST00000319286	T	0.08634	3.07	4.06	2.92	0.33932	.	0.160607	0.29293	N	0.012574	T	0.05273	0.0140	N	0.24115	0.695	0.09310	N	0.999998	B	0.27823	0.19	B	0.27608	0.081	T	0.36456	-0.9747	10	0.27082	T	0.32	-9.0575	7.4137	0.27032	0.8925:0.0:0.1075:0.0	.	70	Q7Z3I7	ZN572_HUMAN	A	70	ENSP00000319305:E70A	ENSP00000319305:E70A	E	+	2	0	ZNF572	126057900	0.024000	0.19004	0.541000	0.28102	0.914000	0.54420	0.846000	0.27682	1.841000	0.53522	0.459000	0.35465	GAA	.	.	.	none		0.378	ZNF572-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381359.1	NM_152412		C	125988719	A	C	125988719	3	2	61	1	0	0	0	0	1	0	0	0	18016	246	9	5	215	5	ZNF572	8	125988719	Missense_Mutation	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	24912598	125988719	20375303	49	4077											
KCNK9	51305	hgsc.bcm.edu	37	chr8	140631226	140631231	+	In_Frame_Del	DEL	TGTTCA	TGTTCA	-																															cagcaggtagcgcacgaaggTgttcatgcgctcgcccaggc																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	TGTTCA	TGTTCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr8:140631226_140631231delTGTTCA	ENST00000520439.1	-	2	458_463	c.395_400delTGAACA	c.(394-402)atgaacacc>acc	p.MN132del	KCNK9_ENST00000523477.1_5'Flank|KCNK9_ENST00000303015.1_In_Frame_Del_p.MN132del	NM_001282534.1	NP_001269463.1	Q9NPC2	KCNK9_HUMAN	potassium channel, subfamily K, member 9	132					cochlea development (GO:0090102)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			NS(1)|endometrium(9)|kidney(1)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)	43	all_cancers(97;3.94e-14)|all_epithelial(106;4.81e-13)|Lung NSC(106;8.18e-05)|all_lung(105;0.00015)|Ovarian(258;0.00235)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;0.134)	BRCA - Breast invasive adenocarcinoma(115;0.0855)		Doxapram(DB00561)|Halothane(DB01159)	CGCACGAAGGTGTTCATGCGCTCGCC	0.587																																					p.132_134del		Atlas-Indel,Pindel	.											.	KCNK9	100	.	0			c.396_401del						PASS	.																																			SO:0001651	inframe_deletion	51305	exon2			.	AF212829	CCDS6377.1	8q24.3	2012-03-07			ENSG00000169427	ENSG00000169427		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6283	protein-coding gene	gene with protein product		605874				10734076, 16382106	Standard	NM_001282534		Approved	K2p9.1, TASK3, TASK-3	uc003yvf.1	Q9NPC2	OTTHUMG00000164186	ENST00000520439.1:c.395_400delTGAACA	chr8.hg19:g.140631226_140631231delTGTTCA	ENSP00000430676:p.Met132_Asn133del	190.0	0.0	0		211.0	27.0	0.127962	NM_016601	Q2M290|Q540F2	In_Frame_Del	DEL	ENST00000520439.1	hg19	CCDS6377.1																																																																																			.	.	.	none		0.587	KCNK9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378473.1	NM_016601		-	140631231	TGTTCA	-	140631226	7	5	61	1	0	1	0	1	0	0	0	0	8079	1696	59	0	728	0	KCNK9	8	140631226	In_Frame_Del	DEL	TGTTCA	TCGA-A4-A48D-01A-11D-A25F-10	14642507	140631226	5732796	50	4078											
ZNF251	90987	hgsc.bcm.edu	37	chr8	145947050	145947050	+	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	taaaaatgtctttcttggaaAatcttcttgatatgaataaa	16	16	5	4	0	4	2	0	2	4	0	4	3	4	3	0	1	0	0	0	1	9	7			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr8:145947050A>T	ENST00000292562.7	-	5	2270	c.1995T>A	c.(1993-1995)atT>atA	p.I665I	ZNF251_ENST00000524394.1_Intron	NM_138367.1	NP_612376.1	Q9BRH9	ZN251_HUMAN	zinc finger protein 251	665					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|kidney(1)|large_intestine(5)|lung(9)|stomach(1)	17	all_cancers(97;3.54e-11)|all_epithelial(106;2.65e-10)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.75e-39)|Epithelial(56;7.54e-38)|all cancers(56;6.19e-33)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.11)	GBM - Glioblastoma multiforme(99;0.198)		TTTCTTGGAAAATCTTCTTGA	0.358																																					p.I665I		Atlas-SNP	.											.	ZNF251	80	.	0			c.T1995A						PASS	.						44	44	44					8																	145947050		1901	4119	6020	SO:0001819	synonymous_variant	90987	exon5			TTGGAAAATCTTC	AK000435	CCDS47944.1	8q24.3	2013-01-08			ENSG00000198169	ENSG00000198169		"Zinc fingers, C2H2-type", "-"	13045	protein-coding gene	gene with protein product							Standard	NM_138367		Approved		uc003zdv.4	Q9BRH9	OTTHUMG00000165189	ENST00000292562.7:c.1995T>A	chr8.hg19:g.145947050A>T		96.0	0.0	.		90.0	28.0	.	NM_138367	Q2M219	Silent	SNP	ENST00000292562.7	hg19	CCDS47944.1																																																																																			.	.	.	none		0.358	ZNF251-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382541.1	NM_138367		T	145947050	A	T	145947050	2	4	61	1	0	0	0	0	0	0	0	1	17808	10	1	5		5	ZNF251	8	145947050	Silent	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	5315824	145947050	416972	51	4079											
BAAT	570	hgsc.bcm.edu	37	chr9	104125253	104125253	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccatagatagtccaatctgTactccttgacatacagagac	13	10	7	11	0	1	3	0	1	1	2	3	4	3	3	3	0	2	1	3	0	5	5			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr9:104125253T>C	ENST00000395051.3	-	3	784	c.714A>G	c.(712-714)gtA>gtG	p.V238V	BAAT_ENST00000259407.2_Silent_p.V238V			Q14032	BAAT_HUMAN	bile acid CoA:amino acid N-acyltransferase	238					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)	GTCCAATCTGTACTCCTTGAC	0.393																																					p.V238V		Atlas-SNP	.											.	BAAT	52	.	0			c.A714G						PASS	.						90	91	91					9																	104125253		2202	4300	6502	SO:0001819	synonymous_variant	570	exon4			AATCTGTACTCCT	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.714A>G	chr9.hg19:g.104125253T>C		62.0	0.0	.		59.0	16.0	.	NM_001127610	Q3B7W9|Q96L31	Silent	SNP	ENST00000395051.3	hg19	CCDS6752.1																																																																																			.	.	.	none		0.393	BAAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053433.1			C	104125253	T	C	104125253	2	2	61	1	0	0	0	0	0	0	0	1	1280	1625	57	3		3	BAAT	9	104125253	Silent	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10		104125253	37088178	52	4080											
GPR107	57720	hgsc.bcm.edu	37	chr9	132845879	132845879	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaagaagtacagtggattcaAaggtaagaactaaccaccct	18	7	8	8	0	1	2	1	0	0	2	1	3	1	3	2	2	3	2	2	2	7	4			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr9:132845879A>G	ENST00000372406.1	+	6	1069	c.562A>G	c.(562-564)Aag>Gag	p.K188E	GPR107_ENST00000347136.6_Missense_Mutation_p.K188E|GPR107_ENST00000372410.3_Missense_Mutation_p.K188E	NM_001136557.1	NP_001130029.1	Q5VW38	GP107_HUMAN	G protein-coupled receptor 107	188						integral component of membrane (GO:0016021)				endometrium(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	11		Ovarian(14;0.000531)				AGTGGATTCAAAGGTAAGAAC	0.348																																					p.K188E		Atlas-SNP	.											.	GPR107	30	.	0			c.A562G						PASS	.						196	174	181					9																	132845879		2203	4300	6503	SO:0001583	missense	57720	exon6			GATTCAAAGGTAA	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.562A>G	chr9.hg19:g.132845879A>G	ENSP00000361483:p.Lys188Glu	243.0	0.0	.		223.0	11.0	.	NM_001136557	A6NJ53|Q2TB81|Q5JPA3|Q5VW39|Q96T26|Q9H658|Q9HCE8	Missense_Mutation	SNP	ENST00000372406.1	hg19	CCDS48041.1	.	.	.	.	.	.	.	.	.	.	A	15.42	2.828233	0.50845	.	.	ENSG00000148358	ENST00000372406;ENST00000347136;ENST00000372410;ENST00000455412	T;T;T	0.22336	1.96;1.97;1.96	5.63	4.42	0.53409	.	0.148254	0.46758	D	0.000276	T	0.14874	0.0359	L	0.42245	1.32	0.32954	D	0.520166	P;P;P	0.40083	0.702;0.696;0.57	B;B;B	0.37650	0.255;0.214;0.255	T	0.05533	-1.0879	10	0.08837	T	0.75	-12.6956	9.084	0.36570	0.8151:0.1849:0.0:0.0	.	188;188;188	G5E994;Q5VW38;Q5VW38-2	.;GP107_HUMAN;.	E	188	ENSP00000361483:K188E;ENSP00000336988:K188E;ENSP00000361487:K188E	ENSP00000336988:K188E	K	+	1	0	GPR107	131885700	0.952000	0.32445	1.000000	0.80357	0.980000	0.70556	0.795000	0.26972	2.145000	0.66743	0.533000	0.62120	AAG	.	.	.	none		0.348	GPR107-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054643.2			G	132845879	A	G	132845879	3	3	61	1	0	0	0	0	1	0	0	0	6630	15	1	3	584	3	GPR107	9	132845879	Missense_Mutation	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	28720626	132845879	8367552	53	4081											
NUDT13	25961	hgsc.bcm.edu	37	chr10	74884990	74884990	+	Missense_Mutation	SNP	T	T	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	gcccttccaataatataatcTattatccacaggtaattatt	14	15	3	9	0	1	0	0	0	1	0	3	0	3	0	3	1	0	1	3	1	8	9			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr10:74884990T>G	ENST00000357321.4	+	6	698	c.580T>G	c.(580-582)Tat>Gat	p.Y194D	NUDT13_ENST00000544879.1_Missense_Mutation_p.Y68D|NUDT13_ENST00000537969.1_5'UTR|RP11-152N13.16_ENST00000608444.1_RNA|SNORA11_ENST00000408237.1_RNA|NUDT13_ENST00000372997.3_Missense_Mutation_p.Y194D|NUDT13_ENST00000488223.1_3'UTR|NUDT13_ENST00000349051.5_Missense_Mutation_p.Y194D	NM_001283016.1|NM_015901.4	NP_001269945.1|NP_056985.3			nudix (nucleoside diphosphate linked moiety X)-type motif 13											large_intestine(2)|lung(5)	7	Prostate(51;0.0119)					TAATATAATCTATTATCCACA	0.478																																					p.Y194D		Atlas-SNP	.											.	NUDT13	16	.	0			c.T580G						PASS	.						68	70	69					10																	74884990		2203	4300	6503	SO:0001583	missense	25961	exon6			ATAATCTATTATC	AL050114	CCDS31220.1, CCDS60551.1, CCDS60552.1, CCDS60553.1, CCDS73148.1	10q22.3	2014-04-24			ENSG00000166321	ENSG00000166321		"Nudix motif containing"	18827	protein-coding gene	gene with protein product		609233				15164054	Standard	NM_001283019		Approved	DKFZp586P2219	uc001jtj.3	Q86X67	OTTHUMG00000018453	ENST00000357321.4:c.580T>G	chr10.hg19:g.74884990T>G	ENSP00000349874:p.Tyr194Asp	115.0	0.0	.		101.0	25.0	.	NM_015901		Missense_Mutation	SNP	ENST00000357321.4	hg19	CCDS31220.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.580430	0.86645	.	.	ENSG00000166321	ENST00000357321;ENST00000349051;ENST00000544879;ENST00000372997	T;T;T;T	0.44083	0.93;1.36;0.93;1.43	5.97	5.97	0.96955	NUDIX hydrolase domain (1);Zinc ribbon, NADH pyrophosphatase (1);NUDIX hydrolase domain-like (1);	0.108901	0.64402	D	0.000004	T	0.57902	0.2085	L	0.42245	1.32	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.979	D;D;P	0.79108	0.992;0.984;0.821	T	0.57556	-0.7791	10	0.52906	T	0.07	.	16.43	0.83839	0.0:0.0:0.0:1.0	.	194;194;194	Q86X67-2;Q5SQM6;Q86X67	.;.;NUD13_HUMAN	D	194;194;68;194	ENSP00000349874:Y194D;ENSP00000335326:Y194D;ENSP00000440760:Y68D;ENSP00000362088:Y194D	ENSP00000335326:Y194D	Y	+	1	0	NUDT13	74554996	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.758000	0.68776	2.283000	0.76528	0.533000	0.62120	TAT	.	.	.	none		0.478	NUDT13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048614.1	NM_015901		G	74884990	T	G	74884990	3	3	61	1	0	0	0	0	1	0	0	0	10736	1522	53	5	598	5	NUDT13	10	74884990	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10		74884990	60649757	54	4082											
MAT1A	4143	hgsc.bcm.edu	37	chr10	82039973	82039973	+	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	ccaggggaggaggccggagcGcctgaggtctgccatccggg	6	4	19	12	3	1	1	0	1	1	0	2	4	2	4	5	7	2	0	5	7	0	0			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr10:82039973G>T	ENST00000372213.3	-	5	765	c.505C>A	c.(505-507)Cgc>Agc	p.R169S		NM_000429.2	NP_000420.1	Q00266	METK1_HUMAN	methionine adenosyltransferase I, alpha	169					cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methionine adenosyltransferase activity (GO:0004478)			endometrium(4)|large_intestine(7)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26			Colorectal(32;0.229)		L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	AGGCCGGAGCGCCTGAGGTCT	0.582																																					p.R169S		Atlas-SNP	.											.	MAT1A	52	.	0			c.C505A						PASS	.						71	79	76					10																	82039973		2203	4300	6503	SO:0001583	missense	4143	exon5			CGGAGCGCCTGAG		CCDS7365.1	10q22	2008-08-01			ENSG00000151224	ENSG00000151224			6903	protein-coding gene	gene with protein product	"S-adenosylmethionine synthetase"	610550				8393662	Standard	XM_005269842		Approved	MAT, SAMS, MATA1, SAMS1	uc001kbw.3	Q00266	OTTHUMG00000018613	ENST00000372213.3:c.505C>A	chr10.hg19:g.82039973G>T	ENSP00000361287:p.Arg169Ser	76.0	0.0	.		86.0	7.0	.	NM_000429	D3DWD5|Q5QP09	Missense_Mutation	SNP	ENST00000372213.3	hg19	CCDS7365.1	.	.	.	.	.	.	.	.	.	.	G	14.12	2.441355	0.43326	.	.	ENSG00000151224	ENST00000372213;ENST00000372206;ENST00000455001	D;D	0.82619	-1.63;-1.63	4.91	4.01	0.46588	S-adenosylmethionine synthetase, central domain (1);S-adenosylmethionine synthetase superfamily (1);	0.097389	0.64402	N	0.000001	D	0.91835	0.7416	M	0.93854	3.465	0.80722	D	1	D	0.60160	0.987	D	0.62955	0.909	D	0.93004	0.6426	10	0.87932	D	0	-22.5394	11.6157	0.51088	0.0885:0.0:0.9115:0.0	.	169	Q00266	METK1_HUMAN	S	169;169;106	ENSP00000361287:R169S;ENSP00000414961:R106S	ENSP00000361280:R169S	R	-	1	0	MAT1A	82029953	1.000000	0.71417	0.858000	0.33744	0.028000	0.11728	6.335000	0.72949	1.217000	0.43442	-0.123000	0.14984	CGC	.	.	.	none		0.582	MAT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049070.1	NM_000429		T	82039973	G	T	82039973	3	4	61	1	0	0	0	0	1	0	0	0	9336	1087	38	4	702	4	MAT1A	10	82039973	Missense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	7154983	82039973	53494774	55	4083											
NRG3	10718	hgsc.bcm.edu	37	chr10	83635455	83635455	+	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	cttcctctccaagcccagctCtttccccaaggccatggaga	8	9	7	17	0	2	1	0	0	2	1	5	2	4	1	6	2	2	1	6	2	2	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr10:83635455C>G	ENST00000404547.1	+	1	359	c.359C>G	c.(358-360)tCt>tGt	p.S120C	NRG3_ENST00000372141.2_Missense_Mutation_p.S120C|NRG3_ENST00000404576.2_5'Flank|NRG3_ENST00000372142.2_5'Flank|NRG3_ENST00000556918.1_5'Flank			P56975	NRG3_HUMAN	neuregulin 3	120	Ser/Thr-rich.				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)		AAGCCCAGCTCTTTCCCCAAG	0.662																																					p.S120C		Atlas-SNP	.											.	NRG3	301	.	0			c.C359G						PASS	.						71	78	75					10																	83635455		2203	4300	6503	SO:0001583	missense	10718	exon1			CCAGCTCTTTCCC	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.359C>G	chr10.hg19:g.83635455C>G	ENSP00000384796:p.Ser120Cys	95.0	0.0	.		113.0	29.0	.	NM_001165972	A4D7U1|Q0PEH2|Q5VYH3	Missense_Mutation	SNP	ENST00000404547.1	hg19	CCDS31233.1	.	.	.	.	.	.	.	.	.	.	c	19.30	3.801788	0.70682	.	.	ENSG00000185737	ENST00000372141;ENST00000404547;ENST00000537287	T;T	0.35973	1.28;1.29	2.97	2.97	0.34412	.	.	.	.	.	T	0.41119	0.1145	N	0.19112	0.55	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.66847	0.947;0.947	T	0.42361	-0.9456	9	0.72032	D	0.01	-10.7268	11.8419	0.52359	0.0:1.0:0.0:0.0	.	120;120	B9EGV5;P56975-4	.;.	C	120	ENSP00000361214:S120C;ENSP00000384796:S120C	ENSP00000361214:S120C	S	+	2	0	NRG3	83625435	0.970000	0.33590	1.000000	0.80357	0.995000	0.86356	2.334000	0.43920	1.680000	0.50976	0.459000	0.35465	TCT	.	.	.	none		0.662	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086		G	83635455	C	G	83635455	3	3	61	1	0	0	0	0	1	0	0	0	10656	913	32	4	361	4	NRG3	10	83635455	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	1595482	83635455	51899292	56	4084											
BMPR1A	657	hgsc.bcm.edu	37	chr10	88681453	88681453	+	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	tcgtcgttgtatcacaggagGtgggagtttgagtagtttct	7	15	14	5	2	2	1	1	1	1	0	4	3	2	3	0	3	0	5	0	3	2	5			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr10:88681453G>A	ENST00000372037.3	+	11	1879		c.e11+1			NM_004329.2	NP_004320.2	P36894	BMR1A_HUMAN	bone morphogenetic protein receptor, type IA						BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|developmental growth (GO:0048589)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic digit morphogenesis (GO:0042733)|embryonic organ development (GO:0048568)|endocardial cushion formation (GO:0003272)|heart formation (GO:0060914)|hindlimb morphogenesis (GO:0035137)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lateral mesoderm development (GO:0048368)|lung development (GO:0030324)|mesendoderm development (GO:0048382)|mesoderm formation (GO:0001707)|Mullerian duct regression (GO:0001880)|negative regulation of neurogenesis (GO:0050768)|neural crest cell development (GO:0014032)|neural plate mediolateral regionalization (GO:0021998)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|paraxial mesoderm structural organization (GO:0048352)|pituitary gland development (GO:0021983)|positive regulation of bone mineralization (GO:0030501)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of lateral mesodermal cell fate specification (GO:0048378)|somitogenesis (GO:0001756)|stem cell maintenance (GO:0019827)|transforming growth factor beta receptor signaling pathway (GO:0007179)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|skin(1)|stomach(1)	24						ATCACAGGAGGTGGGAGTTTG	0.388			"Mis, N, F"			gastrointestinal polyps			Juvenile Polyposis;Hereditary Mixed Polyposis syndrome type 2																												.	Ovarian(190;603 2086 22044 30335 47971)	Atlas-SNP	.	yes	Rec		Juvenile polyposis	10	10q22.3	657	"bone morphogenetic protein receptor, type IA"		E	.	BMPR1A	118	.	0			c.1342+1G>A						PASS	.						112	108	110					10																	88681453		2203	4300	6503	SO:0001630	splice_region_variant	657	exon11	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HMPS2	CAGGAGGTGGGAG	BC028383	CCDS7378.1	10q22.3	2014-09-17			ENSG00000107779	ENSG00000107779		"CD molecules"	1076	protein-coding gene	gene with protein product		601299		ACVRLK3		8397373, 9730621	Standard	NM_004329		Approved	ALK3, CD292	uc001kdy.3	P36894	OTTHUMG00000018657	ENST00000372037.3:c.1342+1G>A	chr10.hg19:g.88681453G>A		163.0	0.0	.		155.0	44.0	.	NM_004329	A8K6U9|Q8NEN8	Splice_Site	SNP	ENST00000372037.3	hg19	CCDS7378.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.039456	0.75617	.	.	ENSG00000107779	ENST00000224764;ENST00000372037	.	.	.	5.63	4.72	0.59763	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3472	0.83146	0.0:0.0:0.867:0.133	.	.	.	.	.	-1	.	.	.	+	.	.	BMPR1A	88671433	1.000000	0.71417	0.989000	0.46669	0.789000	0.44602	9.738000	0.98835	1.511000	0.48818	0.655000	0.94253	.	.	.	.	none		0.388	BMPR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049170.3	NM_004329	Intron	A	88681453	G	A	88681453	5	1	61	1	0	0	0	0	0	0	1	0	1469	1275	44	2	1377	2	BMPR1A	10	88681453	Splice_Site	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	5045998	88681453	46853294	57	4085											
CDHR5	53841	hgsc.bcm.edu	37	chr11	621148	621148	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacgtagccatctgagaaggTgcagggcaggaaccacgggg	11	4	17	9	2	1	1	0	1	1	1	1	4	1	2	2	5	3	3	2	5	3	1			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr11:621148T>C	ENST00000358353.3	-	8	1043	c.721A>G	c.(721-723)Acc>Gcc	p.T241A	CDHR5_ENST00000349570.7_Missense_Mutation_p.T241A|CDHR5_ENST00000397542.2_Missense_Mutation_p.T241A			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	241					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						TCTGAGAAGGTGCAGGGCAGG	0.652																																					p.T241A		Atlas-SNP	.											.	CDHR5	77	.	0			c.A721G						PASS	.						68	64	66					11																	621148		2203	4300	6503	SO:0001583	missense	53841	exon7			AGAAGGTGCAGGG	AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"Cadherins / Cadherin-related"	7521	protein-coding gene	gene with protein product		606839	"mucin and cadherin-like", "mucin-like protocadherin"	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.721A>G	chr11.hg19:g.621148T>C	ENSP00000351118:p.Thr241Ala	112.0	0.0	.		154.0	34.0	.	NM_031264	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Missense_Mutation	SNP	ENST00000358353.3	hg19	CCDS7707.1	.	.	.	.	.	.	.	.	.	.	T	3.798	-0.042254	0.07452	.	.	ENSG00000099834	ENST00000397542;ENST00000358353;ENST00000326366;ENST00000349570	T;T;T	0.45668	0.89;0.89;0.89	4.08	-8.15	0.01065	.	2.323100	0.02445	N	0.084999	T	0.12092	0.0294	N	0.02357	-0.585	0.09310	N	1	B;B;B;B;B	0.13594	0.0;0.005;0.002;0.002;0.008	B;B;B;B;B	0.09377	0.003;0.004;0.004;0.004;0.004	T	0.22977	-1.0201	10	0.10377	T	0.69	-2.285	0.0745	0.00025	0.3221:0.1617:0.2125:0.3037	.	241;241;234;241;241	Q58EZ6;Q9HBB8-4;B4DV98;Q9HBB8-2;Q9HBB8	.;.;.;.;CDHR5_HUMAN	A	241	ENSP00000380676:T241A;ENSP00000351118:T241A;ENSP00000345726:T241A	ENSP00000326527:T241A	T	-	1	0	CDHR5	611148	0.000000	0.05858	0.000000	0.03702	0.184000	0.23303	-1.800000	0.01744	-2.416000	0.00567	-0.496000	0.04628	ACC	.	.	.	none		0.652	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924		C	621148	T	C	621148	3	2	61	1	0	0	0	0	1	0	0	0	3124	1696	59	3	1852	3	CDHR5	11	621148	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10		621148	134385368	58	4086											
MUC2	4583	hgsc.bcm.edu	37	chr11	1093271	1093271	+	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	caccggcacacagaccccaaCatcgacacccatcaccacca	14	2	4	21	2	1	1	1	0	0	1	2	2	1	1	6	1	1	1	6	1	1	0			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr11:1093271C>G	ENST00000441003.2	+	30	5117	c.5090C>G	c.(5089-5091)aCa>aGa	p.T1697R	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.T1664R	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.T1697R(2)|p.T1664R(2)		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)	cagaccccaacatcgacaccc	0.637																																					p.T1697R		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,-1,4	MUC2	614	.	4	Substitution - Missense(4)	kidney(2)|skin(2)	c.C5090G						PASS	.						126	165	151					11																	1093271		1844	3338	5182	SO:0001583	missense	4583	exon30			CCCCAACATCGAC	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.5090C>G	chr11.hg19:g.1093271C>G	ENSP00000415183:p.Thr1697Arg	54.0	0.0	.		70.0	4.0	.	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	C	5.778	0.327961	0.10956	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.13538	2.93;2.58	1.43	1.43	0.22495	.	27.718000	0.04275	U	0.342784	T	0.27027	0.0662	.	.	.	0.20307	N	0.999915	D	0.64830	0.994	D	0.67725	0.953	T	0.19647	-1.0299	9	0.30078	T	0.28	.	6.2291	0.20724	0.0:1.0:0.0:0.0	.	1697	E7EUV1	.	R	1697;1664	ENSP00000415183:T1697R;ENSP00000351956:T1664R	ENSP00000351956:T1664R	T	+	2	0	MUC2	1083271	0.001000	0.12720	0.002000	0.10522	0.003000	0.03518	0.752000	0.26362	0.796000	0.33947	0.184000	0.17185	ACA	.	.	.	none		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		G	1093271	C	G	1093271	3	3	61	1	0	0	0	0	1	0	0	0	9982	478	17	4	5208	4	MUC2	11	1093271	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	472123	1093271	133913245	59	4087											
OR52D1	390066	hgsc.bcm.edu	37	chr11	5510196	5510196	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtgcccaagatgctggccaTtttgtggctccatgctggtg	5	13	13	10	0	0	1	0	0	0	1	1	1	1	1	3	3	3	3	3	3	1	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr11:5510196T>C	ENST00000322641.5	+	1	282	c.260T>C	c.(259-261)aTt>aCt	p.I87T	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron	NM_001005163.2	NP_001005163.1	Q9H346	O52D1_HUMAN	olfactory receptor, family 52, subfamily D, member 1	87					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)		ATGCTGGCCATTTTGTGGCTC	0.498																																					p.I87T		Atlas-SNP	.											.	OR52D1	66	.	0			c.T260C						PASS	.						164	135	144					11																	5510196		2201	4297	6498	SO:0001583	missense	390066	exon1			TGGCCATTTTGTG	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.260T>C	chr11.hg19:g.5510196T>C	ENSP00000326232:p.Ile87Thr	413.0	1.0	.		419.0	115.0	.	NM_001005163	B9EGY9|Q6IFI6	Missense_Mutation	SNP	ENST00000322641.5	hg19	CCDS31384.1	.	.	.	.	.	.	.	.	.	.	T	18.56	3.650929	0.67472	.	.	ENSG00000181609	ENST00000322641	T	0.00384	7.6	5.57	5.57	0.84162	GPCR, rhodopsin-like superfamily (1);	0.088930	0.48767	D	0.000161	T	0.00936	0.0031	M	0.73372	2.23	0.41835	D	0.990092	D	0.89917	1.0	D	0.85130	0.997	T	0.73582	-0.3937	10	0.87932	D	0	.	14.7065	0.69194	0.0:0.0:0.0:1.0	.	87	Q9H346	O52D1_HUMAN	T	87	ENSP00000326232:I87T	ENSP00000326232:I87T	I	+	2	0	OR52D1	5466772	0.008000	0.16893	1.000000	0.80357	0.593000	0.36681	1.557000	0.36299	2.340000	0.79590	0.528000	0.53228	ATT	.	.	.	none		0.498	OR52D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143372.1	NM_001005163		C	5510196	T	C	5510196	3	2	61	1	0	0	0	0	1	0	0	0	11121	1493	52	3	262	3	OR52D1	11	5510196	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	4416925	5510196	129496320	60	4088											
EXPH5	23086	hgsc.bcm.edu	37	chr11	108381937	108381941	+	Frame_Shift_Del	DEL	CTTCT	CTTCT	-																															ttgggaatttccaatattaaCttctgaaagagctggaagac																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	CTTCT	CTTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr11:108381937_108381941delCTTCT	ENST00000265843.4	-	6	4403_4407	c.4293_4297delAGAAG	c.(4291-4299)tcagaagttfs	p.EV1432fs	EXPH5_ENST00000443411.1_Frame_Shift_Del_p.EV1244fs|EXPH5_ENST00000428840.1_Frame_Shift_Del_p.EV1356fs|EXPH5_ENST00000524840.1_5'Flank|EXPH5_ENST00000525344.1_Frame_Shift_Del_p.EV1425fs	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1432					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)		CCAATATTAACTTCTGAAAGAGCTG	0.395																																					p.1432_1433del		Atlas-Indel,Pindel	.											.	EXPH5	193	.	0			c.4294_4298del						PASS	.																																			SO:0001589	frameshift_variant	23086	exon6			.		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.4293_4297delAGAAG	chr11.hg19:g.108381937_108381941delCTTCT	ENSP00000265843:p.Glu1432fs	146.0	0.0	0		123.0	26.0	0.211382	NM_015065	Q2KHM1|Q9Y4D6	Frame_Shift_Del	DEL	ENST00000265843.4	hg19	CCDS8341.1																																																																																			.	.	.	none		0.395	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		-	108381941	CTTCT	-	108381937	7	5	61	1	0	1	0	1	0	0	0	0	5324	565	20	0	1676	0	EXPH5	11	108381937	Frame_Shift_Del	DEL	CTTCT	TCGA-A4-A48D-01A-11D-A25F-10	102871741	108381937	26624579	61	4089											
SIK3	23387	hgsc.bcm.edu	37	chr11	116741113	116741113	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacaggggtaactgctggcActgcctgaagagagacagga	12	5	14	10	0	0	3	0	1	0	2	0	5	0	4	2	4	3	3	2	4	2	1			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr11:116741113A>G	ENST00000292055.4	-	14	1603	c.1568T>C	c.(1567-1569)gTg>gCg	p.V523A	SIK3_ENST00000446921.2_Missense_Mutation_p.V533A|SIK3_ENST00000434315.2_Missense_Mutation_p.V422A|SIK3_ENST00000375300.1_Missense_Mutation_p.V581A|SIK3_ENST00000488337.1_5'Flank|SIK3_ENST00000542607.1_Missense_Mutation_p.V475A|SIK3_ENST00000375288.1_5'UTR	NM_025164.3	NP_079440.3	Q9Y2K2	SIK3_HUMAN	SIK family kinase 3	523					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						AACTGCTGGCACTGCCTGAAG	0.542											OREG0003489	type=REGULATORY REGION|Gene=BC063887|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.V523A		Atlas-SNP	.											.	SIK3	112	.	0			c.T1568C						PASS	.						76	67	70					11																	116741113		2201	4296	6497	SO:0001583	missense	23387	exon14			GCTGGCACTGCCT	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.1568T>C	chr11.hg19:g.116741113A>G	ENSP00000292055:p.Val523Ala	88.0	0.0	.	1475	114.0	25.0	.	NM_025164	A1A5A8|Q59FY2|Q5M9N1|Q6P3R6|Q8IYM8|Q9HA50	Missense_Mutation	SNP	ENST00000292055.4	hg19	CCDS8379.1	.	.	.	.	.	.	.	.	.	.	A	17.96	3.516700	0.64634	.	.	ENSG00000160584	ENST00000375300;ENST00000292055;ENST00000542607;ENST00000434315	T;T;T;T	0.72615	-0.62;-0.65;-0.67;-0.23	5.79	4.66	0.58398	Protein kinase-like domain (1);	0.000000	0.36134	U	0.002766	T	0.66499	0.2795	L	0.29908	0.895	0.80722	D	1	D;P;P	0.53312	0.959;0.929;0.857	P;P;B	0.50192	0.634;0.48;0.396	T	0.68401	-0.5418	10	0.62326	D	0.03	.	11.844	0.52374	0.9311:0.0:0.0689:0.0	.	475;422;523	A1A5A8;A1A5A9;Q9Y2K2	.;.;SIK3_HUMAN	A	581;523;475;422	ENSP00000364449:V581A;ENSP00000292055:V523A;ENSP00000438108:V475A;ENSP00000415873:V422A	ENSP00000292055:V523A	V	-	2	0	SIK3	116246323	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.658000	0.68003	1.011000	0.39340	0.482000	0.46254	GTG	.	.	.	none		0.542	SIK3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_025164		G	116741113	A	G	116741113	3	3	61	1	0	0	0	0	1	0	0	0	14332	159	6	3	2263	3	SIK3	11	116741113	Missense_Mutation	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	8359176	116741113	18265403	62	4090											
USP5	8078	hgsc.bcm.edu	37	chr12	6974373	6974374	+	Frame_Shift_Del	DEL	TG	TG	-																															tcacatgggcacctctaccaTgtgtggtcactacgtctgcc																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr12:6974373_6974374delTG	ENST00000229268.8	+	19	2496_2497	c.2444_2445delTG	c.(2443-2445)atgfs	p.M815fs	USP5_ENST00000389231.5_Frame_Shift_Del_p.M792fs|TPI1_ENST00000229270.4_5'Flank|TPI1_ENST00000488464.2_5'Flank|TPI1_ENST00000396705.5_5'Flank|TPI1_ENST00000535434.1_5'Flank	NM_001098536.1	NP_001092006.1	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 (isopeptidase T)	815	USP.				positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin thiolesterase activity (GO:0004221)|zinc ion binding (GO:0008270)			breast(6)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|skin(2)|urinary_tract(2)	36						ACCTCTACCATGTGTGGTCACT	0.5																																					p.815_815del		Atlas-Indel,Pindel	.											.	USP5	124	.	0			c.2443_2444del						PASS	.																																			SO:0001589	frameshift_variant	8078	exon19			.	U35116	CCDS31733.1, CCDS41743.1	12p13	2007-03-02	2005-08-08		ENSG00000111667	ENSG00000111667		"Ubiquitin-specific peptidases"	12628	protein-coding gene	gene with protein product		601447	"ubiquitin specific protease 5 (isopeptidase T)"			12838346, 8723724	Standard	NM_003481		Approved	IsoT	uc001qri.4	P45974	OTTHUMG00000169233	ENST00000229268.8:c.2444_2445delTG	chr12.hg19:g.6974377_6974378delTG	ENSP00000229268:p.Met815fs	171.0	0.0	0		182.0	32.0	0.175824	NM_001098536	D3DUS7|D3DUS8|Q96J22	Frame_Shift_Del	DEL	ENST00000229268.8	hg19	CCDS41743.1																																																																																			.	.	.	none		0.5	USP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402982.1			-	6974374	TG	-	6974373	7	5	61	1	0	1	0	1	0	0	0	0	17093	1464	51	0	2518	0	USP5	12	6974373	Frame_Shift_Del	DEL	TG	TCGA-A4-A48D-01A-11D-A25F-10		6974373	126877522	63	4091											
LRRK2	120892	hgsc.bcm.edu	37	chr12	40713882	40713882	+	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	tttctttcaaaaaaaaggaaAtttccaaagaactacatgtc	18	12	4	7	0	2	1	1	0	1	1	4	2	3	2	1	1	2	0	1	1	8	4			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr12:40713882A>T	ENST00000298910.7	+	34	4978	c.4920A>T	c.(4918-4920)aaA>aaT	p.K1640N		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1640					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)				AAAAAAGGAAATTTCCAAAGA	0.358											OREG0003827	type=REGULATORY REGION|Gene=LOC486608|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.K1640N		Atlas-SNP	.											.	LRRK2	763	.	0			c.A4920T						PASS	.						52	62	59					12																	40713882		2199	4296	6495	SO:0001583	missense	120892	exon34			AAGGAAATTTCCA	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.4920A>T	chr12.hg19:g.40713882A>T	ENSP00000298910:p.Lys1640Asn	52.0	0.0	.	895	54.0	13.0	.	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	hg19	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	A	13.43	2.234808	0.39498	.	.	ENSG00000188906	ENST00000298910	T	0.71698	-0.59	5.55	4.4	0.53042	.	0.305891	0.37393	N	0.002104	T	0.52451	0.1735	L	0.27053	0.805	0.36820	D	0.886366	B;B	0.24823	0.112;0.005	B;B	0.15484	0.013;0.004	T	0.50233	-0.8852	10	0.17832	T	0.49	.	9.2446	0.37518	0.842:0.0:0.158:0.0	.	1640;1640	Q17RV3;Q5S007	.;LRRK2_HUMAN	N	1640	ENSP00000298910:K1640N	ENSP00000298910:K1640N	K	+	3	2	LRRK2	39000149	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	3.468000	0.53086	0.932000	0.37266	0.482000	0.46254	AAA	.	.	.	none		0.358	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		T	40713882	A	T	40713882	3	4	61	1	0	0	0	0	1	0	0	0	9040	98	4	5	5054	5	LRRK2	12	40713882	Missense_Mutation	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	33739509	40713882	93138013	64	4092											
LRRK2	120892	hgsc.bcm.edu	37	chr12	40745358	40745358	+	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	caggtctttgacattttgaaTtcagctgaattagtctgtct	9	17	8	7	0	4	3	1	3	3	0	4	3	4	3	0	1	1	1	0	1	3	5			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr12:40745358T>A	ENST00000298910.7	+	44	6457	c.6399T>A	c.(6397-6399)aaT>aaA	p.N2133K		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	2133	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				ACATTTTGAATTCAGCTGAAT	0.343																																					p.N2133K		Atlas-SNP	.											.	LRRK2	763	.	0			c.T6399A						PASS	.						48	48	48					12																	40745358		2203	4300	6503	SO:0001583	missense	120892	exon44			TTTGAATTCAGCT	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.6399T>A	chr12.hg19:g.40745358T>A	ENSP00000298910:p.Asn2133Lys	74.0	0.0	.		56.0	6.0	.	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	hg19	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	T	17.95	3.514495	0.64522	.	.	ENSG00000188906	ENST00000298910	T	0.71817	-0.6	6.02	1.09	0.20402	Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.53658	0.1810	N	0.21583	0.68	0.44492	D	0.997434	P;P	0.42692	0.476;0.787	B;B	0.40982	0.246;0.345	T	0.47947	-0.9077	10	0.41790	T	0.15	.	9.6792	0.40059	0.0:0.4062:0.0:0.5938	.	2133;2133	Q17RV3;Q5S007	.;LRRK2_HUMAN	K	2133	ENSP00000298910:N2133K	ENSP00000298910:N2133K	N	+	3	2	LRRK2	39031625	0.999000	0.42202	1.000000	0.80357	0.991000	0.79684	0.493000	0.22451	0.196000	0.20367	0.529000	0.55759	AAT	.	.	.	none		0.343	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		A	40745358	T	A	40745358	3	1	61	1	0	0	0	0	1	0	0	0	9040	1490	52	5	6573	5	LRRK2	12	40745358	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	31476	40745358	93106537	65	4093											
KRT79	338785	hgsc.bcm.edu	37	chr12	53225246	53225246	+	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	ctgagctctgagtccagcctCccccgctcgctctgaagtct	5	10	9	17	2	3	3	0	3	3	0	6	3	5	3	4	0	2	3	4	0	1	0			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr12:53225246C>A	ENST00000330553.5	-	2	676	c.642G>T	c.(640-642)ggG>ggT	p.G214G		NM_175834.2	NP_787028.1	Q5XKE5	K2C79_HUMAN	keratin 79	214	Coil 1B.|Rod.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	enzyme binding (GO:0019899)|structural molecule activity (GO:0005198)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						AGTCCAGCCTCCCCCGCTCGC	0.617																																					p.G214G		Atlas-SNP	.											.	KRT79	78	.	0			c.G642T						PASS	.						114	114	114					12																	53225246		2203	4300	6503	SO:0001819	synonymous_variant	338785	exon2			CAGCCTCCCCCGC	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.642G>T	chr12.hg19:g.53225246C>A		101.0	0.0	.		111.0	27.0	.	NM_175834	Q6P465|Q7Z793	Silent	SNP	ENST00000330553.5	hg19	CCDS8839.1																																																																																			.	.	.	none		0.617	KRT79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406376.1	NM_175834		A	53225246	C	A	53225246	2	1	61	1	0	0	0	0	0	0	0	1	8499	842	30	4		4	KRT79	12	53225246	Silent	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	12479888	53225246	80626649	66	4094											
TIMELESS	8914	hgsc.bcm.edu	37	chr12	56827702	56827703	+	Frame_Shift_Ins	INS	-	-	CACG																															aaatagcggatcagatccttINScacgctctcttcagagacag																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr12:56827702_56827703insCACG	ENST00000553532.1	-	3	255_256	c.105_106insCGTG	c.(103-108)gtgaagfs	p.K36fs	TIMELESS_ENST00000554616.1_Frame_Shift_Ins_p.K36fs|TIMELESS_ENST00000229201.4_Frame_Shift_Ins_p.K36fs					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						ATCAGATCCTTCACGCTCTCTT	0.52																																					p.K36fs		Atlas-Indel,Pindel	.											.	TIMELESS	107	.	0			c.106_107insCGTG						PASS	.																																			SO:0001589	frameshift_variant	8914	exon3			.	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.102_105dupCGTG	chr12.hg19:g.56827703_56827706dupCACG	ENSP00000450607:p.Lys36fs	152.0	0.0	0		156.0	30.0	0.192308	NM_003920		Frame_Shift_Ins	INS	ENST00000553532.1	hg19	CCDS8918.1																																																																																			.	.	.	none		0.52	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920		CACG	56827703	-	CACG	56827702	7	5	61	1	0	1	1	0	0	0	0	0	15916	1792	62	0	3628	0	TIMELESS	12	56827702	Frame_Shift_Ins	INS	-	TCGA-A4-A48D-01A-11D-A25F-10	3602456	56827702	77024193	67	4095											
GPR182	11318	hgsc.bcm.edu	37	chr12	57389791	57389791	+	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	ctgtgcgcctacgtggccgtCtttgtcatgtgctggctgcc	2	13	13	13	3	2	0	1	0	1	0	2	0	2	0	3	2	4	2	3	2	1	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr12:57389791C>G	ENST00000300098.1	+	2	1017	c.798C>G	c.(796-798)gtC>gtG	p.V266V	HBCBP_ENST00000600202.1_5'Flank|RP11-474N8.5_ENST00000556850.1_RNA	NM_007264.3	NP_009195.1	O15218	GP182_HUMAN	G protein-coupled receptor 182	266					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						ACGTGGCCGTCTTTGTCATGT	0.617																																					p.V266V		Atlas-SNP	.											.	GPR182	35	.	0			c.C798G						PASS	.						168	145	153					12																	57389791		2203	4300	6503	SO:0001819	synonymous_variant	11318	exon2			GGCCGTCTTTGTC	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.798C>G	chr12.hg19:g.57389791C>G		46.0	0.0	.		67.0	18.0	.	NM_007264		Silent	SNP	ENST00000300098.1	hg19	CCDS8927.1																																																																																			.	.	.	none		0.617	GPR182-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411212.1	NM_007264		G	57389791	C	G	57389791	2	3	61	1	0	0	0	0	0	0	0	1	6684	900	32	4		4	GPR182	12	57389791	Silent	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	562089	57389791	76462104	68	4096											
TMEM132B	114795	hgsc.bcm.edu	37	chr12	126138829	126138830	+	In_Frame_Ins	INS	-	-	CAA																															tttgctgtgagtgagcagggINScaacatcccccattcccacg																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr12:126138829_126138830insCAA	ENST00000299308.3	+	9	2818_2819	c.2810_2811insCAA	c.(2809-2814)ggcaac>ggCAAcaac	p.938_939insN	TMEM132B_ENST00000535886.1_In_Frame_Ins_p.450_451insN	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	938						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)		AGTGAGCAGGGCAACATCCCCC	0.51																																					p.G937delinsGN		Atlas-Indel,Pindel	.											.	TMEM132B	207	.	0			c.2810_2811insCAA						PASS	.																																			SO:0001652	inframe_insertion	114795	exon9			.	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.2811_2813dupCAA	chr12.hg19:g.126138830_126138832dupCAA	ENSP00000299308:p.Asn938_Asn938dup	139.0	0.0	0		171.0	27.0	0.157895	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	In_Frame_Ins	INS	ENST00000299308.3	hg19	CCDS41859.1																																																																																			.	.	.	none		0.51	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907		CAA	126138830	-	CAA	126138829	7	5	61	1	0	1	1	0	0	0	0	0	16058	1203	42	0	2844	0	TMEM132B	12	126138829	In_Frame_Ins	INS	-	TCGA-A4-A48D-01A-11D-A25F-10	68749038	126138829	7713066	69	4097											
IFT88	8100	hgsc.bcm.edu	37	chr13	21163994	21163994	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcagttactagacctatagcTactggatatggggtaggttt	10	13	12	6	0	0	1	0	0	0	1	0	2	0	2	1	4	3	5	1	4	7	8			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr13:21163994T>C	ENST00000319980.6	+	6	552	c.225T>C	c.(223-225)gcT>gcC	p.A75A	IFT88_ENST00000537103.1_Intron|IFT88_ENST00000351808.5_Silent_p.A66A|IFT88_ENST00000382778.4_Silent_p.A75A	NM_175605.3	NP_783195.2	Q13099	IFT88_HUMAN	intraflagellar transport 88	75					anterior/posterior pattern specification (GO:0009952)|cardiac muscle cell differentiation (GO:0055007)|cardiac septum morphogenesis (GO:0060411)|cilium morphogenesis (GO:0060271)|cochlea development (GO:0090102)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|embryonic digit morphogenesis (GO:0042733)|epidermal stem cell homeostasis (GO:0036334)|epidermis development (GO:0008544)|epithelial cell morphogenesis (GO:0003382)|eye development (GO:0001654)|forebrain morphogenesis (GO:0048853)|heart formation (GO:0060914)|inner ear receptor stereocilium organization (GO:0060122)|kidney development (GO:0001822)|liver development (GO:0001889)|lung vasculature development (GO:0060426)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|protein localization (GO:0008104)|regulation of autophagic vacuole assembly (GO:2000785)|regulation of cilium assembly (GO:1902017)|regulation of fat cell differentiation (GO:0045598)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of protein processing (GO:0070613)|regulation of smoothened signaling pathway (GO:0008589)|response to fluid shear stress (GO:0034405)|smoothened signaling pathway (GO:0007224)|sperm axoneme assembly (GO:0007288)|spermatid nucleus elongation (GO:0007290)|spinal cord dorsal/ventral patterning (GO:0021513)|telencephalon development (GO:0021537)	acrosomal membrane (GO:0002080)|apical part of cell (GO:0045177)|axonemal basal plate (GO:0097541)|centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|kinocilium (GO:0060091)|motile cilium (GO:0031514)|motile primary cilium (GO:0031512)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	27		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)		GACCTATAGCTACTGGATATG	0.328																																					p.A75A		Atlas-SNP	.											.	IFT88	83	.	0			c.T225C						PASS	.						81	82	82					13																	21163994		2203	4299	6502	SO:0001819	synonymous_variant	8100	exon6			TATAGCTACTGGA	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.225T>C	chr13.hg19:g.21163994T>C		61.0	0.0	.		56.0	6.0	.	NM_175605	A2A491|B4DUS2|Q5SZJ6|Q8N719	Silent	SNP	ENST00000319980.6	hg19	CCDS31944.1																																																																																			.	.	.	none		0.328	IFT88-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044075.3	NM_006531		C	21163994	T	C	21163994	2	2	61	1	0	0	0	0	0	0	0	1	7573	1509	53	3		3	IFT88	13	21163994	Silent	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10		21163994	94005884	70	4098											
USP12	219333	hgsc.bcm.edu	37	chr13	27664060	27664060	+	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	gctgcgacactcttcacagtAatacttgtattcactgcaca	11	12	6	12	1	3	0	2	0	1	0	3	1	3	0	0	0	3	4	0	0	3	6			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr13:27664060A>T	ENST00000282344.6	-	6	950	c.694T>A	c.(694-696)Tac>Aac	p.Y232N		NM_182488.3	NP_872294.2	O75317	UBP12_HUMAN	ubiquitin specific peptidase 12	232	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Lung SC(185;0.0161)		all cancers(112;0.0508)|GBM - Glioblastoma multiforme(144;0.168)|Epithelial(112;0.244)|OV - Ovarian serous cystadenocarcinoma(117;0.246)		TCTTCACAGTAATACTTGTAT	0.338																																					p.Y232N	Ovarian(37;808 911 7590 44442 44991)	Atlas-SNP	.											.	USP12	35	.	0			c.T694A						PASS	.						63	62	62					13																	27664060		2203	4300	6503	SO:0001583	missense	219333	exon6			CACAGTAATACTT	AL049221	CCDS31952.1	13q12.13	2010-05-12	2005-08-08	2003-10-08	ENSG00000152484	ENSG00000152484		"Ubiquitin-specific peptidases"	20485	protein-coding gene	gene with protein product			"ubiquitin specific protease 12 like 1", "ubiquitin specific protease 12"	USP12L1		12838346	Standard	NM_182488		Approved		uc001uqy.3	O75317	OTTHUMG00000016626	ENST00000282344.6:c.694T>A	chr13.hg19:g.27664060A>T	ENSP00000282344:p.Tyr232Asn	110.0	0.0	.		115.0	39.0	.	NM_182488	A8K0X0|Q5VZV3|Q8TC49	Missense_Mutation	SNP	ENST00000282344.6	hg19	CCDS31952.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.459009	0.84317	.	.	ENSG00000152484	ENST00000282344	T	0.05649	3.41	5.22	5.22	0.72569	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.16085	0.0387	L	0.42686	1.345	0.80722	D	1	D	0.57571	0.98	P	0.60541	0.876	T	0.00575	-1.1663	10	0.49607	T	0.09	-15.958	15.4004	0.74834	1.0:0.0:0.0:0.0	.	232	O75317	UBP12_HUMAN	N	232	ENSP00000282344:Y232N	ENSP00000282344:Y232N	Y	-	1	0	USP12	26562060	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.803000	0.91915	2.113000	0.64589	0.482000	0.46254	TAC	.	.	.	none		0.338	USP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044264.1	NM_182488		T	27664060	A	T	27664060	3	4	61	1	0	0	0	0	1	0	0	0	17055	362	13	5	434	5	USP12	13	27664060	Missense_Mutation	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	6500066	27664060	87505818	71	4099											
DIAPH3	81624	hgsc.bcm.edu	37	chr13	60686191	60686191	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcattctctgacagtggctTtggaaagttctccatcatct	8	16	7	10	0	5	1	2	1	3	0	7	2	5	2	1	2	0	2	1	2	1	4			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr13:60686191T>C	ENST00000400324.4	-	3	563	c.343A>G	c.(343-345)Aag>Gag	p.K115E	DIAPH3_ENST00000400320.1_Missense_Mutation_p.K104E|DIAPH3_ENST00000377908.2_Missense_Mutation_p.K104E|DIAPH3_ENST00000400319.1_Intron|DIAPH3_ENST00000267215.4_Missense_Mutation_p.K115E|DIAPH3_ENST00000400330.1_Missense_Mutation_p.K115E	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	115	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		GACAGTGGCTTTGGAAAGTTC	0.403																																					p.K115E		Atlas-SNP	.											.	DIAPH3	139	.	0			c.A343G						PASS	.						162	151	154					13																	60686191		1840	4095	5935	SO:0001583	missense	81624	exon3			GTGGCTTTGGAAA	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.343A>G	chr13.hg19:g.60686191T>C	ENSP00000383178:p.Lys115Glu	136.0	0.0	.		88.0	21.0	.	NM_001042517	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Missense_Mutation	SNP	ENST00000400324.4	hg19	CCDS41898.1	.	.	.	.	.	.	.	.	.	.	T	6.162	0.398114	0.11696	.	.	ENSG00000139734	ENST00000400324;ENST00000400330;ENST00000400327;ENST00000413168;ENST00000377908;ENST00000400320;ENST00000267215;ENST00000453990	D;D;D;D;D	0.89485	-2.52;-2.52;-2.52;-1.93;-2.52	5.82	5.82	0.92795	GTPase-binding/formin homology 3 (1);Diaphanous GTPase-binding (1);	0.059630	0.64402	D	0.000004	D	0.82467	0.5043	N	0.25647	0.755	0.33949	D	0.644161	P;P;P	0.50819	0.704;0.485;0.939	B;B;P	0.45753	0.084;0.266;0.492	T	0.82212	-0.0569	10	0.02654	T	1	.	15.1658	0.72825	0.0:0.0:0.0:1.0	.	104;104;115	C9JL55;C9JDG1;Q9NSV4	.;.;DIAP3_HUMAN	E	115;115;104;104;104;104;115;115	ENSP00000383178:K115E;ENSP00000383184:K115E;ENSP00000367141:K104E;ENSP00000383174:K104E;ENSP00000267215:K115E	ENSP00000267215:K115E	K	-	1	0	DIAPH3	59584192	1.000000	0.71417	0.998000	0.56505	0.220000	0.24768	4.210000	0.58500	2.228000	0.72767	0.533000	0.62120	AAG	.	.	.	none		0.403	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517		C	60686191	T	C	60686191	3	2	61	1	0	0	0	0	1	0	0	0	4522	1850	64	3	3362	3	DIAPH3	13	60686191	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	33022131	60686191	54483687	72	4100											
JUB	84962	hgsc.bcm.edu	37	chr14	23444254	23444254	+	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	gggatgccatccaggcacttGttgcaaacaatgcatcggaa	12	8	11	10	1	0	0	0	0	0	0	2	2	1	2	2	3	4	4	2	3	3	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr14:23444254G>A	ENST00000262713.2	-	5	1674	c.1299C>T	c.(1297-1299)aaC>aaT	p.N433N	AJUBA_ENST00000361265.4_Silent_p.N433N|RP11-298I3.5_ENST00000555074.1_Intron|AJUBA_ENST00000397388.3_Silent_p.N16N	NM_032876.4	NP_116265.1	Q96IF1	AJUBA_HUMAN	ajuba LIM protein	433	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)										CCAGGCACTTGTTGCAAACAA	0.522																																					p.N433N		Atlas-SNP	.											.	.	.	.	0			c.C1299T						PASS	.						149	136	141					14																	23444254		2203	4300	6503	SO:0001819	synonymous_variant	84962	exon5			GCACTTGTTGCAA	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.1299C>T	chr14.hg19:g.23444254G>A		58.0	0.0	.		75.0	23.0	.	NM_032876	A8MX18|D3DS37	Silent	SNP	ENST00000262713.2	hg19	CCDS9581.1																																																																																			.	.	.	none		0.522	AJUBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071685.2			A	23444254	G	A	23444254	2	1	61	1	0	0	0	0	0	0	0	1	7975	1368	48	2		2	JUB	14	23444254	Silent	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10		23444254	83905286	73	4101											
C14orf102	55051	hgsc.bcm.edu	37	chr14	90769186	90769186	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttttgatatcgaaaaggtaCtaaactggctctggcaaaat	14	13	8	6	1	1	1	0	1	1	0	2	2	1	1	0	3	2	3	0	3	8	5			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr14:90769186C>T	ENST00000354366.3	-	6	1521	c.1289G>A	c.(1288-1290)aGt>aAt	p.S430N	NRDE2_ENST00000357904.3_Missense_Mutation_p.S199N	NM_017970.3	NP_060440.2	Q9H7Z3	NRDE2_HUMAN	NRDE-2, necessary for RNA interference, domain containing	430																	CGAAAAGGTACTAAACTGGCT	0.423																																					p.S430N		Atlas-SNP	.											.	.	.	.	0			c.G1289A						PASS	.						69	72	71					14																	90769186		2203	4300	6503	SO:0001583	missense	55051	exon6			AAGGTACTAAACT	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.1289G>A	chr14.hg19:g.90769186C>T	ENSP00000346335:p.Ser430Asn	87.0	0.0	.		97.0	16.0	.	NM_017970	B4DH71|Q4G0A7|Q9NWH6	Missense_Mutation	SNP	ENST00000354366.3	hg19	CCDS9890.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.364312	0.82463	.	.	ENSG00000119720	ENST00000354366;ENST00000357904	T;T	0.35973	1.69;1.28	5.51	5.51	0.81932	Domain of unknown function DUF1740 (1);	0.041947	0.85682	D	0.000000	T	0.55986	0.1955	M	0.69185	2.1	0.53005	D	0.999965	D	0.61697	0.99	D	0.63381	0.914	T	0.52124	-0.8617	10	0.38643	T	0.18	-16.8351	16.4406	0.83900	0.0:0.8691:0.1309:0.0	.	430	Q9H7Z3	CN102_HUMAN	N	430;199	ENSP00000346335:S430N;ENSP00000350579:S199N	ENSP00000346335:S430N	S	-	2	0	C14orf102	89838939	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.785000	0.68998	2.586000	0.87340	0.650000	0.86243	AGT	.	.	.	none		0.423	NRDE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411264.1	NM_017970		T	90769186	C	T	90769186	3	4	61	1	0	0	0	0	1	0	0	0	1737	565	20	2	2241	2	C14orf102	14	90769186	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	67324932	90769186	16580354	74	4102											
THBS1	7057	hgsc.bcm.edu	37	chr15	39886356	39886356	+	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	tggaaagatttcaccgcctaCagatggcgtctcagccacag	11	8	10	12	2	2	2	2	0	1	2	3	3	2	3	3	2	2	0	3	2	2	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr15:39886356C>A	ENST00000260356.5	+	20	3489	c.3324C>A	c.(3322-3324)taC>taA	p.Y1108*	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	1108	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		TCACCGCCTACAGATGGCGTC	0.478																																					p.Y1108X		Atlas-SNP	.											.	THBS1	106	.	0			c.C3324A						PASS	.						63	61	62					15																	39886356		2200	4297	6497	SO:0001587	stop_gained	7057	exon20			CGCCTACAGATGG		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.3324C>A	chr15.hg19:g.39886356C>A	ENSP00000260356:p.Tyr1108*	192.0	0.0	.		194.0	47.0	.	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Nonsense_Mutation	SNP	ENST00000260356.5	hg19	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	C	44	10.984739	0.99499	.	.	ENSG00000137801	ENST00000260356	.	.	.	5.83	4.92	0.64577	.	0.000000	0.32852	N	0.005571	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-38.5548	14.6654	0.68904	0.0:0.9305:0.0:0.0695	.	.	.	.	X	1108	.	ENSP00000260356:Y1108X	Y	+	3	2	THBS1	37673648	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.078000	0.57606	1.468000	0.48064	0.655000	0.94253	TAC	.	.	.	none		0.478	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		A	39886356	C	A	39886356	4	1	61	1	0	0	0	0	0	1	0	0	15865	489	17	4	3398	4	THBS1	15	39886356	Nonsense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10		39886356	62645036	75	4103											
MYO9A	4649	hgsc.bcm.edu	37	chr15	72190908	72190908	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtggagactgaaggccttcAggcaccaattctgtagacca	11	8	11	11	1	2	3	1	1	1	2	2	4	2	3	3	3	0	2	3	3	3	3			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr15:72190908A>G	ENST00000356056.5	-	25	4408	c.3936T>C	c.(3934-3936)ccT>ccC	p.P1312P	MYO9A_ENST00000564571.1_Silent_p.P1312P|MYO9A_ENST00000563542.1_5'UTR|MYO9A_ENST00000566885.1_Silent_p.P932P|MYO9A_ENST00000424560.1_Silent_p.P1312P|MYO9A_ENST00000444904.1_Silent_p.P1293P	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1312	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						GAAGGCCTTCAGGCACCAATT	0.453																																					p.P1312P		Atlas-SNP	.											.	MYO9A	203	.	0			c.T3936C						PASS	.						113	113	113					15																	72190908		2199	4297	6496	SO:0001819	synonymous_variant	4649	exon25			GCCTTCAGGCACC	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.3936T>C	chr15.hg19:g.72190908A>G		133.0	0.0	.		120.0	41.0	.	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Silent	SNP	ENST00000356056.5	hg19	CCDS10239.1																																																																																			.	.	.	none		0.453	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		G	72190908	A	G	72190908	2	3	61	1	0	0	0	0	0	0	0	1	10091	175	7	3		3	MYO9A	15	72190908	Silent	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	32304552	72190908	30340484	76	4104											
CLK3	1198	hgsc.bcm.edu	37	chr15	74912367	74912371	+	Frame_Shift_Del	DEL	ACCAG	ACCAG	-																															cagccatgaccgcctgccctAccagaggaggtaccgggagc																								rs373663118|rs371419854		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	ACCAG	ACCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr15:74912367_74912371delACCAG	ENST00000395066.3	+	3	1075_1079	c.614_618delACCAG	c.(613-618)taccagfs	p.YQ205fs	CLK3_ENST00000348245.3_Frame_Shift_Del_p.YQ57fs|CLK3_ENST00000345005.4_Frame_Shift_Del_p.YQ57fs|CLK3_ENST00000352989.5_Frame_Shift_Del_p.YQ57fs	NM_001130028.1	NP_001123500.1	P49761	CLK3_HUMAN	CDC-like kinase 3	205	Arg-rich.				protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)	cytoplasmic vesicle (GO:0031410)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)|stomach(2)|urinary_tract(1)	15						CGCCTGCCCTACCAGAGGAGGTACC	0.58																																					p.205_206del	Ovarian(133;694 1754 28950 29027 31859)	Atlas-Indel,Pindel	.											.	CLK3	78	.	0			c.613_617del						PASS	.																																			SO:0001589	frameshift_variant	1198	exon3			.	L29220	CCDS10265.1, CCDS45304.1	15q24	2008-05-02			ENSG00000179335	ENSG00000179335		"CDC-like kinases"	2071	protein-coding gene	gene with protein product		602990				7990150, 9856501	Standard	NM_003992		Approved	clk3	uc010uln.2	P49761	OTTHUMG00000141320	ENST00000395066.3:c.614_618delACCAG	chr15.hg19:g.74912367_74912371delACCAG	ENSP00000378505:p.Tyr205fs	155.0	0.0	0		176.0	41.0	0.232955	NM_001130028	D3DW59|Q53Y48|Q9BRS3|Q9BUJ7	Frame_Shift_Del	DEL	ENST00000395066.3	hg19	CCDS45304.1																																																																																			.	.	.	none		0.58	CLK3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390442.3			-	74912371	ACCAG	-	74912367	7	5	61	1	0	1	0	1	0	0	0	0	3540	391	14	0	624	0	CLK3	15	74912367	Frame_Shift_Del	DEL	ACCAG	TCGA-A4-A48D-01A-11D-A25F-10	2721459	74912367	27619025	77	4105											
NUBP2	3483	hgsc.bcm.edu	37	chr16	1837701	1837701	+	IGR	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	tgataaagcagtttgtgtccGacgtggcctggggggagctg	7	10	17	7	2	0	1	0	1	0	0	1	3	1	2	2	4	2	3	2	4	2	2	rs533118487		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr16:1837701G>T	ENST00000215539.3	-	0	2116				NUBP2_ENST00000565134.1_Missense_Mutation_p.D120Y|NUBP2_ENST00000543305.1_5'UTR|NUBP2_ENST00000565987.1_Missense_Mutation_p.D60Y|NUBP2_ENST00000568706.1_5'UTR|NUBP2_ENST00000262302.9_Missense_Mutation_p.D120Y			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						GTTTGTGTCCGACGTGGCCTG	0.662																																					p.D120Y		Atlas-SNP	.											.	NUBP2	25	.	0			c.G358T						PASS	.						80	83	82					16																	1837701		2199	4300	6499	SO:0001628	intergenic_variant	10101	exon4			GTGTCCGACGTGG	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		chr16.hg19:g.1837701G>T		42.0	0.0	.		105.0	33.0	.	NM_012225	B4DZY8|E9PGU3	Missense_Mutation	SNP	ENST00000215539.3	hg19	CCDS10446.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.468399	0.84533	.	.	ENSG00000095906	ENST00000262302	T	0.42131	0.98	4.16	4.16	0.48862	.	0.000000	0.85682	D	0.000000	T	0.70885	0.3275	M	0.91818	3.245	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.79500	-0.1778	10	0.87932	D	0	-5.4419	15.1837	0.72982	0.0:0.0:1.0:0.0	.	120	Q9Y5Y2	NUBP2_HUMAN	Y	120	ENSP00000262302:D120Y	ENSP00000262302:D120Y	D	+	1	0	NUBP2	1777702	1.000000	0.71417	0.736000	0.30914	0.976000	0.68499	6.078000	0.71282	2.167000	0.68274	0.561000	0.74099	GAC	.	.	.	none		0.662	IGFALS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250509.2			T	1837701	G	T	1837701	1	4	61	0	1	0	0	0	0	0	0	0	10723	1058	37	4		4	NUBP2	16	1837701	IGR	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10		1837701	88517052	78	4106											
HMOX2	3163	hgsc.bcm.edu	37	chr16	4557884	4557884	+	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	gaaaactgggaggagcaggtGcagtgccccaaggctgccca	11	4	15	11	0	0	0	0	0	0	0	0	3	0	2	3	4	5	3	3	4	3	0			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr16:4557884G>T	ENST00000570646.1	+	4	980	c.375G>T	c.(373-375)gtG>gtT	p.V125V	HMOX2_ENST00000398595.3_Silent_p.V125V|HMOX2_ENST00000219700.6_Silent_p.V125V|HMOX2_ENST00000406590.2_Silent_p.V125V|HMOX2_ENST00000575120.1_Silent_p.V96V|HMOX2_ENST00000414777.1_Silent_p.V125V|HMOX2_ENST00000458134.3_Silent_p.V125V	NM_002134.3	NP_002125.3	P30519	HMOX2_HUMAN	heme oxygenase (decycling) 2	125					cellular iron ion homeostasis (GO:0006879)|heme catabolic process (GO:0042167)|heme oxidation (GO:0006788)|porphyrin-containing compound metabolic process (GO:0006778)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heme oxygenase (decyclizing) activity (GO:0004392)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	8						AGGAGCAGGTGCAGTGCCCCA	0.582																																					p.V125V		Atlas-SNP	.											.	HMOX2	22	.	0			c.G375T						PASS	.						59	55	57					16																	4557884		2197	4300	6497	SO:0001819	synonymous_variant	3163	exon4			GCAGGTGCAGTGC		CCDS10517.1, CCDS66931.1, CCDS73818.1	16p13.3	2008-02-05			ENSG00000103415	ENSG00000103415	1.14.99.3		5014	protein-coding gene	gene with protein product		141251				1575508	Standard	NM_002134		Approved	HO-2	uc002cwq.4	P30519	OTTHUMG00000129473	ENST00000570646.1:c.375G>T	chr16.hg19:g.4557884G>T		126.0	0.0	.		254.0	39.0	.	NM_001127205	A8MT35|D3DUD5|I3L430|O60605	Silent	SNP	ENST00000570646.1	hg19	CCDS10517.1																																																																																			.	.	.	none		0.582	HMOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251636.2			T	4557884	G	T	4557884	2	4	61	1	0	0	0	0	0	0	0	1	7251	1306	46	4		4	HMOX2	16	4557884	Silent	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	2720183	4557884	85796869	79	4107											
SMG1	23049	hgsc.bcm.edu	37	chr16	18861438	18861438	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcctagggtcatcctcaTctaaaggaatctaagagtga	13	9	10	9	0	4	2	2	1	2	1	5	3	5	3	2	2	1	1	2	2	5	3			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr16:18861438T>C	ENST00000446231.2	-	35	5706	c.5294A>G	c.(5293-5295)gAt>gGt	p.D1765G	SMG1_ENST00000389467.3_Missense_Mutation_p.D1765G			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	1765	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.|Interaction with SMG8 and SMG9.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						GTCATCCTCATCTAAAGGAAT	0.388																																					p.D1765G		Atlas-SNP	.											.	SMG1	401	.	0			c.A5294G						PASS	.						64	62	63					16																	18861438		1955	4154	6109	SO:0001583	missense	23049	exon35			TCCTCATCTAAAG	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.5294A>G	chr16.hg19:g.18861438T>C	ENSP00000402515:p.Asp1765Gly	218.0	0.0	.		298.0	99.0	.	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	hg19	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	T	17.47	3.398251	0.62177	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.68479	-0.33;-0.33	5.83	5.83	0.93111	PIK-related kinase (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000002	T	0.68265	0.2982	N	0.14661	0.345	0.50313	D	0.999861	D;D	0.67145	0.996;0.993	D;D	0.74674	0.981;0.984	T	0.68187	-0.5475	10	0.27785	T	0.31	.	16.1982	0.82046	0.0:0.0:0.0:1.0	.	1625;1765	Q96Q15-2;Q96Q15	.;SMG1_HUMAN	G	1765	ENSP00000402515:D1765G;ENSP00000374118:D1765G	ENSP00000374118:D1765G	D	-	2	0	SMG1	18768939	1.000000	0.71417	1.000000	0.80357	0.715000	0.41141	5.891000	0.69782	2.226000	0.72624	0.533000	0.62120	GAT	.	.	.	none		0.388	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		C	18861438	T	C	18861438	3	2	61	1	0	0	0	0	1	0	0	0	14808	1435	50	3	5807	3	SMG1	16	18861438	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10	14303554	18861438	71493315	80	4108											
ACSM2B	348158	hgsc.bcm.edu	37	chr16	20559488	20559488	+	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	ccctccagcgaggcagttctGtagatgggggaacttgtaac	9	9	13	10	1	1	1	0	0	1	1	2	3	2	2	2	3	3	4	2	3	3	4			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr16:20559488G>A	ENST00000329697.6	-	8	1162	c.994C>T	c.(994-996)Cag>Tag	p.Q332*	ACSM2B_ENST00000565322.1_Nonsense_Mutation_p.Q253*|ACSM2B_ENST00000567001.1_Nonsense_Mutation_p.Q332*|ACSM2B_ENST00000567288.1_5'UTR|ACSM2B_ENST00000565232.1_Nonsense_Mutation_p.Q332*	NM_001105069.1	NP_001098539.1	Q68CK6	ACS2B_HUMAN	acyl-CoA synthetase medium-chain family member 2B	332					fatty acid metabolic process (GO:0006631)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(33)|ovary(1)|prostate(1)|skin(5)	57						AGGCAGTTCTGTAGATGGGGG	0.522																																					p.Q332X		Atlas-SNP	.											.	ACSM2B	121	.	0			c.C994T						PASS	.						118	124	122					16																	20559488		2201	4300	6501	SO:0001587	stop_gained	348158	exon9			AGTTCTGTAGATG	AY160217	CCDS10586.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000066813	ENSG00000066813		"Acyl-CoA synthetase family"	30931	protein-coding gene	gene with protein product	"xenobiotic/medium chain fatty acid:CoA ligase"	614359	"acyl-CoA synthetase medium-chain family member 2"	ACSM2		12616642	Standard	NM_182617		Approved	HXMA, HYST1046	uc002dhk.4	Q68CK6	OTTHUMG00000131555	ENST00000329697.6:c.994C>T	chr16.hg19:g.20559488G>A	ENSP00000327453:p.Gln332*	109.0	0.0	.		146.0	39.0	.	NM_182617	Q86YT1	Nonsense_Mutation	SNP	ENST00000329697.6	hg19	CCDS10586.1	.	.	.	.	.	.	.	.	.	.	G	31	5.065183	0.93898	.	.	ENSG00000066813	ENST00000329697	.	.	.	3.37	-1.99	0.07457	.	1.249910	0.05709	N	0.595506	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.16420	T	0.52	-0.7319	14.1154	0.65149	0.0:0.0:0.2719:0.7281	.	.	.	.	X	332	.	ENSP00000327453:Q332X	Q	-	1	0	ACSM2B	20466989	0.000000	0.05858	0.015000	0.15790	0.297000	0.27493	-0.804000	0.04535	-0.475000	0.06852	-0.407000	0.06327	CAG	.	.	.	none		0.522	ACSM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254417.2	NM_182617		A	20559488	G	A	20559488	4	1	61	1	0	0	0	0	0	1	0	0	184	1386	48	2	767	2	ACSM2B	16	20559488	Nonsense_Mutation	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	1698050	20559488	69795265	81	4109											
LOC100132247	100132247	hgsc.bcm.edu	37	chr16	22545744	22545755	+	In_Frame_Del	DEL	TCCACCCTCAGC	TCCACCCTCAGC	-																															gagcgtcagctcactcccctTccaccctcagctccaccctc																								rs373344256		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	TCCACCCTCAGC	TCCACCCTCAGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr16:22545744_22545755delTCCACCCTCAGC	ENST00000517539.1	+	8	1515_1526	c.1440_1451delTCCACCCTCAGC	c.(1438-1452)cttccaccctcagct>ctt	p.PPSA485del	NPIPB5_ENST00000424340.1_In_Frame_Del_p.PPSA485del|NPIPB5_ENST00000415654.1_3'UTR			A8MRT5	NPIB5_HUMAN	nuclear pore complex interacting protein family, member B5	485	Pro-rich.					integral component of membrane (GO:0016021)											TCACTCCCCTTCCACCCTCAGCTCCACCCTCA	0.571																																					p.480_484del		Atlas-INDEL	.											.	.	.	.	0			c.1439_1450del						PASS	.			15,1619		1,13,803							0			1	14,2538		3,8,1265	no	coding	LOC100132247	NM_001135865.1		4,21,2068	A1A1,A1R,RR		0.5486,0.918,0.6928				29,4157				SO:0001651	inframe_deletion	0	exon7			.		CCDS45443.1	16p12.2	2013-06-11			ENSG00000243716	ENSG00000243716			37233	protein-coding gene	gene with protein product							Standard	NM_001135865		Approved			A8MRT5	OTTHUMG00000163573	ENST00000517539.1:c.1440_1451delTCCACCCTCAGC	chr16.hg19:g.22545744_22545755delTCCACCCTCAGC	ENSP00000430633:p.Pro485_Ala488del	39.0	0.0	0		74.0	20.0	0.27027	NM_001135865	B4DK13	In_Frame_Del	DEL	ENST00000517539.1	hg19	CCDS45443.1																																																																																			.	.	.	weak		0.571	NPIPB5-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374343.2	NM_001135865		-	22545755	TCCACCCTCAGC	-	22545744	7	5	61	1	0	1	0	1	0	0	0	0	8875	1770	62	0	1466	0	LOC100132247	16	22545744	In_Frame_Del	DEL	TCCACCCTCAGC	TCGA-A4-A48D-01A-11D-A25F-10	1986256	22545744	67809009	82	4110											
BANP	54971	hgsc.bcm.edu	37	chr16	88105728	88105728	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcctcggaccccgcggcggcGggcgtggatgggtcgccact	3	6	17	15	7	0	0	0	0	0	0	3	2	1	2	4	6	0	0	4	6	0	0			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr16:88105728G>A	ENST00000393207.1	+	13	1619	c.1398G>A	c.(1396-1398)gcG>gcA	p.A466A	BANP_ENST00000286122.7_Silent_p.A466A|BANP_ENST00000393208.2_Silent_p.A438A|BANP_ENST00000355163.5_Silent_p.A444A|BANP_ENST00000479780.2_Silent_p.A413A|BANP_ENST00000538234.1_Silent_p.A455A|BANP_ENST00000481948.1_3'UTR|BANP_ENST00000355022.4_Silent_p.A416A	NM_001173543.1	NP_001167014.1	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein	466					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)		CCGCGGCGGCGGGCGTGGATG	0.711																																					p.A466A		Atlas-SNP	.											.	BANP	67	.	0			c.G1398A						PASS	.						13	15	14					16																	88105728		2187	4283	6470	SO:0001819	synonymous_variant	54971	exon13			GGCGGCGGGCGTG	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.1398G>A	chr16.hg19:g.88105728G>A		1.0	0.0	.		7.0	6.0	.	NM_001173543	A8MU25|A8MX25|B2RCF7|B4DNJ9|F5GZM0|Q96GJ7|Q9NWY1	Silent	SNP	ENST00000393207.1	hg19	CCDS54054.1																																																																																			.	.	.	none		0.711	BANP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269166.1	NM_017869		A	88105728	G	A	88105728	2	1	61	1	0	0	0	0	0	0	0	1	1310	1103	39	1		1	BANP	16	88105728	Silent	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	65559984	88105728	2249025	83	4111											
C17orf37	84299	hgsc.bcm.edu	37	chr17	37886504	37886504	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atactgctccttcacagcacTggccagctccaggtaggtcg	8	9	10	14	1	1	0	1	0	0	0	4	0	3	0	3	3	4	4	3	3	2	3			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr17:37886504T>C	ENST00000394231.3	-	2	421	c.130A>G	c.(130-132)Agt>Ggt	p.S44G	ERBB2_ENST00000584888.1_3'UTR|MIEN1_ENST00000474210.1_Intron|MIEN1_ENST00000577810.1_Missense_Mutation_p.S44G			Q9BRT3	MIEN1_HUMAN	migration and invasion enhancer 1	44					apoptotic process (GO:0006915)|cell redox homeostasis (GO:0045454)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell migration (GO:0030335)|positive regulation of filopodium assembly (GO:0051491)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	selenium binding (GO:0008430)										TTCACAGCACTGGCCAGCTCC	0.657											OREG0024383	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S44G		Atlas-SNP	.											.	.	.	.	0			c.A130G						PASS	.						28	31	30					17																	37886504		2202	4300	6502	SO:0001583	missense	84299	exon2			CAGCACTGGCCAG	AJ308025	CCDS11344.1	17q12	2011-09-21	2011-09-21	2011-09-21	ENSG00000141741	ENSG00000141741			28230	protein-coding gene	gene with protein product		611802	"chromosome 17 open reading frame 37"	C17orf37		17121940, 12739007, 17503775, 21628459	Standard	NM_032339		Approved	MGC14832, ORB3, XTP4, C35, Rdx12	uc002hsq.3	Q9BRT3	OTTHUMG00000133252	ENST00000394231.3:c.130A>G	chr17.hg19:g.37886504T>C	ENSP00000377778:p.Ser44Gly	59.0	0.0	.	874	64.0	18.0	.	NM_032339		Missense_Mutation	SNP	ENST00000394231.3	hg19	CCDS11344.1	.	.	.	.	.	.	.	.	.	.	T	17.92	3.505978	0.64410	.	.	ENSG00000141741	ENST00000394231	T	0.43688	0.94	4.91	4.91	0.64330	.	0.105490	0.64402	D	0.000008	T	0.34948	0.0915	L	0.39898	1.24	0.38895	D	0.957206	B	0.26935	0.164	B	0.22880	0.042	T	0.27773	-1.0064	10	0.48119	T	0.1	-18.1594	13.6518	0.62314	0.0:0.0:0.0:1.0	.	44	Q9BRT3	MIEN1_HUMAN	G	44	ENSP00000377778:S44G	ENSP00000377778:S44G	S	-	1	0	C17orf37	35140030	1.000000	0.71417	0.993000	0.49108	0.973000	0.67179	5.252000	0.65445	2.069000	0.61940	0.402000	0.26972	AGT	.	.	.	none		0.657	MIEN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257020.3	NM_032339		C	37886504	T	C	37886504	3	2	61	1	0	0	0	0	1	0	0	0	1856	1580	55	3	229	3	C17orf37	17	37886504	Missense_Mutation	SNP	T	TCGA-A4-A48D-01A-11D-A25F-10		37886504	43308706	84	4112											
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2703754	2703754	+	Missense_Mutation	SNP	A	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	ggactgtcatgagaagtatgAtaaacaaataaaatttacac	19	10	7	5	0	1	2	1	2	0	1	1	4	1	3	0	1	2	1	0	1	8	5			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr18:2703754A>C	ENST00000320876.6	+	13	2050	c.1712A>C	c.(1711-1713)gAt>gCt	p.D571A	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Missense_Mutation_p.D571A	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	571					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						GAGAAGTATGATAAACAAATA	0.343																																					p.D571A		Atlas-SNP	.											.	SMCHD1	88	.	0			c.A1712C						PASS	.						74	75	75					18																	2703754		1821	4085	5906	SO:0001583	missense	23347	exon13			AGTATGATAAACA	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.1712A>C	chr18.hg19:g.2703754A>C	ENSP00000326603:p.Asp571Ala	152.0	0.0	.		123.0	28.0	.	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	hg19	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	A	14.58	2.577974	0.45902	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	T;T	0.64260	-0.09;-0.06	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.76385	0.3980	L	0.59436	1.845	0.48288	D	0.999625	D	0.89917	1.0	D	0.83275	0.996	T	0.78949	-0.2002	10	0.87932	D	0	-11.3702	15.6552	0.77129	1.0:0.0:0.0:0.0	.	571	A6NHR9	SMHD1_HUMAN	A	571	ENSP00000326603:D571A;ENSP00000261598:D571A	ENSP00000261598:D571A	D	+	2	0	SMCHD1	2693754	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.503000	0.90509	2.088000	0.63022	0.460000	0.39030	GAT	.	.	.	none		0.343	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			C	2703754	A	C	2703754	3	2	61	1	0	0	0	0	1	0	0	0	14801	333	12	5	1762	5	SMCHD1	18	2703754	Missense_Mutation	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10		2703754	75373494	85	4113											
PIK3C3	5289	hgsc.bcm.edu	37	chr18	39542509	39542509	+	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	ctgacctgcccaggaatgccCaagtggccctcaccatatgg	9	7	10	15	0	1	1	1	1	0	0	1	2	1	2	5	3	2	0	5	3	3	1			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr18:39542509C>A	ENST00000262039.4	+	3	399	c.313C>A	c.(313-315)Caa>Aaa	p.Q105K	PIK3C3_ENST00000398870.3_Missense_Mutation_p.Q42K|PIK3C3_ENST00000586545.1_Missense_Mutation_p.Q105K	NM_002647.2	NP_002638.2	Q8NEB9	PK3C3_HUMAN	phosphatidylinositol 3-kinase, catalytic subunit type 3	105	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.				autophagic vacuole assembly (GO:0000045)|cytokinesis (GO:0000910)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein processing (GO:0016485)|regulation of protein secretion (GO:0050708)|response to leucine (GO:0043201)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)|midbody (GO:0030496)|phagocytic vesicle (GO:0045335)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(25)|ovary(1)|skin(2)|urinary_tract(1)	49						CAGGAATGCCCAAGTGGCCCT	0.433										TSP Lung(28;0.18)																											p.Q105K	NSCLC(37;552 1060 2683 16430 37914)	Atlas-SNP	.											.	PIK3C3	138	.	0			c.C313A						PASS	.						101	91	94					18																	39542509		2203	4300	6503	SO:0001583	missense	5289	exon3			AATGCCCAAGTGG	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.313C>A	chr18.hg19:g.39542509C>A	ENSP00000262039:p.Gln105Lys	129.0	0.0	.		139.0	7.0	.	NM_002647	Q15134	Missense_Mutation	SNP	ENST00000262039.4	hg19	CCDS11920.1	.	.	.	.	.	.	.	.	.	.	C	31	5.104641	0.94245	.	.	ENSG00000078142	ENST00000262039;ENST00000398870	T;T	0.76709	-1.04;-1.04	5.88	5.88	0.94601	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (2);	0.000000	0.85682	D	0.000000	T	0.81079	0.4748	M	0.78285	2.405	0.58432	D	0.999994	B;B	0.29341	0.073;0.242	B;B	0.33196	0.067;0.159	T	0.76887	-0.2793	9	.	.	.	.	20.2314	0.98350	0.0:1.0:0.0:0.0	.	42;105	A8MYT4;Q8NEB9	.;PK3C3_HUMAN	K	105;42	ENSP00000262039:Q105K;ENSP00000381845:Q42K	.	Q	+	1	0	PIK3C3	37796507	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.805000	0.69143	2.789000	0.95967	0.591000	0.81541	CAA	.	.	.	none		0.433	PIK3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255804.1	NM_002647		A	39542509	C	A	39542509	3	1	61	1	0	0	0	0	1	0	0	0	11919	595	21	4	323	4	PIK3C3	18	39542509	Missense_Mutation	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10	36838755	39542509	38534739	86	4114											
MYO1F	4542	hgsc.bcm.edu	37	chr19	8642191	8642191	+	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	cccacccttgaaggacttacCatggtggggggctggtgtct	6	10	14	11	0	1	1	0	1	1	0	1	2	1	2	3	6	1	1	3	6	2	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr19:8642191C>G	ENST00000338257.8	-	1	270	c.3G>C	c.(1-3)atG>atC	p.M1I	MYO1F_ENST00000595046.1_5'UTR	NM_012335.3	NP_036467.2	O00160	MYO1F_HUMAN	myosin IF	1					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						AAGGACTTACCATGGTGGGGG	0.587																																					p.M1I		Atlas-SNP	.											.	MYO1F	128	.	0			c.G3C						PASS	.						44	45	44					19																	8642191		1908	4116	6024	SO:0001630	splice_region_variant	4542	exon1			ACTTACCATGGTG	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.3+1G>C	chr19.hg19:g.8642191C>G		70.0	0.0	.		80.0	24.0	.	NM_012335	Q8WWN7	Missense_Mutation	SNP	ENST00000338257.8	hg19	CCDS42494.1	.	.	.	.	.	.	.	.	.	.	C	10.02	1.237181	0.22711	.	.	ENSG00000142347	ENST00000305795;ENST00000338257	D	0.86164	-2.08	3.64	3.64	0.41730	.	0.629994	0.14357	N	0.324717	T	0.78597	0.4308	.	.	.	0.80722	D	1	B;B;B	0.20261	0.0;0.009;0.043	B;B;B	0.14023	0.001;0.003;0.01	T	0.71590	-0.4547	8	.	.	.	.	11.03	0.47767	0.0:1.0:0.0:0.0	.	1;1;1	B4DVP3;B0I1T1;O00160	.;.;MYO1F_HUMAN	I	46;1	ENSP00000344871:M1I	.	M	-	3	0	MYO1F	8548191	1.000000	0.71417	1.000000	0.80357	0.169000	0.22640	3.368000	0.52357	2.028000	0.59812	0.462000	0.41574	ATG	.	.	.	none		0.587	MYO1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342716.2		Missense_Mutation	G	8642191	C	G	8642191	5	3	61	1	0	0	0	0	0	0	1	0	10080	608	21	4	3405	4	MYO1F	19	8642191	Splice_Site	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10		8642191	50486792	87	4115											
ZNF101	94039	hgsc.bcm.edu	37	chr19	19790040	19790040	+	Frame_Shift_Del	DEL	A	A	-																															agaagggaatgaacacagagAaactttcagccagattcctg																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr19:19790040delA	ENST00000592502.1	+	4	352	c.242delA	c.(241-243)gaafs	p.E81fs	ZNF101_ENST00000415784.2_5'UTR|ZNF101_ENST00000444249.2_3'UTR			Q8IZC7	ZN101_HUMAN	zinc finger protein 101	81	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)	17						GAACACAGAGAAACTTTCAGC	0.413																																					p.E81fs		Atlas-Indel,Pindel	.											.	ZNF101	43	.	0			c.241delG						PASS	.						88	82	84					19																	19790040		2203	4300	6503	SO:0001589	frameshift_variant	94039	exon4			.	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.242delA	chr19.hg19:g.19790040delA	ENSP00000468049:p.Glu81fs	136.0	0.0	0		150.0	39.0	0.26	NM_033204	C9JU83|Q0VDG9	Frame_Shift_Del	DEL	ENST00000592502.1	hg19	CCDS32971.1																																																																																			.	.	.	none		0.413	ZNF101-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460559.1	NM_033204		-	19790040	A	-	19790040	7	5	61	1	0	1	0	1	0	0	0	0	17726	246	9	0	256	0	ZNF101	19	19790040	Frame_Shift_Del	DEL	A	TCGA-A4-A48D-01A-11D-A25F-10	11147849	19790040	39338943	88	4116											
GAPDHS	26330	hgsc.bcm.edu	37	chr19	36029207	36029207	+	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	cttcctgtctgtccctggccAgatttggacgcatcggtcgc	4	12	11	14	3	1	1	0	0	1	1	5	2	3	2	3	3	0	1	3	3	0	2	rs111871741		TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr19:36029207A>C	ENST00000222286.4	+	3	361		c.e3-1		AD000090.2_ENST00000590717.1_RNA|AD000090.2_ENST00000590125.1_RNA|AD000090.2_ENST00000589137.1_RNA	NM_014364.4	NP_055179.1	O14556	G3PT_HUMAN	glyceraldehyde-3-phosphate dehydrogenase, spermatogenic						carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|positive regulation of glycolytic process (GO:0045821)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	cytosol (GO:0005829)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity (GO:0004365)|NAD binding (GO:0051287)|NADP binding (GO:0050661)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)	11	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			GTCCCTGGCCAGATTTGGACG	0.567																																					.		Atlas-SNP	.											.	GAPDHS	34	.	0			c.246-2A>C						PASS	.						59	40	46					19																	36029207		2203	4300	6503	SO:0001630	splice_region_variant	26330	exon3			CTGGCCAGATTTG	AJ005371	CCDS12465.1	19q13.1	2008-02-05		2005-05-06		ENSG00000105679			24864	protein-coding gene	gene with protein product		609169		GAPDS		10714828	Standard	NM_014364		Approved	GAPDH-2, GAPD2	uc002oaf.1	O14556		ENST00000222286.4:c.246-1A>C	chr19.hg19:g.36029207A>C		129.0	0.0	.		147.0	34.0	.	NM_014364	B2RC82|O60823|Q6JTT9|Q9HCU6	Splice_Site	SNP	ENST00000222286.4	hg19	CCDS12465.1	.	.	.	.	.	.	.	.	.	.	A	19.98	3.927280	0.73327	.	.	ENSG00000105679	ENST00000222286	.	.	.	5.3	4.29	0.51040	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.0531	0.36389	0.9122:0.0:0.0878:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GAPDHS	40721047	1.000000	0.71417	0.998000	0.56505	0.963000	0.63663	8.908000	0.92640	0.848000	0.35191	0.533000	0.62120	.	.	.	.	alt		0.567	GAPDHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460423.1	NM_014364	Intron	C	36029207	A	C	36029207	5	2	61	1	0	0	0	0	0	0	1	0	6244	202	7	5	254	5	GAPDHS	19	36029207	Splice_Site	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	16239167	36029207	23099776	89	4117											
C20orf46	55321	hgsc.bcm.edu	37	chr20	1161648	1161648	+	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	gggacgaaggtcctccggcgGtacagctcgcccttgcacag	7	6	14	14	4	0	0	0	0	0	0	3	2	2	1	3	4	3	3	3	4	2	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr20:1161648G>A	ENST00000381894.3	-	2	1286	c.615C>T	c.(613-615)taC>taT	p.Y205Y	TMEM74B_ENST00000481747.1_5'Flank	NM_018354.1	NP_060824.1	Q9NUR3	TM74B_HUMAN	transmembrane protein 74B	205						integral component of membrane (GO:0016021)											TCCTCCGGCGGTACAGCTCGC	0.652																																					p.Y205Y		Atlas-SNP	.											.	.	.	.	0			c.C615T						PASS	.						56	50	52					20																	1161648		2203	4300	6503	SO:0001819	synonymous_variant	55321	exon2			CCGGCGGTACAGC	AK002052	CCDS13011.1	20p13	2011-11-23	2011-11-23	2011-11-23	ENSG00000125895	ENSG00000125895			15893	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 46"	C20orf46			Standard	XM_005260748		Approved	FLJ11190	uc002weq.1	Q9NUR3	OTTHUMG00000031655	ENST00000381894.3:c.615C>T	chr20.hg19:g.1161648G>A		78.0	0.0	.		86.0	18.0	.	NM_018354	D3DVW5	Silent	SNP	ENST00000381894.3	hg19	CCDS13011.1																																																																																			.	.	.	none		0.652	TMEM74B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077496.2	NM_018354		A	1161648	G	A	1161648	2	1	61	1	0	0	0	0	0	0	0	1	2115	1256	44	2		2	C20orf46	20	1161648	Silent	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10		1161648	61863872	90	4118											
MYBL2	4605	hgsc.bcm.edu	37	chr20	42310472	42310472	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtttggacagcaggactggAagttcctggccagccacttc	9	9	12	11	0	0	0	0	0	0	0	2	3	1	3	3	4	2	3	3	4	1	3			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr20:42310472A>G	ENST00000217026.4	+	3	290	c.163A>G	c.(163-165)Aag>Gag	p.K55E	MYBL2_ENST00000396863.4_Intron	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	55	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)			GCAGGACTGGAAGTTCCTGGC	0.602																																					p.K55E		Atlas-SNP	.											.	MYBL2	82	.	0			c.A163G						PASS	.						64	52	56					20																	42310472		2203	4300	6503	SO:0001583	missense	4605	exon3			GACTGGAAGTTCC		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.163A>G	chr20.hg19:g.42310472A>G	ENSP00000217026:p.Lys55Glu	95.0	0.0	.		144.0	41.0	.	NM_002466	B2RBS5|B7Z8D9|F8W6N6|Q53F07	Missense_Mutation	SNP	ENST00000217026.4	hg19	CCDS13322.1	.	.	.	.	.	.	.	.	.	.	A	32	5.164691	0.94727	.	.	ENSG00000101057	ENST00000217026	T	0.15718	2.4	5.61	5.61	0.85477	Transcription regulator HTH, Myb-type, DNA-binding (1);Myb, DNA-binding (1);SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	T	0.33089	0.0851	L	0.46567	1.45	0.80722	D	1	D	0.60160	0.987	D	0.62955	0.909	T	0.01613	-1.1312	10	0.54805	T	0.06	-37.5596	15.101	0.72276	1.0:0.0:0.0:0.0	.	55	P10244	MYBB_HUMAN	E	55	ENSP00000217026:K55E	ENSP00000217026:K55E	K	+	1	0	MYBL2	41743886	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.926000	0.92839	2.281000	0.76405	0.533000	0.62120	AAG	.	.	.	none		0.602	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080408.1	NM_002466		G	42310472	A	G	42310472	3	3	61	1	0	0	0	0	1	0	0	0	10017	247	9	3	173	3	MYBL2	20	42310472	Missense_Mutation	SNP	A	TCGA-A4-A48D-01A-11D-A25F-10	41148824	42310472	20715048	91	4119											
SGSM3	27352	hgsc.bcm.edu	37	chr22	40800334	40800334	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgcggtggcaggcccacCtggagttcacccataaccac	8	6	12	15	1	1	0	1	0	0	0	1	1	1	1	4	5	2	3	4	5	1	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr22:40800334C>T	ENST00000248929.9	+	5	430	c.241C>T	c.(241-243)Ctg>Ttg	p.L81L	SGSM3_ENST00000454798.2_Silent_p.L14L	NM_015705.4	NP_056520.2			small G protein signaling modulator 3											cervix(1)|endometrium(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)	19						GCAGGCCCACCTGGAGTTCAC	0.627																																					p.L81L		Atlas-SNP	.											.	SGSM3	48	.	0			c.C241T						PASS	.						53	49	51					22																	40800334		2203	4300	6503	SO:0001819	synonymous_variant	27352	exon5			GCCCACCTGGAGT	AL022238	CCDS14002.1	22q13.1-q13.2	2013-07-09	2007-08-14	2007-08-14	ENSG00000100359	ENSG00000100359		"Small G protein signaling modulators"	25228	protein-coding gene	gene with protein product	"RUN and SH3 containing 3"	610440	"RUN and TBC1 domain containing 3"	RUTBC3		11214971, 17509819	Standard	XM_005261572		Approved	DJ1042K10.2, RUSC3, RabGAP-5, RABGAP5	uc003ayu.1	Q96HU1	OTTHUMG00000151141	ENST00000248929.9:c.241C>T	chr22.hg19:g.40800334C>T		83.0	0.0	.		90.0	24.0	.	NM_015705		Silent	SNP	ENST00000248929.9	hg19	CCDS14002.1																																																																																			.	.	.	none		0.627	SGSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321504.2	NM_015705		T	40800334	C	T	40800334	2	4	61	1	0	0	0	0	0	0	0	1	14237	680	24	2		2	SGSM3	22	40800334	Silent	SNP	C	TCGA-A4-A48D-01A-11D-A25F-10		40800334	10504232	92	4120											
MKL1	57591	hgsc.bcm.edu	37	chr22	40825749	40825749	+	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	agcttcagctgcttggcctgGagggatggctcagccgaggt	6	9	16	10	1	2	0	2	0	0	0	2	3	2	2	2	5	4	4	2	5	0	2			TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chr22:40825749G>A	ENST00000355630.3	-	7	752	c.162C>T	c.(160-162)ctC>ctT	p.L54L	MKL1_ENST00000402042.1_Silent_p.L54L|MKL1_ENST00000396617.3_Silent_p.L54L|MKL1_ENST00000402630.1_Silent_p.L54L|MKL1_ENST00000407029.1_Silent_p.L54L	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	54	Mediates interaction with SCAI and ACTB. {ECO:0000250}.				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)	p.L54L(1)		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						GCTTGGCCTGGAGGGATGGCT	0.577			T	RBM15	acute megakaryocytic leukemia																																p.L54L		Atlas-SNP	.		Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	MKL1,brain,glioma,0,1	MKL1	69	.	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C162T						PASS	.						89	80	83					22																	40825749		2203	4300	6503	SO:0001819	synonymous_variant	57591	exon7			GGCCTGGAGGGAT	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.162C>T	chr22.hg19:g.40825749G>A		101.0	0.0	.		125.0	31.0	.	NM_020831	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Silent	SNP	ENST00000355630.3	hg19	CCDS14003.1																																																																																			.	.	.	none		0.577	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831		A	40825749	G	A	40825749	2	1	61	1	0	0	0	0	0	0	0	1	9608	1161	41	2		2	MKL1	22	40825749	Silent	SNP	G	TCGA-A4-A48D-01A-11D-A25F-10	25415	40825749	10478817	93	4121											
KDM6A	7403	hgsc.bcm.edu	37	chrX	44922715	44922716	+	Nonsense_Mutation	DNP	GG	GG	TA																															gatctactggaattcctaatGggccaacagctgactcatca																										TCGA-A4-A48D-01A-11D-A25F-10	TCGA-A4-A48D-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5ecc88f7-8391-4168-af11-07a6bf9b3652	b87ba993-24fc-4472-bbbc-d4b8af979060	g.chrX:44922715_44922716GG>TA	ENST00000377967.4	+	16	1617_1618	c.1576_1577GG>TA	c.(1576-1578)GGg>TAg	p.G526*	KDM6A_ENST00000382899.4_Nonsense_Mutation_p.G533*|KDM6A_ENST00000543216.1_Nonsense_Mutation_p.G447*|KDM6A_ENST00000536777.1_Nonsense_Mutation_p.G481*	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	526	Interaction with SUPT6H. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0?(6)|p.0(2)		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						AATTCCTAATGGGCCAACAGCT	0.485			"D, N, F, S"		"renal, oesophageal SCC, MM"																																p.G526W|p.G526E	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	.	8	Whole gene deletion(6)|No detectable mRNA/protein(2)	haematopoietic_and_lymphoid_tissue(2)|oesophagus(2)|breast(2)|pancreas(2)	c.G1576T|c.G1577A						PASS	.																																			SO:0001587	stop_gained	7403	exon16			CCTAATGGGCCAA|CTAATGGGCCAAC	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	Exception_encountered	chrX.hg19:g.44922715_44922716delinsTA	ENSP00000367203:p.Gly526*	20.0	0.0	.		28.0	18.0	.	NM_021140	Q52LL9|Q5JVQ7	Missense_Mutation	SNP	ENST00000377967.4	hg19	CCDS14265.1																																																																																			.	.	.	none		0.485	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140		TA	44922716	GG	TA	44922715	4	4	61	1	0	0	0	0	0	1	0	0	8144	1348	47	4	1638	4	KDM6A	23	44922715	Nonsense_Mutation	DNP	GG	TCGA-A4-A48D-01A-11D-A25F-10		44922715	110347845	94	4122											
KIAA1751	85452	hgsc.bcm.edu	37	chr1	1891408	1891409	+	IGR	DEL	GC	GC	-																															gcccctctgactcaccatcgGcttgaaggtgacaagcactt																										TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr1:1891408_1891409delGC								TMEM52 (40696 upstream) : C1orf222 (28153 downstream)																							CTCACCATCGGCTTGAAGGTGA	0.619											OREG0013001	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.586_586del		Atlas-Indel,Pindel	.											.	KIAA1751	92	.	0			c.1756_1757del						PASS	.																																			SO:0001628	intergenic_variant	85452	exon15			.																													chr1.hg19:g.1891408_1891409delGC		259.0	0.0	0	599	214.0	77.0	0.359813	NM_001080484		Frame_Shift_Del	DEL		hg19																																																																																				.	.	.	none	0	0.619									-	1891409	GC	-	1891408	6	5	62	0	1	1	0	1	0	0	0	0	8263	1203	42	0		0	KIAA1751	1	1891408	IGR	DEL	GC	TCGA-A4-A4ZT-01A-11D-A26P-10		1891408	247359213	1	4123											
UBR4	23352	hgsc.bcm.edu	37	chr1	19524166	19524172	+	Frame_Shift_Del	DEL	ATTACGA	ATTACGA	-																															cactgtgaagcaccttacccAttacgaacagcagtggcatc																								rs200068490		TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	ATTACGA	ATTACGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr1:19524166_19524172delATTACGA	ENST00000375254.3	-	7	912_918	c.885_891delTCGTAAT	c.(883-891)gttcgtaatfs	p.VRN295fs	UBR4_ENST00000375226.2_Frame_Shift_Del_p.VRN295fs|UBR4_ENST00000375267.2_Frame_Shift_Del_p.VRN295fs|UBR4_ENST00000375217.2_Frame_Shift_Del_p.VRN295fs	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	295					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)		CACCTTACCCATTACGAACAGCAGTGG	0.464																																					p.296_298del		Atlas-Indel,Pindel	.											.	UBR4	415	.	0			c.886_892del						PASS	.																																			SO:0001589	frameshift_variant	23352	exon7			.	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.885_891delTCGTAAT	chr1.hg19:g.19524166_19524172delATTACGA	ENSP00000364403:p.Val295fs	100.0	0.0	0		77.0	28.0	0.363636	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Frame_Shift_Del	DEL	ENST00000375254.3	hg19	CCDS189.1																																																																																			.	.	.	none		0.464	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		-	19524172	ATTACGA	-	19524166	7	5	62	1	0	1	0	1	0	0	0	0	16916	214	8	0	15060	0	UBR4	1	19524166	Frame_Shift_Del	DEL	ATTACGA	TCGA-A4-A4ZT-01A-11D-A26P-10	17632758	19524166	229726455	2	4124											
CSMD2	114784	hgsc.bcm.edu	37	chr1	34052133	34052133	+	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	tcgggggtggtccttcaaacTgcaggtaggttccaagtttg	7	12	14	8	1	1	0	1	0	0	0	4	0	3	0	2	5	2	4	2	5	3	4			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr1:34052133T>A	ENST00000373381.4	-	46	7198	c.7022A>T	c.(7021-7023)cAg>cTg	p.Q2341L		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2343	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)				TCCTTCAAACTGCAGGTAGGT	0.493																																					p.Q2343L		Atlas-SNP	.											CSMD2_ENST00000373381,NS,carcinoma,0,2	CSMD2	946	.	0			c.A7028T						PASS	.						105	96	99					1																	34052133		2203	4300	6503	SO:0001583	missense	114784	exon47			TCAAACTGCAGGT	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.7022A>T	chr1.hg19:g.34052133T>A	ENSP00000362479:p.Gln2341Leu	180.0	0.0	.		230.0	98.0	.	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	hg19		.	.	.	.	.	.	.	.	.	.	T	18.56	3.650854	0.67472	.	.	ENSG00000121904	ENST00000373381	T	0.66815	-0.23	5.83	5.83	0.93111	Complement control module (2);Sushi/SCR/CCP (3);	0.061993	0.64402	D	0.000004	T	0.65565	0.2703	M	0.64260	1.97	0.80722	D	1	B;B	0.11235	0.004;0.004	B;B	0.24006	0.05;0.029	T	0.60682	-0.7215	10	0.27082	T	0.32	.	15.3817	0.74661	0.0:0.0:0.0:1.0	.	2343;2341	Q7Z408;E7EUA6	CSMD2_HUMAN;.	L	2341	ENSP00000362479:Q2341L	ENSP00000241312:Q2343L	Q	-	2	0	CSMD2	33824720	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.018000	0.70811	2.227000	0.72691	0.528000	0.53228	CAG	.	.	.	none		0.493	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		A	34052133	T	A	34052133	3	1	62	1	0	0	0	0	1	0	0	0	3947	1580	55	5	3527	5	CSMD2	1	34052133	Missense_Mutation	SNP	T	TCGA-A4-A4ZT-01A-11D-A26P-10	14527967	34052133	215198488	3	4125											
KIAA0754	643314	hgsc.bcm.edu	37	chr1	39878312	39878312	+	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	tgagctgaatgtggcatcatCagagggaggggagatggaaa	13	7	17	4	0	2	4	2	2	0	2	2	7	2	6	0	5	1	2	0	5	2	0			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr1:39878312C>T	ENST00000530275.1	+	1	2162	c.1967C>T	c.(1966-1968)tCa>tTa	p.S656L	MACF1_ENST00000289893.4_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000361689.2_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	656										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)			GTGGCATCATCAGAGGGAGGG	0.428																																					p.S792L		Atlas-SNP	.											.	KIAA0754	93	.	0			c.C2375T						PASS	.						85	83	84					1																	39878312		1910	4132	6042	SO:0001583	missense	643314	exon1			CATCATCAGAGGG			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.1967C>T	chr1.hg19:g.39878312C>T	ENSP00000431179:p.Ser656Leu	45.0	0.0	.		57.0	17.0	.	NM_015038	E9PMC2|Q6ZSB2	Missense_Mutation	SNP	ENST00000530275.1	hg19		.	.	.	.	.	.	.	.	.	.	C	10.93	1.491329	0.26774	.	.	ENSG00000255103	ENST00000530275	D	0.86230	-2.09	5.48	-0.479	0.12089	.	.	.	.	.	T	0.74489	0.3723	N	0.24115	0.695	0.09310	N	1	B	0.11235	0.004	B	0.11329	0.006	T	0.63047	-0.6724	9	0.87932	D	0	.	2.2667	0.04080	0.1278:0.5256:0.1262:0.2204	.	656	O94854	K0754_HUMAN	L	656	ENSP00000431179:S656L	ENSP00000431179:S656L	S	+	2	0	RP4-562N20.1	39650899	0.000000	0.05858	0.032000	0.17829	0.874000	0.50279	-0.517000	0.06275	0.188000	0.20168	0.655000	0.94253	TCA	.	.	.	none		0.428	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038		T	39878312	C	T	39878312	3	4	62	1	0	0	0	0	1	0	0	0	8199	838	29	2	2377	2	KIAA0754	1	39878312	Missense_Mutation	SNP	C	TCGA-A4-A4ZT-01A-11D-A26P-10	5826179	39878312	209372309	4	4126											
FNDC7	163479	hgsc.bcm.edu	37	chr1	109265207	109265229	+	Splice_Site	DEL	GAAAACTGGTATGTAAACAAGAG	GAAAACTGGTATGTAAACAAGAG	-																															tcatcttcagcaatgaccctGaaaactggtatgtaaacaag																										TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	GAAAACTGGTATGTAAACAAGAG	GAAAACTGGTATGTAAACAAGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr1:109265207_109265229delGAAAACTGGTATGTAAACAAGAG	ENST00000370017.3	+	5	1126_1133	c.849_856delGAAAACTGGTATGTAAACAAGAG	c.(847-858)ctgaaaactggt>ctgt	p.KTG284fs	FNDC7_ENST00000271311.2_Splice_Site_p.KTG285fs	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	284	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)		CAATGACCCTGAAAACTGGTATGTAAACAAGAGTGAGACTGCT	0.439																																					p.283_286del		Pindel	.											.	FNDC7	113	.	0			c.848_856del						PASS	.																																			SO:0001630	splice_region_variant	163479	exon5			.		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.856+1GAAAACTGGTATGTAAACAAGAG>-	chr1.hg19:g.109265207_109265229delGAAAACTGGTATGTAAACAAGAG		72.0	0.0	.		54.0	13.0	0.241	NM_001144937	A1L468|E9PAZ5|Q6PF16|Q8NA51	In_Frame_Del	DEL	ENST00000370017.3	hg19	CCDS44185.1																																																																																			.	.	.	none		0.439	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532	Frame_Shift_Del	-	109265229	GAAAACTGGTATGTAAACAAGAG	-	109265207	8	5	62	1	0	1	0	1	0	0	1	0	5980	1277	45	0	867	0	FNDC7	1	109265207	Splice_Site	DEL	GAAAACTGGTATGTAAACAAGAG	TCGA-A4-A4ZT-01A-11D-A26P-10	69386895	109265207	139985414	5	4127											
STXBP3	6814	hgsc.bcm.edu	37	chr1	109338856	109338856	+	Splice_Site	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	aatattttattttcattaagGacctggcacttggaactgat	12	16	7	6	0	1	1	1	1	0	0	1	3	1	3	1	3	1	1	1	3	5	7			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr1:109338856G>C	ENST00000370008.3	+	14	1161	c.1111G>C	c.(1111-1113)Gac>Cac	p.D371H		NM_007269.2	NP_009200.2	O00186	STXB3_HUMAN	syntaxin binding protein 3	371					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)		TTTCATTAAGGACCTGGCACT	0.358																																					p.D371H		Atlas-SNP	.											.	STXBP3	44	.	0			c.G1111C						PASS	.						54	54	54					1																	109338856		2203	4300	6503	SO:0001630	splice_region_variant	6814	exon14			ATTAAGGACCTGG	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.1111-1G>C	chr1.hg19:g.109338856G>C		156.0	0.0	.		205.0	53.0	.	NM_007269	A8K269|A8K5K7|Q53FW1|Q86YJ3|Q9UPD7	Missense_Mutation	SNP	ENST00000370008.3	hg19	CCDS790.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.298070	0.81025	.	.	ENSG00000116266	ENST00000370008	T	0.79247	-1.25	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	D	0.89114	0.6623	M	0.87547	2.89	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88884	0.3341	9	.	.	.	-7.6976	20.1392	0.98050	0.0:0.0:1.0:0.0	.	371	O00186	STXB3_HUMAN	H	371	ENSP00000359025:D371H	.	D	+	1	0	STXBP3	109140379	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	8.716000	0.91420	2.751000	0.94390	0.591000	0.81541	GAC	.	.	.	none		0.358	STXBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030591.1	NM_007269	Missense_Mutation	C	109338856	G	C	109338856	5	2	62	1	0	0	0	0	0	0	1	0	15366	1188	41	4	1165	4	STXBP3	1	109338856	Splice_Site	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10	73649	109338856	139911765	6	4128											
ATP6V1B1	525	hgsc.bcm.edu	37	chr2	71188132	71188132	+	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	accatgacgacaacttcgccAtcgtctttgcagccatgggg	9	9	10	13	3	1	1	0	1	1	0	3	2	1	1	3	2	3	1	3	2	1	2			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr2:71188132A>T	ENST00000234396.4	+	7	740	c.667A>T	c.(667-669)Atc>Ttc	p.I223F	ATP6V1B1_ENST00000412314.1_Missense_Mutation_p.I223F|AC007040.11_ENST00000606025.1_Intron	NM_001692.3	NP_001683.2	P15313	VATB1_HUMAN	ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B1	223					ATP hydrolysis coupled proton transport (GO:0015991)|ATP metabolic process (GO:0046034)|calcium ion homeostasis (GO:0055074)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|pH reduction (GO:0045851)|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 plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	ATP binding (GO:0005524)|hydrogen ion transmembrane transporter activity (GO:0015078)|hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances (GO:0016820)			endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(1)	19						CAACTTCGCCATCGTCTTTGC	0.587																																					p.I223F		Atlas-SNP	.											.	ATP6V1B1	66	.	0			c.A667T						PASS	.						94	63	74					2																	71188132		2203	4300	6503	SO:0001583	missense	525	exon7			TTCGCCATCGTCT	AF107466	CCDS1912.1	2p13	2010-04-21	2008-07-31	2002-05-10	ENSG00000116039	ENSG00000116039	3.6.3.14	"ATPases / V-type"	853	protein-coding gene	gene with protein product	"Renal tubular acidosis with deafness"	192132	"vacuolar proton pump 3"	VPP3, ATP6B1		9916796, 2527371	Standard	XM_005264368		Approved	VATB, RTA1B, Vma2	uc002shj.3	P15313	OTTHUMG00000129711	ENST00000234396.4:c.667A>T	chr2.hg19:g.71188132A>T	ENSP00000234396:p.Ile223Phe	219.0	1.0	.		279.0	158.0	.	NM_001692	Q53FY0|Q6P4H6	Missense_Mutation	SNP	ENST00000234396.4	hg19	CCDS1912.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.541872	0.85917	.	.	ENSG00000116039	ENST00000234396;ENST00000483246;ENST00000412314;ENST00000454446	D;D;D	0.81908	-1.55;-1.55;-1.55	5.04	5.04	0.67666	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain (1);	0.000000	0.64402	D	0.000011	D	0.91036	0.7180	M	0.84585	2.705	0.80722	D	1	D;D;D	0.67145	0.996;0.979;0.979	D;D;D	0.74674	0.984;0.93;0.93	D	0.92308	0.5855	10	0.87932	D	0	-35.7839	12.7736	0.57436	1.0:0.0:0.0:0.0	.	198;223;223	B4DWH7;C9JL73;P15313	.;.;VATB1_HUMAN	F	223;198;223;240	ENSP00000234396:I223F;ENSP00000388353:I223F;ENSP00000408361:I240F	ENSP00000234396:I223F	I	+	1	0	ATP6V1B1	71041640	1.000000	0.71417	0.999000	0.59377	0.683000	0.39861	7.140000	0.77322	2.133000	0.65898	0.533000	0.62120	ATC	.	.	.	none		0.587	ATP6V1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251920.2	NM_001692		T	71188132	A	T	71188132	3	4	62	1	0	0	0	0	1	0	0	0	1178	217	8	5	693	5	ATP6V1B1	2	71188132	Missense_Mutation	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10		71188132	172011241	7	4129											
CCDC74A	90557	hgsc.bcm.edu	37	chr2	132290624	132290624	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttccccaaggtctccaccaAgagcctctccaagaaatggt	11	9	7	14	0	2	2	0	0	2	2	5	2	3	2	6	2	1	0	6	2	4	1			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr2:132290624A>G	ENST00000295171.6	+	7	1127	c.989A>G	c.(988-990)aAg>aGg	p.K330R	CCDC74A_ENST00000409856.3_Missense_Mutation_p.K264R|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	330										endometrium(4)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						GTCTCCACCAAGAGCCTCTCC	0.637																																					p.K330R		Atlas-SNP	.											.	CCDC74A	44	.	0			c.A989G						PASS	.						55	62	60					2																	132290624		2202	4280	6482	SO:0001583	missense	90557	exon7			CCACCAAGAGCCT		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.989A>G	chr2.hg19:g.132290624A>G	ENSP00000295171:p.Lys330Arg	456.0	0.0	.		473.0	177.0	.	NM_138770	Q6P4I5	Missense_Mutation	SNP	ENST00000295171.6	hg19	CCDS2167.1	.	.	.	.	.	.	.	.	.	.	.	9.783	1.175737	0.21704	.	.	ENSG00000163040	ENST00000295171;ENST00000409856	T;T	0.32988	1.43;1.43	3.07	3.07	0.35406	.	0.000000	0.34603	U	0.003821	T	0.46229	0.1382	L	0.56769	1.78	0.32221	N	0.57519	D;P	0.67145	0.996;0.927	D;D	0.75484	0.986;0.953	T	0.55379	-0.8150	10	0.66056	D	0.02	.	7.967	0.30104	1.0:0.0:0.0:0.0	.	264;330	Q96AQ1-2;Q96AQ1	.;CC74A_HUMAN	R	330;264	ENSP00000295171:K330R;ENSP00000387009:K264R	ENSP00000295171:K330R	K	+	2	0	CCDC74A	132007094	0.982000	0.34865	0.108000	0.21378	0.014000	0.08584	1.298000	0.33412	1.179000	0.42884	0.352000	0.21897	AAG	.	.	.	none		0.637	CCDC74A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254570.2	NM_138770		G	132290624	A	G	132290624	3	3	62	1	0	0	0	0	1	0	0	0	2849	72	3	3	1015	3	CCDC74A	2	132290624	Missense_Mutation	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10	61102492	132290624	110908749	8	4130											
PTPRN	5798	hgsc.bcm.edu	37	chr2	220161482	220161482	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccactcacaatggggctggCgttgatgtaatcgctccgag	8	9	13	11	3	1	1	1	1	0	0	3	2	2	1	2	3	0	4	2	3	2	2			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr2:220161482C>T	ENST00000295718.2	-	16	2539	c.2299G>A	c.(2299-2301)Gcc>Acc	p.A767T	PTPRN_ENST00000497977.1_5'Flank|PTPRN_ENST00000423636.2_Missense_Mutation_p.A677T|AC114803.3_ENST00000417355.1_RNA|PTPRN_ENST00000409251.3_Missense_Mutation_p.A738T|MIR153-1_ENST00000384914.1_RNA	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	767	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		ATGGGGCTGGCGTTGATGTAA	0.607																																					p.A767T		Atlas-SNP	.											.	PTPRN	138	.	0			c.G2299A						PASS	.						116	99	104					2																	220161482		2203	4300	6503	SO:0001583	missense	5798	exon16			GGCTGGCGTTGAT		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.2299G>A	chr2.hg19:g.220161482C>T	ENSP00000295718:p.Ala767Thr	125.0	0.0	.		199.0	46.0	.	NM_002846	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Missense_Mutation	SNP	ENST00000295718.2	hg19	CCDS2440.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.590157	0.86851	.	.	ENSG00000054356	ENST00000409251;ENST00000295718;ENST00000539342;ENST00000537666	T;T;T	0.59364	0.27;0.27;0.27	4.24	4.24	0.50183	Protein-tyrosine phosphatase, receptor/non-receptor type (4);	0.151418	0.41938	D	0.000789	D	0.85221	0.5647	H	0.98594	4.275	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.956;0.998	D	0.91588	0.5284	10	0.87932	D	0	.	16.4513	0.83991	0.0:1.0:0.0:0.0	.	738;767	Q6NSL1;Q16849	.;PTPRN_HUMAN	T	738;767;738;677	ENSP00000386638:A738T;ENSP00000295718:A767T;ENSP00000444244:A677T	ENSP00000295718:A767T	A	-	1	0	PTPRN	219869726	1.000000	0.71417	0.997000	0.53966	0.982000	0.71751	7.198000	0.77823	2.187000	0.69744	0.563000	0.77884	GCC	.	.	.	none		0.607	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2			T	220161482	C	T	220161482	3	4	62	1	0	0	0	0	1	0	0	0	12820	768	27	1	672	1	PTPRN	2	220161482	Missense_Mutation	SNP	C	TCGA-A4-A4ZT-01A-11D-A26P-10	87870858	220161482	23037891	9	4131											
DOCK10	55619	hgsc.bcm.edu	37	chr2	225688235	225688235	+	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	taccttgagaaatctggcaaCgctgtggtttgcccttcttg	7	14	10	10	1	2	1	0	1	2	1	2	2	2	1	2	2	3	3	2	2	3	5	rs371861682		TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr2:225688235C>T	ENST00000258390.7	-	28	3233	c.3166G>A	c.(3166-3168)Gtt>Att	p.V1056I	DOCK10_ENST00000409592.3_Missense_Mutation_p.V1050I	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1056					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.V1054F(1)		NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		AATCTGGCAACGCTGTGGTTT	0.413																																					p.V1056I		Atlas-SNP	.											DOCK10,NS,carcinoma,0,1	DOCK10	308	.	1	Substitution - Missense(1)	breast(1)	c.G3166A						PASS	.	C	ILE/VAL	0,3770		0,0,1885	191	181	184		3166	4.2	0.8	2		184	2,8232		0,2,4115	no	missense	DOCK10	NM_014689.2	29	0,2,6000	TT,TC,CC		0.0243,0.0,0.0167	benign	1056/2187	225688235	2,12002	1885	4117	6002	SO:0001583	missense	55619	exon28			TGGCAACGCTGTG	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.3166G>A	chr2.hg19:g.225688235C>T	ENSP00000258390:p.Val1056Ile	191.0	0.0	.		224.0	121.0	.	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	hg19	CCDS46528.1	.	.	.	.	.	.	.	.	.	.	C	13.62	2.292507	0.40594	0.0	2.43E-4	ENSG00000135905	ENST00000409592;ENST00000258390	T;T	0.67171	3.85;-0.25	6.0	4.2	0.49525	.	0.302824	0.35349	N	0.003275	T	0.55146	0.1902	L	0.38838	1.175	0.21933	N	0.999469	B;B	0.12013	0.005;0.001	B;B	0.08055	0.002;0.003	T	0.49542	-0.8929	10	0.49607	T	0.09	.	10.9896	0.47541	0.0:0.7834:0.0:0.2166	.	1056;1050	Q96BY6;B3FL70	DOC10_HUMAN;.	I	1050;1056	ENSP00000386694:V1050I;ENSP00000258390:V1056I	ENSP00000258390:V1056I	V	-	1	0	DOCK10	225396479	0.057000	0.20700	0.828000	0.32881	0.970000	0.65996	0.541000	0.23207	0.862000	0.35528	0.643000	0.83706	GTT	.	.	.	weak		0.413	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			T	225688235	C	T	225688235	3	4	62	1	0	0	0	0	1	0	0	0	4687	536	19	1	3510	1	DOCK10	2	225688235	Missense_Mutation	SNP	C	TCGA-A4-A4ZT-01A-11D-A26P-10	5526753	225688235	17511138	10	4132											
SP140L	93349	hgsc.bcm.edu	37	chr2	231264856	231264856	+	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	ttctagatgagaaacttggaTgagtgtgaggtgtgccggga	10	11	16	4	1	1	4	0	3	1	2	1	7	1	6	1	3	2	0	1	3	2	3			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr2:231264856T>A	ENST00000415673.2	+	15	1298	c.1212T>A	c.(1210-1212)gaT>gaA	p.D404E	SP140L_ENST00000444636.1_Missense_Mutation_p.D404E|SP140L_ENST00000243810.6_Missense_Mutation_p.D404E|SP140L_ENST00000396563.4_Missense_Mutation_p.D369E	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	404						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						GAAACTTGGATGAGTGTGAGG	0.512																																					p.D404E		Atlas-SNP	.											.	SP140L	68	.	0			c.T1212A						PASS	.						181	183	182					2																	231264856		2043	4208	6251	SO:0001583	missense	93349	exon15			CTTGGATGAGTGT	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.1212T>A	chr2.hg19:g.231264856T>A	ENSP00000397911:p.Asp404Glu	237.0	0.0	.		389.0	213.0	.	NM_138402	Q2M375|Q4ZG65|Q9BSP3	Missense_Mutation	SNP	ENST00000415673.2	hg19	CCDS46538.1	.	.	.	.	.	.	.	.	.	.	T	15.61	2.883793	0.51908	.	.	ENSG00000185404	ENST00000444636;ENST00000415673;ENST00000243810;ENST00000396563	D;D;D;D	0.87571	-2.27;-2.27;-2.27;-2.27	3.5	-2.37	0.06643	.	.	.	.	.	T	0.81235	0.4780	L	0.52126	1.63	0.09310	N	1	P;P	0.45044	0.849;0.663	B;P	0.45794	0.382;0.493	T	0.71507	-0.4572	9	0.72032	D	0.01	.	0.2987	0.00269	0.1938:0.243:0.1988:0.3644	.	369;404	Q9H930-2;Q9H930-4	.;.	E	404;404;404;369	ENSP00000395195:D404E;ENSP00000397911:D404E;ENSP00000243810:D404E;ENSP00000379811:D369E	ENSP00000243810:D404E	D	+	3	2	SP140L	230973100	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-1.650000	0.01991	-0.178000	0.10672	-0.415000	0.06103	GAT	.	.	.	none		0.512	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402		A	231264856	T	A	231264856	3	1	62	1	0	0	0	0	1	0	0	0	14976	1461	51	5	1270	5	SP140L	2	231264856	Missense_Mutation	SNP	T	TCGA-A4-A4ZT-01A-11D-A26P-10	5576621	231264856	11934517	11	4133											
OXTR	5021	hgsc.bcm.edu	37	chr3	8809352	8809352	+	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	gccacctcgcgcagagagaaGatgtgcacctgcggcgcgct	8	5	14	14	5	0	3	0	0	0	3	1	4	0	3	3	1	2	3	3	1	1	0			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr3:8809352G>T	ENST00000316793.3	-	3	1146	c.522C>A	c.(520-522)atC>atA	p.I174I	CAV3_ENST00000472766.1_Intron	NM_000916.3	NP_000907.2	P30559	OXYR_HUMAN	oxytocin receptor	174					cell surface receptor signaling pathway (GO:0007166)|digestive tract development (GO:0048565)|eating behavior (GO:0042755)|ERK1 and ERK2 cascade (GO:0070371)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|heart development (GO:0007507)|lactation (GO:0007595)|maternal behavior (GO:0042711)|maternal process involved in parturition (GO:0060137)|memory (GO:0007613)|muscle contraction (GO:0006936)|negative regulation of gastric acid secretion (GO:0060455)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of norepinephrine secretion (GO:0010701)|positive regulation of penile erection (GO:0060406)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of uterine smooth muscle contraction (GO:0070474)|response to amphetamine (GO:0001975)|response to anoxia (GO:0034059)|response to cocaine (GO:0042220)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to peptide hormone (GO:0043434)|response to progesterone (GO:0032570)|sleep (GO:0030431)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|suckling behavior (GO:0001967)|telencephalon development (GO:0021537)	apical plasma membrane (GO:0016324)|cell-cell adherens junction (GO:0005913)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	oxytocin receptor activity (GO:0004990)|peptide hormone binding (GO:0017046)|vasopressin receptor activity (GO:0005000)			NS(1)|endometrium(2)|large_intestine(4)|lung(5)|urinary_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(96;0.15)	Carbetocin(DB01282)|Oxytocin(DB00107)	GCAGAGAGAAGATGTGCACCT	0.692																																					p.I174I		Atlas-SNP	.											.	OXTR	31	.	0			c.C522A						PASS	.						34	39	37					3																	8809352		2203	4300	6503	SO:0001819	synonymous_variant	5021	exon3			AGAGAAGATGTGC		CCDS2570.1	3p25	2012-08-08			ENSG00000180914	ENSG00000180914		"GPCR / Class A : Vasopressin and oxytocin receptors"	8529	protein-coding gene	gene with protein product		167055				1313946	Standard	NM_000916		Approved		uc003brc.3	P30559	OTTHUMG00000090537	ENST00000316793.3:c.522C>A	chr3.hg19:g.8809352G>T		86.0	0.0	.		187.0	101.0	.	NM_000916	Q15071	Silent	SNP	ENST00000316793.3	hg19	CCDS2570.1																																																																																			.	.	.	none		0.692	OXTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207061.2			T	8809352	G	T	8809352	2	4	62	1	0	0	0	0	0	0	0	1	11345	932	33	4		4	OXTR	3	8809352	Silent	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10		8809352	189213078	12	4134											
WDR1	9948	hgsc.bcm.edu	37	chr4	10099338	10099338	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagtaagttcacttacgccAattgtgaacttgaacttgaa	15	12	7	7	1	1	3	1	3	0	0	1	3	1	3	1	0	3	2	1	0	7	6			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr4:10099338A>G	ENST00000499869.2	-	5	748	c.555T>C	c.(553-555)atT>atC	p.I185I	WDR1_ENST00000502702.1_Intron|WDR1_ENST00000382452.2_Silent_p.I185I|WDR1_ENST00000382451.2_Intron			O75083	WDR1_HUMAN	WD repeat domain 1	185			I -> V (in dbSNP:rs13441). {ECO:0000269|PubMed:15489334}.		blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|sensory perception of sound (GO:0007605)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)				endometrium(3)|lung(5)|ovary(2)|pancreas(1)|urinary_tract(1)	12				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)		CACTTACGCCAATTGTGAACT	0.507																																					p.I185I		Atlas-SNP	.											.	WDR1	93	.	0			c.T555C						PASS	.						62	66	65					4																	10099338		1963	4144	6107	SO:0001819	synonymous_variant	9948	exon5			TACGCCAATTGTG	AF020260	CCDS54739.1, CCDS54740.1	4p16.1	2013-01-09			ENSG00000071127	ENSG00000071127		"WD repeat domain containing"	12754	protein-coding gene	gene with protein product		604734				10036186	Standard	NM_017491		Approved		uc021xlv.1	O75083	OTTHUMG00000160253	ENST00000499869.2:c.555T>C	chr4.hg19:g.10099338A>G		150.0	0.0	.		124.0	48.0	.	NM_017491	A8K6E9|A8MPU4|O75313|Q8N6E5|Q9UG05|Q9UG78|Q9UQE0	Silent	SNP	ENST00000499869.2	hg19	CCDS54740.1																																																																																			.	.	.	none		0.507	WDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359877.1			G	10099338	A	G	10099338	2	3	62	1	0	0	0	0	0	0	0	1	17284	126	5	3		3	WDR1	4	10099338	Silent	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10		10099338	181054938	13	4135											
UBA6	55236	hgsc.bcm.edu	37	chr4	68536260	68536261	+	Frame_Shift_Ins	INS	-	-	T																															aaacttcaaattcatcaccgINSaaatcacaaaataaccttga																								rs140398587		TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr4:68536260_68536261insT	ENST00000322244.5	-	8	655_656	c.596_597insA	c.(595-597)ttcfs	p.F199fs	UBA6_ENST00000420827.2_Frame_Shift_Ins_p.F199fs	NM_018227.5	NP_060697.4	A0AVT1	UBA6_HUMAN	ubiquitin-like modifier activating enzyme 6	199					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						ATTCATCACCGAAATCACAAAA	0.267																																					p.F199fs		Atlas-INDEL	.											UBA6,NS,carcinoma,0,1	UBA6	98	.	0			c.597_598insA						PASS	.																																			SO:0001589	frameshift_variant	55236	exon8			.	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.596_597insA	chr4.hg19:g.68536260_68536261insT	ENSP00000313454:p.Phe199fs	106.0	0.0	0		96.0	23.0	0.239583	NM_018227	A6N8M7|B2RAV3|Q4W5K0|Q6UV21|Q86T78|Q86TC7|Q8N5T3|Q8N9E4|Q9H3T7|Q9NVC9	Frame_Shift_Ins	INS	ENST00000322244.5	hg19	CCDS3516.1																																																																																			.	.	.	none		0.267	UBA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251429.2	NM_018227		T	68536261	-	T	68536260	7	5	62	1	0	1	1	0	0	0	0	0	16844	1049	37	0	2665	0	UBA6	4	68536260	Frame_Shift_Ins	INS	-	TCGA-A4-A4ZT-01A-11D-A26P-10	58436922	68536260	122618016	14	4136	44	2									
UBA6	55236	hgsc.bcm.edu	37	chr4	68536261	68536262	+	Frame_Shift_Ins	INS	-	-	TT																															aacttcaaattcatcaccgaINSaatcacaaaataaccttgac																										TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr4:68536261_68536262insTT	ENST00000322244.5	-	8	654_655	c.595_596insAA	c.(595-597)ttcfs	p.F199fs	UBA6_ENST00000420827.2_Frame_Shift_Ins_p.F199fs	NM_018227.5	NP_060697.4	A0AVT1	UBA6_HUMAN	ubiquitin-like modifier activating enzyme 6	199					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						TTCATCACCGAAATCACAAAAT	0.272																																					p.F199_G200delinsX		Atlas-INDEL	.											.	UBA6	98	.	0			c.596_597insAA						PASS	.																																			SO:0001589	frameshift_variant	55236	exon8			.	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.595_596insAA	chr4.hg19:g.68536261_68536262insTT	ENSP00000313454:p.Phe199fs	104.0	0.0	0		96.0	23.0	0.239583	NM_018227	A6N8M7|B2RAV3|Q4W5K0|Q6UV21|Q86T78|Q86TC7|Q8N5T3|Q8N9E4|Q9H3T7|Q9NVC9	Frame_Shift_Ins	INS	ENST00000322244.5	hg19	CCDS3516.1																																																																																			.	.	.	none		0.272	UBA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251429.2	NM_018227		TT	68536262	-	TT	68536261	7	5	62	1	0	1	1	0	0	0	0	0	16844	246	9	0	2666	0	UBA6	4	68536261	Frame_Shift_Ins	INS	-	TCGA-A4-A4ZT-01A-11D-A26P-10	1	68536261	122618015	15	4137	44	2									
ANK2	287	hgsc.bcm.edu	37	chr4	114277121	114277121	+	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	ctagaagataactcttcacaCaaaacccctgattctctgga	14	10	5	12	0	3	3	1	1	2	2	4	4	3	4	2	1	2	0	2	1	5	4			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr4:114277121C>A	ENST00000357077.4	+	38	7400	c.7347C>A	c.(7345-7347)caC>caA	p.H2449Q	ANK2_ENST00000509550.1_Intron|ANK2_ENST00000510275.2_Intron|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000264366.6_Missense_Mutation_p.H2416Q|ANK2_ENST00000506722.1_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	2449					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)		ACTCTTCACACAAAACCCCTG	0.502																																					p.H2449Q		Atlas-SNP	.											.	ANK2	576	.	0			c.C7347A						PASS	.						75	74	74					4																	114277121		2203	4300	6503	SO:0001583	missense	287	exon38			TTCACACAAAACC	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.7347C>A	chr4.hg19:g.114277121C>A	ENSP00000349588:p.His2449Gln	87.0	0.0	.		80.0	28.0	.	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	hg19	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.734944	0.48939	.	.	ENSG00000145362	ENST00000357077;ENST00000264366	T;T	0.70516	-0.48;-0.49	5.85	5.01	0.66863	.	0.000000	0.64402	D	0.000013	T	0.69015	0.3064	L	0.54323	1.7	0.80722	D	1	B;P	0.41848	0.144;0.763	B;P	0.44990	0.053;0.466	T	0.67665	-0.5612	9	.	.	.	.	11.2279	0.48895	0.0:0.8096:0.0:0.1904	.	2416;2449	Q01484;Q01484-4	ANK2_HUMAN;.	Q	2449;2416	ENSP00000349588:H2449Q;ENSP00000264366:H2416Q	.	H	+	3	2	ANK2	114496570	0.997000	0.39634	1.000000	0.80357	0.993000	0.82548	0.444000	0.21661	1.488000	0.48433	0.655000	0.94253	CAC	.	.	.	none		0.502	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		A	114277121	C	A	114277121	3	1	62	1	0	0	0	0	1	0	0	0	621	477	17	4	7562	4	ANK2	4	114277121	Missense_Mutation	SNP	C	TCGA-A4-A4ZT-01A-11D-A26P-10	45740860	114277121	76877155	16	4138											
AHRR	57491	hgsc.bcm.edu	37	chr5	353963	353963	+	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	cgcctgacatcatctccaagCtggacaagctttctgtcctg	8	11	8	14	1	3	1	1	1	2	0	5	2	4	2	3	1	2	2	3	1	2	1			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr5:353963C>T	ENST00000505113.1	+	3	237	c.193C>T	c.(193-195)Ctg>Ttg	p.L65L	AHRR_ENST00000512529.1_Intron|AHRR_ENST00000316418.5_Silent_p.L65L|AHRR_ENST00000515206.1_Silent_p.L61L	NM_001242412.1	NP_001229341.1	A9YTQ3	AHRR_HUMAN	aryl-hydrocarbon receptor repressor	65	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				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)	p.L61V(2)		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)			CATCTCCAAGCTGGACAAGCT	0.592																																					p.L65L		Atlas-SNP	.											AHRR,NS,carcinoma,0,1	AHRR	67	.	2	Substitution - Missense(2)	lung(2)	c.C193T						PASS	.						102	115	111					5																	353963		2130	4244	6374	SO:0001819	synonymous_variant	57491	exon3			TCCAAGCTGGACA	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.193C>T	chr5.hg19:g.353963C>T		147.0	0.0	.		193.0	67.0	.	NM_001242412	A7MBN5|D6RAZ1|Q9HAZ3|Q9ULI6	Silent	SNP	ENST00000505113.1	hg19	CCDS56355.1																																																																																			.	.	.	none		0.592	AHRR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367720.1	NM_020731		T	353963	C	T	353963	2	4	62	1	0	0	0	0	0	0	0	1	417	796	28	2		2	AHRR	5	353963	Silent	SNP	C	TCGA-A4-A4ZT-01A-11D-A26P-10		353963	180561297	17	4139											
LIX1	167410	hgsc.bcm.edu	37	chr5	96443096	96443096	+	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	tactgcttcctgaacactttCcataatgaattccttggtga	10	15	6	10	0	0	3	0	3	0	0	3	3	3	3	3	1	3	1	3	1	4	6			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr5:96443096C>A	ENST00000274382.4	-	3	650	c.355G>T	c.(355-357)Gaa>Taa	p.E119*	CTD-2215E18.1_ENST00000509481.1_Intron	NM_153234.4	NP_694966.3	Q8N485	LIX1_HUMAN	Lix1 homolog (chicken)	119										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)	10		all_cancers(142;4.28e-07)|all_epithelial(76;1.06e-09)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0318)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.0733)		TGAACACTTTCCATAATGAAT	0.527																																					p.E119X		Atlas-SNP	.											.	LIX1	41	.	0			c.G355T						PASS	.						109	102	105					5																	96443096		2203	4300	6503	SO:0001587	stop_gained	167410	exon3			CACTTTCCATAAT		CCDS4088.1	5q15	2008-03-06	2008-03-06	2005-02-07	ENSG00000145721	ENSG00000145721			18581	protein-coding gene	gene with protein product		610466	"chromosome 5 open reading frame 11", "Lix1 homolog (mouse)"	C5orf11		11731258	Standard	NM_153234		Approved		uc003kmy.4	Q8N485	OTTHUMG00000128720	ENST00000274382.4:c.355G>T	chr5.hg19:g.96443096C>A	ENSP00000274382:p.Glu119*	131.0	0.0	.		137.0	38.0	.	NM_153234	A8K4R9|Q8N7I2	Nonsense_Mutation	SNP	ENST00000274382.4	hg19	CCDS4088.1	.	.	.	.	.	.	.	.	.	.	C	37	6.428078	0.97559	.	.	ENSG00000145721	ENST00000274382	.	.	.	6.17	6.17	0.99709	.	0.186655	0.64402	D	0.000018	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.9396	13.6552	0.62333	0.0:0.9294:0.0:0.0706	.	.	.	.	X	119	.	ENSP00000274382:E119X	E	-	1	0	LIX1	96468852	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.753000	0.38359	2.941000	0.99782	0.655000	0.94253	GAA	.	.	.	none		0.527	LIX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250625.1	NM_153234		A	96443096	C	A	96443096	4	1	62	1	0	0	0	0	0	1	0	0	8838	864	30	4	509	4	LIX1	5	96443096	Nonsense_Mutation	SNP	C	TCGA-A4-A4ZT-01A-11D-A26P-10	96089133	96443096	84472164	18	4140											
HIST1H2BN	8341	hgsc.bcm.edu	37	chr6	27806755	27806755	+	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	tgcgcctgctgctgccagggGagctggccaagcacgcggtg	5	6	17	13	3	0	0	0	0	0	0	0	1	0	1	3	4	6	4	3	4	1	0			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr6:27806755G>A	ENST00000396980.3	+	1	316	c.316G>A	c.(316-318)Gag>Aag	p.E106K	HIST1H2BN_ENST00000606613.1_Missense_Mutation_p.E106K|HIST1H2AK_ENST00000330180.2_5'Flank	NM_003520.3	NP_003511.1	Q99877	H2B1N_HUMAN	histone cluster 1, H2bn	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)			central_nervous_system(1)|endometrium(3)|lung(3)|prostate(1)	8						GCTGCCAGGGGAGCTGGCCAA	0.677																																					p.E106K		Atlas-SNP	.											.	HIST1H2BN	11	.	0			c.G316A						PASS	.						57	61	60					6																	27806755		2203	4299	6502	SO:0001583	missense	8341	exon1			CCAGGGGAGCTGG	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.316G>A	chr6.hg19:g.27806755G>A	ENSP00000380177:p.Glu106Lys	51.0	0.0	.		62.0	23.0	.	NM_003520	B2R5L4|Q494S8|Q96FB7	Missense_Mutation	SNP	ENST00000396980.3	hg19	CCDS4633.1	.	.	.	.	.	.	.	.	.	.	.	14.44	2.536027	0.45176	.	.	ENSG00000233822	ENST00000449538;ENST00000396980	T;T	0.78126	-1.15;-1.15	4.71	4.71	0.59529	Histone-fold (2);	0.000000	0.43747	U	0.000529	T	0.78710	0.4326	M	0.93106	3.38	0.37318	D	0.90942	B;B	0.28713	0.014;0.22	B;B	0.26202	0.009;0.067	D	0.83433	0.0039	10	0.87932	D	0	.	17.5855	0.87980	0.0:0.0:1.0:0.0	.	106;106	Q99877;B2R4S9	H2B1N_HUMAN;.	K	106	ENSP00000446031:E106K;ENSP00000380177:E106K	ENSP00000380177:E106K	E	+	1	0	HIST1H2BN	27914734	1.000000	0.71417	1.000000	0.80357	0.301000	0.27625	7.723000	0.84788	2.537000	0.85549	0.650000	0.86243	GAG	.	.	.	none		0.677	HIST1H2BN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043840.2	NM_003520		A	27806755	G	A	27806755	3	1	62	1	0	0	0	0	1	0	0	0	7160	1175	41	2	318	2	HIST1H2BN	6	27806755	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10		27806755	143308312	19	4141											
PPP1R10	5514	hgsc.bcm.edu	37	chr6	30572781	30572781	+	Missense_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	gagcccataccttggcagccGtaggtgacagtacttttttt	8	13	10	10	1	0	1	0	1	0	0	0	2	0	1	3	2	4	3	3	2	3	7			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr6:30572781G>A	ENST00000376511.2	-	11	1496	c.944C>T	c.(943-945)aCg>aTg	p.T315M		NM_002714.3	NP_002705.2	Q96QC0	PP1RA_HUMAN	protein phosphatase 1, regulatory subunit 10	315	Interaction with TOX4. {ECO:0000250}.				protein import into nucleus (GO:0006606)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|PTW/PP1 phosphatase complex (GO:0072357)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(3)|skin(1)	25						CTTGGCAGCCGTAGGTGACAG	0.468																																					p.T315M		Atlas-SNP	.											.	PPP1R10	60	.	0			c.C944T						PASS	.						47	57	53					6																	30572781		1511	2709	4220	SO:0001583	missense	5514	exon11			GCAGCCGTAGGTG	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.944C>T	chr6.hg19:g.30572781G>A	ENSP00000365694:p.Thr315Met	73.0	0.0	.		89.0	29.0	.	NM_002714	O00405	Missense_Mutation	SNP	ENST00000376511.2	hg19	CCDS4681.1	.	.	.	.	.	.	.	.	.	.	G	16.30	3.084609	0.55861	.	.	ENSG00000204569	ENST00000376511	T	0.62498	0.02	5.06	5.06	0.68205	.	0.049773	0.85682	D	0.000000	T	0.61362	0.2341	N	0.19112	0.55	0.58432	D	0.999997	D	0.89917	1.0	D	0.83275	0.996	T	0.66799	-0.5832	10	0.56958	D	0.05	-10.3518	17.3696	0.87372	0.0:0.0:1.0:0.0	.	315	Q96QC0	PP1RA_HUMAN	M	315	ENSP00000365694:T315M	ENSP00000365694:T315M	T	-	2	0	PPP1R10	30680760	1.000000	0.71417	0.995000	0.50966	0.762000	0.43233	6.222000	0.72249	2.642000	0.89623	0.561000	0.74099	ACG	.	.	.	none		0.468	PPP1R10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076556.2	NM_002714		A	30572781	G	A	30572781	3	1	62	1	0	0	0	0	1	0	0	0	12362	1145	40	1	1918	1	PPP1R10	6	30572781	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10	2766026	30572781	140542286	20	4142											
UNC5CL	222643	hgsc.bcm.edu	37	chr6	40999454	40999454	+	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	gcatggtgacaatgatctcaTtggttagtgctgaacagtcc	10	12	11	8	0	1	3	1	3	1	0	3	3	2	3	1	2	2	3	1	2	3	2	rs145811250	byFrequency	TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr6:40999454T>A	ENST00000373164.1	-	5	1145	c.1085A>T	c.(1084-1086)aAt>aTt	p.N362I	UNC5CL_ENST00000470102.1_Intron|UNC5CL_ENST00000244565.3_Missense_Mutation_p.N362I			Q8IV45	UN5CL_HUMAN	unc-5 homolog C (C. elegans)-like	362	Interaction with RELA and NFKB1.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|proteolysis (GO:0006508)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	peptidase activity (GO:0008233)			endometrium(1)|kidney(3)|large_intestine(3)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	13	Ovarian(28;0.0418)|Colorectal(47;0.196)					AATGATCTCATTGGTTAGTGC	0.547																																					p.N362I		Atlas-SNP	.											UNC5CL,NS,carcinoma,0,1	UNC5CL	52	.	0			c.A1085T						PASS	.						196	174	181					6																	40999454		2203	4300	6503	SO:0001583	missense	222643	exon6			ATCTCATTGGTTA	BC035284	CCDS4847.1	6p21.1	2013-10-15			ENSG00000124602	ENSG00000124602			21203	protein-coding gene	gene with protein product	"ZU5 and death domain containing"					14769797	Standard	NM_173561		Approved	MGC34763, ZUD	uc003opi.3	Q8IV45	OTTHUMG00000014665	ENST00000373164.1:c.1085A>T	chr6.hg19:g.40999454T>A	ENSP00000362258:p.Asn362Ile	199.0	0.0	.		170.0	64.0	.	NM_173561	Q5TGU1	Missense_Mutation	SNP	ENST00000373164.1	hg19	CCDS4847.1	.	.	.	.	.	.	.	.	.	.	T	12.73	2.024767	0.35701	.	.	ENSG00000124602	ENST00000244565;ENST00000373164	T;T	0.14391	2.51;2.51	4.52	3.34	0.38264	.	0.124350	0.36482	N	0.002565	T	0.02649	0.0080	N	0.24115	0.695	0.37746	D	0.925799	B	0.11235	0.004	B	0.09377	0.004	T	0.35549	-0.9784	10	0.22109	T	0.4	-8.9542	6.7625	0.23548	0.0:0.1071:0.0:0.8929	.	362	Q8IV45	UN5CL_HUMAN	I	362	ENSP00000244565:N362I;ENSP00000362258:N362I	ENSP00000244565:N362I	N	-	2	0	UNC5CL	41107432	1.000000	0.71417	0.996000	0.52242	0.944000	0.59088	0.406000	0.21032	0.770000	0.33336	0.383000	0.25322	AAT	.	T|0.998;C|0.002	.	alt		0.547	UNC5CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040491.1	NM_173561		A	40999454	T	A	40999454	3	1	62	1	0	0	0	0	1	0	0	0	17006	1493	52	5	487	5	UNC5CL	6	40999454	Missense_Mutation	SNP	T	TCGA-A4-A4ZT-01A-11D-A26P-10	10426673	40999454	130115613	21	4143											
ACTB	60	hgsc.bcm.edu	37	chr7	5567473	5567473	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtggacagcgaggccaggAtggagccgccgatccacacg	10	3	16	12	4	0	0	0	0	0	0	1	5	1	3	4	5	2	0	4	5	0	0			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr7:5567473A>G	ENST00000331789.5	-	6	1225	c.1034T>C	c.(1033-1035)aTc>aCc	p.I345T	ACTB_ENST00000464611.1_5'UTR|AC006483.1_ENST00000579427.1_RNA	NM_001101.3	NP_001092.1	P63261	ACTG_HUMAN	actin, beta	345					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)		CGAGGCCAGGATGGAGCCGCC	0.612																																					p.I345T		Atlas-SNP	.											.	ACTB	45	.	0			c.T1034C						PASS	.						67	70	69					7																	5567473		2203	4300	6503	SO:0001583	missense	60	exon6			GCCAGGATGGAGC	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.1034T>C	chr7.hg19:g.5567473A>G	ENSP00000349960:p.Ile345Thr	230.0	1.0	.		407.0	193.0	.	NM_001101	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000331789.5	hg19	CCDS5341.1	.	.	.	.	.	.	.	.	.	.	A	16.84	3.232891	0.58777	.	.	ENSG00000075624	ENST00000331789;ENST00000445914;ENST00000400179;ENST00000320713	D	0.95788	-3.81	5.55	5.55	0.83447	.	0.000000	0.64402	D	0.000013	D	0.98535	0.9511	H	0.94886	3.595	0.53005	D	0.99996	P	0.40032	0.699	D	0.79108	0.992	D	0.99293	1.0899	10	0.87932	D	0	.	14.9227	0.70851	1.0:0.0:0.0:0.0	.	345	P60709	ACTB_HUMAN	T	345;321;317;264	ENSP00000349960:I345T	ENSP00000440549:I264T	I	-	2	0	ACTB	5533999	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	8.991000	0.93514	2.114000	0.64651	0.529000	0.55759	ATC	.	.	.	none		0.612	ACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059589.4	NM_001101		G	5567473	A	G	5567473	3	3	62	1	0	0	0	0	1	0	0	0	193	333	12	3	97	3	ACTB	7	5567473	Missense_Mutation	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10		5567473	153571190	22	4144											
AGK	55750	hgsc.bcm.edu	37	chr7	141352597	141352597	+	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	ttctccccagggagcaggggGctcttttagcattgacagtg	7	11	13	10	0	2	1	0	1	2	0	3	2	2	2	2	3	2	3	2	3	1	4			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr7:141352597G>C	ENST00000355413.4	+	16	1402	c.1142G>C	c.(1141-1143)gGc>gCc	p.G381A	AGK_ENST00000473247.1_Missense_Mutation_p.G353A|RP5-894A10.2_ENST00000467537.1_RNA	NM_018238.3	NP_060708.1	Q53H12	AGK_HUMAN	acylglycerol kinase	381					ceramide biosynthetic process (GO:0046513)|glycerolipid metabolic process (GO:0046486)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acylglycerol kinase activity (GO:0047620)|ATP binding (GO:0005524)|ceramide kinase activity (GO:0001729)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(1)|endometrium(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(3)	17	Melanoma(164;0.0171)					GGAGCAGGGGGCTCTTTTAGC	0.502																																					p.G381A		Atlas-SNP	.											.	AGK	43	.	0			c.G1142C						PASS	.						111	104	107					7																	141352597		2203	4300	6503	SO:0001583	missense	55750	exon16			CAGGGGGCTCTTT	BC022777	CCDS5865.1	7q34	2010-05-04	2007-01-11	2007-01-11	ENSG00000006530	ENSG00000006530	2.7.1.94		21869	protein-coding gene	gene with protein product		610345	"multiple substrate lipid kinase"	MULK		15252046, 15939762, 17135245	Standard	NM_018238		Approved	FLJ10842	uc003vwi.2	Q53H12	OTTHUMG00000157499	ENST00000355413.4:c.1142G>C	chr7.hg19:g.141352597G>C	ENSP00000347581:p.Gly381Ala	102.0	0.0	.		189.0	89.0	.	NM_018238	Q75KN1|Q96GC3|Q9NP48	Missense_Mutation	SNP	ENST00000355413.4	hg19	CCDS5865.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.331077	0.81690	.	.	ENSG00000006530	ENST00000355413;ENST00000473247	T;T	0.12984	2.63;2.63	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.16428	0.0395	L	0.49126	1.545	0.80722	D	1	P	0.37663	0.604	B	0.32533	0.147	T	0.01848	-1.1261	10	0.72032	D	0.01	.	19.2669	0.93990	0.0:0.0:1.0:0.0	.	381	Q53H12	AGK_HUMAN	A	381;353	ENSP00000347581:G381A;ENSP00000420776:G353A	ENSP00000347581:G381A	G	+	2	0	AGK	140999066	1.000000	0.71417	0.986000	0.45419	0.515000	0.34225	8.920000	0.92779	2.549000	0.85964	0.655000	0.94253	GGC	.	.	.	none		0.502	AGK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348969.1	NM_018238		C	141352597	G	C	141352597	3	2	62	1	0	0	0	0	1	0	0	0	383	1203	42	4	1200	4	AGK	7	141352597	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10	135785124	141352597	17786066	23	4145											
C8orf80	389643	hgsc.bcm.edu	37	chr8	27913490	27913490	+	Missense_Mutation	SNP	T	T	G																															ctattaactcaccttcagttTttccttgagaattctagtcc																										TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr8:27913490T>G	ENST00000413272.2	-	10	1340	c.1198A>C	c.(1198-1200)Aaa>Caa	p.K400Q	NUGGC_ENST00000341513.6_Missense_Mutation_p.K400Q	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	400					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)										ACCTTCAGTTTTTCCTTGAGA	0.373																																					p.K400Q		Atlas-SNP	.											.	.	.	.	0			c.A1198C						PASS	.						94	88	89					8																	27913490		1840	4086	5926	SO:0001583	missense	389643	exon10			TCAGTTTTTCCTT	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.1198A>C	chr8.hg19:g.27913490T>G	ENSP00000408697:p.Lys400Gln	62.0	0.0	.		37.0	13.0	.	NM_001010906	Q6ZP73	Missense_Mutation	SNP	ENST00000413272.2	hg19	CCDS47833.1	.	.	.	.	.	.	.	.	.	.	T	18.99	3.739734	0.69304	.	.	ENSG00000189233	ENST00000413272;ENST00000341513	T;T	0.15952	2.38;2.38	5.37	5.37	0.77165	.	0.192094	0.43919	D	0.000520	T	0.14485	0.0350	L	0.32530	0.975	0.37961	D	0.932984	P	0.47350	0.894	B	0.40444	0.329	T	0.05517	-1.0880	10	0.66056	D	0.02	-18.4502	11.7885	0.52055	0.0:0.0:0.0:1.0	.	400	Q68CJ6	SLIP_HUMAN	Q	400	ENSP00000408697:K400Q;ENSP00000345031:K400Q	ENSP00000345031:K400Q	K	-	1	0	C8orf80	27969409	0.999000	0.42202	0.999000	0.59377	0.985000	0.73830	2.663000	0.46774	2.030000	0.59900	0.455000	0.32223	AAA	.	.	.	none		0.373	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906		G	27913490	T	G	27913490	3	3	62	1	0	0	0	0	1	0	0	0	2441	1850	64	5	1232	5	C8orf80	8	27913490	Missense_Mutation	SNP	T	TCGA-A4-A4ZT-01A-11D-A26P-10		27913490	118450532	24	4146	45	2									
C8orf80	389643	hgsc.bcm.edu	37	chr8	27913492	27913492	+	Missense_Mutation	SNP	T	T	C																															attaactcaccttcagttttTccttgagaattctagtcctt																										TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr8:27913492T>C	ENST00000413272.2	-	10	1338	c.1196A>G	c.(1195-1197)gAa>gGa	p.E399G	NUGGC_ENST00000341513.6_Missense_Mutation_p.E399G	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	399					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)										CTTCAGTTTTTCCTTGAGAAT	0.368																																					p.E399G		Atlas-SNP	.											.	.	.	.	0			c.A1196G						PASS	.						93	87	88					8																	27913492		1839	4084	5923	SO:0001583	missense	389643	exon10			AGTTTTTCCTTGA	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.1196A>G	chr8.hg19:g.27913492T>C	ENSP00000408697:p.Glu399Gly	62.0	0.0	.		36.0	13.0	.	NM_001010906	Q6ZP73	Missense_Mutation	SNP	ENST00000413272.2	hg19	CCDS47833.1	.	.	.	.	.	.	.	.	.	.	T	14.94	2.686312	0.47991	.	.	ENSG00000189233	ENST00000413272;ENST00000341513	T;T	0.17054	2.3;2.32	5.37	4.2	0.49525	.	0.367956	0.29205	N	0.012835	T	0.12178	0.0296	L	0.32530	0.975	0.35309	D	0.783741	B	0.32245	0.361	B	0.25140	0.058	T	0.14952	-1.0454	10	0.59425	D	0.04	-7.5105	9.3405	0.38076	0.0:0.0:0.1808:0.8192	.	399	Q68CJ6	SLIP_HUMAN	G	399	ENSP00000408697:E399G;ENSP00000345031:E399G	ENSP00000345031:E399G	E	-	2	0	C8orf80	27969411	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.756000	0.38390	0.851000	0.35264	0.455000	0.32223	GAA	.	.	.	none		0.368	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906		C	27913492	T	C	27913492	3	2	62	1	0	0	0	0	1	0	0	0	2441	1783	62	3	1234	3	C8orf80	8	27913492	Missense_Mutation	SNP	T	TCGA-A4-A4ZT-01A-11D-A26P-10	2	27913492	118450530	25	4147	45	2									
NUP188	23511	hgsc.bcm.edu	37	chr9	131735460	131735460	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaccaccagcactgcatgcAtgtgtgtctatggactgctc	8	10	10	13	0	1	0	0	0	1	0	2	1	1	1	2	1	4	5	2	1	1	1			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr9:131735460A>G	ENST00000372577.2	+	12	1156	c.1135A>G	c.(1135-1137)Atg>Gtg	p.M379V		NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	379					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						CACTGCATGCATGTGTGTCTA	0.493																																					p.M379V		Atlas-SNP	.											.	NUP188	140	.	0			c.A1135G						PASS	.						166	127	140					9																	131735460		2203	4300	6503	SO:0001583	missense	23511	exon12			GCATGCATGTGTG	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.1135A>G	chr9.hg19:g.131735460A>G	ENSP00000361658:p.Met379Val	66.0	0.0	.		57.0	16.0	.	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Missense_Mutation	SNP	ENST00000372577.2	hg19	CCDS35156.1	.	.	.	.	.	.	.	.	.	.	A	11.66	1.706341	0.30232	.	.	ENSG00000095319	ENST00000356693;ENST00000372577	T	0.64618	-0.11	5.01	5.01	0.66863	.	0.175989	0.64402	D	0.000006	T	0.44623	0.1302	N	0.19112	0.55	0.40933	D	0.984408	B	0.11235	0.004	B	0.09377	0.004	T	0.39143	-0.9628	10	0.34782	T	0.22	0.8656	9.6632	0.39967	0.8449:0.0:0.0:0.1551	.	379	Q5SRE5	NU188_HUMAN	V	268;379	ENSP00000361658:M379V	ENSP00000349125:M268V	M	+	1	0	NUP188	130775281	1.000000	0.71417	1.000000	0.80357	0.729000	0.41735	3.448000	0.52943	2.014000	0.59158	0.451000	0.29950	ATG	.	.	.	none		0.493	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2			G	131735460	A	G	131735460	3	3	62	1	0	0	0	0	1	0	0	0	10765	217	8	3	1181	3	NUP188	9	131735460	Missense_Mutation	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10		131735460	9477971	26	4148											
ANK3	288	hgsc.bcm.edu	37	chr10	61832051	61832054	+	Frame_Shift_Del	DEL	TTGT	TTGT	-																															gtttttctttctgagacttaTtgttagtggctcccgaactc																								rs371964932		TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	TTGT	TTGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr10:61832051_61832054delTTGT	ENST00000280772.2	-	37	8776_8779	c.8585_8588delACAA	c.(8584-8589)aacaatfs	p.NN2862fs	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)	2862					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						CTGAGACTTATTGTTAGTGGCTCC	0.402																																					p.2862_2863del		Atlas-INDEL	.											.	ANK3	703	.	0			c.8586_8589del						PASS	.																																			SO:0001589	frameshift_variant	288	exon37			.	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.8585_8588delACAA	chr10.hg19:g.61832051_61832054delTTGT	ENSP00000280772:p.Asn2862fs	129.0	0.0	0		85.0	13.0	0.152941	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Frame_Shift_Del	DEL	ENST00000280772.2	hg19	CCDS7258.1																																																																																			.	.	.	none		0.402	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		-	61832054	TTGT	-	61832051	7	5	62	1	0	1	0	1	0	0	0	0	622	1493	52	0	4886	0	ANK3	10	61832051	Frame_Shift_Del	DEL	TTGT	TCGA-A4-A4ZT-01A-11D-A26P-10		61832051	73702696	27	4149	46	3									
ANK3	288	hgsc.bcm.edu	37	chr10	61832052	61832061	+	Frame_Shift_Del	DEL	TGTTAGTGGC	TGTTAGTGGC	-																															tttttctttctgagacttatTgttagtggctcccgaactct																										TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	TGTTAGTGGC	TGTTAGTGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr10:61832052_61832061delTGTTAGTGGC	ENST00000280772.2	-	37	8769_8778	c.8578_8587delGCCACTAACA	c.(8578-8589)gccactaacaatfs	p.ATNN2860fs	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)	2860					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						TGAGACTTATTGTTAGTGGCTCCCGAACTC	0.41																																					p.2860_2863del		Pindel	.											.	ANK3	703	.	0			c.8579_8588del						PASS	.																																			SO:0001589	frameshift_variant	288	exon37			.	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.8578_8587delGCCACTAACA	chr10.hg19:g.61832052_61832061delTGTTAGTGGC	ENSP00000280772:p.Ala2860fs	130.0	0.0	.		87.0	18.0	0.207	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Frame_Shift_Del	DEL	ENST00000280772.2	hg19	CCDS7258.1																																																																																			.	.	.	none		0.41	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		-	61832061	TGTTAGTGGC	-	61832052	7	5	62	1	0	1	0	1	0	0	0	0	622	1812	63	0	4887	0	ANK3	10	61832052	Frame_Shift_Del	DEL	TGTTAGTGGC	TCGA-A4-A4ZT-01A-11D-A26P-10	1	61832052	73702695	28	4150	46	3									
ANK3	288	hgsc.bcm.edu	37	chr10	61832057	61832061	+	Frame_Shift_Del	DEL	GTGGC	GTGGC	-																															ctttctgagacttattgttaGtggctcccgaactctcccat																										TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	GTGGC	GTGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr10:61832057_61832061delGTGGC	ENST00000280772.2	-	37	8769_8773	c.8578_8582delGCCAC	c.(8578-8583)gccactfs	p.AT2860fs	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)	2860					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						CTTATTGTTAGTGGCTCCCGAACTC	0.415																																					p.2860_2861del		Atlas-INDEL	.											.	ANK3	703	.	0			c.8579_8583del						PASS	.																																			SO:0001589	frameshift_variant	288	exon37			.	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.8578_8582delGCCAC	chr10.hg19:g.61832057_61832061delGTGGC	ENSP00000280772:p.Ala2860fs	128.0	0.0	0		78.0	13.0	0.166667	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Frame_Shift_Del	DEL	ENST00000280772.2	hg19	CCDS7258.1																																																																																			.	.	.	none		0.415	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		-	61832061	GTGGC	-	61832057	7	5	62	1	0	1	0	1	0	0	0	0	622	1029	36	0	4892	0	ANK3	10	61832057	Frame_Shift_Del	DEL	GTGGC	TCGA-A4-A4ZT-01A-11D-A26P-10	5	61832057	73702690	29	4151	46	3									
AIFM2	84883	hgsc.bcm.edu	37	chr10	71874678	71874678	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acatggggcctctcttacccGgcttgtaggcctggagaggc	6	9	14	12	1	1	1	0	0	1	1	2	2	1	1	3	6	1	2	3	6	2	3	rs376374471		TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr10:71874678G>A	ENST00000307864.1	-	8	1181	c.968C>T	c.(967-969)cCg>cTg	p.P323L	AIFM2_ENST00000373248.1_Missense_Mutation_p.P323L|AIFM2_ENST00000482166.1_5'UTR	NM_001198696.1|NM_032797.5	NP_001185625.1|NP_116186.1	Q9BRQ8	AIFM2_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 2	323					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						TCTCTTACCCGGCTTGTAGGC	0.547																																					p.P323L		Atlas-SNP	.											.	AIFM2	33	.	0			c.C968T						PASS	.	G	LEU/PRO,LEU/PRO	0,4406		0,0,2203	29	30	30		968,968	5.8	1	10		30	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	AIFM2	NM_001198696.1,NM_032797.5	98,98	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	possibly-damaging,possibly-damaging	323/374,323/374	71874678	2,13004	2203	4300	6503	SO:0001583	missense	84883	exon8			TTACCCGGCTTGT	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.968C>T	chr10.hg19:g.71874678G>A	ENSP00000312370:p.Pro323Leu	88.0	0.0	.		60.0	16.0	.	NM_001198696	B3KXI0|Q63Z39	Missense_Mutation	SNP	ENST00000307864.1	hg19	CCDS7297.1	.	.	.	.	.	.	.	.	.	.	G	18.31	3.594868	0.66219	0.0	2.33E-4	ENSG00000042286	ENST00000373248;ENST00000307864;ENST00000395039	T;T	0.35421	1.31;1.31	5.8	5.8	0.92144	.	0.052232	0.85682	D	0.000000	T	0.32255	0.0823	M	0.64567	1.98	0.80722	D	1	P	0.39748	0.686	B	0.29598	0.104	T	0.17077	-1.0381	10	0.12766	T	0.61	-6.747	17.8576	0.88771	0.0:0.0:1.0:0.0	.	323	Q9BRQ8	AIFM2_HUMAN	L	323;323;286	ENSP00000362345:P323L;ENSP00000312370:P323L	ENSP00000312370:P323L	P	-	2	0	AIFM2	71544684	1.000000	0.71417	0.996000	0.52242	0.199000	0.23934	8.579000	0.90781	2.758000	0.94735	0.563000	0.77884	CCG	.	.	.	none		0.547	AIFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048487.1	NM_032797		A	71874678	G	A	71874678	3	1	62	1	0	0	0	0	1	0	0	0	427	1116	39	1	161	1	AIFM2	10	71874678	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10	10042621	71874678	63660069	30	4152											
ZMYND17	118490	hgsc.bcm.edu	37	chr10	75185695	75185695	+	Frame_Shift_Del	DEL	T	T	-																															gccaggttccaggggtgaagTtgaggtgctctgtgaaaagc																										TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr10:75185695delT	ENST00000372912.1	-	4	945	c.943delA	c.(943-945)actfs	p.T315fs	MSS51_ENST00000299432.2_Frame_Shift_Del_p.T315fs|AL353731.1_ENST00000584907.1_RNA			Q4VC12	MSS51_HUMAN	MSS51 mitochondrial translational activator	315					social behavior (GO:0035176)		metal ion binding (GO:0046872)										AGGGGTGAAGTTGAGGTGCTC	0.542																																					p.T315fs		Pindel	.											.	.	.	.	0			c.944delC						PASS	.						85	75	78					10																	75185695		2203	4300	6503	SO:0001589	frameshift_variant	118490	exon5			.	AK096884	CCDS31221.1	10q22.3	2013-01-10	2013-01-10	2012-02-24	ENSG00000166343	ENSG00000166343		"Zinc fingers, MYND-type"	21000	protein-coding gene	gene with protein product		614773	"zinc finger, MYND-type containing 17", "MSS51 mitochondrial translational activator homolog (S. cerevisiae)"	ZMYND17		19710419	Standard	NM_001024593		Approved	FLJ39565	uc001jud.3	Q4VC12	OTTHUMG00000018464	ENST00000372912.1:c.943delA	chr10.hg19:g.75185695delT	ENSP00000362003:p.Thr315fs	151.0	0.0	.		140.0	33.0	0.236	NM_001024593	A6NGH6|Q2VP95|Q5F2H5|Q7Z3M9|Q8N8G0	Frame_Shift_Del	DEL	ENST00000372912.1	hg19	CCDS31221.1																																																																																			.	.	.	none		0.542	MSS51-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048652.3	NM_178451		-	75185695	T	-	75185695	7	5	62	1	0	1	0	1	0	0	0	0	17721	1725	60	0	451	0	ZMYND17	10	75185695	Frame_Shift_Del	DEL	T	TCGA-A4-A4ZT-01A-11D-A26P-10	3311017	75185695	60349052	31	4153											
FERMT3	83706	hgsc.bcm.edu	37	chr11	63990576	63990576	+	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	cgccaacaaccgactgatccGcatcgacttggccgtgggcg	8	6	12	15	6	0	1	0	1	0	0	2	3	1	1	4	2	2	1	4	2	2	1			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr11:63990576G>T	ENST00000279227.5	+	14	1834	c.1739G>T	c.(1738-1740)cGc>cTc	p.R580L	FERMT3_ENST00000345728.5_Missense_Mutation_p.R576L|TRPT1_ENST00000540472.1_5'Flank	NM_178443.2	NP_848537.1	Q86UX7	URP2_HUMAN	fermitin family member 3	580					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						CGACTGATCCGCATCGACTTG	0.622																																					p.R580L		Atlas-SNP	.											.	FERMT3	51	.	0			c.G1739T						PASS	.						109	83	92					11																	63990576		2201	4296	6497	SO:0001583	missense	83706	exon14			TGATCCGCATCGA	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.1739G>T	chr11.hg19:g.63990576G>T	ENSP00000279227:p.Arg580Leu	222.0	0.0	.		170.0	65.0	.	NM_178443	Q8IUA1|Q8N207|Q9BT48	Missense_Mutation	SNP	ENST00000279227.5	hg19	CCDS8060.1	.	.	.	.	.	.	.	.	.	.	G	35	5.437985	0.96168	.	.	ENSG00000149781	ENST00000345728;ENST00000279227;ENST00000545896	T;T;T	0.73575	-0.76;-0.76;-0.76	5.19	5.19	0.71726	Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	D	0.86908	0.6046	M	0.81802	2.56	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.993	D	0.87510	0.2439	10	0.52906	T	0.07	-23.8856	17.8551	0.88760	0.0:0.0:1.0:0.0	.	576;580	Q86UX7-2;Q86UX7	.;URP2_HUMAN	L	576;580;97	ENSP00000339950:R576L;ENSP00000279227:R580L;ENSP00000440209:R97L	ENSP00000279227:R580L	R	+	2	0	FERMT3	63747152	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	9.411000	0.97342	2.591000	0.87537	0.561000	0.74099	CGC	.	.	.	none		0.622	FERMT3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396297.1	NM_031471		T	63990576	G	T	63990576	3	4	62	1	0	0	0	0	1	0	0	0	5826	1087	38	4	1789	4	FERMT3	11	63990576	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10		63990576	71015940	32	4154											
C11orf53	341032	hgsc.bcm.edu	37	chr11	111154999	111154999	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggagccctacggagactaccGgcctccggcgctgacgccca	7	4	13	17	5	0	2	0	1	0	1	1	4	1	3	5	4	3	1	5	4	2	2	rs146857088		TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr11:111154999G>A	ENST00000280325.4	+	3	353	c.206G>A	c.(205-207)cGg>cAg	p.R69Q		NM_198498.1	NP_940900.1	Q8IXP5	CK053_HUMAN	chromosome 11 open reading frame 53	69										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)		GGAGACTACCGGCCTCCGGCG	0.692																																					p.R69Q		Atlas-SNP	.											C11orf53,NS,carcinoma,0,1	C11orf53	17	.	0			c.G206A						PASS	.	G	GLN/ARG	0,4402		0,0,2201	41	48	45		206	4.7	1	11	dbSNP_134	45	1,8593	1.2+/-3.3	0,1,4296	no	missense	C11orf53	NM_198498.1	43	0,1,6497	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	69/237	111154999	1,12995	2201	4297	6498	SO:0001583	missense	341032	exon3			ACTACCGGCCTCC	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.206G>A	chr11.hg19:g.111154999G>A	ENSP00000280325:p.Arg69Gln	73.0	2.0	.		85.0	4.0	.	NM_198498		Missense_Mutation	SNP	ENST00000280325.4	hg19	CCDS31674.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.293090	0.80914	0.0	1.16E-4	ENSG00000150750	ENST00000280325	.	.	.	5.66	4.74	0.60224	.	0.057619	0.64402	D	0.000001	T	0.75012	0.3792	M	0.72894	2.215	0.47621	D	0.999472	D	0.89917	1.0	D	0.66497	0.944	T	0.75929	-0.3144	9	0.52906	T	0.07	-34.9344	12.7742	0.57437	0.0795:0.0:0.9205:0.0	.	69	Q8IXP5	CK053_HUMAN	Q	69	.	ENSP00000280325:R69Q	R	+	2	0	C11orf53	110660209	1.000000	0.71417	0.994000	0.49952	0.114000	0.19823	5.606000	0.67641	2.677000	0.91161	0.591000	0.81541	CGG	.	G|1.000;A|0.000	0.000	weak		0.692	C11orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390989.1	NM_198498		A	111154999	G	A	111154999	3	1	62	1	0	0	0	0	1	0	0	0	1650	1116	39	1	212	1	C11orf53	11	111154999	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10	47164423	111154999	23851517	33	4155											
TIMELESS	8914	hgsc.bcm.edu	37	chr12	56814422	56814422	+	Missense_Mutation	SNP	T	T	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	aactgttcgttttccatggcTtcctcattttcctctgtgag	5	18	7	11	1	2	1	1	1	1	0	6	1	5	1	3	1	1	3	3	1	1	6			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr12:56814422T>G	ENST00000553532.1	-	26	3309	c.3159A>C	c.(3157-3159)gaA>gaC	p.E1053D	TIMELESS_ENST00000554616.1_Missense_Mutation_p.E550D|TIMELESS_ENST00000229201.4_Missense_Mutation_p.E1052D					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						TTTCCATGGCTTCCTCATTTT	0.507																																					p.E1053D		Atlas-SNP	.											.	TIMELESS	107	.	0			c.A3159C						PASS	.						133	109	117					12																	56814422		2203	4300	6503	SO:0001583	missense	8914	exon26			CATGGCTTCCTCA	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.3159A>C	chr12.hg19:g.56814422T>G	ENSP00000450607:p.Glu1053Asp	203.0	0.0	.		270.0	135.0	.	NM_003920		Missense_Mutation	SNP	ENST00000553532.1	hg19	CCDS8918.1	.	.	.	.	.	.	.	.	.	.	T	9.732	1.162558	0.21538	.	.	ENSG00000111602	ENST00000229201;ENST00000553532;ENST00000554616	T;T;T	0.15487	2.42;2.42;2.42	5.34	2.91	0.33838	Timeless C-terminal (1);	0.056591	0.64402	D	0.000002	T	0.11024	0.0269	L	0.41961	1.31	0.23589	N	0.99734	B	0.09022	0.002	B	0.14578	0.011	T	0.21348	-1.0248	10	0.15066	T	0.55	-17.0728	4.1508	0.10237	0.3164:0.094:0.0:0.5895	.	1053	Q9UNS1	TIM_HUMAN	D	1052;1053;550	ENSP00000229201:E1052D;ENSP00000450607:E1053D;ENSP00000450848:E550D	ENSP00000229201:E1053D	E	-	3	2	TIMELESS	55100689	0.994000	0.37717	1.000000	0.80357	0.959000	0.62525	0.126000	0.15769	2.150000	0.67090	0.459000	0.35465	GAA	.	.	.	none		0.507	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920		G	56814422	T	G	56814422	3	3	62	1	0	0	0	0	1	0	0	0	15916	1606	56	5	483	5	TIMELESS	12	56814422	Missense_Mutation	SNP	T	TCGA-A4-A4ZT-01A-11D-A26P-10		56814422	77037473	34	4156											
SLC6A15	55117	hgsc.bcm.edu	37	chr12	85279278	85279278	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggggttgctgaaaagactgAgaaaaataaaacaaactcca	20	6	9	6	0	0	3	0	2	0	2	1	4	1	3	1	2	3	2	1	2	7	2			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr12:85279278A>G	ENST00000266682.5	-	4	1051	c.510T>C	c.(508-510)tcT>tcC	p.S170S	SLC6A15_ENST00000450363.3_Silent_p.S170S|SLC6A15_ENST00000551388.1_Intron|SLC6A15_ENST00000552192.1_Silent_p.S63S	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	170					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						GAAAAGACTGAGAAAAATAAA	0.368																																					p.S170S		Atlas-SNP	.											.	SLC6A15	159	.	0			c.T510C						PASS	.						95	94	94					12																	85279278		2203	4300	6503	SO:0001819	synonymous_variant	55117	exon4			AGACTGAGAAAAA	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.510T>C	chr12.hg19:g.85279278A>G		193.0	0.0	.		232.0	62.0	.	NM_018057	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Silent	SNP	ENST00000266682.5	hg19	CCDS9026.1																																																																																			.	.	.	none		0.368	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767		G	85279278	A	G	85279278	2	3	62	1	0	0	0	0	0	0	0	1	14691	291	11	3		3	SLC6A15	12	85279278	Silent	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10	28464856	85279278	48572617	35	4157											
KIAA0564	23078	hgsc.bcm.edu	37	chr13	42185853	42185853	+	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	ctcctttgccacccaggcctGccgtgtctcttccccctgga	3	11	8	19	1	1	0	0	0	1	0	4	1	3	1	7	2	2	0	7	2	0	2			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr13:42185853G>C	ENST00000379310.3	-	39	4804	c.4736C>G	c.(4735-4737)gCa>gGa	p.A1579G		NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	1579						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										ACCCAGGCCTGCCGTGTCTCT	0.522																																					p.A1579G		Atlas-SNP	.											.	.	.	.	0			c.C4736G						PASS	.						53	56	55					13																	42185853		1917	4129	6046	SO:0001583	missense	23078	exon39			AGGCCTGCCGTGT	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"KIAA0564"	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.4736C>G	chr13.hg19:g.42185853G>C	ENSP00000368612:p.Ala1579Gly	94.0	0.0	.		108.0	33.0	.	NM_015058	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Missense_Mutation	SNP	ENST00000379310.3	hg19	CCDS41881.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.015419	0.93404	.	.	ENSG00000102763	ENST00000251030;ENST00000379310	T	0.16457	2.34	5.95	5.95	0.96441	.	0.110644	0.64402	D	0.000012	T	0.46521	0.1397	M	0.87180	2.865	0.80722	D	1	D	0.67145	0.996	P	0.58266	0.836	T	0.50931	-0.8769	10	0.87932	D	0	.	19.9739	0.97296	0.0:0.0:1.0:0.0	.	1579	A3KMH1	K0564_HUMAN	G	1483;1579	ENSP00000368612:A1579G	ENSP00000251030:A1483G	A	-	2	0	KIAA0564	41083853	1.000000	0.71417	0.920000	0.36463	0.903000	0.53119	9.577000	0.98196	2.826000	0.97356	0.563000	0.77884	GCA	.	.	.	none		0.522	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058		C	42185853	G	C	42185853	3	2	62	1	0	0	0	0	1	0	0	0	8192	1319	46	4	1009	4	KIAA0564	13	42185853	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10		42185853	72984025	36	4158											
TUBGCP3	10426	hgsc.bcm.edu	37	chr13	113140459	113140459	+	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	taacaccaaaaactgctgcaCgataccctaaaaagaagcaa	20	5	5	11	1	0	1	0	0	0	1	0	2	0	1	2	0	6	3	2	0	9	3			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr13:113140459C>G	ENST00000261965.3	-	22	2758	c.2572G>C	c.(2572-2574)Gtg>Ctg	p.V858L		NM_006322.4	NP_006313.1	Q96CW5	GCP3_HUMAN	tubulin, gamma complex associated protein 3	858					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)					AACTGCTGCACGATACCCTAA	0.458																																					p.V858L		Atlas-SNP	.											.	TUBGCP3	74	.	0			c.G2572C						PASS	.						26	24	25					13																	113140459		2203	4297	6500	SO:0001583	missense	10426	exon22			GCTGCACGATACC	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.2572G>C	chr13.hg19:g.113140459C>G	ENSP00000261965:p.Val858Leu	343.0	0.0	.		281.0	103.0	.	NM_006322	O43631|O60852|O60853|Q5T8L2|Q7Z4K1|Q96I79	Missense_Mutation	SNP	ENST00000261965.3	hg19	CCDS9525.1	.	.	.	.	.	.	.	.	.	.	C	11.93	1.786517	0.31593	.	.	ENSG00000126216	ENST00000261965	T	0.21932	1.98	4.55	4.55	0.56014	.	0.000000	0.85682	D	0.000000	T	0.22820	0.0551	L	0.58669	1.825	0.80722	D	1	P;P	0.45827	0.867;0.732	B;B	0.41946	0.371;0.371	T	0.08166	-1.0735	10	0.07990	T	0.79	-24.5804	17.6998	0.88291	0.0:1.0:0.0:0.0	.	848;858	B4DYP7;Q96CW5	.;GCP3_HUMAN	L	858	ENSP00000261965:V858L	ENSP00000261965:V858L	V	-	1	0	TUBGCP3	112188460	1.000000	0.71417	0.894000	0.35097	0.023000	0.10783	7.085000	0.76875	2.216000	0.71823	0.655000	0.94253	GTG	.	.	.	none		0.458	TUBGCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045825.2	NM_006322		G	113140459	C	G	113140459	3	3	62	1	0	0	0	0	1	0	0	0	16779	536	19	4	155	4	TUBGCP3	13	113140459	Missense_Mutation	SNP	C	TCGA-A4-A4ZT-01A-11D-A26P-10	70954606	113140459	2029419	37	4159											
SMG1	23049	hgsc.bcm.edu	37	chr16	18849889	18849889	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttacctttttcaaagcaaacAttgtaatctatgtgaacaac	15	14	4	8	0	2	1	1	1	1	0	2	1	2	1	1	0	5	2	1	0	7	6			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr16:18849889A>G	ENST00000446231.2	-	43	7480	c.7068T>C	c.(7066-7068)aaT>aaC	p.N2356N	SMG1_ENST00000389467.3_Silent_p.N2356N			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2356	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						CAAAGCAAACATTGTAATCTA	0.328																																					p.N2356N		Atlas-SNP	.											.	SMG1	401	.	0			c.T7068C						PASS	.						147	136	139					16																	18849889		1828	4078	5906	SO:0001819	synonymous_variant	23049	exon43			GCAAACATTGTAA	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.7068T>C	chr16.hg19:g.18849889A>G		113.0	0.0	.		177.0	42.0	.	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Silent	SNP	ENST00000446231.2	hg19	CCDS45430.1																																																																																			.	.	.	none		0.328	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		G	18849889	A	G	18849889	2	3	62	1	0	0	0	0	0	0	0	1	14808	214	8	3		3	SMG1	16	18849889	Silent	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10		18849889	71504864	38	4160											
CCDC113	29070	hgsc.bcm.edu	37	chr16	58292369	58292370	+	Missense_Mutation	DNP	GG	GG	CT																															agccatatccaagaagaaagGgagtattttggccactcaga																										TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr16:58292369_58292370GG>CT	ENST00000219299.4	+	4	567_568	c.488_489GG>CT	c.(487-489)gGG>gCT	p.G163A	CCDC113_ENST00000443128.2_Missense_Mutation_p.G109A	NM_014157.3	NP_054876.2	Q9H0I3	CC113_HUMAN	coiled-coil domain containing 113	163						cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)				large_intestine(4)|lung(6)|ovary(1)|urinary_tract(1)	12						AAGAAGAAAGGGAGTATTTTGG	0.416																																					p.G163A|p.G163G		Atlas-SNP	.											.	CCDC113	30	.	0			c.G488C|c.G489T						PASS	.																																			SO:0001583	missense	29070	exon4			AGAAAGGGAGTAT|GAAAGGGAGTATT	AL136785	CCDS10795.1, CCDS45497.1	16q21	2008-02-05			ENSG00000103021	ENSG00000103021			25002	protein-coding gene	gene with protein product						11230166, 11042152	Standard	NM_014157		Approved	HSPC065, DKFZp434N1418	uc002ene.3	Q9H0I3	OTTHUMG00000133489	Exception_encountered	chr16.hg19:g.58292369_58292370delinsCT	ENSP00000219299:p.Gly163Ala	138.0	0.0	.		128.0	55.0|53.0	.	NM_014157	B2RAQ7|B4DR20|Q9NZX2	Missense_Mutation|Silent	SNP	ENST00000219299.4	hg19	CCDS10795.1																																																																																			.	.	.	none		0.416	CCDC113-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257387.2	NM_014157		CT	58292370	GG	CT	58292369	3	2	62	1	0	0	0	0	1	0	0	0	2752	1232	43	4	502	4	CCDC113	16	58292369	Missense_Mutation	DNP	GG	TCGA-A4-A4ZT-01A-11D-A26P-10	39442480	58292369	32062384	39	4161											
CAMTA2	23125	hgsc.bcm.edu	37	chr17	4872081	4872081	+	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	agtcccggctggggaagcccTtccagctcctggttctgctt	4	11	12	14	1	1	0	0	0	1	0	4	1	4	1	4	4	3	4	4	4	1	3			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr17:4872081T>A	ENST00000348066.3	-	23	3702	c.3579A>T	c.(3577-3579)gaA>gaT	p.E1193D	CAMTA2_ENST00000414043.3_Missense_Mutation_p.R1216W|SPAG7_ENST00000573366.1_5'Flank|CAMTA2_ENST00000572543.1_Missense_Mutation_p.E1198D|SPAG7_ENST00000575142.1_5'Flank|RP5-1050D4.3_ENST00000576752.1_RNA|SPAG7_ENST00000206020.3_5'Flank|SPAG7_ENST00000571023.1_5'Flank|CAMTA2_ENST00000361571.5_Missense_Mutation_p.E1192D|CAMTA2_ENST00000358183.4_Missense_Mutation_p.E1186D|CAMTA2_ENST00000381311.5_Missense_Mutation_p.E1188D	NM_015099.3	NP_055914.2	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	1193					cardiac muscle hypertrophy in response to stress (GO:0014898)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						GGGGAAGCCCTTCCAGCTCCT	0.612																																					p.R1216W		Atlas-SNP	.											.	CAMTA2	93	.	0			c.A3646T						PASS	.						51	56	55					17																	4872081		2203	4300	6503	SO:0001583	missense	23125	exon23			AAGCCCTTCCAGC	AB020716	CCDS11063.1, CCDS54071.1, CCDS54072.1, CCDS54073.1	17p13.3	2004-09-01			ENSG00000108509	ENSG00000108509			18807	protein-coding gene	gene with protein product		611508				11925432	Standard	NM_015099		Approved	KIAA0909	uc010cku.2	O94983	OTTHUMG00000099417	ENST00000348066.3:c.3579A>T	chr17.hg19:g.4872081T>A	ENSP00000321813:p.Glu1193Asp	81.0	0.0	.		88.0	24.0	.	NM_001171167	B9EGL0|D3DTL5|E7EWU5|Q7Z6M8|Q8N3V0|Q8NDG4|Q96G17	Missense_Mutation	SNP	ENST00000348066.3	hg19	CCDS11063.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.8|20.8	4.044334|4.044334	0.75732|0.75732	.|.	.|.	ENSG00000108509|ENSG00000108509	ENST00000381311;ENST00000361571;ENST00000358183;ENST00000348066|ENST00000414043	T;T;T;T|T	0.40756|0.13538	1.4;1.02;1.4;1.05|2.58	4.7|4.7	-0.79|-0.79	0.10932|0.10932	.|.	0.542415|.	0.14944|.	N|.	0.289350|.	T|T	0.06508|0.06508	0.0167|0.0167	L|L	0.27053|0.27053	0.805|0.805	0.24084|0.24084	N|N	0.995937|0.995937	D;P;D|P	0.56035|0.41643	0.974;0.956;0.974|0.758	D;D;D|B	0.70487|0.30251	0.969;0.931;0.953|0.113	T|T	0.30238|0.30238	-0.9985|-0.9985	10|9	0.62326|0.87932	D|D	0.03|0	0.022|0.022	3.8552|3.8552	0.08973|0.08973	0.0:0.2518:0.4031:0.3451|0.0:0.2518:0.4031:0.3451	.|.	1188;1193;1192|1216	O94983-3;O94983;O94983-4|E7EWU5	.;CMTA2_HUMAN;.|.	D|W	1188;1192;1186;1193|1216	ENSP00000370712:E1188D;ENSP00000354828:E1192D;ENSP00000350910:E1186D;ENSP00000321813:E1193D|ENSP00000412886:R1216W	ENSP00000321813:E1193D|ENSP00000412886:R1216W	E|R	-|-	3|1	2|2	CAMTA2|CAMTA2	4812805|4812805	0.276000|0.276000	0.24211|0.24211	0.999000|0.999000	0.59377|0.59377	0.928000|0.928000	0.56348|0.56348	0.041000|0.041000	0.13927|0.13927	0.162000|0.162000	0.19483|0.19483	0.460000|0.460000	0.39030|0.39030	GAA|AGG	.	.	.	none		0.612	CAMTA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216876.1	NM_015099		A	4872081	T	A	4872081	3	1	62	1	0	0	0	0	1	0	0	0	2616	1609	56	5	83	5	CAMTA2	17	4872081	Missense_Mutation	SNP	T	TCGA-A4-A4ZT-01A-11D-A26P-10		4872081	76323129	40	4162											
SSH2	85464	hgsc.bcm.edu	37	chr17	27958364	27958364	+	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	atttggcgagagaagctgagCgcctcatttgggatggtttg	8	12	15	6	2	1	2	1	1	0	1	1	5	1	3	1	3	2	2	1	3	1	3			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr17:27958364C>T	ENST00000269033.3	-	15	3918	c.3767G>A	c.(3766-3768)cGc>cAc	p.R1256H	RP11-68I3.2_ENST00000581474.1_RNA|SSH2_ENST00000540801.1_Missense_Mutation_p.R1283H	NM_001282129.1|NM_033389.2	NP_001269058.1|NP_203747.2	Q76I76	SSH2_HUMAN	slingshot protein phosphatase 2	1256					actin cytoskeleton organization (GO:0030036)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)		SSH2/SUZ12(2)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						AGAAGCTGAGCGCCTCATTTG	0.532																																					p.R1256H		Atlas-SNP	.											.	SSH2	107	.	0			c.G3767A						PASS	.						103	102	102					17																	27958364		2203	4300	6503	SO:0001583	missense	85464	exon15			GCTGAGCGCCTCA	AB072359	CCDS11253.1, CCDS74024.1	17q11.2	2013-03-05	2013-03-05		ENSG00000141298	ENSG00000141298		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"	30580	protein-coding gene	gene with protein product		606779	"slingshot homolog 2 (Drosophila)"			11832213, 11214970	Standard	XM_005258059		Approved	KIAA1725	uc002heo.1	Q76I76	OTTHUMG00000132752	ENST00000269033.3:c.3767G>A	chr17.hg19:g.27958364C>T	ENSP00000269033:p.Arg1256His	93.0	0.0	.		136.0	81.0	.	NM_033389	Q8TDB5|Q8WYL1|Q8WYL2|Q96F40|Q96H36|Q9C0D8	Missense_Mutation	SNP	ENST00000269033.3	hg19	CCDS11253.1	.	.	.	.	.	.	.	.	.	.	C	15.98	2.991842	0.54041	.	.	ENSG00000141298	ENST00000269033;ENST00000540801	T;T	0.45668	0.89;0.89	6.17	5.19	0.71726	.	0.253540	0.39407	N	0.001375	T	0.34337	0.0894	L	0.39397	1.21	0.80722	D	1	P;B	0.35192	0.489;0.357	B;B	0.29663	0.105;0.048	T	0.17592	-1.0364	10	0.54805	T	0.06	-7.483	14.755	0.69557	0.0:0.9289:0.0:0.0711	.	1283;1256	F5H527;Q76I76	.;SSH2_HUMAN	H	1256;1283	ENSP00000269033:R1256H;ENSP00000444743:R1283H	ENSP00000269033:R1256H	R	-	2	0	SSH2	24982490	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.058000	0.57463	1.560000	0.49568	0.655000	0.94253	CGC	.	.	.	none		0.532	SSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256116.1	NM_033389		T	27958364	C	T	27958364	3	4	62	1	0	0	0	0	1	0	0	0	15197	768	27	1	508	1	SSH2	17	27958364	Missense_Mutation	SNP	C	TCGA-A4-A4ZT-01A-11D-A26P-10	23086283	27958364	53236846	41	4163											
SLFN13	146857	hgsc.bcm.edu	37	chr17	33772567	33772567	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acacgcggcccgtataactcTcgccctctcttggtctctct	5	12	7	17	4	4	0	0	0	4	0	7	0	4	0	2	2	1	1	2	2	2	3			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr17:33772567T>C	ENST00000285013.6	-	3	408	c.133A>G	c.(133-135)Aga>Gga	p.R45G	SLFN13_ENST00000534689.1_Intron|SLFN13_ENST00000542635.1_Missense_Mutation_p.R45G|SLFN13_ENST00000526861.1_Missense_Mutation_p.R45G|SLFN13_ENST00000360502.2_Intron|SLFN13_ENST00000533791.1_Missense_Mutation_p.R45G	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	45						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)		CGTATAACTCTCGCCCTCTCT	0.498																																					p.R45G		Atlas-SNP	.											.	SLFN13	79	.	0			c.A133G						PASS	.						108	111	110					17																	33772567		2203	4300	6503	SO:0001583	missense	146857	exon3			TAACTCTCGCCCT	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.133A>G	chr17.hg19:g.33772567T>C	ENSP00000285013:p.Arg45Gly	73.0	0.0	.		88.0	46.0	.	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Missense_Mutation	SNP	ENST00000285013.6	hg19	CCDS32620.1	.	.	.	.	.	.	.	.	.	.	T	11.35	1.611668	0.28712	.	.	ENSG00000154760	ENST00000285013;ENST00000526861;ENST00000542635;ENST00000524511	T;T;T;T	0.23950	4.48;4.48;4.48;1.88	3.28	3.28	0.37604	.	0.641780	0.12846	U	0.434341	T	0.22820	0.0551	M	0.62723	1.935	0.09310	N	1	B	0.33694	0.421	B	0.24006	0.05	T	0.13202	-1.0518	10	0.46703	T	0.11	.	8.1521	0.31148	0.0:0.0:0.0:1.0	.	45	Q68D06	SLN13_HUMAN	G	45	ENSP00000285013:R45G;ENSP00000434439:R45G;ENSP00000444016:R45G;ENSP00000433181:R45G	ENSP00000285013:R45G	R	-	1	2	SLFN13	30796680	0.001000	0.12720	0.000000	0.03702	0.122000	0.20287	1.012000	0.29924	1.481000	0.48307	0.172000	0.16884	AGA	.	.	.	none		0.498	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682		C	33772567	T	C	33772567	3	2	62	1	0	0	0	0	1	0	0	0	14749	1559	54	3	2576	3	SLFN13	17	33772567	Missense_Mutation	SNP	T	TCGA-A4-A4ZT-01A-11D-A26P-10	5814203	33772567	47422643	42	4164											
LASP1	3927	hgsc.bcm.edu	37	chr17	37070728	37070728	+	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	acatcccgaccagtgccccgGgtgagtgcaggtcctgttgg	6	8	14	13	2	0	1	0	1	0	0	2	2	2	1	5	3	2	2	5	3	0	1			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr17:37070728G>A	ENST00000318008.6	+	5	839	c.508G>A	c.(508-510)Gtt>Att	p.V170I	LASP1_ENST00000433206.2_Splice_Site_p.V114I|LASP1_ENST00000435347.3_Splice_Site_p.V170I	NM_006148.2	NP_006139.1	Q14847	LASP1_HUMAN	LIM and SH3 protein 1	170					ion transport (GO:0006811)|positive regulation of signal transduction (GO:0009967)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	ion transmembrane transporter activity (GO:0015075)|SH3/SH2 adaptor activity (GO:0005070)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(2)|lung(4)|urinary_tract(2)	9						CAGTGCCCCGGGTGAGTGCAG	0.657			T	MLL	AML																																p.V170I		Atlas-SNP	.		Dom	yes		17	17q11-q21.3	3927	LIM and SH3 protein 1		L	.	LASP1	24	.	0			c.G508A						PASS	.						24	30	28					17																	37070728		2202	4299	6501	SO:0001630	splice_region_variant	3927	exon5			GCCCCGGGTGAGT		CCDS11331.1, CCDS62164.1	17q11-q21.3	2008-07-18			ENSG00000002834	ENSG00000002834			6513	protein-coding gene	gene with protein product		602920				7490069	Standard	NM_006148		Approved	MLN50, Lasp-1	uc010cvq.3	Q14847	OTTHUMG00000133182	ENST00000318008.6:c.508+1G>A	chr17.hg19:g.37070728G>A		50.0	0.0	.		100.0	50.0	.	NM_006148	B4DGQ0|Q96ED2|Q96IG0	Missense_Mutation	SNP	ENST00000318008.6	hg19	CCDS11331.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.080367	0.76528	.	.	ENSG00000002834	ENST00000318008;ENST00000433206;ENST00000435347;ENST00000419929	T;T;T;T	0.39997	1.17;1.05;1.17;2.67	5.24	5.24	0.73138	.	0.969776	0.08459	N	0.942649	T	0.33411	0.0862	N	0.24115	0.695	0.41878	D	0.990301	B;B	0.32302	0.363;0.018	B;B	0.24701	0.055;0.016	T	0.11397	-1.0589	10	0.31617	T	0.26	.	17.3957	0.87444	0.0:0.0:1.0:0.0	.	114;170	B4DGQ0;Q14847	.;LASP1_HUMAN	I	170;114;170;134	ENSP00000325240:V170I;ENSP00000401048:V114I;ENSP00000392853:V170I;ENSP00000391897:V134I	ENSP00000325240:V170I	V	+	1	0	LASP1	34324254	1.000000	0.71417	0.713000	0.30519	0.712000	0.41017	4.856000	0.62932	2.431000	0.82371	0.563000	0.77884	GTT	.	.	.	none		0.657	LASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256890.3	NM_006148	Missense_Mutation	A	37070728	G	A	37070728	5	1	62	1	0	0	0	0	0	0	1	0	8644	1246	43	2	526	2	LASP1	17	37070728	Splice_Site	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10	3298161	37070728	44124482	43	4165											
KRT13	3860	hgsc.bcm.edu	37	chr17	39661375	39661375	+	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	gctcagggctagctgggctcTgcttcaggtgccagtcacgg	5	9	15	12	1	4	0	3	0	1	0	4	0	4	0	1	4	3	5	1	4	1	2			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr17:39661375T>A	ENST00000246635.3	-	1	474	c.428A>T	c.(427-429)cAg>cTg	p.Q143L	KRT13_ENST00000587544.1_Missense_Mutation_p.Q143L|KRT13_ENST00000587118.1_5'Flank|AC019349.5_ENST00000411759.1_RNA|KRT13_ENST00000336861.3_Missense_Mutation_p.Q143L	NM_153490.2	NP_705694	P13646	K1C13_HUMAN	keratin 13	143	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)				AGCTGGGCTCTGCTTCAGGTG	0.617																																					p.Q143L		Atlas-SNP	.											.	KRT13	72	.	0			c.A428T						PASS	.						112	104	107					17																	39661375		2203	4300	6503	SO:0001583	missense	3860	exon1			GGGCTCTGCTTCA		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.428A>T	chr17.hg19:g.39661375T>A	ENSP00000246635:p.Gln143Leu	171.0	0.0	.		248.0	155.0	.	NM_002274	Q53G54|Q6AZK5|Q8N240	Missense_Mutation	SNP	ENST00000246635.3	hg19	CCDS11396.1	.	.	.	.	.	.	.	.	.	.	T	14.15	2.448953	0.43531	.	.	ENSG00000171401	ENST00000246635;ENST00000336861;ENST00000157775	D;D	0.89196	-2.48;-2.48	4.9	4.9	0.64082	Filament (1);	0.152962	0.30244	N	0.010071	D	0.94663	0.8279	M	0.87381	2.88	0.35788	D	0.822162	D;D;D;D	0.67145	0.979;0.996;0.989;0.996	P;D;D;D	0.71870	0.905;0.975;0.925;0.975	D	0.97698	1.0183	10	0.62326	D	0.03	.	14.6956	0.69118	0.0:0.0:0.0:1.0	.	131;143;143;143	P13646-2;A1A4E9;P13646-3;P13646	.;.;.;K1C13_HUMAN	L	143;143;131	ENSP00000246635:Q143L;ENSP00000336604:Q143L	ENSP00000157775:Q131L	Q	-	2	0	KRT13	36914901	0.975000	0.34042	0.999000	0.59377	0.052000	0.14988	3.295000	0.51794	2.073000	0.62155	0.533000	0.62120	CAG	.	.	.	none		0.617	KRT13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257297.1	NM_153490		A	39661375	T	A	39661375	3	1	62	1	0	0	0	0	1	0	0	0	8457	1580	55	5	980	5	KRT13	17	39661375	Missense_Mutation	SNP	T	TCGA-A4-A4ZT-01A-11D-A26P-10	2590647	39661375	41533835	44	4166											
CDC27	996	hgsc.bcm.edu	37	chr17	45214536	45214536	+	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	accatgcattataatgtctaGgattgactctgatagcattt	12	15	7	7	0	2	2	0	2	2	0	2	3	2	3	1	1	2	2	1	1	4	6			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr17:45214536G>T	ENST00000066544.3	-	14	1988	c.1895C>A	c.(1894-1896)cCt>cAt	p.P632H	CDC27_ENST00000531206.1_Missense_Mutation_p.P638H|CDC27_ENST00000446365.2_Missense_Mutation_p.P571H|CDC27_ENST00000527547.1_Missense_Mutation_p.P631H	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	632					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						ATAATGTCTAGGATTGACTCT	0.343																																					p.P638H		Atlas-SNP	.											.	CDC27	337	.	0			c.C1913A						PASS	.						41	42	41					17																	45214536		2203	4300	6503	SO:0001583	missense	996	exon14			TGTCTAGGATTGA	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.1895C>A	chr17.hg19:g.45214536G>T	ENSP00000066544:p.Pro632His	28.0	0.0	.		50.0	4.0	.	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	hg19	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.959466	0.74016	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547	T;T;T;T	0.70631	-0.5;-0.5;-0.5;-0.5	5.98	5.98	0.97165	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.266487	0.44688	D	0.000430	D	0.84538	0.5494	M	0.86097	2.795	0.53688	D	0.999971	D;D;D;D	0.65815	0.995;0.991;0.984;0.972	P;P;P;P	0.60117	0.859;0.869;0.779;0.812	D	0.86146	0.1584	10	0.72032	D	0.01	-10.2431	17.9304	0.88994	0.0:0.0:1.0:0.0	.	571;631;638;632	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	H	632;638;571;631	ENSP00000066544:P632H;ENSP00000434614:P638H;ENSP00000392802:P571H;ENSP00000437339:P631H	ENSP00000066544:P632H	P	-	2	0	CDC27	42569535	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.347000	0.59373	2.843000	0.97960	0.585000	0.79938	CCT	.	.	.	none		0.343	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			T	45214536	G	T	45214536	3	4	62	1	0	0	0	0	1	0	0	0	3068	1000	35	4	603	4	CDC27	17	45214536	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10	5553161	45214536	35980674	45	4167											
SCRN2	90507	hgsc.bcm.edu	37	chr17	45918192	45918192	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgcaggaacatggggagtcAgggctcgacgacgccatctg	9	6	15	11	4	2	0	1	0	1	0	4	4	2	2	1	4	1	2	1	4	1	0			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr17:45918192A>G	ENST00000290216.9	-	2	143	c.18T>C	c.(16-18)ccT>ccC	p.P6P	SCRN2_ENST00000584123.1_Silent_p.P14P|SCRN2_ENST00000407215.3_Silent_p.P6P	NM_001145023.1|NM_138355.3	NP_001138495.1|NP_612364.2	Q96FV2	SCRN2_HUMAN	secernin 2	6						extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)			cervix(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	14						ATGGGGAGTCAGGGCTCGACG	0.662																																					p.P6P		Atlas-SNP	.											.	SCRN2	35	.	0			c.T18C						PASS	.						25	31	29					17																	45918192		2203	4299	6502	SO:0001819	synonymous_variant	90507	exon2			GGAGTCAGGGCTC	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.18T>C	chr17.hg19:g.45918192A>G		188.0	0.0	.		243.0	48.0	.	NM_138355	A8K3N1|B7Z8S7|E9PBV5|Q96AC3|Q9BU04	Silent	SNP	ENST00000290216.9	hg19	CCDS11519.1																																																																																			.	.	.	none		0.662	SCRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441383.1	NM_138355		G	45918192	A	G	45918192	2	3	62	1	0	0	0	0	0	0	0	1	13952	175	7	3		3	SCRN2	17	45918192	Silent	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10	703656	45918192	35277018	46	4168											
PPM1E	22843	hgsc.bcm.edu	37	chr17	56833454	56833454	+	Silent	SNP	G	G	A																															tgcggcggcggcgagccggaGccggaacccgaacccgaacc																								rs77856248		TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	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	.	0			c.G96A						PASS	.						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	chr17.hg19:g.56833454G>A		31.0	0.0	.		42.0	9.0	.	NM_014906	Q8N8J9|Q96DB8	Silent	SNP	ENST00000308249.2	hg19	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	62	1	0	0	0	0	0	0	0	1	12348	962	34	2		2	PPM1E	17	56833454	Silent	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10	10915262	56833454	24361756	47	4169	47	2									
PPM1E	22843	hgsc.bcm.edu	37	chr17	56833457	56833457	+	Silent	SNP	G	G	C																															ggcggcggcgagccggagccGgaacccgaacccgaacccga																								rs3834568|rs201186780|rs74256772	byFrequency	TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	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	.	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	chr17.hg19:g.56833457G>C		31.0	0.0	.		42.0	14.0	.	NM_014906	Q8N8J9|Q96DB8	Silent	SNP	ENST00000308249.2	hg19	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	62	1	0	0	0	0	0	0	0	1	12348	1103	39	4		4	PPM1E	17	56833457	Silent	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10	3	56833457	24361753	48	4170	47	2									
AP3D1	8943	hgsc.bcm.edu	37	chr19	2130440	2130440	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctccagcttctccttcagccGgggaaaggcagggcgcagcg	7	6	14	14	3	2	0	1	0	1	0	4	1	3	1	3	4	3	3	3	4	1	2			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr19:2130440G>A	ENST00000345016.5	-	6	790	c.559C>T	c.(559-561)Cgg>Tgg	p.R187W	AP3D1_ENST00000355272.6_Missense_Mutation_p.R187W|AP3D1_ENST00000350812.6_Intron|AP3D1_ENST00000590683.1_5'Flank|AP3D1_ENST00000356926.4_Intron	NM_003938.6	NP_003929.4	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1 subunit	187					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)		TCCTTCAGCCGGGGAAAGGCA	0.597																																					p.R187W		Atlas-SNP	.											.	AP3D1	81	.	0			c.C559T						PASS	.						90	101	97					19																	2130440		2034	4183	6217	SO:0001583	missense	8943	exon6			TCAGCCGGGGAAA	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.559C>T	chr19.hg19:g.2130440G>A	ENSP00000344055:p.Arg187Trp	123.0	0.0	.		106.0	6.0	.	NM_001261826	O00202|O75262|Q59HF5|Q96G11|Q9H3C6	Missense_Mutation	SNP	ENST00000345016.5	hg19	CCDS42459.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.333240	0.81801	.	.	ENSG00000065000	ENST00000345016;ENST00000355272;ENST00000343722	T;T	0.28255	1.62;1.62	4.61	4.61	0.57282	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.65059	0.2655	M	0.92459	3.31	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77004	0.95;0.989	T	0.76187	-0.3051	10	0.87932	D	0	-30.4076	16.444	0.83910	0.0:0.0:1.0:0.0	.	187;187	O14617-5;O14617	.;AP3D1_HUMAN	W	187	ENSP00000344055:R187W;ENSP00000347416:R187W	ENSP00000341579:R187W	R	-	1	2	AP3D1	2081440	1.000000	0.71417	0.999000	0.59377	0.961000	0.63080	6.998000	0.76277	2.116000	0.64780	0.542000	0.68232	CGG	.	.	.	none		0.597	AP3D1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450912.1			A	2130440	G	A	2130440	3	1	62	1	0	0	0	0	1	0	0	0	746	1115	39	1	3160	1	AP3D1	19	2130440	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10		2130440	56998543	49	4171											
ZNF564	163050	hgsc.bcm.edu	37	chr19	12639471	12639471	+	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	cagcaaagcccactcctcaaGtgtgaagttcacagccacat	13	7	7	14	0	2	1	2	1	0	0	3	1	3	1	3	0	3	2	3	0	3	1			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr19:12639471G>T	ENST00000339282.7	-	2	239	c.43C>A	c.(43-45)Ctt>Att	p.L15I	CTD-2192J16.21_ENST00000601420.1_RNA|CTD-2192J16.20_ENST00000593682.1_3'UTR|ZNF709_ENST00000428311.1_Intron	NM_144976.3	NP_659413.1	Q8TBZ8	ZN564_HUMAN	zinc finger protein 564	15	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18						CACTCCTCAAGTGTGAAGTTC	0.468																																					p.L15I		Atlas-SNP	.											.	ZNF564	55	.	0			c.C43A						PASS	.						91	92	91					19																	12639471		2203	4300	6503	SO:0001583	missense	163050	exon2			CCTCAAGTGTGAA	BC028367	CCDS42505.1	19p13.2	2013-09-19			ENSG00000249709	ENSG00000249709		"Zinc fingers, C2H2-type", "-"	31106	protein-coding gene	gene with protein product							Standard	NM_144976		Approved	MGC26914		Q8TBZ8	OTTHUMG00000156418	ENST00000339282.7:c.43C>A	chr19.hg19:g.12639471G>T	ENSP00000340004:p.Leu15Ile	94.0	0.0	.		86.0	18.0	.	NM_144976	B9EGT4|Q6P1K6	Missense_Mutation	SNP	ENST00000339282.7	hg19	CCDS42505.1	.	.	.	.	.	.	.	.	.	.	G	10.57	1.387425	0.25031	.	.	ENSG00000249709	ENST00000339282	T	0.01838	4.61	1.99	0.862	0.19056	Krueppel-associated box (4);	.	.	.	.	T	0.04724	0.0128	M	0.84683	2.71	0.20926	N	0.999823	B	0.29909	0.261	B	0.33196	0.159	T	0.28235	-1.0050	9	0.52906	T	0.07	.	4.2715	0.10789	0.0:0.2591:0.4772:0.2636	.	15	Q8TBZ8	ZN564_HUMAN	I	15	ENSP00000340004:L15I	ENSP00000340004:L15I	L	-	1	0	ZNF564	12500471	0.000000	0.05858	0.452000	0.26994	0.655000	0.38815	-0.253000	0.08794	0.174000	0.19809	0.442000	0.29010	CTT	.	.	.	none		0.468	ZNF564-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344120.2	NM_144976		T	12639471	G	T	12639471	3	4	62	1	0	0	0	0	1	0	0	0	18007	1029	36	4	1630	4	ZNF564	19	12639471	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10	10509031	12639471	46489512	50	4172											
ZNF493	284443	hgsc.bcm.edu	37	chr19	21606232	21606232	+	Missense_Mutation	SNP	A	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	aaccttactacacataagagAattcatactggacagaaacc	18	8	5	10	0	1	2	1	0	0	2	1	4	1	3	2	1	5	0	2	1	7	5			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr19:21606232A>C	ENST00000355504.4	+	2	653	c.387A>C	c.(385-387)agA>agC	p.R129S	ZNF493_ENST00000392288.2_Missense_Mutation_p.R257S|CTD-2561J22.3_ENST00000600810.1_Intron	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	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)|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						CACATAAGAGAATTCATACTG	0.378																																					p.R257S		Atlas-SNP	.											.	ZNF493	178	.	0			c.A771C						PASS	.						38	41	40					19																	21606232		2203	4296	6499	SO:0001583	missense	284443	exon4			TAAGAGAATTCAT	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.387A>C	chr19.hg19:g.21606232A>C	ENSP00000347691:p.Arg129Ser	91.0	0.0	.		72.0	38.0	.	NM_001076678	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	hg19	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	9.658	1.143276	0.21205	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.24151	1.87;1.87	0.927	-1.44	0.08856	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41581	0.1165	M	0.79258	2.445	0.80722	D	1	D;P	0.71674	0.998;0.932	D;B	0.66084	0.941;0.317	T	0.34204	-0.9838	9	0.66056	D	0.02	.	5.0403	0.14456	0.7906:0.0:0.2094:0.0	.	129;257	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	S	257;129	ENSP00000376110:R257S;ENSP00000347691:R129S	ENSP00000347691:R129S	R	+	3	2	ZNF493	21398072	0.000000	0.05858	0.035000	0.18076	0.033000	0.12548	-4.038000	0.00308	-0.593000	0.05844	-0.586000	0.04128	AGA	.	.	.	none		0.378	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		C	21606232	A	C	21606232	3	2	62	1	0	0	0	0	1	0	0	0	17956	243	9	5	848	5	ZNF493	19	21606232	Missense_Mutation	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10	8966761	21606232	37522751	51	4173											
ACSS1	84532	hgsc.bcm.edu	37	chr20	25028726	25028755	+	In_Frame_Del	DEL	GGTGATCCTCACTTCCGTTCCAGGCTCATC	GGTGATCCTCACTTCCGTTCCAGGCTCATC	-																															tcgagggcacagtacctgtaGgtgatcctcacttccgttcc																								rs144423103|rs191234596|rs559373176	byFrequency	TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	GGTGATCCTCACTTCCGTTCCAGGCTCATC	GGTGATCCTCACTTCCGTTCCAGGCTCATC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr20:25028726_25028755delGGTGATCCTCACTTCCGTTCCAGGCTCATC	ENST00000323482.4	-	2	476_505	c.397_426delGATGAGCCTGGAACGGAAGTGAGGATCACC	c.(397-426)gatgagcctggaacggaagtgaggatcaccdel	p.DEPGTEVRIT133del	ACSS1_ENST00000376726.3_In_Frame_Del_p.DEPGTEVRIT133del|ACSS1_ENST00000432802.2_In_Frame_Del_p.DEPGTEVRIT133del	NM_001252675.1|NM_032501.3	NP_001239604.1|NP_115890.2	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	133					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)	p.D133A(1)		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)	AGTACCTGTAGGTGATCCTCACTTCCGTTCCAGGCTCATCGCGCTCCCAG	0.574																																					p.133_143del		Pindel	.											.	ACSS1	46	.	1	Substitution - Missense(1)	lung(1)	c.398_427del						PASS	.																																			SO:0001651	inframe_deletion	84532	exon2			.		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.397_426delGATGAGCCTGGAACGGAAGTGAGGATCACC	chr20.hg19:g.25028726_25028755delGGTGATCCTCACTTCCGTTCCAGGCTCATC	ENSP00000316924:p.Asp133_Thr142del	112.0	0.0	.		72.0	10.0	0.139	NM_001252677	B3KXL2|B4DJZ3|D3DW48|F5H6F4|F8W7Y1|Q5TF42|Q8IV99|Q8N234|Q96JI1|Q96JX6|Q9NU28	In_Frame_Del	DEL	ENST00000323482.4	hg19	CCDS13167.1																																																																																			.	.	.	none		0.574	ACSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078386.2	NM_032501		-	25028755	GGTGATCCTCACTTCCGTTCCAGGCTCATC	-	25028726	7	5	62	1	0	1	0	1	0	0	0	0	188	987	35	0	1695	0	ACSS1	20	25028726	In_Frame_Del	DEL	GGTGATCCTCACTTCCGTTCCAGGCTCATC	TCGA-A4-A4ZT-01A-11D-A26P-10		25028726	37996794	52	4174											
KIAA0406	9675	hgsc.bcm.edu	37	chr20	36641648	36641648	+	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	aagttcatccaatgaccttgGatggtcctgacaatcacact	12	11	7	11	0	2	2	2	2	0	0	4	3	4	3	3	2	0	1	3	2	3	2			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr20:36641648G>C	ENST00000373448.2	-	3	809	c.571C>G	c.(571-573)Cca>Gca	p.P191A	TTI1_ENST00000373447.3_Missense_Mutation_p.P191A|TTI1_ENST00000449821.1_Missense_Mutation_p.P191A|TTI1_ENST00000487362.1_Intron	NM_014657.1	NP_055472.1	O43156	TTI1_HUMAN	TELO2 interacting protein 1	191					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						AATGACCTTGGATGGTCCTGA	0.423																																					p.P191A		Atlas-SNP	.											.	TTI1	104	.	0			c.C571G						PASS	.						61	62	62					20																	36641648		2203	4300	6503	SO:0001583	missense	9675	exon3			ACCTTGGATGGTC	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.571C>G	chr20.hg19:g.36641648G>C	ENSP00000362547:p.Pro191Ala	65.0	0.0	.		64.0	20.0	.	NM_014657	D6W4K3|Q5JX67|Q96A38|Q9BR47|Q9H4K0	Missense_Mutation	SNP	ENST00000373448.2	hg19	CCDS13300.1	.	.	.	.	.	.	.	.	.	.	G	9.292	1.050781	0.19827	.	.	ENSG00000101407	ENST00000373448;ENST00000373447;ENST00000449821	T;T;T	0.13307	2.6;2.6;2.6	5.32	5.32	0.75619	Armadillo-like helical (1);Armadillo-type fold (1);	0.056167	0.64402	D	0.000001	T	0.20455	0.0492	M	0.63428	1.95	0.31399	N	0.676886	D	0.56521	0.976	P	0.49085	0.6	T	0.07443	-1.0772	10	0.07813	T	0.8	-22.5589	16.312	0.82874	0.0:0.0:1.0:0.0	.	191	O43156	TTI1_HUMAN	A	191	ENSP00000362547:P191A;ENSP00000362546:P191A;ENSP00000407270:P191A	ENSP00000362546:P191A	P	-	1	0	TTI1	36075062	0.927000	0.31430	1.000000	0.80357	0.958000	0.62258	1.398000	0.34554	2.767000	0.95098	0.555000	0.69702	CCA	.	.	.	none		0.423	TTI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079138.2	NM_014657		C	36641648	G	C	36641648	3	2	62	1	0	0	0	0	1	0	0	0	8180	1174	41	4	2726	4	KIAA0406	20	36641648	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10	11612922	36641648	26383872	53	4175											
TSHZ2	128553	hgsc.bcm.edu	37	chr20	51871576	51871576	+	Missense_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	tggaaaatactgtcaccacaGccatcaacaaagcccaaaac	18	5	5	13	0	2	0	2	0	0	0	2	1	2	1	3	1	5	0	3	1	7	1			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr20:51871576G>A	ENST00000371497.5	+	2	2466	c.1579G>A	c.(1579-1581)Gcc>Acc	p.A527T	RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000329613.6_Missense_Mutation_p.A524T|TSHZ2_ENST00000603338.2_Missense_Mutation_p.A524T	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	527					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)			TGTCACCACAGCCATCAACAA	0.522																																					p.A527T		Atlas-SNP	.											.	TSHZ2	209	.	0			c.G1579A						PASS	.						50	54	53					20																	51871576		2203	4300	6503	SO:0001583	missense	128553	exon2			ACCACAGCCATCA	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.1579G>A	chr20.hg19:g.51871576G>A	ENSP00000360552:p.Ala527Thr	66.0	0.0	.		67.0	24.0	.	NM_173485	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	hg19	CCDS33490.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.906244	0.92107	.	.	ENSG00000182463	ENST00000371497;ENST00000329613;ENST00000450262	T;T	0.50001	0.76;0.76	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.72334	0.3447	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.73678	-0.3907	10	0.87932	D	0	-23.9458	20.3655	0.98876	0.0:0.0:1.0:0.0	.	527	Q9NRE2	TSH2_HUMAN	T	527;524;53	ENSP00000360552:A527T;ENSP00000333114:A524T	ENSP00000333114:A524T	A	+	1	0	TSHZ2	51304983	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.470000	0.97683	2.822000	0.97130	0.643000	0.83706	GCC	.	.	.	none		0.522	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485		A	51871576	G	A	51871576	3	1	62	1	0	0	0	0	1	0	0	0	16636	971	34	2	1585	2	TSHZ2	20	51871576	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10	15229928	51871576	11153944	54	4176											
IFNAR1	3454	hgsc.bcm.edu	37	chr21	34725063	34725063	+	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	tgatttaattatattttctaGagaaaaattatcgagaaaaa	19	15	5	2	1	1	3	0	1	1	2	2	5	1	3	0	0	0	0	0	0	9	8			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr21:34725063G>A	ENST00000270139.3	+	9	1295		c.e9-1		IFNAR1_ENST00000416947.2_Splice_Site|IFNAR1_ENST00000442357.2_Splice_Site	NM_000629.2	NP_000620.2	P17181	INAR1_HUMAN	interferon (alpha, beta and omega) receptor 1						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)"	ATATTTTCTAGAGAAAAATTA	0.328																																					.	Esophageal Squamous(73;817 1211 32990 35667 42746)	Atlas-SNP	.											.	IFNAR1	44	.	0			c.1144-1G>A						PASS	.						34	39	38					21																	34725063		2200	4297	6497	SO:0001630	splice_region_variant	3454	exon9			TTTCTAGAGAAAA		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.1144-1G>A	chr21.hg19:g.34725063G>A		16.0	0.0	.		18.0	14.0	.	NM_000629	B2R6L9|B4DNT3|D3DSF0|Q53GW9|Q53H11|Q6PKD7|Q7M4L2|Q8WTZ2	Splice_Site	SNP	ENST00000270139.3	hg19	CCDS13624.1	.	.	.	.	.	.	.	.	.	.	G	14.82	2.650324	0.47362	.	.	ENSG00000142166	ENST00000416947;ENST00000270139;ENST00000442357	.	.	.	5.48	4.56	0.56223	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.3702	0.55250	0.0:0.1684:0.8316:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	IFNAR1	33646933	0.956000	0.32656	0.594000	0.28785	0.331000	0.28603	4.213000	0.58520	2.562000	0.86427	0.650000	0.86243	.	.	.	.	none		0.328	IFNAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139823.4		Intron	A	34725063	G	A	34725063	5	1	62	1	0	0	0	0	0	0	1	0	7551	956	33	2	1177	2	IFNAR1	21	34725063	Splice_Site	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10		34725063	13404832	55	4177											
TRIOBP	11078	hgsc.bcm.edu	37	chr22	38119757	38119757	+	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	tctcccaacagaaccactcaAcgagagaattccagaacatc	16	6	5	14	1	2	3	1	0	1	3	5	5	3	3	3	0	4	0	3	0	5	1	rs71322688|rs67890459|rs199535040|rs55745992	byFrequency	TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr22:38119757A>T	ENST00000406386.3	+	7	1449	c.1194A>T	c.(1192-1194)caA>caT	p.Q398H		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	398					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					GAACCACTCAACGAGAGAATT	0.547																																					p.Q398H		Atlas-SNP	.											.	TRIOBP	262	.	0			c.A1194T						PASS	.						118	99	106					22																	38119757		1848	3567	5415	SO:0001583	missense	11078	exon7			CACTCAACGAGAG	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"Pleckstrin homology (PH) domain containing"	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1194A>T	chr22.hg19:g.38119757A>T	ENSP00000384312:p.Gln398His	1.0	0.0	.		13.0	6.0	.	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	hg19	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	A	13.81	2.346788	0.41599	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.34275	1.37	2.47	-1.65	0.08291	.	.	.	.	.	T	0.42177	0.1191	L	0.44542	1.39	0.09310	N	0.999998	D	0.54964	0.969	P	0.62382	0.901	T	0.32402	-0.9908	9	0.49607	T	0.09	.	6.5071	0.22202	0.6093:0.0:0.3907:0.0	.	398	Q9H2D6	TARA_HUMAN	H	398	ENSP00000384312:Q398H	ENSP00000384312:Q398H	Q	+	3	2	TRIOBP	36449703	.	.	0.034000	0.17996	0.078000	0.17371	.	.	-0.503000	0.06586	0.113000	0.15668	CAA	.	.	.	weak		0.547	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			T	38119757	A	T	38119757	3	4	62	1	0	0	0	0	1	0	0	0	16565	40	2	5	1212	5	TRIOBP	22	38119757	Missense_Mutation	SNP	A	TCGA-A4-A4ZT-01A-11D-A26P-10		38119757	13184809	56	4178											
SMC1B	27127	hgsc.bcm.edu	37	chr22	45748333	45748333	+	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	tagcttttgtgaccttacctGtgcacagcaaacaggagagc	11	10	10	10	0	0	2	0	1	0	1	0	3	0	2	2	1	6	3	2	1	3	4			TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chr22:45748333G>T	ENST00000357450.4	-	22	3422	c.3423C>A	c.(3421-3423)caC>caA	p.H1141Q	SMC1B_ENST00000404354.3_Intron	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	1141	Ala/Asp-rich (DA-box).				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)	p.H1143Q(1)		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)		GACCTTACCTGTGCACAGCAA	0.443																																					p.H1141Q		Atlas-SNP	.											SMC1B_ENST00000357450,colon,carcinoma,-1,1	SMC1B	215	.	1	Substitution - Missense(1)	ovary(1)	c.C3423A						PASS	.						74	73	74					22																	45748333		1908	4110	6018	SO:0001583	missense	27127	exon22			TTACCTGTGCACA	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.3423C>A	chr22.hg19:g.45748333G>T	ENSP00000350036:p.His1141Gln	116.0	0.0	.		113.0	32.0	.	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Missense_Mutation	SNP	ENST00000357450.4	hg19	CCDS43027.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.092182	0.76756	.	.	ENSG00000077935	ENST00000357450	T	0.65549	-0.16	6.17	1.52	0.23074	.	0.090318	0.48767	D	0.000179	T	0.64349	0.2590	L	0.59912	1.85	0.80722	D	1	D	0.57257	0.979	P	0.54026	0.74	T	0.65038	-0.6265	10	0.56958	D	0.05	.	8.4322	0.32764	0.1878:0.111:0.7013:0.0	.	1141	Q8NDV3-3	.	Q	1141	ENSP00000350036:H1141Q	ENSP00000350036:H1141Q	H	-	3	2	SMC1B	44126997	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.612000	0.61169	0.948000	0.37687	0.655000	0.94253	CAC	.	.	.	none		0.443	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674		T	45748333	G	T	45748333	3	4	62	1	0	0	0	0	1	0	0	0	14795	1368	48	4	300	4	SMC1B	22	45748333	Missense_Mutation	SNP	G	TCGA-A4-A4ZT-01A-11D-A26P-10	7628576	45748333	5556233	57	4179											
TIMM17B	10245	hgsc.bcm.edu	37	chrX	48751030	48751031	+	Missense_Mutation	DNP	GC	GC	CT																															cctcagtggtactgctgataGctggggtagcctggggccgg																										TCGA-A4-A4ZT-01A-11D-A26P-10	TCGA-A4-A4ZT-10A-01D-A26P-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	483bb781-0179-42e1-bf9c-487b240769b8	3c59a740-98eb-4a0d-8694-ac30ab89b553	g.chrX:48751030_48751031GC>CT	ENST00000376582.3	-	7	648_649	c.500_501GC>AG	c.(499-501)aGC>aAG	p.S167K	TIMM17B_ENST00000465150.2_Missense_Mutation_p.S217K|TIMM17B_ENST00000495490.2_Missense_Mutation_p.S187K|TIMM17B_ENST00000396779.3_Missense_Mutation_p.S217K|TIMM17B_ENST00000472645.1_5'UTR	NM_005834.3	NP_005825.1	O60830	TI17B_HUMAN	translocase of inner mitochondrial membrane 17 homolog B (yeast)	167					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial inner membrane presequence translocase complex (GO:0005744)	P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO:0015450)			kidney(1)|large_intestine(1)|lung(3)|ovary(1)	6						ACTGCTGATAGCTGGGGTAGCC	0.629																																					p.S217R|p.S217N		Atlas-SNP	.											.	TIMM17B	15	.	0			c.C651G|c.G650A						PASS	.																																			SO:0001583	missense	10245	exon8			CTGATAGCTGGGG|TGATAGCTGGGGT	AF034790	CCDS14308.1, CCDS55411.1	Xp11.23	2008-02-05			ENSG00000126768	ENSG00000126768			17310	protein-coding gene	gene with protein product		300249				10339406	Standard	NM_001167947		Approved	DXS9822, JM3	uc004dla.2	O60830	OTTHUMG00000034498	ENST00000376582.3:c.500_501delinsCT	chrX.hg19:g.48751030_48751031delinsCT	ENSP00000365766:p.Ser167Lys	104.0	0.0	.		93.0|92.0	29.0	.	NM_001167947	A8K2E2|J3KPV3|Q9UJV0	Missense_Mutation	SNP	ENST00000376582.3	hg19	CCDS14308.1																																																																																			.	.	.	none		0.629	TIMM17B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083411.2	NM_005834		CT	48751031	GC	CT	48751030	3	2	62	1	0	0	0	0	1	0	0	0	15921	962	34	4	21	4	TIMM17B	23	48751030	Missense_Mutation	DNP	GC	TCGA-A4-A4ZT-01A-11D-A26P-10		48751030	106519530	58	4180											
PRAMEF12	390999	hgsc.bcm.edu	37	chr1	12835789	12835789	+	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	cagaggccctgagtaagagaCgaacagcagggaactgtcca	14	4	13	10	1	0	3	0	1	0	2	1	6	1	4	2	2	3	2	2	2	3	1	rs201386508		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:12835789C>T	ENST00000357726.4	+	2	418	c.391C>T	c.(391-393)Cga>Tga	p.R131*		NM_001080830.1	NP_001074299.1	O95522	PRA12_HUMAN	PRAME family member 12	131					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					NS(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(9)|ovary(3)|skin(1)|urinary_tract(1)	23	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00818)|Colorectal(212;5.04e-06)|Kidney(185;4.99e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000198)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GAGTAAGAGACGAACAGCAGG	0.542																																					p.R131X		Atlas-SNP	.											.	PRAMEF12	69	.	0			c.C391T						PASS	.	C	stop/ARG	1,4345		0,1,2172	109	123	118		391	-2.5	0	1		118	0,8588		0,0,4294	no	stop-gained	PRAMEF12	NM_001080830.1		0,1,6466	TT,TC,CC		0.0,0.023,0.0077		131/484	12835789	1,12933	2173	4294	6467	SO:0001587	stop_gained	390999	exon2			AAGAGACGAACAG		CCDS41254.1	1p36.21	2013-01-17			ENSG00000116726	ENSG00000116726		"-"	22125	protein-coding gene	gene with protein product							Standard	NM_001080830		Approved	OTTHUMG00000001927	uc001aui.3	O95522	OTTHUMG00000001927	ENST00000357726.4:c.391C>T	chr1.hg19:g.12835789C>T	ENSP00000350358:p.Arg131*	137.0	0.0	.		126.0	49.0	.	NM_001080830		Nonsense_Mutation	SNP	ENST00000357726.4	hg19	CCDS41254.1	.	.	.	.	.	.	.	.	.	.	.	14.34	2.507496	0.44558	2.3E-4	0.0	ENSG00000116726	ENST00000357726	.	.	.	2.8	-2.45	0.06481	.	6.292790	0.00896	N	0.002291	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	.	5.4193	0.16392	0.3728:0.2852:0.3419:0.0	.	.	.	.	X	131	.	ENSP00000350358:R131X	R	+	1	2	PRAMEF12	12758376	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-2.908000	0.00700	-0.506000	0.06558	0.313000	0.20887	CGA	.	C|0.999;A|0.001	.	alt		0.542	PRAMEF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005457.1	XM_372760		T	12835789	C	T	12835789	4	4	63	1	0	0	0	0	0	1	0	0	12438	528	19	1	397	1	PRAMEF12	1	12835789	Nonsense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10		12835789	236414832	1	4181											
MYCL1	4610	hgsc.bcm.edu	37	chr1	40366677	40366677	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcgcccagcggacagggggCggcgggcgccgggttgccgg	3	4	21	13	7	0	0	0	0	0	0	1	1	0	1	3	7	2	1	3	7	0	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:40366677C>T	ENST00000372816.2	-	1	877	c.430G>A	c.(430-432)Gcc>Acc	p.A144T	MYCL_ENST00000372815.1_Missense_Mutation_p.A174T|MYCL_ENST00000397332.2_Missense_Mutation_p.A174T|MYCL_ENST00000429311.1_Missense_Mutation_p.A144T|RP1-118J21.5_ENST00000418255.1_RNA			P12524	MYCL_HUMAN	v-myc avian myelocytomatosis viral oncogene lung carcinoma derived homolog	144						nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GGACAGGGGGCGGCGGGCGCC	0.761																																					p.A174T		Atlas-SNP	.											.	MYCL1	36	.	0			c.G520A						PASS	.																																			SO:0001583	missense	4610	exon2			AGGGGGCGGCGGG		CCDS30682.1, CCDS44117.1, CCDS44117.2, CCDS53300.1	1p34.3	2013-07-09	2013-07-09	2013-07-09	ENSG00000116990	ENSG00000116990		"Basic helix-loop-helix proteins"	7555	protein-coding gene	gene with protein product	"l-myc protein", "myc-related gene from lung cancer", "oncogene lmyc"	164850	"v-myc avian myelocytomatosis viral oncogene homolog 1, lung carcinoma derived"	MYCL1		8978772	Standard	NM_001033082		Approved	LMYC, bHLHe38	uc001cer.2	P12524	OTTHUMG00000009243	ENST00000372816.2:c.430G>A	chr1.hg19:g.40366677C>T	ENSP00000361903:p.Ala144Thr	1.0	0.0	.		7.0	4.0	.	NM_005376	A2A2C9|B4DJH2|Q14897|Q5QPL0|Q5QPL1|Q9NUE9	Missense_Mutation	SNP	ENST00000372816.2	hg19	CCDS30682.1	.	.	.	.	.	.	.	.	.	.	C	11.68	1.711171	0.30322	.	.	ENSG00000116990	ENST00000397332;ENST00000372816;ENST00000372815;ENST00000429311	T;T;T;T	0.78003	-0.93;-1.14;1.92;1.51	5.05	1.59	0.23543	.	0.621427	0.17026	N	0.189921	T	0.57814	0.2079	N	0.22421	0.69	0.22531	N	0.999018	B;B	0.10296	0.003;0.001	B;B	0.08055	0.003;0.003	T	0.44050	-0.9353	10	0.41790	T	0.15	-27.6027	2.4699	0.04561	0.233:0.4938:0.1472:0.126	.	144;144	P12524-2;P12524	.;MYCL1_HUMAN	T	174;144;174;144	ENSP00000380494:A174T;ENSP00000361903:A144T;ENSP00000361902:A174T;ENSP00000389358:A144T	ENSP00000361902:A174T	A	-	1	0	MYCL1	40139264	0.999000	0.42202	1.000000	0.80357	0.982000	0.71751	1.103000	0.31062	0.575000	0.29434	0.563000	0.77884	GCC	.	.	.	none		0.761	MYCL-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277004.1	NM_001033082		T	40366677	C	T	40366677	3	4	63	1	0	0	0	0	1	0	0	0	10027	768	27	1	797	1	MYCL1	1	40366677	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	27530888	40366677	208883944	2	4182											
FOXD2	2306	hgsc.bcm.edu	37	chr1	47905224	47905224	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acattcgcctctcgcatcccGgggacgcgctgctgtcctca	5	9	10	17	5	2	0	1	0	1	0	6	1	4	1	3	2	1	3	3	2	0	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:47905224G>A	ENST00000334793.5	+	1	3536	c.1417G>A	c.(1417-1419)Ggg>Agg	p.G473R		NM_004474.3	NP_004465.3	O60548	FOXD2_HUMAN	forkhead box D2	473					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(4)	4				READ - Rectum adenocarcinoma(2;0.0908)		CTCGCATCCCGGGGACGCGCT	0.701																																					p.G473R		Atlas-SNP	.											FOXD2,caecum,carcinoma,0,1	FOXD2	16	.	0			c.G1417A						PASS	.						5	6	6					1																	47905224		2116	4208	6324	SO:0001583	missense	2306	exon1			CATCCCGGGGACG	AF042832	CCDS30708.1	1p34-p32	2008-02-05			ENSG00000186564	ENSG00000186564		"Forkhead boxes"	3803	protein-coding gene	gene with protein product		602211		FKHL17		9403061, 12621056	Standard	NM_004474		Approved	FREAC9	uc001crm.3	O60548	OTTHUMG00000007950	ENST00000334793.5:c.1417G>A	chr1.hg19:g.47905224G>A	ENSP00000335493:p.Gly473Arg	11.0	0.0	.		34.0	21.0	.	NM_004474	Q5SVZ3	Missense_Mutation	SNP	ENST00000334793.5	hg19	CCDS30708.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.990550	0.54041	.	.	ENSG00000186564	ENST00000334793	T	0.61627	0.09	4.99	4.06	0.47325	.	0.529712	0.18195	U	0.148720	T	0.32010	0.0815	N	0.14661	0.345	0.28578	N	0.910271	P	0.38992	0.653	B	0.19946	0.027	T	0.31052	-0.9957	10	0.51188	T	0.08	.	9.9291	0.41512	0.0969:0.0:0.9031:0.0	.	473	O60548	FOXD2_HUMAN	R	473	ENSP00000335493:G473R	ENSP00000335493:G473R	G	+	1	0	FOXD2	47677811	0.000000	0.05858	1.000000	0.80357	0.936000	0.57629	0.303000	0.19210	2.280000	0.76307	0.561000	0.74099	GGG	.	.	.	none		0.701	FOXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021831.1	NM_004474		A	47905224	G	A	47905224	3	1	63	1	0	0	0	0	1	0	0	0	6004	1116	39	1	1419	1	FOXD2	1	47905224	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	7538547	47905224	201345397	3	4183											
C1orf51	148523	hgsc.bcm.edu	37	chr1	150256865	150256882	+	In_Frame_Del	DEL	ATGGACAGGATCCAGCGT	ATGGACAGGATCCAGCGT	-																															gttttcagcagagtgtggcaAtggacaggatccagcgtatt																								rs137955605	byFrequency	TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	ATGGACAGGATCCAGCGT	ATGGACAGGATCCAGCGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:150256865_150256882delATGGACAGGATCCAGCGT	ENST00000290363.5	+	3	921_938	c.472_489delATGGACAGGATCCAGCGT	c.(472-489)atggacaggatccagcgtdel	p.MDRIQR158del	C1orf51_ENST00000469255.1_3'UTR|C1orf51_ENST00000369094.1_In_Frame_Del_p.MDRIQR70del|C1orf51_ENST00000369095.1_In_Frame_Del_p.MDRIQR158del	NM_144697.2	NP_653298.1	Q8N365	CIART_HUMAN		158					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)	p.R163H(1)		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)			GAGTGTGGCAATGGACAGGATCCAGCGTATTGTAGGTG	0.459																																					p.157_163del		Atlas-Indel,Pindel	.											.	C1orf51	35	.	1	Substitution - Missense(1)	urinary_tract(1)	c.471_488del						PASS	.																																			SO:0001651	inframe_deletion	148523	exon3			.																												ENST00000290363.5:c.472_489delATGGACAGGATCCAGCGT	chr1.hg19:g.150256865_150256882delATGGACAGGATCCAGCGT	ENSP00000290363:p.Met158_Arg163del	262.0	0.0	0		171.0	27.0	0.157895	NM_144697	B2RD43|D3DV01|Q8N795|Q96MG6	In_Frame_Del	DEL	ENST00000290363.5	hg19	CCDS949.1																																																																																			.	.	.	none		0.459	C1orf51-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035058.1			-	150256882	ATGGACAGGATCCAGCGT	-	150256865	7	5	63	1	0	1	0	1	0	0	0	0	2045	101	4	0	482	0	C1orf51	1	150256865	In_Frame_Del	DEL	ATGGACAGGATCCAGCGT	TCGA-A4-A57E-01A-11D-A26P-10	102351641	150256865	98993756	4	4184											
PRUNE	58497	hgsc.bcm.edu	37	chr1	151001408	151001408	+	Frame_Shift_Del	DEL	A	A	-																															attttctgtccccatgtggcActccaaacaacggtgagtct																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:151001408delA	ENST00000271620.3	+	7	1077	c.921delA	c.(919-921)gcafs	p.A307fs	PRUNE_ENST00000368935.1_Intron|PRUNE_ENST00000368934.1_Intron|PRUNE_ENST00000368936.1_Frame_Shift_Del_p.A125fs|PRUNE_ENST00000271619.8_Intron|PRUNE_ENST00000467771.1_3'UTR|PRUNE_ENST00000368937.1_Intron	NM_021222.1	NP_067045.1	Q86TP1	PRUNE_HUMAN	prune exopolyphosphatase	307						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)			CCCATGTGGCACTCCAAACAA	0.502																																					p.A307fs		Atlas-Indel,Pindel	.											.	PRUNE	40	.	0			c.920delC						PASS	.						129	94	106					1																	151001408		2203	4300	6503	SO:0001589	frameshift_variant	58497	exon7			.	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.921delA	chr1.hg19:g.151001408delA	ENSP00000271620:p.Ala307fs	143.0	0.0	0		114.0	43.0	0.377193	NM_021222	B2RCH8|B4DFL7|Q5SZF9|Q659E5|Q6P4E0|Q8N654|Q96JU5|Q9C071|Q9C072|Q9UIV0	Frame_Shift_Del	DEL	ENST00000271620.3	hg19	CCDS977.1																																																																																			.	.	.	none		0.502	PRUNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084885.1	NM_021222		-	151001408	A	-	151001408	7	5	63	1	0	1	0	1	0	0	0	0	12650	146	6	0	947	0	PRUNE	1	151001408	Frame_Shift_Del	DEL	A	TCGA-A4-A57E-01A-11D-A26P-10	744543	151001408	98249213	5	4185											
PRDX6	9588	hgsc.bcm.edu	37	chr1	173454563	173454563	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttttcccatcatcgatgatAggaatcgggagcttgccatc	9	12	9	11	2	1	1	1	1	0	0	5	4	2	3	2	2	2	1	2	2	2	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:173454563A>G	ENST00000340385.5	+	3	448	c.316A>G	c.(316-318)Agg>Ggg	p.R106G	PRDX6_ENST00000470017.1_3'UTR	NM_004905.2	NP_004896.1	P30041	PRDX6_HUMAN	peroxiredoxin 6	106	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				hydrogen peroxide catabolic process (GO:0042744)|phospholipid catabolic process (GO:0009395)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|membrane (GO:0016020)	antioxidant activity (GO:0016209)|glutathione peroxidase activity (GO:0004602)|peroxiredoxin activity (GO:0051920)|phospholipase A2 activity (GO:0004623)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	12						CATCGATGATAGGAATCGGGA	0.453																																					p.R106G		Atlas-SNP	.											.	PRDX6	20	.	0			c.A316G						PASS	.						141	133	136					1																	173454563		2203	4300	6503	SO:0001583	missense	9588	exon3			GATGATAGGAATC	D14662	CCDS1307.1	1q24.1	2008-02-05			ENSG00000117592	ENSG00000117592			16753	protein-coding gene	gene with protein product		602316				11233154	Standard	NM_004905		Approved	AOP2, KIAA0106, 1-Cys, NSGPx, PRX, aiPLA2, MGC46173, p29	uc001giy.1	P30041	OTTHUMG00000034804	ENST00000340385.5:c.316A>G	chr1.hg19:g.173454563A>G	ENSP00000342026:p.Arg106Gly	132.0	0.0	.		109.0	44.0	.	NM_004905	A8JZY7|P32077|Q5TAH4|Q5ZEZ8	Missense_Mutation	SNP	ENST00000340385.5	hg19	CCDS1307.1	.	.	.	.	.	.	.	.	.	.	A	5.323	0.244994	0.10077	.	.	ENSG00000117592	ENST00000340385	T	0.30182	1.54	5.27	1.5	0.22942	Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant (1);Thioredoxin-like fold (3);	0.924235	0.09408	N	0.806253	T	0.05318	0.0141	N	0.13299	0.325	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.35847	-0.9772	10	0.35671	T	0.21	-4.8805	2.931	0.05800	0.3634:0.413:0.086:0.1375	.	106	P30041	PRDX6_HUMAN	G	106	ENSP00000342026:R106G	ENSP00000342026:R106G	R	+	1	2	PRDX6	171721186	0.000000	0.05858	0.966000	0.40874	0.149000	0.21700	0.209000	0.17435	0.911000	0.36747	0.528000	0.53228	AGG	.	.	.	none		0.453	PRDX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084222.1	NM_004905		G	173454563	A	G	173454563	3	3	63	1	0	0	0	0	1	0	0	0	12479	411	15	3	326	3	PRDX6	1	173454563	Missense_Mutation	SNP	A	TCGA-A4-A57E-01A-11D-A26P-10	22453155	173454563	75796058	6	4186											
SIPA1L2	57568	hgsc.bcm.edu	37	chr1	232600607	232600607	+	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	actaatcgctgaacaatttcCctgatgtcttcagcacagtt	11	13	6	11	1	2	2	1	2	1	0	4	2	3	2	1	0	2	3	1	0	3	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:232600607C>G	ENST00000366630.1	-	8	3157	c.2799G>C	c.(2797-2799)agG>agC	p.R933S	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.R933S|SIPA1L2_ENST00000308942.4_5'Flank			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	933					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)				GAACAATTTCCCTGATGTCTT	0.408																																					p.R933S		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.G2799C						PASS	.						63	58	60					1																	232600607		1902	4124	6026	SO:0001583	missense	57568	exon7			AATTTCCCTGATG	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.2799G>C	chr1.hg19:g.232600607C>G	ENSP00000355589:p.Arg933Ser	110.0	0.0	.		95.0	37.0	.	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	hg19	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	C	12.18	1.859942	0.32884	.	.	ENSG00000116991	ENST00000366630;ENST00000262861	T;T	0.79554	-1.28;-1.28	6.07	1.09	0.20402	.	0.000000	0.85682	D	0.000000	T	0.81163	0.4765	L	0.52759	1.655	0.51233	D	0.999913	P	0.51351	0.944	P	0.55455	0.776	T	0.77197	-0.2676	10	0.46703	T	0.11	-29.1302	10.0474	0.42195	0.0:0.3607:0.0:0.6393	.	933	Q9P2F8	SI1L2_HUMAN	S	933	ENSP00000355589:R933S;ENSP00000262861:R933S	ENSP00000262861:R933S	R	-	3	2	SIPA1L2	230667230	0.443000	0.25641	0.814000	0.32528	0.705000	0.40729	-0.151000	0.10175	-0.062000	0.13088	-0.136000	0.14681	AGG	.	.	.	none		0.408	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		G	232600607	C	G	232600607	3	3	63	1	0	0	0	0	1	0	0	0	14343	622	22	4	2429	4	SIPA1L2	1	232600607	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	59146044	232600607	16650014	7	4187											
SNTG2	54221	hgsc.bcm.edu	37	chr2	1241762	1241763	+	Missense_Mutation	DNP	CA	CA	AT																															tggctgcgggcggtctcagcCaacatcagggagctgacact																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:1241762_1241763CA>AT	ENST00000308624.5	+	10	951_952	c.822_823CA>AT	c.(820-825)gcCAac>gcATac	p.N275Y	SNTG2_ENST00000407292.1_Missense_Mutation_p.N148Y	NM_018968.3	NP_061841.2	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	275					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|syntrophin complex (GO:0016013)	PDZ domain binding (GO:0030165)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		CGGTCTCAGCCAACATCAGGGA	0.55																																					p.A274A|p.N275Y		Atlas-SNP	.											.	SNTG2	125	.	0			c.C822A|c.A823T						PASS	.																																			SO:0001583	missense	54221	exon10			CTCAGCCAACATC|TCAGCCAACATCA	AJ003029	CCDS46220.1	2p25	2008-05-23			ENSG00000172554	ENSG00000172554			13741	protein-coding gene	gene with protein product		608715				10747910	Standard	NM_018968		Approved	SYN5, G2SYN	uc002qwq.3	Q9NY99	OTTHUMG00000151370	Exception_encountered	chr2.hg19:g.1241762_1241763delinsAT	ENSP00000311837:p.Asn275Tyr	33.0	0.0	.		48.0|47.0	32.0|31.0	.	NM_018968	Q05AH5	Silent|Missense_Mutation	SNP	ENST00000308624.5	hg19	CCDS46220.1																																																																																			.	.	.	none		0.55	SNTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322454.1	NM_018968		AT	1241763	CA	AT	1241762	3	1	63	1	0	0	0	0	1	0	0	0	14888	581	21	4	860	4	SNTG2	2	1241762	Missense_Mutation	DNP	CA	TCGA-A4-A57E-01A-11D-A26P-10		1241762	241957611	8	4188											
IL1A	3552	hgsc.bcm.edu	37	chr2	113540317	113540317	+	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	ttcagagacagatgatcaatGgaggaactgtcttcttcatt	12	13	9	7	0	5	3	3	1	2	2	5	6	5	5	0	2	1	0	0	2	2	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:113540317G>T	ENST00000263339.3	-	3	227	c.72C>A	c.(70-72)tcC>tcA	p.S24S		NM_000575.3	NP_000566.3	P01583	IL1A_HUMAN	interleukin 1, alpha	24					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)	GATGATCAATGGAGGAACTGT	0.373																																					p.S24S		Atlas-SNP	.											.	IL1A	19	.	0			c.C72A						PASS	.						243	215	224					2																	113540317		2203	4300	6503	SO:0001819	synonymous_variant	3552	exon3			ATCAATGGAGGAA	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.72C>A	chr2.hg19:g.113540317G>T		111.0	0.0	.		124.0	25.0	.	NM_000575	Q53QF9|Q7RU02	Silent	SNP	ENST00000263339.3	hg19	CCDS2101.1																																																																																			.	.	.	none		0.373	IL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254084.1	NM_000575		T	113540317	G	T	113540317	2	4	63	1	0	0	0	0	0	0	0	1	7657	1335	47	4		4	IL1A	2	113540317	Silent	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	112298555	113540317	129659056	9	4189											
FAM168B	130074	hgsc.bcm.edu	37	chr2	131812937	131812937	+	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	gagcagggtacaccgttgcaGgcatgccgttgggctgcacc	7	7	15	12	2	0	0	0	0	0	0	0	1	0	0	3	3	5	8	3	3	1	3			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:131812937G>A	ENST00000409185.1	-	5	490	c.383C>T	c.(382-384)cCt>cTt	p.P128L	FAM168B_ENST00000389915.3_Missense_Mutation_p.P128L	NM_001009993.2	NP_001009993.2	A1KXE4	F168B_HUMAN	family with sequence similarity 168, member B	128						cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|lung(2)	5						CACCGTTGCAGGCATGCCGTT	0.622																																					p.P128L		Atlas-SNP	.											.	FAM168B	15	.	0			c.C383T						PASS	.						153	170	164					2																	131812937		2164	4258	6422	SO:0001583	missense	130074	exon5			GTTGCAGGCATGC		CCDS42755.1	2q21.1	2008-08-08			ENSG00000152102	ENSG00000152102			27016	protein-coding gene	gene with protein product							Standard	NM_001009993		Approved	KIAA0280L	uc002tsd.3	A1KXE4	OTTHUMG00000153473	ENST00000409185.1:c.383C>T	chr2.hg19:g.131812937G>A	ENSP00000387051:p.Pro128Leu	196.0	1.0	.		241.0	154.0	.	NM_001009993	Q2TAZ6|Q6NZ40	Missense_Mutation	SNP	ENST00000409185.1	hg19	CCDS42755.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.849158	0.91277	.	.	ENSG00000152102	ENST00000409185;ENST00000389915	.	.	.	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.67524	0.2902	L	0.34521	1.04	0.80722	D	1	D	0.69078	0.997	D	0.78314	0.991	T	0.70364	-0.4892	9	0.87932	D	0	-5.3044	16.8479	0.85986	0.0:0.0:1.0:0.0	.	128	A1KXE4	F168B_HUMAN	L	128	.	ENSP00000374565:P128L	P	-	2	0	FAM168B	131529407	1.000000	0.71417	0.971000	0.41717	0.857000	0.48899	9.249000	0.95470	2.640000	0.89533	0.655000	0.94253	CCT	.	.	.	none		0.622	FAM168B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331299.2	NM_001009993		A	131812937	G	A	131812937	3	1	63	1	0	0	0	0	1	0	0	0	5490	1000	35	2	212	2	FAM168B	2	131812937	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	18272620	131812937	111386436	10	4190											
RAPH1	65059	hgsc.bcm.edu	37	chr2	204304798	204304798	+	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	acacccttgttggagaactcCaggaaggttgactccagaaa	13	8	10	10	0	0	3	0	1	0	2	2	5	2	4	3	3	1	2	3	3	3	3			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:204304798C>G	ENST00000319170.5	-	14	3414	c.3115G>C	c.(3115-3117)Gga>Cga	p.G1039R	RAPH1_ENST00000457812.1_Intron|RAPH1_ENST00000374493.3_Missense_Mutation_p.G1091R|ABI2_ENST00000295851.5_3'UTR	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	1039					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						TGGAGAACTCCAGGAAGGTTG	0.552																																					p.G1039R		Atlas-SNP	.											.	RAPH1	118	.	0			c.G3115C						PASS	.						45	52	50					2																	204304798		2203	4300	6503	SO:0001583	missense	65059	exon14			GAACTCCAGGAAG	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.3115G>C	chr2.hg19:g.204304798C>G	ENSP00000316543:p.Gly1039Arg	56.0	0.0	.		92.0	27.0	.	NM_213589	Q96Q37|Q9C0I2	Missense_Mutation	SNP	ENST00000319170.5	hg19	CCDS2359.1	.	.	.	.	.	.	.	.	.	.	C	14.09	2.432725	0.43224	.	.	ENSG00000173166	ENST00000319170;ENST00000374493	T;T	0.43294	0.95;0.96	4.46	1.62	0.23740	.	.	.	.	.	T	0.19327	0.0464	N	0.08118	0	0.09310	N	0.999998	B	0.31125	0.309	B	0.25884	0.064	T	0.16541	-1.0399	9	0.26408	T	0.33	.	7.532	0.27689	0.0:0.4758:0.0:0.5242	.	1039	Q70E73	RAPH1_HUMAN	R	1039;1091	ENSP00000316543:G1039R;ENSP00000363617:G1091R	ENSP00000316543:G1039R	G	-	1	0	RAPH1	204013043	0.026000	0.19158	0.000000	0.03702	0.668000	0.39293	0.417000	0.21214	0.104000	0.17725	0.467000	0.42956	GGA	.	.	.	none		0.552	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252		G	204304798	C	G	204304798	3	3	63	1	0	0	0	0	1	0	0	0	13063	603	21	4	641	4	RAPH1	2	204304798	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	72491861	204304798	38894575	11	4191											
ZFAND2B	130617	hgsc.bcm.edu	37	chr2	220072714	220072714	+	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	gcatcaagcaccggcatccaCtggaccatgattgctctggg	9	8	11	13	1	2	1	1	1	1	0	3	2	3	2	3	3	2	4	3	3	1	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:220072714C>T	ENST00000289528.5	+	4	583	c.388C>T	c.(388-390)Ctg>Ttg	p.L130L	ZFAND2B_ENST00000444522.2_Silent_p.L130L|ZFAND2B_ENST00000409319.1_Silent_p.L130L|ZFAND2B_ENST00000468301.1_3'UTR|ZFAND2B_ENST00000409097.1_Silent_p.L130L|ZFAND2B_ENST00000409217.1_Silent_p.L130L|ZFAND2B_ENST00000409206.1_Silent_p.L130L|ZFAND2B_ENST00000409594.1_Silent_p.L130L|ZFAND2B_ENST00000409412.1_Silent_p.L130L|ZFAND2B_ENST00000409336.1_Silent_p.L130L	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	130						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)		CCGGCATCCACTGGACCATGA	0.552																																					p.L130L		Atlas-SNP	.											.	ZFAND2B	28	.	0			c.C388T						PASS	.						80	86	84					2																	220072714		2203	4300	6503	SO:0001819	synonymous_variant	130617	exon4			CATCCACTGGACC	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.388C>T	chr2.hg19:g.220072714C>T		250.0	0.0	.		156.0	107.0	.	NM_138802	Q8NB98	Silent	SNP	ENST00000289528.5	hg19	CCDS2435.1																																																																																			.	.	.	none		0.552	ZFAND2B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256824.2	NM_138802		T	220072714	C	T	220072714	2	4	63	1	0	0	0	0	0	0	0	1	17640	564	20	2		2	ZFAND2B	2	220072714	Silent	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	15767916	220072714	23126659	12	4192											
CUL3	8452	hgsc.bcm.edu	37	chr2	225422463	225422463	+	Missense_Mutation	SNP	T	T	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	aaaaccattgtatatgcattTctatagagctcctcaaaact	15	13	4	9	0	2	1	1	0	1	1	3	1	3	1	2	0	4	3	2	0	8	6			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:225422463T>G	ENST00000264414.4	-	2	515	c.177A>C	c.(175-177)agA>agC	p.R59S	CUL3_ENST00000432260.2_5'UTR|CUL3_ENST00000409777.1_Missense_Mutation_p.R35S|CUL3_ENST00000409096.1_Missense_Mutation_p.R35S|CUL3_ENST00000344951.4_Intron	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	59					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)		TATATGCATTTCTATAGAGCT	0.338																																					p.R65S		Atlas-SNP	.											.	CUL3	96	.	0			c.A195C						PASS	.						99	97	98					2																	225422463		2203	4298	6501	SO:0001583	missense	8452	exon2			TGCATTTCTATAG	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.177A>C	chr2.hg19:g.225422463T>G	ENSP00000264414:p.Arg59Ser	47.0	0.0	.		36.0	24.0	.	NM_001257198	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Missense_Mutation	SNP	ENST00000264414.4	hg19	CCDS2462.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.79|16.79	3.221692|3.221692	0.58560|0.58560	.|.	.|.	ENSG00000036257|ENSG00000036257	ENST00000436172|ENST00000264414;ENST00000409096;ENST00000409777	.|T;T;T	.|0.29917	.|1.55;1.55;1.55	5.55|5.55	5.55|5.55	0.83447|0.83447	.|Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.55641|0.55641	0.1933|0.1933	M|M	0.86420|0.86420	2.815|2.815	0.80722|0.80722	D|D	1|1	.|D;D	.|0.76494	.|0.999;0.999	.|D;D	.|0.67725	.|0.953;0.953	T|T	0.62511|0.62511	-0.6839|-0.6839	5|10	.|0.72032	.|D	.|0.01	.|.	8.148|8.148	0.31124|0.31124	0.0:0.1903:0.0:0.8097|0.0:0.1903:0.0:0.8097	.|.	.|37;59	.|Q53S54;Q13618	.|.;CUL3_HUMAN	Q|S	80|59;35;35	.|ENSP00000264414:R59S;ENSP00000387200:R35S;ENSP00000386525:R35S	.|ENSP00000264414:R59S	K|R	-|-	1|3	0|2	CUL3|CUL3	225130707|225130707	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.980000|1.980000	0.40618|0.40618	2.234000|2.234000	0.73211|0.73211	0.533000|0.533000	0.62120|0.62120	AAA|AGA	.	.	.	none		0.338	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2			G	225422463	T	G	225422463	3	3	63	1	0	0	0	0	1	0	0	0	4058	1780	62	5	2189	5	CUL3	2	225422463	Missense_Mutation	SNP	T	TCGA-A4-A57E-01A-11D-A26P-10	5349749	225422463	17776910	13	4193											
KIF1A	547	hgsc.bcm.edu	37	chr2	241658528	241658528	+	Frame_Shift_Del	DEL	G	G	-																															ctgttgtacatgtaggcataGgggcgccgcaccaccacgaa																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:241658528delG	ENST00000320389.7	-	45	4964	c.4806delC	c.(4804-4806)cccfs	p.P1602fs	KIF1A_ENST00000498729.2_Frame_Shift_Del_p.P1703fs	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	1602	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)		TGTAGGCATAGGGGCGCCGCA	0.622																																					p.Y1704fs		Pindel	.											.	KIF1A	152	.	0			c.5110delT						PASS	.						87	100	96					2																	241658528		2166	4274	6440	SO:0001589	frameshift_variant	547	exon47			.	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.4806delC	chr2.hg19:g.241658528delG	ENSP00000322791:p.Pro1602fs	79.0	0.0	.		289.0	95.0	0.329	NM_001244008	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Frame_Shift_Del	DEL	ENST00000320389.7	hg19	CCDS46561.1																																																																																			.	.	.	none		0.622	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483		-	241658528	G	-	241658528	7	5	63	1	0	1	0	1	0	0	0	0	8290	987	35	0	278	0	KIF1A	2	241658528	Frame_Shift_Del	DEL	G	TCGA-A4-A57E-01A-11D-A26P-10	16236065	241658528	1540845	14	4194											
CMTM7	112616	hgsc.bcm.edu	37	chr3	32433539	32433539	+	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	0	0	0	0	0	0	0	0	0	ccccgcacccacgcggccctGctgaaagtggcgcaaatggt	8	5	12	16	4	0	1	0	1	0	0	0	1	0	1	4	3	1	3	4	3	2	0			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr3:32433539G>C	ENST00000334983.5	+	1	377	c.141G>C	c.(139-141)ctG>ctC	p.L47L	CMTM7_ENST00000349718.4_Silent_p.L47L	NM_138410.2	NP_612419.1	Q96FZ5	CKLF7_HUMAN	CKLF-like MARVEL transmembrane domain containing 7	47	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(1)|lung(2)	4						ACGCGGCCCTGCTGAAAGTGG	0.756																																					p.L47L		Atlas-SNP	.											.	CMTM7	14	.	0			c.G141C						PASS	.						2	2	2					3																	32433539		1638	3364	5002	SO:0001819	synonymous_variant	112616	exon1			GGCCCTGCTGAAA	AF479263	CCDS33730.1, CCDS33731.1	3p22.2	2005-11-08	2005-11-08	2005-11-08	ENSG00000153551	ENSG00000153551			19178	protein-coding gene	gene with protein product		607890	"chemokine-like factor super family 7", "chemokine-like factor superfamily 7"	CKLFSF7			Standard	NM_138410		Approved	FLJ30992	uc003cey.1	Q96FZ5	OTTHUMG00000155869	ENST00000334983.5:c.141G>C	chr3.hg19:g.32433539G>C		0.0	0.0	.		4.0	4.0	.	NM_138410	Q5VLK1	Silent	SNP	ENST00000334983.5	hg19	CCDS33730.1																																																																																			.	.	.	none		0.756	CMTM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342084.1			C	32433539	G	C	32433539	2	2	63	1	0	0	0	0	0	0	0	1	3590	1306	46	4		4	CMTM7	3	32433539	Silent	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10		32433539	165588891	15	4195											
KIT	3815	hgsc.bcm.edu	37	chr4	55570036	55570036	+	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	acttttggatcagcaaatgtCacaacaaccttggaagtagt	14	11	8	8	0	2	0	2	0	0	0	2	2	2	2	1	2	3	2	1	2	5	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr4:55570036C>G	ENST00000288135.5	+	5	1000	c.903C>G	c.(901-903)gtC>gtG	p.V301V		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	301	Ig-like C2-type 3.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CAGCAAATGTCACAACAACCT	0.348		1	"Mis, O"		"GIST, AML, TGCT, mastocytosis, mucosal melanoma"	"GIST, epithelioma"	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																												p.V301V		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.C903G						PASS	.						168	163	165					4																	55570036		2203	4300	6503	SO:0001819	synonymous_variant	3815	exon5	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	AAATGTCACAACA	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.903C>G	chr4.hg19:g.55570036C>G		162.0	0.0	.		164.0	58.0	.	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Silent	SNP	ENST00000288135.5	hg19	CCDS3496.1																																																																																			.	.	.	none		0.348	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			G	55570036	C	G	55570036	2	3	63	1	0	0	0	0	0	0	0	1	8336	813	29	4		4	KIT	4	55570036	Silent	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10		55570036	135584240	16	4196											
ADAMTS3	9508	hgsc.bcm.edu	37	chr4	73148995	73148995	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagccatttgtgaagctgaaCtgaggtggaccctcttggtg	8	11	13	9	0	1	3	0	3	1	0	1	4	1	4	2	3	3	1	2	3	2	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr4:73148995C>T	ENST00000286657.4	-	22	3512	c.3476G>A	c.(3475-3477)aGt>aAt	p.S1159N		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	1159					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)			TGAAGCTGAACTGAGGTGGAC	0.498																																					p.S1159N	NSCLC(168;1941 2048 2918 13048 43078)	Atlas-SNP	.											.	ADAMTS3	164	.	0			c.G3476A						PASS	.						195	172	180					4																	73148995		2203	4300	6503	SO:0001583	missense	9508	exon22			GCTGAACTGAGGT	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.3476G>A	chr4.hg19:g.73148995C>T	ENSP00000286657:p.Ser1159Asn	138.0	0.0	.		157.0	51.0	.	NM_014243	A1L3U9|Q9BXZ8	Missense_Mutation	SNP	ENST00000286657.4	hg19	CCDS3553.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.777427	0.00080	.	.	ENSG00000156140	ENST00000286657	T	0.61040	0.14	5.23	-10.5	0.00291	.	1.555640	0.04150	N	0.321125	T	0.22282	0.0537	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27706	-1.0066	10	0.09084	T	0.74	.	11.9585	0.52995	0.0:0.5187:0.2677:0.2136	.	1159	O15072	ATS3_HUMAN	N	1159	ENSP00000286657:S1159N	ENSP00000286657:S1159N	S	-	2	0	ADAMTS3	73367859	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-2.403000	0.01046	-2.504000	0.00508	-0.423000	0.05987	AGT	.	.	.	none		0.498	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2			T	73148995	C	T	73148995	3	4	63	1	0	0	0	0	1	0	0	0	267	565	20	2	145	2	ADAMTS3	4	73148995	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	17578959	73148995	118005281	17	4197											
DMXL1	1657	hgsc.bcm.edu	37	chr5	118451949	118451949	+	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	aaaaacaatcccaaggagaaAttgacttttcttttgtgtat	15	14	6	6	0	1	2	0	1	1	1	2	3	2	2	1	1	1	1	1	1	6	6			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr5:118451949A>T	ENST00000311085.8	+	7	741	c.661A>T	c.(661-663)Att>Ttt	p.I221F	DMXL1_ENST00000539542.1_Missense_Mutation_p.I221F	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	221			I -> M (in dbSNP:rs7700801).							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)		CCAAGGAGAAATTGACTTTTC	0.403																																					p.I221F		Atlas-SNP	.											.	DMXL1	268	.	0			c.A661T						PASS	.						136	130	132					5																	118451949		2202	4300	6502	SO:0001583	missense	1657	exon7			GGAGAAATTGACT	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.661A>T	chr5.hg19:g.118451949A>T	ENSP00000309690:p.Ile221Phe	79.0	0.0	.		95.0	27.0	.	NM_005509		Missense_Mutation	SNP	ENST00000311085.8	hg19	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	A	14.50	2.554283	0.45487	.	.	ENSG00000172869	ENST00000503802;ENST00000311085;ENST00000539542	T;T;T	0.66815	1.93;-0.23;2.94	4.96	2.25	0.28309	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.551167	0.19764	N	0.106592	T	0.46328	0.1387	L	0.28400	0.85	0.25888	N	0.983509	B;B	0.22541	0.071;0.042	B;B	0.23018	0.043;0.019	T	0.17930	-1.0353	10	0.24483	T	0.36	-0.2952	3.3933	0.07297	0.3747:0.2296:0.3958:0.0	.	221;221	F5H269;Q9Y485	.;DMXL1_HUMAN	F	221	ENSP00000427692:I221F;ENSP00000309690:I221F;ENSP00000439479:I221F	ENSP00000309690:I221F	I	+	1	0	DMXL1	118479848	1.000000	0.71417	0.979000	0.43373	0.953000	0.61014	1.200000	0.32247	0.842000	0.35045	0.533000	0.62120	ATT	.	.	.	none		0.403	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		T	118451949	A	T	118451949	3	4	63	1	0	0	0	0	1	0	0	0	4596	101	4	5	687	5	DMXL1	5	118451949	Missense_Mutation	SNP	A	TCGA-A4-A57E-01A-11D-A26P-10		118451949	62463311	18	4198											
ARAP3	64411	hgsc.bcm.edu	37	chr5	141035313	141035313	+	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	gcgtcgtaagaccactggctGctggtcatcgtgctggtggg	5	10	16	10	3	1	1	1	0	0	1	3	1	1	1	1	4	2	4	1	4	1	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr5:141035313G>C	ENST00000239440.4	-	31	4050	c.3985C>G	c.(3985-3987)Cag>Gag	p.Q1329E	ARAP3_ENST00000512390.1_5'UTR|ARAP3_ENST00000513878.1_Missense_Mutation_p.Q991E|ARAP3_ENST00000508305.1_Missense_Mutation_p.Q1160E	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	1329					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						ACCACTGGCTGCTGGTCATCG	0.617																																					p.Q1329E		Atlas-SNP	.											.	ARAP3	139	.	0			c.C3985G						PASS	.						84	79	81					5																	141035313		2203	4300	6503	SO:0001583	missense	64411	exon31			CTGGCTGCTGGTC	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.3985C>G	chr5.hg19:g.141035313G>C	ENSP00000239440:p.Gln1329Glu	135.0	0.0	.		195.0	58.0	.	NM_022481	B4DIT1|D3DQE3	Missense_Mutation	SNP	ENST00000239440.4	hg19	CCDS4266.1	.	.	.	.	.	.	.	.	.	.	G	11.92	1.782249	0.31502	.	.	ENSG00000120318	ENST00000508305;ENST00000239440;ENST00000513878	T;T;T	0.14893	2.47;3.19;3.04	5.66	5.66	0.87406	Pleckstrin homology-type (1);	0.184808	0.46442	D	0.000286	T	0.14960	0.0361	N	0.24115	0.695	0.36230	D	0.852566	P;P;P	0.46220	0.65;0.874;0.637	B;B;B	0.40375	0.306;0.327;0.087	T	0.06844	-1.0804	10	0.35671	T	0.21	.	19.3334	0.94303	0.0:0.0:1.0:0.0	.	991;1160;1329	B4DIT1;G5E9Y3;Q8WWN8	.;.;ARAP3_HUMAN	E	1160;1329;991	ENSP00000421826:Q1160E;ENSP00000239440:Q1329E;ENSP00000421468:Q991E	ENSP00000239440:Q1329E	Q	-	1	0	ARAP3	141015497	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	5.807000	0.69157	2.675000	0.91044	0.655000	0.94253	CAG	.	.	.	none		0.617	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481		C	141035313	G	C	141035313	3	2	63	1	0	0	0	0	1	0	0	0	840	1328	46	4	661	4	ARAP3	5	141035313	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	22583364	141035313	39879947	19	4199											
PCDH12	51294	hgsc.bcm.edu	37	chr5	141334867	141334868	+	Frame_Shift_Ins	INS	-	-	A																															tcctctgcctgggatggttgINSaaaaggaggttgaccgtgtc																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr5:141334867_141334868insA	ENST00000231484.3	-	1	3759_3760	c.2549_2550insT	c.(2548-2550)ttcfs	p.F850fs	PCDH12_ENST00000512221.1_5'Flank|AC005740.6_ENST00000607378.1_RNA	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	850					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)			TGGGATGGTTGAAAAGGAGGTT	0.629																																					p.F850fs		Pindel	.											PCDH12,bladder,carcinoma,0,1	PCDH12	133	.	0			c.2550_2551insT						PASS	.																																			SO:0001589	frameshift_variant	51294	exon1			.	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.2550dupT	chr5.hg19:g.141334871_141334871dupA	ENSP00000231484:p.Phe850fs	68.0	0.0	.		158.0	47.0	0.297	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Frame_Shift_Ins	INS	ENST00000231484.3	hg19	CCDS4269.1																																																																																			.	.	.	none		0.629	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		A	141334868	-	A	141334867	7	5	63	1	0	1	1	0	0	0	0	0	11517	1281	45	0	1020	0	PCDH12	5	141334867	Frame_Shift_Ins	INS	-	TCGA-A4-A57E-01A-11D-A26P-10	299554	141334867	39580393	20	4200											
ADAMTS2	9509	hgsc.bcm.edu	37	chr5	178567002	178567002	+	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	cgtcccgtttgaggatgtcaGgtgtcagccagatgcagtgt	7	11	14	9	2	2	2	2	1	0	1	3	3	3	3	2	2	2	2	2	2	0	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr5:178567002G>A	ENST00000251582.7	-	11	1765	c.1664C>T	c.(1663-1665)cCt>cTt	p.P555L		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	555	Disintegrin.				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)		GAGGATGTCAGGTGTCAGCCA	0.607																																					p.P555L		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.C1664T						PASS	.						162	170	167					5																	178567002		2203	4300	6503	SO:0001583	missense	9509	exon11			ATGTCAGGTGTCA	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.1664C>T	chr5.hg19:g.178567002G>A	ENSP00000251582:p.Pro555Leu	90.0	0.0	.		190.0	56.0	.	NM_014244		Missense_Mutation	SNP	ENST00000251582.7	hg19	CCDS4444.1	.	.	.	.	.	.	.	.	.	.	G	13.86	2.362637	0.41902	.	.	ENSG00000087116	ENST00000251582	T	0.61274	0.12	4.92	4.92	0.64577	.	0.000000	0.53938	D	0.000058	T	0.62841	0.2461	N	0.20685	0.6	0.80722	D	1	D	0.71674	0.998	D	0.68765	0.96	T	0.67201	-0.5730	10	0.52906	T	0.07	.	17.1242	0.86710	0.0:0.0:1.0:0.0	.	555	O95450	ATS2_HUMAN	L	555	ENSP00000251582:P555L	ENSP00000251582:P555L	P	-	2	0	ADAMTS2	178499608	1.000000	0.71417	0.117000	0.21633	0.227000	0.25037	9.282000	0.95840	2.281000	0.76405	0.561000	0.74099	CCT	.	.	.	none		0.607	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244		A	178567002	G	A	178567002	3	1	63	1	0	0	0	0	1	0	0	0	265	1000	35	2	2019	2	ADAMTS2	5	178567002	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	37232135	178567002	2348258	21	4201											
COL21A1	81578	hgsc.bcm.edu	37	chr6	55925556	55925557	+	Frame_Shift_Ins	INS	-	-	A																															acctcttattacatctgtgcINSaaacttgtcgaataaattgt																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr6:55925556_55925557insA	ENST00000244728.5	-	27	2786_2787	c.2389_2390insT	c.(2389-2391)tgcfs	p.C797fs	COL21A1_ENST00000370808.2_Frame_Shift_Ins_p.C197fs|COL21A1_ENST00000535941.1_Frame_Shift_Ins_p.C797fs|COL21A1_ENST00000467045.1_5'UTR|COL21A1_ENST00000370819.1_Frame_Shift_Ins_p.C794fs	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	797					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)			TACATCTGTGCAAACTTGTCGA	0.297																																					p.C797fs		Atlas-Indel,Pindel	.											.	COL21A1	201	.	0			c.2390_2391insT						PASS	.																																			SO:0001589	frameshift_variant	81578	exon27			.	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.2390dupT	chr6.hg19:g.55925559_55925559dupA	ENSP00000244728:p.Cys797fs	69.0	0.0	0		47.0	14.0	0.297872	NM_030820	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Frame_Shift_Ins	INS	ENST00000244728.5	hg19	CCDS55025.1																																																																																			.	.	.	none		0.297	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2			A	55925557	-	A	55925556	7	5	63	1	0	1	1	0	0	0	0	0	3682	710	25	0	499	0	COL21A1	6	55925556	Frame_Shift_Ins	INS	-	TCGA-A4-A57E-01A-11D-A26P-10		55925556	115189511	22	4202											
LAMA2	3908	hgsc.bcm.edu	37	chr6	129766960	129766960	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaccaagctcggaaacaagcCaattctgtaagttcttttta	14	12	6	9	1	2	0	0	0	2	0	3	1	2	1	2	1	4	3	2	1	7	6			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr6:129766960C>T	ENST00000421865.2	+	45	6472	c.6423C>T	c.(6421-6423)gcC>gcT	p.A2141A		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2141	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		GGAAACAAGCCAATTCTGTAA	0.368																																					p.A2141A		Atlas-SNP	.											.	LAMA2	481	.	0			c.C6423T						PASS	.						53	48	50					6																	129766960		2203	4300	6503	SO:0001819	synonymous_variant	3908	exon45			ACAAGCCAATTCT	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.6423C>T	chr6.hg19:g.129766960C>T		54.0	0.0	.		45.0	19.0	.	NM_000426	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	hg19	CCDS5138.1																																																																																			.	.	.	none		0.368	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			T	129766960	C	T	129766960	2	4	63	1	0	0	0	0	0	0	0	1	8613	581	21	2		2	LAMA2	6	129766960	Silent	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	73841404	129766960	41348107	23	4203											
REPS1	85021	hgsc.bcm.edu	37	chr6	139235873	139235873	+	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	ggaggcactgcaggaggatgGgcaacaactccagcctgttg	10	6	15	10	0	0	0	0	0	0	0	1	3	1	3	2	5	4	4	2	5	2	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr6:139235873G>T	ENST00000450536.2	-	15	2320	c.1746C>A	c.(1744-1746)gcC>gcA	p.A582A	REPS1_ENST00000415951.2_Silent_p.A555A|REPS1_ENST00000258062.5_Silent_p.A581A|REPS1_ENST00000367663.4_Silent_p.A555A|REPS1_ENST00000409812.2_Silent_p.A491A			Q96D71	REPS1_HUMAN	RALBP1 associated Eps domain containing 1	582	Pro-rich.				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)		CAGGAGGATGGGCAACAACTC	0.398																																					p.A581A		Atlas-SNP	.											.	REPS1	58	.	0			c.C1743A						PASS	.						142	141	142					6																	139235873		2203	4300	6503	SO:0001819	synonymous_variant	85021	exon15			AGGATGGGCAACA		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.1746C>A	chr6.hg19:g.139235873G>T		108.0	0.0	.		74.0	33.0	.	NM_031922	B7ZBZ8|B7ZBZ9|B7ZC00|J3KP76|Q5JWJ5|Q5JWJ6|Q5JWJ7|Q8NDR7|Q8WU62|Q9BXY9	Silent	SNP	ENST00000450536.2	hg19																																																																																				.	.	.	none		0.398	REPS1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000042447.3			T	139235873	G	T	139235873	2	4	63	1	0	0	0	0	0	0	0	1	13241	1219	43	4		4	REPS1	6	139235873	Silent	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	9468913	139235873	31879194	24	4204											
MEOX2	4223	hgsc.bcm.edu	37	chr7	15725867	15725867	+	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	caaacatgccctcttcgttgGggtatcccgcgattatgcaa	9	11	9	12	3	1	0	0	0	1	0	3	1	2	0	2	2	3	3	2	2	4	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:15725867G>C	ENST00000262041.5	-	1	570	c.161C>G	c.(160-162)cCc>cGc	p.P54R	AC005550.5_ENST00000438923.1_lincRNA|AC005550.4_ENST00000442176.1_lincRNA	NM_005924.4	NP_005915.2	P50222	MEOX2_HUMAN	mesenchyme homeobox 2	54					angiogenesis (GO:0001525)|blood circulation (GO:0008015)|limb development (GO:0060173)|multicellular organismal development (GO:0007275)|neuron death (GO:0070997)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle tissue development (GO:0007519)|somite specification (GO:0001757)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding (GO:0043565)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (126;0.0822)		CTCTTCGTTGGGGTATCCCGC	0.572																																					p.P54R	Esophageal Squamous(140;197 1769 16409 18257 29929)	Atlas-SNP	.											.	MEOX2	68	.	0			c.C161G						PASS	.						59	53	55					7																	15725867		2203	4300	6503	SO:0001583	missense	4223	exon1			TCGTTGGGGTATC		CCDS34605.1	7p22.1-p21.3	2014-07-15	2005-12-22		ENSG00000106511	ENSG00000106511		"Homeoboxes / ANTP class : HOXL subclass"	7014	protein-coding gene	gene with protein product	"growth arrest-specific homeobox"	600535	"mesenchyme homeo box 2 (growth arrest-specific homeo box)", "mesenchyme homeobox 2 (growth arrest-specific homeo box)"	GAX		7713505	Standard	NM_005924		Approved	MOX2	uc003stc.3	P50222	OTTHUMG00000152390	ENST00000262041.5:c.161C>G	chr7.hg19:g.15725867G>C	ENSP00000262041:p.Pro54Arg	91.0	0.0	.		161.0	43.0	.	NM_005924	B2R8I7|O75263|Q9UPL6	Missense_Mutation	SNP	ENST00000262041.5	hg19	CCDS34605.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.877795	0.51801	.	.	ENSG00000106511	ENST00000262041	D	0.91068	-2.78	4.88	4.88	0.63580	.	0.233514	0.43919	D	0.000502	D	0.89269	0.6667	L	0.54323	1.7	0.54753	D	0.999981	B	0.23891	0.093	B	0.26517	0.07	D	0.86520	0.1815	10	0.44086	T	0.13	-23.5827	18.4725	0.90779	0.0:0.0:1.0:0.0	.	54	P50222	MEOX2_HUMAN	R	54	ENSP00000262041:P54R	ENSP00000262041:P54R	P	-	2	0	MEOX2	15692392	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.705000	0.91357	2.424000	0.82194	0.650000	0.86243	CCC	.	.	.	none		0.572	MEOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326058.2	NM_005924		C	15725867	G	C	15725867	3	2	63	1	0	0	0	0	1	0	0	0	9481	1232	43	4	765	4	MEOX2	7	15725867	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10		15725867	143412796	25	4205											
HDAC9	9734	hgsc.bcm.edu	37	chr7	18975517	18975517	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggacatgatctcacagcCatctgtgatgcatcagaagc	12	8	11	10	0	3	3	2	2	2	1	4	5	3	5	1	2	3	1	1	2	1	0	rs534633020		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:18975517C>T	ENST00000432645.2	+	22	2880	c.2880C>T	c.(2878-2880)gcC>gcT	p.A960A	HDAC9_ENST00000401921.1_Silent_p.A919A|HDAC9_ENST00000406451.4_Silent_p.A960A|HDAC9_ENST00000441542.2_Silent_p.A963A	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	960	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)	ATCTCACAGCCATCTGTGATG	0.433																																					p.A963A		Atlas-SNP	.											.	HDAC9	560	.	0			c.C2889T						PASS	.						200	193	195					7																	18975517		1929	4145	6074	SO:0001819	synonymous_variant	9734	exon22			CACAGCCATCTGT	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.2880C>T	chr7.hg19:g.18975517C>T		105.0	0.0	.		203.0	48.0	.	NM_178425	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Silent	SNP	ENST00000432645.2	hg19	CCDS47555.1																																																																																			.	.	.	none		0.433	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1			T	18975517	C	T	18975517	2	4	63	1	0	0	0	0	0	0	0	1	7021	581	21	2		2	HDAC9	7	18975517	Silent	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	3249650	18975517	140163146	26	4206											
C7orf46	340277	hgsc.bcm.edu	37	chr7	23728992	23728992	+	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	cagggcttacctttatgtccCcttgaatggtagccagccca	8	11	9	13	0	0	1	0	1	0	0	1	1	1	1	5	2	3	2	5	2	4	5			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:23728992C>G	ENST00000344962.4	+	3	433	c.344C>G	c.(343-345)cCc>cGc	p.P115R	FAM221A_ENST00000409192.3_Missense_Mutation_p.P115R|FAM221A_ENST00000409994.3_Missense_Mutation_p.P57R|FAM221A_ENST00000409653.1_Missense_Mutation_p.P57R	NM_199136.3	NP_954587.2	A4D161	F221A_HUMAN	family with sequence similarity 221, member A	115																	CTTTATGTCCCCTTGAATGGT	0.493																																					p.P115R		Atlas-SNP	.											.	.	.	.	0			c.C344G						PASS	.						86	78	81					7																	23728992		2203	4300	6503	SO:0001583	missense	340277	exon3			ATGTCCCCTTGAA		CCDS5385.1, CCDS47561.1, CCDS47562.1, CCDS75570.1	7p15.3	2012-04-02	2012-04-02	2012-04-02	ENSG00000188732	ENSG00000188732			27977	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 46"	C7orf46		12477932	Standard	XR_242080		Approved	FLJ45875, MGC72075, DKFZp686F0810	uc003swo.4	A4D161	OTTHUMG00000128463	ENST00000344962.4:c.344C>G	chr7.hg19:g.23728992C>G	ENSP00000342576:p.Pro115Arg	84.0	0.0	.		124.0	34.0	.	NM_199136	Q05CG4|Q4G0Q7|Q6P519	Missense_Mutation	SNP	ENST00000344962.4	hg19	CCDS5385.1	.	.	.	.	.	.	.	.	.	.	C	19.81	3.896270	0.72639	.	.	ENSG00000188732	ENST00000409192;ENST00000344962;ENST00000409653;ENST00000409994	T;T;T;T	0.19394	2.15;2.15;2.15;2.15	5.58	5.58	0.84498	.	0.051181	0.85682	D	0.000000	T	0.57272	0.2042	M	0.90650	3.135	0.53005	D	0.999968	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.83275	0.94;0.996;0.996	T	0.65841	-0.6070	10	0.87932	D	0	-12.9907	19.5733	0.95430	0.0:1.0:0.0:0.0	.	57;115;115	A4D161-3;A4D161-2;A4D161	.;.;CG046_HUMAN	R	115;115;57;57	ENSP00000386927:P115R;ENSP00000342576:P115R;ENSP00000386900:P57R;ENSP00000386631:P57R	ENSP00000342576:P115R	P	+	2	0	C7orf46	23695517	1.000000	0.71417	0.971000	0.41717	0.755000	0.42902	5.491000	0.66887	2.622000	0.88805	0.585000	0.79938	CCC	.	.	.	none		0.493	FAM221A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250261.1	NM_199136		G	23728992	C	G	23728992	3	3	63	1	0	0	0	0	1	0	0	0	2398	623	22	4	354	4	C7orf46	7	23728992	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	4753475	23728992	135409671	27	4207											
NEUROD6	63974	hgsc.bcm.edu	37	chr7	31377935	31377935	+	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	tggctgcgcagatgtaagtcGtaagggaagtggctgtcggt	8	10	17	6	3	0	1	0	0	0	1	2	2	0	2	0	4	1	5	0	4	3	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:31377935G>A	ENST00000297142.3	-	2	1270	c.948C>T	c.(946-948)taC>taT	p.Y316Y		NM_022728.2	NP_073565.2	Q96NK8	NDF6_HUMAN	neuronal differentiation 6	316					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)	p.Y316Y(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	32						GATGTAAGTCGTAAGGGAAGT	0.453																																					p.Y316Y		Atlas-SNP	.											NEUROD6,NS,carcinoma,0,1	NEUROD6	84	.	1	Substitution - coding silent(1)	endometrium(1)	c.C948T						PASS	.						82	81	81					7																	31377935		2203	4300	6503	SO:0001819	synonymous_variant	63974	exon2			TAAGTCGTAAGGG	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.948C>T	chr7.hg19:g.31377935G>A		72.0	0.0	.		107.0	53.0	.	NM_022728	Q548T9|Q9H3H6	Silent	SNP	ENST00000297142.3	hg19	CCDS5434.1																																																																																			.	.	.	none		0.453	NEUROD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215050.1	NM_022728		A	31377935	G	A	31377935	2	1	63	1	0	0	0	0	0	0	0	1	10358	1140	40	1		1	NEUROD6	7	31377935	Silent	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	7648943	31377935	127760728	28	4208											
SAMD9L	219285	hgsc.bcm.edu	37	chr7	92764048	92764048	+	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	aagaatgtaccagtcatagtAtgaattatccagtgagtctc	14	12	8	7	0	2	3	1	2	1	1	4	3	3	3	2	0	1	2	2	0	7	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:92764048A>T	ENST00000318238.4	-	5	2453	c.1237T>A	c.(1237-1239)Tac>Aac	p.Y413N	SAMD9L_ENST00000437805.1_Missense_Mutation_p.Y413N|SAMD9L_ENST00000411955.1_Missense_Mutation_p.Y413N	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	413					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)			CAGTCATAGTATGAATTATCC	0.358																																					p.Y413N		Atlas-SNP	.											.	SAMD9L	227	.	0			c.T1237A						PASS	.						136	138	137					7																	92764048		2203	4299	6502	SO:0001583	missense	219285	exon5			CATAGTATGAATT	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.1237T>A	chr7.hg19:g.92764048A>T	ENSP00000326247:p.Tyr413Asn	17.0	0.0	.		25.0	7.0	.	NM_152703	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Missense_Mutation	SNP	ENST00000318238.4	hg19	CCDS34681.1	.	.	.	.	.	.	.	.	.	.	A	15.64	2.892471	0.52121	.	.	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805	T;T;T	0.13538	2.58;2.58;2.58	4.74	4.74	0.60224	.	0.088161	0.46442	D	0.000299	T	0.31104	0.0786	L	0.51422	1.61	0.42354	D	0.992381	D	0.89917	1.0	D	0.77557	0.99	T	0.03514	-1.1029	10	0.72032	D	0.01	-9.3295	14.0508	0.64734	1.0:0.0:0.0:0.0	.	413	Q8IVG5	SAM9L_HUMAN	N	413	ENSP00000326247:Y413N;ENSP00000405760:Y413N;ENSP00000408796:Y413N	ENSP00000326247:Y413N	Y	-	1	0	SAMD9L	92601984	0.688000	0.27680	0.999000	0.59377	0.977000	0.68977	2.301000	0.43628	1.991000	0.58162	0.377000	0.23210	TAC	.	.	.	none		0.358	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703		T	92764048	A	T	92764048	3	4	63	1	0	0	0	0	1	0	0	0	13840	449	16	5	3521	5	SAMD9L	7	92764048	Missense_Mutation	SNP	A	TCGA-A4-A57E-01A-11D-A26P-10	61386113	92764048	66374615	29	4209											
CCDC132	55610	hgsc.bcm.edu	37	chr7	92953019	92953019	+	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	ttattacttgtatgcaatatAtaccttttttggtcggaatg	10	19	7	5	1	0	0	0	0	0	0	1	1	0	1	1	2	3	2	1	2	8	10			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:92953019A>T	ENST00000305866.5	+	21	2080	c.1952A>T	c.(1951-1953)tAt>tTt	p.Y651F	CCDC132_ENST00000544910.1_Missense_Mutation_p.Y621F|CCDC132_ENST00000535481.1_Missense_Mutation_p.Y371F|CCDC132_ENST00000541136.1_Missense_Mutation_p.Y462F	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	651						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)			TATGCAATATATACCTTTTTT	0.279																																					p.Y651F		Atlas-SNP	.											.	CCDC132	136	.	0			c.A1952T						PASS	.						77	71	73					7																	92953019		1800	4052	5852	SO:0001583	missense	55610	exon21			CAATATATACCTT	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.1952A>T	chr7.hg19:g.92953019A>T	ENSP00000307666:p.Tyr651Phe	28.0	0.0	.		36.0	7.0	.	NM_017667	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	hg19	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.071795	0.76301	.	.	ENSG00000004766	ENST00000305866;ENST00000544910;ENST00000541136;ENST00000535481	.	.	.	4.68	4.68	0.58851	.	0.061363	0.64402	D	0.000002	T	0.53158	0.1779	N	0.12853	0.265	0.80722	D	1	D;D;D	0.64830	0.993;0.994;0.993	D;D;D	0.68192	0.956;0.915;0.956	T	0.57768	-0.7754	9	0.41790	T	0.15	-9.4515	14.0796	0.64912	1.0:0.0:0.0:0.0	.	371;621;651	B4DS55;F5H5U7;Q96JG6	.;.;CC132_HUMAN	F	651;621;462;371	.	ENSP00000307666:Y651F	Y	+	2	0	CCDC132	92790955	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.058000	0.93896	1.877000	0.54381	0.402000	0.26972	TAT	.	.	.	none		0.279	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667		T	92953019	A	T	92953019	3	4	63	1	0	0	0	0	1	0	0	0	2769	449	16	5	2076	5	CCDC132	7	92953019	Missense_Mutation	SNP	A	TCGA-A4-A57E-01A-11D-A26P-10	188971	92953019	66185644	30	4210											
BHLHA15	168620	hgsc.bcm.edu	37	chr7	97842056	97842056	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcccaggcctggaggggccGggccccaagctctaccagca	7	4	13	17	1	1	0	0	0	1	0	2	1	2	1	6	5	3	2	6	5	2	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:97842056G>A	ENST00000609256.1	+	2	561	c.435G>A	c.(433-435)ccG>ccA	p.P145P	BHLHA15_ENST00000314018.2_Silent_p.P145P			Q7RTS1	BHA15_HUMAN	basic helix-loop-helix family, member a15	145					calcium-mediated signaling (GO:0019722)|cell maturation (GO:0048469)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|Golgi organization (GO:0007030)|intracellular distribution of mitochondria (GO:0048312)|mitochondrial calcium ion transport (GO:0006851)	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)										TGGAGGGGCCGGGCCCCAAGC	0.667																																					p.P145P		Atlas-SNP	.											.	BHLHA15	11	.	0			c.G435A						PASS	.						12	12	12					7																	97842056		2137	4189	6326	SO:0001819	synonymous_variant	168620	exon1			GGGGCCGGGCCCC	BK000276	CCDS5655.1	7q21.3	2009-01-12	2009-01-12	2009-01-12	ENSG00000180535	ENSG00000180535		"Basic helix-loop-helix proteins"	22265	protein-coding gene	gene with protein product		608606	"basic helix-loop-helix domain containing, class B, 8"	BHLHB8		14516699, 18557763	Standard	NM_177455		Approved	MIST1, bHLHa15	uc003upf.1	Q7RTS1	OTTHUMG00000154289	ENST00000609256.1:c.435G>A	chr7.hg19:g.97842056G>A		37.0	0.0	.		155.0	7.0	.	NM_177455	A4D271|Q14DE4	Silent	SNP	ENST00000609256.1	hg19	CCDS5655.1																																																																																			.	.	.	none		0.667	BHLHA15-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472733.1	NM_177455		A	97842056	G	A	97842056	2	1	63	1	0	0	0	0	0	0	0	1	1419	1103	39	1		1	BHLHA15	7	97842056	Silent	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	4889037	97842056	61296607	31	4211											
MUC17	140453	hgsc.bcm.edu	37	chr7	100676808	100676808	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacactggtggccagttctgAggctagcaccctttcaacaa	10	9	9	13	0	2	1	1	1	1	0	2	1	2	1	2	3	2	3	2	3	3	3	rs71517134		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:100676808A>G	ENST00000306151.4	+	3	2175	c.2111A>G	c.(2110-2112)gAg>gGg	p.E704G		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	704	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)					GCCAGTTCTGAGGCTAGCACC	0.502																																					p.E704G		Atlas-SNP	.											.	MUC17	804	.	0			c.A2111G						PASS	.						340	344	343					7																	100676808		2203	4300	6503	SO:0001583	missense	140453	exon3			GTTCTGAGGCTAG	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.2111A>G	chr7.hg19:g.100676808A>G	ENSP00000302716:p.Glu704Gly	140.0	0.0	.		234.0	54.0	.	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	1.191	-0.635436	0.03584	.	.	ENSG00000169876	ENST00000306151	T	0.02737	4.18	1.07	-0.378	0.12497	.	.	.	.	.	T	0.01189	0.0039	N	0.11560	0.145	0.09310	N	1	P	0.47604	0.898	B	0.31686	0.134	T	0.51458	-0.8703	9	0.25751	T	0.34	.	5.6279	0.17492	0.4094:0.5906:0.0:0.0	.	704	Q685J3	MUC17_HUMAN	G	704	ENSP00000302716:E704G	ENSP00000302716:E704G	E	+	2	0	MUC17	100463528	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.400000	0.07241	-0.070000	0.12908	-0.949000	0.02662	GAG	.	.	.	none		0.502	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		G	100676808	A	G	100676808	3	3	63	1	0	0	0	0	1	0	0	0	9981	304	11	3	2121	3	MUC17	7	100676808	Missense_Mutation	SNP	A	TCGA-A4-A57E-01A-11D-A26P-10	2834752	100676808	58461855	32	4212											
TRPV5	56302	hgsc.bcm.edu	37	chr7	142606703	142606703	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aattcgcacccacagatcccGgagcgaggccacaggcagcg	11	3	12	15	4	0	1	0	0	0	1	2	3	1	2	3	3	2	2	3	3	1	1	rs368151896	byFrequency	TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:142606703G>A	ENST00000265310.1	-	14	2196	c.1848C>T	c.(1846-1848)tcC>tcT	p.S616S		NM_019841.4	NP_062815.2	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel, subfamily V, member 5	616					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|ion transmembrane transport (GO:0034220)|protein tetramerization (GO:0051262)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(14)|lung(32)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	67	Melanoma(164;0.059)					CACAGATCCCGGAGCGAGGCC	0.597													G|||	7	0.00139776	0	0	5008	,	,		20437	0		0	False		,,,				2504	0.0072				p.S616S		Atlas-SNP	.											.	TRPV5	164	.	0			c.C1848T						PASS	.						79	70	73					7																	142606703		2203	4300	6503	SO:0001819	synonymous_variant	56302	exon14			GATCCCGGAGCGA	AJ271207	CCDS5875.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000127412	ENSG00000127412		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	3145	protein-coding gene	gene with protein product		606679	"epithelial calcium channel 1"	ECAC1		10944439, 10945469, 16382100	Standard	NM_019841		Approved	CaT2	uc003wby.1	Q9NQA5	OTTHUMG00000157157	ENST00000265310.1:c.1848C>T	chr7.hg19:g.142606703G>A		52.0	0.0	.		112.0	6.0	.	NM_019841	A4D2H7|E9PBZ6|Q8N4C1|Q8NDW5|Q8NDX7|Q8NDX8|Q96PM6	Silent	SNP	ENST00000265310.1	hg19	CCDS5875.1																																																																																			.	.	.	weak		0.597	TRPV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347660.1	NM_019841		A	142606703	G	A	142606703	2	1	63	1	0	0	0	0	0	0	0	1	16611	1103	39	1		1	TRPV5	7	142606703	Silent	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	41929895	142606703	16531960	33	4213											
COL22A1	169044	hgsc.bcm.edu	37	chr8	139707076	139707076	+	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	acaagagactcaccggttccCcaggcaggcctggatcgccc	9	5	11	16	2	1	1	1	0	0	1	3	3	2	2	5	4	0	2	5	4	1	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr8:139707076C>T	ENST00000303045.6	-	33	3085	c.2639G>A	c.(2638-2640)gGg>gAg	p.G880E	COL22A1_ENST00000435777.1_Missense_Mutation_p.G880E|COL22A1_ENST00000341807.4_5'UTR	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	880	Collagen-like 7.|Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			CACCGGTTCCCCAGGCAGGCC	0.602										HNSCC(7;0.00092)																											p.G880E		Atlas-SNP	.											.	COL22A1	390	.	0			c.G2639A						PASS	.						104	98	100					8																	139707076		2203	4300	6503	SO:0001583	missense	169044	exon33			GGTTCCCCAGGCA	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.2639G>A	chr8.hg19:g.139707076C>T	ENSP00000303153:p.Gly880Glu	108.0	0.0	.		90.0	38.0	.	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	hg19	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	C	9.130	1.011213	0.19277	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.99353	-5.77;-5.77	4.06	3.19	0.36642	.	0.000000	0.48286	U	0.000190	D	0.99489	0.9818	H	0.96518	3.835	0.43412	D	0.995558	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.99078	1.0836	10	0.87932	D	0	.	7.6856	0.28538	0.0:0.883:0.0:0.117	.	880;880	Q8NFW1-2;Q8NFW1	.;COMA1_HUMAN	E	880;880;593	ENSP00000303153:G880E;ENSP00000387655:G880E	ENSP00000303153:G880E	G	-	2	0	COL22A1	139776258	0.931000	0.31567	0.745000	0.31077	0.080000	0.17528	3.173000	0.50839	1.056000	0.40484	0.551000	0.68910	GGG	.	.	.	none		0.602	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		T	139707076	C	T	139707076	3	4	63	1	0	0	0	0	1	0	0	0	3683	623	22	2	2373	2	COL22A1	8	139707076	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10		139707076	6656946	34	4214											
TOP1MT	116447	hgsc.bcm.edu	37	chr8	144397926	144397926	+	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	ttgccatccccttgggctttGtgctcagccctcgccctcct	2	13	8	18	1	1	0	1	0	0	0	4	0	3	0	6	1	3	2	6	1	0	3			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr8:144397926G>C	ENST00000329245.4	-	12	1558	c.1524C>G	c.(1522-1524)caC>caG	p.H508Q	TOP1MT_ENST00000523676.1_Missense_Mutation_p.H410Q|TOP1MT_ENST00000519148.1_Missense_Mutation_p.H410Q|TOP1MT_ENST00000521193.1_Missense_Mutation_p.H410Q|AC087793.1_ENST00000585120.1_RNA	NM_052963.2	NP_443195.1	Q969P6	TOP1M_HUMAN	topoisomerase (DNA) I, mitochondrial	508					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)	CTTGGGCTTTGTGCTCAGCCC	0.662																																					p.H508Q		Atlas-SNP	.											.	TOP1MT	63	.	0			c.C1524G						PASS	.						131	84	100					8																	144397926		2203	4300	6503	SO:0001583	missense	116447	exon12			GGCTTTGTGCTCA	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.1524C>G	chr8.hg19:g.144397926G>C	ENSP00000328835:p.His508Gln	54.0	0.0	.		75.0	35.0	.	NM_052963	B7ZAR5|E7ES89|Q86ST4|Q86V82	Missense_Mutation	SNP	ENST00000329245.4	hg19	CCDS6400.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	1.192|1.192	-0.634970|-0.634970	0.03584|0.03584	.|.	.|.	ENSG00000184428|ENSG00000184428	ENST00000329245;ENST00000521193;ENST00000519148;ENST00000523676|ENST00000519977	T;T;T;T|.	0.42131|.	0.98;0.98;0.98;0.98|.	3.56|3.56	-0.755|-0.755	0.11061|0.11061	DNA breaking-rejoining enzyme, catalytic core (1);DNA topoisomerase I, C-terminal, eukaryotic-type (1);DNA topoisomerase I, catalytic core, alpha/beta subdomain, eukaryotic-type (1);DNA topoisomerases I, dispensable insert, eukaryotic-type (1);|.	1.222760|.	0.06298|.	U|.	0.700351|.	T|T	0.41119|0.41119	0.1145|0.1145	M|M	0.64997|0.64997	1.995|1.995	0.09310|0.09310	N|N	1|1	P;B|.	0.43826|.	0.818;0.437|.	B;B|.	0.43194|.	0.411;0.131|.	T|T	0.38308|0.38308	-0.9667|-0.9667	10|5	0.18276|.	T|.	0.48|.	.|.	4.746|4.746	0.13038|0.13038	0.4744:0.1621:0.3634:0.0|0.4744:0.1621:0.3634:0.0	.|.	303;508|.	E7ESI1;Q969P6|.	.;TOP1M_HUMAN|.	Q|E	508;410;410;410|18	ENSP00000328835:H508Q;ENSP00000428369:H410Q;ENSP00000429169:H410Q;ENSP00000429181:H410Q|.	ENSP00000328835:H508Q|.	H|Q	-|-	3|1	2|0	TOP1MT|TOP1MT	144469301|144469301	0.018000|0.018000	0.18449|0.18449	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	0.132000|0.132000	0.15891|0.15891	-0.145000|-0.145000	0.11294|0.11294	-0.351000|-0.351000	0.07748|0.07748	CAC|CAA	.	.	.	none		0.662	TOP1MT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381247.3	NM_052963		C	144397926	G	C	144397926	3	2	63	1	0	0	0	0	1	0	0	0	16376	1368	48	4	293	4	TOP1MT	8	144397926	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	4690850	144397926	1966096	35	4215											
KCNT1	57582	hgsc.bcm.edu	37	chr9	138649177	138649177	+	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	cgctgcggaacctgttcatcCccgtctttctgaactgctgg	5	12	10	14	3	3	1	1	1	2	0	4	2	4	2	3	2	4	3	3	2	2	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr9:138649177C>G	ENST00000263604.3	+	9	652	c.652C>G	c.(652-654)Ccc>Gcc	p.P218A	KCNT1_ENST00000487664.1_Missense_Mutation_p.P189A|KCNT1_ENST00000298480.5_Missense_Mutation_p.P237A|KCNT1_ENST00000371757.2_Missense_Mutation_p.P237A|KCNT1_ENST00000488444.2_Missense_Mutation_p.P218A|KCNT1_ENST00000486577.2_Missense_Mutation_p.P198A|KCNT1_ENST00000490355.2_Missense_Mutation_p.P218A|KCNT1_ENST00000491806.2_Missense_Mutation_p.P204A			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	218					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)		CCTGTTCATCCCCGTCTTTCT	0.667																																					p.P237A		Atlas-SNP	.											.	KCNT1	139	.	0			c.C709G						PASS	.						51	58	55					9																	138649177		2203	4300	6503	SO:0001583	missense	57582	exon9			TTCATCCCCGTCT	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.652C>G	chr9.hg19:g.138649177C>G	ENSP00000263604:p.Pro218Ala	34.0	0.0	.		55.0	18.0	.	NM_020822	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Missense_Mutation	SNP	ENST00000263604.3	hg19		.	.	.	.	.	.	.	.	.	.	.	23.4	4.416656	0.83449	.	.	ENSG00000107147	ENST00000487664;ENST00000298480;ENST00000371757;ENST00000473941;ENST00000486577;ENST00000491806;ENST00000488444;ENST00000490355;ENST00000263604	T;T;T;D;T	0.97186	1.86;1.86;1.86;-4.28;1.86	4.63	4.63	0.57726	.	0.000000	0.85682	U	0.000000	D	0.98337	0.9448	M	0.79926	2.475	0.80722	D	1	D;D;D	0.89917	1.0;0.998;0.999	D;D;D	0.91635	0.999;0.989;0.992	D	0.99577	1.0972	10	0.72032	D	0.01	-28.7902	16.4704	0.84109	0.0:1.0:0.0:0.0	.	204;237;189	C9JYL2;B9EGP2;G5E9V0	.;.;.	A	189;237;237;184;198;204;218;218;218	ENSP00000417851:P189A;ENSP00000298480:P237A;ENSP00000360822:P237A;ENSP00000420764:P184A;ENSP00000263604:P218A	ENSP00000263604:P218A	P	+	1	0	KCNT1	137788998	1.000000	0.71417	0.995000	0.50966	0.866000	0.49608	7.427000	0.80284	2.124000	0.65301	0.460000	0.39030	CCC	.	.	.	none		0.667	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822		G	138649177	C	G	138649177	3	3	63	1	0	0	0	0	1	0	0	0	8098	623	22	4	743	4	KCNT1	9	138649177	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10		138649177	2564254	36	4216											
GPRIN2	9721	hgsc.bcm.edu	37	chr10	46999193	46999193	+	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	tgtccaccatgggcggcagtGacctgtgtcgcctgcgggcc	4	8	15	14	3	0	1	0	1	0	0	2	1	1	1	5	3	1	1	5	3	0	0			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr10:46999193G>A	ENST00000374317.1	+	3	586	c.313G>A	c.(313-315)Gac>Aac	p.D105N	GPRIN2_ENST00000374314.4_Missense_Mutation_p.D105N	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	105										breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						GGGCGGCAGTGACCTGTGTCG	0.652																																					p.D105N		Atlas-SNP	.											.	GPRIN2	94	.	0			c.G313A						PASS	.						30	29	29					10																	46999193		2196	4288	6484	SO:0001583	missense	9721	exon3			GGCAGTGACCTGT	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.313G>A	chr10.hg19:g.46999193G>A	ENSP00000363436:p.Asp105Asn	8.0	0.0	.		23.0	8.0	.	NM_014696	Q5SVF0	Missense_Mutation	SNP	ENST00000374317.1	hg19	CCDS31192.1	.	.	.	.	.	.	.	.	.	.	G	17.75	3.467432	0.63625	.	.	ENSG00000204175	ENST00000374317;ENST00000374314	T;T	0.03982	3.74;3.74	5.11	5.11	0.69529	.	0.279617	0.25830	N	0.028026	T	0.11495	0.0280	L	0.54323	1.7	0.09310	N	1	D	0.56746	0.977	P	0.52957	0.714	T	0.04678	-1.0934	10	0.45353	T	0.12	-14.3008	14.245	0.65983	0.0:0.0:1.0:0.0	.	105	O60269	GRIN2_HUMAN	N	105	ENSP00000363436:D105N;ENSP00000363433:D105N	ENSP00000363433:D105N	D	+	1	0	GPRIN2	46419199	0.655000	0.27376	0.709000	0.30452	0.969000	0.65631	3.163000	0.50763	2.833000	0.97629	0.650000	0.86243	GAC	.	.	.	none		0.652	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696		A	46999193	G	A	46999193	3	1	63	1	0	0	0	0	1	0	0	0	6737	1290	45	2	315	2	GPRIN2	10	46999193	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10		46999193	88535554	37	4217											
PNLIPRP1	5407	hgsc.bcm.edu	37	chr10	118357347	118357347	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatctcttttagggttggaTcctgtagaagcaagtttcga	9	15	10	7	1	2	1	1	0	1	1	5	3	3	2	1	2	1	4	1	2	4	5			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr10:118357347T>C	ENST00000528052.1	+	7	653	c.582T>C	c.(580-582)gaT>gaC	p.D194D	PNLIPRP1_ENST00000534537.1_Silent_p.D194D|PNLIPRP1_ENST00000358834.4_Silent_p.D194D			P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1	194					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)		TAGGGTTGGATCCTGTAGAAG	0.507																																					p.D194D		Atlas-SNP	.											.	PNLIPRP1	82	.	0			c.T582C						PASS	.						149	129	136					10																	118357347		2203	4300	6503	SO:0001819	synonymous_variant	5407	exon7			GTTGGATCCTGTA	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.582T>C	chr10.hg19:g.118357347T>C		141.0	0.0	.		149.0	57.0	.	NM_006229	Q68D83|Q68DR6|Q8TAU2|Q9BS82	Silent	SNP	ENST00000528052.1	hg19	CCDS7595.1																																																																																			.	.	.	none		0.507	PNLIPRP1-011	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384633.1	NM_006229		C	118357347	T	C	118357347	2	2	63	1	0	0	0	0	0	0	0	1	12157	1432	50	3		3	PNLIPRP1	10	118357347	Silent	SNP	T	TCGA-A4-A57E-01A-11D-A26P-10	71358154	118357347	17177400	38	4218											
MUC2	4583	hgsc.bcm.edu	37	chr11	1094686	1094686	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacccccactcgcggtaccaCgaccgggtcatcttcagccc	7	6	8	20	4	3	0	2	0	1	0	4	1	3	0	5	2	2	1	5	2	1	2	rs375767205		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr11:1094686C>T	ENST00000441003.2	+	31	5801	c.5774C>T	c.(5773-5775)aCg>aTg	p.T1925M	MUC2_ENST00000361558.6_Missense_Mutation_p.T63M|MUC2_ENST00000333592.6_Missense_Mutation_p.T213M	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4287					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)	CGCGGTACCACGACCGGGTCA	0.637													C|||	1	0.000199681	0	0	5008	,	,		16685	0		0	False		,,,				2504	0.001				p.T1921M		Atlas-SNP	.											.	MUC2	614	.	0			c.C5762T						PASS	.		MET/THR	3,4229		0,3,2113	70	87	82		5759	-0.2	0	11		82	1,8447		0,1,4223	no	missense	MUC2	NM_002457.2	81	0,4,6336	TT,TC,CC		0.0118,0.0709,0.0315	benign	1920/2813	1094686	4,12676	2116	4224	6340	SO:0001583	missense	4583	exon32			GTACCACGACCGG	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.5774C>T	chr11.hg19:g.1094686C>T	ENSP00000415183:p.Thr1925Met	80.0	0.0	.		165.0	64.0	.	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	C	7.600	0.672559	0.14776	7.09E-4	1.18E-4	ENSG00000198788	ENST00000441003;ENST00000361558;ENST00000333592	T;T;T	0.51071	2.55;0.72;3.15	2.06	-0.251	0.13003	.	.	.	.	.	T	0.40094	0.1103	M	0.65975	2.015	0.09310	N	1	B	0.18610	0.029	B	0.04013	0.001	T	0.40869	-0.9540	9	0.62326	D	0.03	.	3.434	0.07438	0.2454:0.5996:0.0:0.155	.	1925	E7EUV1	.	M	1925;63;213	ENSP00000415183:T1925M;ENSP00000354885:T63M;ENSP00000331373:T213M	ENSP00000331373:T213M	T	+	2	0	MUC2	1084686	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	0.419000	0.21247	-0.196000	0.10366	-0.354000	0.07668	ACG	.	.	.	weak		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1094686	C	T	1094686	3	4	63	1	0	0	0	0	1	0	0	0	9982	536	19	1	5888	1	MUC2	11	1094686	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10		1094686	133911830	39	4219											
MRGPRX3	117195	hgsc.bcm.edu	37	chr11	18159591	18159591	+	Frame_Shift_Del	DEL	G	G	-																															cgtgggctcctttaggcagcGtcaaaataggcagaacctga																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr11:18159591delG	ENST00000396275.2	+	3	1203	c.842delG	c.(841-843)cgtfs	p.R281fs		NM_054031.3	NP_473372.3	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	281				R -> L (in Ref. 2; AAL86879). {ECO:0000305}.		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						TTTAGGCAGCGTCAAAATAGG	0.517																																					p.R281fs		Atlas-Indel,Pindel	.											MRGPRX3,mouth,carcinoma,0,1	MRGPRX3	59	.	0			c.841delC						PASS	.						56	60	58					11																	18159591		2200	4290	6490	SO:0001589	frameshift_variant	117195	exon3			.		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.842delG	chr11.hg19:g.18159591delG	ENSP00000379571:p.Arg281fs	82.0	0.0	0		65.0	26.0	0.4	NM_054031	B0M0L1|Q8TDE0|Q8TDE1	Frame_Shift_Del	DEL	ENST00000396275.2	hg19	CCDS7830.1																																																																																			.	.	.	none		0.517	MRGPRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389767.1	NM_054031		-	18159591	G	-	18159591	7	5	63	1	0	1	0	1	0	0	0	0	9775	1145	40	0	844	0	MRGPRX3	11	18159591	Frame_Shift_Del	DEL	G	TCGA-A4-A57E-01A-11D-A26P-10	17064905	18159591	116846925	40	4220											
OR4C3	256144	hgsc.bcm.edu	37	chr11	48347236	48347236	+	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	tcctacattgtcatcctgtaCtccttgaggtcccacagtgc	7	13	7	14	0	1	1	1	1	0	0	5	1	5	1	4	1	3	1	4	1	2	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr11:48347236C>T	ENST00000319856.4	+	1	765	c.744C>T	c.(742-744)taC>taT	p.Y248Y		NM_001004702.1	NP_001004702.1	Q8NH37	OR4C3_HUMAN	olfactory receptor, family 4, subfamily C, member 3	221						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						TCATCCTGTACTCCTTGAGGT	0.493																																					p.Y248Y		Atlas-SNP	.											.	OR4C3	75	.	0			c.C744T						PASS	.						268	192	218					11																	48347236		2201	4298	6499	SO:0001819	synonymous_variant	256144	exon1			CCTGTACTCCTTG	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.744C>T	chr11.hg19:g.48347236C>T		267.0	0.0	.		280.0	46.0	.	NM_001004702	B2RNF2|Q6IFB3	Silent	SNP	ENST00000319856.4	hg19	CCDS31489.1																																																																																			.	.	.	none		0.493	OR4C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390557.1	NM_001004702		T	48347236	C	T	48347236	2	4	63	1	0	0	0	0	0	0	0	1	11057	576	20	2		2	OR4C3	11	48347236	Silent	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	30187645	48347236	86659280	41	4221											
RPS6KA4	8986	hgsc.bcm.edu	37	chr11	64136019	64136019	+	Missense_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	cagcttttctgtgtgtcgccGctgccgccagcgccagagcg	4	9	13	15	5	1	1	0	0	1	1	2	1	1	1	4	0	4	2	4	0	0	2	rs199674030		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr11:64136019G>A	ENST00000334205.4	+	11	1345	c.1280G>A	c.(1279-1281)cGc>cAc	p.R427H	RPS6KA4_ENST00000294261.4_Intron|MIR1237_ENST00000408346.1_RNA|RPS6KA4_ENST00000528057.1_Missense_Mutation_p.R420H	NM_003942.2	NP_003933.1	O75676	KS6A4_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 4	427	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|negative regulation of cytokine production (GO:0001818)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|mitogen-activated protein kinase p38 binding (GO:0048273)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)			breast(1)|endometrium(3)|lung(7)|ovary(1)|prostate(1)	13						GTGTGTCGCCGCTGCCGCCAG	0.701													G|||	1	0.000199681	0	0	5008	,	,		9970	0		0.001	False		,,,				2504	0				p.R427H		Atlas-SNP	.											.	RPS6KA4	85	.	0			c.G1280A						PASS	.	G	HIS/ARG,HIS/ARG	1,4357		0,1,2178	9	11	11		1262,1280	4.5	1	11		11	12,8514		0,12,4251	yes	missense,missense	RPS6KA4	NM_001006944.1,NM_003942.2	29,29	0,13,6429	AA,AG,GG		0.1407,0.0229,0.1009	probably-damaging,probably-damaging	421/767,427/773	64136019	13,12871	2179	4263	6442	SO:0001583	missense	8986	exon11			GTCGCCGCTGCCG	AJ010119	CCDS8073.1, CCDS73313.1	11q11-q13	2011-04-05	2002-08-29		ENSG00000162302	ENSG00000162302			10433	protein-coding gene	gene with protein product		603606	"ribosomal protein S6 kinase, 90kD, polypeptide 4"			9792677, 9687510	Standard	XM_005274379		Approved	RSK-B, MSK2	uc001oae.3	O75676	OTTHUMG00000046094	ENST00000334205.4:c.1280G>A	chr11.hg19:g.64136019G>A	ENSP00000333896:p.Arg427His	1.0	0.0	.		13.0	10.0	.	NM_003942	A8K7Z8|O75585|Q53ES8	Missense_Mutation	SNP	ENST00000334205.4	hg19	CCDS8073.1	.	.	.	.	.	.	.	.	.	.	g	17.24	3.339473	0.60963	2.29E-4	0.001407	ENSG00000162302	ENST00000528057;ENST00000334205;ENST00000530504	T;T;T	0.42513	0.97;0.97;0.97	4.5	4.5	0.54988	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.221656	0.37530	N	0.002053	T	0.47451	0.1446	L	0.33339	1.005	0.09310	N	0.999995	D;D;D	0.69078	0.963;0.997;0.984	P;D;P	0.65323	0.616;0.934;0.843	T	0.32214	-0.9915	10	0.72032	D	0.01	.	8.538	0.33375	0.108:0.0:0.892:0.0	.	420;427;421	E9PJN1;O75676;O75676-2	.;KS6A4_HUMAN;.	H	420;427;405	ENSP00000435580:R420H;ENSP00000333896:R427H;ENSP00000432945:R405H	ENSP00000333896:R427H	R	+	2	0	RPS6KA4	63892595	0.333000	0.24731	0.997000	0.53966	0.668000	0.39293	2.159000	0.42339	2.059000	0.61396	0.462000	0.41574	CGC	.	.	.	weak		0.701	RPS6KA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106246.2	NM_003942		A	64136019	G	A	64136019	3	1	63	1	0	0	0	0	1	0	0	0	13666	1087	38	1	1322	1	RPS6KA4	11	64136019	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	15788783	64136019	70870497	42	4222											
FGF19	9965	hgsc.bcm.edu	37	chr11	69514314	69514314	+	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	atctgggcggatctcctcctCgaaagcacagtcttcctccg	7	10	9	15	3	3	0	0	0	3	0	8	2	6	1	4	2	1	1	4	2	1	1	rs377419016		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr11:69514314C>T	ENST00000294312.3	-	3	1132	c.367G>A	c.(367-369)Gag>Aag	p.E123K		NM_005117.2	NP_005108.1	O95750	FGF19_HUMAN	fibroblast growth factor 19	123					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of bile acid biosynthetic process (GO:0070858)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glucose import (GO:0046326)|positive regulation of JNK cascade (GO:0046330)	extracellular region (GO:0005576)	fibroblast growth factor receptor binding (GO:0005104)			large_intestine(2)|lung(2)|skin(2)	6	all_cancers(3;5.53e-114)|all_epithelial(3;1.34e-121)|Breast(3;9.28e-34)|all_lung(4;1.99e-21)|Lung NSC(4;4.65e-21)|Hepatocellular(3;6.15e-15)|Melanoma(5;1.89e-05)|Ovarian(3;0.0348)		Epithelial(3;3.05e-56)|all cancers(3;2.69e-50)|Lung(3;1.13e-16)|LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)|LUAD - Lung adenocarcinoma(13;0.0537)			ATCTCCTCCTCGAAAGCACAG	0.562																																					p.E123K		Atlas-SNP	.											.	FGF19	11	.	0			c.G367A						PASS	.	C	LYS/GLU	0,4400		0,0,2200	51	47	48		367	2.8	1	11		48	1,8587	1.2+/-3.3	0,1,4293	no	missense	FGF19	NM_005117.2	56	0,1,6493	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	123/217	69514314	1,12987	2200	4294	6494	SO:0001583	missense	9965	exon3			CCTCCTCGAAAGC	AB018122	CCDS8193.1	11q13.1	2008-02-01			ENSG00000162344	ENSG00000162344			3675	protein-coding gene	gene with protein product		603891				9931477, 10525310	Standard	NM_005117		Approved		uc001opf.3	O95750	OTTHUMG00000167886	ENST00000294312.3:c.367G>A	chr11.hg19:g.69514314C>T	ENSP00000294312:p.Glu123Lys	106.0	0.0	.		110.0	5.0	.	NM_005117		Missense_Mutation	SNP	ENST00000294312.3	hg19	CCDS8193.1	.	.	.	.	.	.	.	.	.	.	C	10.10	1.258639	0.23051	0.0	1.16E-4	ENSG00000162344	ENST00000294312	T	0.80304	-1.36	4.9	2.82	0.32997	.	0.379197	0.28659	N	0.014570	T	0.49423	0.1556	N	0.11341	0.13	0.34812	D	0.737793	P	0.40376	0.715	B	0.25759	0.063	T	0.61955	-0.6956	10	0.02654	T	1	-19.2795	7.4934	0.27475	0.0:0.7302:0.166:0.1038	.	123	O95750	FGF19_HUMAN	K	123	ENSP00000294312:E123K	ENSP00000294312:E123K	E	-	1	0	FGF19	69223495	0.833000	0.29383	0.979000	0.43373	0.961000	0.63080	1.017000	0.29989	0.323000	0.23307	0.555000	0.69702	GAG	.	.	.	weak		0.562	FGF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396833.1	NM_005117		T	69514314	C	T	69514314	3	4	63	1	0	0	0	0	1	0	0	0	5854	893	31	1	287	1	FGF19	11	69514314	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	5378295	69514314	65492202	43	4223											
EXPH5	23086	hgsc.bcm.edu	37	chr11	108384826	108384826	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaaatctcctctgttctcCgcttcgtccaaaggtattgc	7	14	6	14	2	3	0	0	0	3	0	8	0	5	0	4	1	1	3	4	1	3	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr11:108384826C>T	ENST00000265843.4	-	6	1518	c.1408G>A	c.(1408-1410)Gga>Aga	p.G470R	EXPH5_ENST00000428840.1_Missense_Mutation_p.G394R|EXPH5_ENST00000524840.1_5'UTR|EXPH5_ENST00000443411.1_Missense_Mutation_p.G282R|EXPH5_ENST00000525344.1_Missense_Mutation_p.G463R	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	470					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)		CTCTGTTCTCCGCTTCGTCCA	0.433																																					p.G470R		Atlas-SNP	.											.	EXPH5	193	.	0			c.G1408A						PASS	.						130	127	128					11																	108384826		2201	4298	6499	SO:0001583	missense	23086	exon6			GTTCTCCGCTTCG		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.1408G>A	chr11.hg19:g.108384826C>T	ENSP00000265843:p.Gly470Arg	96.0	0.0	.		109.0	27.0	.	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	hg19	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	C	1.713	-0.498555	0.04291	.	.	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000439956;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.03152	4.59;4.53;4.37;4.59;4.47;4.03	5.8	4.61	0.57282	.	0.279252	0.31461	N	0.007616	T	0.00815	0.0027	N	0.00104	-2.125	0.19945	N	0.999949	B	0.06786	0.001	B	0.06405	0.002	T	0.43877	-0.9364	10	0.02654	T	1	-6.2184	9.3795	0.38304	0.0:0.0824:0.0:0.9176	.	470	Q8NEV8	EXPH5_HUMAN	R	470;394;282;463;314;394;282	ENSP00000265843:G470R;ENSP00000391966:G394R;ENSP00000411390:G282R;ENSP00000432546:G463R;ENSP00000432683:G394R;ENSP00000446434:G282R	ENSP00000265843:G470R	G	-	1	0	EXPH5	107890036	0.012000	0.17670	0.950000	0.38849	0.930000	0.56654	0.504000	0.22626	1.011000	0.39340	-0.423000	0.05987	GGA	.	.	.	none		0.433	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		T	108384826	C	T	108384826	3	4	63	1	0	0	0	0	1	0	0	0	5324	661	23	1	4565	1	EXPH5	11	108384826	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	38870512	108384826	26621690	44	4224											
ABCG4	64137	hgsc.bcm.edu	37	chr11	119027153	119027153	+	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	agtgccaagctctttgagatGtttgacaaggtgagtgtctc	9	13	12	7	0	2	3	0	3	2	1	3	4	2	3	1	1	2	2	1	1	2	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr11:119027153G>T	ENST00000449422.2	+	7	989	c.801G>T	c.(799-801)atG>atT	p.M267I	ABCG4_ENST00000307417.3_Missense_Mutation_p.M267I|ABCG4_ENST00000531739.1_Missense_Mutation_p.M267I	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	267	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)		TCTTTGAGATGTTTGACAAGG	0.577																																					p.M267I		Atlas-SNP	.											.	ABCG4	77	.	0			c.G801T						PASS	.						141	137	138					11																	119027153		2200	4295	6495	SO:0001583	missense	64137	exon7			TGAGATGTTTGAC	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.801G>T	chr11.hg19:g.119027153G>T	ENSP00000406874:p.Met267Ile	199.0	0.0	.		231.0	131.0	.	NM_022169	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Missense_Mutation	SNP	ENST00000449422.2	hg19	CCDS8415.1	.	.	.	.	.	.	.	.	.	.	G	16.92	3.255972	0.59321	.	.	ENSG00000172350	ENST00000307417;ENST00000449422;ENST00000531739	T;T;T	0.34667	1.35;1.35;1.35	4.82	4.82	0.62117	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.037537	0.85682	D	0.000000	T	0.25382	0.0617	N	0.19112	0.55	0.80722	D	1	B	0.32245	0.361	B	0.25140	0.058	T	0.05971	-1.0853	10	0.38643	T	0.18	-32.7477	18.0972	0.89494	0.0:0.0:1.0:0.0	.	267	Q9H172	ABCG4_HUMAN	I	267	ENSP00000304111:M267I;ENSP00000406874:M267I;ENSP00000434318:M267I	ENSP00000304111:M267I	M	+	3	0	ABCG4	118532363	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.808000	0.86044	2.502000	0.84385	0.655000	0.94253	ATG	.	.	.	none		0.577	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169		T	119027153	G	T	119027153	3	4	63	1	0	0	0	0	1	0	0	0	70	1377	48	4	823	4	ABCG4	11	119027153	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	10642327	119027153	15979363	45	4225											
PIK3C2G	5288	hgsc.bcm.edu	37	chr12	18435382	18435382	+	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	aacctcaaaatacgaataaaGaatgctcctggggaagcccc	16	6	8	11	1	1	1	1	0	0	1	2	3	2	2	4	2	4	1	4	2	9	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:18435382G>A	ENST00000266497.5	+	1	405	c.367G>A	c.(367-369)Gaa>Aaa	p.E123K	PIK3C2G_ENST00000538779.1_Missense_Mutation_p.E123K|RERGL_ENST00000541632.1_Intron|PIK3C2G_ENST00000433979.1_Missense_Mutation_p.E123K|PIK3C2G_ENST00000535651.1_Missense_Mutation_p.E123K			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	123					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)				TACGAATAAAGAATGCTCCTG	0.398																																					p.E123K		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.G367A						PASS	.						69	69	69					12																	18435382		1829	4080	5909	SO:0001583	missense	5288	exon2			AATAAAGAATGCT	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.367G>A	chr12.hg19:g.18435382G>A	ENSP00000266497:p.Glu123Lys	40.0	0.0	.		44.0	6.0	.	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	hg19	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	G	14.26	2.480900	0.44044	.	.	ENSG00000139144	ENST00000535651;ENST00000433979;ENST00000266497;ENST00000538779	T;T;T;T	0.62788	1.35;-0.0;-0.0;-0.0	4.79	2.91	0.33838	.	.	.	.	.	T	0.44138	0.1279	N	0.24115	0.695	0.09310	N	1	B;B	0.31548	0.328;0.22	B;B	0.28011	0.085;0.039	T	0.15809	-1.0424	9	0.15952	T	0.53	-4.9931	11.4633	0.50223	0.0:0.3511:0.6488:0.0	.	123;123	F5H369;O75747	.;P3C2G_HUMAN	K	123	ENSP00000443850:E123K;ENSP00000404845:E123K;ENSP00000266497:E123K;ENSP00000445381:E123K	ENSP00000266497:E123K	E	+	1	0	PIK3C2G	18326649	0.022000	0.18835	0.006000	0.13384	0.083000	0.17756	0.866000	0.27954	0.897000	0.36392	0.655000	0.94253	GAA	.	.	.	none		0.398	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570		A	18435382	G	A	18435382	3	1	63	1	0	0	0	0	1	0	0	0	11918	943	33	2	369	2	PIK3C2G	12	18435382	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10		18435382	115416513	46	4226											
PKP2	5318	hgsc.bcm.edu	37	chr12	33031889	33031889	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggttttaggaacaggggaacGgcctccaacaaaatcatttt	13	10	10	8	1	1	0	1	0	0	0	2	2	2	2	2	5	3	1	2	5	6	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:33031889G>A	ENST00000070846.6	-	2	325	c.301C>T	c.(301-303)Cgt>Tgt	p.R101C	PKP2_ENST00000340811.4_Missense_Mutation_p.R101C	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	101					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)					ACAGGGGAACGGCCTCCAACA	0.378																																					p.R101C		Atlas-SNP	.											.	PKP2	110	.	0			c.C301T						PASS	.						96	91	93					12																	33031889		2203	4300	6503	SO:0001583	missense	5318	exon2			GGGAACGGCCTCC	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.301C>T	chr12.hg19:g.33031889G>A	ENSP00000070846:p.Arg101Cys	70.0	0.0	.		72.0	4.0	.	NM_004572	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Missense_Mutation	SNP	ENST00000070846.6	hg19	CCDS8731.1	.	.	.	.	.	.	.	.	.	.	G	16.45	3.126134	0.56721	.	.	ENSG00000057294	ENST00000340811;ENST00000070846;ENST00000537278	T;T	0.81163	-1.46;-1.42	5.7	3.72	0.42706	.	1.351310	0.04721	N	0.419289	T	0.76076	0.3937	L	0.47716	1.5	0.09310	N	1	B;B;B	0.21381	0.055;0.033;0.033	B;B;B	0.10450	0.005;0.002;0.003	T	0.60835	-0.7184	10	0.52906	T	0.07	-0.1096	8.3857	0.32499	0.0822:0.0:0.7645:0.1533	.	101;101;101	Q99959-2;A0AV37;Q99959	.;.;PKP2_HUMAN	C	101	ENSP00000342800:R101C;ENSP00000070846:R101C	ENSP00000070846:R101C	R	-	1	0	PKP2	32923156	0.000000	0.05858	0.010000	0.14722	0.864000	0.49448	0.261000	0.18442	2.679000	0.91253	0.650000	0.86243	CGT	.	.	.	none		0.378	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572		A	33031889	G	A	33031889	3	1	63	1	0	0	0	0	1	0	0	0	11992	1116	39	1	2396	1	PKP2	12	33031889	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	14596507	33031889	100820006	47	4227											
KRT86	3892	hgsc.bcm.edu	37	chr12	52700004	52700004	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccaggaggtgatgaactccaAgctgggcctggacatcgaga	11	6	14	10	1	0	3	0	2	0	1	2	6	1	5	3	4	2	1	3	4	2	0	rs542735645		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:52700004A>G	ENST00000423955.2	+	9	1365	c.1187A>G	c.(1186-1188)aAg>aGg	p.K396R	KRT86_ENST00000544024.1_Missense_Mutation_p.K396R|KRT86_ENST00000293525.5_Missense_Mutation_p.K396R|RP11-845M18.6_ENST00000552441.1_RNA			O43790	KRT86_HUMAN	keratin 86	396	Coil 2.|Rod.					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)		ATGAACTCCAAGCTGGGCCTG	0.637											OREG0021845	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	a|||	1	0.000199681	0	0.0014	5008	,	,		18796	0		0	False		,,,				2504	0				p.K396R		Atlas-SNP	.											.	KRT86	33	.	0			c.A1187G						PASS	.						78	77	77					12																	52700004		2203	4295	6498	SO:0001583	missense	3892	exon7			ACTCCAAGCTGGG	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.1187A>G	chr12.hg19:g.52700004A>G	ENSP00000444533:p.Lys396Arg	97.0	0.0	.	987	170.0	52.0	.	NM_002284	P78387	Missense_Mutation	SNP	ENST00000423955.2	hg19	CCDS41785.1	.	.	.	.	.	.	.	.	.	.	A	28.8	4.954205	0.92726	.	.	ENSG00000170442;ENSG00000170442;ENSG00000170442;ENSG00000258832	ENST00000544024;ENST00000423955;ENST00000293525;ENST00000553310	D;D;D	0.94376	-3.41;-3.41;-3.41	5.35	5.35	0.76521	Filament (1);	0.000000	0.43747	U	0.000525	D	0.97179	0.9078	M	0.91300	3.195	0.43399	D	0.99552	D	0.89917	1.0	D	0.80764	0.994	D	0.98008	1.0364	10	0.87932	D	0	.	13.9101	0.63862	1.0:0.0:0.0:0.0	.	396	O43790	KRT86_HUMAN	R	396	ENSP00000443169:K396R;ENSP00000444533:K396R;ENSP00000293525:K396R	ENSP00000293525:K396R	K	+	2	0	AC021066.1;KRT86	50986271	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.425000	0.80255	2.020000	0.59435	0.454000	0.30748	AAG	.	.	.	none		0.637	KRT86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404911.1	NM_002284		G	52700004	A	G	52700004	3	3	63	1	0	0	0	0	1	0	0	0	8507	72	3	3	1213	3	KRT86	12	52700004	Missense_Mutation	SNP	A	TCGA-A4-A57E-01A-11D-A26P-10	19668115	52700004	81151891	48	4228											
SRGAP1	57522	hgsc.bcm.edu	37	chr12	64491125	64491125	+	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	aaaaccccctctttcctaagGaaagatttaacgatctgatt	14	12	5	10	1	2	2	0	1	2	1	3	4	3	3	3	1	2	0	3	1	5	5			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:64491125G>C	ENST00000355086.3	+	15	2307	c.1783G>C	c.(1783-1785)Gaa>Caa	p.E595Q	SRGAP1_ENST00000357825.3_Missense_Mutation_p.E572Q|SRGAP1_ENST00000543397.1_Missense_Mutation_p.E532Q|RP11-196H14.2_ENST00000535594.1_RNA	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	595	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		CTTTCCTAAGGAAAGATTTAA	0.398																																					p.E595Q		Atlas-SNP	.											SRGAP1,NS,carcinoma,0,1	SRGAP1	146	.	0			c.G1783C						PASS	.						89	86	87					12																	64491125		2203	4300	6503	SO:0001583	missense	57522	exon15			CCTAAGGAAAGAT	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.1783G>C	chr12.hg19:g.64491125G>C	ENSP00000347198:p.Glu595Gln	49.0	0.0	.		54.0	18.0	.	NM_020762	Q9H8A3|Q9P2P2	Missense_Mutation	SNP	ENST00000355086.3	hg19	CCDS8967.1	.	.	.	.	.	.	.	.	.	.	G	31	5.095528	0.94197	.	.	ENSG00000196935	ENST00000355086;ENST00000357825;ENST00000543397	T;T;T	0.48201	0.82;0.82;0.82	5.48	5.48	0.80851	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.36002	U	0.002860	T	0.62636	0.2444	L	0.53561	1.675	0.80722	D	1	P;P	0.52463	0.953;0.946	P;P	0.59825	0.864;0.786	T	0.57266	-0.7841	9	.	.	.	.	19.7379	0.96215	0.0:0.0:1.0:0.0	.	595;532	Q7Z6B7;G5EA48	SRGP1_HUMAN;.	Q	595;572;532	ENSP00000347198:E595Q;ENSP00000350480:E572Q;ENSP00000437948:E532Q	.	E	+	1	0	SRGAP1	62777392	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.748000	0.98867	2.733000	0.93635	0.655000	0.94253	GAA	.	.	.	none		0.398	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1			C	64491125	G	C	64491125	3	2	63	1	0	0	0	0	1	0	0	0	15157	1175	41	4	1841	4	SRGAP1	12	64491125	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	11791121	64491125	69360770	49	4229											
C12orf12	196477	hgsc.bcm.edu	37	chr12	91347581	91347582	+	In_Frame_Ins	INS	-	-	TCT																															cttcctcctcatcttcgaccINStcttcctcctcatcttcgac																								rs374196591|rs558083520|rs376547014	byFrequency	TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:91347581_91347582insTCT	ENST00000358859.2	-	1	1371_1372	c.938_939insAGA	c.(937-939)gag>gaAGAg	p.313_313E>EE	CCER1_ENST00000548187.1_Intron	NM_152638.2	NP_689851.1	Q8TC90	CCER1_HUMAN	coiled-coil glutamate-rich protein 1	313	Glu-rich.																catcttcgacctcttcctcctc	0.535																																					p.E313delinsEE		Atlas-INDEL	.											.	.	.	.	0			c.939_940insAGA						PASS	.			20,4244		0,20,2112						1.8	0		dbSNP_107	204	107,8147		2,103,4022	no	coding	C12orf12	NM_152638.2		2,123,6134	A1A1,A1R,RR		1.2963,0.469,1.0145				127,12391				SO:0001652	inframe_insertion	196477	exon1			.	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.936_938dupAGA	chr12.hg19:g.91347582_91347584dupTCT	ENSP00000351727:p.Glu313dup	84.0	0.0	0		83.0	12.0	0.144578	NM_152638	Q8TC47	In_Frame_Ins	INS	ENST00000358859.2	hg19	CCDS9036.1																																																																																			.	.	.	weak		0.535	CCER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407142.2	NM_152638		TCT	91347582	-	TCT	91347581	7	5	63	1	0	1	1	0	0	0	0	0	1678	680	24	0	285	0	C12orf12	12	91347581	In_Frame_Ins	INS	-	TCGA-A4-A57E-01A-11D-A26P-10	26856456	91347581	42504314	50	4230			1	12		2	2	13	N	A_-	3.178579e-05
C12orf12	196477	hgsc.bcm.edu	37	chr12	91347593	91347593	+	Missense_Mutation	SNP	A	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	tcttcgacctcttcctcctcAtcttcgacctcttcttcctc	3	17	2	19	2	6	0	1	0	5	0	12	2	9	0	5	0	0	0	5	0	0	5	rs137989103		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:91347593A>C	ENST00000358859.2	-	1	1360	c.927T>G	c.(925-927)gaT>gaG	p.D309E	CCER1_ENST00000548187.1_Intron	NM_152638.2	NP_689851.1	Q8TC90	CCER1_HUMAN	coiled-coil glutamate-rich protein 1	309	Glu-rich.																cttcctcctcatcttcgacct	0.527																																					p.D309E		Atlas-SNP	.											.	.	.	.	0			c.T927G						PASS	.						221	189	200					12																	91347593		2203	4300	6503	SO:0001583	missense	196477	exon1			CTCCTCATCTTCG	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.927T>G	chr12.hg19:g.91347593A>C	ENSP00000351727:p.Asp309Glu	97.0	0.0	.		101.0	9.0	.	NM_152638	Q8TC47	Missense_Mutation	SNP	ENST00000358859.2	hg19	CCDS9036.1	.	.	.	.	.	.	.	.	.	.	A	0.040	-1.288355	0.01387	.	.	ENSG00000197651	ENST00000358859	T	0.15139	2.45	4.85	-9.69	0.00524	.	1.727330	0.03768	N	0.259267	T	0.05686	0.0149	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37934	-0.9684	10	0.02654	T	1	-2.4783	8.0014	0.30299	0.6481:0.1314:0.0:0.2205	.	309	Q8TC90	CL012_HUMAN	E	309	ENSP00000351727:D309E	ENSP00000351727:D309E	D	-	3	2	C12orf12	89871724	0.000000	0.05858	0.000000	0.03702	0.094000	0.18550	-0.544000	0.06077	-1.269000	0.02436	0.378000	0.23410	GAT	.	.	.	weak		0.527	CCER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407142.2	NM_152638		C	91347593	A	C	91347593	3	2	63	1	0	0	0	0	1	0	0	0	1678	214	8	5	297	5	C12orf12	12	91347593	Missense_Mutation	SNP	A	TCGA-A4-A57E-01A-11D-A26P-10	12	91347593	42504302	51	4231			1	12		2	2	13	N	A_-	3.178579e-05
TBX5	6910	hgsc.bcm.edu	37	chr12	114841566	114841566	+	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	ggtctccttacctgctgggtGaaggcggcctgcggggacga	5	8	17	11	3	1	1	0	1	1	0	2	3	1	2	3	6	3	1	3	6	2	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:114841566G>A	ENST00000310346.4	-	2	804	c.138C>T	c.(136-138)ttC>ttT	p.F46F	TBX5_ENST00000526441.1_Silent_p.F46F|TBX5_ENST00000349716.5_Intron|TBX5_ENST00000405440.2_Silent_p.F46F|TBX5_ENST00000552726.1_5'UTR	NM_000192.3	NP_000183.2	Q99593	TBX5_HUMAN	T-box 5	46				GFGLAHTPLEPDAKDLPCDSKPESALGAPSKSPSSPQAAFT QQ -> ALAGAHLWSLTQKTCLRFEPRARSGPPASPPGRPR SRLHPA (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)		CCTGCTGGGTGAAGGCGGCCT	0.632																																					p.F46F	NSCLC(152;1358 1980 4050 23898 40356)	Atlas-SNP	.											.	TBX5	188	.	0			c.C138T						PASS	.						42	52	48					12																	114841566		2199	4299	6498	SO:0001819	synonymous_variant	6910	exon2			CTGGGTGAAGGCG	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.138C>T	chr12.hg19:g.114841566G>A		8.0	0.0	.		29.0	10.0	.	NM_000192	A6ND77|O15301|Q96TB0|Q9Y4I2	Silent	SNP	ENST00000310346.4	hg19	CCDS9173.1																																																																																			.	.	.	none		0.632	TBX5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388297.1	NM_080717		A	114841566	G	A	114841566	2	1	63	1	0	0	0	0	0	0	0	1	15673	1281	45	2		2	TBX5	12	114841566	Silent	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	23493973	114841566	19010329	52	4232											
LRRC43	254050	hgsc.bcm.edu	37	chr12	122669246	122669246	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagacagtttcctgagagaaTtggccatccggaacccgctg	11	8	11	11	2	0	3	0	1	0	2	2	5	2	4	4	2	1	2	4	2	3	2	rs373684289		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:122669246T>C	ENST00000339777.4	+	2	359	c.331T>C	c.(331-333)Ttg>Ctg	p.L111L	LRRC43_ENST00000425921.1_5'UTR	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	111										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)		CCTGAGAGAATTGGCCATCCG	0.592													T|||	1	0.000199681	8e-04	0	5008	,	,		20729	0		0	False		,,,				2504	0				p.L111L		Atlas-SNP	.											.	LRRC43	105	.	0			c.T331C						PASS	.	T	,	1,3991		0,1,1995	51	53	52		331,	4.2	0.8	12		52	0,8312		0,0,4156	no	coding-synonymous,utr-5	LRRC43	NM_001098519.1,NM_152759.4	,	0,1,6151	CC,CT,TT		0.0,0.0251,0.0081	,	111/657,	122669246	1,12303	1996	4156	6152	SO:0001819	synonymous_variant	254050	exon2			AGAGAATTGGCCA	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.331T>C	chr12.hg19:g.122669246T>C		181.0	0.0	.		213.0	92.0	.	NM_001098519	Q6ZVT9	Silent	SNP	ENST00000339777.4	hg19	CCDS45001.1																																																																																			.	.	.	weak		0.592	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759		C	122669246	T	C	122669246	2	2	63	1	0	0	0	0	0	0	0	1	9008	1490	52	3		3	LRRC43	12	122669246	Silent	SNP	T	TCGA-A4-A57E-01A-11D-A26P-10	7827680	122669246	11182649	53	4233											
DNAH10	196385	hgsc.bcm.edu	37	chr12	124335495	124335495	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcttcatcaccatgaaccccGgctacgcaggccgcacggag	9	6	10	16	4	3	1	2	1	1	0	3	2	3	2	4	3	2	3	4	3	2	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:124335495G>A	ENST00000409039.3	+	34	5834	c.5809G>A	c.(5809-5811)Ggc>Agc	p.G1937S		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1937	AAA 1. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		CATGAACCCCGGCTACGCAGG	0.582																																					p.G1937S		Atlas-SNP	.											.	DNAH10	888	.	0			c.G5809A						PASS	.						40	45	44					12																	124335495		2155	4286	6441	SO:0001583	missense	196385	exon34			AACCCCGGCTACG	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.5809G>A	chr12.hg19:g.124335495G>A	ENSP00000386770:p.Gly1937Ser	28.0	0.0	.		94.0	51.0	.	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	35	5.476132	0.96291	.	.	ENSG00000197653	ENST00000409039	T	0.16743	2.32	5.48	5.48	0.80851	ATPase, AAA+ type, core (1);	0.000000	0.64402	U	0.000001	T	0.53546	0.1803	M	0.91510	3.215	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.64232	-0.6456	10	0.87932	D	0	.	19.3709	0.94484	0.0:0.0:1.0:0.0	.	1937	Q8IVF4	DYH10_HUMAN	S	1937	ENSP00000386770:G1937S	ENSP00000386770:G1937S	G	+	1	0	DNAH10	122901448	1.000000	0.71417	0.956000	0.39512	0.972000	0.66771	8.010000	0.88615	2.576000	0.86940	0.655000	0.94253	GGC	.	.	.	none		0.582	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			A	124335495	G	A	124335495	3	1	63	1	0	0	0	0	1	0	0	0	4600	1116	39	1	5943	1	DNAH10	12	124335495	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	1666249	124335495	9516400	54	4234											
BRI3BP	140707	hgsc.bcm.edu	37	chr12	125509696	125509696	+	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	ggtgttcggccgcttcttctGgatcgtgcgggtcgtcctgt	1	14	15	11	5	2	0	0	0	2	0	6	1	3	1	2	4	1	2	2	4	0	3			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:125509696G>T	ENST00000341446.8	+	3	567	c.476G>T	c.(475-477)tGg>tTg	p.W159L		NM_080626.5	NP_542193.3			BRI3 binding protein									p.W159S(1)		large_intestine(1)|lung(8)|ovary(1)	10	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.35e-05)|Epithelial(86;0.000426)|all cancers(50;0.00576)		CGCTTCTTCTGGATCGTGCGG	0.622																																					p.W159L		Atlas-SNP	.											BRI3BP,NS,carcinoma,0,1	BRI3BP	18	.	1	Substitution - Missense(1)	lung(1)	c.G476T						PASS	.						131	99	110					12																	125509696		2203	4300	6503	SO:0001583	missense	140707	exon3			TCTTCTGGATCGT	AF284094	CCDS9262.1	12q24.1	2008-08-04			ENSG00000184992	ENSG00000184992			14251	protein-coding gene	gene with protein product		615627				11860200, 17765869	Standard	NM_080626		Approved	BNAS1, KG19, HCCR-2	uc001uha.1	Q8WY22	OTTHUMG00000168548	ENST00000341446.8:c.476G>T	chr12.hg19:g.125509696G>T	ENSP00000340761:p.Trp159Leu	59.0	1.0	.		90.0	41.0	.	NM_080626		Missense_Mutation	SNP	ENST00000341446.8	hg19	CCDS9262.1	.	.	.	.	.	.	.	.	.	.	g	29.4	5.001126	0.93227	.	.	ENSG00000184992	ENST00000341446	.	.	.	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.77336	0.4115	L	0.57536	1.79	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.79841	-0.1633	9	0.87932	D	0	-1.2314	18.495	0.90861	0.0:0.0:1.0:0.0	.	159	Q8WY22	BRI3B_HUMAN	L	159	.	ENSP00000340761:W159L	W	+	2	0	BRI3BP	124075649	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	9.284000	0.95882	2.344000	0.79699	0.556000	0.70494	TGG	.	.	.	none		0.622	BRI3BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400200.2	NM_080626		T	125509696	G	T	125509696	3	4	63	1	0	0	0	0	1	0	0	0	1515	1357	47	4	486	4	BRI3BP	12	125509696	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	1174201	125509696	8342199	55	4235											
TBC1D4	9882	hgsc.bcm.edu	37	chr13	75923415	75923415	+	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	gccgtactgaaggcctgtttCagagtcagcattacctcatc	9	11	9	12	1	3	2	3	1	0	1	4	2	3	2	3	1	3	3	3	1	3	3			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr13:75923415C>A	ENST00000377636.3	-	5	1645	c.1299G>T	c.(1297-1299)ctG>ctT	p.L433L	TBC1D4_ENST00000425511.1_5'UTR|TBC1D4_ENST00000377625.2_Silent_p.L433L|TBC1D4_ENST00000431480.2_Silent_p.L433L	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	433	PID 2. {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)		AGGCCTGTTTCAGAGTCAGCA	0.473																																					p.L433L		Atlas-SNP	.											.	TBC1D4	142	.	0			c.G1299T						PASS	.						57	58	58					13																	75923415		1948	4168	6116	SO:0001819	synonymous_variant	9882	exon5			CTGTTTCAGAGTC	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.1299G>T	chr13.hg19:g.75923415C>A		72.0	0.0	.		48.0	25.0	.	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Silent	SNP	ENST00000377636.3	hg19	CCDS41901.1																																																																																			.	.	.	none		0.473	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832		A	75923415	C	A	75923415	2	1	63	1	0	0	0	0	0	0	0	1	15634	813	29	4		4	TBC1D4	13	75923415	Silent	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10		75923415	39246463	56	4236											
TEP1	7011	hgsc.bcm.edu	37	chr14	20846267	20846267	+	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	aagccatggtgggcagggaaGgcagccagccgtgccccttc	8	5	15	13	1	0	0	0	0	0	0	1	1	0	1	5	4	4	2	5	4	2	1	rs201698574		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr14:20846267G>C	ENST00000262715.5	-	39	5677	c.5637C>G	c.(5635-5637)gcC>gcG	p.A1879A	TEP1_ENST00000545983.1_Silent_p.A217A|TEP1_ENST00000556935.1_Silent_p.A1771A	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1879					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)		GGGCAGGGAAGGCAGCCAGCC	0.632																																					p.A1879A		Atlas-SNP	.											.	TEP1	224	.	0			c.C5637G						PASS	.						87	85	86					14																	20846267		2203	4300	6503	SO:0001819	synonymous_variant	7011	exon39			AGGGAAGGCAGCC		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.5637C>G	chr14.hg19:g.20846267G>C		33.0	0.0	.		119.0	40.0	.	NM_007110	A0AUV9	Silent	SNP	ENST00000262715.5	hg19	CCDS9548.1																																																																																			.	G|1.000;A|0.000	.	alt		0.632	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		C	20846267	G	C	20846267	2	2	63	1	0	0	0	0	0	0	0	1	15771	987	35	4		4	TEP1	14	20846267	Silent	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10		20846267	86503273	57	4237											
KCNH5	27133	hgsc.bcm.edu	37	chr14	63447729	63447729	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccgggccccacgaaagtcGtgtgaaaatttaaaacgatg	14	7	10	10	4	0	1	0	1	0	0	1	3	0	1	3	1	1	0	3	1	5	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr14:63447729G>A	ENST00000322893.7	-	6	1071	c.803C>T	c.(802-804)aCg>aTg	p.T268M	KCNH5_ENST00000394968.1_Missense_Mutation_p.T210M|KCNH5_ENST00000420622.2_Missense_Mutation_p.T268M|KCNH5_ENST00000394964.2_Missense_Mutation_p.T210M	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	268					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)		CACGAAAGTCGTGTGAAAATT	0.423																																					p.T268M		Atlas-SNP	.											.	KCNH5	320	.	0			c.C803T						PASS	.						70	71	71					14																	63447729		2203	4300	6503	SO:0001583	missense	27133	exon6			AAAGTCGTGTGAA	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.803C>T	chr14.hg19:g.63447729G>A	ENSP00000321427:p.Thr268Met	121.0	0.0	.		94.0	40.0	.	NM_172375	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	hg19	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.325830	0.81580	.	.	ENSG00000140015	ENST00000322893;ENST00000420622;ENST00000394968;ENST00000394964	D;D;D;D	0.95622	-3.76;-3.76;-3.76;-3.76	5.54	5.54	0.83059	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98229	0.9414	M	0.90542	3.125	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.995;1.0;1.0;1.0	D	0.98956	1.0796	10	0.87932	D	0	.	19.4888	0.95042	0.0:0.0:1.0:0.0	.	210;210;268;268	Q86XI1;Q8NCM2-3;Q8NCM2-2;Q8NCM2	.;.;.;KCNH5_HUMAN	M	268;268;210;210	ENSP00000321427:T268M;ENSP00000395439:T268M;ENSP00000378419:T210M;ENSP00000378415:T210M	ENSP00000321427:T268M	T	-	2	0	KCNH5	62517482	1.000000	0.71417	0.992000	0.48379	0.740000	0.42216	9.799000	0.99117	2.607000	0.88179	0.585000	0.79938	ACG	.	.	.	none		0.423	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		A	63447729	G	A	63447729	3	1	63	1	0	0	0	0	1	0	0	0	8042	1145	40	1	2221	1	KCNH5	14	63447729	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	42601462	63447729	43901811	58	4238											
C14orf50	145376	hgsc.bcm.edu	37	chr14	65053588	65053588	+	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	gatacacagaaagactggaaGttctttgaggtgagtcactt	13	11	11	6	0	2	4	1	2	1	2	2	6	2	5	0	2	1	1	0	2	3	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr14:65053588G>A	ENST00000298705.1	+	9	798	c.702G>A	c.(700-702)aaG>aaA	p.K234K	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	234					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										AAGACTGGAAGTTCTTTGAGG	0.353																																					p.K234K		Atlas-SNP	.											.	.	.	.	0			c.G702A						PASS	.						134	126	128					14																	65053588		2203	4300	6503	SO:0001819	synonymous_variant	145376	exon9			CTGGAAGTTCTTT		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.702G>A	chr14.hg19:g.65053588G>A		71.0	0.0	.		51.0	11.0	.	NM_172365	Q6NTH6	Silent	SNP	ENST00000298705.1	hg19	CCDS9767.1																																																																																			.	.	.	none		0.353	PPP1R36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280667.1	NM_172365		A	65053588	G	A	65053588	2	1	63	1	0	0	0	0	0	0	0	1	1779	1020	36	2		2	C14orf50	14	65053588	Silent	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	1605859	65053588	42295952	59	4239											
RIN3	79890	hgsc.bcm.edu	37	chr14	93117951	93117952	+	Frame_Shift_Ins	INS	-	-	T																															tgggactcctcgctgaatccINStccacaagaaagagggaagc																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr14:93117951_93117952insT	ENST00000216487.7	+	6	716_717	c.557_558insT	c.(556-561)cctccafs	p.P187fs	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	187					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)				TCGCTGAATCCTCCACAAGAAA	0.629																																					p.P186fs		Atlas-Indel,Pindel	.											.	RIN3	81	.	0			c.557_558insT						PASS	.																																			SO:0001589	frameshift_variant	79890	exon6			.	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.558dupT	chr14.hg19:g.93117952_93117952dupT	ENSP00000216487:p.Pro187fs	47.0	0.0	0		39.0	24.0	0.615385	NM_024832	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Frame_Shift_Ins	INS	ENST00000216487.7	hg19	CCDS32144.1																																																																																			.	.	.	none		0.629	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1			T	93117952	-	T	93117951	7	5	63	1	0	1	1	0	0	0	0	0	13386	681	24	0	579	0	RIN3	14	93117951	Frame_Shift_Ins	INS	-	TCGA-A4-A57E-01A-11D-A26P-10	28064363	93117951	14231589	60	4240											
RTL1	388015	hgsc.bcm.edu	37	chr14	101350131	101350136	+	In_Frame_Del	DEL	TCGTTG	TCGTTG	-																															atagatagtgcctgatctccTcgttgagcccctggcacaag																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	TCGTTG	TCGTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr14:101350131_101350136delTCGTTG	ENST00000534062.1	-	1	1048_1053	c.990_995delCAACGA	c.(988-996)ctcaacgag>ctg	p.NE331del	MIR136_ENST00000385207.1_RNA|MIR127_ENST00000384876.1_RNA|MIR431_ENST00000385266.1_RNA|MIR433_ENST00000384837.1_RNA|MIR432_ENST00000606207.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	331					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						CCTGATCTCCTCGTTGAGCCCCTGGC	0.563																																					p.331_332del		Atlas-INDEL	.											.	RTL1	120	.	0			c.991_996del						PASS	.																																			SO:0001651	inframe_deletion	388015	exon1			.		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.990_995delCAACGA	chr14.hg19:g.101350131_101350136delTCGTTG	ENSP00000435342:p.Asn331_Glu332del	51.0	0.0	0		46.0	14.0	0.304348	NM_001134888	E9PKS8	In_Frame_Del	DEL	ENST00000534062.1	hg19	CCDS53910.1																																																																																			.	.	.	none		0.563	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888		-	101350136	TCGTTG	-	101350131	7	5	63	1	0	1	0	1	0	0	0	0	13737	1551	54	0	3085	0	RTL1	14	101350131	In_Frame_Del	DEL	TCGTTG	TCGA-A4-A57E-01A-11D-A26P-10	8232180	101350131	5999409	61	4241	48	2									
RTL1	388015	hgsc.bcm.edu	37	chr14	101350138	101350138	+	Frame_Shift_Del	DEL	G	G	-																															gtgcctgatctcctcgttgaGcccctggcacaagtgggcct																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr14:101350138delG	ENST00000534062.1	-	1	1046	c.988delC	c.(988-990)ctcfs	p.L330fs	MIR136_ENST00000385207.1_RNA|MIR127_ENST00000384876.1_RNA|MIR431_ENST00000385266.1_RNA|MIR433_ENST00000384837.1_RNA|MIR432_ENST00000606207.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	330					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						TCCTCGTTGAGCCCCTGGCAC	0.572																																					p.L330fs		Atlas-INDEL	.											.	RTL1	120	.	0			c.989delT						PASS	.						70	67	68					14																	101350138		692	1591	2283	SO:0001589	frameshift_variant	388015	exon1			.		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.988delC	chr14.hg19:g.101350138delG	ENSP00000435342:p.Leu330fs	48.0	0.0	0		45.0	14.0	0.311111	NM_001134888	E9PKS8	Frame_Shift_Del	DEL	ENST00000534062.1	hg19	CCDS53910.1																																																																																			.	.	.	none		0.572	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888		-	101350138	G	-	101350138	7	5	63	1	0	1	0	1	0	0	0	0	13737	971	34	0	3092	0	RTL1	14	101350138	Frame_Shift_Del	DEL	G	TCGA-A4-A57E-01A-11D-A26P-10	7	101350138	5999402	62	4242	48	2									
ARHGAP11A	9824	hgsc.bcm.edu	37	chr15	32929467	32929467	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ataaaagtcaagtcacctctTaagtttcagcgtactcctgt	12	13	6	10	1	4	0	3	0	1	0	5	0	5	0	2	0	2	2	2	0	5	4	rs373558097		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr15:32929467T>C	ENST00000361627.3	+	12	3215	c.2493T>C	c.(2491-2493)ctT>ctC	p.L831L	ARHGAP11A_ENST00000565905.1_Silent_p.L642L|ARHGAP11A_ENST00000543522.1_Silent_p.L642L	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	831					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)		AGTCACCTCTTAAGTTTCAGC	0.388																																					p.L831L	Colon(45;757 1134 30003 36652)	Atlas-SNP	.											.	ARHGAP11A	84	.	0			c.T2493C						PASS	.						99	103	101					15																	32929467		2201	4300	6501	SO:0001819	synonymous_variant	9824	exon12			ACCTCTTAAGTTT	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.2493T>C	chr15.hg19:g.32929467T>C		125.0	0.0	.		117.0	52.0	.	NM_014783	B4DZN9|Q6PI96|Q9Y3S6	Silent	SNP	ENST00000361627.3	hg19	CCDS10028.1																																																																																			.	.	.	alt		0.388	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783		C	32929467	T	C	32929467	2	2	63	1	0	0	0	0	0	0	0	1	863	1741	61	3		3	ARHGAP11A	15	32929467	Silent	SNP	T	TCGA-A4-A57E-01A-11D-A26P-10		32929467	69601925	63	4243											
ZNF770	54989	hgsc.bcm.edu	37	chr15	35275620	35275620	+	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	aatctttagcatttttaaatTgttttcagccatcatattct	11	20	3	7	0	4	0	2	0	2	0	4	0	4	0	1	0	2	2	1	0	5	10			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr15:35275620T>A	ENST00000356321.4	-	3	360	c.16A>T	c.(16-18)Aat>Tat	p.N6Y		NM_014106.3	NP_054825.2	Q6IQ21	ZN770_HUMAN	zinc finger protein 770	6					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)		ATTTTTAAATTGTTTTCAGCC	0.313																																					p.N6Y		Atlas-SNP	.											.	ZNF770	64	.	0			c.A16T						PASS	.						68	62	64					15																	35275620		2201	4298	6499	SO:0001583	missense	54989	exon3			TTAAATTGTTTTC	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.16A>T	chr15.hg19:g.35275620T>A	ENSP00000348673:p.Asn6Tyr	79.0	0.0	.		74.0	27.0	.	NM_014106	Q6ZMZ6|Q9NWV2	Missense_Mutation	SNP	ENST00000356321.4	hg19	CCDS10042.1	.	.	.	.	.	.	.	.	.	.	T	4.657	0.122204	0.08931	.	.	ENSG00000198146	ENST00000356321	T	0.09538	2.97	4.27	3.14	0.36123	.	0.420309	0.21769	N	0.069391	T	0.05227	0.0139	N	0.14661	0.345	0.09310	N	1	B	0.15473	0.013	B	0.11329	0.006	T	0.32481	-0.9905	10	0.66056	D	0.02	-8.2947	0.8062	0.01084	0.1598:0.1796:0.1664:0.4942	.	6	Q6IQ21	ZN770_HUMAN	Y	6	ENSP00000348673:N6Y	ENSP00000348673:N6Y	N	-	1	0	ZNF770	33062912	1.000000	0.71417	0.962000	0.40283	0.306000	0.27790	1.749000	0.38319	0.959000	0.37980	-0.297000	0.09499	AAT	.	.	.	none		0.313	ZNF770-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251896.2	NM_014106		A	35275620	T	A	35275620	3	1	63	1	0	0	0	0	1	0	0	0	18155	1812	63	5	2063	5	ZNF770	15	35275620	Missense_Mutation	SNP	T	TCGA-A4-A57E-01A-11D-A26P-10	2346153	35275620	67255772	64	4244											
PRTG	283659	hgsc.bcm.edu	37	chr15	55931987	55931988	+	Frame_Shift_Ins	INS	-	-	C																															agccttcgcatagagatggtINSggggtggtggtggaggaggg																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr15:55931987_55931988insC	ENST00000389286.4	-	13	2223_2224	c.2176_2177insG	c.(2176-2178)cacfs	p.H726fs		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)		ATAGAGATGGTGGGGTGGTGGT	0.455																																					p.H726fs		Atlas-INDEL	.											.	PRTG	110	.	0			c.2177_2178insG						PASS	.																																			SO:0001589	frameshift_variant	283659	exon13			.	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.2176_2177insG	chr15.hg19:g.55931987_55931988insC	ENSP00000373937:p.His726fs	170.0	0.0	0		138.0	18.0	0.130435	NM_173814		Frame_Shift_Ins	INS	ENST00000389286.4	hg19	CCDS42040.1																																																																																			.	.	.	none		0.455	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814		C	55931988	-	C	55931987	7	5	63	1	0	1	1	0	0	0	0	0	12648	1696	59	0	1307	0	PRTG	15	55931987	Frame_Shift_Ins	INS	-	TCGA-A4-A57E-01A-11D-A26P-10	20656367	55931987	46599405	65	4245	49	3									
PRTG	283659	hgsc.bcm.edu	37	chr15	55931988	55931989	+	In_Frame_Ins	INS	-	-	GGTGGT																															gccttcgcatagagatggtgINSgggtggtggtggaggaggga																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr15:55931988_55931989insGGTGGT	ENST00000389286.4	-	13	2222_2223	c.2175_2176insACCACC	c.(2173-2178)ccccac>cccACCACCcac	p.725_726PH>PTTH		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)		TAGAGATGGTGGGGTGGTGGTG	0.455																																					p.H726delinsTTH		Atlas-INDEL	.											.	PRTG	110	.	0			c.2176_2177insACCACC						PASS	.																																			SO:0001652	inframe_insertion	283659	exon13			.	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.2175_2176insACCACC	chr15.hg19:g.55931988_55931989insGGTGGT	ENSP00000373937:p.Pro725_His726insThrThr	170.0	0.0	0		138.0	18.0	0.130435	NM_173814		In_Frame_Ins	INS	ENST00000389286.4	hg19	CCDS42040.1																																																																																			.	.	.	none		0.455	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814		GGTGGT	55931989	-	GGTGGT	55931988	7	5	63	1	0	1	1	0	0	0	0	0	12648	1348	47	0	1308	0	PRTG	15	55931988	In_Frame_Ins	INS	-	TCGA-A4-A57E-01A-11D-A26P-10	1	55931988	46599404	66	4246	49	3									
PRTG	283659	hgsc.bcm.edu	37	chr15	55931991	55931992	+	Frame_Shift_Ins	INS	-	-	TGGTGGG																															ttcgcatagagatggtggggINStggtggtggaggagggacca																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr15:55931991_55931992insTGGTGGG	ENST00000389286.4	-	13	2219_2220	c.2172_2173insCCCACCA	c.(2170-2175)ccacccfs	p.-725fs		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)		AGATGGTGGGGTGGTGGTGGAG	0.45																																					p.P725fs		Pindel	.											.	PRTG	110	.	0			c.2173_2174insCCCACCA						PASS	.																																			SO:0001589	frameshift_variant	283659	exon13			.	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.2172_2173insCCCACCA	chr15.hg19:g.55931991_55931992insTGGTGGG	ENSP00000373937:p.Pro725fs	168.0	0.0	.		132.0	20.0	0.152	NM_173814		Frame_Shift_Ins	INS	ENST00000389286.4	hg19	CCDS42040.1																																																																																			.	.	.	none		0.45	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814		TGGTGGG	55931992	-	TGGTGGG	55931991	7	5	63	1	0	1	1	0	0	0	0	0	12648	1261	44	0	1311	0	PRTG	15	55931991	Frame_Shift_Ins	INS	-	TCGA-A4-A57E-01A-11D-A26P-10	3	55931991	46599401	67	4247	49	3									
ARMC5	79798	hgsc.bcm.edu	37	chr16	31473812	31473812	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgtgcccagggcctgattcGgcctgcactgggcaatgctg	5	9	15	12	1	0	1	0	1	0	0	1	1	0	1	3	3	3	3	3	3	1	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr16:31473812G>A	ENST00000563544.1	+	4	1490	c.944G>A	c.(943-945)cGg>cAg	p.R315Q	ARMC5_ENST00000268314.4_Missense_Mutation_p.R315Q|ARMC5_ENST00000457010.2_Missense_Mutation_p.R315Q|ARMC5_ENST00000412665.2_Intron|ARMC5_ENST00000538189.1_Missense_Mutation_p.R347Q|ARMC5_ENST00000408912.3_Missense_Mutation_p.R410Q|RP11-452L6.5_ENST00000564629.1_RNA			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5	315										central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						GGCCTGATTCGGCCTGCACTG	0.652																																					p.R315Q		Atlas-SNP	.											.	ARMC5	94	.	0			c.G944A						PASS	.						33	37	36					16																	31473812		2058	4214	6272	SO:0001583	missense	79798	exon3			TGATTCGGCCTGC	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.944G>A	chr16.hg19:g.31473812G>A	ENSP00000456877:p.Arg315Gln	11.0	0.0	.		73.0	34.0	.	NM_024742	Q86WM9|Q9H7P8|Q9H925	Missense_Mutation	SNP	ENST00000563544.1	hg19	CCDS45472.1	.	.	.	.	.	.	.	.	.	.	g	19.23	3.787652	0.70337	.	.	ENSG00000140691	ENST00000408912;ENST00000538189;ENST00000268314;ENST00000457010	T;T;T;T	0.21932	1.98;1.98;1.98;1.98	4.51	4.51	0.55191	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.43411	0.1246	M	0.62723	1.935	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.996;0.996	T	0.35968	-0.9767	10	0.54805	T	0.06	-20.0021	14.7442	0.69477	0.0:0.0:1.0:0.0	.	347;410;315;315	F5H156;B4DIU9;Q96C12;Q96C12-4	.;.;ARMC5_HUMAN;.	Q	410;347;315;315	ENSP00000386125:R410Q;ENSP00000443995:R347Q;ENSP00000268314:R315Q;ENSP00000399561:R315Q	ENSP00000268314:R315Q	R	+	2	0	ARMC5	31381313	1.000000	0.71417	0.970000	0.41538	0.216000	0.24613	5.851000	0.69481	2.060000	0.61445	0.450000	0.29827	CGG	.	.	.	none		0.652	ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432847.1	NM_024742		A	31473812	G	A	31473812	3	1	63	1	0	0	0	0	1	0	0	0	954	1116	39	1	954	1	ARMC5	16	31473812	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10		31473812	58880941	68	4248											
TMCO7	79613	hgsc.bcm.edu	37	chr16	68941414	68941414	+	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	gggccgggtggagcatctcgGggacttgctgtcccactgcc	4	8	16	13	2	1	0	0	0	1	0	3	2	2	2	3	5	3	2	3	5	0	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr16:68941414G>T	ENST00000261778.1	+	10	1748	c.1736G>T	c.(1735-1737)gGg>gTg	p.G579V		NM_024562.1	NP_078838.1	Q9C0B7	TNG6_HUMAN	transport and golgi organization 6 homolog (Drosophila)	579						integral component of membrane (GO:0016021)											GAGCATCTCGGGGACTTGCTG	0.488																																					p.G579V		Atlas-SNP	.											.	.	.	.	0			c.G1736T						PASS	.						93	92	92					16																	68941414		1892	4105	5997	SO:0001583	missense	79613	exon10			ATCTCGGGGACTT		CCDS45516.1	16q22.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000103047	ENSG00000103047			25749	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 7"	TMCO7		11214970	Standard	NM_024562		Approved	FLJ12688, KIAA1746	uc002ewi.4	Q9C0B7	OTTHUMG00000176743	ENST00000261778.1:c.1736G>T	chr16.hg19:g.68941414G>T	ENSP00000261778:p.Gly579Val	86.0	0.0	.		147.0	46.0	.	NM_024562	Q569F9|Q9H9K1	Missense_Mutation	SNP	ENST00000261778.1	hg19	CCDS45516.1	.	.	.	.	.	.	.	.	.	.	G	12.59	1.982626	0.34942	.	.	ENSG00000103047	ENST00000261778	.	.	.	5.95	3.84	0.44239	Armadillo-type fold (1);	0.334836	0.36444	N	0.002597	T	0.30541	0.0768	N	0.11724	0.165	0.51012	D	0.999904	B	0.19706	0.038	B	0.17433	0.018	T	0.08391	-1.0724	9	0.12766	T	0.61	-9.4786	11.0925	0.48123	0.0:0.0:0.5339:0.4661	.	579	Q9C0B7	TMCO7_HUMAN	V	579	.	ENSP00000261778:G579V	G	+	2	0	TMCO7	67498915	1.000000	0.71417	0.996000	0.52242	0.835000	0.47333	2.559000	0.45888	1.483000	0.48342	0.655000	0.94253	GGG	.	.	.	none		0.488	TANGO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433471.2	XM_928235.2		T	68941414	G	T	68941414	3	4	63	1	0	0	0	0	1	0	0	0	16013	1232	43	4	1774	4	TMCO7	16	68941414	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	37467602	68941414	21413339	69	4249											
AP1G1	164	hgsc.bcm.edu	37	chr16	71779166	71779166	+	Missense_Mutation	SNP	T	T	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	ctcccaacaaatccaataaaTcattggcctaaacaaggtaa	18	8	4	11	0	1	0	1	0	0	0	3	0	3	0	3	2	2	1	3	2	9	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr16:71779166T>G	ENST00000299980.4	-	19	2321	c.1880A>C	c.(1879-1881)gAt>gCt	p.D627A	AP1G1_ENST00000569748.1_Missense_Mutation_p.D627A|AP1G1_ENST00000433195.2_Missense_Mutation_p.D650A|AP1G1_ENST00000393512.3_Missense_Mutation_p.D630A|AP1G1_ENST00000423132.2_Missense_Mutation_p.D630A|AP1G1_ENST00000564155.1_Missense_Mutation_p.D52A	NM_001128.5	NP_001119.3	O43747	AP1G1_HUMAN	adaptor-related protein complex 1, gamma 1 subunit	627					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|Golgi to lysosome transport (GO:0090160)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network membrane (GO:0032588)	GTP-dependent protein binding (GO:0030742)|kinesin binding (GO:0019894)|protein transporter activity (GO:0008565)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)			breast(1)|endometrium(8)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|urinary_tract(1)	28		Ovarian(137;0.125)				ATCCAATAAATCATTGGCCTA	0.358																																					p.D630A		Atlas-SNP	.											.	AP1G1	83	.	0			c.A1889C						PASS	.						87	81	83					16																	71779166		2198	4300	6498	SO:0001583	missense	164	exon20			AATAAATCATTGG	Y12226	CCDS32480.1, CCDS45522.1	16q23	2009-08-03				ENSG00000166747			555	protein-coding gene	gene with protein product	"gamma1-adaptin"	603533		CLAPG1, ADTG		9653655, 9733768	Standard	NM_001128		Approved		uc010cgg.3	O43747		ENST00000299980.4:c.1880A>C	chr16.hg19:g.71779166T>G	ENSP00000299980:p.Asp627Ala	78.0	0.0	.		112.0	74.0	.	NM_001030007	O75709|O75842|Q9UG09|Q9Y3U4	Missense_Mutation	SNP	ENST00000299980.4	hg19	CCDS32480.1	.	.	.	.	.	.	.	.	.	.	T	11.24	1.579662	0.28180	.	.	ENSG00000166747	ENST00000299980;ENST00000393512;ENST00000423132;ENST00000433195	T;T;T;T	0.15718	2.41;2.41;2.42;2.4	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.10551	0.0258	N	0.13198	0.31	0.80722	D	1	B;B;B	0.14012	0.001;0.002;0.009	B;B;B	0.17098	0.001;0.004;0.017	T	0.11542	-1.0583	10	0.08599	T	0.76	-12.6522	15.3832	0.74676	0.0:0.0:0.0:1.0	.	627;650;630	O43747;B3KXW5;O43747-2	AP1G1_HUMAN;.;.	A	627;630;630;650	ENSP00000299980:D627A;ENSP00000377148:D630A;ENSP00000409153:D630A;ENSP00000403259:D650A	ENSP00000299980:D627A	D	-	2	0	AP1G1	70336667	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.651000	0.83577	2.054000	0.61138	0.459000	0.35465	GAT	.	.	.	none		0.358	AP1G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434147.1			G	71779166	T	G	71779166	3	3	63	1	0	0	0	0	1	0	0	0	732	1435	50	5	608	5	AP1G1	16	71779166	Missense_Mutation	SNP	T	TCGA-A4-A57E-01A-11D-A26P-10	2837752	71779166	18575587	70	4250											
WDR81	124997	hgsc.bcm.edu	37	chr17	1630298	1630298	+	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	aggtgaccagctgggctcctCcagtcaagcgtcccctggac	7	7	12	15	1	1	1	1	1	0	0	4	2	4	2	5	3	2	2	5	3	1	0			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr17:1630298C>T	ENST00000409644.1	+	1	2045	c.2045C>T	c.(2044-2046)tCc>tTc	p.S682F	WDR81_ENST00000437219.2_Intron|WDR81_ENST00000309182.5_Intron|WDR81_ENST00000419248.1_Intron|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000446363.1_Intron	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	682					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)		CTGGGCTCCTCCAGTCAAGCG	0.607																																					p.S682F		Atlas-SNP	.											.	WDR81	180	.	0			c.C2045T						PASS	.						12	14	14					17																	1630298		691	1588	2279	SO:0001583	missense	124997	exon1			GCTCCTCCAGTCA	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.2045C>T	chr17.hg19:g.1630298C>T	ENSP00000386609:p.Ser682Phe	87.0	0.0	.		45.0	31.0	.	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Missense_Mutation	SNP	ENST00000409644.1	hg19	CCDS54062.1	.	.	.	.	.	.	.	.	.	.	C	2.791	-0.251404	0.05867	.	.	ENSG00000167716	ENST00000409644	T	0.56444	0.46	5.5	4.5	0.54988	.	.	.	.	.	T	0.52158	0.1717	.	.	.	0.29534	N	0.85255	.	.	.	.	.	.	T	0.50180	-0.8858	6	0.37606	T	0.19	.	11.6034	0.51017	0.0:0.8056:0.1247:0.0697	.	.	.	.	F	682	ENSP00000386609:S682F	ENSP00000386609:S682F	S	+	2	0	WDR81	1577048	0.044000	0.20184	0.251000	0.24312	0.026000	0.11368	0.643000	0.24750	2.580000	0.87095	0.561000	0.74099	TCC	.	.	.	none		0.607	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348		T	1630298	C	T	1630298	3	4	63	1	0	0	0	0	1	0	0	0	17342	855	30	2	2109	2	WDR81	17	1630298	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10		1630298	79564912	71	4251											
TP53	7157	hgsc.bcm.edu	37	chr17	7577559	7577559	+	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	ggttcatgccgcccatgcagGaactgttacacatgtagttg	9	11	11	10	1	1	0	1	0	0	0	1	1	1	1	2	2	4	5	2	2	3	4	rs397516437|rs28934573		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr17:7577559G>C	ENST00000269305.4	-	7	911	c.722C>G	c.(721-723)tCc>tGc	p.S241C	TP53_ENST00000413465.2_Missense_Mutation_p.S241C|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000445888.2_Missense_Mutation_p.S241C|TP53_ENST00000420246.2_Missense_Mutation_p.S241C|TP53_ENST00000455263.2_Missense_Mutation_p.S241C|TP53_ENST00000359597.4_Missense_Mutation_p.S241C	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	241	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		S -> A (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074}.|S -> C (in sporadic cancers; somatic mutation).|S -> F (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs28934573). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228}.|S -> P (in sporadic cancers; somatic mutation).|S -> T (in LFS; germline mutation and in sporadic cancers; somatic mutation).|S -> Y (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.S241F(85)|p.S241C(26)|p.0?(8)|p.S241Y(8)|p.C242fs*5(6)|p.?(5)|p.S241del(5)|p.S148F(4)|p.N239_C242delNSSC(3)|p.N239_C242>S(1)|p.C238fs*21(1)|p.S241fs*22(1)|p.N239_C242del(1)|p.Y236_M243delYMCNSSCM(1)|p.S241_G245delSCMGG(1)|p.S148C(1)|p.N239fs*4(1)|p.C238_M246delCNSSCMGGM(1)|p.H233_C242del10(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCCCATGCAGGAACTGTTACA	0.572		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.S241C	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,0,4	TP53	33396	.	160	Substitution - Missense(124)|Deletion - In frame(13)|Deletion - Frameshift(9)|Whole gene deletion(8)|Unknown(5)|Complex - deletion inframe(1)	urinary_tract(19)|large_intestine(18)|breast(17)|endometrium(15)|ovary(15)|lung(12)|skin(9)|biliary_tract(8)|central_nervous_system(8)|haematopoietic_and_lymphoid_tissue(7)|upper_aerodigestive_tract(6)|stomach(6)|oesophagus(5)|bone(5)|liver(3)|pancreas(3)|eye(2)|thyroid(1)|kidney(1)	c.C722G	GRCh37	CM920673	TP53	M	rs28934573	PASS	.						139	108	118					17																	7577559		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;	ATGCAGGAACTGT	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.722C>G	chr17.hg19:g.7577559G>C	ENSP00000269305:p.Ser241Cys	203.0	0.0	.		98.0	72.0	.	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	17.00	3.276619	0.59758	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99857	-7.22;-7.22;-7.22;-7.22;-7.22;-7.22;-7.22;-7.22	4.62	3.64	0.41730	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.120078	0.56097	D	0.000022	D	0.99871	0.9939	M	0.92784	3.345	0.51233	D	0.999916	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;0.999;1.0;1.0;1.0;0.999	D	0.96551	0.9408	10	0.87932	D	0	-35.4617	12.8645	0.57932	0.0:0.1651:0.8349:0.0	.	241;241;148;241;241;241	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	C	241;241;241;241;241;241;230;148;109;148	ENSP00000410739:S241C;ENSP00000352610:S241C;ENSP00000269305:S241C;ENSP00000398846:S241C;ENSP00000391127:S241C;ENSP00000391478:S241C;ENSP00000425104:S109C;ENSP00000423862:S148C	ENSP00000269305:S241C	S	-	2	0	TP53	7518284	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.346000	0.44027	1.295000	0.44724	0.462000	0.41574	TCC	.	.	.	alt		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		C	7577559	G	C	7577559	3	2	63	1	0	0	0	0	1	0	0	0	16393	1174	41	4	568	4	TP53	17	7577559	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	5947261	7577559	73617651	72	4252											
SSH2	85464	hgsc.bcm.edu	37	chr17	27958146	27958146	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgcacaatacactctgttgTtgtgagttgttctacaaaag	11	14	8	8	0	2	1	0	1	2	0	2	1	2	1	0	0	3	5	0	0	5	6			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr17:27958146T>C	ENST00000269033.3	-	15	4136	c.3985A>G	c.(3985-3987)Aca>Gca	p.T1329A	RP11-68I3.2_ENST00000581474.1_RNA|SSH2_ENST00000540801.1_Missense_Mutation_p.T1356A	NM_001282129.1|NM_033389.2	NP_001269058.1|NP_203747.2	Q76I76	SSH2_HUMAN	slingshot protein phosphatase 2	1329					actin cytoskeleton organization (GO:0030036)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)		SSH2/SUZ12(2)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CACTCTGTTGTTGTGAGTTGT	0.532																																					p.T1329A		Atlas-SNP	.											.	SSH2	107	.	0			c.A3985G						PASS	.						57	50	52					17																	27958146		2203	4300	6503	SO:0001583	missense	85464	exon15			CTGTTGTTGTGAG	AB072359	CCDS11253.1, CCDS74024.1	17q11.2	2013-03-05	2013-03-05		ENSG00000141298	ENSG00000141298		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"	30580	protein-coding gene	gene with protein product		606779	"slingshot homolog 2 (Drosophila)"			11832213, 11214970	Standard	XM_005258059		Approved	KIAA1725	uc002heo.1	Q76I76	OTTHUMG00000132752	ENST00000269033.3:c.3985A>G	chr17.hg19:g.27958146T>C	ENSP00000269033:p.Thr1329Ala	72.0	0.0	.		133.0	33.0	.	NM_033389	Q8TDB5|Q8WYL1|Q8WYL2|Q96F40|Q96H36|Q9C0D8	Missense_Mutation	SNP	ENST00000269033.3	hg19	CCDS11253.1	.	.	.	.	.	.	.	.	.	.	T	14.58	2.576881	0.45902	.	.	ENSG00000141298	ENST00000269033;ENST00000540801	T;T	0.58506	0.33;0.33	6.17	6.17	0.99709	.	0.593826	0.17897	N	0.158323	T	0.58509	0.2127	M	0.64997	1.995	0.80722	D	1	P;P	0.41131	0.739;0.622	B;B	0.40782	0.34;0.183	T	0.62234	-0.6897	10	0.59425	D	0.04	-13.774	13.2295	0.59933	0.0:0.0:0.1323:0.8677	.	1356;1329	F5H527;Q76I76	.;SSH2_HUMAN	A	1329;1356	ENSP00000269033:T1329A;ENSP00000444743:T1356A	ENSP00000269033:T1329A	T	-	1	0	SSH2	24982272	1.000000	0.71417	0.999000	0.59377	0.941000	0.58515	2.987000	0.49378	2.371000	0.80710	0.533000	0.62120	ACA	.	.	.	none		0.532	SSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256116.1	NM_033389		C	27958146	T	C	27958146	3	2	63	1	0	0	0	0	1	0	0	0	15197	1725	60	3	290	3	SSH2	17	27958146	Missense_Mutation	SNP	T	TCGA-A4-A57E-01A-11D-A26P-10	20380587	27958146	53237064	73	4253											
CCDC55	84081	hgsc.bcm.edu	37	chr17	28512533	28512533	+	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	cacagactcacagaggaaggGcaagagaagggtaaagaaca	19	2	13	7	0	1	4	1	0	0	4	1	6	1	5	0	3	1	2	0	3	6	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr17:28512533G>T	ENST00000247026.5	+	7	1581	c.1518G>T	c.(1516-1518)ggG>ggT	p.G506G	NSRP1_ENST00000540900.3_3'UTR	NM_001261467.1|NM_032141.3	NP_001248396.1|NP_115517.1	Q9H0G5	NSRP1_HUMAN	nuclear speckle splicing regulatory protein 1	506					developmental process (GO:0032502)|mRNA processing (GO:0006397)|nucleocytoplasmic transport (GO:0006913)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	14						CAGAGGAAGGGCAAGAGAAGG	0.433																																					p.G506G		Atlas-SNP	.											.	NSRP1	49	.	0			c.G1518T						PASS	.						103	101	102					17																	28512533		2203	4300	6503	SO:0001819	synonymous_variant	84081	exon7			GGAAGGGCAAGAG	AL136806	CCDS11255.1, CCDS74025.1	17q11.2	2011-05-24	2011-05-24	2011-05-24	ENSG00000126653	ENSG00000126653			25305	protein-coding gene	gene with protein product			"coiled-coil domain containing 55"	CCDC55		11230166	Standard	NM_032141		Approved	DKFZP434K1421, NSrp70	uc002heu.4	Q9H0G5	OTTHUMG00000132754	ENST00000247026.5:c.1518G>T	chr17.hg19:g.28512533G>T		125.0	0.0	.		170.0	95.0	.	NM_032141	Q6FI71	Silent	SNP	ENST00000247026.5	hg19	CCDS11255.1																																																																																			.	.	.	none		0.433	NSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256121.2	NM_032141		T	28512533	G	T	28512533	2	4	63	1	0	0	0	0	0	0	0	1	2827	1190	42	4		4	CCDC55	17	28512533	Silent	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	554387	28512533	52682677	74	4254											
SAMD14	201191	hgsc.bcm.edu	37	chr17	48191564	48191565	+	Frame_Shift_Del	DEL	TG	TG	-																															tgctcacctcatctgaagacTgagacagcgtgtggtagggg																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr17:48191564_48191565delTG	ENST00000330175.4	-	8	1245_1246	c.928_929delCA	c.(928-930)cagfs	p.Q310fs	SAMD14_ENST00000503734.1_5'Flank|SAMD14_ENST00000503131.1_Frame_Shift_Del_p.Q338fs	NM_001257359.1	NP_001244288.1	Q8IZD0	SAM14_HUMAN	sterile alpha motif domain containing 14	310								p.Q338P(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	15						ATCTGAAGACTGAGACAGCGTG	0.624																																					p.338_338del		Atlas-Indel,Pindel	.											.	SAMD14	36	.	1	Substitution - Missense(1)	large_intestine(1)	c.1013_1014del						PASS	.																																			SO:0001589	frameshift_variant	201191	exon9			.		CCDS11560.1, CCDS58562.1	17q21.33	2013-01-10				ENSG00000167100		"Sterile alpha motif (SAM) domain containing"	27312	protein-coding gene	gene with protein product						8619474	Standard	NM_174920		Approved	FLJ36890	uc002iqg.4	Q8IZD0		ENST00000330175.4:c.928_929delCA	chr17.hg19:g.48191564_48191565delTG	ENSP00000329144:p.Gln310fs	147.0	0.0	0		219.0	58.0	0.26484	NM_174920	A5D8V1|Q8N2X0	Frame_Shift_Del	DEL	ENST00000330175.4	hg19	CCDS58562.1																																																																																			.	.	.	none		0.624	SAMD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366661.1	NM_174920		-	48191565	TG	-	48191564	7	5	63	1	0	1	0	1	0	0	0	0	13832	1580	55	0	336	0	SAMD14	17	48191564	Frame_Shift_Del	DEL	TG	TCGA-A4-A57E-01A-11D-A26P-10	19679031	48191564	33003646	75	4255											
TPM4	7171	hgsc.bcm.edu	37	chr19	16199862	16199862	+	Frame_Shift_Del	DEL	G	G	-																															tgtctttgtgcagaaaatgtGgtgacctggaagaagaactc																										TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr19:16199862delG	ENST00000300933.4	+	5	723	c.463delG	c.(463-465)ggtfs	p.G155fs	TPM4_ENST00000538887.1_Frame_Shift_Del_p.G191fs|TPM4_ENST00000344824.6_Frame_Shift_Del_p.G191fs	NM_003290.2	NP_003281.1	P67936	TPM4_HUMAN	tropomyosin 4	155					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						CAGAAAATGTGGTGACCTGGA	0.428			T	ALK	ALCL						OREG0025329	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C190fs		Atlas-Indel,Pindel	.		Dom	yes		19	19p13.1	7171	tropomyosin 4		L	.	TPM4	28	.	0			c.570delT						PASS	.						125	113	117					19																	16199862		2203	4300	6503	SO:0001589	frameshift_variant	7171	exon6			.		CCDS12338.1, CCDS46007.1	19p13.1	2013-03-11			ENSG00000167460	ENSG00000167460		"Tropomyosins"	12013	protein-coding gene	gene with protein product		600317				8641132	Standard	NM_003290		Approved		uc002ndi.2	P67936	OTTHUMG00000182134	ENST00000300933.4:c.463delG	chr19.hg19:g.16199862delG	ENSP00000300933:p.Gly155fs	101.0	0.0	0	708	80.0	32.0	0.4	NM_001145160	P07226|Q15659|Q5U0D9|Q9BU85|Q9H8Q3|Q9UCS1|Q9UCS2|Q9UCS3|Q9UCS4	Frame_Shift_Del	DEL	ENST00000300933.4	hg19	CCDS12338.1																																																																																			.	.	.	none		0.428	TPM4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459673.2	NM_003290		-	16199862	G	-	16199862	7	5	63	1	0	1	0	1	0	0	0	0	16420	1348	47	0	729	0	TPM4	19	16199862	Frame_Shift_Del	DEL	G	TCGA-A4-A57E-01A-11D-A26P-10		16199862	42929121	76	4256											
YJEFN3	374887	hgsc.bcm.edu	37	chr19	19640278	19640278	+	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	aaacaggcctggggaaggcaGtcatggctagagcagatttg	12	7	15	7	0	1	2	1	0	0	2	1	3	1	3	1	5	2	3	1	5	3	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr19:19640278G>T	ENST00000514277.4	+	2	203	c.165G>T	c.(163-165)caG>caT	p.Q55H	CTC-260F20.3_ENST00000586674.1_3'UTR|YJEFN3_ENST00000436027.5_Intron|YJEFN3_ENST00000608404.1_Intron|CTC-260F20.3_ENST00000555938.1_Intron|NDUFA13_ENST00000512771.3_Missense_Mutation_p.Q177H	NM_198537.3	NP_940939.2	A6XGL0	YJEN3_HUMAN	YjeF N-terminal domain containing 3	55										NS(1)|breast(1)|lung(3)	5						GGGGAAGGCAGTCATGGCTAG	0.577																																					p.Q55H		Atlas-SNP	.											.	YJEFN3	10	.	0			c.G165T						PASS	.						53	58	56					19																	19640278		2035	4179	6214	SO:0001583	missense	374887	exon2			AAGGCAGTCATGG		CCDS42530.1, CCDS54236.1	19p13.11	2014-09-11			ENSG00000250067	ENSG00000250067			24785	protein-coding gene	gene with protein product						17533573	Standard	NM_198537		Approved	hYjeF_N3-19p13.11, FLJ44968	uc002nmt.2	A6XGL0	OTTHUMG00000162251	ENST00000514277.4:c.165G>T	chr19.hg19:g.19640278G>T	ENSP00000426964:p.Gln55His	188.0	0.0	.		172.0	39.0	.	NM_198537	A6XGK9|Q4G1C0	Missense_Mutation	SNP	ENST00000514277.4	hg19	CCDS42530.1	.	.	.	.	.	.	.	.	.	.	G	9.605	1.129720	0.21041	.	.	ENSG00000250067	ENST00000397179;ENST00000514277	T	0.48201	0.82	2.12	2.12	0.27331	.	.	.	.	.	T	0.20981	0.0505	N	0.08118	0	0.58432	D	0.999999	P;B	0.39831	0.69;0.191	B;B	0.35353	0.201;0.008	T	0.02991	-1.1085	9	0.15952	T	0.53	.	7.8598	0.29504	0.0:0.0:1.0:0.0	.	177;55	B4DF76;A6XGL0	.;YJEN3_HUMAN	H	55	ENSP00000426964:Q55H	ENSP00000380364:Q55H	Q	+	3	2	YJEFN3	19501278	0.071000	0.21146	0.059000	0.19551	0.062000	0.15995	1.327000	0.33746	1.530000	0.49136	0.555000	0.69702	CAG	.	.	.	none		0.577	YJEFN3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368157.5	NM_198537		T	19640278	G	T	19640278	3	4	63	1	0	0	0	0	1	0	0	0	17496	1020	36	4	171	4	YJEFN3	19	19640278	Missense_Mutation	SNP	G	TCGA-A4-A57E-01A-11D-A26P-10	3440416	19640278	39488705	77	4257											
TSHZ3	57616	hgsc.bcm.edu	37	chr19	31769063	31769063	+	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	ggcatggatgctgggatagcCcccccagctaggagtgccgt	7	7	15	12	1	0	0	0	0	0	0	0	3	0	3	4	4	4	3	4	4	2	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr19:31769063C>T	ENST00000240587.4	-	2	1963	c.1636G>A	c.(1636-1638)Ggc>Agc	p.G546S		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	546					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)					CTGGGATAGCCCCCCCAGCTA	0.557																																					p.G546S		Atlas-SNP	.											.	TSHZ3	549	.	0			c.G1636A						PASS	.						120	120	120					19																	31769063		2203	4300	6503	SO:0001583	missense	57616	exon2			GATAGCCCCCCCA	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.1636G>A	chr19.hg19:g.31769063C>T	ENSP00000240587:p.Gly546Ser	135.0	0.0	.		171.0	83.0	.	NM_020856	Q9H0G6|Q9P254	Missense_Mutation	SNP	ENST00000240587.4	hg19	CCDS12421.2	.	.	.	.	.	.	.	.	.	.	C	25.9	4.689081	0.88735	.	.	ENSG00000121297	ENST00000240587	T	0.59502	0.26	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.75221	0.3820	M	0.64404	1.975	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.77054	-0.2730	10	0.72032	D	0.01	-41.0424	19.1896	0.93660	0.0:1.0:0.0:0.0	.	546	Q63HK5	TSH3_HUMAN	S	546	ENSP00000240587:G546S	ENSP00000240587:G546S	G	-	1	0	TSHZ3	36460903	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	7.461000	0.80834	2.519000	0.84933	0.655000	0.94253	GGC	.	.	.	none		0.557	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		T	31769063	C	T	31769063	3	4	63	1	0	0	0	0	1	0	0	0	16637	623	22	2	1613	2	TSHZ3	19	31769063	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	12128785	31769063	27359920	78	4258											
RYR1	6261	hgsc.bcm.edu	37	chr19	39019255	39019255	+	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	gcaggcaccgggcatgtaacAtgttcctggagagctacaag	11	7	13	10	1	0	1	0	0	0	1	1	2	1	1	2	3	3	6	2	3	3	3			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr19:39019255A>T	ENST00000359596.3	+	75	10954	c.10954A>T	c.(10954-10956)Atg>Ttg	p.M3652L	RYR1_ENST00000355481.4_Missense_Mutation_p.M3647L|RYR1_ENST00000360985.3_Missense_Mutation_p.M3652L|AC067969.1_ENST00000597015.1_RNA			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3652					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)	GGCATGTAACATGTTCCTGGA	0.612																																					p.M3652L		Atlas-SNP	.											.	RYR1	708	.	0			c.A10954T						PASS	.						106	87	93					19																	39019255		2203	4300	6503	SO:0001583	missense	6261	exon75			TGTAACATGTTCC	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.10954A>T	chr19.hg19:g.39019255A>T	ENSP00000352608:p.Met3652Leu	129.0	0.0	.		219.0	76.0	.	NM_000540	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	A	13.52	2.262183	0.39995	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985;ENST00000538206	D;D;D	0.95518	-3.73;-3.73;-3.73	5.43	5.43	0.79202	.	0.000000	0.85682	U	0.000000	D	0.88901	0.6563	N	0.16307	0.4	0.36251	D	0.853928	B;B;B	0.11235	0.004;0.002;0.001	B;B;B	0.10450	0.005;0.001;0.001	D	0.84199	0.0449	10	0.02654	T	1	.	14.4595	0.67440	1.0:0.0:0.0:0.0	.	3652;3647;3652	P21817-3;P21817-2;P21817	.;.;RYR1_HUMAN	L	3652;3647;3652;572	ENSP00000352608:M3652L;ENSP00000347667:M3647L;ENSP00000354254:M3652L	ENSP00000347667:M3647L	M	+	1	0	RYR1	43711095	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	2.641000	0.46587	2.074000	0.62210	0.459000	0.35465	ATG	.	.	.	none		0.612	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	39019255	A	T	39019255	3	4	63	1	0	0	0	0	1	0	0	0	13781	217	8	5	11252	5	RYR1	19	39019255	Missense_Mutation	SNP	A	TCGA-A4-A57E-01A-11D-A26P-10	7250192	39019255	20109728	79	4259											
POLD1	5424	hgsc.bcm.edu	37	chr19	50918079	50918079	+	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	ggctccctcccaggtctactTcccatacctgcttatcagca	7	11	6	17	0	2	0	1	0	1	0	5	0	5	0	4	2	4	3	4	2	3	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr19:50918079T>A	ENST00000440232.2	+	20	2449	c.2396T>A	c.(2395-2397)tTc>tAc	p.F799Y	POLD1_ENST00000595904.1_Missense_Mutation_p.F825Y|POLD1_ENST00000599857.1_Missense_Mutation_p.F799Y|CTD-2545M3.6_ENST00000599632.1_5'Flank	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	799					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		CAGGTCTACTTCCCATACCTG	0.642								DNA polymerases (catalytic subunits)			OREG0025635	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F799Y		Atlas-SNP	.											.	POLD1	174	.	0			c.T2396A						PASS	.						55	54	54					19																	50918079		2203	4300	6503	SO:0001583	missense	5424	exon20			TCTACTTCCCATA		CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"DNA polymerases"	9175	protein-coding gene	gene with protein product	"CDC2 homolog (S. cerevisiae)"	174761	"polymerase (DNA directed), delta 1, catalytic subunit (125kD)"	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.2396T>A	chr19.hg19:g.50918079T>A	ENSP00000406046:p.Phe799Tyr	75.0	0.0	.	973	96.0	34.0	.	NM_002691	Q8NER3|Q96H98	Missense_Mutation	SNP	ENST00000440232.2	hg19	CCDS12795.1	.	.	.	.	.	.	.	.	.	.	T	14.85	2.657494	0.47467	.	.	ENSG00000062822	ENST00000440232;ENST00000376930	T	0.16597	2.33	4.84	4.84	0.62591	DNA polymerase, palm domain (1);DNA-directed DNA polymerase, family B, multifunctional domain (1);	0.060647	0.64402	D	0.000003	T	0.12305	0.0299	N	0.17764	0.52	0.46521	D	0.999085	B;B	0.12013	0.005;0.002	B;B	0.20384	0.029;0.013	T	0.10636	-1.0621	10	0.27785	T	0.31	-24.2344	13.7358	0.62817	0.0:0.0:0.0:1.0	.	825;799	E7EVW0;P28340	.;DPOD1_HUMAN	Y	799;800	ENSP00000406046:F799Y	ENSP00000366129:F800Y	F	+	2	0	POLD1	55609891	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	2.937000	0.48979	1.970000	0.57323	0.449000	0.29647	TTC	.	.	.	none		0.642	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1			A	50918079	T	A	50918079	3	1	63	1	0	0	0	0	1	0	0	0	12197	1783	62	5	2470	5	POLD1	19	50918079	Missense_Mutation	SNP	T	TCGA-A4-A57E-01A-11D-A26P-10	11898824	50918079	8210904	80	4260											
ZNF548	147694	hgsc.bcm.edu	37	chr19	57908473	57908473	+	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	cccaggaggagtgggggcacCttgatgaggctcagagattg	9	7	17	8	0	1	3	1	2	0	1	1	6	1	5	2	5	0	2	2	5	0	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr19:57908473C>T	ENST00000366197.5	+	2	323	c.73C>T	c.(73-75)Ctt>Ttt	p.L25F	ZNF548_ENST00000336128.7_Missense_Mutation_p.L37F|AC003002.6_ENST00000596400.1_Intron|AC003002.4_ENST00000597658.1_Intron|AC003002.6_ENST00000600421.1_3'UTR|ZNF548_ENST00000597400.1_Missense_Mutation_p.L37F|ZNF548_ENST00000598895.1_Missense_Mutation_p.L37F|AC004076.7_ENST00000597410.1_Intron	NM_152909.3	NP_690873.2	Q8NEK5	ZN548_HUMAN	zinc finger protein 548	25	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GTGGGGGCACCTTGATGAGGC	0.512																																					p.L37F		Atlas-SNP	.											.	ZNF548	64	.	0			c.C109T						PASS	.						377	349	358					19																	57908473		2203	4300	6503	SO:0001583	missense	147694	exon3			GGGCACCTTGATG	AK057494	CCDS46209.1, CCDS54324.1	19q13.43	2013-01-08				ENSG00000188785		"Zinc fingers, C2H2-type", "-"	26561	protein-coding gene	gene with protein product						12477932	Standard	NM_152909		Approved	FLJ32932	uc002qon.3	Q8NEK5		ENST00000366197.5:c.73C>T	chr19.hg19:g.57908473C>T	ENSP00000379482:p.Leu25Phe	331.0	0.0	.		321.0	126.0	.	NM_001172773	Q96M05	Missense_Mutation	SNP	ENST00000366197.5	hg19	CCDS46209.1	.	.	.	.	.	.	.	.	.	.	C	16.79	3.220274	0.58560	.	.	ENSG00000188785	ENST00000336128;ENST00000366197	T;T	0.18960	2.18;2.18	2.55	2.55	0.30701	Krueppel-associated box (4);	.	.	.	.	T	0.61640	0.2363	H	0.99286	4.5	0.21782	N	0.999543	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.55933	-0.8062	9	0.66056	D	0.02	.	8.7465	0.34589	0.0:1.0:0.0:0.0	.	37;25	Q8NEK5-2;Q8NEK5	.;ZN548_HUMAN	F	37;25	ENSP00000337555:L37F;ENSP00000379482:L25F	ENSP00000337555:L37F	L	+	1	0	ZNF548	62600285	0.277000	0.24220	0.716000	0.30569	0.995000	0.86356	1.271000	0.33098	1.763000	0.52060	0.563000	0.77884	CTT	.	.	.	none		0.512	ZNF548-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465937.1	NM_152909		T	57908473	C	T	57908473	3	4	63	1	0	0	0	0	1	0	0	0	17992	681	24	2	119	2	ZNF548	19	57908473	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	6990394	57908473	1220510	81	4261											
PAK7	57144	hgsc.bcm.edu	37	chr20	9525075	9525075	+	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	catccagtagggagtgccaaCcaatgatttcctcttcggca	10	10	9	12	1	1	1	0	1	1	0	4	2	3	2	4	2	2	2	4	2	3	3			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr20:9525075C>A	ENST00000378429.3	-	9	2356	c.1810G>T	c.(1810-1812)Gtt>Ttt	p.V604F	PAK7_ENST00000378423.1_Missense_Mutation_p.V604F|PAK7_ENST00000353224.5_Missense_Mutation_p.V604F	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	604	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> I (in a metastatic melanoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.V604I(1)		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)			GGAGTGCCAACCAATGATTTC	0.478																																					p.V604F		Atlas-SNP	.											PAK7,rectum,carcinoma,+2,1	PAK7	194	.	1	Substitution - Missense(1)	skin(1)	c.G1810T						PASS	.						121	111	114					20																	9525075		2203	4300	6503	SO:0001583	missense	57144	exon8			TGCCAACCAATGA	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.1810G>T	chr20.hg19:g.9525075C>A	ENSP00000367686:p.Val604Phe	141.0	0.0	.		99.0	32.0	.	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	hg19	CCDS13107.1	.	.	.	.	.	.	.	.	.	.	C	35	5.415885	0.96092	.	.	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423	T;T;T	0.70282	-0.47;-0.47;-0.47	5.97	5.97	0.96955	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.86736	0.6004	M	0.84585	2.705	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86251	0.1649	9	.	.	.	.	20.4388	0.99107	0.0:1.0:0.0:0.0	.	604	Q9P286	PAK7_HUMAN	F	604	ENSP00000367686:V604F;ENSP00000322957:V604F;ENSP00000367679:V604F	.	V	-	1	0	PAK7	9473075	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.768000	0.85345	2.836000	0.97738	0.655000	0.94253	GTT	.	.	.	none		0.478	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			A	9525075	C	A	9525075	3	1	63	1	0	0	0	0	1	0	0	0	11412	507	18	4	361	4	PAK7	20	9525075	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10		9525075	53500445	82	4262											
KIAA1755	85449	hgsc.bcm.edu	37	chr20	36869309	36869309	+	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	ggcctgagctgcaccatattCtctgggtttcctagaggtcc	6	12	11	12	0	1	2	0	1	1	1	4	2	3	2	4	3	2	3	4	3	2	4			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr20:36869309C>A	ENST00000279024.4	-	3	1495	c.1224G>T	c.(1222-1224)gaG>gaT	p.E408D		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	408										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)				GCACCATATTCTCTGGGTTTC	0.577																																					p.E408D		Atlas-SNP	.											.	KIAA1755	145	.	0			c.G1224T						PASS	.						67	67	67					20																	36869309		2203	4300	6503	SO:0001583	missense	85449	exon3			CATATTCTCTGGG	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.1224G>T	chr20.hg19:g.36869309C>A	ENSP00000279024:p.Glu408Asp	70.0	0.0	.		53.0	23.0	.	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	hg19	CCDS33467.1	.	.	.	.	.	.	.	.	.	.	C	11.25	1.582898	0.28268	.	.	ENSG00000149633	ENST00000279024	T	0.61040	0.14	4.64	0.4	0.16331	.	0.300502	0.24046	N	0.042048	T	0.62221	0.2410	M	0.67953	2.075	0.09310	N	1	D	0.67145	0.996	P	0.58266	0.836	T	0.53823	-0.8384	10	0.30078	T	0.28	.	7.1114	0.25392	0.0:0.5955:0.0:0.4045	.	408	Q5JYT7	K1755_HUMAN	D	408	ENSP00000279024:E408D	ENSP00000279024:E408D	E	-	3	2	KIAA1755	36302723	0.001000	0.12720	0.026000	0.17262	0.036000	0.12997	-0.298000	0.08265	-0.072000	0.12864	0.655000	0.94253	GAG	.	.	.	none		0.577	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864		A	36869309	C	A	36869309	3	1	63	1	0	0	0	0	1	0	0	0	8264	912	32	4	2426	4	KIAA1755	20	36869309	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10	27344234	36869309	26156211	83	4263											
SGK2	10110	hgsc.bcm.edu	37	chr20	42199308	42199308	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcctggagccccgggccaggTtctacgctgctgaggtggcc	4	8	15	14	2	1	1	0	1	1	0	2	2	2	2	5	5	3	3	5	5	1	2			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr20:42199308T>C	ENST00000341458.4	+	6	811	c.592T>C	c.(592-594)Ttc>Ctc	p.F198L	SGK2_ENST00000485914.1_3'UTR|SGK2_ENST00000373092.3_Missense_Mutation_p.F138L|SGK2_ENST00000426287.1_Missense_Mutation_p.F164L|SGK2_ENST00000423407.3_Missense_Mutation_p.F138L|SGK2_ENST00000373077.1_Missense_Mutation_p.F137L|SGK2_ENST00000373100.1_Missense_Mutation_p.F138L	NM_016276.3	NP_057360.2	Q9HBY8	SGK2_HUMAN	serum/glucocorticoid regulated kinase 2	198	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)			CCGGGCCAGGTTCTACGCTGC	0.627																																					p.F198L		Atlas-SNP	.											.	SGK2	50	.	0			c.T592C						PASS	.						57	60	59					20																	42199308		2203	4300	6503	SO:0001583	missense	10110	exon6			GCCAGGTTCTACG	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.592T>C	chr20.hg19:g.42199308T>C	ENSP00000340608:p.Phe198Leu	45.0	0.0	.		67.0	15.0	.	NM_016276	Q52PK5|Q5H8Y6|Q5H8Z1|Q5TZR3|Q9UKG6	Missense_Mutation	SNP	ENST00000341458.4	hg19	CCDS13320.1	.	.	.	.	.	.	.	.	.	.	T	34	5.328708	0.95733	.	.	ENSG00000101049	ENST00000373100;ENST00000373092;ENST00000373077;ENST00000412111;ENST00000423407;ENST00000341458;ENST00000426287	T;T;T;T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13;-0.13;-0.13;-0.13	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);	0.000000	0.85682	D	0.000000	T	0.75243	0.3823	L	0.59912	1.85	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	0.77448	-0.2584	10	0.62326	D	0.03	.	14.235	0.65919	0.0:0.0:0.0:1.0	.	164;198;138	Q9HBY8-3;Q9HBY8;Q9HBY8-2	.;SGK2_HUMAN;.	L	138;138;137;137;138;198;164	ENSP00000362192:F138L;ENSP00000362184:F138L;ENSP00000362168:F137L;ENSP00000396222:F137L;ENSP00000392795:F138L;ENSP00000340608:F198L;ENSP00000412214:F164L	ENSP00000340608:F198L	F	+	1	0	SGK2	41632722	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	7.860000	0.86993	2.148000	0.66965	0.533000	0.62120	TTC	.	.	.	none		0.627	SGK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080383.1			C	42199308	T	C	42199308	3	2	63	1	0	0	0	0	1	0	0	0	14222	1725	60	3	614	3	SGK2	20	42199308	Missense_Mutation	SNP	T	TCGA-A4-A57E-01A-11D-A26P-10	5329999	42199308	20826212	84	4264											
SREBF2	6721	hgsc.bcm.edu	37	chr22	42289163	42289163	+	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	agagcctgtgtggccccgagCacagtgctgttcctgactcc	6	9	12	14	1	0	2	0	1	0	1	2	3	2	2	5	1	3	3	5	1	0	1			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr22:42289163C>A	ENST00000361204.4	+	12	2417	c.2251C>A	c.(2251-2253)Cac>Aac	p.H751N	SREBF2_ENST00000491541.1_3'UTR	NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	751					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						TGGCCCCGAGCACAGTGCTGT	0.612																																					p.H751N		Atlas-SNP	.											.	SREBF2	99	.	0			c.C2251A						PASS	.						77	77	77					22																	42289163		2203	4300	6503	SO:0001583	missense	6721	exon12			CCCGAGCACAGTG	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.2251C>A	chr22.hg19:g.42289163C>A	ENSP00000354476:p.His751Asn	72.0	0.0	.		78.0	41.0	.	NM_004599	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Missense_Mutation	SNP	ENST00000361204.4	hg19	CCDS14023.1	.	.	.	.	.	.	.	.	.	.	C	5.682	0.310364	0.10733	.	.	ENSG00000198911	ENST00000361204;ENST00000457567	T	0.07216	3.21	5.42	4.36	0.52297	.	0.494236	0.23861	N	0.043856	T	0.03959	0.0111	N	0.03608	-0.345	0.26458	N	0.975491	B	0.14438	0.01	B	0.11329	0.006	T	0.39440	-0.9614	10	0.14252	T	0.57	-3.4319	13.8968	0.63778	0.1516:0.8484:0.0:0.0	.	751	Q12772	SRBP2_HUMAN	N	751	ENSP00000354476:H751N	ENSP00000354476:H751N	H	+	1	0	SREBF2	40619109	0.993000	0.37304	0.234000	0.24042	0.412000	0.31113	2.219000	0.42899	2.543000	0.85770	0.650000	0.86243	CAC	.	.	.	none		0.612	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599		A	42289163	C	A	42289163	3	1	63	1	0	0	0	0	1	0	0	0	15154	710	25	4	2297	4	SREBF2	22	42289163	Missense_Mutation	SNP	C	TCGA-A4-A57E-01A-11D-A26P-10		42289163	9015403	85	4265											
TAS1R1	80835	hgsc.bcm.edu	37	chr1	6639633	6639633	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggactacacgaggcgctgcGgctccacctgaccagtgggt	8	6	14	13	3	0	1	0	1	0	0	1	3	1	2	3	4	2	2	3	4	1	1			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr1:6639633G>A	ENST00000333172.6	+	6	2708	c.2515G>A	c.(2515-2517)Ggc>Agc	p.G839S	TAS1R1_ENST00000328191.4_3'UTR|TAS1R1_ENST00000351136.3_Missense_Mutation_p.G585S|ZBTB48_ENST00000377674.4_5'Flank	NM_138697.3	NP_619642.2	Q7RTX1	TS1R1_HUMAN	taste receptor, type 1, member 1	839					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)		GAGGCGCTGCGGCTCCACCTG	0.632																																					p.G839S		Atlas-SNP	.											.	TAS1R1	76	.	0			c.G2515A						PASS	.						41	41	41					1																	6639633		2203	4299	6502	SO:0001583	missense	80835	exon6			CGCTGCGGCTCCA		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.2515G>A	chr1.hg19:g.6639633G>A	ENSP00000331867:p.Gly839Ser	32.0	0.0	.		32.0	12.0	.	NM_138697	B2RMX0|Q5SY22|Q5SY24|Q8NGZ7|Q8TDJ7|Q8TDJ8|Q8TDJ9|Q8TDK0	Missense_Mutation	SNP	ENST00000333172.6	hg19	CCDS81.1	.	.	.	.	.	.	.	.	.	.	G	2.898	-0.228154	0.06022	.	.	ENSG00000173662	ENST00000333172;ENST00000351136	D;D	0.90900	-2.37;-2.75	5.18	-0.747	0.11091	.	0.840078	0.10725	N	0.641242	T	0.80188	0.4577	N	0.22421	0.69	0.18873	N	0.999982	B;B	0.18310	0.027;0.003	B;B	0.12156	0.007;0.004	T	0.64050	-0.6498	10	0.25751	T	0.34	.	5.538	0.17021	0.3891:0.1411:0.4698:0.0	.	585;839	Q7RTX1-2;Q7RTX1	.;TS1R1_HUMAN	S	839;585	ENSP00000331867:G839S;ENSP00000312558:G585S	ENSP00000331867:G839S	G	+	1	0	TAS1R1	6562220	0.000000	0.05858	0.059000	0.19551	0.071000	0.16799	-0.005000	0.12855	-0.027000	0.13873	-0.216000	0.12614	GGC	.	.	.	none		0.632	TAS1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004211.1			A	6639633	G	A	6639633	3	1	64	1	0	0	0	0	1	0	0	0	15574	1116	39	1	2537	1	TAS1R1	1	6639633	Missense_Mutation	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10		6639633	242610988	1	4266											
HIVEP3	59269	hgsc.bcm.edu	37	chr1	41978641	41978641	+	Missense_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	aggcccacttccctggcggcGctgaccgtggtggtgactcg	4	8	15	14	4	0	2	0	2	0	0	2	2	1	2	3	5	0	1	3	5	0	1			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr1:41978641G>A	ENST00000372583.1	-	8	7136	c.6251C>T	c.(6250-6252)gCg>gTg	p.A2084V	HIVEP3_ENST00000460604.1_5'UTR|HIVEP3_ENST00000372584.1_Missense_Mutation_p.A2084V|HIVEP3_ENST00000247584.5_Missense_Mutation_p.A2084V|HIVEP3_ENST00000429157.2_Missense_Mutation_p.A2084V	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	2084	6 X 4 AA tandem repeats of S-P-X-[RK].				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)				CCCTGGCGGCGCTGACCGTGG	0.701																																					p.A2084V		Atlas-SNP	.											.	HIVEP3	235	.	0			c.C6251T						PASS	.						25	23	23					1																	41978641		2203	4299	6502	SO:0001583	missense	59269	exon8			GGCGGCGCTGACC	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.6251C>T	chr1.hg19:g.41978641G>A	ENSP00000361664:p.Ala2084Val	59.0	0.0	.		98.0	4.0	.	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Missense_Mutation	SNP	ENST00000372583.1	hg19	CCDS463.1	.	.	.	.	.	.	.	.	.	.	G	11.10	1.539774	0.27563	.	.	ENSG00000127124	ENST00000372584;ENST00000372583;ENST00000247584;ENST00000429157	T;T;T;T	0.05258	3.5;3.47;3.47;3.5	4.65	-2.36	0.06663	.	0.979219	0.08323	N	0.963534	T	0.02571	0.0078	N	0.12182	0.205	0.21416	N	0.999695	B;B	0.10296	0.003;0.002	B;B	0.08055	0.003;0.001	T	0.45644	-0.9247	10	0.02654	T	1	-1.2588	4.8403	0.13487	0.3916:0.0:0.4715:0.1369	.	2084;2084	Q5T1R4-2;Q5T1R4	.;ZEP3_HUMAN	V	2084	ENSP00000361665:A2084V;ENSP00000361664:A2084V;ENSP00000247584:A2084V;ENSP00000410828:A2084V	ENSP00000247584:A2084V	A	-	2	0	HIVEP3	41751228	0.084000	0.21492	0.951000	0.38953	0.992000	0.81027	0.117000	0.15583	-0.322000	0.08615	0.655000	0.94253	GCG	.	.	.	none		0.701	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		A	41978641	G	A	41978641	3	1	64	1	0	0	0	0	1	0	0	0	7195	1087	38	1	977	1	HIVEP3	1	41978641	Missense_Mutation	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10	35339008	41978641	207271980	2	4267											
RORC	6097	hgsc.bcm.edu	37	chr1	151785765	151785765	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttgccttcaaaaaagaccGtgcggttgtcagcattgtag	11	12	10	8	2	2	1	2	0	0	1	2	1	2	1	2	1	3	3	2	1	4	5			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr1:151785765G>A	ENST00000318247.6	-	8	1231	c.1124C>T	c.(1123-1125)aCg>aTg	p.T375M	RORC_ENST00000480719.1_5'UTR|RORC_ENST00000356728.6_Missense_Mutation_p.T354M|RORC_ENST00000392697.3_Missense_Mutation_p.T429M	NM_005060.3	NP_005051.2	P51449	RORG_HUMAN	RAR-related orphan receptor C	375	Ligand-binding.				adipose tissue development (GO:0060612)|cellular response to sterol (GO:0036315)|circadian regulation of gene expression (GO:0032922)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|lymph node development (GO:0048535)|negative regulation of thymocyte apoptotic process (GO:0070244)|Peyer's patch development (GO:0048541)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of fat cell differentiation (GO:0045598)|regulation of gamma-delta T cell differentiation (GO:0045586)|regulation of glucose metabolic process (GO:0010906)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription involved in cell fate commitment (GO:0060850)|T cell differentiation in thymus (GO:0033077)|T-helper 17 cell differentiation (GO:0072539)|T-helper cell differentiation (GO:0042093)|transcription initiation from RNA polymerase II promoter (GO:0006367)|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)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(4)|large_intestine(1)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			AAAAAAGACCGTGCGGTTGTC	0.557																																					p.T375M		Atlas-SNP	.											.	RORC	70	.	0			c.C1124T						PASS	.						236	234	235					1																	151785765		2203	4300	6503	SO:0001583	missense	6097	exon8			AAGACCGTGCGGT	U16997	CCDS1004.1, CCDS30856.1	1q21	2013-01-16			ENSG00000143365	ENSG00000143365		"Nuclear hormone receptors"	10260	protein-coding gene	gene with protein product		602943				7811290	Standard	NM_005060		Approved	RZRG, RORG, NR1F3, TOR	uc001ezh.3	P51449	OTTHUMG00000013053	ENST00000318247.6:c.1124C>T	chr1.hg19:g.151785765G>A	ENSP00000327025:p.Thr375Met	79.0	0.0	.		97.0	41.0	.	NM_005060	Q5SZR9|Q8N5V7|Q8NCY8	Missense_Mutation	SNP	ENST00000318247.6	hg19	CCDS1004.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.478730	0.84747	.	.	ENSG00000143365	ENST00000356728;ENST00000392697;ENST00000318247	D;D;D	0.96427	-4.01;-4.01;-4.01	4.62	4.62	0.57501	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.64402	U	0.000012	D	0.97532	0.9192	M	0.71920	2.185	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;1.0	D	0.98360	1.0548	10	0.87932	D	0	.	16.1933	0.82006	0.0:0.0:1.0:0.0	.	375;429;375;354	B6ZGS6;B4DPR1;P51449;F1D8P6	.;.;RORG_HUMAN;.	M	354;429;375	ENSP00000349164:T354M;ENSP00000376461:T429M;ENSP00000327025:T375M	ENSP00000327025:T375M	T	-	2	0	RORC	150052389	1.000000	0.71417	0.997000	0.53966	0.914000	0.54420	9.469000	0.97679	2.391000	0.81399	0.563000	0.77884	ACG	.	.	.	none		0.557	RORC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036626.1			A	151785765	G	A	151785765	3	1	64	1	0	0	0	0	1	0	0	0	13543	1145	40	1	448	1	RORC	1	151785765	Missense_Mutation	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10	109807124	151785765	97464856	3	4268											
FASLG	356	hgsc.bcm.edu	37	chr1	172634980	172634980	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtatccccaggatctggtgAtgatggaggggaagatgatg	11	9	16	5	0	1	4	0	3	1	1	2	7	2	7	2	5	0	1	2	5	2	1	rs111238176		TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr1:172634980A>G	ENST00000367721.2	+	4	854	c.670A>G	c.(670-672)Atg>Gtg	p.M224V	FASLG_ENST00000340030.3_3'UTR	NM_000639.1	NP_000630.1	P48023	TNFL6_HUMAN	Fas ligand (TNF superfamily, member 6)	224					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						GGATCTGGTGATGATGGAGGG	0.507																																					p.M224V	Ovarian(28;486 876 30334 44033)	Atlas-SNP	.											.	FASLG	44	.	0			c.A670G						PASS	.						107	102	104					1																	172634980		2203	4300	6503	SO:0001583	missense	356	exon4			CTGGTGATGATGG	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.670A>G	chr1.hg19:g.172634980A>G	ENSP00000356694:p.Met224Val	94.0	0.0	.		103.0	46.0	.	NM_000639	Q9BZP9	Missense_Mutation	SNP	ENST00000367721.2	hg19	CCDS1304.1	.	.	.	.	.	.	.	.	.	.	A	14.09	2.431408	0.43122	.	.	ENSG00000117560	ENST00000367721	D	0.94457	-3.43	5.34	4.41	0.53225	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	0.257132	0.32624	N	0.005854	T	0.78033	0.4220	N	0.02539	-0.55	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.75068	-0.3448	10	0.66056	D	0.02	-4.9683	13.2687	0.60150	0.1797:0.8202:0.0:0.0	.	224	P48023	TNFL6_HUMAN	V	224	ENSP00000356694:M224V	ENSP00000356694:M224V	M	+	1	0	FASLG	170901603	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	0.680000	0.25306	1.203000	0.43233	0.528000	0.53228	ATG	.	A|0.500;G|0.500	0.500	weak		0.507	FASLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084276.1			G	172634980	A	G	172634980	3	3	64	1	0	0	0	0	1	0	0	0	5689	333	12	3	684	3	FASLG	1	172634980	Missense_Mutation	SNP	A	TCGA-A4-A5DU-01A-11D-A28G-10	20849215	172634980	76615641	4	4269											
PIGR	5284	hgsc.bcm.edu	37	chr1	207112530	207112530	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatgcccaggccacacttgtAgcgcccggagtcatcctggc	7	7	12	15	2	1	0	1	0	0	0	2	2	2	1	4	3	2	1	4	3	1	2			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr1:207112530A>G	ENST00000356495.4	-	3	505	c.322T>C	c.(322-324)Tac>Cac	p.Y108H		NM_002644.3	NP_002635.2	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor	108	Ig-like V-type 1.				detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc receptor signaling pathway (GO:0038093)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|receptor clustering (GO:0043113)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	polymeric immunoglobulin receptor activity (GO:0001792)			central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						CCACACTTGTAGCGCCCGGAG	0.577																																					p.Y108H		Atlas-SNP	.											.	PIGR	98	.	0			c.T322C						PASS	.						75	64	68					1																	207112530		2203	4300	6503	SO:0001583	missense	5284	exon3			ACTTGTAGCGCCC		CCDS1474.1	1q31-q41	2013-01-11			ENSG00000162896	ENSG00000162896		"Immunoglobulin superfamily / V-set domain containing"	8968	protein-coding gene	gene with protein product		173880					Standard	NM_002644		Approved		uc001hez.3	P01833	OTTHUMG00000036581	ENST00000356495.4:c.322T>C	chr1.hg19:g.207112530A>G	ENSP00000348888:p.Tyr108His	149.0	0.0	.		158.0	56.0	.	NM_002644	Q68D81|Q8IZY7	Missense_Mutation	SNP	ENST00000356495.4	hg19	CCDS1474.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.035080	0.75617	.	.	ENSG00000162896	ENST00000356495	D	0.94537	-3.45	5.67	5.67	0.87782	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000008	D	0.97939	0.9322	H	0.95004	3.61	0.44890	D	0.997906	D	0.89917	1.0	D	0.97110	1.0	D	0.98953	1.0795	10	0.87932	D	0	-20.6353	13.9439	0.64073	1.0:0.0:0.0:0.0	.	108	P01833	PIGR_HUMAN	H	108	ENSP00000348888:Y108H	ENSP00000348888:Y108H	Y	-	1	0	PIGR	205179153	1.000000	0.71417	0.979000	0.43373	0.686000	0.39977	5.514000	0.67043	2.288000	0.76882	0.533000	0.62120	TAC	.	.	.	none		0.577	PIGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088975.1	NM_002644		G	207112530	A	G	207112530	3	3	64	1	0	0	0	0	1	0	0	0	11904	420	15	3	2008	3	PIGR	1	207112530	Missense_Mutation	SNP	A	TCGA-A4-A5DU-01A-11D-A28G-10	34477550	207112530	42138091	5	4270											
DISC1	27185	hgsc.bcm.edu	37	chr1	231931003	231931003	+	Frame_Shift_Del	DEL	A	A	-																															tccagcctccaggaaagaatAaaatccctcaacttgtcact																										TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr1:231931003delA	ENST00000602281.1	+	7	1703	c.1650delA	c.(1648-1650)atafs	p.I550fs	TSNAX-DISC1_ENST00000602962.1_3'UTR|DISC1_ENST00000535983.1_Frame_Shift_Del_p.I550fs|DISC1_ENST00000602873.1_Intron|DISC1_ENST00000439617.2_Frame_Shift_Del_p.I550fs|DISC1_ENST00000366633.3_Frame_Shift_Del_p.I550fs|DISC1_ENST00000366636.4_Frame_Shift_Del_p.I550fs|DISC1_ENST00000539444.1_Frame_Shift_Del_p.I550fs|DISC1_ENST00000366637.3_5'UTR|DISC1_ENST00000537876.1_Intron	NM_001164542.1|NM_001164544.1	NP_001158014.1|NP_001158016.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	550	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)				AGGAAAGAATAAAATCCCTCA	0.358																																					p.I582fs		Atlas-Indel,Pindel	.											.	DISC1	207	.	0			c.1745delT						PASS	.						84	85	85					1																	231931003		2203	4300	6503	SO:0001589	frameshift_variant	27185	exon8			.	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.1650delA	chr1.hg19:g.231931003delA	ENSP00000473425:p.Ile550fs	59.0	0.0	0		59.0	27.0	0.457627	NM_001164537	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Frame_Shift_Del	DEL	ENST00000602281.1	hg19	CCDS59205.1																																																																																			.	.	.	none		0.358	DISC1-019	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467451.1	NM_018662		-	231931003	A	-	231931003	7	5	64	1	0	1	0	1	0	0	0	0	4540	352	13	0	2049	0	DISC1	1	231931003	Frame_Shift_Del	DEL	A	TCGA-A4-A5DU-01A-11D-A28G-10	24818473	231931003	17319618	6	4271											
PPM1B	5495	hgsc.bcm.edu	37	chr2	44457731	44457731	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccagctgccacagctacttcTtcgaacagtgatgctggaaa	11	9	9	12	1	1	1	0	1	1	0	2	3	1	2	2	1	6	3	2	1	3	3			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr2:44457731T>C	ENST00000282412.4	+	6	1726	c.1314T>C	c.(1312-1314)tcT>tcC	p.S438S	PPM1B_ENST00000345249.4_Silent_p.S151S|PPM1B_ENST00000378551.2_Intron|PPM1B_ENST00000378540.4_Intron|PPM1B_ENST00000409432.3_3'UTR	NM_002706.4	NP_002697.1	O75688	PPM1B_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1B	438					cytokine-mediated signaling pathway (GO:0019221)|N-terminal protein myristoylation (GO:0006499)|negative regulation of defense response to virus (GO:0050687)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|peptidyl-threonine dephosphorylation (GO:0035970)|protein dephosphorylation (GO:0006470)	cytosol (GO:0005829)|membrane (GO:0016020)	magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)			kidney(4)|large_intestine(3)|lung(7)|skin(2)	16		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				CAGCTACTTCTTCGAACAGTG	0.473																																					p.S438S		Atlas-SNP	.											.	PPM1B	97	.	0			c.T1314C						PASS	.						76	74	75					2																	44457731		2203	4300	6503	SO:0001819	synonymous_variant	5495	exon6			TACTTCTTCGAAC	AJ005801	CCDS1816.1, CCDS1817.1, CCDS1818.1, CCDS46271.1	2p22.1	2012-04-17	2010-03-05		ENSG00000138032	ENSG00000138032	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9276	protein-coding gene	gene with protein product	"protein phosphatase 2C, beta isoform"	603770	"protein phosphatase 1B (formerly 2C), magnesium-dependent, beta isoform"			9684878	Standard	NM_002706		Approved	PPC2BETAX, PP2CB, PP2CBETA	uc002rtt.3	O75688	OTTHUMG00000128757	ENST00000282412.4:c.1314T>C	chr2.hg19:g.44457731T>C		150.0	0.0	.		197.0	131.0	.	NM_002706	Q461Q2|Q4J6C1|Q4J6C2|Q658R4|Q96ER6|Q9HAY8	Silent	SNP	ENST00000282412.4	hg19	CCDS1817.1																																																																																			.	.	.	none		0.473	PPM1B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250672.1	NM_002706		C	44457731	T	C	44457731	2	2	64	1	0	0	0	0	0	0	0	1	12346	1596	56	3		3	PPM1B	2	44457731	Silent	SNP	T	TCGA-A4-A5DU-01A-11D-A28G-10		44457731	198741642	7	4272											
PRKCE	5581	hgsc.bcm.edu	37	chr2	45879246	45879246	+	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	tccccgccccgaccatggtaGtgttcaatggccttcttaag	7	11	9	14	2	2	0	1	0	1	0	3	1	3	0	6	2	0	2	6	2	3	4			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr2:45879246G>C	ENST00000306156.3	+	1	334	c.7G>C	c.(7-9)Gtg>Ctg	p.V3L		NM_005400.2	NP_005391.1	Q02156	KPCE_HUMAN	protein kinase C, epsilon	3	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|cellular response to ethanol (GO:0071361)|cellular response to hypoxia (GO:0071456)|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)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|locomotory exploration behavior (GO:0035641)|macrophage activation involved in immune response (GO:0002281)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cellular glucuronidation (GO:2001031)|positive regulation of cytokinesis (GO:0032467)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of insulin secretion (GO:0032024)|positive regulation of lipid catabolic process (GO:0050996)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|release of sequestered calcium ion into cytosol (GO:0051209)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|TRAM-dependent toll-like receptor 4 signaling pathway (GO:0035669)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|ethanol binding (GO:0035276)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|receptor activator activity (GO:0030546)|signal transducer activity (GO:0004871)		MBOAT2/PRKCE(2)	breast(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(13)|ovary(3)|upper_aerodigestive_tract(2)	34		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)		Tamoxifen(DB00675)	GACCATGGTAGTGTTCAATGG	0.652																																					p.V3L		Atlas-SNP	.											.	PRKCE	58	.	0			c.G7C						PASS	.						31	36	35					2																	45879246		2196	4297	6493	SO:0001583	missense	5581	exon1			ATGGTAGTGTTCA		CCDS1824.1	2p21	2009-07-10			ENSG00000171132	ENSG00000171132	2.7.11.1		9401	protein-coding gene	gene with protein product		176975				1382605, 7877991	Standard	NM_005400		Approved		uc002rut.3	Q02156	OTTHUMG00000128817	ENST00000306156.3:c.7G>C	chr2.hg19:g.45879246G>C	ENSP00000306124:p.Val3Leu	33.0	0.0	.		55.0	28.0	.	NM_005400	B0LPH7|Q32MQ3|Q53SL4|Q53SM5|Q9UE81	Missense_Mutation	SNP	ENST00000306156.3	hg19	CCDS1824.1	.	.	.	.	.	.	.	.	.	.	G	18.18	3.565679	0.65651	.	.	ENSG00000171132	ENST00000421201;ENST00000306156	T;T	0.08458	3.09;3.09	4.71	4.71	0.59529	C2 membrane targeting protein (1);C2 calcium/lipid-binding domain, CaLB (1);	0.080242	0.47852	D	0.000211	T	0.09202	0.0227	L	0.40543	1.245	0.80722	D	1	B	0.13145	0.007	B	0.09377	0.004	T	0.19192	-1.0313	10	0.20519	T	0.43	.	17.673	0.88224	0.0:0.0:1.0:0.0	.	3	Q02156	KPCE_HUMAN	L	3	ENSP00000394574:V3L;ENSP00000306124:V3L	ENSP00000306124:V3L	V	+	1	0	PRKCE	45732750	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.766000	0.98957	2.152000	0.67230	0.561000	0.74099	GTG	.	.	.	none		0.652	PRKCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250751.2			C	45879246	G	C	45879246	3	2	64	1	0	0	0	0	1	0	0	0	12521	1029	36	4	9	4	PRKCE	2	45879246	Missense_Mutation	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10	1421515	45879246	197320127	8	4273											
ABCA12	26154	hgsc.bcm.edu	37	chr2	215865727	215865727	+	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	gtgccagcttctgttagaagGaagcttaaaaataacaccta	15	10	8	8	0	1	1	0	0	1	1	1	2	1	2	2	1	4	3	2	1	8	5			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr2:215865727G>C	ENST00000272895.7	-	22	3100	c.2881C>G	c.(2881-2883)Cct>Gct	p.P961A	ABCA12_ENST00000389661.4_Missense_Mutation_p.P643A	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	961					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)		CTGTTAGAAGGAAGCTTAAAA	0.403																																					p.P961A	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.C2881G						PASS	.						55	58	57					2																	215865727		2202	4300	6502	SO:0001583	missense	26154	exon22			TAGAAGGAAGCTT	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.2881C>G	chr2.hg19:g.215865727G>C	ENSP00000272895:p.Pro961Ala	46.0	0.0	.		51.0	18.0	.	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	hg19	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	G	19.04	3.749673	0.69533	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.86627	-2.15;-2.15	5.9	5.9	0.94986	.	0.627251	0.15788	N	0.244589	D	0.92221	0.7533	L	0.46947	1.48	0.80722	D	1	D;D	0.89917	1.0;0.984	D;P	0.87578	0.998;0.885	D	0.91505	0.5222	10	0.59425	D	0.04	.	20.2664	0.98460	0.0:0.0:1.0:0.0	.	961;643	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	A	961;643	ENSP00000272895:P961A;ENSP00000374312:P643A	ENSP00000272895:P961A	P	-	1	0	ABCA12	215573972	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.627000	0.67784	2.786000	0.95864	0.561000	0.74099	CCT	.	.	.	none		0.403	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		C	215865727	G	C	215865727	3	2	64	1	0	0	0	0	1	0	0	0	30	1174	41	4	5034	4	ABCA12	2	215865727	Missense_Mutation	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10	169986481	215865727	27333646	9	4274											
TNS1	7145	hgsc.bcm.edu	37	chr2	218713569	218713569	+	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	tcccgcttctcctggggactCaaggcagcagtggcactgga	7	8	13	13	1	2	0	1	0	1	0	4	2	3	2	2	5	1	4	2	5	1	1			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr2:218713569C>G	ENST00000171887.4	-	17	1748	c.1296G>C	c.(1294-1296)ttG>ttC	p.L432F	TNS1_ENST00000430930.1_Missense_Mutation_p.L432F|TNS1_ENST00000419504.1_Missense_Mutation_p.L432F|TNS1_ENST00000480665.1_5'UTR	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	432					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)		CCTGGGGACTCAAGGCAGCAG	0.642																																					p.L432F		Atlas-SNP	.											.	TNS1	251	.	0			c.G1296C						PASS	.						64	67	66					2																	218713569		2203	4300	6503	SO:0001583	missense	7145	exon17			GGGACTCAAGGCA	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.1296G>C	chr2.hg19:g.218713569C>G	ENSP00000171887:p.Leu432Phe	98.0	0.0	.		125.0	47.0	.	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	hg19	CCDS2407.1	.	.	.	.	.	.	.	.	.	.	C	14.17	2.454564	0.43634	.	.	ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930;ENST00000446903	D;D;D;D	0.95447	-3.48;-3.47;-3.49;-3.71	4.79	3.9	0.45041	.	0.172150	0.40469	N	0.001094	D	0.96929	0.8997	M	0.76328	2.33	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.996;1.0;0.999;0.999	D;D;D;D;D	0.85130	0.997;0.943;0.974;0.994;0.981	D	0.96213	0.9154	10	0.46703	T	0.11	.	10.7558	0.46237	0.0:0.8443:0.0:0.1557	.	432;486;432;432;432	B2RU35;A1L0S7;Q9HBL0;E9PGF5;E9PF55	.;.;TENS1_HUMAN;.;.	F	432;432;432;557	ENSP00000171887:L432F;ENSP00000408724:L432F;ENSP00000406016:L432F;ENSP00000405460:L557F	ENSP00000171887:L432F	L	-	3	2	TNS1	218421814	1.000000	0.71417	1.000000	0.80357	0.637000	0.38172	1.405000	0.34635	1.227000	0.43598	0.561000	0.74099	TTG	.	.	.	none		0.642	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		G	218713569	C	G	218713569	3	3	64	1	0	0	0	0	1	0	0	0	16355	825	29	4	3979	4	TNS1	2	218713569	Missense_Mutation	SNP	C	TCGA-A4-A5DU-01A-11D-A28G-10	2847842	218713569	24485804	10	4275											
NISCH	11188	hgsc.bcm.edu	37	chr3	52526011	52526011	+	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	ggctgagccagagaaggcccCagccctcagcatcctgctgt	8	6	12	15	0	1	2	1	1	0	1	2	3	2	2	5	2	4	3	5	2	1	0	rs369447186		TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr3:52526011C>T	ENST00000479054.1	+	22	4100	c.4028C>T	c.(4027-4029)cCa>cTa	p.P1343L	NISCH_ENST00000345716.4_Missense_Mutation_p.P1343L			Q9Y2I1	NISCH_HUMAN	nischarin	1343					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)	GAGAAGGCCCCAGCCCTCAGC	0.627																																					p.P1343L		Atlas-SNP	.											.	NISCH	97	.	0			c.C4028T						PASS	.	C	LEU/PRO	0,4406		0,0,2203	71	73	72		4028	4.7	0.1	3		72	2,8598	2.2+/-6.3	0,2,4298	no	missense	NISCH	NM_007184.3	98	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	1343/1505	52526011	2,13004	2203	4300	6503	SO:0001583	missense	11188	exon21			AGGCCCCAGCCCT	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.4028C>T	chr3.hg19:g.52526011C>T	ENSP00000418232:p.Pro1343Leu	107.0	0.0	.		137.0	36.0	.	NM_007184	C9J245|Q6PGP3|Q6PIB4|Q7L8M3|Q7Z2X6|Q9UES6|Q9UEU4|Q9UFW3	Missense_Mutation	SNP	ENST00000479054.1	hg19	CCDS33767.1	.	.	.	.	.	.	.	.	.	.	C	15.14	2.744827	0.49151	0.0	2.33E-4	ENSG00000010322	ENST00000479054;ENST00000345716;ENST00000433196;ENST00000414197	T;T	0.07908	3.15;3.15	5.6	4.7	0.59300	.	0.353140	0.30277	N	0.009998	T	0.07458	0.0188	N	0.24115	0.695	0.09310	N	0.999995	B	0.06786	0.001	B	0.09377	0.004	T	0.24728	-1.0152	10	0.62326	D	0.03	-9.2061	14.0883	0.64973	0.4654:0.5346:0.0:0.0	.	1343	Q9Y2I1	NISCH_HUMAN	L	1343;1343;267;687	ENSP00000418232:P1343L;ENSP00000339958:P1343L	ENSP00000339958:P1343L	P	+	2	0	NISCH	52501051	0.002000	0.14202	0.052000	0.19188	0.991000	0.79684	1.108000	0.31123	1.309000	0.44985	0.491000	0.48974	CCA	.	.	.	weak		0.627	NISCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351357.1	NM_007184		T	52526011	C	T	52526011	3	4	64	1	0	0	0	0	1	0	0	0	10439	594	21	2	4110	2	NISCH	3	52526011	Missense_Mutation	SNP	C	TCGA-A4-A5DU-01A-11D-A28G-10		52526011	145496419	11	4276											
ZNF721	170960	hgsc.bcm.edu	37	chr4	436799	436801	+	In_Frame_Del	DEL	GAG	GAG	-																															tcttatgtttagcaaagcttGaggatgaggtaatgactttg																										TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr4:436799_436801delGAG	ENST00000338977.5	-	2	1467_1469	c.1419_1421delCTC	c.(1417-1422)tcctca>tca	p.473_474SS>S	ZNF721_ENST00000507078.1_Intron|ZNF721_ENST00000506646.1_Intron|ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000511833.2_In_Frame_Del_p.485_486SS>S			Q8TF20	ZN721_HUMAN	zinc finger protein 721	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)			endometrium(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						AGCAAAGCTTGAGGATGAGGTAA	0.369																																					p.486_486del		Atlas-Indel,Pindel	.											.	ZNF721	205	.	0			c.1456_1458del						PASS	.			2,3976		1,0,1988						0.4	0.1			78	1,8109		0,1,4054	no	coding	ZNF721	NM_133474.2		1,1,6042	A1A1,A1R,RR		0.0123,0.0503,0.0248				3,12085				SO:0001651	inframe_deletion	170960	exon3			.	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.1419_1421delCTC	chr4.hg19:g.436799_436801delGAG	ENSP00000340524:p.Ser475del	81.0	0.0	0		80.0	23.0	0.2875	NM_133474	Q69YG7	In_Frame_Del	DEL	ENST00000338977.5	hg19																																																																																				.	.	.	none		0.369	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474		-	436801	GAG	-	436799	7	5	64	1	0	1	0	1	0	0	0	0	18134	1294	45	0	1318	0	ZNF721	4	436799	In_Frame_Del	DEL	GAG	TCGA-A4-A5DU-01A-11D-A28G-10		436799	190717477	12	4277											
DSPP	1834	hgsc.bcm.edu	37	chr4	88537224	88537232	+	In_Frame_Del	DEL	ACAGCAGCA	ACAGCAGCA	-																															cgacagcagtgatagcagtgAcagcagcaacagcagtgaca																								rs201608130|rs140656082|rs200679221|rs564674887	byFrequency	TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	ACAGCAGCA	ACAGCAGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr4:88537224_88537232delACAGCAGCA	ENST00000282478.7	+	4	3443_3451	c.3410_3418delACAGCAGCA	c.(3409-3420)gacagcagcaac>gac	p.SSN1138del	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_In_Frame_Del_p.SSN1138del			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1138	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)		gatagcagtgacagcagcaacagcagtga	0.569																																					p.1137_1139del		Atlas-INDEL	.											.	DSPP	174	.	0			c.3409_3417del						PASS	.																																			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.3410_3418delACAGCAGCA	chr4.hg19:g.88537224_88537232delACAGCAGCA	ENSP00000282478:p.Ser1138_Asn1140del	190.0	0.0	0		250.0	114.0	0.456	NM_014208	A8MUI0|O95815	In_Frame_Del	DEL	ENST00000282478.7	hg19	CCDS43248.1																																																																																			.	.	.	none		0.569	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		-	88537232	ACAGCAGCA	-	88537224	7	5	64	1	0	1	0	1	0	0	0	0	4784	275	10	0	3424	0	DSPP	4	88537224	In_Frame_Del	DEL	ACAGCAGCA	TCGA-A4-A5DU-01A-11D-A28G-10	88100425	88537224	102617052	13	4278											
IL6ST	3572	hgsc.bcm.edu	37	chr5	55237637	55237637	+	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	aatacatttgatcttttgaaTtaaaattgtgctaaggaaga	16	15	7	3	0	1	3	0	2	1	1	1	4	1	4	0	1	2	1	0	1	7	7			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr5:55237637T>A	ENST00000381298.2	-	17	2342	c.2030A>T	c.(2029-2031)aAt>aTt	p.N677I	IL6ST_ENST00000336909.5_Missense_Mutation_p.N677I|IL6ST_ENST00000381294.3_Missense_Mutation_p.N616I|IL6ST_ENST00000381287.4_3'UTR|IL6ST_ENST00000502326.3_Missense_Mutation_p.N677I|IL6ST_ENST00000536319.1_3'UTR|CTD-2031P19.5_ENST00000576302.1_RNA|IL6ST_ENST00000381286.3_Missense_Mutation_p.I53F|IL6ST_ENST00000381293.2_Missense_Mutation_p.I190F	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	677					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)				ATCTTTTGAATTAAAATTGTG	0.343			O		hepatocellular ca																																p.N677I		Atlas-SNP	.		Dom	yes		5	5q11	3572	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"		E	.	IL6ST	75	.	0			c.A2030T						PASS	.						43	47	46					5																	55237637		2199	4298	6497	SO:0001583	missense	3572	exon17			TTTGAATTAAAAT	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.2030A>T	chr5.hg19:g.55237637T>A	ENSP00000370698:p.Asn677Ile	170.0	0.0	.		135.0	55.0	.	NM_002184	A0N0L4|Q5FC04|Q9UQ41	Missense_Mutation	SNP	ENST00000381298.2	hg19	CCDS3971.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.125|9.125	1.009945|1.009945	0.19277|0.19277	.|.	.|.	ENSG00000134352|ENSG00000134352	ENST00000381293;ENST00000381286|ENST00000381298;ENST00000336909;ENST00000381294	T;T|T;T;T	0.56611|0.40225	1.87;0.45|1.31;1.31;1.04	5.68|5.68	1.97|1.97	0.26223|0.26223	.|.	.|0.501171	.|0.23920	.|N	.|0.043246	T|T	0.37732|0.37732	0.1014|0.1014	N|N	0.19112|0.19112	0.55|0.55	0.41896|0.41896	D|D	0.990396|0.990396	P|P;D;P	0.39216|0.60160	0.664|0.822;0.987;0.822	B|B;P;P	0.36030|0.56216	0.216|0.406;0.794;0.534	T|T	0.03608|0.03608	-1.1020|-1.1020	9|10	0.87932|0.22706	D|T	0|0.39	.|.	11.3078|11.3078	0.49345|0.49345	0.0:0.2696:0.0:0.7304|0.0:0.2696:0.0:0.7304	.|.	190|677;616;677	Q5FC05|Q17RA0;Q5FC04;P40189	.|.;.;IL6RB_HUMAN	F|I	190;53|677;677;616	ENSP00000370693:I190F;ENSP00000370686:I53F|ENSP00000370698:N677I;ENSP00000338799:N677I;ENSP00000370694:N616I	ENSP00000370686:I53F|ENSP00000338799:N677I	I|N	-|-	1|2	0|0	IL6ST|IL6ST	55273394|55273394	0.905000|0.905000	0.30787|0.30787	0.932000|0.932000	0.37286|0.37286	0.603000|0.603000	0.37013|0.37013	0.092000|0.092000	0.15066|0.15066	-0.059000|-0.059000	0.13154|0.13154	-1.162000|-1.162000	0.01777|0.01777	ATT|AAT	.	.	.	none		0.343	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		A	55237637	T	A	55237637	3	1	64	1	0	0	0	0	1	0	0	0	7710	1493	52	5	730	5	IL6ST	5	55237637	Missense_Mutation	SNP	T	TCGA-A4-A5DU-01A-11D-A28G-10		55237637	125677623	14	4279											
FHL5	9457	hgsc.bcm.edu	37	chr6	97051597	97051597	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttacatgttatgatcgtgtAttttctaactattgcgagga	10	17	9	5	2	1	1	0	1	1	0	2	3	1	2	0	1	3	3	0	1	5	8			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr6:97051597A>G	ENST00000326771.2	+	3	488	c.108A>G	c.(106-108)gtA>gtG	p.V36V	FHL5_ENST00000541107.1_Silent_p.V36V	NM_020482.4	NP_065228.4	Q5TD97	FHL5_HUMAN	four and a half LIM domains 5	36					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|urinary_tract(1)	27		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)		ATGATCGTGTATTTTCTAACT	0.363																																					p.V36V		Atlas-SNP	.											FHL5,NS,carcinoma,+1,1	FHL5	73	.	0			c.A108G						PASS	.						166	146	153					6																	97051597		2203	4300	6503	SO:0001819	synonymous_variant	9457	exon3			TCGTGTATTTTCT	AF278541	CCDS5035.1	6q16.1-q16.3	2008-02-05			ENSG00000112214	ENSG00000112214			17371	protein-coding gene	gene with protein product		605126					Standard	NM_020482		Approved	FLJ33049, ACT, dJ393D12.2	uc003pot.2	Q5TD97	OTTHUMG00000015239	ENST00000326771.2:c.108A>G	chr6.hg19:g.97051597A>G		85.0	0.0	.		73.0	28.0	.	NM_020482	B2RBD1|E1P526|Q5TD98|Q8WW21|Q9NQU2	Silent	SNP	ENST00000326771.2	hg19	CCDS5035.1																																																																																			.	.	.	none		0.363	FHL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041559.1	NM_020482		G	97051597	A	G	97051597	2	3	64	1	0	0	0	0	0	0	0	1	5888	436	16	3		3	FHL5	6	97051597	Silent	SNP	A	TCGA-A4-A5DU-01A-11D-A28G-10		97051597	74063470	15	4280											
ZMIZ2	83637	hgsc.bcm.edu	37	chr7	44796552	44796552	+	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	ctgcttcctcataggttttgGggaaccccatgggccctgca	6	11	11	13	0	1	0	1	0	0	0	2	1	2	1	4	4	3	3	4	4	2	4			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr7:44796552G>A	ENST00000309315.4	+	4	295	c.172G>A	c.(172-174)Ggg>Agg	p.G58R	ZMIZ2_ENST00000413916.1_Intron|ZMIZ2_ENST00000441627.1_Missense_Mutation_p.G58R|ZMIZ2_ENST00000265346.7_Missense_Mutation_p.G58R|ZMIZ2_ENST00000433667.1_Intron	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2	58	Gly-rich.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						ATAGGTTTTGGGGAACCCCAT	0.592																																					p.G58R	NSCLC(20;604 852 1948 16908 50522)	Atlas-SNP	.											.	ZMIZ2	82	.	0			c.G172A						PASS	.						112	114	113					7																	44796552		1971	4146	6117	SO:0001583	missense	83637	exon3			GTTTTGGGGAACC	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.172G>A	chr7.hg19:g.44796552G>A	ENSP00000311778:p.Gly58Arg	63.0	0.0	.		97.0	43.0	.	NM_174929	A4D2K7|D3DVL1|O94790|Q0VGB4|Q659A8|Q6JKL5|Q8WTX8|Q96Q01|Q9BQH7	Missense_Mutation	SNP	ENST00000309315.4	hg19	CCDS43576.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.707309	0.89018	.	.	ENSG00000122515	ENST00000457123;ENST00000309315;ENST00000441627;ENST00000265346;ENST00000414051	D;D;D;D	0.97731	-4.51;-4.51;-4.51;-4.51	4.8	4.8	0.61643	.	0.000000	0.56097	D	0.000030	D	0.98466	0.9489	M	0.71036	2.16	0.54753	D	0.999989	D;D	0.89917	0.999;1.0	D;D	0.79108	0.962;0.992	D	0.99771	1.1024	10	0.87932	D	0	-8.5125	17.6515	0.88165	0.0:0.0:1.0:0.0	.	58;58	Q8NF64-2;Q8NF64	.;ZMIZ2_HUMAN	R	58	ENSP00000415501:G58R;ENSP00000311778:G58R;ENSP00000414723:G58R;ENSP00000265346:G58R	ENSP00000265346:G58R	G	+	1	0	ZMIZ2	44763077	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	8.810000	0.91950	2.485000	0.83878	0.655000	0.94253	GGG	.	.	.	none		0.592	ZMIZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341790.1	NM_031449		A	44796552	G	A	44796552	3	1	64	1	0	0	0	0	1	0	0	0	17709	1232	43	2	182	2	ZMIZ2	7	44796552	Missense_Mutation	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10		44796552	114342111	16	4281											
PON2	5445	hgsc.bcm.edu	37	chr7	95040981	95040981	+	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	gtaccttggaagaagctcatGtttgactgttttcagatgca	10	14	10	7	0	2	3	2	1	0	2	2	4	2	4	1	1	3	5	1	1	3	5			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr7:95040981G>T	ENST00000222572.3	-	5	724	c.478C>A	c.(478-480)Cat>Aat	p.H160N	PON2_ENST00000483292.1_5'UTR|PON2_ENST00000433091.2_Missense_Mutation_p.H148N|PON2_ENST00000536183.1_Missense_Mutation_p.H181N			Q15165	PON2_HUMAN	paraoxonase 2	160					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)			AGAAGCTCATGTTTGACTGTT	0.358																																					p.H160N	GBM(42;803 823 13649 23368 31463)	Atlas-SNP	.											.	PON2	32	.	0			c.C478A						PASS	.						76	78	78					7																	95040981		2203	4300	6503	SO:0001583	missense	5445	exon5			GCTCATGTTTGAC	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.478C>A	chr7.hg19:g.95040981G>T	ENSP00000222572:p.His160Asn	99.0	0.0	.		98.0	47.0	.	NM_000305	A4D1H7|B2RCP9|B4DJD5|O15114|O15115|O75856|Q5FBX7|Q86YL0	Missense_Mutation	SNP	ENST00000222572.3	hg19	CCDS5640.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.921121	0.33908	.	.	ENSG00000105854	ENST00000536183;ENST00000355659;ENST00000433091;ENST00000222572	T;T;T	0.40476	2.34;1.03;2.34	4.94	3.1	0.35709	Six-bladed beta-propeller, TolB-like (1);	0.093511	0.85682	D	0.000000	T	0.60077	0.2241	M	0.83118	2.625	0.52501	D	0.999956	D;D	0.76494	0.998;0.999	D;D	0.69824	0.946;0.966	T	0.60944	-0.7162	10	0.14252	T	0.57	-9.4713	10.7179	0.46023	0.0717:0.132:0.7963:0.0	.	160;160	A4D1H7;Q15165	.;PON2_HUMAN	N	181;158;148;160	ENSP00000440282:H181N;ENSP00000404622:H148N;ENSP00000222572:H160N	ENSP00000222572:H160N	H	-	1	0	PON2	94878917	1.000000	0.71417	0.894000	0.35097	0.062000	0.15995	7.184000	0.77705	0.774000	0.33427	-0.157000	0.13467	CAT	.	.	.	none		0.358	PON2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333142.1	NM_000305		T	95040981	G	T	95040981	3	4	64	1	0	0	0	0	1	0	0	0	12256	1377	48	4	606	4	PON2	7	95040981	Missense_Mutation	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10	50244429	95040981	64097682	17	4282											
PDP1	54704	hgsc.bcm.edu	37	chr8	94934633	94934633	+	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	tccttggatttgacagcaatCagctgcctgcaaatgcaccc	10	10	8	13	0	1	1	1	1	0	0	2	2	2	2	3	1	5	4	3	1	2	2			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr8:94934633C>T	ENST00000297598.4	+	2	615	c.346C>T	c.(346-348)Cag>Tag	p.Q116*	PDP1_ENST00000517764.1_Nonsense_Mutation_p.Q116*|PDP1_ENST00000520728.1_Nonsense_Mutation_p.Q116*|PDP1_ENST00000396200.3_Nonsense_Mutation_p.Q141*	NM_001161781.1|NM_018444.3	NP_001155253.1|NP_060914.2	Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic subunit 1	116				NVSSILGFDSNQ -> MSVLSLDLTAIK (in Ref. 1; AAF67480). {ECO:0000305}.	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						TGACAGCAATCAGCTGCCTGC	0.463																																					p.Q141X		Atlas-SNP	.											.	PDP1	97	.	0			c.C421T						PASS	.						88	92	90					8																	94934633		2203	4300	6503	SO:0001587	stop_gained	54704	exon3			AGCAATCAGCTGC	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.346C>T	chr8.hg19:g.94934633C>T	ENSP00000297598:p.Gln116*	95.0	0.0	.		81.0	37.0	.	NM_001161780	B3KX71|J3KPU0|Q5U5K1	Nonsense_Mutation	SNP	ENST00000297598.4	hg19	CCDS6259.1	.	.	.	.	.	.	.	.	.	.	C	33	5.196332	0.94960	.	.	ENSG00000164951	ENST00000297598;ENST00000520728;ENST00000396200;ENST00000518573;ENST00000517764;ENST00000518827;ENST00000521144	.	.	.	6.03	6.03	0.97812	.	0.120323	0.64402	D	0.000020	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-14.0857	20.5753	0.99366	0.0:1.0:0.0:0.0	.	.	.	.	X	116;116;141;116;116;116;116	.	ENSP00000297598:Q116X	Q	+	1	0	PDP1	95003809	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.792000	0.85828	2.868000	0.98415	0.557000	0.71058	CAG	.	.	.	none		0.463	PDP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378415.2	NM_018444		T	94934633	C	T	94934633	4	4	64	1	0	0	0	0	0	1	0	0	11692	827	29	2	529	2	PDP1	8	94934633	Nonsense_Mutation	SNP	C	TCGA-A4-A5DU-01A-11D-A28G-10		94934633	51429389	18	4283											
DDX50	79009	hgsc.bcm.edu	37	chr10	70670106	70670106	+	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	aggagccttctccaattttcCtatttctgaagagactataa	12	14	6	9	0	2	2	0	1	2	1	4	4	3	3	3	1	1	0	3	1	5	7			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr10:70670106C>A	ENST00000373585.3	+	3	535	c.428C>A	c.(427-429)cCt>cAt	p.P143H	RNU6-571P_ENST00000384128.1_RNA	NM_024045.1	NP_076950.1	Q9BQ39	DDX50_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	143						membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	29						TCCAATTTTCCTATTTCTGAA	0.378																																					p.P143H		Atlas-SNP	.											.	DDX50	65	.	0			c.C428A						PASS	.						129	133	132					10																	70670106		2203	4300	6503	SO:0001583	missense	79009	exon3			ATTTTCCTATTTC	AF334103	CCDS7283.1	10q22.2	2010-09-30			ENSG00000107625	ENSG00000107625		"DEAD-boxes"	17906	protein-coding gene	gene with protein product		610373				11891046	Standard	NM_024045		Approved	GU2, MGC3199, GUB, RH-II/GuB	uc001jou.3	Q9BQ39	OTTHUMG00000018362	ENST00000373585.3:c.428C>A	chr10.hg19:g.70670106C>A	ENSP00000362687:p.Pro143His	72.0	0.0	.		39.0	11.0	.	NM_024045	Q5VX37|Q8WV76|Q9BWI8	Missense_Mutation	SNP	ENST00000373585.3	hg19	CCDS7283.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.489203	0.64074	.	.	ENSG00000107625	ENST00000373585;ENST00000541832	T	0.21543	2.0	5.23	5.23	0.72850	RNA helicase, DEAD-box type, Q motif (1);	0.210307	0.43110	D	0.000611	T	0.19005	0.0456	L	0.32530	0.975	0.35802	D	0.82318	P;P	0.48016	0.904;0.604	B;B	0.42882	0.401;0.396	T	0.11891	-1.0569	10	0.48119	T	0.1	-3.6785	13.2098	0.59817	0.1588:0.8412:0.0:0.0	.	143;143	Q9BQ39;B4DED6	DDX50_HUMAN;.	H	143	ENSP00000362687:P143H	ENSP00000362687:P143H	P	+	2	0	DDX50	70340112	0.366000	0.25014	1.000000	0.80357	0.993000	0.82548	1.963000	0.40452	2.585000	0.87301	0.555000	0.69702	CCT	.	.	.	none		0.378	DDX50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048363.1	NM_024045		A	70670106	C	A	70670106	3	1	64	1	0	0	0	0	1	0	0	0	4370	681	24	4	438	4	DDX50	10	70670106	Missense_Mutation	SNP	C	TCGA-A4-A5DU-01A-11D-A28G-10		70670106	64864641	19	4284											
INCENP	3619	hgsc.bcm.edu	37	chr11	61897408	61897408	+	Missense_Mutation	SNP	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	cagctgccgcggctaccatgGcattggctgcaccttcttca	6	10	10	15	2	2	0	1	0	1	0	2	0	2	0	3	3	4	5	3	3	1	4			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr11:61897408G>A	ENST00000394818.3	+	4	611	c.409G>A	c.(409-411)Gca>Aca	p.A137T	INCENP_ENST00000278849.4_Missense_Mutation_p.A137T	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	137			A -> V (in dbSNP:rs34441559).		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						GGCTACCATGGCATTGGCTGC	0.627																																					p.A137T		Atlas-SNP	.											.	INCENP	122	.	0			c.G409A						PASS	.						60	60	60					11																	61897408		2201	4299	6500	SO:0001583	missense	3619	exon4			ACCATGGCATTGG	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.409G>A	chr11.hg19:g.61897408G>A	ENSP00000378295:p.Ala137Thr	77.0	0.0	.		72.0	29.0	.	NM_001040694	A8MQD2|Q5Y192	Missense_Mutation	SNP	ENST00000394818.3	hg19	CCDS44624.1	.	.	.	.	.	.	.	.	.	.	G	9.095	1.002664	0.19121	.	.	ENSG00000149503	ENST00000394818;ENST00000533896;ENST00000278849	T;T;T	0.23754	2.52;1.89;2.51	3.14	-3.13	0.05266	.	2.075460	0.02904	N	0.135798	T	0.13884	0.0336	N	0.22421	0.69	0.09310	N	1	B;B;B	0.11235	0.004;0.0;0.0	B;B;B	0.08055	0.003;0.002;0.001	T	0.14671	-1.0464	10	0.10636	T	0.68	.	4.1359	0.10170	0.3443:0.3363:0.3194:0.0	.	137;137;137	B3KPD3;Q9NQS7-2;Q9NQS7	.;.;INCE_HUMAN	T	137	ENSP00000378295:A137T;ENSP00000433100:A137T;ENSP00000278849:A137T	ENSP00000278849:A137T	A	+	1	0	INCENP	61653984	0.000000	0.05858	0.000000	0.03702	0.062000	0.15995	-0.779000	0.04659	-0.725000	0.04901	-0.459000	0.05422	GCA	.	.	.	none		0.627	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238		A	61897408	G	A	61897408	3	1	64	1	0	0	0	0	1	0	0	0	7740	1203	42	2	419	2	INCENP	11	61897408	Missense_Mutation	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10		61897408	73109108	20	4285											
GXYLT1	283464	hgsc.bcm.edu	37	chr12	42481670	42481670	+	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	atattttgtaaatttttccaCagtatgtatgcactgttttt	10	21	5	5	0	0	0	0	0	0	0	1	0	1	0	1	0	1	5	1	0	5	10	rs200973030		TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr12:42481670C>T	ENST00000398675.3	-	8	1473	c.1241G>A	c.(1240-1242)tGt>tAt	p.C414Y	GXYLT1_ENST00000280876.6_Missense_Mutation_p.C383Y	NM_001099650.1|NM_173601.1	NP_001093120.1|NP_775872.1	Q4G148	GXLT1_HUMAN	glucoside xylosyltransferase 1	414					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|O-glycan processing (GO:0016266)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	UDP-xylosyltransferase activity (GO:0035252)			kidney(2)|large_intestine(4)|liver(3)|lung(8)	17						AATTTTTCCACAGTATGTATG	0.313																																					p.C414Y		Atlas-SNP	.											Q8IXV1_HUMAN,NS,carcinoma,-1,2	GXYLT1	47	.	0			c.G1241A						PASS	.						86	77	80					12																	42481670		1809	4072	5881	SO:0001583	missense	283464	exon8			TTTCCACAGTATG	BC015597	CCDS41771.1, CCDS41772.1	12q12	2013-10-11	2009-11-17	2009-11-17	ENSG00000151233	ENSG00000151233		"Glycosyltransferase family 8 domain containing"	27482	protein-coding gene	gene with protein product		613321	"glycosyltransferase 8 domain containing 3"	GLT8D3		19940119	Standard	NM_001099650		Approved	FLJ43151	uc001rms.4	Q4G148	OTTHUMG00000169379	ENST00000398675.3:c.1241G>A	chr12.hg19:g.42481670C>T	ENSP00000381666:p.Cys414Tyr	50.0	1.0	.		40.0	3.0	.	NM_173601	B3KWJ2|Q8IXV1|Q96BH4	Missense_Mutation	SNP	ENST00000398675.3	hg19	CCDS41772.1	.	.	.	.	.	.	.	.	.	.	C	19.85	3.903071	0.72754	.	.	ENSG00000151233	ENST00000398675;ENST00000280876	.	.	.	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	D	0.84083	0.5394	M	0.85197	2.74	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.87025	0.2131	9	0.87932	D	0	-22.3783	18.4282	0.90615	0.0:1.0:0.0:0.0	.	383;414	Q4G148-2;Q4G148	.;GXLT1_HUMAN	Y	414;383	.	ENSP00000280876:C383Y	C	-	2	0	GXYLT1	40767937	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.785000	0.62418	2.435000	0.82474	0.655000	0.94253	TGT	.	.	.	weak		0.313	GXYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403778.1	XM_290597		T	42481670	C	T	42481670	3	4	64	1	0	0	0	0	1	0	0	0	6910	478	17	2	85	2	GXYLT1	12	42481670	Missense_Mutation	SNP	C	TCGA-A4-A5DU-01A-11D-A28G-10		42481670	91370225	21	4286											
SLC25A3	5250	hgsc.bcm.edu	37	chr12	98995295	98995295	+	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	ctctgaagaagaagcttgggTtaactcagtagttagatcaa	14	11	10	6	0	3	4	2	1	1	3	3	4	3	4	0	1	2	4	0	1	7	4			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr12:98995295T>A	ENST00000228318.3	+	8	1198	c.1078T>A	c.(1078-1080)Tta>Ata	p.L360I	SLC25A3_ENST00000552981.1_Missense_Mutation_p.L359I|SLC25A3_ENST00000401722.3_Missense_Mutation_p.L359I|SLC25A3_ENST00000548847.1_Missense_Mutation_p.L322I|SNORA53_ENST00000391141.1_RNA|SLC25A3_ENST00000188376.5_Missense_Mutation_p.L359I|SLC25A3_ENST00000549338.1_Missense_Mutation_p.L359I|SLC25A3_ENST00000551917.1_Missense_Mutation_p.L360I	NM_005888.3	NP_005879.1	Q00325	MPCP_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 3	360					generation of precursor metabolites and energy (GO:0006091)|phosphate ion transmembrane transport (GO:0035435)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	phosphate ion carrier activity (GO:0015320)|protein complex binding (GO:0032403)|symporter activity (GO:0015293)			breast(1)|endometrium(2)|large_intestine(4)|lung(8)|prostate(1)	16		Lung NSC(355;4.08e-05)|Breast(359;0.00191)|Colorectal(145;0.00205)|Myeloproliferative disorder(1001;0.0255)		GBM - Glioblastoma multiforme(134;1.36e-23)|BRCA - Breast invasive adenocarcinoma(302;0.000115)		GAAGCTTGGGTTAACTCAGTA	0.433																																					p.L360I		Atlas-SNP	.											.	SLC25A3	95	.	0			c.T1078A						PASS	.						83	79	80					12																	98995295		2203	4300	6503	SO:0001583	missense	5250	exon8			CTTGGGTTAACTC		CCDS9065.1, CCDS9066.1	12q23.1	2013-05-22			ENSG00000075415	ENSG00000075415		"Solute carriers"	10989	protein-coding gene	gene with protein product		600370		PHC		8168843	Standard	NM_213611		Approved		uc001tfo.3	Q00325	OTTHUMG00000170212	ENST00000228318.3:c.1078T>A	chr12.hg19:g.98995295T>A	ENSP00000228318:p.Leu360Ile	72.0	0.0	.		76.0	48.0	.	NM_005888	B3KS34|Q7Z7N7|Q96A03	Missense_Mutation	SNP	ENST00000228318.3	hg19	CCDS9066.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.008501	0.75046	.	.	ENSG00000075415	ENST00000401722;ENST00000188376;ENST00000228318;ENST00000551917;ENST00000552981;ENST00000549338;ENST00000548847	T;T;T;T;T;T;T	0.78126	-1.15;-1.15;-0.89;-0.89;-1.15;-1.15;-1.13	5.48	3.14	0.36123	.	0.132239	0.49305	D	0.000142	T	0.72112	0.3420	N	0.17674	0.51	0.51012	D	0.999902	B;P;P;B	0.52842	0.135;0.956;0.598;0.135	B;D;B;B	0.65010	0.121;0.931;0.19;0.145	T	0.66324	-0.5952	10	0.09590	T	0.72	-0.9242	7.4149	0.27038	0.0:0.3411:0.0:0.6589	.	322;359;360;359	F8VVM2;B2RE88;Q00325;Q00325-2	.;.;MPCP_HUMAN;.	I	359;359;360;360;359;359;322	ENSP00000383898:L359I;ENSP00000188376:L359I;ENSP00000228318:L360I;ENSP00000447310:L360I;ENSP00000448708:L359I;ENSP00000447740:L359I;ENSP00000449166:L322I	ENSP00000188376:L359I	L	+	1	2	SLC25A3	97519426	0.996000	0.38824	1.000000	0.80357	0.956000	0.61745	0.932000	0.28884	1.022000	0.39626	0.533000	0.62120	TTA	.	.	.	none		0.433	SLC25A3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407989.1	NM_005888		A	98995295	T	A	98995295	3	1	64	1	0	0	0	0	1	0	0	0	14506	1722	60	5	1230	5	SLC25A3	12	98995295	Missense_Mutation	SNP	T	TCGA-A4-A5DU-01A-11D-A28G-10	56513625	98995295	34856600	22	4287											
C12orf45	121053	hgsc.bcm.edu	37	chr12	105385505	105385505	+	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	cacagtattggaccaggtacAgacatttctcccacagatgg	12	9	9	11	0	1	2	0	0	1	2	2	3	1	3	2	3	1	2	2	3	2	4			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr12:105385505A>T	ENST00000552951.1	+	3	261	c.218A>T	c.(217-219)cAg>cTg	p.Q73L	C12orf45_ENST00000280749.5_Intron	NM_152318.2	NP_689531.2	Q8N5I9	CL045_HUMAN	chromosome 12 open reading frame 45	73										large_intestine(1)|lung(2)	3						GACCAGGTACAGACATTTCTC	0.398																																					p.Q73L		Atlas-SNP	.											.	C12orf45	14	.	0			c.A218T						PASS	.						98	91	93					12																	105385505		1855	4099	5954	SO:0001583	missense	121053	exon3			AGGTACAGACATT	BC032326	CCDS41825.1	12q23.3	2012-05-30			ENSG00000151131	ENSG00000151131			28628	protein-coding gene	gene with protein product						12477932	Standard	NM_152318		Approved	MGC40397	uc001tlb.3	Q8N5I9	OTTHUMG00000169822	ENST00000552951.1:c.218A>T	chr12.hg19:g.105385505A>T	ENSP00000447057:p.Gln73Leu	63.0	0.0	.		82.0	4.0	.	NM_152318		Missense_Mutation	SNP	ENST00000552951.1	hg19	CCDS41825.1	.	.	.	.	.	.	.	.	.	.	A	12.99	2.103577	0.37145	.	.	ENSG00000151131	ENST00000552951	T	0.37058	1.22	5.09	3.94	0.45596	.	0.176887	0.51477	D	0.000095	T	0.39517	0.1081	M	0.77820	2.39	0.43372	D	0.995466	P	0.37330	0.59	B	0.37943	0.261	T	0.32955	-0.9887	10	0.72032	D	0.01	.	8.5681	0.33552	0.9109:0.0:0.0891:0.0	.	73	Q8N5I9	CL045_HUMAN	L	73	ENSP00000447057:Q73L	ENSP00000447057:Q73L	Q	+	2	0	C12orf45	103909635	1.000000	0.71417	0.962000	0.40283	0.510000	0.34073	3.094000	0.50227	0.799000	0.34018	0.482000	0.46254	CAG	.	.	.	none		0.398	C12orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406076.1	NM_152318		T	105385505	A	T	105385505	3	4	64	1	0	0	0	0	1	0	0	0	1693	188	7	5	228	5	C12orf45	12	105385505	Missense_Mutation	SNP	A	TCGA-A4-A5DU-01A-11D-A28G-10	6390210	105385505	28466390	23	4288											
RPGRIP1	57096	hgsc.bcm.edu	37	chr14	21793036	21793036	+	Silent	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	ttatctgtggggccacagccCctctatgacttcacctccca	7	11	7	16	0	3	1	1	1	2	0	4	1	4	1	5	2	1	0	5	2	2	3			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr14:21793036C>T	ENST00000400017.2	+	14	2022	c.2022C>T	c.(2020-2022)ccC>ccT	p.P674P	RPGRIP1_ENST00000206660.6_Silent_p.P674P|RPGRIP1_ENST00000382933.4_Intron|RPGRIP1_ENST00000307974.4_Silent_p.P33P|RPGRIP1_ENST00000556336.1_Intron|RPGRIP1_ENST00000557771.1_Silent_p.P636P|RPGRIP1_ENST00000553500.1_Intron	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	674					eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)				breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		GGCCACAGCCCCTCTATGACT	0.512																																					p.P674P		Atlas-SNP	.											.	RPGRIP1	213	.	0			c.C2022T						PASS	.						169	159	162					14																	21793036		1949	4136	6085	SO:0001819	synonymous_variant	57096	exon14			ACAGCCCCTCTAT	AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.2022C>T	chr14.hg19:g.21793036C>T		109.0	0.0	.		126.0	46.0	.	NM_020366	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Silent	SNP	ENST00000400017.2	hg19	CCDS45080.1																																																																																			.	.	.	none		0.512	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366		T	21793036	C	T	21793036	2	4	64	1	0	0	0	0	0	0	0	1	13562	610	22	2		2	RPGRIP1	14	21793036	Silent	SNP	C	TCGA-A4-A5DU-01A-11D-A28G-10		21793036	85556504	24	4289											
FAM98B	283742	hgsc.bcm.edu	37	chr15	38776827	38776827	+	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	ggtggtggtggtggtggtggTggtggtggaggaggtggata	4	11	26	0	0	0	0	0	0	0	0	0	3	0	3	0	13	0	0	0	13	1	1			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr15:38776827T>A	ENST00000491535.1	+	0	3111				FAM98B_ENST00000397609.2_Silent_p.G423G	NM_001042429.1	NP_001035894.1	Q52LJ0	FA98B_HUMAN	family with sequence similarity 98, member B							cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-splicing ligase complex (GO:0072669)	poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|skin(1)	8		all_cancers(109;3.11e-17)|all_epithelial(112;2.64e-15)|Lung NSC(122;2.11e-11)|all_lung(180;5.61e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;9e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0209)		gtggtggtggtggtggtggag	0.443																																					p.G423G		Atlas-SNP	.											FAM98B_ENST00000397609,NS,carcinoma,0,1	FAM98B	53	.	0			c.T1269A						PASS	.						19	18	18					15																	38776827		1515	3413	4928	SO:0001628	intergenic_variant	283742	exon8			TGGTGGTGGTGGT		CCDS10047.2	15q14	2006-11-29		2005-11-20	ENSG00000171262	ENSG00000171262			26773	protein-coding gene	gene with protein product						12477932	Standard	NM_173611		Approved	FLJ38426	uc001zkc.3	Q52LJ0	OTTHUMG00000129831		chr15.hg19:g.38776827T>A		21.0	0.0	.		27.0	4.0	.	NM_173611	A8MUW5|Q8N935	Silent	SNP	ENST00000491535.1	hg19	CCDS42015.1																																																																																			.	.	.	none		0.443	FAM98B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252071.2	NM_173611		A	38776827	T	A	38776827	1	1	64	0	1	0	0	0	0	0	0	0	5664	1683	59	5		5	FAM98B	15	38776827	IGR	SNP	T	TCGA-A4-A5DU-01A-11D-A28G-10		38776827	63754565	25	4290											
KIAA1199	57214	hgsc.bcm.edu	37	chr15	81181040	81181040	+	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	aagggtctcgtttctctgacAggacatcgaggctctgctgc	7	11	12	11	2	3	1	0	1	3	0	6	3	3	2	0	3	2	3	0	3	1	1			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr15:81181040A>T	ENST00000394685.3	+	9	1287		c.e9-1		KIAA1199_ENST00000220244.3_Splice_Site|KIAA1199_ENST00000356249.5_Splice_Site			Q8WUJ3	CEMIP_HUMAN							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						TTTCTCTGACAGGACATCGAG	0.498																																					.		Atlas-SNP	.											.	KIAA1199	118	.	0			c.869-2A>T						PASS	.						101	99	100					15																	81181040		2203	4300	6503	SO:0001630	splice_region_variant	57214	exon8			TCTGACAGGACAT																												ENST00000394685.3:c.869-1A>T	chr15.hg19:g.81181040A>T		57.0	0.0	.		52.0	27.0	.	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Splice_Site	SNP	ENST00000394685.3	hg19	CCDS10315.1	.	.	.	.	.	.	.	.	.	.	A	11.13	1.547385	0.27652	.	.	ENSG00000103888	ENST00000220244;ENST00000394685;ENST00000356249;ENST00000394683	.	.	.	4.87	4.87	0.63330	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6315	0.68660	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KIAA1199	78968095	1.000000	0.71417	0.786000	0.31890	0.035000	0.12851	6.504000	0.73704	2.046000	0.60703	0.455000	0.32223	.	.	.	.	none		0.498	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1		Intron	T	81181040	A	T	81181040	5	4	64	1	0	0	0	0	0	0	1	0	8220	202	7	5	893	5	KIAA1199	15	81181040	Splice_Site	SNP	A	TCGA-A4-A5DU-01A-11D-A28G-10	42404213	81181040	21350352	26	4291											
GLTPD2	388323	hgsc.bcm.edu	37	chr17	4693110	4693110	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cactagggaggccttcaccaAggtgacagacctggaggctc	10	6	13	12	0	1	2	1	1	0	1	2	4	1	4	3	5	0	1	3	5	2	2			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr17:4693110A>G	ENST00000331264.7	+	4	448	c.395A>G	c.(394-396)aAg>aGg	p.K132R		NM_001014985.2	NP_001014985	A6NH11	GLTD2_HUMAN	glycolipid transfer protein domain containing 2	132						cytoplasm (GO:0005737)	glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)	4						GCCTTCACCAAGGTGACAGAC	0.672																																					p.K132R		Atlas-SNP	.											.	GLTPD2	15	.	0			c.A395G						PASS	.						16	17	16					17																	4693110		2178	4256	6434	SO:0001583	missense	388323	exon4			TCACCAAGGTGAC	BC029290	CCDS32534.1	17p13.2	2007-12-19				ENSG00000182327			33756	protein-coding gene	gene with protein product							Standard	NM_001014985		Approved		uc002fza.2	A6NH11		ENST00000331264.7:c.395A>G	chr17.hg19:g.4693110A>G	ENSP00000328070:p.Lys132Arg	86.0	0.0	.		157.0	88.0	.	NM_001014985	A7E2T2	Missense_Mutation	SNP	ENST00000331264.7	hg19	CCDS32534.1	.	.	.	.	.	.	.	.	.	.	A	32	5.182952	0.94885	.	.	ENSG00000182327	ENST00000331264	.	.	.	4.55	4.55	0.56014	Glycolipid transfer protein domain (3);	0.000000	0.85682	D	0.000000	T	0.81312	0.4796	M	0.89601	3.045	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84725	0.0742	9	0.66056	D	0.02	-15.1395	11.95	0.52950	1.0:0.0:0.0:0.0	.	132	A6NH11	GLTD2_HUMAN	R	132	.	ENSP00000328070:K132R	K	+	2	0	GLTPD2	4639850	1.000000	0.71417	0.999000	0.59377	0.879000	0.50718	5.451000	0.66632	1.924000	0.55735	0.454000	0.30748	AAG	.	.	.	none		0.672	GLTPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439781.1	NM_001014985		G	4693110	A	G	4693110	3	3	64	1	0	0	0	0	1	0	0	0	6480	72	3	3	409	3	GLTPD2	17	4693110	Missense_Mutation	SNP	A	TCGA-A4-A5DU-01A-11D-A28G-10		4693110	76502100	27	4292											
CDC37	11140	hgsc.bcm.edu	37	chr19	10506875	10506875	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actgctccatgcgttccaccCgggcctgcgggcagggacgg	5	6	15	15	4	0	0	0	0	0	0	2	1	2	1	4	4	3	3	4	4	0	1			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr19:10506875C>T	ENST00000222005.2	-	2	160	c.107G>A	c.(106-108)cGg>cAg	p.R36Q		NM_007065.3	NP_008996.1	Q16543	CDC37_HUMAN	cell division cycle 37	36					protein targeting (GO:0006605)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	16			OV - Ovarian serous cystadenocarcinoma(20;4.65e-10)|Epithelial(33;6.48e-07)|all cancers(31;2.31e-06)	GBM - Glioblastoma multiforme(1328;0.0318)		GCGTTCCACCCGGGCCTGCGG	0.632																																					p.R36Q		Atlas-SNP	.											.	CDC37	32	.	0			c.G107A						PASS	.						39	42	41					19																	10506875		2203	4300	6503	SO:0001583	missense	11140	exon2			TCCACCCGGGCCT	U63131	CCDS12237.1	19p13.2	2013-01-17	2013-01-17		ENSG00000105401	ENSG00000105401			1735	protein-coding gene	gene with protein product	"CDC37 cell division cycle 37 homolog", "Hsp90 co-chaperone Cdc37", "CDC37 (cell division cycle 37, S. cerevisiae, homolog)"	605065	"CDC37 (cell division cycle 37, S. cerevisiae, homolog)", "CDC37 cell division cycle 37 homolog (S. cerevisiae)", "cell division cycle 37 homolog (S. cerevisiae)"			8703009, 8666233	Standard	NM_007065		Approved	P50CDC37	uc002mof.1	Q16543		ENST00000222005.2:c.107G>A	chr19.hg19:g.10506875C>T	ENSP00000222005:p.Arg36Gln	128.0	0.0	.		141.0	69.0	.	NM_007065	Q53YA2	Missense_Mutation	SNP	ENST00000222005.2	hg19	CCDS12237.1	.	.	.	.	.	.	.	.	.	.	C	33	5.265565	0.95399	.	.	ENSG00000105401	ENST00000222005	T	0.57436	0.4	4.19	4.19	0.49359	Cdc37, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.68568	0.3015	M	0.83852	2.665	0.80722	D	1	D;D	0.71674	0.998;0.998	P;P	0.56216	0.794;0.794	T	0.76130	-0.3072	10	0.87932	D	0	.	14.3942	0.67001	0.0:1.0:0.0:0.0	.	36;36	Q6FG59;Q16543	.;CDC37_HUMAN	Q	36	ENSP00000222005:R36Q	ENSP00000222005:R36Q	R	-	2	0	CDC37	10367875	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.268000	0.78473	2.058000	0.61347	0.555000	0.69702	CGG	.	.	.	none		0.632	CDC37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451987.1	NM_007065		T	10506875	C	T	10506875	3	4	64	1	0	0	0	0	1	0	0	0	3070	652	23	1	1057	1	CDC37	19	10506875	Missense_Mutation	SNP	C	TCGA-A4-A5DU-01A-11D-A28G-10		10506875	48622108	28	4293											
GATA5	140628	hgsc.bcm.edu	37	chr20	61050059	61050059	+	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	gagcccccgcactcaccgaaGgtgggcctgcggcctgggag	6	4	16	15	3	1	0	1	0	0	0	1	3	1	1	5	4	2	1	5	4	1	0			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr20:61050059G>T	ENST00000252997.2	-	2	580	c.519C>A	c.(517-519)acC>acA	p.T173T	RP13-379O24.3_ENST00000606283.1_lincRNA	NM_080473.4	NP_536721.1	Q9BWX5	GATA5_HUMAN	GATA binding protein 5	173					blood coagulation (GO:0007596)|cellular response to BMP stimulus (GO:0071773)|intestinal epithelial cell differentiation (GO:0060575)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|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)|zinc ion binding (GO:0008270)			kidney(1)|lung(3)|ovary(1)|stomach(1)	6	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;3.08e-06)			ACTCACCGAAGGTGGGCCTGC	0.721																																					p.T173T		Atlas-SNP	.											.	GATA5	22	.	0			c.C519A						PASS	.						3	4	3					20																	61050059		1891	3784	5675	SO:0001819	synonymous_variant	140628	exon2			ACCGAAGGTGGGC	BC047790, BC117356	CCDS13499.1	20q13.33	2013-07-17	2001-11-28		ENSG00000130700	ENSG00000130700		"GATA zinc finger domain containing"	15802	protein-coding gene	gene with protein product		611496	"GATA-binding protein 5"			9566909	Standard	NM_080473		Approved	bB379O24.1, GATAS	uc002ycx.1	Q9BWX5	OTTHUMG00000032919	ENST00000252997.2:c.519C>A	chr20.hg19:g.61050059G>T		11.0	0.0	.		83.0	5.0	.	NM_080473	D9ZGF7|Q17RE2|Q86VU4	Silent	SNP	ENST00000252997.2	hg19	CCDS13499.1																																																																																			.	.	.	none		0.721	GATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080038.2	NM_080473		T	61050059	G	T	61050059	2	4	64	1	0	0	0	0	0	0	0	1	6264	987	35	4		4	GATA5	20	61050059	Silent	SNP	G	TCGA-A4-A5DU-01A-11D-A28G-10		61050059	1975461	29	4294											
ACO2	50	hgsc.bcm.edu	37	chr22	41911896	41911896	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcgtggaataccacgggccTggtgtagactccatctcctg	8	10	11	12	2	1	1	0	0	1	1	4	2	2	2	4	3	1	1	4	3	3	2			TCGA-A4-A5DU-01A-11D-A28G-10	TCGA-A4-A5DU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4423a137-3e9c-4910-bff6-0f282d79e89a	61c2e34f-6a63-434c-becd-e6537a9b7df9	g.chr22:41911896T>C	ENST00000216254.4	+	6	832	c.810T>C	c.(808-810)ccT>ccC	p.P270P	ACO2_ENST00000396512.3_Silent_p.P270P|ACO2_ENST00000466237.1_3'UTR	NM_001098.2	NP_001089.1	Q99798	ACON_HUMAN	aconitase 2, mitochondrial	270				P -> H (in Ref. 6; AAH26196). {ECO:0000305}.	cell death (GO:0008219)|cellular metabolic process (GO:0044237)|citrate metabolic process (GO:0006101)|generation of precursor metabolites and energy (GO:0006091)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3 iron, 4 sulfur cluster binding (GO:0051538)|4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron ion binding (GO:0005506)			breast(3)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	23						ACCACGGGCCTGGTGTAGACT	0.607																																					p.P270P		Atlas-SNP	.											.	ACO2	58	.	0			c.T810C						PASS	.						63	48	53					22																	41911896		2203	4300	6503	SO:0001819	synonymous_variant	50	exon6			CGGGCCTGGTGTA	AH006514	CCDS14017.1	22q13.2	2013-05-21			ENSG00000100412	ENSG00000100412	4.2.1.3		118	protein-coding gene	gene with protein product	"aconitate hydratase, mitochondrial"	100850				10591208	Standard	NM_001098		Approved	ACONM	uc003bac.3	Q99798	OTTHUMG00000030544	ENST00000216254.4:c.810T>C	chr22.hg19:g.41911896T>C		114.0	0.0	.		124.0	69.0	.	NM_001098	O75809|Q5JZ41|Q6FHX0|Q8TAQ6	Silent	SNP	ENST00000216254.4	hg19	CCDS14017.1																																																																																			.	.	.	none		0.607	ACO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259151.1	NM_001098		C	41911896	T	C	41911896	2	2	64	1	0	0	0	0	0	0	0	1	147	1567	55	3		3	ACO2	22	41911896	Silent	SNP	T	TCGA-A4-A5DU-01A-11D-A28G-10		41911896	9392670	30	4295											
TMEM52	339456	hgsc.bcm.edu	37	chr1	1850654	1850654	+	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	aggagcggcaggagcggcagGagcggcagcagcagccgcag	10	0	20	11	4	0	0	0	0	0	0	0	3	0	3	1	6	6	6	1	6	0	0			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr1:1850654G>C	ENST00000310991.3	-	1	58	c.51C>G	c.(49-51)ctC>ctG	p.L17L	TMEM52_ENST00000378602.3_5'Flank	NM_178545.3	NP_848640.1	Q8NDY8	TMM52_HUMAN	transmembrane protein 52	17						integral component of membrane (GO:0016021)				NS(1)|prostate(1)|stomach(1)	3	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)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.82e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.75e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		ggagcggcaggagcggcagca	0.771																																					p.L17L		Atlas-SNP	.											TMEM52,NS,carcinoma,0,1	TMEM52	21	.	0			c.C51G						PASS	.						1	2	1					1																	1850654		671	1684	2355	SO:0001819	synonymous_variant	339456	exon1			CGGCAGGAGCGGC	AJ278736	CCDS35.1	1p36.33	2008-02-05			ENSG00000178821	ENSG00000178821			27916	protein-coding gene	gene with protein product							Standard	NM_178545		Approved		uc001aij.2	Q8NDY8	OTTHUMG00000000944	ENST00000310991.3:c.51C>G	chr1.hg19:g.1850654G>C		2.0	0.0	.		3.0	3.0	.	NM_178545	Q4VXS6|Q6UX25	Silent	SNP	ENST00000310991.3	hg19	CCDS35.1	.	.	.	.	.	.	.	.	.	.	.	4.530	0.098402	0.08681	.	.	ENSG00000178821	ENST00000378598	.	.	.	0.149	0.149	0.14863	.	.	.	.	.	T	0.39489	0.1080	.	.	.	0.22446	N	0.999091	.	.	.	.	.	.	T	0.39035	-0.9633	4	0.87932	D	0	.	.	.	.	.	.	.	.	C	15	.	ENSP00000367861:S15C	S	-	2	0	TMEM52	1840514	0.001000	0.12720	0.009000	0.14445	0.010000	0.07245	0.286000	0.18902	0.192000	0.20272	0.195000	0.17529	TCC	.	.	.	none		0.771	TMEM52-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000002781.1	NM_178545		C	1850654	G	C	1850654	2	2	65	1	0	0	0	0	0	0	0	1	16190	1161	41	4		4	TMEM52	1	1850654	Silent	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10		1850654	247399967	1	4296											
PRKCZ	5590	hgsc.bcm.edu	37	chr1	2066777	2066777	+	5'UTR	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacctcttccaagccaagcgCtttaacagggtgagtggccc	9	8	10	14	1	1	1	0	1	1	0	2	1	2	1	4	2	3	1	4	2	3	3			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr1:2066777C>T	ENST00000400921.2	+	0	545				PRKCZ_ENST00000400920.1_5'UTR	NM_001033581.1	NP_001028753.1	Q05513	KPCZ_HUMAN	protein kinase C, zeta						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)	AAGCCAAGCGCTTTAACAGGG	0.552																																					p.R137R		Atlas-SNP	.											.	PRKCZ	84	.	0			c.C411T						PASS	.						48	48	48					1																	2066777		2203	4300	6503	SO:0001623	5_prime_UTR_variant	5590	exon5			CAAGCGCTTTAAC	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.-139C>T	chr1.hg19:g.2066777C>T		41.0	0.0	.		32.0	18.0	.	NM_002744	A8K4N0|A8MU64|B7Z2J7|E9PCW2|Q15207|Q5SYT5|Q969S4	Silent	SNP	ENST00000400921.2	hg19	CCDS41229.1																																																																																			.	.	.	none		0.552	PRKCZ-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000098533.3	NM_002744		T	2066777	C	T	2066777	1	4	65	0	1	0	0	0	0	0	0	0	12527	784	28	2		2	PRKCZ	1	2066777	5'UTR	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10	216123	2066777	247183844	2	4297											
ZNF644	84146	hgsc.bcm.edu	37	chr1	91403569	91403569	+	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	agtggcctctaacatgatttGataatccaattttagtatca	13	15	6	7	0	2	2	1	2	1	0	3	2	3	2	2	1	1	1	2	1	5	6			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr1:91403569G>T	ENST00000370440.1	-	4	3378	c.3161C>A	c.(3160-3162)tCa>tAa	p.S1054*	ZNF644_ENST00000361321.5_Intron|ZNF644_ENST00000347275.5_Intron|ZNF644_ENST00000337393.5_Nonsense_Mutation_p.S1054*|ZNF644_ENST00000467231.1_Intron			Q9H582	ZN644_HUMAN	zinc finger protein 644	1054					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)		AACATGATTTGATAATCCAAT	0.363																																					p.S1054X		Atlas-SNP	.											.	ZNF644	120	.	0			c.C3161A						PASS	.						81	80	81					1																	91403569		2203	4300	6503	SO:0001587	stop_gained	84146	exon4			TGATTTGATAATC	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.3161C>A	chr1.hg19:g.91403569G>T	ENSP00000359469:p.Ser1054*	38.0	0.0	.		37.0	16.0	.	NM_201269	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Nonsense_Mutation	SNP	ENST00000370440.1	hg19	CCDS731.1	.	.	.	.	.	.	.	.	.	.	G	41	9.121790	0.99073	.	.	ENSG00000122482	ENST00000370440;ENST00000337393;ENST00000536941	.	.	.	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.694	20.1634	0.98142	0.0:0.0:1.0:0.0	.	.	.	.	X	1054;1054;626	.	ENSP00000337008:S1054X	S	-	2	0	ZNF644	91176157	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.294000	0.96088	2.773000	0.95371	0.655000	0.94253	TCA	.	.	.	none		0.363	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186		T	91403569	G	T	91403569	4	4	65	1	0	0	0	0	0	1	0	0	18072	1294	45	4	834	4	ZNF644	1	91403569	Nonsense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	89336792	91403569	157847052	3	4298											
SUSD4	55061	hgsc.bcm.edu	37	chr1	223536686	223536686	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggatcacggccaagagtcTctggggggactgaggttgct	8	8	16	9	1	2	2	1	1	1	1	3	4	2	4	1	6	1	2	1	6	1	1			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr1:223536686T>C	ENST00000343846.3	-	1	715	c.82A>G	c.(82-84)Aga>Gga	p.R28G	SUSD4_ENST00000344029.6_Missense_Mutation_p.R28G|SUSD4_ENST00000478605.1_5'UTR|SUSD4_ENST00000366877.3_Missense_Mutation_p.R28G|SUSD4_ENST00000366878.4_Missense_Mutation_p.R28G|SUSD4_ENST00000494793.2_Missense_Mutation_p.R28G|SUSD4_ENST00000484758.2_Missense_Mutation_p.R28G|SUSD4_ENST00000454695.2_5'UTR			Q5VX71	SUSD4_HUMAN	sushi domain containing 4	28						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|skin(1)	17				GBM - Glioblastoma multiforme(131;0.0611)		GCCAAGAGTCTCTGGGGGGAC	0.597																																					p.R28G		Atlas-SNP	.											.	SUSD4	82	.	0			c.A82G						PASS	.						32	32	32					1																	223536686		2202	4299	6501	SO:0001583	missense	55061	exon2			AGAGTCTCTGGGG	AK096265	CCDS31034.1, CCDS41471.1	1q41	2008-05-14			ENSG00000143502	ENSG00000143502			25470	protein-coding gene	gene with protein product		615827				12477932	Standard	NM_017982		Approved	FLJ10052	uc001hny.4	Q5VX71	OTTHUMG00000037936	ENST00000343846.3:c.82A>G	chr1.hg19:g.223536686T>C	ENSP00000344219:p.Arg28Gly	142.0	0.0	.		132.0	44.0	.	NM_017982	D3DTB9|Q6UX62|Q9BSR0|Q9NWG0	Missense_Mutation	SNP	ENST00000343846.3	hg19	CCDS41471.1	.	.	.	.	.	.	.	.	.	.	T	18.90	3.722459	0.68959	.	.	ENSG00000143502	ENST00000343846;ENST00000366878;ENST00000542750;ENST00000271787;ENST00000344029;ENST00000342943;ENST00000366877	T;T;T	0.38560	1.18;1.18;1.13	4.86	4.86	0.63082	.	0.000000	0.46758	D	0.000278	T	0.43322	0.1242	N	0.14661	0.345	0.31376	N	0.679575	D;D;D	0.63880	0.987;0.992;0.993	D;D;P	0.71656	0.942;0.974;0.787	T	0.50939	-0.8768	10	0.66056	D	0.02	-11.375	8.8024	0.34916	0.0:0.0:0.1902:0.8098	.	28;28;28	B7Z369;Q5VX71-3;Q5VX71	.;.;SUSD4_HUMAN	G	28	ENSP00000344219:R28G;ENSP00000355843:R28G;ENSP00000339926:R28G	ENSP00000271787:R28G	R	-	1	2	SUSD4	221603309	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	3.992000	0.56980	1.800000	0.52685	0.459000	0.35465	AGA	.	.	.	none		0.597	SUSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092592.2	NM_017982		C	223536686	T	C	223536686	3	2	65	1	0	0	0	0	1	0	0	0	15422	1559	54	3	1575	3	SUSD4	1	223536686	Missense_Mutation	SNP	T	TCGA-A4-A5XZ-01A-11D-A31X-10	132133117	223536686	25713935	4	4299											
CLEC4F	165530	hgsc.bcm.edu	37	chr2	71036918	71036918	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtcccatctgtccagcgccaGgagccctctgtgcccctgtc	4	9	10	18	1	2	0	0	0	2	0	5	1	4	1	6	1	3	0	6	1	0	0			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr2:71036918G>A	ENST00000272367.2	-	6	1687	c.1611C>T	c.(1609-1611)tcC>tcT	p.S537S	CLEC4F_ENST00000426626.1_Silent_p.S537S	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	537	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				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						TCCAGCGCCAGGAGCCCTCTG	0.552																																					p.S537S	Colon(107;10 2157 6841 26035)	Atlas-SNP	.											.	CLEC4F	95	.	0			c.C1611T						PASS	.						156	141	146					2																	71036918		2203	4300	6503	SO:0001819	synonymous_variant	165530	exon6			GCGCCAGGAGCCC	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.1611C>T	chr2.hg19:g.71036918G>A		57.0	0.0	.		88.0	25.0	.	NM_173535	A4QPA5	Silent	SNP	ENST00000272367.2	hg19	CCDS1910.1																																																																																			.	.	.	none		0.552	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535		A	71036918	G	A	71036918	2	1	65	1	0	0	0	0	0	0	0	1	3518	987	35	2		2	CLEC4F	2	71036918	Silent	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10		71036918	172162455	5	4300											
HDLBP	3069	hgsc.bcm.edu	37	chr2	242196033	242196033	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acctgctcggcagagatgagTaagacttcatggcgagcttt	10	10	12	9	2	1	3	1	1	0	2	2	5	1	3	1	2	2	4	1	2	1	3	rs200251201		TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr2:242196033T>C	ENST00000391975.1	-	6	866	c.639A>G	c.(637-639)ttA>ttG	p.L213L	HDLBP_ENST00000310931.4_Silent_p.L213L|HDLBP_ENST00000427183.2_Silent_p.L249L|HDLBP_ENST00000391976.2_Silent_p.L213L	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	213	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)	cytoplasm (GO:0005737)|high-density lipoprotein particle (GO:0034364)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)			breast(7)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		CAGAGATGAGTAAGACTTCAT	0.567																																					p.L249L		Atlas-SNP	.											.	HDLBP	118	.	0			c.A747G						PASS	.						176	156	163					2																	242196033		2203	4300	6503	SO:0001819	synonymous_variant	3069	exon7			GATGAGTAAGACT		CCDS2547.1, CCDS58760.1	2q37.3	2008-07-18	2008-07-18		ENSG00000115677	ENSG00000115677			4857	protein-coding gene	gene with protein product		142695	"vigilin"	VGL		1318310, 8390966	Standard	NM_005336		Approved	HBP	uc002waz.3	Q00341	OTTHUMG00000133391	ENST00000391975.1:c.639A>G	chr2.hg19:g.242196033T>C		119.0	0.0	.		131.0	35.0	.	NM_001243900	B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Silent	SNP	ENST00000391975.1	hg19	CCDS2547.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	4.630|4.630	0.117115|0.117115	0.08881|0.08881	.|.	.|.	ENSG00000115677|ENSG00000115677	ENST00000373292|ENST00000453141	.|.	.|.	.|.	5.79|5.79	-0.967|-0.967	0.10316|0.10316	.|.	.|.	.|.	.|.	.|.	T|T	0.42223|0.42223	0.1193|0.1193	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.29701|0.29701	-1.0003|-1.0003	4|4	.|.	.|.	.|.	-20.9924|-20.9924	2.4822|2.4822	0.04590|0.04590	0.1601:0.3764:0.3089:0.1546|0.1601:0.3764:0.3089:0.1546	.|.	.|.	.|.	.|.	A|C	91|114	.|.	.|.	T|Y	-|-	1|2	0|0	HDLBP|HDLBP	241844706|241844706	0.522000|0.522000	0.26266|0.26266	0.991000|0.991000	0.47740|0.47740	0.427000|0.427000	0.31564|0.31564	-0.124000|-0.124000	0.10595|0.10595	0.095000|0.095000	0.17434|0.17434	-0.326000|-0.326000	0.08463|0.08463	ACT|TAC	.	T|0.999;C|0.001	0.001	weak		0.567	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	NM_203346		C	242196033	T	C	242196033	2	2	65	1	0	0	0	0	0	0	0	1	7032	1635	57	3		3	HDLBP	2	242196033	Silent	SNP	T	TCGA-A4-A5XZ-01A-11D-A31X-10	171159115	242196033	1003340	6	4301											
ACOX2	8309	hgsc.bcm.edu	37	chr3	58519841	58519842	+	Frame_Shift_Ins	INS	-	-	TATATTT																															gctctcacgaagactctgtgINStatatttaaggccacgtctc																										TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr3:58519841_58519842insTATATTT	ENST00000302819.5	-	4	645_646	c.354_355insAAATATA	c.(352-357)atacacfs	p.H119fs	ACOX2_ENST00000459701.2_Frame_Shift_Ins_p.H119fs	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	119					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)		AAGACTCTGTGTATATTTAAGG	0.54																																					p.H119fs		Pindel	.											.	ACOX2	53	.	0			c.355_356insAAATATA						PASS	.																																			SO:0001589	frameshift_variant	8309	exon4			.	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.348_354dupAAATATA	chr3.hg19:g.58519842_58519848dupTATATTT	ENSP00000307697:p.His119fs	81.0	0.0	.		65.0	12.0	0.185	NM_003500	A6NF16|B2R8U5	Frame_Shift_Ins	INS	ENST00000302819.5	hg19	CCDS33775.1																																																																																			.	.	.	none		0.54	ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1			TATATTT	58519842	-	TATATTT	58519841	7	5	65	1	0	1	1	0	0	0	0	0	159	1377	48	0	1738	0	ACOX2	3	58519841	Frame_Shift_Ins	INS	-	TCGA-A4-A5XZ-01A-11D-A31X-10		58519841	139502589	7	4302											
CADM2	253559	hgsc.bcm.edu	37	chr3	85851274	85851274	+	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	caattttgacctgcagggttGatcaaaatgataacacctcc	13	11	7	10	0	1	3	1	3	0	0	2	3	2	3	3	1	2	2	3	1	4	4			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr3:85851274G>C	ENST00000407528.2	+	2	201	c.139G>C	c.(139-141)Gat>Cat	p.D47H	CADM2_ENST00000405615.2_Missense_Mutation_p.D49H|CADM2-AS2_ENST00000467225.1_RNA|CADM2_ENST00000383699.3_Missense_Mutation_p.D56H	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	47	Ig-like V-type.				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)		CTGCAGGGTTGATCAAAATGA	0.408																																					p.D56H		Atlas-SNP	.											.	CADM2	195	.	0			c.G166C						PASS	.						90	75	80					3																	85851274		2203	4300	6503	SO:0001583	missense	253559	exon3			AGGGTTGATCAAA	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.139G>C	chr3.hg19:g.85851274G>C	ENSP00000384575:p.Asp47His	113.0	0.0	.		110.0	6.0	.	NM_001167675	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Missense_Mutation	SNP	ENST00000407528.2	hg19	CCDS54614.1	.	.	.	.	.	.	.	.	.	.	G	17.26	3.343676	0.61073	.	.	ENSG00000175161	ENST00000383699;ENST00000407528;ENST00000405615	T;T;T	0.64991	-0.13;-0.13;-0.13	5.27	5.27	0.74061	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.162021	0.53938	D	0.000054	T	0.64811	0.2632	L	0.35542	1.07	0.80722	D	1	P;P;P	0.50066	0.805;0.854;0.931	P;P;P	0.53689	0.591;0.517;0.732	T	0.59500	-0.7443	10	0.25751	T	0.34	.	19.2384	0.93871	0.0:0.0:1.0:0.0	.	49;56;47	Q8N3J6-3;G3XHN4;Q8N3J6	.;.;CADM2_HUMAN	H	56;47;49	ENSP00000373200:D56H;ENSP00000384575:D47H;ENSP00000384193:D49H	ENSP00000373200:D56H	D	+	1	0	CADM2	85933964	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	9.420000	0.97426	2.621000	0.88768	0.544000	0.68410	GAT	.	.	.	none		0.408	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184		C	85851274	G	C	85851274	3	2	65	1	0	0	0	0	1	0	0	0	2569	1290	45	4	216	4	CADM2	3	85851274	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	27331433	85851274	112171156	8	4303											
ALDH1L1	10840	hgsc.bcm.edu	37	chr3	125826081	125826081	+	Missense_Mutation	SNP	A	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	tgtgaaaacagttggctcaaAgaagaaccctgcaagagaga	17	6	11	7	0	1	5	1	1	0	4	1	6	1	5	1	1	3	3	1	1	6	1			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr3:125826081A>C	ENST00000393434.2	-	21	2705	c.2356T>G	c.(2356-2358)Ttt>Gtt	p.F786V	ALDH1L1_ENST00000273450.3_Missense_Mutation_p.F796V|ALDH1L1_ENST00000472186.1_Missense_Mutation_p.F786V|ALDH1L1_ENST00000452905.2_Missense_Mutation_p.F685V|ALDH1L1-AS1_ENST00000512384.1_RNA|ALDH1L1_ENST00000393431.2_3'UTR	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	786	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)	GTTGGCTCAAAGAAGAACCCT	0.557																																					p.F796V		Atlas-SNP	.											.	ALDH1L1	138	.	0			c.T2386G						PASS	.						130	115	120					3																	125826081		2203	4300	6503	SO:0001583	missense	10840	exon21			GCTCAAAGAAGAA	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.2356T>G	chr3.hg19:g.125826081A>C	ENSP00000377083:p.Phe786Val	32.0	0.0	.		56.0	36.0	.	NM_001270364	B4DG36|E9PBX3|Q68CS1	Missense_Mutation	SNP	ENST00000393434.2	hg19	CCDS3034.1	.	.	.	.	.	.	.	.	.	.	A	11.51	1.660489	0.29515	.	.	ENSG00000144908	ENST00000273450;ENST00000472186;ENST00000452905;ENST00000393434	T;T;T;T	0.73363	-0.74;-0.74;-0.74;-0.74	3.98	3.98	0.46160	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.85682	D	0.000000	T	0.56093	0.1962	N	0.00450	-1.49	0.80722	D	1	P;D;P	0.54772	0.755;0.968;0.501	P;D;P	0.63793	0.81;0.918;0.673	T	0.65203	-0.6225	10	0.27082	T	0.32	.	10.8723	0.46891	1.0:0.0:0.0:0.0	.	685;321;786	E9PBX3;Q6ZV71;O75891	.;.;AL1L1_HUMAN	V	796;786;685;786	ENSP00000273450:F796V;ENSP00000420293:F786V;ENSP00000395881:F685V;ENSP00000377083:F786V	ENSP00000273450:F796V	F	-	1	0	ALDH1L1	127308771	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	2.579000	0.46059	1.677000	0.50941	0.260000	0.18958	TTT	.	.	.	none		0.557	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190		C	125826081	A	C	125826081	3	2	65	1	0	0	0	0	1	0	0	0	494	72	3	5	364	5	ALDH1L1	3	125826081	Missense_Mutation	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10	39974807	125826081	72196349	9	4304											
DDX60L	91351	hgsc.bcm.edu	37	chr4	169382991	169382991	+	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	attaggaagttaaaaaggtaCgtttgtaaatcactcaggcc	15	11	9	6	1	2	0	2	0	0	0	2	1	2	1	1	3	1	4	1	3	8	5	rs17612630	byFrequency	TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr4:169382991C>T	ENST00000511577.1	-	5	712	c.465G>A	c.(463-465)acG>acA	p.T155T	DDX60L_ENST00000505890.1_Silent_p.T155T|DDX60L_ENST00000260184.7_Silent_p.T155T			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	155							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)		TAAAAAGGTACGTTTGTAAAT	0.368																																					p.T155T		Atlas-SNP	.											.	DDX60L	116	.	0			c.G465A						PASS	.						59	53	55					4																	169382991		1850	4090	5940	SO:0001819	synonymous_variant	91351	exon5			AAGGTACGTTTGT	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.465G>A	chr4.hg19:g.169382991C>T		108.0	0.0	.		93.0	21.0	.	NM_001012967	Q96ND6	Silent	SNP	ENST00000511577.1	hg19																																																																																				.	C|0.904;A|0.096	.	alt		0.368	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		T	169382991	C	T	169382991	2	4	65	1	0	0	0	0	0	0	0	1	4381	523	19	1		1	DDX60L	4	169382991	Silent	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10		169382991	21771285	10	4305											
IK	3550	hgsc.bcm.edu	37	chr5	140034136	140034136	+	Missense_Mutation	SNP	A	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	gccagcaaagagaaagaggaAgaggaactgatggaaaagcc	19	2	14	6	0	0	4	0	1	0	3	0	8	0	7	2	3	3	1	2	3	6	0			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr5:140034136A>C	ENST00000417647.2	+	7	694	c.555A>C	c.(553-555)gaA>gaC	p.E185D		NM_006083.3	NP_006074.2	Q13123	RED_HUMAN	IK cytokine, down-regulator of HLA II	185	Poly-Glu.				cell-cell signaling (GO:0007267)|immune response (GO:0006955)	extracellular space (GO:0005615)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			large_intestine(1)	1		all_hematologic(541;4.8e-07)|all_lung(500;0.000434)|Lung NSC(810;0.00161)|Breast(839;0.128)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGAAAGAGGAAGAGGAACTGA	0.388																																					p.E185D		Atlas-SNP	.											.	IK	46	.	0			c.A555C						PASS	.						44	44	44					5																	140034136		1831	4083	5914	SO:0001583	missense	3550	exon7			AGAGGAAGAGGAA	BC051295	CCDS47280.1	5q31.3	2008-08-07			ENSG00000113141	ENSG00000113141			5958	protein-coding gene	gene with protein product		600549				7970704	Standard	NM_006083		Approved		uc003lgq.3	Q13123	OTTHUMG00000163374	ENST00000417647.2:c.555A>C	chr5.hg19:g.140034136A>C	ENSP00000396301:p.Glu185Asp	516.0	1.0	.		467.0	155.0	.	NM_006083	Q6IPD8	Missense_Mutation	SNP	ENST00000417647.2	hg19	CCDS47280.1	.	.	.	.	.	.	.	.	.	.	A	17.19	3.326795	0.60743	.	.	ENSG00000113141	ENST00000417647;ENST00000508301;ENST00000261812;ENST00000502899	.	.	.	5.86	1.66	0.24008	RED-like, N-terminal (1);	0.042187	0.85682	D	0.000000	T	0.32255	0.0823	N	0.17674	0.51	0.48975	D	0.999737	B;B	0.24132	0.01;0.098	B;B	0.27500	0.026;0.08	T	0.04509	-1.0946	9	0.20519	T	0.43	.	7.8062	0.29204	0.5957:0.0:0.4043:0.0	.	185;185	Q9UK43;Q13123	.;RED_HUMAN	D	185	.	ENSP00000261812:E185D	E	+	3	2	IK	140014320	0.973000	0.33851	1.000000	0.80357	0.990000	0.78478	0.251000	0.18257	0.653000	0.30826	0.460000	0.39030	GAA	.	.	.	none		0.388	IK-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372897.1	NM_006083		C	140034136	A	C	140034136	3	2	65	1	0	0	0	0	1	0	0	0	7615	69	3	5	581	5	IK	5	140034136	Missense_Mutation	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10		140034136	40881124	11	4306											
PCDHA12	56137	hgsc.bcm.edu	37	chr5	140256291	140256291	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcgttggtgctggacagcGccctggaccgcgagagcgtg	6	7	16	12	5	0	1	0	0	0	1	1	4	0	3	2	3	3	2	2	3	0	1			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr5:140256291G>A	ENST00000398631.2	+	1	1234	c.1234G>A	c.(1234-1236)Gcc>Acc	p.A412T	PCDHA4_ENST00000512229.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	412	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)			GCTGGACAGCGCCCTGGACCG	0.607																																					p.A412T	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											PCDHA12,NS,carcinoma,0,2	PCDHA12	196	.	0			c.G1234A						PASS	.						196	189	192					5																	140256291		2203	4300	6503	SO:0001583	missense	56137	exon1			GACAGCGCCCTGG	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.1234G>A	chr5.hg19:g.140256291G>A	ENSP00000381628:p.Ala412Thr	171.0	0.0	.		174.0	8.0	.	NM_018903	O75278|Q2M1N8	Missense_Mutation	SNP	ENST00000398631.2	hg19	CCDS47285.1	.	.	.	.	.	.	.	.	.	.	G	10.75	1.438589	0.25900	.	.	ENSG00000251664	ENST00000398631	T	0.02682	4.2	4.81	-1.86	0.07760	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.02304	0.0071	L	0.35593	1.075	0.09310	N	1	B;B	0.33528	0.056;0.416	B;B	0.37550	0.042;0.253	T	0.45071	-0.9286	9	0.33141	T	0.24	.	0.7087	0.00920	0.22:0.1806:0.3273:0.2721	.	412;412	Q9UN75-2;Q9UN75	.;PCDAC_HUMAN	T	412	ENSP00000381628:A412T	ENSP00000381628:A412T	A	+	1	0	PCDHA12	140236475	0.000000	0.05858	0.001000	0.08648	0.862000	0.49288	-1.193000	0.03049	-0.044000	0.13491	0.655000	0.94253	GCC	.	.	.	none		0.607	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		A	140256291	G	A	140256291	3	1	65	1	0	0	0	0	1	0	0	0	11529	1087	38	1	1236	1	PCDHA12	5	140256291	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	222155	140256291	40658969	12	4307											
NFYA	4800	hgsc.bcm.edu	37	chr6	41059422	41059422	+	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	gcaatgtggtcaattcaggaGggatggtcatggtaagaaaa	14	9	14	4	0	3	1	3	0	0	1	3	3	3	3	0	5	0	2	0	5	5	2			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr6:41059422G>A	ENST00000341376.6	+	7	904	c.703G>A	c.(703-705)Ggg>Agg	p.G235R	NFYA_ENST00000353205.5_Missense_Mutation_p.G206R|OARD1_ENST00000480585.1_Intron	NM_002505.4	NP_002496.1	P23511	NFYA_HUMAN	nuclear transcription factor Y, alpha	235					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)					CAATTCAGGAGGGATGGTCAT	0.418																																					p.G235R		Atlas-SNP	.											.	NFYA	33	.	0			c.G703A						PASS	.						229	209	216					6																	41059422		2203	4300	6503	SO:0001583	missense	4800	exon7			TCAGGAGGGATGG		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.703G>A	chr6.hg19:g.41059422G>A	ENSP00000345702:p.Gly235Arg	58.0	0.0	.		55.0	21.0	.	NM_002505	Q8IXU0	Missense_Mutation	SNP	ENST00000341376.6	hg19	CCDS4849.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.975651	0.92919	.	.	ENSG00000001167	ENST00000341376;ENST00000353205	.	.	.	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.71702	0.3371	L	0.51422	1.61	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.72364	-0.4316	9	0.62326	D	0.03	-10.6151	18.9483	0.92630	0.0:0.0:1.0:0.0	.	206;235	P23511-2;P23511	.;NFYA_HUMAN	R	235;206	.	ENSP00000345702:G235R	G	+	1	0	NFYA	41167400	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.760000	0.98935	2.720000	0.93068	0.655000	0.94253	GGG	.	.	.	none		0.418	NFYA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040496.1			A	41059422	G	A	41059422	3	1	65	1	0	0	0	0	1	0	0	0	10396	1000	35	2	725	2	NFYA	6	41059422	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10		41059422	130055645	13	4308											
YIPF3	25844	hgsc.bcm.edu	37	chr6	43483379	43483379	+	Frame_Shift_Del	DEL	T	T	-																															atcaaagtagggtctgaggaTgtcgatgttggcgtacaagc																										TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr6:43483379delT	ENST00000372422.2	-	3	531	c.349delA	c.(349-351)atcfs	p.I117fs	POLR1C_ENST00000304004.3_5'Flank|POLR1C_ENST00000372344.2_5'Flank|POLR1C_ENST00000372389.3_5'Flank|YIPF3_ENST00000506469.1_Frame_Shift_Del_p.I123fs	NM_015388.3	NP_056203.2	Q9GZM5	YIPF3_HUMAN	Yip1 domain family, member 3	117					cell differentiation (GO:0030154)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)				large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)	9	all_cancers(18;3.79e-05)|Lung NSC(15;0.00217)|all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00736)|OV - Ovarian serous cystadenocarcinoma(102;0.0711)			GGTCTGAGGATGTCGATGTTG	0.517																																					p.I117fs		Atlas-Indel,Pindel	.											.	YIPF3	20	.	0			c.350delT						PASS	.						129	120	123					6																	43483379		2203	4300	6503	SO:0001589	frameshift_variant	25844	exon3			.	AK000946	CCDS4899.1	6p21.1	2009-10-06	2005-07-04	2005-07-04	ENSG00000137207	ENSG00000137207		"Yip1 domain family"	21023	protein-coding gene	gene with protein product		609775	"chromosome 6 open reading frame 109"	C6orf109			Standard	NM_015388		Approved	DKFZp566C243, KLIP1, dJ337H4.3, FinGER3	uc003ovl.2	Q9GZM5	OTTHUMG00000014738	ENST00000372422.2:c.349delA	chr6.hg19:g.43483379delT	ENSP00000361499:p.Ile117fs	102.0	0.0	0		81.0	32.0	0.395062	NM_015388	Q5JTD2|Q6FI85|Q8NI57|Q9NWE3|Q9Y3U9	Frame_Shift_Del	DEL	ENST00000372422.2	hg19	CCDS4899.1																																																																																			.	.	.	none		0.517	YIPF3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040639.2	NM_015388		-	43483379	T	-	43483379	7	5	65	1	0	1	0	1	0	0	0	0	17491	1464	51	0	731	0	YIPF3	6	43483379	Frame_Shift_Del	DEL	T	TCGA-A4-A5XZ-01A-11D-A31X-10	2423957	43483379	127631688	14	4309											
NOD1	10392	hgsc.bcm.edu	37	chr7	30492406	30492406	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcagccgctgtagcagcatGgacttgcccaccccagcatc	8	7	10	16	1	0	0	0	0	0	0	1	1	0	1	4	1	6	6	4	1	1	2			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr7:30492406G>A	ENST00000222823.4	-	6	1152	c.627C>T	c.(625-627)tcC>tcT	p.S209S	NOD1_ENST00000423334.2_Intron	NM_006092.2	NP_006083.1	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain containing 1	209	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				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						GTAGCAGCATGGACTTGCCCA	0.612																																					p.S209S		Atlas-SNP	.											.	NOD1	79	.	0			c.C627T						PASS	.						89	86	87					7																	30492406		2203	4300	6503	SO:0001819	synonymous_variant	10392	exon6			CAGCATGGACTTG	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.627C>T	chr7.hg19:g.30492406G>A		53.0	0.0	.		83.0	23.0	.	NM_006092	B4DTU3|Q549U4|Q8IWF5	Silent	SNP	ENST00000222823.4	hg19	CCDS5427.1																																																																																			.	.	.	none		0.612	NOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250443.2			A	30492406	G	A	30492406	2	1	65	1	0	0	0	0	0	0	0	1	10523	1335	47	2		2	NOD1	7	30492406	Silent	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10		30492406	128646257	15	4310											
OGDH	4967	hgsc.bcm.edu	37	chr7	44747231	44747232	+	Frame_Shift_Ins	INS	-	-	A																															aggaggtgcagaagtaccccINSaatgctgagctggcctggtg																										TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr7:44747231_44747232insA	ENST00000222673.5	+	22	2889_2890	c.2847_2848insA	c.(2848-2850)aatfs	p.N950fs	OGDH_ENST00000543843.1_Frame_Shift_Ins_p.N901fs|OGDH_ENST00000444676.1_Frame_Shift_Ins_p.N965fs|OGDH_ENST00000449767.1_Frame_Shift_Ins_p.N946fs|OGDH_ENST00000439616.2_Frame_Shift_Ins_p.N800fs|OGDH_ENST00000447398.1_Frame_Shift_Ins_p.N961fs	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	950					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)	AGAAGTACCCCAATGCTGAGCT	0.574																																					p.P949fs		Atlas-Indel,Pindel	.											.	OGDH	145	.	0			c.2847_2848insA						PASS	.																																			SO:0001589	frameshift_variant	4967	exon22			.	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.2849dupA	chr7.hg19:g.44747233_44747233dupA	ENSP00000222673:p.Asn950fs	55.0	0.0	0		102.0	38.0	0.372549	NM_002541	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Frame_Shift_Ins	INS	ENST00000222673.5	hg19	CCDS34627.1																																																																																			.	.	.	none		0.574	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1			A	44747232	-	A	44747231	7	5	65	1	0	1	1	0	0	0	0	0	10846	581	21	0	3102	0	OGDH	7	44747231	Frame_Shift_Ins	INS	-	TCGA-A4-A5XZ-01A-11D-A31X-10	14254825	44747231	114391432	16	4311											
ZNF273	10793	hgsc.bcm.edu	37	chr7	64388953	64388953	+	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	agcctttaaacggtccacaaCtcttactaaacataagagaa	17	9	5	10	1	1	1	0	0	1	1	2	2	2	1	2	1	5	0	2	1	8	5			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr7:64388953C>G	ENST00000476120.1	+	4	1318	c.1247C>G	c.(1246-1248)aCt>aGt	p.T416S	ZNF273_ENST00000319636.5_Missense_Mutation_p.T351S|ZNF273_ENST00000527278.1_3'UTR	NM_021148.2	NP_066971.2	Q14593	ZN273_HUMAN	zinc finger protein 273	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(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)				CGGTCCACAACTCTTACTAAA	0.348																																					p.T416S	Ovarian(154;605 895 6696 7659 15316 19321 21716 23848 32322 36932)	Atlas-SNP	.											.	ZNF273	45	.	0			c.C1247G						PASS	.						40	44	42					7																	64388953		2203	4298	6501	SO:0001583	missense	10793	exon4			CCACAACTCTTAC	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.1247C>G	chr7.hg19:g.64388953C>G	ENSP00000418719:p.Thr416Ser	103.0	0.0	.		169.0	77.0	.	NM_021148	B3KQZ5|Q6P3V4	Missense_Mutation	SNP	ENST00000476120.1	hg19	CCDS5528.2	.	.	.	.	.	.	.	.	.	.	.	5.424	0.263316	0.10294	.	.	ENSG00000198039	ENST00000476120;ENST00000319636	T;T	0.03358	3.96;3.96	1.16	1.16	0.20824	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02230	0.0069	N	0.11724	0.165	0.09310	N	1	B	0.19445	0.036	B	0.25405	0.06	T	0.50250	-0.8850	9	0.12103	T	0.63	.	7.3527	0.26700	0.0:1.0:0.0:0.0	.	416	Q14593	ZN273_HUMAN	S	416;351	ENSP00000418719:T416S;ENSP00000324518:T351S	ENSP00000324518:T351S	T	+	2	0	ZNF273	64026388	0.000000	0.05858	0.757000	0.31301	0.755000	0.42902	-6.036000	0.00084	0.202000	0.20498	0.205000	0.17691	ACT	.	.	.	none		0.348	ZNF273-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313502.1			G	64388953	C	G	64388953	3	3	65	1	0	0	0	0	1	0	0	0	17820	565	20	4	1261	4	ZNF273	7	64388953	Missense_Mutation	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10	19641722	64388953	94749710	17	4312											
ABCB4	5244	hgsc.bcm.edu	37	chr7	87049331	87049331	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tacctgtcttagcattgcttTaaaagccattgaccgcagtc	10	13	7	11	1	1	1	0	1	1	0	2	1	1	1	3	0	4	3	3	0	4	6			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr7:87049331T>C	ENST00000265723.4	-	19	2488	c.2377A>G	c.(2377-2379)Aaa>Gaa	p.K793E	ABCB4_ENST00000358400.3_Missense_Mutation_p.K793E|ABCB4_ENST00000359206.3_Missense_Mutation_p.K793E|ABCB4_ENST00000545634.1_Missense_Mutation_p.K793E|ABCB4_ENST00000453593.1_Missense_Mutation_p.K793E	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	793	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	AGCATTGCTTTAAAAGCCATT	0.423																																					p.K793E		Atlas-SNP	.											.	ABCB4	177	.	0			c.A2377G						PASS	.						183	167	173					7																	87049331		2203	4300	6503	SO:0001583	missense	5244	exon19			TTGCTTTAAAAGC	M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"ATP binding cassette transporters / subfamily B"	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.2377A>G	chr7.hg19:g.87049331T>C	ENSP00000265723:p.Lys793Glu	111.0	0.0	.		148.0	64.0	.	NM_018850	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Missense_Mutation	SNP	ENST00000265723.4	hg19	CCDS5606.1	.	.	.	.	.	.	.	.	.	.	T	13.65	2.299295	0.40694	.	.	ENSG00000005471	ENST00000359206;ENST00000358400;ENST00000265723;ENST00000453593;ENST00000545634	D;D;D;D;D	0.89810	-2.57;-2.57;-2.57;-2.57;-2.57	6.03	2.37	0.29283	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.390503	0.30003	N	0.010651	D	0.84543	0.5495	L	0.58101	1.795	0.31324	N	0.685702	B;B;B	0.10296	0.003;0.002;0.003	B;B;B	0.16722	0.016;0.007;0.012	T	0.80286	-0.1446	10	0.62326	D	0.03	-9.0118	6.8919	0.24234	0.0:0.1317:0.1275:0.7408	.	793;793;793	A4D1D5;P21439-2;P21439	.;.;MDR3_HUMAN	E	793	ENSP00000352135:K793E;ENSP00000351172:K793E;ENSP00000265723:K793E;ENSP00000392983:K793E;ENSP00000437465:K793E	ENSP00000265723:K793E	K	-	1	0	ABCB4	86887267	0.999000	0.42202	0.992000	0.48379	0.639000	0.38242	1.584000	0.36589	0.497000	0.27926	-0.256000	0.11100	AAA	.	.	.	none		0.423	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443		C	87049331	T	C	87049331	3	2	65	1	0	0	0	0	1	0	0	0	43	1763	61	3	1523	3	ABCB4	7	87049331	Missense_Mutation	SNP	T	TCGA-A4-A5XZ-01A-11D-A31X-10	22660378	87049331	72089332	18	4313											
ARHGAP22	58504	hgsc.bcm.edu	37	chr10	49659052	49659052	+	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	ttggctgtccctggtgacctCctcggagccccaccccactg	4	9	10	18	1	0	1	0	1	0	0	3	2	2	2	7	3	1	1	7	3	0	1			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr10:49659052C>G	ENST00000249601.4	-	9	1416	c.1120G>C	c.(1120-1122)Gag>Cag	p.E374Q	ARHGAP22_ENST00000477708.2_Missense_Mutation_p.E207Q|ARHGAP22_ENST00000374170.1_Missense_Mutation_p.E215Q|ARHGAP22_ENST00000417912.2_Missense_Mutation_p.E390Q|ARHGAP22_ENST00000435790.2_Missense_Mutation_p.E380Q|ARHGAP22_ENST00000417247.2_Missense_Mutation_p.E284Q|ARHGAP22_ENST00000374172.1_Missense_Mutation_p.E265Q	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	374					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						CTGGTGACCTCCTCGGAGCCC	0.731																																					p.E390Q		Atlas-SNP	.											.	ARHGAP22	94	.	0			c.G1168C						PASS	.						8	9	9					10																	49659052		2008	4065	6073	SO:0001583	missense	58504	exon9			TGACCTCCTCGGA	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.1120G>C	chr10.hg19:g.49659052C>G	ENSP00000249601:p.Glu374Gln	82.0	0.0	.		60.0	25.0	.	NM_001256024	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Missense_Mutation	SNP	ENST00000249601.4	hg19	CCDS7227.1	.	.	.	.	.	.	.	.	.	.	C	18.24	3.580505	0.65992	.	.	ENSG00000128805	ENST00000249601;ENST00000374172;ENST00000374170;ENST00000477708;ENST00000417247;ENST00000435790;ENST00000417912	T;T;T;T;T;T;T	0.37915	2.7;2.36;1.17;1.51;2.34;2.66;2.7	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.62196	0.2408	M	0.81942	2.565	0.50039	D	0.999846	P;D;D;D;D;D	0.89917	0.621;1.0;0.972;1.0;0.959;1.0	B;D;P;D;P;D	0.74348	0.326;0.972;0.742;0.959;0.882;0.983	T	0.66352	-0.5945	10	0.59425	D	0.04	.	15.8862	0.79251	0.0:1.0:0.0:0.0	.	380;374;390;374;284;207	B4DED8;A6NDI7;Q7Z5H3-2;Q7Z5H3;Q7Z5H3-3;D6R9V6	.;.;.;RHG22_HUMAN;.;.	Q	374;265;215;207;284;380;390	ENSP00000249601:E374Q;ENSP00000363287:E265Q;ENSP00000363285:E215Q;ENSP00000422868:E207Q;ENSP00000410054:E284Q;ENSP00000416701:E380Q;ENSP00000412461:E390Q	ENSP00000249601:E374Q	E	-	1	0	ARHGAP22	49329058	1.000000	0.71417	0.573000	0.28510	0.349000	0.29174	6.759000	0.74934	2.440000	0.82611	0.313000	0.20887	GAG	.	.	.	none		0.731	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226		G	49659052	C	G	49659052	3	3	65	1	0	0	0	0	1	0	0	0	872	864	30	4	984	4	ARHGAP22	10	49659052	Missense_Mutation	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10		49659052	85875695	19	4314											
DDN	23109	hgsc.bcm.edu	37	chr12	49390815	49390815	+	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	tgtggcggcggatacgggacAcggcttctcgcagggccccg	5	6	17	13	6	1	0	0	0	1	0	2	2	1	2	2	6	1	2	2	6	1	2			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr12:49390815A>T	ENST00000421952.2	-	2	1865	c.1844T>A	c.(1843-1845)gTg>gAg	p.V615E	RP11-386G11.5_ENST00000552933.1_RNA|RP11-386G11.5_ENST00000547395.1_RNA|RP11-386G11.5_ENST00000547866.1_RNA|RP11-386G11.3_ENST00000549516.1_RNA|RP11-386G11.5_ENST00000552284.1_RNA	NM_015086.1	NP_055901.2	O94850	DEND_HUMAN	dendrin	615	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						GATACGGGACACGGCTTCTCG	0.721																																					p.V615E		Atlas-SNP	.											.	DDN	54	.	0			c.T1844A						PASS	.						5	5	5					12																	49390815		2080	4038	6118	SO:0001583	missense	23109	exon2			CGGGACACGGCTT	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.1844T>A	chr12.hg19:g.49390815A>T	ENSP00000390590:p.Val615Glu	25.0	0.0	.		28.0	13.0	.	NM_015086		Missense_Mutation	SNP	ENST00000421952.2	hg19	CCDS31791.2	.	.	.	.	.	.	.	.	.	.	A	24.9	4.581706	0.86748	.	.	ENSG00000181418	ENST00000421952	T	0.58940	0.3	4.12	4.12	0.48240	.	0.000000	0.41396	D	0.000887	T	0.63462	0.2513	L	0.32530	0.975	0.43936	D	0.99659	D	0.76494	0.999	D	0.71656	0.974	T	0.66783	-0.5836	10	0.87932	D	0	-0.1503	11.4668	0.50243	1.0:0.0:0.0:0.0	.	615	O94850	DEND_HUMAN	E	615	ENSP00000390590:V615E	ENSP00000390590:V615E	V	-	2	0	DDN	47677082	0.983000	0.35010	1.000000	0.80357	0.979000	0.70002	1.446000	0.35090	2.105000	0.64084	0.459000	0.35465	GTG	.	.	.	none		0.721	DDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343335.1			T	49390815	A	T	49390815	3	4	65	1	0	0	0	0	1	0	0	0	4335	159	6	5	295	5	DDN	12	49390815	Missense_Mutation	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10		49390815	84461080	20	4315											
ATP2B1	490	hgsc.bcm.edu	37	chr12	89992987	89992988	+	Frame_Shift_Ins	INS	-	-	AA																															tctcttcaacatcctctgctINSaattcctcctcaggtatttc																										TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr12:89992987_89992988insAA	ENST00000428670.3	-	20	3713_3714	c.3257_3258insTT	c.(3256-3258)ttafs	p.L1086fs	ATP2B1_ENST00000261173.2_Frame_Shift_Ins_p.L1086fs|ATP2B1_ENST00000393164.2_Frame_Shift_Ins_p.L829fs|ATP2B1_ENST00000348959.3_Frame_Shift_Ins_p.L1050fs|ATP2B1_ENST00000359142.3_Frame_Shift_Ins_p.L1086fs			P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1	1086					blood coagulation (GO:0007596)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	45						CATCCTCTGCTAATTCCTCCTC	0.436																																					p.L1086fs		Pindel	.											.	ATP2B1	191	.	0			c.3258_3259insTT						PASS	.																																			SO:0001589	frameshift_variant	490	exon19			.	J04027	CCDS9035.1, CCDS41817.1	12q21.33	2010-04-20			ENSG00000070961	ENSG00000070961	3.6.3.8	"ATPases / P-type"	814	protein-coding gene	gene with protein product	"plasma membrane calcium-transporting ATPase 1"	108731				1674727	Standard	NM_001682		Approved	PMCA1	uc001tbh.3	P20020		ENST00000428670.3:c.3256_3257dupTT	chr12.hg19:g.89992988_89992989dupAA	ENSP00000392043:p.Leu1086fs	66.0	0.0	.		83.0	30.0	0.361	NM_001001323	Q12992|Q12993|Q13819|Q13820|Q13821|Q16504|Q93082	Frame_Shift_Ins	INS	ENST00000428670.3	hg19	CCDS9035.1																																																																																			.	.	.	none		0.436	ATP2B1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406653.1	NM_001682		AA	89992988	-	AA	89992987	7	5	65	1	0	1	1	0	0	0	0	0	1139	1519	53	0	570	0	ATP2B1	12	89992987	Frame_Shift_Ins	INS	-	TCGA-A4-A5XZ-01A-11D-A31X-10	40602172	89992987	43858908	21	4316											
THSD1	55901	hgsc.bcm.edu	37	chr13	52971551	52971551	+	Frame_Shift_Del	DEL	G	G	-																															gtcctcttcccagggtatctGggggcctccttgaagacagt																										TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr13:52971551delG	ENST00000258613.4	-	3	1015	c.837delC	c.(835-837)cccfs	p.P279fs	RNY4P24_ENST00000362735.1_RNA|THSD1_ENST00000544466.1_Intron|THSD1_ENST00000349258.4_Frame_Shift_Del_p.P279fs	NM_018676.3	NP_061146.1	Q9NS62	THSD1_HUMAN	thrombospondin, type I, domain containing 1	279					hematopoietic progenitor cell differentiation (GO:0002244)	cell periphery (GO:0071944)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Breast(56;0.000207)|Lung NSC(96;0.00145)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.8e-08)		CAGGGTATCTGGGGGCCTCCT	0.537																																					p.R280fs		Pindel	.											.	THSD1	89	.	0			c.838delA						PASS	.						75	74	74					13																	52971551		2203	4300	6503	SO:0001589	frameshift_variant	55901	exon3			.	AK096289	CCDS9432.1, CCDS9433.1	13q14.13	2010-04-20	2004-03-11		ENSG00000136114	ENSG00000136114			17754	protein-coding gene	gene with protein product			"thrombospondin, type I, domain 1"				Standard	NM_018676		Approved	TMTSP	uc001vgo.3	Q9NS62	OTTHUMG00000016963	ENST00000258613.4:c.837delC	chr13.hg19:g.52971551delG	ENSP00000258613:p.Pro279fs	84.0	0.0	.		117.0	27.0	0.231	NM_018676	A2A3J3|B2RCF5|Q6P3U1|Q6UXZ2	Frame_Shift_Del	DEL	ENST00000258613.4	hg19	CCDS9432.1																																																																																			.	.	.	none		0.537	THSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045058.3			-	52971551	G	-	52971551	7	5	65	1	0	1	0	1	0	0	0	0	15889	1335	47	0	1733	0	THSD1	13	52971551	Frame_Shift_Del	DEL	G	TCGA-A4-A5XZ-01A-11D-A31X-10		52971551	62198327	22	4317											
ZIC2	7546	hgsc.bcm.edu	37	chr13	100635322	100635322	+	Missense_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	aggcgagaaacccttcccctGccccttcccgggctgtggca	6	7	11	17	2	0	1	0	0	0	1	2	2	2	1	6	3	2	2	6	3	1	2			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr13:100635322G>A	ENST00000376335.3	+	1	1297	c.1004G>A	c.(1003-1005)tGc>tAc	p.C335Y		NM_007129.3	NP_009060.2	O95409	ZIC2_HUMAN	Zic family member 2	335			C -> F (in HPE5). {ECO:0000269|PubMed:19177455}.		brain development (GO:0007420)|developmental pigmentation (GO:0048066)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|retinal ganglion cell axon guidance (GO:0031290)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(2)|liver(2)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CCCTTCCCCTGCCCCTTCCCG	0.617																																					p.C335Y	Pancreas(97;119 1522 31925 44771 48764)	Atlas-SNP	.											.	ZIC2	25	.	0			c.G1004A						PASS	.						81	89	86					13																	100635322		2203	4300	6503	SO:0001583	missense	7546	exon1			TCCCCTGCCCCTT	AF104902	CCDS9495.1	13q32	2013-01-08	2011-05-19		ENSG00000043355	ENSG00000043355		"Zinc fingers, C2H2-type"	12873	protein-coding gene	gene with protein product	"Zinc finger protein of the cerebellum 2"	603073	"Zic family member 2 (odd-paired Drosophila homolog)", "Zic family member 2 (odd-paired homolog, Drosophila)"			9771712	Standard	NM_007129		Approved	HPE5	uc001von.3	O95409	OTTHUMG00000017279	ENST00000376335.3:c.1004G>A	chr13.hg19:g.100635322G>A	ENSP00000365514:p.Cys335Tyr	114.0	0.0	.		87.0	26.0	.	NM_007129	Q5VYA9|Q9H309	Missense_Mutation	SNP	ENST00000376335.3	hg19	CCDS9495.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.224811	0.79576	.	.	ENSG00000043355	ENST00000376335;ENST00000397444	D	0.85088	-1.94	4.69	4.69	0.59074	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	0.93798	0.8017	M	0.90705	3.14	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.94910	0.8064	10	0.87932	D	0	.	18.1567	0.89693	0.0:0.0:1.0:0.0	.	335	O95409	ZIC2_HUMAN	Y	335;84	ENSP00000365514:C335Y	ENSP00000365514:C335Y	C	+	2	0	ZIC2	99433323	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.601000	0.98297	2.610000	0.88304	0.561000	0.74099	TGC	.	.	.	none		0.617	ZIC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045618.2	NM_007129		A	100635322	G	A	100635322	3	1	65	1	0	0	0	0	1	0	0	0	17691	1319	46	2	1006	2	ZIC2	13	100635322	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	47663771	100635322	14534556	23	4318											
SCFD1	23256	hgsc.bcm.edu	37	chr14	31175075	31175075	+	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	cggccagctatggcagcactAccactaaaccaatggggtaa	13	6	10	12	1	0	0	0	0	0	0	0	0	0	0	3	4	4	4	3	4	6	4			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr14:31175075A>T	ENST00000458591.2	+	18	1764	c.1537A>T	c.(1537-1539)Acc>Tcc	p.T513S	SCFD1_ENST00000544052.2_Missense_Mutation_p.T446S|SCFD1_ENST00000554486.1_3'UTR|SCFD1_ENST00000541123.1_Missense_Mutation_p.T328S|SCFD1_ENST00000396629.2_Missense_Mutation_p.T421S|SCFD1_ENST00000421551.3_Missense_Mutation_p.T454S	NM_016106.3	NP_057190.2	Q8WVM8	SCFD1_HUMAN	sec1 family domain containing 1	513					post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|regulation of ER to Golgi vesicle-mediated transport (GO:0060628)|response to hypoxia (GO:0001666)|response to toxic substance (GO:0009636)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle docking involved in exocytosis (GO:0006904)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|Golgi transport complex (GO:0017119)|Golgi-associated vesicle (GO:0005798)|plasma membrane (GO:0005886)	syntaxin binding (GO:0019905)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)	13	Hepatocellular(127;0.0877)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)	GBM - Glioblastoma multiforme(265;0.0181)		TGGCAGCACTACCACTAAACC	0.373																																					p.T513S		Atlas-SNP	.											.	SCFD1	43	.	0			c.A1537T						PASS	.						84	87	86					14																	31175075		2203	4300	6503	SO:0001583	missense	23256	exon18			AGCACTACCACTA	AF110646	CCDS9639.1, CCDS45092.1, CCDS58308.1	14q12	2006-04-04	2004-01-15	2004-01-16	ENSG00000092108	ENSG00000092108			20726	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 163"	C14orf163			Standard	NM_016106		Approved	RA410, KIAA0917, STXBP1L2, SLY1	uc001wqm.2	Q8WVM8	OTTHUMG00000029420	ENST00000458591.2:c.1537A>T	chr14.hg19:g.31175075A>T	ENSP00000390783:p.Thr513Ser	58.0	0.0	.		70.0	20.0	.	NM_016106	A8K2Z5|B7Z4U7|B7Z594|O60754|O94990|Q7Z529|Q9BZI3|Q9UNL3|Q9Y6A8	Missense_Mutation	SNP	ENST00000458591.2	hg19	CCDS9639.1	.	.	.	.	.	.	.	.	.	.	A	9.070	0.996695	0.19043	.	.	ENSG00000092108	ENST00000458591;ENST00000544052;ENST00000421551;ENST00000541123;ENST00000396629	T;T;T;T;T	0.75704	-0.96;-0.96;-0.96;-0.96;-0.96	5.71	4.58	0.56647	.	0.244841	0.38548	N	0.001656	T	0.38188	0.1031	N	0.00985	-1.075	0.33038	D	0.531027	B;B;B;B	0.06786	0.001;0.0;0.001;0.0	B;B;B;B	0.12156	0.003;0.002;0.007;0.005	T	0.43589	-0.9382	10	0.15499	T	0.54	-35.8251	3.8893	0.09111	0.7124:0.0:0.2876:0.0	.	454;446;421;513	B7Z738;B7Z4U7;B7Z594;Q8WVM8	.;.;.;SCFD1_HUMAN	S	513;446;454;328;421	ENSP00000390783:T513S;ENSP00000443010:T446S;ENSP00000388078:T454S;ENSP00000443537:T328S;ENSP00000379870:T421S	ENSP00000309417:T521S	T	+	1	0	SCFD1	30244826	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.464000	0.53057	2.175000	0.68902	0.477000	0.44152	ACC	.	.	.	none		0.373	SCFD1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276612.3	NM_182835		T	31175075	A	T	31175075	3	4	65	1	0	0	0	0	1	0	0	0	13902	391	14	5	1607	5	SCFD1	14	31175075	Missense_Mutation	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10		31175075	76174465	24	4319											
ZFYVE26	23503	hgsc.bcm.edu	37	chr14	68252617	68252617	+	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	cagtgactgaaggacctgatCtagctgctgggagagggtgg	9	8	17	7	0	1	4	0	3	1	1	1	6	1	5	1	4	2	2	1	4	2	1			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr14:68252617C>T	ENST00000347230.4	-	18	3400	c.3262G>A	c.(3262-3264)Gat>Aat	p.D1088N	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.D1088N	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	1088					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)		AGGACCTGATCTAGCTGCTGG	0.557																																					p.D1088N		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.G3262A						PASS	.						218	222	221					14																	68252617		2203	4300	6503	SO:0001583	missense	23503	exon18			CCTGATCTAGCTG	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.3262G>A	chr14.hg19:g.68252617C>T	ENSP00000251119:p.Asp1088Asn	116.0	0.0	.		80.0	26.0	.	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	hg19	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.817287	0.90790	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.30981	1.66;1.51	5.38	5.38	0.77491	.	0.530450	0.20377	N	0.093539	T	0.36908	0.0984	L	0.47716	1.5	0.40782	D	0.983189	P;P	0.39480	0.675;0.546	B;B	0.43658	0.426;0.164	T	0.21621	-1.0240	10	0.59425	D	0.04	0.0013	16.9198	0.86161	0.0:1.0:0.0:0.0	.	1088;1088	G3V2D8;Q68DK2	.;ZFY26_HUMAN	N	1088;1067;1088	ENSP00000251119:D1088N;ENSP00000450603:D1088N	ENSP00000251119:D1088N	D	-	1	0	ZFYVE26	67322370	0.998000	0.40836	0.480000	0.27341	0.939000	0.58152	3.840000	0.55843	2.512000	0.84698	0.655000	0.94253	GAT	.	.	.	none		0.557	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		T	68252617	C	T	68252617	3	4	65	1	0	0	0	0	1	0	0	0	17680	913	32	2	4457	2	ZFYVE26	14	68252617	Missense_Mutation	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10	37077542	68252617	39096923	25	4320											
EXD2	55218	hgsc.bcm.edu	37	chr14	69697234	69697234	+	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	agcctgaagtccctcgctgaGactgttttgaactttcccct	7	13	8	13	1	0	3	0	3	0	1	3	4	2	3	4	0	2	2	4	0	2	3			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr14:69697234G>C	ENST00000409018.3	+	4	764	c.636G>C	c.(634-636)gaG>gaC	p.E212D	EXD2_ENST00000449989.1_Missense_Mutation_p.E87D|EXD2_ENST00000409242.1_Missense_Mutation_p.E87D|EXD2_ENST00000312994.5_Missense_Mutation_p.E212D|EXD2_ENST00000409014.1_Missense_Mutation_p.E87D|EXD2_ENST00000409675.1_Missense_Mutation_p.E87D|EXD2_ENST00000409949.1_Missense_Mutation_p.E87D|EXD2_ENST00000492815.1_3'UTR	NM_001193361.1	NP_001180290.1	Q9NVH0	EXD2_HUMAN	exonuclease 3'-5' domain containing 2	212	3'-5' exonuclease.						3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|urinary_tract(1)	14						CCCTCGCTGAGACTGTTTTGA	0.448																																					p.E212D		Atlas-SNP	.											.	EXD2	43	.	0			c.G636C						PASS	.						178	168	172					14																	69697234		2203	4300	6503	SO:0001583	missense	55218	exon4			CGCTGAGACTGTT	AK001600	CCDS9793.1, CCDS53902.1	14q24.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000081177	ENSG00000081177			20217	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 114", "exonuclease 3'-5' domain-like 2"	C14orf114, EXDL2			Standard	NM_018199		Approved	FLJ10738	uc001xkv.3	Q9NVH0	OTTHUMG00000154496	ENST00000409018.3:c.636G>C	chr14.hg19:g.69697234G>C	ENSP00000387331:p.Glu212Asp	89.0	0.0	.		68.0	21.0	.	NM_001193361	B4DIH6|G5E947|Q6AWB6|Q8N3D3	Missense_Mutation	SNP	ENST00000409018.3	hg19	CCDS53902.1	.	.	.	.	.	.	.	.	.	.	G	17.93	3.507951	0.64410	.	.	ENSG00000081177	ENST00000409018;ENST00000193422;ENST00000409014;ENST00000409675;ENST00000409949;ENST00000409242;ENST00000312994;ENST00000413191;ENST00000449989	T;T;T;T;T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17;-0.17;-0.17;-0.17;-0.17	5.33	2.49	0.30216	-5&apos (1);Ribonuclease H-like (1); exonuclease (1);3&apos (1);	0.093871	0.64402	D	0.000001	T	0.70640	0.3247	M	0.75884	2.315	0.40602	D	0.981598	P;P	0.51057	0.941;0.908	P;P	0.58520	0.84;0.781	T	0.68637	-0.5356	10	0.33141	T	0.24	-25.4424	9.0491	0.36365	0.373:0.0:0.627:0.0	.	212;87	G5E947;Q9NVH0	.;EXD2_HUMAN	D	212;212;87;87;87;87;212;87;87	ENSP00000387331:E212D;ENSP00000386915:E87D;ENSP00000386762:E87D;ENSP00000386632:E87D;ENSP00000386839:E87D;ENSP00000313140:E212D;ENSP00000409089:E87D;ENSP00000392177:E87D	ENSP00000193422:E212D	E	+	3	2	EXD2	68766987	1.000000	0.71417	0.970000	0.41538	0.840000	0.47671	2.350000	0.44063	0.742000	0.32697	-0.136000	0.14681	GAG	.	.	.	none		0.448	EXD2-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000335504.1			C	69697234	G	C	69697234	3	2	65	1	0	0	0	0	1	0	0	0	5300	933	33	4	267	4	EXD2	14	69697234	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	1444617	69697234	37652306	26	4321											
ADAM20	8748	hgsc.bcm.edu	37	chr14	70989617	70989617	+	Missense_Mutation	SNP	A	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	ggcacacttcttacggatgcAgatcttttctggaccacata	10	12	8	11	1	3	1	0	0	3	1	3	3	3	3	1	3	2	2	1	3	2	5			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr14:70989617A>C	ENST00000256389.3	-	2	2252	c.2008T>G	c.(2008-2010)Tgc>Ggc	p.C670G	RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003814.4	NP_003805.3	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20	620					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(2)	27			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)		TTACGGATGCAGATCTTTTCT	0.463																																					p.C670G		Atlas-SNP	.											.	ADAM20	59	.	0			c.T2008G						PASS	.						416	313	348					14																	70989617		2203	4300	6503	SO:0001583	missense	8748	exon2			GGATGCAGATCTT	AF029899	CCDS32111.1	14q24.2	2012-04-30	2005-08-18		ENSG00000134007	ENSG00000134007		"ADAM metallopeptidase domain containing"	199	protein-coding gene	gene with protein product		603712	"a disintegrin and metalloproteinase domain 20"			9469942	Standard	NM_003814		Approved		uc001xme.3	O43506	OTTHUMG00000167548	ENST00000256389.3:c.2008T>G	chr14.hg19:g.70989617A>C	ENSP00000256389:p.Cys670Gly	122.0	0.0	.		103.0	36.0	.	NM_003814	Q6GTZ1|Q9UKJ9	Missense_Mutation	SNP	ENST00000256389.3	hg19	CCDS32111.1	.	.	.	.	.	.	.	.	.	.	A	16.18	3.051177	0.55218	.	.	ENSG00000134007	ENST00000256389	T	0.02763	4.17	4.67	4.67	0.58626	ADAM, cysteine-rich (1);	0.000000	0.42682	D	0.000667	T	0.17066	0.0410	M	0.86805	2.84	0.20196	N	0.999929	D	0.89917	1.0	D	0.91635	0.999	T	0.03166	-1.1065	10	0.87932	D	0	.	12.6491	0.56751	1.0:0.0:0.0:0.0	.	620	O43506	ADA20_HUMAN	G	670	ENSP00000256389:C670G	ENSP00000256389:C670G	C	-	1	0	ADAM20	70059370	0.764000	0.28473	0.184000	0.23157	0.040000	0.13550	4.075000	0.57584	1.856000	0.53863	0.460000	0.39030	TGC	.	.	.	none		0.463	ADAM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395004.2			C	70989617	A	C	70989617	3	2	65	1	0	0	0	0	1	0	0	0	242	188	7	5	326	5	ADAM20	14	70989617	Missense_Mutation	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10	1292383	70989617	36359923	27	4322											
C14orf43	91748	hgsc.bcm.edu	37	chr14	74206660	74206660	+	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	agctggttcctggcccccgaAgaggcaacgcttccgcttgt	6	9	12	14	3	0	1	0	0	0	1	2	2	2	1	4	3	2	5	4	3	2	3			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr14:74206660A>T	ENST00000286523.5	-	2	834	c.52T>A	c.(52-54)Ttc>Atc	p.F18I	ELMSAN1_ENST00000486739.1_5'Flank|ELMSAN1_ENST00000394071.2_Missense_Mutation_p.F18I	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	18					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										TGGCCCCCGAAGAGGCAACGC	0.652																																					p.F18I		Atlas-SNP	.											.	.	.	.	0			c.T52A						PASS	.						44	48	47					14																	74206660		2203	4300	6503	SO:0001583	missense	91748	exon2			CCCCGAAGAGGCA	BF971739	CCDS9819.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000156030	ENSG00000156030			19853	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 117", "chromosome 14 open reading frame 43"	C14orf117, C14orf43			Standard	NM_194278		Approved	LSR68	uc001xou.3	Q6PJG2	OTTHUMG00000150359	ENST00000286523.5:c.52T>A	chr14.hg19:g.74206660A>T	ENSP00000286523:p.Phe18Ile	55.0	0.0	.		39.0	15.0	.	NM_194278	Q6PK13|Q6PK59|Q6ZS23	Missense_Mutation	SNP	ENST00000286523.5	hg19	CCDS9819.1	.	.	.	.	.	.	.	.	.	.	A	15.41	2.824093	0.50739	.	.	ENSG00000156030	ENST00000394071;ENST00000286523;ENST00000423556;ENST00000435371;ENST00000421708	T;T;T;T	0.21734	2.0;2.0;2.0;1.99	4.96	4.96	0.65561	.	0.081627	0.51477	D	0.000084	T	0.15089	0.0364	N	0.24115	0.695	0.47737	D	0.999504	B;B	0.31318	0.319;0.319	B;B	0.27608	0.081;0.081	T	0.05666	-1.0871	10	0.72032	D	0.01	-4.5629	13.0167	0.58762	1.0:0.0:0.0:0.0	.	18;18	A0PJD3;Q6PJG2	.;CN043_HUMAN	I	18	ENSP00000377634:F18I;ENSP00000286523:F18I;ENSP00000407767:F18I;ENSP00000402380:F18I	ENSP00000286523:F18I	F	-	1	0	C14orf43	73276413	1.000000	0.71417	1.000000	0.80357	0.719000	0.41307	6.822000	0.75277	2.089000	0.63090	0.402000	0.26972	TTC	.	.	.	none		0.652	ELMSAN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317793.1	NM_194278		T	74206660	A	T	74206660	3	4	65	1	0	0	0	0	1	0	0	0	1776	72	3	5	3129	5	C14orf43	14	74206660	Missense_Mutation	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10	3217043	74206660	33142880	28	4323											
BCL2L10	10017	hgsc.bcm.edu	37	chr15	52404725	52404725	+	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	gttcccggggtagccgaggtAggcggagaaaaaggaccggt	10	5	18	8	4	0	1	0	0	0	1	1	4	1	2	3	7	1	3	3	7	4	3			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr15:52404725A>T	ENST00000561198.1	-	1	240	c.199T>A	c.(199-201)Tac>Aac	p.Y67N	BCL2L10_ENST00000260442.3_Missense_Mutation_p.Y67N			Q9HD36	B2L10_HUMAN	BCL2-like 10 (apoptosis facilitator)	57					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|female gamete generation (GO:0007292)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|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 apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2				all cancers(107;0.0148)		TAGCCGAGGTAGGCGGAGAAA	0.716																																					p.Y67N		Atlas-SNP	.											.	BCL2L10	10	.	0			c.T199A						PASS	.						12	15	14					15																	52404725		2182	4283	6465	SO:0001583	missense	10017	exon1			CGAGGTAGGCGGA	AF285092	CCDS10148.1	15q21	2007-03-02			ENSG00000137875	ENSG00000137875			993	protein-coding gene	gene with protein product		606910				9829980, 9878060	Standard	NM_020396		Approved	Diva, Boo, BCL-B	uc002abq.3	Q9HD36	OTTHUMG00000131893	ENST00000561198.1:c.199T>A	chr15.hg19:g.52404725A>T	ENSP00000453562:p.Tyr67Asn	61.0	0.0	.		31.0	12.0	.	NM_020396	Q3SX80|Q52LQ9|Q8TCS9	Missense_Mutation	SNP	ENST00000561198.1	hg19		.	.	.	.	.	.	.	.	.	.	A	16.67	3.188072	0.57909	.	.	ENSG00000137875	ENST00000260442	T	0.11930	2.73	4.61	2.26	0.28386	Apoptosis regulator, Bcl-2, BH (2);	1.152810	0.06639	N	0.760739	T	0.27559	0.0677	L	0.51422	1.61	0.09310	N	1	D	0.63880	0.993	D	0.65987	0.94	T	0.13229	-1.0517	10	0.66056	D	0.02	.	5.067	0.14587	0.7532:0.0:0.2468:0.0	.	57	Q9HD36	B2L10_HUMAN	N	67	ENSP00000260442:Y67N	ENSP00000260442:Y67N	Y	-	1	0	BCL2L10	50192017	0.000000	0.05858	0.003000	0.11579	0.015000	0.08874	0.370000	0.20433	0.800000	0.34041	0.533000	0.62120	TAC	.	.	.	none		0.716	BCL2L10-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000419386.1			T	52404725	A	T	52404725	3	4	65	1	0	0	0	0	1	0	0	0	1368	420	15	5	423	5	BCL2L10	15	52404725	Missense_Mutation	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10		52404725	50126667	29	4324											
ULK3	25989	hgsc.bcm.edu	37	chr15	75132623	75132623	+	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	tcttccagctccgagaacgaCctggaggcaaaggggggctg	9	6	15	11	2	1	1	0	0	1	1	3	4	3	2	3	5	2	3	3	5	2	1			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr15:75132623C>T	ENST00000440863.2	-	6	739	c.648G>A	c.(646-648)agG>agA	p.R216R	ULK3_ENST00000568667.1_Silent_p.R227R|ULK3_ENST00000569437.1_Silent_p.R216R	NM_001099436.1	NP_001092906	Q6PHR2	ULK3_HUMAN	unc-51 like kinase 3	216	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						CCGAGAACGACCTGGAGGCAA	0.652																																					p.R216R		Atlas-SNP	.											.	ULK3	30	.	0			c.G648A						PASS	.						25	27	26					15																	75132623		1915	4138	6053	SO:0001819	synonymous_variant	25989	exon6			GAACGACCTGGAG	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.648G>A	chr15.hg19:g.75132623C>T		41.0	0.0	.		40.0	16.0	.	NM_001099436	B2RXK3|B4DRQ7|D3DW68|Q9NPN5|Q9UFS4	Silent	SNP	ENST00000440863.2	hg19	CCDS45305.1																																																																																			.	.	.	none		0.652	ULK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421734.4	NM_015518		T	75132623	C	T	75132623	2	4	65	1	0	0	0	0	0	0	0	1	16989	506	18	2		2	ULK3	15	75132623	Silent	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10	22727898	75132623	27398769	30	4325											
CLDN9	9080	hgsc.bcm.edu	37	chr16	3063765	3063765	+	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	gccggcatcctggtgctcatCcctgtgtgctggacggcgca	4	9	14	14	3	1	0	1	0	0	0	3	1	3	1	3	4	2	4	3	4	0	0			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr16:3063765C>A	ENST00000445369.2	+	1	1309	c.402C>A	c.(400-402)atC>atA	p.I134I		NM_020982.3	NP_066192.1	O95484	CLD9_HUMAN	claudin 9	134					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			endometrium(2)|large_intestine(1)|lung(5)|prostate(2)	10						TGGTGCTCATCCCTGTGTGCT	0.662																																					p.I134I		Atlas-SNP	.											.	CLDN9	33	.	0			c.C402A						PASS	.						82	80	81					16																	3063765		2198	4300	6498	SO:0001819	synonymous_variant	9080	exon1			GCTCATCCCTGTG	AJ130941	CCDS10487.1	16p13.3	2008-08-01			ENSG00000213937	ENSG00000213937		"Claudins"	2051	protein-coding gene	gene with protein product		615799				9441748, 18234789	Standard	NM_020982		Approved		uc010uwo.1	O95484	OTTHUMG00000129000	ENST00000445369.2:c.402C>A	chr16.hg19:g.3063765C>A		82.0	0.0	.		102.0	55.0	.	NM_020982		Silent	SNP	ENST00000445369.2	hg19	CCDS10487.1																																																																																			.	.	.	none		0.662	CLDN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250989.1	NM_020982		A	3063765	C	A	3063765	2	1	65	1	0	0	0	0	0	0	0	1	3494	845	30	4		4	CLDN9	16	3063765	Silent	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10		3063765	87290988	31	4326											
FOXN1	8456	hgsc.bcm.edu	37	chr17	26851949	26851949	+	Frame_Shift_Del	DEL	C	C	-																															gaggcctggtgtaacgggctCccctaccccagccaggagca																								rs548499213	byFrequency	TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr17:26851949delC	ENST00000226247.2	+	2	581	c.552delC	c.(550-552)ctcfs	p.L184fs	FOXN1_ENST00000579795.1_Frame_Shift_Del_p.L184fs	NM_003593.2	NP_003584.2	O15353	FOXN1_HUMAN	forkhead box N1	184					defense response (GO:0006952)|epidermis development (GO:0008544)|epithelial cell proliferation (GO:0050673)|hair follicle development (GO:0001942)|keratinocyte differentiation (GO:0030216)|lymphocyte homeostasis (GO:0002260)|nail development (GO:0035878)|organ morphogenesis (GO:0009887)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(8)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Lung NSC(42;0.00431)					GTAACGGGCTCCCCTACCCCA	0.647																																					p.L184fs		Atlas-Indel,Pindel	.											.	FOXN1	51	.	0			c.551delT						PASS	.						25	27	26					17																	26851949		2202	4300	6502	SO:0001589	frameshift_variant	8456	exon2			.	Y11739	CCDS11232.1	17q11-q12	2014-09-17	2003-06-12	2003-06-13	ENSG00000109101	ENSG00000109101		"Forkhead boxes"	12765	protein-coding gene	gene with protein product		600838	"winged-helix nude", "Rowett nude"	WHN, RONU		9321431	Standard	NM_003593		Approved	FKHL20	uc002hbj.3	O15353	OTTHUMG00000132603	ENST00000226247.2:c.552delC	chr17.hg19:g.26851949delC	ENSP00000226247:p.Leu184fs	25.0	0.0	0		62.0	21.0	0.33871	NM_003593	B2R9Q7|O15352	Frame_Shift_Del	DEL	ENST00000226247.2	hg19	CCDS11232.1																																																																																			.	.	.	none		0.647	FOXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255832.1			-	26851949	C	-	26851949	7	5	65	1	0	1	0	1	0	0	0	0	6026	842	30	0	558	0	FOXN1	17	26851949	Frame_Shift_Del	DEL	C	TCGA-A4-A5XZ-01A-11D-A31X-10		26851949	54343261	32	4327											
C17orf71	55181	hgsc.bcm.edu	37	chr17	57288259	57288259	+	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	aggtagaacctcctcggaacCaagacccagctcatccagac	13	5	8	15	1	1	3	1	0	0	3	4	4	3	4	5	2	3	2	5	2	4	1			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr17:57288259C>A	ENST00000543872.2	+	2	1111	c.847C>A	c.(847-849)Caa>Aaa	p.Q283K	SMG8_ENST00000578922.1_Missense_Mutation_p.Q283K|CTD-2510F5.6_ENST00000577660.1_Intron|SMG8_ENST00000300917.5_Missense_Mutation_p.Q283K|SMG8_ENST00000580498.1_Intron			Q8ND04	SMG8_HUMAN	SMG8 nonsense mediated mRNA decay factor	283					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						TCCTCGGAACCAAGACCCAGC	0.517																																					p.Q283K		Atlas-SNP	.											.	SMG8	79	.	0			c.C847A						PASS	.						66	73	70					17																	57288259		2203	4300	6503	SO:0001583	missense	55181	exon1			CGGAACCAAGACC	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.847C>A	chr17.hg19:g.57288259C>A	ENSP00000438748:p.Gln283Lys	41.0	0.0	.		74.0	5.0	.	NM_018149	Q8N5U5|Q8TDN0|Q9H5P5|Q9NVQ1	Missense_Mutation	SNP	ENST00000543872.2	hg19	CCDS11615.1	.	.	.	.	.	.	.	.	.	.	C	8.062	0.768336	0.15983	.	.	ENSG00000167447	ENST00000300917;ENST00000543872	T;T	0.41400	1.0;1.0	5.88	5.88	0.94601	.	0.345316	0.35179	N	0.003390	T	0.37732	0.1014	L	0.40543	1.245	0.43852	D	0.99644	B	0.19583	0.037	B	0.15052	0.012	T	0.09250	-1.0683	10	0.22706	T	0.39	-16.8779	19.2147	0.93772	0.0:1.0:0.0:0.0	.	283	Q8ND04	SMG8_HUMAN	K	283	ENSP00000300917:Q283K;ENSP00000438748:Q283K	ENSP00000300917:Q283K	Q	+	1	0	SMG8	54643041	0.999000	0.42202	1.000000	0.80357	0.961000	0.63080	3.993000	0.56987	2.769000	0.95229	0.655000	0.94253	CAA	.	.	.	none		0.517	SMG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445960.2	NM_018149		A	57288259	C	A	57288259	3	1	65	1	0	0	0	0	1	0	0	0	1880	595	21	4	849	4	C17orf71	17	57288259	Missense_Mutation	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10	30436310	57288259	23906951	33	4328											
POLRMT	5442	hgsc.bcm.edu	37	chr19	623528	623528	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccctgctggccagctccaTgtggagctgcttctcaaaga	8	9	10	14	0	1	1	1	0	1	1	3	2	2	2	3	2	4	4	3	2	1	1			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr19:623528T>C	ENST00000588649.2	-	6	1300	c.1216A>G	c.(1216-1218)Atg>Gtg	p.M406V	LLNLR-299G3.1_ENST00000607288.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	406					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)		GCCAGCTCCATGTGGAGCTGC	0.632																																					p.M406V		Atlas-SNP	.											.	POLRMT	91	.	0			c.A1216G						PASS	.						54	50	51					19																	623528		2203	4300	6503	SO:0001583	missense	5442	exon6			GCTCCATGTGGAG		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.1216A>G	chr19.hg19:g.623528T>C	ENSP00000465759:p.Met406Val	71.0	0.0	.		52.0	11.0	.	NM_005035	O60370	Missense_Mutation	SNP	ENST00000588649.2	hg19	CCDS12036.1	.	.	.	.	.	.	.	.	.	.	.	0.013	-1.639596	0.00799	.	.	ENSG00000099821	ENST00000215591	T	0.39056	1.1	4.63	-4.26	0.03755	.	0.752409	0.12789	N	0.438968	T	0.08935	0.0221	N	0.01446	-0.86	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31280	-0.9949	10	0.02654	T	1	-12.8428	0.5899	0.00726	0.249:0.2907:0.1226:0.3377	.	406	O00411	RPOM_HUMAN	V	406	ENSP00000215591:M406V	ENSP00000215591:M406V	M	-	1	0	POLRMT	574528	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.196000	0.03041	-0.378000	0.07918	-2.005000	0.00442	ATG	.	.	.	none		0.632	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035		C	623528	T	C	623528	3	2	65	1	0	0	0	0	1	0	0	0	12245	1464	51	3	2540	3	POLRMT	19	623528	Missense_Mutation	SNP	T	TCGA-A4-A5XZ-01A-11D-A31X-10		623528	58505455	34	4329											
KEAP1	9817	hgsc.bcm.edu	37	chr19	10610566	10610566	+	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	gtgtagctgaaggtgcggttGccatgctgggagggcgtcac	6	9	18	8	2	1	1	1	1	0	0	1	2	1	2	1	4	4	4	1	4	2	2			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr19:10610566G>T	ENST00000171111.5	-	2	691	c.144C>A	c.(142-144)ggC>ggA	p.G48G	KEAP1_ENST00000588024.1_5'Flank|KEAP1_ENST00000393623.2_Silent_p.G48G	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	48					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)	AGGTGCGGTTGCCATGCTGGG	0.627																																					p.G48G		Atlas-SNP	.											.	KEAP1	182	.	0			c.C144A						PASS	.						136	108	118					19																	10610566		2203	4300	6503	SO:0001819	synonymous_variant	9817	exon2			GCGGTTGCCATGC	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.144C>A	chr19.hg19:g.10610566G>T		62.0	0.0	.		63.0	24.0	.	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Silent	SNP	ENST00000171111.5	hg19	CCDS12239.1																																																																																			.	.	.	none		0.627	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		T	10610566	G	T	10610566	2	4	65	1	0	0	0	0	0	0	0	1	8148	1306	46	4		4	KEAP1	19	10610566	Silent	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10	9987038	10610566	48518417	35	4330											
MLL4	9757	hgsc.bcm.edu	37	chr19	36229181	36229181	+	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	tctccccacctcatccctgcAgggcatcgggtgctatatgt	6	11	9	15	1	2	0	1	0	1	0	5	0	3	0	4	2	2	3	4	2	2	2			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr19:36229181A>G	ENST00000222270.7	+	37	7872		c.e37-1		IGFLR1_ENST00000587101.1_5'Flank|KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Splice_Site	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B						chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TCATCCCTGCAGGGCATCGGG	0.602																																					.		Atlas-SNP	.											.	MLL4	229	.	0			c.7873-2A>G						PASS	.						60	68	65					19																	36229181		2182	4290	6472	SO:0001630	splice_region_variant	8085	exon37			CCCTGCAGGGCAT	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.7873-1A>G	chr19.hg19:g.36229181A>G		56.0	0.0	.		36.0	15.0	.	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Splice_Site	SNP	ENST00000222270.7	hg19	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	A	12.28	1.890467	0.33348	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	.	.	.	5.42	5.42	0.78866	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4398	0.67309	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AD000671.1	40921021	1.000000	0.71417	0.916000	0.36221	0.245000	0.25701	9.339000	0.96797	2.063000	0.61619	0.379000	0.24179	.	.	.	.	none		0.602	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	Intron	G	36229181	A	G	36229181	5	3	65	1	0	0	0	0	0	0	1	0	9630	202	7	3	8017	3	MLL4	19	36229181	Splice_Site	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10	25618615	36229181	22899802	36	4331											
COL9A3	1299	hgsc.bcm.edu	37	chr20	61467549	61467549	+	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	tcctctgcagtctggcagtcGaggggagctgggccccaaag	7	7	15	12	1	2	0	0	0	2	0	4	2	3	1	3	4	2	3	3	4	1	0			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr20:61467549G>T	ENST00000343916.3	+	28	1415	c.1412G>T	c.(1411-1413)cGa>cTa	p.R471L	COL9A3_ENST00000462700.1_3'UTR	NM_001853.3	NP_001844.3	Q14050	CO9A3_HUMAN	collagen, type IX, alpha 3	471	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)					TCTGGCAGTCGAGGGGAGCTG	0.716																																					p.R471L		Atlas-SNP	.											.	COL9A3	70	.	0			c.G1412T						PASS	.						18	24	22					20																	61467549		2201	4297	6498	SO:0001583	missense	1299	exon28			GCAGTCGAGGGGA	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.1412G>T	chr20.hg19:g.61467549G>T	ENSP00000341640:p.Arg471Leu	82.0	0.0	.		81.0	22.0	.	NM_001853	Q13681|Q9H4G9|Q9UPE2	Missense_Mutation	SNP	ENST00000343916.3	hg19	CCDS13505.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.448038	0.84101	.	.	ENSG00000092758	ENST00000343916	D	0.93712	-3.27	4.63	4.63	0.57726	.	0.283555	0.33127	N	0.005250	D	0.95367	0.8496	L	0.53729	1.69	0.46241	D	0.998947	D	0.89917	1.0	D	0.73380	0.98	D	0.94429	0.7648	10	0.32370	T	0.25	.	17.4821	0.87675	0.0:0.0:1.0:0.0	.	471	Q14050	CO9A3_HUMAN	L	471	ENSP00000341640:R471L	ENSP00000341640:R471L	R	+	2	0	COL9A3	60937994	1.000000	0.71417	0.984000	0.44739	0.994000	0.84299	7.254000	0.78329	2.117000	0.64856	0.561000	0.74099	CGA	.	.	.	none		0.716	COL9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080071.2	NM_001853		T	61467549	G	T	61467549	3	4	65	1	0	0	0	0	1	0	0	0	3711	1058	37	4	1522	4	COL9A3	20	61467549	Missense_Mutation	SNP	G	TCGA-A4-A5XZ-01A-11D-A31X-10		61467549	1557971	37	4332											
C22orf25	128989	hgsc.bcm.edu	37	chr22	20030918	20030918	+	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	gggatgaattctacagccgaCcctccaagttagctgacttc	10	10	9	12	1	1	2	0	2	1	0	3	4	2	3	3	1	3	2	3	1	4	4	rs551072560		TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chr22:20030918C>T	ENST00000327374.4	+	3	275	c.97C>T	c.(97-99)Ccc>Tcc	p.P33S	TANGO2_ENST00000401833.1_Missense_Mutation_p.P74S|TANGO2_ENST00000398042.2_Missense_Mutation_p.P33S|TANGO2_ENST00000434570.2_Missense_Mutation_p.P74S|TANGO2_ENST00000456048.1_Missense_Mutation_p.P38S|TANGO2_ENST00000432883.1_Missense_Mutation_p.P33S|TANGO2_ENST00000447208.2_Missense_Mutation_p.P33S|TANGO2_ENST00000420290.2_5'UTR|TANGO2_ENST00000401886.1_Missense_Mutation_p.P33S|TANGO2_ENST00000479679.1_3'UTR	NM_001283106.1|NM_001283116.1|NM_001283148.1|NM_001283154.1|NM_152906.4	NP_001270035.1|NP_001270045.1|NP_001270077.1|NP_001270083.1|NP_690870.3	Q6ICL3	TNG2_HUMAN	transport and golgi organization 2 homolog (Drosophila)	33																	CTACAGCCGACCCTCCAAGTT	0.542													C|||	1	0.000199681	8e-04	0	5008	,	,		20269	0		0	False		,,,				2504	0				p.P33S		Atlas-SNP	.											.	TANGO2	4	.	0			c.C97T						PASS	.						139	142	141					22																	20030918		2203	4300	6503	SO:0001583	missense	128989	exon3			AGCCGACCCTCCA		CCDS13772.1, CCDS63404.1, CCDS63405.1, CCDS63406.1, CCDS63407.1, CCDS74821.1, CCDS74822.1	22q11.21	2012-12-13	2012-12-13	2012-12-13	ENSG00000183597	ENSG00000183597			25439	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 25"	C22orf25		12477932	Standard	XM_005261222		Approved	DKFZp761P1121	uc002zrc.1	Q6ICL3	OTTHUMG00000150510	ENST00000327374.4:c.97C>T	chr22.hg19:g.20030918C>T	ENSP00000332721:p.Pro33Ser	75.0	0.0	.		95.0	28.0	.	NM_152906	A8MUE9|B7WNV6|B7Z583|B7Z730|D3DX23|Q8IW05|Q8NAL0|Q8TCS0|Q96M16	Missense_Mutation	SNP	ENST00000327374.4	hg19	CCDS13772.1	.	.	.	.	.	.	.	.	.	.	C	13.72	2.320659	0.41096	.	.	ENSG00000183597	ENST00000401886;ENST00000432198;ENST00000447208;ENST00000398042;ENST00000450664;ENST00000327374;ENST00000432883;ENST00000401833;ENST00000434168;ENST00000434570;ENST00000456048	T;T;T;T;T;T;T;T;T;T;T	0.25414	1.8;1.8;1.8;1.8;1.8;1.8;1.8;1.8;1.8;1.8;1.8	4.89	3.87	0.44632	.	0.174725	0.50627	D	0.000101	T	0.57169	0.2035	M	0.92412	3.305	0.80722	D	1	D;D;D;D;D;D;D	0.76494	0.999;0.999;0.994;0.999;0.999;0.999;0.991	D;D;D;D;D;D;D	0.74674	0.984;0.984;0.932;0.984;0.984;0.975;0.933	T	0.66456	-0.5919	10	0.72032	D	0.01	-12.9932	11.3355	0.49500	0.0:0.9094:0.0:0.0906	.	33;74;33;74;33;33;33	B7Z9Q5;B7Z730;B7Z4A5;B7WNV6;Q6AHY1;Q6ICL3;Q6ICL3-2	.;.;.;.;.;CV025_HUMAN;.	S	33;33;33;33;33;33;33;74;33;74;38	ENSP00000385662:P33S;ENSP00000413850:P33S;ENSP00000389797:P33S;ENSP00000381122:P33S;ENSP00000415450:P33S;ENSP00000332721:P33S;ENSP00000402926:P33S;ENSP00000384827:P74S;ENSP00000411602:P33S;ENSP00000391262:P74S;ENSP00000403645:P38S	ENSP00000332721:P33S	P	+	1	0	C22orf25	18410918	1.000000	0.71417	0.061000	0.19648	0.149000	0.21700	4.652000	0.61454	1.197000	0.43143	-0.258000	0.10820	CCC	.	.	.	none		0.542	TANGO2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318689.2	NM_152906		T	20030918	C	T	20030918	3	4	65	1	0	0	0	0	1	0	0	0	2141	507	18	2	103	2	C22orf25	22	20030918	Missense_Mutation	SNP	C	TCGA-A4-A5XZ-01A-11D-A31X-10		20030918	31273648	38	4333											
BCOR	54880	hgsc.bcm.edu	37	chrX	39932148	39932148	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtttggacacgtttgtgtcAgttttagcatctggttcttc	5	18	11	7	1	3	0	1	0	2	0	4	1	3	1	0	3	1	5	0	3	1	6			TCGA-A4-A5XZ-01A-11D-A31X-10	TCGA-A4-A5XZ-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	363096af-a78b-4834-a631-bebac9ce1659	9f1e35f9-8141-463b-a1b9-3fc7a83df607	g.chrX:39932148A>G	ENST00000378444.4	-	4	2679	c.2451T>C	c.(2449-2451)acT>acC	p.T817T	BCOR_ENST00000378455.4_Silent_p.T817T|BCOR_ENST00000342274.4_Silent_p.T817T|BCOR_ENST00000397354.3_Silent_p.T817T	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	817					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						CGTTTGTGTCAGTTTTAGCAT	0.547			"F, N, S, T"	RARA	"retinoblastoma, AML, APL(translocation)"		oculo-facio-cardio-dental genetic																														p.T817T		Atlas-SNP	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	0			c.T2451C						PASS	.						89	87	88					X																	39932148		2202	4300	6502	SO:0001819	synonymous_variant	54880	exon4			TGTGTCAGTTTTA	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.2451T>C	chrX.hg19:g.39932148A>G		97.0	0.0	.		72.0	36.0	.	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Silent	SNP	ENST00000378444.4	hg19	CCDS48093.1																																																																																			.	.	.	none		0.547	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		G	39932148	A	G	39932148	2	3	65	1	0	0	0	0	0	0	0	1	1386	175	7	3		3	BCOR	23	39932148	Silent	SNP	A	TCGA-A4-A5XZ-01A-11D-A31X-10		39932148	115338412	39	4334											
H6PD	9563	hgsc.bcm.edu	37	chr1	9305536	9305536	+	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	ccctttggccatgaccacttCtcagcccagcagctggccac	7	8	8	18	0	1	1	1	1	1	0	2	1	1	1	5	2	3	2	5	2	0	2	rs375431974		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr1:9305536C>T	ENST00000377403.2	+	2	845	c.543C>T	c.(541-543)ttC>ttT	p.F181F	H6PD_ENST00000602477.1_Silent_p.F192F	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	181	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)		ATGACCACTTCTCAGCCCAGC	0.587																																					p.F181F		Atlas-SNP	.											.	H6PD	71	.	0			c.C543T						PASS	.						47	52	50					1																	9305536		2203	4300	6503	SO:0001819	synonymous_variant	9563	exon2			CCACTTCTCAGCC	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.543C>T	chr1.hg19:g.9305536C>T		108.0	0.0	.		101.0	39.0	.	NM_004285	Q4TT33|Q66I35|Q68DT3	Silent	SNP	ENST00000377403.2	hg19	CCDS101.1																																																																																			.	.	.	none		0.587	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285		T	9305536	C	T	9305536	2	4	66	1	0	0	0	0	0	0	0	1	6943	912	32	2		2	H6PD	1	9305536	Silent	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10		9305536	239945085	1	4335											
KANK4	163782	hgsc.bcm.edu	37	chr1	62740357	62740358	+	Frame_Shift_Del	DEL	AA	AA	-																															cctctggctcagcagcttccAactgtctggtggcctctgcc																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr1:62740357_62740358delAA	ENST00000371153.4	-	3	796_797	c.418_419delTT	c.(418-420)ttgfs	p.L140fs	KANK4_ENST00000354381.3_Intron|KANK4_ENST00000371150.1_5'Flank	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	140						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						AGCAGCTTCCAACTGTCTGGTG	0.604																																					p.140_140del		Pindel	.											.	KANK4	135	.	0			c.419_420del						PASS	.																																			SO:0001589	frameshift_variant	163782	exon3			.	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.418_419delTT	chr1.hg19:g.62740357_62740358delAA	ENSP00000360195:p.Leu140fs	51.0	0.0	.		62.0	15.0	0.242	NM_181712	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Frame_Shift_Del	DEL	ENST00000371153.4	hg19	CCDS620.1																																																																																			.	.	.	none		0.604	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712		-	62740358	AA	-	62740357	7	5	66	1	0	1	0	1	0	0	0	0	7986	131	5	0	2600	0	KANK4	1	62740357	Frame_Shift_Del	DEL	AA	TCGA-A4-A5Y0-01A-11D-A31X-10	53434821	62740357	186510264	2	4336											
RABGGTB	5876	hgsc.bcm.edu	37	chr1	76253203	76253203	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcactccacagaaggatgttAttatcaagtcagatgcaccg	13	9	9	10	1	2	2	2	0	0	2	3	3	3	3	2	1	1	3	2	1	4	2			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr1:76253203A>G	ENST00000319942.3	+	2	96	c.25A>G	c.(25-27)Att>Gtt	p.I9V	SNORD45A_ENST00000384512.1_RNA|RABGGTB_ENST00000496055.1_3'UTR|SNORD45B_ENST00000364617.1_RNA|SNORD45C_ENST00000383893.1_RNA|RABGGTB_ENST00000370826.3_Missense_Mutation_p.I9V|RABGGTB_ENST00000535300.1_5'UTR	NM_004582.3	NP_004573.2	P53611	PGTB2_HUMAN	Rab geranylgeranyltransferase, beta subunit	9					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						GAAGGATGTTATTATCAAGTC	0.368																																					p.I9V		Atlas-SNP	.											.	RABGGTB	37	.	0			c.A25G						PASS	.						147	134	139					1																	76253203		2203	4300	6503	SO:0001583	missense	5876	exon2			GATGTTATTATCA	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.25A>G	chr1.hg19:g.76253203A>G	ENSP00000317473:p.Ile9Val	127.0	0.0	.		162.0	72.0	.	NM_004582	Q92697	Missense_Mutation	SNP	ENST00000319942.3	hg19	CCDS669.1	.	.	.	.	.	.	.	.	.	.	A	9.952	1.220540	0.22457	.	.	ENSG00000137955	ENST00000319942;ENST00000370824;ENST00000370826	.	.	.	5.05	0.547	0.17202	.	0.830524	0.11309	N	0.577349	T	0.07683	0.0193	N	0.05199	-0.095	0.18873	N	0.999984	B	0.02656	0.0	B	0.01281	0.0	T	0.39292	-0.9621	9	0.29301	T	0.29	-8.2035	10.2082	0.43126	0.5747:0.0:0.4253:0.0	.	9	P53611	PGTB2_HUMAN	V	9	.	ENSP00000317473:I9V	I	+	1	0	RABGGTB	76025791	0.001000	0.12720	0.210000	0.23637	0.847000	0.48162	0.335000	0.19806	0.044000	0.15775	0.533000	0.62120	ATT	.	.	.	none		0.368	RABGGTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026972.1	NM_004582		G	76253203	A	G	76253203	3	3	66	1	0	0	0	0	1	0	0	0	12981	449	16	3	31	3	RABGGTB	1	76253203	Missense_Mutation	SNP	A	TCGA-A4-A5Y0-01A-11D-A31X-10	13512846	76253203	172997418	3	4337											
OVGP1	5016	hgsc.bcm.edu	37	chr1	111957940	111957940	+	Missense_Mutation	SNP	A	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	cacagcagatgacagccaaaAttgtggtaaagaagttgaac	17	7	10	7	0	0	4	0	2	0	2	0	4	0	4	1	1	3	3	1	1	6	3			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr1:111957940A>C	ENST00000369732.3	-	11	1238	c.1183T>G	c.(1183-1185)Ttt>Gtt	p.F395V	OVGP1_ENST00000540696.1_3'UTR	NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	395					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)		GACAGCCAAAATTGTGGTAAA	0.433																																					p.F395V		Atlas-SNP	.											.	OVGP1	177	.	0			c.T1183G						PASS	.						48	46	47					1																	111957940		2203	4300	6503	SO:0001583	missense	5016	exon11			GCCAAAATTGTGG	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.1183T>G	chr1.hg19:g.111957940A>C	ENSP00000358747:p.Phe395Val	91.0	0.0	.		98.0	38.0	.	NM_002557	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	hg19	CCDS834.1	.	.	.	.	.	.	.	.	.	.	A	11.95	1.791958	0.31685	.	.	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000434331	T	0.03860	3.78	4.43	0.705	0.18127	.	0.784649	0.10922	N	0.619328	T	0.00875	0.0029	L	0.36672	1.1	0.09310	N	1	B;P	0.39831	0.105;0.69	B;B	0.29598	0.014;0.104	T	0.47623	-0.9103	10	0.22109	T	0.4	-2.4013	3.3373	0.07106	0.5411:0.0:0.0994:0.3595	.	395;459	Q12889;Q59HH5	OVGP1_HUMAN;.	V	395;459;203	ENSP00000358747:F395V	ENSP00000358743:F459V	F	-	1	0	OVGP1	111759463	0.000000	0.05858	0.000000	0.03702	0.103000	0.19146	0.154000	0.16343	0.097000	0.17492	0.477000	0.44152	TTT	.	.	.	none		0.433	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557		C	111957940	A	C	111957940	3	2	66	1	0	0	0	0	1	0	0	0	11332	101	4	5	857	5	OVGP1	1	111957940	Missense_Mutation	SNP	A	TCGA-A4-A5Y0-01A-11D-A31X-10	35704737	111957940	137292681	4	4338											
CCT3	7203	hgsc.bcm.edu	37	chr1	156294858	156294858	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctgctccaggaagtgctcAgctacagacagcatttcccc	9	9	9	14	0	1	1	1	0	0	1	3	2	3	2	3	1	6	5	3	1	2	2			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr1:156294858A>G	ENST00000295688.3	-	6	607	c.327T>C	c.(325-327)gcT>gcC	p.A109A	CCT3_ENST00000368261.3_Silent_p.A64A|CCT3_ENST00000472765.2_Silent_p.A64A|CCT3_ENST00000368259.2_Silent_p.A71A	NM_005998.4	NP_005989.3	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 (gamma)	109					'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)					GGAAGTGCTCAGCTACAGACA	0.413																																					p.A109A		Atlas-SNP	.											.	CCT3	61	.	0			c.T327C						PASS	.						92	84	87					1																	156294858		2203	4300	6503	SO:0001819	synonymous_variant	7203	exon6			GTGCTCAGCTACA	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.327T>C	chr1.hg19:g.156294858A>G		30.0	0.0	.		36.0	17.0	.	NM_005998	A6NE14|Q5SZY1|Q9BR64	Silent	SNP	ENST00000295688.3	hg19	CCDS1140.2																																																																																			.	.	.	none		0.413	CCT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060602.3	NM_005998		G	156294858	A	G	156294858	2	3	66	1	0	0	0	0	0	0	0	1	2956	175	7	3		3	CCT3	1	156294858	Silent	SNP	A	TCGA-A4-A5Y0-01A-11D-A31X-10	44336918	156294858	92955763	5	4339											
HHIPL2	79802	hgsc.bcm.edu	37	chr1	222705394	222705394	+	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	aggacgtggtgctgcccaggCaaagatcctgcttcttccat	8	10	11	12	1	1	1	0	0	1	1	3	2	3	2	3	3	3	3	3	3	1	2			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr1:222705394C>T	ENST00000343410.6	-	6	1695	c.1637G>A	c.(1636-1638)tGc>tAc	p.C546Y		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	546					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)		GCTGCCCAGGCAAAGATCCTG	0.428																																					p.C546Y		Atlas-SNP	.											.	HHIPL2	122	.	0			c.G1637A						PASS	.						87	87	87					1																	222705394		2203	4300	6503	SO:0001583	missense	79802	exon6			CCCAGGCAAAGAT	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.1637G>A	chr1.hg19:g.222705394C>T	ENSP00000342118:p.Cys546Tyr	56.0	0.0	.		65.0	31.0	.	NM_024746	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Missense_Mutation	SNP	ENST00000343410.6	hg19	CCDS1530.2	.	.	.	.	.	.	.	.	.	.	C	22.9	4.343683	0.82022	.	.	ENSG00000143512	ENST00000343410	T	0.13307	2.6	5.0	5.0	0.66597	Soluble quinoprotein glucose/sorbosone dehydrogenase (1);Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.47600	0.1454	M	0.91510	3.215	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.58532	-0.7620	10	0.51188	T	0.08	-17.4954	17.9254	0.88982	0.0:1.0:0.0:0.0	.	546	Q6UWX4	HIPL2_HUMAN	Y	546	ENSP00000342118:C546Y	ENSP00000342118:C546Y	C	-	2	0	HHIPL2	220772017	1.000000	0.71417	0.980000	0.43619	0.936000	0.57629	5.693000	0.68264	2.304000	0.77564	0.591000	0.81541	TGC	.	.	.	none		0.428	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746		T	222705394	C	T	222705394	3	4	66	1	0	0	0	0	1	0	0	0	7101	710	25	2	553	2	HHIPL2	1	222705394	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	66410536	222705394	26545227	6	4340											
C1orf95	375057	hgsc.bcm.edu	37	chr1	226784625	226784625	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaaatcctcactgccatcGtcatggtgggctggatcatg	8	11	10	12	1	3	0	3	0	0	0	6	1	5	1	3	3	1	1	3	3	1	0	rs531129279		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr1:226784625G>A	ENST00000366788.3	+	2	430	c.325G>A	c.(325-327)Gtc>Atc	p.V109I	C1orf95_ENST00000366789.4_Missense_Mutation_p.V109I	NM_001003665.3	NP_001003665.1	Q69YW2	STUM_HUMAN	chromosome 1 open reading frame 95	109						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)		CACTGCCATCGTCATGGTGGG	0.612													G|||	1	0.000199681	8e-04	0	5008	,	,		22256	0		0	False		,,,				2504	0				p.V109I		Atlas-SNP	.											.	C1orf95	16	.	0			c.G325A						PASS	.						167	143	151					1																	226784625		2203	4300	6503	SO:0001583	missense	375057	exon2			GCCATCGTCATGG	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.325G>A	chr1.hg19:g.226784625G>A	ENSP00000355752:p.Val109Ile	84.0	0.0	.		91.0	38.0	.	NM_001003665	A6NGL2	Missense_Mutation	SNP	ENST00000366788.3	hg19	CCDS31044.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.469818	0.43839	.	.	ENSG00000203685	ENST00000366788;ENST00000366789	.	.	.	5.82	5.82	0.92795	.	0.154593	0.43919	D	0.000509	T	0.34658	0.0905	N	0.03324	-0.35	0.38912	D	0.957563	B	0.24368	0.102	B	0.17979	0.02	T	0.34825	-0.9813	9	0.08599	T	0.76	1.3905	19.6956	0.96023	0.0:0.0:1.0:0.0	.	109	Q69YW2	CA095_HUMAN	I	109	.	ENSP00000355752:V109I	V	+	1	0	C1orf95	224851248	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.144000	0.71762	2.756000	0.94617	0.561000	0.74099	GTC	.	.	.	none		0.612	C1orf95-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091634.1	NM_001003665		A	226784625	G	A	226784625	3	1	66	1	0	0	0	0	1	0	0	0	2074	1145	40	1	331	1	C1orf95	1	226784625	Missense_Mutation	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10	4079231	226784625	22465996	7	4341											
ZNF804A	91752	hgsc.bcm.edu	37	chr2	185802210	185802211	+	Missense_Mutation	DNP	AC	AC	CA																															taaaaaccactgtaaaaagaAcacaatacttttaaatggac																								rs5836928|rs3046266	byFrequency	TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr2:185802210_185802211AC>CA	ENST00000302277.6	+	4	2681_2682	c.2087_2088AC>CA	c.(2086-2088)aAC>aCA	p.N696T		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	696							metal ion binding (GO:0046872)	p.N696K(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						TGTAAAAAGAACACAATACTTT	0.292																																					p.N696T|p.N696K		Atlas-SNP	.											.|ZNF804A,NS,carcinoma,0,1	ZNF804A	322	.	1	Substitution - Missense(1)	ovary(1)	c.A2087C|c.C2088A						PASS	.																																			SO:0001583	missense	91752	exon4			AAAAGAACACAAT|AAAGAACACAATA	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	Exception_encountered	chr2.hg19:g.185802210_185802211delinsCA	ENSP00000303252:p.Asn696Thr	135.0|137.0	0.0	.		570.0	24.0|32.0	.	NM_194250	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	hg19	CCDS2291.1																																																																																			.	.	.	none		0.292	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		CA	185802211	AC	CA	185802210	3	2	66	1	0	0	0	0	1	0	0	0	18182	43	2	5	2101	5	ZNF804A	2	185802210	Missense_Mutation	DNP	AC	TCGA-A4-A5Y0-01A-11D-A31X-10		185802210	57397163	8	4342	50	2									
ZNF804A	91752	hgsc.bcm.edu	37	chr2	185802216	185802216	+	Missense_Mutation	SNP	T	T	C																															ccactgtaaaaagaacacaaTacttttaaatggacaatcaa																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr2:185802216T>C	ENST00000302277.6	+	4	2687	c.2093T>C	c.(2092-2094)aTa>aCa	p.I698T		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	698							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						AAGAACACAATACTTTTAAAT	0.294																																					p.I698T		Atlas-SNP	.											.	ZNF804A	322	.	0			c.T2093C						PASS	.						73	67	69					2																	185802216		2194	4291	6485	SO:0001583	missense	91752	exon4			ACACAATACTTTT	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.2093T>C	chr2.hg19:g.185802216T>C	ENSP00000303252:p.Ile698Thr	137.0	0.0	.		569.0	30.0	.	NM_194250	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	hg19	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	T	3.795	-0.042847	0.07452	.	.	ENSG00000170396	ENST00000302277	T	0.05258	3.47	5.63	0.374	0.16183	.	1.826620	0.02817	N	0.125135	T	0.04227	0.0117	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40776	-0.9545	10	0.27082	T	0.32	-0.3078	8.4113	0.32644	0.0:0.5963:0.0:0.4037	.	698	Q7Z570	Z804A_HUMAN	T	698	ENSP00000303252:I698T	ENSP00000303252:I698T	I	+	2	0	ZNF804A	185510461	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	0.483000	0.22292	0.077000	0.16863	0.533000	0.62120	ATA	.	.	.	none		0.294	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		C	185802216	T	C	185802216	3	2	66	1	0	0	0	0	1	0	0	0	18182	1406	49	3	2107	3	ZNF804A	2	185802216	Missense_Mutation	SNP	T	TCGA-A4-A5Y0-01A-11D-A31X-10	6	185802216	57397157	9	4343	50	2									
CUL3	8452	hgsc.bcm.edu	37	chr2	225362540	225362540	+	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	gatgctggagtgtgagctgtCgaccactgtgtttggctaag	7	12	15	7	1	0	1	0	1	0	0	1	4	0	2	1	2	2	4	1	2	1	2			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr2:225362540C>G	ENST00000264414.4	-	12	1975	c.1637G>C	c.(1636-1638)cGa>cCa	p.R546P	CUL3_ENST00000344951.4_Missense_Mutation_p.R480P|CUL3_ENST00000409777.1_Missense_Mutation_p.R522P|CUL3_ENST00000409096.1_Missense_Mutation_p.R522P	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	546					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)		TGTGAGCTGTCGACCACTGTG	0.353																																					p.R552P		Atlas-SNP	.											CUL3,NS,adenocarcinoma,0,1	CUL3	96	.	0			c.G1655C						PASS	.						150	140	143					2																	225362540		2203	4300	6503	SO:0001583	missense	8452	exon12			AGCTGTCGACCAC	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.1637G>C	chr2.hg19:g.225362540C>G	ENSP00000264414:p.Arg546Pro	122.0	0.0	.		52.0	48.0	.	NM_001257198	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Missense_Mutation	SNP	ENST00000264414.4	hg19	CCDS2462.1	.	.	.	.	.	.	.	.	.	.	C	34	5.352209	0.95830	.	.	ENSG00000036257	ENST00000264414;ENST00000344951;ENST00000409096;ENST00000409777	D;D;D;D	0.87887	-2.31;-2.31;-2.31;-2.31	6.16	6.16	0.99307	Cullin, N-terminal (1);Cullin homology (3);	0.000000	0.85682	D	0.000000	D	0.96719	0.8929	H	0.98276	4.19	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	0.97283	0.9919	10	0.87932	D	0	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	480;524;546	Q13618-3;Q53S54;Q13618	.;.;CUL3_HUMAN	P	546;480;522;522	ENSP00000264414:R546P;ENSP00000343601:R480P;ENSP00000387200:R522P;ENSP00000386525:R522P	ENSP00000264414:R546P	R	-	2	0	CUL3	225070784	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	7.802000	0.85969	2.937000	0.99478	0.650000	0.86243	CGA	.	.	.	none		0.353	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2			G	225362540	C	G	225362540	3	3	66	1	0	0	0	0	1	0	0	0	4058	884	31	4	689	4	CUL3	2	225362540	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	39560324	225362540	17836833	10	4344											
ULK4	54986	hgsc.bcm.edu	37	chr3	41795965	41795965	+	Frame_Shift_Del	DEL	T	T	-																															gctgtcaagtaaacggataaTtgtggagacaaaaccctgta																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr3:41795965delT	ENST00000301831.4	-	22	2671	c.2209delA	c.(2209-2211)attfs	p.I738fs		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	738					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)		AAACGGATAATTGTGGAGACA	0.358																																					p.I737fs		Pindel	.											.	ULK4	150	.	0			c.2210delT						PASS	.						82	79	80					3																	41795965		1820	4081	5901	SO:0001589	frameshift_variant	54986	exon22			.	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.2209delA	chr3.hg19:g.41795965delT	ENSP00000301831:p.Ile738fs	106.0	0.0	.		123.0	42.0	0.341	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Frame_Shift_Del	DEL	ENST00000301831.4	hg19	CCDS43071.1																																																																																			.	.	.	none		0.358	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989		-	41795965	T	-	41795965	7	5	66	1	0	1	0	1	0	0	0	0	16990	1493	52	0	1682	0	ULK4	3	41795965	Frame_Shift_Del	DEL	T	TCGA-A4-A5Y0-01A-11D-A31X-10		41795965	156226465	11	4345											
CISH	1154	hgsc.bcm.edu	37	chr3	50645901	50645901	+	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	tctgtctgggctggggtaccCtctgccacctcctcgaggaa	5	10	12	14	1	3	0	0	0	3	0	5	2	4	1	4	4	2	2	4	4	2	1			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr3:50645901C>A	ENST00000348721.3	-	2	324	c.144G>T	c.(142-144)gaG>gaT	p.E48D	CISH_ENST00000443053.2_Missense_Mutation_p.E65D	NM_145071.2	NP_659508.1	Q9NSE2	CISH_HUMAN	cytokine inducible SH2-containing protein	48					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)		CTGGGGTACCCTCTGCCACCT	0.642																																					p.E65D		Atlas-SNP	.											.	CISH	27	.	0			c.G195T						PASS	.						54	49	51					3																	50645901		2203	4300	6503	SO:0001583	missense	1154	exon3			GGTACCCTCTGCC	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.144G>T	chr3.hg19:g.50645901C>A	ENSP00000294173:p.Glu48Asp	64.0	0.0	.		49.0	28.0	.	NM_013324	B2R9N1|G5E9R1|Q9NS38|Q9Y5R1	Missense_Mutation	SNP	ENST00000348721.3	hg19	CCDS2831.1	.	.	.	.	.	.	.	.	.	.	C	7.873	0.728634	0.15507	.	.	ENSG00000114737	ENST00000443053;ENST00000348721	T;T	0.47177	0.85;0.87	6.03	2.26	0.28386	.	0.367420	0.28209	N	0.016181	T	0.35885	0.0947	L	0.57536	1.79	0.28436	N	0.917019	B;B	0.28082	0.2;0.048	B;B	0.23574	0.047;0.012	T	0.21690	-1.0238	10	0.14656	T	0.56	-8.0475	6.8677	0.24102	0.0:0.587:0.119:0.294	.	65;48	G5E9R1;Q9NSE2	.;CISH_HUMAN	D	65;48	ENSP00000409346:E65D;ENSP00000294173:E48D	ENSP00000294173:E48D	E	-	3	2	CISH	50620905	0.991000	0.36638	1.000000	0.80357	0.071000	0.16799	0.437000	0.21543	0.441000	0.26529	-0.150000	0.13652	GAG	.	.	.	none		0.642	CISH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346245.1	NM_145071		A	50645901	C	A	50645901	3	1	66	1	0	0	0	0	1	0	0	0	3439	680	24	4	640	4	CISH	3	50645901	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	8849936	50645901	147376529	12	4346											
DNAH1	25981	hgsc.bcm.edu	37	chr3	52380547	52380547	+	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	aaggtggccatgcgcagcagCctgcgcgacatgagcaaggg	10	4	16	11	3	0	1	0	1	0	0	0	2	0	1	2	3	5	3	2	3	2	0			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr3:52380547C>A	ENST00000420323.2	+	11	1977	c.1716C>A	c.(1714-1716)agC>agA	p.S572R		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	572	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)		TGCGCAGCAGCCTGCGCGACA	0.572																																					p.S572R		Atlas-SNP	.											.	DNAH1	534	.	0			c.C1716A						PASS	.						55	57	56					3																	52380547		2141	4243	6384	SO:0001583	missense	25981	exon11			CAGCAGCCTGCGC	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.1716C>A	chr3.hg19:g.52380547C>A	ENSP00000401514:p.Ser572Arg	36.0	0.0	.		42.0	11.0	.	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	hg19	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	C	16.45	3.127059	0.56721	.	.	ENSG00000114841	ENST00000420323	T	0.24350	1.86	4.53	4.53	0.55603	.	0.443881	0.19011	N	0.125064	T	0.34513	0.0900	M	0.72894	2.215	0.39055	D	0.960409	P;P	0.45957	0.713;0.869	B;P	0.47981	0.434;0.563	T	0.15263	-1.0443	10	0.23302	T	0.38	.	11.8369	0.52330	0.0:0.9149:0.0:0.0851	.	572;572	C9JXH6;Q9P2D7-3	.;.	R	572	ENSP00000401514:S572R	ENSP00000401514:S572R	S	+	3	2	DNAH1	52355587	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	2.033000	0.41136	2.085000	0.62840	0.563000	0.77884	AGC	.	.	.	none		0.572	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		A	52380547	C	A	52380547	3	1	66	1	0	0	0	0	1	0	0	0	4599	738	26	4	1754	4	DNAH1	3	52380547	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	1734646	52380547	145641883	13	4347											
IL17RB	55540	hgsc.bcm.edu	37	chr3	53886139	53886147	+	In_Frame_Del	DEL	CCCTCTGGT	CCCTCTGGT	-																															ccttccagactcagaccagaCcctctggtggtaaagtaagc																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	CCCTCTGGT	CCCTCTGGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr3:53886139_53886147delCCCTCTGGT	ENST00000288167.3	+	4	349_357	c.340_348delCCCTCTGGT	c.(340-348)ccctctggtdel	p.PSG114del		NM_018725.3	NP_061195.2	Q9NRM6	I17RB_HUMAN	interleukin 17 receptor B	114					cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|regulation of cell growth (GO:0001558)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	cytokine receptor activity (GO:0004896)			breast(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)	13				BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)		TCAGACCAGACCCTCTGGTGGTAAAGTAA	0.478																																					p.113_116del		Atlas-Indel,Pindel	.											.	IL17RB	27	.	0			c.339_347del						PASS	.																																			SO:0001651	inframe_deletion	55540	exon4			.	AF212365	CCDS2874.1	3p21.1	2008-02-05		2003-07-09	ENSG00000056736	ENSG00000056736		"Interleukins and interleukin receptors"	18015	protein-coding gene	gene with protein product		605458	"interleukin 17B receptor"	IL17BR		10749887, 10815801	Standard	NM_018725		Approved	IL17RH1, EVI27, CRL4	uc003dha.3	Q9NRM6	OTTHUMG00000158280	ENST00000288167.3:c.340_348delCCCTCTGGT	chr3.hg19:g.53886139_53886147delCCCTCTGGT	ENSP00000288167:p.Pro114_Gly116del	126.0	0.0	0		103.0	35.0	0.339806	NM_018725	Q9BPZ0|Q9NRL4|Q9NRM5	In_Frame_Del	DEL	ENST00000288167.3	hg19	CCDS2874.1																																																																																			.	.	.	none		0.478	IL17RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350563.1	NM_172234		-	53886147	CCCTCTGGT	-	53886139	7	5	66	1	0	1	0	1	0	0	0	0	7647	507	18	0	354	0	IL17RB	3	53886139	In_Frame_Del	DEL	CCCTCTGGT	TCGA-A4-A5Y0-01A-11D-A31X-10	1505592	53886139	144136291	14	4348											
A4GNT	51146	hgsc.bcm.edu	37	chr3	137849689	137849689	+	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	ttaagtttccctaaacacttActtgattgtaccatgaaaac	14	14	4	9	0	0	2	0	2	0	0	1	2	1	2	2	0	4	2	2	0	7	7			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr3:137849689A>C	ENST00000236709.3	-	2	610		c.e2+1			NM_016161.2	NP_057245.1	Q9UNA3	A4GCT_HUMAN	alpha-1,4-N-acetylglucosaminyltransferase						carbohydrate metabolic process (GO:0005975)|glycoprotein biosynthetic process (GO:0009101)|negative regulation of epithelial cell proliferation (GO:0050680)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylglucosaminyltransferase activity (GO:0008375)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)	16						CTAAACACTTACTTGATTGTA	0.403																																					.		Atlas-SNP	.											.	A4GNT	42	.	0			c.408+2T>G						PASS	.						65	65	65					3																	137849689		2202	4300	6502	SO:0001630	splice_region_variant	51146	exon3			ACACTTACTTGAT	AF141315	CCDS3097.1	3p14.3	2010-12-14			ENSG00000118017	ENSG00000118017			17968	protein-coding gene	gene with protein product						10430883	Standard	NM_016161		Approved	alpha4GnT	uc003ers.2	Q9UNA3	OTTHUMG00000159820	ENST00000236709.3:c.408+1T>G	chr3.hg19:g.137849689A>C		136.0	0.0	.		195.0	96.0	.	NM_016161	Q0VDK1|Q0VDK2	Splice_Site	SNP	ENST00000236709.3	hg19	CCDS3097.1	.	.	.	.	.	.	.	.	.	.	A	13.58	2.279090	0.40294	.	.	ENSG00000118017	ENST00000236709	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4479	0.75248	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	A4GNT	139332379	1.000000	0.71417	0.995000	0.50966	0.387000	0.30353	6.414000	0.73318	2.046000	0.60703	0.454000	0.30748	.	.	.	.	none		0.403	A4GNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357557.1	NM_016161	Intron	C	137849689	A	C	137849689	5	2	66	1	0	0	0	0	0	0	1	0	7	405	14	5	620	5	A4GNT	3	137849689	Splice_Site	SNP	A	TCGA-A4-A5Y0-01A-11D-A31X-10	83963550	137849689	60172741	15	4349											
PRKCI	5584	hgsc.bcm.edu	37	chr3	170020905	170020905	+	Frame_Shift_Del	DEL	A	A	-																															tcttttgatgtctgcagaagAatgtgtctgatcctcatttt																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr3:170020905delA	ENST00000295797.4	+	18	2086	c.1781delA	c.(1780-1782)gaafs	p.E594fs		NM_002740.5	NP_002731.4	P41743	KPCI_HUMAN	protein kinase C, iota	594	AGC-kinase C-terminal.				actin filament organization (GO:0007015)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell junction organization (GO:0045216)|cellular response to insulin stimulus (GO:0032869)|cytoskeleton organization (GO:0007010)|establishment of apical/basal cell polarity (GO:0035089)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|eye photoreceptor cell development (GO:0042462)|Golgi vesicle budding (GO:0048194)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of glucose import (GO:0046326)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein phosphorylation (GO:0006468)|protein targeting to membrane (GO:0006612)|response to interleukin-1 (GO:0070555)|secretion (GO:0046903)|tight junction assembly (GO:0070830)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Schmidt-Lanterman incisure (GO:0043220)	ATP binding (GO:0005524)|phospholipid binding (GO:0005543)|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)|endometrium(5)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	36	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|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;0.197)		Tamoxifen(DB00675)	TCTGCAGAAGAATGTGTCTGA	0.333																																					p.E594fs		Atlas-Indel,Pindel	.											.	PRKCI	82	.	0			c.1780delG						PASS	.						154	140	145					3																	170020905		2203	4300	6503	SO:0001589	frameshift_variant	5584	exon18			.		CCDS3212.2	3q26.3	2008-07-18			ENSG00000163558	ENSG00000163558	2.7.11.13		9404	protein-coding gene	gene with protein product		600539		DXS1179E		7607695, 11978974	Standard	NM_002740		Approved	PKCI	uc003fgs.2	P41743	OTTHUMG00000150214	ENST00000295797.4:c.1781delA	chr3.hg19:g.170020905delA	ENSP00000295797:p.Glu594fs	71.0	0.0	0		86.0	36.0	0.418605	NM_002740	D3DNQ4|Q8WW06	Frame_Shift_Del	DEL	ENST00000295797.4	hg19	CCDS3212.2																																																																																			.	.	.	none		0.333	PRKCI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316866.3	NM_002740		-	170020905	A	-	170020905	7	5	66	1	0	1	0	1	0	0	0	0	12524	246	9	0	1851	0	PRKCI	3	170020905	Frame_Shift_Del	DEL	A	TCGA-A4-A5Y0-01A-11D-A31X-10	32171216	170020905	28001525	16	4350											
WDFY3	23001	hgsc.bcm.edu	37	chr4	85722839	85722839	+	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	ccagagcctgagaggctaatCgttcaaacatccgctgcagg	11	7	11	12	2	1	2	1	1	0	2	3	3	2	2	3	2	3	4	3	2	2	2			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr4:85722839C>A	ENST00000295888.4	-	17	3193	c.2786G>T	c.(2785-2787)cGa>cTa	p.R929L	WDFY3_ENST00000322366.6_Missense_Mutation_p.R929L|WDFY3_ENST00000512267.1_5'Flank|WDFY3-AS1_ENST00000510449.1_RNA	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	929					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)		AGAGGCTAATCGTTCAAACAT	0.493																																					p.R929L		Atlas-SNP	.											.	WDFY3	314	.	0			c.G2786T						PASS	.						109	112	111					4																	85722839		2203	4300	6503	SO:0001583	missense	23001	exon17			GCTAATCGTTCAA	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.2786G>T	chr4.hg19:g.85722839C>A	ENSP00000295888:p.Arg929Leu	24.0	0.0	.		36.0	16.0	.	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	hg19	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.890055	0.91889	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.57107	0.42;0.42	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.73489	0.3593	M	0.73217	2.22	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	T	0.72475	-0.4282	10	0.54805	T	0.06	.	20.4024	0.99000	0.0:1.0:0.0:0.0	.	929	Q8IZQ1	WDFY3_HUMAN	L	929	ENSP00000318466:R929L;ENSP00000295888:R929L	ENSP00000295888:R929L	R	-	2	0	WDFY3	85941863	1.000000	0.71417	0.883000	0.34634	0.737000	0.42083	7.487000	0.81328	2.827000	0.97445	0.650000	0.86243	CGA	.	.	.	none		0.493	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		A	85722839	C	A	85722839	3	1	66	1	0	0	0	0	1	0	0	0	17282	884	31	4	8002	4	WDFY3	4	85722839	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10		85722839	105431437	17	4351											
ADAMTS12	81792	hgsc.bcm.edu	37	chr5	33534943	33534943	+	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	aacccattcacccaccggcaCttttcttgcaggcctgctgg	7	10	8	16	1	2	0	1	0	1	0	2	0	2	0	4	3	3	3	4	3	1	4			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr5:33534943C>A	ENST00000504830.1	-	23	4936	c.4601G>T	c.(4600-4602)aGt>aTt	p.S1534I	ADAMTS12_ENST00000352040.3_Missense_Mutation_p.S1449I	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	1534					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						CCCACCGGCACTTTTCTTGCA	0.433										HNSCC(64;0.19)																											p.S1534I		Atlas-SNP	.											.	ADAMTS12	464	.	0			c.G4601T						PASS	.						130	124	126					5																	33534943		2203	4300	6503	SO:0001583	missense	81792	exon23			CCGGCACTTTTCT	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.4601G>T	chr5.hg19:g.33534943C>A	ENSP00000422554:p.Ser1534Ile	65.0	0.0	.		91.0	44.0	.	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	hg19	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	C	12.52	1.963656	0.34659	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.60548	0.19;0.18	4.98	0.386	0.16254	.	0.588898	0.19280	N	0.118200	T	0.43366	0.1244	L	0.52364	1.645	0.53005	D	0.999961	P;B	0.36837	0.571;0.435	B;B	0.36989	0.238;0.12	T	0.14392	-1.0474	10	0.30854	T	0.27	.	3.6087	0.08052	0.0:0.3846:0.2143:0.401	.	1449;1534	P58397-3;P58397	.;ATS12_HUMAN	I	1534;1449	ENSP00000422554:S1534I;ENSP00000344847:S1449I	ENSP00000344847:S1449I	S	-	2	0	ADAMTS12	33570700	0.000000	0.05858	0.922000	0.36590	0.973000	0.67179	0.033000	0.13754	0.202000	0.20498	0.563000	0.77884	AGT	.	.	.	none		0.433	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		A	33534943	C	A	33534943	3	1	66	1	0	0	0	0	1	0	0	0	257	565	20	4	191	4	ADAMTS12	5	33534943	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10		33534943	147380317	18	4352											
PCDHB14	56122	hgsc.bcm.edu	37	chr5	140605127	140605127	+	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	ccccggcccaggcccaggccGactccctcaccgtctacctg	5	5	9	22	3	2	0	1	0	1	0	3	1	3	0	8	3	1	0	8	3	1	1			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr5:140605127G>A	ENST00000239449.4	+	1	2050	c.2050G>A	c.(2050-2052)Gac>Aac	p.D684N	PCDHB14_ENST00000515856.2_Missense_Mutation_p.D531N	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	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)			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)			GGCCCAGGCCGACTCCCTCAC	0.701																																					p.D684N	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.G2050A						PASS	.						69	77	74					5																	140605127		2187	4284	6471	SO:0001583	missense	56122	exon1			CAGGCCGACTCCC	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.2050G>A	chr5.hg19:g.140605127G>A	ENSP00000239449:p.Asp684Asn	85.0	0.0	.		73.0	5.0	.	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Missense_Mutation	SNP	ENST00000239449.4	hg19	CCDS4256.1	.	.	.	.	.	.	.	.	.	.	-	11.91	1.778390	0.31502	.	.	ENSG00000120327	ENST00000515856;ENST00000239449	T;T	0.52983	0.65;0.64	4.17	4.17	0.49024	.	.	.	.	.	T	0.47135	0.1429	M	0.83483	2.645	0.09310	N	1	P	0.35575	0.51	B	0.30572	0.117	T	0.52540	-0.8562	9	0.59425	D	0.04	.	6.9347	0.24461	0.0935:0.0:0.7321:0.1744	.	684	Q9Y5E9	PCDBE_HUMAN	N	531;684	ENSP00000444518:D531N;ENSP00000239449:D684N	ENSP00000239449:D684N	D	+	1	0	PCDHB14	140585311	0.747000	0.28283	0.039000	0.18376	0.064000	0.16182	2.451000	0.44952	2.022000	0.59522	0.650000	0.86243	GAC	.	.	.	none		0.701	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934		A	140605127	G	A	140605127	3	1	66	1	0	0	0	0	1	0	0	0	11546	1058	37	1	2052	1	PCDHB14	5	140605127	Missense_Mutation	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10	107070184	140605127	40310133	19	4353											
CD83	9308	hgsc.bcm.edu	37	chr6	14133946	14133946	+	Frame_Shift_Del	DEL	C	C	-																															ggagattgtcctgctgctggCtctggttattttctacttaa																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr6:14133946delC	ENST00000379153.3	+	4	620	c.449delC	c.(448-450)gctfs	p.A150fs		NM_001040280.1|NM_001251901.1|NM_004233.3	NP_001035370.1|NP_001238830.1|NP_004224.1	Q01151	CD83_HUMAN	CD83 molecule	150					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)				CTGCTGCTGGCTCTGGTTATT	0.383																																					p.A150fs		Atlas-Indel,Pindel	.											.	CD83	23	.	0			c.448delG						PASS	.						132	132	132					6																	14133946		2203	4300	6503	SO:0001589	frameshift_variant	9308	exon4			.	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.449delC	chr6.hg19:g.14133946delC	ENSP00000368450:p.Ala150fs	73.0	0.0	0		107.0	49.0	0.457944	NM_004233	Q5THX9	Frame_Shift_Del	DEL	ENST00000379153.3	hg19	CCDS4532.1																																																																																			.	.	.	none		0.383	CD83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039916.1			-	14133946	C	-	14133946	7	5	66	1	0	1	0	1	0	0	0	0	3043	797	28	0	463	0	CD83	6	14133946	Frame_Shift_Del	DEL	C	TCGA-A4-A5Y0-01A-11D-A31X-10		14133946	156981121	20	4354											
E2F3	1871	hgsc.bcm.edu	37	chr6	20490451	20490451	+	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	tgctcagtttctatgggaaaCctttctcctctggcctcccc	5	14	7	15	0	4	0	1	0	3	0	6	1	5	1	5	2	2	2	5	2	2	3			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr6:20490451C>G	ENST00000346618.3	+	7	1254	c.1188C>G	c.(1186-1188)aaC>aaG	p.N396K	E2F3_ENST00000535432.1_Missense_Mutation_p.N265K	NM_001949.4	NP_001940.1	O00716	E2F3_HUMAN	E2F transcription factor 3	396	Transactivation. {ECO:0000255}.				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)			CTATGGGAAACCTTTCTCCTC	0.443																																					p.N396K		Atlas-SNP	.											.	E2F3	30	.	0			c.C1188G						PASS	.						72	71	71					6																	20490451		2203	4300	6503	SO:0001583	missense	1871	exon7			GGGAAACCTTTCT	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.1188C>G	chr6.hg19:g.20490451C>G	ENSP00000262904:p.Asn396Lys	83.0	0.0	.		101.0	52.0	.	NM_001949	Q15000|Q68DT0|Q9BZ44	Missense_Mutation	SNP	ENST00000346618.3	hg19	CCDS4545.1	.	.	.	.	.	.	.	.	.	.	C	0.070	-1.205397	0.01568	.	.	ENSG00000112242	ENST00000346618;ENST00000535432	T;T	0.06294	3.32;3.35	5.49	2.71	0.32032	.	0.637186	0.17731	N	0.163882	T	0.00637	0.0021	N	0.08118	0	0.20489	N	0.999892	B	0.15473	0.013	B	0.11329	0.006	T	0.46190	-0.9209	10	0.06236	T	0.91	.	3.2605	0.06846	0.2493:0.5042:0.1104:0.1361	.	396	O00716	E2F3_HUMAN	K	396;265	ENSP00000262904:N396K;ENSP00000443418:N265K	ENSP00000262904:N396K	N	+	3	2	E2F3	20598430	0.274000	0.24191	0.948000	0.38648	0.975000	0.68041	0.955000	0.29188	0.355000	0.24131	-0.224000	0.12420	AAC	.	.	.	none		0.443	E2F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043828.1			G	20490451	C	G	20490451	3	3	66	1	0	0	0	0	1	0	0	0	4870	506	18	4	1214	4	E2F3	6	20490451	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	6356505	20490451	150624616	21	4355											
HLA-A	3105	hgsc.bcm.edu	37	chr6	29910554	29910554	+	Missense_Mutation	SNP	T	T	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	gctcccactccatgaggtatTtcttcacatccgtgtcccgg	6	12	8	15	2	2	1	1	1	1	0	6	1	6	1	4	2	0	2	4	2	1	3			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr6:29910554T>G	ENST00000396634.1	+	4	435	c.94T>G	c.(94-96)Ttc>Gtc	p.F32V	HLA-A_ENST00000376809.5_Missense_Mutation_p.F32V|HLA-A_ENST00000376806.5_Missense_Mutation_p.F32V|HLA-A_ENST00000376802.2_Missense_Mutation_p.F32V			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	32	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						CATGAGGTATTTCTTCACATC	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.F32V		Atlas-SNP	.											.	HLA-A	89	.	0			c.T94G						PASS	.						15	15	15					6																	29910554		2179	4265	6444	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	AGGTATTTCTTCA	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.94T>G	chr6.hg19:g.29910554T>G	ENSP00000379873:p.Phe32Val	109.0	0.0	.		134.0	38.0	.	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	hg19	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	10.84	1.463317	0.26248	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00932	5.53;5.53;5.53;5.53	3.72	2.53	0.30540	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	0.35349	U	0.003271	T	0.03178	0.0093	H	0.96142	3.775	0.09310	N	1	D;D;D;D;D	0.76494	0.999;0.998;0.999;0.998;0.999	D;D;D;D;D	0.91635	0.999;0.998;0.999;0.998;0.999	T	0.29971	-0.9994	10	0.87932	D	0	.	5.839	0.18623	0.0:0.1258:0.0:0.8742	.	32;32;32;32;32	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	V	32	ENSP00000379873:F32V;ENSP00000366002:F32V;ENSP00000366005:F32V;ENSP00000365998:F32V	ENSP00000348012:F32V	F	+	1	0	HLA-A	30018533	0.004000	0.15560	0.034000	0.17996	0.201000	0.24016	0.452000	0.21795	0.620000	0.30215	0.391000	0.25812	TTC	.	.	.	none		0.726	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116		G	29910554	T	G	29910554	3	3	66	1	0	0	0	0	1	0	0	0	7202	1841	64	5	100	5	HLA-A	6	29910554	Missense_Mutation	SNP	T	TCGA-A4-A5Y0-01A-11D-A31X-10	9420103	29910554	141204513	22	4356											
BRD2	6046	hgsc.bcm.edu	37	chr6	32944714	32944714	+	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	tggacctcagcactgtcaagGtacccactgcatggggcaga	10	7	12	12	0	2	1	2	0	0	1	2	2	2	2	2	4	3	4	2	4	2	1			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr6:32944714G>A	ENST00000374825.4	+	7	2901		c.e7+1		BRD2_ENST00000443797.2_Splice_Site|BRD2_ENST00000395287.1_Splice_Site|BRD2_ENST00000374831.4_Splice_Site|BRD2_ENST00000449085.2_Splice_Site|BRD2_ENST00000395289.2_Splice_Site	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2						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)	p.?(1)		central_nervous_system(3)|stomach(2)	5						CACTGTCAAGGTACCCACTGC	0.507																																					.		Atlas-SNP	.											BRD2_ENST00000395289,mouth,carcinoma,0,1	BRD2	70	.	1	Unknown(1)	upper_aerodigestive_tract(1)	c.1200+1G>A						PASS	.						60	64	63					6																	32944714		1472	2670	4142	SO:0001630	splice_region_variant	6046	exon7			GTCAAGGTACCCA	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.1200+1G>A	chr6.hg19:g.32944714G>A		29.0	0.0	.		42.0	21.0	.	NM_005104	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Splice_Site	SNP	ENST00000374825.4	hg19	CCDS4762.1	.	.	.	.	.	.	.	.	.	.	G	17.86	3.493736	0.64186	.	.	ENSG00000204256	ENST00000374825;ENST00000374831;ENST00000395289;ENST00000443797;ENST00000395287;ENST00000449025;ENST00000449085	.	.	.	4.84	4.84	0.62591	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8266	0.78711	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BRD2	33052692	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.592000	0.98245	2.679000	0.91253	0.637000	0.83480	.	.	.	.	none		0.507	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2		Intron	A	32944714	G	A	32944714	5	1	66	1	0	0	0	0	0	0	1	0	1504	1275	44	2	1223	2	BRD2	6	32944714	Splice_Site	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10	3034160	32944714	138170353	23	4357											
ASCC3	10973	hgsc.bcm.edu	37	chr6	101075824	101075824	+	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	gtgatgagataaaatttgttCgagatacaatgacctctaga	15	12	9	5	1	1	5	0	3	1	3	2	7	1	5	1	0	1	1	1	0	5	5			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr6:101075824C>A	ENST00000369162.2	-	28	4759	c.4415G>T	c.(4414-4416)cGa>cTa	p.R1472L		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	1472	Helicase ATP-binding 2. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		AAAATTTGTTCGAGATACAAT	0.393																																					p.R1472L		Atlas-SNP	.											.	ASCC3	205	.	0			c.G4415T						PASS	.						108	105	106					6																	101075824		2203	4300	6503	SO:0001583	missense	10973	exon28			TTTGTTCGAGATA	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.4415G>T	chr6.hg19:g.101075824C>A	ENSP00000358159:p.Arg1472Leu	74.0	0.0	.		69.0	30.0	.	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	hg19	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	C	32	5.124487	0.94429	.	.	ENSG00000112249	ENST00000369162	T	0.14640	2.49	6.17	6.17	0.99709	DEAD-like helicase (2);ATPase, AAA+ type, core (1);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.52224	0.1721	H	0.97516	4.02	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68383	-0.5423	10	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	1472	Q8N3C0	HELC1_HUMAN	L	1472	ENSP00000358159:R1472L	ENSP00000358159:R1472L	R	-	2	0	ASCC3	101182545	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.941000	0.99782	0.655000	0.94253	CGA	.	.	.	none		0.393	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		A	101075824	C	A	101075824	3	1	66	1	0	0	0	0	1	0	0	0	1033	884	31	4	2253	4	ASCC3	6	101075824	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	68131110	101075824	70039243	24	4358											
NRCAM	4897	hgsc.bcm.edu	37	chr7	107807453	107807453	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttgtatgctgttcctggcaTtagaccctttaacccaaaga	10	14	7	10	0	0	2	0	0	0	2	1	2	1	2	3	1	2	4	3	1	4	6			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr7:107807453T>C	ENST00000425651.2	-	27	3378	c.3379A>G	c.(3379-3381)Atg>Gtg	p.M1127V	NRCAM_ENST00000351718.4_Intron|NRCAM_ENST00000413765.2_Intron|NRCAM_ENST00000379024.4_Intron|NRCAM_ENST00000379022.4_Missense_Mutation_p.M1127V|NRCAM_ENST00000379028.3_Missense_Mutation_p.M1127V	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	1127	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						GTTCCTGGCATTAGACCCTTT	0.433																																					p.M1127V		Atlas-SNP	.											.	NRCAM	267	.	0			c.A3379G						PASS	.						76	81	79					7																	107807453		1972	4151	6123	SO:0001583	missense	4897	exon27			CTGGCATTAGACC		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.3379A>G	chr7.hg19:g.107807453T>C	ENSP00000401244:p.Met1127Val	123.0	0.0	.		133.0	50.0	.	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	hg19	CCDS47686.1	.	.	.	.	.	.	.	.	.	.	T	9.859	1.195856	0.22037	.	.	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000425651;ENST00000379022	T;T;T	0.55760	0.5;0.5;0.5	5.67	3.17	0.36434	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.360043	0.35838	N	0.002958	T	0.29945	0.0749	N	0.14661	0.345	0.27571	N	0.949892	B	0.02656	0.0	B	0.01281	0.0	T	0.14531	-1.0469	10	0.14656	T	0.56	.	8.9597	0.35840	0.0:0.0674:0.126:0.8066	.	1127	Q92823	NRCAM_HUMAN	V	1127	ENSP00000368314:M1127V;ENSP00000401244:M1127V;ENSP00000368308:M1127V	ENSP00000368308:M1127V	M	-	1	0	NRCAM	107594689	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.529000	0.60588	1.086000	0.41228	0.523000	0.50628	ATG	.	.	.	none		0.433	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		C	107807453	T	C	107807453	3	2	66	1	0	0	0	0	1	0	0	0	10651	1493	52	3	581	3	NRCAM	7	107807453	Missense_Mutation	SNP	T	TCGA-A4-A5Y0-01A-11D-A31X-10		107807453	51331210	25	4359											
OR6V1	346517	hgsc.bcm.edu	37	chr7	142750247	142750247	+	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	cactctgtgcaagtcaggaaGgtcgtggccttggtgacttc	7	11	13	10	1	2	1	1	1	1	0	4	2	2	2	1	4	1	1	1	4	2	2			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr7:142750247G>C	ENST00000418316.1	+	1	831	c.810G>C	c.(808-810)aaG>aaC	p.K270N		NM_001001667.1	NP_001001667.1	Q8N148	OR6V1_HUMAN	olfactory receptor, family 6, subfamily V, 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)			endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)	20	Melanoma(164;0.059)					AAGTCAGGAAGGTCGTGGCCT	0.507																																					p.K270N		Atlas-SNP	.											.	OR6V1	77	.	0			c.G810C						PASS	.						104	112	110					7																	142750247		2053	4182	6235	SO:0001583	missense	346517	exon1			CAGGAAGGTCGTG		CCDS47728.1	7q34	2014-05-06			ENSG00000225781	ENSG00000225781		"GPCR / Class A : Olfactory receptors"	15090	protein-coding gene	gene with protein product						12732197	Standard	NM_001001667		Approved	GPR138	uc011ksv.2	Q8N148	OTTHUMG00000158385	ENST00000418316.1:c.810G>C	chr7.hg19:g.142750247G>C	ENSP00000396085:p.Lys270Asn	72.0	0.0	.		80.0	41.0	.	NM_001001667	A4D2I0|B9EH48|Q6IF70	Missense_Mutation	SNP	ENST00000418316.1	hg19	CCDS47728.1	.	.	.	.	.	.	.	.	.	.	G	13.01	2.109344	0.37242	.	.	ENSG00000225781	ENST00000418316	T	0.00207	8.55	4.52	4.52	0.55395	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00666	0.0022	M	0.85041	2.73	0.09310	N	1	D	0.89917	1.0	D	0.79784	0.993	T	0.48103	-0.9064	9	0.87932	D	0	.	14.772	0.69688	0.0:0.0:1.0:0.0	.	270	Q8N148	OR6V1_HUMAN	N	270	ENSP00000396085:K270N	ENSP00000396085:K270N	K	+	3	2	OR6V1	142460369	0.000000	0.05858	0.506000	0.27664	0.262000	0.26303	0.085000	0.14912	2.349000	0.79799	0.655000	0.94253	AAG	.	.	.	none		0.507	OR6V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350860.1			C	142750247	G	C	142750247	3	2	66	1	0	0	0	0	1	0	0	0	11218	991	35	4	812	4	OR6V1	7	142750247	Missense_Mutation	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10	34942794	142750247	16388416	26	4360											
SNAI2	6591	hgsc.bcm.edu	37	chr8	49833817	49833817	+	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	gcttcttgaccaggaaggagCgcggcatcttgccagcgggt	7	8	15	11	3	2	1	0	1	2	0	2	3	2	3	2	4	3	2	2	4	1	3			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr8:49833817C>G	ENST00000396822.1	-	2	365	c.8G>C	c.(7-9)cGc>cCc	p.R3P	SNAI2_ENST00000020945.1_Missense_Mutation_p.R3P			O43623	SNAI2_HUMAN	snail family zinc finger 2	3	SNAG domain. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|cartilage morphogenesis (GO:0060536)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to ionizing radiation (GO:0071479)|desmosome disassembly (GO:0035921)|embryo development (GO:0009790)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|epithelium development (GO:0060429)|negative regulation of anoikis (GO:2000811)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell-cell adhesion by negative regulation of transcription from RNA polymerase II promoter (GO:1900387)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of stem cell proliferation (GO:2000647)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|negative regulation of vitamin D receptor signaling pathway (GO:0070563)|neural crest cell development (GO:0014032)|Notch signaling pathway (GO:0007219)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone acetylation (GO:0035066)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of chemokine production (GO:0032642)|regulation of osteoblast differentiation (GO:0045667)|regulation of tight junction assembly (GO:2000810)|sensory perception of sound (GO:0007605)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|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 distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)	18		all_cancers(86;0.0368)|all_epithelial(80;0.000624)|Lung NSC(129;0.0019)|all_lung(136;0.00502)				CAGGAAGGAGCGCGGCATCTT	0.587																																					p.R3P		Atlas-SNP	.											SNAI2,NS,carcinoma,0,1	SNAI2	53	.	0			c.G8C						PASS	.						107	108	107					8																	49833817		2203	4300	6503	SO:0001583	missense	6591	exon1			AAGGAGCGCGGCA	U97060	CCDS6146.1	8q11.21	2013-05-23	2013-05-23	2002-02-28	ENSG00000019549	ENSG00000019549		"Snail homologs", "Zinc fingers, C2H2-type"	11094	protein-coding gene	gene with protein product		602150	"slug homolog, zinc finger protein (chicken)", "snail homolog 2 (Drosophila)"	SLUG		9337409, 9721220	Standard	NM_003068		Approved	SLUGH1, SNAIL2	uc003xqp.3	O43623	OTTHUMG00000149912	ENST00000396822.1:c.8G>C	chr8.hg19:g.49833817C>G	ENSP00000380034:p.Arg3Pro	36.0	0.0	.		38.0	22.0	.	NM_003068	B2R6P6|Q53FC1	Missense_Mutation	SNP	ENST00000396822.1	hg19	CCDS6146.1	.	.	.	.	.	.	.	.	.	.	C	32	5.143242	0.94560	.	.	ENSG00000019549	ENST00000020945;ENST00000396822	T;T	0.19938	2.11;2.11	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.52885	0.1762	M	0.84948	2.725	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.58808	-0.7571	9	.	.	.	-21.1684	18.5472	0.91052	0.0:1.0:0.0:0.0	.	3	O43623	SNAI2_HUMAN	P	3	ENSP00000020945:R3P;ENSP00000380034:R3P	.	R	-	2	0	SNAI2	49996370	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.380000	0.79704	2.377000	0.81083	0.313000	0.20887	CGC	.	.	.	none		0.587	SNAI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313873.2	NM_003068		G	49833817	C	G	49833817	3	3	66	1	0	0	0	0	1	0	0	0	14840	768	27	4	810	4	SNAI2	8	49833817	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10		49833817	96530205	27	4361											
MTSS1	9788	hgsc.bcm.edu	37	chr8	125570101	125570101	+	Frame_Shift_Del	DEL	A	A	-																															acttgataaactatagtgagAaaacccgttagacaactgga																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr8:125570101delA	ENST00000518547.1	-	11	1524	c.1051delT	c.(1051-1053)tctfs	p.S351fs	MTSS1_ENST00000378017.3_Intron|MTSS1_ENST00000325064.5_Frame_Shift_Del_p.S355fs|NDUFB9_ENST00000522532.1_Intron|MTSS1_ENST00000431961.2_Intron|MTSS1_ENST00000354184.4_Intron|MTSS1_ENST00000395508.2_Frame_Shift_Del_p.S125fs|MTSS1_ENST00000523587.1_5'UTR|MTSS1_ENST00000524090.1_Frame_Shift_Del_p.S241fs	NM_001282971.1|NM_014751.4	NP_001269900.1|NP_055566.3	O43312	MTSS1_HUMAN	metastasis suppressor 1	351	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)			CTATAGTGAGAAAACCCGTTA	0.498																																					p.S351fs	Esophageal Squamous(160;622 1893 3862 8546 12509)	Pindel	.											.	MTSS1	79	.	0			c.1052delC						PASS	.						22	23	23					8																	125570101		2196	4297	6493	SO:0001589	frameshift_variant	9788	exon11			.	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.1051delT	chr8.hg19:g.125570101delA	ENSP00000429064:p.Ser351fs	67.0	0.0	.		56.0	17.0	0.304	NM_014751	J3KNK6|Q8TCA2|Q96RX2	Frame_Shift_Del	DEL	ENST00000518547.1	hg19	CCDS6353.1																																																																																			.	.	.	none		0.498	MTSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109625.3	NM_014751		-	125570101	A	-	125570101	7	5	66	1	0	1	0	1	0	0	0	0	9969	246	9	0	1232	0	MTSS1	8	125570101	Frame_Shift_Del	DEL	A	TCGA-A4-A5Y0-01A-11D-A31X-10	75736284	125570101	20793921	28	4362											
RFX3	5991	hgsc.bcm.edu	37	chr9	3301560	3301560	+	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	acttacatggctgttgagaaGagagcttctgtgagtggaca	11	11	13	6	0	1	3	0	2	1	2	1	6	1	4	0	2	2	3	0	2	2	3			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr9:3301560G>A	ENST00000382004.3	-	6	846	c.535C>T	c.(535-537)Ctt>Ttt	p.L179F	RFX3_ENST00000302303.1_Missense_Mutation_p.L179F|RFX3_ENST00000358730.2_Missense_Mutation_p.L179F	NM_001282116.1|NM_134428.1	NP_001269045.1|NP_602304.1	P48380	RFX3_HUMAN	regulatory factor X, 3 (influences HLA class II expression)	179					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)		CTGTTGAGAAGAGAGCTTCTG	0.398																																					p.L179F		Atlas-SNP	.											.	RFX3	156	.	0			c.C535T						PASS	.						157	135	143					9																	3301560		2203	4300	6503	SO:0001583	missense	5991	exon6			TGAGAAGAGAGCT	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.535C>T	chr9.hg19:g.3301560G>A	ENSP00000371434:p.Leu179Phe	75.0	0.0	.		87.0	44.0	.	NM_134428	A8K0H5|D3DRH8|D3DRH9|Q5JTL7|Q5JTL8|Q6NW13|Q8WTU4|Q95HL5|Q95HL6	Missense_Mutation	SNP	ENST00000382004.3	hg19	CCDS6449.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.832324	0.91036	.	.	ENSG00000080298	ENST00000382004;ENST00000358730;ENST00000302303;ENST00000451859	D;D;D;T	0.83075	-1.68;-1.68;-1.68;0.27	5.87	5.87	0.94306	.	0.137392	0.50627	D	0.000106	T	0.75110	0.3805	N	0.02011	-0.69	0.58432	D	0.999994	D;B;D	0.58620	0.983;0.037;0.965	P;B;P	0.55345	0.731;0.037;0.774	T	0.82536	-0.0408	10	0.56958	D	0.05	-9.8293	16.4906	0.84200	0.0:0.0:0.8686:0.1314	.	179;179;179	P48380-3;P48380-2;P48380	.;.;RFX3_HUMAN	F	179	ENSP00000371434:L179F;ENSP00000351574:L179F;ENSP00000303847:L179F;ENSP00000411756:L179F	ENSP00000303847:L179F	L	-	1	0	RFX3	3291560	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.781000	0.95711	0.655000	0.94253	CTT	.	.	.	none		0.398	RFX3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051545.1	NM_002919		A	3301560	G	A	3301560	3	1	66	1	0	0	0	0	1	0	0	0	13277	942	33	2	1922	2	RFX3	9	3301560	Missense_Mutation	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10		3301560	137911871	29	4363											
EXOSC2	23404	hgsc.bcm.edu	37	chr9	133579154	133579154	+	Frame_Shift_Del	DEL	A	A	-																															ccagaggcttttggaacaggAgggataaggaggtgctccag																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr9:133579154delA	ENST00000372358.5	+	9	946	c.875delA	c.(874-876)gagfs	p.E292fs	EXOSC2_ENST00000546165.1_Frame_Shift_Del_p.E266fs|EXOSC2_ENST00000372351.3_Frame_Shift_Del_p.E262fs|EXOSC2_ENST00000372352.3_Frame_Shift_Del_p.E284fs|EXOSC2_ENST00000467138.1_3'UTR			Q13868	EXOS2_HUMAN	exosome component 2	292					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)		TTGGAACAGGAGGGATAAGGA	0.478																																					p.E292fs	Pancreas(134;1683 1824 10118 27928 31640)	Atlas-Indel,Pindel	.											.	EXOSC2	15	.	0			c.874delG						PASS	.						118	127	124					9																	133579154		2203	4300	6503	SO:0001589	frameshift_variant	23404	exon9			.	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.875delA	chr9.hg19:g.133579154delA	ENSP00000361433:p.Glu292fs	67.0	0.0	0		92.0	46.0	0.5	NM_014285	A3KFL3|B4DKK6|Q9NUY4	Frame_Shift_Del	DEL	ENST00000372358.5	hg19	CCDS6935.1																																																																																			.	.	.	none		0.478	EXOSC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054673.1	NM_014285		-	133579154	A	-	133579154	7	5	66	1	0	1	0	1	0	0	0	0	5317	304	11	0	909	0	EXOSC2	9	133579154	Frame_Shift_Del	DEL	A	TCGA-A4-A5Y0-01A-11D-A31X-10	130277594	133579154	7634277	30	4364											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1276776	1276776	+	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	gtgactggcgaggtgcaaccGgtggcctgtgcggtgagtgg	5	8	20	8	3	0	2	0	2	0	0	0	3	0	2	2	6	3	1	2	6	1	0			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr11:1276776G>T	ENST00000529681.1	+	37	16112	c.16054G>T	c.(16054-16056)Ggt>Tgt	p.G5352C	MUC5B_ENST00000447027.1_Missense_Mutation_p.G5355C	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5352					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)		AGGTGCAACCGGTGGCCTGTG	0.746																																					p.G5352C		Atlas-SNP	.											.	MUC5B	473	.	0			c.G16054T						PASS	.						6	7	7					11																	1276776		1853	3899	5752	SO:0001583	missense	727897	exon37			GCAACCGGTGGCC	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.16054G>T	chr11.hg19:g.1276776G>T	ENSP00000436812:p.Gly5352Cys	53.0	0.0	.		62.0	4.0	.	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	hg19	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	g	7.246	0.602241	0.13939	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000546052;ENST00000406844	T;T	0.17054	2.3;2.47	4.01	-2.42	0.06542	.	.	.	.	.	T	0.34513	0.0900	M	0.79475	2.455	0.09310	N	1	D;D	0.76494	0.999;0.999	D;D	0.72338	0.977;0.977	T	0.16012	-1.0417	9	0.87932	D	0	.	5.244	0.15487	0.4649:0.181:0.3541:0.0	.	5689;5355	A7Y9J9;E9PBJ0	.;.	C	5352;5355;5296;251;5064	ENSP00000436812:G5352C;ENSP00000415793:G5355C	ENSP00000343037:G5296C	G	+	1	0	MUC5B	1233352	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-3.094000	0.00607	-0.833000	0.04245	0.448000	0.29417	GGT	.	.	.	none		0.746	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		T	1276776	G	T	1276776	3	4	66	1	0	0	0	0	1	0	0	0	9986	1116	39	4	16209	4	MUC5B	11	1276776	Missense_Mutation	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10		1276776	133729740	31	4365											
SF3B2	10992	hgsc.bcm.edu	37	chr11	65826742	65826742	+	Missense_Mutation	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	caaactggagaactctgcagCccccaagaagaagggatttg	14	6	11	10	0	1	3	0	0	1	3	1	5	1	4	2	2	4	1	2	2	5	1			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr11:65826742C>T	ENST00000322535.6	+	11	1302	c.1253C>T	c.(1252-1254)gCc>gTc	p.A418V	SF3B2_ENST00000528302.1_Missense_Mutation_p.A401V	NM_006842.2	NP_006833.2	Q13435	SF3B2_HUMAN	splicing factor 3b, subunit 2, 145kDa	418					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	41						AACTCTGCAGCCCCCAAGAAG	0.532																																					p.A418V		Atlas-SNP	.											.	SF3B2	85	.	0			c.C1253T						PASS	.						62	55	58					11																	65826742		2201	4295	6496	SO:0001583	missense	10992	exon11			CTGCAGCCCCCAA	U41371	CCDS31612.1	11q13	2010-07-21	2002-08-29		ENSG00000087365	ENSG00000087365			10769	protein-coding gene	gene with protein product		605591	"splicing factor 3b, subunit 2, 145kD"			8566756	Standard	XM_005273726		Approved	SAP145, SF3b1, Cus1, SF3b145	uc001ogy.1	Q13435	OTTHUMG00000166751	ENST00000322535.6:c.1253C>T	chr11.hg19:g.65826742C>T	ENSP00000318861:p.Ala418Val	132.0	0.0	.		141.0	6.0	.	NM_006842	A8K485|B4DT19|Q7L4T5|Q7Z627|Q969K1|Q96CM6|Q9BWD2	Missense_Mutation	SNP	ENST00000322535.6	hg19	CCDS31612.1	.	.	.	.	.	.	.	.	.	.	C	10.31	1.315405	0.23908	.	.	ENSG00000087365	ENST00000528302;ENST00000322535;ENST00000355456	.	.	.	5.06	-0.939	0.10408	.	0.379232	0.29073	N	0.013223	T	0.23289	0.0563	L	0.27053	0.805	0.19575	N	0.999966	B	0.02656	0.0	B	0.04013	0.001	T	0.20140	-1.0284	9	0.18276	T	0.48	0.0053	8.4596	0.32921	0.0:0.4852:0.0:0.5148	.	418	Q13435	SF3B2_HUMAN	V	401;418;322	.	ENSP00000318861:A418V	A	+	2	0	SF3B2	65583318	0.339000	0.24784	0.028000	0.17463	0.984000	0.73092	0.269000	0.18589	-0.516000	0.06470	0.555000	0.69702	GCC	.	.	.	none		0.532	SF3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391352.2			T	65826742	C	T	65826742	3	4	66	1	0	0	0	0	1	0	0	0	14164	739	26	2	1295	2	SF3B2	11	65826742	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	64549966	65826742	69179774	32	4366											
TMTC2	160335	hgsc.bcm.edu	37	chr12	83251132	83251132	+	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	tcgtgggacgagccgatgtcGgggccagtctcttctttctc	4	12	13	12	4	3	0	0	0	3	0	7	3	3	1	2	3	1	0	2	3	0	2			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr12:83251132G>T	ENST00000321196.3	+	2	1134	c.427G>T	c.(427-429)Ggg>Tgg	p.G143W	TMTC2_ENST00000549919.1_Missense_Mutation_p.G137W|TMTC2_ENST00000548305.1_Missense_Mutation_p.G143W	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2	143					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						AGCCGATGTCGGGGCCAGTCT	0.547																																					p.G143W		Atlas-SNP	.											TMTC2,NS,carcinoma,0,1	TMTC2	100	.	0			c.G427T						PASS	.						115	95	102					12																	83251132		2203	4300	6503	SO:0001583	missense	160335	exon2			GATGTCGGGGCCA	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.427G>T	chr12.hg19:g.83251132G>T	ENSP00000322300:p.Gly143Trp	82.0	0.0	.		84.0	37.0	.	NM_152588	B2RCU7|Q8N2K8	Missense_Mutation	SNP	ENST00000321196.3	hg19	CCDS9025.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.146896	0.77888	.	.	ENSG00000179104	ENST00000321196;ENST00000548305;ENST00000549919	T;T;T	0.60797	0.82;0.16;0.72	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.78342	0.4268	M	0.80616	2.505	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	T	0.80171	-0.1493	10	0.72032	D	0.01	-15.2295	18.1624	0.89712	0.0:0.0:1.0:0.0	.	143;143	Q8N394;F8VSH2	TMTC2_HUMAN;.	W	143;143;137	ENSP00000322300:G143W;ENSP00000448292:G143W;ENSP00000447609:G137W	ENSP00000322300:G143W	G	+	1	0	TMTC2	81775263	1.000000	0.71417	0.941000	0.38009	0.945000	0.59286	9.174000	0.94824	2.788000	0.95919	0.650000	0.86243	GGG	.	.	.	none		0.547	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405663.1	NM_152588		T	83251132	G	T	83251132	3	4	66	1	0	0	0	0	1	0	0	0	16273	1116	39	4	433	4	TMTC2	12	83251132	Missense_Mutation	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10		83251132	50600763	33	4367											
FOXA1	3169	hgsc.bcm.edu	37	chr14	38060788	38060788	+	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	ggacatgaggttgttgatggAgaacgggtggttgaaggagt	10	10	19	2	1	0	4	0	3	0	1	0	7	0	6	0	6	1	3	0	6	2	3			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr14:38060788A>T	ENST00000250448.2	-	2	1262	c.1201T>A	c.(1201-1203)Tcc>Acc	p.S401T	FOXA1_ENST00000545425.2_5'UTR|FOXA1_ENST00000540786.1_Missense_Mutation_p.S368T	NM_004496.3	NP_004487.2	P55317	FOXA1_HUMAN	forkhead box A1	401					anatomical structure formation involved in morphogenesis (GO:0048646)|chromatin remodeling (GO:0006338)|dorsal/ventral neural tube patterning (GO:0021904)|epithelial cell maturation involved in prostate gland development (GO:0060743)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|epithelial-mesenchymal signaling involved in prostate gland development (GO:0060738)|glucose homeostasis (GO:0042593)|hormone metabolic process (GO:0042445)|lung epithelial cell differentiation (GO:0060487)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate specification (GO:0048665)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland epithelium morphogenesis (GO:0060740)|prostate gland stromal morphogenesis (GO:0060741)|response to estradiol (GO:0032355)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)	microvillus (GO:0005902)|nucleus (GO:0005634)	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)|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(1)|large_intestine(2)|lung(3)|prostate(12)	19	Breast(36;0.0954)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;5.41e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.0454)|LUSC - Lung squamous cell carcinoma(13;0.0917)|all cancers(34;0.0925)|BRCA - Breast invasive adenocarcinoma(188;0.239)	GBM - Glioblastoma multiforme(112;0.0222)		TTGTTGATGGAGAACGGGTGG	0.602																																					p.S401T		Atlas-SNP	.											.	FOXA1	56	.	0			c.T1201A						PASS	.						109	78	89					14																	38060788		2203	4300	6503	SO:0001583	missense	3169	exon2			TGATGGAGAACGG	U39840	CCDS9665.1	14q12-q13	2008-04-10		2002-09-20	ENSG00000129514	ENSG00000129514		"Forkhead boxes"	5021	protein-coding gene	gene with protein product		602294	"hepatocyte nuclear factor 3, alpha"	HNF3A		9119385, 8652662	Standard	NM_004496		Approved		uc001wuf.4	P55317	OTTHUMG00000140253	ENST00000250448.2:c.1201T>A	chr14.hg19:g.38060788A>T	ENSP00000250448:p.Ser401Thr	98.0	0.0	.		116.0	63.0	.	NM_004496	B2R9H6|B7ZAP5|Q9H2A0	Missense_Mutation	SNP	ENST00000250448.2	hg19	CCDS9665.1	.	.	.	.	.	.	.	.	.	.	A	19.62	3.861765	0.71949	.	.	ENSG00000129514	ENST00000250448;ENST00000540786	T;T	0.72051	-0.62;-0.62	4.29	4.29	0.51040	Forkhead box protein, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.83727	0.5317	M	0.83384	2.64	0.80722	D	1	D	0.69078	0.997	D	0.79108	0.992	D	0.86303	0.1681	10	0.87932	D	0	.	12.5253	0.56083	1.0:0.0:0.0:0.0	.	401	P55317	FOXA1_HUMAN	T	401;368	ENSP00000250448:S401T;ENSP00000440178:S368T	ENSP00000250448:S401T	S	-	1	0	FOXA1	37130539	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.050000	0.93843	1.798000	0.52647	0.329000	0.21502	TCC	.	.	.	none		0.602	FOXA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276735.1			T	38060788	A	T	38060788	3	4	66	1	0	0	0	0	1	0	0	0	5996	304	11	5	221	5	FOXA1	14	38060788	Missense_Mutation	SNP	A	TCGA-A4-A5Y0-01A-11D-A31X-10		38060788	69288752	34	4368											
RAGE	5891	hgsc.bcm.edu	37	chr14	102718326	102718326	+	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	ttttttctgataatgggtatCttctccctgtacaatcaagg	9	17	7	8	0	4	1	1	1	3	0	5	1	4	1	1	2	1	2	1	2	5	7			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr14:102718326C>A	ENST00000361847.2	-	5	521	c.290G>T	c.(289-291)aGa>aTa	p.R97I	MOK_ENST00000193029.6_5'UTR|MOK_ENST00000522874.1_Missense_Mutation_p.R97I|MOK_ENST00000524214.1_Missense_Mutation_p.R67I	NM_014226.1	NP_055041.1	Q9UQ07	MOK_HUMAN	MOK protein kinase	97	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)										TAATGGGTATCTTCTCCCTGT	0.333																																					p.R97I		Atlas-SNP	.											.	.	.	.	0			c.G290T						PASS	.						73	80	78					14																	102718326		2203	4299	6502	SO:0001583	missense	5891	exon5			GGGTATCTTCTCC	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.290G>T	chr14.hg19:g.102718326C>A	ENSP00000355304:p.Arg97Ile	124.0	0.0	.		130.0	60.0	.	NM_014226	B2R6Z4|B7Z7P6|E7ER76|E7ERR8|Q92790|Q93067	Missense_Mutation	SNP	ENST00000361847.2	hg19	CCDS9971.1	.	.	.	.	.	.	.	.	.	.	C	15.00	2.703155	0.48412	.	.	ENSG00000080823	ENST00000522874;ENST00000361847;ENST00000524214	T;T;T	0.45668	0.89;0.89;0.89	5.42	4.52	0.55395	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.177262	0.50627	D	0.000113	T	0.49762	0.1576	L	0.55481	1.735	0.80722	D	1	D;D	0.53151	0.958;0.958	P;P	0.55667	0.781;0.781	T	0.51395	-0.8711	10	0.72032	D	0.01	-8.7163	8.6721	0.34156	0.0:0.765:0.154:0.081	.	67;97	E7ERR8;Q9UQ07	.;MOK_HUMAN	I	97;97;67	ENSP00000429469:R97I;ENSP00000355304:R97I;ENSP00000428942:R67I	ENSP00000355304:R97I	R	-	2	0	RAGE	101788079	1.000000	0.71417	0.988000	0.46212	0.863000	0.49368	1.056000	0.30480	1.273000	0.44346	0.650000	0.86243	AGA	.	.	.	none		0.333	MOK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380848.3			A	102718326	C	A	102718326	3	1	66	1	0	0	0	0	1	0	0	0	13019	913	32	4	1001	4	RAGE	14	102718326	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	64657538	102718326	4631214	35	4369											
C15orf56	644809	hgsc.bcm.edu	37	chr15	40544920	40544920	+	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	ccccggctgccccggaggttCgcggcgagaggacgggcctc	4	4	17	16	6	0	1	0	0	0	1	2	4	0	3	5	6	1	2	5	6	0	1			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr15:40544920C>T	ENST00000319503.3	-	1	191	c.170G>A	c.(169-171)cGa>cAa	p.R57Q	RP11-133K1.2_ENST00000558658.1_Intron|PAK6_ENST00000542403.2_5'Flank|PAK6_ENST00000441369.1_Intron|PAK6_ENST00000260404.4_Intron|C15orf56_ENST00000559727.1_Missense_Mutation_p.R57Q|PAK6_ENST00000455577.2_Intron|PAK6_ENST00000453867.1_Intron|PAK6_ENST00000560346.1_Intron	NM_001039905.1	NP_001034994.1	Q8N910	CO056_HUMAN	chromosome 15 open reading frame 56	57										lung(1)	1		all_cancers(109;1.62e-14)|all_epithelial(112;7.09e-12)|Lung NSC(122;3.4e-09)|all_lung(180;6.88e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.28e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0503)		CCCGGAGGTTCGCGGCGAGAG	0.756																																					p.R57Q		Atlas-SNP	.											.	C15orf56	3	.	0			c.G170A						PASS	.						4	5	5					15																	40544920		2008	3995	6003	SO:0001583	missense	644809	exon1			GAGGTTCGCGGCG		CCDS32197.1	15q15.1	2012-05-30			ENSG00000176753	ENSG00000176753			33868	protein-coding gene	gene with protein product							Standard	NM_001039905		Approved	FLJ38596	uc001zla.2	Q8N910	OTTHUMG00000172399	ENST00000319503.3:c.170G>A	chr15.hg19:g.40544920C>T	ENSP00000315794:p.Arg57Gln	121.0	0.0	.		137.0	59.0	.	NM_001039905		Missense_Mutation	SNP	ENST00000319503.3	hg19	CCDS32197.1	.	.	.	.	.	.	.	.	.	.	C	10.76	1.440220	0.25900	.	.	ENSG00000176753	ENST00000319503	T	0.30714	1.52	2.0	-1.71	0.08133	.	.	.	.	.	T	0.10035	0.0246	N	0.08118	0	0.09310	N	0.999999	P	0.44241	0.829	B	0.29353	0.101	T	0.17868	-1.0355	9	0.87932	D	0	.	3.9423	0.09333	0.0:0.3247:0.4801:0.1952	.	57	Q8N910	CO056_HUMAN	Q	57	ENSP00000315794:R57Q	ENSP00000315794:R57Q	R	-	2	0	C15orf56	38332212	.	.	0.000000	0.03702	0.001000	0.01503	.	.	-0.435000	0.07264	-1.253000	0.01494	CGA	.	.	.	none		0.756	C15orf56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418370.2	NM_001039905		T	40544920	C	T	40544920	3	4	66	1	0	0	0	0	1	0	0	0	1806	884	31	1	323	1	C15orf56	15	40544920	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10		40544920	61986472	36	4370											
CASC5	57082	hgsc.bcm.edu	37	chr15	40914359	40914359	+	Frame_Shift_Del	DEL	A	A	-																															cagacataatagccaaaaacAgcttaaccgacacctggaac																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr15:40914359delA	ENST00000346991.5	+	11	2365	c.1975delA	c.(1975-1977)agcfs	p.S659fs	CASC5_ENST00000399668.2_Frame_Shift_Del_p.S633fs|CASC5_ENST00000527044.1_3'UTR			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	659	Interaction with BUB1 and BUB1B.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		AGCCAAAAACAGCTTAACCGA	0.388																																					p.N658fs		Atlas-Indel,Pindel	.											.	CASC5	269	.	0			c.1974delC						PASS	.						82	79	80					15																	40914359		1881	4102	5983	SO:0001589	frameshift_variant	57082	exon11			.	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.1975delA	chr15.hg19:g.40914359delA	ENSP00000335463:p.Ser659fs	103.0	0.0	0		111.0	45.0	0.405405	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Frame_Shift_Del	DEL	ENST00000346991.5	hg19	CCDS42023.1																																																																																			.	.	.	none		0.388	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		-	40914359	A	-	40914359	7	5	66	1	0	1	0	1	0	0	0	0	2665	188	7	0	2013	0	CASC5	15	40914359	Frame_Shift_Del	DEL	A	TCGA-A4-A5Y0-01A-11D-A31X-10	369439	40914359	61617033	37	4371											
EME2	197342	hgsc.bcm.edu	37	chr16	1826070	1826070	+	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	tgcctttgcctgctcctaggCgctggaggcctgcagcacgg	4	9	14	14	2	0	0	0	0	0	0	1	1	1	1	4	4	5	4	4	4	1	2			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr16:1826070C>T	ENST00000568449.1	+	8	992	c.971C>T	c.(970-972)gCg>gTg	p.A324V	EME2_ENST00000307394.7_Splice_Site_p.A389V|MRPS34_ENST00000177742.3_5'Flank|MRPS34_ENST00000397375.2_5'Flank	NM_001257370.1	NP_001244299.1	A4GXA9	EME2_HUMAN	essential meiotic structure-specific endonuclease subunit 2	324					DNA recombination (GO:0006310)|DNA repair (GO:0006281)	nucleus (GO:0005634)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)			central_nervous_system(1)|kidney(2)|lung(5)|pancreas(1)	9						TGCTCCTAGGCGCTGGAGGCC	0.726								Direct reversal of damage;Homologous recombination																													p.A324V		Atlas-SNP	.											.	EME2	40	.	0			c.C971T						PASS	.						20	23	22					16																	1826070		2187	4278	6465	SO:0001630	splice_region_variant	197342	exon8			CCTAGGCGCTGGA	AK074080	CCDS58404.1	16p13.3	2013-07-03	2013-07-03			ENSG00000197774			27289	protein-coding gene	gene with protein product	"SLX2 structure-specific endonuclease subunit homolog B (S. cerevisiae)"	610886	"essential meiotic endonuclease 1 homolog 2 (S. pombe)"			12721304	Standard	NM_001257370		Approved	FLJ00151, SLX2B	uc010brw.1	A4GXA9		ENST00000568449.1:c.970-1C>T	chr16.hg19:g.1826070C>T		39.0	0.0	.		62.0	22.0	.	NM_001257370	Q8TEP2|Q96RY3	Missense_Mutation	SNP	ENST00000568449.1	hg19	CCDS58404.1	.	.	.	.	.	.	.	.	.	.	C	18.87	3.716192	0.68844	.	.	ENSG00000197774	ENST00000307394;ENST00000454910	.	.	.	3.4	2.43	0.29744	ERCC4 domain (2);	0.097008	0.41396	D	0.000895	T	0.75664	0.3880	M	0.80847	2.515	0.53688	D	0.999978	D;D	0.89917	1.0;0.977	D;B	0.91635	0.999;0.425	T	0.74405	-0.3676	9	0.49607	T	0.09	-7.8093	8.3214	0.32132	0.0:0.883:0.0:0.117	.	338;190	A4GXA9;A4GXA9-2	EME2_HUMAN;.	V	389;345	.	ENSP00000303779:A389V	A	+	2	0	EME2	1766071	0.931000	0.31567	0.515000	0.27774	0.021000	0.10359	1.875000	0.39578	0.756000	0.33013	0.561000	0.74099	GCG	.	.	.	none		0.726	EME2-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433185.2	NM_001010865	Missense_Mutation	T	1826070	C	T	1826070	5	4	66	1	0	0	0	0	0	0	1	0	5091	782	27	1	1196	1	EME2	16	1826070	Splice_Site	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10		1826070	88528683	38	4372											
ABCA3	21	hgsc.bcm.edu	37	chr16	2369834	2369834	+	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	acggccaggaagccttcccgGatgtaccctgggtgcgggag	7	6	16	12	3	0	0	0	0	0	0	1	3	1	3	4	5	3	1	4	5	2	2			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr16:2369834G>C	ENST00000301732.5	-	8	1321	c.621C>G	c.(619-621)atC>atG	p.I207M	ABCA3_ENST00000382381.3_Missense_Mutation_p.I207M	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	207					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)	AGCCTTCCCGGATGTACCCTG	0.652																																					p.I207M		Atlas-SNP	.											.	ABCA3	176	.	0			c.C621G						PASS	.						71	62	65					16																	2369834		2198	4300	6498	SO:0001583	missense	21	exon8			TTCCCGGATGTAC	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.621C>G	chr16.hg19:g.2369834G>C	ENSP00000301732:p.Ile207Met	34.0	0.0	.		33.0	10.0	.	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Missense_Mutation	SNP	ENST00000301732.5	hg19	CCDS10466.1	.	.	.	.	.	.	.	.	.	.	G	10.68	1.419127	0.25552	.	.	ENSG00000167972	ENST00000301732;ENST00000382381	D	0.89939	-2.59	5.04	3.05	0.35203	.	0.339378	0.32314	N	0.006271	D	0.91858	0.7423	M	0.78637	2.42	0.80722	D	1	B;P;B	0.37370	0.302;0.592;0.287	B;P;B	0.54590	0.297;0.756;0.217	D	0.89048	0.3453	10	0.42905	T	0.14	.	6.8397	0.23955	0.148:0.1482:0.7038:0.0	.	207;269;207	A7MBM9;Q4LE27;Q99758	.;.;ABCA3_HUMAN	M	207;269	ENSP00000301732:I207M	ENSP00000301732:I207M	I	-	3	3	ABCA3	2309835	1.000000	0.71417	0.843000	0.33291	0.138000	0.21146	3.628000	0.54259	0.688000	0.31529	0.655000	0.94253	ATC	.	.	.	none		0.652	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089		C	2369834	G	C	2369834	3	2	66	1	0	0	0	0	1	0	0	0	33	1164	41	4	4597	4	ABCA3	16	2369834	Missense_Mutation	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10	543764	2369834	87984919	39	4373											
ADCY9	115	hgsc.bcm.edu	37	chr16	4042307	4042307	+	Frame_Shift_Del	DEL	C	C	-																															ctgactgttggtgagcttctCctcttggggagggctgagga																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr16:4042307delC	ENST00000294016.3	-	5	2585	c.2047delG	c.(2047-2049)gagfs	p.E683fs	ADCY9_ENST00000571889.1_Intron	NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	683					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						GTGAGCTTCTCCTCTTGGGGA	0.582																																					p.E683fs		Pindel	.											.	ADCY9	151	.	0			c.2048delA						PASS	.						72	67	69					16																	4042307		2197	4300	6497	SO:0001589	frameshift_variant	115	exon5			.	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.2047delG	chr16.hg19:g.4042307delC	ENSP00000294016:p.Glu683fs	69.0	0.0	.		76.0	26.0	0.342	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Frame_Shift_Del	DEL	ENST00000294016.3	hg19	CCDS32382.1																																																																																			.	.	.	none		0.582	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1			-	4042307	C	-	4042307	7	5	66	1	0	1	0	1	0	0	0	0	301	864	30	0	2042	0	ADCY9	16	4042307	Frame_Shift_Del	DEL	C	TCGA-A4-A5Y0-01A-11D-A31X-10	1672473	4042307	86312446	40	4374											
PRM3	5620	hgsc.bcm.edu	37	chr16	11367405	11367405	+	IGR	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	cccgtgctgtggcctgggctGtggcctgggctctggcctgt	0	11	17	13	1	1	0	0	0	1	0	1	0	1	0	4	5	1	3	4	5	0	0			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr16:11367405G>C	ENST00000241808.4	-	0	680				RMI2_ENST00000572173.1_Intron|PRM3_ENST00000327157.2_Missense_Mutation_p.H16Q|SNORA48_ENST00000390926.1_RNA	NM_002762.2	NP_002753.2	P04554	PRM2_HUMAN	protamine 2						cell differentiation (GO:0030154)|chromosome condensation (GO:0030261)|DNA packaging (GO:0006323)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.0?(1)		central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(2)	7						ggcctgggctgtggcctgggc	0.617																																					p.H16Q		Atlas-SNP	.											.	PRM3	8	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.C48G						PASS	.						28	30	29					16																	11367405		1980	4149	6129	SO:0001628	intergenic_variant	58531	exon1			TGGGCTGTGGCCT		CCDS42118.1, CCDS66944.1	16p13.13	2013-10-17			ENSG00000122304	ENSG00000122304			9448	protein-coding gene	gene with protein product	"cancer/testis antigen family 94, member 2"	182890				16632464	Standard	NM_001286356		Approved	CT94.2	uc002dau.1	P04554	OTTHUMG00000172317		chr16.hg19:g.11367405G>C		15.0	0.0	.		21.0	7.0	.	NM_021247	Q6ZMM0	Missense_Mutation	SNP	ENST00000241808.4	hg19	CCDS42118.1	.	.	.	.	.	.	.	.	.	.	G	2.311	-0.357977	0.05138	.	.	ENSG00000178257	ENST00000327157	T	0.53640	0.61	0.559	-1.12	0.09808	.	.	.	.	.	T	0.39963	0.1098	N	0.19112	0.55	0.09310	N	0.999999	P	0.47106	0.89	P	0.55055	0.767	T	0.31081	-0.9956	8	0.66056	D	0.02	.	.	.	.	.	16	Q9NNZ6	PRM3_HUMAN	Q	16	ENSP00000325638:H16Q	ENSP00000325638:H16Q	H	-	3	2	PRM3	11274906	0.193000	0.23313	0.002000	0.10522	0.005000	0.04900	-0.194000	0.09559	-1.041000	0.03266	-1.036000	0.02392	CAC	.	.	.	none		0.617	PRM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417808.1			C	11367405	G	C	11367405	1	2	66	0	1	0	0	0	0	0	0	0	12544	1368	48	4		4	PRM3	16	11367405	IGR	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10	7325098	11367405	78987348	41	4375											
DCTPP1	79077	hgsc.bcm.edu	37	chr16	30435583	30435583	+	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	ggtctggcctgtggagtcacAgggaatgtccgcaggcccca	7	7	15	12	1	2	0	1	0	1	0	3	2	3	2	4	5	0	1	4	5	1	0	rs36092481		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr16:30435583A>T	ENST00000319285.4	-	3	578	c.484T>A	c.(484-486)Tgt>Agt	p.C162S	DCTPP1_ENST00000568434.1_Missense_Mutation_p.C41S|ZNF771_ENST00000566625.1_Intron|DCTPP1_ENST00000568973.1_Missense_Mutation_p.C41S|DCTPP1_ENST00000565758.1_Missense_Mutation_p.C41S|DCTPP1_ENST00000567983.1_Missense_Mutation_p.C63S	NM_024096.1	NP_077001.1	Q9H773	DCTP1_HUMAN	dCTP pyrophosphatase 1	162					nucleoside triphosphate catabolic process (GO:0009143)|protein homotetramerization (GO:0051289)	cytosol (GO:0005829)	dCTP diphosphatase activity (GO:0047840)|magnesium ion binding (GO:0000287)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|pyrimidine deoxyribonucleotide binding (GO:0032556)			kidney(1)|large_intestine(3)|upper_aerodigestive_tract(1)	5						GTGGAGTCACAGGGAATGTCC	0.597																																					p.C162S		Atlas-SNP	.											.	DCTPP1	12	.	0			c.T484A						PASS	.						40	37	38					16																	30435583		2197	4300	6497	SO:0001583	missense	79077	exon3			AGTCACAGGGAAT	BC001344	CCDS10680.1	16p11.2	2009-02-11			ENSG00000179958	ENSG00000179958	3.6.1.12		28777	protein-coding gene	gene with protein product	"XTP3-transactivated protein A"	615840				15740738	Standard	NM_024096		Approved	MGC5627, RS21C6, CDA03, XTP3TPA	uc002dyf.3	Q9H773	OTTHUMG00000132416	ENST00000319285.4:c.484T>A	chr16.hg19:g.30435583A>T	ENSP00000322524:p.Cys162Ser	54.0	0.0	.		80.0	43.0	.	NM_024096		Missense_Mutation	SNP	ENST00000319285.4	hg19	CCDS10680.1	.	.	.	.	.	.	.	.	.	.	A	1.012	-0.687538	0.03328	.	.	ENSG00000179958	ENST00000319285	.	.	.	3.72	-0.855	0.10700	.	1.452180	0.04273	N	0.342559	T	0.23611	0.0571	N	0.20685	0.6	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.17531	-1.0366	9	0.05525	T	0.97	-32.526	6.9119	0.24340	0.5009:0.0:0.4991:0.0	.	162	Q9H773	DCTP1_HUMAN	S	162	.	ENSP00000322524:C162S	C	-	1	0	DCTPP1	30343084	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.017000	0.12590	-0.100000	0.12241	-0.353000	0.07706	TGT	.	.	.	none		0.597	DCTPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255553.2	NM_024096		T	30435583	A	T	30435583	3	4	66	1	0	0	0	0	1	0	0	0	4314	188	7	5	32	5	DCTPP1	16	30435583	Missense_Mutation	SNP	A	TCGA-A4-A5Y0-01A-11D-A31X-10	19068178	30435583	59919170	42	4376											
DHX38	9785	hgsc.bcm.edu	37	chr16	72142801	72142801	+	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	ccccagattacatagtgtatCacgagttggtcatgaccacc	11	10	8	12	1	2	2	2	1	0	1	2	3	2	2	4	1	1	2	4	1	3	4			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr16:72142801C>T	ENST00000268482.3	+	24	3867	c.3358C>T	c.(3358-3360)Cac>Tac	p.H1120Y	DHX38_ENST00000536867.1_Missense_Mutation_p.H432Y	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	1120					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)				CATAGTGTATCACGAGTTGGT	0.542																																					p.H1120Y	Melanoma(97;711 1442 7855 13832 28836)	Atlas-SNP	.											.	DHX38	91	.	0			c.C3358T						PASS	.						78	64	69					16																	72142801		2198	4300	6498	SO:0001583	missense	9785	exon24			GTGTATCACGAGT	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.3358C>T	chr16.hg19:g.72142801C>T	ENSP00000268482:p.His1120Tyr	80.0	0.0	.		62.0	23.0	.	NM_014003	B4DVG8|D3DWS7|O75212|Q96HN7	Missense_Mutation	SNP	ENST00000268482.3	hg19	CCDS10907.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.922424	0.92319	.	.	ENSG00000140829	ENST00000268482;ENST00000536867	T;T	0.02656	4.21;4.21	5.14	5.14	0.70334	Domain of unknown function DUF1605 (1);	0.000000	0.85682	D	0.000000	T	0.22126	0.0533	M	0.91972	3.26	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.02683	-1.1124	10	0.52906	T	0.07	.	18.8078	0.92045	0.0:1.0:0.0:0.0	.	432;1120	B4DVG8;Q92620	.;PRP16_HUMAN	Y	1120;432	ENSP00000268482:H1120Y;ENSP00000437898:H432Y	ENSP00000268482:H1120Y	H	+	1	0	DHX38	70700302	1.000000	0.71417	0.989000	0.46669	0.996000	0.88848	7.097000	0.76967	2.677000	0.91161	0.655000	0.94253	CAC	.	.	.	none		0.542	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003		T	72142801	C	T	72142801	3	4	66	1	0	0	0	0	1	0	0	0	4513	826	29	2	3448	2	DHX38	16	72142801	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	41707218	72142801	18211952	43	4377											
MYH13	8735	hgsc.bcm.edu	37	chr17	10215392	10215392	+	Splice_Site	DEL	A	A	-																															tttgcttccactctgcaaggAcctgggagatgacaaaggga																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr17:10215392delA	ENST00000418404.3	-	31	4530	c.4367delT	c.(4366-4368)gtc>gc	p.V1456fs	MYH13_ENST00000252172.4_Splice_Site_p.V1456fs|RP11-401O9.4_ENST00000609088.1_RNA			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	1456					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						CTCTGCAAGGACCTGGGAGAT	0.517																																					p.V1456fs		Atlas-Indel,Pindel	.											MYH13_ENST00000252172,NS,carcinoma,0,2	MYH13	533	.	0			c.4368delC						PASS	.						56	54	55					17																	10215392		1981	4180	6161	SO:0001630	splice_region_variant	8735	exon32			.	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.4366-1T>-	chr17.hg19:g.10215392delA		63.0	0.0	0		93.0	30.0	0.322581	NM_003802	O95252|Q9P0U8	Frame_Shift_Del	DEL	ENST00000418404.3	hg19	CCDS45613.1																																																																																			.	.	.	none		0.517	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	Frame_Shift_Del	-	10215392	A	-	10215392	8	5	66	1	0	1	0	1	0	0	1	0	10039	289	10	0	1489	0	MYH13	17	10215392	Splice_Site	DEL	A	TCGA-A4-A5Y0-01A-11D-A31X-10		10215392	70979818	44	4378											
NCOR1	9611	hgsc.bcm.edu	37	chr17	15971431	15971431	+	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	gtagacttgttagaagaaatTgtaactggaaaaaaagagcc	18	9	10	4	0	0	4	0	0	0	4	0	5	0	5	1	1	2	3	1	1	8	5			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr17:15971431T>G	ENST00000268712.3	-	32	4775	c.4518A>C	c.(4516-4518)acA>acC	p.T1506T	NCOR1_ENST00000395851.1_Silent_p.T1522T|NCOR1_ENST00000395857.3_Silent_p.T90T	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1506	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)		TAGAAGAAATTGTAACTGGAA	0.403																																					p.T1522T		Atlas-SNP	.											.	NCOR1	240	.	0			c.A4566C						PASS	.						33	33	33					17																	15971431		2203	4300	6503	SO:0001819	synonymous_variant	9611	exon31			AGAAATTGTAACT	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.4518A>C	chr17.hg19:g.15971431T>G		90.0	0.0	.		117.0	32.0	.	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Silent	SNP	ENST00000268712.3	hg19	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	T	13.19	2.162182	0.38217	.	.	ENSG00000141027	ENST00000395849	.	.	.	5.76	-9.98	0.00438	.	.	.	.	.	.	.	.	.	.	.	0.36017	D	0.8385	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.3886	0.07281	0.1594:0.3155:0.0807:0.4444	.	.	.	.	.	-1	.	.	.	-	.	.	NCOR1	15912156	0.000000	0.05858	0.041000	0.18516	0.927000	0.56198	-0.918000	0.04021	-1.256000	0.02478	0.460000	0.39030	.	.	.	.	none		0.403	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		G	15971431	T	G	15971431	2	3	66	1	0	0	0	0	0	0	0	1	10242	1799	63	5		5	NCOR1	17	15971431	Silent	SNP	T	TCGA-A4-A5Y0-01A-11D-A31X-10	5756039	15971431	65223779	45	4379											
CCR7	1236	hgsc.bcm.edu	37	chr17	38711306	38711306	+	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	accccattgtagggcagctgGaagactatgaagaccacgac	13	6	11	11	1	0	3	0	1	0	2	0	5	0	4	3	2	1	3	3	2	4	3			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr17:38711306G>T	ENST00000246657.2	-	3	887	c.825C>A	c.(823-825)ttC>ttA	p.F275L	CCR7_ENST00000579344.1_Missense_Mutation_p.F269L	NM_001838.3	NP_001829.1	P32248	CCR7_HUMAN	chemokine (C-C motif) receptor 7	275					activation of Rho GTPase activity (GO:0032862)|cellular response to cytokine stimulus (GO:0071345)|chemokine (C-C motif) ligand 19 signaling pathway (GO:0038115)|chemokine (C-C motif) ligand 21 signaling pathway (GO:0038116)|chemokine-mediated signaling pathway (GO:0070098)|dendritic cell chemotaxis (GO:0002407)|establishment of T cell polarity (GO:0001768)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interleukin-12 secretion (GO:0072610)|lymphocyte migration into lymph node (GO:0097022)|mature dendritic cell differentiation (GO:0097029)|myeloid dendritic cell chemotaxis (GO:0002408)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative thymic T cell selection (GO:0045060)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell motility (GO:2000147)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of glycoprotein biosynthetic process involved in immunological synapse formation (GO:2000526)|positive regulation of humoral immune response (GO:0002922)|positive regulation of hypersensitivity (GO:0002885)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of immunological synapse formation (GO:2000522)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of T cell costimulation (GO:2000525)|positive regulation of T cell receptor signaling pathway (GO:0050862)|regulation of dendritic cell dendrite assembly (GO:2000547)|regulation of interferon-gamma production (GO:0032649)|regulation of interleukin-1 beta secretion (GO:0050706)|release of sequestered calcium ion into cytosol (GO:0051209)|response to lipopolysaccharide (GO:0032496)|response to nitric oxide (GO:0071731)|response to prostaglandin E (GO:0034695)|ruffle organization (GO:0031529)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|C-C motif chemokine 19 receptor activity (GO:0038117)|C-C motif chemokine 21 receptor activity (GO:0038121)|chemokine (C-C motif) ligand 19 binding (GO:0035757)|chemokine (C-C motif) ligand 21 binding (GO:0035758)|G-protein coupled receptor activity (GO:0004930)			breast(1)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		Breast(137;0.000496)				AGGGCAGCTGGAAGACTATGA	0.552																																					p.F275L		Atlas-SNP	.											.	CCR7	31	.	0			c.C825A						PASS	.						209	173	185					17																	38711306		2203	4300	6503	SO:0001583	missense	1236	exon3			CAGCTGGAAGACT		CCDS11369.1	17q12-q21.2	2012-08-08			ENSG00000126353	ENSG00000126353		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1608	protein-coding gene	gene with protein product		600242		CMKBR7, EBI1		8383238	Standard	NM_001838		Approved	BLR2, CDw197, CD197	uc002huw.3	P32248	OTTHUMG00000133375	ENST00000246657.2:c.825C>A	chr17.hg19:g.38711306G>T	ENSP00000246657:p.Phe275Leu	72.0	0.0	.		129.0	41.0	.	NM_001838		Missense_Mutation	SNP	ENST00000246657.2	hg19	CCDS11369.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.286284	0.80803	.	.	ENSG00000126353	ENST00000246657	T	0.35973	1.28	5.83	5.83	0.93111	GPCR, rhodopsin-like superfamily (1);	0.225560	0.45867	D	0.000323	T	0.43033	0.1229	L	0.58669	1.825	0.80722	D	1	B	0.22541	0.071	B	0.30401	0.115	T	0.18023	-1.0350	10	0.35671	T	0.21	.	20.1082	0.97900	0.0:0.0:1.0:0.0	.	275	P32248	CCR7_HUMAN	L	275	ENSP00000246657:F275L	ENSP00000246657:F275L	F	-	3	2	CCR7	35964832	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.869000	0.99810	2.764000	0.94973	0.555000	0.69702	TTC	.	.	.	none		0.552	CCR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257222.1			T	38711306	G	T	38711306	3	4	66	1	0	0	0	0	1	0	0	0	2948	1165	41	4	315	4	CCR7	17	38711306	Missense_Mutation	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10	22739875	38711306	42483904	46	4380											
KIF2B	84643	hgsc.bcm.edu	37	chr17	51901648	51901648	+	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	acttccaggcaaacacctgtCaacgctcactcatccaggag	12	7	7	15	1	3	0	3	0	0	0	5	1	5	1	3	2	2	2	3	2	2	1			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr17:51901648C>T	ENST00000268919.4	+	1	1410	c.1254C>T	c.(1252-1254)gtC>gtT	p.V418V		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	418	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						AAACACCTGTCAACGCTCACT	0.512																																					p.V418V		Atlas-SNP	.											.	KIF2B	254	.	0			c.C1254T						PASS	.						102	76	85					17																	51901648		2203	4300	6503	SO:0001819	synonymous_variant	84643	exon1			ACCTGTCAACGCT	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.1254C>T	chr17.hg19:g.51901648C>T		137.0	0.0	.		221.0	68.0	.	NM_032559	Q96MA2|Q9BXG6	Silent	SNP	ENST00000268919.4	hg19	CCDS32685.1																																																																																			.	.	.	none		0.512	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559		T	51901648	C	T	51901648	2	4	66	1	0	0	0	0	0	0	0	1	8305	813	29	2		2	KIF2B	17	51901648	Silent	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	13190342	51901648	29293562	47	4381											
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9257703	9257703	+	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	tgccaggaaactcttgtgctCaggatccggcatcctttatg	8	12	10	11	1	2	0	1	0	1	0	4	2	4	2	3	3	3	2	3	3	2	3			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr18:9257703C>G	ENST00000262126.4	+	9	4678	c.4438C>G	c.(4438-4440)Cag>Gag	p.Q1480E	RP11-888D10.4_ENST00000609701.1_RNA|ANKRD12_ENST00000383440.2_Missense_Mutation_p.Q1457E|ANKRD12_ENST00000400020.3_Missense_Mutation_p.Q1457E	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1480						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						CTCTTGTGCTCAGGATCCGGC	0.418																																					p.Q1480E		Atlas-SNP	.											.	ANKRD12	167	.	0			c.C4438G						PASS	.						49	52	51					18																	9257703		2200	4299	6499	SO:0001583	missense	23253	exon9			TGTGCTCAGGATC	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.4438C>G	chr18.hg19:g.9257703C>G	ENSP00000262126:p.Gln1480Glu	118.0	0.0	.		104.0	40.0	.	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	hg19	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.234306	0.39498	.	.	ENSG00000101745	ENST00000383440;ENST00000262126	T;T	0.68479	-0.33;-0.33	5.69	5.69	0.88448	.	0.303615	0.32444	N	0.006084	T	0.55768	0.1941	L	0.29908	0.895	0.44946	D	0.997969	P;P	0.38195	0.571;0.622	B;B	0.31101	0.124;0.097	T	0.58967	-0.7542	10	0.48119	T	0.1	-11.1383	19.8263	0.96618	0.0:1.0:0.0:0.0	.	1457;1480	Q6UB98-2;Q6UB98	.;ANR12_HUMAN	E	1457;1480	ENSP00000372932:Q1457E;ENSP00000262126:Q1480E	ENSP00000262126:Q1480E	Q	+	1	0	ANKRD12	9247703	1.000000	0.71417	1.000000	0.80357	0.791000	0.44710	5.359000	0.66074	2.676000	0.91093	0.655000	0.94253	CAG	.	.	.	none		0.418	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		G	9257703	C	G	9257703	3	3	66	1	0	0	0	0	1	0	0	0	640	827	29	4	4468	4	ANKRD12	18	9257703	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10		9257703	68819545	48	4382											
MBP	4155	hgsc.bcm.edu	37	chr18	74700845	74700845	+	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	ggtcttacctttccctgcgaCgggggtggtgtgcgaggcgt	3	11	17	10	4	1	0	0	0	1	0	2	2	2	0	2	5	3	0	2	5	1	2	rs112511603		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr18:74700845C>T	ENST00000397869.3	-	3	352	c.306G>A	c.(304-306)ccG>ccA	p.P102P	MBP_ENST00000397865.5_Silent_p.P102P|MBP_ENST00000580402.1_Silent_p.P235P|MBP_ENST00000526111.1_Silent_p.P80P|MBP_ENST00000354542.4_Intron|MBP_ENST00000397875.3_Silent_p.P112P|MBP_ENST00000355994.2_Silent_p.P235P|MBP_ENST00000527041.1_Intron|MBP_ENST00000578193.1_Silent_p.P102P|MBP_ENST00000359645.3_Silent_p.P128P|MBP_ENST00000528160.1_Intron|MBP_ENST00000579129.1_Silent_p.P235P|MBP_ENST00000382582.3_Silent_p.P128P|MBP_ENST00000397866.4_Silent_p.P102P			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)	TTCCCTGCGACGGGGGTGGTG	0.527																																					p.P235P	NSCLC(17;72 1131 19392)	Atlas-SNP	.											.	MBP	45	.	0			c.G705A						PASS	.						121	130	127					18																	74700845		2203	4300	6503	SO:0001819	synonymous_variant	4155	exon6			CTGCGACGGGGGT		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.306G>A	chr18.hg19:g.74700845C>T		80.0	0.0	.		65.0	28.0	.	NM_001025101	A6XMW0|B2R5I1|P81448|Q14227|Q6ICT2	Silent	SNP	ENST00000397869.3	hg19																																																																																				.	C|0.500;T|0.500	0.500	weak		0.527	MBP-024	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000267964.1	NM_001025081		T	74700845	C	T	74700845	2	4	66	1	0	0	0	0	0	0	0	1	9366	523	19	1		1	MBP	18	74700845	Silent	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10	65443142	74700845	3376403	49	4383											
XAB2	56949	hgsc.bcm.edu	37	chr19	7691039	7691039	+	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	cacctggtagttggacttgcCggccttagacacgaaacgct	9	9	11	12	3	0	1	0	0	0	1	0	3	0	2	3	3	2	3	3	3	3	4			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr19:7691039C>A	ENST00000358368.4	-	5	677	c.640G>T	c.(640-642)Ggc>Tgc	p.G214C	XAB2_ENST00000534844.1_Missense_Mutation_p.G211C	NM_020196.2	NP_064581.2	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	214					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)		p.G211S(1)		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						TTGGACTTGCCGGCCTTAGAC	0.642								Direct reversal of damage;Nucleotide excision repair (NER)																													p.G214C		Atlas-SNP	.											XAB2,NS,carcinoma,0,1	XAB2	69	.	1	Substitution - Missense(1)	lung(1)	c.G640T						PASS	.						63	69	67					19																	7691039		2203	4299	6502	SO:0001583	missense	56949	exon5			ACTTGCCGGCCTT	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.640G>T	chr19.hg19:g.7691039C>A	ENSP00000351137:p.Gly214Cys	37.0	0.0	.		40.0	2.0	.	NM_020196	Q8TET6|Q96HB0|Q96IW0|Q9NRG6|Q9ULP3	Missense_Mutation	SNP	ENST00000358368.4	hg19	CCDS32892.1	.	.	.	.	.	.	.	.	.	.	C	17.42	3.386274	0.61956	.	.	ENSG00000076924	ENST00000358368;ENST00000534844	T;T	0.63417	-0.04;-0.04	4.84	3.8	0.43715	.	0.000000	0.85682	D	0.000000	T	0.81221	0.4777	M	0.91300	3.195	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.83505	0.0077	10	0.87932	D	0	-43.9904	10.2415	0.43314	0.0:0.9057:0.0:0.0943	.	214	Q9HCS7	SYF1_HUMAN	C	214;211	ENSP00000351137:G214C;ENSP00000438225:G211C	ENSP00000351137:G214C	G	-	1	0	XAB2	7597039	1.000000	0.71417	0.986000	0.45419	0.502000	0.33828	7.343000	0.79319	1.033000	0.39918	0.455000	0.32223	GGC	.	.	.	none		0.642	XAB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461021.1	NM_020196		A	7691039	C	A	7691039	3	1	66	1	0	0	0	0	1	0	0	0	17430	652	23	4	1987	4	XAB2	19	7691039	Missense_Mutation	SNP	C	TCGA-A4-A5Y0-01A-11D-A31X-10		7691039	51437944	50	4384											
ZNF43	7594	hgsc.bcm.edu	37	chr19	21990696	21990696	+	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	aaggtttgaggatcggttaaAagctttgccacatttttcac	11	14	9	7	1	1	1	1	1	0	0	2	2	1	2	1	3	2	3	1	3	3	5			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr19:21990696A>T	ENST00000354959.4	-	4	2312	c.2143T>A	c.(2143-2145)Ttt>Att	p.F715I	ZNF43_ENST00000598381.1_Missense_Mutation_p.F709I|ZNF43_ENST00000594012.1_Missense_Mutation_p.F709I|ZNF43_ENST00000595461.1_Missense_Mutation_p.F709I	NM_003423.3	NP_003414.2	P17038	ZNF43_HUMAN	zinc finger protein 43	715					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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)		GATCGGTTAAAAGCTTTGCCA	0.363																																					p.F724I		Atlas-SNP	.											.	ZNF43	152	.	0			c.T2170A						PASS	.						50	54	53					19																	21990696		2203	4299	6502	SO:0001583	missense	7594	exon4			GGTTAAAAGCTTT	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.2143T>A	chr19.hg19:g.21990696A>T	ENSP00000347045:p.Phe715Ile	27.0	0.0	.		37.0	20.0	.	NM_001256653	A8K5N8|P28160|Q53XQ2|Q5H9T3|Q96DG1	Missense_Mutation	SNP	ENST00000354959.4	hg19	CCDS12413.2	.	.	.	.	.	.	.	.	.	.	A	17.13	3.311136	0.60414	.	.	ENSG00000198521	ENST00000397148;ENST00000354959	T	0.46451	0.87	1.76	1.76	0.24704	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.66499	0.2795	M	0.91972	3.26	0.36120	D	0.845417	D	0.89917	1.0	D	0.81914	0.995	T	0.73953	-0.3820	9	0.87932	D	0	.	8.2856	0.31926	1.0:0.0:0.0:0.0	.	715	P17038	ZNF43_HUMAN	I	714;715	ENSP00000347045:F715I	ENSP00000347045:F715I	F	-	1	0	ZNF43	21782536	0.986000	0.35501	0.177000	0.23020	0.629000	0.37895	6.109000	0.71528	0.808000	0.34231	0.254000	0.18369	TTT	.	.	.	none		0.363	ZNF43-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250380.2	NM_003423		T	21990696	A	T	21990696	3	4	66	1	0	0	0	0	1	0	0	0	17915	14	1	5	290	5	ZNF43	19	21990696	Missense_Mutation	SNP	A	TCGA-A4-A5Y0-01A-11D-A31X-10	14299657	21990696	37138287	51	4385											
FBXO46	23403	hgsc.bcm.edu	37	chr19	46215847	46215847	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtataagtcacatgtgatctTgtccttggctcgggccccag	7	12	11	11	1	2	1	1	1	1	0	4	1	3	1	3	2	0	2	3	2	2	4			TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr19:46215847T>C	ENST00000317683.3	-	2	1040	c.907A>G	c.(907-909)Aag>Gag	p.K303E		NM_001080469.1	NP_001073938.1	Q6PJ61	FBX46_HUMAN	F-box protein 46	303										breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(2)|skin(1)	15		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00568)|GBM - Glioblastoma multiforme(486;0.0844)|Epithelial(262;0.201)		CATGTGATCTTGTCCTTGGCT	0.682																																					p.K303E		Atlas-SNP	.											.	FBXO46	34	.	0			c.A907G						PASS	.						31	36	34					19																	46215847		2004	4156	6160	SO:0001583	missense	23403	exon2			TGATCTTGTCCTT	BC021978	CCDS46116.1	19q13.3	2008-02-05	2004-06-15	2004-06-16		ENSG00000177051		"F-boxes /  "other""	25069	protein-coding gene	gene with protein product		609117	"F-box only protein 34-like"	FBXO34L		9585442	Standard	NM_001080469		Approved	20D7-FC4, Fbx46	uc002pcz.3	Q6PJ61		ENST00000317683.3:c.907A>G	chr19.hg19:g.46215847T>C	ENSP00000410007:p.Lys303Glu	75.0	0.0	.		101.0	47.0	.	NM_001080469		Missense_Mutation	SNP	ENST00000317683.3	hg19	CCDS46116.1	.	.	.	.	.	.	.	.	.	.	T	10.96	1.498092	0.26861	.	.	ENSG00000177051	ENST00000317683	.	.	.	4.39	3.37	0.38596	.	.	.	.	.	T	0.32194	0.0821	N	0.22421	0.69	0.38310	D	0.943215	B	0.31705	0.336	B	0.27796	0.083	T	0.12915	-1.0529	8	0.28530	T	0.3	-10.0116	6.4522	0.21910	0.0:0.1111:0.0:0.8889	.	303	Q6PJ61	FBX46_HUMAN	E	303	.	ENSP00000410007:K303E	K	-	1	0	FBXO46	50907687	1.000000	0.71417	1.000000	0.80357	0.414000	0.31173	3.177000	0.50871	0.737000	0.32582	-0.371000	0.07208	AAG	.	.	.	none		0.682	FBXO46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459661.1	XM_371179		C	46215847	T	C	46215847	3	2	66	1	0	0	0	0	1	0	0	0	5762	1821	63	3	908	3	FBXO46	19	46215847	Missense_Mutation	SNP	T	TCGA-A4-A5Y0-01A-11D-A31X-10	24225151	46215847	12913136	52	4386											
EDN3	1908	hgsc.bcm.edu	37	chr20	57876603	57876603	+	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	tgtggctggccctggcgaggGgactgtggccccgacagcac	5	6	17	13	2	0	0	0	0	0	0	0	3	0	1	3	6	1	2	3	6	0	0	rs457651		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chr20:57876603G>T	ENST00000337938.2	+	2	577	c.191G>T	c.(190-192)gGg>gTg	p.G64V	EDN3_ENST00000371025.3_Missense_Mutation_p.G64V|EDN3_ENST00000395654.3_Missense_Mutation_p.G64V|EDN3_ENST00000371028.2_Missense_Mutation_p.G64V|EDN3_ENST00000311585.7_Missense_Mutation_p.G64V	NM_207034.1	NP_996917.1	P14138	EDN3_HUMAN	endothelin 3	64					blood circulation (GO:0008015)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|inositol phosphate-mediated signaling (GO:0048016)|melanocyte differentiation (GO:0030318)|multicellular organismal development (GO:0007275)|neural crest cell migration (GO:0001755)|neuron differentiation (GO:0030182)|neutrophil chemotaxis (GO:0030593)|peptide hormone secretion (GO:0030072)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart rate (GO:0010460)|positive regulation of hormone secretion (GO:0046887)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|regulation of developmental pigmentation (GO:0048070)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|signal transduction (GO:0007165)|vasoconstriction (GO:0042310)|vein smooth muscle contraction (GO:0014826)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)|receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	19	all_lung(29;0.0115)					CCTGGCGAGGGGACTGTGGCC	0.716																																					p.G64V		Atlas-SNP	.											.	EDN3	83	.	0			c.G191T						PASS	.						33	37	35					20																	57876603		2201	4300	6501	SO:0001583	missense	1908	exon2			GCGAGGGGACTGT	X52001	CCDS13477.1, CCDS13478.1, CCDS13479.1	20q13.2-q13.3	2013-02-26			ENSG00000124205	ENSG00000124205		"Endogenous ligands"	3178	protein-coding gene	gene with protein product		131242					Standard	NM_000114		Approved	ET3	uc002yaq.3	P14138	OTTHUMG00000032867	ENST00000337938.2:c.191G>T	chr20.hg19:g.57876603G>T	ENSP00000337128:p.Gly64Val	77.0	0.0	.		94.0	43.0	.	NM_207034	E1P5I5|Q03229|Q7Z6D2|Q9UGT7	Missense_Mutation	SNP	ENST00000337938.2	hg19	CCDS13477.1	.	.	.	.	.	.	.	.	.	.	G	11.71	1.720028	0.30503	.	.	ENSG00000124205	ENST00000337938;ENST00000311585;ENST00000371028;ENST00000371025;ENST00000395654	D;D;D;D;D	0.87179	-2.22;-2.22;-2.22;-2.22;-2.22	3.59	-7.18	0.01505	.	.	.	.	.	T	0.63105	0.2483	N	0.08118	0	0.09310	N	1	P;P;P;P	0.38110	0.618;0.543;0.483;0.51	B;B;B;B	0.33690	0.168;0.138;0.081;0.067	T	0.61053	-0.7140	9	0.36615	T	0.2	1.9985	0.3953	0.00417	0.2776:0.1274:0.2815:0.3135	.	64;64;64;64	P14138-2;Q7Z6D2;P14138;Q4FAT2	.;.;EDN3_HUMAN;.	V	64	ENSP00000337128:G64V;ENSP00000311854:G64V;ENSP00000360067:G64V;ENSP00000360064:G64V;ENSP00000379015:G64V	ENSP00000311854:G64V	G	+	2	0	EDN3	57309998	0.000000	0.05858	0.000000	0.03702	0.221000	0.24807	-0.348000	0.07740	-1.885000	0.01118	0.313000	0.20887	GGG	.	G|1.000;A|0.000	.	alt		0.716	EDN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079919.2	NM_000114		T	57876603	G	T	57876603	3	4	66	1	0	0	0	0	1	0	0	0	4920	1232	43	4	197	4	EDN3	20	57876603	Missense_Mutation	SNP	G	TCGA-A4-A5Y0-01A-11D-A31X-10		57876603	5148917	53	4387											
AR	367	hgsc.bcm.edu	37	chrX	66765207	66765208	+	Missense_Mutation	DNP	GC	GC	AG																															cagcagcagcagcagcagcaGcagcagcagcagcagcagca																										TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	g.chrX:66765207_66765208GC>AG	ENST00000374690.3	+	1	743_744	c.219_220GC>AG	c.(217-222)caGCag>caAGag	p.Q74E	AR_ENST00000504326.1_Missense_Mutation_p.Q74E|AR_ENST00000396044.3_Missense_Mutation_p.Q74E|AR_ENST00000513847.1_3'UTR	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	74	Gln-rich.|Modulating.|Poly-Gln.		Missing.		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)	agcagcagcagcagcagcagca	0.668									Androgen Insensitivity Syndrome																												p.Q73Q|p.Q74E		Atlas-SNP	.											.	AR	249	.	0			c.G219A|c.C220G						PASS	.																																			SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	GCAGCAGCAGCAG|CAGCAGCAGCAGC	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	Exception_encountered	chrX.hg19:g.66765207_66765208delinsAG	ENSP00000363822:p.Gln74Glu	97.0	0.0	.		102.0|104.0	9.0|8.0	.	NM_000044	A2RUN2|B1AKD7|Q9UD95	Silent|Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1																																																																																			.	.	.	none		0.668	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		AG	66765208	GC	AG	66765207	3	1	66	1	0	0	0	0	1	0	0	0	836	962	34	2	221	2	AR	23	66765207	Missense_Mutation	DNP	GC	TCGA-A4-A5Y0-01A-11D-A31X-10		66765207	88505353	54	4388											
KLHL17	339451	hgsc.bcm.edu	37	chr1	898748	898748	+	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	cctcagacctggctaccgtgGagtcctacgaccccgtgact	7	8	10	16	3	1	2	1	1	0	1	2	4	2	3	6	2	2	1	6	2	2	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr1:898748G>A	ENST00000338591.3	+	8	1326	c.1219G>A	c.(1219-1221)Gag>Aag	p.E407K		NM_198317.2	NP_938073.1	Q6TDP4	KLH17_HUMAN	kelch-like family member 17	407	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)		GGCTACCGTGGAGTCCTACGA	0.622																																					p.E407K		Atlas-SNP	.											.	KLHL17	31	.	0			c.G1219A						PASS	.						90	75	80					1																	898748		2202	4300	6502	SO:0001583	missense	339451	exon8			ACCGTGGAGTCCT	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.1219G>A	chr1.hg19:g.898748G>A	ENSP00000343930:p.Glu407Lys	166.0	1.0	.		177.0	124.0	.	NM_198317	Q5SV94	Missense_Mutation	SNP	ENST00000338591.3	hg19	CCDS30550.1	.	.	.	.	.	.	.	.	.	.	G	36	5.935264	0.97122	.	.	ENSG00000187961	ENST00000338591;ENST00000455747;ENST00000540863	D	0.84516	-1.86	5.37	5.37	0.77165	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	D	0.95452	0.8523	H	0.98965	4.385	0.80722	D	1	D	0.57571	0.98	P	0.60012	0.867	D	0.97376	0.9979	10	0.87932	D	0	.	19.0966	0.93255	0.0:0.0:1.0:0.0	.	407	Q6TDP4	KLH17_HUMAN	K	407;283;130	ENSP00000343930:E407K	ENSP00000343930:E407K	E	+	1	0	KLHL17	888611	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.708000	0.98727	2.532000	0.85374	0.448000	0.29417	GAG	.	.	.	none		0.622	KLHL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097875.3	NM_198317		A	898748	G	A	898748	3	1	67	1	0	0	0	0	1	0	0	0	8379	1175	41	2	1249	2	KLHL17	1	898748	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10		898748	248351873	1	4389											
FGGY	55277	hgsc.bcm.edu	37	chr1	60019871	60019884	+	Frame_Shift_Del	DEL	TCTGTGGAACGTCT	TCTGTGGAACGTCT	-																															gacgtcacggctggctgtcaTctgtggaacgtcttcttgtc																								rs144977691|rs116481036|rs147926450	byFrequency	TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	TCTGTGGAACGTCT	TCTGTGGAACGTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr1:60019871_60019884delTCTGTGGAACGTCT	ENST00000303721.7	+	8	1049_1062	c.875_888delTCTGTGGAACGTCT	c.(874-888)atctgtggaacgtctfs	p.ICGTS292fs	FGGY_ENST00000371212.1_Frame_Shift_Del_p.ICGTS204fs|FGGY_ENST00000371218.4_Frame_Shift_Del_p.ICGTS292fs|FGGY_ENST00000474476.1_3'UTR|FGGY_ENST00000371210.1_5'UTR	NM_018291.3	NP_060761.3	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing	292					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)					CTGGCTGTCATCTGTGGAACGTCTTCTTGTCACA	0.561																																					p.292_296del		Pindel	.											.	FGGY	99	.	0			c.874_887del						PASS	.																																			SO:0001589	frameshift_variant	55277	exon8			.		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.875_888delTCTGTGGAACGTCT	chr1.hg19:g.60019871_60019884delTCTGTGGAACGTCT	ENSP00000305922:p.Ile292fs	236.0	0.0	.		157.0	48.0	0.306	NM_001113411	B1AK92|B1AK93|B1AK94|B2RDR8|D3DQ56|Q9HA63|Q9NV20	Frame_Shift_Del	DEL	ENST00000303721.7	hg19	CCDS611.2																																																																																			.	.	.	none		0.561	FGGY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023210.2	NM_001113411		-	60019884	TCTGTGGAACGTCT	-	60019871	7	5	67	1	0	1	0	1	0	0	0	0	5878	1435	50	0	901	0	FGGY	1	60019871	Frame_Shift_Del	DEL	TCTGTGGAACGTCT	TCGA-A4-A5Y1-01A-11D-A28G-10	59121123	60019871	189230750	2	4390											
CD1C	911	hgsc.bcm.edu	37	chr1	158261919	158261919	+	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	gggctgtgagctgcattctgGaaagagcccagaaggcttct	9	9	14	9	0	2	3	0	1	2	2	2	4	2	4	1	3	3	4	1	3	2	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr1:158261919G>A	ENST00000368170.3	+	3	653	c.374G>A	c.(373-375)gGa>gAa	p.G125E		NM_001765.2	NP_001756.2	P29017	CD1C_HUMAN	CD1c molecule	125					antigen processing and presentation (GO:0019882)|T cell activation involved in immune response (GO:0002286)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	endogenous lipid antigen binding (GO:0030883)|exogenous lipid antigen binding (GO:0030884)|glycolipid binding (GO:0051861)|lipopeptide binding (GO:0071723)			NS(1)|endometrium(3)|large_intestine(4)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	39	all_hematologic(112;0.0378)					CTGCATTCTGGAAAGAGCCCA	0.448																																					p.G125E		Atlas-SNP	.											.	CD1C	100	.	0			c.G374A						PASS	.						91	98	95					1																	158261919		2203	4300	6503	SO:0001583	missense	911	exon3			ATTCTGGAAAGAG	M28827	CCDS1175.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158481	ENSG00000158481		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1636	protein-coding gene	gene with protein product		188340	"CD1C antigen, c polypeptide", "CD1c antigen"	CD1		2447586	Standard	NM_001765		Approved		uc001fru.3	P29017	OTTHUMG00000017514	ENST00000368170.3:c.374G>A	chr1.hg19:g.158261919G>A	ENSP00000357152:p.Gly125Glu	154.0	0.0	.		192.0	89.0	.	NM_001765	Q5TDJ7|Q6IAS4|Q9UMM0|Q9UN96	Missense_Mutation	SNP	ENST00000368170.3	hg19	CCDS1175.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	13.26|13.26	2.185038|2.185038	0.38609|0.38609	.|.	.|.	ENSG00000158481|ENSG00000158481	ENST00000368169;ENST00000368170|ENST00000443761	T|.	0.06294|.	3.32|.	3.92|3.92	-0.561|-0.561	0.11785|0.11785	MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	2.458490|.	0.01726|.	N|.	0.028603|.	T|.	0.19805|.	0.0476|.	M|M	0.64997|0.64997	1.995|1.995	0.09310|0.09310	N|N	1|1	P|.	0.52577|.	0.954|.	B|.	0.44278|.	0.445|.	T|.	0.33803|.	-0.9854|.	10|.	0.87932|.	D|.	0|.	.|.	1.0278|1.0278	0.01531|0.01531	0.1994:0.1834:0.4297:0.1875|0.1994:0.1834:0.4297:0.1875	.|.	125|.	P29017|.	CD1C_HUMAN|.	E|X	125|59	ENSP00000357152:G125E|.	ENSP00000357151:G125E|.	G|W	+|+	2|3	0|0	CD1C|CD1C	156528543|156528543	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.020000|0.020000	0.10135|0.10135	-0.226000|-0.226000	0.09139|0.09139	0.093000|0.093000	0.17368|0.17368	0.644000|0.644000	0.83932|0.83932	GGA|TGG	.	.	.	none		0.448	CD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046351.2	NM_001765		A	158261919	G	A	158261919	3	1	67	1	0	0	0	0	1	0	0	0	2978	1174	41	2	384	2	CD1C	1	158261919	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	98242048	158261919	90988702	3	4391											
C1orf14	81626	hgsc.bcm.edu	37	chr1	182898789	182898789	+	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	gtttatttcttaccatttcaGtagtcatcatttttgctaca	9	20	4	8	0	4	0	3	0	1	0	4	0	4	0	1	0	3	3	1	0	4	9			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr1:182898789G>T	ENST00000367547.3	-	6	1411	c.1175C>A	c.(1174-1176)aCt>aAt	p.T392N	SHCBP1L_ENST00000488956.1_5'UTR|SHCBP1L_ENST00000423786.1_Missense_Mutation_p.T273N	NM_030933.2	NP_112195.2	Q9BZQ2	SHP1L_HUMAN	SHC SH2-domain binding protein 1-like	464										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|pancreas(1)|prostate(1)|skin(2)	15						TACCATTTCAGTAGTCATCAT	0.343																																					p.T392N		Atlas-SNP	.											.	SHCBP1L	64	.	0			c.C1175A						PASS	.						97	94	95					1																	182898789		2202	4297	6499	SO:0001583	missense	81626	exon6			ATTTCAGTAGTCA	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.1175C>A	chr1.hg19:g.182898789G>T	ENSP00000356518:p.Thr392Asn	21.0	0.0	.		38.0	16.0	.	NM_030933	Q4G195|Q9BZQ3|Q9H2B6	Missense_Mutation	SNP	ENST00000367547.3	hg19	CCDS30955.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.470487	0.43942	.	.	ENSG00000157060	ENST00000367547;ENST00000287709;ENST00000423786	T;T	0.47869	0.83;0.84	5.88	4.94	0.65067	Carbohydrate-binding/sugar hydrolysis domain (1);	0.212652	0.33092	N	0.005289	T	0.43277	0.1240	L	0.43152	1.355	0.25433	N	0.988169	B;B;B	0.26258	0.09;0.078;0.145	B;B;B	0.29785	0.024;0.034;0.107	T	0.38520	-0.9657	10	0.42905	T	0.14	-11.1083	14.1389	0.65306	0.0:0.1504:0.8496:0.0	.	464;273;392	Q9BZQ2;Q9BZQ2-2;Q9BZQ2-3	SHP1L_HUMAN;.;.	N	392;461;273	ENSP00000356518:T392N;ENSP00000397308:T273N	ENSP00000287709:T461N	T	-	2	0	SHCBP1L	181165412	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.607000	0.67648	1.463000	0.47967	0.644000	0.83932	ACT	.	.	.	none		0.343	SHCBP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085956.1	NM_030933		T	182898789	G	T	182898789	3	4	67	1	0	0	0	0	1	0	0	0	2002	1029	36	4	806	4	C1orf14	1	182898789	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	24636870	182898789	66351832	4	4392											
SMC6	79677	hgsc.bcm.edu	37	chr2	17847696	17847696	+	Missense_Mutation	SNP	T	T	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	taaaaagttacctcatgcttTgaggtgtgagcaagataaac	15	11	9	6	0	1	3	1	2	0	1	1	3	1	3	1	1	4	3	1	1	7	4			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:17847696T>G	ENST00000448223.2	-	27	3421	c.3152A>C	c.(3151-3153)cAa>cCa	p.Q1051P	SMC6_ENST00000351948.4_Missense_Mutation_p.Q1051P|SMC6_ENST00000381272.4_Missense_Mutation_p.Q1077P|SMC6_ENST00000402989.1_Missense_Mutation_p.Q1051P	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	1051					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					CCTCATGCTTTGAGGTGTGAG	0.308																																					p.Q1051P		Atlas-SNP	.											.	SMC6	102	.	0			c.A3152C						PASS	.						76	72	74					2																	17847696		2203	4300	6503	SO:0001583	missense	79677	exon27			ATGCTTTGAGGTG	AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"Structural maintenance of chromosomes proteins"	20466	protein-coding gene	gene with protein product		609387	"SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.3152A>C	chr2.hg19:g.17847696T>G	ENSP00000404092:p.Gln1051Pro	33.0	0.0	.		43.0	22.0	.	NM_001142286	A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Missense_Mutation	SNP	ENST00000448223.2	hg19	CCDS1690.1	.	.	.	.	.	.	.	.	.	.	T	19.23	3.786888	0.70337	.	.	ENSG00000163029	ENST00000448223;ENST00000351948;ENST00000381272;ENST00000402989	T;T;T;T	0.68181	-0.31;-0.31;2.02;-0.31	6.08	6.08	0.98989	RecF/RecN/SMC (1);	0.054551	0.85682	D	0.000000	T	0.79516	0.4459	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.81291	-0.0999	10	0.72032	D	0.01	.	12.8158	0.57665	0.1222:0.0:0.0:0.8778	.	1051	Q96SB8	SMC6_HUMAN	P	1051;1051;1077;1051	ENSP00000404092:Q1051P;ENSP00000323439:Q1051P;ENSP00000370672:Q1077P;ENSP00000384539:Q1051P	ENSP00000323439:Q1051P	Q	-	2	0	SMC6	17711177	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.920000	0.56446	2.333000	0.79357	0.482000	0.46254	CAA	.	.	.	none		0.308	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207359.1	NM_024624		G	17847696	T	G	17847696	3	3	67	1	0	0	0	0	1	0	0	0	14800	1812	63	5	131	5	SMC6	2	17847696	Missense_Mutation	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10		17847696	225351677	5	4393											
ITGA6	3655	hgsc.bcm.edu	37	chr2	173352476	173352476	+	Frame_Shift_Del	DEL	A	A	-																															gtcactttttatttggttttAagtacaactgaagtcacctt																										TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:173352476delA	ENST00000264106.6	+	18	2585	c.2382delA	c.(2380-2382)ttafs	p.L794fs	ITGA6_ENST00000409080.1_Frame_Shift_Del_p.L755fs|AC093818.1_ENST00000442417.1_RNA|ITGA6_ENST00000264107.7_Frame_Shift_Del_p.L755fs|ITGA6_ENST00000409532.1_Frame_Shift_Del_p.L636fs|ITGA6_ENST00000343713.4_Frame_Shift_Del_p.L750fs|ITGA6_ENST00000375221.2_Frame_Shift_Del_p.L794fs			P23229	ITA6_HUMAN	integrin, alpha 6	794					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)			ATTTGGTTTTAAGTACAACTG	0.333																																					p.L755X		Atlas-Indel,Pindel	.											.	ITGA6	171	.	0			c.2264delT						PASS	.						123	118	120					2																	173352476		2203	4300	6503	SO:0001589	frameshift_variant	3655	exon17			.		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.2382delA	chr2.hg19:g.173352476delA	ENSP00000264106:p.Leu794fs	81.0	0.0	0		73.0	14.0	0.191781	NM_000210	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Frame_Shift_Del	DEL	ENST00000264106.6	hg19																																																																																				.	.	.	none		0.333	ITGA6-201	KNOWN	basic	protein_coding	protein_coding				-	173352476	A	-	173352476	7	5	67	1	0	1	0	1	0	0	0	0	7887	359	13	0	2331	0	ITGA6	2	173352476	Frame_Shift_Del	DEL	A	TCGA-A4-A5Y1-01A-11D-A28G-10	155504780	173352476	69846897	6	4394											
TTN	7273	hgsc.bcm.edu	37	chr2	179547441	179547441	+	Missense_Mutation	SNP	T	T	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	tacctgtgatgtattcttcaTgctcttcatatcgttcatac	8	18	5	10	1	5	1	3	1	2	0	6	1	5	1	1	0	3	3	1	0	4	8			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:179547441T>G	ENST00000591111.1	-	133	32350	c.32126A>C	c.(32125-32127)cAt>cCt	p.H10709P	TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.H9782P|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.H11026P|TTN-AS1_ENST00000431752.1_RNA			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)			GTATTCTTCATGCTCTTCATA	0.338																																					p.H11026P		Atlas-SNP	.											.	TTN	18412	.	0			c.A33077C						PASS	.						257	246	249					2																	179547441		1899	4119	6018	SO:0001583	missense	7273	exon135			TCTTCATGCTCTT	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.32126A>C	chr2.hg19:g.179547441T>G	ENSP00000465570:p.His10709Pro	82.0	0.0	.		107.0	55.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	3.299	-0.143379	0.06669	.	.	ENSG00000155657	ENST00000342992;ENST00000414766	T;T	0.68331	-0.32;-0.1	4.98	2.59	0.31030	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.46889	0.1416	N	0.19112	0.55	0.58432	D	0.999996	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.35674	-0.9779	9	0.87932	D	0	.	5.0483	0.14496	0.0:0.1647:0.1536:0.6817	.	10709;10445	Q8WZ42;Q8WZ42-5	TITIN_HUMAN;.	P	9782;640	ENSP00000343764:H9782P;ENSP00000401501:H640P	ENSP00000343764:H9782P	H	-	2	0	TTN	179255686	0.000000	0.05858	0.989000	0.46669	0.230000	0.25150	-0.913000	0.04042	0.338000	0.23692	-0.256000	0.11100	CAT	.	.	.	none		0.338	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179547441	T	G	179547441	3	3	67	1	0	0	0	0	1	0	0	0	16747	1464	51	5	71364	5	TTN	2	179547441	Missense_Mutation	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10	6194965	179547441	63651932	7	4395											
SSFA2	6744	hgsc.bcm.edu	37	chr2	182765617	182765618	+	Frame_Shift_Ins	INS	-	-	T																															atggaagtagaaaacccaaaINSttatgctttaacaagtaaga																										TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:182765617_182765618insT	ENST00000431877.2	+	7	877_878	c.698_699insT	c.(697-702)aattatfs	p.Y234fs	SSFA2_ENST00000409001.1_Frame_Shift_Ins_p.Y234fs|SSFA2_ENST00000320370.7_Frame_Shift_Ins_p.Y234fs|SSFA2_ENST00000428267.2_Frame_Shift_Ins_p.Y81fs	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	234						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)			GAAAACCCAAATTATGCTTTAA	0.302																																					p.N233fs		Atlas-Indel,Pindel	.											.	SSFA2	130	.	0			c.698_699insT						PASS	.																																			SO:0001589	frameshift_variant	6744	exon7			.	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.700dupT	chr2.hg19:g.182765619_182765619dupT	ENSP00000388731:p.Tyr234fs	69.0	0.0	0		84.0	19.0	0.22619	NM_001130445	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Frame_Shift_Ins	INS	ENST00000431877.2	hg19	CCDS46467.1																																																																																			.	.	.	none		0.302	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2	NM_006751		T	182765618	-	T	182765617	7	5	67	1	0	1	1	0	0	0	0	0	15195	101	4	0	724	0	SSFA2	2	182765617	Frame_Shift_Ins	INS	-	TCGA-A4-A5Y1-01A-11D-A28G-10	3218176	182765617	60433756	8	4396											
FSIP2	401024	hgsc.bcm.edu	37	chr2	186671593	186671593	+	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	tcaggccagataagggaaatCagttccctgggggtaaagtg	12	8	14	7	0	2	1	2	0	0	1	3	2	3	2	2	4	0	2	2	4	4	3			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:186671593C>T	ENST00000424728.1	+	17	17560	c.17560C>T	c.(17560-17562)Cag>Tag	p.Q5854*	FSIP2_ENST00000343098.5_Nonsense_Mutation_p.Q5943*			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	5854										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						TAAGGGAAATCAGTTCCCTGG	0.408																																					p.Q5943X		Atlas-SNP	.											.	FSIP2	251	.	0			c.C17827T						PASS	.						87	79	82					2																	186671593		1841	4085	5926	SO:0001587	stop_gained	401024	exon17			GGAAATCAGTTCC	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.17560C>T	chr2.hg19:g.186671593C>T	ENSP00000401306:p.Gln5854*	65.0	0.0	.		90.0	23.0	.	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Nonsense_Mutation	SNP	ENST00000424728.1	hg19		.	.	.	.	.	.	.	.	.	.	C	55	24.779395	0.99962	.	.	ENSG00000188738	ENST00000343098;ENST00000424728	.	.	.	4.87	1.8	0.24995	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	.	6.7948	0.23719	0.3174:0.4362:0.2464:0.0	.	.	.	.	X	5943;5854	.	ENSP00000344403:Q5943X	Q	+	1	0	FSIP2	186379838	0.000000	0.05858	0.002000	0.10522	0.014000	0.08584	-0.056000	0.11787	0.131000	0.18576	0.591000	0.81541	CAG	.	.	.	none		0.408	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		T	186671593	C	T	186671593	4	4	67	1	0	0	0	0	0	1	0	0	6082	827	29	2	17893	2	FSIP2	2	186671593	Nonsense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	3905976	186671593	56527780	9	4397											
TNP1	7141	hgsc.bcm.edu	37	chr2	217724631	217724631	+	Missense_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	tcactcaccgtcatcgccccGtttcctacttttcaggttgc	5	14	6	16	3	4	0	4	0	0	0	6	0	5	0	4	1	2	2	4	1	1	5	rs561435538		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:217724631G>A	ENST00000236979.2	-	1	156	c.127C>T	c.(127-129)Cgg>Tgg	p.R43W	AC007563.5_ENST00000607591.1_RNA|AC007563.5_ENST00000447289.1_RNA	NM_003284.3	NP_003275.1	P09430	STP1_HUMAN	transition protein 1 (during histone to protamine replacement)	43					chromatin remodeling (GO:0006338)|chromatin silencing (GO:0006342)|fertilization, exchange of chromosomal proteins (GO:0035042)|multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|sexual reproduction (GO:0019953)|single strand break repair (GO:0000012)|sperm motility (GO:0030317)|spermatid development (GO:0007286)|spermatid nucleus differentiation (GO:0007289)|spermatid nucleus elongation (GO:0007290)	male germ cell nucleus (GO:0001673)|nucleosome (GO:0000786)	DNA binding (GO:0003677)			large_intestine(1)|lung(1)|stomach(1)	3		Renal(207;0.0822)		Epithelial(149;8.97e-07)|all cancers(144;2.46e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCATCGCCCCGTTTCCTACTT	0.552													G|||	1	0.000199681	0	0	5008	,	,		20388	0.001		0	False		,,,				2504	0				p.R43W		Atlas-SNP	.											TNP1,NS,carcinoma,0,1	TNP1	10	.	0			c.C127T						PASS	.						217	195	203					2																	217724631		2203	4300	6503	SO:0001583	missense	7141	exon1			CGCCCCGTTTCCT		CCDS2406.1	2q35-q36	2008-06-03			ENSG00000118245	ENSG00000118245			11951	protein-coding gene	gene with protein product		190231				2249851	Standard	NM_003284		Approved		uc002vgk.3	P09430	OTTHUMG00000133057	ENST00000236979.2:c.127C>T	chr2.hg19:g.217724631G>A	ENSP00000236979:p.Arg43Trp	126.0	0.0	.		156.0	74.0	.	NM_003284		Missense_Mutation	SNP	ENST00000236979.2	hg19	CCDS2406.1	.	.	.	.	.	.	.	.	.	.	G	12.50	1.957505	0.34565	.	.	ENSG00000118245	ENST00000236979	.	.	.	5.55	-1.5	0.08691	.	0.000000	0.52532	D	0.000080	T	0.64918	0.2642	.	.	.	0.21105	N	0.99979	D	0.89917	1.0	D	0.76071	0.987	T	0.64807	-0.6320	8	0.87932	D	0	-0.9614	15.5104	0.75776	0.0:0.0:0.2376:0.7624	.	43	P09430	STP1_HUMAN	W	43	.	ENSP00000236979:R43W	R	-	1	2	TNP1	217432876	0.771000	0.28555	0.434000	0.26772	0.816000	0.46133	0.173000	0.16724	-0.090000	0.12462	-0.182000	0.12963	CGG	.	.	.	none		0.552	TNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256673.1	NM_003284		A	217724631	G	A	217724631	3	1	67	1	0	0	0	0	1	0	0	0	16345	1144	40	1	48	1	TNP1	2	217724631	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	31053038	217724631	25474742	10	4398											
AGFG1	3267	hgsc.bcm.edu	37	chr2	228399580	228399580	+	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	ggtggtgatcagggaagtggCtttgggaccacaggtaaagc	10	8	17	6	0	1	1	1	1	0	0	1	3	1	3	1	6	1	2	1	6	3	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:228399580C>G	ENST00000310078.8	+	8	1304	c.1044C>G	c.(1042-1044)ggC>ggG	p.G348G	AGFG1_ENST00000409315.1_Intron|AGFG1_ENST00000373671.3_Silent_p.G308G|AGFG1_ENST00000409979.2_Silent_p.G372G|AGFG1_ENST00000409171.1_Silent_p.G348G	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	348					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						AGGGAAGTGGCTTTGGGACCA	0.433																																					p.G372G		Atlas-SNP	.											.	AGFG1	80	.	0			c.C1116G						PASS	.						154	145	148					2																	228399580		2203	4300	6503	SO:0001819	synonymous_variant	3267	exon9			AAGTGGCTTTGGG		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.1044C>G	chr2.hg19:g.228399580C>G		186.0	1.0	.		218.0	130.0	.	NM_001135187	B3KUL1|E9PHX7|Q15277|Q4VAS0|Q4VAS1|Q4VAS3|Q53QT8|Q53R11	Silent	SNP	ENST00000310078.8	hg19	CCDS2467.1																																																																																			.	.	.	none		0.433	AGFG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256895.2	NM_004504		G	228399580	C	G	228399580	2	3	67	1	0	0	0	0	0	0	0	1	380	784	28	4		4	AGFG1	2	228399580	Silent	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	10674949	228399580	14799793	11	4399											
SH3BP4	23677	hgsc.bcm.edu	37	chr2	235943690	235943690	+	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	ggccaactccaatggcctccCtcgctgcaagtcagagggga	9	6	12	14	1	1	1	1	0	0	1	4	2	3	2	4	4	2	2	4	4	3	0			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr2:235943690C>T	ENST00000409212.1	+	3	551	c.44C>T	c.(43-45)cCt>cTt	p.P15L	SH3BP4_ENST00000392011.2_Missense_Mutation_p.P15L|SH3BP4_ENST00000344528.4_Missense_Mutation_p.P15L			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	15					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)		AATGGCCTCCCTCGCTGCAAG	0.547																																					p.P15L		Atlas-SNP	.											.	SH3BP4	109	.	0			c.C44T						PASS	.						51	53	52					2																	235943690		2203	4300	6503	SO:0001583	missense	23677	exon3			GCCTCCCTCGCTG	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.44C>T	chr2.hg19:g.235943690C>T	ENSP00000386862:p.Pro15Leu	76.0	0.0	.		80.0	30.0	.	NM_014521	O95082|Q309A3|Q53QD0|Q53TD1	Missense_Mutation	SNP	ENST00000409212.1	hg19	CCDS2513.1	.	.	.	.	.	.	.	.	.	.	C	14.31	2.496478	0.44352	.	.	ENSG00000130147	ENST00000392011;ENST00000420127;ENST00000416021;ENST00000409212;ENST00000344528;ENST00000444916;ENST00000446904;ENST00000454947	T;T;T;T;T	0.38560	2.49;1.18;2.49;2.49;1.13	4.91	4.03	0.46877	.	0.000000	0.85682	D	0.000000	T	0.32315	0.0825	L	0.34521	1.04	0.80722	D	1	B;B	0.13594	0.008;0.005	B;B	0.10450	0.005;0.005	T	0.11348	-1.0591	10	0.59425	D	0.04	-11.6851	11.1019	0.48179	0.0:0.9093:0.0:0.0907	.	15;15	A8K594;Q9P0V3	.;SH3B4_HUMAN	L	15	ENSP00000375867:P15L;ENSP00000403251:P15L;ENSP00000386862:P15L;ENSP00000340237:P15L;ENSP00000415391:P15L	ENSP00000340237:P15L	P	+	2	0	SH3BP4	235608429	0.999000	0.42202	0.870000	0.34147	0.360000	0.29518	4.311000	0.59147	1.064000	0.40671	0.655000	0.94253	CCT	.	.	.	none		0.547	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1			T	235943690	C	T	235943690	3	4	67	1	0	0	0	0	1	0	0	0	14259	681	24	2	46	2	SH3BP4	2	235943690	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	7544110	235943690	7255683	12	4400											
SETD2	29072	hgsc.bcm.edu	37	chr3	47098859	47098859	+	Frame_Shift_Del	DEL	G	G	-																															tcccaggttctgcatctgttGctgttgtttctgagcctccc																										TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr3:47098859delG	ENST00000409792.3	-	15	6457	c.6415delC	c.(6415-6417)caafs	p.Q2140fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2140	Low charge region.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TGCATCTGTTGCTGTTGTTTC	0.478			"N, F, S, Mis"		clear cell renal carcinoma																																p.Q2139fs		Atlas-INDEL	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.6416delA						PASS	.						160	148	152					3																	47098859		2203	4300	6503	SO:0001589	frameshift_variant	29072	exon15			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.6415delC	chr3.hg19:g.47098859delG	ENSP00000386759:p.Gln2140fs	164.0	0.0	0		112.0	83.0	0.741071	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Del	DEL	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.	.	none		0.478	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		-	47098859	G	-	47098859	7	5	67	1	0	1	0	1	0	0	0	0	14144	1328	46	0	1307	0	SETD2	3	47098859	Frame_Shift_Del	DEL	G	TCGA-A4-A5Y1-01A-11D-A28G-10		47098859	150923571	13	4401											
ARMC8	25852	hgsc.bcm.edu	37	chr3	137964017	137964040	+	Splice_Site	DEL	CGGAAGAAGGTGAGTCTGGGAGAG	CGGAAGAAGGTGAGTCTGGGAGAG	-																															gagcaaatgatgaagacatcCggaagaaggtgagtctggga																										TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	CGGAAGAAGGTGAGTCTGGGAGAG	CGGAAGAAGGTGAGTCTGGGAGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr3:137964017_137964040delCGGAAGAAGGTGAGTCTGGGAGAG	ENST00000469044.1	+	12	1397_1405	c.1126_1134delCGGAAGAAGGTGAGTCTGGGAGAG	c.(1126-1134)cggaagaagdel	p.RKK376del	ARMC8_ENST00000461822.1_Splice_Site_p.RKK309del|ARMC8_ENST00000538260.1_Splice_Site_p.RKK345del|ARMC8_ENST00000491704.1_Splice_Site_p.RKK334del|ARMC8_ENST00000471453.1_In_Frame_Del_p.RKKVSLGE362del|ARMC8_ENST00000358441.2_In_Frame_Del_p.RKKVSLGE362del|ARMC8_ENST00000470821.1_In_Frame_Del_p.RKKVSLGE376del|ARMC8_ENST00000485396.1_Splice_Site_p.RKK303del|ARMC8_ENST00000489213.1_In_Frame_Del_p.RKKVSLGE334del|ARMC8_ENST00000393058.3_Splice_Site_p.RKK366del|ARMC8_ENST00000481646.1_Splice_Site_p.RKK362del	NM_001267041.1|NM_001267042.1	NP_001253970.1|NP_001253971.1	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8	376										endometrium(2)|kidney(1)|large_intestine(7)|lung(5)|upper_aerodigestive_tract(1)	16						TGAAGACATCCGGAAGAAGGTGAGTCTGGGAGAGGGGCGTCCCC	0.491																																					p.361_364del		Atlas-Indel,Pindel	.											.	ARMC8	79	.	0			c.1083_1092del						PASS	.																																			SO:0001630	splice_region_variant	25852	exon13			.		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.1134+1CGGAAGAAGGTGAGTCTGGGAGAG>-	chr3.hg19:g.137964017_137964040delCGGAAGAAGGTGAGTCTGGGAGAG		147.0	0.0	0		139.0	22.0	0.158273	NM_015396	A8K0L2|B7Z441|B7Z453|D3DNE6|F5GWK4|Q6PIL2|Q96D19|Q96HZ5|Q9NV02|Q9NV94|Q9Y4R9	Frame_Shift_Del	DEL	ENST00000469044.1	hg19																																																																																				.	.	.	none		0.491	ARMC8-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000357560.1	NM_015396	In_Frame_Del	-	137964040	CGGAAGAAGGTGAGTCTGGGAGAG	-	137964017	8	5	67	1	0	1	0	1	0	0	1	0	957	643	23	0	1130	0	ARMC8	3	137964017	Splice_Site	DEL	CGGAAGAAGGTGAGTCTGGGAGAG	TCGA-A4-A5Y1-01A-11D-A28G-10	90865158	137964017	60058413	14	4402											
GPR87	53836	hgsc.bcm.edu	37	chr3	151012432	151012432	+	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	tgactgccgtatgccatttgAcccccaaaggacttttaagt	10	12	8	11	1	0	2	0	2	0	0	0	3	0	3	4	1	2	1	4	1	3	4			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr3:151012432A>T	ENST00000260843.4	-	3	1066	c.602T>A	c.(601-603)gTc>gAc	p.V201D	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	201					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)			ATGCCATTTGACCCCCAAAGG	0.453																																					p.V201D		Atlas-SNP	.											.	GPR87	52	.	0			c.T602A						PASS	.						119	114	116					3																	151012432		2203	4300	6503	SO:0001583	missense	53836	exon3			CATTTGACCCCCA	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.602T>A	chr3.hg19:g.151012432A>T	ENSP00000260843:p.Val201Asp	125.0	0.0	.		178.0	36.0	.	NM_023915	Q5KU35|Q96JZ8|Q9BXC2	Missense_Mutation	SNP	ENST00000260843.4	hg19	CCDS3157.1	.	.	.	.	.	.	.	.	.	.	A	11.72	1.721769	0.30503	.	.	ENSG00000138271	ENST00000260843	T	0.36699	1.24	5.45	1.74	0.24563	GPCR, rhodopsin-like superfamily (1);	0.457951	0.21222	N	0.078134	T	0.25082	0.0609	L	0.29908	0.895	0.20821	N	0.999843	B	0.31274	0.317	B	0.38842	0.283	T	0.29027	-1.0025	10	0.10902	T	0.67	-6.9007	8.0205	0.30406	0.6554:0.0:0.3446:0.0	.	201	Q9BY21	GPR87_HUMAN	D	201	ENSP00000260843:V201D	ENSP00000260843:V201D	V	-	2	0	GPR87	152495122	0.000000	0.05858	0.009000	0.14445	0.543000	0.35085	1.208000	0.32345	0.120000	0.18254	-0.408000	0.06270	GTC	.	.	.	none		0.453	GPR87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357788.1			T	151012432	A	T	151012432	3	4	67	1	0	0	0	0	1	0	0	0	6723	275	10	5	478	5	GPR87	3	151012432	Missense_Mutation	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	13048415	151012432	47009998	15	4403											
SENP5	205564	hgsc.bcm.edu	37	chr3	196612951	196612952	+	Frame_Shift_Ins	INS	-	-	T																															ccagaacctaaagacccttcINSttgtcggcatcagccgtact																								rs148425489		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr3:196612951_196612952insT	ENST00000323460.5	+	2	1148_1149	c.899_900insT	c.(898-903)tcttgtfs	p.C301fs	SENP5_ENST00000445299.2_Frame_Shift_Ins_p.C301fs|SENP5_ENST00000419026.1_Intron	NM_152699.4	NP_689912.2	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	301					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)		AAAGACCCTTCTTGTCGGCATC	0.53																																					p.S300fs	Ovarian(47;891 1095 11174 13858 51271)	Atlas-Indel,Pindel	.											.	SENP5	68	.	0			c.899_900insT						PASS	.																																			SO:0001589	frameshift_variant	205564	exon2			.	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.901dupT	chr3.hg19:g.196612953_196612953dupT	ENSP00000327197:p.Cys301fs	72.0	0.0	0		94.0	46.0	0.489362	NM_152699	B4DY82|Q96SA5	Frame_Shift_Ins	INS	ENST00000323460.5	hg19	CCDS3322.1																																																																																			.	.	.	none		0.53	SENP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340524.1	NM_152699		T	196612952	-	T	196612951	7	5	67	1	0	1	1	0	0	0	0	0	14062	913	32	0	901	0	SENP5	3	196612951	Frame_Shift_Ins	INS	-	TCGA-A4-A5Y1-01A-11D-A28G-10	45600519	196612951	1409479	16	4404											
BOD1L	259282	hgsc.bcm.edu	37	chr4	13602646	13602646	+	Missense_Mutation	SNP	T	T	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	atcctttcctgagactgcacTggtcacactgctttctacaa	9	13	6	13	0	2	1	1	1	1	1	4	2	4	1	2	1	3	2	2	1	2	3			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr4:13602646T>G	ENST00000040738.5	-	10	6013	c.5878A>C	c.(5878-5880)Agt>Cgt	p.S1960R		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1960						nucleus (GO:0005634)	DNA binding (GO:0003677)										GAGACTGCACTGGTCACACTG	0.448																																					p.S1960R		Atlas-SNP	.											.	.	.	.	0			c.A5878C						PASS	.						140	135	136					4																	13602646		2203	4300	6503	SO:0001583	missense	259282	exon10			CTGCACTGGTCAC	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.5878A>C	chr4.hg19:g.13602646T>G	ENSP00000040738:p.Ser1960Arg	114.0	0.0	.		152.0	14.0	.	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	hg19	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	T	17.39	3.376793	0.61735	.	.	ENSG00000038219	ENST00000040738	T	0.17691	2.26	5.55	4.35	0.52113	.	0.000000	0.64402	D	0.000002	T	0.13970	0.0338	L	0.34521	1.04	0.39358	D	0.96587	P	0.41673	0.759	B	0.38327	0.271	T	0.03315	-1.1049	10	0.72032	D	0.01	-6.7552	11.456	0.50183	0.0:0.0:0.1507:0.8493	.	1960	Q8NFC6	BOD1L_HUMAN	R	1960	ENSP00000040738:S1960R	ENSP00000040738:S1960R	S	-	1	0	BOD1L	13211744	1.000000	0.71417	1.000000	0.80357	0.715000	0.41141	4.808000	0.62583	0.904000	0.36572	0.459000	0.35465	AGT	.	.	.	none		0.448	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		G	13602646	T	G	13602646	3	3	67	1	0	0	0	0	1	0	0	0	1483	1580	55	5	3345	5	BOD1L	4	13602646	Missense_Mutation	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10		13602646	177551630	17	4405											
PDS5A	23244	hgsc.bcm.edu	37	chr4	39851206	39851213	+	Frame_Shift_Del	DEL	CTTCATAA	CTTCATAA	-																															ttgatgttctctgccatcttCttcataaaggcatggctatt																										TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	CTTCATAA	CTTCATAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr4:39851206_39851213delCTTCATAA	ENST00000303538.8	-	27	3685_3692	c.3146_3153delTTATGAAG	c.(3145-3153)tttatgaagfs	p.FMK1049fs		NM_001100399.1	NP_001093869.1			PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)											breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						CTGCCATCTTCTTCATAAAGGCATGGCT	0.38																																					p.1049_1052del		Atlas-INDEL	.											.	PDS5A	114	.	0			c.3147_3154del						PASS	.																																			SO:0001589	frameshift_variant	23244	exon27			.	AF294791	CCDS47045.1, CCDS54759.1	4p14	2007-06-20			ENSG00000121892	ENSG00000121892			29088	protein-coding gene	gene with protein product		613200				11076961, 15855230	Standard	NM_001100399		Approved	KIAA0648, PIG54, SCC-112	uc003guv.4	Q29RF7	OTTHUMG00000160582	ENST00000303538.8:c.3146_3153delTTATGAAG	chr4.hg19:g.39851206_39851213delCTTCATAA	ENSP00000303427:p.Phe1049fs	95.0	0.0	0		82.0	23.0	0.280488	NM_001100399		Frame_Shift_Del	DEL	ENST00000303538.8	hg19	CCDS47045.1																																																																																			.	.	.	none		0.38	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200		-	39851213	CTTCATAA	-	39851206	7	5	67	1	0	1	0	1	0	0	0	0	11698	912	32	0	888	0	PDS5A	4	39851206	Frame_Shift_Del	DEL	CTTCATAA	TCGA-A4-A5Y1-01A-11D-A28G-10	26248560	39851206	151303070	18	4406											
SLC10A4	201780	hgsc.bcm.edu	37	chr4	48485850	48485850	+	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	gttccctcggccctgggcgcCccacgcgctcccgttctggg	1	8	13	19	5	1	0	0	0	1	0	4	0	3	0	5	3	0	3	5	3	0	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr4:48485850C>G	ENST00000273861.4	+	1	491	c.272C>G	c.(271-273)cCc>cGc	p.P91R		NM_152679.3	NP_689892.1	Q96EP9	NTCP4_HUMAN	solute carrier family 10, member 4	91						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						CCCTGGGCGCCCCACGCGCTC	0.756																																					p.P91R		Atlas-SNP	.											.	SLC10A4	23	.	0			c.C272G						PASS	.																																			SO:0001583	missense	201780	exon1			GGGCGCCCCACGC	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.272C>G	chr4.hg19:g.48485850C>G	ENSP00000273861:p.Pro91Arg	2.0	0.0	.		34.0	10.0	.	NM_152679	Q8WUZ2	Missense_Mutation	SNP	ENST00000273861.4	hg19	CCDS3482.1	.	.	.	.	.	.	.	.	.	.	c	14.82	2.648971	0.47362	.	.	ENSG00000145248	ENST00000273861	T	0.09255	3.0	4.58	3.74	0.42951	.	0.434744	0.26692	N	0.022981	T	0.08802	0.0218	L	0.40543	1.245	0.19575	N	0.999969	B	0.09022	0.002	B	0.06405	0.002	T	0.21690	-1.0238	10	0.45353	T	0.12	-26.3851	6.3555	0.21398	0.0:0.6733:0.1543:0.1724	.	91	Q96EP9	NTCP4_HUMAN	R	91	ENSP00000273861:P91R	ENSP00000273861:P91R	P	+	2	0	SLC10A4	48180607	0.004000	0.15560	0.599000	0.28851	0.923000	0.55619	1.782000	0.38654	1.159000	0.42565	-0.348000	0.07805	CCC	.	.	.	none		0.756	SLC10A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219926.3	NM_152679		G	48485850	C	G	48485850	3	3	67	1	0	0	0	0	1	0	0	0	14389	623	22	4	274	4	SLC10A4	4	48485850	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	8634644	48485850	142668426	19	4407											
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123260393	123260393	+	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	caaatttagctgtttaccagTatcaagagtagaatgcatgt	14	13	8	6	0	1	2	1	0	0	2	1	2	1	2	1	0	3	5	1	0	7	6			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr4:123260393T>A	ENST00000264501.4	+	72	12555	c.12182T>A	c.(12181-12183)gTa>gAa	p.V4061E	KIAA1109_ENST00000388738.3_Missense_Mutation_p.V4061E			Q2LD37	K1109_HUMAN	KIAA1109	4061					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						TGTTTACCAGTATCAAGAGTA	0.368																																					p.V4061E		Atlas-SNP	.											.	KIAA1109	424	.	0			c.T12182A						PASS	.						134	120	124					4																	123260393		1830	4088	5918	SO:0001583	missense	84162	exon70			TACCAGTATCAAG	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.12182T>A	chr4.hg19:g.123260393T>A	ENSP00000264501:p.Val4061Glu	115.0	0.0	.		121.0	66.0	.	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	28.3|28.3|28.3	4.907716|4.907716|4.907716	0.92107|0.92107|0.92107	.|.|.	.|.|.	ENSG00000138688|ENSG00000138688|ENSG00000138688	ENST00000442707|ENST00000264501;ENST00000388738;ENST00000438707|ENST00000306802	.|T;T;T|.	.|0.35789|.	.|2.31;2.31;1.29|.	5.81|5.81|5.81	5.81|5.81|5.81	0.92471|0.92471|0.92471	.|.|.	.|0.067355|.	.|0.64402|.	.|D|.	.|0.000010|.	T|T|T	0.68540|0.68540|0.68540	0.3012|0.3012|0.3012	L|L|L	0.49126|0.49126|0.49126	1.545|1.545|1.545	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|P;P|.	.|0.49961|.	.|0.899;0.93|.	.|P;P|.	.|0.45232|.	.|0.474;0.462|.	T|T|T	0.65853|0.65853|0.65853	-0.6067|-0.6067|-0.6067	5|10|5	.|0.66056|.	.|D|.	.|0.02|.	.|.|.	16.1637|16.1637|16.1637	0.81739|0.81739|0.81739	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.|.	.|4060;4061|.	.|Q2LD37-4;Q2LD37|.	.|.;K1109_HUMAN|.	R|E|N	6|4061;4061;730|437	.|ENSP00000264501:V4061E;ENSP00000373390:V4061E;ENSP00000410874:V730E|.	.|ENSP00000264501:V4061E|.	S|V|Y	+|+|+	3|2|1	2|0|0	KIAA1109|KIAA1109|KIAA1109	123479843|123479843|123479843	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.997000|0.997000|0.997000	0.53966|0.53966|0.53966	0.999000|0.999000|0.999000	0.98932|0.98932|0.98932	7.963000|7.963000|7.963000	0.87922|0.87922|0.87922	2.216000|2.216000|2.216000	0.71823|0.71823|0.71823	0.533000|0.533000|0.533000	0.62120|0.62120|0.62120	AGT|GTA|TAT	.	.	.	none		0.368	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		A	123260393	T	A	123260393	3	1	67	1	0	0	0	0	1	0	0	0	8215	1638	57	5	12460	5	KIAA1109	4	123260393	Missense_Mutation	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10	74774543	123260393	67893883	20	4408											
ODZ3	55714	hgsc.bcm.edu	37	chr4	183713663	183713663	+	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	ttgggtacaagtcggagggtCttattcaaatacagaaggca	13	10	12	6	1	2	1	1	0	1	1	3	2	2	2	0	4	2	2	0	4	6	5			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr4:183713663C>T	ENST00000511685.1	+	26	5961	c.5838C>T	c.(5836-5838)gtC>gtT	p.V1946V	TENM3_ENST00000406950.2_Silent_p.V1946V			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1946					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)										GTCGGAGGGTCTTATTCAAAT	0.448																																					p.V1946V		Atlas-SNP	.											.	.	.	.	0			c.C5838T						PASS	.						63	63	63					4																	183713663		1880	4104	5984	SO:0001819	synonymous_variant	55714	exon25			GAGGGTCTTATTC	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.5838C>T	chr4.hg19:g.183713663C>T		149.0	0.0	.		206.0	69.0	.	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Silent	SNP	ENST00000511685.1	hg19	CCDS47165.1																																																																																			.	.	.	none		0.448	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			T	183713663	C	T	183713663	2	4	67	1	0	0	0	0	0	0	0	1	10843	900	32	2		2	ODZ3	4	183713663	Silent	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	60453270	183713663	7440613	21	4409											
NKD2	85409	hgsc.bcm.edu	37	chr5	1033498	1033498	+	Missense_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	tccccctagtggcactccccGctgagaaagctgagggccgc	7	6	12	16	2	0	2	0	2	0	1	2	3	2	2	5	2	1	3	5	2	2	1	rs144426465		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr5:1033498G>A	ENST00000296849.5	+	5	443	c.214G>A	c.(214-216)Gct>Act	p.A72T	NKD2_ENST00000537972.1_Missense_Mutation_p.A72T|NKD2_ENST00000274150.4_Missense_Mutation_p.A72T	NM_033120.3	NP_149111.1	Q969F2	NKD2_HUMAN	naked cuticle homolog 2 (Drosophila)	72	Targeting to the basolateral cell membrane.				exocytosis (GO:0006887)|Golgi vesicle fusion to target membrane (GO:0048210)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein processing (GO:0010954)|protein targeting to plasma membrane (GO:0072661)|Wnt signaling pathway (GO:0016055)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cytoplasmic vesicle (GO:0031410)	calcium ion binding (GO:0005509)|growth factor binding (GO:0019838)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(3)|large_intestine(1)|lung(8)|pancreas(1)	14	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)		Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)			GGCACTCCCCGCTGAGAAAGC	0.692																																					p.A72T		Atlas-SNP	.											.	NKD2	39	.	0			c.G214A						PASS	.	C	THR/ALA	0,4370		0,0,2185	18	22	20		214	-0.3	0	5	dbSNP_134	20	6,8568		0,6,4281	yes	missense	NKD2	NM_033120.2	58	0,6,6466	AA,AG,GG		0.07,0.0,0.0464	benign	72/452	1033498	6,12938	2185	4287	6472	SO:0001583	missense	85409	exon5			CTCCCCGCTGAGA	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.214G>A	chr5.hg19:g.1033498G>A	ENSP00000296849:p.Ala72Thr	90.0	0.0	.		226.0	51.0	.	NM_001271082	Q96EK8|Q9BSN0	Missense_Mutation	SNP	ENST00000296849.5	hg19	CCDS3859.1	.	.	.	.	.	.	.	.	.	.	N	10.61	1.399838	0.25291	0.0	7.0E-4	ENSG00000145506	ENST00000296849;ENST00000274150;ENST00000537972	T;T;T	0.00535	6.73;6.73;6.73	3.69	-0.271	0.12922	.	0.159534	0.41396	N	0.000898	T	0.00328	0.0010	N	0.22421	0.69	0.80722	D	1	B;B	0.33022	0.002;0.394	B;B	0.25506	0.002;0.061	T	0.72721	-0.4208	10	0.66056	D	0.02	-8.4045	2.08	0.03633	0.1396:0.4077:0.273:0.1798	.	72;72	Q969F2-2;Q969F2	.;NKD2_HUMAN	T	72	ENSP00000296849:A72T;ENSP00000274150:A72T;ENSP00000440925:A72T	ENSP00000274150:A72T	A	+	1	0	NKD2	1086498	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.116000	0.10724	-0.934000	0.03733	-5.484000	0.00000	GCT	.	G|1.000;A|0.000	0.000	weak		0.692	NKD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206720.2	NM_033120		A	1033498	G	A	1033498	3	1	67	1	0	0	0	0	1	0	0	0	10449	1087	38	1	232	1	NKD2	5	1033498	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10		1033498	179881762	22	4410											
DEPDC1B	55789	hgsc.bcm.edu	37	chr5	59893587	59893587	+	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	tgtggaagtattattacattCgaaaacttctagttctttga	12	17	7	5	1	2	1	0	1	2	0	3	3	2	2	0	1	2	2	0	1	7	8			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr5:59893587C>T	ENST00000265036.5	-	11	1650	c.1583G>A	c.(1582-1584)cGa>cAa	p.R528Q	DEPDC1B_ENST00000453022.2_Missense_Mutation_p.R466Q|DEPDC1B_ENST00000545085.1_Missense_Mutation_p.R439Q	NM_018369.2	NP_060839.2	Q8WUY9	DEP1B_HUMAN	DEP domain containing 1B	528					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(2)|skin(2)	17		Lung NSC(810;0.000214)|Prostate(74;0.0147)|Breast(144;0.0991)|Ovarian(174;0.17)				TTATTACATTCGAAAACTTCT	0.418																																					p.R528Q		Atlas-SNP	.											DEPDC1B,NS,carcinoma,-1,1	DEPDC1B	56	.	0			c.G1583A						PASS	.						174	167	170					5																	59893587		2203	4300	6503	SO:0001583	missense	55789	exon11			TACATTCGAAAAC	AF303178	CCDS3977.1, CCDS47214.1	5q12	2008-02-05			ENSG00000035499	ENSG00000035499			24902	protein-coding gene	gene with protein product	"breast cancer cell 3"					12477932	Standard	NM_001145208		Approved	XTP1, BRCC3	uc003jsh.3	Q8WUY9	OTTHUMG00000097083	ENST00000265036.5:c.1583G>A	chr5.hg19:g.59893587C>T	ENSP00000265036:p.Arg528Gln	71.0	0.0	.		77.0	21.0	.	NM_018369	A8K3R9|B4DUT4|Q86WJ3|Q8IZY6|Q9NUN3|Q9NW57	Missense_Mutation	SNP	ENST00000265036.5	hg19	CCDS3977.1	.	.	.	.	.	.	.	.	.	.	C	34	5.383654	0.95967	.	.	ENSG00000035499	ENST00000265036;ENST00000453022;ENST00000545085	T;T;T	0.49432	1.96;1.18;0.78	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.67767	0.2928	M	0.68593	2.085	0.53688	D	0.999979	D;D	0.89917	0.997;1.0	D;D	0.70227	0.968;0.941	T	0.64850	-0.6310	9	.	.	.	-9.0991	19.4868	0.95032	0.0:1.0:0.0:0.0	.	466;528	B4DUT4;Q8WUY9	.;DEP1B_HUMAN	Q	528;466;439	ENSP00000265036:R528Q;ENSP00000389101:R466Q;ENSP00000438320:R439Q	.	R	-	2	0	DEPDC1B	59929344	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.694000	0.74587	2.838000	0.97847	0.591000	0.81541	CGA	.	.	.	none		0.418	DEPDC1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214207.1	NM_018369		T	59893587	C	T	59893587	3	4	67	1	0	0	0	0	1	0	0	0	4442	884	31	1	10	1	DEPDC1B	5	59893587	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	58860089	59893587	121021673	23	4411											
AP3B1	8546	hgsc.bcm.edu	37	chr5	77521385	77521385	+	Missense_Mutation	SNP	A	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	ctgtgcttttatctttcagaAgtttttcaattacttcaatt	9	21	4	7	0	4	1	3	0	1	1	4	1	4	1	0	0	2	2	0	0	5	8			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr5:77521385A>C	ENST00000255194.6	-	6	759	c.584T>G	c.(583-585)cTt>cGt	p.L195R	AP3B1_ENST00000519295.1_Missense_Mutation_p.L146R	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	195					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)		ATCTTTCAGAAGTTTTTCAAT	0.239									Hermansky-Pudlak syndrome																												p.L195R		Atlas-SNP	.											.	AP3B1	94	.	0			c.T584G						PASS	.						55	55	55					5																	77521385		2193	4276	6469	SO:0001583	missense	8546	exon6	Familial Cancer Database	HPS, HPS1-8	TTCAGAAGTTTTT	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.584T>G	chr5.hg19:g.77521385A>C	ENSP00000255194:p.Leu195Arg	46.0	0.0	.		88.0	54.0	.	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Missense_Mutation	SNP	ENST00000255194.6	hg19	CCDS4041.1	.	.	.	.	.	.	.	.	.	.	A	18.69	3.678934	0.68042	.	.	ENSG00000132842	ENST00000255194;ENST00000519295;ENST00000535760;ENST00000535667	T;T	0.18502	2.21;2.21	5.59	4.44	0.53790	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.54431	0.1858	H	0.97023	3.925	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.67023	-0.5775	10	0.87932	D	0	-1.7217	11.3981	0.49854	0.9293:0.0:0.0707:0.0	.	195	O00203	AP3B1_HUMAN	R	195;146;195;99	ENSP00000255194:L195R;ENSP00000430597:L146R	ENSP00000255194:L195R	L	-	2	0	AP3B1	77557141	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	9.245000	0.95431	0.959000	0.37980	-0.361000	0.07541	CTT	.	.	.	none		0.239	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2			C	77521385	A	C	77521385	3	2	67	1	0	0	0	0	1	0	0	0	744	72	3	5	2788	5	AP3B1	5	77521385	Missense_Mutation	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	17627798	77521385	103393875	24	4412											
IK	3550	hgsc.bcm.edu	37	chr5	140037217	140037217	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	catacctgaggcagggaaccCgtaacaagaagcttaagaag	16	5	11	9	1	0	3	0	1	0	2	0	4	0	4	2	2	4	3	2	2	7	3			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr5:140037217C>T	ENST00000417647.2	+	10	1019	c.880C>T	c.(880-882)Cgt>Tgt	p.R294C		NM_006083.3	NP_006074.2	Q13123	RED_HUMAN	IK cytokine, down-regulator of HLA II	294					cell-cell signaling (GO:0007267)|immune response (GO:0006955)	extracellular space (GO:0005615)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			large_intestine(1)	1		all_hematologic(541;4.8e-07)|all_lung(500;0.000434)|Lung NSC(810;0.00161)|Breast(839;0.128)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAGGGAACCCGTAACAAGAA	0.473																																					p.R294C		Atlas-SNP	.											.	IK	46	.	0			c.C880T						PASS	.						129	116	120					5																	140037217		1910	4122	6032	SO:0001583	missense	3550	exon10			GGAACCCGTAACA	BC051295	CCDS47280.1	5q31.3	2008-08-07			ENSG00000113141	ENSG00000113141			5958	protein-coding gene	gene with protein product		600549				7970704	Standard	NM_006083		Approved		uc003lgq.3	Q13123	OTTHUMG00000163374	ENST00000417647.2:c.880C>T	chr5.hg19:g.140037217C>T	ENSP00000396301:p.Arg294Cys	203.0	0.0	.		269.0	59.0	.	NM_006083	Q6IPD8	Missense_Mutation	SNP	ENST00000417647.2	hg19	CCDS47280.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.584507	0.86748	.	.	ENSG00000113141	ENST00000417647	.	.	.	5.48	5.48	0.80851	RED-like, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.80722	0.4677	M	0.85373	2.75	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.83092	-0.0132	9	0.72032	D	0.01	.	14.198	0.65684	0.1496:0.8504:0.0:0.0	.	294;294	Q9UK43;Q13123	.;RED_HUMAN	C	294	.	ENSP00000396301:R294C	R	+	1	0	IK	140017401	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.692000	0.54727	2.730000	0.93505	0.655000	0.94253	CGT	.	.	.	none		0.473	IK-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372897.1	NM_006083		T	140037217	C	T	140037217	3	4	67	1	0	0	0	0	1	0	0	0	7615	652	23	1	918	1	IK	5	140037217	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	62515832	140037217	40878043	25	4413											
FAM65B	9750	hgsc.bcm.edu	37	chr6	24836059	24836059	+	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	tgtgtcttcagtgagcgcttCactgagatgccccctggctt	5	13	11	12	1	3	2	2	2	1	1	3	3	3	2	2	1	2	2	2	1	0	3			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr6:24836059C>T	ENST00000259698.4	-	16	2318	c.2143G>A	c.(2143-2145)Gaa>Aaa	p.E715K	FAM65B_ENST00000538035.1_Missense_Mutation_p.E694K	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	715					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						GTGAGCGCTTCACTGAGATGC	0.527																																					p.E715K		Atlas-SNP	.											.	FAM65B	134	.	0			c.G2143A						PASS	.						105	90	94					6																	24836059		692	1591	2283	SO:0001583	missense	9750	exon16			GCGCTTCACTGAG	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.2143G>A	chr6.hg19:g.24836059C>T	ENSP00000259698:p.Glu715Lys	170.0	0.0	.		252.0	75.0	.	NM_014722	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Missense_Mutation	SNP	ENST00000259698.4	hg19	CCDS47383.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.966222	0.74131	.	.	ENSG00000111913	ENST00000259698;ENST00000538035	T;T	0.35789	1.29;1.29	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.24084	0.0583	L	0.43152	1.355	0.80722	D	1	B;B	0.31548	0.264;0.328	B;B	0.30495	0.085;0.116	T	0.09640	-1.0665	10	0.66056	D	0.02	-10.1386	19.1916	0.93669	0.0:1.0:0.0:0.0	.	694;715	F5GX51;Q9Y4F9	.;FA65B_HUMAN	K	715;694	ENSP00000259698:E715K;ENSP00000441138:E694K	ENSP00000259698:E715K	E	-	1	0	FAM65B	24944038	1.000000	0.71417	0.595000	0.28798	0.748000	0.42578	7.452000	0.80683	2.541000	0.85698	0.655000	0.94253	GAA	.	.	.	none		0.527	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2			T	24836059	C	T	24836059	3	4	67	1	0	0	0	0	1	0	0	0	5607	835	29	2	1095	2	FAM65B	6	24836059	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10		24836059	146279008	26	4414											
HIST1H1C	3006	hgsc.bcm.edu	37	chr6	26056096	26056096	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcacagccttagcagcactTttggcagctttcttgggctt	6	15	9	11	0	2	0	1	0	1	0	2	0	2	0	1	2	4	5	1	2	1	7			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr6:26056096T>C	ENST00000343677.2	-	1	603	c.561A>G	c.(559-561)aaA>aaG	p.K187K		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	187					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						TAGCAGCACTTTTGGCAGCTT	0.547																																					p.K187K		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.A561G						PASS	.						89	96	93					6																	26056096		2203	4300	6503	SO:0001819	synonymous_variant	3006	exon1			AGCACTTTTGGCA	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.561A>G	chr6.hg19:g.26056096T>C		95.0	0.0	.		143.0	12.0	.	NM_005319	A8K4I2	Silent	SNP	ENST00000343677.2	hg19	CCDS4577.1																																																																																			.	.	.	none		0.547	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319		C	26056096	T	C	26056096	2	2	67	1	0	0	0	0	0	0	0	1	7131	1838	64	3		3	HIST1H1C	6	26056096	Silent	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10	1220037	26056096	145058971	27	4415											
SLC26A5	375611	hgsc.bcm.edu	37	chr7	103050896	103050896	+	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	caaacagatattttaacatgGaggtgaagacatgcacagct	16	9	9	7	0	0	3	0	1	0	2	0	4	0	4	0	2	4	2	0	2	4	3			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr7:103050896G>C	ENST00000306312.3	-	7	932	c.671C>G	c.(670-672)tCc>tGc	p.S224C	SLC26A5_ENST00000393729.1_Missense_Mutation_p.S187C|SLC26A5_ENST00000393735.2_Missense_Mutation_p.S224C|SLC26A5_ENST00000432958.2_Missense_Mutation_p.S224C|SLC26A5_ENST00000339444.6_Missense_Mutation_p.S224C|SLC26A5_ENST00000393723.1_Missense_Mutation_p.S224C|SLC26A5_ENST00000393727.1_Missense_Mutation_p.S224C|SLC26A5_ENST00000356767.4_Missense_Mutation_p.S224C|SLC26A5_ENST00000393730.1_Missense_Mutation_p.S224C|SLC26A5_ENST00000354356.4_5'UTR	NM_198999.2	NP_945350.1	P58743	S26A5_HUMAN	solute carrier family 26 (anion exchanger), member 5	224					regulation of cell shape (GO:0008360)|regulation of membrane potential (GO:0042391)|sensory perception of sound (GO:0007605)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)	secondary active sulfate transmembrane transporter activity (GO:0008271)			endometrium(5)|kidney(2)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)	43						TTTTAACATGGAGGTGAAGAC	0.443																																					p.S224C		Atlas-SNP	.											.	SLC26A5	231	.	0			c.C671G						PASS	.						73	71	71					7																	103050896		2203	4300	6503	SO:0001583	missense	375611	exon7			AACATGGAGGTGA	AC005064	CCDS5733.1, CCDS43630.1, CCDS55150.1, CCDS5732.1, CCDS43629.1	7q22	2013-07-18	2013-07-18	2005-09-13	ENSG00000170615	ENSG00000170615		"Solute carriers"	9359	protein-coding gene	gene with protein product	"deafness, neurosensory, autosomal recessive, 61"	604943	"prestin (motor protein)"	PRES		10821263	Standard	NM_206883		Approved	DFNB61	uc003vbz.3	P58743	OTTHUMG00000149911	ENST00000306312.3:c.671C>G	chr7.hg19:g.103050896G>C	ENSP00000304783:p.Ser224Cys	86.0	0.0	.		83.0	26.0	.	NM_206883	Q496J2|Q7Z7F3|Q86UF8|Q86UF9|Q86UG0	Missense_Mutation	SNP	ENST00000306312.3	hg19	CCDS5733.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.816614	0.90790	.	.	ENSG00000170615	ENST00000339444;ENST00000356767;ENST00000393735;ENST00000306312;ENST00000393730;ENST00000432958;ENST00000393729;ENST00000393727;ENST00000393723	D;D;D;D;D;D;D;D;D	0.93859	-3.3;-3.3;-3.3;-3.3;-3.3;-3.3;-3.3;-3.3;-3.3	5.72	5.72	0.89469	Sulphate transporter (1);	0.000000	0.85682	D	0.000000	D	0.97898	0.9309	H	0.95365	3.66	0.80722	D	1	D;D;D;D;D	0.76494	0.997;0.998;0.999;0.997;0.999	D;D;D;D;D	0.73380	0.98;0.974;0.967;0.931;0.956	D	0.98561	1.0641	10	0.87932	D	0	.	19.885	0.96909	0.0:0.0:1.0:0.0	.	224;224;224;224;224	P58743;Q496J2;P58743-4;P58743-3;P58743-2	S26A5_HUMAN;.;.;.;.	C	224;224;224;224;224;224;187;224;224	ENSP00000342396:S224C;ENSP00000349210:S224C;ENSP00000377336:S224C;ENSP00000304783:S224C;ENSP00000377331:S224C;ENSP00000389733:S224C;ENSP00000377330:S187C;ENSP00000377328:S224C;ENSP00000377324:S224C	ENSP00000304783:S224C	S	-	2	0	SLC26A5	102838132	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.330000	0.96422	2.708000	0.92522	0.591000	0.81541	TCC	.	.	.	none		0.443	SLC26A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313860.1	NM_198999		C	103050896	G	C	103050896	3	2	67	1	0	0	0	0	1	0	0	0	14533	1174	41	4	1660	4	SLC26A5	7	103050896	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10		103050896	56087767	28	4416											
STAU2	27067	hgsc.bcm.edu	37	chr8	74464271	74464271	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagccttgaatccttgctaaAtattccagttgttttgaagg	11	15	8	7	0	0	2	0	2	0	0	2	2	2	2	3	1	2	3	3	1	6	8			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr8:74464271A>G	ENST00000521451.1	-	8	1222	c.846T>C	c.(844-846)taT>taC	p.Y282Y	STAU2_ENST00000517542.1_Silent_p.Y464Y|STAU2_ENST00000523558.1_Silent_p.Y330Y|STAU2_ENST00000521210.1_Silent_p.Y398Y|STAU2_ENST00000524300.1_Silent_p.Y502Y|STAU2_ENST00000522695.1_Silent_p.Y470Y|STAU2_ENST00000519961.1_Silent_p.Y502Y|STAU2_ENST00000355780.5_Silent_p.Y470Y|STAU2_ENST00000521727.1_Silent_p.Y482Y|STAU2_ENST00000522509.1_Silent_p.Y470Y			Q9NUL3	STAU2_HUMAN	staufen double-stranded RNA binding protein 2	502					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)			TCCTTGCTAAATATTCCAGTT	0.363																																					p.Y502Y		Atlas-SNP	.											.	STAU2	148	.	0			c.T1506C						PASS	.						56	61	59					8																	74464271		2203	4297	6500	SO:0001819	synonymous_variant	27067	exon13			TGCTAAATATTCC	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.846T>C	chr8.hg19:g.74464271A>G		152.0	0.0	.		143.0	61.0	.	NM_001164380	B7Z1I6|B7Z292|B7Z8B4|E7ER74|E9PEI3|E9PF26|E9PF50|Q6AHY7|Q96HM0|Q96HM1|Q9NVI5|Q9UGG6	Silent	SNP	ENST00000521451.1	hg19																																																																																				.	.	.	none		0.363	STAU2-006	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000379006.4	NM_001164380		G	74464271	A	G	74464271	2	3	67	1	0	0	0	0	0	0	0	1	15285	108	4	3		3	STAU2	8	74464271	Silent	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10		74464271	71899751	29	4417											
PSIP1	11168	hgsc.bcm.edu	37	chr9	15468982	15468982	+	Frame_Shift_Del	DEL	G	G	-																															agtgtagtaatcatctctgtGtgtttctgagcttgttgcat																										TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr9:15468982delG	ENST00000380733.4	-	13	1522	c.1179delC	c.(1177-1179)cacfs	p.H393fs	PSIP1_ENST00000380738.4_Frame_Shift_Del_p.H393fs			O75475	PSIP1_HUMAN	PC4 and SFRS1 interacting protein 1	393					establishment of integrated proviral latency (GO:0075713)|mRNA 5'-splice site recognition (GO:0000395)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to heat (GO:0009408)|response to oxidative stress (GO:0006979)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear heterochromatin (GO:0005720)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription coactivator activity (GO:0001105)|supercoiled DNA binding (GO:0097100)			breast(2)|endometrium(2)|kidney(1)|lung(3)|prostate(1)	9				GBM - Glioblastoma multiforme(50;2.38e-06)		TCATCTCTGTGTGTTTCTGAG	0.328																																					p.T394fs		Atlas-Indel,Pindel	.											.	PSIP1	93	.	0			c.1180delA						PASS	.						89	82	84					9																	15468982		2202	4300	6502	SO:0001589	frameshift_variant	11168	exon13			.	AF098482	CCDS6479.1, CCDS6480.1	9p22.2	2008-02-05	2004-02-24		ENSG00000164985	ENSG00000164985			9527	protein-coding gene	gene with protein product		603620	"PC4 and SFRS1 interacting protein 2"	PSIP2		9822615, 9885563	Standard	NM_033222		Approved	p52, LEDGF, p75	uc003zlw.4	O75475	OTTHUMG00000021021	ENST00000380733.4:c.1179delC	chr9.hg19:g.15468982delG	ENSP00000370109:p.His393fs	99.0	0.0	0		51.0	28.0	0.54902	NM_001128217	D3DRI9|O00256|O95368|Q6P391|Q86YB9|Q9NZI3|Q9UER6	Frame_Shift_Del	DEL	ENST00000380733.4	hg19	CCDS6479.1																																																																																			.	.	.	none		0.328	PSIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055445.1	NM_033222		-	15468982	G	-	15468982	7	5	67	1	0	1	0	1	0	0	0	0	12673	1368	48	0	429	0	PSIP1	9	15468982	Frame_Shift_Del	DEL	G	TCGA-A4-A5Y1-01A-11D-A28G-10		15468982	125744449	30	4418											
OR13F1	138805	hgsc.bcm.edu	37	chr9	107267461	107267461	+	Missense_Mutation	SNP	T	T	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	gccttgaaaaaattgctgatTagaaatcattttaatactgc	15	14	6	6	0	1	3	1	2	0	1	1	3	1	3	1	0	3	1	1	0	7	6			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr9:107267461T>G	ENST00000334726.2	+	1	1007	c.918T>G	c.(916-918)atT>atG	p.I306M		NM_001004485.1	NP_001004485.1	Q8NGS4	O13F1_HUMAN	olfactory receptor, family 13, subfamily F, member 1	306						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						AATTGCTGATTAGAAATCATT	0.353																																					p.I306M		Atlas-SNP	.											.	OR13F1	75	.	0			c.T918G						PASS	.						39	42	41					9																	107267461		2203	4300	6503	SO:0001583	missense	138805	exon1			GCTGATTAGAAAT		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.918T>G	chr9.hg19:g.107267461T>G	ENSP00000334452:p.Ile306Met	69.0	0.0	.		44.0	18.0	.	NM_001004485	Q6IF50	Missense_Mutation	SNP	ENST00000334726.2	hg19	CCDS35087.1	.	.	.	.	.	.	.	.	.	.	T	2.865	-0.235310	0.05983	.	.	ENSG00000186881	ENST00000334726	T	0.37411	1.2	4.3	-3.06	0.05379	.	0.941008	0.08732	N	0.901923	T	0.15262	0.0368	N	0.10972	0.075	0.09310	N	1	B	0.16166	0.016	B	0.10450	0.005	T	0.20207	-1.0282	10	0.33141	T	0.24	.	3.0534	0.06176	0.1435:0.0881:0.443:0.3254	.	306	Q8NGS4	O13F1_HUMAN	M	306	ENSP00000334452:I306M	ENSP00000334452:I306M	I	+	3	3	OR13F1	106307282	0.000000	0.05858	0.004000	0.12327	0.446000	0.32137	-0.563000	0.05943	-0.521000	0.06426	-0.290000	0.09829	ATT	.	.	.	none		0.353	OR13F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053475.1			G	107267461	T	G	107267461	3	3	67	1	0	0	0	0	1	0	0	0	10948	1742	61	5	920	5	OR13F1	9	107267461	Missense_Mutation	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10	91798479	107267461	33945970	31	4419											
SPTAN1	6709	hgsc.bcm.edu	37	chr9	131379924	131379924	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccatctctcattcagggagaAgaagctgctggtgggctcag	9	9	13	10	0	4	2	3	0	1	2	5	3	4	2	1	3	2	3	1	3	2	1			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr9:131379924A>G	ENST00000372731.4	+	41	5458	c.5348A>G	c.(5347-5349)aAg>aGg	p.K1783R	SPTAN1_ENST00000372739.3_Missense_Mutation_p.K1788R|SPTAN1_ENST00000358161.5_Missense_Mutation_p.K1788R	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1783					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						TTCAGGGAGAAGAAGCTGCTG	0.567																																					p.K1788R	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.A5363G						PASS	.						53	54	54					9																	131379924		2203	4300	6503	SO:0001583	missense	6709	exon42			GGGAGAAGAAGCT	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.5348A>G	chr9.hg19:g.131379924A>G	ENSP00000361816:p.Lys1783Arg	118.0	0.0	.		143.0	50.0	.	NM_001130438	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Missense_Mutation	SNP	ENST00000372731.4	hg19	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.628279	0.87560	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719;ENST00000372721	T;T;T	0.56444	0.46;0.46;0.46	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.68622	0.3021	L	0.55103	1.725	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.97110	1.0;0.996;0.998	T	0.71101	-0.4690	10	0.66056	D	0.02	.	15.8191	0.78626	1.0:0.0:0.0:0.0	.	1763;1788;1783	Q13813-3;Q13813-2;Q13813	.;.;SPTA2_HUMAN	R	1788;1783;1788;1763;32	ENSP00000350882:K1788R;ENSP00000361816:K1783R;ENSP00000361824:K1788R	ENSP00000350882:K1788R	K	+	2	0	SPTAN1	130419745	1.000000	0.71417	1.000000	0.80357	0.685000	0.39939	8.824000	0.92023	2.202000	0.70862	0.379000	0.24179	AAG	.	.	.	none		0.567	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		G	131379924	A	G	131379924	3	3	67	1	0	0	0	0	1	0	0	0	15129	72	3	3	5525	3	SPTAN1	9	131379924	Missense_Mutation	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	24112463	131379924	9833507	32	4420											
EHMT1	79813	hgsc.bcm.edu	37	chr9	140710514	140710514	+	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	cgtcgtacagaatggtctcaGgtgagaggcagcttcctgcc	8	9	13	11	2	1	2	1	1	1	2	4	3	2	2	2	3	3	3	2	3	2	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr9:140710514G>A	ENST00000460843.1	+	23	3401	c.3374G>A	c.(3373-3375)aGg>aAg	p.R1125K		NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	1125					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)		AATGGTCTCAGGTGAGAGGCA	0.552																																					p.R1125K		Atlas-SNP	.											.	EHMT1	196	.	0			c.G3374A						PASS	.						52	45	48					9																	140710514		2203	4300	6503	SO:0001630	splice_region_variant	79813	exon23			GTCTCAGGTGAGA	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.3374+1G>A	chr9.hg19:g.140710514G>A		57.0	0.0	.		67.0	35.0	.	NM_024757	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Missense_Mutation	SNP	ENST00000460843.1	hg19	CCDS7050.2	.	.	.	.	.	.	.	.	.	.	G	10.78	1.447711	0.26074	.	.	ENSG00000181090	ENST00000371400;ENST00000460843	D	0.88741	-2.42	5.11	5.11	0.69529	SET domain (1);	0.042517	0.85682	D	0.000000	T	0.73048	0.3537	N	0.04805	-0.155	0.80722	D	1	B	0.12013	0.005	B	0.08055	0.003	T	0.68379	-0.5424	10	0.02654	T	1	.	11.9694	0.53055	0.0798:0.0:0.9202:0.0	.	1125	Q9H9B1	EHMT1_HUMAN	K	1094;1125	ENSP00000417980:R1125K	ENSP00000360453:R1094K	R	+	2	0	EHMT1	139830335	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	7.876000	0.87215	2.357000	0.79964	0.591000	0.81541	AGG	.	.	.	none		0.552	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757	Missense_Mutation	A	140710514	G	A	140710514	5	1	67	1	0	0	0	0	0	0	1	0	4985	1014	35	2	3513	2	EHMT1	9	140710514	Splice_Site	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	9330590	140710514	502917	33	4421											
CUBN	8029	hgsc.bcm.edu	37	chr10	17169853	17169853	+	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	aattaagctgatagatttgaCtagatatattttgaggcaga	15	14	9	3	0	0	6	0	3	0	3	0	6	0	6	0	1	1	2	0	1	6	8	rs543983858		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr10:17169853C>A	ENST00000377833.4	-	3	388	c.323G>T	c.(322-324)aGt>aTt	p.S108I	CUBN_ENST00000377823.1_Missense_Mutation_p.S108I	NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	108					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)	ATAGATTTGACTAGATATATT	0.338																																					p.S108I		Atlas-SNP	.											.	CUBN	515	.	0			c.G323T						PASS	.						202	199	200					10																	17169853		2202	4300	6502	SO:0001583	missense	8029	exon3			ATTTGACTAGATA	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.323G>T	chr10.hg19:g.17169853C>A	ENSP00000367064:p.Ser108Ile	58.0	0.0	.		39.0	19.0	.	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	C	14.20	2.465566	0.43839	.	.	ENSG00000107611	ENST00000377833;ENST00000377823	T;D	0.89939	-1.04;-2.59	5.39	-1.65	0.08291	.	0.658141	0.14204	N	0.334504	T	0.77103	0.4081	N	0.19112	0.55	0.24501	N	0.994254	P	0.41265	0.744	B	0.36030	0.216	T	0.66991	-0.5783	10	0.33940	T	0.23	.	11.3077	0.49345	0.0:0.445:0.0:0.555	.	108	O60494	CUBN_HUMAN	I	108	ENSP00000367064:S108I;ENSP00000367054:S108I	ENSP00000367054:S108I	S	-	2	0	CUBN	17209859	0.964000	0.33143	0.979000	0.43373	0.946000	0.59487	-0.127000	0.10547	-0.237000	0.09739	0.650000	0.86243	AGT	.	.	.	none		0.338	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		A	17169853	C	A	17169853	3	1	67	1	0	0	0	0	1	0	0	0	4053	565	20	4	10808	4	CUBN	10	17169853	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10		17169853	118364894	34	4422											
SLC25A28	81894	hgsc.bcm.edu	37	chr10	101370968	101370968	+	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	ctcctgcaggaattcataggTcatgaagtgaatggcttgga	11	11	12	7	0	2	2	2	2	0	0	3	4	3	4	1	4	1	2	1	4	4	3			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr10:101370968T>A	ENST00000370495.4	-	4	761	c.733A>T	c.(733-735)Acc>Tcc	p.T245S	SLC25A28_ENST00000496035.1_5'UTR	NM_031212.3	NP_112489.3	Q96A46	MFRN2_HUMAN	solute carrier family 25 (mitochondrial iron transporter), member 28	245					ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|stomach(1)	11		Colorectal(252;0.234)		Epithelial(162;2.57e-10)|all cancers(201;2.01e-08)		AATTCATAGGTCATGAAGTGA	0.567																																					p.T245S		Atlas-SNP	.											.	SLC25A28	34	.	0			c.A733T						PASS	.						66	69	68					10																	101370968		2005	4172	6177	SO:0001583	missense	81894	exon4			CATAGGTCATGAA	AF327402	CCDS41559.1	10q24.2	2013-05-22	2012-03-29		ENSG00000155287	ENSG00000155287		"Solute carriers"	23472	protein-coding gene	gene with protein product	"mitoferrin 2"	609767	"solute carrier family 25, member 28"			11297739	Standard	NM_031212		Approved	MRS3/4, MRS4L	uc001kpx.2	Q96A46	OTTHUMG00000018886	ENST00000370495.4:c.733A>T	chr10.hg19:g.101370968T>A	ENSP00000359526:p.Thr245Ser	185.0	0.0	.		137.0	44.0	.	NM_031212	Q4VBZ0|Q5T777|Q86VX5|Q969G8|Q9H2J3	Missense_Mutation	SNP	ENST00000370495.4	hg19	CCDS41559.1	.	.	.	.	.	.	.	.	.	.	T	18.84	3.710038	0.68730	.	.	ENSG00000155287	ENST00000434701;ENST00000370495	T;T	0.80123	-1.34;-1.34	5.41	5.41	0.78517	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	T	0.76681	0.4021	L	0.49126	1.545	0.58432	D	0.999999	P	0.42456	0.78	B	0.42138	0.377	T	0.78175	-0.2306	10	0.52906	T	0.07	-32.8904	10.7365	0.46128	0.0:0.0735:0.0:0.9265	.	245	Q96A46	MFRN2_HUMAN	S	106;245	ENSP00000399102:T106S;ENSP00000359526:T245S	ENSP00000359526:T245S	T	-	1	0	SLC25A28	101360958	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.678000	0.61641	2.271000	0.75665	0.459000	0.35465	ACC	.	.	.	none		0.567	SLC25A28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049801.1	NM_031212		A	101370968	T	A	101370968	3	1	67	1	0	0	0	0	1	0	0	0	14504	1667	58	5	365	5	SLC25A28	10	101370968	Missense_Mutation	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10	84201115	101370968	34163779	35	4423											
VAX1	11023	hgsc.bcm.edu	37	chr10	118893699	118893699	+	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	ccgagcagcgagggcaccggCaggctgaagaggctgtggcc	8	3	18	12	3	0	2	0	1	0	1	0	4	0	2	3	5	2	5	3	5	1	0			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr10:118893699C>T	ENST00000369206.5	-	3	824	c.825G>A	c.(823-825)ctG>ctA	p.L275L	VAX1_ENST00000277905.2_Intron	NM_001112704.1	NP_001106175.1	Q5SQQ9	VAX1_HUMAN	ventral anterior homeobox 1	275					axon guidance (GO:0007411)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|palate development (GO:0060021)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(1)|lung(8)|ovary(2)	12				all cancers(201;0.0108)		AGGGCACCGGCAGGCTGAAGA	0.736																																					p.L275L		Atlas-SNP	.											.	VAX1	50	.	0			c.G825A						PASS	.						18	20	19					10																	118893699		692	1591	2283	SO:0001819	synonymous_variant	11023	exon3			CACCGGCAGGCTG	AK127095	CCDS7597.1, CCDS44483.1	10q26.11	2011-06-20			ENSG00000148704	ENSG00000148704		"Homeoboxes / ANTP class : NKL subclass"	12660	protein-coding gene	gene with protein product		604294				9636075, 10485894	Standard	NM_199131		Approved		uc009xyx.3	Q5SQQ9	OTTHUMG00000019117	ENST00000369206.5:c.825G>A	chr10.hg19:g.118893699C>T		7.0	0.0	.		15.0	8.0	.	NM_001112704	B1AVW5|Q6ZSX0	Silent	SNP	ENST00000369206.5	hg19	CCDS44483.1																																																																																			.	.	.	none		0.736	VAX1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050559.3	XM_301242		T	118893699	C	T	118893699	2	4	67	1	0	0	0	0	0	0	0	1	17146	697	25	2		2	VAX1	10	118893699	Silent	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	17522731	118893699	16641048	36	4424											
KCNQ1	3784	hgsc.bcm.edu	37	chr11	2798240	2798240	+	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	gaccagtccattgggaagccCtcactgttcatctccgtctc	7	11	8	15	1	4	0	2	0	2	0	7	2	5	1	4	1	1	1	4	1	1	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr11:2798240C>G	ENST00000155840.5	+	14	1818	c.1710C>G	c.(1708-1710)ccC>ccG	p.P570P	KCNQ1_ENST00000335475.5_Silent_p.P443P	NM_000218.2	NP_000209.2	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 1	570					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)	TTGGGAAGCCCTCACTGTTCA	0.602																																					p.P570P		Atlas-SNP	.											.	KCNQ1	60	.	0			c.C1710G	GRCh37	CD057258	KCNQ1	D		PASS	.						249	175	200					11																	2798240		2202	4299	6501	SO:0001819	synonymous_variant	3784	exon14			GAAGCCCTCACTG	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.1710C>G	chr11.hg19:g.2798240C>G		142.0	0.0	.		185.0	53.0	.	NM_000218	O00347|O60607|O94787|Q14D14|Q7Z6G9|Q92960|Q9UMN8|Q9UMN9	Silent	SNP	ENST00000155840.5	hg19	CCDS7736.1																																																																																			.	.	.	none		0.602	KCNQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027382.2	NM_000218		G	2798240	C	G	2798240	2	3	67	1	0	0	0	0	0	0	0	1	8089	668	24	4		4	KCNQ1	11	2798240	Silent	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10		2798240	132208276	37	4425											
KCNA4	3739	hgsc.bcm.edu	37	chr11	30032894	30032894	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcggaccagacgaatgatTctgaggatggcaaaggacat	14	7	12	8	2	1	3	0	2	1	1	2	7	1	6	1	4	0	1	1	4	2	1			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr11:30032894T>C	ENST00000328224.6	-	2	2565	c.1332A>G	c.(1330-1332)agA>agG	p.R444R	KCNA4_ENST00000526518.1_5'Flank	NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	444					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	GACGAATGATTCTGAGGATGG	0.572																																					p.R444R		Atlas-SNP	.											.	KCNA4	158	.	0			c.A1332G						PASS	.						70	68	69					11																	30032894		2059	4216	6275	SO:0001819	synonymous_variant	3739	exon2			AATGATTCTGAGG	M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6222	protein-coding gene	gene with protein product		176266	"potassium voltage-gated channel, shaker-related subfamily, member 4-like"	KCNA4L		2263489, 16382104	Standard	NM_002233		Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.1332A>G	chr11.hg19:g.30032894T>C		71.0	0.0	.		104.0	30.0	.	NM_002233		Silent	SNP	ENST00000328224.6	hg19	CCDS41629.1																																																																																			.	.	.	none		0.572	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388074.2	NM_002233		C	30032894	T	C	30032894	2	2	67	1	0	0	0	0	0	0	0	1	8012	1780	62	3		3	KCNA4	11	30032894	Silent	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10	27234654	30032894	104973622	38	4426											
TRIM44	54765	hgsc.bcm.edu	37	chr11	35684955	35684956	+	Frame_Shift_Ins	INS	-	-	T																															agcgaggcaggggaagagagINStgagtcggaggaagagagcg																								rs534573468	byFrequency	TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr11:35684955_35684956insT	ENST00000299413.5	+	1	603_604	c.296_297insT	c.(295-300)agtgagfs	p.E100fs	RP1-276E15.1_ENST00000525573.2_lincRNA	NM_017583.4	NP_060053.2	Q96DX7	TRI44_HUMAN	tripartite motif containing 44	100	Glu-rich.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18	all_lung(20;0.0317)|Lung NSC(22;0.0661)|all_epithelial(35;0.115)	all_hematologic(20;0.107)				ggggaagagagtgagtcggagg	0.589																																					p.S99fs		Atlas-Indel,Pindel	.											.	TRIM44	29	.	0			c.296_297insT						PASS	.																																			SO:0001589	frameshift_variant	54765	exon1			.	BC024031	CCDS31461.1	11p13	2011-04-20	2011-01-25		ENSG00000166326	ENSG00000166326		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19016	protein-coding gene	gene with protein product		612298	"tripartite motif-containing 44"				Standard	NM_017583		Approved	DIPB, MC7	uc001mwi.2	Q96DX7	OTTHUMG00000166312	ENST00000299413.5:c.297dupT	chr11.hg19:g.35684956_35684956dupT	ENSP00000299413:p.Glu100fs	174.0	0.0	0		253.0	66.0	0.26087	NM_017583	D3DR14|Q96QY2|Q9UGK0	Frame_Shift_Ins	INS	ENST00000299413.5	hg19	CCDS31461.1																																																																																			.	.	.	none		0.589	TRIM44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389081.1	NM_017583		T	35684956	-	T	35684955	7	5	67	1	0	1	1	0	0	0	0	0	16531	1029	36	0	298	0	TRIM44	11	35684955	Frame_Shift_Ins	INS	-	TCGA-A4-A5Y1-01A-11D-A28G-10	5652061	35684955	99321561	39	4427											
C12orf39	80763	hgsc.bcm.edu	37	chr12	21680692	21680692	+	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	ttcatctccgaccagagccgGagaaaggacctctccgaccg	10	6	10	15	4	3	2	1	0	2	2	5	6	3	3	6	2	1	0	6	2	1	1			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr12:21680692G>C	ENST00000256969.2	+	4	343	c.177G>C	c.(175-177)cgG>cgC	p.R59R		NM_030572.2	NP_085049.1	Q9BT56	SPXN_HUMAN		59					long-chain fatty acid import (GO:0044539)|negative regulation of appetite (GO:0032099)|negative regulation of heart rate (GO:0010459)|negative regulation of renal sodium excretion (GO:0035814)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of sensory perception of pain (GO:0051930)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)	neuropeptide hormone activity (GO:0005184)|type 2 galanin receptor binding (GO:0031765)|type 3 galanin receptor binding (GO:0031766)			endometrium(3)|large_intestine(1)|lung(2)|urinary_tract(1)	7						ACCAGAGCCGGAGAAAGGACC	0.647																																					p.R59R		Atlas-SNP	.											.	C12orf39	18	.	0			c.G177C						PASS	.						20	21	21					12																	21680692		2195	4272	6467	SO:0001819	synonymous_variant	80763	exon4			GAGCCGGAGAAAG																												ENST00000256969.2:c.177G>C	chr12.hg19:g.21680692G>C		203.0	1.0	.		215.0	158.0	.	NM_030572	B3KND6	Silent	SNP	ENST00000256969.2	hg19	CCDS31757.1																																																																																			.	.	.	none		0.647	C12orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402389.1			C	21680692	G	C	21680692	2	2	67	1	0	0	0	0	0	0	0	1	1686	1161	41	4		4	C12orf39	12	21680692	Silent	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10		21680692	112171203	40	4428											
MLL2	8085	hgsc.bcm.edu	37	chr12	49436945	49436945	+	Missense_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	ggtcactgggcactggggatGccttcacgcccccatcctca	6	8	11	16	1	3	0	3	0	0	0	4	1	4	1	4	4	1	1	4	4	0	1			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr12:49436945G>A	ENST00000301067.7	-	25	5557	c.5558C>T	c.(5557-5559)gCa>gTa	p.A1853V		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1853					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)										CACTGGGGATGCCTTCACGCC	0.587																																					p.A1853V		Atlas-SNP	.											.	MLL2	1173	.	0			c.C5558T						PASS	.						69	71	71					12																	49436945		2031	4183	6214	SO:0001583	missense	8085	exon25			GGGGATGCCTTCA	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.5558C>T	chr12.hg19:g.49436945G>A	ENSP00000301067:p.Ala1853Val	96.0	0.0	.		104.0	8.0	.	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	12.58	1.980996	0.34942	.	.	ENSG00000167548	ENST00000301067	T	0.79554	-1.28	5.61	4.72	0.59763	.	0.000000	0.36303	N	0.002670	T	0.69504	0.3118	L	0.29908	0.895	0.30174	N	0.801069	B	0.26363	0.147	B	0.19391	0.025	T	0.69472	-0.5136	10	0.87932	D	0	.	10.4356	0.44433	0.0892:0.0:0.9108:0.0	.	1853	O14686	MLL2_HUMAN	V	1853	ENSP00000301067:A1853V	ENSP00000301067:A1853V	A	-	2	0	MLL2	47723212	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	2.943000	0.49026	1.371000	0.46172	0.655000	0.94253	GCA	.	.	.	none		0.587	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49436945	G	A	49436945	3	1	67	1	0	0	0	0	1	0	0	0	9628	1319	46	2	11175	2	MLL2	12	49436945	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	27756253	49436945	84414950	41	4429											
PABPC3	5042	hgsc.bcm.edu	37	chr13	25671122	25671122	+	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	ctcaatggaaaacaaatttaCgttggtcgagctcagaaaaa	17	9	8	7	2	2	1	2	0	0	1	3	3	2	2	0	2	3	2	0	2	7	3	rs79072440		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr13:25671122C>T	ENST00000281589.3	+	1	823	c.786C>T	c.(784-786)taC>taT	p.Y262Y		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	262	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				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)		AACAAATTTACGTTGGTCGAG	0.408																																					p.Y262Y		Atlas-SNP	.											.	PABPC3	129	.	0			c.C786T						PASS	.																																			SO:0001819	synonymous_variant	5042	exon1			AATTTACGTTGGT	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.786C>T	chr13.hg19:g.25671122C>T		134.0	0.0	.		196.0	12.0	.	NM_030979	Q8NHV0|Q9H086	Silent	SNP	ENST00000281589.3	hg19	CCDS9311.1																																																																																			.	C|0.500;T|0.500	0.500	weak		0.408	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979		T	25671122	C	T	25671122	2	4	67	1	0	0	0	0	0	0	0	1	11372	547	19	1		1	PABPC3	13	25671122	Silent	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10		25671122	89498756	42	4430											
MYH7	4625	hgsc.bcm.edu	37	chr14	23886422	23886422	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccagggactcctcataggCgttcttgagtttgaagagct	8	13	11	9	1	2	3	1	2	1	1	4	4	4	4	2	2	1	3	2	2	2	5			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr14:23886422C>T	ENST00000355349.3	-	32	4621	c.4459G>A	c.(4459-4461)Gcc>Acc	p.A1487T	CTD-2201G16.1_ENST00000557368.1_RNA|MIR208B_ENST00000401172.1_RNA	NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1487					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		TCCTCATAGGCGTTCTTGAGT	0.597																																					p.A1487T		Atlas-SNP	.											.	MYH7	349	.	0			c.G4459A						PASS	.						118	124	122					14																	23886422		2203	4300	6503	SO:0001583	missense	4625	exon32			CATAGGCGTTCTT	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.4459G>A	chr14.hg19:g.23886422C>T	ENSP00000347507:p.Ala1487Thr	97.0	0.0	.		83.0	34.0	.	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	hg19	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.374149	0.82573	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	T	0.78364	-1.17	5.27	5.27	0.74061	Myosin tail (1);	.	.	.	.	D	0.84000	0.5376	M	0.81942	2.565	0.39473	D	0.967754	P	0.43662	0.814	P	0.50440	0.641	D	0.86199	0.1617	9	0.59425	D	0.04	.	13.987	0.64341	0.1513:0.8487:0.0:0.0	.	1487	P12883	MYH7_HUMAN	T	1487;1492	ENSP00000347507:A1487T	ENSP00000347507:A1487T	A	-	1	0	MYH7	22956262	0.987000	0.35691	0.998000	0.56505	0.982000	0.71751	2.764000	0.47613	2.746000	0.94184	0.591000	0.81541	GCC	.	.	.	none		0.597	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		T	23886422	C	T	23886422	3	4	67	1	0	0	0	0	1	0	0	0	10046	768	27	1	1384	1	MYH7	14	23886422	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10		23886422	83463118	43	4431											
ABHD12B	145447	hgsc.bcm.edu	37	chr14	51368558	51368558	+	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	taaaaatagatttaccggaaCattccaggatttttacgtac	15	13	6	7	2	0	1	0	0	0	1	1	3	1	3	2	2	4	1	2	2	8	9			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr14:51368558C>T	ENST00000337334.2	+	10	807	c.792C>T	c.(790-792)aaC>aaT	p.N264N	ABHD12B_ENST00000353130.1_Silent_p.N187N|ABHD12B_ENST00000395752.1_Silent_p.N157N|PYGL_ENST00000532462.1_Intron	NM_001206673.1	NP_001193602.1	Q7Z5M8	AB12B_HUMAN	abhydrolase domain containing 12B	264							hydrolase activity (GO:0016787)			breast(2)|endometrium(1)|large_intestine(2)|lung(5)	10	all_epithelial(31;0.00481)|Breast(41;0.148)					TTTACCGGAACATTCCAGGAT	0.308																																					p.N264N		Atlas-SNP	.											.	ABHD12B	53	.	0			c.C792T						PASS	.						58	54	55					14																	51368558		2202	4297	6499	SO:0001819	synonymous_variant	145447	exon10			CCGGAACATTCCA	BG698443	CCDS9702.1, CCDS55916.1	14q21.3	2009-10-09	2007-04-03	2007-04-03	ENSG00000131969	ENSG00000131969		"Abhydrolase domain containing"	19837	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 29"	C14orf29			Standard	NM_181814		Approved	BEM46L3	uc001wys.3	Q7Z5M8	OTTHUMG00000140286	ENST00000337334.2:c.792C>T	chr14.hg19:g.51368558C>T		108.0	0.0	.		68.0	45.0	.	NM_001206673	Q3KNR9|Q3KNS0|Q7Z5M6|Q7Z5M7|Q8N4D2	Silent	SNP	ENST00000337334.2	hg19	CCDS55916.1																																																																																			.	.	.	none		0.308	ABHD12B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411030.1			T	51368558	C	T	51368558	2	4	67	1	0	0	0	0	0	0	0	1	77	477	17	2		2	ABHD12B	14	51368558	Silent	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	27482136	51368558	55980982	44	4432											
MPP5	64398	hgsc.bcm.edu	37	chr14	67787027	67787027	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ataggaagagacctatcatcTtgattggtccacagaactgt	13	11	9	8	0	2	3	1	1	1	2	3	5	3	4	2	2	1	0	2	2	4	4			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr14:67787027T>C	ENST00000261681.4	+	12	2111	c.1450T>C	c.(1450-1452)Ttg>Ctg	p.L484L	MPP5_ENST00000555925.1_Silent_p.L450L|ATP6V1D_ENST00000553974.1_Intron	NM_022474.3	NP_071919.2	Q8N3R9	MPP5_HUMAN	membrane protein, palmitoylated 5 (MAGUK p55 subfamily member 5)	484	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|establishment of protein localization to plasma membrane (GO:0090002)|morphogenesis of an epithelial sheet (GO:0002011)|myelin assembly (GO:0032288)|peripheral nervous system myelin maintenance (GO:0032287)|protein localization to myelin sheath abaxonal region (GO:0035750)|tight junction assembly (GO:0070830)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lateral loop (GO:0043219)|myelin sheath adaxonal region (GO:0035749)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein domain specific binding (GO:0019904)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|skin(1)	18				all cancers(60;0.000388)|OV - Ovarian serous cystadenocarcinoma(108;0.00762)|BRCA - Breast invasive adenocarcinoma(234;0.0106)		ACCTATCATCTTGATTGGTCC	0.408																																					p.L484L		Atlas-SNP	.											.	MPP5	46	.	0			c.T1450C						PASS	.						111	104	107					14																	67787027		2203	4300	6503	SO:0001819	synonymous_variant	64398	exon12			ATCATCTTGATTG	AK022677	CCDS9779.1, CCDS58325.1	14q23.3	2008-08-11				ENSG00000072415			18669	protein-coding gene	gene with protein product	"stardust"	606958				11927608	Standard	NM_022474		Approved	PALS1, FLJ12615	uc001xjc.4	Q8N3R9		ENST00000261681.4:c.1450T>C	chr14.hg19:g.67787027T>C		47.0	0.0	.		40.0	30.0	.	NM_022474	A1L380|Q7Z631|Q86T98|Q8N7I5|Q9H9Q0	Silent	SNP	ENST00000261681.4	hg19	CCDS9779.1																																																																																			.	.	.	none		0.408	MPP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412498.1	NM_022474		C	67787027	T	C	67787027	2	2	67	1	0	0	0	0	0	0	0	1	9744	1606	56	3		3	MPP5	14	67787027	Silent	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10	16418469	67787027	39562513	45	4433											
YLPM1	56252	hgsc.bcm.edu	37	chr14	75248111	75248111	+	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	1	0	0	0	0	0	0	0	0	caacatctttaccaagaatgGgagcgagagtttcagctatg	13	10	10	8	1	2	2	1	0	1	2	2	4	2	3	1	1	4	2	1	1	5	4			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr14:75248111G>A	ENST00000552421.1	+	4	1489	c.1365G>A	c.(1363-1365)tgG>tgA	p.W455*	YLPM1_ENST00000238571.3_Intron|YLPM1_ENST00000325680.7_Nonsense_Mutation_p.W455*			P49750	YLPM1_HUMAN	YLP motif containing 1	0					regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		ACCAAGAATGGGAGCGAGAGT	0.423																																					p.W455X		Atlas-SNP	.											.	YLPM1	298	.	0			c.G1365A						PASS	.						40	37	38					14																	75248111		1917	4135	6052	SO:0001587	stop_gained	56252	exon4			AGAATGGGAGCGA	AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 169"		"chromosome 14 open reading frame 170"	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000552421.1:c.1365G>A	chr14.hg19:g.75248111G>A	ENSP00000447921:p.Trp455*	197.0	0.0	.		166.0	124.0	.	NM_019589	P49752|Q96I64|Q9P1V7	Nonsense_Mutation	SNP	ENST00000552421.1	hg19		.	.	.	.	.	.	.	.	.	.	G	35	5.452918	0.96223	.	.	ENSG00000119596	ENST00000552421;ENST00000325680;ENST00000423680	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.0557	0.97650	0.0:0.0:1.0:0.0	.	.	.	.	X	455;455;168	.	ENSP00000324463:W455X	W	+	3	0	YLPM1	74317864	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.471000	0.97696	2.732000	0.93576	0.591000	0.81541	TGG	.	.	.	none		0.423	YLPM1-008	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404450.1	NM_019589		A	75248111	G	A	75248111	4	1	67	1	0	0	0	0	0	1	0	0	17498	1241	43	2	1379	2	YLPM1	14	75248111	Nonsense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	7461084	75248111	32101429	46	4434											
CATSPERB	79820	hgsc.bcm.edu	37	chr14	92195753	92195753	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctgaaacttacctttattaTatactattcctgatgaaaat	14	17	3	7	0	1	3	0	3	1	0	2	3	2	3	2	0	3	0	2	0	9	8			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr14:92195753T>C	ENST00000256343.3	-	2	227	c.71A>G	c.(70-72)tAt>tGt	p.Y24C		NM_024764.2	NP_079040.2	Q9H7T0	CTSRB_HUMAN	catsper channel auxiliary subunit beta	24					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)				ACCTTTATTATATACTATTCC	0.279																																					p.Y24C		Atlas-SNP	.											.	CATSPERB	114	.	0			c.A71G						PASS	.						32	36	35					14																	92195753		2194	4276	6470	SO:0001583	missense	79820	exon2			TTATTATATACTA	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.71A>G	chr14.hg19:g.92195753T>C	ENSP00000256343:p.Tyr24Cys	173.0	0.0	.		152.0	68.0	.	NM_024764	A0AV51	Missense_Mutation	SNP	ENST00000256343.3	hg19	CCDS32142.1	.	.	.	.	.	.	.	.	.	.	T	13.15	2.150476	0.37923	.	.	ENSG00000133962	ENST00000256343;ENST00000553329;ENST00000554560;ENST00000556661;ENST00000553676	T	0.56941	0.43	5.22	4.05	0.47172	.	0.528936	0.15705	N	0.248736	T	0.58935	0.2157	L	0.47716	1.5	0.26423	N	0.976068	D	0.65815	0.995	P	0.58873	0.847	T	0.50550	-0.8815	10	0.66056	D	0.02	-4.0069	8.4676	0.32966	0.1734:0.0:0.0:0.8266	.	24	Q9H7T0	CTSRB_HUMAN	C	24	ENSP00000256343:Y24C	ENSP00000256343:Y24C	Y	-	2	0	CATSPERB	91265506	0.928000	0.31464	0.216000	0.23742	0.648000	0.38561	2.017000	0.40981	0.893000	0.36288	0.397000	0.26171	TAT	.	.	.	none		0.279	CATSPERB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411769.1	NM_024764		C	92195753	T	C	92195753	3	2	67	1	0	0	0	0	1	0	0	0	2693	1406	49	3	3383	3	CATSPERB	14	92195753	Missense_Mutation	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10	16947642	92195753	15153787	47	4435											
CASC5	57082	hgsc.bcm.edu	37	chr15	40913801	40913801	+	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	ccaaatgtctctcaaatatgAgagaggagaaaaatttgcta	17	10	8	6	0	2	3	1	1	1	2	3	5	2	3	1	1	1	1	1	1	6	3			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr15:40913801A>T	ENST00000346991.5	+	11	1807	c.1417A>T	c.(1417-1419)Aga>Tga	p.R473*	CASC5_ENST00000399668.2_Nonsense_Mutation_p.R447*|CASC5_ENST00000527044.1_3'UTR			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	473	Interaction with BUB1 and BUB1B.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		CTCAAATATGAGAGAGGAGAA	0.328																																					p.R473X		Atlas-SNP	.											.	CASC5	269	.	0			c.A1417T						PASS	.						67	65	65					15																	40913801		1822	4080	5902	SO:0001587	stop_gained	57082	exon11			AATATGAGAGAGG	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.1417A>T	chr15.hg19:g.40913801A>T	ENSP00000335463:p.Arg473*	184.0	0.0	.		146.0	57.0	.	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Nonsense_Mutation	SNP	ENST00000346991.5	hg19	CCDS42023.1	.	.	.	.	.	.	.	.	.	.	A	38	7.205877	0.98136	.	.	ENSG00000137812	ENST00000346991;ENST00000260369;ENST00000399668	.	.	.	5.94	2.3	0.28687	.	1.023320	0.07757	N	0.949536	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.4785	0.16710	0.5262:0.2673:0.2064:0.0	.	.	.	.	X	473;447;447	.	ENSP00000260369:R447X	R	+	1	2	CASC5	38701093	0.001000	0.12720	0.969000	0.41365	0.966000	0.64601	0.013000	0.13310	0.490000	0.27771	0.455000	0.32223	AGA	.	.	.	none		0.328	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		T	40913801	A	T	40913801	4	4	67	1	0	0	0	0	0	1	0	0	2665	296	11	5	1455	5	CASC5	15	40913801	Nonsense_Mutation	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10		40913801	61617591	48	4436											
RNF111	54778	hgsc.bcm.edu	37	chr15	59344604	59344604	+	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	tcaactgacagtgaagtggaGattgtaacagttggagaaag	15	9	13	4	0	1	4	1	2	0	2	1	6	1	4	0	2	2	2	0	2	4	3	rs137923008	byFrequency	TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr15:59344604G>T	ENST00000557998.1	+	3	1268	c.981G>T	c.(979-981)gaG>gaT	p.E327D	RNF111_ENST00000559209.1_Missense_Mutation_p.E327D|RNF111_ENST00000434298.1_Missense_Mutation_p.E327D|RNF111_ENST00000348370.4_Missense_Mutation_p.E327D|RNF111_ENST00000561186.1_Missense_Mutation_p.E327D	NM_001270530.1	NP_001257459.1	Q6ZNA4	RN111_HUMAN	ring finger protein 111	327	Interaction with AXIN1.|Ser-rich.				gene expression (GO:0010467)|pattern specification process (GO:0007389)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein polyubiquitination (GO:0000209)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|SUMO polymer binding (GO:0032184)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35				all cancers(107;0.194)		GTGAAGTGGAGATTGTAACAG	0.333																																					p.E327D	NSCLC(72;983 1365 10746 34387 47081)	Atlas-SNP	.											.	RNF111	179	.	0			c.G981T						PASS	.						119	108	112					15																	59344604		2192	4291	6483	SO:0001583	missense	54778	exon3			AGTGGAGATTGTA	AL157474	CCDS10169.1, CCDS58365.1, CCDS58366.1	15q21	2013-01-09			ENSG00000157450	ENSG00000157450		"RING-type (C3HC4) zinc fingers"	17384	protein-coding gene	gene with protein product		605840				11298452	Standard	NM_017610		Approved	ARK, Arkadia, FLJ38008, DKFZP761D081	uc002aft.4	Q6ZNA4	OTTHUMG00000132716	ENST00000557998.1:c.981G>T	chr15.hg19:g.59344604G>T	ENSP00000452732:p.Glu327Asp	74.0	0.0	.		61.0	23.0	.	NM_017610	C9JUS4|H0YN55|Q6P9A4|Q6ZMU2|Q7L428|Q7Z346|Q8N1P9|Q8WUA3|Q9NSR1	Missense_Mutation	SNP	ENST00000557998.1	hg19	CCDS58366.1	.	.	.	.	.	.	.	.	.	.	G	12.55	1.972394	0.34848	.	.	ENSG00000157450	ENST00000348370;ENST00000434298	T;T	0.39997	1.05;1.06	5.6	1.64	0.23874	.	0.000000	0.85682	D	0.000000	T	0.36082	0.0954	L	0.59436	1.845	0.51012	D	0.9999	B;B;B	0.27732	0.187;0.117;0.187	B;B;B	0.29267	0.1;0.046;0.1	T	0.15607	-1.0431	10	0.87932	D	0	-5.7934	6.825	0.23878	0.1993:0.0:0.6759:0.1248	.	327;327;327	Q6ZNA4-3;Q6ZNA4;Q6ZNA4-2	.;RN111_HUMAN;.	D	327	ENSP00000288199:E327D;ENSP00000393641:E327D	ENSP00000288199:E327D	E	+	3	2	RNF111	57131896	1.000000	0.71417	0.997000	0.53966	0.284000	0.27059	4.092000	0.57707	0.051000	0.15978	-0.241000	0.12123	GAG	.	G|0.998;A|0.002	.	alt		0.333	RNF111-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000416012.1	NM_017610		T	59344604	G	T	59344604	3	4	67	1	0	0	0	0	1	0	0	0	13438	933	33	4	987	4	RNF111	15	59344604	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	18430803	59344604	43186788	49	4437											
VPS13C	54832	hgsc.bcm.edu	37	chr15	62155703	62155703	+	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	acagtggtatcggtaagtctCtccttccaactttttgatat	9	16	7	9	1	1	1	0	1	1	0	5	1	3	1	2	2	1	2	2	2	4	6			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr15:62155703C>A	ENST00000261517.5	-	82	10961	c.10888G>T	c.(10888-10890)Gag>Tag	p.E3630*	VPS13C_ENST00000249837.3_Nonsense_Mutation_p.E3587*	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						CGGTAAGTCTCTCCTTCCAAC	0.353																																					p.E3630X		Atlas-SNP	.											.	VPS13C	506	.	0			c.G10888T						PASS	.						156	136	143					15																	62155703		2203	4300	6503	SO:0001587	stop_gained	54832	exon82			AAGTCTCTCCTTC	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.10888G>T	chr15.hg19:g.62155703C>A	ENSP00000261517:p.Glu3630*	151.0	0.0	.		115.0	41.0	.	NM_020821		Nonsense_Mutation	SNP	ENST00000261517.5	hg19	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	C	53	21.012209	0.99936	.	.	ENSG00000129003	ENST00000249837;ENST00000261517	.	.	.	5.68	5.68	0.88126	.	0.055754	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	20.1554	0.98111	0.0:1.0:0.0:0.0	.	.	.	.	X	3587;3630	.	ENSP00000249837:E3587X	E	-	1	0	VPS13C	59942995	1.000000	0.71417	0.981000	0.43875	0.992000	0.81027	6.594000	0.74104	2.838000	0.97847	0.591000	0.81541	GAG	.	.	.	none		0.353	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		A	62155703	C	A	62155703	4	1	67	1	0	0	0	0	0	1	0	0	17203	922	32	4	389	4	VPS13C	15	62155703	Nonsense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	2811099	62155703	40375689	50	4438											
PIAS1	8554	hgsc.bcm.edu	37	chr15	68434644	68434644	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctagggatatttctgggaccAaatgtgacttcacagtacag	12	11	10	8	0	2	1	1	1	1	0	2	3	2	3	1	2	1	1	1	2	4	5			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr15:68434644A>G	ENST00000249636.6	+	4	719	c.571A>G	c.(571-573)Aaa>Gaa	p.K191E	PIAS1_ENST00000545237.1_Missense_Mutation_p.K193E	NM_016166.1	NP_057250.1	O75925	PIAS1_HUMAN	protein inhibitor of activated STAT, 1	191	PINIT. {ECO:0000255|PROSITE- ProRule:PRU00799}.				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						TTCTGGGACCAAATGTGACTT	0.353																																					p.K191E		Atlas-SNP	.											.	PIAS1	42	.	0			c.A571G						PASS	.						55	51	53					15																	68434644		1818	4073	5891	SO:0001583	missense	8554	exon4			GGGACCAAATGTG	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.571A>G	chr15.hg19:g.68434644A>G	ENSP00000249636:p.Lys191Glu	131.0	0.0	.		150.0	55.0	.	NM_016166	B2RB67|B3KSY9|C5J4B4|Q147X4|Q99751|Q9UN02	Missense_Mutation	SNP	ENST00000249636.6	hg19	CCDS45290.1	.	.	.	.	.	.	.	.	.	.	A	27.7	4.858688	0.91433	.	.	ENSG00000033800	ENST00000249636;ENST00000545237	T;T	0.36340	1.26;1.26	5.39	5.39	0.77823	PINIT domain (1);	0.000000	0.85682	D	0.000000	T	0.58750	0.2144	M	0.73217	2.22	0.80722	D	1	D;B	0.54047	0.964;0.107	D;P	0.65773	0.938;0.475	T	0.62793	-0.6779	10	0.72032	D	0.01	-13.0322	15.4074	0.74890	1.0:0.0:0.0:0.0	.	191;191	C5J4B4;O75925	.;PIAS1_HUMAN	E	191;193	ENSP00000249636:K191E;ENSP00000438574:K193E	ENSP00000249636:K191E	K	+	1	0	PIAS1	66221698	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.883000	0.92426	2.042000	0.60477	0.477000	0.44152	AAA	.	.	.	none		0.353	PIAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419642.2			G	68434644	A	G	68434644	3	3	67	1	0	0	0	0	1	0	0	0	11882	131	5	3	585	3	PIAS1	15	68434644	Missense_Mutation	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	6278941	68434644	34096748	51	4439											
IL16	3603	hgsc.bcm.edu	37	chr15	81517938	81517938	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgtgcagctggcagacacAtcggaggctgggcccagcag	8	6	15	12	1	1	1	0	0	1	1	2	2	1	2	1	4	3	5	1	4	0	0			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr15:81517938A>G	ENST00000302987.4	+	1	198	c.198A>G	c.(196-198)acA>acG	p.T66T	IL16_ENST00000394660.2_Silent_p.T66T			Q14005	IL16_HUMAN	interleukin 16	66					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						TGGCAGACACATCGGAGGCTG	0.552																																					p.T66T		Atlas-SNP	.											.	IL16	254	.	0			c.A198G						PASS	.						65	65	65					15																	81517938		2006	4190	6196	SO:0001819	synonymous_variant	3603	exon2			AGACACATCGGAG	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.198A>G	chr15.hg19:g.81517938A>G		127.0	0.0	.		116.0	29.0	.	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Silent	SNP	ENST00000302987.4	hg19	CCDS42069.1																																																																																			.	.	.	none		0.552	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217		G	81517938	A	G	81517938	2	3	67	1	0	0	0	0	0	0	0	1	7640	204	8	3		3	IL16	15	81517938	Silent	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	13083294	81517938	21013454	52	4440											
FANCI	55215	hgsc.bcm.edu	37	chr15	89856164	89856164	+	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	aagagcctgaactatacgggAgagaaaaaggagaaacctgc	18	4	12	7	1	0	4	0	1	0	3	0	7	0	5	2	2	5	0	2	2	7	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr15:89856164A>T	ENST00000310775.7	+	35	3767	c.3681A>T	c.(3679-3681)ggA>ggT	p.G1227G	FANCI_ENST00000566615.1_3'UTR|FANCI_ENST00000300027.8_Silent_p.G1167G	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	1227					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)					ACTATACGGGAGAGAAAAAGG	0.423								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.G1227G		Atlas-SNP	.											.	FANCI	129	.	0			c.A3681T						PASS	.						77	76	76					15																	89856164		2200	4299	6499	SO:0001819	synonymous_variant	55215	exon35	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TACGGGAGAGAAA	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.3681A>T	chr15.hg19:g.89856164A>T		61.0	0.0	.		51.0	21.0	.	NM_001113378	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Silent	SNP	ENST00000310775.7	hg19	CCDS45346.1																																																																																			.	.	.	none		0.423	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193		T	89856164	A	T	89856164	2	4	67	1	0	0	0	0	0	0	0	1	5676	291	11	5		5	FANCI	15	89856164	Silent	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	8338226	89856164	12675228	53	4441											
FAHD1	81889	hgsc.bcm.edu	37	chr16	1877593	1877593	+	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	aaggggctgccctggactctGgcgaagagcttcacggcgtc	7	7	15	12	3	2	1	1	0	1	1	3	3	2	2	1	5	2	2	1	5	2	1			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr16:1877593G>T	ENST00000427358.2	+	1	369	c.363G>T	c.(361-363)ctG>ctT	p.L121L	HAGH_ENST00000455446.2_5'Flank|FAHD1_ENST00000382666.4_Silent_p.L121L|HAGH_ENST00000397353.2_5'Flank|HAGH_ENST00000566709.1_5'Flank|HAGH_ENST00000397356.3_5'Flank|FAHD1_ENST00000382668.4_Silent_p.L121L	NM_031208.3	NP_112485.1	Q6P587	FAHD1_HUMAN	fumarylacetoacetate hydrolase domain containing 1	121						cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetylpyruvate hydrolase activity (GO:0018773)|acylpyruvate hydrolase activity (GO:0047621)|fumarylpyruvate hydrolase activity (GO:0034545)|metal ion binding (GO:0046872)			NS(1)|large_intestine(1)|liver(1)|ovary(2)|urinary_tract(1)	6						CCTGGACTCTGGCGAAGAGCT	0.642																																					p.L121L		Atlas-SNP	.											.	FAHD1	18	.	0			c.G363T						PASS	.						38	34	36					16																	1877593		2199	4300	6499	SO:0001819	synonymous_variant	81889	exon1			GACTCTGGCGAAG	BC063017	CCDS10448.1, CCDS32367.1, CCDS45380.1	16p13.3	2011-10-21	2004-08-19	2004-08-26	ENSG00000180185	ENSG00000180185			14169	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 36"	C16orf36		21878618	Standard	NM_001018104		Approved	DKFZP566J2046	uc002cnd.3	Q6P587	OTTHUMG00000128663	ENST00000427358.2:c.363G>T	chr16.hg19:g.1877593G>T		114.0	0.0	.		273.0	39.0	.	NM_031208	B1AK40|B1AK41|Q6FIC7|Q96RY1|Q9H0N6	Silent	SNP	ENST00000427358.2	hg19	CCDS10448.1																																																																																			.	.	.	none		0.642	FAHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250550.2	NM_001018104		T	1877593	G	T	1877593	2	4	67	1	0	0	0	0	0	0	0	1	5376	1335	47	4		4	FAHD1	16	1877593	Silent	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10		1877593	88477160	54	4442											
CMTM4	146223	hgsc.bcm.edu	37	chr16	66670440	66670440	+	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	aggccttcacacggggagcaTgccatgatggtctctatgca	9	9	12	11	1	2	1	1	1	1	0	3	2	2	2	2	4	3	2	2	4	1	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr16:66670440T>A	ENST00000330687.4	-	2	412	c.231A>T	c.(229-231)gcA>gcT	p.A77A	CMTM4_ENST00000563952.1_Silent_p.A48A|CMTM4_ENST00000394106.2_Silent_p.A77A	NM_178818.2|NM_181521.2	NP_848933.1|NP_852662.1	Q8IZR5	CKLF4_HUMAN	CKLF-like MARVEL transmembrane domain containing 4	77	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0811)|Epithelial(162;0.214)		ACGGGGAGCATGCCATGATGG	0.443																																					p.A77A		Atlas-SNP	.											.	CMTM4	19	.	0			c.A231T						PASS	.						117	103	108					16																	66670440		2201	4300	6501	SO:0001819	synonymous_variant	146223	exon2			GGAGCATGCCATG	AF479814	CCDS10817.1, CCDS42170.1	16q22.1-q22.3	2008-02-05	2005-11-08	2005-11-08	ENSG00000183723	ENSG00000183723			19175	protein-coding gene	gene with protein product		607887	"chemokine-like factor super family 4", "chemokine-like factor superfamily 4"	CKLFSF4		12782130	Standard	NM_178818		Approved		uc002epz.3	Q8IZR5	OTTHUMG00000137500	ENST00000330687.4:c.231A>T	chr16.hg19:g.66670440T>A		120.0	0.0	.		95.0	5.0	.	NM_178818	Q52M40|Q8IZR4|Q8IZV1	Silent	SNP	ENST00000330687.4	hg19	CCDS10817.1																																																																																			.	.	.	none		0.443	CMTM4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268807.1			A	66670440	T	A	66670440	2	1	67	1	0	0	0	0	0	0	0	1	3587	1451	51	5		5	CMTM4	16	66670440	Silent	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10	64792847	66670440	23684313	55	4443											
PRDM7	11105	hgsc.bcm.edu	37	chr16	90127007	90127007	+	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	gccaccaggttctgctcttcAtcatcccgggcacagttcac	7	10	8	16	1	5	0	3	0	2	0	6	0	6	0	3	2	1	4	3	2	0	3			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr16:90127007A>T	ENST00000449207.2	-	9	994	c.975T>A	c.(973-975)gaT>gaA	p.D325E	PRDM7_ENST00000407825.1_Intron|PRDM7_ENST00000325921.6_Intron	NM_001098173.1	NP_001091643.1	Q9NQW5	PRDM7_HUMAN	PR domain containing 7	325	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				regulation of transcription, DNA-templated (GO:0006355)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleic acid binding (GO:0003676)			lung(2)|ovary(2)|stomach(1)	5		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		TCTGCTCTTCATCATCCCGGG	0.547																																					p.D325E		Atlas-SNP	.											.	PRDM7	53	.	0			c.T975A						PASS	.						78	77	77					16																	90127007		1938	4120	6058	SO:0001583	missense	11105	exon9			CTCTTCATCATCC	AF274347	CCDS45557.1	16q24.3	2013-01-09			ENSG00000126856	ENSG00000126856		"Zinc fingers, C2H2-type", "-"	9351	protein-coding gene	gene with protein product		609759				17916234	Standard	NM_001098173		Approved	ZNF910	uc010cje.3	Q9NQW5	OTTHUMG00000138990	ENST00000449207.2:c.975T>A	chr16.hg19:g.90127007A>T	ENSP00000396732:p.Asp325Glu	343.0	0.0	.		210.0	119.0	.	NM_001098173	A4Q9G8|Q08EM4|Q9NQW4	Missense_Mutation	SNP	ENST00000449207.2	hg19	CCDS45557.1	.	.	.	.	.	.	.	.	.	.	.	0.006	-2.026388	0.00414	.	.	ENSG00000126856	ENST00000449207	T	0.41065	1.01	2.23	-4.45	0.03546	SET domain (2);	.	.	.	.	T	0.10594	0.0259	N	0.01297	-0.9	0.09310	N	0.999998	B	0.06786	0.001	B	0.06405	0.002	T	0.17137	-1.0379	8	.	.	.	-0.9636	1.139	0.01761	0.2061:0.3427:0.2807:0.1705	.	325	Q9NQW5	PRDM7_HUMAN	E	325	ENSP00000396732:D325E	.	D	-	3	2	PRDM7	88654508	0.000000	0.05858	0.092000	0.20876	0.342000	0.28953	-2.198000	0.01239	-1.546000	0.01717	0.397000	0.26171	GAT	.	.	.	none		0.547	PRDM7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420560.1			T	90127007	A	T	90127007	3	4	67	1	0	0	0	0	1	0	0	0	12471	214	8	5	511	5	PRDM7	16	90127007	Missense_Mutation	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	23456567	90127007	227746	56	4444											
SHPK	23729	hgsc.bcm.edu	37	chr17	3514081	3514081	+	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	caggttctgaacaatgcctcGgcacagagcccgggtcacgt	9	7	12	13	3	2	2	1	1	1	1	3	2	2	2	2	3	3	2	2	3	2	1			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr17:3514081G>T	ENST00000225519.3	-	7	1312	c.1210C>A	c.(1210-1212)Cga>Aga	p.R404R	SHPK_ENST00000572705.1_5'Flank	NM_013276.2	NP_037408	Q9UHJ6	SHPK_HUMAN	sedoheptulokinase	404					carbohydrate metabolic process (GO:0005975)|cellular response to interleukin-13 (GO:0035963)|cellular response to interleukin-4 (GO:0071353)|cellular response to lipopolysaccharide (GO:0071222)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|phosphorylation (GO:0016310)|regulation of inflammatory response (GO:0050727)|regulation of macrophage activation (GO:0043030)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|sedoheptulokinase activity (GO:0050277)			breast(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				COAD - Colon adenocarcinoma(5;0.0828)		ACAATGCCTCGGCACAGAGCC	0.642																																					p.R404R		Atlas-SNP	.											.	SHPK	34	.	0			c.C1210A						PASS	.						110	111	111					17																	3514081		2203	4300	6503	SO:0001819	synonymous_variant	23729	exon7			TGCCTCGGCACAG	AF163573	CCDS11030.1	17p13	2008-02-08	2008-02-08	2008-02-08	ENSG00000197417	ENSG00000197417	2.7.1.14		1492	protein-coding gene	gene with protein product		605060	"carbohydrate kinase-like"	CARKL		10673275, 18186520	Standard	NM_013276		Approved	SHK	uc002fvz.1	Q9UHJ6	OTTHUMG00000090694	ENST00000225519.3:c.1210C>A	chr17.hg19:g.3514081G>T		126.0	0.0	.		169.0	99.0	.	NM_013276	B2R640|Q8WUH3	Silent	SNP	ENST00000225519.3	hg19	CCDS11030.1																																																																																			.	.	.	none		0.642	SHPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207378.2			T	3514081	G	T	3514081	2	4	67	1	0	0	0	0	0	0	0	1	14303	1124	39	4		4	SHPK	17	3514081	Silent	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10		3514081	77681129	57	4445											
P2RX1	5023	hgsc.bcm.edu	37	chr17	3808622	3808622	+	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	gagacactgctgatgaggccGctcgaggtctggtagccctt	7	9	14	11	2	1	3	0	2	1	1	2	5	1	3	2	3	2	3	2	3	1	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr17:3808622G>C	ENST00000225538.3	-	2	451	c.177C>G	c.(175-177)agC>agG	p.S59R		NM_002558.2	NP_002549.1	P51575	P2RX1_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 1	59					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ceramide biosynthetic process (GO:0046513)|insemination (GO:0007320)|ion transport (GO:0006811)|neuronal action potential (GO:0019228)|platelet activation (GO:0030168)|positive regulation of ion transport (GO:0043270)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of vascular smooth muscle contraction (GO:0003056)|response to ATP (GO:0033198)|serotonin secretion by platelet (GO:0002554)|signal transduction (GO:0007165)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|vasoconstriction (GO:0042310)	external side of cell outer membrane (GO:0031240)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	13				LUAD - Lung adenocarcinoma(2;1.9e-05)|Lung(3;0.0173)		TGATGAGGCCGCTCGAGGTCT	0.627																																					p.S59R		Atlas-SNP	.											.	P2RX1	38	.	0			c.C177G						PASS	.						56	60	59					17																	3808622		2203	4300	6503	SO:0001583	missense	5023	exon2			GAGGCCGCTCGAG	X83688	CCDS11040.1	17p13.3	2012-01-17				ENSG00000108405		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8533	protein-coding gene	gene with protein product		600845				8834001	Standard	NM_002558		Approved	P2X1	uc002fww.3	P51575		ENST00000225538.3:c.177C>G	chr17.hg19:g.3808622G>C	ENSP00000225538:p.Ser59Arg	99.0	0.0	.		117.0	31.0	.	NM_002558	Q9UK84	Missense_Mutation	SNP	ENST00000225538.3	hg19	CCDS11040.1	.	.	.	.	.	.	.	.	.	.	G	19.16	3.773763	0.69992	.	.	ENSG00000108405	ENST00000225538	T	0.04551	3.6	5.84	-11.4	0.00090	.	0.368613	0.32671	N	0.005781	T	0.05273	0.0140	L	0.43152	1.355	0.09310	N	1	P	0.37122	0.583	P	0.46299	0.511	T	0.17167	-1.0378	10	0.87932	D	0	-16.9741	10.8476	0.46751	0.5956:0.089:0.3154:0.0	.	59	P51575	P2RX1_HUMAN	R	59	ENSP00000225538:S59R	ENSP00000225538:S59R	S	-	3	2	P2RX1	3755371	0.011000	0.17503	0.000000	0.03702	0.860000	0.49131	-0.937000	0.03942	-2.012000	0.00950	-0.291000	0.09656	AGC	.	.	.	none		0.627	P2RX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438391.1	NM_002558		C	3808622	G	C	3808622	3	2	67	1	0	0	0	0	1	0	0	0	11346	1078	38	4	1066	4	P2RX1	17	3808622	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	294541	3808622	77386588	58	4446											
MYO15A	51168	hgsc.bcm.edu	37	chr17	18023902	18023902	+	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	aggggcagccagaaggcccgGgcgggcggccctgctgtcag	6	3	19	13	3	1	1	1	0	0	1	1	1	1	1	3	6	2	2	3	6	1	0			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr17:18023902G>C	ENST00000205890.5	+	2	2126	c.1788G>C	c.(1786-1788)cgG>cgC	p.R596R		NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	596					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)					AGAAGGCCCGGGCGGGCGGCC	0.697																																					p.R596R		Atlas-SNP	.											.	MYO15A	268	.	0			c.G1788C						PASS	.						5	6	6					17																	18023902		1638	3647	5285	SO:0001819	synonymous_variant	51168	exon2			GGCCCGGGCGGGC	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.1788G>C	chr17.hg19:g.18023902G>C		12.0	0.0	.		88.0	4.0	.	NM_016239	B4DFC7	Silent	SNP	ENST00000205890.5	hg19	CCDS42271.1																																																																																			.	.	.	none		0.697	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		C	18023902	G	C	18023902	2	2	67	1	0	0	0	0	0	0	0	1	10070	1219	43	4		4	MYO15A	17	18023902	Silent	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	14215280	18023902	63171308	59	4447											
TP53I13	90313	hgsc.bcm.edu	37	chr17	27899239	27899239	+	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	tcaagggcccaggcagccctCttctagtggtgccaagaggc	8	7	13	13	0	3	1	1	0	2	1	3	1	3	1	3	4	2	1	3	4	3	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr17:27899239C>G	ENST00000301057.7	+	6	708	c.593C>G	c.(592-594)tCt>tGt	p.S198C	RP11-68I3.2_ENST00000581474.1_RNA|RP11-68I3.4_ENST00000579050.1_RNA	NM_138349.2	NP_612358.3	Q8NBR0	P5I13_HUMAN	tumor protein p53 inducible protein 13	198						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|lung(1)|urinary_tract(1)	4				READ - Rectum adenocarcinoma(3;0.236)		AGGCAGCCCTCTTCTAGTGGT	0.657																																					p.S198C		Atlas-SNP	.											.	TP53I13	17	.	0			c.C593G						PASS	.						22	24	24					17																	27899239		1986	4140	6126	SO:0001583	missense	90313	exon6			AGCCCTCTTCTAG	AK075341	CCDS42289.1	17q11.2	2006-01-16				ENSG00000167543			25102	protein-coding gene	gene with protein product						14767535	Standard	NM_138349		Approved	DSCP1	uc002hee.3	Q8NBR0		ENST00000301057.7:c.593C>G	chr17.hg19:g.27899239C>G	ENSP00000301057:p.Ser198Cys	32.0	0.0	.		37.0	15.0	.	NM_138349	Q7L5U3	Missense_Mutation	SNP	ENST00000301057.7	hg19	CCDS42289.1	.	.	.	.	.	.	.	.	.	.	C	15.38	2.816310	0.50527	.	.	ENSG00000167543	ENST00000301057	.	.	.	3.94	1.89	0.25635	.	0.645758	0.14735	N	0.301505	T	0.51550	0.1681	M	0.63428	1.95	0.09310	N	1	D	0.69078	0.997	P	0.60345	0.873	T	0.36939	-0.9727	9	0.87932	D	0	-2.2609	5.6779	0.17759	0.0:0.7387:0.0:0.2613	.	198	Q8NBR0	P5I13_HUMAN	C	198	.	ENSP00000301057:S198C	S	+	2	0	TP53I13	24923365	0.000000	0.05858	0.002000	0.10522	0.018000	0.09664	-0.070000	0.11523	0.412000	0.25729	0.462000	0.41574	TCT	.	.	.	none		0.657	TP53I13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447804.2	NM_138349		G	27899239	C	G	27899239	3	3	67	1	0	0	0	0	1	0	0	0	16398	913	32	4	615	4	TP53I13	17	27899239	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	9875337	27899239	53295971	60	4448											
ATAD5	79915	hgsc.bcm.edu	37	chr17	29220519	29220519	+	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	gtatgaattgtcttgctaggAaacactctgaaagagaacag	15	10	10	6	0	2	3	0	2	2	1	2	5	2	4	0	1	3	2	0	1	6	4			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr17:29220519A>T	ENST00000321990.4	+	21	5026	c.4648A>T	c.(4648-4650)Aaa>Taa	p.K1550*		NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1550					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)				TCTTGCTAGGAAACACTCTGA	0.358																																					p.K1550X		Atlas-SNP	.											.	ATAD5	150	.	0			c.A4648T						PASS	.						42	50	47					17																	29220519		2201	4297	6498	SO:0001587	stop_gained	79915	exon21			GCTAGGAAACACT		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.4648A>T	chr17.hg19:g.29220519A>T	ENSP00000313171:p.Lys1550*	70.0	0.0	.		93.0	54.0	.	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Nonsense_Mutation	SNP	ENST00000321990.4	hg19	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	A	42	9.739259	0.99252	.	.	ENSG00000176208	ENST00000321990	.	.	.	6.08	5.01	0.66863	.	0.805371	0.11834	N	0.524975	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	2.577	0.04808	0.6185:0.1452:0.0786:0.1577	.	.	.	.	X	1550	.	ENSP00000313171:K1550X	K	+	1	0	ATAD5	26244645	0.002000	0.14202	0.899000	0.35326	0.203000	0.24098	0.236000	0.17967	2.333000	0.79357	0.482000	0.46254	AAA	.	.	.	none		0.358	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		T	29220519	A	T	29220519	4	4	67	1	0	0	0	0	0	1	0	0	1076	247	9	5	4730	5	ATAD5	17	29220519	Nonsense_Mutation	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	1321280	29220519	51974691	61	4449											
AZI1	22994	hgsc.bcm.edu	37	chr17	79166615	79166615	+	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	ccgttgctgctgcagcgcccActgctcctgctccaggtgct	3	10	11	17	2	0	0	0	0	0	0	2	0	2	0	4	1	7	7	4	1	0	1			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr17:79166615A>T	ENST00000269392.4	-	19	2606	c.2359T>A	c.(2359-2361)Tgg>Agg	p.W787R	AZI1_ENST00000450824.2_Missense_Mutation_p.W784R|AZI1_ENST00000374782.3_Intron|AZI1_ENST00000575907.1_Intron	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		787					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)			tgcagcgcccactgctcctgc	0.736																																					p.W784R		Atlas-SNP	.											.	AZI1	145	.	0			c.T2350A						PASS	.						14	17	16					17																	79166615		2089	4202	6291	SO:0001583	missense	22994	exon19			GCGCCCACTGCTC																												ENST00000269392.4:c.2359T>A	chr17.hg19:g.79166615A>T	ENSP00000269392:p.Trp787Arg	3.0	0.0	.		97.0	4.0	.	NM_014984	A6NHI8|B2RN11|Q96F50	Missense_Mutation	SNP	ENST00000269392.4	hg19		.	.	.	.	.	.	.	.	.	.	A	0.069	-1.206900	0.01568	.	.	ENSG00000141577	ENST00000450824;ENST00000269392	T;T	0.12255	2.7;2.7	3.32	-0.767	0.11016	.	0.637872	0.14277	N	0.329778	T	0.02455	0.0075	N	0.00538	-1.39	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.41805	-0.9488	10	0.09338	T	0.73	-14.4324	3.6545	0.08215	0.1041:0.1576:0.5766:0.1617	.	787;784	Q9UPN4;Q9UPN4-2	AZI1_HUMAN;.	R	784;787	ENSP00000393583:W784R;ENSP00000269392:W787R	ENSP00000269392:W787R	W	-	1	0	AZI1	76781210	0.999000	0.42202	0.980000	0.43619	0.571000	0.35966	0.724000	0.25954	0.039000	0.15632	0.383000	0.25322	TGG	.	.	.	none		0.736	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1			T	79166615	A	T	79166615	3	4	67	1	0	0	0	0	1	0	0	0	1240	159	6	5	924	5	AZI1	17	79166615	Missense_Mutation	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	49946096	79166615	2028595	62	4450											
FAM38B	63895	hgsc.bcm.edu	37	chr18	10691260	10691260	+	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	gttgacgtaattgtagctctTggtgaggaagttccccagga	9	12	13	7	1	1	2	0	2	1	0	2	4	2	4	2	3	1	5	2	3	3	6			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr18:10691260T>A	ENST00000503781.3	-	44	6972	c.6973A>T	c.(6973-6975)Aag>Tag	p.K2325*	PIEZO2_ENST00000302079.6_Nonsense_Mutation_p.K2325*|PIEZO2_ENST00000285141.4_Nonsense_Mutation_p.K180*|PIEZO2_ENST00000580640.1_Nonsense_Mutation_p.K2350*|PIEZO2_ENST00000538948.1_Nonsense_Mutation_p.K282*	NM_022068.2	NP_071351.2	Q9H5I5	PIEZ2_HUMAN	piezo-type mechanosensitive ion channel component 2	2325					cation transport (GO:0006812)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|regulation of membrane potential (GO:0042391)|response to mechanical stimulus (GO:0009612)	integral component of membrane (GO:0016021)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)										TTGTAGCTCTTGGTGAGGAAG	0.493																																					p.K2325X		Atlas-SNP	.											.	.	.	.	0			c.A6973T						PASS	.						128	112	118					18																	10691260		2203	4300	6503	SO:0001587	stop_gained	63895	exon44			AGCTCTTGGTGAG	AK027056		18p11.21	2012-11-19	2011-08-31	2011-08-31	ENSG00000154864	ENSG00000154864			26270	protein-coding gene	gene with protein product		613629	"chromosome 18 open reading frame 30", "chromosome 18 open reading frame 58", "family with sequence similarity 38, member B"	FAM38B2, C18orf30, C18orf58, FAM38B		20813920, 21056836, 21299953	Standard	NM_022068		Approved	FLJ23403, FLJ23144, HsT748, HsT771, FLJ34907	uc002kos.2	Q9H5I5	OTTHUMG00000178507	ENST00000503781.3:c.6973A>T	chr18.hg19:g.10691260T>A	ENSP00000421377:p.Lys2325*	194.0	0.0	.		272.0	76.0	.	NM_022068	B7Z812|M4GPJ9|Q6ZS91|Q8N787|Q8NAR6|Q9H5R4	Nonsense_Mutation	SNP	ENST00000503781.3	hg19		.	.	.	.	.	.	.	.	.	.	T	43	9.868735	0.99284	.	.	ENSG00000154864	ENST00000503781;ENST00000302079;ENST00000538948;ENST00000285141	.	.	.	5.62	5.62	0.85841	.	0.142737	0.47455	D	0.000228	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.1189	0.81329	0.0:0.0:0.0:1.0	.	.	.	.	X	282;2325;282;180	.	ENSP00000285141:K180X	K	-	1	0	FAM38B	10681260	1.000000	0.71417	0.998000	0.56505	0.966000	0.64601	8.005000	0.88553	2.263000	0.75096	0.533000	0.62120	AAG	.	.	.	none		0.493	PIEZO2-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442385.4	NM_022068		A	10691260	T	A	10691260	4	1	67	1	0	0	0	0	0	1	0	0	5562	1821	63	5	1321	5	FAM38B	18	10691260	Nonsense_Mutation	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10		10691260	67385988	63	4451											
RBBP8	5932	hgsc.bcm.edu	37	chr18	20606136	20606136	+	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	ggaagatcttgatccttgtcCtcgtccaaaaagacgtcagc	11	10	9	11	2	2	3	1	1	1	2	6	4	5	4	3	1	1	0	3	1	3	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr18:20606136C>G	ENST00000399722.2	+	19	2978	c.2627C>G	c.(2626-2628)cCt>cGt	p.P876R	RBBP8_ENST00000327155.5_Missense_Mutation_p.P876R|RBBP8_ENST00000399725.2_Missense_Mutation_p.L844V|Y_RNA_ENST00000411091.1_RNA|RBBP8_ENST00000360790.5_Missense_Mutation_p.P881R|RBBP8_ENST00000581687.1_Missense_Mutation_p.P54R	NM_203291.1	NP_976036.1	Q99708	COM1_HUMAN	retinoblastoma binding protein 8	876					blastocyst hatching (GO:0001835)|cell cycle checkpoint (GO:0000075)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|G2 DNA damage checkpoint (GO:0031572)|meiotic nuclear division (GO:0007126)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	damaged DNA binding (GO:0003684)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)	p.P876L(1)|p.L844F(1)		central_nervous_system(1)|cervix(2)|endometrium(5)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	24	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)		OV - Ovarian serous cystadenocarcinoma(1;0.00196)			GATCCTTGTCCTCGTCCAAAA	0.368								Homologous recombination																													p.P876R		Atlas-SNP	.											RBBP8_ENST00000399725,NS,carcinoma,0,2	RBBP8	138	.	2	Substitution - Missense(2)	prostate(2)	c.C2627G						PASS	.						128	114	119					18																	20606136		2203	4300	6503	SO:0001583	missense	5932	exon19			CTTGTCCTCGTCC	AF043431	CCDS11874.1, CCDS11875.1	18q11.2	2012-11-05	2001-11-28		ENSG00000101773	ENSG00000101773			9891	protein-coding gene	gene with protein product	"CTBP-interacting protein"	604124	"retinoblastoma-binding protein 8", "Seckel syndrome 2"	SCKL2		9721205, 17965729, 21998596	Standard	NM_002894		Approved	CtIP, RIM, COM1	uc002ktw.3	Q99708	OTTHUMG00000131769	ENST00000399722.2:c.2627C>G	chr18.hg19:g.20606136C>G	ENSP00000382628:p.Pro876Arg	232.0	0.0	.		305.0	78.0	.	NM_002894	A6NKN2|A8K8W6|E7ETY1|O75371|Q8NHQ3	Missense_Mutation	SNP	ENST00000399722.2	hg19	CCDS11875.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.52|11.52	1.661903|1.661903	0.29515|0.29515	.|.	.|.	ENSG00000101773|ENSG00000101773	ENST00000399725;ENST00000399721|ENST00000327155;ENST00000399722;ENST00000360790	T|T;T;T	0.35048|0.30182	1.33|1.54;1.54;1.54	5.75|5.75	5.75|5.75	0.90469|0.90469	.|.	.|0.429012	.|0.25735	.|N	.|0.028643	T|T	0.24967|0.24967	0.0606|0.0606	N|N	0.14661|0.14661	0.345|0.345	0.30511|0.30511	N|N	0.769444|0.769444	P|D;D	0.42827|0.59767	0.791|0.986;0.986	B|P;P	0.38378|0.48873	0.272|0.593;0.593	T|T	0.07481|0.07481	-1.0770|-1.0770	9|10	0.87932|0.38643	D|T	0|0.18	-7.0083|-7.0083	12.5437|12.5437	0.56186|0.56186	0.2615:0.7385:0.0:0.0|0.2615:0.7385:0.0:0.0	.|.	844|881;876	A6NKN2|E7ETY1;Q99708	.|.;COM1_HUMAN	V|R	844|876;876;881	ENSP00000382630:L844V|ENSP00000323050:P876R;ENSP00000382628:P876R;ENSP00000354024:P881R	ENSP00000382627:L844V|ENSP00000323050:P876R	L|P	+|+	1|2	0|0	RBBP8|RBBP8	18860134|18860134	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.979000|0.979000	0.70002|0.70002	1.895000|1.895000	0.39778|0.39778	2.716000|2.716000	0.92895|0.92895	0.655000|0.655000	0.94253|0.94253	CTC|CCT	.	.	.	none		0.368	RBBP8-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446387.1	NM_203291		G	20606136	C	G	20606136	3	3	67	1	0	0	0	0	1	0	0	0	13118	681	24	4	2697	4	RBBP8	18	20606136	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	9914876	20606136	57471112	64	4452											
PCSK4	148223	hgsc.bcm.edu	37	chr19	1481811	1481811	+	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	ggtgggggtggccctggcacGggagagccaggcgtatagtg	6	6	21	8	2	0	1	0	0	0	1	0	2	0	1	2	7	1	2	2	7	2	2	rs377189780		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr19:1481811G>A	ENST00000436106.2	-	0	0				C19orf25_ENST00000591027.1_5'Flank|CTB-25B13.6_ENST00000585643.1_RNA|C19orf25_ENST00000427685.2_5'Flank|C19orf25_ENST00000585675.1_5'Flank|C19orf25_ENST00000586564.1_5'Flank|C19orf25_ENST00000588849.1_5'Flank|C19orf25_ENST00000592872.1_5'Flank|C19orf25_ENST00000588871.1_5'Flank|PCSK4_ENST00000300954.5_Missense_Mutation_p.R739C|C19orf25_ENST00000588427.1_5'Flank			Q9UFG5	CS025_HUMAN	chromosome 19 open reading frame 25														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)		GCCCTGGCACGGGAGAGCCAG	0.672																																					p.R739C		Atlas-SNP	.											.	PCSK4	44	.	0			c.C2215T						PASS	.						21	25	24					19																	1481811		2202	4296	6498	SO:0001631	upstream_gene_variant	54760	exon15			TGGCACGGGAGAG	AK075267	CCDS45898.1	19p13.3	2012-10-24			ENSG00000119559	ENSG00000119559			26711	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_152482		Approved	FLJ36666	uc010dsk.3	Q9UFG5	OTTHUMG00000180092		chr19.hg19:g.1481811G>A	Exception_encountered	75.0	0.0	.		104.0	12.0	.	NM_017573	B3KQN6|Q8N9R7|Q8WV94	Missense_Mutation	SNP	ENST00000436106.2	hg19	CCDS45898.1	.	.	.	.	.	.	.	.	.	.	g	8.277	0.814622	0.16607	.	.	ENSG00000115257	ENST00000300954	T	0.70749	-0.51	1.2	-2.4	0.06583	.	.	.	.	.	T	0.46268	0.1384	L	0.36672	1.1	0.09310	N	1	P	0.46457	0.878	B	0.26094	0.066	T	0.30880	-0.9963	9	0.52906	T	0.07	.	4.3765	0.11272	0.0:0.4776:0.2063:0.3161	.	739	Q6UW60	PCSK4_HUMAN	C	739	ENSP00000300954:R739C	ENSP00000300954:R739C	R	-	1	0	PCSK4	1432811	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-3.167000	0.00575	-2.042000	0.00914	-1.041000	0.02371	CGT	.	.	.	alt		0.672	C19orf25-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449694.1	NM_152482		A	1481811	G	A	1481811	1	1	67	0	1	0	0	0	0	0	0	0	11609	1116	39	1		1	PCSK4	19	1481811	5'Flank	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10		1481811	57647172	65	4453											
NRTN	4902	hgsc.bcm.edu	37	chr19	5827909	5827909	+	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	cgcggccttgcgggctgcgcGagctggaggtgcgcgtgagc	3	6	20	12	7	0	1	0	1	0	0	0	3	0	2	1	4	5	2	1	4	0	1	rs375707068		TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr19:5827909G>A	ENST00000303212.2	+	2	683	c.319G>A	c.(319-321)Gag>Aag	p.E107K		NM_004558.3	NP_004549.1	Q99748	NRTN_HUMAN	neurturin	107					axon guidance (GO:0007411)|MAPK cascade (GO:0000165)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neuron projection development (GO:0031175)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|extracellular region (GO:0005576)	receptor binding (GO:0005102)			large_intestine(1)	1						CGGGCTGCGCGAGCTGGAGGT	0.806																																					p.E107K		Atlas-SNP	.											.	NRTN	4	.	0			c.G319A						PASS	.	G	LYS/GLU	0,3794		0,0,1897	5	5	5		319	4.3	1	19		5	1,7493		0,1,3746	no	missense	NRTN	NM_004558.3	56	0,1,5643	AA,AG,GG		0.0133,0.0,0.0089	possibly-damaging	107/198	5827909	1,11287	1897	3747	5644	SO:0001583	missense	4902	exon2			CTGCGCGAGCTGG	U78110	CCDS12151.1	19p13.3	2014-01-30				ENSG00000171119		"Endogenous ligands"	8007	protein-coding gene	gene with protein product	"prepro-neurturin"	602018				8945474	Standard	NM_004558		Approved	NTN	uc002mde.3	Q99748		ENST00000303212.2:c.319G>A	chr19.hg19:g.5827909G>A	ENSP00000302648:p.Glu107Lys	0.0	0.0	.		9.0	8.0	.	NM_004558	B2RPE8	Missense_Mutation	SNP	ENST00000303212.2	hg19	CCDS12151.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.650912	0.87958	0.0	1.33E-4	ENSG00000171119	ENST00000303212	D	0.84146	-1.81	4.33	4.33	0.51752	Transforming growth factor-beta, C-terminal (3);	0.128790	0.51477	D	0.000084	D	0.82513	0.5053	L	0.34521	1.04	0.39656	D	0.970533	D	0.63046	0.992	P	0.54856	0.762	T	0.81088	-0.1091	10	0.33940	T	0.23	-8.9466	8.5435	0.33406	0.1094:0.0:0.8906:0.0	.	107	Q99748	NRTN_HUMAN	K	107	ENSP00000302648:E107K	ENSP00000302648:E107K	E	+	1	0	NRTN	5778909	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	3.082000	0.50128	2.153000	0.67306	0.491000	0.48974	GAG	.	.	.	weak		0.806	NRTN-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451882.2	NM_004558		A	5827909	G	A	5827909	3	1	67	1	0	0	0	0	1	0	0	0	10671	1059	37	1	325	1	NRTN	19	5827909	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	4346098	5827909	53301074	66	4454											
TBCB	1155	hgsc.bcm.edu	37	chr19	36606539	36606539	+	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	caacaccttccgctccgagaAgcgatacagccgcagcctca	11	5	8	17	4	1	1	1	0	0	1	3	3	3	1	5	0	5	2	5	0	3	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr19:36606539A>T	ENST00000221855.3	+	1	652	c.77A>T	c.(76-78)aAg>aTg	p.K26M	TBCB_ENST00000589996.1_Missense_Mutation_p.K26M|TBCB_ENST00000585746.1_5'Flank|TBCB_ENST00000392178.4_3'UTR|TBCB_ENST00000586868.1_5'Flank|POLR2I_ENST00000221859.4_5'Flank	NM_001281.2	NP_001272.2	Q99426	TBCB_HUMAN	tubulin folding cofactor B	26					'de novo' posttranslational protein folding (GO:0051084)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	5	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			CGCTCCGAGAAGCGATACAGC	0.662																																					p.K26M		Atlas-SNP	.											.	TBCB	13	.	0			c.A77T						PASS	.						34	23	27					19																	36606539		2202	4299	6501	SO:0001583	missense	1155	exon1			CCGAGAAGCGATA	AF013488	CCDS12488.1, CCDS74344.1	19q13.11-q13.12	2008-02-05	2006-11-22	2006-11-22	ENSG00000105254	ENSG00000105254			1989	protein-coding gene	gene with protein product		601303	"cytoskeleton-associated protein 1", "cytoskeleton associated protein 1"	CKAP1		8978778	Standard	NM_001281		Approved	CG22, CKAPI	uc002odg.1	Q99426	OTTHUMG00000048143	ENST00000221855.3:c.77A>T	chr19.hg19:g.36606539A>T	ENSP00000221855:p.Lys26Met	98.0	0.0	.		159.0	72.0	.	NM_001281	O00111|O00674|O14728|Q6FGY5	Missense_Mutation	SNP	ENST00000221855.3	hg19	CCDS12488.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.024046	0.75390	.	.	ENSG00000105254	ENST00000221855;ENST00000392178	D	0.92249	-3.0	5.33	4.31	0.51392	.	0.180969	0.47852	D	0.000214	D	0.90964	0.7159	M	0.76002	2.32	0.80722	D	1	P	0.44260	0.83	B	0.42422	0.387	D	0.89084	0.3478	10	0.54805	T	0.06	-27.6416	9.2292	0.37425	0.9131:0.0:0.0869:0.0	.	26	Q99426	TBCB_HUMAN	M	26	ENSP00000221855:K26M	ENSP00000221855:K26M	K	+	2	0	TBCB	41298379	1.000000	0.71417	0.979000	0.43373	0.871000	0.50021	2.209000	0.42806	0.863000	0.35553	0.397000	0.26171	AAG	.	.	.	none		0.662	TBCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156291.2	NM_001281		T	36606539	A	T	36606539	3	4	67	1	0	0	0	0	1	0	0	0	15642	72	3	5	79	5	TBCB	19	36606539	Missense_Mutation	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	30778630	36606539	22522444	67	4455											
FBL	2091	hgsc.bcm.edu	37	chr19	40330915	40330915	+	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	ccataaactgattccccaggGaccaggttcttggtgaccag	10	9	10	12	0	1	2	0	2	1	0	2	3	2	3	5	3	1	1	5	3	2	4			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr19:40330915G>A	ENST00000221801.3	-	4	449	c.336C>T	c.(334-336)gtC>gtT	p.V112V	FBL_ENST00000593503.1_5'Flank	NM_001436.3	NP_001427.2	P22087	FBRL_HUMAN	fibrillarin	112					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)		ATTCCCCAGGGACCAGGTTCT	0.577																																					p.V112V		Atlas-SNP	.											.	FBL	37	.	0			c.C336T						PASS	.						103	91	95					19																	40330915		2203	4300	6503	SO:0001819	synonymous_variant	2091	exon4			CCCAGGGACCAGG	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.336C>T	chr19.hg19:g.40330915G>A		172.0	0.0	.		93.0	26.0	.	NM_001436	B5BUE8|O75259|Q6IAT5|Q9UPI6	Silent	SNP	ENST00000221801.3	hg19	CCDS12545.1																																																																																			.	.	.	none		0.577	FBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462509.4	NM_001436		A	40330915	G	A	40330915	2	1	67	1	0	0	0	0	0	0	0	1	5703	1161	41	2		2	FBL	19	40330915	Silent	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	3724376	40330915	18798068	68	4456											
KLK5	25818	hgsc.bcm.edu	37	chr19	51451945	51451945	+	Missense_Mutation	SNP	T	T	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	cggcgcagaacatggtgtcaTctatctgtctcgggtaagca	9	10	12	10	3	4	1	1	0	3	1	5	1	4	1	0	3	2	3	0	3	3	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr19:51451945T>G	ENST00000336334.3	-	5	1029	c.677A>C	c.(676-678)gAt>gCt	p.D226A	CTB-147C22.8_ENST00000594939.1_RNA|KLK5_ENST00000391809.2_Missense_Mutation_p.D226A|KLK5_ENST00000593428.1_Missense_Mutation_p.D226A|CTB-147C22.8_ENST00000601506.1_RNA	NM_012427.4	NP_036559	Q9Y337	KLK5_HUMAN	kallikrein-related peptidase 5	226	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				epidermis development (GO:0008544)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)	epidermal lamellar body (GO:0097209)|extracellular space (GO:0005615)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|urinary_tract(1)	15		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00379)|GBM - Glioblastoma multiforme(134;0.00888)		CATGGTGTCATCTATCTGTCT	0.507																																					p.D226A		Atlas-SNP	.											.	KLK5	37	.	0			c.A677C						PASS	.						170	133	146					19																	51451945		2203	4300	6503	SO:0001583	missense	25818	exon5			GTGTCATCTATCT	AF135028	CCDS12810.1	19q13.33	2008-02-05	2006-10-27			ENSG00000167754		"Kallikreins"	6366	protein-coding gene	gene with protein product		605643	"kallikrein 5"			10514489, 10608802, 1680072, 4, 16800723, 17012259	Standard	NM_012427		Approved	SCTE, KLK-L2	uc002puf.3	Q9Y337		ENST00000336334.3:c.677A>C	chr19.hg19:g.51451945T>G	ENSP00000337733:p.Asp226Ala	138.0	0.0	.		114.0	53.0	.	NM_012427	Q53ZR3|Q9HBG8	Missense_Mutation	SNP	ENST00000336334.3	hg19	CCDS12810.1	.	.	.	.	.	.	.	.	.	.	t	10.10	1.257295	0.22965	.	.	ENSG00000167754	ENST00000336334;ENST00000391809	D;D	0.88201	-2.35;-2.35	4.67	2.49	0.30216	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.34386	U	0.004020	T	0.79776	0.4504	N	0.16066	0.365	0.09310	N	1	P	0.40398	0.716	B	0.41036	0.346	T	0.71111	-0.4687	10	0.51188	T	0.08	.	10.2185	0.43184	0.0:0.0:0.5204:0.4796	.	226	Q9Y337	KLK5_HUMAN	A	226	ENSP00000337733:D226A;ENSP00000375685:D226A	ENSP00000337733:D226A	D	-	2	0	KLK5	56143757	1.000000	0.71417	0.006000	0.13384	0.020000	0.10135	5.146000	0.64845	0.262000	0.21774	-0.316000	0.08728	GAT	.	.	.	none		0.507	KLK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465057.1	NM_012427		G	51451945	T	G	51451945	3	3	67	1	0	0	0	0	1	0	0	0	8414	1435	50	5	212	5	KLK5	19	51451945	Missense_Mutation	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10	11121030	51451945	7677038	69	4457											
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-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	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_ENST00000600634.1_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	chr19.hg19:g.58385793C>T	ENSP00000410545:p.Arg322Lys	86.0	0.0	.		86.0	16.0	.	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	hg19	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	67	1	0	0	0	0	1	0	0	0	18188	913	32	2	1606	2	ZNF814	19	58385793	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	6933848	58385793	743190	70	4458											
PCSK2	5126	hgsc.bcm.edu	37	chr20	17417493	17417493	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagtggatgggccccgggagCtcacgctgcaggccatggcc	6	5	16	14	2	1	0	1	0	0	0	1	2	1	2	4	5	2	3	4	5	0	0			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr20:17417493C>T	ENST00000262545.2	+	8	1165	c.850C>T	c.(850-852)Ctc>Ttc	p.L284F	PCSK2_ENST00000536609.1_Missense_Mutation_p.L249F|PCSK2_ENST00000377899.1_Missense_Mutation_p.L265F	NM_002594.3	NP_002585.2	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	284	Peptidase S8.			EL -> DV (in Ref. 1; AAA60032). {ECO:0000305}.	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)"	GCCCCGGGAGCTCACGCTGCA	0.642																																					p.L284F		Atlas-SNP	.											.	PCSK2	112	.	0			c.C850T						PASS	.						34	32	33					20																	17417493		2203	4300	6503	SO:0001583	missense	5126	exon8			CGGGAGCTCACGC	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.850C>T	chr20.hg19:g.17417493C>T	ENSP00000262545:p.Leu284Phe	81.0	0.0	.		174.0	65.0	.	NM_002594	B1ANH9|B4DFQ3|Q14927|Q5JYQ1|Q8IWA8|Q9NQG3|Q9NUG1|Q9UJC6	Missense_Mutation	SNP	ENST00000262545.2	hg19	CCDS13125.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.421696	0.83559	.	.	ENSG00000125851	ENST00000377899;ENST00000262545;ENST00000536609	D;D;D	0.87887	-2.31;-2.31;-2.31	5.38	5.38	0.77491	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.000000	0.85682	D	0.000000	D	0.92192	0.7524	M	0.79693	2.465	0.80722	D	1	B;D	0.53745	0.24;0.962	B;P	0.55391	0.146;0.775	D	0.92722	0.6192	10	0.56958	D	0.05	-19.6799	17.6879	0.88261	0.0:1.0:0.0:0.0	.	249;284	B4DFQ3;P16519	.;NEC2_HUMAN	F	265;284;249	ENSP00000367131:L265F;ENSP00000262545:L284F;ENSP00000437458:L249F	ENSP00000262545:L284F	L	+	1	0	PCSK2	17365493	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.647000	0.61418	2.519000	0.84933	0.655000	0.94253	CTC	.	.	.	none		0.642	PCSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078120.2	NM_002594		T	17417493	C	T	17417493	3	4	67	1	0	0	0	0	1	0	0	0	11608	797	28	2	880	2	PCSK2	20	17417493	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10		17417493	45608027	71	4459											
C20orf114	92747	hgsc.bcm.edu	37	chr20	31892698	31892698	+	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	ctgggattggctggttccaaGtaagtgttaacaggtggtgc	8	12	15	6	0	0	0	0	0	0	0	1	1	1	1	1	5	2	4	1	5	3	4			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr20:31892698G>A	ENST00000253354.1	+	13	1415		c.e13+1		BPIFB1_ENST00000464032.1_Splice_Site	NM_033197.2	NP_149974.2	Q8TDL5	BPIB1_HUMAN	BPI fold containing family B, member 1						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)										CTGGTTCCAAGTAAGTGTTAA	0.532																																					.		Atlas-SNP	.											.	.	.	.	0			c.1254+1G>A						PASS	.						104	86	92					20																	31892698		2203	4300	6503	SO:0001630	splice_region_variant	92747	exon13			TTCCAAGTAAGTG	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.1254+1G>A	chr20.hg19:g.31892698G>A		98.0	0.0	.		201.0	73.0	.	NM_033197	A8K2H8|Q5QP43|Q6UWY1|Q6ZRU7|Q96HK6|Q9BQP8|Q9BWZ6|Q9H4V6	Splice_Site	SNP	ENST00000253354.1	hg19	CCDS13218.1	.	.	.	.	.	.	.	.	.	.	G	12.79	2.043780	0.36085	.	.	ENSG00000125999	ENST00000253354	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.217	0.65800	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BPIFB1	31356359	0.999000	0.42202	0.998000	0.56505	0.266000	0.26442	4.225000	0.58600	2.740000	0.93945	0.561000	0.74099	.	.	.	.	none		0.532	BPIFB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106499.2	NM_033197	Intron	A	31892698	G	A	31892698	5	1	67	1	0	0	0	0	0	0	1	0	2084	1043	36	2	1301	2	C20orf114	20	31892698	Splice_Site	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10	14475205	31892698	31132822	72	4460											
MYT1	4661	hgsc.bcm.edu	37	chr20	62859303	62859303	+	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	ggcacccaccaaggacgacaAggaggaccccgagctgatga	13	2	13	13	2	0	2	0	2	0	0	0	7	0	5	4	4	1	2	4	4	2	0			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr20:62859303A>T	ENST00000328439.1	+	18	3018	c.2654A>T	c.(2653-2655)aAg>aTg	p.K885M	MYT1_ENST00000536311.1_Missense_Mutation_p.K912M|MYT1_ENST00000360149.4_Missense_Mutation_p.K564M	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(12)|liver(1)|lung(17)|ovary(5)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					AAGGACGACAAGGAGGACCCC	0.483																																					p.K885M	GBM(59;481 1041 20555 21139 33705)	Atlas-SNP	.											.	MYT1	152	.	0			c.A2654T						PASS	.						89	88	88					20																	62859303		2203	4300	6503	SO:0001583	missense	4661	exon18			ACGACAAGGAGGA	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.2654A>T	chr20.hg19:g.62859303A>T	ENSP00000327465:p.Lys885Met	141.0	0.0	.		213.0	82.0	.	NM_004535	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000328439.1	hg19	CCDS13558.1	.	.	.	.	.	.	.	.	.	.	A	17.01	3.279871	0.59758	.	.	ENSG00000196132	ENST00000360149;ENST00000328439;ENST00000536311	T;T;T	0.54071	0.59;0.65;0.61	5.67	4.58	0.56647	.	0.115126	0.64402	D	0.000018	T	0.69251	0.3090	M	0.78637	2.42	0.53688	D	0.999978	D;D;D	0.67145	0.996;0.993;0.986	D;P;P	0.64144	0.922;0.886;0.621	T	0.72272	-0.4342	10	0.72032	D	0.01	-30.9363	11.5655	0.50802	0.9301:0.0:0.0699:0.0	.	912;885;564	F5H7M8;Q01538;Q6P6D5	.;MYT1_HUMAN;.	M	564;885;912	ENSP00000353269:K564M;ENSP00000327465:K885M;ENSP00000442412:K912M	ENSP00000327465:K885M	K	+	2	0	MYT1	62329747	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	6.166000	0.71896	0.990000	0.38787	0.533000	0.62120	AAG	.	.	.	none		0.483	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535		T	62859303	A	T	62859303	3	4	67	1	0	0	0	0	1	0	0	0	10113	72	3	5	2716	5	MYT1	20	62859303	Missense_Mutation	SNP	A	TCGA-A4-A5Y1-01A-11D-A28G-10	30966605	62859303	166217	73	4461											
ZNF280A	129025	hgsc.bcm.edu	37	chr22	22869192	22869192	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgacttgctagacttgaaaTgtctgtcattgccaggccag	9	13	10	9	0	2	3	1	2	1	1	2	3	2	3	2	1	2	1	2	1	2	5			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chr22:22869192T>C	ENST00000302097.3	-	2	1015	c.763A>G	c.(763-765)Att>Gtt	p.I255V	snoU13_ENST00000459485.1_RNA	NM_080740.3	NP_542778.1	P59817	Z280A_HUMAN	zinc finger protein 280A	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)			endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	18	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		AGACTTGAAATGTCTGTCATT	0.413																																					p.I255V		Atlas-SNP	.											.	ZNF280A	67	.	0			c.A763G						PASS	.						126	115	119					22																	22869192		2203	4300	6503	SO:0001583	missense	129025	exon2			TTGAAATGTCTGT	D87009	CCDS13800.1	22q11.21	2007-09-20	2007-09-20	2007-09-20	ENSG00000169548	ENSG00000169548			18597	protein-coding gene	gene with protein product			"zinc finger protein 280", "suppressor of hairy wing homolog 1 (Drosophila)"	ZNF280, SUHW1		9074928	Standard	NM_080740		Approved	3'OY11.1, ZNF636	uc002zwe.3	P59817	OTTHUMG00000030545	ENST00000302097.3:c.763A>G	chr22.hg19:g.22869192T>C	ENSP00000302855:p.Ile255Val	129.0	1.0	.		121.0	100.0	.	NM_080740		Missense_Mutation	SNP	ENST00000302097.3	hg19	CCDS13800.1	.	.	.	.	.	.	.	.	.	.	T	2.685	-0.274412	0.05679	.	.	ENSG00000169548	ENST00000302097	T	0.01126	5.3	3.66	1.52	0.23074	.	.	.	.	.	T	0.00695	0.0023	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.48163	-0.9059	9	0.20519	T	0.43	-0.1797	4.2473	0.10677	0.5866:0.2055:0.0:0.2079	.	255	P59817	Z280A_HUMAN	V	255	ENSP00000302855:I255V	ENSP00000302855:I255V	I	-	1	0	ZNF280A	21199192	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.195000	0.17155	0.264000	0.21851	-1.173000	0.01734	ATT	.	.	.	none		0.413	ZNF280A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075433.3	NM_080740		C	22869192	T	C	22869192	3	2	67	1	0	0	0	0	1	0	0	0	17826	1464	51	3	869	3	ZNF280A	22	22869192	Missense_Mutation	SNP	T	TCGA-A4-A5Y1-01A-11D-A28G-10		22869192	28435374	74	4462											
CSF2RA	1438	hgsc.bcm.edu	37	chrX	1407702	1407702	+	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	cctgtttcatctacaatgcgGatttaatgaactgtacctgg	10	14	8	9	1	2	1	1	1	1	0	2	2	2	2	2	2	4	2	2	2	5	5			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chrX:1407702G>T	ENST00000381524.3	+	6	580	c.394G>T	c.(394-396)Gat>Tat	p.D132Y	CSF2RA_ENST00000417535.2_Missense_Mutation_p.D132Y|CSF2RA_ENST00000432318.2_Missense_Mutation_p.D132Y|CSF2RA_ENST00000381529.3_Missense_Mutation_p.D132Y|CSF2RA_ENST00000381509.3_Missense_Mutation_p.D132Y|CSF2RA_ENST00000355805.2_Missense_Mutation_p.D132Y|CSF2RA_ENST00000501036.2_5'UTR|CSF2RA_ENST00000355432.3_Missense_Mutation_p.D132Y|BX649553.3_ENST00000581137.1_RNA|CSF2RA_ENST00000494969.2_Intron|CSF2RA_ENST00000361536.3_Missense_Mutation_p.D132Y|CSF2RA_ENST00000381500.1_Missense_Mutation_p.D132Y			P15509	CSF2R_HUMAN	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	132					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)	CTACAATGCGGATTTAATGAA	0.468																																					p.D132Y	Esophageal Squamous(131;723 1707 25334 40494 41806)	Atlas-SNP	.											.	CSF2RA	153	.	0			c.G394T						PASS	.						173	182	179					X																	1407702		2203	4296	6499	SO:0001583	missense	1438	exon4			AATGCGGATTTAA	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.394G>T	chrX.hg19:g.1407702G>T	ENSP00000370935:p.Asp132Tyr	282.0	0.0	.		389.0	127.0	.	NM_172247	A7J003|A8KAM1|B4DW68|J3JS76|J3JS77|O00207|Q14429|Q14430|Q14431|Q16564	Missense_Mutation	SNP	ENST00000381524.3	hg19	CCDS35191.1	.	.	.	.	.	.	.	.	.	.	.	3.532	-0.095615	0.07010	.	.	ENSG00000198223	ENST00000381529;ENST00000432318;ENST00000361536;ENST00000381507;ENST00000381524;ENST00000412290;ENST00000419094;ENST00000381509;ENST00000355805;ENST00000355432;ENST00000417535;ENST00000381500	D;D;T;D;T;T;D;T;T;D;T	0.96104	-3.91;-3.91;0.5;-3.91;0.5;0.5;-3.91;0.5;0.5;-3.91;0.5	2.02	-0.156	0.13391	Interleukin-6 receptor alpha chain, binding (1);Fibronectin, type III (1);Immunoglobulin-like fold (1);	1.244990	0.06574	U	0.749174	D	0.95896	0.8664	.	.	.	0.18873	N	0.999989	P;P;P;D;B;P	0.57899	0.488;0.483;0.685;0.981;0.428;0.483	B;B;B;P;B;B	0.60012	0.092;0.239;0.269;0.867;0.154;0.157	D	0.86489	0.1796	9	0.66056	D	0.02	.	3.1267	0.06409	0.1944:0.2787:0.5269:0.0	.	132;132;132;132;132;132	P15509-2;A7J003;P15509-3;P15509-6;P15509-5;P15509	.;.;.;.;.;CSF2R_HUMAN	Y	132	ENSP00000370940:D132Y;ENSP00000416437:D132Y;ENSP00000354836:D132Y;ENSP00000370935:D132Y;ENSP00000410667:D132Y;ENSP00000397452:D132Y;ENSP00000370920:D132Y;ENSP00000348058:D132Y;ENSP00000347606:D132Y;ENSP00000394227:D132Y;ENSP00000370911:D132Y	ENSP00000347606:D132Y	D	+	1	0	CSF2RA	1367702	0.006000	0.16342	0.001000	0.08648	0.041000	0.13682	-0.778000	0.04664	-0.259000	0.09432	0.280000	0.19369	GAT	.	.	.	none		0.468	CSF2RA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000035013.2			T	1407702	G	T	1407702	3	4	67	1	0	0	0	0	1	0	0	0	3936	1174	41	4	408	4	CSF2RA	23	1407702	Missense_Mutation	SNP	G	TCGA-A4-A5Y1-01A-11D-A28G-10		1407702	153862858	75	4463											
NAA10	8260	hgsc.bcm.edu	37	chrX	153198018	153198018	+	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	ggtgatatgtccatggggcaCatcatctgggtcctcttccc	6	12	11	12	0	3	1	1	1	2	0	6	1	6	1	3	4	0	1	3	4	1	2			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chrX:153198018C>T	ENST00000464845.1	-	4	517	c.199G>A	c.(199-201)Gtg>Atg	p.V67M	NAA10_ENST00000393712.3_Missense_Mutation_p.V67M|NAA10_ENST00000370009.1_Missense_Mutation_p.V67M|NAA10_ENST00000393710.3_5'UTR|NAA10_ENST00000370015.4_Missense_Mutation_p.V67M	NM_001256120.1|NM_003491.3	NP_001243049.1|NP_003482.1	P41227	NAA10_HUMAN	N(alpha)-acetyltransferase 10, NatA catalytic subunit	67	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				DNA packaging (GO:0006323)|internal protein amino acid acetylation (GO:0006475)|N-terminal protein amino acid acetylation (GO:0006474)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)|NatA complex (GO:0031415)|nucleolus (GO:0005730)|nucleus (GO:0005634)	N-acetyltransferase activity (GO:0008080)|peptide alpha-N-acetyltransferase activity (GO:0004596)			breast(1)|endometrium(3)|kidney(1)|lung(3)|ovary(1)|prostate(1)	10						CCATGGGGCACATCATCTGGG	0.587																																					p.V67M	Ovarian(94;1099 1433 38814 45882 51063)	Atlas-SNP	.											.	NAA10	18	.	0			c.G199A						PASS	.						68	49	55					X																	153198018		2202	4297	6499	SO:0001583	missense	8260	exon4			GGGGCACATCATC	BC000308	CCDS14737.1, CCDS59179.1	Xq28	2010-05-07	2010-01-14	2010-01-14	ENSG00000102030	ENSG00000102030	2.3.1.88	"N(alpha)-acetyltransferase subunits"	18704	protein-coding gene	gene with protein product		300013	"ARD1 homolog, N-acetyltransferase (S. cerevisiae)", "ARD1 homolog A, N-acetyltransferase (S. cerevisiae)"	ARD1, ARD1A		7981673, 19660095	Standard	NM_003491		Approved	DXS707, TE2	uc004fjm.2	P41227	OTTHUMG00000024225	ENST00000464845.1:c.199G>A	chrX.hg19:g.153198018C>T	ENSP00000417763:p.Val67Met	51.0	0.0	.		87.0	32.0	.	NM_001256119	A6NM98	Missense_Mutation	SNP	ENST00000464845.1	hg19	CCDS14737.1	.	.	.	.	.	.	.	.	.	.	C	15.36	2.811472	0.50527	.	.	ENSG00000102030	ENST00000464845;ENST00000370015;ENST00000393712;ENST00000370009;ENST00000545734;ENST00000370011;ENST00000432089	T;T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51;1.51	5.04	3.25	0.37280	GCN5-related N-acetyltransferase (GNAT) domain (2);Acyl-CoA N-acyltransferase (2);	0.000000	0.85682	D	0.000000	T	0.37892	0.1020	L	0.47016	1.485	0.54753	D	0.999981	B;P;P	0.44195	0.251;0.454;0.828	B;P;P	0.53954	0.375;0.738;0.738	T	0.08330	-1.0727	10	0.46703	T	0.11	-18.5174	9.0852	0.36577	0.0:0.8122:0.0:0.1878	.	67;67;67	B7Z9N2;A6NM98;P41227	.;.;NAA10_HUMAN	M	67;67;67;67;67;61;61	ENSP00000417763:V67M;ENSP00000359032:V67M;ENSP00000377315:V67M;ENSP00000359026:V67M;ENSP00000359028:V61M;ENSP00000413668:V61M	ENSP00000359026:V67M	V	-	1	0	NAA10	152851212	1.000000	0.71417	0.899000	0.35326	0.948000	0.59901	4.628000	0.61282	0.909000	0.36697	0.525000	0.51046	GTG	.	.	.	none		0.587	NAA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061108.2	NM_003491		T	153198018	C	T	153198018	3	4	67	1	0	0	0	0	1	0	0	0	10123	478	17	2	528	2	NAA10	23	153198018	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	151790316	153198018	2072542	76	4464											
PLXNA3	55558	hgsc.bcm.edu	37	chrX	153700940	153700940	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctctcccccagattctcaCggctctggaccgagatgcct	6	10	8	17	2	3	2	1	0	3	2	6	4	4	3	5	2	1	1	5	2	0	1			TCGA-A4-A5Y1-01A-11D-A28G-10	TCGA-A4-A5Y1-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39eb3bc2-c190-47cb-b9c7-20278d7e1692	2eeacc32-d82b-4e45-908f-19cb21710b93	g.chrX:153700940C>T	ENST00000369682.3	+	33	5703	c.5528C>T	c.(5527-5529)aCg>aTg	p.T1843M		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	1843					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)					CAGATTCTCACGGCTCTGGAC	0.607																																					p.T1843M		Atlas-SNP	.											.	PLXNA3	156	.	0			c.C5528T						PASS	.						122	101	108					X																	153700940		2203	4300	6503	SO:0001583	missense	55558	exon33			TTCTCACGGCTCT	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.5528C>T	chrX.hg19:g.153700940C>T	ENSP00000358696:p.Thr1843Met	137.0	0.0	.		205.0	178.0	.	NM_017514	Q5HY36	Missense_Mutation	SNP	ENST00000369682.3	hg19	CCDS14752.1	.	.	.	.	.	.	.	.	.	.	C	12.00	1.807947	0.31961	.	.	ENSG00000130827	ENST00000369682	T	0.01015	5.44	5.32	0.143	0.14820	.	0.182827	0.46758	D	0.000265	T	0.01029	0.0034	L	0.52011	1.625	0.44295	D	0.997164	B	0.19583	0.037	B	0.14578	0.011	T	0.58880	-0.7558	10	0.46703	T	0.11	.	5.7954	0.18383	0.1253:0.3656:0.4303:0.0788	.	1843	P51805	PLXA3_HUMAN	M	1843	ENSP00000358696:T1843M	ENSP00000358696:T1843M	T	+	2	0	PLXNA3	153354134	0.000000	0.05858	0.001000	0.08648	0.032000	0.12392	0.251000	0.18257	-0.517000	0.06461	-0.191000	0.12829	ACG	.	.	.	none		0.607	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514		T	153700940	C	T	153700940	3	4	67	1	0	0	0	0	1	0	0	0	12128	536	19	1	5654	1	PLXNA3	23	153700940	Missense_Mutation	SNP	C	TCGA-A4-A5Y1-01A-11D-A28G-10	502922	153700940	1569620	77	4465											
AGRN	375790	hgsc.bcm.edu	37	chr1	987003	987003	+	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	tgcctgtgtcccgggggattCtcaggaccgcactgcgagaa	7	8	14	12	3	1	1	1	0	1	1	3	4	2	3	3	3	2	1	3	3	1	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:987003C>A	ENST00000379370.2	+	32	5591	c.5541C>A	c.(5539-5541)ttC>ttA	p.F1847L		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	1851	EGF-like 4. {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)		CCGGGGGATTCTCAGGACCGC	0.711																																					p.F1847L		Atlas-SNP	.											.	AGRN	110	.	0			c.C5541A						PASS	.						24	25	25					1																	987003		2199	4296	6495	SO:0001583	missense	375790	exon32			GGGATTCTCAGGA	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.5541C>A	chr1.hg19:g.987003C>A	ENSP00000368678:p.Phe1847Leu	17.0	0.0	.		54.0	19.0	.	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Missense_Mutation	SNP	ENST00000379370.2	hg19	CCDS30551.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.64|15.64	2.893312|2.893312	0.52121|0.52121	.|.	.|.	ENSG00000188157|ENSG00000188157	ENST00000379370;ENST00000379364|ENST00000419249	D|.	0.94000|.	-3.33|.	4.96|4.96	4.05|4.05	0.47172|0.47172	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);EGF (1);Epidermal growth factor-like (1);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.75177|0.75177	0.3814|0.3814	M|M	0.83118|0.83118	2.625|2.625	0.58432|0.58432	D|D	0.999995|0.999995	D|.	0.61080|.	0.989|.	P|.	0.62298|.	0.9|.	T|T	0.76782|0.76782	-0.2832|-0.2832	10|5	0.48119|.	T|.	0.1|.	-27.1498|-27.1498	12.382|12.382	0.55311|0.55311	0.0:0.9177:0.0:0.0823|0.0:0.9177:0.0:0.0823	.|.	1847|.	O00468|.	AGRIN_HUMAN|.	L|I	1847;190|150	ENSP00000368678:F1847L|.	ENSP00000368671:F190L|.	F|L	+|+	3|1	2|0	AGRN|AGRN	976866|976866	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.032000|0.032000	0.12392|0.12392	2.087000|2.087000	0.41653|0.41653	1.112000|1.112000	0.41740|0.41740	0.555000|0.555000	0.69702|0.69702	TTC|CTC	.	.	.	none		0.711	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576		A	987003	C	A	987003	3	1	68	1	0	0	0	0	1	0	0	0	397	912	32	4	5667	4	AGRN	1	987003	Missense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10		987003	248263618	1	4466											
KLHL21	9903	hgsc.bcm.edu	37	chr1	6659179	6659179	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggcgggagctggccgcagTccaccagcgaccacaggtcg	8	3	16	14	4	0	0	0	0	0	0	2	2	1	1	4	4	2	2	4	4	0	0			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:6659179T>C	ENST00000377658.4	-	2	1406	c.1355A>G	c.(1354-1356)gAc>gGc	p.D452G	KLHL21_ENST00000463043.1_Missense_Mutation_p.D85G|KLHL21_ENST00000467612.1_Missense_Mutation_p.D85G|KLHL21_ENST00000377663.3_Missense_Mutation_p.D452G	NM_014851.2	NP_055666.2	Q9UJP4	KLH21_HUMAN	kelch-like family member 21	452					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)		CTGGCCGCAGTCCACCAGCGA	0.642																																					p.D452G		Atlas-SNP	.											.	KLHL21	27	.	0			c.A1355G						PASS	.						47	45	46					1																	6659179		2203	4300	6503	SO:0001583	missense	9903	exon2			CCGCAGTCCACCA	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.1355A>G	chr1.hg19:g.6659179T>C	ENSP00000366886:p.Asp452Gly	90.0	0.0	.		170.0	56.0	.	NM_014851	B3KQP2|O75057|Q5SY26|Q5SY28|Q8N4I6|Q8NF10	Missense_Mutation	SNP	ENST00000377658.4	hg19	CCDS30575.1	.	.	.	.	.	.	.	.	.	.	T	13.54	2.269130	0.40095	.	.	ENSG00000162413	ENST00000377658;ENST00000377663	T;T	0.74209	-0.72;-0.82	5.14	3.99	0.46301	Galactose oxidase, beta-propeller (1);	0.179251	0.64402	D	0.000019	T	0.54013	0.1832	N	0.08118	0	0.31114	N	0.70964	B;B	0.28933	0.02;0.228	B;B	0.30855	0.007;0.121	T	0.55036	-0.8203	10	0.27082	T	0.32	.	11.6365	0.51207	0.0:0.0:0.1489:0.851	.	452;452	Q9UJP4;Q9UJP4-2	KLH21_HUMAN;.	G	452	ENSP00000366886:D452G;ENSP00000366891:D452G	ENSP00000366886:D452G	D	-	2	0	KLHL21	6581766	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	3.336000	0.52113	0.877000	0.35895	0.533000	0.62120	GAC	.	.	.	none		0.642	KLHL21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004188.1	NM_014851		C	6659179	T	C	6659179	3	2	68	1	0	0	0	0	1	0	0	0	8383	1667	58	3	450	3	KLHL21	1	6659179	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	5672176	6659179	242591442	2	4467											
INPP5B	3633	hgsc.bcm.edu	37	chr1	38343988	38343988	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaccaggcaggagcacggcActtctcactgaaatgcaaag	14	5	10	12	1	1	1	1	1	1	0	2	2	1	2	1	3	2	4	1	3	2	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:38343988A>G	ENST00000373026.1	-	15	1789	c.1789T>C	c.(1789-1791)Tgc>Cgc	p.C597R	INPP5B_ENST00000373023.2_Missense_Mutation_p.C597R|INPP5B_ENST00000373024.3_Missense_Mutation_p.C517R|INPP5B_ENST00000373027.1_Missense_Mutation_p.C353R|INPP5B_ENST00000458109.2_3'UTR			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	597	5-phosphatase. {ECO:0000250}.|Substrate binding.			GSDDWDTSEKCRAPAWCDRI -> RALTTGIPVRSAVLLPG VIGF (in Ref. 5; AA sequence). {ECO:0000305}.	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)				GGAGCACGGCACTTCTCACTG	0.547																																					p.C517R		Atlas-SNP	.											.	INPP5B	76	.	0			c.T1549C						PASS	.						66	67	67					1																	38343988		2087	4203	6290	SO:0001583	missense	3633	exon16			CACGGCACTTCTC	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.1789T>C	chr1.hg19:g.38343988A>G	ENSP00000362117:p.Cys597Arg	42.0	0.0	.		80.0	19.0	.	NM_005540	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	Missense_Mutation	SNP	ENST00000373026.1	hg19		.	.	.	.	.	.	.	.	.	.	A	19.27	3.796203	0.70567	.	.	ENSG00000204084	ENST00000373027;ENST00000373023;ENST00000373029;ENST00000373026;ENST00000373024	T;T;T;T	0.79554	-1.28;-1.28;-1.28;-1.28	5.43	5.43	0.79202	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.000000	0.85682	D	0.000000	D	0.83473	0.5262	L	0.33624	1.015	0.80722	D	1	D;P	0.89917	1.0;0.861	D;B	0.68765	0.96;0.31	T	0.82133	-0.0608	10	0.30854	T	0.27	.	15.4883	0.75584	1.0:0.0:0.0:0.0	.	597;517	P32019;P32019-2	I5P2_HUMAN;.	R	353;597;597;597;517	ENSP00000362118:C353R;ENSP00000362114:C597R;ENSP00000362117:C597R;ENSP00000362115:C517R	ENSP00000362114:C597R	C	-	1	0	INPP5B	38116575	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	8.855000	0.92236	2.078000	0.62432	0.460000	0.39030	TGC	.	.	.	none		0.547	INPP5B-003	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000012968.1	NM_005540		G	38343988	A	G	38343988	3	3	68	1	0	0	0	0	1	0	0	0	7762	159	6	3	1228	3	INPP5B	1	38343988	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	31684809	38343988	210906633	3	4468											
ACOT11	26027	hgsc.bcm.edu	37	chr1	55059680	55059687	+	Frame_Shift_Del	DEL	GCCACCTT	GCCACCTT	-																															ggaatgtgtgcaaggccttgGccaccttcgtggcccgccga																								rs35306628|rs370568235		TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	GCCACCTT	GCCACCTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:55059680_55059687delGCCACCTT	ENST00000371316.3	+	5	521_528	c.439_446delGCCACCTT	c.(439-447)gccaccttcfs	p.ATF147fs	ACOT11_ENST00000481208.1_3'UTR|ACOT11_ENST00000343744.2_Frame_Shift_Del_p.ATF147fs	NM_015547.3	NP_056362.1	Q8WXI4	ACO11_HUMAN	acyl-CoA thioesterase 11	147	Acyl coenzyme A hydrolase 1.				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						CAAGGCCTTGGCCACCTTCGTGGCCCGC	0.625																																					p.146_149del	Ovarian(148;1440 1861 22015 32453 51933)	Atlas-Indel,Pindel	.											.	ACOT11	105	.	0			c.438_445del						PASS	.																																			SO:0001589	frameshift_variant	26027	exon5			.	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.439_446delGCCACCTT	chr1.hg19:g.55059680_55059687delGCCACCTT	ENSP00000360366:p.Ala147fs	43.0	0.0	0		49.0	13.0	0.265306	NM_147161	B1AQ22|D3DQ50|O75187|Q52LP1|Q53ER9|Q96DI1|Q9H883	Frame_Shift_Del	DEL	ENST00000371316.3	hg19	CCDS592.1																																																																																			.	.	.	none		0.625	ACOT11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027356.1	NM_015547		-	55059687	GCCACCTT	-	55059680	7	5	68	1	0	1	0	1	0	0	0	0	149	1203	42	0	457	0	ACOT11	1	55059680	Frame_Shift_Del	DEL	GCCACCTT	TCGA-A4-A6HP-01A-11D-A31X-10	16715692	55059680	194190941	4	4469											
PTGFR	5737	hgsc.bcm.edu	37	chr1	78959108	78959108	+	Missense_Mutation	SNP	T	T	C																															tgcaatcacaggaattacacTtttaagagttaaatttaaaa																										TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:78959108T>C	ENST00000370757.3	+	2	917	c.680T>C	c.(679-681)cTt>cCt	p.L227P	PTGFR_ENST00000370756.3_Missense_Mutation_p.L227P|PTGFR_ENST00000370758.1_Missense_Mutation_p.L227P	NM_000959.3	NP_000950.1	P43088	PF2R_HUMAN	prostaglandin F receptor (FP)	227					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)	GGAATTACACTTTTAAGAGTT	0.383																																					p.L227P		Atlas-SNP	.											.	PTGFR	121	.	0			c.T680C						PASS	.						58	60	59					1																	78959108		2203	4300	6503	SO:0001583	missense	5737	exon2			TTACACTTTTAAG	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.680T>C	chr1.hg19:g.78959108T>C	ENSP00000359793:p.Leu227Pro	54.0	0.0	.		133.0	39.0	.	NM_000959	A8K9Y0|Q2KHP3|Q6RYQ6|Q9P1X4	Missense_Mutation	SNP	ENST00000370757.3	hg19	CCDS686.1	.	.	.	.	.	.	.	.	.	.	T	19.84	3.901960	0.72754	.	.	ENSG00000122420	ENST00000370758;ENST00000370757;ENST00000370756	T;T;T	0.52754	0.65;0.65;0.65	5.85	5.85	0.93711	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.63954	0.2555	M	0.76170	2.325	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.68685	-0.5343	10	0.87932	D	0	-21.0338	16.5479	0.84454	0.0:0.0:0.0:1.0	.	227;227	P43088;P43088-2	PF2R_HUMAN;.	P	227	ENSP00000359794:L227P;ENSP00000359793:L227P;ENSP00000359792:L227P	ENSP00000359792:L227P	L	+	2	0	PTGFR	78731696	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.698000	0.84413	2.371000	0.80710	0.533000	0.62120	CTT	.	.	.	none		0.383	PTGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026582.1	NM_000959		C	78959108	T	C	78959108	3	2	68	1	0	0	0	0	1	0	0	0	12760	1609	56	3	682	3	PTGFR	1	78959108	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	23899428	78959108	170291513	5	4470	51	2									
PTGFR	5737	hgsc.bcm.edu	37	chr1	78959111	78959111	+	Missense_Mutation	SNP	T	T	C																															aatcacaggaattacactttTaagagttaaatttaaaagtc																										TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:78959111T>C	ENST00000370757.3	+	2	920	c.683T>C	c.(682-684)tTa>tCa	p.L228S	PTGFR_ENST00000370756.3_Missense_Mutation_p.L228S|PTGFR_ENST00000370758.1_Missense_Mutation_p.L228S	NM_000959.3	NP_000950.1	P43088	PF2R_HUMAN	prostaglandin F receptor (FP)	228					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)	ATTACACTTTTAAGAGTTAAA	0.388																																					p.L228S		Atlas-SNP	.											.	PTGFR	121	.	0			c.T683C						PASS	.						57	59	58					1																	78959111		2203	4300	6503	SO:0001583	missense	5737	exon2			CACTTTTAAGAGT	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.683T>C	chr1.hg19:g.78959111T>C	ENSP00000359793:p.Leu228Ser	55.0	0.0	.		131.0	38.0	.	NM_000959	A8K9Y0|Q2KHP3|Q6RYQ6|Q9P1X4	Missense_Mutation	SNP	ENST00000370757.3	hg19	CCDS686.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.020614	0.75275	.	.	ENSG00000122420	ENST00000370758;ENST00000370757;ENST00000370756	T;T;T	0.39997	1.05;1.05;1.05	5.85	5.85	0.93711	GPCR, rhodopsin-like superfamily (1);	0.074264	0.56097	D	0.000033	T	0.50514	0.1620	L	0.52573	1.65	0.54753	D	0.999985	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.989	T	0.45731	-0.9241	10	0.40728	T	0.16	-5.6031	16.5479	0.84454	0.0:0.0:0.0:1.0	.	228;228	P43088;P43088-2	PF2R_HUMAN;.	S	228	ENSP00000359794:L228S;ENSP00000359793:L228S;ENSP00000359792:L228S	ENSP00000359792:L228S	L	+	2	0	PTGFR	78731699	1.000000	0.71417	0.995000	0.50966	0.988000	0.76386	7.643000	0.83403	2.371000	0.80710	0.533000	0.62120	TTA	.	.	.	none		0.388	PTGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026582.1	NM_000959		C	78959111	T	C	78959111	3	2	68	1	0	0	0	0	1	0	0	0	12760	1764	61	3	685	3	PTGFR	1	78959111	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	3	78959111	170291510	6	4471	51	2									
SLC6A17	388662	hgsc.bcm.edu	37	chr1	110740214	110740214	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggctacagcgcctggatcaAggaggaggtgaggggtgggg	8	5	22	6	1	1	1	1	1	0	0	1	4	1	4	1	9	2	1	1	9	2	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:110740214A>G	ENST00000331565.4	+	11	2293	c.1808A>G	c.(1807-1809)aAg>aGg	p.K603R		NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	603					alanine transport (GO:0032328)|glycine transport (GO:0015816)|leucine transport (GO:0015820)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		GCCTGGATCAAGGAGGAGGTG	0.582											OREG0013652	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K603R		Atlas-SNP	.											.	SLC6A17	86	.	0			c.A1808G						PASS	.						24	27	26					1																	110740214		2203	4300	6503	SO:0001583	missense	388662	exon11			GGATCAAGGAGGA		CCDS30799.1	1p13.2	2013-07-19	2013-07-19		ENSG00000197106	ENSG00000197106		"Solute carriers"	31399	protein-coding gene	gene with protein product		610299	"solute carrier family 6 (neurotransmitter transporter), member 17", "solute carrier family 6, member 17"				Standard	NM_001010898		Approved		uc009wfq.3	Q9H1V8	OTTHUMG00000011761	ENST00000331565.4:c.1808A>G	chr1.hg19:g.110740214A>G	ENSP00000330199:p.Lys603Arg	7.0	0.0	.	1429	22.0	11.0	.	NM_001010898	A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Missense_Mutation	SNP	ENST00000331565.4	hg19	CCDS30799.1	.	.	.	.	.	.	.	.	.	.	A	11.56	1.673675	0.29693	.	.	ENSG00000197106	ENST00000331565;ENST00000450985	T	0.74315	-0.83	5.03	2.63	0.31362	.	0.288442	0.37669	N	0.001989	T	0.23727	0.0574	N	0.04508	-0.205	0.26690	N	0.971361	B	0.02656	0.0	B	0.09377	0.004	T	0.29941	-0.9995	10	0.15066	T	0.55	.	7.503	0.27528	0.6046:0.0:0.3954:0.0	.	603	Q9H1V8	S6A17_HUMAN	R	603	ENSP00000330199:K603R	ENSP00000330199:K603R	K	+	2	0	SLC6A17	110541737	0.080000	0.21391	0.999000	0.59377	0.978000	0.69477	1.878000	0.39608	0.235000	0.21160	0.455000	0.32223	AAG	.	.	.	none		0.582	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2	XM_371280		G	110740214	A	G	110740214	3	3	68	1	0	0	0	0	1	0	0	0	14693	72	3	3	1846	3	SLC6A17	1	110740214	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	31781103	110740214	138510407	7	4472											
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144874782	144874782	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	catcagacaggaaagaggtgCtgctgggagagcggtgggag	11	5	19	6	1	1	3	1	0	0	3	1	6	1	5	0	5	3	2	0	5	1	0			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:144874782C>T	ENST00000369354.3	-	30	5015	c.4826G>A	c.(4825-4827)aGc>aAc	p.S1609N	RP4-791M13.5_ENST00000531288.1_RNA|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.S1745N|AL138796.1_ENST00000582173.1_RNA|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.S1609N|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.S1565N|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.S1745N			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1609	NBPF. {ECO:0000255|PROSITE- ProRule:PRU00647}.				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)		GAAAGAGGTGCTGCTGGGAGA	0.537			T	PDGFRB	MPD																																p.S1609N		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.G4826A						PASS	.						253	241	245					1																	144874782		2203	4296	6499	SO:0001583	missense	9659	exon30			GAGGTGCTGCTGG	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.4826G>A	chr1.hg19:g.144874782C>T	ENSP00000358360:p.Ser1609Asn	92.0	0.0	.		170.0	24.0	.	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	hg19	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.058459	0.76074	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01767	4.65;4.76;4.76;4.73;4.78	5.91	2.8	0.32819	DUF1220 (2);	.	.	.	.	T	0.01558	0.0050	L	0.61218	1.895	0.80722	D	1	P;P	0.40970	0.634;0.734	B;B	0.43575	0.3;0.424	T	0.57046	-0.7878	9	0.56958	D	0.05	.	10.7557	0.46234	0.1347:0.622:0.2433:0.0	.	1565;1609	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	N	1565;1609;1609;1745;1745	ENSP00000327209:S1565N;ENSP00000358360:S1609N;ENSP00000358363:S1609N;ENSP00000435654:S1745N;ENSP00000358366:S1745N	ENSP00000327209:S1565N	S	-	2	0	PDE4DIP	143586139	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	4.387000	0.59626	0.794000	0.33899	0.650000	0.86243	AGC	.	.	.	none		0.537	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		T	144874782	C	T	144874782	3	4	68	1	0	0	0	0	1	0	0	0	11650	797	28	2	2274	2	PDE4DIP	1	144874782	Missense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	34134568	144874782	104375839	8	4473											
CELF3	11189	hgsc.bcm.edu	37	chr1	151678722	151678722	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctctttgctgctgctgctgTtgctgctgctgctgctgctg	0	17	12	12	0	1	0	0	0	1	0	2	0	1	0	0	0	10	11	0	0	0	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:151678722T>C	ENST00000290583.4	-	10	1897	c.1104A>G	c.(1102-1104)caA>caG	p.Q368Q	CELF3_ENST00000290585.4_Silent_p.Q318Q|CELF3_ENST00000392706.3_Silent_p.Q163Q|RP11-98D18.1_ENST00000457548.1_RNA|CELF3_ENST00000470688.1_5'UTR	NM_001172648.1|NM_007185.4	NP_001166119.1|NP_009116.3	Q5SZQ8	CELF3_HUMAN	CUGBP, Elav-like family member 3	368	Gln-rich.				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	21						gctgctgctgttgctgctgct	0.657																																					p.Q368Q		Atlas-SNP	.											CELF3,caecum,carcinoma,0,1	CELF3	49	.	0			c.A1104G						PASS	.						19	20	20					1																	151678722		2200	4297	6497	SO:0001819	synonymous_variant	11189	exon10			CTGCTGTTGCTGC	U80759	CCDS1002.1, CCDS53367.1	1q21	2013-02-12	2010-02-19	2010-02-19	ENSG00000159409	ENSG00000159409		"Trinucleotide (CAG) repeat containing", "RNA binding motif (RRM) containing"	11967	protein-coding gene	gene with protein product	"expanded repeat domain, CAG/CTG 4", "CAG repeat domain", "CUG-BP and ETR-3 like factor 3"	612678	"trinucleotide repeat containing 4"	TNRC4		9225980	Standard	XM_005244859		Approved	CAGH4, BRUNOL1, ERDA4, MGC57297	uc001eys.2	Q5SZQ8	OTTHUMG00000013064	ENST00000290583.4:c.1104A>G	chr1.hg19:g.151678722T>C		23.0	0.0	.		34.0	4.0	.	NM_007185	B7ZKK6|O15414|Q499Y6|Q5SZQ7|Q6NVK0|Q8IZ98|Q9BZC2|Q9HB30	Silent	SNP	ENST00000290583.4	hg19	CCDS1002.1	.	.	.	.	.	.	.	.	.	.	.	4.938	0.174339	0.09391	.	.	ENSG00000159409	ENST00000420342	.	.	.	3.25	1.39	0.22231	.	.	.	.	.	T	0.36496	0.0969	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.19943	-1.0290	4	.	.	.	-0.0118	5.4728	0.16680	0.0:0.7409:0.0:0.2591	.	.	.	.	S	369	.	.	N	-	2	0	CELF3	149945346	0.076000	0.21285	1.000000	0.80357	0.644000	0.38419	-0.812000	0.04496	0.416000	0.25844	-0.389000	0.06534	AAC	.	.	.	none		0.657	CELF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036663.2	NM_007185		C	151678722	T	C	151678722	2	2	68	1	0	0	0	0	0	0	0	1	3219	1722	60	3		3	CELF3	1	151678722	Silent	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	6803940	151678722	97571899	9	4474											
RNPEP	6051	hgsc.bcm.edu	37	chr1	201958580	201958590	+	Frame_Shift_Del	DEL	TTCCAGATGTG	TTCCAGATGTG	-																															gaggtccaaataagttcttcTtccagatgtgtcagcccatc																										TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	TTCCAGATGTG	TTCCAGATGTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:201958580_201958590delTTCCAGATGTG	ENST00000295640.4	+	3	701_711	c.658_668delTTCCAGATGTG	c.(658-669)ttccagatgtgtfs	p.FQMC220fs	RNPEP_ENST00000367286.3_Frame_Shift_Del_p.FQMC220fs|RNPEP_ENST00000471105.1_Intron	NM_020216.3	NP_064601.3	Q9H4A4	AMPB_HUMAN	arginyl aminopeptidase (aminopeptidase B)	220					leukotriene biosynthetic process (GO:0019370)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|epoxide hydrolase activity (GO:0004301)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|large_intestine(4)|lung(6)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21				KIRC - Kidney renal clear cell carcinoma(1967;3.23e-08)|Colorectal(1306;0.005)		TAAGTTCTTCTTCCAGATGTGTCAGCCCATC	0.507																																					p.219_223del	GBM(19;39 479 7473 13131 19462)	Atlas-Indel,Pindel	.											.	RNPEP	39	.	0			c.657_667del						PASS	.																																			SO:0001589	frameshift_variant	6051	exon3			.	BC001064	CCDS1418.1	1q32	2008-02-05			ENSG00000176393	ENSG00000176393	3.4.11.6		10078	protein-coding gene	gene with protein product		602675				9533033, 10467730	Standard	NM_020216		Approved		uc001gxd.3	Q9H4A4	OTTHUMG00000035866	ENST00000295640.4:c.658_668delTTCCAGATGTG	chr1.hg19:g.201958580_201958590delTTCCAGATGTG	ENSP00000295640:p.Phe220fs	70.0	0.0	0		161.0	36.0	0.223602	NM_020216	Q9BVM9|Q9H1D4|Q9NPT7	Frame_Shift_Del	DEL	ENST00000295640.4	hg19	CCDS1418.1																																																																																			.	.	.	none		0.507	RNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087345.1	NM_020216		-	201958590	TTCCAGATGTG	-	201958580	7	5	68	1	0	1	0	1	0	0	0	0	13522	1609	56	0	668	0	RNPEP	1	201958580	Frame_Shift_Del	DEL	TTCCAGATGTG	TCGA-A4-A6HP-01A-11D-A31X-10	50279858	201958580	47292041	10	4475											
CR1L	1379	hgsc.bcm.edu	37	chr1	207881586	207881586	+	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	ggcaatactgcccattggagCatgaagccaccaatttgtca	12	9	9	11	0	1	1	1	1	0	0	1	2	1	2	3	2	4	2	3	2	4	3			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:207881586C>G	ENST00000508064.2	+	10	1452	c.1392C>G	c.(1390-1392)agC>agG	p.S464R	CR1L_ENST00000530905.1_Intron	NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	464	Sushi 7. {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						CCCATTGGAGCATGAAGCCAC	0.428																																					p.S464R		Atlas-SNP	.											.	CR1L	97	.	0			c.C1392G						PASS	.						268	258	261					1																	207881586		1901	4113	6014	SO:0001583	missense	1379	exon10			TTGGAGCATGAAG	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.1392C>G	chr1.hg19:g.207881586C>G	ENSP00000421736:p.Ser464Arg	147.0	0.0	.		267.0	72.0	.	NM_175710	Q32MC9|Q8NEU7	Missense_Mutation	SNP	ENST00000508064.2	hg19	CCDS44310.1	.	.	.	.	.	.	.	.	.	.	.	5.589	0.293432	0.10567	.	.	ENSG00000197721	ENST00000508064	T	0.68765	-0.35	1.67	-3.04	0.05412	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.61110	0.2321	M	0.80332	2.49	0.09310	N	1	B	0.15473	0.013	B	0.23018	0.043	T	0.55315	-0.8160	9	0.48119	T	0.1	.	2.9622	0.05896	0.0:0.3631:0.2498:0.3871	.	464	Q2VPA4	CR1L_HUMAN	R	464	ENSP00000421736:S464R	ENSP00000421736:S464R	S	+	3	2	CR1L	205948209	0.007000	0.16637	0.000000	0.03702	0.046000	0.14306	-0.702000	0.05069	-0.814000	0.04352	0.298000	0.19748	AGC	.	.	.	none		0.428	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735		G	207881586	C	G	207881586	3	3	68	1	0	0	0	0	1	0	0	0	3843	709	25	4	1430	4	CR1L	1	207881586	Missense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	5923006	207881586	41369035	11	4476											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228520936	228520936	+	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	acagagtccaccactgatgaGggccagctgccccaggtggt	9	6	13	13	0	0	3	0	2	0	1	1	3	1	3	5	3	2	1	5	3	0	0			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr1:228520936G>C	ENST00000422127.1	+	58	15812	c.15768G>C	c.(15766-15768)gaG>gaC	p.E5256D	OBSCN_ENST00000366707.4_Missense_Mutation_p.E2890D|OBSCN_ENST00000570156.2_Missense_Mutation_p.E6213D|OBSCN_ENST00000366709.4_Missense_Mutation_p.E2375D|OBSCN_ENST00000284548.11_Missense_Mutation_p.E5256D	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5256					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)				CCACTGATGAGGGCCAGCTGC	0.632																																					p.E6213D		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G18639C						PASS	.						14	16	15					1																	228520936		1999	4165	6164	SO:0001583	missense	84033	exon69			TGATGAGGGCCAG	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.15768G>C	chr1.hg19:g.228520936G>C	ENSP00000409493:p.Glu5256Asp	60.0	0.0	.		140.0	50.0	.	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	17.79	3.475444	0.63737	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.65364	0.27;-0.15;-0.1;0.41	5.29	-2.78	0.05859	.	0.204869	0.40818	N	0.001014	T	0.30039	0.0752	N	0.04880	-0.145	0.34900	D	0.746403	B;B	0.16166	0.009;0.016	B;B	0.19148	0.011;0.024	T	0.01684	-1.1296	10	0.44086	T	0.13	.	2.9874	0.05972	0.3769:0.104:0.4128:0.1063	.	5256;5256	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	D	5256;5256;2890;2375	ENSP00000284548:E5256D;ENSP00000409493:E5256D;ENSP00000355668:E2890D;ENSP00000355670:E2375D	ENSP00000284548:E5256D	E	+	3	2	OBSCN	226587559	0.939000	0.31865	0.987000	0.45799	0.212000	0.24457	-0.019000	0.12546	-0.128000	0.11641	-0.254000	0.11334	GAG	.	.	.	none		0.632	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		C	228520936	G	C	228520936	3	2	68	1	0	0	0	0	1	0	0	0	10819	991	35	4	15994	4	OBSCN	1	228520936	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	20639350	228520936	20729685	12	4477											
ANXA4	307	hgsc.bcm.edu	37	chr2	70039804	70039804	+	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	gggtgggagggatgaaggaaAttatctggacgatgctctcg	10	9	17	5	2	2	1	0	1	2	0	3	6	2	5	0	5	1	1	0	5	3	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr2:70039804A>T	ENST00000394295.4	+	8	745	c.497A>T	c.(496-498)aAt>aTt	p.N166I	ANXA4_ENST00000409920.1_Missense_Mutation_p.N144I|ANXA4_ENST00000536030.1_Missense_Mutation_p.N82I	NM_001153.3	NP_001144.1	P09525	ANXA4_HUMAN	annexin A4	164					epithelial cell differentiation (GO:0030855)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of interleukin-8 secretion (GO:2000483)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phospholipase inhibitor activity (GO:0004859)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)	11						GATGAAGGAAATTATCTGGAC	0.443																																					p.N166I		Atlas-SNP	.											.	ANXA4	34	.	0			c.A497T						PASS	.						113	101	105					2																	70039804		2203	4300	6503	SO:0001583	missense	307	exon8			AAGGAAATTATCT	M82809	CCDS1894.1	2p13.3	2008-02-05			ENSG00000196975	ENSG00000196975		"Annexins"	542	protein-coding gene	gene with protein product		106491		ANX4		1346776	Standard	NM_001153		Approved		uc002sfr.4	P09525	OTTHUMG00000129649	ENST00000394295.4:c.497A>T	chr2.hg19:g.70039804A>T	ENSP00000377833:p.Asn166Ile	19.0	0.0	.		78.0	28.0	.	NM_001153	B4DDF9|Q96F33|Q9BWK1	Missense_Mutation	SNP	ENST00000394295.4	hg19	CCDS1894.1	.	.	.	.	.	.	.	.	.	.	A	12.92	2.083724	0.36758	.	.	ENSG00000196975	ENST00000409920;ENST00000394295;ENST00000536030	T;T;T	0.12147	2.71;2.71;2.71	5.67	3.15	0.36227	.	0.343196	0.34268	N	0.004120	T	0.13670	0.0331	M	0.64567	1.98	0.33200	D	0.551962	B;B;B	0.33135	0.155;0.399;0.155	B;B;B	0.35039	0.105;0.194;0.105	T	0.10497	-1.0627	9	.	.	.	.	5.8848	0.18876	0.635:0.2795:0.0855:0.0	.	164;144;166	P09525;Q6P452;Q6LES2	ANXA4_HUMAN;.;.	I	144;166;82	ENSP00000386756:N144I;ENSP00000377833:N166I;ENSP00000441931:N82I	.	N	+	2	0	ANXA4	69893308	0.145000	0.22656	0.915000	0.36163	0.808000	0.45660	1.316000	0.33620	0.982000	0.38575	0.533000	0.62120	AAT	.	.	.	none		0.443	ANXA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251848.2	NM_001153		T	70039804	A	T	70039804	3	4	68	1	0	0	0	0	1	0	0	0	720	101	4	5	523	5	ANXA4	2	70039804	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10		70039804	173159569	13	4478											
MPHOSPH10	10199	hgsc.bcm.edu	37	chr2	71360588	71360588	+	Missense_Mutation	SNP	T	T	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	ggaggcctatttagaaaacaTagaaaaagaagaggaacgaa	21	5	11	4	1	0	4	0	0	0	4	0	7	0	6	1	3	2	0	1	3	10	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr2:71360588T>G	ENST00000244230.2	+	2	1002	c.650T>G	c.(649-651)aTa>aGa	p.I217R	MPHOSPH10_ENST00000498451.2_Missense_Mutation_p.I217R	NM_005791.2	NP_005782.1	O00566	MPP10_HUMAN	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	217					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						TTAGAAAACATAGAAAAAGAA	0.353																																					p.I217R		Atlas-SNP	.											.	MPHOSPH10	81	.	0			c.T650G						PASS	.						63	70	68					2																	71360588		2202	4300	6502	SO:0001583	missense	10199	exon2			AAAACATAGAAAA	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.650T>G	chr2.hg19:g.71360588T>G	ENSP00000244230:p.Ile217Arg	186.0	0.0	.		394.0	162.0	.	NM_005791	A0AVJ8	Missense_Mutation	SNP	ENST00000244230.2	hg19	CCDS1916.1	.	.	.	.	.	.	.	.	.	.	T	13.86	2.363316	0.41902	.	.	ENSG00000124383	ENST00000244230;ENST00000425650	T;T	0.09817	2.94;2.94	5.04	5.04	0.67666	.	0.585812	0.20103	N	0.099190	T	0.09555	0.0235	N	0.19112	0.55	0.22389	N	0.999144	P;P	0.49696	0.927;0.655	P;B	0.46419	0.516;0.305	T	0.27434	-1.0074	10	0.17369	T	0.5	.	13.0251	0.58810	0.0:0.0:0.0:1.0	.	217;217	B3KPV5;O00566	.;MPP10_HUMAN	R	217;77	ENSP00000244230:I217R;ENSP00000393034:I77R	ENSP00000244230:I217R	I	+	2	0	MPHOSPH10	71214096	0.146000	0.22672	0.072000	0.20136	0.923000	0.55619	1.710000	0.37920	2.040000	0.60383	0.397000	0.26171	ATA	.	.	.	none		0.353	MPHOSPH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251924.2	NM_005791		G	71360588	T	G	71360588	3	3	68	1	0	0	0	0	1	0	0	0	9732	1406	49	5	656	5	MPHOSPH10	2	71360588	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	1320784	71360588	171838785	14	4479											
IMMT	10989	hgsc.bcm.edu	37	chr2	86371557	86371557	+	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	tgacaaactttgctgctagcTccagatcaccatgctcaatg	11	11	7	12	0	2	2	2	1	0	1	3	2	3	2	2	0	5	4	2	0	3	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr2:86371557T>A	ENST00000410111.3	-	15	2498	c.2111A>T	c.(2110-2112)gAg>gTg	p.E704V	IMMT_ENST00000449247.2_Missense_Mutation_p.E693V|IMMT_ENST00000254636.5_Missense_Mutation_p.E605V|IMMT_ENST00000442664.2_Missense_Mutation_p.E703V|IMMT_ENST00000409051.2_Missense_Mutation_p.E657V	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	704					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						TGCTGCTAGCTCCAGATCACC	0.488																																					p.E704V		Atlas-SNP	.											.	IMMT	65	.	0			c.A2111T						PASS	.						102	97	98					2																	86371557		1969	4166	6135	SO:0001583	missense	10989	exon15			GCTAGCTCCAGAT	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.2111A>T	chr2.hg19:g.86371557T>A	ENSP00000387262:p.Glu704Val	58.0	0.0	.		146.0	43.0	.	NM_006839	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Missense_Mutation	SNP	ENST00000410111.3	hg19	CCDS46355.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.501330	0.85176	.	.	ENSG00000132305	ENST00000254636;ENST00000449247;ENST00000410111;ENST00000442664;ENST00000409051;ENST00000545283;ENST00000377310;ENST00000398211;ENST00000409715	T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.57431	0.2053	M	0.78049	2.395	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;1.0;1.0;1.0;1.0	T	0.59820	-0.7382	10	0.51188	T	0.08	-20.9731	15.8107	0.78561	0.0:0.0:0.0:1.0	.	657;692;693;672;704	B9A067;B4DKR1;Q16891-2;Q16891-3;Q16891	.;.;.;.;IMMT_HUMAN	V	605;693;704;703;657;693;672;318;605	ENSP00000254636:E605V;ENSP00000396899:E693V;ENSP00000387262:E704V;ENSP00000407788:E703V;ENSP00000387227:E657V	ENSP00000254636:E605V	E	-	2	0	IMMT	86225068	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.868000	0.87116	2.320000	0.78422	0.529000	0.55759	GAG	.	.	.	none		0.488	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839		A	86371557	T	A	86371557	3	1	68	1	0	0	0	0	1	0	0	0	7725	1551	54	5	169	5	IMMT	2	86371557	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	15010969	86371557	156827816	15	4480											
SMPD4	55627	hgsc.bcm.edu	37	chr2	130912744	130912744	+	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	caccatgagcgcgtgcttggGgctgaccaggtctgtgcgga	6	8	16	11	3	1	2	0	2	1	0	1	3	1	3	2	4	3	2	2	4	0	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr2:130912744G>A	ENST00000409031.1	-	15	2643	c.1495C>T	c.(1495-1497)Ccc>Tcc	p.P499S	SMPD4_ENST00000452225.2_Missense_Mutation_p.P240S|SMPD4_ENST00000426662.2_Missense_Mutation_p.P135S|SMPD4_ENST00000339679.7_Missense_Mutation_p.P357S|SMPD4_ENST00000443958.2_Missense_Mutation_p.P163S|SMPD4_ENST00000431183.2_Missense_Mutation_p.P397S|SMPD4_ENST00000453750.1_Missense_Mutation_p.P248S|SMPD4_ENST00000351288.6_Missense_Mutation_p.P470S|SMPD4_ENST00000473720.1_5'Flank	NM_017951.4	NP_060421.2	Q9NXE4	NSMA3_HUMAN	sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)	460					cellular response to tumor necrosis factor (GO:0071356)|ceramide biosynthetic process (GO:0046513)|glycerophospholipid catabolic process (GO:0046475)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)|sphingomyelin phosphodiesterase D activity (GO:0050290)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(17)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29	Colorectal(110;0.1)				Phosphatidylserine(DB00144)	GCGTGCTTGGGGCTGACCAGG	0.597																																					p.P499S		Atlas-SNP	.											.	SMPD4	67	.	0			c.C1495T						PASS	.						89	85	86					2																	130912744		2203	4300	6503	SO:0001583	missense	55627	exon15			GCTTGGGGCTGAC	AF052134	CCDS2156.2, CCDS42751.1, CCDS54398.1	2q21.1	2009-11-06			ENSG00000136699	ENSG00000136699			32949	protein-coding gene	gene with protein product		610457				16517606	Standard	NM_001171083		Approved	FLJ20297, FLJ20756, nSMase-3, KIAA1418, NSMASE3, NET13	uc002tqr.2	Q9NXE4	OTTHUMG00000131624	ENST00000409031.1:c.1495C>T	chr2.hg19:g.130912744G>A	ENSP00000386531:p.Pro499Ser	59.0	0.0	.		83.0	20.0	.	NM_017951	B4DM23|B4DQ31|B4DRB8|B4DWK7|B4E0L6|E7ESA2|E9PCE6|Q6FI76|Q6P1P7|Q6ZT43|Q9H0M2|Q9NW20|Q9NWL2|Q9P2C9	Missense_Mutation	SNP	ENST00000409031.1	hg19	CCDS42751.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	18.79|18.79	3.698485|3.698485	0.68386|0.68386	.|.	.|.	ENSG00000136699|ENSG00000136699	ENST00000430682|ENST00000351288;ENST00000409031;ENST00000431183;ENST00000453750;ENST00000443958;ENST00000339679;ENST00000452225;ENST00000426662;ENST00000457039;ENST00000449159;ENST00000451542	.|.	.|.	.|.	4.24|4.24	4.24|4.24	0.50183|0.50183	.|.	0.182604|0.182604	0.47852|0.47852	D|D	0.000216|0.000216	T|T	0.76449|0.76449	0.3989|0.3989	M|M	0.74881|0.74881	2.28|2.28	0.42852|0.42852	D|D	0.994089|0.994089	.|D;D;D;D;P;D;P;D;D	.|0.71674	.|0.997;0.967;0.988;0.988;0.793;0.975;0.939;0.99;0.998	.|D;P;P;P;B;P;P;P;D	.|0.80764	.|0.931;0.595;0.896;0.896;0.258;0.644;0.745;0.878;0.994	T|T	0.75895|0.75895	-0.3156|-0.3156	6|9	.|0.29301	.|T	.|0.29	.|.	14.1436|14.1436	0.65336|0.65336	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|135;240;397;357;248;431;460;499;506	.|B4E0L6;B4DQ31;E7ESA2;B4E0T5;B4DM23;Q9NXE4-2;Q9NXE4;B1PBA3;Q9NXE4-4	.|.;.;.;.;.;.;NSMA3_HUMAN;.;.	L|S	180|470;499;397;248;163;357;240;135;96;35;241	.|.	.|ENSP00000339721:P357S	P|P	-|-	2|1	0|0	SMPD4|SMPD4	130629214|130629214	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.637000|0.637000	0.38172|0.38172	5.392000|5.392000	0.66272|0.66272	1.886000|1.886000	0.54624|0.54624	0.305000|0.305000	0.20034|0.20034	CCC|CCC	.	.	.	none		0.597	SMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254516.3	NM_017751		A	130912744	G	A	130912744	3	1	68	1	0	0	0	0	1	0	0	0	14820	1232	43	2	1129	2	SMPD4	2	130912744	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	44541187	130912744	112286629	16	4481											
DNAJC10	54431	hgsc.bcm.edu	37	chr2	183594619	183594619	+	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	agatcaaaggagagtttagtGagttttgcaatgcagcatgt	13	12	12	4	0	1	3	1	1	0	2	1	4	1	3	0	1	3	5	0	1	3	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr2:183594619G>T	ENST00000264065.7	+	8	1093	c.678G>T	c.(676-678)gtG>gtT	p.V226V	DNAJC10_ENST00000537515.1_Silent_p.V226V	NM_018981.1	NP_061854.1	Q8IXB1	DJC10_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 10	226	Thioredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00691}.				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)			AGAGTTTAGTGAGTTTTGCAA	0.323																																					p.V226V	Pancreas(56;860 1183 25669 35822 48585)	Atlas-SNP	.											.	DNAJC10	76	.	0			c.G678T						PASS	.						148	159	155					2																	183594619		2203	4300	6503	SO:0001819	synonymous_variant	54431	exon8			TTTAGTGAGTTTT		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.678G>T	chr2.hg19:g.183594619G>T		147.0	0.0	.		346.0	111.0	.	NM_001271581	Q17RJ6|Q3B7W8|Q4ZG06|Q53QT7|Q6UWZ6|Q86T61|Q8NC82|Q8TD87|Q96K38|Q96K44|Q96K54|Q9NSY6	Silent	SNP	ENST00000264065.7	hg19	CCDS33345.1																																																																																			.	.	.	none		0.323	DNAJC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334418.2	NM_018981		T	183594619	G	T	183594619	2	4	68	1	0	0	0	0	0	0	0	1	4631	1277	45	4		4	DNAJC10	2	183594619	Silent	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	52681875	183594619	59604754	17	4482											
HSPE1	3336	hgsc.bcm.edu	37	chr2	198365881	198365881	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgaaactgtaaccaaaggAggcattatgcttccagaaaa	16	8	9	8	0	0	2	0	1	0	1	1	3	1	3	2	2	3	4	2	2	6	3			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr2:198365881A>G	ENST00000233893.5	+	2	530	c.87A>G	c.(85-87)ggA>ggG	p.G29G	HSPD1_ENST00000345042.2_5'Flank|HSPE1_ENST00000409729.1_Intron|HSPD1_ENST00000544407.1_5'Flank|HSPE1_ENST00000409468.1_Silent_p.G29G|HSPE1-MOB4_ENST00000604458.1_Silent_p.G29G|HSPE1_ENST00000465573.1_Intron|HSPD1_ENST00000388968.3_5'Flank	NM_002157.2	NP_002148.1	P61604	CH10_HUMAN	heat shock 10kDa protein 1	29					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|osteoblast differentiation (GO:0001649)|protein folding (GO:0006457)|response to unfolded protein (GO:0006986)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			lung(1)	1			Epithelial(96;0.225)			TAACCAAAGGAGGCATTATGC	0.438																																					p.G29G		Atlas-SNP	.											.	HSPE1	2	.	0			c.A87G						PASS	.						59	60	60					2																	198365881		2203	4297	6500	SO:0001819	synonymous_variant	3336	exon2			CAAAGGAGGCATT	AF109872	CCDS2320.1	2q33.1	2013-10-17	2013-10-17		ENSG00000115541	ENSG00000115541		"Heat Shock Proteins / Chaperonins"	5269	protein-coding gene	gene with protein product	"chaperonin 10"	600141	"heat shock 10kD protein 1 (chaperonin 10)"			7914093, 7698325	Standard	NM_002157		Approved	CPN10, GROES		P61604	OTTHUMG00000132749	ENST00000233893.5:c.87A>G	chr2.hg19:g.198365881A>G		187.0	0.0	.		367.0	141.0	.	NM_002157	O95421|Q04984|Q53X54|Q9UDH0	Silent	SNP	ENST00000233893.5	hg19	CCDS2320.1																																																																																			.	.	.	none		0.438	HSPE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256112.1	NM_002157		G	198365881	A	G	198365881	2	3	68	1	0	0	0	0	0	0	0	1	7436	291	11	3		3	HSPE1	2	198365881	Silent	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	14771262	198365881	44833492	18	4483											
NIF3L1	60491	hgsc.bcm.edu	37	chr2	201768315	201768315	+	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	aacgaggctttctttctgacCttcgagatatgctggattct	8	15	9	9	2	3	2	0	1	3	1	4	5	3	3	1	2	2	2	1	2	2	5			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr2:201768315C>A	ENST00000409020.1	+	7	1342	c.1048C>A	c.(1048-1050)Ctt>Att	p.L350I	NIF3L1_ENST00000359683.4_Missense_Mutation_p.L323I|NIF3L1_ENST00000409357.1_Missense_Mutation_p.L350I|NIF3L1_ENST00000416651.1_Missense_Mutation_p.L350I|NIF3L1_ENST00000409588.1_3'UTR			Q9GZT8	GTPC1_HUMAN	NIF3 NGG1 interacting factor 3-like 1 (S. cerevisiae)	350					7,8-dihydroneopterin 3'-triphosphate biosynthetic process (GO:0035998)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTP cyclohydrolase I activity (GO:0003934)|metal ion binding (GO:0046872)|transcription factor binding (GO:0008134)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(1)|urinary_tract(2)	13						TCTTTCTGACCTTCGAGATAT	0.423																																					p.L350I		Atlas-SNP	.											.	NIF3L1	51	.	0			c.C1048A						PASS	.						140	131	134					2																	201768315		1885	4113	5998	SO:0001583	missense	60491	exon7			TCTGACCTTCGAG	AB038949	CCDS42797.1, CCDS46485.1, CCDS46486.1	2q33	2011-11-10	2011-11-10		ENSG00000196290	ENSG00000196290			13390	protein-coding gene	gene with protein product		605778	"NIF3 (Ngg1 interacting factor 3, S.pombe homolog)-like 1", "NIF3 NGG1 interacting factor 3-like 1 (S. pombe)"	ALS2CR1		11124544, 11161814, 12522100	Standard	NM_001136039		Approved	CALS-7, MDS015	uc002uwm.2	Q9GZT8	OTTHUMG00000154588	ENST00000409020.1:c.1048C>A	chr2.hg19:g.201768315C>A	ENSP00000386394:p.Leu350Ile	106.0	0.0	.		241.0	85.0	.	NM_001136039	Q53TX4|Q6X735|Q9H2D2|Q9HC18	Missense_Mutation	SNP	ENST00000409020.1	hg19	CCDS46485.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.267008	0.80469	.	.	ENSG00000196290	ENST00000416651;ENST00000409020;ENST00000359683;ENST00000409357	T;T;T;T	0.52754	0.65;0.65;0.65;0.65	5.33	5.33	0.75918	.	0.052331	0.85682	D	0.000000	T	0.67618	0.2912	M	0.72624	2.21	0.46437	D	0.999043	D	0.69078	0.997	D	0.65573	0.936	T	0.65631	-0.6121	10	0.39692	T	0.17	-14.3245	19.3851	0.94553	0.0:1.0:0.0:0.0	.	350	Q9GZT8	NIF3L_HUMAN	I	350;350;323;350	ENSP00000400787:L350I;ENSP00000386394:L350I;ENSP00000352711:L323I;ENSP00000387315:L350I	ENSP00000352711:L323I	L	+	1	0	NIF3L1	201476560	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.771000	0.47670	2.656000	0.90262	0.557000	0.71058	CTT	.	.	.	none		0.423	NIF3L1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336201.1	NM_021824		A	201768315	C	A	201768315	3	1	68	1	0	0	0	0	1	0	0	0	10423	681	24	4	1070	4	NIF3L1	2	201768315	Missense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	3402434	201768315	41431058	19	4484											
KLHL18	23276	hgsc.bcm.edu	37	chr3	47374712	47374713	+	Missense_Mutation	DNP	GC	GC	TA																															aggggtccctacctgcctgaGctgctgtccaatatccgcct																										TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr3:47374712_47374713GC>TA	ENST00000232766.5	+	5	686_687	c.666_667GC>TA	c.(664-669)gaGCtg>gaTAtg	p.222_223EL>DM	KLHL18_ENST00000455924.2_Missense_Mutation_p.110_111EL>DM	NM_025010.4	NP_079286.2	O94889	KLH18_HUMAN	kelch-like family member 18	222	BACK.									endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	21		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00645)|Kidney(197;0.00741)		ACCTGCCTGAGCTGCTGTCCAA	0.569																																					p.E222D|p.L223M		Atlas-SNP	.											.	KLHL18	46	.	0			c.G666T|c.C667A						PASS	.																																			SO:0001583	missense	23276	exon5			GCCTGAGCTGCTG|CCTGAGCTGCTGT	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	Exception_encountered	chr3.hg19:g.47374712_47374713delinsTA	ENSP00000232766:p.E222_L223delinsDM	44.0|45.0	0.0	.		79.0|81.0	21.0|23.0	.	NM_025010	A8K612|Q7Z3E8|Q8N125	Missense_Mutation	SNP	ENST00000232766.5	hg19	CCDS33749.1																																																																																			.	.	.	none		0.569	KLHL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344493.1	NM_025010		TA	47374713	GC	TA	47374712	3	4	68	1	0	0	0	0	1	0	0	0	8380	962	34	4	684	4	KLHL18	3	47374712	Missense_Mutation	DNP	GC	TCGA-A4-A6HP-01A-11D-A31X-10		47374712	150647718	20	4485											
TMF1	7110	hgsc.bcm.edu	37	chr3	69072460	69072460	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgcagaatagtgttgtacctTtgatccaaatcctgaaaaat	14	13	7	7	0	0	3	0	2	0	1	2	3	2	3	3	0	2	3	3	0	6	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr3:69072460T>C	ENST00000398559.2	-	17	3366	c.3150A>G	c.(3148-3150)caA>caG	p.Q1050Q	CTD-2013N24.2_ENST00000599467.1_RNA|CTD-2013N24.2_ENST00000601735.1_RNA|CTD-2013N24.2_ENST00000597950.1_RNA|CTD-2013N24.2_ENST00000598783.1_RNA|CTD-2013N24.2_ENST00000482368.2_RNA|CTD-2013N24.2_ENST00000601511.1_RNA|TMF1_ENST00000489370.1_5'Flank|CTD-2013N24.2_ENST00000595925.1_RNA|TMF1_ENST00000543976.1_Silent_p.Q1053Q|CTD-2013N24.2_ENST00000597366.1_RNA|CTD-2013N24.2_ENST00000596732.1_RNA|CTD-2013N24.2_ENST00000596523.1_RNA			P82094	TMF1_HUMAN	TATA element modulatory factor 1	1050					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)		TGTTGTACCTTTGATCCAAAT	0.299																																					p.Q1050Q		Atlas-SNP	.											.	TMF1	77	.	0			c.A3150G						PASS	.						93	78	82					3																	69072460		1810	4067	5877	SO:0001819	synonymous_variant	7110	exon17			GTACCTTTGATCC		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.3150A>G	chr3.hg19:g.69072460T>C		80.0	0.0	.		196.0	61.0	.	NM_007114	B7ZLJ2|Q17R87|Q59GK0	Silent	SNP	ENST00000398559.2	hg19	CCDS43105.1																																																																																			.	.	.	none		0.299	TMF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352106.1	NM_007114		C	69072460	T	C	69072460	2	2	68	1	0	0	0	0	0	0	0	1	16240	1838	64	3		3	TMF1	3	69072460	Silent	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	21697748	69072460	128949970	21	4486											
NDUFB4	4710	hgsc.bcm.edu	37	chr3	120320001	120320001	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcctatgcaagaacaataaAtgtctatcctaatttcagac	15	11	6	9	0	2	2	1	0	1	2	3	2	3	2	2	1	2	1	2	1	8	5			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr3:120320001A>G	ENST00000184266.2	+	2	275	c.224A>G	c.(223-225)aAt>aGt	p.N75S	NDUFB4_ENST00000485064.1_Missense_Mutation_p.N75S|NDUFB4_ENST00000492739.1_Intron	NM_004547.5	NP_004538.2	O95168	NDUB4_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 4, 15kDa	75					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|large_intestine(1)|lung(3)	5				GBM - Glioblastoma multiforme(114;0.14)		AGAACAATAAATGTCTATCCT	0.363																																					p.N75S		Atlas-SNP	.											.	NDUFB4	21	.	0			c.A224G						PASS	.						132	142	139					3																	120320001		2203	4296	6499	SO:0001583	missense	4710	exon2			CAATAAATGTCTA	AF044957	CCDS2999.1, CCDS54630.1	3q13.33	2011-07-04	2002-08-29		ENSG00000065518	ENSG00000065518		"Mitochondrial respiratory chain complex / Complex I"	7699	protein-coding gene	gene with protein product	"complex I B15 subunit"	603840	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 4 (15kD, B15)"			9878551	Standard	NM_004547		Approved	B15	uc003edu.3	O95168	OTTHUMG00000159442	ENST00000184266.2:c.224A>G	chr3.hg19:g.120320001A>G	ENSP00000184266:p.Asn75Ser	60.0	0.0	.		179.0	71.0	.	NM_004547	B2RUY3|B9EJC7	Missense_Mutation	SNP	ENST00000184266.2	hg19	CCDS2999.1	.	.	.	.	.	.	.	.	.	.	A	11.43	1.635688	0.29068	.	.	ENSG00000065518	ENST00000184266;ENST00000485064	.	.	.	5.45	5.45	0.79879	.	0.052553	0.85682	D	0.000000	T	0.57562	0.2062	M	0.71581	2.175	0.80722	D	1	B;P	0.38129	0.103;0.619	B;B	0.38921	0.047;0.285	T	0.60929	-0.7165	9	0.45353	T	0.12	2.7254	11.8278	0.52278	1.0:0.0:0.0:0.0	.	75;75	O95168;B2RUY3	NDUB4_HUMAN;.	S	75	.	ENSP00000184266:N75S	N	+	2	0	NDUFB4	121802691	0.971000	0.33674	0.492000	0.27490	0.082000	0.17680	3.410000	0.52664	2.288000	0.76882	0.533000	0.62120	AAT	.	.	.	none		0.363	NDUFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355420.1	NM_004547		G	120320001	A	G	120320001	3	3	68	1	0	0	0	0	1	0	0	0	10290	101	4	3	230	3	NDUFB4	3	120320001	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	51247541	120320001	77702429	22	4487											
NMD3	51068	hgsc.bcm.edu	37	chr3	160964158	160964158	+	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	agtctgggtacagaagacatCtgaaatgaatacagataaac	18	8	9	6	0	2	5	0	2	2	3	2	5	2	5	0	1	3	1	0	1	7	3			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr3:160964158C>T	ENST00000460469.1	+	11	1507	c.1052C>T	c.(1051-1053)tCt>tTt	p.S351F	NMD3_ENST00000472947.1_Missense_Mutation_p.S351F|NMD3_ENST00000351193.2_Missense_Mutation_p.S351F			Q96D46	NMD3_HUMAN	NMD3 ribosome export adaptor	351					protein transport (GO:0015031)|ribosomal large subunit export from nucleus (GO:0000055)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|ribosomal large subunit binding (GO:0043023)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(10)|ovary(1)|skin(1)|urinary_tract(2)	25			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)			CAGAAGACATCTGAAATGAAT	0.353																																					p.S351F		Atlas-SNP	.											.	NMD3	49	.	0			c.C1052T						PASS	.						75	77	76					3																	160964158		2203	4300	6503	SO:0001583	missense	51068	exon12			AGACATCTGAAAT	BC013317	CCDS3194.1	3q26.1	2013-08-06	2013-08-06		ENSG00000169251	ENSG00000169251			24250	protein-coding gene	gene with protein product		611021	"NMD3 homolog (S. cerevisiae)"			10810093, 23782956, 12773398	Standard	NM_015938		Approved	CGI-07	uc003feb.1	Q96D46	OTTHUMG00000159063	ENST00000460469.1:c.1052C>T	chr3.hg19:g.160964158C>T	ENSP00000419004:p.Ser351Phe	30.0	0.0	.		79.0	33.0	.	NM_015938	D3DNM7|Q9Y2Z6	Missense_Mutation	SNP	ENST00000460469.1	hg19	CCDS3194.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.751897	0.89753	.	.	ENSG00000169251	ENST00000351193;ENST00000472947;ENST00000460469;ENST00000540137	T;T;T	0.24723	1.84;1.84;1.84	5.01	5.01	0.66863	.	0.055185	0.85682	D	0.000000	T	0.57388	0.2050	M	0.91354	3.2	0.80722	D	1	D;D;D	0.56968	0.972;0.978;0.976	P;P;P	0.59703	0.781;0.862;0.556	T	0.68213	-0.5468	10	0.87932	D	0	-30.719	18.1915	0.89808	0.0:1.0:0.0:0.0	.	351;351;351	B3KT11;C9JA08;Q96D46	.;.;NMD3_HUMAN	F	351;351;351;231	ENSP00000307525:S351F;ENSP00000417559:S351F;ENSP00000419004:S351F	ENSP00000307525:S351F	S	+	2	0	NMD3	162446852	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.963000	0.76055	2.709000	0.92574	0.655000	0.94253	TCT	.	.	.	none		0.353	NMD3-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353114.1	NM_015938		T	160964158	C	T	160964158	3	4	68	1	0	0	0	0	1	0	0	0	10495	913	32	2	1094	2	NMD3	3	160964158	Missense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	40644157	160964158	37058272	23	4488											
PARL	55486	hgsc.bcm.edu	37	chr3	183602604	183602604	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacgcctggccgcagccccAgcctctctgcgcccagcctc	4	5	9	23	3	1	0	0	0	1	0	3	0	1	0	8	1	4	1	8	1	0	0			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr3:183602604A>G	ENST00000317096.4	-	1	91	c.31T>C	c.(31-33)Tgg>Cgg	p.W11R	MIR4448_ENST00000584360.1_RNA|PARL_ENST00000311101.5_Missense_Mutation_p.W11R|PARL_ENST00000435888.1_Missense_Mutation_p.W11R|RP11-315J22.5_ENST00000445165.1_RNA	NM_018622.5	NP_061092.3	Q9H300	PARL_HUMAN	presenilin associated, rhomboid-like	11					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)			CCGCAGCCCCAGCCTCTCTGC	0.697											OREG0015941	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.W11R		Atlas-SNP	.											.	PARL	32	.	0			c.T31C						PASS	.						10	11	11					3																	183602604		2174	4246	6420	SO:0001583	missense	55486	exon1			AGCCCCAGCCTCT	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.31T>C	chr3.hg19:g.183602604A>G	ENSP00000325421:p.Trp11Arg	17.0	0.0	.	1985	37.0	13.0	.	NM_018622	Q96CQ4|Q9BTJ6|Q9P1E3	Missense_Mutation	SNP	ENST00000317096.4	hg19	CCDS3248.1	.	.	.	.	.	.	.	.	.	.	A	18.56	3.650621	0.67472	.	.	ENSG00000175193	ENST00000317096;ENST00000311101;ENST00000435888	T;T;T	0.58652	0.42;0.32;0.33	4.72	4.72	0.59763	.	0.104022	0.38217	N	0.001779	T	0.51770	0.1694	L	0.40543	1.245	0.37352	D	0.910834	P;P	0.40107	0.703;0.664	B;B	0.42692	0.395;0.296	T	0.62959	-0.6743	10	0.87932	D	0	-25.2787	10.7723	0.46330	1.0:0.0:0.0:0.0	.	11;11	Q9H300-2;Q9H300	.;PARL_HUMAN	R	11	ENSP00000325421:W11R;ENSP00000310676:W11R;ENSP00000402137:W11R	ENSP00000310676:W11R	W	-	1	0	PARL	185085298	0.998000	0.40836	1.000000	0.80357	0.719000	0.41307	3.655000	0.54460	2.118000	0.64928	0.533000	0.62120	TGG	.	.	.	none		0.697	PARL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346465.1	NM_018622		G	183602604	A	G	183602604	3	3	68	1	0	0	0	0	1	0	0	0	11458	188	7	3	1148	3	PARL	3	183602604	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	22638446	183602604	14419826	24	4489											
ZNF721	170960	hgsc.bcm.edu	37	chr4	436719	436719	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtttagtaagggttgtggAactagtaaacgctttaccac	12	13	10	6	1	0	0	0	0	0	0	0	1	0	1	1	2	3	5	1	2	7	8			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr4:436719A>G	ENST00000338977.5	-	2	1549	c.1501T>C	c.(1501-1503)Tcc>Ccc	p.S501P	ZNF721_ENST00000511833.2_Missense_Mutation_p.S513P|ZNF721_ENST00000506646.1_Intron|ZNF721_ENST00000507078.1_Intron|ABCA11P_ENST00000451020.2_RNA			Q8TF20	ZN721_HUMAN	zinc finger protein 721	501					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						AGGGTTGTGGAACTAGTAAAC	0.398																																					p.G513R		Atlas-SNP	.											.	ZNF721	205	.	0			c.G1537C						PASS	.						84	92	89					4																	436719		2098	4242	6340	SO:0001583	missense	170960	exon3			TTGTGGAACTAGT	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.1501T>C	chr4.hg19:g.436719A>G	ENSP00000340524:p.Ser501Pro	31.0	0.0	.		126.0	41.0	.	NM_133474	Q69YG7	Missense_Mutation	SNP	ENST00000338977.5	hg19		.	.	.	.	.	.	.	.	.	.	A	3.452	-0.111794	0.06881	.	.	ENSG00000182903	ENST00000338977;ENST00000511833	T;T	0.07908	3.15;3.15	0.419	-0.837	0.10766	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13927	0.0337	L	0.55743	1.74	0.09310	N	1	P;P;P	0.45348	0.856;0.669;0.777	P;P;P	0.55112	0.592;0.592;0.769	T	0.16217	-1.0410	9	0.42905	T	0.14	.	4.3636	0.11213	0.3506:0.0:0.6494:0.0	.	501;513;513	Q8TF20;D9N162;Q8TF20-2	ZN721_HUMAN;.;.	P	501;513	ENSP00000340524:S501P;ENSP00000428878:S513P	ENSP00000340524:S501P	S	-	1	0	ZNF721	426719	0.000000	0.05858	0.002000	0.10522	0.089000	0.18198	-1.976000	0.01497	-0.428000	0.07339	0.155000	0.16302	TCC	.	.	.	none		0.398	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474		G	436719	A	G	436719	3	3	68	1	0	0	0	0	1	0	0	0	18134	246	9	3	1238	3	ZNF721	4	436719	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10		436719	190717557	25	4490											
TMEM192	201931	hgsc.bcm.edu	37	chr4	166000935	166000935	+	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	cttttcaacaatttcttctaGgcttgaaatagttctgcaag	11	16	6	8	0	4	1	1	1	3	0	4	1	4	1	0	1	2	3	0	1	6	8			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr4:166000935G>T	ENST00000306480.6	-	6	836	c.691C>A	c.(691-693)Cta>Ata	p.L231I	TMEM192_ENST00000506087.1_Missense_Mutation_p.L227I	NM_001100389.1	NP_001093859.1	Q8IY95	TM192_HUMAN	transmembrane protein 192	231						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)	protein homodimerization activity (GO:0042803)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	7	all_hematologic(180;0.221)	Prostate(90;0.0959)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.0926)		ATTTCTTCTAGGCTTGAAATA	0.388																																					p.L231I		Atlas-SNP	.											.	TMEM192	21	.	0			c.C691A						PASS	.						94	88	90					4																	166000935		1868	4109	5977	SO:0001583	missense	201931	exon6			CTTCTAGGCTTGA	BC036301	CCDS43279.1	4q32.3	2008-04-22			ENSG00000170088	ENSG00000170088			26775	protein-coding gene	gene with protein product						12477932	Standard	NM_001100389		Approved	FLJ38482	uc003iqz.4	Q8IY95	OTTHUMG00000161254	ENST00000306480.6:c.691C>A	chr4.hg19:g.166000935G>T	ENSP00000305069:p.Leu231Ile	36.0	0.0	.		76.0	27.0	.	NM_001100389	Q7Z3A1|Q8N928	Missense_Mutation	SNP	ENST00000306480.6	hg19	CCDS43279.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.692853	0.30052	.	.	ENSG00000170088	ENST00000306480;ENST00000506087	.	.	.	5.97	3.32	0.38043	.	0.000000	0.85682	D	0.000000	T	0.59487	0.2197	M	0.73962	2.25	0.41322	D	0.987189	B	0.27997	0.197	B	0.30716	0.119	T	0.60627	-0.7226	9	0.66056	D	0.02	-38.5919	6.9529	0.24556	0.3323:0.0:0.6677:0.0	.	231	Q8IY95	TM192_HUMAN	I	231;227	.	ENSP00000305069:L231I	L	-	1	2	TMEM192	166220385	1.000000	0.71417	0.172000	0.22920	0.509000	0.34042	2.379000	0.44318	0.868000	0.35678	0.591000	0.81541	CTA	.	.	.	none		0.388	TMEM192-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364310.3	NM_152681		T	166000935	G	T	166000935	3	4	68	1	0	0	0	0	1	0	0	0	16127	991	35	4	128	4	TMEM192	4	166000935	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	165564216	166000935	25153341	26	4491											
PPARGC1B	133522	hgsc.bcm.edu	37	chr5	149213062	149213062	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggagagctctgtgtgccccGtgcggcgttctcggagactg	4	10	16	11	4	2	2	0	0	2	2	3	4	2	2	2	3	3	2	2	3	0	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr5:149213062G>A	ENST00000309241.5	+	5	1458	c.1426G>A	c.(1426-1428)Gtg>Atg	p.V476M	PPARGC1B_ENST00000360453.4_Missense_Mutation_p.V437M|PPARGC1B_ENST00000403750.1_Missense_Mutation_p.V412M|PPARGC1B_ENST00000394320.3_Missense_Mutation_p.V476M	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	476					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)			TGTGTGCCCCGTGCGGCGTTC	0.637																																					p.V476M		Atlas-SNP	.											PPARGC1B,colon,carcinoma,0,1	PPARGC1B	74	.	0			c.G1426A						PASS	.						42	44	43					5																	149213062		2182	4277	6459	SO:0001583	missense	133522	exon5			TGCCCCGTGCGGC	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.1426G>A	chr5.hg19:g.149213062G>A	ENSP00000312649:p.Val476Met	52.0	0.0	.		82.0	27.0	.	NM_133263	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Missense_Mutation	SNP	ENST00000309241.5	hg19	CCDS4298.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.80|18.80	3.700810|3.700810	0.68501|0.68501	.|.	.|.	ENSG00000155846|ENSG00000155846	ENST00000434684|ENST00000360453;ENST00000394320;ENST00000309241;ENST00000403750	.|T;T;T;T	.|0.14266	.|2.53;2.52;2.54;2.52	5.38|5.38	5.38|5.38	0.77491|0.77491	.|.	.|0.000000	.|0.64402	.|D	.|0.000002	T|T	0.29749|0.29749	0.0743|0.0743	L|L	0.36672|0.36672	1.1|1.1	0.43207|0.43207	D|D	0.995068|0.995068	.|D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D	.|0.91635	.|0.999;0.999;0.999;0.999;0.999	T|T	0.01294|0.01294	-1.1393|-1.1393	5|10	.|0.66056	.|D	.|0.02	-15.2485|-15.2485	17.3201|17.3201	0.87233|0.87233	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|455;455;437;476;476	.|Q86YN6-2;Q86YN6-4;Q86YN6-5;Q86YN6;Q86YN6-3	.|.;.;.;PRGC2_HUMAN;.	H|M	162|437;476;476;412	.|ENSP00000353638:V437M;ENSP00000377855:V476M;ENSP00000312649:V476M;ENSP00000384403:V412M	.|ENSP00000312649:V476M	R|V	+|+	2|1	0|0	PPARGC1B|PPARGC1B	149193255|149193255	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.758000|0.758000	0.43043|0.43043	4.727000|4.727000	0.61993|0.61993	2.521000|2.521000	0.84997|0.84997	0.462000|0.462000	0.41574|0.41574	CGT|GTG	.	.	.	none		0.637	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263		A	149213062	G	A	149213062	3	1	68	1	0	0	0	0	1	0	0	0	12308	1145	40	1	1451	1	PPARGC1B	5	149213062	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10		149213062	31702198	27	4492											
GALNT10	55568	hgsc.bcm.edu	37	chr5	153755929	153755929	+	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	gggaagggctgataaggaccCgaatgctgggggcctcagtg	9	6	18	8	1	1	1	1	1	0	0	1	4	1	3	2	5	1	2	2	5	3	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr5:153755929C>T	ENST00000297107.6	+	5	798	c.661C>T	c.(661-663)Cga>Tga	p.R221*	GALNT10_ENST00000519544.1_3'UTR|GALNT10_ENST00000425427.2_Nonsense_Mutation_p.R221*|GALNT10_ENST00000377661.2_Intron|SAP30L-AS1_ENST00000519727.1_RNA	NM_198321.3	NP_938080.1	Q86SR1	GLT10_HUMAN	polypeptide N-acetylgalactosaminyltransferase 10	221	Catalytic subdomain A.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			cervix(1)|endometrium(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)			GATAAGGACCCGAATGCTGGG	0.522																																					p.R221X		Atlas-SNP	.											.	GALNT10	70	.	0			c.C661T						PASS	.						90	89	90					5																	153755929		2203	4300	6503	SO:0001587	stop_gained	55568	exon5			AGGACCCGAATGC	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.661C>T	chr5.hg19:g.153755929C>T	ENSP00000297107:p.Arg221*	88.0	0.0	.		159.0	61.0	.	NM_198321	B3KXC9|Q6IN56|Q86VP8|Q8IXJ2|Q8TEJ2|Q96IV2|Q9H8E1|Q9Y4M4	Nonsense_Mutation	SNP	ENST00000297107.6	hg19	CCDS4325.1	.	.	.	.	.	.	.	.	.	.	C	38	7.017290	0.98006	.	.	ENSG00000164574	ENST00000425427;ENST00000297107	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.6439	0.99570	0.0:1.0:0.0:0.0	.	.	.	.	X	221	.	ENSP00000297107:R221X	R	+	1	2	GALNT10	153736122	0.997000	0.39634	1.000000	0.80357	0.936000	0.57629	3.644000	0.54381	2.884000	0.98904	0.655000	0.94253	CGA	.	.	.	none		0.522	GALNT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252453.1	NM_198321		T	153755929	C	T	153755929	4	4	68	1	0	0	0	0	0	1	0	0	6215	644	23	1	679	1	GALNT10	5	153755929	Nonsense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	4542867	153755929	27159331	28	4493											
CPEB4	80315	hgsc.bcm.edu	37	chr5	173317154	173317154	+	Missense_Mutation	SNP	T	T	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	taaggatcgaatctccagtgTtgacagggtttgattatcaa	12	13	10	6	1	2	2	1	2	1	0	4	4	2	3	1	2	0	2	1	2	4	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr5:173317154T>G	ENST00000265085.5	+	1	1872	c.418T>G	c.(418-420)Ttg>Gtg	p.L140V	CPEB4_ENST00000519835.1_Missense_Mutation_p.L140V|CPEB4_ENST00000517880.1_5'Flank|CPEB4_ENST00000520867.1_Missense_Mutation_p.L140V|CPEB4_ENST00000522336.1_5'Flank|CPEB4_ENST00000334035.5_Missense_Mutation_p.L140V	NM_030627.2	NP_085130.2	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding protein 4	140					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)			ATCTCCAGTGTTGACAGGGTT	0.448																																					p.L140V		Atlas-SNP	.											.	CPEB4	54	.	0			c.T418G						PASS	.						103	105	105					5																	173317154		2203	4300	6503	SO:0001583	missense	80315	exon1			CCAGTGTTGACAG	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.418T>G	chr5.hg19:g.173317154T>G	ENSP00000265085:p.Leu140Val	51.0	0.0	.		111.0	8.0	.	NM_030627	B7ZLQ7|Q7Z310|Q8N405|Q9C0J0	Missense_Mutation	SNP	ENST00000265085.5	hg19	CCDS4390.1	.	.	.	.	.	.	.	.	.	.	T	14.40	2.525591	0.44969	.	.	ENSG00000113742	ENST00000265085;ENST00000520867;ENST00000334035;ENST00000519835	T;T;T;T	0.55234	0.53;0.53;0.53;0.53	5.96	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.59838	0.2223	L	0.34521	1.04	0.80722	D	1	D;D;D;D	0.71674	0.997;0.998;0.997;0.997	D;D;D;D	0.87578	0.996;0.998;0.996;0.996	T	0.61686	-0.7012	10	0.72032	D	0.01	-9.5609	9.6678	0.39994	0.0:0.1383:0.0:0.8617	.	140;140;140;140	B7ZLQ8;Q17RY0-2;E5RJM0;Q17RY0	.;.;.;CPEB4_HUMAN	V	140	ENSP00000265085:L140V;ENSP00000429092:L140V;ENSP00000334533:L140V;ENSP00000429048:L140V	ENSP00000265085:L140V	L	+	1	2	CPEB4	173249760	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	1.961000	0.40432	1.089000	0.41292	0.533000	0.62120	TTG	.	.	.	none		0.448	CPEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252964.2	NM_030627		G	173317154	T	G	173317154	3	3	68	1	0	0	0	0	1	0	0	0	3805	1722	60	5	420	5	CPEB4	5	173317154	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	19561225	173317154	7598106	29	4494											
CDHR2	54825	hgsc.bcm.edu	37	chr5	176018324	176018324	+	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	taacatgtacaacactgagcGgtgagcaggggtcaaagggt	13	7	14	7	1	1	2	1	2	0	0	1	2	1	2	0	4	5	2	0	4	4	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr5:176018324G>A	ENST00000510636.1	+	29	3927	c.3653G>A	c.(3652-3654)cGa>cAa	p.R1218Q	CDHR2_ENST00000506348.1_Splice_Site_p.R1218Q|CDHR2_ENST00000261944.5_Splice_Site_p.R1218Q	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	1218					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						AACACTGAGCGGTGAGCAGGG	0.597																																					p.R1218Q		Atlas-SNP	.											.	CDHR2	152	.	0			c.G3653A						PASS	.						66	64	65					5																	176018324		2203	4300	6503	SO:0001630	splice_region_variant	54825	exon29			CTGAGCGGTGAGC	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.3653+1G>A	chr5.hg19:g.176018324G>A		52.0	0.0	.		122.0	44.0	.	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	hg19	CCDS34297.1	.	.	.	.	.	.	.	.	.	.	g	12.10	1.836140	0.32421	.	.	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.56103	0.48;0.48;0.48	4.24	2.24	0.28232	.	.	.	.	.	T	0.45236	0.1332	M	0.70595	2.14	0.32458	N	0.544539	P	0.52061	0.95	B	0.38428	0.273	T	0.56378	-0.7989	9	0.25751	T	0.34	-7.212	9.1617	0.37028	0.203:0.0:0.797:0.0	.	1218	Q9BYE9	CDHR2_HUMAN	Q	1218	ENSP00000424565:R1218Q;ENSP00000261944:R1218Q;ENSP00000421078:R1218Q	ENSP00000261944:R1218Q	R	+	2	0	CDHR2	175950930	1.000000	0.71417	0.933000	0.37362	0.367000	0.29736	3.600000	0.54052	1.036000	0.39998	0.459000	0.35465	CGA	.	.	.	none		0.597	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675	Missense_Mutation	A	176018324	G	A	176018324	5	1	68	1	0	0	0	0	0	0	1	0	3121	1130	39	1	3763	1	CDHR2	5	176018324	Splice_Site	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	2701170	176018324	4896936	30	4495											
DSP	1832	hgsc.bcm.edu	37	chr6	7583589	7583589	+	Missense_Mutation	SNP	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	ctaaggaaaaatactctttgGtagaggccaagagaaagaaa	19	7	10	5	0	1	3	0	0	1	3	1	5	1	4	1	3	1	1	1	3	8	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr6:7583589G>A	ENST00000379802.3	+	24	6435	c.6094G>A	c.(6094-6096)Gta>Ata	p.V2032I	DSP_ENST00000418664.2_Missense_Mutation_p.V1433I	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2032	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)		ATACTCTTTGGTAGAGGCCAA	0.478																																					p.V2032I		Atlas-SNP	.											.	DSP	306	.	0			c.G6094A						PASS	.						49	54	52					6																	7583589		2203	4300	6503	SO:0001583	missense	1832	exon24			TCTTTGGTAGAGG	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.6094G>A	chr6.hg19:g.7583589G>A	ENSP00000369129:p.Val2032Ile	49.0	0.0	.		114.0	32.0	.	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	hg19	CCDS4501.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.877522	0.51801	.	.	ENSG00000096696	ENST00000379802;ENST00000418664	T;T	0.67523	-0.27;-0.27	4.98	4.98	0.66077	.	0.000000	0.52532	D	0.000074	T	0.44456	0.1294	L	0.36672	1.1	0.25902	N	0.983344	P;P	0.45078	0.85;0.779	B;B	0.41236	0.278;0.351	T	0.45131	-0.9282	10	0.22109	T	0.4	.	18.6091	0.91277	0.0:0.0:1.0:0.0	.	1480;2032	Q4LE79;P15924	.;DESP_HUMAN	I	2032;1433	ENSP00000369129:V2032I;ENSP00000396591:V1433I	ENSP00000369129:V2032I	V	+	1	0	DSP	7528588	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	4.384000	0.59607	2.459000	0.83118	0.655000	0.94253	GTA	.	.	.	none		0.478	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		A	7583589	G	A	7583589	3	1	68	1	0	0	0	0	1	0	0	0	4783	1261	44	2	6188	2	DSP	6	7583589	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10		7583589	163531478	31	4496											
TMEM170B	100113407	hgsc.bcm.edu	37	chr6	11575733	11575733	+	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	tttggaagcgctggtatgggGcgttggacagactgtactga	8	11	16	6	2	0	2	0	1	0	1	0	4	0	4	0	5	2	4	0	5	3	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr6:11575733G>T	ENST00000379426.1	+	3	338	c.338G>T	c.(337-339)gGc>gTc	p.G113V	TMEM170B_ENST00000543875.1_Missense_Mutation_p.G113V	NM_001100829.1	NP_001094299.1	Q5T4T1	T170B_HUMAN	transmembrane protein 170B	113						integral component of membrane (GO:0016021)				large_intestine(3)|lung(5)	8						CTGGTATGGGGCGTTGGACAG	0.473																																					p.G113V		Atlas-SNP	.											.	TMEM170B	9	.	0			c.G338T						PASS	.						203	196	198					6																	11575733		1966	4141	6107	SO:0001583	missense	100113407	exon3			TATGGGGCGTTGG		CCDS43425.1	6p24.1	2008-08-08			ENSG00000205269	ENSG00000205269			34244	protein-coding gene	gene with protein product							Standard	NM_001100829		Approved		uc010jpa.4	Q5T4T1	OTTHUMG00000014259	ENST00000379426.1:c.338G>T	chr6.hg19:g.11575733G>T	ENSP00000368737:p.Gly113Val	75.0	0.0	.		134.0	36.0	.	NM_001100829		Missense_Mutation	SNP	ENST00000379426.1	hg19	CCDS43425.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.373246	0.82573	.	.	ENSG00000205269	ENST00000543875;ENST00000379426	.	.	.	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.72859	0.3513	L	0.59436	1.845	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	T	0.75645	-0.3246	9	0.87932	D	0	-20.3795	19.0673	0.93116	0.0:0.0:1.0:0.0	.	113	Q5T4T1	T170B_HUMAN	V	113	.	ENSP00000368737:G113V	G	+	2	0	TMEM170B	11683719	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	9.466000	0.97665	2.502000	0.84385	0.579000	0.79373	GGC	.	.	.	none		0.473	TMEM170B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000039862.1	NM_001100829		T	11575733	G	T	11575733	3	4	68	1	0	0	0	0	1	0	0	0	16099	1203	42	4	348	4	TMEM170B	6	11575733	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	3992144	11575733	159539334	32	4497											
RIMS1	22999	hgsc.bcm.edu	37	chr6	73017054	73017055	+	Frame_Shift_Del	DEL	AT	AT	-																															tggttctagtcaagaacttgAtcgcgagcaatattccaagg																										TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr6:73017054_73017055delAT	ENST00000521978.1	+	27	3944_3945	c.3944_3945delAT	c.(3943-3945)gatfs	p.D1315fs	RIMS1_ENST00000517960.1_Frame_Shift_Del_p.D1107fs|RIMS1_ENST00000522291.1_Intron|RIMS1_ENST00000520567.1_Intron|RIMS1_ENST00000264839.7_Frame_Shift_Del_p.D1164fs|RIMS1_ENST00000491071.2_Frame_Shift_Del_p.D1138fs|RIMS1_ENST00000523963.1_Intron|RIMS1_ENST00000518273.1_Intron|RIMS1_ENST00000348717.5_Frame_Shift_Del_p.D1107fs|RIMS1_ENST00000401910.3_Frame_Shift_Del_p.D635fs|RIMS1_ENST00000517827.1_Intron|RIMS1_ENST00000538414.1_Frame_Shift_Del_p.D121fs|RIMS1_ENST00000425662.2_Intron	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	1315					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)				CAAGAACTTGATCGCGAGCAAT	0.401																																					p.1315_1315del		Atlas-Indel,Pindel	.											.	RIMS1	278	.	0			c.3943_3944del						PASS	.																																			SO:0001589	frameshift_variant	22999	exon27			.	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.3944_3945delAT	chr6.hg19:g.73017054_73017055delAT	ENSP00000428417:p.Asp1315fs	64.0	0.0	0		118.0	34.0	0.288136	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	Frame_Shift_Del	DEL	ENST00000521978.1	hg19	CCDS47449.1																																																																																			.	.	.	none		0.401	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			-	73017055	AT	-	73017054	7	5	68	1	0	1	0	1	0	0	0	0	13380	333	12	0	4213	0	RIMS1	6	73017054	Frame_Shift_Del	DEL	AT	TCGA-A4-A6HP-01A-11D-A31X-10	61441321	73017054	98098013	33	4498											
ECT2L	345930	hgsc.bcm.edu	37	chr6	139135653	139135653	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcaggaaagagtggctcttaTaagtcattggtttgacctct	10	14	10	7	0	4	2	2	1	2	1	4	3	4	3	1	3	0	2	1	3	3	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr6:139135653T>C	ENST00000423192.1	+	3	253	c.92T>C	c.(91-93)aTa>aCa	p.I31T	ECT2L_ENST00000367682.2_Missense_Mutation_p.I31T|ECT2L_ENST00000541398.1_5'Flank			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	31							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						GTGGCTCTTATAAGTCATTGG	0.368			"N, Splice, Mis"		ETP ALL																																p.I31T		Atlas-SNP	.		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	.	ECT2L	75	.	0			c.T92C						PASS	.						77	75	76					6																	139135653		1836	4092	5928	SO:0001583	missense	345930	exon3			CTCTTATAAGTCA		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.92T>C	chr6.hg19:g.139135653T>C	ENSP00000387388:p.Ile31Thr	48.0	0.0	.		112.0	45.0	.	NM_001195037	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Missense_Mutation	SNP	ENST00000423192.1	hg19	CCDS43508.1	.	.	.	.	.	.	.	.	.	.	T	15.36	2.809410	0.50421	.	.	ENSG00000203734	ENST00000423192;ENST00000401414;ENST00000367682	T;T;T	0.62498	0.02;0.65;0.02	5.43	5.43	0.79202	.	.	.	.	.	T	0.44477	0.1295	L	0.33485	1.01	0.80722	D	1	D	0.54047	0.964	P	0.45310	0.476	T	0.55347	-0.8155	9	0.87932	D	0	.	13.0191	0.58775	0.0:0.0:0.0:1.0	.	31	Q008S8	ECT2L_HUMAN	T	31	ENSP00000387388:I31T;ENSP00000385187:I31T;ENSP00000356655:I31T	ENSP00000356655:I31T	I	+	2	0	ECT2L	139177346	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.876000	0.63079	2.066000	0.61787	0.533000	0.62120	ATA	.	.	.	none		0.368	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706		C	139135653	T	C	139135653	3	2	68	1	0	0	0	0	1	0	0	0	4904	1406	49	3	98	3	ECT2L	6	139135653	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	66118599	139135653	31979414	34	4499											
CITED2	10370	hgsc.bcm.edu	37	chr6	139694869	139694869	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagtccccggccccatcgcAtgcctgatgccgctcgtggc	5	7	11	18	4	0	1	0	1	0	0	3	1	1	1	6	2	2	2	6	2	0	0			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr6:139694869A>G	ENST00000367651.2	-	2	428	c.213T>C	c.(211-213)caT>caC	p.H71H	CITED2_ENST00000537332.1_Silent_p.H71H|CITED2_ENST00000536159.1_Silent_p.H71H	NM_006079.4	NP_006070.2	Q99967	CITE2_HUMAN	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	71					adrenal cortex formation (GO:0035802)|bone morphogenesis (GO:0060349)|cardiac neural crest cell development involved in heart development (GO:0061308)|cell aging (GO:0007569)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|cranial nerve morphogenesis (GO:0021602)|decidualization (GO:0046697)|determination of left/right symmetry (GO:0007368)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|endocardial cushion development (GO:0003197)|erythrocyte development (GO:0048821)|granulocyte differentiation (GO:0030851)|heart development (GO:0007507)|heart looping (GO:0001947)|hematopoietic progenitor cell differentiation (GO:0002244)|left/right axis specification (GO:0070986)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell migration (GO:0030336)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900164)|outflow tract morphogenesis (GO:0003151)|peripheral nervous system development (GO:0007422)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of gene expression (GO:0010628)|positive regulation of male gonad development (GO:2000020)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|pulmonary artery morphogenesis (GO:0061156)|regulation of organ formation (GO:0003156)|regulation of RNA biosynthetic process (GO:2001141)|response to estrogen (GO:0043627)|response to fluid shear stress (GO:0034405)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|sex determination (GO:0007530)|skeletal muscle cell differentiation (GO:0035914)|spleen development (GO:0048536)|thymus development (GO:0048538)|transforming growth factor beta receptor signaling pathway (GO:0007179)|trophectodermal cell differentiation (GO:0001829)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|LBD domain binding (GO:0050693)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			large_intestine(1)|lung(4)	5	Breast(32;0.226)			GBM - Glioblastoma multiforme(68;0.000171)|OV - Ovarian serous cystadenocarcinoma(155;0.00134)		GCCCCATCGCATGCCTGATGC	0.672																																					p.H76H	NSCLC(98;1219 1550 33720 43229 49330)	Atlas-SNP	.											.	CITED2	16	.	0			c.T228C						PASS	.						34	34	34					6																	139694869		2203	4299	6502	SO:0001819	synonymous_variant	10370	exon2			CATCGCATGCCTG	U65093	CCDS5195.1, CCDS75530.1	6q23.3	2008-08-29			ENSG00000164442	ENSG00000164442			1987	protein-coding gene	gene with protein product		602937				8901575, 10552932	Standard	NM_006079		Approved	MRG1	uc021zfz.2	Q99967	OTTHUMG00000015691	ENST00000367651.2:c.213T>C	chr6.hg19:g.139694869A>G		20.0	0.0	.		33.0	11.0	.	NM_001168389	O95426|Q5VTF4	Silent	SNP	ENST00000367651.2	hg19	CCDS5195.1																																																																																			.	.	.	none		0.672	CITED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042463.1			G	139694869	A	G	139694869	2	3	68	1	0	0	0	0	0	0	0	1	3442	214	8	3		3	CITED2	6	139694869	Silent	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	559216	139694869	31420198	35	4500											
RADIL	55698	hgsc.bcm.edu	37	chr7	4841357	4841357	+	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	agcgcttttccacaggggccGccggactctggccagtcggg	5	7	15	14	4	1	0	0	0	1	0	3	1	2	1	4	5	1	1	4	5	0	2	rs369296363	byFrequency	TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr7:4841357G>A	ENST00000399583.3	-	12	2956	c.2769C>T	c.(2767-2769)ggC>ggT	p.G923G	RADIL_ENST00000536091.1_3'UTR|RADIL_ENST00000538469.1_Silent_p.G683G	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	923	Pro-rich.				multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		CACAGGGGCCGCCGGACTCTG	0.711													G|||	2	0.000399361	0.0015	0	5008	,	,		14081	0		0	False		,,,				2504	0				p.G923G		Atlas-SNP	.											RADIL,right_upper_lobe,carcinoma,0,1	RADIL	110	.	0			c.C2769T						PASS	.	G		2,3724		0,2,1861	8	10	10		2769	-3.9	0	7		10	0,8120		0,0,4060	no	coding-synonymous	RADIL	NM_018059.4		0,2,5921	AA,AG,GG		0.0,0.0537,0.0169		923/1076	4841357	2,11844	1863	4060	5923	SO:0001819	synonymous_variant	55698	exon12			GGGGCCGCCGGAC	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.2769C>T	chr7.hg19:g.4841357G>A		111.0	0.0	.		300.0	118.0	.	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Silent	SNP	ENST00000399583.3	hg19	CCDS43544.1																																																																																			.	.	.	weak		0.711	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059		A	4841357	G	A	4841357	2	1	68	1	0	0	0	0	0	0	0	1	13010	1074	38	1		1	RADIL	7	4841357	Silent	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10		4841357	154297306	36	4501											
RINT1	60561	hgsc.bcm.edu	37	chr7	105189036	105189036	+	Frame_Shift_Del	DEL	A	A	-																															tgagccaaagcaactcccagAaaaatactctcttcctgcct																										TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr7:105189036delA	ENST00000257700.2	+	7	1106	c.875delA	c.(874-876)gaafs	p.E292fs		NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	292	RINT1/TIP20. {ECO:0000255|PROSITE- ProRule:PRU00717}.				G2 DNA damage checkpoint (GO:0031572)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						CAACTCCCAGAAAAATACTCT	0.428																																					p.E292fs		Atlas-Indel,Pindel	.											.	RINT1	65	.	0			c.874delG						PASS	.						190	164	173					7																	105189036		2203	4300	6503	SO:0001589	frameshift_variant	60561	exon7			.	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.875delA	chr7.hg19:g.105189036delA	ENSP00000257700:p.Glu292fs	53.0	0.0	0		197.0	62.0	0.314721	NM_021930	Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Frame_Shift_Del	DEL	ENST00000257700.2	hg19	CCDS34726.1																																																																																			.	.	.	none		0.428	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	NM_021930		-	105189036	A	-	105189036	7	5	68	1	0	1	0	1	0	0	0	0	13389	246	9	0	901	0	RINT1	7	105189036	Frame_Shift_Del	DEL	A	TCGA-A4-A6HP-01A-11D-A31X-10	100347679	105189036	53949627	37	4502											
SGK196	84197	hgsc.bcm.edu	37	chr8	42977953	42977953	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgcccaggacgttctggAgacctaccagaaggtcttgg	9	8	12	12	1	2	2	0	0	2	2	2	4	2	3	3	4	2	1	3	4	2	3			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr8:42977953A>G	ENST00000331373.5	+	5	1241	c.986A>G	c.(985-987)gAg>gGg	p.E329G		NM_001277971.1|NM_032237.3	NP_001264900.1|NP_115613.1	Q9H5K3	SG196_HUMAN	protein-O-mannose kinase	329	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)										GACGTTCTGGAGACCTACCAG	0.478																																					p.E329G		Atlas-SNP	.											.	.	.	.	0			c.A986G						PASS	.						87	94	91					8																	42977953		2203	4300	6503	SO:0001583	missense	0	exon5			TTCTGGAGACCTA		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.986A>G	chr8.hg19:g.42977953A>G	ENSP00000331258:p.Glu329Gly	33.0	0.0	.		64.0	23.0	.	NM_032237		Missense_Mutation	SNP	ENST00000331373.5	hg19	CCDS6141.1	.	.	.	.	.	.	.	.	.	.	A	10.75	1.439110	0.25900	.	.	ENSG00000185900	ENST00000331373	T	0.23348	1.91	5.45	5.45	0.79879	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.258956	0.44483	D	0.000449	T	0.19446	0.0467	L	0.29908	0.895	0.26493	N	0.974911	B	0.22604	0.072	B	0.19391	0.025	T	0.12293	-1.0553	9	.	.	.	-20.8671	13.4611	0.61227	1.0:0.0:0.0:0.0	.	329	Q9H5K3	SG196_HUMAN	G	329	ENSP00000331258:E329G	.	E	+	2	0	AC113191.1	43097110	1.000000	0.71417	0.760000	0.31359	0.425000	0.31504	3.808000	0.55598	2.065000	0.61736	0.482000	0.46254	GAG	.	.	.	none		0.478	POMK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377291.2	NM_032237		G	42977953	A	G	42977953	3	3	68	1	0	0	0	0	1	0	0	0	14221	304	11	3	992	3	SGK196	8	42977953	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10		42977953	103386069	38	4503											
FER1L6	654463	hgsc.bcm.edu	37	chr8	124992806	124992806	+	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	aaatgaacgaaggctttgggGaaggtgtgtcattcaggggc	11	9	16	5	1	2	1	2	1	0	0	2	3	2	2	0	6	1	1	0	6	4	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr8:124992806G>A	ENST00000522917.1	+	11	1371	c.1165G>A	c.(1165-1167)Gaa>Aaa	p.E389K	FER1L6_ENST00000399018.1_Missense_Mutation_p.E389K	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	389						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)			AGGCTTTGGGGAAGGTGTGTC	0.512											OREG0018964	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E389K		Atlas-SNP	.											.	FER1L6	268	.	0			c.G1165A						PASS	.						161	159	160					8																	124992806		1882	4115	5997	SO:0001583	missense	654463	exon11			TTTGGGGAAGGTG	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.1165G>A	chr8.hg19:g.124992806G>A	ENSP00000428280:p.Glu389Lys	115.0	0.0	.	1538	278.0	93.0	.	NM_001039112		Missense_Mutation	SNP	ENST00000522917.1	hg19	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	G	35	5.527427	0.96431	.	.	ENSG00000214814	ENST00000522917;ENST00000399018	D;D	0.83673	-1.75;-1.75	5.53	5.53	0.82687	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.64402	U	0.000003	D	0.91882	0.7430	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.90993	0.4836	10	0.40728	T	0.16	.	19.466	0.94939	0.0:0.0:1.0:0.0	.	389	Q2WGJ9	FR1L6_HUMAN	K	389	ENSP00000428280:E389K;ENSP00000381982:E389K	ENSP00000381982:E389K	E	+	1	0	FER1L6	125061987	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	9.813000	0.99286	2.607000	0.88179	0.655000	0.94253	GAA	.	.	.	none		0.512	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		A	124992806	G	A	124992806	3	1	68	1	0	0	0	0	1	0	0	0	5822	1175	41	2	1203	2	FER1L6	8	124992806	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	82014853	124992806	21371216	39	4504											
ZBTB5	9925	hgsc.bcm.edu	37	chr9	37441549	37441549	+	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	ctgaggctcaggtgagctcaGgggctcagatttaaccacca	10	8	12	11	0	3	3	3	2	0	1	3	3	3	3	2	4	2	3	2	4	1	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr9:37441549G>T	ENST00000307750.4	-	2	1188	c.1000C>A	c.(1000-1002)Ctg>Atg	p.L334M		NM_014872.2	NP_055687.1	O15062	ZBTB5_HUMAN	zinc finger and BTB domain containing 5	334					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	8				GBM - Glioblastoma multiforme(29;0.00733)|Lung(182;0.226)		GGTGAGCTCAGGGGCTCAGAT	0.522																																					p.L334M		Atlas-SNP	.											.	ZBTB5	43	.	0			c.C1000A						PASS	.						103	94	97					9																	37441549		2203	4300	6503	SO:0001583	missense	9925	exon2			AGCTCAGGGGCTC	AB002352	CCDS6610.1	9p13.1	2013-01-09			ENSG00000168795	ENSG00000168795		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	23836	protein-coding gene	gene with protein product						9205841	Standard	NM_014872		Approved	KIAA0354	uc003zzx.3	O15062	OTTHUMG00000019918	ENST00000307750.4:c.1000C>A	chr9.hg19:g.37441549G>T	ENSP00000307604:p.Leu334Met	20.0	0.0	.		45.0	12.0	.	NM_014872		Missense_Mutation	SNP	ENST00000307750.4	hg19	CCDS6610.1	.	.	.	.	.	.	.	.	.	.	G	13.16	2.155723	0.38021	.	.	ENSG00000168795	ENST00000307750	T	0.16196	2.36	5.49	1.43	0.22495	.	0.167314	0.39985	N	0.001220	T	0.22360	0.0539	N	0.24115	0.695	0.48395	D	0.999648	D	0.71674	0.998	D	0.80764	0.994	T	0.01225	-1.1413	10	0.29301	T	0.29	.	10.2477	0.43352	0.3912:0.0:0.6088:0.0	.	334	O15062	ZBTB5_HUMAN	M	334	ENSP00000307604:L334M	ENSP00000307604:L334M	L	-	1	2	ZBTB5	37431549	0.995000	0.38212	0.998000	0.56505	0.932000	0.56968	1.979000	0.40608	0.457000	0.26962	-0.136000	0.14681	CTG	.	.	.	none		0.522	ZBTB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052462.1	NM_014872		T	37441549	G	T	37441549	3	4	68	1	0	0	0	0	1	0	0	0	17563	991	35	4	1037	4	ZBTB5	9	37441549	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10		37441549	103771882	40	4505											
ABCA1	19	hgsc.bcm.edu	37	chr9	107578436	107578436	+	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	taacttacttcttccagggtCgtctctgagatgccataact	9	14	7	11	1	2	1	0	1	2	1	5	2	3	1	2	1	4	0	2	1	3	5	rs548468204	byFrequency	TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr9:107578436C>T	ENST00000374736.3	-	25	4120	c.3726G>A	c.(3724-3726)acG>acA	p.T1242T		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	1242					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)	CTTCCAGGGTCGTCTCTGAGA	0.483													C|||	4	0.000798722	0	0	5008	,	,		19115	0		0	False		,,,				2504	0.0041				p.T1242T		Atlas-SNP	.											.	ABCA1	244	.	0			c.G3726A						PASS	.						166	178	174					9																	107578436		2203	4300	6503	SO:0001819	synonymous_variant	19	exon25			CAGGGTCGTCTCT	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.3726G>A	chr9.hg19:g.107578436C>T		44.0	0.0	.		120.0	51.0	.	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Silent	SNP	ENST00000374736.3	hg19	CCDS6762.1																																																																																			.	.	.	none		0.483	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		T	107578436	C	T	107578436	2	4	68	1	0	0	0	0	0	0	0	1	28	871	31	1		1	ABCA1	9	107578436	Silent	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	70136887	107578436	33634995	41	4506											
COQ4	51117	hgsc.bcm.edu	37	chr9	131095205	131095205	+	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	ctgggtgcattctttggaccGatccgacttggcgctcagta	6	12	12	11	3	2	0	1	0	1	0	3	3	3	1	2	3	1	3	2	3	1	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr9:131095205G>A	ENST00000300452.3	+	6	932	c.609G>A	c.(607-609)ccG>ccA	p.P203P	COQ4_ENST00000461102.1_3'UTR	NM_016035.3	NP_057119			coenzyme Q4											endometrium(4)|large_intestine(1)|lung(4)	9						TCTTTGGACCGATCCGACTTG	0.557																																					p.P203P		Atlas-SNP	.											.	COQ4	20	.	0			c.G609A						PASS	.						194	158	171					9																	131095205		2203	4300	6503	SO:0001819	synonymous_variant	51117	exon6			TGGACCGATCCGA	AF151850	CCDS6898.1	9q34.2	2013-10-18	2013-10-18		ENSG00000167113	ENSG00000167113			19693	protein-coding gene	gene with protein product		612898	"coenzyme Q4 homolog (yeast)", "coenzyme Q4 homolog (S. cerevisiae)"			11469793, 18474229	Standard	NM_016035		Approved	CGI-92	uc004bur.4	Q9Y3A0	OTTHUMG00000020743	ENST00000300452.3:c.609G>A	chr9.hg19:g.131095205G>A		86.0	0.0	.		184.0	68.0	.	NM_016035		Silent	SNP	ENST00000300452.3	hg19	CCDS6898.1																																																																																			.	.	.	none		0.557	COQ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054427.1	NM_016035		A	131095205	G	A	131095205	2	1	68	1	0	0	0	0	0	0	0	1	3749	1045	37	1		1	COQ4	9	131095205	Silent	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	23516769	131095205	10118226	42	4507											
SURF2	6835	hgsc.bcm.edu	37	chr9	136227264	136227264	+	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	gaaggccactgatgagagcaGgagagagacgaccgtgtacc	13	4	15	9	2	0	4	0	2	0	3	0	9	0	4	3	2	2	2	3	2	2	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr9:136227264G>T	ENST00000371964.4	+	5	682	c.641G>T	c.(640-642)aGg>aTg	p.R214M		NM_017503.3	NP_059973.4	Q15527	SURF2_HUMAN	surfeit 2	214						nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|large_intestine(1)|lung(4)	6				OV - Ovarian serous cystadenocarcinoma(145;4.87e-07)|Epithelial(140;4.02e-06)|all cancers(34;3.71e-05)		GATGAGAGCAGGAGAGAGACG	0.557																																					p.R214M		Atlas-SNP	.											.	SURF2	9	.	0			c.G641T						PASS	.						131	111	118					9																	136227264		2203	4300	6503	SO:0001583	missense	6835	exon5			AGAGCAGGAGAGA		CCDS6967.1	9q33-q34	2008-07-21			ENSG00000148291	ENSG00000148291			11475	protein-coding gene	gene with protein product	"surfeit locus protein 2"	185630					Standard	NM_017503		Approved		uc004cdi.2	Q15527	OTTHUMG00000020867	ENST00000371964.4:c.641G>T	chr9.hg19:g.136227264G>T	ENSP00000361032:p.Arg214Met	30.0	0.0	.		52.0	19.0	.	NM_017503	Q6IBP9|Q96CD1	Missense_Mutation	SNP	ENST00000371964.4	hg19	CCDS6967.1	.	.	.	.	.	.	.	.	.	.	G	13.28	2.190148	0.38707	.	.	ENSG00000148291	ENST00000371964	T	0.33216	1.42	2.84	0.71	0.18157	.	0.792035	0.11077	N	0.602308	T	0.28566	0.0707	L	0.51422	1.61	0.09310	N	1	P	0.50710	0.938	P	0.45343	0.477	T	0.14227	-1.0480	10	0.54805	T	0.06	-4.7868	5.4059	0.16320	0.1238:0.2056:0.6706:0.0	.	214	Q15527	SURF2_HUMAN	M	214	ENSP00000361032:R214M	ENSP00000361032:R214M	R	+	2	0	SURF2	135217085	0.005000	0.15991	0.000000	0.03702	0.030000	0.12068	1.572000	0.36461	0.015000	0.14971	0.462000	0.41574	AGG	.	.	.	none		0.557	SURF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054883.1	NM_017503		T	136227264	G	T	136227264	3	4	68	1	0	0	0	0	1	0	0	0	15416	1000	35	4	659	4	SURF2	9	136227264	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	5132059	136227264	4986167	43	4508											
NOTCH1	4851	hgsc.bcm.edu	37	chr9	139407915	139407915	+	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	aggtgccgccgttgacacaaGggttggattcacactcattg	9	10	12	10	2	2	1	2	1	0	0	2	2	2	2	2	3	1	2	2	3	1	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr9:139407915G>T	ENST00000277541.6	-	14	2357	c.2282C>A	c.(2281-2283)cCt>cAt	p.P761H		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	761	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)		GTTGACACAAGGGTTGGATTC	0.587			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)																											p.P761H		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	.	NOTCH1	1980	.	0			c.C2282A						PASS	.						104	118	113					9																	139407915		2187	4274	6461	SO:0001583	missense	4851	exon14			ACACAAGGGTTGG	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.2282C>A	chr9.hg19:g.139407915G>T	ENSP00000277541:p.Pro761His	30.0	0.0	.		68.0	20.0	.	NM_017617	Q59ED8|Q5SXM3	Missense_Mutation	SNP	ENST00000277541.6	hg19	CCDS43905.1	.	.	.	.	.	.	.	.	.	.	G	17.88	3.497270	0.64186	.	.	ENSG00000148400	ENST00000277541	D	0.93189	-3.18	4.76	4.76	0.60689	EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.97539	0.9194	M	0.93638	3.44	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98725	1.0710	10	0.72032	D	0.01	.	16.7491	0.85480	0.0:0.0:1.0:0.0	.	761	P46531	NOTC1_HUMAN	H	761	ENSP00000277541:P761H	ENSP00000277541:P761H	P	-	2	0	NOTCH1	138527736	1.000000	0.71417	1.000000	0.80357	0.223000	0.24884	9.349000	0.97066	2.199000	0.70637	0.455000	0.32223	CCT	.	.	.	none		0.587	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		T	139407915	G	T	139407915	3	4	68	1	0	0	0	0	1	0	0	0	10554	1000	35	4	5469	4	NOTCH1	9	139407915	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	3180651	139407915	1805516	44	4509											
BMS1	9790	hgsc.bcm.edu	37	chr10	43294061	43294061	+	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	gtggaggccccccatgactgGgatttagaggaggtaagtct	9	9	15	8	0	1	2	0	1	1	1	1	5	1	5	3	5	0	1	3	5	2	3			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr10:43294061G>T	ENST00000374518.5	+	12	2298	c.2235G>T	c.(2233-2235)tgG>tgT	p.W745C		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	745					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						CCCATGACTGGGATTTAGAGG	0.428																																					p.W745C		Atlas-SNP	.											.	BMS1	132	.	0			c.G2235T						PASS	.						91	97	95					10																	43294061		2203	4300	6503	SO:0001583	missense	9790	exon12			TGACTGGGATTTA	BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"BMS1-like, ribosome assembly protein (yeast)", "BMS1 homolog, ribosome assembly protein (yeast)"	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.2235G>T	chr10.hg19:g.43294061G>T	ENSP00000363642:p.Trp745Cys	80.0	0.0	.		173.0	7.0	.	NM_014753	Q5QPT5|Q86XJ9	Missense_Mutation	SNP	ENST00000374518.5	hg19	CCDS7199.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.986911	0.74589	.	.	ENSG00000165733	ENST00000374518	T	0.53857	0.6	5.92	5.92	0.95590	.	0.060191	0.64402	D	0.000001	T	0.76314	0.3970	M	0.79805	2.47	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.77219	-0.2668	10	0.66056	D	0.02	.	20.3734	0.98896	0.0:0.0:1.0:0.0	.	745	Q14692	BMS1_HUMAN	C	745	ENSP00000363642:W745C	ENSP00000363642:W745C	W	+	3	0	BMS1	42614067	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	9.218000	0.95166	2.820000	0.97059	0.650000	0.86243	TGG	.	.	.	none		0.428	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753		T	43294061	G	T	43294061	3	4	68	1	0	0	0	0	1	0	0	0	1472	1241	43	4	2277	4	BMS1	10	43294061	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10		43294061	92240686	45	4510											
C10orf12	26148	hgsc.bcm.edu	37	chr10	98741939	98741939	+	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	cctagcaaggaaatcacctcTcacgaggaaggaggtggaga	14	5	13	9	1	2	1	2	0	1	1	3	6	2	4	2	5	1	1	2	5	4	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr10:98741939T>G	ENST00000286067.2	+	1	899	c.792T>G	c.(790-792)tcT>tcG	p.S264S		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	264										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)		AAATCACCTCTCACGAGGAAG	0.512																																					p.S264S		Atlas-SNP	.											.	C10orf12	94	.	0			c.T792G						PASS	.						89	90	90					10																	98741939		2203	4300	6503	SO:0001819	synonymous_variant	26148	exon1			CACCTCTCACGAG	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.792T>G	chr10.hg19:g.98741939T>G		65.0	0.0	.		110.0	37.0	.	NM_015652	Q9H945|Q9Y457	Silent	SNP	ENST00000286067.2	hg19	CCDS7452.1																																																																																			.	.	.	none		0.512	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652		G	98741939	T	G	98741939	2	3	68	1	0	0	0	0	0	0	0	1	1591	1538	54	5		5	C10orf12	10	98741939	Silent	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	55447878	98741939	36792808	46	4511											
PDCD4	27250	hgsc.bcm.edu	37	chr10	112655819	112655819	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caggctggaataatttccaaAcaactcagagatctttgtcc	13	11	7	10	0	2	1	1	0	1	1	4	3	4	2	2	2	2	1	2	2	4	3			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr10:112655819A>G	ENST00000280154.7	+	11	1597	c.1323A>G	c.(1321-1323)aaA>aaG	p.K441K	PDCD4_ENST00000393104.2_Silent_p.K430K|MIR4680_ENST00000580906.1_RNA	NM_001199492.1|NM_014456.4	NP_001186421.1|NP_055271.2	Q53EL6	PDCD4_HUMAN	programmed cell death 4 (neoplastic transformation inhibitor)	441	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)		TAATTTCCAAACAACTCAGAG	0.358																																					p.K441K	Ovarian(115;1498 1603 9363 40056 40885)	Atlas-SNP	.											.	PDCD4	39	.	0			c.A1323G						PASS	.						78	78	78					10																	112655819		2202	4300	6502	SO:0001819	synonymous_variant	27250	exon11			TTCCAAACAACTC	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.1323A>G	chr10.hg19:g.112655819A>G		86.0	0.0	.		205.0	64.0	.	NM_014456	B2RCV4|B5ME91|O15501|Q5VZS6|Q6PJI5|Q8TAR5|Q99834	Silent	SNP	ENST00000280154.7	hg19	CCDS7567.1																																																																																			.	.	.	none		0.358	PDCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050361.1	NM_014456		G	112655819	A	G	112655819	2	3	68	1	0	0	0	0	0	0	0	1	11628	40	2	3		3	PDCD4	10	112655819	Silent	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	13913880	112655819	22878928	47	4512											
SLC22A10	387775	hgsc.bcm.edu	37	chr11	63065116	63065116	+	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	attggacagataatcctgggAggcttggcttatgtcttccg	8	13	12	8	1	1	1	0	0	1	1	3	3	3	3	2	4	0	2	2	4	2	5			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr11:63065116A>T	ENST00000332793.6	+	4	749	c.747A>T	c.(745-747)ggA>ggT	p.G249G	SLC22A10_ENST00000526800.1_Intron|SLC22A10_ENST00000544661.1_Silent_p.G94G|SLC22A10_ENST00000525620.1_3'UTR|SLC22A10_ENST00000535888.1_Silent_p.G39G	NM_001039752.3	NP_001034841.3	Q63ZE4	S22AA_HUMAN	solute carrier family 22, member 10	249						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28					Conjugated Estrogens(DB00286)|Probenecid(DB01032)|Salicylic acid(DB00936)	TAATCCTGGGAGGCTTGGCTT	0.463																																					p.G249G		Atlas-SNP	.											.	SLC22A10	79	.	0			c.A747T						PASS	.						159	149	152					11																	63065116		1933	4127	6060	SO:0001819	synonymous_variant	387775	exon4			CCTGGGAGGCTTG	AP003420	CCDS41661.1	11q12.3	2013-05-22	2008-01-11		ENSG00000184999	ENSG00000184999		"Solute carriers"	18057	protein-coding gene	gene with protein product		607580	"solute carrier family 22 (organic anion/cation transporter), member 10"			11327718	Standard	NM_001039752		Approved	OAT5, hOAT5	uc009yor.3	Q63ZE4	OTTHUMG00000165197	ENST00000332793.6:c.747A>T	chr11.hg19:g.63065116A>T		85.0	0.0	.		156.0	64.0	.	NM_001039752	Q68CJ0	Silent	SNP	ENST00000332793.6	hg19	CCDS41661.1																																																																																			.	.	.	none		0.463	SLC22A10-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382622.3	NM_001039752		T	63065116	A	T	63065116	2	4	68	1	0	0	0	0	0	0	0	1	14454	291	11	5		5	SLC22A10	11	63065116	Silent	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10		63065116	71941400	48	4513											
SLC22A10	387775	hgsc.bcm.edu	37	chr11	63071636	63071636	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaatcggctgttctgctgctActttttccagtgttgctgtt	4	18	10	9	1	1	0	0	0	1	0	3	1	2	0	1	1	4	7	1	1	2	6			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr11:63071636A>G	ENST00000332793.6	+	8	1344	c.1342A>G	c.(1342-1344)Act>Gct	p.T448A	SLC22A10_ENST00000526800.1_Intron|SLC22A10_ENST00000544661.1_Silent_p.L246L|SLC22A10_ENST00000525620.1_Intron|SLC22A10_ENST00000535888.1_Intron	NM_001039752.3	NP_001034841.3	Q63ZE4	S22AA_HUMAN	solute carrier family 22, member 10	448						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28					Conjugated Estrogens(DB00286)|Probenecid(DB01032)|Salicylic acid(DB00936)	TTCTGCTGCTACTTTTTCCAG	0.483																																					p.T448A		Atlas-SNP	.											.	SLC22A10	79	.	0			c.A1342G						PASS	.						212	217	215					11																	63071636		2073	4247	6320	SO:0001583	missense	387775	exon8			GCTGCTACTTTTT	AP003420	CCDS41661.1	11q12.3	2013-05-22	2008-01-11		ENSG00000184999	ENSG00000184999		"Solute carriers"	18057	protein-coding gene	gene with protein product		607580	"solute carrier family 22 (organic anion/cation transporter), member 10"			11327718	Standard	NM_001039752		Approved	OAT5, hOAT5	uc009yor.3	Q63ZE4	OTTHUMG00000165197	ENST00000332793.6:c.1342A>G	chr11.hg19:g.63071636A>G	ENSP00000327569:p.Thr448Ala	41.0	0.0	.		75.0	26.0	.	NM_001039752	Q68CJ0	Missense_Mutation	SNP	ENST00000332793.6	hg19	CCDS41661.1	.	.	.	.	.	.	.	.	.	.	A	0	-2.853818	0.00066	.	.	ENSG00000184999	ENST00000332793	T	0.74526	-0.85	3.05	-6.11	0.02131	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.214933	0.39020	N	0.001483	T	0.27594	0.0678	N	0.00525	-1.395	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.33137	-0.9880	10	0.05351	T	0.99	.	5.742	0.18100	0.3421:0.0:0.1242:0.5336	.	448	Q63ZE4	S22AA_HUMAN	A	448	ENSP00000327569:T448A	ENSP00000327569:T448A	T	+	1	0	SLC22A10	62828212	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.437000	0.01018	-3.799000	0.00105	-1.485000	0.00982	ACT	.	.	.	none		0.483	SLC22A10-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382622.3	NM_001039752		G	63071636	A	G	63071636	3	3	68	1	0	0	0	0	1	0	0	0	14454	391	14	3	1372	3	SLC22A10	11	63071636	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	6520	63071636	71934880	49	4514											
MAML2	84441	hgsc.bcm.edu	37	chr11	95825254	95825254	+	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	tgttgttgctgctgctgctgCtgttgttgctgctgctgctg	0	18	14	9	0	0	0	0	0	0	0	0	0	0	0	0	0	9	13	0	0	0	4	rs61749250		TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr11:95825254C>T	ENST00000524717.1	-	2	3225	c.1941G>A	c.(1939-1941)caG>caA	p.Q647Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	647					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.Q647Q(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)				gctgctgctgctgttgttgct	0.512			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.Q647Q		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	MAML2,caecum,carcinoma,0,2	MAML2	94	.	1	Substitution - coding silent(1)	endometrium(1)	c.G1941A						PASS	.	C		0,4198		0,0,2099	35	40	38		1941	1.7	0.1	11	dbSNP_129	38	5,8237		0,5,4116	no	coding-synonymous	MAML2	NM_032427.1		0,5,6215	TT,TC,CC		0.0607,0.0,0.0402		647/1157	95825254	5,12435	2099	4121	6220	SO:0001819	synonymous_variant	84441	exon2			CTGCTGCTGTTGT	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.1941G>A	chr11.hg19:g.95825254C>T		40.0	1.0	.		76.0	4.0	.	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	hg19	CCDS44714.1																																																																																			.	.	.	weak		0.512	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95825254	C	T	95825254	2	4	68	1	0	0	0	0	0	0	0	1	9213	796	28	2		2	MAML2	11	95825254	Silent	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	32753618	95825254	39181262	50	4515											
NPAT	4863	hgsc.bcm.edu	37	chr11	108043550	108043550	+	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	gttgctagaaggtttatcatCagtattttgggactcagggt	9	15	12	5	0	3	1	3	0	0	1	3	2	3	2	0	3	1	4	0	3	4	7			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr11:108043550C>T	ENST00000278612.8	-	13	2266	c.2161G>A	c.(2161-2163)Gat>Aat	p.D721N	NPAT_ENST00000610253.1_5'UTR	NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	721					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)		GGTTTATCATCAGTATTTTGG	0.428																																					p.D721N		Atlas-SNP	.											.	NPAT	124	.	0			c.G2161A						PASS	.						120	110	113					11																	108043550		1892	4120	6012	SO:0001583	missense	4863	exon13			TATCATCAGTATT	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.2161G>A	chr11.hg19:g.108043550C>T	ENSP00000278612:p.Asp721Asn	36.0	0.0	.		66.0	21.0	.	NM_002519	A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	Missense_Mutation	SNP	ENST00000278612.8	hg19	CCDS41710.1	.	.	.	.	.	.	.	.	.	.	C	1.672	-0.508824	0.04231	.	.	ENSG00000149308	ENST00000278612	T	0.03982	3.74	5.55	-1.3	0.09259	.	1.001340	0.08051	N	0.996678	T	0.02418	0.0074	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.49204	-0.8964	10	0.18710	T	0.47	3.2313	6.8937	0.24245	0.1138:0.3772:0.0:0.509	.	721;721	B9EG70;Q14207	.;NPAT_HUMAN	N	721	ENSP00000278612:D721N	ENSP00000278612:D721N	D	-	1	0	NPAT	107548760	0.145000	0.22656	0.022000	0.16811	0.316000	0.28119	0.773000	0.26661	-0.127000	0.11661	-0.136000	0.14681	GAT	.	.	.	none		0.428	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389506.2	NM_002519		T	108043550	C	T	108043550	3	4	68	1	0	0	0	0	1	0	0	0	10573	826	29	2	2146	2	NPAT	11	108043550	Missense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	12218296	108043550	26962966	51	4516											
BCL9L	283149	hgsc.bcm.edu	37	chr11	118773516	118773516	+	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	ggcggggcactgccaggggcCgggggtggcggcggcggcag	3	2	25	11	5	0	0	0	0	0	0	0	0	0	0	2	11	1	2	2	11	0	0			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr11:118773516C>A	ENST00000334801.3	-	6	1900	c.936G>T	c.(934-936)ccG>ccT	p.P312P	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	312	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)		TGCCAGGGGCCGGGGGTGGCG	0.731																																					p.P312P		Atlas-SNP	.											.	BCL9L	254	.	0			c.G936T						PASS	.						5	7	6					11																	118773516		2014	4005	6019	SO:0001819	synonymous_variant	283149	exon6			AGGGGCCGGGGGT	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.936G>T	chr11.hg19:g.118773516C>A		3.0	0.0	.		10.0	5.0	.	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Silent	SNP	ENST00000334801.3	hg19	CCDS8403.1																																																																																			.	.	.	none		0.731	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557		A	118773516	C	A	118773516	2	1	68	1	0	0	0	0	0	0	0	1	1382	639	23	4		4	BCL9L	11	118773516	Silent	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	10729966	118773516	16233000	52	4517											
SOX5	6660	hgsc.bcm.edu	37	chr12	23757377	23757377	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgtgaatgctggtaggagAtacagcagcaccaaggttgc	11	9	14	7	0	0	2	0	1	0	1	0	3	0	2	1	3	5	5	1	3	4	3			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr12:23757377A>G	ENST00000451604.2	-	9	1209	c.1108T>C	c.(1108-1110)Tct>Cct	p.S370P	SOX5_ENST00000545921.1_Missense_Mutation_p.S360P|SOX5_ENST00000381381.2_Missense_Mutation_p.S357P|SOX5_ENST00000537393.1_Missense_Mutation_p.S335P|SOX5_ENST00000541536.1_Missense_Mutation_p.S357P|SOX5_ENST00000546136.1_Missense_Mutation_p.S357P|SOX5_ENST00000309359.1_Missense_Mutation_p.S357P			P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5	370					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						CTGGTAGGAGATACAGCAGCA	0.502																																					p.S370P		Atlas-SNP	.											SOX5,colon,carcinoma,0,1	SOX5	134	.	0			c.T1108C						PASS	.						164	133	144					12																	23757377		2203	4300	6503	SO:0001583	missense	6660	exon9			TAGGAGATACAGC	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.1108T>C	chr12.hg19:g.23757377A>G	ENSP00000398273:p.Ser370Pro	51.0	0.0	.		125.0	33.0	.	NM_006940	B7Z8V0|F5H5B0|Q86UK8|Q8J017|Q8J018|Q8J019|Q8J020|Q8N1D9|Q8N7E0|Q8TEA4	Missense_Mutation	SNP	ENST00000451604.2	hg19	CCDS8699.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.520861	0.85495	.	.	ENSG00000134532	ENST00000546136;ENST00000309359;ENST00000381381;ENST00000451604;ENST00000435266;ENST00000537393;ENST00000541536;ENST00000545921	D;D;D;D;D;D;D	0.97831	-4.54;-4.54;-4.24;-4.55;-4.56;-4.24;-4.55	6.16	6.16	0.99307	.	0.171135	0.53938	D	0.000045	D	0.98251	0.9421	M	0.64567	1.98	0.53688	D	0.999975	D;P;D	0.60160	0.987;0.945;0.978	P;D;P	0.68621	0.907;0.959;0.809	D	0.98503	1.0615	10	0.41790	T	0.15	.	16.8061	0.85666	1.0:0.0:0.0:0.0	.	335;357;370	F5H0I3;P35711-4;P35711	.;.;SOX5_HUMAN	P	357;357;357;370;322;335;357;360	ENSP00000437487:S357P;ENSP00000308927:S357P;ENSP00000370788:S357P;ENSP00000398273:S370P;ENSP00000439832:S335P;ENSP00000441973:S357P;ENSP00000443520:S360P	ENSP00000308927:S357P	S	-	1	0	SOX5	23648644	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	5.618000	0.67722	2.367000	0.80283	0.528000	0.53228	TCT	.	.	.	none		0.502	SOX5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402006.2	NM_006940		G	23757377	A	G	23757377	3	3	68	1	0	0	0	0	1	0	0	0	14967	333	12	3	1221	3	SOX5	12	23757377	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10		23757377	110094518	53	4518											
ADCY6	112	hgsc.bcm.edu	37	chr12	49168249	49168249	+	Missense_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	tgccaactgcggtgctatgtGcccgtgagcggacaatgctg	7	9	14	11	3	0	1	0	1	0	0	0	2	0	2	2	2	7	2	2	2	3	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr12:49168249G>A	ENST00000307885.4	-	13	2913	c.2219C>T	c.(2218-2220)gCa>gTa	p.A740V	ADCY6_ENST00000550422.1_Missense_Mutation_p.A740V|ADCY6_ENST00000357869.3_Missense_Mutation_p.A740V|ADCY6_ENST00000552090.1_5'UTR|MIR4701_ENST00000583094.1_RNA	NM_015270.3	NP_056085.1	O43306	ADCY6_HUMAN	adenylate cyclase 6	740					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						GGTGCTATGTGCCCGTGAGCG	0.537																																					p.A740V		Atlas-SNP	.											.	ADCY6	81	.	0			c.C2219T						PASS	.						134	112	119					12																	49168249		2203	4300	6503	SO:0001583	missense	112	exon14			CTATGTGCCCGTG		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.2219C>T	chr12.hg19:g.49168249G>A	ENSP00000311405:p.Ala740Val	84.0	0.0	.		182.0	88.0	.	NM_020983	Q9NR75|Q9UDB0	Missense_Mutation	SNP	ENST00000307885.4	hg19	CCDS8767.1	.	.	.	.	.	.	.	.	.	.	G	12.99	2.103172	0.37145	.	.	ENSG00000174233	ENST00000357869;ENST00000550422;ENST00000307885	T;T;T	0.39787	1.06;1.06;1.06	4.42	3.51	0.40186	.	0.303154	0.30820	N	0.008801	T	0.28896	0.0717	L	0.36672	1.1	0.28148	N	0.929491	B;B	0.26041	0.14;0.004	B;B	0.28139	0.086;0.01	T	0.18618	-1.0331	10	0.13470	T	0.59	.	8.2466	0.31693	0.202:0.0:0.798:0.0	.	740;740	O43306-2;O43306	.;ADCY6_HUMAN	V	740	ENSP00000350536:A740V;ENSP00000446730:A740V;ENSP00000311405:A740V	ENSP00000311405:A740V	A	-	2	0	ADCY6	47454516	0.679000	0.27596	1.000000	0.80357	0.892000	0.51952	2.661000	0.46758	0.963000	0.38082	0.561000	0.74099	GCA	.	.	.	none		0.537	ADCY6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408863.1	NM_020983		A	49168249	G	A	49168249	3	1	68	1	0	0	0	0	1	0	0	0	298	1319	46	2	1323	2	ADCY6	12	49168249	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	25410872	49168249	84683646	54	4519											
HOXC4	3221	hgsc.bcm.edu	37	chr12	54447788	54447788	+	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	aagaatattcgcaaaatagcTacatccctgaacacagtccg	16	8	6	11	2	0	2	0	1	0	1	3	2	2	2	2	0	3	2	2	0	8	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr12:54447788T>A	ENST00000430889.2	+	1	128	c.82T>A	c.(82-84)Tac>Aac	p.Y28N	HOXC4_ENST00000303406.4_Missense_Mutation_p.Y28N|HOXC4_ENST00000609810.1_Missense_Mutation_p.Y28N	NM_153633.2	NP_705897.1	P09017	HXC4_HUMAN	homeobox C4	28					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	13						GCAAAATAGCTACATCCCTGA	0.493																																					p.Y28N		Atlas-SNP	.											.	HOXC4	29	.	0			c.T82A						PASS	.						127	129	128					12																	54447788		2203	4300	6503	SO:0001583	missense	3221	exon3			AATAGCTACATCC		CCDS8873.1	12q13.13	2011-06-20	2005-12-22		ENSG00000198353	ENSG00000198353		"Homeoboxes / ANTP class : HOXL subclass"	5126	protein-coding gene	gene with protein product		142974	"homeo box C4"	HOX3, HOX3E		1973146, 1358459	Standard	NM_014620		Approved		uc001sex.3	P09017	OTTHUMG00000160036	ENST00000430889.2:c.82T>A	chr12.hg19:g.54447788T>A	ENSP00000399808:p.Tyr28Asn	72.0	0.0	.		205.0	40.0	.	NM_014620		Missense_Mutation	SNP	ENST00000430889.2	hg19	CCDS8873.1	.	.	.	.	.	.	.	.	.	.	T	18.84	3.710126	0.68730	.	.	ENSG00000198353	ENST00000303406;ENST00000430889	D;D	0.83992	-1.79;-1.79	3.41	3.41	0.39046	.	0.152719	0.44902	D	0.000404	D	0.92014	0.7470	M	0.92317	3.295	0.80722	D	1	D	0.71674	0.998	D	0.76071	0.987	D	0.93212	0.6601	10	0.72032	D	0.01	.	11.785	0.52037	0.0:0.0:0.0:1.0	.	28	P09017	HXC4_HUMAN	N	28	ENSP00000305973:Y28N;ENSP00000399808:Y28N	ENSP00000305973:Y28N	Y	+	1	0	HOXC4	52734055	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.592000	0.61027	1.775000	0.52247	0.379000	0.24179	TAC	.	.	.	none		0.493	HOXC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358963.1			A	54447788	T	A	54447788	3	1	68	1	0	0	0	0	1	0	0	0	7320	1522	53	5	84	5	HOXC4	12	54447788	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	5279539	54447788	79404107	55	4520											
GPR81	27198	hgsc.bcm.edu	37	chr12	123214112	123214112	+	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	gctgagggttatgtgcagggCcccatggacagagggatcgc	8	7	17	9	1	0	2	0	1	0	1	1	4	0	4	2	4	1	3	2	4	1	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr12:123214112C>T	ENST00000436083.2	-	1	1278	c.775G>A	c.(775-777)Gcc>Acc	p.A259T	HCAR1_ENST00000432564.1_Missense_Mutation_p.A259T|HCAR1_ENST00000356987.2_Missense_Mutation_p.A259T			Q9BXC0	HCAR1_HUMAN	hydroxycarboxylic acid receptor 1	259					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						ATGTGCAGGGCCCCATGGACA	0.522																																					p.A259T		Atlas-SNP	.											.	HCAR1	21	.	0			c.G775A						PASS	.						81	81	81					12																	123214112		2203	4300	6503	SO:0001583	missense	27198	exon1			GCAGGGCCCCATG	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.775G>A	chr12.hg19:g.123214112C>T	ENSP00000409980:p.Ala259Thr	78.0	0.0	.		213.0	92.0	.	NM_032554	B2R9X4|Q3Y5J3|Q4VBN1|Q6NXU5	Missense_Mutation	SNP	ENST00000436083.2	hg19	CCDS9236.1	.	.	.	.	.	.	.	.	.	.	C	15.54	2.864791	0.51482	.	.	ENSG00000196917	ENST00000356987;ENST00000432564;ENST00000436083	T;T;T	0.38401	1.14;1.14;1.14	5.62	4.72	0.59763	GPCR, rhodopsin-like superfamily (1);	0.162482	0.38272	N	0.001754	T	0.50292	0.1607	L	0.55481	1.735	0.37418	D	0.913513	D	0.61697	0.99	D	0.64877	0.93	T	0.49872	-0.8893	10	0.33141	T	0.24	-12.0983	12.8086	0.57628	0.0:0.9183:0.0:0.0817	.	259	Q9BXC0	HCAR1_HUMAN	T	259	ENSP00000349478:A259T;ENSP00000389255:A259T;ENSP00000409980:A259T	ENSP00000349478:A259T	A	-	1	0	HCAR1	121780065	0.985000	0.35326	0.946000	0.38457	0.043000	0.13939	2.721000	0.47260	2.653000	0.90120	0.655000	0.94253	GCC	.	.	.	none		0.522	HCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401415.1			T	123214112	C	T	123214112	3	4	68	1	0	0	0	0	1	0	0	0	6718	739	26	2	269	2	GPR81	12	123214112	Missense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	68766324	123214112	10637783	56	4521											
GPR133	283383	hgsc.bcm.edu	37	chr12	131471648	131471648	+	Missense_Mutation	SNP	T	T	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	actcttttccaggcccctatTggactcatgtcctatttaca	8	15	5	13	0	2	0	1	0	1	0	4	1	4	1	4	2	1	0	4	2	3	7			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr12:131471648T>G	ENST00000261654.5	+	6	1058	c.499T>G	c.(499-501)Tgg>Ggg	p.W167G	GPR133_ENST00000535015.1_Missense_Mutation_p.W199G	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	167					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(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)		AGGCCCCTATTGGACTCATGT	0.493																																					p.W167G		Atlas-SNP	.											.	GPR133	136	.	0			c.T499G						PASS	.						59	57	58					12																	131471648		2203	4300	6503	SO:0001583	missense	283383	exon6			CCCTATTGGACTC	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.499T>G	chr12.hg19:g.131471648T>G	ENSP00000261654:p.Trp167Gly	46.0	0.0	.		120.0	25.0	.	NM_198827	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Missense_Mutation	SNP	ENST00000261654.5	hg19	CCDS9272.1	.	.	.	.	.	.	.	.	.	.	T	15.41	2.826517	0.50739	.	.	ENSG00000111452	ENST00000261654;ENST00000542091;ENST00000535015	D;D;D	0.86769	-2.17;-2.17;-2.17	4.55	4.55	0.56014	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.85682	D	0.000000	D	0.94679	0.8284	M	0.93898	3.47	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.99	D	0.95634	0.8692	10	0.72032	D	0.01	.	13.1073	0.59253	0.0:0.0:0.0:1.0	.	199;167	B7ZLF7;Q6QNK2	.;GP133_HUMAN	G	167;107;199	ENSP00000261654:W167G;ENSP00000442501:W107G;ENSP00000444425:W199G	ENSP00000261654:W167G	W	+	1	0	GPR133	130037601	1.000000	0.71417	1.000000	0.80357	0.406000	0.30931	7.078000	0.76821	1.685000	0.51034	0.533000	0.62120	TGG	.	.	.	none		0.493	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827		G	131471648	T	G	131471648	3	3	68	1	0	0	0	0	1	0	0	0	6650	1812	63	5	521	5	GPR133	12	131471648	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	8257536	131471648	2380247	57	4522											
COG6	57511	hgsc.bcm.edu	37	chr13	40251678	40251678	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aactgacttctgatgaaatgAgtcttctccgaggtacaaga	13	11	9	8	1	3	5	0	4	3	1	4	6	3	5	1	1	2	1	1	1	4	3			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr13:40251678A>G	ENST00000455146.3	+	5	552	c.502A>G	c.(502-504)Agt>Ggt	p.S168G	COG6_ENST00000416691.1_Missense_Mutation_p.S168G	NM_020751.2	NP_065802.1	Q9Y2V7	COG6_HUMAN	component of oligomeric golgi complex 6	168					glycosylation (GO:0070085)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				NS(1)|kidney(2)|large_intestine(5)|lung(4)|skin(1)	13		Lung NSC(96;0.000124)|Breast(139;0.0199)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.03e-09)|Epithelial(112;7e-07)|OV - Ovarian serous cystadenocarcinoma(117;0.00015)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.0168)		TGATGAAATGAGTCTTCTCCG	0.348																																					p.S168G		Atlas-SNP	.											.	COG6	49	.	0			c.A502G						PASS	.						87	81	83					13																	40251678		2203	4300	6503	SO:0001583	missense	57511	exon5			GAAATGAGTCTTC	AK026638	CCDS9370.1, CCDS45042.1	13q13.2	2011-08-01			ENSG00000133103	ENSG00000133103		"Components of oligomeric golgi complex"	18621	protein-coding gene	gene with protein product		606977				11980916	Standard	NM_020751		Approved	COD2, KIAA1134	uc001uxh.2	Q9Y2V7	OTTHUMG00000016768	ENST00000455146.3:c.502A>G	chr13.hg19:g.40251678A>G	ENSP00000397441:p.Ser168Gly	53.0	0.0	.		113.0	36.0	.	NM_001145079	Q5T0U1|Q6AI19|Q86V49|Q9ULT5	Missense_Mutation	SNP	ENST00000455146.3	hg19	CCDS9370.1	.	.	.	.	.	.	.	.	.	.	A	12.40	1.927586	0.34002	.	.	ENSG00000133103	ENST00000416691;ENST00000255468;ENST00000422759;ENST00000455146	T;T;T	0.55588	0.51;0.51;0.51	5.78	-1.08	0.09936	.	0.333784	0.40640	N	0.001058	T	0.29321	0.0730	N	0.24115	0.695	0.28989	N	0.888159	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.10989	-1.0606	10	0.22109	T	0.4	-11.1167	5.8826	0.18864	0.5582:0.1302:0.3116:0.0	.	189;168	Q5T0U2;Q9Y2V7	.;COG6_HUMAN	G	168;199;168;168	ENSP00000403733:S168G;ENSP00000412877:S168G;ENSP00000397441:S168G	ENSP00000255468:S199G	S	+	1	0	COG6	39149678	1.000000	0.71417	0.941000	0.38009	0.875000	0.50365	2.795000	0.47861	-0.395000	0.07715	-0.334000	0.08254	AGT	.	.	.	none		0.348	COG6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044622.3			G	40251678	A	G	40251678	3	3	68	1	0	0	0	0	1	0	0	0	3664	304	11	3	520	3	COG6	13	40251678	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10		40251678	74918200	58	4523											
IPO5	3843	hgsc.bcm.edu	37	chr13	98667795	98667795	+	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	cctcattagtgcattgaagtAatgggagatggatgccttaa	12	12	11	6	0	1	2	1	1	0	1	1	4	1	3	2	2	2	2	2	2	4	4	rs61750357		TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr13:98667795A>T	ENST00000490680.1	+	20	2402	c.2337A>T	c.(2335-2337)gtA>gtT	p.V779V	IPO5_ENST00000539640.1_Silent_p.V654V|IPO5_ENST00000261574.5_Silent_p.V797V			O00410	IPO5_HUMAN	importin 5	779					cellular response to amino acid stimulus (GO:0071230)|negative regulation of catalytic activity (GO:0043086)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein import into nucleus (GO:0042307)|ribosomal protein import into nucleus (GO:0006610)|viral process (GO:0016032)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|Ran GTPase binding (GO:0008536)			breast(2)|endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	27						GCATTGAAGTAATGGGAGATG	0.348																																					p.V797V		Atlas-SNP	.											.	IPO5	90	.	0			c.A2391T						PASS	.						108	107	107					13																	98667795		2203	4300	6503	SO:0001819	synonymous_variant	3843	exon23			TGAAGTAATGGGA	U72761	CCDS31999.1	13q32.2	2012-05-02	2008-04-15	2008-04-15	ENSG00000065150	ENSG00000065150		"Importins"	6402	protein-coding gene	gene with protein product		602008	"karyopherin (importin) beta 3", "RAN binding protein 5"	KPNB3, RANBP5		9114010, 9271386, 17005651	Standard	NM_002271		Approved	IMB3, MGC2068, Pse1	uc001vne.3	O00410	OTTHUMG00000017244	ENST00000490680.1:c.2337A>T	chr13.hg19:g.98667795A>T		85.0	0.0	.		167.0	61.0	.	NM_002271	B4DZA0|O15257|Q5T578|Q86XC7	Silent	SNP	ENST00000490680.1	hg19		.	.	.	.	.	.	.	.	.	.	A	10.56	1.383369	0.25031	.	.	ENSG00000065150	ENST00000469360	.	.	.	5.72	-3.39	0.04868	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-8.1611	7.7355	0.28812	0.295:0.5469:0.06:0.0981	.	.	.	.	L	781	.	.	X	+	2	2	IPO5	97465796	0.965000	0.33210	0.966000	0.40874	0.996000	0.88848	0.136000	0.15974	-0.832000	0.04251	0.533000	0.62120	TAA	.	.	.	alt		0.348	IPO5-006	NOVEL	alternative_5_UTR|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000354655.1	NM_002271		T	98667795	A	T	98667795	2	4	68	1	0	0	0	0	0	0	0	1	7803	349	13	5		5	IPO5	13	98667795	Silent	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	58416117	98667795	16502083	59	4524											
ATP11A	23250	hgsc.bcm.edu	37	chr13	113474213	113474213	+	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	acgtggcttttctgtcgccaGgttcgtgggtcgcatcaacg	5	12	13	11	5	2	0	1	0	1	0	5	0	2	0	1	3	1	3	1	3	1	3			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr13:113474213G>A	ENST00000487903.1	+	8	762		c.e8-1		ATP11A_ENST00000375630.2_Splice_Site|ATP11A_ENST00000375645.3_Splice_Site|ATP11A_ENST00000283558.8_Splice_Site			P98196	AT11A_HUMAN	ATPase, class VI, type 11A						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)				TCTGTCGCCAGGTTCGTGGGT	0.637																																					.		Atlas-SNP	.											.	ATP11A	225	.	0			c.675-1G>A						PASS	.						125	89	101					13																	113474213		2203	4300	6503	SO:0001630	splice_region_variant	23250	exon8			TCGCCAGGTTCGT	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.675-1G>A	chr13.hg19:g.113474213G>A		10.0	0.0	.		57.0	18.0	.	NM_015205	Q5VXT2	Splice_Site	SNP	ENST00000487903.1	hg19	CCDS32011.1	.	.	.	.	.	.	.	.	.	.	G	12.40	1.927015	0.34002	.	.	ENSG00000068650	ENST00000487903;ENST00000375630;ENST00000375645;ENST00000283558;ENST00000418678	.	.	.	4.87	4.87	0.63330	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8794	0.63674	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ATP11A	112522214	1.000000	0.71417	0.997000	0.53966	0.023000	0.10783	6.506000	0.73712	2.406000	0.81754	0.591000	0.81541	.	.	.	.	none		0.637	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205	Intron	A	113474213	G	A	113474213	5	1	68	1	0	0	0	0	0	0	1	0	1119	1014	35	2	704	2	ATP11A	13	113474213	Splice_Site	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	14806418	113474213	1695665	60	4525											
ZSCAN29	146050	hgsc.bcm.edu	37	chr15	43653718	43653718	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagtcaagacatttataaggTttctctccagtgtggattct	10	15	8	8	0	3	1	1	0	2	1	5	2	4	2	1	2	0	1	1	2	3	5			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr15:43653718T>C	ENST00000396976.2	-	5	2246	c.2112A>G	c.(2110-2112)aaA>aaG	p.K704K	ZSCAN29_ENST00000568898.1_Silent_p.K314K|ZSCAN29_ENST00000562072.1_3'UTR|ZSCAN29_ENST00000396972.1_Silent_p.K315K	NM_152455.3	NP_689668.3	Q8IWY8	ZSC29_HUMAN	zinc finger and SCAN domain containing 29	704					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)		ATTTATAAGGTTTCTCTCCAG	0.438																																					p.K704K		Atlas-SNP	.											.	ZSCAN29	57	.	0			c.A2112G						PASS	.						60	57	58					15																	43653718		2201	4299	6500	SO:0001819	synonymous_variant	146050	exon5			ATAAGGTTTCTCT	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.2112A>G	chr15.hg19:g.43653718T>C		64.0	0.0	.		155.0	43.0	.	NM_152455	B3KVB9|Q32M75|Q32M76|Q8NA40	Silent	SNP	ENST00000396976.2	hg19	CCDS10095.2																																																																																			.	.	.	none		0.438	ZSCAN29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253278.1	NM_152455		C	43653718	T	C	43653718	2	2	68	1	0	0	0	0	0	0	0	1	18248	1722	60	3		3	ZSCAN29	15	43653718	Silent	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10		43653718	58877674	61	4526											
FAM154B	283726	hgsc.bcm.edu	37	chr15	82575198	82575198	+	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	gccacatgaattgatcccaaCagagagttgcaaacctttaa	15	9	7	10	0	0	3	0	2	0	1	1	4	1	3	3	0	3	2	3	0	4	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr15:82575198C>A	ENST00000339465.5	+	3	1061	c.992C>A	c.(991-993)aCa>aAa	p.T331K	FAM154B_ENST00000565501.1_3'UTR|FAM154B_ENST00000427381.2_Missense_Mutation_p.T316K	NM_001008226.1	NP_001008227.1	Q658L1	F154B_HUMAN	family with sequence similarity 154, member B	331										autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(2)	19						TTGATCCCAACAGAGAGTTGC	0.388																																					p.T331K		Atlas-SNP	.											.	FAM154B	50	.	0			c.C992A						PASS	.						74	74	74					15																	82575198		2203	4300	6503	SO:0001583	missense	283726	exon3			TCCCAACAGAGAG	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.992C>A	chr15.hg19:g.82575198C>A	ENSP00000340445:p.Thr331Lys	171.0	0.0	.		402.0	132.0	.	NM_001008226	B4E2M2	Missense_Mutation	SNP	ENST00000339465.5	hg19	CCDS32310.1	.	.	.	.	.	.	.	.	.	.	C	12.76	2.034412	0.35893	.	.	ENSG00000188659	ENST00000339465;ENST00000427381	T;T	0.16743	2.32;2.32	4.22	3.28	0.37604	.	0.172782	0.36628	N	0.002496	T	0.36248	0.0960	M	0.82323	2.585	0.09310	N	0.999996	D;D	0.76494	0.999;0.984	D;P	0.68765	0.96;0.881	T	0.24693	-1.0153	10	0.14656	T	0.56	-8.4012	8.8098	0.34961	0.0:0.7627:0.1525:0.0849	.	316;331	B4E2M2;Q658L1	.;F154B_HUMAN	K	331;316	ENSP00000340445:T331K;ENSP00000403743:T316K	ENSP00000340445:T331K	T	+	2	0	FAM154B	80362253	0.114000	0.22134	0.015000	0.15790	0.341000	0.28922	0.879000	0.28146	0.867000	0.35654	0.404000	0.27445	ACA	.	.	.	none		0.388	FAM154B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419644.1	NM_001008226		A	82575198	C	A	82575198	3	1	68	1	0	0	0	0	1	0	0	0	5468	478	17	4	1002	4	FAM154B	15	82575198	Missense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	38921480	82575198	19956194	62	4527											
ALPK3	57538	hgsc.bcm.edu	37	chr15	85407685	85407685	+	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	atgtttaggatcatcccactGtatctgatctaccggcctgc	8	13	8	12	1	3	1	1	1	2	0	4	2	4	2	3	2	2	2	3	2	3	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr15:85407685G>A	ENST00000258888.5	+	12	5285	c.5118G>A	c.(5116-5118)ctG>ctA	p.L1706L		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1706	Alpha-type protein kinase. {ECO:0000255|PROSITE-ProRule:PRU00501}.				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)			TCATCCCACTGTATCTGATCT	0.512																																					p.L1706L		Atlas-SNP	.											.	ALPK3	289	.	0			c.G5118A						PASS	.						94	84	87					15																	85407685		2203	4299	6502	SO:0001819	synonymous_variant	57538	exon12			CCCACTGTATCTG	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.5118G>A	chr15.hg19:g.85407685G>A		55.0	0.0	.		122.0	47.0	.	NM_020778	Q9P2L6	Silent	SNP	ENST00000258888.5	hg19	CCDS10333.1																																																																																			.	.	.	none		0.512	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778		A	85407685	G	A	85407685	2	1	68	1	0	0	0	0	0	0	0	1	546	1364	48	2		2	ALPK3	15	85407685	Silent	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	2832487	85407685	17123707	63	4528											
NDUFB10	4716	hgsc.bcm.edu	37	chr16	2011289	2011289	+	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	cgaaatgcagtggaagagggActagtacgtgagccatgctg	12	7	15	7	2	0	2	0	1	0	1	0	5	0	4	1	2	4	3	1	2	4	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr16:2011289A>T	ENST00000268668.6	+	2	383	c.266A>T	c.(265-267)gAc>gTc	p.D89V	SNORA64_ENST00000384674.1_RNA|SNORA10_ENST00000384084.1_RNA|NDUFB10_ENST00000543683.2_Missense_Mutation_p.D89V|NDUFB10_ENST00000569148.1_Intron	NM_004548.2	NP_004539.1	O96000	NDUBA_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 10, 22kDa	89					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			lung(1)|urinary_tract(1)	2						TGGAAGAGGGACTAGTACGTG	0.567																																					p.D89V		Atlas-SNP	.											.	NDUFB10	17	.	0			c.A266T						PASS	.						194	142	160					16																	2011289		2199	4300	6499	SO:0001583	missense	4716	exon2			AGAGGGACTAGTA	AF044954	CCDS10451.1	16p13.3	2011-07-04	2002-08-29		ENSG00000140990	ENSG00000140990		"Mitochondrial respiratory chain complex / Complex I"	7696	protein-coding gene	gene with protein product	"complex I PDSW subunit"	603843	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 10 (22kD, PDSW)"			9763677, 9878551	Standard	NM_004548		Approved	PDSW	uc002cni.2	O96000	OTTHUMG00000128709	ENST00000268668.6:c.266A>T	chr16.hg19:g.2011289A>T	ENSP00000268668:p.Asp89Val	38.0	0.0	.		94.0	32.0	.	NM_004548	Q96II6	Missense_Mutation	SNP	ENST00000268668.6	hg19	CCDS10451.1	.	.	.	.	.	.	.	.	.	.	A	17.97	3.519366	0.64634	.	.	ENSG00000140990	ENST00000268668;ENST00000543683	.	.	.	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.81767	0.4892	M	0.88105	2.93	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.85631	0.1270	9	0.87932	D	0	-38.553	14.1338	0.65273	1.0:0.0:0.0:0.0	.	89;89	Q96II6;O96000	.;NDUBA_HUMAN	V	89	.	ENSP00000268668:D89V	D	+	2	0	NDUFB10	1951290	1.000000	0.71417	1.000000	0.80357	0.253000	0.25986	8.564000	0.90726	1.936000	0.56123	0.533000	0.62120	GAC	.	.	.	none		0.567	NDUFB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250614.2	NM_004548		T	2011289	A	T	2011289	3	4	68	1	0	0	0	0	1	0	0	0	10286	275	10	5	272	5	NDUFB10	16	2011289	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10		2011289	88343464	64	4529											
TRAP1	10131	hgsc.bcm.edu	37	chr16	3712967	3712967	+	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	ttctctgataggcactcggcGgctgcggaagagcaggcgac	8	7	15	11	4	1	2	0	1	1	1	3	4	1	3	0	5	2	3	0	5	2	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr16:3712967G>A	ENST00000246957.5	-	15	1798	c.1710C>T	c.(1708-1710)gcC>gcT	p.A570A	DNASE1_ENST00000575152.1_3'UTR|TRAP1_ENST00000538171.1_Splice_Site_p.A517A|DNASE1_ENST00000414110.2_Intron|TRAP1_ENST00000575671.1_Splice_Site_p.A361A	NM_016292.2	NP_057376.2	Q12931	TRAP1_HUMAN	TNF receptor-associated protein 1	570					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)				GGCACTCGGCGGCTGCGGAAG	0.642																																					p.A570A		Atlas-SNP	.											.	TRAP1	53	.	0			c.C1710T						PASS	.						60	46	51					16																	3712967		2197	4300	6497	SO:0001630	splice_region_variant	10131	exon15			CTCGGCGGCTGCG	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.1709-1C>T	chr16.hg19:g.3712967G>A		12.0	0.0	.		27.0	10.0	.	NM_016292	B4DR68|D3DUC8|F5H897|O43642|O75235|Q9UHL5	Silent	SNP	ENST00000246957.5	hg19	CCDS10508.1																																																																																			.	.	.	none		0.642	TRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251586.2	NM_016292	Silent	A	3712967	G	A	3712967	5	1	68	1	0	0	0	0	0	0	1	0	16467	1130	39	1	420	1	TRAP1	16	3712967	Splice_Site	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	1701678	3712967	86641786	65	4530											
ZZEF1	23140	hgsc.bcm.edu	37	chr17	3980188	3980189	+	Frame_Shift_Ins	INS	-	-	T																															cgagctgccattgaaaacacINStgagttacataatctttcta																										TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr17:3980188_3980189insT	ENST00000381638.2	-	20	3208_3209	c.3084_3085insA	c.(3082-3087)tcagtgfs	p.V1029fs	ZZEF1_ENST00000574474.1_5'UTR	NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	1029							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						ATTGAAAACACTGAGTTACATA	0.47																																					p.V1029fs		Atlas-Indel,Pindel	.											.	ZZEF1	195	.	0			c.3085_3086insA						PASS	.																																			SO:0001589	frameshift_variant	23140	exon20			.	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.3085dupA	chr17.hg19:g.3980189_3980189dupT	ENSP00000371051:p.Val1029fs	71.0	0.0	0		222.0	121.0	0.545045	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Frame_Shift_Ins	INS	ENST00000381638.2	hg19	CCDS11043.1																																																																																			.	.	.	none		0.47	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		T	3980189	-	T	3980188	7	5	68	1	0	1	1	0	0	0	0	0	18267	565	20	0	5944	0	ZZEF1	17	3980188	Frame_Shift_Ins	INS	-	TCGA-A4-A6HP-01A-11D-A31X-10		3980188	77215022	66	4531											
KDM6B	23135	hgsc.bcm.edu	37	chr17	7748926	7748926	+	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	gctgcacgggaagcctttgcCcttgggggcctgagctgtgc	4	9	16	12	1	0	1	0	1	0	0	0	2	0	2	3	3	5	3	3	3	1	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr17:7748926C>A	ENST00000448097.2	+	4	385	c.54C>A	c.(52-54)gcC>gcA	p.A18A	KDM6B_ENST00000254846.5_Silent_p.A18A			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	18					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						AAGCCTTTGCCCTTGGGGGCC	0.642																																					p.A18A		Atlas-SNP	.											.	KDM6B	95	.	0			c.C54A						PASS	.						56	59	58					17																	7748926		2203	4300	6503	SO:0001819	synonymous_variant	23135	exon4			CTTTGCCCTTGGG	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.54C>A	chr17.hg19:g.7748926C>A		72.0	0.0	.		184.0	40.0	.	NM_001080424	C9IZ40|Q96G33	Silent	SNP	ENST00000448097.2	hg19																																																																																				.	.	.	none		0.642	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272		A	7748926	C	A	7748926	2	1	68	1	0	0	0	0	0	0	0	1	8145	610	22	4		4	KDM6B	17	7748926	Silent	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	3768738	7748926	73446284	67	4532											
ELAC2	60528	hgsc.bcm.edu	37	chr17	12898190	12898190	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcttgcagtgccgcaccagAcaggtctgaaactgaaaggg	11	7	13	10	1	1	3	0	2	1	1	1	3	1	3	2	2	4	3	2	2	2	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr17:12898190A>G	ENST00000338034.4	-	21	2159	c.1920T>C	c.(1918-1920)tgT>tgC	p.C640C	ELAC2_ENST00000395962.2_Silent_p.C621C|ELAC2_ENST00000426905.3_Silent_p.C600C	NM_018127.6|NM_173717.1	NP_060597.4|NP_776065.1	Q9BQ52	RNZ2_HUMAN	elaC ribonuclease Z 2	640					mitochondrial tRNA 3'-trailer cleavage, endonucleolytic (GO:0072684)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|skin(1)	23						GCCGCACCAGACAGGTCTGAA	0.622																																					p.C640C		Atlas-SNP	.											.	ELAC2	48	.	0			c.T1920C						PASS	.						72	78	76					17																	12898190		2203	4300	6503	SO:0001819	synonymous_variant	60528	exon21			CACCAGACAGGTC	AF304370	CCDS11164.1, CCDS54093.1	17p11.2	2013-05-24	2013-05-24		ENSG00000006744	ENSG00000006744	3.1.26.11		14198	protein-coding gene	gene with protein product	"tRNase Z (long form)"	605367	"elaC (E. coli) homolog 2", "elaC homolog 2 (E. coli)"			10986046, 16636667, 21559454	Standard	NM_018127		Approved	FLJ10530, HPC2	uc010vvr.2	Q9BQ52	OTTHUMG00000058764	ENST00000338034.4:c.1920T>C	chr17.hg19:g.12898190A>G		41.0	0.0	.		121.0	60.0	.	NM_018127	B4DPL9|Q6IA94|Q9HAS8|Q9HAS9|Q9NVT1	Silent	SNP	ENST00000338034.4	hg19	CCDS11164.1																																																																																			.	.	.	none		0.622	ELAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129934.5			G	12898190	A	G	12898190	2	3	68	1	0	0	0	0	0	0	0	1	5049	273	10	3		3	ELAC2	17	12898190	Silent	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	5149264	12898190	68297020	68	4533											
TBC1D28	254272	hgsc.bcm.edu	37	chr17	18541949	18541949	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttaccttcttggtgctcctAtattttgtccagtctgcaag	6	17	8	10	0	2	0	0	0	2	0	4	0	4	0	3	1	3	3	3	1	4	7			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr17:18541949A>G	ENST00000345096.4	-	6	963	c.264T>C	c.(262-264)taT>taC	p.Y88Y	TBC1D28_ENST00000405044.1_Silent_p.Y88Y			Q2M2D7	TBC28_HUMAN	TBC1 domain family, member 28	88							Rab GTPase activator activity (GO:0005097)			breast(1)|large_intestine(5)|lung(2)|ovary(1)	9						TGGTGCTCCTATATTTTGTCC	0.542																																					p.Y88Y		Atlas-SNP	.											.	TBC1D28	14	.	0			c.T264C						PASS	.						120	117	118					17																	18541949		1942	4126	6068	SO:0001819	synonymous_variant	254272	exon7			GCTCCTATATTTT		CCDS42273.1	17p11.2	2008-10-27			ENSG00000189375	ENSG00000189375			26858	protein-coding gene	gene with protein product							Standard	NM_001039397		Approved	FLJ40244	uc002gud.2	Q2M2D7	OTTHUMG00000059054	ENST00000345096.4:c.264T>C	chr17.hg19:g.18541949A>G		59.0	0.0	.		142.0	60.0	.	NM_001039397	Q2M2E1	Silent	SNP	ENST00000345096.4	hg19	CCDS42273.1																																																																																			.	.	.	none		0.542	TBC1D28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130672.2	NM_001039397		G	18541949	A	G	18541949	2	3	68	1	0	0	0	0	0	0	0	1	15629	456	16	3		3	TBC1D28	17	18541949	Silent	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	5643759	18541949	62653261	69	4534											
MSL1	339287	hgsc.bcm.edu	37	chr17	38282491	38282491	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcagctggtaaagaaggataAcgagaaagaaaggcacaagc	19	3	13	6	1	0	3	0	0	0	3	0	5	0	4	0	3	3	4	0	3	7	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr17:38282491A>G	ENST00000398532.4	+	2	1139	c.824A>G	c.(823-825)aAc>aGc	p.N275S	MSL1_ENST00000578648.1_Missense_Mutation_p.N275S|MSL1_ENST00000577454.1_Missense_Mutation_p.N275S|MSL1_ENST00000579565.1_Missense_Mutation_p.N12S	NM_001012241.1	NP_001012241.1	Q68DK7	MSL1_HUMAN	male-specific lethal 1 homolog (Drosophila)	275					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						AAGAAGGATAACGAGAAAGAA	0.428																																					p.N12S		Atlas-SNP	.											.	MSL1	21	.	0			c.A35G						PASS	.						98	98	98					17																	38282491		1949	4139	6088	SO:0001583	missense	339287	exon3			AGGATAACGAGAA		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.824A>G	chr17.hg19:g.38282491A>G	ENSP00000381543:p.Asn275Ser	92.0	0.0	.		231.0	110.0	.	NM_001012241	Q0VF46|Q69Z03	Missense_Mutation	SNP	ENST00000398532.4	hg19		.	.	.	.	.	.	.	.	.	.	A	11.43	1.637733	0.29157	.	.	ENSG00000188895	ENST00000339569;ENST00000398532	.	.	.	5.79	5.79	0.91817	.	0.270557	0.44688	D	0.000434	T	0.22820	0.0551	N	0.19112	0.55	0.26940	N	0.966276	B	0.16396	0.017	B	0.18263	0.021	T	0.28776	-1.0033	9	0.05436	T	0.98	-11.0278	8.4872	0.33078	0.8546:0.0:0.1454:0.0	.	275	Q68DK7	MSL1_HUMAN	S	12;275	.	ENSP00000341409:N12S	N	+	2	0	MSL1	35536017	0.994000	0.37717	1.000000	0.80357	0.965000	0.64279	2.451000	0.44952	2.208000	0.71279	0.533000	0.62120	AAC	.	.	.	none		0.428	MSL1-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000447409.2	NM_001012241		G	38282491	A	G	38282491	3	3	68	1	0	0	0	0	1	0	0	0	9884	43	2	3	37	3	MSL1	17	38282491	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	19740542	38282491	42912719	70	4535											
C17orf64	124773	hgsc.bcm.edu	37	chr17	58503225	58503225	+	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	tgcgccatgccaagggcctgGatcaggacaccttcaaaact	11	7	10	13	1	2	0	2	0	0	0	2	2	2	2	4	3	3	0	4	3	3	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr17:58503225G>A	ENST00000269127.4	+	2	217	c.133G>A	c.(133-135)Gat>Aat	p.D45N		NM_181707.2	NP_859058.2	Q86WR6	CQ064_HUMAN	chromosome 17 open reading frame 64	45										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)			CAAGGGCCTGGATCAGGACAC	0.587																																					p.D45N		Atlas-SNP	.											.	C17orf64	19	.	0			c.G133A						PASS	.						49	50	50					17																	58503225		692	1591	2283	SO:0001583	missense	124773	exon2			GGCCTGGATCAGG	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.133G>A	chr17.hg19:g.58503225G>A	ENSP00000269127:p.Asp45Asn	64.0	0.0	.		118.0	62.0	.	NM_181707	Q8IY87	Missense_Mutation	SNP	ENST00000269127.4	hg19	CCDS32698.2	.	.	.	.	.	.	.	.	.	.	G	8.915	0.959686	0.18507	.	.	ENSG00000141371	ENST00000428000;ENST00000269127	.	.	.	5.8	1.57	0.23409	.	1.190680	0.06014	N	0.650076	T	0.35422	0.0931	L	0.38838	1.175	0.09310	N	0.999999	B	0.22983	0.078	B	0.25614	0.062	T	0.35475	-0.9787	9	0.51188	T	0.08	0.2409	8.0582	0.30617	0.4133:0.0:0.5867:0.0	.	45	Q86WR6	CQ064_HUMAN	N	39;45	.	ENSP00000269127:D45N	D	+	1	0	C17orf64	55858007	0.078000	0.21339	0.143000	0.22291	0.070000	0.16714	0.157000	0.16402	0.087000	0.17167	-0.136000	0.14681	GAT	.	.	.	none		0.587	C17orf64-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000347743.1	NM_181707		A	58503225	G	A	58503225	3	1	68	1	0	0	0	0	1	0	0	0	1874	1174	41	2	139	2	C17orf64	17	58503225	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10	20220734	58503225	22691985	71	4536											
PIAS2	9063	hgsc.bcm.edu	37	chr18	44416377	44416377	+	Missense_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	cacacacaggacaaatccagGtgggctttttctcattcatt	11	12	7	11	0	2	0	2	0	1	0	4	1	3	1	1	3	0	1	1	3	1	4			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr18:44416377G>A	ENST00000585916.1	-	9	1144	c.1145C>T	c.(1144-1146)aCc>aTc	p.T382I	PIAS2_ENST00000545673.1_Missense_Mutation_p.T92I|PIAS2_ENST00000324794.7_Missense_Mutation_p.T382I	NM_004671.3	NP_004662.2	O75928	PIAS2_HUMAN	protein inhibitor of activated STAT, 2	382					androgen receptor signaling pathway (GO:0030521)|negative regulation of androgen receptor signaling pathway (GO:0060766)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein sumoylation (GO:0016925)|regulation of osteoblast differentiation (GO:0045667)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|SUMO ligase activity (GO:0019789)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	22						ACAAATCCAGGTGGGCTTTTT	0.408																																					p.T382I		Atlas-SNP	.											.	PIAS2	85	.	0			c.C1145T						PASS	.						118	114	115					18																	44416377		2203	4300	6503	SO:0001583	missense	9063	exon9			ATCCAGGTGGGCT	AF077953	CCDS32824.1, CCDS32825.1	18q12.1-q12.3	2011-10-11				ENSG00000078043		"Zinc fingers, MIZ-type"	17311	protein-coding gene	gene with protein product	"zinc finger, MIZ-type containing 4"	603567				9724754, 9256341	Standard	NM_004671		Approved	PIASX-BETA, miz, PIASX-ALPHA, ZMIZ4	uc002lck.3	O75928		ENST00000585916.1:c.1145C>T	chr18.hg19:g.44416377G>A	ENSP00000465676:p.Thr382Ile	153.0	0.0	.		329.0	44.0	.	NM_173206	O75927|Q96BT5|Q96KE3	Missense_Mutation	SNP	ENST00000585916.1	hg19	CCDS32824.1	.	.	.	.	.	.	.	.	.	.	G	32	5.124311	0.94429	.	.	ENSG00000078043	ENST00000398654;ENST00000262161;ENST00000398651;ENST00000545673;ENST00000324794	T;T	0.53640	0.61;1.12	5.62	5.62	0.85841	Zinc finger, MIZ-type (2);	0.000000	0.85682	D	0.000000	T	0.74876	0.3774	M	0.87038	2.855	0.80722	D	1	D;D;D;D;D	0.89917	0.998;1.0;1.0;0.999;1.0	D;D;D;D;D	0.97110	0.996;1.0;0.994;0.992;1.0	T	0.78971	-0.1993	10	0.87932	D	0	-11.3089	19.6407	0.95757	0.0:0.0:1.0:0.0	.	92;386;382;382;382	B4DGW0;O75928-3;Q2TA77;O75928-2;O75928	.;.;.;.;PIAS2_HUMAN	I	382;382;378;92;382	ENSP00000443238:T92I;ENSP00000317163:T382I	ENSP00000262161:T382I	T	-	2	0	PIAS2	42670375	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.864000	0.99589	2.640000	0.89533	0.460000	0.39030	ACC	.	.	.	none		0.408	PIAS2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445656.2	NM_004671		A	44416377	G	A	44416377	3	1	68	1	0	0	0	0	1	0	0	0	11883	1261	44	2	819	2	PIAS2	18	44416377	Missense_Mutation	SNP	G	TCGA-A4-A6HP-01A-11D-A31X-10		44416377	33660871	72	4537											
ILVBL	10994	hgsc.bcm.edu	37	chr19	15226103	15226103	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgcggaagtccgtcctcccaAtgaggatgttgaccacaacc	10	7	10	14	3	0	2	0	2	0	0	3	4	3	4	5	2	1	1	5	2	3	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr19:15226103A>G	ENST00000263383.3	-	16	1998	c.1859T>C	c.(1858-1860)aTt>aCt	p.I620T	ILVBL_ENST00000534378.1_Missense_Mutation_p.I513T	NM_006844.3	NP_006835.2	A1L0T0	ILVBL_HUMAN	ilvB (bacterial acetolactate synthase)-like	620						integral component of membrane (GO:0016021)|membrane (GO:0016020)	magnesium ion binding (GO:0000287)|thiamine pyrophosphate binding (GO:0030976)|transferase activity (GO:0016740)			NS(3)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)	26						CGTCCTCCCAATGAGGATGTT	0.607																																					p.I620T		Atlas-SNP	.											.	ILVBL	54	.	0			c.T1859C						PASS	.						138	103	115					19																	15226103		2203	4300	6503	SO:0001583	missense	10994	exon16			CTCCCAATGAGGA	U61263	CCDS12325.1	19p13.1	2008-07-16			ENSG00000105135	ENSG00000105135			6041	protein-coding gene	gene with protein product	"acetolactate synthase homolog"	605770				8954801	Standard	NM_006844		Approved	209L8, AHAS, ILV2H, MGC1269, FLJ39061, MGC19535	uc002nam.3	A1L0T0	OTTHUMG00000165630	ENST00000263383.3:c.1859T>C	chr19.hg19:g.15226103A>G	ENSP00000263383:p.Ile620Thr	58.0	0.0	.		76.0	24.0	.	NM_006844	O43341|Q96F08|Q99651|Q9BWN5|Q9UEB2	Missense_Mutation	SNP	ENST00000263383.3	hg19	CCDS12325.1	.	.	.	.	.	.	.	.	.	.	A	19.86	3.905085	0.72868	.	.	ENSG00000105135	ENST00000263383	T	0.42900	0.96	5.37	5.37	0.77165	.	0.056671	0.64402	D	0.000002	T	0.58264	0.2110	M	0.68952	2.095	0.80722	D	1	D	0.71674	0.998	D	0.63877	0.919	T	0.59542	-0.7435	10	0.46703	T	0.11	-18.752	11.7697	0.51951	1.0:0.0:0.0:0.0	.	620	A1L0T0	ILVBL_HUMAN	T	620	ENSP00000263383:I620T	ENSP00000263383:I620T	I	-	2	0	ILVBL	15087103	1.000000	0.71417	0.998000	0.56505	0.840000	0.47671	6.822000	0.75277	2.044000	0.60594	0.533000	0.62120	ATT	.	.	.	none		0.607	ILVBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385439.1	NM_006844		G	15226103	A	G	15226103	3	3	68	1	0	0	0	0	1	0	0	0	7722	101	4	3	43	3	ILVBL	19	15226103	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10		15226103	43902880	73	4538											
ZNF536	9745	hgsc.bcm.edu	37	chr19	31040126	31040126	+	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	ctgtctgccctcagcaaagaCagcagcagcgatggcgggga	10	5	14	12	2	2	1	1	0	1	1	2	3	2	2	1	3	5	3	1	3	1	0	rs545401755		TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr19:31040126C>G	ENST00000355537.3	+	4	3747	c.3600C>G	c.(3598-3600)gaC>gaG	p.D1200E		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	1200					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)					TCAGCAAAGACAGCAGCAGCG	0.592																																					p.D1200E		Atlas-SNP	.											.	ZNF536	424	.	0			c.C3600G						PASS	.						62	63	63					19																	31040126		2203	4300	6503	SO:0001583	missense	9745	exon4			CAAAGACAGCAGC		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.3600C>G	chr19.hg19:g.31040126C>G	ENSP00000347730:p.Asp1200Glu	59.0	0.0	.		81.0	30.0	.	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	hg19	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	C	0.147	-1.095522	0.01858	.	.	ENSG00000198597	ENST00000355537	T	0.08546	3.08	5.59	3.11	0.35812	.	0.444542	0.25789	N	0.028284	T	0.03871	0.0109	N	0.12746	0.255	0.21675	N	0.999597	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.44298	-0.9337	10	0.13108	T	0.6	-38.7005	6.6261	0.22830	0.2337:0.5954:0.0:0.1709	.	1200;1200	A7E228;O15090	.;ZN536_HUMAN	E	1200	ENSP00000347730:D1200E	ENSP00000347730:D1200E	D	+	3	2	ZNF536	35731966	0.207000	0.23482	0.966000	0.40874	0.051000	0.14879	0.146000	0.16180	1.319000	0.45190	0.655000	0.94253	GAC	.	.	.	none		0.592	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		G	31040126	C	G	31040126	3	3	68	1	0	0	0	0	1	0	0	0	17986	477	17	4	3610	4	ZNF536	19	31040126	Missense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	15814023	31040126	28088857	74	4539											
ZNF146	7705	hgsc.bcm.edu	37	chr19	36727612	36727612	+	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	aaggaaaacctccttacgcaCcagaaaattcacactggaga	17	6	7	11	1	1	2	1	0	0	2	2	4	2	3	3	2	2	1	3	2	6	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr19:36727612C>A	ENST00000443387.2	+	4	1262	c.270C>A	c.(268-270)caC>caA	p.H90Q	ZNF565_ENST00000355114.5_Intron|ZNF146_ENST00000456324.1_Missense_Mutation_p.H90Q	NM_007145.2	NP_009076.2	Q15072	OZF_HUMAN	zinc finger protein 146	90					regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	11	Esophageal squamous(110;0.162)					TCCTTACGCACCAGAAAATTC	0.403																																					p.H90Q		Atlas-SNP	.											.	ZNF146	32	.	0			c.C270A						PASS	.						67	72	70					19																	36727612		2203	4300	6503	SO:0001583	missense	7705	exon3			TACGCACCAGAAA	X70394	CCDS12492.1	19q13.1	2013-01-08				ENSG00000167635		"Zinc fingers, C2H2-type"	12931	protein-coding gene	gene with protein product		601505				10449921, 8641144	Standard	NM_001099639		Approved	OZF	uc010eeu.3	Q15072		ENST00000443387.2:c.270C>A	chr19.hg19:g.36727612C>A	ENSP00000392095:p.His90Gln	90.0	0.0	.		190.0	79.0	.	NM_001099638	Q2TB94	Missense_Mutation	SNP	ENST00000443387.2	hg19	CCDS12492.1	.	.	.	.	.	.	.	.	.	.	C	15.56	2.870414	0.51588	.	.	ENSG00000167635	ENST00000443387;ENST00000456324	D;D	0.86865	-2.18;-2.18	4.46	3.34	0.38264	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.41396	D	0.000891	D	0.94135	0.8119	H	0.95402	3.665	0.33426	D	0.580462	D	0.62365	0.991	D	0.73708	0.981	D	0.94447	0.7664	10	0.87932	D	0	-10.1539	6.9293	0.24432	0.0:0.2248:0.0:0.7752	.	90	Q15072	OZF_HUMAN	Q	90	ENSP00000392095:H90Q;ENSP00000400391:H90Q	ENSP00000392095:H90Q	H	+	3	2	ZNF146	41419452	0.874000	0.30092	1.000000	0.80357	0.991000	0.79684	-0.067000	0.11579	0.946000	0.37632	-0.355000	0.07637	CAC	.	.	.	none		0.403	ZNF146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451706.1	NM_007145		A	36727612	C	A	36727612	3	1	68	1	0	0	0	0	1	0	0	0	17745	506	18	4	272	4	ZNF146	19	36727612	Missense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	5687486	36727612	22401371	75	4540											
GYS1	2997	hgsc.bcm.edu	37	chr19	49485593	49485593	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aactcatagcggccggcgatAaagaagtataaggtcttgtc	13	9	11	8	3	2	1	1	0	1	1	3	2	2	1	1	3	2	1	1	3	7	5			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr19:49485593A>G	ENST00000323798.3	-	7	1177	c.981T>C	c.(979-981)ttT>ttC	p.F327F	GYS1_ENST00000541188.1_Silent_p.F247F|GYS1_ENST00000263276.6_Silent_p.F263F|GYS1_ENST00000540532.1_Missense_Mutation_p.L208S|GYS1_ENST00000544287.1_5'UTR	NM_002103.4	NP_002094.2	P13807	GYS1_HUMAN	glycogen synthase 1 (muscle)	327					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|heart development (GO:0007507)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|inclusion body (GO:0016234)|membrane (GO:0016020)	glucose binding (GO:0005536)|glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000164)|all cancers(93;0.000226)|GBM - Glioblastoma multiforme(486;0.00561)|Epithelial(262;0.0286)		GGCCGGCGATAAAGAAGTATA	0.542																																					p.F327F		Atlas-SNP	.											.	GYS1	59	.	0			c.T981C						PASS	.						88	79	82					19																	49485593		2203	4300	6503	SO:0001819	synonymous_variant	2997	exon7			GGCGATAAAGAAG		CCDS12747.1, CCDS54292.1	19q13.3	2013-02-22			ENSG00000104812	ENSG00000104812	2.4.1.11	"Glycosyltransferase group 1 domain containing"	4706	protein-coding gene	gene with protein product		138570		GYS			Standard	NM_002103		Approved	GSY	uc002plp.3	P13807	OTTHUMG00000150723	ENST00000323798.3:c.981T>C	chr19.hg19:g.49485593A>G		82.0	0.0	.		171.0	62.0	.	NM_002103	Q9BTT9	Silent	SNP	ENST00000323798.3	hg19	CCDS12747.1	.	.	.	.	.	.	.	.	.	.	A	15.40	2.821993	0.50739	.	.	ENSG00000104812	ENST00000540532	T	0.27890	1.64	5.1	-3.84	0.04256	.	.	.	.	.	T	0.34366	0.0895	.	.	.	0.22754	N	0.998773	.	.	.	.	.	.	T	0.42965	-0.9420	6	0.41790	T	0.15	-14.4659	15.6467	0.77061	0.234:0.0:0.766:0.0	.	.	.	.	S	208	ENSP00000445197:L208S	ENSP00000445197:L208S	L	-	2	0	GYS1	54177405	1.000000	0.71417	0.849000	0.33467	0.997000	0.91878	1.654000	0.37334	-0.742000	0.04790	0.528000	0.53228	TTA	.	.	.	none		0.542	GYS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319791.1	NM_002103		G	49485593	A	G	49485593	2	3	68	1	0	0	0	0	0	0	0	1	6919	359	13	3		3	GYS1	19	49485593	Silent	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	12757981	49485593	9643390	76	4541											
TMEM86B	255043	hgsc.bcm.edu	37	chr19	55740079	55740079	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggctgagcagtgagtctTcagggtctgccccgctttgc	4	11	14	12	1	3	2	1	2	2	0	3	2	3	2	2	2	3	3	2	2	0	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr19:55740079T>C	ENST00000327042.4	-	1	553	c.31A>G	c.(31-33)Aag>Gag	p.K11E	AC010327.2_ENST00000598855.1_3'UTR	NM_173804.4	NP_776165.3	Q8N661	TM86B_HUMAN	transmembrane protein 86B	11					ether lipid metabolic process (GO:0046485)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alkenylglycerophosphocholine hydrolase activity (GO:0047408)|alkenylglycerophosphoethanolamine hydrolase activity (GO:0047409)			skin(2)	2			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0443)		CAGTGAGTCTTCAGGGTCTGC	0.672																																					p.K11E		Atlas-SNP	.											.	TMEM86B	12	.	0			c.A31G						PASS	.						25	26	26					19																	55740079		2203	4299	6502	SO:0001583	missense	255043	exon1			GAGTCTTCAGGGT	BC023000	CCDS12920.1	19q13.42	2011-07-12					3.3.2.2, 3.3.2.5		28448	protein-coding gene	gene with protein product						21515882	Standard	NM_173804		Approved	MGC30208	uc002qju.3	Q8N661		ENST00000327042.4:c.31A>G	chr19.hg19:g.55740079T>C	ENSP00000321038:p.Lys11Glu	68.0	0.0	.		107.0	40.0	.	NM_173804		Missense_Mutation	SNP	ENST00000327042.4	hg19	CCDS12920.1	.	.	.	.	.	.	.	.	.	.	T	8.776	0.926998	0.18056	.	.	ENSG00000180089	ENST00000327042	T	0.22743	1.94	4.76	-1.37	0.09056	.	2.056380	0.01961	N	0.043375	T	0.12944	0.0314	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.31223	-0.9951	10	0.33940	T	0.23	.	11.2263	0.48886	0.0:0.5941:0.0:0.4059	.	11	Q8N661	TM86B_HUMAN	E	11	ENSP00000321038:K11E	ENSP00000321038:K11E	K	-	1	0	TMEM86B	60431891	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.228000	0.09114	-0.525000	0.06391	0.379000	0.24179	AAG	.	.	.	none		0.672	TMEM86B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452659.1	NM_173804		C	55740079	T	C	55740079	3	2	68	1	0	0	0	0	1	0	0	0	16221	1792	62	3	661	3	TMEM86B	19	55740079	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	6254486	55740079	3388904	77	4542											
AHCY	191	hgsc.bcm.edu	37	chr20	32878681	32878681	+	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	cttgccggcaatcatcacatCtgtggcccgcttgatgccat	7	11	9	14	2	3	1	2	1	1	0	3	1	3	1	3	2	2	2	3	2	1	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr20:32878681C>T	ENST00000217426.2	-	6	699	c.622G>A	c.(622-624)Gat>Aat	p.D208N	AHCY_ENST00000538132.1_Missense_Mutation_p.D180N|AHCY_ENST00000468908.1_5'Flank	NM_000687.2	NP_000678.1	P23526	SAHH_HUMAN	adenosylhomocysteinase	208					cellular nitrogen compound metabolic process (GO:0034641)|chronic inflammatory response to antigenic stimulus (GO:0002439)|circadian sleep/wake cycle (GO:0042745)|homocysteine biosynthetic process (GO:0071268)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|S-adenosylhomocysteine catabolic process (GO:0019510)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|nucleus (GO:0005634)	adenosylhomocysteinase activity (GO:0004013)|adenyl nucleotide binding (GO:0030554)|NAD binding (GO:0051287)			endometrium(6)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						ATCATCACATCTGTGGCCCGC	0.587																																					p.D208N		Atlas-SNP	.											.	AHCY	43	.	0			c.G622A						PASS	.						50	47	48					20																	32878681		2203	4300	6503	SO:0001583	missense	191	exon6			TCACATCTGTGGC	M61832	CCDS13233.1, CCDS54457.1	20q11.22	2009-06-12	2009-06-12		ENSG00000101444	ENSG00000101444	3.3.1.1		343	protein-coding gene	gene with protein product		180960	"S-adenosylhomocysteine hydrolase"			7079734, 6580258	Standard	NM_001161766		Approved	SAHH	uc002xai.3	P23526	OTTHUMG00000140098	ENST00000217426.2:c.622G>A	chr20.hg19:g.32878681C>T	ENSP00000217426:p.Asp208Asn	60.0	0.0	.		112.0	42.0	.	NM_000687	A8K307|B3KUN3|E1P5P2|F5H737|Q96A36	Missense_Mutation	SNP	ENST00000217426.2	hg19	CCDS13233.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.766291	0.90020	.	.	ENSG00000101444	ENST00000217426;ENST00000538132	T;T	0.79352	-1.23;-1.26	4.74	3.78	0.43462	S-adenosyl-L-homocysteine hydrolase, NAD binding (1);	0.089011	0.85682	D	0.000000	D	0.86218	0.5880	M	0.67700	2.07	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	D	0.88144	0.2846	10	0.87932	D	0	.	15.2705	0.73696	0.0:0.859:0.141:0.0	.	208	P23526	SAHH_HUMAN	N	208;180	ENSP00000217426:D208N;ENSP00000442820:D180N	ENSP00000217426:D208N	D	-	1	0	AHCY	32342342	1.000000	0.71417	0.977000	0.42913	0.981000	0.71138	7.529000	0.81952	1.333000	0.45449	0.561000	0.74099	GAT	.	.	.	none		0.587	AHCY-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078773.2	NM_000687		T	32878681	C	T	32878681	3	4	68	1	0	0	0	0	1	0	0	0	409	913	32	2	696	2	AHCY	20	32878681	Missense_Mutation	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10		32878681	30146839	78	4543											
KIAA1755	85449	hgsc.bcm.edu	37	chr20	36874404	36874404	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagaaggaagctcagcccaTccccctggaagccagagtcc	11	4	10	16	0	1	2	1	0	0	2	3	4	3	4	6	2	3	1	6	2	3	0			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr20:36874404T>C	ENST00000279024.4	-	2	399	c.128A>G	c.(127-129)gAt>gGt	p.D43G		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	43										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)				GCTCAGCCCATCCCCCTGGAA	0.602																																					p.D43G		Atlas-SNP	.											.	KIAA1755	145	.	0			c.A128G						PASS	.						76	67	70					20																	36874404		2203	4300	6503	SO:0001583	missense	85449	exon2			AGCCCATCCCCCT	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.128A>G	chr20.hg19:g.36874404T>C	ENSP00000279024:p.Asp43Gly	41.0	0.0	.		84.0	4.0	.	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	hg19	CCDS33467.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.846553	0.91277	.	.	ENSG00000149633	ENST00000279024	T	0.39056	1.1	5.4	5.4	0.78164	.	0.000000	0.50627	D	0.000112	T	0.66607	0.2806	M	0.81942	2.565	0.58432	D	0.999998	D	0.89917	1.0	D	0.87578	0.998	T	0.71583	-0.4549	10	0.72032	D	0.01	.	14.9112	0.70758	0.0:0.0:0.0:1.0	.	43	Q5JYT7	K1755_HUMAN	G	43	ENSP00000279024:D43G	ENSP00000279024:D43G	D	-	2	0	KIAA1755	36307818	1.000000	0.71417	0.899000	0.35326	0.867000	0.49689	7.984000	0.88150	2.172000	0.68678	0.533000	0.62120	GAT	.	.	.	none		0.602	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864		C	36874404	T	C	36874404	3	2	68	1	0	0	0	0	1	0	0	0	8264	1435	50	3	3526	3	KIAA1755	20	36874404	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10	3995723	36874404	26151116	79	4544											
SLC13A3	64849	hgsc.bcm.edu	37	chr20	45217868	45217868	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tatcttctgcattggttcttAtctcagatttattcttcctc	6	21	4	10	0	5	1	1	0	5	1	8	1	6	1	1	1	1	2	1	1	3	9			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr20:45217868A>G	ENST00000279027.4	-	7	965	c.947T>C	c.(946-948)aTa>aCa	p.I316T	SLC13A3_ENST00000464518.1_5'Flank|SLC13A3_ENST00000472148.1_Missense_Mutation_p.I269T|SLC13A3_ENST00000396360.1_Missense_Mutation_p.I269T|SLC13A3_ENST00000413164.2_Missense_Mutation_p.I266T|SLC13A3_ENST00000435032.1_5'UTR|SLC13A3_ENST00000290317.5_Missense_Mutation_p.I269T|SLC13A3_ENST00000495082.1_Missense_Mutation_p.I269T|SLC13A3_ENST00000372121.1_Missense_Mutation_p.I266T	NM_001193342.1|NM_022829.5	NP_001180271.1|NP_073740.2	Q8WWT9	S13A3_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	316					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-affinity sodium:dicarboxylate symporter activity (GO:0015362)			breast(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	ATTGGTTCTTATCTCAGATTT	0.488																																					p.I316T		Atlas-SNP	.											.	SLC13A3	88	.	0			c.T947C						PASS	.						115	114	114					20																	45217868		2203	4300	6503	SO:0001583	missense	64849	exon7			GTTCTTATCTCAG	AF154121	CCDS13400.1, CCDS42886.1, CCDS54469.1, CCDS54470.1	20q13.12	2013-05-22			ENSG00000158296	ENSG00000158296		"Solute carriers"	14430	protein-coding gene	gene with protein product		606411				10794676, 10992006	Standard	NM_001011554		Approved	NADC3, SDCT2	uc002xsf.2	Q8WWT9	OTTHUMG00000033042	ENST00000279027.4:c.947T>C	chr20.hg19:g.45217868A>G	ENSP00000279027:p.Ile316Thr	77.0	0.0	.		152.0	35.0	.	NM_022829	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Missense_Mutation	SNP	ENST00000279027.4	hg19	CCDS13400.1	.	.	.	.	.	.	.	.	.	.	A	0.563	-0.844580	0.02671	.	.	ENSG00000158296	ENST00000290317;ENST00000396360;ENST00000279027;ENST00000472148;ENST00000413164;ENST00000495082;ENST00000468915;ENST00000420568;ENST00000372121	T;T;T;T;T;T;T;T;T	0.10099	3.84;3.75;4.1;3.75;3.57;3.84;3.26;2.92;2.91	5.84	4.74	0.60224	.	1.055960	0.07196	N	0.856503	T	0.10981	0.0268	L	0.27053	0.805	0.28449	N	0.916409	P;B;P;P	0.42161	0.772;0.128;0.515;0.571	B;B;B;B	0.43701	0.428;0.144;0.22;0.328	T	0.15178	-1.0446	10	0.13470	T	0.59	-3.1173	10.4316	0.44411	0.9264:0.0:0.0736:0.0	.	266;269;269;316	B4DIR8;Q8WWT9-3;F6WI18;Q8WWT9	.;.;.;S13A3_HUMAN	T	269;269;316;269;266;269;269;229;266	ENSP00000290317:I269T;ENSP00000379648:I269T;ENSP00000279027:I316T;ENSP00000420177:I269T;ENSP00000415852:I266T;ENSP00000419621:I269T;ENSP00000417784:I269T;ENSP00000395095:I229T;ENSP00000361193:I266T	ENSP00000279027:I316T	I	-	2	0	SLC13A3	44651275	0.575000	0.26692	0.001000	0.08648	0.055000	0.15305	3.364000	0.52328	1.044000	0.40200	0.529000	0.55759	ATA	.	.	.	none		0.488	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2			G	45217868	A	G	45217868	3	3	68	1	0	0	0	0	1	0	0	0	14406	449	16	3	889	3	SLC13A3	20	45217868	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10	8343464	45217868	17807652	80	4545											
MTMR3	8897	hgsc.bcm.edu	37	chr22	30403186	30403186	+	Missense_Mutation	SNP	A	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	gcgaaatgcagatgatgagcAtctggtacagtcagtagcca	13	8	12	8	1	2	3	1	2	1	1	2	4	2	3	1	1	4	4	1	1	3	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr22:30403186A>C	ENST00000401950.2	+	10	1097	c.755A>C	c.(754-756)cAt>cCt	p.H252P	MTMR3_ENST00000323630.5_Missense_Mutation_p.H116P|MTMR3_ENST00000333027.3_Missense_Mutation_p.H252P|CTA-85E5.10_ENST00000429350.1_RNA|MTMR3_ENST00000351488.3_Missense_Mutation_p.H252P|MTMR3_ENST00000406629.1_Missense_Mutation_p.H252P	NM_021090.3	NP_066576.1	Q13615	MTMR3_HUMAN	myotubularin related protein 3	252	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)			GATGATGAGCATCTGGTACAG	0.547																																					p.H252P		Atlas-SNP	.											.	MTMR3	106	.	0			c.A755C						PASS	.						94	87	89					22																	30403186		2203	4300	6503	SO:0001583	missense	8897	exon10			ATGAGCATCTGGT	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.755A>C	chr22.hg19:g.30403186A>C	ENSP00000384651:p.His252Pro	40.0	0.0	.		92.0	28.0	.	NM_153050	A5PL26|A7MD32|Q9NYN5|Q9NYN6|Q9UDX6|Q9UEG3	Missense_Mutation	SNP	ENST00000401950.2	hg19	CCDS13870.1	.	.	.	.	.	.	.	.	.	.	A	27.9	4.872970	0.91664	.	.	ENSG00000100330	ENST00000401950;ENST00000333027;ENST00000323630;ENST00000351488;ENST00000406629	D;D;D;D;D	0.92752	-3.1;-3.1;-3.1;-3.1;-3.1	5.87	5.87	0.94306	Myotubularin phosphatase domain (1);Myotubularin-related (1);	0.087453	0.85682	D	0.000000	D	0.95310	0.8478	M	0.69823	2.125	0.80722	D	1	D;P;D	0.69078	0.997;0.931;0.997	D;P;D	0.66847	0.947;0.781;0.947	D	0.95552	0.8621	10	0.66056	D	0.02	.	15.4554	0.75308	1.0:0.0:0.0:0.0	.	252;252;252	Q13615-3;Q13615;Q13615-2	.;MTMR3_HUMAN;.	P	252;252;116;252;252	ENSP00000384651:H252P;ENSP00000331649:H252P;ENSP00000318070:H116P;ENSP00000307271:H252P;ENSP00000384077:H252P	ENSP00000318070:H116P	H	+	2	0	MTMR3	28733186	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	8.962000	0.93254	2.253000	0.74438	0.533000	0.62120	CAT	.	.	.	none		0.547	MTMR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322066.1	NM_021090		C	30403186	A	C	30403186	3	2	68	1	0	0	0	0	1	0	0	0	9952	217	8	5	785	5	MTMR3	22	30403186	Missense_Mutation	SNP	A	TCGA-A4-A6HP-01A-11D-A31X-10		30403186	20901380	81	4546											
CARD10	29775	hgsc.bcm.edu	37	chr22	37898635	37898635	+	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	aggaagtccaggccacagccCcgagccaggaggccttccgg	9	3	14	15	2	0	0	0	0	0	0	2	3	2	2	7	5	2	0	7	5	1	1			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chr22:37898635C>G	ENST00000403299.1	-	12	1977	c.1761G>C	c.(1759-1761)cgG>cgC	p.R587R	CARD10_ENST00000406271.3_Silent_p.R301R|CARD10_ENST00000251973.5_Silent_p.R587R			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	587					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)					GGCCACAGCCCCGAGCCAGGA	0.617																																					p.R587R		Atlas-SNP	.											.	CARD10	55	.	0			c.G1761C						PASS	.						54	48	50					22																	37898635		2203	4300	6503	SO:0001819	synonymous_variant	29775	exon11			ACAGCCCCGAGCC	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.1761G>C	chr22.hg19:g.37898635C>G		27.0	0.0	.		63.0	21.0	.	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Silent	SNP	ENST00000403299.1	hg19	CCDS13948.1																																																																																			.	.	.	none		0.617	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550		G	37898635	C	G	37898635	2	3	68	1	0	0	0	0	0	0	0	1	2646	610	22	4		4	CARD10	22	37898635	Silent	SNP	C	TCGA-A4-A6HP-01A-11D-A31X-10	7495449	37898635	13405931	82	4547											
SLC6A8	6535	hgsc.bcm.edu	37	chrX	152958793	152958793	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccctcacagccctgggcagcTacaaccgcttcaacaacaac	12	5	6	18	1	2	0	2	0	0	0	2	0	2	0	3	1	7	3	3	1	5	2			TCGA-A4-A6HP-01A-11D-A31X-10	TCGA-A4-A6HP-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d1845e20-13c6-473e-a607-d5010b214486	1fbfe3f1-dbc6-4e89-a9f6-0adbf2672b92	g.chrX:152958793T>C	ENST00000253122.5	+	6	1464	c.988T>C	c.(988-990)Tac>Cac	p.Y330H	SLC6A8_ENST00000430077.2_Missense_Mutation_p.Y215H|SLC6A8_ENST00000485324.1_3'UTR	NM_001142805.1|NM_005629.3	NP_001136277.1|NP_005620.1	P48029	SC6A8_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 8	330					cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|creatine transmembrane transport (GO:1902598)|creatine transport (GO:0015881)|muscle contraction (GO:0006936)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	creatine transmembrane transporter activity (GO:0005308)|creatine:sodium symporter activity (GO:0005309)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|pancreas(1)|upper_aerodigestive_tract(1)	13	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				Creatine(DB00148)	CCTGGGCAGCTACAACCGCTT	0.632																																					p.Y330H		Atlas-SNP	.											.	SLC6A8	34	.	0			c.T988C						PASS	.						45	49	48					X																	152958793		2203	4300	6503	SO:0001583	missense	6535	exon6			GGCAGCTACAACC		CCDS14726.1, CCDS48190.1	Xq28	2013-07-19	2013-07-19		ENSG00000130821	ENSG00000130821		"Solute carriers"	11055	protein-coding gene	gene with protein product	"creatine transporter"	300036	"solute carrier family 6 (neurotransmitter transporter, creatine), member 8"			7774949	Standard	NM_001142805		Approved	CRTR, CT1	uc004fib.3	P48029	OTTHUMG00000024208	ENST00000253122.5:c.988T>C	chrX.hg19:g.152958793T>C	ENSP00000253122:p.Tyr330His	79.0	0.0	.		114.0	5.0	.	NM_005629	B2KY47|B4DIA3|E9PFC0|Q13032|Q66I36	Missense_Mutation	SNP	ENST00000253122.5	hg19	CCDS14726.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	26.1|26.1	4.700265|4.700265	0.88924|0.88924	.|.	.|.	ENSG00000130821|ENSG00000130821	ENST00000413787|ENST00000253122;ENST00000430077;ENST00000328897	T|D;D	0.79653|0.84516	-1.29|-1.86;-1.86	5.16|5.16	5.16|5.16	0.70880|0.70880	.|.	.|0.000000	.|0.64402	.|U	.|0.000003	D|D	0.92980|0.92980	0.7766|0.7766	M|M	0.89214|0.89214	3.015|3.015	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.87578	.|0.998;0.993	D|D	0.94080|0.94080	0.7343|0.7343	7|10	0.87932|0.87932	D|D	0|0	.|.	12.9947|12.9947	0.58640|0.58640	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|349;330	.|Q59EV7;P48029	.|.;SC6A8_HUMAN	P|H	45|330;215;336	ENSP00000400463:L45P|ENSP00000253122:Y330H;ENSP00000403041:Y215H	ENSP00000400463:L45P|ENSP00000253122:Y330H	L|Y	+|+	2|1	0|0	SLC6A8|SLC6A8	152611987|152611987	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.753000|7.753000	0.85153|0.85153	1.914000|1.914000	0.55421|0.55421	0.430000|0.430000	0.28490|0.28490	CTA|TAC	.	.	.	none		0.632	SLC6A8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061003.1			C	152958793	T	C	152958793	3	2	68	1	0	0	0	0	1	0	0	0	14703	1522	53	3	1010	3	SLC6A8	23	152958793	Missense_Mutation	SNP	T	TCGA-A4-A6HP-01A-11D-A31X-10		152958793	2311767	83	4548											
NRD1	4898	hgsc.bcm.edu	37	chr1	52260504	52260504	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caaatacttactcaacaacaTatttcaggaaatccatagat	18	11	3	9	0	2	1	2	0	0	1	3	2	3	2	1	1	4	0	1	1	8	5			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr1:52260504T>C	ENST00000354831.7	-	25	3020	c.2831A>G	c.(2830-2832)tAt>tGt	p.Y944C	RP4-657D16.3_ENST00000591675.1_RNA|NRD1_ENST00000352171.7_Missense_Mutation_p.Y876C|NRD1_ENST00000485608.1_5'UTR|NRD1_ENST00000544028.1_3'UTR|RP4-657D16.3_ENST00000586761.1_RNA|NRD1_ENST00000539524.1_Missense_Mutation_p.Y812C|RP4-657D16.3_ENST00000588291.1_RNA	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	875					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						CTCAACAACATATTTCAGGAA	0.368																																					p.Y944C		Atlas-SNP	.											.	NRD1	89	.	0			c.A2831G						PASS	.						84	88	87					1																	52260504		2203	4300	6503	SO:0001583	missense	4898	exon25			ACAACATATTTCA	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.2831A>G	chr1.hg19:g.52260504T>C	ENSP00000346890:p.Tyr944Cys	356.0	0.0	.		232.0	89.0	.	NM_002525	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Missense_Mutation	SNP	ENST00000354831.7	hg19	CCDS559.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.59|14.59	2.581623|2.581623	0.46006|0.46006	.|.	.|.	ENSG00000078618|ENSG00000078618	ENST00000440943|ENST00000352171;ENST00000354831;ENST00000539524;ENST00000371665;ENST00000546169	.|T;T;T	.|0.07800	.|3.16;3.16;3.16	5.65|5.65	4.51|4.51	0.55191|0.55191	.|Peptidase M16, C-terminal (1);Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	.|0.120475	.|0.64402	.|D	.|0.000018	T|T	0.09598|0.09598	0.0236|0.0236	L|L	0.43701|0.43701	1.375|1.375	0.80722|0.80722	D|D	1|1	.|B;B;B	.|0.27264	.|0.076;0.094;0.173	.|B;B;B	.|0.30105	.|0.037;0.063;0.111	T|T	0.10800|0.10800	-1.0614|-1.0614	5|10	.|0.40728	.|T	.|0.16	-7.7067|-7.7067	12.2317|12.2317	0.54492|0.54492	0.1275:0.0:0.0:0.8725|0.1275:0.0:0.0:0.8725	.|.	.|876;875;944	.|F5H6R2;O43847;B1AKJ5	.|.;NRDC_HUMAN;.	M|C	290|876;944;812;306;876	.|ENSP00000262679:Y876C;ENSP00000346890:Y944C;ENSP00000444416:Y812C	.|ENSP00000262679:Y876C	I|Y	-|-	3|2	3|0	NRD1|NRD1	52033092|52033092	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.993000|0.993000	0.82548|0.82548	5.393000|5.393000	0.66279|0.66279	1.134000|1.134000	0.42165|0.42165	0.533000|0.533000	0.62120|0.62120	ATA|TAT	.	.	.	none		0.368	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525		C	52260504	T	C	52260504	3	2	69	1	0	0	0	0	1	0	0	0	10652	1406	49	3	864	3	NRD1	1	52260504	Missense_Mutation	SNP	T	TCGA-A4-A772-01A-11D-A33Q-10		52260504	196990117	1	4549											
MSH4	4438	hgsc.bcm.edu	37	chr1	76378456	76378456	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccactaggcttgttcaaactGctcgaaactctcaattggat	11	12	7	11	1	2	0	2	0	1	0	4	2	2	1	1	2	3	3	1	2	4	4			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr1:76378456G>A	ENST00000263187.3	+	20	2799	c.2695G>A	c.(2695-2697)Gct>Act	p.A899T		NM_002440.3	NP_002431.2	O15457	MSH4_HUMAN	mutS homolog 4	899					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|female gamete generation (GO:0007292)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						TGTTCAAACTGCTCGAAACTC	0.383								Mismatch excision repair (MMR)																													p.A899T		Atlas-SNP	.											.	MSH4	147	.	0			c.G2695A						PASS	.						51	53	52					1																	76378456		2203	4300	6503	SO:0001583	missense	4438	exon20			CAAACTGCTCGAA	U89293	CCDS670.1	1p31	2013-09-12	2013-09-12		ENSG00000057468	ENSG00000057468			7327	protein-coding gene	gene with protein product		602105	"mutS (E. coli) homolog 4", "mutS homolog 4 (E. coli)"			9299235	Standard	NM_002440		Approved		uc001dhd.2	O15457	OTTHUMG00000009788	ENST00000263187.3:c.2695G>A	chr1.hg19:g.76378456G>A	ENSP00000263187:p.Ala899Thr	214.0	0.0	.		138.0	37.0	.	NM_002440	Q5T4U6|Q8NEB3|Q9UNP8	Missense_Mutation	SNP	ENST00000263187.3	hg19	CCDS670.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.265047	0.80358	.	.	ENSG00000057468	ENST00000263187	D	0.88664	-2.41	5.2	5.2	0.72013	.	0.057075	0.64402	D	0.000001	D	0.86694	0.5994	M	0.63843	1.955	0.44155	D	0.996952	D	0.55605	0.972	P	0.50490	0.642	D	0.84547	0.0642	10	0.25751	T	0.34	-39.1665	13.9996	0.64424	0.0:0.0:0.8486:0.1514	.	899	O15457	MSH4_HUMAN	T	899	ENSP00000263187:A899T	ENSP00000263187:A899T	A	+	1	0	MSH4	76151044	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.301000	0.72782	2.582000	0.87167	0.453000	0.30009	GCT	.	.	.	none		0.383	MSH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026983.1	NM_002440		A	76378456	G	A	76378456	3	1	69	1	0	0	0	0	1	0	0	0	9879	1319	46	2	2773	2	MSH4	1	76378456	Missense_Mutation	SNP	G	TCGA-A4-A772-01A-11D-A33Q-10	24117952	76378456	172872165	2	4550											
STXBP3	6814	hgsc.bcm.edu	37	chr1	109338883	109338883	+	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	cacttggaactgatgcagaaGgacagaaggtgaaagattcc	15	7	12	7	0	0	5	0	2	0	3	1	7	1	7	1	3	2	1	1	3	4	2			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr1:109338883G>A	ENST00000370008.3	+	14	1188	c.1138G>A	c.(1138-1140)Gga>Aga	p.G380R		NM_007269.2	NP_009200.2	O00186	STXB3_HUMAN	syntaxin binding protein 3	380					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)		TGATGCAGAAGGACAGAAGGT	0.313																																					p.G380R		Atlas-SNP	.											.	STXBP3	44	.	0			c.G1138A						PASS	.						68	67	68					1																	109338883		2203	4300	6503	SO:0001583	missense	6814	exon14			GCAGAAGGACAGA	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.1138G>A	chr1.hg19:g.109338883G>A	ENSP00000359025:p.Gly380Arg	364.0	0.0	.		258.0	82.0	.	NM_007269	A8K269|A8K5K7|Q53FW1|Q86YJ3|Q9UPD7	Missense_Mutation	SNP	ENST00000370008.3	hg19	CCDS790.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.823061	0.90873	.	.	ENSG00000116266	ENST00000370008	T	0.81330	-1.48	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	D	0.90256	0.6953	M	0.85041	2.73	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89811	0.3982	10	0.54805	T	0.06	-19.5687	20.1392	0.98050	0.0:0.0:1.0:0.0	.	380	O00186	STXB3_HUMAN	R	380	ENSP00000359025:G380R	ENSP00000359025:G380R	G	+	1	0	STXBP3	109140406	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	8.716000	0.91420	2.751000	0.94390	0.591000	0.81541	GGA	.	.	.	none		0.313	STXBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030591.1	NM_007269		A	109338883	G	A	109338883	3	1	69	1	0	0	0	0	1	0	0	0	15366	1001	35	2	1192	2	STXBP3	1	109338883	Missense_Mutation	SNP	G	TCGA-A4-A772-01A-11D-A33Q-10	32960427	109338883	139911738	3	4551											
ARHGEF11	9826	hgsc.bcm.edu	37	chr1	156911226	156911226	+	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	ctgagtcatccagttctaccCtgaggaaggaaaccaacaca	14	7	8	12	0	2	2	1	2	1	0	3	4	3	4	3	2	3	1	3	2	4	2			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr1:156911226C>T	ENST00000361409.2	-	34	4075		c.e34-1		ARHGEF11_ENST00000315174.8_Splice_Site|ARHGEF11_ENST00000368194.3_Splice_Site|ARHGEF11_ENST00000487682.1_Splice_Site	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)					CAGTTCTACCCTGAGGAAGGA	0.552																																					.		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.3333-1G>A						PASS	.						98	86	90					1																	156911226		2203	4300	6503	SO:0001630	splice_region_variant	9826	exon35			TCTACCCTGAGGA	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.3333-1G>A	chr1.hg19:g.156911226C>T		92.0	0.0	.		68.0	25.0	.	NM_014784	D3DVD0|Q5VY40|Q6PFW2	Splice_Site	SNP	ENST00000361409.2	hg19	CCDS1162.1	.	.	.	.	.	.	.	.	.	.	C	18.32	3.598788	0.66332	.	.	ENSG00000132694	ENST00000368194;ENST00000361409;ENST00000315174	.	.	.	4.72	4.72	0.59763	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.369	0.60703	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ARHGEF11	155177850	0.999000	0.42202	0.986000	0.45419	0.504000	0.33889	3.269000	0.51592	2.608000	0.88229	0.462000	0.41574	.	.	.	.	none		0.552	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236	Intron	T	156911226	C	T	156911226	5	4	69	1	0	0	0	0	0	0	1	0	896	695	24	2	1264	2	ARHGEF11	1	156911226	Splice_Site	SNP	C	TCGA-A4-A772-01A-11D-A33Q-10	47572343	156911226	92339395	4	4552											
TP53BP2	7159	hgsc.bcm.edu	37	chr1	223989924	223989924	+	Frame_Shift_Del	DEL	C	C	-																															ccatccggcagggctggcttCaccagcaattcaggccttga																										TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr1:223989924delC	ENST00000343537.7	-	9	1410	c.1119delG	c.(1117-1119)gtgfs	p.V373fs	TP53BP2_ENST00000391878.2_Frame_Shift_Del_p.V244fs|TP53BP2_ENST00000498843.1_5'UTR|TP53BP2_ENST00000391879.2_5'Flank	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	367					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)		GGGCTGGCTTCACCAGCAATT	0.572																																					p.K374fs		Atlas-Indel,Pindel	.											.	TP53BP2	144	.	0			c.1120delA						PASS	.						76	77	77					1																	223989924		2203	4300	6503	SO:0001589	frameshift_variant	7159	exon9			.	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.1119delG	chr1.hg19:g.223989924delC	ENSP00000341957:p.Val373fs	100.0	0.0	0		90.0	26.0	0.288889	NM_001031685	B4DG66|Q12892|Q86X75|Q96KQ3	Frame_Shift_Del	DEL	ENST00000343537.7	hg19	CCDS44319.1																																																																																			.	.	.	none		0.572	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3	NM_001031685, NM_005426		-	223989924	C	-	223989924	7	5	69	1	0	1	0	1	0	0	0	0	16396	813	29	0	2325	0	TP53BP2	1	223989924	Frame_Shift_Del	DEL	C	TCGA-A4-A772-01A-11D-A33Q-10	67078698	223989924	25260697	5	4553											
SLC35F5	80255	hgsc.bcm.edu	37	chr2	114513036	114513036	+	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	aaacgtggaatctaccttgtCttaagagcccttctgagatc	11	12	8	10	1	3	2	0	1	3	2	4	4	3	3	2	1	3	0	2	1	4	4			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr2:114513036C>G	ENST00000245680.2	-	2	539	c.126G>C	c.(124-126)aaG>aaC	p.K42N	SLC35F5_ENST00000409342.1_Missense_Mutation_p.K36N	NM_025181.2	NP_079457.2	Q8WV83	S35F5_HUMAN	solute carrier family 35, member F5	42					transport (GO:0006810)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(4)|large_intestine(2)|lung(7)|ovary(2)|prostate(3)|skin(1)	20						TCTACCTTGTCTTAAGAGCCC	0.383																																					p.K42N		Atlas-SNP	.											.	SLC35F5	60	.	0			c.G126C						PASS	.						104	102	102					2																	114513036		2203	4300	6503	SO:0001583	missense	80255	exon2			CCTTGTCTTAAGA	AF529364	CCDS2119.1	2q14.1	2013-05-22			ENSG00000115084	ENSG00000115084		"Solute carriers"	23617	protein-coding gene	gene with protein product							Standard	XM_005263799		Approved	FLJ22004	uc002tku.1	Q8WV83	OTTHUMG00000131361	ENST00000245680.2:c.126G>C	chr2.hg19:g.114513036C>G	ENSP00000245680:p.Lys42Asn	207.0	0.0	.		143.0	58.0	.	NM_025181	Q9H6P8|Q9H7D8	Missense_Mutation	SNP	ENST00000245680.2	hg19	CCDS2119.1	.	.	.	.	.	.	.	.	.	.	C	8.367	0.834366	0.16820	.	.	ENSG00000115084	ENST00000245680;ENST00000409106;ENST00000409342	T;T	0.50001	0.76;0.76	5.13	-1.54	0.08584	.	0.871411	0.10144	N	0.710493	T	0.28333	0.0700	N	0.22421	0.69	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	0.17077	-1.0381	10	0.42905	T	0.14	-0.0951	4.9347	0.13935	0.0:0.2162:0.2783:0.5055	.	42;36;42	B2RDY0;B8ZZV6;Q8WV83	.;.;S35F5_HUMAN	N	42;36;36	ENSP00000245680:K42N;ENSP00000386754:K36N	ENSP00000245680:K42N	K	-	3	2	SLC35F5	114229506	0.041000	0.20044	0.034000	0.17996	0.117000	0.20001	0.299000	0.19138	-0.420000	0.07427	-0.903000	0.02851	AAG	.	.	.	none		0.383	SLC35F5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254150.1	NM_025181		G	114513036	C	G	114513036	3	3	69	1	0	0	0	0	1	0	0	0	14605	912	32	4	1501	4	SLC35F5	2	114513036	Missense_Mutation	SNP	C	TCGA-A4-A772-01A-11D-A33Q-10		114513036	128686337	6	4554											
RAB3GAP1	22930	hgsc.bcm.edu	37	chr2	135815643	135815643	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gattggaaactctttgggaaAgccactcgaaaaggtcagat	14	9	11	7	1	2	1	1	0	1	1	3	5	2	3	1	3	2	0	1	3	4	2			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr2:135815643A>G	ENST00000264158.8	+	3	180	c.137A>G	c.(136-138)aAg>aGg	p.K46R	RAB3GAP1_ENST00000425393.1_Missense_Mutation_p.K46R|RAB3GAP1_ENST00000539493.1_5'UTR|RAB3GAP1_ENST00000442034.1_Missense_Mutation_p.K46R	NM_012233.2	NP_036365.1	Q15042	RB3GP_HUMAN	RAB3 GTPase activating protein subunit 1 (catalytic)	46					brain development (GO:0007420)|camera-type eye development (GO:0043010)|establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|face morphogenesis (GO:0060325)|hypothalamus development (GO:0021854)|lipid particle organization (GO:0034389)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of calcium ion-dependent exocytosis of neurotransmitter (GO:1903233)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of GTPase activity (GO:0043087)|regulation of short-term neuronal synaptic plasticity (GO:0048172)	cytoplasm (GO:0005737)|endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(10)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32				BRCA - Breast invasive adenocarcinoma(221;0.117)		TCTTTGGGAAAGCCACTCGAA	0.388																																					p.K46R		Atlas-SNP	.											.	RAB3GAP1	87	.	0			c.A137G						PASS	.						93	88	90					2																	135815643		2203	4300	6503	SO:0001583	missense	22930	exon3			TGGGAAAGCCACT	D31886	CCDS33294.1, CCDS54402.1	2q21.3	2013-07-09			ENSG00000115839	ENSG00000115839			17063	protein-coding gene	gene with protein product		602536				9030515, 15696165	Standard	NM_012233		Approved	RAB3GAP, KIAA0066, RAB3GAP130, WARBM1	uc010fnf.3	Q15042	OTTHUMG00000154889	ENST00000264158.8:c.137A>G	chr2.hg19:g.135815643A>G	ENSP00000264158:p.Lys46Arg	85.0	0.0	.		77.0	26.0	.	NM_001172435	A6H8Z3|C9J837|Q659F5|Q8TBB4	Missense_Mutation	SNP	ENST00000264158.8	hg19	CCDS33294.1	.	.	.	.	.	.	.	.	.	.	A	14.70	2.613130	0.46631	.	.	ENSG00000115839	ENST00000264158;ENST00000442034;ENST00000425393	T;T	0.44482	0.92;0.92	5.62	-1.08	0.09936	.	0.287773	0.36932	N	0.002336	T	0.24392	0.0591	L	0.47716	1.5	0.80722	D	1	B;P	0.38335	0.0;0.627	B;B	0.32677	0.0;0.15	T	0.07233	-1.0783	10	0.19147	T	0.46	-7.7819	5.3457	0.16008	0.5453:0.144:0.3107:0.0	.	46;46	C9J837;Q15042	.;RB3GP_HUMAN	R	46	ENSP00000264158:K46R;ENSP00000411418:K46R	ENSP00000264158:K46R	K	+	2	0	RAB3GAP1	135532113	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	0.810000	0.27183	-0.106000	0.12110	0.533000	0.62120	AAG	.	.	.	none		0.388	RAB3GAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337514.2	NM_012233		G	135815643	A	G	135815643	3	3	69	1	0	0	0	0	1	0	0	0	12948	72	3	3	147	3	RAB3GAP1	2	135815643	Missense_Mutation	SNP	A	TCGA-A4-A772-01A-11D-A33Q-10	21302607	135815643	107383730	7	4555											
PKP4	8502	hgsc.bcm.edu	37	chr2	159488407	159488407	+	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	cgcagcccaaaccatggaacTgtggagctccaaggatcgca	12	5	11	13	2	0	0	0	0	0	0	2	3	1	3	3	3	4	3	3	3	3	0			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr2:159488407T>A	ENST00000389759.3	+	8	1408	c.1296T>A	c.(1294-1296)acT>acA	p.T432T	PKP4_ENST00000389757.3_Silent_p.T432T	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	432					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						ACCATGGAACTGTGGAGCTCC	0.517										HNSCC(62;0.18)																											p.T432T		Atlas-SNP	.											.	PKP4	133	.	0			c.T1296A						PASS	.						123	111	115					2																	159488407		2203	4300	6503	SO:0001819	synonymous_variant	8502	exon8			TGGAACTGTGGAG	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.1296T>A	chr2.hg19:g.159488407T>A		132.0	0.0	.		79.0	19.0	.	NM_001005476	Q86W91	Silent	SNP	ENST00000389759.3	hg19	CCDS33305.1																																																																																			.	.	.	none		0.517	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1			A	159488407	T	A	159488407	2	1	69	1	0	0	0	0	0	0	0	1	11994	1567	55	5		5	PKP4	2	159488407	Silent	SNP	T	TCGA-A4-A772-01A-11D-A33Q-10	23672764	159488407	83710966	8	4556											
KCNH7	90134	hgsc.bcm.edu	37	chr2	163256852	163256852	+	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	tgccaaagctctaaggcaacCtttacttgccccccgaaagg	11	8	8	14	1	1	0	0	0	1	0	1	1	1	0	5	2	5	2	5	2	5	4			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr2:163256852C>T	ENST00000332142.5	-	10	2353	c.2254G>A	c.(2254-2256)Ggt>Agt	p.G752S		NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	752					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)	CTAAGGCAACCTTTACTTGCC	0.478																																					p.G752S	GBM(196;1492 2208 17507 24132 45496)	Atlas-SNP	.											.	KCNH7	378	.	0			c.G2254A						PASS	.						148	149	148					2																	163256852		2203	4300	6503	SO:0001583	missense	90134	exon10			GGCAACCTTTACT	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.2254G>A	chr2.hg19:g.163256852C>T	ENSP00000331727:p.Gly752Ser	120.0	0.0	.		85.0	26.0	.	NM_033272	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Missense_Mutation	SNP	ENST00000332142.5	hg19	CCDS2219.1	.	.	.	.	.	.	.	.	.	.	C	35	5.436882	0.96168	.	.	ENSG00000184611	ENST00000332142	D	0.96427	-4.01	5.57	5.57	0.84162	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (2);	0.000000	0.85682	D	0.000000	D	0.97259	0.9104	M	0.67569	2.06	0.80722	D	1	D	0.56035	0.974	P	0.55615	0.78	D	0.97606	1.0126	10	0.72032	D	0.01	.	19.5531	0.95330	0.0:1.0:0.0:0.0	.	752	Q9NS40	KCNH7_HUMAN	S	752	ENSP00000331727:G752S	ENSP00000331727:G752S	G	-	1	0	KCNH7	162965098	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.807000	0.86032	2.628000	0.89032	0.591000	0.81541	GGT	.	.	.	none		0.478	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1	NM_033272		T	163256852	C	T	163256852	3	4	69	1	0	0	0	0	1	0	0	0	8044	681	24	2	1364	2	KCNH7	2	163256852	Missense_Mutation	SNP	C	TCGA-A4-A772-01A-11D-A33Q-10	3768445	163256852	79942521	9	4557											
SLC6A6	6533	hgsc.bcm.edu	37	chr3	14526398	14526417	+	Frame_Shift_Del	DEL	AAGGGAACCCAACCGCTGGG	AAGGGAACCCAACCGCTGGG	-																															gtcaagtacctgctgaccccAagggaacccaaccgctgggc																								rs376586731		TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	AAGGGAACCCAACCGCTGGG	AAGGGAACCCAACCGCTGGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr3:14526398_14526417delAAGGGAACCCAACCGCTGGG	ENST00000454876.2	+	15	2075_2094	c.1746_1765delAAGGGAACCCAACCGCTGGG	c.(1744-1767)ccaagggaacccaaccgctgggctfs	p.REPNRWA583fs	SLC6A6_ENST00000360861.3_Frame_Shift_Del_p.REPNRWA583fs			P31641	SC6A6_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 6	583					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						TGCTGACCCCAAGGGAACCCAACCGCTGGGCTGTGGAGCG	0.609																																					p.582_588del		Atlas-Indel,Pindel	.											.	SLC6A6	58	.	0			c.1745_1764del						PASS	.																																			SO:0001589	frameshift_variant	6533	exon15			.		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.1746_1765delAAGGGAACCCAACCGCTGGG	chr3.hg19:g.14526398_14526417delAAGGGAACCCAACCGCTGGG	ENSP00000398063:p.Arg583fs	33.0	0.0	0		37.0	10.0	0.27027	NM_003043	B2RNU7|Q9BRI2|Q9BXB0	Frame_Shift_Del	DEL	ENST00000454876.2	hg19	CCDS33705.1																																																																																			.	.	.	none		0.609	SLC6A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340507.1	NM_003043		-	14526417	AAGGGAACCCAACCGCTGGG	-	14526398	7	5	69	1	0	1	0	1	0	0	0	0	14701	117	5	0	1800	0	SLC6A6	3	14526398	Frame_Shift_Del	DEL	AAGGGAACCCAACCGCTGGG	TCGA-A4-A772-01A-11D-A33Q-10		14526398	183496032	10	4558											
ACOX2	8309	hgsc.bcm.edu	37	chr3	58494718	58494718	+	Missense_Mutation	SNP	A	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	atttaaacactgatcggtgaAgtcaaaagcatcagttaaca	17	10	7	7	1	2	2	2	2	0	0	3	2	2	2	0	1	3	2	0	1	6	3			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr3:58494718A>C	ENST00000302819.5	-	14	2176	c.1885T>G	c.(1885-1887)Ttc>Gtc	p.F629V	ACOX2_ENST00000481527.1_5'UTR|ACOX2_ENST00000459701.2_Missense_Mutation_p.F615V	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	629					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)		TGATCGGTGAAGTCAAAAGCA	0.418																																					p.F629V		Atlas-SNP	.											.	ACOX2	53	.	0			c.T1885G						PASS	.						120	106	111					3																	58494718		2203	4300	6503	SO:0001583	missense	8309	exon14			CGGTGAAGTCAAA	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.1885T>G	chr3.hg19:g.58494718A>C	ENSP00000307697:p.Phe629Val	124.0	0.0	.		108.0	26.0	.	NM_003500	A6NF16|B2R8U5	Missense_Mutation	SNP	ENST00000302819.5	hg19	CCDS33775.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.408425	0.83340	.	.	ENSG00000168306	ENST00000459701;ENST00000302819	T;T	0.42900	0.96;0.96	5.43	5.43	0.79202	Acyl-CoA oxidase, C-terminal (1);Acyl-CoA dehydrogenase/oxidase C-terminal (1);	0.093665	0.46442	D	0.000282	T	0.53158	0.1779	M	0.76938	2.355	0.44702	D	0.997696	P	0.46395	0.877	P	0.46885	0.53	T	0.58387	-0.7645	10	0.48119	T	0.1	-29.0011	15.5185	0.75846	1.0:0.0:0.0:0.0	.	629	Q99424	ACOX2_HUMAN	V	615;629	ENSP00000418562:F615V;ENSP00000307697:F629V	ENSP00000307697:F629V	F	-	1	0	ACOX2	58469758	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.308000	0.72820	2.088000	0.63022	0.472000	0.43445	TTC	.	.	.	none		0.418	ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1			C	58494718	A	C	58494718	3	2	69	1	0	0	0	0	1	0	0	0	159	72	3	5	168	5	ACOX2	3	58494718	Missense_Mutation	SNP	A	TCGA-A4-A772-01A-11D-A33Q-10	43968320	58494718	139527712	11	4559											
CADM2	253559	hgsc.bcm.edu	37	chr3	86114787	86114787	+	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	tggctggccagaatggccctGaccatgctctcataggagga	9	8	13	11	0	1	2	1	1	1	1	2	4	1	4	3	5	1	2	3	5	2	1			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr3:86114787G>A	ENST00000407528.2	+	9	1158	c.1096G>A	c.(1096-1098)Gac>Aac	p.D366N	CADM2_ENST00000383699.3_Missense_Mutation_p.D335N|CADM2_ENST00000405615.2_Missense_Mutation_p.D368N	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	366					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)		p.D335H(1)|p.D368H(1)		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)		GAATGGCCCTGACCATGCTCT	0.403																																					p.D368N		Atlas-SNP	.											CADM2_ENST00000383699,NS,carcinoma,0,1	CADM2	195	.	2	Substitution - Missense(2)	lung(2)	c.G1102A						PASS	.						157	140	146					3																	86114787		2203	4300	6503	SO:0001583	missense	253559	exon9			GGCCCTGACCATG	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.1096G>A	chr3.hg19:g.86114787G>A	ENSP00000384575:p.Asp366Asn	100.0	0.0	.		103.0	55.0	.	NM_153184	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Missense_Mutation	SNP	ENST00000407528.2	hg19	CCDS54614.1	.	.	.	.	.	.	.	.	.	.	G	36	5.603574	0.96626	.	.	ENSG00000175161	ENST00000383699;ENST00000407528;ENST00000405615	T;T;T	0.69175	-0.22;-0.38;-0.38	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.75752	0.3892	L	0.41824	1.3	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.83275	0.996;0.995;0.996	T	0.68281	-0.5450	10	0.17832	T	0.49	.	19.964	0.97260	0.0:0.0:1.0:0.0	.	368;335;366	Q8N3J6-3;G3XHN4;Q8N3J6	.;.;CADM2_HUMAN	N	335;366;368	ENSP00000373200:D335N;ENSP00000384575:D366N;ENSP00000384193:D368N	ENSP00000373200:D335N	D	+	1	0	CADM2	86197477	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.869000	0.99810	2.721000	0.93114	0.650000	0.86243	GAC	.	.	.	none		0.403	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184		A	86114787	G	A	86114787	3	1	69	1	0	0	0	0	1	0	0	0	2569	1290	45	2	1201	2	CADM2	3	86114787	Missense_Mutation	SNP	G	TCGA-A4-A772-01A-11D-A33Q-10	27620069	86114787	111907643	12	4560											
QTRTD1	79691	hgsc.bcm.edu	37	chr3	113795727	113795727	+	Silent	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	tttcaaggaaatccaacaacCctggaggctagactacgctt	13	9	8	11	1	1	1	1	0	0	1	2	3	2	3	2	3	3	2	2	3	6	4			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr3:113795727C>T	ENST00000493014.1	+	3	434	c.366C>T	c.(364-366)acC>acT	p.T122T	QTRTD1_ENST00000485050.1_Silent_p.T240T|QTRTD1_ENST00000479882.1_Silent_p.T105T|QTRTD1_ENST00000281273.4_Silent_p.T228T	NM_001256836.1	NP_001243765.1			queuine tRNA-ribosyltransferase domain containing 1											central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|skin(2)	10						ATCCAACAACCCTGGAGGCTA	0.567																																					p.T240T		Atlas-SNP	.											.	QTRTD1	29	.	0			c.C720T						PASS	.						90	75	80					3																	113795727		2203	4300	6503	SO:0001819	synonymous_variant	79691	exon6			AACAACCCTGGAG	AK023022	CCDS33828.1, CCDS58846.1, CCDS58845.1, CCDS58844.1	3q13.31	2010-11-16			ENSG00000151576	ENSG00000151576			25771	protein-coding gene	gene with protein product						12477932	Standard	NM_024638		Approved	FLJ12960	uc003eaz.4	Q9H974	OTTHUMG00000159336	ENST00000493014.1:c.366C>T	chr3.hg19:g.113795727C>T		152.0	0.0	.		138.0	25.0	.	NM_001256835		Silent	SNP	ENST00000493014.1	hg19	CCDS58845.1																																																																																			.	.	.	none		0.567	QTRTD1-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000354711.1	NM_024638		T	113795727	C	T	113795727	2	4	69	1	0	0	0	0	0	0	0	1	12899	610	22	2		2	QTRTD1	3	113795727	Silent	SNP	C	TCGA-A4-A772-01A-11D-A33Q-10	27680940	113795727	84226703	13	4561											
NDUFB4	4710	hgsc.bcm.edu	37	chr3	120321109	120321109	+	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	tggatcgaacatttcacctcTcatattaagtctggcaatga	12	13	7	9	1	3	1	2	1	2	0	5	3	3	2	1	2	1	1	1	2	4	3			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr3:120321109T>A	ENST00000184266.2	+	3	433	c.382T>A	c.(382-384)Tca>Aca	p.S128T	NDUFB4_ENST00000485064.1_3'UTR|NDUFB4_ENST00000492739.1_Missense_Mutation_p.S79T	NM_004547.5	NP_004538.2	O95168	NDUB4_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 4, 15kDa	128					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|large_intestine(1)|lung(3)	5				GBM - Glioblastoma multiforme(114;0.14)		ATTTCACCTCTCATATTAAGT	0.303																																					p.S128T		Atlas-SNP	.											.	NDUFB4	21	.	0			c.T382A						PASS	.						82	90	87					3																	120321109		2203	4295	6498	SO:0001583	missense	4710	exon3			CACCTCTCATATT	AF044957	CCDS2999.1, CCDS54630.1	3q13.33	2011-07-04	2002-08-29		ENSG00000065518	ENSG00000065518		"Mitochondrial respiratory chain complex / Complex I"	7699	protein-coding gene	gene with protein product	"complex I B15 subunit"	603840	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 4 (15kD, B15)"			9878551	Standard	NM_004547		Approved	B15	uc003edu.3	O95168	OTTHUMG00000159442	ENST00000184266.2:c.382T>A	chr3.hg19:g.120321109T>A	ENSP00000184266:p.Ser128Thr	118.0	0.0	.		99.0	42.0	.	NM_004547	B2RUY3|B9EJC7	Missense_Mutation	SNP	ENST00000184266.2	hg19	CCDS2999.1	.	.	.	.	.	.	.	.	.	.	T	6.494	0.459339	0.12342	.	.	ENSG00000065518	ENST00000184266;ENST00000492739	.	.	.	4.88	-0.947	0.10382	.	0.721652	0.12974	N	0.423890	T	0.39860	0.1094	M	0.64567	1.98	0.09310	N	1	B	0.22746	0.074	B	0.23574	0.047	T	0.41070	-0.9529	9	0.59425	D	0.04	-3.6658	5.2004	0.15260	0.47:0.0:0.1616:0.3683	.	128	O95168	NDUB4_HUMAN	T	128;79	.	ENSP00000184266:S128T	S	+	1	0	NDUFB4	121803799	0.001000	0.12720	0.547000	0.28179	0.010000	0.07245	0.040000	0.13905	0.054000	0.16065	-0.336000	0.08194	TCA	.	.	.	none		0.303	NDUFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355420.1	NM_004547		A	120321109	T	A	120321109	3	1	69	1	0	0	0	0	1	0	0	0	10290	1551	54	5	428	5	NDUFB4	3	120321109	Missense_Mutation	SNP	T	TCGA-A4-A772-01A-11D-A33Q-10	6525382	120321109	77701321	14	4562											
EFNA5	1946	hgsc.bcm.edu	37	chr5	106763191	106763191	+	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	attgatacagacatcaatatGgtagtcacccctctggaatc	13	11	7	10	0	3	2	2	1	1	1	4	3	3	3	2	2	1	1	2	2	5	4			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr5:106763191G>A	ENST00000333274.6	-	2	426	c.145C>T	c.(145-147)Cat>Tat	p.H49Y	EFNA5_ENST00000509503.1_Missense_Mutation_p.H49Y	NM_001962.2	NP_001953.1	P52803	EFNA5_HUMAN	ephrin-A5	49	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.				axon guidance (GO:0007411)|ephrin receptor signaling pathway (GO:0048013)|nervous system development (GO:0007399)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell-cell adhesion (GO:0022407)|regulation of focal adhesion assembly (GO:0051893)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rho GTPase activity (GO:0032319)|retinal ganglion cell axon guidance (GO:0031290)	anchored component of external side of plasma membrane (GO:0031362)|plasma membrane (GO:0005886)	chemorepellent activity (GO:0045499)|ephrin receptor binding (GO:0046875)			large_intestine(6)	6		all_cancers(142;5.15e-06)|all_epithelial(76;4.39e-07)|Prostate(80;0.00726)|Lung NSC(167;0.0736)|Ovarian(225;0.0797)|all_lung(232;0.0854)|Colorectal(57;0.241)		Epithelial(69;1.25e-12)|OV - Ovarian serous cystadenocarcinoma(64;1.32e-11)|BRCA - Breast invasive adenocarcinoma(61;0.0376)|COAD - Colon adenocarcinoma(37;0.109)		ACATCAATATGGTAGTCACCC	0.408																																					p.H49Y		Atlas-SNP	.											.	EFNA5	16	.	0			c.C145T						PASS	.						106	107	106					5																	106763191		2202	4300	6502	SO:0001583	missense	1946	exon2			CAATATGGTAGTC	U26403	CCDS4097.1	5q21	2011-03-09			ENSG00000184349	ENSG00000184349		"Ephrins"	3225	protein-coding gene	gene with protein product		601535		EPLG7		8661153, 9245480	Standard	NM_001962		Approved	AF1, LERK7	uc003kol.3	P52803	OTTHUMG00000128741	ENST00000333274.6:c.145C>T	chr5.hg19:g.106763191G>A	ENSP00000328777:p.His49Tyr	74.0	0.0	.		81.0	33.0	.	NM_001962		Missense_Mutation	SNP	ENST00000333274.6	hg19	CCDS4097.1	.	.	.	.	.	.	.	.	.	.	G	11.77	1.737704	0.30774	.	.	ENSG00000184349	ENST00000333274;ENST00000509503	D;D	0.92965	-3.14;-3.14	6.06	6.06	0.98353	Cupredoxin (2);	0.041559	0.85682	D	0.000000	D	0.89483	0.6728	L	0.40543	1.245	0.80722	D	1	P;P	0.49559	0.925;0.629	P;P	0.47915	0.561;0.478	D	0.85995	0.1491	10	0.08599	T	0.76	-23.2864	15.3505	0.74380	0.0:0.0:0.8605:0.1395	.	49;49	D6RDV5;P52803	.;EFNA5_HUMAN	Y	49	ENSP00000328777:H49Y;ENSP00000426989:H49Y	ENSP00000328777:H49Y	H	-	1	0	EFNA5	106791090	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.500000	0.81588	2.882000	0.98803	0.655000	0.94253	CAT	.	.	.	none		0.408	EFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250652.1	NM_001962		A	106763191	G	A	106763191	3	1	69	1	0	0	0	0	1	0	0	0	4956	1348	47	2	557	2	EFNA5	5	106763191	Missense_Mutation	SNP	G	TCGA-A4-A772-01A-11D-A33Q-10		106763191	74152069	15	4563											
RING1	6015	hgsc.bcm.edu	37	chr6	33179580	33179580	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctgcgcattgccctcgagcGgaggcaacagcaggaagcag	10	4	14	13	3	0	0	0	0	0	0	1	3	0	2	2	3	6	4	2	3	2	1	rs528777843		TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr6:33179580G>A	ENST00000374656.4	+	6	1128	c.920G>A	c.(919-921)cGg>cAg	p.R307Q	RING1_ENST00000478431.1_3'UTR	NM_002931.3	NP_002922.2	Q06587	RING1_HUMAN	ring finger protein 1	307	Necessary for interaction with CBX2. {ECO:0000250}.				anterior/posterior pattern specification (GO:0009952)|camera-type eye morphogenesis (GO:0048593)|histone H2A monoubiquitination (GO:0035518)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(5)|large_intestine(1)|lung(3)|ovary(2)|prostate(2)|skin(4)	17						GCCCTCGAGCGGAGGCAACAG	0.647													G|||	1	0.000199681	0	0.0014	5008	,	,		13950	0		0	False		,,,				2504	0				p.R307Q		Atlas-SNP	.											.	RING1	40	.	0			c.G920A						PASS	.						71	73	72					6																	33179580		2203	4299	6502	SO:0001583	missense	6015	exon6			TCGAGCGGAGGCA		CCDS34424.1	6p21.3	2013-01-09			ENSG00000204227	ENSG00000204227		"RING-type (C3HC4) zinc fingers"	10018	protein-coding gene	gene with protein product		602045				1906426	Standard	NM_002931		Approved	RNF1	uc003odk.3	Q06587	OTTHUMG00000031278	ENST00000374656.4:c.920G>A	chr6.hg19:g.33179580G>A	ENSP00000363787:p.Arg307Gln	38.0	0.0	.		51.0	20.0	.	NM_002931	A8JZZ0|Q5JP96|Q5SQW2|Q86V19	Missense_Mutation	SNP	ENST00000374656.4	hg19	CCDS34424.1	.	.	.	.	.	.	.	.	.	.	G	6.906	0.536803	0.13188	.	.	ENSG00000204227	ENST00000374656	D	0.83335	-1.71	3.89	3.89	0.44902	.	0.281756	0.28671	N	0.014523	T	0.38957	0.1060	N	0.08118	0	0.31260	N	0.693011	P	0.41420	0.749	B	0.23419	0.046	T	0.41342	-0.9514	10	0.13853	T	0.58	-20.2778	11.2237	0.48871	0.0:0.0:1.0:0.0	.	307	Q06587	RING1_HUMAN	Q	307	ENSP00000363787:R307Q	ENSP00000363787:R307Q	R	+	2	0	RING1	33287558	0.991000	0.36638	0.986000	0.45419	0.113000	0.19764	0.000000	0.12993	1.965000	0.57142	0.448000	0.29417	CGG	.	.	.	none		0.647	RING1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076609.2			A	33179580	G	A	33179580	3	1	69	1	0	0	0	0	1	0	0	0	13387	1116	39	1	938	1	RING1	6	33179580	Missense_Mutation	SNP	G	TCGA-A4-A772-01A-11D-A33Q-10		33179580	137935487	16	4564											
ABCA13	154664	hgsc.bcm.edu	37	chr7	48654963	48654963	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcttggttctcctcagcacAtcaaaaataggtgcgttgaa	11	12	9	9	1	4	1	2	1	2	0	5	1	4	1	1	2	2	3	1	2	4	4			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr7:48654963A>G	ENST00000435803.1	+	59	14851	c.14827A>G	c.(14827-14829)Atc>Gtc	p.I4943V	ABCA13_ENST00000544596.1_Missense_Mutation_p.I673V	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4943	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TCCTCAGCACATCAAAAATAG	0.418																																					p.I4943V		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A14827G						PASS	.						97	94	95					7																	48654963		1926	4132	6058	SO:0001583	missense	154664	exon59			CAGCACATCAAAA	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.14827A>G	chr7.hg19:g.48654963A>G	ENSP00000411096:p.Ile4943Val	149.0	0.0	.		162.0	46.0	.	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	A	17.37	3.371572	0.61624	.	.	ENSG00000179869	ENST00000435803;ENST00000411975;ENST00000544596	D;D;D	0.97906	-4.6;-4.6;-4.6	5.99	2.22	0.28083	ABC transporter-like (1);	0.254751	0.27469	N	0.019238	D	0.94968	0.8372	N	0.25245	0.725	0.29963	N	0.819227	P;D;P	0.58268	0.679;0.982;0.921	B;P;B	0.50934	0.264;0.654;0.401	D	0.91892	0.5524	10	0.72032	D	0.01	.	7.8742	0.29584	0.4999:0.4258:0.0743:0.0	.	673;2645;4943	F5H7B7;Q86UQ4-3;Q86UQ4	.;.;ABCAD_HUMAN	V	4943;716;673	ENSP00000411096:I4943V;ENSP00000391042:I716V;ENSP00000442634:I673V	ENSP00000391042:I716V	I	+	1	0	ABCA13	48625509	0.221000	0.23642	0.940000	0.37924	0.947000	0.59692	0.258000	0.18387	0.492000	0.27815	-0.316000	0.08728	ATC	.	.	.	none		0.418	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		G	48654963	A	G	48654963	3	3	69	1	0	0	0	0	1	0	0	0	31	217	8	3	14890	3	ABCA13	7	48654963	Missense_Mutation	SNP	A	TCGA-A4-A772-01A-11D-A33Q-10		48654963	110483700	17	4565											
KEL	3792	hgsc.bcm.edu	37	chr7	142658912	142658912	+	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	cagagagttcccattccaccTgcctggctgcgttccctcgg	5	10	10	16	2	0	1	0	0	0	1	4	2	3	1	5	2	2	3	5	2	0	3			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr7:142658912T>G	ENST00000355265.2	-	2	525	c.51A>C	c.(49-51)gcA>gcC	p.A17A	KEL_ENST00000479768.2_5'UTR	NM_000420.2	NP_000411.1	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	17					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)					CCATTCCACCTGCCTGGCTGC	0.547																																					p.A17A		Atlas-SNP	.											.	KEL	128	.	0			c.A51C						PASS	.						283	240	255					7																	142658912		2203	4300	6503	SO:0001819	synonymous_variant	3792	exon2			TCCACCTGCCTGG	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.51A>C	chr7.hg19:g.142658912T>G		129.0	0.0	.		143.0	77.0	.	NM_000420	B2RBV4|Q96RS8|Q99885	Silent	SNP	ENST00000355265.2	hg19	CCDS34766.1																																																																																			.	.	.	none		0.547	KEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347671.2	NM_000420		G	142658912	T	G	142658912	2	3	69	1	0	0	0	0	0	0	0	1	8149	1567	55	5		5	KEL	7	142658912	Silent	SNP	T	TCGA-A4-A772-01A-11D-A33Q-10	94003949	142658912	16479751	18	4566											
LRP12	29967	hgsc.bcm.edu	37	chr8	105509750	105509750	+	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	tatctgtccagaagaagaaaCaactgtaagaggtgcatgag	16	8	11	6	0	1	5	0	1	1	4	2	5	2	5	1	1	3	2	1	1	6	2			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr8:105509750C>G	ENST00000276654.5	-	5	1138	c.1030G>C	c.(1030-1032)Gtt>Ctt	p.V344L	LRP12_ENST00000518375.1_5'Flank|LRP12_ENST00000424843.2_Missense_Mutation_p.V325L	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	344	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			GAAGAAGAAACAACTGTAAGA	0.388																																					p.V344L		Atlas-SNP	.											.	LRP12	124	.	0			c.G1030C						PASS	.						69	68	68					8																	105509750		2203	4300	6503	SO:0001583	missense	29967	exon5			AAGAAACAACTGT	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.1030G>C	chr8.hg19:g.105509750C>G	ENSP00000276654:p.Val344Leu	177.0	0.0	.		120.0	51.0	.	NM_013437	A8K137|B4DRQ2	Missense_Mutation	SNP	ENST00000276654.5	hg19	CCDS6303.1	.	.	.	.	.	.	.	.	.	.	C	19.27	3.795513	0.70452	.	.	ENSG00000147650	ENST00000424843;ENST00000276654	T;T	0.27402	1.67;1.67	5.95	5.95	0.96441	CUB (5);	0.000000	0.85682	D	0.000000	T	0.45074	0.1324	L	0.35487	1.065	0.80722	D	1	D;D	0.69078	0.99;0.997	D;D	0.79108	0.98;0.992	T	0.07290	-1.0780	10	0.12766	T	0.61	-26.5114	20.3748	0.98911	0.0:1.0:0.0:0.0	.	325;344	Q9Y561-2;Q9Y561	.;LRP12_HUMAN	L	325;344	ENSP00000399148:V325L;ENSP00000276654:V344L	ENSP00000276654:V344L	V	-	1	0	LRP12	105578926	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.263000	0.78421	2.817000	0.96982	0.563000	0.77884	GTT	.	.	.	none		0.388	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	NM_013437		G	105509750	C	G	105509750	3	3	69	1	0	0	0	0	1	0	0	0	8961	478	17	4	1561	4	LRP12	8	105509750	Missense_Mutation	SNP	C	TCGA-A4-A772-01A-11D-A33Q-10		105509750	40854272	19	4567											
FRMD3	257019	hgsc.bcm.edu	37	chr9	86004612	86004615	+	Frame_Shift_Del	DEL	TTTG	TTTG	-																															tggtcaatgagaaactgcccTttggtttccctctgcaaagg																								rs145028837		TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	TTTG	TTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr9:86004612_86004615delTTTG	ENST00000304195.3	-	2	362_365	c.156_159delCAAA	c.(154-159)accaaafs	p.TK52fs	FRMD3_ENST00000376438.1_Frame_Shift_Del_p.TK52fs	NM_001244960.1|NM_174938.5	NP_001231889.1|NP_777598.3	A2A2Y4	FRMD3_HUMAN	FERM domain containing 3	52	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)				breast(2)|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						GAAACTGCCCTTTGGTTTCCCTCT	0.5																																					p.53_54del		Atlas-Indel,Pindel	.											.	FRMD3	96	.	0			c.157_160del						PASS	.																																			SO:0001589	frameshift_variant	257019	exon2			.	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.156_159delCAAA	chr9.hg19:g.86004612_86004615delTTTG	ENSP00000303508:p.Thr52fs	109.0	0.0	0		80.0	30.0	0.375	NM_001244959	A8MQB0|B4DN14|Q53EP2|Q5JV59|Q5VZA1|Q86WP8|Q8IZ44|Q8N3Y5|Q8N9L2	Frame_Shift_Del	DEL	ENST00000304195.3	hg19	CCDS43840.1																																																																																			.	.	.	none		0.5	FRMD3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157355.1	NM_174938		-	86004615	TTTG	-	86004612	7	5	69	1	0	1	0	1	0	0	0	0	6057	1606	56	0	1686	0	FRMD3	9	86004612	Frame_Shift_Del	DEL	TTTG	TCGA-A4-A772-01A-11D-A33Q-10		86004612	55208819	20	4568											
SOHLH1	402381	hgsc.bcm.edu	37	chr9	138589408	138589408	+	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	acacctgcttgaatctgactCgacaacgtcaactgtaaaac	14	9	6	12	2	2	2	1	2	1	0	3	3	2	2	1	0	4	2	1	0	5	2	rs561649799		TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr9:138589408C>G	ENST00000298466.5	-	4	471	c.411G>C	c.(409-411)tcG>tcC	p.S137S	SOHLH1_ENST00000425225.1_Silent_p.S137S	NM_001012415.2	NP_001012415	Q5JUK2	SOLH1_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 1	137					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)		GAATCTGACTCGACAACGTCA	0.527																																					p.S137S		Atlas-SNP	.											.	SOHLH1	70	.	0			c.G411C						PASS	.						78	65	70					9																	138589408		2202	4300	6502	SO:0001819	synonymous_variant	402381	exon4			CTGACTCGACAAC	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.411G>C	chr9.hg19:g.138589408C>G		99.0	0.0	.		39.0	12.0	.	NM_001012415	C9JG81|Q5EE14|Q5EGC2|Q8NEE3	Silent	SNP	ENST00000298466.5	hg19	CCDS35174.1																																																																																			.	.	.	none		0.527	SOHLH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055018.2	NM_001012415		G	138589408	C	G	138589408	2	3	69	1	0	0	0	0	0	0	0	1	14936	871	31	4		4	SOHLH1	9	138589408	Silent	SNP	C	TCGA-A4-A772-01A-11D-A33Q-10	52584796	138589408	2624023	21	4569											
CACNA1B	774	hgsc.bcm.edu	37	chr9	140952502	140952502	+	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	tgctctcctctttgcccaggGtgctgaaacactccgtggat	6	12	10	13	1	2	1	0	1	2	0	4	2	3	2	3	2	4	2	3	2	1	1			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr9:140952502G>C	ENST00000371372.1	+	28	4253	c.4108G>C	c.(4108-4110)Gtg>Ctg	p.V1370L	CACNA1B_ENST00000371363.1_Splice_Site_p.V1370L|CACNA1B_ENST00000371355.4_Splice_Site_p.V1371L|CACNA1B_ENST00000277551.2_Splice_Site_p.V1370L|CACNA1B_ENST00000371357.1_Splice_Site_p.V1371L|CACNA1B_ENST00000277549.5_Splice_Site_p.V566L	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	1370					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	TTTGCCCAGGGTGCTGAAACA	0.567																																					p.V1370L		Atlas-SNP	.											.	CACNA1B	266	.	0			c.G4108C						PASS	.						119	112	114					9																	140952502		2003	4183	6186	SO:0001630	splice_region_variant	774	exon28			CCCAGGGTGCTGA	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.4107-1G>C	chr9.hg19:g.140952502G>C		104.0	0.0	.		95.0	33.0	.	NM_001243812	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	hg19	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.911067	0.92178	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000277549;ENST00000371363;ENST00000371357;ENST00000371355	D;D;D;D;D;D	0.97480	-4.4;-4.4;-4.4;-4.4;-4.4;-4.4	5.33	5.33	0.75918	.	0.062804	0.64402	D	0.000004	D	0.97501	0.9182	L	0.51853	1.615	0.80722	D	1	B;D;D	0.76494	0.008;0.999;0.999	B;D;D	0.74348	0.016;0.983;0.983	D	0.95747	0.8788	10	0.13108	T	0.6	.	19.4443	0.94840	0.0:0.0:1.0:0.0	.	1370;1371;1370	B1AQK4;B1AQK7;B1AQK6	.;.;.	L	1370;1370;566;1370;1371;1371	ENSP00000360423:V1370L;ENSP00000277551:V1370L;ENSP00000277549:V566L;ENSP00000360414:V1370L;ENSP00000360408:V1371L;ENSP00000360406:V1371L	ENSP00000277549:V566L	V	+	1	0	CACNA1B	140072323	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	9.725000	0.98778	2.682000	0.91365	0.555000	0.69702	GTG	.	.	.	none		0.567	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718	Missense_Mutation	C	140952502	G	C	140952502	5	2	69	1	0	0	0	0	0	0	1	0	2541	1275	44	4	4218	4	CACNA1B	9	140952502	Splice_Site	SNP	G	TCGA-A4-A772-01A-11D-A33Q-10	2363094	140952502	260929	22	4570											
KRTAP5-2	440021	hgsc.bcm.edu	37	chr11	1619255	1619255	+	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	cccacaggagccacagctggTgcaggaacaggctggcaccc	10	3	13	15	0	0	0	0	0	0	0	0	2	0	2	3	5	4	4	3	5	1	0			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr11:1619255T>A	ENST00000412090.1	-	1	269	c.226A>T	c.(226-228)Acc>Tcc	p.T76S	KRTAP5-AS1_ENST00000424148.1_RNA|KRTAP5-AS1_ENST00000534077.1_RNA|KRTAP5-AS1_ENST00000532922.1_RNA|KRTAP5-AS1_ENST00000524947.1_RNA	NM_001004325.1	NP_001004325.1	Q701N4	KRA52_HUMAN	keratin associated protein 5-2	76	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)		CCACAGCTGGTGCAGGAACAG	0.677																																					p.T76S		Atlas-SNP	.											KRTAP5-2,NS,malignant_melanoma,0,1	KRTAP5-2	38	.	0			c.A226T						PASS	.						79	101	94					11																	1619255		2202	4299	6501	SO:0001583	missense	440021	exon1			AGCTGGTGCAGGA	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.226A>T	chr11.hg19:g.1619255T>A	ENSP00000400041:p.Thr76Ser	68.0	1.0	.		46.0	2.0	.	NM_001004325	A9JTZ1	Missense_Mutation	SNP	ENST00000412090.1	hg19	CCDS31331.1	.	.	.	.	.	.	.	.	.	.	N	7.373	0.627221	0.14257	.	.	ENSG00000205867	ENST00000412090	T	0.00603	6.28	2.65	-0.183	0.13284	.	.	.	.	.	T	0.00178	0.0005	N	0.00210	-1.845	0.09310	N	0.999993	B	0.11235	0.004	B	0.06405	0.002	T	0.34153	-0.9840	9	0.07644	T	0.81	.	3.2935	0.06957	0.5374:0.0:0.1142:0.3484	.	76	Q701N4	KRA52_HUMAN	S	76	ENSP00000400041:T76S	ENSP00000400041:T76S	T	-	1	0	KRTAP5-2	1575831	0.111000	0.22076	0.725000	0.30721	0.572000	0.35998	-0.241000	0.08940	-0.911000	0.03843	-3.088000	0.00065	ACC	.	.	.	none		0.677	KRTAP5-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384775.1	NM_001004325		A	1619255	T	A	1619255	3	1	69	1	0	0	0	0	1	0	0	0	8568	1696	59	5	311	5	KRTAP5-2	11	1619255	Missense_Mutation	SNP	T	TCGA-A4-A772-01A-11D-A33Q-10		1619255	133387261	23	4571											
CREB3L1	90993	hgsc.bcm.edu	37	chr11	46334184	46334184	+	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	tctcagcccaggagagccgtCgtaagaagaaggagtatgtg	12	7	14	8	2	1	3	1	0	1	3	3	5	1	4	2	2	2	2	2	2	4	2			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr11:46334184C>T	ENST00000529193.1	+	7	1376	c.925C>T	c.(925-927)Cgt>Tgt	p.R309C	CREB3L1_ENST00000288400.3_Missense_Mutation_p.R309C			Q96BA8	CR3L1_HUMAN	cAMP responsive element binding protein 3-like 1	309	Basic motif. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				regulation of bone mineralization (GO:0030500)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)		FUS/CREB3L1(6)	NS(2)|breast(1)|large_intestine(4)|lung(2)|ovary(3)	12				GBM - Glioblastoma multiforme(35;0.0285)		GGAGAGCCGTCGTAAGAAGAA	0.562			T	FUS	myxofibrosarcoma																																p.R309C	Pancreas(3;159 194 19597 26278 47995)	Atlas-SNP	.		Dom	yes		11	11p11.2	90993	cAMP responsive element binding protein 3-like 1		M	.	CREB3L1	30	.	0			c.C925T						PASS	.						39	40	40					11																	46334184		1886	4102	5988	SO:0001583	missense	90993	exon7			AGCCGTCGTAAGA		CCDS53620.1	11q11	2013-01-10				ENSG00000157613		"basic leucine zipper proteins"	18856	protein-coding gene	gene with protein product	"BBF-2 homolog (drosophila)"						Standard	NM_052854		Approved	OASIS	uc021qil.1	Q96BA8		ENST00000529193.1:c.925C>T	chr11.hg19:g.46334184C>T	ENSP00000434939:p.Arg309Cys	115.0	0.0	.		71.0	29.0	.	NM_052854	Q8N2D5|Q96CP0	Missense_Mutation	SNP	ENST00000529193.1	hg19	CCDS53620.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.141715	0.77775	.	.	ENSG00000157613	ENST00000529193;ENST00000288400;ENST00000446415;ENST00000530518	T;T;T	0.77358	-1.09;-1.09;-1.09	4.69	4.69	0.59074	Basic-leucine zipper (bZIP) transcription factor (3);Eukaryotic transcription factor, Skn-1-like, DNA-binding (1);bZIP transcription factor, bZIP-1 (1);	0.168110	0.50627	D	0.000103	D	0.90376	0.6988	H	0.95294	3.65	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	D	0.92077	0.5669	10	0.87932	D	0	-9.1036	10.8454	0.46741	0.3258:0.6742:0.0:0.0	.	309	Q96BA8	CR3L1_HUMAN	C	309;309;221;69	ENSP00000434939:R309C;ENSP00000288400:R309C;ENSP00000436574:R69C	ENSP00000288400:R309C	R	+	1	0	CREB3L1	46290760	0.997000	0.39634	1.000000	0.80357	0.970000	0.65996	3.088000	0.50175	2.439000	0.82584	0.462000	0.41574	CGT	.	.	.	none		0.562	CREB3L1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389702.1	NM_052854		T	46334184	C	T	46334184	3	4	69	1	0	0	0	0	1	0	0	0	3858	884	31	1	951	1	CREB3L1	11	46334184	Missense_Mutation	SNP	C	TCGA-A4-A772-01A-11D-A33Q-10	44714929	46334184	88672332	24	4572											
NXF1	10482	hgsc.bcm.edu	37	chr11	62563986	62563986	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggaacagcaggccccatcaTggtaggcatccaggagccct	10	5	13	13	0	1	0	1	0	0	0	2	2	2	2	4	5	3	3	4	5	2	1			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr11:62563986T>C	ENST00000532297.1	-	15	1861	c.1232A>G	c.(1231-1233)cAt>cGt	p.H411R	NXF1_ENST00000294172.2_Missense_Mutation_p.H411R|NXF1_ENST00000533048.1_5'UTR|NXF1_ENST00000531709.2_3'UTR			Q9UBU9	NXF1_HUMAN	nuclear RNA export factor 1	411	NTF2. {ECO:0000255|PROSITE- ProRule:PRU00137}.				gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear inclusion body (GO:0042405)|nuclear pore (GO:0005643)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GGCCCCATCATGGTAGGCATC	0.517																																					p.H411R		Atlas-SNP	.											.	NXF1	67	.	0			c.A1232G						PASS	.						113	112	112					11																	62563986		2201	4299	6500	SO:0001583	missense	10482	exon14			CCATCATGGTAGG	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.1232A>G	chr11.hg19:g.62563986T>C	ENSP00000436679:p.His411Arg	113.0	0.0	.		87.0	38.0	.	NM_006362	B4E269|Q99799|Q9UQL2	Missense_Mutation	SNP	ENST00000532297.1	hg19	CCDS8037.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.552072	0.86127	.	.	ENSG00000162231	ENST00000294172;ENST00000532297;ENST00000530875	T;T;T	0.66638	-0.22;-0.22;-0.22	5.11	5.11	0.69529	Nuclear transport factor 2, Eukaryote (1);Nuclear transport factor 2 (1);	0.000000	0.85682	D	0.000000	D	0.84224	0.5425	M	0.91561	3.22	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.86541	0.1828	10	0.49607	T	0.09	-27.1453	12.906	0.58152	0.0:0.0:0.0:1.0	.	454;411	E9PIN3;Q9UBU9	.;NXF1_HUMAN	R	411;411;454	ENSP00000294172:H411R;ENSP00000436679:H411R;ENSP00000435742:H454R	ENSP00000294172:H411R	H	-	2	0	NXF1	62320562	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	7.548000	0.82154	2.159000	0.67721	0.443000	0.29094	CAT	.	.	.	none		0.517	NXF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395365.2	NM_006362		C	62563986	T	C	62563986	3	2	69	1	0	0	0	0	1	0	0	0	10789	1464	51	3	659	3	NXF1	11	62563986	Missense_Mutation	SNP	T	TCGA-A4-A772-01A-11D-A33Q-10	16229802	62563986	72442530	25	4573											
PKP2	5318	hgsc.bcm.edu	37	chr12	33003716	33003716	+	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	ctacctgttatttgttttttAgtctccaagtctctggtttg	5	21	7	8	0	2	0	0	0	2	0	4	0	2	0	2	1	1	3	2	1	4	7			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr12:33003716A>T	ENST00000070846.6	-	5	1386	c.1362T>A	c.(1360-1362)acT>acA	p.T454T	PKP2_ENST00000340811.4_Silent_p.T454T	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	454					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)					TTTGTTTTTTAGTCTCCAAGT	0.418																																					p.T454T		Atlas-SNP	.											.	PKP2	110	.	0			c.T1362A						PASS	.						135	132	133					12																	33003716		2203	4300	6503	SO:0001819	synonymous_variant	5318	exon5			TTTTTTAGTCTCC	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.1362T>A	chr12.hg19:g.33003716A>T		66.0	0.0	.		63.0	14.0	.	NM_004572	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Silent	SNP	ENST00000070846.6	hg19	CCDS8731.1																																																																																			.	.	.	none		0.418	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572		T	33003716	A	T	33003716	2	4	69	1	0	0	0	0	0	0	0	1	11992	407	15	5		5	PKP2	12	33003716	Silent	SNP	A	TCGA-A4-A772-01A-11D-A33Q-10		33003716	100848179	26	4574											
UBC	7316	hgsc.bcm.edu	37	chr12	125397821	125397821	+	Missense_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	cactgggctccacctcgaggGtgatggtcttaccagtcagg	7	9	13	12	1	2	1	1	1	1	0	4	2	3	1	3	4	1	1	3	4	1	1			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr12:125397821G>A	ENST00000536769.1	-	1	2073	c.497C>T	c.(496-498)aCc>aTc	p.T166I	UBC_ENST00000538617.1_Intron|UBC_ENST00000546120.1_Intron|MIR5188_ENST00000583467.1_RNA|UBC_ENST00000339647.5_Missense_Mutation_p.T166I|UBC_ENST00000536661.1_5'Flank			P0CG48	UBC_HUMAN	ubiquitin C	166	Ubiquitin-like 3. {ECO:0000255|PROSITE- ProRule:PRU00214}.				activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protease binding (GO:0002020)			breast(3)|endometrium(4)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.17e-05)|Epithelial(86;0.000207)|all cancers(50;0.00308)		CACCTCGAGGGTGATGGTCTT	0.517																																					p.T166I		Atlas-SNP	.											.	UBC	79	.	0			c.C497T						PASS	.						169	168	169					12																	125397821		2203	4298	6501	SO:0001583	missense	7316	exon2			TCGAGGGTGATGG		CCDS9260.1	12q24.3	2008-09-08			ENSG00000150991	ENSG00000150991			12468	protein-coding gene	gene with protein product	"polyubiquitin-C"	191340				1315303, 11872750	Standard	NM_021009		Approved		uc001ugs.4	P0CG48		ENST00000536769.1:c.497C>T	chr12.hg19:g.125397821G>A	ENSP00000441543:p.Thr166Ile	169.0	0.0	.		161.0	7.0	.	NM_021009	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Missense_Mutation	SNP	ENST00000536769.1	hg19	CCDS9260.1	.	.	.	.	.	.	.	.	.	.	-	17.15	3.316028	0.60524	.	.	ENSG00000150991	ENST00000536769;ENST00000535460;ENST00000339647	T;T	0.75477	-0.94;-0.94	3.91	3.91	0.45181	Ubiquitin supergroup (1);Ubiquitin (2);	0.000000	0.49305	U	0.000150	D	0.86879	0.6039	M	0.85041	2.73	0.80722	D	1	D;D;D	0.65815	0.995;0.994;0.995	D;D;D	0.87578	0.998;0.975;0.998	D	0.89541	0.3792	10	0.87932	D	0	.	14.8482	0.70275	0.0:0.0:1.0:0.0	.	255;166;166	Q66K58;F5H7K6;P0CG48	.;.;UBC_HUMAN	I	166	ENSP00000441543:T166I;ENSP00000344818:T166I	ENSP00000344818:T166I	T	-	2	0	UBC	123963774	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	8.136000	0.89610	1.897000	0.54924	0.555000	0.69702	ACC	.	.	.	none		0.517	UBC-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400177.1	NM_021009		A	125397821	G	A	125397821	3	1	69	1	0	0	0	0	1	0	0	0	16854	1261	44	2	1564	2	UBC	12	125397821	Missense_Mutation	SNP	G	TCGA-A4-A772-01A-11D-A33Q-10	92394105	125397821	8454074	27	4575											
TMTC4	84899	hgsc.bcm.edu	37	chr13	101287287	101287287	+	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	tcagttgatacctttttcttGgtatgtttgctcagggctcc	5	18	9	9	0	3	1	2	1	1	0	4	1	4	1	2	2	2	5	2	2	2	7			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr13:101287287G>T	ENST00000376234.3	-	10	1497	c.1308C>A	c.(1306-1308)acC>acA	p.T436T	TMTC4_ENST00000328767.5_Silent_p.T325T|TMTC4_ENST00000342624.5_Silent_p.T455T|TMTC4_ENST00000462211.1_5'UTR	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	436						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)					CCTTTTTCTTGGTATGTTTGC	0.502																																					p.T455T		Atlas-SNP	.											.	TMTC4	103	.	0			c.C1365A						PASS	.						86	81	82					13																	101287287		2203	4300	6503	SO:0001819	synonymous_variant	84899	exon11			TTTCTTGGTATGT		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.1308C>A	chr13.hg19:g.101287287G>T		97.0	0.0	.		89.0	38.0	.	NM_032813	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Silent	SNP	ENST00000376234.3	hg19	CCDS41904.1																																																																																			.	.	.	none		0.502	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813		T	101287287	G	T	101287287	2	4	69	1	0	0	0	0	0	0	0	1	16275	1335	47	4		4	TMTC4	13	101287287	Silent	SNP	G	TCGA-A4-A772-01A-11D-A33Q-10		101287287	13882591	28	4576											
OXA1L	9056	hgsc.bcm.edu	37	chr14	23240318	23240318	+	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	0	0	0	0	0	0	0	agtacgcactgtacttaaaaTcccccagcgtgttgtacatg	11	11	8	11	2	0	0	0	0	0	0	1	0	1	0	2	0	4	5	2	0	5	5			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr14:23240318T>C	ENST00000397532.3	-	0	2447				OXA1L_ENST00000412791.1_Missense_Mutation_p.I344T|OXA1L_ENST00000285848.5_Missense_Mutation_p.I404T|SLC7A7_ENST00000554061.1_5'Flank|OXA1L_ENST00000604262.1_Missense_Mutation_p.I344T|OXA1L_ENST00000358043.5_Missense_Mutation_p.I328T			Q9UM01	YLAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, y+L system), member 7						amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(2)	20	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.00741)		GTACTTAAAATCCCCCAGCGT	0.488																																					p.I404T		Atlas-SNP	.											.	OXA1L	49	.	0			c.T1211C						PASS	.						117	104	108					14																	23240318		2203	4300	6503	SO:0001628	intergenic_variant	5018	exon8			TTAAAATCCCCCA	AF092032	CCDS9574.1	14q11.2	2014-09-17	2011-07-12		ENSG00000155465	ENSG00000155465		"Solute carriers"	11065	protein-coding gene	gene with protein product		603593		LPI		9829974	Standard	NM_001126106		Approved	y+LAT-1	uc001wgs.4	Q9UM01	OTTHUMG00000028692		chr14.hg19:g.23240318T>C		135.0	0.0	.		84.0	36.0	.	NM_005015	B2RAU0|D3DS26|O95984|Q53XC1|Q86U07|Q9P2V5	Missense_Mutation	SNP	ENST00000397532.3	hg19	CCDS9574.1	.	.	.	.	.	.	.	.	.	.	T	16.12	3.034342	0.54896	.	.	ENSG00000155463	ENST00000285848;ENST00000412791;ENST00000358043	T;T;T	0.42900	0.96;1.05;0.98	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.67449	0.2894	M	0.82630	2.6	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.78314	0.987;0.991;0.975	T	0.72959	-0.4133	10	0.87932	D	0	-21.7899	14.954	0.71098	0.0:0.0:0.0:1.0	.	344;344;404	E7EVY0;Q15070;Q2M1J6	.;OXA1L_HUMAN;.	T	404;344;328	ENSP00000285848:I404T;ENSP00000387601:I344T;ENSP00000350740:I328T	ENSP00000285848:I404T	I	+	2	0	OXA1L	22310158	1.000000	0.71417	1.000000	0.80357	0.036000	0.12997	6.496000	0.73670	2.162000	0.67917	0.496000	0.49642	ATC	.	.	.	none		0.488	SLC7A7-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071636.3			C	23240318	T	C	23240318	1	2	69	0	1	0	0	0	0	0	0	0	11335	1435	50	3		3	OXA1L	14	23240318	IGR	SNP	T	TCGA-A4-A772-01A-11D-A33Q-10		23240318	84109222	29	4577											
IPO4	79711	hgsc.bcm.edu	37	chr14	24656090	24656090	+	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	cactccaggctcacctccagGcagaatgtgaggacttcaga	11	7	10	13	0	2	3	2	1	0	2	4	4	4	4	3	3	0	2	3	3	1	1			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr14:24656090G>T	ENST00000354464.6	-	8	926	c.750C>A	c.(748-750)tgC>tgA	p.C250*	RP11-468E2.2_ENST00000561419.1_3'UTR	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4	250					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)		TCACCTCCAGGCAGAATGTGA	0.552																																					p.C250X		Atlas-SNP	.											.	IPO4	74	.	0			c.C750A						PASS	.						56	62	60					14																	24656090		2120	4256	6376	SO:0001587	stop_gained	79711	exon8			CTCCAGGCAGAAT	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.750C>A	chr14.hg19:g.24656090G>T	ENSP00000346453:p.Cys250*	89.0	0.0	.		65.0	17.0	.	NM_024658	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Nonsense_Mutation	SNP	ENST00000354464.6	hg19	CCDS9616.1	.	.	.	.	.	.	.	.	.	.	G	36	5.871003	0.97049	.	.	ENSG00000196497	ENST00000354464	.	.	.	4.96	4.07	0.47477	.	0.117958	0.64402	D	0.000019	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.6276	10.7129	0.45995	0.0895:0.0:0.9105:0.0	.	.	.	.	X	250	.	ENSP00000346453:C250X	C	-	3	2	IPO4	23725930	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.957000	0.49137	1.454000	0.47793	0.655000	0.94253	TGC	.	.	.	none		0.552	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658		T	24656090	G	T	24656090	4	4	69	1	0	0	0	0	0	1	0	0	7802	1195	42	4	2587	4	IPO4	14	24656090	Nonsense_Mutation	SNP	G	TCGA-A4-A772-01A-11D-A33Q-10	1415772	24656090	82693450	30	4578											
SERPINA5	5104	hgsc.bcm.edu	37	chr14	95053705	95053705	+	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	caaagaacagccaccatgcaGctcttcctcctcttgtgcct	9	10	6	16	0	2	1	0	0	2	1	4	1	4	1	5	0	5	2	5	0	2	2			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr14:95053705G>A	ENST00000554866.1	+	2	120	c.6G>A	c.(4-6)caG>caA	p.Q2Q	SERPINA5_ENST00000329597.7_Silent_p.Q2Q|SERPINA5_ENST00000554276.1_Silent_p.Q2Q|SERPINA5_ENST00000553780.1_Silent_p.Q2Q			P05154	IPSP_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5	2					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)	CCACCATGCAGCTCTTCCTCC	0.587																																					p.Q2Q		Atlas-SNP	.											.	SERPINA5	69	.	0			c.G6A						PASS	.						80	89	86					14																	95053705		2203	4300	6503	SO:0001819	synonymous_variant	5104	exon3			CATGCAGCTCTTC	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.6G>A	chr14.hg19:g.95053705G>A		24.0	0.0	.		22.0	10.0	.	NM_000624	Q07616|Q9UG30	Silent	SNP	ENST00000554866.1	hg19	CCDS9928.1																																																																																			.	.	.	none		0.587	SERPINA5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410726.1	NM_000624		A	95053705	G	A	95053705	2	1	69	1	0	0	0	0	0	0	0	1	14105	962	34	2		2	SERPINA5	14	95053705	Silent	SNP	G	TCGA-A4-A772-01A-11D-A33Q-10	70397615	95053705	12295835	31	4579											
SPTBN5	51332	hgsc.bcm.edu	37	chr15	42142086	42142086	+	Frame_Shift_Del	DEL	G	G	-																															cctgagtagacatccaggccGggcatccttggtcgtgcact																										TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr15:42142086delG	ENST00000320955.6	-	67	11220	c.10993delC	c.(10993-10995)cggfs	p.R3665fs	RNA5SP393_ENST00000363423.1_RNA	NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	3665					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)		CATCCAGGCCGGGCATCCTTG	0.602																																					p.R3630fs		Atlas-Indel,Pindel	.											.	SPTBN5	171	.	0			c.10889delG						PASS	.						56	59	58					15																	42142086		1926	4125	6051	SO:0001589	frameshift_variant	51332	exon67			.	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.10993delC	chr15.hg19:g.42142086delG	ENSP00000317790:p.Arg3665fs	67.0	0.0	0		74.0	31.0	0.418919	NM_016642		Frame_Shift_Del	DEL	ENST00000320955.6	hg19																																																																																				.	.	.	none		0.602	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		-	42142086	G	-	42142086	7	5	69	1	0	1	0	1	0	0	0	0	15134	1115	39	0	39	0	SPTBN5	15	42142086	Frame_Shift_Del	DEL	G	TCGA-A4-A772-01A-11D-A33Q-10		42142086	60389306	32	4580											
CLEC16A	23274	hgsc.bcm.edu	37	chr16	11214588	11214588	+	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	agcctgatgtgtccaggcttGgctggggagtggtcaagttt	6	12	16	7	0	1	1	1	1	0	0	2	2	2	2	2	5	1	3	2	5	1	2			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr16:11214588G>T	ENST00000409790.1	+	20	2463	c.2233G>T	c.(2233-2235)Ggc>Tgc	p.G745C	CLEC16A_ENST00000465491.1_3'UTR|CLEC16A_ENST00000409552.3_Missense_Mutation_p.G727C	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						GTCCAGGCTTGGCTGGGGAGT	0.527																																					p.G745C		Atlas-SNP	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2233T						PASS	.						112	115	114					16																	11214588		2054	4203	6257	SO:0001583	missense	23274	exon19			AGGCTTGGCTGGG	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.2233G>T	chr16.hg19:g.11214588G>T	ENSP00000387122:p.Gly745Cys	73.0	0.0	.		92.0	4.0	.	NM_015226		Missense_Mutation	SNP	ENST00000409790.1	hg19	CCDS45409.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.592315	0.86953	.	.	ENSG00000038532	ENST00000409790;ENST00000542102;ENST00000409552	T	0.65549	-0.16	5.58	4.59	0.56863	.	0.000000	0.85682	D	0.000000	T	0.80099	0.4561	M	0.83118	2.625	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.971	T	0.83060	-0.0148	10	0.87932	D	0	-26.9241	14.9754	0.71267	0.0:0.0:0.8573:0.1427	.	745;727	Q2KHT3;Q2KHT3-2	CL16A_HUMAN;.	C	745;745;727	ENSP00000387122:G745C	ENSP00000386495:G727C	G	+	1	0	CLEC16A	11122089	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.516000	0.81772	2.640000	0.89533	0.561000	0.74099	GGC	.	.	.	none		0.527	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226		T	11214588	G	T	11214588	3	4	69	1	0	0	0	0	1	0	0	0	3502	1348	47	4	2307	4	CLEC16A	16	11214588	Missense_Mutation	SNP	G	TCGA-A4-A772-01A-11D-A33Q-10		11214588	79140165	33	4581											
NT5M	56953	hgsc.bcm.edu	37	chr17	17209883	17209883	+	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	gccatcagcatttgggagtcAaagaatttcttttttgaact	11	15	8	7	0	3	2	2	1	1	1	3	3	3	3	1	1	2	1	1	1	3	5			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr17:17209883A>T	ENST00000389022.4	+	2	510	c.294A>T	c.(292-294)tcA>tcT	p.S98S		NM_020201.3	NP_064586.1	Q9NPB1	NT5M_HUMAN	5',3'-nucleotidase, mitochondrial	98					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						TTTGGGAGTCAAAGAATTTCT	0.507																																					p.S98S		Atlas-SNP	.											.	NT5M	17	.	0			c.A294T						PASS	.						147	155	152					17																	17209883		2203	4300	6503	SO:0001819	synonymous_variant	56953	exon2			GGAGTCAAAGAAT	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.294A>T	chr17.hg19:g.17209883A>T		65.0	0.0	.		68.0	15.0	.	NM_020201		Silent	SNP	ENST00000389022.4	hg19	CCDS32581.1																																																																																			.	.	.	none		0.507	NT5M-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446045.1			T	17209883	A	T	17209883	2	4	69	1	0	0	0	0	0	0	0	1	10701	117	5	5		5	NT5M	17	17209883	Silent	SNP	A	TCGA-A4-A772-01A-11D-A33Q-10		17209883	63985327	34	4582											
TBX21	30009	hgsc.bcm.edu	37	chr17	45822561	45822561	+	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	ccccccttggtgtggactgaGattgcccccatccggccgga	5	8	12	16	2	0	1	0	1	0	1	1	4	1	3	7	4	1	0	7	4	0	2			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr17:45822561G>C	ENST00000177694.1	+	6	1648	c.1437G>C	c.(1435-1437)gaG>gaC	p.E479D		NM_013351.1	NP_037483.1	Q9UL17	TBX21_HUMAN	T-box 21	479					cellular response to organic substance (GO:0071310)|lymphocyte migration (GO:0072676)|multicellular organismal development (GO:0007275)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	neuronal cell body (GO:0043025)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|endometrium(1)|large_intestine(3)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	22						TGTGGACTGAGATTGCCCCCA	0.642																																					p.E479D		Atlas-SNP	.											.	TBX21	50	.	0			c.G1437C						PASS	.						42	43	43					17																	45822561		2203	4300	6503	SO:0001583	missense	30009	exon6			GACTGAGATTGCC	AF093098	CCDS11514.1	17q21.2	2008-06-23				ENSG00000073861		"T-boxes"	11599	protein-coding gene	gene with protein product		604895					Standard	NM_013351		Approved	TBLYM, T-bet	uc002ilv.1	Q9UL17		ENST00000177694.1:c.1437G>C	chr17.hg19:g.45822561G>C	ENSP00000177694:p.Glu479Asp	71.0	0.0	.		87.0	43.0	.	NM_013351		Missense_Mutation	SNP	ENST00000177694.1	hg19	CCDS11514.1	.	.	.	.	.	.	.	.	.	.	G	11.24	1.581500	0.28180	.	.	ENSG00000073861	ENST00000177694	D	0.87179	-2.22	4.65	-0.982	0.10266	.	0.577561	0.17764	N	0.162817	T	0.76069	0.3936	L	0.47016	1.485	0.42346	D	0.99235	B	0.10296	0.003	B	0.10450	0.005	T	0.59768	-0.7392	10	0.29301	T	0.29	.	0.7332	0.00961	0.2942:0.1842:0.3602:0.1614	.	479	Q9UL17	TBX21_HUMAN	D	479	ENSP00000177694:E479D	ENSP00000177694:E479D	E	+	3	2	TBX21	43177560	0.955000	0.32602	0.856000	0.33681	0.903000	0.53119	-0.086000	0.11233	-0.012000	0.14223	-0.137000	0.14449	GAG	.	.	.	none		0.642	TBX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441365.1	NM_013351		C	45822561	G	C	45822561	3	2	69	1	0	0	0	0	1	0	0	0	15669	933	33	4	1459	4	TBX21	17	45822561	Missense_Mutation	SNP	G	TCGA-A4-A772-01A-11D-A33Q-10	28612678	45822561	35372649	35	4583											
ABCC3	8714	hgsc.bcm.edu	37	chr17	48755182	48755182	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctatctactcccacttttcGgagacagtgactggtgccag	8	11	9	13	1	1	2	0	1	1	1	3	3	2	2	3	2	2	0	3	2	2	4	rs142831476		TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr17:48755182G>A	ENST00000285238.8	+	24	3536	c.3456G>A	c.(3454-3456)tcG>tcA	p.S1152S		NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	1152	ABC transmembrane type-1 2. {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)	CCCACTTTTCGGAGACAGTGA	0.542																																					p.S1152S		Atlas-SNP	.											.	ABCC3	138	.	0			c.G3456A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	134	137	136		3456	-0.4	1	17	dbSNP_134	136	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ABCC3	NM_003786.3		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		1152/1528	48755182	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	8714	exon24			CTTTTCGGAGACA	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.3456G>A	chr17.hg19:g.48755182G>A		97.0	0.0	.		130.0	40.0	.	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Silent	SNP	ENST00000285238.8	hg19	CCDS32681.1	.	.	.	.	.	.	.	.	.	.	G	10.28	1.307492	0.23821	2.27E-4	1.16E-4	ENSG00000108846	ENST00000513745	.	.	.	5.7	-0.425	0.12317	.	.	.	.	.	T	0.40015	0.1100	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.28650	-1.0037	4	.	.	.	-6.2185	1.0684	0.01616	0.2099:0.2093:0.361:0.2199	.	.	.	.	R	256	.	.	G	+	1	0	ABCC3	46110181	0.079000	0.21365	0.999000	0.59377	0.994000	0.84299	-0.672000	0.05244	0.340000	0.23745	0.655000	0.94253	GGA	.	G|1.000;A|0.000	0.000	weak		0.542	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038		A	48755182	G	A	48755182	2	1	69	1	0	0	0	0	0	0	0	1	54	1103	39	1		1	ABCC3	17	48755182	Silent	SNP	G	TCGA-A4-A772-01A-11D-A33Q-10	2932621	48755182	32440028	36	4584											
MED13	9969	hgsc.bcm.edu	37	chr17	60112944	60112944	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctgtctccatgcaagaaaaAggtgaaggagcaggacaagt	15	6	13	7	0	1	2	0	1	1	1	2	4	1	4	1	3	2	3	1	3	5	0			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr17:60112944A>G	ENST00000397786.2	-	4	572	c.496T>C	c.(496-498)Ttt>Ctt	p.F166L	Y_RNA_ENST00000363972.1_RNA	NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	166					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						TGCAAGAAAAAGGTGAAGGAG	0.373																																					p.F166L		Atlas-SNP	.											.	MED13	181	.	0			c.T496C						PASS	.						90	81	84					17																	60112944		1896	4123	6019	SO:0001583	missense	9969	exon4			AGAAAAAGGTGAA	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.496T>C	chr17.hg19:g.60112944A>G	ENSP00000380888:p.Phe166Leu	62.0	0.0	.		79.0	4.0	.	NM_005121	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	hg19	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	A	32	5.162757	0.94727	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	T	0.80653	-1.4	5.33	5.33	0.75918	Mediator complex, subunit Med13, N-terminal, metazoa/fungi (1);	0.000000	0.85682	D	0.000000	D	0.90721	0.7088	M	0.87381	2.88	0.80722	D	1	D	0.63046	0.992	D	0.76071	0.987	D	0.92397	0.5926	10	0.87932	D	0	-7.7639	15.5854	0.76479	1.0:0.0:0.0:0.0	.	166	Q9UHV7	MED13_HUMAN	L	166;165	ENSP00000380888:F166L	ENSP00000262436:F165L	F	-	1	0	MED13	57467726	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.867000	0.92314	2.139000	0.66308	0.482000	0.46254	TTT	.	.	.	none		0.373	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		G	60112944	A	G	60112944	3	3	69	1	0	0	0	0	1	0	0	0	9437	72	3	3	6136	3	MED13	17	60112944	Missense_Mutation	SNP	A	TCGA-A4-A772-01A-11D-A33Q-10	11357762	60112944	21082266	37	4585											
SLC44A2	57153	hgsc.bcm.edu	37	chr19	10738606	10738606	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttccacagcctggactcaTggagaccctcgaaaggtgat	10	9	10	12	1	1	2	1	1	0	1	3	5	2	3	3	3	1	0	3	3	1	1	rs376552555		TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr19:10738606T>C	ENST00000335757.5	+	4	547	c.171T>C	c.(169-171)caT>caC	p.H57H	SLC44A2_ENST00000407327.4_Silent_p.H55H|SLC44A2_ENST00000586078.1_Silent_p.H57H			Q8IWA5	CTL2_HUMAN	solute carrier family 44 (choline transporter), member 2	57					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)	CCTGGACTCATGGAGACCCTC	0.597																																					p.H57H		Atlas-SNP	.											.	SLC44A2	56	.	0			c.T171C						PASS	.	T	,	0,4406		0,0,2203	72	62	66		165,171	-4.8	0.9	19		66	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	SLC44A2	NM_001145056.1,NM_020428.3	,	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	,	55/705,57/707	10738606	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	57153	exon4			GACTCATGGAGAC	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.171T>C	chr19.hg19:g.10738606T>C		188.0	0.0	.		125.0	49.0	.	NM_020428	B2RBB1|B3KNH3|B4DFJ0|F2Q9D7|Q658V1|Q658Z2|Q6PJV7|Q8N2F0|Q9NY68	Silent	SNP	ENST00000335757.5	hg19	CCDS12245.1																																																																																			.	.	.	weak		0.597	SLC44A2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452045.1			C	10738606	T	C	10738606	2	2	69	1	0	0	0	0	0	0	0	1	14649	1461	51	3		3	SLC44A2	19	10738606	Silent	SNP	T	TCGA-A4-A772-01A-11D-A33Q-10		10738606	48390377	38	4586											
OR10H2	26538	hgsc.bcm.edu	37	chr19	15838984	15838984	+	Missense_Mutation	SNP	T	T	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	cacgctgctgggcaacctgcTcatcatggccaccgtctgga	7	8	11	15	2	3	0	2	0	1	0	3	1	3	1	3	3	3	4	3	3	1	0			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr19:15838984T>G	ENST00000305899.3	+	1	151	c.131T>G	c.(130-132)cTc>cGc	p.L44R		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	44						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(1)	27	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					GGCAACCTGCTCATCATGGCC	0.592																																					p.L44R		Atlas-SNP	.											.	OR10H2	59	.	0			c.T131G						PASS	.						210	173	186					19																	15838984		2203	4297	6500	SO:0001583	missense	26538	exon1			ACCTGCTCATCAT	AC004597	CCDS12333.1	19p13.1	2012-08-09				ENSG00000171942		"GPCR / Class A : Olfactory receptors"	8173	protein-coding gene	gene with protein product							Standard	NM_013939		Approved		uc002nbm.2	O60403		ENST00000305899.3:c.131T>G	chr19.hg19:g.15838984T>G	ENSP00000306095:p.Leu44Arg	92.0	0.0	.		95.0	41.0	.	NM_013939	Q6IFQ1|Q96R58	Missense_Mutation	SNP	ENST00000305899.3	hg19	CCDS12333.1	.	.	.	.	.	.	.	.	.	.	.	16.26	3.074499	0.55646	.	.	ENSG00000171942	ENST00000305899	T	0.02863	4.13	2.88	2.88	0.33553	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44285	D	0.000469	T	0.17577	0.0422	H	0.94306	3.52	0.35461	D	0.796538	D	0.59357	0.985	D	0.65233	0.933	T	0.22521	-1.0214	10	0.87932	D	0	.	8.94	0.35725	0.0:0.0:0.0:1.0	.	44	O60403	O10H2_HUMAN	R	44	ENSP00000306095:L44R	ENSP00000306095:L44R	L	+	2	0	OR10H2	15699984	0.001000	0.12720	1.000000	0.80357	0.961000	0.63080	0.586000	0.23894	1.186000	0.42985	0.438000	0.28831	CTC	.	.	.	none		0.592	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1			G	15838984	T	G	15838984	3	3	69	1	0	0	0	0	1	0	0	0	10913	1551	54	5	133	5	OR10H2	19	15838984	Missense_Mutation	SNP	T	TCGA-A4-A772-01A-11D-A33Q-10	5100378	15838984	43289999	39	4587											
HAMP	57817	hgsc.bcm.edu	37	chr19	35775707	35775707	+	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	cacagacgggacaacttgcaGagctgcaaccccaggacaga	14	3	11	13	1	0	3	0	0	0	3	0	5	0	5	2	2	5	3	2	2	2	1			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr19:35775707G>T	ENST00000598398.1	+	3	402	c.106G>T	c.(106-108)Gag>Tag	p.E36*	HAMP_ENST00000222304.3_Nonsense_Mutation_p.E36*	NM_021175.2	NP_066998.1	P81172	HEPC_HUMAN	hepcidin antimicrobial peptide	36					cellular iron ion homeostasis (GO:0006879)|defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|immune response (GO:0006955)|killing of cells of other organism (GO:0031640)	apical cortex (GO:0045179)|extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|large_intestine(1)|lung(1)	4	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)		Epithelial(14;7.4e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.47e-19)|all cancers(14;4.17e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			ACAACTTGCAGAGCTGCAACC	0.632																																					p.E36X		Atlas-SNP	.											.	HAMP	14	.	0			c.G106T						PASS	.						81	79	80					19																	35775707		2203	4300	6503	SO:0001587	stop_gained	57817	exon2			CTTGCAGAGCTGC	AF309489	CCDS12454.1	19q13.1	2014-09-17				ENSG00000105697			15598	protein-coding gene	gene with protein product		606464				11034317, 11113132	Standard	NM_021175		Approved	LEAP-1, HEPC, HFE2B, LEAP1	uc002nyw.3	P81172		ENST00000598398.1:c.106G>T	chr19.hg19:g.35775707G>T	ENSP00000471894:p.Glu36*	90.0	0.0	.		80.0	20.0	.	NM_021175	Q1HE14|Q9BY68	Nonsense_Mutation	SNP	ENST00000598398.1	hg19	CCDS12454.1	.	.	.	.	.	.	.	.	.	.	G	15.41	2.825924	0.50739	.	.	ENSG00000105697	ENST00000222304	.	.	.	4.51	4.51	0.55191	.	0.875034	0.09823	N	0.751245	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-6.4081	12.6114	0.56554	0.0:0.0:1.0:0.0	.	.	.	.	X	36	.	ENSP00000222304:E36X	E	+	1	0	HAMP	40467547	0.001000	0.12720	0.009000	0.14445	0.004000	0.04260	0.677000	0.25262	2.348000	0.79779	0.561000	0.74099	GAG	.	.	.	none		0.632	HAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466067.1	NM_021175		T	35775707	G	T	35775707	4	4	69	1	0	0	0	0	0	1	0	0	6955	943	33	4	112	4	HAMP	19	35775707	Nonsense_Mutation	SNP	G	TCGA-A4-A772-01A-11D-A33Q-10	19936723	35775707	23353276	40	4588											
MYH7B	57644	hgsc.bcm.edu	37	chr20	33586408	33586408	+	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	caaagcctggaagagttgcgGcgccagctagaggaggaaag	13	4	16	8	2	0	2	0	0	0	2	0	5	0	5	2	4	3	2	2	4	4	2			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr20:33586408G>T	ENST00000262873.7	+	32	4187	c.4095G>T	c.(4093-4095)cgG>cgT	p.R1365R		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	1323						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)			AAGAGTTGCGGCGCCAGCTAG	0.632																																					p.R1365R		Atlas-SNP	.											MYH7B,NS,adenocarcinoma,0,1	MYH7B	145	.	0			c.G4095T						PASS	.						32	37	36					20																	33586408		2075	4214	6289	SO:0001819	synonymous_variant	57644	exon34			GTTGCGGCGCCAG	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.4095G>T	chr20.hg19:g.33586408G>T		49.0	0.0	.		33.0	15.0	.	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Silent	SNP	ENST00000262873.7	hg19	CCDS42869.1																																																																																			.	.	.	none		0.632	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884		T	33586408	G	T	33586408	2	4	69	1	0	0	0	0	0	0	0	1	10047	1190	42	4		4	MYH7B	20	33586408	Silent	SNP	G	TCGA-A4-A772-01A-11D-A33Q-10		33586408	29439112	41	4589											
SLCO4A1	28231	hgsc.bcm.edu	37	chr20	61299155	61299155	+	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	gcaacgctgcctgcagctgcCagccagaacactacagccct	10	5	9	17	1	0	1	0	0	0	1	0	1	0	1	4	0	9	4	4	0	3	1			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr20:61299155C>A	ENST00000370507.1	+	7	1627	c.1531C>A	c.(1531-1533)Cag>Aag	p.Q511K	RP11-93B14.5_ENST00000451648.1_RNA|RP11-93B14.5_ENST00000411824.1_RNA|SLCO4A1_ENST00000217159.1_Missense_Mutation_p.Q511K|RP11-93B14.5_ENST00000433126.1_RNA|SLCO4A1_ENST00000470412.1_3'UTR			Q96BD0	SO4A1_HUMAN	solute carrier organic anion transporter family, member 4A1	511	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				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)	CTGCAGCTGCCAGCCAGAACA	0.652																																					p.Q511K	Pancreas(168;741 2006 10379 40139 45334)	Atlas-SNP	.											.	SLCO4A1	65	.	0			c.C1531A						PASS	.						68	66	66					20																	61299155		2203	4300	6503	SO:0001583	missense	28231	exon8			AGCTGCCAGCCAG	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.1531C>A	chr20.hg19:g.61299155C>A	ENSP00000359538:p.Gln511Lys	111.0	0.0	.		75.0	29.0	.	NM_016354	Q9H4T7|Q9H4T8|Q9H8P2|Q9NWX8|Q9UI35|Q9UIG7	Missense_Mutation	SNP	ENST00000370507.1	hg19	CCDS13501.1	.	.	.	.	.	.	.	.	.	.	C	0.994	-0.692948	0.03303	.	.	ENSG00000101187	ENST00000217159;ENST00000370512;ENST00000370507;ENST00000342674	T;T	0.04083	3.71;3.71	5.06	2.0	0.26442	Proteinase inhibitor I1, Kazal (1);Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);Protease inhibitor, Kazal-type (1);	1.148120	0.06393	N	0.717436	T	0.03959	0.0111	L	0.33245	0.995	0.09310	N	0.999998	B	0.06786	0.001	B	0.12156	0.007	T	0.47315	-0.9127	10	0.06099	T	0.92	.	5.8255	0.18550	0.0:0.5806:0.1286:0.2908	.	511	Q96BD0	SO4A1_HUMAN	K	511;511;511;363	ENSP00000217159:Q511K;ENSP00000359538:Q511K	ENSP00000217159:Q511K	Q	+	1	0	SLCO4A1	60769600	0.000000	0.05858	0.157000	0.22605	0.015000	0.08874	-0.466000	0.06672	0.143000	0.18926	0.655000	0.94253	CAG	.	.	.	none		0.652	SLCO4A1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080048.2	NM_016354		A	61299155	C	A	61299155	3	1	69	1	0	0	0	0	1	0	0	0	14742	595	21	4	1557	4	SLCO4A1	20	61299155	Missense_Mutation	SNP	C	TCGA-A4-A772-01A-11D-A33Q-10	27712747	61299155	1726365	42	4590											
TRIOBP	11078	hgsc.bcm.edu	37	chr22	38153684	38153684	+	Missense_Mutation	SNP	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	cccagaagggccccctgaagGcaggggagcagcgggcgggc	8	1	19	13	2	0	2	0	1	0	1	0	3	0	3	3	6	2	2	3	6	2	0			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chr22:38153684G>A	ENST00000406386.3	+	16	6007	c.5752G>A	c.(5752-5754)Gca>Aca	p.A1918T	TRIOBP_ENST00000407319.2_Missense_Mutation_p.A205T|TRIOBP_ENST00000403663.2_Missense_Mutation_p.A205T	NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	1918					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)					CCCCCTGAAGGCAGGGGAGCA	0.677																																					p.A1918T		Atlas-SNP	.											.	TRIOBP	262	.	0			c.G5752A						PASS	.						14	15	14					22																	38153684		2184	4289	6473	SO:0001583	missense	11078	exon16			CTGAAGGCAGGGG	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.5752G>A	chr22.hg19:g.38153684G>A	ENSP00000384312:p.Ala1918Thr	41.0	0.0	.		38.0	19.0	.	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	hg19	CCDS43015.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	4.919|4.919	0.170774|0.170774	0.09391|0.09391	.|.	.|.	ENSG00000100106|ENSG00000100106	ENST00000406386;ENST00000407319;ENST00000403663;ENST00000418339;ENST00000417857|ENST00000428075	T|.	0.20881|.	2.04|.	5.5|5.5	2.09|2.09	0.27110|0.27110	.|.	.|.	.|.	.|.	.|.	T|T	0.34629|0.34629	0.0904|0.0904	L|L	0.44542|0.44542	1.39|1.39	0.09310|0.09310	N|N	0.999996|0.999996	B;B;B|.	0.25486|.	0.007;0.04;0.127|.	B;B;B|.	0.19148|.	0.007;0.009;0.024|.	T|T	0.24621|0.24621	-1.0155|-1.0155	9|5	0.15952|.	T|.	0.53|.	.|.	3.9861|3.9861	0.09516|0.09516	0.1377:0.2332:0.5093:0.1199|0.1377:0.2332:0.5093:0.1199	.|.	205;205;1918|.	F8W6V6;F2Z2W0;Q9H2D6|.	.;.;TARA_HUMAN|.	T|D	1918;205;205;164;134|158	ENSP00000384312:A1918T|.	ENSP00000386026:A205T|.	A|G	+|+	1|2	0|0	TRIOBP|TRIOBP	36483630|36483630	0.004000|0.004000	0.15560|0.15560	0.612000|0.612000	0.29024|0.29024	0.312000|0.312000	0.27988|0.27988	-0.063000|-0.063000	0.11655|0.11655	0.652000|0.652000	0.30806|0.30806	-0.315000|-0.315000	0.08773|0.08773	GCA|GGC	.	.	.	none		0.677	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			A	38153684	G	A	38153684	3	1	69	1	0	0	0	0	1	0	0	0	16565	1203	42	2	5993	2	TRIOBP	22	38153684	Missense_Mutation	SNP	G	TCGA-A4-A772-01A-11D-A33Q-10		38153684	13150882	43	4591											
PNPLA4	8228	hgsc.bcm.edu	37	chrX	7894062	7894062	+	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	gcgaaggctttgacatccttCacaagttttttgccatgtct	8	15	8	10	1	2	1	1	1	1	0	3	2	3	1	2	1	1	2	2	1	2	5			TCGA-A4-A772-01A-11D-A33Q-10	TCGA-A4-A772-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e7e4d69c-b66c-4aa5-b7ac-573ab82472ff	280b0962-0e12-4148-b679-dd642d7f0b3e	g.chrX:7894062C>G	ENST00000381042.4	-	2	269	c.99G>C	c.(97-99)gtG>gtC	p.V33V	PNPLA4_ENST00000444736.1_Silent_p.V33V|PNPLA4_ENST00000537427.1_Intron	NM_004650.2	NP_004641.1	P41247	PLPL4_HUMAN	patatin-like phospholipase domain containing 4	33	Patatin.				lipid catabolic process (GO:0016042)		triglyceride lipase activity (GO:0004806)			kidney(1)|large_intestine(3)|lung(2)|prostate(1)	7		Colorectal(8;0.0329)|Medulloblastoma(8;0.232)				TGACATCCTTCACAAGTTTTT	0.458											OREG0019651	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V33V		Atlas-SNP	.											.	PNPLA4	24	.	0			c.G99C						PASS	.						94	78	84					X																	7894062		2203	4299	6502	SO:0001819	synonymous_variant	8228	exon2			ATCCTTCACAAGT	U03886	CCDS14129.1, CCDS55368.1	Xp22.3	2014-03-14			ENSG00000006757	ENSG00000006757	3.1.1.3	"Patatin-like phospholipase domain containing"	24887	protein-coding gene	gene with protein product		300102				7806223, 16799181, 19029121	Standard	NM_004650		Approved	DXS1283E, GS2, iPLA2eta	uc011mhr.1	P41247	OTTHUMG00000021103	ENST00000381042.4:c.99G>C	chrX.hg19:g.7894062C>G		216.0	0.0	.	645	158.0	27.0	.	NM_004650	A8K1H3|B4E362|Q8WW83	Silent	SNP	ENST00000381042.4	hg19	CCDS14129.1																																																																																			.	.	.	none		0.458	PNPLA4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055687.1	NM_004650		G	7894062	C	G	7894062	2	3	69	1	0	0	0	0	0	0	0	1	12174	813	29	4		4	PNPLA4	23	7894062	Silent	SNP	C	TCGA-A4-A772-01A-11D-A33Q-10		7894062	147376498	44	4592											
MOV10	4343	hgsc.bcm.edu	37	chr1	113236732	113236732	+	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	acacaccaggaggaccccatCacatataagggctttgtgca	13	7	9	12	0	1	0	1	0	0	0	1	2	1	2	3	3	1	2	3	3	2	3			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr1:113236732C>T	ENST00000413052.2	+	8	1623	c.1233C>T	c.(1231-1233)atC>atT	p.I411I	MOV10_ENST00000468624.1_3'UTR|MOV10_ENST00000357443.2_Silent_p.I411I|MOV10_ENST00000369645.1_Silent_p.I411I|RP11-426L16.3_ENST00000421943.1_RNA|MOV10_ENST00000369644.1_Silent_p.I355I	NM_001130079.1|NM_020963.3	NP_001123551.1|NP_066014.1	Q9HCE1	MOV10_HUMAN	Mov10 RISC complex RNA helicase	411					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(3)	38	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)		AGGACCCCATCACATATAAGG	0.577																																					p.I411I		Atlas-SNP	.											.	MOV10	74	.	0			c.C1233T						PASS	.						139	134	136					1																	113236732		2203	4300	6503	SO:0001819	synonymous_variant	4343	exon8			CCCCATCACATAT	AL833353	CCDS853.1, CCDS65615.1	1p13.2	2014-07-02	2014-07-02		ENSG00000155363	ENSG00000155363			7200	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 113"	610742	"Mov10 (Moloney leukemia virus 10, mouse) homolog", "Mov10, Moloney leukemia virus 10, homolog (mouse)"			12226669	Standard	NM_001286072		Approved	gb110, MGC2948, fSAP113	uc001eck.3	Q9HCE1	OTTHUMG00000011906	ENST00000413052.2:c.1233C>T	chr1.hg19:g.113236732C>T		97.0	0.0	.		101.0	26.0	.	NM_020963	Q5JR03|Q8TEF0|Q9BSY3|Q9BUJ9	Silent	SNP	ENST00000413052.2	hg19	CCDS853.1																																																																																			.	.	.	none		0.577	MOV10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032906.1	NM_020963		T	113236732	C	T	113236732	2	4	70	1	0	0	0	0	0	0	0	1	9725	816	29	2		2	MOV10	1	113236732	Silent	SNP	C	TCGA-A4-A7UZ-01A-12D-A34Z-10		113236732	136013889	1	4593											
SYCP1	6847	hgsc.bcm.edu	37	chr1	115488960	115488960	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gactcagaattaggactttaTaagagcaaagaacaagaaca	20	7	8	6	0	1	4	1	0	0	4	1	6	1	5	0	1	3	1	0	1	8	4			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr1:115488960T>C	ENST00000369522.3	+	26	2445	c.2205T>C	c.(2203-2205)taT>taC	p.Y735Y	SYCP1_ENST00000369518.1_Silent_p.Y735Y	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	735					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)		TAGGACTTTATAAGAGCAAAG	0.328																																					p.Y735Y		Atlas-SNP	.											.	SYCP1	149	.	0			c.T2205C						PASS	.						67	70	69					1																	115488960		2203	4300	6503	SO:0001819	synonymous_variant	6847	exon26			ACTTTATAAGAGC	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.2205T>C	chr1.hg19:g.115488960T>C		318.0	0.0	.		368.0	98.0	.	NM_003176	O14963|Q5VXJ6	Silent	SNP	ENST00000369522.3	hg19	CCDS879.1																																																																																			.	.	.	none		0.328	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176		C	115488960	T	C	115488960	2	2	70	1	0	0	0	0	0	0	0	1	15443	1413	49	3		3	SYCP1	1	115488960	Silent	SNP	T	TCGA-A4-A7UZ-01A-12D-A34Z-10	2252228	115488960	133761661	2	4594											
CFHR5	81494	hgsc.bcm.edu	37	chr1	196952181	196952181	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgcataacatgcacagaagaAggatggtcaccaacaccgaa	17	4	9	11	2	1	2	1	0	0	2	1	4	1	3	2	2	3	2	2	2	5	1			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr1:196952181A>G	ENST00000256785.4	+	2	334	c.225A>G	c.(223-225)gaA>gaG	p.E75E	CFHR5_ENST00000367414.5_Silent_p.E99E			Q9BXR6	FHR5_HUMAN	complement factor H-related 5	75	Sushi 1. {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						GCACAGAAGAAGGATGGTCAC	0.408																																					p.E75E		Atlas-SNP	.											.	CFHR5	150	.	0			c.A225G						PASS	.						122	106	111					1																	196952181		2203	4300	6503	SO:0001819	synonymous_variant	81494	exon2			AGAAGAAGGATGG	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.225A>G	chr1.hg19:g.196952181A>G		234.0	0.0	.		209.0	53.0	.	NM_030787	Q2NKK2	Silent	SNP	ENST00000256785.4	hg19	CCDS1387.1																																																																																			.	.	.	none		0.408	CFHR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088814.2	NM_030787		G	196952181	A	G	196952181	2	3	70	1	0	0	0	0	0	0	0	1	3290	69	3	3		3	CFHR5	1	196952181	Silent	SNP	A	TCGA-A4-A7UZ-01A-12D-A34Z-10	81463221	196952181	52298440	3	4595											
PIK3C2B	5287	hgsc.bcm.edu	37	chr1	204433195	204433198	+	Frame_Shift_Del	DEL	CATT	CATT	-																															cacaaagtcacccacgtccaCattcctcaggtcatcatggg																										TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	CATT	CATT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr1:204433195_204433198delCATT	ENST00000367187.3	-	6	1808_1811	c.1252_1255delAATG	c.(1252-1257)aatgtgfs	p.NV418fs	PIK3C2B_ENST00000424712.2_Frame_Shift_Del_p.NV418fs	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	418	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)			CCCACGTCCACATTCCTCAGGTCA	0.539																																					p.418_419del		Atlas-Indel,Pindel	.											.	PIK3C2B	142	.	0			c.1253_1256del						PASS	.																																			SO:0001589	frameshift_variant	5287	exon6			.	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.1252_1255delAATG	chr1.hg19:g.204433195_204433198delCATT	ENSP00000356155:p.Asn418fs	63.0	0.0	0		69.0	12.0	0.173913	NM_002646	O95666|Q5SW99	Frame_Shift_Del	DEL	ENST00000367187.3	hg19	CCDS1446.1																																																																																			.	.	.	none		0.539	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646		-	204433198	CATT	-	204433195	7	5	70	1	0	1	0	1	0	0	0	0	11917	478	17	0	3765	0	PIK3C2B	1	204433195	Frame_Shift_Del	DEL	CATT	TCGA-A4-A7UZ-01A-12D-A34Z-10	7481014	204433195	44817426	4	4596											
OR2T4	127074	hgsc.bcm.edu	37	chr1	248524967	248524969	+	In_Frame_Del	DEL	ATG	ATG	-																															tcagacaatccaaacatccaAtggccaatatcacctggatg																								rs200915140	byFrequency	TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	ATG	ATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr1:248524967_248524969delATG	ENST00000366475.1	+	1	85_87	c.85_87delATG	c.(85-87)atgdel	p.M29del		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	29						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)			CAAACATCCAATGGCCAATATCA	0.498																																					p.28_29del		Atlas-INDEL	.											.	OR2T4	126	.	0			c.84_86del						PASS	.																																			SO:0001651	inframe_deletion	127074	exon1			.	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.85_87delATG	chr1.hg19:g.248524967_248524969delATG	ENSP00000355431:p.Met29del	11.0	0.0	0		15.0	14.0	0.933333	NM_001004696	Q6IEZ8	In_Frame_Del	DEL	ENST00000366475.1	hg19	CCDS31113.1																																																																																			.	.	.	none		0.498	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696		-	248524969	ATG	-	248524967	7	5	70	1	0	1	0	1	0	0	0	0	11034	101	4	0	87	0	OR2T4	1	248524967	In_Frame_Del	DEL	ATG	TCGA-A4-A7UZ-01A-12D-A34Z-10	44091772	248524967	725654	5	4597											
ARHGEF4	50649	hgsc.bcm.edu	37	chr2	131803640	131803640	+	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	ggccctgctacctgacgcgcCagaagcacccagccctgccc	7	4	10	20	2	0	2	0	1	0	1	0	2	0	2	6	1	5	2	6	1	2	1			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr2:131803640C>A	ENST00000326016.5	+	14	2470	c.1951C>A	c.(1951-1953)Cag>Aag	p.Q651K	ARHGEF4_ENST00000525839.1_3'UTR|ARHGEF4_ENST00000409303.1_Missense_Mutation_p.Q591K|ARHGEF4_ENST00000392953.3_3'UTR|ARHGEF4_ENST00000355771.3_Missense_Mutation_p.Q580K|ARHGEF4_ENST00000428230.2_Missense_Mutation_p.Q153K	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	651					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)		CCTGACGCGCCAGAAGCACCC	0.677																																					p.Q651K		Atlas-SNP	.											.	ARHGEF4	89	.	0			c.C1951A						PASS	.						52	63	60					2																	131803640		2203	4300	6503	SO:0001583	missense	50649	exon14			ACGCGCCAGAAGC	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.1951C>A	chr2.hg19:g.131803640C>A	ENSP00000316845:p.Gln651Lys	100.0	0.0	.		68.0	19.0	.	NM_015320	Q9HDC6|Q9UPP0	Missense_Mutation	SNP	ENST00000326016.5	hg19	CCDS2165.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.354512	0.82243	.	.	ENSG00000136002	ENST00000326016;ENST00000438985;ENST00000428230;ENST00000409303;ENST00000355771	T;T;T;T;T	0.35789	1.29;1.29;1.29;1.29;1.29	5.71	5.71	0.89125	.	0.059818	0.64402	D	0.000002	T	0.38878	0.1057	M	0.61703	1.905	0.80722	D	1	P;P	0.41420	0.616;0.749	B;B	0.38264	0.199;0.269	T	0.19582	-1.0301	10	0.36615	T	0.2	.	17.337	0.87285	0.0:1.0:0.0:0.0	.	591;651	E9PEM0;Q9NR80	.;ARHG4_HUMAN	K	651;333;153;591;580	ENSP00000316845:Q651K;ENSP00000389661:Q333K;ENSP00000398455:Q153K;ENSP00000387285:Q591K;ENSP00000348017:Q580K	ENSP00000316845:Q651K	Q	+	1	0	ARHGEF4	131520110	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.251000	0.78297	2.700000	0.92200	0.462000	0.41574	CAG	.	.	.	none		0.677	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254554.4			A	131803640	C	A	131803640	3	1	70	1	0	0	0	0	1	0	0	0	908	595	21	4	2089	4	ARHGEF4	2	131803640	Missense_Mutation	SNP	C	TCGA-A4-A7UZ-01A-12D-A34Z-10		131803640	111395733	6	4598											
IRS1	3667	hgsc.bcm.edu	37	chr2	227661691	227661691	+	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	cgacgctccaaggggtgcatTtccagaccctcctctgggta	7	9	11	14	2	1	1	0	0	1	1	4	2	4	1	4	3	1	3	4	3	2	2			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr2:227661691T>A	ENST00000305123.5	-	1	2784	c.1764A>T	c.(1762-1764)gaA>gaT	p.E588D	IRS1_ENST00000498335.1_5'Flank	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN	insulin receptor substrate 1	588					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)		AGGGGTGCATTTCCAGACCCT	0.687											OREG0015248	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E588D		Atlas-SNP	.											.	IRS1	141	.	0			c.A1764T						PASS	.						33	35	34					2																	227661691		2203	4299	6502	SO:0001583	missense	3667	exon1			GTGCATTTCCAGA		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.1764A>T	chr2.hg19:g.227661691T>A	ENSP00000304895:p.Glu588Asp	48.0	0.0	.	2321	58.0	17.0	.	NM_005544		Missense_Mutation	SNP	ENST00000305123.5	hg19	CCDS2463.1	.	.	.	.	.	.	.	.	.	.	T	0.689	-0.795221	0.02862	.	.	ENSG00000169047	ENST00000305123	T	0.55588	0.51	4.98	-2.09	0.07232	.	0.080047	0.52532	D	0.000061	T	0.18882	0.0453	N	0.02916	-0.46	0.24828	N	0.992544	B	0.19200	0.034	B	0.14023	0.01	T	0.35624	-0.9781	10	0.02654	T	1	-14.305	9.8521	0.41064	0.0:0.5701:0.1155:0.3144	.	588	P35568	IRS1_HUMAN	D	588	ENSP00000304895:E588D	ENSP00000304895:E588D	E	-	3	2	IRS1	227369935	0.067000	0.21026	0.981000	0.43875	0.963000	0.63663	-0.781000	0.04648	-0.222000	0.09958	0.459000	0.35465	GAA	.	.	.	none		0.687	IRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256886.3	NM_005544		A	227661691	T	A	227661691	3	1	70	1	0	0	0	0	1	0	0	0	7847	1838	64	5	1968	5	IRS1	2	227661691	Missense_Mutation	SNP	T	TCGA-A4-A7UZ-01A-12D-A34Z-10	95858051	227661691	15537682	7	4599											
MLH1	4292	hgsc.bcm.edu	37	chr3	37092015	37092015	+	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	attccaaactcctggaagtgGactgtggaacacattgtcta	12	11	9	9	0	1	0	0	0	1	0	3	3	3	3	2	3	2	0	2	3	4	3	rs63750978		TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr3:37092015G>T	ENST00000231790.2	+	19	2358	c.2142G>T	c.(2140-2142)tgG>tgT	p.W714C	MLH1_ENST00000539477.1_Missense_Mutation_p.W473C|MLH1_ENST00000536378.1_Intron|MLH1_ENST00000458205.2_Missense_Mutation_p.W473C|MLH1_ENST00000435176.1_Missense_Mutation_p.W616C|MLH1_ENST00000455445.2_Missense_Mutation_p.W473C	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	714					ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.0?(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						CCTGGAAGTGGACTGTGGAAC	0.468		1	"D, Mis, N, F, S"		"colorectal, endometrial, ovarian, CNS"	"colorectal, endometrial, ovarian, CNS"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.W714C		Atlas-SNP	.	yes	Rec	yes	"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	3	3p21.3	4292	E.coli MutL homolog gene		"E, O"	.	MLH1	226	.	1	Whole gene deletion(1)	ovary(1)	c.G2142T	GRCh37	CM960977	MLH1	M	rs63750978	PASS	.						106	96	99					3																	37092015		2203	4300	6503	SO:0001583	missense	4292	exon19	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	GAAGTGGACTGTG	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.2142G>T	chr3.hg19:g.37092015G>T	ENSP00000231790:p.Trp714Cys	71.0	0.0	.		65.0	18.0	.	NM_000249	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	hg19	CCDS2663.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.5|24.5	4.543467|4.543467	0.86022|0.86022	.|.	.|.	ENSG00000076242|ENSG00000076242	ENST00000396438;ENST00000456676;ENST00000413740|ENST00000231790;ENST00000383761;ENST00000421440;ENST00000458205;ENST00000539477;ENST00000455445;ENST00000435176	D|D;D;D;D;D	0.96745|0.93906	-4.11|-3.31;-3.31;-3.31;-3.31;-3.31	5.41|5.41	5.41|5.41	0.78517|0.78517	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.97495|0.97495	0.9180|0.9180	M|M	0.91768|0.91768	3.24|3.24	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	.|0.77557	.|0.99;0.977;0.977;0.977;0.983	D|D	0.98012|0.98012	1.0366|1.0366	7|10	0.87932|0.66056	D|D	0|0.02	-9.6335|-9.6335	19.2553|19.2553	0.93944|0.93944	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|616;714;473;714;714	.|E9PCU2;B2R6K0;B4DI13;Q53GX1;P40692	.|.;.;.;.;MLH1_HUMAN	V|C	112;637;110|714;509;132;473;473;473;616	ENSP00000416476:G110V|ENSP00000231790:W714C;ENSP00000402667:W473C;ENSP00000443665:W473C;ENSP00000398272:W473C;ENSP00000402564:W616C	ENSP00000379715:G112V|ENSP00000231790:W714C	G|W	+|+	2|3	0|0	MLH1|MLH1	37067019|37067019	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	9.572000|9.572000	0.98179|0.98179	2.557000|2.557000	0.86248|0.86248	0.650000|0.650000	0.86243|0.86243	GGA|TGG	.	.	.	alt		0.468	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249		T	37092015	G	T	37092015	3	4	70	1	0	0	0	0	1	0	0	0	9624	1183	41	4	2216	4	MLH1	3	37092015	Missense_Mutation	SNP	G	TCGA-A4-A7UZ-01A-12D-A34Z-10		37092015	160930415	8	4600											
DNAH1	25981	hgsc.bcm.edu	37	chr3	52397032	52397032	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctcttccgacccgtggccAtgatggttccagattacgcc	6	10	10	15	4	1	2	0	1	1	1	3	3	3	2	5	2	1	2	5	2	1	3			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr3:52397032A>G	ENST00000420323.2	+	32	5377	c.5116A>G	c.(5116-5118)Atg>Gtg	p.M1706V		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1706	AAA 1. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		ACCCGTGGCCATGATGGTTCC	0.552																																					p.M1706V		Atlas-SNP	.											.	DNAH1	534	.	0			c.A5116G						PASS	.						193	198	196					3																	52397032		2137	4254	6391	SO:0001583	missense	25981	exon32			GTGGCCATGATGG	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.5116A>G	chr3.hg19:g.52397032A>G	ENSP00000401514:p.Met1706Val	80.0	0.0	.		96.0	33.0	.	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	hg19	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.439957	0.83885	.	.	ENSG00000114841	ENST00000420323	T	0.36340	1.26	4.93	4.93	0.64822	.	0.000000	0.64402	D	0.000003	T	0.65626	0.2709	M	0.88512	2.96	0.58432	D	0.999997	D	0.76494	0.999	D	0.76575	0.988	T	0.73770	-0.3878	10	0.87932	D	0	.	14.7323	0.69391	1.0:0.0:0.0:0.0	.	1706	C9JXH6	.	V	1706	ENSP00000401514:M1706V	ENSP00000401514:M1706V	M	+	1	0	DNAH1	52372072	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.147000	0.71783	2.080000	0.62538	0.533000	0.62120	ATG	.	.	.	none		0.552	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		G	52397032	A	G	52397032	3	3	70	1	0	0	0	0	1	0	0	0	4599	217	8	3	5238	3	DNAH1	3	52397032	Missense_Mutation	SNP	A	TCGA-A4-A7UZ-01A-12D-A34Z-10	15305017	52397032	145625398	9	4601											
EIF4A2	1974	hgsc.bcm.edu	37	chr3	186505347	186505348	+	Frame_Shift_Ins	INS	-	-	A																															attccggtcagggtcaagtcINSgtgttctgatcactactgac																										TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr3:186505347_186505348insA	ENST00000323963.5	+	9	1037_1038	c.973_974insA	c.(973-975)cgtfs	p.R325fs	EIF4A2_ENST00000440191.2_Frame_Shift_Ins_p.R326fs|EIF4A2_ENST00000356531.5_Frame_Shift_Ins_p.R230fs|SNORA63_ENST00000363548.1_RNA|SNORA81_ENST00000408493.2_RNA|SNORD2_ENST00000459163.1_RNA|SNORA4_ENST00000584302.1_RNA|SNORA63_ENST00000363450.1_RNA			Q14240	IF4A2_HUMAN	eukaryotic translation initiation factor 4A2	325	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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)		AGGGTCAAGTCGTGTTCTGATC	0.396			T	BCL6	NHL																																p.R325fs		Atlas-Indel,Pindel	.		Dom	yes		3	3q27.3	1974	"eukaryotic translation initiation factor 4A, isoform 2"		L	.	EIF4A2	55	.	0			c.973_974insA						PASS	.																																			SO:0001589	frameshift_variant	1974	exon9			.	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	Exception_encountered	chr3.hg19:g.186505347_186505348insA	ENSP00000326381:p.Arg325fs	174.0	0.0	0		200.0	28.0	0.14	NM_001967	D3DNU9|Q53XJ6|Q96B90|Q96EA8	Frame_Shift_Ins	INS	ENST00000323963.5	hg19	CCDS3282.1																																																																																			.	.	.	none		0.396	EIF4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344609.1	NM_001967		A	186505348	-	A	186505347	7	5	70	1	0	1	1	0	0	0	0	0	5027	884	31	0	1007	0	EIF4A2	3	186505347	Frame_Shift_Ins	INS	-	TCGA-A4-A7UZ-01A-12D-A34Z-10	134108315	186505347	11517083	10	4602											
ANKRD17	26057	hgsc.bcm.edu	37	chr4	73986056	73986056	+	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	ttagtggtgtgagaccagtcTaagtttagtgtaaaattaaa	14	14	10	3	0	1	1	0	1	1	1	1	2	1	1	1	1	0	2	1	1	7	6			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr4:73986056T>C	ENST00000358602.4	-	21	3966		c.e21-2		ANKRD17_ENST00000514252.1_Splice_Site|ANKRD17_ENST00000330838.6_Splice_Site|ANKRD17_ENST00000509867.2_Splice_Site	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17						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)			GAGACCAGTCTAAGTTTAGTG	0.398																																					.		Atlas-SNP	.											.	ANKRD17	214	.	0			c.3097-2A>G						PASS	.						55	52	53					4																	73986056		2203	4300	6503	SO:0001630	splice_region_variant	26057	exon21			CCAGTCTAAGTTT	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.3850-2A>G	chr4.hg19:g.73986056T>C		81.0	0.0	.		92.0	4.0	.	NM_198889	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Splice_Site	SNP	ENST00000358602.4	hg19	CCDS34004.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.294121	0.81025	.	.	ENSG00000132466	ENST00000358602;ENST00000330838;ENST00000509867	.	.	.	5.68	5.68	0.88126	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9332	0.79683	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	ANKRD17	74204920	1.000000	0.71417	0.997000	0.53966	0.839000	0.47603	8.040000	0.89188	2.164000	0.68074	0.477000	0.44152	.	.	.	.	none		0.398	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217	Intron	C	73986056	T	C	73986056	5	2	70	1	0	0	0	0	0	0	1	0	646	1536	53	3	4019	3	ANKRD17	4	73986056	Splice_Site	SNP	T	TCGA-A4-A7UZ-01A-12D-A34Z-10		73986056	117168220	11	4603											
CENPE	1062	hgsc.bcm.edu	37	chr4	104064497	104064497	+	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	aacaatccctcttagtttatCaatagtttcttggtgctcct	9	17	5	10	0	3	0	1	0	2	0	5	0	5	0	2	1	2	3	2	1	6	6			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr4:104064497C>G	ENST00000265148.3	-	34	5301	c.5212G>C	c.(5212-5214)Gat>Cat	p.D1738H	CENPE_ENST00000380026.3_Missense_Mutation_p.D1713H	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	1738					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)	p.D1738H(1)		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)		CTTAGTTTATCAATAGTTTCT	0.303																																					p.D1738H		Atlas-SNP	.											CENPE,NS,carcinoma,0,1	CENPE	253	.	1	Substitution - Missense(1)	lung(1)	c.G5212C						PASS	.						170	169	169					4																	104064497		2203	4298	6501	SO:0001583	missense	1062	exon34			GTTTATCAATAGT	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.5212G>C	chr4.hg19:g.104064497C>G	ENSP00000265148:p.Asp1738His	314.0	1.0	.		351.0	72.0	.	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	hg19	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	C	11.66	1.706339	0.30232	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026	T;T	0.72282	-0.64;-0.64	5.16	3.42	0.39159	.	.	.	.	.	T	0.73289	0.3568	L	0.48642	1.525	0.09310	N	1	D;B	0.57257	0.979;0.376	P;B	0.57911	0.829;0.08	T	0.61317	-0.7087	9	0.56958	D	0.05	.	7.6167	0.28163	0.0:0.8007:0.0:0.1993	.	1713;1738	Q02224-3;Q02224	.;CENPE_HUMAN	H	1738;1738;1713	ENSP00000265148:D1738H;ENSP00000369365:D1713H	ENSP00000265148:D1738H	D	-	1	0	CENPE	104283946	0.000000	0.05858	0.053000	0.19242	0.428000	0.31595	0.140000	0.16056	0.665000	0.31066	0.643000	0.83706	GAT	.	.	.	none		0.303	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	104064497	C	G	104064497	3	3	70	1	0	0	0	0	1	0	0	0	3232	826	29	4	2957	4	CENPE	4	104064497	Missense_Mutation	SNP	C	TCGA-A4-A7UZ-01A-12D-A34Z-10	30078441	104064497	87089779	12	4604											
LNPEP	4012	hgsc.bcm.edu	37	chr5	96315035	96315035	+	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	gaggatgaagaggattatgaGtcatcagcaaagctgctggg	13	8	15	5	0	2	3	2	2	0	1	2	6	2	5	0	3	3	3	0	3	3	1			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr5:96315035G>A	ENST00000231368.5	+	2	905	c.213G>A	c.(211-213)gaG>gaA	p.E71E	LNPEP_ENST00000395770.3_Silent_p.E57E	NM_005575.2	NP_005566.2	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase	71					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)		AGGATTATGAGTCATCAGCAA	0.547																																					p.E71E		Atlas-SNP	.											.	LNPEP	80	.	0			c.G213A						PASS	.						77	82	80					5																	96315035		2203	4300	6503	SO:0001819	synonymous_variant	4012	exon2			TTATGAGTCATCA	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.213G>A	chr5.hg19:g.96315035G>A		121.0	0.0	.		96.0	26.0	.	NM_005575	O00769|Q15145|Q59H76|Q9TNQ2|Q9TNQ3|Q9UIQ7	Silent	SNP	ENST00000231368.5	hg19	CCDS4087.1																																																																																			.	.	.	none		0.547	LNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250624.1	NM_005575		A	96315035	G	A	96315035	2	1	70	1	0	0	0	0	0	0	0	1	8871	1020	36	2		2	LNPEP	5	96315035	Silent	SNP	G	TCGA-A4-A7UZ-01A-12D-A34Z-10		96315035	84600225	13	4605											
AQPEP	206338	hgsc.bcm.edu	37	chr5	115350221	115350221	+	Missense_Mutation	SNP	A	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	atgggtggatcatccagaaaAtgagtaagagtaatatcata	17	10	10	4	0	2	3	2	1	0	2	3	4	3	4	1	2	0	2	1	2	6	4			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr5:115350221A>C	ENST00000357872.4	+	16	2571	c.2447A>C	c.(2446-2448)aAt>aCt	p.N816T	AQPEP_ENST00000515454.1_3'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		816						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										CATCCAGAAAATGAGTAAGAG	0.388																																					p.N816T		Atlas-SNP	.											.	.	.	.	0			c.A2447C						PASS	.						88	84	85					5																	115350221		2202	4300	6502	SO:0001583	missense	0	exon16			CAGAAAATGAGTA																												ENST00000357872.4:c.2447A>C	chr5.hg19:g.115350221A>C	ENSP00000350541:p.Asn816Thr	66.0	0.0	.		57.0	19.0	.	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Missense_Mutation	SNP	ENST00000357872.4	hg19	CCDS4124.1	.	.	.	.	.	.	.	.	.	.	A	5.191	0.220737	0.09863	.	.	ENSG00000172901	ENST00000357872;ENST00000379578	T	0.05447	3.44	5.37	1.42	0.22433	.	0.797068	0.10818	N	0.630826	T	0.06371	0.0164	L	0.42686	1.345	0.19300	N	0.999976	B	0.10296	0.003	B	0.10450	0.005	T	0.32561	-0.9902	10	0.54805	T	0.06	.	5.9133	0.19041	0.575:0.3337:0.0914:0.0	.	816	Q6Q4G3	AMPQ_HUMAN	T	816;805	ENSP00000350541:N816T	ENSP00000350541:N816T	N	+	2	0	AC010282.1	115378120	0.768000	0.28519	0.784000	0.31847	0.077000	0.17291	1.419000	0.34793	0.851000	0.35264	0.482000	0.46254	AAT	.	.	.	none		0.388	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1			C	115350221	A	C	115350221	3	2	70	1	0	0	0	0	1	0	0	0	834	101	4	5	2509	5	AQPEP	5	115350221	Missense_Mutation	SNP	A	TCGA-A4-A7UZ-01A-12D-A34Z-10	19035186	115350221	65565039	14	4606											
BTN3A1	11119	hgsc.bcm.edu	37	chr6	26411792	26411792	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttcctttcagaatggaaaaAggccctcttcaagcctggtg	10	11	9	11	0	3	1	2	0	1	1	4	2	4	2	3	3	1	0	3	3	4	3			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr6:26411792A>G	ENST00000289361.6	+	9	1369	c.1001A>G	c.(1000-1002)aAg>aGg	p.K334R	BTN3A1_ENST00000425234.2_Missense_Mutation_p.K334R|BTN3A1_ENST00000476549.2_Missense_Mutation_p.K334R|BTN3A1_ENST00000414912.2_Missense_Mutation_p.K282R	NM_001145008.1|NM_001145009.1|NM_007048.5	NP_001138480.1|NP_001138481.1|NP_008979.3	O00481	BT3A1_HUMAN	butyrophilin, subfamily 3, member A1	334	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				activated T cell proliferation (GO:0050798)|cytokine secretion (GO:0050663)|interferon-gamma secretion (GO:0072643)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						GAATGGAAAAAGGCCCTCTTC	0.438																																					p.K334R		Atlas-SNP	.											.	BTN3A1	80	.	0			c.A1001G						PASS	.						185	156	166					6																	26411792		2203	4300	6503	SO:0001583	missense	11119	exon9			GGAAAAAGGCCCT	U90552	CCDS4608.1, CCDS4609.1, CCDS47388.1, CCDS47389.1	6p22.1	2014-01-14			ENSG00000026950	ENSG00000026950		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Butyrophilins"	1138	protein-coding gene	gene with protein product		613593				9149941	Standard	NM_007048		Approved	BT3.1, BTF5, CD277, BTN3.1	uc003nhv.3	O00481	OTTHUMG00000014449	ENST00000289361.6:c.1001A>G	chr6.hg19:g.26411792A>G	ENSP00000289361:p.Lys334Arg	105.0	0.0	.		92.0	4.0	.	NM_007048	A2A278|A8K2C8|B4DIQ1|B4DRM2|E9PGB4|E9PHG8|Q0P515|Q147X5|Q53F15|Q99420|Q9HCY1	Missense_Mutation	SNP	ENST00000289361.6	hg19	CCDS4608.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.703738	0.00096	.	.	ENSG00000026950	ENST00000476549;ENST00000289361;ENST00000425234;ENST00000414912	T;T;T;T	0.60424	3.8;0.19;3.71;0.19	1.32	-2.63	0.06133	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.11495	0.0280	N	0.26130	0.795	0.09310	N	1	B;B;B;B	0.13145	0.0;0.007;0.002;0.0	B;B;B;B	0.12156	0.001;0.007;0.003;0.001	T	0.23440	-1.0188	9	0.08837	T	0.75	.	2.5592	0.04768	0.3119:0.2317:0.0:0.4564	.	282;334;334;334	E9PGB4;O00481-3;O00481-2;O00481	.;.;.;BT3A1_HUMAN	R	334;334;334;282	ENSP00000420010:K334R;ENSP00000289361:K334R;ENSP00000396684:K334R;ENSP00000406667:K282R	ENSP00000289361:K334R	K	+	2	0	BTN3A1	26519771	0.003000	0.15002	0.001000	0.08648	0.050000	0.14768	-2.542000	0.00935	-1.617000	0.01570	-1.416000	0.01114	AAG	.	.	.	none		0.438	BTN3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040112.3			G	26411792	A	G	26411792	3	3	70	1	0	0	0	0	1	0	0	0	1564	72	3	3	1031	3	BTN3A1	6	26411792	Missense_Mutation	SNP	A	TCGA-A4-A7UZ-01A-12D-A34Z-10		26411792	144703275	15	4607											
OR2J2	26707	hgsc.bcm.edu	37	chr6	29141971	29141971	+	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	gtgaagttccagcacttctgCgtttatcatgtgttgacacc	8	14	9	10	1	2	2	1	2	1	0	3	2	3	2	2	0	2	4	2	0	2	5	rs371365216		TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr6:29141971C>T	ENST00000377167.2	+	1	661	c.559C>T	c.(559-561)Cgt>Tgt	p.R187C		NM_030905.2	NP_112167.2	O76002	OR2J2_HUMAN	olfactory receptor, family 2, subfamily J, member 2	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)|kidney(2)|large_intestine(1)|liver(2)|lung(17)|ovary(1)|upper_aerodigestive_tract(1)	25						AGCACTTCTGCGTTTATCATG	0.443																																					p.R187C		Atlas-SNP	.											.	OR2J2	51	.	0			c.C559T						PASS	.	C	CYS/ARG	1,3883		0,1,1941	171	149	156		559	-4.2	0	6		156	0,8302		0,0,4151	no	missense	OR2J2	NM_030905.2	180	0,1,6092	TT,TC,CC		0.0,0.0257,0.0082	probably-damaging	187/313	29141971	1,12185	1942	4151	6093	SO:0001583	missense	26707	exon1			CTTCTGCGTTTAT		CCDS43434.1	6p22.2-p21.31	2012-08-09			ENSG00000204700	ENSG00000204700		"GPCR / Class A : Olfactory receptors"	8260	protein-coding gene	gene with protein product							Standard	NM_030905		Approved	OR6-8, hs6M1-6, dJ80I19.4	uc011dlm.2	O76002	OTTHUMG00000031091	ENST00000377167.2:c.559C>T	chr6.hg19:g.29141971C>T	ENSP00000366372:p.Arg187Cys	172.0	0.0	.		188.0	27.0	.	NM_030905	A6NCU9|A6NLD0|B0UY53|Q32N09|Q5ST39|Q5SUJ6|Q6IF24|Q9GZK2|Q9GZL3	Missense_Mutation	SNP	ENST00000377167.2	hg19	CCDS43434.1	.	.	.	.	.	.	.	.	.	.	C	10.36	1.328083	0.24080	2.57E-4	0.0	ENSG00000204700	ENST00000377167	T	0.00158	8.65	2.3	-4.17	0.03857	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00073	0.0002	L	0.53671	1.685	0.09310	N	1	D	0.65815	0.995	D	0.63192	0.912	T	0.49293	-0.8955	9	0.87932	D	0	.	1.8745	0.03215	0.4347:0.2998:0.1449:0.1206	.	187	O76002	OR2J2_HUMAN	C	187	ENSP00000366372:R187C	ENSP00000366372:R187C	R	+	1	0	OR2J2	29249950	0.000000	0.05858	0.015000	0.15790	0.438000	0.31896	-1.750000	0.01822	-0.693000	0.05121	0.205000	0.17691	CGT	.	.	.	weak		0.443	OR2J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076131.2			T	29141971	C	T	29141971	3	4	70	1	0	0	0	0	1	0	0	0	11010	768	27	1	561	1	OR2J2	6	29141971	Missense_Mutation	SNP	C	TCGA-A4-A7UZ-01A-12D-A34Z-10	2730179	29141971	141973096	16	4608											
GJB7	375519	hgsc.bcm.edu	37	chr6	87994224	87994224	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaataaaacaaggaagccaAtttcaaaaccagttttaaca	22	8	4	7	0	1	0	1	0	0	0	1	1	1	1	2	1	4	1	2	1	10	4			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr6:87994224A>G	ENST00000525899.1	-	3	752	c.407T>C	c.(406-408)aTt>aCt	p.I136T	GJB7_ENST00000296882.3_Missense_Mutation_p.I136T	NM_198568.2	NP_940970.1	Q6PEY0	CXB7_HUMAN	gap junction protein, beta 7, 25kDa	136					cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(3)	5		all_cancers(76;1.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;7.38e-10)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00323)		BRCA - Breast invasive adenocarcinoma(108;0.0167)		AAGGAAGCCAATTTCAAAACC	0.403																																					p.I136T		Atlas-SNP	.											.	GJB7	28	.	0			c.T407C						PASS	.						77	77	77					6																	87994224		2203	4300	6503	SO:0001583	missense	375519	exon3			AAGCCAATTTCAA	AJ414563	CCDS5008.1	6q15	2008-02-05	2007-11-06			ENSG00000164411		"Ion channels / Gap junction proteins (connexins)"	16690	protein-coding gene	gene with protein product	"connexin 25"	611921	"gap junction protein, beta 7"				Standard	NM_198568		Approved	CX25, bA136M9.1	uc003plo.2	Q6PEY0		ENST00000525899.1:c.407T>C	chr6.hg19:g.87994224A>G	ENSP00000435355:p.Ile136Thr	91.0	0.0	.		110.0	32.0	.	NM_198568	B3KXL0|Q96KP0	Missense_Mutation	SNP	ENST00000525899.1	hg19	CCDS5008.1	.	.	.	.	.	.	.	.	.	.	A	11.99	1.803020	0.31869	.	.	ENSG00000164411	ENST00000525899;ENST00000296882;ENST00000369576	D;D;D	0.95622	-3.76;-3.76;-3.76	4.71	4.71	0.59529	Gap junction protein, cysteine-rich domain (1);	0.368503	0.24240	U	0.040275	D	0.91348	0.7271	M	0.70903	2.155	0.24359	N	0.994881	B	0.19583	0.037	B	0.22152	0.038	D	0.87908	0.2695	10	0.62326	D	0.03	.	13.0176	0.58766	1.0:0.0:0.0:0.0	.	136	Q6PEY0	CXB7_HUMAN	T	136	ENSP00000435355:I136T;ENSP00000296882:I136T;ENSP00000358589:I136T	ENSP00000296882:I136T	I	-	2	0	GJB7	88050943	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	3.955000	0.56715	1.751000	0.51876	0.379000	0.24179	ATT	.	.	.	none		0.403	GJB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394780.1			G	87994224	A	G	87994224	3	3	70	1	0	0	0	0	1	0	0	0	6420	101	4	3	268	3	GJB7	6	87994224	Missense_Mutation	SNP	A	TCGA-A4-A7UZ-01A-12D-A34Z-10	58852253	87994224	83120843	17	4609											
CRHR2	1395	hgsc.bcm.edu	37	chr7	30702464	30702464	+	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	gtgatgcagcggcaccagacCtgtgtgcagggcagagaggc	9	5	17	10	1	0	3	0	1	0	2	0	4	0	3	2	3	3	4	2	3	0	0			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr7:30702464C>T	ENST00000471646.1	-	6	961		c.e6-1		CRHR2_ENST00000341843.4_Splice_Site|CRHR2_ENST00000506074.2_Splice_Site|CRHR2_ENST00000348438.4_Splice_Site	NM_001202482.1|NM_001202483.1|NM_001883.4	NP_001189411.1|NP_001189412.1|NP_001874.2	Q13324	CRFR2_HUMAN	corticotropin releasing hormone receptor 2						adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|positive regulation of cAMP-mediated signaling (GO:0043950)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotrophin-releasing factor receptor activity (GO:0015056)			breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						GGCACCAGACCTGTGTGCAGG	0.587																																					.		Atlas-SNP	.											.	CRHR2	104	.	0			c.541-1G>A						PASS	.						84	61	69					7																	30702464		2203	4300	6503	SO:0001630	splice_region_variant	1395	exon7			CCAGACCTGTGTG		CCDS5429.1, CCDS56477.1, CCDS56478.1, CCDS75576.1	7p21-p15	2012-08-10			ENSG00000106113	ENSG00000106113		"GPCR / Class B : Corticotropin-releasing factor receptors"	2358	protein-coding gene	gene with protein product		602034				8536644	Standard	NM_001883		Approved	CRF2, CRF-RB, HM-CRF	uc003tbp.3	Q13324	OTTHUMG00000023218	ENST00000471646.1:c.544-1G>A	chr7.hg19:g.30702464C>T		64.0	0.0	.		79.0	16.0	.	NM_001202482	B2R967|B3SXS6|B3SXS7|B3SXS8|B3SXT0|F8WA81|O43461|Q4QRJ4|Q99431	Splice_Site	SNP	ENST00000471646.1	hg19	CCDS5429.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.070432	0.76301	.	.	ENSG00000106113	ENST00000471646;ENST00000348438;ENST00000341843;ENST00000506074	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.0535	0.86526	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CRHR2	30668989	1.000000	0.71417	1.000000	0.80357	0.742000	0.42306	7.493000	0.81493	2.717000	0.92951	0.655000	0.94253	.	.	.	.	none		0.587	CRHR2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250448.3		Intron	T	30702464	C	T	30702464	5	4	70	1	0	0	0	0	0	0	1	0	3874	695	24	2	720	2	CRHR2	7	30702464	Splice_Site	SNP	C	TCGA-A4-A7UZ-01A-12D-A34Z-10		30702464	128436199	18	4610											
MUC17	140453	hgsc.bcm.edu	37	chr7	100692139	100692139	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcctcagggccaccggagacTatctctgcccaaatggaact	10	7	10	14	1	2	1	1	0	1	1	3	3	2	2	4	3	2	0	4	3	3	1			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr7:100692139T>C	ENST00000306151.4	+	5	12613	c.12549T>C	c.(12547-12549)acT>acC	p.T4183T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	4183					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)					CACCGGAGACTATCTCTGCCC	0.522																																					p.T4183T		Atlas-SNP	.											.	MUC17	804	.	0			c.T12549C						PASS	.						101	90	94					7																	100692139		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon5			GGAGACTATCTCT	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.12549T>C	chr7.hg19:g.100692139T>C		106.0	0.0	.		178.0	11.0	.	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	hg19	CCDS34711.1																																																																																			.	.	.	none		0.522	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		C	100692139	T	C	100692139	2	2	70	1	0	0	0	0	0	0	0	1	9981	1509	53	3		3	MUC17	7	100692139	Silent	SNP	T	TCGA-A4-A7UZ-01A-12D-A34Z-10	69989675	100692139	58446524	19	4611											
SYPL1	6856	hgsc.bcm.edu	37	chr7	105752601	105752601	+	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	ctcacccactcgaggaccttGatgaagccgagtggctcctt	8	9	10	14	2	1	2	1	2	0	0	3	5	2	3	4	2	1	1	4	2	1	2			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr7:105752601G>A	ENST00000011473.2	-	2	154	c.108C>T	c.(106-108)atC>atT	p.I36I	SYPL1_ENST00000470347.1_Silent_p.I18I|SYPL1_ENST00000455385.2_Silent_p.I18I	NM_006754.3	NP_006745.1	Q16563	SYPL1_HUMAN	synaptophysin-like 1	36	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|integral component of synaptic vesicle membrane (GO:0030285)|secretory granule (GO:0030141)	transporter activity (GO:0005215)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)	7						CGAGGACCTTGATGAAGCCGA	0.697																																					p.I36I		Atlas-SNP	.											.	SYPL1	20	.	0			c.C108T						PASS	.						35	36	35					7																	105752601		2203	4300	6503	SO:0001819	synonymous_variant	6856	exon2			GACCTTGATGAAG		CCDS5736.1, CCDS47685.1	7q22.2	2005-05-24	2005-05-24	2005-05-24	ENSG00000008282	ENSG00000008282			11507	protein-coding gene	gene with protein product			"synaptophysin-like protein"	SYPL			Standard	NM_006754		Approved		uc003vdp.4	Q16563	OTTHUMG00000157587	ENST00000011473.2:c.108C>T	chr7.hg19:g.105752601G>A		18.0	0.0	.		34.0	18.0	.	NM_006754	A4D0R2|Q96AR8	Silent	SNP	ENST00000011473.2	hg19	CCDS5736.1																																																																																			.	.	.	none		0.697	SYPL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349221.1			A	105752601	G	A	105752601	2	1	70	1	0	0	0	0	0	0	0	1	15474	1280	45	2		2	SYPL1	7	105752601	Silent	SNP	G	TCGA-A4-A7UZ-01A-12D-A34Z-10	5060462	105752601	53386062	20	4612											
ADAM18	8749	hgsc.bcm.edu	37	chr8	39468142	39468142	+	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	tttatcaaatgaaaaataatGatccaaatgtatccatttta	18	15	3	5	0	1	2	1	2	0	0	3	2	3	2	2	0	0	1	2	0	8	6			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr8:39468142G>C	ENST00000265707.5	+	6	484	c.439G>C	c.(439-441)Gat>Cat	p.D147H	ADAM18_ENST00000520772.1_Missense_Mutation_p.D147H|ADAM18_ENST00000541111.1_Intron|ADAM18_ENST00000379866.1_Missense_Mutation_p.D147H	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	147					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)			GAAAAATAATGATCCAAATGT	0.333																																					p.D147H		Atlas-SNP	.											.	ADAM18	169	.	0			c.G439C						PASS	.						51	52	52					8																	39468142		2203	4298	6501	SO:0001583	missense	8749	exon6			AATAATGATCCAA	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.439G>C	chr8.hg19:g.39468142G>C	ENSP00000265707:p.Asp147His	403.0	0.0	.		379.0	86.0	.	NM_001190956	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	hg19	CCDS6113.1	.	.	.	.	.	.	.	.	.	.	G	9.536	1.112036	0.20795	.	.	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000520772;ENST00000522198	T;T;T	0.12465	5.24;4.8;2.68	5.25	-2.98	0.05513	.	0.836611	0.10471	N	0.670788	T	0.05823	0.0152	N	0.08118	0	0.09310	N	1	B;B;B	0.13594	0.005;0.003;0.008	B;B;B	0.17433	0.018;0.008;0.014	T	0.35847	-0.9772	10	0.44086	T	0.13	.	5.278	0.15661	0.3482:0.3014:0.3504:0.0	.	147;147;147	Q9Y3Q7-2;Q9Y3Q7;Q6IRW9	.;ADA18_HUMAN;.	H	147;147;147;103	ENSP00000265707:D147H;ENSP00000369195:D147H;ENSP00000429908:D147H	ENSP00000265707:D147H	D	+	1	0	ADAM18	39587299	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	0.482000	0.22276	-0.700000	0.05070	-0.302000	0.09304	GAT	.	.	.	none		0.333	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237		C	39468142	G	C	39468142	3	2	70	1	0	0	0	0	1	0	0	0	239	1290	45	4	461	4	ADAM18	8	39468142	Missense_Mutation	SNP	G	TCGA-A4-A7UZ-01A-12D-A34Z-10		39468142	106895880	21	4613											
IFNA2	3440	hgsc.bcm.edu	37	chr9	21385222	21385222	+	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	gtgccaggagcatcaaggtcCtcctgctacccaggctgtgg	7	8	13	13	0	1	0	1	0	0	0	3	1	3	1	4	4	4	3	4	4	2	1			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr9:21385222C>T	ENST00000380206.2	-	1	174	c.107G>A	c.(106-108)aGg>aAg	p.R36K		NM_000605.3	NP_000596.2	P01563	IFNA2_HUMAN	interferon, alpha 2	36					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of gene expression (GO:0010629)|negative regulation of interleukin-13 secretion (GO:2000666)|negative regulation of interleukin-5 secretion (GO:2000663)|negative regulation of T cell differentiation (GO:0045581)|negative regulation of T-helper 2 cell cytokine production (GO:2000552)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral entry into host cell (GO:0046597)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	type I interferon receptor binding (GO:0005132)			breast(2)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)	13				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0173)		CATCAAGGTCCTCCTGCTACC	0.537																																					p.R36K		Atlas-SNP	.											.	IFNA2	32	.	0			c.G107A						PASS	.						113	109	110					9																	21385222		2203	4300	6503	SO:0001583	missense	3440	exon1			AAGGTCCTCCTGC		CCDS6506.1	9p22	2010-08-24			ENSG00000188379	ENSG00000188379		"Interferons"	5423	protein-coding gene	gene with protein product	"alpha-2a interferon", "interferon alpha 2b", "interferon alpha A"	147562				1385305	Standard	NM_000605		Approved	IFNA, IFN-alphaA	uc003zpb.3	P01563	OTTHUMG00000019674	ENST00000380206.2:c.107G>A	chr9.hg19:g.21385222C>T	ENSP00000369554:p.Arg36Lys	61.0	0.0	.		52.0	8.0	.	NM_000605	H2DF54|H2DF55|P01564|Q14606|Q6DJX8|Q96KI6	Missense_Mutation	SNP	ENST00000380206.2	hg19	CCDS6506.1	.	.	.	.	.	.	.	.	.	.	C	10.73	1.432634	0.25813	.	.	ENSG00000188379	ENST00000380206	T	0.03242	4.0	3.24	1.01	0.19927	.	0.727652	0.13301	N	0.398209	T	0.04048	0.0113	L	0.49455	1.56	0.09310	N	1	B	0.10296	0.003	B	0.24974	0.057	T	0.40270	-0.9572	10	0.38643	T	0.18	.	3.0905	0.06293	0.0:0.4701:0.231:0.2989	.	36	Q6DJX8	.	K	36	ENSP00000369554:R36K	ENSP00000369554:R36K	R	-	2	0	IFNA2	21375222	0.000000	0.05858	0.015000	0.15790	0.209000	0.24338	-0.746000	0.04829	0.528000	0.28580	0.484000	0.47621	AGG	.	.	.	none		0.537	IFNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051903.1	NM_000605		T	21385222	C	T	21385222	3	4	70	1	0	0	0	0	1	0	0	0	7544	681	24	2	463	2	IFNA2	9	21385222	Missense_Mutation	SNP	C	TCGA-A4-A7UZ-01A-12D-A34Z-10		21385222	119828209	22	4614											
ALDOB	229	hgsc.bcm.edu	37	chr9	104187772	104187773	+	Frame_Shift_Ins	INS	-	-	A																															cagtacggtggagagctgttINSacggtggccatagctacttg																										TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr9:104187772_104187773insA	ENST00000374855.4	-	7	885_886	c.761_762insT	c.(760-762)gtafs	p.V254fs	ALDOB_ENST00000468981.3_5'Flank	NM_000035.3	NP_000026.2	P05062	ALDOB_HUMAN	aldolase B, fructose-bisphosphate	254					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)				GGAGAGCTGTTACGGTGGCCAT	0.51																																					p.V254fs		Atlas-Indel,Pindel	.											.	ALDOB	69	.	0			c.762_763insT						PASS	.																																			SO:0001589	frameshift_variant	229	exon7			.	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.762dupT	chr9.hg19:g.104187773_104187773dupA	ENSP00000363988:p.Val254fs	100.0	0.0	0		110.0	26.0	0.236364	NM_000035	Q13741|Q13742|Q5T7D6	Frame_Shift_Ins	INS	ENST00000374855.4	hg19	CCDS6756.1																																																																																			.	.	.	none		0.51	ALDOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053434.2			A	104187773	-	A	104187772	7	5	70	1	0	1	1	0	0	0	0	0	508	1741	61	0	344	0	ALDOB	9	104187772	Frame_Shift_Ins	INS	-	TCGA-A4-A7UZ-01A-12D-A34Z-10	82802550	104187772	37025659	23	4615											
RC3H2	54542	hgsc.bcm.edu	37	chr9	125612089	125612089	+	Missense_Mutation	SNP	T	T	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	gaagttaccggcagaattgtTttttgctcctccctgagaaa	10	13	9	9	1	0	2	0	1	0	2	2	4	2	2	3	1	2	4	3	1	4	5			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr9:125612089T>G	ENST00000373670.1	-	20	3993	c.3393A>C	c.(3391-3393)aaA>aaC	p.K1131N	RC3H2_ENST00000357244.2_Missense_Mutation_p.K1131N			Q9HBD1	RC3H2_HUMAN	ring finger and CCCH-type domains 2	1131					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						GCAGAATTGTTTTTTGCTCCT	0.413																																					p.K1131N		Atlas-SNP	.											.	RC3H2	150	.	0			c.A3393C						PASS	.						53	51	52					9																	125612089		1849	4092	5941	SO:0001583	missense	54542	exon21			AATTGTTTTTTGC	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.3393A>C	chr9.hg19:g.125612089T>G	ENSP00000362774:p.Lys1131Asn	144.0	0.0	.		125.0	39.0	.	NM_001100588	Q4VXB1|Q5JPD7|Q86ST6|Q8N3D6|Q96F27|Q9H5J2|Q9HBD2|Q9NWN9|Q9NXE1	Missense_Mutation	SNP	ENST00000373670.1	hg19	CCDS43874.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.83|16.83	3.231922|3.231922	0.58777|0.58777	.|.	.|.	ENSG00000056586|ENSG00000056586	ENST00000373670;ENST00000357244|ENST00000454740	T;T|.	0.50277|.	0.75;0.75|.	5.57|5.57	4.42|4.42	0.53409|0.53409	.|.	0.143354|.	0.48286|.	D|.	0.000191|.	T|T	0.33118|0.33118	0.0852|0.0852	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	D|.	0.57899|.	0.981|.	D|.	0.67231|.	0.95|.	T|T	0.09465|0.09465	-1.0673|-1.0673	10|5	0.87932|.	D|.	0|.	-17.8216|-17.8216	9.2704|9.2704	0.37668|0.37668	0.0:0.0817:0.0:0.9183|0.0:0.0817:0.0:0.9183	.|.	1131|.	Q9HBD1|.	RC3H2_HUMAN|.	N|H	1131|184	ENSP00000362774:K1131N;ENSP00000349783:K1131N|.	ENSP00000349783:K1131N|.	K|N	-|-	3|1	2|0	RC3H2|RC3H2	124651910|124651910	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.894000|0.894000	0.52154|0.52154	1.967000|1.967000	0.40491|0.40491	0.939000|0.939000	0.37446|0.37446	0.460000|0.460000	0.39030|0.39030	AAA|AAC	.	.	.	none		0.413	RC3H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053966.1	NM_018835		G	125612089	T	G	125612089	3	3	70	1	0	0	0	0	1	0	0	0	13180	1838	64	5	186	5	RC3H2	9	125612089	Missense_Mutation	SNP	T	TCGA-A4-A7UZ-01A-12D-A34Z-10	21424317	125612089	15601342	24	4616											
KAZALD1	81621	hgsc.bcm.edu	37	chr10	102824381	102824381	+	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	tgggtcaagtggaggcccctGctagcttgacagtgctcaca	8	9	13	11	0	2	1	2	1	0	0	2	2	2	2	2	3	3	3	2	3	2	2			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr10:102824381G>T	ENST00000370200.5	+	4	1122	c.796G>T	c.(796-798)Gct>Tct	p.A266S		NM_030929.4	NP_112191.2	Q96I82	KAZD1_HUMAN	Kazal-type serine peptidase inhibitor domain 1	266	Ig-like C2-type.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|regulation of cell growth (GO:0001558)	interstitial matrix (GO:0005614)				endometrium(1)|ovary(1)|prostate(2)	4				Epithelial(162;6.21e-09)|all cancers(201;3.14e-07)		GGAGGCCCCTGCTAGCTTGAC	0.582																																					p.A266S		Atlas-SNP	.											.	KAZALD1	14	.	0			c.G796T						PASS	.						51	49	50					10																	102824381		2203	4300	6503	SO:0001583	missense	81621	exon4			GCCCCTGCTAGCT	AF333487	CCDS7509.1	10q24.32	2013-01-11	2005-08-17		ENSG00000107821	ENSG00000107821		"Immunoglobulin superfamily / I-set domain containing"	25460	protein-coding gene	gene with protein product		609208	"Kazal-type serine protease inhibitor domain 1"			12975309	Standard	NM_030929		Approved	FKSG40, FKSG28	uc001ksr.3	Q96I82	OTTHUMG00000018918	ENST00000370200.5:c.796G>T	chr10.hg19:g.102824381G>T	ENSP00000359219:p.Ala266Ser	34.0	0.0	.		42.0	7.0	.	NM_030929	D3DR74|Q6ZMB1|Q9BQ73	Missense_Mutation	SNP	ENST00000370200.5	hg19	CCDS7509.1	.	.	.	.	.	.	.	.	.	.	G	34	5.318477	0.95682	.	.	ENSG00000107821	ENST00000370200	T	0.70516	-0.49	5.71	5.71	0.89125	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.86121	0.5857	M	0.83603	2.65	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86242	0.1644	10	0.52906	T	0.07	-1.6084	19.8575	0.96767	0.0:0.0:1.0:0.0	.	266	Q96I82	KAZD1_HUMAN	S	266	ENSP00000359219:A266S	ENSP00000359219:A266S	A	+	1	0	KAZALD1	102814371	1.000000	0.71417	0.959000	0.39883	0.953000	0.61014	9.821000	0.99360	2.698000	0.92095	0.561000	0.74099	GCT	.	.	.	none		0.582	KAZALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049891.2	NM_030929		T	102824381	G	T	102824381	3	4	70	1	0	0	0	0	1	0	0	0	7996	1319	46	4	806	4	KAZALD1	10	102824381	Missense_Mutation	SNP	G	TCGA-A4-A7UZ-01A-12D-A34Z-10		102824381	32710366	25	4617											
PPRC1	23082	hgsc.bcm.edu	37	chr10	103900008	103900008	+	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	tcattggtcgactctgcccaAgccagccccatgccagttga	8	9	9	15	1	2	1	1	1	1	0	3	2	2	1	5	1	4	1	5	1	1	2			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr10:103900008A>T	ENST00000278070.2	+	5	1782	c.1743A>T	c.(1741-1743)caA>caT	p.Q581H	PPRC1_ENST00000413464.2_Missense_Mutation_p.Q581H|PPRC1_ENST00000370012.1_5'Flank	NM_015062.3	NP_055877.3	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator-related 1	581					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(10)|lung(19)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		ACTCTGCCCAAGCCAGCCCCA	0.542																																					p.Q581H		Atlas-SNP	.											.	PPRC1	151	.	0			c.A1743T						PASS	.						133	114	120					10																	103900008		2203	4300	6503	SO:0001583	missense	23082	exon5			TGCCCAAGCCAGC	AF325193	CCDS7529.1, CCDS73186.1	10q24.32	2013-02-12	2006-10-17		ENSG00000148840	ENSG00000148840		"RNA binding motif (RRM) containing"	30025	protein-coding gene	gene with protein product			"peroxisome proliferative activated receptor, gamma, coactivator-related 1"			9628581, 11340167	Standard	XM_005269656		Approved	PRC, KIAA0595, MGC74642	uc001kum.3	Q5VV67	OTTHUMG00000018948	ENST00000278070.2:c.1743A>T	chr10.hg19:g.103900008A>T	ENSP00000278070:p.Gln581His	112.0	0.0	.		135.0	28.0	.	NM_015062	Q5VV66|Q6P3U5|Q6P3W1|Q76N31|Q9BUJ3|Q9BZE5|Q9Y4E0	Missense_Mutation	SNP	ENST00000278070.2	hg19	CCDS7529.1	.	.	.	.	.	.	.	.	.	.	A	12.76	2.034985	0.35893	.	.	ENSG00000148840	ENST00000278070;ENST00000413464	T;T	0.55413	0.52;0.52	4.77	-4.45	0.03546	.	2.468930	0.01573	N	0.020686	T	0.32406	0.0828	N	0.19112	0.55	0.09310	N	1	P;B;P	0.35600	0.511;0.412;0.511	B;B;B	0.35688	0.145;0.208;0.094	T	0.12837	-1.0532	10	0.54805	T	0.06	.	0.1789	0.00121	0.2863:0.2485:0.2237:0.2416	.	581;461;581	E7EVG6;Q5VV67-2;Q5VV67	.;.;PPRC1_HUMAN	H	581	ENSP00000278070:Q581H;ENSP00000399743:Q581H	ENSP00000278070:Q581H	Q	+	3	2	PPRC1	103889998	0.102000	0.21896	0.000000	0.03702	0.010000	0.07245	0.172000	0.16704	-0.920000	0.03799	-1.357000	0.01221	CAA	.	.	.	none		0.542	PPRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050021.1	NM_015062		T	103900008	A	T	103900008	3	4	70	1	0	0	0	0	1	0	0	0	12420	69	3	5	1761	5	PPRC1	10	103900008	Missense_Mutation	SNP	A	TCGA-A4-A7UZ-01A-12D-A34Z-10	1075627	103900008	31634739	26	4618											
PRDX5	25824	hgsc.bcm.edu	37	chr11	64085710	64085710	+	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	gggactagctggcgtgtgcgCcctgagacgctcagcgggct	5	7	17	12	4	1	1	1	1	0	1	1	3	1	2	1	3	3	3	1	3	1	1	rs368539290		TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr11:64085710C>T	ENST00000265462.4	+	1	151	c.23C>T	c.(22-24)gCc>gTc	p.A8V	TRMT112_ENST00000535750.1_5'Flank|PRDX5_ENST00000352435.4_Missense_Mutation_p.A8V|PRDX5_ENST00000347941.4_Missense_Mutation_p.A8V|TRMT112_ENST00000535126.1_5'Flank|TRMT112_ENST00000539854.1_5'Flank|TRMT112_ENST00000544844.1_5'Flank|TRMT112_ENST00000308774.2_5'Flank	NM_012094.4	NP_036226	P30044	PRDX5_HUMAN	peroxiredoxin 5	8					cellular response to reactive oxygen species (GO:0034614)|hydrogen peroxide catabolic process (GO:0042744)|inflammatory response (GO:0006954)|NADPH oxidation (GO:0070995)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of transcription from RNA polymerase III promoter (GO:0016480)|positive regulation of collagen biosynthetic process (GO:0032967)|reactive nitrogen species metabolic process (GO:2001057)|regulation of apoptosis involved in tissue homeostasis (GO:0060785)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	antioxidant activity (GO:0016209)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|peroxidase activity (GO:0004601)|peroxiredoxin activity (GO:0051920)|peroxynitrite reductase activity (GO:0072541)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase III regulatory region DNA binding (GO:0001016)			breast(1)|kidney(1)|lung(1)|skin(1)	4					Auranofin(DB00995)	GGCGTGTGCGCCCTGAGACGC	0.697																																					p.A8V		Atlas-SNP	.											.	PRDX5	16	.	0			c.C23T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA	0,4400		0,0,2200	34	36	35		23,23,23	-2.2	0	11		35	1,8591	1.2+/-3.3	0,1,4295	no	missense,missense,missense	PRDX5	NM_012094.4,NM_181651.2,NM_181652.2	64,64,64	0,1,6495	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	8/215,8/171,8/126	64085710	1,12991	2200	4296	6496	SO:0001583	missense	25824	exon1			TGTGCGCCCTGAG	AF197952	CCDS8069.1, CCDS8070.1, CCDS8071.1	11q13	2008-07-21			ENSG00000126432	ENSG00000126432			9355	protein-coding gene	gene with protein product	"antioxidant enzyme B166", "thioredoxin peroxidase PMP20", "peroxisomal antioxidant enzyme", "TPx type VI", "liver tissue 2D-page spot 71B", "Alu co-repressor 1"	606583				10514471, 10521424	Standard	NM_012094		Approved	ACR1, AOEB166, MGC142285, PRXV, PMP20, B166, PRDX6, PLP, SBBI10, MGC117264, MGC142283	uc001nzu.3	P30044	OTTHUMG00000168805	ENST00000265462.4:c.23C>T	chr11.hg19:g.64085710C>T	ENSP00000265462:p.Ala8Val	91.0	0.0	.		67.0	24.0	.	NM_181651	A6NC19|A6NG06|B7ZLJ4|B7ZVW3|Q14CK0|Q6IAF2|Q9UBU5|Q9UJU4|Q9UKX4	Missense_Mutation	SNP	ENST00000265462.4	hg19	CCDS8069.1	.	.	.	.	.	.	.	.	.	.	C	1.653	-0.513546	0.04200	0.0	1.16E-4	ENSG00000126432	ENST00000265462;ENST00000352435;ENST00000347941	T;T;T	0.42900	0.96;0.97;1.04	3.31	-2.16	0.07080	.	.	.	.	.	T	0.11452	0.0279	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	0.29912	-0.9996	9	0.02654	T	1	-0.1379	3.904	0.09174	0.0:0.3617:0.2031:0.4352	.	8;8;8	A6NC19;A6NG06;P30044	.;.;PRDX5_HUMAN	V	8	ENSP00000265462:A8V;ENSP00000335334:A8V;ENSP00000335363:A8V	ENSP00000265462:A8V	A	+	2	0	PRDX5	63842286	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-0.504000	0.06375	-0.389000	0.07786	-0.518000	0.04402	GCC	.	.	.	weak		0.697	PRDX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401148.1	NM_181651		T	64085710	C	T	64085710	3	4	70	1	0	0	0	0	1	0	0	0	12478	739	26	2	25	2	PRDX5	11	64085710	Missense_Mutation	SNP	C	TCGA-A4-A7UZ-01A-12D-A34Z-10		64085710	70920806	27	4619											
SYVN1	84447	hgsc.bcm.edu	37	chr11	64897359	64897359	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggtcagcccagcaaagccCgcagggggcacaggcattgg	9	3	17	12	1	1	0	1	0	0	0	1	0	1	0	2	6	3	4	2	6	1	1			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr11:64897359C>T	ENST00000377190.3	-	14	1531	c.1437G>A	c.(1435-1437)gcG>gcA	p.A479A	SYVN1_ENST00000526060.1_Silent_p.A478A|SYVN1_ENST00000526121.1_5'Flank|SYVN1_ENST00000294256.8_Silent_p.A478A|SYVN1_ENST00000307289.6_Silent_p.A427A	NM_172230.2	NP_757385.1	Q86TM6	SYVN1_HUMAN	synovial apoptosis inhibitor 1, synoviolin	479					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						CAGCAAAGCCCGCAGGGGGCA	0.652																																					p.A479A		Atlas-SNP	.											.	SYVN1	55	.	0			c.G1437A						PASS	.						26	32	30					11																	64897359		2201	4297	6498	SO:0001819	synonymous_variant	84447	exon14			AAAGCCCGCAGGG	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.1437G>A	chr11.hg19:g.64897359C>T		41.0	0.0	.		27.0	7.0	.	NM_172230	Q8N3K3|Q8N6E8|Q96JL5|Q96PK3	Silent	SNP	ENST00000377190.3	hg19	CCDS31605.1																																																																																			.	.	.	none		0.652	SYVN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385274.1	NM_032431		T	64897359	C	T	64897359	2	4	70	1	0	0	0	0	0	0	0	1	15499	639	23	1		1	SYVN1	11	64897359	Silent	SNP	C	TCGA-A4-A7UZ-01A-12D-A34Z-10	811649	64897359	70109157	28	4620											
HEPHL1	341208	hgsc.bcm.edu	37	chr11	93796840	93796840	+	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	tcgcacatcgacgccccaaaGgacatctgctctgggctaat	10	8	9	14	3	2	0	0	0	2	0	4	2	2	1	2	2	1	3	2	2	2	1	rs557063968		TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr11:93796840G>T	ENST00000315765.9	+	3	590	c.582G>T	c.(580-582)aaG>aaT	p.K194N		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	194	Plastocyanin-like 1.				copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				ACGCCCCAAAGGACATCTGCT	0.522																																					p.K194N		Atlas-SNP	.											.	HEPHL1	144	.	0			c.G582T						PASS	.						108	106	107					11																	93796840		1965	4153	6118	SO:0001583	missense	341208	exon3			CCCAAAGGACATC	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.582G>T	chr11.hg19:g.93796840G>T	ENSP00000313699:p.Lys194Asn	99.0	0.0	.		91.0	24.0	.	NM_001098672	Q3C1W7	Missense_Mutation	SNP	ENST00000315765.9	hg19	CCDS44710.1	.	.	.	.	.	.	.	.	.	.	G	17.47	3.397872	0.62177	.	.	ENSG00000181333	ENST00000315765	D	0.99483	-5.99	5.33	3.47	0.39725	Cupredoxin (2);Multicopper oxidase, type 3 (1);	0.146963	0.64402	D	0.000010	D	0.98909	0.9630	L	0.49513	1.565	0.44762	D	0.99776	D	0.67145	0.996	D	0.70016	0.967	D	0.97634	1.0144	10	0.30854	T	0.27	.	6.7985	0.23738	0.3943:0.0:0.6057:0.0	.	194	Q6MZM0	HPHL1_HUMAN	N	194	ENSP00000313699:K194N	ENSP00000313699:K194N	K	+	3	2	HEPHL1	93436488	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	1.877000	0.39598	0.642000	0.30620	0.655000	0.94253	AAG	.	.	.	none		0.522	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947		T	93796840	G	T	93796840	3	4	70	1	0	0	0	0	1	0	0	0	7062	991	35	4	592	4	HEPHL1	11	93796840	Missense_Mutation	SNP	G	TCGA-A4-A7UZ-01A-12D-A34Z-10	28899481	93796840	41209676	29	4621											
IL18	3606	hgsc.bcm.edu	37	chr11	112019383	112019384	+	Frame_Shift_Del	DEL	AG	AG	-																															gaaattttctcacacttcacAgagatagttacagccatacc																										TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr11:112019383_112019384delAG	ENST00000280357.7	-	5	521_522	c.302_303delCT	c.(301-303)tctfs	p.S101fs	IL18_ENST00000524595.1_Frame_Shift_Del_p.S97fs|SDHD_ENST00000532699.1_Intron|IL18_ENST00000528832.1_Frame_Shift_Del_p.S101fs|IL18_ENST00000533858.1_5'UTR	NM_001562.3	NP_001553.1	Q14116	IL18_HUMAN	interleukin 18	101					angiogenesis (GO:0001525)|cell-cell signaling (GO:0007267)|cellular response to organic cyclic compound (GO:0071407)|chemokine biosynthetic process (GO:0042033)|granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0042253)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma biosynthetic process (GO:0042095)|interleukin-13 biosynthetic process (GO:0042231)|interleukin-2 biosynthetic process (GO:0042094)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|natural killer cell activation (GO:0030101)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of gene expression (GO:0010628)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NK T cell proliferation (GO:0051142)|positive regulation of tissue remodeling (GO:0034105)|regulation of cell adhesion (GO:0030155)|sleep (GO:0030431)|T-helper 1 type immune response (GO:0042088)|type 2 immune response (GO:0042092)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)						all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;6.72e-07)|Epithelial(105;8.15e-07)|all cancers(92;1.43e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.055)		CACACTTCACAGAGATAGTTAC	0.317																																					p.101_102del		Atlas-Indel,Pindel	.											.	IL18	10	.	0			c.303_304del						PASS	.																																			SO:0001589	frameshift_variant	3606	exon5			.	U90434	CCDS44731.1, CCDS58180.1	11q22.2-q22.3	2014-04-04	2014-04-04		ENSG00000150782	ENSG00000150782		"Interleukins and interleukin receptors"	5986	protein-coding gene	gene with protein product	"interferon-gamma-inducing factor"	600953	"interleukin 18 (interferon-gamma-inducing factor)"			7477296, 9693051	Standard	NM_001562		Approved	IGIF, IL1F4, IL-1g, IL-18	uc001pnb.2	Q14116	OTTHUMG00000167006	ENST00000280357.7:c.302_303delCT	chr11.hg19:g.112019385_112019386delAG	ENSP00000280357:p.Ser101fs	172.0	0.0	0		144.0	39.0	0.270833	NM_001562	O75599|Q6FGY3|Q6WWJ7	Frame_Shift_Del	DEL	ENST00000280357.7	hg19	CCDS44731.1																																																																																			.	.	.	none		0.317	IL18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392409.1	NM_001562		-	112019384	AG	-	112019383	7	5	70	1	0	1	0	1	0	0	0	0	7652	175	7	0	286	0	IL18	11	112019383	Frame_Shift_Del	DEL	AG	TCGA-A4-A7UZ-01A-12D-A34Z-10	18222543	112019383	22987133	30	4622											
LIMA1	51474	hgsc.bcm.edu	37	chr12	50571415	50571415	+	Frame_Shift_Del	DEL	A	A	-																															gcttcttcagatctagatcgAcatcctcaggaacttcgggc																										TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr12:50571415delA	ENST00000341247.4	-	11	1861	c.1712delT	c.(1711-1713)gtcfs	p.V571fs	LIMA1_ENST00000552491.1_Frame_Shift_Del_p.V268fs|LIMA1_ENST00000552909.1_Frame_Shift_Del_p.V410fs|LIMA1_ENST00000552783.1_Frame_Shift_Del_p.V412fs|LIMA1_ENST00000394943.3_Frame_Shift_Del_p.V572fs|LIMA1_ENST00000552823.1_Frame_Shift_Del_p.V411fs|LIMA1_ENST00000547825.1_Frame_Shift_Del_p.V269fs	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	571					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						ATCTAGATCGACATCCTCAGG	0.478																																					p.V572fs		Atlas-Indel,Pindel	.											LIMA1,NS,carcinoma,0,1	LIMA1	67	.	0			c.1716delC						PASS	.						123	123	123					12																	50571415		2203	4300	6503	SO:0001589	frameshift_variant	51474	exon11			.	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.1712delT	chr12.hg19:g.50571415delA	ENSP00000340184:p.Val571fs	116.0	0.0	0		138.0	51.0	0.369565	NM_001113546	B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Frame_Shift_Del	DEL	ENST00000341247.4	hg19	CCDS8802.1																																																																																			.	.	.	none		0.478	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357		-	50571415	A	-	50571415	7	5	70	1	0	1	0	1	0	0	0	0	8803	275	10	0	571	0	LIMA1	12	50571415	Frame_Shift_Del	DEL	A	TCGA-A4-A7UZ-01A-12D-A34Z-10		50571415	83280480	31	4623											
LIMA1	51474	hgsc.bcm.edu	37	chr12	50594621	50594621	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggcacattctccttttgcTccattttatgaattttgatt	7	19	7	8	0	1	2	0	2	1	0	3	2	2	2	2	2	1	2	2	2	2	8			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr12:50594621T>C	ENST00000341247.4	-	7	1060	c.911A>G	c.(910-912)gAg>gGg	p.E304G	LIMA1_ENST00000552491.1_Missense_Mutation_p.E2G|LIMA1_ENST00000552909.1_Missense_Mutation_p.E144G|LIMA1_ENST00000552783.1_Missense_Mutation_p.E144G|LIMA1_ENST00000394943.3_Missense_Mutation_p.E304G|LIMA1_ENST00000552823.1_Missense_Mutation_p.E144G|LIMA1_ENST00000547825.1_Missense_Mutation_p.E2G|LIMA1_ENST00000552008.1_5'UTR	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	304					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						CTCCTTTTGCTCCATTTTATG	0.408																																					p.E304G		Atlas-SNP	.											.	LIMA1	67	.	0			c.A911G						PASS	.						251	249	249					12																	50594621		2203	4300	6503	SO:0001583	missense	51474	exon7			TTTTGCTCCATTT	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.911A>G	chr12.hg19:g.50594621T>C	ENSP00000340184:p.Glu304Gly	90.0	0.0	.		91.0	19.0	.	NM_016357	B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Missense_Mutation	SNP	ENST00000341247.4	hg19	CCDS8802.1	.	.	.	.	.	.	.	.	.	.	T	12.71	2.020309	0.35606	.	.	ENSG00000050405	ENST00000552491;ENST00000547825;ENST00000552823;ENST00000394943;ENST00000341247;ENST00000552783;ENST00000552909;ENST00000420992	T;T;D;D;T;D;D	0.84944	-1.32;-1.32;-1.51;-1.92;-1.19;-1.51;-1.51	5.44	5.44	0.79542	.	0.394381	0.29119	N	0.013087	D	0.82724	0.5099	M	0.67953	2.075	0.43868	D	0.996471	B;B;B	0.23990	0.095;0.06;0.034	B;B;B	0.18871	0.023;0.018;0.023	T	0.78966	-0.1995	10	0.32370	T	0.25	.	13.1177	0.59309	0.0:0.0:0.0:1.0	.	313;304;144	Q59FE8;Q9UHB6;F8VQE1	.;LIMA1_HUMAN;.	G	2;2;144;304;304;144;144;223	ENSP00000448463:E2G;ENSP00000448706:E2G;ENSP00000450266:E144G;ENSP00000378400:E304G;ENSP00000340184:E304G;ENSP00000448779:E144G;ENSP00000450087:E144G	ENSP00000340184:E304G	E	-	2	0	LIMA1	48880888	0.997000	0.39634	0.995000	0.50966	0.281000	0.26958	2.852000	0.48310	2.284000	0.76573	0.528000	0.53228	GAG	.	.	.	none		0.408	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357		C	50594621	T	C	50594621	3	2	70	1	0	0	0	0	1	0	0	0	8803	1551	54	3	1391	3	LIMA1	12	50594621	Missense_Mutation	SNP	T	TCGA-A4-A7UZ-01A-12D-A34Z-10	23206	50594621	83257274	32	4624											
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-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	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,0,2	KRT3	65	.	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	chr12.hg19:g.53183951C>T	ENSP00000413479:p.Gly588Ser	36.0	0.0	.		68.0	13.0	.	NM_057088	A6NIS2|Q701L8	Missense_Mutation	SNP	ENST00000417996.2	hg19	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	70	1	0	0	0	0	1	0	0	0	8473	652	23	1	128	1	KRT3	12	53183951	Missense_Mutation	SNP	C	TCGA-A4-A7UZ-01A-12D-A34Z-10	2589330	53183951	80667944	33	4625											
ANO4	121601	hgsc.bcm.edu	37	chr12	101514351	101514351	+	Missense_Mutation	SNP	T	T	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	ggtgccctatggctacacacTgcagttttggcatgtcctag	7	12	11	11	0	0	0	0	0	0	0	1	0	1	0	2	3	3	4	2	3	3	5			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr12:101514351T>G	ENST00000392977.3	+	26	2834	c.2624T>G	c.(2623-2625)cTg>cGg	p.L875R	ANO4_ENST00000392979.3_Missense_Mutation_p.L840R|ANO4_ENST00000299222.9_Missense_Mutation_p.L395R|ANO4_ENST00000550015.1_Missense_Mutation_p.L395R			Q32M45	ANO4_HUMAN	anoctamin 4	875					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						GGCTACACACTGCAGTTTTGG	0.408										HNSCC(74;0.22)																											p.L840R		Atlas-SNP	.											.	ANO4	183	.	0			c.T2519G						PASS	.						160	138	145					12																	101514351		2203	4300	6503	SO:0001583	missense	121601	exon25			ACACACTGCAGTT	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.2624T>G	chr12.hg19:g.101514351T>G	ENSP00000376703:p.Leu875Arg	178.0	0.0	.		182.0	48.0	.	NM_178826	Q8NAJ0|Q8NB39|Q8NB53	Missense_Mutation	SNP	ENST00000392977.3	hg19		.	.	.	.	.	.	.	.	.	.	T	24.2	4.506997	0.85282	.	.	ENSG00000151572	ENST00000392979;ENST00000299222;ENST00000392977;ENST00000550015	T;T;T;T	0.69685	-0.41;-0.26;-0.42;-0.26	5.9	5.9	0.94986	.	0.000000	0.64402	D	0.000018	T	0.77089	0.4079	L	0.53249	1.67	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.999;0.996;0.999	T	0.72207	-0.4360	10	0.16420	T	0.52	.	16.3322	0.83039	0.0:0.0:0.0:1.0	.	395;875;840	Q32M45-3;Q32M45;Q32M45-2	.;ANO4_HUMAN;.	R	840;395;875;395	ENSP00000376705:L840R;ENSP00000299222:L395R;ENSP00000376703:L875R;ENSP00000450192:L395R	ENSP00000299222:L395R	L	+	2	0	ANO4	100038482	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.040000	0.89188	2.251000	0.74343	0.528000	0.53228	CTG	.	.	.	none		0.408	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826		G	101514351	T	G	101514351	3	3	70	1	0	0	0	0	1	0	0	0	699	1580	55	5	2613	5	ANO4	12	101514351	Missense_Mutation	SNP	T	TCGA-A4-A7UZ-01A-12D-A34Z-10	48330400	101514351	32337544	34	4626											
ATXN2	6311	hgsc.bcm.edu	37	chr12	111951273	111951273	+	Frame_Shift_Del	DEL	G	G	-																															aattctaggccactggatatGgaacccctcccagcagaaac																										TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr12:111951273delG	ENST00000377617.3	-	11	2087	c.1926delC	c.(1924-1926)tccfs	p.S642fs	ATXN2_ENST00000550104.1_Frame_Shift_Del_p.S642fs|ATXN2_ENST00000608853.1_Frame_Shift_Del_p.S482fs|ATXN2_ENST00000389153.4_Frame_Shift_Del_p.S377fs|ATXN2_ENST00000542287.2_Frame_Shift_Del_p.S377fs|ATXN2_ENST00000535949.1_Frame_Shift_Del_p.S353fs	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	642	Pro-rich.				cell death (GO:0008219)|cerebellar Purkinje cell differentiation (GO:0021702)|cytoplasmic mRNA processing body assembly (GO:0033962)|homeostasis of number of cells (GO:0048872)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of receptor internalization (GO:0002091)|neuromuscular process (GO:0050905)|neuron projection morphogenesis (GO:0048812)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA transport (GO:0050658)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|trans-Golgi network (GO:0005802)	epidermal growth factor receptor binding (GO:0005154)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						CACTGGATATGGAACCCCTCC	0.532																																					p.I643fs		Atlas-Indel,Pindel	.											.	ATXN2	99	.	0			c.1927delA						PASS	.						94	80	84					12																	111951273		2203	4300	6503	SO:0001589	frameshift_variant	6311	exon11			.	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.1926delC	chr12.hg19:g.111951273delG	ENSP00000366843:p.Ser642fs	95.0	0.0	0		126.0	24.0	0.190476	NM_002973	A6NLD4|Q6ZQZ7|Q99493	Frame_Shift_Del	DEL	ENST00000377617.3	hg19	CCDS31902.1																																																																																			.	.	.	none		0.532	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973		-	111951273	G	-	111951273	7	5	70	1	0	1	0	1	0	0	0	0	1211	1335	47	0	2075	0	ATXN2	12	111951273	Frame_Shift_Del	DEL	G	TCGA-A4-A7UZ-01A-12D-A34Z-10	10436922	111951273	21900622	35	4627											
SUCLA2	8803	hgsc.bcm.edu	37	chr13	48528276	48528276	+	Splice_Site	DEL	T	T	-																															tatcaagccctgcccttaccTttttatctgaagtgataagc																										TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr13:48528276delT	ENST00000378654.3	-	8	1162	c.1106delA	c.(1105-1107)aag>ag	p.K369fs	SUCLA2_ENST00000534875.1_Splice_Site_p.K311fs|SUCLA2_ENST00000544100.1_Splice_Site_p.K235fs|SUCLA2_ENST00000543413.1_Splice_Site_p.K311fs	NM_003850.2	NP_003841.1	Q9P2R7	SUCB1_HUMAN	succinate-CoA ligase, ADP-forming, beta subunit	369					cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|succinyl-CoA metabolic process (GO:0006104)|succinyl-CoA pathway (GO:0006781)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(3)|skin(4)	15		all_cancers(8;1.13e-24)|all_epithelial(8;1.78e-13)|all_lung(13;2.85e-06)|Breast(56;0.000141)|Lung NSC(96;0.000226)|all_hematologic(8;0.000885)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.0167)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;2.1e-06)	Succinic acid(DB00139)	TGCCCTTACCTTTTTATCTGA	0.303																																					p.K369fs		Pindel	.											.	SUCLA2	40	.	0			c.1107delG						PASS	.						36	36	36					13																	48528276		2203	4300	6503	SO:0001630	splice_region_variant	8803	exon8			.	AF058953	CCDS9406.1	13q12.2-q13.3	2010-04-16			ENSG00000136143	ENSG00000136143	6.2.1.5		11448	protein-coding gene	gene with protein product		603921				9765291	Standard	NM_003850		Approved		uc001vbs.3	Q9P2R7	OTTHUMG00000016889	ENST00000378654.3:c.1107+1A>-	chr13.hg19:g.48528276delT		136.0	0.0	.		140.0	15.0	0.107	NM_003850	B2RDE7|O95194|Q5T9Q4|Q5T9Q6|Q9NV21|Q9NVP7	Frame_Shift_Del	DEL	ENST00000378654.3	hg19	CCDS9406.1																																																																																			.	.	.	none		0.303	SUCLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044852.1		Frame_Shift_Del	-	48528276	T	-	48528276	8	5	70	1	0	1	0	1	0	0	1	0	15375	1623	56	0	301	0	SUCLA2	13	48528276	Splice_Site	DEL	T	TCGA-A4-A7UZ-01A-12D-A34Z-10		48528276	66641602	36	4628											
PCNX	22990	hgsc.bcm.edu	37	chr14	71572155	71572155	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cacatcttatcctccaacacTaggtaatgtgaaacaaagtt	15	11	5	10	0	1	1	0	1	1	0	3	1	3	1	2	1	2	2	2	1	6	4			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr14:71572155T>C	ENST00000304743.2	+	33	6745	c.6299T>C	c.(6298-6300)cTa>cCa	p.L2100P	PCNX_ENST00000439984.3_Missense_Mutation_p.L1989P|PCNX_ENST00000238570.5_Missense_Mutation_p.L2028P|PCNX_ENST00000556272.1_3'UTR	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	2100						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)		CCTCCAACACTAGGTAATGTG	0.448																																					p.L2100P		Atlas-SNP	.											.	PCNX	198	.	0			c.T6299C						PASS	.						91	80	84					14																	71572155		2203	4300	6503	SO:0001583	missense	22990	exon33			CAACACTAGGTAA	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.6299T>C	chr14.hg19:g.71572155T>C	ENSP00000304192:p.Leu2100Pro	90.0	0.0	.		75.0	13.0	.	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	hg19	CCDS9806.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.11|13.11	2.138849|2.138849	0.37728|0.37728	.|.	.|.	ENSG00000100731|ENSG00000100731	ENST00000304743;ENST00000238570;ENST00000439984|ENST00000554691	T;T;T|.	0.10860|.	3.25;3.28;2.83|.	5.26|5.26	5.26|5.26	0.73747|0.73747	.|.	0.505695|.	0.18696|.	N|.	0.133734|.	T|.	0.64114|.	0.2569|.	L|L	0.54323|0.54323	1.7|1.7	0.58432|0.58432	D|D	0.999997|0.999997	D;D;D|.	0.76494|.	0.999;0.998;0.998|.	D;D;D|.	0.87578|.	0.998;0.995;0.995|.	T|.	0.62572|.	-0.6826|.	10|.	0.22706|.	T|.	0.39|.	.|.	14.1629|14.1629	0.65457|0.65457	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	2028;1989;2100|.	Q96RV3-3;B2RTR6;Q96RV3|.	.;.;PCX1_HUMAN|.	P|Q	2100;2028;1989|1087	ENSP00000304192:L2100P;ENSP00000238570:L2028P;ENSP00000396617:L1989P|.	ENSP00000238570:L2028P|.	L|X	+|+	2|1	0|0	PCNX|PCNX	70641908|70641908	1.000000|1.000000	0.71417|0.71417	0.843000|0.843000	0.33291|0.33291	0.193000|0.193000	0.23685|0.23685	3.097000|3.097000	0.50251|0.50251	1.988000|1.988000	0.58038|0.58038	0.533000|0.533000	0.62120|0.62120	CTA|TAG	.	.	.	none		0.448	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		C	71572155	T	C	71572155	3	2	70	1	0	0	0	0	1	0	0	0	11598	1522	53	3	6429	3	PCNX	14	71572155	Missense_Mutation	SNP	T	TCGA-A4-A7UZ-01A-12D-A34Z-10		71572155	35777385	37	4629											
C15orf44	81556	hgsc.bcm.edu	37	chr15	65892192	65892192	+	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	aaacctgttgctctcacttcGttgattttgagtggctaggg	7	15	11	8	1	1	2	1	2	1	0	3	2	1	2	1	2	2	4	1	2	2	6			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr15:65892192G>C	ENST00000395644.4	-	4	741	c.406C>G	c.(406-408)Cga>Gga	p.R136G	VWA9_ENST00000567744.1_Missense_Mutation_p.R172G|VWA9_ENST00000569491.1_Missense_Mutation_p.R87G|VWA9_ENST00000431261.2_Missense_Mutation_p.R57G|VWA9_ENST00000442903.3_Missense_Mutation_p.R100G|VWA9_ENST00000313182.2_Missense_Mutation_p.R136G|VWA9_ENST00000420799.2_Missense_Mutation_p.R79G			Q96SY0	VWA9_HUMAN	von Willebrand factor A domain containing 9	136	VWFA.																CTCTCACTTCGTTGATTTTGA	0.448																																					p.R119G		Atlas-SNP	.											.	VWA9	15	.	0			c.C355G						PASS	.						163	121	136					15																	65892192		2201	4299	6500	SO:0001583	missense	81556	exon4			CACTTCGTTGATT	AL136662	CCDS55969.1, CCDS45283.1	15q22.31	2012-09-27	2012-09-27	2012-09-27	ENSG00000138614	ENSG00000138614			25372	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 44"	C15orf44		11230166	Standard	NM_001136043		Approved	DKFZP564O1664	uc010uja.2	Q96SY0	OTTHUMG00000133159	ENST00000395644.4:c.406C>G	chr15.hg19:g.65892192G>C	ENSP00000379006:p.Arg136Gly	79.0	0.0	.		120.0	34.0	.	NM_001207058	B4DDI6|B4DVD5|Q49AH8|Q96HX5|Q9H0S5	Missense_Mutation	SNP	ENST00000395644.4	hg19		.	.	.	.	.	.	.	.	.	.	G	14.98	2.696264	0.48202	.	.	ENSG00000138614	ENST00000395644;ENST00000313182;ENST00000431261;ENST00000420799;ENST00000442903	T;T;T	0.67345	-0.26;-0.26;-0.26	5.79	2.77	0.32553	von Willebrand factor, type A (1);	0.000000	0.85682	D	0.000000	T	0.68467	0.3004	L	0.59436	1.845	0.58432	D	0.999996	P;P;P;D;P	0.53619	0.884;0.884;0.901;0.961;0.924	B;B;B;P;B	0.48815	0.347;0.361;0.233;0.591;0.436	T	0.68187	-0.5475	10	0.44086	T	0.13	-12.6037	14.8532	0.70313	0.0:0.0:0.5019:0.4981	.	79;87;100;172;136	B4DDI6;B4DWZ3;B4DVT3;B4DJL6;Q96SY0	.;.;.;.;CO044_HUMAN	G	136;136;57;79;100	ENSP00000379006:R136G;ENSP00000326379:R136G;ENSP00000396314:R100G	ENSP00000326379:R136G	R	-	1	2	C15orf44	63679245	0.991000	0.36638	0.312000	0.25196	0.975000	0.68041	2.072000	0.41510	0.291000	0.22468	-0.127000	0.14921	CGA	.	.	.	none		0.448	VWA9-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420604.3	NM_030800		C	65892192	G	C	65892192	3	2	70	1	0	0	0	0	1	0	0	0	1800	1153	40	4	1186	4	C15orf44	15	65892192	Missense_Mutation	SNP	G	TCGA-A4-A7UZ-01A-12D-A34Z-10		65892192	36639200	38	4630											
RASGRF1	5923	hgsc.bcm.edu	37	chr15	79265658	79265658	+	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	aacgcaccatcctcatcttgGagaagttgaccaggccgtct	10	9	9	13	2	3	2	1	1	2	1	4	3	4	2	4	2	1	2	4	2	2	2			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr15:79265658G>C	ENST00000419573.3	-	26	3921	c.3647C>G	c.(3646-3648)tCc>tGc	p.S1216C	RASGRF1_ENST00000394745.3_Missense_Mutation_p.S432C|RASGRF1_ENST00000558480.2_Missense_Mutation_p.S1200C	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	1216	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						CCTCATCTTGGAGAAGTTGAC	0.632																																					p.S1216C		Atlas-SNP	.											.	RASGRF1	168	.	0			c.C3647G						PASS	.						164	129	141					15																	79265658		2196	4293	6489	SO:0001583	missense	5923	exon26			ATCTTGGAGAAGT	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.3647C>G	chr15.hg19:g.79265658G>C	ENSP00000405963:p.Ser1216Cys	49.0	0.0	.		50.0	14.0	.	NM_002891	F8VPA5|H0YKF2|J3KQP9|Q16027	Missense_Mutation	SNP	ENST00000419573.3	hg19	CCDS10309.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.193004	0.78902	.	.	ENSG00000058335	ENST00000419573;ENST00000394741;ENST00000394745	T;T	0.32753	1.44;1.44	4.08	4.08	0.47627	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine-nucleotide exchange factor, conserved site (1);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.53722	0.1814	M	0.74467	2.265	0.80722	D	1	D;B	0.69078	0.997;0.445	D;B	0.70016	0.967;0.401	T	0.59392	-0.7463	10	0.66056	D	0.02	.	14.1711	0.65510	0.0:0.0:1.0:0.0	.	1218;1200	Q13972;F8VPA5	RGRF1_HUMAN;.	C	1216;1200;432	ENSP00000405963:S1216C;ENSP00000378228:S432C	ENSP00000378224:S1200C	S	-	2	0	RASGRF1	77052713	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.359000	0.97115	2.250000	0.74265	0.591000	0.81541	TCC	.	.	.	none		0.632	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891		C	79265658	G	C	79265658	3	2	70	1	0	0	0	0	1	0	0	0	13085	1174	41	4	186	4	RASGRF1	15	79265658	Missense_Mutation	SNP	G	TCGA-A4-A7UZ-01A-12D-A34Z-10	13373466	79265658	23265734	39	4631											
TELO2	9894	hgsc.bcm.edu	37	chr16	1550652	1550653	+	Missense_Mutation	DNP	GG	GG	AT																															ctgggcatgatcgtggcagaGgtcgttagtgcccggatcca																										TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr16:1550652_1550653GG>AT	ENST00000262319.6	+	9	1512_1513	c.1233_1234GG>AT	c.(1231-1236)gaGGtc>gaATtc	p.V412F		NM_016111.3	NP_057195.2	Q9Y4R8	TELO2_HUMAN	telomere maintenance 2	412					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)				TCGTGGCAGAGGTCGTTAGTGC	0.698																																					p.E411E|p.V412F		Atlas-SNP	.											.	TELO2	44	.	0			c.G1233A|c.G1234T						PASS	.																																			SO:0001583	missense	9894	exon9			GGCAGAGGTCGTT|GCAGAGGTCGTTA	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	Exception_encountered	chr16.hg19:g.1550652_1550653delinsAT	ENSP00000262319:p.Val412Phe	89.0	0.0	.		120.0	23.0|24.0	.	NM_016111	D3DU73|O75168|Q7LDV4|Q9BR21	Silent|Missense_Mutation	SNP	ENST00000262319.6	hg19	CCDS32363.1																																																																																			.	.	.	none		0.698	TELO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103602.2	NM_016111		AT	1550653	GG	AT	1550652	3	1	70	1	0	0	0	0	1	0	0	0	15769	991	35	2	1263	2	TELO2	16	1550652	Missense_Mutation	DNP	GG	TCGA-A4-A7UZ-01A-12D-A34Z-10		1550652	88804101	40	4632											
A2BP1	54715	hgsc.bcm.edu	37	chr16	7703911	7703911	+	Silent	SNP	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	accgtgtacaacaccttcagGgccgcggcgcccccgccccc	6	4	10	21	5	1	0	1	0	0	0	1	0	1	0	7	2	2	1	7	2	2	2			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr16:7703911G>A	ENST00000550418.1	+	12	1840	c.852G>A	c.(850-852)agG>agA	p.R284R	RBFOX1_ENST00000355637.4_Silent_p.R304R|RBFOX1_ENST00000311745.5_Silent_p.R304R|RBFOX1_ENST00000436368.2_Silent_p.R304R|RBFOX1_ENST00000552089.1_Silent_p.R301R|RBFOX1_ENST00000547372.1_Silent_p.R327R|RBFOX1_ENST00000553186.1_Silent_p.R257R|RBFOX1_ENST00000547338.1_Silent_p.R284R|RBFOX1_ENST00000422070.4_Silent_p.R327R|RBFOX1_ENST00000535565.2_Silent_p.R241R|RBFOX1_ENST00000340209.4_Silent_p.R289R	NM_018723.3	NP_061193.2	Q9NWB1	RFOX1_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 1	284					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						ACACCTTCAgggccgcggcgc	0.756																																					p.R304R	Ovarian(157;934 2567 15163 39509)	Atlas-SNP	.											.	RBFOX1	341	.	0			c.G912A						PASS	.						9	11	10					16																	7703911		1833	3814	5647	SO:0001819	synonymous_variant	54715	exon9			CTTCAGGGCCGCG	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.852G>A	chr16.hg19:g.7703911G>A		19.0	0.0	.		14.0	6.0	.	NM_145891	Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20	Silent	SNP	ENST00000550418.1	hg19	CCDS55983.1																																																																																			.	.	.	none		0.756	RBFOX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409492.2	NM_145891		A	7703911	G	A	7703911	2	1	70	1	0	0	0	0	0	0	0	1	3	1223	43	2		2	A2BP1	16	7703911	Silent	SNP	G	TCGA-A4-A7UZ-01A-12D-A34Z-10	6153259	7703911	82650842	41	4633											
BFAR	51283	hgsc.bcm.edu	37	chr16	14758841	14758841	+	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	gttggaggtccattactggaCatcacggtttctcatcatca	9	13	9	10	1	4	0	4	0	1	0	6	2	5	2	1	4	1	2	1	4	1	3			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr16:14758841C>T	ENST00000261658.2	+	7	1350	c.1073C>T	c.(1072-1074)aCa>aTa	p.T358I	BFAR_ENST00000426842.2_Missense_Mutation_p.T230I|BFAR_ENST00000563971.1_Missense_Mutation_p.T233I	NM_016561.2	NP_057645.1	Q9NZS9	BFAR_HUMAN	bifunctional apoptosis regulator	358					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						CATTACTGGACATCACGGTTT	0.438																																					p.T358I		Atlas-SNP	.											.	BFAR	38	.	0			c.C1073T						PASS	.						248	206	220					16																	14758841		2197	4300	6497	SO:0001583	missense	51283	exon7			ACTGGACATCACG	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.1073C>T	chr16.hg19:g.14758841C>T	ENSP00000261658:p.Thr358Ile	258.0	0.0	.		272.0	56.0	.	NM_016561	A8K4Z9|B4DUT0|D3DUG8	Missense_Mutation	SNP	ENST00000261658.2	hg19	CCDS10554.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.556706	0.86231	.	.	ENSG00000103429	ENST00000261658;ENST00000426842	T;T	0.54279	2.92;0.58	5.81	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.59404	0.2191	L	0.27053	0.805	0.58432	D	0.999999	P;D;D	0.89917	0.908;1.0;1.0	B;D;D	0.69307	0.325;0.963;0.963	T	0.64415	-0.6413	10	0.87932	D	0	.	14.1846	0.65598	0.0:0.9282:0.0:0.0718	.	230;358;358	B4DUT0;B2R9R6;Q9NZS9	.;.;BFAR_HUMAN	I	358;230	ENSP00000261658:T358I;ENSP00000400634:T230I	ENSP00000261658:T358I	T	+	2	0	BFAR	14666342	1.000000	0.71417	0.934000	0.37439	0.996000	0.88848	7.555000	0.82223	1.455000	0.47813	0.655000	0.94253	ACA	.	.	.	none		0.438	BFAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252088.1	NM_016561		T	14758841	C	T	14758841	3	4	70	1	0	0	0	0	1	0	0	0	1414	478	17	2	1095	2	BFAR	16	14758841	Missense_Mutation	SNP	C	TCGA-A4-A7UZ-01A-12D-A34Z-10	7054930	14758841	75595912	42	4634											
ABCC1	4363	hgsc.bcm.edu	37	chr16	16228223	16228223	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcaggtcggcatcgtggggcGgacgggagctgggaagtcgt	6	6	21	8	5	0	0	0	0	0	0	3	3	0	3	0	7	1	3	0	7	1	0	rs370672850		TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr16:16228223G>A	ENST00000399410.3	+	28	4158	c.3983G>A	c.(3982-3984)cGg>cAg	p.R1328Q	ABCC1_ENST00000351154.5_Missense_Mutation_p.R1269Q|ABCC1_ENST00000349029.5_Missense_Mutation_p.R1213Q|ABCC1_ENST00000346370.5_Missense_Mutation_p.R1272Q|ABCC1_ENST00000399408.2_Missense_Mutation_p.R1338Q|ABCC1_ENST00000345148.5_Missense_Mutation_p.R1328Q	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	1328	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)	ATCGTGGGGCGGACGGGAGCT	0.607																																					p.R1328Q		Atlas-SNP	.											.	ABCC1	156	.	0			c.G3983A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	1,4205		0,1,2102	81	89	86		3983,3806,3815,3638,3983	5.8	1	16		86	0,8444		0,0,4222	no	missense,missense,missense,missense,missense	ABCC1	NM_004996.3,NM_019862.2,NM_019898.2,NM_019899.2,NM_019900.2	43,43,43,43,43	0,1,6324	AA,AG,GG		0.0,0.0238,0.0079	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	1328/1532,1269/1473,1272/1476,1213/1417,1328/1467	16228223	1,12649	2103	4222	6325	SO:0001583	missense	4363	exon28			TGGGGCGGACGGG	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.3983G>A	chr16.hg19:g.16228223G>A	ENSP00000382342:p.Arg1328Gln	49.0	0.0	.		48.0	7.0	.	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Missense_Mutation	SNP	ENST00000399410.3	hg19	CCDS42122.1	.	.	.	.	.	.	.	.	.	.	G	18.47	3.630940	0.67015	2.38E-4	0.0	ENSG00000103222	ENST00000399410;ENST00000399408;ENST00000346370;ENST00000351154;ENST00000345148;ENST00000349029;ENST00000536381	D;D;D;D;D;D	0.94000	-3.33;-3.33;-3.33;-3.33;-3.33;-3.33	5.81	5.81	0.92471	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.85682	D	0.000000	D	0.96661	0.8910	M	0.76328	2.33	0.58432	D	0.999997	D;D;D;D;D;D	0.89917	0.971;1.0;1.0;1.0;1.0;1.0	P;D;D;D;D;D	0.97110	0.669;1.0;0.999;0.996;0.997;0.999	D	0.96746	0.9550	10	0.87932	D	0	-28.0643	19.0707	0.93134	0.0:0.0:1.0:0.0	.	1213;1328;1272;1269;1328;1338	P33527-5;P33527-4;P33527-3;P33527-2;P33527;P33527-9	.;.;.;.;MRP1_HUMAN;.	Q	1328;1338;1272;1269;1328;1213;1012	ENSP00000382342:R1328Q;ENSP00000382340:R1338Q;ENSP00000263019:R1272Q;ENSP00000263017:R1269Q;ENSP00000263014:R1328Q;ENSP00000263016:R1213Q	ENSP00000263014:R1328Q	R	+	2	0	ABCC1	16135724	1.000000	0.71417	1.000000	0.80357	0.153000	0.21895	9.831000	0.99420	2.746000	0.94184	0.655000	0.94253	CGG	.	.	.	weak		0.607	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996		A	16228223	G	A	16228223	3	1	70	1	0	0	0	0	1	0	0	0	49	1116	39	1	4093	1	ABCC1	16	16228223	Missense_Mutation	SNP	G	TCGA-A4-A7UZ-01A-12D-A34Z-10	1469382	16228223	74126530	43	4635											
GTF3C1	2975	hgsc.bcm.edu	37	chr16	27561107	27561108	+	Frame_Shift_Ins	INS	-	-	A																															agggttccaaaggcagcgggINSaagggcggcactcgcgtctc																										TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr16:27561107_27561108insA	ENST00000356183.4	-	1	119_120	c.104_105insT	c.(103-105)ttcfs	p.F35fs	GTF3C1_ENST00000561623.1_Frame_Shift_Ins_p.F35fs|KIAA0556_ENST00000261588.4_5'Flank	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	35					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						AAGGCAGCGGGAAGGGCGGCAC	0.678																																					p.F35fs		Atlas-Indel,Pindel	.											.	GTF3C1	210	.	0			c.105_106insT						PASS	.																																			SO:0001589	frameshift_variant	2975	exon1			.	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.105dupT	chr16.hg19:g.27561109_27561109dupA	ENSP00000348510:p.Phe35fs	97.0	0.0	0		140.0	65.0	0.464286	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Frame_Shift_Ins	INS	ENST00000356183.4	hg19	CCDS32414.1																																																																																			.	.	.	none		0.678	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520		A	27561108	-	A	27561107	7	5	70	1	0	1	1	0	0	0	0	0	6879	1165	41	0	6372	0	GTF3C1	16	27561107	Frame_Shift_Ins	INS	-	TCGA-A4-A7UZ-01A-12D-A34Z-10	11332884	27561107	62793646	44	4636											
ITFG1	81533	hgsc.bcm.edu	37	chr16	47195736	47195736	+	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	ttgcagtccactcttgttttCgtatagactggaagaagaat	11	14	9	7	1	1	3	0	0	1	3	3	4	2	4	1	1	1	3	1	1	5	6	rs141409020		TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr16:47195736C>T	ENST00000320640.6	-	16	1814	c.1586G>A	c.(1585-1587)cGa>cAa	p.R529Q	ITFG1_ENST00000544001.2_Missense_Mutation_p.R416Q|RP11-329J18.2_ENST00000564705.1_RNA|ITFG1_ENST00000568047.1_5'UTR|RP11-329J18.2_ENST00000565694.1_RNA	NM_030790.3	NP_110417.2	Q8TB96	TIP_HUMAN	integrin alpha FG-GAP repeat containing 1	529						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)				CTCTTGTTTTCGTATAGACTG	0.323																																					p.R529Q		Atlas-SNP	.											.	ITFG1	49	.	0			c.G1586A						PASS	.	C	GLN/ARG	0,4404		0,0,2202	180	166	171		1586	5.4	1	16	dbSNP_134	171	1,8599	1.2+/-3.3	0,1,4299	no	missense	ITFG1	NM_030790.3	43	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	529/613	47195736	1,13003	2202	4300	6502	SO:0001583	missense	81533	exon16			TGTTTTCGTATAG	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.1586G>A	chr16.hg19:g.47195736C>T	ENSP00000319918:p.Arg529Gln	95.0	0.0	.		118.0	19.0	.	NM_030790	Q96SR4|Q9BRE2|Q9H2V9	Missense_Mutation	SNP	ENST00000320640.6	hg19	CCDS10728.1	.	.	.	.	.	.	.	.	.	.	C	33	5.197986	0.94997	0.0	1.16E-4	ENSG00000129636	ENST00000320640;ENST00000537184;ENST00000542691;ENST00000544001	T;T	0.63096	-0.02;-0.02	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.71779	0.3380	L	0.41824	1.3	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.99;0.999	T	0.64892	-0.6300	10	0.16896	T	0.51	-4.0712	19.1974	0.93695	0.0:1.0:0.0:0.0	.	416;529	F5GXC5;Q8TB96	.;TIP_HUMAN	Q	529;189;274;416	ENSP00000319918:R529Q;ENSP00000441062:R416Q	ENSP00000319918:R529Q	R	-	2	0	ITFG1	45753237	1.000000	0.71417	0.976000	0.42696	0.992000	0.81027	7.270000	0.78493	2.538000	0.85594	0.467000	0.42956	CGA	.	C|1.000;T|0.000	0.000	weak		0.323	ITFG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256768.3	NM_030790		T	47195736	C	T	47195736	3	4	70	1	0	0	0	0	1	0	0	0	7876	884	31	1	264	1	ITFG1	16	47195736	Missense_Mutation	SNP	C	TCGA-A4-A7UZ-01A-12D-A34Z-10	19634629	47195736	43159017	45	4637											
RBL2	5934	hgsc.bcm.edu	37	chr16	53504377	53504377	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacaagctgtgacaggctcCatccagcccctcagtgctca	9	7	9	16	0	2	1	2	1	0	0	4	1	4	1	4	1	3	4	4	1	1	0			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr16:53504377C>T	ENST00000262133.6	+	16	2465	c.2328C>T	c.(2326-2328)tcC>tcT	p.S776S	RBL2_ENST00000379935.4_3'UTR|RBL2_ENST00000544545.1_Intron	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	776	Pocket; binds E1A.|Spacer.				chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TGACAGGCTCCATCCAGCCCC	0.512																																					p.S776S		Atlas-SNP	.											.	RBL2	115	.	0			c.C2328T						PASS	.						53	52	52					16																	53504377		2198	4300	6498	SO:0001819	synonymous_variant	5934	exon16			AGGCTCCATCCAG	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.2328C>T	chr16.hg19:g.53504377C>T		62.0	0.0	.		81.0	21.0	.	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Silent	SNP	ENST00000262133.6	hg19	CCDS10748.1																																																																																			.	.	.	none		0.512	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611		T	53504377	C	T	53504377	2	4	70	1	0	0	0	0	0	0	0	1	13123	581	21	2		2	RBL2	16	53504377	Silent	SNP	C	TCGA-A4-A7UZ-01A-12D-A34Z-10	6308641	53504377	36850376	46	4638											
NLRP1	22861	hgsc.bcm.edu	37	chr17	5424855	5424865	+	Frame_Shift_Del	DEL	AGCAGTCACTT	AGCAGTCACTT	-																															tagtgtcaccttccgaatggAgcagtcacttgggatcaggt																								rs556315689|rs200659907		TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	AGCAGTCACTT	AGCAGTCACTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr17:5424855_5424865delAGCAGTCACTT	ENST00000572272.1	-	13	3761_3771	c.3762_3772delAAGTGACTGCT	c.(3760-3774)ccaagtgactgctccfs	p.SDCS1255fs	NLRP1_ENST00000354411.3_Frame_Shift_Del_p.SDCS1225fs|NLRP1_ENST00000577119.1_Frame_Shift_Del_p.SDCS1225fs|NLRP1_ENST00000345221.3_Frame_Shift_Del_p.SDCS1255fs|NLRP1_ENST00000269280.4_Frame_Shift_Del_p.SDCS1255fs|NLRP1_ENST00000262467.5_Frame_Shift_Del_p.SDCS1259fs			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	1255					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)				TTCCGAATGGAGCAGTCACTTGGGATCAGGT	0.545																																					p.1259_1262del		Atlas-INDEL	.											.	NLRP1	358	.	0			c.3775_3785del						PASS	.																																			SO:0001589	frameshift_variant	22861	exon13			.	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.3762_3772delAAGTGACTGCT	chr17.hg19:g.5424855_5424865delAGCAGTCACTT	ENSP00000460475:p.Ser1255fs	51.0	0.0	0		76.0	10.0	0.131579	NM_001033053	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Frame_Shift_Del	DEL	ENST00000572272.1	hg19	CCDS42246.1																																																																																			.	.	.	none		0.545	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004		-	5424865	AGCAGTCACTT	-	5424855	7	5	70	1	0	1	0	1	0	0	0	0	10478	304	11	0	732	0	NLRP1	17	5424855	Frame_Shift_Del	DEL	AGCAGTCACTT	TCGA-A4-A7UZ-01A-12D-A34Z-10		5424855	75770355	47	4639											
ZNF287	57336	hgsc.bcm.edu	37	chr17	16455883	16455885	+	In_Frame_Del	DEL	GAA	GAA	-																															agtatgtattttttgatgctGaagaaggtgtgtactctgac																										TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr17:16455883_16455885delGAA	ENST00000395824.1	-	6	2188_2190	c.1571_1573delTTC	c.(1570-1575)cttcag>cag	p.L524del	ZNF287_ENST00000395825.3_In_Frame_Del_p.L524del			Q9HBT7	ZN287_HUMAN	zinc finger protein 287	517					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)		TTTTGATGCTGAAGAAGGTGTGT	0.35																																					p.524_525del		Atlas-Indel,Pindel	.											.	ZNF287	60	.	0			c.1572_1574del						PASS	.																																			SO:0001651	inframe_deletion	57336	exon6			.	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.1571_1573delTTC	chr17.hg19:g.16455886_16455888delGAA	ENSP00000379168:p.Leu524del	165.0	0.0	0		233.0	32.0	0.137339	NM_020653	Q6IAG1	In_Frame_Del	DEL	ENST00000395824.1	hg19	CCDS11179.2																																																																																			.	.	.	none		0.35	ZNF287-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130504.1			-	16455885	GAA	-	16455883	7	5	70	1	0	1	0	1	0	0	0	0	17837	1299	45	0	716	0	ZNF287	17	16455883	In_Frame_Del	DEL	GAA	TCGA-A4-A7UZ-01A-12D-A34Z-10	11031028	16455883	64739327	48	4640											
ACACA	31	hgsc.bcm.edu	37	chr17	35620716	35620716	+	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	agcattgccatattggtccgCtaagatctgcacctccagat	10	11	8	12	1	1	2	0	0	1	2	3	2	3	2	4	1	3	3	4	1	2	4			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr17:35620716C>G	ENST00000394406.2	-	11	1280	c.1090G>C	c.(1090-1092)Gcg>Ccg	p.A364P	ACACA_ENST00000335166.5_Missense_Mutation_p.A286P|ACACA_ENST00000353139.5_Missense_Mutation_p.A401P|ACACA_ENST00000360679.3_Missense_Mutation_p.A306P	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	364	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.			A -> V (in Ref. 2; AAP94122). {ECO:0000305}.	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)	TATTGGTCCGCTAAGATCTGC	0.443																																					p.A401P	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-SNP	.											.	ACACA	395	.	0			c.G1201C						PASS	.						205	179	188					17																	35620716		2203	4300	6503	SO:0001583	missense	31	exon11			GGTCCGCTAAGAT	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.1090G>C	chr17.hg19:g.35620716C>G	ENSP00000377928:p.Ala364Pro	103.0	0.0	.		137.0	11.0	.	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	hg19	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.981395	0.93044	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166	D;D;D;D	0.97553	-4.43;-4.43;-4.43;-4.43	5.78	5.78	0.91487	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);Biotin carboxylation domain (1);	0.050076	0.85682	D	0.000000	D	0.99102	0.9691	H	0.98466	4.24	0.80722	D	1	D;D;D	0.89917	0.979;1.0;0.999	D;D;D	0.78314	0.913;0.991;0.985	D	0.99007	1.0813	10	0.87932	D	0	-14.7209	14.8047	0.69945	0.1441:0.8559:0.0:0.0	.	401;364;306	Q13085-4;Q13085;Q13085-2	.;ACACA_HUMAN;.	P	401;306;364;388;286	ENSP00000344789:A401P;ENSP00000353898:A306P;ENSP00000377928:A364P;ENSP00000335323:A286P	ENSP00000335323:A286P	A	-	1	0	ACACA	32694829	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.930000	0.70104	2.722000	0.93159	0.655000	0.94253	GCG	.	.	.	none		0.443	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		G	35620716	C	G	35620716	3	3	70	1	0	0	0	0	1	0	0	0	106	797	28	4	6134	4	ACACA	17	35620716	Missense_Mutation	SNP	C	TCGA-A4-A7UZ-01A-12D-A34Z-10	19164833	35620716	45574494	49	4641											
SYNRG	11276	hgsc.bcm.edu	37	chr17	35946557	35946557	+	Missense_Mutation	SNP	T	T	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	cggcaaactgcttctgcatgTctggagtgtactgtgggcct	6	12	13	10	1	2	0	0	0	2	0	2	1	2	1	1	3	4	4	1	3	2	2			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr17:35946557T>G	ENST00000339208.6	-	4	481	c.341A>C	c.(340-342)gAc>gCc	p.D114A	SYNRG_ENST00000346661.4_Missense_Mutation_p.D114A|SYNRG_ENST00000345615.4_Missense_Mutation_p.D114A|SYNRG_ENST00000591288.1_Missense_Mutation_p.D114A|SYNRG_ENST00000585472.1_Missense_Mutation_p.D113A|SYNRG_ENST00000502449.2_Missense_Mutation_p.D114A|SYNRG_ENST00000394378.2_Missense_Mutation_p.D114A	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma	114					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						CTTCTGCATGTCTGGAGTGTA	0.473																																					p.D114A		Atlas-SNP	.											.	SYNRG	101	.	0			c.A341C						PASS	.						133	118	123					17																	35946557		2203	4300	6503	SO:0001583	missense	11276	exon4			TGCATGTCTGGAG	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.341A>C	chr17.hg19:g.35946557T>G	ENSP00000343610:p.Asp114Ala	139.0	0.0	.		193.0	73.0	.	NM_001163544	A8MWU4|B7ZKZ2|B7ZKZ3|Q17RI2|Q5BKU5|Q6ZT17	Missense_Mutation	SNP	ENST00000339208.6	hg19	CCDS11321.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.463539	0.84425	.	.	ENSG00000006114	ENST00000346661;ENST00000339208;ENST00000345615;ENST00000502449;ENST00000394378;ENST00000394379	T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6	4.74	4.74	0.60224	.	0.050722	0.85682	D	0.000000	T	0.48295	0.1492	M	0.61703	1.905	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.998;0.999;0.999;0.999;0.999;1.0;1.0	D;D;D;D;D;D;D	0.85130	0.941;0.951;0.951;0.951;0.951;0.997;0.997	T	0.43442	-0.9391	10	0.09084	T	0.74	-4.1366	14.5161	0.67821	0.0:0.0:0.0:1.0	.	114;114;114;114;114;114;114	A8MYE0;B7ZKZ2;Q9UMZ2-3;A8MWU4;Q9UMZ2-4;Q9UMZ2-5;Q9UMZ2	.;.;.;.;.;.;SYNRG_HUMAN	A	114	ENSP00000005279:D114A;ENSP00000343610:D114A;ENSP00000315722:D114A;ENSP00000424893:D114A;ENSP00000377903:D114A	ENSP00000343610:D114A	D	-	2	0	SYNRG	33020670	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.604000	0.82830	1.876000	0.54355	0.482000	0.46254	GAC	.	.	.	none		0.473	SYNRG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256811.2	NM_007247		G	35946557	T	G	35946557	3	3	70	1	0	0	0	0	1	0	0	0	15472	1667	58	5	3752	5	SYNRG	17	35946557	Missense_Mutation	SNP	T	TCGA-A4-A7UZ-01A-12D-A34Z-10	325841	35946557	45248653	50	4642											
DHX8	1659	hgsc.bcm.edu	37	chr17	41584425	41584426	+	Frame_Shift_Del	DEL	AC	AC	-																															gtgagacaggatctggaaagAcaacacagatcacccagtac																										TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr17:41584425_41584426delAC	ENST00000262415.3	+	13	1855_1856	c.1783_1784delAC	c.(1783-1785)acafs	p.T596fs	DHX8_ENST00000540306.1_Frame_Shift_Del_p.T596fs	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	596	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		ATCTGGAAAGACAACACAGATC	0.49																																					p.594_595del	NSCLC(56;1548 1661 49258 49987)	Atlas-Indel,Pindel	.											.	DHX8	98	.	0			c.1782_1783del						PASS	.																																			SO:0001589	frameshift_variant	1659	exon13			.	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.1783_1784delAC	chr17.hg19:g.41584425_41584426delAC	ENSP00000262415:p.Thr596fs	52.0	0.0	0		80.0	12.0	0.15	NM_004941		Frame_Shift_Del	DEL	ENST00000262415.3	hg19	CCDS11464.1																																																																																			.	.	.	none		0.49	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453485.1			-	41584426	AC	-	41584425	7	5	70	1	0	1	0	1	0	0	0	0	4517	275	10	0	1833	0	DHX8	17	41584425	Frame_Shift_Del	DEL	AC	TCGA-A4-A7UZ-01A-12D-A34Z-10	5637868	41584425	39610785	51	4643											
CPLX4	339302	hgsc.bcm.edu	37	chr18	56964141	56964141	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctccagccatctggatttgaTtctcatccatttcactctat	8	16	4	13	0	4	1	2	1	3	0	7	2	6	2	3	1	1	0	3	1	1	4			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr18:56964141T>C	ENST00000299721.3	-	3	458	c.272A>G	c.(271-273)aAt>aGt	p.N91S	CPLX4_ENST00000587244.1_Intron	NM_181654.3	NP_857637.1	Q7Z7G2	CPLX4_HUMAN	complexin 4	91					exocytosis (GO:0006887)|neurotransmitter transport (GO:0006836)|regulation of neurotransmitter secretion (GO:0046928)	cell junction (GO:0030054)|membrane (GO:0016020)|synapse (GO:0045202)				autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)	16		Colorectal(73;0.175)				CTGGATTTGATTCTCATCCAT	0.318																																					p.N91S		Atlas-SNP	.											.	CPLX4	35	.	0			c.A272G						PASS	.						66	60	62					18																	56964141		2203	4300	6503	SO:0001583	missense	339302	exon3			ATTTGATTCTCAT	AY286502	CCDS11973.1	18q21.32	2005-08-02			ENSG00000166569	ENSG00000166569			24330	protein-coding gene	gene with protein product		609586				15911881	Standard	NM_181654		Approved	CPX-IV	uc002lhy.3	Q7Z7G2	OTTHUMG00000132756	ENST00000299721.3:c.272A>G	chr18.hg19:g.56964141T>C	ENSP00000299721:p.Asn91Ser	138.0	0.0	.		159.0	8.0	.	NM_181654	F1T0L6	Missense_Mutation	SNP	ENST00000299721.3	hg19	CCDS11973.1	.	.	.	.	.	.	.	.	.	.	T	4.797	0.148248	0.09134	.	.	ENSG00000166569	ENST00000299721	.	.	.	5.66	-1.56	0.08532	.	0.177771	0.64402	N	0.000012	T	0.47173	0.1431	L	0.50333	1.59	0.44780	D	0.997788	B	0.06786	0.001	B	0.11329	0.006	T	0.40534	-0.9558	9	0.07644	T	0.81	-7.2865	11.4238	0.49998	0.0:0.0644:0.5712:0.3644	.	91	Q7Z7G2	CPLX4_HUMAN	S	91	.	ENSP00000299721:N91S	N	-	2	0	CPLX4	55115121	1.000000	0.71417	0.969000	0.41365	0.974000	0.67602	2.143000	0.42187	-0.158000	0.11040	-0.396000	0.06452	AAT	.	.	.	none		0.318	CPLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256127.1	NM_181654		C	56964141	T	C	56964141	3	2	70	1	0	0	0	0	1	0	0	0	3809	1493	52	3	214	3	CPLX4	18	56964141	Missense_Mutation	SNP	T	TCGA-A4-A7UZ-01A-12D-A34Z-10		56964141	21113107	52	4644											
ATP9B	374868	hgsc.bcm.edu	37	chr18	77013436	77013436	+	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	gaaagcgctatttttggcttTagttgctctttccattgtta	7	19	8	7	1	1	0	0	0	1	0	2	1	2	0	1	1	2	5	1	1	4	9			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr18:77013436T>G	ENST00000426216.2	+	12	1180	c.1163T>G	c.(1162-1164)tTa>tGa	p.L388*	RP11-1136J12.1_ENST00000591742.1_RNA|ATP9B_ENST00000307671.7_Nonsense_Mutation_p.L388*	NM_198531.3	NP_940933.3	O43861	ATP9B_HUMAN	ATPase, class II, type 9B	388					establishment of protein localization to Golgi (GO:0072600)|phospholipid translocation (GO:0045332)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(3)|prostate(1)|skin(2)|stomach(1)	38		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		TTTTTGGCTTTAGTTGCTCTT	0.408																																					p.L388X		Atlas-SNP	.											.	ATP9B	96	.	0			c.T1163G						PASS	.						303	279	287					18																	77013436		2203	4300	6503	SO:0001587	stop_gained	374868	exon12			TGGCTTTAGTTGC	R51412	CCDS12014.1	18q23	2010-04-20	2007-09-19		ENSG00000166377	ENSG00000166377		"ATPases / P-type"	13541	protein-coding gene	gene with protein product		614446	"ATPase, Class II, type 9B"			9548971, 11015572	Standard	NM_198531		Approved	ATPIIB	uc002lmx.3	O43861	OTTHUMG00000132898	ENST00000426216.2:c.1163T>G	chr18.hg19:g.77013436T>G	ENSP00000398076:p.Leu388*	526.0	1.0	.		550.0	128.0	.	NM_198531	O60872|Q08AD8|Q08AD9	Nonsense_Mutation	SNP	ENST00000426216.2	hg19	CCDS12014.1	.	.	.	.	.	.	.	.	.	.	T	37	6.321691	0.97471	.	.	ENSG00000166377	ENST00000426216;ENST00000307671	.	.	.	5.95	5.95	0.96441	.	0.071724	0.53938	D	0.000050	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.4237	0.83790	0.0:0.0:0.0:1.0	.	.	.	.	X	388	.	ENSP00000304500:L388X	L	+	2	0	ATP9B	75114424	0.426000	0.25506	0.004000	0.12327	0.963000	0.63663	3.606000	0.54095	2.279000	0.76181	0.533000	0.62120	TTA	.	.	.	none		0.408	ATP9B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256402.3	NM_198531		G	77013436	T	G	77013436	4	3	70	1	0	0	0	0	0	1	0	0	1199	1764	61	5	1209	5	ATP9B	18	77013436	Nonsense_Mutation	SNP	T	TCGA-A4-A7UZ-01A-12D-A34Z-10	20049295	77013436	1063812	53	4645											
CPXM1	56265	hgsc.bcm.edu	37	chr20	2779177	2779177	+	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	gggactccagacccaaaggaGgacagcctggggcggggata	11	3	17	10	1	0	1	0	0	0	1	1	5	1	5	3	7	1	0	3	7	2	1			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr20:2779177G>T	ENST00000380605.2	-	3	411	c.347C>A	c.(346-348)cCt>cAt	p.P116H		NM_001184699.1|NM_019609.4	NP_001171628.1|NP_062555.1	Q96SM3	CPXM1_HUMAN	carboxypeptidase X (M14 family), member 1	116	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)			endometrium(5)|kidney(5)|large_intestine(8)|lung(17)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						ACCCAAAGGAGGACAGCCTGG	0.602																																					p.P116H		Atlas-SNP	.											.	CPXM1	107	.	0			c.C347A						PASS	.						39	41	40					20																	2779177		2203	4300	6503	SO:0001583	missense	56265	exon3			AAAGGAGGACAGC	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.347C>A	chr20.hg19:g.2779177G>T	ENSP00000369979:p.Pro116His	19.0	0.0	.		35.0	6.0	.	NM_001184699	Q6P4G8|Q6UW65|Q9NUB5	Missense_Mutation	SNP	ENST00000380605.2	hg19	CCDS13033.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.346218	0.82022	.	.	ENSG00000088882	ENST00000380605	D	0.98914	-5.23	4.6	4.6	0.57074	Coagulation factor 5/8 C-terminal type domain (2);Galactose-binding domain-like (1);	0.000000	0.64402	D	0.000001	D	0.98779	0.9589	M	0.64080	1.96	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.99564	1.0969	10	0.87932	D	0	-18.0862	14.9658	0.71193	0.0:0.0:1.0:0.0	.	116;116	Q8N2E1;Q96SM3	.;CPXM1_HUMAN	H	116	ENSP00000369979:P116H	ENSP00000369979:P116H	P	-	2	0	CPXM1	2727177	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	9.455000	0.97625	2.398000	0.81561	0.563000	0.77884	CCT	.	.	.	none		0.602	CPXM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077643.2	NM_019609		T	2779177	G	T	2779177	3	4	70	1	0	0	0	0	1	0	0	0	3839	1000	35	4	1905	4	CPXM1	20	2779177	Missense_Mutation	SNP	G	TCGA-A4-A7UZ-01A-12D-A34Z-10		2779177	60246343	54	4646											
C20orf151	140893	hgsc.bcm.edu	37	chr20	60988918	60988918	+	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	ctgctctggcactctggtccCcttggtgccattgctgagtg	3	13	12	13	0	2	1	0	1	2	0	3	1	3	1	3	3	3	3	3	3	0	2			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr20:60988918C>G	ENST00000252998.1	-	10	1645	c.1489G>C	c.(1489-1491)Ggg>Cgg	p.G497R		NM_080833.2	NP_543023.2	Q8NC74	RB8NL_HUMAN	RBBP8 N-terminal like	497	Pro-rich.					extracellular space (GO:0005615)											ACTCTGGTCCCCTTGGTGCCA	0.692																																					p.G497R		Atlas-SNP	.											.	.	.	.	0			c.G1489C						PASS	.						12	11	11					20																	60988918		2184	4286	6470	SO:0001583	missense	140893	exon10			TGGTCCCCTTGGT	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.1489G>C	chr20.hg19:g.60988918C>G	ENSP00000252998:p.Gly497Arg	106.0	0.0	.		110.0	50.0	.	NM_080833	B2RP98|Q8N4Z9|Q9BR75|Q9H0Y9	Missense_Mutation	SNP	ENST00000252998.1	hg19	CCDS13498.1	.	.	.	.	.	.	.	.	.	.	C	14.40	2.525223	0.44969	.	.	ENSG00000130701	ENST00000252998	T	0.19532	2.14	3.49	1.32	0.21799	.	1.401760	0.04423	N	0.367918	T	0.24044	0.0582	L	0.43152	1.355	0.09310	N	1	D	0.60160	0.987	P	0.49012	0.598	T	0.16988	-1.0384	10	0.41790	T	0.15	-3.3453	4.3029	0.10933	0.0:0.6278:0.238:0.1342	.	497	Q8NC74	CT151_HUMAN	R	497	ENSP00000252998:G497R	ENSP00000252998:G497R	G	-	1	0	C20orf151	60422313	0.000000	0.05858	0.020000	0.16555	0.119000	0.20118	0.123000	0.15708	0.822000	0.34565	-0.339000	0.08088	GGG	.	.	.	none		0.692	RBBP8NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080029.1	NM_080833		G	60988918	C	G	60988918	3	3	70	1	0	0	0	0	1	0	0	0	2093	623	22	4	525	4	C20orf151	20	60988918	Missense_Mutation	SNP	C	TCGA-A4-A7UZ-01A-12D-A34Z-10	58209741	60988918	2036602	55	4647											
DIDO1	11083	hgsc.bcm.edu	37	chr20	61513486	61513486	+	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	ggtttgagggatgacagcacTtttagcaccggtggttctgg	7	12	15	7	1	1	2	0	2	1	0	1	3	1	3	1	5	2	4	1	5	1	4			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chr20:61513486T>A	ENST00000266070.4	-	16	4147	c.3822A>T	c.(3820-3822)aaA>aaT	p.K1274N	DIDO1_ENST00000395343.1_Missense_Mutation_p.K1274N	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	1274	Pro-rich.				apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					ATGACAGCACTTTTAGCACCG	0.647																																					p.K1274N	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.A3822T						PASS	.						73	80	78					20																	61513486		2203	4300	6503	SO:0001583	missense	11083	exon16			CAGCACTTTTAGC	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.3822A>T	chr20.hg19:g.61513486T>A	ENSP00000266070:p.Lys1274Asn	78.0	0.0	.		90.0	42.0	.	NM_001193369	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	hg19	CCDS33506.1	.	.	.	.	.	.	.	.	.	.	T	18.13	3.556495	0.65425	.	.	ENSG00000101191	ENST00000266070;ENST00000395343	T;T	0.09445	2.98;2.98	5.3	-3.1	0.05315	.	0.000000	0.45867	D	0.000337	T	0.17280	0.0415	M	0.76838	2.35	0.18873	N	0.999989	P	0.51933	0.949	P	0.46585	0.521	T	0.16630	-1.0396	10	0.62326	D	0.03	-20.2186	14.5469	0.68038	0.0:0.5842:0.0:0.4158	.	1274	Q9BTC0	DIDO1_HUMAN	N	1274	ENSP00000266070:K1274N;ENSP00000378752:K1274N	ENSP00000266070:K1274N	K	-	3	2	DIDO1	60983931	0.002000	0.14202	0.000000	0.03702	0.012000	0.07955	-0.248000	0.08854	-0.761000	0.04670	-0.376000	0.06991	AAA	.	.	.	none		0.647	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		A	61513486	T	A	61513486	3	1	70	1	0	0	0	0	1	0	0	0	4524	1606	56	5	2904	5	DIDO1	20	61513486	Missense_Mutation	SNP	T	TCGA-A4-A7UZ-01A-12D-A34Z-10	524568	61513486	1512034	56	4648											
KLHL34	257240	hgsc.bcm.edu	37	chrX	21674429	21674429	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggacgtataagtcccggAggctgctcgctccgccctcg	6	7	12	16	5	0	0	0	0	0	0	4	2	2	2	4	3	1	4	4	3	2	2			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chrX:21674429A>G	ENST00000379499.2	-	1	2019	c.1478T>C	c.(1477-1479)cTc>cCc	p.L493P		NM_153270.1	NP_695002.1	Q8N239	KLH34_HUMAN	kelch-like family member 34	493						extracellular space (GO:0005615)				cervix(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(11)|ovary(2)|urinary_tract(1)	26						TAAGTCCCGGAGGCTGCTCGC	0.697																																					p.L493P		Atlas-SNP	.											.	KLHL34	76	.	0			c.T1478C						PASS	.						30	18	22					X																	21674429		2201	4298	6499	SO:0001583	missense	257240	exon1			TCCCGGAGGCTGC	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.1478T>C	chrX.hg19:g.21674429A>G	ENSP00000368813:p.Leu493Pro	55.0	0.0	.		52.0	17.0	.	NM_153270		Missense_Mutation	SNP	ENST00000379499.2	hg19	CCDS14199.1	.	.	.	.	.	.	.	.	.	.	A	11.33	1.607556	0.28623	.	.	ENSG00000185915	ENST00000379499	T	0.54675	0.56	5.54	5.54	0.83059	Kelch-type beta propeller (1);	0.486321	0.17614	N	0.167973	T	0.67711	0.2922	M	0.78916	2.43	0.49483	D	0.99979	D	0.61080	0.989	P	0.61070	0.883	T	0.70371	-0.4890	10	0.62326	D	0.03	.	8.8221	0.35032	0.8129:0.1871:0.0:0.0	.	493	Q8N239	KLH34_HUMAN	P	493	ENSP00000368813:L493P	ENSP00000368813:L493P	L	-	2	0	KLHL34	21584350	1.000000	0.71417	1.000000	0.80357	0.653000	0.38743	3.067000	0.50010	1.849000	0.53698	0.486000	0.48141	CTC	.	.	.	none		0.697	KLHL34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056022.1	NM_153270		G	21674429	A	G	21674429	3	3	70	1	0	0	0	0	1	0	0	0	8394	304	11	3	460	3	KLHL34	23	21674429	Missense_Mutation	SNP	A	TCGA-A4-A7UZ-01A-12D-A34Z-10		21674429	133596131	57	4649											
KLHL15	80311	hgsc.bcm.edu	37	chrX	24024135	24024157	+	Frame_Shift_Del	DEL	AGCAAAACCGGATATTCTGAATG	AGCAAAACCGGATATTCTGAATG	-																															aacgctggttggggtcatcaAgcaaaaccggatattctgaa																										TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	AGCAAAACCGGATATTCTGAATG	AGCAAAACCGGATATTCTGAATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chrX:24024135_24024157delAGCAAAACCGGATATTCTGAATG	ENST00000328046.8	-	3	909_931	c.654_676delCATTCAGAATATCCGGTTTTGCT	c.(652-678)atcattcagaatatccggttttgcttgfs	p.IQNIRFCL219fs		NM_030624.2	NP_085127.2	Q96M94	KLH15_HUMAN	kelch-like family member 15	219	BACK.				protein ubiquitination (GO:0016567)					autonomic_ganglia(1)|breast(1)|endometrium(8)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	22						GGGGTCATCAAGCAAAACCGGATATTCTGAATGATGGTATCGG	0.43																																					p.219_226del		Pindel	.											.	KLHL15	50	.	0			c.655_677del						PASS	.																																			SO:0001589	frameshift_variant	80311	exon3			.	AB051464	CCDS35217.1	Xp22.1-p21	2013-01-30	2013-01-30		ENSG00000174010	ENSG00000174010		"Kelch-like", "BTB/POZ domain containing"	29347	protein-coding gene	gene with protein product			"kelch-like 15 (Drosophila)"			11214970, 14702039	Standard	NM_030624		Approved	KIAA1677	uc004dba.4	Q96M94	OTTHUMG00000021261	ENST00000328046.8:c.654_676delCATTCAGAATATCCGGTTTTGCT	chrX.hg19:g.24024135_24024157delAGCAAAACCGGATATTCTGAATG	ENSP00000332791:p.Ile219fs	77.0	0.0	.		66.0	12.0	0.182	NM_030624	Q32MN3|Q8NDA3|Q96BM6|Q9C0I6	Frame_Shift_Del	DEL	ENST00000328046.8	hg19	CCDS35217.1																																																																																			.	.	.	none		0.43	KLHL15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056078.1	XM_040383		-	24024157	AGCAAAACCGGATATTCTGAATG	-	24024135	7	5	70	1	0	1	0	1	0	0	0	0	8378	69	3	0	1146	0	KLHL15	23	24024135	Frame_Shift_Del	DEL	AGCAAAACCGGATATTCTGAATG	TCGA-A4-A7UZ-01A-12D-A34Z-10	2349706	24024135	131246425	58	4650											
UTP14A	10813	hgsc.bcm.edu	37	chrX	129058817	129058817	+	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	gaattgagagtactatctcaGaaattgaaggaaaaccatca	18	9	8	6	0	2	3	2	2	1	2	3	6	2	4	1	1	2	1	1	1	7	4			TCGA-A4-A7UZ-01A-12D-A34Z-10	TCGA-A4-A7UZ-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	991be3fd-4490-49c9-8019-27879e3192bd	fc283c2e-af56-4460-b252-9f1dc8940a6e	g.chrX:129058817G>A	ENST00000394422.3	+	12	1423	c.1395G>A	c.(1393-1395)caG>caA	p.Q465Q	UTP14A_ENST00000425117.2_Silent_p.Q413Q|UTP14A_ENST00000371042.3_Silent_p.Q297Q|UTP14A_ENST00000371051.5_Silent_p.Q411Q|RP4-537K23.4_ENST00000432062.1_RNA	NM_006649.3	NP_006640.2	Q9BVJ6	UT14A_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog A (yeast)	465					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						TACTATCTCAGAAATTGAAGG	0.473																																					p.Q465Q		Atlas-SNP	.											.	UTP14A	74	.	0			c.G1395A						PASS	.						132	142	139					X																	129058817		2203	4300	6503	SO:0001819	synonymous_variant	10813	exon12			ATCTCAGAAATTG	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.1395G>A	chrX.hg19:g.129058817G>A		83.0	0.0	.		102.0	55.0	.	NM_006649	A8K7A3|A8MVQ1|B4DQ08|E9PEL7|Q5JYF1	Silent	SNP	ENST00000394422.3	hg19	CCDS14615.1																																																																																			.	.	.	none		0.473	UTP14A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058221.1	NM_006649		A	129058817	G	A	129058817	2	1	70	1	0	0	0	0	0	0	0	1	17107	933	33	2		2	UTP14A	23	129058817	Silent	SNP	G	TCGA-A4-A7UZ-01A-12D-A34Z-10	105034682	129058817	26211743	59	4651											
CSMD2	114784	hgsc.bcm.edu	37	chr1	34112388	34112388	+	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	tgagagggctgagagagtccCgtccgtcgtagatatggagg	9	8	17	7	3	0	4	0	2	0	3	3	7	2	5	2	3	0	2	2	3	2	2			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr1:34112388C>A	ENST00000373380.1	-	8	1473	c.1253G>T	c.(1252-1254)cGg>cTg	p.R418L	CSMD2_ENST00000373388.2_5'UTR|CSMD2_ENST00000373381.4_Missense_Mutation_p.R1545L			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1505	CUB 3. {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)				GAGAGAGTCCCGTCCGTCGTA	0.547																																					p.R1505L		Atlas-SNP	.											.	CSMD2	946	.	0			c.G4514T						PASS	.						52	49	50					1																	34112388		2203	4300	6503	SO:0001583	missense	114784	exon29			GAGTCCCGTCCGT	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.1253G>T	chr1.hg19:g.34112388C>A	ENSP00000362478:p.Arg418Leu	74.0	0.0	.		54.0	4.0	.	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373380.1	hg19		.	.	.	.	.	.	.	.	.	.	C	14.49	2.551842	0.45487	.	.	ENSG00000121904	ENST00000373381;ENST00000373380	T;T	0.17370	2.28;2.28	5.95	2.84	0.33178	CUB (5);	0.303339	0.31747	N	0.007126	T	0.06142	0.0159	N	0.04387	-0.21	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.09377	0.001;0.004;0.004	T	0.28267	-1.0049	10	0.23891	T	0.37	.	4.0978	0.09998	0.175:0.3786:0.3631:0.0833	.	418;1505;1545	Q7Z408-2;Q7Z408;E7EUA6	.;CSMD2_HUMAN;.	L	1545;418	ENSP00000362479:R1545L;ENSP00000362478:R418L	ENSP00000241312:R1505L	R	-	2	0	CSMD2	33884975	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	3.988000	0.56951	0.856000	0.35383	0.655000	0.94253	CGG	.	.	.	none		0.547	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896		A	34112388	C	A	34112388	3	1	71	1	0	0	0	0	1	0	0	0	3947	652	23	4	6113	4	CSMD2	1	34112388	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08		34112388	215138233	1	4652											
SASS6	163786	hgsc.bcm.edu	37	chr1	100572938	100572938	+	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	aatattaactacctcttgctCtttaattcgaagagactgtc	12	15	5	9	1	2	1	0	0	2	1	4	3	2	1	1	0	3	1	1	0	6	7			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr1:100572938C>G	ENST00000287482.5	-	11	1458	c.1318G>C	c.(1318-1320)Gag>Cag	p.E440Q	SASS6_ENST00000462159.1_5'UTR|SASS6_ENST00000535161.1_Missense_Mutation_p.E273Q	NM_194292.1	NP_919268.1	Q6UVJ0	SAS6_HUMAN	spindle assembly 6 homolog (C. elegans)	440					centriole replication (GO:0007099)|centrosome duplication (GO:0051298)	centriole (GO:0005814)|centrosome (GO:0005813)|deuterosome (GO:0098536)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	19		all_epithelial(167;4.58e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.085)|all cancers(265;0.139)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.197)		ACCTCTTGCTCTTTAATTCGA	0.294																																					p.E440Q		Atlas-SNP	.											.	SASS6	61	.	0			c.G1318C						PASS	.						57	53	54					1																	100572938		2201	4289	6490	SO:0001583	missense	163786	exon11			CTTGCTCTTTAAT	AL834265	CCDS764.1	1p21.3	2008-02-05			ENSG00000156876	ENSG00000156876			25403	protein-coding gene	gene with protein product		609321				15665853, 14654843	Standard	NM_194292		Approved	DKFZp761A078, SAS-6, FLJ22097, SAS6	uc001dsu.3	Q6UVJ0	OTTHUMG00000010754	ENST00000287482.5:c.1318G>C	chr1.hg19:g.100572938C>G	ENSP00000287482:p.Glu440Gln	143.0	0.0	.		88.0	13.0	.	NM_194292	D3DT55|Q8N3K0	Missense_Mutation	SNP	ENST00000287482.5	hg19	CCDS764.1	.	.	.	.	.	.	.	.	.	.	C	12.02	1.812823	0.32053	.	.	ENSG00000156876	ENST00000287482;ENST00000539329;ENST00000535161	T;T	0.29397	1.57;1.57	5.38	5.38	0.77491	.	0.047861	0.85682	D	0.000000	T	0.23451	0.0567	L	0.60455	1.87	0.58432	D	0.999999	P	0.41546	0.754	B	0.39339	0.297	T	0.02743	-1.1116	10	0.35671	T	0.21	-9.3422	19.1244	0.93376	0.0:1.0:0.0:0.0	.	440	Q6UVJ0	SAS6_HUMAN	Q	440;413;273	ENSP00000287482:E440Q;ENSP00000440169:E273Q	ENSP00000287482:E440Q	E	-	1	0	SASS6	100345526	1.000000	0.71417	1.000000	0.80357	0.064000	0.16182	5.050000	0.64251	2.515000	0.84797	0.585000	0.79938	GAG	.	.	.	none		0.294	SASS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029656.2	NM_194292		G	100572938	C	G	100572938	3	3	71	1	0	0	0	0	1	0	0	0	13863	922	32	4	683	4	SASS6	1	100572938	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08	66460550	100572938	148677683	2	4653											
RPTN	126638	hgsc.bcm.edu	37	chr1	152127802	152127802	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagtacttattttgcccttgTatttccccagtctgtgattg	7	18	7	9	0	1	1	0	1	1	0	2	1	2	1	3	0	2	2	3	0	4	8			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr1:152127802T>C	ENST00000316073.3	-	3	1837	c.1773A>G	c.(1771-1773)atA>atG	p.I591M		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	591	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						TTTGCCCTTGTATTTCCCCAG	0.453																																					p.I591M		Atlas-SNP	.											.	RPTN	123	.	0			c.A1773G						PASS	.						371	334	345					1																	152127802		1568	3582	5150	SO:0001583	missense	126638	exon3			CCCTTGTATTTCC	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.1773A>G	chr1.hg19:g.152127802T>C	ENSP00000317895:p.Ile591Met	594.0	0.0	.		769.0	224.0	.	NM_001122965	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	hg19	CCDS41397.1	.	.	.	.	.	.	.	.	.	.	T	2.328	-0.353972	0.05173	.	.	ENSG00000215853	ENST00000316073;ENST00000541545	T	0.13307	2.6	3.14	1.75	0.24633	.	.	.	.	.	T	0.01765	0.0056	N	0.08118	0	0.09310	N	1	P	0.41265	0.744	B	0.36608	0.229	T	0.42413	-0.9453	9	0.32370	T	0.25	0.0237	6.2084	0.20615	0.3116:0.0:0.0:0.6884	.	591	Q6XPR3	RPTN_HUMAN	M	591;246	ENSP00000317895:I591M	ENSP00000317895:I591M	I	-	3	3	RPTN	150394426	0.005000	0.15991	0.015000	0.15790	0.332000	0.28634	-0.725000	0.04942	0.119000	0.18210	0.450000	0.29827	ATA	.	.	.	none		0.453	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312		C	152127802	T	C	152127802	3	2	71	1	0	0	0	0	1	0	0	0	13677	1628	57	3	585	3	RPTN	1	152127802	Missense_Mutation	SNP	T	TCGA-AL-3466-01A-01D-1252-08	51554864	152127802	97122819	3	4654											
FAM129A	116496	hgsc.bcm.edu	37	chr1	184767228	184767228	+	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	cttacctttcagagtttcatCaagcaggatctgatgtaaaa	13	13	7	8	0	4	2	3	1	1	1	4	3	4	3	1	1	2	3	1	1	4	4			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr1:184767228C>A	ENST00000367511.3	-	13	1844	c.1651G>T	c.(1651-1653)Gat>Tat	p.D551Y	FAM129A_ENST00000487074.1_5'UTR	NM_052966.2	NP_443198.1	Q9BZQ8	NIBAN_HUMAN	family with sequence similarity 129, member A	551					negative regulation of protein phosphorylation (GO:0001933)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(6)|liver(1)|lung(22)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	45						AGAGTTTCATCAAGCAGGATC	0.453																																					p.D551Y		Atlas-SNP	.											.	FAM129A	98	.	0			c.G1651T						PASS	.						87	78	81					1																	184767228		2203	4300	6503	SO:0001583	missense	116496	exon13			TTTCATCAAGCAG	AF288391	CCDS1364.1	1q25	2008-10-08	2006-11-23	2006-11-23	ENSG00000135842	ENSG00000135842			16784	protein-coding gene	gene with protein product	"cell growth inhibiting protein 39"		"chromosome 1 open reading frame 24"	C1orf24		15085203, 16444351	Standard	NM_052966		Approved	NIBAN, GIG39	uc001gra.4	Q9BZQ8	OTTHUMG00000035388	ENST00000367511.3:c.1651G>T	chr1.hg19:g.184767228C>A	ENSP00000356481:p.Asp551Tyr	69.0	0.0	.		87.0	8.0	.	NM_052966	Q2TTR2|Q5TEM8|Q8TEI5|Q9H593|Q9H9Y8|Q9HCB9	Missense_Mutation	SNP	ENST00000367511.3	hg19	CCDS1364.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.62|16.62	3.173955|3.173955	0.57692|0.57692	.|.	.|.	ENSG00000135842|ENSG00000135842	ENST00000367511|ENST00000417056	T|.	0.13307|.	2.6|.	5.37|5.37	4.44|4.44	0.53790|0.53790	.|.	0.408987|.	0.29225|.	N|.	0.012780|.	T|.	0.63189|.	0.2490|.	L|L	0.54323|0.54323	1.7|1.7	0.34170|0.34170	D|D	0.669652|0.669652	D;D|.	0.89917|.	0.986;1.0|.	P;D|.	0.73380|.	0.742;0.98|.	T|.	0.71794|.	-0.4485|.	10|.	0.72032|.	D|.	0.01|.	-7.0804|-7.0804	14.591|14.591	0.68365|0.68365	0.0:0.8548:0.1452:0.0|0.0:0.8548:0.1452:0.0	.|.	82;551|.	Q5TEY9;Q9BZQ8|.	.;NIBAN_HUMAN|.	Y|L	551|82	ENSP00000356481:D551Y|.	ENSP00000356481:D551Y|.	D|X	-|-	1|2	0|2	FAM129A|FAM129A	183033851|183033851	0.876000|0.876000	0.30132|0.30132	0.985000|0.985000	0.45067|0.45067	0.994000|0.994000	0.84299|0.84299	2.463000|2.463000	0.45058|0.45058	1.233000|1.233000	0.43693|0.43693	0.655000|0.655000	0.94253|0.94253	GAT|TGA	.	.	.	none		0.453	FAM129A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085786.1			A	184767228	C	A	184767228	3	1	71	1	0	0	0	0	1	0	0	0	5440	826	29	4	1143	4	FAM129A	1	184767228	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08	32639426	184767228	64483393	4	4655											
PTPN14	5784	hgsc.bcm.edu	37	chr1	214557259	214557259	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgccccgcaccatgctgtTcatcacctccaggctgtggc	6	9	9	17	1	2	0	2	0	0	0	3	0	3	0	5	2	2	4	5	2	0	1			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr1:214557259T>C	ENST00000366956.5	-	13	2133	c.1939A>G	c.(1939-1941)Aac>Gac	p.N647D	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	647					lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)			NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		ACCATGCTGTTCATCACCTCC	0.662																																					p.N647D	Colon(92;557 1424 24372 34121 40073)	Atlas-SNP	.											.	PTPN14	168	.	0			c.A1939G						PASS	.						50	42	45					1																	214557259		2203	4300	6503	SO:0001583	missense	5784	exon13			TGCTGTTCATCAC	X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.1939A>G	chr1.hg19:g.214557259T>C	ENSP00000355923:p.Asn647Asp	71.0	0.0	.		169.0	55.0	.	NM_005401	Q5VSI0	Missense_Mutation	SNP	ENST00000366956.5	hg19	CCDS1514.1	.	.	.	.	.	.	.	.	.	.	T	14.65	2.600155	0.46423	.	.	ENSG00000152104	ENST00000366956	T	0.66815	-0.23	5.66	4.43	0.53597	.	0.373344	0.33217	N	0.005146	T	0.45458	0.1343	N	0.08118	0	0.80722	D	1	B	0.12630	0.006	B	0.10450	0.005	T	0.35525	-0.9785	10	0.62326	D	0.03	.	9.7306	0.40359	0.0:0.1:0.0:0.9	.	647	Q15678	PTN14_HUMAN	D	647	ENSP00000355923:N647D	ENSP00000355923:N647D	N	-	1	0	PTPN14	212623882	1.000000	0.71417	0.970000	0.41538	0.991000	0.79684	3.785000	0.55424	0.847000	0.35167	0.455000	0.32223	AAC	.	.	.	none		0.662	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401		C	214557259	T	C	214557259	3	2	71	1	0	0	0	0	1	0	0	0	12794	1783	62	3	1652	3	PTPN14	1	214557259	Missense_Mutation	SNP	T	TCGA-AL-3466-01A-01D-1252-08	29790031	214557259	34693362	5	4656											
MOSC1	64757	hgsc.bcm.edu	37	chr1	220971317	220971317	+	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	gttaaagcaaccaacttcagGcccaatattgtaatttcagg	14	11	7	9	0	2	0	2	0	0	0	2	0	2	0	2	2	3	3	2	2	7	6			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr1:220971317G>A	ENST00000366910.5	+	4	900	c.714G>A	c.(712-714)agG>agA	p.R238R	MARC1_ENST00000496110.1_3'UTR	NM_022746.3	NP_073583.3	Q5VT66	MARC1_HUMAN	mitochondrial amidoxime reducing component 1	238	MOSC. {ECO:0000255|PROSITE- ProRule:PRU00670}.				detoxification of nitrogen compound (GO:0051410)|nitrate metabolic process (GO:0042126)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	molybdenum ion binding (GO:0030151)|molybdopterin cofactor binding (GO:0043546)|nitrate reductase activity (GO:0008940)|pyridoxal phosphate binding (GO:0030170)										CCAACTTCAGGCCCAATATTG	0.443																																					p.R238R		Atlas-SNP	.											.	.	.	.	0			c.G714A						PASS	.						168	167	167					1																	220971317		2203	4300	6503	SO:0001819	synonymous_variant	64757	exon4			CTTCAGGCCCAAT	AK026043	CCDS1526.1	1q41	2011-11-02	2011-11-02	2011-11-02	ENSG00000186205	ENSG00000186205			26189	protein-coding gene	gene with protein product		614126	"MOCO sulphurase C-terminal domain containing 1"	MOSC1		11886751	Standard	NM_022746		Approved	FLJ22390	uc001hms.3	Q5VT66	OTTHUMG00000037353	ENST00000366910.5:c.714G>A	chr1.hg19:g.220971317G>A		376.0	0.0	.		498.0	119.0	.	NM_022746	A8K447|B2D078|Q5VVS9|Q5VVT0|Q5VVT1|Q8N9P5|Q96FN8|Q9H6C7	Silent	SNP	ENST00000366910.5	hg19	CCDS1526.1	.	.	.	.	.	.	.	.	.	.	G	2.055	-0.416878	0.04766	.	.	ENSG00000186205	ENST00000407981	.	.	.	4.95	3.04	0.35103	.	.	.	.	.	T	0.47875	0.1469	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39057	-0.9632	4	.	.	.	-19.1717	4.6342	0.12516	0.2726:0.1776:0.5497:0.0	.	.	.	.	T	147	.	.	A	+	1	0	MOSC1	219037940	0.990000	0.36364	0.996000	0.52242	0.079000	0.17450	0.098000	0.15189	1.211000	0.43351	0.655000	0.94253	GCC	.	.	.	none		0.443	MARC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090904.1	NM_022746		A	220971317	G	A	220971317	2	1	71	1	0	0	0	0	0	0	0	1	9720	1194	42	2		2	MOSC1	1	220971317	Silent	SNP	G	TCGA-AL-3466-01A-01D-1252-08	6414058	220971317	28279304	6	4657											
SLC35F3	148641	hgsc.bcm.edu	37	chr1	234458910	234458910	+	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	caaagtgaggaagaaggaggAgcctgcagagggcgctgccg	12	3	18	8	2	0	3	0	1	0	2	0	6	0	6	2	4	3	2	2	4	3	0			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr1:234458910A>T	ENST00000366617.3	+	7	1415	c.1187A>T	c.(1186-1188)gAg>gTg	p.E396V	SLC35F3_ENST00000366618.3_Missense_Mutation_p.E465V			Q8IY50	S35F3_HUMAN	solute carrier family 35, member F3	396					thiamine transport (GO:0015888)	integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|urinary_tract(1)	32	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)			AAGAAGGAGGAGCCTGCAGAG	0.587											OREG0014330	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E465V		Atlas-SNP	.											.	SLC35F3	81	.	0			c.A1394T						PASS	.						74	73	74					1																	234458910		2203	4300	6503	SO:0001583	missense	148641	exon8			AGGAGGAGCCTGC		CCDS1600.1, CCDS73050.1	1q42.3	2013-05-22			ENSG00000183780	ENSG00000183780		"Solute carriers"	23616	protein-coding gene	gene with protein product							Standard	XM_005273070		Approved	FLJ37712	uc001hvy.1	Q8IY50	OTTHUMG00000037929	ENST00000366617.3:c.1187A>T	chr1.hg19:g.234458910A>T	ENSP00000355576:p.Glu396Val	160.0	0.0	.	2373	281.0	36.0	.	NM_173508	Q5TDD6|Q8N9C9	Missense_Mutation	SNP	ENST00000366617.3	hg19		.	.	.	.	.	.	.	.	.	.	A	25.5	4.643874	0.87859	.	.	ENSG00000183780	ENST00000366618;ENST00000366617	T;T	0.53857	0.6;0.62	5.62	5.62	0.85841	.	0.214041	0.48767	D	0.000163	T	0.58623	0.2135	L	0.50333	1.59	0.51482	D	0.999922	D;D	0.57571	0.966;0.98	P;P	0.51229	0.543;0.663	T	0.61983	-0.6950	10	0.59425	D	0.04	-20.2302	15.7908	0.78364	1.0:0.0:0.0:0.0	.	396;465	Q8IY50;Q8IY50-2	S35F3_HUMAN;.	V	465;396	ENSP00000355577:E465V;ENSP00000355576:E396V	ENSP00000355576:E396V	E	+	2	0	SLC35F3	232525533	1.000000	0.71417	0.996000	0.52242	0.989000	0.77384	8.954000	0.93051	2.132000	0.65825	0.402000	0.26972	GAG	.	.	.	none		0.587	SLC35F3-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000128322.1	NM_173508		T	234458910	A	T	234458910	3	4	71	1	0	0	0	0	1	0	0	0	14603	304	11	5	1424	5	SLC35F3	1	234458910	Missense_Mutation	SNP	A	TCGA-AL-3466-01A-01D-1252-08	13487593	234458910	14791711	7	4658											
RAB11FIP5	26056	hgsc.bcm.edu	37	chr2	73315269	73315269	+	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	ggatgagtgatgtggggaggCccccaggatgggacccccct	7	6	17	11	0	0	2	0	2	0	0	0	6	0	6	5	6	0	0	5	6	0	0			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr2:73315269C>T	ENST00000258098.6	-	3	1717	c.1477G>A	c.(1477-1479)Gcc>Acc	p.A493T	RAB11FIP5_ENST00000493523.2_5'UTR	NM_015470.2	NP_056285.1	Q9BXF6	RFIP5_HUMAN	RAB11 family interacting protein 5 (class I)	493					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						TGTGGGGAGGCCCCCAGGATG	0.607																																					p.A493T		Atlas-SNP	.											.	RAB11FIP5	66	.	0			c.G1477A						PASS	.						69	74	72					2																	73315269		2203	4300	6503	SO:0001583	missense	26056	exon3			GGGAGGCCCCCAG	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.1477G>A	chr2.hg19:g.73315269C>T	ENSP00000258098:p.Ala493Thr	249.0	0.0	.		484.0	55.0	.	NM_015470	O94939|Q9P0M1	Missense_Mutation	SNP	ENST00000258098.6	hg19	CCDS1923.1	.	.	.	.	.	.	.	.	.	.	C	16.78	3.217658	0.58560	.	.	ENSG00000135631	ENST00000258098	T	0.50548	0.74	4.52	4.52	0.55395	.	0.334564	0.25935	N	0.027344	T	0.50905	0.1643	N	0.19112	0.55	0.34421	D	0.697508	D;D	0.63880	0.993;0.993	D;D	0.74674	0.971;0.984	T	0.55780	-0.8087	10	0.23891	T	0.37	-11.0892	14.4444	0.67340	0.0:1.0:0.0:0.0	.	493;493	Q9BXF6;Q2Z1P3	RFIP5_HUMAN;.	T	493	ENSP00000258098:A493T	ENSP00000258098:A493T	A	-	1	0	RAB11FIP5	73168777	0.002000	0.14202	0.992000	0.48379	0.966000	0.64601	-0.184000	0.09698	2.527000	0.85204	0.491000	0.48974	GCC	.	.	.	none		0.607	RAB11FIP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251995.1	NM_015470		T	73315269	C	T	73315269	3	4	71	1	0	0	0	0	1	0	0	0	12910	739	26	2	496	2	RAB11FIP5	2	73315269	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08		73315269	169884104	8	4659											
FAM124B	79843	hgsc.bcm.edu	37	chr2	225266233	225266233	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgctggagagagtccaggaCgcgaaatagcctatcctctc	11	8	11	11	2	1	1	0	0	1	1	4	5	3	3	3	2	2	1	3	2	3	2			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr2:225266233C>T	ENST00000409685.3	-	1	518	c.253G>A	c.(253-255)Gtc>Atc	p.V85I	FAM124B_ENST00000243806.2_Missense_Mutation_p.V85I|FAM124B_ENST00000389874.3_Missense_Mutation_p.V85I	NM_001122779.1	NP_001116251.1	Q9H5Z6	F124B_HUMAN	family with sequence similarity 124B	85								p.V85I(2)		endometrium(2)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	16		Renal(207;0.0112)|all_lung(227;0.0126)|Lung NSC(271;0.0161)|all_hematologic(139;0.138)		Epithelial(121;4.4e-10)|all cancers(144;2.02e-07)|Lung(261;0.00766)|LUSC - Lung squamous cell carcinoma(224;0.00825)		GAGTCCAGGACGCGAAATAGC	0.552																																					p.V85I		Atlas-SNP	.											FAM124B_ENST00000409685,NS,carcinoma,0,4	FAM124B	71	.	2	Substitution - Missense(2)	endometrium(2)	c.G253A						PASS	.						59	57	58					2																	225266233		2203	4300	6503	SO:0001583	missense	79843	exon1			CCAGGACGCGAAA	AK075126	CCDS2461.1, CCDS46527.1	2q36.2	2008-02-05			ENSG00000124019	ENSG00000124019			26224	protein-coding gene	gene with protein product						12477932	Standard	NM_001122779		Approved	FLJ22746	uc002vnx.3	Q9H5Z6	OTTHUMG00000133168	ENST00000409685.3:c.253G>A	chr2.hg19:g.225266233C>T	ENSP00000386895:p.Val85Ile	105.0	0.0	.		145.0	20.0	.	NM_024785	A6NNC7|Q8NBZ4|Q8TAV7	Missense_Mutation	SNP	ENST00000409685.3	hg19	CCDS46527.1	.	.	.	.	.	.	.	.	.	.	C	4.854	0.158738	0.09236	.	.	ENSG00000124019	ENST00000389874;ENST00000409685;ENST00000243806	T;T;T	0.46063	0.88;0.88;0.88	5.69	1.32	0.21799	.	0.311841	0.33691	N	0.004645	T	0.30510	0.0767	L	0.42686	1.345	0.09310	N	1	B;B	0.21452	0.056;0.004	B;B	0.17433	0.018;0.003	T	0.18871	-1.0323	10	0.44086	T	0.13	-7.8837	7.6061	0.28103	0.0:0.574:0.22:0.206	.	85;85	Q9H5Z6;Q9H5Z6-2	F124B_HUMAN;.	I	85	ENSP00000374524:V85I;ENSP00000386895:V85I;ENSP00000243806:V85I	ENSP00000243806:V85I	V	-	1	0	FAM124B	224974477	0.625000	0.27111	0.000000	0.03702	0.001000	0.01503	1.550000	0.36223	0.332000	0.23536	-0.137000	0.14449	GTC	.	.	.	none		0.552	FAM124B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330873.1	NM_024785		T	225266233	C	T	225266233	3	4	71	1	0	0	0	0	1	0	0	0	5430	536	19	1	1213	1	FAM124B	2	225266233	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08	151950964	225266233	17933140	9	4660											
PFKFB4	5210	hgsc.bcm.edu	37	chr3	48577177	48577177	+	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	aaagatggtcgctctccgttCtcgggtggtgtttgtggcat	5	14	14	8	3	2	1	0	0	2	1	5	1	2	1	1	4	0	4	1	4	1	2			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr3:48577177C>A	ENST00000232375.3	-	5	518	c.406G>T	c.(406-408)Gaa>Taa	p.E136*	PFKFB4_ENST00000490115.1_5'UTR|PFKFB4_ENST00000541519.1_Nonsense_Mutation_p.E102*|PFKFB4_ENST00000416568.1_Nonsense_Mutation_p.E136*|PFKFB4_ENST00000536104.1_Nonsense_Mutation_p.E125*|PFKFB4_ENST00000545984.1_Missense_Mutation_p.E113D|PFKFB4_ENST00000383734.2_Nonsense_Mutation_p.E136*	NM_004567.2	NP_004558.1	Q16877	F264_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4	136	6-phosphofructo-2-kinase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|urinary_tract(1)	14				BRCA - Breast invasive adenocarcinoma(193;0.0003)|KIRC - Kidney renal clear cell carcinoma(197;0.00596)|Kidney(197;0.00684)		GCTCTCCGTTCTCGGGTGGTG	0.567																																					p.E136X		Atlas-SNP	.											.	PFKFB4	39	.	0			c.G406T						PASS	.						114	107	109					3																	48577177		2203	4300	6503	SO:0001587	stop_gained	5210	exon5			TCCGTTCTCGGGT	BC010269	CCDS2771.1	3p22-p21	2004-03-02			ENSG00000114268	ENSG00000114268			8875	protein-coding gene	gene with protein product		605320				8830046, 10095107	Standard	NM_004567		Approved		uc003ctv.3	Q16877	OTTHUMG00000133528	ENST00000232375.3:c.406G>T	chr3.hg19:g.48577177C>A	ENSP00000232375:p.Glu136*	143.0	0.0	.		124.0	49.0	.	NM_004567	Q5S3G5|Q5XLC2|Q64EX5	Nonsense_Mutation	SNP	ENST00000232375.3	hg19	CCDS2771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.32|15.32	2.797337|2.797337	0.50208|0.50208	.|.	.|.	ENSG00000114268|ENSG00000114268	ENST00000545984|ENST00000232375;ENST00000536104;ENST00000416568;ENST00000383734;ENST00000541519;ENST00000452531;ENST00000412035	.|.	.|.	.|.	4.62|4.62	4.62|4.62	0.57501|0.57501	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|.	0.63307|.	0.2500|.	.|.	.|.	.|.	0.31708|0.31708	N|N	0.639831|0.639831	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.71906|.	-0.4451|.	6|.	0.02654|0.87932	T|D	1|0	-15.7704|-15.7704	15.0132|15.0132	0.71565|0.71565	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	D|X	113|136;125;136;136;102;125;102	.|.	ENSP00000437844:E113D|ENSP00000232375:E136X	E|E	-|-	3|1	2|0	PFKFB4|PFKFB4	48552181|48552181	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.769000|0.769000	0.43574|0.43574	7.645000|7.645000	0.83430|0.83430	2.419000|2.419000	0.82065|0.82065	0.467000|0.467000	0.42956|0.42956	GAG|GAA	.	.	.	none		0.567	PFKFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257503.2	NM_004567		A	48577177	C	A	48577177	4	1	71	1	0	0	0	0	0	1	0	0	11770	922	32	4	1043	4	PFKFB4	3	48577177	Nonsense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08		48577177	149445253	10	4661											
TKT	7086	hgsc.bcm.edu	37	chr3	53264627	53264627	+	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	gtgcctgcccgtaggccttgCgggtggctatctgtgaggaa	5	10	16	10	2	1	1	0	1	1	0	1	2	1	2	3	4	3	2	3	4	3	3			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr3:53264627C>T	ENST00000462138.1	-	8	1041	c.953G>A	c.(952-954)cGc>cAc	p.R318H	TKT_ENST00000461139.1_5'UTR|TKT_ENST00000296289.6_Missense_Mutation_p.R271H|TKT_ENST00000423525.2_Missense_Mutation_p.R318H|TKT_ENST00000423516.1_Missense_Mutation_p.R326H			P29401	TKT_HUMAN	transketolase	318					carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|glyceraldehyde-3-phosphate biosynthetic process (GO:0046166)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|regulation of growth (GO:0040008)|small molecule metabolic process (GO:0044281)|xylulose biosynthetic process (GO:0005999)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|peroxisome (GO:0005777)|vesicle (GO:0031982)	cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|transketolase activity (GO:0004802)			endometrium(5)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17		Prostate(884;0.0959)		BRCA - Breast invasive adenocarcinoma(193;0.000159)|OV - Ovarian serous cystadenocarcinoma(275;0.000314)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)		GTAGGCCTTGCGGGTGGCTAT	0.587																																					p.R326H	Colon(133;1506 2347 35238 42177)	Atlas-SNP	.											.	TKT	38	.	0			c.G977A						PASS	.						59	56	57					3																	53264627		2203	4300	6503	SO:0001583	missense	7086	exon9			GCCTTGCGGGTGG		CCDS2871.1, CCDS58834.1	3p14.3	2008-07-31	2008-07-31		ENSG00000163931	ENSG00000163931	2.2.1.1		11834	protein-coding gene	gene with protein product	"Wernicke-Korsakoff syndrome"	606781				1567394	Standard	NM_001064		Approved		uc011beq.2	P29401	OTTHUMG00000158192	ENST00000462138.1:c.953G>A	chr3.hg19:g.53264627C>T	ENSP00000417773:p.Arg318His	72.0	0.0	.		98.0	6.0	.	NM_001258028	A8K089|B4DE31|E7EPA7|Q8TBA3|Q96HH3	Missense_Mutation	SNP	ENST00000462138.1	hg19	CCDS2871.1	.	.	.	.	.	.	.	.	.	.	C	35	5.563617	0.96527	.	.	ENSG00000163931	ENST00000462138;ENST00000423525;ENST00000423516;ENST00000296289;ENST00000414014	D;D;D;D	0.92965	-3.14;-3.14;-3.14;-3.14	5.69	5.69	0.88448	Transketolase-like, pyrimidine-binding domain (2);	0.047547	0.85682	D	0.000000	D	0.97763	0.9266	H	0.97682	4.055	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.72338	0.963;0.977;0.971	D	0.98701	1.0700	10	0.87932	D	0	-15.8701	19.8045	0.96525	0.0:1.0:0.0:0.0	.	326;235;318	E7EPA7;B3KSI4;P29401	.;.;TKT_HUMAN	H	318;318;326;271;152	ENSP00000417773:R318H;ENSP00000405455:R318H;ENSP00000391481:R326H;ENSP00000296289:R271H	ENSP00000296289:R271H	R	-	2	0	TKT	53239667	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.818000	0.86416	2.676000	0.91093	0.655000	0.94253	CGC	.	.	.	none		0.587	TKT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350356.1			T	53264627	C	T	53264627	3	4	71	1	0	0	0	0	1	0	0	0	15946	768	27	1	946	1	TKT	3	53264627	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08	4687450	53264627	144757803	11	4662											
PPP4R2	151987	hgsc.bcm.edu	37	chr3	73110176	73110176	+	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	tgatttttgttattgcagaaTgtgatggttgttagctgtgt	7	20	12	2	0	0	3	0	2	0	1	0	3	0	3	0	1	2	5	0	1	3	6			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr3:73110176T>A	ENST00000356692.5	+	5	637	c.384T>A	c.(382-384)aaT>aaA	p.N128K	PPP4R2_ENST00000394284.3_Missense_Mutation_p.N71K|EBLN2_ENST00000533473.1_5'Flank|PPP4R2_ENST00000295862.9_Missense_Mutation_p.N72K			Q9NY27	PP4R2_HUMAN	protein phosphatase 4, regulatory subunit 2	128					cellular protein modification process (GO:0006464)|hematopoietic progenitor cell differentiation (GO:0002244)|mRNA processing (GO:0006397)|regulation of catalytic activity (GO:0050790)|regulation of double-strand break repair via homologous recombination (GO:0010569)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)	protein binding, bridging (GO:0030674)|protein phosphatase type 4 regulator activity (GO:0030362)			breast(2)|endometrium(1)|large_intestine(1)|lung(3)|skin(2)|stomach(1)|urinary_tract(2)	12		Prostate(10;0.0187)|Lung SC(41;0.236)		Epithelial(33;1.76e-07)|BRCA - Breast invasive adenocarcinoma(55;9.42e-05)|LUSC - Lung squamous cell carcinoma(21;0.00211)|Lung(16;0.00643)|KIRC - Kidney renal clear cell carcinoma(39;0.0164)|Kidney(39;0.0193)|OV - Ovarian serous cystadenocarcinoma(275;0.031)		TATTGCAGAATGTGATGGTTG	0.259																																					p.N128K		Atlas-SNP	.											.	PPP4R2	30	.	0			c.T384A						PASS	.						102	96	98					3																	73110176		2199	4292	6491	SO:0001583	missense	151987	exon5			GCAGAATGTGATG	AJ271448	CCDS2917.1	3q29	2010-06-18			ENSG00000163605	ENSG00000163605		"Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"	18296	protein-coding gene	gene with protein product		613822				10769191	Standard	NM_174907		Approved		uc003dph.1	Q9NY27	OTTHUMG00000158816	ENST00000356692.5:c.384T>A	chr3.hg19:g.73110176T>A	ENSP00000349124:p.Asn128Lys	68.0	0.0	.		34.0	8.0	.	NM_174907	A8K1I6|Q2TAJ9|Q498B8|Q8WXX6	Missense_Mutation	SNP	ENST00000356692.5	hg19	CCDS2917.1	.	.	.	.	.	.	.	.	.	.	T	17.55	3.417029	0.62511	.	.	ENSG00000163605	ENST00000356692;ENST00000488810;ENST00000394284;ENST00000295862	T;T;T;T	0.54071	0.59;0.59;0.59;0.59	4.96	2.54	0.30619	.	0.000000	0.85682	D	0.000000	T	0.57036	0.2026	M	0.86178	2.8	0.80722	D	1	P;P	0.39903	0.694;0.505	B;B	0.41374	0.353;0.355	T	0.59467	-0.7449	10	0.72032	D	0.01	.	9.3514	0.38140	0.0:0.1471:0.0:0.8529	.	71;128	Q9NY27-2;Q9NY27	.;PP4R2_HUMAN	K	128;128;71;72	ENSP00000349124:N128K;ENSP00000418750:N128K;ENSP00000377825:N71K;ENSP00000295862:N72K	ENSP00000295862:N72K	N	+	3	2	PPP4R2	73192866	1.000000	0.71417	1.000000	0.80357	0.829000	0.46940	3.134000	0.50538	0.329000	0.23460	-0.297000	0.09499	AAT	.	.	.	none		0.259	PPP4R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352321.1	NM_174907		A	73110176	T	A	73110176	3	1	71	1	0	0	0	0	1	0	0	0	12414	1461	51	5	402	5	PPP4R2	3	73110176	Missense_Mutation	SNP	T	TCGA-AL-3466-01A-01D-1252-08	19845549	73110176	124912254	12	4663											
MED12L	116931	hgsc.bcm.edu	37	chr3	151072983	151072983	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggagactgtgttcactaaaCtccagctcctttcatatttt	9	16	6	10	0	2	1	2	0	0	1	4	2	4	1	2	1	2	2	2	1	3	6	rs200848773		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr3:151072983C>T	ENST00000474524.1	+	16	2406	c.2368C>T	c.(2368-2370)Ctc>Ttc	p.L790F	MED12L_ENST00000273432.4_Missense_Mutation_p.L650F|P2RY12_ENST00000302632.3_Intron|MED12L_ENST00000491549.1_3'UTR	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	790						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)			GTTCACTAAACTCCAGCTCCT	0.358																																					p.L790F		Atlas-SNP	.											.	MED12L	271	.	0			c.C2368T						PASS	.						103	104	103					3																	151072983		2203	4300	6503	SO:0001583	missense	116931	exon16			ACTAAACTCCAGC	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.2368C>T	chr3.hg19:g.151072983C>T	ENSP00000417235:p.Leu790Phe	151.0	0.0	.		61.0	17.0	.	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	hg19	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	C	3.897	-0.022893	0.07634	.	.	ENSG00000144893	ENST00000474524;ENST00000273432	T;T	0.71341	-0.56;-0.56	5.35	5.35	0.76521	.	0.059800	0.64402	D	0.000002	T	0.31918	0.0812	N	0.00186	-1.895	0.80722	D	1	B;B	0.15141	0.006;0.012	B;B	0.17098	0.017;0.012	T	0.46830	-0.9163	10	0.11182	T	0.66	-18.4403	12.407	0.55445	0.0:0.922:0.0:0.078	.	650;790	F8WAE6;Q86YW9	.;MD12L_HUMAN	F	790;650	ENSP00000417235:L790F;ENSP00000273432:L650F	ENSP00000273432:L650F	L	+	1	0	MED12L	152555673	1.000000	0.71417	1.000000	0.80357	0.545000	0.35147	3.177000	0.50871	2.656000	0.90262	0.650000	0.86243	CTC	.	C|0.999;G|0.001	.	alt		0.358	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		T	151072983	C	T	151072983	3	4	71	1	0	0	0	0	1	0	0	0	9436	565	20	2	2430	2	MED12L	3	151072983	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08	77962807	151072983	46949447	13	4664											
HAVCR1	26762	hgsc.bcm.edu	37	chr5	156482352	156482362	+	Frame_Shift_Del	DEL	AATAGCTTATA	AATAGCTTATA	-																															cccttcttgaaaggtcccccAatagcttatagcgtgtgtcc																								rs111358310	byFrequency	TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	AATAGCTTATA	AATAGCTTATA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr5:156482352_156482362delAATAGCTTATA	ENST00000339252.3	-	2	761_771	c.229_239delTATAAGCTATT	c.(229-240)tataagctattgfs	p.YKLL77fs	HAVCR1_ENST00000523175.1_Frame_Shift_Del_p.YKLL77fs|HAVCR1_ENST00000544197.1_Frame_Shift_Del_p.YKLL77fs|HAVCR1_ENST00000522693.1_Frame_Shift_Del_p.YKLL77fs|HAVCR1_ENST00000425854.1_Frame_Shift_Del_p.YKLL77fs	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)			AAGGTCCCCCAATAGCTTATAGCGTGTGTCC	0.479																																					p.77_80del		Atlas-INDEL	.											.	HAVCR1	84	.	0			c.230_240del						PASS	.																																			SO:0001589	frameshift_variant	26762	exon3			.	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.229_239delTATAAGCTATT	chr5.hg19:g.156482352_156482362delAATAGCTTATA	ENSP00000344844:p.Tyr77fs	128.0	0.0	0		271.0	52.0	0.191882	NM_001099414	O43656	Frame_Shift_Del	DEL	ENST00000339252.3	hg19	CCDS43392.1																																																																																			.	.	.	none		0.479	HAVCR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373698.1			-	156482362	AATAGCTTATA	-	156482352	7	5	71	1	0	1	0	1	0	0	0	0	6980	131	5	0	883	0	HAVCR1	5	156482352	Frame_Shift_Del	DEL	AATAGCTTATA	TCGA-AL-3466-01A-01D-1252-08		156482352	24432908	14	4665											
HIST1H2BL	8340	hgsc.bcm.edu	37	chr6	27775403	27775403	+	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	aggcgcacggcggtctggatCtccctggaggtgatggtcga	6	8	17	10	4	2	1	0	1	2	0	4	4	2	3	1	7	0	1	1	7	0	0	rs141648774		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr6:27775403C>T	ENST00000377401.2	-	1	306	c.282G>A	c.(280-282)gaG>gaA	p.E94E	HIST1H3H_ENST00000369163.2_5'Flank|HIST1H2AI_ENST00000358739.3_5'Flank	NM_003519.3	NP_003510.1	Q99880	H2B1L_HUMAN	histone cluster 1, H2bl	94					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						CGGTCTGGATCTCCCTGGAGG	0.617																																					p.E94E		Atlas-SNP	.											.	HIST1H2BL	48	.	0			c.G282A						PASS	.						92	94	93					6																	27775403		2203	4300	6503	SO:0001819	synonymous_variant	8340	exon1			CTGGATCTCCCTG	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.282G>A	chr6.hg19:g.27775403C>T		176.0	0.0	.		197.0	143.0	.	NM_003519	B2R5A3|Q52LW9	Silent	SNP	ENST00000377401.2	hg19	CCDS4625.1																																																																																			.	C|1.000;A|0.000	.	alt		0.617	HIST1H2BL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040153.1	NM_003519		T	27775403	C	T	27775403	2	4	71	1	0	0	0	0	0	0	0	1	7158	912	32	2		2	HIST1H2BL	6	27775403	Silent	SNP	C	TCGA-AL-3466-01A-01D-1252-08		27775403	143339664	15	4666											
C6orf142	90523	hgsc.bcm.edu	37	chr6	53989447	53989447	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagctgaatatgtccttatTgtggactccgaaggggaaga	13	10	12	6	1	0	2	0	1	0	1	2	5	2	4	2	3	1	1	2	3	6	3			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr6:53989447T>C	ENST00000274897.5	+	3	509	c.396T>C	c.(394-396)atT>atC	p.I132I	MLIP_ENST00000511744.1_3'UTR|MLIP_ENST00000514921.1_Silent_p.I132I|MLIP_ENST00000509997.1_Silent_p.I80I|MLIP_ENST00000370876.2_Silent_p.I70I|MLIP_ENST00000502396.1_Silent_p.I143I|MLIP_ENST00000370877.2_Silent_p.I80I|MLIP_ENST00000358276.5_Silent_p.I126I	NM_138569.2	NP_612636.2	Q5VWP3	MLIP_HUMAN	muscular LMNA-interacting protein	132						nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|PML body (GO:0016605)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(16)|ovary(8)|skin(4)|stomach(1)|urinary_tract(1)	34						ATGTCCTTATTGTGGACTCCG	0.502																																					p.I132I		Atlas-SNP	.											.	MLIP	84	.	0			c.T396C						PASS	.						100	99	100					6																	53989447		2203	4300	6503	SO:0001819	synonymous_variant	90523	exon3			CCTTATTGTGGAC	AK055530	CCDS4954.1, CCDS64448.1, CCDS64449.1	6p12.2-p12.1	2011-04-29	2011-04-29	2011-04-29	ENSG00000146147	ENSG00000146147			21355	protein-coding gene	gene with protein product	"muscle-enriched A-type lamin interacting protein"	614106	"chromosome 6 open reading frame 142"	C6orf142		21498514	Standard	NM_138569		Approved	MGC18257	uc011dxa.2	Q5VWP3	OTTHUMG00000014891	ENST00000274897.5:c.396T>C	chr6.hg19:g.53989447T>C		250.0	0.0	.		166.0	127.0	.	NM_138569	B7Z2N0|D6RE05|Q96H08|Q96NF7	Silent	SNP	ENST00000274897.5	hg19	CCDS4954.1																																																																																			.	.	.	none		0.502	MLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040979.3	NM_138569		C	53989447	T	C	53989447	2	2	71	1	0	0	0	0	0	0	0	1	2335	1800	63	3		3	C6orf142	6	53989447	Silent	SNP	T	TCGA-AL-3466-01A-01D-1252-08	26214044	53989447	117125620	16	4667											
NOS3	4846	hgsc.bcm.edu	37	chr7	150698913	150698913	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttcctctcccgcagcgccGtgaagatctccgcctcgctc	4	9	8	20	5	2	2	0	1	2	1	7	2	3	2	6	0	1	2	6	0	1	1			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr7:150698913G>A	ENST00000484524.1	+	12	1507	c.1507G>A	c.(1507-1509)Gtg>Atg	p.V503M	NOS3_ENST00000297494.3_Missense_Mutation_p.V503M|NOS3_ENST00000461406.1_Missense_Mutation_p.V297M|NOS3_ENST00000467517.1_Missense_Mutation_p.V503M	NM_001160111.1	NP_001153583.1	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	0					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCGCAGCGCCGTGAAGATCTC	0.642																																					p.V503M		Atlas-SNP	.											.	NOS3	131	.	0			c.G1507A						PASS	.						53	51	52					7																	150698913		2203	4300	6503	SO:0001583	missense	4846	exon12			AGCGCCGTGAAGA		CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"endothelial nitric oxide synthase"	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000484524.1:c.1507G>A	chr7.hg19:g.150698913G>A	ENSP00000420215:p.Val503Met	148.0	0.0	.		174.0	53.0	.	NM_001160111	Q495E5	Missense_Mutation	SNP	ENST00000484524.1	hg19	CCDS55182.1	.	.	.	.	.	.	.	.	.	.	G	19.87	3.907322	0.72868	.	.	ENSG00000164867	ENST00000297494;ENST00000461406;ENST00000484524;ENST00000467517	T;T;T;T	0.17691	4.46;4.33;2.67;2.26	4.8	4.8	0.61643	.	0.000000	0.48767	D	0.000162	T	0.48660	0.1512	M	0.89414	3.03	0.58432	D	0.99999	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.79784	0.98;0.98;0.991;0.993;0.991	T	0.58869	-0.7560	10	0.87932	D	0	-4.5235	15.7394	0.77876	0.0:0.0:1.0:0.0	.	503;503;503;297;503	A0S0A6;E9PFR2;A0S0A8;E7ESA7;P29474	.;.;.;.;NOS3_HUMAN	M	503;297;503;503	ENSP00000297494:V503M;ENSP00000417143:V297M;ENSP00000420215:V503M;ENSP00000420551:V503M	ENSP00000297494:V503M	V	+	1	0	NOS3	150329846	1.000000	0.71417	0.946000	0.38457	0.522000	0.34438	9.261000	0.95576	2.376000	0.81061	0.655000	0.94253	GTG	.	.	.	none		0.642	NOS3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351550.1	NM_000603		A	150698913	G	A	150698913	3	1	71	1	0	0	0	0	1	0	0	0	10551	1145	40	1	1553	1	NOS3	7	150698913	Missense_Mutation	SNP	G	TCGA-AL-3466-01A-01D-1252-08		150698913	8439750	17	4668											
OXR1	55074	hgsc.bcm.edu	37	chr8	107752622	107752622	+	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	gctatccatggactcttgttTatggtactggaaaacatggc	10	13	10	8	0	1	0	0	0	1	0	2	2	2	2	1	4	2	3	1	4	5	5			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr8:107752622T>A	ENST00000442977.2	+	13	2317	c.2218T>A	c.(2218-2220)Tat>Aat	p.Y740N	OXR1_ENST00000312046.6_Missense_Mutation_p.Y705N|OXR1_ENST00000445937.1_Missense_Mutation_p.Y712N|OXR1_ENST00000531443.1_Missense_Mutation_p.Y712N|OXR1_ENST00000452423.2_Missense_Mutation_p.Y160N|OXR1_ENST00000297447.6_Missense_Mutation_p.Y109N|OXR1_ENST00000521592.1_De_novo_Start_OutOfFrame|OXR1_ENST00000517566.2_Missense_Mutation_p.Y739N|OXR1_ENST00000449762.2_Missense_Mutation_p.Y82N	NM_001198532.1	NP_001185461.1	Q8N573	OXR1_HUMAN	oxidation resistance 1	740	TLD.				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)			GACTCTTGTTTATGGTACTGG	0.383																																					p.Y740N		Atlas-SNP	.											.	OXR1	190	.	0			c.T2218A						PASS	.						129	119	122					8																	107752622		2203	4300	6503	SO:0001583	missense	55074	exon13			CTTGTTTATGGTA	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.2218T>A	chr8.hg19:g.107752622T>A	ENSP00000405424:p.Tyr740Asn	234.0	0.0	.		75.0	11.0	.	NM_001198532	A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7	Missense_Mutation	SNP	ENST00000442977.2	hg19	CCDS56548.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.4|25.4	4.629261|4.629261	0.87560|0.87560	.|.	.|.	ENSG00000164830|ENSG00000164830	ENST00000519415|ENST00000445937;ENST00000531443;ENST00000517566;ENST00000452423;ENST00000442977;ENST00000312046;ENST00000449762;ENST00000297447	.|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	5.48|5.48	5.48|5.48	0.80851|0.80851	.|TLDc (2);	.|0.054965	.|0.85682	.|D	.|0.000000	T|T	0.82204|0.82204	0.4986|0.4986	H|H	0.97540|0.97540	4.025|4.025	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D	.|0.89917	.|0.999;0.999;1.0;0.999;0.992;0.998	.|D;D;D;D;D;D	.|0.81914	.|0.991;0.987;0.995;0.977;0.942;0.983	D|D	0.88810|0.88810	0.3291|0.3291	5|10	.|0.87932	.|D	.|0	-15.1603|-15.1603	15.5747|15.5747	0.76368|0.76368	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|705;740;739;82;109;712	.|Q8N573-2;Q8N573;D3HIS6;B7Z8N5;Q8N573-4;Q8N573-5	.|.;OXR1_HUMAN;.;.;.;.	L|N	383|712;712;739;160;740;705;82;109	.|ENSP00000402918:Y712N;ENSP00000431966:Y712N;ENSP00000429205:Y739N;ENSP00000395032:Y160N;ENSP00000405424:Y740N;ENSP00000311026:Y705N;ENSP00000408659:Y82N;ENSP00000297447:Y109N	.|ENSP00000297447:Y109N	F|Y	+|+	3|1	2|0	OXR1|OXR1	107821798|107821798	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.040000|8.040000	0.89188|0.89188	2.066000|2.066000	0.61787|0.61787	0.533000|0.533000	0.62120|0.62120	TTT|TAT	.	.	.	none		0.383	OXR1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_181354		A	107752622	T	A	107752622	3	1	71	1	0	0	0	0	1	0	0	0	11341	1754	61	5	2383	5	OXR1	8	107752622	Missense_Mutation	SNP	T	TCGA-AL-3466-01A-01D-1252-08		107752622	38611400	18	4669											
AKNA	80709	hgsc.bcm.edu	37	chr9	117139726	117139726	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccatctggctcctcttcagTcatgtccagctgacggccct	5	11	8	17	1	4	1	2	1	2	0	6	1	6	1	4	2	1	2	4	2	0	1	rs371041163		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr9:117139726T>C	ENST00000307564.4	-	3	522	c.361A>G	c.(361-363)Act>Gct	p.T121A	AKNA_ENST00000223791.3_5'Flank|AKNA_ENST00000374088.3_Missense_Mutation_p.T121A|AKNA_ENST00000374075.5_Missense_Mutation_p.T40A|AKNA_ENST00000312033.3_Missense_Mutation_p.T121A	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	121					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						TCCTCTTCAGTCATGTCCAGC	0.602																																					p.T121A		Atlas-SNP	.											.	AKNA	119	.	0			c.A361G						PASS	.						44	45	45					9																	117139726		2203	4300	6503	SO:0001583	missense	80709	exon3			CTTCAGTCATGTC	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.361A>G	chr9.hg19:g.117139726T>C	ENSP00000303769:p.Thr121Ala	129.0	0.0	.		163.0	84.0	.	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	hg19	CCDS6805.1	.	.	.	.	.	.	.	.	.	.	T	17.95	3.512748	0.64522	.	.	ENSG00000106948	ENST00000307564;ENST00000374088;ENST00000374075;ENST00000312033;ENST00000394574	T;T;T;T	0.32272	2.69;2.69;2.7;1.46	4.58	0.597	0.17504	.	0.519095	0.16285	N	0.221162	T	0.18759	0.0450	L	0.27053	0.805	0.80722	D	1	B;B;B	0.33807	0.22;0.075;0.426	B;B;B	0.37692	0.208;0.035;0.256	T	0.06954	-1.0798	10	0.34782	T	0.22	-4.4222	3.703	0.08390	0.3391:0.1032:0.0:0.5577	.	121;121;40	Q7Z591-6;Q7Z591;Q7Z591-2	.;AKNA_HUMAN;.	A	121;121;40;121;121	ENSP00000303769:T121A;ENSP00000363201:T121A;ENSP00000363188:T40A;ENSP00000309222:T121A	ENSP00000303769:T121A	T	-	1	0	AKNA	116179547	0.975000	0.34042	0.174000	0.22961	0.155000	0.21991	0.491000	0.22419	0.172000	0.19760	0.379000	0.24179	ACT	.	.	.	alt		0.602	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767		C	117139726	T	C	117139726	3	2	71	1	0	0	0	0	1	0	0	0	463	1667	58	3	4038	3	AKNA	9	117139726	Missense_Mutation	SNP	T	TCGA-AL-3466-01A-01D-1252-08		117139726	24073705	19	4670											
DBC1	1620	hgsc.bcm.edu	37	chr9	121930244	121930244	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgaactgctcgctccgctcCgagtccacgttctgtggttc	5	12	10	14	4	1	1	0	1	1	0	6	2	4	1	3	1	2	5	3	1	1	2	rs370346617		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr9:121930244C>T	ENST00000265922.3	-	8	1865	c.1404G>A	c.(1402-1404)tcG>tcA	p.S468S	BRINP1_ENST00000482797.1_Intron	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	468					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)											CGCTCCGCTCCGAGTCCACGT	0.592																																					p.S468S		Atlas-SNP	.											.	DBC1	194	.	0			c.G1404A						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	149	122	131		1404	0.4	1	9		131	0,8600		0,0,4300	no	coding-synonymous	DBC1	NM_014618.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		468/762	121930244	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1620	exon8			CCGCTCCGAGTCC	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.1404G>A	chr9.hg19:g.121930244C>T		92.0	0.0	.		107.0	26.0	.	NM_014618	Q6IPV6|Q6P1A0|Q8WU22	Silent	SNP	ENST00000265922.3	hg19	CCDS6822.1																																																																																			.	.	.	weak		0.592	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618		T	121930244	C	T	121930244	2	4	71	1	0	0	0	0	0	0	0	1	4249	639	23	1		1	DBC1	9	121930244	Silent	SNP	C	TCGA-AL-3466-01A-01D-1252-08	4790518	121930244	19283187	20	4671											
GTPBP4	23560	hgsc.bcm.edu	37	chr10	1043230	1043230	+	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	gggtacccaaatgttgggaaGtccagcttcatcaacaaggt	12	9	11	9	0	2	0	2	0	0	0	3	1	3	1	2	3	3	3	2	3	5	3			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr10:1043230G>A	ENST00000360803.4	+	5	625	c.543G>A	c.(541-543)aaG>aaA	p.K181K	GTPBP4_ENST00000538293.1_Silent_p.K65K|GTPBP4_ENST00000491635.1_3'UTR|GTPBP4_ENST00000545048.1_Silent_p.K134K	NM_012341.2	NP_036473.2	Q9BZE4	NOG1_HUMAN	GTP binding protein 4	181	OBG-type G. {ECO:0000255|PROSITE- ProRule:PRU01047}.				GTP catabolic process (GO:0006184)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of collagen binding (GO:0033342)|negative regulation of DNA replication (GO:0008156)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein stabilization (GO:0050821)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|ribosome biogenesis (GO:0042254)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(1)	21		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)		ATGTTGGGAAGTCCAGCTTCA	0.443																																					p.K181K		Atlas-SNP	.											.	GTPBP4	57	.	0			c.G543A						PASS	.						180	169	172					10																	1043230		2203	4300	6503	SO:0001819	synonymous_variant	23560	exon5			TGGGAAGTCCAGC	AK001548	CCDS31132.1	10p15-p14	2007-07-27			ENSG00000107937	ENSG00000107937			21535	protein-coding gene	gene with protein product	"G protein-binding protein CRFG", " GTP-binding protein"					11316846	Standard	NM_012341		Approved	CRFG, NGB, FLJ10690, FLJ10686, NOG1	uc001ift.3	Q9BZE4	OTTHUMG00000017538	ENST00000360803.4:c.543G>A	chr10.hg19:g.1043230G>A		390.0	1.0	.		456.0	204.0	.	NM_012341	B3KMC5|B4DY13|B7Z7A3|O95446|Q5T3R8|Q9NVJ8	Silent	SNP	ENST00000360803.4	hg19	CCDS31132.1																																																																																			.	.	.	none		0.443	GTPBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046412.1	NM_012341		A	1043230	G	A	1043230	2	1	71	1	0	0	0	0	0	0	0	1	6889	1020	36	2		2	GTPBP4	10	1043230	Silent	SNP	G	TCGA-AL-3466-01A-01D-1252-08		1043230	134491517	21	4672											
PIK3C2A	5286	hgsc.bcm.edu	37	chr11	17190402	17190402	+	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	gatcctttgctagcaaacttGaaacatttttctcttcctca	10	16	4	11	0	2	1	1	1	1	0	5	2	4	1	2	0	4	2	2	0	3	6			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr11:17190402G>A	ENST00000265970.7	-	1	886	c.887C>T	c.(886-888)tCa>tTa	p.S296L	PIK3C2A_ENST00000531428.1_Intron|PIK3C2A_ENST00000540361.1_Intron	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	296					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						TAGCAAACTTGAAACATTTTT	0.393																																					p.S296L		Atlas-SNP	.											.	PIK3C2A	148	.	0			c.C887T						PASS	.						176	170	172					11																	17190402		2200	4293	6493	SO:0001583	missense	5286	exon1			AAACTTGAAACAT	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.887C>T	chr11.hg19:g.17190402G>A	ENSP00000265970:p.Ser296Leu	276.0	0.0	.		278.0	59.0	.	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	hg19	CCDS7824.1	.	.	.	.	.	.	.	.	.	.	G	10.03	1.239126	0.22711	.	.	ENSG00000011405	ENST00000265970;ENST00000544896	T	0.62639	0.01	5.49	5.49	0.81192	.	1.281530	0.04815	N	0.435973	T	0.54838	0.1883	N	0.19112	0.55	0.54753	D	0.999987	B;B	0.26258	0.145;0.0	B;B	0.21708	0.036;0.0	T	0.09422	-1.0675	10	0.51188	T	0.08	-3.6563	15.6995	0.77533	0.0:0.137:0.863:0.0	.	296;296	F5H5W9;O00443	.;P3C2A_HUMAN	L	296	ENSP00000265970:S296L	ENSP00000265970:S296L	S	-	2	0	PIK3C2A	17146978	0.228000	0.23718	0.359000	0.25824	0.485000	0.33311	1.793000	0.38764	2.570000	0.86706	0.563000	0.77884	TCA	.	.	.	none		0.393	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		A	17190402	G	A	17190402	3	1	71	1	0	0	0	0	1	0	0	0	11916	1294	45	2	4301	2	PIK3C2A	11	17190402	Missense_Mutation	SNP	G	TCGA-AL-3466-01A-01D-1252-08		17190402	117816114	22	4673											
MS4A12	54860	hgsc.bcm.edu	37	chr11	60268545	60268545	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agatcatggttggattgatgCacattggttttggaattgtt	9	17	12	3	0	1	2	1	1	0	1	1	4	1	4	0	4	1	4	0	4	1	7			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr11:60268545C>T	ENST00000016913.4	+	3	361	c.304C>T	c.(304-306)Cac>Tac	p.H102Y	MS4A12_ENST00000537076.1_Intron	NM_017716.2	NP_060186.2	Q9NXJ0	M4A12_HUMAN	membrane-spanning 4-domains, subfamily A, member 12	102						integral component of membrane (GO:0016021)				breast(1)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)	17						TGGATTGATGCACATTGGTTT	0.373																																					p.H102Y		Atlas-SNP	.											.	MS4A12	44	.	0			c.C304T						PASS	.						292	286	288					11																	60268545		2203	4300	6503	SO:0001583	missense	54860	exon3			TTGATGCACATTG	AK000224	CCDS7988.1, CCDS53638.1	11q12	2008-03-25				ENSG00000071203			13370	protein-coding gene	gene with protein product		606550				11401424, 11486273	Standard	NM_017716		Approved	Ms4a10, FLJ20217	uc001npr.3	Q9NXJ0		ENST00000016913.4:c.304C>T	chr11.hg19:g.60268545C>T	ENSP00000016913:p.His102Tyr	591.0	0.0	.		298.0	44.0	.	NM_017716	F5GX98|Q8N6L4	Missense_Mutation	SNP	ENST00000016913.4	hg19	CCDS7988.1	.	.	.	.	.	.	.	.	.	.	C	13.57	2.277327	0.40294	.	.	ENSG00000071203	ENST00000016913;ENST00000530007	T;T	0.58506	4.27;0.33	5.14	5.14	0.70334	.	0.454353	0.25506	N	0.030212	T	0.66177	0.2763	L	0.55990	1.75	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.62243	-0.6895	10	0.02654	T	1	.	14.0807	0.64919	0.0:1.0:0.0:0.0	.	102	Q9NXJ0	M4A12_HUMAN	Y	102	ENSP00000016913:H102Y;ENSP00000434783:H102Y	ENSP00000016913:H102Y	H	+	1	0	MS4A12	60025121	0.679000	0.27596	0.572000	0.28498	0.095000	0.18619	2.340000	0.43974	2.375000	0.81037	0.462000	0.41574	CAC	.	.	.	none		0.373	MS4A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383627.1			T	60268545	C	T	60268545	3	4	71	1	0	0	0	0	1	0	0	0	9863	710	25	2	310	2	MS4A12	11	60268545	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08	43078143	60268545	74737971	23	4674											
VWCE	220001	hgsc.bcm.edu	37	chr11	61026692	61026692	+	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	gctacagttgacaggggcctCagtgtctccatgcaggctcc	7	9	12	13	0	2	1	1	1	1	0	4	1	3	1	3	3	2	4	3	3	1	2			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr11:61026692C>A	ENST00000335613.5	-	20	2709	c.2323G>T	c.(2323-2325)Gag>Tag	p.E775*	VWCE_ENST00000535710.1_Nonsense_Mutation_p.E240*	NM_152718.2	NP_689931.2	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	775						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						ACAGGGGCCTCAGTGTCTCCA	0.567																																					p.E775X		Atlas-SNP	.											.	VWCE	84	.	0			c.G2323T						PASS	.						40	42	41					11																	61026692		2203	4299	6502	SO:0001587	stop_gained	220001	exon20			GGGCCTCAGTGTC	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.2323G>T	chr11.hg19:g.61026692C>A	ENSP00000334186:p.Glu775*	117.0	0.0	.		112.0	22.0	.	NM_152718	A5PKV0|Q7Z7L6|Q86WK8	Nonsense_Mutation	SNP	ENST00000335613.5	hg19	CCDS8002.1	.	.	.	.	.	.	.	.	.	.	C	37	6.304859	0.97458	.	.	ENSG00000167992	ENST00000335613;ENST00000535710	.	.	.	4.63	-0.214	0.13161	.	0.840398	0.09913	N	0.739540	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	.	3.1614	0.06521	0.1831:0.4481:0.0:0.3689	.	.	.	.	X	775;240	.	ENSP00000334186:E775X	E	-	1	0	VWCE	60783268	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.666000	0.05280	0.047000	0.15862	-0.982000	0.02568	GAG	.	.	.	none		0.567	VWCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398811.1	NM_152718		A	61026692	C	A	61026692	4	1	71	1	0	0	0	0	0	1	0	0	17257	835	29	4	548	4	VWCE	11	61026692	Nonsense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08	758147	61026692	73979824	24	4675											
M6PR	4074	hgsc.bcm.edu	37	chr12	9096395	9096395	+	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	tatacaacacagggtgcctcAccgctagggtgtgtcgattg	9	10	12	10	2	1	0	1	0	0	0	2	1	1	0	2	2	3	1	2	2	4	4			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr12:9096395A>G	ENST00000000412.3	-	4	922		c.e4+1			NM_002355.3	NP_002346.1	P20645	MPRD_HUMAN	mannose-6-phosphate receptor (cation dependent)						endosome to lysosome transport (GO:0008333)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	mannose binding (GO:0005537)|mannose transmembrane transporter activity (GO:0015578)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(1)	11		Hepatocellular(102;0.137)		BRCA - Breast invasive adenocarcinoma(232;0.0146)	Alglucosidase alfa(DB01272)	AGGGTGCCTCACCGCTAGGGT	0.527																																					.		Atlas-SNP	.											.	M6PR	33	.	0			c.453+2T>C						PASS	.						79	64	69					12																	9096395		2203	4300	6503	SO:0001630	splice_region_variant	4074	exon5			TGCCTCACCGCTA		CCDS8598.1, CCDS73440.1	12p13.31	2013-09-20			ENSG00000003056	ENSG00000003056			6752	protein-coding gene	gene with protein product		154540					Standard	NM_002355		Approved		uc001qvf.3	P20645	OTTHUMG00000168276	ENST00000000412.3:c.453+1T>C	chr12.hg19:g.9096395A>G		150.0	0.0	.		100.0	18.0	.	NM_002355	A8K528|D3DUV5	Splice_Site	SNP	ENST00000000412.3	hg19	CCDS8598.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.111457	0.77210	.	.	ENSG00000003056	ENST00000000412;ENST00000537621	.	.	.	5.71	5.71	0.89125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6658	0.77227	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	M6PR	8987662	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.075000	0.76798	2.191000	0.70037	0.528000	0.53228	.	.	.	.	none		0.527	M6PR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399130.1		Intron	G	9096395	A	G	9096395	5	3	71	1	0	0	0	0	0	0	1	0	9147	173	6	3	394	3	M6PR	12	9096395	Splice_Site	SNP	A	TCGA-AL-3466-01A-01D-1252-08		9096395	124755500	25	4676											
MEIS2	4212	hgsc.bcm.edu	37	chr15	37184626	37184626	+	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	ctcattcccataggaccaccCtgagaaacgtagtcccctgg	10	8	8	15	1	1	1	1	1	0	1	3	3	3	2	5	2	1	1	5	2	3	3			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr15:37184626C>A	ENST00000561208.1	-	12	1600	c.1182G>T	c.(1180-1182)caG>caT	p.Q394H	MEIS2_ENST00000559408.1_5'Flank|MEIS2_ENST00000444725.1_3'UTR|MEIS2_ENST00000397620.2_3'UTR|MEIS2_ENST00000557796.2_3'UTR|MEIS2_ENST00000382766.2_Missense_Mutation_p.Q387H|MEIS2_ENST00000340545.5_3'UTR|MEIS2_ENST00000338564.5_Missense_Mutation_p.Q387H|MEIS2_ENST00000559085.1_3'UTR|MEIS2_ENST00000397624.3_3'UTR|MEIS2_ENST00000219869.9_3'UTR|MEIS2_ENST00000424352.2_3'UTR			O14770	MEIS2_HUMAN	Meis homeobox 2	394	Transcriptional activation domain.				eye development (GO:0001654)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas development (GO:0031016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	36		all_epithelial(112;9.77e-14)|Lung NSC(122;1.42e-09)|all_lung(180;2.2e-08)|Ovarian(310;0.134)|Melanoma(134;0.155)		all cancers(64;9.33e-21)|GBM - Glioblastoma multiforme(113;1.71e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0288)		TAGGACCACCCTGAGAAACGT	0.458																																					p.Q394H		Atlas-SNP	.											MEIS2,right_lower_lobe,carcinoma,0,1	MEIS2	99	.	0			c.G1182T						PASS	.						187	188	188					15																	37184626		2201	4297	6498	SO:0001583	missense	4212	exon12			ACCACCCTGAGAA	AF017418	CCDS10044.1, CCDS10045.1, CCDS42014.1, CCDS45217.1, CCDS45218.1, CCDS45219.1, CCDS45220.1	15q14	2011-06-20	2007-02-15		ENSG00000134138	ENSG00000134138		"Homeoboxes / TALE class"	7001	protein-coding gene	gene with protein product		601740	"Meis (mouse) homolog 2", "Meis1, myeloid ecotropic viral integration site 1 homolog 2 (mouse)"			9383298	Standard	NM_172315		Approved	MRG1, HsT18361	uc001zjr.4	O14770	OTTHUMG00000129781	ENST00000561208.1:c.1182G>T	chr15.hg19:g.37184626C>A	ENSP00000453793:p.Gln394His	591.0	1.0	.		214.0	59.0	.	NM_170675	A6NJI5|A8MWD5|B3KP98|B3KPQ6|Q96DI2|Q96KI4|Q96KI5|Q9NRS1|Q9NRS2|Q9NRS3	Missense_Mutation	SNP	ENST00000561208.1	hg19	CCDS10044.1	.	.	.	.	.	.	.	.	.	.	C	11.46	1.645203	0.29246	.	.	ENSG00000134138	ENST00000314177;ENST00000338564;ENST00000382766	D;D	0.86627	-2.15;-2.15	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.78046	0.4222	N	0.12182	0.205	0.80722	D	1	B;B;B;B	0.13145	0.001;0.002;0.001;0.007	B;B;B;B	0.13407	0.002;0.002;0.002;0.009	T	0.71087	-0.4694	10	0.22706	T	0.39	-1.914	18.9968	0.92817	0.0:1.0:0.0:0.0	.	387;394;374;90	O14770-4;O14770;B7Z6F6;Q6V703	.;MEIS2_HUMAN;.;.	H	394;387;387	ENSP00000341400:Q387H;ENSP00000372216:Q387H	ENSP00000326296:Q394H	Q	-	3	2	MEIS2	34971918	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.801000	0.69115	2.705000	0.92388	0.655000	0.94253	CAG	.	.	.	none		0.458	MEIS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252003.2	NM_170677		A	37184626	C	A	37184626	3	1	71	1	0	0	0	0	1	0	0	0	9475	680	24	4	255	4	MEIS2	15	37184626	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08		37184626	65346766	26	4677											
CRISPLD2	83716	hgsc.bcm.edu	37	chr16	84940197	84940197	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttcttctttttttcagcctGgggactcctcgggatggaaa	6	16	10	9	1	3	0	1	0	2	0	5	3	4	3	2	4	1	0	2	4	1	5			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr16:84940197G>A	ENST00000262424.5	+	15	1667	c.1443G>A	c.(1441-1443)ctG>ctA	p.L481L	CRISPLD2_ENST00000567845.1_Silent_p.L480L	NM_031476.3	NP_113664.1	Q9H0B8	CRLD2_HUMAN	cysteine-rich secretory protein LCCL domain containing 2	481	LCCL 2. {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						TTTTCAGCCTGGGGACTCCTC	0.597																																					p.L481L		Atlas-SNP	.											.	CRISPLD2	36	.	0			c.G1443A						PASS	.						54	58	57					16																	84940197		2199	4300	6499	SO:0001819	synonymous_variant	83716	exon15			CAGCCTGGGGACT	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.1443G>A	chr16.hg19:g.84940197G>A		256.0	0.0	.		282.0	59.0	.	NM_031476	D3DUM0|Q6P590|Q6UWH0|Q6UXC6|Q96IB1|Q96K61	Silent	SNP	ENST00000262424.5	hg19	CCDS10949.1																																																																																			.	.	.	none		0.597	CRISPLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269086.2	NM_031476		A	84940197	G	A	84940197	2	1	71	1	0	0	0	0	0	0	0	1	3885	1335	47	2		2	CRISPLD2	16	84940197	Silent	SNP	G	TCGA-AL-3466-01A-01D-1252-08		84940197	5414556	27	4678											
NGFR	4804	hgsc.bcm.edu	37	chr17	47588006	47588006	+	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	gctgtggttgtgggccttgtGgcctacatagccttcaagag	6	12	14	9	0	1	1	1	0	0	1	1	1	1	1	3	3	2	2	3	3	3	5			TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr17:47588006G>T	ENST00000172229.3	+	4	926	c.801G>T	c.(799-801)gtG>gtT	p.V267V	RP5-1029K10.2_ENST00000514506.1_RNA|NGFR_ENST00000504201.1_Silent_p.V173V	NM_002507.3	NP_002498.1	P08138	TNR16_HUMAN	nerve growth factor receptor	267					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)					TGGGCCTTGTGGCCTACATAG	0.577																																					p.V267V		Atlas-SNP	.											.	NGFR	46	.	0			c.G801T						PASS	.						112	101	105					17																	47588006		2203	4300	6503	SO:0001819	synonymous_variant	4804	exon4			CCTTGTGGCCTAC	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.801G>T	chr17.hg19:g.47588006G>T		205.0	0.0	.		333.0	56.0	.	NM_002507	B2R961|B4E096	Silent	SNP	ENST00000172229.3	hg19	CCDS11549.1																																																																																			.	.	.	none		0.577	NGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365150.1			T	47588006	G	T	47588006	2	4	71	1	0	0	0	0	0	0	0	1	10403	1335	47	4		4	NGFR	17	47588006	Silent	SNP	G	TCGA-AL-3466-01A-01D-1252-08		47588006	33607204	28	4679											
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43514887	43514888	+	Frame_Shift_Ins	INS	-	-	A																															tccacagcatttgcacagacINSagagtcccaaagggcatctc																										TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chr18:43514887_43514888insA	ENST00000282041.5	-	11	2178_2179	c.2144_2145insT	c.(2143-2145)ctgfs	p.L715fs		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	715					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						TTTGCACAGACAGAGTCCCAAA	0.495																																					p.L715fs		Atlas-INDEL	.											.	EPG5	199	.	0			c.2145_2146insT						PASS	.																																			SO:0001589	frameshift_variant	57724	exon11			.	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.2145dupT	chr18.hg19:g.43514888_43514888dupA	ENSP00000282041:p.Leu715fs	123.0	0.0	0		151.0	34.0	0.225166	NM_020964	A2BDF3|Q9H8C8	Frame_Shift_Ins	INS	ENST00000282041.5	hg19	CCDS11926.2																																																																																			.	.	.	none		0.495	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		A	43514888	-	A	43514887	7	5	71	1	0	1	1	0	0	0	0	0	8256	465	17	0	5730	0	KIAA1632	18	43514887	Frame_Shift_Ins	INS	-	TCGA-AL-3466-01A-01D-1252-08		43514887	34562361	29	4680											
MAOB	4129	hgsc.bcm.edu	37	chrX	43655071	43655071	+	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	caggcctctccagcttcactCggtctccaaggaggtccatt	7	10	9	15	1	3	0	1	0	2	0	7	1	4	1	4	4	1	1	4	4	1	2	rs143144504		TCGA-AL-3466-01A-01D-1252-08	TCGA-AL-3466-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	75de0b05-e8e7-4591-99ef-c50d0772ca3b	656d840f-c095-487f-9c3a-712f21c7cdc8	g.chrX:43655071C>A	ENST00000378069.4	-	7	830	c.683G>T	c.(682-684)cGa>cTa	p.R228L	MAOB_ENST00000536181.1_Missense_Mutation_p.R212L|MAOB_ENST00000538942.1_Missense_Mutation_p.R212L|MAOB_ENST00000487544.1_5'Flank	NM_000898.4	NP_000889.3	P27338	AOFB_HUMAN	monoamine oxidase B	228					negative regulation of serotonin secretion (GO:0014063)|positive regulation of dopamine metabolic process (GO:0045964)|response to aluminum ion (GO:0010044)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|primary amine oxidase activity (GO:0008131)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(2)|skin(5)	21					Amantadine(DB00915)|Amphetamine(DB00182)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Procaine(DB00721)|Rasagiline(DB01367)|Selegiline(DB01037)|Sertraline(DB01104)|Tranylcypromine(DB00752)|Zonisamide(DB00909)	CAGCTTCACTCGGTCTCCAAG	0.478																																					p.R228L		Atlas-SNP	.											.	MAOB	52	.	0			c.G683T						PASS	.						152	126	135					X																	43655071		2203	4300	6503	SO:0001583	missense	4129	exon7			TTCACTCGGTCTC		CCDS14261.1	Xp11.4-p11.3	2008-02-05			ENSG00000069535	ENSG00000069535	1.4.3.4		6834	protein-coding gene	gene with protein product		309860					Standard	NM_000898		Approved		uc004dfz.4	P27338	OTTHUMG00000021388	ENST00000378069.4:c.683G>T	chrX.hg19:g.43655071C>A	ENSP00000367309:p.Arg228Leu	103.0	0.0	.		117.0	6.0	.	NM_000898	B2R6R3|B7Z5H3|D3DWC3|Q7Z6S2	Missense_Mutation	SNP	ENST00000378069.4	hg19	CCDS14261.1	.	.	.	.	.	.	.	.	.	.	C	14.05	2.420375	0.42918	.	.	ENSG00000069535	ENST00000378069;ENST00000536181;ENST00000538942	T;T;T	0.10477	2.87;2.87;2.87	5.29	3.53	0.40419	Amine oxidase (1);	0.127637	0.53938	D	0.000045	T	0.16171	0.0389	M	0.84683	2.71	0.58432	D	0.999996	B;B	0.23316	0.083;0.007	B;B	0.25140	0.058;0.037	T	0.01810	-1.1269	10	0.40728	T	0.16	-3.8481	7.0564	0.25102	0.1391:0.7088:0.0:0.1521	.	212;228	B7Z5H3;P27338	.;AOFB_HUMAN	L	228;212;212	ENSP00000367309:R228L;ENSP00000441613:R212L;ENSP00000442240:R212L	ENSP00000367309:R228L	R	-	2	0	MAOB	43540015	0.561000	0.26578	0.751000	0.31187	0.638000	0.38207	1.705000	0.37867	0.550000	0.28991	0.529000	0.55759	CGA	.	C|1.000;T|0.000	.	alt		0.478	MAOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056303.1	NM_000898		A	43655071	C	A	43655071	3	1	71	1	0	0	0	0	1	0	0	0	9233	884	31	4	915	4	MAOB	23	43655071	Missense_Mutation	SNP	C	TCGA-AL-3466-01A-01D-1252-08		43655071	111615489	30	4681											
AMD1	262	hgsc.bcm.edu	37	chr6	111208734	111208734	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgggacatacttttgaaggAtgtgcaatgttcaatcataa	13	13	10	5	0	2	1	2	1	0	0	2	3	2	3	0	2	2	2	0	2	5	5			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr6:111208734A>G	ENST00000368885.3	+	2	473	c.137A>G	c.(136-138)gAt>gGt	p.D46G	AMD1_ENST00000451850.2_Intron|AMD1_ENST00000368877.5_Intron|AMD1_ENST00000368876.1_5'UTR|AMD1_ENST00000368882.3_Intron	NM_001634.4	NP_001625.2	P17707	DCAM_HUMAN	adenosylmethionine decarboxylase 1	46					cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|S-adenosylmethioninamine biosynthetic process (GO:0006557)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)|spermine biosynthetic process (GO:0006597)	cytosol (GO:0005829)	adenosylmethionine decarboxylase activity (GO:0004014)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(2)	8		all_cancers(87;3.83e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0209)		OV - Ovarian serous cystadenocarcinoma(136;0.0522)|Epithelial(106;0.111)|all cancers(137;0.143)	S-Adenosylmethionine(DB00118)	CTTTTGAAGGATGTGCAATGT	0.353																																					p.D46G		Atlas-SNP	.											.	AMD1	23	.	0			c.A137G						PASS	.						180	175	177					6																	111208734		2203	4300	6503	SO:0001583	missense	262	exon2			TGAAGGATGTGCA	M88006	CCDS5086.1, CCDS75504.1, CCDS75505.1	6q21	2014-05-13			ENSG00000123505	ENSG00000123505	4.1.1.50		457	protein-coding gene	gene with protein product		180980	"S-adenosylmethionine decarboxylase 1"				Standard	NM_001634		Approved	SAMDC	uc003puk.1	P17707	OTTHUMG00000015369	ENST00000368885.3:c.137A>G	chr6.hg19:g.111208734A>G	ENSP00000357880:p.Asp46Gly	271.0	0.0	.		305.0	53.0	.	NM_001634	E1P5F7|Q5VXN4|Q5VXN6|Q9BWK4	Missense_Mutation	SNP	ENST00000368885.3	hg19	CCDS5086.1	.	.	.	.	.	.	.	.	.	.	A	12.71	2.020888	0.35606	.	.	ENSG00000123505	ENST00000368885	.	.	.	5.46	4.31	0.51392	S-adenosylmethionine decarboxylase, core (2);	0.184022	0.56097	N	0.000026	T	0.18002	0.0432	N	0.08118	0	0.80722	D	1	B	0.06786	0.001	B	0.16722	0.016	T	0.06391	-1.0829	9	0.21014	T	0.42	.	11.2686	0.49124	0.9284:0.0:0.0716:0.0	.	46	P17707	DCAM_HUMAN	G	46	.	ENSP00000357880:D46G	D	+	2	0	AMD1	111315427	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	8.803000	0.91915	1.021000	0.39600	0.482000	0.46254	GAT	.	.	.	none		0.353	AMD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041816.1			G	111208734	A	G	111208734	3	3	72	1	0	0	0	0	1	0	0	0	566	333	12	3	143	3	AMD1	6	111208734	Missense_Mutation	SNP	A	TCGA-AL-3467-01A-01D-1252-08		111208734	59906333	1	4682											
SNX13	23161	hgsc.bcm.edu	37	chr7	17836512	17836512	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctcattcgaatacttttaTctctgcatggaacagcctct	9	16	5	11	1	3	0	1	0	3	0	6	2	3	1	1	1	4	1	1	1	4	5			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr7:17836512T>C	ENST00000409389.1	-	25	2769	c.2597A>G	c.(2596-2598)gAt>gGt	p.D866G	SNX13_ENST00000496855.1_5'UTR|SNX13_ENST00000428135.3_Missense_Mutation_p.D855G			Q9Y5W8	SNX13_HUMAN	sorting nexin 13	866					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)					AATACTTTTATCTCTGCATGG	0.318																																					p.D855G		Atlas-SNP	.											.	SNX13	113	.	0			c.A2564G						PASS	.						186	172	176					7																	17836512		1832	4093	5925	SO:0001583	missense	23161	exon25			CTTTTATCTCTGC	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.2597A>G	chr7.hg19:g.17836512T>C	ENSP00000386705:p.Asp866Gly	288.0	0.0	.		149.0	14.0	.	NM_015132	B2RCI9|O94821|Q8WVZ2|Q8WXH8	Missense_Mutation	SNP	ENST00000409389.1	hg19		.	.	.	.	.	.	.	.	.	.	T	24.8	4.576015	0.86645	.	.	ENSG00000071189	ENST00000409389;ENST00000428135;ENST00000242044	T;T	0.30714	1.52;1.52	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.52901	0.1763	M	0.65498	2.005	0.80722	D	1	D;P;D	0.67145	0.996;0.943;0.995	D;P;D	0.67548	0.952;0.867;0.94	T	0.55509	-0.8130	10	0.59425	D	0.04	-15.4175	15.4601	0.75349	0.0:0.0:0.0:1.0	.	652;866;855	B3KN60;B8ZZT9;Q9Y5W8-2	.;.;.	G	866;855;903	ENSP00000386705:D866G;ENSP00000398789:D855G	ENSP00000242044:D903G	D	-	2	0	SNX13	17803037	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.698000	0.84413	2.046000	0.60703	0.455000	0.32223	GAT	.	.	.	none		0.318	SNX13-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000327608.1	NM_015132		C	17836512	T	C	17836512	3	2	72	1	0	0	0	0	1	0	0	0	14897	1435	50	3	317	3	SNX13	7	17836512	Missense_Mutation	SNP	T	TCGA-AL-3467-01A-01D-1252-08		17836512	141302151	2	4683											
BRAF	673	hgsc.bcm.edu	37	chr7	140453136	140453136	+	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	acccactccatcgagatttcActgtagctagaccaaaatca	14	9	5	13	1	2	2	2	0	0	2	4	3	3	2	3	0	1	2	3	0	4	3	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		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.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(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)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	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.V600E	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,adenoma,0,1	BRAF	36346	.	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	c.T1799A						PASS	.						112	104	107					7																	140453136		2203	4300	6503	SO:0001583	missense	673	exon15	Familial Cancer Database	CFC, CFCS	GATTTCACTGTAG	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.1799T>A	chr7.hg19:g.140453136A>T	ENSP00000288602:p.Val600Glu	189.0	0.0	.		127.0	50.0	.	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	hg19	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	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|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA	.	.	.	weak		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		T	140453136	A	T	140453136	3	4	72	1	0	0	0	0	1	0	0	0	1498	159	6	5	517	5	BRAF	7	140453136	Missense_Mutation	SNP	A	TCGA-AL-3467-01A-01D-1252-08	122616624	140453136	18685527	3	4684											
GYLTL1B	120071	hgsc.bcm.edu	37	chr11	45948105	45948105	+	Missense_Mutation	SNP	A	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	tgggaacctgctgcggagagAgctctttgtgtgccccagcc	6	9	14	12	1	1	1	0	0	1	1	1	4	1	3	4	2	6	2	4	2	1	1			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr11:45948105A>C	ENST00000531526.1	+	9	1232	c.1121A>C	c.(1120-1122)gAg>gCg	p.E374A	GYLTL1B_ENST00000389968.3_Missense_Mutation_p.E101A|GYLTL1B_ENST00000529052.1_Missense_Mutation_p.E343A|GYLTL1B_ENST00000536139.1_Missense_Mutation_p.E343A|GYLTL1B_ENST00000401752.1_Missense_Mutation_p.E374A|GYLTL1B_ENST00000325468.5_Missense_Mutation_p.E374A	NM_152312.3	NP_689525.3	Q8N3Y3	LARG2_HUMAN	glycosyltransferase-like 1B	374					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)		CTGCGGAGAGAGCTCTTTGTG	0.567																																					p.E374A		Atlas-SNP	.											.	GYLTL1B	45	.	0			c.A1121C						PASS	.						72	74	74					11																	45948105		2203	4299	6502	SO:0001583	missense	120071	exon9			GGAGAGAGCTCTT		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.1121A>C	chr11.hg19:g.45948105A>C	ENSP00000432869:p.Glu374Ala	92.0	0.0	.		104.0	35.0	.	NM_152312	A6NN75|Q8N8Y6|Q8NAK3|Q8WY62	Missense_Mutation	SNP	ENST00000531526.1	hg19	CCDS31473.1	.	.	.	.	.	.	.	.	.	.	A	16.53	3.148701	0.57151	.	.	ENSG00000165905	ENST00000529052;ENST00000531526;ENST00000401752;ENST00000389968;ENST00000325468;ENST00000536139;ENST00000534410	T;T;T;D;T;T	0.83419	0.88;0.87;0.87;-1.72;0.87;0.88	5.45	4.32	0.51571	.	0.000000	0.85682	D	0.000000	T	0.80854	0.4703	M	0.66939	2.045	0.80722	D	1	P;B;B	0.36027	0.533;0.204;0.102	B;B;B	0.36418	0.224;0.099;0.068	T	0.79135	-0.1928	10	0.52906	T	0.07	-26.8748	11.3948	0.49836	0.9288:0.0:0.0712:0.0	.	343;343;374	B3KP69;E9PIZ2;Q8N3Y3	.;.;LARG2_HUMAN	A	343;374;374;101;374;343;35	ENSP00000431932:E343A;ENSP00000432869:E374A;ENSP00000385235:E374A;ENSP00000374618:E101A;ENSP00000324570:E374A;ENSP00000445044:E343A	ENSP00000324570:E374A	E	+	2	0	GYLTL1B	45904681	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	7.158000	0.77470	0.909000	0.36697	-0.411000	0.06167	GAG	.	.	.	none		0.567	GYLTL1B-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392572.1	NM_152312		C	45948105	A	C	45948105	3	2	72	1	0	0	0	0	1	0	0	0	6914	304	11	5	1151	5	GYLTL1B	11	45948105	Missense_Mutation	SNP	A	TCGA-AL-3467-01A-01D-1252-08		45948105	89058411	4	4685											
CPNE6	9362	hgsc.bcm.edu	37	chr14	24544466	24544466	+	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	ccaggagatgcaggaagggaCggcaaaccctgggcaggagg	12	2	18	9	1	0	1	0	0	0	1	0	5	0	4	2	7	2	3	2	7	2	0			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr14:24544466C>A	ENST00000397016.2	+	9	1069	c.758C>A	c.(757-759)aCg>aAg	p.T253K	CPNE6_ENST00000537691.1_Missense_Mutation_p.T308K|CPNE6_ENST00000216775.2_Missense_Mutation_p.T253K	NM_001280558.1	NP_001267487.1	O95741	CPNE6_HUMAN	copine VI (neuronal)	253					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)		CAGGAAGGGACGGCAAACCCT	0.567																																					p.T253K		Atlas-SNP	.											.	CPNE6	40	.	0			c.C758A						PASS	.						111	106	107					14																	24544466		2203	4300	6503	SO:0001583	missense	9362	exon8			AAGGGACGGCAAA	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.758C>A	chr14.hg19:g.24544466C>A	ENSP00000380211:p.Thr253Lys	250.0	1.0	.		271.0	121.0	.	NM_006032	B2RAG6|B7Z1M3|D3DS55|F5GXN1|Q53HA6|Q8WVG1	Missense_Mutation	SNP	ENST00000397016.2	hg19	CCDS9607.1	.	.	.	.	.	.	.	.	.	.	C	3.945	-0.013372	0.07727	.	.	ENSG00000100884	ENST00000537691;ENST00000397016;ENST00000216775	T;T;T	0.06294	3.32;3.34;3.34	5.13	5.13	0.70059	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.64402	D	0.000007	T	0.03783	0.0107	N	0.05487	-0.04	0.21020	N	0.999808	P;B	0.39326	0.668;0.192	B;B	0.40901	0.343;0.122	T	0.39165	-0.9627	10	0.05721	T	0.95	-31.3802	13.9546	0.64140	0.0:1.0:0.0:0.0	.	308;253	F5GXN1;O95741	.;CPNE6_HUMAN	K	308;253;253	ENSP00000440077:T308K;ENSP00000380211:T253K;ENSP00000216775:T253K	ENSP00000216775:T253K	T	+	2	0	CPNE6	23614306	0.908000	0.30866	0.997000	0.53966	0.900000	0.52787	0.035000	0.13797	2.676000	0.91093	0.467000	0.42956	ACG	.	.	.	none		0.567	CPNE6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071869.5			A	24544466	C	A	24544466	3	1	72	1	0	0	0	0	1	0	0	0	3818	536	19	4	784	4	CPNE6	14	24544466	Missense_Mutation	SNP	C	TCGA-AL-3467-01A-01D-1252-08		24544466	82805074	5	4686											
NPAS3	64067	hgsc.bcm.edu	37	chr14	34263109	34263109	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttttttttcgccagtgctgaAtaagggtcagtgtgtgacaa	9	15	11	6	1	1	2	1	2	0	0	2	2	1	2	1	1	1	1	1	1	3	5			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr14:34263109A>G	ENST00000356141.4	+	10	1160	c.1160A>G	c.(1159-1161)aAt>aGt	p.N387S	NPAS3_ENST00000346562.2_Missense_Mutation_p.N355S|NPAS3_ENST00000548645.1_Missense_Mutation_p.N357S|NPAS3_ENST00000357798.5_Missense_Mutation_p.N374S|NPAS3_ENST00000551492.1_Missense_Mutation_p.N392S			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3	387	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)		CCAGTGCTGAATAAGGGTCAG	0.368																																					p.N387S		Atlas-SNP	.											.	NPAS3	266	.	0			c.A1160G						PASS	.						107	102	103					14																	34263109		2203	4300	6503	SO:0001583	missense	64067	exon10			TGCTGAATAAGGG	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.1160A>G	chr14.hg19:g.34263109A>G	ENSP00000348460:p.Asn387Ser	196.0	0.0	.		199.0	16.0	.	NM_001164749	Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	Missense_Mutation	SNP	ENST00000356141.4	hg19	CCDS53891.1	.	.	.	.	.	.	.	.	.	.	A	12.93	2.085130	0.36758	.	.	ENSG00000151322	ENST00000551634;ENST00000551492;ENST00000346562;ENST00000548645;ENST00000356141;ENST00000357798	T;T;T;T;T;T	0.16743	2.32;2.32;2.32;2.32;2.32;2.32	5.79	5.79	0.91817	PAS fold-3 (1);PAS (2);	0.000000	0.85682	D	0.000000	T	0.10766	0.0263	N	0.04297	-0.235	0.80722	D	1	P;B;P;P	0.35542	0.508;0.351;0.508;0.508	B;B;B;B	0.37304	0.234;0.246;0.234;0.234	T	0.31696	-0.9934	10	0.39692	T	0.17	.	16.1299	0.81422	1.0:0.0:0.0:0.0	.	357;387;355;374	Q8IXF0-2;Q8IXF0;Q8IXF0-4;Q8IXF0-3	.;NPAS3_HUMAN;.;.	S	364;392;355;357;387;374	ENSP00000448373:N364S;ENSP00000450392:N392S;ENSP00000319610:N355S;ENSP00000448916:N357S;ENSP00000348460:N387S;ENSP00000350446:N374S	ENSP00000319610:N355S	N	+	2	0	NPAS3	33332860	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.292000	0.72725	2.213000	0.71641	0.455000	0.32223	AAT	.	.	.	none		0.368	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1			G	34263109	A	G	34263109	3	3	72	1	0	0	0	0	1	0	0	0	10571	101	4	3	1253	3	NPAS3	14	34263109	Missense_Mutation	SNP	A	TCGA-AL-3467-01A-01D-1252-08	9718643	34263109	73086431	6	4687											
GCOM1	100820829	hgsc.bcm.edu	37	chr15	57922023	57922023	+	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	agaggcagttggaggtagcgCaagttgaaaaccagctgcta	13	7	14	7	1	0	2	0	1	0	1	0	3	0	3	1	3	4	7	1	3	5	4			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr15:57922023C>G	ENST00000267853.5	+	6	743	c.649C>G	c.(649-651)Caa>Gaa	p.Q217E	GCOM1_ENST00000587652.1_Missense_Mutation_p.Q217E|GCOM1_ENST00000396180.1_Missense_Mutation_p.Q186E|GCOM1_ENST00000380569.2_Missense_Mutation_p.Q217E|GCOM1_ENST00000572390.1_Missense_Mutation_p.Q217E|GCOM1_ENST00000380560.2_Missense_Mutation_p.Q148E|POLR2M_ENST00000380563.2_5'UTR|GCOM1_ENST00000380568.3_Missense_Mutation_p.Q217E|GCOM1_ENST00000574161.1_Missense_Mutation_p.Q217E|MYZAP_ENST00000380565.4_Missense_Mutation_p.Q217E|GCOM1_ENST00000380561.2_Missense_Mutation_p.Q186E			P0CAP1	MYZAP_HUMAN	myocardial zonula adherens protein	217					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)											GGAGGTAGCGCAAGTTGAAAA	0.413																																					p.Q217E		Atlas-SNP	.											.	GCOM1	66	.	0			c.C649G						PASS	.						95	90	92					15																	57922023		2192	4292	6484	SO:0001583	missense	145781	exon6			GTAGCGCAAGTTG	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.649C>G	chr15.hg19:g.57922023C>G	ENSP00000267853:p.Gln217Glu	114.0	0.0	.		109.0	5.0	.	NM_001018090	D2E9U7|Q6EER8|Q6EES2|Q6EEV3|Q6EF00|Q6EF01|Q6EF02|Q6EF46|Q6EFN8|Q6EM48|Q6K046|Q6K050|Q6K051|Q6ZQZ3|Q8NC58|Q8NCF3|Q96DI5|Q96JB7|Q96NF5	Missense_Mutation	SNP	ENST00000267853.5	hg19	CCDS10162.1	.	.	.	.	.	.	.	.	.	.	C	8.397	0.841141	0.16891	.	.	ENSG00000137878	ENST00000380569;ENST00000380561;ENST00000396180;ENST00000380560;ENST00000267853;ENST00000380565;ENST00000380568	T;T;T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01;1.01;1.01	5.43	3.54	0.40534	.	0.231577	0.44688	D	0.000424	T	0.37652	0.1011	L	0.56769	1.78	0.43326	D	0.995354	P;P;P;B	0.43024	0.544;0.798;0.544;0.402	B;B;B;B	0.44044	0.346;0.439;0.346;0.346	T	0.14172	-1.0482	10	0.13108	T	0.6	-7.7731	7.7864	0.29095	0.2881:0.6345:0.0:0.0774	.	217;217;217;217	P0CAP1-2;P0CAP1-11;P0CAP1-4;P0CAP1	.;.;.;GCOM1_HUMAN	E	217;186;186;148;217;217;217	ENSP00000369943:Q217E;ENSP00000369935:Q186E;ENSP00000379483:Q186E;ENSP00000369933:Q148E;ENSP00000267853:Q217E;ENSP00000369939:Q217E;ENSP00000369942:Q217E	ENSP00000267853:Q217E	Q	+	1	0	GCOM1	55709315	0.992000	0.36948	0.004000	0.12327	0.268000	0.26511	3.376000	0.52417	0.642000	0.30620	0.650000	0.86243	CAA	.	.	.	none		0.413	MYZAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255716.2	NM_001018100		G	57922023	C	G	57922023	3	3	72	1	0	0	0	0	1	0	0	0	6311	711	25	4	671	4	GCOM1	15	57922023	Missense_Mutation	SNP	C	TCGA-AL-3467-01A-01D-1252-08		57922023	44609369	7	4688											
SRCAP	10847	hgsc.bcm.edu	37	chr16	30745323	30745323	+	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	aacttcaccacagcctatttCaaacaggtactaagtaagat	16	10	5	10	0	2	1	2	0	0	1	2	1	2	1	2	1	4	2	2	1	6	6			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr16:30745323C>G	ENST00000262518.4	+	30	6988	c.6603C>G	c.(6601-6603)ttC>ttG	p.F2201L	SRCAP_ENST00000395059.2_Missense_Mutation_p.F2139L|SRCAP_ENST00000344771.4_Missense_Mutation_p.F2043L	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	2201					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)			CAGCCTATTTCAAACAGGTAC	0.453																																					p.F2201L		Atlas-SNP	.											SRCAP,NS,carcinoma,0,2	SRCAP	298	.	0			c.C6603G						PASS	.						67	60	63					16																	30745323		2197	4300	6497	SO:0001583	missense	10847	exon30			CTATTTCAAACAG	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.6603C>G	chr16.hg19:g.30745323C>G	ENSP00000262518:p.Phe2201Leu	27.0	0.0	.		34.0	2.0	.	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	hg19	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	C	11.79	1.744801	0.30865	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	T;T;T	0.07800	3.16;3.16;3.16	5.24	2.95	0.34219	.	0.380726	0.22784	N	0.055681	T	0.11367	0.0277	N	0.13003	0.285	0.31625	N	0.649832	D;D	0.71674	0.998;0.997	D;D	0.80764	0.994;0.985	T	0.11446	-1.0587	10	0.34782	T	0.22	-14.3882	7.2742	0.26275	0.0:0.329:0.0:0.671	.	2139;2201	Q6ZRS2-2;Q6ZRS2	.;SRCAP_HUMAN	L	2201;2139;2043	ENSP00000262518:F2201L;ENSP00000378499:F2139L;ENSP00000343042:F2043L	ENSP00000262518:F2201L	F	+	3	2	SRCAP	30652824	0.995000	0.38212	1.000000	0.80357	0.948000	0.59901	0.370000	0.20433	0.414000	0.25790	-0.414000	0.06135	TTC	.	.	.	none		0.453	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		G	30745323	C	G	30745323	3	3	72	1	0	0	0	0	1	0	0	0	15147	825	29	4	6713	4	SRCAP	16	30745323	Missense_Mutation	SNP	C	TCGA-AL-3467-01A-01D-1252-08		30745323	59609430	8	4689											
CDH8	1006	hgsc.bcm.edu	37	chr16	61891030	61891031	+	Missense_Mutation	DNP	AG	AG	CT																															ttaggccacaaacctgtttcAggctcaatggaaaaataagg																										TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr16:61891030_61891031AG>CT	ENST00000577390.1	-	4	1613_1614	c.659_660CT>AG	c.(658-660)cCT>cAG	p.P220Q	CDH8_ENST00000584337.1_Missense_Mutation_p.P220Q|CDH8_ENST00000299345.6_Missense_Mutation_p.P220Q|CDH8_ENST00000577730.1_Missense_Mutation_p.P220Q	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	220	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|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)		AACCTGTTTCAGGCTCAATGGA	0.391																																					p.P220P|p.P220H		Atlas-SNP	.											.	CDH8	273	.	0			c.T660G|c.C659A						PASS	.																																			SO:0001583	missense	1006	exon4			TGTTTCAGGCTCA|GTTTCAGGCTCAA	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.659_660delinsCT	chr16.hg19:g.61891030_61891031delinsCT	ENSP00000462701:p.Pro220Gln	146.0|145.0	0.0	.		109.0|108.0	35.0|34.0	.	NM_001796	B3KWC1|Q14DC6|Q9ULB2	Silent|Missense_Mutation	SNP	ENST00000577390.1	hg19	CCDS10802.1																																																																																			.	.	.	none		0.391	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		CT	61891031	AG	CT	61891030	3	2	72	1	0	0	0	0	1	0	0	0	3118	175	7	5	1775	5	CDH8	16	61891030	Missense_Mutation	DNP	AG	TCGA-AL-3467-01A-01D-1252-08	31145707	61891030	28463723	9	4690											
ZMYND15	84225	hgsc.bcm.edu	37	chr17	4645266	4645266	+	Frame_Shift_Del	DEL	G	G	-																															gttagccaaaaccccaatgcGgacatggggtccccggccag																								rs200238712		TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr17:4645266delG	ENST00000433935.1	+	4	941	c.884delG	c.(883-885)cggfs	p.R295fs	CXCL16_ENST00000293778.6_5'Flank|CXCL16_ENST00000574412.1_5'Flank|ZMYND15_ENST00000592813.1_Frame_Shift_Del_p.R295fs|ZMYND15_ENST00000269289.6_Frame_Shift_Del_p.R295fs|ZMYND15_ENST00000573751.2_Frame_Shift_Del_p.R295fs	NM_001136046.2|NM_001267822.1	NP_001129518.1|NP_001254751.1	Q9H091	ZMY15_HUMAN	zinc finger, MYND-type containing 15	295					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						ACCCCAATGCGGACATGGGGT	0.577																																					p.R295fs		Atlas-INDEL	.											.	ZMYND15	87	.	0			c.883delC						PASS	.						79	84	82					17																	4645266		2203	4300	6503	SO:0001589	frameshift_variant	84225	exon4			.	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.884delG	chr17.hg19:g.4645266delG	ENSP00000391742:p.Arg295fs	222.0	0.0	0		224.0	83.0	0.370536	NM_001136046	B4DXY5|I3L296	Frame_Shift_Del	DEL	ENST00000433935.1	hg19	CCDS45584.1																																																																																			.	.	.	none		0.577	ZMYND15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439580.1	NM_032265		-	4645266	G	-	4645266	7	5	72	1	0	1	0	1	0	0	0	0	17720	1116	39	0	894	0	ZMYND15	17	4645266	Frame_Shift_Del	DEL	G	TCGA-AL-3467-01A-01D-1252-08		4645266	76549944	10	4691											
CDC27	996	hgsc.bcm.edu	37	chr17	45249350	45249350	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtagtacaactgtgtccttTcaagagtctatatgctttat	10	17	7	7	0	2	1	1	0	1	1	3	1	3	1	1	0	3	3	1	0	7	7			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr17:45249350T>C	ENST00000066544.3	-	3	277	c.184A>G	c.(184-186)Aaa>Gaa	p.K62E	CDC27_ENST00000527547.1_Missense_Mutation_p.K62E|RP5-867C24.5_ENST00000572193.1_RNA|CDC27_ENST00000531206.1_Missense_Mutation_p.K62E|CDC27_ENST00000528748.1_5'UTR|CDC27_ENST00000446365.2_Intron	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	62					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						CTGTGTCCTTTCAAGAGTCTA	0.348																																					p.K62E		Atlas-SNP	.											CDC27_ENST00000531206,NS,carcinoma,0,2	CDC27	337	.	0			c.A184G						PASS	.						42	41	41					17																	45249350		2202	4300	6502	SO:0001583	missense	996	exon3			GTCCTTTCAAGAG	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.184A>G	chr17.hg19:g.45249350T>C	ENSP00000066544:p.Lys62Glu	99.0	2.0	.		80.0	4.0	.	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	hg19	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	T	19.40	3.820387	0.71028	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000527547;ENST00000526866	T;T;T;T	0.73575	-0.76;-0.76;-0.76;-0.76	5.69	5.69	0.88448	Tetratricopeptide-like helical (1);	0.518646	0.23036	N	0.052667	T	0.70971	0.3285	L	0.39467	1.215	0.80722	D	1	B;P;P	0.46578	0.314;0.499;0.88	B;B;P	0.45099	0.082;0.112;0.469	T	0.74754	-0.3558	10	0.72032	D	0.01	-34.4674	13.8831	0.63693	0.0:0.0:0.0:1.0	.	62;62;62	G5EA36;G3V1C4;P30260	.;.;CDC27_HUMAN	E	62	ENSP00000066544:K62E;ENSP00000434614:K62E;ENSP00000437339:K62E;ENSP00000432105:K62E	ENSP00000066544:K62E	K	-	1	0	CDC27	42604349	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.803000	0.85983	2.173000	0.68751	0.482000	0.46254	AAA	.	.	.	none		0.348	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			C	45249350	T	C	45249350	3	2	72	1	0	0	0	0	1	0	0	0	3068	1792	62	3	2376	3	CDC27	17	45249350	Missense_Mutation	SNP	T	TCGA-AL-3467-01A-01D-1252-08	40604084	45249350	35945860	11	4692											
TBX4	9496	hgsc.bcm.edu	37	chr17	59560359	59560359	+	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	tccgttccccccctccctacGaccagcaaatgctgagcccc	7	7	6	21	2	0	1	0	1	0	0	3	2	3	1	8	0	4	3	8	0	2	2			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr17:59560359G>A	ENST00000240335.1	+	8	1165	c.1120G>A	c.(1120-1122)Gac>Aac	p.D374N	TBX4_ENST00000393853.4_Missense_Mutation_p.D375N|TBX4_ENST00000589449.1_3'UTR	NM_018488.2	NP_060958.2	P57082	TBX4_HUMAN	T-box 4	374					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						CCCTCCCTACGACCAGCAAAT	0.597																																					p.D374N		Atlas-SNP	.											TBX4,colon,carcinoma,0,1	TBX4	69	.	0			c.G1120A						PASS	.						66	58	61					17																	59560359		2203	4300	6503	SO:0001583	missense	9496	exon8			CCCTACGACCAGC	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.1120G>A	chr17.hg19:g.59560359G>A	ENSP00000240335:p.Asp374Asn	91.0	0.0	.		91.0	6.0	.	NM_018488	A5PKU7|B2RMT1|B7ZLV3	Missense_Mutation	SNP	ENST00000240335.1	hg19	CCDS11629.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.231687	0.79688	.	.	ENSG00000121075	ENST00000393853;ENST00000240335	D;D	0.85702	-2.02;-2.02	5.51	5.51	0.81932	.	0.377447	0.27455	N	0.019283	T	0.78805	0.4341	L	0.40543	1.245	0.58432	D	0.999997	P;P	0.47545	0.896;0.897	B;B	0.35971	0.215;0.212	T	0.79127	-0.1931	9	.	.	.	.	18.4116	0.90554	0.0:0.0:1.0:0.0	.	375;374	A5PKU7;P57082	.;TBX4_HUMAN	N	375;374	ENSP00000377435:D375N;ENSP00000240335:D374N	.	D	+	1	0	TBX4	56915141	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.574000	0.82434	2.590000	0.87494	0.655000	0.94253	GAC	.	.	.	none		0.597	TBX4-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449649.1	NM_018488		A	59560359	G	A	59560359	3	1	72	1	0	0	0	0	1	0	0	0	15672	1058	37	1	1150	1	TBX4	17	59560359	Missense_Mutation	SNP	G	TCGA-AL-3467-01A-01D-1252-08	14311009	59560359	21634851	12	4693											
CELSR1	9620	hgsc.bcm.edu	37	chr22	46785299	46785299	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgcacgtcattgccaaagAgcgtgcccgtgtgctgtgta	7	10	13	11	4	1	1	1	0	0	1	1	1	1	1	2	0	5	3	2	0	2	2			TCGA-AL-3467-01A-01D-1252-08	TCGA-AL-3467-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a74ffd4b-fa89-49ae-aa1d-3052a5440fa2	2ab402fb-392f-4441-a979-713a602c9cd3	g.chr22:46785299A>G	ENST00000262738.3	-	18	6442	c.6443T>C	c.(6442-6444)cTc>cCc	p.L2148P		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2148					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)		ATTGCCAAAGAGCGTGCCCGT	0.667																																					p.L2148P		Atlas-SNP	.											.	CELSR1	242	.	0			c.T6443C						PASS	.						48	41	43					22																	46785299		2203	4300	6503	SO:0001583	missense	9620	exon18			CCAAAGAGCGTGC	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.6443T>C	chr22.hg19:g.46785299A>G	ENSP00000262738:p.Leu2148Pro	93.0	0.0	.		107.0	6.0	.	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	hg19	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	A	8.527	0.870135	0.17322	.	.	ENSG00000075275	ENST00000262738	T	0.14516	2.5	4.99	3.96	0.45880	Domain of unknown function DUF3497 (1);	0.304522	0.25386	N	0.031042	T	0.20373	0.0490	M	0.68952	2.095	0.38634	D	0.951442	B;B	0.29136	0.234;0.097	B;B	0.37451	0.25;0.16	T	0.03728	-1.1009	10	0.66056	D	0.02	.	10.2827	0.43550	0.9208:0.0:0.0792:0.0	.	469;2148	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	P	2148	ENSP00000262738:L2148P	ENSP00000262738:L2148P	L	-	2	0	CELSR1	45163963	1.000000	0.71417	0.594000	0.28785	0.090000	0.18270	2.630000	0.46494	0.763000	0.33175	0.533000	0.62120	CTC	.	.	.	none		0.667	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		G	46785299	A	G	46785299	3	3	72	1	0	0	0	0	1	0	0	0	3223	304	11	3	2673	3	CELSR1	22	46785299	Missense_Mutation	SNP	A	TCGA-AL-3467-01A-01D-1252-08		46785299	4519267	13	4694											
ADAM15	8751	hgsc.bcm.edu	37	chr1	155032387	155032387	+	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	gtacctcctaggtctgtgacAgcaacaggcactgctactgt	9	10	10	12	0	1	1	0	1	1	0	2	1	2	1	2	2	5	4	2	2	4	3			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr1:155032387A>T	ENST00000356955.2	+	17	2106	c.2005A>T	c.(2005-2007)Agc>Tgc	p.S669C	ADAM15_ENST00000359280.4_Missense_Mutation_p.S669C|ADAM15_ENST00000449910.2_Missense_Mutation_p.S669C|ADAM15_ENST00000360674.4_Missense_Mutation_p.S669C|ADAM15_ENST00000368410.2_Missense_Mutation_p.S375C|ADAM15_ENST00000355956.2_Missense_Mutation_p.S669C|ADAM15_ENST00000531455.1_Missense_Mutation_p.S679C|ADAM15_ENST00000368412.3_Missense_Mutation_p.S669C|ADAM15_ENST00000472434.1_3'UTR|ADAM15_ENST00000368413.1_Missense_Mutation_p.S375C|ADAM15_ENST00000271836.6_Missense_Mutation_p.S669C	NM_207197.2	NP_997080.1	Q13444	ADA15_HUMAN	ADAM metallopeptidase domain 15	669	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)			GGTCTGTGACAGCAACAGGCA	0.557																																					p.S679C		Atlas-SNP	.											.	ADAM15	92	.	0			c.A2035T						PASS	.						143	141	142					1																	155032387		2203	4300	6503	SO:0001583	missense	8751	exon17			TGTGACAGCAACA	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.2005A>T	chr1.hg19:g.155032387A>T	ENSP00000349436:p.Ser669Cys	406.0	0.0	.		458.0	179.0	.	NM_001261464	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	hg19	CCDS1087.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.657238	0.88154	.	.	ENSG00000143537	ENST00000356955;ENST00000449910;ENST00000359280;ENST00000360674;ENST00000368412;ENST00000355956;ENST00000368410;ENST00000271836;ENST00000368413;ENST00000531455	D;D;D;D;D;D;D;D;D;D	0.88741	-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42	5.55	5.55	0.83447	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.53938	D	0.000051	D	0.94798	0.8320	M	0.91717	3.235	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;0.999;1.0;1.0;1.0;0.998;0.999;1.0	D;D;D;D;D;D;D;D;D;D	0.85130	0.986;0.971;0.981;0.969;0.994;0.994;0.997;0.967;0.989;0.986	D	0.95706	0.8753	10	0.87932	D	0	.	13.6954	0.62575	1.0:0.0:0.0:0.0	.	679;686;669;669;669;669;669;669;669;666	E9PN65;B7Z390;Q13444-10;Q13444-2;Q13444-4;Q13444-5;Q13444-3;Q13444-9;Q13444;Q59GF2	.;.;.;.;.;.;.;.;ADA15_HUMAN;.	C	669;669;669;669;669;669;375;669;375;679	ENSP00000349436:S669C;ENSP00000403843:S669C;ENSP00000352226:S669C;ENSP00000353892:S669C;ENSP00000357397:S669C;ENSP00000348227:S669C;ENSP00000357395:S375C;ENSP00000271836:S669C;ENSP00000357398:S375C;ENSP00000432927:S679C	ENSP00000271836:S669C	S	+	1	0	ADAM15	153299011	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.114000	0.89570	2.333000	0.79357	0.533000	0.62120	AGC	.	.	.	none		0.557	ADAM15-019	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387168.1	NM_003815		T	155032387	A	T	155032387	3	4	73	1	0	0	0	0	1	0	0	0	237	188	7	5	2071	5	ADAM15	1	155032387	Missense_Mutation	SNP	A	TCGA-AL-3468-01A-01D-1252-08		155032387	94218234	1	4695											
ASH1L	55870	hgsc.bcm.edu	37	chr1	155408153	155408153	+	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	tgctcttcttcctctggtaaTggcttctgcttttttctggt	2	21	8	10	0	5	0	0	0	5	0	6	0	6	0	1	3	2	4	1	3	1	7	rs369367522		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr1:155408153T>A	ENST00000368346.3	-	5	6432	c.5793A>T	c.(5791-5793)ccA>ccT	p.P1931P	ASH1L_ENST00000392403.3_Silent_p.P1931P			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	1931					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)			CCTCTGGTAATGGCTTCTGCT	0.363																																					p.P1931P		Atlas-SNP	.											.	ASH1L	279	.	0			c.A5793T						PASS	.						145	142	143					1																	155408153		2203	4300	6503	SO:0001819	synonymous_variant	55870	exon5			TGGTAATGGCTTC	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.5793A>T	chr1.hg19:g.155408153T>A		331.0	0.0	.		228.0	76.0	.	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Silent	SNP	ENST00000368346.3	hg19																																																																																				.	.	.	none		0.363	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		A	155408153	T	A	155408153	2	1	73	1	0	0	0	0	0	0	0	1	1041	1451	51	5		5	ASH1L	1	155408153	Silent	SNP	T	TCGA-AL-3468-01A-01D-1252-08	375766	155408153	93842468	2	4696											
ISG20L2	81875	hgsc.bcm.edu	37	chr1	156693972	156693972	+	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	gtttagcagcttcttggtgaGatgcttcagagacatggtgg	8	13	14	6	0	2	2	1	1	1	2	2	4	2	2	0	3	3	4	0	3	1	5			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr1:156693972G>A	ENST00000313146.6	-	2	1698	c.916C>T	c.(916-918)Ctc>Ttc	p.L306F	ISG20L2_ENST00000368219.1_Missense_Mutation_p.L306F|ISG20L2_ENST00000472824.2_5'UTR	NM_030980.1	NP_112242.1	Q9H9L3	I20L2_HUMAN	interferon stimulated exonuclease gene 20kDa-like 2	306	Exonuclease.				ribosome biogenesis (GO:0042254)	nucleus (GO:0005634)	exonuclease activity (GO:0004527)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TTCTTGGTGAGATGCTTCAGA	0.587																																					p.L306F		Atlas-SNP	.											.	ISG20L2	43	.	0			c.C916T						PASS	.						116	115	116					1																	156693972		2203	4300	6503	SO:0001583	missense	81875	exon2			TGGTGAGATGCTT	AK095697	CCDS1153.1	1q23.1	2013-10-11			ENSG00000143319	ENSG00000143319			25745	protein-coding gene	gene with protein product		611930				18065403	Standard	NM_030980		Approved	FLJ12671	uc001fps.1	Q9H9L3	OTTHUMG00000041301	ENST00000313146.6:c.916C>T	chr1.hg19:g.156693972G>A	ENSP00000323424:p.Leu306Phe	239.0	0.0	.		226.0	21.0	.	NM_030980	D3DVC6|Q64KA2	Missense_Mutation	SNP	ENST00000313146.6	hg19	CCDS1153.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.787888	0.90367	.	.	ENSG00000143319	ENST00000313146;ENST00000368219	T;T	0.34472	1.36;1.36	5.73	4.81	0.61882	Exonuclease (1);Exonuclease, RNase T/DNA polymerase III (1);Ribonuclease H-like (1);	0.146642	0.47093	D	0.000259	T	0.67618	0.2912	H	0.97291	3.975	0.58432	D	0.999995	D	0.76494	0.999	D	0.70227	0.968	T	0.78502	-0.2179	10	0.87932	D	0	-18.3136	13.9197	0.63923	0.0752:0.0:0.9248:0.0	.	306	Q9H9L3	I20L2_HUMAN	F	306	ENSP00000323424:L306F;ENSP00000357202:L306F	ENSP00000323424:L306F	L	-	1	0	ISG20L2	154960596	1.000000	0.71417	0.964000	0.40570	0.954000	0.61252	5.268000	0.65536	2.722000	0.93159	0.655000	0.94253	CTC	.	.	.	none		0.587	ISG20L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098969.1	NM_030980		A	156693972	G	A	156693972	3	1	73	1	0	0	0	0	1	0	0	0	7862	942	33	2	153	2	ISG20L2	1	156693972	Missense_Mutation	SNP	G	TCGA-AL-3468-01A-01D-1252-08	1285819	156693972	92556649	3	4697											
IGSF9	57549	hgsc.bcm.edu	37	chr1	159898194	159898194	+	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	agtcagccagggctgtgtaaGggggctctgcagtggcccca	7	7	16	11	0	2	0	1	0	1	0	2	0	2	0	3	4	2	4	3	4	1	1	rs374964822	byFrequency	TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr1:159898194G>T	ENST00000368094.1	-	19	3181	c.2984C>A	c.(2983-2985)cCt>cAt	p.P995H	TAGLN2_ENST00000478033.1_5'Flank|TAGLN2_ENST00000368097.4_5'Flank|IGSF9_ENST00000361509.3_Missense_Mutation_p.P979H|IGSF9_ENST00000493195.1_5'UTR	NM_001135050.1	NP_001128522.1	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9	995					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)			GGCTGTGTAAGGGGGCTCTGC	0.647																																					p.P995H		Atlas-SNP	.											.	IGSF9	123	.	0			c.C2984A						PASS	.						12	14	13					1																	159898194		2189	4271	6460	SO:0001583	missense	57549	exon19			GTGTAAGGGGGCT	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.2984C>A	chr1.hg19:g.159898194G>T	ENSP00000357073:p.Pro995His	26.0	0.0	.		15.0	8.0	.	NM_001135050		Missense_Mutation	SNP	ENST00000368094.1	hg19	CCDS44254.1	.	.	.	.	.	.	.	.	.	.	g	8.178	0.793234	0.16327	.	.	ENSG00000085552	ENST00000361509;ENST00000368094;ENST00000198587	T;T	0.68181	-0.31;-0.23	4.21	2.34	0.29019	.	0.791526	0.10306	U	0.690564	T	0.32376	0.0827	N	0.19112	0.55	0.20873	N	0.999834	P;P	0.46327	0.876;0.876	B;B	0.43360	0.417;0.237	T	0.07046	-1.0793	9	.	.	.	-0.7754	8.3059	0.32042	0.1977:0.0:0.8023:0.0	.	995;533	Q9P2J2;C9JI81	TUTLA_HUMAN;.	H	979;995;533	ENSP00000355049:P979H;ENSP00000357073:P995H	.	P	-	2	0	IGSF9	158164818	0.440000	0.25618	0.583000	0.28640	0.038000	0.13279	1.608000	0.36847	0.426000	0.26116	-0.119000	0.15052	CCT	.	.	.	none		0.647	IGSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059115.1	NM_020789		T	159898194	G	T	159898194	3	4	73	1	0	0	0	0	1	0	0	0	7612	1000	35	4	567	4	IGSF9	1	159898194	Missense_Mutation	SNP	G	TCGA-AL-3468-01A-01D-1252-08	3204222	159898194	89352427	4	4698											
LY9	4063	hgsc.bcm.edu	37	chr1	160771585	160771585	+	Intron	DEL	T	T	-																															attcaattttcccagcaccaTttattgaaaagttgtccgtc																										TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr1:160771585delT	ENST00000263285.6	+	2	484				LY9_ENST00000471816.1_Intron|LY9_ENST00000368039.2_Frame_Shift_Del_p.F154fs|LY9_ENST00000341032.4_Intron|LY9_ENST00000368037.5_Intron|LY9_ENST00000392203.4_Intron|LY9_ENST00000368040.1_Intron|LY9_ENST00000368041.2_Intron			Q9HBG7	LY9_HUMAN	lymphocyte antigen 9						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)			cccagcaccatttattgaaaa	0.473																																					p.P153fs		Atlas-INDEL	.											.	LY9	115	.	0			c.459delA						PASS	.						84	92	89					1																	160771585		2203	4300	6503	SO:0001627	intron_variant	4063	exon3			.	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.454+1713T>-	chr1.hg19:g.160771585delT		251.0	0.0	0		284.0	121.0	0.426056	NM_001033667	A8K7N3|Q14775|Q5VYI3|Q6P2J4|Q9H4N5|Q9NQ24	Frame_Shift_Del	DEL	ENST00000263285.6	hg19	CCDS30916.1																																																																																			.	.	.	none		0.473	LY9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060457.3	NM_002348		-	160771585	T	-	160771585	6	5	73	0	1	1	0	1	0	0	0	0	9108	1493	52	0		0	LY9	1	160771585	Intron	DEL	T	TCGA-AL-3468-01A-01D-1252-08	873391	160771585	88479036	5	4699											
PROX1	5629	hgsc.bcm.edu	37	chr1	214178606	214178606	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgctgaagacctacttctcCgacgtaaaggtagggacttt	11	11	10	9	2	1	2	0	1	1	1	2	4	1	3	2	2	2	3	2	2	5	5	rs369204553	byFrequency	TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr1:214178606C>T	ENST00000366958.4	+	3	2432	c.1824C>T	c.(1822-1824)tcC>tcT	p.S608S	PROX1_ENST00000435016.1_Silent_p.S608S|PROX1_ENST00000261454.4_Silent_p.S608S|PROX1_ENST00000498508.2_Silent_p.S608S	NM_001270616.1	NP_001257545.1	Q92786	PROX1_HUMAN	prospero homeobox 1	608					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)	p.S608S(2)		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)		CCTACTTCTCCGACGTAAAGG	0.378													C|||	3	0.000599042	0	0	5008	,	,		20446	0		0	False		,,,				2504	0.0031				p.S608S		Atlas-SNP	.											PROX1,NS,carcinoma,0,2	PROX1	124	.	2	Substitution - coding silent(2)	prostate(1)|endometrium(1)	c.C1824T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	96	94	94		1824	-7.2	0.9	1		94	0,8600		0,0,4300	no	coding-synonymous	PROX1	NM_002763.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		608/738	214178606	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	5629	exon3			CTTCTCCGACGTA	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.1824C>T	chr1.hg19:g.214178606C>T		148.0	0.0	.		91.0	29.0	.	NM_001270616	A6NK29|A8K2B1|Q5SW76|Q8TB91	Silent	SNP	ENST00000366958.4	hg19	CCDS31021.1																																																																																			.	.	.	none		0.378	PROX1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089727.6	NM_002763		T	214178606	C	T	214178606	2	4	73	1	0	0	0	0	0	0	0	1	12570	639	23	1		1	PROX1	1	214178606	Silent	SNP	C	TCGA-AL-3468-01A-01D-1252-08	53407021	214178606	35072015	6	4700											
BPNT1	10380	hgsc.bcm.edu	37	chr1	220232228	220232229	+	Frame_Shift_Ins	INS	-	-	GCATA																															tagattctggaactcggcttINSgcatagtagtcataattcct																										TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr1:220232228_220232229insGCATA	ENST00000469520.2	-	10	1333_1334	c.884_885insTATGC	c.(883-885)gcafs	p.-295fs	BPNT1_ENST00000544404.1_Frame_Shift_Ins_p.-240fs|BPNT1_ENST00000414869.2_Frame_Shift_Ins_p.-259fs|BPNT1_ENST00000354807.3_Intron|BPNT1_ENST00000322067.7_Frame_Shift_Ins_p.-295fs			O95861	BPNT1_HUMAN	3'(2'), 5'-bisphosphate nucleotidase 1						3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|dephosphorylation (GO:0016311)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|phosphatidylinositol phosphorylation (GO:0046854)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3'(2'),5'-bisphosphate nucleotidase activity (GO:0008441)|inositol-1,4-bisphosphate 1-phosphatase activity (GO:0004441)|magnesium ion binding (GO:0000287)			breast(1)|endometrium(1)|large_intestine(1)|lung(9)|ovary(1)|skin(1)	14				GBM - Glioblastoma multiforme(131;0.0558)		GAACTCGGCTTGCATAGTAGTC	0.46																																					p.A295fs		Atlas-INDEL	.											.	BPNT1	29	.	0			c.885_886insTATGC						PASS	.																																			SO:0001589	frameshift_variant	10380	exon9			.	AF125042	CCDS41469.1, CCDS65787.1, CCDS65788.1	1q42	2008-02-05			ENSG00000162813	ENSG00000162813	3.1.3.7		1096	protein-coding gene	gene with protein product		604053				10224133	Standard	XM_005272998		Approved		uc001hma.3	O95861	OTTHUMG00000037435	ENST00000469520.2:c.880_884dupTATGC	chr1.hg19:g.220232229_220232233dupGCATA	ENSP00000446828:p.Ala295fs	413.0	0.0	0		296.0	28.0	0.0945946	NM_006085	A8K7C8|B4DPS5|B4DUS9|D3DTA9|Q8WVL5|Q9UGJ3	Frame_Shift_Ins	INS	ENST00000469520.2	hg19	CCDS41469.1																																																																																			.	.	.	none		0.46	BPNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091137.2	NM_006085		GCATA	220232229	-	GCATA	220232228	7	5	73	1	0	1	1	0	0	0	0	0	1496	1799	63	0	45	0	BPNT1	1	220232228	Frame_Shift_Ins	INS	-	TCGA-AL-3468-01A-01D-1252-08	6053622	220232228	29018393	7	4701	52	2									
BPNT1	10380	hgsc.bcm.edu	37	chr1	220232235	220232235	+	Missense_Mutation	SNP	T	T	C																															ctggaactcggcttgcatagTagtcataattcctcagtgtg																										TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr1:220232235T>C	ENST00000469520.2	-	10	1327	c.878A>G	c.(877-879)tAc>tGc	p.Y293C	BPNT1_ENST00000544404.1_Missense_Mutation_p.Y238C|BPNT1_ENST00000414869.2_Missense_Mutation_p.Y257C|BPNT1_ENST00000354807.3_Intron|BPNT1_ENST00000322067.7_Missense_Mutation_p.Y293C			O95861	BPNT1_HUMAN	3'(2'), 5'-bisphosphate nucleotidase 1	293					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|dephosphorylation (GO:0016311)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|phosphatidylinositol phosphorylation (GO:0046854)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3'(2'),5'-bisphosphate nucleotidase activity (GO:0008441)|inositol-1,4-bisphosphate 1-phosphatase activity (GO:0004441)|magnesium ion binding (GO:0000287)			breast(1)|endometrium(1)|large_intestine(1)|lung(9)|ovary(1)|skin(1)	14				GBM - Glioblastoma multiforme(131;0.0558)		GCTTGCATAGTAGTCATAATT	0.463																																					p.Y293C		Atlas-SNP	.											.	BPNT1	29	.	0			c.A878G						PASS	.						176	166	169					1																	220232235		1915	4149	6064	SO:0001583	missense	10380	exon9			GCATAGTAGTCAT	AF125042	CCDS41469.1, CCDS65787.1, CCDS65788.1	1q42	2008-02-05			ENSG00000162813	ENSG00000162813	3.1.3.7		1096	protein-coding gene	gene with protein product		604053				10224133	Standard	XM_005272998		Approved		uc001hma.3	O95861	OTTHUMG00000037435	ENST00000469520.2:c.878A>G	chr1.hg19:g.220232235T>C	ENSP00000446828:p.Tyr293Cys	383.0	0.0	.		268.0	74.0	.	NM_006085	A8K7C8|B4DPS5|B4DUS9|D3DTA9|Q8WVL5|Q9UGJ3	Missense_Mutation	SNP	ENST00000469520.2	hg19	CCDS41469.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.266127	0.80358	.	.	ENSG00000162813	ENST00000322067;ENST00000469520;ENST00000544404;ENST00000414869	T;T;T;T	0.50813	0.73;0.73;0.73;0.73	5.41	5.41	0.78517	.	.	.	.	.	T	0.65228	0.2671	M	0.67953	2.075	0.80722	D	1	P;D	0.67145	0.951;0.996	P;D	0.66602	0.886;0.945	T	0.65438	-0.6168	9	0.42905	T	0.14	.	15.7585	0.78058	0.0:0.0:0.0:1.0	.	257;293	B4DUS9;O95861	.;BPNT1_HUMAN	C	293;293;238;257	ENSP00000318852:Y293C;ENSP00000446828:Y293C;ENSP00000444398:Y238C;ENSP00000410348:Y257C	ENSP00000318852:Y293C	Y	-	2	0	BPNT1	218298858	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.164000	0.71885	2.191000	0.70037	0.528000	0.53228	TAC	.	.	.	none		0.463	BPNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091137.2	NM_006085		C	220232235	T	C	220232235	3	2	73	1	0	0	0	0	1	0	0	0	1496	1638	57	3	52	3	BPNT1	1	220232235	Missense_Mutation	SNP	T	TCGA-AL-3468-01A-01D-1252-08	7	220232235	29018386	8	4702	52	2									
PRKCE	5581	hgsc.bcm.edu	37	chr2	46372319	46372319	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcaaggaagggattctgaaTggtgtgacgaccaccacgtt	11	9	13	8	2	1	2	0	2	1	0	1	5	1	4	2	3	1	2	2	3	3	2			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr2:46372319T>C	ENST00000306156.3	+	12	2007	c.1680T>C	c.(1678-1680)aaT>aaC	p.N560N		NM_005400.2	NP_005391.1	Q02156	KPCE_HUMAN	protein kinase C, epsilon	560	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|cellular response to ethanol (GO:0071361)|cellular response to hypoxia (GO:0071456)|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)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|locomotory exploration behavior (GO:0035641)|macrophage activation involved in immune response (GO:0002281)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cellular glucuronidation (GO:2001031)|positive regulation of cytokinesis (GO:0032467)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of insulin secretion (GO:0032024)|positive regulation of lipid catabolic process (GO:0050996)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|release of sequestered calcium ion into cytosol (GO:0051209)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|TRAM-dependent toll-like receptor 4 signaling pathway (GO:0035669)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|ethanol binding (GO:0035276)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|receptor activator activity (GO:0030546)|signal transducer activity (GO:0004871)		MBOAT2/PRKCE(2)	breast(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(13)|ovary(3)|upper_aerodigestive_tract(2)	34		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)		Tamoxifen(DB00675)	GGATTCTGAATGGTGTGACGA	0.537																																					p.N560N		Atlas-SNP	.											.	PRKCE	58	.	0			c.T1680C						PASS	.						176	173	174					2																	46372319		2114	4130	6244	SO:0001819	synonymous_variant	5581	exon12			TCTGAATGGTGTG		CCDS1824.1	2p21	2009-07-10			ENSG00000171132	ENSG00000171132	2.7.11.1		9401	protein-coding gene	gene with protein product		176975				1382605, 7877991	Standard	NM_005400		Approved		uc002rut.3	Q02156	OTTHUMG00000128817	ENST00000306156.3:c.1680T>C	chr2.hg19:g.46372319T>C		264.0	1.0	.		266.0	108.0	.	NM_005400	B0LPH7|Q32MQ3|Q53SL4|Q53SM5|Q9UE81	Silent	SNP	ENST00000306156.3	hg19	CCDS1824.1																																																																																			.	.	.	none		0.537	PRKCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250751.2			C	46372319	T	C	46372319	2	2	73	1	0	0	0	0	0	0	0	1	12521	1461	51	3		3	PRKCE	2	46372319	Silent	SNP	T	TCGA-AL-3468-01A-01D-1252-08		46372319	196827054	9	4703											
DCTN1	1639	hgsc.bcm.edu	37	chr2	74589259	74589259	+	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	ctgagatactgtctccttgaGgacctcatcctagggaaggg	9	10	12	10	0	2	2	1	2	1	1	4	5	3	4	3	3	1	0	3	3	3	3			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr2:74589259G>C	ENST00000361874.3	-	31	3936	c.3619C>G	c.(3619-3621)Ctc>Gtc	p.L1207V	DCTN1_ENST00000409567.3_Missense_Mutation_p.L1182V|DCTN1_ENST00000407639.2_Missense_Mutation_p.L1073V|RP11-287D1.3_ENST00000451608.2_Missense_Mutation_p.L120V|DCTN1_ENST00000409868.1_Missense_Mutation_p.L1185V|DCTN1_ENST00000394003.3_Missense_Mutation_p.L1200V|DCTN1_ENST00000409240.1_Missense_Mutation_p.L1165V|DCTN1_ENST00000409438.1_Missense_Mutation_p.L1068V	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	1207					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						GTCTCCTTGAGGACCTCATCC	0.557																																					p.L1207V		Atlas-SNP	.											.	DCTN1	110	.	0			c.C3619G						PASS	.						99	81	87					2																	74589259		2203	4300	6503	SO:0001583	missense	1639	exon31			CCTTGAGGACCTC		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.3619C>G	chr2.hg19:g.74589259G>C	ENSP00000354791:p.Leu1207Val	89.0	0.0	.		80.0	41.0	.	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Missense_Mutation	SNP	ENST00000361874.3	hg19	CCDS1939.1	.	.	.	.	.	.	.	.	.	.	G	11.74	1.729642	0.30684	.	.	ENSG00000204843	ENST00000361874;ENST00000394003;ENST00000393999;ENST00000407639;ENST00000409438;ENST00000409240;ENST00000409868;ENST00000409567	T;T;T;T;T;T;T	0.77620	-0.7;-0.89;-0.7;-0.71;-1.11;-0.9;-0.89	5.24	3.05	0.35203	.	0.486591	0.15698	N	0.249059	T	0.53110	0.1776	N	0.08118	0	0.41825	D	0.990044	B;B;B;B;B;B;B	0.18968	0.009;0.0;0.003;0.032;0.022;0.006;0.025	B;B;B;B;B;B;B	0.21708	0.004;0.002;0.003;0.021;0.014;0.006;0.036	T	0.39014	-0.9634	10	0.15952	T	0.53	-0.2731	4.924	0.13883	0.1277:0.0:0.4745:0.3979	.	1182;1165;1207;1200;1073;1068;1190	E9PGE1;E9PFS5;Q14203;A8MY36;Q14203-2;G5E9H4;A8MWX9	.;.;DCTN1_HUMAN;.;.;.;.	V	1207;1200;1190;1073;1068;1165;1185;1182	ENSP00000354791:L1207V;ENSP00000377571:L1200V;ENSP00000384844:L1073V;ENSP00000387270:L1068V;ENSP00000386406:L1165V;ENSP00000387327:L1185V;ENSP00000386843:L1182V	ENSP00000354791:L1207V	L	-	1	0	DCTN1	74442767	0.998000	0.40836	1.000000	0.80357	0.966000	0.64601	2.517000	0.45529	1.057000	0.40506	0.491000	0.48974	CTC	.	.	.	none		0.557	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082		C	74589259	G	C	74589259	3	2	73	1	0	0	0	0	1	0	0	0	4308	1000	35	4	225	4	DCTN1	2	74589259	Missense_Mutation	SNP	G	TCGA-AL-3468-01A-01D-1252-08	28216940	74589259	168610114	10	4704											
RGPD3	653489	hgsc.bcm.edu	37	chr2	107049613	107049613	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttggtaggagatggtgtagaAtgttttatttctgaatccgc	9	16	12	4	1	1	3	0	1	1	2	2	4	2	3	1	3	0	3	1	3	5	6			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr2:107049613A>G	ENST00000409886.3	-	16	2421	c.2334T>C	c.(2332-2334)caT>caC	p.H778H	RGPD3_ENST00000304514.7_Silent_p.H778H	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	778					protein targeting to Golgi (GO:0000042)			p.H778Q(2)		breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						ATGGTGTAGAATGTTTTATTT	0.353																																					p.H778H		Atlas-SNP	.											RGPD3_ENST00000304514,NS,carcinoma,0,2	RGPD3	316	.	2	Substitution - Missense(2)	lung(2)	c.T2334C						PASS	.						8	17	14					2																	107049613		632	1470	2102	SO:0001819	synonymous_variant	653489	exon16			TGTAGAATGTTTT		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.2334T>C	chr2.hg19:g.107049613A>G		593.0	0.0	.		381.0	104.0	.	NM_001144013	B8ZZM4	Silent	SNP	ENST00000409886.3	hg19	CCDS46379.1																																																																																			.	.	.	none		0.353	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931		G	107049613	A	G	107049613	2	3	73	1	0	0	0	0	0	0	0	1	13300	98	4	3		3	RGPD3	2	107049613	Silent	SNP	A	TCGA-AL-3468-01A-01D-1252-08	32460354	107049613	136149760	11	4705											
DPP10	57628	hgsc.bcm.edu	37	chr2	116598392	116598392	+	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	aaaagctggagtgaattataCtatgcaggtaagctactttc	14	12	9	6	0	0	1	0	1	0	0	1	2	0	2	0	2	5	4	0	2	8	6	rs201639501		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr2:116598392C>A	ENST00000410059.1	+	25	2729	c.2249C>A	c.(2248-2250)aCt>aAt	p.T750N	DPP10_ENST00000310323.8_Missense_Mutation_p.T743N|DPP10_ENST00000409163.1_Missense_Mutation_p.T700N|DPP10_ENST00000393147.2_Missense_Mutation_p.T754N	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	750						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						GTGAATTATACTATGCAGGTA	0.358																																					p.T754N		Atlas-SNP	.											.	DPP10	415	.	0			c.C2261A						PASS	.						96	94	94					2																	116598392		2203	4300	6503	SO:0001583	missense	57628	exon25			ATTATACTATGCA	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.2249C>A	chr2.hg19:g.116598392C>A	ENSP00000386565:p.Thr750Asn	109.0	0.0	.		74.0	34.0	.	NM_001178034	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	hg19	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.635056	0.87760	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393147;ENST00000310323	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	5.99	5.99	0.97316	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.056130	0.64402	D	0.000001	T	0.53883	0.1824	L	0.31294	0.92	0.54753	D	0.999989	D;D;D;D	0.67145	0.995;0.978;0.996;0.996	D;P;D;D	0.68621	0.931;0.832;0.959;0.959	T	0.44937	-0.9295	10	0.37606	T	0.19	-19.3701	19.4659	0.94939	0.0:1.0:0.0:0.0	.	743;754;746;750	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	N	750;700;754;743	ENSP00000386565:T750N;ENSP00000387038:T700N;ENSP00000376855:T754N;ENSP00000309066:T743N	ENSP00000309066:T743N	T	+	2	0	DPP10	116314862	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.723000	0.74742	2.840000	0.97914	0.655000	0.94253	ACT	.	C|0.999;G|0.001	.	alt		0.358	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		A	116598392	C	A	116598392	3	1	73	1	0	0	0	0	1	0	0	0	4729	565	20	4	2518	4	DPP10	2	116598392	Missense_Mutation	SNP	C	TCGA-AL-3468-01A-01D-1252-08	9548779	116598392	126600981	12	4706											
ITGB6	3694	hgsc.bcm.edu	37	chr2	160982928	160982928	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcaccacaggtaggacatcgTtcacaggttggtcctgaggc	9	9	12	11	1	2	1	2	1	0	0	4	2	3	2	2	5	0	3	2	5	1	3			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr2:160982928T>C	ENST00000283249.2	-	11	2082	c.1845A>G	c.(1843-1845)gaA>gaG	p.E615E	ITGB6_ENST00000409967.2_Intron|ITGB6_ENST00000428609.2_Silent_p.E573E|ITGB6_ENST00000409872.1_Silent_p.E615E	NM_001282353.1|NM_001282354.1|NM_001282388.1	NP_001269282.1|NP_001269283.1|NP_001269317.1	P18564	ITB6_HUMAN	integrin, beta 6	615	Cysteine-rich tandem repeats.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|multicellular organismal development (GO:0007275)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23						TAGGACATCGTTCACAGGTTG	0.502																																					p.E615E		Atlas-SNP	.											.	ITGB6	68	.	0			c.A1845G						PASS	.						97	85	89					2																	160982928		2203	4300	6503	SO:0001819	synonymous_variant	3694	exon11			ACATCGTTCACAG		CCDS2212.1, CCDS63040.1, CCDS74596.1, CCDS74597.1	2q24.2	2010-03-23			ENSG00000115221	ENSG00000115221		"Integrins"	6161	protein-coding gene	gene with protein product		147558				1729173, 8120056	Standard	NM_001282353		Approved		uc002ubh.2	P18564	OTTHUMG00000132026	ENST00000283249.2:c.1845A>G	chr2.hg19:g.160982928T>C		149.0	0.0	.		161.0	15.0	.	NM_000888	B2R9W5|C9JA97|Q0VA95|Q16500|Q53RG5|Q53RR6	Silent	SNP	ENST00000283249.2	hg19	CCDS2212.1																																																																																			.	.	.	none		0.502	ITGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255036.1	NM_000888		C	160982928	T	C	160982928	2	2	73	1	0	0	0	0	0	0	0	1	7906	1722	60	3		3	ITGB6	2	160982928	Silent	SNP	T	TCGA-AL-3468-01A-01D-1252-08	44384536	160982928	82216445	13	4707											
ACADL	33	hgsc.bcm.edu	37	chr2	211081149	211081149	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggaataaagtgcttaatcTgttcttctgagccatggttt	9	15	11	6	0	3	1	0	1	3	0	3	2	3	2	1	3	2	3	1	3	4	5			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr2:211081149T>C	ENST00000233710.3	-	4	685	c.458A>G	c.(457-459)cAg>cGg	p.Q153R	AC006994.2_ENST00000412065.1_RNA	NM_001608.3	NP_001599.1	P28330	ACADL_HUMAN	acyl-CoA dehydrogenase, long chain	153					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)		GTGCTTAATCTGTTCTTCTGA	0.383																																					p.Q153R		Atlas-SNP	.											.	ACADL	38	.	0			c.A458G						PASS	.						161	149	153					2																	211081149		2203	4300	6503	SO:0001583	missense	33	exon4			TTAATCTGTTCTT	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.458A>G	chr2.hg19:g.211081149T>C	ENSP00000233710:p.Gln153Arg	258.0	0.0	.		68.0	22.0	.	NM_001608	B2R8T3|Q8IUN8	Missense_Mutation	SNP	ENST00000233710.3	hg19	CCDS2389.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.667847	0.88348	.	.	ENSG00000115361	ENST00000233710	D	0.99869	-7.33	5.63	5.63	0.86233	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, N-terminal (1);Acyl-CoA dehydrogenase/oxidase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99921	0.9963	H	0.99026	4.405	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.96051	0.9031	10	0.72032	D	0.01	.	16.1307	0.81436	0.0:0.0:0.0:1.0	.	153	P28330	ACADL_HUMAN	R	153	ENSP00000233710:Q153R	ENSP00000233710:Q153R	Q	-	2	0	ACADL	210789394	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.422000	0.80217	2.263000	0.75096	0.533000	0.62120	CAG	.	.	.	none		0.383	ACADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256561.2	NM_001608		C	211081149	T	C	211081149	3	2	73	1	0	0	0	0	1	0	0	0	112	1580	55	3	866	3	ACADL	2	211081149	Missense_Mutation	SNP	T	TCGA-AL-3468-01A-01D-1252-08	50098221	211081149	32118224	14	4708											
BARD1	580	hgsc.bcm.edu	37	chr2	215593624	215593624	+	Missense_Mutation	SNP	T	T	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	gtctggcttgggctttctacTgaggatctggcccccacctg	4	12	12	13	0	3	1	0	1	3	0	3	2	3	2	3	4	1	2	3	4	1	3			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr2:215593624T>G	ENST00000260947.4	-	11	2244	c.2110A>C	c.(2110-2112)Agt>Cgt	p.S704R	BARD1_ENST00000432456.1_Missense_Mutation_p.S75R|BARD1_ENST00000449967.2_Silent_p.S558S	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	704	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.				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)		GGCTTTCTACTGAGGATCTGG	0.493									Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.S704R		Atlas-SNP	.											.	BARD1	138	.	0			c.A2110C						PASS	.						144	111	122					2																	215593624		2203	4300	6503	SO:0001583	missense	580	exon11	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	TTCTACTGAGGAT		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.2110A>C	chr2.hg19:g.215593624T>G	ENSP00000260947:p.Ser704Arg	107.0	0.0	.		59.0	36.0	.	NM_000465	F6MDH7|F6MDH8|F6MDH9|O43574|Q53SS5	Missense_Mutation	SNP	ENST00000260947.4	hg19	CCDS2397.1	.	.	.	.	.	.	.	.	.	.	T	12.86	2.064962	0.36470	.	.	ENSG00000138376	ENST00000260947;ENST00000432456	T;T	0.73363	-0.74;1.95	5.81	5.81	0.92471	BRCT (3);	0.268513	0.40908	N	0.000992	T	0.60431	0.2268	L	0.36672	1.1	0.80722	D	1	B	0.15930	0.015	B	0.09377	0.004	T	0.56269	-0.8007	10	0.25106	T	0.35	-7.0699	6.3187	0.21204	0.1431:0.0794:0.0:0.7775	.	704	Q99728	BARD1_HUMAN	R	704;75	ENSP00000260947:S704R;ENSP00000405020:S75R	ENSP00000260947:S704R	S	-	1	0	BARD1	215301869	0.102000	0.21896	0.975000	0.42487	0.984000	0.73092	0.357000	0.20199	2.217000	0.71921	0.482000	0.46254	AGT	.	.	.	none		0.493	BARD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256602.1	NM_000465		G	215593624	T	G	215593624	3	3	73	1	0	0	0	0	1	0	0	0	1312	1580	55	5	227	5	BARD1	2	215593624	Missense_Mutation	SNP	T	TCGA-AL-3468-01A-01D-1252-08	4512475	215593624	27605749	15	4709											
STK25	10494	hgsc.bcm.edu	37	chr2	242437690	242437690	+	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	ccgtccccttgtgaagcttgCtgtgtggactcggccggatg	4	11	14	12	3	0	1	0	1	0	0	2	3	1	3	4	3	2	2	4	3	1	2			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr2:242437690C>A	ENST00000316586.4	-	9	1341	c.992G>T	c.(991-993)aGc>aTc	p.S331I	STK25_ENST00000405585.1_Missense_Mutation_p.S254I|STK25_ENST00000478403.1_5'UTR|STK25_ENST00000405883.3_Missense_Mutation_p.S254I|STK25_ENST00000543554.1_Missense_Mutation_p.S237I|STK25_ENST00000403346.3_Missense_Mutation_p.S331I|STK25_ENST00000535007.1_Missense_Mutation_p.S237I|STK25_ENST00000401869.1_Missense_Mutation_p.S331I	NM_001271977.1|NM_001271978.1|NM_001282308.1	NP_001258906.1|NP_001258907.1|NP_001269237.1	O00506	STK25_HUMAN	serine/threonine kinase 25	331					establishment or maintenance of cell polarity (GO:0007163)|Golgi localization (GO:0051645)|positive regulation of axonogenesis (GO:0050772)|response to oxidative stress (GO:0006979)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|kidney(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	10		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;8.24e-34)|all cancers(36;3.46e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.6e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.1e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0839)		GTGAAGCTTGCTGTGTGGACT	0.652																																					p.S331I	NSCLC(99;1100 1566 7679 28647 48345)	Atlas-SNP	.											.	STK25	32	.	0			c.G992T						PASS	.						152	134	140					2																	242437690		2203	4300	6503	SO:0001583	missense	10494	exon9			AGCTTGCTGTGTG	D63780	CCDS2549.1, CCDS63199.1, CCDS63200.1	2q37.3	2010-06-25	2010-06-25		ENSG00000115694	ENSG00000115694			11404	protein-coding gene	gene with protein product		602255	"serine/threonine kinase 25 (Ste20, yeast homolog)"			8887545, 9160885, 15037601	Standard	NM_001271977		Approved	SOK1, YSK1	uc002wbp.4	O00506	OTTHUMG00000133408	ENST00000316586.4:c.992G>T	chr2.hg19:g.242437690C>A	ENSP00000325748:p.Ser331Ile	228.0	0.0	.		237.0	10.0	.	NM_006374	A8K6Z3|A8K7D2|B7Z9K1|Q15522|Q5BJF1	Missense_Mutation	SNP	ENST00000316586.4	hg19	CCDS2549.1	.	.	.	.	.	.	.	.	.	.	C	13.08	2.130649	0.37630	.	.	ENSG00000115694	ENST00000316586;ENST00000403346;ENST00000401869;ENST00000405883;ENST00000545437;ENST00000405585;ENST00000543554;ENST00000535007	T;T;T;T;T;T;T	0.36520	1.25;1.25;1.25;1.25;1.25;1.25;1.25	4.97	2.17	0.27698	.	0.191571	0.56097	D	0.000038	T	0.23370	0.0565	L	0.29908	0.895	0.48236	D	0.99961	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.06405	0.002;0.002;0.001	T	0.05131	-1.0904	10	0.41790	T	0.15	.	7.7734	0.29021	0.0:0.6788:0.0:0.3212	.	257;254;331	B4DVS7;A8K6Z3;O00506	.;.;STK25_HUMAN	I	331;331;331;254;237;254;237;237	ENSP00000325748:S331I;ENSP00000384162:S331I;ENSP00000385687:S331I;ENSP00000384444:S254I;ENSP00000385541:S254I;ENSP00000444886:S237I;ENSP00000446008:S237I	ENSP00000325748:S331I	S	-	2	0	STK25	242086363	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	0.472000	0.22116	0.629000	0.30376	0.561000	0.74099	AGC	.	.	.	none		0.652	STK25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257265.4	NM_006374		A	242437690	C	A	242437690	3	1	73	1	0	0	0	0	1	0	0	0	15306	797	28	4	304	4	STK25	2	242437690	Missense_Mutation	SNP	C	TCGA-AL-3468-01A-01D-1252-08	26844066	242437690	761683	16	4710											
BHLHE40	8553	hgsc.bcm.edu	37	chr3	5024904	5024904	+	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	cggagaagggcgacttgcgcAgtgagcagccgtgcttcaaa	10	6	15	10	4	1	2	1	1	0	1	1	4	1	2	1	2	4	3	1	2	2	2			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr3:5024904A>T	ENST00000256495.3	+	5	1369	c.766A>T	c.(766-768)Agt>Tgt	p.S256C		NM_003670.2	NP_003661.1	O14503	BHE40_HUMAN	basic helix-loop-helix family, member e40	256					circadian regulation of gene expression (GO:0032922)|entrainment of circadian clock by photoperiod (GO:0043153)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|MRF binding (GO:0043426)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(2)	12						CGACTTGCGCAGTGAGCAGCC	0.572																																					p.S256C		Atlas-SNP	.											.	BHLHE40	35	.	0			c.A766T						PASS	.						69	64	66					3																	5024904		2203	4300	6503	SO:0001583	missense	8553	exon5			TTGCGCAGTGAGC	AB004066	CCDS2565.1	3p26	2009-01-12	2009-01-12	2009-01-12	ENSG00000134107	ENSG00000134107		"Basic helix-loop-helix proteins"	1046	protein-coding gene	gene with protein product	"differentially expressed in chondrocytes 1", " differentiated embryo chondrocyte expressed gene 1"	604256	"basic helix-loop-helix domain containing, class B, 2"	STRA13, BHLHB2		9240428, 10449910, 18557763	Standard	NM_003670		Approved	DEC1, bHLHe40	uc003bqf.3	O14503	OTTHUMG00000119035	ENST00000256495.3:c.766A>T	chr3.hg19:g.5024904A>T	ENSP00000256495:p.Ser256Cys	98.0	0.0	.		146.0	92.0	.	NM_003670	Q96TD3	Missense_Mutation	SNP	ENST00000256495.3	hg19	CCDS2565.1	.	.	.	.	.	.	.	.	.	.	A	6.428	0.447160	0.12223	.	.	ENSG00000134107	ENST00000256495	T	0.65364	-0.15	5.2	-2.51	0.06365	.	1.437920	0.04279	N	0.343497	T	0.49047	0.1534	L	0.34521	1.04	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.41502	-0.9505	10	0.62326	D	0.03	.	6.2929	0.21069	0.1557:0.0922:0.6603:0.0918	.	256	O14503	BHE40_HUMAN	C	256	ENSP00000256495:S256C	ENSP00000256495:S256C	S	+	1	0	BHLHE40	4999904	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	0.454000	0.21827	-0.536000	0.06298	-0.290000	0.09829	AGT	.	.	.	none		0.572	BHLHE40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239244.2	NM_003670		T	5024904	A	T	5024904	3	4	73	1	0	0	0	0	1	0	0	0	1423	188	7	5	784	5	BHLHE40	3	5024904	Missense_Mutation	SNP	A	TCGA-AL-3468-01A-01D-1252-08		5024904	192997526	17	4711											
SLC6A6	6533	hgsc.bcm.edu	37	chr3	14508150	14508150	+	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	ctgacatcacccgccttgagGacccacaggtactgtggggc	8	7	12	14	1	1	2	1	2	0	0	1	3	1	3	3	4	1	1	3	4	1	2			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr3:14508150G>A	ENST00000454876.2	+	7	1188	c.859G>A	c.(859-861)Gac>Aac	p.D287N	SLC6A6_ENST00000360861.3_Missense_Mutation_p.D287N			P31641	SC6A6_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 6	287					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						CCGCCTTGAGGACCCACAGGT	0.642																																					p.D287N		Atlas-SNP	.											.	SLC6A6	58	.	0			c.G859A						PASS	.						60	56	57					3																	14508150		2203	4300	6503	SO:0001583	missense	6533	exon7			CTTGAGGACCCAC		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.859G>A	chr3.hg19:g.14508150G>A	ENSP00000398063:p.Asp287Asn	121.0	0.0	.		191.0	115.0	.	NM_003043	B2RNU7|Q9BRI2|Q9BXB0	Missense_Mutation	SNP	ENST00000454876.2	hg19	CCDS33705.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.616123	0.87359	.	.	ENSG00000131389	ENST00000454876;ENST00000360861	T;T	0.74526	-0.85;-0.85	4.55	4.55	0.56014	.	0.047664	0.85682	D	0.000000	T	0.76709	0.4025	L	0.42487	1.325	0.80722	D	1	P	0.44044	0.825	P	0.50934	0.654	T	0.77264	-0.2652	10	0.42905	T	0.14	.	17.6676	0.88207	0.0:0.0:1.0:0.0	.	287	P31641	SC6A6_HUMAN	N	287	ENSP00000398063:D287N;ENSP00000354107:D287N	ENSP00000354107:D287N	D	+	1	0	SLC6A6	14483154	1.000000	0.71417	0.994000	0.49952	0.928000	0.56348	7.696000	0.84270	2.241000	0.73720	0.491000	0.48974	GAC	.	.	.	none		0.642	SLC6A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340507.1	NM_003043		A	14508150	G	A	14508150	3	1	73	1	0	0	0	0	1	0	0	0	14701	1174	41	2	881	2	SLC6A6	3	14508150	Missense_Mutation	SNP	G	TCGA-AL-3468-01A-01D-1252-08	9483246	14508150	183514280	18	4712											
BAP1	8314	hgsc.bcm.edu	37	chr3	52441417	52441417	+	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	cccacagctcccacacacctGgcatggctattatgggcctt	8	9	8	16	0	0	0	0	0	0	0	1	0	1	0	4	3	1	3	4	3	2	3			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr3:52441417G>C	ENST00000460680.1	-	6	906	c.435C>G	c.(433-435)gcC>gcG	p.A145A	BAP1_ENST00000296288.5_Silent_p.A145A	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0	Interaction with HIP2.				anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		CCACACACCTGGCATGGCTAT	0.547			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.A145A	GBM(101;493 1458 7992 21037 25532)	Atlas-SNP	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	0			c.C435G						PASS	.						88	92	91					3																	52441417		2203	4300	6503	SO:0001819	synonymous_variant	8314	exon6			ACACCTGGCATGG	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.435C>G	chr3.hg19:g.52441417G>C		191.0	0.0	.		235.0	68.0	.	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Silent	SNP	ENST00000460680.1	hg19	CCDS2853.1																																																																																			.	.	.	none		0.547	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			C	52441417	G	C	52441417	2	2	73	1	0	0	0	0	0	0	0	1	1311	1335	47	4		4	BAP1	3	52441417	Silent	SNP	G	TCGA-AL-3468-01A-01D-1252-08	37933267	52441417	145581013	19	4713											
PDZRN3	23024	hgsc.bcm.edu	37	chr3	73432828	73432828	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccatcttcatctcgctcacCgcgtcgtcgtcggtggtcat	4	12	9	16	6	5	0	3	0	2	0	9	0	5	0	2	2	0	1	2	2	0	1			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr3:73432828C>T	ENST00000263666.4	-	10	3003	c.2889G>A	c.(2887-2889)gcG>gcA	p.A963A	PDZRN3_ENST00000466780.1_Silent_p.A620A|PDZRN3_ENST00000462146.2_Silent_p.A620A|PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000479530.1_Silent_p.A680A|PDZRN3_ENST00000535920.1_Silent_p.A685A	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	963					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)	p.A963A(1)		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)		TCTCGCTCACCGCGTCGTCGT	0.672																																					p.A963A		Atlas-SNP	.											PDZRN3,rectum,carcinoma,0,2	PDZRN3	196	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2889A						PASS	.						75	72	73					3																	73432828		2203	4300	6503	SO:0001819	synonymous_variant	23024	exon10			GCTCACCGCGTCG	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.2889G>A	chr3.hg19:g.73432828C>T		147.0	0.0	.		278.0	79.0	.	NM_015009	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Silent	SNP	ENST00000263666.4	hg19	CCDS33789.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	5.192|5.192	0.220967|0.220967	0.09863|0.09863	.|.	.|.	ENSG00000121440|ENSG00000121440	ENST00000416926|ENST00000494559	.|.	.|.	.|.	5.21|5.21	-1.55|-1.55	0.08558|0.08558	.|.	.|.	.|.	.|.	.|.	T|T	0.80149|0.80149	0.4570|0.4570	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.78157|0.78157	-0.2313|-0.2313	5|4	0.09590|.	T|.	0.72|.	.|.	25.5553|25.5553	0.99994|0.99994	0.0:0.1209:0.8791:0.0|0.0:0.1209:0.8791:0.0	.|.	.|.	.|.	.|.	S|Q	683|279	.|.	ENSP00000392657:G683S|.	G|R	-|-	1|2	0|0	PDZRN3|PDZRN3	73515518|73515518	0.370000|0.370000	0.25047|0.25047	0.008000|0.008000	0.14137|0.14137	0.813000|0.813000	0.45954|0.45954	-0.257000|-0.257000	0.08745|0.08745	-0.749000|-0.749000	0.04747|0.04747	0.563000|0.563000	0.77884|0.77884	GGT|CGG	.	.	.	none		0.672	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363		T	73432828	C	T	73432828	2	4	73	1	0	0	0	0	0	0	0	1	11716	639	23	1		1	PDZRN3	3	73432828	Silent	SNP	C	TCGA-AL-3468-01A-01D-1252-08	20991411	73432828	124589602	20	4714											
SLC2A2	6514	hgsc.bcm.edu	37	chr3	170732492	170732492	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcatccagtggaacacccAaaacatgtctatagtgagat	14	9	9	9	0	2	1	1	1	1	1	3	3	3	2	2	2	2	0	2	2	5	2			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr3:170732492A>G	ENST00000314251.3	-	3	216	c.137T>C	c.(136-138)tTg>tCg	p.L46S	SLC2A2_ENST00000382808.4_Intron	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	46					carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)			central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	TGGAACACCCAAAACATGTCT	0.333																																					p.L46S		Atlas-SNP	.											.	SLC2A2	71	.	0			c.T137C	GRCh37	CD972446	SLC2A2	D		PASS	.						124	124	124					3																	170732492		2203	4300	6503	SO:0001583	missense	6514	exon3			ACACCCAAAACAT	J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"Solute carriers"	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.137T>C	chr3.hg19:g.170732492A>G	ENSP00000323568:p.Leu46Ser	238.0	0.0	.		201.0	53.0	.	NM_000340	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Missense_Mutation	SNP	ENST00000314251.3	hg19	CCDS3215.1	.	.	.	.	.	.	.	.	.	.	A	16.72	3.200977	0.58234	.	.	ENSG00000163581	ENST00000314251	D	0.84589	-1.87	5.84	5.84	0.93424	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.207774	0.41500	D	0.000861	D	0.88768	0.6526	M	0.89840	3.065	0.80722	D	1	P	0.37423	0.594	B	0.40982	0.345	D	0.87926	0.2707	10	0.30854	T	0.27	.	14.4575	0.67425	1.0:0.0:0.0:0.0	.	46	P11168	GTR2_HUMAN	S	46	ENSP00000323568:L46S	ENSP00000323568:L46S	L	-	2	0	SLC2A2	172215186	1.000000	0.71417	0.703000	0.30354	0.233000	0.25261	6.862000	0.75484	2.243000	0.73865	0.533000	0.62120	TTG	.	.	.	none		0.333	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340		G	170732492	A	G	170732492	3	3	73	1	0	0	0	0	1	0	0	0	14557	131	5	3	1473	3	SLC2A2	3	170732492	Missense_Mutation	SNP	A	TCGA-AL-3468-01A-01D-1252-08	97299664	170732492	27289938	21	4715											
EIF2B5	8893	hgsc.bcm.edu	37	chr3	183861938	183861938	+	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	actacataaagcgcgcagccGaccatttggaagcgttagca	13	7	10	11	4	0	0	0	0	0	0	0	2	0	1	2	1	5	3	2	1	5	4			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr3:183861938G>A	ENST00000273783.3	+	14	2043	c.1921G>A	c.(1921-1923)Gac>Aac	p.D641N	EIF2B5_ENST00000444495.1_Missense_Mutation_p.D641N	NM_003907.2	NP_003898.2	Q13144	EI2BE_HUMAN	eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82kDa	641	W2. {ECO:0000255|PROSITE- ProRule:PRU00695}.				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)			GCGCGCAGCCGACCATTTGGA	0.473																																					p.D641N		Atlas-SNP	.											EIF2B5,NS,carcinoma,0,1	EIF2B5	62	.	0			c.G1921A						PASS	.						157	158	158					3																	183861938		2203	4300	6503	SO:0001583	missense	8893	exon14			GCAGCCGACCATT	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.1921G>A	chr3.hg19:g.183861938G>A	ENSP00000273783:p.Asp641Asn	410.0	1.0	.		515.0	142.0	.	NM_003907	Q541Z1|Q96D04	Missense_Mutation	SNP	ENST00000273783.3	hg19	CCDS3252.1	.	.	.	.	.	.	.	.	.	.	g	21.4	4.137002	0.77775	.	.	ENSG00000145191	ENST00000273783;ENST00000444495	T;T	0.81330	-1.48;-1.48	5.83	5.83	0.93111	eIF4-gamma/eIF5/eIF2-epsilon (3);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.000000	0.85682	D	0.000000	D	0.89753	0.6806	M	0.82056	2.57	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.71414	0.966;0.973	D	0.86277	0.1665	10	0.22109	T	0.4	.	20.1218	0.97964	0.0:0.0:1.0:0.0	.	641;641	E9PC74;Q13144	.;EI2BE_HUMAN	N	641	ENSP00000273783:D641N;ENSP00000409142:D641N	ENSP00000273783:D641N	D	+	1	0	EIF2B5	185344632	1.000000	0.71417	1.000000	0.80357	0.248000	0.25809	9.095000	0.94175	2.763000	0.94921	0.561000	0.74099	GAC	.	.	.	none		0.473	EIF2B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346168.1			A	183861938	G	A	183861938	3	1	73	1	0	0	0	0	1	0	0	0	5006	1058	37	1	1975	1	EIF2B5	3	183861938	Missense_Mutation	SNP	G	TCGA-AL-3468-01A-01D-1252-08	13129446	183861938	14160492	22	4716											
CD180	4064	hgsc.bcm.edu	37	chr5	66479676	66479676	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgacacaattgatcgaaaTgatttacactgagaactaat	16	13	6	6	1	0	4	0	4	0	1	1	6	0	4	0	0	2	0	0	0	5	5			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr5:66479676T>C	ENST00000256447.4	-	3	1152	c.995A>G	c.(994-996)cAt>cGt	p.H332R		NM_005582.2	NP_005573.2	Q99467	CD180_HUMAN	CD180 molecule	332					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)		TTGATCGAAATGATTTACACT	0.448																																					p.H332R		Atlas-SNP	.											.	CD180	78	.	0			c.A995G						PASS	.						112	108	109					5																	66479676		2203	4300	6503	SO:0001583	missense	4064	exon3			TCGAAATGATTTA	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.995A>G	chr5.hg19:g.66479676T>C	ENSP00000256447:p.His332Arg	286.0	1.0	.		210.0	89.0	.	NM_005582	B2R7Z7|Q32MM5	Missense_Mutation	SNP	ENST00000256447.4	hg19	CCDS3992.1	.	.	.	.	.	.	.	.	.	.	T	0.320	-0.962736	0.02249	.	.	ENSG00000134061	ENST00000256447	T	0.22945	1.93	4.93	-6.2	0.02072	.	2.214440	0.01592	N	0.021638	T	0.08358	0.0208	N	0.02685	-0.53	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.19778	-1.0295	10	0.12430	T	0.62	.	3.8381	0.08903	0.0947:0.3857:0.1905:0.3291	.	332	Q99467	CD180_HUMAN	R	332	ENSP00000256447:H332R	ENSP00000256447:H332R	H	-	2	0	CD180	66515432	0.000000	0.05858	0.000000	0.03702	0.455000	0.32408	-1.582000	0.02117	-0.862000	0.04089	0.528000	0.53228	CAT	.	.	.	none		0.448	CD180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253973.2	NM_005582		C	66479676	T	C	66479676	3	2	73	1	0	0	0	0	1	0	0	0	2974	1464	51	3	994	3	CD180	5	66479676	Missense_Mutation	SNP	T	TCGA-AL-3468-01A-01D-1252-08		66479676	114435584	23	4717											
SPINK5	11005	hgsc.bcm.edu	37	chr5	147505159	147505159	+	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	ctgggcgttccttggcctctGttgccaggatgagtacagtg	5	12	14	10	1	1	1	0	1	1	0	2	2	2	2	3	3	2	3	3	3	1	4			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr5:147505159G>T	ENST00000256084.7	+	29	2781				SPINK5_ENST00000359874.3_Missense_Mutation_p.V938F	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5						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)			CTTGGCCTCTGTTGCCAGGAT	0.453																																					p.V938F		Atlas-SNP	.											.	SPINK5	245	.	0			c.G2812T						PASS	.						81	72	75					5																	147505159		1568	3582	5150	SO:0001627	intron_variant	11005	exon29			GCCTCTGTTGCCA	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.2740-127G>T	chr5.hg19:g.147505159G>T		100.0	0.0	.		57.0	27.0	.	NM_001127698	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	hg19	CCDS43382.1	.	.	.	.	.	.	.	.	.	.	G	0.012	-1.647508	0.00792	.	.	ENSG00000133710	ENST00000359874	T	0.48836	0.8	4.84	-6.57	0.01842	.	3.884710	0.00531	N	0.000217	T	0.33352	0.0860	.	.	.	0.09310	N	1	B	0.20052	0.041	B	0.28553	0.091	T	0.21895	-1.0232	9	0.36615	T	0.2	2.1949	6.42	0.21738	0.3875:0.236:0.3766:0.0	.	938	Q9NQ38-3	.	F	938	ENSP00000352936:V938F	ENSP00000352936:V938F	V	+	1	0	SPINK5	147485352	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-1.352000	0.02619	-1.402000	0.02056	-0.889000	0.02933	GTT	.	.	.	none		0.453	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698		T	147505159	G	T	147505159	1	4	73	0	1	0	0	0	0	0	0	0	15074	1377	48	4		4	SPINK5	5	147505159	Intron	SNP	G	TCGA-AL-3468-01A-01D-1252-08	81025483	147505159	33410101	24	4718											
OR2J3	442186	hgsc.bcm.edu	37	chr6	29080474	29080475	+	Frame_Shift_Del	DEL	TT	TT	-																															ctccagccaccatcaggaaaTtctcaagatcaaggcaagtt																										TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr6:29080474_29080475delTT	ENST00000377169.1	+	1	807_808	c.807_808delTT	c.(805-810)aattctfs	p.S270fs		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	270						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						CATCAGGAAATTCTCAAGATCA	0.441																																					p.269_269del		Atlas-INDEL	.											.	OR2J3	53	.	0			c.806_807del						PASS	.																																			SO:0001589	frameshift_variant	442186	exon1			.		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.807_808delTT	chr6.hg19:g.29080474_29080475delTT	ENSP00000366374:p.Ser270fs	216.0	0.0	0		89.0	79.0	0.88764	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Frame_Shift_Del	DEL	ENST00000377169.1	hg19	CCDS43433.1																																																																																			.	.	.	none		0.441	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2			-	29080475	TT	-	29080474	7	5	73	1	0	1	0	1	0	0	0	0	11011	1490	52	0	809	0	OR2J3	6	29080474	Frame_Shift_Del	DEL	TT	TCGA-AL-3468-01A-01D-1252-08		29080474	142034593	25	4719											
MSH5	4439	hgsc.bcm.edu	37	chr6	31712029	31712029	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaatcggggttgaactggaAgactataatgtcagcgtccc	12	9	12	8	2	1	3	1	1	0	2	3	4	2	4	1	3	2	1	1	3	5	3			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr6:31712029A>G	ENST00000375755.3	+	7	886	c.600A>G	c.(598-600)gaA>gaG	p.E200E	MSH5_ENST00000375750.3_Silent_p.E200E|MSH5_ENST00000375740.3_Silent_p.E217E|MSH5_ENST00000375703.3_Silent_p.E200E|MSH5_ENST00000431848.2_5'Flank|MSH5_ENST00000534153.4_Silent_p.E217E|MSH5_ENST00000375742.3_Silent_p.E217E|MSH5-SAPCD1_ENST00000493662.2_Silent_p.E217E|MSH5_ENST00000482280.1_3'UTR	NM_002441.4	NP_002432.1	O43196	MSH5_HUMAN	mutS homolog 5	200					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|reciprocal meiotic recombination (GO:0007131)	synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|ovary(2)|skin(2)	5						TTGAACTGGAAGACTATAATG	0.502								Direct reversal of damage;Mismatch excision repair (MMR)																													p.E217E		Atlas-SNP	.											.	MSH5	108	.	0			c.A651G						PASS	.						100	100	100					6																	31712029		2203	4300	6503	SO:0001819	synonymous_variant	4439	exon7			ACTGGAAGACTAT	AF070071	CCDS4720.1, CCDS34409.1, CCDS34410.1, CCDS34409.2	6p21.3	2013-09-12	2013-09-12		ENSG00000204410	ENSG00000204410			7328	protein-coding gene	gene with protein product		603382	"mutS (E. coli) homolog 5", "mutS homolog 5 (E. coli)"			9740671, 9787078, 17977839	Standard	NM_002441		Approved		uc011hbg.2	O43196	OTTHUMG00000167551	ENST00000375755.3:c.600A>G	chr6.hg19:g.31712029A>G		211.0	0.0	.		195.0	63.0	.	NM_025259	B0V033|B0V034|O60586|Q5BLU9|Q5SSR1|Q8IW44|Q9BQC7	Silent	SNP	ENST00000375755.3	hg19	CCDS4720.1																																																																																			.	.	.	none		0.502	MSH5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076243.4			G	31712029	A	G	31712029	2	3	73	1	0	0	0	0	0	0	0	1	9880	69	3	3		3	MSH5	6	31712029	Silent	SNP	A	TCGA-AL-3468-01A-01D-1252-08	2631555	31712029	139403038	26	4720											
LRRC1	55227	hgsc.bcm.edu	37	chr6	53787458	53787458	+	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	acttctaaggcgagccactcCacacccaggggagttaaagc	12	6	10	13	1	1	0	0	0	1	0	2	2	2	1	3	3	2	1	3	3	3	3			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr6:53787458C>A	ENST00000370888.1	+	14	1719	c.1442C>A	c.(1441-1443)cCa>cAa	p.P481Q	RP3-523E19.2_ENST00000474641.2_RNA	NM_018214.4	NP_060684.4	Q9BTT6	LRRC1_HUMAN	leucine rich repeat containing 1	481						cytoplasm (GO:0005737)|membrane (GO:0016020)				cervix(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)		CGAGCCACTCCACACCCAGGG	0.408																																					p.P481Q		Atlas-SNP	.											.	LRRC1	59	.	0			c.C1442A						PASS	.						145	144	144					6																	53787458		1898	4118	6016	SO:0001583	missense	55227	exon14			CCACTCCACACCC	AF332199	CCDS4953.2	6p12.2	2014-07-30	2003-11-19		ENSG00000137269	ENSG00000137269			14307	protein-coding gene	gene with protein product		608195	"leucine-rich repeat-containing 1"				Standard	NM_018214		Approved	dJ523E19.1, LANO, FLJ10775, FLJ11834	uc003pcd.1	Q9BTT6	OTTHUMG00000014885	ENST00000370888.1:c.1442C>A	chr6.hg19:g.53787458C>A	ENSP00000359925:p.Pro481Gln	237.0	0.0	.		214.0	189.0	.	NM_018214	Q5TGN3|Q9HAC0|Q9NVF1	Missense_Mutation	SNP	ENST00000370888.1	hg19	CCDS4953.2	.	.	.	.	.	.	.	.	.	.	C	23.5	4.429142	0.83776	.	.	ENSG00000137269	ENST00000370888	T	0.77358	-1.09	5.91	5.91	0.95273	.	0.059723	0.64402	D	0.000002	D	0.87505	0.6194	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.87812	0.2632	10	0.87932	D	0	.	19.2934	0.94112	0.0:1.0:0.0:0.0	.	481	Q9BTT6	LRRC1_HUMAN	Q	481	ENSP00000359925:P481Q	ENSP00000359925:P481Q	P	+	2	0	LRRC1	53895417	1.000000	0.71417	0.980000	0.43619	0.992000	0.81027	7.394000	0.79862	2.808000	0.96608	0.655000	0.94253	CCA	.	.	.	none		0.408	LRRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040970.2	NM_025168		A	53787458	C	A	53787458	3	1	73	1	0	0	0	0	1	0	0	0	8973	594	21	4	1496	4	LRRC1	6	53787458	Missense_Mutation	SNP	C	TCGA-AL-3468-01A-01D-1252-08	22075429	53787458	117327609	27	4721											
BAI3	577	hgsc.bcm.edu	37	chr6	69759168	69759168	+	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	atttattctttctagaattaGatgaatcatctgtatttgtt	11	21	5	4	0	4	3	1	1	3	2	4	3	4	3	0	0	0	2	0	0	6	9	rs267601102		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr6:69759168G>C	ENST00000370598.1	+	15	3084	c.2263G>C	c.(2263-2265)Gat>Cat	p.D755H		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	755					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.D755N(2)		NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				TCTAGAATTAGATGAATCATC	0.289																																					p.D755H		Atlas-SNP	.											BAI3,colon,carcinoma,-1,3	BAI3	451	.	2	Substitution - Missense(2)	skin(2)	c.G2263C						PASS	.						62	61	62					6																	69759168		2202	4295	6497	SO:0001583	missense	577	exon15			GAATTAGATGAAT	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.2263G>C	chr6.hg19:g.69759168G>C	ENSP00000359630:p.Asp755His	112.0	0.0	.		27.0	2.0	.	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	hg19	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.097887	0.76870	.	.	ENSG00000135298	ENST00000370598	T	0.22134	1.97	5.3	5.3	0.74995	Domain of unknown function DUF3497 (1);	0.055134	0.64402	D	0.000001	T	0.32436	0.0829	L	0.58810	1.83	0.80722	D	1	P	0.50819	0.939	P	0.57548	0.823	T	0.03945	-1.0990	10	0.87932	D	0	.	19.3983	0.94617	0.0:0.0:1.0:0.0	.	755	O60242	BAI3_HUMAN	H	755	ENSP00000359630:D755H	ENSP00000359630:D755H	D	+	1	0	BAI3	69815889	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.425000	0.73370	2.650000	0.89964	0.650000	0.86243	GAT	.	.	.	none		0.289	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			C	69759168	G	C	69759168	3	2	73	1	0	0	0	0	1	0	0	0	1300	942	33	4	2313	4	BAI3	6	69759168	Missense_Mutation	SNP	G	TCGA-AL-3468-01A-01D-1252-08	15971710	69759168	101355899	28	4722											
ARL4A	10124	hgsc.bcm.edu	37	chr7	12728407	12728407	+	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	atcataggagatggcctaaaGgaaggacttgagaaactaca	17	7	11	6	0	1	2	1	1	0	2	1	6	1	4	1	4	2	0	1	4	6	4			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr7:12728407G>C	ENST00000396663.1	+	2	1010	c.528G>C	c.(526-528)aaG>aaC	p.K176N	ARL4A_ENST00000396662.1_Missense_Mutation_p.K176N|ARL4A_ENST00000404894.1_Missense_Mutation_p.K176N|ARL4A_ENST00000356797.3_Missense_Mutation_p.K176N|ARL4A_ENST00000396664.2_Missense_Mutation_p.K176N	NM_001037164.2|NM_001195396.1|NM_005738.4|NM_212460.3	NP_001032241.1|NP_001182325.1|NP_005729.1|NP_997625.1	P40617	ARL4A_HUMAN	ADP-ribosylation factor-like 4A	176					brown fat cell differentiation (GO:0050873)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			NS(2)|lung(3)|ovary(1)	6				UCEC - Uterine corpus endometrioid carcinoma (126;0.176)		ATGGCCTAAAGGAAGGACTTG	0.368																																					p.K176N		Atlas-SNP	.											.	ARL4A	15	.	0			c.G528C						PASS	.						58	57	58					7																	12728407		2203	4294	6497	SO:0001583	missense	10124	exon2			CCTAAAGGAAGGA	U73960	CCDS5359.1	7p21.3	2014-05-09	2005-11-03	2005-11-03	ENSG00000122644	ENSG00000122644		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	695	protein-coding gene	gene with protein product		604786	"ADP-ribosylation factor-like 4"	ARL4			Standard	NM_212460		Approved		uc003ssq.3	P40617	OTTHUMG00000023374	ENST00000396663.1:c.528G>C	chr7.hg19:g.12728407G>C	ENSP00000379898:p.Lys176Asn	197.0	0.0	.		168.0	70.0	.	NM_001037164	A4D119|P80418|Q49AF5	Missense_Mutation	SNP	ENST00000396663.1	hg19	CCDS5359.1	.	.	.	.	.	.	.	.	.	.	G	9.982	1.228338	0.22542	.	.	ENSG00000122644	ENST00000396662;ENST00000356797;ENST00000396664;ENST00000396663;ENST00000404894	D;D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63;-1.63	4.52	2.56	0.30785	.	0.309199	0.29730	N	0.011351	T	0.66752	0.2821	N	0.20610	0.595	0.38338	D	0.943985	B	0.33000	0.393	B	0.31101	0.124	T	0.67894	-0.5552	10	0.87932	D	0	.	5.1052	0.14781	0.2333:0.1757:0.591:0.0	.	176	P40617	ARL4A_HUMAN	N	176	ENSP00000379897:K176N;ENSP00000349250:K176N;ENSP00000379899:K176N;ENSP00000379898:K176N;ENSP00000385236:K176N	ENSP00000349250:K176N	K	+	3	2	ARL4A	12694932	0.997000	0.39634	0.999000	0.59377	0.980000	0.70556	0.531000	0.23052	1.232000	0.43678	0.650000	0.86243	AAG	.	.	.	none		0.368	ARL4A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326036.1	NM_005738		C	12728407	G	C	12728407	3	2	73	1	0	0	0	0	1	0	0	0	936	991	35	4	530	4	ARL4A	7	12728407	Missense_Mutation	SNP	G	TCGA-AL-3468-01A-01D-1252-08		12728407	146410256	29	4723											
CAMK2B	816	hgsc.bcm.edu	37	chr7	44259810	44259810	+	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	ctgcgtgagccggatgtaagCgatgcaggcggcatcctctc	7	8	14	12	4	1	1	0	1	1	0	3	3	2	2	2	3	4	3	2	3	1	1			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr7:44259810C>T	ENST00000395749.2	-	23	1928	c.1852G>A	c.(1852-1854)Gct>Act	p.A618T	CAMK2B_ENST00000440254.2_Missense_Mutation_p.A494T|CAMK2B_ENST00000489429.1_5'UTR|CAMK2B_ENST00000358707.3_Missense_Mutation_p.A455T|CAMK2B_ENST00000502837.2_3'UTR|CAMK2B_ENST00000395747.2_Missense_Mutation_p.A470T|CAMK2B_ENST00000258682.6_Missense_Mutation_p.A469T|CAMK2B_ENST00000346990.4_Missense_Mutation_p.A401T|CAMK2B_ENST00000350811.3_Missense_Mutation_p.A494T|CAMK2B_ENST00000353625.4_Missense_Mutation_p.A431T|CAMK2B_ENST00000347193.4_Missense_Mutation_p.A444T|CAMK2B_ENST00000457475.1_Missense_Mutation_p.A470T	NM_001220.4	NP_001211.3	Q13554	KCC2B_HUMAN	calcium/calmodulin-dependent protein kinase II beta	618					activation of meiosis involved in egg activation (GO:0060466)|calcium ion transport (GO:0006816)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|inhibitory G-protein coupled receptor phosphorylation (GO:0002030)|interferon-gamma-mediated signaling pathway (GO:0060333)|neuromuscular process controlling balance (GO:0050885)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of neuron projection development (GO:0010976)|positive regulation of synapse maturation (GO:0090129)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of calcium ion transport (GO:0051924)|regulation of dendritic spine development (GO:0060998)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of skeletal muscle adaptation (GO:0014733)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, cholinergic (GO:0032222)|response to cadmium ion (GO:0046686)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)	18						CGGATGTAAGCGATGCAGGCG	0.652																																					p.A618T		Atlas-SNP	.											.	CAMK2B	56	.	0			c.G1852A						PASS	.						100	63	76					7																	44259810		2203	4300	6503	SO:0001583	missense	816	exon23			TGTAAGCGATGCA	U50358	CCDS5483.1, CCDS5484.1, CCDS5485.1, CCDS5486.1, CCDS5487.1, CCDS5488.1, CCDS5489.1, CCDS43573.1	7p14.3-p14.1	2008-10-30	2008-10-30		ENSG00000058404	ENSG00000058404			1461	protein-coding gene	gene with protein product	"CaM-kinase II beta chain", "calcium/calmodulin-dependent protein kinase type II beta chain", "CaM kinase II beta subunit", "proline rich calmodulin-dependent protein kinase"	607707	"calcium/calmodulin-dependent protein kinase (CaM kinase) II beta"	CAMKB			Standard	NM_172079		Approved	CAM2, CAMK2	uc003tkq.2	Q13554	OTTHUMG00000023491	ENST00000395749.2:c.1852G>A	chr7.hg19:g.44259810C>T	ENSP00000379098:p.Ala618Thr	45.0	0.0	.		76.0	8.0	.	NM_001220	A4D2K0|A4D2K1|A4D2K2|A4D2K3|A4D2K4|A4D2K5|A4D2K6|O95437|O95438|O95599|Q9UGH7|Q9UGH8|Q9UGH9|Q9UNX0|Q9UNX7|Q9UP00|Q9Y5N4|Q9Y6F4	Missense_Mutation	SNP	ENST00000395749.2	hg19	CCDS5483.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.432187	0.83776	.	.	ENSG00000058404	ENST00000350811;ENST00000457475;ENST00000395749;ENST00000425809;ENST00000440254;ENST00000358707;ENST00000353625;ENST00000347193;ENST00000346990;ENST00000258682;ENST00000395747	T;T;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;0.3;0.3	4.43	4.43	0.53597	Calcium/calmodulin-dependent protein kinase II, association-domain (1);	.	.	.	.	T	0.70937	0.3281	L	0.52905	1.665	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	0.968;1.0;0.987;1.0;1.0;0.974;0.988;1.0;0.999;1.0	P;D;P;D;D;P;P;D;P;D	0.91635	0.592;0.993;0.773;0.999;0.994;0.715;0.467;0.998;0.824;0.998	T	0.70608	-0.4825	9	0.40728	T	0.16	.	15.9546	0.79876	0.0:1.0:0.0:0.0	.	469;401;431;455;444;469;470;618;494;618	Q13554-8;Q13554-7;Q13554-4;Q13554-3;Q13554-6;A4D2K5;Q13554-5;Q13554;Q13554-2;A4D2J9	.;.;.;.;.;.;.;KCC2B_HUMAN;.;.	T	494;470;618;136;494;455;431;444;401;469;470	ENSP00000326375:A494T;ENSP00000390292:A470T;ENSP00000379098:A618T;ENSP00000410445:A136T;ENSP00000397937:A494T;ENSP00000351542:A455T;ENSP00000326427:A431T;ENSP00000326544:A444T;ENSP00000326518:A401T;ENSP00000258682:A469T;ENSP00000379096:A470T	ENSP00000258682:A469T	A	-	1	0	CAMK2B	44226335	1.000000	0.71417	1.000000	0.80357	0.579000	0.36224	7.303000	0.78871	2.305000	0.77605	0.462000	0.41574	GCT	.	.	.	none		0.652	CAMK2B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251138.2	NM_172084		T	44259810	C	T	44259810	3	4	73	1	0	0	0	0	1	0	0	0	2602	768	27	1	152	1	CAMK2B	7	44259810	Missense_Mutation	SNP	C	TCGA-AL-3468-01A-01D-1252-08	31531403	44259810	114878853	30	4724											
LANCL2	55915	hgsc.bcm.edu	37	chr7	55459595	55459595	+	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	tgactgctctgcttatactgGctggacaggtgaggctgtgg	6	12	15	8	0	1	2	0	2	1	0	1	3	1	3	0	5	3	4	0	5	2	2			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr7:55459595G>C	ENST00000254770.2	+	2	892	c.314G>C	c.(313-315)gGc>gCc	p.G105A		NM_018697.3	NP_061167.1	Q9NS86	LANC2_HUMAN	LanC lantibiotic synthetase component C-like 2 (bacterial)	105					negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of abscisic acid-activated signaling pathway (GO:0009789)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|GTP binding (GO:0005525)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(2)|lung(11)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	25	Breast(14;0.0379)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00128)|Epithelial(13;0.0706)			GCTTATACTGGCTGGACAGGT	0.393																																					p.G105A		Atlas-SNP	.											.	LANCL2	54	.	0			c.G314C						PASS	.						93	96	95					7																	55459595		2203	4300	6503	SO:0001583	missense	55915	exon2			ATACTGGCTGGAC	AJ278245	CCDS5517.1	7q31.1-q31.33	2008-07-18	2001-12-04		ENSG00000132434	ENSG00000132434			6509	protein-coding gene	gene with protein product	"testis-specific adriamycin sensitivity protein", "G protein-coupled receptor 69B"	612919	"LanC (bacterial lantibiotic synthetase component C)-like 2"	GPR69B		11762191	Standard	NM_018697		Approved	TASP	uc003tqp.3	Q9NS86	OTTHUMG00000023779	ENST00000254770.2:c.314G>C	chr7.hg19:g.55459595G>C	ENSP00000254770:p.Gly105Ala	142.0	0.0	.		214.0	34.0	.	NM_018697	B2R8D4|Q6NSL4|Q8TCQ3|Q9BSR1	Missense_Mutation	SNP	ENST00000254770.2	hg19	CCDS5517.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.661548	0.88154	.	.	ENSG00000132434	ENST00000254770	D	0.91631	-2.88	5.79	5.79	0.91817	Six-hairpin glycosidase-like (1);	0.000000	0.85682	D	0.000000	D	0.97046	0.9035	M	0.91612	3.225	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97510	1.0066	10	0.87932	D	0	.	18.5771	0.91159	0.0:0.0:1.0:0.0	.	105	Q9NS86	LANC2_HUMAN	A	105	ENSP00000254770:G105A	ENSP00000254770:G105A	G	+	2	0	LANCL2	55427089	1.000000	0.71417	0.983000	0.44433	0.808000	0.45660	9.150000	0.94667	2.727000	0.93392	0.655000	0.94253	GGC	.	.	.	none		0.393	LANCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251459.1	NM_018697		C	55459595	G	C	55459595	3	2	73	1	0	0	0	0	1	0	0	0	8628	1203	42	4	320	4	LANCL2	7	55459595	Missense_Mutation	SNP	G	TCGA-AL-3468-01A-01D-1252-08	11199785	55459595	103679068	31	4725											
ABCB1	5243	hgsc.bcm.edu	37	chr7	87148688	87148688	+	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	tttatgtgccaccaagtaggCtccaaaccggaaacatccag	13	8	8	12	1	0	0	0	0	0	0	2	1	2	1	5	2	3	2	5	2	5	3			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr7:87148688C>T	ENST00000265724.3	-	24	3298	c.2881G>A	c.(2881-2883)Gcc>Acc	p.A961T	ABCB1_ENST00000543898.1_Missense_Mutation_p.A897T|ABCB1_ENST00000488737.2_5'UTR	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	961	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	ACCAAGTAGGCTCCAAACCGG	0.383																																					p.A961T		Atlas-SNP	.											.	ABCB1	263	.	0			c.G2881A						PASS	.						98	89	92					7																	87148688		2203	4300	6503	SO:0001583	missense	5243	exon24			AGTAGGCTCCAAA	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.2881G>A	chr7.hg19:g.87148688C>T	ENSP00000265724:p.Ala961Thr	140.0	0.0	.		104.0	40.0	.	NM_000927	A8K294|B5AK60|Q12755|Q14812	Missense_Mutation	SNP	ENST00000265724.3	hg19	CCDS5608.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.171264	0.78452	.	.	ENSG00000085563	ENST00000543174;ENST00000265724;ENST00000543898	D;D	0.89123	-2.47;-2.47	5.79	5.79	0.91817	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.047985	0.85682	D	0.000000	D	0.93501	0.7926	M	0.88640	2.97	0.54753	D	0.999982	B;P	0.45348	0.225;0.856	B;P	0.48598	0.116;0.583	D	0.94005	0.7279	10	0.66056	D	0.02	-19.2761	20.0366	0.97561	0.0:1.0:0.0:0.0	.	897;961	B5AK60;P08183	.;MDR1_HUMAN	T	742;961;897	ENSP00000265724:A961T;ENSP00000444095:A897T	ENSP00000265724:A961T	A	-	1	0	ABCB1	86986624	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	5.801000	0.69115	2.736000	0.93811	0.561000	0.74099	GCC	.	.	.	none		0.383	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927		T	87148688	C	T	87148688	3	4	73	1	0	0	0	0	1	0	0	0	40	797	28	2	985	2	ABCB1	7	87148688	Missense_Mutation	SNP	C	TCGA-AL-3468-01A-01D-1252-08	31689093	87148688	71989975	32	4726											
CALD1	800	hgsc.bcm.edu	37	chr7	134618538	134618538	+	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	aggaagagaaaagggcagcaGaggagaggcagaggataaag	19	1	18	3	0	0	4	0	0	0	4	0	8	0	6	0	5	1	3	0	5	5	1			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr7:134618538G>A	ENST00000361675.2	+	5	1247	c.1018G>A	c.(1018-1020)Gag>Aag	p.E340K	CALD1_ENST00000417172.1_Intron|CALD1_ENST00000495522.1_Intron|CALD1_ENST00000422748.1_Intron|CALD1_ENST00000361388.2_Intron|CALD1_ENST00000424922.1_Intron|CALD1_ENST00000361901.2_Intron|CALD1_ENST00000543443.1_Intron|CALD1_ENST00000393118.2_Intron			Q05682	CALD1_HUMAN	caldesmon 1	340	3 X 14 AA tandem repeats of E-E-E-K-R-A- A-E-E-R-Q-R-I-K.				cellular component movement (GO:0006928)|muscle contraction (GO:0006936)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|calmodulin binding (GO:0005516)|tropomyosin binding (GO:0005523)	p.E340K(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(15)|lung(10)	43						aagggcagcagaggagaggca	0.527																																					p.E340K		Atlas-SNP	.											CALD1,NS,carcinoma,0,1	CALD1	150	.	1	Substitution - Missense(1)	endometrium(1)	c.G1018A						PASS	.																																			SO:0001583	missense	800	exon5			GCAGCAGAGGAGA	M64110	CCDS5834.1, CCDS5835.1, CCDS5836.1, CCDS47716.1, CCDS47717.1, CCDS5836.2	7q33	2007-04-23			ENSG00000122786	ENSG00000122786			1441	protein-coding gene	gene with protein product		114213				1885618	Standard	NM_004342		Approved	CDM, H-CAD, L-CAD	uc003vrz.3	Q05682	OTTHUMG00000155407	ENST00000361675.2:c.1018G>A	chr7.hg19:g.134618538G>A	ENSP00000354826:p.Glu340Lys	14.0	0.0	.		31.0	2.0	.	NM_033138	A8K0X1|Q13978|Q13979|Q14741|Q14742|Q9UD91	Missense_Mutation	SNP	ENST00000361675.2	hg19	CCDS5835.1	.	.	.	.	.	.	.	.	.	.	G	0.886	-0.727229	0.03158	.	.	ENSG00000122786	ENST00000361675	T	0.40225	1.04	3.67	1.57	0.23409	.	.	.	.	.	T	0.31104	0.0786	L	0.29908	0.895	0.80722	D	1	P	0.47253	0.892	P	0.45681	0.49	T	0.02639	-1.1130	8	.	.	.	.	7.2358	0.26070	0.0:0.1886:0.6169:0.1946	.	340	Q05682	CALD1_HUMAN	K	340	ENSP00000354826:E340K	.	E	+	1	0	CALD1	134269078	1.000000	0.71417	0.018000	0.16275	0.194000	0.23727	3.554000	0.53720	-0.013000	0.14199	0.462000	0.41574	GAG	.	.	.	none		0.527	CALD1-005	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339939.1	NM_033138		A	134618538	G	A	134618538	3	1	73	1	0	0	0	0	1	0	0	0	2583	943	33	2	1085	2	CALD1	7	134618538	Missense_Mutation	SNP	G	TCGA-AL-3468-01A-01D-1252-08	47469850	134618538	24520125	33	4727											
TMEM67	91147	hgsc.bcm.edu	37	chr8	94792858	94792858	+	Missense_Mutation	SNP	A	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	atcttgtcaagctcttggaaAtatgtgtgtgatgaacatga	12	14	10	5	0	3	3	1	3	2	0	3	4	3	4	0	1	2	1	0	1	4	3			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr8:94792858A>C	ENST00000453321.3	+	8	810	c.752A>C	c.(751-753)aAt>aCt	p.N251T	TMEM67_ENST00000425545.2_3'UTR|TMEM67_ENST00000409623.3_Missense_Mutation_p.N170T	NM_153704.5	NP_714915.3	Q5HYA8	MKS3_HUMAN	transmembrane protein 67	251				N -> S (in Ref. 1; BAG52507). {ECO:0000305}.	cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of centrosome duplication (GO:0010826)	centrosome (GO:0005813)|ciliary membrane (GO:0060170)|cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)	filamin binding (GO:0031005)|unfolded protein binding (GO:0051082)			breast(3)|endometrium(8)|kidney(5)|large_intestine(4)|liver(2)|lung(15)|ovary(2)|skin(1)|urinary_tract(1)	41	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)			GCTCTTGGAAATATGTGTGTG	0.363																																					p.N251T		Atlas-SNP	.											.	TMEM67	187	.	0			c.A752C						PASS	.						257	245	249					8																	94792858		2203	4300	6503	SO:0001583	missense	91147	exon8			TTGGAAATATGTG	BX648768	CCDS6258.2, CCDS47893.1	8q22.1	2014-09-17			ENSG00000164953	ENSG00000164953			28396	protein-coding gene	gene with protein product	"Meckelin"	609884	"Meckel syndrome, type 3"	MKS3		12384791, 16415887, 19508969	Standard	NM_153704		Approved	MGC26979, JBTS6, NPHP11	uc011lgk.2	Q5HYA8	OTTHUMG00000153119	ENST00000453321.3:c.752A>C	chr8.hg19:g.94792858A>C	ENSP00000389998:p.Asn251Thr	444.0	1.0	.		291.0	134.0	.	NM_153704	B3KRU5|B3KT47|G5E9H2|Q3ZCX3|Q7Z5T8|Q8IZ06	Missense_Mutation	SNP	ENST00000453321.3	hg19	CCDS6258.2	.	.	.	.	.	.	.	.	.	.	A	25.0	4.588377	0.86851	.	.	ENSG00000164953	ENST00000452276;ENST00000453321;ENST00000409623	D;D;D	0.99167	-5.51;-5.51;-5.51	5.86	5.86	0.93980	.	0.091847	0.64402	D	0.000001	D	0.99318	0.9761	M	0.86028	2.79	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99150	1.0858	10	0.87932	D	0	-22.3661	16.2559	0.82517	1.0:0.0:0.0:0.0	.	251;170	Q5HYA8;G5E9H2	MKS3_HUMAN;.	T	148;251;170	ENSP00000388671:N148T;ENSP00000389998:N251T;ENSP00000386966:N170T	ENSP00000314488:N241T	N	+	2	0	TMEM67	94862034	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.629000	0.90983	2.239000	0.73571	0.528000	0.53228	AAT	.	.	.	none		0.363	TMEM67-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329641.2	NM_153704		C	94792858	A	C	94792858	3	2	73	1	0	0	0	0	1	0	0	0	16208	101	4	5	920	5	TMEM67	8	94792858	Missense_Mutation	SNP	A	TCGA-AL-3468-01A-01D-1252-08		94792858	51571164	34	4728											
KCNS2	3788	hgsc.bcm.edu	37	chr8	99441466	99441466	+	Frame_Shift_Del	DEL	A	A	-																															ctcccacttttaccggcgccAaaagcaacttgagagtgcca																										TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr8:99441466delA	ENST00000287042.4	+	2	1609	c.1259delA	c.(1258-1260)caafs	p.Q420fs	KCNS2_ENST00000521839.1_Frame_Shift_Del_p.Q420fs	NM_020697.2	NP_065748.1	Q9ULS6	KCNS2_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 2	420					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			autonomic_ganglia(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	31	Breast(36;2.4e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.0448)			TACCGGCGCCAAAAGCAACTT	0.498																																					p.Q420fs	Pancreas(138;844 2489 9202 24627)	Atlas-INDEL	.											.	KCNS2	93	.	0			c.1258delC						PASS	.						116	116	116					8																	99441466		2203	4300	6503	SO:0001589	frameshift_variant	3788	exon2			.	AB032970	CCDS6279.1	8q22	2011-07-05			ENSG00000156486	ENSG00000156486		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6301	protein-coding gene	gene with protein product		602906				9305895, 16382104	Standard	NM_020697		Approved	Kv9.2	uc003yin.3	Q9ULS6	OTTHUMG00000044337	ENST00000287042.4:c.1259delA	chr8.hg19:g.99441466delA	ENSP00000287042:p.Gln420fs	273.0	0.0	0		271.0	114.0	0.420664	NM_020697	A8KAN1	Frame_Shift_Del	DEL	ENST00000287042.4	hg19	CCDS6279.1																																																																																			.	.	.	none		0.498	KCNS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103134.1	NM_020697		-	99441466	A	-	99441466	7	5	73	1	0	1	0	1	0	0	0	0	8096	130	5	0	1261	0	KCNS2	8	99441466	Frame_Shift_Del	DEL	A	TCGA-AL-3468-01A-01D-1252-08	4648608	99441466	46922556	35	4729											
ZNF658	26149	hgsc.bcm.edu	37	chr9	40774146	40774146	+	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	agaaaggtagaatttatcttCtgtgtgaattctctgatgtg	11	16	10	4	0	3	4	0	2	3	2	4	4	3	4	0	1	0	1	0	1	5	5			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr9:40774146C>A	ENST00000602553.1	-	5	1423	c.1129G>T	c.(1129-1131)Gaa>Taa	p.E377*	ZNF658_ENST00000441795.1_Nonsense_Mutation_p.E375*|ZNF658_ENST00000377626.3_Nonsense_Mutation_p.E377*			Q5TYW1	ZN658_HUMAN	zinc finger protein 658	377					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(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)		AATTTATCTTCTGTGTGAATT	0.403																																					p.E377X		Atlas-SNP	.											.	ZNF658	100	.	0			c.G1129T						PASS	.						205	209	207					9																	40774146		2203	4300	6503	SO:0001587	stop_gained	26149	exon5			TATCTTCTGTGTG	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.1129G>T	chr9.hg19:g.40774146C>A	ENSP00000473484:p.Glu377*	701.0	0.0	.		251.0	105.0	.	NM_033160	Q6PIP3|Q96M55|Q9H9S6|Q9UG02	Nonsense_Mutation	SNP	ENST00000602553.1	hg19	CCDS35023.1	.	.	.	.	.	.	.	.	.	.	c	28.0	4.885852	0.91814	.	.	ENSG00000196409	ENST00000441795;ENST00000377626	.	.	.	1.96	0.962	0.19643	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	8.0678	0.30672	0.0:0.7452:0.2548:0.0	.	.	.	.	X	375;377	.	ENSP00000366853:E377X	E	-	1	0	ZNF658	40764146	0.022000	0.18835	0.016000	0.15963	0.058000	0.15608	1.461000	0.35255	0.360000	0.24265	0.384000	0.25694	GAA	.	.	.	none		0.403	ZNF658-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467800.1	NM_033160		A	40774146	C	A	40774146	4	1	73	1	0	0	0	0	0	1	0	0	18081	922	32	4	2054	4	ZNF658	9	40774146	Nonsense_Mutation	SNP	C	TCGA-AL-3468-01A-01D-1252-08		40774146	100439285	36	4730											
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84609703	84609703	+	Frame_Shift_Del	DEL	A	A	-																															ccttcccagtggggcttgggAaagctcagcacaacccagaa																										TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr9:84609703delA	ENST00000344803.2	+	4	4365	c.4318delA	c.(4318-4320)aaafs	p.K1440fs		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	1440					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GGGGCTTGGGAAAGCTCAGCA	0.552																																					p.G1439fs		Atlas-INDEL	.											.	.	.	.	0			c.4317delG						PASS	.						41	41	41					9																	84609703		1915	4112	6027	SO:0001589	frameshift_variant	389763	exon4			.		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.4318delA	chr9.hg19:g.84609703delA	ENSP00000341988:p.Lys1440fs	87.0	0.0	0		85.0	29.0	0.341176	NM_001001670		Frame_Shift_Del	DEL	ENST00000344803.2	hg19	CCDS47986.1																																																																																			.	.	.	none		0.552	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		-	84609703	A	-	84609703	7	5	73	1	0	1	0	1	0	0	0	0	5939	247	9	0	4332	0	FLJ46321	9	84609703	Frame_Shift_Del	DEL	A	TCGA-AL-3468-01A-01D-1252-08	43835557	84609703	56603728	37	4731											
COL5A1	1289	hgsc.bcm.edu	37	chr9	137714852	137714852	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctctctgcagggtccgccTggtccaaaaggtgctaaggg	7	9	13	12	1	2	0	0	0	2	0	5	0	4	0	3	4	2	2	3	4	3	1			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr9:137714852T>C	ENST00000371817.3	+	60	5031	c.4617T>C	c.(4615-4617)ccT>ccC	p.P1539P		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1539	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		AGGGTCCGCCTGGTCCAAAAG	0.657																																					p.P1539P		Atlas-SNP	.											.	COL5A1	323	.	0			c.T4617C						PASS	.						101	77	85					9																	137714852		2203	4300	6503	SO:0001819	synonymous_variant	1289	exon60			TCCGCCTGGTCCA	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.4617T>C	chr9.hg19:g.137714852T>C		53.0	0.0	.		61.0	12.0	.	NM_000093	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	hg19	CCDS6982.1																																																																																			.	.	.	none		0.657	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		C	137714852	T	C	137714852	2	2	73	1	0	0	0	0	0	0	0	1	3698	1567	55	3		3	COL5A1	9	137714852	Silent	SNP	T	TCGA-AL-3468-01A-01D-1252-08	53105149	137714852	3498579	38	4732											
ZNF503	84858	hgsc.bcm.edu	37	chr10	77159027	77159027	+	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	aggagtgcacaccgtgcagcGggtgcgtggggtacaccagc	8	5	17	11	3	0	0	0	0	0	0	0	1	0	1	2	4	6	3	2	4	1	1			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr10:77159027G>T	ENST00000372524.4	-	2	1907	c.1421C>A	c.(1420-1422)cCg>cAg	p.P474Q	ZNF503_ENST00000535216.1_Missense_Mutation_p.P474Q|ZNF503-AS2_ENST00000466942.2_RNA|RP11-399K21.11_ENST00000418818.2_lincRNA	NM_032772.4	NP_116161.2	Q96F45	ZN503_HUMAN	zinc finger protein 503	474	Ala-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)					ACCGTGCAGCGGGTGCGTGGG	0.721																																					p.P474Q		Atlas-SNP	.											.	ZNF503	25	.	0			c.C1421A						PASS	.						10	13	12					10																	77159027		2191	4274	6465	SO:0001583	missense	84858	exon2			TGCAGCGGGTGCG	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.1421C>A	chr10.hg19:g.77159027G>T	ENSP00000361602:p.Pro474Gln	20.0	0.0	.		50.0	32.0	.	NM_032772	Q8NAC5|Q96E25|Q96IJ0	Missense_Mutation	SNP	ENST00000372524.4	hg19	CCDS7350.1	.	.	.	.	.	.	.	.	.	.	G	16.38	3.106906	0.56291	.	.	ENSG00000165655	ENST00000372524;ENST00000535216;ENST00000372516	T;T	0.49432	0.78;0.78	4.45	3.54	0.40534	.	0.119276	0.64402	D	0.000019	T	0.57272	0.2042	M	0.69358	2.11	0.46416	D	0.999039	D	0.65815	0.995	P	0.56865	0.808	T	0.59716	-0.7402	10	0.66056	D	0.02	-17.0629	9.0142	0.36159	0.0794:0.0:0.7743:0.1463	.	474	Q96F45	ZN503_HUMAN	Q	474;474;437	ENSP00000361602:P474Q;ENSP00000438988:P474Q	ENSP00000361594:P437Q	P	-	2	0	ZNF503	76829033	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.106000	0.71511	1.088000	0.41272	0.643000	0.83706	CCG	.	.	.	none		0.721	ZNF503-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048826.1	NM_032772		T	77159027	G	T	77159027	3	4	73	1	0	0	0	0	1	0	0	0	17963	1116	39	4	523	4	ZNF503	10	77159027	Missense_Mutation	SNP	G	TCGA-AL-3468-01A-01D-1252-08		77159027	58375720	39	4733											
CTBP2	1488	hgsc.bcm.edu	37	chr10	126715159	126715159	+	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	ggggatgctgtctgcagaggAgccgcagcgcccagagaagc	9	4	17	11	2	1	2	0	0	1	2	1	5	1	4	2	3	5	3	2	3	1	0	rs529129641|rs372118432	byFrequency	TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr10:126715159A>G	ENST00000337195.5	-	3	458				CTBP2_ENST00000494626.2_Intron|CTBP2_ENST00000309035.6_Silent_p.A390A|CTBP2_ENST00000411419.2_Intron|CTBP2_ENST00000531469.1_Intron	NM_001329.2	NP_001320.1	P56545	CTBP2_HUMAN	C-terminal binding protein 2						negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)|white fat cell differentiation (GO:0050872)	cell junction (GO:0030054)|nucleus (GO:0005634)|synapse (GO:0045202)|transcriptional repressor complex (GO:0017053)	NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		TCTGCAGAGGAGCCGCAGCGC	0.701																																					p.A390A		Atlas-SNP	.											.,1	CTBP2	100	.	0			c.T1170C						PASS	.						9	7	8					10																	126715159		2126	4169	6295	SO:0001627	intron_variant	1488	exon1			CAGAGGAGCCGCA	AF016507	CCDS7643.1, CCDS7644.1	10q26.13	2008-08-01			ENSG00000175029	ENSG00000175029			2495	protein-coding gene	gene with protein product		602619				9479502, 11864595	Standard	NM_022802		Approved	ribeye	uc001lie.4	P56545	OTTHUMG00000019224	ENST00000337195.5:c.58+12406T>C	chr10.hg19:g.126715159A>G		4.0	0.0	.		15.0	3.0	.	NM_022802	A8K2X5|D3DRF5|O43449|Q5SQP7|Q69YI3|Q86SV0|Q9H2T8	Silent	SNP	ENST00000337195.5	hg19	CCDS7643.1																																																																																			.	.	.	none		0.701	CTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050900.3	NM_001083914		G	126715159	A	G	126715159	1	3	73	0	1	0	0	0	0	0	0	0	4000	291	11	3		3	CTBP2	10	126715159	Intron	SNP	A	TCGA-AL-3468-01A-01D-1252-08	49556132	126715159	8819588	40	4734											
KNDC1	85442	hgsc.bcm.edu	37	chr10	135009191	135009191	+	Missense_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	ctgtgtactgtgtggccgccGttctgtggaccgcagccaag	5	10	14	12	3	1	0	0	0	1	0	1	1	1	1	4	2	2	3	4	2	2	2	rs541722509		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr10:135009191G>A	ENST00000304613.3	+	10	1621	c.1600G>A	c.(1600-1602)Gtt>Att	p.V534I	KNDC1_ENST00000368572.2_Missense_Mutation_p.V534I|KNDC1_ENST00000368571.2_Missense_Mutation_p.V469I			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	534	KIND 2. {ECO:0000255|PROSITE- ProRule:PRU00709}.				cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		TGTGGCCGCCGTTCTGTGGAC	0.667													G|||	1	0.000199681	8e-04	0	5008	,	,		15057	0		0	False		,,,				2504	0				p.V534I		Atlas-SNP	.											.	KNDC1	155	.	0			c.G1600A						PASS	.						48	44	45					10																	135009191		2202	4300	6502	SO:0001583	missense	85442	exon10			GCCGCCGTTCTGT	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"RasGEF domain family, member 2"	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.1600G>A	chr10.hg19:g.135009191G>A	ENSP00000304437:p.Val534Ile	44.0	0.0	.		55.0	21.0	.	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	hg19	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	G	10.94	1.494320	0.26774	.	.	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.41400	1.0;1.0;1.0	4.63	2.32	0.28847	KIND (2);	0.189090	0.34067	N	0.004291	T	0.24851	0.0603	L	0.45581	1.43	0.38564	D	0.949782	P;B	0.45428	0.858;0.221	B;B	0.32928	0.155;0.051	T	0.08806	-1.0704	10	0.32370	T	0.25	-39.5659	4.8812	0.13681	0.3953:0.0:0.6047:0.0	.	469;534	Q76NI1-2;Q76NI1	.;VKIND_HUMAN	I	534;534;469	ENSP00000304437:V534I;ENSP00000357561:V534I;ENSP00000357560:V469I	ENSP00000304437:V534I	V	+	1	0	KNDC1	134859181	0.108000	0.22018	0.624000	0.29186	0.129000	0.20672	1.040000	0.30278	1.085000	0.41206	0.306000	0.20318	GTT	.	.	.	none		0.667	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		A	135009191	G	A	135009191	3	1	73	1	0	0	0	0	1	0	0	0	8433	1145	40	1	1638	1	KNDC1	10	135009191	Missense_Mutation	SNP	G	TCGA-AL-3468-01A-01D-1252-08	8294032	135009191	525556	41	4735											
OR5P2	120065	hgsc.bcm.edu	37	chr11	7817940	7817940	+	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	gacactgatatcagaacaggAgagttcaagtaagggagcga	16	6	13	6	1	2	3	2	1	0	2	2	7	2	4	0	2	2	2	0	2	4	3			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr11:7817940A>T	ENST00000329434.2	-	1	580	c.550T>A	c.(550-552)Tcc>Acc	p.S184T	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	184						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)|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)		TCAGAACAGGAGAGTTCAAGT	0.398																																					p.S184T		Atlas-SNP	.											.	OR5P2	68	.	0			c.T550A						PASS	.						72	83	80					11																	7817940		2102	4292	6394	SO:0001583	missense	120065	exon1			AACAGGAGAGTTC	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.550T>A	chr11.hg19:g.7817940A>T	ENSP00000331823:p.Ser184Thr	128.0	0.0	.		82.0	31.0	.	NM_153444	Q3MIS8	Missense_Mutation	SNP	ENST00000329434.2	hg19	CCDS7782.1	.	.	.	.	.	.	.	.	.	.	A	12.70	2.016481	0.35606	.	.	ENSG00000183303	ENST00000329434	T	0.00282	8.31	5.5	5.5	0.81552	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000005	T	0.00468	0.0015	M	0.78637	2.42	0.29905	N	0.824079	P	0.40000	0.698	P	0.48524	0.58	T	0.31110	-0.9955	10	0.52906	T	0.07	-52.8073	13.6117	0.62083	1.0:0.0:0.0:0.0	.	184	Q8WZ92	OR5P2_HUMAN	T	184	ENSP00000331823:S184T	ENSP00000331823:S184T	S	-	1	0	OR5P2	7774516	0.339000	0.24784	0.995000	0.50966	0.033000	0.12548	0.825000	0.27393	2.313000	0.78055	0.454000	0.30748	TCC	.	.	.	none		0.398	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444		T	7817940	A	T	7817940	3	4	73	1	0	0	0	0	1	0	0	0	11185	304	11	5	422	5	OR5P2	11	7817940	Missense_Mutation	SNP	A	TCGA-AL-3468-01A-01D-1252-08		7817940	127188576	42	4736											
NXF1	10482	hgsc.bcm.edu	37	chr11	62567920	62567921	+	Frame_Shift_Ins	INS	-	-	G																															gccagagctcttctagcttcINSagcccctttatcttgtccaa																										TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr11:62567920_62567921insG	ENST00000532297.1	-	11	1573_1574	c.944_945insC	c.(943-945)ctgfs	p.L315fs	NXF1_ENST00000439713.2_Frame_Shift_Ins_p.L315fs|NXF1_ENST00000531131.1_Frame_Shift_Ins_p.L178fs|NXF1_ENST00000294172.2_Frame_Shift_Ins_p.L315fs|NXF1_ENST00000531709.2_Frame_Shift_Ins_p.L315fs			Q9UBU9	NXF1_HUMAN	nuclear RNA export factor 1	315					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						CTTCTAGCTTCAGCCCCTTTAT	0.55																																					p.L315fs		Atlas-INDEL	.											.	NXF1	67	.	0			c.945_946insC						PASS	.																																			SO:0001589	frameshift_variant	10482	exon10			.	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.944_945insC	chr11.hg19:g.62567920_62567921insG	ENSP00000436679:p.Leu315fs	95.0	0.0	0		87.0	23.0	0.264368	NM_006362	B4E269|Q99799|Q9UQL2	Frame_Shift_Ins	INS	ENST00000532297.1	hg19	CCDS8037.1																																																																																			.	.	.	none		0.55	NXF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395365.2	NM_006362		G	62567921	-	G	62567920	7	5	73	1	0	1	1	0	0	0	0	0	10789	813	29	0	1017	0	NXF1	11	62567920	Frame_Shift_Ins	INS	-	TCGA-AL-3468-01A-01D-1252-08	54749980	62567920	72438596	43	4737	53	2									
NXF1	10482	hgsc.bcm.edu	37	chr11	62567921	62567921	+	Missense_Mutation	SNP	A	A	G																															gccagagctcttctagcttcAgcccctttatcttgtccaat																										TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr11:62567921A>G	ENST00000532297.1	-	11	1573	c.944T>C	c.(943-945)cTg>cCg	p.L315P	NXF1_ENST00000439713.2_Missense_Mutation_p.L315P|NXF1_ENST00000531131.1_Missense_Mutation_p.L178P|NXF1_ENST00000294172.2_Missense_Mutation_p.L315P|NXF1_ENST00000531709.2_Missense_Mutation_p.L315P			Q9UBU9	NXF1_HUMAN	nuclear RNA export factor 1	315					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						TTCTAGCTTCAGCCCCTTTAT	0.547																																					p.L315P		Atlas-SNP	.											.	NXF1	67	.	0			c.T944C						PASS	.						150	105	120					11																	62567921		2201	4299	6500	SO:0001583	missense	10482	exon10			AGCTTCAGCCCCT	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.944T>C	chr11.hg19:g.62567921A>G	ENSP00000436679:p.Leu315Pro	92.0	0.0	.		80.0	27.0	.	NM_006362	B4E269|Q99799|Q9UQL2	Missense_Mutation	SNP	ENST00000532297.1	hg19	CCDS8037.1	.	.	.	.	.	.	.	.	.	.	A	16.72	3.200863	0.58234	.	.	ENSG00000162231	ENST00000294172;ENST00000532297;ENST00000530875;ENST00000439713	T;T;T;T	0.56941	0.43;0.43;0.43;0.43	4.91	3.78	0.43462	.	0.074476	0.56097	D	0.000032	T	0.78622	0.4312	H	0.96996	3.92	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.91635	0.998;0.975;0.997;0.999	T	0.80160	-0.1498	10	0.49607	T	0.09	-11.668	8.613	0.33815	0.9087:0.0:0.0913:0.0	.	178;358;328;315	B4E227;E9PIN3;Q59E96;Q9UBU9	.;.;.;NXF1_HUMAN	P	315;315;358;315	ENSP00000294172:L315P;ENSP00000436679:L315P;ENSP00000435742:L358P;ENSP00000408864:L315P	ENSP00000294172:L315P	L	-	2	0	NXF1	62324497	1.000000	0.71417	1.000000	0.80357	0.867000	0.49689	8.818000	0.91991	0.902000	0.36520	0.528000	0.53228	CTG	.	.	.	none		0.547	NXF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395365.2	NM_006362		G	62567921	A	G	62567921	3	3	73	1	0	0	0	0	1	0	0	0	10789	188	7	3	1018	3	NXF1	11	62567921	Missense_Mutation	SNP	A	TCGA-AL-3468-01A-01D-1252-08	1	62567921	72438595	44	4738	53	2									
CD248	57124	hgsc.bcm.edu	37	chr11	66082566	66082566	+	Frame_Shift_Del	DEL	T	T	-																															ggggccatcttcccttgggaTttggggggctttggaatggg																										TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr11:66082566delT	ENST00000311330.3	-	1	1949	c.1933delA	c.(1933-1935)atcfs	p.I645fs	RP11-867G23.13_ENST00000534065.1_RNA	NM_020404.2	NP_065137.1	Q9HCU0	CD248_HUMAN	CD248 molecule, endosialin	645	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						TCCCTTGGGATTTGGGGGGCT	0.657																																					p.I645fs		Atlas-INDEL	.											.	CD248	69	.	0			c.1934delT						PASS	.						33	37	36					11																	66082566		2199	4291	6490	SO:0001589	frameshift_variant	57124	exon1			.	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.1933delA	chr11.hg19:g.66082566delT	ENSP00000308117:p.Ile645fs	143.0	0.0	0		148.0	64.0	0.432432	NM_020404	Q2M2V5|Q3SX55|Q96KB6	Frame_Shift_Del	DEL	ENST00000311330.3	hg19	CCDS8134.1																																																																																			.	.	.	none		0.657	CD248-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392922.2	NM_020404		-	66082566	T	-	66082566	7	5	73	1	0	1	0	1	0	0	0	0	2991	1493	52	0	344	0	CD248	11	66082566	Frame_Shift_Del	DEL	T	TCGA-AL-3468-01A-01D-1252-08	3514645	66082566	68923950	45	4739											
LTBR	4055	hgsc.bcm.edu	37	chr12	6494285	6494285	+	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	cactggaactacctgaccatCtgccagctgtgccgcccctg	7	8	9	17	1	1	1	0	1	1	0	1	2	1	2	6	1	5	1	6	1	2	1			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr12:6494285C>T	ENST00000228918.4	+	3	617	c.291C>T	c.(289-291)atC>atT	p.I97I	LTBR_ENST00000543190.1_5'UTR|LTBR_ENST00000546296.1_3'UTR|LTBR_ENST00000541102.1_5'UTR|LTBR_ENST00000539925.1_Silent_p.I78I	NM_002342.2	NP_002333.1	P36941	TNR3_HUMAN	lymphotoxin beta receptor (TNFR superfamily, member 3)	97					apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|cervix(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	15						ACCTGACCATCTGCCAGCTGT	0.617																																					p.I97I		Atlas-SNP	.											.	LTBR	30	.	0			c.C291T						PASS	.						152	142	145					12																	6494285		2203	4300	6503	SO:0001819	synonymous_variant	4055	exon3			GACCATCTGCCAG	L04270	CCDS8544.1, CCDS59233.1	12p13	2013-05-22				ENSG00000111321		"Tumor necrosis factor receptor superfamily"	6718	protein-coding gene	gene with protein product		600979		D12S370		8171323, 8486360	Standard	NM_002342		Approved	TNFCR, TNFR-RP, TNFR2-RP, TNF-R-III, TNFRSF3	uc001qny.2	P36941		ENST00000228918.4:c.291C>T	chr12.hg19:g.6494285C>T		280.0	0.0	.		446.0	261.0	.	NM_002342	B7Z1D2|D3DUR2|F5GXE7	Silent	SNP	ENST00000228918.4	hg19	CCDS8544.1																																																																																			.	.	.	none		0.617	LTBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399422.1			T	6494285	C	T	6494285	2	4	73	1	0	0	0	0	0	0	0	1	9084	903	32	2		2	LTBR	12	6494285	Silent	SNP	C	TCGA-AL-3468-01A-01D-1252-08		6494285	127357610	46	4740											
TM7SF3	51768	hgsc.bcm.edu	37	chr12	27156249	27156249	+	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	cacattgcttgaaatatcatGcaaaatagcttcctctggaa	14	12	6	9	0	2	1	1	1	1	0	3	2	3	2	1	1	3	3	1	1	6	5			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr12:27156249G>T	ENST00000343028.4	-	2	391	c.166C>A	c.(166-168)Cat>Aat	p.H56N	TM7SF3_ENST00000542667.1_Intron	NM_016551.2	NP_057635.1	Q9NS93	TM7S3_HUMAN	transmembrane 7 superfamily member 3	56						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)					GAAATATCATGCAAAATAGCT	0.343																																					p.H56N		Atlas-SNP	.											.	TM7SF3	41	.	0			c.C166A						PASS	.						61	58	59					12																	27156249		2203	4297	6500	SO:0001583	missense	51768	exon2			TATCATGCAAAAT	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.166C>A	chr12.hg19:g.27156249G>T	ENSP00000342322:p.His56Asn	103.0	0.0	.		65.0	23.0	.	NM_016551	B3KMZ3|Q9NUS4	Missense_Mutation	SNP	ENST00000343028.4	hg19	CCDS8710.1	.	.	.	.	.	.	.	.	.	.	G	11.88	1.771441	0.31320	.	.	ENSG00000064115	ENST00000343028;ENST00000512808;ENST00000545600	T	0.28255	1.62	5.57	5.57	0.84162	.	0.502867	0.22125	N	0.064269	T	0.20170	0.0485	N	0.22421	0.69	0.20074	N	0.999935	B	0.21520	0.057	B	0.15870	0.014	T	0.11348	-1.0591	10	0.19590	T	0.45	-2.76	12.4317	0.55577	0.0:0.0:0.8326:0.1674	.	56	Q9NS93	TM7S3_HUMAN	N	56;35;61	ENSP00000342322:H56N	ENSP00000342322:H56N	H	-	1	0	TM7SF3	27047516	0.757000	0.28394	0.164000	0.22755	0.847000	0.48162	1.951000	0.40333	2.788000	0.95919	0.650000	0.86243	CAT	.	.	.	none		0.343	TM7SF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403033.1	NM_016551		T	27156249	G	T	27156249	3	4	73	1	0	0	0	0	1	0	0	0	15987	1319	46	4	1590	4	TM7SF3	12	27156249	Missense_Mutation	SNP	G	TCGA-AL-3468-01A-01D-1252-08	20661964	27156249	106695646	47	4741											
TIMELESS	8914	hgsc.bcm.edu	37	chr12	56822670	56822670	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaaccatcccactcaccggCgtgcccaggaggcagcttcc	8	6	10	17	2	1	0	1	0	0	0	3	1	3	1	5	3	3	3	5	3	1	2			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr12:56822670C>T	ENST00000553532.1	-	11	1451	c.1301G>A	c.(1300-1302)cGc>cAc	p.R434H	TIMELESS_ENST00000229201.4_Missense_Mutation_p.R433H|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						CACTCACCGGCGTGCCCAGGA	0.517																																					p.R434H		Atlas-SNP	.											.	TIMELESS	107	.	0			c.G1301A						PASS	.						88	77	81					12																	56822670		2203	4300	6503	SO:0001583	missense	8914	exon11			CACCGGCGTGCCC	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.1301G>A	chr12.hg19:g.56822670C>T	ENSP00000450607:p.Arg434His	90.0	0.0	.		116.0	32.0	.	NM_003920		Missense_Mutation	SNP	ENST00000553532.1	hg19	CCDS8918.1	.	.	.	.	.	.	.	.	.	.	C	32	5.163112	0.94727	.	.	ENSG00000111602	ENST00000229201;ENST00000553532	T;T	0.10005	2.92;2.93	4.95	4.95	0.65309	.	0.057662	0.64402	D	0.000001	T	0.32645	0.0836	M	0.83012	2.62	0.80722	D	1	D;D	0.76494	0.999;0.999	P;P	0.58780	0.845;0.704	T	0.12243	-1.0555	10	0.51188	T	0.08	.	17.3351	0.87278	0.0:1.0:0.0:0.0	.	433;434	Q9UNS1-2;Q9UNS1	.;TIM_HUMAN	H	433;434	ENSP00000229201:R433H;ENSP00000450607:R434H	ENSP00000229201:R434H	R	-	2	0	TIMELESS	55108937	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	7.503000	0.81632	2.454000	0.82982	0.462000	0.41574	CGC	.	.	.	none		0.517	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920		T	56822670	C	T	56822670	3	4	73	1	0	0	0	0	1	0	0	0	15916	768	27	1	2401	1	TIMELESS	12	56822670	Missense_Mutation	SNP	C	TCGA-AL-3468-01A-01D-1252-08	29666421	56822670	77029225	48	4742											
GRIP1	23426	hgsc.bcm.edu	37	chr12	66765685	66765685	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcatgattcaaactcatcGtgctccccgacatgattgtt	9	13	6	13	2	3	2	3	2	0	0	5	3	4	2	3	0	2	2	3	0	1	3	rs367781032		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr12:66765685G>A	ENST00000398016.3	-	22	2713	c.2645C>T	c.(2644-2646)aCg>aTg	p.T882M	GRIP1_ENST00000359742.4_Missense_Mutation_p.T934M|GRIP1_ENST00000286445.7_Missense_Mutation_p.T919M	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)	p.T882K(1)		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)		CAAACTCATCGTGCTCCCCGA	0.512																																					p.T882M		Atlas-SNP	.											GRIP1,NS,carcinoma,0,1	GRIP1	106	.	1	Substitution - Missense(1)	lung(1)	c.C2645T						PASS	.	G	MET/THR,MET/THR	0,4056		0,0,2028	53	57	56		2600,2645	6.1	1	12		56	2,8392		0,2,4195	no	missense,missense	GRIP1	NM_001178074.1,NM_021150.3	81,81	0,2,6223	AA,AG,GG		0.0238,0.0,0.0161	benign,benign	867/1062,882/1077	66765685	2,12448	2028	4197	6225	SO:0001583	missense	23426	exon22			CTCATCGTGCTCC	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.2645C>T	chr12.hg19:g.66765685G>A	ENSP00000381098:p.Thr882Met	133.0	0.0	.		187.0	51.0	.	NM_021150	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Missense_Mutation	SNP	ENST00000398016.3	hg19	CCDS41807.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.77|13.77	2.337198|2.337198	0.41398|0.41398	0.0|0.0	2.38E-4|2.38E-4	ENSG00000155974|ENSG00000155974	ENST00000538164|ENST00000398016;ENST00000359742;ENST00000286445;ENST00000538211;ENST00000540433;ENST00000536215	.|T;T;T;T;T;T	.|0.79352	.|-1.26;-1.26;-1.26;-1.26;-1.26;-1.26	6.07|6.07	6.07|6.07	0.98685|0.98685	.|.	.|0.147302	.|0.64402	.|D	.|0.000014	.|D	.|0.84633	.|0.5515	L|L	0.56769|0.56769	1.78|1.78	0.46185|0.46185	D|D	0.998915|0.998915	.|B;D;B;D	.|0.61080	.|0.11;0.981;0.405;0.989	.|B;P;B;P	.|0.57283	.|0.04;0.563;0.058;0.817	.|T	.|0.82078	.|-0.0635	.|9	.|.	.|.	.|.	-13.6657|-13.6657	20.6593|20.6593	0.99626|0.99626	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|867;934;882;919	.|F5H4N6;Q9Y3R0;Q9Y3R0-3;Q9Y3R0-2	.|.;GRIP1_HUMAN;.;.	X|M	734|882;934;919;867;826;759	.|ENSP00000381098:T882M;ENSP00000352780:T934M;ENSP00000286445:T919M;ENSP00000446047:T867M;ENSP00000446024:T826M;ENSP00000446011:T759M	.|.	R|T	-|-	1|2	2|0	GRIP1|GRIP1	65051952|65051952	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.717000|0.717000	0.41224|0.41224	5.059000|5.059000	0.64306|0.64306	2.885000|2.885000	0.99019|0.99019	0.655000|0.655000	0.94253|0.94253	CGA|ACG	.	.	.	weak		0.512	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2			A	66765685	G	A	66765685	3	1	73	1	0	0	0	0	1	0	0	0	6794	1145	40	1	597	1	GRIP1	12	66765685	Missense_Mutation	SNP	G	TCGA-AL-3468-01A-01D-1252-08	9943015	66765685	67086210	49	4743											
SSH1	54434	hgsc.bcm.edu	37	chr12	109182194	109182194	+	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	cttttgagaaactactggtgTggtccaggcggtagaagaaa	12	10	13	6	1	0	3	0	1	0	3	1	4	1	3	1	4	2	1	1	4	5	4			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr12:109182194T>A	ENST00000326495.5	-	15	2813	c.2720A>T	c.(2719-2721)cAc>cTc	p.H907L	SSH1_ENST00000360239.3_Missense_Mutation_p.H595L	NM_018984.3	NP_061857.3	Q8WYL5	SSH1_HUMAN	slingshot protein phosphatase 1	907	Interaction with YWHAG.				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						ACTACTGGTGTGGTCCAGGCG	0.587																																					p.H907L		Atlas-SNP	.											.	SSH1	144	.	0			c.A2720T						PASS	.						37	39	38					12																	109182194		2190	4270	6460	SO:0001583	missense	54434	exon15			CTGGTGTGGTCCA	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.2720A>T	chr12.hg19:g.109182194T>A	ENSP00000315713:p.His907Leu	94.0	0.0	.		200.0	133.0	.	NM_018984	Q6P6C0|Q8N9A7|Q8WYL3|Q8WYL4|Q9P2P8	Missense_Mutation	SNP	ENST00000326495.5	hg19	CCDS9121.1	.	.	.	.	.	.	.	.	.	.	T	13.84	2.357131	0.41801	.	.	ENSG00000084112	ENST00000360239;ENST00000326495	T;T	0.12147	2.84;2.71	5.64	4.43	0.53597	.	0.418583	0.26345	N	0.024917	T	0.32526	0.0832	M	0.62723	1.935	0.36858	D	0.888238	P;D	0.89917	0.842;1.0	P;D	0.83275	0.477;0.996	T	0.26916	-1.0089	10	0.66056	D	0.02	-33.6502	11.6178	0.51099	0.1332:0.0:0.0:0.8668	.	907;595	Q8WYL5;Q8WYL5-4	SSH1_HUMAN;.	L	595;907	ENSP00000353374:H595L;ENSP00000315713:H907L	ENSP00000315713:H907L	H	-	2	0	SSH1	107706323	1.000000	0.71417	0.999000	0.59377	0.775000	0.43874	1.902000	0.39848	2.160000	0.67779	0.528000	0.53228	CAC	.	.	.	none		0.587	SSH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403724.1	NM_018984		A	109182194	T	A	109182194	3	1	73	1	0	0	0	0	1	0	0	0	15196	1696	59	5	433	5	SSH1	12	109182194	Missense_Mutation	SNP	T	TCGA-AL-3468-01A-01D-1252-08	42416509	109182194	24669701	50	4744											
ATP7B	540	hgsc.bcm.edu	37	chr13	52548120	52548120	+	Frame_Shift_Del	DEL	T	T	-																															tcttctatagcagctctgagTtcttctgggctaattacaga																										TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr13:52548120delT	ENST00000242839.4	-	2	1392	c.1236delA	c.(1234-1236)gaafs	p.E412fs	ATP7B_ENST00000482841.1_5'UTR|ATP7B_ENST00000400366.3_Frame_Shift_Del_p.E301fs|ATP7B_ENST00000344297.5_Frame_Shift_Del_p.E412fs|ATP7B_ENST00000418097.2_Frame_Shift_Del_p.E412fs|ATP7B_ENST00000400370.3_Frame_Shift_Del_p.E412fs|ATP7B_ENST00000542656.1_Frame_Shift_Del_p.E380fs|ATP7B_ENST00000448424.2_Frame_Shift_Del_p.E412fs	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	412	HMA 4. {ECO:0000255|PROSITE- ProRule:PRU00280}.				cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	CAGCTCTGAGTTCTTCTGGGC	0.468									Wilson disease																												p.L413fs		Atlas-INDEL	.											.	ATP7B	123	.	0			c.1237delC						PASS	.						105	101	102					13																	52548120		1930	4134	6064	SO:0001589	frameshift_variant	540	exon2	Familial Cancer Database		.	U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"ATPases / P-type"	870	protein-coding gene	gene with protein product	"Wilson disease", "copper pump 2", "copper-transporting ATPase 2"	606882	"ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.1236delA	chr13.hg19:g.52548120delT	ENSP00000242839:p.Glu412fs	163.0	0.0	0		147.0	59.0	0.401361	NM_000053	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Frame_Shift_Del	DEL	ENST00000242839.4	hg19	CCDS41892.1																																																																																			.	.	.	none		0.468	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053		-	52548120	T	-	52548120	7	5	73	1	0	1	0	1	0	0	0	0	1191	1722	60	0	3241	0	ATP7B	13	52548120	Frame_Shift_Del	DEL	T	TCGA-AL-3468-01A-01D-1252-08		52548120	62621758	51	4745											
KIAA0586	9786	hgsc.bcm.edu	37	chr14	58949256	58949256	+	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	ggaacaagcagtggcgccctCcagctttttgttgatgctgg	7	11	13	10	1	0	1	0	1	0	0	1	2	1	2	2	3	4	4	2	3	2	3			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr14:58949256C>T	ENST00000556134.1	+	22	3199	c.2925C>T	c.(2923-2925)ctC>ctT	p.L975L	KIAA0586_ENST00000261244.5_Silent_p.L914L|KIAA0586_ENST00000354386.6_Silent_p.L1043L|KIAA0586_ENST00000423743.3_Silent_p.L946L|KIAA0586_ENST00000538571.2_3'UTR	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	975					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						GTGGCGCCCTCCAGCTTTTTG	0.378																																					p.L1043L		Atlas-SNP	.											.	KIAA0586	180	.	0			c.C3129T						PASS	.						51	49	49					14																	58949256		1851	4103	5954	SO:0001819	synonymous_variant	9786	exon23			CGCCCTCCAGCTT	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.2925C>T	chr14.hg19:g.58949256C>T		77.0	0.0	.		55.0	26.0	.	NM_001244189	B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	Silent	SNP	ENST00000556134.1	hg19	CCDS58321.1																																																																																			.	.	.	none		0.378	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1	NM_014749		T	58949256	C	T	58949256	2	4	73	1	0	0	0	0	0	0	0	1	8193	842	30	2		2	KIAA0586	14	58949256	Silent	SNP	C	TCGA-AL-3468-01A-01D-1252-08		58949256	48400284	52	4746											
TRIP11	9321	hgsc.bcm.edu	37	chr14	92491671	92491671	+	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	tacctctttttgttgaagttGatttcggtaacttgtagatt	8	20	8	5	1	1	3	0	2	1	1	2	3	1	3	1	1	2	4	1	1	4	10			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr14:92491671G>C	ENST00000267622.4	-	3	668	c.295C>G	c.(295-297)Caa>Gaa	p.Q99E		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	99					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)		TGTTGAAGTTGATTTCGGTAA	0.308			T	PDGFRB	AML																																p.Q99E	Ovarian(84;609 1888 9852 42686)	Atlas-SNP	.		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	.	TRIP11	184	.	0			c.C295G						PASS	.						189	161	170					14																	92491671		2203	4299	6502	SO:0001583	missense	9321	exon3			GAAGTTGATTTCG	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.295C>G	chr14.hg19:g.92491671G>C	ENSP00000267622:p.Gln99Glu	116.0	0.0	.		53.0	28.0	.	NM_004239	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	hg19	CCDS9899.1	.	.	.	.	.	.	.	.	.	.	g	10.13	1.265895	0.23136	.	.	ENSG00000100815	ENST00000267622	T	0.65732	-0.17	5.5	4.6	0.57074	.	0.159691	0.45606	N	0.000356	T	0.57519	0.2059	L	0.55481	1.735	0.32399	N	0.552188	B	0.09022	0.002	B	0.11329	0.006	T	0.60110	-0.7327	10	0.20046	T	0.44	.	16.3096	0.82864	0.0:0.1325:0.8675:0.0	.	99	Q15643	TRIPB_HUMAN	E	99	ENSP00000267622:Q99E	ENSP00000267622:Q99E	Q	-	1	0	TRIP11	91561424	1.000000	0.71417	0.026000	0.17262	0.472000	0.32918	3.533000	0.53561	1.303000	0.44873	0.563000	0.77884	CAA	.	.	.	none		0.308	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1			C	92491671	G	C	92491671	3	2	73	1	0	0	0	0	1	0	0	0	16567	1299	45	4	5720	4	TRIP11	14	92491671	Missense_Mutation	SNP	G	TCGA-AL-3468-01A-01D-1252-08	33542415	92491671	14857869	53	4747											
EIF5	1983	hgsc.bcm.edu	37	chr14	103807312	103807312	+	Frame_Shift_Del	DEL	A	A	-																															cttaacaggtggtgtattcgAaggctgccagtgtaccgaaa																										TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr14:103807312delA	ENST00000216554.3	+	12	1895	c.1219delA	c.(1219-1221)aagfs	p.K407fs	EIF5_ENST00000558506.1_Frame_Shift_Del_p.K407fs|EIF5_ENST00000392715.2_Frame_Shift_Del_p.K407fs	NM_001969.4	NP_001960.2	P55010	IF5_HUMAN	eukaryotic translation initiation factor 5	407					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|regulation of translational initiation (GO:0006446)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(3)|kidney(2)|large_intestine(3)|lung(5)|pancreas(2)|skin(2)|upper_aerodigestive_tract(1)	18		Melanoma(154;0.155)	Epithelial(46;0.182)			GGTGTATTCGAAGGCTGCCAG	0.378																																					p.S406fs		Atlas-INDEL	.											.	EIF5	40	.	0			c.1218delG						PASS	.						133	112	119					14																	103807312		2203	4300	6503	SO:0001589	frameshift_variant	1983	exon11			.	U49436	CCDS9980.1	14q32.32	2006-05-11				ENSG00000100664			3299	protein-coding gene	gene with protein product		601710				8663286	Standard	NM_001969		Approved		uc001ymq.4	P55010		ENST00000216554.3:c.1219delA	chr14.hg19:g.103807312delA	ENSP00000216554:p.Lys407fs	118.0	0.0	0		54.0	16.0	0.296296	NM_183004	Q53XB3|Q9H5N2|Q9UG48	Frame_Shift_Del	DEL	ENST00000216554.3	hg19	CCDS9980.1																																																																																			.	.	.	none		0.378	EIF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415329.2	NM_001969		-	103807312	A	-	103807312	7	5	73	1	0	1	0	1	0	0	0	0	5042	247	9	0	1257	0	EIF5	14	103807312	Frame_Shift_Del	DEL	A	TCGA-AL-3468-01A-01D-1252-08	11315641	103807312	3542228	54	4748											
USP3	9960	hgsc.bcm.edu	37	chr15	63882867	63882867	+	Missense_Mutation	SNP	T	T	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	tttgcctttacagggttggtTctggacattacacagcatac	9	14	9	9	0	1	0	0	0	1	0	1	1	1	1	1	3	5	3	1	3	3	7			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr15:63882867T>G	ENST00000380324.3	+	15	1534	c.1405T>G	c.(1405-1407)Tct>Gct	p.S469A	USP3_ENST00000539772.1_Missense_Mutation_p.S220A|USP3-AS1_ENST00000560962.1_RNA|USP3-AS1_ENST00000561191.1_RNA|USP3_ENST00000268049.7_Missense_Mutation_p.S447A|USP3-AS1_ENST00000559861.1_RNA|USP3_ENST00000558285.1_Missense_Mutation_p.S452A|USP3-AS1_ENST00000561256.1_RNA|USP3-AS1_ENST00000560622.1_RNA|USP3-AS1_ENST00000560350.1_RNA|USP3-AS1_ENST00000559357.1_RNA|USP3_ENST00000559711.1_Missense_Mutation_p.S380A|USP3_ENST00000558218.1_3'UTR|USP3-AS1_ENST00000558831.1_RNA|USP3_ENST00000540797.1_Missense_Mutation_p.S425A|USP3-AS1_ENST00000559737.1_RNA	NM_006537.3	NP_006528.2	Q9Y6I4	UBP3_HUMAN	ubiquitin specific peptidase 3	469	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)		CAGGGTTGGTTCTGGACATTA	0.403																																					p.S469A		Atlas-SNP	.											.	USP3	37	.	0			c.T1405G						PASS	.						119	113	115					15																	63882867		2203	4300	6503	SO:0001583	missense	9960	exon15			GTTGGTTCTGGAC	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.1405T>G	chr15.hg19:g.63882867T>G	ENSP00000369681:p.Ser469Ala	179.0	0.0	.		207.0	79.0	.	NM_006537	B4DVU5|F5H1A6|Q8WVD0	Missense_Mutation	SNP	ENST00000380324.3	hg19	CCDS32265.1	.	.	.	.	.	.	.	.	.	.	T	18.13	3.555531	0.65425	.	.	ENSG00000140455	ENST00000540797;ENST00000380324;ENST00000268049;ENST00000539772;ENST00000538686	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	6.07	6.07	0.98685	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (1);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.29093	0.0723	L	0.48174	1.505	0.58432	D	0.999999	B;B;B;B	0.29378	0.204;0.243;0.131;0.243	B;B;B;B	0.28849	0.058;0.095;0.078;0.078	T	0.06303	-1.0834	10	0.15066	T	0.55	.	16.6288	0.85011	0.0:0.0:0.0:1.0	.	425;425;447;469	F5H1A6;B4DVU5;Q6JHV3;Q9Y6I4	.;.;.;UBP3_HUMAN	A	425;469;447;220;300	ENSP00000445828:S425A;ENSP00000369681:S469A;ENSP00000268049:S447A;ENSP00000445642:S220A	ENSP00000268049:S447A	S	+	1	0	USP3	61669920	1.000000	0.71417	0.995000	0.50966	0.957000	0.61999	8.012000	0.88631	2.326000	0.78906	0.533000	0.62120	TCT	.	.	.	none		0.403	USP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417773.1			G	63882867	T	G	63882867	3	3	73	1	0	0	0	0	1	0	0	0	17072	1783	62	5	1463	5	USP3	15	63882867	Missense_Mutation	SNP	T	TCGA-AL-3468-01A-01D-1252-08		63882867	38648525	55	4749											
CRTC3	64784	hgsc.bcm.edu	37	chr15	91161146	91161146	+	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	cctggcccattgaaagaagaGaatctgttaaatgttccgaa	14	10	9	8	1	1	3	0	1	1	2	2	5	2	3	3	1	0	2	3	1	6	3			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr15:91161146G>C	ENST00000268184.6	+	8	649	c.645G>C	c.(643-645)gaG>gaC	p.E215D	CRTC3_ENST00000420329.2_Missense_Mutation_p.E215D|RP11-387D10.2_ENST00000559531.1_RNA			Q6UUV7	CRTC3_HUMAN	CREB regulated transcription coactivator 3	215					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)			TGAAAGAAGAGAATCTGTTAA	0.473			T	MAML2	salivary gland mucoepidermoid																																p.E215D		Atlas-SNP	.		Dom	yes		15	15q26.1	64784	CREB regulated transcription coactivator 3		E	.	CRTC3	47	.	0			c.G645C						PASS	.						96	87	90					15																	91161146		2198	4298	6496	SO:0001583	missense	64784	exon8			AGAAGAGAATCTG		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.645G>C	chr15.hg19:g.91161146G>C	ENSP00000268184:p.Glu215Asp	99.0	0.0	.		102.0	42.0	.	NM_022769	Q6DK61|Q6DK62|Q8NF38|Q9H6U2	Missense_Mutation	SNP	ENST00000268184.6	hg19	CCDS32331.1	.	.	.	.	.	.	.	.	.	.	G	18.97	3.735287	0.69189	.	.	ENSG00000140577	ENST00000437186;ENST00000268184;ENST00000420329	T;T	0.47528	0.84;0.84	5.12	1.05	0.20165	Transducer of regulated CREB activity, middle domain (1);	0.179858	0.47093	D	0.000248	T	0.47192	0.1432	L	0.44542	1.39	0.47123	D	0.999322	P;P	0.37370	0.592;0.537	P;P	0.51516	0.672;0.542	T	0.32903	-0.9889	10	0.39692	T	0.17	-15.2878	5.8106	0.18463	0.2477:0.1421:0.6102:0.0	.	215;215	Q6UUV7;Q6UUV7-3	CRTC3_HUMAN;.	D	179;215;215	ENSP00000268184:E215D;ENSP00000416573:E215D	ENSP00000268184:E215D	E	+	3	2	CRTC3	88962150	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.158000	0.31737	0.318000	0.23185	0.467000	0.42956	GAG	.	.	.	none		0.473	CRTC3-001	KNOWN	NAGNAG_splice_site|non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417716.2	NM_022769		C	91161146	G	C	91161146	3	2	73	1	0	0	0	0	1	0	0	0	3903	933	33	4	675	4	CRTC3	15	91161146	Missense_Mutation	SNP	G	TCGA-AL-3468-01A-01D-1252-08	27278279	91161146	11370246	56	4750											
NR2F2	7026	hgsc.bcm.edu	37	chr15	96875754	96875755	+	Frame_Shift_Ins	INS	-	-	T																															gccgcctcaaaaagtgcctcINSaaagtgggcatgagacggga																										TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr15:96875754_96875755insT	ENST00000394166.3	+	1	1809_1810	c.420_421insT	c.(421-423)aaafs	p.K141fs	NR2F2_ENST00000421109.2_Intron|MIR1469_ENST00000410719.1_RNA|NR2F2_ENST00000453270.2_5'Flank|NR2F2_ENST00000394171.2_5'Flank	NM_021005.3	NP_066285.1	P24468	COT2_HUMAN	nuclear receptor subfamily 2, group F, member 2	141	Interaction with ZFPM2. {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)			AAAAGTGCCTCAAAGTGGGCAT	0.604																																					p.L140fs		Atlas-INDEL	.											.	NR2F2	35	.	0			c.420_421insT						PASS	.																																			SO:0001589	frameshift_variant	7026	exon1			.	M64497	CCDS10375.1, CCDS45358.1, CCDS45359.1	15q26	2013-01-16			ENSG00000185551	ENSG00000185551		"Nuclear hormone receptors"	7976	protein-coding gene	gene with protein product		107773		ARP1, TFCOUP2		8530078, 11544252	Standard	NM_021005		Approved	COUP-TFII, COUPTFB, SVP40, NF-E3	uc010uri.2	P24468	OTTHUMG00000149848	Exception_encountered	chr15.hg19:g.96875754_96875755insT	ENSP00000377721:p.Lys141fs	72.0	0.0	0		87.0	23.0	0.264368	NM_021005	B4DQJ2|B6ZGU1|Q03754|Q3KQR7	Frame_Shift_Ins	INS	ENST00000394166.3	hg19	CCDS10375.1																																																																																			.	.	.	none		0.604	NR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313534.1			T	96875755	-	T	96875754	7	5	73	1	0	1	1	0	0	0	0	0	10635	813	29	0	469	0	NR2F2	15	96875754	Frame_Shift_Ins	INS	-	TCGA-AL-3468-01A-01D-1252-08	5714608	96875754	5655638	57	4751											
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1263882	1263882	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcttcatcaccttcatcaTctgtgtcaacgtcatcacca	9	13	3	16	1	9	0	7	0	2	0	9	0	9	0	3	0	1	0	3	0	1	2			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr16:1263882T>C	ENST00000348261.5	+	27	5128	c.4880T>C	c.(4879-4881)aTc>aCc	p.I1627T	CACNA1H_ENST00000358590.4_Missense_Mutation_p.I1621T|CACNA1H_ENST00000565831.1_Missense_Mutation_p.I1621T	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1627					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)	ACCTTCATCATCTGTGTCAAC	0.637																																					p.I1627T		Atlas-SNP	.											.	CACNA1H	317	.	0			c.T4880C						PASS	.						77	76	76					16																	1263882		2103	4238	6341	SO:0001583	missense	8912	exon27			TCATCATCTGTGT	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.4880T>C	chr16.hg19:g.1263882T>C	ENSP00000334198:p.Ile1627Thr	20.0	0.0	.		34.0	21.0	.	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	hg19	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	T	18.38	3.611627	0.66558	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.98192	-4.78;-4.78	3.99	3.99	0.46301	.	0.000000	0.85682	D	0.000000	D	0.98950	0.9643	M	0.89904	3.07	0.49798	D	0.999823	D;D;D;D;P	0.89917	0.999;1.0;0.998;0.999;0.893	P;D;D;D;P	0.79108	0.895;0.992;0.964;0.986;0.626	D	0.99449	1.0940	10	0.87932	D	0	.	12.4929	0.55909	0.0:0.0:0.0:1.0	.	373;362;368;1621;1627	A2SX38;A2SX35;A2SX37;O95180-2;O95180	.;.;.;.;CAC1H_HUMAN	T	1627;1621	ENSP00000334198:I1627T;ENSP00000351401:I1621T	ENSP00000334198:I1627T	I	+	2	0	CACNA1H	1203883	1.000000	0.71417	0.955000	0.39395	0.467000	0.32768	7.236000	0.78154	1.807000	0.52817	0.482000	0.46254	ATC	.	.	.	none		0.637	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		C	1263882	T	C	1263882	3	2	73	1	0	0	0	0	1	0	0	0	2547	1435	50	3	4982	3	CACNA1H	16	1263882	Missense_Mutation	SNP	T	TCGA-AL-3468-01A-01D-1252-08		1263882	89090871	58	4752											
SRCAP	10847	hgsc.bcm.edu	37	chr16	30736125	30736125	+	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	cactgaccttgagccctgccCcagttcctaccctgggcccg	5	8	9	19	1	0	2	0	2	0	0	1	2	1	2	7	1	3	1	7	1	1	3	rs371358460		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr16:30736125C>G	ENST00000262518.4	+	25	5765	c.5380C>G	c.(5380-5382)Cca>Gca	p.P1794A	SRCAP_ENST00000344771.4_Missense_Mutation_p.P1636A|SRCAP_ENST00000395059.2_Missense_Mutation_p.P1732A	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1794	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)			gagccctgccccagttcctac	0.652																																					p.P1794A		Atlas-SNP	.											.	SRCAP	298	.	0			c.C5380G						PASS	.	C	ALA/PRO	0,4394		0,0,2197	47	41	43		5380	3.9	0.9	16		43	1,8597	1.2+/-3.3	0,1,4298	no	missense	SRCAP	NM_006662.2	27	0,1,6495	GG,GC,CC		0.0116,0.0,0.0077	benign	1794/3231	30736125	1,12991	2197	4299	6496	SO:0001583	missense	10847	exon25			CCTGCCCCAGTTC	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.5380C>G	chr16.hg19:g.30736125C>G	ENSP00000262518:p.Pro1794Ala	49.0	0.0	.		98.0	32.0	.	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	hg19	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	C	9.997	1.232471	0.22626	0.0	1.16E-4	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.92446	-2.7;-2.96;-3.04	5.81	3.86	0.44501	.	0.131464	0.35207	N	0.003362	D	0.83170	0.5196	N	0.19112	0.55	0.23533	N	0.997471	B;B;B	0.12630	0.002;0.006;0.001	B;B;B	0.10450	0.005;0.005;0.002	T	0.72944	-0.4138	10	0.54805	T	0.06	-6.3761	5.5202	0.16927	0.0:0.664:0.1649:0.1711	.	1636;1732;1794	Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2	.;.;SRCAP_HUMAN	A	1794;1732;1636	ENSP00000262518:P1794A;ENSP00000378499:P1732A;ENSP00000343042:P1636A	ENSP00000262518:P1794A	P	+	1	0	SRCAP	30643626	0.022000	0.18835	0.931000	0.37212	0.814000	0.46013	2.321000	0.43805	1.458000	0.47871	0.655000	0.94253	CCA	.	.	.	weak		0.652	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		G	30736125	C	G	30736125	3	3	73	1	0	0	0	0	1	0	0	0	15147	623	22	4	5470	4	SRCAP	16	30736125	Missense_Mutation	SNP	C	TCGA-AL-3468-01A-01D-1252-08	29472243	30736125	59618628	59	4753											
NEK8	284086	hgsc.bcm.edu	37	chr17	27067537	27067537	+	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	gcccccagcaggtgcccatgCccccaggacaggaagctcag	9	3	12	17	0	1	0	1	0	0	0	1	2	1	2	5	3	4	2	5	3	1	0			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr17:27067537C>G	ENST00000268766.6	+	11	1508	c.1474C>G	c.(1474-1476)Ccc>Gcc	p.P492A	AC010761.6_ENST00000582536.1_RNA|AC010761.6_ENST00000584779.1_RNA	NM_178170.2	NP_835464.1	Q86SG6	NEK8_HUMAN	NIMA-related kinase 8	492					organ morphogenesis (GO:0009887)|regulation of hippo signaling (GO:0035330)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|primary cilium (GO:0072372)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Lung NSC(42;0.0158)					GGTGCCCATGCCCCCAGGACA	0.567																																					p.P492A	NSCLC(6;19 293 14866 25253 49845)	Atlas-SNP	.											.	NEK8	76	.	0			c.C1474G						PASS	.						103	96	99					17																	27067537		2203	4300	6503	SO:0001583	missense	284086	exon11			CCCATGCCCCCAG	AY267371	CCDS32597.1	17q11.1	2012-11-15	2012-11-15			ENSG00000160602			13387	protein-coding gene	gene with protein product		609799	"NIMA (never in mitosis gene a)- related kinase 8"			18199800	Standard	NM_178170		Approved	NPHP9	uc002hcp.3	Q86SG6		ENST00000268766.6:c.1474C>G	chr17.hg19:g.27067537C>G	ENSP00000268766:p.Pro492Ala	202.0	0.0	.		324.0	87.0	.	NM_178170	A6NIC5|Q14CL7|Q2M1S6|Q8NDH1	Missense_Mutation	SNP	ENST00000268766.6	hg19	CCDS32597.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.947298	0.73672	.	.	ENSG00000160602	ENST00000268766	T	0.80824	-1.42	5.36	4.37	0.52481	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.108661	0.64402	N	0.000005	D	0.89979	0.6872	M	0.84683	2.71	0.53688	D	0.999979	D	0.89917	1.0	D	0.76071	0.987	D	0.90846	0.4727	10	0.52906	T	0.07	.	14.7766	0.69736	0.0:0.8496:0.1504:0.0	.	492	Q86SG6	NEK8_HUMAN	A	492	ENSP00000268766:P492A	ENSP00000268766:P492A	P	+	1	0	NEK8	24091664	1.000000	0.71417	0.913000	0.36048	0.984000	0.73092	3.608000	0.54109	1.218000	0.43458	0.555000	0.69702	CCC	.	.	.	none		0.567	NEK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446467.2			G	27067537	C	G	27067537	3	3	73	1	0	0	0	0	1	0	0	0	10337	739	26	4	1516	4	NEK8	17	27067537	Missense_Mutation	SNP	C	TCGA-AL-3468-01A-01D-1252-08		27067537	54127673	60	4754											
CACNB1	782	hgsc.bcm.edu	37	chr17	37331566	37331566	+	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	ccccggttccggttgtcggtCagctcttcctcatagtcttc	3	14	9	15	3	4	0	2	0	2	0	8	0	6	0	4	3	1	3	4	3	1	5			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr17:37331566C>T	ENST00000394303.3	-	14	1884	c.1677G>A	c.(1675-1677)ctG>ctA	p.L559L	RP5-906A24.2_ENST00000579256.1_RNA	NM_000723.4	NP_000714.3	Q02641	CACB1_HUMAN	calcium channel, voltage-dependent, beta 1 subunit	559				L -> M (in Ref. 3; AAA36167). {ECO:0000305}.	axon guidance (GO:0007411)|protein targeting to membrane (GO:0006612)|transport (GO:0006810)	sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	16					Dronedarone(DB04855)|Ibutilide(DB00308)|Magnesium Sulfate(DB00653)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	GGTTGTCGGTCAGCTCTTCCT	0.662											OREG0024371	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L559L	Esophageal Squamous(5;100 366 38393 41452 45827)	Atlas-SNP	.											.	CACNB1	89	.	0			c.G1677A						PASS	.						145	161	156					17																	37331566		1894	4098	5992	SO:0001819	synonymous_variant	782	exon14			GTCGGTCAGCTCT		CCDS11334.1, CCDS42311.1, CCDS45665.1	17q21-q22	2013-03-20			ENSG00000067191	ENSG00000067191		"Calcium channel subunits"	1401	protein-coding gene	gene with protein product		114207		CACNLB1		8381767, 8395940	Standard	NM_000723		Approved		uc002hrm.2	Q02641	OTTHUMG00000133217	ENST00000394303.3:c.1677G>A	chr17.hg19:g.37331566C>T		575.0	1.0	.	869	853.0	268.0	.	NM_000723	A8K114|O15331|Q02639|Q02640|Q8N3X9|Q9C085|Q9UD79	Silent	SNP	ENST00000394303.3	hg19	CCDS42311.1																																																																																			.	.	.	none		0.662	CACNB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256945.3			T	37331566	C	T	37331566	2	4	73	1	0	0	0	0	0	0	0	1	2554	813	29	2		2	CACNB1	17	37331566	Silent	SNP	C	TCGA-AL-3468-01A-01D-1252-08	10264029	37331566	43863644	61	4755											
CDC6	990	hgsc.bcm.edu	37	chr17	38447499	38447499	+	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	ccaaaacaaaatactttcttCagttagaaaaagtcaagaga	20	9	5	7	0	3	2	2	0	1	2	3	3	3	2	1	0	2	1	1	0	9	4			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr17:38447499C>T	ENST00000209728.4	+	3	839	c.368C>T	c.(367-369)tCa>tTa	p.S123L		NM_001254.3	NP_001245.1	Q99741	CDC6_HUMAN	cell division cycle 6	123					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						ATACTTTCTTCAGTTAGAAAA	0.373																																					p.S123L		Atlas-SNP	.											.	CDC6	53	.	0			c.C368T						PASS	.						80	77	78					17																	38447499		2203	4300	6503	SO:0001583	missense	990	exon3			TTTCTTCAGTTAG	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.368C>T	chr17.hg19:g.38447499C>T	ENSP00000209728:p.Ser123Leu	123.0	0.0	.		184.0	108.0	.	NM_001254	Q8TB30	Missense_Mutation	SNP	ENST00000209728.4	hg19	CCDS11365.1	.	.	.	.	.	.	.	.	.	.	C	15.04	2.715080	0.48622	.	.	ENSG00000094804	ENST00000209728	T	0.52295	0.67	5.34	5.34	0.76211	.	0.815336	0.11356	N	0.572480	T	0.50103	0.1596	M	0.63428	1.95	0.09310	N	1	B	0.17852	0.024	B	0.08055	0.003	T	0.36016	-0.9765	10	0.32370	T	0.25	-0.9791	18.3299	0.90264	0.0:1.0:0.0:0.0	.	123	Q99741	CDC6_HUMAN	L	123	ENSP00000209728:S123L	ENSP00000209728:S123L	S	+	2	0	CDC6	35701025	0.320000	0.24616	0.023000	0.16930	0.065000	0.16274	3.873000	0.56093	2.937000	0.99478	0.650000	0.86243	TCA	.	.	.	none		0.373	CDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257129.1			T	38447499	C	T	38447499	3	4	73	1	0	0	0	0	1	0	0	0	3085	838	29	2	374	2	CDC6	17	38447499	Missense_Mutation	SNP	C	TCGA-AL-3468-01A-01D-1252-08	1115933	38447499	42747711	62	4756											
DDX5	1655	hgsc.bcm.edu	37	chr17	62500099	62500102	+	Splice_Site	DEL	ACAG	ACAG	-																															tcaagagttctcccaaacttAcagacaatgttttcccagat																										TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	ACAG	ACAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr17:62500099_62500102delACAG	ENST00000225792.5	-	4	841_843	c.440_442delCTGT	c.(439-444)tctgta>tta	p.SV147fs	DDX5_ENST00000580026.1_5'Flank|MIR5047_ENST00000579212.1_RNA|DDX5_ENST00000578804.1_Splice_Site_p.SV147fs|DDX5_ENST00000450599.2_Intron|CEP95_ENST00000556440.2_5'Flank	NM_004396.3	NP_004387.1	P17844	DDX5_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 5	147	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)			TCCCAAACTTACAGACAATGTTTT	0.397			T	ETV4	prostate																																p.147_147del	NSCLC(22;406 813 4871 19580 40307)	Atlas-INDEL	.		Dom	yes		17	17q21	1655	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5		E	.	DDX5	101	.	0			c.441_441del						PASS	.																																			SO:0001630	splice_region_variant	1655	exon4			.	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.441+1CTGT>-	chr17.hg19:g.62500099_62500102delACAG		294.0	0.0	0		179.0	45.0	0.251397	NM_004396	B4DLW8|B5BU21|D3DU32|E7ETL9|O75681|Q53Y61	Frame_Shift_Del	DEL	ENST00000225792.5	hg19	CCDS11659.1																																																																																			.	.	.	none		0.397	DDX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444030.1	NM_004396	Frame_Shift_Del	-	62500102	ACAG	-	62500099	8	5	73	1	0	1	0	1	0	0	1	0	4369	405	14	0	1441	0	DDX5	17	62500099	Splice_Site	DEL	ACAG	TCGA-AL-3468-01A-01D-1252-08	24052600	62500099	18695111	63	4757											
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-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	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	chr17.hg19:g.68171425G>A	ENSP00000243457:p.Arg82Gln	256.0	0.0	.		310.0	108.0	.	NM_000891	O15110|P48049	Missense_Mutation	SNP	ENST00000243457.3	hg19	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	73	1	0	0	0	0	1	0	0	0	8058	1116	39	1	247	1	KCNJ2	17	68171425	Missense_Mutation	SNP	G	TCGA-AL-3468-01A-01D-1252-08	5671326	68171425	13023785	64	4758											
RAB37	326624	hgsc.bcm.edu	37	chr17	72736931	72736931	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcttctgggagacacaggcGtcggcaaaacatgtttcctg	9	10	12	10	2	1	1	0	0	1	1	3	2	2	1	1	3	2	3	1	3	2	2			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr17:72736931G>A	ENST00000392613.5	+	2	174	c.118G>A	c.(118-120)Gtc>Atc	p.V40I	RAB37_ENST00000340415.3_Intron|RAB37_ENST00000392615.5_Intron|RAB37_ENST00000392614.4_Missense_Mutation_p.V45I|RAB37_ENST00000402449.4_Intron|RAB37_ENST00000392612.3_Intron|RAB37_ENST00000392610.1_Missense_Mutation_p.V40I|RAB37_ENST00000528438.1_Missense_Mutation_p.V13I	NM_001006638.2	NP_001006639.1	Q96AX2	RAB37_HUMAN	RAB37, member RAS oncogene family	40					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|secretory granule (GO:0030141)	GTP binding (GO:0005525)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	12						AGACACAGGCGTCGGCAAAAC	0.567																																					p.V45I		Atlas-SNP	.											.	RAB37	69	.	0			c.G133A						PASS	.						153	154	153					17																	72736931		2203	4300	6503	SO:0001583	missense	326624	exon2			ACAGGCGTCGGCA	BC040547	CCDS11703.1, CCDS32722.1, CCDS54161.1, CCDS54162.1	17q25.2	2008-02-05			ENSG00000172794	ENSG00000172794		"RAB, member RAS oncogene"	30268	protein-coding gene	gene with protein product		609956				10722846	Standard	NM_175738		Approved		uc002jlk.3	Q96AX2	OTTHUMG00000134282	ENST00000392613.5:c.118G>A	chr17.hg19:g.72736931G>A	ENSP00000376389:p.Val40Ile	351.0	0.0	.		508.0	34.0	.	NM_001163989	A8MXF5|A8MYT0|Q8IWA7	Missense_Mutation	SNP	ENST00000392613.5	hg19	CCDS32722.1	.	.	.	.	.	.	.	.	.	.	G	19.29	3.799506	0.70567	.	.	ENSG00000172794	ENST00000528438;ENST00000392614;ENST00000392613;ENST00000533530;ENST00000392610	D;D;D;D	0.82081	-1.57;-1.57;-1.57;-1.57	5.27	5.27	0.74061	Small GTP-binding protein domain (1);	0.072360	0.53938	D	0.000052	D	0.91442	0.7299	M	0.93241	3.395	0.80722	D	1	P;P	0.50369	0.739;0.934	P;P	0.52627	0.503;0.704	D	0.93664	0.6984	10	0.87932	D	0	.	17.663	0.88197	0.0:0.0:1.0:0.0	.	45;40	A8MYT0;Q96AX2	.;RAB37_HUMAN	I	13;45;40;40;40	ENSP00000432086:V13I;ENSP00000376390:V45I;ENSP00000376389:V40I;ENSP00000376387:V40I	ENSP00000376387:V40I	V	+	1	0	RAB37	70248526	1.000000	0.71417	0.992000	0.48379	0.052000	0.14988	9.248000	0.95456	2.469000	0.83416	0.561000	0.74099	GTC	.	.	.	none		0.567	RAB37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258872.2	NM_175738		A	72736931	G	A	72736931	3	1	73	1	0	0	0	0	1	0	0	0	12940	1145	40	1	427	1	RAB37	17	72736931	Missense_Mutation	SNP	G	TCGA-AL-3468-01A-01D-1252-08	4565506	72736931	8458279	65	4759											
ACOX1	51	hgsc.bcm.edu	37	chr17	73945931	73945931	+	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	tcaaataggacaccatgccaCacaccaactttcctgagtgc	13	8	6	14	0	1	1	1	1	0	0	2	2	2	2	4	1	3	0	4	1	3	2			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr17:73945931C>T	ENST00000301608.4	-	10	1406	c.1346G>A	c.(1345-1347)tGt>tAt	p.C449Y	ACOX1_ENST00000293217.5_Missense_Mutation_p.C449Y|ACOX1_ENST00000537812.1_Missense_Mutation_p.C411Y	NM_007292.5	NP_009223.2	Q15067	ACOX1_HUMAN	acyl-CoA oxidase 1, palmitoyl	449				C -> R (in Ref. 2; AAA18595). {ECO:0000305}.	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)	CACCATGCCACACACCAACTT	0.468																																					p.C449Y		Atlas-SNP	.											.	ACOX1	85	.	0			c.G1346A						PASS	.						123	101	108					17																	73945931		2203	4300	6503	SO:0001583	missense	51	exon10			ATGCCACACACCA	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.1346G>A	chr17.hg19:g.73945931C>T	ENSP00000301608:p.Cys449Tyr	138.0	0.0	.		178.0	100.0	.	NM_007292	A8K6X8|A8KAA0|B4DK61|F5GYQ8|Q12863|Q15068|Q15101|Q16131|Q7Z3W5|Q9UD31	Missense_Mutation	SNP	ENST00000301608.4	hg19	CCDS11735.1	.	.	.	.	.	.	.	.	.	.	C	8.054	0.766632	0.15983	.	.	ENSG00000161533	ENST00000301608;ENST00000293217;ENST00000537812;ENST00000539791;ENST00000538781	T;T;T	0.69175	-0.38;-0.38;-0.38	5.9	2.59	0.31030	Acyl-CoA dehydrogenase/oxidase C-terminal (1);	0.983847	0.08367	N	0.956805	T	0.45856	0.1363	N	0.14661	0.345	0.20074	N	0.999931	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	0.28839	-1.0031	10	0.18276	T	0.48	-0.6261	6.3539	0.21390	0.0:0.5984:0.1198:0.2817	.	381;411;449;449	F5H0M0;F5GYQ8;Q15067;Q15067-2	.;.;ACOX1_HUMAN;.	Y	449;449;411;449;381	ENSP00000301608:C449Y;ENSP00000293217:C449Y;ENSP00000441257:C411Y	ENSP00000293217:C449Y	C	-	2	0	ACOX1	71457526	0.001000	0.12720	0.520000	0.27837	0.349000	0.29174	1.001000	0.29783	0.314000	0.23086	-0.157000	0.13467	TGT	.	.	.	none		0.468	ACOX1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439503.1			T	73945931	C	T	73945931	3	4	73	1	0	0	0	0	1	0	0	0	158	478	17	2	656	2	ACOX1	17	73945931	Missense_Mutation	SNP	C	TCGA-AL-3468-01A-01D-1252-08	1209000	73945931	7249279	66	4760											
FAM59A	64762	hgsc.bcm.edu	37	chr18	29867890	29867890	+	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	ttgcatctgaagttccagggGacttcgggtgctaaatctgc	8	12	12	9	1	2	1	0	1	2	0	4	2	3	2	1	3	3	3	1	3	3	4			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr18:29867890G>A	ENST00000269209.6	-	4	673	c.670C>T	c.(670-672)Ccc>Tcc	p.P224S	GAREM_ENST00000578619.1_5'UTR|GAREM_ENST00000399218.4_Missense_Mutation_p.P224S|RP11-344B2.2_ENST00000579580.1_RNA			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	224	CABIT.				cellular response to epidermal growth factor stimulus (GO:0071364)|epidermal growth factor receptor signaling pathway (GO:0007173)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)										AGTTCCAGGGGACTTCGGGTG	0.522																																					p.P224S		Atlas-SNP	.											.	.	.	.	0			c.C670T						PASS	.						135	114	121					18																	29867890		2203	4300	6503	SO:0001583	missense	64762	exon4			CCAGGGGACTTCG	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.670C>T	chr18.hg19:g.29867890G>A	ENSP00000269209:p.Pro224Ser	187.0	0.0	.		139.0	55.0	.	NM_022751	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	Missense_Mutation	SNP	ENST00000269209.6	hg19	CCDS56057.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.672770	0.88445	.	.	ENSG00000141441	ENST00000399218;ENST00000269209	T;T	0.15487	2.42;2.42	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.43366	0.1244	M	0.69823	2.125	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.66351	0.93;0.943	T	0.20672	-1.0268	10	0.72032	D	0.01	-23.7807	20.1095	0.97908	0.0:0.0:1.0:0.0	.	224;224	Q9H706;Q9H706-3	FA59A_HUMAN;.	S	224	ENSP00000382165:P224S;ENSP00000269209:P224S	ENSP00000269209:P224S	P	-	1	0	FAM59A	28121888	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	9.357000	0.97099	2.831000	0.97527	0.655000	0.94253	CCC	.	.	.	none		0.522	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255365.1	NM_022751		A	29867890	G	A	29867890	3	1	73	1	0	0	0	0	1	0	0	0	5599	1174	41	2	1969	2	FAM59A	18	29867890	Missense_Mutation	SNP	G	TCGA-AL-3468-01A-01D-1252-08		29867890	48209358	67	4761											
HMSD	284293	hgsc.bcm.edu	37	chr18	61621714	61621714	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcagtcacttcttgttgcaAttaacagaactgacactgaa	13	13	6	9	0	3	3	2	2	1	1	3	3	3	3	0	0	3	2	0	0	4	5			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr18:61621714A>G	ENST00000408945.3	+	3	347	c.145A>G	c.(145-147)Att>Gtt	p.I49V	HMSD_ENST00000526932.1_Silent_p.Q14Q|HMSD_ENST00000481726.1_3'UTR	NM_001123366.1	NP_001116838.1	A8MTL9	HMSD_HUMAN	histocompatibility (minor) serpin domain containing	49						extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			kidney(1)|large_intestine(2)|lung(2)|stomach(1)	6						TCTTGTTGCAATTAACAGAAC	0.348																																					p.I49V		Atlas-SNP	.											.	HMSD	16	.	0			c.A145G						PASS	.						151	141	144					18																	61621714		1568	3582	5150	SO:0001583	missense	284293	exon3			GTTGCAATTAACA	AC009802	CCDS42441.1	18q21.33	2008-02-04			ENSG00000221887	ENSG00000221887			23037	protein-coding gene	gene with protein product		612086		C18orf53		17409267	Standard	NM_001123366		Approved	ACC-6	uc010dqj.3	A8MTL9	OTTHUMG00000060593	ENST00000408945.3:c.145A>G	chr18.hg19:g.61621714A>G	ENSP00000386207:p.Ile49Val	269.0	0.0	.		156.0	13.0	.	NM_001123366		Missense_Mutation	SNP	ENST00000408945.3	hg19	CCDS42441.1	.	.	.	.	.	.	.	.	.	.	A	0.059	-1.229197	0.01518	.	.	ENSG00000221887	ENST00000408945	D	0.84442	-1.85	3.19	-5.08	0.02929	Serpin domain (2);	.	.	.	.	T	0.67277	0.2876	N	0.10809	0.05	0.27000	N	0.964924	B	0.15930	0.015	B	0.28139	0.086	T	0.57376	-0.7822	9	0.08599	T	0.76	.	10.4449	0.44488	0.6618:0.0:0.3382:0.0	.	49	A8MTL9	HMSD_HUMAN	V	49	ENSP00000386207:I49V	ENSP00000386207:I49V	I	+	1	0	HMSD	59772694	0.078000	0.21339	0.000000	0.03702	0.000000	0.00434	0.203000	0.17315	-1.378000	0.02120	-1.411000	0.01122	ATT	.	.	.	none		0.348	HMSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134010.2	XM_209104		G	61621714	A	G	61621714	3	3	73	1	0	0	0	0	1	0	0	0	7253	101	4	3	151	3	HMSD	18	61621714	Missense_Mutation	SNP	A	TCGA-AL-3468-01A-01D-1252-08	31753824	61621714	16455534	68	4762											
COL5A3	50509	hgsc.bcm.edu	37	chr19	10096525	10096525	+	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	cccagcttcctaccttaggtCcagggcgtcctggataacct	7	10	9	15	1	0	0	0	0	0	0	3	1	3	1	6	3	3	1	6	3	3	4			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr19:10096525C>T	ENST00000264828.3	-	31	2484	c.2399G>A	c.(2398-2400)gGa>gAa	p.G800E		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	800	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)			TACCTTAGGTCCAGGGCGTCC	0.582																																					p.G800E		Atlas-SNP	.											.	COL5A3	243	.	0			c.G2399A						PASS	.						121	138	132					19																	10096525		2203	4300	6503	SO:0001583	missense	50509	exon31			TTAGGTCCAGGGC	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.2399G>A	chr19.hg19:g.10096525C>T	ENSP00000264828:p.Gly800Glu	571.0	1.0	.		473.0	258.0	.	NM_015719	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	hg19	CCDS12222.1	.	.	.	.	.	.	.	.	.	.	C	16.90	3.250158	0.59212	.	.	ENSG00000080573	ENST00000264828	D	0.96992	-4.2	4.6	4.6	0.57074	.	0.075366	0.51477	U	0.000084	D	0.98520	0.9506	M	0.93550	3.43	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99620	1.0983	10	0.87932	D	0	.	15.2861	0.73828	0.0:1.0:0.0:0.0	.	800	P25940	CO5A3_HUMAN	E	800	ENSP00000264828:G800E	ENSP00000264828:G800E	G	-	2	0	COL5A3	9957525	1.000000	0.71417	0.999000	0.59377	0.220000	0.24768	6.386000	0.73186	2.267000	0.75376	0.462000	0.41574	GGA	.	.	.	none		0.582	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719		T	10096525	C	T	10096525	3	4	73	1	0	0	0	0	1	0	0	0	3700	855	30	2	2986	2	COL5A3	19	10096525	Missense_Mutation	SNP	C	TCGA-AL-3468-01A-01D-1252-08		10096525	49032458	69	4763											
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11141551	11141551	+	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	actgtgatcatttttgacagCgactggaatcctcaccaggt	10	12	9	10	1	2	2	2	2	0	0	3	4	3	3	2	2	1	0	2	2	1	2	rs573885719		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr19:11141551C>G	ENST00000429416.3	+	26	3809	c.3528C>G	c.(3526-3528)agC>agG	p.S1176R	SMARCA4_ENST00000358026.2_Missense_Mutation_p.S1176R|SMARCA4_ENST00000413806.3_Missense_Mutation_p.S1176R|SMARCA4_ENST00000590574.1_Missense_Mutation_p.S1176R|SMARCA4_ENST00000450717.3_Missense_Mutation_p.S1176R|SMARCA4_ENST00000589677.1_Missense_Mutation_p.S1176R|SMARCA4_ENST00000344626.4_Missense_Mutation_p.S1176R|SMARCA4_ENST00000444061.3_Missense_Mutation_p.S1176R|SMARCA4_ENST00000541122.2_Missense_Mutation_p.S1176R	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1176	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				TTTTTGACAGCGACTGGAATC	0.622			"F, N, Mis"		NSCLC																																p.S1176R		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.C3528G						PASS	.						23	23	23					19																	11141551		2200	4298	6498	SO:0001583	missense	6597	exon25			TGACAGCGACTGG	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.3528C>G	chr19.hg19:g.11141551C>G	ENSP00000395654:p.Ser1176Arg	22.0	0.0	.		37.0	19.0	.	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	C	17.39	3.376857	0.61735	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.96651	-4.08;-4.08;-4.08;-4.08;-4.08;-4.08;-4.08	4.59	-2.64	0.06114	Helicase, C-terminal (3);	0.099658	0.64402	D	0.000003	D	0.97198	0.9084	M	0.78285	2.405	0.51482	D	0.999927	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.95549	0.8619	10	0.87932	D	0	-24.9368	11.693	0.51527	0.0:0.1538:0.0:0.8462	.	1176;1176;1176;1176;1176;396;1176;1176	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;A7E2E1;P51532	.;.;.;.;.;.;.;SMCA4_HUMAN	R	1176;1176;1240;1176;1176;1176;1176;1176	ENSP00000395654:S1176R;ENSP00000350720:S1176R;ENSP00000343896:S1176R;ENSP00000445036:S1176R;ENSP00000392837:S1176R;ENSP00000397783:S1176R;ENSP00000414727:S1176R	ENSP00000343896:S1176R	S	+	3	2	SMARCA4	11002551	0.002000	0.14202	0.983000	0.44433	0.991000	0.79684	-1.403000	0.02497	-0.701000	0.05063	0.563000	0.77884	AGC	.	.	.	none		0.622	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		G	11141551	C	G	11141551	3	3	73	1	0	0	0	0	1	0	0	0	14783	767	27	4	3622	4	SMARCA4	19	11141551	Missense_Mutation	SNP	C	TCGA-AL-3468-01A-01D-1252-08	1045026	11141551	47987432	70	4764											
PLEKHG2	64857	hgsc.bcm.edu	37	chr19	39915323	39915323	+	Missense_Mutation	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	ctgcacctccacttccggagCcaagccttacagatacacag	11	7	7	16	1	0	1	0	0	0	1	2	2	2	2	5	1	5	1	5	1	3	3			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr19:39915323C>T	ENST00000409794.3	+	19	4400	c.3550C>T	c.(3550-3552)Cca>Tca	p.P1184S	PLEKHG2_ENST00000458508.2_Missense_Mutation_p.P1125S|PLEKHG2_ENST00000409797.2_Intron|PLEKHG2_ENST00000378550.1_Intron|CTB-60E11.4_ENST00000601124.1_lincRNA|PLEKHG2_ENST00000425673.1_Missense_Mutation_p.P1155S	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	1184	Pro-rich.				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)			ACTTCCGGAGCCAAGCCTTAC	0.562																																					p.P1184S		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.C3550T						PASS	.						137	138	138					19																	39915323		2203	4300	6503	SO:0001583	missense	64857	exon19			CCGGAGCCAAGCC	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.3550C>T	chr19.hg19:g.39915323C>T	ENSP00000386733:p.Pro1184Ser	292.0	0.0	.		319.0	126.0	.	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	hg19	CCDS33022.2	.	.	.	.	.	.	.	.	.	.	C	11.34	1.610668	0.28712	.	.	ENSG00000090924	ENST00000409794;ENST00000425673;ENST00000458508	T;T;T	0.69040	-0.24;-0.27;-0.37	4.07	1.85	0.25348	.	1.332870	0.05347	N	0.531168	T	0.52108	0.1714	L	0.39898	1.24	0.09310	N	1	B;B;B	0.33694	0.403;0.281;0.421	B;B;B	0.25291	0.059;0.027;0.026	T	0.42565	-0.9444	9	.	.	.	.	4.6767	0.12715	0.0:0.6467:0.2297:0.1236	.	1155;1184;1125	Q9H7P9-3;Q9H7P9;E7ESZ3	.;PKHG2_HUMAN;.	S	1184;1155;1125	ENSP00000386733:P1184S;ENSP00000392906:P1155S;ENSP00000408857:P1125S	.	P	+	1	0	PLEKHG2	44607163	0.006000	0.16342	0.064000	0.19789	0.058000	0.15608	0.781000	0.26774	0.976000	0.38417	0.511000	0.50034	CCA	.	.	.	none		0.562	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835		T	39915323	C	T	39915323	3	4	73	1	0	0	0	0	1	0	0	0	12076	739	26	2	3620	2	PLEKHG2	19	39915323	Missense_Mutation	SNP	C	TCGA-AL-3468-01A-01D-1252-08	28773772	39915323	19213660	71	4765											
MEGF8	1954	hgsc.bcm.edu	37	chr19	42872696	42872696	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagagctgctccctgggctgTgctcaggcaactcagtgcgc	6	8	14	13	1	2	1	2	0	0	1	3	2	3	1	1	2	5	5	1	2	1	0			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr19:42872696T>C	ENST00000251268.6	+	36	6363	c.6363T>C	c.(6361-6363)tgT>tgC	p.C2121C	MEGF8_ENST00000378073.4_5'Flank|MEGF8_ENST00000334370.4_Silent_p.C2054C	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	2121	PSI 7.				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)				CCCTGGGCTGTGCTCAGGCAA	0.697																																					p.C2121C		Atlas-SNP	.											.	MEGF8	358	.	0			c.T6363C						PASS	.						10	10	10					19																	42872696		2193	4277	6470	SO:0001819	synonymous_variant	1954	exon36			GGGCTGTGCTCAG	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.6363T>C	chr19.hg19:g.42872696T>C		28.0	0.0	.		29.0	13.0	.	NM_001271938	A8KAY0|O75097	Silent	SNP	ENST00000251268.6	hg19																																																																																				.	.	.	none		0.697	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		C	42872696	T	C	42872696	2	2	73	1	0	0	0	0	0	0	0	1	9470	1702	59	3		3	MEGF8	19	42872696	Silent	SNP	T	TCGA-AL-3468-01A-01D-1252-08	2957373	42872696	16256287	72	4766											
PPP1R12C	54776	hgsc.bcm.edu	37	chr19	55603617	55603617	+	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	gcccgctccagctccaccttGagctgcgccagccgcagcgt	5	6	11	19	4	0	1	0	1	0	0	2	1	2	1	6	0	5	4	6	0	0	1			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr19:55603617G>C	ENST00000263433.3	-	19	2148	c.2133C>G	c.(2131-2133)ctC>ctG	p.L711L	PPP1R12C_ENST00000376393.2_Silent_p.L648L|PPP1R12C_ENST00000435544.2_Silent_p.L636L	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)		GCTCCACCTTGAGCTGCGCCA	0.692																																					p.L711L		Atlas-SNP	.											.	PPP1R12C	46	.	0			c.C2133G						PASS	.						9	9	9					19																	55603617		2170	4262	6432	SO:0001819	synonymous_variant	54776	exon19			CACCTTGAGCTGC	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.2133C>G	chr19.hg19:g.55603617G>C		16.0	0.0	.		18.0	5.0	.	NM_017607		Silent	SNP	ENST00000263433.3	hg19	CCDS12916.1																																																																																			.	.	.	none		0.692	PPP1R12C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451814.2	NM_017607		C	55603617	G	C	55603617	2	2	73	1	0	0	0	0	0	0	0	1	12366	1277	45	4		4	PPP1R12C	19	55603617	Silent	SNP	G	TCGA-AL-3468-01A-01D-1252-08	12730921	55603617	3525366	73	4767											
ZNF17	7565	hgsc.bcm.edu	37	chr19	57931956	57931959	+	Frame_Shift_Del	DEL	TTCT	TTCT	-																															attgctgtgaatgtgggaaaTtctttatggacagctgcaca																										TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	TTCT	TTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr19:57931956_57931959delTTCT	ENST00000601808.1	+	3	1309_1312	c.1096_1099delTTCT	c.(1096-1101)ttctttfs	p.FF366fs	ZNF17_ENST00000307658.7_Frame_Shift_Del_p.FF368fs|AC004076.7_ENST00000597410.1_Intron	NM_006959.2	NP_008890.2	P17021	ZNF17_HUMAN	zinc finger protein 17	366					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0234)|GBM - Glioblastoma multiforme(193;0.000426)|Lung(386;0.176)		ATGTGGGAAATTCTTTATGGACAG	0.387																																					p.365_366del	Melanoma(149;1637 1853 29914 42869 44988)	Atlas-INDEL	.											.	ZNF17	49	.	0			c.1095_1098del						PASS	.																																			SO:0001589	frameshift_variant	7565	exon3			.	X52341	CCDS42636.1	19q13.43	2013-01-08	2006-05-10			ENSG00000186272		"Zinc fingers, C2H2-type", "-"	12958	protein-coding gene	gene with protein product			"zinc finger protein 17 (HPF3, KOX 10)"			2115127, 2014798	Standard	NM_006959		Approved	HPF3, KOX10, KIAA1947, FLJ40864, FLJ46058, FLJ46615	uc002qoo.1	P17021		ENST00000601808.1:c.1096_1099delTTCT	chr19.hg19:g.57931956_57931959delTTCT	ENSP00000471905:p.Phe366fs	245.0	0.0	0		145.0	15.0	0.103448	NM_006959	B3KXU2|B3KY20|Q8N7M1|Q8N893|Q8TF54	Frame_Shift_Del	DEL	ENST00000601808.1	hg19	CCDS42636.1																																																																																			.	.	.	none		0.387	ZNF17-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466384.1	NM_006959		-	57931959	TTCT	-	57931956	7	5	73	1	0	1	0	1	0	0	0	0	17755	1493	52	0	1106	0	ZNF17	19	57931956	Frame_Shift_Del	DEL	TTCT	TCGA-AL-3468-01A-01D-1252-08	2328339	57931956	1197027	74	4768											
FASTKD5	60493	hgsc.bcm.edu	37	chr20	3128940	3128940	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaaaaaatgtttaaaaacctAggtactttgcggcctaagta	16	11	8	6	1	0	0	0	0	0	0	0	1	0	0	2	2	3	3	2	2	10	7			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr20:3128940A>G	ENST00000380266.3	-	2	1098	c.777T>C	c.(775-777)ccT>ccC	p.P259P	UBOX5_ENST00000348031.2_Intron|UBOX5_ENST00000217173.2_Intron|UBOX5-AS1_ENST00000446537.1_RNA	NM_021826.4	NP_068598.1	Q7L8L6	FAKD5_HUMAN	FAST kinase domains 5	259					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(2)|endometrium(2)|large_intestine(2)|lung(8)|prostate(2)|skin(1)|urinary_tract(2)	19						TTAAAAACCTAGGTACTTTGC	0.393																																					p.P259P		Atlas-SNP	.											.	FASTKD5	63	.	0			c.T777C						PASS	.						44	46	45					20																	3128940		2200	4300	6500	SO:0001819	synonymous_variant	60493	exon2			AAACCTAGGTACT	BC007413	CCDS13048.1	20p13	2006-07-07			ENSG00000215251	ENSG00000215251			25790	protein-coding gene	gene with protein product		614272				11347906	Standard	NM_021826		Approved	FLJ13149	uc002whz.4	Q7L8L6	OTTHUMG00000031727	ENST00000380266.3:c.777T>C	chr20.hg19:g.3128940A>G		126.0	0.0	.		122.0	36.0	.	NM_021826	Q96JN3|Q9H5D1|Q9H8Y3	Silent	SNP	ENST00000380266.3	hg19	CCDS13048.1																																																																																			.	.	.	none		0.393	FASTKD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077701.2	NM_021826		G	3128940	A	G	3128940	2	3	73	1	0	0	0	0	0	0	0	1	5695	407	15	3		3	FASTKD5	20	3128940	Silent	SNP	A	TCGA-AL-3468-01A-01D-1252-08		3128940	59896580	75	4769											
ZHX3	23051	hgsc.bcm.edu	37	chr20	39831715	39831715	+	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	ggggctctctccttgtatttGgttggtgtgaagtcaggagt	5	15	15	6	0	2	1	1	1	1	0	4	2	3	2	1	5	0	3	1	5	2	4			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr20:39831715G>T	ENST00000309060.3	-	4	2257	c.1842C>A	c.(1840-1842)acC>acA	p.T614T	ZHX3_ENST00000540170.1_Silent_p.T614T|ZHX3_ENST00000544979.2_Silent_p.T614T|ZHX3_ENST00000559234.1_Silent_p.T614T|ZHX3_ENST00000558993.1_Intron|ZHX3_ENST00000557816.1_Intron|ZHX3_ENST00000432768.2_Silent_p.T614T|ZHX3_ENST00000560361.1_Silent_p.T614T			Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3	614					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of osteoblast differentiation (GO:0045669)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(2)|kidney(5)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		Myeloproliferative disorder(115;0.00425)				CCTTGTATTTGGTTGGTGTGA	0.537																																					p.T614T		Atlas-SNP	.											.	ZHX3	78	.	0			c.C1842A						PASS	.						161	151	154					20																	39831715		2203	4300	6503	SO:0001819	synonymous_variant	23051	exon3			GTATTTGGTTGGT	AB007855	CCDS13315.1	20q12	2012-03-09	2004-01-29	2004-01-30	ENSG00000174306	ENSG00000174306		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	15935	protein-coding gene	gene with protein product		609598	"triple homeobox 1"	TIX1		9455477	Standard	XM_005260343		Approved	KIAA0395	uc002xjs.1	Q9H4I2	OTTHUMG00000032481	ENST00000309060.3:c.1842C>A	chr20.hg19:g.39831715G>T		164.0	0.0	.		281.0	176.0	.	NM_015035	E1P5W5|F5H820|O43145|Q6NUJ7	Silent	SNP	ENST00000309060.3	hg19	CCDS13315.1	.	.	.	.	.	.	.	.	.	.	G	4.135	0.023393	0.08006	.	.	ENSG00000174306	ENST00000421422	.	.	.	6.06	3.94	0.45596	.	.	.	.	.	T	0.60715	0.2290	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58719	-0.7587	4	.	.	.	-16.3993	10.5172	0.44896	0.0731:0.0:0.7373:0.1895	.	.	.	.	K	323	.	.	Q	-	1	0	ZHX3	39265129	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.636000	0.24644	1.567000	0.49668	0.650000	0.86243	CAA	.	.	.	none		0.537	ZHX3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079262.3	NM_015035		T	39831715	G	T	39831715	2	4	73	1	0	0	0	0	0	0	0	1	17689	1335	47	4		4	ZHX3	20	39831715	Silent	SNP	G	TCGA-AL-3468-01A-01D-1252-08	36702775	39831715	23193805	76	4770											
DSCAM	1826	hgsc.bcm.edu	37	chr21	41710196	41710196	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaagcaggttagagttctTgtaccatttaatggagtaat	13	13	11	4	0	1	1	0	0	1	1	1	3	1	3	1	3	2	5	1	3	5	7			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr21:41710196T>C	ENST00000400454.1	-	8	2092	c.1615A>G	c.(1615-1617)Aag>Gag	p.K539E		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	539	Ig-like C2-type 6.				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)				TTAGAGTTCTTGTACCATTTA	0.438																																					p.K539E	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.A1615G						PASS	.						179	171	173					21																	41710196		1946	4147	6093	SO:0001583	missense	1826	exon8			AGTTCTTGTACCA	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.1615A>G	chr21.hg19:g.41710196T>C	ENSP00000383303:p.Lys539Glu	235.0	0.0	.		103.0	80.0	.	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	hg19	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.204393	0.79127	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.81330	-1.48;-1.48	5.77	5.77	0.91146	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.93048	0.7787	H	0.97291	3.975	0.43489	D	0.995729	D	0.64830	0.994	D	0.64506	0.926	D	0.95287	0.8391	10	0.72032	D	0.01	.	16.0742	0.80958	0.0:0.0:0.0:1.0	.	539	O60469	DSCAM_HUMAN	E	539;291	ENSP00000383303:K539E;ENSP00000385342:K291E	ENSP00000383303:K539E	K	-	1	0	DSCAM	40632066	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.028000	0.70889	2.198000	0.70561	0.533000	0.62120	AAG	.	.	.	none		0.438	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		C	41710196	T	C	41710196	3	2	73	1	0	0	0	0	1	0	0	0	4770	1821	63	3	4527	3	DSCAM	21	41710196	Missense_Mutation	SNP	T	TCGA-AL-3468-01A-01D-1252-08		41710196	6419699	77	4771											
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23237695	23237695	+	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	cctggaaggcagatggcagcCccgtcaaggcgggagtggag	9	4	18	10	2	1	1	1	0	0	1	1	4	1	4	3	6	1	2	3	6	2	0			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr22:23237695C>T	ENST00000526893.1	+	3	740	c.466C>T	c.(466-468)Ccc>Tcc	p.P156S	IGLC1_ENST00000390321.2_RNA|IGLJ1_ENST00000390320.2_RNA|IGLL5_ENST00000532223.2_Missense_Mutation_p.P157S|IGLL5_ENST00000531372.1_3'UTR	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	156	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						AGATGGCAGCCCCGTCAAGGC	0.597																																					p.P156S		Atlas-SNP	.											.	IGLL5	26	.	0			c.C466T						PASS	.						76	80	79					22																	23237695		2202	4295	6497	SO:0001583	missense	100423062	exon3			GGCAGCCCCGTCA	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.466C>T	chr22.hg19:g.23237695C>T	ENSP00000431254:p.Pro156Ser	48.0	0.0	.		54.0	21.0	.	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	hg19	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	C	3.861	-0.029965	0.07543	.	.	ENSG00000254709	ENST00000532223;ENST00000526893	T;T	0.02837	4.14;4.14	3.54	-7.09	0.01553	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	.	.	.	.	T	0.02688	0.0081	L	0.42632	1.34	0.09310	N	0.999998	B	0.10296	0.003	B	0.19946	0.027	T	0.37291	-0.9712	9	0.72032	D	0.01	.	5.0659	0.14582	0.1683:0.4504:0.2909:0.0904	.	156	B9A064	IGLL5_HUMAN	S	157;156	ENSP00000436353:P157S;ENSP00000431254:P156S	ENSP00000431254:P156S	P	+	1	0	IGLL5	21567695	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.956000	0.00326	-4.369000	0.00053	-1.188000	0.01700	CCC	.	.	.	none		0.597	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		T	23237695	C	T	23237695	3	4	73	1	0	0	0	0	1	0	0	0	7601	623	22	2	476	2	IGLL5	22	23237695	Missense_Mutation	SNP	C	TCGA-AL-3468-01A-01D-1252-08		23237695	28066871	78	4772											
EIF4ENIF1	56478	hgsc.bcm.edu	37	chr22	31837941	31837941	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgccaaggtgggtgttttTctcccagttgctttaggtcg	5	15	13	8	1	1	0	0	0	1	0	3	1	1	0	2	3	2	3	2	3	2	5			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr22:31837941T>C	ENST00000397525.1	-	17	2593	c.2370A>G	c.(2368-2370)agA>agG	p.R790R	EIF4ENIF1_ENST00000344710.5_Silent_p.R616R|EIF4ENIF1_ENST00000330125.5_Silent_p.R790R|EIF4ENIF1_ENST00000397523.1_Silent_p.R766R|EIF4ENIF1_ENST00000382180.2_Silent_p.R445R|EIF4ENIF1_ENST00000441289.1_5'Flank	NM_001164501.1	NP_001157973.1	Q9NRA8	4ET_HUMAN	eukaryotic translation initiation factor 4E nuclear import factor 1	790						cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						TGGGTGTTTTTCTCCCAGTTG	0.527																																					p.R790R		Atlas-SNP	.											.	EIF4ENIF1	80	.	0			c.A2370G						PASS	.						321	298	306					22																	31837941		2203	4300	6503	SO:0001819	synonymous_variant	56478	exon17			TGTTTTTCTCCCA	AF240775	CCDS13898.1, CCDS54520.1	22q11.2	2007-01-16			ENSG00000184708	ENSG00000184708			16687	protein-coding gene	gene with protein product		607445				10856257	Standard	NM_019843		Approved	4E-T, FLJ21601, Clast4, 2610509L04Rik	uc003akz.2	Q9NRA8	OTTHUMG00000030793	ENST00000397525.1:c.2370A>G	chr22.hg19:g.31837941T>C		185.0	0.0	.		184.0	19.0	.	NM_019843	B1AKL2|B1AKL3|B2RBF1|Q8NCF2|Q9H708	Silent	SNP	ENST00000397525.1	hg19	CCDS13898.1																																																																																			.	.	.	none		0.527	EIF4ENIF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127926.1	NM_019843		C	31837941	T	C	31837941	2	2	73	1	0	0	0	0	0	0	0	1	5037	1780	62	3		3	EIF4ENIF1	22	31837941	Silent	SNP	T	TCGA-AL-3468-01A-01D-1252-08	8600246	31837941	19466625	79	4773											
POLDIP3	84271	hgsc.bcm.edu	37	chr22	42998037	42998037	+	Frame_Shift_Del	DEL	G	G	-																															cggcaggatggggatgaagtGgtgccatggctttctgctgt																								rs569033722		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr22:42998037delG	ENST00000252115.5	-	3	580	c.476delC	c.(475-477)ccafs	p.P159fs	POLDIP3_ENST00000451060.2_Frame_Shift_Del_p.P3fs|POLDIP3_ENST00000339677.6_Intron|POLDIP3_ENST00000491021.1_5'UTR|POLDIP3_ENST00000348657.2_Intron	NM_032311.3	NP_115687.2	Q9BY77	PDIP3_HUMAN	polymerase (DNA-directed), delta interacting protein 3	159					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						GGGATGAAGTGGTGCCATGGC	0.498																																					p.P159fs	Ovarian(52;967 1128 5875 19997 42537)	Atlas-INDEL	.											.	POLDIP3	58	.	0			c.477delA						PASS	.						245	211	222					22																	42998037		2203	4300	6503	SO:0001589	frameshift_variant	84271	exon3			.		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.476delC	chr22.hg19:g.42998037delG	ENSP00000252115:p.Pro159fs	243.0	0.0	0		201.0	80.0	0.39801	NM_032311	A8K6F8|A8K6V9|Q009A7|Q5H972|Q6PGN6|Q7Z6Z0|Q9NSP5|Q9NSP6	Frame_Shift_Del	DEL	ENST00000252115.5	hg19	CCDS14038.1																																																																																			.	.	.	none		0.498	POLDIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320433.1	NM_032311		-	42998037	G	-	42998037	7	5	73	1	0	1	0	1	0	0	0	0	12202	1348	47	0	817	0	POLDIP3	22	42998037	Frame_Shift_Del	DEL	G	TCGA-AL-3468-01A-01D-1252-08	11160096	42998037	8306529	80	4774											
CELSR1	9620	hgsc.bcm.edu	37	chr22	46931045	46931045	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attcacgtccagcaccgtgaTggacacgctggtggaggagc	9	7	14	11	3	1	1	1	1	0	0	2	4	2	4	2	4	2	2	2	4	0	1			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr22:46931045T>C	ENST00000262738.3	-	1	2022	c.2023A>G	c.(2023-2025)Atc>Gtc	p.I675V	CELSR1_ENST00000395964.1_Missense_Mutation_p.I675V|CELSR1_ENST00000497509.1_5'Flank	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	675	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		AGCACCGTGATGGACACGCTG	0.657																																					p.I675V		Atlas-SNP	.											.	CELSR1	242	.	0			c.A2023G						PASS	.						33	23	26					22																	46931045		2198	4299	6497	SO:0001583	missense	9620	exon1			CCGTGATGGACAC	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.2023A>G	chr22.hg19:g.46931045T>C	ENSP00000262738:p.Ile675Val	26.0	0.0	.		43.0	13.0	.	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	hg19	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	T	0.117	-1.131052	0.01756	.	.	ENSG00000075275	ENST00000262738;ENST00000395964	T;T	0.48522	0.81;1.31	4.51	2.38	0.29361	Cadherin (5);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.64402	U	0.000002	T	0.25975	0.0633	N	0.20845	0.615	0.32913	D	0.514725	B	0.31040	0.305	B	0.33750	0.169	T	0.35400	-0.9790	10	0.05436	T	0.98	.	7.9257	0.29872	0.0:0.1734:0.0:0.8266	.	675	Q9NYQ6	CELR1_HUMAN	V	675	ENSP00000262738:I675V;ENSP00000379293:I675V	ENSP00000262738:I675V	I	-	1	0	CELSR1	45309709	1.000000	0.71417	1.000000	0.80357	0.779000	0.44077	1.649000	0.37281	0.608000	0.30000	0.254000	0.18369	ATC	.	.	.	none		0.657	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		C	46931045	T	C	46931045	3	2	73	1	0	0	0	0	1	0	0	0	3223	1464	51	3	7161	3	CELSR1	22	46931045	Missense_Mutation	SNP	T	TCGA-AL-3468-01A-01D-1252-08	3933008	46931045	4373521	81	4775											
MBTPS2	51360	hgsc.bcm.edu	37	chrX	21857904	21857904	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgggtggctggactgtcgtcTacctgaccgacttggtgctg	4	12	15	10	2	1	1	0	1	1	0	2	3	1	2	2	4	2	2	2	4	1	2			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chrX:21857904T>C	ENST00000379484.5	+	1	151	c.52T>C	c.(52-54)Tac>Cac	p.Y18H	MBTPS2_ENST00000465888.1_3'UTR|MBTPS2_ENST00000365779.2_Missense_Mutation_p.Y18H	NM_015884.3	NP_056968.1	O43462	MBTP2_HUMAN	membrane-bound transcription factor peptidase, site 2	18					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)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|endometrium(3)|large_intestine(3)|lung(13)|ovary(1)|skin(2)	24						GACTGTCGTCTACCTGACCGA	0.672																																					p.Y18H		Atlas-SNP	.											.	MBTPS2	52	.	0			c.T52C						PASS	.						116	50	72					X																	21857904		2196	4291	6487	SO:0001583	missense	51360	exon1			GTCGTCTACCTGA	AF019612	CCDS14201.1	Xp22.12-p22.11	2014-02-03	2005-08-17		ENSG00000012174	ENSG00000012174			15455	protein-coding gene	gene with protein product		300294	"membrane-bound transcription factor protease, site 2", "keratosis follicularis spinulosa decalvans"	KFSD		9847074, 9659902, 20672378	Standard	NM_015884		Approved	S2P	uc004dae.3	O43462	OTTHUMG00000021237	ENST00000379484.5:c.52T>C	chrX.hg19:g.21857904T>C	ENSP00000368798:p.Tyr18His	9.0	0.0	.		5.0	5.0	.	NM_015884	Q9UM70|Q9UMD3	Missense_Mutation	SNP	ENST00000379484.5	hg19	CCDS14201.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.095893	0.76870	.	.	ENSG00000012174	ENST00000379484;ENST00000365779	D;D	0.94280	-3.39;-2.25	5.29	5.29	0.74685	.	0.121945	0.56097	D	0.000021	D	0.95582	0.8564	M	0.62723	1.935	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.83275	0.996;0.946;0.946	D	0.95070	0.8203	10	0.42905	T	0.14	-7.7197	13.24	0.59992	0.0:0.0:0.0:1.0	.	18;18;18	A8KA68;O43462;B9ZVQ3	.;MBTP2_HUMAN;.	H	18	ENSP00000368798:Y18H;ENSP00000368796:Y18H	ENSP00000368796:Y18H	Y	+	1	0	MBTPS2	21767825	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	5.780000	0.68956	1.768000	0.52137	0.486000	0.48141	TAC	.	.	.	none		0.672	MBTPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056026.1			C	21857904	T	C	21857904	3	2	73	1	0	0	0	0	1	0	0	0	9369	1522	53	3	54	3	MBTPS2	23	21857904	Missense_Mutation	SNP	T	TCGA-AL-3468-01A-01D-1252-08		21857904	133412656	82	4776											
SPIN3	169981	hgsc.bcm.edu	37	chrX	57021007	57021007	+	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	ctttgccaaccattatttctGccaagtgtgtatcactgatt	9	16	6	10	0	2	1	1	1	1	0	2	1	2	1	3	0	3	1	3	0	4	5			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chrX:57021007G>C	ENST00000374919.3	-	2	696	c.374C>G	c.(373-375)gCa>gGa	p.A125G		NM_001010862.2	NP_001010862.2	Q5JUX0	SPIN3_HUMAN	spindlin family, member 3	125					gamete generation (GO:0007276)					central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)	4						CATTATTTCTGCCAAGTGTGT	0.418																																					p.A125G		Atlas-SNP	.											.	SPIN3	33	.	0			c.C374G						PASS	.						144	141	142					X																	57021007		2073	4205	6278	SO:0001583	missense	169981	exon2			ATTTCTGCCAAGT	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.374C>G	chrX.hg19:g.57021007G>C	ENSP00000364054:p.Ala125Gly	287.0	0.0	.		217.0	11.0	.	NM_001010862	B2RUW3|B7Z8W2|Q8N5D9	Missense_Mutation	SNP	ENST00000374919.3	hg19	CCDS43963.1	.	.	.	.	.	.	.	.	.	.	G	6.700	0.497740	0.12762	.	.	ENSG00000204271	ENST00000374919	T	0.52057	0.68	2.3	1.43	0.22495	.	0.090478	0.42548	U	0.000686	T	0.46268	0.1384	M	0.81497	2.545	0.31005	N	0.719843	B	0.18610	0.029	B	0.21708	0.036	T	0.52419	-0.8578	10	0.87932	D	0	-0.3707	6.6117	0.22755	0.1624:0.0:0.8376:0.0	.	125	Q5JUX0	SPIN3_HUMAN	G	125	ENSP00000364054:A125G	ENSP00000364054:A125G	A	-	2	0	SPIN3	57037732	1.000000	0.71417	0.072000	0.20136	0.179000	0.23085	3.759000	0.55227	0.418000	0.25898	0.600000	0.82982	GCA	.	.	.	none		0.418	SPIN3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056908.1	XM_093024		C	57021007	G	C	57021007	3	2	73	1	0	0	0	0	1	0	0	0	15067	1319	46	4	406	4	SPIN3	23	57021007	Missense_Mutation	SNP	G	TCGA-AL-3468-01A-01D-1252-08	35163103	57021007	98249553	83	4777											
GRIK3	2899	hgsc.bcm.edu	37	chr1	37307384	37307384	+	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	gttccactggcccttgtcatCctgtgccccgtacttgccgt	3	13	9	16	2	1	0	1	0	0	0	3	0	3	0	6	1	3	2	6	1	1	4			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr1:37307384C>T	ENST00000373091.3	-	10	1499	c.1483G>A	c.(1483-1485)Gat>Aat	p.D495N	GRIK3_ENST00000373093.4_Missense_Mutation_p.D495N	NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	495					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)				CCCTTGTCATCCTGTGCCCCG	0.597																																					p.D495N		Atlas-SNP	.											.	GRIK3	195	.	0			c.G1483A						PASS	.						176	151	159					1																	37307384		2203	4300	6503	SO:0001583	missense	2899	exon10			TGTCATCCTGTGC	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.1483G>A	chr1.hg19:g.37307384C>T	ENSP00000362183:p.Asp495Asn	245.0	0.0	.		371.0	177.0	.	NM_000831	A9Z1Z8|B1AMS6|Q13004|Q16136	Missense_Mutation	SNP	ENST00000373091.3	hg19	CCDS416.1	.	.	.	.	.	.	.	.	.	.	C	5.820	0.335627	0.11013	.	.	ENSG00000163873	ENST00000373091;ENST00000373093	T;T	0.76060	-0.99;-0.99	4.86	4.86	0.63082	Glutamate receptor, L-glutamate/glycine-binding (2);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	T	0.60932	0.2307	N	0.20881	0.62	0.54753	D	0.999986	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.004	T	0.57312	-0.7833	10	0.09338	T	0.73	.	18.3613	0.90375	0.0:1.0:0.0:0.0	.	495;495	A9Z1Z8;Q13003	.;GRIK3_HUMAN	N	495	ENSP00000362183:D495N;ENSP00000362185:D495N	ENSP00000362183:D495N	D	-	1	0	GRIK3	37079971	1.000000	0.71417	0.993000	0.49108	0.530000	0.34684	4.928000	0.63447	2.398000	0.81561	0.591000	0.81541	GAT	.	.	.	none		0.597	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1	NM_000831		T	37307384	C	T	37307384	3	4	74	1	0	0	0	0	1	0	0	0	6782	855	30	2	1304	2	GRIK3	1	37307384	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08		37307384	211943237	1	4778											
CRTC2	200186	hgsc.bcm.edu	37	chr1	153924730	153924730	+	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	tggcaggctggtcaggagatGgaaagatgctaggggaagga	12	6	19	4	0	1	2	1	0	0	2	1	6	1	5	0	8	1	3	0	8	3	1			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr1:153924730G>A	ENST00000368633.1	-	10	888	c.761C>T	c.(760-762)cCa>cTa	p.P254L	CRTC2_ENST00000476883.1_5'Flank|CRTC2_ENST00000368630.3_Intron	NM_181715.2	NP_859066.1	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2	254					gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|histone H3-K9 acetylation (GO:0043970)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cAMP response element binding protein binding (GO:0008140)			NS(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	27	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			GTCAGGAGATGGAAAGATGCT	0.552																																					p.P254L		Atlas-SNP	.											.	CRTC2	58	.	0			c.C761T						PASS	.						57	62	60					1																	153924730		2203	4300	6503	SO:0001583	missense	200186	exon10			GGAGATGGAAAGA	AY360172	CCDS30875.1	1q21.3	2008-02-05			ENSG00000160741	ENSG00000160741			27301	protein-coding gene	gene with protein product		608972				14506290, 14536081	Standard	NM_181715		Approved	TORC2	uc021pab.1	Q53ET0	OTTHUMG00000037156	ENST00000368633.1:c.761C>T	chr1.hg19:g.153924730G>A	ENSP00000357622:p.Pro254Leu	117.0	0.0	.		176.0	72.0	.	NM_181715	Q6UUV8|Q7Z3X7|Q8N332	Missense_Mutation	SNP	ENST00000368633.1	hg19	CCDS30875.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.966111	0.74131	.	.	ENSG00000160741	ENST00000368633	T	0.71817	-0.6	4.67	3.76	0.43208	Transducer of regulated CREB activity, middle domain (1);	0.213044	0.40554	N	0.001070	T	0.76385	0.3980	M	0.80332	2.49	0.51767	D	0.999939	D	0.58970	0.984	D	0.62955	0.909	T	0.80086	-0.1529	10	0.87932	D	0	-3.0813	10.3415	0.43882	0.0961:0.0:0.9039:0.0	.	254	Q53ET0	CRTC2_HUMAN	L	254	ENSP00000357622:P254L	ENSP00000357622:P254L	P	-	2	0	CRTC2	152191354	1.000000	0.71417	0.961000	0.40146	0.979000	0.70002	6.923000	0.75817	1.195000	0.43115	0.455000	0.32223	CCA	.	.	.	none		0.552	CRTC2-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090272.3	NM_181715		A	153924730	G	A	153924730	3	1	74	1	0	0	0	0	1	0	0	0	3902	1348	47	2	1340	2	CRTC2	1	153924730	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08	116617346	153924730	95325891	2	4779											
HAPLN2	60484	hgsc.bcm.edu	37	chr1	156593855	156593855	+	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	cgactagacgcctccctggtCatcgcgggcgtgcgcctgga	5	7	14	15	6	1	1	1	0	0	1	3	3	2	2	3	3	1	0	3	3	1	1			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr1:156593855C>T	ENST00000255039.1	+	4	749	c.342C>T	c.(340-342)gtC>gtT	p.V114V		NM_021817.2	NP_068589.1	Q9GZV7	HPLN2_HUMAN	hyaluronan and proteoglycan link protein 2	114	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)					CCTCCCTGGTCATCGCGGGCG	0.692																																					p.V114V		Atlas-SNP	.											.	HAPLN2	20	.	0			c.C342T						PASS	.						30	29	30					1																	156593855		2191	4256	6447	SO:0001819	synonymous_variant	60484	exon4			CCTGGTCATCGCG	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.342C>T	chr1.hg19:g.156593855C>T		53.0	0.0	.		76.0	45.0	.	NM_021817	Q5T3J0	Silent	SNP	ENST00000255039.1	hg19	CCDS1148.1																																																																																			.	.	.	none		0.692	HAPLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081039.1	NM_021817		T	156593855	C	T	156593855	2	4	74	1	0	0	0	0	0	0	0	1	6962	813	29	2		2	HAPLN2	1	156593855	Silent	SNP	C	TCGA-AL-3472-01A-01D-1252-08	2669125	156593855	92656766	3	4780											
USH2A	7399	hgsc.bcm.edu	37	chr1	216073458	216073458	+	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	gaatccaagaactatgtgcaCtgccaaatccattggaggca	14	8	9	10	0	0	1	0	0	0	1	2	3	2	2	3	2	3	2	3	2	5	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr1:216073458C>T	ENST00000307340.3	-	40	7939	c.7553G>A	c.(7552-7554)aGt>aAt	p.S2518N	USH2A_ENST00000366943.2_Missense_Mutation_p.S2518N|RP5-1111A8.3_ENST00000414995.1_RNA	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2518	Fibronectin type-III 11. {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)		ACTATGTGCACTGCCAAATCC	0.423										HNSCC(13;0.011)																											p.S2518N		Atlas-SNP	.											.	USH2A	1168	.	0			c.G7553A						PASS	.						146	120	129					1																	216073458		2203	4300	6503	SO:0001583	missense	7399	exon40			TGTGCACTGCCAA	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.7553G>A	chr1.hg19:g.216073458C>T	ENSP00000305941:p.Ser2518Asn	217.0	0.0	.		34.0	17.0	.	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	15.26	2.781126	0.49891	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.54071	0.59;0.59	6.16	4.3	0.51218	Fibronectin, type III (5);Immunoglobulin-like fold (1);	0.558407	0.16087	N	0.230233	T	0.47783	0.1464	L	0.46157	1.445	0.09310	N	1	P	0.43231	0.801	P	0.46419	0.516	T	0.33727	-0.9857	10	0.32370	T	0.25	.	4.9527	0.14023	0.0:0.5906:0.1598:0.2496	.	2518	O75445	USH2A_HUMAN	N	2518	ENSP00000305941:S2518N;ENSP00000355910:S2518N	ENSP00000305941:S2518N	S	-	2	0	USH2A	214140081	0.558000	0.26554	0.182000	0.23118	0.991000	0.79684	1.002000	0.29796	0.923000	0.37045	0.650000	0.86243	AGT	.	.	.	none		0.423	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216073458	C	T	216073458	3	4	74	1	0	0	0	0	1	0	0	0	17048	565	20	2	8187	2	USH2A	1	216073458	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08	59479603	216073458	33177163	4	4781											
KIDINS220	57498	hgsc.bcm.edu	37	chr2	8871568	8871568	+	Frame_Shift_Del	DEL	T	T	-																															catctttgagcagtggagtgTtatctgattcttctgtgcca																										TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr2:8871568delT	ENST00000256707.3	-	30	4779	c.4598delA	c.(4597-4599)aacfs	p.N1533fs	KIDINS220_ENST00000418530.1_Frame_Shift_Del_p.N1434fs|KIDINS220_ENST00000427284.1_Frame_Shift_Del_p.N1514fs|KIDINS220_ENST00000473731.1_Frame_Shift_Del_p.N1514fs	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	1533					activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234)	PDZ domain binding (GO:0030165)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					CAGTGGAGTGTTATCTGATTC	0.478																																					p.N1533fs		Atlas-INDEL	.											.	KIDINS220	136	.	0			c.4599delC						PASS	.						82	83	82					2																	8871568		1930	4146	6076	SO:0001589	frameshift_variant	57498	exon30			.	AK025528	CCDS42650.1	2p24	2013-01-10			ENSG00000134313	ENSG00000134313		"Ankyrin repeat domain containing"	29508	protein-coding gene	gene with protein product	"ankyrin repeat-rich membrane-spanning protein"	615759				10998417, 10574462	Standard	NM_020738		Approved	ARMS	uc002qzc.2	Q9ULH0	OTTHUMG00000151658	ENST00000256707.3:c.4598delA	chr2.hg19:g.8871568delT	ENSP00000256707:p.Asn1533fs	233.0	0.0	0		145.0	57.0	0.393103	NM_020738	A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Frame_Shift_Del	DEL	ENST00000256707.3	hg19	CCDS42650.1																																																																																			.	.	.	none		0.478	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738		-	8871568	T	-	8871568	7	5	74	1	0	1	0	1	0	0	0	0	8278	1725	60	0	721	0	KIDINS220	2	8871568	Frame_Shift_Del	DEL	T	TCGA-AL-3472-01A-01D-1252-08		8871568	234327805	5	4782											
TSGA10	80705	hgsc.bcm.edu	37	chr2	99689479	99689479	+	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	atttgttgcacgactgatttAccttgatgcctgttccatct	7	17	7	10	1	1	2	0	2	1	0	2	3	2	2	3	0	3	3	3	0	1	6			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr2:99689479A>C	ENST00000393483.3	-	13	1783		c.e13+1		TSGA10_ENST00000355053.4_Splice_Site|TSGA10_ENST00000410001.1_Splice_Site|TSGA10_ENST00000539964.1_Splice_Site|TSGA10_ENST00000542655.1_Intron|TSGA10_ENST00000478090.1_Splice_Site	NM_025244.2	NP_079520.1	Q9BZW7	TSG10_HUMAN	testis specific, 10						cell projection assembly (GO:0030031)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|membrane (GO:0016020)|motile cilium (GO:0031514)|neuron projection (GO:0043005)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	34						CGACTGATTTACCTTGATGCC	0.353																																					.		Atlas-SNP	.											.	TSGA10	81	.	0			c.938+2T>G						PASS	.						158	136	144					2																	99689479		2203	4300	6503	SO:0001630	splice_region_variant	80705	exon14			TGATTTACCTTGA	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.938+1T>G	chr2.hg19:g.99689479A>C		405.0	0.0	.		212.0	105.0	.	NM_025244	B7Z925|D3DVH7|Q8NEP0|Q9BWX0	Splice_Site	SNP	ENST00000393483.3	hg19	CCDS2037.1	.	.	.	.	.	.	.	.	.	.	A	17.47	3.398383	0.62177	.	.	ENSG00000135951	ENST00000393483;ENST00000410001;ENST00000355053;ENST00000539964;ENST00000409564;ENST00000393482	.	.	.	4.94	4.94	0.65067	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.9136	0.47122	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TSGA10	99055911	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	5.076000	0.64413	2.092000	0.63282	0.477000	0.44152	.	.	.	.	none		0.353	TSGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253125.1	NM_182911	Intron	C	99689479	A	C	99689479	5	2	74	1	0	0	0	0	0	0	1	0	16629	405	14	5	1192	5	TSGA10	2	99689479	Splice_Site	SNP	A	TCGA-AL-3472-01A-01D-1252-08	90817911	99689479	143509894	6	4783											
SLC25A12	8604	hgsc.bcm.edu	37	chr2	172647961	172647961	+	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	aaaaaaaaatttgtagttacCtgccatggctccagctgcaa	15	10	7	9	0	0	0	0	0	0	0	1	0	1	0	3	1	4	5	3	1	7	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr2:172647961C>G	ENST00000422440.2	-	15	1622	c.1585G>C	c.(1585-1587)Ggt>Cgt	p.G529R	SLC25A12_ENST00000392592.4_Splice_Site_p.G422R	NM_003705.4	NP_003696.2	O75746	CMC1_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 12	529					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)	TTGTAGTTACCTGCCATGGCT	0.353																																					p.G529R		Atlas-SNP	.											.	SLC25A12	59	.	0			c.G1585C						PASS	.						68	70	69					2																	172647961		2203	4300	6503	SO:0001630	splice_region_variant	8604	exon15			AGTTACCTGCCAT	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.1585+1G>C	chr2.hg19:g.172647961C>G		191.0	0.0	.		146.0	60.0	.	NM_003705	B3KR64|Q96AM8	Missense_Mutation	SNP	ENST00000422440.2	hg19	CCDS33327.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.952520	0.92660	.	.	ENSG00000115840	ENST00000422440;ENST00000392592	D;D	0.85339	-1.97;-1.97	5.92	5.92	0.95590	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.95242	0.8457	H	0.95712	3.71	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.95808	0.8839	9	.	.	.	-13.0108	20.3206	0.98668	0.0:1.0:0.0:0.0	.	422;529	B3KR64;O75746	.;CMC1_HUMAN	R	529;422	ENSP00000388658:G529R;ENSP00000376371:G422R	.	G	-	1	0	SLC25A12	172356207	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.784000	0.85713	2.809000	0.96659	0.655000	0.94253	GGT	.	.	.	none		0.353	SLC25A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259010.2	NM_003705	Missense_Mutation	G	172647961	C	G	172647961	5	3	74	1	0	0	0	0	0	0	1	0	14487	695	24	4	467	4	SLC25A12	2	172647961	Splice_Site	SNP	C	TCGA-AL-3472-01A-01D-1252-08	72958482	172647961	70551412	7	4784											
SF3B1	23451	hgsc.bcm.edu	37	chr2	198260814	198260814	+	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	atcttcaagtaacggtgttaCggcataaatgtagtcttttc	11	15	8	7	2	3	0	1	0	2	0	4	0	3	0	0	2	2	4	0	2	6	7			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr2:198260814C>T	ENST00000335508.6	-	23	3596	c.3505G>A	c.(3505-3507)Gta>Ata	p.V1169I		NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	1169					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)			AACGGTGTTACGGCATAAATG	0.323			Mis		myelodysplastic syndrome																																p.V1169I		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1	1038	.	0			c.G3505A						PASS	.						111	108	109					2																	198260814		2203	4300	6503	SO:0001583	missense	23451	exon23			GTGTTACGGCATA	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.3505G>A	chr2.hg19:g.198260814C>T	ENSP00000335321:p.Val1169Ile	322.0	0.0	.		105.0	43.0	.	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	hg19	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	C	14.40	2.524051	0.44866	.	.	ENSG00000115524	ENST00000335508	T	0.63744	-0.06	5.11	5.11	0.69529	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.58949	0.2158	L	0.50847	1.595	0.80722	D	1	D	0.56035	0.974	B	0.42361	0.385	T	0.57289	-0.7837	10	0.24483	T	0.36	.	19.0887	0.93217	0.0:1.0:0.0:0.0	.	1169	O75533	SF3B1_HUMAN	I	1169	ENSP00000335321:V1169I	ENSP00000335321:V1169I	V	-	1	0	SF3B1	197969059	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.534000	0.82004	2.826000	0.97356	0.655000	0.94253	GTA	.	.	.	none		0.323	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			T	198260814	C	T	198260814	3	4	74	1	0	0	0	0	1	0	0	0	14162	536	19	1	421	1	SF3B1	2	198260814	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08	25612853	198260814	44938559	8	4785											
PER2	8864	hgsc.bcm.edu	37	chr2	239176835	239176850	+	Splice_Site	DEL	GGACACTGCGGAGAAG	GGACACTGCGGAGAAG	-																															ttcattctcgtggcttttccGgacactgcggagaagagcca																								rs373179670|rs377264399|rs202102579|rs374332427		TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	GGACACTGCGGAGAAG	GGACACTGCGGAGAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr2:239176835_239176850delGGACACTGCGGAGAAG	ENST00000254657.3	-	8	1104_1108	c.825_829delCTTCTCCGCAGTGTCC	c.(823-831)agcttctcc>agcc	p.SFS275fs	PER2_ENST00000355768.2_Splice_Site_p.SFS275fs|PER2_ENST00000440245.1_Splice_Site_p.SFS275fs|PER2_ENST00000254658.3_Splice_Site_p.SFS275fs	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	275					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)		TGGCTTTTCCGGACACTGCGGAGAAGAGCCACGCTC	0.574																																					p.275_277del		Atlas-INDEL	.											.	PER2	85	.	0			c.825_830del						PASS	.																																			SO:0001630	splice_region_variant	8864	exon8			.	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.825-1CTTCTCCGCAGTGTCC>-	chr2.hg19:g.239176835_239176850delGGACACTGCGGAGAAG		76.0	0.0	0		129.0	35.0	0.271318	NM_022817	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	In_Frame_Del	DEL	ENST00000254657.3	hg19	CCDS2528.1																																																																																			.	.	.	none		0.574	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817	Frame_Shift_Del	-	239176850	GGACACTGCGGAGAAG	-	239176835	8	5	74	1	0	1	0	1	0	0	1	0	11737	1115	39	0	3002	0	PER2	2	239176835	Splice_Site	DEL	GGACACTGCGGAGAAG	TCGA-AL-3472-01A-01D-1252-08	40916021	239176835	4022538	9	4786											
ITIH3	3699	hgsc.bcm.edu	37	chr3	52830615	52830615	+	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	agacacggccaaggaggtttCctttgatgtggagctgccca	9	9	13	10	1	0	2	0	1	0	1	1	4	1	4	3	4	2	2	3	4	1	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr3:52830615C>T	ENST00000449956.2	+	3	239	c.233C>T	c.(232-234)tCc>tTc	p.S78F	ITIH3_ENST00000416872.2_Missense_Mutation_p.S78F	NM_002217.3	NP_002208.3	Q06033	ITIH3_HUMAN	inter-alpha-trypsin inhibitor heavy chain 3	78	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				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)		AAGGAGGTTTCCTTTGATGTG	0.562																																					p.S78F		Atlas-SNP	.											.	ITIH3	132	.	0			c.C233T						PASS	.						76	82	80					3																	52830615		2122	4276	6398	SO:0001583	missense	3699	exon3			AGGTTTCCTTTGA		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.233C>T	chr3.hg19:g.52830615C>T	ENSP00000415769:p.Ser78Phe	42.0	0.0	.		48.0	18.0	.	NM_002217	Q3B7H5|Q53F06|Q6LAM2|Q99085	Missense_Mutation	SNP	ENST00000449956.2	hg19	CCDS46845.1	.	.	.	.	.	.	.	.	.	.	C	7.116	0.576936	0.13686	.	.	ENSG00000162267	ENST00000398670;ENST00000536431;ENST00000273291;ENST00000416872;ENST00000449956	T;T	0.23552	1.9;1.9	4.43	2.45	0.29901	Vault protein inter-alpha-trypsin (2);Vault protein inter-alpha-trypsin, metazoa (1);	0.175288	0.50627	N	0.000112	T	0.10423	0.0255	N	0.10972	0.075	0.35532	D	0.802333	B;B	0.06786	0.001;0.001	B;B	0.13407	0.002;0.009	T	0.15694	-1.0428	10	0.17369	T	0.5	-12.815	4.7553	0.13080	0.0:0.6593:0.0:0.3407	.	78;78	E7ET33;Q06033	.;ITIH3_HUMAN	F	78;78;73;78;78	ENSP00000413922:S78F;ENSP00000415769:S78F	ENSP00000273291:S73F	S	+	2	0	ITIH3	52805655	0.000000	0.05858	0.973000	0.42090	0.946000	0.59487	-0.476000	0.06591	1.088000	0.41272	0.591000	0.81541	TCC	.	.	.	none		0.562	ITIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352668.2	NM_002217		T	52830615	C	T	52830615	3	4	74	1	0	0	0	0	1	0	0	0	7912	855	30	2	243	2	ITIH3	3	52830615	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08		52830615	145191815	10	4787											
ZNF654	55279	hgsc.bcm.edu	37	chr3	88190087	88190087	+	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	tgtataaaaaatcagtgaaaAgattaagatgtggcaaatgc	19	10	9	3	0	1	3	1	1	0	2	1	3	1	3	0	1	1	2	0	1	8	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr3:88190087A>T	ENST00000309495.5	+	1	1834	c.1627A>T	c.(1627-1629)Aga>Tga	p.R543*	CGGBP1_ENST00000462901.1_Intron	NM_018293.2	NP_060763.2	Q8IZM8	ZN654_HUMAN	zinc finger protein 654	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)			breast(2)|endometrium(1)|large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(3)	12		Lung NSC(201;0.0283)		UCEC - Uterine corpus endometrioid carcinoma (27;0.194)|LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00661)		ATCAGTGAAAAGATTAAGATG	0.383																																					p.R543X		Atlas-SNP	.											.	ZNF654	56	.	0			c.A1627T						PASS	.						77	71	73					3																	88190087		1854	4098	5952	SO:0001587	stop_gained	55279	exon1			GTGAAAAGATTAA	AF543494	CCDS46874.1	3p11.1	2005-01-10			ENSG00000175105	ENSG00000175105			25612	protein-coding gene	gene with protein product							Standard	NM_018293		Approved	FLJ10997, FLJ21142	uc003dqv.3	Q8IZM8	OTTHUMG00000159097	ENST00000309495.5:c.1627A>T	chr3.hg19:g.88190087A>T	ENSP00000312141:p.Arg543*	119.0	0.0	.		19.0	6.0	.	NM_018293	Q9H791|Q9NV14	Nonsense_Mutation	SNP	ENST00000309495.5	hg19	CCDS46874.1	.	.	.	.	.	.	.	.	.	.	a	39	7.456045	0.98296	.	.	ENSG00000175105	ENST00000309495	.	.	.	5.48	5.48	0.80851	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.7425	0.69467	1.0:0.0:0.0:0.0	.	.	.	.	X	543	.	ENSP00000312141:R543X	R	+	1	2	ZNF654	88272777	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.207000	0.72159	2.069000	0.61940	0.468000	0.43344	AGA	.	.	.	none		0.383	ZNF654-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353285.2	NM_018293		T	88190087	A	T	88190087	4	4	74	1	0	0	0	0	0	1	0	0	18079	64	3	5	1629	5	ZNF654	3	88190087	Nonsense_Mutation	SNP	A	TCGA-AL-3472-01A-01D-1252-08	35359472	88190087	109832343	11	4788											
LYAR	55646	hgsc.bcm.edu	37	chr4	4276342	4276342	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcttttccttttcttctgcCgttcttcctttctttctctt	0	25	2	14	1	6	0	0	0	6	0	9	0	8	0	3	0	1	1	3	0	0	10			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr4:4276342C>T	ENST00000343470.4	-	7	824	c.584G>A	c.(583-585)cGg>cAg	p.R195Q	LYAR_ENST00000452476.1_Missense_Mutation_p.R195Q	NM_017816.2	NP_060286	Q9NX58	LYAR_HUMAN	Ly1 antibody reactive	195	Lys-rich.					nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(6)|liver(2)|lung(5)|ovary(1)|prostate(1)	17				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		tttcttctgccgttcttcctt	0.438																																					p.R195Q		Atlas-SNP	.											.	LYAR	36	.	0			c.G584A						PASS	.						138	128	132					4																	4276342		2203	4300	6503	SO:0001583	missense	55646	exon7			TTCTGCCGTTCTT	AL136750	CCDS3374.1	4p16.3	2013-01-10	2012-12-07		ENSG00000145220	ENSG00000145220		"Zinc fingers, C2HC-type containing"	26021	protein-coding gene	gene with protein product			"Ly1 antibody reactive homolog (mouse)"			11230166, 8491376	Standard	NM_001145725		Approved	ZC2HC2, ZLYAR	uc003ght.3	Q9NX58	OTTHUMG00000125477	ENST00000343470.4:c.584G>A	chr4.hg19:g.4276342C>T	ENSP00000345917:p.Arg195Gln	256.0	0.0	.		301.0	137.0	.	NM_017816	D3DVS4|Q6FI78|Q9NYS1	Missense_Mutation	SNP	ENST00000343470.4	hg19	CCDS3374.1	.	.	.	.	.	.	.	.	.	.	C	12.94	2.089165	0.36855	.	.	ENSG00000145220	ENST00000343470;ENST00000452476	T;T	0.32753	1.44;1.44	5.19	5.19	0.71726	.	0.286976	0.36338	N	0.002645	T	0.30230	0.0758	M	0.72894	2.215	0.46222	D	0.998937	P	0.48503	0.911	B	0.31946	0.138	T	0.33523	-0.9865	10	0.44086	T	0.13	-12.7208	16.5728	0.84629	0.0:1.0:0.0:0.0	.	195	Q9NX58	LYAR_HUMAN	Q	195	ENSP00000345917:R195Q;ENSP00000397367:R195Q	ENSP00000345917:R195Q	R	-	2	0	LYAR	4327243	1.000000	0.71417	0.986000	0.45419	0.130000	0.20726	2.673000	0.46858	2.571000	0.86741	0.655000	0.94253	CGG	.	.	.	none		0.438	LYAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246800.2	NM_017816		T	4276342	C	T	4276342	3	4	74	1	0	0	0	0	1	0	0	0	9110	652	23	1	571	1	LYAR	4	4276342	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08		4276342	186877934	12	4789											
NSUN7	79730	hgsc.bcm.edu	37	chr4	40810405	40810405	+	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	tgctggatgggattgagttgGgtaaatcatcaaaacgggag	12	10	15	4	1	2	1	2	1	0	0	2	4	2	4	0	4	2	3	0	4	4	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr4:40810405G>C	ENST00000381782.2	+	12	2101	c.1606G>C	c.(1606-1608)Ggt>Cgt	p.G536R	NSUN7_ENST00000316607.5_3'UTR	NM_024677.4	NP_078953	Q8NE18	NSUN7_HUMAN	NOP2/Sun domain family, member 7	536							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|cervix(1)|large_intestine(1)|lung(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	12						GATTGAGTTGGGTAAATCATC	0.428																																					p.G536R		Atlas-SNP	.											.	NSUN7	70	.	0			c.G1606C						PASS	.						81	67	71					4																	40810405		692	1591	2283	SO:0001583	missense	79730	exon12			GAGTTGGGTAAAT	BC036568	CCDS3461.2	4p14	2013-10-11	2009-11-23		ENSG00000179299	ENSG00000179299		"NOP2/Sun domain containing"	25857	protein-coding gene	gene with protein product			"NOL1/NOP2/Sun domain family, member 7"			17442852	Standard	NM_024677		Approved	FLJ14001	uc003gvj.4	Q8NE18	OTTHUMG00000128597	ENST00000381782.2:c.1606G>C	chr4.hg19:g.40810405G>C	ENSP00000371201:p.Gly536Arg	162.0	0.0	.		145.0	63.0	.	NM_024677	C9JI19|Q8N9K8|Q9H815	Missense_Mutation	SNP	ENST00000381782.2	hg19	CCDS3461.2	.	.	.	.	.	.	.	.	.	.	G	15.27	2.783124	0.49891	.	.	ENSG00000179299	ENST00000381782	T	0.14640	2.49	5.6	3.87	0.44632	.	0.804730	0.11512	N	0.556627	T	0.11623	0.0283	L	0.47716	1.5	0.09310	N	0.999999	P	0.48089	0.905	B	0.39258	0.295	T	0.16837	-1.0389	10	0.31617	T	0.26	-7.9775	6.9881	0.24739	0.1529:0.1439:0.7032:0.0	.	536	Q8NE18	NSUN7_HUMAN	R	536	ENSP00000371201:G536R	ENSP00000371201:G536R	G	+	1	0	NSUN7	40505162	0.935000	0.31712	0.983000	0.44433	0.993000	0.82548	2.018000	0.40991	1.364000	0.46038	0.591000	0.81541	GGT	.	.	.	none		0.428	NSUN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250454.2	NM_024677		C	40810405	G	C	40810405	3	2	74	1	0	0	0	0	1	0	0	0	10690	1232	43	4	1648	4	NSUN7	4	40810405	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08	36534063	40810405	150343871	13	4790											
INTU	27152	hgsc.bcm.edu	37	chr4	128564929	128564929	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcaataaaaaaaatagcAatgacaatggaccagtatcc	19	7	7	8	0	0	1	0	1	0	0	1	2	1	2	2	1	2	4	2	1	9	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr4:128564929A>G	ENST00000335251.6	+	2	503	c.400A>G	c.(400-402)Aat>Gat	p.N134D	INTU_ENST00000296461.5_Missense_Mutation_p.N134D	NM_015693.3	NP_056508.2	Q9ULD6	INTU_HUMAN	inturned planar cell polarity protein	134					cilium assembly (GO:0042384)|hair follicle morphogenesis (GO:0031069)|keratinocyte differentiation (GO:0030216)|limb development (GO:0060173)|negative regulation of cell division (GO:0051782)|negative regulation of keratinocyte proliferation (GO:0010839)|nervous system development (GO:0007399)|positive regulation of smoothened signaling pathway (GO:0045880)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord dorsal/ventral patterning (GO:0021513)	cytoplasm (GO:0005737)				breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	43						AAAAAATAGCAATGACAATGG	0.358																																					p.N134D		Atlas-SNP	.											.	INTU	92	.	0			c.A400G						PASS	.						69	71	71					4																	128564929		2203	4300	6503	SO:0001583	missense	27152	exon2			AATAGCAATGACA	BC051698	CCDS34061.1	4q28.2	2013-03-05	2013-03-05	2006-10-24	ENSG00000164066	ENSG00000164066			29239	protein-coding gene	gene with protein product		610621	"PDZ domain containing 6", "inturned planar cell polarity effector homolog (Drosophila)"	PDZK6, PDZD6		10574462, 21761479	Standard	NM_015693		Approved	KIAA1284	uc003ifk.2	Q9ULD6	OTTHUMG00000161202	ENST00000335251.6:c.400A>G	chr4.hg19:g.128564929A>G	ENSP00000334003:p.Asn134Asp	167.0	0.0	.		36.0	17.0	.	NM_015693	A1L4N5|D6RAE6|D6RBT4|Q4W5I8|Q86V55	Missense_Mutation	SNP	ENST00000335251.6	hg19	CCDS34061.1	.	.	.	.	.	.	.	.	.	.	A	1.750	-0.489422	0.04352	.	.	ENSG00000164066	ENST00000504491;ENST00000335251;ENST00000296461	T	0.44083	0.93	5.1	2.61	0.31194	.	0.890844	0.09986	N	0.730400	T	0.24736	0.0600	N	0.22421	0.69	0.22127	N	0.999348	B	0.06786	0.001	B	0.04013	0.001	T	0.25152	-1.0140	10	0.25751	T	0.34	-1.097	2.9593	0.05887	0.5157:0.2769:0.0738:0.1336	.	134	Q9ULD6	PDZD6_HUMAN	D	115;134;134	ENSP00000296461:N134D	ENSP00000296461:N134D	N	+	1	0	INTU	128784379	0.341000	0.24801	0.129000	0.21949	0.028000	0.11728	2.259000	0.43259	0.393000	0.25203	0.533000	0.62120	AAT	.	.	.	none		0.358	INTU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364147.2	XM_371707		G	128564929	A	G	128564929	3	3	74	1	0	0	0	0	1	0	0	0	7793	130	5	3	406	3	INTU	4	128564929	Missense_Mutation	SNP	A	TCGA-AL-3472-01A-01D-1252-08	87754524	128564929	62589347	14	4791											
PSD2	84249	hgsc.bcm.edu	37	chr5	139193773	139193773	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgaccccagcctgaaggaTggcctgtcagactcagactc	10	7	11	13	0	2	4	2	2	0	2	3	5	2	5	4	2	1	0	4	2	1	0			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr5:139193773T>C	ENST00000274710.3	+	4	1045	c.840T>C	c.(838-840)gaT>gaC	p.D280D		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	280	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCTGAAGGATGGCCTGTCAG	0.632																																					p.D280D		Atlas-SNP	.											.	PSD2	88	.	0			c.T840C						PASS	.						108	101	103					5																	139193773		2203	4300	6503	SO:0001819	synonymous_variant	84249	exon4			GAAGGATGGCCTG	AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"Pleckstrin homology (PH) domain containing"	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.840T>C	chr5.hg19:g.139193773T>C		329.0	0.0	.		577.0	261.0	.	NM_032289	D3DQD3|Q8N3J8	Silent	SNP	ENST00000274710.3	hg19	CCDS4216.1																																																																																			.	.	.	none		0.632	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289		C	139193773	T	C	139193773	2	2	74	1	0	0	0	0	0	0	0	1	12657	1461	51	3		3	PSD2	5	139193773	Silent	SNP	T	TCGA-AL-3472-01A-01D-1252-08		139193773	41721487	15	4792											
SLC25A2	83884	hgsc.bcm.edu	37	chr5	140683030	140683030	+	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	ctccatttcatacatggtctGtagccggcacttcacaagct	9	12	7	13	1	3	0	2	0	1	0	4	0	4	0	2	2	3	3	2	2	3	4			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr5:140683030G>A	ENST00000239451.4	-	1	582	c.403C>T	c.(403-405)Cag>Tag	p.Q135*		NM_031947.2	NP_114153.1	Q9BXI2	ORNT2_HUMAN	solute carrier family 25 (mitochondrial carrier; ornithine transporter) member 2	135					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)|urea cycle (GO:0000050)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				breast(3)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	19		all_lung(500;0.000249)|Lung NSC(810;0.0011)|Ovarian(839;0.00556)|Breast(839;0.0173)|all_hematologic(541;0.152)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.00204)	L-Ornithine(DB00129)	TACATGGTCTGTAGCCGGCAC	0.522																																					p.Q135X		Atlas-SNP	.											.	SLC25A2	68	.	0			c.C403T						PASS	.						100	108	105					5																	140683030		2203	4300	6503	SO:0001587	stop_gained	83884	exon1			TGGTCTGTAGCCG	AF332005	CCDS4258.1	5q31.3	2013-05-22			ENSG00000120329	ENSG00000120329		"Solute carriers"	22921	protein-coding gene	gene with protein product		608157				11004451	Standard	NM_031947		Approved	ORNT2	uc003ljf.3	Q9BXI2	OTTHUMG00000129604	ENST00000239451.4:c.403C>T	chr5.hg19:g.140683030G>A	ENSP00000239451:p.Gln135*	353.0	1.0	.		503.0	204.0	.	NM_031947	Q496C1|Q6XUI0|Q8NFZ2	Nonsense_Mutation	SNP	ENST00000239451.4	hg19	CCDS4258.1	.	.	.	.	.	.	.	.	.	.	G	33	5.250551	0.95305	.	.	ENSG00000120329	ENST00000239451	.	.	.	3.78	3.78	0.43462	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-5.487	13.9383	0.64039	0.0:0.0:1.0:0.0	.	.	.	.	X	135	.	ENSP00000239451:Q135X	Q	-	1	0	SLC25A2	140663214	1.000000	0.71417	0.982000	0.44146	0.942000	0.58702	8.721000	0.91446	2.424000	0.82194	0.650000	0.86243	CAG	.	.	.	none		0.522	SLC25A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251799.2	NM_031947		A	140683030	G	A	140683030	4	1	74	1	0	0	0	0	0	1	0	0	14495	1386	48	2	506	2	SLC25A2	5	140683030	Nonsense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08	1489257	140683030	40232230	16	4793											
SLC22A23	63027	hgsc.bcm.edu	37	chr6	3410472	3410472	+	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	ccaggcaaaatccttcaaagAacctgagtgtgctgaacatt	14	9	8	10	0	1	3	1	2	0	1	2	3	2	3	3	1	3	2	3	1	5	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr6:3410472A>T	ENST00000406686.3	-	3	862	c.863T>A	c.(862-864)tTc>tAc	p.F288Y	SLC22A23_ENST00000436008.2_Missense_Mutation_p.F288Y|SLC22A23_ENST00000380302.4_Missense_Mutation_p.F7Y|SLC22A23_ENST00000490273.1_Missense_Mutation_p.F7Y|SLC22A23_ENST00000380298.2_Missense_Mutation_p.F288Y	NM_015482.1	NP_056297.1	A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23	288					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)				TCCTTCAAAGAACCTGAGTGT	0.448																																					p.F288Y		Atlas-SNP	.											.	SLC22A23	89	.	0			c.T863A						PASS	.						112	96	101					6																	3410472		2203	4300	6503	SO:0001583	missense	63027	exon3			TCAAAGAACCTGA	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.863T>A	chr6.hg19:g.3410472A>T	ENSP00000385028:p.Phe288Tyr	144.0	0.0	.		64.0	61.0	.	NM_015482	A1A5C8|Q5T8B8|Q6ZMH3|Q8IW73	Missense_Mutation	SNP	ENST00000406686.3	hg19	CCDS47363.1	.	.	.	.	.	.	.	.	.	.	A	29.1	4.980895	0.92982	.	.	ENSG00000137266	ENST00000436008;ENST00000406686;ENST00000380302;ENST00000490273;ENST00000485307;ENST00000467177;ENST00000380298	T;T;T;T;T;T;T	0.62788	0.0;0.0;0.0;0.0;0.0;0.0;0.0	5.17	5.17	0.71159	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.71239	0.3316	M	0.64997	1.995	0.52501	D	0.999957	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.997	T	0.76110	-0.3079	10	0.87932	D	0	-30.1819	15.0144	0.71573	1.0:0.0:0.0:0.0	.	288;288	C9J4Z0;A1A5C7	.;S22AN_HUMAN	Y	288;288;7;7;116;114;288	ENSP00000410245:F288Y;ENSP00000385028:F288Y;ENSP00000369657:F7Y;ENSP00000419463:F7Y;ENSP00000418134:F116Y;ENSP00000418985:F114Y;ENSP00000369653:F288Y	ENSP00000369653:F288Y	F	-	2	0	SLC22A23	3355471	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.770000	0.91746	1.960000	0.56953	0.460000	0.39030	TTC	.	.	.	none		0.448	SLC22A23-006	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353059.1	NM_021945		T	3410472	A	T	3410472	3	4	74	1	0	0	0	0	1	0	0	0	14465	246	9	5	1229	5	SLC22A23	6	3410472	Missense_Mutation	SNP	A	TCGA-AL-3472-01A-01D-1252-08		3410472	167704595	17	4794											
TRIM15	89870	hgsc.bcm.edu	37	chr6	30140094	30140094	+	Frame_Shift_Del	DEL	A	A	-																															tccctttctttgccgtctggAaaaaaggttcctgccttacg																										TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr6:30140094delA	ENST00000376694.4	+	7	1835	c.1366delA	c.(1366-1368)aaafs	p.K457fs	TRIM15_ENST00000376688.1_Intron	NM_033229.2	NP_150232.2	Q9C019	TRI15_HUMAN	tripartite motif containing 15	457	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						TGCCGTCTGGAAAAAAGGTTC	0.637																																					p.W455X		Atlas-INDEL	.											.	TRIM15	34	.	0			c.1365delG						PASS	.						36	45	42					6																	30140094		1506	2707	4213	SO:0001589	frameshift_variant	89870	exon7			.	AF220132, U34249	CCDS4677.1	6p21.33	2013-01-09	2011-01-25		ENSG00000204610	ENSG00000204610		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16284	protein-coding gene	gene with protein product			"zinc finger protein 178", "tripartite motif-containing 15"	ZNF178		11331580, 8304341, 8812418	Standard	NM_033229		Approved	ZNFB7, RNF93	uc010jrx.3	Q9C019	OTTHUMG00000031031	ENST00000376694.4:c.1366delA	chr6.hg19:g.30140094delA	ENSP00000365884:p.Lys457fs	135.0	0.0	0		184.0	81.0	0.440217	NM_033229	A2BEC9|O95604|Q8IUX9|Q9C018	Frame_Shift_Del	DEL	ENST00000376694.4	hg19	CCDS4677.1																																																																																			.	.	.	none		0.637	TRIM15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076026.2	NM_033229		-	30140094	A	-	30140094	7	5	74	1	0	1	0	1	0	0	0	0	16502	247	9	0	1392	0	TRIM15	6	30140094	Frame_Shift_Del	DEL	A	TCGA-AL-3472-01A-01D-1252-08	26729622	30140094	140974973	18	4795											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51712728	51712728	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatctgtgtgcaccagcagtAggtaattaccaggagcaaag	14	8	11	8	0	1	0	0	0	1	0	1	1	1	1	2	2	4	5	2	2	5	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr6:51712728A>G	ENST00000371117.3	-	50	8227	c.7952T>C	c.(7951-7953)cTa>cCa	p.L2651P	PKHD1_ENST00000340994.4_Missense_Mutation_p.L2651P	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2651					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)					CACCAGCAGTAGGTAATTACC	0.458																																					p.L2651P		Atlas-SNP	.											.	PKHD1	927	.	0			c.T7952C						PASS	.						127	126	127					6																	51712728		2203	4300	6503	SO:0001583	missense	5314	exon50			AGCAGTAGGTAAT	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.7952T>C	chr6.hg19:g.51712728A>G	ENSP00000360158:p.Leu2651Pro	267.0	0.0	.		81.0	72.0	.	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	A	15.27	2.784987	0.49997	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.89123	-2.28;-2.47	5.47	5.47	0.80525	.	0.128004	0.36409	N	0.002604	D	0.91606	0.7348	L	0.59436	1.845	0.58432	D	0.999997	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.73708	0.98;0.965;0.981	D	0.92508	0.6014	10	0.62326	D	0.03	.	15.0183	0.71605	1.0:0.0:0.0:0.0	.	2651;2651;2651	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	P	2651	ENSP00000360158:L2651P;ENSP00000341097:L2651P	ENSP00000341097:L2651P	L	-	2	0	PKHD1	51820687	1.000000	0.71417	0.992000	0.48379	0.153000	0.21895	6.098000	0.71458	2.196000	0.70406	0.528000	0.53228	CTA	.	.	.	none		0.458	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		G	51712728	A	G	51712728	3	3	74	1	0	0	0	0	1	0	0	0	11978	420	15	3	4383	3	PKHD1	6	51712728	Missense_Mutation	SNP	A	TCGA-AL-3472-01A-01D-1252-08	21572634	51712728	119402339	19	4796											
AHI1	54806	hgsc.bcm.edu	37	chr6	135732541	135732541	+	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	tcttcgttgaagaactttcaGtgtggacaaattcatcaatc	12	14	7	8	1	4	2	3	1	1	1	6	3	4	3	0	1	1	1	0	1	4	4			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr6:135732541G>C	ENST00000367800.4	-	19	3122	c.2906C>G	c.(2905-2907)aCt>aGt	p.T969S	AHI1_ENST00000417892.2_Missense_Mutation_p.T323S|AHI1_ENST00000327035.6_Missense_Mutation_p.T969S|AHI1_ENST00000457866.2_Missense_Mutation_p.T969S	NM_001134830.1	NP_001128302.1	Q8N157	AHI1_HUMAN	Abelson helper integration site 1	969					cellular protein localization (GO:0034613)|central nervous system development (GO:0007417)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|cloaca development (GO:0035844)|heart looping (GO:0001947)|hindbrain development (GO:0030902)|Kupffer's vesicle development (GO:0070121)|left/right axis specification (GO:0070986)|morphogenesis of a polarized epithelium (GO:0001738)|negative regulation of apoptotic process (GO:0043066)|otic vesicle development (GO:0071599)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of polarized epithelial cell differentiation (GO:0030862)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pronephric duct morphogenesis (GO:0039023)|pronephric nephron tubule morphogenesis (GO:0039008)|protein localization to organelle (GO:0033365)|regulation of behavior (GO:0050795)|retina layer formation (GO:0010842)|specification of axis polarity (GO:0065001)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vesicle targeting (GO:0006903)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|nonmotile primary cilium (GO:0031513)|photoreceptor outer segment (GO:0001750)|primary cilium (GO:0072372)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)	37	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		AGAACTTTCAGTGTGGACAAA	0.373																																					p.T969S		Atlas-SNP	.											.	AHI1	81	.	0			c.C2906G						PASS	.						143	137	139					6																	135732541		1847	4102	5949	SO:0001583	missense	54806	exon20			CTTTCAGTGTGGA	AJ459824	CCDS47483.1, CCDS47484.1	6q23.2	2013-01-10	2005-11-29		ENSG00000135541	ENSG00000135541		"WD repeat domain containing"	21575	protein-coding gene	gene with protein product	"Jouberin"	608894	"Abelson helper integration site"			15060101, 16240161	Standard	NM_017651		Approved	FLJ20069, ORF1, JBTS3	uc003qgj.3	Q8N157	OTTHUMG00000015631	ENST00000367800.4:c.2906C>G	chr6.hg19:g.135732541G>C	ENSP00000356774:p.Thr969Ser	200.0	0.0	.		33.0	27.0	.	NM_001134832	E1P584|Q4FD35|Q504T3|Q5TCP9|Q6P098|Q6PIT6|Q8NDX0|Q9H0H2	Missense_Mutation	SNP	ENST00000367800.4	hg19	CCDS47483.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.95|12.95	2.090823|2.090823	0.36855|0.36855	.|.	.|.	ENSG00000135541|ENSG00000135541	ENST00000367799;ENST00000529865|ENST00000367800;ENST00000457866;ENST00000417892;ENST00000265602;ENST00000327035;ENST00000367801	.|T;T;T;T;T	.|0.37411	.|1.2;1.2;1.2;1.2;1.2	5.69|5.69	2.9|2.9	0.33743|0.33743	.|.	.|0.402955	.|0.30830	.|N	.|0.008787	T|T	0.13114|0.13114	0.0318|0.0318	N|N	0.22421|0.22421	0.69|0.69	0.80722|0.80722	D|D	1|1	.|P;P;B	.|0.40431	.|0.717;0.595;0.451	.|B;B;B	.|0.41271	.|0.352;0.192;0.112	T|T	0.03662|0.03662	-1.1015|-1.1015	5|10	.|0.54805	.|T	.|0.06	-12.9903|-12.9903	9.4417|9.4417	0.38673|0.38673	0.0:0.2946:0.5522:0.1532|0.0:0.2946:0.5522:0.1532	.|.	.|969;969;969	.|Q8N157-2;Q8N157;Q4FD35	.|.;AHI1_HUMAN;.	V|S	469;36|969;969;323;969;969;969	.|ENSP00000356774:T969S;ENSP00000388650:T969S;ENSP00000416867:T323S;ENSP00000265602:T969S;ENSP00000322478:T969S	.|ENSP00000265602:T969S	L|T	-|-	1|2	2|0	AHI1|AHI1	135774234|135774234	0.951000|0.951000	0.32395|0.32395	0.977000|0.977000	0.42913|0.42913	0.960000|0.960000	0.62799|0.62799	0.749000|0.749000	0.26320|0.26320	0.311000|0.311000	0.23014|0.23014	-0.127000|-0.127000	0.14921|0.14921	CTG|ACT	.	.	.	none		0.373	AHI1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391948.1	NM_017651		C	135732541	G	C	135732541	3	2	74	1	0	0	0	0	1	0	0	0	413	1029	36	4	777	4	AHI1	6	135732541	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08	84019813	135732541	35382526	20	4797											
RADIL	55698	hgsc.bcm.edu	37	chr7	4876021	4876021	+	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	gtagccctgcagaaggagcaGatgcggggactggtacagcg	10	5	17	9	2	0	2	0	0	0	2	0	4	0	4	1	4	6	4	1	4	3	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr7:4876021G>T	ENST00000399583.3	-	3	938	c.751C>A	c.(751-753)Ctg>Atg	p.L251M	RADIL_ENST00000538469.1_Missense_Mutation_p.L11M|RADIL_ENST00000536091.1_Missense_Mutation_p.L251M	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	251					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)		AGAAGGAGCAGATGCGGGGAC	0.701																																					p.L251M		Atlas-SNP	.											.	RADIL	110	.	0			c.C751A						PASS	.						16	23	20					7																	4876021		2086	4206	6292	SO:0001583	missense	55698	exon3			GGAGCAGATGCGG	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.751C>A	chr7.hg19:g.4876021G>T	ENSP00000382492:p.Leu251Met	12.0	0.0	.		29.0	8.0	.	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	hg19	CCDS43544.1	.	.	.	.	.	.	.	.	.	.	G	12.62	1.993465	0.35131	.	.	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000536091;ENST00000538469	T;T;T	0.06849	3.25;3.25;3.25	4.85	3.96	0.45880	Forkhead-associated (FHA) domain (1);SMAD/FHA domain (1);	0.000000	0.64402	D	0.000002	T	0.29914	0.0748	M	0.82630	2.6	0.35445	D	0.795246	D	0.89917	1.0	D	0.69307	0.963	T	0.43750	-0.9372	10	0.62326	D	0.03	-21.7944	13.6214	0.62138	0.0828:0.0:0.9172:0.0	.	251	Q96JH8	RADIL_HUMAN	M	251;225;251;11	ENSP00000382492:L251M;ENSP00000442533:L251M;ENSP00000442966:L11M	ENSP00000320946:L225M	L	-	1	2	RADIL	4842547	1.000000	0.71417	0.993000	0.49108	0.126000	0.20510	3.872000	0.56085	0.473000	0.27368	-1.598000	0.00824	CTG	.	.	.	none		0.701	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059		T	4876021	G	T	4876021	3	4	74	1	0	0	0	0	1	0	0	0	13010	933	33	4	2528	4	RADIL	7	4876021	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08		4876021	154262642	21	4798											
MET	4233	hgsc.bcm.edu	37	chr7	116415115	116415115	+	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	ccaggcagtgcagcatgtagTgattgggcccagtagcctga	9	8	14	10	0	0	2	0	2	0	0	0	2	0	2	3	2	3	5	3	2	2	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr7:116415115T>A	ENST00000318493.6	+	15	3450	c.3263T>A	c.(3262-3264)gTg>gAg	p.V1088E	MET_ENST00000539704.1_5'Flank|MET_ENST00000397752.3_Missense_Mutation_p.V1070E			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.V1088E(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)			CAGCATGTAGTGATTGGGCCC	0.433			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.V1088E		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	Substitution - Missense(1)	kidney(1)	c.T3263A						PASS	.						174	172	172					7																	116415115		2077	4220	6297	SO:0001583	missense	4233	exon15	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	ATGTAGTGATTGG	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.3263T>A	chr7.hg19:g.116415115T>A	ENSP00000317272:p.Val1088Glu	316.0	2.0	.		283.0	165.0	.	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	T	28.0	4.885631	0.91814	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000454623	T;T	0.73681	-0.77;-0.77	5.62	5.62	0.85841	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	D	0.84469	0.5479	M	0.62723	1.935	0.80722	D	1	D;D	0.69078	0.996;0.997	D;D	0.80764	0.994;0.989	D	0.86091	0.1550	10	0.87932	D	0	-15.0307	16.1067	0.81230	0.0:0.0:0.0:1.0	.	1088;1070	P08581-2;P08581	.;MET_HUMAN	E	1070;1088;155	ENSP00000380860:V1070E;ENSP00000317272:V1088E	ENSP00000317272:V1088E	V	+	2	0	MET	116202351	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.310000	0.78947	2.255000	0.74692	0.533000	0.62120	GTG	.	.	.	none		0.433	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			A	116415115	T	A	116415115	3	1	74	1	0	0	0	0	1	0	0	0	9492	1696	59	5	3317	5	MET	7	116415115	Missense_Mutation	SNP	T	TCGA-AL-3472-01A-01D-1252-08	111539094	116415115	42723548	22	4799											
KLHL9	55958	hgsc.bcm.edu	37	chr9	21334413	21334413	+	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	caacacagttatccaaagagActcctgatataagaaatact	18	9	5	9	0	0	3	0	1	0	2	2	4	2	3	2	0	2	1	2	0	7	4			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr9:21334413A>T	ENST00000359039.4	-	1	966	c.446T>A	c.(445-447)gTc>gAc	p.V149D	KLHL9_ENST00000537938.1_Missense_Mutation_p.V81D			Q9P2J3	KLHL9_HUMAN	kelch-like family member 9	149					cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|midbody (GO:0030496)				endometrium(9)|large_intestine(7)|lung(10)|ovary(4)|skin(2)	32				Lung(24;8.52e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.118)		ATCCAAAGAGACTCCTGATAT	0.338																																					p.V149D		Atlas-SNP	.											.	KLHL9	61	.	0			c.T446A						PASS	.						39	43	42					9																	21334413		2203	4297	6500	SO:0001583	missense	55958	exon1			AAAGAGACTCCTG	AB037775	CCDS6503.1	9p22	2013-01-30	2013-01-30		ENSG00000198642	ENSG00000198642		"Kelch-like", "BTB/POZ domain containing"	18732	protein-coding gene	gene with protein product		611201	"kelch-like 9 (Drosophila)"				Standard	NM_018847		Approved	KIAA1354, FLJ13568	uc003zoy.3	Q9P2J3	OTTHUMG00000019669	ENST00000359039.4:c.446T>A	chr9.hg19:g.21334413A>T	ENSP00000351933:p.Val149Asp	145.0	0.0	.		133.0	61.0	.	NM_018847	Q8TCQ2	Missense_Mutation	SNP	ENST00000359039.4	hg19	CCDS6503.1	.	.	.	.	.	.	.	.	.	.	A	14.17	2.455753	0.43634	.	.	ENSG00000198642	ENST00000359039;ENST00000537938	T;T	0.73152	-0.7;-0.72	5.21	5.21	0.72293	BTB/POZ-like (1);BTB/POZ fold (1);	0.136382	0.48286	D	0.000181	T	0.72236	0.3435	M	0.68317	2.08	0.80722	D	1	B	0.28933	0.228	B	0.36289	0.221	T	0.74423	-0.3670	10	0.87932	D	0	.	13.3494	0.60593	1.0:0.0:0.0:0.0	.	149	Q9P2J3	KLHL9_HUMAN	D	149;81	ENSP00000351933:V149D;ENSP00000437733:V81D	ENSP00000351933:V149D	V	-	2	0	KLHL9	21324413	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.891000	0.92485	2.111000	0.64477	0.528000	0.53228	GTC	.	.	.	none		0.338	KLHL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051898.2	NM_018847		T	21334413	A	T	21334413	3	4	74	1	0	0	0	0	1	0	0	0	8403	275	10	5	1411	5	KLHL9	9	21334413	Missense_Mutation	SNP	A	TCGA-AL-3472-01A-01D-1252-08		21334413	119879018	23	4800											
PSAT1	29968	hgsc.bcm.edu	37	chr9	80942983	80942984	+	Frame_Shift_Ins	INS	-	-	A																															cagttgtccagtggagccccINSaaaatagaagcaagatgaat																										TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr9:80942983_80942984insA	ENST00000376588.3	+	8	954_955	c.886_887insA	c.(886-888)caafs	p.Q296fs	PSAT1_ENST00000347159.2_Intron	NM_058179.2	NP_478059.1	Q9Y617	SERC_HUMAN	phosphoserine aminotransferase 1	296					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-serine biosynthetic process (GO:0006564)|pyridoxine biosynthetic process (GO:0008615)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	O-phospho-L-serine:2-oxoglutarate aminotransferase activity (GO:0004648)|pyridoxal phosphate binding (GO:0030170)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	20						AGTGGAGCCCCAAAATAGAAGC	0.337																																					p.Q296fs	Colon(34;187 791 10662 18313 37609)	Atlas-INDEL	.											.	PSAT1	33	.	0			c.886_887insA						PASS	.																																			SO:0001589	frameshift_variant	29968	exon8			.	BC004863	CCDS6659.1, CCDS6660.1	9q21.2	2008-08-11			ENSG00000135069	ENSG00000135069			19129	protein-coding gene	gene with protein product		610936				12633500, 3651428	Standard	NM_058179		Approved	PSA	uc004ala.3	Q9Y617	OTTHUMG00000020066	ENST00000376588.3:c.890dupA	chr9.hg19:g.80942987_80942987dupA	ENSP00000365773:p.Gln296fs	111.0	0.0	0		44.0	21.0	0.477273	NM_058179	Q5T7G5|Q5T7G6|Q96AW2|Q9BQ12	Frame_Shift_Ins	INS	ENST00000376588.3	hg19	CCDS6660.1																																																																																			.	.	.	none		0.337	PSAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052777.1	NM_021154		A	80942984	-	A	80942983	7	5	74	1	0	1	1	0	0	0	0	0	12654	595	21	0	916	0	PSAT1	9	80942983	Frame_Shift_Ins	INS	-	TCGA-AL-3472-01A-01D-1252-08	59608570	80942983	60270448	24	4801											
RPL12	6136	hgsc.bcm.edu	37	chr9	130213582	130213582	+	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	actttgatctcgttggggtcGaacttcggcggcatggtgga	6	12	15	8	4	1	1	0	1	1	0	4	3	1	2	0	6	1	2	0	6	1	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr9:130213582G>A	ENST00000361436.5	-	1	102	c.15C>T	c.(13-15)ttC>ttT	p.F5F	RPL12_ENST00000497322.1_5'UTR|RPL12_ENST00000536368.1_Silent_p.F5F|SNORA65_ENST00000364432.1_RNA|LRSAM1_ENST00000323301.4_5'Flank|LRSAM1_ENST00000373322.1_5'Flank|LRSAM1_ENST00000373324.4_5'Flank|LRSAM1_ENST00000300417.6_5'Flank	NM_000976.3	NP_000967.1	P30050	RL12_HUMAN	ribosomal protein L12	5					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)|structural constituent of ribosome (GO:0003735)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|prostate(1)	4						CGTTGGGGTCGAACTTCGGCG	0.652																																					p.F5F		Atlas-SNP	.											.	RPL12	11	.	0			c.C15T						PASS	.						33	36	35					9																	130213582		2199	4296	6495	SO:0001819	synonymous_variant	6136	exon1			GGGGTCGAACTTC		CCDS6872.1	9q34	2011-04-06			ENSG00000197958	ENSG00000197958		"L ribosomal proteins"	10302	protein-coding gene	gene with protein product		180475				8441690	Standard	NM_000976		Approved	L12	uc004bqy.2	P30050	OTTHUMG00000020704	ENST00000361436.5:c.15C>T	chr9.hg19:g.130213582G>A		110.0	0.0	.		171.0	68.0	.	NM_000976	Q5VVV2|Q6PB27	Silent	SNP	ENST00000361436.5	hg19	CCDS6872.1																																																																																			.	.	.	none		0.652	RPL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054189.1			A	130213582	G	A	130213582	2	1	74	1	0	0	0	0	0	0	0	1	13571	1049	37	1		1	RPL12	9	130213582	Silent	SNP	G	TCGA-AL-3472-01A-01D-1252-08	49270599	130213582	10999849	25	4802											
AKR1E2	83592	hgsc.bcm.edu	37	chr10	4877871	4877871	+	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	ctctccttcttcgcagcctcCtcatccagaatggatcatga	8	12	6	15	1	4	2	2	1	2	1	8	3	6	3	4	1	1	1	4	1	1	2	rs149822509	byFrequency	TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr10:4877871C>A	ENST00000298375.7	+	4	400	c.329C>A	c.(328-330)cCt>cAt	p.P110H	AKR1E2_ENST00000532248.1_Missense_Mutation_p.P110H|AKR1E2_ENST00000525281.1_3'UTR|AKR1E2_ENST00000334019.4_Missense_Mutation_p.P110H|AKR1E2_ENST00000345253.5_Missense_Mutation_p.P110H	NM_001040177.2	NP_001035267.1	Q96JD6	AKCL2_HUMAN	aldo-keto reductase family 1, member E2	110						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	1,5-anhydro-D-fructose reductase activity (GO:0050571)			NS(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)	15						TCGCAGCCTCCTCATCCAGAA	0.483																																					p.P110H	NSCLC(43;343 1097 20371 28813 45509)	Atlas-SNP	.											.	AKR1E2	30	.	0			c.C329A						PASS	.						82	68	73					10																	4877871		2203	4300	6503	SO:0001583	missense	83592	exon4			AGCCTCCTCATCC	AB040820	CCDS31134.1, CCDS59210.1, CCDS59209.1	10p15.2	2009-09-09	2009-09-09	2009-09-09	ENSG00000165568	ENSG00000165568		"Aldo-keto reductases"	23437	protein-coding gene	gene with protein product			"aldo-keto reductase family 1, member C-like 2"	AKRDC1, AKR1CL2			Standard	NM_001271021		Approved	MGC10612	uc001ihi.4	Q96JD6	OTTHUMG00000017577	ENST00000298375.7:c.329C>A	chr10.hg19:g.4877871C>A	ENSP00000298375:p.Pro110His	105.0	0.0	.		73.0	26.0	.	NM_001271025	Q86Z16|Q86Z17|Q86Z18|Q9BU71	Missense_Mutation	SNP	ENST00000298375.7	hg19	CCDS31134.1	.	.	.	.	.	.	.	.	.	.	C	12.44	1.940130	0.34283	.	.	ENSG00000165568	ENST00000462718;ENST00000533295;ENST00000298375;ENST00000532248;ENST00000334019;ENST00000345253	T;T;T;T;T	0.50277	0.75;2.3;2.3;2.3;1.87	3.39	2.47	0.30058	NADP-dependent oxidoreductase domain (3);	.	.	.	.	T	0.38268	0.1034	N	0.11201	0.11	0.09310	N	1	B;D;D;D;D	0.55385	0.007;0.965;0.965;0.971;0.965	B;P;P;P;P	0.54372	0.014;0.634;0.634;0.75;0.634	T	0.13764	-1.0497	9	0.72032	D	0.01	.	6.973	0.24658	0.0:0.8714:0.0:0.1286	.	71;110;110;110;110	B7Z7K2;Q96JD6-5;Q96JD6-2;Q96JD6;Q96JD6-3	.;.;.;AKCL2_HUMAN;.	H	6;114;110;110;110;110	ENSP00000435436:P114H;ENSP00000298375:P110H;ENSP00000432947:P110H;ENSP00000335034:P110H;ENSP00000335603:P110H	ENSP00000298375:P110H	P	+	2	0	AKR1E2	4867871	0.000000	0.05858	0.001000	0.08648	0.031000	0.12232	0.340000	0.19892	0.964000	0.38108	0.561000	0.74099	CCT	.	C|0.994;G|0.006	.	alt		0.483	AKR1E2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046520.4	NM_031436		A	4877871	C	A	4877871	3	1	74	1	0	0	0	0	1	0	0	0	474	681	24	4	343	4	AKR1E2	10	4877871	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08		4877871	130656876	26	4803											
OR10G8	219869	hgsc.bcm.edu	37	chr11	123900948	123900948	+	Missense_Mutation	SNP	T	T	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	tgactgttggaatagtggccTcgggctgctttgtcctgata	6	14	13	8	1	0	2	0	2	0	0	2	3	1	3	2	3	1	3	2	3	3	4			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr11:123900948T>G	ENST00000431524.1	+	1	652	c.619T>G	c.(619-621)Tcg>Gcg	p.S207A		NM_001004464.1	NP_001004464.1	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G, member 8	207						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|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)		AATAGTGGCCTCGGGCTGCTT	0.537																																					p.S207A		Atlas-SNP	.											.	OR10G8	132	.	0			c.T619G						PASS	.						193	169	177					11																	123900948		2201	4299	6500	SO:0001583	missense	219869	exon1			GTGGCCTCGGGCT	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.619T>G	chr11.hg19:g.123900948T>G	ENSP00000389072:p.Ser207Ala	209.0	0.0	.		173.0	71.0	.	NM_001004464	B2RNJ3|Q6IEV2	Missense_Mutation	SNP	ENST00000431524.1	hg19	CCDS31704.1	.	.	.	.	.	.	.	.	.	.	T	2.750	-0.260282	0.05791	.	.	ENSG00000234560	ENST00000431524	T	0.36157	1.27	2.91	2.91	0.33838	GPCR, rhodopsin-like superfamily (1);	0.953949	0.08599	N	0.921764	T	0.23330	0.0564	N	0.01482	-0.84	0.09310	N	1	B	0.30914	0.3	B	0.43194	0.411	T	0.46456	-0.9190	10	0.45353	T	0.12	.	11.0743	0.48021	0.0:0.0:0.0:1.0	.	207	Q8NGN5	O10G8_HUMAN	A	207	ENSP00000389072:S207A	ENSP00000389072:S207A	S	+	1	0	OR10G8	123406158	0.000000	0.05858	0.780000	0.31762	0.263000	0.26337	0.369000	0.20416	1.319000	0.45190	0.455000	0.32223	TCG	.	.	.	none		0.537	OR10G8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387270.1	NM_001004464		G	123900948	T	G	123900948	3	3	74	1	0	0	0	0	1	0	0	0	10910	1551	54	5	621	5	OR10G8	11	123900948	Missense_Mutation	SNP	T	TCGA-AL-3472-01A-01D-1252-08		123900948	11105568	27	4804											
ST14	6768	hgsc.bcm.edu	37	chr11	130066334	130066334	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaggactacgtggagatcaAcggggagaagtgagtccccg	12	5	15	9	3	1	3	1	1	0	2	2	6	2	4	2	4	2	0	2	4	4	1			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr11:130066334A>G	ENST00000278742.5	+	10	1632	c.1214A>G	c.(1213-1215)aAc>aGc	p.N405S		NM_021978.3	NP_068813.1	Q9Y5Y6	ST14_HUMAN	suppression of tumorigenicity 14 (colon carcinoma)	405	CUB 2. {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)	GTGGAGATCAACGGGGAGAAG	0.677																																					p.N405S		Atlas-SNP	.											.	ST14	82	.	0			c.A1214G						PASS	.						30	27	28					11																	130066334		2201	4296	6497	SO:0001583	missense	6768	exon10			AGATCAACGGGGA	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.1214A>G	chr11.hg19:g.130066334A>G	ENSP00000278742:p.Asn405Ser	39.0	0.0	.		39.0	10.0	.	NM_021978	Q9BS01|Q9H3S0|Q9HB36|Q9HCA3	Missense_Mutation	SNP	ENST00000278742.5	hg19	CCDS8487.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.146950	0.77888	.	.	ENSG00000149418	ENST00000278742;ENST00000525779	T	0.18960	2.18	4.62	4.62	0.57501	CUB (5);	0.000000	0.41097	D	0.000956	T	0.32102	0.0818	L	0.41710	1.295	0.58432	D	0.999999	D;D	0.67145	0.996;0.993	D;D	0.69654	0.936;0.965	T	0.03374	-1.1043	10	0.17832	T	0.49	.	12.2663	0.54681	1.0:0.0:0.0:0.0	.	215;405	B4DYI7;Q9Y5Y6	.;ST14_HUMAN	S	405;307	ENSP00000278742:N405S	ENSP00000278742:N405S	N	+	2	0	ST14	129571544	0.997000	0.39634	0.972000	0.41901	0.891000	0.51852	3.696000	0.54757	1.730000	0.51580	0.533000	0.62120	AAC	.	.	.	none		0.677	ST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386119.1			G	130066334	A	G	130066334	3	3	74	1	0	0	0	0	1	0	0	0	15223	43	2	3	1252	3	ST14	11	130066334	Missense_Mutation	SNP	A	TCGA-AL-3472-01A-01D-1252-08	6165386	130066334	4940182	28	4805											
FGF6	2251	hgsc.bcm.edu	37	chr12	4554499	4554500	+	Missense_Mutation	DNP	CC	CC	AG																															ccgctgccgcttgatccccaCcaaatagccactttcccagt																										TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr12:4554499_4554500CC>AG	ENST00000228837.2	-	1	280_281	c.237_238GG>CT	c.(235-240)ttGGtg>ttCTtg	p.79_80LV>FL		NM_020996.1	NP_066276.2	P10767	FGF6_HUMAN	fibroblast growth factor 6	79					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)			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)			TTGATCCCCACCAAATAGCCAC	0.653																																					p.V80L|p.L79F		Atlas-SNP	.											.	FGF6	40	.	0			c.G238T|c.G237C						PASS	.																																			SO:0001583	missense	2251	exon1			TCCCCACCAAATA|CCCCACCAAATAG	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.237_238delinsAG	chr12.hg19:g.4554499_4554500delinsAG	ENSP00000228837:p.L79_V80delinsFL	175.0|179.0	0.0	.		244.0|241.0	116.0	.	NM_020996	Q0VAE1	Missense_Mutation	SNP	ENST00000228837.2	hg19	CCDS8527.1																																																																																			.	.	.	none		0.653	FGF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398939.1	NM_020996		AG	4554500	CC	AG	4554499	3	1	74	1	0	0	0	0	1	0	0	0	5863	507	18	4	400	4	FGF6	12	4554499	Missense_Mutation	DNP	CC	TCGA-AL-3472-01A-01D-1252-08		4554499	129297396	29	4806											
LAG3	3902	hgsc.bcm.edu	37	chr12	6886462	6886462	+	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	cctttgggtcacctggatccCtggggaagctgctttgtgag	5	12	14	10	0	1	1	1	1	0	0	2	3	2	3	3	4	2	2	3	4	1	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr12:6886462C>A	ENST00000203629.2	+	6	1423	c.1090C>A	c.(1090-1092)Ctg>Atg	p.L364M		NM_002286.5	NP_002277.4	P18627	LAG3_HUMAN	lymphocyte-activation gene 3	364	Ig-like C2-type 3.				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						ACCTGGATCCCTGGGGAAGCT	0.512																																					p.L364M		Atlas-SNP	.											.	LAG3	35	.	0			c.C1090A						PASS	.						113	112	112					12																	6886462		2203	4300	6503	SO:0001583	missense	3902	exon6			GGATCCCTGGGGA		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.1090C>A	chr12.hg19:g.6886462C>A	ENSP00000203629:p.Leu364Met	255.0	0.0	.		383.0	171.0	.	NM_002286	A8K7T9|Q7Z643	Missense_Mutation	SNP	ENST00000203629.2	hg19	CCDS8561.1	.	.	.	.	.	.	.	.	.	.	C	14.51	2.556120	0.45487	.	.	ENSG00000089692	ENST00000203629	T	0.11604	2.76	4.55	2.53	0.30540	.	1.747540	0.02897	N	0.134825	T	0.10937	0.0267	N	0.24115	0.695	0.09310	N	1	P	0.46277	0.875	P	0.44732	0.459	T	0.24584	-1.0156	10	0.33940	T	0.23	2.878	7.2879	0.26350	0.1917:0.6226:0.1858:0.0	.	364	P18627	LAG3_HUMAN	M	364	ENSP00000203629:L364M	ENSP00000203629:L364M	L	+	1	2	LAG3	6756723	0.025000	0.19082	0.471000	0.27229	0.889000	0.51656	-0.025000	0.12413	1.073000	0.40885	0.561000	0.74099	CTG	.	.	.	none		0.512	LAG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402846.1			A	6886462	C	A	6886462	3	1	74	1	0	0	0	0	1	0	0	0	8607	680	24	4	1112	4	LAG3	12	6886462	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08	2331963	6886462	126965433	30	4807											
TMTC1	83857	hgsc.bcm.edu	37	chr12	29670368	29670368	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catcctactcaccagtgccaAgcggagctccctctgagaag	10	7	9	15	1	2	1	1	1	1	1	4	3	4	2	4	1	4	1	4	1	3	1			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr12:29670368A>G	ENST00000539277.1	-	14	2219	c.2161T>C	c.(2161-2163)Ttg>Ctg	p.L721L	TMTC1_ENST00000319685.8_5'UTR|TMTC1_ENST00000256062.5_Silent_p.L613L|TMTC1_ENST00000552618.1_Silent_p.L745L|TMTC1_ENST00000551659.1_Silent_p.L783L|RP11-310I24.1_ENST00000549070.1_RNA	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	721						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)					ACCAGTGCCAAGCGGAGCTCC	0.517																																					p.L721L		Atlas-SNP	.											.	TMTC1	147	.	0			c.T2161C						PASS	.						117	114	115					12																	29670368		2203	4300	6503	SO:0001819	synonymous_variant	83857	exon14			GTGCCAAGCGGAG		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.2161T>C	chr12.hg19:g.29670368A>G		203.0	0.0	.		80.0	34.0	.	NM_001193451	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Silent	SNP	ENST00000539277.1	hg19	CCDS53772.1																																																																																			.	.	.	none		0.517	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403509.1	NM_031920		G	29670368	A	G	29670368	2	3	74	1	0	0	0	0	0	0	0	1	16272	69	3	3		3	TMTC1	12	29670368	Silent	SNP	A	TCGA-AL-3472-01A-01D-1252-08	22783906	29670368	104181527	31	4808											
RBM19	9904	hgsc.bcm.edu	37	chr12	114397941	114397941	+	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	ctgggcatgtttgctccaggCtctgggtttggccgggtccc	2	12	15	12	1	1	0	0	0	1	0	3	0	3	0	3	5	1	5	3	5	0	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr12:114397941C>T	ENST00000545145.2	-	3	340	c.262G>A	c.(262-264)Gcc>Acc	p.A88T	RBM19_ENST00000261741.5_Missense_Mutation_p.A88T|RBM19_ENST00000392561.3_Missense_Mutation_p.A88T	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	88					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)					TTGCTCCAGGCTCTGGGTTTG	0.532																																					p.A88T		Atlas-SNP	.											.	RBM19	117	.	0			c.G262A						PASS	.						100	99	99					12																	114397941		2203	4300	6503	SO:0001583	missense	9904	exon3			TCCAGGCTCTGGG	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.262G>A	chr12.hg19:g.114397941C>T	ENSP00000442053:p.Ala88Thr	103.0	0.0	.		144.0	54.0	.	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	hg19	CCDS9172.1	.	.	.	.	.	.	.	.	.	.	C	16.36	3.102307	0.56183	.	.	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.74315	-0.83;-0.83;-0.83	4.86	4.86	0.63082	Nucleotide-binding, alpha-beta plait (1);	0.116689	0.56097	D	0.000023	T	0.76716	0.4026	M	0.79258	2.445	0.48288	D	0.999627	P	0.44478	0.836	B	0.41374	0.355	T	0.79381	-0.1827	10	0.40728	T	0.16	-26.8541	18.1761	0.89761	0.0:1.0:0.0:0.0	.	88	Q9Y4C8	RBM19_HUMAN	T	88	ENSP00000442053:A88T;ENSP00000376344:A88T;ENSP00000261741:A88T	ENSP00000261741:A88T	A	-	1	0	RBM19	112882324	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	3.397000	0.52572	2.513000	0.84729	0.557000	0.71058	GCC	.	.	.	none		0.532	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196		T	114397941	C	T	114397941	3	4	74	1	0	0	0	0	1	0	0	0	13134	797	28	2	2708	2	RBM19	12	114397941	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08	84727573	114397941	19453954	32	4809											
ULK1	8408	hgsc.bcm.edu	37	chr12	132393457	132393457	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcagctgacttcggcttcGcgcggtacctccagagcaac	7	7	11	16	5	0	2	0	1	0	1	3	2	1	2	3	2	4	5	3	2	2	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr12:132393457G>A	ENST00000321867.4	+	7	856	c.505G>A	c.(505-507)Gcg>Acg	p.A169T		NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	169	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|cellular response to nutrient levels (GO:0031669)|cerebellar granule cell differentiation (GO:0021707)|negative regulation of collateral sprouting (GO:0048671)|neuron projection development (GO:0031175)|neuron projection regeneration (GO:0031102)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|protein autophosphorylation (GO:0046777)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|radial glia guided migration of cerebellar granule cell (GO:0021933)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of autophagy (GO:0010506)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|response to starvation (GO:0042594)	ATG1/UKL1 signaling complex (GO:0034273)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extrinsic component of autophagic vacuole membrane (GO:0097635)|extrinsic component of omegasome membrane (GO:0097629)|extrinsic component of pre-autophagosomal structure membrane (GO:0097632)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)	ATP binding (GO:0005524)|protein complex binding (GO:0032403)|protein serine/threonine kinase activity (GO:0004674)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	29	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		CTTCGGCTTCGCGCGGTACCT	0.711																																					p.A169T		Atlas-SNP	.											.	ULK1	92	.	0			c.G505A						PASS	.						60	59	59					12																	132393457		2203	4300	6503	SO:0001583	missense	8408	exon7			GGCTTCGCGCGGT	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.505G>A	chr12.hg19:g.132393457G>A	ENSP00000324560:p.Ala169Thr	105.0	0.0	.		139.0	60.0	.	NM_003565	Q9UQ28	Missense_Mutation	SNP	ENST00000321867.4	hg19	CCDS9274.1	.	.	.	.	.	.	.	.	.	.	G	36	5.828944	0.96996	.	.	ENSG00000177169	ENST00000321867;ENST00000537421;ENST00000542313	T;T;D	0.90133	0.97;0.97;-2.62	5.32	5.32	0.75619	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.95959	0.8684	M	0.86178	2.8	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96254	0.9185	10	0.87932	D	0	-34.7466	19.3607	0.94436	0.0:0.0:1.0:0.0	.	169	O75385	ULK1_HUMAN	T	169;86;63	ENSP00000324560:A169T;ENSP00000438953:A86T;ENSP00000444983:A63T	ENSP00000324560:A169T	A	+	1	0	ULK1	130959410	1.000000	0.71417	0.295000	0.24960	0.974000	0.67602	7.537000	0.82033	2.651000	0.90000	0.455000	0.32223	GCG	.	.	.	none		0.711	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3			A	132393457	G	A	132393457	3	1	74	1	0	0	0	0	1	0	0	0	16987	1087	38	1	531	1	ULK1	12	132393457	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08	17995516	132393457	1458438	33	4810											
ACYP1	97	hgsc.bcm.edu	37	chr14	75528414	75528414	+	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	actggtagcaaagctaactgGaacacagctcttgctgtgag	12	9	11	9	0	1	1	0	1	1	0	1	2	1	2	0	2	6	5	0	2	4	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr14:75528414G>C	ENST00000238618.3	-	2	188				ACYP1_ENST00000555135.1_Missense_Mutation_p.P46A|ACYP1_ENST00000555463.1_Intron|ACYP1_ENST00000357971.3_Missense_Mutation_p.P46A|ACYP1_ENST00000555694.1_Intron	NM_001107.3	NP_001098.1	P07311	ACYP1_HUMAN	acylphosphatase 1, erythrocyte (common) type						phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)	acylphosphatase activity (GO:0003998)			large_intestine(2)	2				BRCA - Breast invasive adenocarcinoma(234;0.00646)		AAGCTAACTGGAACACAGCTC	0.358																																					p.P46A		Atlas-SNP	.											.	ACYP1	6	.	0			c.C136G						PASS	.						69	67	68					14																	75528414		1872	4101	5973	SO:0001627	intron_variant	97	exon3			TAACTGGAACACA	X84194	CCDS9838.1, CCDS45137.1	14q24.3	2014-08-08			ENSG00000119640	ENSG00000119640	3.6.1.7		179	protein-coding gene	gene with protein product		600875				7796909, 9730610	Standard	NM_001107		Approved		uc001xrg.3	P07311	OTTHUMG00000171767	ENST00000238618.3:c.84+1758C>G	chr14.hg19:g.75528414G>C		65.0	0.0	.		53.0	18.0	.	NM_203488	A6NDV8|B2R590	Missense_Mutation	SNP	ENST00000238618.3	hg19	CCDS9838.1	.	.	.	.	.	.	.	.	.	.	G	9.868	1.198229	0.22037	.	.	ENSG00000119640	ENST00000357971;ENST00000555135	.	.	.	3.01	0.887	0.19200	.	.	.	.	.	T	0.36908	0.0984	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.35450	-0.9788	7	0.87932	D	0	.	9.8551	0.41082	0.0:0.5438:0.4562:0.0	.	46	A6NDV8	.	A	46	.	ENSP00000350655:P46A	P	-	1	0	ACYP1	74598167	0.003000	0.15002	0.054000	0.19295	0.203000	0.24098	0.172000	0.16704	0.176000	0.19873	0.543000	0.68304	CCA	.	.	.	none		0.358	ACYP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415013.1			C	75528414	G	C	75528414	1	2	74	0	1	0	0	0	0	0	0	0	228	1174	41	4		4	ACYP1	14	75528414	Intron	SNP	G	TCGA-AL-3472-01A-01D-1252-08		75528414	31821126	34	4811											
LRRK1	79705	hgsc.bcm.edu	37	chr15	101592098	101592098	+	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	acttcatctcctgccccagaCacccggacctccccgtgccg	6	7	7	21	3	2	1	1	0	1	1	4	2	3	2	8	1	2	0	8	1	0	1			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr15:101592098C>A	ENST00000388948.3	+	24	3981	c.3622C>A	c.(3622-3624)Cac>Aac	p.H1208N	RP11-505E24.3_ENST00000558979.1_RNA|RP11-505E24.2_ENST00000559857.1_RNA|LRRK1_ENST00000284395.5_Missense_Mutation_p.H1205N	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)			CTGCCCCAGACACCCGGACCT	0.617																																					p.H1208N		Atlas-SNP	.											.	LRRK1	310	.	0			c.C3622A						PASS	.						53	62	59					15																	101592098		2037	4192	6229	SO:0001583	missense	79705	exon24			CCCAGACACCCGG	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.3622C>A	chr15.hg19:g.101592098C>A	ENSP00000373600:p.His1208Asn	90.0	0.0	.		125.0	55.0	.	NM_024652		Missense_Mutation	SNP	ENST00000388948.3	hg19	CCDS42086.1	.	.	.	.	.	.	.	.	.	.	C	33	5.194800	0.94960	.	.	ENSG00000154237	ENST00000388948;ENST00000284395	T;T	0.73789	-0.76;-0.78	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.81356	0.4805	L	0.32530	0.975	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	T	0.83156	-0.0101	10	0.72032	D	0.01	.	19.2014	0.93713	0.0:1.0:0.0:0.0	.	1208	Q38SD2	LRRK1_HUMAN	N	1208;1205	ENSP00000373600:H1208N;ENSP00000284395:H1205N	ENSP00000284395:H1205N	H	+	1	0	LRRK1	99409621	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.669000	0.83911	2.541000	0.85698	0.655000	0.94253	CAC	.	.	.	none		0.617	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		A	101592098	C	A	101592098	3	1	74	1	0	0	0	0	1	0	0	0	9039	478	17	4	3712	4	LRRK1	15	101592098	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08		101592098	939294	35	4812											
SRRM2	23524	hgsc.bcm.edu	37	chr16	2814808	2814809	+	Frame_Shift_Ins	INS	-	-	T																															ttctgcatcttctcctgaaaINStgaaagatggtttacccaga																										TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr16:2814808_2814809insT	ENST00000301740.8	+	11	4828_4829	c.4279_4280insT	c.(4279-4281)atgfs	p.M1427fs		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	1427	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						TTCTCCTGAAATGAAAGATGGT	0.505																																					p.M1427fs		Atlas-INDEL	.											.	SRRM2	263	.	0			c.4279_4280insT						PASS	.																																			SO:0001589	frameshift_variant	23524	exon11			.	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.4280dupT	chr16.hg19:g.2814809_2814809dupT	ENSP00000301740:p.Met1427fs	336.0	0.0	0		367.0	150.0	0.408719	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Frame_Shift_Ins	INS	ENST00000301740.8	hg19	CCDS32373.1																																																																																			.	.	.	none		0.505	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			T	2814809	-	T	2814808	7	5	74	1	0	1	1	0	0	0	0	0	15181	101	4	0	4317	0	SRRM2	16	2814808	Frame_Shift_Ins	INS	-	TCGA-AL-3472-01A-01D-1252-08		2814808	87539945	36	4813											
CLEC16A	23274	hgsc.bcm.edu	37	chr16	11066855	11066855	+	Missense_Mutation	SNP	A	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	tgctgttccttacttctccaAtttggtctggttcattggga	5	18	9	9	0	3	0	1	0	2	0	5	1	4	1	2	3	2	3	2	3	2	6			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr16:11066855A>C	ENST00000409790.1	+	7	895	c.665A>C	c.(664-666)aAt>aCt	p.N222T	CLEC16A_ENST00000409552.3_Missense_Mutation_p.N220T	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						TACTTCTCCAATTTGGTCTGG	0.463																																					p.N222T		Atlas-SNP	.											.	CLEC16A	101	.	0			c.A665C						PASS	.						86	83	84					16																	11066855		1967	4159	6126	SO:0001583	missense	23274	exon6			TCTCCAATTTGGT	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.665A>C	chr16.hg19:g.11066855A>C	ENSP00000387122:p.Asn222Thr	54.0	0.0	.		39.0	17.0	.	NM_015226		Missense_Mutation	SNP	ENST00000409790.1	hg19	CCDS45409.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.575730	0.86645	.	.	ENSG00000038532	ENST00000409790;ENST00000542102;ENST00000409552	T	0.50813	0.73	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.67813	0.2933	M	0.70595	2.14	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.78314	0.987;0.991	T	0.69161	-0.5218	10	0.51188	T	0.08	-24.4217	15.5133	0.75802	1.0:0.0:0.0:0.0	.	222;220	Q2KHT3;Q2KHT3-2	CL16A_HUMAN;.	T	222;222;220	ENSP00000387122:N222T	ENSP00000386495:N220T	N	+	2	0	CLEC16A	10974356	1.000000	0.71417	0.937000	0.37676	0.978000	0.69477	9.228000	0.95250	2.251000	0.74343	0.528000	0.53228	AAT	.	.	.	none		0.463	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226		C	11066855	A	C	11066855	3	2	74	1	0	0	0	0	1	0	0	0	3502	101	4	5	687	5	CLEC16A	16	11066855	Missense_Mutation	SNP	A	TCGA-AL-3472-01A-01D-1252-08	8252047	11066855	79287898	37	4814											
ZNF423	23090	hgsc.bcm.edu	37	chr16	49670867	49670867	+	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	aggtgcacctggatggacacCttggagtcgaagacctcctg	9	8	13	11	1	0	1	0	0	0	1	2	5	1	4	4	4	1	1	4	4	1	1	rs373085653		TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr16:49670867C>G	ENST00000561648.1	-	4	2249	c.2196G>C	c.(2194-2196)aaG>aaC	p.K732N	ZNF423_ENST00000567169.1_Missense_Mutation_p.K615N|ZNF423_ENST00000562871.1_Missense_Mutation_p.K672N|ZNF423_ENST00000535559.1_Missense_Mutation_p.K615N|ZNF423_ENST00000562520.1_Missense_Mutation_p.K672N|ZNF423_ENST00000563137.2_Missense_Mutation_p.K672N|ZNF423_ENST00000262383.2_Missense_Mutation_p.K732N	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	732					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)				GGATGGACACCTTGGAGTCGA	0.567																																					p.K732N		Atlas-SNP	.											.	ZNF423	463	.	0			c.G2196C						PASS	.						100	93	95					16																	49670867		2198	4300	6498	SO:0001583	missense	23090	exon4			GGACACCTTGGAG	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.2196G>C	chr16.hg19:g.49670867C>G	ENSP00000455426:p.Lys732Asn	76.0	0.0	.		136.0	71.0	.	NM_015069	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	hg19	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	C	15.57	2.872977	0.51695	.	.	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.30448	1.53;1.53	5.05	5.05	0.67936	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.85682	D	0.000000	T	0.46946	0.1419	L	0.38531	1.155	0.53005	D	0.999969	D	0.89917	1.0	D	0.91635	0.999	T	0.31364	-0.9946	9	.	.	.	.	18.4141	0.90562	0.0:1.0:0.0:0.0	.	732	Q2M1K9	ZN423_HUMAN	N	732;615	ENSP00000262383:K732N;ENSP00000442321:K615N	.	K	-	3	2	ZNF423	48228368	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.361000	0.52306	2.352000	0.79861	0.561000	0.74099	AAG	.	.	.	alt		0.567	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		G	49670867	C	G	49670867	3	3	74	1	0	0	0	0	1	0	0	0	17910	680	24	4	1678	4	ZNF423	16	49670867	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08	38604012	49670867	40683886	38	4815											
KIAA0513	9764	hgsc.bcm.edu	37	chr16	85100829	85100829	+	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	gagtgagaccactgagtctgCggacagtgagaatgacatgg	12	7	15	7	1	1	4	0	4	1	2	1	8	1	5	1	2	1	0	1	2	1	0	rs148950418		TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr16:85100829C>T	ENST00000566428.1	+	2	783	c.152C>T	c.(151-153)gCg>gTg	p.A51V	KIAA0513_ENST00000258180.3_Missense_Mutation_p.A51V|KIAA0513_ENST00000567328.1_Missense_Mutation_p.A51V|KIAA0513_ENST00000538274.1_Missense_Mutation_p.A51V			O60268	K0513_HUMAN	KIAA0513	51						cytoplasm (GO:0005737)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(9)|pancreas(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.234)		ACTGAGTCTGCGGACAGTGAG	0.647																																					p.A51V		Atlas-SNP	.											.	KIAA0513	43	.	0			c.C152T						PASS	.	C	VAL/ALA	1,4397	2.1+/-5.4	0,1,2198	72	58	63		152	4.5	0.2	16	dbSNP_134	63	0,8600		0,0,4300	no	missense	KIAA0513	NM_014732.2	64	0,1,6498	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	51/412	85100829	1,12997	2199	4300	6499	SO:0001583	missense	9764	exon2			AGTCTGCGGACAG	AB011085	CCDS32499.1, CCDS67091.1, CCDS73919.1	16q24.1	2012-11-29			ENSG00000135709	ENSG00000135709			29058	protein-coding gene	gene with protein product		611675				9628581	Standard	XM_005256265		Approved		uc002fiu.3	O60268	OTTHUMG00000176597	ENST00000566428.1:c.152C>T	chr16.hg19:g.85100829C>T	ENSP00000457408:p.Ala51Val	66.0	0.0	.		113.0	34.0	.	NM_014732	B4DSS5|D3DUM2|Q8N6G0	Missense_Mutation	SNP	ENST00000566428.1	hg19	CCDS32499.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.700612	0.88924	2.27E-4	0.0	ENSG00000135709	ENST00000538274;ENST00000258180	T;T	0.38240	1.15;1.15	4.54	4.54	0.55810	.	0.000000	0.85682	D	0.000000	T	0.57755	0.2075	M	0.67953	2.075	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.986	T	0.58239	-0.7671	10	0.41790	T	0.15	-15.5029	16.2567	0.82522	0.0:1.0:0.0:0.0	.	51;51	B4DSS5;O60268	.;K0513_HUMAN	V	51	ENSP00000446439:A51V;ENSP00000258180:A51V	ENSP00000258180:A51V	A	+	2	0	KIAA0513	83658330	1.000000	0.71417	0.218000	0.23776	0.820000	0.46376	6.939000	0.75911	2.234000	0.73211	0.561000	0.74099	GCG	.	C|1.000;T|0.000	0.000	weak		0.647	KIAA0513-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432736.1	NM_014732		T	85100829	C	T	85100829	3	4	74	1	0	0	0	0	1	0	0	0	8188	768	27	1	154	1	KIAA0513	16	85100829	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08	35429962	85100829	5253924	39	4816											
MYH13	8735	hgsc.bcm.edu	37	chr17	10258306	10258306	+	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	gtcactctggatttttctaaCagatctaaggtaacaaaaat	15	13	6	7	0	4	1	1	0	3	1	4	2	4	2	0	2	2	1	0	2	5	5			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr17:10258306C>G	ENST00000418404.3	-	9	970	c.807G>C	c.(805-807)ctG>ctC	p.L269L	MYH13_ENST00000252172.4_Silent_p.L269L			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	269	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						ATTTTTCTAACAGATCTAAGG	0.368																																					p.L269L		Atlas-SNP	.											.	MYH13	533	.	0			c.G807C						PASS	.						71	70	71					17																	10258306		1848	4092	5940	SO:0001819	synonymous_variant	8735	exon10			TTCTAACAGATCT	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.807G>C	chr17.hg19:g.10258306C>G		80.0	0.0	.		91.0	16.0	.	NM_003802	O95252|Q9P0U8	Silent	SNP	ENST00000418404.3	hg19	CCDS45613.1																																																																																			.	.	.	none		0.368	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		G	10258306	C	G	10258306	2	3	74	1	0	0	0	0	0	0	0	1	10039	465	17	4		4	MYH13	17	10258306	Silent	SNP	C	TCGA-AL-3472-01A-01D-1252-08		10258306	70936904	40	4817											
MPRIP	23164	hgsc.bcm.edu	37	chr17	17080727	17080727	+	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	tgccacggtgtccggatatgGtgcgtcctcgggtcatgccc	4	10	14	13	4	1	0	1	0	0	0	4	1	3	1	4	4	3	0	4	4	1	1			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr17:17080727G>A	ENST00000341712.4	+	21	2959		c.e21+1		MPRIP_ENST00000395804.3_Splice_Site|RP11-45M22.3_ENST00000584203.1_RNA|MPRIP_ENST00000395811.5_Splice_Site|RN7SL775P_ENST00000498361.2_RNA|MPRIP_ENST00000444976.1_Splice_Site			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein							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						TCCGGATATGGTGCGTCCTCG	0.582																																					.		Atlas-SNP	.											.	MPRIP	87	.	0			c.2959+1G>A						PASS	.						64	57	59					17																	17080727		2203	4300	6503	SO:0001630	splice_region_variant	23164	exon21			GATATGGTGCGTC	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.2959+1G>A	chr17.hg19:g.17080727G>A		91.0	0.0	.		250.0	73.0	.	NM_015134	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Splice_Site	SNP	ENST00000341712.4	hg19	CCDS32578.1	.	.	.	.	.	.	.	.	.	.	G	13.42	2.232815	0.39498	.	.	ENSG00000133030	ENST00000444976;ENST00000395811;ENST00000395804;ENST00000341712;ENST00000313485;ENST00000414263;ENST00000429184	.	.	.	5.13	5.13	0.70059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.9433	0.92612	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MPRIP	17021452	1.000000	0.71417	0.960000	0.40013	0.094000	0.18550	9.358000	0.97109	2.539000	0.85634	0.563000	0.77884	.	.	.	.	none		0.582	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134	Intron	A	17080727	G	A	17080727	5	1	74	1	0	0	0	0	0	0	1	0	9750	1275	44	2	3042	2	MPRIP	17	17080727	Splice_Site	SNP	G	TCGA-AL-3472-01A-01D-1252-08	6822421	17080727	64114483	41	4818											
NDUFS7	374291	hgsc.bcm.edu	37	chr19	1391140	1391140	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctacgaccagatgccggagcCgcgctacgtggtctccatgg	7	7	13	14	5	1	1	0	0	1	1	2	3	1	2	4	3	4	1	4	3	2	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr19:1391140C>T	ENST00000233627.9	+	6	727	c.431C>T	c.(430-432)cCg>cTg	p.P144L	NDUFS7_ENST00000414651.2_Missense_Mutation_p.P174L|NDUFS7_ENST00000546283.1_Missense_Mutation_p.P144L|NDUFS7_ENST00000540530.1_3'UTR|NDUFS7_ENST00000313408.7_Missense_Mutation_p.P144L|AC005329.7_ENST00000501448.1_RNA|NDUFS7_ENST00000539480.1_Missense_Mutation_p.P144L|AC005329.7_ENST00000589734.1_RNA|AC005329.7_ENST00000585596.1_RNA	NM_024407.4	NP_077718.3	O75251	NDUS7_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 7, 20kDa (NADH-coenzyme Q reductase)	144					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|mitochondrial respiratory chain complex I assembly (GO:0032981)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|synaptic membrane (GO:0097060)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|quinone binding (GO:0048038)			ovary(1)	1		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)|Breast(49;0.00186)|Lung NSC(49;0.00292)|all_lung(49;0.00419)		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)	Doxorubicin(DB00997)	ATGCCGGAGCCGCGCTACGTG	0.687																																					p.P144L		Atlas-SNP	.											.	NDUFS7	4	.	0			c.C431T						PASS	.						22	24	23					19																	1391140		2201	4298	6499	SO:0001583	missense	374291	exon6			CGGAGCCGCGCTA	AF115969	CCDS12063.1	19p13	2011-07-04	2002-08-29		ENSG00000115286	ENSG00000115286		"Mitochondrial respiratory chain complex / Complex I"	7714	protein-coding gene	gene with protein product	"complex I 20kDa subunit", "NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial"	601825	"NADH dehydrogenase (ubiquinone) Fe-S protein 7 (20kD) (NADH-coenzyme Q reductase)"			8938450	Standard	NM_024407		Approved	PSST, FLJ46880, FLJ45860, CI-20	uc002lse.4	O75251	OTTHUMG00000168077	ENST00000233627.9:c.431C>T	chr19.hg19:g.1391140C>T	ENSP00000233627:p.Pro144Leu	44.0	0.0	.		58.0	24.0	.	NM_024407	B3KRI2|Q2T9H7|Q9BV17	Missense_Mutation	SNP	ENST00000233627.9	hg19	CCDS12063.1	.	.	.	.	.	.	.	.	.	.	C	13.64	2.298050	0.40694	.	.	ENSG00000115286	ENST00000546283;ENST00000233627;ENST00000539480;ENST00000313408;ENST00000414651;ENST00000538929;ENST00000538523;ENST00000540530;ENST00000535382	D;D;D;D;D	0.88354	-2.37;-2.37;-2.37;-2.37;-2.37	4.44	4.44	0.53790	NADH:ubiquinone oxidoreductase-like, 20kDa subunit (2);	.	.	.	.	D	0.96358	0.8812	H	0.97051	3.93	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.995;1.0;0.998;0.993	D	0.97936	1.0323	9	0.87932	D	0	.	15.6509	0.77091	0.0:1.0:0.0:0.0	.	144;151;144;144	F5H5N1;Q8NAS7;B3KRI2;O75251	.;.;.;NDUS7_HUMAN	L	144;144;144;144;174;63;63;63;63	ENSP00000440348:P144L;ENSP00000233627:P144L;ENSP00000443273:P144L;ENSP00000364262:P144L;ENSP00000406630:P174L	ENSP00000233627:P144L	P	+	2	0	NDUFS7	1342140	1.000000	0.71417	0.807000	0.32361	0.032000	0.12392	7.076000	0.76806	2.016000	0.59253	0.511000	0.50034	CCG	.	.	.	none		0.687	NDUFS7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397984.1	NM_024407		T	1391140	C	T	1391140	3	4	74	1	0	0	0	0	1	0	0	0	10304	652	23	1	453	1	NDUFS7	19	1391140	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08		1391140	57737843	42	4819											
EEF2	1938	hgsc.bcm.edu	37	chr19	3983291	3983293	+	Splice_Site	DEL	TGA	TGA	-																															gtagaagagggagatggcacTgatggagggagggactcgtc																								rs111408370		TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr19:3983291_3983293delTGA	ENST00000309311.6	-	3	307		c.e3-2		EEF2_ENST00000600720.1_Splice_Site|SNORD37_ENST00000384048.1_RNA	NM_001961.3	NP_001952.1	P13639	EF2_HUMAN	eukaryotic translation elongation factor 2						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)		GAGATGGCACTGATGGAGGGAGG	0.586																																					.	Colon(165;1804 1908 4071 6587 18799)	Atlas-INDEL	.											.	EEF2	57	.	0			.						PASS	.																																			SO:0001630	splice_region_variant	1938	.			.	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.219-2TCA>-	chr19.hg19:g.3983291_3983293delTGA		28.0	0.0	0		64.0	19.0	0.296875	.	B2RMP5|D6W618|Q58J86	Splice_Site	DEL	ENST00000309311.6	hg19	CCDS12117.1																																																																																			.	.	.	none		0.586	EEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457615.2	NM_001961	Intron	-	3983293	TGA	-	3983291	8	5	74	1	0	1	0	1	0	0	1	0	4931	1594	55	0	2411	0	EEF2	19	3983291	Splice_Site	DEL	TGA	TCGA-AL-3472-01A-01D-1252-08	2592151	3983291	55145692	43	4820											
MUC16	94025	hgsc.bcm.edu	37	chr19	9063328	9063328	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctgtggtgacttcagaggTggccagtatttcaactgagg	9	12	13	7	0	3	3	2	2	1	1	3	3	3	3	1	4	1	1	1	4	2	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr19:9063328T>C	ENST00000397910.4	-	3	24321	c.24118A>G	c.(24118-24120)Acc>Gcc	p.T8040A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	8042	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						ACTTCAGAGGTGGCCAGTATT	0.458																																					p.T8040A		Atlas-SNP	.											.	MUC16	4315	.	0			c.A24118G						PASS	.						130	120	124					19																	9063328		1946	4144	6090	SO:0001583	missense	94025	exon3			CAGAGGTGGCCAG	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.24118A>G	chr19.hg19:g.9063328T>C	ENSP00000381008:p.Thr8040Ala	188.0	0.0	.		79.0	40.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	8.827	0.938900	0.18281	.	.	ENSG00000181143	ENST00000397910	T	0.24908	1.83	2.66	-2.24	0.06909	.	.	.	.	.	T	0.28067	0.0692	L	0.35854	1.095	.	.	.	P	0.49961	0.93	P	0.54664	0.758	T	0.39313	-0.9620	8	0.87932	D	0	.	7.4725	0.27357	0.7363:0.0:0.0:0.2637	.	8040	B5ME49	.	A	8040	ENSP00000381008:T8040A	ENSP00000381008:T8040A	T	-	1	0	MUC16	8924328	0.000000	0.05858	0.000000	0.03702	0.445000	0.32107	-1.059000	0.03479	-0.657000	0.05373	0.332000	0.21555	ACC	.	.	.	none		0.458	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9063328	T	C	9063328	3	2	74	1	0	0	0	0	1	0	0	0	9980	1696	59	3	19733	3	MUC16	19	9063328	Missense_Mutation	SNP	T	TCGA-AL-3472-01A-01D-1252-08	5080037	9063328	50065655	44	4821											
GGN	199720	hgsc.bcm.edu	37	chr19	38876904	38876904	+	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	gtggcggcggtagggcccggGcttgggacgcaggcgccgag	4	4	22	11	6	0	0	0	0	0	0	0	2	0	1	2	7	0	3	2	7	1	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr19:38876904G>T	ENST00000334928.6	-	3	1130	c.998C>A	c.(997-999)gCc>gAc	p.A333D	SPRED3_ENST00000587013.1_5'Flank|AC005789.9_ENST00000585411.1_RNA|GGN_ENST00000591809.1_Intron	NM_152657.3	NP_689870.3	Q86UU5	GGN_HUMAN	gametogenetin	333	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)			TAGGGCCCGGGCTTGGGACGC	0.677																																					p.A333D		Atlas-SNP	.											.	GGN	50	.	0			c.C998A						PASS	.						28	32	30					19																	38876904		2201	4299	6500	SO:0001583	missense	199720	exon3			GCCCGGGCTTGGG	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.998C>A	chr19.hg19:g.38876904G>T	ENSP00000334940:p.Ala333Asp	23.0	0.0	.		62.0	27.0	.	NM_152657	Q7RTU6|Q86UU4|Q8NAA1	Missense_Mutation	SNP	ENST00000334928.6	hg19	CCDS12516.1	.	.	.	.	.	.	.	.	.	.	G	6.337	0.430216	0.12045	.	.	ENSG00000179168	ENST00000334928	.	.	.	3.33	0.957	0.19613	.	1.070480	0.07455	N	0.899668	T	0.21227	0.0511	N	0.24115	0.695	0.09310	N	1	B;B	0.32829	0.386;0.386	B;B	0.25405	0.06;0.06	T	0.18650	-1.0330	9	0.45353	T	0.12	0.4297	5.4042	0.16312	0.0:0.2275:0.5387:0.2338	.	250;333	Q86UU5-2;Q86UU5	.;GGN_HUMAN	D	333	.	ENSP00000334940:A333D	A	-	2	0	GGN	43568744	0.000000	0.05858	0.000000	0.03702	0.073000	0.16967	-0.059000	0.11731	0.082000	0.17018	0.462000	0.41574	GCC	.	.	.	none		0.677	GGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459205.1	NM_152657		T	38876904	G	T	38876904	3	4	74	1	0	0	0	0	1	0	0	0	6365	1203	42	4	968	4	GGN	19	38876904	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08	29813576	38876904	20252079	45	4822											
PRR12	57479	hgsc.bcm.edu	37	chr19	50102854	50102854	+	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	cacccctgctgtgccacatcCcccaccttccggagcctttg	5	9	7	20	1	0	0	0	0	0	0	2	1	2	1	8	1	3	1	8	1	0	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr19:50102854C>T	ENST00000418929.2	+	5	4016	c.4004C>T	c.(4003-4005)cCc>cTc	p.P1335L		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	0							DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		GTGCCACATCCCCCACCTTCC	0.697																																					p.P1335L		Atlas-SNP	.											.	PRR12	157	.	0			c.C4004T						PASS	.						12	15	14					19																	50102854		1955	4119	6074	SO:0001583	missense	57479	exon5			CACATCCCCCACC	AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"KIAA1205"	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.4004C>T	chr19.hg19:g.50102854C>T	ENSP00000394510:p.Pro1335Leu	24.0	0.0	.		29.0	11.0	.	NM_020719	E9PB06|Q8N4J6	Missense_Mutation	SNP	ENST00000418929.2	hg19	CCDS46143.1	.	.	.	.	.	.	.	.	.	.	C	4.945	0.175637	0.09391	.	.	ENSG00000126464	ENST00000418929;ENST00000246798;ENST00000314734	.	.	.	4.34	4.34	0.51931	.	0.157267	0.30338	N	0.009842	T	0.56949	0.2020	L	0.42245	1.32	0.48762	D	0.999702	B	0.20164	0.042	B	0.28709	0.093	T	0.58907	-0.7553	9	0.56958	D	0.05	-10.4584	14.2367	0.65932	0.0:1.0:0.0:0.0	.	1335	Q9ULL5-3	.	L	1335;515;515	.	ENSP00000246798:P515L	P	+	2	0	PRR12	54794666	0.029000	0.19370	0.156000	0.22583	0.027000	0.11550	3.359000	0.52292	2.424000	0.82194	0.563000	0.77884	CCC	.	.	.	none		0.697	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719		T	50102854	C	T	50102854	3	4	74	1	0	0	0	0	1	0	0	0	12594	623	22	2	4022	2	PRR12	19	50102854	Missense_Mutation	SNP	C	TCGA-AL-3472-01A-01D-1252-08	11225950	50102854	9026129	46	4823											
NLRP8	126205	hgsc.bcm.edu	37	chr19	56459468	56459468	+	Missense_Mutation	SNP	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	actgactgagctcagtactgGcaccatgcccatcacctggg	9	8	10	14	0	2	2	2	2	0	0	2	2	2	2	3	2	3	3	3	2	1	1			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr19:56459468G>A	ENST00000291971.3	+	1	271	c.200G>A	c.(199-201)gGc>gAc	p.G67D	NLRP8_ENST00000590542.1_Missense_Mutation_p.G67D	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	67	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				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)		CTCAGTACTGGCACCATGCCC	0.557																																					p.G67D		Atlas-SNP	.											.	NLRP8	225	.	0			c.G200A						PASS	.						105	84	91					19																	56459468		2203	4300	6503	SO:0001583	missense	126205	exon1			GTACTGGCACCAT	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.200G>A	chr19.hg19:g.56459468G>A	ENSP00000291971:p.Gly67Asp	59.0	0.0	.		50.0	24.0	.	NM_176811	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	hg19	CCDS12937.1	.	.	.	.	.	.	.	.	.	.	G	5.435	0.265352	0.10294	.	.	ENSG00000179709	ENST00000291971	T	0.59083	0.29	1.98	-0.375	0.12509	Pyrin (2);DEATH-like (2);	.	.	.	.	T	0.45094	0.1325	L	0.47716	1.5	0.09310	N	1	B;B	0.24576	0.1;0.106	B;B	0.33295	0.056;0.161	T	0.38478	-0.9659	9	0.20046	T	0.44	.	2.9915	0.05984	0.1879:0.2955:0.5166:0.0	.	67;67	Q86W28-2;Q86W28	.;NALP8_HUMAN	D	67	ENSP00000291971:G67D	ENSP00000291971:G67D	G	+	2	0	NLRP8	61151280	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	0.665000	0.25083	-0.014000	0.14175	0.514000	0.50259	GGC	.	.	.	none		0.557	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811		A	56459468	G	A	56459468	3	1	74	1	0	0	0	0	1	0	0	0	10490	1203	42	2	202	2	NLRP8	19	56459468	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08	6356614	56459468	2669515	47	4824											
ZNF583	147949	hgsc.bcm.edu	37	chr19	56934490	56934490	+	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	aaatccttccagaagttcaaAataaagaatataacaaatct	21	10	3	7	0	2	2	1	0	1	2	4	2	4	2	2	0	1	1	2	0	10	5			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr19:56934490A>T	ENST00000333201.9	+	5	673	c.463A>T	c.(463-465)Aat>Tat	p.N155Y	ZNF583_ENST00000291598.7_Missense_Mutation_p.N155Y	NM_001159861.1|NM_152478.2	NP_001153333.1|NP_689691.2	Q96ND8	ZN583_HUMAN	zinc finger protein 583	155					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(2)|prostate(1)|skin(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0564)		AGAAGTTCAAAATAAAGAATA	0.363																																					p.N155Y		Atlas-SNP	.											.	ZNF583	83	.	0			c.A463T						PASS	.						71	78	76					19																	56934490		2202	4300	6502	SO:0001583	missense	147949	exon5			GTTCAAAATAAAG	AK055592	CCDS12943.1	19q13.43	2013-09-20			ENSG00000198440	ENSG00000198440		"Zinc fingers, C2H2-type", "-"	26427	protein-coding gene	gene with protein product							Standard	NM_152478		Approved	FLJ31030	uc010ygl.1	Q96ND8	OTTHUMG00000168874	ENST00000333201.9:c.463A>T	chr19.hg19:g.56934490A>T	ENSP00000388502:p.Asn155Tyr	246.0	0.0	.		52.0	23.0	.	NM_001159861	O14850|Q2NKK3	Missense_Mutation	SNP	ENST00000333201.9	hg19	CCDS12943.1	.	.	.	.	.	.	.	.	.	.	A	13.43	2.236222	0.39498	.	.	ENSG00000198440	ENST00000291598;ENST00000333201	T;T	0.01034	5.42;5.42	4.19	3.17	0.36434	.	0.536023	0.17228	N	0.182048	T	0.00468	0.0015	N	0.01464	-0.85	0.24096	N	0.995892	B	0.11235	0.004	B	0.06405	0.002	T	0.45731	-0.9241	9	.	.	.	.	7.714	0.28694	0.8962:0.0:0.1038:0.0	.	155	Q96ND8	ZN583_HUMAN	Y	155	ENSP00000291598:N155Y;ENSP00000388502:N155Y	.	N	+	1	0	ZNF583	61626302	0.000000	0.05858	0.416000	0.26546	0.379000	0.30106	0.567000	0.23608	0.776000	0.33473	0.379000	0.24179	AAT	.	.	.	none		0.363	ZNF583-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401453.1	NM_152478		T	56934490	A	T	56934490	3	4	74	1	0	0	0	0	1	0	0	0	18027	14	1	5	477	5	ZNF583	19	56934490	Missense_Mutation	SNP	A	TCGA-AL-3472-01A-01D-1252-08	475022	56934490	2194493	48	4825											
PLTP	5360	hgsc.bcm.edu	37	chr20	44534919	44534919	+	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	cagctcacccggaagtccatGtccaggttgctggtggaagc	8	8	13	12	1	1	0	1	0	0	0	3	2	3	2	3	4	3	3	3	4	2	1			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr20:44534919G>A	ENST00000477313.1	-	7	1287	c.693C>T	c.(691-693)gaC>gaT	p.D231D	PLTP_ENST00000372420.1_Silent_p.D143D|PLTP_ENST00000420868.2_Silent_p.D136D|PLTP_ENST00000354050.4_Silent_p.D179D|PLTP_ENST00000372431.3_Silent_p.D231D|PLTP_ENST00000542937.1_Silent_p.D251D			P55058	PLTP_HUMAN	phospholipid transfer protein	231					lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|sperm motility (GO:0030317)|vitamin E biosynthetic process (GO:0010189)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)			endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)	21		Myeloproliferative disorder(115;0.0122)				GGAAGTCCATGTCCAGGTTGC	0.507																																					p.D231D		Atlas-SNP	.											.	PLTP	49	.	0			c.C693T						PASS	.						102	82	89					20																	44534919		2203	4300	6503	SO:0001819	synonymous_variant	5360	exon8			GTCCATGTCCAGG	L26232	CCDS13386.1, CCDS13387.1, CCDS56196.1, CCDS56197.1	20q13.12	2011-08-16			ENSG00000100979	ENSG00000100979		"BPI fold containing"	9093	protein-coding gene	gene with protein product	"BPI fold containing family E"	172425					Standard	NM_006227		Approved	BPIFE	uc002xqn.2	P55058	OTTHUMG00000033047	ENST00000477313.1:c.693C>T	chr20.hg19:g.44534919G>A		64.0	0.0	.		82.0	34.0	.	NM_006227	A8K006|B4DDD5|B4DRB4|E1P5N8|E7EV16|Q8WTT1|Q9BR07|Q9BSH8	Silent	SNP	ENST00000477313.1	hg19	CCDS13386.1																																																																																			.	.	.	none		0.507	PLTP-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354633.1	NM_006227		A	44534919	G	A	44534919	2	1	74	1	0	0	0	0	0	0	0	1	12121	1368	48	2		2	PLTP	20	44534919	Silent	SNP	G	TCGA-AL-3472-01A-01D-1252-08		44534919	18490601	49	4826											
SLC12A5	57468	hgsc.bcm.edu	37	chr20	44670175	44670175	+	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	ggtgctgccagtggcctcatCaaaggtctgcggagggacaa	9	7	15	10	1	3	0	2	0	1	0	3	2	3	2	2	5	3	1	2	5	2	0			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr20:44670175C>T	ENST00000454036.2	+	8	1180	c.1131C>T	c.(1129-1131)atC>atT	p.I377I	SLC12A5_ENST00000243964.3_Silent_p.I354I	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5	377					cellular ion homeostasis (GO:0006873)|chloride transmembrane transport (GO:1902476)|ion transport (GO:0006811)|learning (GO:0007612)|multicellular organism growth (GO:0035264)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|thermosensory behavior (GO:0040040)|transmembrane transport (GO:0055085)|transport (GO:0006810)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(1)|lung(38)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	80		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	GTGGCCTCATCAAAGGTCTGC	0.557																																					p.I377I		Atlas-SNP	.											.	SLC12A5	181	.	0			c.C1131T						PASS	.						53	50	51					20																	44670175		2203	4300	6503	SO:0001819	synonymous_variant	57468	exon8			CCTCATCAAAGGT	AB033002	CCDS13391.1, CCDS46610.1	20q13.12	2013-05-22	2010-04-20		ENSG00000124140	ENSG00000124140		"Solute carriers"	13818	protein-coding gene	gene with protein product		606726					Standard	NM_020708		Approved	KIAA1176, KCC2	uc010zxl.1	Q9H2X9	OTTHUMG00000032638	ENST00000454036.2:c.1131C>T	chr20.hg19:g.44670175C>T		93.0	0.0	.		93.0	37.0	.	NM_001134771	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Silent	SNP	ENST00000454036.2	hg19	CCDS46610.1																																																																																			.	.	.	none		0.557	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1			T	44670175	C	T	44670175	2	4	74	1	0	0	0	0	0	0	0	1	14399	816	29	2		2	SLC12A5	20	44670175	Silent	SNP	C	TCGA-AL-3472-01A-01D-1252-08	135256	44670175	18355345	50	4827											
PCK1	5105	hgsc.bcm.edu	37	chr20	56140816	56140817	+	Frame_Shift_Del	DEL	GA	GA	-																															ccgacctcccctgtgaaatcGagagagagatccttgccttg																								rs17847705		TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	GA	GA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr20:56140816_56140817delGA	ENST00000319441.4	+	10	1989_1990	c.1825_1826delGA	c.(1825-1827)gagfs	p.E609fs	PCK1_ENST00000543666.1_Frame_Shift_Del_p.E292fs	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	609					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			CTGTGAAATCGAGAGAGAGATC	0.47																																					p.608_609del		Atlas-INDEL	.											.	PCK1	95	.	0			c.1824_1825del						PASS	.																																			SO:0001589	frameshift_variant	5105	exon10			.		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.1825_1826delGA	chr20.hg19:g.56140824_56140825delGA	ENSP00000319814:p.Glu609fs	115.0	0.0	0		102.0	32.0	0.313726	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Frame_Shift_Del	DEL	ENST00000319441.4	hg19	CCDS13460.1																																																																																			.	.	.	none		0.47	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2			-	56140817	GA	-	56140816	7	5	74	1	0	1	0	1	0	0	0	0	11588	1059	37	0	1859	0	PCK1	20	56140816	Frame_Shift_Del	DEL	GA	TCGA-AL-3472-01A-01D-1252-08	11470641	56140816	6884704	51	4828											
PFKL	5211	hgsc.bcm.edu	37	chr21	45743723	45743723	+	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	tgcatcgtcatgtgtgtcatCccagccaccatcagcaacaa	11	9	7	14	1	3	0	3	0	0	0	5	0	4	0	3	0	4	2	3	0	2	0			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr21:45743723C>T	ENST00000349048.4	+	16	1627	c.1572C>T	c.(1570-1572)atC>atT	p.I524I	PFKL_ENST00000403390.1_Silent_p.I571I	NM_002626.4	NP_002617.3	P17858	PFKAL_HUMAN	phosphofructokinase, liver	524	C-terminal regulatory PFK domain 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 1,6-bisphosphate metabolic process (GO:0030388)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|negative regulation of insulin secretion (GO:0046676)|protein homotetramerization (GO:0051289)|protein oligomerization (GO:0051259)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	6-phosphofructokinase complex (GO:0005945)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|fructose binding (GO:0070061)|fructose-6-phosphate binding (GO:0070095)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	23				Colorectal(79;0.0811)		TGTGTGTCATCCCAGCCACCA	0.642																																					p.I524I		Atlas-SNP	.											.	PFKL	65	.	0			c.C1572T						PASS	.						114	78	91					21																	45743723		2201	4300	6501	SO:0001819	synonymous_variant	5211	exon16			TGTCATCCCAGCC		CCDS33582.1	21q22.3	1992-12-17			ENSG00000141959	ENSG00000141959	2.7.1.11		8876	protein-coding gene	gene with protein product		171860					Standard	NR_024108		Approved		uc002zel.3	P17858	OTTHUMG00000086910	ENST00000349048.4:c.1572C>T	chr21.hg19:g.45743723C>T		54.0	0.0	.		89.0	38.0	.	NM_002626	Q96A64|Q96IH4|Q9BR91	Silent	SNP	ENST00000349048.4	hg19	CCDS33582.1																																																																																			.	.	.	none		0.642	PFKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195805.1			T	45743723	C	T	45743723	2	4	74	1	0	0	0	0	0	0	0	1	11771	845	30	2		2	PFKL	21	45743723	Silent	SNP	C	TCGA-AL-3472-01A-01D-1252-08		45743723	2386172	52	4829											
INPP5J	27124	hgsc.bcm.edu	37	chr22	31523948	31523948	+	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	cccaaacagcctcgtgttctGgttcggggacctgaacttcc	7	10	10	14	2	1	1	0	1	1	0	4	2	2	2	4	3	3	2	4	3	2	3			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr22:31523948G>C	ENST00000331075.5	+	7	1848	c.1799G>C	c.(1798-1800)tGg>tCg	p.W600S	INPP5J_ENST00000400294.2_Missense_Mutation_p.W233S|INPP5J_ENST00000412277.2_Missense_Mutation_p.W533S|INPP5J_ENST00000401755.1_5'UTR|INPP5J_ENST00000404390.3_Missense_Mutation_p.W232S|INPP5J_ENST00000402238.1_5'UTR|INPP5J_ENST00000404453.1_5'UTR|INPP5J_ENST00000405300.1_Missense_Mutation_p.W233S	NM_001284285.1	NP_001271214.1	Q15735	PI5PA_HUMAN	inositol polyphosphate-5-phosphatase J	600	Catalytic. {ECO:0000255}.				inositol phosphate metabolic process (GO:0043647)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of neuron projection development (GO:0010977)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|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)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:0034485)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(1)	12						CTCGTGTTCTGGTTCGGGGAC	0.577																																					p.W232S		Atlas-SNP	.											.	INPP5J	94	.	0			c.G695C						PASS	.						47	45	45					22																	31523948		1913	4119	6032	SO:0001583	missense	27124	exon7			TGTTCTGGTTCGG	U45975	CCDS46687.1, CCDS63453.1, CCDS63454.1, CCDS63455.1, CCDS74847.1	22q12.2	2008-09-09	2008-09-09	2008-09-09	ENSG00000185133	ENSG00000185133			8956	protein-coding gene	gene with protein product		606481	"phosphatidylinositol (4,5) bisphosphate 5-phosphatase, A"	PIB5PA		10591208	Standard	NM_001284287		Approved	INPP5	uc003aju.4	Q15735	OTTHUMG00000151206	ENST00000331075.5:c.1799G>C	chr22.hg19:g.31523948G>C	ENSP00000333262:p.Trp600Ser	73.0	0.0	.		110.0	46.0	.	NM_001002837	B3KS54|Q32M61|Q6ZTH6|Q8N902|Q9UDT9	Missense_Mutation	SNP	ENST00000331075.5	hg19		.	.	.	.	.	.	.	.	.	.	G	19.90	3.913228	0.72983	.	.	ENSG00000185133	ENST00000331075;ENST00000412277;ENST00000400294;ENST00000405300;ENST00000404390	D;D;D;D;D	0.81499	-1.5;-1.5;-1.5;-1.5;-1.5	4.76	4.76	0.60689	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.000000	0.85682	D	0.000000	D	0.93792	0.8015	H	0.98068	4.14	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.997	D	0.96283	0.9208	10	0.87932	D	0	.	17.7408	0.88406	0.0:0.0:1.0:0.0	.	533;600;232	B4DF95;Q15735;Q15735-3	.;PI5PA_HUMAN;.	S	600;533;233;233;232	ENSP00000333262:W600S;ENSP00000392924:W533S;ENSP00000383150:W233S;ENSP00000384596:W233S;ENSP00000384534:W232S	ENSP00000333262:W600S	W	+	2	0	INPP5J	29853948	1.000000	0.71417	1.000000	0.80357	0.748000	0.42578	9.343000	0.97047	2.329000	0.79093	0.655000	0.94253	TGG	.	.	.	none		0.577	INPP5J-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000321784.1	NM_001002837		C	31523948	G	C	31523948	3	2	74	1	0	0	0	0	1	0	0	0	7766	1357	47	4	721	4	INPP5J	22	31523948	Missense_Mutation	SNP	G	TCGA-AL-3472-01A-01D-1252-08		31523948	19780618	53	4830											
MEI1	150365	hgsc.bcm.edu	37	chr22	42191444	42191444	+	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	taccggagtagcagtgtcctCtctcatgaagaggtgggtga	9	10	14	8	1	2	3	1	2	1	1	4	4	3	4	2	3	2	2	2	3	3	2			TCGA-AL-3472-01A-01D-1252-08	TCGA-AL-3472-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f246dd1b-eedd-4105-b80e-77c3cb63a450	a80cc8a1-24ad-41f0-bdad-9c05f2ad4901	g.chr22:42191444C>A	ENST00000401548.3	+	29	3604	c.3564C>A	c.(3562-3564)ctC>ctA	p.L1188L	MEI1_ENST00000400107.1_Silent_p.L521L|MEI1_ENST00000476893.1_3'UTR|MEI1_ENST00000300398.4_Intron	NM_152513.3	NP_689726.3			meiosis inhibitor 1											breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						GCAGTGTCCTCTCTCATGAAG	0.542																																					p.L1188L		Atlas-SNP	.											.	MEI1	87	.	0			c.C3564A						PASS	.						154	156	155					22																	42191444		2039	4204	6243	SO:0001819	synonymous_variant	150365	exon29			TGTCCTCTCTCAT	AK092934	CCDS46718.1	22q13.2	2013-10-11			ENSG00000167077	ENSG00000167077			28613	protein-coding gene	gene with protein product	"spermatogenesis associated 38"	608797				16683055	Standard	XM_006724154		Approved	MGC40042, SPATA38	uc003baz.1	Q5TIA1	OTTHUMG00000030083	ENST00000401548.3:c.3564C>A	chr22.hg19:g.42191444C>A		150.0	0.0	.		207.0	78.0	.	NM_152513		Silent	SNP	ENST00000401548.3	hg19	CCDS46718.1	.	.	.	.	.	.	.	.	.	.	c	0.075	-1.194186	0.01594	.	.	ENSG00000167077	ENST00000423900	.	.	.	5.01	1.65	0.23941	.	0.552403	0.16357	N	0.217956	T	0.56108	0.1963	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54906	-0.8223	6	0.87932	D	0	-15.0087	2.2726	0.04095	0.1575:0.5189:0.1526:0.171	.	.	.	.	I	7	.	ENSP00000410973:L7I	L	+	1	0	MEI1	40521390	0.219000	0.23619	0.509000	0.27700	0.069000	0.16628	-0.099000	0.11007	0.139000	0.18822	-0.521000	0.04368	CTC	.	.	.	none		0.542	MEI1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000074937.3	NM_152513		A	42191444	C	A	42191444	2	1	74	1	0	0	0	0	0	0	0	1	9472	900	32	4		4	MEI1	22	42191444	Silent	SNP	C	TCGA-AL-3472-01A-01D-1252-08	10667496	42191444	9113122	54	4831											
SCMH1	22955	hgsc.bcm.edu	37	chr1	41503104	41503104	+	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	caggatgaaagcaagggccgGtgcctttgggaggtgctgac	9	7	17	8	1	0	2	0	2	0	0	0	4	0	4	2	5	3	2	2	5	2	1			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr1:41503104G>A	ENST00000326197.7	-	12	1877	c.1578C>T	c.(1576-1578)caC>caT	p.H526H	SCMH1_ENST00000372597.1_Silent_p.H479H|SCMH1_ENST00000361705.3_Silent_p.H479H|SCMH1_ENST00000402904.2_Silent_p.H526H|SCMH1_ENST00000372596.1_Silent_p.H465H|SCMH1_ENST00000456518.2_Silent_p.H368H|SCMH1_ENST00000472037.1_5'UTR|SCMH1_ENST00000397171.2_Silent_p.H465H|SCMH1_ENST00000337495.5_Silent_p.H536H|SCMH1_ENST00000361191.5_Silent_p.H465H|SCMH1_ENST00000397174.2_Silent_p.H506H|SCMH1_ENST00000372595.1_Silent_p.H465H					sex comb on midleg homolog 1 (Drosophila)											breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(2)|pancreas(2)|upper_aerodigestive_tract(1)	15	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162)	Myeloproliferative disorder(586;0.0393)				GCAAGGGCCGGTGCCTTTGGG	0.587																																					p.H536H		Atlas-SNP	.											.	SCMH1	120	.	0			c.C1608T						PASS	.						200	179	186					1																	41503104		2203	4300	6503	SO:0001819	synonymous_variant	22955	exon13			GGGCCGGTGCCTT	AF149045	CCDS461.1, CCDS30688.1, CCDS53301.1, CCDS53302.1, CCDS53303.1, CCDS53304.1	1p34	2013-01-10			ENSG00000010803	ENSG00000010803		"Sterile alpha motif (SAM) domain containing"	19003	protein-coding gene	gene with protein product						10524249	Standard	NM_012236		Approved	Scml3	uc001cgs.3	Q96GD3	OTTHUMG00000005720	ENST00000326197.7:c.1578C>T	chr1.hg19:g.41503104G>A		225.0	0.0	.		181.0	24.0	.	NM_001172219		Silent	SNP	ENST00000326197.7	hg19	CCDS30688.1																																																																																			.	.	.	none		0.587	SCMH1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015656.1			A	41503104	G	A	41503104	2	1	75	1	0	0	0	0	0	0	0	1	13921	1252	44	2		2	SCMH1	1	41503104	Silent	SNP	G	TCGA-AL-3473-01A-01D-1252-08		41503104	207747517	1	4832											
PTGFR	5737	hgsc.bcm.edu	37	chr1	78959187	78959187	+	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	atggtaatccagctcctggcGataatgtgtgtctcctgtat	8	14	10	9	1	1	0	0	0	1	0	4	1	3	0	3	2	1	3	3	2	3	3			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr1:78959187G>A	ENST00000370757.3	+	2	996	c.759G>A	c.(757-759)gcG>gcA	p.A253A	PTGFR_ENST00000370756.3_Silent_p.A253A|PTGFR_ENST00000370758.1_Silent_p.A253A	NM_000959.3	NP_000950.1	P43088	PF2R_HUMAN	prostaglandin F receptor (FP)	253					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)	p.A253A(2)		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)	AGCTCCTGGCGATAATGTGTG	0.393																																					p.A253A		Atlas-SNP	.											PTGFR_ENST00000370758,rectum,carcinoma,0,4	PTGFR	121	.	2	Substitution - coding silent(2)	skin(2)	c.G759A						PASS	.						52	49	50					1																	78959187		2203	4300	6503	SO:0001819	synonymous_variant	5737	exon2			CCTGGCGATAATG	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.759G>A	chr1.hg19:g.78959187G>A		153.0	0.0	.		127.0	17.0	.	NM_000959	A8K9Y0|Q2KHP3|Q6RYQ6|Q9P1X4	Silent	SNP	ENST00000370757.3	hg19	CCDS686.1																																																																																			.	.	.	none		0.393	PTGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026582.1	NM_000959		A	78959187	G	A	78959187	2	1	75	1	0	0	0	0	0	0	0	1	12760	1045	37	1		1	PTGFR	1	78959187	Silent	SNP	G	TCGA-AL-3473-01A-01D-1252-08	37456083	78959187	170291434	2	4833											
PEX19	5824	hgsc.bcm.edu	37	chr1	160253370	160253370	+	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	gggccccgaagcatcaggggCcgtggtggtagaagggggtg	7	5	21	8	2	1	1	1	0	0	1	1	2	1	1	3	7	1	2	3	7	3	1			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr1:160253370C>T	ENST00000368072.5	-	2	151	c.130G>A	c.(130-132)Gcc>Acc	p.A44T	DCAF8_ENST00000556710.1_Intron|PEX19_ENST00000532508.1_5'UTR|PEX19_ENST00000440949.3_5'UTR|DCAF8_ENST00000608310.1_Intron	NM_001193644.1|NM_002857.3	NP_001180573.1|NP_002848.1	P40855	PEX19_HUMAN	peroxisomal biogenesis factor 19	44	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)			GCATCAGGGGCCGTGGTGGTA	0.562																																					p.A44T		Atlas-SNP	.											.	PEX19	34	.	0			c.G130A						PASS	.						65	67	66					1																	160253370		2203	4300	6503	SO:0001583	missense	5824	exon2			CAGGGGCCGTGGT	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.130G>A	chr1.hg19:g.160253370C>T	ENSP00000357051:p.Ala44Thr	186.0	0.0	.		200.0	27.0	.	NM_002857	D3DVE7|Q5QNY4|Q8NI97	Missense_Mutation	SNP	ENST00000368072.5	hg19	CCDS1201.1	.	.	.	.	.	.	.	.	.	.	C	17.55	3.417114	0.62511	.	.	ENSG00000162735	ENST00000368072;ENST00000429425;ENST00000392220	.	.	.	4.61	0.66	0.17868	.	0.463549	0.23343	N	0.049217	T	0.12263	0.0298	N	0.19112	0.55	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11792	-1.0573	9	0.13853	T	0.58	-0.5735	5.3692	0.16131	0.0:0.5415:0.1411:0.3175	.	44	P40855	PEX19_HUMAN	T	44;24;24	.	ENSP00000357051:A44T	A	-	1	0	PEX19	158519994	0.994000	0.37717	0.887000	0.34795	0.892000	0.51952	3.040000	0.49799	-0.022000	0.13986	-0.217000	0.12591	GCC	.	.	.	none		0.562	PEX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080642.2	NM_002857		T	160253370	C	T	160253370	3	4	75	1	0	0	0	0	1	0	0	0	11751	739	26	2	797	2	PEX19	1	160253370	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08	81294183	160253370	88997251	3	4834											
SPHKAP	80309	hgsc.bcm.edu	37	chr2	228882137	228882137	+	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	atagtaatccagcagtaactCaaatcctctcccttcatttt	12	14	3	12	0	3	0	2	0	1	0	6	0	5	0	3	0	2	3	3	0	4	6			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr2:228882137C>T	ENST00000392056.3	-	7	3479	c.3433G>A	c.(3433-3435)Gag>Aag	p.E1145K	SPHKAP_ENST00000344657.5_Missense_Mutation_p.E1145K	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1145						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)		AGCAGTAACTCAAATCCTCTC	0.527																																					p.E1145K		Atlas-SNP	.											.	SPHKAP	750	.	0			c.G3433A						PASS	.						65	54	58					2																	228882137		2203	4300	6503	SO:0001583	missense	80309	exon7			GTAACTCAAATCC		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.3433G>A	chr2.hg19:g.228882137C>T	ENSP00000375909:p.Glu1145Lys	121.0	0.0	.		157.0	25.0	.	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	hg19	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	C	30	5.054264	0.93793	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.62498	0.02;0.02	5.57	5.57	0.84162	.	0.089852	0.85682	D	0.000000	T	0.65842	0.2730	N	0.19112	0.55	0.58432	D	0.999995	P;D;D	0.65815	0.952;0.995;0.99	P;P;P	0.59487	0.601;0.82;0.858	T	0.69793	-0.5049	10	0.72032	D	0.01	.	18.8971	0.92427	0.0:1.0:0.0:0.0	.	176;1145;1145	B3KR30;Q2M3C7;Q2M3C7-2	.;SPKAP_HUMAN;.	K	1145	ENSP00000375909:E1145K;ENSP00000339886:E1145K	ENSP00000339886:E1145K	E	-	1	0	SPHKAP	228590381	1.000000	0.71417	0.983000	0.44433	0.989000	0.77384	7.152000	0.77419	2.785000	0.95823	0.655000	0.94253	GAG	.	.	.	none		0.527	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		T	228882137	C	T	228882137	3	4	75	1	0	0	0	0	1	0	0	0	15060	835	29	2	1693	2	SPHKAP	2	228882137	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08		228882137	14317236	4	4835											
VHL	7428	hgsc.bcm.edu	37	chr3	10188203	10188204	+	Frame_Shift_Ins	INS	-	-	T																															gcttgtcccgataggtcaccINStttggctcttcagagatgca																										TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr3:10188203_10188204insT	ENST00000256474.2	+	2	1186_1187	c.346_347insT	c.(346-348)cttfs	p.L116fs	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Intron	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	116	Involved in binding to CCT complex.		L -> V (in VHLD). {ECO:0000269|PubMed:8730290}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|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)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.?(3)|p.L116fs*43(3)|p.W117fs*14(2)|p.L116V(1)|p.H115fs*15(1)|p.L116fs*16(1)|p.W117fs*42(1)|p.H115fs*41(1)|p.H115fs*42(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GATAGGTCACCTTTGGCTCTTC	0.53		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																												p.L116fs		Atlas-INDEL	.	yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	VHL,colon,carcinoma,-1,3	VHL	2192	.	14	Deletion - Frameshift(9)|Unknown(3)|Substitution - Missense(1)|Insertion - Frameshift(1)	kidney(14)	c.346_347insT	GRCh37	CM961424	VHL	M		PASS	.																																			SO:0001589	frameshift_variant	7428	exon2	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	.	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.349dupT	chr3.hg19:g.10188206_10188206dupT	ENSP00000256474:p.Leu116fs	308.0	0.0	0		443.0	81.0	0.182844	NM_000551	B2RE45|Q13599|Q6PDA9	Frame_Shift_Ins	INS	ENST00000256474.2	hg19	CCDS2597.1																																																																																			.	.	.	none		0.53	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		T	10188204	-	T	10188203	7	5	75	1	0	1	1	0	0	0	0	0	17174	681	24	0	352	0	VHL	3	10188203	Frame_Shift_Ins	INS	-	TCGA-AL-3473-01A-01D-1252-08		10188203	187834227	5	4836											
OXSM	54995	hgsc.bcm.edu	37	chr3	25832524	25832524	+	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	tcttaatcatgtccaactgcCtgcaaaatttcctgaaaatt	13	14	4	10	0	2	1	1	1	1	0	4	1	4	1	3	0	3	1	3	0	6	3			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr3:25832524C>A	ENST00000280701.3	+	2	112	c.13C>A	c.(13-15)Ctg>Atg	p.L5M	OXSM_ENST00000449808.1_3'UTR|NGLY1_ENST00000417874.2_5'Flank|OXSM_ENST00000420173.2_Missense_Mutation_p.L5M	NM_017897.2	NP_060367.1	Q9NWU1	OXSM_HUMAN	3-oxoacyl-ACP synthase, mitochondrial	5					acyl-CoA metabolic process (GO:0006637)|medium-chain fatty acid biosynthetic process (GO:0051792)|short-chain fatty acid biosynthetic process (GO:0051790)	mitochondrion (GO:0005739)	3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	25						GTCCAACTGCCTGCAAAATTT	0.368																																					p.L5M		Atlas-SNP	.											.	OXSM	54	.	0			c.C13A						PASS	.						83	88	86					3																	25832524		2203	4300	6503	SO:0001583	missense	54995	exon2			AACTGCCTGCAAA	BC008202	CCDS2643.1, CCDS46780.1	3p24.2	2010-03-19			ENSG00000151093	ENSG00000151093	2.3.1.41		26063	protein-coding gene	gene with protein product	"beta-ketoacyl synthase"	610324				12477932	Standard	NM_017897		Approved	KS, FLJ20604, FASN2D	uc003cdn.3	Q9NWU1	OTTHUMG00000130477	ENST00000280701.3:c.13C>A	chr3.hg19:g.25832524C>A	ENSP00000280701:p.Leu5Met	278.0	0.0	.		196.0	36.0	.	NM_017897		Missense_Mutation	SNP	ENST00000280701.3	hg19	CCDS2643.1	.	.	.	.	.	.	.	.	.	.	C	7.760	0.705106	0.15172	.	.	ENSG00000151093	ENST00000452098;ENST00000280701;ENST00000420173;ENST00000428266	.	.	.	4.84	3.7	0.42460	.	1.003210	0.08029	N	0.993289	T	0.24774	0.0601	N	0.08118	0	0.24531	N	0.994111	P;P	0.47677	0.899;0.838	P;B	0.51355	0.667;0.372	T	0.14117	-1.0484	9	0.52906	T	0.07	-10.4228	5.7793	0.18297	0.0:0.0885:0.1686:0.7429	.	5;5	Q9NWU1-2;Q9NWU1	.;OXSM_HUMAN	M	5	.	ENSP00000280701:L5M	L	+	1	2	OXSM	25807528	0.036000	0.19791	0.572000	0.28498	0.418000	0.31294	0.834000	0.27518	0.992000	0.38840	-0.367000	0.07326	CTG	.	.	.	none		0.368	OXSM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252876.2	NM_017897		A	25832524	C	A	25832524	3	1	75	1	0	0	0	0	1	0	0	0	11342	680	24	4	15	4	OXSM	3	25832524	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08	15644321	25832524	172189906	6	4837											
LAMB2	3913	hgsc.bcm.edu	37	chr3	49167097	49167098	+	Frame_Shift_Del	DEL	GG	GG	-																															cagtaacaggatccactgttGgggtcacaaggagtgctccc																										TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr3:49167097_49167098delGG	ENST00000418109.1	-	12	1621_1622	c.1457_1458delCC	c.(1456-1458)cccfs	p.P486fs	LAMB2_ENST00000305544.4_Frame_Shift_Del_p.P486fs	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	486	Laminin EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00460}.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		ATCCACTGTTGGGGTCACAAGG	0.559																																					p.486_487del		Atlas-INDEL	.											.	LAMB2	156	.	0			c.1458_1459del						PASS	.																																			SO:0001589	frameshift_variant	3913	exon11			.		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.1457_1458delCC	chr3.hg19:g.49167099_49167100delGG	ENSP00000388325:p.Pro486fs	92.0	0.0	0		127.0	12.0	0.0944882	NM_002292	Q16321	Frame_Shift_Del	DEL	ENST00000418109.1	hg19	CCDS2789.1																																																																																			.	.	.	none		0.559	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		-	49167098	GG	-	49167097	7	5	75	1	0	1	0	1	0	0	0	0	8618	1335	47	0	4026	0	LAMB2	3	49167097	Frame_Shift_Del	DEL	GG	TCGA-AL-3473-01A-01D-1252-08	23334573	49167097	148855333	7	4838											
BAP1	8314	hgsc.bcm.edu	37	chr3	52437889	52437889	+	Frame_Shift_Del	DEL	C	C	-																															ccgctcaatgcccctggcttCcctgttcccttccccttata																										TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr3:52437889delC	ENST00000460680.1	-	13	1743	c.1272delG	c.(1270-1272)gggfs	p.G424fs	BAP1_ENST00000296288.5_Frame_Shift_Del_p.G406fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K425fs*4(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		CCCCTGGCTTCCCTGTTCCCT	0.557			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.K425fs	GBM(101;493 1458 7992 21037 25532)	Atlas-INDEL	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	1	Deletion - Frameshift(1)	kidney(1)	c.1273delA						PASS	.						85	89	88					3																	52437889		2203	4300	6503	SO:0001589	frameshift_variant	8314	exon13			.	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1272delG	chr3.hg19:g.52437889delC	ENSP00000417132:p.Gly424fs	158.0	0.0	0		333.0	62.0	0.186186	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Frame_Shift_Del	DEL	ENST00000460680.1	hg19	CCDS2853.1																																																																																			.	.	.	none		0.557	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			-	52437889	C	-	52437889	7	5	75	1	0	1	0	1	0	0	0	0	1311	842	30	0	937	0	BAP1	3	52437889	Frame_Shift_Del	DEL	C	TCGA-AL-3473-01A-01D-1252-08	3270792	52437889	145584541	8	4839											
PROS1	5627	hgsc.bcm.edu	37	chr3	93624723	93624723	+	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	cacaaatttgactgcaacctCcatttatatttgagggatct	12	14	6	9	0	1	2	0	2	1	0	2	3	2	3	2	1	2	1	2	1	4	5			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr3:93624723C>G	ENST00000394236.3	-	6	822	c.506G>C	c.(505-507)gGa>gCa	p.G169A	PROS1_ENST00000407433.1_Missense_Mutation_p.G38A	NM_000313.3	NP_000304.2	P07225	PROS_HUMAN	protein S (alpha)	169	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|negative regulation of endopeptidase activity (GO:0010951)|peptidyl-glutamic acid carboxylation (GO:0017187)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|endopeptidase inhibitor activity (GO:0004866)			endometrium(3)|kidney(5)|large_intestine(8)|lung(26)|ovary(1)|skin(2)|urinary_tract(1)	46					Drotrecogin alfa(DB00055)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)	ACTGCAACCTCCATTTATATT	0.299																																					p.G169A		Atlas-SNP	.											.	PROS1	126	.	0			c.G506C						PASS	.						77	79	78					3																	93624723		2199	4296	6495	SO:0001583	missense	5627	exon6			CAACCTCCATTTA		CCDS2923.1	3q11.1	2013-06-03			ENSG00000184500	ENSG00000184500			9456	protein-coding gene	gene with protein product		176880		PROS		214811, 1833851	Standard	NM_000313		Approved		uc003drb.4	P07225	OTTHUMG00000150354	ENST00000394236.3:c.506G>C	chr3.hg19:g.93624723C>G	ENSP00000377783:p.Gly169Ala	268.0	0.0	.		287.0	47.0	.	NM_000313	A8KAC9|D3DN28|Q15518|Q7Z715|Q9UCZ8	Missense_Mutation	SNP	ENST00000394236.3	hg19	CCDS2923.1	.	.	.	.	.	.	.	.	.	.	C	17.74	3.464378	0.63513	.	.	ENSG00000184500	ENST00000394236;ENST00000407433;ENST00000348974;ENST00000472684	D;D;D;D	0.98329	-4.87;-4.87;-4.87;-1.67	4.44	4.44	0.53790	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.125904	0.53938	D	0.000053	D	0.96334	0.8804	M	0.67397	2.05	0.40346	D	0.979083	P	0.46064	0.872	B	0.35655	0.207	D	0.96712	0.9526	10	0.62326	D	0.03	.	13.0646	0.59025	0.0:0.8385:0.1615:0.0	.	169	P07225	PROS_HUMAN	A	169;38;201;38	ENSP00000377783:G169A;ENSP00000385794:G38A;ENSP00000330021:G201A;ENSP00000419616:G38A	ENSP00000330021:G201A	G	-	2	0	PROS1	95107413	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	2.172000	0.42463	2.314000	0.78098	0.484000	0.47621	GGA	.	.	.	none		0.299	PROS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317762.1	NM_000313		G	93624723	C	G	93624723	3	3	75	1	0	0	0	0	1	0	0	0	12568	855	30	4	1564	4	PROS1	3	93624723	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08	41186834	93624723	104397707	9	4840											
GPBP1	65056	hgsc.bcm.edu	37	chr5	56542173	56542173	+	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	gctccaaggatgctggtcatTaagaaaggtaatacaaaaga	17	8	10	6	0	1	2	1	0	0	2	2	3	2	3	1	3	2	3	1	3	7	3	rs371740495		TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr5:56542173T>A	ENST00000506184.2	+	7	1630	c.525T>A	c.(523-525)atT>atA	p.I175I	GPBP1_ENST00000454432.2_Silent_p.I195I|GPBP1_ENST00000424459.3_Silent_p.I195I|GPBP1_ENST00000264779.6_Silent_p.I182I|GPBP1_ENST00000538707.1_Silent_p.I182I|GPBP1_ENST00000511209.1_Silent_p.I182I|GPBP1_ENST00000514387.2_Silent_p.I4I			Q86WP2	GPBP1_HUMAN	GC-rich promoter binding protein 1	175					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	19		Lung NSC(810;0.000861)|Prostate(74;0.0305)|Breast(144;0.222)		OV - Ovarian serous cystadenocarcinoma(10;7.64e-39)		TGCTGGTCATTAAGAAAGGTA	0.383																																					p.I182I		Atlas-SNP	.											.	GPBP1	51	.	0			c.T546A						PASS	.						84	86	85					5																	56542173		2203	4300	6503	SO:0001819	synonymous_variant	65056	exon6			GGTCATTAAGAAA		CCDS34162.1, CCDS47211.1, CCDS47212.1, CCDS47212.2, CCDS56368.1	5q11.2	2008-02-05				ENSG00000062194			29520	protein-coding gene	gene with protein product		608412				12842993	Standard	NM_022913		Approved	DKFZp761C169, vasculin	uc003jrk.4	Q86WP2		ENST00000506184.2:c.525T>A	chr5.hg19:g.56542173T>A		124.0	0.0	.		68.0	10.0	.	NM_001127236	A6NKW3|Q6NSH6|Q9H0D4|Q9H785|Q9NSN4	Silent	SNP	ENST00000506184.2	hg19	CCDS34162.1																																																																																			.	.	.	alt		0.383	GPBP1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000374496.1	NM_022913		A	56542173	T	A	56542173	2	1	75	1	0	0	0	0	0	0	0	1	6602	1742	61	5		5	GPBP1	5	56542173	Silent	SNP	T	TCGA-AL-3473-01A-01D-1252-08		56542173	124373087	10	4841											
PCDHA4	56144	hgsc.bcm.edu	37	chr5	140188710	140188710	+	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	acggacgctccgcgccaccgCctactggtactggtgaagga	8	6	13	14	5	0	1	0	1	0	0	1	3	1	3	4	4	2	2	4	4	3	2			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr5:140188710C>T	ENST00000530339.1	+	1	1938	c.1938C>T	c.(1936-1938)cgC>cgT	p.R646R	PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Silent_p.R646R|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000356878.4_Silent_p.R646R|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	646	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)			CGCGCCACCGCCTACTGGTAC	0.682																																					p.R646R		Atlas-SNP	.											.	PCDHA4	419	.	0			c.C1938T						PASS	.						74	76	75					5																	140188710		2203	4300	6503	SO:0001819	synonymous_variant	56144	exon1			CCACCGCCTACTG	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.1938C>T	chr5.hg19:g.140188710C>T		156.0	0.0	.		345.0	50.0	.	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	hg19	CCDS54916.1																																																																																			.	.	.	none		0.682	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		T	140188710	C	T	140188710	2	4	75	1	0	0	0	0	0	0	0	1	11533	726	26	2		2	PCDHA4	5	140188710	Silent	SNP	C	TCGA-AL-3473-01A-01D-1252-08	83646537	140188710	40726550	11	4842											
ARSI	340075	hgsc.bcm.edu	37	chr5	149677875	149677875	+	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	agcatagtggagtactggccGctgagcccccaggccacatt	9	7	12	13	1	0	1	0	1	0	0	0	2	0	2	4	3	3	3	4	3	2	3			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr5:149677875G>T	ENST00000328668.7	-	2	1191	c.612C>A	c.(610-612)agC>agA	p.S204R		NM_001012301.2	NP_001012301.1	Q5FYB1	ARSI_HUMAN	arylsulfatase family, member I	204					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)			AGTACTGGCCGCTGAGCCCCC	0.607																																					p.S204R		Atlas-SNP	.											.	ARSI	65	.	0			c.C612A						PASS	.						59	56	57					5																	149677875		2203	4300	6503	SO:0001583	missense	340075	exon2			CTGGCCGCTGAGC	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.612C>A	chr5.hg19:g.149677875G>T	ENSP00000333395:p.Ser204Arg	47.0	0.0	.		92.0	4.0	.	NM_001012301	A1L3B0|B3KV22|B7XD03	Missense_Mutation	SNP	ENST00000328668.7	hg19	CCDS34275.1	.	.	.	.	.	.	.	.	.	.	G	9.783	1.175888	0.21704	.	.	ENSG00000183876	ENST00000328668;ENST00000515301;ENST00000509146	D;D;D	0.98633	-5.04;-5.04;-5.04	4.31	-3.25	0.05079	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.346719	0.35772	N	0.002983	D	0.91236	0.7238	N	0.01257	-0.925	0.32291	N	0.566281	B	0.06786	0.001	B	0.12156	0.007	T	0.82244	-0.0553	10	0.20046	T	0.44	.	13.7168	0.62702	0.7322:0.0:0.2678:0.0	.	204	Q5FYB1	ARSI_HUMAN	R	204;61;61	ENSP00000333395:S204R;ENSP00000426879:S61R;ENSP00000420955:S61R	ENSP00000333395:S204R	S	-	3	2	ARSI	149658068	0.000000	0.05858	0.974000	0.42286	0.992000	0.81027	-1.644000	0.02002	-0.629000	0.05575	0.555000	0.69702	AGC	.	.	.	none		0.607	ARSI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373681.1	NM_001012301		T	149677875	G	T	149677875	3	4	75	1	0	0	0	0	1	0	0	0	994	1078	38	4	1101	4	ARSI	5	149677875	Missense_Mutation	SNP	G	TCGA-AL-3473-01A-01D-1252-08	9489165	149677875	31237385	12	4843											
NOD1	10392	hgsc.bcm.edu	37	chr7	30472766	30472766	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctgccaaactctctgccActtcatcgttgagttcattt	7	17	5	12	1	4	1	2	1	2	0	6	1	4	1	2	0	3	2	2	0	1	5			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr7:30472766A>G	ENST00000222823.4	-	12	3176	c.2651T>C	c.(2650-2652)gTg>gCg	p.V884A		NM_006092.2	NP_006083.1	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain containing 1	884					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						ACTCTCTGCCACTTCATCGTT	0.393																																					p.V884A		Atlas-SNP	.											.	NOD1	79	.	0			c.T2651C						PASS	.						133	117	123					7																	30472766		2203	4300	6503	SO:0001583	missense	10392	exon12			TCTGCCACTTCAT	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.2651T>C	chr7.hg19:g.30472766A>G	ENSP00000222823:p.Val884Ala	125.0	0.0	.		44.0	8.0	.	NM_006092	B4DTU3|Q549U4|Q8IWF5	Missense_Mutation	SNP	ENST00000222823.4	hg19	CCDS5427.1	.	.	.	.	.	.	.	.	.	.	A	3.545	-0.092917	0.07053	.	.	ENSG00000106100	ENST00000222823	T	0.51574	0.7	5.74	0.404	0.16355	.	0.399974	0.28544	N	0.014963	T	0.14013	0.0339	N	0.00815	-1.16	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.09885	-1.0654	10	0.12103	T	0.63	.	8.3537	0.32318	0.5662:0.0:0.4338:0.0	.	884	Q9Y239	NOD1_HUMAN	A	884	ENSP00000222823:V884A	ENSP00000222823:V884A	V	-	2	0	NOD1	30439291	0.488000	0.25996	0.983000	0.44433	0.937000	0.57800	0.908000	0.28545	0.117000	0.18138	0.460000	0.39030	GTG	.	.	.	none		0.393	NOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250443.2			G	30472766	A	G	30472766	3	3	75	1	0	0	0	0	1	0	0	0	10523	159	6	3	222	3	NOD1	7	30472766	Missense_Mutation	SNP	A	TCGA-AL-3473-01A-01D-1252-08		30472766	128665897	13	4844											
KIAA1967	57805	hgsc.bcm.edu	37	chr8	22474942	22474942	+	Frame_Shift_Del	DEL	G	G	-																															tgcctctgtagaaggaggatGggcttttgcccaaaccactc																										TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr8:22474942delG	ENST00000308511.4	+	15	2104	c.1855delG	c.(1855-1857)gggfs	p.G619fs	CCAR2_ENST00000389279.3_Frame_Shift_Del_p.G619fs|CCAR2_ENST00000520861.1_Frame_Shift_Del_p.G294fs|RP11-582J16.5_ENST00000521025.1_RNA			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	619					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)										GAAGGAGGATGGGCTTTTGCC	0.502																																					p.D618fs		Atlas-INDEL	.											.	KIAA1967	72	.	0			c.1854delT						PASS	.						101	113	109					8																	22474942		2203	4300	6503	SO:0001589	frameshift_variant	57805	exon15			.	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.1855delG	chr8.hg19:g.22474942delG	ENSP00000310670:p.Gly619fs	332.0	0.0	0		678.0	97.0	0.143068	NM_021174	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Frame_Shift_Del	DEL	ENST00000308511.4	hg19	CCDS34863.1																																																																																			.	.	.	none		0.502	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174		-	22474942	G	-	22474942	7	5	75	1	0	1	0	1	0	0	0	0	8272	1348	47	0	1909	0	KIAA1967	8	22474942	Frame_Shift_Del	DEL	G	TCGA-AL-3473-01A-01D-1252-08		22474942	123889080	14	4845											
CUEDC2	79004	hgsc.bcm.edu	37	chr10	104184514	104184514	+	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	ggcccaggtcctccaggaccCcaagcacataggagaagatg	12	4	12	13	0	0	2	0	0	0	2	2	4	2	3	5	4	1	1	5	4	3	1			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr10:104184514C>T	ENST00000369937.4	-	3	255	c.110G>A	c.(109-111)gGg>gAg	p.G37E	CUEDC2_ENST00000465409.1_5'Flank	NM_024040.2	NP_076945.2	Q9H467	CUED2_HUMAN	CUE domain containing 2	37						cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(1)|stomach(1)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.122)		Epithelial(162;9.17e-09)|all cancers(201;2.16e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		CTCCAGGACCCCAAGCACATA	0.592																																					p.G37E		Atlas-SNP	.											.	CUEDC2	22	.	0			c.G110A						PASS	.						45	49	48					10																	104184514		1955	4136	6091	SO:0001583	missense	79004	exon3			AGGACCCCAAGCA	BC000262	CCDS41566.1	10q24.32	2008-10-23	2004-03-04	2004-03-05	ENSG00000107874	ENSG00000107874			28352	protein-coding gene	gene with protein product		614142	"chromosome 10 open reading frame 66"	C10orf66		12477932	Standard	NM_024040		Approved	MGC2491	uc001kvn.2	Q9H467	OTTHUMG00000018958	ENST00000369937.4:c.110G>A	chr10.hg19:g.104184514C>T	ENSP00000358953:p.Gly37Glu	106.0	0.0	.		216.0	30.0	.	NM_024040	D3DR88|Q9BWG8	Missense_Mutation	SNP	ENST00000369937.4	hg19	CCDS41566.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.419316	0.83559	.	.	ENSG00000107874	ENST00000369937	D	0.85088	-1.94	5.36	5.36	0.76844	.	0.051192	0.85682	D	0.000000	D	0.89061	0.6608	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90111	0.4192	10	0.87932	D	0	-28.8879	18.4607	0.90737	0.0:1.0:0.0:0.0	.	37	Q9H467	CUED2_HUMAN	E	37	ENSP00000358953:G37E	ENSP00000358953:G37E	G	-	2	0	CUEDC2	104174504	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.245000	0.78237	2.688000	0.91661	0.561000	0.74099	GGG	.	.	.	none		0.592	CUEDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050060.1	NM_024040		T	104184514	C	T	104184514	3	4	75	1	0	0	0	0	1	0	0	0	4055	623	22	2	781	2	CUEDC2	10	104184514	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08		104184514	31350233	15	4846											
SORCS3	22986	hgsc.bcm.edu	37	chr10	107022222	107022222	+	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	cggagcctgaggagctgctgGacaaagagctggacacgcgg	10	4	17	10	3	0	2	0	1	0	1	0	6	0	6	1	5	4	3	1	5	1	0			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr10:107022222G>C	ENST00000369701.3	+	26	3804	c.3577G>C	c.(3577-3579)Gac>Cac	p.D1193H		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	1193					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)		GGAGCTGCTGGACAAAGAGCT	0.542																																					p.D1193H	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-SNP	.											SORCS3,NS,carcinoma,0,1	SORCS3	282	.	0			c.G3577C						PASS	.						69	55	60					10																	107022222		2203	4300	6503	SO:0001583	missense	22986	exon26			CTGCTGGACAAAG	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.3577G>C	chr10.hg19:g.107022222G>C	ENSP00000358715:p.Asp1193His	122.0	0.0	.		27.0	2.0	.	NM_014978	Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	ENST00000369701.3	hg19	CCDS7558.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.902493	0.92035	.	.	ENSG00000156395	ENST00000369701	T	0.19394	2.15	5.84	5.84	0.93424	.	0.105330	0.64402	D	0.000004	T	0.34106	0.0886	N	0.24115	0.695	0.58432	D	0.999998	D	0.76494	0.999	D	0.70935	0.971	T	0.02512	-1.1148	9	.	.	.	.	20.1579	0.98126	0.0:0.0:1.0:0.0	.	1193	Q9UPU3	SORC3_HUMAN	H	1193	ENSP00000358715:D1193H	.	D	+	1	0	SORCS3	107012212	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.476000	0.97823	2.767000	0.95098	0.555000	0.69702	GAC	.	.	.	none		0.542	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		C	107022222	G	C	107022222	3	2	75	1	0	0	0	0	1	0	0	0	14945	1174	41	4	3679	4	SORCS3	10	107022222	Missense_Mutation	SNP	G	TCGA-AL-3473-01A-01D-1252-08	2837708	107022222	28512525	16	4847											
MUC2	4583	hgsc.bcm.edu	37	chr11	1104253	1104253	+	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	gcgctcccctaggcatctggGgagcgggtgagcggggtggg	4	6	21	10	3	1	1	0	1	1	0	2	2	2	2	2	7	2	2	2	7	1	1			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr11:1104253G>A	ENST00000441003.2	+	49	8471	c.8444G>A	c.(8443-8445)gGg>gAg	p.G2815E		NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	5177					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)	AGGCATCTGGGGAGCGGGTGA	0.692																																					p.G2811E		Atlas-SNP	.											.	MUC2	614	.	0			c.G8432A						PASS	.						27	31	30					11																	1104253		1848	4082	5930	SO:0001583	missense	4583	exon50			ATCTGGGGAGCGG	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.8444G>A	chr11.hg19:g.1104253G>A	ENSP00000415183:p.Gly2815Glu	36.0	0.0	.		111.0	17.0	.	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	G	6.142	0.394436	0.11638	.	.	ENSG00000198788	ENST00000441003	T	0.14516	2.5	2.52	0.508	0.16972	.	.	.	.	.	T	0.10594	0.0259	L	0.44542	1.39	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.33471	-0.9867	9	0.87932	D	0	.	3.1167	0.06377	0.153:0.0:0.5868:0.2602	.	2815	E7EUV1	.	E	2815	ENSP00000415183:G2815E	ENSP00000415183:G2815E	G	+	2	0	MUC2	1094253	0.029000	0.19370	0.000000	0.03702	0.009000	0.06853	2.405000	0.44548	0.131000	0.18576	0.491000	0.48974	GGG	.	.	.	none		0.692	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1104253	G	A	1104253	3	1	75	1	0	0	0	0	1	0	0	0	9982	1232	43	2	8630	2	MUC2	11	1104253	Missense_Mutation	SNP	G	TCGA-AL-3473-01A-01D-1252-08		1104253	133902263	17	4848											
KRTAP5-5	439915	hgsc.bcm.edu	37	chr11	1651483	1651483	+	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	ctgtggggggtccaagggggGctgtggctcctgtggggggt	2	9	23	7	0	0	0	0	0	0	0	2	0	2	0	2	10	0	2	2	10	1	0			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr11:1651483G>C	ENST00000399676.2	+	1	451	c.413G>C	c.(412-414)gGc>gCc	p.G138A		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	138	8 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)		p.G138A(1)		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)		TCCAAGGGGGGCTGTGGCTCC	0.692																																					p.G138A		Atlas-SNP	.											KRTAP5-5,NS,carcinoma,0,2	KRTAP5-5	86	.	1	Substitution - Missense(1)	lung(1)	c.G413C						PASS	.						13	19	17					11																	1651483		2129	4198	6327	SO:0001583	missense	439915	exon1			AGGGGGGCTGTGG	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.413G>C	chr11.hg19:g.1651483G>C	ENSP00000382584:p.Gly138Ala	105.0	1.0	.		221.0	11.0	.	NM_001001480	A8MWN2	Missense_Mutation	SNP	ENST00000399676.2	hg19	CCDS41592.1	.	.	.	.	.	.	.	.	.	.	g	0	-2.606108	0.00121	.	.	ENSG00000185940	ENST00000399676;ENST00000422553	T	0.01203	5.18	3.03	2.11	0.27256	.	.	.	.	.	T	0.01695	0.0054	M	0.82823	2.61	0.22601	N	0.998945	B	0.25667	0.131	B	0.19666	0.026	T	0.52366	-0.8585	9	0.02654	T	1	.	6.1318	0.20209	0.1478:0.0:0.8522:0.0	.	138	Q701N2	KRA55_HUMAN	A	138;109	ENSP00000382584:G138A	ENSP00000382584:G138A	G	+	2	0	KRTAP5-5	1608059	1.000000	0.71417	0.411000	0.26484	0.028000	0.11728	2.598000	0.46223	0.497000	0.27926	-0.360000	0.07572	GGC	.	.	.	none		0.692	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1			C	1651483	G	C	1651483	3	2	75	1	0	0	0	0	1	0	0	0	8571	1203	42	4	415	4	KRTAP5-5	11	1651483	Missense_Mutation	SNP	G	TCGA-AL-3473-01A-01D-1252-08	547230	1651483	133355033	18	4849											
MRGPRX3	117195	hgsc.bcm.edu	37	chr11	18159638	18159638	+	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	ttctccagagggctctgcagGacacgcctgaggtggatgaa	9	8	14	10	1	2	3	0	2	2	1	3	5	2	5	2	4	1	2	2	4	1	1			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr11:18159638G>A	ENST00000396275.2	+	3	1250	c.889G>A	c.(889-891)Gac>Aac	p.D297N		NM_054031.3	NP_473372.3	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	297						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						GGCTCTGCAGGACACGCCTGA	0.557																																					p.D297N		Atlas-SNP	.											.	MRGPRX3	59	.	0			c.G889A						PASS	.						45	48	47					11																	18159638		2200	4292	6492	SO:0001583	missense	117195	exon3			CTGCAGGACACGC		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.889G>A	chr11.hg19:g.18159638G>A	ENSP00000379571:p.Asp297Asn	132.0	0.0	.		168.0	10.0	.	NM_054031	B0M0L1|Q8TDE0|Q8TDE1	Missense_Mutation	SNP	ENST00000396275.2	hg19	CCDS7830.1	.	.	.	.	.	.	.	.	.	.	G	17.59	3.428032	0.62844	.	.	ENSG00000179826	ENST00000396275	T	0.25912	1.77	1.3	1.3	0.21679	.	0.429218	0.22048	N	0.065351	T	0.47469	0.1447	M	0.84433	2.695	0.24902	N	0.9921	D	0.89917	1.0	D	0.76575	0.988	T	0.18461	-1.0336	10	0.87932	D	0	.	5.9358	0.19165	0.0:0.0:1.0:0.0	.	297	Q96LB0	MRGX3_HUMAN	N	297	ENSP00000379571:D297N	ENSP00000379571:D297N	D	+	1	0	MRGPRX3	18116214	0.485000	0.25972	0.781000	0.31783	0.068000	0.16541	1.158000	0.31737	1.011000	0.39340	0.195000	0.17529	GAC	.	.	.	none		0.557	MRGPRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389767.1	NM_054031		A	18159638	G	A	18159638	3	1	75	1	0	0	0	0	1	0	0	0	9775	1174	41	2	891	2	MRGPRX3	11	18159638	Missense_Mutation	SNP	G	TCGA-AL-3473-01A-01D-1252-08	16508155	18159638	116846878	19	4850											
SNX15	29907	hgsc.bcm.edu	37	chr11	64802325	64802325	+	Missense_Mutation	SNP	T	T	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	cctgggggccgtaggccggtTtgaagcctcagtgatcgagg	6	8	17	10	3	1	2	1	2	0	0	2	3	1	2	4	5	1	2	4	5	2	2			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr11:64802325T>G	ENST00000377244.3	+	4	393	c.263T>G	c.(262-264)tTt>tGt	p.F88C	RP11-399J13.3_ENST00000301886.3_3'UTR|SNX15_ENST00000352068.5_Missense_Mutation_p.F88C	NM_013306.4|NM_147777.3	NP_037438.2|NP_680086.2	Q9NRS6	SNX15_HUMAN	sorting nexin 15	88	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				intracellular protein transport (GO:0006886)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14						GTAGGCCGGTTTGAAGCCTCA	0.622																																					p.F88C	Esophageal Squamous(56;269 1304 3324 8253)	Atlas-SNP	.											.	SNX15	35	.	0			c.T263G						PASS	.						55	54	54					11																	64802325		2201	4297	6498	SO:0001583	missense	29907	exon4			GCCGGTTTGAAGC	AF175267	CCDS8089.1, CCDS8090.1	11q12	2008-05-22			ENSG00000110025	ENSG00000110025		"Sorting nexins"	14978	protein-coding gene	gene with protein product		605964				11208079	Standard	NM_013306		Approved			Q9NRS6	OTTHUMG00000037387	ENST00000377244.3:c.263T>G	chr11.hg19:g.64802325T>G	ENSP00000366452:p.Phe88Cys	123.0	0.0	.		237.0	27.0	.	NM_147777	E5KQS6|Q9NRS5	Missense_Mutation	SNP	ENST00000377244.3	hg19	CCDS8089.1	.	.	.	.	.	.	.	.	.	.	T	9.953	1.220623	0.22457	.	.	ENSG00000110025	ENST00000377244;ENST00000534637;ENST00000524831;ENST00000352068	T;T;T;T	0.38722	1.12;1.12;1.12;1.12	5.24	5.24	0.73138	Phox homologous domain (5);	0.000000	0.85682	D	0.000000	T	0.72922	0.3521	M	0.94142	3.5	0.80722	D	1	B;B;D	0.89917	0.002;0.032;1.0	B;B;D	0.91635	0.004;0.031;0.999	T	0.81028	-0.1118	10	0.87932	D	0	-11.7965	13.084	0.59129	0.0:0.0:0.0:1.0	.	88;88;88	E5KQS5;E5KQS6;Q9NRS6	.;.;SNX15_HUMAN	C	88;84;76;88	ENSP00000366452:F88C;ENSP00000437277:F84C;ENSP00000431690:F76C;ENSP00000316410:F88C	ENSP00000316410:F88C	F	+	2	0	SNX15	64558901	1.000000	0.71417	0.793000	0.32043	0.045000	0.14185	7.364000	0.79526	1.991000	0.58162	0.374000	0.22700	TTT	.	.	.	none		0.622	SNX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091004.3			G	64802325	T	G	64802325	3	3	75	1	0	0	0	0	1	0	0	0	14899	1841	64	5	277	5	SNX15	11	64802325	Missense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08	46642687	64802325	70204191	20	4851											
BIRC3	330	hgsc.bcm.edu	37	chr11	102206814	102206814	+	Missense_Mutation	SNP	T	T	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	taatgaacaagaacatgatgTtattaaacagaagacacaga	21	8	7	5	0	0	6	0	2	0	4	0	6	0	6	0	0	3	1	0	0	8	3			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr11:102206814T>G	ENST00000263464.3	+	7	4192	c.1442T>G	c.(1441-1443)gTt>gGt	p.V481G	BIRC3_ENST00000532808.1_Missense_Mutation_p.V481G	NM_001165.4	NP_001156.1	Q13489	BIRC3_HUMAN	baculoviral IAP repeat containing 3	481	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				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)		GAACATGATGTTATTAAACAG	0.353			T	MALT1	MALT																																p.V481G		Atlas-SNP	.		Dom	yes		11	11q22-q23	330	baculoviral IAP repeat-containing 3		L	.	BIRC3	56	.	0			c.T1442G						PASS	.						104	107	106					11																	102206814		2203	4298	6501	SO:0001583	missense	330	exon7			ATGATGTTATTAA	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.1442T>G	chr11.hg19:g.102206814T>G	ENSP00000263464:p.Val481Gly	243.0	0.0	.		63.0	12.0	.	NM_001165	Q16628|Q9HC27|Q9UP46	Missense_Mutation	SNP	ENST00000263464.3	hg19	CCDS8315.1	.	.	.	.	.	.	.	.	.	.	T	9.986	1.229473	0.22542	.	.	ENSG00000023445	ENST00000263464;ENST00000532808;ENST00000532609	T;T	0.19532	2.14;2.14	4.98	1.35	0.21983	DEATH-like (2);Caspase Recruitment (3);	0.559991	0.21816	N	0.068695	T	0.16981	0.0408	L	0.58669	1.825	0.31062	N	0.71399	B	0.10296	0.003	B	0.15484	0.013	T	0.12915	-1.0529	10	0.27785	T	0.31	.	4.8847	0.13697	0.0:0.231:0.1477:0.6212	.	481	Q13489	BIRC3_HUMAN	G	481;481;249	ENSP00000263464:V481G;ENSP00000432907:V481G	ENSP00000263464:V481G	V	+	2	0	BIRC3	101712024	0.052000	0.20516	0.281000	0.24762	0.902000	0.53008	0.187000	0.16998	0.130000	0.18549	-0.316000	0.08728	GTT	.	.	.	none		0.353	BIRC3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394159.1	NM_001165		G	102206814	T	G	102206814	3	3	75	1	0	0	0	0	1	0	0	0	1436	1725	60	5	1464	5	BIRC3	11	102206814	Missense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08	37404489	102206814	32799702	21	4852											
OR8G1	219865	hgsc.bcm.edu	37	chr11	124135727	124135727	+	Silent	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	aataaagatgtccacgttgcCctgaagaaaacgctagggaa	16	7	10	8	2	0	3	0	1	0	2	1	4	1	4	2	1	2	2	2	1	8	3			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr11:124135727C>T	ENST00000524943.2	+	1	1005	c.1005C>T	c.(1003-1005)gcC>gcT	p.A335A	OR8G1_ENST00000341493.2_RNA	NM_001005198.1	NP_001005198.1	Q8NG78	OR8G5_HUMAN	olfactory receptor, family 8, subfamily G, member 5	335						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)		TCCACGTTGCCCTGAAGAAAA	0.403																																					p.A335A	Ovarian(169;523 1969 8640 31295 51256)	Atlas-SNP	.											.	.	.	.	0			c.C1005T						PASS	.						54	52	53					11																	124135727		2018	4203	6221	SO:0001819	synonymous_variant	219865	exon1			CGTTGCCCTGAAG	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.1005C>T	chr11.hg19:g.124135727C>T		87.0	0.0	.		46.0	11.0	.	NM_001005198	B2RND3|Q6IEU6	Silent	SNP	ENST00000524943.2	hg19																																																																																				.	.	.	none		0.403	OR8G5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387283.2	NM_001005198		T	124135727	C	T	124135727	2	4	75	1	0	0	0	0	0	0	0	1	11241	610	22	2		2	OR8G1	11	124135727	Silent	SNP	C	TCGA-AL-3473-01A-01D-1252-08	21928913	124135727	10870789	22	4853											
PKNOX2	63876	hgsc.bcm.edu	37	chr11	125280693	125280693	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtggagccttataccaacCggttaccatggtaacctccc	10	9	9	13	1	0	0	0	0	0	0	1	1	1	1	6	4	5	2	6	4	5	4			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr11:125280693C>T	ENST00000298282.9	+	9	1008	c.737C>T	c.(736-738)cCg>cTg	p.P246L	PKNOX2_ENST00000530517.1_3'UTR|PKNOX2_ENST00000542175.1_Missense_Mutation_p.P182L	NM_022062.2	NP_071345.2	Q96KN3	PKNX2_HUMAN	PBX/knotted 1 homeobox 2	246					regulation of transcription from RNA polymerase II promoter (GO:0006357)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(14)|ovary(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	29		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)		TTATACCAACCGGTTACCATG	0.577																																					p.P246L		Atlas-SNP	.											.	PKNOX2	60	.	0			c.C737T						PASS	.						94	91	92					11																	125280693		1947	4142	6089	SO:0001583	missense	63876	exon9			ACCAACCGGTTAC	AK023136	CCDS41730.1	11q24.2	2014-09-04			ENSG00000165495	ENSG00000165495		"Homeoboxes / TALE class"	16714	protein-coding gene	gene with protein product		613066				11549286	Standard	NM_022062		Approved		uc001qbu.3	Q96KN3	OTTHUMG00000165884	ENST00000298282.9:c.737C>T	chr11.hg19:g.125280693C>T	ENSP00000298282:p.Pro246Leu	110.0	0.0	.		137.0	27.0	.	NM_022062	B7Z5I5|F5GZ15|Q63HL6|Q86XD1	Missense_Mutation	SNP	ENST00000298282.9	hg19	CCDS41730.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.066060	0.76187	.	.	ENSG00000165495	ENST00000530517;ENST00000531116;ENST00000298282;ENST00000542175;ENST00000535518	D;D;D;D	0.88277	-2.36;-2.36;-2.36;-2.25	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.93324	0.7872	L	0.54323	1.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.995	D	0.93357	0.6723	10	0.59425	D	0.04	-12.9127	19.0405	0.92997	0.0:1.0:0.0:0.0	.	182;246	F5GZ15;Q96KN3	.;PKNX2_HUMAN	L	217;217;246;182;234	ENSP00000434732:P217L;ENSP00000433971:P217L;ENSP00000298282:P246L;ENSP00000441470:P182L	ENSP00000298282:P246L	P	+	2	0	PKNOX2	124785903	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.191000	0.77763	2.586000	0.87340	0.655000	0.94253	CCG	.	.	.	none		0.577	PKNOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386866.3			T	125280693	C	T	125280693	3	4	75	1	0	0	0	0	1	0	0	0	11990	652	23	1	759	1	PKNOX2	11	125280693	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08	1144966	125280693	9725823	23	4854											
WNK1	65125	hgsc.bcm.edu	37	chr12	978188	978188	+	Intron	SNP	T	T	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	gttacaagaatccccactttTcttctgtttcccccaaggaa	10	13	5	13	0	2	1	0	0	2	1	4	2	4	2	4	1	1	2	4	1	5	5			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr12:978188T>A	ENST00000315939.6	+	9	2782				WNK1_ENST00000535572.1_Intron|WNK1_ENST00000530271.2_Missense_Mutation_p.F1184Y|WNK1_ENST00000340908.4_Intron|WNK1_ENST00000537687.1_Missense_Mutation_p.F1099Y|WNK1_ENST00000574564.1_Missense_Mutation_p.F398Y	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1						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)			TCCCCACTTTTCTTCTGTTTC	0.493																																					p.F1184Y	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.T3551A						PASS	.						323	310	314					12																	978188		1914	4143	6057	SO:0001627	intron_variant	65125	exon10			CACTTTTCTTCTG	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.2140-2243T>A	chr12.hg19:g.978188T>A		735.0	1.0	.		315.0	51.0	.	NM_213655	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	hg19	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	T	14.12	2.440816	0.43326	.	.	ENSG00000060237	ENST00000537687;ENST00000530271	T;T	0.16743	2.32;2.32	5.85	5.85	0.93711	.	.	.	.	.	T	0.23133	0.0559	.	.	.	0.80722	D	1	P	0.46656	0.882	B	0.44278	0.445	T	0.00842	-1.1544	8	0.52906	T	0.07	.	14.8154	0.70031	0.0:0.0:0.0:1.0	.	1184	F5H2M7	.	Y	1099;1184	ENSP00000444465:F1099Y;ENSP00000433548:F1184Y	ENSP00000433548:F1184Y	F	+	2	0	WNK1	848449	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.421000	0.52742	2.233000	0.73108	0.455000	0.32223	TTC	.	.	.	none		0.493	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		A	978188	T	A	978188	1	1	75	0	1	0	0	0	0	0	0	0	17389	1783	62	5		5	WNK1	12	978188	Intron	SNP	T	TCGA-AL-3473-01A-01D-1252-08		978188	132873707	24	4855											
CD27	939	hgsc.bcm.edu	37	chr12	6554287	6554287	+	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	acggccacatccctggtggcTgtgcgttctggggaccctgg	4	9	15	13	2	1	0	0	0	1	0	2	1	2	1	3	6	1	2	3	6	0	1			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr12:6554287T>A	ENST00000266557.3	+	1	255	c.26T>A	c.(25-27)cTg>cAg	p.L9Q	CD27-AS1_ENST00000399492.2_RNA|CD27-AS1_ENST00000545339.1_RNA	NM_001242.4	NP_001233	P26842	CD27_HUMAN	CD27 molecule	9					cell surface receptor signaling pathway (GO:0007166)|extrinsic apoptotic signaling pathway (GO:0097191)|immunoglobulin mediated immune response (GO:0016064)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of T cell apoptotic process (GO:0070233)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of JNK cascade (GO:0046330)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|response to ethanol (GO:0045471)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|transmembrane signaling receptor activity (GO:0004888)			kidney(1)|large_intestine(5)|lung(1)|urinary_tract(3)	10						CCCTGGTGGCTGTGCGTTCTG	0.642																																					p.L9Q		Atlas-SNP	.											.	CD27	17	.	0			c.T26A						PASS	.						18	24	22					12																	6554287		2202	4299	6501	SO:0001583	missense	939	exon1			GGTGGCTGTGCGT	M63928	CCDS8545.1	12p13	2014-09-17	2006-10-27	2006-10-27	ENSG00000139193	ENSG00000139193		"Tumor necrosis factor receptor superfamily", "CD molecules"	11922	protein-coding gene	gene with protein product		186711	"tumor necrosis factor receptor superfamily, member 7"	TNFRSF7		2442250, 8530100	Standard	NM_001242		Approved	S152, Tp55	uc001qod.3	P26842	OTTHUMG00000168316	ENST00000266557.3:c.26T>A	chr12.hg19:g.6554287T>A	ENSP00000266557:p.Leu9Gln	25.0	0.0	.		41.0	6.0	.	NM_001242	B2RDZ0	Missense_Mutation	SNP	ENST00000266557.3	hg19	CCDS8545.1	.	.	.	.	.	.	.	.	.	.	T	17.78	3.473069	0.63737	.	.	ENSG00000139193	ENST00000266557	D	0.95788	-3.81	4.91	4.91	0.64330	.	0.254840	0.25922	N	0.027424	D	0.95726	0.8610	L	0.36672	1.1	0.41219	D	0.986497	D	0.89917	1.0	D	0.85130	0.997	D	0.95798	0.8830	10	0.72032	D	0.01	-12.3828	10.8657	0.46853	0.0:0.0:0.0:1.0	.	9	P26842	CD27_HUMAN	Q	9	ENSP00000266557:L9Q	ENSP00000266557:L9Q	L	+	2	0	CD27	6424548	1.000000	0.71417	1.000000	0.80357	0.604000	0.37047	3.432000	0.52824	2.064000	0.61679	0.455000	0.32223	CTG	.	.	.	none		0.642	CD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399258.1			A	6554287	T	A	6554287	3	1	75	1	0	0	0	0	1	0	0	0	2992	1580	55	5	28	5	CD27	12	6554287	Missense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08	5576099	6554287	127297608	25	4856											
SOX5	6660	hgsc.bcm.edu	37	chr12	24102509	24102509	+	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	tgtactcacctttcaaactcCtgaggtaaatcagggtcagt	11	12	8	10	0	4	1	4	1	0	0	5	1	5	1	2	2	2	2	2	2	4	3			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr12:24102509C>G	ENST00000451604.2	-	1	128	c.27G>C	c.(25-27)caG>caC	p.Q9H	SOX5_ENST00000541847.1_Intron|SOX5_ENST00000545921.1_Intron|SOX5_ENST00000309359.1_5'UTR|SOX5_ENST00000381381.2_5'UTR|SOX5_ENST00000441133.2_Missense_Mutation_p.Q9H|SOX5_ENST00000536850.1_5'UTR|SOX5_ENST00000537393.1_Missense_Mutation_p.Q9H			P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5	9					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						TTTCAAACTCCTGAGGTAAAT	0.433																																					p.Q9H		Atlas-SNP	.											.	SOX5	134	.	0			c.G27C						PASS	.						112	102	106					12																	24102509		2203	4300	6503	SO:0001583	missense	6660	exon1			AAACTCCTGAGGT	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.27G>C	chr12.hg19:g.24102509C>G	ENSP00000398273:p.Gln9His	140.0	0.0	.		98.0	17.0	.	NM_006940	B7Z8V0|F5H5B0|Q86UK8|Q8J017|Q8J018|Q8J019|Q8J020|Q8N1D9|Q8N7E0|Q8TEA4	Missense_Mutation	SNP	ENST00000451604.2	hg19	CCDS8699.1	.	.	.	.	.	.	.	.	.	.	c	15.91	2.971147	0.53614	.	.	ENSG00000134532	ENST00000451604;ENST00000537393;ENST00000441133	D;D	0.97378	-4.34;-4.36	5.28	5.28	0.74379	.	0.154071	0.45126	D	0.000386	D	0.96222	0.8768	L	0.54323	1.7	0.80722	D	1	P;P	0.44309	0.832;0.826	P;B	0.44990	0.466;0.276	D	0.96291	0.9214	10	0.52906	T	0.07	.	17.0691	0.86568	0.0:1.0:0.0:0.0	.	9;9	G3V0H1;P35711	.;SOX5_HUMAN	H	9	ENSP00000398273:Q9H;ENSP00000439832:Q9H	ENSP00000393240:Q9H	Q	-	3	2	SOX5	23993776	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.509000	0.73725	2.631000	0.89168	0.645000	0.84053	CAG	.	.	.	none		0.433	SOX5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402006.2	NM_006940		G	24102509	C	G	24102509	3	3	75	1	0	0	0	0	1	0	0	0	14967	680	24	4	2334	4	SOX5	12	24102509	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08	17548222	24102509	109749386	26	4857											
SRGAP1	57522	hgsc.bcm.edu	37	chr12	64377805	64377805	+	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	agttcagcttctccaggatcTgcaagatttcttccgaaaaa	12	12	7	10	1	4	1	1	0	3	1	6	3	5	2	2	1	2	3	2	1	3	4			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr12:64377805T>A	ENST00000355086.3	+	2	670	c.146T>A	c.(145-147)cTg>cAg	p.L49Q	SRGAP1_ENST00000357825.3_Missense_Mutation_p.L49Q|SRGAP1_ENST00000543397.1_Missense_Mutation_p.L9Q	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	49	F-BAR domain.|FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		CTCCAGGATCTGCAAGATTTC	0.428																																					p.L49Q		Atlas-SNP	.											.	SRGAP1	146	.	0			c.T146A						PASS	.						110	114	113					12																	64377805		2203	4300	6503	SO:0001583	missense	57522	exon2			AGGATCTGCAAGA	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.146T>A	chr12.hg19:g.64377805T>A	ENSP00000347198:p.Leu49Gln	207.0	0.0	.		86.0	12.0	.	NM_020762	Q9H8A3|Q9P2P2	Missense_Mutation	SNP	ENST00000355086.3	hg19	CCDS8967.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.690212	0.88735	.	.	ENSG00000196935	ENST00000355086;ENST00000357825;ENST00000543397	T;T;T	0.56611	0.45;0.45;1.94	5.1	5.1	0.69264	Fps/Fes/Fer/CIP4 homology (3);	0.000000	0.28600	U	0.014776	T	0.74261	0.3693	M	0.83603	2.65	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.87578	0.998;0.987;0.987	T	0.77648	-0.2509	9	.	.	.	.	15.199	0.73120	0.0:0.0:0.0:1.0	.	49;9;49	Q7Z6B7;G5EA48;Q7Z6B7-2	SRGP1_HUMAN;.;.	Q	49;49;9	ENSP00000347198:L49Q;ENSP00000350480:L49Q;ENSP00000437948:L9Q	.	L	+	2	0	SRGAP1	62664072	1.000000	0.71417	0.997000	0.53966	0.933000	0.57130	7.975000	0.88055	2.060000	0.61445	0.477000	0.44152	CTG	.	.	.	none		0.428	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1			A	64377805	T	A	64377805	3	1	75	1	0	0	0	0	1	0	0	0	15157	1580	55	5	152	5	SRGAP1	12	64377805	Missense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08	40275296	64377805	69474090	27	4858											
METT11D1	64745	hgsc.bcm.edu	37	chr14	21464719	21464719	+	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	aggaagaaaagttctctatgGtgatccttgctcgggggtct	9	12	13	7	1	2	2	0	1	2	1	5	3	3	3	1	4	1	2	1	4	4	3			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr14:21464719G>T	ENST00000339374.6	+	13	1347	c.1114G>T	c.(1114-1116)Gtg>Ttg	p.V372L	RP11-84C10.4_ENST00000557335.1_RNA|METTL17_ENST00000556670.2_Missense_Mutation_p.V372L|SLC39A2_ENST00000298681.4_5'Flank|METTL17_ENST00000382985.4_Missense_Mutation_p.V372L|SLC39A2_ENST00000554422.1_5'Flank	NM_001029991.1|NM_022734.2	NP_001025162.1|NP_073571.1	Q9H7H0	MET17_HUMAN	methyltransferase like 17	372					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	copper ion binding (GO:0005507)|methyltransferase activity (GO:0008168)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|skin(2)	20						GTTCTCTATGGTGATCCTTGC	0.463																																					p.V372L		Atlas-SNP	.											.	METTL17	46	.	0			c.G1114T						PASS	.						53	50	51					14																	21464719		2203	4300	6503	SO:0001583	missense	64745	exon13			TCTATGGTGATCC	AK024512	CCDS9562.1, CCDS41913.1	14q11.2	2011-03-03	2011-03-02	2011-03-02	ENSG00000165792	ENSG00000165792			19280	protein-coding gene	gene with protein product			"methyltransferase 11 domain containing 1"	METT11D1		11278769	Standard	XM_006720235		Approved	FLJ20859	uc001vyn.3	Q9H7H0	OTTHUMG00000029610	ENST00000339374.6:c.1114G>T	chr14.hg19:g.21464719G>T	ENSP00000343041:p.Val372Leu	171.0	0.0	.		164.0	25.0	.	NM_022734	Q9BSH1|Q9BZH2|Q9BZH3	Missense_Mutation	SNP	ENST00000339374.6	hg19	CCDS9562.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.25|13.25	2.180366|2.180366	0.38511|0.38511	.|.	.|.	ENSG00000165792|ENSG00000165792	ENST00000556733|ENST00000339374;ENST00000382985	.|T;T	.|0.35789	.|1.33;1.29	5.12|5.12	5.12|5.12	0.69794|0.69794	.|.	.|0.222302	.|0.37577	.|N	.|0.002038	T|T	0.20941|0.20941	0.0504|0.0504	N|N	0.17838|0.17838	0.53|0.53	0.34359|0.34359	D|D	0.690735|0.690735	.|B;B;B	.|0.12630	.|0.006;0.003;0.002	.|B;B;B	.|0.10450	.|0.005;0.005;0.003	T|T	0.24154|0.24154	-1.0168|-1.0168	5|10	.|0.12766	.|T	.|0.61	.|.	9.6516|9.6516	0.39902|0.39902	0.0949:0.0:0.9051:0.0|0.0949:0.0:0.9051:0.0	.|.	.|372;372;372	.|Q9H7H0-3;Q9H7H0;Q9H7H0-2	.|.;MET17_HUMAN;.	V|L	47|372	.|ENSP00000343041:V372L;ENSP00000372445:V372L	.|ENSP00000343041:V372L	G|V	+|+	2|1	0|0	METTL17|METTL17	20534559|20534559	0.995000|0.995000	0.38212|0.38212	0.998000|0.998000	0.56505|0.56505	0.906000|0.906000	0.53458|0.53458	1.316000|1.316000	0.33620|0.33620	2.392000|2.392000	0.81423|0.81423	0.655000|0.655000	0.94253|0.94253	GGT|GTG	.	.	.	none		0.463	METTL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073804.4	NM_022734		T	21464719	G	T	21464719	3	4	75	1	0	0	0	0	1	0	0	0	9498	1261	44	4	1164	4	METT11D1	14	21464719	Missense_Mutation	SNP	G	TCGA-AL-3473-01A-01D-1252-08		21464719	85884821	28	4859											
NID2	22795	hgsc.bcm.edu	37	chr14	52485956	52485956	+	Missense_Mutation	SNP	A	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	ccgggccccagggtaggcatActgggcctgggcatggcgct	5	6	17	13	2	0	0	0	0	0	0	0	0	0	0	4	6	1	4	4	6	2	2			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr14:52485956A>C	ENST00000216286.5	-	14	2850	c.2851T>G	c.(2851-2853)Tat>Gat	p.Y951D	NID2_ENST00000541773.1_Missense_Mutation_p.Y850D	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	951	Thyroglobulin type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					GGGTAGGCATACTGGGCCTGG	0.577																																					p.Y951D		Atlas-SNP	.											.	NID2	201	.	0			c.T2851G						PASS	.						52	46	48					14																	52485956		2203	4300	6503	SO:0001583	missense	22795	exon14			AGGCATACTGGGC	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.2851T>G	chr14.hg19:g.52485956A>C	ENSP00000216286:p.Tyr951Asp	74.0	0.0	.		103.0	27.0	.	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	hg19	CCDS9706.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.654|9.654	1.142329|1.142329	0.21205|0.21205	.|.	.|.	ENSG00000087303|ENSG00000087303	ENST00000556572|ENST00000216286;ENST00000316204;ENST00000541773;ENST00000395707	.|T;T	.|0.61742	.|0.08;0.08	5.32|5.32	0.0082|0.0082	0.14073|0.14073	.|Thyroglobulin type-1 (4);	.|1.030560	.|0.07634	.|N	.|0.929216	T|T	0.40473|0.40473	0.1118|0.1118	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.27997	.|0.0;0.021;0.197;0.117	.|B;B;B;B	.|0.29862	.|0.002;0.023;0.108;0.009	T|T	0.30387|0.30387	-0.9980|-0.9980	5|10	.|0.33940	.|T	.|0.23	.|.	5.3979|5.3979	0.16278|0.16278	0.0652:0.2279:0.4723:0.2346|0.0652:0.2279:0.4723:0.2346	.|.	.|545;850;953;951	.|E7EPP3;Q14112-2;Q5CZI2;Q14112	.|.;.;.;NID2_HUMAN	G|D	219|951;545;850;953	.|ENSP00000216286:Y951D;ENSP00000443730:Y850D	.|ENSP00000216286:Y951D	V|Y	-|-	2|1	0|0	NID2|NID2	51555706|51555706	0.419000|0.419000	0.25449|0.25449	0.019000|0.019000	0.16419|0.16419	0.026000|0.026000	0.11368|0.11368	1.277000|1.277000	0.33167|0.33167	-0.092000|-0.092000	0.12417|0.12417	-0.242000|-0.242000	0.12053|0.12053	GTA|TAT	.	.	.	none		0.577	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			C	52485956	A	C	52485956	3	2	75	1	0	0	0	0	1	0	0	0	10422	391	14	5	1312	5	NID2	14	52485956	Missense_Mutation	SNP	A	TCGA-AL-3473-01A-01D-1252-08	31021237	52485956	54863584	29	4860											
C15orf23	90417	hgsc.bcm.edu	37	chr15	40685795	40685795	+	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	atggagcagctattagaaatGtaagaagaagcaagtggcca	17	7	12	5	0	0	3	0	0	0	3	0	4	0	4	1	2	3	4	1	2	7	3			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr15:40685795G>T	ENST00000249776.8	+	9	1063	c.948G>T	c.(946-948)atG>atT	p.M316I	KNSTRN_ENST00000416151.2_3'UTR|KNSTRN_ENST00000448395.2_3'UTR|KNSTRN_ENST00000608100.1_Missense_Mutation_p.M238I	NM_033286.3	NP_150628.3			kinetochore-localized astrin/SPAG5 binding protein																		TATTAGAAATGTAAGAAGaag	0.423																																					p.M316I		Atlas-SNP	.											.	.	.	.	0			c.G948T						PASS	.						83	76	78					15																	40685795		1885	4111	5996	SO:0001583	missense	90417	exon9			AGAAATGTAAGAA	AK027408	CCDS42021.1, CCDS45226.1, CCDS45227.1	15q15.1	2013-01-17	2012-12-04	2012-12-04	ENSG00000128944	ENSG00000128944			30767	protein-coding gene	gene with protein product	"small kinetochore-associated protein", "kinetochore-localized astrin-binding protein", "TRAF4 associated factor 1"	614718	"chromosome 15 open reading frame 23"	C15orf23		12477932	Standard	NM_033286		Approved	FLJ14502, SKAP, kinastrin, TRAF4AF1	uc001zll.3	Q9Y448	OTTHUMG00000172454	ENST00000249776.8:c.948G>T	chr15.hg19:g.40685795G>T	ENSP00000249776:p.Met316Ile	97.0	0.0	.		90.0	18.0	.	NM_033286		Missense_Mutation	SNP	ENST00000249776.8	hg19	CCDS42021.1	.	.	.	.	.	.	.	.	.	.	G	12.89	2.074155	0.36566	.	.	ENSG00000128944	ENST00000249776	T	0.27720	1.65	5.02	3.02	0.34903	.	0.171826	0.41938	D	0.000798	T	0.16128	0.0388	N	0.14661	0.345	0.80722	D	1	B	0.11235	0.004	B	0.11329	0.006	T	0.06267	-1.0836	10	0.62326	D	0.03	-5.1946	5.8118	0.18469	0.0965:0.0:0.7133:0.1903	.	316	Q9Y448	T4AF1_HUMAN	I	316	ENSP00000249776:M316I	ENSP00000249776:M316I	M	+	3	0	C15orf23	38473087	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	1.826000	0.39092	1.491000	0.48482	0.650000	0.86243	ATG	.	.	.	none		0.423	KNSTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418636.1	NM_001142761		T	40685795	G	T	40685795	3	4	75	1	0	0	0	0	1	0	0	0	1787	1377	48	4	1025	4	C15orf23	15	40685795	Missense_Mutation	SNP	G	TCGA-AL-3473-01A-01D-1252-08		40685795	61845597	30	4861											
RAB27A	5873	hgsc.bcm.edu	37	chr15	55516128	55516128	+	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	atggcttcctcctctttcacTactctctggtcctccagatc	5	15	5	16	0	3	1	1	0	2	1	9	1	7	1	4	2	1	1	4	2	1	3			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr15:55516128T>A	ENST00000396307.2	-	5	677	c.426A>T	c.(424-426)gtA>gtT	p.V142V	RAB27A_ENST00000569493.1_Silent_p.V142V|RAB27A_ENST00000336787.1_Silent_p.V142V|RAB27A_ENST00000564609.1_Silent_p.V142V	NM_004580.4	NP_004571.2	P51159	RB27A_HUMAN	RAB27A, member RAS oncogene family	142					antigen processing and presentation (GO:0019882)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cytotoxic T cell degranulation (GO:0043316)|exocytosis (GO:0006887)|exosomal secretion (GO:1990182)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|multivesicular body organization (GO:0036257)|multivesicular body sorting pathway (GO:0071985)|natural killer cell degranulation (GO:0043320)|positive regulation of exocytosis (GO:0045921)|positive regulation of gene expression (GO:0010628)|protein targeting (GO:0006605)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle transport (GO:0048489)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|exocytic vesicle (GO:0070382)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|multivesicular body membrane (GO:0032585)|photoreceptor outer segment (GO:0001750)|secretory granule membrane (GO:0030667)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(2)|liver(1)|lung(3)|ovary(1)|skin(1)	9				all cancers(107;0.0273)|GBM - Glioblastoma multiforme(80;0.0993)		CCTCTTTCACTACTCTCTGGT	0.398																																					p.V142V		Atlas-SNP	.											.	RAB27A	18	.	0			c.A426T						PASS	.						167	168	167					15																	55516128		2193	4292	6485	SO:0001819	synonymous_variant	5873	exon6			TTTCACTACTCTC	U38654	CCDS10153.1	15q15-q21.1	2014-09-17			ENSG00000069974	ENSG00000069974		"RAB, member RAS oncogene"	9766	protein-coding gene	gene with protein product		603868				7592656	Standard	NM_183235		Approved	RAB27, RAM, GS2, HsT18676	uc002acq.3	P51159	OTTHUMG00000131959	ENST00000396307.2:c.426A>T	chr15.hg19:g.55516128T>A		447.0	0.0	.		91.0	12.0	.	NM_183235	O00195|Q6FI40|Q9UIR9|Q9Y5U3	Silent	SNP	ENST00000396307.2	hg19	CCDS10153.1																																																																																			.	.	.	none		0.398	RAB27A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254918.1	NM_004580, NM_183236		A	55516128	T	A	55516128	2	1	75	1	0	0	0	0	0	0	0	1	12927	1509	53	5		5	RAB27A	15	55516128	Silent	SNP	T	TCGA-AL-3473-01A-01D-1252-08	14830333	55516128	47015264	31	4862											
TMC7	79905	hgsc.bcm.edu	37	chr16	19073098	19073098	+	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	atgtgaacttattattttttAggaaagtcgtgacaagtgct	12	16	9	4	1	0	2	0	2	0	0	1	3	0	3	0	1	2	1	0	1	6	5			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr16:19073098A>T	ENST00000304381.5	+	16	2236		c.e16-1		RP11-626G11.5_ENST00000568971.1_RNA|RP11-626G11.5_ENST00000571934.1_RNA|TMC7_ENST00000421369.3_Splice_Site|RP11-626G11.5_ENST00000567047.1_RNA|RP11-626G11.5_ENST00000576433.1_RNA	NM_024847.3	NP_079123.3	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7						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						ATTATTTTTTAGGAAAGTCGT	0.403																																					.		Atlas-SNP	.											.	TMC7	75	.	0			c.2107-2A>T						PASS	.						87	80	82					16																	19073098		2197	4300	6497	SO:0001630	splice_region_variant	79905	exon16			TTTTTTAGGAAAG	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.2107-1A>T	chr16.hg19:g.19073098A>T		83.0	0.0	.		90.0	13.0	.	NM_024847	E7ERB6|Q5H9Q8|Q7Z5M4|Q86WX0|Q9H766	Splice_Site	SNP	ENST00000304381.5	hg19	CCDS10573.1	.	.	.	.	.	.	.	.	.	.	A	14.61	2.586609	0.46110	.	.	ENSG00000170537	ENST00000304381;ENST00000421369	.	.	.	5.03	5.03	0.67393	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.2868	0.60247	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TMC7	18980599	1.000000	0.71417	0.916000	0.36221	0.545000	0.35147	6.318000	0.72866	2.012000	0.59069	0.533000	0.62120	.	.	.	.	none		0.403	TMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254276.3	NM_024847	Intron	T	19073098	A	T	19073098	5	4	75	1	0	0	0	0	0	0	1	0	16002	434	15	5	2167	5	TMC7	16	19073098	Splice_Site	SNP	A	TCGA-AL-3473-01A-01D-1252-08		19073098	71281655	32	4863											
DNAH3	55567	hgsc.bcm.edu	37	chr16	21080893	21080893	+	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	catccaaattgtcttgtatgCgaattagcttttcttcccat	9	17	5	10	1	2	0	0	0	2	0	4	1	4	0	2	0	2	2	2	0	4	7	rs577456196		TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr16:21080893C>T	ENST00000261383.3	-	23	3223	c.3224G>A	c.(3223-3225)cGc>cAc	p.R1075H	DNAH3_ENST00000415178.1_Missense_Mutation_p.R1075H	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1075	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.R1075P(2)		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)		GTCTTGTATGCGAATTAGCTT	0.453													C|||	1	0.000199681	0	0	5008	,	,		19175	0.001		0	False		,,,				2504	0				p.R1075H		Atlas-SNP	.											DNAH3_ENST00000261383,NS,carcinoma,-1,2	DNAH3	1142	.	2	Substitution - Missense(2)	lung(2)	c.G3224A						PASS	.						173	130	144					16																	21080893		2201	4300	6501	SO:0001583	missense	55567	exon23			TGTATGCGAATTA	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.3224G>A	chr16.hg19:g.21080893C>T	ENSP00000261383:p.Arg1075His	176.0	0.0	.		96.0	14.0	.	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	hg19	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	C	10.65	1.410395	0.25465	.	.	ENSG00000158486	ENST00000261383;ENST00000415178	T;T	0.61859	0.07;0.07	5.4	4.22	0.49857	Dynein heavy chain, domain-2 (1);	0.726956	0.12981	N	0.423277	T	0.44519	0.1297	L	0.28192	0.835	0.09310	N	1	D	0.65815	0.995	P	0.49332	0.607	T	0.36625	-0.9740	10	0.26408	T	0.33	.	2.0715	0.03614	0.3159:0.4174:0.1475:0.1193	.	1075	Q8TD57	DYH3_HUMAN	H	1075	ENSP00000261383:R1075H;ENSP00000394245:R1075H	ENSP00000261383:R1075H	R	-	2	0	DNAH3	20988394	0.001000	0.12720	0.952000	0.39060	0.634000	0.38068	0.318000	0.19504	2.696000	0.92011	0.655000	0.94253	CGC	.	.	.	none		0.453	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		T	21080893	C	T	21080893	3	4	75	1	0	0	0	0	1	0	0	0	4605	768	27	1	9285	1	DNAH3	16	21080893	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08	2007795	21080893	69273860	33	4864											
TMEM107	84314	hgsc.bcm.edu	37	chr17	8079579	8079579	+	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	ggagcgtcaggaagcgagagGgcacaagccctgagacccgg	11	2	17	11	3	1	2	1	1	0	2	1	6	1	4	2	4	3	1	2	4	2	0			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr17:8079579G>T	ENST00000437139.2	-	1	113	c.26C>A	c.(25-27)cCc>cAc	p.P9H	TMEM107_ENST00000449985.2_Missense_Mutation_p.P9H|RP11-599B13.7_ENST00000581248.1_lincRNA|TMEM107_ENST00000431792.2_Missense_Mutation_p.P9H|TMEM107_ENST00000532998.1_Missense_Mutation_p.P9H|SNORD118_ENST00000363593.1_RNA|TMEM107_ENST00000316425.5_Missense_Mutation_p.P9H|TMEM107_ENST00000533070.1_Missense_Mutation_p.P9H	NM_183065.2	NP_898888.1	Q6UX40	TM107_HUMAN	transmembrane protein 107	9					cilium assembly (GO:0042384)|embryonic digit morphogenesis (GO:0042733)|neural tube patterning (GO:0021532)	integral component of membrane (GO:0016021)				large_intestine(1)|lung(4)|ovary(1)	6						GAAGCGAGAGGGCACAAGCCC	0.632																																					p.P9H		Atlas-SNP	.											.	TMEM107	16	.	0			c.C26A						PASS	.						58	48	51					17																	8079579		2203	4300	6503	SO:0001583	missense	84314	exon1			CGAGAGGGCACAA	AF311338	CCDS11132.1, CCDS45607.1	17p13.1	2005-12-19				ENSG00000179029			28128	protein-coding gene	gene with protein product						12477932	Standard	NM_032354		Approved	MGC10744	uc002gkh.4	Q6UX40		ENST00000437139.2:c.26C>A	chr17.hg19:g.8079579G>T	ENSP00000402732:p.Pro9His	84.0	0.0	.		159.0	21.0	.	NM_183065	A0PJV7|Q6NSE3|Q6ZRX9|Q96T82	Missense_Mutation	SNP	ENST00000437139.2	hg19	CCDS45607.1	.	.	.	.	.	.	.	.	.	.	G	17.61	3.431906	0.62844	.	.	ENSG00000179029	ENST00000449985;ENST00000532998;ENST00000437139;ENST00000533070;ENST00000316425;ENST00000431792;ENST00000415860	.	.	.	5.6	4.63	0.57726	.	0.000000	0.85682	D	0.000000	T	0.77465	0.4134	M	0.79475	2.455	0.49915	D	0.999835	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;0.982	T	0.79948	-0.1588	9	0.87932	D	0	-37.9001	10.8172	0.46583	0.0877:0.0:0.9123:0.0	.	9;9;9;9	B3KNL7;Q6UX40-3;Q6UX40-4;Q6UX40	.;.;.;TM107_HUMAN	H	9	.	ENSP00000314116:P9H	P	-	2	0	TMEM107	8020304	1.000000	0.71417	1.000000	0.80357	0.028000	0.11728	8.301000	0.89951	1.511000	0.48818	-0.158000	0.13435	CCC	.	.	.	none		0.632	TMEM107-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388844.1	NM_032354		T	8079579	G	T	8079579	3	4	75	1	0	0	0	0	1	0	0	0	16035	1232	43	4	434	4	TMEM107	17	8079579	Missense_Mutation	SNP	G	TCGA-AL-3473-01A-01D-1252-08		8079579	73115631	34	4865											
TMEM106A	113277	hgsc.bcm.edu	37	chr17	41365849	41365849	+	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	caccttctctctctctagagCtggagaagcagttggtggct	7	12	11	11	0	3	2	0	0	3	2	5	3	3	2	1	3	2	4	1	3	2	3			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr17:41365849C>T	ENST00000331615.3	+	4	451	c.214C>T	c.(214-216)Ctg>Ttg	p.L72L	TMEM106A_ENST00000541594.1_Silent_p.L24L|TMEM106A_ENST00000588659.1_Silent_p.L72L|TMEM106A_ENST00000592564.1_3'UTR|TMEM106A_ENST00000536052.1_Silent_p.L72L	NM_145041.1	NP_659478.1	Q96A25	T106A_HUMAN	transmembrane protein 106A	72						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)	11		Breast(137;0.0164)		BRCA - Breast invasive adenocarcinoma(366;0.0917)		CTCTCTAGAGCTGGAGAAGCA	0.552																																					p.L72L		Atlas-SNP	.											.	TMEM106A	20	.	0			c.C214T						PASS	.						97	74	82					17																	41365849		2203	4296	6499	SO:0001819	synonymous_variant	113277	exon4			CTAGAGCTGGAGA	AK056132	CCDS11462.1, CCDS74073.1	17q21.31	2012-01-23			ENSG00000184988	ENSG00000184988			28288	protein-coding gene	gene with protein product							Standard	XM_006721658		Approved	MGC20235	uc002idn.1	Q96A25		ENST00000331615.3:c.214C>T	chr17.hg19:g.41365849C>T		108.0	0.0	.		165.0	17.0	.	NM_145041	A8K2X2|B7Z698	Silent	SNP	ENST00000331615.3	hg19	CCDS11462.1																																																																																			.	.	.	none		0.552	TMEM106A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453470.2	NM_145041		T	41365849	C	T	41365849	2	4	75	1	0	0	0	0	0	0	0	1	16032	796	28	2		2	TMEM106A	17	41365849	Silent	SNP	C	TCGA-AL-3473-01A-01D-1252-08	33286270	41365849	39829361	35	4866											
PHB	5245	hgsc.bcm.edu	37	chr17	47486482	47486483	+	Frame_Shift_Del	DEL	CT	CT	-																															ctcacctgcctggagaccagCtctctctgggtgattagttc																										TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr17:47486482_47486483delCT	ENST00000300408.3	-	5	503_504	c.431_432delAG	c.(430-432)gagfs	p.E144fs	PHB_ENST00000511832.1_Intron|RP11-81K2.1_ENST00000576461.1_Intron|PHB_ENST00000508009.1_5'UTR	NM_001281496.1|NM_001281715.1|NM_002634.2	NP_001268425.1|NP_001268644.1|NP_002625.1	P35232	PHB_HUMAN	prohibitin	144					cellular response to interleukin-6 (GO:0071354)|DNA replication (GO:0006260)|histone deacetylation (GO:0016575)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone receptor signaling pathway (GO:0050847)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|transcription regulatory region DNA binding (GO:0044212)			endometrium(4)|large_intestine(2)|lung(4)	10	all_cancers(4;2.62e-14)|Breast(4;4.21e-29)|all_epithelial(4;6.9e-18)		Epithelial(5;8.1e-06)|all cancers(6;7.71e-05)			TGGAGACCAGCTCTCTCTGGGT	0.554																																					p.144_145del		Atlas-INDEL	.											.	PHB	25	.	0			c.432_433del						PASS	.																																			SO:0001589	frameshift_variant	5245	exon5			.		CCDS11548.1, CCDS62244.1	17q21	2010-11-25			ENSG00000167085	ENSG00000167085			8912	protein-coding gene	gene with protein product		176705				10376528, 8244394	Standard	NM_001281496		Approved	PHB1	uc002iox.1	P35232	OTTHUMG00000134271	ENST00000300408.3:c.431_432delAG	chr17.hg19:g.47486488_47486489delCT	ENSP00000300408:p.Glu144fs	77.0	0.0	0		137.0	17.0	0.124088	NM_002634	B4DY47|Q4VBQ0	Frame_Shift_Del	DEL	ENST00000300408.3	hg19	CCDS11548.1																																																																																			.	.	.	none		0.554	PHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258826.1	NM_002634		-	47486483	CT	-	47486482	7	5	75	1	0	1	0	1	0	0	0	0	11821	796	28	0	398	0	PHB	17	47486482	Frame_Shift_Del	DEL	CT	TCGA-AL-3473-01A-01D-1252-08	6120633	47486482	33708728	36	4867											
ME2	4200	hgsc.bcm.edu	37	chr18	48442562	48442562	+	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	ttatttatttcgatctcagaCagaggtcatgttagatcaat	12	16	7	6	1	3	3	3	0	1	3	5	4	3	3	0	1	0	1	0	1	4	5			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr18:48442562C>G	ENST00000321341.5	+	5	689	c.417C>G	c.(415-417)gaC>gaG	p.D139E	ME2_ENST00000382927.3_Missense_Mutation_p.D139E	NM_002396.4	NP_002387.1	P23368	MAOM_HUMAN	malic enzyme 2, NAD(+)-dependent, mitochondrial	139					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)		CGATCTCAGACAGAGGTCATG	0.333																																					p.D139E		Atlas-SNP	.											.	ME2	49	.	0			c.C417G						PASS	.						186	177	180					18																	48442562		2203	4300	6503	SO:0001583	missense	4200	exon5			CTCAGACAGAGGT	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.417C>G	chr18.hg19:g.48442562C>G	ENSP00000321070:p.Asp139Glu	234.0	0.0	.		38.0	4.0	.	NM_001168335	B2R8J2|Q9BWL6|Q9BYG1|Q9H4B2	Missense_Mutation	SNP	ENST00000321341.5	hg19	CCDS11948.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.129308	0.77549	.	.	ENSG00000082212	ENST00000321341;ENST00000382927	T;T	0.45668	0.89;0.89	5.8	5.8	0.92144	Malic enzyme, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.63698	0.2533	M	0.77712	2.385	0.58432	D	0.999994	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.61950	-0.6957	10	0.36615	T	0.2	-22.0057	12.879	0.58006	0.0:0.9218:0.0:0.0782	.	139;139	Q9BWL6;P23368	.;MAOM_HUMAN	E	139	ENSP00000321070:D139E;ENSP00000372384:D139E	ENSP00000321070:D139E	D	+	3	2	ME2	46696560	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.392000	0.52537	2.741000	0.93983	0.650000	0.86243	GAC	.	.	.	none		0.333	ME2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255991.1	NM_002396		G	48442562	C	G	48442562	3	3	75	1	0	0	0	0	1	0	0	0	9425	477	17	4	431	4	ME2	18	48442562	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08		48442562	29634686	37	4868											
SLC25A42	284439	hgsc.bcm.edu	37	chr19	19221630	19221630	+	Frame_Shift_Del	DEL	T	T	-																															gggtcccatcgccgtgggcaTcagcttcaccaccttcgacc																										TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr19:19221630delT	ENST00000318596.7	+	8	1053	c.902delT	c.(901-903)atcfs	p.I301fs		NM_178526.4	NP_848621.2	Q86VD7	S2542_HUMAN	solute carrier family 25, member 42	301					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)			GCCGTGGGCATCAGCTTCACC	0.657																																					p.I301fs		Atlas-INDEL	.											.	SLC25A42	18	.	0			c.901delA						PASS	.						68	52	57					19																	19221630		2203	4300	6503	SO:0001589	frameshift_variant	284439	exon8			.		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.902delT	chr19.hg19:g.19221630delT	ENSP00000326693:p.Ile301fs	106.0	0.0	0		198.0	24.0	0.121212	NM_178526	D2T2J5|O14553|O43378	Frame_Shift_Del	DEL	ENST00000318596.7	hg19	CCDS32966.1																																																																																			.	.	.	none		0.657	SLC25A42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465931.1	NM_178526		-	19221630	T	-	19221630	7	5	75	1	0	1	0	1	0	0	0	0	14520	1435	50	0	928	0	SLC25A42	19	19221630	Frame_Shift_Del	DEL	T	TCGA-AL-3473-01A-01D-1252-08		19221630	39907353	38	4869											
APLP1	333	hgsc.bcm.edu	37	chr19	36362560	36362560	+	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	gcacggctcgggcatgctctTaccctgtggctcggatcggt	4	10	14	13	4	1	0	0	0	1	0	4	1	1	1	1	5	2	5	1	5	1	1			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr19:36362560T>A	ENST00000221891.4	+	5	776	c.584T>A	c.(583-585)tTa>tAa	p.L195*	APLP1_ENST00000537454.2_Nonsense_Mutation_p.L156*|APLP1_ENST00000586861.1_Nonsense_Mutation_p.L189*|NPHS1_ENST00000591817.1_5'Flank	NM_001024807.1|NM_005166.3	NP_001019978.1|NP_005157.1	P51693	APLP1_HUMAN	amyloid beta (A4) precursor-like protein 1	195					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)			GGCATGCTCTTACCCTGTGGC	0.642																																					p.L195X		Atlas-SNP	.											.	APLP1	77	.	0			c.T584A						PASS	.						111	105	107					19																	36362560		2203	4300	6503	SO:0001587	stop_gained	333	exon5			TGCTCTTACCCTG	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.584T>A	chr19.hg19:g.36362560T>A	ENSP00000221891:p.Leu195*	155.0	0.0	.		345.0	57.0	.	NM_005166	O00113|Q96A92	Nonsense_Mutation	SNP	ENST00000221891.4	hg19	CCDS32997.1	.	.	.	.	.	.	.	.	.	.	T	36	5.888940	0.97068	.	.	ENSG00000105290	ENST00000537454;ENST00000221891	.	.	.	4.41	4.41	0.53225	.	0.000000	0.33515	N	0.004832	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.3771	11.5688	0.50822	0.0:0.0:0.0:1.0	.	.	.	.	X	156;195	.	ENSP00000221891:L195X	L	+	2	0	APLP1	41054400	1.000000	0.71417	1.000000	0.80357	0.713000	0.41058	7.189000	0.77747	1.630000	0.50440	0.379000	0.24179	TTA	.	.	.	none		0.642	APLP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452564.1	NM_001024807		A	36362560	T	A	36362560	4	1	75	1	0	0	0	0	0	1	0	0	778	1764	61	5	602	5	APLP1	19	36362560	Nonsense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08	17140930	36362560	22766423	39	4870											
ZNF585B	92285	hgsc.bcm.edu	37	chr19	37678072	37678072	+	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	ggatttttccccagaataaaTtttttgatcttgagaggaag	12	15	9	5	0	1	3	0	2	1	2	2	6	2	5	2	2	0	0	2	2	4	7			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr19:37678072T>A	ENST00000532828.2	-	5	618	c.367A>T	c.(367-369)Att>Ttt	p.I123F	CTC-454I21.3_ENST00000585860.2_Intron|ZNF585B_ENST00000312908.5_5'Flank|ZNF585B_ENST00000531805.1_Missense_Mutation_p.I68F|ZNF585B_ENST00000527838.1_Missense_Mutation_p.I123F	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	123					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)			CCAGAATAAATTTTTTGATCT	0.373																																					p.I123F	Melanoma(93;882 1454 18863 28917 48427)	Atlas-SNP	.											.	ZNF585B	91	.	0			c.A367T						PASS	.						59	64	62					19																	37678072		2202	4299	6501	SO:0001583	missense	92285	exon5			AATAAATTTTTTG	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.367A>T	chr19.hg19:g.37678072T>A	ENSP00000433773:p.Ile123Phe	174.0	0.0	.		88.0	9.0	.	NM_152279	Q8IZD3|Q96JW6	Missense_Mutation	SNP	ENST00000532828.2	hg19	CCDS12500.1	.	.	.	.	.	.	.	.	.	.	T	4.132	0.022795	0.08006	.	.	ENSG00000245680	ENST00000531805;ENST00000532828;ENST00000527838	T;T;T	0.08634	3.07;3.15;6.5	2.32	2.32	0.28847	.	0.230506	0.22120	U	0.064354	T	0.10551	0.0258	M	0.65498	2.005	0.80722	D	1	B	0.22909	0.077	B	0.20184	0.028	T	0.06427	-1.0827	10	0.72032	D	0.01	.	9.2461	0.37527	0.0:0.0:0.0:1.0	.	123	Q52M93	Z585B_HUMAN	F	68;123;123	ENSP00000436774:I68F;ENSP00000433773:I123F;ENSP00000435268:I123F	ENSP00000435268:I123F	I	-	1	0	ZNF585B	42369912	0.614000	0.27017	0.755000	0.31263	0.021000	0.10359	0.914000	0.28624	1.052000	0.40392	0.374000	0.22700	ATT	.	.	.	none		0.373	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279		A	37678072	T	A	37678072	3	1	75	1	0	0	0	0	1	0	0	0	18030	1493	52	5	1946	5	ZNF585B	19	37678072	Missense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08	1315512	37678072	21450911	40	4871											
CSE1L	1434	hgsc.bcm.edu	37	chr20	47675025	47675025	+	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	aactcagcgatgcaaatctgCaaacactaacagaatattta	18	9	5	9	1	2	1	1	0	1	1	2	2	2	1	0	0	6	2	0	0	7	4			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr20:47675025C>A	ENST00000262982.2	+	2	148	c.25C>A	c.(25-27)Caa>Aaa	p.Q9K	CSE1L_ENST00000542325.1_5'UTR|CSE1L_ENST00000396192.3_Missense_Mutation_p.Q9K	NM_001256135.1|NM_001316.3	NP_001243064.1|NP_001307.2	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like (yeast)	9					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	importin-alpha export receptor activity (GO:0008262)			breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(11)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	35			BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)			TGCAAATCTGCAAACACTAAC	0.333																																					p.Q9K		Atlas-SNP	.											.	CSE1L	83	.	0			c.C25A						PASS	.						100	109	106					20																	47675025		2203	4300	6503	SO:0001583	missense	1434	exon2			AATCTGCAAACAC	U33286	CCDS13412.1, CCDS58773.1	20q13	2013-05-01	2001-11-28		ENSG00000124207	ENSG00000124207		"Exportins"	2431	protein-coding gene	gene with protein product	"cellular apoptosis susceptibility"	601342	"chromosome segregation 1 (yeast homolog)-like"			8963895, 7479798	Standard	NM_001316		Approved	CAS, XPO2, CSE1	uc002xty.4	P55060	OTTHUMG00000033046	ENST00000262982.2:c.25C>A	chr20.hg19:g.47675025C>A	ENSP00000262982:p.Gln9Lys	173.0	0.0	.		234.0	24.0	.	NM_001256135	A3RLL6|B2R5T4|E1P5Y0|F8W904|O75432|Q32M40|Q9H5B7|Q9NTS0|Q9UP98|Q9UP99|Q9UPA0	Missense_Mutation	SNP	ENST00000262982.2	hg19	CCDS13412.1	.	.	.	.	.	.	.	.	.	.	C	14.53	2.561981	0.45590	.	.	ENSG00000124207	ENST00000262982;ENST00000396192	T;T	0.68624	-0.34;-0.34	5.3	4.36	0.52297	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.58004	0.2092	L	0.59436	1.845	0.80722	D	1	B;P	0.36990	0.24;0.577	B;B	0.33042	0.157;0.13	T	0.55431	-0.8142	10	0.10902	T	0.67	-1.2095	14.1142	0.65142	0.0:0.927:0.0:0.073	.	9;9	F8W904;P55060	.;XPO2_HUMAN	K	9	ENSP00000262982:Q9K;ENSP00000379495:Q9K	ENSP00000262982:Q9K	Q	+	1	0	CSE1L	47108432	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	7.272000	0.78516	1.222000	0.43521	0.591000	0.81541	CAA	.	.	.	none		0.333	CSE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080345.2	NM_001316		A	47675025	C	A	47675025	3	1	75	1	0	0	0	0	1	0	0	0	3932	711	25	4	27	4	CSE1L	20	47675025	Missense_Mutation	SNP	C	TCGA-AL-3473-01A-01D-1252-08		47675025	15350495	41	4872											
ZNF512B	57473	hgsc.bcm.edu	37	chr20	62598870	62598870	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctgtccaccacggaccaccGgcatccctgcagcacacaac	10	5	7	19	2	1	0	0	0	1	0	3	1	3	1	5	2	3	3	5	2	1	0			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr20:62598870G>A	ENST00000450537.1	-	3	188	c.128C>T	c.(127-129)cCg>cTg	p.P43L	ZNF512B_ENST00000217130.3_Missense_Mutation_p.P43L|ZNF512B_ENST00000369888.1_Missense_Mutation_p.P43L			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	43					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)					ACGGACCACCGGCATCCCTGC	0.637																																					p.P43L		Atlas-SNP	.											.	ZNF512B	72	.	0			c.C128T						PASS	.						79	84	82					20																	62598870		2203	4300	6503	SO:0001583	missense	57473	exon3			ACCACCGGCATCC	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.128C>T	chr20.hg19:g.62598870G>A	ENSP00000393795:p.Pro43Leu	198.0	0.0	.		417.0	69.0	.	NM_020713	Q08AK9|Q9ULM4	Missense_Mutation	SNP	ENST00000450537.1	hg19	CCDS13548.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.158963	0.78226	.	.	ENSG00000196700	ENST00000369888;ENST00000450537;ENST00000217130	T;T;T	0.25414	1.8;1.8;1.8	3.86	3.86	0.44501	.	0.253119	0.27917	N	0.017321	T	0.35508	0.0934	N	0.24115	0.695	0.46586	D	0.999114	D	0.89917	1.0	D	0.81914	0.995	T	0.23583	-1.0184	10	0.87932	D	0	-13.686	13.7319	0.62792	0.0:0.0:1.0:0.0	.	43	Q96KM6	Z512B_HUMAN	L	43	ENSP00000358904:P43L;ENSP00000393795:P43L;ENSP00000217130:P43L	ENSP00000217130:P43L	P	-	2	0	ZNF512B	62069314	0.845000	0.29573	0.989000	0.46669	0.848000	0.48234	1.891000	0.39738	2.444000	0.82710	0.462000	0.41574	CCG	.	.	.	none		0.637	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713		A	62598870	G	A	62598870	3	1	75	1	0	0	0	0	1	0	0	0	17969	1116	39	1	2610	1	ZNF512B	20	62598870	Missense_Mutation	SNP	G	TCGA-AL-3473-01A-01D-1252-08	14923845	62598870	426650	42	4873											
COL4A6	1288	hgsc.bcm.edu	37	chrX	107433650	107433650	+	Missense_Mutation	SNP	T	T	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	cctttgaggcctaggtttccTtttggaccttgttctcctcg	3	17	9	12	1	1	1	0	1	1	0	4	2	2	2	5	3	0	2	5	3	1	7			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chrX:107433650T>G	ENST00000372216.4	-	20	1501	c.1401A>C	c.(1399-1401)aaA>aaC	p.K467N	COL4A6_ENST00000545689.1_Missense_Mutation_p.K466N|COL4A6_ENST00000394872.2_Missense_Mutation_p.K467N|COL4A6_ENST00000334504.7_Missense_Mutation_p.K466N|COL4A6_ENST00000538570.1_Missense_Mutation_p.K466N	NM_001847.2	NP_001838.2	Q14031	CO4A6_HUMAN	collagen, type IV, alpha 6	467	Triple-helical region.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(41)|ovary(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	92						CTAGGTTTCCTTTTGGACCTT	0.443									Alport syndrome with Diffuse Leiomyomatosis																												p.K467N	Melanoma(87;1895 1945 2589 7165)	Atlas-SNP	.											.	COL4A6	270	.	0			c.A1401C						PASS	.						130	118	122					X																	107433650		2203	4300	6503	SO:0001583	missense	1288	exon20	Familial Cancer Database		GTTTCCTTTTGGA	U04845	CCDS14541.1, CCDS14542.1, CCDS76008.1, CCDS76009.1, CCDS76010.1	Xq22	2014-09-17			ENSG00000197565	ENSG00000197565		"Collagens"	2208	protein-coding gene	gene with protein product		303631				8356449	Standard	NM_033641		Approved		uc004env.4	Q14031	OTTHUMG00000022179	ENST00000372216.4:c.1401A>C	chrX.hg19:g.107433650T>G	ENSP00000361290:p.Lys467Asn	179.0	0.0	.		99.0	38.0	.	NM_001847	Q12823|Q14053|Q5JYH6|Q5JYH8|Q9NQM5|Q9NTX3|Q9UJ76|Q9UMG6|Q9Y4L4	Missense_Mutation	SNP	ENST00000372216.4	hg19	CCDS14541.1	.	.	.	.	.	.	.	.	.	.	T	12.36	1.915515	0.33815	.	.	ENSG00000197565	ENST00000372216;ENST00000334504;ENST00000394872;ENST00000541389;ENST00000545689;ENST00000538570	D;D;D;D;D	0.94232	-3.38;-3.38;-3.38;-3.25;-3.38	5.3	2.74	0.32292	.	0.000000	0.45361	D	0.000370	D	0.92506	0.7620	L	0.52206	1.635	0.33503	D	0.590155	D;D;D;D	0.61697	0.982;0.982;0.983;0.99	P;P;P;P	0.59487	0.764;0.764;0.725;0.858	D	0.91531	0.5242	10	0.59425	D	0.04	.	2.7178	0.05192	0.1932:0.2036:0.0:0.6032	.	466;466;467;466	F5H851;F5H3Q5;Q14031;Q14031-2	.;.;CO4A6_HUMAN;.	N	467;466;467;466;466;466	ENSP00000361290:K467N;ENSP00000334733:K466N;ENSP00000378340:K467N;ENSP00000443707:K466N;ENSP00000445236:K466N	ENSP00000334733:K466N	K	-	3	2	COL4A6	107320306	0.993000	0.37304	0.998000	0.56505	0.987000	0.75469	0.944000	0.29043	0.886000	0.36113	0.486000	0.48141	AAA	.	.	.	none		0.443	COL4A6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057875.2			G	107433650	T	G	107433650	3	3	75	1	0	0	0	0	1	0	0	0	3697	1606	56	5	3778	5	COL4A6	23	107433650	Missense_Mutation	SNP	T	TCGA-AL-3473-01A-01D-1252-08		107433650	47836910	43	4874											
RERE	473	hgsc.bcm.edu	37	chr1	8415616	8415616	+	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	agctggtgggctgctgacatGgggggtgggatggccccagg	5	7	21	8	0	0	1	0	1	0	0	0	2	0	2	2	8	2	3	2	8	0	0			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr1:8415616G>T	ENST00000337907.3	-	23	5164	c.4530C>A	c.(4528-4530)ccC>ccA	p.P1510P	RERE_ENST00000400908.2_Silent_p.P1510P|RERE_ENST00000377464.1_Silent_p.P1242P|RERE_ENST00000400907.2_Silent_p.P528P|RERE_ENST00000476556.1_Silent_p.P956P	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	1510	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)		CTGCTGACATGGGGGGTGGGA	0.642																																					p.P1510P		Atlas-SNP	.											.	RERE	129	.	0			c.C4530A						PASS	.						16	17	17					1																	8415616		2201	4295	6496	SO:0001819	synonymous_variant	473	exon23			TGACATGGGGGGT	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.4530C>A	chr1.hg19:g.8415616G>T		39.0	0.0	.		36.0	9.0	.	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Silent	SNP	ENST00000337907.3	hg19	CCDS95.1																																																																																			.	.	.	none		0.642	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1			T	8415616	G	T	8415616	2	4	76	1	0	0	0	0	0	0	0	1	13244	1335	47	4		4	RERE	1	8415616	Silent	SNP	G	TCGA-AL-7173-01A-11D-2136-08		8415616	240835005	1	4875											
TSPAN2	10100	hgsc.bcm.edu	37	chr1	115601516	115601516	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttactcactgttgagtggaaGgtgatgagtgtcccattgcc	8	13	12	8	0	1	3	1	3	0	0	2	4	2	4	2	2	2	1	2	2	2	3			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr1:115601516G>A	ENST00000369516.2	-	5	463	c.432C>T	c.(430-432)acC>acT	p.T144T	TSPAN2_ENST00000369515.2_Silent_p.T119T|TSPAN2_ENST00000491992.1_5'Flank|TSPAN2_ENST00000369514.2_Silent_p.T144T	NM_005725.4	NP_005716.2	O60636	TSN2_HUMAN	tetraspanin 2	144					astrocyte development (GO:0014002)|axon development (GO:0061564)|brain development (GO:0007420)|inflammatory response (GO:0006954)|microglia development (GO:0014005)|myelination (GO:0042552)|oligodendrocyte differentiation (GO:0048709)	integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|plasma membrane (GO:0005886)				central_nervous_system(1)|large_intestine(4)|lung(3)|pancreas(1)|prostate(1)	10	Lung SC(450;0.211)	all_cancers(81;2.9e-07)|all_epithelial(167;1.42e-06)|all_lung(203;6.72e-06)|Lung NSC(69;1.13e-05)|Acute lymphoblastic leukemia(138;0.191)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179)		TTGAGTGGAAGGTGATGAGTG	0.398																																					p.T144T		Atlas-SNP	.											.	TSPAN2	37	.	0			c.C432T						PASS	.						256	232	240					1																	115601516		2203	4300	6503	SO:0001819	synonymous_variant	10100	exon5			GTGGAAGGTGATG	AF054839	CCDS881.1	1p13.1	2013-02-14			ENSG00000134198	ENSG00000134198		"Tetraspanins"	20659	protein-coding gene	gene with protein product		613133				9714763, 11739647	Standard	NM_005725		Approved	TSPAN-2, TSN2, FLJ12082	uc001eft.3	O60636	OTTHUMG00000011878	ENST00000369516.2:c.432C>T	chr1.hg19:g.115601516G>A		203.0	0.0	.		167.0	40.0	.	NM_005725	D6PTH4|Q5TET2|Q8WU05	Silent	SNP	ENST00000369516.2	hg19	CCDS881.1																																																																																			.	.	.	none		0.398	TSPAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032828.1	NM_005725		A	115601516	G	A	115601516	2	1	76	1	0	0	0	0	0	0	0	1	16656	987	35	2		2	TSPAN2	1	115601516	Silent	SNP	G	TCGA-AL-7173-01A-11D-2136-08	107185900	115601516	133649105	2	4876											
RGL1	23179	hgsc.bcm.edu	37	chr1	183885638	183885638	+	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	ccatggacacaaattcctcaGggatgtcttccttaatcaac	12	11	6	12	0	3	0	2	0	1	0	5	2	5	2	3	2	1	0	3	2	3	3			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr1:183885638G>C	ENST00000360851.3	+	16	1985	c.1807G>C	c.(1807-1809)Ggg>Cgg	p.G603R	RGL1_ENST00000536277.1_Missense_Mutation_p.G601R|RGL1_ENST00000539189.1_Missense_Mutation_p.G574R|RGL1_ENST00000304685.4_Missense_Mutation_p.G638R			Q9NZL6	RGL1_HUMAN	ral guanine nucleotide dissociation stimulator-like 1	603	Ser-rich.				cellular lipid metabolic process (GO:0044255)|positive regulation of Ral GTPase activity (GO:0032852)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(5)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(17)|ovary(4)|prostate(3)|stomach(1)	51						AAATTCCTCAGGGATGTCTTC	0.502																																					p.G638R		Atlas-SNP	.											RGL1,NS,carcinoma,0,1	RGL1	91	.	0			c.G1912C						PASS	.						186	182	183					1																	183885638		2203	4300	6503	SO:0001583	missense	23179	exon17			TCCTCAGGGATGT	AF186780	CCDS1359.1, CCDS72992.1	1q25.2	2008-02-05			ENSG00000143344	ENSG00000143344			30281	protein-coding gene	gene with protein product		605667				10760592, 10231032	Standard	XM_005245010		Approved	RGL	uc001gqm.3	Q9NZL6	OTTHUMG00000035328	ENST00000360851.3:c.1807G>C	chr1.hg19:g.183885638G>C	ENSP00000354097:p.Gly603Arg	153.0	0.0	.		169.0	47.0	.	NM_015149	Q5SXQ2|Q5SXQ6|Q9HBY3|Q9HBY4|Q9NZL5|Q9UG43|Q9Y2G6	Missense_Mutation	SNP	ENST00000360851.3	hg19		.	.	.	.	.	.	.	.	.	.	G	16.32	3.090748	0.55968	.	.	ENSG00000143344	ENST00000304685;ENST00000367531;ENST00000536277;ENST00000360851;ENST00000539189	T;T;T;T;T	0.50548	0.76;0.76;0.79;0.78;0.74	5.05	5.05	0.67936	.	0.057165	0.64402	D	0.000001	T	0.48502	0.1503	L	0.40543	1.245	0.47245	D	0.999364	D;D;D;D	0.58268	0.982;0.969;0.969;0.969	P;P;B;P	0.51866	0.682;0.585;0.348;0.585	T	0.48670	-0.9015	10	0.54805	T	0.06	.	11.5322	0.50616	0.0831:0.0:0.9169:0.0	.	574;601;603;638	F5H6U6;B7Z2W5;Q9NZL6;Q5SXQ6	.;.;RGL1_HUMAN;.	R	638;638;601;603;574	ENSP00000303192:G638R;ENSP00000356501:G638R;ENSP00000438662:G601R;ENSP00000354097:G603R;ENSP00000437355:G574R	ENSP00000303192:G638R	G	+	1	0	RGL1	182152261	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.475000	0.53136	2.345000	0.79718	0.650000	0.86243	GGG	.	.	.	none		0.502	RGL1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000085742.1	NM_015149		C	183885638	G	C	183885638	3	2	76	1	0	0	0	0	1	0	0	0	13289	1000	35	4	1974	4	RGL1	1	183885638	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08	68284122	183885638	65364983	3	4877											
TTC15	51112	hgsc.bcm.edu	37	chr2	3483103	3483103	+	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	cactacctgcacgagagcgtGctcttcaacctgaccaccat	10	8	7	16	2	2	2	1	1	1	1	2	3	2	2	4	0	5	2	4	0	2	2			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr2:3483103G>A	ENST00000324266.5	+	12	2274	c.2079G>A	c.(2077-2079)gtG>gtA	p.V693V	TRAPPC12-AS1_ENST00000453806.1_RNA|TRAPPC12_ENST00000382110.2_Silent_p.V693V	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	693					vesicle-mediated transport (GO:0016192)												ACGAGAGCGTGCTCTTCAACC	0.632																																					p.V693V		Atlas-SNP	.											.	.	.	.	0			c.G2079A						PASS	.						123	115	118					2																	3483103		2203	4300	6503	SO:0001819	synonymous_variant	51112	exon12			GAGCGTGCTCTTC	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.2079G>A	chr2.hg19:g.3483103G>A		160.0	0.0	.		124.0	30.0	.	NM_016030	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Silent	SNP	ENST00000324266.5	hg19	CCDS1652.1	.	.	.	.	.	.	.	.	.	.	G	9.411	1.080605	0.20309	.	.	ENSG00000171853	ENST00000416918	.	.	.	4.55	-2.5	0.06384	.	.	.	.	.	T	0.50086	0.1595	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44436	-0.9328	4	.	.	.	.	6.1178	0.20136	0.0754:0.4917:0.1948:0.2381	.	.	.	.	T	80	.	.	A	+	1	0	TTC15	3462110	0.943000	0.32029	0.965000	0.40720	0.990000	0.78478	-0.009000	0.12765	-0.267000	0.09325	-0.150000	0.13652	GCT	.	.	.	none		0.632	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030		A	3483103	G	A	3483103	2	1	76	1	0	0	0	0	0	0	0	1	16694	1306	46	2		2	TTC15	2	3483103	Silent	SNP	G	TCGA-AL-7173-01A-11D-2136-08		3483103	239716270	4	4878											
RHOQ	23433	hgsc.bcm.edu	37	chr2	46803262	46803262	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgaggcctttatcttacccaAtgaccgatgtcttccttata	9	15	6	11	1	2	2	0	2	2	0	3	3	3	2	4	1	1	0	4	1	5	6	rs557488131		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr2:46803262A>G	ENST00000238738.4	+	3	557	c.238A>G	c.(238-240)Atg>Gtg	p.M80V	RHOQ_ENST00000465198.1_3'UTR|RP11-417F21.1_ENST00000506009.2_RNA	NM_012249.3	NP_036381.2	P17081	RHOQ_HUMAN	ras homolog family member Q	80					cellular response to insulin stimulus (GO:0032869)|cortical actin cytoskeleton organization (GO:0030866)|GTP catabolic process (GO:0006184)|insulin receptor signaling pathway (GO:0008286)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|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)	actin filament (GO:0005884)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	GBD domain binding (GO:0032427)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|profilin binding (GO:0005522)	p.M80V(1)		skin(2)	2		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			ATCTTACCCAATGACCGATGT	0.393													A|||	1	0.000199681	0	0	5008	,	,		18452	0		0.001	False		,,,				2504	0				p.M80V		Atlas-SNP	.											RHOQ_ENST00000238738,NS,carcinoma,0,1	RHOQ	22	.	1	Substitution - Missense(1)	endometrium(1)	c.A238G						PASS	.						99	89	92					2																	46803262		2203	4300	6503	SO:0001583	missense	23433	exon3			TACCCAATGACCG	M31470	CCDS33191.1	2p21	2012-02-27	2012-02-27	2004-03-24	ENSG00000119729	ENSG00000119729			17736	protein-coding gene	gene with protein product		605857	"RAS-like, family 7, member A", "ras homolog gene family, member Q"	RASL7A, ARHQ		2108320	Standard	NM_012249		Approved	TC10	uc002rva.3	P17081	OTTHUMG00000150653	ENST00000238738.4:c.238A>G	chr2.hg19:g.46803262A>G	ENSP00000238738:p.Met80Val	84.0	2.0	.		74.0	3.0	.	NM_012249	D6W5A6|Q0VGN1|Q52LS8|Q53SJ1|Q6NS39|Q6P146|Q7Z480	Missense_Mutation	SNP	ENST00000238738.4	hg19	CCDS33191.1	.	.	.	.	.	.	.	.	.	.	A	13.87	2.367334	0.41902	.	.	ENSG00000119729	ENST00000238738;ENST00000482449	T;T	0.76186	-1.0;3.4	5.43	4.26	0.50523	Small GTP-binding protein domain (1);	0.034638	0.85682	D	0.000000	T	0.65637	0.2710	L	0.38175	1.15	0.58432	D	0.99999	B	0.15141	0.012	B	0.12156	0.007	T	0.63202	-0.6690	10	0.87932	D	0	.	12.6767	0.56897	0.862:0.1379:0.0:0.0	.	80	P17081	RHOQ_HUMAN	V	80;1	ENSP00000238738:M80V;ENSP00000428006:M1V	ENSP00000238738:M80V	M	+	1	0	RHOQ	46656766	1.000000	0.71417	0.993000	0.49108	0.882000	0.50991	7.317000	0.79018	1.055000	0.40461	-0.316000	0.08728	ATG	.	.	.	none		0.393	RHOQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319409.1	NM_012249		G	46803262	A	G	46803262	3	3	76	1	0	0	0	0	1	0	0	0	13355	101	4	3	248	3	RHOQ	2	46803262	Missense_Mutation	SNP	A	TCGA-AL-7173-01A-11D-2136-08	43320159	46803262	196396111	5	4879											
SESTD1	91404	hgsc.bcm.edu	37	chr2	180016091	180016091	+	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	gcatggttctatataacgagTcaatttgttggcggacacta	11	13	10	7	2	2	0	1	0	1	0	2	2	2	1	0	3	1	3	0	3	5	7			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr2:180016091T>A	ENST00000428443.3	-	6	713	c.397A>T	c.(397-399)Act>Tct	p.T133S		NM_178123.4	NP_835224.3	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	133	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.						phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(3)	30			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)			ATATAACGAGTCAATTTGTTG	0.353																																					p.T133S		Atlas-SNP	.											.	SESTD1	66	.	0			c.A397T						PASS	.						71	70	70					2																	180016091		2203	4300	6503	SO:0001583	missense	91404	exon6			AACGAGTCAATTT	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.397A>T	chr2.hg19:g.180016091T>A	ENSP00000415332:p.Thr133Ser	46.0	0.0	.		41.0	17.0	.	NM_178123	Q53R38|Q53SP3|Q5GM69|Q8N6M1|Q96LQ2	Missense_Mutation	SNP	ENST00000428443.3	hg19	CCDS33338.1	.	.	.	.	.	.	.	.	.	.	T	15.75	2.926704	0.52759	.	.	ENSG00000187231	ENST00000428443;ENST00000440010;ENST00000435047	T;T;T	0.21734	1.99;1.99;1.99	5.68	5.68	0.88126	Cellular retinaldehyde-binding/triple function, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.26412	0.0645	N	0.05383	-0.06	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	T	0.26710	-1.0095	9	.	.	.	-17.9645	16.2237	0.82280	0.0:0.0:0.0:1.0	.	133	Q86VW0	SESD1_HUMAN	S	133	ENSP00000415332:T133S;ENSP00000416164:T133S;ENSP00000410286:T133S	.	T	-	1	0	SESTD1	179724336	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.962000	0.87912	2.289000	0.77006	0.482000	0.46254	ACT	.	.	.	none		0.353	SESTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335916.2	NM_178123		A	180016091	T	A	180016091	3	1	76	1	0	0	0	0	1	0	0	0	14140	1667	58	5	1745	5	SESTD1	2	180016091	Missense_Mutation	SNP	T	TCGA-AL-7173-01A-11D-2136-08	133212829	180016091	63183282	6	4880											
CUL3	8452	hgsc.bcm.edu	37	chr2	225422410	225422410	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttcggtaacaacttctcttAgtccagtgtagagcttttct	8	16	8	9	1	2	1	0	0	2	1	5	1	3	1	1	1	3	4	1	1	4	7			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr2:225422410A>G	ENST00000264414.4	-	2	568	c.230T>C	c.(229-231)cTa>cCa	p.L77P	CUL3_ENST00000344951.4_Intron|CUL3_ENST00000409096.1_Missense_Mutation_p.L53P|CUL3_ENST00000409777.1_Missense_Mutation_p.L53P|CUL3_ENST00000432260.2_5'UTR	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	77					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)		AACTTCTCTTAGTCCAGTGTA	0.333																																					p.L83P		Atlas-SNP	.											.	CUL3	96	.	0			c.T248C						PASS	.						84	86	85					2																	225422410		2202	4299	6501	SO:0001583	missense	8452	exon2			TCTCTTAGTCCAG	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.230T>C	chr2.hg19:g.225422410A>G	ENSP00000264414:p.Leu77Pro	35.0	0.0	.		53.0	16.0	.	NM_001257198	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Missense_Mutation	SNP	ENST00000264414.4	hg19	CCDS2462.1	.	.	.	.	.	.	.	.	.	.	A	19.94	3.920164	0.73098	.	.	ENSG00000036257	ENST00000264414;ENST00000409096;ENST00000409777	T;T;T	0.79940	-1.32;-1.32;-1.32	5.61	5.61	0.85477	Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	0.000000	0.64402	D	0.000001	D	0.92857	0.7728	H	0.96239	3.79	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74348	0.983;0.983	D	0.95014	0.8154	10	0.87932	D	0	.	15.8142	0.78586	1.0:0.0:0.0:0.0	.	55;77	Q53S54;Q13618	.;CUL3_HUMAN	P	77;53;53	ENSP00000264414:L77P;ENSP00000387200:L53P;ENSP00000386525:L53P	ENSP00000264414:L77P	L	-	2	0	CUL3	225130654	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.194000	0.94962	2.143000	0.66587	0.533000	0.62120	CTA	.	.	.	none		0.333	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2			G	225422410	A	G	225422410	3	3	76	1	0	0	0	0	1	0	0	0	4058	420	15	3	2136	3	CUL3	2	225422410	Missense_Mutation	SNP	A	TCGA-AL-7173-01A-11D-2136-08	45406319	225422410	17776963	7	4881											
CUL3	8452	hgsc.bcm.edu	37	chr2	225449722	225449722	+	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	ccgtgcctttgctcagattcGacatggtgctcgtcccctcc	4	12	9	16	3	1	1	1	0	0	1	5	2	3	1	5	1	3	2	5	1	0	2			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr2:225449722G>T	ENST00000264414.4	-	1	343	c.5C>A	c.(4-6)tCg>tAg	p.S2*	CUL3_ENST00000344951.4_Nonsense_Mutation_p.S2*	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	2					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)		GCTCAGATTCGACATGGTGCT	0.706																																					p.S2X		Atlas-SNP	.											.	CUL3	96	.	0			c.C5A						PASS	.						34	31	32					2																	225449722		2199	4300	6499	SO:0001587	stop_gained	8452	exon1			AGATTCGACATGG	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.5C>A	chr2.hg19:g.225449722G>T	ENSP00000264414:p.Ser2*	39.0	0.0	.		33.0	8.0	.	NM_003590	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Nonsense_Mutation	SNP	ENST00000264414.4	hg19	CCDS2462.1	.	.	.	.	.	.	.	.	.	.	G	40	8.107774	0.98657	.	.	ENSG00000036257	ENST00000264414;ENST00000344951	.	.	.	3.18	0.952	0.19584	.	0.432093	0.18593	U	0.136664	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.6371	0.45571	0.0:0.375:0.625:0.0	.	.	.	.	X	2	.	ENSP00000264414:S2X	S	-	2	0	CUL3	225157966	1.000000	0.71417	0.999000	0.59377	0.977000	0.68977	2.063000	0.41423	0.257000	0.21650	0.305000	0.20034	TCG	.	.	.	none		0.706	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2			T	225449722	G	T	225449722	4	4	76	1	0	0	0	0	0	1	0	0	4058	1059	37	4	2365	4	CUL3	2	225449722	Nonsense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08	27312	225449722	17749651	8	4882											
CRBN	51185	hgsc.bcm.edu	37	chr3	3209360	3209360	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttatatgaacattggtcttcTcttgagacaggttttgaagg	10	16	10	5	0	2	3	0	3	2	1	3	4	2	3	0	3	1	1	0	3	4	7			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr3:3209360T>C	ENST00000231948.4	-	5	667	c.645A>G	c.(643-645)agA>agG	p.R215R	CRBN_ENST00000432408.2_Silent_p.R214R	NM_016302.3	NP_057386.2	Q96SW2	CRBN_HUMAN	cereblon	215	Lon.				negative regulation of ion transmembrane transport (GO:0034766)|negative regulation of protein homooligomerization (GO:0032463)|positive regulation of protein homodimerization activity (GO:0090073)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP-dependent peptidase activity (GO:0004176)			endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	11				Epithelial(13;0.00244)|OV - Ovarian serous cystadenocarcinoma(96;0.00617)|all cancers(10;0.0079)	Lenalidomide(DB00480)|Pomalidomide(DB08910)|Thalidomide(DB01041)	ATTGGTCTTCTCTTGAGACAG	0.363																																					p.R215R		Atlas-SNP	.											.	CRBN	29	.	0			c.A645G						PASS	.						134	139	137					3																	3209360		2203	4300	6503	SO:0001819	synonymous_variant	51185	exon5			GTCTTCTCTTGAG	BC017419	CCDS2562.1, CCDS54547.1	3p26.3	2014-05-27			ENSG00000113851	ENSG00000113851			30185	protein-coding gene	gene with protein product		609262	"mental retardation, non-syndromic, autosomal recessive, 2A"	MRT2A		15557513	Standard	NM_016302		Approved	MRT2	uc003bpq.3	Q96SW2	OTTHUMG00000090261	ENST00000231948.4:c.645A>G	chr3.hg19:g.3209360T>C		171.0	0.0	.		155.0	13.0	.	NM_016302	B2R6H4|C9IZA9|C9JAH6|Q6AI62|Q6NVZ0|Q9UHW4	Silent	SNP	ENST00000231948.4	hg19	CCDS2562.1	.	.	.	.	.	.	.	.	.	.	C	10.22	1.290994	0.23564	.	.	ENSG00000113851	ENST00000424814;ENST00000450014	.	.	.	5.1	4.22	0.49857	.	.	.	.	.	T	0.57198	0.2037	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52049	-0.8627	4	.	.	.	-0.4216	6.8828	0.24183	0.1419:0.7141:0.0:0.144	.	.	.	.	G	211	.	.	E	-	2	0	CRBN	3184360	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.276000	0.43408	0.666000	0.31087	-0.119000	0.15052	GAG	.	.	.	none		0.363	CRBN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206579.3	NM_016302		C	3209360	T	C	3209360	2	2	76	1	0	0	0	0	0	0	0	1	3853	1548	54	3		3	CRBN	3	3209360	Silent	SNP	T	TCGA-AL-7173-01A-11D-2136-08		3209360	194813070	9	4883											
CAPN7	23473	hgsc.bcm.edu	37	chr3	15288291	15288291	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gattccttcaccatacacctTatcaaaacgggtgagaaaat	15	10	6	10	1	2	1	2	1	0	1	3	3	3	1	3	1	2	0	3	1	6	4			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr3:15288291T>C	ENST00000253693.2	+	18	2316	c.2063T>C	c.(2062-2064)tTa>tCa	p.L688S		NM_014296.2	NP_055111.1	Q9Y6W3	CAN7_HUMAN	calpain 7	688	Domain III.				positive regulation of epithelial cell migration (GO:0010634)|self proteolysis (GO:0097264)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|endopeptidase activity (GO:0004175)|MIT domain binding (GO:0090541)			breast(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|skin(2)	22						CCATACACCTTATCAAAACGG	0.284																																					p.L688S		Atlas-SNP	.											CAPN7,NS,carcinoma,0,1	CAPN7	63	.	0			c.T2063C						PASS	.						74	73	73					3																	15288291		2202	4300	6502	SO:0001583	missense	23473	exon18			ACACCTTATCAAA	AB028639	CCDS2624.1	3p24	2008-07-18			ENSG00000131375	ENSG00000131375			1484	protein-coding gene	gene with protein product	"calpain like protease", "homolog of Aspergillus Nidulans PALB"	606400				8163008, 10051333	Standard	NM_014296		Approved	PalBH	uc003bzn.3	Q9Y6W3	OTTHUMG00000129863	ENST00000253693.2:c.2063T>C	chr3.hg19:g.15288291T>C	ENSP00000253693:p.Leu688Ser	39.0	0.0	.		37.0	2.0	.	NM_014296		Missense_Mutation	SNP	ENST00000253693.2	hg19	CCDS2624.1	.	.	.	.	.	.	.	.	.	.	T	11.57	1.677192	0.29783	.	.	ENSG00000131375	ENST00000253693	D	0.86627	-2.15	5.48	5.48	0.80851	Peptidase C2, calpain, large subunit, domain III (1);Peptidase C2, calpain, domain III (1);	0.998190	0.08112	N	0.996014	D	0.82641	0.5081	L	0.29908	0.895	0.33618	D	0.604407	B	0.15141	0.012	B	0.15052	0.012	T	0.74097	-0.3775	10	0.25751	T	0.34	-1.9331	15.2344	0.73416	0.0:0.0:0.0:1.0	.	688	Q9Y6W3	CAN7_HUMAN	S	688	ENSP00000253693:L688S	ENSP00000253693:L688S	L	+	2	0	CAPN7	15263295	0.999000	0.42202	1.000000	0.80357	0.969000	0.65631	2.913000	0.48790	2.092000	0.63282	0.533000	0.62120	TTA	.	.	.	none		0.284	CAPN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252105.2	NM_014296		C	15288291	T	C	15288291	3	2	76	1	0	0	0	0	1	0	0	0	2633	1764	61	3	2133	3	CAPN7	3	15288291	Missense_Mutation	SNP	T	TCGA-AL-7173-01A-11D-2136-08	12078931	15288291	182734139	10	4884											
ACAD9	28976	hgsc.bcm.edu	37	chr3	128612493	128612493	+	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	ttgggctgcaagtcccagaaGaatatggtaagtcaagcaaa	15	8	11	7	0	1	2	1	0	0	2	2	2	2	2	1	2	2	4	1	2	7	3			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr3:128612493G>C	ENST00000308982.7	+	3	421	c.340G>C	c.(340-342)Gaa>Caa	p.E114Q		NM_014049.4	NP_054768.2	Q9H845	ACAD9_HUMAN	acyl-CoA dehydrogenase family, member 9	114						dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	30						AGTCCCAGAAGAATATGGTAA	0.448																																					p.E114Q		Atlas-SNP	.											ACAD9,NS,carcinoma,0,1	ACAD9	51	.	0			c.G340C						PASS	.						40	45	43					3																	128612493		2203	4300	6503	SO:0001583	missense	28976	exon3			CCAGAAGAATATG	AF078854	CCDS3053.1	3q21.3	2013-05-24	2010-04-30		ENSG00000177646	ENSG00000177646		"Mitochondrial respiratory chain complex assembly factors"	21497	protein-coding gene	gene with protein product		611103	"acyl-Coenzyme A dehydrogenase family, member 9"			12359260, 21057504, 20816094	Standard	NM_014049		Approved	NPD002, MGC14452	uc003ela.4	Q9H845	OTTHUMG00000159942	ENST00000308982.7:c.340G>C	chr3.hg19:g.128612493G>C	ENSP00000312618:p.Glu114Gln	43.0	0.0	.		40.0	2.0	.	NM_014049	D3DNB8|Q8WXX3	Missense_Mutation	SNP	ENST00000308982.7	hg19	CCDS3053.1	.	.	.	.	.	.	.	.	.	.	G	18.91	3.723058	0.68959	.	.	ENSG00000177646	ENST00000308982;ENST00000514336	D;D	0.99809	-6.86;-6.86	5.94	5.94	0.96194	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, N-terminal (1);Acyl-CoA dehydrogenase/oxidase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99124	0.9698	L	0.53249	1.67	0.80722	D	1	P	0.40970	0.734	B	0.37480	0.251	D	0.99909	1.1193	10	0.56958	D	0.05	.	17.8532	0.88754	0.0:0.0:1.0:0.0	.	114	Q9H845	ACAD9_HUMAN	Q	114;126	ENSP00000312618:E114Q;ENSP00000423758:E126Q	ENSP00000312618:E114Q	E	+	1	0	ACAD9	130095183	1.000000	0.71417	1.000000	0.80357	0.671000	0.39405	8.237000	0.89807	2.816000	0.96949	0.563000	0.77884	GAA	.	.	.	none		0.448	ACAD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358405.1	NM_014049		C	128612493	G	C	128612493	3	2	76	1	0	0	0	0	1	0	0	0	111	943	33	4	350	4	ACAD9	3	128612493	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08	113324202	128612493	69409937	11	4885											
COMMD2	51122	hgsc.bcm.edu	37	chr3	149468478	149468478	+	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	gctatacctgtacatctagtCgccattcaaggttatgataa	12	13	7	9	1	2	1	1	1	1	0	3	1	2	1	2	1	2	3	2	1	7	7			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr3:149468478C>T	ENST00000473414.1	-	4	443	c.389G>A	c.(388-390)cGa>cAa	p.R130Q		NM_016094.3	NP_057178.2	Q86X83	COMD2_HUMAN	COMM domain containing 2	130	COMM. {ECO:0000255|PROSITE- ProRule:PRU00602}.									NS(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)|urinary_tract(1)	9			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			TACATCTAGTCGCCATTCAAG	0.333																																					p.R130Q		Atlas-SNP	.											.	COMMD2	21	.	0			c.G389A						PASS	.						138	131	133					3																	149468478		2203	4300	6503	SO:0001583	missense	51122	exon4			TCTAGTCGCCATT	AY542158	CCDS3145.1	3q25.1	2004-02-20			ENSG00000114744	ENSG00000114744			24993	protein-coding gene	gene with protein product						15799966	Standard	NM_016094		Approved	HSPC042	uc003exj.2	Q86X83	OTTHUMG00000159616	ENST00000473414.1:c.389G>A	chr3.hg19:g.149468478C>T	ENSP00000419475:p.Arg130Gln	103.0	0.0	.		123.0	25.0	.	NM_016094	Q561V4|Q9H3L5|Q9Y5V1	Missense_Mutation	SNP	ENST00000473414.1	hg19	CCDS3145.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.480742	0.84747	.	.	ENSG00000114744	ENST00000473414	T	0.27104	1.69	5.36	4.49	0.54785	COMM domain (1);	0.000000	0.85682	D	0.000000	T	0.57858	0.2082	M	0.89715	3.055	0.58432	D	0.999991	D	0.89917	1.0	D	0.97110	1.0	T	0.68104	-0.5497	10	0.87932	D	0	-2.9867	13.9104	0.63864	0.0:0.9268:0.0:0.0732	.	130	Q86X83	COMD2_HUMAN	Q	130	ENSP00000419475:R130Q	ENSP00000419475:R130Q	R	-	2	0	COMMD2	150951168	1.000000	0.71417	0.996000	0.52242	0.823000	0.46562	6.402000	0.73260	1.397000	0.46682	0.650000	0.86243	CGA	.	.	.	none		0.333	COMMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356515.1	NM_016094		T	149468478	C	T	149468478	3	4	76	1	0	0	0	0	1	0	0	0	3718	884	31	1	218	1	COMMD2	3	149468478	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08	20855985	149468478	48553952	12	4886											
FAM194A	131831	hgsc.bcm.edu	37	chr3	150421569	150421569	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcctcctcctcctccacctcTtcctcctcctcctccacctc	2	13	0	26	0	1	0	0	0	1	0	12	0	11	0	12	0	0	0	12	0	0	1			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr3:150421569T>C	ENST00000295910.6	-	1	169	c.117A>G	c.(115-117)gaA>gaG	p.E39E	RP11-103G8.2_ENST00000475393.1_RNA|RP11-103G8.2_ENST00000471093.1_RNA|FAM194A_ENST00000491361.1_Intron	NM_152394.3	NP_689607.2												p.E39E(1)		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						cctccacctcttcctcctcct	0.627																																					p.E39E		Atlas-SNP	.											FAM194A,NS,carcinoma,0,2	FAM194A	91	.	1	Substitution - coding silent(1)	prostate(1)	c.A117G						PASS	.						92	78	83					3																	150421569		2203	4298	6501	SO:0001819	synonymous_variant	131831	exon1			CACCTCTTCCTCC																												ENST00000295910.6:c.117A>G	chr3.hg19:g.150421569T>C		22.0	1.0	.		20.0	3.0	.	NM_152394		Silent	SNP	ENST00000295910.6	hg19	CCDS3151.2																																																																																			.	.	.	none		0.627	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1			C	150421569	T	C	150421569	2	2	76	1	0	0	0	0	0	0	0	1	5530	1606	56	3		3	FAM194A	3	150421569	Silent	SNP	T	TCGA-AL-7173-01A-11D-2136-08	953091	150421569	47600861	13	4887											
FETUB	26998	hgsc.bcm.edu	37	chr3	186362554	186362554	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacagtttcaaaaaaaaagAtttacatgacgtgccctgac	17	9	6	9	1	1	3	1	2	0	1	1	3	1	3	1	0	3	1	1	0	6	3			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr3:186362554A>G	ENST00000265029.3	+	4	540	c.439A>G	c.(439-441)Att>Gtt	p.I147V	RP11-134F2.2_ENST00000428501.1_RNA|RP11-134F2.2_ENST00000455926.1_RNA|FETUB_ENST00000539949.1_5'UTR|FETUB_ENST00000382134.3_Missense_Mutation_p.I82V|FETUB_ENST00000488561.1_3'UTR|FETUB_ENST00000450521.1_Missense_Mutation_p.I147V|FETUB_ENST00000382136.3_Missense_Mutation_p.I110V	NM_014375.2	NP_055190.2	Q9UGM5	FETUB_HUMAN	fetuin B	147					binding of sperm to zona pellucida (GO:0007339)|negative regulation of endopeptidase activity (GO:0010951)|single fertilization (GO:0007338)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)			endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)	20	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0479)		AAAAAAAAAGATTTACATGAC	0.408																																					p.I147V		Atlas-SNP	.											.	FETUB	53	.	0			c.A439G						PASS	.						102	96	98					3																	186362554		2203	4300	6503	SO:0001583	missense	26998	exon4			AAAAAGATTTACA	AJ242928	CCDS3279.1	3q27.3	2008-05-15			ENSG00000090512	ENSG00000090512			3658	protein-coding gene	gene with protein product		605954				10947975	Standard	XM_005247350		Approved		uc003fqn.3	Q9UGM5	OTTHUMG00000156586	ENST00000265029.3:c.439A>G	chr3.hg19:g.186362554A>G	ENSP00000265029:p.Ile147Val	156.0	0.0	.		106.0	27.0	.	NM_014375	B2RCW6|E9PG06|Q1RMZ0|Q5J876|Q6DK58|Q6GRB6|Q9Y6Z0	Missense_Mutation	SNP	ENST00000265029.3	hg19	CCDS3279.1	.	.	.	.	.	.	.	.	.	.	A	5.125	0.208699	0.09757	.	.	ENSG00000090512	ENST00000450521;ENST00000265029;ENST00000382134;ENST00000382136	T;T;T;T	0.39406	3.17;3.17;1.08;3.14	5.29	-0.0385	0.13880	Proteinase inhibitor I25C, fetuin, conserved site (1);	0.418485	0.23250	N	0.050254	T	0.22085	0.0532	N	0.21583	0.68	0.19300	N	0.999976	B;B;B	0.13145	0.002;0.007;0.007	B;B;B	0.13407	0.004;0.009;0.004	T	0.11227	-1.0596	10	0.27785	T	0.31	-2.9015	4.6541	0.12610	0.592:0.1544:0.2537:0.0	.	110;82;147	E9PG06;E9PG08;Q9UGM5	.;.;FETUB_HUMAN	V	147;147;82;110	ENSP00000404288:I147V;ENSP00000265029:I147V;ENSP00000371569:I82V;ENSP00000371571:I110V	ENSP00000265029:I147V	I	+	1	0	FETUB	187845248	0.004000	0.15560	0.000000	0.03702	0.001000	0.01503	0.250000	0.18235	-0.155000	0.11098	-0.274000	0.10170	ATT	.	.	.	none		0.408	FETUB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344679.1	NM_014375		G	186362554	A	G	186362554	3	3	76	1	0	0	0	0	1	0	0	0	5828	333	12	3	453	3	FETUB	3	186362554	Missense_Mutation	SNP	A	TCGA-AL-7173-01A-11D-2136-08	35940985	186362554	11659876	14	4888											
ST6GAL1	6480	hgsc.bcm.edu	37	chr3	186790685	186790685	+	Frame_Shift_Del	DEL	G	G	-																															aagacagtttgtacaatgaaGgaatcctaattgtatgggac																										TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr3:186790685delG	ENST00000169298.3	+	6	1428	c.754delG	c.(754-756)ggafs	p.G252fs	ST6GAL1_ENST00000448044.1_Frame_Shift_Del_p.G252fs|ST6GAL1_ENST00000457772.2_Frame_Shift_Del_p.G21fs	NM_173216.2	NP_775323.1	P15907	SIAT1_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 1	252					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)		GTACAATGAAGGAATCCTAAT	0.433																																					p.E251fs		Atlas-INDEL	.											.	ST6GAL1	36	.	0			c.753delA						PASS	.						142	139	140					3																	186790685		2203	4300	6503	SO:0001589	frameshift_variant	6480	exon5			.	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.754delG	chr3.hg19:g.186790685delG	ENSP00000169298:p.Gly252fs	145.0	0.0	0		142.0	29.0	0.204225	NM_003032	A8KA14|B2R513|D3DNV3	Frame_Shift_Del	DEL	ENST00000169298.3	hg19	CCDS3285.1																																																																																			.	.	.	none		0.433	ST6GAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344399.1	NM_173216		-	186790685	G	-	186790685	7	5	76	1	0	1	0	1	0	0	0	0	15233	1001	35	0	764	0	ST6GAL1	3	186790685	Frame_Shift_Del	DEL	G	TCGA-AL-7173-01A-11D-2136-08	428131	186790685	11231745	15	4889											
EGF	1950	hgsc.bcm.edu	37	chr4	110865158	110865158	+	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	ttcagtacaacagagaaggaAgcaattctcttatttgctcc	13	12	7	9	0	2	1	1	0	1	1	4	3	3	2	1	1	4	3	1	1	6	5			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr4:110865158A>T	ENST00000265171.5	+	4	1115	c.670A>T	c.(670-672)Agc>Tgc	p.S224C	EGF_ENST00000509793.1_Missense_Mutation_p.S224C|EGF_ENST00000503392.1_Missense_Mutation_p.S224C	NM_001178130.1|NM_001963.4	NP_001171601.1|NP_001954.2	P01133	EGF_HUMAN	epidermal growth factor	224					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)	CAGAGAAGGAAGCAATTCTCT	0.388																																					p.S224C		Atlas-SNP	.											.	EGF	113	.	0			c.A670T						PASS	.						140	143	142					4																	110865158		2203	4300	6503	SO:0001583	missense	1950	exon4			GAAGGAAGCAATT	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.670A>T	chr4.hg19:g.110865158A>T	ENSP00000265171:p.Ser224Cys	75.0	0.0	.		70.0	20.0	.	NM_001963	B4DRK7|E7EVD2|E9PBF0|Q52LZ6	Missense_Mutation	SNP	ENST00000265171.5	hg19	CCDS3689.1	.	.	.	.	.	.	.	.	.	.	A	17.66	3.444933	0.63178	.	.	ENSG00000138798	ENST00000509793;ENST00000265171;ENST00000503392	D;D;D	0.91464	-2.85;-2.85;-2.85	5.71	-0.638	0.11500	Six-bladed beta-propeller, TolB-like (1);	0.594017	0.19957	N	0.102292	D	0.91019	0.7175	L	0.57536	1.79	0.09310	N	1	D;D;D	0.64830	0.99;0.994;0.983	P;P;P	0.55999	0.619;0.789;0.619	D	0.85276	0.1059	10	0.72032	D	0.01	.	11.2107	0.48797	0.3476:0.0:0.6524:0.0	.	224;224;224	E7EVD2;P01133-2;P01133	.;.;EGF_HUMAN	C	224	ENSP00000424316:S224C;ENSP00000265171:S224C;ENSP00000421384:S224C	ENSP00000265171:S224C	S	+	1	0	EGF	111084607	0.211000	0.23529	0.001000	0.08648	0.160000	0.22226	0.879000	0.28146	-0.085000	0.12573	0.533000	0.62120	AGC	.	.	.	none		0.388	EGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255065.1			T	110865158	A	T	110865158	3	4	76	1	0	0	0	0	1	0	0	0	4964	72	3	5	684	5	EGF	4	110865158	Missense_Mutation	SNP	A	TCGA-AL-7173-01A-11D-2136-08		110865158	80289118	16	4890											
MND1	84057	hgsc.bcm.edu	37	chr4	154330168	154330168	+	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	agctgctaacagatggactgGtatgtactataataatgctg	13	12	10	6	0	0	1	0	0	0	1	0	2	0	2	0	2	5	5	0	2	6	6			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr4:154330168G>C	ENST00000504860.1	+	6	510	c.467G>C	c.(466-468)gGt>gCt	p.G156A	MND1_ENST00000240488.3_Splice_Site					meiotic nuclear divisions 1 homolog (S. cerevisiae)											large_intestine(2)|lung(1)	3	all_hematologic(180;0.093)					AGATGGACTGGTATGTACTAT	0.299																																					.		Atlas-SNP	.											MND1,colon,carcinoma,0,1	MND1	18	.	0			c.511+1G>C						PASS	.						88	88	88					4																	154330168		2203	4300	6503	SO:0001583	missense	84057	exon7			GGACTGGTATGTA	AY028916	CCDS3782.1, CCDS75202.1	4q31.3	2008-02-05			ENSG00000121211	ENSG00000121211			24839	protein-coding gene	gene with protein product		611422				11940665	Standard	NM_032117		Approved	GAJ	uc003ink.2	Q9BWT6	OTTHUMG00000161523	ENST00000504860.1:c.467G>C	chr4.hg19:g.154330168G>C	ENSP00000422933:p.Gly156Ala	44.0	0.0	.		46.0	2.0	.	NM_032117		Splice_Site	SNP	ENST00000504860.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.71|17.71	3.455955|3.455955	0.63401|0.63401	.|.	.|.	ENSG00000121211|ENSG00000121211	ENST00000240488|ENST00000504860	.|.	.|.	.|.	5.18|5.18	5.18|5.18	0.71444|0.71444	.|.	.|.	.|.	.|.	.|.	.|T	.|0.67316	.|0.2880	.|.	.|.	.|.	0.32963|0.32963	D|D	0.521356|0.521356	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.72577	.|-0.4251	.|4	.|.	.|.	.|.	.|-14.8667	17.8243|17.8243	0.88660|0.88660	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	.|A	-1|156	.|.	.|.	.|G	+|+	.|2	.|0	MND1|MND1	154549618|154549618	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.947000|0.947000	0.59692|0.59692	6.338000|6.338000	0.72963|0.72963	2.576000|2.576000	0.86940|0.86940	0.591000|0.591000	0.81541|0.81541	.|GGT	.	.	.	none		0.299	MND1-002	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365195.1	NM_032117		C	154330168	G	C	154330168	3	2	76	1	0	0	0	0	1	0	0	0	9682	1275	44	4	538	4	MND1	4	154330168	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08	43465010	154330168	36824108	17	4891											
C5orf42	65250	hgsc.bcm.edu	37	chr5	37187887	37187887	+	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	gatattgcctgcaactatagGataacttatcacggacatgc	13	11	8	9	1	1	0	1	0	0	0	1	3	1	2	1	2	5	1	1	2	6	6			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr5:37187887G>C	ENST00000508244.1	-	21	3962	c.3869C>G	c.(3868-3870)tCc>tGc	p.S1290C	C5orf42_ENST00000425232.2_Missense_Mutation_p.S1290C|C5orf42_ENST00000274258.7_Missense_Mutation_p.S171C			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	1290						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)			GCAACTATAGGATAACTTATC	0.373																																					p.S1290C		Atlas-SNP	.											.	C5orf42	422	.	0			c.C3869G						PASS	.						109	102	104					5																	37187887		2203	4300	6503	SO:0001583	missense	65250	exon22			CTATAGGATAACT		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.3869C>G	chr5.hg19:g.37187887G>C	ENSP00000421690:p.Ser1290Cys	56.0	0.0	.		26.0	5.0	.	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	hg19	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	G	19.65	3.867793	0.72065	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28	5.49	5.49	0.81192	.	0.080123	0.49305	D	0.000159	T	0.75228	0.3821	L	0.29908	0.895	0.46701	D	0.999167	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.991	T	0.77525	-0.2555	10	0.87932	D	0	.	19.7365	0.96208	0.0:0.0:1.0:0.0	.	1290;171	E9PH94;Q9H799	.;CE042_HUMAN	C	1290;1290;171;338;171	ENSP00000421690:S1290C;ENSP00000389014:S1290C;ENSP00000274258:S171C;ENSP00000424223:S338C	ENSP00000274258:S171C	S	-	2	0	C5orf42	37223644	1.000000	0.71417	0.982000	0.44146	0.176000	0.22953	8.290000	0.89925	2.749000	0.94314	0.491000	0.48974	TCC	.	.	.	none		0.373	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		C	37187887	G	C	37187887	3	2	76	1	0	0	0	0	1	0	0	0	2303	1174	41	4	5848	4	C5orf42	5	37187887	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08		37187887	143727373	18	4892											
C7	730	hgsc.bcm.edu	37	chr5	40964972	40964972	+	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	ttgttggggaaatgcattgtCagagtgagtggcgtcagttg	8	13	16	4	1	2	2	2	1	0	1	2	3	2	3	0	3	1	3	0	3	1	4			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr5:40964972C>G	ENST00000313164.9	+	14	2238	c.1879C>G	c.(1879-1881)Cag>Gag	p.Q627E		NM_000587.2	NP_000578.2	P10643	CO7_HUMAN	complement component 7	627	CCP 2.|Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				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)				AATGCATTGTCAGAGTGAGTG	0.403																																					p.Q627E		Atlas-SNP	.											.	C7	136	.	0			c.C1879G						PASS	.						147	147	147					5																	40964972		1988	4163	6151	SO:0001583	missense	730	exon14			CATTGTCAGAGTG	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.1879C>G	chr5.hg19:g.40964972C>G	ENSP00000322061:p.Gln627Glu	180.0	0.0	.		159.0	8.0	.	NM_000587	Q6P3T5|Q92489	Missense_Mutation	SNP	ENST00000313164.9	hg19	CCDS47201.1	.	.	.	.	.	.	.	.	.	.	C	17.08	3.296653	0.60086	.	.	ENSG00000112936	ENST00000313164;ENST00000440677	T	0.44881	0.91	6.04	6.04	0.98038	Complement control module (2);Sushi/SCR/CCP (1);	0.184818	0.47455	D	0.000226	T	0.36276	0.0961	L	0.32530	0.975	0.49687	D	0.999811	P	0.46395	0.877	B	0.37480	0.251	T	0.21690	-1.0238	10	0.56958	D	0.05	-8.4484	20.5948	0.99439	0.0:1.0:0.0:0.0	.	627	P10643	CO7_HUMAN	E	627;467	ENSP00000322061:Q627E	ENSP00000322061:Q627E	Q	+	1	0	C7	41000729	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	2.443000	0.44881	2.873000	0.98535	0.563000	0.77884	CAG	.	.	.	none		0.403	C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317680.1			G	40964972	C	G	40964972	3	3	76	1	0	0	0	0	1	0	0	0	2377	827	29	4	1933	4	C7	5	40964972	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08	3777085	40964972	139950288	19	4893											
ITGA1	3672	hgsc.bcm.edu	37	chr5	52204750	52204750	+	Frame_Shift_Del	DEL	T	T	-																															tggttcctactttggcagtaTtttaacaacaactgacattg																										TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr5:52204750delT	ENST00000282588.6	+	13	1936	c.1478delT	c.(1477-1479)attfs	p.I493fs		NM_181501.1	NP_852478.1	P56199	ITA1_HUMAN	integrin, alpha 1	493					activation of MAPK activity (GO:0000187)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular extravasation (GO:0045123)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neutrophil chemotaxis (GO:0030593)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|vasodilation (GO:0042311)	acrosomal vesicle (GO:0001669)|basal part of cell (GO:0045178)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha1-beta1 complex (GO:0034665)|integrin complex (GO:0008305)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|protein phosphatase binding (GO:0019903)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(19)|ovary(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				TTTGGCAGTATTTTAACAACA	0.383																																					p.I493fs		Atlas-INDEL	.											.	ITGA1	112	.	0			c.1477delA						PASS	.						154	149	151					5																	52204750		2203	4300	6503	SO:0001589	frameshift_variant	3672	exon13			.	X68742	CCDS3955.1	5q11.1	2010-03-23			ENSG00000213949	ENSG00000213949		"CD molecules", "Integrins"	6134	protein-coding gene	gene with protein product		192968				8428973, 11937138	Standard	NM_181501		Approved	VLA1, CD49a	uc003jou.3	P56199	OTTHUMG00000131163	ENST00000282588.6:c.1478delT	chr5.hg19:g.52204750delT	ENSP00000282588:p.Ile493fs	168.0	0.0	0		145.0	31.0	0.213793	NM_181501	B2RNU0	Frame_Shift_Del	DEL	ENST00000282588.6	hg19	CCDS3955.1																																																																																			.	.	.	none		0.383	ITGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253855.3	NM_181501		-	52204750	T	-	52204750	7	5	76	1	0	1	0	1	0	0	0	0	7879	1493	52	0	1528	0	ITGA1	5	52204750	Frame_Shift_Del	DEL	T	TCGA-AL-7173-01A-11D-2136-08	11239778	52204750	128710510	20	4894											
LARS	51520	hgsc.bcm.edu	37	chr5	145552256	145552256	+	Frame_Shift_Del	DEL	T	T	-																															tagggaaacattacctcacaTttggataaagaaaacgtgtg																										TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr5:145552256delT	ENST00000394434.2	-	3	373	c.207delA	c.(205-207)aaafs	p.K69fs	LARS_ENST00000274562.9_Frame_Shift_Del_p.K69fs|LARS_ENST00000510191.1_Frame_Shift_Del_p.K15fs|LARS_ENST00000545646.1_Frame_Shift_Del_p.K69fs|LARS_ENST00000511505.1_5'UTR	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	69					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)	TTACCTCACATTTGGATAAAG	0.353																																					p.C70fs		Atlas-INDEL	.											.	LARS	100	.	0			c.208delT						PASS	.						94	87	90					5																	145552256		2203	4300	6503	SO:0001589	frameshift_variant	51520	exon3			.	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.207delA	chr5.hg19:g.145552256delT	ENSP00000377954:p.Lys69fs	48.0	0.0	0		62.0	23.0	0.370968	NM_020117	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	Frame_Shift_Del	DEL	ENST00000394434.2	hg19	CCDS34265.1																																																																																			.	.	.	none		0.353	LARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000373367.1	NM_020117		-	145552256	T	-	145552256	7	5	76	1	0	1	0	1	0	0	0	0	8641	1490	52	0	3443	0	LARS	5	145552256	Frame_Shift_Del	DEL	T	TCGA-AL-7173-01A-11D-2136-08	93347506	145552256	35363004	21	4895											
SPINK5	11005	hgsc.bcm.edu	37	chr5	147510840	147510840	+	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	aggattctgagatgtgcaaaGactaccgagtattgcccagg	12	9	12	8	1	1	2	0	1	1	2	1	5	1	3	2	2	3	2	2	2	3	4			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr5:147510840G>C	ENST00000256084.7	+	31	3025	c.2983G>C	c.(2983-2985)Gac>Cac	p.D995H	SPINK5_ENST00000359874.3_Missense_Mutation_p.D1025H	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	995	Kazal-like 15. {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)			GATGTGCAAAGACTACCGAGT	0.433																																					p.D1025H		Atlas-SNP	.											.	SPINK5	245	.	0			c.G3073C						PASS	.						250	232	238					5																	147510840		1894	4123	6017	SO:0001583	missense	11005	exon32			TGCAAAGACTACC	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.2983G>C	chr5.hg19:g.147510840G>C	ENSP00000256084:p.Asp995His	276.0	0.0	.		239.0	44.0	.	NM_001127698	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	hg19	CCDS43382.1	.	.	.	.	.	.	.	.	.	.	G	4.580	0.107817	0.08780	.	.	ENSG00000133710	ENST00000359874;ENST00000256084	T;T	0.75367	-0.93;-0.93	4.69	0.694	0.18062	Proteinase inhibitor I1, Kazal (1);	0.707951	0.13366	N	0.393281	T	0.44180	0.1281	N	0.02539	-0.55	0.24542	N	0.994066	B;B	0.10296	0.003;0.0	B;B	0.09377	0.003;0.004	T	0.29274	-1.0017	10	0.22109	T	0.4	-0.8408	7.0127	0.24871	0.2944:0.3745:0.3311:0.0	.	1025;995	Q9NQ38-3;Q9NQ38	.;ISK5_HUMAN	H	1025;995	ENSP00000352936:D1025H;ENSP00000256084:D995H	ENSP00000256084:D995H	D	+	1	0	SPINK5	147491033	0.961000	0.32948	0.962000	0.40283	0.816000	0.46133	-0.005000	0.12855	-0.016000	0.14127	-0.136000	0.14681	GAC	.	.	.	none		0.433	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698		C	147510840	G	C	147510840	3	2	76	1	0	0	0	0	1	0	0	0	15074	942	33	4	3211	4	SPINK5	5	147510840	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08	1958584	147510840	33404420	22	4896											
SERPINB9	5272	hgsc.bcm.edu	37	chr6	2890546	2890546	+	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	gctcgacgctgccgctgcctCggtgccttcttcattcacct	3	12	9	17	4	3	0	2	0	1	0	5	1	3	0	4	1	3	3	4	1	0	3	rs375600576		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr6:2890546C>A	ENST00000380698.4	-	7	1071	c.982G>T	c.(982-984)Gag>Tag	p.E328*		NM_004155.5	NP_004146.1	P50453	SPB9_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 9	328					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)				GCCGCTGCCTCGGTGCCTTCT	0.547																																					p.E328X		Atlas-SNP	.											.	SERPINB9	37	.	0			c.G982T						PASS	.						104	92	96					6																	2890546		2203	4300	6503	SO:0001587	stop_gained	5272	exon7			CTGCCTCGGTGCC	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.982G>T	chr6.hg19:g.2890546C>A	ENSP00000370074:p.Glu328*	91.0	0.0	.		125.0	10.0	.	NM_004155	B2RBW3|Q5TD03	Nonsense_Mutation	SNP	ENST00000380698.4	hg19	CCDS4478.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.487921	0.84854	.	.	ENSG00000170542	ENST00000380698	.	.	.	4.66	4.66	0.58398	.	0.045448	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	17.4207	0.87514	0.0:1.0:0.0:0.0	.	.	.	.	X	328	.	ENSP00000370074:E328X	E	-	1	0	SERPINB9	2835545	1.000000	0.71417	0.695000	0.30226	0.086000	0.17979	5.692000	0.68256	2.502000	0.84385	0.655000	0.94253	GAG	.	.	.	alt		0.547	SERPINB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039656.1			A	2890546	C	A	2890546	4	1	76	1	0	0	0	0	0	1	0	0	14121	893	31	4	152	4	SERPINB9	6	2890546	Nonsense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08		2890546	168224521	23	4897											
HOXA1	3198	hgsc.bcm.edu	37	chr7	27134334	27134334	+	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	gttgaagtggaactccttctCcagttccgtgagctgcttgg	6	13	12	10	1	1	2	0	2	1	0	4	3	3	3	3	2	3	4	3	2	2	4			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr7:27134334C>T	ENST00000343060.4	-	2	794	c.733G>A	c.(733-735)Gag>Aag	p.E245K	HOTAIRM1_ENST00000425358.2_RNA|HOTAIRM1_ENST00000495032.1_RNA|HOTAIRM1_ENST00000429611.3_RNA|HOXA1_ENST00000355633.5_3'UTR|HOTAIRM1_ENST00000434063.3_RNA	NM_005522.4	NP_005513	P49639	HXA1_HUMAN	homeobox A1	245					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						AACTCCTTCTCCAGTTCCGTG	0.582																																					p.E245K		Atlas-SNP	.											.	HOXA1	64	.	0			c.G733A						PASS	.						120	109	113					7																	27134334		2203	4300	6503	SO:0001583	missense	3198	exon2			CCTTCTCCAGTTC		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.733G>A	chr7.hg19:g.27134334C>T	ENSP00000343246:p.Glu245Lys	155.0	0.0	.		205.0	46.0	.	NM_005522	A4D184|B2R8U7|O43363	Missense_Mutation	SNP	ENST00000343060.4	hg19	CCDS5401.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.901126	0.92035	.	.	ENSG00000105991	ENST00000343060	D	0.97575	-4.44	5.31	5.31	0.75309	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.046170	0.85682	D	0.000000	D	0.98848	0.9611	M	0.92317	3.295	0.80722	D	1	D	0.69078	0.997	D	0.80764	0.994	D	0.99686	1.1000	10	0.87932	D	0	.	18.98	0.92752	0.0:1.0:0.0:0.0	.	245	P49639	HXA1_HUMAN	K	245	ENSP00000343246:E245K	ENSP00000343246:E245K	E	-	1	0	HOXA1	27100859	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.770000	0.85390	2.495000	0.84180	0.655000	0.94253	GAG	.	.	.	none		0.582	HOXA1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358454.1			T	27134334	C	T	27134334	3	4	76	1	0	0	0	0	1	0	0	0	7295	864	30	2	278	2	HOXA1	7	27134334	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08		27134334	132004329	24	4898											
MAGI2	9863	hgsc.bcm.edu	37	chr7	78131031	78131031	+	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	agctcctcaggctgactgtaCactggtgcaggataaggctg	9	9	13	10	0	1	1	1	1	0	0	2	2	2	2	1	4	3	5	1	4	2	2			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr7:78131031C>A	ENST00000354212.4	-	5	1081	c.828G>T	c.(826-828)gtG>gtT	p.V276V	MAGI2_ENST00000419488.1_Silent_p.V276V|MAGI2_ENST00000535697.1_Silent_p.V113V|MAGI2_ENST00000522391.1_Silent_p.V276V|MAGI2_ENST00000536571.1_Silent_p.V108V	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	276	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)			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)				GCTGACTGTACACTGGTGCAG	0.493																																					p.V276V		Atlas-SNP	.											.	MAGI2	246	.	0			c.G828T						PASS	.						233	184	201					7																	78131031		2203	4300	6503	SO:0001819	synonymous_variant	9863	exon5			ACTGTACACTGGT	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.828G>T	chr7.hg19:g.78131031C>A		77.0	0.0	.		105.0	22.0	.	NM_012301	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Silent	SNP	ENST00000354212.4	hg19	CCDS5594.1																																																																																			.	.	.	none		0.493	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		A	78131031	C	A	78131031	2	1	76	1	0	0	0	0	0	0	0	1	9198	465	17	4		4	MAGI2	7	78131031	Silent	SNP	C	TCGA-AL-7173-01A-11D-2136-08	50996697	78131031	81007632	25	4899											
PCLO	27445	hgsc.bcm.edu	37	chr7	82763823	82763823	+	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	tgttctttttactgttggagCttgttcagctttgggctcta	4	20	10	7	0	3	0	1	0	2	0	3	1	3	1	0	2	3	6	0	2	2	9			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr7:82763823C>G	ENST00000333891.9	-	3	3380	c.3043G>C	c.(3043-3045)Gct>Cct	p.A1015P	PCLO_ENST00000423517.2_Missense_Mutation_p.A1015P	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						ACTGTTGGAGCTTGTTCAGCT	0.428																																					p.A1015P		Atlas-SNP	.											.	PCLO	1506	.	0			c.G3043C						PASS	.						87	84	85					7																	82763823		1833	4087	5920	SO:0001583	missense	27445	exon3			TTGGAGCTTGTTC	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.3043G>C	chr7.hg19:g.82763823C>G	ENSP00000334319:p.Ala1015Pro	60.0	0.0	.		57.0	16.0	.	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	7.239	0.600956	0.13939	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.76839	-1.05;-1.05	6.07	2.21	0.28008	.	.	.	.	.	T	0.66626	0.2808	L	0.36672	1.1	0.09310	N	0.999994	B;B	0.12630	0.006;0.006	B;B	0.10450	0.005;0.005	T	0.57659	-0.7773	9	0.87932	D	0	.	6.642	0.22914	0.1221:0.6245:0.0:0.2534	.	1015;1015	Q9Y6V0-5;Q9Y6V0-6	.;.	P	961;1015;1015	ENSP00000334319:A1015P;ENSP00000388393:A1015P	ENSP00000334319:A1015P	A	-	1	0	PCLO	82601759	0.000000	0.05858	0.011000	0.14972	0.864000	0.49448	0.079000	0.14782	0.126000	0.18424	-0.136000	0.14681	GCT	.	.	.	none		0.428	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		G	82763823	C	G	82763823	3	3	76	1	0	0	0	0	1	0	0	0	11590	797	28	4	12494	4	PCLO	7	82763823	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08	4632792	82763823	76374840	26	4900											
CYP3A7	1551	hgsc.bcm.edu	37	chr7	99328744	99328744	+	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	gggccctggaattccaagctTcttaaaaagtccatgtgtac	11	11	9	10	0	1	0	0	0	1	0	3	1	3	1	3	2	2	2	3	2	6	4			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr7:99328744T>A	ENST00000336374.2	-	2	105	c.103A>T	c.(103-105)Aag>Tag	p.K35*		NM_000765.3	NP_000756.2	P24462	CP3A7_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 7	35					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)	ATTCCAAGCTTCTTAAAAAGT	0.423																																					p.K35X		Atlas-SNP	.											.	CYP3A7	59	.	0			c.A103T						PASS	.						105	98	100					7																	99328744		2203	4300	6503	SO:0001587	stop_gained	1551	exon2			CAAGCTTCTTAAA	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.103A>T	chr7.hg19:g.99328744T>A	ENSP00000337450:p.Lys35*	104.0	0.0	.		152.0	56.0	.	NM_000765	A4D288|Q9H241	Nonsense_Mutation	SNP	ENST00000336374.2	hg19	CCDS5673.1	.	.	.	.	.	.	.	.	.	.	T	11.23	1.576557	0.28092	.	.	ENSG00000160870	ENST00000292414;ENST00000336374	.	.	.	3.52	3.52	0.40303	.	0.100727	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.5745	0.33590	0.0:0.0:0.0:1.0	.	.	.	.	X	35	.	ENSP00000292414:K35X	K	-	1	0	CYP3A7	99166680	1.000000	0.71417	0.974000	0.42286	0.205000	0.24178	4.328000	0.59253	1.598000	0.50083	0.418000	0.28097	AAG	.	.	.	none		0.423	CYP3A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345484.1			A	99328744	T	A	99328744	4	1	76	1	0	0	0	0	0	1	0	0	4183	1792	62	5	1456	5	CYP3A7	7	99328744	Nonsense_Mutation	SNP	T	TCGA-AL-7173-01A-11D-2136-08	16564921	99328744	59809919	27	4901											
CUX1	1523	hgsc.bcm.edu	37	chr7	101845410	101845410	+	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	acatgtaccaggaggtggacAccatcgagctcacccggcag	11	5	12	13	2	1	0	1	0	0	0	2	3	1	2	3	4	2	3	3	4	1	1			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr7:101845410A>T	ENST00000292535.7	+	18	2871	c.2833A>T	c.(2833-2835)Acc>Tcc	p.T945S	CUX1_ENST00000360264.3_Missense_Mutation_p.T956S|CUX1_ENST00000546411.2_Missense_Mutation_p.T843S|CUX1_ENST00000549414.2_Missense_Mutation_p.T923S|CUX1_ENST00000550008.2_Missense_Mutation_p.T889S|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000556210.1_Missense_Mutation_p.T787S|CUX1_ENST00000292538.4_Intron|CUX1_ENST00000560541.1_Intron|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000437600.4_Intron	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	945					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						GGAGGTGGACACCATCGAGCT	0.612																																					p.T956S		Atlas-SNP	.											.	CUX1	253	.	0			c.A2866T						PASS	.						111	113	112					7																	101845410		2203	4300	6503	SO:0001583	missense	1523	exon18			GTGGACACCATCG	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.2833A>T	chr7.hg19:g.101845410A>T	ENSP00000292535:p.Thr945Ser	172.0	0.0	.		230.0	78.0	.	NM_001202543	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000292535.7	hg19	CCDS5721.1	.	.	.	.	.	.	.	.	.	.	A	33	5.209946	0.95069	.	.	ENSG00000257923	ENST00000360264;ENST00000292535;ENST00000549414;ENST00000550008;ENST00000546411;ENST00000556210	T;T;T;T;T;T	0.79845	-1.28;-1.28;-1.3;-1.31;-1.22;-1.23	5.29	5.29	0.74685	Homeodomain protein CUT (2);Lambda repressor-like, DNA-binding (2);	0.132166	0.51477	D	0.000092	D	0.89511	0.6736	M	0.82056	2.57	0.80722	D	1	D;D	0.71674	0.992;0.998	D;D	0.80764	0.987;0.994	D	0.90018	0.4126	10	0.48119	T	0.1	-33.7771	15.2336	0.73411	1.0:0.0:0.0:0.0	.	945;956	P39880;P39880-3	CUX1_HUMAN;.	S	956;945;923;889;843;787	ENSP00000353401:T956S;ENSP00000292535:T945S;ENSP00000446630:T923S;ENSP00000447373:T889S;ENSP00000450125:T843S;ENSP00000451558:T787S	ENSP00000292535:T945S	T	+	1	0	CUX1	101632130	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.010000	0.58986	0.533000	0.62120	ACC	.	.	.	none		0.612	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913		T	101845410	A	T	101845410	3	4	76	1	0	0	0	0	1	0	0	0	4066	159	6	5	2970	5	CUX1	7	101845410	Missense_Mutation	SNP	A	TCGA-AL-7173-01A-11D-2136-08	2516666	101845410	57293253	28	4902											
MET	4233	hgsc.bcm.edu	37	chr7	116417463	116417463	+	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	ggcattttggttgtgtatatCatgggactttgttggacaat	8	17	12	4	0	1	0	1	0	0	0	1	2	1	2	0	4	0	4	0	4	3	7	rs121913244		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr7:116417463C>T	ENST00000318493.6	+	16	3521	c.3334C>T	c.(3334-3336)Cat>Tat	p.H1112Y	MET_ENST00000397752.3_Missense_Mutation_p.H1094Y|MET_ENST00000539704.1_5'UTR			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.H1112Y(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)			TTGTGTATATCATGGGACTTT	0.343			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.H1112Y		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,colon,carcinoma,0,2	MET	412	.	1	Substitution - Missense(1)	kidney(1)	c.C3334T	GRCh37	CM993668	MET	M	rs121913244	PASS	.						188	175	179					7																	116417463		1832	4086	5918	SO:0001583	missense	4233	exon16	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	GTATATCATGGGA	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.3334C>T	chr7.hg19:g.116417463C>T	ENSP00000317272:p.His1112Tyr	161.0	0.0	.		181.0	62.0	.	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.615896	0.87359	.	.	ENSG00000105976	ENST00000397752;ENST00000318493	T;T	0.33654	1.4;1.4	5.29	5.29	0.74685	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	0.43919	0.1269	N	0.11364	0.135	0.80722	D	1	P;D	0.89917	0.937;1.0	P;D	0.91635	0.854;0.999	T	0.52711	-0.8539	10	0.51188	T	0.08	-16.8984	19.2953	0.94119	0.0:1.0:0.0:0.0	.	1112;1094	P08581-2;P08581	.;MET_HUMAN	Y	1094;1112	ENSP00000380860:H1094Y;ENSP00000317272:H1112Y	ENSP00000317272:H1112Y	H	+	1	0	MET	116204699	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.776000	0.85560	2.628000	0.89032	0.655000	0.94253	CAT	.	.	.	weak		0.343	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			T	116417463	C	T	116417463	3	4	76	1	0	0	0	0	1	0	0	0	9492	826	29	2	3392	2	MET	7	116417463	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08	14572053	116417463	42721200	29	4903											
C7orf55	154791	hgsc.bcm.edu	37	chr7	139030365	139030365	+	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	acatcaggaatttcatggcaAgggtgagcgctcggtggagg	10	8	16	7	2	2	1	2	1	0	0	3	3	2	3	0	6	1	2	0	6	2	1			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr7:139030365A>T	ENST00000297534.6	+	2	510	c.257A>T	c.(256-258)aAg>aTg	p.K86M	LUC7L2_ENST00000541515.3_Missense_Mutation_p.K86M|C7orf55_ENST00000481123.1_3'UTR|C7orf55-LUC7L2_ENST00000541170.3_Intron	NM_197964.4	NP_932068.2	Q96HJ9	CG055_HUMAN	chromosome 7 open reading frame 55	86						mitochondrion (GO:0005739)				breast(1)|lung(2)	3						TTTCATGGCAAGGGTGAGCGC	0.562																																					p.K86M		Atlas-SNP	.											.	.	.	.	0			c.A257T						PASS	.						76	68	71					7																	139030365		2203	4300	6503	SO:0001583	missense	100996928	exon2			ATGGCAAGGGTGA	AF161386	CCDS5853.1	7q34	2009-01-22	2009-01-22	2009-01-22	ENSG00000164898	ENSG00000164898			26946	protein-coding gene	gene with protein product	"formation of mitochondrial complexes 1 homolog (S. cerevisiae)"					12477932	Standard	NM_197964		Approved	HSPC268, FMC1		Q96HJ9	OTTHUMG00000151719	ENST00000297534.6:c.257A>T	chr7.hg19:g.139030365A>T	ENSP00000297534:p.Lys86Met	68.0	0.0	.		81.0	16.0	.	NM_001244584	B7Z4Q3|Q75M90|Q9P0B3	Missense_Mutation	SNP	ENST00000297534.6	hg19	CCDS5853.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.963741	0.74016	.	.	ENSG00000164898;ENSG00000146963	ENST00000297534;ENST00000541515	T;T	0.53423	0.62;1.33	5.62	3.25	0.37280	.	.	.	.	.	T	0.44244	0.1284	M	0.71581	2.175	0.32737	N	0.508162	B;B	0.10296	0.003;0.003	B;B	0.14578	0.011;0.011	T	0.53968	-0.8363	9	0.87932	D	0	-0.2264	5.3084	0.15817	0.7154:0.0:0.1316:0.1531	.	86;86	B7Z4Q3;Q96HJ9	.;CG055_HUMAN	M	86	ENSP00000297534:K86M;ENSP00000440222:K86M	ENSP00000297534:K86M	K	+	2	0	LUC7L2;C7orf55	138680905	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.533000	0.36040	0.928000	0.37168	0.455000	0.32223	AAG	.	.	.	none		0.562	C7orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323626.1	NM_197964		T	139030365	A	T	139030365	3	4	76	1	0	0	0	0	1	0	0	0	2405	72	3	5	263	5	C7orf55	7	139030365	Missense_Mutation	SNP	A	TCGA-AL-7173-01A-11D-2136-08	22612902	139030365	20108298	30	4904											
KEL	3792	hgsc.bcm.edu	37	chr7	142658089	142658089	+	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	tattggtctctttggcccttCcacaggcaaagctgaagaag	10	11	10	10	0	1	2	0	1	1	1	3	2	2	2	2	3	1	2	2	3	4	4			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr7:142658089C>A	ENST00000355265.2	-	4	800	c.326G>T	c.(325-327)gGa>gTa	p.G109V	KEL_ENST00000479768.2_5'UTR	NM_000420.2	NP_000411.1	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	109					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)					TTTGGCCCTTCCACAGGCAAA	0.512																																					p.G109V		Atlas-SNP	.											.	KEL	128	.	0			c.G326T						PASS	.						133	133	133					7																	142658089		2203	4300	6503	SO:0001583	missense	3792	exon4			GCCCTTCCACAGG	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.326G>T	chr7.hg19:g.142658089C>A	ENSP00000347409:p.Gly109Val	191.0	0.0	.		208.0	40.0	.	NM_000420	B2RBV4|Q96RS8|Q99885	Missense_Mutation	SNP	ENST00000355265.2	hg19	CCDS34766.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.61|12.61	1.990455|1.990455	0.35131|0.35131	.|.	.|.	ENSG00000197993|ENSG00000197993	ENST00000355265;ENST00000476829;ENST00000467543|ENST00000460479	D;D;D|.	0.88741|.	-2.42;-2.42;-2.42|.	5.66|5.66	2.87|2.87	0.33458|0.33458	Peptidase M13 (1);|.	0.255042|.	0.27792|.	N|.	0.017836|.	T|T	0.71576|0.71576	0.3356|0.3356	M|M	0.83223|0.83223	2.63|2.63	0.45607|0.45607	D|D	0.998543|0.998543	D|.	0.89917|.	1.0|.	D|.	0.80764|.	0.994|.	T|T	0.68458|0.68458	-0.5403|-0.5403	10|5	0.87932|.	D|.	0|.	-14.3801|-14.3801	7.6264|7.6264	0.28214|0.28214	0.0:0.7371:0.0:0.2629|0.0:0.7371:0.0:0.2629	.|.	109|.	P23276|.	KELL_HUMAN|.	V|C	109;109;90|119	ENSP00000347409:G109V;ENSP00000419889:G109V;ENSP00000420011:G90V|.	ENSP00000347409:G109V|.	G|W	-|-	2|3	0|0	KEL|KEL	142368211|142368211	0.745000|0.745000	0.28261|0.28261	0.447000|0.447000	0.26932|0.26932	0.040000|0.040000	0.13550|0.13550	1.084000|1.084000	0.30828|0.30828	0.317000|0.317000	0.23160|0.23160	0.655000|0.655000	0.94253|0.94253	GGA|TGG	.	.	.	none		0.512	KEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347671.2	NM_000420		A	142658089	C	A	142658089	3	1	76	1	0	0	0	0	1	0	0	0	8149	855	30	4	1936	4	KEL	7	142658089	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08	3627724	142658089	16480574	31	4905											
FBXO43	286151	hgsc.bcm.edu	37	chr8	101152996	101152996	+	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	ttttaattctgttaagatgtCcagtttttctatacccattt	9	21	4	7	0	2	1	0	0	2	1	3	1	3	1	2	0	1	2	2	0	4	9			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr8:101152996C>G	ENST00000428847.2	-	2	1802	c.1486G>C	c.(1486-1488)Gac>Cac	p.D496H		NM_001029860.3	NP_001025031.2	Q4G163	FBX43_HUMAN	F-box protein 43	496	F-box.				meiotic nuclear division (GO:0007126)|negative regulation of meiosis (GO:0045835)|negative regulation of protein catabolic process (GO:0042177)|protein ubiquitination (GO:0016567)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(5)|lung(14)|prostate(1)|skin(5)|urinary_tract(1)	31	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)			GTTAAGATGTCCAGTTTTTCT	0.388																																					p.D496H		Atlas-SNP	.											.	FBXO43	155	.	0			c.G1486C						PASS	.						144	134	137					8																	101152996		1822	4082	5904	SO:0001583	missense	286151	exon2			AGATGTCCAGTTT	BC028709	CCDS47904.1	8q22.3	2004-08-24			ENSG00000156509	ENSG00000156509		"F-boxes /  "other""	28521	protein-coding gene	gene with protein product		609110					Standard	NR_036491		Approved	Fbx43	uc003yjd.3	Q4G163	OTTHUMG00000164803	ENST00000428847.2:c.1486G>C	chr8.hg19:g.101152996C>G	ENSP00000403293:p.Asp496His	167.0	0.0	.		160.0	36.0	.	NM_001029860		Missense_Mutation	SNP	ENST00000428847.2	hg19	CCDS47904.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.070318	0.76301	.	.	ENSG00000156509	ENST00000428847	T	0.64618	-0.11	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.81394	0.4813	M	0.83223	2.63	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.84731	0.0745	10	0.87932	D	0	-12.012	18.3634	0.90383	0.0:1.0:0.0:0.0	.	462;496	C9J908;Q4G163	.;FBX43_HUMAN	H	496	ENSP00000403293:D496H	ENSP00000403293:D496H	D	-	1	0	FBXO43	101222172	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.034000	0.76511	2.398000	0.81561	0.655000	0.94253	GAC	.	.	.	none		0.388	FBXO43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380380.1	XM_209918		G	101152996	C	G	101152996	3	3	76	1	0	0	0	0	1	0	0	0	5759	855	30	4	656	4	FBXO43	8	101152996	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08		101152996	45211026	32	4906											
FREM1	158326	hgsc.bcm.edu	37	chr9	14801824	14801824	+	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	ctggggaatgtccaggtccaCagcgctgatgatggaagagt	10	8	15	8	1	0	3	0	2	0	1	2	5	2	5	2	4	1	1	2	4	2	0			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr9:14801824C>G	ENST00000380880.3	-	20	4303	c.3520G>C	c.(3520-3522)Gtg>Ctg	p.V1174L	FREM1_ENST00000380881.4_Missense_Mutation_p.V1175L|FREM1_ENST00000422223.2_Missense_Mutation_p.V1174L			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1174					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)		TCCAGGTCCACAGCGCTGATG	0.493																																					p.V1174L		Atlas-SNP	.											.	FREM1	261	.	0			c.G3520C						PASS	.						150	147	148					9																	14801824		2053	4219	6272	SO:0001583	missense	158326	exon21			GGTCCACAGCGCT	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.3520G>C	chr9.hg19:g.14801824C>G	ENSP00000370262:p.Val1174Leu	227.0	0.0	.		160.0	36.0	.	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	hg19	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	C	8.474	0.858155	0.17178	.	.	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.49432	0.78;0.78;0.78	5.51	-0.193	0.13244	.	0.808695	0.12113	N	0.498353	T	0.32793	0.0841	L	0.33339	1.005	0.22017	N	0.999411	B	0.12013	0.005	B	0.09377	0.004	T	0.22556	-1.0213	10	0.21540	T	0.41	-0.3702	10.4355	0.44433	0.0:0.6222:0.0:0.3778	.	1174	Q5H8C1	FREM1_HUMAN	L	1175;1174;1174	ENSP00000370263:V1175L;ENSP00000412940:V1174L;ENSP00000370262:V1174L	ENSP00000370257:V1177L	V	-	1	0	FREM1	14791824	0.010000	0.17322	0.071000	0.20095	0.038000	0.13279	0.139000	0.16036	0.033000	0.15463	0.591000	0.81541	GTG	.	.	.	none		0.493	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		G	14801824	C	G	14801824	3	3	76	1	0	0	0	0	1	0	0	0	6051	478	17	4	3141	4	FREM1	9	14801824	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08		14801824	126411607	33	4907											
FCN1	2219	hgsc.bcm.edu	37	chr9	137801883	137801883	+	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	gttgttgttgtggcccgttaGagaattacctgctcacagaa	9	13	11	8	1	1	2	1	0	0	2	1	3	1	2	2	1	2	5	2	1	4	5			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr9:137801883G>C	ENST00000371806.3	-	9	833	c.742C>G	c.(742-744)Cta>Gta	p.L248V		NM_002003.3	NP_001994.2	O00602	FCN1_HUMAN	ficolin (collagen/fibrinogen domain containing) 1	248	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell surface pattern recognition receptor signaling pathway (GO:0002752)|complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|opsonization (GO:0008228)|positive regulation of interleukin-8 secretion (GO:2000484)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extrinsic component of external side of plasma membrane (GO:0031232)	antigen binding (GO:0003823)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|G-protein coupled receptor binding (GO:0001664)|signaling pattern recognition receptor activity (GO:0008329)			endometrium(3)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	37		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.46e-08)|Epithelial(140;6.01e-08)|all cancers(34;3.69e-07)		TGGCCCGTTAGAGAATTACCT	0.507																																					p.L248V		Atlas-SNP	.											.	FCN1	62	.	0			c.C742G						PASS	.						170	177	175					9																	137801883		2203	4300	6503	SO:0001583	missense	2219	exon9			CCGTTAGAGAATT	D83920	CCDS6985.1	9q34	2013-02-06	2002-01-14		ENSG00000085265	ENSG00000085265		"Fibrinogen C domain containing"	3623	protein-coding gene	gene with protein product		601252	"ficolin (collagen/fibrinogen domain-containing) 1"			8573080, 8884275	Standard	NM_002003		Approved	FCNM	uc004cfi.3	O00602	OTTHUMG00000020895	ENST00000371806.3:c.742C>G	chr9.hg19:g.137801883G>C	ENSP00000360871:p.Leu248Val	283.0	0.0	.		253.0	53.0	.	NM_002003	Q5VYV5|Q92596	Missense_Mutation	SNP	ENST00000371806.3	hg19	CCDS6985.1	.	.	.	.	.	.	.	.	.	.	G	13.50	2.254797	0.39896	.	.	ENSG00000085265	ENST00000371806	T	0.78246	-1.16	3.29	1.19	0.21007	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	.	.	.	.	D	0.88742	0.6519	H	0.96833	3.89	0.33292	D	0.56369	D	0.67145	0.996	D	0.68765	0.96	D	0.85951	0.1464	9	0.87932	D	0	.	2.548	0.04742	0.2654:0.0:0.5025:0.2321	.	248	O00602	FCN1_HUMAN	V	248	ENSP00000360871:L248V	ENSP00000360871:L248V	L	-	1	2	FCN1	136941704	0.980000	0.34600	0.042000	0.18584	0.143000	0.21401	2.020000	0.41010	0.705000	0.31890	0.643000	0.83706	CTA	.	.	.	none		0.507	FCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054963.1	NM_002003		C	137801883	G	C	137801883	3	2	76	1	0	0	0	0	1	0	0	0	5798	933	33	4	242	4	FCN1	9	137801883	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08	123000059	137801883	3411548	34	4908											
PLAU	414236	hgsc.bcm.edu	37	chr10	75672687	75672687	+	Intron	SNP	T	T	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	cctgtccccttgtagataagTcaaaaacctgctatgagggg	11	10	10	10	0	1	2	1	1	0	1	2	2	2	2	4	2	2	2	4	2	5	4			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr10:75672687T>A	ENST00000409178.1	-	3	301				PLAU_ENST00000372762.4_Missense_Mutation_p.S31T|PLAU_ENST00000446342.1_Missense_Mutation_p.S50T|PLAU_ENST00000494287.1_3'UTR|PLAU_ENST00000372764.3_Missense_Mutation_p.S67T|C10orf55_ENST00000412307.2_Intron	NM_001001791.2	NP_001001791.2	Q5SWW7	CJ055_HUMAN	chromosome 10 open reading frame 55											endometrium(1)	1	Prostate(51;0.0112)					TGTAGATAAGTCAAAAACCTG	0.468																																					p.S67T		Atlas-SNP	.											.	PLAU	47	.	0			c.T199A						PASS	.						50	49	49					10																	75672687		2203	4300	6503	SO:0001627	intron_variant	5328	exon5			GATAAGTCAAAAA		CCDS53541.1	10q22.2	2012-05-24			ENSG00000222047	ENSG00000222047			31008	protein-coding gene	gene with protein product							Standard	NM_001001791		Approved	bA417O11.3	uc001jvz.2	Q5SWW7	OTTHUMG00000018496	ENST00000409178.1:c.39+113A>T	chr10.hg19:g.75672687T>A		75.0	0.0	.		62.0	6.0	.	NM_002658	Q3KRG4|Q8NAK4	Missense_Mutation	SNP	ENST00000409178.1	hg19	CCDS53541.1	.	.	.	.	.	.	.	.	.	.	T	10.76	1.440884	0.25900	.	.	ENSG00000122861	ENST00000446342;ENST00000372764;ENST00000372762;ENST00000372761	T;T;T	0.62364	0.03;0.03;0.03	5.78	3.47	0.39725	Kringle-like fold (1);	0.659026	0.14635	N	0.307599	T	0.47875	0.1469	L	0.38692	1.165	0.09310	N	0.999999	B;B;B;B	0.24823	0.022;0.112;0.022;0.027	B;B;B;B	0.26864	0.026;0.074;0.014;0.018	T	0.34428	-0.9829	10	0.33141	T	0.24	.	5.3638	0.16103	0.0:0.0896:0.1988:0.7116	.	50;31;67;67	E7ET40;E7ESM2;B2R7F2;P00749	.;.;.;UROK_HUMAN	T	50;67;31;31	ENSP00000388474:S50T;ENSP00000361850:S67T;ENSP00000361848:S31T	ENSP00000361847:S31T	S	+	1	0	PLAU	75342693	0.000000	0.05858	0.022000	0.16811	0.143000	0.21401	0.117000	0.15583	1.009000	0.39289	-0.340000	0.08031	TCA	.	.	.	none		0.468	C10orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048746.1	NM_001001791		A	75672687	T	A	75672687	1	1	76	0	1	0	0	0	0	0	0	0	12029	1667	58	5		5	PLAU	10	75672687	Intron	SNP	T	TCGA-AL-7173-01A-11D-2136-08		75672687	59862060	35	4909											
WDR74	54663	hgsc.bcm.edu	37	chr11	62606983	62606983	+	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	cgagcctgccacccacctttCaagatcccagtctcggtgcc	7	8	8	18	2	2	1	1	0	1	1	4	2	3	1	6	1	3	0	6	1	1	1			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr11:62606983C>G	ENST00000525239.1	-	2	597	c.60G>C	c.(58-60)ttG>ttC	p.L20F	WDR74_ENST00000311713.7_Missense_Mutation_p.L20F|WDR74_ENST00000529106.1_Missense_Mutation_p.L20F|RNU2-2P_ENST00000410396.1_RNA|WDR74_ENST00000540620.1_5'UTR|WDR74_ENST00000278856.4_Missense_Mutation_p.L20F|WDR74_ENST00000525752.1_Intron			Q6RFH5	WDR74_HUMAN	WD repeat domain 74	20					blastocyst formation (GO:0001825)|RNA metabolic process (GO:0016070)	nucleolus (GO:0005730)|nucleus (GO:0005634)				kidney(2)|large_intestine(1)|liver(1)|lung(3)|ovary(1)	8						ACCCACCTTTCAAGATCCCAG	0.632																																					p.L20F		Atlas-SNP	.											.	WDR74	36	.	0			c.G60C						PASS	.						39	45	43					11																	62606983		2086	4226	6312	SO:0001583	missense	54663	exon2			ACCTTTCAAGATC		CCDS44630.1	11q12.3	2013-01-09				ENSG00000133316		"WD repeat domain containing"	25529	protein-coding gene	gene with protein product							Standard	NM_018093		Approved	FLJ10439	uc001nvm.2	Q6RFH5		ENST00000525239.1:c.60G>C	chr11.hg19:g.62606983C>G	ENSP00000432119:p.Leu20Phe	104.0	0.0	.		97.0	26.0	.	NM_018093	A8K8G5|Q9BRC9|Q9H6X8|Q9NVY2	Missense_Mutation	SNP	ENST00000525239.1	hg19	CCDS44630.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.49|18.49	3.634308|3.634308	0.67130|0.67130	.|.	.|.	ENSG00000133316|ENSG00000133316	ENST00000535048|ENST00000311713;ENST00000529106;ENST00000525239;ENST00000278856;ENST00000538098	.|T;T;T;T;T	.|0.39406	.|1.35;1.35;1.35;1.35;1.08	4.28|4.28	1.21|1.21	0.21127|0.21127	.|.	.|0.000000	.|0.64402	.|D	.|0.000007	T|T	0.48502|0.48502	0.1503|0.1503	L|L	0.43554|0.43554	1.36|1.36	0.48632|0.48632	D|D	0.999681|0.999681	.|D;D;D	.|0.89917	.|1.0;0.999;1.0	.|D;D;D	.|0.97110	.|0.997;0.953;1.0	T|T	0.39057|0.39057	-0.9632|-0.9632	5|10	.|0.48119	.|T	.|0.1	-8.5329|-8.5329	5.8248|5.8248	0.18548|0.18548	0.0:0.6468:0.161:0.1922|0.0:0.6468:0.161:0.1922	.|.	.|20;20;20	.|B4E018;Q6RFH5;Q6RFH5-2	.|.;WDR74_HUMAN;.	Q|F	12|20	.|ENSP00000308931:L20F;ENSP00000435726:L20F;ENSP00000432119:L20F;ENSP00000278856:L20F;ENSP00000440612:L20F	.|ENSP00000278856:L20F	E|L	-|-	1|3	0|2	WDR74|WDR74	62363559|62363559	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.936000|0.936000	0.57629|0.57629	1.056000|1.056000	0.30480|0.30480	0.415000|0.415000	0.25817|0.25817	0.655000|0.655000	0.94253|0.94253	GAA|TTG	.	.	.	none		0.632	WDR74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395678.1	NM_018093		G	62606983	C	G	62606983	3	3	76	1	0	0	0	0	1	0	0	0	17336	825	29	4	1141	4	WDR74	11	62606983	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08		62606983	72399533	36	4910											
MMP13	4322	hgsc.bcm.edu	37	chr11	102822873	102822873	+	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	acctaaggagtggccgaactCatgcgcagcaacaagaaaca	16	4	10	11	2	1	1	1	0	0	1	1	3	1	2	2	2	5	2	2	2	5	1			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr11:102822873C>G	ENST00000260302.3	-	5	695	c.667G>C	c.(667-669)Gag>Cag	p.E223Q	MMP13_ENST00000340273.4_Missense_Mutation_p.E223Q	NM_002427.3	NP_002418.1	P45452	MMP13_HUMAN	matrix metallopeptidase 13 (collagenase 3)	223	Interaction with TIMP2.				bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cartilage development (GO:0051216)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.E223K(1)		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)	TGGCCGAACTCATGCGCAGCA	0.433																																					p.E223Q		Atlas-SNP	.											MMP13,NS,NS,0,1	MMP13	75	.	1	Substitution - Missense(1)	NS(1)	c.G667C						PASS	.						160	152	154					11																	102822873		2202	4299	6501	SO:0001583	missense	4322	exon5			CGAACTCATGCGC	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.667G>C	chr11.hg19:g.102822873C>G	ENSP00000260302:p.Glu223Gln	175.0	0.0	.		179.0	32.0	.	NM_002427	A8K846|B2RCZ3|Q6NWN6	Missense_Mutation	SNP	ENST00000260302.3	hg19	CCDS8324.1	.	.	.	.	.	.	.	.	.	.	C	34	5.305406	0.95601	.	.	ENSG00000137745	ENST00000260302;ENST00000546012;ENST00000340273	D;D	0.83075	-1.68;-1.68	5.75	5.75	0.90469	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.94355	0.8185	H	0.95365	3.66	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95140	0.8263	10	0.87932	D	0	.	20.312	0.98644	0.0:1.0:0.0:0.0	.	223	P45452	MMP13_HUMAN	Q	223	ENSP00000260302:E223Q;ENSP00000339672:E223Q	ENSP00000260302:E223Q	E	-	1	0	MMP13	102328083	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.772000	0.85439	2.866000	0.98385	0.650000	0.86243	GAG	.	.	.	none		0.433	MMP13-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386648.1	NM_002427		G	102822873	C	G	102822873	3	3	76	1	0	0	0	0	1	0	0	0	9659	835	29	4	772	4	MMP13	11	102822873	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08	40215890	102822873	32183643	37	4911											
FKBP4	2288	hgsc.bcm.edu	37	chr12	2910328	2910328	+	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	agaagggcctcttccgccggGgagaggcccacctggccgtg	6	5	16	14	3	1	2	0	0	1	2	2	3	2	2	6	5	0	0	6	5	1	1			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr12:2910328G>A	ENST00000001008.4	+	9	1265	c.1078G>A	c.(1078-1080)Gga>Aga	p.G360R	RP4-816N1.7_ENST00000547042.1_RNA|RP4-816N1.6_ENST00000547834.1_RNA	NM_002014.3	NP_002005.1	Q02790	FKBP4_HUMAN	FK506 binding protein 4, 59kDa	360	Interaction with tubulin. {ECO:0000250}.				androgen receptor signaling pathway (GO:0030521)|chaperone-mediated protein folding (GO:0061077)|copper ion transport (GO:0006825)|embryo implantation (GO:0007566)|male sex differentiation (GO:0046661)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)|negative regulation of neuron projection development (GO:0010977)|prostate gland development (GO:0030850)|protein complex localization (GO:0031503)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|steroid hormone receptor complex assembly (GO:0006463)	axonal growth cone (GO:0044295)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|FK506 binding (GO:0005528)|GTP binding (GO:0005525)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(1)	14			OV - Ovarian serous cystadenocarcinoma(31;0.00105)			CTTCCGCCGGGGAGAGGCCCA	0.572																																					p.G360R		Atlas-SNP	.											.	FKBP4	29	.	0			c.G1078A						PASS	.						56	61	59					12																	2910328		2203	4300	6503	SO:0001583	missense	2288	exon9			CGCCGGGGAGAGG	M88279	CCDS8512.1	12p13.33	2013-01-10	2002-08-29		ENSG00000004478	ENSG00000004478		"Tetratricopeptide (TTC) repeat domain containing"	3720	protein-coding gene	gene with protein product		600611	"FK506-binding protein 4 (59kD)"			1279700	Standard	NM_002014		Approved	FKBP59, FKBP52	uc001qkz.3	Q02790	OTTHUMG00000090429	ENST00000001008.4:c.1078G>A	chr12.hg19:g.2910328G>A	ENSP00000001008:p.Gly360Arg	115.0	0.0	.		150.0	33.0	.	NM_002014	D3DUQ1|Q9UCP1|Q9UCV7	Missense_Mutation	SNP	ENST00000001008.4	hg19	CCDS8512.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.166076	0.78339	.	.	ENSG00000004478	ENST00000001008	T	0.66995	-0.24	5.57	4.68	0.58851	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.047223	0.85682	N	0.000000	D	0.87577	0.6212	H	0.97564	4.03	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91165	0.4964	10	0.72032	D	0.01	-18.3148	13.2702	0.60155	0.0758:0.0:0.9242:0.0	.	360	Q02790	FKBP4_HUMAN	R	360	ENSP00000001008:G360R	ENSP00000001008:G360R	G	+	1	0	FKBP4	2780589	1.000000	0.71417	0.913000	0.36048	0.591000	0.36615	9.383000	0.97214	1.355000	0.45865	0.561000	0.74099	GGA	.	.	.	none		0.572	FKBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206861.1			A	2910328	G	A	2910328	3	1	76	1	0	0	0	0	1	0	0	0	5917	1233	43	2	1112	2	FKBP4	12	2910328	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08		2910328	130941567	38	4912											
LRRC23	10233	hgsc.bcm.edu	37	chr12	7023220	7023220	+	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	ctctgggcagtgtggggtgcAgaatggggtgcctaggcctg	5	9	19	8	0	1	1	0	0	1	1	1	1	1	1	2	6	2	2	2	6	2	1			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr12:7023220A>C	ENST00000007969.8	+	0	1442				ENO2_ENST00000544774.1_5'Flank|LRRC23_ENST00000323702.5_Silent_p.A308A|ENO2_ENST00000541477.1_5'Flank|ENO2_ENST00000545045.2_5'Flank|ENO2_ENST00000535366.1_5'Flank|ENO2_ENST00000229277.1_5'Flank|LRRC23_ENST00000443597.2_3'UTR|LRRC23_ENST00000429740.1_3'UTR|ENO2_ENST00000538763.1_5'Flank	NM_001135217.1|NM_201650.2	NP_001128689.1|NP_964013.1	Q53EV4	LRC23_HUMAN	leucine rich repeat containing 23											NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|stomach(1)	13						TGTGGGGTGCAGAATGGGGTG	0.657																																					p.A308A		Atlas-SNP	.											.	LRRC23	46	.	0			c.A924C						PASS	.						94	90	92					12																	7023220		2203	4300	6503	SO:0001624	3_prime_UTR_variant	10233	exon7			GGGTGCAGAATGG	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.*190A>C	chr12.hg19:g.7023220A>C		153.0	0.0	.		170.0	65.0	.	NM_006992	A8K8C6|D3DUT1|Q8N6K6|Q92977|Q99620	Silent	SNP	ENST00000007969.8	hg19	CCDS8569.1																																																																																			.	.	.	none		0.657	LRRC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345214.1	NM_006992		C	7023220	A	C	7023220	1	2	76	0	1	0	0	0	0	0	0	0	8985	175	7	5		5	LRRC23	12	7023220	3'UTR	SNP	A	TCGA-AL-7173-01A-11D-2136-08	4112892	7023220	126828675	39	4913											
CD163	9332	hgsc.bcm.edu	37	chr12	7640255	7640255	+	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	ggtcttgccattcaccaagcGaatttctgtgtatcctggaa	9	13	9	10	1	3	0	1	0	2	0	4	2	4	1	3	2	2	1	3	2	4	4	rs373039092		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr12:7640255G>A	ENST00000359156.4	-	8	1952	c.1750C>T	c.(1750-1752)Cgc>Tgc	p.R584C	CD163_ENST00000396620.3_Missense_Mutation_p.R617C|CD163_ENST00000539632.1_5'Flank|CD163_ENST00000541972.1_Missense_Mutation_p.R572C|CD163_ENST00000432237.2_Missense_Mutation_p.R584C	NM_004244.5	NP_004235.4	Q86VB7	C163A_HUMAN	CD163 molecule	584	SRCR 6. {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)	p.R584C(1)		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)	TTCACCAAGCGAATTTCTGTG	0.488																																					p.R584C		Atlas-SNP	.											CD163_ENST00000396620,NS,lymphoid_neoplasm,+1,1	CD163	221	.	1	Substitution - Missense(1)	skin(1)	c.C1750T						PASS	.	G	CYS/ARG,CYS/ARG	0,4406		0,0,2203	70	71	71		1750,1750	5.2	0.9	12		71	1,8599		0,1,4299	no	missense,missense	CD163	NM_004244.5,NM_203416.3	180,180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	584/1157,584/1122	7640255	1,13005	2203	4300	6503	SO:0001583	missense	9332	exon8			CCAAGCGAATTTC	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.1750C>T	chr12.hg19:g.7640255G>A	ENSP00000352071:p.Arg584Cys	114.0	0.0	.		166.0	9.0	.	NM_203416	C9JIG2|Q07898|Q07899|Q07900|Q07901|Q2VLH7	Missense_Mutation	SNP	ENST00000359156.4	hg19	CCDS8578.1	.	.	.	.	.	.	.	.	.	.	G	16.62	3.173313	0.57584	0.0	1.16E-4	ENSG00000177575	ENST00000359156;ENST00000541972;ENST00000396620;ENST00000432237	T;T;T;T	0.54479	0.57;0.57;0.57;0.57	5.21	5.21	0.72293	Speract/scavenger receptor (1);Speract/scavenger receptor-related (2);	0.076247	0.51477	D	0.000083	T	0.79627	0.4478	M	0.93763	3.455	0.26882	N	0.967512	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.76575	0.988;0.917;0.988	T	0.76509	-0.2933	10	0.87932	D	0	.	16.6253	0.84968	0.0:0.0:1.0:0.0	.	617;584;584	C9JHR8;Q86VB7-3;Q86VB7	.;.;C163A_HUMAN	C	584;572;617;584	ENSP00000352071:R584C;ENSP00000444071:R572C;ENSP00000379863:R617C;ENSP00000403885:R584C	ENSP00000352071:R584C	R	-	1	0	CD163	7531522	0.513000	0.26194	0.917000	0.36280	0.574000	0.36063	1.594000	0.36697	2.592000	0.87571	0.655000	0.94253	CGC	.	.	.	weak		0.488	CD163-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399396.2	NM_004244, NM_203416		A	7640255	G	A	7640255	3	1	76	1	0	0	0	0	1	0	0	0	2969	1058	37	1	1756	1	CD163	12	7640255	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08	617035	7640255	126211640	40	4914											
KERA	11081	hgsc.bcm.edu	37	chr12	91449805	91449805	+	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	caaatggcttttcaggaatgGtttctatcaggttgttttga	9	17	10	5	0	3	1	2	1	1	0	3	2	3	2	0	4	0	4	0	4	3	7			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr12:91449805G>C	ENST00000266719.3	-	2	501	c.254C>G	c.(253-255)aCc>aGc	p.T85S		NM_007035.3	NP_008966.1	O60938	KERA_HUMAN	keratocan	85					carbohydrate metabolic process (GO:0005975)|cornea development in camera-type eye (GO:0061303)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|response to stimulus (GO:0050896)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)				breast(2)|large_intestine(8)|lung(5)|prostate(2)|skin(2)	19						TTCAGGAATGGTTTCTATCAG	0.353																																					p.T85S		Atlas-SNP	.											.	KERA	62	.	0			c.C254G						PASS	.						119	112	115					12																	91449805		2202	4297	6499	SO:0001583	missense	11081	exon2			GGAATGGTTTCTA	AF063301	CCDS9037.1	12q21.3-q22	2014-09-17				ENSG00000139330		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	6309	protein-coding gene	gene with protein product	"keratocan proteoglycan"	603288		CNA2		10565548, 10802664	Standard	NM_007035		Approved	SLRR2B	uc001tbl.3	O60938		ENST00000266719.3:c.254C>G	chr12.hg19:g.91449805G>C	ENSP00000266719:p.Thr85Ser	116.0	0.0	.		115.0	19.0	.	NM_007035		Missense_Mutation	SNP	ENST00000266719.3	hg19	CCDS9037.1	.	.	.	.	.	.	.	.	.	.	G	8.585	0.883190	0.17467	.	.	ENSG00000139330	ENST00000266719	T	0.56444	0.46	6.04	6.04	0.98038	.	0.296558	0.42821	N	0.000642	T	0.28001	0.0690	N	0.02368	-0.58	0.25604	N	0.986567	B	0.10296	0.003	B	0.15870	0.014	T	0.04650	-1.0936	10	0.10111	T	0.7	-17.6051	16.8507	0.85993	0.0:0.0:0.8711:0.1289	.	85	O60938	KERA_HUMAN	S	85	ENSP00000266719:T85S	ENSP00000266719:T85S	T	-	2	0	KERA	89973936	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.631000	0.54280	2.890000	0.99128	0.650000	0.86243	ACC	.	.	.	none		0.353	KERA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407149.2	NM_007035		C	91449805	G	C	91449805	3	2	76	1	0	0	0	0	1	0	0	0	8150	1261	44	4	812	4	KERA	12	91449805	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08	83809550	91449805	42402090	41	4915											
DDX54	79039	hgsc.bcm.edu	37	chr12	113610194	113610194	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagtttgcccttggcggggaAgctgtagttgatgacattgt	7	13	15	6	1	0	2	0	2	0	0	0	4	0	3	1	3	2	4	1	3	2	5			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr12:113610194A>G	ENST00000306014.5	-	11	1270	c.1243T>C	c.(1243-1245)Ttc>Ctc	p.F415L	DDX54_ENST00000314045.7_Missense_Mutation_p.F415L	NM_024072.3	NP_076977.3	Q8TDD1	DDX54_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	415	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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						TTGGCGGGGAAGCTGTAGTTG	0.637																																					p.F415L		Atlas-SNP	.											.	DDX54	73	.	0			c.T1243C						PASS	.						80	65	70					12																	113610194		2203	4300	6503	SO:0001583	missense	79039	exon11			CGGGGAAGCTGTA	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.1243T>C	chr12.hg19:g.113610194A>G	ENSP00000304072:p.Phe415Leu	48.0	0.0	.		51.0	21.0	.	NM_024072	Q86YT8|Q9BRZ1	Missense_Mutation	SNP	ENST00000306014.5	hg19	CCDS31907.1	.	.	.	.	.	.	.	.	.	.	A	32	5.178425	0.94846	.	.	ENSG00000123064	ENST00000314045;ENST00000306014	T;T	0.72835	-0.69;-0.69	5.18	5.18	0.71444	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.75302	0.3831	L	0.28274	0.84	0.80722	D	1	D;D	0.71674	0.997;0.998	D;D	0.73380	0.966;0.98	T	0.79047	-0.1963	10	0.87932	D	0	.	14.7275	0.69354	1.0:0.0:0.0:0.0	.	415;415	Q8TDD1-2;Q8TDD1	.;DDX54_HUMAN	L	415	ENSP00000323858:F415L;ENSP00000304072:F415L	ENSP00000304072:F415L	F	-	1	0	DDX54	112094577	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.294000	0.96088	1.966000	0.57179	0.528000	0.53228	TTC	.	.	.	none		0.637	DDX54-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405435.1	NM_024072		G	113610194	A	G	113610194	3	3	76	1	0	0	0	0	1	0	0	0	4374	72	3	3	1445	3	DDX54	12	113610194	Missense_Mutation	SNP	A	TCGA-AL-7173-01A-11D-2136-08	22160389	113610194	20241701	42	4916											
CDK8	1024	hgsc.bcm.edu	37	chr13	26975735	26975736	+	Frame_Shift_Del	DEL	GG	GG	-																															ctcctaccactacctcaggtGgacttatcatgacctcagac																										TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr13:26975735_26975736delGG	ENST00000381527.3	+	12	1746_1747	c.1243_1244delGG	c.(1243-1245)ggafs	p.G415fs	CDK8_ENST00000536792.1_3'UTR|CDK8_ENST00000480323.1_3'UTR	NM_001260.1	NP_001251.1	P49336	CDK8_HUMAN	cyclin-dependent kinase 8	415					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	25	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0384)|Epithelial(112;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.188)		TACCTCAGGTGGACTTATCATG	0.446																																					p.414_415del		Atlas-INDEL	.											.	CDK8	61	.	0			c.1242_1243del						PASS	.																																			SO:0001589	frameshift_variant	1024	exon12			.	X85753	CCDS9317.1	13q12	2011-11-08			ENSG00000132964	ENSG00000132964		"Cyclin-dependent kinases"	1779	protein-coding gene	gene with protein product		603184				7568034	Standard	NM_001260		Approved	K35	uc001uqr.1	P49336	OTTHUMG00000016617	ENST00000381527.3:c.1243_1244delGG	chr13.hg19:g.26975735_26975736delGG	ENSP00000370938:p.Gly415fs	117.0	0.0	0		95.0	11.0	0.115789	NM_001260	Q5VUF3|Q6ISB5	Frame_Shift_Del	DEL	ENST00000381527.3	hg19	CCDS9317.1																																																																																			.	.	.	none		0.446	CDK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044250.1			-	26975736	GG	-	26975735	7	5	76	1	0	1	0	1	0	0	0	0	3152	1349	47	0	1289	0	CDK8	13	26975735	Frame_Shift_Del	DEL	GG	TCGA-AL-7173-01A-11D-2136-08		26975735	88194143	43	4917	54	2									
CDK8	1024	hgsc.bcm.edu	37	chr13	26975738	26975738	+	Missense_Mutation	SNP	C	C	A																															ctaccactacctcaggtggaCttatcatgacctcagactat																										TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr13:26975738C>A	ENST00000381527.3	+	12	1749	c.1246C>A	c.(1246-1248)Ctt>Att	p.L416I	CDK8_ENST00000536792.1_3'UTR|CDK8_ENST00000480323.1_3'UTR	NM_001260.1	NP_001251.1	P49336	CDK8_HUMAN	cyclin-dependent kinase 8	416					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	25	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0384)|Epithelial(112;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.188)		CTCAGGTGGACTTATCATGAC	0.438																																					p.L416I		Atlas-SNP	.											.	CDK8	61	.	0			c.C1246A						PASS	.						144	125	131					13																	26975738		2203	4300	6503	SO:0001583	missense	1024	exon12			GGTGGACTTATCA	X85753	CCDS9317.1	13q12	2011-11-08			ENSG00000132964	ENSG00000132964		"Cyclin-dependent kinases"	1779	protein-coding gene	gene with protein product		603184				7568034	Standard	NM_001260		Approved	K35	uc001uqr.1	P49336	OTTHUMG00000016617	ENST00000381527.3:c.1246C>A	chr13.hg19:g.26975738C>A	ENSP00000370938:p.Leu416Ile	117.0	0.0	.		97.0	12.0	.	NM_001260	Q5VUF3|Q6ISB5	Missense_Mutation	SNP	ENST00000381527.3	hg19	CCDS9317.1	.	.	.	.	.	.	.	.	.	.	C	15.68	2.903879	0.52333	.	.	ENSG00000132964	ENST00000381527	T	0.68025	-0.3	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.49490	0.1560	N	0.08118	0	0.80722	D	1	P;P	0.39282	0.666;0.586	B;B	0.37833	0.259;0.146	T	0.51957	-0.8639	10	0.28530	T	0.3	-6.9656	18.9814	0.92756	0.0:1.0:0.0:0.0	.	415;416	P49336-2;P49336	.;CDK8_HUMAN	I	416	ENSP00000370938:L416I	ENSP00000370938:L416I	L	+	1	0	CDK8	25873738	1.000000	0.71417	0.995000	0.50966	0.993000	0.82548	7.440000	0.80464	2.491000	0.84063	0.655000	0.94253	CTT	.	.	.	none		0.438	CDK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044250.1			A	26975738	C	A	26975738	3	1	76	1	0	0	0	0	1	0	0	0	3152	565	20	4	1292	4	CDK8	13	26975738	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08	3	26975738	88194140	44	4918	54	2									
DIAPH3	81624	hgsc.bcm.edu	37	chr13	60566699	60566699	+	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	agatgtaaccagggcattgaTgagctgcatacaagctacct	13	9	10	9	0	0	3	0	2	0	1	0	3	0	3	2	1	6	5	2	1	4	4			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr13:60566699T>A	ENST00000400324.4	-	10	1253	c.1033A>T	c.(1033-1035)Atc>Ttc	p.I345F	DIAPH3_ENST00000400330.1_Missense_Mutation_p.I345F|DIAPH3_ENST00000465066.1_5'UTR|DIAPH3_ENST00000400319.1_Missense_Mutation_p.I275F|DIAPH3_ENST00000377908.2_Missense_Mutation_p.I334F|DIAPH3_ENST00000400320.1_Missense_Mutation_p.I299F|DIAPH3_ENST00000267215.4_Missense_Mutation_p.I345F	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	345	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		AGGGCATTGATGAGCTGCATA	0.393																																					p.I345F		Atlas-SNP	.											.	DIAPH3	139	.	0			c.A1033T						PASS	.						65	60	62					13																	60566699		1908	4138	6046	SO:0001583	missense	81624	exon10			CATTGATGAGCTG	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.1033A>T	chr13.hg19:g.60566699T>A	ENSP00000383178:p.Ile345Phe	42.0	0.0	.		52.0	8.0	.	NM_001042517	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Missense_Mutation	SNP	ENST00000400324.4	hg19	CCDS41898.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.490483	0.84962	.	.	ENSG00000139734	ENST00000400324;ENST00000400330;ENST00000400327;ENST00000413168;ENST00000400329;ENST00000377908;ENST00000400319;ENST00000400320;ENST00000267215;ENST00000267214;ENST00000453990	D;D;D;D;D;D	0.91894	-2.93;-2.93;-2.93;-2.93;-2.93;-2.93	5.77	5.77	0.91146	GTPase-binding/formin homology 3 (1);Diaphanous FH3 (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.97334	0.9128	H	0.95114	3.625	0.54753	D	0.999989	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.996	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.98	D	0.98505	1.0616	10	0.87932	D	0	.	16.0865	0.81056	0.0:0.0:0.0:1.0	.	275;299;334;82;345	A8MYX0;C9JL55;C9JDG1;Q9NSV4-1;Q9NSV4	.;.;.;.;DIAP3_HUMAN	F	345;345;334;299;275;334;275;299;345;82;345	ENSP00000383178:I345F;ENSP00000383184:I345F;ENSP00000367141:I334F;ENSP00000383173:I275F;ENSP00000383174:I299F;ENSP00000267215:I345F	ENSP00000267214:I82F	I	-	1	0	DIAPH3	59464700	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.606000	0.82863	2.194000	0.70268	0.377000	0.23210	ATC	.	.	.	none		0.393	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517		A	60566699	T	A	60566699	3	1	76	1	0	0	0	0	1	0	0	0	4522	1464	51	5	2644	5	DIAPH3	13	60566699	Missense_Mutation	SNP	T	TCGA-AL-7173-01A-11D-2136-08	33590961	60566699	54603179	45	4919											
CPNE6	9362	hgsc.bcm.edu	37	chr14	24545747	24545747	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttgctatcaactttgacccGgaaaatcctgaatgtgaagg	12	12	9	8	1	1	3	1	3	0	0	2	4	2	4	2	2	2	1	2	2	6	3			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr14:24545747G>A	ENST00000397016.2	+	14	1457	c.1146G>A	c.(1144-1146)ccG>ccA	p.P382P	CPNE6_ENST00000216775.2_Silent_p.P382P|CPNE6_ENST00000537691.1_Silent_p.P437P	NM_001280558.1	NP_001267487.1	O95741	CPNE6_HUMAN	copine VI (neuronal)	382	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				lipid metabolic process (GO:0006629)|nervous system development (GO:0007399)|synaptic transmission (GO:0007268)|vesicle-mediated transport (GO:0016192)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			endometrium(4)|large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(265;0.0184)		ACTTTGACCCGGAAAATCCTG	0.587																																					p.P382P		Atlas-SNP	.											.	CPNE6	40	.	0			c.G1146A						PASS	.						100	103	102					14																	24545747		2203	4300	6503	SO:0001819	synonymous_variant	9362	exon13			TGACCCGGAAAAT	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.1146G>A	chr14.hg19:g.24545747G>A		139.0	0.0	.		94.0	30.0	.	NM_006032	B2RAG6|B7Z1M3|D3DS55|F5GXN1|Q53HA6|Q8WVG1	Silent	SNP	ENST00000397016.2	hg19	CCDS9607.1																																																																																			.	.	.	none		0.587	CPNE6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071869.5			A	24545747	G	A	24545747	2	1	76	1	0	0	0	0	0	0	0	1	3818	1103	39	1		1	CPNE6	14	24545747	Silent	SNP	G	TCGA-AL-7173-01A-11D-2136-08		24545747	82803793	46	4920											
ANKDD1A	348094	hgsc.bcm.edu	37	chr15	65214185	65214185	+	Frame_Shift_Del	DEL	A	A	-																															cgaatcctccagatcttggtAaactcaggggccaagatcca																										TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr15:65214185delA	ENST00000380230.3	+	4	362	c.333delA	c.(331-333)gtafs	p.V111fs	ANKDD1A_ENST00000395723.1_Frame_Shift_Del_p.V20fs|ANKDD1A_ENST00000491145.1_3'UTR|ANKDD1A_ENST00000319580.8_Frame_Shift_Del_p.K34fs|ANKDD1A_ENST00000496660.1_Frame_Shift_Del_p.V20fs|ANKDD1A_ENST00000357698.3_Frame_Shift_Del_p.V111fs|ANKDD1A_ENST00000395720.1_Frame_Shift_Del_p.V111fs|AC069368.3_ENST00000437723.1_Frame_Shift_Del_p.V183fs	NM_182703.3	NP_874362.3	Q495B1	AKD1A_HUMAN	ankyrin repeat and death domain containing 1A	111					signal transduction (GO:0007165)					NS(1)|endometrium(1)|large_intestine(10)|liver(2)|lung(4)|ovary(1)|prostate(2)	21						AGATCTTGGTAAACTCAGGGG	0.577																																					p.V111fs		Atlas-INDEL	.											.	ANKDD1A	47	.	0			c.332delT						PASS	.						113	90	98					15																	65214185		2202	4299	6501	SO:0001589	frameshift_variant	348094	exon4			.		CCDS10197.2	15q22.31	2013-01-10	2006-02-16		ENSG00000166839	ENSG00000166839		"Ankyrin repeat domain containing"	28002	protein-coding gene	gene with protein product						12477932	Standard	NM_182703		Approved	FLJ25870	uc002aoa.3	Q495B1	OTTHUMG00000133051	ENST00000380230.3:c.333delA	chr15.hg19:g.65214185delA	ENSP00000369579:p.Val111fs	76.0	0.0	0		80.0	17.0	0.2125	NM_182703	Q495B2|Q495B3|Q8N7A0|Q8NBS5	Frame_Shift_Del	DEL	ENST00000380230.3	hg19	CCDS10197.2																																																																																			.	.	.	none		0.577	ANKDD1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256705.2	NM_182703		-	65214185	A	-	65214185	7	5	76	1	0	1	0	1	0	0	0	0	624	349	13	0	347	0	ANKDD1A	15	65214185	Frame_Shift_Del	DEL	A	TCGA-AL-7173-01A-11D-2136-08		65214185	37317207	47	4921											
SEMA7A	8482	hgsc.bcm.edu	37	chr15	74708932	74708932	+	Missense_Mutation	SNP	A	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	tcaccctgcacaactgggccAcacgggacacattgagagga	12	5	11	13	1	1	1	1	1	0	1	1	4	1	3	2	3	2	1	2	3	1	1			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr15:74708932A>C	ENST00000261918.4	-	7	1333	c.785T>G	c.(784-786)gTg>gGg	p.V262G	SEMA7A_ENST00000543145.2_Missense_Mutation_p.V248G|SEMA7A_ENST00000542748.1_Missense_Mutation_p.V97G	NM_003612.3	NP_003603.1	O75326	SEM7A_HUMAN	semaphorin 7A, GPI membrane anchor (John Milton Hagen blood group)	262	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						CAACTGGGCCACACGGGACAC	0.552																																					p.V262G		Atlas-SNP	.											.	SEMA7A	58	.	0			c.T785G						PASS	.						204	168	180					15																	74708932		2197	4296	6493	SO:0001583	missense	8482	exon7			TGGGCCACACGGG	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.785T>G	chr15.hg19:g.74708932A>C	ENSP00000261918:p.Val262Gly	68.0	0.0	.		63.0	18.0	.	NM_003612	B4DDP7|F5H1S0|Q1XE81|Q1XE82|Q1XE83|Q1XE84|Q3MIY5	Missense_Mutation	SNP	ENST00000261918.4	hg19	CCDS10262.1	.	.	.	.	.	.	.	.	.	.	A	16.84	3.235032	0.58886	.	.	ENSG00000138623	ENST00000261918;ENST00000543145;ENST00000542748	T;T;T	0.35789	1.29;1.29;1.29	5.39	5.39	0.77823	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.065645	0.64402	D	0.000009	T	0.67316	0.2880	M	0.91354	3.2	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.75622	-0.3254	10	0.87932	D	0	-18.6242	13.6573	0.62346	1.0:0.0:0.0:0.0	.	248;262	F5H1S0;O75326	.;SEM7A_HUMAN	G	262;248;97	ENSP00000261918:V262G;ENSP00000438966:V248G;ENSP00000441493:V97G	ENSP00000261918:V262G	V	-	2	0	SEMA7A	72495985	1.000000	0.71417	0.993000	0.49108	0.169000	0.22640	5.449000	0.66619	2.043000	0.60533	0.533000	0.62120	GTG	.	.	.	none		0.552	SEMA7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272904.3	NM_003612		C	74708932	A	C	74708932	3	2	76	1	0	0	0	0	1	0	0	0	14056	159	6	5	1247	5	SEMA7A	15	74708932	Missense_Mutation	SNP	A	TCGA-AL-7173-01A-11D-2136-08	9494747	74708932	27822460	48	4922											
ARID3B	10620	hgsc.bcm.edu	37	chr15	74884140	74884140	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagctccccatgaagatcAggatcaacggcaggggtgag	11	5	15	10	1	2	3	2	2	0	1	3	4	3	4	2	5	2	3	2	5	2	0			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr15:74884140A>G	ENST00000346246.5	+	7	1636	c.1405A>G	c.(1405-1407)Agg>Ggg	p.R469G		NM_006465.2	NP_006456.1	Q8IVW6	ARI3B_HUMAN	AT rich interactive domain 3B (BRIGHT-like)	469	REKLES. {ECO:0000255|PROSITE- ProRule:PRU00819}.					nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)			NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(2)	14						CATGAAGATCAGGATCAACGG	0.637																																					p.R469G		Atlas-SNP	.											.	ARID3B	35	.	0			c.A1405G						PASS	.						43	45	44					15																	74884140		2196	4296	6492	SO:0001583	missense	10620	exon7			AAGATCAGGATCA		CCDS10264.1	15q24	2013-02-07	2006-11-08		ENSG00000179361	ENSG00000179361		"-"	14350	protein-coding gene	gene with protein product		612457	"AT rich interactive domain 3B (BRIGHT- like)"				Standard	NM_006465		Approved	BDP, DRIL2	uc002ayd.3	Q8IVW6	OTTHUMG00000141321	ENST00000346246.5:c.1405A>G	chr15.hg19:g.74884140A>G	ENSP00000343126:p.Arg469Gly	109.0	0.0	.		114.0	5.0	.	NM_006465	O95443|Q59HC9|Q6P9C9	Missense_Mutation	SNP	ENST00000346246.5	hg19	CCDS10264.1	.	.	.	.	.	.	.	.	.	.	A	16.97	3.268903	0.59540	.	.	ENSG00000179361	ENST00000346246	T	0.47177	0.85	5.31	-0.252	0.12999	REKLES domain (1);	1.496780	0.03536	N	0.223239	T	0.51329	0.1668	L	0.49126	1.545	0.39186	D	0.962875	P;P	0.43352	0.501;0.804	B;P	0.44860	0.081;0.462	T	0.50224	-0.8853	10	0.33141	T	0.24	-15.6404	14.4155	0.67148	0.4611:0.5389:0.0:0.0	.	469;469	Q8IVW6;Q8IVW6-4	ARI3B_HUMAN;.	G	469	ENSP00000343126:R469G	ENSP00000343126:R469G	R	+	1	2	ARID3B	72671193	0.082000	0.21442	0.638000	0.29380	0.820000	0.46376	1.178000	0.31981	-0.309000	0.08779	0.533000	0.62120	AGG	.	.	.	none		0.637	ARID3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280688.2	NM_006465		G	74884140	A	G	74884140	3	3	76	1	0	0	0	0	1	0	0	0	917	179	7	3	1427	3	ARID3B	15	74884140	Missense_Mutation	SNP	A	TCGA-AL-7173-01A-11D-2136-08	175208	74884140	27647252	49	4923											
SGK269	79834	hgsc.bcm.edu	37	chr15	77406689	77406689	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagggtgttcctctgtactaGgctagggcaggcggtgaaag	8	9	16	8	1	1	1	0	1	1	0	2	1	2	1	1	5	1	4	1	5	4	4			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr15:77406689G>A	ENST00000560626.2	-	7	5525	c.5050C>T	c.(5050-5052)Cta>Tta	p.L1684L	PEAK1_ENST00000312493.4_Silent_p.L1684L			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	1684					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										CTCTGTACTAGGCTAGGGCAG	0.542																																					p.L1684L		Atlas-SNP	.											.	.	.	.	0			c.C5050T						PASS	.						93	96	95					15																	77406689		1943	4130	6073	SO:0001819	synonymous_variant	0	exon8			GTACTAGGCTAGG		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.5050C>T	chr15.hg19:g.77406689G>A		143.0	0.0	.		137.0	34.0	.	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Silent	SNP	ENST00000560626.2	hg19	CCDS42062.1																																																																																			.	.	.	none		0.542	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3			A	77406689	G	A	77406689	2	1	76	1	0	0	0	0	0	0	0	1	14224	991	35	2		2	SGK269	15	77406689	Silent	SNP	G	TCGA-AL-7173-01A-11D-2136-08	2522549	77406689	25124703	50	4924											
ZNF423	23090	hgsc.bcm.edu	37	chr16	49670185	49670185	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaccacagatgggacacaTgtagtgcttggcagggcccc	9	7	12	13	0	1	1	1	0	0	1	1	2	1	2	3	3	1	3	3	3	1	2			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr16:49670185T>C	ENST00000561648.1	-	4	2931	c.2878A>G	c.(2878-2880)Atg>Gtg	p.M960V	ZNF423_ENST00000567169.1_Missense_Mutation_p.M843V|ZNF423_ENST00000262383.2_Missense_Mutation_p.M960V|ZNF423_ENST00000563137.2_Missense_Mutation_p.M900V|ZNF423_ENST00000562520.1_Missense_Mutation_p.M900V|ZNF423_ENST00000562871.1_Missense_Mutation_p.M900V|ZNF423_ENST00000535559.1_Missense_Mutation_p.M843V	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	960					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)				ATGGGACACATGTAGTGCTTG	0.602																																					p.M960V		Atlas-SNP	.											.	ZNF423	463	.	0			c.A2878G						PASS	.						72	54	60					16																	49670185		2198	4300	6498	SO:0001583	missense	23090	exon4			GACACATGTAGTG	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.2878A>G	chr16.hg19:g.49670185T>C	ENSP00000455426:p.Met960Val	61.0	0.0	.		62.0	12.0	.	NM_015069	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	hg19	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	T	19.12	3.766597	0.69878	.	.	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.16897	2.31;2.31	4.81	4.81	0.61882	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	0.18551	0.0445	N	0.04043	-0.29	0.45648	D	0.998576	D	0.61697	0.99	D	0.67548	0.952	T	0.32375	-0.9909	9	.	.	.	-30.7346	14.3758	0.66874	0.0:0.0:0.0:1.0	.	960	Q2M1K9	ZN423_HUMAN	V	960;843	ENSP00000262383:M960V;ENSP00000442321:M843V	.	M	-	1	0	ZNF423	48227686	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.289000	0.72696	1.814000	0.52955	0.459000	0.35465	ATG	.	.	.	none		0.602	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		C	49670185	T	C	49670185	3	2	76	1	0	0	0	0	1	0	0	0	17910	1464	51	3	996	3	ZNF423	16	49670185	Missense_Mutation	SNP	T	TCGA-AL-7173-01A-11D-2136-08		49670185	40684568	51	4925											
FLII	2314	hgsc.bcm.edu	37	chr17	18150655	18150655	+	Missense_Mutation	SNP	A	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	acacatcgtcccaattcttgAacttggccttgaacacctgc	10	11	6	14	1	1	2	0	2	1	0	3	2	2	2	3	1	3	0	3	1	3	4			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr17:18150655A>C	ENST00000327031.4	-	21	2729	c.2504T>G	c.(2503-2505)tTc>tGc	p.F835C	FLII_ENST00000545457.2_Missense_Mutation_p.F780C|FLII_ENST00000579294.1_Missense_Mutation_p.F824C|FLII_ENST00000379450.4_Missense_Mutation_p.F749C|FLII_ENST00000578558.1_Intron	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	835					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)					CCAATTCTTGAACTTGGCCTT	0.602																																					p.F835C		Atlas-SNP	.											.	FLII	79	.	0			c.T2504G						PASS	.						108	92	97					17																	18150655		2203	4300	6503	SO:0001583	missense	2314	exon21			TTCTTGAACTTGG	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.2504T>G	chr17.hg19:g.18150655A>C	ENSP00000324573:p.Phe835Cys	119.0	0.0	.		109.0	18.0	.	NM_002018	B4DIL0|F5H407|J3QLG3	Missense_Mutation	SNP	ENST00000327031.4	hg19	CCDS11192.1	.	.	.	.	.	.	.	.	.	.	A	19.68	3.872270	0.72180	.	.	ENSG00000177731	ENST00000327031;ENST00000379450	T;T	0.45276	0.9;0.9	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.67785	0.2930	M	0.82323	2.585	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.97110	0.996;0.996;1.0;0.993	T	0.73685	-0.3905	10	0.87932	D	0	-23.7587	15.4271	0.75061	1.0:0.0:0.0:0.0	.	749;749;835;804	E7EPM0;B4DIL0;Q13045;B4DIX0	.;.;FLII_HUMAN;.	C	835;749	ENSP00000324573:F835C;ENSP00000368763:F749C	ENSP00000324573:F835C	F	-	2	0	FLII	18091380	1.000000	0.71417	1.000000	0.80357	0.553000	0.35397	8.532000	0.90613	2.045000	0.60652	0.460000	0.39030	TTC	.	.	.	none		0.602	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018		C	18150655	A	C	18150655	3	2	76	1	0	0	0	0	1	0	0	0	5932	246	9	5	1345	5	FLII	17	18150655	Missense_Mutation	SNP	A	TCGA-AL-7173-01A-11D-2136-08		18150655	63044555	52	4926											
ZPBP2	124626	hgsc.bcm.edu	37	chr17	38027753	38027753	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tataactgaaactggacagcTgatggtgaaagattttttgg	13	13	11	4	0	0	4	0	3	0	1	0	5	0	5	0	3	3	1	0	3	4	5			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr17:38027753T>C	ENST00000348931.4	+	4	472	c.281T>C	c.(280-282)cTg>cCg	p.L94P	ZPBP2_ENST00000584588.1_Missense_Mutation_p.L94P|ZPBP2_ENST00000377940.3_Missense_Mutation_p.L72P	NM_199321.2	NP_955353.1	Q6X784	ZPBP2_HUMAN	zona pellucida binding protein 2	94					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)			ACTGGACAGCTGATGGTGAAA	0.294																																					p.L94P		Atlas-SNP	.											.	ZPBP2	33	.	0			c.T281C						PASS	.						93	98	96					17																	38027753		2203	4298	6501	SO:0001583	missense	124626	exon4			GACAGCTGATGGT	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.281T>C	chr17.hg19:g.38027753T>C	ENSP00000335384:p.Leu94Pro	96.0	0.0	.		59.0	15.0	.	NM_199321	A8K8L8|Q6X783|Q86XL5	Missense_Mutation	SNP	ENST00000348931.4	hg19	CCDS11352.1	.	.	.	.	.	.	.	.	.	.	T	19.59	3.855999	0.71834	.	.	ENSG00000186075	ENST00000348931;ENST00000377940	D;D	0.92397	-3.03;-3.03	5.46	5.46	0.80206	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.49305	D	0.000158	D	0.95698	0.8601	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.96132	0.9093	10	0.87932	D	0	-7.3583	13.7798	0.63077	0.0:0.0:0.0:1.0	.	72;94	Q6X784-2;Q6X784	.;ZPBP2_HUMAN	P	94;72	ENSP00000335384:L94P;ENSP00000367174:L72P	ENSP00000335384:L94P	L	+	2	0	ZPBP2	35281279	1.000000	0.71417	0.994000	0.49952	0.981000	0.71138	4.645000	0.61404	2.072000	0.62099	0.377000	0.23210	CTG	.	.	.	none		0.294	ZPBP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256609.2	NM_198844		C	38027753	T	C	38027753	3	2	76	1	0	0	0	0	1	0	0	0	18232	1580	55	3	295	3	ZPBP2	17	38027753	Missense_Mutation	SNP	T	TCGA-AL-7173-01A-11D-2136-08	19877098	38027753	43167457	53	4927											
TIMP2	7077	hgsc.bcm.edu	37	chr17	76867041	76867047	+	Frame_Shift_Del	DEL	GGGGGCC	GGGGGCC	-																															accccacacactgccgaggaGggggccgtgtagataaactc																								rs372752139		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	GGGGGCC	GGGGGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr17:76867041_76867047delGGGGGCC	ENST00000262768.7	-	3	571_577	c.273_279delGGCCCCC	c.(271-279)acggcccccfs	p.TAP91fs	TIMP2_ENST00000586057.1_Frame_Shift_Del_p.TAP14fs|TIMP2_ENST00000585421.1_Frame_Shift_Del_p.TAP14fs|TIMP2_ENST00000536189.2_Frame_Shift_Del_p.TAP14fs	NM_003255.4	NP_003246.1	P16035	TIMP2_HUMAN	TIMP metallopeptidase inhibitor 2	91	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				aging (GO:0007568)|cellular response to organic substance (GO:0071310)|central nervous system development (GO:0007417)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of proteolysis (GO:0045861)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|regulation of Rap protein signal transduction (GO:0032487)|response to cytokine (GO:0034097)|response to drug (GO:0042493)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)	p.A92V(1)|p.S94fs*43(1)		central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.194)			CTGCCGAGGAGGGGGCCGTGTAGATAA	0.541																																					p.92_94del		Atlas-INDEL	.											.	TIMP2	27	.	2	Substitution - Missense(1)|Deletion - Frameshift(1)	ovary(1)|prostate(1)	c.274_280del						PASS	.																																			SO:0001589	frameshift_variant	7077	exon3			.		CCDS11758.1	17q25	2008-07-18	2005-08-08		ENSG00000035862	ENSG00000035862			11821	protein-coding gene	gene with protein product		188825	"tissue inhibitor of metalloproteinase 2"			1427908	Standard	NM_003255		Approved	CSC-21K	uc002jwf.3	P16035	OTTHUMG00000154517	ENST00000262768.7:c.273_279delGGCCCCC	chr17.hg19:g.76867041_76867047delGGGGGCC	ENSP00000262768:p.Thr91fs	180.0	0.0	0		161.0	10.0	0.0621118	NM_003255	Q16121|Q93006|Q9UDF7	Frame_Shift_Del	DEL	ENST00000262768.7	hg19	CCDS11758.1																																																																																			.	.	.	none		0.541	TIMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335662.1	NM_003255		-	76867047	GGGGGCC	-	76867041	7	5	76	1	0	1	0	1	0	0	0	0	15930	987	35	0	395	0	TIMP2	17	76867041	Frame_Shift_Del	DEL	GGGGGCC	TCGA-AL-7173-01A-11D-2136-08	38839288	76867041	4328169	54	4928											
PLVAP	83483	hgsc.bcm.edu	37	chr19	17476968	17476968	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgcttctcactcaagatgaTggcagccatgtacctctgat	9	13	8	11	0	3	3	2	2	2	1	4	3	3	3	2	1	3	3	2	1	2	3			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr19:17476968T>C	ENST00000252590.4	-	2	467	c.406A>G	c.(406-408)Atc>Gtc	p.I136V		NM_031310.1	NP_112600.1	Q9BX97	PLVAP_HUMAN	plasmalemma vesicle associated protein	136					MAPK cascade (GO:0000165)|positive regulation of cellular extravasation (GO:0002693)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CTCAAGATGATGGCAGCCATG	0.552																																					p.I136V		Atlas-SNP	.											.	PLVAP	64	.	0			c.A406G						PASS	.						237	203	215					19																	17476968		2203	4300	6503	SO:0001583	missense	83483	exon2			AGATGATGGCAGC	AF326591	CCDS32952.1	19p13.2	2008-07-17				ENSG00000130300			13635	protein-coding gene	gene with protein product	"fenestrated-endothelial linked structure protein; PV-1 protein"	607647				11401446	Standard	NM_031310		Approved	gp68, PV-1, PV1, FELS	uc002ngk.1	Q9BX97		ENST00000252590.4:c.406A>G	chr19.hg19:g.17476968T>C	ENSP00000252590:p.Ile136Val	196.0	0.0	.		191.0	52.0	.	NM_031310	Q86VP0|Q8N8Y0|Q8ND68|Q8TER8|Q9BZD5	Missense_Mutation	SNP	ENST00000252590.4	hg19	CCDS32952.1	.	.	.	.	.	.	.	.	.	.	T	11.14	1.551302	0.27739	.	.	ENSG00000130300	ENST00000252590	T	0.31247	1.5	4.07	3.05	0.35203	.	0.289259	0.35708	N	0.003037	T	0.33818	0.0876	L	0.34521	1.04	0.26494	N	0.974888	D	0.69078	0.997	D	0.80764	0.994	T	0.15178	-1.0446	10	0.10111	T	0.7	-51.4771	6.1733	0.20429	0.0:0.114:0.0:0.886	.	136	Q9BX97	PLVAP_HUMAN	V	136	ENSP00000252590:I136V	ENSP00000252590:I136V	I	-	1	0	PLVAP	17337968	1.000000	0.71417	0.994000	0.49952	0.058000	0.15608	2.845000	0.48254	0.915000	0.36847	0.459000	0.35465	ATC	.	.	.	none		0.552	PLVAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463655.1	NM_031310		C	17476968	T	C	17476968	3	2	76	1	0	0	0	0	1	0	0	0	12123	1464	51	3	942	3	PLVAP	19	17476968	Missense_Mutation	SNP	T	TCGA-AL-7173-01A-11D-2136-08		17476968	41652015	55	4929											
ZNF780A	284323	hgsc.bcm.edu	37	chr19	40581903	40581903	+	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	aagcatgaggagtatgagtaGgcagtttttcatagctgatc	12	12	12	5	0	1	3	1	3	0	0	2	4	1	4	0	2	2	6	0	2	4	5			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr19:40581903G>C	ENST00000595687.2	-	6	655	c.446C>G	c.(445-447)cCt>cGt	p.P149R	ZNF780A_ENST00000455521.1_Missense_Mutation_p.P150R|ZNF780A_ENST00000450241.2_Missense_Mutation_p.P115R|ZNF780A_ENST00000594395.1_Missense_Mutation_p.P150R|ZNF780A_ENST00000340963.5_Missense_Mutation_p.P149R|AC005614.5_ENST00000595508.1_RNA|ZNF780A_ENST00000414720.2_Intron	NM_001010880.2	NP_001010880.2	O75290	Z780A_HUMAN	zinc finger protein 780A	149					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|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)					AGTATGAGTAGGCAGTTTTTC	0.333																																					p.P150R		Atlas-SNP	.											.	ZNF780A	156	.	0			c.C449G						PASS	.						198	170	179					19																	40581903		2203	4300	6503	SO:0001583	missense	284323	exon6			TGAGTAGGCAGTT	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.446C>G	chr19.hg19:g.40581903G>C	ENSP00000472189:p.Pro149Arg	97.0	0.0	.		76.0	17.0	.	NM_001142577	E9PB48|Q6ZN87	Missense_Mutation	SNP	ENST00000595687.2	hg19	CCDS33026.2	.	.	.	.	.	.	.	.	.	.	G	0.101	-1.152082	0.01700	.	.	ENSG00000197782	ENST00000450241;ENST00000455521;ENST00000340963	T;T	0.05447	3.44;3.46	0.928	0.928	0.19443	.	.	.	.	.	T	0.07413	0.0187	M	0.64404	1.975	0.09310	N	1	P;P	0.48162	0.51;0.906	B;B	0.44163	0.099;0.443	T	0.27872	-1.0061	9	0.15499	T	0.54	.	4.8476	0.13521	0.0:0.3981:0.6019:0.0	.	150;149	E9PB48;O75290	.;Z780A_HUMAN	R	149;150;149	ENSP00000400997:P150R;ENSP00000341507:P149R	ENSP00000341507:P149R	P	-	2	0	ZNF780A	45273743	0.000000	0.05858	0.009000	0.14445	0.048000	0.14542	-1.367000	0.02583	0.796000	0.33947	0.305000	0.20034	CCT	.	.	.	none		0.333	ZNF780A-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000470066.1	NM_001010880		C	40581903	G	C	40581903	3	2	76	1	0	0	0	0	1	0	0	0	18164	1000	35	4	1610	4	ZNF780A	19	40581903	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08	23104935	40581903	18547080	56	4930											
NLRP7	199713	hgsc.bcm.edu	37	chr19	55449434	55449434	+	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	cactttctgcagatgacaggTgctacgggttacgtggtcac	8	11	12	10	2	2	2	1	1	1	1	2	2	2	2	0	3	4	3	0	3	2	3			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr19:55449434T>A	ENST00000590030.1	-	4	2147	c.2107A>T	c.(2107-2109)Acc>Tcc	p.T703S	NLRP7_ENST00000340844.2_Missense_Mutation_p.T703S|NLRP7_ENST00000588756.1_Missense_Mutation_p.T703S|NLRP7_ENST00000448121.2_Missense_Mutation_p.T675S|NLRP7_ENST00000446217.1_Missense_Mutation_p.T731S|NLRP7_ENST00000328092.5_Missense_Mutation_p.T675S|NLRP7_ENST00000592784.1_Missense_Mutation_p.T703S			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	703							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)		AGATGACAGGTGCTACGGGTT	0.428																																					p.T703S		Atlas-SNP	.											.	NLRP7	411	.	0			c.A2107T						PASS	.						243	252	249					19																	55449434		2203	4300	6503	SO:0001583	missense	199713	exon5			GACAGGTGCTACG	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.2107A>T	chr19.hg19:g.55449434T>A	ENSP00000465520:p.Thr703Ser	421.0	0.0	.		418.0	101.0	.	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	hg19	CCDS33109.1	.	.	.	.	.	.	.	.	.	.	T	3.493	-0.103411	0.06967	.	.	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217;ENST00000399724	T;T;T	0.51325	0.71;0.71;0.71	2.19	-1.51	0.08664	.	0.529447	0.14299	N	0.328408	T	0.26159	0.0638	L	0.40543	1.245	0.09310	N	1	B;B;B;B	0.32203	0.264;0.151;0.151;0.36	B;B;B;B	0.26416	0.057;0.032;0.032;0.069	T	0.16041	-1.0416	10	0.16896	T	0.51	.	2.3	0.04160	0.4111:0.2735:0.0:0.3154	.	731;703;703;675	E7EPM2;Q32MH9;Q8WX94;Q8WX94-2	.;.;NALP7_HUMAN;.	S	703;675;703;731;470	ENSP00000409137:T675S;ENSP00000339491:T703S;ENSP00000414273:T731S	ENSP00000329568:T703S	T	-	1	0	NLRP7	60141246	0.002000	0.14202	0.002000	0.10522	0.002000	0.02628	-0.473000	0.06615	-0.505000	0.06568	-1.288000	0.01363	ACC	.	.	.	none		0.428	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		A	55449434	T	A	55449434	3	1	76	1	0	0	0	0	1	0	0	0	10489	1696	59	5	1034	5	NLRP7	19	55449434	Missense_Mutation	SNP	T	TCGA-AL-7173-01A-11D-2136-08	14867531	55449434	3679549	57	4931											
CHRNA4	1137	hgsc.bcm.edu	37	chr20	61982183	61982183	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggtccacgcggctgtgcaTgttcaccaggtcgatcttgg	5	11	13	12	3	2	0	1	0	1	0	4	1	3	0	2	4	1	3	2	4	0	2			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr20:61982183T>C	ENST00000370263.4	-	5	801	c.580A>G	c.(580-582)Atg>Gtg	p.M194V	CHRNA4_ENST00000463705.1_5'UTR	NM_000744.6|NM_001256573.1	NP_000735.1|NP_001243502.1	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 (neuronal)	194					action potential (GO:0001508)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cognition (GO:0050890)|DNA repair (GO:0006281)|exploration behavior (GO:0035640)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|neurological system process (GO:0050877)|regulation of dopamine secretion (GO:0014059)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(19)|prostate(3)|skin(3)|soft_tissue(1)	33	all_cancers(38;1.71e-10)				Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	CGGCTGTGCATGTTCACCAGG	0.587																																					p.M194V		Atlas-SNP	.											.	CHRNA4	98	.	0			c.A580G						PASS	.						138	114	122					20																	61982183		2203	4299	6502	SO:0001583	missense	1137	exon5			TGTGCATGTTCAC		CCDS13517.1	20q13.33	2013-09-20	2012-02-07		ENSG00000101204	ENSG00000101204		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1958	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 4 (neuronal)"	118504	"cholinergic receptor, nicotinic, alpha polypeptide 4"	EBN, EBN1		1505988	Standard	NM_000744		Approved	BFNC	uc002yes.3	P43681	OTTHUMG00000033080	ENST00000370263.4:c.580A>G	chr20.hg19:g.61982183T>C	ENSP00000359285:p.Met194Val	97.0	0.0	.		96.0	25.0	.	NM_000744	Q4JGR7|Q4VAQ5|Q4VAQ6	Missense_Mutation	SNP	ENST00000370263.4	hg19	CCDS13517.1	.	.	.	.	.	.	.	.	.	.	T	12.02	1.814091	0.32053	.	.	ENSG00000101204	ENST00000370258;ENST00000370263;ENST00000539366	T	0.78707	-1.2	4.87	2.6	0.31112	Neurotransmitter-gated ion-channel ligand-binding (3);	0.074711	0.85682	N	0.000000	T	0.61527	0.2354	N	0.16233	0.39	0.58432	D	0.999998	B;B	0.31125	0.309;0.017	B;B	0.31946	0.138;0.052	T	0.57382	-0.7821	10	0.72032	D	0.01	.	8.8251	0.35050	0.0:0.1556:0.0:0.8444	.	123;194	Q4VAQ5;P43681	.;ACHA4_HUMAN	V	100;194;123	ENSP00000359285:M194V	ENSP00000359280:M100V	M	-	1	0	CHRNA4	61452627	1.000000	0.71417	0.980000	0.43619	0.625000	0.37756	4.841000	0.62824	0.225000	0.20959	-0.379000	0.06801	ATG	.	.	.	none		0.587	CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3			C	61982183	T	C	61982183	3	2	76	1	0	0	0	0	1	0	0	0	3387	1464	51	3	1311	3	CHRNA4	20	61982183	Missense_Mutation	SNP	T	TCGA-AL-7173-01A-11D-2136-08		61982183	1043337	58	4932											
ARFRP1	10139	hgsc.bcm.edu	37	chr20	62333531	62333531	+	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	agcctctcctcgtcggtggaGtcaatgacgtagatgacgcc	8	9	12	12	4	2	3	1	2	1	1	5	4	2	4	3	2	1	1	3	2	2	1			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr20:62333531G>C	ENST00000359715.5	-	4	869	c.303C>G	c.(301-303)gaC>gaG	p.D101E	ARFRP1_ENST00000324228.2_Missense_Mutation_p.D101E|ARFRP1_ENST00000485858.1_5'Flank|ARFRP1_ENST00000607873.1_Missense_Mutation_p.D54E|ARFRP1_ENST00000609142.1_Missense_Mutation_p.D101E|ARFRP1_ENST00000440854.1_Missense_Mutation_p.D101E			Q13795	ARFRP_HUMAN	ADP-ribosylation factor related protein 1	101					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)			CGTCGGTGGAGTCAATGACGT	0.632																																					p.D101E		Atlas-SNP	.											.	ARFRP1	17	.	0			c.C303G						PASS	.						102	82	89					20																	62333531		2203	4297	6500	SO:0001583	missense	10139	exon5			GGTGGAGTCAATG	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.303C>G	chr20.hg19:g.62333531G>C	ENSP00000352746:p.Asp101Glu	75.0	0.0	.		69.0	20.0	.	NM_001134758	B7ZKX7|E1P5J9|Q6IBQ0	Missense_Mutation	SNP	ENST00000359715.5	hg19	CCDS13533.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.178823	0.78564	.	.	ENSG00000101246	ENST00000440854;ENST00000359715;ENST00000324228	T;T;T	0.79247	-1.25;-1.25;-1.25	5.53	-0.912	0.10504	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.91895	0.7434	H	0.99726	4.73	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90445	0.4434	10	0.87932	D	0	-27.1276	9.796	0.40735	0.4997:0.0:0.5003:0.0	.	101;101	B3KTR4;Q13795	.;ARFRP_HUMAN	E	101	ENSP00000403942:D101E;ENSP00000352746:D101E;ENSP00000326884:D101E	ENSP00000326884:D101E	D	-	3	2	ARFRP1	61803975	1.000000	0.71417	0.998000	0.56505	0.751000	0.42716	1.177000	0.31969	-0.026000	0.13895	0.462000	0.41574	GAC	.	.	.	none		0.632	ARFRP1-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472024.1			C	62333531	G	C	62333531	3	2	76	1	0	0	0	0	1	0	0	0	856	1020	36	4	322	4	ARFRP1	20	62333531	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08	351348	62333531	691989	59	4933											
ZDHHC8	29801	hgsc.bcm.edu	37	chr22	20130720	20130720	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acccgccacggcccctacccCgcagcttcagccccgtgctg	5	5	9	22	4	1	0	1	0	0	0	1	0	1	0	8	1	4	3	8	1	1	2	rs532240635		TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr22:20130720C>T	ENST00000334554.7	+	10	1708	c.1567C>T	c.(1567-1569)Cgc>Tgc	p.R523C	ZDHHC8_ENST00000405930.3_Missense_Mutation_p.R523C|ZDHHC8_ENST00000320602.7_Missense_Mutation_p.R431C	NM_013373.3	NP_037505.1	Q9ULC8	ZDHC8_HUMAN	zinc finger, DHHC-type containing 8	523					locomotory behavior (GO:0007626)|protein palmitoylation (GO:0018345)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	20	Colorectal(54;0.0993)					GCCCCTACCCCGCAGCTTCAG	0.706																																					p.R523C		Atlas-SNP	.											.	ZDHHC8	77	.	0			c.C1567T						PASS	.						17	21	19					22																	20130720		2173	4267	6440	SO:0001583	missense	29801	exon10			CTACCCCGCAGCT	AB033118	CCDS13776.1, CCDS54502.1	22q11.21	2009-10-06		2003-02-28	ENSG00000099904	ENSG00000099904		"Zinc fingers, DHHC-type"	18474	protein-coding gene	gene with protein product		608784				10574462, 15184899	Standard	NM_013373		Approved	ZNF378, KIAA1292	uc002zrr.2	Q9ULC8	OTTHUMG00000150499	ENST00000334554.7:c.1567C>T	chr22.hg19:g.20130720C>T	ENSP00000334490:p.Arg523Cys	74.0	0.0	.		56.0	14.0	.	NM_001185024	Q2TGE9|Q6ICL1|Q6ZNF5|Q7Z6L9	Missense_Mutation	SNP	ENST00000334554.7	hg19	CCDS13776.1	.	.	.	.	.	.	.	.	.	.	.	16.52	3.147388	0.57151	.	.	ENSG00000099904	ENST00000334554;ENST00000320602;ENST00000405930	T;T;T	0.74002	1.22;-0.8;1.19	4.79	3.77	0.43336	.	1.375280	0.04372	N	0.359278	T	0.79411	0.4441	L	0.29908	0.895	0.49213	D	0.999762	D;D;D	0.69078	0.981;0.996;0.997	P;P;P	0.59703	0.635;0.862;0.642	T	0.65302	-0.6201	10	0.56958	D	0.05	.	12.8482	0.57842	0.0:0.9203:0.0:0.0797	.	431;523;523	Q9ULC8-2;Q9ULC8-3;Q9ULC8	.;.;ZDHC8_HUMAN	C	523;431;523	ENSP00000334490:R523C;ENSP00000317804:R431C;ENSP00000384716:R523C	ENSP00000317804:R431C	R	+	1	0	ZDHHC8	18510720	0.996000	0.38824	1.000000	0.80357	0.387000	0.30353	3.788000	0.55446	1.025000	0.39708	-0.339000	0.08088	CGC	.	.	.	none		0.706	ZDHHC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318564.1	NM_013373		T	20130720	C	T	20130720	3	4	76	1	0	0	0	0	1	0	0	0	17633	652	23	1	1605	1	ZDHHC8	22	20130720	Missense_Mutation	SNP	C	TCGA-AL-7173-01A-11D-2136-08		20130720	31173846	60	4934											
ADSL	158	hgsc.bcm.edu	37	chr22	40745897	40745897	+	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	gaaatcaaacctggagaacaTcgacttcaagatggcagctg	15	7	10	9	1	2	2	2	0	0	2	3	5	2	2	1	2	3	2	1	2	4	1			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr22:40745897T>A	ENST00000216194.7	+	2	271	c.215T>A	c.(214-216)aTc>aAc	p.I72N	ADSL_ENST00000454266.2_Missense_Mutation_p.I72N|ADSL_ENST00000342312.6_Missense_Mutation_p.I72N	NM_000026.2	NP_000017.1	P30566	PUR8_HUMAN	adenylosuccinate lyase	72			I -> V (in ADSL deficiency; severe). {ECO:0000269|PubMed:10090474}.		'de novo' AMP biosynthetic process (GO:0044208)|'de novo' IMP biosynthetic process (GO:0006189)|aerobic respiration (GO:0009060)|AMP biosynthetic process (GO:0006167)|metabolic process (GO:0008152)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein tetramerization (GO:0051262)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to hypoxia (GO:0001666)|response to muscle activity (GO:0014850)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate AMP-lyase (fumarate-forming) activity (GO:0070626)|N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity (GO:0004018)			breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(2)|ovary(1)|prostate(1)	19						CTGGAGAACATCGACTTCAAG	0.433																																					p.I72N	Colon(4;65 130 1097 1516)	Atlas-SNP	.											.	ADSL	98	.	0			c.T215A						PASS	.						119	94	102					22																	40745897		2203	4300	6503	SO:0001583	missense	158	exon2			AGAACATCGACTT	X65867	CCDS14001.1, CCDS46714.1	22q13.1	2011-02-17			ENSG00000239900	ENSG00000239900	4.3.2.2		291	protein-coding gene	gene with protein product		608222				8404037	Standard	NM_000026		Approved		uc003ayp.4	P30566	OTTHUMG00000166425	ENST00000216194.7:c.215T>A	chr22.hg19:g.40745897T>A	ENSP00000216194:p.Ile72Asn	88.0	0.0	.		56.0	11.0	.	NM_001123378	B0QY76|O75495|Q5TI34	Missense_Mutation	SNP	ENST00000216194.7	hg19	CCDS14001.1	.	.	.	.	.	.	.	.	.	.	T	32	5.145835	0.94603	.	.	ENSG00000239900	ENST00000216194;ENST00000544206;ENST00000425605;ENST00000454266;ENST00000342312	D;D;D	0.95518	-3.73;-3.73;-3.64	5.59	5.59	0.84812	L-Aspartase-like (1);L-Aspartase-like, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98273	0.9428	M	0.93638	3.44	0.80722	D	1	D;D;D;D	0.71674	0.978;0.983;0.998;0.998	P;D;D;D	0.76575	0.822;0.929;0.988;0.988	D	0.99433	1.0936	10	0.72032	D	0.01	-8.6026	15.8537	0.78956	0.0:0.0:0.0:1.0	.	72;72;72;72	E7ERF4;P30566-2;Q71UA4;P30566	.;.;.;PUR8_HUMAN	N	72	ENSP00000216194:I72N;ENSP00000390107:I72N;ENSP00000341429:I72N	ENSP00000216194:I72N	I	+	2	0	ADSL	39075843	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	7.757000	0.85209	2.141000	0.66446	0.529000	0.55759	ATC	.	.	.	none		0.433	ADSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321386.1	NM_000026		A	40745897	T	A	40745897	3	1	76	1	0	0	0	0	1	0	0	0	346	1435	50	5	221	5	ADSL	22	40745897	Missense_Mutation	SNP	T	TCGA-AL-7173-01A-11D-2136-08	20615177	40745897	10558669	61	4935											
PARVG	64098	hgsc.bcm.edu	37	chr22	44581694	44581694	+	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	cactctgcttccaggaggaaAgaagaaatacctgccaccca	14	6	8	13	0	1	2	0	0	1	2	2	4	2	4	4	2	3	1	4	2	4	2			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr22:44581694A>T	ENST00000444313.3	+	4	570	c.86A>T	c.(85-87)aAg>aTg	p.K29M	PARVG_ENST00000415224.1_Missense_Mutation_p.K29M|PARVG_ENST00000453888.3_3'UTR|PARVG_ENST00000422871.1_Missense_Mutation_p.K29M	NM_022141.5	NP_071424.1	Q9HBI0	PARVG_HUMAN	parvin, gamma	29					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)				CCAGGAGGAAAGAAGAAATAC	0.577																																					p.K96M		Atlas-SNP	.											.	PARVG	41	.	0			c.A287T						PASS	.						68	55	60					22																	44581694		2203	4300	6503	SO:0001583	missense	64098	exon3			GAGGAAAGAAGAA	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.86A>T	chr22.hg19:g.44581694A>T	ENSP00000391583:p.Lys29Met	29.0	0.0	.		46.0	11.0	.	NM_001254742	B4DDW5|E7EVM6|Q9BQX5|Q9NSG1	Missense_Mutation	SNP	ENST00000444313.3	hg19	CCDS14057.1	.	.	.	.	.	.	.	.	.	.	A	16.30	3.083589	0.55861	.	.	ENSG00000138964	ENST00000422871;ENST00000453888;ENST00000444313;ENST00000415224	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	4.79	4.79	0.61399	Calponin homology domain (1);	0.161867	0.39985	N	0.001210	T	0.63733	0.2536	M	0.70595	2.14	0.42735	D	0.993721	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.944	T	0.66945	-0.5795	10	0.66056	D	0.02	3.0E-4	7.9054	0.29759	0.8163:0.0:0.0:0.1837	.	96;29	B4DDW5;Q9HBI0	.;PARVG_HUMAN	M	29;96;29;29	ENSP00000391453:K29M;ENSP00000416104:K96M;ENSP00000391583:K29M;ENSP00000416761:K29M	ENSP00000349378:K29M	K	+	2	0	PARVG	42913027	1.000000	0.71417	0.994000	0.49952	0.692000	0.40212	3.551000	0.53698	1.781000	0.52344	0.533000	0.62120	AAG	.	.	.	none		0.577	PARVG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318238.4	NM_022141		T	44581694	A	T	44581694	3	4	76	1	0	0	0	0	1	0	0	0	11477	72	3	5	92	5	PARVG	22	44581694	Missense_Mutation	SNP	A	TCGA-AL-7173-01A-11D-2136-08	3835797	44581694	6722872	62	4936											
HDAC10	83933	hgsc.bcm.edu	37	chr22	50684494	50684494	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caggggcagcaccaagcccaAgatgcagctcaggaaaccac	14	2	11	14	0	1	1	1	0	0	1	1	2	1	2	3	3	5	4	3	3	3	0			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chr22:50684494A>G	ENST00000216271.5	-	18	2030	c.1678T>C	c.(1678-1680)Ttg>Ctg	p.L560L	HDAC10_ENST00000349505.4_Silent_p.L540L|HDAC10_ENST00000448072.1_Silent_p.L510L|HDAC10_ENST00000498366.1_5'UTR|TUBGCP6_ENST00000439308.2_5'Flank|TUBGCP6_ENST00000248846.5_5'Flank|MAPK12_ENST00000497036.1_5'UTR	NM_001159286.1|NM_032019.5	NP_001152758.1|NP_114408.3	Q969S8	HDA10_HUMAN	histone deacetylase 10	560					chromatin modification (GO:0016568)|histone deacetylation (GO:0016575)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|oligodendrocyte development (GO:0014003)|protein deacetylation (GO:0006476)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)			endometrium(2)|kidney(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	8		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		ACCAAGCCCAAGATGCAGCTC	0.657																																					p.L560L		Atlas-SNP	.											.	HDAC10	29	.	0			c.T1678C						PASS	.						41	44	43					22																	50684494		2201	4300	6501	SO:0001819	synonymous_variant	83933	exon18			AGCCCAAGATGCA	AF393962	CCDS14088.1, CCDS54545.1	22q13.31	2008-06-10			ENSG00000100429	ENSG00000100429			18128	protein-coding gene	gene with protein product		608544				11677242, 11726666	Standard	NM_032019		Approved	DKFZP761B039	uc003bkg.3	Q969S8	OTTHUMG00000044647	ENST00000216271.5:c.1678T>C	chr22.hg19:g.50684494A>G		48.0	0.0	.		47.0	5.0	.	NM_032019	Q08AP4|Q6STF9|Q96P77|Q96P78|Q9H028|Q9UGX1|Q9UGX2	Silent	SNP	ENST00000216271.5	hg19	CCDS14088.1																																																																																			.	.	.	none		0.657	HDAC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104141.4	NM_032019		G	50684494	A	G	50684494	2	3	76	1	0	0	0	0	0	0	0	1	7012	69	3	3		3	HDAC10	22	50684494	Silent	SNP	A	TCGA-AL-7173-01A-11D-2136-08	6102800	50684494	620072	63	4937											
PRKX	5613	hgsc.bcm.edu	37	chrX	3544550	3544550	+	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	ggttgtcatcaaaaaacggaGgaaacctgttagaaaaacaa	19	7	9	6	1	2	1	2	0	0	1	2	3	2	3	1	3	3	2	1	3	8	2			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chrX:3544550G>C	ENST00000262848.5	-	5	1079	c.725C>G	c.(724-726)cCt>cGt	p.P242R	PRKX_ENST00000425240.1_5'UTR	NM_005044.4	NP_005035.1	P51817	PRKX_HUMAN	protein kinase, X-linked	242	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial tube morphogenesis (GO:0060562)|kidney morphogenesis (GO:0060993)|myeloid cell differentiation (GO:0030099)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of epithelial cell differentiation involved in kidney development (GO:2000696)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)			kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|skin(2)	12		all_lung(23;0.000396)|Lung NSC(23;0.00123)				AAAAAACGGAGGAAACCTGTT	0.373																																					p.P242R		Atlas-SNP	.											.	PRKX	29	.	0			c.C725G						PASS	.						108	93	98					X																	3544550		2203	4300	6503	SO:0001583	missense	5613	exon5			AACGGAGGAAACC		CCDS14125.1	Xp22.3	2008-08-01			ENSG00000183943	ENSG00000183943	2.7.11.1		9441	protein-coding gene	gene with protein product		300083				7633447	Standard	NM_005044		Approved	PKX1	uc010nde.3	P51817	OTTHUMG00000021087	ENST00000262848.5:c.725C>G	chrX.hg19:g.3544550G>C	ENSP00000262848:p.Pro242Arg	24.0	0.0	.		25.0	7.0	.	NM_005044		Missense_Mutation	SNP	ENST00000262848.5	hg19	CCDS14125.1	.	.	.	.	.	.	.	.	.	.	G	12.63	1.994637	0.35226	.	.	ENSG00000183943	ENST00000262848	T	0.09073	3.02	3.47	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);	0.000000	0.85682	D	0.000000	T	0.19167	0.0460	L	0.39147	1.195	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.00909	-1.1518	10	0.87932	D	0	-3.9448	12.0899	0.53719	0.0:0.0:1.0:0.0	.	242	P51817	PRKX_HUMAN	R	242	ENSP00000262848:P242R	ENSP00000262848:P242R	P	-	2	0	PRKX	3554550	1.000000	0.71417	0.936000	0.37596	0.310000	0.27922	6.948000	0.75965	1.374000	0.46228	0.529000	0.55759	CCT	.	.	.	none		0.373	PRKX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055659.1	NM_005044		C	3544550	G	C	3544550	3	2	76	1	0	0	0	0	1	0	0	0	12537	1000	35	4	367	4	PRKX	23	3544550	Missense_Mutation	SNP	G	TCGA-AL-7173-01A-11D-2136-08		3544550	151726010	64	4938											
KIAA2022	340533	hgsc.bcm.edu	37	chrX	73961092	73961092	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaatggtcctgggacaccCtcttggaacccctttagtgt	7	12	9	13	0	1	0	0	0	1	0	3	2	3	2	5	3	1	0	5	3	3	3			TCGA-AL-7173-01A-11D-2136-08	TCGA-AL-7173-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2fd86890-1842-4e9e-9100-f10814f8db6a	d279d1dd-cfd3-4527-8aaf-d880d7862c30	g.chrX:73961092C>T	ENST00000055682.6	-	3	3911	c.3300G>A	c.(3298-3300)gaG>gaA	p.E1100E		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	1100					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						CTGGGACACCCTCTTGGAACC	0.478																																					p.E1100E		Atlas-SNP	.											.	KIAA2022	262	.	0			c.G3300A						PASS	.						75	70	72					X																	73961092		2203	4300	6503	SO:0001819	synonymous_variant	340533	exon3			GACACCCTCTTGG		CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"XLMR-related protein, neurite extension"	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.3300G>A	chrX.hg19:g.73961092C>T		109.0	0.0	.		85.0	4.0	.	NM_001008537	A7YY87|Q5JUX9|Q8IVE9	Silent	SNP	ENST00000055682.6	hg19	CCDS35337.1																																																																																			.	.	.	none		0.478	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537		T	73961092	C	T	73961092	2	4	76	1	0	0	0	0	0	0	0	1	8276	680	24	2		2	KIAA2022	23	73961092	Silent	SNP	C	TCGA-AL-7173-01A-11D-2136-08	70416542	73961092	81309468	65	4939											
MEGF6	1953	hgsc.bcm.edu	37	chr1	3425692	3425692	+	Missense_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	actctgcctcttcctcatcgGccccgacgtcgtcatcctgg	4	11	8	18	4	4	0	2	0	2	0	8	1	6	0	5	2	1	0	5	2	0	1			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr1:3425692G>A	ENST00000356575.4	-	12	1701	c.1475C>T	c.(1474-1476)gCc>gTc	p.A492V	MEGF6_ENST00000294599.4_Missense_Mutation_p.A387V	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	492						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)		TTCCTCATCGGCCCCGACGTC	0.682																																					p.A492V	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.C1475T						PASS	.						16	20	18					1																	3425692		1999	4145	6144	SO:0001583	missense	1953	exon12			TCATCGGCCCCGA	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.1475C>T	chr1.hg19:g.3425692G>A	ENSP00000348982:p.Ala492Val	65.0	0.0	.		56.0	13.0	.	NM_001409	Q4AC86|Q5VV39	Missense_Mutation	SNP	ENST00000356575.4	hg19	CCDS41237.1	.	.	.	.	.	.	.	.	.	.	G	0.860	-0.735532	0.03111	.	.	ENSG00000162591	ENST00000294599;ENST00000356575	D;D	0.86627	-2.15;-1.89	3.74	2.76	0.32466	.	0.812464	0.10434	N	0.675134	T	0.81297	0.4793	L	0.47716	1.5	0.09310	N	1	B;B	0.16396	0.007;0.017	B;B	0.12156	0.007;0.006	T	0.67444	-0.5669	10	0.30854	T	0.27	-0.505	7.6695	0.28451	0.0:0.1513:0.6354:0.2133	.	492;387	O75095;O75095-2	MEGF6_HUMAN;.	V	387;492	ENSP00000294599:A387V;ENSP00000348982:A492V	ENSP00000294599:A387V	A	-	2	0	MEGF6	3415552	0.011000	0.17503	0.017000	0.16124	0.027000	0.11550	1.272000	0.33109	1.906000	0.55180	0.462000	0.41574	GCC	.	.	.	none		0.682	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409		A	3425692	G	A	3425692	3	1	77	1	0	0	0	0	1	0	0	0	9469	1203	42	2	3254	2	MEGF6	1	3425692	Missense_Mutation	SNP	G	TCGA-AL-A5DJ-01A-11D-A26P-10		3425692	245824929	1	4940											
MYCN	4613	hgsc.bcm.edu	37	chr2	16085781	16085781	+	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	gctcagtccagcgagctgatCctcaaacgatgccttcccat	9	9	8	15	2	2	1	2	1	0	0	5	3	5	1	4	0	4	2	4	0	1	1			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr2:16085781C>T	ENST00000281043.3	+	3	1254	c.957C>T	c.(955-957)atC>atT	p.I319I		NM_005378.4	NP_005369.2	P04198	MYCN_HUMAN	v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog	319					branching morphogenesis of an epithelial tube (GO:0048754)|cartilage condensation (GO:0001502)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|lung development (GO:0030324)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|positive regulation of cell death (GO:0010942)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin (GO:0000785)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	31	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)			GCGAGCTGATCCTCAAACGAT	0.592			A		neuroblastoma																																p.I319I		Atlas-SNP	.		Dom	yes		2	2p24.1	4613	"v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)"		O	.	MYCN	63	.	0			c.C957T						PASS	.						87	72	77					2																	16085781		2203	4300	6503	SO:0001819	synonymous_variant	4613	exon3			GCTGATCCTCAAA	BC002712	CCDS1687.1	2p24.3	2013-08-14	2013-07-09		ENSG00000134323	ENSG00000134323		"Basic helix-loop-helix proteins"	7559	protein-coding gene	gene with protein product		164840		NMYC			Standard	XM_006711886		Approved	bHLHe37, N-myc, MYCNOT	uc002rci.3	P04198	OTTHUMG00000039579	ENST00000281043.3:c.957C>T	chr2.hg19:g.16085781C>T		336.0	0.0	.		463.0	105.0	.	NM_005378	Q53XS5|Q6LDT9	Silent	SNP	ENST00000281043.3	hg19	CCDS1687.1																																																																																			.	.	.	none		0.592	MYCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095469.2	NM_005378		T	16085781	C	T	16085781	2	4	77	1	0	0	0	0	0	0	0	1	10028	845	30	2		2	MYCN	2	16085781	Silent	SNP	C	TCGA-AL-A5DJ-01A-11D-A26P-10		16085781	227113592	2	4941											
EIF2AK3	9451	hgsc.bcm.edu	37	chr2	88913362	88913362	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccatctaaagtgctgataatTactaatgacctgtaaatatt	15	14	5	7	0	1	2	0	2	1	0	1	2	1	2	2	0	2	2	2	0	8	7			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr2:88913362T>C	ENST00000303236.3	-	2	619	c.318A>G	c.(316-318)gtA>gtG	p.V106V	EIF2AK3_ENST00000419748.1_5'UTR	NM_004836.5	NP_004827.4	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 3	106					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						TGCTGATAATTACTAATGACC	0.373																																					p.V106V	GBM(138;671 1851 16235 39058 45249)	Atlas-SNP	.											.	EIF2AK3	160	.	0			c.A318G						PASS	.						73	67	69					2																	88913362		2203	4300	6503	SO:0001819	synonymous_variant	9451	exon2			GATAATTACTAAT	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.318A>G	chr2.hg19:g.88913362T>C		33.0	0.0	.		29.0	13.0	.	NM_004836	A0AVH1|A0AVH2|B2RCU9|O95846|Q53QY0|Q53SB1	Silent	SNP	ENST00000303236.3	hg19	CCDS33241.1																																																																																			.	.	.	none		0.373	EIF2AK3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000338233.2	NM_004836		C	88913362	T	C	88913362	2	2	77	1	0	0	0	0	0	0	0	1	5000	1741	61	3		3	EIF2AK3	2	88913362	Silent	SNP	T	TCGA-AL-A5DJ-01A-11D-A26P-10	72827581	88913362	154286011	3	4942											
RANBP2	5903	hgsc.bcm.edu	37	chr2	109399079	109399079	+	Missense_Mutation	SNP	T	T	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	ttgaagaatgtcagcagaatTtaatgaaactccagaaagga	18	9	9	5	0	1	5	1	2	0	3	2	6	2	6	1	1	2	1	1	1	6	3			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr2:109399079T>G	ENST00000283195.6	+	28	9256	c.9130T>G	c.(9130-9132)Tta>Gta	p.L3044V		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	3044	RanBD1 4. {ECO:0000255|PROSITE- ProRule:PRU00164}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						TCAGCAGAATTTAATGAAACT	0.393																																					p.L3044V		Atlas-SNP	.											.	RANBP2	488	.	0			c.T9130G						PASS	.						89	90	90					2																	109399079		2203	4300	6503	SO:0001583	missense	5903	exon28			CAGAATTTAATGA	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.9130T>G	chr2.hg19:g.109399079T>G	ENSP00000283195:p.Leu3044Val	93.0	0.0	.		86.0	20.0	.	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	hg19	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	T	11.15	1.552949	0.27739	.	.	ENSG00000153201	ENST00000409491;ENST00000283195	T	0.48522	0.81	5.57	3.14	0.36123	Ran binding protein 1 (1);	.	.	.	.	T	0.32971	0.0847	L	0.31526	0.94	0.22096	N	0.999367	B	0.10296	0.003	B	0.13407	0.009	T	0.24440	-1.0160	9	0.46703	T	0.11	-10.6162	5.3388	0.15973	0.135:0.144:0.0:0.721	.	3044	P49792	RBP2_HUMAN	V	2068;3044	ENSP00000283195:L3044V	ENSP00000283195:L3044V	L	+	1	2	RANBP2	108765511	0.955000	0.32602	1.000000	0.80357	0.922000	0.55478	0.403000	0.20982	0.385000	0.24970	0.456000	0.33151	TTA	.	.	.	none		0.393	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		G	109399079	T	G	109399079	3	3	77	1	0	0	0	0	1	0	0	0	13041	1838	64	5	9240	5	RANBP2	2	109399079	Missense_Mutation	SNP	T	TCGA-AL-A5DJ-01A-11D-A26P-10	20485717	109399079	133800294	4	4943											
ZC3H6	376940	hgsc.bcm.edu	37	chr2	113079400	113079400	+	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	ggagacaactgtaaattttcCcatgatgatctaactaaaga	16	11	7	7	0	1	4	0	2	1	2	2	5	2	4	1	1	2	1	1	1	6	5			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr2:113079400C>G	ENST00000409871.1	+	8	1445	c.1044C>G	c.(1042-1044)tcC>tcG	p.S348S	ZC3H6_ENST00000343936.4_Silent_p.S348S	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	348							metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						GTAAATTTTCCCATGATGATC	0.308																																					p.S348S		Atlas-SNP	.											.	ZC3H6	93	.	0			c.C1044G						PASS	.						46	41	43					2																	113079400		1800	4066	5866	SO:0001819	synonymous_variant	376940	exon8			ATTTTCCCATGAT	AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"Zinc fingers, CCCH-type domain containing"	24762	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 6"	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.1044C>G	chr2.hg19:g.113079400C>G		136.0	0.0	.		162.0	49.0	.	NM_198581	A9JR71|Q6ZW96	Silent	SNP	ENST00000409871.1	hg19	CCDS46393.1																																																																																			.	.	.	none		0.308	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581		G	113079400	C	G	113079400	2	3	77	1	0	0	0	0	0	0	0	1	17583	610	22	4		4	ZC3H6	2	113079400	Silent	SNP	C	TCGA-AL-A5DJ-01A-11D-A26P-10	3680321	113079400	130119973	5	4944											
CRYGD	1421	hgsc.bcm.edu	37	chr2	208988981	208988981	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagccgctgtccacgcgcGccgagttgcagcggctcaag	7	5	14	15	6	1	0	1	0	0	0	2	1	2	0	3	1	4	5	3	1	1	1	rs200234608		TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr2:208988981G>A	ENST00000264376.4	-	2	134	c.107C>T	c.(106-108)gCg>gTg	p.A36V		NM_006891.3	NP_008822.2	P07320	CRGD_HUMAN	crystallin, gamma D	36	Beta/gamma crystallin 'Greek key' 1. {ECO:0000255|PROSITE-ProRule:PRU00028}.				cellular response to reactive oxygen species (GO:0034614)|lens development in camera-type eye (GO:0002088)|lens fiber cell differentiation (GO:0070306)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	structural constituent of eye lens (GO:0005212)			breast(1)|endometrium(1)|lung(3)	5				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.0858)|Lung(261;0.133)		GTCCACGCGCGCCGAGTTGCA	0.652																																					p.A36V		Atlas-SNP	.											CRYGD,NS,neuroblastoma,0,1	CRYGD	18	.	0			c.C107T						PASS	.						11	13	12					2																	208988981		2179	4274	6453	SO:0001583	missense	1421	exon2			ACGCGCGCCGAGT		CCDS2378.1	2q33.3	2013-02-14			ENSG00000118231	ENSG00000118231			2411	protein-coding gene	gene with protein product		123690		CRYG4			Standard	NM_006891		Approved		uc002vcn.4	P07320	OTTHUMG00000132944	ENST00000264376.4:c.107C>T	chr2.hg19:g.208988981G>A	ENSP00000264376:p.Ala36Val	72.0	0.0	.		55.0	6.0	.	NM_006891	Q17RF7|Q53R51|Q99681	Missense_Mutation	SNP	ENST00000264376.4	hg19	CCDS2378.1	.	.	.	.	.	.	.	.	.	.	G	11.40	1.627591	0.28978	.	.	ENSG00000118231	ENST00000264376	T	0.72051	-0.62	4.35	3.19	0.36642	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.184420	0.36703	N	0.002444	T	0.29389	0.0732	N	0.00166	-1.94	0.09310	N	0.999995	B	0.02656	0.0	B	0.01281	0.0	T	0.34875	-0.9811	10	0.32370	T	0.25	.	8.1681	0.31239	0.9021:0.0:0.0979:0.0	.	36	P07320	CRGD_HUMAN	V	36	ENSP00000264376:A36V	ENSP00000264376:A36V	A	-	2	0	CRYGD	208697226	0.280000	0.24249	0.067000	0.19924	0.966000	0.64601	2.073000	0.41519	0.695000	0.31675	-0.573000	0.04149	GCG	.	G|0.998;A|0.002	0.002	weak		0.652	CRYGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256476.2	NM_006891		A	208988981	G	A	208988981	3	1	77	1	0	0	0	0	1	0	0	0	3919	1087	38	1	425	1	CRYGD	2	208988981	Missense_Mutation	SNP	G	TCGA-AL-A5DJ-01A-11D-A26P-10	95909581	208988981	34210392	6	4945											
ZNF502	91392	hgsc.bcm.edu	37	chr3	44762365	44762365	+	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	attctgctgttttctttcagGctgggtaaacaagaacaagc	11	13	9	8	0	3	1	1	0	2	1	3	1	3	1	0	2	4	4	0	2	5	5			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr3:44762365G>T	ENST00000296091.4	+	4	312	c.56G>T	c.(55-57)gGc>gTc	p.G19V	ZNF502_ENST00000449836.1_Splice_Site_p.G19V|ZNF502_ENST00000436624.2_Splice_Site_p.G19V	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	19					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			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)		TTTCTTTCAGGCTGGGTAAAC	0.443																																					p.G19V		Atlas-SNP	.											.	ZNF502	58	.	0			c.G56T						PASS	.						52	56	55					3																	44762365		2202	4300	6502	SO:0001630	splice_region_variant	91392	exon4			TTTCAGGCTGGGT	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.56-1G>T	chr3.hg19:g.44762365G>T		58.0	0.0	.		62.0	29.0	.	NM_001134440		Missense_Mutation	SNP	ENST00000296091.4	hg19	CCDS2719.1	.	.	.	.	.	.	.	.	.	.	G	10.89	1.479567	0.26511	.	.	ENSG00000196653	ENST00000449836;ENST00000296091;ENST00000436624;ENST00000427783;ENST00000411443	T;T;T;T	0.52983	3.17;3.17;3.17;0.64	4.77	-1.71	0.08133	.	.	.	.	.	T	0.18964	0.0455	N	0.08118	0	0.28556	N	0.9114	B	0.13145	0.007	B	0.11329	0.006	T	0.20840	-1.0263	8	.	.	.	.	0.412	0.00443	0.3647:0.1308:0.2221:0.2825	.	19	Q8TBZ5	ZN502_HUMAN	V	19	ENSP00000397390:G19V;ENSP00000296091:G19V;ENSP00000406469:G19V;ENSP00000401717:G19V	.	G	+	2	0	ZNF502	44737369	0.011000	0.17503	0.016000	0.15963	0.013000	0.08279	-0.325000	0.07976	-0.210000	0.10140	-0.140000	0.14226	GGC	.	.	.	none		0.443	ZNF502-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256744.4	NM_033210	Missense_Mutation	T	44762365	G	T	44762365	5	4	77	1	0	0	0	0	0	0	1	0	17962	1217	42	4	62	4	ZNF502	3	44762365	Splice_Site	SNP	G	TCGA-AL-A5DJ-01A-11D-A26P-10		44762365	153260065	7	4946											
QARS	5859	hgsc.bcm.edu	37	chr3	49135888	49135888	+	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	cccgtctgcaggtcacctccAgactctctacacaaccactg	9	8	6	18	1	3	1	1	0	2	1	5	1	4	1	4	1	3	1	4	1	2	1			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr3:49135888A>T	ENST00000306125.6	-	21	2319	c.1982T>A	c.(1981-1983)cTg>cAg	p.L661Q	QARS_ENST00000470225.1_5'Flank|QARS_ENST00000414533.1_Missense_Mutation_p.L650Q			P47897	SYQ_HUMAN	glutaminyl-tRNA synthetase	661					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)	GGTCACCTCCAGACTCTCTAC	0.562																																					p.L661Q		Atlas-SNP	.											.	QARS	55	.	0			c.T1982A						PASS	.						54	57	56					3																	49135888		2203	4300	6503	SO:0001583	missense	5859	exon21			ACCTCCAGACTCT	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.1982T>A	chr3.hg19:g.49135888A>T	ENSP00000307567:p.Leu661Gln	84.0	0.0	.		123.0	38.0	.	NM_005051	B4DWJ2	Missense_Mutation	SNP	ENST00000306125.6	hg19	CCDS2788.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.130027	0.77549	.	.	ENSG00000172053	ENST00000453392;ENST00000306125;ENST00000414533	T;T	0.27402	1.67;1.67	5.8	5.8	0.92144	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);	0.068752	0.64402	D	0.000013	T	0.67420	0.2891	H	0.94886	3.595	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.77699	-0.2490	10	0.87932	D	0	-12.8433	15.8218	0.78654	1.0:0.0:0.0:0.0	.	650;661	B4DWJ2;P47897	.;SYQ_HUMAN	Q	181;661;650	ENSP00000307567:L661Q;ENSP00000390015:L650Q	ENSP00000307567:L661Q	L	-	2	0	QARS	49110892	1.000000	0.71417	0.870000	0.34147	0.599000	0.36880	8.794000	0.91867	2.226000	0.72624	0.459000	0.35465	CTG	.	.	.	none		0.562	QARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345689.2	NM_005051		T	49135888	A	T	49135888	3	4	77	1	0	0	0	0	1	0	0	0	12884	188	7	5	361	5	QARS	3	49135888	Missense_Mutation	SNP	A	TCGA-AL-A5DJ-01A-11D-A26P-10	4373523	49135888	148886542	8	4947											
PCBP4	57060	hgsc.bcm.edu	37	chr3	51994252	51994252	+	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	agccttcccaatcagtgagcCacactgactggcagggatga	11	7	11	12	0	1	3	1	3	0	0	2	4	2	4	3	2	2	1	3	2	1	1			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr3:51994252C>T	ENST00000461554.1	-	7	671	c.340G>A	c.(340-342)Ggc>Agc	p.G114S	RP11-155D18.12_ENST00000488257.1_RNA|PCBP4_ENST00000395014.2_Missense_Mutation_p.G80S|PCBP4_ENST00000484633.1_Missense_Mutation_p.G114S|PCBP4_ENST00000471622.1_Missense_Mutation_p.G114S|PCBP4_ENST00000322099.7_Missense_Mutation_p.G114S|PCBP4_ENST00000395013.3_Missense_Mutation_p.G37S|PCBP4_ENST00000355852.2_Missense_Mutation_p.G114S|PCBP4_ENST00000428823.2_Missense_Mutation_p.G114S	NM_001174100.1	NP_001167571.1	P57723	PCBP4_HUMAN	poly(rC) binding protein 4	114	KH 2. {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)		ATCAGTGAGCCACACTGACTG	0.587																																					p.G114S		Atlas-SNP	.											.	PCBP4	35	.	0			c.G340A						PASS	.						60	56	57					3																	51994252		2203	4300	6503	SO:0001583	missense	57060	exon6			GTGAGCCACACTG	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.340G>A	chr3.hg19:g.51994252C>T	ENSP00000417196:p.Gly114Ser	228.0	0.0	.		283.0	55.0	.	NM_033008	Q96AH7	Missense_Mutation	SNP	ENST00000461554.1	hg19	CCDS2839.1	.	.	.	.	.	.	.	.	.	.	C	35	5.589850	0.96590	.	.	ENSG00000090097	ENST00000355852;ENST00000322099;ENST00000461554;ENST00000484633;ENST00000395013;ENST00000428823;ENST00000395014;ENST00000471622;ENST00000294192;ENST00000468324;ENST00000466412	T;T;T;T;T;T;T;T;T;T	0.49432	0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.78	4.96	4.96	0.65561	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.72977	0.3528	M	0.84773	2.715	0.36967	D	0.89361	D;D;B;P;P;D;D	0.76494	0.966;0.971;0.0;0.954;0.954;0.999;0.998	D;D;B;P;D;D;D	0.87578	0.961;0.929;0.0;0.899;0.924;0.984;0.998	T	0.81929	-0.0708	10	0.87932	D	0	-5.5523	17.8155	0.88632	0.0:1.0:0.0:0.0	.	114;114;37;114;114;80;80	C9J0A4;P57723-2;B3KM64;E7EST1;P57723;Q9GZT1;Q9HCU2	.;.;.;.;PCBP4_HUMAN;.;.	S	114;114;114;114;37;114;80;114;114;114;114	ENSP00000348111:G114S;ENSP00000322341:G114S;ENSP00000417196:G114S;ENSP00000417100:G114S;ENSP00000378460:G37S;ENSP00000395030:G114S;ENSP00000378461:G80S;ENSP00000418925:G114S;ENSP00000419694:G114S;ENSP00000419557:G114S	ENSP00000294192:G114S	G	-	1	0	PCBP4	51969292	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.751000	0.85126	2.281000	0.76405	0.563000	0.77884	GGC	.	.	.	none		0.587	PCBP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348597.1	NM_020418		T	51994252	C	T	51994252	3	4	77	1	0	0	0	0	1	0	0	0	11510	594	21	2	903	2	PCBP4	3	51994252	Missense_Mutation	SNP	C	TCGA-AL-A5DJ-01A-11D-A26P-10	2858364	51994252	146028178	9	4948											
XRN1	54464	hgsc.bcm.edu	37	chr3	142031582	142031582	+	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	ttgagccaaagagatgagacGacgaaggcattatattagct	15	9	11	6	2	0	3	0	2	0	2	0	7	0	3	1	1	2	2	1	1	5	4	rs552700387		TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr3:142031582G>A	ENST00000264951.4	-	41	4793	c.4676C>T	c.(4675-4677)tCg>tTg	p.S1559L	XRN1_ENST00000392981.2_Missense_Mutation_p.S1547L	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	1559					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						GAGATGAGACGACGAAGGCAT	0.443													G|||	1	0.000199681	0	0	5008	,	,		14945	0		0	False		,,,				2504	0.001				p.S1559L		Atlas-SNP	.											.	XRN1	138	.	0			c.C4676T						PASS	.						115	120	118					3																	142031582		2203	4300	6503	SO:0001583	missense	54464	exon41			TGAGACGACGAAG	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.4676C>T	chr3.hg19:g.142031582G>A	ENSP00000264951:p.Ser1559Leu	111.0	0.0	.		127.0	27.0	.	NM_019001	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Missense_Mutation	SNP	ENST00000264951.4	hg19	CCDS3123.1	.	.	.	.	.	.	.	.	.	.	G	17.78	3.472860	0.63737	.	.	ENSG00000114127	ENST00000264951;ENST00000392981	T;T	0.34072	1.39;1.38	5.18	5.18	0.71444	.	0.358063	0.27052	N	0.021166	T	0.30386	0.0763	L	0.29908	0.895	0.80722	D	1	B;B	0.31680	0.335;0.226	B;B	0.27170	0.077;0.035	T	0.09751	-1.0660	10	0.51188	T	0.08	-1.1955	19.0575	0.93072	0.0:0.0:1.0:0.0	.	1547;1559	Q8IZH2-2;Q8IZH2	.;XRN1_HUMAN	L	1559;1547	ENSP00000264951:S1559L;ENSP00000376707:S1547L	ENSP00000264951:S1559L	S	-	2	0	XRN1	143514272	0.997000	0.39634	0.956000	0.39512	0.965000	0.64279	6.412000	0.73303	2.554000	0.86153	0.655000	0.94253	TCG	.	.	.	none		0.443	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001		A	142031582	G	A	142031582	3	1	77	1	0	0	0	0	1	0	0	0	17471	1059	37	1	452	1	XRN1	3	142031582	Missense_Mutation	SNP	G	TCGA-AL-A5DJ-01A-11D-A26P-10	90037330	142031582	55990848	10	4949											
HS3ST1	9957	hgsc.bcm.edu	37	chr4	11401255	11401255	+	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	cgctcaggcactttgggcgaCgtgaaatacgcgggggtctt	7	9	15	10	5	2	1	1	1	1	0	2	2	2	1	0	4	1	2	0	4	2	3			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr4:11401255C>T	ENST00000002596.5	-	2	1549	c.375G>A	c.(373-375)acG>acA	p.T125T		NM_005114.2	NP_005105.1	O14792	HS3S1_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	125					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						CTTTGGGCGACGTGAAATACG	0.617																																					p.T125T		Atlas-SNP	.											.	HS3ST1	41	.	0			c.G375A						PASS	.						67	66	66					4																	11401255		2203	4300	6503	SO:0001819	synonymous_variant	9957	exon2			GGGCGACGTGAAA	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.375G>A	chr4.hg19:g.11401255C>T		178.0	0.0	.		162.0	7.0	.	NM_005114	B3KUA6|Q6PEY8	Silent	SNP	ENST00000002596.5	hg19	CCDS3408.1																																																																																			.	.	.	none		0.617	HS3ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207073.3	NM_005114		T	11401255	C	T	11401255	2	4	77	1	0	0	0	0	0	0	0	1	7370	523	19	1		1	HS3ST1	4	11401255	Silent	SNP	C	TCGA-AL-A5DJ-01A-11D-A26P-10		11401255	179753021	11	4950											
CLCN3	1182	hgsc.bcm.edu	37	chr4	170625204	170625204	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggagcgatcgcaggaaggaTtgtggggattgcggtggagc	8	8	20	5	3	0	0	0	0	0	0	1	6	0	5	0	7	3	1	0	7	1	2			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr4:170625204T>C	ENST00000513761.1	+	10	2178	c.1619T>C	c.(1618-1620)aTt>aCt	p.I540T	CLCN3_ENST00000504131.2_Missense_Mutation_p.I523T|CLCN3_ENST00000347613.4_Missense_Mutation_p.I540T|CLCN3_ENST00000360642.3_Missense_Mutation_p.I513T	NM_001829.3	NP_001820.2	P51790	CLCN3_HUMAN	chloride channel, voltage-sensitive 3	540					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)		GCAGGAAGGATTGTGGGGATT	0.507																																					p.I540T		Atlas-SNP	.											.	CLCN3	85	.	0			c.T1619C						PASS	.						232	194	207					4																	170625204		2203	4300	6503	SO:0001583	missense	1182	exon10			GAAGGATTGTGGG	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.1619T>C	chr4.hg19:g.170625204T>C	ENSP00000424603:p.Ile540Thr	254.0	0.0	.		208.0	61.0	.	NM_001829	B7Z932|B9EGJ9|D3DP34|E9PB97|O14918|Q86Z21	Missense_Mutation	SNP	ENST00000513761.1	hg19	CCDS34101.1	.	.	.	.	.	.	.	.	.	.	T	17.41	3.381367	0.61845	.	.	ENSG00000109572	ENST00000513761;ENST00000347613;ENST00000360642;ENST00000504131;ENST00000507875	D;D;D;D;D	0.94613	-3.47;-3.47;-3.47;-3.47;-3.47	5.22	4.03	0.46877	Chloride channel, core (2);	0.087869	0.85682	D	0.000000	D	0.93897	0.8047	L	0.49350	1.555	0.80722	D	1	B;P;B;B;B	0.34462	0.318;0.454;0.27;0.318;0.05	P;P;B;P;B	0.45794	0.493;0.493;0.41;0.493;0.135	D	0.92858	0.6303	10	0.72032	D	0.01	-2.771	11.2757	0.49165	0.0:0.0726:0.0:0.9274	.	513;523;513;540;540	B7Z932;B9EGJ9;E9PE15;P51790;P51790-2	.;.;.;CLCN3_HUMAN;.	T	540;540;513;523;513	ENSP00000424603:I540T;ENSP00000261514:I540T;ENSP00000353857:I513T;ENSP00000424540:I523T;ENSP00000425323:I513T	ENSP00000261514:I540T	I	+	2	0	CLCN3	170861779	1.000000	0.71417	0.746000	0.31095	0.658000	0.38924	7.994000	0.88315	0.936000	0.37367	0.449000	0.29647	ATT	.	.	.	none		0.507	CLCN3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363210.2			C	170625204	T	C	170625204	3	2	77	1	0	0	0	0	1	0	0	0	3466	1493	52	3	1653	3	CLCN3	4	170625204	Missense_Mutation	SNP	T	TCGA-AL-A5DJ-01A-11D-A26P-10	159223949	170625204	20529072	12	4951											
GFM2	84340	hgsc.bcm.edu	37	chr5	74018240	74018240	+	Missense_Mutation	SNP	T	T	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	ggaacaaatccaataacaacTttgttgtcctggcgagtctg	12	11	9	9	1	1	0	0	0	1	0	3	2	3	1	2	2	3	1	2	2	5	3			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr5:74018240T>G	ENST00000296805.3	-	20	2632	c.2175A>C	c.(2173-2175)aaA>aaC	p.K725N	RNU6-658P_ENST00000384606.1_RNA|GFM2_ENST00000515125.1_5'UTR|GFM2_ENST00000345239.2_Missense_Mutation_p.K678N|GFM2_ENST00000509430.1_Missense_Mutation_p.K725N	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)		CAATAACAACTTTGTTGTCCT	0.388																																					p.K725N		Atlas-SNP	.											.	GFM2	38	.	0			c.A2175C						PASS	.						146	144	144					5																	74018240		2203	4300	6503	SO:0001583	missense	84340	exon20			AACAACTTTGTTG	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.2175A>C	chr5.hg19:g.74018240T>G	ENSP00000296805:p.Lys725Asn	56.0	0.0	.		100.0	6.0	.	NM_032380		Missense_Mutation	SNP	ENST00000296805.3	hg19	CCDS4023.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.391627	0.83011	.	.	ENSG00000164347	ENST00000296805;ENST00000345239;ENST00000546082;ENST00000509430	T;T;T	0.63913	-0.07;-0.07;-0.07	5.96	4.8	0.61643	Elongation factor G/III/V (1);Translation elongation factor EFG/EF2, C-terminal (3);	0.352841	0.38663	N	0.001604	T	0.69646	0.3134	M	0.68952	2.095	0.80722	D	1	B;P;B	0.50369	0.202;0.934;0.123	B;P;B	0.52646	0.185;0.705;0.282	T	0.72503	-0.4273	10	0.87932	D	0	-1.7306	11.9157	0.52763	0.0:0.0678:0.0:0.9322	.	723;678;725	Q969S9-3;Q969S9-2;Q969S9	.;.;RRF2M_HUMAN	N	725;678;547;725	ENSP00000296805:K725N;ENSP00000296804:K678N;ENSP00000427004:K725N	ENSP00000296805:K725N	K	-	3	2	GFM2	74053996	0.999000	0.42202	0.792000	0.32020	0.989000	0.77384	1.529000	0.35996	1.079000	0.41038	0.528000	0.53228	AAA	.	.	.	none		0.388	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380		G	74018240	T	G	74018240	3	3	77	1	0	0	0	0	1	0	0	0	6349	1606	56	5	172	5	GFM2	5	74018240	Missense_Mutation	SNP	T	TCGA-AL-A5DJ-01A-11D-A26P-10		74018240	106897020	13	4952											
HIST1H2AE	3012	hgsc.bcm.edu	37	chr6	26217562	26217562	+	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	gccgtattgctgcctaagaaGacggagagccaccataaggc	12	6	12	11	2	0	3	0	0	0	3	0	4	0	3	4	2	3	2	4	2	4	4			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr6:26217562G>A	ENST00000303910.2	+	1	398	c.360G>A	c.(358-360)aaG>aaA	p.K120K	HIST1H2BG_ENST00000244601.3_5'Flank	NM_021052.2	NP_066390.1	P04908	H2A1B_HUMAN	histone cluster 1, H2ae	120						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.K120N(1)		central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)	10		all_hematologic(11;0.196)				TGCCTAAGAAGACGGAGAGCC	0.542																																					p.K120K		Atlas-SNP	.											HIST1H2AE,NS,carcinoma,0,1	HIST1H2AE	25	.	1	Substitution - Missense(1)	lung(1)	c.G360A						PASS	.						55	56	55					6																	26217562		2203	4300	6503	SO:0001819	synonymous_variant	3012	exon1			TAAGAAGACGGAG	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.360G>A	chr6.hg19:g.26217562G>A		145.0	0.0	.		144.0	92.0	.	NM_021052	P28001|Q76P63	Silent	SNP	ENST00000303910.2	hg19	CCDS4595.1																																																																																			.	.	.	none		0.542	HIST1H2AE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040103.1	NM_021052		A	26217562	G	A	26217562	2	1	77	1	0	0	0	0	0	0	0	1	7139	933	33	2		2	HIST1H2AE	6	26217562	Silent	SNP	G	TCGA-AL-A5DJ-01A-11D-A26P-10		26217562	144897505	14	4953											
PNPLA1	285848	hgsc.bcm.edu	37	chr6	36238386	36238386	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaaacagcccaccgctttgcGgggacatcggcaggtgctgt	8	7	14	12	3	0	0	0	0	0	0	1	2	0	1	2	4	4	3	2	4	1	1			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr6:36238386G>A	ENST00000394571.2	+	1	150	c.150G>A	c.(148-150)gcG>gcA	p.A50A	PNPLA1_ENST00000312917.5_Intron|PNPLA1_ENST00000388715.3_Intron	NM_001145717.1	NP_001139189.2	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	50	Patatin.				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						ACCGCTTTGCGGGGACATCGG	0.652																																					p.A50A		Atlas-SNP	.											.	PNPLA1	92	.	0			c.G150A						PASS	.						16	21	19					6																	36238386		692	1591	2283	SO:0001819	synonymous_variant	285848	exon1			CTTTGCGGGGACA		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.150G>A	chr6.hg19:g.36238386G>A		74.0	0.0	.		101.0	85.0	.	NM_001145717	A3RMU3|J3JS20|Q2A6N1|Q3SY95|Q3SY96|Q5R3L2	Silent	SNP	ENST00000394571.2	hg19	CCDS54997.1																																																																																			.	.	.	none		0.652	PNPLA1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_173676		A	36238386	G	A	36238386	2	1	77	1	0	0	0	0	0	0	0	1	12171	1103	39	1		1	PNPLA1	6	36238386	Silent	SNP	G	TCGA-AL-A5DJ-01A-11D-A26P-10	10020824	36238386	134876681	15	4954											
TBP	6908	hgsc.bcm.edu	37	chr6	170871004	170871004	+	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	gagcaacaaaggcagcagcaGcaacaacaacagcagcagca	19	0	10	12	0	0	0	0	0	0	0	0	1	0	0	0	1	11	8	0	1	5	0			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr6:170871004G>A	ENST00000392092.2	+	3	459	c.180G>A	c.(178-180)caG>caA	p.Q60Q	TBP_ENST00000230354.6_Silent_p.Q60Q|TBP_ENST00000540980.1_Silent_p.Q40Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	60	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		Ggcagcagcagcaacaacaac	0.542																																					p.Q60Q		Atlas-SNP	.											.	TBP	58	.	0			c.G180A						PASS	.						43	45	44					6																	170871004		2203	4300	6503	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAACAA	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"General transcription factors"	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.180G>A	chr6.hg19:g.170871004G>A		79.0	0.0	.		108.0	13.0	.	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	hg19	CCDS5315.1																																																																																			.	.	.	none		0.542	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		A	170871004	G	A	170871004	2	1	77	1	0	0	0	0	0	0	0	1	15656	962	34	2		2	TBP	6	170871004	Silent	SNP	G	TCGA-AL-A5DJ-01A-11D-A26P-10	134632618	170871004	244063	16	4955											
ZNF679	168417	hgsc.bcm.edu	37	chr7	63720609	63720609	+	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	tgtttttcagggactgttgaCattcagagatgtagtcatag	10	15	11	5	0	3	2	3	1	0	1	3	4	3	3	0	1	0	3	0	1	2	6			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr7:63720609C>A	ENST00000421025.1	+	3	319	c.50C>A	c.(49-51)aCa>aAa	p.T17K	ZNF679_ENST00000255746.4_Missense_Mutation_p.T17K	NM_001159524.1|NM_153363.2	NP_001152996.1|NP_699194.2	Q8IYX0	ZN679_HUMAN	zinc finger protein 679	17	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|skin(1)|stomach(1)	18						GGACTGTTGACATTCAGAGAT	0.388																																					p.T17K		Atlas-SNP	.											.	ZNF679	80	.	0			c.C50A						PASS	.						55	48	50					7																	63720609		692	1591	2283	SO:0001583	missense	168417	exon3			TGTTGACATTCAG	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.50C>A	chr7.hg19:g.63720609C>A	ENSP00000416809:p.Thr17Lys	135.0	0.0	.		159.0	9.0	.	NM_153363		Missense_Mutation	SNP	ENST00000421025.1	hg19	CCDS47592.1	.	.	.	.	.	.	.	.	.	.	c	11.22	1.573678	0.28092	.	.	ENSG00000197123	ENST00000421025;ENST00000255746	T;T	0.02974	4.09;4.09	0.195	0.195	0.15151	Krueppel-associated box (4);	.	.	.	.	T	0.09291	0.0229	M	0.82923	2.615	0.23126	N	0.998254	D	0.58268	0.982	P	0.57620	0.824	T	0.16808	-1.0390	9	0.62326	D	0.03	.	3.1108	0.06357	0.4763:0.5235:1.0E-4:1.0E-4	.	17	Q8IYX0	ZN679_HUMAN	K	17	ENSP00000416809:T17K;ENSP00000255746:T17K	ENSP00000255746:T17K	T	+	2	0	ZNF679	63358044	0.064000	0.20934	0.196000	0.23383	0.196000	0.23810	0.148000	0.16224	0.300000	0.22699	0.306000	0.20318	ACA	.	.	.	none		0.388	ZNF679-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344317.2	NM_153363		A	63720609	C	A	63720609	3	1	77	1	0	0	0	0	1	0	0	0	18098	478	17	4	56	4	ZNF679	7	63720609	Missense_Mutation	SNP	C	TCGA-AL-A5DJ-01A-11D-A26P-10		63720609	95418054	17	4956											
NUP205	23165	hgsc.bcm.edu	37	chr7	135282924	135282924	+	Missense_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	ctctgtgtttctacgattccGtacaagagcttaccggagag	9	12	10	10	3	2	2	0	0	2	2	3	4	3	2	2	1	4	3	2	1	4	5	rs375295025		TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr7:135282924G>A	ENST00000285968.6	+	15	2269	c.2243G>A	c.(2242-2244)cGt>cAt	p.R748H	NUP205_ENST00000440390.2_3'UTR	NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	748					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						CTACGATTCCGTACAAGAGCT	0.428																																					p.R748H		Atlas-SNP	.											.	NUP205	198	.	0			c.G2243A						PASS	.	G	HIS/ARG	0,4406		0,0,2203	159	164	162		2243	5.7	1	7		162	1,8599	1.2+/-3.3	0,1,4299	no	missense	NUP205	NM_015135.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	748/2013	135282924	1,13005	2203	4300	6503	SO:0001583	missense	23165	exon15			GATTCCGTACAAG	D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"chromosome 7 open reading frame 14"	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.2243G>A	chr7.hg19:g.135282924G>A	ENSP00000285968:p.Arg748His	82.0	0.0	.		100.0	31.0	.	NM_015135	A6H8X3|Q86YC1	Missense_Mutation	SNP	ENST00000285968.6	hg19	CCDS34759.1	.	.	.	.	.	.	.	.	.	.	G	14.29	2.490520	0.44249	0.0	1.16E-4	ENSG00000155561	ENST00000285968	T	0.32753	1.44	5.73	5.73	0.89815	.	0.098316	0.64402	D	0.000001	T	0.21387	0.0515	N	0.13098	0.295	0.80722	D	1	B	0.31655	0.334	B	0.24394	0.053	T	0.03473	-1.1033	10	0.40728	T	0.16	-22.9195	19.8824	0.96903	0.0:0.0:1.0:0.0	.	748	Q92621	NU205_HUMAN	H	748	ENSP00000285968:R748H	ENSP00000285968:R748H	R	+	2	0	NUP205	134933464	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.954000	0.76001	2.696000	0.92011	0.591000	0.81541	CGT	.	.	.	weak		0.428	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1			A	135282924	G	A	135282924	3	1	77	1	0	0	0	0	1	0	0	0	10766	1145	40	1	2301	1	NUP205	7	135282924	Missense_Mutation	SNP	G	TCGA-AL-A5DJ-01A-11D-A26P-10	71562315	135282924	23855739	18	4957											
MLL3	58508	hgsc.bcm.edu	37	chr7	151859226	151859226	+	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	ccttcagctgggttctgcttCtcaactagtttattatcctt	6	18	6	11	0	3	0	2	0	2	0	5	0	4	0	2	1	3	4	2	1	4	8			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr7:151859226C>A	ENST00000262189.6	-	43	11654	c.11436G>T	c.(11434-11436)gaG>gaT	p.E3812D	KMT2C_ENST00000355193.2_Missense_Mutation_p.E3812D	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	3812					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)										GGTTCTGCTTCTCAACTAGTT	0.328																																					p.E3812D		Atlas-SNP	.											.	MLL3	1564	.	0			c.G11436T						PASS	.						44	48	47					7																	151859226		2201	4298	6499	SO:0001583	missense	58508	exon43			CTGCTTCTCAACT	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.11436G>T	chr7.hg19:g.151859226C>A	ENSP00000262189:p.Glu3812Asp	26.0	0.0	.		40.0	7.0	.	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.21|11.21	1.570903|1.570903	0.28003|0.28003	.|.	.|.	ENSG00000055609|ENSG00000055609	ENST00000262189;ENST00000355193;ENST00000424877;ENST00000418061|ENST00000360104	D;D;D|.	0.89050|.	-1.81;-1.8;-2.46|.	5.51|5.51	2.72|2.72	0.32119|0.32119	.|.	0.311841|0.311841	0.22245|0.22245	U|U	0.062629|0.062629	T|.	0.40719|.	0.1128|.	L|L	0.35723|0.35723	1.085|1.085	0.80722|0.80722	D|D	1|1	B;B;B|.	0.15141|.	0.012;0.01;0.01|.	B;B;B|.	0.13407|.	0.006;0.009;0.009|.	T|.	0.08027|.	-1.0742|.	10|.	0.18276|0.12103	T|T	0.48|0.63	.|.	6.7615|6.7615	0.23542|0.23542	0.0:0.5573:0.2457:0.197|0.0:0.5573:0.2457:0.197	.|.	3812;2873;3812|.	Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3|.	MLL3_HUMAN;.;.|.	D|X	3812;3812;398;8|1318	ENSP00000262189:E3812D;ENSP00000347325:E3812D;ENSP00000410411:E398D|.	ENSP00000262189:E3812D|ENSP00000353218:E1318X	E|E	-|-	3|1	2|0	MLL3|MLL3	151490159|151490159	0.998000|0.998000	0.40836|0.40836	0.728000|0.728000	0.30774|0.30774	0.974000|0.974000	0.67602|0.67602	0.397000|0.397000	0.20883|0.20883	0.689000|0.689000	0.31550|0.31550	0.650000|0.650000	0.86243|0.86243	GAG|GAA	.	.	.	none		0.328	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			A	151859226	C	A	151859226	3	1	77	1	0	0	0	0	1	0	0	0	9629	912	32	4	3367	4	MLL3	7	151859226	Missense_Mutation	SNP	C	TCGA-AL-A5DJ-01A-11D-A26P-10	16576302	151859226	7279437	19	4958											
KCNK9	51305	hgsc.bcm.edu	37	chr8	140630623	140630623	+	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	tgtgcttggtgagatctcctCgatcttgtaagagatggagt	8	14	13	6	1	2	2	0	1	2	2	4	6	2	3	1	2	1	2	1	2	1	3			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr8:140630623C>T	ENST00000520439.1	-	2	1066	c.1003G>A	c.(1003-1005)Gag>Aag	p.E335K	KCNK9_ENST00000523477.1_5'Flank|KCNK9_ENST00000303015.1_Missense_Mutation_p.E335K	NM_001282534.1	NP_001269463.1	Q9NPC2	KCNK9_HUMAN	potassium channel, subfamily K, member 9	335					cochlea development (GO:0090102)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			NS(1)|endometrium(9)|kidney(1)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)	43	all_cancers(97;3.94e-14)|all_epithelial(106;4.81e-13)|Lung NSC(106;8.18e-05)|all_lung(105;0.00015)|Ovarian(258;0.00235)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;0.134)	BRCA - Breast invasive adenocarcinoma(115;0.0855)		Doxapram(DB00561)|Halothane(DB01159)	GAGATCTCCTCGATCTTGTAA	0.552																																					p.E335K		Atlas-SNP	.											.	KCNK9	100	.	0			c.G1003A						PASS	.						115	113	113					8																	140630623		2203	4300	6503	SO:0001583	missense	51305	exon2			TCTCCTCGATCTT	AF212829	CCDS6377.1	8q24.3	2012-03-07			ENSG00000169427	ENSG00000169427		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6283	protein-coding gene	gene with protein product		605874				10734076, 16382106	Standard	NM_001282534		Approved	K2p9.1, TASK3, TASK-3	uc003yvf.1	Q9NPC2	OTTHUMG00000164186	ENST00000520439.1:c.1003G>A	chr8.hg19:g.140630623C>T	ENSP00000430676:p.Glu335Lys	193.0	0.0	.		213.0	89.0	.	NM_016601	Q2M290|Q540F2	Missense_Mutation	SNP	ENST00000520439.1	hg19	CCDS6377.1	.	.	.	.	.	.	.	.	.	.	C	16.05	3.013189	0.54468	.	.	ENSG00000169427	ENST00000522317;ENST00000303015;ENST00000520439	T;T;T	0.16324	2.35;2.35;2.35	5.85	5.85	0.93711	.	0.062019	0.64402	D	0.000005	T	0.19446	0.0467	M	0.70595	2.14	0.58432	D	0.999999	P	0.40083	0.702	B	0.34038	0.174	T	0.11494	-1.0585	10	0.07325	T	0.83	.	19.1531	0.93496	0.0:1.0:0.0:0.0	.	335	Q9NPC2	KCNK9_HUMAN	K	335	ENSP00000429847:E335K;ENSP00000302166:E335K;ENSP00000430676:E335K	ENSP00000302166:E335K	E	-	1	0	KCNK9	140699805	1.000000	0.71417	0.969000	0.41365	0.752000	0.42762	5.595000	0.67563	2.753000	0.94483	0.655000	0.94253	GAG	.	.	.	none		0.552	KCNK9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378473.1	NM_016601		T	140630623	C	T	140630623	3	4	77	1	0	0	0	0	1	0	0	0	8079	893	31	1	125	1	KCNK9	8	140630623	Missense_Mutation	SNP	C	TCGA-AL-A5DJ-01A-11D-A26P-10		140630623	5733399	20	4959											
ST6GALNAC4	27090	hgsc.bcm.edu	37	chr9	130674884	130674884	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctcggcactgtcgatctcagCacccaggcctgagcccagca	8	6	10	17	2	1	1	1	1	1	0	4	2	1	1	3	2	3	3	3	2	0	0			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr9:130674884C>T	ENST00000335791.5	-	4	549	c.274G>A	c.(274-276)Gct>Act	p.A92T	ST6GALNAC4_ENST00000495983.1_5'UTR|ST6GALNAC4_ENST00000343609.2_Missense_Mutation_p.A8T	NM_175039.3	NP_778204.1	Q9H4F1	SIA7D_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 4	92					cellular protein metabolic process (GO:0044267)|glycolipid metabolic process (GO:0006664)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	(alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl-galactosaminide 6-alpha-sialyltransferase activity (GO:0047290)|sialyltransferase activity (GO:0008373)			endometrium(1)|large_intestine(2)|lung(2)|prostate(2)	7						TCGATCTCAGCACCCAGGCCT	0.682																																					p.A92T		Atlas-SNP	.											.	ST6GALNAC4	29	.	0			c.G274A						PASS	.						31	26	27					9																	130674884		2203	4299	6502	SO:0001583	missense	27090	exon4			TCTCAGCACCCAG	AB035172	CCDS6883.1	9q34	2013-03-01	2005-02-07	2005-02-07	ENSG00000136840	ENSG00000136840	2.4.99.7	"Sialyltransferases"	17846	protein-coding gene	gene with protein product		606378	"sialyltransferase 7D ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase)"	SIAT7D		10207017, 11062056	Standard	XM_005251922		Approved	ST6GALNACIV, SIAT3C	uc004bss.3	Q9H4F1	OTTHUMG00000020724	ENST00000335791.5:c.274G>A	chr9.hg19:g.130674884C>T	ENSP00000336733:p.Ala92Thr	4.0	0.0	.		18.0	6.0	.	NM_175039	Q5T9D0|Q9NWU6|Q9UKU1|Q9ULB9|Q9Y3G3|Q9Y3G4	Missense_Mutation	SNP	ENST00000335791.5	hg19	CCDS6883.1	.	.	.	.	.	.	.	.	.	.	C	12.47	1.947277	0.34377	.	.	ENSG00000136840	ENST00000541933;ENST00000335791;ENST00000343609;ENST00000361444	T;T;T	0.30714	1.52;1.52;1.52	5.58	-4.4	0.03600	.	0.720248	0.13564	N	0.378592	T	0.14874	0.0359	N	0.26092	0.79	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.13926	-1.0491	10	0.35671	T	0.21	-23.1112	4.2604	0.10739	0.0897:0.1894:0.4714:0.2496	.	92	Q9H4F1	SIA7D_HUMAN	T	8;92;8;8	ENSP00000336733:A92T;ENSP00000340382:A8T;ENSP00000355130:A8T	ENSP00000336733:A92T	A	-	1	0	ST6GALNAC4	129714705	0.000000	0.05858	0.001000	0.08648	0.554000	0.35429	-0.081000	0.11321	-0.632000	0.05553	-0.379000	0.06801	GCT	.	.	.	none		0.682	ST6GALNAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054317.2	NM_175040		T	130674884	C	T	130674884	3	4	77	1	0	0	0	0	1	0	0	0	15238	710	25	2	646	2	ST6GALNAC4	9	130674884	Missense_Mutation	SNP	C	TCGA-AL-A5DJ-01A-11D-A26P-10		130674884	10538547	21	4960											
OR51S1	119692	hgsc.bcm.edu	37	chr11	4869479	4869479	+	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	catcctactcactgagcaccAcccaccttcctgggctgcaa	9	8	6	18	0	1	1	1	1	0	0	3	1	3	1	5	1	3	3	5	1	2	2			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr11:4869479A>T	ENST00000322101.2	-	1	1035	c.960T>A	c.(958-960)ggT>ggA	p.G320G	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	320						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)		ACTGAGCACCACCCACCTTCC	0.448																																					p.G320G		Atlas-SNP	.											.	OR51S1	83	.	0			c.T960A						PASS	.						142	135	138					11																	4869479		2201	4298	6499	SO:0001819	synonymous_variant	119692	exon1			AGCACCACCCACC	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.960T>A	chr11.hg19:g.4869479A>T		92.0	0.0	.		110.0	22.0	.	NM_001004758	B9EGZ1|Q6IFI2	Silent	SNP	ENST00000322101.2	hg19	CCDS31362.1																																																																																			.	.	.	none		0.448	OR51S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142179.1	NM_001004758		T	4869479	A	T	4869479	2	4	77	1	0	0	0	0	0	0	0	1	11112	146	6	5		5	OR51S1	11	4869479	Silent	SNP	A	TCGA-AL-A5DJ-01A-11D-A26P-10		4869479	130137037	22	4961											
C11orf45	219833	hgsc.bcm.edu	37	chr11	128772504	128772504	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgagggggtagcccaggCggccctctctactatcatgg	7	8	13	13	1	2	1	1	1	1	0	3	1	2	1	2	5	2	1	2	5	3	3	rs545751134		TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr11:128772504C>T	ENST00000524878.1	-	4	556	c.386G>A	c.(385-387)cGc>cAc	p.R129H	C11orf45_ENST00000530168.1_5'UTR|KCNJ5_ENST00000338350.4_Intron|C11orf45_ENST00000310799.3_Missense_Mutation_p.R129H|KCNJ5_ENST00000529694.1_Intron			Q8TAV5	CK045_HUMAN	chromosome 11 open reading frame 45	129						extracellular region (GO:0005576)				endometrium(1)|kidney(1)|lung(2)|pancreas(1)|prostate(2)	7	all_hematologic(175;0.0641)	Lung NSC(97;0.00521)|Breast(109;0.00715)|all_lung(97;0.0111)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.00531)|LUSC - Lung squamous cell carcinoma(976;0.0193)|Lung(977;0.0195)		GTAGCCCAGGCGGCCCTCTCT	0.607																																					p.R129H		Atlas-SNP	.											.	C11orf45	14	.	0			c.G386A						PASS	.						67	59	61					11																	128772504		2201	4297	6498	SO:0001583	missense	219833	exon4			CCCAGGCGGCCCT	AK125634	CCDS8478.1	11q24.3	2012-05-30			ENSG00000174370	ENSG00000174370			28584	protein-coding gene	gene with protein product							Standard	NM_001256088		Approved	MGC35558, FLJ43646	uc001qeu.3	Q8TAV5	OTTHUMG00000165796	ENST00000524878.1:c.386G>A	chr11.hg19:g.128772504C>T	ENSP00000431922:p.Arg129His	74.0	0.0	.		67.0	30.0	.	NM_145013	B2RAD0	Missense_Mutation	SNP	ENST00000524878.1	hg19	CCDS8478.1	.	.	.	.	.	.	.	.	.	.	C	8.914	0.959417	0.18507	.	.	ENSG00000174370	ENST00000310799;ENST00000524878	.	.	.	2.51	-4.9	0.03094	.	.	.	.	.	T	0.13713	0.0332	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18808	-1.0325	8	0.87932	D	0	.	0.223	0.00170	0.2826:0.2756:0.207:0.2348	.	129	Q8TAV5	CK045_HUMAN	H	129	.	ENSP00000307879:R129H	R	-	2	0	C11orf45	128277714	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.211000	0.02997	-1.303000	0.02332	-2.745000	0.00126	CGC	.	.	.	none		0.607	C11orf45-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386243.1	NM_145013		T	128772504	C	T	128772504	3	4	77	1	0	0	0	0	1	0	0	0	1644	768	27	1	55	1	C11orf45	11	128772504	Missense_Mutation	SNP	C	TCGA-AL-A5DJ-01A-11D-A26P-10	123903025	128772504	6234012	23	4962											
CD163	9332	hgsc.bcm.edu	37	chr12	7651490	7651490	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaatcactccagcatcctcaGcatgatcacagttatgcttt	12	12	5	12	0	3	1	3	1	0	0	5	1	5	1	2	0	3	4	2	0	2	2			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr12:7651490G>A	ENST00000359156.4	-	4	954	c.752C>T	c.(751-753)gCt>gTt	p.A251V	CD163_ENST00000541972.1_Missense_Mutation_p.A239V|CD163_ENST00000396620.3_Missense_Mutation_p.A251V|CD163_ENST00000432237.2_Missense_Mutation_p.A251V	NM_004244.5	NP_004235.4	Q86VB7	C163A_HUMAN	CD163 molecule	251	SRCR 2. {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)	AGCATCCTCAGCATGATCACA	0.433																																					p.A251V		Atlas-SNP	.											.	CD163	221	.	0			c.C752T						PASS	.						180	168	172					12																	7651490		2203	4300	6503	SO:0001583	missense	9332	exon4			TCCTCAGCATGAT	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.752C>T	chr12.hg19:g.7651490G>A	ENSP00000352071:p.Ala251Val	101.0	0.0	.		119.0	24.0	.	NM_203416	C9JIG2|Q07898|Q07899|Q07900|Q07901|Q2VLH7	Missense_Mutation	SNP	ENST00000359156.4	hg19	CCDS8578.1	.	.	.	.	.	.	.	.	.	.	G	12.85	2.061841	0.36373	.	.	ENSG00000177575	ENST00000359156;ENST00000541972;ENST00000396620;ENST00000432237	T;T;T;T	0.35605	1.3;1.3;1.3;1.3	5.16	3.02	0.34903	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	1.445290	0.04133	N	0.318256	T	0.30355	0.0762	L	0.27975	0.815	0.09310	N	0.999992	P;B;P	0.45428	0.772;0.225;0.858	B;B;B	0.43701	0.428;0.047;0.428	T	0.19614	-1.0300	10	0.41790	T	0.15	.	5.6612	0.17670	0.0941:0.0:0.4895:0.4164	.	251;251;251	C9JHR8;Q86VB7-3;Q86VB7	.;.;C163A_HUMAN	V	251;239;251;251	ENSP00000352071:A251V;ENSP00000444071:A239V;ENSP00000379863:A251V;ENSP00000403885:A251V	ENSP00000352071:A251V	A	-	2	0	CD163	7542757	0.000000	0.05858	0.278000	0.24718	0.945000	0.59286	-0.236000	0.09003	1.300000	0.44818	0.650000	0.86243	GCT	.	.	.	none		0.433	CD163-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399396.2	NM_004244, NM_203416		A	7651490	G	A	7651490	3	1	77	1	0	0	0	0	1	0	0	0	2969	971	34	2	2770	2	CD163	12	7651490	Missense_Mutation	SNP	G	TCGA-AL-A5DJ-01A-11D-A26P-10		7651490	126200405	24	4963											
PIK3C2G	5288	hgsc.bcm.edu	37	chr12	18478009	18478009	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagaaaatatgacttccacCtgaaatacctattgaaaacc	17	10	4	10	0	1	4	1	3	0	1	2	4	2	4	4	0	2	0	4	0	8	5			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr12:18478009C>T	ENST00000266497.5	+	7	1287	c.1249C>T	c.(1249-1251)Ctg>Ttg	p.L417L	PIK3C2G_ENST00000538779.1_Silent_p.L417L|PIK3C2G_ENST00000433979.1_Silent_p.L417L|PIK3C2G_ENST00000535651.1_Silent_p.L417L			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	417					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)				TGACTTCCACCTGAAATACCT	0.299																																					p.L417L		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.C1249T						PASS	.						83	81	82					12																	18478009		1800	4061	5861	SO:0001819	synonymous_variant	5288	exon8			TTCCACCTGAAAT	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.1249C>T	chr12.hg19:g.18478009C>T		33.0	0.0	.		36.0	15.0	.	NM_004570	A1L3U0	Silent	SNP	ENST00000266497.5	hg19	CCDS44839.1																																																																																			.	.	.	none		0.299	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570		T	18478009	C	T	18478009	2	4	77	1	0	0	0	0	0	0	0	1	11918	680	24	2		2	PIK3C2G	12	18478009	Silent	SNP	C	TCGA-AL-A5DJ-01A-11D-A26P-10	10826519	18478009	115373886	25	4964											
C14orf104	55172	hgsc.bcm.edu	37	chr14	50092296	50092296	+	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	agcaaagaattctgaaaactGaatgcacaattggtcacatg	17	9	8	7	0	2	3	1	2	1	1	2	3	2	3	0	1	3	2	0	1	6	2			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr14:50092296G>T	ENST00000298292.8	-	3	2558	c.2478C>A	c.(2476-2478)ttC>ttA	p.F826L	RP11-649E7.5_ENST00000555043.1_RNA|DNAAF2_ENST00000406043.3_Missense_Mutation_p.F778L	NM_018139.2	NP_060609.2	Q9NVR5	KTU_HUMAN	dynein, axonemal, assembly factor 2	826					axonemal dynein complex assembly (GO:0070286)|bacterial-type flagellum-dependent cell motility (GO:0071973)|cilium-dependent cell motility (GO:0060285)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)				kidney(1)|lung(4)	5						TCTGAAAACTGAATGCACAAT	0.308																																					p.F826L		Atlas-SNP	.											.	DNAAF2	47	.	0			c.C2478A						PASS	.						99	91	94					14																	50092296		2202	4300	6502	SO:0001583	missense	55172	exon3			AAAACTGAATGCA	AK001425	CCDS9691.2, CCDS45100.1	14q21.3	2012-05-03	2011-06-09	2011-06-09	ENSG00000165506	ENSG00000165506			20188	protein-coding gene	gene with protein product	"kintoun"	612517	"chromosome 14 open reading frame 104"	C14orf104			Standard	NM_001083908		Approved	FLJ10563, KTU, PF13, CILD10	uc001wws.4	Q9NVR5	OTTHUMG00000152331	ENST00000298292.8:c.2478C>A	chr14.hg19:g.50092296G>T	ENSP00000298292:p.Phe826Leu	104.0	0.0	.		80.0	21.0	.	NM_018139	B9WS54|C0JAP7|Q86TR1|Q86TY8|Q969Z5	Missense_Mutation	SNP	ENST00000298292.8	hg19	CCDS9691.2	.	.	.	.	.	.	.	.	.	.	G	22.8	4.339347	0.81911	.	.	ENSG00000165506	ENST00000298292;ENST00000406043	T;T	0.08282	3.11;3.11	5.9	5.0	0.66597	.	0.163612	0.40302	N	0.001129	T	0.21145	0.0509	M	0.66939	2.045	0.33550	D	0.596045	D;D	0.65815	0.995;0.991	P;P	0.59424	0.857;0.795	T	0.09143	-1.0688	10	0.72032	D	0.01	.	10.6878	0.45854	0.1484:0.0:0.8516:0.0	.	778;826	Q9NVR5-2;Q9NVR5	.;KTU_HUMAN	L	826;778	ENSP00000298292:F826L;ENSP00000384862:F778L	ENSP00000298292:F826L	F	-	3	2	DNAAF2	49162046	0.911000	0.30947	1.000000	0.80357	0.850000	0.48378	0.932000	0.28884	2.808000	0.96608	0.551000	0.68910	TTC	.	.	.	none		0.308	DNAAF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276813.1			T	50092296	G	T	50092296	3	4	77	1	0	0	0	0	1	0	0	0	1738	1281	45	4	39	4	C14orf104	14	50092296	Missense_Mutation	SNP	G	TCGA-AL-A5DJ-01A-11D-A26P-10		50092296	57257244	26	4965											
DYX1C1	161582	hgsc.bcm.edu	37	chr15	55731768	55731768	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctcttcgtgcctcagcttgTttgtgtagccactagaatga	7	14	10	10	1	2	2	1	1	1	1	3	2	2	2	2	0	3	4	2	0	3	5			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr15:55731768T>C	ENST00000321149.3	-	7	1162	c.795A>G	c.(793-795)aaA>aaG	p.K265K	DYX1C1_ENST00000448430.2_Silent_p.K265K|DYX1C1_ENST00000380679.1_Silent_p.K265K|DYX1C1_ENST00000348518.3_Silent_p.K265K|DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000457155.2_Silent_p.K265K	NM_130810.3	NP_570722.2	Q8WXU2	DYXC1_HUMAN	dyslexia susceptibility 1 candidate 1	265					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)		CCTCAGCTTGTTTGTGTAGCC	0.348																																					p.K265K		Atlas-SNP	.											.	DYX1C1	54	.	0			c.A795G						PASS	.						66	67	66					15																	55731768		2193	4292	6485	SO:0001819	synonymous_variant	161582	exon7			AGCTTGTTTGTGT		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.795A>G	chr15.hg19:g.55731768T>C		42.0	0.0	.		85.0	23.0	.	NM_001033560	Q6P5Y9|Q8N1S6	Silent	SNP	ENST00000321149.3	hg19	CCDS10154.1																																																																																			.	.	.	none		0.348	DYX1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254976.1	NM_130810		C	55731768	T	C	55731768	2	2	77	1	0	0	0	0	0	0	0	1	4864	1722	60	3		3	DYX1C1	15	55731768	Silent	SNP	T	TCGA-AL-A5DJ-01A-11D-A26P-10		55731768	46799624	27	4966											
ADCY9	115	hgsc.bcm.edu	37	chr16	4163953	4163953	+	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	ctcctcatgcccaggatgccGcaaaggacggtgcccgtgtg	7	7	13	14	3	1	0	1	0	0	0	2	2	2	2	4	3	3	1	4	3	1	0			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr16:4163953G>A	ENST00000294016.3	-	2	2029	c.1491C>T	c.(1489-1491)tgC>tgT	p.C497C		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	497	Guanylate cyclase 1. {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						CCAGGATGCCGCAAAGGACGG	0.562																																					p.C497C		Atlas-SNP	.											.	ADCY9	151	.	0			c.C1491T						PASS	.						122	126	125					16																	4163953		2197	4300	6497	SO:0001819	synonymous_variant	115	exon2			GATGCCGCAAAGG	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.1491C>T	chr16.hg19:g.4163953G>A		152.0	0.0	.		194.0	138.0	.	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Silent	SNP	ENST00000294016.3	hg19	CCDS32382.1																																																																																			.	.	.	none		0.562	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1			A	4163953	G	A	4163953	2	1	77	1	0	0	0	0	0	0	0	1	301	1079	38	1		1	ADCY9	16	4163953	Silent	SNP	G	TCGA-AL-A5DJ-01A-11D-A26P-10		4163953	86190800	28	4967											
ADCY9	115	hgsc.bcm.edu	37	chr16	4164162	4164162	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttggtctcctcacacaggcGgtcgaagcgaccgaacagat	10	7	11	13	4	2	1	1	0	1	1	4	4	2	1	2	3	2	0	2	3	2	1			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr16:4164162G>A	ENST00000294016.3	-	2	1820	c.1282C>T	c.(1282-1284)Cgc>Tgc	p.R428C		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	428	Guanylate cyclase 1. {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						TCACACAGGCGGTCGAAGCGA	0.572																																					p.R428C		Atlas-SNP	.											ADCY9,NS,carcinoma,0,1	ADCY9	151	.	0			c.C1282T						PASS	.						67	70	69					16																	4164162		2197	4300	6497	SO:0001583	missense	115	exon2			ACAGGCGGTCGAA	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.1282C>T	chr16.hg19:g.4164162G>A	ENSP00000294016:p.Arg428Cys	106.0	0.0	.		126.0	23.0	.	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Missense_Mutation	SNP	ENST00000294016.3	hg19	CCDS32382.1	.	.	.	.	.	.	.	.	.	.	G	16.75	3.210746	0.58343	.	.	ENSG00000162104	ENST00000294016	D	0.81996	-1.56	5.28	5.28	0.74379	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.061240	0.64402	D	0.000003	D	0.90518	0.7029	M	0.81614	2.55	0.58432	D	0.999996	D	0.76494	0.999	P	0.59761	0.863	D	0.91803	0.5453	10	0.87932	D	0	.	18.9505	0.92640	0.0:0.0:1.0:0.0	.	428	O60503	ADCY9_HUMAN	C	428	ENSP00000294016:R428C	ENSP00000294016:R428C	R	-	1	0	ADCY9	4104163	1.000000	0.71417	0.993000	0.49108	0.907000	0.53573	3.072000	0.50049	2.481000	0.83766	0.555000	0.69702	CGC	.	.	.	none		0.572	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1			A	4164162	G	A	4164162	3	1	77	1	0	0	0	0	1	0	0	0	301	1116	39	1	2819	1	ADCY9	16	4164162	Missense_Mutation	SNP	G	TCGA-AL-A5DJ-01A-11D-A26P-10	209	4164162	86190591	29	4968											
NDRG4	65009	hgsc.bcm.edu	37	chr16	58541744	58541744	+	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	ggacattaaccggcctggaaCggtgcccaatgccaagacgc	11	5	12	13	3	0	1	0	0	0	1	0	3	0	3	4	4	4	0	4	4	4	1	rs200391051		TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr16:58541744C>T	ENST00000570248.1	+	9	759	c.653C>T	c.(652-654)aCg>aTg	p.T218M	NDRG4_ENST00000566192.1_Missense_Mutation_p.T218M|NDRG4_ENST00000394279.2_Missense_Mutation_p.T250M|NDRG4_ENST00000258187.5_Missense_Mutation_p.T250M|NDRG4_ENST00000569923.1_Missense_Mutation_p.T163M|NDRG4_ENST00000562999.1_Missense_Mutation_p.T218M|NDRG4_ENST00000568640.1_Missense_Mutation_p.T236M|NDRG4_ENST00000394282.4_Missense_Mutation_p.T270M|NDRG4_ENST00000356752.4_Missense_Mutation_p.T248M|NDRG4_ENST00000563799.1_Missense_Mutation_p.T236M	NM_001242835.1	NP_001229764.1	Q9ULP0	NDRG4_HUMAN	NDRG family member 4	218					cell differentiation (GO:0030154)|cell growth (GO:0016049)|response to stress (GO:0006950)	cytoplasm (GO:0005737)				breast(1)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	11						CGGCCTGGAACGGTGCCCAAT	0.667																																					p.T270M		Atlas-SNP	.											NDRG4,NS,malignant_melanoma,0,1	NDRG4	29	.	0			c.C809T						PASS	.	C	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	0,4396		0,0,2198	68	66	67		809,743,707,653,653,749,749	4.6	1	16		67	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense,missense	NDRG4	NM_001130487.1,NM_001242833.1,NM_001242834.1,NM_001242835.1,NM_001242836.1,NM_020465.3,NM_022910.3	81,81,81,81,81,81,81	0,1,6497	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	270/392,248/370,236/358,218/353,218/340,250/372,250/372	58541744	1,12995	2198	4300	6498	SO:0001583	missense	65009	exon11			CTGGAACGGTGCC	AB044947	CCDS10797.1, CCDS45500.1, CCDS55999.1, CCDS58465.1, CCDS58466.1, CCDS58467.1	16q21-q22.3	2008-07-04			ENSG00000103034	ENSG00000103034			14466	protein-coding gene	gene with protein product		614463				11352569, 16408304	Standard	NM_020465		Approved	KIAA1180, SMAP-8	uc002enk.3	Q9ULP0	OTTHUMG00000133485	ENST00000570248.1:c.653C>T	chr16.hg19:g.58541744C>T	ENSP00000457659:p.Thr218Met	104.0	0.0	.		109.0	16.0	.	NM_001130487	B3KNU2|B4DK66|B4DSW5|H7C600|Q6ZNE7|Q6ZTI7|Q96PL9|Q9GZM1|Q9GZN3|Q9GZX0	Missense_Mutation	SNP	ENST00000570248.1	hg19	CCDS58466.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.947408	0.73672	0.0	1.16E-4	ENSG00000103034	ENST00000258187;ENST00000421602;ENST00000394282;ENST00000394279;ENST00000356752	T;T;T;T	0.18338	2.22;2.22;2.22;2.22	5.59	4.63	0.57726	.	0.097461	0.64402	D	0.000001	T	0.30135	0.0755	L	0.34521	1.04	0.58432	D	0.999998	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;0.979;0.999;1.0;0.999	D;D;D;P;P;P;P	0.68192	0.956;0.956;0.927;0.636;0.861;0.897;0.855	T	0.02917	-1.1094	10	0.52906	T	0.07	-0.368	15.0366	0.71751	0.143:0.857:0.0:0.0	.	236;248;236;218;218;270;250	B4DK66;B4DSW5;Q9ULP0-5;Q9ULP0-2;Q9ULP0;Q9ULP0-6;Q9ULP0-3	.;.;.;.;NDRG4_HUMAN;.;.	M	250;163;270;250;248	ENSP00000258187:T250M;ENSP00000377823:T270M;ENSP00000377820:T250M;ENSP00000349193:T248M	ENSP00000258187:T250M	T	+	2	0	NDRG4	57099245	1.000000	0.71417	0.980000	0.43619	0.680000	0.39746	4.398000	0.59697	1.340000	0.45581	0.655000	0.94253	ACG	.	C|0.999;T|0.001	0.001	weak		0.667	NDRG4-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422671.2			T	58541744	C	T	58541744	3	4	77	1	0	0	0	0	1	0	0	0	10261	536	19	1	851	1	NDRG4	16	58541744	Missense_Mutation	SNP	C	TCGA-AL-A5DJ-01A-11D-A26P-10	54377582	58541744	31813009	30	4969											
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11129655	11129655	+	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	cgctgtccaactgggcgtacGagtttgacaagtgggccccc	7	8	13	13	3	0	1	0	1	0	0	1	2	1	1	3	2	2	3	3	2	3	2			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr19:11129655G>A	ENST00000429416.3	+	18	2742	c.2461G>A	c.(2461-2463)Gag>Aag	p.E821K	SMARCA4_ENST00000590574.1_Missense_Mutation_p.E821K|SMARCA4_ENST00000541122.2_Missense_Mutation_p.E821K|SMARCA4_ENST00000450717.3_Missense_Mutation_p.E821K|SMARCA4_ENST00000589677.1_Missense_Mutation_p.E821K|SMARCA4_ENST00000344626.4_Missense_Mutation_p.E821K|CTC-215O4.4_ENST00000587831.1_RNA|SMARCA4_ENST00000444061.3_Missense_Mutation_p.E821K|SMARCA4_ENST00000413806.3_Missense_Mutation_p.E821K|SMARCA4_ENST00000358026.2_Missense_Mutation_p.E821K	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	821	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				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.E821K(3)|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)				CTGGGCGTACGAGTTTGACAA	0.557			"F, N, Mis"		NSCLC																																p.E821K		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"		E	SMARCA4,NS,lymphoid_neoplasm,0,3	SMARCA4	502	.	4	Substitution - Missense(3)|Unknown(1)	central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)	c.G2461A						PASS	.						173	148	157					19																	11129655		2203	4300	6503	SO:0001583	missense	6597	exon17			GCGTACGAGTTTG	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.2461G>A	chr19.hg19:g.11129655G>A	ENSP00000395654:p.Glu821Lys	170.0	1.0	.		264.0	194.0	.	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.317520	0.81469	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.95690	-3.78;-3.78;-3.78;-3.78;-3.78;-3.78;-3.78	4.95	4.95	0.65309	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.98629	0.9541	H	0.97291	3.975	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;0.999;1.0;1.0	D	0.99624	1.0984	10	0.87932	D	0	-27.2359	17.1078	0.86668	0.0:0.0:1.0:0.0	.	821;821;821;821;821;821;821	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;A7E2E1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	K	821;821;885;821;821;821;821;821	ENSP00000395654:E821K;ENSP00000350720:E821K;ENSP00000343896:E821K;ENSP00000445036:E821K;ENSP00000392837:E821K;ENSP00000397783:E821K;ENSP00000414727:E821K	ENSP00000343896:E821K	E	+	1	0	SMARCA4	10990655	1.000000	0.71417	0.924000	0.36721	0.213000	0.24496	9.625000	0.98406	2.571000	0.86741	0.591000	0.81541	GAG	.	.	.	none		0.557	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		A	11129655	G	A	11129655	3	1	77	1	0	0	0	0	1	0	0	0	14783	1059	37	1	2523	1	SMARCA4	19	11129655	Missense_Mutation	SNP	G	TCGA-AL-A5DJ-01A-11D-A26P-10		11129655	47999328	31	4970											
GCDH	2639	hgsc.bcm.edu	37	chr19	13002761	13002761	+	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	gccaggagagactcatgcctCgcatcctgttggccaatcgc	8	8	11	14	2	1	1	1	0	0	1	4	3	2	2	4	2	1	2	4	2	1	1			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr19:13002761C>T	ENST00000222214.5	+	4	455	c.244C>T	c.(244-246)Cgc>Tgc	p.R82C	GCDH_ENST00000591470.1_Missense_Mutation_p.R82C|GCDH_ENST00000457854.1_Missense_Mutation_p.R82C|GCDH_ENST00000422947.2_Silent_p.L19L			Q92947	GCDH_HUMAN	glutaryl-CoA dehydrogenase	82					cellular nitrogen compound metabolic process (GO:0034641)|fatty acid oxidation (GO:0019395)|fatty-acyl-CoA biosynthetic process (GO:0046949)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tryptophan metabolic process (GO:0006568)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|glutaryl-CoA dehydrogenase activity (GO:0004361)			autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)	19					Flavin adenine dinucleotide(DB03147)	ACTCATGCCTCGCATCCTGTT	0.637																																					p.F82F	GBM(123;875 1636 7726 16444 26754)	Atlas-SNP	.											.	GCDH	76	.	0			c.T244T						PASS	.						79	63	68					19																	13002761		2203	4300	6503	SO:0001583	missense	2639	exon4			ATGCCTCGCATCC	AF012342	CCDS12286.1	19p13.2	2010-04-30	2010-04-30			ENSG00000105607	1.3.99.7		4189	protein-coding gene	gene with protein product		608801	"glutaryl-Coenzyme A dehydrogenase"			1438360, 8088809	Standard	NM_000159		Approved	ACAD5	uc002mvq.4	Q92947		ENST00000222214.5:c.244C>T	chr19.hg19:g.13002761C>T	ENSP00000222214:p.Arg82Cys	131.0	0.0	.		144.0	22.0	.	NM_013976	A8K2Z2|O14719	Silent	SNP	ENST00000222214.5	hg19	CCDS12286.1	.	.	.	.	.	.	.	.	.	.	C	35	5.478034	0.96291	.	.	ENSG00000105607	ENST00000457854;ENST00000222214;ENST00000421816	D;D	0.99722	-6.53;-6.53	5.31	5.31	0.75309	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, N-terminal (1);Acyl-CoA dehydrogenase/oxidase, N-terminal (1);	0.054691	0.85682	D	0.000000	D	0.99859	0.9934	H	0.98866	4.355	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.75020	0.931;0.985;0.985	D	0.96498	0.9369	10	0.87932	D	0	.	16.4613	0.84055	0.0:1.0:0.0:0.0	.	70;82;82	B4DQF2;Q92947;Q92947-2	.;GCDH_HUMAN;.	C	82;82;70	ENSP00000394872:R82C;ENSP00000222214:R82C	ENSP00000222214:R82C	R	+	1	0	GCDH	12863761	0.996000	0.38824	0.997000	0.53966	0.993000	0.82548	3.457000	0.53007	2.488000	0.83962	0.563000	0.77884	CGC	.	.	.	none		0.637	GCDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451897.1			T	13002761	C	T	13002761	3	4	77	1	0	0	0	0	1	0	0	0	6294	884	31	1	254	1	GCDH	19	13002761	Missense_Mutation	SNP	C	TCGA-AL-A5DJ-01A-11D-A26P-10	1873106	13002761	46126222	32	4971											
HAO1	54363	hgsc.bcm.edu	37	chr20	7894923	7894923	+	Missense_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	gcccatcttctctgcctgccGcactagcttcttggtgactt	4	14	8	15	1	3	1	0	1	3	0	4	1	3	1	3	1	3	2	3	1	1	5	rs200785017		TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr20:7894923G>A	ENST00000378789.3	-	3	484	c.433C>T	c.(433-435)Cgg>Tgg	p.R145W		NM_017545.2	NP_060015.1	Q9UJM8	HAOX1_HUMAN	hydroxyacid oxidase (glycolate oxidase) 1	145	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						TCTGCCTGCCGCACTAGCTTC	0.517																																					p.R145W		Atlas-SNP	.											HAO1,NS,carcinoma,0,3	HAO1	71	.	0			c.C433T						PASS	.						198	121	147					20																	7894923		2203	4300	6503	SO:0001583	missense	54363	exon3			CCTGCCGCACTAG	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.433C>T	chr20.hg19:g.7894923G>A	ENSP00000368066:p.Arg145Trp	212.0	0.0	.		304.0	74.0	.	NM_017545	Q14CQ0|Q9UPZ0|Q9Y3I7	Missense_Mutation	SNP	ENST00000378789.3	hg19	CCDS13100.1	.	.	.	.	.	.	.	.	.	.	G	13.38	2.218570	0.39201	.	.	ENSG00000101323	ENST00000378789	T	0.34072	1.38	6.17	0.404	0.16355	Aldolase-type TIM barrel (1);FMN-dependent dehydrogenase (1);	0.915368	0.09558	N	0.786011	T	0.61438	0.2347	M	0.92923	3.36	0.09310	N	1	D;D	0.56287	0.975;0.975	P;P	0.61592	0.891;0.891	T	0.48570	-0.9024	10	0.87932	D	0	0.281	6.8057	0.23777	0.0708:0.0792:0.4783:0.3717	.	145;145	A8K058;Q9UJM8	.;HAOX1_HUMAN	W	145	ENSP00000368066:R145W	ENSP00000368066:R145W	R	-	1	2	HAO1	7842923	0.057000	0.20700	0.316000	0.25252	0.058000	0.15608	0.662000	0.25038	0.398000	0.25338	0.655000	0.94253	CGG	.	G|0.999;A|0.001	0.001	weak		0.517	HAO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077926.2			A	7894923	G	A	7894923	3	1	77	1	0	0	0	0	1	0	0	0	6958	1086	38	1	703	1	HAO1	20	7894923	Missense_Mutation	SNP	G	TCGA-AL-A5DJ-01A-11D-A26P-10		7894923	55130597	33	4972											
BIK	638	hgsc.bcm.edu	37	chr22	43523734	43523734	+	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	ccctgcggctggcctgcatcGgggacgagatggacgtgagc	6	6	17	12	4	0	2	0	1	0	1	1	5	0	4	2	5	3	2	2	5	0	0			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chr22:43523734G>T	ENST00000216115.2	+	3	256	c.193G>T	c.(193-195)Ggg>Tgg	p.G65W		NM_001197.4	NP_001188.1	Q13323	BIK_HUMAN	BCL2-interacting killer (apoptosis-inducing)	65					apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|male gonad development (GO:0008584)|positive regulation of protein homooligomerization (GO:0032464)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|mitochondrial envelope (GO:0005740)				breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|urinary_tract(1)	5		Ovarian(80;0.0694)				GGCCTGCATCGGGGACGAGAT	0.677																																					p.G65W		Atlas-SNP	.											.	BIK	11	.	0			c.G193T						PASS	.						24	20	21					22																	43523734		2147	4197	6344	SO:0001583	missense	638	exon3			TGCATCGGGGACG	U34584	CCDS14044.1	22q13.31	2014-03-07			ENSG00000100290	ENSG00000100290			1051	protein-coding gene	gene with protein product		603392				7478623, 10591208	Standard	NM_001197		Approved	NBK	uc003bdk.3	Q13323	OTTHUMG00000150703	ENST00000216115.2:c.193G>T	chr22.hg19:g.43523734G>T	ENSP00000216115:p.Gly65Trp	18.0	0.0	.		44.0	10.0	.	NM_001197	Q16582|Q6FH93	Missense_Mutation	SNP	ENST00000216115.2	hg19	CCDS14044.1	.	.	.	.	.	.	.	.	.	.	G	14.25	2.480785	0.44044	.	.	ENSG00000100290	ENST00000216115	T	0.40476	1.03	3.8	3.8	0.43715	Apoptosis regulator, Bcl-2, BH3 motif, conserved site (1);	0.441185	0.16893	N	0.195260	T	0.50514	0.1620	L	0.29908	0.895	0.37261	D	0.907003	D	0.89917	1.0	D	0.91635	0.999	T	0.57312	-0.7833	10	0.87932	D	0	-25.3198	11.4735	0.50284	0.0:0.0:1.0:0.0	.	65	Q13323	BIK_HUMAN	W	65	ENSP00000216115:G65W	ENSP00000216115:G65W	G	+	1	0	BIK	41853678	0.100000	0.21855	0.806000	0.32338	0.168000	0.22595	2.576000	0.46033	2.410000	0.81850	0.561000	0.74099	GGG	.	.	.	none		0.677	BIK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319676.1	NM_001197		T	43523734	G	T	43523734	3	4	77	1	0	0	0	0	1	0	0	0	1431	1116	39	4	199	4	BIK	22	43523734	Missense_Mutation	SNP	G	TCGA-AL-A5DJ-01A-11D-A26P-10		43523734	7780832	34	4973											
MAGEC1	9947	hgsc.bcm.edu	37	chrX	140996146	140996146	+	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	cattagacctcacctctgagGggtgtctgagtgatgagcag	9	10	13	9	0	3	5	1	4	2	1	3	5	3	5	2	2	1	1	2	2	1	1			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chrX:140996146G>T	ENST00000285879.4	+	4	3242	c.2956G>T	c.(2956-2958)Ggg>Tgg	p.G986W	MAGEC1_ENST00000406005.2_Missense_Mutation_p.G53W	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	986	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									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)					CACCTCTGAGGGGTGTCTGAG	0.478										HNSCC(15;0.026)																											p.G986W		Atlas-SNP	.											.	MAGEC1	317	.	0			c.G2956T						PASS	.						112	105	107					X																	140996146		2203	4300	6503	SO:0001583	missense	9947	exon4			TCTGAGGGGTGTC	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.2956G>T	chrX.hg19:g.140996146G>T	ENSP00000285879:p.Gly986Trp	101.0	0.0	.		146.0	42.0	.	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	hg19	CCDS35417.1	.	.	.	.	.	.	.	.	.	.	g	5.313	0.243052	0.10077	.	.	ENSG00000155495	ENST00000285879;ENST00000406005	T;T	0.05513	3.43;3.43	0.626	0.626	0.17670	.	.	.	.	.	T	0.27489	0.0675	M	0.91972	3.26	0.09310	N	1	D	0.76494	0.999	D	0.78314	0.991	T	0.02950	-1.1090	8	0.87932	D	0	.	.	.	.	.	986	O60732	MAGC1_HUMAN	W	986;53	ENSP00000285879:G986W;ENSP00000385500:G53W	ENSP00000285879:G986W	G	+	1	0	MAGEC1	140823812	0.000000	0.05858	0.005000	0.12908	0.012000	0.07955	0.510000	0.22723	0.564000	0.29238	0.279000	0.19357	GGG	.	.	.	none		0.478	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462		T	140996146	G	T	140996146	3	4	77	1	0	0	0	0	1	0	0	0	9187	1232	43	4	2962	4	MAGEC1	23	140996146	Missense_Mutation	SNP	G	TCGA-AL-A5DJ-01A-11D-A26P-10		140996146	14274414	35	4974											
GABRA3	2556	hgsc.bcm.edu	37	chrX	151532942	151532942	+	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	caaagtccccgggttcttgtCgtcttgattccccttgacca	6	13	8	14	2	2	2	0	2	2	0	5	2	4	2	5	1	0	1	5	1	1	5			TCGA-AL-A5DJ-01A-11D-A26P-10	TCGA-AL-A5DJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4f515ce-5bee-4e40-a66a-01f41e92181e	7c64233c-871d-4df4-8c4d-d60713a4ac1e	g.chrX:151532942C>T	ENST00000370314.4	-	2	339	c.101G>A	c.(100-102)cGa>cAa	p.R34Q	GABRA3_ENST00000535043.1_Missense_Mutation_p.R34Q	NM_000808.3	NP_000799.1	P34903	GBRA3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 3	34					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)	GGGTTCTTGTCGTCTTGATTC	0.443																																					p.R34Q	NSCLC(142;2578 2613 10251 16743)	Atlas-SNP	.											.	GABRA3	97	.	0			c.G101A						PASS	.						177	168	171					X																	151532942		2203	4300	6503	SO:0001583	missense	2556	exon2			TCTTGTCGTCTTG		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.101G>A	chrX.hg19:g.151532942C>T	ENSP00000359337:p.Arg34Gln	91.0	0.0	.		119.0	56.0	.	NM_000808	Q8TAF9	Missense_Mutation	SNP	ENST00000370314.4	hg19	CCDS14706.1	.	.	.	.	.	.	.	.	.	.	C	15.22	2.770224	0.49680	.	.	ENSG00000011677	ENST00000370314;ENST00000370311;ENST00000535043	T;T;T	0.71103	-0.54;-0.54;-0.54	5.01	5.01	0.66863	.	2.366800	0.01730	N	0.028823	T	0.75664	0.3880	N	0.19112	0.55	0.27649	N	0.947442	D	0.58620	0.983	P	0.61201	0.885	T	0.65651	-0.6116	10	0.37606	T	0.19	.	12.6556	0.56786	0.0:1.0:0.0:0.0	.	34	P34903	GBRA3_HUMAN	Q	34	ENSP00000359337:R34Q;ENSP00000359334:R34Q;ENSP00000443527:R34Q	ENSP00000359334:R34Q	R	-	2	0	GABRA3	151283598	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.443000	0.52907	2.039000	0.60335	0.600000	0.82982	CGA	.	.	.	none		0.443	GABRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060921.1	NM_000808		T	151532942	C	T	151532942	3	4	77	1	0	0	0	0	1	0	0	0	6169	884	31	1	1413	1	GABRA3	23	151532942	Missense_Mutation	SNP	C	TCGA-AL-A5DJ-01A-11D-A26P-10	10536796	151532942	3737618	36	4975											
SPATA6	54558	hgsc.bcm.edu	37	chr1	48918785	48918785	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcctctttgtctttaagcaCgactcctgggcaagttacct	7	14	8	12	1	2	0	0	0	2	0	4	1	4	0	3	1	2	3	3	1	3	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr1:48918785C>T	ENST00000371847.3	-	2	234	c.70G>A	c.(70-72)Gtg>Atg	p.V24M	SPATA6_ENST00000463938.1_5'UTR|SPATA6_ENST00000371843.3_Missense_Mutation_p.V24M|SPATA6_ENST00000396199.3_De_novo_Start_InFrame	NM_019073.2	NP_061946.1	Q9NWH7	SPAT6_HUMAN	spermatogenesis associated 6	24					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						TCTTTAAGCACGACTCCTGGG	0.373																																					p.V24M		Atlas-SNP	.											.	SPATA6	45	.	0			c.G70A						PASS	.						124	118	120					1																	48918785		2203	4300	6503	SO:0001583	missense	54558	exon2			TAAGCACGACTCC	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.70G>A	chr1.hg19:g.48918785C>T	ENSP00000360913:p.Val24Met	72.0	0.0	.		71.0	30.0	.	NM_019073	Q5T3N7|Q8WUE6	Missense_Mutation	SNP	ENST00000371847.3	hg19	CCDS551.1	.	.	.	.	.	.	.	.	.	.	C	10.52	1.373114	0.24857	.	.	ENSG00000132122	ENST00000371847;ENST00000371843	T;T	0.12569	2.67;2.67	5.12	1.99	0.26369	.	0.662370	0.14247	N	0.331705	T	0.04815	0.0130	N	0.08118	0	0.80722	D	1	B;B	0.33073	0.396;0.153	B;B	0.24394	0.053;0.053	T	0.41088	-0.9528	10	0.30854	T	0.27	.	3.3052	0.06997	0.1575:0.4045:0.3416:0.0963	.	24;24	Q9NWH7-2;Q9NWH7	.;SPAT6_HUMAN	M	24	ENSP00000360913:V24M;ENSP00000360909:V24M	ENSP00000360909:V24M	V	-	1	0	SPATA6	48691372	0.208000	0.23494	1.000000	0.80357	0.990000	0.78478	-0.170000	0.09897	1.163000	0.42636	0.555000	0.69702	GTG	.	.	.	none		0.373	SPATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021347.1	NM_019073		T	48918785	C	T	48918785	3	4	78	1	0	0	0	0	1	0	0	0	15025	536	19	1	1444	1	SPATA6	1	48918785	Missense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10		48918785	200331836	1	4976											
GTF2B	2959	hgsc.bcm.edu	37	chr1	89352944	89352944	+	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	aaaccataataacaactcacCtacaaccaagccacattcag	19	6	2	14	0	2	0	2	0	0	0	2	0	2	0	4	0	6	0	4	0	7	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr1:89352944C>G	ENST00000370500.5	-	2	242	c.124G>C	c.(124-126)Ggt>Cgt	p.G42R	GTF2B_ENST00000494819.1_5'UTR	NM_001514.5	NP_001505.1	Q00403	TF2B_HUMAN	general transcription factor IIB	42					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)	core promoter binding (GO:0001047)|thyroid hormone receptor binding (GO:0046966)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	10		Lung NSC(277;0.123)		all cancers(265;0.0131)|Epithelial(280;0.0255)		AACAACTCACCTACAACCAAG	0.473																																					p.G42R		Atlas-SNP	.											.	GTF2B	32	.	0			c.G124C						PASS	.						293	301	298					1																	89352944		2203	4300	6503	SO:0001630	splice_region_variant	2959	exon2			ACTCACCTACAAC	M76766	CCDS715.1	1p22-p21	2010-03-23			ENSG00000137947	ENSG00000137947		"General transcription factors"	4648	protein-coding gene	gene with protein product		189963				1876184, 8162052	Standard	NM_001514		Approved	TFIIB	uc001dmo.4	Q00403	OTTHUMG00000010611	ENST00000370500.5:c.124+1G>C	chr1.hg19:g.89352944C>G		85.0	0.0	.		82.0	39.0	.	NM_001514	A8K1A7|Q5JS30	Missense_Mutation	SNP	ENST00000370500.5	hg19	CCDS715.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.002123	0.74932	.	.	ENSG00000137947	ENST00000370500;ENST00000448623	T;T	0.43294	0.95;0.95	5.67	5.67	0.87782	Zinc finger, TFIIB-type (2);	0.000000	0.85682	D	0.000000	T	0.37156	0.0993	M	0.77103	2.36	0.80722	D	1	B	0.13145	0.007	B	0.23574	0.047	T	0.24977	-1.0145	9	.	.	.	-12.0703	19.7698	0.96359	0.0:1.0:0.0:0.0	.	42	Q00403	TF2B_HUMAN	R	42;41	ENSP00000359531:G42R;ENSP00000415741:G41R	.	G	-	1	0	GTF2B	89125532	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.125000	0.77193	2.659000	0.90383	0.655000	0.94253	GGT	.	.	.	none		0.473	GTF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029279.1	NM_001514	Missense_Mutation	G	89352944	C	G	89352944	5	3	78	1	0	0	0	0	0	0	1	0	6862	695	24	4	850	4	GTF2B	1	89352944	Splice_Site	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	40434159	89352944	159897677	2	4977											
C1orf146	388649	hgsc.bcm.edu	37	chr1	92707844	92707844	+	Missense_Mutation	SNP	A	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	attcagtggaaaatggatcaAttatattttctctttctggt	11	18	7	5	0	4	0	2	0	2	0	5	2	4	2	0	3	0	0	0	3	5	6			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr1:92707844A>C	ENST00000370375.3	+	3	290	c.142A>C	c.(142-144)Att>Ctt	p.I48L	C1orf146_ENST00000370373.2_5'UTR	NM_001012425.1	NP_001012425.1	Q5VVC0	CA146_HUMAN	chromosome 1 open reading frame 146	48										breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	8		all_lung(203;0.00528)|Lung NSC(277;0.0193)		all cancers(265;0.00846)|Epithelial(280;0.0952)		AAATGGATCAATTATATTTTC	0.308																																					p.I48L		Atlas-SNP	.											.	C1orf146	21	.	0			c.A142C						PASS	.						111	112	112					1																	92707844		2203	4298	6501	SO:0001583	missense	388649	exon3			GGATCAATTATAT		CCDS30772.1	1p22.1	2008-02-05			ENSG00000203910	ENSG00000203910			24032	protein-coding gene	gene with protein product						15496913	Standard	NM_001012425		Approved		uc001doq.3	Q5VVC0	OTTHUMG00000010285	ENST00000370375.3:c.142A>C	chr1.hg19:g.92707844A>C	ENSP00000359401:p.Ile48Leu	13.0	0.0	.		20.0	10.0	.	NM_001012425	Q5VVC4	Missense_Mutation	SNP	ENST00000370375.3	hg19	CCDS30772.1	.	.	.	.	.	.	.	.	.	.	A	14.39	2.520239	0.44866	.	.	ENSG00000203910	ENST00000370375;ENST00000370373	.	.	.	5.15	2.85	0.33270	.	0.254660	0.34067	N	0.004296	T	0.11750	0.0286	N	0.24115	0.695	0.28249	N	0.92534	B	0.32507	0.373	B	0.30572	0.117	T	0.07986	-1.0744	9	0.59425	D	0.04	0.0214	8.2971	0.31993	0.7519:0.0:0.2481:0.0	.	48	Q5VVC0	CA146_HUMAN	L	48;27	.	ENSP00000359399:I27L	I	+	1	0	C1orf146	92480432	0.955000	0.32602	0.999000	0.59377	0.994000	0.84299	1.221000	0.32503	0.445000	0.26639	0.533000	0.62120	ATT	.	.	.	none		0.308	C1orf146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028364.1	NM_001012425		C	92707844	A	C	92707844	3	2	78	1	0	0	0	0	1	0	0	0	2005	101	4	5	148	5	C1orf146	1	92707844	Missense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10	3354900	92707844	156542777	3	4978											
ZNF697	90874	hgsc.bcm.edu	37	chr1	120165395	120165395	+	Missense_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	ggaagcctttgccgcagcccGcacacttgtgcggcttgttg	5	10	13	13	3	0	0	0	0	0	0	0	1	0	1	3	2	4	4	3	2	1	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr1:120165395G>A	ENST00000421812.2	-	3	1690	c.1571C>T	c.(1570-1572)gCg>gTg	p.A524V		NM_001080470.1	NP_001073939.1	Q5TEC3	ZN697_HUMAN	zinc finger protein 697	524					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)		GCCGCAGCCCGCACACTTGTG	0.637																																					p.A524V		Atlas-SNP	.											.	ZNF697	26	.	0			c.C1571T						PASS	.						13	17	16					1																	120165395		2127	4266	6393	SO:0001583	missense	90874	exon3			CAGCCCGCACACT	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.1571C>T	chr1.hg19:g.120165395G>A	ENSP00000396857:p.Ala524Val	53.0	0.0	.		86.0	36.0	.	NM_001080470	Q96IT2	Missense_Mutation	SNP	ENST00000421812.2	hg19	CCDS44202.1	.	.	.	.	.	.	.	.	.	.	G	2.237	-0.374694	0.05034	.	.	ENSG00000143067	ENST00000421812	T	0.17691	2.26	4.99	4.07	0.47477	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.216152	0.23519	N	0.047302	T	0.03915	0.0110	N	0.20574	0.59	0.09310	N	1	B	0.23128	0.08	B	0.25291	0.059	T	0.32188	-0.9916	10	0.37606	T	0.19	-8.4913	8.9809	0.35964	0.0:0.1625:0.6694:0.1681	.	524	Q5TEC3	ZN697_HUMAN	V	524	ENSP00000396857:A524V	ENSP00000396857:A524V	A	-	2	0	ZNF697	119966918	0.000000	0.05858	0.026000	0.17262	0.005000	0.04900	0.294000	0.19047	1.414000	0.47017	-0.175000	0.13238	GCG	.	.	.	none		0.637	ZNF697-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036349.3	XM_371286		A	120165395	G	A	120165395	3	1	78	1	0	0	0	0	1	0	0	0	18112	1087	38	1	70	1	ZNF697	1	120165395	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	27457551	120165395	129085226	4	4979											
CREG1	8804	hgsc.bcm.edu	37	chr1	167515417	167515417	+	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	caggacccagatattggttaTattcaacttagcaaagaacc	15	10	7	9	0	1	2	1	0	0	2	1	3	1	3	2	2	3	2	2	2	7	6			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr1:167515417T>A	ENST00000370509.4	-	3	605	c.580A>T	c.(580-582)Ata>Tta	p.I194L	CREG1_ENST00000466652.1_5'UTR	NM_003851.2	NP_003842.1	O75629	CREG1_HUMAN	cellular repressor of E1A-stimulated genes 1	194					cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	extracellular vesicular exosome (GO:0070062)|transcription factor complex (GO:0005667)	FMN binding (GO:0010181)|oxidoreductase activity (GO:0016491)|transcription corepressor activity (GO:0003714)										ATATTGGTTATATTCAACTTA	0.383																																					p.I194L		Atlas-SNP	.											.	CREG1	6	.	0			c.A580T						PASS	.						73	75	74					1																	167515417		2203	4300	6503	SO:0001583	missense	8804	exon3			TGGTTATATTCAA	AF084523	CCDS1262.1	1q24	2008-02-05	2004-09-22	2004-09-22	ENSG00000143162	ENSG00000143162			2351	protein-coding gene	gene with protein product			"cellular repressor of E1A-stimulated genes"	CREG		9710587	Standard	NM_003851		Approved		uc001gel.3	O75629	OTTHUMG00000034682	ENST00000370509.4:c.580A>T	chr1.hg19:g.167515417T>A	ENSP00000359540:p.Ile194Leu	128.0	0.0	.		105.0	46.0	.	NM_003851	B2RDD4|Q8N9A3	Missense_Mutation	SNP	ENST00000370509.4	hg19	CCDS1262.1	.	.	.	.	.	.	.	.	.	.	T	33	5.194241	0.94960	.	.	ENSG00000143162	ENST00000370509	.	.	.	5.86	5.86	0.93980	FMN-binding split barrel-related (1);FMN-binding split barrel (1);	0.000000	0.85682	D	0.000000	T	0.76111	0.3942	M	0.82923	2.615	0.51012	D	0.999905	D	0.58620	0.983	D	0.68192	0.956	T	0.79102	-0.1941	8	0.52906	T	0.07	0.6411	16.2453	0.82441	0.0:0.0:0.0:1.0	.	194	O75629	CREG1_HUMAN	L	194	.	ENSP00000359540:I194L	I	-	1	0	CREG1	165782041	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	7.549000	0.82163	2.241000	0.73720	0.533000	0.62120	ATA	.	.	.	none		0.383	CREG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083911.1	NM_003851		A	167515417	T	A	167515417	3	1	78	1	0	0	0	0	1	0	0	0	3866	1406	49	5	90	5	CREG1	1	167515417	Missense_Mutation	SNP	T	TCGA-AT-A5NU-01A-11D-A28G-10	47350022	167515417	81735204	5	4980											
MOSC1	64757	hgsc.bcm.edu	37	chr1	220960439	220960439	+	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	cccacgcggcgccggcggctGctgcagcaggtgggcacagt	5	4	17	15	5	0	0	0	0	0	0	0	0	0	0	2	5	3	5	2	5	0	0	rs367900610		TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr1:220960439G>T	ENST00000366910.5	+	1	339	c.153G>T	c.(151-153)ctG>ctT	p.L51L		NM_022746.3	NP_073583.3	Q5VT66	MARC1_HUMAN	mitochondrial amidoxime reducing component 1	51					detoxification of nitrogen compound (GO:0051410)|nitrate metabolic process (GO:0042126)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	molybdenum ion binding (GO:0030151)|molybdopterin cofactor binding (GO:0043546)|nitrate reductase activity (GO:0008940)|pyridoxal phosphate binding (GO:0030170)										GCCGGCGGCTGCTGCAGCAGG	0.756																																					p.L51L		Atlas-SNP	.											.	.	.	.	0			c.G153T						PASS	.	G		0,3888		0,0,1944	5	6	6		153	0.2	0.9	1		6	2,7704		0,2,3851	no	coding-synonymous	MOSC1	NM_022746.3		0,2,5795	TT,TG,GG		0.026,0.0,0.0173		51/338	220960439	2,11592	1944	3853	5797	SO:0001819	synonymous_variant	64757	exon1			GCGGCTGCTGCAG	AK026043	CCDS1526.1	1q41	2011-11-02	2011-11-02	2011-11-02	ENSG00000186205	ENSG00000186205			26189	protein-coding gene	gene with protein product		614126	"MOCO sulphurase C-terminal domain containing 1"	MOSC1		11886751	Standard	NM_022746		Approved	FLJ22390	uc001hms.3	Q5VT66	OTTHUMG00000037353	ENST00000366910.5:c.153G>T	chr1.hg19:g.220960439G>T		3.0	0.0	.		25.0	10.0	.	NM_022746	A8K447|B2D078|Q5VVS9|Q5VVT0|Q5VVT1|Q8N9P5|Q96FN8|Q9H6C7	Silent	SNP	ENST00000366910.5	hg19	CCDS1526.1																																																																																			.	.	.	none		0.756	MARC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090904.1	NM_022746		T	220960439	G	T	220960439	2	4	78	1	0	0	0	0	0	0	0	1	9720	1306	46	4		4	MOSC1	1	220960439	Silent	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	53445022	220960439	28290182	6	4981											
CEBPZ	10153	hgsc.bcm.edu	37	chr2	37455042	37455042	+	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	ttgagctttggagctgatatTtgagcggaagagtagccttt	9	14	13	5	1	0	4	0	3	0	1	0	6	0	6	1	2	4	3	1	2	3	6			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr2:37455042T>A	ENST00000234170.5	-	2	1439	c.1294A>T	c.(1294-1296)Aat>Tat	p.N432Y		NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	432					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)				GAGCTGATATTTGAGCGGAAG	0.363																																					p.N432Y		Atlas-SNP	.											.	CEBPZ	68	.	0			c.A1294T						PASS	.						102	104	103					2																	37455042		2203	4300	6503	SO:0001583	missense	10153	exon2			TGATATTTGAGCG	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.1294A>T	chr2.hg19:g.37455042T>A	ENSP00000234170:p.Asn432Tyr	74.0	0.0	.		113.0	37.0	.	NM_005760	Q8NE75	Missense_Mutation	SNP	ENST00000234170.5	hg19	CCDS1787.1	.	.	.	.	.	.	.	.	.	.	T	19.75	3.885601	0.72410	.	.	ENSG00000115816	ENST00000234170;ENST00000545744	T	0.13420	2.59	5.31	5.31	0.75309	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.46814	0.1412	M	0.91300	3.195	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.59289	-0.7482	10	0.87932	D	0	.	15.3016	0.73955	0.0:0.0:0.0:1.0	.	432	Q03701	CEBPZ_HUMAN	Y	432	ENSP00000234170:N432Y	ENSP00000234170:N432Y	N	-	1	0	CEBPZ	37308546	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.525000	0.81892	2.017000	0.59298	0.528000	0.53228	AAT	.	.	.	none		0.363	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760		A	37455042	T	A	37455042	3	1	78	1	0	0	0	0	1	0	0	0	3206	1841	64	5	1930	5	CEBPZ	2	37455042	Missense_Mutation	SNP	T	TCGA-AT-A5NU-01A-11D-A28G-10		37455042	205744331	7	4982											
C2orf34	79823	hgsc.bcm.edu	37	chr2	44589184	44589184	+	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	ggacgctgggaccggcgagaCcgcgcgagcagcgggcggga	7	1	21	12	8	0	1	0	0	0	1	0	6	0	4	2	5	2	2	2	5	0	0			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr2:44589184C>T	ENST00000378494.3	+	1	82	c.38C>T	c.(37-39)aCc>aTc	p.T13I	PREPL_ENST00000409936.1_5'Flank|PREPL_ENST00000378511.3_5'Flank|PREPL_ENST00000540817.1_5'Flank|PREPL_ENST00000409411.1_5'Flank|PREPL_ENST00000410081.1_5'Flank|CAMKMT_ENST00000402247.1_Missense_Mutation_p.T13I|PREPL_ENST00000409957.1_5'Flank|CAMKMT_ENST00000403853.3_Missense_Mutation_p.T13I|PREPL_ENST00000260648.6_5'Flank|PREPL_ENST00000409272.1_5'Flank|CAMKMT_ENST00000407131.1_Missense_Mutation_p.T13I|PREPL_ENST00000541738.1_5'Flank|PREPL_ENST00000378520.3_5'Flank	NM_024766.4	NP_079042.1	Q7Z624	CMKMT_HUMAN	calmodulin-lysine N-methyltransferase	13						Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	calmodulin-lysine N-methyltransferase activity (GO:0018025)			breast(2)|large_intestine(3)|lung(5)	10						ACCGGCGAGACCGCGCGAGCA	0.741																																					p.T13I		Atlas-SNP	.											.	CAMKMT	20	.	0			c.C38T						PASS	.						4	7	6					2																	44589184		2073	4050	6123	SO:0001583	missense	79823	exon1			GCGAGACCGCGCG		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.38C>T	chr2.hg19:g.44589184C>T	ENSP00000367755:p.Thr13Ile	2.0	0.0	.		62.0	31.0	.	NM_024766	Q4ZG15|Q53SS6|Q8N6P5|Q9H5G8	Missense_Mutation	SNP	ENST00000378494.3	hg19	CCDS1820.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.846091	0.51164	.	.	ENSG00000143919	ENST00000402247;ENST00000454848;ENST00000407131;ENST00000378494;ENST00000403853	.	.	.	4.91	4.91	0.64330	.	0.320112	0.26262	N	0.025387	T	0.41419	0.1158	L	0.40543	1.245	0.09310	N	0.999994	B;P	0.47762	0.079;0.9	B;P	0.47645	0.051;0.553	T	0.30765	-0.9967	9	0.39692	T	0.17	-0.7064	13.4872	0.61373	0.0:1.0:0.0:0.0	.	13;13	Q7Z624;Q7Z624-2	CMKMT_HUMAN;.	I	13	.	ENSP00000367755:T13I	T	+	2	0	CAMKMT	44442688	0.000000	0.05858	0.278000	0.24718	0.011000	0.07611	0.616000	0.24344	2.549000	0.85964	0.655000	0.94253	ACC	.	.	.	none		0.741	CAMKMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250678.2	NM_024766		T	44589184	C	T	44589184	3	4	78	1	0	0	0	0	1	0	0	0	2165	507	18	2	40	2	C2orf34	2	44589184	Missense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	7134142	44589184	198610189	8	4983											
GCC2	9648	hgsc.bcm.edu	37	chr2	109087879	109087879	+	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	gaggaaaacaataaactcagTtcagaaaaaaaacagttgag	22	6	8	5	0	2	2	2	1	0	1	2	4	2	3	0	1	3	2	0	1	9	3			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr2:109087879T>A	ENST00000309863.6	+	6	2808	c.2094T>A	c.(2092-2094)agT>agA	p.S698R		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	698					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						ATAAACTCAGTTCAGAAAAAA	0.308																																					p.S698R		Atlas-SNP	.											.	GCC2	129	.	0			c.T2094A						PASS	.						114	143	133					2																	109087879		2203	4299	6502	SO:0001583	missense	9648	exon6			ACTCAGTTCAGAA	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.2094T>A	chr2.hg19:g.109087879T>A	ENSP00000307939:p.Ser698Arg	95.0	0.0	.		172.0	39.0	.	NM_181453	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Missense_Mutation	SNP	ENST00000309863.6	hg19	CCDS33268.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	3.987|3.987	-0.005307|-0.005307	0.07773|0.07773	.|.	.|.	ENSG00000135968|ENSG00000135968	ENST00000309863;ENST00000409896|ENST00000393318	T|.	0.32023|.	1.47|.	5.5|5.5	4.27|4.27	0.50696|0.50696	.|.	0.676432|.	0.15756|.	N|.	0.246200|.	T|T	0.34019|0.34019	0.0883|0.0883	L|L	0.41236|0.41236	1.265|1.265	0.24442|0.24442	N|N	0.994523|0.994523	B|.	0.27625|.	0.183|.	B|.	0.22386|.	0.039|.	T|T	0.18840|0.18840	-1.0324|-1.0324	10|6	0.19590|0.12103	T|T	0.45|0.63	.|.	8.3633|8.3633	0.32372|0.32372	0.1299:0.0:0.1353:0.7349|0.1299:0.0:0.1353:0.7349	.|.	698|.	Q8IWJ2|.	GCC2_HUMAN|.	R|D	698;661|443	ENSP00000307939:S698R|.	ENSP00000307939:S698R|ENSP00000376993:V443D	S|V	+|+	3|2	2|0	GCC2|GCC2	108454311|108454311	0.010000|0.010000	0.17322|0.17322	0.942000|0.942000	0.38095|0.38095	0.386000|0.386000	0.30323|0.30323	0.472000|0.472000	0.22116|0.22116	2.213000|2.213000	0.71641|0.71641	0.528000|0.528000	0.53228|0.53228	AGT|GTT	.	.	.	none		0.308	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635		A	109087879	T	A	109087879	3	1	78	1	0	0	0	0	1	0	0	0	6293	1722	60	5	2116	5	GCC2	2	109087879	Missense_Mutation	SNP	T	TCGA-AT-A5NU-01A-11D-A28G-10	64498695	109087879	134111494	9	4984											
ORC4L	5000	hgsc.bcm.edu	37	chr2	148695764	148695764	+	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	aaacggaatgtgctttccttTgaacaaacttctgaaactct	13	13	6	9	1	2	2	0	2	2	0	3	3	3	3	1	1	5	1	1	1	5	3			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr2:148695764T>A	ENST00000392857.5	-	13	1180	c.1073A>T	c.(1072-1074)cAa>cTa	p.Q358L	ORC4_ENST00000264169.2_Missense_Mutation_p.Q358L|ORC4_ENST00000536575.1_Missense_Mutation_p.Q274L|ORC4_ENST00000392858.1_Missense_Mutation_p.Q358L|ORC4_ENST00000540442.1_Missense_Mutation_p.Q284L|AC009480.1_ENST00000584553.1_RNA|ORC4_ENST00000535373.1_Missense_Mutation_p.Q358L|ORC4_ENST00000488761.1_5'Flank|ORC4_ENST00000542387.1_Missense_Mutation_p.Q141L	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	358					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						TGCTTTCCTTTGAACAAACTT	0.328																																					p.Q358L		Atlas-SNP	.											.	ORC4	40	.	0			c.A1073T						PASS	.						50	52	51					2																	148695764		2201	4299	6500	SO:0001583	missense	5000	exon13			TTCCTTTGAACAA	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.1073A>T	chr2.hg19:g.148695764T>A	ENSP00000376597:p.Gln358Leu	141.0	0.0	.		156.0	8.0	.	NM_002552	B7Z3D0|B7Z5F1|D3DP86|F5H069|Q96C42	Missense_Mutation	SNP	ENST00000392857.5	hg19	CCDS2187.1	.	.	.	.	.	.	.	.	.	.	T	16.58	3.162605	0.57368	.	.	ENSG00000115947	ENST00000264169;ENST00000535373;ENST00000392858;ENST00000540442;ENST00000536575;ENST00000392857;ENST00000542387	T;T;T;T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07;-1.07;-1.07;-1.07	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.76478	0.3993	M	0.66939	2.045	0.80722	D	1	B	0.32573	0.376	B	0.30943	0.122	T	0.75445	-0.3315	10	0.41790	T	0.15	-17.6101	16.4116	0.83717	0.0:0.0:0.0:1.0	.	358	O43929	ORC4_HUMAN	L	358;358;358;284;274;358;141	ENSP00000264169:Q358L;ENSP00000441953:Q358L;ENSP00000376598:Q358L;ENSP00000438326:Q284L;ENSP00000441502:Q274L;ENSP00000376597:Q358L;ENSP00000437440:Q141L	ENSP00000264169:Q358L	Q	-	2	0	ORC4	148412234	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.684000	0.84104	2.276000	0.75962	0.528000	0.53228	CAA	.	.	.	none		0.328	ORC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254797.3	NM_181742		A	148695764	T	A	148695764	3	1	78	1	0	0	0	0	1	0	0	0	11271	1812	63	5	245	5	ORC4L	2	148695764	Missense_Mutation	SNP	T	TCGA-AT-A5NU-01A-11D-A28G-10	39607885	148695764	94503609	10	4985											
NEB	4703	hgsc.bcm.edu	37	chr2	152579988	152579989	+	Frame_Shift_Ins	INS	-	-	A																															ttgtctgcttcccagtcttcINSagtgtacagtttctaaatca																										TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr2:152579988_152579989insA	ENST00000172853.10	-	9	771_772	c.624_625insT	c.(622-627)actgaafs	p.E209fs	NEB_ENST00000427231.2_Frame_Shift_Ins_p.E209fs|NEB_ENST00000603639.1_Frame_Shift_Ins_p.E209fs|NEB_ENST00000409198.1_Frame_Shift_Ins_p.E209fs|NEB_ENST00000397345.3_Frame_Shift_Ins_p.E209fs|NEB_ENST00000604864.1_Frame_Shift_Ins_p.E209fs			P20929	NEBU_HUMAN	nebulin	209					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.E209*(1)		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)		TCCCAGTCTTCAGTGTACAGTT	0.391																																					p.E209_D210delinsX		Atlas-Indel,Pindel	.											NEB,NS,neuroblastoma,0,1	NEB	1697	.	1	Substitution - Nonsense(1)	autonomic_ganglia(1)	c.625_626insT						PASS	.																																			SO:0001589	frameshift_variant	4703	exon9			.	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.625dupT	chr2.hg19:g.152579989_152579989dupA	ENSP00000172853:p.Glu209fs	72.0	0.0	0		120.0	67.0	0.558333	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Frame_Shift_Ins	INS	ENST00000172853.10	hg19																																																																																				.	.	.	none		0.391	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152579989	-	A	152579988	7	5	78	1	0	1	1	0	0	0	0	0	10309	835	29	0	25757	0	NEB	2	152579988	Frame_Shift_Ins	INS	-	TCGA-AT-A5NU-01A-11D-A28G-10	3884224	152579988	90619385	11	4986											
PKP4	8502	hgsc.bcm.edu	37	chr2	159459582	159459582	+	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	ttttctttctttttctttagCtcaactgagaagtcatttcc	7	21	4	9	0	5	1	2	1	3	1	6	2	6	1	1	0	2	1	1	0	3	8			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr2:159459582C>A	ENST00000389759.3	+	4	358	c.246C>A	c.(244-246)agC>agA	p.S82R	PKP4_ENST00000389757.3_Splice_Site_p.S82R	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	82					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						TTTTCTTTAGCTCAACTGAGA	0.259										HNSCC(62;0.18)																											p.S82R		Atlas-SNP	.											.	PKP4	133	.	0			c.C246A						PASS	.						39	47	45					2																	159459582		2180	4267	6447	SO:0001630	splice_region_variant	8502	exon4			CTTTAGCTCAACT	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.246-1C>A	chr2.hg19:g.159459582C>A		117.0	0.0	.		104.0	23.0	.	NM_001005476	Q86W91	Missense_Mutation	SNP	ENST00000389759.3	hg19	CCDS33305.1	.	.	.	.	.	.	.	.	.	.	C	15.17	2.754453	0.49362	.	.	ENSG00000144283	ENST00000389757;ENST00000389759	T;T	0.79653	-1.28;-1.29	5.48	5.48	0.80851	.	0.095284	0.64402	D	0.000001	T	0.75258	0.3825	L	0.59436	1.845	0.80722	D	1	B;P	0.42456	0.339;0.78	B;B	0.34779	0.189;0.18	T	0.76046	-0.3102	9	.	.	.	.	15.2074	0.73190	0.0:1.0:0.0:0.0	.	82;82	Q99569-2;Q99569	.;PKP4_HUMAN	R	82	ENSP00000374407:S82R;ENSP00000374409:S82R	.	S	+	3	2	PKP4	159167828	1.000000	0.71417	1.000000	0.80357	0.731000	0.41821	2.706000	0.47135	2.745000	0.94114	0.484000	0.47621	AGC	.	.	.	none		0.259	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1		Missense_Mutation	A	159459582	C	A	159459582	5	1	78	1	0	0	0	0	0	0	1	0	11994	811	28	4	256	4	PKP4	2	159459582	Splice_Site	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	6879594	159459582	83739791	12	4987											
GPR155	151556	hgsc.bcm.edu	37	chr2	175331330	175331330	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgtttatatttcttactcAaaagaagaatagccagagac	15	12	7	7	0	2	3	1	0	1	3	2	4	2	3	1	0	2	2	1	0	8	6			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr2:175331330A>G	ENST00000392552.2	-	6	1446	c.1208T>C	c.(1207-1209)tTg>tCg	p.L403S	GPR155_ENST00000295500.4_Missense_Mutation_p.L403S|GPR155_ENST00000392551.2_Missense_Mutation_p.L403S	NM_001267051.1|NM_152529.6	NP_001253980.1|NP_689742.4	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155	403					cognition (GO:0050890)|intracellular signal transduction (GO:0035556)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	26						TTTCTTACTCAAAAGAAGAAT	0.274																																					p.L403S		Atlas-SNP	.											.	GPR155	76	.	0			c.T1208C						PASS	.						78	87	84					2																	175331330		2202	4287	6489	SO:0001583	missense	151556	exon7			TTACTCAAAAGAA	AY255528	CCDS2259.1, CCDS74605.1	2q31.1	2012-04-10			ENSG00000163328	ENSG00000163328			22951	protein-coding gene	gene with protein product						12679517	Standard	NM_001033045		Approved	DEPDC3, DEP.7, FLJ31819, PGR22	uc002uiu.4	Q7Z3F1	OTTHUMG00000132336	ENST00000392552.2:c.1208T>C	chr2.hg19:g.175331330A>G	ENSP00000376335:p.Leu403Ser	106.0	0.0	.		150.0	47.0	.	NM_001033045	B2RCI2|D3DPE2|Q4G0Y6|Q53SJ3|Q53TA8|Q69YG8|Q86SP9|Q8N261|Q8N639|Q8N8K3|Q96MV6	Missense_Mutation	SNP	ENST00000392552.2	hg19	CCDS2259.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.485820	0.84854	.	.	ENSG00000163328	ENST00000392552;ENST00000392551;ENST00000295500	T;T;T	0.52983	0.64;0.64;0.64	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.67496	0.2899	M	0.71581	2.175	0.58432	D	0.999998	D	0.89917	1.0	D	0.78314	0.991	T	0.66881	-0.5811	10	0.38643	T	0.18	-8.6419	16.0125	0.80411	1.0:0.0:0.0:0.0	.	403	Q7Z3F1	GP155_HUMAN	S	403	ENSP00000376335:L403S;ENSP00000376334:L403S;ENSP00000295500:L403S	ENSP00000295500:L403S	L	-	2	0	GPR155	175039576	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.737000	0.91562	2.178000	0.69098	0.528000	0.53228	TTG	.	.	.	none		0.274	GPR155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255455.1	NM_152529		G	175331330	A	G	175331330	3	3	78	1	0	0	0	0	1	0	0	0	6667	131	5	3	1448	3	GPR155	2	175331330	Missense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10	15871748	175331330	67868043	13	4988											
NBEAL1	65065	hgsc.bcm.edu	37	chr2	203972839	203972839	+	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	tgccttttctttcagtgcttGgttttgcttagaccaggatc	5	18	9	9	0	2	1	1	0	1	1	3	2	2	2	2	2	3	3	2	2	1	7			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr2:203972839G>A	ENST00000449802.1	+	13	2123	c.1790G>A	c.(1789-1791)tGg>tAg	p.W597*		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	597										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						TTCAGTGCTTGGTTTTGCTTA	0.408																																					p.W597X		Atlas-SNP	.											.	NBEAL1	266	.	0			c.G1790A						PASS	.						60	50	53					2																	203972839		692	1591	2283	SO:0001587	stop_gained	65065	exon13			GTGCTTGGTTTTG	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.1790G>A	chr2.hg19:g.203972839G>A	ENSP00000399903:p.Trp597*	117.0	0.0	.		121.0	71.0	.	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Nonsense_Mutation	SNP	ENST00000449802.1	hg19	CCDS46495.1	.	.	.	.	.	.	.	.	.	.	G	41	8.993174	0.99029	.	.	ENSG00000144426	ENST00000449802;ENST00000340268	.	.	.	5.38	5.38	0.77491	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.1076	0.93303	0.0:0.0:1.0:0.0	.	.	.	.	X	597	.	ENSP00000344985:W597X	W	+	2	0	NBEAL1	203681084	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.476000	0.97823	2.500000	0.84329	0.557000	0.71058	TGG	.	.	.	none		0.408	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4			A	203972839	G	A	203972839	4	1	78	1	0	0	0	0	0	1	0	0	10195	1357	47	2	1836	2	NBEAL1	2	203972839	Nonsense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	28641509	203972839	39226534	14	4989											
C2orf62	375307	hgsc.bcm.edu	37	chr2	219222408	219222408	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tactgcctcttcgtgcatgcCtctagccgaggcttcttgga	5	13	10	13	2	3	0	0	0	3	0	4	2	3	1	3	2	5	2	3	2	2	5			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr2:219222408C>T	ENST00000289388.3	+	3	299	c.270C>T	c.(268-270)gcC>gcT	p.A90A	AC021016.8_ENST00000411433.1_RNA	NM_198559.1	NP_940961.1	Q7Z7H3	CATIP_HUMAN		90					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Renal(207;0.0915)		Epithelial(149;8.08e-07)|all cancers(144;0.000146)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCGTGCATGCCTCTAGCCGAG	0.567																																					p.A90A		Atlas-SNP	.											.	C2orf62	28	.	0			c.C270T						PASS	.						75	72	73					2																	219222408		2203	4300	6503	SO:0001819	synonymous_variant	375307	exon3			GCATGCCTCTAGC																												ENST00000289388.3:c.270C>T	chr2.hg19:g.219222408C>T		60.0	0.0	.		73.0	37.0	.	NM_198559		Silent	SNP	ENST00000289388.3	hg19	CCDS2414.1																																																																																			.	.	.	none		0.567	C2orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256771.1			T	219222408	C	T	219222408	2	4	78	1	0	0	0	0	0	0	0	1	2183	668	24	2		2	C2orf62	2	219222408	Silent	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	15249569	219222408	23976965	15	4990											
LAMB2	3913	hgsc.bcm.edu	37	chr3	49161312	49161312	+	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	acccgtctgttgcaactcctGcgcccgctgctctaggcgct	4	10	10	17	4	2	0	0	0	2	0	3	0	3	0	3	1	4	5	3	1	2	2			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr3:49161312G>C	ENST00000418109.1	-	25	3810	c.3646C>G	c.(3646-3648)Cag>Gag	p.Q1216E	USP19_ENST00000453664.1_5'Flank|USP19_ENST00000398888.2_5'Flank|LAMB2_ENST00000464891.1_5'Flank|USP19_ENST00000488993.1_5'Flank|USP19_ENST00000398892.3_5'Flank|LAMB2_ENST00000305544.4_Missense_Mutation_p.Q1216E	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	1216	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)		TGCAACTCCTGCGCCCGCTGC	0.612																																					p.Q1216E		Atlas-SNP	.											.	LAMB2	156	.	0			c.C3646G						PASS	.						42	43	42					3																	49161312		2203	4300	6503	SO:0001583	missense	3913	exon24			ACTCCTGCGCCCG		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.3646C>G	chr3.hg19:g.49161312G>C	ENSP00000388325:p.Gln1216Glu	72.0	0.0	.		84.0	57.0	.	NM_002292	Q16321	Missense_Mutation	SNP	ENST00000418109.1	hg19	CCDS2789.1	.	.	.	.	.	.	.	.	.	.	G	0.910	-0.719263	0.03182	.	.	ENSG00000172037	ENST00000418109;ENST00000305544	T;T	0.34072	1.38;1.38	5.84	2.97	0.34412	.	0.513188	0.21549	N	0.072764	T	0.27933	0.0688	L	0.44542	1.39	0.21675	N	0.999593	B	0.17465	0.022	B	0.14023	0.01	T	0.26087	-1.0113	10	0.07175	T	0.84	.	14.3514	0.66705	0.0:0.0:0.4875:0.5125	.	1216	P55268	LAMB2_HUMAN	E	1216	ENSP00000388325:Q1216E;ENSP00000307156:Q1216E	ENSP00000307156:Q1216E	Q	-	1	0	LAMB2	49136316	0.007000	0.16637	0.323000	0.25347	0.532000	0.34746	0.332000	0.19751	0.326000	0.23384	0.561000	0.74099	CAG	.	.	.	none		0.612	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		C	49161312	G	C	49161312	3	2	78	1	0	0	0	0	1	0	0	0	8618	1328	46	4	1786	4	LAMB2	3	49161312	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10		49161312	148861118	16	4991											
ANAPC10	10393	hgsc.bcm.edu	37	chr4	145916549	145916549	+	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	cttattgaacgatacatcatGaaatctatagttgtacatct	14	15	5	7	1	3	2	1	2	2	0	3	3	3	2	0	0	3	2	0	0	7	7			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr4:145916549G>T	ENST00000507656.1	-	5	627	c.534C>A	c.(532-534)ttC>ttA	p.F178L	ANAPC10_ENST00000451299.2_Missense_Mutation_p.F178L|ANAPC10_ENST00000309439.5_Missense_Mutation_p.F178L|ANAPC10_ENST00000510270.1_5'UTR	NM_001256706.1	NP_001243635.1	Q9UM13	APC10_HUMAN	anaphase promoting complex subunit 10	178	DOC. {ECO:0000255|PROSITE- ProRule:PRU00614}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				endometrium(1)|large_intestine(3)|lung(1)|skin(1)	6	all_hematologic(180;0.151)					GATACATCATGAAATCTATAG	0.303																																					p.F189L		Atlas-SNP	.											.	ANAPC10	12	.	0			c.C567A						PASS	.						119	115	116					4																	145916549		1815	4079	5894	SO:0001583	missense	10393	exon7			CATCATGAAATCT	AF132794	CCDS43273.1	4q31	2011-06-15			ENSG00000164162	ENSG00000164162		"Anaphase promoting complex subunits"	24077	protein-coding gene	gene with protein product		613745				10318877, 11230166	Standard	NM_001256706		Approved	APC10, DOC1, DKFZP564L0562	uc031shk.1	Q9UM13	OTTHUMG00000161477	ENST00000507656.1:c.534C>A	chr4.hg19:g.145916549G>T	ENSP00000423995:p.Phe178Leu	48.0	0.0	.		51.0	27.0	.	NM_001256709	D3DNZ7|Q2V500|Q9UG51|Q9Y5R0	Missense_Mutation	SNP	ENST00000507656.1	hg19	CCDS43273.1	.	.	.	.	.	.	.	.	.	.	G	14.68	2.607532	0.46527	.	.	ENSG00000164162	ENST00000507656;ENST00000309439;ENST00000451299	T;T;T	0.72615	-0.67;-0.67;-0.67	5.82	3.2	0.36748	Anaphase-promoting complex, subunit 10/DOC domain (2);	0.000000	0.85682	D	0.000000	T	0.62502	0.2433	L	0.57536	1.79	0.80722	D	1	B	0.09022	0.002	B	0.20384	0.029	T	0.51687	-0.8674	10	0.19147	T	0.46	-9.7039	8.8754	0.35343	0.2784:0.0:0.7216:0.0	.	178	Q9UM13	APC10_HUMAN	L	178	ENSP00000423995:F178L;ENSP00000310071:F178L;ENSP00000403891:F178L	ENSP00000310071:F178L	F	-	3	2	ANAPC10	146135999	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.820000	0.48057	0.400000	0.25396	0.484000	0.47621	TTC	.	.	.	none		0.303	ANAPC10-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365090.1	NM_014885		T	145916549	G	T	145916549	3	4	78	1	0	0	0	0	1	0	0	0	599	1281	45	4	27	4	ANAPC10	4	145916549	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10		145916549	45237727	17	4992											
ADAMTS12	81792	hgsc.bcm.edu	37	chr5	33658354	33658354	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaatcttcattgatgttacaActgcggtgaggctgacacat	11	12	10	8	1	2	3	1	3	1	0	2	4	2	3	0	2	3	2	0	2	3	3			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr5:33658354A>G	ENST00000504830.1	-	7	1460	c.1125T>C	c.(1123-1125)agT>agC	p.S375S	ADAMTS12_ENST00000352040.3_Silent_p.S375S|ADAMTS12_ENST00000504582.1_5'UTR	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	375	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				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						TGATGTTACAACTGCGGTGAG	0.507										HNSCC(64;0.19)																											p.S375S		Atlas-SNP	.											.	ADAMTS12	464	.	0			c.T1125C						PASS	.						145	145	145					5																	33658354		2203	4300	6503	SO:0001819	synonymous_variant	81792	exon7			GTTACAACTGCGG	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.1125T>C	chr5.hg19:g.33658354A>G		196.0	0.0	.		169.0	10.0	.	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Silent	SNP	ENST00000504830.1	hg19	CCDS34140.1																																																																																			.	.	.	none		0.507	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		G	33658354	A	G	33658354	2	3	78	1	0	0	0	0	0	0	0	1	257	40	2	3		3	ADAMTS12	5	33658354	Silent	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10		33658354	147256906	18	4993											
GPR98	84059	hgsc.bcm.edu	37	chr5	90281309	90281309	+	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	aatctatcatcagagcatgtCacagatctatggactcattc	13	12	6	10	0	6	2	4	0	2	2	7	3	6	3	0	1	1	1	0	1	3	3			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr5:90281309C>T	ENST00000405460.2	+	85	18218	c.18122C>T	c.(18121-18123)tCa>tTa	p.S6041L	GPR98_ENST00000425867.2_Missense_Mutation_p.S1702L	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	6041					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)		CAGAGCATGTCACAGATCTAT	0.433																																					p.S6041L		Atlas-SNP	.											.	GPR98	605	.	0			c.C18122T						PASS	.						181	166	171					5																	90281309		1920	4145	6065	SO:0001583	missense	84059	exon85			GCATGTCACAGAT	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.18122C>T	chr5.hg19:g.90281309C>T	ENSP00000384582:p.Ser6041Leu	193.0	0.0	.		157.0	54.0	.	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	C	13.82	2.352252	0.41700	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.29917	1.61;1.55	5.7	5.7	0.88788	GPCR, family 2-like (1);	0.379457	0.28989	N	0.013487	T	0.22399	0.0540	N	0.14661	0.345	0.22835	N	0.998674	B;B;B	0.24317	0.101;0.042;0.082	B;B;B	0.25506	0.061;0.061;0.036	T	0.10042	-1.0647	9	.	.	.	.	19.8221	0.96602	0.0:1.0:0.0:0.0	.	1702;6041;1702	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	L	6041;6041;1702	ENSP00000384582:S6041L;ENSP00000392618:S1702L	.	S	+	2	0	GPR98	90317065	0.993000	0.37304	0.750000	0.31169	0.347000	0.29111	4.029000	0.57253	2.690000	0.91761	0.557000	0.71058	TCA	.	.	.	none		0.433	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		T	90281309	C	T	90281309	3	4	78	1	0	0	0	0	1	0	0	0	6728	838	29	2	18460	2	GPR98	5	90281309	Missense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	56622955	90281309	90633951	19	4994											
TRPC7	57113	hgsc.bcm.edu	37	chr5	135561911	135561911	+	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	taagacagccagagttttgcTcgggcgaacttccattccac	10	10	9	12	2	0	2	0	0	0	2	3	3	2	2	3	1	3	2	3	1	2	5			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr5:135561911T>A	ENST00000513104.1	-	9	2355	c.2073A>T	c.(2071-2073)cgA>cgT	p.R691R	TRPC7_ENST00000355180.3_Silent_p.R630R|TRPC7_ENST00000426057.2_Silent_p.R575R	NM_020389.2	NP_065122.1	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel, subfamily C, member 7	691					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|manganese ion transport (GO:0006828)|platelet activation (GO:0030168)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(3)	46			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGAGTTTTGCTCGGGCGAACT	0.443																																					p.R691R		Atlas-SNP	.											.	TRPC7	126	.	0			c.A2073T						PASS	.						37	36	36					5																	135561911		1848	3950	5798	SO:0001819	synonymous_variant	57113	exon9			TTTTGCTCGGGCG	AJ272034	CCDS47267.1, CCDS47267.2, CCDS54905.1, CCDS54906.1	5q31.2	2011-12-14			ENSG00000069018	ENSG00000069018		"Voltage-gated ion channels / Transient receptor potential cation channels"	20754	protein-coding gene	gene with protein product						11805119, 16382100	Standard	NM_020389		Approved		uc003lbn.2	Q9HCX4	OTTHUMG00000162035	ENST00000513104.1:c.2073A>T	chr5.hg19:g.135561911T>A		108.0	0.0	.		96.0	47.0	.	NM_020389	A1A4Z4|F5H5U9|Q70T26|Q8IWP7	Silent	SNP	ENST00000513104.1	hg19	CCDS47267.2	.	.	.	.	.	.	.	.	.	.	T	10.27	1.303877	0.23736	.	.	ENSG00000069018	ENST00000352189;ENST00000378459;ENST00000502753	.	.	.	4.99	-2.08	0.07254	.	.	.	.	.	T	0.38161	0.1030	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.28073	-1.0055	4	.	.	.	-6.643	0.5481	0.00657	0.2789:0.2612:0.1187:0.3412	.	.	.	.	C	575;630;636	.	.	S	-	1	0	TRPC7	135589810	0.029000	0.19370	0.942000	0.38095	0.996000	0.88848	-0.795000	0.04580	-0.526000	0.06383	0.482000	0.46254	AGC	.	.	.	none		0.443	TRPC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366975.1	NM_020389		A	135561911	T	A	135561911	2	1	78	1	0	0	0	0	0	0	0	1	16596	1538	54	5		5	TRPC7	5	135561911	Silent	SNP	T	TCGA-AT-A5NU-01A-11D-A28G-10	45280602	135561911	45353349	20	4995											
HSPA9	3313	hgsc.bcm.edu	37	chr5	137903216	137903216	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cattaatcacccgaagcacaTtcagtccagatatctggcca	13	9	6	13	1	3	1	2	0	1	1	4	2	4	1	3	1	1	1	3	1	3	3			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr5:137903216T>C	ENST00000297185.3	-	7	769	c.644A>G	c.(643-645)aAt>aGt	p.N215S	HSPA9_ENST00000501917.2_5'Flank	NM_004134.6	NP_004125.3	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 (mortalin)	215					cellular protein metabolic process (GO:0044267)|negative regulation of apoptotic process (GO:0043066)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(1)|kidney(4)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CCGAAGCACATTCAGTCCAGA	0.423																																					p.N215S		Atlas-SNP	.											.	HSPA9	49	.	0			c.A644G						PASS	.						96	97	96					5																	137903216		2203	4300	6503	SO:0001583	missense	3313	exon7			AGCACATTCAGTC	L11066	CCDS4208.1	5q31.1	2011-09-02	2006-10-31	2006-10-31	ENSG00000113013	ENSG00000113013		"Heat shock proteins / HSP70"	5244	protein-coding gene	gene with protein product		600548	"heat shock 70kDa protein 9B (mortalin-2)"	HSPA9B		7684501	Standard	NM_004134		Approved	GRP75, PBP74, mot-2, mthsp75	uc003ldf.3	P38646	OTTHUMG00000129206	ENST00000297185.3:c.644A>G	chr5.hg19:g.137903216T>C	ENSP00000297185:p.Asn215Ser	90.0	0.0	.		69.0	7.0	.	NM_004134	B2RCM1|P30036|P31932|Q1HB43|Q53H23|Q6GU03|Q9BWB7|Q9UC56	Missense_Mutation	SNP	ENST00000297185.3	hg19	CCDS4208.1	.	.	.	.	.	.	.	.	.	.	T	18.79	3.699341	0.68501	.	.	ENSG00000113013	ENST00000297185;ENST00000541333;ENST00000540484	T	0.01203	5.18	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.04952	0.0133	H	0.95328	3.655	0.80722	D	1	B;B	0.24651	0.002;0.108	B;B	0.25884	0.006;0.064	T	0.01330	-1.1383	10	0.66056	D	0.02	-21.9951	15.0791	0.72099	0.0:0.0:0.0:1.0	.	146;215	B7Z1V7;P38646	.;GRP75_HUMAN	S	215;168;201	ENSP00000297185:N215S	ENSP00000297185:N215S	N	-	2	0	HSPA9	137931115	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.250000	0.72435	2.095000	0.63458	0.533000	0.62120	AAT	.	.	.	none		0.423	HSPA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251285.1	NM_004134		C	137903216	T	C	137903216	3	2	78	1	0	0	0	0	1	0	0	0	7424	1493	52	3	1439	3	HSPA9	5	137903216	Missense_Mutation	SNP	T	TCGA-AT-A5NU-01A-11D-A28G-10	2341305	137903216	43012044	21	4996											
PCDHA2	56146	hgsc.bcm.edu	37	chr5	140176265	140176265	+	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	ttggcgcctagggctggcacCgctgctggcgcagtgagtga	5	8	17	11	3	0	2	0	2	0	0	0	2	0	2	2	4	1	5	2	4	1	2			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr5:140176265C>A	ENST00000526136.1	+	1	1716	c.1716C>A	c.(1714-1716)acC>acA	p.T572T	PCDHA2_ENST00000520672.2_Silent_p.T572T|PCDHA2_ENST00000378132.1_Silent_p.T572T|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018905.2	NP_061728.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	572					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)			GGGCTGGCACCGCTGCTGGCG	0.682																																					p.T572T		Atlas-SNP	.											.	PCDHA2	404	.	0			c.C1716A						PASS	.						97	92	93					5																	140176265		2203	4298	6501	SO:0001819	synonymous_variant	56146	exon1			TGGCACCGCTGCT	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.1716C>A	chr5.hg19:g.140176265C>A		7.0	0.0	.		177.0	13.0	.	NM_031495	O75287|Q9BTV3	Silent	SNP	ENST00000526136.1	hg19	CCDS54914.1																																																																																			.	.	.	none		0.682	PCDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372877.3	NM_018905		A	140176265	C	A	140176265	2	1	78	1	0	0	0	0	0	0	0	1	11531	639	23	4		4	PCDHA2	5	140176265	Silent	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	2273049	140176265	40738995	22	4997											
DIAPH1	1729	hgsc.bcm.edu	37	chr5	140953451	140953451	+	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	gccaacaccctcaggcaaagGagggggtggagggatggtag	11	4	18	8	0	1	0	1	0	0	0	1	3	1	3	2	7	1	2	2	7	3	1			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr5:140953451G>T	ENST00000398557.4	-	16	2106	c.1966C>A	c.(1966-1968)Cct>Act	p.P656T	DIAPH1_ENST00000389057.5_Missense_Mutation_p.P647T|DIAPH1_ENST00000398566.3_Missense_Mutation_p.P647T|DIAPH1_ENST00000389054.3_Missense_Mutation_p.P656T|DIAPH1_ENST00000398562.2_Missense_Mutation_p.P635T|DIAPH1_ENST00000520569.1_Missense_Mutation_p.P602T|DIAPH1_ENST00000518047.1_Missense_Mutation_p.P647T|DIAPH1_ENST00000253811.6_Missense_Mutation_p.P656T	NM_005219.4	NP_005210.3	O60610	DIAP1_HUMAN	diaphanous-related formin 1	656	FH1.				actin filament polymerization (GO:0030041)|cellular response to histamine (GO:0071420)|cytoskeleton organization (GO:0007010)|positive regulation of cell migration (GO:0030335)|protein localization to microtubule (GO:0035372)|regulation of cell shape (GO:0008360)|regulation of microtubule-based process (GO:0032886)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|ruffle membrane (GO:0032587)	ion channel binding (GO:0044325)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|pancreas(1)|skin(2)|stomach(2)	23			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCAGGCAAAGGAGGGGGTGGA	0.592																																					p.P656T		Atlas-SNP	.											.	DIAPH1	64	.	0			c.C1966A						PASS	.						9	9	9					5																	140953451		1969	4113	6082	SO:0001583	missense	1729	exon16			GCAAAGGAGGGGG	BC007411		5q31	2013-05-24	2013-05-24		ENSG00000131504	ENSG00000131504			2876	protein-coding gene	gene with protein product		602121	"diaphanous (Drosophila, homolog) 1", "diaphanous homolog 1 (Drosophila)"	DFNA1		9360932, 1350680	Standard	NM_005219		Approved	hDIA1, LFHL1	uc003llb.4	O60610	OTTHUMG00000149893	ENST00000398557.4:c.1966C>A	chr5.hg19:g.140953451G>T	ENSP00000381565:p.Pro656Thr	49.0	0.0	.		54.0	25.0	.	NM_005219	A6NF18|B7ZKW2|E9PEZ2|Q17RN4|Q59FH8|Q9UC76	Missense_Mutation	SNP	ENST00000398557.4	hg19	CCDS43374.1	.	.	.	.	.	.	.	.	.	.	g	13.06	2.124083	0.37533	.	.	ENSG00000131504	ENST00000389054;ENST00000520569;ENST00000398562;ENST00000389057;ENST00000398566;ENST00000398557;ENST00000253811;ENST00000518047;ENST00000546094	T;T;T;T;T;T;T;T	0.65364	-0.15;-0.15;-0.13;-0.15;-0.15;-0.15;-0.15;-0.15	4.73	4.73	0.59995	Formin Homology 1 (1);	0.242758	0.33875	N	0.004470	T	0.70430	0.3223	M	0.85373	2.75	0.48511	D	0.999665	P;P;P	0.43938	0.822;0.645;0.645	P;B;B	0.44477	0.451;0.41;0.41	T	0.73780	-0.3875	10	0.36615	T	0.2	.	16.9924	0.86357	0.0:0.0:1.0:0.0	.	602;647;656	E7ERW8;E9PEZ2;O60610	.;.;DIAP1_HUMAN	T	656;602;635;647;647;656;656;647;95	ENSP00000373706:P656T;ENSP00000429282:P602T;ENSP00000381570:P635T;ENSP00000373709:P647T;ENSP00000381572:P647T;ENSP00000381565:P656T;ENSP00000253811:P656T;ENSP00000428268:P647T	ENSP00000253811:P656T	P	-	1	0	DIAPH1	140933635	0.998000	0.40836	1.000000	0.80357	0.566000	0.35808	3.542000	0.53625	2.629000	0.89072	0.472000	0.43445	CCT	.	.	.	none		0.592	DIAPH1-203	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_005219		T	140953451	G	T	140953451	3	4	78	1	0	0	0	0	1	0	0	0	4520	1174	41	4	1904	4	DIAPH1	5	140953451	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	777186	140953451	39961809	23	4998											
PCYOX1L	78991	hgsc.bcm.edu	37	chr5	148747898	148747898	+	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	cttccggcgaaagcagccccAggaggcagctgtttggcgag	8	6	15	12	3	0	0	0	0	0	0	1	3	1	1	3	4	3	4	3	4	1	2			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr5:148747898A>T	ENST00000274569.4	+	6	1228	c.1166A>T	c.(1165-1167)cAg>cTg	p.Q389L	PCYOX1L_ENST00000514349.1_Missense_Mutation_p.Q299L	NM_024028.3	NP_076933.3	Q8NBM8	PCYXL_HUMAN	prenylcysteine oxidase 1 like	389					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)			AAGCAGCCCCAGGAGGCAGCT	0.557											OREG0016912	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q389L	Ovarian(62;1136 1477 27277 27495)	Atlas-SNP	.											.	PCYOX1L	32	.	0			c.A1166T						PASS	.						92	99	97					5																	148747898		2203	4300	6503	SO:0001583	missense	78991	exon6			AGCCCCAGGAGGC		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.1166A>T	chr5.hg19:g.148747898A>T	ENSP00000274569:p.Gln389Leu	125.0	0.0	.	1719	107.0	42.0	.	NM_024028	Q7Z4S2|Q8NCY5|Q8NF69|Q9BTE8|Q9BWS3	Missense_Mutation	SNP	ENST00000274569.4	hg19	CCDS4296.1	.	.	.	.	.	.	.	.	.	.	A	16.43	3.122001	0.56613	.	.	ENSG00000145882	ENST00000274569;ENST00000514349	T;T	0.15718	2.4;2.4	5.51	5.51	0.81932	Prenylcysteine lyase (1);	0.000000	0.85682	D	0.000000	T	0.39759	0.1090	M	0.66939	2.045	0.80722	D	1	D;B;D	0.69078	0.997;0.216;0.993	D;B;P	0.80764	0.994;0.09;0.874	T	0.08994	-1.0695	10	0.32370	T	0.25	-22.8691	15.6328	0.76926	1.0:0.0:0.0:0.0	.	271;299;389	B3KXF9;E7EVZ5;Q8NBM8	.;.;PCYXL_HUMAN	L	389;299	ENSP00000274569:Q389L;ENSP00000428512:Q299L	ENSP00000274569:Q389L	Q	+	2	0	PCYOX1L	148728091	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	6.075000	0.71261	2.084000	0.62774	0.459000	0.35465	CAG	.	.	.	none		0.557	PCYOX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252331.2	NM_024028		T	148747898	A	T	148747898	3	4	78	1	0	0	0	0	1	0	0	0	11616	188	7	5	1188	5	PCYOX1L	5	148747898	Missense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10	7794447	148747898	32167362	24	4999											
RARS	5917	hgsc.bcm.edu	37	chr5	167937680	167937680	+	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	tggacaagttgaaggaaaaaGaaagagacaaggtaattcaa	21	6	11	3	0	1	3	1	1	0	2	1	6	1	5	0	3	0	2	0	3	8	3	rs148161788		TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr5:167937680G>T	ENST00000231572.3	+	12	1495	c.1441G>T	c.(1441-1443)Gaa>Taa	p.E481*	RARS_ENST00000538719.1_Nonsense_Mutation_p.E275*	NM_002887.3	NP_002878.2	P54136	SYRC_HUMAN	arginyl-tRNA synthetase	481					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	arginine binding (GO:0034618)|arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|tRNA binding (GO:0000049)	p.E481K(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|stomach(1)	22	Renal(175;0.000159)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0208)|all_neural(177;0.0227)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0693)|Epithelial(171;0.131)|OV - Ovarian serous cystadenocarcinoma(192;0.156)		GAAGGAAAAAGAAAGAGACAA	0.373																																					p.E481X		Atlas-SNP	.											RARS,NS,carcinoma,0,2	RARS	58	.	1	Substitution - Missense(1)	skin(1)	c.G1441T						PASS	.						65	65	65					5																	167937680		2203	4300	6503	SO:0001587	stop_gained	5917	exon12			GAAAAAGAAAGAG	BC000528	CCDS4367.1	5q35.1	2011-07-01			ENSG00000113643	ENSG00000113643	6.1.1.19	"Aminoacyl tRNA synthetases / Class I"	9870	protein-coding gene	gene with protein product	"arginine tRNA ligase 1, cytoplasmic"	107820				7590355	Standard	NM_002887		Approved	DALRD1	uc003lzx.3	P54136	OTTHUMG00000130411	ENST00000231572.3:c.1441G>T	chr5.hg19:g.167937680G>T	ENSP00000231572:p.Glu481*	135.0	0.0	.		128.0	51.0	.	NM_002887	B2RBS9|Q53GY4|Q9BWA1	Nonsense_Mutation	SNP	ENST00000231572.3	hg19	CCDS4367.1	.	.	.	.	.	.	.	.	.	.	G	38	6.721281	0.97788	.	.	ENSG00000113643	ENST00000231572;ENST00000538719	.	.	.	4.99	4.12	0.48240	.	0.150792	0.64402	D	0.000018	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	-22.9725	15.7934	0.78384	0.0:0.1366:0.8634:0.0	.	.	.	.	X	481;275	.	ENSP00000231572:E481X	E	+	1	0	RARS	167870258	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.498000	0.81546	1.218000	0.43458	-0.150000	0.13652	GAA	.	.	.	alt		0.373	RARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252794.2	NM_002887		T	167937680	G	T	167937680	4	4	78	1	0	0	0	0	0	1	0	0	13071	943	33	4	1487	4	RARS	5	167937680	Nonsense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	19189782	167937680	12977580	25	5000											
DDX41	51428	hgsc.bcm.edu	37	chr5	176943307	176943307	+	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	accttcagccttctctttaaGgtgctggtgctgatccagga	7	13	10	11	0	2	1	1	1	1	0	4	2	3	2	3	3	3	2	3	3	1	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr5:176943307G>C	ENST00000507955.1	-	3	803	c.280C>G	c.(280-282)Ctt>Gtt	p.L94V	DDX41_ENST00000506965.1_5'UTR	NM_016222.2	NP_057306.2	Q9UJV9	DDX41_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 41	94					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)			TTCTCTTTAAGGTGCTGGTGC	0.582																																					p.L94V		Atlas-SNP	.											.	DDX41	49	.	0			c.C280G						PASS	.						161	161	161					5																	176943307		2203	4300	6503	SO:0001583	missense	51428	exon3			CTTTAAGGTGCTG	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.280C>G	chr5.hg19:g.176943307G>C	ENSP00000422753:p.Leu94Val	102.0	0.0	.		84.0	36.0	.	NM_016222	B2RDC8|Q96BK6|Q96K05|Q9NT96|Q9NW04	Missense_Mutation	SNP	ENST00000507955.1	hg19	CCDS4427.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.008160	0.75046	.	.	ENSG00000183258	ENST00000330503;ENST00000507955	T;T	0.29142	1.58;1.59	5.38	4.5	0.54988	.	0.000000	0.64402	D	0.000003	T	0.48150	0.1484	L	0.56340	1.77	0.58432	D	0.999999	D	0.76494	0.999	D	0.68621	0.959	T	0.37244	-0.9714	10	0.42905	T	0.14	-23.2967	14.3294	0.66545	0.0725:0.0:0.9274:0.0	.	94	Q9UJV9	DDX41_HUMAN	V	112;94	ENSP00000330349:L112V;ENSP00000422753:L94V	ENSP00000330349:L112V	L	-	1	0	DDX41	176875913	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.218000	0.72224	2.513000	0.84729	0.491000	0.48974	CTT	.	.	.	none		0.582	DDX41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253432.2	NM_016222		C	176943307	G	C	176943307	3	2	78	1	0	0	0	0	1	0	0	0	4363	1000	35	4	1648	4	DDX41	5	176943307	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	9005627	176943307	3971953	26	5001											
DCDC2	51473	hgsc.bcm.edu	37	chr6	24357769	24357769	+	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	agcttccggattcggtggccAgtccgcggggtgtagatgtt	5	11	16	9	4	0	1	0	0	0	1	3	2	2	2	3	5	1	3	3	5	1	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr6:24357769A>T	ENST00000378454.3	-	1	511	c.210T>A	c.(208-210)acT>acA	p.T70T	KAAG1_ENST00000274766.1_5'UTR	NM_001195610.1|NM_016356.3	NP_001182539.1|NP_057440.2	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2	70	Doublecortin 1. {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)				TTCGGTGGCCAGTCCGCGGGG	0.597																																					p.T70T		Atlas-SNP	.											.	DCDC2	53	.	0			c.T210A						PASS	.						39	38	38					6																	24357769		2203	4299	6502	SO:0001819	synonymous_variant	51473	exon2			GTGGCCAGTCCGC	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.210T>A	chr6.hg19:g.24357769A>T		70.0	0.0	.		74.0	4.0	.	NM_001195610	Q5VTR8|Q5VTR9|Q86W35|Q9UFD1|Q9UHG1|Q9ULR6	Silent	SNP	ENST00000378454.3	hg19	CCDS4550.1	.	.	.	.	.	.	.	.	.	.	A	4.106	0.017843	0.07959	.	.	ENSG00000146038	ENST00000436313	.	.	.	5.56	-4.43	0.03568	.	.	.	.	.	T	0.19248	0.0462	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41179	-0.9523	4	.	.	.	-10.2342	0.669	0.00856	0.2741:0.2931:0.2257:0.2071	.	.	.	.	Q	38	.	.	L	-	2	0	DCDC2	24465748	0.027000	0.19231	0.078000	0.20375	0.442000	0.32017	-0.787000	0.04618	-0.539000	0.06273	-1.491000	0.00971	CTG	.	.	.	none		0.597	DCDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043604.1	NM_016356		T	24357769	A	T	24357769	2	4	78	1	0	0	0	0	0	0	0	1	4287	175	7	5		5	DCDC2	6	24357769	Silent	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10		24357769	146757298	27	5002											
LRFN2	57497	hgsc.bcm.edu	37	chr6	40399589	40399589	+	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	cacaagcacagcccgttccgGggggcttttgggaggctctc	6	8	14	13	2	1	0	0	0	1	0	3	1	2	1	2	5	2	4	2	5	1	3			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr6:40399589G>T	ENST00000338305.6	-	2	1806	c.1264C>A	c.(1264-1266)Ccg>Acg	p.P422T		NM_020737.1	NP_065788.1	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III domain containing 2	422	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.					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)					GCCCGTTCCGGGGGGCTTTTG	0.642																																					p.P422T		Atlas-SNP	.											.	LRFN2	133	.	0			c.C1264A						PASS	.						44	48	47					6																	40399589		2203	4300	6503	SO:0001583	missense	57497	exon2			GTTCCGGGGGGCT	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.1264C>A	chr6.hg19:g.40399589G>T	ENSP00000345985:p.Pro422Thr	56.0	0.0	.		56.0	23.0	.	NM_020737	A5PKU3|Q5SYP9	Missense_Mutation	SNP	ENST00000338305.6	hg19	CCDS34443.1	.	.	.	.	.	.	.	.	.	.	G	10.62	1.400939	0.25291	.	.	ENSG00000156564	ENST00000338305	T	0.72282	-0.64	5.38	5.38	0.77491	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.50718	0.1632	L	0.50333	1.59	0.80722	D	1	B	0.19445	0.036	B	0.20577	0.03	T	0.51309	-0.8722	10	0.13853	T	0.58	.	16.6167	0.84918	0.0:0.0:1.0:0.0	.	422	Q9ULH4	LRFN2_HUMAN	T	422	ENSP00000345985:P422T	ENSP00000345985:P422T	P	-	1	0	LRFN2	40507567	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	9.578000	0.98200	2.525000	0.85131	0.561000	0.74099	CCG	.	.	.	none		0.642	LRFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040488.1	XM_166372		T	40399589	G	T	40399589	3	4	78	1	0	0	0	0	1	0	0	0	8945	1232	43	4	1113	4	LRFN2	6	40399589	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	16041820	40399589	130715478	28	5003											
BVES	11149	hgsc.bcm.edu	37	chr6	105563684	105563684	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtgcagaggctgagctgatGttccagctttttggctttct	5	16	12	8	0	1	3	0	2	1	1	2	3	2	3	1	2	3	6	1	2	0	4	rs370149373		TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr6:105563684G>A	ENST00000314641.5	-	7	1051	c.835C>T	c.(835-837)Cat>Tat	p.H279Y	BVES_ENST00000446408.2_Missense_Mutation_p.H279Y|BVES_ENST00000336775.5_Missense_Mutation_p.H279Y	NM_001199563.1	NP_001186492.1	Q8NE79	POPD1_HUMAN	blood vessel epicardial substance	279					epithelial cell-cell adhesion (GO:0090136)|hematopoietic progenitor cell differentiation (GO:0002244)|muscle organ development (GO:0007517)|positive regulation of locomotion (GO:0040017)|positive regulation of receptor recycling (GO:0001921)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|regulation of Rac GTPase activity (GO:0032314)|sinoatrial node cell development (GO:0060931)|substrate adhesion-dependent cell spreading (GO:0034446)|vesicle-mediated transport (GO:0016192)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	cAMP binding (GO:0030552)|structural molecule activity (GO:0005198)			NS(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|urinary_tract(1)	21		all_cancers(87;2.83e-05)|Acute lymphoblastic leukemia(125;1.95e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0101)|Colorectal(196;0.204)|Lung NSC(302;0.238)				CTGAGCTGATGTTCCAGCTTT	0.443																																					p.H279Y		Atlas-SNP	.											.	BVES	33	.	0			c.C835T						PASS	.	G	TYR/HIS,TYR/HIS,TYR/HIS	0,4406		0,0,2203	145	121	129		835,835,835	4.8	1	6		129	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	BVES	NM_001199563.1,NM_007073.4,NM_147147.3	83,83,83	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign	279/361,279/361,279/361	105563684	1,13005	2203	4300	6503	SO:0001583	missense	11149	exon7			GCTGATGTTCCAG	AF124512	CCDS5051.1	6q21	2008-11-25			ENSG00000112276	ENSG00000112276			1152	protein-coding gene	gene with protein product	"popeye domain containing 1"	604577				10441744, 10882522	Standard	NM_147147		Approved	HBVES, POP1, POPDC1	uc003pqx.3	Q8NE79	OTTHUMG00000015291	ENST00000314641.5:c.835C>T	chr6.hg19:g.105563684G>A	ENSP00000313172:p.His279Tyr	95.0	0.0	.		97.0	32.0	.	NM_001199563	A8K1R4|E1P5D8|Q5T550|Q5T551|Q8IWC6|Q9HBV0|Q9UNG6	Missense_Mutation	SNP	ENST00000314641.5	hg19	CCDS5051.1	.	.	.	.	.	.	.	.	.	.	G	10.32	1.317534	0.23908	0.0	1.16E-4	ENSG00000112276	ENST00000314641;ENST00000336775;ENST00000446408	T;T;T	0.17213	2.29;2.29;2.29	5.71	4.79	0.61399	.	0.279017	0.39544	N	0.001325	T	0.02688	0.0081	N	0.22421	0.69	0.27859	N	0.940468	P	0.40398	0.716	B	0.30495	0.116	T	0.34104	-0.9842	10	0.02654	T	1	-25.5861	13.3716	0.60717	0.0:0.0:0.7242:0.2758	.	279	Q8NE79	POPD1_HUMAN	Y	279	ENSP00000313172:H279Y;ENSP00000337259:H279Y;ENSP00000397310:H279Y	ENSP00000313172:H279Y	H	-	1	0	BVES	105670377	1.000000	0.71417	0.985000	0.45067	0.994000	0.84299	4.940000	0.63533	2.706000	0.92434	0.563000	0.77884	CAT	.	.	.	weak		0.443	BVES-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406075.1	NM_147147		A	105563684	G	A	105563684	3	1	78	1	0	0	0	0	1	0	0	0	1577	1377	48	2	255	2	BVES	6	105563684	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	65164095	105563684	65551383	29	5004											
CITED2	10370	hgsc.bcm.edu	37	chr6	139694300	139694309	+	Frame_Shift_Del	DEL	CACACGAAGT	CACACGAAGT	-																															ctctgctgggctgctgtttgCacacgaagtccgtcataaaa																										TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	CACACGAAGT	CACACGAAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr6:139694300_139694309delCACACGAAGT	ENST00000367651.2	-	2	988_997	c.773_782delACTTCGTGTG	c.(772-783)gacttcgtgtgcfs	p.DFVC258fs	CITED2_ENST00000537332.1_Frame_Shift_Del_p.DFVC258fs|CITED2_ENST00000536159.1_Frame_Shift_Del_p.DFVC258fs	NM_006079.4	NP_006070.2	Q99967	CITE2_HUMAN	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	258	Asp/Glu-rich (acidic).				adrenal cortex formation (GO:0035802)|bone morphogenesis (GO:0060349)|cardiac neural crest cell development involved in heart development (GO:0061308)|cell aging (GO:0007569)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|cranial nerve morphogenesis (GO:0021602)|decidualization (GO:0046697)|determination of left/right symmetry (GO:0007368)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|endocardial cushion development (GO:0003197)|erythrocyte development (GO:0048821)|granulocyte differentiation (GO:0030851)|heart development (GO:0007507)|heart looping (GO:0001947)|hematopoietic progenitor cell differentiation (GO:0002244)|left/right axis specification (GO:0070986)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell migration (GO:0030336)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900164)|outflow tract morphogenesis (GO:0003151)|peripheral nervous system development (GO:0007422)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of gene expression (GO:0010628)|positive regulation of male gonad development (GO:2000020)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|pulmonary artery morphogenesis (GO:0061156)|regulation of organ formation (GO:0003156)|regulation of RNA biosynthetic process (GO:2001141)|response to estrogen (GO:0043627)|response to fluid shear stress (GO:0034405)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|sex determination (GO:0007530)|skeletal muscle cell differentiation (GO:0035914)|spleen development (GO:0048536)|thymus development (GO:0048538)|transforming growth factor beta receptor signaling pathway (GO:0007179)|trophectodermal cell differentiation (GO:0001829)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|LBD domain binding (GO:0050693)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			large_intestine(1)|lung(4)	5	Breast(32;0.226)			GBM - Glioblastoma multiforme(68;0.000171)|OV - Ovarian serous cystadenocarcinoma(155;0.00134)		CTGCTGTTTGCACACGAAGTCCGTCATAAA	0.49																																					p.263_266del	NSCLC(98;1219 1550 33720 43229 49330)	Atlas-Indel,Pindel	.											.	CITED2	16	.	0			c.789_798del						PASS	.																																			SO:0001589	frameshift_variant	10370	exon2			.	U65093	CCDS5195.1, CCDS75530.1	6q23.3	2008-08-29			ENSG00000164442	ENSG00000164442			1987	protein-coding gene	gene with protein product		602937				8901575, 10552932	Standard	NM_006079		Approved	MRG1	uc021zfz.2	Q99967	OTTHUMG00000015691	ENST00000367651.2:c.773_782delACTTCGTGTG	chr6.hg19:g.139694300_139694309delCACACGAAGT	ENSP00000356623:p.Asp258fs	89.0	0.0	0		57.0	15.0	0.263158	NM_001168389	O95426|Q5VTF4	Frame_Shift_Del	DEL	ENST00000367651.2	hg19	CCDS5195.1																																																																																			.	.	.	none		0.49	CITED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042463.1			-	139694309	CACACGAAGT	-	139694300	7	5	78	1	0	1	0	1	0	0	0	0	3442	710	25	0	34	0	CITED2	6	139694300	Frame_Shift_Del	DEL	CACACGAAGT	TCGA-AT-A5NU-01A-11D-A28G-10	34130616	139694300	31420767	30	5005											
FBXL13	222235	hgsc.bcm.edu	37	chr7	102553614	102553614	+	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	tactgtaagcctttgtctgtGaaccgtctgcaataagccaa	11	12	8	10	1	2	1	0	1	2	0	2	1	2	1	3	0	5	2	3	0	6	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr7:102553614G>A	ENST00000313221.4	-	11	1353	c.927C>T	c.(925-927)ttC>ttT	p.F309F	FBXL13_ENST00000455112.2_Silent_p.F309F|LRRC17_ENST00000339431.4_Intron|FBXL13_ENST00000436908.1_Silent_p.F309F|FBXL13_ENST00000379306.3_Silent_p.F309F|LRRC17_ENST00000249377.4_Intron|FBXL13_ENST00000379305.3_Silent_p.F309F|FBXL13_ENST00000379308.3_Silent_p.F309F|FBXL13_ENST00000456695.1_Silent_p.F309F|FBXL13_ENST00000393772.2_Silent_p.F309F	NM_145032.3	NP_659469.3	Q8NEE6	FXL13_HUMAN	F-box and leucine-rich repeat protein 13	309										NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|skin(3)|stomach(1)	27						CTTTGTCTGTGAACCGTCTGC	0.443																																					p.F309F		Atlas-SNP	.											.	FBXL13	65	.	0			c.C927T						PASS	.						146	131	136					7																	102553614		2203	4300	6503	SO:0001819	synonymous_variant	222235	exon11			GTCTGTGAACCGT	BC031285	CCDS5726.1, CCDS47678.1, CCDS75649.1	7q22.1	2014-07-18			ENSG00000161040	ENSG00000161040		"F-boxes / Leucine-rich repeats"	21658	protein-coding gene	gene with protein product		609080					Standard	NM_145032		Approved	MGC21636, Fbl13	uc003vaq.2	Q8NEE6	OTTHUMG00000157224	ENST00000313221.4:c.927C>T	chr7.hg19:g.102553614G>A		170.0	0.0	.		169.0	38.0	.	NM_001111038	C9J565|C9J566|Q6UVW7|Q6UVW8|Q75MN5|Q86UJ5|Q8N7Y4|Q8TCL2|Q8WUF9|Q8WUG0	Silent	SNP	ENST00000313221.4	hg19	CCDS5726.1																																																																																			.	.	.	none		0.443	FBXL13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348001.1	NM_145032		A	102553614	G	A	102553614	2	1	78	1	0	0	0	0	0	0	0	1	5716	1281	45	2		2	FBXL13	7	102553614	Silent	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10		102553614	56585049	31	5006											
LAMB1	3912	hgsc.bcm.edu	37	chr7	107605061	107605061	+	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	gggtggcaaagtagtaaccaGgttccacttcgttgcactga	10	10	12	9	1	0	1	0	1	0	0	2	1	1	1	2	3	2	6	2	3	3	5			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr7:107605061G>C	ENST00000222399.6	-	14	1864	c.1634C>G	c.(1633-1635)cCt>cGt	p.P545R	LAMB1_ENST00000393561.1_Missense_Mutation_p.P569R|LAMB1_ENST00000393560.1_Missense_Mutation_p.P545R	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	545					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						GTAGTAACCAGGTTCCACTTC	0.567																																					p.P545R		Atlas-SNP	.											.	LAMB1	185	.	0			c.C1634G						PASS	.						173	143	153					7																	107605061		2203	4300	6503	SO:0001583	missense	3912	exon14			TAACCAGGTTCCA	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.1634C>G	chr7.hg19:g.107605061G>C	ENSP00000222399:p.Pro545Arg	153.0	0.0	.		202.0	73.0	.	NM_002291	Q14D91	Missense_Mutation	SNP	ENST00000222399.6	hg19	CCDS5750.1	.	.	.	.	.	.	.	.	.	.	G	18.39	3.614445	0.66672	.	.	ENSG00000091136	ENST00000393561;ENST00000222399;ENST00000393560	T;T;T	0.63096	-0.02;-0.02;0.91	4.64	4.64	0.57946	EGF-like, laminin (3);	.	.	.	.	T	0.72606	0.3481	M	0.69463	2.115	0.38209	D	0.940402	B;B;B	0.33777	0.213;0.425;0.321	B;P;B	0.47645	0.229;0.553;0.126	T	0.76737	-0.2849	9	0.49607	T	0.09	.	17.501	0.87732	0.0:0.0:1.0:0.0	.	545;545;569	E7EPA6;P07942;G3XAI2	.;LAMB1_HUMAN;.	R	569;545;545	ENSP00000377191:P569R;ENSP00000222399:P545R;ENSP00000377190:P545R	ENSP00000222399:P545R	P	-	2	0	LAMB1	107392297	1.000000	0.71417	0.631000	0.29282	0.798000	0.45092	9.435000	0.97529	2.129000	0.65627	0.563000	0.77884	CCT	.	.	.	none		0.567	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291		C	107605061	G	C	107605061	3	2	78	1	0	0	0	0	1	0	0	0	8617	1000	35	4	3810	4	LAMB1	7	107605061	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	5051447	107605061	51533602	32	5007											
ASAH1	427	hgsc.bcm.edu	37	chr8	17916973	17916973	+	Splice_Site	DEL	T	T	-																															ctaccctgcttagcatcgagTctagatacaaaaggagagat																										TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr8:17916973delT	ENST00000262097.6	-	12	1229	c.918delA	c.(916-918)gaa>ga	p.E306fs	ASAH1_ENST00000314146.10_Splice_Site_p.E300fs|ASAH1_ENST00000520781.1_Splice_Site_p.E281fs|ASAH1_ENST00000417108.2_Splice_Site_p.E216fs|ASAH1_ENST00000381733.4_Splice_Site_p.E322fs	NM_177924.3	NP_808592.2	Q13510	ASAH1_HUMAN	N-acylsphingosine amidohydrolase (acid ceramidase) 1	306					cell death (GO:0008219)|ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|lung development (GO:0030324)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	catalytic activity (GO:0003824)|ceramidase activity (GO:0017040)			breast(1)|endometrium(2)|large_intestine(4)|lung(2)	9				Colorectal(111;0.0646)|COAD - Colon adenocarcinoma(73;0.228)		TAGCATCGAGTCTAGATACAA	0.398																																					p.L323fs		Atlas-Indel,Pindel	.											.	ASAH1	71	.	0			c.967delC						PASS	.						185	167	173					8																	17916973		2203	4300	6503	SO:0001630	splice_region_variant	427	exon12			.	U70063	CCDS6005.1, CCDS6006.1, CCDS47813.1	8p22	2007-03-27	2002-09-11	2002-09-13	ENSG00000104763	ENSG00000104763			735	protein-coding gene	gene with protein product		613468	"N-acylsphingosine amidohydrolase (acid ceramidase)"	ASAH		8955159, 10610716	Standard	NM_004315		Approved	AC, PHP32, FLJ21558	uc003wyn.2	Q13510	OTTHUMG00000096997	ENST00000262097.6:c.918-1A>-	chr8.hg19:g.17916973delT		77.0	0.0	0		66.0	25.0	0.378788	NM_004315	E9PDS0|Q6W898|Q96AS2	Frame_Shift_Del	DEL	ENST00000262097.6	hg19	CCDS6006.1																																																																																			.	.	.	none		0.398	ASAH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214077.2	NM_004315	Frame_Shift_Del	-	17916973	T	-	17916973	8	5	78	1	0	1	0	1	0	0	1	0	1006	1681	58	0	281	0	ASAH1	8	17916973	Splice_Site	DEL	T	TCGA-AT-A5NU-01A-11D-A28G-10		17916973	128447049	33	5008											
STMN4	81551	hgsc.bcm.edu	37	chr8	27097616	27097616	+	Frame_Shift_Del	DEL	G	G	-																															gttttcctcaatggccttttGgatcacctctctctcatgtt																										TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr8:27097616delG	ENST00000265770.7	-	5	518	c.382delC	c.(382-384)caafs	p.Q128fs	STMN4_ENST00000522908.1_Frame_Shift_Del_p.Q155fs|STMN4_ENST00000350889.4_Frame_Shift_Del_p.Q155fs|STMN4_ENST00000519997.1_Frame_Shift_Del_p.Q119fs|STMN4_ENST00000523048.1_Frame_Shift_Del_p.Q155fs|STMN4_ENST00000519614.1_Frame_Shift_Del_p.Q128fs			Q9H169	STMN4_HUMAN	stathmin-like 4	128	SLD. {ECO:0000255|PROSITE- ProRule:PRU00998}.				regulation of microtubule polymerization or depolymerization (GO:0031110)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)	11		Ovarian(32;0.00167)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0214)|Epithelial(17;9.82e-10)|Colorectal(74;0.142)	Lomustine(DB01206)	ATGGCCTTTTGGATCACCTCT	0.512																																					p.Q155fs		Atlas-INDEL	.											.	STMN4	28	.	0			c.464delA						PASS	.						220	205	210					8																	27097616		2203	4300	6503	SO:0001589	frameshift_variant	81551	exon6			.		CCDS6055.1, CCDS64851.1, CCDS64852.1, CCDS64854.1	8p21.2	2006-12-09			ENSG00000015592	ENSG00000015592			16078	protein-coding gene	gene with protein product						11230166	Standard	NM_001283054		Approved	RB3	uc003xfj.3	Q9H169	OTTHUMG00000099461	ENST00000265770.7:c.382delC	chr8.hg19:g.27097616delG	ENSP00000265770:p.Gln128fs	164.0	0.0	0		129.0	10.0	0.0775194	NM_030795	B7Z2Z7|B7Z4I9|D3DSS8|D3DSS9|G5EA16|Q2TAB9	Frame_Shift_Del	DEL	ENST00000265770.7	hg19																																																																																				.	.	.	none		0.512	STMN4-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000375941.1	NM_030795		-	27097616	G	-	27097616	7	5	78	1	0	1	0	1	0	0	0	0	15323	1357	47	0	195	0	STMN4	8	27097616	Frame_Shift_Del	DEL	G	TCGA-AT-A5NU-01A-11D-A28G-10	9180643	27097616	119266406	34	5009											
FAM108B1	51104	hgsc.bcm.edu	37	chr9	74489541	74489541	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaatttaccttgtcctaagAgcaagccaagcagcttcaat	14	10	6	11	0	1	1	1	0	0	1	2	1	2	1	3	0	5	3	3	0	6	5			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr9:74489541A>G	ENST00000333421.6	-	2	567	c.456T>C	c.(454-456)gcT>gcC	p.A152A	ABHD17B_ENST00000377041.2_Silent_p.A152A	NM_001025780.1	NP_001020951.1	Q5VST6	AB17B_HUMAN	abhydrolase domain containing 17B	152						extracellular region (GO:0005576)|membrane (GO:0016020)	hydrolase activity (GO:0016787)										TTGTCCTAAGAGCAAGCCAAG	0.353																																					p.A152A		Atlas-SNP	.											.	FAM108B1	24	.	0			c.T456C						PASS	.						53	49	50					9																	74489541		2203	4300	6503	SO:0001819	synonymous_variant	51104	exon2			CCTAAGAGCAAGC	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.456T>C	chr9.hg19:g.74489541A>G		86.0	0.0	.		90.0	4.0	.	NM_016014	A8KAJ5|Q5VST7|Q86YB6|Q8IY03|Q9Y377	Silent	SNP	ENST00000333421.6	hg19	CCDS35043.1																																																																																			.	.	.	none		0.353	ABHD17B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052625.1	NM_016014		G	74489541	A	G	74489541	2	3	78	1	0	0	0	0	0	0	0	1	5396	291	11	3		3	FAM108B1	9	74489541	Silent	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10		74489541	66723890	35	5010											
FAM178A	55719	hgsc.bcm.edu	37	chr10	102675796	102675796	+	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	tcttcaaaccagcttcaaaaCaaggtatgtacactgttgat	14	12	6	9	0	3	1	2	1	1	0	3	1	3	1	1	1	4	4	1	1	6	5			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr10:102675796C>T	ENST00000238961.4	+	2	723	c.181C>T	c.(181-183)Caa>Taa	p.Q61*	FAM178A_ENST00000370271.3_Nonsense_Mutation_p.Q61*|FAM178A_ENST00000370269.3_Nonsense_Mutation_p.Q61*	NM_018121.3	NP_060591.3	Q8IX21	F178A_HUMAN	family with sequence similarity 178, member A	61						chromatin (GO:0000785)|extracellular space (GO:0005615)|nucleus (GO:0005634)											AGCTTCAAAACAAGGTATGTA	0.333																																					p.Q61X		Atlas-SNP	.											.	FAM178A	9	.	0			c.C181T						PASS	.						145	150	148					10																	102675796		2203	4300	6503	SO:0001587	stop_gained	55719	exon2			TCAAAACAAGGTA	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.181C>T	chr10.hg19:g.102675796C>T	ENSP00000238961:p.Gln61*	66.0	0.0	.		55.0	20.0	.	NM_001136123	A8K950|B1AL17|Q5W0L8|Q6GMU6|Q9NPE8	Nonsense_Mutation	SNP	ENST00000238961.4	hg19	CCDS7500.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.510828	0.85389	.	.	ENSG00000119906	ENST00000370271;ENST00000238961;ENST00000370269	.	.	.	5.65	5.65	0.86999	.	0.136815	0.34386	N	0.004001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	-7.1251	16.8133	0.85726	0.0:1.0:0.0:0.0	.	.	.	.	X	61	.	ENSP00000238961:Q61X	Q	+	1	0	FAM178A	102665786	1.000000	0.71417	1.000000	0.80357	0.448000	0.32197	4.535000	0.60629	2.819000	0.97034	0.650000	0.86243	CAA	.	.	.	none		0.333	FAM178A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049897.3			T	102675796	C	T	102675796	4	4	78	1	0	0	0	0	0	1	0	0	5507	479	17	2	187	2	FAM178A	10	102675796	Nonsense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10		102675796	32858951	36	5011											
WDR11	55717	hgsc.bcm.edu	37	chr10	122665493	122665493	+	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	aggctctcctggttctcctcTctctgggctgcttttttagc	2	17	9	13	0	4	0	0	0	4	0	7	0	4	0	2	3	2	4	2	3	1	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr10:122665493T>A	ENST00000263461.6	+	27	3643	c.3397T>A	c.(3397-3399)Tct>Act	p.S1133T	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						GGTTCTCCTCTCTCTGGGCTG	0.512																																					p.S1133T		Atlas-SNP	.											.	WDR11	95	.	0			c.T3397A						PASS	.						117	106	110					10																	122665493		2203	4300	6503	SO:0001583	missense	55717	exon27			CTCCTCTCTCTGG	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.3397T>A	chr10.hg19:g.122665493T>A	ENSP00000263461:p.Ser1133Thr	115.0	0.0	.		122.0	48.0	.	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000263461.6	hg19	CCDS7619.1	.	.	.	.	.	.	.	.	.	.	T	16.56	3.158729	0.57368	.	.	ENSG00000120008	ENST00000263461	D	0.91843	-2.92	5.63	4.48	0.54585	.	0.000000	0.85682	D	0.000000	D	0.94069	0.8099	L	0.58669	1.825	0.52501	D	0.999954	P;P;P;P	0.52842	0.956;0.956;0.911;0.682	D;D;P;B	0.65010	0.931;0.931;0.558;0.129	D	0.93073	0.6484	10	0.48119	T	0.1	-11.2569	11.9916	0.53178	0.1299:0.0:0.0:0.8701	.	1133;1133;424;662	Q9BZH6;B2RCJ6;Q9NWV7;Q659C9	WDR11_HUMAN;.;.;.	T	1133	ENSP00000263461:S1133T	ENSP00000263461:S1133T	S	+	1	0	WDR11	122655483	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	5.888000	0.69758	0.923000	0.37045	0.455000	0.32223	TCT	.	.	.	none		0.512	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2			A	122665493	T	A	122665493	3	1	78	1	0	0	0	0	1	0	0	0	17285	1551	54	5	3503	5	WDR11	10	122665493	Missense_Mutation	SNP	T	TCGA-AT-A5NU-01A-11D-A28G-10	19989697	122665493	12869254	37	5012											
OR5T2	219464	hgsc.bcm.edu	37	chr11	56000572	56000573	+	Frame_Shift_Del	DEL	AA	AA	-																															acaaacttgaagatatgcatAaagttacagttcatattatg																										TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr11:56000572_56000573delAA	ENST00000313264.4	-	1	164_165	c.89_90delTT	c.(88-90)tttfs	p.F30fs		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	30						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)					AGATATGCATAAAGTTACAGTT	0.351																																					p.30_31del		Atlas-Indel,Pindel	.											.	OR5T2	107	.	0			c.90_91del						PASS	.																																			SO:0001589	frameshift_variant	219464	exon1			.	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"GPCR / Class A : Olfactory receptors"	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.89_90delTT	chr11.hg19:g.56000572_56000573delAA	ENSP00000323688:p.Phe30fs	110.0	0.0	0		106.0	39.0	0.367925	NM_001004746	B9EGX5|Q6IFC8	Frame_Shift_Del	DEL	ENST00000313264.4	hg19	CCDS31523.1																																																																																			.	.	.	none		0.351	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746		-	56000573	AA	-	56000572	7	5	78	1	0	1	0	1	0	0	0	0	11189	359	13	0	988	0	OR5T2	11	56000572	Frame_Shift_Del	DEL	AA	TCGA-AT-A5NU-01A-11D-A28G-10		56000572	79005944	38	5013											
CDC42BPG	55561	hgsc.bcm.edu	37	chr11	64603951	64603963	+	Frame_Shift_Del	DEL	CCAGCTGGGGGCC	CCAGCTGGGGGCC	-																															cactgtcctgacctgggctaCcagctgggggcccatccgtc																										TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	CCAGCTGGGGGCC	CCAGCTGGGGGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr11:64603951_64603963delCCAGCTGGGGGCC	ENST00000342711.5	-	12	1423_1435	c.1424_1436delGGCCCCCAGCTGG	c.(1423-1437)gggcccccagctggtfs	p.GPPAG475fs		NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						ACCTGGGCTACCAGCTGGGGGCCCATCCGTCTG	0.653											OREG0004017	type=REGULATORY REGION|Gene=CDC42BPG|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.475_479del		Pindel	.											.	CDC42BPG	101	.	0			c.1425_1437del						PASS	.																																			SO:0001589	frameshift_variant	55561	exon12			.	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.1424_1436delGGCCCCCAGCTGG	chr11.hg19:g.64603951_64603963delCCAGCTGGGGGCC	ENSP00000345133:p.Gly475fs	99.0	0.0	.	1077	62.0	10.0	0.161	NM_017525		Frame_Shift_Del	DEL	ENST00000342711.5	hg19	CCDS31601.1																																																																																			.	.	.	none		0.653	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516		-	64603963	CCAGCTGGGGGCC	-	64603951	7	5	78	1	0	1	0	1	0	0	0	0	3076	507	18	0	3323	0	CDC42BPG	11	64603951	Frame_Shift_Del	DEL	CCAGCTGGGGGCC	TCGA-AT-A5NU-01A-11D-A28G-10	8603379	64603951	70402565	39	5014											
TCIRG1	10312	hgsc.bcm.edu	37	chr11	67817430	67817430	+	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	ctgcctgctcatgccccaggAggaaaacaaggccgggttgc	9	6	13	13	1	1	0	1	0	0	0	1	2	1	2	4	4	5	2	4	4	3	1			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr11:67817430A>G	ENST00000265686.3	+	17	2123	c.2015A>G	c.(2014-2016)gAg>gGg	p.E672G	RP11-802E16.3_ENST00000526897.1_RNA|TCIRG1_ENST00000532635.1_Splice_Site_p.E456G|RP11-802E16.3_ENST00000529934.1_RNA|RP11-802E16.3_ENST00000534517.1_RNA	NM_006019.3	NP_006010.2	Q13488	VPP3_HUMAN	T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 subunit A3	672					ATP hydrolysis coupled proton transport (GO:0015991)|cellular defense response (GO:0006968)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of cell proliferation (GO:0008284)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	hydrogen ion transmembrane transporter activity (GO:0015078)|transporter activity (GO:0005215)			breast(1)|endometrium(4)|large_intestine(3)|lung(4)|ovary(3)|prostate(1)	16						ATGCCCCAGGAGGAAAACAAG	0.637																																					p.E672G		Atlas-SNP	.											.	TCIRG1	40	.	0			c.A2015G						PASS	.						38	39	39					11																	67817430		2199	4292	6491	SO:0001630	splice_region_variant	10312	exon17			CCCAGGAGGAAAA	AF025374	CCDS8177.1, CCDS53670.1	11q13.2	2014-09-17	2006-01-20		ENSG00000110719	ENSG00000110719		"ATPases / V-type"	11647	protein-coding gene	gene with protein product	"T-cell immune response cDNA 7"	604592	"T-cell, immune regulator 1", "T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein a isoform 3", "T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3"			8579597, 9806637	Standard	NM_006019		Approved	TIRC7, OC-116, OC116, ATP6N1C, Atp6i, a3, ATP6V0A3	uc001one.3	Q13488	OTTHUMG00000167358	ENST00000265686.3:c.2014-1A>G	chr11.hg19:g.67817430A>G		62.0	0.0	.		72.0	38.0	.	NM_006019	O75877|Q8WVC5	Missense_Mutation	SNP	ENST00000265686.3	hg19	CCDS8177.1	.	.	.	.	.	.	.	.	.	.	A	8.644	0.896745	0.17686	.	.	ENSG00000110719	ENST00000265686;ENST00000532635;ENST00000546315	D;D	0.89123	-1.95;-2.47	4.21	1.83	0.25207	.	1.186560	0.05814	N	0.614544	T	0.78666	0.4319	N	0.17082	0.46	0.45194	D	0.998206	B	0.02656	0.0	B	0.06405	0.002	T	0.64024	-0.6504	10	0.15066	T	0.55	-4.3465	6.3839	0.21550	0.7598:0.0:0.2402:0.0	.	672	Q13488	VPP3_HUMAN	G	672;456;30	ENSP00000265686:E672G;ENSP00000434407:E456G	ENSP00000265686:E672G	E	+	2	0	TCIRG1	67574006	0.009000	0.17119	0.006000	0.13384	0.156000	0.22039	0.207000	0.17395	0.671000	0.31185	0.379000	0.24179	GAG	.	.	.	none		0.637	TCIRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394305.1	NM_006019	Missense_Mutation	G	67817430	A	G	67817430	5	3	78	1	0	0	0	0	0	0	1	0	15715	318	11	3	2077	3	TCIRG1	11	67817430	Splice_Site	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10	3213479	67817430	67189086	40	5015											
NAALAD2	10003	hgsc.bcm.edu	37	chr11	89868775	89868775	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccacttctgtgcgctatcAtcaaagtatacggtggaaac	12	10	9	10	2	3	0	2	0	1	0	3	2	3	1	1	2	3	2	1	2	5	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr11:89868775A>G	ENST00000534061.1	+	2	361	c.131A>G	c.(130-132)cAt>cGt	p.H44R	NAALAD2_ENST00000321955.4_Missense_Mutation_p.H44R|NAALAD2_ENST00000375944.3_Missense_Mutation_p.H44R|NAALAD2_ENST00000525171.1_Missense_Mutation_p.H44R	NM_005467.3	NP_005458.1	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	44					neurotransmitter catabolic process (GO:0042135)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|N-formylglutamate deformylase activity (GO:0050129)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(32)|pancreas(1)|prostate(3)|skin(5)|stomach(2)	59		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				GTGCGCTATCATCAAAGTATA	0.343																																					p.H44R		Atlas-SNP	.											.	NAALAD2	113	.	0			c.A131G						PASS	.						112	113	112					11																	89868775		2201	4299	6500	SO:0001583	missense	10003	exon2			GCTATCATCAAAG	AJ012370	CCDS8288.1, CCDS73364.1	11q14.3-q21	2011-08-16			ENSG00000077616	ENSG00000077616	3.4.17.21		14526	protein-coding gene	gene with protein product	"glutamate carboxypeptidase III"	611636				10085079	Standard	NM_005467		Approved	NAALADASE2, NAADALASE2, GPCIII	uc001pdf.4	Q9Y3Q0	OTTHUMG00000166368	ENST00000534061.1:c.131A>G	chr11.hg19:g.89868775A>G	ENSP00000432481:p.His44Arg	30.0	0.0	.		58.0	10.0	.	NM_005467	B3KQR4|Q4KKV4|Q4VAM9	Missense_Mutation	SNP	ENST00000534061.1	hg19	CCDS8288.1	.	.	.	.	.	.	.	.	.	.	A	7.614	0.675410	0.14841	.	.	ENSG00000077616	ENST00000525497;ENST00000534061;ENST00000321955;ENST00000525171;ENST00000375944	T;T;T;T;T	0.42513	0.97;1.39;1.53;1.01;2.81	5.08	-0.0308	0.13912	.	0.762404	0.12673	N	0.448598	T	0.21674	0.0522	N	0.20986	0.625	0.09310	N	1	B;B;B;B;B	0.06786	0.0;0.001;0.0;0.001;0.0	B;B;B;B;B	0.08055	0.0;0.003;0.001;0.001;0.0	T	0.18241	-1.0343	9	.	.	.	-1.591	2.7544	0.05289	0.5012:0.285:0.0769:0.1368	.	44;44;44;44;44	Q4KKV4;E9PJV2;Q9Y3Q0;E9PKX5;Q8IUX3	.;.;NALD2_HUMAN;.;.	R	44	ENSP00000431989:H44R;ENSP00000432481:H44R;ENSP00000320083:H44R;ENSP00000435249:H44R;ENSP00000365111:H44R	.	H	+	2	0	NAALAD2	89508423	0.776000	0.28616	0.094000	0.20943	0.701000	0.40568	0.409000	0.21082	-0.159000	0.11021	-0.305000	0.09177	CAT	.	.	.	none		0.343	NAALAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389424.2	NM_005467		G	89868775	A	G	89868775	3	3	78	1	0	0	0	0	1	0	0	0	10135	217	8	3	137	3	NAALAD2	11	89868775	Missense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10	22051345	89868775	45137741	41	5016											
NT5DC3	51559	hgsc.bcm.edu	37	chr12	104182695	104182695	+	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	tctcattcatctttcggaaaGgcctaacaacagaaatggga	14	10	8	9	1	3	1	2	0	2	1	5	3	3	3	1	3	2	0	1	3	4	3			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr12:104182695G>C	ENST00000392876.3	-	10	1062	c.1022C>G	c.(1021-1023)cCt>cGt	p.P341R		NM_001031701.2	NP_001026871.1	Q86UY8	NT5D3_HUMAN	5'-nucleotidase domain containing 3	341						cytosol (GO:0005829)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|ovary(2)|skin(1)|stomach(2)	30						CTTTCGGAAAGGCCTAACAAC	0.423																																					p.P341R		Atlas-SNP	.											.	NT5DC3	113	.	0			c.C1022G						PASS	.						192	183	186					12																	104182695		2203	4300	6503	SO:0001583	missense	51559	exon10			CGGAAAGGCCTAA	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.1022C>G	chr12.hg19:g.104182695G>C	ENSP00000376615:p.Pro341Arg	117.0	0.0	.		106.0	46.0	.	NM_001031701	Q9NUM7|Q9P2T2|Q9P2T3	Missense_Mutation	SNP	ENST00000392876.3	hg19	CCDS41824.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.625073	0.87560	.	.	ENSG00000111696	ENST00000392876	T	0.26223	1.75	6.07	6.07	0.98685	HAD-like domain (1);	0.000000	0.85682	D	0.000000	T	0.59473	0.2196	M	0.86028	2.79	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.60622	-0.7227	10	0.59425	D	0.04	-12.7708	20.6593	0.99626	0.0:0.0:1.0:0.0	.	341	Q86UY8	NT5D3_HUMAN	R	341	ENSP00000376615:P341R	ENSP00000376615:P341R	P	-	2	0	NT5DC3	102706825	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	9.515000	0.98015	2.885000	0.99019	0.655000	0.94253	CCT	.	.	.	none		0.423	NT5DC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347118.2	NM_016575		C	104182695	G	C	104182695	3	2	78	1	0	0	0	0	1	0	0	0	10699	1000	35	4	644	4	NT5DC3	12	104182695	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10		104182695	29669200	42	5017											
C13orf15	28984	hgsc.bcm.edu	37	chr13	42031876	42031876	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcggcgcagggcagccccgcGgccgccgcggccgcaggtga	4	1	19	17	8	0	1	0	1	0	0	0	1	0	1	5	5	1	3	5	5	0	0			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr13:42031876G>A	ENST00000379359.3	+	1	182	c.33G>A	c.(31-33)gcG>gcA	p.A11A		NM_014059.2	NP_054778.2	Q9H4X1	RGCC_HUMAN	regulator of cell cycle	11	Ala-rich.				cellular response to hypoxia (GO:0071456)|complement activation (GO:0006956)|fibroblast activation (GO:0072537)|mitotic cell cycle arrest (GO:0071850)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of exit from mitosis (GO:0001100)|negative regulation of fibroblast growth factor production (GO:0090272)|negative regulation of mitotic cell cycle phase transition (GO:1901991)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|positive regulation of gene expression (GO:0010628)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of mitosis (GO:0045840)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stress fiber assembly (GO:0051496)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|R-SMAD binding (GO:0070412)										gcagccccgcggccgccgcgg	0.741																																					p.A11A		Atlas-SNP	.											.	.	.	.	0			c.G33A						PASS	.						1	1	1					13																	42031876		410	1255	1665	SO:0001819	synonymous_variant	28984	exon1			CCCCGCGGCCGCC	AF036549	CCDS41880.1	13q14.11	2012-02-20	2012-02-20	2012-02-20	ENSG00000102760	ENSG00000102760			20369	protein-coding gene	gene with protein product	"response gene to complement 32"	610077	"chromosome 13 open reading frame 15"	C13orf15		17146433, 19158077, 19652095	Standard	NM_014059		Approved	bA157L14.2, RGC-32, RGC32	uc001uyi.2	Q9H4X1	OTTHUMG00000016796	ENST00000379359.3:c.33G>A	chr13.hg19:g.42031876G>A		0.0	0.0	.		25.0	14.0	.	NM_014059	Q6NZ48|Q9UL69	Silent	SNP	ENST00000379359.3	hg19	CCDS41880.1																																																																																			.	.	.	none		0.741	RGCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044684.1	NM_014059		A	42031876	G	A	42031876	2	1	78	1	0	0	0	0	0	0	0	1	1720	1103	39	1		1	C13orf15	13	42031876	Silent	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10		42031876	73138002	43	5018											
NKX2-1	7080	hgsc.bcm.edu	37	chr14	36988288	36988288	+	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	gcggcagctcgctcatgttgCccaggttgccgttgcagtag	5	10	14	12	3	1	0	1	0	0	0	2	0	1	0	2	2	4	8	2	2	1	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr14:36988288C>A	ENST00000518149.1	-	2	880	c.275G>T	c.(274-276)gGc>gTc	p.G92V	NKX2-1_ENST00000354822.5_Missense_Mutation_p.G122V|NKX2-1-AS1_ENST00000521292.2_RNA|RP11-896J10.3_ENST00000521945.1_RNA|NKX2-1_ENST00000522719.2_Missense_Mutation_p.G92V|NKX2-1_ENST00000498187.2_Missense_Mutation_p.G92V			P43699	NKX21_HUMAN	NK2 homeobox 1	92					anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|brain development (GO:0007420)|cerebral cortex cell migration (GO:0021795)|cerebral cortex GABAergic interneuron differentiation (GO:0021892)|Clara cell differentiation (GO:0060486)|developmental induction (GO:0031128)|endoderm development (GO:0007492)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|forebrain development (GO:0030900)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain neuron fate commitment (GO:0021877)|globus pallidus development (GO:0021759)|hippocampus development (GO:0021766)|Leydig cell differentiation (GO:0033327)|locomotory behavior (GO:0007626)|lung development (GO:0030324)|lung saccule development (GO:0060430)|menarche (GO:0042696)|negative regulation of cell migration (GO:0030336)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|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 migration (GO:0001764)|oligodendrocyte differentiation (GO:0048709)|phospholipid metabolic process (GO:0006644)|pituitary gland development (GO:0021983)|positive regulation of circadian rhythm (GO:0042753)|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)|response to hormone (GO:0009725)|rhythmic process (GO:0048511)|thyroid gland development (GO:0030878)|Type II pneumocyte differentiation (GO:0060510)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|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)	p.G92D(1)		large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(2)	7	all_cancers(3;4.47e-51)|Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)|Breast(36;0.165)		Lung(8;1.8e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.014)|all cancers(34;0.0366)|LUSC - Lung squamous cell carcinoma(13;0.132)	GBM - Glioblastoma multiforme(112;0.0171)		GCTCATGTTGCCCAGGTTGCC	0.716			A		NSCLC																																p.G122V		Atlas-SNP	.		Dom	yes		14	14q13	7080	NK2 homeobox 1		E	NKX2-1,NS,malignant_melanoma,0,1	NKX2-1	21	.	1	Substitution - Missense(1)	skin(1)	c.G365T						PASS	.						10	14	13					14																	36988288		2088	4220	6308	SO:0001583	missense	7080	exon2			ATGTTGCCCAGGT		CCDS9659.1, CCDS41945.1	14q13.3	2012-03-09	2007-07-26	2007-07-26	ENSG00000136352	ENSG00000136352		"Homeoboxes / ANTP class : NKL subclass"	11825	protein-coding gene	gene with protein product		600635	"benign chorea", "thyroid transcription factor 1"	NKX2A, BCH, TITF1		1976511	Standard	NM_001079668		Approved	TTF-1, TTF1	uc001wtu.3	P43699	OTTHUMG00000140225	ENST00000518149.1:c.275G>T	chr14.hg19:g.36988288C>A	ENSP00000428341:p.Gly92Val	5.0	1.0	.		26.0	13.0	.	NM_001079668	D3DSA3|O14954|O14955|Q7KZF6|Q9BRJ8	Missense_Mutation	SNP	ENST00000518149.1	hg19	CCDS9659.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.357912	0.82243	.	.	ENSG00000136352	ENST00000354822;ENST00000498187;ENST00000518149;ENST00000522719	D;D;D;D	0.91521	-2.86;-2.82;-2.82;-2.82	4.7	4.7	0.59300	.	0.056339	0.64402	D	0.000001	D	0.94843	0.8334	M	0.84683	2.71	0.80722	D	1	D;P	0.57257	0.979;0.935	P;P	0.59546	0.859;0.544	D	0.94962	0.8109	10	0.49607	T	0.09	.	16.7821	0.85565	0.0:1.0:0.0:0.0	.	122;92	P43699-3;P43699	.;NKX21_HUMAN	V	122;92;92;92	ENSP00000346879:G122V;ENSP00000429607:G92V;ENSP00000428341:G92V;ENSP00000429519:G92V	ENSP00000346879:G122V	G	-	2	0	NKX2-1	36058039	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.934000	0.75880	2.442000	0.82660	0.455000	0.32223	GGC	.	.	.	none		0.716	NKX2-1-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376225.2	NM_003317		A	36988288	C	A	36988288	3	1	78	1	0	0	0	0	1	0	0	0	10456	739	26	4	848	4	NKX2-1	14	36988288	Missense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10		36988288	70361252	44	5019											
ARID4A	5926	hgsc.bcm.edu	37	chr14	58796735	58796735	+	Missense_Mutation	SNP	A	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	tcttagggcttcagaaagcaAgcatcttcttaaaaactaga	15	11	7	8	0	4	2	1	0	3	2	4	2	4	2	0	1	3	3	0	1	7	5			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr14:58796735A>C	ENST00000355431.3	+	11	1127	c.754A>C	c.(754-756)Agc>Cgc	p.S252R	ARID4A_ENST00000431317.2_Missense_Mutation_p.S252R|ARID4A_ENST00000395168.3_Missense_Mutation_p.S252R|ARID4A_ENST00000348476.3_Missense_Mutation_p.S252R	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	252					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						TCAGAAAGCAAGCATCTTCTT	0.388																																					p.S252R		Atlas-SNP	.											.	ARID4A	222	.	0			c.A754C						PASS	.						97	104	101					14																	58796735		2203	4300	6503	SO:0001583	missense	5926	exon11			AAAGCAAGCATCT	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.754A>C	chr14.hg19:g.58796735A>C	ENSP00000347602:p.Ser252Arg	171.0	0.0	.		151.0	66.0	.	NM_002892	Q15991|Q15992|Q15993	Missense_Mutation	SNP	ENST00000355431.3	hg19	CCDS9732.1	.	.	.	.	.	.	.	.	.	.	A	17.03	3.284422	0.59867	.	.	ENSG00000032219	ENST00000355431;ENST00000348476;ENST00000395168;ENST00000445108;ENST00000431317	T;T;T;T	0.14391	2.51;2.51;2.51;2.51	6.07	4.94	0.65067	RBB1NT (1);	0.208574	0.64402	D	0.000015	T	0.24851	0.0603	L	0.57536	1.79	0.39498	D	0.96815	P;B;P	0.46277	0.875;0.139;0.702	P;B;P	0.52454	0.699;0.394;0.556	T	0.01420	-1.1359	10	0.42905	T	0.14	-12.6657	12.3445	0.55114	0.9343:0.0:0.0657:0.0	.	252;252;252	P29374-3;P29374;P29374-2	.;ARI4A_HUMAN;.	R	252;252;252;215;252	ENSP00000347602:S252R;ENSP00000344556:S252R;ENSP00000378597:S252R;ENSP00000397368:S252R	ENSP00000344556:S252R	S	+	1	0	ARID4A	57866488	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.593000	0.54001	1.112000	0.41740	-0.274000	0.10170	AGC	.	.	.	none		0.388	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001		C	58796735	A	C	58796735	3	2	78	1	0	0	0	0	1	0	0	0	919	72	3	5	792	5	ARID4A	14	58796735	Missense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10	21808447	58796735	48552805	45	5020											
TTC8	123016	hgsc.bcm.edu	37	chr14	89338717	89338717	+	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	ccatcagtgcttcaggctggCtctggtcaacaacaacaacc	11	8	8	14	0	4	0	3	0	1	0	4	0	4	0	2	3	5	3	2	3	4	1			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr14:89338717C>T	ENST00000345383.5	+	12	1322	c.1238C>T	c.(1237-1239)gCt>gTt	p.A413V	TTC8_ENST00000358622.5_Missense_Mutation_p.A225V|TTC8_ENST00000536576.1_Missense_Mutation_p.A184V|TTC8_ENST00000338104.6_Missense_Mutation_p.A439V|TTC8_ENST00000354441.6_Missense_Mutation_p.A158V|TTC8_ENST00000380656.2_Missense_Mutation_p.A423V|TTC8_ENST00000346301.4_Missense_Mutation_p.A383V	NM_198309.2	NP_938051.1	Q8TAM2	TTC8_HUMAN	tetratricopeptide repeat domain 8	449					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						TTCAGGCTGGCTCTGGTCAAC	0.532																																					p.A423V		Atlas-SNP	.											.	TTC8	42	.	0			c.C1268T						PASS	.						123	105	111					14																	89338717		2203	4300	6503	SO:0001583	missense	123016	exon13			GGCTGGCTCTGGT	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.1238C>T	chr14.hg19:g.89338717C>T	ENSP00000339486:p.Ala413Val	138.0	0.0	.		122.0	58.0	.	NM_144596	A6NFG2|B3KWA5|Q67B97|Q86SY0|Q86TV9|Q86U26|Q8NDH9|Q96DG8	Missense_Mutation	SNP	ENST00000345383.5	hg19	CCDS9885.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.2|28.2	4.900692|4.900692	0.92035|0.92035	.|.	.|.	ENSG00000165533|ENSG00000165533	ENST00000345383;ENST00000536576;ENST00000346301;ENST00000338104;ENST00000354441;ENST00000380656;ENST00000358622|ENST00000554686	T;T;T;T;T;T;T|.	0.74106|.	-0.81;-0.81;-0.81;-0.81;-0.81;-0.81;-0.81|.	5.59|5.59	5.59|5.59	0.84812|0.84812	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);|.	0.101143|.	0.64402|.	D|.	0.000002|.	D|D	0.85733|0.85733	0.5765|0.5765	M|M	0.89904|0.89904	3.07|3.07	0.58432|0.58432	D|D	0.999999|0.999999	P;P;P;P;P|.	0.48089|.	0.905;0.604;0.885;0.55;0.685|.	P;B;P;B;B|.	0.47346|.	0.544;0.394;0.492;0.382;0.382|.	D|D	0.87391|0.87391	0.2363|0.2363	10|5	0.41790|.	T|.	0.15|.	-15.7808|-15.7808	19.96|19.96	0.97242|0.97242	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	158;184;449;393;423|.	Q8TAM2-2;B3KSL8;Q8TAM2;Q8TAM2-3;Q8TAM2-4|.	.;.;TTC8_HUMAN;.;.|.	V|F	413;184;383;439;158;423;225|373	ENSP00000339486:A413V;ENSP00000445067:A184V;ENSP00000298324:A383V;ENSP00000337653:A439V;ENSP00000346427:A158V;ENSP00000370031:A423V;ENSP00000351439:A225V|.	ENSP00000337653:A439V|.	A|L	+|+	2|1	0|0	TTC8|TTC8	88408470|88408470	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	5.670000|5.670000	0.68088|0.68088	2.793000|2.793000	0.96121|0.96121	0.561000|0.561000	0.74099|0.74099	GCT|CTC	.	.	.	none		0.532	TTC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410861.1	NM_144596		T	89338717	C	T	89338717	3	4	78	1	0	0	0	0	1	0	0	0	16726	797	28	2	1318	2	TTC8	14	89338717	Missense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	30541982	89338717	18010823	46	5021											
TRPM1	4308	hgsc.bcm.edu	37	chr15	31342655	31342655	+	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	gggggtcagtttcttcctccActtcctctttcactttccct	3	17	6	15	0	4	0	2	0	2	0	8	0	8	0	4	2	0	1	4	2	0	5			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr15:31342655A>T	ENST00000256552.6	-	12	1541	c.1394T>A	c.(1393-1395)gTg>gAg	p.V465E	TRPM1_ENST00000542188.1_Missense_Mutation_p.V482E|TRPM1_ENST00000397795.2_Missense_Mutation_p.V443E	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)		Ttcttcctccacttcctcttt	0.542																																					p.V482E		Atlas-SNP	.											.	TRPM1	183	.	0			c.T1445A						PASS	.						208	217	214					15																	31342655		2000	4152	6152	SO:0001583	missense	4308	exon11			TCCTCCACTTCCT	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.1394T>A	chr15.hg19:g.31342655A>T	ENSP00000256552:p.Val465Glu	117.0	0.0	.		100.0	38.0	.	NM_001252020		Missense_Mutation	SNP	ENST00000256552.6	hg19	CCDS58346.1	.	.	.	.	.	.	.	.	.	.	A	3.172	-0.169735	0.06461	.	.	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	T;T;T	0.72051	-0.62;-0.62;-0.62	4.8	-0.746	0.11095	.	0.495264	0.20727	N	0.086800	T	0.44074	0.1276	N	0.08118	0	0.09310	N	1	B;B	0.12013	0.005;0.003	B;B	0.12156	0.007;0.003	T	0.29822	-0.9999	10	0.66056	D	0.02	-6.1648	5.5491	0.17081	0.5174:0.0:0.3552:0.1273	.	437;443	Q7Z4N2-3;Q7Z4N2	.;TRPM1_HUMAN	E	443;482;465;443	ENSP00000380897:V443E;ENSP00000437849:V482E;ENSP00000256552:V465E	ENSP00000256552:V465E	V	-	2	0	TRPM1	29129947	0.010000	0.17322	0.812000	0.32479	0.123000	0.20343	0.172000	0.16704	-0.389000	0.07786	-1.843000	0.00578	GTG	.	.	.	none		0.542	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420		T	31342655	A	T	31342655	3	4	78	1	0	0	0	0	1	0	0	0	16597	159	6	5	3551	5	TRPM1	15	31342655	Missense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10		31342655	71188737	47	5022											
AQR	9716	hgsc.bcm.edu	37	chr15	35189882	35189882	+	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	tctttccttttcttccctttTccacttcttactggaaaagt	6	20	3	12	0	3	0	0	0	3	0	6	1	6	1	3	1	1	0	3	1	3	8			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr15:35189882T>G	ENST00000156471.5	-	21	2493	c.2268A>C	c.(2266-2268)ggA>ggC	p.G756G		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	756					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		TCTTCCCTTTTCCACTTCTTA	0.393																																					p.G756G		Atlas-SNP	.											.	AQR	139	.	0			c.A2268C						PASS	.						111	102	105					15																	35189882		1844	4108	5952	SO:0001819	synonymous_variant	9716	exon21			CCCTTTTCCACTT	AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 164"	610548	"aquarius homolog (mouse)"			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.2268A>C	chr15.hg19:g.35189882T>G		63.0	0.0	.		79.0	30.0	.	NM_014691	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Silent	SNP	ENST00000156471.5	hg19	CCDS42013.1																																																																																			.	.	.	none		0.393	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691		G	35189882	T	G	35189882	2	3	78	1	0	0	0	0	0	0	0	1	835	1770	62	5		5	AQR	15	35189882	Silent	SNP	T	TCGA-AT-A5NU-01A-11D-A28G-10	3847227	35189882	67341510	48	5023											
CDH11	1009	hgsc.bcm.edu	37	chr16	64981793	64981793	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagcccaggtctaggcatgtActgatactcaggtttgatgt	9	12	12	8	0	2	2	1	2	1	0	2	3	2	2	1	3	3	3	1	3	3	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr16:64981793A>G	ENST00000268603.4	-	13	2719	c.2104T>C	c.(2104-2106)Tac>Cac	p.Y702H	CDH11_ENST00000394156.3_3'UTR|CDH11_ENST00000566827.1_Missense_Mutation_p.Y576H	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	702					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.Y702H(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		CTAGGCATGTACTGATACTCA	0.522			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																											p.Y702H		Atlas-SNP	.		Dom	yes		16	16q22.1	1009	"cadherin 11, type 2, OB-cadherin (osteoblast)"		M	CDH11,colon,carcinoma,0,1	CDH11	260	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2104C						PASS	.						135	128	130					16																	64981793		2203	4300	6503	SO:0001583	missense	1009	exon13			GCATGTACTGATA	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.2104T>C	chr16.hg19:g.64981793A>G	ENSP00000268603:p.Tyr702His	106.0	0.0	.		223.0	117.0	.	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Missense_Mutation	SNP	ENST00000268603.4	hg19	CCDS10803.1	.	.	.	.	.	.	.	.	.	.	A	15.04	2.715271	0.48622	.	.	ENSG00000140937	ENST00000268603;ENST00000538390	T	0.76060	-0.99	6.17	6.17	0.99709	Cadherin, cytoplasmic domain (1);	0.054697	0.85682	D	0.000000	T	0.76054	0.3934	L	0.31926	0.97	0.80722	D	1	D	0.55800	0.973	P	0.59115	0.852	T	0.71182	-0.4668	10	0.15499	T	0.54	.	16.0034	0.80327	1.0:0.0:0.0:0.0	.	702	P55287	CAD11_HUMAN	H	702;685	ENSP00000268603:Y702H	ENSP00000268603:Y702H	Y	-	1	0	CDH11	63539294	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.371000	0.80710	0.533000	0.62120	TAC	.	.	.	none		0.522	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664		G	64981793	A	G	64981793	3	3	78	1	0	0	0	0	1	0	0	0	3099	391	14	3	290	3	CDH11	16	64981793	Missense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10		64981793	25372960	49	5024											
SERPINF1	5176	hgsc.bcm.edu	37	chr17	1679947	1679953	+	Frame_Shift_Del	DEL	GAGAACT	GAGAACT	-																															gttcattcatgacatagaccGagaactgaagaccgtgcagg																								rs146939364	byFrequency	TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	GAGAACT	GAGAACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr17:1679947_1679953delGAGAACT	ENST00000254722.4	+	7	1071_1077	c.908_914delGAGAACT	c.(907-915)cgagaactgfs	p.REL303fs		NM_002615.5	NP_002606.3	P36955	PEDF_HUMAN	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1	303					aging (GO:0007568)|cell proliferation (GO:0008283)|kidney development (GO:0001822)|multicellular organismal development (GO:0007275)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of inflammatory response (GO:0050728)|positive regulation of neurogenesis (GO:0050769)|regulation of proteolysis (GO:0030162)|response to glucocorticoid (GO:0051384)|response to retinoic acid (GO:0032526)|short-term memory (GO:0007614)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.L305V(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	16						GACATAGACCGAGAACTGAAGACCGTG	0.512																																					p.303_305del		Atlas-Indel,Pindel	.											.	SERPINF1	31	.	1	Substitution - Missense(1)	stomach(1)	c.907_913del						PASS	.																																			SO:0001589	frameshift_variant	5176	exon7			.	M76979	CCDS11012.1	17p13.3	2014-02-18	2005-08-18		ENSG00000132386	ENSG00000132386		"Serine (or cysteine) peptidase inhibitors"	8824	protein-coding gene	gene with protein product	"pigment epithelium-derived factor", "proliferation-inducing protein 35"	172860	"serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1"	PEDF		8434014, 24172014	Standard	NM_002615		Approved	EPC-1, PIG35	uc002ftl.3	P36955	OTTHUMG00000090571	ENST00000254722.4:c.908_914delGAGAACT	chr17.hg19:g.1679947_1679953delGAGAACT	ENSP00000254722:p.Arg303fs	137.0	0.0	0		133.0	60.0	0.451128	NM_002615	F1T092|Q13236|Q2TU83|Q96CT1|Q96R01|Q9BWA4	Frame_Shift_Del	DEL	ENST00000254722.4	hg19	CCDS11012.1																																																																																			.	.	.	none		0.512	SERPINF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207109.4	NM_002615		-	1679953	GAGAACT	-	1679947	7	5	78	1	0	1	0	1	0	0	0	0	14127	1058	37	0	930	0	SERPINF1	17	1679947	Frame_Shift_Del	DEL	GAGAACT	TCGA-AT-A5NU-01A-11D-A28G-10		1679947	79515263	50	5025											
WDR16	146845	hgsc.bcm.edu	37	chr17	9501596	9501596	+	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	gatcttccaaatagaaaaatCtggccaactgagtgccaaac	16	8	7	10	0	2	2	0	1	2	1	3	3	3	2	3	1	3	0	3	1	6	2			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr17:9501596C>A	ENST00000352665.5	+	5	651	c.582C>A	c.(580-582)atC>atA	p.I194I	WDR16_ENST00000299764.5_Silent_p.I204I|WDR16_ENST00000396219.3_Silent_p.I126I	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						ATAGAAAAATCTGGCCAACTG	0.328																																					p.I194I		Atlas-SNP	.											.	WDR16	67	.	0			c.C582A						PASS	.						92	98	96					17																	9501596		2203	4300	6503	SO:0001819	synonymous_variant	146845	exon5			AAAAATCTGGCCA	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.582C>A	chr17.hg19:g.9501596C>A		31.0	0.0	.		54.0	14.0	.	NM_145054		Silent	SNP	ENST00000352665.5	hg19	CCDS11149.2																																																																																			.	.	.	none		0.328	WDR16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316569.2	NM_145054		A	9501596	C	A	9501596	2	1	78	1	0	0	0	0	0	0	0	1	17288	903	32	4		4	WDR16	17	9501596	Silent	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	7821649	9501596	71693614	51	5026											
MFSD11	79157	hgsc.bcm.edu	37	chr17	74738356	74738356	+	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	tgggcacttctgcagtctagGtaattatccttttgaggttc	7	16	10	8	0	2	1	0	1	2	0	4	1	3	1	1	3	1	4	1	3	3	7			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr17:74738356G>A	ENST00000588460.1	+	5	2479		c.e5+1		MFSD11_ENST00000355954.3_Intron|MFSD11_ENST00000586622.1_Splice_Site|MFSD11_ENST00000590514.1_Splice_Site|MFSD11_ENST00000336509.4_Splice_Site|MFSD11_ENST00000593181.1_Intron	NM_001242534.1	NP_001229463.1	O43934	MFS11_HUMAN	major facilitator superfamily domain containing 11							integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)	17						TGCAGTCTAGGTAATTATCCT	0.403																																					.		Atlas-SNP	.											.	MFSD11	47	.	0			c.437+1G>A						PASS	.						140	140	140					17																	74738356		2203	4300	6503	SO:0001630	splice_region_variant	79157	exon6			GTCTAGGTAATTA	BC002753	CCDS11750.1, CCDS56045.1	17q25.1	2012-03-09			ENSG00000092931	ENSG00000092931			25458	protein-coding gene	gene with protein product						9358160	Standard	NM_001242532		Approved	FLJ22196, FLJ20226	uc002jte.3	O43934		ENST00000588460.1:c.437+1G>A	chr17.hg19:g.74738356G>A		120.0	0.0	.		180.0	10.0	.	NM_001242534	O43442|Q9NXI5	Splice_Site	SNP	ENST00000588460.1	hg19	CCDS11750.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.234688	0.79800	.	.	ENSG00000092931	ENST00000336509	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.9326	0.97124	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MFSD11	72249951	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	9.471000	0.97696	2.720000	0.93068	0.650000	0.86243	.	.	.	.	none		0.403	MFSD11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451516.1	NM_024311	Intron	A	74738356	G	A	74738356	5	1	78	1	0	0	0	0	0	0	1	0	9536	1275	44	2	456	2	MFSD11	17	74738356	Splice_Site	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	65236760	74738356	6456854	52	5027											
CABLES1	91768	hgsc.bcm.edu	37	chr18	20768825	20768825	+	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	gcgcctcatctcccagagatCttccttggagaccctggaag	8	9	10	14	1	3	2	1	0	2	2	5	5	4	3	4	2	0	0	4	2	1	2			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr18:20768825C>T	ENST00000256925.7	+	2	869	c.869C>T	c.(868-870)tCt>tTt	p.S290F	CABLES1_ENST00000400473.2_5'UTR|CABLES1_ENST00000420687.2_Missense_Mutation_p.S25F|CABLES1_ENST00000585061.1_3'UTR	NM_001100619.2	NP_001094089.1	Q8TDN4	CABL1_HUMAN	Cdk5 and Abl enzyme substrate 1	290	Interacts with CDK3. {ECO:0000250}.				blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|nervous system development (GO:0007399)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)	cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			breast(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|stomach(1)	11	all_cancers(21;0.000102)|all_epithelial(16;2.48e-06)|Lung NSC(20;0.00696)|all_lung(20;0.0197)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TCCCAGAGATCTTCCTTGGAG	0.433																																					p.S290F		Atlas-SNP	.											.	CABLES1	32	.	0			c.C869T						PASS	.						67	63	64					18																	20768825		1814	4069	5883	SO:0001583	missense	91768	exon2			AGAGATCTTCCTT	BC037218	CCDS42417.1, CCDS42418.1, CCDS58615.1	18q11.2	2005-08-16				ENSG00000134508			25097	protein-coding gene	gene with protein product		609194				12477932	Standard	NM_138375		Approved	HsT2563, FLJ35924	uc002kuc.2	Q8TDN4		ENST00000256925.7:c.869C>T	chr18.hg19:g.20768825C>T	ENSP00000256925:p.Ser290Phe	29.0	0.0	.		24.0	7.0	.	NM_001100619	B4DK60|Q8N3Y8|Q8NA22|Q9BTG1	Missense_Mutation	SNP	ENST00000256925.7	hg19	CCDS42417.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.817292	0.90790	.	.	ENSG00000134508	ENST00000256925;ENST00000420687	T;T	0.50548	0.74;0.78	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.65091	0.2658	L	0.47716	1.5	0.80722	D	1	D;D	0.76494	0.994;0.999	D;D	0.83275	0.989;0.996	T	0.66705	-0.5856	10	0.87932	D	0	-11.7652	19.4124	0.94679	0.0:1.0:0.0:0.0	.	25;290	Q8TDN4-2;Q8TDN4	.;CABL1_HUMAN	F	290;25	ENSP00000256925:S290F;ENSP00000413851:S25F	ENSP00000256925:S290F	S	+	2	0	CABLES1	19022823	1.000000	0.71417	0.958000	0.39756	0.852000	0.48524	7.345000	0.79337	2.595000	0.87683	0.556000	0.70494	TCT	.	.	.	none		0.433	CABLES1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445198.2	NM_138375		T	20768825	C	T	20768825	3	4	78	1	0	0	0	0	1	0	0	0	2531	913	32	2	929	2	CABLES1	18	20768825	Missense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10		20768825	57308423	53	5028											
FHOD3	80206	hgsc.bcm.edu	37	chr18	34310626	34310626	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaaaactgctgcagatggAaaaaggcaagagatcattgt	18	7	11	5	0	1	3	1	0	0	3	1	5	1	4	0	2	3	3	0	2	6	1			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr18:34310626A>G	ENST00000359247.4	+	16	2859	c.2859A>G	c.(2857-2859)ggA>ggG	p.G953G	FHOD3_ENST00000257209.4_Silent_p.G970G|FHOD3_ENST00000590592.1_Silent_p.G1145G|FHOD3_ENST00000592128.1_5'UTR|FHOD3_ENST00000445677.1_Silent_p.G932G|FHOD3_ENST00000591635.1_Silent_p.G166G	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	953	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				CTGCAGATGGAAAAAGGCAAG	0.413																																					p.G970G		Atlas-SNP	.											.	FHOD3	210	.	0			c.A2910G						PASS	.						113	105	108					18																	34310626		2203	4300	6503	SO:0001819	synonymous_variant	80206	exon17			AGATGGAAAAAGG	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.2859A>G	chr18.hg19:g.34310626A>G		79.0	0.0	.		85.0	4.0	.	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Silent	SNP	ENST00000359247.4	hg19																																																																																				.	.	.	none		0.413	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		G	34310626	A	G	34310626	2	3	78	1	0	0	0	0	0	0	0	1	5890	233	9	3		3	FHOD3	18	34310626	Silent	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10	13541801	34310626	43766622	54	5029											
ABCA7	10347	hgsc.bcm.edu	37	chr19	1041554	1041554	+	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	ggcctctcttcctcttcttcAtcctggtggctgttcgccac	2	15	8	16	1	4	0	1	0	3	0	8	0	6	0	4	3	0	2	4	3	0	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr19:1041554A>T	ENST00000263094.6	+	3	343	c.112A>T	c.(112-114)Atc>Ttc	p.I38F	AC011558.5_ENST00000585757.1_RNA|ABCA7_ENST00000433129.1_Missense_Mutation_p.I38F|ABCA7_ENST00000435683.2_5'Flank	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	38					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)		CCTCTTCTTCATCCTGGTGGC	0.637																																					p.I38F		Atlas-SNP	.											.	ABCA7	174	.	0			c.A112T						PASS	.						103	107	106					19																	1041554		2203	4300	6503	SO:0001583	missense	10347	exon3			TTCTTCATCCTGG	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.112A>T	chr19.hg19:g.1041554A>T	ENSP00000263094:p.Ile38Phe	26.0	0.0	.		25.0	9.0	.	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	hg19	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	A	29.2	4.986185	0.93044	.	.	ENSG00000064687	ENST00000263094;ENST00000524850;ENST00000531467;ENST00000433129	D;D;D;D	0.99194	-5.54;-5.54;-5.54;-5.54	4.78	4.78	0.61160	.	.	.	.	.	D	0.98839	0.9608	L	0.53729	1.69	0.47905	D	0.999542	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.997	D	0.99744	1.1016	9	0.87932	D	0	.	12.2354	0.54512	1.0:0.0:0.0:0.0	.	38;38	B4DVJ5;Q8IZY2	.;ABCA7_HUMAN	F	38;38;36;38	ENSP00000263094:I38F;ENSP00000431473:I38F;ENSP00000433545:I36F;ENSP00000414062:I38F	ENSP00000263094:I38F	I	+	1	0	ABCA7	992554	1.000000	0.71417	1.000000	0.80357	0.676000	0.39594	5.979000	0.70508	1.794000	0.52575	0.460000	0.39030	ATC	.	.	.	none		0.637	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		T	1041554	A	T	1041554	3	4	78	1	0	0	0	0	1	0	0	0	37	217	8	5	118	5	ABCA7	19	1041554	Missense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10		1041554	58087429	55	5030											
EVI5L	115704	hgsc.bcm.edu	37	chr19	7927064	7927064	+	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	ccacggaagctggtcgtgggCgagctgcaggacgagctgat	8	6	17	10	4	0	1	0	1	0	0	1	5	0	3	1	4	4	4	1	4	1	0			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr19:7927064C>T	ENST00000270530.4	+	15	1864	c.1668C>T	c.(1666-1668)ggC>ggT	p.G556G	EVI5L_ENST00000538904.2_Silent_p.G567G	NM_145245.3	NP_660288.1	Q96CN4	EVI5L_HUMAN	ecotropic viral integration site 5-like	556					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						TGGTCGTGGGCGAGCTGCAGG	0.731																																					p.G567G		Atlas-SNP	.											.	EVI5L	43	.	0			c.C1701T						PASS	.						5	6	6					19																	7927064		2077	4154	6231	SO:0001819	synonymous_variant	115704	exon15			CGTGGGCGAGCTG	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.1668C>T	chr19.hg19:g.7927064C>T		4.0	0.0	.		15.0	10.0	.	NM_001159944	B9A6I9	Silent	SNP	ENST00000270530.4	hg19	CCDS12188.1																																																																																			.	.	.	none		0.731	EVI5L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461347.1	NM_145245		T	7927064	C	T	7927064	2	4	78	1	0	0	0	0	0	0	0	1	5292	755	27	1		1	EVI5L	19	7927064	Silent	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	6885510	7927064	51201919	56	5031											
TSHZ3	57616	hgsc.bcm.edu	37	chr19	31768208	31768208	+	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	cgagtttgacatgaatgataCgacggcagatgtctttgccg	10	11	12	8	4	1	4	0	3	1	1	1	6	1	4	1	1	2	2	1	1	2	3	rs201694059		TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr19:31768208C>T	ENST00000240587.4	-	2	2818	c.2491G>A	c.(2491-2493)Gta>Ata	p.V831I		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	831					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)					ATGAATGATACGACGGCAGAT	0.527													C|||	1	0.000199681	0	0	5008	,	,		19141	0.001		0	False		,,,				2504	0				p.V831I		Atlas-SNP	.											.	TSHZ3	549	.	0			c.G2491A						PASS	.						143	130	135					19																	31768208		2203	4300	6503	SO:0001583	missense	57616	exon2			ATGATACGACGGC	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.2491G>A	chr19.hg19:g.31768208C>T	ENSP00000240587:p.Val831Ile	199.0	0.0	.		199.0	81.0	.	NM_020856	Q9H0G6|Q9P254	Missense_Mutation	SNP	ENST00000240587.4	hg19	CCDS12421.2	.	.	.	.	.	.	.	.	.	.	C	14.20	2.465152	0.43839	.	.	ENSG00000121297	ENST00000240587	T	0.11930	2.73	5.37	4.32	0.51571	.	0.118294	0.56097	D	0.000026	T	0.07593	0.0191	N	0.08118	0	0.48040	D	0.999571	B	0.21452	0.056	B	0.16722	0.016	T	0.33420	-0.9869	10	0.23302	T	0.38	-9.1996	14.4459	0.67349	0.0:0.9276:0.0:0.0723	.	831	Q63HK5	TSH3_HUMAN	I	831	ENSP00000240587:V831I	ENSP00000240587:V831I	V	-	1	0	TSHZ3	36460048	1.000000	0.71417	0.961000	0.40146	0.937000	0.57800	5.745000	0.68672	2.501000	0.84356	0.655000	0.94253	GTA	.	C|0.999;A|0.001	.	alt		0.527	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		T	31768208	C	T	31768208	3	4	78	1	0	0	0	0	1	0	0	0	16637	536	19	1	758	1	TSHZ3	19	31768208	Missense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	23841144	31768208	27360775	57	5032											
ZNF181	339318	hgsc.bcm.edu	37	chr19	35231657	35231657	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taagaagaatttggaatataTagagaagttggaagggaagc	18	9	13	1	0	0	3	0	0	0	3	0	7	0	6	0	3	1	1	0	3	10	6			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr19:35231657T>C	ENST00000492450.1	+	4	460	c.371T>C	c.(370-372)aTa>aCa	p.I124T	ZNF181_ENST00000459757.2_Missense_Mutation_p.I123T|ZNF181_ENST00000392232.3_Missense_Mutation_p.I168T			Q2M3W8	ZN181_HUMAN	zinc finger protein 181	124					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)			TTGGAATATATAGAGAAGTTG	0.348																																					p.I124T		Atlas-SNP	.											.	ZNF181	65	.	0			c.T371C						PASS	.						45	50	48					19																	35231657		2194	4294	6488	SO:0001583	missense	339318	exon4			AATATATAGAGAA	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.371T>C	chr19.hg19:g.35231657T>C	ENSP00000420727:p.Ile124Thr	103.0	0.0	.		107.0	29.0	.	NM_001029997	B7ZKX3|Q49A75	Missense_Mutation	SNP	ENST00000492450.1	hg19	CCDS32990.2	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.579817	0.00129	.	.	ENSG00000197841	ENST00000392232;ENST00000425140;ENST00000492450;ENST00000459757	T;T;T	0.05717	3.4;3.49;3.46	2.89	-0.737	0.11129	.	.	.	.	.	T	0.04182	0.0116	L	0.38175	1.15	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.002	T	0.46119	-0.9214	9	0.23302	T	0.38	.	1.2006	0.01884	0.1774:0.117:0.3517:0.3539	.	123;124	B7ZKX3;Q2M3W8	.;ZN181_HUMAN	T	168;123;124;123	ENSP00000376065:I168T;ENSP00000420727:I124T;ENSP00000419435:I123T	ENSP00000376065:I168T	I	+	2	0	ZNF181	39923497	0.286000	0.24305	0.000000	0.03702	0.058000	0.15608	0.956000	0.29202	-0.238000	0.09724	-0.512000	0.04463	ATA	.	.	.	none		0.348	ZNF181-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349005.3	NM_001029997		C	35231657	T	C	35231657	3	2	78	1	0	0	0	0	1	0	0	0	17761	1406	49	3	385	3	ZNF181	19	35231657	Missense_Mutation	SNP	T	TCGA-AT-A5NU-01A-11D-A28G-10	3463449	35231657	23897326	58	5033											
CATSPERG	57828	hgsc.bcm.edu	37	chr19	38850108	38850108	+	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	ctctccatctctgtccctgcAgctctaacaaggaaaacttc	10	11	5	15	0	3	0	0	0	3	0	7	1	4	1	2	1	4	2	2	1	4	2			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr19:38850108A>T	ENST00000409235.3	+	14	1611		c.e14-1		CATSPERG_ENST00000410018.1_Splice_Site|CATSPERG_ENST00000215069.4_Intron|AC005625.1_ENST00000590304.1_RNA	NM_021185.4	NP_067008.3	Q6ZRH7	CTSRG_HUMAN	catsper channel auxiliary subunit gamma						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						CTGTCCCTGCAGCTCTAACAA	0.527																																					.		Atlas-SNP	.											.	CATSPERG	121	.	0			c.1497-2A>T						PASS	.						75	61	66					19																	38850108		2203	4300	6503	SO:0001630	splice_region_variant	57828	exon14			CCCTGCAGCTCTA	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.1497-1A>T	chr19.hg19:g.38850108A>T		88.0	0.0	.		69.0	33.0	.	NM_021185	A6NEG6|Q659E1	Splice_Site	SNP	ENST00000409235.3	hg19	CCDS12514.2	.	.	.	.	.	.	.	.	.	.	A	14.07	2.426002	0.43020	.	.	ENSG00000099338	ENST00000410018;ENST00000409235;ENST00000409410	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.1118	0.53844	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CATSPERG	43541948	1.000000	0.71417	0.268000	0.24571	0.124000	0.20399	5.184000	0.65070	2.172000	0.68678	0.533000	0.62120	.	.	.	.	none		0.527	CATSPERG-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330204.1	NM_021185	Intron	T	38850108	A	T	38850108	5	4	78	1	0	0	0	0	0	0	1	0	2694	202	7	5	1545	5	CATSPERG	19	38850108	Splice_Site	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10	3618451	38850108	20278875	59	5034											
SUPT5H	6829	hgsc.bcm.edu	37	chr19	39966780	39966780	+	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	gttgtcagcatttccagtgaGcacctggagcctatcacccc	8	10	9	14	0	2	1	2	1	0	0	3	2	3	2	5	1	3	3	5	1	1	3			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr19:39966780G>C	ENST00000599117.1	+	30	3451	c.3084G>C	c.(3082-3084)gaG>gaC	p.E1028D	SUPT5H_ENST00000359191.6_Missense_Mutation_p.E1024D|SUPT5H_ENST00000432763.2_Missense_Mutation_p.E1028D|SUPT5H_ENST00000598725.1_Missense_Mutation_p.E1028D|SUPT5H_ENST00000402194.2_Missense_Mutation_p.E1024D			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	1028					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)			TTTCCAGTGAGCACCTGGAGC	0.577																																					p.E1028D		Atlas-SNP	.											.	SUPT5H	119	.	0			c.G3084C						PASS	.						90	72	79					19																	39966780		2203	4300	6503	SO:0001583	missense	6829	exon28			CAGTGAGCACCTG	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.3084G>C	chr19.hg19:g.39966780G>C	ENSP00000470252:p.Glu1028Asp	112.0	0.0	.		86.0	10.0	.	NM_003169	O43279|Q59G52|Q99639	Missense_Mutation	SNP	ENST00000599117.1	hg19	CCDS12536.1	.	.	.	.	.	.	.	.	.	.	G	9.397	1.076981	0.20227	.	.	ENSG00000196235	ENST00000432763;ENST00000402194;ENST00000378524;ENST00000359191	.	.	.	4.42	-0.361	0.12564	.	0.102463	0.64402	D	0.000003	T	0.25901	0.0631	N	0.16201	0.385	0.51233	D	0.999916	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.03202	-1.1061	8	.	.	.	-29.1312	4.6807	0.12734	0.3392:0.0:0.5198:0.1409	.	1024;1028	O00267-2;O00267	.;SPT5H_HUMAN	D	1028;1024;1006;1028	.	.	E	+	3	2	SUPT5H	44658620	0.986000	0.35501	1.000000	0.80357	0.996000	0.88848	0.154000	0.16343	0.130000	0.18549	0.462000	0.41574	GAG	.	.	.	none		0.577	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1	NM_003169		C	39966780	G	C	39966780	3	2	78	1	0	0	0	0	1	0	0	0	15411	962	34	4	3194	4	SUPT5H	19	39966780	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	1116672	39966780	19162203	60	5035											
CCDC9	26093	hgsc.bcm.edu	37	chr19	47763935	47763935	+	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	ggactcctccacagcagggaGgccgggccggcatgggccga	7	3	17	14	3	0	0	0	0	0	0	2	3	2	2	5	6	1	2	5	6	0	0			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr19:47763935G>A	ENST00000221922.6	+	5	523	c.301G>A	c.(301-303)Ggc>Agc	p.G101S		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	101	Gly-rich.						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)		ACAGCAGGGAGGCCGGGCCGG	0.756																																					p.G101S		Atlas-SNP	.											.	CCDC9	37	.	0			c.G301A						PASS	.						13	15	14					19																	47763935		1920	4024	5944	SO:0001583	missense	26093	exon5			CAGGGAGGCCGGG	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.301G>A	chr19.hg19:g.47763935G>A	ENSP00000221922:p.Gly101Ser	0.0	0.0	.		7.0	6.0	.	NM_015603		Missense_Mutation	SNP	ENST00000221922.6	hg19	CCDS12698.1	.	.	.	.	.	.	.	.	.	.	-	10.73	1.433672	0.25813	.	.	ENSG00000105321	ENST00000221922;ENST00000504556	T	0.31769	1.48	3.32	2.26	0.28386	.	0.589357	0.16586	N	0.207978	T	0.26048	0.0635	L	0.54323	1.7	0.27250	N	0.958919	P	0.40180	0.705	B	0.40864	0.342	T	0.08046	-1.0741	10	0.25751	T	0.34	-10.5089	5.4967	0.16807	0.2634:0.0:0.7366:0.0	.	101	Q9Y3X0	CCDC9_HUMAN	S	101	ENSP00000221922:G101S	ENSP00000221922:G101S	G	+	1	0	CCDC9	52455775	0.926000	0.31397	0.964000	0.40570	0.633000	0.38033	1.380000	0.34351	0.731000	0.32448	0.431000	0.28591	GGC	.	.	.	none		0.756	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603		A	47763935	G	A	47763935	3	1	78	1	0	0	0	0	1	0	0	0	2869	1000	35	2	315	2	CCDC9	19	47763935	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	7797155	47763935	11365048	61	5036											
GLTSCR1	29998	hgsc.bcm.edu	37	chr19	48205552	48205552	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccggccggacgcccgcgccCtcgtacccccacgctgcctc	3	4	10	24	7	0	0	0	0	0	0	2	1	0	1	7	2	2	2	7	2	1	1			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr19:48205552C>T	ENST00000396720.3	+	15	4757	c.4563C>T	c.(4561-4563)ccC>ccT	p.P1521P	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	1521										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)		CGCCCGCGCCCTCGTACCCCC	0.741																																					p.P1521P		Atlas-SNP	.											.	GLTSCR1	79	.	0			c.C4563T						PASS	.						11	13	12					19																	48205552		2094	4176	6270	SO:0001819	synonymous_variant	29998	exon15			CGCGCCCTCGTAC	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.4563C>T	chr19.hg19:g.48205552C>T		0.0	0.0	.		13.0	7.0	.	NM_015711	A8MW01	Silent	SNP	ENST00000396720.3	hg19	CCDS46134.1																																																																																			.	.	.	none		0.741	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711		T	48205552	C	T	48205552	2	4	78	1	0	0	0	0	0	0	0	1	6481	668	24	2		2	GLTSCR1	19	48205552	Silent	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	441617	48205552	10923431	62	5037											
OLIG1	116448	hgsc.bcm.edu	37	chr21	34442850	34442850	+	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	gcgcccggccggacgccaagGaggagcagcagcagcagctg	9	1	17	14	4	0	0	0	0	0	0	0	3	0	3	3	4	5	5	3	4	1	0			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr21:34442850G>C	ENST00000382348.1	+	1	401	c.298G>C	c.(298-300)Gag>Cag	p.E100Q	OLIG1_ENST00000333063.5_Missense_Mutation_p.E84Q|AP000282.2_ENST00000420356.1_RNA|AP000282.2_ENST00000454622.1_RNA	NM_138983.2	NP_620450.2	Q8TAK6	OLIG1_HUMAN	oligodendrocyte transcription factor 1	100					neuron fate commitment (GO:0048663)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)	1						ggACGCCAAGGAGGAGCAGCA	0.746																																					p.E100Q		Atlas-SNP	.											.	OLIG1	4	.	0			c.G298C						PASS	.						4	5	5					21																	34442850		1905	3895	5800	SO:0001583	missense	116448	exon1			GCCAAGGAGGAGC	AP000109	CCDS42920.1, CCDS42920.2	21q22.11	2013-05-21			ENSG00000184221	ENSG00000184221		"Basic helix-loop-helix proteins"	16983	protein-coding gene	gene with protein product	"oligodendrocyte-specific bHLH transcription factor 1", "oligodendrocyte lineage transcription factor 1", "basic domain, helix-loop-helix protein, class B, 6"	606385				11526205	Standard	NM_138983		Approved	BHLHB6, bHLHe21	uc002yqz.3	Q8TAK6	OTTHUMG00000065064	ENST00000382348.1:c.298G>C	chr21.hg19:g.34442850G>C	ENSP00000371785:p.Glu100Gln	0.0	0.0	.		22.0	13.0	.	NM_138983	Q7RTS0	Missense_Mutation	SNP	ENST00000382348.1	hg19	CCDS42920.2	.	.	.	.	.	.	.	.	.	.	G	14.96	2.691676	0.48097	.	.	ENSG00000184221	ENST00000382348;ENST00000333063	D;D	0.98585	-5.01;-2.75	4.35	3.45	0.39498	.	0.466103	0.16859	U	0.196606	D	0.93802	0.8018	N	0.14661	0.345	0.29416	N	0.860923	P	0.38978	0.652	B	0.39027	0.288	D	0.90917	0.4780	10	0.33940	T	0.23	-11.8771	8.2305	0.31595	0.0932:0.1572:0.7496:0.0	.	100	Q8TAK6	OLIG1_HUMAN	Q	100;84	ENSP00000371785:E100Q;ENSP00000331066:E84Q	ENSP00000331066:E84Q	E	+	1	0	OLIG1	33364720	1.000000	0.71417	0.999000	0.59377	0.929000	0.56500	3.498000	0.53302	1.996000	0.58369	0.479000	0.44913	GAG	.	.	.	none		0.746	OLIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139730.1	NM_138983		C	34442850	G	C	34442850	3	2	78	1	0	0	0	0	1	0	0	0	10867	1175	41	4	300	4	OLIG1	21	34442850	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10		34442850	13687045	63	5038											
KRTAP10-3	386682	hgsc.bcm.edu	37	chr21	45978023	45978023	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagaggagggacacgcaggaGgccgggcggcagcagctggg	9	1	21	10	3	0	1	0	0	0	1	0	4	0	4	1	7	2	4	1	7	0	0			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr21:45978023G>A	ENST00000391620.1	-	1	620	c.576C>T	c.(574-576)gcC>gcT	p.A192A	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198696.2	NP_941969.2	P60369	KR103_HUMAN	keratin associated protein 10-3	192	18 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				kidney(1)|lung(4)|prostate(1)|skin(1)	7						ACACGCAGGAGGCCGGGCGGC	0.721																																					p.A192A		Atlas-SNP	.											.	KRTAP10-3	17	.	0			c.C576T						PASS	.						32	39	36					21																	45978023		2200	4298	6498	SO:0001819	synonymous_variant	386682	exon1			GCAGGAGGCCGGG	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.576C>T	chr21.hg19:g.45978023G>A		14.0	0.0	.		165.0	9.0	.	NM_198696	A3KN67|Q70LJ4	Silent	SNP	ENST00000391620.1	hg19	CCDS42956.1																																																																																			.	.	.	none		0.721	KRTAP10-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128031.1			A	45978023	G	A	45978023	2	1	78	1	0	0	0	0	0	0	0	1	8517	987	35	2		2	KRTAP10-3	21	45978023	Silent	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	11535173	45978023	2151872	64	5039											
SEC14L2	23541	hgsc.bcm.edu	37	chr22	30818390	30818391	+	Frame_Shift_Ins	INS	-	-	A																															agctgggggcaggcaccccgINSaaataacaccttctcctata																										TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr22:30818390_30818391insA	ENST00000312932.9	+	12	1466_1467	c.1206_1207insA	c.(1207-1209)aaafs	p.K403fs	RP4-539M6.21_ENST00000608952.1_RNA|RP4-539M6.19_ENST00000439838.1_Intron|SEC14L2_ENST00000403484.1_Frame_Shift_Ins_p.K329fs|SEC14L2_ENST00000402592.3_Frame_Shift_Ins_p.K320fs|RP4-539M6.20_ENST00000608677.1_RNA|RNU6-564P_ENST00000410983.1_RNA	NM_012429.3	NP_036561.1	O76054	S14L2_HUMAN	SEC14-like 2 (S. cerevisiae)	403					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cholesterol biosynthetic process (GO:0045540)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	phospholipid binding (GO:0005543)|transporter activity (GO:0005215)|vitamin E binding (GO:0008431)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|urinary_tract(1)	10					Vitamin E(DB00163)	CAGGCACCCCGAAATAACACCT	0.515																																					p.P402fs		Atlas-Indel,Pindel	.											.	SEC14L2	24	.	0			c.1206_1207insA						PASS	.																																			SO:0001589	frameshift_variant	23541	exon12			.	AL096881	CCDS13876.1, CCDS46685.1, CCDS56228.1	22q12.2	2010-08-19	2001-11-28		ENSG00000100003	ENSG00000100003			10699	protein-coding gene	gene with protein product	"supernatant protein factor"	607558	"SEC14 (S. cerevisiae)-like 2"	C22orf6		10591208	Standard	NM_033382		Approved	TAP, SPF, KIAA1186, KIAA1658	uc003ahr.3	O76054	OTTHUMG00000151024	ENST00000312932.9:c.1209dupA	chr22.hg19:g.30818393_30818393dupA	ENSP00000316203:p.Lys403fs	82.0	0.0	0		62.0	21.0	0.33871	NM_012429	B7Z8Q1|F5H3U4|Q53EQ2|Q6PD61|Q9ULN4	Frame_Shift_Ins	INS	ENST00000312932.9	hg19	CCDS13876.1																																																																																			.	.	.	none		0.515	SEC14L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321018.4	NM_012429		A	30818391	-	A	30818390	7	5	78	1	0	1	1	0	0	0	0	0	13995	1045	37	0	1350	0	SEC14L2	22	30818390	Frame_Shift_Ins	INS	-	TCGA-AT-A5NU-01A-11D-A28G-10		30818390	20486176	65	5040											
EIF3L	51386	hgsc.bcm.edu	37	chr22	38273745	38273745	+	Missense_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	cctcacgatgtaccccatgcGtattgatgagagcattcacc	10	10	8	13	2	2	2	2	2	0	1	2	4	2	2	4	0	3	3	4	0	2	4			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr22:38273745G>A	ENST00000412331.2	+	11	1724	c.1142G>A	c.(1141-1143)cGt>cAt	p.R381H	EIF3L_ENST00000406934.1_Missense_Mutation_p.R283H|EIF3L_ENST00000381683.6_Missense_Mutation_p.R333H	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						TACCCCATGCGTATTGATGAG	0.507																																					p.R381H		Atlas-SNP	.											.	EIF3L	35	.	0			c.G1142A						PASS	.						109	91	97					22																	38273745		2203	4300	6503	SO:0001583	missense	51386	exon11			CCATGCGTATTGA	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.1142G>A	chr22.hg19:g.38273745G>A	ENSP00000416892:p.Arg381His	260.0	1.0	.		198.0	77.0	.	NM_016091		Missense_Mutation	SNP	ENST00000412331.2	hg19	CCDS13960.1	.	.	.	.	.	.	.	.	.	.	g	17.83	3.484330	0.63962	.	.	ENSG00000100129	ENST00000412331;ENST00000425539;ENST00000381683;ENST00000262832;ENST00000406934	T;T;T	0.47177	0.85;0.85;0.85	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.50205	0.1602	M	0.64170	1.965	0.80722	D	1	B;B;B;B	0.33755	0.424;0.205;0.241;0.391	B;B;B;B	0.34779	0.185;0.086;0.067;0.189	T	0.54912	-0.8222	10	0.52906	T	0.07	-11.4514	18.5732	0.91144	0.0:0.0:1.0:0.0	.	333;283;381;424	B4DYB2;B0QY90;Q9Y262;B0QY89	.;.;EIF3L_HUMAN;.	H	381;424;333;348;283	ENSP00000416892:R381H;ENSP00000371099:R333H;ENSP00000384634:R283H	ENSP00000262832:R348H	R	+	2	0	EIF3L	36603691	1.000000	0.71417	0.983000	0.44433	0.982000	0.71751	9.824000	0.99380	2.436000	0.82500	0.436000	0.28706	CGT	.	.	.	none		0.507	EIF3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319551.2	NM_016091		A	38273745	G	A	38273745	3	1	78	1	0	0	0	0	1	0	0	0	5024	1145	40	1	1184	1	EIF3L	22	38273745	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	7455355	38273745	13030821	66	5041											
ENTHD1	150350	hgsc.bcm.edu	37	chr22	40283710	40283710	+	Missense_Mutation	SNP	A	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	gacttttatttcagcatctgAgtaatttttcacaaagtttt	11	19	5	6	0	3	1	2	1	1	0	3	2	3	1	0	0	1	3	0	0	3	8			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr22:40283710A>C	ENST00000325157.6	-	2	293	c.43T>G	c.(43-45)Tca>Gca	p.S15A		NM_152512.3	NP_689725.2	Q8IYW4	ENTD1_HUMAN	ENTH domain containing 1	15	ENTH. {ECO:0000255|PROSITE- ProRule:PRU00243}.									breast(2)|endometrium(1)|kidney(6)|large_intestine(6)|lung(11)|ovary(3)|skin(3)	32	Melanoma(58;0.0749)					TCAGCATCTGAGTAATTTTTC	0.388																																					p.S15A		Atlas-SNP	.											.	ENTHD1	83	.	0			c.T43G						PASS	.						79	77	78					22																	40283710		2203	4300	6503	SO:0001583	missense	150350	exon2			CATCTGAGTAATT	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.43T>G	chr22.hg19:g.40283710A>C	ENSP00000317431:p.Ser15Ala	39.0	0.0	.		22.0	8.0	.	NM_152512	B0QYD5|Q5H9F7|Q96LK3	Missense_Mutation	SNP	ENST00000325157.6	hg19	CCDS13998.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.238534	0.79800	.	.	ENSG00000176177	ENST00000325157	T	0.51574	0.7	5.72	5.72	0.89469	Epsin domain, N-terminal (1);ENTH/VHS (2);Epsin-like, N-terminal (2);	0.000000	0.56097	D	0.000026	T	0.74336	0.3703	M	0.89968	3.075	0.46336	D	0.998993	P	0.45348	0.856	D	0.64687	0.928	T	0.79598	-0.1737	10	0.87932	D	0	-12.6774	15.6751	0.77311	1.0:0.0:0.0:0.0	.	15	Q8IYW4	ENTD1_HUMAN	A	15	ENSP00000317431:S15A	ENSP00000317431:S15A	S	-	1	0	ENTHD1	38613656	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.127000	0.64727	2.183000	0.69458	0.533000	0.62120	TCA	.	.	.	none		0.388	ENTHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321302.1	NM_152512		C	40283710	A	C	40283710	3	2	78	1	0	0	0	0	1	0	0	0	5139	304	11	5	1804	5	ENTHD1	22	40283710	Missense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10	2009965	40283710	11020856	67	5042											
CENPM	79019	hgsc.bcm.edu	37	chr22	42339699	42339699	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatgctgcagtggctctccCgcccagctggaaagaagcca	10	6	12	13	1	1	1	0	0	1	1	2	3	1	2	3	2	4	4	3	2	3	0	rs138744954		TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr22:42339699C>T	ENST00000215980.5	-	5	404	c.317G>A	c.(316-318)cGg>cAg	p.R106Q	CENPM_ENST00000404067.1_Intron|CENPM_ENST00000402420.1_Silent_p.A100A|CENPM_ENST00000402338.1_Missense_Mutation_p.R72Q|CENPM_ENST00000407253.3_Intron	NM_024053.3	NP_076958.1	Q9NSP4	CENPM_HUMAN	centromere protein M	106					mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)				kidney(1)|large_intestine(1)|prostate(1)	3						GTGGCTCTCCCGCCCAGCTGG	0.572																																					p.R106Q		Atlas-SNP	.											.	CENPM	8	.	0			c.G317A						PASS	.	C	,GLN/ARG	0,4406		0,0,2203	78	59	65		,317	-4.7	1	22	dbSNP_134	65	2,8598	2.2+/-6.3	0,2,4298	yes	intron,missense	CENPM	NM_001002876.1,NM_024053.3	,43	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,benign	,106/181	42339699	2,13004	2203	4300	6503	SO:0001583	missense	79019	exon5			CTCTCCCGCCCAG	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.317G>A	chr22.hg19:g.42339699C>T	ENSP00000215980:p.Arg106Gln	138.0	0.0	.		94.0	37.0	.	NM_024053	A7LM22|B1AHQ9|Q6I9W3	Missense_Mutation	SNP	ENST00000215980.5	hg19	CCDS14025.1	.	.	.	.	.	.	.	.	.	.	C	13.00	2.106900	0.37145	0.0	2.33E-4	ENSG00000100162	ENST00000215980;ENST00000402338	.	.	.	5.25	-4.72	0.03269	.	0.976709	0.08428	N	0.947321	T	0.26448	0.0646	N	0.16656	0.425	0.29767	N	0.83507	B	0.15930	0.015	B	0.10450	0.005	T	0.41070	-0.9529	9	0.11182	T	0.66	-34.5962	11.9913	0.53176	0.0:0.4651:0.0:0.5349	.	106	Q9NSP4	CENPM_HUMAN	Q	106;72	.	ENSP00000215980:R106Q	R	-	2	0	CENPM	40669645	0.002000	0.14202	0.956000	0.39512	0.972000	0.66771	-0.717000	0.04986	-0.651000	0.05415	-0.218000	0.12543	CGG	.	C|1.000;T|0.000	0.000	weak		0.572	CENPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322058.1	NM_024053		T	42339699	C	T	42339699	3	4	78	1	0	0	0	0	1	0	0	0	3239	652	23	1	273	1	CENPM	22	42339699	Missense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	2055989	42339699	8964867	68	5043											
MCAT	27349	hgsc.bcm.edu	37	chr22	43539309	43539309	+	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	ggcgccgcggcggtagctggCgcccaagcccctgacccacg	5	3	15	18	6	0	1	0	1	0	0	0	1	0	1	5	4	2	2	5	4	2	1	rs200527554	byFrequency	TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chr22:43539309C>A	ENST00000290429.6	-	1	91	c.46G>T	c.(46-48)Gcc>Tcc	p.A16S	MCAT_ENST00000327555.5_Missense_Mutation_p.A16S|MCAT_ENST00000464244.1_5'Flank	NM_173467.4	NP_775738.3	Q8IVS2	FABD_HUMAN	malonyl CoA:ACP acyltransferase (mitochondrial)	16					fatty acid biosynthetic process (GO:0006633)|metabolic process (GO:0008152)	mitochondrion (GO:0005739)	[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|poly(A) RNA binding (GO:0044822)|transferase activity (GO:0016740)			breast(1)|endometrium(3)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(1)	11		Ovarian(80;0.0694)				CGGTAGCTGGCGCCCAAGCCC	0.761													C|||	44	0.00878594	8e-04	0.0014	5008	,	,		12066	0.001		0	False		,,,				2504	0.0419				p.A16S		Atlas-SNP	.											.	MCAT	26	.	0			c.G46T						PASS	.	C	SER/ALA,SER/ALA	2,2788		0,2,1393	2	3	3		46,46	0.4	0	22		3	12,6196		0,12,3092	no	missense,missense	MCAT	NM_014507.3,NM_173467.4	99,99	0,14,4485	AA,AC,CC		0.1933,0.0717,0.1556	benign,benign	16/181,16/391	43539309	14,8984	1395	3104	4499	SO:0001583	missense	27349	exon1			AGCTGGCGCCCAA	AL359401	CCDS14045.1, CCDS33660.1	22q13.2	2010-04-27			ENSG00000100294	ENSG00000100294	2.3.1.39		29622	protein-coding gene	gene with protein product		614479				12882974	Standard	NM_173467		Approved	MT, MCT, fabD, FASN2C, NET62	uc003bdl.1	Q8IVS2	OTTHUMG00000150704	ENST00000290429.6:c.46G>T	chr22.hg19:g.43539309C>A	ENSP00000290429:p.Ala16Ser	0.0	0.0	.		6.0	6.0	.	NM_014507	B0QY72|O95510|O95511	Missense_Mutation	SNP	ENST00000290429.6	hg19	CCDS33660.1	.	.	.	.	.	.	.	.	.	.	C	12.66	2.005171	0.35415	7.17E-4	0.001933	ENSG00000100294	ENST00000327555;ENST00000290429	T	0.44482	0.92	5.13	0.374	0.16183	.	1.107710	0.06871	N	0.800769	T	0.19208	0.0461	N	0.08118	0	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.11329	0.006;0.006	T	0.24977	-1.0145	10	0.09590	T	0.72	-2.6285	4.8423	0.13496	0.1466:0.5099:0.2666:0.0768	.	16;16	B0QY72;Q8IVS2	.;FABD_HUMAN	S	16	ENSP00000290429:A16S	ENSP00000290429:A16S	A	-	1	0	MCAT	41869253	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.231000	0.09069	-0.090000	0.12462	-0.463000	0.05309	GCC	.	.	.	weak		0.761	MCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319677.2	NM_173467		A	43539309	C	A	43539309	3	1	78	1	0	0	0	0	1	0	0	0	9379	768	27	4	1142	4	MCAT	22	43539309	Missense_Mutation	SNP	C	TCGA-AT-A5NU-01A-11D-A28G-10	1199610	43539309	7765257	69	5044											
HDAC6	10013	hgsc.bcm.edu	37	chrX	48676773	48676773	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccccgcatgggtgatgctgActacctagctgcctggcatc	6	9	12	14	1	0	2	0	2	0	0	1	2	0	2	4	2	4	4	4	2	2	2			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chrX:48676773A>G	ENST00000334136.5	+	22	2319	c.2141A>G	c.(2140-2142)gAc>gGc	p.D714G	HDAC6_ENST00000376619.2_Missense_Mutation_p.D714G|HDAC6_ENST00000444343.2_Missense_Mutation_p.D728G			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	714	Histone deacetylase 2.				aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	GGTGATGCTGACTACCTAGCT	0.637																																					p.D714G	Pancreas(112;205 1675 2305 8976 15959)	Atlas-SNP	.											.	HDAC6	111	.	0			c.A2141G						PASS	.						53	42	45					X																	48676773		2203	4300	6503	SO:0001583	missense	10013	exon22			ATGCTGACTACCT	AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 90"	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.2141A>G	chrX.hg19:g.48676773A>G	ENSP00000334061:p.Asp714Gly	95.0	0.0	.		88.0	77.0	.	NM_006044	O94975|Q6NT75|Q7L3E5|Q96CY0	Missense_Mutation	SNP	ENST00000334136.5	hg19	CCDS14306.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.672707	0.88445	.	.	ENSG00000094631	ENST00000444343;ENST00000334136;ENST00000376619;ENST00000436813	T;T;T	0.71222	-0.55;-0.55;-0.55	5.35	5.35	0.76521	Histone deacetylase domain (2);	0.237016	0.41294	D	0.000917	T	0.76786	0.4036	L	0.43923	1.385	0.80722	D	1	P;D;P	0.57571	0.931;0.98;0.931	P;D;P	0.63703	0.848;0.917;0.848	T	0.79090	-0.1946	10	0.87932	D	0	-11.0343	12.2017	0.54331	1.0:0.0:0.0:0.0	.	704;362;714	B4DZN1;B3KVK5;Q9UBN7	.;.;HDAC6_HUMAN	G	728;714;714;714	ENSP00000398566:D728G;ENSP00000334061:D714G;ENSP00000365804:D714G	ENSP00000334061:D714G	D	+	2	0	HDAC6	48561717	1.000000	0.71417	0.932000	0.37286	0.989000	0.77384	8.533000	0.90617	1.785000	0.52413	0.486000	0.48141	GAC	.	.	.	none		0.637	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044		G	48676773	A	G	48676773	3	3	78	1	0	0	0	0	1	0	0	0	7018	275	10	3	2223	3	HDAC6	23	48676773	Missense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10		48676773	106593787	70	5045											
SERPINA7	6906	hgsc.bcm.edu	37	chrX	105280775	105280775	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgaaccccaaggtctccacaAtctcagtttgggtgctgcag	9	10	10	12	0	2	1	1	1	2	0	4	1	2	1	3	2	3	3	3	2	3	1			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chrX:105280775A>G	ENST00000327674.4	-	1	610	c.275T>C	c.(274-276)aTt>aCt	p.I92T	SERPINA7_ENST00000487487.1_5'Flank|SERPINA7_ENST00000372563.1_Missense_Mutation_p.I92T			P05543	THBG_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7	92					aging (GO:0007568)|negative regulation of endopeptidase activity (GO:0010951)|post-embryonic development (GO:0009791)|regulation of proteolysis (GO:0030162)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to peptide hormone (GO:0043434)|response to prostaglandin E (GO:0034695)|response to vitamin A (GO:0033189)|thyroid hormone transport (GO:0070327)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	hormone binding (GO:0042562)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|ovary(1)|skin(3)	24					Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	GGTCTCCACAATCTCAGTTTG	0.483																																					p.I92T		Atlas-SNP	.											.	SERPINA7	72	.	0			c.T275C						PASS	.						82	75	78					X																	105280775		2203	4300	6503	SO:0001583	missense	6906	exon2			TCCACAATCTCAG	M14091	CCDS14518.1	Xq21-q22	2014-02-18	2005-08-18		ENSG00000123561	ENSG00000123561		"Serine (or cysteine) peptidase inhibitors"	11583	protein-coding gene	gene with protein product	"thyroxin-binding globulin", "thyroxine-binding globulin", "alpha-1 antiproteinase, antitrypsin"	314200	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 7"	TBG		24172014	Standard	NM_000354		Approved		uc004eme.2	P05543	OTTHUMG00000022144	ENST00000327674.4:c.275T>C	chrX.hg19:g.105280775A>G	ENSP00000329374:p.Ile92Thr	45.0	0.0	.		46.0	6.0	.	NM_000354	D3DUX1	Missense_Mutation	SNP	ENST00000327674.4	hg19	CCDS14518.1	.	.	.	.	.	.	.	.	.	.	A	11.85	1.760784	0.31137	.	.	ENSG00000123561	ENST00000327674;ENST00000372563	D;D	0.85773	-2.03;-2.03	4.91	4.91	0.64330	Serpin domain (3);	0.073669	0.56097	D	0.000032	D	0.94298	0.8168	H	0.96175	3.78	0.40968	D	0.984676	D	0.89917	1.0	D	0.87578	0.998	D	0.95648	0.8704	10	0.87932	D	0	.	11.5511	0.50721	1.0:0.0:0.0:0.0	.	92	P05543	THBG_HUMAN	T	92	ENSP00000329374:I92T;ENSP00000361644:I92T	ENSP00000329374:I92T	I	-	2	0	SERPINA7	105167431	1.000000	0.71417	0.055000	0.19348	0.009000	0.06853	8.589000	0.90817	1.930000	0.55929	0.486000	0.48141	ATT	.	.	.	none		0.483	SERPINA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057790.1	NM_000354		G	105280775	A	G	105280775	3	3	78	1	0	0	0	0	1	0	0	0	14107	101	4	3	988	3	SERPINA7	23	105280775	Missense_Mutation	SNP	A	TCGA-AT-A5NU-01A-11D-A28G-10	56604002	105280775	49989785	71	5046											
ODZ1	10178	hgsc.bcm.edu	37	chrX	123637524	123637524	+	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	ctcccagagaataaagtcagGgcacgtttcatattcatatc	13	11	7	10	1	3	1	3	0	0	1	5	2	4	1	1	1	0	2	1	1	5	5			TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chrX:123637524G>T	ENST00000371130.3	-	19	3394	c.3331C>A	c.(3331-3333)Cct>Act	p.P1111T	TENM1_ENST00000422452.2_Missense_Mutation_p.P1111T	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1111					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)										ATAAAGTCAGGGCACGTTTCA	0.363																																					p.P1111T		Atlas-SNP	.											.	.	.	.	0			c.C3331A						PASS	.						165	160	162					X																	123637524		2203	4300	6503	SO:0001583	missense	10178	exon19			AGTCAGGGCACGT	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.3331C>A	chrX.hg19:g.123637524G>T	ENSP00000360171:p.Pro1111Thr	134.0	1.0	.		155.0	132.0	.	NM_001163278	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	hg19	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	G	13.66	2.302140	0.40694	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.85773	-2.03;-2.0	5.7	5.7	0.88788	.	0.060698	0.64402	D	0.000002	T	0.77955	0.4208	L	0.38953	1.18	0.51233	D	0.999913	B;B;B	0.17852	0.024;0.011;0.007	B;B;B	0.12156	0.007;0.005;0.004	T	0.71768	-0.4493	10	0.16420	T	0.52	.	13.7872	0.63117	0.0:0.0:0.8469:0.1531	.	1110;1111;1111	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	T	1111	ENSP00000360171:P1111T;ENSP00000403954:P1111T	ENSP00000360171:P1111T	P	-	1	0	ODZ1	123465205	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.633000	0.74286	2.402000	0.81655	0.600000	0.82982	CCT	.	.	.	none		0.363	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		T	123637524	G	T	123637524	3	4	78	1	0	0	0	0	1	0	0	0	10841	1232	43	4	4923	4	ODZ1	23	123637524	Missense_Mutation	SNP	G	TCGA-AT-A5NU-01A-11D-A28G-10	18356749	123637524	31633036	72	5047											
RENBP	5973	hgsc.bcm.edu	37	chrX	153200984	153200985	+	Frame_Shift_Ins	INS	-	-	T																															gagagggccaccttgccctcINStcggctcaggtagccaaacc																										TCGA-AT-A5NU-01A-11D-A28G-10	TCGA-AT-A5NU-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	573e6af3-cd69-43ac-8dbf-b2f3331d520d	f93a95f6-7503-431f-9f12-d22c659ce92b	g.chrX:153200984_153200985insT	ENST00000393700.3	-	10	1202_1203	c.1122_1123insA	c.(1120-1125)cgagagfs	p.E375fs	NAA10_ENST00000464845.1_5'Flank|RENBP_ENST00000369997.3_Frame_Shift_Ins_p.E361fs|NAA10_ENST00000370009.1_5'Flank|NAA10_ENST00000393712.3_5'Flank|RENBP_ENST00000412763.1_3'UTR|NAA10_ENST00000393710.3_5'Flank|NAA10_ENST00000370015.4_5'Flank	NM_002910.5	NP_002901.2	P51606	RENBP_HUMAN	renin binding protein	375					N-acetylglucosamine metabolic process (GO:0006044)|N-acetylmannosamine metabolic process (GO:0006051)|N-acetylneuraminate catabolic process (GO:0019262)|regulation of blood pressure (GO:0008217)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|endopeptidase inhibitor activity (GO:0004866)|N-acylglucosamine 2-epimerase activity (GO:0050121)			breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	20	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)				N-Acetyl-D-glucosamine(DB00141)	ACCTTGCCCTCTCGGCTCAGGT	0.644																																					p.E375fs		Atlas-Indel,Pindel	.											.	RENBP	69	.	0			c.1123_1124insA						PASS	.																																			SO:0001589	frameshift_variant	5973	exon10			.		CCDS14738.2	Xq28	2013-09-23	2001-11-28		ENSG00000102032	ENSG00000102032			9959	protein-coding gene	gene with protein product	"N-acylglucosamine 2-epimerase", "GlcNAc 2-epimerase", "N-acetyl-D-glucosamine 2-epimerase"	312420	"renin-binding protein"			1618798	Standard	NM_002910		Approved	RNBP, RBP	uc004fjo.2	P51606	OTTHUMG00000024224	ENST00000393700.3:c.1123dupA	chrX.hg19:g.153200985_153200985dupT	ENSP00000377303:p.Glu375fs	139.0	0.0	0		171.0	144.0	0.842105	NM_002910	B4DNZ3|Q96BI6	Frame_Shift_Ins	INS	ENST00000393700.3	hg19	CCDS14738.2																																																																																			.	.	.	none		0.644	RENBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061103.3	NM_002910		T	153200985	-	T	153200984	7	5	78	1	0	1	1	0	0	0	0	0	13238	922	32	0	168	0	RENBP	23	153200984	Frame_Shift_Ins	INS	-	TCGA-AT-A5NU-01A-11D-A28G-10	29563460	153200984	2069576	73	5048											
ANGPTL3	27329	hgsc.bcm.edu	37	chr1	63066787	63066787	+	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	tattcaagaacccacagaaaTttctctatcttccaagccaa	15	11	3	12	0	3	2	1	0	2	2	5	2	4	2	3	0	2	0	3	0	7	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr1:63066787T>A	ENST00000371129.3	+	3	721	c.641T>A	c.(640-642)aTt>aAt	p.I214N	DOCK7_ENST00000251157.5_Intron|DOCK7_ENST00000340370.5_Intron|DOCK7_ENST00000404627.2_Intron	NM_014495.2	NP_055310.1	Q9Y5C1	ANGL3_HUMAN	angiopoietin-like 3	214					acylglycerol homeostasis (GO:0055090)|artery morphogenesis (GO:0048844)|cell-matrix adhesion (GO:0007160)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|fatty acid metabolic process (GO:0006631)|glycerol metabolic process (GO:0006071)|integrin-mediated signaling pathway (GO:0007229)|lipid homeostasis (GO:0055088)|lipid storage (GO:0019915)|negative regulation of lipoprotein lipase activity (GO:0051005)|negative regulation of phospholipase activity (GO:0010519)|phospholipid catabolic process (GO:0009395)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of lipid catabolic process (GO:0050996)|response to hormone (GO:0009725)|signal transduction (GO:0007165)|triglyceride homeostasis (GO:0070328)	cell surface (GO:0009986)|extracellular space (GO:0005615)	enzyme inhibitor activity (GO:0004857)|growth factor activity (GO:0008083)|integrin binding (GO:0005178)|phospholipase inhibitor activity (GO:0004859)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(3)|urinary_tract(1)	13						CCCACAGAAATTTCTCTATCT	0.338																																					p.K214K		Atlas-SNP	.											.	ANGPTL3	42	.	0			c.A641A						PASS	.						92	90	91					1																	63066787		2203	4298	6501	SO:0001583	missense	27329	exon3			CAGAAATTTCTCT	AF152562	CCDS622.1	1p31.3	2013-02-06			ENSG00000132855	ENSG00000132855		"Fibrinogen C domain containing"	491	protein-coding gene	gene with protein product	"angiopoietin 5"	604774		ANGPT5		10644446	Standard	NM_014495		Approved		uc001das.2	Q9Y5C1	OTTHUMG00000009146	ENST00000371129.3:c.641T>A	chr1.hg19:g.63066787T>A	ENSP00000360170:p.Ile214Asn	142.0	0.0	.		128.0	18.0	.	NM_014495	A0JLS0|B1ALJ0|B2RCW1	Silent	SNP	ENST00000371129.3	hg19	CCDS622.1	.	.	.	.	.	.	.	.	.	.	T	6.726	0.502609	0.12822	.	.	ENSG00000132855	ENST00000371129	T	0.62498	0.02	5.36	-1.93	0.07594	.	1.409980	0.04232	N	0.335475	T	0.09555	0.0235	N	0.01576	-0.805	0.20764	N	0.999851	B	0.02656	0.0	B	0.01281	0.0	T	0.04413	-1.0953	10	0.17369	T	0.5	.	1.6612	0.02792	0.3425:0.1379:0.0856:0.4341	.	214	Q9Y5C1	ANGL3_HUMAN	N	214	ENSP00000360170:I214N	ENSP00000360170:I214N	I	+	2	0	ANGPTL3	62839375	0.740000	0.28207	0.994000	0.49952	0.801000	0.45260	0.181000	0.16880	-0.002000	0.14469	-0.649000	0.03915	ATT	.	.	.	none		0.338	ANGPTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025344.1	NM_014495		A	63066787	T	A	63066787	3	1	79	1	0	0	0	0	1	0	0	0	615	1493	52	5	651	5	ANGPTL3	1	63066787	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08		63066787	186183834	1	5049											
ANKRD35	148741	hgsc.bcm.edu	37	chr1	145562384	145562384	+	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	ggaggccacagagaagctgcGgaagctcctggcctcccaga	10	4	14	13	1	0	2	0	0	0	2	2	5	2	4	4	4	3	2	4	4	2	0			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr1:145562384G>C	ENST00000355594.4	+	10	2159	c.2072G>C	c.(2071-2073)cGg>cCg	p.R691P		NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	691										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)					GAGAAGCTGCGGAAGCTCCTG	0.632																																					p.R691P	Melanoma(9;127 754 22988 51047)	Atlas-SNP	.											.	ANKRD35	96	.	0			c.G2072C						PASS	.						33	38	36					1																	145562384		2203	4300	6503	SO:0001583	missense	148741	exon10			AGCTGCGGAAGCT	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.2072G>C	chr1.hg19:g.145562384G>C	ENSP00000347802:p.Arg691Pro	61.0	0.0	.		49.0	7.0	.	NM_144698	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	hg19	CCDS919.1	.	.	.	.	.	.	.	.	.	.	G	13.91	2.376931	0.42105	.	.	ENSG00000198483	ENST00000453670;ENST00000355594	T	0.57107	0.42	4.97	4.06	0.47325	.	0.000000	0.45361	D	0.000361	T	0.42675	0.1213	M	0.70595	2.14	0.80722	D	1	P	0.49862	0.929	P	0.46510	0.519	T	0.48186	-0.9057	10	0.52906	T	0.07	-21.9317	9.1164	0.36760	0.0988:0.0:0.9012:0.0	.	691	Q8N283	ANR35_HUMAN	P	600;691	ENSP00000347802:R691P	ENSP00000347802:R691P	R	+	2	0	ANKRD35	144273741	0.998000	0.40836	0.991000	0.47740	0.842000	0.47809	4.005000	0.57075	1.319000	0.45190	0.563000	0.77884	CGG	.	.	.	none		0.632	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698		C	145562384	G	C	145562384	3	2	79	1	0	0	0	0	1	0	0	0	664	1116	39	4	2110	4	ANKRD35	1	145562384	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	82495597	145562384	103688237	2	5050											
ATP1B1	481	hgsc.bcm.edu	37	chr1	169094257	169094257	+	Missense_Mutation	SNP	T	T	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	ttcagcccagagggatgacaTgatttttgaagattgtggcg	10	12	13	6	1	1	5	1	3	0	2	1	6	1	6	1	2	1	0	1	2	1	4			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr1:169094257T>G	ENST00000367816.1	+	4	891	c.362T>G	c.(361-363)aTg>aGg	p.M121R	ATP1B1_ENST00000499679.3_Missense_Mutation_p.M65R|ATP1B1_ENST00000367813.3_Missense_Mutation_p.M113R|ATP1B1_ENST00000367815.4_Missense_Mutation_p.M121R			P05026	AT1B1_HUMAN	ATPase, Na+/K+ transporting, beta 1 polypeptide	121					blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular potassium ion homeostasis (GO:0030007)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|leukocyte migration (GO:0050900)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|positive regulation of ATP catabolic process (GO:1903291)|positive regulation of ATPase activity (GO:0032781)|positive regulation of calcium:sodium antiporter activity (GO:1903281)|positive regulation of potassium ion import (GO:1903288)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of sodium ion export from cell (GO:1903278)|potassium ion import (GO:0010107)|protein localization to plasma membrane (GO:0072659)|protein stabilization (GO:0050821)|protein transport into plasma membrane raft (GO:0044861)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression (GO:0010468)|relaxation of cardiac muscle (GO:0055119)|response to hypoxia (GO:0001666)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|vesicle (GO:0031982)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|MHC class II protein complex binding (GO:0023026)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	14	all_hematologic(923;0.208)					AGGGATGACATGATTTTTGAA	0.373																																					p.M121R		Atlas-SNP	.											.	ATP1B1	29	.	0			c.T362G						PASS	.						170	167	168					1																	169094257		2203	4300	6503	SO:0001583	missense	481	exon3			ATGACATGATTTT	U16799	CCDS1276.1	1q24.2	2012-10-22			ENSG00000143153	ENSG00000143153		"ATPases / P-type"	804	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit beta-1", "sodium pump subunit beta-1", "sodium-potassium ATPase subunit beta 1 (non-catalytic)"	182330		ATP1B			Standard	NM_001677		Approved		uc001gfr.1	P05026	OTTHUMG00000034590	ENST00000367816.1:c.362T>G	chr1.hg19:g.169094257T>G	ENSP00000356790:p.Met121Arg	302.0	0.0	.		320.0	60.0	.	NM_001677	Q5TGZ3	Missense_Mutation	SNP	ENST00000367816.1	hg19	CCDS1276.1	.	.	.	.	.	.	.	.	.	.	T	4.424	0.078374	0.08533	.	.	ENSG00000143153	ENST00000367816;ENST00000367815;ENST00000499679;ENST00000367813	T;T;T;T	0.28255	1.63;1.63;1.62;1.63	5.57	5.57	0.84162	.	0.083753	0.85682	D	0.000000	T	0.12732	0.0309	L	0.54323	1.7	0.43830	D	0.996406	B	0.28233	0.204	B	0.24269	0.052	T	0.09037	-1.0693	9	0.15952	T	0.53	-21.6982	10.9096	0.47101	0.14:0.0:0.0:0.86	.	121	P05026	AT1B1_HUMAN	R	121;121;65;113	ENSP00000356790:M121R;ENSP00000356789:M121R;ENSP00000423450:M65R;ENSP00000356787:M113R	ENSP00000356787:M113R	M	+	2	0	ATP1B1	167360881	0.023000	0.18921	1.000000	0.80357	0.432000	0.31715	1.328000	0.33758	2.114000	0.64651	0.533000	0.62120	ATG	.	.	.	none		0.373	ATP1B1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083696.1			G	169094257	T	G	169094257	3	3	79	1	0	0	0	0	1	0	0	0	1132	1464	51	5	372	5	ATP1B1	1	169094257	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	23531873	169094257	80156364	3	5051											
ARID4B	51742	hgsc.bcm.edu	37	chr1	235386544	235386544	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagagattcaaatttcgataTccaagtacaggtcgtttgtt	13	14	8	6	2	1	1	1	0	0	1	4	3	2	1	1	1	1	3	1	1	5	6			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr1:235386544T>C	ENST00000264183.3	-	13	1499	c.1002A>G	c.(1000-1002)ggA>ggG	p.G334G	ARID4B_ENST00000366603.2_Silent_p.G334G|ARID4B_ENST00000349213.3_Silent_p.G334G	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	334	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.|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)			AATTTCGATATCCAAGTACAG	0.299																																					p.G334G		Atlas-SNP	.											.	ARID4B	142	.	0			c.A1002G						PASS	.						106	100	102					1																	235386544		2203	4298	6501	SO:0001819	synonymous_variant	51742	exon13			TCGATATCCAAGT	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.1002A>G	chr1.hg19:g.235386544T>C		48.0	0.0	.		42.0	6.0	.	NM_016374	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	Silent	SNP	ENST00000264183.3	hg19	CCDS31061.1																																																																																			.	.	.	none		0.299	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374		C	235386544	T	C	235386544	2	2	79	1	0	0	0	0	0	0	0	1	920	1422	50	3		3	ARID4B	1	235386544	Silent	SNP	T	TCGA-B1-5398-01A-02D-1589-08	66292287	235386544	13864077	4	5052											
PSME4	23198	hgsc.bcm.edu	37	chr2	54135515	54135515	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccatcgggagtcaaattcaTgcttgtgagatccttggaat	10	13	10	8	1	2	1	2	1	0	1	5	4	4	3	2	2	1	1	2	2	2	3			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr2:54135515T>C	ENST00000404125.1	-	24	2781	c.2726A>G	c.(2725-2727)cAt>cGt	p.H909R	PSME4_ENST00000421748.2_Missense_Mutation_p.H53R	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	909					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)			GTCAAATTCATGCTTGTGAGA	0.338																																					p.H909R		Atlas-SNP	.											.	PSME4	247	.	0			c.A2726G						PASS	.						57	57	57					2																	54135515		2203	4298	6501	SO:0001583	missense	23198	exon24			AATTCATGCTTGT	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.2726A>G	chr2.hg19:g.54135515T>C	ENSP00000384211:p.His909Arg	62.0	0.0	.		46.0	8.0	.	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	hg19	CCDS33197.2	.	.	.	.	.	.	.	.	.	.	T	10.65	1.409628	0.25465	.	.	ENSG00000068878	ENST00000421748;ENST00000404125	T;T	0.10960	2.82;2.82	5.36	5.36	0.76844	Armadillo-like helical (1);Armadillo-type fold (1);	0.050889	0.85682	D	0.000000	T	0.09291	0.0229	L	0.29908	0.895	0.54753	D	0.999982	B;B;B	0.16603	0.007;0.001;0.018	B;B;B	0.12837	0.005;0.003;0.008	T	0.20706	-1.0267	10	0.16420	T	0.52	.	15.3474	0.74350	0.0:0.0:0.0:1.0	.	284;53;909	Q14997-2;Q14997-3;Q14997	.;.;PSME4_HUMAN	R	53;909	ENSP00000410830:H53R;ENSP00000384211:H909R	ENSP00000384211:H909R	H	-	2	0	PSME4	53989019	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.033000	0.64146	2.012000	0.59069	0.533000	0.62120	CAT	.	.	.	none		0.338	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		C	54135515	T	C	54135515	3	2	79	1	0	0	0	0	1	0	0	0	12719	1464	51	3	2897	3	PSME4	2	54135515	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08		54135515	189063858	5	5053											
PCBP1	5093	hgsc.bcm.edu	37	chr2	70314950	70314950	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttatgcacggaaaggaagtAggaagcatcattgggaagaa	16	7	13	5	1	1	1	1	0	0	1	1	5	1	5	0	4	2	3	0	4	7	3			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr2:70314950A>G	ENST00000303577.5	+	1	366	c.75A>G	c.(73-75)gtA>gtG	p.V25V	PCBP1-AS1_ENST00000457076.1_RNA|PCBP1-AS1_ENST00000413791.1_RNA|PCBP1-AS1_ENST00000425333.1_RNA|PCBP1-AS1_ENST00000423402.1_RNA|PCBP1-AS1_ENST00000437456.1_RNA|PCBP1-AS1_ENST00000609075.1_RNA|PCBP1-AS1_ENST00000444410.1_RNA|PCBP1-AS1_ENST00000421843.1_RNA|PCBP1-AS1_ENST00000420309.1_RNA|PCBP1-AS1_ENST00000458698.2_RNA|PCBP1-AS1_ENST00000415060.2_RNA|PCBP1-AS1_ENST00000594548.1_RNA|PCBP1-AS1_ENST00000596665.1_RNA|PCBP1-AS1_ENST00000437019.1_RNA|PCBP1-AS1_ENST00000413069.1_RNA|PCBP1-AS1_ENST00000610168.1_RNA|PCBP1-AS1_ENST00000415742.1_RNA|PCBP1-AS1_ENST00000425601.1_RNA|PCBP1-AS1_ENST00000457770.1_RNA|PCBP1-AS1_ENST00000416395.1_RNA|PCBP1-AS1_ENST00000599673.1_RNA|PCBP1-AS1_ENST00000415222.1_RNA|PCBP1-AS1_ENST00000442040.1_RNA|PCBP1-AS1_ENST00000444320.1_RNA|PCBP1-AS1_ENST00000432604.1_RNA|PCBP1-AS1_ENST00000458686.1_RNA|PCBP1-AS1_ENST00000419963.1_RNA|PCBP1-AS1_ENST00000456161.1_RNA|PCBP1-AS1_ENST00000366234.3_RNA|PCBP1-AS1_ENST00000434781.1_RNA|AC016700.2_ENST00000455541.1_lincRNA|PCBP1-AS1_ENST00000418564.1_RNA|PCBP1-AS1_ENST00000421255.1_RNA|PCBP1-AS1_ENST00000452431.1_RNA|PCBP1-AS1_ENST00000596028.1_RNA|PCBP1-AS1_ENST00000413436.1_RNA|PCBP1-AS1_ENST00000411429.1_RNA|PCBP1-AS1_ENST00000429599.2_RNA|PCBP1-AS1_ENST00000449178.1_RNA|PCBP1-AS1_ENST00000595459.1_RNA|PCBP1-AS1_ENST00000601396.1_RNA|PCBP1-AS1_ENST00000439892.1_RNA|PCBP1-AS1_ENST00000596573.1_RNA|PCBP1-AS1_ENST00000435880.2_RNA|PCBP1-AS1_ENST00000439670.2_RNA|PCBP1-AS1_ENST00000422515.1_RNA|PCBP1-AS1_ENST00000416068.1_RNA|PCBP1-AS1_ENST00000418308.1_RNA	NM_006196.3	NP_006187.2	Q15365	PCBP1_HUMAN	poly(rC) binding protein 1	25	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|skin(1)	12						GAAAGGAAGTAGGAAGCATCA	0.567																																					p.V25V	Colon(85;1146 1307 3484 18706 25380)	Atlas-SNP	.											.	PCBP1	28	.	0			c.A75G						PASS	.						111	114	113					2																	70314950		2203	4300	6503	SO:0001819	synonymous_variant	5093	exon1			GGAAGTAGGAAGC		CCDS1898.1	2p13-p12	2013-07-16	2001-11-28		ENSG00000169564	ENSG00000169564			8647	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein E1"	601209	"poly(rC)-binding protein 1"			8833161	Standard	NM_006196		Approved	HNRPE1, hnRNP-E1, HNRPX, hnRNP-X	uc002sgf.3	Q15365	OTTHUMG00000129645	ENST00000303577.5:c.75A>G	chr2.hg19:g.70314950A>G		176.0	0.0	.		164.0	40.0	.	NM_006196	Q13157|Q14975	Silent	SNP	ENST00000303577.5	hg19	CCDS1898.1																																																																																			.	.	.	none		0.567	PCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251844.1	NM_006196		G	70314950	A	G	70314950	2	3	79	1	0	0	0	0	0	0	0	1	11507	407	15	3		3	PCBP1	2	70314950	Silent	SNP	A	TCGA-B1-5398-01A-02D-1589-08	16179435	70314950	172884423	6	5054											
SCN1A	6323	hgsc.bcm.edu	37	chr2	166915109	166915109	+	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	aaaatcttaatagctattttCctaagaggattgaagggagt	15	13	9	4	0	1	2	0	1	1	1	2	4	2	4	1	2	1	1	1	2	7	7	rs121917959		TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr2:166915109C>T	ENST00000303395.4	-	2	353	c.354G>A	c.(352-354)agG>agA	p.R118R	SCN1A_ENST00000409050.1_Silent_p.R118R|SCN1A_ENST00000423058.2_Silent_p.R118R|AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000599041.1_RNA|AC010127.3_ENST00000595268.1_RNA|SCN1A_ENST00000375405.3_Silent_p.R118R			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	118			R -> S (in EIEE6; dbSNP:rs121917959). {ECO:0000269|PubMed:18413471}.		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)	TAGCTATTTTCCTAAGAGGAT	0.338																																					p.R118R		Atlas-SNP	.											.	SCN1A	641	.	0			c.G354A	GRCh37	CM081422	SCN1A	M	rs121917959	PASS	.						64	65	65					2																	166915109		2202	4298	6500	SO:0001819	synonymous_variant	6323	exon2			TATTTTCCTAAGA	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.354G>A	chr2.hg19:g.166915109C>T		80.0	0.0	.		95.0	13.0	.	NM_001165964	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Silent	SNP	ENST00000303395.4	hg19	CCDS54413.1																																																																																			.	.	.	alt		0.338	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		T	166915109	C	T	166915109	2	4	79	1	0	0	0	0	0	0	0	1	13927	854	30	2		2	SCN1A	2	166915109	Silent	SNP	C	TCGA-B1-5398-01A-02D-1589-08	96600159	166915109	76284264	7	5055											
UBR3	130507	hgsc.bcm.edu	37	chr2	170815017	170815017	+	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	tcacgacagaaaagctttatGgaaactgcaatggatgttgg	14	10	11	6	1	1	1	1	0	0	1	1	4	1	3	0	3	3	3	0	3	5	3			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr2:170815017G>A	ENST00000272793.5	+	24	3665	c.3615G>A	c.(3613-3615)atG>atA	p.M1205I	UBR3_ENST00000418381.1_Missense_Mutation_p.M1205I			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	1205					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						AAAGCTTTATGGAAACTGCAA	0.343																																					p.M1205I		Atlas-SNP	.											.	UBR3	182	.	0			c.G3615A						PASS	.						95	101	99					2																	170815017		2203	4300	6503	SO:0001583	missense	130507	exon24			CTTTATGGAAACT	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.3615G>A	chr2.hg19:g.170815017G>A	ENSP00000272793:p.Met1205Ile	123.0	0.0	.		134.0	26.0	.	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Missense_Mutation	SNP	ENST00000272793.5	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.5|25.5	4.648848|4.648848	0.87958|0.87958	.|.	.|.	ENSG00000144357|ENSG00000144357	ENST00000272793;ENST00000442603;ENST00000418381|ENST00000392632	T;T|.	0.52983|.	0.64;0.64|.	6.04|6.04	6.04|6.04	0.98038|0.98038	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.75391|.	0.3843|.	M|M	0.64567|0.64567	1.98|1.98	0.80722|0.80722	D|D	1|1	P;P|.	0.50528|.	0.936;0.851|.	P;P|.	0.61201|.	0.885;0.838|.	T|.	0.70880|.	-0.4752|.	10|.	0.16420|.	T|.	0.52|.	.|.	20.5801|20.5801	0.99389|0.99389	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1205;1205|.	Q6ZT12;E7EVK3|.	UBR3_HUMAN;.|.	I|X	1205|263	ENSP00000272793:M1205I;ENSP00000396068:M1205I|.	ENSP00000272793:M1205I|.	M|W	+|+	3|2	0|0	UBR3|UBR3	170523263|170523263	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	9.828000|9.828000	0.99408|0.99408	2.873000|2.873000	0.98535|0.98535	0.643000|0.643000	0.83706|0.83706	ATG|TGG	.	.	.	none		0.343	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070		A	170815017	G	A	170815017	3	1	79	1	0	0	0	0	1	0	0	0	16915	1348	47	2	3709	2	UBR3	2	170815017	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	3899908	170815017	72384356	8	5056											
SSFA2	6744	hgsc.bcm.edu	37	chr2	182765433	182765433	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttttgtagtgtttcagaaTtgttggaactttatgaggaa	10	19	10	2	0	1	2	1	1	0	1	1	4	1	4	0	2	1	3	0	2	5	9			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr2:182765433T>C	ENST00000431877.2	+	7	693	c.514T>C	c.(514-516)Ttg>Ctg	p.L172L	SSFA2_ENST00000428267.2_Silent_p.L19L|SSFA2_ENST00000320370.7_Silent_p.L172L|SSFA2_ENST00000409001.1_Silent_p.L172L	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	172						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)			TGTTTCAGAATTGTTGGAACT	0.299																																					p.L172L		Atlas-SNP	.											.	SSFA2	130	.	0			c.T514C						PASS	.						55	57	56					2																	182765433		2203	4299	6502	SO:0001819	synonymous_variant	6744	exon7			TCAGAATTGTTGG	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.514T>C	chr2.hg19:g.182765433T>C		99.0	0.0	.		103.0	18.0	.	NM_001130445	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Silent	SNP	ENST00000431877.2	hg19	CCDS46467.1																																																																																			.	.	.	none		0.299	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2	NM_006751		C	182765433	T	C	182765433	2	2	79	1	0	0	0	0	0	0	0	1	15195	1490	52	3		3	SSFA2	2	182765433	Silent	SNP	T	TCGA-B1-5398-01A-02D-1589-08	11950416	182765433	60433940	9	5057											
AOX1	316	hgsc.bcm.edu	37	chr2	201478584	201478584	+	Silent	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	cttattctgaatgaagtctcCcttttgggctcggcgccagg	6	13	11	11	2	2	2	0	2	2	0	4	2	2	2	2	3	0	1	2	3	3	4			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr2:201478584C>T	ENST00000374700.2	+	15	1747	c.1506C>T	c.(1504-1506)tcC>tcT	p.S502S	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	502					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)			breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	ATGAAGTCTCCCTTTTGGGCT	0.478																																					p.S502S		Atlas-SNP	.											.	AOX1	152	.	0			c.C1506T						PASS	.						91	87	88					2																	201478584		2203	4300	6503	SO:0001819	synonymous_variant	316	exon15			AGTCTCCCTTTTG	AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.1506C>T	chr2.hg19:g.201478584C>T		71.0	0.0	.		76.0	17.0	.	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Silent	SNP	ENST00000374700.2	hg19	CCDS33360.1																																																																																			.	.	.	none		0.478	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159		T	201478584	C	T	201478584	2	4	79	1	0	0	0	0	0	0	0	1	729	610	22	2		2	AOX1	2	201478584	Silent	SNP	C	TCGA-B1-5398-01A-02D-1589-08	18713151	201478584	41720789	10	5058											
DNAJB3	54578	hgsc.bcm.edu	37	chr2	234652372	234652372	+	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	cctcgccatagcggtcatagAtatcgcgtttcttggcgtcc	6	12	10	13	5	2	1	1	0	1	1	5	1	3	1	3	2	1	1	3	2	3	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr2:234652372A>G	ENST00000305139.6	+	2	1000				UGT1A9_ENST00000354728.4_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A3_ENST00000482026.1_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A1_ENST00000609767.1_Intron|DNAJB3_ENST00000449667.1_RNA|UGT1A1_ENST00000373450.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A10_ENST00000344644.5_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)	GCGGTCATAGATATCGCGTTT	0.632																																					p.I64T		Atlas-SNP	.											.	.	.	.	0			c.T191C						PASS	.						131	143	139					2																	234652372		2045	4204	6249	SO:0001627	intron_variant	414061	exon1			TCATAGATATCGC	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.862-23308A>G	chr2.hg19:g.234652372A>G		254.0	0.0	.		239.0	37.0	.	NM_001001394	A6NKK6|B8K289|Q96TE7	Missense_Mutation	SNP	ENST00000305139.6	hg19	CCDS2507.1																																																																																			.	.	.	none		0.632	UGT1A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130988.1	NM_205862		G	234652372	A	G	234652372	1	3	79	0	1	0	0	0	0	0	0	0	4623	333	12	3		3	DNAJB3	2	234652372	Intron	SNP	A	TCGA-B1-5398-01A-02D-1589-08	33173788	234652372	8547001	11	5059											
SH3BP4	23677	hgsc.bcm.edu	37	chr2	235962373	235962373	+	Frame_Shift_Del	DEL	C	C	-																															accaagcgctggaagcacctCactgggactctgatcttggt																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr2:235962373delC	ENST00000409212.1	+	6	3312	c.2805delC	c.(2803-2805)ctcfs	p.L935fs	SH3BP4_ENST00000344528.4_Frame_Shift_Del_p.L935fs|SH3BP4_ENST00000392011.2_Frame_Shift_Del_p.L935fs			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	935					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)		GGAAGCACCTCACTGGGACTC	0.592																																					p.L935fs		Atlas-INDEL	.											.	SH3BP4	109	.	0			c.2804delT						PASS	.						173	164	167					2																	235962373		2203	4300	6503	SO:0001589	frameshift_variant	23677	exon6			.	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.2805delC	chr2.hg19:g.235962373delC	ENSP00000386862:p.Leu935fs	247.0	0.0	0		163.0	34.0	0.208589	NM_014521	O95082|Q309A3|Q53QD0|Q53TD1	Frame_Shift_Del	DEL	ENST00000409212.1	hg19	CCDS2513.1																																																																																			.	.	.	none		0.592	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1			-	235962373	C	-	235962373	7	5	79	1	0	1	0	1	0	0	0	0	14259	813	29	0	2819	0	SH3BP4	2	235962373	Frame_Shift_Del	DEL	C	TCGA-B1-5398-01A-02D-1589-08	1310001	235962373	7237000	12	5060											
COL6A3	1293	hgsc.bcm.edu	37	chr2	238234213	238234213	+	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	aatcacttaccaggagcgcaAaccttttcacattctttctg	11	13	5	12	1	4	0	2	0	2	0	4	1	4	1	2	1	3	1	2	1	3	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr2:238234213A>T	ENST00000295550.4	-	43	9935	c.9483T>A	c.(9481-9483)gtT>gtA	p.V3161V	COL6A3_ENST00000353578.4_Silent_p.V2955V|COL6A3_ENST00000473258.1_5'UTR|COL6A3_ENST00000347401.3_Silent_p.V2960V|COL6A3_ENST00000409809.1_Silent_p.V2955V|COL6A3_ENST00000472056.1_Silent_p.V2554V|COL6A3_ENST00000346358.4_Silent_p.V2961V	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	3161	BPTI/Kunitz inhibitor. {ECO:0000255|PROSITE-ProRule:PRU00031}.|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)		CAGGAGCGCAAACCTTTTCAC	0.383																																					p.V3161V		Atlas-SNP	.											.	COL6A3	608	.	0			c.T9483A						PASS	.						178	181	180					2																	238234213		2203	4300	6503	SO:0001819	synonymous_variant	1293	exon43			AGCGCAAACCTTT	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.9483T>A	chr2.hg19:g.238234213A>T		224.0	0.0	.		231.0	53.0	.	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	hg19	CCDS33412.1																																																																																			.	.	.	none		0.383	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238234213	A	T	238234213	2	4	79	1	0	0	0	0	0	0	0	1	3703	1	1	5		5	COL6A3	2	238234213	Silent	SNP	A	TCGA-B1-5398-01A-02D-1589-08	2271840	238234213	4965160	13	5061											
PER2	8864	hgsc.bcm.edu	37	chr2	239184526	239184526	+	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	ttgtgtgtgtccactttcgaAgactggtcgctactgcagga	7	13	12	9	2	0	1	0	0	0	1	3	3	1	2	1	2	2	2	1	2	2	3			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr2:239184526A>C	ENST00000254657.3	-	4	585	c.306T>G	c.(304-306)tcT>tcG	p.S102S	PER2_ENST00000355768.2_Silent_p.S102S|PER2_ENST00000440245.1_Silent_p.S102S|PER2_ENST00000254658.3_Silent_p.S102S	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	102					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)		CCACTTTCGAAGACTGGTCGC	0.502																																					p.S102S		Atlas-SNP	.											.	PER2	85	.	0			c.T306G						PASS	.						173	169	170					2																	239184526		2203	4300	6503	SO:0001819	synonymous_variant	8864	exon4			TTTCGAAGACTGG	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.306T>G	chr2.hg19:g.239184526A>C		110.0	0.0	.		116.0	19.0	.	NM_022817	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Silent	SNP	ENST00000254657.3	hg19	CCDS2528.1																																																																																			.	.	.	none		0.502	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817		C	239184526	A	C	239184526	2	2	79	1	0	0	0	0	0	0	0	1	11737	59	3	5		5	PER2	2	239184526	Silent	SNP	A	TCGA-B1-5398-01A-02D-1589-08	950313	239184526	4014847	14	5062											
SCN11A	11280	hgsc.bcm.edu	37	chr3	38891987	38891988	+	Frame_Shift_Del	DEL	GC	GC	-																															cttactaacaatggaaagaaGcacgaccacacagtcaaata																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr3:38891987_38891988delGC	ENST00000302328.3	-	25	4509_4510	c.4311_4312delGC	c.(4309-4314)gtgcttfs	p.L1439fs	SCN11A_ENST00000444237.2_Frame_Shift_Del_p.L1439fs|SCN11A_ENST00000456224.3_Frame_Shift_Del_p.L1401fs|SCN11A_ENST00000450244.1_Frame_Shift_Del_p.L1439fs	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	1439					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)	ATGGAAAGAAGCACGACCACAC	0.347																																					p.1438_1438del		Atlas-INDEL	.											.	SCN11A	296	.	0			c.4312_4313del						PASS	.																																			SO:0001589	frameshift_variant	11280	exon25			.	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.4311_4312delGC	chr3.hg19:g.38891987_38891988delGC	ENSP00000307599:p.Leu1439fs	121.0	0.0	0		136.0	39.0	0.286765	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Frame_Shift_Del	DEL	ENST00000302328.3	hg19	CCDS33737.1																																																																																			.	.	.	none		0.347	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		-	38891988	GC	-	38891987	7	5	79	1	0	1	0	1	0	0	0	0	13926	971	34	0	1071	0	SCN11A	3	38891987	Frame_Shift_Del	DEL	GC	TCGA-B1-5398-01A-02D-1589-08		38891987	159130443	15	5063											
NDUFB5	4711	hgsc.bcm.edu	37	chr3	179334831	179334831	+	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	agaacactgggaatattataAggtttgtataggacattgac	15	12	10	4	0	0	2	0	1	0	1	0	4	0	4	0	3	1	2	0	3	7	7			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr3:179334831A>C	ENST00000259037.3	+	4	455	c.341A>C	c.(340-342)aAg>aCg	p.K114T	snoU13_ENST00000459278.1_RNA|NDUFB5_ENST00000493866.1_Splice_Site_p.K62T|NDUFB5_ENST00000473500.1_3'UTR|NDUFB5_ENST00000472629.1_Splice_Site_p.K102T	NM_002492.3	NP_002483.1	O43674	NDUB5_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5, 16kDa	114					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			endometrium(1)|lung(6)|skin(1)	8	all_cancers(143;9.62e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.18)			GAATATTATAAGGTTTGTATA	0.343																																					p.K114T		Atlas-SNP	.											.	NDUFB5	22	.	0			c.A341C						PASS	.						79	78	78					3																	179334831		2203	4300	6503	SO:0001630	splice_region_variant	4711	exon4			ATTATAAGGTTTG	AF047181	CCDS3234.1, CCDS56297.1, CCDS75054.1	3q27.1	2011-07-04	2002-08-29		ENSG00000136521	ENSG00000136521		"Mitochondrial respiratory chain complex / Complex I"	7700	protein-coding gene	gene with protein product	"complex I SGDH subunit"	603841	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5 (16kD, SGDH)"			9425316	Standard	NM_002492		Approved	SGDH, CI-SGDH, MGC12314	uc003fkc.3	O43674	OTTHUMG00000157480	ENST00000259037.3:c.342+1A>C	chr3.hg19:g.179334831A>C		77.0	0.0	.		76.0	28.0	.	NM_002492	Q561V6	Missense_Mutation	SNP	ENST00000259037.3	hg19	CCDS3234.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.66|15.66	2.899232|2.899232	0.52227|0.52227	.|.	.|.	ENSG00000136521|ENSG00000136521	ENST00000259037;ENST00000493866;ENST00000472629;ENST00000471112|ENST00000482604	T;T;T;T|.	0.55413|.	0.52;0.52;0.52;0.52|.	5.54|5.54	4.37|4.37	0.52481|0.52481	.|.	0.044583|.	0.85682|.	D|.	0.000000|.	T|T	0.74275|0.74275	0.3695|0.3695	M|M	0.86740|0.86740	2.835|2.835	0.80722|0.80722	D|D	1|1	D;P|.	0.63046|.	0.992;0.933|.	D;P|.	0.63703|.	0.917;0.827|.	T|T	0.74466|0.74466	-0.3656|-0.3656	10|5	0.87932|.	D|.	0|.	-13.9029|-13.9029	7.2091|7.2091	0.25923|0.25923	0.776:0.1461:0.0779:0.0|0.776:0.1461:0.0779:0.0	.|.	62;114|.	Q561V6;O43674|.	.;NDUB5_HUMAN|.	T|R	114;62;102;35|131	ENSP00000259037:K114T;ENSP00000419656:K62T;ENSP00000419248:K102T;ENSP00000419501:K35T|.	ENSP00000259037:K114T|.	K|S	+|+	2|1	0|0	NDUFB5|NDUFB5	180817525|180817525	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.531000|0.531000	0.34715|0.34715	6.924000|6.924000	0.75823|0.75823	0.923000|0.923000	0.37045|0.37045	-0.304000|-0.304000	0.09214|0.09214	AAG|AGC	.	.	.	none		0.343	NDUFB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348937.2	NM_002492	Missense_Mutation	C	179334831	A	C	179334831	5	2	79	1	0	0	0	0	0	0	1	0	10291	86	3	5	355	5	NDUFB5	3	179334831	Splice_Site	SNP	A	TCGA-B1-5398-01A-02D-1589-08	140442844	179334831	18687599	16	5064											
C4orf35	85438	hgsc.bcm.edu	37	chr4	71201158	71201158	+	Frame_Shift_Del	DEL	T	T	-																															actactgtttctttaatagaTttttccactgacatagcaaa																								rs367634444		TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr4:71201158delT	ENST00000273936.5	+	1	476	c.402delT	c.(400-402)gatfs	p.D134fs		NM_033122.3	NP_149113.3	Q96KC9	CABS1_HUMAN	calcium-binding protein, spermatid-specific 1	134					spermatogenesis (GO:0007283)	mitochondrial inner membrane (GO:0005743)|motile cilium (GO:0031514)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(4)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						CTTTAATAGATTTTTCCACTG	0.383																																					p.D134fs		Atlas-INDEL	.											.,1	CABS1	75	.	0			c.401delA						PASS	.						54	54	54					4																	71201158		2203	4298	6501	SO:0001589	frameshift_variant	85438	exon1			.	AF380838	CCDS3539.1	4q13.3	2013-10-11	2011-01-25	2011-01-25	ENSG00000145309	ENSG00000145309			30710	protein-coding gene	gene with protein product	"casein-like phosphoprotein"		"chromosome 4 open reading frame 35"	C4orf35		19208547, 19271754	Standard	NM_033122		Approved	NYD-SP26, FLJ32897, CLPH	uc003hff.3	Q96KC9	OTTHUMG00000129405	ENST00000273936.5:c.402delT	chr4.hg19:g.71201158delT	ENSP00000273936:p.Asp134fs	95.0	0.0	0		116.0	23.0	0.198276	NM_033122	B2RCB5|Q86UE0|Q96M17	Frame_Shift_Del	DEL	ENST00000273936.5	hg19	CCDS3539.1																																																																																			.	.	.	none		0.383	CABS1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251561.3	NM_033122		-	71201158	T	-	71201158	7	5	79	1	0	1	0	1	0	0	0	0	2267	1490	52	0	404	0	C4orf35	4	71201158	Frame_Shift_Del	DEL	T	TCGA-B1-5398-01A-02D-1589-08		71201158	119953118	17	5065											
ANKRD17	26057	hgsc.bcm.edu	37	chr4	74014608	74014608	+	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	tggtgtataaccttcatcatTgacctcttccaggctagctc	8	14	7	12	0	3	1	2	1	1	0	5	1	4	1	3	2	2	3	3	2	3	6			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr4:74014608T>A	ENST00000358602.4	-	8	1605	c.1489A>T	c.(1489-1491)Aat>Tat	p.N497Y	ANKRD17_ENST00000509867.2_Missense_Mutation_p.N384Y|ANKRD17_ENST00000330838.6_Missense_Mutation_p.N497Y|ANKRD17_ENST00000514252.1_5'UTR	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	497					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)			CCTTCATCATTGACCTCTTCC	0.443																																					p.N497Y		Atlas-SNP	.											.	ANKRD17	214	.	0			c.A1489T						PASS	.						115	97	103					4																	74014608		2203	4300	6503	SO:0001583	missense	26057	exon8			CATCATTGACCTC	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.1489A>T	chr4.hg19:g.74014608T>A	ENSP00000351416:p.Asn497Tyr	91.0	0.0	.		90.0	15.0	.	NM_198889	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Missense_Mutation	SNP	ENST00000358602.4	hg19	CCDS34004.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.059277	0.76074	.	.	ENSG00000132466	ENST00000358602;ENST00000426990;ENST00000330838;ENST00000509867;ENST00000411811	T;T;T	0.16897	2.31;2.31;2.31	5.43	4.25	0.50352	Ankyrin repeat-containing domain (5);	0.000000	0.64402	D	0.000002	T	0.37128	0.0992	M	0.61703	1.905	0.30866	N	0.732937	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.998;0.999;0.999;1.0;0.999	T	0.40478	-0.9561	10	0.72032	D	0.01	.	11.4205	0.49978	0.0:0.071:0.0:0.929	.	82;497;497;497;384	B4DR08;O75179-2;G5E964;O75179;E7EUV3	.;.;.;ANR17_HUMAN;.	Y	497;497;497;384;497	ENSP00000351416:N497Y;ENSP00000332265:N497Y;ENSP00000427151:N384Y	ENSP00000332265:N497Y	N	-	1	0	ANKRD17	74233472	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.885000	0.87282	1.002000	0.39104	0.482000	0.46254	AAT	.	.	.	none		0.443	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217		A	74014608	T	A	74014608	3	1	79	1	0	0	0	0	1	0	0	0	646	1812	63	5	6430	5	ANKRD17	4	74014608	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	2813450	74014608	117139668	18	5066											
SCD5	79966	hgsc.bcm.edu	37	chr4	83719607	83719607	+	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	ctctccgggccgccgccgccCtcagagctttcgagcccggc	3	6	12	20	6	2	1	1	0	1	1	4	2	2	1	6	2	2	1	6	2	0	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr4:83719607C>G	ENST00000319540.4	-	1	403	c.84G>C	c.(82-84)gaG>gaC	p.E28D	SCD5_ENST00000273908.4_Missense_Mutation_p.E28D|SCD5_ENST00000282709.4_Missense_Mutation_p.E28D	NM_001037582.2	NP_001032671.2	Q86SK9	SCD5_HUMAN	stearoyl-CoA desaturase 5	28					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)	p.E28D(2)		endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	13		Colorectal(4;0.0323)|Hepatocellular(203;0.115)				CGCCGCCGCCCTCAGAGCTTT	0.692																																					p.E28D		Atlas-SNP	.											SCD5_ENST00000273908,NS,carcinoma,0,2	SCD5	58	.	2	Substitution - Missense(2)	lung(2)	c.G84C						PASS	.						21	23	22					4																	83719607		2200	4295	6495	SO:0001583	missense	79966	exon1			GCCGCCCTCAGAG	AF389338	CCDS3595.1, CCDS34024.1	4q21.3	2013-01-25	2005-06-09	2005-06-09	ENSG00000145284	ENSG00000145284		"Fatty acid desaturases"	21088	protein-coding gene	gene with protein product		608370	"stearoyl-CoA desaturase 4"	SCD4		12477932	Standard	NM_024906		Approved	ACOD4, FLJ21032, FADS4, HSCD5	uc003hna.2	Q86SK9	OTTHUMG00000130293	ENST00000319540.4:c.84G>C	chr4.hg19:g.83719607C>G	ENSP00000316329:p.Glu28Asp	33.0	0.0	.		39.0	5.0	.	NM_024906	B2RPG0|Q4W5Q5|Q8NDS0|Q9H7D1	Missense_Mutation	SNP	ENST00000319540.4	hg19	CCDS34024.1	.	.	.	.	.	.	.	.	.	.	C	9.274	1.046479	0.19748	.	.	ENSG00000145284	ENST00000319540;ENST00000273908;ENST00000282709	T	0.44083	0.93	4.24	2.39	0.29439	.	0.474937	0.20549	N	0.090143	T	0.16557	0.0398	N	0.08118	0	0.09310	N	1	B;B;B	0.24721	0.034;0.11;0.008	B;B;B	0.19946	0.027;0.027;0.003	T	0.11867	-1.0570	10	0.16896	T	0.51	-2.1795	2.9623	0.05896	0.1795:0.542:0.1749:0.1035	.	28;28;28	Q9BSN4;Q86SK9-2;Q86SK9	.;.;SCD5_HUMAN	D	28	ENSP00000316329:E28D	ENSP00000273908:E28D	E	-	3	2	SCD5	83938631	0.000000	0.05858	0.008000	0.14137	0.176000	0.22953	-0.141000	0.10327	0.973000	0.38340	0.471000	0.43371	GAG	.	.	.	none		0.692	SCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252635.1	NM_024906		G	83719607	C	G	83719607	3	3	79	1	0	0	0	0	1	0	0	0	13900	680	24	4	1134	4	SCD5	4	83719607	Missense_Mutation	SNP	C	TCGA-B1-5398-01A-02D-1589-08	9704999	83719607	107434669	19	5067											
GUCY1B3	2983	hgsc.bcm.edu	37	chr4	156725753	156725753	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcttttttgcagataacaatAgggatacacactggagaggt	13	12	10	6	0	1	2	0	0	1	2	1	4	1	3	0	3	3	1	0	3	4	6			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr4:156725753A>G	ENST00000264424.8	+	12	1645	c.1563A>G	c.(1561-1563)atA>atG	p.I521M	GUCY1B3_ENST00000503520.1_Missense_Mutation_p.I488M|GUCY1B3_ENST00000513437.1_Missense_Mutation_p.I453M|GUCY1B3_ENST00000507146.1_Missense_Mutation_p.I496M|GUCY1B3_ENST00000502959.1_Missense_Mutation_p.I543M|GUCY1B3_ENST00000505764.1_Missense_Mutation_p.I501M|GUCY1B3_ENST00000505154.1_Missense_Mutation_p.I453M	NM_000857.2	NP_000848.1	Q02153	GCYB1_HUMAN	guanylate cyclase 1, soluble, beta 3	521	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)	cytoplasm (GO:0005737)|guanylate cyclase complex, soluble (GO:0008074)|intracellular membrane-bounded organelle (GO:0043231)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.148)		AGATAACAATAGGGATACACA	0.373																																					p.I521M		Atlas-SNP	.											GUCY1B3,colon,carcinoma,0,1	GUCY1B3	65	.	0			c.A1563G						PASS	.						114	117	116					4																	156725753		1863	4098	5961	SO:0001583	missense	2983	exon12			AACAATAGGGATA	AF020340	CCDS47154.1, CCDS75203.1	4q31.3-q33	2008-03-18			ENSG00000061918	ENSG00000061918	4.6.1.2		4687	protein-coding gene	gene with protein product		139397		GUC1B3		1352257	Standard	XM_005262959		Approved	GC-SB3, GC-S-beta-1	uc003ipc.3	Q02153	OTTHUMG00000161698	ENST00000264424.8:c.1563A>G	chr4.hg19:g.156725753A>G	ENSP00000264424:p.Ile521Met	161.0	0.0	.		165.0	21.0	.	NM_000857	B7Z426|Q86WY5	Missense_Mutation	SNP	ENST00000264424.8	hg19	CCDS47154.1	.	.	.	.	.	.	.	.	.	.	A	16.65	3.181816	0.57800	.	.	ENSG00000061918	ENST00000505154;ENST00000502959;ENST00000505764;ENST00000507146;ENST00000264424;ENST00000503520;ENST00000513437	D;D;D;D;D;D;D	0.85955	-2.05;-2.05;-2.05;-2.05;-2.05;-2.05;-2.05	5.54	-0.268	0.12934	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.85682	D	0.000000	D	0.92912	0.7745	H	0.94264	3.515	0.52501	D	0.999953	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;0.996;0.998;0.991;0.995	D	0.91851	0.5491	10	0.87932	D	0	.	10.0789	0.42377	0.3827:0.5019:0.0:0.1153	.	501;543;496;488;521	B7Z426;E9PCN2;D6RC99;Q02153-2;Q02153	.;.;.;.;GCYB1_HUMAN	M	453;543;501;496;521;488;453	ENSP00000427226:I453M;ENSP00000426786:I543M;ENSP00000426319:I501M;ENSP00000422313:I496M;ENSP00000264424:I521M;ENSP00000420842:I488M;ENSP00000425065:I453M	ENSP00000264424:I521M	I	+	3	3	GUCY1B3	156945203	0.972000	0.33761	0.998000	0.56505	0.987000	0.75469	0.228000	0.17814	0.045000	0.15804	-0.323000	0.08544	ATA	.	.	.	none		0.373	GUCY1B3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365770.2			G	156725753	A	G	156725753	3	3	79	1	0	0	0	0	1	0	0	0	6902	410	15	3	1609	3	GUCY1B3	4	156725753	Missense_Mutation	SNP	A	TCGA-B1-5398-01A-02D-1589-08	73006146	156725753	34428523	20	5068											
CCDC110	256309	hgsc.bcm.edu	37	chr4	186380443	186380443	+	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	gcacagattcttttaggtaaTtctgtaagtactgaattttt	11	18	7	5	0	2	2	0	1	2	1	2	2	2	2	0	1	1	4	0	1	5	9			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr4:186380443T>A	ENST00000307588.3	-	6	1373	c.1298A>T	c.(1297-1299)aAt>aTt	p.N433I	CCDC110_ENST00000393540.3_Missense_Mutation_p.N396I|CCDC110_ENST00000507501.1_5'Flank|CCDC110_ENST00000510617.1_Missense_Mutation_p.N433I	NM_152775.3	NP_689988.1	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110	433						nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(9)	30		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)		TTTTAGGTAATTCTGTAAGTA	0.318																																					p.N433I		Atlas-SNP	.											.	CCDC110	78	.	0			c.A1298T						PASS	.						94	98	97					4																	186380443		2203	4297	6500	SO:0001583	missense	256309	exon6			AGGTAATTCTGTA	AB080722	CCDS3843.1, CCDS47170.1	4q35.1	2010-12-24			ENSG00000168491	ENSG00000168491			28504	protein-coding gene	gene with protein product	"cancer/testis antigen 52"	609488				18160854	Standard	NM_152775		Approved	KM-HN-1, MGC33607, CT52	uc003ixu.4	Q8TBZ0	OTTHUMG00000160415	ENST00000307588.3:c.1298A>T	chr4.hg19:g.186380443T>A	ENSP00000306776:p.Asn433Ile	285.0	0.0	.		261.0	51.0	.	NM_152775	Q86YI9|Q8N7W0	Missense_Mutation	SNP	ENST00000307588.3	hg19	CCDS3843.1	.	.	.	.	.	.	.	.	.	.	T	16.17	3.046799	0.55110	.	.	ENSG00000168491	ENST00000393540;ENST00000307588;ENST00000510617	T;T;T	0.08807	3.06;3.05;3.05	5.66	5.66	0.87406	.	0.000000	0.64402	D	0.000007	T	0.24699	0.0599	M	0.66939	2.045	0.30797	N	0.740247	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.12167	-1.0558	10	0.51188	T	0.08	-18.2543	10.1029	0.42515	0.1493:0.0:0.0:0.8507	.	433;396;433	B4DZA2;Q8TBZ0-2;Q8TBZ0	.;.;CC110_HUMAN	I	396;433;433	ENSP00000377172:N396I;ENSP00000306776:N433I;ENSP00000427246:N433I	ENSP00000306776:N433I	N	-	2	0	CCDC110	186617437	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.671000	0.54576	2.161000	0.67846	0.533000	0.62120	AAT	.	.	.	none		0.318	CCDC110-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360519.2	NM_152775		A	186380443	T	A	186380443	3	1	79	1	0	0	0	0	1	0	0	0	2749	1493	52	5	1211	5	CCDC110	4	186380443	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	29654690	186380443	4773833	21	5069											
PDZD2	23037	hgsc.bcm.edu	37	chr5	31983432	31983432	+	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	gcgaaaaaggggaaacgaacCagaaagtttggggtcatctc	15	6	13	7	2	2	1	1	0	1	1	3	4	2	2	1	4	2	1	1	4	5	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr5:31983432C>G	ENST00000438447.1	+	3	1036	c.648C>G	c.(646-648)acC>acG	p.T216T	PDZD2_ENST00000282493.3_Silent_p.T216T			O15018	PDZD2_HUMAN	PDZ domain containing 2	216					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						GGAAACGAACCAGAAAGTTTG	0.557																																					p.T216T		Atlas-SNP	.											.	PDZD2	306	.	0			c.C648G						PASS	.						87	85	85					5																	31983432		2203	4300	6503	SO:0001819	synonymous_variant	23037	exon2			ACGAACCAGAAAG	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.648C>G	chr5.hg19:g.31983432C>G		149.0	0.0	.		138.0	30.0	.	NM_178140	Q9BXD4	Silent	SNP	ENST00000438447.1	hg19	CCDS34137.1																																																																																			.	.	.	none		0.557	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			G	31983432	C	G	31983432	2	3	79	1	0	0	0	0	0	0	0	1	11708	581	21	4		4	PDZD2	5	31983432	Silent	SNP	C	TCGA-B1-5398-01A-02D-1589-08		31983432	148931828	22	5070											
ISL1	3670	hgsc.bcm.edu	37	chr5	50683584	50683584	+	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	gcggccactgcaaatggcagGtactcctctgcccggctcgg	6	7	13	15	3	1	0	0	0	1	0	3	0	2	0	3	5	3	4	3	5	2	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr5:50683584G>T	ENST00000230658.7	+	3	1063		c.e3+1		ISL1_ENST00000511384.1_Splice_Site|ISL1_ENST00000505475.2_Splice_Site	NM_002202.2	NP_002193.2	P61371	ISL1_HUMAN	ISL LIM homeobox 1						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)				CAAATGGCAGGTACTCCTCTG	0.637																																					.		Atlas-SNP	.											.	ISL1	65	.	0			c.478+1G>T						PASS	.						23	25	24					5																	50683584		2037	4162	6199	SO:0001630	splice_region_variant	3670	exon3			TGGCAGGTACTCC	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.478+1G>T	chr5.hg19:g.50683584G>T		43.0	0.0	.		51.0	18.0	.	NM_002202	P20663|P47894	Splice_Site	SNP	ENST00000230658.7	hg19	CCDS43314.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.649867	0.87958	.	.	ENSG00000016082	ENST00000230658;ENST00000503187;ENST00000511384;ENST00000505475	.	.	.	5.41	5.41	0.78517	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.2404	0.93879	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ISL1	50719341	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	7.502000	0.81614	2.538000	0.85594	0.456000	0.33151	.	.	.	.	none		0.637	ISL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368413.3	NM_002202	Intron	T	50683584	G	T	50683584	5	4	79	1	0	0	0	0	0	0	1	0	7863	1275	44	4	489	4	ISL1	5	50683584	Splice_Site	SNP	G	TCGA-B1-5398-01A-02D-1589-08	18700152	50683584	130231676	23	5071											
ZNF366	167465	hgsc.bcm.edu	37	chr5	71739940	71739940	+	Nonsense_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	gggctgtagggctccacctcGtagcagttatcctcctcttc	5	12	10	14	1	1	0	0	0	1	0	6	0	4	0	4	2	1	6	4	2	3	4	rs373642159		TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr5:71739940G>C	ENST00000318442.5	-	5	2368	c.1878C>G	c.(1876-1878)taC>taG	p.Y626*	RP11-389C8.2_ENST00000564956.1_RNA	NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	626	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)		GCTCCACCTCGTAGCAGTTAT	0.667																																					p.Y626X		Atlas-SNP	.											ZNF366,NS,carcinoma,0,1	ZNF366	108	.	0			c.C1878G						PASS	.						94	108	103					5																	71739940		2203	4300	6503	SO:0001587	stop_gained	167465	exon5			CACCTCGTAGCAG	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.1878C>G	chr5.hg19:g.71739940G>C	ENSP00000313158:p.Tyr626*	343.0	0.0	.		372.0	65.0	.	NM_152625	Q5HYI9|Q7RTV4	Nonsense_Mutation	SNP	ENST00000318442.5	hg19	CCDS4015.1	.	.	.	.	.	.	.	.	.	.	G	38	7.253100	0.98164	.	.	ENSG00000178175	ENST00000318442	.	.	.	5.78	-7.21	0.01490	.	0.868154	0.10255	N	0.696665	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.173	17.8813	0.88841	0.6695:0.0:0.3305:0.0	.	.	.	.	X	626	.	ENSP00000313158:Y626X	Y	-	3	2	ZNF366	71775696	0.385000	0.25172	0.000000	0.03702	0.206000	0.24218	-0.180000	0.09754	-1.491000	0.01840	-0.136000	0.14681	TAC	.	.	.	alt		0.667	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3			C	71739940	G	C	71739940	4	2	79	1	0	0	0	0	0	1	0	0	17882	1140	40	4	360	4	ZNF366	5	71739940	Nonsense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	21056356	71739940	109175320	24	5072											
PCDHA8	56140	hgsc.bcm.edu	37	chr5	140222316	140222316	+	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	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-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr5:140222316G>C	ENST00000531613.1	+	1	1410	c.1410G>C	c.(1408-1410)ccG>ccC	p.P470P	PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA8_ENST00000378123.3_Silent_p.P470P|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_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	.	0			c.G1410C						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>C	chr5.hg19:g.140222316G>C		139.0	0.0	.		123.0	16.0	.	NM_031856	B9EGT7|O75281	Silent	SNP	ENST00000531613.1	hg19	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		C	140222316	G	C	140222316	2	2	79	1	0	0	0	0	0	0	0	1	11537	1103	39	4		4	PCDHA8	5	140222316	Silent	SNP	G	TCGA-B1-5398-01A-02D-1589-08	68482376	140222316	40692944	25	5073											
ARHGAP26	23092	hgsc.bcm.edu	37	chr5	142513635	142513635	+	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	gtcctgcagcgagaggccccTgacgctcttccacaccgttc	6	8	10	17	3	1	2	0	1	1	1	4	3	3	2	5	1	2	3	5	1	0	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr5:142513635T>A	ENST00000274498.4	+	19	2180	c.1802T>A	c.(1801-1803)cTg>cAg	p.L601Q	ARHGAP26_ENST00000378004.3_Missense_Mutation_p.L601Q	NM_015071.4	NP_055886.1	Q9UNA1	RHG26_HUMAN	Rho GTPase activating protein 26	601	Ser-rich.				actin cytoskeleton organization (GO:0030036)|filopodium assembly (GO:0046847)|nervous system development (GO:0007399)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(7)|ovary(1)	25		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GAGAGGCCCCTGACGCTCTTC	0.582																																					p.L601Q		Atlas-SNP	.											.	ARHGAP26	57	.	0			c.T1802A						PASS	.						129	110	116					5																	142513635		2203	4300	6503	SO:0001583	missense	23092	exon19			GGCCCCTGACGCT	AB014521	CCDS4277.1, CCDS47297.1	5q31	2011-06-29			ENSG00000145819	ENSG00000145819		"Rho GTPase activating proteins"	17073	protein-coding gene	gene with protein product	"GTPase regulator associated with the focal adhesion kinase pp125"	605370				9858476, 8649427	Standard	NM_001135608		Approved	GRAF, KIAA0621, OPHN1L, OPHN1L1	uc011dbj.2	Q9UNA1	OTTHUMG00000059705	ENST00000274498.4:c.1802T>A	chr5.hg19:g.142513635T>A	ENSP00000274498:p.Leu601Gln	188.0	0.0	.		187.0	31.0	.	NM_015071	O75117|Q5D035|Q9BYS6|Q9BYS7|Q9UJ00	Missense_Mutation	SNP	ENST00000274498.4	hg19	CCDS4277.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.4|24.4	4.531454|4.531454	0.85706|0.85706	.|.	.|.	ENSG00000145819|ENSG00000145819	ENST00000274498;ENST00000378004;ENST00000418668|ENST00000443674;ENST00000418236	T;T|.	0.09630|.	2.96;2.97|.	5.95|5.95	5.95|5.95	0.96441|0.96441	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.55878|.	0.1948|.	L|L	0.29908|0.29908	0.895|0.895	0.51767|0.51767	D|D	0.99993|0.99993	D;D;D|.	0.76494|.	0.998;0.994;0.999|.	D;P;D|.	0.87578|.	0.995;0.852;0.998|.	T|.	0.52298|.	-0.8594|.	10|.	0.42905|.	T|.	0.14|.	.|.	15.3985|15.3985	0.74816|0.74816	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	601;174;601|.	Q9UNA1;B3KT96;Q9UNA1-2|.	RHG26_HUMAN;.;.|.	Q|R	601;601;174|220;173	ENSP00000274498:L601Q;ENSP00000367243:L601Q|.	ENSP00000274498:L601Q|.	L|X	+|+	2|1	0|0	ARHGAP26|ARHGAP26	142493828|142493828	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.934000|0.934000	0.57294|0.57294	5.763000|5.763000	0.68818|0.68818	2.279000|2.279000	0.76181|0.76181	0.533000|0.533000	0.62120|0.62120	CTG|TGA	.	.	.	none		0.582	ARHGAP26-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132744.3	NM_015071		A	142513635	T	A	142513635	3	1	79	1	0	0	0	0	1	0	0	0	875	1580	55	5	1876	5	ARHGAP26	5	142513635	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	2291319	142513635	38401625	26	5074											
RBM27	54439	hgsc.bcm.edu	37	chr5	145641187	145641187	+	Missense_Mutation	SNP	T	T	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	acaaccgattcattcgagtcTtgtggcatagggaaaataat	14	11	9	7	2	2	0	1	0	1	0	3	3	2	1	1	2	1	1	1	2	5	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr5:145641187T>G	ENST00000265271.5	+	13	2174	c.2008T>G	c.(2008-2010)Ttg>Gtg	p.L670V	RBM27_ENST00000506502.1_Missense_Mutation_p.L615V	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	670	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CATTCGAGTCTTGTGGCATAG	0.478																																					p.L670V		Atlas-SNP	.											.	RBM27	119	.	0			c.T2008G						PASS	.						174	156	161					5																	145641187		1568	3582	5150	SO:0001583	missense	54439	exon13			CGAGTCTTGTGGC	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.2008T>G	chr5.hg19:g.145641187T>G	ENSP00000265271:p.Leu670Val	176.0	0.0	.		229.0	34.0	.	NM_018989	Q8IYW9	Missense_Mutation	SNP	ENST00000265271.5	hg19	CCDS43378.1	.	.	.	.	.	.	.	.	.	.	T	14.23	2.473230	0.43942	.	.	ENSG00000091009	ENST00000265271	T	0.44083	0.93	5.5	-1.73	0.08081	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.106316	0.40222	N	0.001141	T	0.30634	0.0771	N	0.19112	0.55	0.09310	N	1	P;P	0.41748	0.568;0.761	B;P	0.45310	0.301;0.476	T	0.33701	-0.9858	10	0.66056	D	0.02	-6.6533	11.6531	0.51301	0.0:0.4781:0.0:0.5219	.	670;615	Q9P2N5;B3KY61	RBM27_HUMAN;.	V	670	ENSP00000265271:L670V	ENSP00000265271:L670V	L	+	1	2	RBM27	145621380	0.692000	0.27719	0.167000	0.22817	0.977000	0.68977	1.212000	0.32394	-0.779000	0.04560	-0.379000	0.06801	TTG	.	.	.	none		0.478	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128		G	145641187	T	G	145641187	3	3	79	1	0	0	0	0	1	0	0	0	13140	1606	56	5	2058	5	RBM27	5	145641187	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	3127552	145641187	35274073	27	5075											
CPEB4	80315	hgsc.bcm.edu	37	chr5	173370039	173370039	+	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	tgacatgcagcaaggacataTgggcgaaggagaggtaacat	15	6	14	6	1	0	2	0	1	0	1	0	5	0	3	0	4	3	3	0	4	4	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr5:173370039T>G	ENST00000265085.5	+	4	2723	c.1269T>G	c.(1267-1269)taT>taG	p.Y423*	CPEB4_ENST00000520867.1_Intron|CPEB4_ENST00000522336.1_Intron|CPEB4_ENST00000334035.5_Nonsense_Mutation_p.Y406*|CPEB4_ENST00000517880.1_Intron|CPEB4_ENST00000519467.1_3'UTR|CPEB4_ENST00000519835.1_Intron	NM_030627.2	NP_085130.2	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding protein 4	423					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)			CAAGGACATATGGGCGAAGGA	0.348																																					p.Y423X		Atlas-SNP	.											.	CPEB4	54	.	0			c.T1269G						PASS	.						187	195	192					5																	173370039		2203	4300	6503	SO:0001587	stop_gained	80315	exon4			GACATATGGGCGA	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.1269T>G	chr5.hg19:g.173370039T>G	ENSP00000265085:p.Tyr423*	266.0	0.0	.		328.0	44.0	.	NM_030627	B7ZLQ7|Q7Z310|Q8N405|Q9C0J0	Nonsense_Mutation	SNP	ENST00000265085.5	hg19	CCDS4390.1	.	.	.	.	.	.	.	.	.	.	T	41	8.729920	0.98931	.	.	ENSG00000113742	ENST00000265085;ENST00000334035	.	.	.	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.6823	16.2484	0.82467	0.0:0.0:0.0:1.0	.	.	.	.	X	423;406	.	ENSP00000265085:Y423X	Y	+	3	2	CPEB4	173302645	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.965000	0.87945	2.291000	0.77112	0.533000	0.62120	TAT	.	.	.	none		0.348	CPEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252964.2	NM_030627		G	173370039	T	G	173370039	4	3	79	1	0	0	0	0	0	1	0	0	3805	1471	51	5	1283	5	CPEB4	5	173370039	Nonsense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	27728852	173370039	7545221	28	5076											
MAK	4117	hgsc.bcm.edu	37	chr6	10796389	10796389	+	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	gggttgtccaacaacctgatCgattatatccggcagaggct	10	10	11	10	2	0	2	0	1	0	1	3	3	2	2	3	3	2	3	3	3	4	3	rs201812469	byFrequency	TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr6:10796389C>G	ENST00000313243.2	-	9	1367	c.985G>C	c.(985-987)Gat>Cat	p.D329H	MAK_ENST00000354489.2_Missense_Mutation_p.D329H|MAK_ENST00000536370.1_3'UTR|RP11-637O19.3_ENST00000480294.1_Intron|MAK_ENST00000474039.1_Missense_Mutation_p.D329H|SYCP2L_ENST00000543878.1_Intron|MAK_ENST00000538030.1_Missense_Mutation_p.D329H			P20794	MAK_HUMAN	male germ cell-associated kinase	329	Glu/Pro-rich.		D -> E (in dbSNP:rs17579447).		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)				ACAACCTGATCGATTATATCC	0.483																																					p.D329H		Atlas-SNP	.											.	MAK	47	.	0			c.G985C						PASS	.						120	124	123					6																	10796389		2203	4300	6503	SO:0001583	missense	4117	exon9			CCTGATCGATTAT		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.985G>C	chr6.hg19:g.10796389C>G	ENSP00000313021:p.Asp329His	142.0	0.0	.		130.0	26.0	.	NM_005906	F1T0K6|G1FL29|Q547D0|Q9NUH7	Missense_Mutation	SNP	ENST00000313243.2	hg19	CCDS4516.1	.	.	.	.	.	.	.	.	.	.	C	13.92	2.380100	0.42207	.	.	ENSG00000111837	ENST00000313243;ENST00000354489;ENST00000538030	T;T;T	0.72167	-0.63;-0.63;-0.63	4.96	4.09	0.47781	.	0.539095	0.20661	N	0.088033	T	0.51024	0.1650	L	0.32530	0.975	0.45108	D	0.998127	P	0.46512	0.879	P	0.47673	0.554	T	0.53878	-0.8376	10	0.42905	T	0.14	.	9.0292	0.36249	0.0:0.7735:0.1482:0.0784	.	329	P20794	MAK_HUMAN	H	329	ENSP00000313021:D329H;ENSP00000346484:D329H;ENSP00000442250:D329H	ENSP00000313021:D329H	D	-	1	0	MAK	10904375	0.415000	0.25416	0.068000	0.19968	0.049000	0.14656	1.369000	0.34227	1.220000	0.43490	0.448000	0.29417	GAT	.	C|1.000;T|0.000	.	alt		0.483	MAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039841.1	NM_005906		G	10796389	C	G	10796389	3	3	79	1	0	0	0	0	1	0	0	0	9204	884	31	4	910	4	MAK	6	10796389	Missense_Mutation	SNP	C	TCGA-B1-5398-01A-02D-1589-08		10796389	160318678	29	5077											
MDC1	9656	hgsc.bcm.edu	37	chr6	30679993	30679993	+	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	ctctgcatctgtttcacagtCcccatgcagaggccaggctt	7	11	9	14	0	3	1	1	0	2	1	4	1	4	1	3	2	2	4	3	2	0	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr6:30679993C>T	ENST00000376406.3	-	5	2373	c.1726G>A	c.(1726-1728)Gac>Aac	p.D576N	MDC1_ENST00000376405.2_Missense_Mutation_p.D576N|MDC1_ENST00000494654.1_5'Flank|MDC1-AS1_ENST00000442150.1_RNA	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	576					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						GTTTCACAGTCCCCATGCAGA	0.542								Other conserved DNA damage response genes																													p.D576N		Atlas-SNP	.											MDC1_ENST00000376406,NS,carcinoma,0,1	MDC1	218	.	0			c.G1726A						PASS	.						58	57	58					6																	30679993		1509	2709	4218	SO:0001583	missense	9656	exon5			CACAGTCCCCATG	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.1726G>A	chr6.hg19:g.30679993C>T	ENSP00000365588:p.Asp576Asn	74.0	0.0	.		63.0	15.0	.	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Missense_Mutation	SNP	ENST00000376406.3	hg19	CCDS34384.1	.	.	.	.	.	.	.	.	.	.	C	8.320	0.824001	0.16678	.	.	ENSG00000137337	ENST00000376406;ENST00000376405;ENST00000429610;ENST00000422104	T;T	0.03553	3.97;3.89	4.32	1.5	0.22942	.	.	.	.	.	T	0.00875	0.0029	L	0.44542	1.39	0.09310	N	1	B;B;P;B	0.37466	0.037;0.054;0.596;0.003	B;B;B;B	0.35470	0.049;0.028;0.203;0.018	T	0.45906	-0.9229	9	0.15499	T	0.54	-2.5972	2.8168	0.05458	0.1874:0.5287:0.1815:0.1023	.	576;448;576;576	Q14676-2;B4DYH4;Q14676;Q14676-4	.;.;MDC1_HUMAN;.	N	576;576;576;448	ENSP00000365588:D576N;ENSP00000365587:D576N	ENSP00000365587:D576N	D	-	1	0	MDC1	30787972	0.031000	0.19500	0.001000	0.08648	0.006000	0.05464	1.511000	0.35801	0.106000	0.17784	-0.467000	0.05162	GAC	.	.	.	none		0.542	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641		T	30679993	C	T	30679993	3	4	79	1	0	0	0	0	1	0	0	0	9410	855	30	2	4587	2	MDC1	6	30679993	Missense_Mutation	SNP	C	TCGA-B1-5398-01A-02D-1589-08	19883604	30679993	140435074	30	5078											
SLC39A7	7922	hgsc.bcm.edu	37	chr6	33169242	33169242	+	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	ctcacgagagcatctggcatGgacatacccacgatcacgac	12	6	9	14	3	3	1	2	0	1	1	3	5	3	2	1	2	2	2	1	2	1	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr6:33169242G>C	ENST00000374677.3	+	1	593	c.220G>C	c.(220-222)Gga>Cga	p.G74R	RNY4P10_ENST00000365571.1_RNA|RXRB_ENST00000374685.4_5'Flank|SLC39A7_ENST00000374675.3_Missense_Mutation_p.G74R|RXRB_ENST00000413614.2_5'Flank|RXRB_ENST00000544186.1_5'Flank|RXRB_ENST00000374680.3_5'Flank	NM_006979.2	NP_008910.2	Q92504	S39A7_HUMAN	solute carrier family 39 (zinc transporter), member 7	74	His-rich.				transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion transmembrane transporter activity (GO:0046873)			NS(1)|breast(3)|endometrium(2)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						CATCTGGCATGGACATACCCA	0.552																																					p.G74R		Atlas-SNP	.											.	SLC39A7	32	.	0			c.G220C						PASS	.						122	123	122					6																	33169242		2134	4244	6378	SO:0001583	missense	7922	exon1			TGGCATGGACATA	AF117221	CCDS43453.1	6p21.3	2014-01-28		2003-10-27	ENSG00000112473	ENSG00000112473		"Solute carriers"	4927	protein-coding gene	gene with protein product		601416	"HLA class II region expressed gene KE4"	HKE4		8812499, 1855816, 19246244, 15705588	Standard	NM_006979		Approved	H2-KE4, D6S2244E, KE4, RING5, ZIP7	uc003odf.3	Q92504	OTTHUMG00000031238	ENST00000374677.3:c.220G>C	chr6.hg19:g.33169242G>C	ENSP00000363809:p.Gly74Arg	115.0	0.0	.		100.0	21.0	.	NM_006979	B0UXF6|Q5STP8|Q9UIQ0	Missense_Mutation	SNP	ENST00000374677.3	hg19	CCDS43453.1	.	.	.	.	.	.	.	.	.	.	G	15.46	2.840008	0.51057	.	.	ENSG00000112473	ENST00000374675;ENST00000446283;ENST00000374677	T;T	0.60920	0.15;0.15	4.75	4.75	0.60458	.	0.374050	0.27802	N	0.017796	T	0.30510	0.0767	L	0.27053	0.805	0.45946	D	0.99877	P	0.48162	0.906	B	0.44163	0.443	T	0.06643	-1.0815	10	0.13853	T	0.58	-11.1163	13.1907	0.59709	0.0:0.0:1.0:0.0	.	74	Q92504	S39A7_HUMAN	R	74;55;74	ENSP00000363807:G74R;ENSP00000363809:G74R	ENSP00000363807:G74R	G	+	1	0	SLC39A7	33277220	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	3.576000	0.53878	2.507000	0.84556	0.289000	0.19496	GGA	.	.	.	none		0.552	SLC39A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076499.2	NM_006979		C	33169242	G	C	33169242	3	2	79	1	0	0	0	0	1	0	0	0	14636	1349	47	4	222	4	SLC39A7	6	33169242	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	2489249	33169242	137945825	31	5079											
LMBRD1	55788	hgsc.bcm.edu	37	chr6	70451754	70451755	+	Frame_Shift_Ins	INS	-	-	AA																															ttttgttattgggaacattcINSaatggaacaaaggcactaca																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr6:70451754_70451755insAA	ENST00000370577.3	-	6	717_718	c.488_489insTT	c.(487-489)ttgfs	p.L163fs	LMBRD1_ENST00000370570.1_Frame_Shift_Ins_p.L90fs	NM_018368.3	NP_060838.3	Q9NUN5	LMBD1_HUMAN	LMBR1 domain containing 1	163					cobalamin metabolic process (GO:0009235)|insulin receptor internalization (GO:0038016)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein kinase B signaling (GO:0051898)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	clathrin-coated endocytic vesicle (GO:0045334)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cobalamin binding (GO:0031419)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	31						TGGGAACATTCAATGGAACAAA	0.267																																					p.L163fs		Atlas-INDEL	.											.	LMBRD1	61	.	0			c.489_490insTT						PASS	.																																			SO:0001589	frameshift_variant	55788	exon6			.	AF113224	CCDS4969.1	6q13	2011-05-12	2005-07-25	2005-07-25	ENSG00000168216	ENSG00000168216			23038	protein-coding gene	gene with protein product		612625	"chromosome 6 open reading frame 209"	C6orf209		19136951	Standard	NM_018368		Approved	FLJ11240, bA810I22.1, cblF	uc003pfa.3	Q9NUN5	OTTHUMG00000014985	ENST00000370577.3:c.487_488dupTT	chr6.hg19:g.70451755_70451756dupAA	ENSP00000359609:p.Leu163fs	95.0	0.0	0		90.0	14.0	0.155556	NM_018368	A8K204|E1P531|Q5VUN6|Q86Y70|Q96FW4|Q9BY56|Q9NZD6	Frame_Shift_Ins	INS	ENST00000370577.3	hg19	CCDS4969.1																																																																																			.	.	.	none		0.267	LMBRD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041124.1	NM_018368		AA	70451755	-	AA	70451754	7	5	79	1	0	1	1	0	0	0	0	0	8849	825	29	0	1177	0	LMBRD1	6	70451754	Frame_Shift_Ins	INS	-	TCGA-B1-5398-01A-02D-1589-08	37282512	70451754	100663313	32	5080											
TPBG	7162	hgsc.bcm.edu	37	chr6	83075159	83075159	+	Frame_Shift_Del	DEL	G	G	-																															tggccgacctcagtcccttcGctttctcgggcagcaatgcc																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr6:83075159delG	ENST00000369750.3	+	2	1098	c.481delG	c.(481-483)gctfs	p.A161fs	TPBG_ENST00000543496.1_Frame_Shift_Del_p.A161fs|TPBG_ENST00000535040.1_Frame_Shift_Del_p.A161fs			Q13641	TPBG_HUMAN	trophoblast glycoprotein	161					cell adhesion (GO:0007155)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	15		all_cancers(76;0.000805)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.0897)		BRCA - Breast invasive adenocarcinoma(397;0.107)		CAGTCCCTTCGCTTTCTCGGG	0.667																																					p.F160fs		Atlas-INDEL	.											.	TPBG	37	.	0			c.480delC						PASS	.						76	82	80					6																	83075159		2203	4300	6503	SO:0001589	frameshift_variant	7162	exon2			.	AJ012159	CCDS4995.1	6q14-q15	2008-07-29			ENSG00000146242	ENSG00000146242			12004	protein-coding gene	gene with protein product		190920				8132670	Standard	NM_006670		Approved	5T4-AG, 5T4	uc003pjo.3	Q13641	OTTHUMG00000015103	ENST00000369750.3:c.481delG	chr6.hg19:g.83075159delG	ENSP00000358765:p.Ala161fs	245.0	0.0	0		204.0	31.0	0.151961	NM_001166392	A8K555	Frame_Shift_Del	DEL	ENST00000369750.3	hg19	CCDS4995.1																																																																																			.	.	.	none		0.667	TPBG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041340.1			-	83075159	G	-	83075159	7	5	79	1	0	1	0	1	0	0	0	0	16406	1087	38	0	483	0	TPBG	6	83075159	Frame_Shift_Del	DEL	G	TCGA-B1-5398-01A-02D-1589-08	12623405	83075159	88039908	33	5081											
FIG4	9896	hgsc.bcm.edu	37	chr6	110086287	110086287	+	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	gcacagtttatggtgggaaaAtgtgctctggcctatcagct	9	12	12	8	0	2	0	1	0	1	0	2	1	2	1	1	3	2	4	1	3	4	3			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr6:110086287A>T	ENST00000230124.3	+	14	1630	c.1506A>T	c.(1504-1506)aaA>aaT	p.K502N	FIG4_ENST00000441478.2_Missense_Mutation_p.K225N	NM_014845.5	NP_055660.1	Q92562	FIG4_HUMAN	FIG4 phosphoinositide 5-phosphatase	502	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				cell death (GO:0008219)|locomotory behavior (GO:0007626)|myelin assembly (GO:0032288)|negative regulation of myelination (GO:0031642)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of neuron projection development (GO:0010976)|small molecule metabolic process (GO:0044281)|vacuole organization (GO:0007033)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)	phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)	32		all_cancers(87;8.63e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000124)|all_lung(197;0.0187)|Colorectal(196;0.0492)|Lung SC(18;0.0548)		OV - Ovarian serous cystadenocarcinoma(136;0.0355)|Epithelial(106;0.038)|all cancers(137;0.0425)|BRCA - Breast invasive adenocarcinoma(108;0.079)		TGGTGGGAAAATGTGCTCTGG	0.393																																					p.K502N		Atlas-SNP	.											.	FIG4	77	.	0			c.A1506T						PASS	.						162	144	150					6																	110086287		2203	4300	6503	SO:0001583	missense	9896	exon14			GGGAAAATGTGCT	D87464	CCDS5078.1	6q21	2014-09-17	2014-08-04	2007-07-30	ENSG00000112367	ENSG00000112367			16873	protein-coding gene	gene with protein product		609390	"KIAA0274", "FIG4 homolog (S. cerevisiae)", "FIG4 homolog, SAC1 lipid phosphatase domain containing (S. cerevisiae)"	KIAA0274		9039502, 11274189, 17572665	Standard	NM_014845		Approved	SAC3, hSac3, dJ249I4.1, ALS11, CMT4J	uc003ptt.2	Q92562	OTTHUMG00000015352	ENST00000230124.3:c.1506A>T	chr6.hg19:g.110086287A>T	ENSP00000230124:p.Lys502Asn	114.0	0.0	.		135.0	25.0	.	NM_014845	Q53H49|Q5TCS6	Missense_Mutation	SNP	ENST00000230124.3	hg19	CCDS5078.1	.	.	.	.	.	.	.	.	.	.	A	18.84	3.709792	0.68730	.	.	ENSG00000112367	ENST00000441478;ENST00000230124	T;T	0.57436	1.65;0.4	5.22	-7.1	0.01547	Synaptojanin, N-terminal (1);	0.052794	0.64402	D	0.000001	T	0.57198	0.2037	M	0.85859	2.78	0.52501	D	0.999955	D;D	0.64830	0.994;0.973	P;P	0.59424	0.857;0.496	T	0.76130	-0.3072	10	0.59425	D	0.04	-25.2243	16.78	0.85561	0.4032:0.0:0.5968:0.0	.	225;502	F5H8L9;Q92562	.;FIG4_HUMAN	N	225;502	ENSP00000399443:K225N;ENSP00000230124:K502N	ENSP00000230124:K502N	K	+	3	2	FIG4	110192980	0.983000	0.35010	0.502000	0.27614	0.869000	0.49853	0.299000	0.19138	-1.402000	0.02056	-0.924000	0.02725	AAA	.	.	.	none		0.393	FIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041768.1	NM_014845		T	110086287	A	T	110086287	3	4	79	1	0	0	0	0	1	0	0	0	5895	98	4	5	1560	5	FIG4	6	110086287	Missense_Mutation	SNP	A	TCGA-B1-5398-01A-02D-1589-08	27011128	110086287	61028780	34	5082											
AGR2	10551	hgsc.bcm.edu	37	chr7	16837318	16837319	+	Splice_Site	DNP	AC	AC	GA																															gtgtttgtcagttgtttcatActaaaataaaaagaaaagca																								rs571596748		TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr7:16837318_16837319AC>GA	ENST00000419304.2	-	6	483	c.331_331GT>TC	c.(331-333)GTta>TCtta	p.V111S	AGR2_ENST00000401412.1_Splice_Site_p.V111S|AGR2_ENST00000419572.2_Splice_Site_p.V131S	NM_006408.3	NP_006399.1	O95994	AGR2_HUMAN	anterior gradient 2	111					lung goblet cell differentiation (GO:0060480)|mucus secretion (GO:0070254)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)	dystroglycan binding (GO:0002162)			endometrium(2)|lung(1)|prostate(1)|skin(2)	6	Lung NSC(10;0.0376)|all_lung(11;0.0855)			UCEC - Uterine corpus endometrioid carcinoma (126;0.184)		GTTGTTTCATACTAAAATAAAA	0.381																																					p.Y111H|.		Atlas-SNP	.											.	AGR2	14	.	0			c.T331C|c.331-1G>T						PASS	.																																			SO:0001630	splice_region_variant	10551	exon6|exon7			TTTCATACTAAAA|TTCATACTAAAAT	AF038451	CCDS5364.1	7p21.3	2013-07-31	2013-07-31		ENSG00000106541	ENSG00000106541		"Protein disulfide isomerases"	328	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 17"	606358	"anterior gradient 2 homolog (Xenopus laevis)"			9790916	Standard	NM_006408		Approved	XAG-2, HAG-2, AG2, PDIA17	uc003str.3	O95994	OTTHUMG00000023446	ENST00000419304.2:c.331_331delinsGA	chr7.hg19:g.16837318_16837319delinsGA		63.0|64.0	0.0	.		60.0|59.0	14.0|13.0	.	NM_006408		Missense_Mutation|Splice_Site	SNP	ENST00000419304.2	hg19	CCDS5364.1																																																																																			.	.	.	none		0.381	AGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207594.2	NM_006408	Missense_Mutation	GA	16837319	AC	GA	16837318	5	3	79	1	0	0	0	0	0	0	1	0	395	405	14	3	208	3	AGR2	7	16837318	Splice_Site	DNP	AC	TCGA-B1-5398-01A-02D-1589-08		16837318	142301345	35	5083											
ABCB5	340273	hgsc.bcm.edu	37	chr7	20778604	20778604	+	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	caaatgctttatcttttgatAgagtttttactgcaattgca	11	18	6	6	0	1	2	0	1	1	1	1	2	1	2	0	0	4	4	0	0	5	9			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr7:20778604A>G	ENST00000404938.2	+	24	3519		c.e24-1		ABCB5_ENST00000258738.6_Splice_Site	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5						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						ATCTTTTGATAGAGTTTTTAC	0.393																																					.		Atlas-SNP	.											ABCB5_ENST00000404938,mucosal,malignant_melanoma,0,2	ABCB5	357	.	0			c.2868-2A>G						PASS	.						59	57	58					7																	20778604		2203	4300	6503	SO:0001630	splice_region_variant	340273	exon24			TTTGATAGAGTTT	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.2868-1A>G	chr7.hg19:g.20778604A>G		51.0	0.0	.		48.0	7.0	.	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Splice_Site	SNP	ENST00000404938.2	hg19	CCDS55090.1	.	.	.	.	.	.	.	.	.	.	A	13.43	2.236102	0.39498	.	.	ENSG00000004846	ENST00000404938;ENST00000258738	.	.	.	4.99	4.99	0.66335	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.9637	0.58472	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ABCB5	20745129	1.000000	0.71417	0.931000	0.37212	0.329000	0.28539	8.421000	0.90259	2.238000	0.73509	0.397000	0.26171	.	.	.	.	none		0.393	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	Intron	G	20778604	A	G	20778604	5	3	79	1	0	0	0	0	0	0	1	0	44	434	15	3	2997	3	ABCB5	7	20778604	Splice_Site	SNP	A	TCGA-B1-5398-01A-02D-1589-08	3941286	20778604	138360059	36	5084											
SBDS	51119	hgsc.bcm.edu	37	chr7	66459200	66459200	+	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	tgctgcagctgttacccaccTgcttacagatttcagtttgg	7	14	9	11	0	1	1	1	0	0	1	1	1	1	1	2	1	6	6	2	1	2	4			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr7:66459200T>C	ENST00000246868.2	-	2	440	c.257A>G	c.(256-258)cAg>cGg	p.Q86R	TYW1_ENST00000359626.5_5'Flank	NM_016038.2	NP_057122.2	Q9Y3A5	SBDS_HUMAN	Shwachman-Bodian-Diamond syndrome	86					bone marrow development (GO:0048539)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|inner cell mass cell proliferation (GO:0001833)|leukocyte chemotaxis (GO:0030595)|mature ribosome assembly (GO:0042256)|mitotic spindle stabilization (GO:0043148)|ribosomal large subunit biogenesis (GO:0042273)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|rRNA binding (GO:0019843)			cervix(1)|endometrium(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	7						GTTACCCACCTGCTTACAGAT	0.378			Gene Conversion			"AML, MDS"			Shwachman-Diamond syndrome																												p.Q86R		Atlas-SNP	.	yes	Rec		Schwachman-Diamond syndrome	7	7q11	51119	Shwachman-Bodian-Diamond syndrome protein		L	.	SBDS	20	.	0			c.A257G						PASS	.						153	133	139					7																	66459200		2203	4300	6503	SO:0001630	splice_region_variant	51119	exon2	Familial Cancer Database	Shwachman syndrome, Shwachman-Bodian syndrome, Congenital Lipomatosis of the Pancreas	CCCACCTGCTTAC	AF151855	CCDS5537.1	7q11.22	2014-09-17			ENSG00000126524	ENSG00000126524			19440	protein-coding gene	gene with protein product		607444				12496757	Standard	NM_016038		Approved	CGI-97, FLJ10917, SDS, SWDS	uc003tvm.1	Q9Y3A5	OTTHUMG00000023165	ENST00000246868.2:c.258+1A>G	chr7.hg19:g.66459200T>C		151.0	0.0	.		188.0	33.0	.	NM_016038	A8K0P4|Q96FX0|Q9NV53	Missense_Mutation	SNP	ENST00000246868.2	hg19	CCDS5537.1	.	.	.	.	.	.	.	.	.	.	T	16.75	3.209588	0.58343	.	.	ENSG00000126524	ENST00000246868	D	0.96011	-3.88	4.73	4.73	0.59995	Ribosome maturation protein SBDS, N-terminal (2);	0.104529	0.64402	D	0.000002	D	0.92886	0.7737	L	0.45422	1.42	0.58432	D	0.999999	B	0.15930	0.015	B	0.31016	0.123	D	0.89696	0.3901	10	0.32370	T	0.25	-14.8213	12.2034	0.54339	0.0:0.0:0.0:1.0	.	86	Q9Y3A5	SBDS_HUMAN	R	86	ENSP00000246868:Q86R	ENSP00000246868:Q86R	Q	-	2	0	SBDS	66096635	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.470000	0.53100	1.998000	0.58463	0.459000	0.35465	CAG	.	.	.	none		0.378	SBDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251746.2	NM_016038	Missense_Mutation	C	66459200	T	C	66459200	5	2	79	1	0	0	0	0	0	0	1	0	13870	1594	55	3	511	3	SBDS	7	66459200	Splice_Site	SNP	T	TCGA-B1-5398-01A-02D-1589-08	45680596	66459200	92679463	37	5085											
GPR22	2845	hgsc.bcm.edu	37	chr7	107115465	107115465	+	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	atgtctttattgattatttcTacatttcttctctgctggac	7	21	5	8	0	4	1	0	1	4	0	5	2	4	2	0	1	2	1	0	1	3	8			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr7:107115465T>A	ENST00000304402.4	+	3	2303	c.960T>A	c.(958-960)tcT>tcA	p.S320S	COG5_ENST00000393603.2_Intron|COG5_ENST00000347053.3_Intron|COG5_ENST00000475638.2_Intron|COG5_ENST00000297135.3_Intron	NM_005295.2	NP_005286.2	Q99680	GPR22_HUMAN	G protein-coupled receptor 22	320					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			large_intestine(3)|lung(6)|ovary(2)|stomach(1)	12						TGATTATTTCTACATTTCTTC	0.373																																					p.S320S		Atlas-SNP	.											.	GPR22	43	.	0			c.T960A						PASS	.						112	115	114					7																	107115465		2203	4300	6503	SO:0001819	synonymous_variant	2845	exon3			TATTTCTACATTT	U66581	CCDS5744.1	7q22-q31.1	2012-08-21			ENSG00000172209	ENSG00000172209		"GPCR / Class A : Orphans"	4477	protein-coding gene	gene with protein product		601910				9073069	Standard	NM_005295		Approved		uc003vef.3	Q99680	OTTHUMG00000154902	ENST00000304402.4:c.960T>A	chr7.hg19:g.107115465T>A		129.0	0.0	.		116.0	22.0	.	NM_005295	O14554	Silent	SNP	ENST00000304402.4	hg19	CCDS5744.1																																																																																			.	.	.	none		0.373	GPR22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337598.1			A	107115465	T	A	107115465	2	1	79	1	0	0	0	0	0	0	0	1	6689	1509	53	5		5	GPR22	7	107115465	Silent	SNP	T	TCGA-B1-5398-01A-02D-1589-08	40656265	107115465	52023198	38	5086											
IQUB	154865	hgsc.bcm.edu	37	chr7	123136764	123136764	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acttacattctaatgcattaTaaagaaattcaaaatcttca	18	14	2	7	0	4	1	2	0	2	1	4	1	4	1	0	0	2	1	0	0	8	7	rs567499713		TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr7:123136764T>C	ENST00000466202.1	-	7	1796	c.1220A>G	c.(1219-1221)tAt>tGt	p.Y407C	IQUB_ENST00000434450.1_Missense_Mutation_p.Y407C|IQUB_ENST00000324698.6_Missense_Mutation_p.Y407C	NM_001282855.1	NP_001269784.1	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	407					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						TAATGCATTATAAAGAAATTC	0.308													T|||	1	0.000199681	8e-04	0	5008	,	,		16913	0		0	False		,,,				2504	0				p.Y407C		Atlas-SNP	.											.	IQUB	117	.	0			c.A1220G						PASS	.						63	60	61					7																	123136764		2203	4298	6501	SO:0001583	missense	154865	exon7			GCATTATAAAGAA	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.1220A>G	chr7.hg19:g.123136764T>C	ENSP00000417769:p.Tyr407Cys	85.0	0.0	.		84.0	17.0	.	NM_178827	A4D0X0|Q49AL6|Q4G189|Q5BJD9|Q6NUH6|Q8N9Y2	Missense_Mutation	SNP	ENST00000466202.1	hg19	CCDS5787.1	.	.	.	.	.	.	.	.	.	.	T	11.58	1.680750	0.29872	.	.	ENSG00000164675	ENST00000466202;ENST00000324698;ENST00000434450	T;T;T	0.58652	1.37;1.37;0.32	5.17	0.946	0.19549	.	0.119152	0.64402	D	0.000016	T	0.73705	0.3621	M	0.83692	2.655	0.45295	D	0.998293	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.969	T	0.75434	-0.3319	10	0.87932	D	0	.	10.8458	0.46743	0.3381:0.0:0.0:0.6619	.	407;407	Q8NA54-2;Q8NA54	.;IQUB_HUMAN	C	407	ENSP00000417769:Y407C;ENSP00000324882:Y407C;ENSP00000388498:Y407C	ENSP00000324882:Y407C	Y	-	2	0	IQUB	122924000	1.000000	0.71417	1.000000	0.80357	0.099000	0.18886	1.936000	0.40183	0.309000	0.22966	0.533000	0.62120	TAT	.	.	.	none		0.308	IQUB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348529.1	NM_178827		C	123136764	T	C	123136764	3	2	79	1	0	0	0	0	1	0	0	0	7827	1406	49	3	1183	3	IQUB	7	123136764	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	16021299	123136764	36001899	39	5087											
BRAF	673	hgsc.bcm.edu	37	chr7	140453193	140453193	+	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	ggtcttcatgaagaaatataTctgaggtgtagtaagtaaag	15	12	11	3	0	3	3	1	2	2	1	3	3	3	3	0	2	0	3	0	2	8	6	rs121913370		TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr7:140453193T>C	ENST00000288602.6	-	15	1802	c.1742A>G	c.(1741-1743)aAt>aGt	p.N581S		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	581	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		N -> D (in CFC1). {ECO:0000269|PubMed:16439621, ECO:0000269|PubMed:16474404, ECO:0000269|PubMed:18042262}.|N -> S (in a colorectal adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		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.N581S(9)|p.N581I(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)	AAGAAATATATCTGAGGTGTA	0.358		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.N581S	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,0,16	BRAF	36346	.	10	Substitution - Missense(10)	large_intestine(3)|lung(3)|skin(2)|ovary(1)|soft_tissue(1)	c.A1742G						PASS	.						86	83	84					7																	140453193		2203	4298	6501	SO:0001630	splice_region_variant	673	exon15	Familial Cancer Database	CFC, CFCS	AATATATCTGAGG	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.1742-1A>G	chr7.hg19:g.140453193T>C		104.0	0.0	.		106.0	18.0	.	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	hg19	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.68|17.68	3.450518|3.450518	0.63290|0.63290	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000496384|ENST00000288602	.|D	.|0.99803	.|-6.82	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	D|D	0.99864|0.99864	0.9936|0.9936	H|H	0.96970|0.96970	3.915|3.915	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.87578	.|0.998	D|D	0.96655|0.96655	0.9484|0.9484	5|10	.|0.59425	.|D	.|0.04	.|.	15.9326|15.9326	0.79675|0.79675	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|581	.|P15056	.|BRAF_HUMAN	V|S	189|581	.|ENSP00000288602:N581S	.|ENSP00000288602:N581S	I|N	-|-	1|2	0|0	BRAF|BRAF	140099662|140099662	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.921000|7.921000	0.87530|0.87530	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	ATA|AAT	.	.	.	weak		0.358	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333	Missense_Mutation	C	140453193	T	C	140453193	5	2	79	1	0	0	0	0	0	0	1	0	1498	1449	50	3	574	3	BRAF	7	140453193	Splice_Site	SNP	T	TCGA-B1-5398-01A-02D-1589-08	17316429	140453193	18685470	40	5088											
KIF27	55582	hgsc.bcm.edu	37	chr9	86485505	86485505	+	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	tgcatcaaggtcctcagcttTcggttttagaccttcttcct	6	16	7	12	1	3	1	2	0	1	1	6	1	5	1	3	2	2	3	3	2	2	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr9:86485505T>A	ENST00000297814.2	-	12	2829	c.2686A>T	c.(2686-2688)Aaa>Taa	p.K896*	KIF27_ENST00000334204.2_Intron|KIF27_ENST00000413982.1_Nonsense_Mutation_p.K830*|RP11-575L7.4_ENST00000589817.1_RNA|RP11-575L7.4_ENST00000591217.1_RNA|RP11-575L7.4_ENST00000421734.3_RNA|RP11-575L7.4_ENST00000590368.1_RNA|RP11-575L7.4_ENST00000589233.1_RNA|RP11-575L7.4_ENST00000586211.1_RNA	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	896					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						TCCTCAGCTTTCGGTTTTAGA	0.363																																					p.K896X		Atlas-SNP	.											.	KIF27	103	.	0			c.A2686T						PASS	.						93	88	90					9																	86485505		2202	4300	6502	SO:0001587	stop_gained	55582	exon12			CAGCTTTCGGTTT	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.2686A>T	chr9.hg19:g.86485505T>A	ENSP00000297814:p.Lys896*	128.0	0.0	.		143.0	18.0	.	NM_017576	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Nonsense_Mutation	SNP	ENST00000297814.2	hg19	CCDS6665.1	.	.	.	.	.	.	.	.	.	.	T	28.9	4.962159	0.92791	.	.	ENSG00000165115	ENST00000297814;ENST00000413982	.	.	.	3.74	3.74	0.42951	.	0.000000	0.52532	U	0.000067	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.9954	0.36050	0.0:0.0:0.0:1.0	.	.	.	.	X	896;830	.	ENSP00000297814:K896X	K	-	1	0	KIF27	85675325	0.392000	0.25229	0.385000	0.26158	0.016000	0.09150	0.777000	0.26718	1.682000	0.51000	0.240000	0.17902	AAA	.	.	.	none		0.363	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576		A	86485505	T	A	86485505	4	1	79	1	0	0	0	0	0	1	0	0	8303	1792	62	5	1547	5	KIF27	9	86485505	Nonsense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08		86485505	54727926	41	5089											
DAPK1	1612	hgsc.bcm.edu	37	chr9	90254289	90254289	+	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	cctgagaacataatgcttttGgatagaaatgtccccaaacc	14	10	7	10	0	0	2	0	1	0	2	1	4	1	3	4	1	3	1	4	1	5	4			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr9:90254289G>C	ENST00000408954.3	+	5	779	c.444G>C	c.(442-444)ttG>ttC	p.L148F	DAPK1_ENST00000469640.2_Missense_Mutation_p.L148F|DAPK1_ENST00000358077.5_Missense_Mutation_p.L148F|DAPK1_ENST00000491893.1_Missense_Mutation_p.L148F|DAPK1_ENST00000472284.1_Missense_Mutation_p.L148F	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	148	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						TAATGCTTTTGGATAGAAATG	0.363									Chronic Lymphocytic Leukemia, Familial Clustering of																												p.L148F		Atlas-SNP	.											.	DAPK1	329	.	0			c.G444C						PASS	.						86	82	83					9																	90254289		1807	4078	5885	SO:0001583	missense	1612	exon5	Familial Cancer Database	Familial CLL	GCTTTTGGATAGA	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.444G>C	chr9.hg19:g.90254289G>C	ENSP00000386135:p.Leu148Phe	165.0	0.0	.		179.0	27.0	.	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	hg19	CCDS43842.1	.	.	.	.	.	.	.	.	.	.	G	16.96	3.264980	0.59431	.	.	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16	5.42	3.59	0.41128	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.40728	N	0.001036	T	0.61714	0.2369	N	0.17800	0.525	0.58432	D	0.999993	P;P;D	0.76494	0.838;0.93;0.999	B;P;D	0.81914	0.41;0.51;0.995	T	0.62258	-0.6892	10	0.59425	D	0.04	.	7.0523	0.25079	0.1427:0.0:0.7183:0.139	.	148;148;148	B7ZLE7;B7Z454;P53355	.;.;DAPK1_HUMAN	F	148	ENSP00000350785:L148F;ENSP00000417076:L148F;ENSP00000418885:L148F;ENSP00000386135:L148F;ENSP00000419026:L148F	ENSP00000350785:L148F	L	+	3	2	DAPK1	89444109	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	2.692000	0.47018	0.850000	0.35239	-0.244000	0.11960	TTG	.	.	.	none		0.363	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938		C	90254289	G	C	90254289	3	2	79	1	0	0	0	0	1	0	0	0	4237	1339	47	4	458	4	DAPK1	9	90254289	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	3768784	90254289	50959142	42	5090											
PSMD5	5711	hgsc.bcm.edu	37	chr9	123591454	123591454	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtggtacagtagtttaaagaTtctggtgacacggaagaaat	14	11	12	4	1	1	3	0	1	1	2	1	4	1	4	0	3	1	3	0	3	6	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr9:123591454T>C	ENST00000210313.3	-	5	668	c.594A>G	c.(592-594)gaA>gaG	p.E198E	PSMD5-AS1_ENST00000589026.1_RNA|PSMD5_ENST00000373904.5_Silent_p.E155E	NM_001270427.1|NM_005047.3	NP_001257356.1|NP_005038.1	Q16401	PSMD5_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 5	198					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome regulatory particle assembly (GO:0070682)|protein folding (GO:0006457)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)				endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|prostate(1)	10						AGTTTAAAGATTCTGGTGACA	0.398																																					p.E198E		Atlas-SNP	.											.	PSMD5	34	.	0			c.A594G						PASS	.						99	100	100					9																	123591454		2203	4300	6503	SO:0001819	synonymous_variant	5711	exon5			TAAAGATTCTGGT	AK001065	CCDS6824.1, CCDS59143.1	9q34.11	2008-02-05			ENSG00000095261	ENSG00000095261		"Proteasome (prosome, macropain) subunits"	9563	protein-coding gene	gene with protein product		604452				7559544	Standard	NM_005047		Approved	S5B, KIAA0072	uc004bko.4	Q16401	OTTHUMG00000020573	ENST00000210313.3:c.594A>G	chr9.hg19:g.123591454T>C		94.0	0.0	.		110.0	17.0	.	NM_005047	B4DZM8|Q15045|Q4VXG8	Silent	SNP	ENST00000210313.3	hg19	CCDS6824.1																																																																																			.	.	.	none		0.398	PSMD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053825.2	NM_005047		C	123591454	T	C	123591454	2	2	79	1	0	0	0	0	0	0	0	1	12711	1490	52	3		3	PSMD5	9	123591454	Silent	SNP	T	TCGA-B1-5398-01A-02D-1589-08	33337165	123591454	17621977	43	5091											
SPTAN1	6709	hgsc.bcm.edu	37	chr9	131339498	131339498	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacctggcaagtgttcaggcTctgcttcggaagcacgaggg	8	8	15	10	2	2	0	1	0	1	0	3	3	2	1	1	4	2	5	1	4	2	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr9:131339498T>C	ENST00000372731.4	+	7	986	c.876T>C	c.(874-876)gcT>gcC	p.A292A	SPTAN1_ENST00000372739.3_Silent_p.A292A|SPTAN1_ENST00000358161.5_Silent_p.A292A	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	292					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						GTGTTCAGGCTCTGCTTCGGA	0.473																																					p.A292A	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.T876C						PASS	.						134	136	135					9																	131339498		2203	4300	6503	SO:0001819	synonymous_variant	6709	exon7			TCAGGCTCTGCTT	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.876T>C	chr9.hg19:g.131339498T>C		201.0	0.0	.		203.0	43.0	.	NM_003127	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Silent	SNP	ENST00000372731.4	hg19	CCDS6905.1																																																																																			.	.	.	none		0.473	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		C	131339498	T	C	131339498	2	2	79	1	0	0	0	0	0	0	0	1	15129	1538	54	3		3	SPTAN1	9	131339498	Silent	SNP	T	TCGA-B1-5398-01A-02D-1589-08	7748044	131339498	9873933	44	5092											
KCNT1	57582	hgsc.bcm.edu	37	chr9	138683918	138683918	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctccgaccccctggctcacGtggccagcagctcccagagc	6	5	11	19	2	1	1	1	0	0	1	3	2	3	1	5	2	3	4	5	2	0	0			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr9:138683918G>A	ENST00000263604.3	+	31	3604	c.3604G>A	c.(3604-3606)Gtg>Atg	p.V1202M	KCNT1_ENST00000298480.5_Missense_Mutation_p.V1228M|KCNT1_ENST00000371757.2_Missense_Mutation_p.V1207M|KCNT1_ENST00000488444.2_Missense_Mutation_p.V1207M|KCNT1_ENST00000486577.2_Missense_Mutation_p.V1185M|KCNT1_ENST00000491806.2_Missense_Mutation_p.V1193M|KCNT1_ENST00000487664.1_Missense_Mutation_p.V1183M|KCNT1_ENST00000490355.2_Missense_Mutation_p.V1206M			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	1202					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)		CCTGGCTCACGTGGCCAGCAG	0.677																																					p.V1207M		Atlas-SNP	.											.	KCNT1	139	.	0			c.G3619A						PASS	.						23	25	25					9																	138683918		2201	4299	6500	SO:0001583	missense	57582	exon31			GCTCACGTGGCCA	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.3604G>A	chr9.hg19:g.138683918G>A	ENSP00000263604:p.Val1202Met	24.0	0.0	.		42.0	7.0	.	NM_020822	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Missense_Mutation	SNP	ENST00000263604.3	hg19		.	.	.	.	.	.	.	.	.	.	G	13.10	2.136017	0.37728	.	.	ENSG00000107147	ENST00000487664;ENST00000298480;ENST00000371757;ENST00000486577;ENST00000491806;ENST00000488444;ENST00000490355;ENST00000263604	T;T;T;T	0.25912	1.84;1.86;1.77;1.84	4.86	2.02	0.26589	.	0.135507	0.49305	N	0.000146	T	0.19565	0.0470	L	0.46157	1.445	0.43043	D	0.994636	B;B;B	0.32365	0.058;0.251;0.367	B;B;B	0.27500	0.027;0.037;0.08	T	0.03898	-1.0994	10	0.41790	T	0.15	-41.9415	9.4906	0.38958	0.2237:0.0:0.7763:0.0	.	1195;1207;1183	C9JYL2;B9EGP2;G5E9V0	.;.;.	M	1183;1228;1207;1187;1195;1209;1207;1202	ENSP00000417851:V1183M;ENSP00000298480:V1228M;ENSP00000360822:V1207M;ENSP00000263604:V1202M	ENSP00000263604:V1202M	V	+	1	0	KCNT1	137823739	1.000000	0.71417	0.999000	0.59377	0.475000	0.33008	2.313000	0.43735	0.132000	0.18615	0.561000	0.74099	GTG	.	.	.	none		0.677	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822		A	138683918	G	A	138683918	3	1	79	1	0	0	0	0	1	0	0	0	8098	1145	40	1	3741	1	KCNT1	9	138683918	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	7344420	138683918	2529513	45	5093											
RHOBTB1	9886	hgsc.bcm.edu	37	chr10	62648933	62648933	+	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	tgggggcaaaatatcccctcTctttatgggcctgaaataga	11	11	10	9	0	1	2	0	1	1	1	3	2	2	2	3	3	0	1	3	3	6	4			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr10:62648933T>A	ENST00000337910.5	-	6	830	c.493A>T	c.(493-495)Aga>Tga	p.R165*	RHOBTB1_ENST00000357917.4_Nonsense_Mutation_p.R165*	NM_001242359.1|NM_014836.4	NP_001229288.1|NP_055651.1	O94844	RHBT1_HUMAN	Rho-related BTB domain containing 1	165	Rho-like.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(6)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	Prostate(12;0.0112)					ATATCCCCTCTCTTTATGGGC	0.388																																					p.R165X		Atlas-SNP	.											.	RHOBTB1	61	.	0			c.A493T						PASS	.						57	59	58					10																	62648933		2203	4300	6503	SO:0001587	stop_gained	9886	exon6			CCCCTCTCTTTAT	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.493A>T	chr10.hg19:g.62648933T>A	ENSP00000338671:p.Arg165*	107.0	0.0	.		122.0	14.0	.	NM_014836		Nonsense_Mutation	SNP	ENST00000337910.5	hg19	CCDS7261.1	.	.	.	.	.	.	.	.	.	.	T	40	8.172729	0.98688	.	.	ENSG00000072422	ENST00000357917;ENST00000337910	.	.	.	5.83	4.65	0.58169	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.3328	0.66569	0.0:0.0:0.1313:0.8686	.	.	.	.	X	165	.	ENSP00000338671:R165X	R	-	1	2	RHOBTB1	62318939	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.586000	0.46119	2.219000	0.72066	0.482000	0.46254	AGA	.	.	.	none		0.388	RHOBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048220.1			A	62648933	T	A	62648933	4	1	79	1	0	0	0	0	0	1	0	0	13346	1559	54	5	1621	5	RHOBTB1	10	62648933	Nonsense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08		62648933	72885814	46	5094											
ENTPD7	57089	hgsc.bcm.edu	37	chr10	101458575	101458575	+	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	agaggatgtgttgcgcattgGtggccgctaccatgggccaa	8	9	15	9	2	0	1	0	0	0	1	0	2	0	2	3	4	2	3	3	4	2	3			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr10:101458575G>C	ENST00000370489.4	+	10	1473	c.1295G>C	c.(1294-1296)gGt>gCt	p.G432A		NM_020354.3	NP_065087.1	Q9NQZ7	ENTP7_HUMAN	ectonucleoside triphosphate diphosphohydrolase 7	432						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)		TTGCGCATTGGTGGCCGCTAC	0.438																																					p.G432A		Atlas-SNP	.											.	ENTPD7	44	.	0			c.G1295C						PASS	.						58	57	57					10																	101458575		2203	4300	6503	SO:0001583	missense	57089	exon10			GCATTGGTGGCCG	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.1295G>C	chr10.hg19:g.101458575G>C	ENSP00000359520:p.Gly432Ala	83.0	0.0	.		69.0	12.0	.	NM_020354	B2RB83|B3KP21|D3DR64	Missense_Mutation	SNP	ENST00000370489.4	hg19	CCDS7480.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.310593	0.81358	.	.	ENSG00000198018	ENST00000370489	T	0.12879	2.64	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	T	0.37128	0.0992	M	0.71036	2.16	0.80722	D	1	D	0.60575	0.988	D	0.70935	0.971	T	0.03278	-1.1053	10	0.37606	T	0.19	-17.123	18.3825	0.90455	0.0:0.0:1.0:0.0	.	432	Q9NQZ7	ENTP7_HUMAN	A	432	ENSP00000359520:G432A	ENSP00000359520:G432A	G	+	2	0	ENTPD7	101448565	1.000000	0.71417	0.982000	0.44146	0.720000	0.41350	9.578000	0.98200	2.583000	0.87209	0.655000	0.94253	GGT	.	.	.	none		0.438	ENTPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049809.2	NM_020354		C	101458575	G	C	101458575	3	2	79	1	0	0	0	0	1	0	0	0	5146	1261	44	4	1329	4	ENTPD7	10	101458575	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	38809642	101458575	34076172	47	5095											
NFKB2	4791	hgsc.bcm.edu	37	chr10	104156717	104156717	+	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	gacctggtaacacacagtgaCccacctcgtgctcatgccca	10	7	8	16	1	1	1	1	1	0	0	2	2	1	1	4	1	3	2	4	1	1	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr10:104156717C>T	ENST00000369966.3	+	6	550	c.300C>T	c.(298-300)gaC>gaT	p.D100D	NFKB2_ENST00000189444.6_Silent_p.D100D|NFKB2_ENST00000428099.1_Silent_p.D100D	NM_001077494.2	NP_001070962.1	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)	100	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)	CACACAGTGACCCACCTCGTG	0.597			T	IGH@	B-NHL																																p.D100D		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.C300T						PASS	.						78	84	82					10																	104156717		2080	4213	6293	SO:0001819	synonymous_variant	4791	exon6			CAGTGACCCACCT	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.300C>T	chr10.hg19:g.104156717C>T		53.0	0.0	.		54.0	7.0	.	NM_001077494	A8K9D9|D3DR83|Q04860|Q9BU75|Q9H471|Q9H472	Silent	SNP	ENST00000369966.3	hg19	CCDS41564.1																																																																																			.	.	.	none		0.597	NFKB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050080.2			T	104156717	C	T	104156717	2	4	79	1	0	0	0	0	0	0	0	1	10383	506	18	2		2	NFKB2	10	104156717	Silent	SNP	C	TCGA-B1-5398-01A-02D-1589-08	2698142	104156717	31378030	48	5096											
CCKBR	887	hgsc.bcm.edu	37	chr11	6291417	6291417	+	Missense_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	ggcacgagtgtggcagacgcGctcccacgcggctcgcgtga	6	5	16	14	7	0	2	0	1	0	1	2	3	1	2	1	3	0	4	1	3	0	0			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:6291417G>A	ENST00000334619.2	+	3	696	c.503G>A	c.(502-504)cGc>cAc	p.R168H	CCKBR_ENST00000525462.1_Missense_Mutation_p.R168H|CCKBR_ENST00000525014.1_3'UTR|CCKBR_ENST00000532715.1_Missense_Mutation_p.R84H	NM_176875.3	NP_795344.1	P32239	GASR_HUMAN	cholecystokinin B receptor	168					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)	TGGCAGACGCGCTCCCACGCG	0.647																																					p.R168H		Atlas-SNP	.											.	CCKBR	232	.	0			c.G503A						PASS	.						46	38	41					11																	6291417		2197	4290	6487	SO:0001583	missense	887	exon3			AGACGCGCTCCCA	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.503G>A	chr11.hg19:g.6291417G>A	ENSP00000335544:p.Arg168His	52.0	0.0	.		51.0	11.0	.	NM_176875	A8K7P9|O75824|Q16144|Q92492|Q96LC6|Q9NYK7|Q9UBV1	Missense_Mutation	SNP	ENST00000334619.2	hg19	CCDS7761.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.371373	0.82573	.	.	ENSG00000110148	ENST00000334619;ENST00000532715;ENST00000525462	T;T;T	0.72725	-0.68;-0.68;-0.68	4.81	4.81	0.61882	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.84197	0.5419	M	0.88377	2.95	0.51012	D	0.999906	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.75020	0.937;0.975;0.985	D	0.85468	0.1171	10	0.52906	T	0.07	.	10.2312	0.43256	0.0916:0.0:0.9084:0.0	.	168;102;168	P32239-2;P32239-3;P32239	.;.;GASR_HUMAN	H	168;84;168	ENSP00000335544:R168H;ENSP00000432079:R84H;ENSP00000435534:R168H	ENSP00000335544:R168H	R	+	2	0	CCKBR	6247993	0.101000	0.21875	1.000000	0.80357	0.942000	0.58702	2.571000	0.45990	2.505000	0.84491	0.655000	0.94253	CGC	.	.	.	none		0.647	CCKBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257230.2	NM_176875		A	6291417	G	A	6291417	3	1	79	1	0	0	0	0	1	0	0	0	2883	1087	38	1	513	1	CCKBR	11	6291417	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08		6291417	128715099	49	5097											
MAPK8IP1	9479	hgsc.bcm.edu	37	chr11	45926284	45926284	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtagattgccaccacccgcCggctcaccgtgcactttaac	8	9	8	16	3	1	1	1	0	0	1	1	1	1	1	5	1	3	3	5	1	2	4			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:45926284C>T	ENST00000241014.2	+	9	1962	c.1792C>T	c.(1792-1794)Cgg>Tgg	p.R598W	MAPK8IP1_ENST00000395629.2_Missense_Mutation_p.R588W|RP11-618K13.2_ENST00000533218.1_RNA	NM_005456.3	NP_005447.1	Q9UQF2	JIP1_HUMAN	mitogen-activated protein kinase 8 interacting protein 1	598	Interaction with VRK2.|PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				JUN phosphorylation (GO:0007258)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|positive regulation of signal transduction (GO:0009967)|regulation of JNK cascade (GO:0046328)|regulation of transcription, DNA-templated (GO:0006355)|vesicle-mediated transport (GO:0016192)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic growth cone (GO:0044294)|dentate gyrus mossy fiber (GO:0044302)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)|protein kinase inhibitor activity (GO:0004860)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)	24				GBM - Glioblastoma multiforme(35;0.231)		CACCACCCGCCGGCTCACCGT	0.612																																					p.R598W		Atlas-SNP	.											MAPK8IP1,NS,carcinoma,0,1	MAPK8IP1	51	.	0			c.C1792T						PASS	.						77	80	79					11																	45926284		2203	4299	6502	SO:0001583	missense	9479	exon9			ACCCGCCGGCTCA		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.1792C>T	chr11.hg19:g.45926284C>T	ENSP00000241014:p.Arg598Trp	149.0	0.0	.		116.0	21.0	.	NM_005456	D3DQP4|O43407	Missense_Mutation	SNP	ENST00000241014.2	hg19	CCDS7916.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.560899	0.86335	.	.	ENSG00000121653	ENST00000241014;ENST00000395629	T;T	0.14766	2.48;2.48	5.84	4.87	0.63330	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.056704	0.64402	D	0.000002	T	0.35653	0.0939	L	0.61218	1.895	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.03503	-1.1030	10	0.87932	D	0	-26.4988	16.4247	0.83810	0.0:0.8687:0.1313:0.0	.	598	Q9UQF2	JIP1_HUMAN	W	598;588	ENSP00000241014:R598W;ENSP00000378991:R588W	ENSP00000241014:R598W	R	+	1	2	MAPK8IP1	45882860	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.985000	0.29578	2.768000	0.95171	0.561000	0.74099	CGG	.	.	.	none		0.612	MAPK8IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259405.1	NM_005456		T	45926284	C	T	45926284	3	4	79	1	0	0	0	0	1	0	0	0	9291	643	23	1	1826	1	MAPK8IP1	11	45926284	Missense_Mutation	SNP	C	TCGA-B1-5398-01A-02D-1589-08	39634867	45926284	89080232	50	5098											
MADD	8567	hgsc.bcm.edu	37	chr11	47345285	47345285	+	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	tgtatgagcgctggtggtacGagaagctcatcaacatgacc	11	9	12	9	2	2	3	2	2	0	1	2	4	2	3	1	2	4	4	1	2	4	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:47345285G>C	ENST00000311027.5	+	31	4606	c.4441G>C	c.(4441-4443)Gag>Cag	p.E1481Q	MADD_ENST00000405573.2_Missense_Mutation_p.E291Q|MADD_ENST00000395336.3_Missense_Mutation_p.E1481Q|MADD_ENST00000407859.3_Missense_Mutation_p.E1399Q|MADD_ENST00000395344.3_Missense_Mutation_p.E1375Q|MADD_ENST00000402799.1_Missense_Mutation_p.E1379Q|MADD_ENST00000402192.2_Missense_Mutation_p.E1421Q|MADD_ENST00000406482.1_Missense_Mutation_p.E1379Q|MADD_ENST00000342922.4_Missense_Mutation_p.E1422Q|MADD_ENST00000349238.3_Missense_Mutation_p.E1442Q	NM_003682.3	NP_003673.3			MAP-kinase activating death domain											breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		CTGGTGGTACGAGAAGCTCAT	0.498																																					p.E1481Q		Atlas-SNP	.											.	MADD	172	.	0			c.G4441C						PASS	.						223	167	186					11																	47345285		2201	4298	6499	SO:0001583	missense	8567	exon31			TGGTACGAGAAGC	AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"DENN/MADD domain containing"	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.4441G>C	chr11.hg19:g.47345285G>C	ENSP00000310933:p.Glu1481Gln	88.0	0.0	.		96.0	18.0	.	NM_130475		Missense_Mutation	SNP	ENST00000311027.5	hg19	CCDS7930.1	.	.	.	.	.	.	.	.	.	.	G	33	5.270702	0.95429	.	.	ENSG00000110514	ENST00000342922;ENST00000395342;ENST00000402799;ENST00000406482;ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395344;ENST00000395336;ENST00000402192;ENST00000405573	T;T;T;T;T;T;T;T;T;T	0.57436	2.85;2.72;2.75;2.83;2.86;2.72;2.72;2.87;2.85;0.4	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.70762	0.3261	L	0.53561	1.675	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;0.999;1.0;0.999;0.999	D;D;D;D;D;D;D;D;D;D;D	0.91635	0.999;0.998;0.998;0.999;0.999;0.999;0.999;0.999;0.998;0.997;0.998	T	0.71724	-0.4506	10	0.87932	D	0	-24.9261	19.903	0.96995	0.0:0.0:1.0:0.0	.	291;1375;1375;1481;1379;1379;1379;1442;1399;1481;1422	F8W8U2;B5MEE5;A8K8S7;Q8WXG6-7;F8W9P9;Q8WXG6-6;Q8WXG6-5;Q8WXG6-2;Q8WXG6-4;Q8WXG6;Q8WXG6-3	.;.;.;.;.;.;.;.;.;MADD_HUMAN;.	Q	1422;1379;1379;1379;1442;1481;1399;1375;1481;1421;291	ENSP00000343902:E1422Q;ENSP00000385585:E1379Q;ENSP00000384435:E1379Q;ENSP00000304505:E1442Q;ENSP00000310933:E1481Q;ENSP00000384204:E1399Q;ENSP00000378753:E1375Q;ENSP00000378745:E1481Q;ENSP00000384287:E1421Q;ENSP00000384483:E291Q	ENSP00000310933:E1481Q	E	+	1	0	MADD	47301861	1.000000	0.71417	0.992000	0.48379	0.988000	0.76386	8.947000	0.93000	2.705000	0.92388	0.549000	0.68633	GAG	.	.	.	none		0.498	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1			C	47345285	G	C	47345285	3	2	79	1	0	0	0	0	1	0	0	0	9159	1059	37	4	4559	4	MADD	11	47345285	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	1419001	47345285	87661231	51	5099											
OR5D14	219436	hgsc.bcm.edu	37	chr11	55563325	55563326	+	Missense_Mutation	DNP	CT	CT	AA																															aaaagcatcttctactttagCtgcatgatgcagtacttcct																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:55563325_55563326CT>AA	ENST00000335605.1	+	1	294_295	c.294_295CT>AA	c.(292-297)agCTgc>agAAgc	p.98_99SC>RS		NM_001004735.1	NP_001004735.1	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D, member 14	98						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(30)|ovary(2)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	48		all_epithelial(135;0.196)				TCTACTTTAGCTGCATGATGCA	0.455																																					p.S98R|p.C99S		Atlas-SNP	.											.	OR5D14	116	.	0			c.C294A|c.T295A						PASS	.																																			SO:0001583	missense	219436	exon1			CTTTAGCTGCATG|TTTAGCTGCATGA	AB065779	CCDS31508.1	11q11	2012-08-09			ENSG00000186113	ENSG00000186113		"GPCR / Class A : Olfactory receptors"	15281	protein-coding gene	gene with protein product							Standard	NM_001004735		Approved		uc010rim.2	Q8NGL3	OTTHUMG00000166809	Exception_encountered	chr11.hg19:g.55563325_55563326delinsAA	ENSP00000334456:p.S98_C99delinsRS	89.0|91.0	0.0	.		82.0|81.0	7.0	.	NM_001004735	Q6IF69|Q6IFD4|Q96RB5	Missense_Mutation	SNP	ENST00000335605.1	hg19	CCDS31508.1																																																																																			.	.	.	none		0.455	OR5D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391513.1	NM_001004735		AA	55563326	CT	AA	55563325	3	1	79	1	0	0	0	0	1	0	0	0	11162	796	28	4	296	4	OR5D14	11	55563325	Missense_Mutation	DNP	CT	TCGA-B1-5398-01A-02D-1589-08	8218040	55563325	79443191	52	5100											
SLC22A10	387775	hgsc.bcm.edu	37	chr11	63064875	63064875	+	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	tccctgtttactgtgtactaCgcttcttggcaggtttttct	4	19	8	10	1	2	0	0	0	2	0	3	0	3	0	1	2	3	5	1	2	3	8	rs200183991		TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:63064875C>T	ENST00000332793.6	+	3	609	c.607C>T	c.(607-609)Cgc>Tgc	p.R203C	SLC22A10_ENST00000544661.1_Missense_Mutation_p.R48C|SLC22A10_ENST00000535888.1_5'UTR|SLC22A10_ENST00000525620.1_3'UTR|SLC22A10_ENST00000526800.1_Intron	NM_001039752.3	NP_001034841.3	Q63ZE4	S22AA_HUMAN	solute carrier family 22, member 10	203						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28					Conjugated Estrogens(DB00286)|Probenecid(DB01032)|Salicylic acid(DB00936)	CTGTGTACTACGCTTCTTGGC	0.408																																					p.R203C		Atlas-SNP	.											.	SLC22A10	79	.	0			c.C607T						PASS	.	C	CYS/ARG	2,4092		0,2,2045	170	169	169		607	2.3	0.3	11		169	0,8428		0,0,4214	yes	missense	SLC22A10	NM_001039752.3	180	0,2,6259	TT,TC,CC		0.0,0.0489,0.016	probably-damaging	203/542	63064875	2,12520	2047	4214	6261	SO:0001583	missense	387775	exon3			GTACTACGCTTCT	AP003420	CCDS41661.1	11q12.3	2013-05-22	2008-01-11		ENSG00000184999	ENSG00000184999		"Solute carriers"	18057	protein-coding gene	gene with protein product		607580	"solute carrier family 22 (organic anion/cation transporter), member 10"			11327718	Standard	NM_001039752		Approved	OAT5, hOAT5	uc009yor.3	Q63ZE4	OTTHUMG00000165197	ENST00000332793.6:c.607C>T	chr11.hg19:g.63064875C>T	ENSP00000327569:p.Arg203Cys	217.0	0.0	.		232.0	31.0	.	NM_001039752	Q68CJ0	Missense_Mutation	SNP	ENST00000332793.6	hg19	CCDS41661.1	.	.	.	.	.	.	.	.	.	.	C	17.11	3.306314	0.60305	4.89E-4	0.0	ENSG00000184999	ENST00000544661;ENST00000332793	D;D	0.90261	-2.64;-2.64	3.26	2.34	0.29019	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.066213	0.64402	N	0.000009	D	0.93341	0.7877	M	0.92077	3.27	0.80722	D	1	P	0.50819	0.939	P	0.50352	0.638	D	0.92539	0.6040	10	0.72032	D	0.01	.	8.4548	0.32893	0.0:0.8776:0.0:0.1224	.	203	Q63ZE4	S22AA_HUMAN	C	48;203	ENSP00000445667:R48C;ENSP00000327569:R203C	ENSP00000327569:R203C	R	+	1	0	SLC22A10	62821451	0.772000	0.28567	0.265000	0.24526	0.132000	0.20833	1.238000	0.32707	0.751000	0.32900	0.447000	0.29281	CGC	.	.	.	weak		0.408	SLC22A10-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382622.3	NM_001039752		T	63064875	C	T	63064875	3	4	79	1	0	0	0	0	1	0	0	0	14454	536	19	1	617	1	SLC22A10	11	63064875	Missense_Mutation	SNP	C	TCGA-B1-5398-01A-02D-1589-08	7501550	63064875	71941641	53	5101											
NUMA1	4926	hgsc.bcm.edu	37	chr11	71724282	71724282	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctctgcccgcagctgctgagCtgttcgctcctgctctgcca	3	11	10	17	2	2	1	0	1	2	0	4	1	3	1	3	0	6	7	3	0	0	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:71724282C>T	ENST00000393695.3	-	15	4598	c.4267G>A	c.(4267-4269)Gct>Act	p.A1423T	RP11-849H4.4_ENST00000502284.1_RNA|NUMA1_ENST00000358965.6_Missense_Mutation_p.A1423T|NUMA1_ENST00000351960.6_Intron	NM_006185.2	NP_006176.2			nuclear mitotic apparatus protein 1											central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(12)|lung(20)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	65						AGCTGCTGAGCTGTTCGCTCC	0.672			T	RARA	APL																																p.A1423T		Atlas-SNP	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.G4267A						PASS	.						46	48	47					11																	71724282		2200	4293	6493	SO:0001583	missense	4926	exon15			GCTGAGCTGTTCG	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.4267G>A	chr11.hg19:g.71724282C>T	ENSP00000377298:p.Ala1423Thr	119.0	0.0	.		123.0	25.0	.	NM_006185		Missense_Mutation	SNP	ENST00000393695.3	hg19	CCDS31633.1	.	.	.	.	.	.	.	.	.	.	C	13.42	2.231361	0.39399	.	.	ENSG00000137497	ENST00000358965;ENST00000393695;ENST00000359652;ENST00000536544	T;T	0.13307	2.6;2.6	5.14	4.23	0.50019	.	0.000000	0.53938	D	0.000051	T	0.06645	0.0170	N	0.14661	0.345	0.20563	N	0.999885	P;B;B;P	0.39480	0.675;0.447;0.241;0.675	B;B;B;B	0.35550	0.205;0.148;0.148;0.205	T	0.25779	-1.0122	10	0.33940	T	0.23	.	5.9903	0.19456	0.1541:0.6873:0.0:0.1586	.	1429;907;1423;1423	Q4LE64;Q59HB8;Q14980-2;Q14980	.;.;.;NUMA1_HUMAN	T	1423;1423;986;392	ENSP00000351851:A1423T;ENSP00000377298:A1423T	ENSP00000351851:A1423T	A	-	1	0	NUMA1	71401930	0.000000	0.05858	0.838000	0.33150	0.876000	0.50452	-0.321000	0.08018	1.391000	0.46566	0.655000	0.94253	GCT	.	.	.	none		0.672	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1			T	71724282	C	T	71724282	3	4	79	1	0	0	0	0	1	0	0	0	10757	797	28	2	2132	2	NUMA1	11	71724282	Missense_Mutation	SNP	C	TCGA-B1-5398-01A-02D-1589-08	8659407	71724282	63282234	54	5102											
ARHGEF17	9828	hgsc.bcm.edu	37	chr11	73021440	73021440	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggatccgctgcccctcaTcgtccaggaccaatatgtgc	8	8	11	14	2	1	0	1	0	0	0	4	3	3	3	5	3	2	1	5	3	2	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:73021440T>C	ENST00000263674.3	+	1	2107	c.1757T>C	c.(1756-1758)aTc>aCc	p.I586T	RP11-800A3.7_ENST00000546324.1_RNA	NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	586					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						CTGCCCCTCATCGTCCAGGAC	0.647																																					p.I586T		Atlas-SNP	.											.	ARHGEF17	117	.	0			c.T1757C						PASS	.						48	50	49					11																	73021440		2200	4293	6493	SO:0001583	missense	9828	exon1			CCCTCATCGTCCA	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.1757T>C	chr11.hg19:g.73021440T>C	ENSP00000263674:p.Ile586Thr	84.0	0.0	.		88.0	13.0	.	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Missense_Mutation	SNP	ENST00000263674.3	hg19	CCDS8221.1	.	.	.	.	.	.	.	.	.	.	T	9.868	1.198064	0.22037	.	.	ENSG00000110237	ENST00000263674	T	0.55588	0.51	4.62	4.62	0.57501	.	1.144840	0.06515	N	0.738667	T	0.36608	0.0973	N	0.08118	0	0.09310	N	1	B	0.13594	0.008	B	0.16722	0.016	T	0.20974	-1.0259	10	0.87932	D	0	-9.7864	9.3506	0.38136	0.0:0.0:0.1804:0.8196	.	586	Q96PE2	ARHGH_HUMAN	T	586	ENSP00000263674:I586T	ENSP00000263674:I586T	I	+	2	0	ARHGEF17	72699088	0.963000	0.33076	0.006000	0.13384	0.872000	0.50106	3.475000	0.53136	1.931000	0.55961	0.459000	0.35465	ATC	.	.	.	none		0.647	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		C	73021440	T	C	73021440	3	2	79	1	0	0	0	0	1	0	0	0	900	1435	50	3	1759	3	ARHGEF17	11	73021440	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	1297158	73021440	61985076	55	5103											
GDPD4	220032	hgsc.bcm.edu	37	chr11	76944148	76944148	+	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	gagttaatcctggagcaccaGgccagtgagaaaagccaagg	14	5	13	9	0	0	1	0	1	0	1	1	4	1	2	4	3	2	2	4	3	4	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:76944148G>C	ENST00000376217.2	-	13	1561	c.1311C>G	c.(1309-1311)gcC>gcG	p.A437A	GDPD4_ENST00000315938.4_Silent_p.A437A			Q6W3E5	GDPD4_HUMAN	glycerophosphodiester phosphodiesterase domain containing 4	437	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						TGGAGCACCAGGCCAGTGAGA	0.468																																					p.A437A		Atlas-SNP	.											.	GDPD4	49	.	0			c.C1311G						PASS	.						168	146	153					11																	76944148		2200	4292	6492	SO:0001819	synonymous_variant	220032	exon13			GCACCAGGCCAGT	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.1311C>G	chr11.hg19:g.76944148G>C		83.0	0.0	.		87.0	9.0	.	NM_182833	Q7Z5B0	Silent	SNP	ENST00000376217.2	hg19																																																																																				.	.	.	none		0.468	GDPD4-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382075.1	NM_182833		C	76944148	G	C	76944148	2	2	79	1	0	0	0	0	0	0	0	1	6333	987	35	4		4	GDPD4	11	76944148	Silent	SNP	G	TCGA-B1-5398-01A-02D-1589-08	3922708	76944148	58062368	56	5104											
PCF11	51585	hgsc.bcm.edu	37	chr11	82877690	82877690	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggcactgaaccaaaggagaAtgtagaaaactggcaaagtt	18	6	11	6	0	0	3	0	1	0	2	0	4	0	3	1	3	2	4	1	3	7	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:82877690A>G	ENST00000298281.4	+	5	2203	c.1751A>G	c.(1750-1752)aAt>aGt	p.N584S		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	584					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						CCAAAGGAGAATGTAGAAAAC	0.393																																					p.N584S		Atlas-SNP	.											PCF11_ENST00000298281,NS,carcinoma,0,4	PCF11	220	.	0			c.A1751G						PASS	.						66	66	66					11																	82877690		1824	4044	5868	SO:0001583	missense	51585	exon5			AGGAGAATGTAGA	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.1751A>G	chr11.hg19:g.82877690A>G	ENSP00000298281:p.Asn584Ser	113.0	0.0	.		104.0	20.0	.	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	hg19	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	A	13.22	2.172383	0.38315	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.50813	1.68;0.74;0.73	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000005	T	0.34483	0.0899	N	0.19112	0.55	0.29519	N	0.853609	P;P	0.43788	0.473;0.817	B;B	0.38500	0.091;0.275	T	0.25433	-1.0132	9	.	.	.	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	584;584	E9PQ01;O94913	.;PCF11_HUMAN	S	584	ENSP00000298281:N584S;ENSP00000434540:N584S;ENSP00000431567:N584S	.	N	+	2	0	PCF11	82555338	1.000000	0.71417	0.991000	0.47740	0.967000	0.64934	3.827000	0.55745	2.326000	0.78906	0.533000	0.62120	AAT	.	.	.	none		0.393	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		G	82877690	A	G	82877690	3	3	79	1	0	0	0	0	1	0	0	0	11580	101	4	3	1769	3	PCF11	11	82877690	Missense_Mutation	SNP	A	TCGA-B1-5398-01A-02D-1589-08	5933542	82877690	52128826	57	5105											
CASP4	837	hgsc.bcm.edu	37	chr11	104825523	104825523	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttaaaaaaggtttgaagaagCatttgtcctgccatacgttg	13	13	9	6	1	0	2	0	1	0	1	1	2	1	2	2	1	3	3	2	1	6	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr11:104825523C>T	ENST00000444739.2	-	2	1123	c.213G>A	c.(211-213)atG>atA	p.M71I	CASP4_ENST00000531333.1_5'UTR|CASP4_ENST00000393150.3_Missense_Mutation_p.M15I	NM_001225.3	NP_001216.1	P49662	CASP4_HUMAN	caspase 4, apoptosis-related cysteine peptidase	71	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				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)		TTTGAAGAAGCATTTGTCCTG	0.353																																					p.M71I		Atlas-SNP	.											.	CASP4	57	.	0			c.G213A						PASS	.						187	177	181					11																	104825523		2202	4299	6501	SO:0001583	missense	837	exon2			AAGAAGCATTTGT	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.213G>A	chr11.hg19:g.104825523C>T	ENSP00000388566:p.Met71Ile	222.0	0.0	.		224.0	37.0	.	NM_001225	A2NHL8|A2NHM0	Missense_Mutation	SNP	ENST00000444739.2	hg19	CCDS8327.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.174|0.174	-1.068340|-1.068340	0.01934|0.01934	.|.	.|.	ENSG00000196954|ENSG00000196954	ENST00000355546|ENST00000444739;ENST00000393150;ENST00000417440	.|T;T;T	.|0.18174	.|2.23;4.52;2.23	3.6|3.6	-1.75|-1.75	0.08031|0.08031	.|DEATH-like (2);Caspase Recruitment (3);	.|1.351520	.|0.05087	.|N	.|0.484541	T|T	0.06371|0.06371	0.0164|0.0164	N|N	0.12182|0.12182	0.205|0.205	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.11235	.|0.004;0.001;0.0	.|B;B;B	.|0.13407	.|0.009;0.004;0.002	T|T	0.26710|0.26710	-1.0095|-1.0095	6|10	0.02654|0.02654	T|T	1|1	.|.	0.1298|0.1298	0.00073|0.00073	0.3445:0.2198:0.1837:0.252|0.3445:0.2198:0.1837:0.252	.|.	.|71;71;71	.|B4DJH5;B4E2D2;P49662	.|.;.;CASP4_HUMAN	Y|I	25|71;15;71	.|ENSP00000388566:M71I;ENSP00000376857:M15I;ENSP00000401673:M71I	ENSP00000347741:C25Y|ENSP00000376857:M15I	C|M	-|-	2|3	0|0	CASP4|CASP4	104330733|104330733	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.004000|0.004000	0.04260|0.04260	-2.136000|-2.136000	0.01305|0.01305	-0.231000|-0.231000	0.09825|0.09825	-0.150000|-0.150000	0.13652|0.13652	TGC|ATG	.	.	.	none		0.353	CASP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387751.1	NM_001225		T	104825523	C	T	104825523	3	4	79	1	0	0	0	0	1	0	0	0	2675	710	25	2	948	2	CASP4	11	104825523	Missense_Mutation	SNP	C	TCGA-B1-5398-01A-02D-1589-08	21947833	104825523	30180993	58	5106											
FKBP4	2288	hgsc.bcm.edu	37	chr12	2909578	2909578	+	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	gaaggtaaatacaagcaagcTttactacagtataagaagat	19	9	8	5	0	0	2	0	0	0	2	0	3	0	2	0	1	5	4	0	1	11	7			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr12:2909578T>G	ENST00000001008.4	+	8	1054	c.867T>G	c.(865-867)gcT>gcG	p.A289A	RP4-816N1.6_ENST00000547834.1_RNA|RP4-816N1.7_ENST00000547042.1_RNA	NM_002014.3	NP_002005.1	Q02790	FKBP4_HUMAN	FK506 binding protein 4, 59kDa	289	Interaction with tubulin. {ECO:0000250}.				androgen receptor signaling pathway (GO:0030521)|chaperone-mediated protein folding (GO:0061077)|copper ion transport (GO:0006825)|embryo implantation (GO:0007566)|male sex differentiation (GO:0046661)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)|negative regulation of neuron projection development (GO:0010977)|prostate gland development (GO:0030850)|protein complex localization (GO:0031503)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|steroid hormone receptor complex assembly (GO:0006463)	axonal growth cone (GO:0044295)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|FK506 binding (GO:0005528)|GTP binding (GO:0005525)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(1)	14			OV - Ovarian serous cystadenocarcinoma(31;0.00105)			ACAAGCAAGCTTTACTACAGT	0.483																																					p.A289A		Atlas-SNP	.											.	FKBP4	29	.	0			c.T867G						PASS	.						76	69	71					12																	2909578		2203	4300	6503	SO:0001819	synonymous_variant	2288	exon8			GCAAGCTTTACTA	M88279	CCDS8512.1	12p13.33	2013-01-10	2002-08-29		ENSG00000004478	ENSG00000004478		"Tetratricopeptide (TTC) repeat domain containing"	3720	protein-coding gene	gene with protein product		600611	"FK506-binding protein 4 (59kD)"			1279700	Standard	NM_002014		Approved	FKBP59, FKBP52	uc001qkz.3	Q02790	OTTHUMG00000090429	ENST00000001008.4:c.867T>G	chr12.hg19:g.2909578T>G		49.0	0.0	.		58.0	10.0	.	NM_002014	D3DUQ1|Q9UCP1|Q9UCV7	Silent	SNP	ENST00000001008.4	hg19	CCDS8512.1																																																																																			.	.	.	none		0.483	FKBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206861.1			G	2909578	T	G	2909578	2	3	79	1	0	0	0	0	0	0	0	1	5917	1596	56	5		5	FKBP4	12	2909578	Silent	SNP	T	TCGA-B1-5398-01A-02D-1589-08		2909578	130942317	59	5107											
CHD4	1108	hgsc.bcm.edu	37	chr12	6707540	6707540	+	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	tggtgtgggagatggtggctGaccccacttccagattagga	8	10	15	8	0	0	3	0	1	0	2	1	5	1	4	3	5	0	1	3	5	1	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr12:6707540G>A	ENST00000357008.2	-	11	1697	c.1534C>T	c.(1534-1536)Cag>Tag	p.Q512*	CHD4_ENST00000309577.6_Nonsense_Mutation_p.Q512*|CHD4_ENST00000544484.1_Nonsense_Mutation_p.Q509*|CHD4_ENST00000544040.1_Nonsense_Mutation_p.Q505*	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	512	Chromo 1. {ECO:0000255|PROSITE- ProRule:PRU00053}.				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						GATGGTGGCTGACCCCACTTC	0.547																																					p.Q512X	Colon(32;586 792 4568 16848 45314)	Atlas-SNP	.											.	CHD4	539	.	0			c.C1534T						PASS	.						137	140	139					12																	6707540		2203	4300	6503	SO:0001587	stop_gained	1108	exon11			GTGGCTGACCCCA	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.1534C>T	chr12.hg19:g.6707540G>A	ENSP00000349508:p.Gln512*	285.0	0.0	.		278.0	43.0	.	NM_001273	Q8IXZ5	Nonsense_Mutation	SNP	ENST00000357008.2	hg19	CCDS8552.1	.	.	.	.	.	.	.	.	.	.	G	39	7.490672	0.98316	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464	.	.	.	3.86	3.86	0.44501	.	0.127870	0.53938	D	0.000057	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	9.8645	12.2938	0.54833	0.0:0.1709:0.8291:0.0	.	.	.	.	X	509;505;512;512;486	.	ENSP00000312419:Q512X	Q	-	1	0	CHD4	6577801	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	4.469000	0.60169	2.149000	0.67028	0.305000	0.20034	CAG	.	.	.	none		0.547	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273		A	6707540	G	A	6707540	4	1	79	1	0	0	0	0	0	1	0	0	3329	1299	45	2	4324	2	CHD4	12	6707540	Nonsense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	3797962	6707540	127144355	60	5108											
RASSF8	11228	hgsc.bcm.edu	37	chr12	26217472	26217472	+	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	ttatagagaaatggagagatActgaaagacacttagcacct	17	9	9	6	0	0	4	0	1	0	3	0	7	0	5	1	1	2	1	1	1	6	4			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr12:26217472A>T	ENST00000405154.2	+	3	344	c.145A>T	c.(145-147)Act>Tct	p.T49S	RASSF8_ENST00000541490.1_Missense_Mutation_p.T49S|RASSF8_ENST00000542865.1_Missense_Mutation_p.T49S|RASSF8_ENST00000381352.3_Missense_Mutation_p.T49S|RASSF8_ENST00000282884.9_Missense_Mutation_p.T49S	NM_001164748.1	NP_001158220.1	Q8NHQ8	RASF8_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 8	49	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				signal transduction (GO:0007165)					cervix(2)|endometrium(1)|large_intestine(6)|lung(15)|urinary_tract(1)	25	Colorectal(261;0.0847)					ATGGAGAGATACTGAAAGACA	0.388																																					p.T49S		Atlas-SNP	.											.	RASSF8	56	.	0			c.A145T						PASS	.						111	115	113					12																	26217472		2203	4300	6503	SO:0001583	missense	11228	exon4			AGAGATACTGAAA	U82396	CCDS8705.1, CCDS53765.1	12p12.3	2013-05-30	2008-02-22	2005-09-14	ENSG00000123094	ENSG00000123094			13232	protein-coding gene	gene with protein product		608231	"chromosome 12 open reading frame 2"	C12orf2			Standard	NM_007211		Approved	HoJ-1	uc001rgx.3	Q8NHQ8	OTTHUMG00000169087	ENST00000405154.2:c.145A>T	chr12.hg19:g.26217472A>T	ENSP00000384491:p.Thr49Ser	164.0	0.0	.		179.0	32.0	.	NM_007211	A8K1Z0|O95647|Q5SCI2|Q76KB6	Missense_Mutation	SNP	ENST00000405154.2	hg19	CCDS53765.1	.	.	.	.	.	.	.	.	.	.	A	15.41	2.826488	0.50739	.	.	ENSG00000123094	ENST00000381352;ENST00000535907;ENST00000405154;ENST00000542865;ENST00000541490;ENST00000542004;ENST00000542315;ENST00000541218;ENST00000282884;ENST00000545413;ENST00000541934	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	5.38	4.21	0.49690	Ras-association (3);	0.046729	0.85682	D	0.000000	T	0.21674	0.0522	N	0.17723	0.515	0.58432	D	0.999995	B;D	0.63046	0.383;0.992	B;D	0.64042	0.19;0.921	T	0.03008	-1.1083	10	0.21014	T	0.42	-11.7935	11.9163	0.52767	0.8541:0.1459:0.0:0.0	.	49;49	Q8NHQ8-2;Q8NHQ8	.;RASF8_HUMAN	S	49	ENSP00000370756:T49S;ENSP00000442036:T49S;ENSP00000384491:T49S;ENSP00000439839:T49S;ENSP00000443096:T49S;ENSP00000442485:T49S;ENSP00000441294:T49S;ENSP00000445970:T49S;ENSP00000282884:T49S;ENSP00000443696:T49S	ENSP00000282884:T49S	T	+	1	0	RASSF8	26108739	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.609000	0.61148	0.970000	0.38263	0.528000	0.53228	ACT	.	.	.	none		0.388	RASSF8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402209.2	NM_007211		T	26217472	A	T	26217472	3	4	79	1	0	0	0	0	1	0	0	0	13105	391	14	5	151	5	RASSF8	12	26217472	Missense_Mutation	SNP	A	TCGA-B1-5398-01A-02D-1589-08	19509932	26217472	107634423	61	5109											
LRRK2	120892	hgsc.bcm.edu	37	chr12	40681240	40681240	+	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	agcctcaggcagcgatggaaAtttttctgaagatgtgctgt	10	12	12	7	1	2	2	1	1	1	1	2	4	2	3	1	2	3	2	1	2	2	2	rs555679009		TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr12:40681240A>T	ENST00000298910.7	+	20	2646	c.2588A>T	c.(2587-2589)aAt>aTt	p.N863I	LRRK2_ENST00000343742.2_Missense_Mutation_p.N863I	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	863					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)				AGCGATGGAAATTTTTCTGAA	0.398																																					p.N863I		Atlas-SNP	.											.	LRRK2	763	.	0			c.A2588T						PASS	.						123	118	119					12																	40681240		2202	4299	6501	SO:0001583	missense	120892	exon20			ATGGAAATTTTTC	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.2588A>T	chr12.hg19:g.40681240A>T	ENSP00000298910:p.Asn863Ile	94.0	0.0	.		110.0	22.0	.	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	hg19	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	A	7.572	0.666963	0.14710	.	.	ENSG00000188906	ENST00000343742;ENST00000298910	T;T	0.71579	2.25;-0.58	5.5	1.35	0.21983	.	0.449692	0.24999	N	0.033934	T	0.50309	0.1608	N	0.19112	0.55	0.09310	N	1	B;B	0.30455	0.28;0.121	B;B	0.30401	0.115;0.032	T	0.41016	-0.9532	10	0.46703	T	0.11	.	6.406	0.21664	0.6611:0.1269:0.212:0.0	.	863;863	E9PC85;Q5S007	.;LRRK2_HUMAN	I	863	ENSP00000341930:N863I;ENSP00000298910:N863I	ENSP00000298910:N863I	N	+	2	0	LRRK2	38967507	0.002000	0.14202	0.001000	0.08648	0.111000	0.19643	0.146000	0.16180	0.363000	0.24346	0.402000	0.26972	AAT	.	.	.	none		0.398	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		T	40681240	A	T	40681240	3	4	79	1	0	0	0	0	1	0	0	0	9040	101	4	5	2666	5	LRRK2	12	40681240	Missense_Mutation	SNP	A	TCGA-B1-5398-01A-02D-1589-08	14463768	40681240	93170655	62	5110											
PRICKLE1	144165	hgsc.bcm.edu	37	chr12	42858293	42858293	+	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	cagggaatcttcataccactGtgtttcatcatgattatacc	11	14	6	10	0	4	1	3	1	1	0	4	2	4	2	2	1	2	1	2	1	4	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr12:42858293G>A	ENST00000455697.1	-	7	1828	c.1543C>T	c.(1543-1545)Cag>Tag	p.Q515*	PRICKLE1_ENST00000552240.1_Nonsense_Mutation_p.Q515*|PRICKLE1_ENST00000445766.2_Nonsense_Mutation_p.Q515*|RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000548696.1_Nonsense_Mutation_p.Q515*|PRICKLE1_ENST00000345127.3_Nonsense_Mutation_p.Q515*	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	515					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)		TCATACCACTGTGTTTCATCA	0.488																																					p.Q515X		Atlas-SNP	.											.	PRICKLE1	105	.	0			c.C1543T						PASS	.						106	101	103					12																	42858293		2203	4300	6503	SO:0001587	stop_gained	144165	exon7			ACCACTGTGTTTC	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.1543C>T	chr12.hg19:g.42858293G>A	ENSP00000401060:p.Gln515*	131.0	0.0	.		157.0	29.0	.	NM_001144882	Q14C83|Q71QF8|Q96N00	Nonsense_Mutation	SNP	ENST00000455697.1	hg19	CCDS8742.1	.	.	.	.	.	.	.	.	.	.	G	39	7.452020	0.98292	.	.	ENSG00000139174	ENST00000455697;ENST00000445766;ENST00000548696;ENST00000345127;ENST00000552240	.	.	.	5.76	4.85	0.62838	.	0.319538	0.38959	N	0.001519	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	-13.6227	16.3438	0.83116	0.0:0.0:0.8668:0.1332	.	.	.	.	X	515	.	ENSP00000345064:Q515X	Q	-	1	0	PRICKLE1	41144560	1.000000	0.71417	0.760000	0.31359	0.887000	0.51463	5.953000	0.70290	1.531000	0.49152	0.650000	0.86243	CAG	.	.	.	none		0.488	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1			A	42858293	G	A	42858293	4	1	79	1	0	0	0	0	0	1	0	0	12496	1386	48	2	960	2	PRICKLE1	12	42858293	Nonsense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	2177053	42858293	90993602	63	5111											
SFRS2IP	9169	hgsc.bcm.edu	37	chr12	46318586	46318586	+	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	gggggagggggtggtggtggTggtagtccctgagatacact	6	9	21	5	0	0	1	0	1	0	1	1	3	1	2	1	8	1	1	1	8	2	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr12:46318586T>A	ENST00000369367.3	-	12	4064	c.3831A>T	c.(3829-3831)ccA>ccT	p.P1277P	SCAF11_ENST00000550629.1_5'Flank|SCAF11_ENST00000465950.1_Silent_p.P962P|SCAF11_ENST00000549162.1_Silent_p.P1085P|SCAF11_ENST00000419565.2_Silent_p.P1277P	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	1277	Pro-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						GTGGTGGTGGTGGTAGTCCCT	0.493																																					p.P1277P		Atlas-SNP	.											.	SCAF11	145	.	0			c.A3831T						PASS	.						99	85	90					12																	46318586		2203	4300	6503	SO:0001819	synonymous_variant	9169	exon12			TGGTGGTGGTAGT	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.3831A>T	chr12.hg19:g.46318586T>A		127.0	0.0	.		92.0	18.0	.	NM_004719	A6NEU9|A6NLW5|Q8IW59	Silent	SNP	ENST00000369367.3	hg19	CCDS8748.2																																																																																			.	.	.	none		0.493	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719		A	46318586	T	A	46318586	2	1	79	1	0	0	0	0	0	0	0	1	14190	1683	59	5		5	SFRS2IP	12	46318586	Silent	SNP	T	TCGA-B1-5398-01A-02D-1589-08	3460293	46318586	87533309	64	5112											
MBD6	114785	hgsc.bcm.edu	37	chr12	57922959	57922959	+	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	ttaggcagctgtccctctgcCtccccgggcccgccctggcc	2	8	11	20	2	1	0	0	0	1	0	3	0	3	0	7	3	2	2	7	3	1	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr12:57922959C>T	ENST00000355673.3	+	13	3310	c.2954C>T	c.(2953-2955)cCt>cTt	p.P985L	MBD6_ENST00000431731.2_Missense_Mutation_p.P985L	NM_052897.3	NP_443129.3	Q96DN6	MBD6_HUMAN	methyl-CpG binding domain protein 6	985						chromocenter (GO:0010369)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|urinary_tract(1)	31						GTCCCTCTGCCTCCCCGGGCC	0.562																																					p.P985L		Atlas-SNP	.											.	MBD6	99	.	0			c.C2954T						PASS	.						80	79	79					12																	57922959		2203	4300	6503	SO:0001583	missense	114785	exon13			CTCTGCCTCCCCG	AB067474	CCDS8944.1	12q13.2	2008-02-05				ENSG00000166987			20445	protein-coding gene	gene with protein product						12529184	Standard	NM_052897		Approved	KIAA1887	uc001soj.1	Q96DN6		ENST00000355673.3:c.2954C>T	chr12.hg19:g.57922959C>T	ENSP00000347896:p.Pro985Leu	121.0	0.0	.		93.0	23.0	.	NM_052897	Q8N3M0|Q8NA81|Q96Q00	Missense_Mutation	SNP	ENST00000355673.3	hg19	CCDS8944.1	.	.	.	.	.	.	.	.	.	.	c	15.34	2.804649	0.50315	.	.	ENSG00000166987	ENST00000355673;ENST00000431731	.	.	.	4.81	4.81	0.61882	.	0.000000	0.53938	D	0.000055	T	0.28532	0.0706	N	0.08118	0	0.49389	D	0.999785	P;P	0.46784	0.884;0.728	B;B	0.39562	0.303;0.199	T	0.28902	-1.0029	9	0.87932	D	0	-4.6123	13.5981	0.62002	0.0:1.0:0.0:0.0	.	985;985	Q6P0P0;Q96DN6	.;MBD6_HUMAN	L	985	.	ENSP00000347896:P985L	P	+	2	0	MBD6	56209226	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.576000	0.53878	2.683000	0.91414	0.558000	0.71614	CCT	.	.	.	none		0.562	MBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407250.1			T	57922959	C	T	57922959	3	4	79	1	0	0	0	0	1	0	0	0	9355	681	24	2	2996	2	MBD6	12	57922959	Missense_Mutation	SNP	C	TCGA-B1-5398-01A-02D-1589-08	11604373	57922959	75928936	65	5113											
USP15	9958	hgsc.bcm.edu	37	chr12	62795034	62795034	+	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	gatgacagtagtgtctccacTgcatctgaagaccaaattgt	12	11	9	9	0	2	3	0	2	2	1	3	4	2	3	2	0	1	2	2	0	3	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr12:62795034T>A	ENST00000280377.5	+	21	2800	c.2742T>A	c.(2740-2742)acT>acA	p.T914T	USP15_ENST00000393654.3_Silent_p.T889T|USP15_ENST00000353364.3_Silent_p.T885T	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	914	USP.				BMP signaling pathway (GO:0030509)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|protein deubiquitination (GO:0016579)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|identical protein binding (GO:0042802)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(15)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	37			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		GTGTCTCCACTGCATCTGAAG	0.323																																					p.T914T	Melanoma(181;615 2041 39364 49691 50001)	Atlas-SNP	.											.	USP15	105	.	0			c.T2742A						PASS	.						69	68	68					12																	62795034		2203	4297	6500	SO:0001819	synonymous_variant	9958	exon21			CTCCACTGCATCT	AB011101	CCDS8963.1, CCDS58250.1, CCDS58251.1	12q14	2006-07-18	2005-08-08					"Ubiquitin-specific peptidases"	12613	protein-coding gene	gene with protein product		604731	"ubiquitin specific protease 15"			12838346	Standard	NM_001252078		Approved	KIAA0529, UNPH4	uc001src.2	Q9Y4E8	OTTHUMG00000170186	ENST00000280377.5:c.2742T>A	chr12.hg19:g.62795034T>A		82.0	0.0	.		71.0	17.0	.	NM_001252078	Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Silent	SNP	ENST00000280377.5	hg19	CCDS58251.1																																																																																			.	.	.	none		0.323	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2	NM_006313		A	62795034	T	A	62795034	2	1	79	1	0	0	0	0	0	0	0	1	17058	1567	55	5		5	USP15	12	62795034	Silent	SNP	T	TCGA-B1-5398-01A-02D-1589-08	4872075	62795034	71056861	66	5114											
GRIP1	23426	hgsc.bcm.edu	37	chr12	66838463	66838463	+	Frame_Shift_Del	DEL	T	T	-																															ggtgctgtcttctgttggaaTtccattgatggccatcactc																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr12:66838463delT	ENST00000398016.3	-	12	1500	c.1432delA	c.(1432-1434)attfs	p.I478fs	GRIP1_ENST00000286445.7_Frame_Shift_Del_p.I530fs|GRIP1_ENST00000359742.4_Frame_Shift_Del_p.I530fs	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)		TCTGTTGGAATTCCATTGATG	0.458																																					p.I478fs		Atlas-INDEL	.											.	GRIP1	106	.	0			c.1433delT						PASS	.						136	131	133					12																	66838463		1962	4135	6097	SO:0001589	frameshift_variant	23426	exon12			.	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.1432delA	chr12.hg19:g.66838463delT	ENSP00000381098:p.Ile478fs	118.0	0.0	0		106.0	22.0	0.207547	NM_001178074	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Frame_Shift_Del	DEL	ENST00000398016.3	hg19	CCDS41807.1																																																																																			.	.	.	none		0.458	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2			-	66838463	T	-	66838463	7	5	79	1	0	1	0	1	0	0	0	0	6794	1493	52	0	1850	0	GRIP1	12	66838463	Frame_Shift_Del	DEL	T	TCGA-B1-5398-01A-02D-1589-08	4043429	66838463	67013432	67	5115											
ALDH1L2	160428	hgsc.bcm.edu	37	chr12	105433493	105433493	+	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	acattttaaaaccaatacctCttcatgatctgtttgccaat	13	15	3	10	0	3	1	1	1	2	0	3	1	3	1	3	0	3	1	3	0	5	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr12:105433493C>T	ENST00000258494.9	-	17	2183	c.2043G>A	c.(2041-2043)aaG>aaA	p.K681K	C12orf45_ENST00000548583.1_Intron	NM_001034173.3	NP_001029345.2	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2	681	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|prostate(2)|skin(3)|stomach(2)	35						ACCAATACCTCTTCATGATCT	0.388																																					p.K681K		Atlas-SNP	.											.	ALDH1L2	71	.	0			c.G2043A						PASS	.						148	136	140					12																	105433493		2203	4300	6503	SO:0001819	synonymous_variant	160428	exon17			ATACCTCTTCATG	AK095827	CCDS31891.1	12q23.3	2014-09-11			ENSG00000136010	ENSG00000136010	1.5.1.6	"Aldehyde dehydrogenases"	26777	protein-coding gene	gene with protein product	"mitochondrial 10-formyltetrahydrofolate dehydrogenase"	613584				20498374	Standard	NM_001034173		Approved	FLJ38508, mtFDH	uc001tlc.3	Q3SY69	OTTHUMG00000169823	ENST00000258494.9:c.2043G>A	chr12.hg19:g.105433493C>T		98.0	0.0	.		115.0	17.0	.	NM_001034173	Q3SY68|Q68D62|Q6AI55|Q8N922	Silent	SNP	ENST00000258494.9	hg19	CCDS31891.1																																																																																			.	.	.	none		0.388	ALDH1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406098.1	XM_090294		T	105433493	C	T	105433493	2	4	79	1	0	0	0	0	0	0	0	1	495	912	32	2		2	ALDH1L2	12	105433493	Silent	SNP	C	TCGA-B1-5398-01A-02D-1589-08	38595030	105433493	28418402	68	5116											
PXN	5829	hgsc.bcm.edu	37	chr12	120653399	120653399	+	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	cctccggggctgctccgcccGccgtcccgaggccagccggc	2	4	14	21	6	0	0	0	0	0	0	3	1	3	0	8	4	2	2	8	4	0	0	rs374919882	byFrequency	TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr12:120653399G>A	ENST00000228307.7	-	7	1038	c.897C>T	c.(895-897)ggC>ggT	p.G299G	PXN_ENST00000267257.7_Intron|PXN_ENST00000536957.1_Silent_p.G297G|PXN_ENST00000397506.3_Silent_p.G63G|PXN_ENST00000424649.2_Intron|PXN_ENST00000538144.1_Intron|PXN_ENST00000458477.2_Intron|PXN-AS1_ENST00000542265.1_RNA|PXN-AS1_ENST00000535200.1_RNA	NM_001080855.2	NP_001074324.1	P49023	PAXI_HUMAN	paxillin	299					activation of MAPK activity (GO:0000187)|branching morphogenesis of an epithelial tube (GO:0048754)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cellular component movement (GO:0006928)|cellular response to reactive oxygen species (GO:0034614)|cytoskeleton organization (GO:0007010)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|growth hormone receptor signaling pathway (GO:0060396)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|muscle contraction (GO:0006936)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of cell shape (GO:0008360)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	beta-catenin binding (GO:0008013)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TGCTCCGCCCGCCGTCCCGAG	0.672													G|||	4	0.000798722	0	0	5008	,	,		11205	0		0	False		,,,				2504	0.0041				p.G299G		Atlas-SNP	.											.	PXN	69	.	0			c.C897T						PASS	.	G	,,	1,3119		0,1,1559	27	35	32		897,,	3	0.7	12		32	0,7154		0,0,3577	no	coding-synonymous,intron,intron	PXN	NM_001080855.2,NM_002859.3,NM_025157.4	,,	0,1,5136	AA,AG,GG		0.0,0.0321,0.0097	,,	299/592,,	120653399	1,10273	1560	3577	5137	SO:0001819	synonymous_variant	5829	exon7			CCGCCCGCCGTCC	U14588	CCDS44996.1, CCDS44997.1, CCDS44998.1, CCDS58281.1	12q24	2006-01-23			ENSG00000089159	ENSG00000089159			9718	protein-coding gene	gene with protein product		602505				7534286	Standard	NM_001080855		Approved		uc001txv.3	P49023	OTTHUMG00000169169	ENST00000228307.7:c.897C>T	chr12.hg19:g.120653399G>A		110.0	0.0	.		75.0	15.0	.	NM_001080855	B2RAI3|B7ZMB4|O14970|O14971|O60360|Q5HYA4	Silent	SNP	ENST00000228307.7	hg19	CCDS44997.1	.	.	.	.	.	.	.	.	.	.	G	0.728	-0.780857	0.02929	3.21E-4	0.0	ENSG00000089159	ENST00000550795	.	.	.	4.89	3.03	0.35002	.	.	.	.	.	T	0.35480	0.0933	.	.	.	0.24856	N	0.992376	.	.	.	.	.	.	T	0.19976	-1.0289	4	.	.	.	.	8.1293	0.31018	0.1991:0.0:0.8009:0.0	.	.	.	.	V	48	.	.	A	-	2	0	PXN	119137782	0.004000	0.15560	0.679000	0.29978	0.009000	0.06853	0.629000	0.24538	1.209000	0.43321	-0.148000	0.13756	GCG	.	.	.	weak		0.672	PXN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402679.4	NM_002859		A	120653399	G	A	120653399	2	1	79	1	0	0	0	0	0	0	0	1	12865	1074	38	1		1	PXN	12	120653399	Silent	SNP	G	TCGA-B1-5398-01A-02D-1589-08	15219906	120653399	13198496	69	5117											
DCLK1	9201	hgsc.bcm.edu	37	chr13	36382392	36382396	+	Frame_Shift_Del	DEL	GGAGA	GGAGA	-																															cggaaacattatcccagtatGgagaaggaaagtccacctgc																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	GGAGA	GGAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr13:36382392_36382396delGGAGA	ENST00000360631.3	-	14	2039_2043	c.1828_1832delTCTCC	c.(1828-1833)tctccafs	p.SP610fs	DCLK1_ENST00000379893.1_Frame_Shift_Del_p.SP303fs|DCLK1_ENST00000255448.4_Frame_Shift_Del_p.SP610fs			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	610	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)	p.P611S(1)		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)		ATCCCAGTATGGAGAAGGAAAGTCC	0.424																																					p.610_611del		Atlas-INDEL	.											.	DCLK1	350	.	1	Substitution - Missense(1)	skin(1)	c.1829_1833del						PASS	.																																			SO:0001589	frameshift_variant	9201	exon14			.	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.1828_1832delTCTCC	chr13.hg19:g.36382392_36382396delGGAGA	ENSP00000353846:p.Ser610fs	170.0	0.0	0		175.0	35.0	0.2	NM_004734	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Frame_Shift_Del	DEL	ENST00000360631.3	hg19																																																																																				.	.	.	none		0.424	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734		-	36382396	GGAGA	-	36382392	7	5	79	1	0	1	0	1	0	0	0	0	4293	1348	47	0	377	0	DCLK1	13	36382392	Frame_Shift_Del	DEL	GGAGA	TCGA-B1-5398-01A-02D-1589-08		36382392	78787486	70	5118											
F10	2159	hgsc.bcm.edu	37	chr13	113803360	113803360	+	Frame_Shift_Del	DEL	C	C	-																															ctccggctcaagacccccatCaccttccgcatgaacgtggc																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr13:113803360delC	ENST00000375559.3	+	8	1034	c.996delC	c.(994-996)atcfs	p.I332fs	F10_ENST00000375551.3_Frame_Shift_Del_p.S329fs|F10_ENST00000409306.1_Frame_Shift_Del_p.S331fs	NM_000504.3	NP_000495.1	P00742	FA10_HUMAN	coagulation factor X	332	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|blood coagulation, intrinsic pathway (GO:0007597)|cellular protein metabolic process (GO:0044267)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of cell migration (GO:0030335)|positive regulation of protein kinase B signaling (GO:0051897)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|intrinsic component of external side of plasma membrane (GO:0031233)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(4)|lung(10)|pancreas(1)|stomach(1)	18	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.113)|all_lung(25;0.0364)|all_epithelial(44;0.0373)|Lung NSC(25;0.128)|Breast(118;0.188)	all cancers(43;0.0805)|Epithelial(84;0.231)		Antihemophilic Factor(DB00025)|Apixaban(DB06605)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)|Menadione(DB00170)|Rivaroxaban(DB06228)	AGACCCCCATCACCTTCCGCA	0.632																																					p.I332fs		Atlas-INDEL	.											.	F10	53	.	0			c.995delT						PASS	.						154	120	132					13																	113803360		2203	4300	6503	SO:0001589	frameshift_variant	2159	exon8			.		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.996delC	chr13.hg19:g.113803360delC	ENSP00000364709:p.Ile332fs	174.0	0.0	0		191.0	28.0	0.146597	NM_000504	Q14340	Frame_Shift_Del	DEL	ENST00000375559.3	hg19	CCDS9530.1																																																																																			.	.	.	none		0.632	F10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045841.3			-	113803360	C	-	113803360	7	5	79	1	0	1	0	1	0	0	0	0	5338	816	29	0	1026	0	F10	13	113803360	Frame_Shift_Del	DEL	C	TCGA-B1-5398-01A-02D-1589-08	77420968	113803360	1366518	71	5119											
OR4N5	390437	hgsc.bcm.edu	37	chr14	20612708	20612708	+	Missense_Mutation	SNP	T	T	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	tcccagctgacaaggtagttTctcttttccatactgtcatc	8	15	6	12	0	2	1	1	1	1	0	6	1	4	1	2	1	2	3	2	1	3	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr14:20612708T>G	ENST00000333629.1	+	1	814	c.814T>G	c.(814-816)Tct>Gct	p.S272A	RNA5SP381_ENST00000516076.1_RNA	NM_001004724.1	NP_001004724.1	Q8IXE1	OR4N5_HUMAN	olfactory receptor, family 4, subfamily N, member 5	272						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|lung(23)|ovary(1)|skin(2)|urinary_tract(1)	29	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.84e-06)	GBM - Glioblastoma multiforme(265;0.0143)		CAAGGTAGTTTCTCTTTTCCA	0.418																																					p.S272A		Atlas-SNP	.											.	OR4N5	72	.	0			c.T814G						PASS	.						165	167	167					14																	20612708		2203	4300	6503	SO:0001583	missense	390437	exon1			GTAGTTTCTCTTT		CCDS32031.1	14q11.2	2013-09-23			ENSG00000184394	ENSG00000184394		"GPCR / Class A : Olfactory receptors"	15358	protein-coding gene	gene with protein product							Standard	NM_001004724		Approved		uc010tla.2	Q8IXE1	OTTHUMG00000170784	ENST00000333629.1:c.814T>G	chr14.hg19:g.20612708T>G	ENSP00000332110:p.Ser272Ala	374.0	0.0	.		437.0	79.0	.	NM_001004724	Q6IF11	Missense_Mutation	SNP	ENST00000333629.1	hg19	CCDS32031.1	.	.	.	.	.	.	.	.	.	.	T	1.597	-0.527459	0.04141	.	.	ENSG00000184394	ENST00000333629	T	0.00198	8.57	4.0	-2.2	0.06994	GPCR, rhodopsin-like superfamily (1);	0.172594	0.28198	N	0.016223	T	0.00109	0.0003	L	0.41492	1.28	0.09310	N	1	B	0.14012	0.009	B	0.21708	0.036	T	0.47586	-0.9106	10	0.02654	T	1	.	6.6619	0.23018	0.1429:0.0:0.4373:0.4197	.	272	Q8IXE1	OR4N5_HUMAN	A	272	ENSP00000332110:S272A	ENSP00000332110:S272A	S	+	1	0	OR4N5	19682548	0.000000	0.05858	0.534000	0.28014	0.087000	0.18053	-0.284000	0.08422	-0.115000	0.11915	-0.313000	0.08912	TCT	.	.	.	none		0.418	OR4N5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410347.1			G	20612708	T	G	20612708	3	3	79	1	0	0	0	0	1	0	0	0	11086	1783	62	5	816	5	OR4N5	14	20612708	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08		20612708	86736832	72	5120											
FANCM	57697	hgsc.bcm.edu	37	chr14	45667882	45667882	+	Frame_Shift_Del	DEL	T	T	-																															tgtttaggagaacaaagagcTatgacagcctgctgactacc																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr14:45667882delT	ENST00000267430.5	+	22	5837	c.5752delT	c.(5752-5754)tatfs	p.Y1918fs	FANCM_ENST00000542564.2_Frame_Shift_Del_p.Y1892fs	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1918	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						AACAAAGAGCTATGACAGCCT	0.363								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.S1917fs		Atlas-INDEL	.											.	FANCM	225	.	0			c.5751delC						PASS	.						84	83	83					14																	45667882		2203	4300	6503	SO:0001589	frameshift_variant	57697	exon22	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	.	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"Fanconi anemia, complementation groups"	23168	protein-coding gene	gene with protein product		609644	"KIAA1596"	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.5752delT	chr14.hg19:g.45667882delT	ENSP00000267430:p.Tyr1918fs	126.0	0.0	0		107.0	22.0	0.205607	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Frame_Shift_Del	DEL	ENST00000267430.5	hg19	CCDS32070.1																																																																																			.	.	.	none		0.363	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		-	45667882	T	-	45667882	7	5	79	1	0	1	0	1	0	0	0	0	5678	1522	53	0	5838	0	FANCM	14	45667882	Frame_Shift_Del	DEL	T	TCGA-B1-5398-01A-02D-1589-08	25055174	45667882	61681658	73	5121											
C14orf182	283551	hgsc.bcm.edu	37	chr14	50472313	50472313	+	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	ttccacatggcacacggaccTtggaggcacagagggatggg	10	6	15	10	1	0	1	0	0	0	1	1	4	1	4	2	6	0	2	2	6	0	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr14:50472313T>C	ENST00000399206.1	-	1	1925	c.205A>G	c.(205-207)Agg>Ggg	p.R69G	C14orf182_ENST00000529902.1_5'UTR	NM_001012706.1	NP_001012724.1	A1A4T8	CN182_HUMAN	chromosome 14 open reading frame 182	69										large_intestine(2)|urinary_tract(1)	3						CACACGGACCTTGGAGGCACA	0.537																																					p.R69G		Atlas-SNP	.											.	C14orf182	8	.	0			c.A205G						PASS	.						126	138	134					14																	50472313		2049	4187	6236	SO:0001630	splice_region_variant	283551	exon1			CGGACCTTGGAGG	AK090420	CCDS41949.1	14q22.1	2009-02-24			ENSG00000214900	ENSG00000214900			27503	protein-coding gene	gene with protein product							Standard	NM_001012706		Approved		uc001wxi.1	A1A4T8		ENST00000399206.1:c.206+1A>G	chr14.hg19:g.50472313T>C		183.0	0.0	.		160.0	24.0	.	NM_001012706	A8MYX4	Missense_Mutation	SNP	ENST00000399206.1	hg19	CCDS41949.1	.	.	.	.	.	.	.	.	.	.	T	4.441	0.081550	0.08533	.	.	ENSG00000214900	ENST00000399206	T	0.59906	0.23	3.15	0.664	0.17890	.	.	.	.	.	T	0.43986	0.1272	.	.	.	0.09310	N	1	B	0.24426	0.103	B	0.23419	0.046	T	0.40757	-0.9546	8	0.87932	D	0	.	5.9656	0.19322	0.6219:0.0:0.0:0.3781	.	69	A1A4T8-2	.	G	69	ENSP00000382157:R69G	ENSP00000382157:R69G	R	-	1	2	C14orf182	49542063	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.033000	0.13754	0.130000	0.18549	-0.509000	0.04479	AGG	.	.	.	none		0.537	C14orf182-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395717.1	NM_001012706	Missense_Mutation	C	50472313	T	C	50472313	5	2	79	1	0	0	0	0	0	0	1	0	1767	1623	56	3	130	3	C14orf182	14	50472313	Splice_Site	SNP	T	TCGA-B1-5398-01A-02D-1589-08	4804431	50472313	56877227	74	5122											
MLH3	27030	hgsc.bcm.edu	37	chr14	75516130	75516130	+	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	gtcctgtaccgagtggcattTactggtgaaataacgatttc	10	13	10	8	2	0	1	0	1	0	0	2	3	1	1	2	2	3	2	2	2	4	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr14:75516130T>A	ENST00000556740.1	-	1	264	c.229A>T	c.(229-231)Aaa>Taa	p.K77*	MLH3_ENST00000555671.1_5'Flank|MLH3_ENST00000556257.1_Nonsense_Mutation_p.K77*|MLH3_ENST00000238662.7_Nonsense_Mutation_p.K77*|MLH3_ENST00000355774.2_Nonsense_Mutation_p.K77*|MLH3_ENST00000544985.1_5'Flank|MLH3_ENST00000380968.2_5'UTR			Q9UHC1	MLH3_HUMAN	mutL homolog 3	77					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		GAGTGGCATTTACTGGTGAAA	0.448								Mismatch excision repair (MMR)																													p.K77X		Atlas-SNP	.											.	MLH3	200	.	0			c.A229T						PASS	.						101	90	94					14																	75516130		2203	4300	6503	SO:0001587	stop_gained	27030	exon2			GGCATTTACTGGT	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)"			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.229A>T	chr14.hg19:g.75516130T>A	ENSP00000452316:p.Lys77*	110.0	0.0	.		100.0	17.0	.	NM_014381	P49751|Q56DK9|Q9P292|Q9UHC0	Nonsense_Mutation	SNP	ENST00000556740.1	hg19	CCDS32123.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.646105	0.87958	.	.	ENSG00000119684	ENST00000355774;ENST00000238662;ENST00000556257;ENST00000556740;ENST00000553263;ENST00000557648	.	.	.	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.7094	15.6637	0.77209	0.0:0.0:0.0:1.0	.	.	.	.	X	77	.	ENSP00000238662:K77X	K	-	1	0	MLH3	74585883	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.036000	0.88901	2.095000	0.63458	0.533000	0.62120	AAA	.	.	.	none		0.448	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		A	75516130	T	A	75516130	4	1	79	1	0	0	0	0	0	1	0	0	9625	1763	61	5	4180	5	MLH3	14	75516130	Nonsense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	25043817	75516130	31833410	75	5123											
C14orf159	80017	hgsc.bcm.edu	37	chr14	91642321	91642321	+	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	tccaaacctgcctacggggaTgccatggtgtgtcccccagg	7	8	12	14	1	0	0	0	0	0	0	2	1	2	1	6	4	4	0	6	4	2	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr14:91642321T>A	ENST00000523771.1	+	7	1239	c.636T>A	c.(634-636)gaT>gaA	p.D212E	C14orf159_ENST00000523816.1_Missense_Mutation_p.D212E|C14orf159_ENST00000520328.1_Missense_Mutation_p.D200E|C14orf159_ENST00000518868.1_Missense_Mutation_p.D217E|C14orf159_ENST00000412671.2_Missense_Mutation_p.D217E|C14orf159_ENST00000525393.2_Missense_Mutation_p.D88E|C14orf159_ENST00000256324.10_Missense_Mutation_p.D217E|C14orf159_ENST00000428926.2_Missense_Mutation_p.D212E|C14orf159_ENST00000521077.2_Missense_Mutation_p.D217E|C14orf159_ENST00000522322.1_Missense_Mutation_p.D212E			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	212						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)		CCTACGGGGATGCCATGGTGT	0.527																																					p.D217E		Atlas-SNP	.											.	C14orf159	57	.	0			c.T651A						PASS	.						102	90	94					14																	91642321		2203	4300	6503	SO:0001583	missense	80017	exon7			CGGGGATGCCATG	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.636T>A	chr14.hg19:g.91642321T>A	ENSP00000429655:p.Asp212Glu	94.0	0.0	.		102.0	18.0	.	NM_001102368	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Missense_Mutation	SNP	ENST00000523771.1	hg19	CCDS32141.1	.	.	.	.	.	.	.	.	.	.	T	3.538	-0.094274	0.07053	.	.	ENSG00000133943	ENST00000520328;ENST00000256324;ENST00000521077;ENST00000518868;ENST00000523816;ENST00000517518;ENST00000525393;ENST00000428926;ENST00000522322;ENST00000523771;ENST00000412671	T;T;T;T;T;T;T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73	5.06	-10.1	0.00402	.	0.938675	0.09028	N	0.859166	T	0.22166	0.0534	N	0.20807	0.61	0.09310	N	1	B;B;B;B;B;B	0.11235	0.003;0.004;0.003;0.0;0.001;0.003	B;B;B;B;B;B	0.16289	0.009;0.014;0.015;0.005;0.005;0.007	T	0.15378	-1.0439	10	0.39692	T	0.17	.	3.0379	0.06128	0.2001:0.225:0.4295:0.1454	.	212;88;217;200;217;217	Q7Z3D6;Q8NB88;B3KVU6;Q7Z3D6-5;Q7Z3D6-2;Q7Z3D6-3	CN159_HUMAN;.;.;.;.;.	E	200;217;217;217;212;217;88;212;212;212;217	ENSP00000429453:D200E;ENSP00000256324:D217E;ENSP00000430137:D217E;ENSP00000428263:D217E;ENSP00000428974:D212E;ENSP00000428652:D217E;ENSP00000435459:D88E;ENSP00000404343:D212E;ENSP00000427953:D212E;ENSP00000429655:D212E;ENSP00000404196:D217E	ENSP00000256324:D217E	D	+	3	2	C14orf159	90712074	0.000000	0.05858	0.000000	0.03702	0.072000	0.16883	-1.173000	0.03108	-3.740000	0.00113	0.459000	0.35465	GAT	.	.	.	none		0.527	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952		A	91642321	T	A	91642321	3	1	79	1	0	0	0	0	1	0	0	0	1757	1461	51	5	669	5	C14orf159	14	91642321	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	16126191	91642321	15707219	76	5124											
PPP2R5C	5527	hgsc.bcm.edu	37	chr14	102323022	102323022	+	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	actttgctttctgcttttcaGatgttcctcctgctgatcaa	6	18	6	11	0	3	2	2	1	1	1	5	2	5	2	2	0	3	4	2	0	1	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr14:102323022G>A	ENST00000334743.5	+	2	142		c.e2-1		PPP2R5C_ENST00000328724.5_Splice_Site|PPP2R5C_ENST00000422945.2_Splice_Site|PPP2R5C_ENST00000557095.1_Splice_Site|PPP2R5C_ENST00000445439.3_Splice_Site|PPP2R5C_ENST00000350249.3_Splice_Site	NM_002719.3	NP_002710.2	Q13362	2A5G_HUMAN	protein phosphatase 2, regulatory subunit B', gamma						DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of cell proliferation (GO:0008285)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20						CTGCTTTTCAGATGTTCCTCC	0.353																																					.		Atlas-SNP	.											.	PPP2R5C	74	.	0			c.188-1G>A						PASS	.						177	165	169					14																	102323022		2203	4300	6503	SO:0001630	splice_region_variant	5527	exon4			TTTTCAGATGTTC	L42375	CCDS9964.1, CCDS9965.1, CCDS45163.1, CCDS53911.1, CCDS53912.1	14q32.31	2010-06-18	2010-04-14		ENSG00000078304	ENSG00000078304		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9311	protein-coding gene	gene with protein product		601645	"protein phosphatase 2, regulatory subunit B (B56), gamma isoform", "protein phosphatase 2, regulatory subunit B', gamma isoform"			7592815	Standard	NM_002719		Approved	B56G, PR61G	uc001ykk.3	Q13362		ENST00000334743.5:c.95-1G>A	chr14.hg19:g.102323022G>A		353.0	0.0	.		311.0	56.0	.	NM_001161725	B4DYJ8|B5BUA5|F5GWP3|Q14391|Q15060|Q15174|Q6ZN33	Splice_Site	SNP	ENST00000334743.5	hg19	CCDS9964.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.633499	0.87660	.	.	ENSG00000078304	ENST00000422945;ENST00000328724;ENST00000557268;ENST00000350249;ENST00000557621;ENST00000445439;ENST00000334743;ENST00000557095	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.3772	0.94517	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PPP2R5C	101392775	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.813000	0.99286	2.573000	0.86826	0.511000	0.50034	.	.	.	.	none		0.353	PPP2R5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414373.2	NM_002719	Intron	A	102323022	G	A	102323022	5	1	79	1	0	0	0	0	0	0	1	0	12404	956	33	2	469	2	PPP2R5C	14	102323022	Splice_Site	SNP	G	TCGA-B1-5398-01A-02D-1589-08	10680701	102323022	5026518	77	5125											
BAG5	9529	hgsc.bcm.edu	37	chr14	104027517	104027517	+	5'UTR	SNP	A	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	tccatacttttgttgtgttcAgtttcacaagcactaaaaga	12	15	6	8	0	2	1	2	0	0	1	3	1	3	1	1	0	2	4	1	0	4	7			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr14:104027517A>T	ENST00000445922.2	-	0	231				BAG5_ENST00000337322.4_Silent_p.T36T|APOPT1_ENST00000247618.4_5'Flank|APOPT1_ENST00000556253.2_5'Flank|BAG5_ENST00000299204.4_5'UTR|RP11-73M18.2_ENST00000472726.2_5'Flank|APOPT1_ENST00000409074.2_5'Flank|RP11-894P9.2_ENST00000556332.1_RNA	NM_004873.3	NP_004864.1	Q9UL15	BAG5_HUMAN	BCL2-associated athanogene 5						negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein refolding (GO:0061084)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|neuron death (GO:0070997)|protein folding (GO:0006457)|regulation of inclusion body assembly (GO:0090083)	inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	chaperone binding (GO:0051087)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	24		Melanoma(154;0.155)	Epithelial(46;0.144)			TGTTGTGTTCAGTTTCACAAG	0.353																																					p.T36T	NSCLC(171;1832 2055 18950 31566 41632)	Atlas-SNP	.											.	BAG5	47	.	0			c.T108A						PASS	.						57	61	60					14																	104027517		2199	4285	6484	SO:0001623	5_prime_UTR_variant	9529	exon2			GTGTTCAGTTTCA	AF095195	CCDS9982.1, CCDS41995.1	14q32	2008-08-01				ENSG00000166170			941	protein-coding gene	gene with protein product		603885				9873016, 15603737	Standard	NM_001015048		Approved		uc001ynh.2	Q9UL15		ENST00000445922.2:c.-16T>A	chr14.hg19:g.104027517A>T		169.0	0.0	.		179.0	34.0	.	NM_001015049	O94950|Q86W59	Silent	SNP	ENST00000445922.2	hg19	CCDS9982.1																																																																																			.	.	.	none		0.353	BAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414990.1			T	104027517	A	T	104027517	1	4	79	0	1	0	0	0	0	0	0	0	1290	175	7	5		5	BAG5	14	104027517	5'UTR	SNP	A	TCGA-B1-5398-01A-02D-1589-08	1704495	104027517	3322023	78	5126											
SCG3	29106	hgsc.bcm.edu	37	chr15	51993377	51993377	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagatggaaaaggaatatggAagcttgaaggattccacaaa	19	7	11	4	0	0	2	0	1	0	1	1	6	1	6	1	4	1	1	1	4	8	3			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr15:51993377A>G	ENST00000220478.3	+	10	1546	c.1143A>G	c.(1141-1143)ggA>ggG	p.G381G	SCG3_ENST00000542355.2_Silent_p.G149G	NM_013243.3	NP_037375.2	Q8WXD2	SCG3_HUMAN	secretogranin III	381					blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|membrane (GO:0016020)|secretory granule lumen (GO:0034774)	poly(A) RNA binding (GO:0044822)			breast(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21				all cancers(107;0.00488)		AGGAATATGGAAGCTTGAAGG	0.413																																					p.G381G		Atlas-SNP	.											.	SCG3	50	.	0			c.A1143G						PASS	.						185	171	176					15																	51993377		2195	4293	6488	SO:0001819	synonymous_variant	29106	exon10			ATATGGAAGCTTG	AF078851	CCDS10142.1, CCDS53947.1	15q21.2	2013-09-23			ENSG00000104112	ENSG00000104112			13707	protein-coding gene	gene with protein product		611796				2053134, 8825061	Standard	NM_013243		Approved	SGIII, FLJ90833	uc002abh.3	Q8WXD2	OTTHUMG00000131748	ENST00000220478.3:c.1143A>G	chr15.hg19:g.51993377A>G		123.0	0.0	.		104.0	24.0	.	NM_013243	A8K2B0|B3KQP6|B4DK99|F5H3R8|Q96C83|Q96GE8|Q9Y6G7	Silent	SNP	ENST00000220478.3	hg19	CCDS10142.1																																																																																			.	.	.	none		0.413	SCG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254670.2	NM_013243		G	51993377	A	G	51993377	2	3	79	1	0	0	0	0	0	0	0	1	13905	233	9	3		3	SCG3	15	51993377	Silent	SNP	A	TCGA-B1-5398-01A-02D-1589-08		51993377	50538015	79	5127											
SRRM2	23524	hgsc.bcm.edu	37	chr16	2807812	2807812	+	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	actcaccagttggcagaattAaatgagaagaagaatgaaag	19	7	10	5	0	1	5	1	2	0	4	1	6	1	5	1	1	0	2	1	1	7	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr16:2807812A>T	ENST00000301740.8	+	4	930	c.381A>T	c.(379-381)ttA>ttT	p.L127F		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	127					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						tggcagaattaaatgagaaga	0.443																																					p.L127F		Atlas-SNP	.											.	SRRM2	263	.	0			c.A381T						PASS	.						92	99	96					16																	2807812		2198	4300	6498	SO:0001583	missense	23524	exon4			AGAATTAAATGAG	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.381A>T	chr16.hg19:g.2807812A>T	ENSP00000301740:p.Leu127Phe	149.0	0.0	.		207.0	32.0	.	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	hg19	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	A	12.64	1.997285	0.35226	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000396975;ENST00000426305	T	0.23348	1.91	4.96	1.41	0.22369	.	0.000000	0.40908	D	0.000991	T	0.25232	0.0613	N	0.14661	0.345	0.28270	N	0.924446	D	0.69078	0.997	D	0.63488	0.915	T	0.04900	-1.0919	10	0.51188	T	0.08	-4.0677	7.5072	0.27551	0.3974:0.0:0.6026:0.0	.	127	Q9UQ35	SRRM2_HUMAN	F	127;127;31;92	ENSP00000301740:L127F	ENSP00000301740:L127F	L	+	3	2	SRRM2	2747813	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	0.918000	0.28678	0.497000	0.27926	-0.414000	0.06135	TTA	.	.	.	none		0.443	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			T	2807812	A	T	2807812	3	4	79	1	0	0	0	0	1	0	0	0	15181	359	13	5	391	5	SRRM2	16	2807812	Missense_Mutation	SNP	A	TCGA-B1-5398-01A-02D-1589-08		2807812	87546941	80	5128											
XPO6	23214	hgsc.bcm.edu	37	chr16	28157419	28157419	+	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	tgtttgaggagtttacctgtTgagaactgcttccttgtctc	6	17	10	8	0	1	2	0	2	1	1	3	4	2	3	2	1	3	4	2	1	2	6			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr16:28157419T>A	ENST00000304658.5	-	9	1830	c.1330A>T	c.(1330-1332)Aac>Tac	p.N444Y	XPO6_ENST00000565698.1_Missense_Mutation_p.N430Y	NM_015171.3	NP_055986.1	Q96QU8	XPO6_HUMAN	exportin 6	444					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						GTTTACCTGTTGAGAACTGCT	0.398																																					p.N444Y		Atlas-SNP	.											.	XPO6	177	.	0			c.A1330T						PASS	.						209	195	199					16																	28157419		1880	4095	5975	SO:0001583	missense	23214	exon9			ACCTGTTGAGAAC	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.1330A>T	chr16.hg19:g.28157419T>A	ENSP00000302790:p.Asn444Tyr	242.0	0.0	.		292.0	80.0	.	NM_015171	A1L3W4|D3DWF9|Q2YDX3|Q53G88|Q68G50|Q76N88|Q96CP8|Q9BT21	Missense_Mutation	SNP	ENST00000304658.5	hg19	CCDS42135.1	.	.	.	.	.	.	.	.	.	.	T	14.34	2.507676	0.44558	.	.	ENSG00000169180	ENST00000304658	T	0.47528	0.84	5.07	5.07	0.68467	Armadillo-like helical (1);Armadillo-type fold (1);	0.197221	0.52532	D	0.000061	T	0.33702	0.0872	L	0.29908	0.895	0.39270	D	0.964376	P;P	0.48162	0.906;0.79	B;B	0.41723	0.272;0.365	T	0.24012	-1.0172	10	0.42905	T	0.14	.	7.6658	0.28430	0.0:0.0948:0.0:0.9052	.	444;444	B7ZM10;Q96QU8	.;XPO6_HUMAN	Y	444	ENSP00000302790:N444Y	ENSP00000302790:N444Y	N	-	1	0	XPO6	28064920	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.790000	0.62453	1.925000	0.55765	0.524000	0.50904	AAC	.	.	.	none		0.398	XPO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433732.1	XM_055195		A	28157419	T	A	28157419	3	1	79	1	0	0	0	0	1	0	0	0	17460	1812	63	5	2111	5	XPO6	16	28157419	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	25349607	28157419	62197334	81	5129											
SRCAP	10847	hgsc.bcm.edu	37	chr16	30723210	30723210	+	Frame_Shift_Del	DEL	A	A	-																															tgaacattcagaggaggaagAaacaagtggaagttcagcat																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr16:30723210delA	ENST00000262518.4	+	12	1932	c.1547delA	c.(1546-1548)gaafs	p.E516fs	SRCAP_ENST00000395059.2_Frame_Shift_Del_p.E516fs|SNORA30_ENST00000384028.1_RNA|SRCAP_ENST00000344771.4_Frame_Shift_Del_p.E516fs	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	516	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)			GAGGAGGAAGAAACAAGTGGA	0.473																																					p.E516fs		Atlas-INDEL	.											.	SRCAP	298	.	0			c.1546delG						PASS	.						74	71	72					16																	30723210		2197	4300	6497	SO:0001589	frameshift_variant	10847	exon12			.	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.1547delA	chr16.hg19:g.30723210delA	ENSP00000262518:p.Glu516fs	73.0	0.0	0		78.0	13.0	0.166667	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Frame_Shift_Del	DEL	ENST00000262518.4	hg19	CCDS10689.2																																																																																			.	.	.	none		0.473	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		-	30723210	A	-	30723210	7	5	79	1	0	1	0	1	0	0	0	0	15147	246	9	0	1585	0	SRCAP	16	30723210	Frame_Shift_Del	DEL	A	TCGA-B1-5398-01A-02D-1589-08	2565791	30723210	59631543	82	5130											
ZNF646	9726	hgsc.bcm.edu	37	chr16	31090723	31090723	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggagatgccaagtctcaagaGggagcaggcacccccttggg	10	5	15	11	0	1	2	1	0	1	2	2	4	1	3	3	4	2	2	3	4	2	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr16:31090723G>A	ENST00000394979.2	+	1	3501	c.3078G>A	c.(3076-3078)gaG>gaA	p.E1026E	ZNF646_ENST00000300850.5_Silent_p.E1026E			O15015	ZN646_HUMAN	zinc finger protein 646	1026					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						AGTCTCAAGAGGGAGCAGGCA	0.587																																					p.E1026E		Atlas-SNP	.											.	ZNF646	133	.	0			c.G3078A						PASS	.						121	118	119					16																	31090723		2197	4300	6497	SO:0001819	synonymous_variant	9726	exon2			TCAAGAGGGAGCA	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.3078G>A	chr16.hg19:g.31090723G>A		252.0	0.0	.		232.0	34.0	.	NM_014699	Q8IVD8	Silent	SNP	ENST00000394979.2	hg19																																																																																				.	.	.	none		0.587	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699		A	31090723	G	A	31090723	2	1	79	1	0	0	0	0	0	0	0	1	18074	991	35	2		2	ZNF646	16	31090723	Silent	SNP	G	TCGA-B1-5398-01A-02D-1589-08	367513	31090723	59264030	83	5131											
CNOT1	23019	hgsc.bcm.edu	37	chr16	58633189	58633190	+	Frame_Shift_Ins	INS	-	-	CCAC																															atttttcttggttaaattgtINSccaccaggtagctgatttga																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr16:58633189_58633190insCCAC	ENST00000317147.5	-	2	384_385	c.52_53insGTGG	c.(52-54)gacfs	p.D18fs	CNOT1_ENST00000441024.2_Frame_Shift_Ins_p.D18fs|CNOT1_ENST00000569240.1_Frame_Shift_Ins_p.D18fs	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	18				D -> G (in Ref. 1; CAD97851). {ECO:0000305}.	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)		GGTTAAATTGTCCACCAGGTAG	0.49																																					p.D18fs		Atlas-INDEL	.											.	CNOT1	359	.	0			c.53_54insGTGG						PASS	.																																			SO:0001589	frameshift_variant	23019	exon2			.	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.49_52dupGTGG	chr16.hg19:g.58633190_58633193dupCCAC	ENSP00000320949:p.Asp18fs	95.0	0.0	0		121.0	25.0	0.206612	NM_001265612	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Frame_Shift_Ins	INS	ENST00000317147.5	hg19	CCDS10799.1																																																																																			.	.	.	none		0.49	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		CCAC	58633190	-	CCAC	58633189	7	5	79	1	0	1	1	0	0	0	0	0	3619	1667	58	0	7491	0	CNOT1	16	58633189	Frame_Shift_Ins	INS	-	TCGA-B1-5398-01A-02D-1589-08	27542466	58633189	31721564	84	5132											
HAS3	3038	hgsc.bcm.edu	37	chr16	69143465	69143465	+	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	cgccatcctgggcctgcaccTgctcattcagagcctttttg	5	12	9	15	1	2	1	2	0	0	1	3	1	3	1	5	1	3	2	5	1	0	3			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr16:69143465T>A	ENST00000306560.1	+	2	323	c.167T>A	c.(166-168)cTg>cAg	p.L56Q	HAS3_ENST00000569188.1_Missense_Mutation_p.L56Q|HAS3_ENST00000219322.3_Missense_Mutation_p.L56Q	NM_005329.2	NP_005320.2	O00219	HYAS3_HUMAN	hyaluronan synthase 3	56					carbohydrate metabolic process (GO:0005975)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|positive regulation of hyaluranon cable assembly (GO:1900106)|positive regulation of transcription, DNA-templated (GO:0045893)|small molecule metabolic process (GO:0044281)	hyaluranon cable (GO:0036117)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|urinary_tract(2)	16		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.0694)		GGCCTGCACCTGCTCATTCAG	0.657																																					p.L56Q		Atlas-SNP	.											.	HAS3	61	.	0			c.T167A						PASS	.						93	79	84					16																	69143465		2198	4300	6498	SO:0001583	missense	3038	exon2			TGCACCTGCTCAT	BC021853	CCDS10870.1, CCDS10871.1	16q22.1	2013-02-22			ENSG00000103044	ENSG00000103044	2.4.1.212	"Glycosyltransferase family 2 domain containing"	4820	protein-coding gene	gene with protein product		602428				9169154, 9083017	Standard	NM_005329		Approved		uc010cfh.3	O00219	OTTHUMG00000137562	ENST00000306560.1:c.167T>A	chr16.hg19:g.69143465T>A	ENSP00000304440:p.Leu56Gln	88.0	0.0	.		100.0	13.0	.	NM_138612	A8K5T5|Q8WTZ0|Q9NYP0	Missense_Mutation	SNP	ENST00000306560.1	hg19	CCDS10871.1	.	.	.	.	.	.	.	.	.	.	T	26.9	4.778165	0.90195	.	.	ENSG00000103044	ENST00000219322;ENST00000306560	T;T	0.55930	0.49;0.63	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.73393	0.3581	M	0.77486	2.375	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.959;0.999	T	0.77370	-0.2613	10	0.87932	D	0	12.4482	15.438	0.75162	0.0:0.0:0.0:1.0	.	56;56	O00219;O00219-2	HAS3_HUMAN;.	Q	56	ENSP00000219322:L56Q;ENSP00000304440:L56Q	ENSP00000219322:L56Q	L	+	2	0	HAS3	67700966	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.924000	0.87555	2.143000	0.66587	0.459000	0.35465	CTG	.	.	.	none		0.657	HAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268898.2	NM_138612		A	69143465	T	A	69143465	3	1	79	1	0	0	0	0	1	0	0	0	6970	1580	55	5	169	5	HAS3	16	69143465	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	10510276	69143465	21211288	85	5133											
SLC38A8	146167	hgsc.bcm.edu	37	chr16	84063153	84063153	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacacagaggtccaggaggcAgggctgtaaacagacaagaa	17	3	13	8	0	0	3	0	0	0	3	1	4	1	4	1	4	2	3	1	4	5	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr16:84063153A>G	ENST00000299709.3	-	5	635	c.636T>C	c.(634-636)ccT>ccC	p.P212P		NM_001080442.1	NP_001073911.1	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8	212					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						TCCAGGAGGCAGGGCTGTAAA	0.493																																					p.P212P		Atlas-SNP	.											.	SLC38A8	60	.	0			c.T636C						PASS	.						94	92	93					16																	84063153		2200	4300	6500	SO:0001819	synonymous_variant	146167	exon5			GGAGGCAGGGCTG		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.636T>C	chr16.hg19:g.84063153A>G		68.0	0.0	.		81.0	29.0	.	NM_001080442		Silent	SNP	ENST00000299709.3	hg19	CCDS32495.1																																																																																			.	.	.	none		0.493	SLC38A8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432623.1	NM_001080442		G	84063153	A	G	84063153	2	3	79	1	0	0	0	0	0	0	0	1	14623	175	7	3		3	SLC38A8	16	84063153	Silent	SNP	A	TCGA-B1-5398-01A-02D-1589-08	14919688	84063153	6291600	86	5134											
TMEM220	388335	hgsc.bcm.edu	37	chr17	10626593	10626593	+	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	agttgaatacttactttgagGaactgtggcacaggataatc	13	12	10	6	0	0	2	0	2	0	0	1	4	0	4	0	3	3	2	0	3	5	5			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr17:10626593G>C	ENST00000341871.3	-	5	805	c.341C>G	c.(340-342)tCc>tGc	p.S114C	TMEM220_ENST00000455996.2_Missense_Mutation_p.S104C|TMEM220_ENST00000578345.1_Intron|TMEM220_ENST00000580186.1_5'UTR	NM_001004313.1	NP_001004313.1	Q6QAJ8	TM220_HUMAN	transmembrane protein 220	114						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)|lung(1)|prostate(2)	5						TTACTTTGAGGAACTGTGGCA	0.468																																					p.S114C		Atlas-SNP	.											.	TMEM220	11	.	0			c.C341G						PASS	.						163	145	151					17																	10626593		2203	4300	6503	SO:0001583	missense	388335	exon5			TTTGAGGAACTGT		CCDS32567.1	17p13.1	2008-08-08			ENSG00000187824	ENSG00000187824			33757	protein-coding gene	gene with protein product							Standard	NM_001004313		Approved		uc002gmx.3	Q6QAJ8		ENST00000341871.3:c.341C>G	chr17.hg19:g.10626593G>C	ENSP00000339830:p.Ser114Cys	117.0	0.0	.		125.0	18.0	.	NM_001004313	A1YRJ4|B2RNE4|B4DJ52|B9EGW3	Missense_Mutation	SNP	ENST00000341871.3	hg19	CCDS32567.1	.	.	.	.	.	.	.	.	.	.	G	16.73	3.205169	0.58234	.	.	ENSG00000187824	ENST00000341871;ENST00000455996	.	.	.	5.63	4.66	0.58398	.	0.096587	0.41938	D	0.000796	T	0.77046	0.4073	M	0.74881	2.28	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.948;0.998	T	0.79403	-0.1818	9	0.87932	D	0	-22.2883	11.3464	0.49563	0.0848:0.0:0.9152:0.0	.	104;114	Q6QAJ8-2;Q6QAJ8	.;TM220_HUMAN	C	114;104	.	ENSP00000339830:S114C	S	-	2	0	TMEM220	10567318	1.000000	0.71417	0.137000	0.22149	0.714000	0.41099	3.006000	0.49529	1.379000	0.46325	0.563000	0.77884	TCC	.	.	.	none		0.468	TMEM220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440333.1	NM_001004313		C	10626593	G	C	10626593	3	2	79	1	0	0	0	0	1	0	0	0	16156	1174	41	4	149	4	TMEM220	17	10626593	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08		10626593	70568617	87	5135											
FBXW10	10517	hgsc.bcm.edu	37	chr17	18653137	18653137	+	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	gtacgatccctgcaatctatTggttgacctggatgacatca	10	12	9	10	1	2	2	1	2	1	0	3	4	3	3	2	2	2	3	2	2	3	4			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr17:18653137T>A	ENST00000395665.4	+	3	994	c.773T>A	c.(772-774)tTg>tAg	p.L258*	FBXW10_ENST00000395667.1_Nonsense_Mutation_p.L258*|FBXW10_ENST00000301938.4_Nonsense_Mutation_p.L258*|FBXW10_ENST00000308799.4_Nonsense_Mutation_p.L258*			Q5XX13	FBW10_HUMAN	F-box and WD repeat domain containing 10	258										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						TGCAATCTATTGGTTGACCTG	0.468																																					p.L258X		Atlas-SNP	.											.	FBXW10	82	.	0			c.T773A						PASS	.						146	115	126					17																	18653137		2203	4300	6503	SO:0001587	stop_gained	10517	exon3			ATCTATTGGTTGA	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.773T>A	chr17.hg19:g.18653137T>A	ENSP00000379025:p.Leu258*	302.0	0.0	.		314.0	49.0	.	NM_001267585	C9JRY8|C9JZD7|Q8TC00|Q9H0F0	Nonsense_Mutation	SNP	ENST00000395665.4	hg19	CCDS11199.3	.	.	.	.	.	.	.	.	.	.	T	37	6.578584	0.97680	.	.	ENSG00000171931	ENST00000395667;ENST00000308799;ENST00000301938;ENST00000395665	.	.	.	2.49	2.49	0.30216	.	0.395534	0.14928	U	0.290234	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.5156	0.33244	0.0:0.0:0.0:1.0	.	.	.	.	X	258	.	ENSP00000306937:L258X	L	+	2	0	FBXW10	18593862	0.026000	0.19158	0.002000	0.10522	0.803000	0.45373	1.573000	0.36472	1.144000	0.42321	0.333000	0.21579	TTG	.	.	.	none		0.468	FBXW10-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313531.2	NM_031456		A	18653137	T	A	18653137	4	1	79	1	0	0	0	0	0	1	0	0	5770	1821	63	5	783	5	FBXW10	17	18653137	Nonsense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	8026544	18653137	62542073	88	5136											
DHX58	79132	hgsc.bcm.edu	37	chr17	40262859	40262859	+	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	ggagtttaagttctaggtacTggctcatgatgacgttgtag	9	14	13	5	1	2	2	1	2	1	0	2	3	2	3	0	3	1	6	0	3	4	7			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr17:40262859T>A	ENST00000251642.3	-	5	665	c.443A>T	c.(442-444)cAg>cTg	p.Q148L		NM_024119.2	NP_077024.2	Q96C10	DHX58_HUMAN	DEXH (Asp-Glu-X-His) box polypeptide 58	148	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of innate immune response (GO:0045824)|negative regulation of MDA-5 signaling pathway (GO:0039534)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|positive regulation of type I interferon production (GO:0032481)|regulation of innate immune response (GO:0045088)|response to virus (GO:0009615)|viral process (GO:0016032)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_cancers(22;9.73e-07)|all_epithelial(22;3.58e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		TTCTAGGTACTGGCTCATGAT	0.612																																					p.Q148L		Atlas-SNP	.											.	DHX58	39	.	0			c.A443T						PASS	.						189	163	172					17																	40262859		2203	4300	6503	SO:0001583	missense	79132	exon5			AGGTACTGGCTCA	BC014949	CCDS11416.1	17q21.2	2008-02-05			ENSG00000108771	ENSG00000108771			29517	protein-coding gene	gene with protein product	"RNA helicase LGP2"	608588				11735219	Standard	NM_024119		Approved	LGP2, D11LGP2	uc002hyw.3	Q96C10	OTTHUMG00000133493	ENST00000251642.3:c.443A>T	chr17.hg19:g.40262859T>A	ENSP00000251642:p.Gln148Leu	152.0	0.0	.		140.0	24.0	.	NM_024119	Q9HAM6	Missense_Mutation	SNP	ENST00000251642.3	hg19	CCDS11416.1	.	.	.	.	.	.	.	.	.	.	T	14.83	2.653438	0.47362	.	.	ENSG00000108771	ENST00000251642;ENST00000423748;ENST00000413196;ENST00000430773	T;T;T	0.33438	3.64;1.41;1.94	4.93	-2.66	0.06077	DEAD-like helicase (2);Helicase/UvrB domain (1);	0.568788	0.18403	N	0.142315	T	0.17874	0.0429	N	0.17800	0.525	0.19575	N	0.999962	B;B	0.22746	0.074;0.007	B;B	0.27500	0.08;0.015	T	0.22487	-1.0215	10	0.36615	T	0.2	.	11.295	0.49274	0.0:0.5209:0.0:0.4791	.	141;148	B7Z455;Q96C10	.;DHX58_HUMAN	L	148;111;148;148	ENSP00000251642:Q148L;ENSP00000416389:Q148L;ENSP00000404639:Q148L	ENSP00000251642:Q148L	Q	-	2	0	DHX58	37516385	0.000000	0.05858	0.973000	0.42090	0.876000	0.50452	-0.928000	0.03980	-0.318000	0.08665	-1.063000	0.02288	CAG	.	.	.	none		0.612	DHX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257396.1	NM_024119		A	40262859	T	A	40262859	3	1	79	1	0	0	0	0	1	0	0	0	4516	1580	55	5	1633	5	DHX58	17	40262859	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08	21609722	40262859	40932351	89	5137											
MYO5B	4645	hgsc.bcm.edu	37	chr18	47375980	47375980	+	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	atgtaaatcttcagttgcttTttgagcttcctctcattctt	7	20	5	9	0	4	1	2	1	3	0	6	1	5	1	1	0	2	4	1	0	2	8			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr18:47375980T>A	ENST00000285039.7	-	32	4571	c.4272A>T	c.(4270-4272)aaA>aaT	p.K1424N	SCARNA17_ENST00000589499.1_RNA|MYO5B_ENST00000324581.6_Missense_Mutation_p.K539N|MYO5B_ENST00000592688.1_5'UTR	NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	1424					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)		TCAGTTGCTTTTTGAGCTTCC	0.483																																					p.K1424N		Atlas-SNP	.											.	MYO5B	178	.	0			c.A4272T						PASS	.						336	326	330					18																	47375980		1961	4155	6116	SO:0001583	missense	4645	exon32			TTGCTTTTTGAGC	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.4272A>T	chr18.hg19:g.47375980T>A	ENSP00000285039:p.Lys1424Asn	475.0	0.0	.		494.0	65.0	.	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Missense_Mutation	SNP	ENST00000285039.7	hg19	CCDS42436.1	.	.	.	.	.	.	.	.	.	.	T	19.99	3.929283	0.73327	.	.	ENSG00000167306	ENST00000285039;ENST00000324581	T;T	0.27720	1.65;1.65	4.63	-8.81	0.00813	.	0.000000	0.85682	D	0.000000	T	0.48132	0.1483	M	0.75615	2.305	0.45914	D	0.998753	D;D	0.89917	0.999;1.0	D;D	0.85130	0.986;0.997	T	0.70737	-0.4790	10	0.42905	T	0.14	.	18.1767	0.89764	0.0:0.7032:0.0:0.2968	.	1424;539	Q9ULV0;Q9H6Y6	MYO5B_HUMAN;.	N	1424;539	ENSP00000285039:K1424N;ENSP00000315531:K539N	ENSP00000285039:K1424N	K	-	3	2	MYO5B	45629978	0.939000	0.31865	0.188000	0.23233	0.960000	0.62799	0.054000	0.14205	-1.861000	0.01153	-0.441000	0.05720	AAA	.	.	.	none		0.483	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2			A	47375980	T	A	47375980	3	1	79	1	0	0	0	0	1	0	0	0	10086	1838	64	5	1310	5	MYO5B	18	47375980	Missense_Mutation	SNP	T	TCGA-B1-5398-01A-02D-1589-08		47375980	30701268	90	5138											
ZNF254	9534	hgsc.bcm.edu	37	chr19	24309780	24309780	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaccctacaagtgtgaagaAtgtggcaaagcatttatatg	16	10	9	6	0	0	2	0	1	0	1	0	2	0	2	1	1	3	2	1	1	8	4			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr19:24309780A>G	ENST00000357002.4	+	4	1093	c.978A>G	c.(976-978)gaA>gaG	p.E326E	ZNF254_ENST00000342944.6_Silent_p.E241E	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	326					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)				AGTGTGAAGAATGTGGCAAAG	0.388																																					p.E326E		Atlas-SNP	.											.	ZNF254	88	.	0			c.A978G						PASS	.						50	50	50					19																	24309780		2203	4300	6503	SO:0001819	synonymous_variant	9534	exon4			TGAAGAATGTGGC	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.978A>G	chr19.hg19:g.24309780A>G		123.0	0.0	.		94.0	12.0	.	NM_203282	A4QPC0|Q86XL7	Silent	SNP	ENST00000357002.4	hg19	CCDS32983.1																																																																																			.	.	.	none		0.388	ZNF254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466453.1	NM_004876		G	24309780	A	G	24309780	2	3	79	1	0	0	0	0	0	0	0	1	17810	98	4	3		3	ZNF254	19	24309780	Silent	SNP	A	TCGA-B1-5398-01A-02D-1589-08		24309780	34819203	91	5139											
UBA2	10054	hgsc.bcm.edu	37	chr19	34924279	34924279	+	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	ctataatgtggaatttttccGacagtttatactggttatga	11	17	8	5	1	0	1	0	1	0	0	1	3	1	2	1	2	1	2	1	2	6	8	rs370848936		TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr19:34924279G>A	ENST00000246548.4	+	4	390	c.320G>A	c.(319-321)cGa>cAa	p.R107Q	UBA2_ENST00000439527.2_Missense_Mutation_p.R11Q	NM_005499.2	NP_005490.1	Q9UBT2	SAE2_HUMAN	ubiquitin-like modifier activating enzyme 2	107					cellular protein metabolic process (GO:0044267)|positive regulation of catalytic activity (GO:0043085)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)|SMT3-dependent protein catabolic process (GO:0019950)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|SUMO activating enzyme complex (GO:0031510)	ATP binding (GO:0005524)|enzyme activator activity (GO:0008047)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|SUMO activating enzyme activity (GO:0019948)			breast(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	20	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			GAATTTTTCCGACAGTTTATA	0.308																																					p.R107Q		Atlas-SNP	.											.	UBA2	53	.	0			c.G320A						PASS	.	G	GLN/ARG	0,4404		0,0,2202	98	105	103		320	4.6	1	19		103	1,8599	1.2+/-3.3	0,1,4299	no	missense	UBA2	NM_005499.2	43	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	benign	107/641	34924279	1,13003	2202	4300	6502	SO:0001583	missense	10054	exon4			TTTTCCGACAGTT	BC003153	CCDS12439.1	19q13.11	2008-02-05	2007-11-30	2007-11-30		ENSG00000126261		"Ubiquitin-like modifier activating enzymes"	30661	protein-coding gene	gene with protein product	"UBA2, ubiquitin-activating enzyme E1 homolog (yeast)"	613295	"SUMO1 activating enzyme subunit 2"	SAE2		10187858, 9920803	Standard	NM_005499		Approved	FLJ13058, HRIHFB2115, ARX	uc002nvk.3	Q9UBT2		ENST00000246548.4:c.320G>A	chr19.hg19:g.34924279G>A	ENSP00000246548:p.Arg107Gln	223.0	0.0	.		197.0	36.0	.	NM_005499	B3KWB9|O95605|Q59H87|Q6IBP6|Q9NTJ1|Q9UED2	Missense_Mutation	SNP	ENST00000246548.4	hg19	CCDS12439.1	.	.	.	.	.	.	.	.	.	.	G	14.59	2.582155	0.46006	0.0	1.16E-4	ENSG00000126261	ENST00000246548;ENST00000439527	T;T	0.29917	1.55;1.55	5.65	4.62	0.57501	UBA/THIF-type NAD/FAD binding fold (1);Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.111742	0.56097	D	0.000021	T	0.15132	0.0365	N	0.11000	0.08	0.47621	D	0.99947	B	0.20459	0.045	B	0.15484	0.013	T	0.09207	-1.0685	10	0.16896	T	0.51	-8.9388	9.9261	0.41494	0.1577:0.0:0.8423:0.0	.	107	Q9UBT2	SAE2_HUMAN	Q	107;11	ENSP00000246548:R107Q;ENSP00000437484:R11Q	ENSP00000246548:R107Q	R	+	2	0	UBA2	39616119	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.620000	0.67736	1.396000	0.46663	0.591000	0.81541	CGA	.	.	.	weak		0.308	UBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459257.3	NM_005499		A	34924279	G	A	34924279	3	1	79	1	0	0	0	0	1	0	0	0	16840	1058	37	1	334	1	UBA2	19	34924279	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	10614499	34924279	24204704	92	5140											
LAIR1	3903	hgsc.bcm.edu	37	chr19	54872527	54872527	+	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	caggtgacgtcctcacctttCaccagcagctccaggtagtc	8	9	9	15	1	2	1	2	1	0	0	5	1	4	1	4	2	2	3	4	2	1	2			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr19:54872527C>A	ENST00000391742.2	-	3	512	c.360G>T	c.(358-360)gtG>gtT	p.V120V	LAIR1_ENST00000348231.4_Silent_p.V120V|LAIR1_ENST00000463489.1_Intron|LAIR1_ENST00000391743.3_Silent_p.V102V|LAIR1_ENST00000313038.6_Silent_p.V113V|LAIR1_ENST00000474878.1_Silent_p.V119V|LAIR1_ENST00000434277.2_Silent_p.V119V			Q6GTX8	LAIR1_HUMAN	leukocyte-associated immunoglobulin-like receptor 1	120					immune system process (GO:0002376)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(9)|ovary(4)|prostate(1)|stomach(3)	26	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0573)		CCTCACCTTTCACCAGCAGCT	0.582																																					p.V120V		Atlas-SNP	.											.	LAIR1	44	.	0			c.G360T						PASS	.						105	100	102					19																	54872527		2203	4300	6503	SO:0001819	synonymous_variant	3903	exon3			ACCTTTCACCAGC	AF013249	CCDS12891.1, CCDS12892.1, CCDS74448.1, CCDS74449.1, CCDS74450.1	19q13.4	2013-01-29	2006-03-23		ENSG00000167613	ENSG00000167613		"Leukocyte-associated Ig like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6477	protein-coding gene	gene with protein product		602992	"leukocyte-associated Ig-like receptor 1"			9285412	Standard	XM_005258924		Approved	CD305	uc002qfk.1	Q6GTX8	OTTHUMG00000065545	ENST00000391742.2:c.360G>T	chr19.hg19:g.54872527C>A		226.0	0.0	.		197.0	37.0	.	NM_021706		Silent	SNP	ENST00000391742.2	hg19	CCDS12891.1																																																																																			.	.	.	none		0.582	LAIR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140506.1			A	54872527	C	A	54872527	2	1	79	1	0	0	0	0	0	0	0	1	8609	813	29	4		4	LAIR1	19	54872527	Silent	SNP	C	TCGA-B1-5398-01A-02D-1589-08	19948248	54872527	4256456	93	5141											
ZNF773	374928	hgsc.bcm.edu	37	chr19	58018029	58018029	+	Missense_Mutation	SNP	G	G	A																															ggcctttcatgctggaaaaaGgcattacaaatgcagtgaat																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr19:58018029G>A	ENST00000282292.4	+	4	706	c.566G>A	c.(565-567)aGg>aAg	p.R189K	ZNF773_ENST00000598770.1_Missense_Mutation_p.R188K|ZNF773_ENST00000599847.1_Intron|ZNF773_ENST00000593916.1_Intron	NM_198542.1	NP_940944.1	Q6PK81	ZN773_HUMAN	zinc finger protein 773	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)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	22		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;0.0254)		GCTGGAAAAAGGCATTACAAA	0.473																																					p.R189K		Atlas-SNP	.											.	ZNF773	62	.	0			c.G566A						PASS	.						48	48	48					19																	58018029		2203	4297	6500	SO:0001583	missense	374928	exon4			GAAAAAGGCATTA	BC005167	CCDS33134.1	19q13.43	2013-01-08	2006-12-15	2006-12-15		ENSG00000152439		"Zinc fingers, C2H2-type", "-"	30487	protein-coding gene	gene with protein product			"zinc finger protein 419B"	ZNF419B		12477932	Standard	NM_198542		Approved	MGC4728	uc002qox.3	Q6PK81		ENST00000282292.4:c.566G>A	chr19.hg19:g.58018029G>A	ENSP00000282292:p.Arg189Lys	45.0	0.0	.		56.0	5.0	.	NM_198542	Q96DL8	Missense_Mutation	SNP	ENST00000282292.4	hg19	CCDS33134.1	.	.	.	.	.	.	.	.	.	.	G	1.360	-0.589074	0.03799	.	.	ENSG00000152439	ENST00000282292	T	0.21543	2.0	1.25	0.169	0.15017	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06962	0.0177	N	0.05259	-0.085	0.09310	N	1	B;B	0.28233	0.204;0.01	B;B	0.27076	0.076;0.003	T	0.36744	-0.9735	9	0.02654	T	1	.	4.9147	0.13840	0.3681:0.0:0.6319:0.0	.	188;189	Q6PK81-2;Q6PK81	.;ZN773_HUMAN	K	189	ENSP00000282292:R189K	ENSP00000282292:R189K	R	+	2	0	ZNF773	62709841	0.000000	0.05858	0.006000	0.13384	0.429000	0.31625	-0.057000	0.11768	0.097000	0.17492	0.313000	0.20887	AGG	.	.	.	none		0.473	ZNF773-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466475.1	NM_198542		A	58018029	G	A	58018029	3	1	79	1	0	0	0	0	1	0	0	0	18158	1000	35	2	580	2	ZNF773	19	58018029	Missense_Mutation	SNP	G	TCGA-B1-5398-01A-02D-1589-08	3145502	58018029	1110954	94	5142	55	2									
ZNF773	374928	hgsc.bcm.edu	37	chr19	58018032	58018032	+	Missense_Mutation	SNP	A	A	G																															ctttcatgctggaaaaaggcAttacaaatgcagtgaatgtg																										TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr19:58018032A>G	ENST00000282292.4	+	4	709	c.569A>G	c.(568-570)cAt>cGt	p.H190R	ZNF773_ENST00000598770.1_Missense_Mutation_p.H189R|ZNF773_ENST00000599847.1_Intron|ZNF773_ENST00000593916.1_Intron	NM_198542.1	NP_940944.1	Q6PK81	ZN773_HUMAN	zinc finger protein 773	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)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	22		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;0.0254)		GGAAAAAGGCATTACAAATGC	0.473																																					p.H190R		Atlas-SNP	.											.	ZNF773	62	.	0			c.A569G						PASS	.						49	49	49					19																	58018032		2203	4297	6500	SO:0001583	missense	374928	exon4			AAAGGCATTACAA	BC005167	CCDS33134.1	19q13.43	2013-01-08	2006-12-15	2006-12-15		ENSG00000152439		"Zinc fingers, C2H2-type", "-"	30487	protein-coding gene	gene with protein product			"zinc finger protein 419B"	ZNF419B		12477932	Standard	NM_198542		Approved	MGC4728	uc002qox.3	Q6PK81		ENST00000282292.4:c.569A>G	chr19.hg19:g.58018032A>G	ENSP00000282292:p.His190Arg	45.0	0.0	.		61.0	5.0	.	NM_198542	Q96DL8	Missense_Mutation	SNP	ENST00000282292.4	hg19	CCDS33134.1	.	.	.	.	.	.	.	.	.	.	A	1.777	-0.482865	0.04383	.	.	ENSG00000152439	ENST00000282292	T	0.07327	3.2	1.25	0.141	0.14811	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04452	0.0122	N	0.13098	0.295	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.002	T	0.40098	-0.9581	9	0.66056	D	0.02	.	3.1074	0.06346	0.3454:0.4308:0.0:0.2238	.	189;190	Q6PK81-2;Q6PK81	.;ZN773_HUMAN	R	190	ENSP00000282292:H190R	ENSP00000282292:H190R	H	+	2	0	ZNF773	62709844	0.000000	0.05858	0.002000	0.10522	0.468000	0.32798	-0.492000	0.06467	-0.023000	0.13963	0.260000	0.18958	CAT	.	.	.	none		0.473	ZNF773-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466475.1	NM_198542		G	58018032	A	G	58018032	3	3	79	1	0	0	0	0	1	0	0	0	18158	217	8	3	583	3	ZNF773	19	58018032	Missense_Mutation	SNP	A	TCGA-B1-5398-01A-02D-1589-08	3	58018032	1110951	95	5143	55	2									
COL18A1	80781	hgsc.bcm.edu	37	chr21	46902710	46902710	+	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	cctgctcttttccgtacaggGtgaagcaggcgccccaggac	7	8	12	14	2	1	1	0	1	1	0	2	2	2	2	4	3	3	3	4	3	2	3			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr21:46902710G>A	ENST00000359759.4	+	14	2942	c.2921G>A	c.(2920-2922)gGt>gAt	p.G974D	COL18A1_ENST00000400337.2_Splice_Site_p.G559D|COL18A1_ENST00000355480.5_Splice_Site_p.G739D			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	974	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)		TCCGTACAGGGTGAAGCAGGC	0.592																																					p.G739D		Atlas-SNP	.											.	COL18A1	129	.	0			c.G2216A						PASS	.						116	125	122					21																	46902710		2050	4191	6241	SO:0001630	splice_region_variant	80781	exon14			TACAGGGTGAAGC		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.2920-1G>A	chr21.hg19:g.46902710G>A		126.0	0.0	.		98.0	16.0	.	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	hg19		.	.	.	.	.	.	.	.	.	.	G	14.50	2.553832	0.45487	.	.	ENSG00000182871	ENST00000400337;ENST00000355480;ENST00000359759	D;D;D	0.99532	-5.77;-6.1;-6.1	2.62	2.62	0.31277	.	.	.	.	.	D	0.99651	0.9871	H	0.95294	3.65	0.39801	D	0.972573	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.98225	1.0480	9	0.87932	D	0	.	8.8912	0.35434	0.0:0.0:1.0:0.0	.	974;739;559	P39060;P39060-1;P39060-2	COIA1_HUMAN;.;.	D	559;739;974	ENSP00000383191:G559D;ENSP00000347665:G739D;ENSP00000352798:G974D	ENSP00000347665:G739D	G	+	2	0	COL18A1	45727138	0.971000	0.33674	0.522000	0.27862	0.058000	0.15608	1.738000	0.38207	1.799000	0.52666	0.549000	0.68633	GGT	.	.	.	none		0.592	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		Missense_Mutation	A	46902710	G	A	46902710	5	1	79	1	0	0	0	0	0	0	1	0	3677	1275	44	2	3089	2	COL18A1	21	46902710	Splice_Site	SNP	G	TCGA-B1-5398-01A-02D-1589-08		46902710	1227185	96	5144											
MCHR1	2847	hgsc.bcm.edu	37	chr22	41076973	41076973	+	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	gatcacctcctcgcacggggAgcatctcctacatcaacatc	10	8	7	16	2	3	0	2	0	1	0	7	2	4	1	3	2	3	2	3	2	2	1			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr22:41076973A>T	ENST00000249016.4	+	2	1006	c.310A>T	c.(310-312)Agc>Tgc	p.S104C	MCHR1_ENST00000381433.2_Missense_Mutation_p.S104C|MCHR1_ENST00000498400.1_3'UTR	NM_005297.3	NP_005288.3	Q99705	MCHR1_HUMAN	melanin-concentrating hormone receptor 1	104					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						TCGCACGGGGAGCATCTCCTA	0.567																																					p.S104C		Atlas-SNP	.											.	MCHR1	45	.	0			c.A310T						PASS	.						139	105	117					22																	41076973		2203	4300	6503	SO:0001583	missense	2847	exon2			ACGGGGAGCATCT		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.310A>T	chr22.hg19:g.41076973A>T	ENSP00000249016:p.Ser104Cys	81.0	0.0	.		89.0	12.0	.	NM_005297	B2RBX6|Q5R3J1|Q96S47|Q9BV08	Missense_Mutation	SNP	ENST00000249016.4	hg19	CCDS14004.1	.	.	.	.	.	.	.	.	.	.	A	8.701	0.909808	0.17833	.	.	ENSG00000128285	ENST00000249016;ENST00000381433	T;T	0.38077	1.16;1.16	4.87	3.77	0.43336	.	0.596448	0.17749	N	0.163281	T	0.21631	0.0521	N	0.14661	0.345	0.22866	N	0.998638	P	0.39576	0.679	B	0.37047	0.24	T	0.11421	-1.0588	10	0.59425	D	0.04	.	10.4074	0.44272	0.8375:0.1625:0.0:0.0	.	104	Q99705	MCHR1_HUMAN	C	104	ENSP00000249016:S104C;ENSP00000370841:S104C	ENSP00000249016:S104C	S	+	1	0	MCHR1	39406919	0.902000	0.30710	0.457000	0.27056	0.381000	0.30169	1.471000	0.35365	1.959000	0.56917	0.533000	0.62120	AGC	.	.	.	none		0.567	MCHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317142.1	NM_005297		T	41076973	A	T	41076973	3	4	79	1	0	0	0	0	1	0	0	0	9389	304	11	5	316	5	MCHR1	22	41076973	Missense_Mutation	SNP	A	TCGA-B1-5398-01A-02D-1589-08		41076973	10227593	97	5145											
CELSR1	9620	hgsc.bcm.edu	37	chr22	46790151	46790151	+	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	accagcctctggggcacggaAggtcgagtctgtggggaaaa	10	6	16	9	2	2	0	0	0	2	0	3	3	2	2	2	6	1	1	2	6	3	0			TCGA-B1-5398-01A-02D-1589-08	TCGA-B1-5398-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de6c652a-86c7-4cc3-b7ad-db199a1c4c7a	b2dcd77d-e773-4e2b-9af9-173ffcc421d0	g.chr22:46790151A>T	ENST00000262738.3	-	14	5851	c.5852T>A	c.(5851-5853)cTt>cAt	p.L1951H		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1951	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				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)		GGGGCACGGAAGGTCGAGTCT	0.567																																					p.L1951H		Atlas-SNP	.											.	CELSR1	242	.	0			c.T5852A						PASS	.						40	39	39					22																	46790151		2203	4300	6503	SO:0001583	missense	9620	exon14			CACGGAAGGTCGA	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.5852T>A	chr22.hg19:g.46790151A>T	ENSP00000262738:p.Leu1951His	68.0	0.0	.		60.0	10.0	.	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	hg19	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	A	8.280	0.815341	0.16607	.	.	ENSG00000075275	ENST00000262738	D	0.92199	-2.99	3.47	3.47	0.39725	.	0.204155	0.30011	U	0.010631	D	0.92831	0.7720	L	0.40543	1.245	0.80722	D	1	D;B	0.76494	0.999;0.048	D;B	0.68765	0.96;0.025	D	0.92188	0.5757	10	0.48119	T	0.1	.	11.945	0.52924	1.0:0.0:0.0:0.0	.	272;1951	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	H	1951	ENSP00000262738:L1951H	ENSP00000262738:L1951H	L	-	2	0	CELSR1	45168815	0.967000	0.33354	0.996000	0.52242	0.436000	0.31835	2.258000	0.43249	1.360000	0.45960	0.379000	0.24179	CTT	.	.	.	none		0.567	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		T	46790151	A	T	46790151	3	4	79	1	0	0	0	0	1	0	0	0	3223	72	3	5	3280	5	CELSR1	22	46790151	Missense_Mutation	SNP	A	TCGA-B1-5398-01A-02D-1589-08	5713178	46790151	4514415	98	5146											
TMEM201	199953	hgsc.bcm.edu	37	chr1	9656944	9656944	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actacaacaagccgatccccGcccagtacttggagcacctg	11	6	8	16	2	0	0	0	0	0	0	1	2	1	1	5	1	5	2	5	1	4	3			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr1:9656944G>A	ENST00000340381.6	+	3	271	c.262G>A	c.(262-264)Gcc>Acc	p.A88T	TMEM201_ENST00000340305.5_Missense_Mutation_p.A88T|TMEM201_ENST00000377376.4_Missense_Mutation_p.A88T	NM_001130924.2	NP_001124396.2	Q5SNT2	TM201_HUMAN	transmembrane protein 201	88					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)		GCCGATCCCCGCCCAGTACTT	0.672																																					p.A88T		Atlas-SNP	.											TMEM201_ENST00000340381,NS,carcinoma,0,2	TMEM201	63	.	0			c.G262A						PASS	.						66	60	62					1																	9656944		2203	4300	6503	SO:0001583	missense	199953	exon3			ATCCCCGCCCAGT		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.262G>A	chr1.hg19:g.9656944G>A	ENSP00000344503:p.Ala88Thr	102.0	0.0	.		58.0	19.0	.	NM_001010866	B9EH90|Q5SNT3	Missense_Mutation	SNP	ENST00000340381.6	hg19	CCDS44055.2	.	.	.	.	.	.	.	.	.	.	G	36	5.608642	0.96626	.	.	ENSG00000188807	ENST00000377376;ENST00000340305;ENST00000340381	.	.	.	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.77572	0.4150	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;0.952	T	0.79090	-0.1946	9	0.59425	D	0.04	-25.3478	16.0587	0.80822	0.0:0.0:1.0:0.0	.	88;88	E9PBR6;Q5SNT2-2	.;.	T	88	.	ENSP00000344772:A88T	A	+	1	0	TMEM201	9579531	1.000000	0.71417	0.952000	0.39060	0.975000	0.68041	9.102000	0.94226	2.447000	0.82792	0.655000	0.94253	GCC	.	.	.	none		0.672	TMEM201-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127672.1	NM_001010866		A	9656944	G	A	9656944	3	1	80	1	0	0	0	0	1	0	0	0	16138	1087	38	1	272	1	TMEM201	1	9656944	Missense_Mutation	SNP	G	TCGA-B1-7332-01A-11D-2136-08		9656944	239593677	1	5147											
HNRNPCL1	343069	hgsc.bcm.edu	37	chr1	12907282	12907285	+	Frame_Shift_Del	DEL	GGTG	GGTG	-																															taagagtcatcctggccattGgtgctgtctctgtcatcctc																								rs139731855|rs149796618|rs148930640		TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	GGTG	GGTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr1:12907282_12907285delGGTG	ENST00000317869.6	-	2	1083_1086	c.858_861delCACC	c.(856-861)agcaccfs	p.ST286fs		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	286						nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.S286R(1)|p.T287A(1)|p.T287T(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|stomach(2)	29						CCTGGCCATTGGTGCTGTCTCTGT	0.436																																					p.287_288del		Pindel	.											.	HNRNPCL1	68	.	3	Substitution - Missense(2)|Substitution - coding silent(1)	stomach(2)|lung(1)	c.859_862del						PASS	.																																			SO:0001589	frameshift_variant	343069	exon2			.	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.858_861delCACC	chr1.hg19:g.12907282_12907285delGGTG	ENSP00000365370:p.Ser286fs	380.0	0.0	.		233.0	16.0	0.069	NM_001013631	B2RP44	Frame_Shift_Del	DEL	ENST00000317869.6	hg19	CCDS30591.1																																																																																			.	.	.	none		0.436	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631		-	12907285	GGTG	-	12907282	7	5	80	1	0	1	0	1	0	0	0	0	7270	1335	47	0	22	0	HNRNPCL1	1	12907282	Frame_Shift_Del	DEL	GGTG	TCGA-B1-7332-01A-11D-2136-08	3250338	12907282	236343339	2	5148											
ZBTB40	9923	hgsc.bcm.edu	37	chr1	22850847	22850847	+	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	ctctgtggggaactcttcacCtcccaggcccagcttgacag	7	9	10	15	0	3	1	1	1	2	0	4	2	4	2	3	3	2	1	3	3	1	2			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr1:22850847C>A	ENST00000375647.4	+	17	3642	c.3435C>A	c.(3433-3435)acC>acA	p.T1145T	ZBTB40_ENST00000404138.1_Silent_p.T1145T|ZBTB40_ENST00000374651.4_Silent_p.T1033T	NM_014870.3	NP_055685.3	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40	1145					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)		AACTCTTCACCTCCCAGGCCC	0.577																																					p.T1145T		Atlas-SNP	.											.	ZBTB40	87	.	0			c.C3435A						PASS	.						78	76	76					1																	22850847		2203	4300	6503	SO:0001819	synonymous_variant	9923	exon18			CTTCACCTCCCAG	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.3435C>A	chr1.hg19:g.22850847C>A		91.0	0.0	.		35.0	8.0	.	NM_001083621	O75066|Q5TFU5|Q8N1R1	Silent	SNP	ENST00000375647.4	hg19	CCDS224.1																																																																																			.	.	.	none		0.577	ZBTB40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008094.1	NM_014870		A	22850847	C	A	22850847	2	1	80	1	0	0	0	0	0	0	0	1	17554	668	24	4		4	ZBTB40	1	22850847	Silent	SNP	C	TCGA-B1-7332-01A-11D-2136-08	9943565	22850847	226399774	3	5149											
DLGAP3	58512	hgsc.bcm.edu	37	chr1	35365842	35365842	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atctccccatccttgccaccGgtggggtaacccccccagtc	6	8	8	19	1	1	0	0	0	1	0	4	0	2	0	8	3	2	1	8	3	1	2	rs149715442		TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr1:35365842G>A	ENST00000373347.1	-	4	1408	c.1140C>T	c.(1138-1140)acC>acT	p.T380T	DLGAP3_ENST00000235180.4_Silent_p.T380T			O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated protein 3	380					cell-cell signaling (GO:0007267)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)	p.T380T(1)		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)				CCTTGCCACCGGTGGGGTAAC	0.612																																					p.T380T		Atlas-SNP	.											DLGAP3,right_upper_lobe,carcinoma,0,2	DLGAP3	107	.	1	Substitution - coding silent(1)	lung(1)	c.C1140T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	85	86	86		1140	-0.6	1	1	dbSNP_134	86	0,8600		0,0,4300	no	coding-synonymous	DLGAP3	NM_001080418.1		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		380/980	35365842	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	58512	exon2			GCCACCGGTGGGG	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.1140C>T	chr1.hg19:g.35365842G>A		234.0	0.0	.		113.0	43.0	.	NM_001080418	Q5TDD5|Q9H3X7	Silent	SNP	ENST00000373347.1	hg19	CCDS30670.1																																																																																			.	G|1.000;A|0.000	0.000	weak		0.612	DLGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011554.1	NM_021234		A	35365842	G	A	35365842	2	1	80	1	0	0	0	0	0	0	0	1	4563	1103	39	1		1	DLGAP3	1	35365842	Silent	SNP	G	TCGA-B1-7332-01A-11D-2136-08	12514995	35365842	213884779	4	5150											
ROR1	4919	hgsc.bcm.edu	37	chr1	64603076	64603076	+	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	gagtatgaagaagatggattCtgtcagccatacagagggat	14	9	13	5	0	2	4	1	1	1	3	2	7	2	6	1	2	2	1	1	2	4	3			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr1:64603076C>A	ENST00000371079.1	+	5	882	c.507C>A	c.(505-507)ttC>ttA	p.F169L	ROR1_ENST00000545203.1_5'UTR|ROR1_ENST00000371080.1_Missense_Mutation_p.F169L|RP11-24J23.2_ENST00000424995.1_RNA|ROR1_ENST00000482426.1_3'UTR	NM_005012.3	NP_005003.2	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1	169	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				peptidyl-tyrosine phosphorylation (GO:0018108)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			breast(7)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(10)|ovary(6)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	51						AAGATGGATTCTGTCAGCCAT	0.443																																					p.F169L		Atlas-SNP	.											.	ROR1	113	.	0			c.C507A						PASS	.						162	158	159					1																	64603076		2203	4300	6503	SO:0001583	missense	4919	exon5			TGGATTCTGTCAG	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.507C>A	chr1.hg19:g.64603076C>A	ENSP00000360120:p.Phe169Leu	163.0	0.0	.		108.0	44.0	.	NM_001083592	Q5VVX6|Q66K77|Q92776	Missense_Mutation	SNP	ENST00000371079.1	hg19	CCDS626.1	.	.	.	.	.	.	.	.	.	.	C	18.56	3.651034	0.67472	.	.	ENSG00000185483	ENST00000371080;ENST00000371079;ENST00000544776	T;T	0.75154	0.01;-0.91	6.07	5.16	0.70880	Frizzled domain (1);	0.000000	0.44902	D	0.000404	T	0.59211	0.2177	L	0.59436	1.845	0.80722	D	1	B;B	0.33477	0.413;0.243	B;B	0.35114	0.196;0.068	T	0.67233	-0.5722	10	0.72032	D	0.01	.	9.7049	0.40209	0.0:0.8053:0.0:0.1947	.	169;169	Q01973;Q66K77	ROR1_HUMAN;.	L	169;169;172	ENSP00000360121:F169L;ENSP00000360120:F169L	ENSP00000360120:F169L	F	+	3	2	ROR1	64375664	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.658000	0.37376	1.571000	0.49722	0.655000	0.94253	TTC	.	.	.	none		0.443	ROR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025002.1	NM_005012		A	64603076	C	A	64603076	3	1	80	1	0	0	0	0	1	0	0	0	13539	912	32	4	525	4	ROR1	1	64603076	Missense_Mutation	SNP	C	TCGA-B1-7332-01A-11D-2136-08	29237234	64603076	184647545	5	5151											
ATP1B1	481	hgsc.bcm.edu	37	chr1	169096573	169096573	+	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	ttgctctggattaaatgatgAaacttatggctacaaagagg	14	12	10	5	0	1	3	0	2	1	1	1	4	1	4	0	3	3	2	0	3	6	4			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr1:169096573A>T	ENST00000367816.1	+	5	1023	c.494A>T	c.(493-495)gAa>gTa	p.E165V	ATP1B1_ENST00000499679.3_Missense_Mutation_p.E109V|ATP1B1_ENST00000367815.4_Missense_Mutation_p.E165V|ATP1B1_ENST00000367813.3_Missense_Mutation_p.E157V			P05026	AT1B1_HUMAN	ATPase, Na+/K+ transporting, beta 1 polypeptide	165					blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular potassium ion homeostasis (GO:0030007)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|leukocyte migration (GO:0050900)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|positive regulation of ATP catabolic process (GO:1903291)|positive regulation of ATPase activity (GO:0032781)|positive regulation of calcium:sodium antiporter activity (GO:1903281)|positive regulation of potassium ion import (GO:1903288)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of sodium ion export from cell (GO:1903278)|potassium ion import (GO:0010107)|protein localization to plasma membrane (GO:0072659)|protein stabilization (GO:0050821)|protein transport into plasma membrane raft (GO:0044861)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression (GO:0010468)|relaxation of cardiac muscle (GO:0055119)|response to hypoxia (GO:0001666)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|vesicle (GO:0031982)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|MHC class II protein complex binding (GO:0023026)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	14	all_hematologic(923;0.208)					TTAAATGATGAAACTTATGGC	0.393																																					p.E165V		Atlas-SNP	.											.	ATP1B1	29	.	0			c.A494T						PASS	.						104	101	102					1																	169096573		2203	4300	6503	SO:0001583	missense	481	exon4			ATGATGAAACTTA	U16799	CCDS1276.1	1q24.2	2012-10-22			ENSG00000143153	ENSG00000143153		"ATPases / P-type"	804	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit beta-1", "sodium pump subunit beta-1", "sodium-potassium ATPase subunit beta 1 (non-catalytic)"	182330		ATP1B			Standard	NM_001677		Approved		uc001gfr.1	P05026	OTTHUMG00000034590	ENST00000367816.1:c.494A>T	chr1.hg19:g.169096573A>T	ENSP00000356790:p.Glu165Val	110.0	0.0	.		60.0	25.0	.	NM_001677	Q5TGZ3	Missense_Mutation	SNP	ENST00000367816.1	hg19	CCDS1276.1	.	.	.	.	.	.	.	.	.	.	A	12.14	1.849985	0.32699	.	.	ENSG00000143153	ENST00000367816;ENST00000367815;ENST00000499679;ENST00000367813	T;T;T;T	0.32515	1.45;1.45;1.45;1.45	6.02	4.84	0.62591	.	0.673655	0.16466	N	0.213169	T	0.17450	0.0419	L	0.55481	1.735	0.25560	N	0.987001	B	0.11235	0.004	B	0.12156	0.007	T	0.06058	-1.0848	9	0.48119	T	0.1	-7.8189	12.903	0.58135	0.7578:0.2422:0.0:0.0	.	165	P05026	AT1B1_HUMAN	V	165;165;109;157	ENSP00000356790:E165V;ENSP00000356789:E165V;ENSP00000423450:E109V;ENSP00000356787:E157V	ENSP00000356787:E157V	E	+	2	0	ATP1B1	167363197	0.003000	0.15002	0.866000	0.34008	0.333000	0.28666	1.278000	0.33179	2.311000	0.77944	0.533000	0.62120	GAA	.	.	.	none		0.393	ATP1B1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083696.1			T	169096573	A	T	169096573	3	4	80	1	0	0	0	0	1	0	0	0	1132	246	9	5	508	5	ATP1B1	1	169096573	Missense_Mutation	SNP	A	TCGA-B1-7332-01A-11D-2136-08	104493497	169096573	80154048	6	5152											
NMNAT2	23057	hgsc.bcm.edu	37	chr1	183253891	183253891	+	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	gggcggacacagcagatccgGctgaggctttctcccacctt	7	8	12	14	2	1	2	0	1	1	1	3	3	2	3	3	4	1	3	3	4	0	2			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr1:183253891G>C	ENST00000287713.6	-	6	817	c.483C>G	c.(481-483)agC>agG	p.S161R	NMNAT2_ENST00000473046.1_5'UTR|NMNAT2_ENST00000294868.4_Missense_Mutation_p.S156R	NM_015039.3	NP_055854.1	Q9BZQ4	NMNA2_HUMAN	nicotinamide nucleotide adenylyltransferase 2	161					NAD biosynthetic process (GO:0009435)|NAD metabolic process (GO:0019674)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|late endosome (GO:0005770)|synapse (GO:0045202)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|nicotinamide-nucleotide adenylyltransferase activity (GO:0000309)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(7)|skin(2)	18						AGCAGATCCGGCTGAGGCTTT	0.542																																					p.S161R		Atlas-SNP	.											.	NMNAT2	48	.	0			c.C483G						PASS	.						58	59	59					1																	183253891		2203	4300	6503	SO:0001583	missense	23057	exon6			GATCCGGCTGAGG	AF288395	CCDS1353.1, CCDS1354.1	1q25	2008-02-05	2003-04-30	2003-05-02	ENSG00000157064	ENSG00000157064			16789	protein-coding gene	gene with protein product		608701	"chromosome 1 open reading frame 15"	C1orf15		11318611, 12359228	Standard	NM_015039		Approved	KIAA0479, PNAT2	uc001gqc.2	Q9BZQ4	OTTHUMG00000035519	ENST00000287713.6:c.483C>G	chr1.hg19:g.183253891G>C	ENSP00000287713:p.Ser161Arg	145.0	0.0	.		58.0	16.0	.	NM_015039	O75067|Q5T1Q3|Q8WU99|Q96QW1	Missense_Mutation	SNP	ENST00000287713.6	hg19	CCDS1353.1	.	.	.	.	.	.	.	.	.	.	.	15.18	2.757497	0.49468	.	.	ENSG00000157064	ENST00000287713;ENST00000294868	D;D	0.97430	-4.38;-4.24	5.32	5.32	0.75619	Cytidylyltransferase (1);	0.248777	0.46758	D	0.000270	D	0.94945	0.8365	N	0.08118	0	0.44254	D	0.997101	D;P;B	0.62365	0.991;0.918;0.226	D;P;B	0.64877	0.93;0.604;0.246	D	0.92751	0.6216	10	0.16420	T	0.52	-14.3221	13.3395	0.60537	0.0777:0.0:0.9223:0.0	.	161;161;156	A8K5S5;Q9BZQ4;Q9BZQ4-2	.;NMNA2_HUMAN;.	R	161;156	ENSP00000287713:S161R;ENSP00000294868:S156R	ENSP00000287713:S161R	S	-	3	2	NMNAT2	181520514	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.939000	0.28978	2.498000	0.84270	0.561000	0.74099	AGC	.	.	.	none		0.542	NMNAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086255.1			C	183253891	G	C	183253891	3	2	80	1	0	0	0	0	1	0	0	0	10506	1194	42	4	464	4	NMNAT2	1	183253891	Missense_Mutation	SNP	G	TCGA-B1-7332-01A-11D-2136-08	14157318	183253891	65996730	7	5153											
C1orf107	27042	hgsc.bcm.edu	37	chr1	210006621	210006621	+	Frame_Shift_Del	DEL	A	A	-																															cccgaagagttcacagatgcAaaacacgagtcactgttcag																										TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr1:210006621delA	ENST00000491415.2	+	4	537	c.480delA	c.(478-480)gcafs	p.A160fs		NM_014388.6	NP_055203.4	Q68CQ4	DIEXF_HUMAN	digestive organ expansion factor homolog (zebrafish)	160	Glu-rich.				multicellular organismal development (GO:0007275)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(15)|large_intestine(7)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(2)	53						TCACAGATGCAAAACACGAGT	0.478																																					p.A160fs		Atlas-Indel,Pindel	.											.	DIEXF	97	.	0			c.479delC						PASS	.						113	103	107					1																	210006621		2203	4300	6503	SO:0001589	frameshift_variant	27042	exon4			.	BC022964	CCDS1493.1	1q32.2	2011-08-12	2011-02-16	2011-02-16	ENSG00000117597	ENSG00000117597			28440	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 107"	C1orf107		16322560	Standard	NM_014388		Approved	MGC29875, DEF, UTP25	uc001hhr.2	Q68CQ4	OTTHUMG00000036654	ENST00000491415.2:c.480delA	chr1.hg19:g.210006621delA	ENSP00000419005:p.Ala160fs	104.0	0.0	0		81.0	31.0	0.382716	NM_014388	O75992|Q4VY00|Q63HL9	Frame_Shift_Del	DEL	ENST00000491415.2	hg19	CCDS1493.1																																																																																			.	.	.	none		0.478	DIEXF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089127.2	NM_014388		-	210006621	A	-	210006621	7	5	80	1	0	1	0	1	0	0	0	0	1983	117	5	0	494	0	C1orf107	1	210006621	Frame_Shift_Del	DEL	A	TCGA-B1-7332-01A-11D-2136-08	26752730	210006621	39244000	8	5154											
USH2A	7399	hgsc.bcm.edu	37	chr1	215953196	215953196	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttctcacctgtgaccgtaTgctgtctcctgtcagtggtg	4	16	10	11	1	3	1	2	1	2	0	5	1	3	1	3	1	1	2	3	1	1	3			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr1:215953196T>C	ENST00000307340.3	-	55	11314	c.10928A>G	c.(10927-10929)cAt>cGt	p.H3643R	USH2A_ENST00000366943.2_Missense_Mutation_p.H3643R	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3643	Fibronectin type-III 21. {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)		TGTGACCGTATGCTGTCTCCT	0.483										HNSCC(13;0.011)																											p.H3643R		Atlas-SNP	.											.	USH2A	1168	.	0			c.A10928G						PASS	.						156	130	139					1																	215953196		2203	4300	6503	SO:0001583	missense	7399	exon55			ACCGTATGCTGTC	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.10928A>G	chr1.hg19:g.215953196T>C	ENSP00000305941:p.His3643Arg	76.0	0.0	.		54.0	25.0	.	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	T	19.34	3.808890	0.70797	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.57273	0.41;0.41	5.9	5.9	0.94986	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.46442	D	0.000296	T	0.71273	0.3320	M	0.73598	2.24	0.40934	D	0.984414	D	0.76494	0.999	D	0.68483	0.958	T	0.71547	-0.4560	10	0.35671	T	0.21	.	16.3217	0.82953	0.0:0.0:0.0:1.0	.	3643	O75445	USH2A_HUMAN	R	3643	ENSP00000305941:H3643R;ENSP00000355910:H3643R	ENSP00000305941:H3643R	H	-	2	0	USH2A	214019819	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.390000	0.73204	2.251000	0.74343	0.528000	0.53228	CAT	.	.	.	none		0.483	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		C	215953196	T	C	215953196	3	2	80	1	0	0	0	0	1	0	0	0	17048	1464	51	3	4752	3	USH2A	1	215953196	Missense_Mutation	SNP	T	TCGA-B1-7332-01A-11D-2136-08	5946575	215953196	33297425	9	5155											
IARS2	55699	hgsc.bcm.edu	37	chr1	220267643	220267643	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggggacgccccgccttcccTgcagcccgggatggcaaggg	5	4	17	15	3	0	0	0	0	0	0	1	2	1	2	5	5	2	2	5	5	1	1			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr1:220267643T>C	ENST00000302637.5	+	1	189	c.85T>C	c.(85-87)Tgc>Cgc	p.C29R	IARS2_ENST00000366922.1_5'UTR	NM_018060.3	NP_060530.3	Q9NSE4	SYIM_HUMAN	isoleucyl-tRNA synthetase 2, mitochondrial	29					gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)			NS(1)|breast(1)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(7)|lung(17)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)	CCGCCTTCCCTGCAGCCCGGG	0.711																																					p.C29R		Atlas-SNP	.											.	IARS2	106	.	0			c.T85C						PASS	.						13	18	16					1																	220267643		2185	4287	6472	SO:0001583	missense	55699	exon1			CTTCCCTGCAGCC	AK022665	CCDS1523.1	1q41	2011-07-01	2007-02-26		ENSG00000067704	ENSG00000067704	6.1.1.5	"Aminoacyl tRNA synthetases / Class I"	29685	protein-coding gene	gene with protein product	"isoleucine tRNA ligase 2, mitochondrial"	612801					Standard	NM_018060		Approved	FLJ10326	uc001hmc.3	Q9NSE4	OTTHUMG00000037287	ENST00000302637.5:c.85T>C	chr1.hg19:g.220267643T>C	ENSP00000303279:p.Cys29Arg	37.0	0.0	.		12.0	7.0	.	NM_018060	B2RPG8|Q1M2P9|Q6PI85|Q7L439|Q86WU9|Q96D91|Q9H9Q8|Q9NW42	Missense_Mutation	SNP	ENST00000302637.5	hg19	CCDS1523.1	.	.	.	.	.	.	.	.	.	.	T	8.040	0.763710	0.15914	.	.	ENSG00000067704	ENST00000302637	T	0.16457	2.34	4.13	-6.24	0.02046	.	0.684586	0.13548	N	0.379704	T	0.11239	0.0274	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11372	-1.0590	10	0.35671	T	0.21	-6.2347	11.9767	0.53096	0.1113:0.6427:0.0:0.246	.	29	Q9NSE4	SYIM_HUMAN	R	29	ENSP00000303279:C29R	ENSP00000303279:C29R	C	+	1	0	IARS2	218334266	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.122000	0.03267	-1.621000	0.01562	-0.353000	0.07706	TGC	.	.	.	none		0.711	IARS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018060		C	220267643	T	C	220267643	3	2	80	1	0	0	0	0	1	0	0	0	7481	1580	55	3	87	3	IARS2	1	220267643	Missense_Mutation	SNP	T	TCGA-B1-7332-01A-11D-2136-08	4314447	220267643	28982978	10	5156											
LRP2	4036	hgsc.bcm.edu	37	chr2	170058174	170058174	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagtgttattatcatggcAgttgtctacaccattgcaga	11	14	9	7	0	2	2	1	1	1	1	2	2	2	2	1	1	2	4	1	1	4	5			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr2:170058174A>G	ENST00000263816.3	-	44	8701	c.8416T>C	c.(8416-8418)Tgc>Cgc	p.C2806R		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2806	LDL-receptor class A 18. {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)"	TTATCATGGCAGTTGTCTACA	0.428																																					p.C2806R		Atlas-SNP	.											.	LRP2	751	.	0			c.T8416C						PASS	.						145	134	138					2																	170058174		2203	4300	6503	SO:0001583	missense	4036	exon44			CATGGCAGTTGTC		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.8416T>C	chr2.hg19:g.170058174A>G	ENSP00000263816:p.Cys2806Arg	73.0	0.0	.		104.0	19.0	.	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	hg19	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.386704	0.82902	.	.	ENSG00000081479	ENST00000263816	D	0.99919	-8.0	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	D	0.99953	0.9980	H	0.98738	4.315	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96044	0.9026	10	0.87932	D	0	.	16.3678	0.83341	1.0:0.0:0.0:0.0	.	2806	P98164	LRP2_HUMAN	R	2806	ENSP00000263816:C2806R	ENSP00000263816:C2806R	C	-	1	0	LRP2	169766420	1.000000	0.71417	1.000000	0.80357	0.802000	0.45316	9.195000	0.94971	2.254000	0.74563	0.528000	0.53228	TGC	.	.	.	none		0.428	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		G	170058174	A	G	170058174	3	3	80	1	0	0	0	0	1	0	0	0	8963	188	7	3	5695	3	LRP2	2	170058174	Missense_Mutation	SNP	A	TCGA-B1-7332-01A-11D-2136-08		170058174	73141199	11	5157											
SLC25A12	8604	hgsc.bcm.edu	37	chr2	172691265	172691266	+	Frame_Shift_Del	DEL	GC	GC	-																															acttcaacatctttccttgtGccagctagagtgctatatat																										TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr2:172691265_172691266delGC	ENST00000422440.2	-	7	759_760	c.722_723delGC	c.(721-723)ggcfs	p.G241fs	SLC25A12_ENST00000392592.4_Frame_Shift_Del_p.G134fs	NM_003705.4	NP_003696.2	O75746	CMC1_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 12	241					aspartate transport (GO:0015810)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|upper_aerodigestive_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)	CTTTCCTTGTGCCAGCTAGAGT	0.361																																					p.241_242del		Atlas-Indel,Pindel	.											.	SLC25A12	59	.	0			c.723_724del						PASS	.																																			SO:0001589	frameshift_variant	8604	exon7			.	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.722_723delGC	chr2.hg19:g.172691265_172691266delGC	ENSP00000388658:p.Gly241fs	87.0	0.0	0		134.0	16.0	0.119403	NM_003705	B3KR64|Q96AM8	Frame_Shift_Del	DEL	ENST00000422440.2	hg19	CCDS33327.1																																																																																			.	.	.	none		0.361	SLC25A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259010.2	NM_003705		-	172691266	GC	-	172691265	7	5	80	1	0	1	0	1	0	0	0	0	14487	1306	46	0	1361	0	SLC25A12	2	172691265	Frame_Shift_Del	DEL	GC	TCGA-B1-7332-01A-11D-2136-08	2633091	172691265	70508108	12	5158											
FZD7	8324	hgsc.bcm.edu	37	chr2	202900338	202900338	+	Missense_Mutation	SNP	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	ggagcgcttctcggacgatgGctaccgcacggtggcgcagg	6	6	17	12	6	1	0	0	0	1	0	2	3	1	2	1	6	2	4	1	6	1	2			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr2:202900338G>A	ENST00000286201.1	+	1	1029	c.968G>A	c.(967-969)gGc>gAc	p.G323D	RP11-107N15.1_ENST00000608741.1_lincRNA	NM_003507.1	NP_003498.1	O75084	FZD7_HUMAN	frizzled class receptor 7	323					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						TCGGACGATGGCTACCGCACG	0.627											OREG0015146	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G323D		Atlas-SNP	.											.	FZD7	70	.	0			c.G968A						PASS	.						66	65	65					2																	202900338		2203	4300	6503	SO:0001583	missense	8324	exon1			ACGATGGCTACCG	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.968G>A	chr2.hg19:g.202900338G>A	ENSP00000286201:p.Gly323Asp	110.0	0.0	.	2133	120.0	23.0	.	NM_003507	O94816|Q53S59|Q96B74	Missense_Mutation	SNP	ENST00000286201.1	hg19	CCDS2351.1	.	.	.	.	.	.	.	.	.	.	G	14.56	2.572271	0.45798	.	.	ENSG00000155760	ENST00000286201	D	0.81739	-1.53	5.54	5.54	0.83059	GPCR, family 2-like (1);	0.178643	0.48286	D	0.000181	D	0.83344	0.5234	M	0.85462	2.755	0.53688	D	0.999975	B	0.12013	0.005	B	0.18561	0.022	T	0.79317	-0.1853	10	0.24483	T	0.36	.	19.4882	0.95039	0.0:0.0:1.0:0.0	.	323	O75084	FZD7_HUMAN	D	323	ENSP00000286201:G323D	ENSP00000286201:G323D	G	+	2	0	FZD7	202608583	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.698000	0.54771	2.618000	0.88619	0.563000	0.77884	GGC	.	.	.	none		0.627	FZD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256314.1	NM_003507		A	202900338	G	A	202900338	3	1	80	1	0	0	0	0	1	0	0	0	6142	1203	42	2	970	2	FZD7	2	202900338	Missense_Mutation	SNP	G	TCGA-B1-7332-01A-11D-2136-08	30209073	202900338	40299035	13	5159											
UGT1A9	54600	hgsc.bcm.edu	37	chr2	234580593	234580593	+	Frame_Shift_Del	DEL	G	G	-																															gttctctgatggcttgcacaGggtggaccagcccccttcct																										TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr2:234580593delG	ENST00000354728.4	+	1	95	c.13delG	c.(13-15)gggfs	p.G5fs	UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000609637.1_Frame_Shift_Del_p.G5fs			O60656	UD19_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A9	5					cellular glucuronidation (GO:0052695)|cellular lipid metabolic process (GO:0044255)|drug metabolic process (GO:0017144)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|metabolic process (GO:0008152)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|small molecule metabolic process (GO:0044281)|xenobiotic glucuronidation (GO:0052697)|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)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)			breast(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	37		Breast(86;0.000766)|all_lung(227;0.00269)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0331)|Lung NSC(271;0.0459)|Lung SC(224;0.128)		Epithelial(121;1.26e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000436)|Lung(119;0.00347)|LUSC - Lung squamous cell carcinoma(224;0.00757)	Acetaminophen(DB00316)|Buprenorphine(DB00921)|Canagliflozin(DB08907)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Entacapone(DB00494)|Etodolac(DB00749)|Ezogabine(DB04953)|Flurbiprofen(DB00712)|Haloperidol(DB00502)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ketobemidone(DB06738)|Lumiracoxib(DB01283)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Nateglinide(DB00731)|Niflumic Acid(DB04552)|Oxazepam(DB00842)|Propofol(DB00818)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sulfamethoxazole(DB01015)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zileuton(DB00744)	GGCTTGCACAGGGTGGACCAG	0.557																																					p.T4fs		Atlas-Indel,Pindel	.											.	UGT1A9	79	.	0			c.12delA						PASS	.						66	61	63					2																	234580593		2203	4300	6503	SO:0001589	frameshift_variant	54600	exon1			.	AF056188	CCDS2505.1	2q37	2010-03-05	2005-07-20		ENSG00000241119	ENSG00000241119		"UDP glucuronosyltransferases"	12541	other	complex locus constituent		606434	"UDP glycosyltransferase 1 family, polypeptide A9"			9295054, 1910331	Standard	NM_021027		Approved	HLUGP4, LUGP4, UGT1AI		O60656	OTTHUMG00000059124	ENST00000354728.4:c.13delG	chr2.hg19:g.234580593delG	ENSP00000346768:p.Gly5fs	67.0	0.0	0		71.0	18.0	0.253521	NM_021027	B8K285|P36509|Q9HAX0	Frame_Shift_Del	DEL	ENST00000354728.4	hg19	CCDS2505.1																																																																																			.	.	.	none		0.557	UGT1A9-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130995.1	NM_021027		-	234580593	G	-	234580593	7	5	80	1	0	1	0	1	0	0	0	0	16964	1000	35	0	15	0	UGT1A9	2	234580593	Frame_Shift_Del	DEL	G	TCGA-B1-7332-01A-11D-2136-08	31680255	234580593	8618780	14	5160											
COL6A3	1293	hgsc.bcm.edu	37	chr2	238289848	238289848	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agccggctgaactcgtgaatAggttgttacgaacaaagtct	12	10	11	8	3	1	2	0	2	1	0	2	3	1	2	1	2	4	3	1	2	6	3			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr2:238289848A>G	ENST00000295550.4	-	5	2059	c.1607T>C	c.(1606-1608)cTa>cCa	p.L536P	COL6A3_ENST00000353578.4_Missense_Mutation_p.L330P|COL6A3_ENST00000346358.4_Missense_Mutation_p.L536P|COL6A3_ENST00000392004.3_Missense_Mutation_p.L330P|COL6A3_ENST00000392003.2_Missense_Mutation_p.L129P|COL6A3_ENST00000409809.1_Missense_Mutation_p.L330P|COL6A3_ENST00000472056.1_Missense_Mutation_p.L129P|COL6A3_ENST00000347401.3_Missense_Mutation_p.L335P	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	536	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			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)		ACTCGTGAATAGGTTGTTACG	0.547																																					p.L536P		Atlas-SNP	.											.	COL6A3	608	.	0			c.T1607C						PASS	.						73	83	80					2																	238289848		2203	4300	6503	SO:0001583	missense	1293	exon5			GTGAATAGGTTGT	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.1607T>C	chr2.hg19:g.238289848A>G	ENSP00000295550:p.Leu536Pro	203.0	0.0	.		191.0	30.0	.	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	A	13.45	2.239904	0.39598	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358;ENST00000392004;ENST00000392003;ENST00000433762	D;D;D;D;D;D;D;D;D	0.87334	-2.24;-2.24;-2.24;-2.24;-2.24;-2.24;-2.24;-2.24;-2.24	5.6	5.6	0.85130	von Willebrand factor, type A (3);	0.138230	0.32161	N	0.006489	D	0.92848	0.7725	M	0.75150	2.29	0.43907	D	0.996547	D;D;P;P;D;D	0.69078	0.989;0.997;0.953;0.953;0.993;0.989	P;D;P;P;D;P	0.70227	0.883;0.968;0.905;0.898;0.935;0.883	D	0.93510	0.6852	10	0.66056	D	0.02	.	15.7932	0.78384	1.0:0.0:0.0:0.0	.	536;129;129;330;330;536	E9PCV6;E9PFQ6;A8MT30;E9PGQ9;P12111-2;P12111	.;.;.;.;.;CO6A3_HUMAN	P	536;335;330;129;330;536;330;129;536	ENSP00000295550:L536P;ENSP00000315609:L335P;ENSP00000315873:L330P;ENSP00000418285:L129P;ENSP00000386844:L330P;ENSP00000295546:L536P;ENSP00000375861:L330P;ENSP00000375860:L129P;ENSP00000389539:L536P	ENSP00000295550:L536P	L	-	2	0	COL6A3	237954587	1.000000	0.71417	0.996000	0.52242	0.015000	0.08874	5.769000	0.68865	2.124000	0.65301	0.533000	0.62120	CTA	.	.	.	none		0.547	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		G	238289848	A	G	238289848	3	3	80	1	0	0	0	0	1	0	0	0	3703	420	15	3	8133	3	COL6A3	2	238289848	Missense_Mutation	SNP	A	TCGA-B1-7332-01A-11D-2136-08	3709255	238289848	4909525	15	5161											
ZDHHC3	51304	hgsc.bcm.edu	37	chr3	44986685	44986687	+	In_Frame_Del	DEL	TGA	TGA	-																															gtggtgggctcggtcgggctTgatgctgcagcatttggggc																										TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr3:44986685_44986687delTGA	ENST00000424952.2	-	3	672_674	c.404_406delTCA	c.(403-408)atcaag>aag	p.I135del	ZDHHC3_ENST00000296127.3_In_Frame_Del_p.I135del|ZDHHC3_ENST00000342790.4_In_Frame_Del_p.I169del	NM_001135179.1	NP_001128651.1	Q9NYG2	ZDHC3_HUMAN	zinc finger, DHHC-type containing 3	135					protein palmitoylation (GO:0018345)|protein targeting (GO:0006605)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(193;0.00943)|KIRC - Kidney renal clear cell carcinoma(197;0.053)|Kidney(197;0.0665)		CGGTCGGGCTTGATGCTGCAGCA	0.591																																					p.135_136del		Atlas-Indel,Pindel	.											.	ZDHHC3	25	.	0			c.405_407del						PASS	.																																			SO:0001651	inframe_deletion	51304	exon3			.	AF247703	CCDS2724.1, CCDS46811.1	3p21.31	2010-02-09			ENSG00000163812	ENSG00000163812		"Zinc fingers, DHHC-type"	18470	protein-coding gene	gene with protein product	"golgi-specific DHHC Zinc Finger Protein"					19955568	Standard	NM_016598		Approved	ZNF373, GODZ	uc003cod.3	Q9NYG2	OTTHUMG00000133093	ENST00000424952.2:c.404_406delTCA	chr3.hg19:g.44986685_44986687delTGA	ENSP00000395502:p.Ile135del	133.0	0.0	0		154.0	28.0	0.181818	NM_001135179	Q53A17|Q96BL0	In_Frame_Del	DEL	ENST00000424952.2	hg19	CCDS46811.1																																																																																			.	.	.	none		0.591	ZDHHC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347004.1	NM_016598		-	44986687	TGA	-	44986685	7	5	80	1	0	1	0	1	0	0	0	0	17628	1821	63	0	854	0	ZDHHC3	3	44986685	In_Frame_Del	DEL	TGA	TCGA-B1-7332-01A-11D-2136-08		44986685	153035745	16	5162											
DAG1	1605	hgsc.bcm.edu	37	chr3	49568799	49568799	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccctgccagggagggcgcAatgtctgctcagcttggcta	6	8	14	13	1	2	0	1	0	1	0	2	1	2	1	3	3	3	4	3	3	2	2			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr3:49568799A>G	ENST00000539901.1	+	3	1413	c.855A>G	c.(853-855)gcA>gcG	p.A285A	DAG1_ENST00000308775.2_Silent_p.A285A|DAG1_ENST00000545947.1_Silent_p.A285A|DAG1_ENST00000538711.1_Silent_p.A285A|DAG1_ENST00000515359.2_Silent_p.A285A|DAG1_ENST00000541308.1_Silent_p.A285A	NM_001177644.2	NP_001171115	Q14118	DAG1_HUMAN	dystroglycan 1 (dystrophin-associated glycoprotein 1)	285	Required for laminin recognition.				basement membrane organization (GO:0071711)|branching involved in salivary gland morphogenesis (GO:0060445)|calcium-dependent cell-matrix adhesion (GO:0016340)|commissural neuron axon guidance (GO:0071679)|cytoskeletal anchoring at plasma membrane (GO:0007016)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|microtubule anchoring (GO:0034453)|modulation by virus of host morphology or physiology (GO:0019048)|morphogenesis of an epithelial sheet (GO:0002011)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell migration (GO:0030336)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase B signaling (GO:0051898)|nerve maturation (GO:0021682)|NLS-bearing protein import into nucleus (GO:0006607)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell outer membrane (GO:0009279)|cell-cell adherens junction (GO:0005913)|contractile ring (GO:0070938)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystroglycan complex (GO:0016011)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|node of Ranvier (GO:0033268)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|alpha-actinin binding (GO:0051393)|calcium ion binding (GO:0005509)|laminin-1 binding (GO:0043237)|SH2 domain binding (GO:0042169)|structural constituent of muscle (GO:0008307)|tubulin binding (GO:0015631)|vinculin binding (GO:0017166)|virus receptor activity (GO:0001618)			NS(1)|autonomic_ganglia(2)|breast(2)|endometrium(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	23				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.00241)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		GGGAGGGCGCAATGTCTGCTC	0.597																																					p.A285A		Atlas-SNP	.											.	DAG1	60	.	0			c.A855G						PASS	.						82	77	79					3																	49568799		2203	4300	6503	SO:0001819	synonymous_variant	1605	exon4			GGGCGCAATGTCT	L19711	CCDS2799.1	3p21	2014-09-17			ENSG00000173402	ENSG00000173402			2666	protein-coding gene	gene with protein product	"alpha-dystroglycan", "dystrophin-associated glycoprotein-1", "beta-dystroglycan"	128239				7774920, 1741056	Standard	NM_001177643		Approved	A3a, 156DAG, AGRNR, DAG	uc021wyd.1	Q14118	OTTHUMG00000156869	ENST00000539901.1:c.855A>G	chr3.hg19:g.49568799A>G		113.0	0.0	.		104.0	44.0	.	NM_001177642	A8K6M7|Q969J9	Silent	SNP	ENST00000539901.1	hg19	CCDS2799.1																																																																																			.	.	.	none		0.597	DAG1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346326.1			G	49568799	A	G	49568799	2	3	80	1	0	0	0	0	0	0	0	1	4227	117	5	3		3	DAG1	3	49568799	Silent	SNP	A	TCGA-B1-7332-01A-11D-2136-08	4582114	49568799	148453631	17	5163											
DHX15	1665	hgsc.bcm.edu	37	chr4	24543620	24543620	+	Frame_Shift_Del	DEL	T	T	-																															tagctgtcaccaaaagggacTcaactctgattcgaggattg																										TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr4:24543620delT	ENST00000336812.4	-	8	1517	c.1361delA	c.(1360-1362)gagfs	p.E454fs	DHX15_ENST00000508032.1_5'Flank	NM_001358.2	NP_001349.2	O43143	DHX15_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 15	454	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)				CAAAAGGGACTCAACTCTGAT	0.423																																					p.E454fs		Atlas-Indel,Pindel	.											.	DHX15	69	.	0			c.1362delG						PASS	.						91	90	91					4																	24543620		2203	4300	6503	SO:0001589	frameshift_variant	1665	exon8			.	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.1361delA	chr4.hg19:g.24543620delT	ENSP00000336741:p.Glu454fs	53.0	0.0	0		56.0	17.0	0.303571	NM_001358	Q9NQT7	Frame_Shift_Del	DEL	ENST00000336812.4	hg19	CCDS33966.1																																																																																			.	.	.	none		0.423	DHX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360143.1	NM_001358		-	24543620	T	-	24543620	7	5	80	1	0	1	0	1	0	0	0	0	4503	1551	54	0	1054	0	DHX15	4	24543620	Frame_Shift_Del	DEL	T	TCGA-B1-7332-01A-11D-2136-08		24543620	166610656	18	5164											
C4orf51	646603	hgsc.bcm.edu	37	chr4	146653660	146653660	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctcatctgaggattcagaagCtgatcgatactccgattatg	11	12	9	9	2	3	3	2	2	1	1	5	6	4	4	1	1	2	1	1	1	3	3			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr4:146653660C>T	ENST00000438731.1	+	6	557	c.557C>T	c.(556-558)gCt>gTt	p.A186V	C4orf51_ENST00000508981.1_3'UTR	NM_001080531.1	NP_001074000.1	C9J302	CD051_HUMAN	chromosome 4 open reading frame 51	186										haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)	6						GATTCAGAAGCTGATCGATAC	0.488																																					p.A186V		Atlas-SNP	.											.	C4orf51	18	.	0			c.C557T						PASS	.						66	67	67					4																	146653660		1941	4147	6088	SO:0001583	missense	646603	exon6			CAGAAGCTGATCG		CCDS47140.1	4q31.21	2009-09-09			ENSG00000237136	ENSG00000237136			37264	protein-coding gene	gene with protein product							Standard	NM_001080531		Approved		uc003ikk.3	C9J302	OTTHUMG00000161367	ENST00000438731.1:c.557C>T	chr4.hg19:g.146653660C>T	ENSP00000391404:p.Ala186Val	39.0	0.0	.		19.0	9.0	.	NM_001080531		Missense_Mutation	SNP	ENST00000438731.1	hg19	CCDS47140.1	.	.	.	.	.	.	.	.	.	.	C	12.12	1.842007	0.32513	.	.	ENSG00000237136	ENST00000438731	.	.	.	3.65	-2.95	0.05564	.	.	.	.	.	T	0.15565	0.0375	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.16867	-1.0388	8	0.45353	T	0.12	.	4.9044	0.13791	0.0:0.3232:0.3035:0.3734	.	186	C9J302	CD051_HUMAN	V	186	.	ENSP00000391404:A186V	A	+	2	0	C4orf51	146873110	0.000000	0.05858	0.000000	0.03702	0.180000	0.23129	-0.547000	0.06055	-0.767000	0.04633	-0.391000	0.06502	GCT	.	.	.	none		0.488	C4orf51-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080531		T	146653660	C	T	146653660	3	4	80	1	0	0	0	0	1	0	0	0	2279	797	28	2	579	2	C4orf51	4	146653660	Missense_Mutation	SNP	C	TCGA-B1-7332-01A-11D-2136-08	122110040	146653660	44500616	19	5165											
POU4F2	5458	hgsc.bcm.edu	37	chr4	147561825	147561825	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgctcgaagcctactttgcCattcagcctcggccctcctc	5	11	7	18	3	1	0	1	0	0	0	6	1	2	0	5	1	4	1	5	1	2	3			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr4:147561825C>T	ENST00000281321.3	+	2	1343	c.1095C>T	c.(1093-1095)gcC>gcT	p.A365A	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	365					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)					CCTACTTTGCCATTCAGCCTC	0.587																																					p.A365A		Atlas-SNP	.											.	POU4F2	83	.	0			c.C1095T						PASS	.						65	70	68					4																	147561825		2203	4300	6503	SO:0001819	synonymous_variant	5458	exon2			CTTTGCCATTCAG	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.1095C>T	chr4.hg19:g.147561825C>T		181.0	0.0	.		89.0	30.0	.	NM_004575	B1PJR6|B2RC84|Q13883|Q14987	Silent	SNP	ENST00000281321.3	hg19	CCDS34074.1																																																																																			.	.	.	none		0.587	POU4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367020.1	NM_004575		T	147561825	C	T	147561825	2	4	80	1	0	0	0	0	0	0	0	1	12286	581	21	2		2	POU4F2	4	147561825	Silent	SNP	C	TCGA-B1-7332-01A-11D-2136-08	908165	147561825	43592451	20	5166											
RNASEN	29102	hgsc.bcm.edu	37	chr5	31409241	31409241	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaagctgggatttggggtcaTtccaatcctgattcaaaatg	11	12	11	7	0	2	1	2	1	0	0	4	3	4	2	2	3	1	1	2	3	4	3			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr5:31409241T>C	ENST00000511367.2	-	32	4020	c.3776A>G	c.(3775-3777)aAt>aGt	p.N1259S	DROSHA_ENST00000513349.1_Missense_Mutation_p.N1222S|DROSHA_ENST00000442743.1_Missense_Mutation_p.N1222S|DROSHA_ENST00000344624.3_Missense_Mutation_p.N1259S	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	1259	Necessary for interaction with DGCR8 and pri-miRNA processing activity.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|gene expression (GO:0010467)|miRNA metabolic process (GO:0010586)|pre-miRNA processing (GO:0031054)|primary miRNA processing (GO:0031053)|ribosome biogenesis (GO:0042254)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA catabolic process (GO:0016075)	nucleoplasm (GO:0005654)	lipopolysaccharide binding (GO:0001530)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)			breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66						TTTGGGGTCATTCCAATCCTG	0.433																																					p.N1259S		Atlas-SNP	.											.	DROSHA	130	.	0			c.A3776G						PASS	.						70	66	67					5																	31409241		1857	4109	5966	SO:0001583	missense	29102	exon32			GGGTCATTCCAAT	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.3776A>G	chr5.hg19:g.31409241T>C	ENSP00000425979:p.Asn1259Ser	37.0	0.0	.		36.0	22.0	.	NM_013235	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Missense_Mutation	SNP	ENST00000511367.2	hg19	CCDS47195.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.527326	0.85706	.	.	ENSG00000113360	ENST00000511367;ENST00000344624;ENST00000442743;ENST00000513349;ENST00000265075	T;T;T;T	0.40756	1.02;1.02;1.02;1.02	5.34	5.34	0.76211	Ribonuclease III (2);	0.000000	0.85682	D	0.000000	T	0.58750	0.2144	M	0.67953	2.075	0.80722	D	1	D;P	0.62365	0.991;0.683	P;B	0.58331	0.837;0.18	T	0.63453	-0.6634	10	0.72032	D	0.01	-23.6224	15.3311	0.74212	0.0:0.0:0.0:1.0	.	1222;1259	E7EMP9;Q9NRR4	.;RNC_HUMAN	S	1259;1259;1222;1222;1184	ENSP00000425979:N1259S;ENSP00000339845:N1259S;ENSP00000409335:N1222S;ENSP00000424161:N1222S	ENSP00000265075:N1184S	N	-	2	0	DROSHA	31444998	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.586000	0.82596	2.030000	0.59900	0.533000	0.62120	AAT	.	.	.	none		0.433	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235		C	31409241	T	C	31409241	3	2	80	1	0	0	0	0	1	0	0	0	13430	1493	52	3	364	3	RNASEN	5	31409241	Missense_Mutation	SNP	T	TCGA-B1-7332-01A-11D-2136-08		31409241	149506019	21	5167											
POLR3G	10622	hgsc.bcm.edu	37	chr5	89797779	89797779	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaggcacaccactcactaatActgaagatgtgttgaaaaaa	18	8	7	8	0	1	3	1	2	0	1	1	3	1	3	1	1	1	2	1	1	7	3			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr5:89797779A>G	ENST00000399107.1	+	6	612	c.412A>G	c.(412-414)Act>Gct	p.T138A	POLR3G_ENST00000504930.1_Missense_Mutation_p.T138A	NM_006467.2	NP_006458.2	O15318	RPC7_HUMAN	polymerase (RNA) III (DNA directed) polypeptide G (32kD)	138					cell proliferation (GO:0008283)|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)|transcription initiation from RNA polymerase III promoter (GO:0006384)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	DNA-directed RNA polymerase activity (GO:0003899)			cervix(1)|endometrium(1)|kidney(2)|lung(4)|prostate(1)	9		all_cancers(142;5.03e-09)|all_epithelial(76;1.23e-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;2.74e-31)|Epithelial(54;8.2e-26)|all cancers(79;3.86e-22)		ACTCACTAATACTGAAGATGT	0.383																																					p.T138A		Atlas-SNP	.											.	POLR3G	19	.	0			c.A412G						PASS	.						72	68	69					5																	89797779		1862	4108	5970	SO:0001583	missense	10622	exon6			ACTAATACTGAAG	U93868	CCDS43337.1	5q14.3	2014-06-05			ENSG00000113356	ENSG00000113356		"RNA polymerase subunits"	30075	protein-coding gene	gene with protein product						9171375, 12391170	Standard	NM_006467		Approved	RPC32, RPC7	uc003kjq.3	O15318	OTTHUMG00000162809	ENST00000399107.1:c.412A>G	chr5.hg19:g.89797779A>G	ENSP00000382058:p.Thr138Ala	35.0	0.0	.		38.0	11.0	.	NM_006467	A8MTH0	Missense_Mutation	SNP	ENST00000399107.1	hg19	CCDS43337.1	.	.	.	.	.	.	.	.	.	.	A	7.354	0.623448	0.14193	.	.	ENSG00000113356	ENST00000503373;ENST00000399107;ENST00000504930	.	.	.	5.76	-3.4	0.04853	.	1.429180	0.04034	N	0.301916	T	0.23410	0.0566	L	0.36672	1.1	0.09310	N	1	P	0.40144	0.704	B	0.39217	0.294	T	0.13361	-1.0512	9	0.09084	T	0.74	-1.7336	4.8923	0.13733	0.305:0.4951:0.0729:0.127	.	138	O15318	RPC7_HUMAN	A	138	.	ENSP00000382058:T138A	T	+	1	0	POLR3G	89833535	0.039000	0.19947	0.000000	0.03702	0.135000	0.20990	0.724000	0.25954	-0.710000	0.05001	-0.316000	0.08728	ACT	.	.	.	none		0.383	POLR3G-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370462.1	NM_006467		G	89797779	A	G	89797779	3	3	80	1	0	0	0	0	1	0	0	0	12241	391	14	3	430	3	POLR3G	5	89797779	Missense_Mutation	SNP	A	TCGA-B1-7332-01A-11D-2136-08	58388538	89797779	91117481	22	5168											
C6orf105	84830	hgsc.bcm.edu	37	chr6	11735821	11735821	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggctgatgtaagcaatgctGgcagcagccagcaaggtgag	11	6	15	9	1	0	2	0	2	0	0	0	2	0	2	1	3	5	7	1	3	3	1			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr6:11735821G>A	ENST00000414691.3	-	4	896	c.486C>T	c.(484-486)gcC>gcT	p.A162A	ADTRP_ENST00000229583.5_Silent_p.A180A|ADTRP_ENST00000514824.1_5'UTR|ADTRP_ENST00000379413.2_Silent_p.A162A	NM_032744.3	NP_116133.1	Q96IZ2	ADTRP_HUMAN	androgen-dependent TFPI-regulating protein	162						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											AAGCAATGCTGGCAGCAGCCA	0.483																																					p.A180A		Atlas-SNP	.											.	ADTRP	3	.	0			c.C540T						PASS	.						66	60	62					6																	11735821		2203	4300	6503	SO:0001819	synonymous_variant	84830	exon5			AATGCTGGCAGCA	AJ420520	CCDS4521.1, CCDS47374.1	6p24.1	2012-01-30	2012-01-27	2012-01-27	ENSG00000111863	ENSG00000111863			21214	protein-coding gene	gene with protein product	"androgen-induced 1-like"	614348	"chromosome 6 open reading frame 105"	C6orf105		21868574	Standard	NM_032744		Approved	dJ413H6.1, AIG1L	uc011dip.2	Q96IZ2	OTTHUMG00000014260	ENST00000414691.3:c.486C>T	chr6.hg19:g.11735821G>A		57.0	0.0	.		41.0	8.0	.	NM_001143948	B2R7T9|B4DV39|Q5THW1	Silent	SNP	ENST00000414691.3	hg19	CCDS4521.1																																																																																			.	.	.	none		0.483	ADTRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039864.3	NM_032744		A	11735821	G	A	11735821	2	1	80	1	0	0	0	0	0	0	0	1	2320	1335	47	2		2	C6orf105	6	11735821	Silent	SNP	G	TCGA-B1-7332-01A-11D-2136-08		11735821	159379246	23	5169											
MET	4233	hgsc.bcm.edu	37	chr7	116422117	116422117	+	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	aatatcttgcaagcaaaaagTttgtccacagagacttggct	14	11	8	8	0	1	1	0	0	1	1	2	2	2	1	1	1	2	4	1	1	5	4			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr7:116422117T>A	ENST00000318493.6	+	18	3839	c.3652T>A	c.(3652-3654)Ttt>Att	p.F1218I	MET_ENST00000397752.3_Missense_Mutation_p.F1200I|MET_ENST00000539704.1_Missense_Mutation_p.F70I			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.F1218V(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)			AAGCAAAAAGTTTGTCCACAG	0.393			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.F1218I		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	Substitution - Missense(1)	kidney(1)	c.T3652A						PASS	.						57	55	56					7																	116422117		1836	4092	5928	SO:0001583	missense	4233	exon18	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	AAAAAGTTTGTCC	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.3652T>A	chr7.hg19:g.116422117T>A	ENSP00000317272:p.Phe1218Ile	44.0	0.0	.		30.0	11.0	.	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.735740	0.89482	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000539704	T;T;T	0.25414	1.8;1.8;1.8	5.87	5.87	0.94306	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	0.37128	0.0992	N	0.16862	0.45	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.35201	-0.9798	10	0.87932	D	0	.	16.5764	0.84681	0.0:0.0:0.0:1.0	.	1218;1200	P08581-2;P08581	.;MET_HUMAN	I	1200;1218;70	ENSP00000380860:F1200I;ENSP00000317272:F1218I;ENSP00000445020:F70I	ENSP00000317272:F1218I	F	+	1	0	MET	116209353	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.972000	0.88022	2.371000	0.80710	0.533000	0.62120	TTT	.	.	.	none		0.393	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			A	116422117	T	A	116422117	3	1	80	1	0	0	0	0	1	0	0	0	9492	1725	60	5	3718	5	MET	7	116422117	Missense_Mutation	SNP	T	TCGA-B1-7332-01A-11D-2136-08		116422117	42716546	24	5170											
DOCK5	80005	hgsc.bcm.edu	37	chr8	25226181	25226181	+	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	ctccggaaagccacaatcccCattttctttgatatgatgca	11	12	6	12	1	1	2	0	2	1	0	3	3	3	3	4	1	2	1	4	1	3	4			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr8:25226181C>A	ENST00000276440.7	+	33	3422	c.3378C>A	c.(3376-3378)ccC>ccA	p.P1126P		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	1126					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)		CCACAATCCCCATTTTCTTTG	0.443																																					p.P1126P	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											.	DOCK5	167	.	0			c.C3378A						PASS	.						73	71	72					8																	25226181		2203	4300	6503	SO:0001819	synonymous_variant	80005	exon33			AATCCCCATTTTC		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.3378C>A	chr8.hg19:g.25226181C>A		55.0	0.0	.		40.0	16.0	.	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Silent	SNP	ENST00000276440.7	hg19	CCDS6047.1	.	.	.	.	.	.	.	.	.	.	C	9.817	1.184776	0.21870	.	.	ENSG00000147459	ENST00000444569	.	.	.	5.8	4.93	0.64822	.	.	.	.	.	T	0.60612	0.2282	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59010	-0.7534	4	.	.	.	.	9.6931	0.40141	0.0:0.6721:0.257:0.0709	.	.	.	.	N	898	.	.	H	+	1	0	DOCK5	25282098	0.998000	0.40836	1.000000	0.80357	0.999000	0.98932	0.603000	0.24149	1.461000	0.47929	0.655000	0.94253	CAT	.	.	.	none		0.443	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940		A	25226181	C	A	25226181	2	1	80	1	0	0	0	0	0	0	0	1	4692	581	21	4		4	DOCK5	8	25226181	Silent	SNP	C	TCGA-B1-7332-01A-11D-2136-08		25226181	121137841	25	5171											
TRPS1	7227	hgsc.bcm.edu	37	chr8	116631588	116631588	+	Missense_Mutation	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	tcagatctgtggggtcgttgCcgtagtaaccatatccacag	9	11	11	10	2	2	1	1	0	1	1	4	1	3	1	3	2	2	3	3	2	3	4			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr8:116631588C>T	ENST00000220888.5	-	2	857	c.698G>A	c.(697-699)gGc>gAc	p.G233D	TRPS1_ENST00000519076.1_Missense_Mutation_p.G187D|TRPS1_ENST00000520276.1_Missense_Mutation_p.G237D|TRPS1_ENST00000395715.3_Missense_Mutation_p.G246D|TRPS1_ENST00000519674.1_Missense_Mutation_p.G233D			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	233					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)			GGGGTCGTTGCCGTAGTAACC	0.483									Langer-Giedion syndrome																												p.G246D		Atlas-SNP	.											.	TRPS1	516	.	0			c.G737A						PASS	.						113	113	113					8																	116631588		1958	4180	6138	SO:0001583	missense	7227	exon3	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	TCGTTGCCGTAGT	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.698G>A	chr8.hg19:g.116631588C>T	ENSP00000220888:p.Gly233Asp	122.0	0.0	.		117.0	38.0	.	NM_014112	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Missense_Mutation	SNP	ENST00000220888.5	hg19		.	.	.	.	.	.	.	.	.	.	C	22.7	4.320687	0.81469	.	.	ENSG00000104447	ENST00000395715;ENST00000220888;ENST00000519076;ENST00000520276;ENST00000519674	T;T;T;T;T	0.06528	3.29;3.29;3.29;3.29;3.29	5.56	5.56	0.83823	Zinc finger, C2H2-like (1);	0.000000	0.85682	D	0.000000	T	0.16471	0.0396	N	0.24115	0.695	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	0.02797	-1.1109	10	0.87932	D	0	0.3311	19.5324	0.95234	0.0:1.0:0.0:0.0	.	237;233;246	Q9UHF7-3;Q9UHF7;Q9UHF7-2	.;TRPS1_HUMAN;.	D	246;233;187;237;233	ENSP00000379065:G246D;ENSP00000220888:G233D;ENSP00000428910:G187D;ENSP00000428680:G237D;ENSP00000429174:G233D	ENSP00000220888:G233D	G	-	2	0	TRPS1	116700763	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.818000	0.86416	2.619000	0.88677	0.460000	0.39030	GGC	.	.	.	none		0.483	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		T	116631588	C	T	116631588	3	4	80	1	0	0	0	0	1	0	0	0	16605	739	26	2	3167	2	TRPS1	8	116631588	Missense_Mutation	SNP	C	TCGA-B1-7332-01A-11D-2136-08	91405407	116631588	29732434	26	5172											
ATAD2	29028	hgsc.bcm.edu	37	chr8	124382171	124382185	+	In_Frame_Del	DEL	TCATCATCATCATCG	TCATCATCATCATCG	-																															catcatcttcatcatcatcaTcatcatcatcatcgtcatca																								rs139406007|rs539981908|rs370549201|rs200543112|rs117211505|rs113160199|rs148244463	byFrequency	TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	TCATCATCATCATCG	TCATCATCATCATCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr8:124382171_124382185delTCATCATCATCATCG	ENST00000287394.5	-	7	914_928	c.807_821delCGATGATGATGATGA	c.(805-822)gacgatgatgatgatgat>gat	p.269_274DDDDDD>D	ATAD2_ENST00000521903.1_De_novo_Start_InFrame|ATAD2_ENST00000534257.1_5'Flank	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	269	Asp-rich.				ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			atcatcatcatcatcatcatcatcgtcatcatcat	0.372																																					p.270_274del		Pindel	.											.	ATAD2	160	.	0			c.808_822del						PASS	.																																			SO:0001651	inframe_deletion	29028	exon7			.	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.807_821delCGATGATGATGATGA	chr8.hg19:g.124382171_124382185delTCATCATCATCATCG	ENSP00000287394:p.Asp269_Asp273del	48.0	0.0	.		45.0	12.0	0.267	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	In_Frame_Del	DEL	ENST00000287394.5	hg19	CCDS6343.1																																																																																			.	.	.	none		0.372	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109		-	124382185	TCATCATCATCATCG	-	124382171	7	5	80	1	0	1	0	1	0	0	0	0	1071	1435	50	0	3439	0	ATAD2	8	124382171	In_Frame_Del	DEL	TCATCATCATCATCG	TCGA-B1-7332-01A-11D-2136-08	7750583	124382171	21981851	27	5173											
EPPK1	83481	hgsc.bcm.edu	37	chr8	144941596	144941596	+	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	agcttctggcgggtgcagggGtccaggaggaacccggtggc	6	6	19	10	2	1	0	0	0	1	0	2	2	2	2	2	8	3	2	2	8	1	1	rs576788732		TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr8:144941596G>A	ENST00000525985.1	-	2	5897	c.5826C>T	c.(5824-5826)gaC>gaT	p.D1942D				P58107	EPIPL_HUMAN	epiplakin 1	1942						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)			GGGTGCAGGGGTCCAGGAGGA	0.637																																					p.D1942D		Atlas-SNP	.											.	EPPK1	199	.	0			c.C5826T						PASS	.						39	47	44					8																	144941596		1996	4166	6162	SO:0001819	synonymous_variant	83481	exon1			GCAGGGGTCCAGG	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.5826C>T	chr8.hg19:g.144941596G>A		166.0	0.0	.		63.0	27.0	.	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	hg19																																																																																				.	.	.	none		0.637	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		A	144941596	G	A	144941596	2	1	80	1	0	0	0	0	0	0	0	1	5192	1252	44	2		2	EPPK1	8	144941596	Silent	SNP	G	TCGA-B1-7332-01A-11D-2136-08	20559425	144941596	1422426	28	5174											
SMU1	55234	hgsc.bcm.edu	37	chr9	33048146	33048146	+	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	0	0	0	0	0	0	0	0	0	ccagtgactgtactgaaacaGtagagcacaaagtcctcccc	13	7	8	13	0	0	3	0	2	0	1	2	3	2	3	4	0	3	3	4	0	4	2			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr9:33048146G>C	ENST00000397149.3	-	11	1451	c.1401C>G	c.(1399-1401)taC>taG	p.Y467*	SMU1_ENST00000536631.1_Nonsense_Mutation_p.Y306*	NM_018225.2	NP_060695.2	Q2TAY7	SMU1_HUMAN	smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans)	467						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)		TACTGAAACAGTAGAGCACAA	0.443																																					p.Y467X		Atlas-SNP	.											.	SMU1	29	.	0			c.C1401G						PASS	.						117	98	104					9																	33048146		2203	4300	6503	SO:0001587	stop_gained	55234	exon11			GAAACAGTAGAGC	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.1401C>G	chr9.hg19:g.33048146G>C	ENSP00000380336:p.Tyr467*	89.0	0.0	.		63.0	13.0	.	NM_018225	B4E3L0|Q9BU59|Q9HA96|Q9NVD1	Nonsense_Mutation	SNP	ENST00000397149.3	hg19	CCDS6534.1	.	.	.	.	.	.	.	.	.	.	G	36	5.657265	0.96724	.	.	ENSG00000122692	ENST00000397149;ENST00000536631	.	.	.	5.25	3.35	0.38373	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.9692	9.5331	0.39207	0.182:0.0:0.818:0.0	.	.	.	.	X	467;306	.	ENSP00000380336:Y467X	Y	-	3	2	SMU1	33038146	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.318000	0.51975	0.648000	0.30732	0.591000	0.81541	TAC	.	.	.	none		0.443	SMU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052022.1	NM_018225		C	33048146	G	C	33048146	4	2	80	1	0	0	0	0	0	1	0	0	14830	1024	36	4	148	4	SMU1	9	33048146	Nonsense_Mutation	SNP	G	TCGA-B1-7332-01A-11D-2136-08		33048146	108165285	29	5175											
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84607291	84607291	+	Missense_Mutation	SNP	T	T	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	tgcagaaagtgcaggaaagtTtgtggggcttaccctctgtg	9	11	14	7	0	1	1	0	0	1	1	1	2	1	2	1	3	3	4	1	3	3	2	rs201182137	byFrequency	TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr9:84607291T>G	ENST00000344803.2	+	4	1953	c.1906T>G	c.(1906-1908)Ttg>Gtg	p.L636V		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	636					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GCAGGAAAGTTTGTGGGGCTT	0.478													G|||	3	0.000599042	8e-04	0	5008	,	,		19868	0		0.001	False		,,,				2504	0.001				p.L636V		Atlas-SNP	.											FAM75D4,NS,carcinoma,0,2	.	.	.	0			c.T1906G						PASS	.	G	VAL/LEU	0,3730		0,0,1865	101	98	99		1906	-3.7	0	9		99	1,8223		0,1,4111	no	missense	FAM75D1	NM_001001670.2	32	0,1,5976	GG,GT,TT		0.0122,0.0,0.0084	benign	636/1577	84607291	1,11953	1865	4112	5977	SO:0001583	missense	389763	exon4			GAAAGTTTGTGGG		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.1906T>G	chr9.hg19:g.84607291T>G	ENSP00000341988:p.Leu636Val	70.0	0.0	.		102.0	5.0	.	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	hg19	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	G	4.363	0.066840	0.08388	0.0	1.22E-4	ENSG00000214929	ENST00000344803	T	0.05786	3.39	3.83	-3.67	0.04476	.	1.454400	0.04584	N	0.395509	T	0.02970	0.0088	N	0.11023	0.085	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.43261	-0.9402	10	0.16420	T	0.52	0.4754	3.7406	0.08528	0.108:0.096:0.4463:0.3497	.	636	Q6ZQQ2	F75D1_HUMAN	V	636	ENSP00000341988:L636V	ENSP00000341988:L636V	L	+	1	2	FAM75D1	83797111	0.011000	0.17503	0.002000	0.10522	0.000000	0.00434	-0.756000	0.04777	-1.293000	0.02362	-0.729000	0.03580	TTG	.	.	.	weak		0.478	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		G	84607291	T	G	84607291	3	3	80	1	0	0	0	0	1	0	0	0	5939	1838	64	5	1920	5	FLJ46321	9	84607291	Missense_Mutation	SNP	T	TCGA-B1-7332-01A-11D-2136-08	51559145	84607291	56606140	30	5176											
OR5C1	392391	hgsc.bcm.edu	37	chr9	125551413	125551413	+	Missense_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	cacctatgtacttcttcctgGccaacctctccctgctggat	6	13	6	16	0	2	0	0	0	2	0	4	1	3	1	5	2	3	2	5	2	3	4			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr9:125551413G>A	ENST00000373680.2	+	1	264	c.202G>A	c.(202-204)Gcc>Acc	p.A68T		NM_001001923.1	NP_001001923.1	Q8NGR4	OR5C1_HUMAN	olfactory receptor, family 5, subfamily C, member 1	68						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|large_intestine(5)|lung(6)|pancreas(1)|prostate(5)|skin(1)	20						CTTCTTCCTGGCCAACCTCTC	0.617																																					p.A68T		Atlas-SNP	.											.	OR5C1	45	.	0			c.G202A						PASS	.						149	139	142					9																	125551413		2203	4300	6503	SO:0001583	missense	392391	exon1			TTCCTGGCCAACC	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.202G>A	chr9.hg19:g.125551413G>A	ENSP00000362784:p.Ala68Thr	237.0	0.0	.		175.0	8.0	.	NM_001001923	B2RN54|B9EGT0|Q96RC4	Missense_Mutation	SNP	ENST00000373680.2	hg19	CCDS35131.1	.	.	.	.	.	.	.	.	.	.	G	14.79	2.639367	0.47153	.	.	ENSG00000148215	ENST00000373680	T	0.01099	5.34	5.17	4.27	0.50696	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36234	U	0.002710	T	0.00875	0.0029	L	0.28608	0.87	0.28228	N	0.926248	P	0.42827	0.791	B	0.32677	0.15	T	0.51100	-0.8748	10	0.62326	D	0.03	.	4.1132	0.10068	0.0841:0.1619:0.5858:0.1681	.	68	Q8NGR4	OR5C1_HUMAN	T	68	ENSP00000362784:A68T	ENSP00000362784:A68T	A	+	1	0	OR5C1	124591234	0.000000	0.05858	1.000000	0.80357	0.998000	0.95712	0.075000	0.14686	1.391000	0.46566	0.650000	0.86243	GCC	.	.	.	none		0.617	OR5C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053953.1			A	125551413	G	A	125551413	3	1	80	1	0	0	0	0	1	0	0	0	11160	1203	42	2	204	2	OR5C1	9	125551413	Missense_Mutation	SNP	G	TCGA-B1-7332-01A-11D-2136-08	40944122	125551413	15662018	31	5177											
KIAA1279	26128	hgsc.bcm.edu	37	chr10	70749011	70749011	+	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	atctctctctgcatccaggcGcaggtgagagcgagcccggc	7	7	13	14	3	2	1	0	1	2	1	5	3	3	1	2	3	3	2	2	3	0	0			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr10:70749011G>C	ENST00000361983.4	+	1	525	c.423G>C	c.(421-423)gcG>gcC	p.A141A		NM_015634.3	NP_056449.1	Q96EK5	KBP_HUMAN	KIAA1279	141					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						GCATCCAGGCGCAGGTGAGAG	0.677																																					p.A141A		Atlas-SNP	.											.	KIAA1279	35	.	0			c.G423C						PASS	.						12	15	14					10																	70749011		2196	4277	6473	SO:0001819	synonymous_variant	26128	exon1			CCAGGCGCAGGTG	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.423G>C	chr10.hg19:g.70749011G>C		41.0	0.0	.		24.0	15.0	.	NM_015634	A8K5M8|Q9BR89|Q9ULE1|Q9Y428	Silent	SNP	ENST00000361983.4	hg19	CCDS7284.1																																																																																			.	.	.	none		0.677	KIAA1279-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048370.1	NM_015634		C	70749011	G	C	70749011	2	2	80	1	0	0	0	0	0	0	0	1	8228	1074	38	4		4	KIAA1279	10	70749011	Silent	SNP	G	TCGA-B1-7332-01A-11D-2136-08		70749011	64785736	32	5178											
KATNAL1	84056	hgsc.bcm.edu	37	chr13	30814673	30814673	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagcttcccttagcaacttcTtagcttcttccagatctgct	7	15	5	14	0	3	1	0	0	3	1	5	1	5	1	2	0	5	4	2	0	3	6			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr13:30814673T>C	ENST00000380615.3	-	6	817	c.650A>G	c.(649-651)aAg>aGg	p.K217R	KATNAL1_ENST00000380617.3_Missense_Mutation_p.K217R	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)		TAGCAACTTCTTAGCTTCTTC	0.363																																					p.K217R		Atlas-SNP	.											.	KATNAL1	53	.	0			c.A650G						PASS	.						112	103	106					13																	30814673		2203	4300	6503	SO:0001583	missense	84056	exon6			AACTTCTTAGCTT	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.650A>G	chr13.hg19:g.30814673T>C	ENSP00000369989:p.Lys217Arg	102.0	0.0	.		63.0	33.0	.	NM_001014380		Missense_Mutation	SNP	ENST00000380615.3	hg19	CCDS31956.1	.	.	.	.	.	.	.	.	.	.	T	33	5.206604	0.95033	.	.	ENSG00000102781	ENST00000380615;ENST00000380617	D;D	0.95656	-3.77;-3.77	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	D	0.97685	0.9241	M	0.93678	3.445	0.80722	D	1	D	0.54964	0.969	P	0.53401	0.725	D	0.98333	1.0534	10	0.66056	D	0.02	-18.253	16.5582	0.84512	0.0:0.0:0.0:1.0	.	217	Q9BW62	KATL1_HUMAN	R	217	ENSP00000369989:K217R;ENSP00000369991:K217R	ENSP00000369989:K217R	K	-	2	0	KATNAL1	29712673	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.040000	0.89188	2.308000	0.77769	0.533000	0.62120	AAG	.	.	.	none		0.363	KATNAL1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044346.2	NM_032116		C	30814673	T	C	30814673	3	2	80	1	0	0	0	0	1	0	0	0	7992	1609	56	3	846	3	KATNAL1	13	30814673	Missense_Mutation	SNP	T	TCGA-B1-7332-01A-11D-2136-08		30814673	84355205	33	5179											
HEXA	3073	hgsc.bcm.edu	37	chr15	72637848	72637848	+	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	aaatgtcaggtcagatgtcaActtgttgctccacagccttt	10	13	8	10	0	3	1	3	0	0	1	4	1	4	1	2	1	3	2	2	1	2	3			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr15:72637848A>T	ENST00000268097.5	-	13	1968	c.1465T>A	c.(1465-1467)Ttg>Atg	p.L489M	HEXA_ENST00000567159.1_Missense_Mutation_p.L489M|HEXA_ENST00000457859.2_3'UTR|RP11-106M3.3_ENST00000570175.1_RNA|RP11-106M3.2_ENST00000379915.4_RNA|HEXA_ENST00000566304.1_Missense_Mutation_p.L500M	NM_000520.4	NP_000511.2	P06865	HEXA_HUMAN	hexosaminidase A (alpha polypeptide)	489					carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-N-acetylhexosaminidase activity (GO:0004563)|protein heterodimerization activity (GO:0046982)			breast(2)|cervix(1)|endometrium(3)|kidney(3)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	24						TCAGATGTCAACTTGTTGCTC	0.567																																					p.L489M		Atlas-SNP	.											.	HEXA	48	.	0			c.T1465A						PASS	.						148	111	124					15																	72637848		2199	4297	6496	SO:0001583	missense	3073	exon13			ATGTCAACTTGTT	M13520	CCDS10243.1	15q24.1	2012-10-02			ENSG00000213614	ENSG00000213614	3.2.1.52		4878	protein-coding gene	gene with protein product	"Tay Sachs disease", "GM2 gangliosidosis"	606869				2952641, 3013851	Standard	NM_000520		Approved		uc002aun.4	P06865	OTTHUMG00000133445	ENST00000268097.5:c.1465T>A	chr15.hg19:g.72637848A>T	ENSP00000268097:p.Leu489Met	88.0	0.0	.		71.0	10.0	.	NM_000520	B4DKE7|E7ENH7|Q53HS8|Q6AI32	Missense_Mutation	SNP	ENST00000268097.5	hg19	CCDS10243.1	.	.	.	.	.	.	.	.	.	.	A	13.26	2.184859	0.38609	.	.	ENSG00000213614	ENST00000268097	D	0.96651	-4.08	5.71	-11.4	0.00090	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	2.683750	0.01267	N	0.009357	D	0.87533	0.6201	N	0.08118	0	0.09310	N	0.999998	B;B;B	0.15930	0.015;0.0;0.006	B;B;B	0.17098	0.017;0.005;0.014	T	0.79351	-0.1839	10	0.51188	T	0.08	4.1018	4.1333	0.10159	0.1012:0.1303:0.3717:0.3968	.	500;369;489	B4DVA7;Q9BVJ8;P06865	.;.;HEXA_HUMAN	M	489	ENSP00000268097:L489M	ENSP00000268097:L489M	L	-	1	2	HEXA	70424902	0.000000	0.05858	0.000000	0.03702	0.155000	0.21991	-0.794000	0.04584	-2.858000	0.00328	-0.290000	0.09829	TTG	.	.	.	none		0.567	HEXA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257317.2	NM_000520		T	72637848	A	T	72637848	3	4	80	1	0	0	0	0	1	0	0	0	7080	40	2	5	132	5	HEXA	15	72637848	Missense_Mutation	SNP	A	TCGA-B1-7332-01A-11D-2136-08		72637848	29893544	34	5180											
METTL9	51108	hgsc.bcm.edu	37	chr16	21666647	21666647	+	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	tgaagttttcagaaaagctgGttttgttatcgaagctttca	11	16	9	5	1	2	2	2	1	0	1	3	3	2	2	0	1	2	5	0	1	5	6			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr16:21666647G>T	ENST00000358154.3	+	5	1109	c.851G>T	c.(850-852)gGt>gTt	p.G284V	IGSF6_ENST00000268389.4_5'Flank|METTL9_ENST00000396014.4_Missense_Mutation_p.G283V	NM_001077180.1|NM_016025.3	NP_001070648.1|NP_057109.3	Q9H1A3	METL9_HUMAN	methyltransferase like 9	284										endometrium(1)|kidney(3)|large_intestine(1)|lung(1)|ovary(1)	7				GBM - Glioblastoma multiforme(48;0.0759)		AGAAAAGCTGGTTTTGTTATC	0.423																																					p.G284V		Atlas-SNP	.											.	METTL9	18	.	0			c.G851T						PASS	.						116	105	109					16																	21666647		2199	4300	6499	SO:0001583	missense	51108	exon5			AAGCTGGTTTTGT	NM_016025, AF151839	CCDS10598.2, CCDS45440.1	16p12.2	2008-11-06			ENSG00000197006	ENSG00000197006			24586	protein-coding gene	gene with protein product	"DORA reverse strand protein 1"	609388				10810093, 11132146	Standard	NM_001077180		Approved	DREV1	uc002dje.3	Q9H1A3	OTTHUMG00000131584	ENST00000358154.3:c.851G>T	chr16.hg19:g.21666647G>T	ENSP00000350874:p.Gly284Val	73.0	0.0	.		66.0	16.0	.	NM_016025	Q8NBT8|Q9BWJ7|Q9H1A2|Q9Y390	Missense_Mutation	SNP	ENST00000358154.3	hg19	CCDS10598.2	.	.	.	.	.	.	.	.	.	.	G	22.6	4.309820	0.81247	.	.	ENSG00000197006	ENST00000358154;ENST00000396014;ENST00000540294	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.84817	0.5556	M	0.87456	2.885	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.995	D	0.86314	0.1688	9	0.87932	D	0	-12.9082	18.1377	0.89624	0.0:0.0:1.0:0.0	.	283;284	Q9H1A3-2;Q9H1A3	.;METL9_HUMAN	V	284;283;248	.	ENSP00000350874:G284V	G	+	2	0	METTL9	21574148	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.445000	0.97587	2.890000	0.99128	0.650000	0.86243	GGT	.	.	.	none		0.423	METTL9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254465.1	NM_016025		T	21666647	G	T	21666647	3	4	80	1	0	0	0	0	1	0	0	0	9515	1261	44	4	869	4	METTL9	16	21666647	Missense_Mutation	SNP	G	TCGA-B1-7332-01A-11D-2136-08		21666647	68688106	35	5181											
FAM83G	644815	hgsc.bcm.edu	37	chr17	18881908	18881908	+	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	gagatcttggcaatctcgtcGacgctcttggccttgacaag	8	11	11	11	3	3	2	0	1	3	1	5	4	3	2	1	2	0	2	1	2	2	3			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr17:18881908G>A	ENST00000388995.6	-	5	1294	c.1071C>T	c.(1069-1071)gtC>gtT	p.V357V	FAM83G_ENST00000585154.2_Silent_p.V357V|SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000395647.2_Intron|SLC5A10_ENST00000395643.2_Intron|SLC5A10_ENST00000395645.3_Intron|FAM83G_ENST00000345041.4_Silent_p.V357V|SLC5A10_ENST00000317977.6_Intron|SLC5A10_ENST00000417251.2_Intron			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	357					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						CAATCTCGTCGACGCTCTTGG	0.627																																					p.V357V		Atlas-SNP	.											.	FAM83G	51	.	0			c.C1071T						PASS	.						67	74	72					17																	18881908		1996	4157	6153	SO:0001819	synonymous_variant	644815	exon5			CTCGTCGACGCTC	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.1071C>T	chr17.hg19:g.18881908G>A		153.0	0.0	.		146.0	21.0	.	NM_001039999	Q3KQZ4|Q6ZW60	Silent	SNP	ENST00000388995.6	hg19	CCDS42276.1																																																																																			.	.	.	none		0.627	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4			A	18881908	G	A	18881908	2	1	80	1	0	0	0	0	0	0	0	1	5646	1045	37	1		1	FAM83G	17	18881908	Silent	SNP	G	TCGA-B1-7332-01A-11D-2136-08		18881908	62313302	36	5182											
KIAA1267	284058	hgsc.bcm.edu	37	chr17	44109553	44109553	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctaggggactgaccatgggAgtattctgacaaagagtggc	11	8	14	8	0	1	3	0	2	1	1	1	5	1	5	2	4	0	1	2	4	3	3			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr17:44109553A>G	ENST00000262419.6	-	14	3420	c.2950T>C	c.(2950-2952)Tcc>Ccc	p.S984P	KANSL1_ENST00000432791.1_Missense_Mutation_p.S984P|KANSL1_ENST00000393476.3_Missense_Mutation_p.S278P|KANSL1_ENST00000574590.1_Missense_Mutation_p.S984P|KANSL1_ENST00000575318.1_Missense_Mutation_p.S920P|KANSL1_ENST00000572904.1_Missense_Mutation_p.S984P	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	984	Sufficient for interaction with KAT8.				chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											TGACCATGGGAGTATTCTGAC	0.632																																					p.S984P		Atlas-SNP	.											.	.	.	.	0			c.T2950C						PASS	.						54	59	58					17																	44109553		2203	4300	6503	SO:0001583	missense	284058	exon14			CATGGGAGTATTC	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.2950T>C	chr17.hg19:g.44109553A>G	ENSP00000262419:p.Ser984Pro	145.0	0.0	.		103.0	38.0	.	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	hg19	CCDS11503.1	.	.	.	.	.	.	.	.	.	.	A	13.49	2.252579	0.39797	.	.	ENSG00000120071	ENST00000262419;ENST00000432791;ENST00000393476	T;T;T	0.26660	2.54;2.54;1.72	5.2	2.98	0.34508	.	0.285019	0.36482	N	0.002570	T	0.16171	0.0389	L	0.33485	1.01	0.33040	D	0.531312	B;B;B;B	0.12013	0.005;0.002;0.004;0.004	B;B;B;B	0.14578	0.01;0.007;0.011;0.011	T	0.20438	-1.0275	10	0.19590	T	0.45	-3.7274	7.0976	0.25319	0.7735:0.1488:0.0778:0.0	.	252;315;984;984	B3KT49;Q7Z3B3-2;C9JHY2;Q7Z3B3	.;.;.;K1267_HUMAN	P	984;984;278	ENSP00000262419:S984P;ENSP00000387393:S984P;ENSP00000377117:S278P	ENSP00000262419:S984P	S	-	1	0	KIAA1267	41465400	1.000000	0.71417	0.998000	0.56505	0.228000	0.25075	1.224000	0.32539	0.443000	0.26582	-0.429000	0.05907	TCC	.	.	.	none		0.632	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443		G	44109553	A	G	44109553	3	3	80	1	0	0	0	0	1	0	0	0	8226	304	11	3	375	3	KIAA1267	17	44109553	Missense_Mutation	SNP	A	TCGA-B1-7332-01A-11D-2136-08	25227645	44109553	37085657	37	5183											
ZNF652	22834	hgsc.bcm.edu	37	chr17	47388762	47388762	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgaactgtttgtgcccaatAtgaatgctcatgtgggagcg	10	12	12	7	1	1	2	1	2	0	0	1	3	1	3	1	1	4	2	1	1	4	2			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr17:47388762A>G	ENST00000362063.2	-	5	1539	c.1221T>C	c.(1219-1221)caT>caC	p.H407H	ZNF652_ENST00000430262.2_Silent_p.H407H	NM_014897.2	NP_055712.1	Q9Y2D9	ZN652_HUMAN	zinc finger protein 652	407					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)			TGTGCCCAATATGAATGCTCA	0.433																																					p.H407H		Atlas-SNP	.											.	ZNF652	54	.	0			c.T1221C						PASS	.						271	235	248					17																	47388762		2203	4300	6503	SO:0001819	synonymous_variant	22834	exon5			CCCAATATGAATG	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.1221T>C	chr17.hg19:g.47388762A>G		245.0	0.0	.		248.0	33.0	.	NM_001145365	A4QPD9|Q5H9Q0	Silent	SNP	ENST00000362063.2	hg19	CCDS32677.1																																																																																			.	.	.	none		0.433	ZNF652-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364524.1	NM_014897		G	47388762	A	G	47388762	2	3	80	1	0	0	0	0	0	0	0	1	18077	446	16	3		3	ZNF652	17	47388762	Silent	SNP	A	TCGA-B1-7332-01A-11D-2136-08	3279209	47388762	33806448	38	5184											
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2772342	2772342	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgtactcttccaaactataCtaaaggcagtggagatgttt	12	13	9	7	0	1	1	0	0	1	1	2	2	2	1	1	2	3	3	1	2	6	6			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr18:2772342C>T	ENST00000320876.6	+	41	5485	c.5147C>T	c.(5146-5148)aCt>aTt	p.T1716I	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Missense_Mutation_p.T1716I|snoU13_ENST00000459147.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1716					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						CCAAACTATACTAAAGGCAGT	0.348																																					p.T1716I		Atlas-SNP	.											.	SMCHD1	88	.	0			c.C5147T						PASS	.						97	92	94					18																	2772342		1830	4076	5906	SO:0001583	missense	23347	exon41			ACTATACTAAAGG	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.5147C>T	chr18.hg19:g.2772342C>T	ENSP00000326603:p.Thr1716Ile	98.0	0.0	.		46.0	19.0	.	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	hg19	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	C	11.11	1.541676	0.27563	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	D;D	0.85411	-1.98;-1.98	5.66	5.66	0.87406	SMCs flexible hinge (1);	0.303958	0.37053	N	0.002277	T	0.75554	0.3865	N	0.22421	0.69	0.37791	D	0.92734	P	0.39391	0.671	B	0.32289	0.143	T	0.75929	-0.3144	10	0.21014	T	0.42	-19.063	19.7468	0.96255	0.0:1.0:0.0:0.0	.	1716	A6NHR9	SMHD1_HUMAN	I	1716	ENSP00000326603:T1716I;ENSP00000261598:T1716I	ENSP00000261598:T1716I	T	+	2	0	SMCHD1	2762342	0.996000	0.38824	0.997000	0.53966	0.780000	0.44128	4.014000	0.57145	2.678000	0.91216	0.563000	0.77884	ACT	.	.	.	none		0.348	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			T	2772342	C	T	2772342	3	4	80	1	0	0	0	0	1	0	0	0	14801	565	20	2	5309	2	SMCHD1	18	2772342	Missense_Mutation	SNP	C	TCGA-B1-7332-01A-11D-2136-08		2772342	75304906	39	5185											
WIZ	58525	hgsc.bcm.edu	37	chr19	15558957	15558957	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agaatgtctcgggggccctcCttggtgacaggcaggtaacg	8	8	15	10	2	1	2	0	1	1	1	3	2	2	2	2	5	1	2	2	5	2	2			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr19:15558957C>T	ENST00000389282.4	-	2	375	c.162G>A	c.(160-162)aaG>aaA	p.K54K	MIR1470_ENST00000600745.1_RNA|WIZ_ENST00000263381.7_Silent_p.K54K			O95785	WIZ_HUMAN	widely interspaced zinc finger motifs	54					positive regulation of nuclear cell cycle DNA replication (GO:0010571)|protein heterotrimerization (GO:0070208)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	24						GGGGGCCCTCCTTGGTGACAG	0.647																																					p.K54K		Atlas-SNP	.											.	WIZ	152	.	0			c.G162A						PASS	.						68	74	73					19																	15558957		1957	4128	6085	SO:0001819	synonymous_variant	58525	exon2			GCCCTCCTTGGTG	AK091183	CCDS42516.1	19p13.12	2012-10-05	2007-01-18		ENSG00000011451	ENSG00000011451		"Zinc fingers, C2H2-type"	30917	protein-coding gene	gene with protein product			"WIZ zinc finger"			9795207, 12226707	Standard	NM_021241		Approved	ZNF803	uc002nbb.4	O95785		ENST00000389282.4:c.162G>A	chr19.hg19:g.15558957C>T		223.0	0.0	.		76.0	30.0	.	NM_021241	B3KVH1|B7ZM82|M0QY21|Q4G0E0|Q6P6B0|Q6ZN24|Q7LDY6|Q7LDZ1|Q96IG5|Q96SQ6|Q9BUR8|Q9NPT1	Silent	SNP	ENST00000389282.4	hg19																																																																																				.	.	.	none		0.647	WIZ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_021241		T	15558957	C	T	15558957	2	4	80	1	0	0	0	0	0	0	0	1	17387	680	24	2		2	WIZ	19	15558957	Silent	SNP	C	TCGA-B1-7332-01A-11D-2136-08		15558957	43570026	40	5186											
PLVAP	83483	hgsc.bcm.edu	37	chr19	17476947	17476947	+	Missense_Mutation	SNP	A	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	gtccttgaattgatctctgcAttgcttctcactcaagatga	9	15	7	10	0	3	4	2	3	2	1	6	4	4	4	1	0	2	2	1	0	2	4			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr19:17476947A>C	ENST00000252590.4	-	2	488	c.427T>G	c.(427-429)Tgc>Ggc	p.C143G		NM_031310.1	NP_112600.1	Q9BX97	PLVAP_HUMAN	plasmalemma vesicle associated protein	143					MAPK cascade (GO:0000165)|positive regulation of cellular extravasation (GO:0002693)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						TGATCTCTGCATTGCTTCTCA	0.552																																					p.C143G		Atlas-SNP	.											.	PLVAP	64	.	0			c.T427G						PASS	.						242	205	217					19																	17476947		2203	4300	6503	SO:0001583	missense	83483	exon2			CTCTGCATTGCTT	AF326591	CCDS32952.1	19p13.2	2008-07-17				ENSG00000130300			13635	protein-coding gene	gene with protein product	"fenestrated-endothelial linked structure protein; PV-1 protein"	607647				11401446	Standard	NM_031310		Approved	gp68, PV-1, PV1, FELS	uc002ngk.1	Q9BX97		ENST00000252590.4:c.427T>G	chr19.hg19:g.17476947A>C	ENSP00000252590:p.Cys143Gly	293.0	1.0	.		138.0	52.0	.	NM_031310	Q86VP0|Q8N8Y0|Q8ND68|Q8TER8|Q9BZD5	Missense_Mutation	SNP	ENST00000252590.4	hg19	CCDS32952.1	.	.	.	.	.	.	.	.	.	.	A	13.54	2.268758	0.40095	.	.	ENSG00000130300	ENST00000252590	T	0.29142	1.58	4.06	4.06	0.47325	.	0.379023	0.30455	N	0.009594	T	0.38374	0.1038	L	0.34521	1.04	0.09310	N	0.999998	D	0.89917	1.0	D	0.91635	0.999	T	0.12426	-1.0548	10	0.20519	T	0.43	-58.5488	9.6793	0.40061	1.0:0.0:0.0:0.0	.	143	Q9BX97	PLVAP_HUMAN	G	143	ENSP00000252590:C143G	ENSP00000252590:C143G	C	-	1	0	PLVAP	17337947	0.326000	0.24669	0.096000	0.21009	0.003000	0.03518	3.317000	0.51968	2.071000	0.62044	0.454000	0.30748	TGC	.	.	.	none		0.552	PLVAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463655.1	NM_031310		C	17476947	A	C	17476947	3	2	80	1	0	0	0	0	1	0	0	0	12123	217	8	5	921	5	PLVAP	19	17476947	Missense_Mutation	SNP	A	TCGA-B1-7332-01A-11D-2136-08	1917990	17476947	41652036	41	5187											
PRX	57716	hgsc.bcm.edu	37	chr19	40903295	40903295	+	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	cacatccagggtgggcaccaCtaccgacacagccccttccc	9	5	8	19	1	0	0	0	0	0	0	2	1	2	0	6	2	2	1	6	2	1	2			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr19:40903295C>T	ENST00000324001.7	-	7	1234	c.964G>A	c.(964-966)Gtg>Atg	p.V322M	PRX_ENST00000291825.7_3'UTR	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	periaxin	322					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)			GTGGGCACCACTACCGACACA	0.687																																					p.V322M		Atlas-SNP	.											.	PRX	151	.	0			c.G964A						PASS	.						13	13	13					19																	40903295		2068	4088	6156	SO:0001583	missense	57716	exon7			GCACCACTACCGA	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.964G>A	chr19.hg19:g.40903295C>T	ENSP00000326018:p.Val322Met	49.0	0.0	.		33.0	9.0	.	NM_181882	Q9BXL9|Q9HCF2	Missense_Mutation	SNP	ENST00000324001.7	hg19	CCDS33028.1	.	.	.	.	.	.	.	.	.	.	C	1.262	-0.615608	0.03663	.	.	ENSG00000105227	ENST00000324001;ENST00000341562	T	0.01092	5.35	4.56	1.19	0.21007	.	0.747813	0.11845	N	0.523898	T	0.00608	0.0020	N	0.02539	-0.55	0.09310	N	0.999999	B	0.18610	0.029	B	0.10450	0.005	T	0.47623	-0.9103	10	0.46703	T	0.11	-5.234	4.3329	0.11073	0.0:0.205:0.1751:0.6198	.	322	Q9BXM0	PRAX_HUMAN	M	322	ENSP00000326018:V322M	ENSP00000326018:V322M	V	-	1	0	PRX	45595135	0.003000	0.15002	0.072000	0.20136	0.072000	0.16883	0.502000	0.22594	0.794000	0.33899	-0.367000	0.07326	GTG	.	.	.	none		0.687	PRX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462582.1	NM_020956		T	40903295	C	T	40903295	3	4	80	1	0	0	0	0	1	0	0	0	12652	565	20	2	3425	2	PRX	19	40903295	Missense_Mutation	SNP	C	TCGA-B1-7332-01A-11D-2136-08	23426348	40903295	18225688	42	5188											
APOL5	80831	hgsc.bcm.edu	37	chr22	36123235	36123235	+	Missense_Mutation	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	gaggatcccgtgtggttaaaCcagaaggtaggaaggcagcg	12	6	16	7	2	0	1	0	0	0	1	1	4	1	3	2	5	2	3	2	5	5	2			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chr22:36123235C>T	ENST00000249044.2	+	3	1120	c.1120C>T	c.(1120-1122)Cca>Tca	p.P374S		NM_030642.1	NP_085145.1	Q9BWW9	APOL5_HUMAN	apolipoprotein L, 5	374					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						TGTGGTTAAACCAGAAGGTAG	0.597																																					p.P374S		Atlas-SNP	.											.	APOL5	45	.	0			c.C1120T						PASS	.						42	46	45					22																	36123235		2196	4290	6486	SO:0001583	missense	80831	exon3			GTTAAACCAGAAG	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.1120C>T	chr22.hg19:g.36123235C>T	ENSP00000249044:p.Pro374Ser	105.0	0.0	.		40.0	16.0	.	NM_030642	Q5TFL9|Q9UGW5	Missense_Mutation	SNP	ENST00000249044.2	hg19	CCDS13920.1	.	.	.	.	.	.	.	.	.	.	C	8.430	0.848333	0.17034	.	.	ENSG00000128313	ENST00000249044	T	0.06142	3.34	1.94	-1.84	0.07809	.	3.921800	0.02219	U	0.063822	T	0.03608	0.0103	N	0.08118	0	0.09310	N	1	B	0.28552	0.215	B	0.23018	0.043	T	0.37911	-0.9685	10	0.87932	D	0	.	4.2557	0.10715	0.0:0.3635:0.4734:0.1631	.	374	Q9BWW9	APOL5_HUMAN	S	374	ENSP00000249044:P374S	ENSP00000249044:P374S	P	+	1	0	APOL5	34453181	0.000000	0.05858	0.001000	0.08648	0.029000	0.11900	-0.970000	0.03810	-0.348000	0.08286	0.462000	0.41574	CCA	.	.	.	none		0.597	APOL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318979.1	NM_030642		T	36123235	C	T	36123235	3	4	80	1	0	0	0	0	1	0	0	0	809	507	18	2	1130	2	APOL5	22	36123235	Missense_Mutation	SNP	C	TCGA-B1-7332-01A-11D-2136-08		36123235	15181331	43	5189											
DDX3X	1654	hgsc.bcm.edu	37	chrX	41203029	41203029	+	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	atttctgttgcccatcttgaGtcagatttattcagatggtc	8	17	8	8	0	4	3	2	1	2	2	5	3	4	3	1	1	1	1	1	1	1	6			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chrX:41203029G>T	ENST00000399959.2	+	8	1574	c.719G>T	c.(718-720)aGt>aTt	p.S240I	DDX3X_ENST00000478993.1_3'UTR|DDX3X_ENST00000542215.1_Intron|DDX3X_ENST00000441189.2_Intron|DDX3X_ENST00000457138.2_Missense_Mutation_p.S224I|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	240	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.|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						CCCATCTTGAGTCAGATTTAT	0.398										HNSCC(61;0.18)																											p.S240I		Atlas-SNP	.											.	DDX3X	138	.	0			c.G719T						PASS	.						90	78	82					X																	41203029		1934	4159	6093	SO:0001583	missense	1654	exon8			TCTTGAGTCAGAT	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.719G>T	chrX.hg19:g.41203029G>T	ENSP00000382840:p.Ser240Ile	154.0	0.0	.		89.0	10.0	.	NM_001193416	A8K538|B4E3E8|O15536	Missense_Mutation	SNP	ENST00000399959.2	hg19	CCDS43931.1	.	.	.	.	.	.	.	.	.	.	G	33	5.205754	0.95033	.	.	ENSG00000215301	ENST00000399959;ENST00000457138	T;T	0.15718	2.4;2.4	5.42	5.42	0.78866	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.30166	0.0756	N	0.20328	0.56	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.997;0.992;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.941;0.932;0.999;0.999	T	0.14643	-1.0465	10	0.87932	D	0	-15.9903	18.5561	0.91085	0.0:0.0:1.0:0.0	.	240;224;240;252;240	B4DLU5;B4E3E8;B5BTY4;Q59GX6;O00571	.;.;.;.;DDX3X_HUMAN	I	240;224	ENSP00000382840:S240I;ENSP00000392494:S224I	ENSP00000382840:S240I	S	+	2	0	DDX3X	41087973	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.636000	0.98440	2.411000	0.81874	0.600000	0.82982	AGT	.	.	.	none		0.398	DDX3X-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056253.1	NM_024005		T	41203029	G	T	41203029	3	4	80	1	0	0	0	0	1	0	0	0	4360	1029	36	4	749	4	DDX3X	23	41203029	Missense_Mutation	SNP	G	TCGA-B1-7332-01A-11D-2136-08		41203029	114067531	44	5190											
ATP11C	286410	hgsc.bcm.edu	37	chrX	138844142	138844142	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tatagaagaagtactgtacaAggtgtgctattctcacataa	15	12	8	6	0	1	2	1	0	1	2	2	2	1	2	0	1	3	3	0	1	9	7			TCGA-B1-7332-01A-11D-2136-08	TCGA-B1-7332-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d453dcec-6bab-4b59-a593-ee38835cbe15	9d012012-57fb-4523-a066-ad674ddb3d3f	g.chrX:138844142A>G	ENST00000327569.3	-	22	2725	c.2627T>C	c.(2626-2628)cTt>cCt	p.L876P	ATP11C_ENST00000370543.1_Missense_Mutation_p.L876P|ATP11C_ENST00000359686.2_Missense_Mutation_p.L876P|ATP11C_ENST00000370557.1_Missense_Mutation_p.L870P|ATP11C_ENST00000361648.2_Missense_Mutation_p.L876P|ATP11C_ENST00000460773.1_5'UTR	NM_173694.4	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C	876					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|positive regulation of B cell differentiation (GO:0045579)|pre-B cell differentiation (GO:0002329)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(31)|ovary(5)|prostate(1)|skin(3)	75	Acute lymphoblastic leukemia(192;0.000127)					GTACTGTACAAGGTGTGCTAT	0.343																																					p.L876P		Atlas-SNP	.											.	ATP11C	319	.	0			c.T2627C						PASS	.						112	100	104					X																	138844142		2203	4300	6503	SO:0001583	missense	286410	exon22			TGTACAAGGTGTG	AJ580094	CCDS14668.1, CCDS35410.1	Xq27.1	2011-06-09	2007-09-19		ENSG00000101974	ENSG00000101974		"ATPases / P-type"	13554	protein-coding gene	gene with protein product		300516	"ATPase, Class VI, type 11C"			11015572	Standard	NM_173694		Approved	ATPIG, ATPIQ	uc004faz.3	Q8NB49	OTTHUMG00000022538	ENST00000327569.3:c.2627T>C	chrX.hg19:g.138844142A>G	ENSP00000332756:p.Leu876Pro	75.0	0.0	.		152.0	69.0	.	NM_001010986	Q5JT69|Q5JT70|Q5JT71|Q5JT72|Q5JT73|Q6ZND5|Q6ZU50|Q6ZUP7|Q70IJ9|Q70IK0|Q8WX24	Missense_Mutation	SNP	ENST00000327569.3	hg19	CCDS14668.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.010046	0.75046	.	.	ENSG00000101974	ENST00000370557;ENST00000361648;ENST00000327569;ENST00000370543;ENST00000359686	T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.78394	0.4276	H	0.96518	3.835	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.85280	0.1061	10	0.72032	D	0.01	.	14.1997	0.65693	1.0:0.0:0.0:0.0	.	876;876;876	Q8NB49-3;Q8NB49;Q8NB49-2	.;AT11C_HUMAN;.	P	870;876;876;876;876	ENSP00000359588:L870P;ENSP00000355165:L876P;ENSP00000332756:L876P;ENSP00000359574:L876P;ENSP00000352715:L876P	ENSP00000332756:L876P	L	-	2	0	ATP11C	138671808	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.962000	0.93254	1.952000	0.56665	0.441000	0.28932	CTT	.	.	.	none		0.343	ATP11C-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354945.1	NM_173694		G	138844142	A	G	138844142	3	3	80	1	0	0	0	0	1	0	0	0	1121	72	3	3	870	3	ATP11C	23	138844142	Missense_Mutation	SNP	A	TCGA-B1-7332-01A-11D-2136-08	97641113	138844142	16426418	45	5191											
ERRFI1	54206	hgsc.bcm.edu	37	chr1	8074134	8074135	+	Frame_Shift_Del	DEL	AG	AG	-																															aggaagtctgtatctgagctAgttaggaattccacctcaca																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr1:8074134_8074135delAG	ENST00000377482.5	-	4	747_748	c.524_525delCT	c.(523-525)actfs	p.T175fs	ERRFI1_ENST00000469499.1_3'UTR|ERRFI1_ENST00000474874.1_Intron|ERRFI1_ENST00000467067.1_3'UTR	NM_018948.3	NP_061821.1	Q9UJM3	ERRFI_HUMAN	ERBB receptor feedback inhibitor 1	175					lung alveolus development (GO:0048286)|lung epithelium development (GO:0060428)|lung vasculature development (GO:0060426)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of protein autophosphorylation (GO:0031953)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of keratinocyte differentiation (GO:0045616)|response to stress (GO:0006950)|skin morphogenesis (GO:0043589)	cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|Rho GTPase activator activity (GO:0005100)			breast(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(3)|ovary(1)|prostate(1)|skin(2)	16	Ovarian(185;0.06)|all_lung(157;0.151)	all_epithelial(116;1.76e-16)|all_lung(118;3.66e-05)|Lung NSC(185;0.000163)|Renal(390;0.000469)|Colorectal(325;0.0033)|Breast(348;0.0044)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.33e-70)|GBM - Glioblastoma multiforme(8;8.05e-37)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;6.9e-06)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.000985)|READ - Rectum adenocarcinoma(331;0.0642)		TATCTGAGCTAGTTAGGAATTC	0.48																																					p.175_176del		Atlas-Indel,Pindel	.											.	ERRFI1	42	.	0			c.525_526del						PASS	.																																			SO:0001589	frameshift_variant	54206	exon4			.	BC025337	CCDS94.1	1p36.23	2008-02-05			ENSG00000116285	ENSG00000116285			18185	protein-coding gene	gene with protein product		608069				10749885, 2780291, 12226756, 11003669	Standard	NM_018948		Approved	MIG-6, GENE-33, RALT	uc001aoz.3	Q9UJM3	OTTHUMG00000001221	ENST00000377482.5:c.524_525delCT	chr1.hg19:g.8074134_8074135delAG	ENSP00000366702:p.Thr175fs	79.0	0.0	0		99.0	41.0	0.414141	NM_018948	B2RDX9|Q9NTG9|Q9UD05	Frame_Shift_Del	DEL	ENST00000377482.5	hg19	CCDS94.1																																																																																			.	.	.	none		0.48	ERRFI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003617.1	NM_018948		-	8074135	AG	-	8074134	7	5	81	1	0	1	0	1	0	0	0	0	5246	407	15	0	867	0	ERRFI1	1	8074134	Frame_Shift_Del	DEL	AG	TCGA-B1-A47M-01A-11D-A25F-10		8074134	241176487	1	5192											
KDM1A	23028	hgsc.bcm.edu	37	chr1	23383993	23383993	+	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	acaggatcgtgtgggtggacGagttgccacatttcgcaaag	10	9	14	8	3	0	0	0	0	0	0	2	3	0	2	1	3	1	2	1	3	1	2			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr1:23383993G>A	ENST00000356634.3	+	7	1096	c.947G>A	c.(946-948)cGa>cAa	p.R316Q	RP1-184J9.2_ENST00000427154.1_RNA|KDM1A_ENST00000542151.1_Missense_Mutation_p.R336Q|MIR4419A_ENST00000583845.1_RNA|KDM1A_ENST00000400181.4_Missense_Mutation_p.R336Q	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A	316	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						GTGGGTGGACGAGTTGCCACA	0.428																																					p.R336Q		Atlas-SNP	.											.	KDM1A	49	.	0			c.G1007A						PASS	.						206	194	198					1																	23383993		2203	4300	6503	SO:0001583	missense	23028	exon8			GTGGACGAGTTGC	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.947G>A	chr1.hg19:g.23383993G>A	ENSP00000349049:p.Arg316Gln	135.0	0.0	.		113.0	6.0	.	NM_001009999	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Missense_Mutation	SNP	ENST00000356634.3	hg19	CCDS30627.1	.	.	.	.	.	.	.	.	.	.	G	36	5.777153	0.96929	.	.	ENSG00000004487	ENST00000356634;ENST00000400181;ENST00000542151	D;D;D	0.97710	-4.5;-4.5;-4.5	5.48	5.48	0.80851	Amine oxidase (1);	0.000000	0.85682	D	0.000000	D	0.99196	0.9721	H	0.96269	3.795	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.984;0.991	D	0.99113	1.0847	10	0.87932	D	0	-9.5301	18.3409	0.90304	0.0:0.0:1.0:0.0	.	336;316	O60341-2;O60341	.;KDM1A_HUMAN	Q	316;336;336	ENSP00000349049:R316Q;ENSP00000383042:R336Q;ENSP00000439072:R336Q	ENSP00000349049:R316Q	R	+	2	0	KDM1A	23256580	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.634000	0.98435	2.572000	0.86782	0.585000	0.79938	CGA	.	.	.	none		0.428	KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013		A	23383993	G	A	23383993	3	1	81	1	0	0	0	0	1	0	0	0	8129	1058	37	1	1037	1	KDM1A	1	23383993	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	15309859	23383993	225866628	2	5193											
GNL2	29889	hgsc.bcm.edu	37	chr1	38042060	38042060	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgcaatgggagccacgttgCaaactttcttagaacgcaat	12	10	9	10	2	1	1	0	0	1	1	1	2	1	2	1	1	5	4	1	1	5	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr1:38042060C>T	ENST00000373062.3	-	9	1105	c.1007G>A	c.(1006-1008)tGc>tAc	p.C336Y		NM_013285.2	NP_037417.1	Q13823	NOG2_HUMAN	guanine nucleotide binding protein-like 2 (nucleolar)	336	CP-type G. {ECO:0000255|PROSITE- ProRule:PRU01058}.				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)				AGCCACGTTGCAAACTTTCTT	0.423																																					p.C336Y		Atlas-SNP	.											.	GNL2	58	.	0			c.G1007A						PASS	.						190	170	177					1																	38042060		2203	4300	6503	SO:0001583	missense	29889	exon9			ACGTTGCAAACTT	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.1007G>A	chr1.hg19:g.38042060C>T	ENSP00000362153:p.Cys336Tyr	91.0	0.0	.		69.0	24.0	.	NM_013285	Q9BWN7	Missense_Mutation	SNP	ENST00000373062.3	hg19	CCDS421.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	32|32	5.162979|5.162979	0.94727|0.94727	.|.	.|.	ENSG00000134697|ENSG00000134697	ENST00000538069|ENST00000373062;ENST00000545489	.|T	.|0.13538	.|2.58	6.14|6.14	6.14|6.14	0.99180|0.99180	.|GTP-binding domain, HSR1-related (1);	.|0.041714	.|0.85682	.|D	.|0.000000	T|T	0.55657|0.55657	0.1934|0.1934	H|H	0.96996|0.96996	3.92|3.92	0.80722|0.80722	D|D	1|1	.|D	.|0.65815	.|0.995	.|D	.|0.70016	.|0.967	T|T	0.69045|0.69045	-0.5249|-0.5249	5|10	.|0.87932	.|D	.|0	-7.4933|-7.4933	20.8597|20.8597	0.99761|0.99761	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|336	.|Q13823	.|NOG2_HUMAN	T|Y	188|336;177	.|ENSP00000362153:C336Y	.|ENSP00000362153:C336Y	A|C	-|-	1|2	0|0	GNL2|GNL2	37814647|37814647	1.000000|1.000000	0.71417|0.71417	0.865000|0.865000	0.33974|0.33974	0.986000|0.986000	0.74619|0.74619	7.786000|7.786000	0.85741|0.85741	2.937000|2.937000	0.99478|0.99478	0.650000|0.650000	0.86243|0.86243	GCA|TGC	.	.	.	none		0.423	GNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012478.1	NM_013285		T	38042060	C	T	38042060	3	4	81	1	0	0	0	0	1	0	0	0	6543	710	25	2	1220	2	GNL2	1	38042060	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	14658067	38042060	211208561	3	5194											
GLIS1	148979	hgsc.bcm.edu	37	chr1	53995548	53995548	+	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	cccgggtgctggcacaggtaCggcttctcgcccgtgtggct	3	9	15	14	4	1	0	0	0	1	0	2	0	1	0	2	5	2	5	2	5	1	2	rs549794466		TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr1:53995548C>T	ENST00000312233.2	-	4	1439	c.873G>A	c.(871-873)ccG>ccA	p.P291P		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						GGCACAGGTACGGCTTCTCGC	0.637																																					p.P291P		Atlas-SNP	.											.	GLIS1	52	.	0			c.G873A						PASS	.						72	74	74					1																	53995548		2203	4300	6503	SO:0001819	synonymous_variant	148979	exon4			CAGGTACGGCTTC	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.873G>A	chr1.hg19:g.53995548C>T		45.0	0.0	.		52.0	27.0	.	NM_147193		Silent	SNP	ENST00000312233.2	hg19	CCDS582.1																																																																																			.	.	.	none		0.637	GLIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022109.1	NM_147193		T	53995548	C	T	53995548	2	4	81	1	0	0	0	0	0	0	0	1	6452	523	19	1		1	GLIS1	1	53995548	Silent	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	15953488	53995548	195255073	4	5195											
SAMD13	148418	hgsc.bcm.edu	37	chr1	84768963	84768963	+	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	aggaaaatggctctgtcggtGtaaaaaagtaagtgaagctg	15	9	13	4	1	1	1	0	1	1	0	2	2	1	2	0	3	1	4	0	3	7	2	rs556493054		TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr1:84768963G>T	ENST00000370671.3	+	2	165	c.106G>T	c.(106-108)Gta>Tta	p.V36L	SAMD13_ENST00000394834.3_Missense_Mutation_p.V16L|SAMD13_ENST00000370669.1_Missense_Mutation_p.V16L|SAMD13_ENST00000370668.3_Missense_Mutation_p.V16L|SAMD13_ENST00000370670.2_Missense_Mutation_p.V16L|SAMD13_ENST00000370673.3_Missense_Mutation_p.V30L			Q5VXD3	SAM13_HUMAN	sterile alpha motif domain containing 13	36										lung(4)	4				all cancers(265;0.00667)|Epithelial(280;0.0219)|OV - Ovarian serous cystadenocarcinoma(397;0.136)		CTCTGTCGGTGTAAAAAAGTA	0.408																																					p.V30L		Atlas-SNP	.											.	SAMD13	5	.	0			c.G88T						PASS	.						72	65	67					1																	84768963		2203	4300	6503	SO:0001583	missense	148418	exon2			GTCGGTGTAAAAA		CCDS30760.1, CCDS44166.1	1p31.1	2013-01-10			ENSG00000203943	ENSG00000203943		"Sterile alpha motif (SAM) domain containing"	24582	protein-coding gene	gene with protein product							Standard	NM_001010971		Approved		uc001djr.3	Q5VXD3	OTTHUMG00000009859	ENST00000370671.3:c.106G>T	chr1.hg19:g.84768963G>T	ENSP00000359705:p.Val36Leu	69.0	0.0	.		53.0	22.0	.	NM_001010971	B3KPW8|D3DT11|Q53AI4|Q5VXD2|Q5VXD4	Missense_Mutation	SNP	ENST00000370671.3	hg19		.	.	.	.	.	.	.	.	.	.	G	10.75	1.439172	0.25900	.	.	ENSG00000203943	ENST00000370673;ENST00000370671;ENST00000394834;ENST00000370669;ENST00000370668;ENST00000370670	.	.	.	5.34	5.34	0.76211	.	0.391477	0.25631	N	0.029344	T	0.18130	0.0435	N	0.24115	0.695	0.80722	D	1	B;B	0.32101	0.032;0.356	B;B	0.27608	0.023;0.081	T	0.06516	-1.0822	9	0.13470	T	0.59	-11.7208	10.4571	0.44557	0.0893:0.0:0.9107:0.0	.	36;30	Q5VXD3;Q5VXD3-2	SAM13_HUMAN;.	L	30;36;16;16;16;16	.	ENSP00000359702:V16L	V	+	1	0	SAMD13	84541551	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.486000	0.60286	2.657000	0.90304	0.655000	0.94253	GTA	.	.	.	none		0.408	SAMD13-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000027243.1	NM_001010971		T	84768963	G	T	84768963	3	4	81	1	0	0	0	0	1	0	0	0	13831	1377	48	4	94	4	SAMD13	1	84768963	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	30773415	84768963	164481658	5	5196											
CD58	965	hgsc.bcm.edu	37	chr1	117078689	117078689	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggaagatcattttccatctTaaaatatatactggttgagt	13	16	7	5	0	2	2	1	1	1	1	3	3	3	3	1	2	1	1	1	2	6	7			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr1:117078689T>C	ENST00000369489.5	-	3	592	c.526A>G	c.(526-528)Aag>Gag	p.K176E	CD58_ENST00000369487.3_Missense_Mutation_p.K176E|CD58_ENST00000457047.2_Missense_Mutation_p.K176E	NM_001779.2	NP_001770.1	P19256	LFA3_HUMAN	CD58 molecule	176					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)		TTTTCCATCTTAAAATATATA	0.353																																					p.K176E		Atlas-SNP	.											.	CD58	40	.	0			c.A526G						PASS	.						115	111	112					1																	117078689		2203	4300	6503	SO:0001583	missense	965	exon3			CCATCTTAAAATA	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.526A>G	chr1.hg19:g.117078689T>C	ENSP00000358501:p.Lys176Glu	56.0	0.0	.		48.0	16.0	.	NM_001144822	A8K7G5|Q5U053|Q6IB65|Q96KI9	Missense_Mutation	SNP	ENST00000369489.5	hg19	CCDS888.1	.	.	.	.	.	.	.	.	.	.	T	12.10	1.835666	0.32421	.	.	ENSG00000116815	ENST00000369489;ENST00000457047;ENST00000369487	T;T;T	0.41758	0.99;0.99;1.02	3.59	-6.97	0.01616	.	9.277070	0.00166	N	0.000001	T	0.07818	0.0196	L	0.29908	0.895	0.09310	N	1	P;B;P	0.50528	0.936;0.4;0.936	P;B;P	0.45167	0.472;0.118;0.472	T	0.41698	-0.9494	10	0.02654	T	1	.	2.2982	0.04155	0.1357:0.3744:0.2766:0.2133	.	176;176;176	P19256-3;B1AMW1;P19256	.;.;LFA3_HUMAN	E	176	ENSP00000358501:K176E;ENSP00000409080:K176E;ENSP00000358499:K176E	ENSP00000358499:K176E	K	-	1	0	CD58	116880212	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.440000	0.06888	-1.664000	0.01479	-0.290000	0.09829	AAG	.	.	.	none		0.353	CD58-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059036.1	NM_001779		C	117078689	T	C	117078689	3	2	81	1	0	0	0	0	1	0	0	0	3027	1763	61	3	246	3	CD58	1	117078689	Missense_Mutation	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10	32309726	117078689	132171932	6	5197											
POGZ	23126	hgsc.bcm.edu	37	chr1	151381040	151381040	+	Silent	SNP	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	acagttcgtggctgccctcgGgaagcccggattgtcacctg	6	9	13	13	3	1	0	1	0	0	0	3	2	1	2	3	3	2	2	3	3	1	2			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr1:151381040G>A	ENST00000271715.2	-	14	2393	c.2079C>T	c.(2077-2079)tcC>tcT	p.S693S	POGZ_ENST00000392723.1_Silent_p.S640S|POGZ_ENST00000368863.2_Silent_p.S598S|POGZ_ENST00000409503.1_Silent_p.S684S|POGZ_ENST00000361398.3_Silent_p.S640S|POGZ_ENST00000491586.1_Silent_p.S649S|POGZ_ENST00000540984.1_Silent_p.S55S|POGZ_ENST00000531094.1_Silent_p.S631S	NM_001194937.1|NM_015100.3	NP_001181866.1|NP_055915.2	Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain	693					kinetochore assembly (GO:0051382)|mitotic sister chromatid cohesion (GO:0007064)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(10)|kidney(3)|large_intestine(10)|liver(2)|lung(11)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	47	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			GCTGCCCTCGGGAAGCCCGGA	0.532																																					p.S693S		Atlas-SNP	.											.	POGZ	211	.	0			c.C2079T						PASS	.						90	99	96					1																	151381040		2203	4300	6503	SO:0001819	synonymous_variant	23126	exon14			CCCTCGGGAAGCC	AB007930	CCDS997.1, CCDS998.1, CCDS44222.1, CCDS44222.2, CCDS53365.1, CCDS53366.1	1q21.1	2013-07-22			ENSG00000143442	ENSG00000143442			18801	protein-coding gene	gene with protein product	"zinc finger protein 280E", "putative protein product of Nbla00003"	614787				10976766	Standard	NM_015100		Approved	KIAA0461, ZNF635m, ZNF280E	uc001eyd.2	Q7Z3K3	OTTHUMG00000012499	ENST00000271715.2:c.2079C>T	chr1.hg19:g.151381040G>A		75.0	0.0	.		48.0	17.0	.	NM_015100	B4DTP8|B4DYL9|B7ZBY5|E9PM80|O75049|Q3LIC4|Q5SZS1|Q5SZS2|Q5SZS3|Q5SZS4|Q8TDZ7|Q9Y4X7	Silent	SNP	ENST00000271715.2	hg19	CCDS997.1																																																																																			.	.	.	none		0.532	POGZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034915.2	NM_207171		A	151381040	G	A	151381040	2	1	81	1	0	0	0	0	0	0	0	1	12193	1219	43	2		2	POGZ	1	151381040	Silent	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	34302351	151381040	97869581	7	5198											
VHLL	391104	hgsc.bcm.edu	37	chr1	156268771	156268771	+	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	agcttgccatagtagttgagCcacacaggcagcacgattcg	11	8	11	11	2	0	1	0	1	0	0	1	2	0	1	2	1	4	5	2	1	2	5			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr1:156268771C>T	ENST00000339922.3	-	1	657	c.210G>A	c.(208-210)tgG>tgA	p.W70*		NM_001004319.2	NP_001004319.1	Q6RSH7	VHLL_HUMAN	von Hippel-Lindau tumor suppressor-like	70	Beta-domain.									endometrium(1)|lung(2)|ovary(1)	4	Hepatocellular(266;0.158)					AGTAGTTGAGCCACACAGGCA	0.597																																					p.W70X		Atlas-SNP	.											.	VHLL	12	.	0			c.G210A						PASS	.						84	75	78					1																	156268771		2203	4300	6503	SO:0001587	stop_gained	391104	exon1			GTTGAGCCACACA			1q22	2013-09-24			ENSG00000189030	ENSG00000189030			30666	protein-coding gene	gene with protein product			"VHL pseudogene"	VHLP		14757845	Standard	NM_001004319		Approved	VLP	uc001fok.3	Q6RSH7	OTTHUMG00000024058	ENST00000339922.3:c.210G>A	chr1.hg19:g.156268771C>T	ENSP00000464258:p.Trp70*	98.0	0.0	.		63.0	17.0	.	NM_001004319	A1L4M4	Nonsense_Mutation	SNP	ENST00000339922.3	hg19																																																																																				.	.	.	none		0.597	VHLL-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000060590.3	NM_001004319		T	156268771	C	T	156268771	4	4	81	1	0	0	0	0	0	1	0	0	17175	740	26	2	213	2	VHLL	1	156268771	Nonsense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	4887731	156268771	92981850	8	5199											
KLHL12	59349	hgsc.bcm.edu	37	chr1	202866048	202866048	+	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	acatcaatgggagactgctgGcttccaaagcccccaaccac	12	6	8	15	0	1	1	1	0	0	1	2	2	2	1	4	2	3	2	4	2	3	1			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr1:202866048G>A	ENST00000367261.3	-	7	1091	c.873C>T	c.(871-873)agC>agT	p.S291S	KLHL12_ENST00000367259.1_Silent_p.S24S|KLHL12_ENST00000435533.3_Silent_p.S329S	NM_021633.2	NP_067646.1	Q53G59	KLH12_HUMAN	kelch-like family member 12	291					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)			GAGACTGCTGGCTTCCAAAGC	0.473																																					p.S291S		Atlas-SNP	.											.	KLHL12	50	.	0			c.C873T						PASS	.						201	210	207					1																	202866048		2203	4300	6503	SO:0001819	synonymous_variant	59349	exon7			CTGCTGGCTTCCA	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.873C>T	chr1.hg19:g.202866048G>A		106.0	0.0	.		116.0	47.0	.	NM_021633	A6NEN8|B7Z7B8|Q9HBX5	Silent	SNP	ENST00000367261.3	hg19	CCDS1429.1																																																																																			.	.	.	none		0.473	KLHL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099151.1	NM_021633		A	202866048	G	A	202866048	2	1	81	1	0	0	0	0	0	0	0	1	8375	1194	42	2		2	KLHL12	1	202866048	Silent	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	46597277	202866048	46384573	9	5200											
C4BPB	725	hgsc.bcm.edu	37	chr1	207271520	207271520	+	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	acttagtgggcgtgcaggagCagcaatgcgttgatggggag	9	8	18	6	2	0	1	0	1	0	0	0	3	0	3	0	4	4	4	0	4	2	2			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr1:207271520C>A	ENST00000243611.5	+	5	823	c.529C>A	c.(529-531)Cag>Aag	p.Q177K	C4BPB_ENST00000367076.3_Missense_Mutation_p.Q176K|C4BPB_ENST00000391923.1_Missense_Mutation_p.Q177K|C4BPB_ENST00000367078.3_Missense_Mutation_p.Q177K|C4BPB_ENST00000470767.1_3'UTR	NM_000716.3	NP_000707.1	P20851	C4BPB_HUMAN	complement component 4 binding protein, beta	177	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation (GO:0007596)|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)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)				breast(2)|lung(1)|ovary(1)	4						CGTGCAGGAGCAGCAATGCGT	0.478																																					p.Q177K		Atlas-SNP	.											.	C4BPB	19	.	0			c.C529A						PASS	.						167	146	153					1																	207271520		2203	4300	6503	SO:0001583	missense	725	exon6			CAGGAGCAGCAAT	L11245	CCDS1476.1, CCDS31005.1	1q32	2008-07-18	2001-11-28		ENSG00000123843	ENSG00000123843			1328	protein-coding gene	gene with protein product	"complement component 4 binding protein, beta chain", "C4b binding protein, beta chain"	120831	"complement component 4-binding protein, beta"	C4BP		2300577, 8325877	Standard	XM_005273255		Approved		uc001hfj.3	P20851	OTTHUMG00000036035	ENST00000243611.5:c.529C>A	chr1.hg19:g.207271520C>A	ENSP00000243611:p.Gln177Lys	102.0	0.0	.		78.0	26.0	.	NM_001017365	A5JYP8|D3DT81|Q5VVR0|Q9BS25	Missense_Mutation	SNP	ENST00000243611.5	hg19	CCDS1476.1	.	.	.	.	.	.	.	.	.	.	C	11.86	1.763769	0.31228	.	.	ENSG00000123843	ENST00000367078;ENST00000452902;ENST00000243611;ENST00000367076;ENST00000391923	T;T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09;-0.09	5.0	3.07	0.35406	Complement control module (2);Sushi/SCR/CCP (3);	0.511839	0.16242	N	0.223086	T	0.60353	0.2262	M	0.62723	1.935	0.09310	N	0.999992	P;P	0.52170	0.951;0.939	P;P	0.52710	0.707;0.583	T	0.53788	-0.8389	10	0.02654	T	1	-3.3863	7.1729	0.25728	0.0:0.7347:0.1719:0.0935	.	177;176	P20851;P20851-2	C4BPB_HUMAN;.	K	177;177;177;176;177	ENSP00000356045:Q177K;ENSP00000392237:Q177K;ENSP00000243611:Q177K;ENSP00000356043:Q176K;ENSP00000375790:Q177K	ENSP00000243611:Q177K	Q	+	1	0	C4BPB	205338143	0.017000	0.18338	0.006000	0.13384	0.024000	0.10985	1.187000	0.32090	1.317000	0.45149	0.655000	0.94253	CAG	.	.	.	none		0.478	C4BPB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087847.2	NM_000716		A	207271520	C	A	207271520	3	1	81	1	0	0	0	0	1	0	0	0	2252	711	25	4	547	4	C4BPB	1	207271520	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	4405472	207271520	41979101	10	5201											
RPS6KC1	26750	hgsc.bcm.edu	37	chr1	213251150	213251150	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcctccatttgctaaaggaaTagtgtttggtaagtgattat	11	16	9	5	0	0	1	0	1	0	0	2	2	2	2	2	2	1	3	2	2	6	6			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr1:213251150T>C	ENST00000366960.3	+	3	404	c.254T>C	c.(253-255)aTa>aCa	p.I85T	RPS6KC1_ENST00000490299.1_3'UTR|RPS6KC1_ENST00000543470.1_5'UTR|RPS6KC1_ENST00000543354.1_5'UTR|RPS6KC1_ENST00000366959.3_Missense_Mutation_p.I73T	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	85	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				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)		GCTAAAGGAATAGTGTTTGGT	0.279																																					p.I85T		Atlas-SNP	.											.	RPS6KC1	114	.	0			c.T254C						PASS	.						77	74	75					1																	213251150		2202	4294	6496	SO:0001583	missense	26750	exon3			AAGGAATAGTGTT	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.254T>C	chr1.hg19:g.213251150T>C	ENSP00000355927:p.Ile85Thr	129.0	0.0	.		84.0	44.0	.	NM_012424	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Missense_Mutation	SNP	ENST00000366960.3	hg19	CCDS1513.1	.	.	.	.	.	.	.	.	.	.	T	1.213	-0.629208	0.03610	.	.	ENSG00000136643	ENST00000366960;ENST00000366959	T;T	0.38887	1.11;1.11	5.4	0.0644	0.14353	Phox homologous domain (5);	0.247652	0.39909	N	0.001239	T	0.15349	0.0370	N	0.10760	0.04	0.80722	D	1	B;B	0.09022	0.002;0.002	B;B	0.16722	0.016;0.016	T	0.32929	-0.9888	10	0.02654	T	1	1.7807	5.8179	0.18506	0.5179:0.0738:0.0:0.4083	.	85;73	Q96S38;B1APS8	KS6C1_HUMAN;.	T	85;73	ENSP00000355927:I85T;ENSP00000355926:I73T	ENSP00000355926:I73T	I	+	2	0	RPS6KC1	211317773	1.000000	0.71417	0.979000	0.43373	0.998000	0.95712	1.559000	0.36320	-0.258000	0.09446	0.533000	0.62120	ATA	.	.	.	none		0.279	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3	NM_012424		C	213251150	T	C	213251150	3	2	81	1	0	0	0	0	1	0	0	0	13671	1406	49	3	264	3	RPS6KC1	1	213251150	Missense_Mutation	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10	5979630	213251150	35999471	11	5202											
TLR5	7100	hgsc.bcm.edu	37	chr1	223286361	223286361	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cactcctaggagaaggtccaGgtggtctcccatgatcctat	9	10	10	12	0	1	2	0	1	1	1	5	3	4	2	4	4	0	0	4	4	3	2			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr1:223286361G>A	ENST00000540964.1	-	4	474	c.13C>T	c.(13-15)Ctg>Ttg	p.L5L	TLR5_ENST00000342210.6_Silent_p.L5L			O60602	TLR5_HUMAN	toll-like receptor 5	5					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)		AGAAGGTCCAGGTGGTCTCCC	0.498																																					p.L5L		Atlas-SNP	.											.	TLR5	86	.	0			c.C13T						PASS	.						37	38	38					1																	223286361		2203	4298	6501	SO:0001819	synonymous_variant	7100	exon6			GGTCCAGGTGGTC		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.13C>T	chr1.hg19:g.223286361G>A		210.0	0.0	.		154.0	57.0	.	NM_003268	B1AZ05|B3Y633|B9VJ63|D1CS80|D3DTB8|O15456|Q32MI2|Q32MI3	Silent	SNP	ENST00000540964.1	hg19	CCDS31033.1																																																																																			.	.	.	none		0.498	TLR5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003268		A	223286361	G	A	223286361	2	1	81	1	0	0	0	0	0	0	0	1	15966	991	35	2		2	TLR5	1	223286361	Silent	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	10035211	223286361	25964260	12	5203											
TRIB2	28951	hgsc.bcm.edu	37	chr2	12858616	12858616	+	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	tcgcattgcgtttcttgtatCgggaaatacttattgttgga	8	17	10	6	3	1	0	0	0	1	0	3	2	1	2	0	2	2	4	0	2	4	8			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr2:12858616C>A	ENST00000405331.3	+	1	253	c.183C>A	c.(181-183)atC>atA	p.I61I	RP11-333O1.1_ENST00000569860.1_lincRNA|TRIB2_ENST00000155926.4_Silent_p.I61I|TRIB2_ENST00000381465.2_Intron					tribbles pseudokinase 2											breast(1)|cervix(1)|endometrium(1)|large_intestine(8)|lung(5)|prostate(1)|skin(1)|stomach(1)	19	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					TTTCTTGTATCGGGAAATACT	0.577											OREG0014450	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I61I		Atlas-SNP	.											.	TRIB2	61	.	0			c.C183A						PASS	.						74	78	76					2																	12858616		2203	4300	6503	SO:0001819	synonymous_variant	28951	exon1			TTGTATCGGGAAA	AY245544	CCDS1683.1	2p25.1	2013-10-03	2013-10-03		ENSG00000071575	ENSG00000071575			30809	protein-coding gene	gene with protein product		609462	"tribbles homolog 2 (Drosophila)"			12736262, 17097562, 16715410	Standard	NM_021643		Approved	TRB2, GS3955	uc002rbv.4	Q92519	OTTHUMG00000090575	ENST00000405331.3:c.183C>A	chr2.hg19:g.12858616C>A		97.0	0.0	.	683	73.0	29.0	.	NM_021643		Silent	SNP	ENST00000405331.3	hg19																																																																																				.	.	.	none		0.577	TRIB2-004	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000323585.1	NM_021643		A	12858616	C	A	12858616	2	1	81	1	0	0	0	0	0	0	0	1	16495	874	31	4		4	TRIB2	2	12858616	Silent	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10		12858616	230340757	13	5204											
IL1RL2	8808	hgsc.bcm.edu	37	chr2	102805602	102805602	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccagccttttgcttttaattGtacattccctcccataacat	9	16	3	13	0	0	0	0	0	0	0	2	0	2	0	4	0	4	2	4	0	3	8			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr2:102805602G>A	ENST00000264257.2	+	3	251	c.125G>A	c.(124-126)tGt>tAt	p.C42Y	IL1RL2_ENST00000441515.2_Intron|IL1RL2_ENST00000481806.1_Intron|IL1RL2_ENST00000539491.1_Missense_Mutation_p.C42Y	NM_003854.2	NP_003845.2	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2	42	Ig-like C2-type 1.				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						GCTTTTAATTGTACATTCCCT	0.358																																					p.C42Y		Atlas-SNP	.											.	IL1RL2	118	.	0			c.G125A						PASS	.						90	89	89					2																	102805602		2203	4300	6503	SO:0001583	missense	8808	exon3			TTAATTGTACATT	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.125G>A	chr2.hg19:g.102805602G>A	ENSP00000264257:p.Cys42Tyr	38.0	0.0	.		49.0	18.0	.	NM_003854	A4FU63|Q13525|Q45H74|Q53TU8|Q587I8	Missense_Mutation	SNP	ENST00000264257.2	hg19	CCDS2056.1	.	.	.	.	.	.	.	.	.	.	G	18.68	3.676325	0.67928	.	.	ENSG00000115598	ENST00000264257;ENST00000421464;ENST00000539491	D;D;D	0.94537	-3.45;-3.45;-3.45	5.86	4.94	0.65067	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.274660	0.40908	D	0.000981	D	0.96448	0.8841	M	0.78637	2.42	0.45867	D	0.998726	D	0.55800	0.973	P	0.62560	0.904	D	0.95878	0.8896	10	0.59425	D	0.04	.	13.5643	0.61807	0.0:0.1562:0.8438:0.0	.	42	Q9HB29	ILRL2_HUMAN	Y	42	ENSP00000264257:C42Y;ENSP00000387611:C42Y;ENSP00000442184:C42Y	ENSP00000264257:C42Y	C	+	2	0	IL1RL2	102172034	0.992000	0.36948	0.966000	0.40874	0.967000	0.64934	3.468000	0.53086	2.937000	0.99478	0.650000	0.86243	TGT	.	.	.	none		0.358	IL1RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253290.1	NM_003854		A	102805602	G	A	102805602	3	1	81	1	0	0	0	0	1	0	0	0	7671	1377	48	2	131	2	IL1RL2	2	102805602	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	89946986	102805602	140393771	14	5205											
R3HDM1	23518	hgsc.bcm.edu	37	chr2	136393707	136393707	+	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	aagcaaatctatagaagaaaGagaagaagagtaccagagag	22	4	11	4	0	1	6	0	0	1	6	1	8	1	6	1	0	2	2	1	0	9	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr2:136393707G>T	ENST00000264160.4	+	11	1227	c.857G>T	c.(856-858)aGa>aTa	p.R286I	R3HDM1_ENST00000409478.1_Missense_Mutation_p.R242I|R3HDM1_ENST00000329971.3_Missense_Mutation_p.R242I|R3HDM1_ENST00000409606.1_Missense_Mutation_p.R286I|R3HDM1_ENST00000410054.1_Missense_Mutation_p.R230I	NM_001282798.1|NM_015361.2	NP_001269727.1|NP_056176.2	Q15032	R3HD1_HUMAN	R3H domain containing 1	286	SUZ. {ECO:0000255|PROSITE- ProRule:PRU01009}.						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)		ATAGAAGAAAGAGAAGAAGAG	0.343																																					p.R286I		Atlas-SNP	.											.	R3HDM1	84	.	0			c.G857T						PASS	.						150	164	159					2																	136393707		2203	4300	6503	SO:0001583	missense	23518	exon11			AAGAAAGAGAAGA	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.857G>T	chr2.hg19:g.136393707G>T	ENSP00000264160:p.Arg286Ile	141.0	0.0	.		84.0	26.0	.	NM_015361	A8K1V0|B3KXQ9|E9PBB4|E9PG42|G5E9G8|Q8IW32	Missense_Mutation	SNP	ENST00000264160.4	hg19	CCDS2177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.2|24.2	4.500931|4.500931	0.85176|0.85176	.|.	.|.	ENSG00000048991|ENSG00000048991	ENST00000456040|ENST00000422577;ENST00000409478;ENST00000264160;ENST00000329971;ENST00000410054;ENST00000409606	.|D;D;D;D;D	.|0.82526	.|-1.62;-1.62;-1.62;-1.62;-1.62	5.58|5.58	4.7|4.7	0.59300|0.59300	.|SUZ domain (1);	.|0.151795	.|0.64402	.|D	.|0.000020	.|D	.|0.90745	.|0.7095	M|M	0.79475|0.79475	2.455|2.455	0.48395|0.48395	D|D	0.999647|0.999647	.|D;D;D;D	.|0.89917	.|1.0;1.0;0.999;1.0	.|D;D;D;D	.|0.91635	.|0.997;0.999;0.998;0.999	.|D	.|0.92028	.|0.5631	.|10	.|0.87932	.|D	.|0	-12.4326|-12.4326	15.055|15.055	0.71908|0.71908	0.0685:0.0:0.9315:0.0|0.0685:0.0:0.9315:0.0	.|.	.|242;286;230;286	.|G5E9G8;E9PBB4;E9PG42;Q15032	.|.;.;.;R3HD1_HUMAN	X|I	269|242;242;286;242;230;286	.|ENSP00000386457:R242I;ENSP00000264160:R286I;ENSP00000331396:R242I;ENSP00000386877:R230I;ENSP00000387010:R286I	.|ENSP00000264160:R286I	E|R	+|+	1|2	0|0	R3HDM1|R3HDM1	136110177|136110177	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.821000|0.821000	0.46438|0.46438	7.981000|7.981000	0.88123|0.88123	1.501000|1.501000	0.48654|0.48654	-0.126000|-0.126000	0.14955|0.14955	GAG|AGA	.	.	.	none		0.343	R3HDM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254659.1	NM_015361		T	136393707	G	T	136393707	3	4	81	1	0	0	0	0	1	0	0	0	12900	942	33	4	891	4	R3HDM1	2	136393707	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	33588105	136393707	106805666	15	5206											
SCN1A	6323	hgsc.bcm.edu	37	chr2	166848746	166848746	+	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	agatggcgtagatgaacatgActaggaagagtaggaggccg	14	6	16	5	2	0	5	0	2	0	3	0	7	0	7	1	4	1	2	1	4	5	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr2:166848746A>T	ENST00000303395.4	-	26	5038	c.5039T>A	c.(5038-5040)gTc>gAc	p.V1680D	SCN1A_ENST00000409050.1_Missense_Mutation_p.V1652D|AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000375405.3_Missense_Mutation_p.V1669D|AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000423058.2_Missense_Mutation_p.V1680D			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1680					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)	GATGAACATGACTAGGAAGAG	0.478																																					p.V1680D		Atlas-SNP	.											.	SCN1A	641	.	0			c.T5039A						PASS	.						178	164	169					2																	166848746		2203	4300	6503	SO:0001583	missense	6323	exon26			AACATGACTAGGA	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.5039T>A	chr2.hg19:g.166848746A>T	ENSP00000303540:p.Val1680Asp	314.0	0.0	.		268.0	89.0	.	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	hg19	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.331387	0.81690	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.98926	-5.24;-5.24;-5.24;-5.24	5.41	5.41	0.78517	.	0.000000	0.53938	D	0.000051	D	0.99423	0.9796	H	0.96015	3.755	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98389	1.0562	10	0.87932	D	0	.	15.4593	0.75342	1.0:0.0:0.0:0.0	.	1669	P35498-2	.	D	1680;1680;1669;1652	ENSP00000407030:V1680D;ENSP00000303540:V1680D;ENSP00000364554:V1669D;ENSP00000386312:V1652D	ENSP00000303540:V1680D	V	-	2	0	SCN1A	166556992	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.106000	0.94253	2.049000	0.60858	0.528000	0.53228	GTC	.	.	.	none		0.478	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		T	166848746	A	T	166848746	3	4	81	1	0	0	0	0	1	0	0	0	13927	275	10	5	994	5	SCN1A	2	166848746	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	30455039	166848746	76350627	16	5207											
NFE2L2	4780	hgsc.bcm.edu	37	chr2	178098806	178098806	+	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	gaattgggagaaattcacctGtctcttcatctagttgtaac	11	14	8	8	0	4	1	2	0	2	1	5	3	4	1	1	1	1	2	1	1	4	6			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr2:178098806G>T	ENST00000397062.3	-	2	793	c.239C>A	c.(238-240)aCa>aAa	p.T80K	NFE2L2_ENST00000423513.1_Missense_Mutation_p.T64K|NFE2L2_ENST00000446151.2_Missense_Mutation_p.T64K|NFE2L2_ENST00000464747.1_Missense_Mutation_p.T64K|NFE2L2_ENST00000397063.4_Missense_Mutation_p.T64K	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	80					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T80K(3)|p.T80R(2)|p.T80I(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			AAATTCACCTGTCTCTTCATC	0.443			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.T80K		Atlas-SNP	.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	NFE2L2,NS,carcinoma,0,8	NFE2L2	225	.	6	Substitution - Missense(6)	lung(2)|oesophagus(2)|upper_aerodigestive_tract(1)|endometrium(1)	c.C239A						PASS	.						146	145	145					2																	178098806		1901	4109	6010	SO:0001583	missense	4780	exon2			TCACCTGTCTCTT		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.239C>A	chr2.hg19:g.178098806G>T	ENSP00000380252:p.Thr80Lys	63.0	0.0	.		65.0	20.0	.	NM_006164	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	hg19	CCDS42782.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.264788	0.80358	.	.	ENSG00000116044	ENST00000397063;ENST00000397062;ENST00000446151;ENST00000449627;ENST00000448782;ENST00000421929;ENST00000423513	T;T;T;T;T;T;T	0.32988	1.43;1.43;1.43;1.43;1.43;1.43;1.43	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.64327	0.2588	M	0.87180	2.865	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.91635	0.997;0.994;0.999;0.997	T	0.69087	-0.5238	10	0.87932	D	0	.	19.9976	0.97389	0.0:0.0:1.0:0.0	.	64;64;64;80	E9PGJ7;B4DNB0;C9JFL6;Q16236	.;.;.;NF2L2_HUMAN	K	64;80;64;64;64;64;64	ENSP00000380253:T64K;ENSP00000380252:T80K;ENSP00000411575:T64K;ENSP00000391590:T64K;ENSP00000400073:T64K;ENSP00000412191:T64K;ENSP00000410015:T64K	ENSP00000380252:T80K	T	-	2	0	NFE2L2	177807052	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.229000	0.95273	2.737000	0.93849	0.563000	0.77884	ACA	.	.	.	none		0.443	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		T	178098806	G	T	178098806	3	4	81	1	0	0	0	0	1	0	0	0	10375	1377	48	4	1594	4	NFE2L2	2	178098806	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	11250060	178098806	65100567	17	5208											
FAM117B	150864	hgsc.bcm.edu	37	chr2	203560690	203560690	+	Frame_Shift_Del	DEL	G	G	-																															ctcttgctgcaccgtatcttGctggacactggcctcgggat																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr2:203560690delG	ENST00000392238.2	+	2	688	c.688delG	c.(688-690)gctfs	p.A230fs	FAM117B_ENST00000303116.6_5'UTR			Q6P1L5	F117B_HUMAN	family with sequence similarity 117, member B	230										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)	17						ACCGTATCTTGCTGGACACTG	0.483																																					p.L229fs		Atlas-Indel,Pindel	.											.	FAM117B	73	.	0			c.687delT						PASS	.						86	75	79					2																	203560690		2203	4300	6503	SO:0001589	frameshift_variant	150864	exon2			.	AB053315	CCDS33362.1, CCDS33362.2	2q33	2008-08-18	2008-08-18	2008-08-18	ENSG00000138439	ENSG00000138439			14440	protein-coding gene	gene with protein product			"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13"	ALS2CR13		11586298	Standard	NM_173511		Approved	FLJ38771	uc010zhx.2	Q6P1L5	OTTHUMG00000154550	ENST00000392238.2:c.688delG	chr2.hg19:g.203560690delG	ENSP00000376071:p.Ala230fs	87.0	0.0	0		92.0	32.0	0.347826	NM_173511	Q53QZ5|Q585T9|Q8N8W1|Q96Q34	Frame_Shift_Del	DEL	ENST00000392238.2	hg19	CCDS33362.2																																																																																			.	.	.	none		0.483	FAM117B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335888.3	NM_173511		-	203560690	G	-	203560690	7	5	81	1	0	1	0	1	0	0	0	0	5414	1319	46	0	694	0	FAM117B	2	203560690	Frame_Shift_Del	DEL	G	TCGA-B1-A47M-01A-11D-A25F-10	25461884	203560690	39638683	18	5209											
CHPF	79586	hgsc.bcm.edu	37	chr2	220404816	220404816	+	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	agcagggtcagggctgccgcAgcatcaccaggctccagtgc	8	5	14	14	1	2	0	2	0	0	0	3	0	3	0	3	3	4	5	3	3	0	0			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr2:220404816A>T	ENST00000243776.6	-	4	1865	c.1617T>A	c.(1615-1617)gcT>gcA	p.A539A	CHPF_ENST00000535926.1_Silent_p.A377A	NM_024536.5	NP_078812	Q8IZ52	CHSS2_HUMAN	chondroitin polymerizing factor	539	Ala-rich.				carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	21		Renal(207;0.0183)		Epithelial(149;3.02e-08)|all cancers(144;3.41e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		GGGCTGCCGCAGCATCACCAG	0.657																																					p.A539A		Atlas-SNP	.											.	CHPF	56	.	0			c.T1617A						PASS	.						15	15	15					2																	220404816		2197	4292	6489	SO:0001819	synonymous_variant	79586	exon4			TGCCGCAGCATCA	BC008878	CCDS2443.1, CCDS56169.1	2q35	2014-02-12			ENSG00000123989	ENSG00000123989	2.4.1.175, 2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	24291	protein-coding gene	gene with protein product	"chondroitin sulfate synthase 2"	610405				11230166, 12716890	Standard	NM_024536		Approved	CSS2, CHSY2	uc002vmc.4	Q8IZ52	OTTHUMG00000058929	ENST00000243776.6:c.1617T>A	chr2.hg19:g.220404816A>T		51.0	0.0	.		18.0	9.0	.	NM_024536	B4DXU0|Q6UXD6|Q7L4G1|Q9H0F8|Q9H618	Silent	SNP	ENST00000243776.6	hg19	CCDS2443.1																																																																																			.	.	.	none		0.657	CHPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130268.1	NM_024536		T	220404816	A	T	220404816	2	4	81	1	0	0	0	0	0	0	0	1	3370	175	7	5		5	CHPF	2	220404816	Silent	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	16844126	220404816	22794557	19	5210											
COL6A3	1293	hgsc.bcm.edu	37	chr2	238259816	238259816	+	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	tgcctcgttctccaggagcaCcagcggcacctccgcttccc	5	8	9	19	3	1	0	0	0	1	0	5	1	3	1	6	2	3	4	6	2	0	2			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr2:238259816C>G	ENST00000295550.4	-	27	7225	c.6773G>C	c.(6772-6774)gGt>gCt	p.G2258A	COL6A3_ENST00000472056.1_Missense_Mutation_p.G1651A|COL6A3_ENST00000409809.1_Missense_Mutation_p.G2052A|COL6A3_ENST00000353578.4_Missense_Mutation_p.G2052A|COL6A3_ENST00000346358.4_Missense_Mutation_p.G2058A|COL6A3_ENST00000347401.3_Missense_Mutation_p.G2057A	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2258	Collagen-like 4.|Triple-helical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TCCAGGAGCACCAGCGGCACC	0.572																																					p.G2258A		Atlas-SNP	.											.	COL6A3	608	.	0			c.G6773C						PASS	.						102	83	89					2																	238259816		2203	4300	6503	SO:0001583	missense	1293	exon27			GGAGCACCAGCGG	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.6773G>C	chr2.hg19:g.238259816C>G	ENSP00000295550:p.Gly2258Ala	90.0	0.0	.		93.0	28.0	.	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	11.17	1.558422	0.27827	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.97850	-4.16;-4.16;-4.57;-4.16;-4.57;-4.16	5.42	5.42	0.78866	.	0.000000	0.56097	D	0.000040	D	0.99372	0.9779	H	0.99238	4.48	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.91635	0.998;0.997;0.999;0.998	D	0.98306	1.0521	10	0.87932	D	0	.	17.4191	0.87510	0.0:1.0:0.0:0.0	.	1651;1651;2052;2258	E9PFQ6;B7ZMJ7;P12111-2;P12111	.;.;.;CO6A3_HUMAN	A	2258;2057;2052;1651;2052;2058	ENSP00000295550:G2258A;ENSP00000315609:G2057A;ENSP00000315873:G2052A;ENSP00000418285:G1651A;ENSP00000386844:G2052A;ENSP00000295546:G2058A	ENSP00000295550:G2258A	G	-	2	0	COL6A3	237924555	0.999000	0.42202	0.110000	0.21437	0.435000	0.31806	5.960000	0.70348	2.543000	0.85770	0.650000	0.86243	GGT	.	.	.	none		0.572	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		G	238259816	C	G	238259816	3	3	81	1	0	0	0	0	1	0	0	0	3703	507	18	4	2832	4	COL6A3	2	238259816	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	17855000	238259816	4939557	20	5211											
ILKAP	80895	hgsc.bcm.edu	37	chr2	239093869	239093869	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatgcaaattctgtgcagcaAattttgaggctcgaattcct	11	13	9	8	1	1	1	0	1	1	0	3	3	2	1	1	1	3	4	1	1	3	4			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr2:239093869A>G	ENST00000254654.3	-	6	660	c.485T>C	c.(484-486)tTt>tCt	p.F162S		NM_030768.2	NP_110395.1	Q9H0C8	ILKAP_HUMAN	integrin-linked kinase-associated serine/threonine phosphatase	162	PP2C-like.				protein dephosphorylation (GO:0006470)|regulation of nuclear cell cycle DNA replication (GO:0033262)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			endometrium(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_lung(227;0.152)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;5.49e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.93e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.82e-08)|BRCA - Breast invasive adenocarcinoma(100;0.00012)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0163)		CTGTGCAGCAAATTTTGAGGC	0.353																																					p.F162S		Atlas-SNP	.											.	ILKAP	42	.	0			c.T485C						PASS	.						110	104	106					2																	239093869		2203	4300	6503	SO:0001583	missense	80895	exon6			GCAGCAAATTTTG	AY024365	CCDS2526.1	2q37.3	2012-04-17	2010-10-25		ENSG00000132323	ENSG00000132323	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	15566	protein-coding gene	gene with protein product			"integrin-linked kinase-associated serine/threonine phosphatase 2C"				Standard	NM_030768		Approved	DKFZP434J2031, FLJ10181	uc002vxv.3	Q9H0C8	OTTHUMG00000133334	ENST00000254654.3:c.485T>C	chr2.hg19:g.239093869A>G	ENSP00000254654:p.Phe162Ser	103.0	0.0	.		125.0	33.0	.	NM_030768	B3KM39	Missense_Mutation	SNP	ENST00000254654.3	hg19	CCDS2526.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.082008	0.76528	.	.	ENSG00000132323	ENST00000254654;ENST00000457149	T;T	0.18810	2.19;2.19	5.86	5.86	0.93980	Protein phosphatase 2C-like (5);	0.000000	0.85682	D	0.000000	T	0.48768	0.1518	M	0.87617	2.895	0.80722	D	1	D	0.61080	0.989	D	0.67103	0.949	T	0.55425	-0.8143	10	0.66056	D	0.02	-4.2693	10.9192	0.47154	0.8595:0.0:0.0:0.1405	.	162	Q9H0C8	ILKAP_HUMAN	S	162;160	ENSP00000254654:F162S;ENSP00000395301:F160S	ENSP00000254654:F162S	F	-	2	0	ILKAP	238758608	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	3.341000	0.52151	2.241000	0.73720	0.528000	0.53228	TTT	.	.	.	none		0.353	ILKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257163.2	NM_030768		G	239093869	A	G	239093869	3	3	81	1	0	0	0	0	1	0	0	0	7721	14	1	3	721	3	ILKAP	2	239093869	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	834053	239093869	4105504	21	5212											
ABHD5	51099	hgsc.bcm.edu	37	chr3	43744053	43744053	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctaggtggattcttggctgcTgcttactcgctgaagtaccc	6	13	11	11	1	1	1	0	1	1	0	2	2	1	2	1	3	4	5	1	3	4	5			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr3:43744053T>C	ENST00000458276.2	+	3	603	c.480T>C	c.(478-480)gcT>gcC	p.A160A		NM_016006.4	NP_057090.2	Q8WTS1	ABHD5_HUMAN	abhydrolase domain containing 5	160					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)		TCTTGGCTGCTGCTTACTCGC	0.468																																					p.A160A		Atlas-SNP	.											.	ABHD5	33	.	0			c.T480C						PASS	.						205	195	198					3																	43744053		2203	4300	6503	SO:0001819	synonymous_variant	51099	exon3			GGCTGCTGCTTAC	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.480T>C	chr3.hg19:g.43744053T>C		188.0	0.0	.		199.0	46.0	.	NM_016006	B2R9K0|Q9Y369	Silent	SNP	ENST00000458276.2	hg19	CCDS2711.1																																																																																			.	.	.	none		0.468	ABHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256644.2	NM_016006		C	43744053	T	C	43744053	2	2	81	1	0	0	0	0	0	0	0	1	85	1567	55	3		3	ABHD5	3	43744053	Silent	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10		43744053	154278377	22	5213											
RG9MTD1	54931	hgsc.bcm.edu	37	chr3	101284214	101284214	+	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	caatgggctggaagggtgccCaggccatgcagtttggacaa	10	7	15	9	0	0	0	0	0	0	0	0	2	0	2	2	5	2	3	2	5	3	1			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr3:101284214C>T	ENST00000309922.6	+	2	743	c.589C>T	c.(589-591)Cag>Tag	p.Q197*		NM_017819.2	NP_060289.2	Q7L0Y3	MRRP1_HUMAN	tRNA methyltransferase 10 homolog C (S. cerevisiae)	197	SAM-dependent MTase TRM10-type. {ECO:0000255|PROSITE-ProRule:PRU01012}.				mitochondrial RNA 5'-end processing (GO:0000964)|tRNA processing (GO:0008033)	mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)										GAAGGGTGCCCAGGCCATGCA	0.398																																					p.Q197X		Atlas-SNP	.											.	.	.	.	0			c.C589T						PASS	.						103	95	97					3																	101284214		1849	4094	5943	SO:0001587	stop_gained	54931	exon2			GGTGCCCAGGCCA	AK000439	CCDS43122.1	3q12.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000174173	ENSG00000174173			26022	protein-coding gene	gene with protein product	"mitochondrial RNase P subunit 1"	615423	"RNA (guanine-9-) methyltransferase domain containing 1"	RG9MTD1		18984158	Standard	NM_017819		Approved	FLJ20432, MRPP1	uc003duz.4	Q7L0Y3	OTTHUMG00000159114	ENST00000309922.6:c.589C>T	chr3.hg19:g.101284214C>T	ENSP00000312356:p.Gln197*	42.0	0.0	.		50.0	16.0	.	NM_017819	Q9NRG5|Q9NX54|Q9Y596	Nonsense_Mutation	SNP	ENST00000309922.6	hg19	CCDS43122.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.956006	0.92726	.	.	ENSG00000174173	ENST00000309922;ENST00000495642	.	.	.	5.96	5.96	0.96718	.	0.120526	0.64402	D	0.000020	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	-25.6056	20.422	0.99049	0.0:1.0:0.0:0.0	.	.	.	.	X	197	.	ENSP00000312356:Q197X	Q	+	1	0	RG9MTD1	102766904	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.736000	0.68597	2.832000	0.97577	0.655000	0.94253	CAG	.	.	.	none		0.398	TRMT10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353400.2	NM_017819		T	101284214	C	T	101284214	4	4	81	1	0	0	0	0	0	1	0	0	13284	595	21	2	591	2	RG9MTD1	3	101284214	Nonsense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	57540161	101284214	96738216	23	5214											
LRCH3	84859	hgsc.bcm.edu	37	chr3	197592302	197592302	+	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	gtttctccacagagtgatgaCagacctaatgctctattaag	12	12	8	9	0	2	4	0	2	2	2	3	4	2	4	2	0	1	2	2	0	3	4	rs201375313		TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr3:197592302C>G	ENST00000425562.2	+	16	1725	c.1725C>G	c.(1723-1725)gaC>gaG	p.D575E	LRCH3_ENST00000334859.4_Missense_Mutation_p.D575E|LRCH3_ENST00000414675.2_Missense_Mutation_p.D523E|LRCH3_ENST00000441090.2_Missense_Mutation_p.D421E|LRCH3_ENST00000438796.2_Missense_Mutation_p.D575E|LRCH3_ENST00000536618.1_Missense_Mutation_p.D170E			Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 3	575						cytoplasm (GO:0005737)|extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.119)		AGAGTGATGACAGACCTAATG	0.274																																					p.D575E		Atlas-SNP	.											.	LRCH3	96	.	0			c.C1725G						PASS	.						39	38	39					3																	197592302		2203	4300	6503	SO:0001583	missense	84859	exon16			TGATGACAGACCT	AL137527	CCDS3330.1	3q29	2006-04-12			ENSG00000186001	ENSG00000186001			28637	protein-coding gene	gene with protein product						12477932	Standard	NM_032773		Approved	MGC4126	uc003fyj.1	Q96II8	OTTHUMG00000155378	ENST00000425562.2:c.1725C>G	chr3.hg19:g.197592302C>G	ENSP00000393579:p.Asp575Glu	125.0	0.0	.		154.0	41.0	.	NM_032773	B4E0T7|Q96FP9|Q9NT52	Missense_Mutation	SNP	ENST00000425562.2	hg19		.	.	.	.	.	.	.	.	.	.	C	4.270	0.049197	0.08243	.	.	ENSG00000186001	ENST00000438796;ENST00000441090;ENST00000414675;ENST00000334859;ENST00000425562;ENST00000536618;ENST00000452660;ENST00000433298	T;T;T;T;T;T;T;T	0.46451	2.09;1.5;2.1;2.36;2.11;0.89;0.87;0.97	4.97	2.98	0.34508	.	0.475028	0.22270	N	0.062279	T	0.26340	0.0643	L	0.29908	0.895	0.20563	N	0.999887	B;B;B;B;P	0.37663	0.102;0.058;0.056;0.033;0.604	B;B;B;B;B	0.33042	0.028;0.012;0.029;0.008;0.157	T	0.07539	-1.0767	10	0.31617	T	0.26	-1.0728	8.8539	0.35217	0.0:0.8043:0.0:0.1957	.	421;523;575;575;575	E9PD99;B4E0T7;Q96II8-2;Q96II8;Q96II8-3	.;.;.;LRCH3_HUMAN;.	E	575;421;523;575;575;170;86;48	ENSP00000399751:D575E;ENSP00000394609:D421E;ENSP00000394965:D523E;ENSP00000334375:D575E;ENSP00000393579:D575E;ENSP00000439083:D170E;ENSP00000395309:D86E;ENSP00000400164:D48E	ENSP00000334375:D575E	D	+	3	2	LRCH3	199076699	1.000000	0.71417	0.975000	0.42487	0.064000	0.16182	0.457000	0.21875	0.390000	0.25115	-0.480000	0.04831	GAC	.	C|0.999;T|0.001	.	alt		0.274	LRCH3-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000339965.1	NM_032773		G	197592302	C	G	197592302	3	3	81	1	0	0	0	0	1	0	0	0	8941	477	17	4	1787	4	LRCH3	3	197592302	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	96308088	197592302	430128	24	5215											
KCTD8	386617	hgsc.bcm.edu	37	chr4	44450334	44450334	+	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	ggcgagaacatgctggccaaAgtactgtccgggacgctgag	10	6	15	10	3	0	2	0	1	0	1	1	4	1	3	2	3	3	3	2	3	3	1			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr4:44450334A>T	ENST00000360029.3	-	1	490	c.207T>A	c.(205-207)acT>acA	p.T69T	AC131951.1_ENST00000584757.1_RNA	NM_198353.2	NP_938167.1	Q6ZWB6	KCTD8_HUMAN	potassium channel tetramerization domain containing 8	69	BTB.				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						TGCTGGCCAAAGTACTGTCCG	0.677										HNSCC(17;0.042)																											p.T69T		Atlas-SNP	.											.	KCTD8	96	.	0			c.T207A						PASS	.						24	21	22					4																	44450334		2191	4278	6469	SO:0001819	synonymous_variant	386617	exon1			GGCCAAAGTACTG	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.207T>A	chr4.hg19:g.44450334A>T		44.0	0.0	.		33.0	16.0	.	NM_198353	A2RU39	Silent	SNP	ENST00000360029.3	hg19	CCDS3467.1																																																																																			.	.	.	none		0.677	KCTD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216868.1			T	44450334	A	T	44450334	2	4	81	1	0	0	0	0	0	0	0	1	8122	59	3	5		5	KCTD8	4	44450334	Silent	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10		44450334	146703942	25	5216											
AFF1	4299	hgsc.bcm.edu	37	chr4	88053423	88053423	+	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	acttctgtctttgttcatagCatgcgttgccagtccatttt	6	18	7	10	1	3	0	1	0	2	0	4	0	4	0	2	0	3	3	2	0	1	7			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr4:88053423C>T	ENST00000307808.6	+	18	3573	c.3153C>T	c.(3151-3153)tgC>tgT	p.C1051C	AFF1_ENST00000395146.4_Splice_Site_p.C1058C|AFF1_ENST00000544085.1_Splice_Site_p.C689C	NM_005935.2	NP_005926.1	P51825	AFF1_HUMAN	AF4/FMR2 family, member 1	1051					positive regulation of transcription, DNA-templated (GO:0045893)	transcription elongation factor complex (GO:0008023)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(2)	3		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		TTGTTCATAGCATGCGTTGCC	0.393																																					p.C1058C		Atlas-SNP	.											.	AFF1	102	.	0			c.C3174T						PASS	.						118	107	111					4																	88053423		2203	4300	6503	SO:0001630	splice_region_variant	4299	exon19			TCATAGCATGCGT	L22179	CCDS3616.1, CCDS54775.1	4q21.3	2009-08-04	2005-06-27	2005-06-27	ENSG00000172493	ENSG00000172493			7135	protein-coding gene	gene with protein product		159557	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 2", "pre-B-cell monocytic leukemia partner 1"	PBM1, MLLT2		7689231, 1423625, 8353274	Standard	NM_005935		Approved	AF-4, AF4	uc011ccz.2	P51825	OTTHUMG00000130603	ENST00000307808.6:c.3153-1C>T	chr4.hg19:g.88053423C>T		131.0	0.0	.		118.0	34.0	.	NM_001166693	B4DTU1|E9PBM3	Silent	SNP	ENST00000307808.6	hg19	CCDS3616.1																																																																																			.	.	.	none		0.393	AFF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253053.3	NM_005935	Silent	T	88053423	C	T	88053423	5	4	81	1	0	0	0	0	0	0	1	0	356	724	25	2	3265	2	AFF1	4	88053423	Splice_Site	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	43603089	88053423	103100853	26	5217											
ADH4	127	hgsc.bcm.edu	37	chr4	100057629	100057629	+	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	ccatttaccttggcattgttGattgcagccccatagccagt	8	13	8	12	0	0	1	0	1	0	0	0	1	0	1	5	1	4	3	5	1	2	7			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr4:100057629G>T	ENST00000265512.7	-	5	644	c.570C>A	c.(568-570)atC>atA	p.I190I	RP11-696N14.1_ENST00000500358.2_RNA|ADH4_ENST00000508393.1_Silent_p.I209I|ADH4_ENST00000423445.1_Silent_p.I209I|ADH4_ENST00000505590.1_Silent_p.I209I	NM_000670.3	NP_000661.2	P08319	ADH4_HUMAN	alcohol dehydrogenase 4 (class II), pi polypeptide	190					alcohol catabolic process (GO:0046164)|alcohol metabolic process (GO:0006066)|cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|quinone metabolic process (GO:1901661)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|all-trans retinal binding (GO:0005503)|benzaldehyde dehydrogenase activity (GO:0019115)|ethanol binding (GO:0035276)|NAD binding (GO:0051287)|NADPH:quinone reductase activity (GO:0003960)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)|skin(2)	18				OV - Ovarian serous cystadenocarcinoma(123;4.48e-08)		TGGCATTGTTGATTGCAGCCC	0.388																																					p.I190I		Atlas-SNP	.											.	ADH4	35	.	0			c.C570A						PASS	.						162	144	150					4																	100057629		2203	4300	6503	SO:0001819	synonymous_variant	127	exon5			ATTGTTGATTGCA	M15943	CCDS34032.1	4q22	2008-02-05				ENSG00000198099	1.1.1.1	"Alcohol dehydrogenases"	252	protein-coding gene	gene with protein product		103740					Standard	NM_000670		Approved	ADH-2	uc003hun.3	P08319		ENST00000265512.7:c.570C>A	chr4.hg19:g.100057629G>T		50.0	0.0	.		45.0	14.0	.	NM_000670	A8K470|B4DIE7|C9J4A9|Q8TCD7	Silent	SNP	ENST00000265512.7	hg19	CCDS34032.1																																																																																			.	.	.	none		0.388	ADH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364220.2	NM_000670		T	100057629	G	T	100057629	2	4	81	1	0	0	0	0	0	0	0	1	310	1280	45	4		4	ADH4	4	100057629	Silent	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	12004206	100057629	91096647	27	5218											
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123109188	123109188	+	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	ttgtgaaaggaaagcttgaaAatgttcgagtcatgcttgtt	12	14	11	4	1	1	2	1	2	0	0	2	4	1	3	0	1	2	4	0	1	4	5			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr4:123109188A>T	ENST00000264501.4	+	9	1139	c.766A>T	c.(766-768)Aat>Tat	p.N256Y	KIAA1109_ENST00000388738.3_Missense_Mutation_p.N256Y|KIAA1109_ENST00000455637.1_Missense_Mutation_p.N256Y			Q2LD37	K1109_HUMAN	KIAA1109	256					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						AAAGCTTGAAAATGTTCGAGT	0.313																																					p.N256Y		Atlas-SNP	.											.	KIAA1109	424	.	0			c.A766T						PASS	.						103	94	97					4																	123109188		1842	4093	5935	SO:0001583	missense	84162	exon7			CTTGAAAATGTTC	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.766A>T	chr4.hg19:g.123109188A>T	ENSP00000264501:p.Asn256Tyr	34.0	0.0	.		19.0	6.0	.	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.3|24.3	4.519360|4.519360	0.85495|0.85495	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000424425|ENST00000264501;ENST00000388738;ENST00000455637	.|D;D;D	.|0.95272	.|-3.66;-3.66;-3.66	5.44|5.44	5.44|5.44	0.79542|0.79542	.|.	.|7739.210000	.|0.00604	.|U	.|0.000398	D|D	0.97204|0.97204	0.9086|0.9086	L|L	0.55213|0.55213	1.73|1.73	0.80722|0.80722	D|D	1|1	.|D	.|0.71674	.|0.998	.|D	.|0.80764	.|0.994	D|D	0.87444|0.87444	0.2397|0.2397	5|10	.|0.87932	.|D	.|0	.|.	15.4917|15.4917	0.75611|0.75611	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|256	.|Q2LD37	.|K1109_HUMAN	I|Y	88|256	.|ENSP00000264501:N256Y;ENSP00000373390:N256Y;ENSP00000389925:N256Y	.|ENSP00000264501:N256Y	K|N	+|+	2|1	0|0	KIAA1109|KIAA1109	123328638|123328638	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	9.232000|9.232000	0.95325|0.95325	2.065000|2.065000	0.61736|0.61736	0.459000|0.459000	0.35465|0.35465	AAA|AAT	.	.	.	none		0.313	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		T	123109188	A	T	123109188	3	4	81	1	0	0	0	0	1	0	0	0	8215	14	1	5	792	5	KIAA1109	4	123109188	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	23051559	123109188	68045088	28	5219											
SMARCA5	8467	hgsc.bcm.edu	37	chr4	144457751	144457751	+	Missense_Mutation	SNP	A	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	agcagaacctggtccaccttAtacaacagatatgcatctag	14	9	7	11	0	1	2	0	0	1	2	2	2	2	2	3	1	5	2	3	1	6	4			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr4:144457751A>C	ENST00000283131.3	+	11	1877	c.1415A>C	c.(1414-1416)tAt>tCt	p.Y472S		NM_003601.3	NP_003592.3	O60264	SMCA5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	472					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)					GGTCCACCTTATACAACAGAT	0.398																																					p.Y472S		Atlas-SNP	.											.	SMARCA5	73	.	0			c.A1415C						PASS	.						102	95	97					4																	144457751		2203	4300	6503	SO:0001583	missense	8467	exon11			CACCTTATACAAC	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.1415A>C	chr4.hg19:g.144457751A>C	ENSP00000283131:p.Tyr472Ser	351.0	0.0	.		327.0	128.0	.	NM_003601		Missense_Mutation	SNP	ENST00000283131.3	hg19	CCDS3761.1	.	.	.	.	.	.	.	.	.	.	A	25.7	4.668376	0.88348	.	.	ENSG00000153147	ENST00000283131;ENST00000536484;ENST00000535006	T	0.75050	-0.9	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	D	0.85720	0.5762	M	0.88906	2.99	0.80722	D	1	P	0.44380	0.834	P	0.53912	0.737	D	0.87814	0.2633	10	0.56958	D	0.05	-21.194	15.7551	0.78018	1.0:0.0:0.0:0.0	.	472	O60264	SMCA5_HUMAN	S	472;415;415	ENSP00000283131:Y472S	ENSP00000283131:Y472S	Y	+	2	0	SMARCA5	144677201	1.000000	0.71417	0.977000	0.42913	0.985000	0.73830	9.231000	0.95317	2.192000	0.70111	0.533000	0.62120	TAT	.	.	.	none		0.398	SMARCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365077.3			C	144457751	A	C	144457751	3	2	81	1	0	0	0	0	1	0	0	0	14784	449	16	5	1457	5	SMARCA5	4	144457751	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	21348563	144457751	46696525	29	5220											
CDH6	1004	hgsc.bcm.edu	37	chr5	31294229	31294229	+	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	ttacatccttcgagctcaagCtataaacagaaggacaggga	15	8	9	9	1	1	1	1	0	0	1	3	4	2	3	1	2	4	2	1	2	6	4			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr5:31294229C>A	ENST00000265071.2	+	3	654	c.389C>A	c.(388-390)gCt>gAt	p.A130D	CDH6_ENST00000514738.1_Missense_Mutation_p.A75D	NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	130	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CGAGCTCAAGCTATAAACAGA	0.458																																					p.A130D		Atlas-SNP	.											.	CDH6	175	.	0			c.C389A						PASS	.						128	127	127					5																	31294229		2203	4300	6503	SO:0001583	missense	1004	exon3			CTCAAGCTATAAA	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.389C>A	chr5.hg19:g.31294229C>A	ENSP00000265071:p.Ala130Asp	72.0	0.0	.		68.0	21.0	.	NM_004932	A8K5H5|Q9BWS0	Missense_Mutation	SNP	ENST00000265071.2	hg19	CCDS3894.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.436456	0.83885	.	.	ENSG00000113361	ENST00000514738;ENST00000265071	T;T	0.71934	-0.61;-0.61	5.77	5.77	0.91146	Cadherin (4);Cadherin-like (1);	0.096902	0.64402	D	0.000001	D	0.90964	0.7159	H	0.98089	4.145	0.53688	D	0.999972	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.93441	0.6794	10	0.87932	D	0	.	20.3627	0.98863	0.0:1.0:0.0:0.0	.	130;130	P55285;P55285-2	CADH6_HUMAN;.	D	75;130	ENSP00000424843:A75D;ENSP00000265071:A130D	ENSP00000265071:A130D	A	+	2	0	CDH6	31329986	0.995000	0.38212	1.000000	0.80357	0.993000	0.82548	3.261000	0.51530	2.885000	0.99019	0.655000	0.94253	GCT	.	.	.	none		0.458	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207355.2	NM_004932		A	31294229	C	A	31294229	3	1	81	1	0	0	0	0	1	0	0	0	3116	797	28	4	395	4	CDH6	5	31294229	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10		31294229	149621031	30	5221											
SKP2	6502	hgsc.bcm.edu	37	chr5	36183992	36183992	+	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	0	0	0	0	0	0	0	0	0	0	0	gttggactctgacatcggatGccctcaaacatacagaactt	12	10	8	11	1	2	2	1	1	1	1	3	4	2	4	1	2	4	1	1	2	3	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr5:36183992G>A	ENST00000274255.6	+	0	3330				SKP2_ENST00000274254.5_Missense_Mutation_p.C371Y	NM_005983.3	NP_005974.2	Q13309	SKP2_HUMAN	S-phase kinase-associated protein 2, E3 ubiquitin protein ligase						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)			GACATCGGATGCCCTCAAACA	0.358																																					p.C371Y		Atlas-SNP	.											.	SKP2	70	.	0			c.G1112A						PASS	.						100	95	96					5																	36183992		2203	4300	6503	SO:0001624	3_prime_UTR_variant	6502	exon10			TCGGATGCCCTCA	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.*1859G>A	chr5.hg19:g.36183992G>A		131.0	0.0	.		155.0	7.0	.	NM_032637	A8K5E0|B4DJT4|Q8TDZ0|Q8TDZ1|Q9BV69	Missense_Mutation	SNP	ENST00000274255.6	hg19	CCDS3916.1	.	.	.	.	.	.	.	.	.	.	G	10.41	1.342740	0.24339	.	.	ENSG00000145604	ENST00000274254	T	0.09630	2.96	5.53	3.5	0.40072	.	0.203110	0.53938	D	0.000058	T	0.07908	0.0198	.	.	.	0.09310	N	0.999995	B	0.02656	0.0	B	0.06405	0.002	T	0.22382	-1.0218	9	0.72032	D	0.01	-5.9	5.4712	0.16670	0.2751:0.0:0.7248:0.0	.	371	Q13309-2	.	Y	371	ENSP00000274254:C371Y	ENSP00000274254:C371Y	C	+	2	0	SKP2	36219749	0.013000	0.17824	0.442000	0.26870	0.014000	0.08584	0.596000	0.24044	1.358000	0.45922	0.650000	0.86243	TGC	.	.	.	none		0.358	SKP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253769.2	NM_005983		A	36183992	G	A	36183992	1	1	81	0	1	0	0	0	0	0	0	0	14375	1319	46	2		2	SKP2	5	36183992	3'UTR	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	4889763	36183992	144731268	31	5222											
DTWD2	285605	hgsc.bcm.edu	37	chr5	118183873	118183873	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atctattagtcggctgcatcCgaattacatactgactagaa	13	12	7	9	2	1	2	0	1	1	1	3	3	2	2	1	1	3	2	1	1	7	5			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr5:118183873C>T	ENST00000510708.1	-	5	671	c.638G>A	c.(637-639)cGg>cAg	p.R213Q	DTWD2_ENST00000304058.4_Missense_Mutation_p.R147Q|DTWD2_ENST00000515439.3_Missense_Mutation_p.R117Q	NM_173666.2	NP_775937.1	Q8NBA8	DTWD2_HUMAN	DTW domain containing 2	213										breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)	13		all_epithelial(76;0.0982)|Prostate(80;0.121)		OV - Ovarian serous cystadenocarcinoma(64;0.000228)|Epithelial(69;0.000941)|all cancers(49;0.00939)		CGGCTGCATCCGAATTACATA	0.318																																					p.R213Q		Atlas-SNP	.											.	DTWD2	27	.	0			c.G638A						PASS	.						67	64	65					5																	118183873		2202	4300	6502	SO:0001583	missense	285605	exon5			TGCATCCGAATTA		CCDS34216.1	5q23.1	2008-02-05			ENSG00000169570	ENSG00000169570			19334	protein-coding gene	gene with protein product							Standard	NM_173666		Approved	FLJ33977	uc003ksa.3	Q8NBA8	OTTHUMG00000162956	ENST00000510708.1:c.638G>A	chr5.hg19:g.118183873C>T	ENSP00000425048:p.Arg213Gln	136.0	0.0	.		136.0	41.0	.	NM_173666		Missense_Mutation	SNP	ENST00000510708.1	hg19	CCDS34216.1	.	.	.	.	.	.	.	.	.	.	C	33	5.223594	0.95139	.	.	ENSG00000169570	ENST00000304058;ENST00000510708;ENST00000515439	.	.	.	5.36	5.36	0.76844	DTW (1);	0.000000	0.85682	D	0.000000	D	0.86134	0.5860	M	0.91768	3.24	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89151	0.3523	9	0.87932	D	0	-25.3975	18.6918	0.91586	0.0:1.0:0.0:0.0	.	213	Q8NBA8	DTWD2_HUMAN	Q	147;213;117	.	ENSP00000302892:R147Q	R	-	2	0	DTWD2	118211772	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.267000	0.78462	2.511000	0.84671	0.455000	0.32223	CGG	.	.	.	none		0.318	DTWD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371167.2	NM_173666		T	118183873	C	T	118183873	3	4	81	1	0	0	0	0	1	0	0	0	4794	652	23	1	266	1	DTWD2	5	118183873	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	81999881	118183873	62731387	32	5223											
FAM13B	51306	hgsc.bcm.edu	37	chr5	137346798	137346798	+	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	tccagccattatcctgctcaCtatttcttgctctttcatgt	6	18	4	13	0	4	0	2	0	2	0	6	0	6	0	3	0	3	2	3	0	2	5			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr5:137346798C>G	ENST00000033079.3	-	6	1040	c.589G>C	c.(589-591)Gtg>Ctg	p.V197L	FAM13B_ENST00000420893.2_Missense_Mutation_p.V197L|FAM13B_ENST00000425075.2_Missense_Mutation_p.V79L	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	197	Glu-rich.|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						ATCCTGCTCACTATTTCTTGC	0.338																																					p.V197L		Atlas-SNP	.											.	FAM13B	46	.	0			c.G589C						PASS	.						155	147	150					5																	137346798		2203	4300	6503	SO:0001583	missense	51306	exon6			TGCTCACTATTTC	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.589G>C	chr5.hg19:g.137346798C>G	ENSP00000033079:p.Val197Leu	22.0	0.0	.		31.0	18.0	.	NM_001101800	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Missense_Mutation	SNP	ENST00000033079.3	hg19	CCDS4195.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.818248	0.90790	.	.	ENSG00000031003	ENST00000033079;ENST00000425075;ENST00000420893	T;T;T	0.41400	1.0;2.01;1.0	5.59	5.59	0.84812	Rho GTPase-activating protein domain (3);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.58495	0.2126	L	0.40543	1.245	0.80722	D	1	D;D;P	0.67145	0.996;0.996;0.461	D;D;B	0.77557	0.987;0.99;0.299	T	0.57476	-0.7805	10	0.54805	T	0.06	-6.8245	19.5907	0.95509	0.0:1.0:0.0:0.0	.	79;197;197	G3V0H9;Q9NYF5-2;Q9NYF5	.;.;FA13B_HUMAN	L	197;79;197	ENSP00000033079:V197L;ENSP00000394669:V79L;ENSP00000388521:V197L	ENSP00000033079:V197L	V	-	1	0	FAM13B	137374697	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.005000	0.63972	2.640000	0.89533	0.655000	0.94253	GTG	.	.	.	none		0.338	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1			G	137346798	C	G	137346798	3	3	81	1	0	0	0	0	1	0	0	0	5457	565	20	4	2300	4	FAM13B	5	137346798	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	19162925	137346798	43568462	33	5224											
PCDHB10	56126	hgsc.bcm.edu	37	chr5	140572491	140572494	+	Frame_Shift_Del	DEL	AGTC	AGTC	-																															atttaccgggctgagctgagAgtcagggatataaatgatca																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	AGTC	AGTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr5:140572491_140572494delAGTC	ENST00000239446.4	+	1	550_553	c.366_369delAGTC	c.(364-369)agagtcfs	p.RV122fs		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	122	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(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)			CTGAGCTGAGAGTCAGGGATATAA	0.422																																					p.122_123del		Atlas-Indel,Pindel	.											.	PCDHB10	177	.	0			c.365_368del						PASS	.																																			SO:0001589	frameshift_variant	56126	exon1			.	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"Cadherins / Protocadherins : Clustered"	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.366_369delAGTC	chr5.hg19:g.140572491_140572494delAGTC	ENSP00000239446:p.Arg122fs	175.0	0.0	0		182.0	54.0	0.296703	NM_018930	Q96T99	Frame_Shift_Del	DEL	ENST00000239446.4	hg19	CCDS4252.1																																																																																			.	.	.	none		0.422	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		-	140572494	AGTC	-	140572491	7	5	81	1	0	1	0	1	0	0	0	0	11542	301	11	0	368	0	PCDHB10	5	140572491	Frame_Shift_Del	DEL	AGTC	TCGA-B1-A47M-01A-11D-A25F-10	3225693	140572491	40342769	34	5225											
FAM71B	153745	hgsc.bcm.edu	37	chr5	156590131	156590131	+	Missense_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	tttctgctgcacacttgctgGtcgtaatactgcctgcaaac	8	13	8	12	1	1	0	0	0	1	0	2	0	1	0	1	1	7	5	1	1	3	4			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr5:156590131G>A	ENST00000302938.4	-	2	1240	c.1145C>T	c.(1144-1146)aCc>aTc	p.T382I		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	382						nucleus (GO:0005634)		p.T382N(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)			ACACTTGCTGGTCGTAATACT	0.572																																					p.T382I		Atlas-SNP	.											FAM71B,NS,carcinoma,0,1	FAM71B	145	.	1	Substitution - Missense(1)	lung(1)	c.C1145T						PASS	.						47	49	48					5																	156590131		2203	4300	6503	SO:0001583	missense	153745	exon2			TTGCTGGTCGTAA		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.1145C>T	chr5.hg19:g.156590131G>A	ENSP00000305596:p.Thr382Ile	30.0	0.0	.		51.0	11.0	.	NM_130899	Q1EDD9|Q8TC64|Q96LY8	Missense_Mutation	SNP	ENST00000302938.4	hg19	CCDS4335.1	.	.	.	.	.	.	.	.	.	.	G	14.90	2.673011	0.47781	.	.	ENSG00000170613	ENST00000302938	T	0.18960	2.18	3.83	2.95	0.34219	.	0.314558	0.23165	N	0.051186	T	0.37598	0.1009	M	0.78801	2.425	0.09310	N	1	D	0.62365	0.991	P	0.57101	0.813	T	0.13548	-1.0505	10	0.72032	D	0.01	-18.4181	9.0093	0.36131	0.0:0.0:0.781:0.219	.	382	Q8TC56	FA71B_HUMAN	I	382	ENSP00000305596:T382I	ENSP00000305596:T382I	T	-	2	0	FAM71B	156522709	0.045000	0.20229	0.011000	0.14972	0.002000	0.02628	2.344000	0.44010	1.174000	0.42811	0.561000	0.74099	ACC	.	.	.	none		0.572	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899		A	156590131	G	A	156590131	3	1	81	1	0	0	0	0	1	0	0	0	5615	1261	44	2	676	2	FAM71B	5	156590131	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	16017640	156590131	24325129	35	5226											
CLK4	57396	hgsc.bcm.edu	37	chr5	178030682	178030683	+	Frame_Shift_Ins	INS	-	-	T																															atccaaggtaattctttgagINSttggatcatattctaacatt																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr5:178030682_178030683insT	ENST00000316308.4	-	13	1549_1550	c.1381_1382insA	c.(1381-1383)actfs	p.T461fs		NM_020666.2	NP_065717.1	Q9HAZ1	CLK4_HUMAN	CDC-like kinase 4	461	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(2)	21	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.235)		AATTCTTTGAGTTGGATCATAT	0.342																																					p.T461fs		Atlas-Indel,Pindel	.											.	CLK4	103	.	0			c.1382_1383insA						PASS	.																																			SO:0001589	frameshift_variant	57396	exon13			.	AF294429	CCDS4437.1	5q35	2008-05-02			ENSG00000113240	ENSG00000113240		"CDC-like kinases"	13659	protein-coding gene	gene with protein product		607969				11170754	Standard	NM_020666		Approved		uc003mjf.1	Q9HAZ1	OTTHUMG00000130893	ENST00000316308.4:c.1382dupA	chr5.hg19:g.178030684_178030684dupT	ENSP00000316948:p.Thr461fs	79.0	0.0	0		61.0	30.0	0.491803	NM_020666		Frame_Shift_Ins	INS	ENST00000316308.4	hg19	CCDS4437.1																																																																																			.	.	.	none		0.342	CLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253479.2			T	178030683	-	T	178030682	7	5	81	1	0	1	1	0	0	0	0	0	3541	1029	36	0	67	0	CLK4	5	178030682	Frame_Shift_Ins	INS	-	TCGA-B1-A47M-01A-11D-A25F-10	21440551	178030682	2884578	36	5227											
EHMT2	10919	hgsc.bcm.edu	37	chr6	31852462	31852462	+	Frame_Shift_Del	DEL	G	G	-																															ctcccgagctgcgatgtgcaGgggggtgtccccatggtagt																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr6:31852462delG	ENST00000375537.4	-	20	2569	c.2563delC	c.(2563-2565)ctgfs	p.L855fs	EHMT2_ENST00000395728.3_Frame_Shift_Del_p.L912fs|EHMT2_ENST00000375528.4_Frame_Shift_Del_p.L878fs|EHMT2_ENST00000375530.4_Frame_Shift_Del_p.L821fs|EHMT2-AS1_ENST00000434689.1_RNA|EHMT2_ENST00000480912.1_5'UTR	NM_006709.3	NP_006700.3	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	855					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						GCGATGTGCAGGGGGGTGTCC	0.657																																					p.L855fs		Atlas-Indel,Pindel	.											.	EHMT2	45	.	0			c.2564delT						PASS	.						39	34	36					6																	31852462		1511	2708	4219	SO:0001589	frameshift_variant	10919	exon20			.	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.2563delC	chr6.hg19:g.31852462delG	ENSP00000364687:p.Leu855fs	96.0	0.0	0		66.0	27.0	0.409091	NM_006709	B0UZY2|Q14349|Q5JP83|Q5JQ92|Q5JQA1|Q5JQG3|Q6PK06|Q96MH5|Q96QD0|Q9UQL8|Q9Y331	Frame_Shift_Del	DEL	ENST00000375537.4	hg19	CCDS4725.1																																																																																			.	.	.	none		0.657	EHMT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076355.5	NM_006709		-	31852462	G	-	31852462	7	5	81	1	0	1	0	1	0	0	0	0	4986	991	35	0	1105	0	EHMT2	6	31852462	Frame_Shift_Del	DEL	G	TCGA-B1-A47M-01A-11D-A25F-10		31852462	139262605	37	5228	56	2									
EHMT2	10919	hgsc.bcm.edu	37	chr6	31852467	31852467	+	Missense_Mutation	SNP	G	G	A																															gagctgcgatgtgcagggggGtgtccccatggtagttgaca																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr6:31852467G>A	ENST00000375537.4	-	20	2564	c.2558C>T	c.(2557-2559)aCc>aTc	p.T853I	EHMT2_ENST00000395728.3_Missense_Mutation_p.T910I|EHMT2_ENST00000375528.4_Missense_Mutation_p.T876I|EHMT2_ENST00000375530.4_Missense_Mutation_p.T819I|EHMT2-AS1_ENST00000434689.1_RNA|EHMT2_ENST00000480912.1_5'UTR	NM_006709.3	NP_006700.3	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	853					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						GTGCAGGGGGGTGTCCCCATG	0.647																																					p.T853I		Atlas-SNP	.											.	EHMT2	45	.	0			c.C2558T						PASS	.						39	33	36					6																	31852467		1511	2709	4220	SO:0001583	missense	10919	exon20			AGGGGGGTGTCCC	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.2558C>T	chr6.hg19:g.31852467G>A	ENSP00000364687:p.Thr853Ile	104.0	0.0	.		68.0	28.0	.	NM_006709	B0UZY2|Q14349|Q5JP83|Q5JQ92|Q5JQA1|Q5JQG3|Q6PK06|Q96MH5|Q96QD0|Q9UQL8|Q9Y331	Missense_Mutation	SNP	ENST00000375537.4	hg19	CCDS4725.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.175053	0.78564	.	.	ENSG00000204371	ENST00000395728;ENST00000375528;ENST00000375530;ENST00000375537;ENST00000442298	D;D;D;D	0.82255	-1.59;-1.59;-1.59;-1.59	5.14	5.14	0.70334	Ankyrin repeat-containing domain (3);	0.055749	0.64402	D	0.000001	D	0.94245	0.8152	H	0.97829	4.085	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;1.0;1.0	D;D;D;D	0.81914	0.99;0.983;0.995;0.995	D	0.96314	0.9231	10	0.87932	D	0	.	17.3716	0.87380	0.0:0.0:1.0:0.0	.	876;819;853;674	A2ABF8;Q96KQ7-2;Q96KQ7;Q59FM7	.;.;EHMT2_HUMAN;.	I	910;876;819;853;674	ENSP00000379078:T910I;ENSP00000364678:T876I;ENSP00000364680:T819I;ENSP00000364687:T853I	ENSP00000364678:T876I	T	-	2	0	EHMT2	31960446	1.000000	0.71417	0.978000	0.43139	0.313000	0.28021	9.634000	0.98435	2.396000	0.81511	0.555000	0.69702	ACC	.	.	.	none		0.647	EHMT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076355.5	NM_006709		A	31852467	G	A	31852467	3	1	81	1	0	0	0	0	1	0	0	0	4986	1261	44	2	1110	2	EHMT2	6	31852467	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	5	31852467	139262600	38	5229	56	2									
CUL9	23113	hgsc.bcm.edu	37	chr6	43184050	43184050	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcagcaccttttggctcatTcccactggggcgctgaacag	7	10	10	14	1	2	1	2	1	0	0	3	1	3	1	2	3	2	3	2	3	1	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr6:43184050T>C	ENST00000252050.4	+	31	6175	c.6091T>C	c.(6091-6093)Tcc>Ccc	p.S2031P	CUL9_ENST00000354495.3_Missense_Mutation_p.S1921P|RP3-330M21.5_ENST00000500590.1_RNA|CUL9_ENST00000372647.2_Missense_Mutation_p.S2003P	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	2031					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						TTTGGCTCATTCCCACTGGGG	0.602																																					p.S2031P		Atlas-SNP	.											.	CUL9	248	.	0			c.T6091C						PASS	.						51	43	46					6																	43184050		2203	4300	6503	SO:0001583	missense	23113	exon31			GCTCATTCCCACT	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.6091T>C	chr6.hg19:g.43184050T>C	ENSP00000252050:p.Ser2031Pro	97.0	0.0	.		58.0	18.0	.	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	hg19	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	T	18.17	3.563689	0.65651	.	.	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.04156	3.69;3.69;3.69	5.82	3.11	0.35812	.	0.282909	0.37809	N	0.001923	T	0.01835	0.0058	L	0.36672	1.1	0.28092	N	0.93174	P;P;P	0.38642	0.467;0.641;0.641	B;B;B	0.38562	0.26;0.276;0.276	T	0.41161	-0.9524	10	0.54805	T	0.06	-12.2048	9.9765	0.41786	0.1212:0.0:0.1122:0.7665	.	1921;2003;2031	Q8IWT3-3;E9PEZ1;Q8IWT3	.;.;CUL9_HUMAN	P	2031;1921;2003	ENSP00000252050:S2031P;ENSP00000346490:S1921P;ENSP00000361730:S2003P	ENSP00000252050:S2031P	S	+	1	0	CUL9	43292028	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.643000	0.46604	1.001000	0.39076	0.533000	0.62120	TCC	.	.	.	none		0.602	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		C	43184050	T	C	43184050	3	2	81	1	0	0	0	0	1	0	0	0	4063	1783	62	3	6209	3	CUL9	6	43184050	Missense_Mutation	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10	11331583	43184050	127931017	39	5230											
COL10A1	1300	hgsc.bcm.edu	37	chr6	116441541	116441541	+	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	agtccttgggtcataatgctGttgcctgttatacaaaattt	10	16	8	7	0	1	0	1	0	0	0	2	0	2	0	2	1	3	3	2	1	5	6			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr6:116441541G>T	ENST00000327673.4	-	2	2145	c.1738C>A	c.(1738-1740)Cag>Aag	p.Q580K	NT5DC1_ENST00000319550.4_Intron|AL121963.1_ENST00000430695.1_5'Flank|COL10A1_ENST00000243222.4_Missense_Mutation_p.Q580K			Q03692	COAA1_HUMAN	collagen, type X, alpha 1	580	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.|Nonhelical region (NC1).				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	cell cortex (GO:0005938)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|lung(6)|skin(3)|upper_aerodigestive_tract(1)	13		all_cancers(87;0.0176)|all_epithelial(87;0.0263)|Colorectal(196;0.234)		all cancers(137;0.0157)|OV - Ovarian serous cystadenocarcinoma(136;0.0325)|GBM - Glioblastoma multiforme(226;0.0446)|Epithelial(106;0.0711)		TCATAATGCTGTTGCCTGTTA	0.398																																					p.Q580K		Atlas-SNP	.											.	COL10A1	51	.	0			c.C1738A						PASS	.						96	98	97					6																	116441541		2203	4300	6503	SO:0001583	missense	1300	exon3			AATGCTGTTGCCT		CCDS5105.1	6q21-q22	2013-01-16	2008-07-29		ENSG00000123500	ENSG00000123500		"Collagens"	2185	protein-coding gene	gene with protein product	"Schmid metaphyseal chondrodysplasia"	120110				2037056	Standard	XM_006715332		Approved		uc003pwm.3	Q03692	OTTHUMG00000015426	ENST00000327673.4:c.1738C>A	chr6.hg19:g.116441541G>T	ENSP00000327368:p.Gln580Lys	76.0	0.0	.		78.0	21.0	.	NM_000493	A1L4P2	Missense_Mutation	SNP	ENST00000327673.4	hg19	CCDS5105.1	.	.	.	.	.	.	.	.	.	.	G	12.08	1.829889	0.32329	.	.	ENSG00000123500	ENST00000243222;ENST00000327673	D;D	0.85556	-2.0;-2.0	4.74	2.88	0.33553	Tumour necrosis factor-like (2);Complement C1q protein (4);	0.188788	0.47455	D	0.000223	T	0.56366	0.1980	L	0.41415	1.275	0.40364	D	0.97927	B	0.06786	0.001	B	0.08055	0.003	T	0.53767	-0.8392	10	0.02654	T	1	.	9.3923	0.38381	0.0:0.1413:0.5663:0.2925	.	580	Q03692	COAA1_HUMAN	K	580	ENSP00000243222:Q580K;ENSP00000327368:Q580K	ENSP00000243222:Q580K	Q	-	1	0	COL10A1	116548234	1.000000	0.71417	0.986000	0.45419	0.996000	0.88848	2.258000	0.43249	0.487000	0.27698	0.455000	0.32223	CAG	.	.	.	none		0.398	COL10A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041926.1			T	116441541	G	T	116441541	3	4	81	1	0	0	0	0	1	0	0	0	3668	1386	48	4	308	4	COL10A1	6	116441541	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	73257491	116441541	54673526	40	5231											
SBDS	51119	hgsc.bcm.edu	37	chr7	66456178	66456178	+	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	atgaccttgatcagtggcttGagcttttctttcagcttctt	6	18	8	9	0	4	3	2	3	2	0	4	3	4	3	1	1	2	3	1	1	0	7			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr7:66456178G>C	ENST00000246868.2	-	4	753	c.570C>G	c.(568-570)ctC>ctG	p.L190L		NM_016038.2	NP_057122.2	Q9Y3A5	SBDS_HUMAN	Shwachman-Bodian-Diamond syndrome	190					bone marrow development (GO:0048539)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|inner cell mass cell proliferation (GO:0001833)|leukocyte chemotaxis (GO:0030595)|mature ribosome assembly (GO:0042256)|mitotic spindle stabilization (GO:0043148)|ribosomal large subunit biogenesis (GO:0042273)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|rRNA binding (GO:0019843)			cervix(1)|endometrium(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	7						TCAGTGGCTTGAGCTTTTCTT	0.368			Gene Conversion			"AML, MDS"			Shwachman-Diamond syndrome																												p.L190L		Atlas-SNP	.	yes	Rec		Schwachman-Diamond syndrome	7	7q11	51119	Shwachman-Bodian-Diamond syndrome protein		L	.	SBDS	20	.	0			c.C570G						PASS	.						142	119	127					7																	66456178		2203	4300	6503	SO:0001819	synonymous_variant	51119	exon4	Familial Cancer Database	Shwachman syndrome, Shwachman-Bodian syndrome, Congenital Lipomatosis of the Pancreas	TGGCTTGAGCTTT	AF151855	CCDS5537.1	7q11.22	2014-09-17			ENSG00000126524	ENSG00000126524			19440	protein-coding gene	gene with protein product		607444				12496757	Standard	NM_016038		Approved	CGI-97, FLJ10917, SDS, SWDS	uc003tvm.1	Q9Y3A5	OTTHUMG00000023165	ENST00000246868.2:c.570C>G	chr7.hg19:g.66456178G>C		77.0	0.0	.		95.0	20.0	.	NM_016038	A8K0P4|Q96FX0|Q9NV53	Silent	SNP	ENST00000246868.2	hg19	CCDS5537.1																																																																																			.	.	.	none		0.368	SBDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251746.2	NM_016038		C	66456178	G	C	66456178	2	2	81	1	0	0	0	0	0	0	0	1	13870	1277	45	4		4	SBDS	7	66456178	Silent	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10		66456178	92682485	41	5232											
ZNF498	221785	hgsc.bcm.edu	37	chr7	99219063	99219063	+	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	aggcgcttgggagccaggcaTccagctggggccagtggagg	7	5	19	10	1	0	0	0	0	0	0	1	2	1	2	3	7	2	3	3	7	0	1			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr7:99219063T>A	ENST00000394152.2	+	5	782	c.455T>A	c.(454-456)aTc>aAc	p.I152N	ZSCAN25_ENST00000262941.6_Missense_Mutation_p.I152N|ZSCAN25_ENST00000334715.3_Missense_Mutation_p.I152N|ZSCAN25_ENST00000466948.1_Intron	NM_145115.2	NP_660090.2	Q6NSZ9	ZSC25_HUMAN	zinc finger and SCAN domain containing 25	152					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GAGCCAGGCATCCAGCTGGGG	0.592																																					p.I152N		Atlas-SNP	.											.	.	.	.	0			c.T455A						PASS	.						73	71	72					7																	99219063		2203	4300	6503	SO:0001583	missense	221785	exon5			CAGGCATCCAGCT	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.455T>A	chr7.hg19:g.99219063T>A	ENSP00000377708:p.Ile152Asn	108.0	0.0	.		169.0	66.0	.	NM_145115	A4D290|D6W5T5|Q14C82|Q14C99|Q5EBM9|Q6DJZ0|Q6N032|Q6ZML3	Missense_Mutation	SNP	ENST00000394152.2	hg19	CCDS5671.2	.	.	.	.	.	.	.	.	.	.	T	13.88	2.370520	0.42003	.	.	ENSG00000197037	ENST00000394152;ENST00000334715;ENST00000262941	T;T;T	0.08896	3.1;3.1;3.04	5.08	5.08	0.68730	.	0.491076	0.17227	N	0.182081	T	0.06962	0.0177	N	0.24115	0.695	0.32243	N	0.572403	P;P	0.37276	0.589;0.454	B;B	0.37888	0.26;0.133	T	0.18053	-1.0349	10	0.26408	T	0.33	-10.0218	11.8202	0.52235	0.0:0.0:0.0:1.0	.	152;152	Q6NSZ9-2;Q6NSZ9	.;ZN498_HUMAN	N	152	ENSP00000377708:I152N;ENSP00000334800:I152N;ENSP00000262941:I152N	ENSP00000262941:I152N	I	+	2	0	ZNF498	99056999	0.009000	0.17119	0.884000	0.34674	0.768000	0.43524	1.283000	0.33237	2.210000	0.71456	0.533000	0.62120	ATC	.	.	.	none		0.592	ZSCAN25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157203.4	NM_145115		A	99219063	T	A	99219063	3	1	81	1	0	0	0	0	1	0	0	0	17959	1435	50	5	461	5	ZNF498	7	99219063	Missense_Mutation	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10	32762885	99219063	59919600	42	5233											
AASS	10157	hgsc.bcm.edu	37	chr7	121769482	121769482	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttattgtgtgggagaaaaatGcataagtcttcctggacatt	12	14	10	5	0	1	1	0	0	1	1	2	3	2	2	1	2	1	1	1	2	4	5			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr7:121769482G>A	ENST00000393376.1	-	2	415	c.320C>T	c.(319-321)gCa>gTa	p.A107V	AASS_ENST00000473553.1_Intron|AASS_ENST00000417368.2_Missense_Mutation_p.A107V			Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase	107	Lysine-ketoglutarate reductase.				cellular nitrogen compound metabolic process (GO:0034641)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity (GO:0047131)|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity (GO:0047130)			autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(6)|large_intestine(12)|lung(27)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	54						GGAGAAAAATGCATAAGTCTT	0.348																																					p.A107V		Atlas-SNP	.											.	AASS	123	.	0			c.C320T						PASS	.						59	61	60					7																	121769482		2202	4300	6502	SO:0001583	missense	10157	exon3			AAAAATGCATAAG	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.320C>T	chr7.hg19:g.121769482G>A	ENSP00000377040:p.Ala107Val	47.0	0.0	.		50.0	18.0	.	NM_005763	O95462	Missense_Mutation	SNP	ENST00000393376.1	hg19	CCDS5783.1	.	.	.	.	.	.	.	.	.	.	.	13.69	2.312716	0.40895	.	.	ENSG00000008311	ENST00000393376;ENST00000417368	T;T	0.74737	-0.87;-0.87	5.39	5.39	0.77823	Alanine dehydrogenase/PNT, N-terminal (1);	0.096191	0.64402	D	0.000001	T	0.63674	0.2531	N	0.20483	0.58	0.80722	D	1	B	0.32526	0.374	B	0.38225	0.268	T	0.59434	-0.7455	10	0.06365	T	0.9	-20.188	19.4914	0.95050	0.0:0.0:1.0:0.0	.	107	Q9UDR5	AASS_HUMAN	V	107	ENSP00000377040:A107V;ENSP00000403768:A107V	ENSP00000351834:A107V	A	-	2	0	AASS	121556718	1.000000	0.71417	0.929000	0.37066	0.990000	0.78478	9.799000	0.99117	2.681000	0.91329	0.655000	0.94253	GCA	.	.	.	none		0.348	AASS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347300.1	NM_005763		A	121769482	G	A	121769482	3	1	81	1	0	0	0	0	1	0	0	0	24	1319	46	2	2548	2	AASS	7	121769482	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	22550419	121769482	37369181	43	5234											
VIPR2	7434	hgsc.bcm.edu	37	chr7	158828654	158828654	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggactcacccggtgtcttcTaagtagagcctggccgcagt	7	10	12	12	2	3	1	1	0	2	1	3	2	3	2	3	3	1	2	3	3	2	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr7:158828654T>C	ENST00000262178.2	-	8	983	c.798A>G	c.(796-798)ttA>ttG	p.L266L	VIPR2_ENST00000377633.3_Silent_p.L250L|VIPR2_ENST00000402066.1_Silent_p.L407L	NM_003382.4	NP_003373.2	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2	266					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)		CGGTGTCTTCTAAGTAGAGCC	0.597																																					p.L266L	Pancreas(154;1876 1931 2329 17914 20079)	Atlas-SNP	.											.	VIPR2	53	.	0			c.A798G						PASS	.						81	60	67					7																	158828654		2203	4300	6503	SO:0001819	synonymous_variant	7434	exon8			GTCTTCTAAGTAG	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.798A>G	chr7.hg19:g.158828654T>C		59.0	0.0	.		144.0	68.0	.	NM_003382	Q13053|Q15870|Q53Y09|Q6ZN22|Q9UCW0	Silent	SNP	ENST00000262178.2	hg19	CCDS5950.1																																																																																			.	.	.	none		0.597	VIPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322675.1	NM_003382		C	158828654	T	C	158828654	2	2	81	1	0	0	0	0	0	0	0	1	17182	1519	53	3		3	VIPR2	7	158828654	Silent	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10	37059172	158828654	310009	44	5235											
MSR1	4481	hgsc.bcm.edu	37	chr8	16021617	16021617	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaggtctgagaatgttcccaAtctttcagtctgagatcatt	11	14	8	8	0	5	2	2	2	3	2	6	4	6	2	1	1	0	1	1	1	3	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr8:16021617A>G	ENST00000262101.5	-	5	895	c.774T>C	c.(772-774)gaT>gaC	p.D258D	MSR1_ENST00000355282.2_Silent_p.D258D|MSR1_ENST00000445506.2_Silent_p.D276D|MSR1_ENST00000350896.3_Silent_p.D258D|MSR1_ENST00000536385.1_Silent_p.D32D|MSR1_ENST00000381998.4_Silent_p.D258D			P21757	MSRE_HUMAN	macrophage scavenger receptor 1	258					cholesterol transport (GO:0030301)|lipoprotein transport (GO:0042953)|plasma lipoprotein particle clearance (GO:0034381)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)			haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(7)|lung(14)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	37				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)		AATGTTCCCAATCTTTCAGTC	0.303																																					p.D258D		Atlas-SNP	.											.	MSR1	140	.	0			c.T774C						PASS	.						168	150	156					8																	16021617		2203	4299	6502	SO:0001819	synonymous_variant	4481	exon5			TTCCCAATCTTTC	D13263	CCDS5995.1, CCDS5996.1, CCDS5997.1	8p22	2006-02-22			ENSG00000038945	ENSG00000038945		"CD molecules"	7376	protein-coding gene	gene with protein product		153622				2251254	Standard	NM_138715		Approved	SCARA1, CD204	uc003wwz.3	P21757	OTTHUMG00000094809	ENST00000262101.5:c.774T>C	chr8.hg19:g.16021617A>G		77.0	0.0	.		55.0	13.0	.	NM_138715	D3DSP3|O60505|P21759|Q45F10	Silent	SNP	ENST00000262101.5	hg19	CCDS5995.1																																																																																			.	.	.	none		0.303	MSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211627.2			G	16021617	A	G	16021617	2	3	81	1	0	0	0	0	0	0	0	1	9893	98	4	3		3	MSR1	8	16021617	Silent	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10		16021617	130342405	45	5236											
EYA1	2138	hgsc.bcm.edu	37	chr8	72182014	72182014	+	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	taggacccagtaagcaaggaGtggaaaacaatgattgtctc	15	8	11	7	0	1	1	0	1	1	0	2	4	1	4	1	3	2	2	1	3	6	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr8:72182014G>A	ENST00000340726.3	-	11	1650	c.1011C>T	c.(1009-1011)caC>caT	p.H337H	EYA1_ENST00000419131.1_Silent_p.H332H|EYA1_ENST00000388743.2_Silent_p.H336H|EYA1_ENST00000303824.7_Silent_p.H331H|EYA1_ENST00000388741.2_Silent_p.H303H|EYA1_ENST00000388742.4_Silent_p.H337H|EYA1_ENST00000388740.3_Silent_p.H304H	NM_000503.4	NP_000494.2	Q99502	EYA1_HUMAN	EYA transcriptional coactivator and phosphatase 1	337					anatomical structure morphogenesis (GO:0009653)|aorta morphogenesis (GO:0035909)|branching involved in ureteric bud morphogenesis (GO:0001658)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|double-strand break repair (GO:0006302)|embryonic skeletal system morphogenesis (GO:0048704)|establishment of mitotic spindle orientation (GO:0000132)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|histone dephosphorylation (GO:0016576)|lung epithelial cell differentiation (GO:0060487)|metanephros development (GO:0001656)|middle ear morphogenesis (GO:0042474)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neuron fate specification (GO:0048665)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of DNA repair (GO:0045739)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of neuron differentiation (GO:0045664)|response to ionizing radiation (GO:0010212)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)|RNA binding (GO:0003723)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(15)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	44	Breast(64;0.046)		Epithelial(68;0.0837)|all cancers(69;0.247)			TAAGCAAGGAGTGGAAAACAA	0.403																																					p.H337H		Atlas-SNP	.											.	EYA1	108	.	0			c.C1011T						PASS	.						172	156	161					8																	72182014		2203	4300	6503	SO:0001819	synonymous_variant	2138	exon11			CAAGGAGTGGAAA	AJ000098	CCDS34906.1, CCDS34907.1, CCDS47873.1, CCDS75750.1	8q13.3	2014-06-19	2014-06-19		ENSG00000104313	ENSG00000104313		"Protein tyrosine phosphatases / Asp-based PTPs"	3519	protein-coding gene	gene with protein product		601653	"eyes absent (Drosophila) homolog 1", "eyes absent homolog 1 (Drosophila)"	BOR		9020840	Standard	XM_005251184		Approved		uc003xys.4	Q99502	OTTHUMG00000149894	ENST00000340726.3:c.1011C>T	chr8.hg19:g.72182014G>A		102.0	0.0	.		110.0	33.0	.	NM_000503	A6NHQ0|G5E9R4|Q0P516|Q8WX80	Silent	SNP	ENST00000340726.3	hg19	CCDS34906.1																																																																																			.	.	.	none		0.403	EYA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313788.2	NM_000503, NM_172060		A	72182014	G	A	72182014	2	1	81	1	0	0	0	0	0	0	0	1	5330	1020	36	2		2	EYA1	8	72182014	Silent	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	56160397	72182014	74182008	46	5237											
FER1L6	654463	hgsc.bcm.edu	37	chr8	124989660	124989660	+	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	cctggctgtgtttttaggggCgaaccacagtgcagaagaac	10	9	13	9	1	0	2	0	0	0	2	0	3	0	2	2	3	3	3	2	3	4	3	rs535471573		TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr8:124989660C>T	ENST00000522917.1	+	10	1080	c.874C>T	c.(874-876)Cga>Tga	p.R292*	FER1L6_ENST00000399018.1_Nonsense_Mutation_p.R292*	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	292	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.					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)			TTTTTAGGGGCGAACCACAGT	0.478													C|||	1	0.000199681	0	0.0014	5008	,	,		21723	0		0	False		,,,				2504	0				p.R292X		Atlas-SNP	.											.	FER1L6	268	.	0			c.C874T						PASS	.						128	126	127					8																	124989660		2043	4204	6247	SO:0001587	stop_gained	654463	exon10			TAGGGGCGAACCA	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.874C>T	chr8.hg19:g.124989660C>T	ENSP00000428280:p.Arg292*	122.0	0.0	.		124.0	46.0	.	NM_001039112		Nonsense_Mutation	SNP	ENST00000522917.1	hg19	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	C	38	7.224901	0.98146	.	.	ENSG00000214814	ENST00000522917;ENST00000399018	.	.	.	5.53	1.04	0.20106	.	0.091536	0.44688	U	0.000426	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	.	16.3285	0.82997	0.4563:0.5437:0.0:0.0	.	.	.	.	X	292	.	ENSP00000381982:R292X	R	+	1	2	FER1L6	125058841	0.002000	0.14202	0.996000	0.52242	0.952000	0.60782	0.481000	0.22260	0.264000	0.21851	-0.268000	0.10319	CGA	.	.	.	none		0.478	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		T	124989660	C	T	124989660	4	4	81	1	0	0	0	0	0	1	0	0	5822	760	27	1	908	1	FER1L6	8	124989660	Nonsense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	52807646	124989660	21374362	47	5238											
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79325026	79325026	+	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	attgctacccagttcaggctGaccaaattcagactcccagg	11	9	8	13	0	2	2	2	1	0	1	3	2	3	2	3	2	2	3	3	2	2	4			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr9:79325026G>A	ENST00000376718.3	-	8	2287	c.2164C>T	c.(2164-2166)Cag>Tag	p.Q722*	PRUNE2_ENST00000428286.1_Nonsense_Mutation_p.Q363*	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	722					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						AGTTCAGGCTGACCAAATTCA	0.458																																					p.Q722X		Atlas-SNP	.											.	PRUNE2	331	.	0			c.C2164T						PASS	.						54	49	51					9																	79325026		1568	3582	5150	SO:0001587	stop_gained	158471	exon8			CAGGCTGACCAAA	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.2164C>T	chr9.hg19:g.79325026G>A	ENSP00000365908:p.Gln722*	98.0	0.0	.		69.0	36.0	.	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Nonsense_Mutation	SNP	ENST00000376718.3	hg19	CCDS47982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.95|13.95	2.388631|2.388631	0.42308|0.42308	.|.	.|.	ENSG00000106772|ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033|ENST00000426088	.|.	.|.	.|.	5.97|5.97	5.97|5.97	0.96955|0.96955	.|.	0.000000|.	0.50627|.	D|.	0.000114|.	.|T	.|0.72128	.|0.3422	.|.	.|.	.|.	0.46149|0.46149	D|D	0.998894|0.998894	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.69217	.|-0.5203	.|4	0.38643|.	T|.	0.18|.	-6.3717|-6.3717	15.6992|15.6992	0.77528|0.77528	0.0:0.1355:0.8645:0.0|0.0:0.1355:0.8645:0.0	.|.	.|.	.|.	.|.	X|L	722;363;721|43	.|.	ENSP00000365908:Q722X|.	Q|S	-|-	1|2	0|0	PRUNE2|PRUNE2	78514846|78514846	0.736000|0.736000	0.28164|0.28164	0.024000|0.024000	0.17045|0.17045	0.138000|0.138000	0.21146|0.21146	2.887000|2.887000	0.48586|0.48586	2.836000|2.836000	0.97738|0.97738	0.655000|0.655000	0.94253|0.94253	CAG|TCA	.	.	.	none		0.458	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		A	79325026	G	A	79325026	4	1	81	1	0	0	0	0	0	1	0	0	12651	1299	45	2	7150	2	PRUNE2	9	79325026	Nonsense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10		79325026	61888405	48	5239											
WNK2	65268	hgsc.bcm.edu	37	chr9	96079890	96079890	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcattcccggagccgcccCgaccctgtccgtgcccacac	5	6	10	20	4	1	0	1	0	0	0	3	2	3	1	7	2	2	0	7	2	0	1	rs377748076		TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr9:96079890C>T	ENST00000297954.4	+	29	6716	c.6716C>T	c.(6715-6717)cCg>cTg	p.P2239L	WNK2_ENST00000427277.2_Missense_Mutation_p.P1814L|WNK2_ENST00000349097.3_Missense_Mutation_p.P1851L|WNK2_ENST00000356055.3_3'UTR|WNK2_ENST00000395477.2_Missense_Mutation_p.P2202L|WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000471076.1_3'UTR	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	2239					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						GGAGCCGCCCCGACCCTGTCC	0.667																																					p.P2202L		Atlas-SNP	.											.	WNK2	277	.	0			c.C6605T						PASS	.	A	LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	52	44	47		6605	2.6	0	9		47	0,8596		0,0,4298	no	missense	WNK2	NM_006648.3	98	0,1,6500	TT,TC,CC		0.0,0.0227,0.0077	benign	2202/2218	96079890	1,13001	2203	4298	6501	SO:0001583	missense	65268	exon28			CCGCCCCGACCCT	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.6716C>T	chr9.hg19:g.96079890C>T	ENSP00000297954:p.Pro2239Leu	60.0	0.0	.		18.0	5.0	.	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Missense_Mutation	SNP	ENST00000297954.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	6.441|6.441	0.449533|0.449533	0.12223|0.12223	2.27E-4|2.27E-4	0.0|0.0	ENSG00000165238|ENSG00000165238	ENST00000297954;ENST00000395477;ENST00000349097;ENST00000427277|ENST00000432730;ENST00000448251	T;T;T;T|.	0.74842|.	-0.77;-0.88;-0.2;-0.01|.	5.73|5.73	2.64|2.64	0.31445|0.31445	.|.	0.398049|.	0.21391|.	N|.	0.075314|.	T|.	0.37073|.	0.0990|.	L|L	0.48642|0.48642	1.525|1.525	0.21967|0.21967	N|N	0.999449|0.999449	P;B;B;B|.	0.38195|.	0.622;0.066;0.108;0.255|.	B;B;B;B|.	0.32393|.	0.145;0.008;0.012;0.024|.	T|.	0.24977|.	-1.0145|.	10|.	0.87932|.	D|.	0|.	.|.	5.2308|5.2308	0.15420|0.15420	0.1562:0.6551:0.0:0.1887|0.1562:0.6551:0.0:0.1887	.|.	2202;1693;2202;2239|.	Q9Y3S1-2;A6PVR4;F8W9F9;Q9Y3S1|.	.;.;.;WNK2_HUMAN|.	L|X	2239;2202;1851;1814|2198;999	ENSP00000297954:P2239L;ENSP00000378860:P2202L;ENSP00000297876:P1851L;ENSP00000411181:P1814L|.	ENSP00000297954:P2239L|.	P|R	+|+	2|1	0|2	WNK2|WNK2	95119711|95119711	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.006000|0.006000	0.05464|0.05464	0.676000|0.676000	0.25247|0.25247	0.229000|0.229000	0.21039|0.21039	-0.127000|-0.127000	0.14921|0.14921	CCG|CGA	.	.	.	weak		0.667	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648		T	96079890	C	T	96079890	3	4	81	1	0	0	0	0	1	0	0	0	17390	652	23	1	6715	1	WNK2	9	96079890	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	16754864	96079890	45133541	49	5240											
TDRD7	23424	hgsc.bcm.edu	37	chr9	100227199	100227199	+	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	gaatattacagtaagaatccTaagatcacaccagtccaggc	16	8	7	10	0	1	2	1	0	0	2	3	3	3	2	3	1	1	1	3	1	6	4			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr9:100227199T>G	ENST00000355295.4	+	8	1813	c.1518T>G	c.(1516-1518)ccT>ccG	p.P506P	TDRD7_ENST00000422139.2_Silent_p.P432P	NM_014290.2	NP_055105.2	Q8NHU6	TDRD7_HUMAN	tudor domain containing 7	506					germ cell development (GO:0007281)|lens fiber cell differentiation (GO:0070306)|lens morphogenesis in camera-type eye (GO:0002089)|posttranscriptional regulation of gene expression (GO:0010608)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|P granule (GO:0043186)|ribonucleoprotein granule (GO:0035770)	mRNA binding (GO:0003729)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Acute lymphoblastic leukemia(62;0.158)				GTAAGAATCCTAAGATCACAC	0.458																																					p.P506P		Atlas-SNP	.											.	TDRD7	78	.	0			c.T1518G						PASS	.						115	106	109					9																	100227199		2203	4300	6503	SO:0001819	synonymous_variant	23424	exon8			GAATCCTAAGATC	AB025254	CCDS6725.1	9q22.33	2013-01-23			ENSG00000196116	ENSG00000196116		"Tudor domain containing"	30831	protein-coding gene	gene with protein product		611258				21436445	Standard	NM_014290		Approved	PCTAIRE2BP	uc004axj.3	Q8NHU6	OTTHUMG00000020326	ENST00000355295.4:c.1518T>G	chr9.hg19:g.100227199T>G		134.0	0.0	.		126.0	27.0	.	NM_014290	A6NCI6|B2RBX3|B4DG99|B4DXF7|E7EQD4|Q5VV27|Q96JT1|Q9UFF0|Q9Y2M3	Silent	SNP	ENST00000355295.4	hg19	CCDS6725.1																																																																																			.	.	.	none		0.458	TDRD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053322.1	NM_014290		G	100227199	T	G	100227199	2	3	81	1	0	0	0	0	0	0	0	1	15747	1509	53	5		5	TDRD7	9	100227199	Silent	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10	4147309	100227199	40986232	50	5241											
CTNNAL1	8727	hgsc.bcm.edu	37	chr9	111761412	111761413	+	Missense_Mutation	DNP	AT	AT	CC																															aatcccagttttcattggctAtagcttctcctactttaaca																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A|T	A|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr9:111761412_111761413AT>CC	ENST00000325551.4	-	2	351_352	c.265_266AT>GG	c.(265-267)ATa>GGa	p.I89G	CTNNAL1_ENST00000325580.6_Missense_Mutation_p.I89G|CTNNAL1_ENST00000374593.4_Missense_Mutation_p.I89G|CTNNAL1_ENST00000374595.4_Missense_Mutation_p.I89G	NM_003798.2	NP_003789.1	Q9UBT7	CTNL1_HUMAN	catenin (cadherin-associated protein), alpha-like 1	89					cell adhesion (GO:0007155)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(4)|urinary_tract(2)	25				STAD - Stomach adenocarcinoma(157;0.0768)		TTCATTGGCTATAGCTTCTCCT	0.356																																					p.I89R|p.I89V		Atlas-SNP	.											.	CTNNAL1	51	.	0			c.T266G|c.A265G						PASS	.																																			SO:0001583	missense	8727	exon2			TTGGCTATAGCTT|TGGCTATAGCTTC	AF030233	CCDS6775.1, CCDS69638.1	9q31.2	2008-07-21			ENSG00000119326	ENSG00000119326			2512	protein-coding gene	gene with protein product	"alpha-catulin", "alpha2-catulin"	604785				9806841	Standard	XM_005252291		Approved	CLLP, alpha-CATU	uc004bdo.1	Q9UBT7	OTTHUMG00000020466	ENST00000325551.4:c.265_266delinsCC	chr9.hg19:g.111761412_111761413delinsCC	ENSP00000320434:p.Ile89Gly	44.0	0.0	.		54.0|55.0	14.0	.	NM_003798	B5BU47|O76084|Q53FQ2|Q5JTQ7|Q5JTQ8|Q9Y401	Missense_Mutation	SNP	ENST00000325551.4	hg19	CCDS6775.1																																																																																			.	.	.	none		0.356	CTNNAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053577.1	NM_003798		CC	111761413	AT	CC	111761412	3	2	81	1	0	0	0	0	1	0	0	0	4017	449	16	5	2010	5	CTNNAL1	9	111761412	Missense_Mutation	DNP	AT	TCGA-B1-A47M-01A-11D-A25F-10	11534213	111761412	29452019	51	5242											
ZBTB6	10773	hgsc.bcm.edu	37	chr9	125673886	125673886	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcacagtctttatcagaatTttcatcttcattcttaacat	11	18	2	10	0	7	1	4	0	3	1	7	1	7	1	0	0	1	0	0	0	3	7			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr9:125673886T>C	ENST00000373659.3	-	2	554	c.466A>G	c.(466-468)Aat>Gat	p.N156D		NM_006626.5	NP_006617.1	Q15916	ZBTB6_HUMAN	zinc finger and BTB domain containing 6	156					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(1)|skin(1)	11						TTATCAGAATTTTCATCTTCA	0.338																																					p.N156D		Atlas-SNP	.											.	ZBTB6	32	.	0			c.A466G						PASS	.						57	57	57					9																	125673886		2203	4300	6503	SO:0001583	missense	10773	exon2			CAGAATTTTCATC	X82018	CCDS6846.1	9q33.1-q33.3	2013-01-08	2006-04-10	2006-04-10	ENSG00000186130	ENSG00000186130		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16764	protein-coding gene	gene with protein product		605976	"zinc finger protein 482"	ZNF482		7958847	Standard	NM_006626		Approved	ZID	uc004bnh.4	Q15916	OTTHUMG00000020628	ENST00000373659.3:c.466A>G	chr9.hg19:g.125673886T>C	ENSP00000362763:p.Asn156Asp	21.0	0.0	.		24.0	6.0	.	NM_006626	A8K8N6	Missense_Mutation	SNP	ENST00000373659.3	hg19	CCDS6846.1	.	.	.	.	.	.	.	.	.	.	T	1.533	-0.543782	0.04053	.	.	ENSG00000186130	ENST00000373659	T	0.09073	3.02	5.96	3.54	0.40534	.	1.010830	0.07908	N	0.973873	T	0.04363	0.0120	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.47129	-0.9141	10	0.10902	T	0.67	.	6.968	0.24632	0.0:0.0766:0.2858:0.6376	.	156	Q15916	ZBTB6_HUMAN	D	156	ENSP00000362763:N156D	ENSP00000362763:N156D	N	-	1	0	ZBTB6	124713707	0.001000	0.12720	0.992000	0.48379	0.995000	0.86356	0.967000	0.29344	0.460000	0.27045	0.533000	0.62120	AAT	.	.	.	none		0.338	ZBTB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053962.1	NM_006626		C	125673886	T	C	125673886	3	2	81	1	0	0	0	0	1	0	0	0	17564	1841	64	3	812	3	ZBTB6	9	125673886	Missense_Mutation	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10	13912474	125673886	15539545	52	5243											
ODF2	4957	hgsc.bcm.edu	37	chr9	131250301	131250301	+	Frame_Shift_Del	DEL	G	G	-																															aagctggagaatgagaggctGaaggttcgcagtgagagctg																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr9:131250301delG	ENST00000434106.3	+	14	1896	c.1533delG	c.(1531-1533)ctgfs	p.L511fs	ODF2_ENST00000372807.5_Frame_Shift_Del_p.L506fs|ODF2_ENST00000604420.1_Frame_Shift_Del_p.L511fs|ODF2_ENST00000546203.1_Frame_Shift_Del_p.L492fs|ODF2_ENST00000372791.3_Frame_Shift_Del_p.L492fs|ODF2_ENST00000351030.3_Frame_Shift_Del_p.L506fs|ODF2_ENST00000393533.2_Frame_Shift_Del_p.L511fs|ODF2_ENST00000372814.3_Frame_Shift_Del_p.L555fs|ODF2_ENST00000448249.3_Frame_Shift_Del_p.L430fs|ODF2_ENST00000393527.3_Frame_Shift_Del_p.L487fs|ODF2_ENST00000444119.2_Frame_Shift_Del_p.L487fs	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	511					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						ATGAGAGGCTGAAGGTTCGCA	0.587																																					p.L575fs		Atlas-Indel,Pindel	.											.	ODF2	227	.	0			c.1724delT						PASS	.						72	63	66					9																	131250301		2203	4300	6503	SO:0001589	frameshift_variant	4957	exon14			.	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.1533delG	chr9.hg19:g.131250301delG	ENSP00000403453:p.Leu511fs	64.0	0.0	0		46.0	16.0	0.347826	NM_153435	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Frame_Shift_Del	DEL	ENST00000434106.3	hg19	CCDS56588.1																																																																																			.	.	.	none		0.587	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3			-	131250301	G	-	131250301	7	5	81	1	0	1	0	1	0	0	0	0	10834	1277	45	0	1638	0	ODF2	9	131250301	Frame_Shift_Del	DEL	G	TCGA-B1-A47M-01A-11D-A25F-10	5576415	131250301	9963130	53	5244											
PARG	8505	hgsc.bcm.edu	37	chr10	51028288	51028288	+	Frame_Shift_Del	DEL	A	A	-																															attctgagtccccaaaggtgAaataaaccacatctcgctca																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr10:51028288delA	ENST00000402038.3	-	13	1243	c.1244delT	c.(1243-1245)ttcfs	p.F415fs		NM_003631.2	NP_003622.2	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase	900	A-domain.				carbohydrate metabolic process (GO:0005975)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(ADP-ribose) glycohydrolase activity (GO:0004649)			endometrium(5)|kidney(2)|lung(1)|ovary(2)	10				Epithelial(53;0.213)		CCCAAAGGTGAAATAAACCAC	0.423																																					p.F900fs		Atlas-Indel,Pindel	.											.	PARG	46	.	0			c.2700delC						PASS	.						139	114	122					10																	51028288		692	1591	2283	SO:0001589	frameshift_variant	8505	exon17			.	AF005043	CCDS73130.1	10q11.23	2012-04-20			ENSG00000227345	ENSG00000227345	3.2.1.143		8605	protein-coding gene	gene with protein product		603501				9115250, 10449915	Standard	NM_003631		Approved		uc001jif.3	Q86W56	OTTHUMG00000018201	ENST00000402038.3:c.1244delT	chr10.hg19:g.51028288delA	ENSP00000384408:p.Phe415fs	89.0	0.0	0		75.0	21.0	0.28	NM_003631	A5YBK3|B2RC24|B4DIU5|B4DYR4|I6RUV3|Q6E4P6|Q6E4P7|Q7Z742|Q9Y4W7	Frame_Shift_Del	DEL	ENST00000402038.3	hg19																																																																																				.	.	.	none		0.423	PARG-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048011.2	NM_003631		-	51028288	A	-	51028288	7	5	81	1	0	1	0	1	0	0	0	0	11455	246	9	0	239	0	PARG	10	51028288	Frame_Shift_Del	DEL	A	TCGA-B1-A47M-01A-11D-A25F-10		51028288	84506459	54	5245	57	2									
PARG	8505	hgsc.bcm.edu	37	chr10	51028292	51028292	+	Missense_Mutation	SNP	A	A	T																															tgagtccccaaaggtgaaatAaaccacatctcgctcagctg																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr10:51028292A>T	ENST00000402038.3	-	13	1239	c.1240T>A	c.(1240-1242)Tat>Aat	p.Y414N		NM_003631.2	NP_003622.2	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase	899	A-domain.			F -> L (in Ref. 3; AAB61614). {ECO:0000305}.	carbohydrate metabolic process (GO:0005975)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(ADP-ribose) glycohydrolase activity (GO:0004649)			endometrium(5)|kidney(2)|lung(1)|ovary(2)	10				Epithelial(53;0.213)		AAGGTGAAATAAACCACATCT	0.418																																					p.Y899N		Atlas-SNP	.											.	PARG	46	.	0			c.T2695A						PASS	.						129	108	114					10																	51028292		692	1591	2283	SO:0001583	missense	8505	exon17			TGAAATAAACCAC	AF005043	CCDS73130.1	10q11.23	2012-04-20			ENSG00000227345	ENSG00000227345	3.2.1.143		8605	protein-coding gene	gene with protein product		603501				9115250, 10449915	Standard	NM_003631		Approved		uc001jif.3	Q86W56	OTTHUMG00000018201	ENST00000402038.3:c.1240T>A	chr10.hg19:g.51028292A>T	ENSP00000384408:p.Tyr414Asn	87.0	0.0	.		77.0	22.0	.	NM_003631	A5YBK3|B2RC24|B4DIU5|B4DYR4|I6RUV3|Q6E4P6|Q6E4P7|Q7Z742|Q9Y4W7	Missense_Mutation	SNP	ENST00000402038.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	28.5|28.5	4.922052|4.922052	0.92319|0.92319	.|.	.|.	ENSG00000227345|ENSG00000227345	ENST00000432127|ENST00000402038	.|.	.|.	.|.	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	.|.	.|.	.|.	.|.	D|D	0.84447|0.84447	0.5474|0.5474	M|M	0.87971|0.87971	2.92|2.92	.|.	.|.	.|.	.|D;D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D;D;D	.|0.97110	.|0.999;1.0;0.999;0.999;0.999;0.999;1.0	D|D	0.87072|0.87072	0.2160|0.2160	4|7	.|0.87932	.|D	.|0	-13.0842|-13.0842	16.5582|16.5582	0.84512|0.84512	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|817;899;450;167;414;439;899	.|Q86W56-2;Q86W56;A5YBK3;B4DHS4;Q5SQP4;B4DX76;Q0MQR4	.|.;PARG_HUMAN;.;.;.;.;.	L|N	114|414	.|.	.|ENSP00000384408:Y414N	F|Y	-|-	3|1	2|0	PARG|PARG	50698298|50698298	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.383000|8.383000	0.90157|0.90157	2.308000|2.308000	0.77769|0.77769	0.533000|0.533000	0.62120|0.62120	TTT|TAT	.	.	.	none		0.418	PARG-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048011.2	NM_003631		T	51028292	A	T	51028292	3	4	81	1	0	0	0	0	1	0	0	0	11455	362	13	5	243	5	PARG	10	51028292	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	4	51028292	84506455	55	5246	57	2									
TET1	80312	hgsc.bcm.edu	37	chr10	70446307	70446307	+	Frame_Shift_Del	DEL	G	G	-																															aaaagaacgtgtttcactcaGcctgttccccgttctggaaa																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr10:70446307delG	ENST00000373644.4	+	11	5456	c.5247delG	c.(5245-5247)cagfs	p.Q1749fs		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1749					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						GTTTCACTCAGCCTGTTCCCC	0.507																																					p.Q1749fs		Atlas-Indel,Pindel	.											.	TET1	255	.	0			c.5246delA						PASS	.						104	105	105					10																	70446307		2203	4300	6503	SO:0001589	frameshift_variant	80312	exon11			.	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.5247delG	chr10.hg19:g.70446307delG	ENSP00000362748:p.Gln1749fs	130.0	0.0	0		136.0	44.0	0.323529	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Frame_Shift_Del	DEL	ENST00000373644.4	hg19	CCDS7281.1																																																																																			.	.	.	none		0.507	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		-	70446307	G	-	70446307	7	5	81	1	0	1	0	1	0	0	0	0	15781	962	34	0	5285	0	TET1	10	70446307	Frame_Shift_Del	DEL	G	TCGA-B1-A47M-01A-11D-A25F-10	19418015	70446307	65088440	56	5247											
SMC3	9126	hgsc.bcm.edu	37	chr10	112361757	112361757	+	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	ttgagcagtgcaacacagaaTtaaagaagtacagccatgtt	16	9	9	7	0	0	3	0	1	0	2	0	3	0	3	1	0	5	4	1	0	6	4			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr10:112361757T>A	ENST00000361804.4	+	25	3052	c.2926T>A	c.(2926-2928)Tta>Ata	p.L976I		NM_005445.3	NP_005436.1	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3	976					DNA repair (GO:0006281)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid cohesion (GO:0007064)|mitotic spindle organization (GO:0007052)|negative regulation of DNA endoreduplication (GO:0032876)|regulation of DNA replication (GO:0006275)|signal transduction (GO:0007165)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	basement membrane (GO:0005604)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cohesin core heterodimer (GO:0008280)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear matrix (GO:0016363)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|dynein binding (GO:0045502)|microtubule motor activity (GO:0003777)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(5)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		CAACACAGAATTAAAGAAGTA	0.303																																					p.L976I		Atlas-SNP	.											.	SMC3	103	.	0			c.T2926A						PASS	.						46	48	47					10																	112361757		2201	4300	6501	SO:0001583	missense	9126	exon25			ACAGAATTAAAGA	AF020043	CCDS31285.1	10q25	2014-09-17	2006-07-06	2006-07-06	ENSG00000108055	ENSG00000108055		"Structural maintenance of chromosomes proteins", "Proteoglycans / Extracellular Matrix : Other"	2468	protein-coding gene	gene with protein product	"bamacan proteoglycan"	606062	"chondroitin sulfate proteoglycan 6 (bamacan)"	CSPG6		9506951, 10358101	Standard	NM_005445		Approved	HCAP, BAM, SMC3L1, bamacan	uc001kze.3	Q9UQE7	OTTHUMG00000019042	ENST00000361804.4:c.2926T>A	chr10.hg19:g.112361757T>A	ENSP00000354720:p.Leu976Ile	56.0	0.0	.		47.0	9.0	.	NM_005445	A8K156|O60464|Q5T482	Missense_Mutation	SNP	ENST00000361804.4	hg19	CCDS31285.1	.	.	.	.	.	.	.	.	.	.	T	18.65	3.669080	0.67814	.	.	ENSG00000108055	ENST00000361804	T	0.76839	-1.05	5.32	1.32	0.21799	RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	T	0.80243	0.4587	M	0.75884	2.315	0.80722	D	1	D	0.62365	0.991	D	0.63283	0.913	T	0.78021	-0.2367	10	0.07175	T	0.84	.	6.5259	0.22301	0.0:0.5503:0.0:0.4497	.	976	Q9UQE7	SMC3_HUMAN	I	976	ENSP00000354720:L976I	ENSP00000354720:L976I	L	+	1	2	SMC3	112351747	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	3.542000	0.53625	0.427000	0.26145	0.477000	0.44152	TTA	.	.	.	none		0.303	SMC3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050337.1	NM_005445		A	112361757	T	A	112361757	3	1	81	1	0	0	0	0	1	0	0	0	14797	1490	52	5	3024	5	SMC3	10	112361757	Missense_Mutation	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10	41915450	112361757	23172990	57	5248											
RAB11FIP2	22841	hgsc.bcm.edu	37	chr10	119798692	119798692	+	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	aggctaactttctcccttttCtctcttttattttcttttct	4	24	2	11	0	5	0	0	0	5	0	7	0	5	0	1	1	1	1	1	1	2	10			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr10:119798692C>A	ENST00000355624.3	-	3	1495	c.1056G>T	c.(1054-1056)gaG>gaT	p.E352D	RAB11FIP2_ENST00000369199.3_Missense_Mutation_p.E352D|RP11-354M20.3_ENST00000417968.4_RNA|RP11-354M20.3_ENST00000451610.2_RNA	NM_014904.2	NP_055719.1	Q7L804	RFIP2_HUMAN	RAB11 family interacting protein 2 (class I)	352					establishment of cell polarity (GO:0030010)|insulin secretion involved in cellular response to glucose stimulus (GO:0035773)|protein transport (GO:0015031)|regulated secretory pathway (GO:0045055)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasmic vesicle membrane (GO:0030659)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(8)	19		Colorectal(252;0.235)		all cancers(201;0.0238)		TCTCCCTTTTCTCTCTTTTAT	0.353																																					p.E352D		Atlas-SNP	.											.	RAB11FIP2	39	.	0			c.G1056T						PASS	.						150	161	157					10																	119798692		2202	4300	6502	SO:0001583	missense	22841	exon3			CCTTTTCTCTCTT	AY037299	CCDS7602.1	10q26.12	2004-07-22			ENSG00000107560	ENSG00000107560			29152	protein-coding gene	gene with protein product		608599				11994279, 10231032	Standard	NM_014904		Approved	KIAA0941, nRip11, Rab11-FIP2	uc001ldj.2	Q7L804	OTTHUMG00000019128	ENST00000355624.3:c.1056G>T	chr10.hg19:g.119798692C>A	ENSP00000347839:p.Glu352Asp	67.0	0.0	.		57.0	17.0	.	NM_014904	A6NEI4|Q3I768|Q9Y2F0	Missense_Mutation	SNP	ENST00000355624.3	hg19	CCDS7602.1	.	.	.	.	.	.	.	.	.	.	C	9.205	1.029505	0.19512	.	.	ENSG00000107560	ENST00000355624;ENST00000369199	T;T	0.66638	-0.21;-0.22	5.76	0.259	0.15583	.	0.171402	0.53938	D	0.000046	T	0.51584	0.1683	L	0.50333	1.59	0.44627	D	0.997603	B;B	0.16166	0.016;0.007	B;B	0.13407	0.009;0.004	T	0.27157	-1.0082	10	0.17369	T	0.5	-21.6296	6.802	0.23756	0.0:0.5332:0.1101:0.3567	.	352;352	Q3I768;Q7L804	.;RFIP2_HUMAN	D	352	ENSP00000347839:E352D;ENSP00000358200:E352D	ENSP00000347839:E352D	E	-	3	2	RAB11FIP2	119788682	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	1.171000	0.31896	0.067000	0.16545	-0.355000	0.07637	GAG	.	.	.	none		0.353	RAB11FIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050583.1	NM_014904		A	119798692	C	A	119798692	3	1	81	1	0	0	0	0	1	0	0	0	12907	912	32	4	494	4	RAB11FIP2	10	119798692	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	7436935	119798692	15736055	58	5249											
OR51E1	143503	hgsc.bcm.edu	37	chr11	4674486	4674486	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaaggcatttggcacttgcGtctctcatgtgtgtgctgtg	5	14	12	10	1	2	0	1	0	1	0	3	0	2	0	1	2	2	3	1	2	1	2	rs148787592		TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr11:4674486G>A	ENST00000396952.5	+	2	1380	c.730G>A	c.(730-732)Gtc>Atc	p.V244I	OR51E1_ENST00000530215.1_Intron	NM_152430.3	NP_689643.2	Q8TCB6	O51E1_HUMAN	olfactory receptor, family 51, subfamily E, member 1	243						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V243I(1)		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)		TGGCACTTGCGTCTCTCATGT	0.498																																					p.V244I		Atlas-SNP	.											OR51E1,colon,carcinoma,-1,1	OR51E1	67	.	1	Substitution - Missense(1)	large_intestine(1)	c.G730A						PASS	.	G	ILE/VAL	0,4402		0,0,2201	243	229	234		730	4	1	11	dbSNP_134	234	3,8593	3.0+/-9.4	0,3,4295	yes	missense	OR51E1	NM_152430.3	29	0,3,6496	AA,AG,GG		0.0349,0.0,0.0231	possibly-damaging	244/319	4674486	3,12995	2201	4298	6499	SO:0001583	missense	143503	exon2			ACTTGCGTCTCTC	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.730G>A	chr11.hg19:g.4674486G>A	ENSP00000380155:p.Val244Ile	99.0	0.0	.		77.0	26.0	.	NM_152430	A8KAM6|Q5S4P5|Q66X57|Q6IF93	Missense_Mutation	SNP	ENST00000396952.5	hg19	CCDS31358.2	.	.	.	.	.	.	.	.	.	.	G	9.642	1.139187	0.21205	0.0	3.49E-4	ENSG00000180785	ENST00000396952	T	0.37584	1.19	4.89	3.98	0.46160	GPCR, rhodopsin-like superfamily (1);	0.255092	0.27563	N	0.018809	T	0.18551	0.0445	N	0.20881	0.62	0.80722	D	1	P	0.43826	0.818	B	0.37239	0.244	T	0.05007	-1.0912	10	0.07644	T	0.81	.	9.4332	0.38624	0.1719:0.0:0.8281:0.0	.	243	Q8TCB6	O51E1_HUMAN	I	244	ENSP00000380155:V244I	ENSP00000380155:V244I	V	+	1	0	OR51E1	4631062	0.000000	0.05858	1.000000	0.80357	0.830000	0.47004	0.514000	0.22786	1.435000	0.47434	0.655000	0.94253	GTC	.	G|1.000;A|0.000	0.000	weak		0.498	OR51E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347136.2	NM_152430		A	4674486	G	A	4674486	3	1	81	1	0	0	0	0	1	0	0	0	11101	1145	40	1	732	1	OR51E1	11	4674486	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10		4674486	130332030	59	5250											
ZDHHC5	25921	hgsc.bcm.edu	37	chr11	57466844	57466844	+	Missense_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	gccaaaaagcccaacctggtGtctctgagacagaagaagtg	14	6	11	10	0	1	3	0	1	1	3	2	4	1	3	3	1	2	0	3	1	5	0			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr11:57466844G>A	ENST00000287169.3	+	11	3298	c.1936G>A	c.(1936-1938)Gtc>Atc	p.V646I	ZDHHC5_ENST00000527985.1_Missense_Mutation_p.V593I	NM_015457.2	NP_056272.2	Q9C0B5	ZDHC5_HUMAN	zinc finger, DHHC-type containing 5	646					protein palmitoylation (GO:0018345)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(3)|large_intestine(3)|lung(5)|skin(1)	18						CCAACCTGGTGTCTCTGAGAC	0.527																																					p.V646I		Atlas-SNP	.											.	ZDHHC5	49	.	0			c.G1936A						PASS	.						60	62	61					11																	57466844		2201	4296	6497	SO:0001583	missense	25921	exon11			CCTGGTGTCTCTG	AB051535	CCDS7965.1	11q13.1	2008-05-02			ENSG00000156599	ENSG00000156599		"Zinc fingers, DHHC-type"	18472	protein-coding gene	gene with protein product		614586				11214970	Standard	NM_015457		Approved	KIAA1748, ZNF375	uc001nkx.1	Q9C0B5	OTTHUMG00000167198	ENST00000287169.3:c.1936G>A	chr11.hg19:g.57466844G>A	ENSP00000287169:p.Val646Ile	44.0	0.0	.		33.0	13.0	.	NM_015457	Q2TGF0|Q6ZMF0|Q8TAK8|Q9H923|Q9UFI7	Missense_Mutation	SNP	ENST00000287169.3	hg19	CCDS7965.1	.	.	.	.	.	.	.	.	.	.	G	8.863	0.947386	0.18356	.	.	ENSG00000156599	ENST00000527985;ENST00000287169	T;T	0.57436	0.4;1.41	5.83	5.83	0.93111	.	1.629370	0.03465	N	0.212746	T	0.55242	0.1908	N	0.11427	0.14	0.43043	D	0.994634	P	0.42584	0.784	P	0.55391	0.775	T	0.48525	-0.9028	10	0.08381	T	0.77	-21.3343	17.8915	0.88874	0.0:0.0:1.0:0.0	.	646	Q9C0B5	ZDHC5_HUMAN	I	593;646	ENSP00000432202:V593I;ENSP00000287169:V646I	ENSP00000287169:V646I	V	+	1	0	ZDHHC5	57223420	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.646000	0.46630	2.769000	0.95229	0.655000	0.94253	GTC	.	.	.	none		0.527	ZDHHC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393694.1	NM_015457		A	57466844	G	A	57466844	3	1	81	1	0	0	0	0	1	0	0	0	17630	1377	48	2	1974	2	ZDHHC5	11	57466844	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	52792358	57466844	77539672	60	5251											
ARL2	402	hgsc.bcm.edu	37	chr11	64789247	64789247	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgcatccagggctgcagcGccgtcaccggggagaacctg	7	5	16	13	3	1	1	1	0	0	1	2	2	2	1	4	4	4	3	4	4	1	0			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr11:64789247G>A	ENST00000246747.4	+	5	570	c.475G>A	c.(475-477)Gcc>Acc	p.A159T	ARL2_ENST00000533729.1_Missense_Mutation_p.A132T|ARL2_ENST00000529384.1_Missense_Mutation_p.A159T|RP11-399J13.3_ENST00000301886.3_Intron	NM_001667.3	NP_001658.2	P36404	ARL2_HUMAN	ADP-ribosylation factor-like 2	159					cell cycle (GO:0007049)|centrosome organization (GO:0051297)|GTP catabolic process (GO:0006184)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of GTPase activity (GO:0034260)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of microtubule polymerization (GO:0031116)|regulation of microtubule polymerization (GO:0031113)|small GTPase mediated signal transduction (GO:0007264)|tight junction assembly (GO:0070830)|tubulin complex assembly (GO:0007021)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|lateral plasma membrane (GO:0016328)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|GTPase inhibitor activity (GO:0005095)	p.A159T(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	5						GGGCTGCAGCGCCGTCACCGG	0.627																																					p.A159T		Atlas-SNP	.											.	ARL2	11	.	1	Substitution - Missense(1)	lung(1)	c.G475A						PASS	.						56	49	51					11																	64789247		2201	4297	6498	SO:0001583	missense	402	exon5			TGCAGCGCCGTCA	AF493888	CCDS8088.1, CCDS55770.1	11q13	2014-05-09			ENSG00000213465	ENSG00000213465		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	693	protein-coding gene	gene with protein product		601175				8415637, 9253601	Standard	NM_001667		Approved	ARFL2	uc001och.4	P36404	OTTHUMG00000165728	ENST00000246747.4:c.475G>A	chr11.hg19:g.64789247G>A	ENSP00000246747:p.Ala159Thr	49.0	0.0	.		25.0	12.0	.	NM_001667	G3V184|Q9BUK8	Missense_Mutation	SNP	ENST00000246747.4	hg19	CCDS8088.1	.	.	.	.	.	.	.	.	.	.	G	32	5.153338	0.94645	.	.	ENSG00000213465	ENST00000246747;ENST00000529384;ENST00000533729	D;D;D	0.91351	-2.83;-2.83;-2.83	4.5	4.5	0.54988	.	0.000000	0.85682	U	0.000000	D	0.96222	0.8768	H	0.94385	3.53	0.80722	D	1	D	0.71674	0.998	D	0.66196	0.942	D	0.97253	0.9899	10	0.87932	D	0	-17.1644	14.7471	0.69496	0.0:0.0:1.0:0.0	.	159	P36404	ARL2_HUMAN	T	159;159;132	ENSP00000246747:A159T;ENSP00000436021:A159T;ENSP00000432971:A132T	ENSP00000246747:A159T	A	+	1	0	ARL2	64545823	1.000000	0.71417	0.984000	0.44739	0.890000	0.51754	8.981000	0.93465	2.343000	0.79666	0.484000	0.47621	GCC	.	.	.	none		0.627	ARL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385963.1	NM_001667		A	64789247	G	A	64789247	3	1	81	1	0	0	0	0	1	0	0	0	933	1087	38	1	493	1	ARL2	11	64789247	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	7322403	64789247	70217269	61	5252											
IL10RA	3587	hgsc.bcm.edu	37	chr11	117869943	117869943	+	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	aagaagacccagctgctgtgGcattccagggttacctgagg	10	8	13	10	0	0	3	0	1	0	2	1	3	1	3	3	3	3	4	3	3	3	2			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr11:117869943G>T	ENST00000227752.3	+	7	1444	c.1324G>T	c.(1324-1326)Gca>Tca	p.A442S	IL10RA_ENST00000541785.1_Missense_Mutation_p.A422S|IL10RA_ENST00000545409.1_Missense_Mutation_p.A293S|IL10RA_ENST00000533700.1_3'UTR	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	442					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)		AGCTGCTGTGGCATTCCAGGG	0.637																																					p.A442S		Atlas-SNP	.											.	IL10RA	46	.	0			c.G1324T						PASS	.						79	77	78					11																	117869943		2200	4296	6496	SO:0001583	missense	3587	exon7			GCTGTGGCATTCC	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.1324G>T	chr11.hg19:g.117869943G>T	ENSP00000227752:p.Ala442Ser	107.0	0.0	.		63.0	18.0	.	NM_001558	A8K6I0|B0YJ27	Missense_Mutation	SNP	ENST00000227752.3	hg19	CCDS8388.1	.	.	.	.	.	.	.	.	.	.	G	12.67	2.007738	0.35415	.	.	ENSG00000110324	ENST00000227752;ENST00000541785;ENST00000545409;ENST00000536858	T;T;T	0.24723	1.84;1.84;1.84	5.83	2.69	0.31865	.	4.801410	0.00447	N	0.000099	T	0.28566	0.0707	L	0.60455	1.87	0.09310	N	1	B;B	0.26845	0.161;0.1	B;B	0.23852	0.049;0.024	T	0.20605	-1.0270	10	0.41790	T	0.15	-4.9837	6.4798	0.22057	0.1701:0.1494:0.6805:0.0	.	422;442	F5GYV8;Q13651	.;I10R1_HUMAN	S	442;422;293;422	ENSP00000227752:A442S;ENSP00000441397:A422S;ENSP00000443019:A293S	ENSP00000227752:A442S	A	+	1	0	IL10RA	117375153	0.268000	0.24133	0.043000	0.18650	0.009000	0.06853	0.801000	0.27055	1.438000	0.47492	0.563000	0.77884	GCA	.	.	.	none		0.637	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1			T	117869943	G	T	117869943	3	4	81	1	0	0	0	0	1	0	0	0	7627	1203	42	4	1350	4	IL10RA	11	117869943	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	53080696	117869943	17136573	62	5253											
NAB2	4665	hgsc.bcm.edu	37	chr12	57486863	57486863	+	Frame_Shift_Del	DEL	C	C	-																															caggttggagaacagagtcaCcctgaaatccagcagcctcc																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr12:57486863delC	ENST00000300131.3	+	5	1539	c.1161delC	c.(1159-1161)cacfs	p.H387fs	NAB2_ENST00000342556.6_Frame_Shift_Del_p.H387fs|NAB2_ENST00000357680.4_3'UTR	NM_005967.3	NP_005958.1	Q15742	NAB2_HUMAN	NGFI-A binding protein 2 (EGR1 binding protein 2)	387					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						AACAGAGTCACCCTGAAATCC	0.622																																					p.H387fs		Atlas-Indel,Pindel	.											.	NAB2	47	.	0			c.1160delA						PASS	.						108	118	115					12																	57486863		2203	4300	6503	SO:0001589	frameshift_variant	4665	exon5			.	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.1161delC	chr12.hg19:g.57486863delC	ENSP00000300131:p.His387fs	61.0	0.0	0		54.0	19.0	0.351852	NM_005967	B2RAK3|O76006|Q14797	Frame_Shift_Del	DEL	ENST00000300131.3	hg19	CCDS8930.1																																																																																			.	.	.	none		0.622	NAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412222.1	NM_005967		-	57486863	C	-	57486863	7	5	81	1	0	1	0	1	0	0	0	0	10139	506	18	0	1179	0	NAB2	12	57486863	Frame_Shift_Del	DEL	C	TCGA-B1-A47M-01A-11D-A25F-10		57486863	76365032	63	5254											
SLC25A15	10166	hgsc.bcm.edu	37	chr13	41381598	41381598	+	Splice_Site	DEL	A	A	-																															gggagatcaaaagatgaattAggtaaatgtgtttgcattga																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr13:41381598delA	ENST00000338625.4	+	5	857	c.621delA	c.(619-621)tta>tt	p.L207fs	SLC25A15_ENST00000478827.1_3'UTR	NM_014252.3	NP_055067.1	Q9Y619	ORNT1_HUMAN	solute carrier family 25 (mitochondrial carrier; ornithine transporter) member 15	207					cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|L-ornithine transmembrane transport (GO:1903352)|mitochondrial ornithine transport (GO:0000066)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	L-ornithine transmembrane transporter activity (GO:0000064)			endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|stomach(1)|urinary_tract(1)	14		Lung NSC(96;3.55e-06)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;1.48e-08)|Epithelial(112;7.51e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000191)|GBM - Glioblastoma multiforme(144;0.00231)|BRCA - Breast invasive adenocarcinoma(63;0.0704)	L-Ornithine(DB00129)	AAGATGAATTAGGTAAATGTG	0.473																																					p.L207X		Atlas-Indel,Pindel	.											.	SLC25A15	30	.	0			c.620delT						PASS	.						129	122	124					13																	41381598		2203	4300	6503	SO:0001630	splice_region_variant	10166	exon5			.	AF112968	CCDS9373.1	13q14	2013-05-22			ENSG00000102743	ENSG00000102743		"Solute carriers"	10985	protein-coding gene	gene with protein product	"ornithine transporter 1"	603861		ORNT1, HHH		10369256	Standard	NM_014252		Approved	ORC1, D13S327	uc001uxn.3	Q9Y619	OTTHUMG00000016776	ENST00000338625.4:c.622+1A>-	chr13.hg19:g.41381598delA		69.0	0.0	0		63.0	29.0	0.460317	NM_014252	Q5VZD8|Q9HC45	Frame_Shift_Del	DEL	ENST00000338625.4	hg19	CCDS9373.1																																																																																			.	.	.	none		0.473	SLC25A15-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276149.2	NM_014252	Frame_Shift_Del	-	41381598	A	-	41381598	8	5	81	1	0	1	0	1	0	0	1	0	14490	434	15	0	635	0	SLC25A15	13	41381598	Splice_Site	DEL	A	TCGA-B1-A47M-01A-11D-A25F-10		41381598	73788280	64	5255											
FBXO33	254170	hgsc.bcm.edu	37	chr14	39871674	39871674	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acaaacttccttgctgttgtAgaacacttatgtctccaaaa	13	13	5	10	0	1	1	0	0	1	1	3	1	2	1	2	0	3	3	2	0	6	5			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr14:39871674A>G	ENST00000298097.7	-	2	978	c.641T>C	c.(640-642)cTa>cCa	p.L214P	FBXO33_ENST00000554190.1_Intron	NM_203301.3	NP_976046.1	Q7Z6M2	FBX33_HUMAN	F-box protein 33	214					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)		TTGCTGTTGTAGAACACTTAT	0.308																																					p.L214P		Atlas-SNP	.											.	FBXO33	21	.	0			c.T641C						PASS	.						100	92	95					14																	39871674		2203	4298	6501	SO:0001583	missense	254170	exon2			TGTTGTAGAACAC	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.641T>C	chr14.hg19:g.39871674A>G	ENSP00000298097:p.Leu214Pro	34.0	0.0	.		20.0	6.0	.	NM_203301	Q6PIR2|Q86TR2|Q86YE0	Missense_Mutation	SNP	ENST00000298097.7	hg19	CCDS9677.1	.	.	.	.	.	.	.	.	.	.	A	13.87	2.366608	0.41902	.	.	ENSG00000165355	ENST00000298097	T	0.01279	5.06	6.08	6.08	0.98989	.	0.072360	0.56097	D	0.000025	T	0.02929	0.0087	L	0.32530	0.975	0.80722	D	1	P	0.50272	0.933	P	0.50440	0.641	T	0.69232	-0.5199	9	.	.	.	-1.7988	16.6438	0.85155	1.0:0.0:0.0:0.0	.	214	Q7Z6M2	FBX33_HUMAN	P	214	ENSP00000298097:L214P	.	L	-	2	0	FBXO33	38941425	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	8.486000	0.90451	2.333000	0.79357	0.533000	0.62120	CTA	.	.	.	none		0.308	FBXO33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276769.2			G	39871674	A	G	39871674	3	3	81	1	0	0	0	0	1	0	0	0	5750	420	15	3	1038	3	FBXO33	14	39871674	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10		39871674	67477866	65	5256											
L2HGDH	79944	hgsc.bcm.edu	37	chr14	50713788	50713788	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcattatttataattcaaaTctttgttgtacttcatctgc	10	21	3	7	0	5	0	3	0	2	0	5	0	5	0	0	0	2	2	0	0	5	10			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr14:50713788T>C	ENST00000267436.4	-	10	1777	c.1380A>G	c.(1378-1380)agA>agG	p.R460R	L2HGDH_ENST00000421284.3_Silent_p.R460R|L2HGDH_ENST00000261699.4_Intron			Q9H9P8	L2HDH_HUMAN	L-2-hydroxyglutarate dehydrogenase	460					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular protein metabolic process (GO:0044267)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	2-hydroxyglutarate dehydrogenase activity (GO:0047545)			kidney(1)|large_intestine(4)|lung(3)|ovary(2)	10	all_epithelial(31;0.000599)|Breast(41;0.0102)					ATAATTCAAATCTTTGTTGTA	0.328																																					p.R460R		Atlas-SNP	.											.	L2HGDH	33	.	0			c.A1380G						PASS	.						49	48	49					14																	50713788		2203	4300	6503	SO:0001819	synonymous_variant	79944	exon10			TTCAAATCTTTGT		CCDS9698.1	14q22.1	2006-04-28	2005-05-25	2005-05-25	ENSG00000087299	ENSG00000087299	1.1.99.2		20499	protein-coding gene	gene with protein product	"2-hydroxyglutarate dehydrogenase"	609584	"chromosome 14 open reading frame 160"	C14orf160		16005139	Standard	NM_024884		Approved	FLJ12618	uc001wxu.3	Q9H9P8	OTTHUMG00000140289	ENST00000267436.4:c.1380A>G	chr14.hg19:g.50713788T>C		110.0	0.0	.		103.0	38.0	.	NM_024884	Q9BRR1	Silent	SNP	ENST00000267436.4	hg19	CCDS9698.1																																																																																			.	.	.	none		0.328	L2HGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276870.2	NM_024884		C	50713788	T	C	50713788	2	2	81	1	0	0	0	0	0	0	0	1	8597	1432	50	3		3	L2HGDH	14	50713788	Silent	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10	10842114	50713788	56635752	66	5257											
ADAM20	8748	hgsc.bcm.edu	37	chr14	70990728	70990729	+	Frame_Shift_Del	DEL	CT	CT	-																															ccagtcaaaattacatcaacCtccaaaggatgatagaagga																								rs112672973		TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr14:70990728_70990729delCT	ENST00000256389.3	-	2	1140_1141	c.896_897delAG	c.(895-897)gagfs	p.E299fs	RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003814.4	NP_003805.3	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20	249	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(2)	27			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)		TTACATCAACCTCCAAAGGATG	0.347																																					p.299_300del		Atlas-INDEL	.											.	ADAM20	59	.	0			c.897_898del						PASS	.																																			SO:0001589	frameshift_variant	8748	exon2			.	AF029899	CCDS32111.1	14q24.2	2012-04-30	2005-08-18		ENSG00000134007	ENSG00000134007		"ADAM metallopeptidase domain containing"	199	protein-coding gene	gene with protein product		603712	"a disintegrin and metalloproteinase domain 20"			9469942	Standard	NM_003814		Approved		uc001xme.3	O43506	OTTHUMG00000167548	ENST00000256389.3:c.896_897delAG	chr14.hg19:g.70990728_70990729delCT	ENSP00000256389:p.Glu299fs	42.0	0.0	0		44.0	13.0	0.295455	NM_003814	Q6GTZ1|Q9UKJ9	Frame_Shift_Del	DEL	ENST00000256389.3	hg19	CCDS32111.1																																																																																			.	.	.	none		0.347	ADAM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395004.2			-	70990729	CT	-	70990728	7	5	81	1	0	1	0	1	0	0	0	0	242	680	24	0	1437	0	ADAM20	14	70990728	Frame_Shift_Del	DEL	CT	TCGA-B1-A47M-01A-11D-A25F-10	20276940	70990728	36358812	67	5258											
C14orf115	55237	hgsc.bcm.edu	37	chr14	74824279	74824279	+	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	ttccagccctggccccactcTcatcgccggccaagaccctg	6	7	8	20	2	1	1	1	0	1	1	4	1	2	1	7	2	1	0	7	2	1	1			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr14:74824279T>A	ENST00000256362.4	+	2	1034	c.793T>A	c.(793-795)Tca>Aca	p.S265T		NM_018228.2	NP_060698.2	Q9H8Y1	VRTN_HUMAN	vertebrae development associated	265					transposition, DNA-mediated (GO:0006313)		sequence-specific DNA binding (GO:0043565)|transposase activity (GO:0004803)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(15)|ovary(5)|prostate(2)|skin(1)|urinary_tract(1)	41						GGCCCCACTCTCATCGCCGGC	0.637																																					p.S265T		Atlas-SNP	.											.	VRTN	79	.	0			c.T793A						PASS	.						39	39	39					14																	74824279		2203	4300	6503	SO:0001583	missense	55237	exon2			CCACTCTCATCGC	AK001673	CCDS9830.1	14q24.2	2012-12-07	2012-12-07	2010-10-20	ENSG00000133980	ENSG00000133980			20223	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 115", "vertebrae development homolog (pig)"	C14orf115		21232157	Standard	NM_018228		Approved	FLJ10811, vertnin	uc001xpw.4	Q9H8Y1	OTTHUMG00000171208	ENST00000256362.4:c.793T>A	chr14.hg19:g.74824279T>A	ENSP00000256362:p.Ser265Thr	107.0	0.0	.		47.0	18.0	.	NM_018228	Q9NVC7	Missense_Mutation	SNP	ENST00000256362.4	hg19	CCDS9830.1	.	.	.	.	.	.	.	.	.	.	T	0.012	-1.670536	0.00758	.	.	ENSG00000133980	ENST00000256362	T	0.42131	0.98	4.34	2.42	0.29668	.	0.896444	0.09544	N	0.787929	T	0.20047	0.0482	N	0.08118	0	0.09310	N	1	B	0.15141	0.012	B	0.12837	0.008	T	0.27191	-1.0081	10	0.18276	T	0.48	0.001	5.0154	0.14333	0.0:0.5664:0.2316:0.202	.	265	Q9H8Y1	VRTN_HUMAN	T	265	ENSP00000256362:S265T	ENSP00000256362:S265T	S	+	1	0	VRTN	73894032	0.614000	0.27017	0.014000	0.15608	0.005000	0.04900	2.793000	0.47845	0.762000	0.33152	-0.337000	0.08149	TCA	.	.	.	none		0.637	VRTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412339.1	NM_018228		A	74824279	T	A	74824279	3	1	81	1	0	0	0	0	1	0	0	0	1742	1551	54	5	795	5	C14orf115	14	74824279	Missense_Mutation	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10	3833551	74824279	32525261	68	5259											
GALC	2581	hgsc.bcm.edu	37	chr14	88412007	88412007	+	Missense_Mutation	SNP	A	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	tgatgctcgccagggtcttcAatatttgtaaaatattcaaa	13	14	7	7	1	3	1	2	1	1	0	4	1	3	1	1	1	1	2	1	1	6	6			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr14:88412007A>C	ENST00000261304.2	-	14	1666	c.1560T>G	c.(1558-1560)atT>atG	p.I520M	GALC_ENST00000544807.2_Missense_Mutation_p.I464M|GALC_ENST00000393569.2_Missense_Mutation_p.I494M|GALC_ENST00000393568.4_Missense_Mutation_p.I497M	NM_000153.3|NM_001201401.1	NP_000144.2|NP_001188330.1	P54803	GALC_HUMAN	galactosylceramidase	520					carbohydrate metabolic process (GO:0005975)|galactosylceramide catabolic process (GO:0006683)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	galactosylceramidase activity (GO:0004336)			endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CAGGGTCTTCAATATTTGTAA	0.398																																					p.I520M		Atlas-SNP	.											.	GALC	48	.	0			c.T1560G						PASS	.						88	87	87					14																	88412007		1838	4079	5917	SO:0001583	missense	2581	exon14			GTCTTCAATATTT	L23116	CCDS9878.2, CCDS55936.1, CCDS55937.1	14q31	2009-01-06	2005-11-29		ENSG00000054983	ENSG00000054983	3.2.1.46		4115	protein-coding gene	gene with protein product	"Krabbe disease"	606890	"galactosylceramidase (Krabbe disease)"				Standard	NM_000153		Approved		uc001xvt.3	P54803	OTTHUMG00000028646	ENST00000261304.2:c.1560T>G	chr14.hg19:g.88412007A>C	ENSP00000261304:p.Ile520Met	36.0	0.0	.		39.0	10.0	.	NM_000153	B4DKE8|B4DYN1|B4DZJ8|B7Z7Z2|J3KN25|J3KPP8|Q8J030	Missense_Mutation	SNP	ENST00000261304.2	hg19	CCDS9878.2	.	.	.	.	.	.	.	.	.	.	A	0.019	-1.451307	0.01080	.	.	ENSG00000054983	ENST00000261304;ENST00000544807;ENST00000393569;ENST00000539620;ENST00000393568	D;D;D;D	0.93604	-3.25;-3.25;-3.25;-3.25	5.51	-11.0	0.00169	.	2.091110	0.01473	N	0.016351	D	0.85796	0.5780	N	0.12746	0.255	0.09310	N	1	B;B;B;B	0.11235	0.004;0.001;0.002;0.001	B;B;B;B	0.15052	0.007;0.012;0.012;0.012	T	0.76288	-0.3014	10	0.46703	T	0.11	4.0145	13.9406	0.64052	0.283:0.3027:0.4142:0.0	.	464;497;494;520	P54803-5;E7EPA4;P54803-4;P54803	.;.;.;GALC_HUMAN	M	520;464;494;309;497	ENSP00000261304:I520M;ENSP00000437513:I464M;ENSP00000377199:I494M;ENSP00000377198:I497M	ENSP00000261304:I520M	I	-	3	3	GALC	87481760	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.299000	0.01139	-6.093000	0.00006	-2.649000	0.00149	ATT	.	.	.	none		0.398	GALC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071559.2			C	88412007	A	C	88412007	3	2	81	1	0	0	0	0	1	0	0	0	6208	126	5	5	513	5	GALC	14	88412007	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	13587728	88412007	18937533	69	5260											
CALM1	801	hgsc.bcm.edu	37	chr14	90870815	90870815	+	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	gaagaagtagatgaaatgatCagagaagcagatattgatgg	18	8	13	2	0	1	7	1	3	0	4	1	9	1	7	0	1	1	2	0	1	6	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr14:90870815C>T	ENST00000356978.4	+	5	626	c.378C>T	c.(376-378)atC>atT	p.I126I	RP11-471B22.2_ENST00000555853.1_RNA|CALM1_ENST00000544280.2_Silent_p.I90I|CALM1_ENST00000553542.1_Silent_p.I90I|CALM1_ENST00000447653.3_Silent_p.I127I	NM_006888.4	NP_008819.1	P62158	CALM_HUMAN	calmodulin 1 (phosphorylase kinase, delta)	126	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)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(1)	10		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.208)	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)	ATGAAATGATCAGAGAAGCAG	0.388																																					p.I126I		Atlas-SNP	.											.	CALM1	16	.	0			c.C378T						PASS	.						135	127	130					14																	90870815		2203	4300	6503	SO:0001819	synonymous_variant	801	exon5			AATGATCAGAGAA		CCDS9892.1	14q32.11	2013-02-25			ENSG00000198668	ENSG00000198668	2.7.11.19	"EF-hand domain containing", "Endogenous ligands"	1442	protein-coding gene	gene with protein product	"prepro-calmodulin 1"	114180		CALML2		6385987	Standard	NM_006888		Approved	CAMI, PHKD, DD132	uc001xyl.2	P62158	OTTHUMG00000171044	ENST00000356978.4:c.378C>T	chr14.hg19:g.90870815C>T		173.0	0.0	.		149.0	38.0	.	NM_006888	P02593|P70667|P99014|Q13942|Q53S29|Q61379|Q61380|Q96HK3	Silent	SNP	ENST00000356978.4	hg19	CCDS9892.1																																																																																			.	.	.	none		0.388	CALM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411346.1			T	90870815	C	T	90870815	2	4	81	1	0	0	0	0	0	0	0	1	2586	816	29	2		2	CALM1	14	90870815	Silent	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	2458808	90870815	16478725	70	5261											
ATP10A	57194	hgsc.bcm.edu	37	chr15	25981205	25981205	+	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	cagacacacgatactcacatGcagccgcgaaacctactcag	14	5	7	15	3	2	1	2	0	0	1	2	3	2	1	2	0	5	1	2	0	3	2			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr15:25981205G>A	ENST00000356865.6	-	3	849	c.738C>T	c.(736-738)tgC>tgT	p.C246C	RNA5SP390_ENST00000410191.1_RNA	NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	246					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)		ATACTCACATGCAGCCGCGAA	0.448																																					p.C246C		Atlas-SNP	.											.	ATP10A	270	.	0			c.C738T						PASS	.						148	100	116					15																	25981205		2203	4300	6503	SO:0001819	synonymous_variant	57194	exon3			TCACATGCAGCCG	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.738C>T	chr15.hg19:g.25981205G>A		103.0	0.0	.		99.0	38.0	.	NM_024490	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	hg19	CCDS32178.1																																																																																			.	.	.	none		0.448	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		A	25981205	G	A	25981205	2	1	81	1	0	0	0	0	0	0	0	1	1116	1311	46	2		2	ATP10A	15	25981205	Silent	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10		25981205	76550187	71	5262											
SECISBP2L	9728	hgsc.bcm.edu	37	chr15	49293279	49293279	+	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	tcatcaatctctttacaaagAacctgattacaatacctgta	15	13	3	10	0	3	2	2	1	1	1	4	2	3	2	2	0	4	1	2	0	8	5			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr15:49293279A>C	ENST00000559471.1	-	15	2306	c.2043T>G	c.(2041-2043)gtT>gtG	p.V681V	SECISBP2L_ENST00000559122.1_5'UTR|SECISBP2L_ENST00000261847.3_Silent_p.V636V	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	681							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						CTTTACAAAGAACCTGATTAC	0.338																																					p.V681V		Atlas-SNP	.											.	SECISBP2L	118	.	0			c.T2043G						PASS	.						60	54	56					15																	49293279		2197	4295	6492	SO:0001819	synonymous_variant	9728	exon15			ACAAAGAACCTGA	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.2043T>G	chr15.hg19:g.49293279A>C		20.0	0.0	.		42.0	16.0	.	NM_001193489	Q8N767	Silent	SNP	ENST00000559471.1	hg19	CCDS53942.1																																																																																			.	.	.	none		0.338	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701		C	49293279	A	C	49293279	2	2	81	1	0	0	0	0	0	0	0	1	14020	233	9	5		5	SECISBP2L	15	49293279	Silent	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	23312074	49293279	53238113	72	5263											
TEX9	374618	hgsc.bcm.edu	37	chr15	56686956	56686956	+	Frame_Shift_Del	DEL	A	A	-																															tatgcaacagtctcaagtagAaaaatacaaaactcttttcg																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr15:56686956delA	ENST00000352903.2	+	9	776	c.752delA	c.(751-753)gaafs	p.E251fs	TEX9_ENST00000537232.1_Frame_Shift_Del_p.E176fs|RP11-48G14.2_ENST00000564401.1_lincRNA|TEX9_ENST00000560582.1_Frame_Shift_Del_p.E7fs|TEX9_ENST00000561221.2_Frame_Shift_Del_p.E251fs|TEX9_ENST00000558083.2_Frame_Shift_Del_p.E176fs	NM_198524.1	NP_940926.1	Q8N6V9	TEX9_HUMAN	testis expressed 9	251										cervix(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	14				all cancers(107;0.0394)|GBM - Glioblastoma multiforme(80;0.056)		TCTCAAGTAGAAAAATACAAA	0.303																																					p.E251fs		Atlas-Indel,Pindel	.											TEX9,NS,carcinoma,0,1	TEX9	29	.	0			c.751delG						PASS	.						46	50	49					15																	56686956		2191	4284	6475	SO:0001589	frameshift_variant	374618	exon9			.	BC028119	CCDS10157.1, CCDS66776.1	15q21.3	2007-03-13	2007-03-13		ENSG00000151575	ENSG00000151575			29585	protein-coding gene	gene with protein product			"testis expressed sequence 9"				Standard	XM_005254361		Approved		uc002adp.3	Q8N6V9	OTTHUMG00000132035	ENST00000352903.2:c.752delA	chr15.hg19:g.56686956delA	ENSP00000342169:p.Glu251fs	102.0	0.0	0		85.0	29.0	0.341176	NM_198524	B4DH73	Frame_Shift_Del	DEL	ENST00000352903.2	hg19	CCDS10157.1																																																																																			.	.	.	none		0.303	TEX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255048.2	NM_198524		-	56686956	A	-	56686956	7	5	81	1	0	1	0	1	0	0	0	0	15796	246	9	0	786	0	TEX9	15	56686956	Frame_Shift_Del	DEL	A	TCGA-B1-A47M-01A-11D-A25F-10	7393677	56686956	45844436	73	5264											
ARL2BP	23568	hgsc.bcm.edu	37	chr16	57283687	57283687	+	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	ccactgttgcagatttctttGgtagaaaaatacattgaaga	14	13	8	6	0	1	4	0	1	1	3	1	4	1	4	1	1	2	3	1	1	5	6			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr16:57283687G>T	ENST00000219204.3	+	4	486	c.216G>T	c.(214-216)ttG>ttT	p.L72F	RP11-407G23.3_ENST00000564376.1_RNA|ARL2BP_ENST00000562023.1_Intron|RP11-407G23.4_ENST00000562409.1_RNA	NM_012106.3	NP_036238.1	Q9Y2Y0	AR2BP_HUMAN	ADP-ribosylation factor-like 2 binding protein	72					maintenance of protein location in nucleus (GO:0051457)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of catalytic activity (GO:0050790)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	centrosome (GO:0005813)|cilium (GO:0005929)|midbody (GO:0030496)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)	small GTPase regulator activity (GO:0005083)|transcription coactivator activity (GO:0003713)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(4)|urinary_tract(1)	12						AGATTTCTTTGGTAGAAAAAT	0.423																																					p.L72F		Atlas-SNP	.											.	ARL2BP	20	.	0			c.G216T						PASS	.						126	128	127					16																	57283687		2198	4300	6498	SO:0001583	missense	23568	exon4			TTCTTTGGTAGAA	AF126062	CCDS10776.1	16q13	2014-01-30			ENSG00000102931	ENSG00000102931			17146	protein-coding gene	gene with protein product	"binder of Arl2"	615407	"retinitis pigmentosa 66 (autosomal recessive)"	RP66		10488091, 18981177, 23849777	Standard	NM_012106		Approved	BART1, BART	uc002elf.1	Q9Y2Y0	OTTHUMG00000133459	ENST00000219204.3:c.216G>T	chr16.hg19:g.57283687G>T	ENSP00000219204:p.Leu72Phe	50.0	0.0	.		50.0	7.0	.	NM_012106	B3KQJ5|Q504R0	Missense_Mutation	SNP	ENST00000219204.3	hg19	CCDS10776.1	.	.	.	.	.	.	.	.	.	.	G	16.50	3.139821	0.56936	.	.	ENSG00000102931	ENST00000219204	T	0.54071	0.59	5.95	2.95	0.34219	ADP-ribosylation factor-like 2-binding protein, domain (2);	0.127524	0.37095	U	0.002259	T	0.70360	0.3215	M	0.88310	2.945	0.80722	D	1	D;D	0.71674	0.998;0.991	D;D	0.70716	0.97;0.934	T	0.68372	-0.5426	10	0.62326	D	0.03	-7.9781	5.1654	0.15082	0.2858:0.0:0.5774:0.1368	.	40;72	B4DQD8;Q9Y2Y0	.;AR2BP_HUMAN	F	72	ENSP00000219204:L72F	ENSP00000219204:L72F	L	+	3	2	ARL2BP	55841188	1.000000	0.71417	0.996000	0.52242	0.684000	0.39900	2.160000	0.42348	0.418000	0.25898	0.655000	0.94253	TTG	.	.	.	none		0.423	ARL2BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257334.2	NM_012106		T	57283687	G	T	57283687	3	4	81	1	0	0	0	0	1	0	0	0	934	1339	47	4	230	4	ARL2BP	16	57283687	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10		57283687	33071066	74	5265											
KCTD11	147040	hgsc.bcm.edu	37	chr17	7256621	7256621	+	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	ctgagctccgtccaggtggaCaccttccgagccaacctttt	7	10	9	15	2	0	1	0	1	0	0	3	3	3	2	6	2	3	1	6	2	1	3	rs79616684		TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr17:7256621C>T	ENST00000333751.3	+	1	1414	c.360C>T	c.(358-360)gaC>gaT	p.D120D	TMEM95_ENST00000330767.4_5'Flank|RP11-542C16.1_ENST00000572417.1_RNA|TMEM95_ENST00000389982.4_5'Flank|TMEM95_ENST00000576060.1_5'Flank	NM_001002914.2	NP_001002914.1	Q693B1	KCD11_HUMAN	potassium channel tetramerization domain containing 11	120					cell cycle (GO:0007049)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)				kidney(1)|large_intestine(2)|lung(1)	4		Prostate(122;0.157)				TCCAGGTGGACACCTTCCGAG	0.627																																					p.D120D		Atlas-SNP	.											.	KCTD11	17	.	0			c.C360T						PASS	.						89	72	78					17																	7256621		2203	4300	6503	SO:0001819	synonymous_variant	147040	exon1			GGTGGACACCTTC	AK056227	CCDS32545.1	17p13.2	2013-06-20	2013-06-20	2003-11-26	ENSG00000213859	ENSG00000213859			21302	protein-coding gene	gene with protein product		609848	"chromosome 17 open reading frame 36", "potassium channel tetramerisation domain containing 11"	C17orf36		12186855, 21472142	Standard	NM_001002914		Approved	REN, KCASH1	uc002gge.4	Q693B1	OTTHUMG00000132061	ENST00000333751.3:c.360C>T	chr17.hg19:g.7256621C>T		68.0	0.0	.		62.0	17.0	.	NM_001002914	B3KPE0	Silent	SNP	ENST00000333751.3	hg19	CCDS32545.1																																																																																			.	C|0.500;T|0.500	0.500	weak		0.627	KCTD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255084.2	NM_001002914		T	7256621	C	T	7256621	2	4	81	1	0	0	0	0	0	0	0	1	8105	477	17	2		2	KCTD11	17	7256621	Silent	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10		7256621	73938589	75	5266											
PEX12	5193	hgsc.bcm.edu	37	chr17	33904481	33904481	+	Missense_Mutation	SNP	A	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	aattctctttaagccgtaaaAgttttcagaaaatgaggcac	15	12	7	7	1	2	2	1	1	1	1	3	2	2	2	1	1	1	3	1	1	6	6			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr17:33904481A>C	ENST00000225873.4	-	2	863	c.256T>G	c.(256-258)Ttt>Gtt	p.F86V	RP11-1094M14.11_ENST00000592381.1_lincRNA	NM_000286.2	NP_000277.1	O00623	PEX12_HUMAN	peroxisomal biogenesis factor 12	86					peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	integral component of peroxisomal membrane (GO:0005779)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(8)	18				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		AAGCCGTAAAAGTTTTCAGAA	0.423																																					p.F86V		Atlas-SNP	.											.	PEX12	36	.	0			c.T256G						PASS	.						149	167	161					17																	33904481		2203	4300	6503	SO:0001583	missense	5193	exon2			CGTAAAAGTTTTC	U91521	CCDS11296.1	17q21.1	2011-02-10			ENSG00000108733	ENSG00000108733			8854	protein-coding gene	gene with protein product		601758				9090384	Standard	NM_000286		Approved		uc002hjp.3	O00623	OTTHUMG00000132951	ENST00000225873.4:c.256T>G	chr17.hg19:g.33904481A>C	ENSP00000225873:p.Phe86Val	27.0	0.0	.		37.0	11.0	.	NM_000286	B2R6M2	Missense_Mutation	SNP	ENST00000225873.4	hg19	CCDS11296.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.845090	0.91197	.	.	ENSG00000108733	ENST00000424525;ENST00000225873	D	0.85171	-1.95	5.63	5.63	0.86233	Pex, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.93093	0.7801	M	0.86420	2.815	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.94107	0.7367	10	0.72032	D	0.01	-21.3132	15.0234	0.71650	1.0:0.0:0.0:0.0	.	86	O00623	PEX12_HUMAN	V	86	ENSP00000225873:F86V	ENSP00000225873:F86V	F	-	1	0	PEX12	30928594	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.736000	0.74811	2.142000	0.66516	0.528000	0.53228	TTT	.	.	.	none		0.423	PEX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256489.2	NM_000286		C	33904481	A	C	33904481	3	2	81	1	0	0	0	0	1	0	0	0	11747	72	3	5	831	5	PEX12	17	33904481	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	26647860	33904481	47290729	76	5267											
CDC6	990	hgsc.bcm.edu	37	chr17	38447445	38447445	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgacaatcagctgacaattaAgtctcctagcaaaagagaac	17	8	7	9	0	2	3	1	2	1	1	3	4	2	3	1	0	3	2	1	0	7	2			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr17:38447445A>G	ENST00000209728.4	+	3	785	c.314A>G	c.(313-315)aAg>aGg	p.K105R		NM_001254.3	NP_001245.1	Q99741	CDC6_HUMAN	cell division cycle 6	105					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						CTGACAATTAAGTCTCCTAGC	0.398																																					p.K105R		Atlas-SNP	.											.	CDC6	53	.	0			c.A314G						PASS	.						121	110	114					17																	38447445		2203	4300	6503	SO:0001583	missense	990	exon3			CAATTAAGTCTCC	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.314A>G	chr17.hg19:g.38447445A>G	ENSP00000209728:p.Lys105Arg	77.0	0.0	.		120.0	14.0	.	NM_001254	Q8TB30	Missense_Mutation	SNP	ENST00000209728.4	hg19	CCDS11365.1	.	.	.	.	.	.	.	.	.	.	A	12.04	1.819366	0.32145	.	.	ENSG00000094804	ENST00000209728	T	0.51071	0.72	5.52	4.25	0.50352	.	0.245750	0.38959	N	0.001502	T	0.36166	0.0957	M	0.63428	1.95	0.22666	N	0.998871	B	0.14805	0.011	B	0.10450	0.005	T	0.24476	-1.0159	10	0.09338	T	0.73	-12.0983	4.517	0.11939	0.7131:0.0:0.1193:0.1676	.	105	Q99741	CDC6_HUMAN	R	105	ENSP00000209728:K105R	ENSP00000209728:K105R	K	+	2	0	CDC6	35700971	0.007000	0.16637	0.979000	0.43373	0.951000	0.60555	0.662000	0.25038	2.227000	0.72691	0.454000	0.30748	AAG	.	.	.	none		0.398	CDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257129.1			G	38447445	A	G	38447445	3	3	81	1	0	0	0	0	1	0	0	0	3085	72	3	3	320	3	CDC6	17	38447445	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	4542964	38447445	42747765	77	5268											
HDAC5	10014	hgsc.bcm.edu	37	chr17	42160014	42160014	+	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	gtaggagttttgcggtgatgGctacagagttgaagaagcag	11	10	16	4	1	0	4	0	2	0	2	0	5	0	5	0	3	3	5	0	3	4	5			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr17:42160014G>C	ENST00000393622.2	-	20	2877	c.2546C>G	c.(2545-2547)gCc>gGc	p.A849G	HDAC5_ENST00000225983.6_Missense_Mutation_p.A850G|HDAC5_ENST00000586802.1_Missense_Mutation_p.A849G|HDAC5_ENST00000336057.5_Missense_Mutation_p.A764G	NM_001015053.1|NM_005474.4	NP_001015053.1|NP_005465.2	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5	849	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|chromatin silencing (GO:0006342)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|inflammatory response (GO:0006954)|multicellular organismal response to stress (GO:0033555)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|osteoblast development (GO:0002076)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression, epigenetic (GO:0040029)|regulation of myotube differentiation (GO:0010830)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|histone deacetylase complex (GO:0000118)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	21		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		TGCGGTGATGGCTACAGAGTT	0.592																																					p.A850G		Atlas-SNP	.											.	HDAC5	67	.	0			c.C2549G						PASS	.						104	91	95					17																	42160014		2203	4300	6503	SO:0001583	missense	10014	exon20			GTGATGGCTACAG	AF249731	CCDS32663.1, CCDS45696.1	17q21	2008-07-18					3.5.1.98		14068	protein-coding gene	gene with protein product		605315				10220385, 9610721	Standard	XM_005256905		Approved	KIAA0600, NY-CO-9, FLJ90614	uc002iff.1	Q9UQL6		ENST00000393622.2:c.2546C>G	chr17.hg19:g.42160014G>C	ENSP00000377244:p.Ala849Gly	129.0	0.0	.		176.0	51.0	.	NM_001015053	C9JFV9|O60340|O60528|Q96DY4	Missense_Mutation	SNP	ENST00000393622.2	hg19	CCDS45696.1	.	.	.	.	.	.	.	.	.	.	G	32	5.172286	0.94807	.	.	ENSG00000108840	ENST00000225983;ENST00000393622;ENST00000336057	T;T;T	0.74737	-0.87;-0.87;-0.87	4.98	4.98	0.66077	Histone deacetylase domain (2);	0.000000	0.85682	D	0.000000	D	0.89093	0.6617	M	0.91818	3.245	0.80722	D	1	D;D;P;B	0.69078	0.987;0.997;0.512;0.235	D;D;P;P	0.87578	0.976;0.998;0.511;0.744	D	0.91712	0.5382	10	0.87932	D	0	-14.2335	17.0238	0.86440	0.0:0.0:1.0:0.0	.	764;849;850;849	Q9UQL6-2;B4DGT4;Q9UQL6-3;Q9UQL6	.;.;.;HDAC5_HUMAN	G	850;849;764	ENSP00000225983:A850G;ENSP00000377244:A849G;ENSP00000337290:A764G	ENSP00000225983:A850G	A	-	2	0	HDAC5	39515540	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	9.842000	0.99487	2.317000	0.78254	0.561000	0.74099	GCC	.	.	.	none		0.592	HDAC5-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457686.1	NM_001015053		C	42160014	G	C	42160014	3	2	81	1	0	0	0	0	1	0	0	0	7017	1203	42	4	854	4	HDAC5	17	42160014	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	3712569	42160014	39035196	78	5269											
WNT9B	7484	hgsc.bcm.edu	37	chr17	44952592	44952592	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actctccggggctggagagcCggcaggcctggcagtggggc	5	5	19	12	2	1	1	0	0	1	1	2	2	1	1	3	8	1	3	3	8	0	0			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr17:44952592C>T	ENST00000290015.2	+	3	513	c.460C>T	c.(460-462)Cgg>Tgg	p.R154W	WNT9B_ENST00000393461.2_Missense_Mutation_p.R154W	NM_003396.1	NP_003387.1	O14905	WNT9B_HUMAN	wingless-type MMTV integration site family, member 9B	154					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)			GCTGGAGAGCCGGCAGGCCTG	0.662																																					p.R154W		Atlas-SNP	.											.	WNT9B	37	.	0			c.C460T						PASS	.						58	61	60					17																	44952592		2203	4300	6503	SO:0001583	missense	7484	exon3			GAGAGCCGGCAGG	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.460C>T	chr17.hg19:g.44952592C>T	ENSP00000290015:p.Arg154Trp	87.0	0.0	.		93.0	4.0	.	NM_003396	Q6UXT4|Q96Q09	Missense_Mutation	SNP	ENST00000290015.2	hg19	CCDS11506.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.707667	0.89018	.	.	ENSG00000158955	ENST00000376843;ENST00000393461;ENST00000290015	T;T	0.76709	-1.04;-1.04	4.61	3.63	0.41609	.	0.058491	0.64402	D	0.000001	D	0.88672	0.6500	M	0.87097	2.86	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.983	D	0.90582	0.4530	10	0.66056	D	0.02	.	14.3984	0.67027	0.1489:0.8511:0.0:0.0	.	154;154	E7EPC3;O14905	.;WNT9B_HUMAN	W	148;154;154	ENSP00000377105:R154W;ENSP00000290015:R154W	ENSP00000290015:R154W	R	+	1	2	WNT9B	42307591	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.904000	0.56325	1.262000	0.44165	0.462000	0.41574	CGG	.	.	.	none		0.662	WNT9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440433.1	NM_003396		T	44952592	C	T	44952592	3	4	81	1	0	0	0	0	1	0	0	0	17411	643	23	1	470	1	WNT9B	17	44952592	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	2792578	44952592	36242618	79	5270											
NOL11	25926	hgsc.bcm.edu	37	chr17	65739904	65739904	+	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	agattgaagtaagttttcggGagctacagaaattaaatcaa	17	11	9	4	1	1	3	1	1	0	2	2	4	1	4	0	1	2	3	0	1	7	6	rs370393293		TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr17:65739904G>A	ENST00000253247.4	+	18	2204	c.2089G>A	c.(2089-2091)Gag>Aag	p.E697K	SNORA38B_ENST00000363524.1_RNA|NOL11_ENST00000535137.1_Missense_Mutation_p.E515K	NM_015462.3	NP_056277.2	Q9H8H0	NOL11_HUMAN	nucleolar protein 11	697					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)			AAGTTTTCGGGAGCTACAGAA	0.299																																					p.E697K		Atlas-SNP	.											.	NOL11	48	.	0			c.G2089A						PASS	.	G	LYS/GLU	0,4404		0,0,2202	45	49	47		2089	4.2	1	17		47	1,8595	1.2+/-3.3	0,1,4297	no	missense	NOL11	NM_015462.3	56	0,1,6499	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	697/720	65739904	1,12999	2202	4298	6500	SO:0001583	missense	25926	exon18			TTTCGGGAGCTAC	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.2089G>A	chr17.hg19:g.65739904G>A	ENSP00000253247:p.Glu697Lys	17.0	0.0	.		36.0	9.0	.	NM_015462	B7Z5V9|Q7L5S1|Q9UG18	Missense_Mutation	SNP	ENST00000253247.4	hg19	CCDS11671.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.954162	0.73902	0.0	1.16E-4	ENSG00000130935	ENST00000253247;ENST00000535137	T	0.48836	0.8	5.27	4.25	0.50352	.	0.057766	0.64402	D	0.000002	T	0.51686	0.1689	M	0.74258	2.255	0.50813	D	0.999891	P	0.48294	0.908	B	0.44224	0.444	T	0.59994	-0.7349	10	0.56958	D	0.05	-20.9764	13.8316	0.63384	0.0:0.1531:0.8468:0.0	.	697	Q9H8H0	NOL11_HUMAN	K	697;515	ENSP00000253247:E697K	ENSP00000253247:E697K	E	+	1	0	NOL11	63170366	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.909000	0.63314	2.626000	0.88956	0.655000	0.94253	GAG	.	.	.	weak		0.299	NOL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448074.1	NM_015462		A	65739904	G	A	65739904	3	1	81	1	0	0	0	0	1	0	0	0	10528	1175	41	2	2159	2	NOL11	17	65739904	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	20787312	65739904	15455306	80	5271											
TTR	7276	hgsc.bcm.edu	37	chr18	29178601	29178601	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctgctgagcccctactcctAttccaccacggctgtcgtca	6	10	7	18	2	1	1	1	1	0	0	4	1	3	1	6	1	3	2	6	1	2	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr18:29178601A>G	ENST00000237014.3	+	4	584	c.407A>G	c.(406-408)tAt>tGt	p.Y136C		NM_000371.3	NP_000362.1	P02766	TTHY_HUMAN	transthyretin	136	Thyroid hormone binding.		Y -> S (in AMYL-TTR; amyloid polyneuropathy). {ECO:0000269|PubMed:10627135}.|Y -> V (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:3675594}.		extracellular matrix organization (GO:0030198)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	hormone binding (GO:0042562)|identical protein binding (GO:0042802)			cervix(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)	13			OV - Ovarian serous cystadenocarcinoma(10;0.00523)		Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diflunisal(DB00861)|Dimethyl sulfoxide(DB01093)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	CCCTACTCCTATTCCACCACG	0.552																																					p.Y136C		Atlas-SNP	.											.	TTR	21	.	0			c.A407G	GRCh37	CM971541	TTR	M		PASS	.						80	67	72					18																	29178601		2203	4300	6503	SO:0001583	missense	7276	exon4			ACTCCTATTCCAC	M10605	CCDS11899.1	18q12.1	2014-09-17	2008-07-31		ENSG00000118271	ENSG00000118271			12405	protein-coding gene	gene with protein product		176300	"prealbumin, amyloidosis type I", "carpal tunnel syndrome 1"	PALB, CTS1		8309582	Standard	NM_000371		Approved	HsT2651, CTS	uc002kwx.4	P02766	OTTHUMG00000131984	ENST00000237014.3:c.407A>G	chr18.hg19:g.29178601A>G	ENSP00000237014:p.Tyr136Cys	85.0	0.0	.		78.0	21.0	.	NM_000371	Q549C7|Q6IB96|Q9UBZ6|Q9UCM9	Missense_Mutation	SNP	ENST00000237014.3	hg19	CCDS11899.1	.	.	.	.	.	.	.	.	.	.	A	16.32	3.089090	0.55968	.	.	ENSG00000118271	ENST00000237014;ENST00000432547;ENST00000541025	D	0.98120	-4.73	6.08	3.5	0.40072	Transthyretin, conserved site (1);Transthyretin/hydroxyisourate hydrolase, superfamily (4);	0.246709	0.42294	D	0.000722	D	0.98957	0.9645	H	0.96301	3.8	0.52501	D	0.999955	D	0.89917	1.0	D	0.87578	0.998	D	0.98496	1.0612	10	0.87932	D	0	-18.6558	10.7142	0.46002	0.7084:0.0:0.0:0.2916	.	136	P02766	TTHY_HUMAN	C	136;173;128	ENSP00000237014:Y136C	ENSP00000237014:Y136C	Y	+	2	0	TTR	27432599	0.995000	0.38212	0.908000	0.35775	0.474000	0.32979	3.175000	0.50855	2.333000	0.79357	0.482000	0.46254	TAT	.	.	.	none		0.552	TTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254948.1	NM_000371		G	29178601	A	G	29178601	3	3	81	1	0	0	0	0	1	0	0	0	16750	449	16	3	421	3	TTR	18	29178601	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10		29178601	48898647	81	5272											
C18orf21	83608	hgsc.bcm.edu	37	chr18	33558958	33558958	+	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	tatcttctctgaagggtggaCttttaaaataagaaatgcct	13	14	8	6	0	2	2	0	1	2	1	3	3	2	3	1	2	1	0	1	2	6	5			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr18:33558958C>G	ENST00000592875.1	+	5	1298	c.652C>G	c.(652-654)Ctt>Gtt	p.L218V	C18orf21_ENST00000333234.5_Missense_Mutation_p.L130V	NM_031446.4	NP_113634.3	Q32NC0	CR021_HUMAN	chromosome 18 open reading frame 21	218										endometrium(1)|kidney(1)|large_intestine(1)|skin(2)	5						GAAGGGTGGACTTTTAAAATA	0.308																																					p.L218V		Atlas-SNP	.											.	C18orf21	15	.	0			c.C652G						PASS	.						50	54	53					18																	33558958		2202	4300	6502	SO:0001583	missense	83608	exon5			GGTGGACTTTTAA	BC025950	CCDS11916.2, CCDS56064.1, CCDS74212.1	18q12.2	2004-05-05			ENSG00000141428	ENSG00000141428			28802	protein-coding gene	gene with protein product						12477932	Standard	NM_031446		Approved	PNAS-131, PNAS-124, HsT3108	uc002kzc.3	Q32NC0	OTTHUMG00000128531	ENST00000592875.1:c.652C>G	chr18.hg19:g.33558958C>G	ENSP00000465517:p.Leu218Val	57.0	0.0	.		54.0	17.0	.	NM_031446	Q6GW03|Q9BXV6|Q9BXW2	Missense_Mutation	SNP	ENST00000592875.1	hg19	CCDS11916.2	.	.	.	.	.	.	.	.	.	.	C	14.98	2.697544	0.48307	.	.	ENSG00000141428	ENST00000333234;ENST00000269194	.	.	.	5.34	1.6	0.23607	.	.	.	.	.	T	0.17577	0.0422	N	0.08118	0	0.09310	N	1	B	0.18741	0.03	B	0.21151	0.033	T	0.20405	-1.0276	8	0.87932	D	0	.	3.9349	0.09301	0.1694:0.5002:0.0:0.3305	.	218	Q32NC0	CR021_HUMAN	V	218;130	.	ENSP00000269194:L130V	L	+	1	0	C18orf21	31812956	0.136000	0.22515	0.033000	0.17914	0.167000	0.22549	-0.006000	0.12833	0.641000	0.30601	0.655000	0.94253	CTT	.	.	.	none		0.308	C18orf21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250364.1	NM_031446		G	33558958	C	G	33558958	3	3	81	1	0	0	0	0	1	0	0	0	1899	565	20	4	670	4	C18orf21	18	33558958	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	4380357	33558958	44518290	82	5273											
TSHZ1	10194	hgsc.bcm.edu	37	chr18	72999467	72999468	+	Frame_Shift_Ins	INS	-	-	A																															gaggccgagactgggaaggcINScaaaaaggagggaccgctgg																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr18:72999467_72999468insA	ENST00000580243.1	+	2	2453_2454	c.2105_2106insA	c.(2104-2109)gccaaafs	p.K703fs	TSHZ1_ENST00000322038.5_Frame_Shift_Ins_p.K658fs			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	703					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)		ACTGGGAAGGCCAAAAAGGAGG	0.55																																					p.A657fs		Atlas-INDEL	.											.	TSHZ1	104	.	0			c.1970_1971insA						PASS	.																																			SO:0001589	frameshift_variant	10194	exon2			.	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	Exception_encountered	chr18.hg19:g.72999467_72999468insA	ENSP00000464391:p.Lys703fs	136.0	0.0	0		103.0	31.0	0.300971	NM_005786	O60534|Q4LE29|Q53EU4	Frame_Shift_Ins	INS	ENST00000580243.1	hg19																																																																																				.	.	.	none		0.55	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786		A	72999468	-	A	72999467	7	5	81	1	0	1	1	0	0	0	0	0	16635	739	26	0	1972	0	TSHZ1	18	72999467	Frame_Shift_Ins	INS	-	TCGA-B1-A47M-01A-11D-A25F-10	39440509	72999467	5077781	83	5274	58	3									
TSHZ1	10194	hgsc.bcm.edu	37	chr18	72999468	72999468	+	Silent	SNP	C	C	A																															gaggccgagactgggaaggcCaaaaaggagggaccgctgga																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr18:72999468C>A	ENST00000580243.1	+	2	2454	c.2106C>A	c.(2104-2106)gcC>gcA	p.A702A	TSHZ1_ENST00000322038.5_Silent_p.A657A			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	702					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)		CTGGGAAGGCCAAAAAGGAGG	0.547																																					p.A657A		Atlas-SNP	.											.	TSHZ1	104	.	0			c.C1971A						PASS	.						99	88	92					18																	72999468		2203	4300	6503	SO:0001819	synonymous_variant	10194	exon2			GAAGGCCAAAAAG	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.2106C>A	chr18.hg19:g.72999468C>A		136.0	0.0	.		102.0	35.0	.	NM_005786	O60534|Q4LE29|Q53EU4	Silent	SNP	ENST00000580243.1	hg19																																																																																				.	.	.	none		0.547	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786		A	72999468	C	A	72999468	2	1	81	1	0	0	0	0	0	0	0	1	16635	581	21	4		4	TSHZ1	18	72999468	Silent	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	1	72999468	5077780	84	5275	58	3									
TSHZ1	10194	hgsc.bcm.edu	37	chr18	72999471	72999472	+	Frame_Shift_Ins	INS	-	-	A																															ccgagactgggaaggccaaaINSaaggagggaccgctggacgt																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr18:72999471_72999472insA	ENST00000580243.1	+	2	2457_2458	c.2109_2110insA	c.(2110-2112)aagfs	p.K704fs	TSHZ1_ENST00000322038.5_Frame_Shift_Ins_p.K659fs			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	704					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)		GGAAGGCCAAAAAGGAGGGACC	0.545																																					p.K658fs		Pindel	.											.	TSHZ1	104	.	0			c.1974_1975insA						PASS	.																																			SO:0001589	frameshift_variant	10194	exon2			.	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.2111dupA	chr18.hg19:g.72999473_72999473dupA	ENSP00000464391:p.Lys704fs	137.0	0.0	.		103.0	25.0	0.243	NM_005786	O60534|Q4LE29|Q53EU4	Frame_Shift_Ins	INS	ENST00000580243.1	hg19																																																																																				.	.	.	none		0.545	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786		A	72999472	-	A	72999471	7	5	81	1	0	1	1	0	0	0	0	0	16635	11	1	0	1976	0	TSHZ1	18	72999471	Frame_Shift_Ins	INS	-	TCGA-B1-A47M-01A-11D-A25F-10	3	72999471	5077777	85	5276	58	3									
SF4	57794	hgsc.bcm.edu	37	chr19	19427332	19427332	+	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	ttctgagcgatgagctcttcCtggtgaaggatgttcatgtt	7	15	12	7	1	3	3	1	3	2	0	4	5	4	4	1	2	2	3	1	2	1	4			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr19:19427332C>G	ENST00000247001.5	-	2	452	c.105G>C	c.(103-105)caG>caC	p.Q35H	SUGP1_ENST00000334782.5_Missense_Mutation_p.Q35H|SUGP1_ENST00000585763.1_5'UTR	NM_172231.3	NP_757386.2	Q8IWZ8	SUGP1_HUMAN	SURP and G patch domain containing 1	35					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						TGAGCTCTTCCTGGTGAAGGA	0.517																																					p.Q35H		Atlas-SNP	.											.	SUGP1	63	.	0			c.G105C						PASS	.						137	103	114					19																	19427332		2203	4300	6503	SO:0001583	missense	57794	exon2			CTCTTCCTGGTGA	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.105G>C	chr19.hg19:g.19427332C>G	ENSP00000247001:p.Gln35His	124.0	0.0	.		99.0	30.0	.	NM_172231	O60378|Q6P3X9|Q8TCQ4|Q8WWT4|Q8WWT5|Q9NTG3	Missense_Mutation	SNP	ENST00000247001.5	hg19	CCDS12399.1	.	.	.	.	.	.	.	.	.	.	C	17.73	3.460953	0.63513	.	.	ENSG00000105705	ENST00000247001;ENST00000535070;ENST00000334782	T	0.54279	0.58	4.88	-3.34	0.04943	.	0.000000	0.85682	D	0.000000	T	0.64832	0.2634	M	0.73962	2.25	0.50039	D	0.999841	D	0.71674	0.998	D	0.79784	0.993	T	0.67237	-0.5721	10	0.87932	D	0	.	10.2244	0.43216	0.0:0.2929:0.0:0.7071	.	35	Q8IWZ8	SUGP1_HUMAN	H	35	ENSP00000247001:Q35H	ENSP00000247001:Q35H	Q	-	3	2	SUGP1	19288332	0.067000	0.21026	0.993000	0.49108	0.968000	0.65278	-1.275000	0.02817	-0.260000	0.09418	-0.258000	0.10820	CAG	.	.	.	none		0.517	SUGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460128.4	NM_021164		G	19427332	C	G	19427332	3	3	81	1	0	0	0	0	1	0	0	0	14168	680	24	4	1884	4	SF4	19	19427332	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10		19427332	39701651	86	5277											
ZNF567	163081	hgsc.bcm.edu	37	chr19	37210700	37210701	+	Missense_Mutation	DNP	TC	TC	AT																															ctcattcgtcatcagagaacTcacacgggagagaaaccata																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr19:37210700_37210701TC>AT	ENST00000536254.2	+	6	1296_1297	c.1074_1075TC>AT	c.(1072-1077)acTCac>acATac	p.H359Y	ZNF850_ENST00000589390.1_Intron|ZNF567_ENST00000360729.4_Missense_Mutation_p.H328Y|ZNF567_ENST00000588311.1_Missense_Mutation_p.H328Y|ZNF567_ENST00000392163.2_Missense_Mutation_p.H328Y|ZNF567_ENST00000585696.1_Missense_Mutation_p.H328Y			Q8N184	ZN567_HUMAN	zinc finger protein 567	359					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			ATCAGAGAACTCACACGGGAGA	0.455																																					p.T327T|p.H328Y		Atlas-SNP	.											.	ZNF567	61	.	0			c.T981A|c.C982T						PASS	.																																			SO:0001583	missense	163081	exon4			GAGAACTCACACG|AGAACTCACACGG	AK093034	CCDS12495.1, CCDS74349.1	19q13.12	2013-10-08				ENSG00000189042		"Zinc fingers, C2H2-type", "-"	28696	protein-coding gene	gene with protein product						12477932	Standard	XM_006723064		Approved	MGC45586	uc002oep.4	Q8N184		Exception_encountered	chr19.hg19:g.37210700_37210701delinsAT	ENSP00000441838:p.His359Tyr	91.0|89.0	0.0	.		84.0|82.0	33.0|32.0	.	NM_152603	B3KX49|Q6N044	Silent|Missense_Mutation	SNP	ENST00000536254.2	hg19																																																																																				.	.	.	none		0.455	ZNF567-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000453549.1	NM_152603		AT	37210701	TC	AT	37210700	3	1	81	1	0	0	0	0	1	0	0	0	18010	1538	54	5	991	5	ZNF567	19	37210700	Missense_Mutation	DNP	TC	TCGA-B1-A47M-01A-11D-A25F-10	17783368	37210700	21918283	87	5278											
ZNF569	148266	hgsc.bcm.edu	37	chr19	37904781	37904781	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccagtatgaattctttgaTgtctaatgagatttgacatt	11	17	7	6	0	2	4	0	4	2	1	3	5	3	4	1	0	0	1	1	0	3	6			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr19:37904781T>C	ENST00000316950.6	-	6	1336	c.779A>G	c.(778-780)cAt>cGt	p.H260R	ZNF569_ENST00000392149.2_Missense_Mutation_p.H260R|ZNF569_ENST00000392150.2_Missense_Mutation_p.H101R	NM_152484.2	NP_689697.2	Q5MCW4	ZN569_HUMAN	zinc finger protein 569	260					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(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)			AATTCTTTGATGTCTAATGAG	0.313																																					p.H260R		Atlas-SNP	.											.	ZNF569	101	.	0			c.A779G						PASS	.						74	81	79					19																	37904781		2203	4299	6502	SO:0001583	missense	148266	exon6			CTTTGATGTCTAA	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.779A>G	chr19.hg19:g.37904781T>C	ENSP00000325018:p.His260Arg	16.0	0.0	.		17.0	9.0	.	NM_152484	A8K1S2|Q15925|Q17RR6|Q96MQ2	Missense_Mutation	SNP	ENST00000316950.6	hg19	CCDS12503.1	.	.	.	.	.	.	.	.	.	.	T	16.52	3.145205	0.57044	.	.	ENSG00000196437	ENST00000316950;ENST00000392150	D;D	0.86865	-2.18;-2.18	3.8	2.75	0.32379	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.38897	N	0.001523	D	0.93265	0.7854	M	0.92555	3.32	0.42876	D	0.994154	D;D	0.76494	0.999;0.999	D;D	0.62955	0.909;0.909	D	0.92892	0.6332	10	0.87932	D	0	.	9.5174	0.39113	0.0:0.0:0.1787:0.8213	.	101;260	Q17RR6;Q5MCW4	.;ZN569_HUMAN	R	260;101	ENSP00000325018:H260R;ENSP00000375993:H101R	ENSP00000325018:H260R	H	-	2	0	ZNF569	42596621	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.150000	0.50662	0.597000	0.29811	0.482000	0.46254	CAT	.	.	.	none		0.313	ZNF569-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109594.2	NM_152484		C	37904781	T	C	37904781	3	2	81	1	0	0	0	0	1	0	0	0	18012	1464	51	3	1285	3	ZNF569	19	37904781	Missense_Mutation	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10	694081	37904781	21224202	88	5279											
RABAC1	10567	hgsc.bcm.edu	37	chr19	42461228	42461228	+	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	cagaagaaggggaaggagatGcctccagccagagcatactg	14	4	14	9	0	0	4	0	0	0	4	1	6	1	5	3	3	4	1	3	3	4	1			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr19:42461228G>T	ENST00000222008.6	-	4	508	c.411C>A	c.(409-411)ggC>ggA	p.G137G	RABAC1_ENST00000601078.1_Silent_p.G43G|RABAC1_ENST00000601891.1_Intron	NM_006423.2	NP_006414.2	Q9UI14	PRAF1_HUMAN	Rab acceptor 1 (prenylated)	137						cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|synapse (GO:0045202)	identical protein binding (GO:0042802)			central_nervous_system(1)|kidney(1)|prostate(1)	3						GGAAGGAGATGCCTCCAGCCA	0.642																																					p.G137G		Atlas-SNP	.											.	RABAC1	6	.	0			c.C411A						PASS	.						77	75	76					19																	42461228		2203	4300	6503	SO:0001819	synonymous_variant	10567	exon4			GGAGATGCCTCCA	AJ133534	CCDS12593.1	19q13.2	2012-09-20			ENSG00000105404	ENSG00000105404			9794	protein-coding gene	gene with protein product	"PRA1 domain family 1", "prenylated Rab acceptor 1"	604925				10329441, 10751420	Standard	NM_006423		Approved	PRA1, PRAF1, YIP3	uc002osf.3	Q9UI14		ENST00000222008.6:c.411C>A	chr19.hg19:g.42461228G>T		281.0	0.0	.		143.0	54.0	.	NM_006423	Q7Z4Y2|Q9Y3R1	Silent	SNP	ENST00000222008.6	hg19	CCDS12593.1																																																																																			.	.	.	none		0.642	RABAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463388.1	NM_006423		T	42461228	G	T	42461228	2	4	81	1	0	0	0	0	0	0	0	1	12973	1306	46	4		4	RABAC1	19	42461228	Silent	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	4556447	42461228	16667755	89	5280											
CCDC155	147872	hgsc.bcm.edu	37	chr19	49920441	49920441	+	Missense_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	cgcggcgggaactccagcaaGccctggtgcctgtgatgaaa	9	6	14	12	3	0	2	0	2	0	0	1	3	1	3	3	3	4	1	3	3	3	0			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr19:49920441G>A	ENST00000447857.3	+	19	1670	c.1465G>A	c.(1465-1467)Gcc>Acc	p.A489T		NM_144688.4	NP_653289.3	Q8N6L0	KASH5_HUMAN	coiled-coil domain containing 155	489						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						ACTCCAGCAAGCCCTGGTGCC	0.652																																					p.A489T		Atlas-SNP	.											.	CCDC155	46	.	0			c.G1465A						PASS	.						23	26	25					19																	49920441		1938	4124	6062	SO:0001583	missense	147872	exon19			CAGCAAGCCCTGG		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.1465G>A	chr19.hg19:g.49920441G>A	ENSP00000404220:p.Ala489Thr	60.0	0.0	.		42.0	19.0	.	NM_144688	Q96MC3	Missense_Mutation	SNP	ENST00000447857.3	hg19	CCDS46140.1	.	.	.	.	.	.	.	.	.	.	g	16.07	3.019479	0.54576	.	.	ENSG00000161609	ENST00000447857	T	0.57595	0.39	3.88	3.88	0.44766	.	0.000000	0.46758	D	0.000279	T	0.68824	0.3043	M	0.72118	2.19	0.28879	N	0.89453	D;D	0.67145	0.996;0.996	D;D	0.79784	0.993;0.993	T	0.65179	-0.6231	10	0.87932	D	0	-7.7039	12.1446	0.54016	0.0:0.0:1.0:0.0	.	489;489	C9JGW3;Q8N6L0	.;CC155_HUMAN	T	489	ENSP00000404220:A489T	ENSP00000404220:A489T	A	+	1	0	CCDC155	54612253	0.984000	0.35163	0.893000	0.35052	0.131000	0.20780	4.606000	0.61126	2.123000	0.65237	0.444000	0.29173	GCC	.	.	.	none		0.652	CCDC155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465436.2	NM_144688		A	49920441	G	A	49920441	3	1	81	1	0	0	0	0	1	0	0	0	2790	971	34	2	1535	2	CCDC155	19	49920441	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10	7459213	49920441	9208542	90	5281											
AP2A1	160	hgsc.bcm.edu	37	chr19	50285918	50285918	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggccctgcactgcatcgccaAcgtgggcagccgggagatgg	7	5	16	13	3	0	1	0	0	0	1	1	2	0	1	3	4	4	3	3	4	1	0			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr19:50285918A>G	ENST00000359032.5	+	4	410	c.410A>G	c.(409-411)aAc>aGc	p.N137S	AP2A1_ENST00000354293.5_Missense_Mutation_p.N137S|AP2A1_ENST00000600199.1_3'UTR	NM_014203.2	NP_055018.2	O95782	AP2A1_HUMAN	adaptor-related protein complex 2, alpha 1 subunit	137					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	AP-2 adaptor complex (GO:0030122)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)	19		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0023)|GBM - Glioblastoma multiforme(134;0.0157)		TGCATCGCCAACGTGGGCAGC	0.657																																					p.N137S		Atlas-SNP	.											.	AP2A1	108	.	0			c.A410G						PASS	.						32	33	32					19																	50285918		2157	4257	6414	SO:0001583	missense	160	exon4			TCGCCAACGTGGG	AA993745	CCDS46148.1, CCDS46149.1	19q13.3	2008-05-23				ENSG00000196961			561	protein-coding gene	gene with protein product		601026		CLAPA1, ADTAA		2564002	Standard	NM_014203		Approved		uc002ppn.3	O95782		ENST00000359032.5:c.410A>G	chr19.hg19:g.50285918A>G	ENSP00000351926:p.Asn137Ser	51.0	0.0	.		30.0	12.0	.	NM_130787	Q96CI7|Q96PP6|Q96PP7|Q9H070	Missense_Mutation	SNP	ENST00000359032.5	hg19	CCDS46148.1	.	.	.	.	.	.	.	.	.	.	A	18.01	3.527703	0.64860	.	.	ENSG00000196961	ENST00000354293;ENST00000359032	T;T	0.23950	1.88;1.88	5.54	5.54	0.83059	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.32133	0.0819	M	0.65975	2.015	0.80722	D	1	B;B	0.24533	0.025;0.105	B;B	0.28465	0.029;0.09	T	0.08617	-1.0713	10	0.52906	T	0.07	.	14.6526	0.68808	1.0:0.0:0.0:0.0	.	137;137	O95782-2;O95782	.;AP2A1_HUMAN	S	137	ENSP00000346246:N137S;ENSP00000351926:N137S	ENSP00000346246:N137S	N	+	2	0	AP2A1	54977730	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.309000	0.96252	2.103000	0.63969	0.455000	0.32223	AAC	.	.	.	none		0.657	AP2A1-008	NOVEL	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465809.1			G	50285918	A	G	50285918	3	3	81	1	0	0	0	0	1	0	0	0	739	43	2	3	424	3	AP2A1	19	50285918	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	365477	50285918	8843065	91	5282											
JAG1	182	hgsc.bcm.edu	37	chr20	10639160	10639160	+	Missense_Mutation	SNP	T	T	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	agccttccatgcaagttttgTtgccattctggtcacaggca	8	13	9	11	0	2	0	1	0	1	0	3	0	3	0	3	2	3	4	3	2	1	5			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr20:10639160T>G	ENST00000254958.5	-	4	1165	c.650A>C	c.(649-651)aAc>aCc	p.N217T	JAG1_ENST00000423891.2_Missense_Mutation_p.N58T	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	217	DSL. {ECO:0000255|PROSITE- ProRule:PRU00377}.				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						GCAAGTTTTGTTGCCATTCTG	0.493									Alagille Syndrome																												p.N217T		Atlas-SNP	.											.	JAG1	213	.	0			c.A650C						PASS	.						126	119	121					20																	10639160		2203	4300	6503	SO:0001583	missense	182	exon4	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	GTTTTGTTGCCAT	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.650A>C	chr20.hg19:g.10639160T>G	ENSP00000254958:p.Asn217Thr	89.0	0.0	.		58.0	25.0	.	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Missense_Mutation	SNP	ENST00000254958.5	hg19	CCDS13112.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.463155	0.84425	.	.	ENSG00000101384	ENST00000254958;ENST00000423891	D;D	0.96011	-3.88;-3.88	5.58	5.58	0.84498	Delta/Serrate/lag-2 (DSL) protein (3);	0.000000	0.85682	D	0.000000	D	0.95382	0.8501	L	0.50333	1.59	0.80722	D	1	D	0.52996	0.957	P	0.51833	0.681	D	0.95419	0.8505	10	0.54805	T	0.06	.	15.7475	0.77958	0.0:0.0:0.0:1.0	.	217	P78504	JAG1_HUMAN	T	217;58	ENSP00000254958:N217T;ENSP00000389519:N58T	ENSP00000254958:N217T	N	-	2	0	JAG1	10587160	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.040000	0.89188	2.124000	0.65301	0.460000	0.39030	AAC	.	.	.	none		0.493	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214		G	10639160	T	G	10639160	3	3	81	1	0	0	0	0	1	0	0	0	7941	1725	60	5	3098	5	JAG1	20	10639160	Missense_Mutation	SNP	T	TCGA-B1-A47M-01A-11D-A25F-10		10639160	52386360	92	5283											
CTCFL	140690	hgsc.bcm.edu	37	chr20	56098141	56098141	+	Frame_Shift_Del	DEL	T	T	-																															taccctttgtctttctttgaTtttttgtagatttggccttt																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr20:56098141delT	ENST00000608263.1	-	2	1398	c.737delA	c.(736-738)aatfs	p.N246fs	CTCFL_ENST00000432255.2_Frame_Shift_Del_p.N246fs|CTCFL_ENST00000609232.1_Frame_Shift_Del_p.N246fs|CTCFL_ENST00000433949.3_Frame_Shift_Del_p.N41fs|CTCFL_ENST00000608858.1_Intron|CTCFL_ENST00000429804.3_Frame_Shift_Del_p.N246fs|CTCFL_ENST00000608425.1_Frame_Shift_Del_p.N246fs|CTCFL_ENST00000422869.2_Frame_Shift_Del_p.N246fs|CTCFL_ENST00000539382.1_Frame_Shift_Del_p.N41fs|CTCFL_ENST00000243914.3_Frame_Shift_Del_p.N246fs|CTCFL_ENST00000608158.1_Frame_Shift_Del_p.N246fs|CTCFL_ENST00000608903.1_Intron|CTCFL_ENST00000502686.2_Intron|CTCFL_ENST00000608440.1_Frame_Shift_Del_p.N246fs|CTCFL_ENST00000481655.2_Frame_Shift_Del_p.N246fs|CTCFL_ENST00000423479.3_Frame_Shift_Del_p.N246fs|CTCFL_ENST00000371196.2_Frame_Shift_Del_p.N246fs	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	246					cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			CTTTCTTTGATTTTTTGTAGA	0.398																																					p.N246fs		Atlas-Indel,Pindel	.											.	CTCFL	97	.	0			c.738delT						PASS	.						197	176	183					20																	56098141		2202	4300	6502	SO:0001589	frameshift_variant	140690	exon2			.		CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"Zinc fingers, C2H2-type"	16234	protein-coding gene	gene with protein product	"cancer/testis antigen 27"	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.737delA	chr20.hg19:g.56098141delT	ENSP00000476783:p.Asn246fs	85.0	0.0	0		72.0	24.0	0.333333	NM_001269044	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Frame_Shift_Del	DEL	ENST00000608263.1	hg19	CCDS13459.1																																																																																			.	.	.	none		0.398	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618		-	56098141	T	-	56098141	7	5	81	1	0	1	0	1	0	0	0	0	4003	1493	52	0	1290	0	CTCFL	20	56098141	Frame_Shift_Del	DEL	T	TCGA-B1-A47M-01A-11D-A25F-10	45458981	56098141	6927379	93	5284											
MYT1	4661	hgsc.bcm.edu	37	chr20	62851117	62851117	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctggacttgagcatgcacAaacaccgcaaacgagaaaat	16	5	8	12	2	0	2	0	1	0	1	0	4	0	3	2	1	4	3	2	1	4	1			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr20:62851117A>G	ENST00000328439.1	+	13	2387	c.2023A>G	c.(2023-2025)Aaa>Gaa	p.K675E	MYT1_ENST00000536311.1_Missense_Mutation_p.K702E|MYT1_ENST00000360149.4_Missense_Mutation_p.K377E	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(12)|liver(1)|lung(17)|ovary(5)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					GAGCATGCACAAACACCGCAA	0.557																																					p.K675E	GBM(59;481 1041 20555 21139 33705)	Atlas-SNP	.											.	MYT1	152	.	0			c.A2023G						PASS	.						107	99	102					20																	62851117		2203	4300	6503	SO:0001583	missense	4661	exon13			ATGCACAAACACC	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.2023A>G	chr20.hg19:g.62851117A>G	ENSP00000327465:p.Lys675Glu	191.0	0.0	.		174.0	67.0	.	NM_004535	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000328439.1	hg19	CCDS13558.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.049072	0.75846	.	.	ENSG00000196132	ENST00000360149;ENST00000328439;ENST00000536311	T;T;T	0.59083	0.29;0.29;0.29	5.75	5.75	0.90469	Myelin transcription factor 1 (1);	0.000000	0.85682	D	0.000000	T	0.74344	0.3704	M	0.73598	2.24	0.58432	D	0.999999	D;D;P	0.55800	0.971;0.973;0.716	P;P;P	0.61874	0.641;0.895;0.487	T	0.77816	-0.2447	10	0.87932	D	0	-17.2533	16.0591	0.80826	1.0:0.0:0.0:0.0	.	702;675;377	F5H7M8;Q01538;Q6P6D5	.;MYT1_HUMAN;.	E	377;675;702	ENSP00000353269:K377E;ENSP00000327465:K675E;ENSP00000442412:K702E	ENSP00000327465:K675E	K	+	1	0	MYT1	62321561	1.000000	0.71417	0.598000	0.28837	0.888000	0.51559	8.826000	0.92034	2.185000	0.69588	0.533000	0.62120	AAA	.	.	.	none		0.557	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535		G	62851117	A	G	62851117	3	3	81	1	0	0	0	0	1	0	0	0	10113	131	5	3	2065	3	MYT1	20	62851117	Missense_Mutation	SNP	A	TCGA-B1-A47M-01A-11D-A25F-10	6752976	62851117	174403	94	5285											
DYRK1A	1859	hgsc.bcm.edu	37	chr21	38884349	38884349	+	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	atgcattgcatcatcaccatGgtaacagttcccatcaccat	12	11	5	13	0	3	0	3	0	0	0	4	0	4	0	3	1	3	4	3	1	1	3			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr21:38884349G>A	ENST00000398960.2	+	11	1882	c.1807G>A	c.(1807-1809)Ggt>Agt	p.G603S	DYRK1A_ENST00000455387.2_Missense_Mutation_p.G375S|DYRK1A_ENST00000339659.4_Missense_Mutation_p.G594S|DYRK1A_ENST00000338785.3_3'UTR	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	603					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						TCATCACCATGGTAACAGTTC	0.502																																					p.G603S	Melanoma(114;464 1602 31203 43785 45765)	Atlas-SNP	.											.	DYRK1A	85	.	0			c.G1807A						PASS	.						115	98	104					21																	38884349		2203	4300	6503	SO:0001583	missense	1859	exon11			CACCATGGTAACA	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.1807G>A	chr21.hg19:g.38884349G>A	ENSP00000381932:p.Gly603Ser	154.0	0.0	.		129.0	45.0	.	NM_001396	O60769|Q92582|Q92810|Q9UNM5	Missense_Mutation	SNP	ENST00000398960.2	hg19	CCDS42925.1	.	.	.	.	.	.	.	.	.	.	G	16.79	3.221682	0.58560	.	.	ENSG00000157540	ENST00000339659;ENST00000398960;ENST00000455387	T;T;T	0.55760	0.5;0.5;1.09	5.21	5.21	0.72293	.	0.298408	0.32459	N	0.006064	T	0.52725	0.1752	N	0.14661	0.345	0.53688	D	0.999979	D;D	0.60575	0.98;0.988	P;D	0.65010	0.855;0.931	T	0.44329	-0.9335	10	0.08599	T	0.76	.	18.785	0.91951	0.0:0.0:1.0:0.0	.	603;594	Q13627;Q13627-2	DYR1A_HUMAN;.	S	594;603;375	ENSP00000340373:G594S;ENSP00000381932:G603S;ENSP00000407854:G375S	ENSP00000340373:G594S	G	+	1	0	DYRK1A	37806219	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.746000	0.74866	2.434000	0.82447	0.655000	0.94253	GGT	.	.	.	none		0.502	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1	NM_001396		A	38884349	G	A	38884349	3	1	81	1	0	0	0	0	1	0	0	0	4856	1348	47	2	1933	2	DYRK1A	21	38884349	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10		38884349	9245546	95	5286											
SMARCB1	6598	hgsc.bcm.edu	37	chr22	24175838	24175839	+	Frame_Shift_Ins	INS	-	-	TT																															gtgcccactgctggagactcINStgacagacgctgagatggag																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr22:24175838_24175839insTT	ENST00000263121.7	+	8	1262_1263	c.1066_1067insTT	c.(1066-1068)ctgfs	p.L356fs	SMARCB1_ENST00000407422.3_Frame_Shift_Ins_p.L347fs|DERL3_ENST00000464023.1_5'Flank|SMARCB1_ENST00000344921.6_Frame_Shift_Ins_p.L365fs|SMARCB1_ENST00000407082.3_Frame_Shift_Ins_p.L310fs	NM_003073.3	NP_003064.2	Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	356					ATP-dependent chromatin remodeling (GO:0043044)|blastocyst hatching (GO:0001835)|cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|DNA integration (GO:0015074)|DNA repair (GO:0006281)|mitotic cell cycle phase transition (GO:0044772)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	p53 binding (GO:0002039)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)	p.?(2)|p.L266_*386del(1)		bone(4)|central_nervous_system(198)|endometrium(4)|haematopoietic_and_lymphoid_tissue(25)|kidney(3)|large_intestine(5)|liver(2)|lung(5)|meninges(5)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|soft_tissue(194)	458		Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05)				GCTGGAGACTCTGACAGACGCT	0.629			"D, N, F, S"		malignant rhabdoid	malignant rhabdoid																															p.L356fs		Atlas-Indel,Pindel	.	yes	Rec	yes	Rhabdoid predisposition syndrome	22	22q11	6598	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1"		M	.	SMARCB1	586	.	3	Unknown(2)|Deletion - In frame(1)	central_nervous_system(3)	c.1066_1067insTT						PASS	.																																			SO:0001589	frameshift_variant	6598	exon8			.	U04847	CCDS13817.1, CCDS46671.1	22q11.23	2014-09-17			ENSG00000099956	ENSG00000099956			11103	protein-coding gene	gene with protein product	"sucrose nonfermenting, yeast, homolog-like 1", "integrase interactor 1", "malignant rhabdoid tumor suppressor", "protein phosphatase 1, regulatory subunit 144"	601607		SNF5L1		7801128, 10319872, 10365963	Standard	NM_003073		Approved	BAF47, Ini1, Snr1, hSNFS, Sfh1p, RDT, PPP1R144	uc002zyb.3	Q12824	OTTHUMG00000150737	Exception_encountered	chr22.hg19:g.24175838_24175839insTT	ENSP00000263121:p.Leu356fs	83.0	0.0	0		90.0	24.0	0.266667	NM_003073	O75784|O95474|Q17S11|Q38GA1|Q76N08|Q9UBH2	Frame_Shift_Ins	INS	ENST00000263121.7	hg19	CCDS13817.1																																																																																			.	.	.	none		0.629	SMARCB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319872.1	NM_003073		TT	24175839	-	TT	24175838	7	5	81	1	0	1	1	0	0	0	0	0	14787	912	32	0	1096	0	SMARCB1	22	24175838	Frame_Shift_Ins	INS	-	TCGA-B1-A47M-01A-11D-A25F-10		24175838	27128728	96	5287											
NF2	4771	hgsc.bcm.edu	37	chr22	30038228	30038229	+	Missense_Mutation	DNP	CT	CT	AC																															agatgaaaagatctactgccCtcctgaggcttctgtgctcc																										TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chr22:30038228_30038229CT>AC	ENST00000338641.4	+	4	842_843	c.401_402CT>AC	c.(400-402)cCT>cAC	p.P134H	NF2_ENST00000347330.5_Missense_Mutation_p.P51H|NF2_ENST00000397789.3_Missense_Mutation_p.P134H|NF2_ENST00000334961.7_Missense_Mutation_p.P51H|NF2_ENST00000361452.4_Missense_Mutation_p.P93H|NF2_ENST00000361676.4_Missense_Mutation_p.P92H|NF2_ENST00000353887.4_Missense_Mutation_p.P51H|NF2_ENST00000413209.2_Missense_Mutation_p.P134H|NF2_ENST00000403435.1_Missense_Mutation_p.P134H|NF2_ENST00000361166.4_Missense_Mutation_p.P134H|NF2_ENST00000403999.3_Missense_Mutation_p.P134H	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	134	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.V122_K149del(5)|p.?(3)|p.L127_P134del(1)|p.K123fs*2(1)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						ATCTACTGCCCTCCTGAGGCTT	0.47			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																												p.P134H|p.P134P		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	.,1|.	NF2	1312	.	10	Deletion - In frame(6)|Unknown(3)|Deletion - Frameshift(1)	soft_tissue(8)|large_intestine(1)|stomach(1)	c.C401A|c.T402C						PASS	.																																			SO:0001583	missense	4771	exon4	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	ACTGCCCTCCTGA|CTGCCCTCCTGAG	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"A-kinase anchor proteins"	7773	protein-coding gene	gene with protein product	"moesin-ezrin-radixin like", "schwannomin"	607379	"neurofibromin 2 (bilateral acoustic neuroma)"			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	Exception_encountered	chr22.hg19:g.30038228_30038229delinsAC	ENSP00000344666:p.Pro134His	76.0	0.0	.		50.0|49.0	20.0	.	NM_000268	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Missense_Mutation|Silent	SNP	ENST00000338641.4	hg19	CCDS13861.1																																																																																			.	.	.	none		0.47	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268		AC	30038229	CT	AC	30038228	3	1	81	1	0	0	0	0	1	0	0	0	10364	681	24	4	415	4	NF2	22	30038228	Missense_Mutation	DNP	CT	TCGA-B1-A47M-01A-11D-A25F-10	5862390	30038228	21266338	97	5288											
SLC35A2	7355	hgsc.bcm.edu	37	chrX	48762075	48762075	+	Missense_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	acggtgggaagacagctgcgGtggtggtggctgcccgggag	6	6	21	8	3	0	1	0	0	0	1	0	3	0	3	1	7	3	2	1	7	1	0			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chrX:48762075G>A	ENST00000247138.5	-	4	1114	c.1111C>T	c.(1111-1113)Ccg>Tcg	p.P371S	SLC35A2_ENST00000413561.2_Missense_Mutation_p.P310S|SLC35A2_ENST00000376515.3_Missense_Mutation_p.T150I|SLC35A2_ENST00000452555.2_Missense_Mutation_p.P399S|SLC35A2_ENST00000376521.1_Missense_Mutation_p.P371S|SLC35A2_ENST00000376529.3_Missense_Mutation_p.T174I|SLC35A2_ENST00000445167.2_Missense_Mutation_p.T174I	NM_005660.1	NP_005651.1	P78381	S35A2_HUMAN	solute carrier family 35 (UDP-galactose transporter), member A2	371					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						GACAGCTGCGGTGGTGGTGGC	0.652																																					p.P371S		Atlas-SNP	.											.	SLC35A2	46	.	0			c.C1111T						PASS	.						40	34	36					X																	48762075		2203	4300	6503	SO:0001583	missense	7355	exon4			GCTGCGGTGGTGG	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.1111C>T	chrX.hg19:g.48762075G>A	ENSP00000247138:p.Pro371Ser	44.0	0.0	.		23.0	13.0	.	NM_001042498	A8K2L9|A8K9V1|B4DE11|B4DPT2|E7EW45|Q8IV21|Q92553	Missense_Mutation	SNP	ENST00000247138.5	hg19	CCDS14311.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.494|7.494	0.651284|0.651284	0.14516|0.14516	.|.	.|.	ENSG00000102100|ENSG00000102100	ENST00000247138;ENST00000376521;ENST00000413561;ENST00000452555|ENST00000376529;ENST00000445167;ENST00000376515	T;T;T;T|.	0.42131|.	0.98;0.99;0.99;1.0|.	3.67|3.67	0.966|0.966	0.19667|0.19667	.|.	1.403590|.	0.04571|.	N|.	0.393258|.	T|T	0.16342|0.16342	0.0393|0.0393	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	B;B;D;B;B|B	0.54601|0.02656	0.003;0.0;0.967;0.002;0.001|0.0	B;B;P;B;B|B	0.62382|0.08055	0.003;0.0;0.901;0.001;0.001|0.003	T|T	0.29941|0.29941	-0.9995|-0.9995	10|8	0.32370|0.13470	T|T	0.25|0.59	-0.5438|-0.5438	3.4371|3.4371	0.07449|0.07449	0.3602:0.1976:0.4422:0.0|0.3602:0.1976:0.4422:0.0	.|.	310;399;384;371;371|174	B4DE11;E7EW45;B4DE15;P78381-2;P78381|P78381-3	.;.;.;.;S35A2_HUMAN|.	S|I	371;371;310;399|174;174;150	ENSP00000247138:P371S;ENSP00000365704:P371S;ENSP00000393233:P310S;ENSP00000416002:P399S|.	ENSP00000247138:P371S|ENSP00000365698:T150I	P|T	-|-	1|2	0|0	SLC35A2|SLC35A2	48647019|48647019	0.169000|0.169000	0.23002|0.23002	0.010000|0.010000	0.14722|0.14722	0.354000|0.354000	0.29330|0.29330	0.674000|0.674000	0.25218|0.25218	0.064000|0.064000	0.16427|0.16427	-0.881000|-0.881000	0.02953|0.02953	CCG|ACC	.	.	.	none		0.652	SLC35A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060790.1	NM_005660		A	48762075	G	A	48762075	3	1	81	1	0	0	0	0	1	0	0	0	14584	1261	44	2	243	2	SLC35A2	23	48762075	Missense_Mutation	SNP	G	TCGA-B1-A47M-01A-11D-A25F-10		48762075	106508485	98	5289											
LPAR4	2846	hgsc.bcm.edu	37	chrX	78011381	78011381	+	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	ccctgtttaagactgaaacaCctttgaccacaaagccttcc	12	10	5	14	0	0	3	0	2	0	1	1	3	1	3	5	0	2	1	5	0	3	4			TCGA-B1-A47M-01A-11D-A25F-10	TCGA-B1-A47M-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8fb7fcac-6c1d-40c2-9309-b53821cbef30	68d9e30c-356a-4fd1-a9e9-6e535a0a963d	g.chrX:78011381C>T	ENST00000435339.3	+	2	1401	c.1015C>T	c.(1015-1017)Cct>Tct	p.P339S		NM_005296.2	NP_005287.1	Q99677	LPAR4_HUMAN	lysophosphatidic acid receptor 4	339					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)|lipid binding (GO:0008289)			breast(3)|endometrium(3)|kidney(4)|large_intestine(4)|lung(16)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	38						GACTGAAACACCTTTGACCAC	0.403																																					p.P339S		Atlas-SNP	.											.	LPAR4	83	.	0			c.C1015T						PASS	.						151	134	140					X																	78011381		2203	4300	6503	SO:0001583	missense	2846	exon2			GAAACACCTTTGA	U90322	CCDS14441.1	Xq21.1	2012-08-08	2008-04-11	2008-04-11	ENSG00000147145	ENSG00000147145		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	4478	protein-coding gene	gene with protein product		300086	"G protein-coupled receptor 23"	GPR23			Standard	NM_005296		Approved	P2Y9, P2Y5-LIKE, P2RY9, LPA4	uc010nme.3	Q99677	OTTHUMG00000021895	ENST00000435339.3:c.1015C>T	chrX.hg19:g.78011381C>T	ENSP00000408205:p.Pro339Ser	64.0	0.0	.		66.0	47.0	.	NM_005296	B2RAC7|O15132|Q502U9|Q6NSP5	Missense_Mutation	SNP	ENST00000435339.3	hg19	CCDS14441.1	.	.	.	.	.	.	.	.	.	.	C	8.708	0.911460	0.17833	.	.	ENSG00000147145	ENST00000435339;ENST00000373301	T;T	0.70631	-0.5;-0.5	4.26	4.26	0.50523	.	0.407810	0.24314	N	0.039618	T	0.41259	0.1151	N	0.08118	0	0.38155	D	0.938872	B	0.34103	0.437	B	0.30401	0.115	T	0.50890	-0.8774	10	0.02654	T	1	.	8.4939	0.33117	0.0:0.8889:0.0:0.1111	.	339	Q99677	LPAR4_HUMAN	S	339	ENSP00000408205:P339S;ENSP00000362398:P339S	ENSP00000362398:P339S	P	+	1	0	LPAR4	77898037	0.970000	0.33590	1.000000	0.80357	0.927000	0.56198	1.463000	0.35277	1.961000	0.56991	0.422000	0.28245	CCT	.	.	.	none		0.403	LPAR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057322.2	NM_005296		T	78011381	C	T	78011381	3	4	81	1	0	0	0	0	1	0	0	0	8914	507	18	2	1017	2	LPAR4	23	78011381	Missense_Mutation	SNP	C	TCGA-B1-A47M-01A-11D-A25F-10	29249306	78011381	77259179	99	5290											
DOCK7	85440	hgsc.bcm.edu	37	chr1	63119731	63119731	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcaatatcatctggaggaaAttcaatcaaatcccgtaaag	16	11	6	8	1	5	0	4	0	1	0	6	2	6	2	1	2	0	1	1	2	7	4			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr1:63119731A>G	ENST00000340370.5	-	3	261	c.244T>C	c.(244-246)Ttt>Ctt	p.F82L	DOCK7_ENST00000251157.5_Missense_Mutation_p.F82L|DOCK7_ENST00000404627.2_Missense_Mutation_p.F82L	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	82					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						TCTGGAGGAAATTCAATCAAA	0.428																																					p.F82L		Atlas-SNP	.											.	DOCK7	184	.	0			c.T244C						PASS	.						67	66	66					1																	63119731		2203	4300	6503	SO:0001583	missense	85440	exon3			GAGGAAATTCAAT		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.244T>C	chr1.hg19:g.63119731A>G	ENSP00000340742:p.Phe82Leu	83.0	0.0	.		85.0	27.0	.	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	hg19	CCDS30734.1	.	.	.	.	.	.	.	.	.	.	A	34	5.346120	0.95807	.	.	ENSG00000116641	ENST00000371140;ENST00000251157;ENST00000340370;ENST00000404627	T;T;T	0.63580	-0.05;-0.05;-0.05	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.73799	0.3633	M	0.84156	2.68	0.80722	D	1	P;D;P	0.56521	0.911;0.976;0.861	P;P;P	0.62382	0.895;0.901;0.73	T	0.78314	-0.2252	10	0.59425	D	0.04	.	15.1374	0.72579	1.0:0.0:0.0:0.0	.	82;82;82	Q96NI0;Q96N67-2;Q96N67-5	.;.;.	L	82	ENSP00000251157:F82L;ENSP00000340742:F82L;ENSP00000384446:F82L	ENSP00000251157:F82L	F	-	1	0	DOCK7	62892319	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.683000	0.91236	2.162000	0.67917	0.533000	0.62120	TTT	.	.	.	none		0.428	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		G	63119731	A	G	63119731	3	3	82	1	0	0	0	0	1	0	0	0	4694	101	4	3	6273	3	DOCK7	1	63119731	Missense_Mutation	SNP	A	TCGA-B1-A47N-01A-11D-A25F-10		63119731	186130890	1	5291											
HBXIP	10542	hgsc.bcm.edu	37	chr1	110950347	110950347	+	5'Flank	DEL	C	C	-																															gggcgtggaccgtaacggcgCctccaaagggacaaaattga																								rs201420127		TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr1:110950347delC	ENST00000602318.1	-	0	0				LAMTOR5_ENST00000602858.1_5'Flank|LAMTOR5-AS1_ENST00000598454.1_RNA|LAMTOR5-AS1_ENST00000608499.1_RNA|LAMTOR5-AS1_ENST00000457535.1_RNA|LAMTOR5-AS1_ENST00000609244.1_RNA|LAMTOR5_ENST00000256644.4_Frame_Shift_Del_p.A48fs|LAMTOR5-AS1_ENST00000608486.1_RNA|LAMTOR5_ENST00000474861.2_5'Flank|LAMTOR5-AS1_ENST00000610148.1_RNA|LAMTOR5-AS1_ENST00000608602.1_RNA|LAMTOR5_ENST00000483260.1_5'Flank|LAMTOR5-AS1_ENST00000587691.1_RNA|LAMTOR5-AS1_ENST00000590413.1_RNA|LAMTOR5-AS1_ENST00000609512.1_RNA|LAMTOR5-AS1_ENST00000608253.1_RNA|LAMTOR5-AS1_ENST00000590826.1_RNA|LAMTOR5-AS1_ENST00000609709.1_RNA|LAMTOR5-AS1_ENST00000608067.1_RNA			O43504	LTOR5_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 5						cellular response to amino acid stimulus (GO:0071230)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of GTPase activity (GO:0043547)|positive regulation of TOR signaling (GO:0032008)|protein localization to lysosome (GO:0061462)|regulation of cell size (GO:0008361)|response to virus (GO:0009615)|viral genome replication (GO:0019079)	cytosol (GO:0005829)|lysosome (GO:0005764)|Ragulator complex (GO:0071986)											CGTAACGGCGCCTCCAAAGGG	0.617																																					p.A48fs		Pindel	.											.	.	.	.	0			c.143delC						PASS	.						87	74	78					1																	110950347		2203	4300	6503	SO:0001631	upstream_gene_variant	10542	exon1			.	AF029890	CCDS824.1	1p12	2012-09-24	2012-09-24	2012-09-24	ENSG00000134248	ENSG00000134248			17955	protein-coding gene	gene with protein product	"HBx-interacting protein", "hepatitis B virus x-interacting protein (9.6kD)"	608521	"hepatitis B virus x interacting protein"	HBXIP		9499022, 22980980	Standard	NM_006402		Approved	XIP, MGC71071	uc001dzr.3	O43504	OTTHUMG00000011568		chr1.hg19:g.110950347delC	Exception_encountered	297.0	0.0	.		216.0	42.0	0.194	NM_006402	Q6IBD8	Frame_Shift_Del	DEL	ENST00000602318.1	hg19																																																																																				.	.	.	none		0.617	LAMTOR5-007	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467909.1	NM_006402		-	110950347	C	-	110950347	6	5	82	0	1	1	0	1	0	0	0	0	6995	739	26	0		0	HBXIP	1	110950347	5'Flank	DEL	C	TCGA-B1-A47N-01A-11D-A25F-10	47830616	110950347	138300274	2	5292											
PLEKHO1	51177	hgsc.bcm.edu	37	chr1	150131515	150131515	+	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	ccaaggacccccctcggtctCcgccggattctgagtcagag	7	7	11	16	3	3	2	1	1	2	1	5	4	3	4	6	3	0	0	6	3	1	1			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr1:150131515C>A	ENST00000369124.4	+	6	1305	c.1027C>A	c.(1027-1029)Ccg>Acg	p.P343T	PLEKHO1_ENST00000025469.6_Missense_Mutation_p.P309T|PLEKHO1_ENST00000369126.1_Missense_Mutation_p.P160T	NM_016274.4	NP_057358.2	Q53GL0	PKHO1_HUMAN	pleckstrin homology domain containing, family O member 1	343	Negative regulator of AP-1 activity.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	22	Lung NSC(24;7.78e-28)|Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCCTCGGTCTCCGCCGGATTC	0.607																																					p.P343T		Atlas-SNP	.											.	PLEKHO1	37	.	0			c.C1027A						PASS	.						50	54	53					1																	150131515		2203	4300	6503	SO:0001583	missense	51177	exon6			CGGTCTCCGCCGG	AF073836	CCDS945.1	1q21.2	2013-01-10			ENSG00000023902	ENSG00000023902		"Pleckstrin homology (PH) domain containing"	24310	protein-coding gene	gene with protein product		608335				10799509	Standard	NM_016274		Approved	CKIP-1, OC120	uc001ett.3	Q53GL0	OTTHUMG00000012510	ENST00000369124.4:c.1027C>A	chr1.hg19:g.150131515C>A	ENSP00000358120:p.Pro343Thr	132.0	0.0	.		127.0	19.0	.	NM_016274	Q336K5|Q8IZ51|Q9NRV3|Q9UL48	Missense_Mutation	SNP	ENST00000369124.4	hg19	CCDS945.1	.	.	.	.	.	.	.	.	.	.	C	15.60	2.880995	0.51801	.	.	ENSG00000023902	ENST00000369126;ENST00000025469;ENST00000369124;ENST00000441340	T;T	0.41758	0.99;0.99	5.24	5.24	0.73138	.	0.515831	0.21943	N	0.066842	T	0.13329	0.0323	N	0.14661	0.345	0.35920	D	0.831769	B	0.34103	0.437	B	0.32090	0.14	T	0.07309	-1.0779	10	0.52906	T	0.07	-17.5791	8.9859	0.35994	0.0:0.899:0.0:0.101	.	343	Q53GL0	PKHO1_HUMAN	T	160;309;343;223	ENSP00000025469:P309T;ENSP00000358120:P343T	ENSP00000025469:P309T	P	+	1	0	PLEKHO1	148398139	0.278000	0.24230	1.000000	0.80357	0.732000	0.41865	1.272000	0.33109	2.726000	0.93360	0.655000	0.94253	CCG	.	.	.	none		0.607	PLEKHO1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034962.1	NM_016274		A	150131515	C	A	150131515	3	1	82	1	0	0	0	0	1	0	0	0	12091	855	30	4	1049	4	PLEKHO1	1	150131515	Missense_Mutation	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10	39181168	150131515	99119106	3	5293											
C2orf61	285051	hgsc.bcm.edu	37	chr2	47382353	47382353	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacccaccaggtcttcccttAttgaggtggaagcggtggcg	7	9	13	12	2	1	1	0	1	1	0	2	2	2	2	3	5	1	0	3	5	2	3			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr2:47382353A>G	ENST00000445927.2	-	1	164	c.38T>C	c.(37-39)aTa>aCa	p.I13T	RP11-761B3.1_ENST00000422269.1_Intron|C2orf61_ENST00000294947.2_Missense_Mutation_p.I13T	NM_001163561.1	NP_001157033.1	Q8N801	CB061_HUMAN	chromosome 2 open reading frame 61	13								p.0?(2)		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)			GTCTTCCCTTATTGAGGTGGA	0.632																																					p.I13T		Atlas-SNP	.											.	C2orf61	31	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.T38C						PASS	.						103	86	91					2																	47382353		2203	4300	6503	SO:0001583	missense	285051	exon1			TCCCTTATTGAGG	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.38T>C	chr2.hg19:g.47382353A>G	ENSP00000408527:p.Ile13Thr	118.0	0.0	.		100.0	31.0	.	NM_173649	H7C2Z2	Missense_Mutation	SNP	ENST00000445927.2	hg19	CCDS54356.1	.	.	.	.	.	.	.	.	.	.	A	7.690	0.690952	0.15039	.	.	ENSG00000239605	ENST00000445927;ENST00000294947	T;T	0.32988	1.43;1.44	3.27	-2.91	0.05631	.	.	.	.	.	T	0.15219	0.0367	N	0.22421	0.69	0.09310	N	1	B	0.16396	0.017	B	0.14023	0.01	T	0.27806	-1.0063	9	0.59425	D	0.04	-0.0687	0.6125	0.00764	0.3325:0.172:0.1132:0.3822	.	13	Q8N801	CB061_HUMAN	T	13	ENSP00000408527:I13T;ENSP00000294947:I13T	ENSP00000294947:I13T	I	-	2	0	C2orf61	47235857	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.157000	0.16402	-0.545000	0.06224	-0.527000	0.04329	ATA	.	.	.	none		0.632	C2orf61-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173649		G	47382353	A	G	47382353	3	3	82	1	0	0	0	0	1	0	0	0	2182	449	16	3	751	3	C2orf61	2	47382353	Missense_Mutation	SNP	A	TCGA-B1-A47N-01A-11D-A25F-10		47382353	195817020	4	5294											
ZNF2	7549	hgsc.bcm.edu	37	chr2	95847510	95847510	+	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	taatccacactggcaggaagCcttatgagtgtaacgagtgc	12	9	11	9	1	0	1	0	1	0	0	1	3	1	2	2	2	3	2	2	2	4	3			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr2:95847510C>G	ENST00000340539.5	+	5	1399	c.937C>G	c.(937-939)Cct>Gct	p.P313A	ZNF2_ENST00000425369.1_Missense_Mutation_p.P233A|ZNF2_ENST00000398107.2_Missense_Mutation_p.P271A|ZNF2_ENST00000453539.2_Missense_Mutation_p.P326A|ZNF2_ENST00000295210.6_Missense_Mutation_p.P275A	NM_021088.2	NP_066574	Q9BSG1	ZNF2_HUMAN	zinc finger protein 2	313					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1)	12		Ovarian(717;0.00768)		READ - Rectum adenocarcinoma(193;0.0222)		TGGCAGGAAGCCTTATGAGTG	0.468																																					p.P313A		Atlas-SNP	.											.	ZNF2	21	.	0			c.C937G						PASS	.						72	78	76					2																	95847510		2117	4248	6365	SO:0001583	missense	7549	exon5			AGGAAGCCTTATG	X60152	CCDS42712.1, CCDS42713.1, CCDS62957.1	2q11.1	2013-09-24	2005-02-07		ENSG00000163067	ENSG00000275111		"Zinc fingers, C2H2-type", "-"	12991	protein-coding gene	gene with protein product		194500	"zinc finger protein 2 (A1-5)"			8183940, 1945843	Standard	NM_021088		Approved	A1-5, ZNF661, Zfp661	uc002suf.3	Q9BSG1	OTTHUMG00000155150	ENST00000340539.5:c.937C>G	chr2.hg19:g.95847510C>G	ENSP00000345392:p.Pro313Ala	168.0	0.0	.		153.0	53.0	.	NM_021088	A8MWV7|B4DIR4|Q4ZFY6|Q96G44|Q9UMC5	Missense_Mutation	SNP	ENST00000340539.5	hg19	CCDS42712.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.197452	0.79015	.	.	ENSG00000163067	ENST00000398107;ENST00000340539;ENST00000425369;ENST00000295210;ENST00000453539	T;T;T;T;T	0.16457	2.34;2.34;2.34;2.34;2.34	5.31	5.31	0.75309	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49305	D	0.000154	T	0.43233	0.1238	M	0.77406	2.37	0.53688	D	0.999974	D;D;D	0.76494	0.986;0.999;0.962	P;D;P	0.66847	0.766;0.947;0.514	T	0.35051	-0.9804	10	0.87932	D	0	-19.4509	16.5178	0.84305	0.0:1.0:0.0:0.0	.	275;271;312	B4DIR4;A8MWV7;Q9BSG1	.;.;ZNF2_HUMAN	A	271;313;233;275;326	ENSP00000381178:P271A;ENSP00000345392:P313A;ENSP00000406017:P233A;ENSP00000295210:P275A;ENSP00000411051:P326A	ENSP00000295210:P275A	P	+	1	0	ZNF2	95211237	1.000000	0.71417	0.998000	0.56505	0.591000	0.36615	7.297000	0.78799	2.765000	0.95021	0.655000	0.94253	CCT	.	.	.	none		0.468	ZNF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338595.2	NM_021088		G	95847510	C	G	95847510	3	3	82	1	0	0	0	0	1	0	0	0	17772	739	26	4	951	4	ZNF2	2	95847510	Missense_Mutation	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10	48465157	95847510	147351863	5	5295											
HOXD8	3234	hgsc.bcm.edu	37	chr2	176996164	176996165	+	Frame_Shift_Ins	INS	-	-	CCCTAGCCCT																															aagaatcgaggtttcccacgINSccctagccctcaccgagaga																										TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr2:176996164_176996165insCCCTAGCCCT	ENST00000313173.4	+	2	1324_1325	c.697_698insCCCTAGCCCT	c.(697-699)gccfs	p.-236fs	HOXD8_ENST00000429017.1_Frame_Shift_Ins_p.-52fs|HOXD8_ENST00000544999.1_Frame_Shift_Ins_p.-235fs|HOXD8_ENST00000450510.2_Frame_Shift_Ins_p.-235fs|HOXD-AS2_ENST00000440016.2_RNA|HOXD8_ENST00000548663.1_Frame_Shift_Ins_p.-132fs	NM_001199746.1|NM_019558.3	NP_001186675.1|NP_062458.1	P13378	HXD8_HUMAN	homeobox D8						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)		GGTTTCCCACGCCCTAGCCCTC	0.446																																					p.A233fs		Atlas-Indel,Pindel	.											.	HOXD8	24	.	0			c.697_698insCCCTAGCCCT						PASS	.																																			SO:0001589	frameshift_variant	3234	exon2			.		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.698_707dupCCCTAGCCCT	chr2.hg19:g.176996165_176996174dupCCCTAGCCCT	ENSP00000315949:p.Leu236fs	87.0	0.0	0		52.0	11.0	0.211538	NM_019558	F8WBG7|Q5BL00|Q8IXZ1	Frame_Shift_Ins	INS	ENST00000313173.4	hg19	CCDS2268.1																																																																																			.	.	.	none		0.446	HOXD8-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255694.1			CCCTAGCCCT	176996165	-	CCCTAGCCCT	176996164	7	5	82	1	0	1	1	0	0	0	0	0	7332	1087	38	0	703	0	HOXD8	2	176996164	Frame_Shift_Ins	INS	-	TCGA-B1-A47N-01A-11D-A25F-10	81148654	176996164	66203209	6	5296											
PGAP1	80055	hgsc.bcm.edu	37	chr2	197750195	197750195	+	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	ccatgataaatcaaccccttGcaggctttgaaataaatatg	15	11	6	9	0	1	2	1	2	0	0	1	2	1	2	3	1	2	2	3	1	7	5			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr2:197750195G>T	ENST00000354764.4	-	12	1339	c.1225C>A	c.(1225-1227)Caa>Aaa	p.Q409K	PGAP1_ENST00000409188.1_3'UTR|PGAP1_ENST00000409475.1_Missense_Mutation_p.Q409K	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	409					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						TCAACCCCTTGCAGGCTTTGA	0.284																																					p.Q409K		Atlas-SNP	.											.	PGAP1	84	.	0			c.C1225A						PASS	.						52	59	57					2																	197750195		2191	4286	6477	SO:0001583	missense	80055	exon12			CCCCTTGCAGGCT		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.1225C>A	chr2.hg19:g.197750195G>T	ENSP00000346809:p.Gln409Lys	105.0	0.0	.		71.0	5.0	.	NM_024989	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Missense_Mutation	SNP	ENST00000354764.4	hg19	CCDS2318.1	.	.	.	.	.	.	.	.	.	.	G	14.07	2.425404	0.43020	.	.	ENSG00000197121	ENST00000422382;ENST00000354764;ENST00000409475	.	.	.	5.26	5.26	0.73747	.	0.261976	0.38778	N	0.001561	T	0.56630	0.1998	N	0.24115	0.695	0.80722	D	1	B;P	0.49447	0.228;0.924	B;P	0.62298	0.083;0.9	T	0.46373	-0.9196	9	0.06891	T	0.86	-10.914	14.225	0.65853	0.0:0.0:1.0:0.0	.	409;409	Q75T13-3;Q75T13	.;PGAP1_HUMAN	K	189;409;409	.	ENSP00000346809:Q409K	Q	-	1	0	PGAP1	197458440	0.997000	0.39634	0.967000	0.41034	0.825000	0.46686	3.380000	0.52448	2.732000	0.93576	0.591000	0.81541	CAA	.	.	.	none		0.284	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989		T	197750195	G	T	197750195	3	4	82	1	0	0	0	0	1	0	0	0	11784	1328	46	4	1607	4	PGAP1	2	197750195	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	20754031	197750195	45449178	7	5297											
TPRG1	285386	hgsc.bcm.edu	37	chr3	188925189	188925189	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaaatgtcaacaattgggAgttttgaaggattccaggct	14	11	11	5	0	1	2	1	1	0	1	2	4	2	4	1	3	1	2	1	3	5	4			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr3:188925189A>G	ENST00000345063.3	+	2	183	c.16A>G	c.(16-18)Agt>Ggt	p.S6G	TPRG1_ENST00000433971.1_Missense_Mutation_p.S6G	NM_198485.3	NP_940887.1	Q6ZUI0	TPRG1_HUMAN	tumor protein p63 regulated 1	6						cytoplasm (GO:0005737)				endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|skin(2)|urinary_tract(1)	16	all_cancers(143;6.12e-12)|all_hematologic(3;0.0359)|Ovarian(172;0.0925)	all_lung(153;8.23e-09)|Lung NSC(153;3.55e-06)|all_neural(597;0.0019)|Myeloproliferative disorder(1037;0.0255)	Lung(62;6.93e-06)	GBM - Glioblastoma multiforme(93;4.77e-14)		AACAATTGGGAGTTTTGAAGG	0.458																																					p.S6G		Atlas-SNP	.											.	TPRG1	32	.	0			c.A16G						PASS	.						97	95	96					3																	188925189		2203	4300	6503	SO:0001583	missense	285386	exon2			ATTGGGAGTTTTG	AK125682	CCDS3292.1	3q28	2008-02-04	2008-01-16	2008-01-16	ENSG00000188001	ENSG00000188001			24759	protein-coding gene	gene with protein product			"family with sequence similarity 79, member B"	FAM79B			Standard	NM_198485		Approved	FLJ41238, FLJ43694	uc003frw.2	Q6ZUI0	OTTHUMG00000156321	ENST00000345063.3:c.16A>G	chr3.hg19:g.188925189A>G	ENSP00000341031:p.Ser6Gly	132.0	0.0	.		149.0	23.0	.	NM_198485		Missense_Mutation	SNP	ENST00000345063.3	hg19	CCDS3292.1	.	.	.	.	.	.	.	.	.	.	A	14.92	2.678779	0.47886	.	.	ENSG00000188001	ENST00000433971;ENST00000412373;ENST00000345063;ENST00000456832	.	.	.	5.83	5.83	0.93111	.	0.488214	0.25631	N	0.029360	T	0.39410	0.1077	L	0.34521	1.04	0.31374	N	0.679799	B	0.26363	0.147	B	0.29077	0.098	T	0.48681	-0.9014	9	0.45353	T	0.12	-5.1687	12.5927	0.56451	1.0:0.0:0.0:0.0	.	6	Q6ZUI0	TPRG1_HUMAN	G	6	.	ENSP00000341031:S6G	S	+	1	0	TPRG1	190407883	1.000000	0.71417	0.982000	0.44146	0.737000	0.42083	2.764000	0.47613	2.235000	0.73313	0.533000	0.62120	AGT	.	.	.	none		0.458	TPRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343931.1	NM_198485		G	188925189	A	G	188925189	3	3	82	1	0	0	0	0	1	0	0	0	16430	304	11	3	18	3	TPRG1	3	188925189	Missense_Mutation	SNP	A	TCGA-B1-A47N-01A-11D-A25F-10		188925189	9097241	8	5298											
MUC4	4585	hgsc.bcm.edu	37	chr3	195490958	195490958	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcacagcccacgtggggccGcctctgctggtacagggcac	7	5	14	15	2	1	0	0	0	1	0	1	0	1	0	3	4	4	4	3	4	1	1			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr3:195490958G>A	ENST00000346145.4	-	10	1333	c.1294C>T	c.(1294-1296)Cgg>Tgg	p.R432W	MUC4_ENST00000349607.4_Missense_Mutation_p.R381W|MUC4_ENST00000475231.1_Missense_Mutation_p.R4616W|MUC4_ENST00000463781.3_Missense_Mutation_p.R4668W	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1425					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)		ACGTGGGGCCGCCTCTGCTGG	0.662																																					p.R4668W		Atlas-SNP	.											.	MUC4	1505	.	0			c.C14002T						PASS	.						18	16	16					3																	195490958		2200	4299	6499	SO:0001583	missense	4585	exon11			GGGGCCGCCTCTG	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.1294C>T	chr3.hg19:g.195490958G>A	ENSP00000304207:p.Arg432Trp	330.0	0.0	.		210.0	10.0	.	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000346145.4	hg19	CCDS3310.1	.	.	.	.	.	.	.	.	.	.	.	9.013	0.982982	0.18889	.	.	ENSG00000145113	ENST00000349607;ENST00000346145;ENST00000463781;ENST00000475231	T;T;T;T	0.78126	-1.15;-0.44;-0.46;-0.33	5.25	-4.79	0.03200	AMOP (2);	0.750787	0.11391	N	0.568766	T	0.73814	0.3635	M	0.76002	2.32	0.25565	N	0.986958	P;P;P;P;B;B;D	0.53619	0.469;0.922;0.779;0.91;0.027;0.027;0.961	B;P;B;B;B;B;P	0.49451	0.107;0.611;0.199;0.303;0.019;0.019;0.466	T	0.65553	-0.6140	10	0.87932	D	0	-4.1234	1.1024	0.01687	0.3996:0.1018:0.1745:0.324	.	4540;1425;381;432;4668;4616;1373	E7ESK3;Q99102;Q99102-12;Q99102-13;E9PDY6;E7ENC5;Q99102-10	.;MUC4_HUMAN;.;.;.;.;.	W	381;432;4668;4616	ENSP00000338109:R381W;ENSP00000304207:R432W;ENSP00000417498:R4668W;ENSP00000420243:R4616W	ENSP00000304207:R432W	R	-	1	2	MUC4	196976629	0.021000	0.18746	0.104000	0.21259	0.021000	0.10359	-0.327000	0.07955	-0.553000	0.06158	-0.187000	0.12897	CGG	.	.	.	none		0.662	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406		A	195490958	G	A	195490958	3	1	82	1	0	0	0	0	1	0	0	0	9985	1086	38	1	2296	1	MUC4	3	195490958	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	6565769	195490958	2531472	9	5299											
UBA6	55236	hgsc.bcm.edu	37	chr4	68534339	68534339	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaaatgttaggaattgtccTgtctccagtttgtgaggatg	9	14	12	6	1	1	1	0	1	1	0	3	4	2	3	2	2	0	2	2	2	3	3			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr4:68534339T>C	ENST00000322244.5	-	9	782	c.723A>G	c.(721-723)acA>acG	p.T241T	UBA6_ENST00000420827.2_Silent_p.T241T	NM_018227.5	NP_060697.4	A0AVT1	UBA6_HUMAN	ubiquitin-like modifier activating enzyme 6	241					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						GGAATTGTCCTGTCTCCAGTT	0.303																																					p.T241T		Atlas-SNP	.											.	UBA6	98	.	0			c.A723G						PASS	.						123	120	121					4																	68534339		2203	4300	6503	SO:0001819	synonymous_variant	55236	exon9			TTGTCCTGTCTCC	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.723A>G	chr4.hg19:g.68534339T>C		76.0	0.0	.		94.0	5.0	.	NM_018227	A6N8M7|B2RAV3|Q4W5K0|Q6UV21|Q86T78|Q86TC7|Q8N5T3|Q8N9E4|Q9H3T7|Q9NVC9	Silent	SNP	ENST00000322244.5	hg19	CCDS3516.1																																																																																			.	.	.	none		0.303	UBA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251429.2	NM_018227		C	68534339	T	C	68534339	2	2	82	1	0	0	0	0	0	0	0	1	16844	1567	55	3		3	UBA6	4	68534339	Silent	SNP	T	TCGA-B1-A47N-01A-11D-A25F-10		68534339	122619937	10	5300											
ACCN5	51802	hgsc.bcm.edu	37	chr4	156784757	156784757	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagaaccaccaccaaccagaGcaccctgcgaattttgctcc	12	6	6	17	1	0	2	0	0	0	2	1	3	1	2	6	0	5	2	6	0	3	2			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr4:156784757G>A	ENST00000537611.2	-	2	236	c.190C>T	c.(190-192)Ctc>Ttc	p.L64F	TDO2_ENST00000506181.1_Intron	NM_017419.2	NP_059115.1	Q9NY37	ASIC5_HUMAN	acid-sensing (proton-gated) ion channel family member 5	64					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)										ACCAACCAGAGCACCCTGCGA	0.483																																					p.L64F		Atlas-SNP	.											.	.	.	.	0			c.C190T						PASS	.						131	116	121					4																	156784757		2203	4300	6503	SO:0001583	missense	51802	exon2			ACCAGAGCACCCT	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.190C>T	chr4.hg19:g.156784757G>A	ENSP00000442477:p.Leu64Phe	144.0	0.0	.		149.0	56.0	.	NM_017419		Missense_Mutation	SNP	ENST00000537611.2	hg19	CCDS3793.1	.	.	.	.	.	.	.	.	.	.	G	6.118	0.390031	0.11581	.	.	ENSG00000256394	ENST00000537611	T	0.65732	-0.17	4.24	1.65	0.23941	.	0.825563	0.10479	N	0.669867	T	0.38878	0.1057	N	0.11651	0.15	0.58432	D	0.999998	B	0.10296	0.003	B	0.17979	0.02	T	0.26744	-1.0094	10	0.02654	T	1	-0.483	12.6071	0.56529	0.0:0.0:0.5103:0.4896	.	64	Q9NY37	ACCN5_HUMAN	F	64	ENSP00000442477:L64F	ENSP00000264432:L64F	L	-	1	0	ACCN5	157004207	0.075000	0.21258	0.386000	0.26170	0.148000	0.21650	0.106000	0.15354	0.224000	0.20940	-0.271000	0.10264	CTC	.	.	.	none		0.483	ASIC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366464.1			A	156784757	G	A	156784757	3	1	82	1	0	0	0	0	1	0	0	0	132	971	34	2	1363	2	ACCN5	4	156784757	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	88250418	156784757	34369519	11	5301											
BTN2A2	10385	hgsc.bcm.edu	37	chr6	26384118	26384118	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcctcctgctcctcctcctTctcagcctgtgtgcactggt	2	14	7	18	0	1	0	1	0	1	0	7	0	6	0	6	1	3	2	6	1	0	1			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr6:26384118T>C	ENST00000356709.4	+	2	180	c.69T>C	c.(67-69)ctT>ctC	p.L23L	BTN2A2_ENST00000482536.1_Silent_p.L23L|BTN2A2_ENST00000469230.1_Silent_p.L23L|BTN2A2_ENST00000416795.2_Silent_p.L23L|BTN2A2_ENST00000432533.2_Silent_p.L23L|BTN2A2_ENST00000352867.2_Silent_p.L23L	NM_001197240.1|NM_006995.4	NP_001184169.1|NP_008926.2	Q8WVV5	BT2A2_HUMAN	butyrophilin, subfamily 2, member A2	23					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						tcctcctccttctcAGCCTGT	0.577																																					p.L23L		Atlas-SNP	.											.	BTN2A2	87	.	0			c.T69C						PASS	.						151	111	124					6																	26384118		2203	4300	6503	SO:0001819	synonymous_variant	10385	exon2			CCTCCTTCTCAGC	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.69T>C	chr6.hg19:g.26384118T>C		148.0	0.0	.		143.0	10.0	.	NM_181531	A6NM84|B4DE97|B4DQ01|E9PH07|O00480	Silent	SNP	ENST00000356709.4	hg19	CCDS4606.1																																																																																			.	.	.	none		0.577	BTN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040117.1			C	26384118	T	C	26384118	2	2	82	1	0	0	0	0	0	0	0	1	1563	1770	62	3		3	BTN2A2	6	26384118	Silent	SNP	T	TCGA-B1-A47N-01A-11D-A25F-10		26384118	144730949	12	5302											
SYNGAP1	8831	hgsc.bcm.edu	37	chr6	33400480	33400480	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaaggcttcctgagccgaCggctaaaaagctccatcaaa	14	6	9	12	2	1	1	1	1	0	0	3	2	3	1	3	2	3	4	3	2	5	2			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr6:33400480C>T	ENST00000418600.2	+	5	507	c.406C>T	c.(406-408)Cgg>Tgg	p.R136W	SYNGAP1_ENST00000428982.2_Missense_Mutation_p.R77W|SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000293748.5_Missense_Mutation_p.R136W	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	136					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						CCTGAGCCGACGGCTAAAAAG	0.577																																					p.R136W		Atlas-SNP	.											.	SYNGAP1	202	.	0			c.C406T						PASS	.						56	49	51					6																	33400480		2203	4300	6503	SO:0001583	missense	8831	exon5			AGCCGACGGCTAA	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.406C>T	chr6.hg19:g.33400480C>T	ENSP00000403636:p.Arg136Trp	59.0	0.0	.		54.0	16.0	.	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Missense_Mutation	SNP	ENST00000418600.2	hg19	CCDS34434.2	.	.	.	.	.	.	.	.	.	.	C	15.30	2.792591	0.50102	.	.	ENSG00000197283	ENST00000293748;ENST00000418600;ENST00000449372;ENST00000428982	T;T;T	0.28666	1.6;1.71;1.77	4.06	-1.15	0.09709	Pleckstrin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.34048	0.0884	M	0.69358	2.11	0.58432	D	0.999996	D;D;D	0.71674	0.965;0.98;0.998	B;P;P	0.62382	0.416;0.621;0.901	T	0.43065	-0.9414	10	0.87932	D	0	.	11.9927	0.53184	0.6778:0.3221:0.0:0.0	.	136;136;136	Q96PV0;Q96PV0-4;B7ZCA0	SYGP1_HUMAN;.;.	W	136;136;136;77	ENSP00000293748:R136W;ENSP00000403636:R136W;ENSP00000412475:R77W	ENSP00000293748:R136W	R	+	1	2	SYNGAP1	33508458	0.994000	0.37717	0.996000	0.52242	0.938000	0.57974	1.265000	0.33027	0.002000	0.14630	0.467000	0.42956	CGG	.	.	.	none		0.577	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407		T	33400480	C	T	33400480	3	4	82	1	0	0	0	0	1	0	0	0	15459	527	19	1	424	1	SYNGAP1	6	33400480	Missense_Mutation	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10	7016362	33400480	137714587	13	5303											
LPA	4018	hgsc.bcm.edu	37	chr6	161026202	161026202	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actctgtccatttccgtggtAgcactcctgcaccccaggcc	6	10	8	17	1	1	0	0	0	1	0	4	0	4	0	6	2	2	3	6	2	1	2			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr6:161026202A>G	ENST00000316300.5	-	18	2865	c.2821T>C	c.(2821-2823)Tac>Cac	p.Y941H	LPA_ENST00000447678.1_Missense_Mutation_p.Y941H			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3449	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)	TTTCCGTGGTAGCACTCCTGC	0.458																																					p.Y941H		Atlas-SNP	.											.	LPA	237	.	0			c.T2821C						PASS	.						269	278	275					6																	161026202		2200	4298	6498	SO:0001583	missense	4018	exon19			CGTGGTAGCACTC	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.2821T>C	chr6.hg19:g.161026202A>G	ENSP00000321334:p.Tyr941His	66.0	0.0	.		55.0	32.0	.	NM_005577	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	hg19	CCDS43523.1	.	.	.	.	.	.	.	.	.	.	a	10.16	1.275243	0.23307	.	.	ENSG00000198670	ENST00000316300;ENST00000447678	T;T	0.65364	-0.15;-0.15	2.16	2.16	0.27623	Kringle (4);Kringle-like fold (1);	.	.	.	.	T	0.72087	0.3417	H	0.95816	3.725	0.21782	N	0.999546	D	0.60160	0.987	D	0.70227	0.968	T	0.61004	-0.7150	9	0.26408	T	0.33	.	6.2159	0.20656	1.0:0.0:0.0:0.0	.	3449	P08519	APOA_HUMAN	H	941	ENSP00000321334:Y941H;ENSP00000395608:Y941H	ENSP00000321334:Y941H	Y	-	1	0	LPA	160946192	0.988000	0.35896	0.913000	0.36048	0.097000	0.18754	2.967000	0.49216	0.999000	0.39023	0.155000	0.16302	TAC	.	.	.	none		0.458	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		G	161026202	A	G	161026202	3	3	82	1	0	0	0	0	1	0	0	0	8910	420	15	3	3389	3	LPA	6	161026202	Missense_Mutation	SNP	A	TCGA-B1-A47N-01A-11D-A25F-10	127625722	161026202	10088865	14	5304											
TAX1BP1	8887	hgsc.bcm.edu	37	chr7	27856559	27856559	+	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	aaatacaaaggccacctgtcAgagtcccctcttggggactg	11	8	10	12	0	2	1	1	0	1	1	3	2	3	2	4	3	1	0	4	3	3	2			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr7:27856559A>T	ENST00000396319.2	+	15	2075	c.1987A>T	c.(1987-1989)Aga>Tga	p.R663*	TAX1BP1_ENST00000265393.6_Nonsense_Mutation_p.R621*|TAX1BP1_ENST00000543117.1_Nonsense_Mutation_p.R621*|TAX1BP1_ENST00000433216.2_Nonsense_Mutation_p.R464*|TAX1BP1_ENST00000409980.1_Nonsense_Mutation_p.R687*	NM_006024.6	NP_006015.4	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I) binding protein 1	663					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	kinase binding (GO:0019900)			breast(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(8)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31			GBM - Glioblastoma multiforme(3;0.0823)			GCCACCTGTCAGAGTCCCCTC	0.453																																					p.R663X		Atlas-SNP	.											.	TAX1BP1	71	.	0			c.A1987T						PASS	.						63	65	65					7																	27856559		2203	4300	6503	SO:0001587	stop_gained	8887	exon15			CCTGTCAGAGTCC	U33821	CCDS5415.1, CCDS43561.1, CCDS56471.1	7p15	2010-08-05			ENSG00000106052	ENSG00000106052			11575	protein-coding gene	gene with protein product		605326				10435631	Standard	NM_006024		Approved	TXBP151, CALCOCO3	uc003szl.3	Q86VP1	OTTHUMG00000023377	ENST00000396319.2:c.1987A>T	chr7.hg19:g.27856559A>T	ENSP00000379612:p.Arg663*	31.0	0.0	.		74.0	44.0	.	NM_006024	B4DKU7|E7ENV2|O60398|O95770|Q13311|Q9BQG5|Q9UI88	Nonsense_Mutation	SNP	ENST00000396319.2	hg19	CCDS5415.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.886755	0.91814	.	.	ENSG00000106052	ENST00000543117;ENST00000265393;ENST00000409980;ENST00000433216;ENST00000396319;ENST00000457186	.	.	.	5.67	4.5	0.54988	.	0.000000	0.56097	D	0.000023	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05620	T	0.96	-17.6197	12.6545	0.56780	0.857:0.143:0.0:0.0	.	.	.	.	X	621;621;687;464;663;200	.	ENSP00000265393:R621X	R	+	1	2	TAX1BP1	27823084	1.000000	0.71417	0.999000	0.59377	0.808000	0.45660	2.947000	0.49058	0.975000	0.38392	0.533000	0.62120	AGA	.	.	.	none		0.453	TAX1BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214142.1	NM_006024		T	27856559	A	T	27856559	4	4	82	1	0	0	0	0	0	1	0	0	15606	180	7	5	2041	5	TAX1BP1	7	27856559	Nonsense_Mutation	SNP	A	TCGA-B1-A47N-01A-11D-A25F-10		27856559	131282104	15	5305											
NFX1	4799	hgsc.bcm.edu	37	chr9	33319097	33319097	+	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	ccttcatgtggaaaagtgtgCggcaagcctctgccttgtgg	7	11	13	10	1	2	0	1	0	1	0	2	1	2	1	3	3	3	1	3	3	3	2			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr9:33319097C>T	ENST00000379540.3	+	9	1940	c.1878C>T	c.(1876-1878)tgC>tgT	p.C626C	NFX1_ENST00000379521.4_Silent_p.C626C|NFX1_ENST00000318524.6_Silent_p.C626C	NM_002504.4	NP_002495.2	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1	626					inflammatory response (GO:0006954)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)		GAAAAGTGTGCGGCAAGCCTC	0.453																																					p.C626C		Atlas-SNP	.											.	NFX1	85	.	0			c.C1878T						PASS	.						70	70	70					9																	33319097		2203	4300	6503	SO:0001819	synonymous_variant	4799	exon9			AGTGTGCGGCAAG	U19759	CCDS6538.1, CCDS6539.1, CCDS6540.1	9p12	2013-12-13			ENSG00000086102	ENSG00000086102			7803	protein-coding gene	gene with protein product		603255				7964459, 2511169	Standard	NM_002504		Approved	NFX2, MGC20369, Tex42, TEG-42	uc003zsq.3	Q12986	OTTHUMG00000019772	ENST00000379540.3:c.1878C>T	chr9.hg19:g.33319097C>T		97.0	0.0	.		96.0	4.0	.	NM_147134	A8K6H8|Q5VXW6|Q96EL5|Q9BXI1	Silent	SNP	ENST00000379540.3	hg19	CCDS6538.1																																																																																			.	.	.	none		0.453	NFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052069.1			T	33319097	C	T	33319097	2	4	82	1	0	0	0	0	0	0	0	1	10394	776	27	1		1	NFX1	9	33319097	Silent	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10		33319097	107894334	16	5306											
LAMC3	10319	hgsc.bcm.edu	37	chr9	133948708	133948708	+	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	ggcccgtgccctcgccaggaGgtgagtcccaagacatggtg	7	6	15	13	2	0	2	0	1	0	1	2	3	1	3	4	4	1	0	4	4	1	0			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr9:133948708G>A	ENST00000361069.4	+	20	3627	c.3494G>A	c.(3493-3495)aGc>aAc	p.S1165N	LAMC3_ENST00000480883.1_Intron	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	1165	Domain II and I.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		CTCGCCAGGAGGTGAGTCCCA	0.607																																					p.S1165N		Atlas-SNP	.											.	LAMC3	167	.	0			c.G3494A						PASS	.						46	46	46					9																	133948708		2203	4300	6503	SO:0001630	splice_region_variant	10319	exon20			CCAGGAGGTGAGT	AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"Laminins"	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.3494+1G>A	chr9.hg19:g.133948708G>A		55.0	0.0	.		17.0	7.0	.	NM_006059	B1APX9|B1APY0|Q59H72	Missense_Mutation	SNP	ENST00000361069.4	hg19	CCDS6938.1	.	.	.	.	.	.	.	.	.	.	G	10.79	1.450700	0.26074	.	.	ENSG00000050555	ENST00000361069;ENST00000355048	T	0.29655	1.56	4.23	4.23	0.50019	.	0.177619	0.64402	D	0.000012	T	0.34221	0.0890	M	0.68317	2.08	0.39455	D	0.967477	P	0.36789	0.57	B	0.40038	0.317	T	0.15093	-1.0449	10	0.17832	T	0.49	.	14.3309	0.66556	0.0:0.0:1.0:0.0	.	1165	Q9Y6N6	LAMC3_HUMAN	N	1165	ENSP00000354360:S1165N	ENSP00000347156:S1165N	S	+	2	0	LAMC3	132938529	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	6.044000	0.71012	2.365000	0.80145	0.555000	0.69702	AGC	.	.	.	none		0.607	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059	Missense_Mutation	A	133948708	G	A	133948708	5	1	82	1	0	0	0	0	0	0	1	0	8623	1014	35	2	3572	2	LAMC3	9	133948708	Splice_Site	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	100629611	133948708	7264723	17	5307											
ARHGAP21	57584	hgsc.bcm.edu	37	chr10	24873803	24873803	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcggtagcatctctgtgcccTcctagtgtatgtctgcgccg	4	13	11	13	3	2	0	0	0	2	0	5	0	3	0	3	1	3	3	3	1	3	3			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr10:24873803T>C	ENST00000396432.2	-	26	5901	c.5415A>G	c.(5413-5415)ggA>ggG	p.G1805G		NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	1804	Interaction with CTNNA1.				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						CTCTGTGCCCTCCTAGTGTAT	0.488																																					p.G1805G		Atlas-SNP	.											.	ARHGAP21	185	.	0			c.A5415G						PASS	.						50	50	50					10																	24873803		2203	4300	6503	SO:0001819	synonymous_variant	57584	exon26			GTGCCCTCCTAGT	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.5415A>G	chr10.hg19:g.24873803T>C		77.0	0.0	.		86.0	32.0	.	NM_020824	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Silent	SNP	ENST00000396432.2	hg19	CCDS7144.2																																																																																			.	.	.	none		0.488	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824		C	24873803	T	C	24873803	2	2	82	1	0	0	0	0	0	0	0	1	871	1538	54	3		3	ARHGAP21	10	24873803	Silent	SNP	T	TCGA-B1-A47N-01A-11D-A25F-10		24873803	110660944	18	5308											
ARHGAP1	392	hgsc.bcm.edu	37	chr11	46702650	46702650	+	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	acatagaagatcttctgcccGaacttgaagctgttggtgga	11	11	11	8	1	2	3	0	1	2	2	2	5	2	4	1	2	3	2	1	2	4	4			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr11:46702650G>A	ENST00000311956.4	-	7	643	c.546C>T	c.(544-546)ttC>ttT	p.F182F		NM_004308.3	NP_004299.1	Q07960	RHG01_HUMAN	Rho GTPase activating protein 1	182	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				positive regulation of signal transduction (GO:0009967)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	Rac GTPase activator activity (GO:0030675)|Rho GTPase activator activity (GO:0005100)|SH3/SH2 adaptor activity (GO:0005070)			endometrium(1)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	11		Lung NSC(402;1.76e-12)|all_lung(304;1.3e-11)		GBM - Glioblastoma multiforme(35;5.17e-06)|BRCA - Breast invasive adenocarcinoma(625;0.00112)|Lung(87;0.153)		TCTTCTGCCCGAACTTGAAGC	0.602																																					p.F182F		Atlas-SNP	.											ARHGAP1,NS,carcinoma,0,1	ARHGAP1	27	.	0			c.C546T						PASS	.						84	90	88					11																	46702650		2201	4299	6500	SO:0001819	synonymous_variant	392	exon7			CTGCCCGAACTTG	BC018118	CCDS7922.1	11p11.2	2006-04-11			ENSG00000175220	ENSG00000175220		"Rho GTPase activating proteins"	673	protein-coding gene	gene with protein product		602732				8288572	Standard	NM_004308		Approved	RhoGAP, p50rhoGAP, CDC42GAP, Cdc42GAP	uc001ndd.4	Q07960	OTTHUMG00000166567	ENST00000311956.4:c.546C>T	chr11.hg19:g.46702650G>A		106.0	0.0	.		58.0	5.0	.	NM_004308	D3DQQ6	Silent	SNP	ENST00000311956.4	hg19	CCDS7922.1	.	.	.	.	.	.	.	.	.	.	G	9.301	1.052993	0.19907	.	.	ENSG00000175220	ENST00000528837	.	.	.	5.28	1.37	0.22104	.	.	.	.	.	T	0.57770	0.2076	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51356	-0.8716	4	.	.	.	.	9.3727	0.38264	0.7873:0.0:0.2127:0.0	.	.	.	.	W	136	.	.	R	-	1	2	ARHGAP1	46659226	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	1.205000	0.32308	0.323000	0.23307	-0.459000	0.05422	CGG	.	.	.	none		0.602	ARHGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390472.1	NM_004308		A	46702650	G	A	46702650	2	1	82	1	0	0	0	0	0	0	0	1	861	1049	37	1		1	ARHGAP1	11	46702650	Silent	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10		46702650	88303866	19	5309											
AHNAK	79026	hgsc.bcm.edu	37	chr11	62296065	62296065	+	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	ctccaattttggcaccgacaCatccacatcccctttgactt	9	12	4	16	1	0	1	0	1	0	0	3	2	3	1	5	1	0	1	5	1	1	4			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr11:62296065C>T	ENST00000378024.4	-	5	6098	c.5824G>A	c.(5824-5826)Gtg>Atg	p.V1942M	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	1942					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)				GGCACCGACACATCCACATCC	0.502																																					p.V1942M		Atlas-SNP	.											.	AHNAK	532	.	0			c.G5824A						PASS	.						216	226	223					11																	62296065		2202	4299	6501	SO:0001583	missense	79026	exon5			CCGACACATCCAC	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.5824G>A	chr11.hg19:g.62296065C>T	ENSP00000367263:p.Val1942Met	194.0	0.0	.		188.0	14.0	.	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	hg19	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	c	6.228	0.410192	0.11812	.	.	ENSG00000124942	ENST00000244934;ENST00000378024	T	0.01272	5.07	2.29	1.33	0.21861	.	.	.	.	.	T	0.03608	0.0103	M	0.88105	2.93	0.27412	N	0.95455	P	0.41131	0.739	B	0.40602	0.334	T	0.14643	-1.0465	9	0.66056	D	0.02	.	7.0623	0.25133	0.0:0.8577:0.0:0.1423	.	1942	Q09666	AHNK_HUMAN	M	31;1942	ENSP00000367263:V1942M	ENSP00000244934:V31M	V	-	1	0	AHNAK	62052641	0.700000	0.27796	0.013000	0.15412	0.006000	0.05464	-0.172000	0.09868	0.317000	0.23160	0.186000	0.17326	GTG	.	.	.	none		0.502	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		T	62296065	C	T	62296065	3	4	82	1	0	0	0	0	1	0	0	0	414	478	17	2	11968	2	AHNAK	11	62296065	Missense_Mutation	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10	15593415	62296065	72710451	20	5310											
PC	5091	hgsc.bcm.edu	37	chr11	66636384	66636384	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacctcgatgaagtagtgctTgccgtgcctgtccaccagga	8	9	12	12	2	0	1	0	1	0	0	2	4	1	2	5	1	3	2	5	1	2	2			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr11:66636384T>C	ENST00000393958.2	-	9	1048	c.955A>G	c.(955-957)Aag>Gag	p.K319E	PC_ENST00000393955.2_Missense_Mutation_p.K319E|PC_ENST00000524491.1_Missense_Mutation_p.K279E|PC_ENST00000393960.1_Missense_Mutation_p.K319E|PC_ENST00000355677.3_Missense_Mutation_p.K319E	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	319	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)	AAGTAGTGCTTGCCGTGCCTG	0.687																																					p.K319E		Atlas-SNP	.											.	PC	116	.	0			c.A955G						PASS	.						92	81	84					11																	66636384		2200	4295	6495	SO:0001583	missense	5091	exon9			AGTGCTTGCCGTG	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.955A>G	chr11.hg19:g.66636384T>C	ENSP00000377530:p.Lys319Glu	336.0	1.0	.		190.0	65.0	.	NM_000920	B4DN00|Q16705	Missense_Mutation	SNP	ENST00000393958.2	hg19	CCDS8152.1	.	.	.	.	.	.	.	.	.	.	T	13.76	2.333430	0.41297	.	.	ENSG00000173599	ENST00000393955;ENST00000393958;ENST00000393960;ENST00000524491;ENST00000355677	D;D;D;D;D	0.97256	-4.31;-4.31;-4.31;-4.31;-4.31	4.65	4.65	0.58169	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);Biotin carboxylation domain (1);	0.063886	0.64402	D	0.000015	D	0.91643	0.7359	N	0.13352	0.335	0.43226	D	0.995117	B	0.09022	0.002	B	0.21360	0.034	D	0.87584	0.2486	10	0.13108	T	0.6	-19.2405	12.029	0.53388	0.0:0.0:0.0:1.0	.	319	P11498	PYC_HUMAN	E	319;319;319;279;319	ENSP00000377527:K319E;ENSP00000377530:K319E;ENSP00000377532:K319E;ENSP00000434192:K279E;ENSP00000347900:K319E	ENSP00000347900:K319E	K	-	1	0	PC	66392960	0.994000	0.37717	1.000000	0.80357	0.938000	0.57974	1.707000	0.37888	1.730000	0.51580	0.459000	0.35465	AAG	.	.	.	none		0.687	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716		C	66636384	T	C	66636384	3	2	82	1	0	0	0	0	1	0	0	0	11504	1821	63	3	2637	3	PC	11	66636384	Missense_Mutation	SNP	T	TCGA-B1-A47N-01A-11D-A25F-10	4340319	66636384	68370132	21	5311											
MAML2	84441	hgsc.bcm.edu	37	chr11	95825248	95825248	+	Silent	SNP	C	C	T																															tgctgttgttgttgctgctgCtgctgctgttgttgctgctg																										TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr11:95825248C>T	ENST00000524717.1	-	2	3231	c.1947G>A	c.(1945-1947)caG>caA	p.Q649Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	649					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)				gttgctgctgctgctgctgtt	0.517			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.Q649Q		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2	94	.	0			c.G1947A						PASS	.						33	39	37					11																	95825248		2115	4166	6281	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.1947G>A	chr11.hg19:g.95825248C>T		80.0	0.0	.		139.0	25.0	.	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	hg19	CCDS44714.1																																																																																			.	.	.	none		0.517	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95825248	C	T	95825248	2	4	82	1	0	0	0	0	0	0	0	1	9213	796	28	2		2	MAML2	11	95825248	Silent	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10	29188864	95825248	39181268	22	5312	59	2									
MAML2	84441	hgsc.bcm.edu	37	chr11	95825254	95825254	+	Silent	SNP	C	C	T																															tgttgttgctgctgctgctgCtgttgttgctgctgctgctg																								rs61749250		TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr11:95825254C>T	ENST00000524717.1	-	2	3225	c.1941G>A	c.(1939-1941)caG>caA	p.Q647Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	647					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.Q647Q(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)				gctgctgctgctgttgttgct	0.512			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.Q647Q		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	MAML2,caecum,carcinoma,0,2	MAML2	94	.	1	Substitution - coding silent(1)	endometrium(1)	c.G1941A						PASS	.	C		0,4198		0,0,2099	35	40	38		1941	1.7	0.1	11	dbSNP_129	38	5,8237		0,5,4116	no	coding-synonymous	MAML2	NM_032427.1		0,5,6215	TT,TC,CC		0.0607,0.0,0.0402		647/1157	95825254	5,12435	2099	4121	6220	SO:0001819	synonymous_variant	84441	exon2			CTGCTGCTGTTGT	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.1941G>A	chr11.hg19:g.95825254C>T		75.0	1.0	.		140.0	28.0	.	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	hg19	CCDS44714.1																																																																																			.	.	.	weak		0.512	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95825254	C	T	95825254	2	4	82	1	0	0	0	0	0	0	0	1	9213	796	28	2		2	MAML2	11	95825254	Silent	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10	6	95825254	39181262	23	5313	59	2									
SLC6A12	6539	hgsc.bcm.edu	37	chr12	306024	306024	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatagtcacagccttggggAaggcgatgaaggccagccca	11	6	13	11	1	2	1	2	1	0	0	2	3	2	2	3	4	2	0	3	4	3	2			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr12:306024A>G	ENST00000428720.1	-	11	1843	c.1100T>C	c.(1099-1101)tTc>tCc	p.F367S	SLC6A12_ENST00000538272.1_5'Flank|RP11-283I3.1_ENST00000544067.1_RNA|SLC6A12_ENST00000536824.1_Missense_Mutation_p.F367S|SLC6A12_ENST00000424061.2_Missense_Mutation_p.F367S|SLC6A12_ENST00000359674.4_Missense_Mutation_p.F367S|SLC6A12_ENST00000397296.2_Missense_Mutation_p.F367S	NM_001122848.2	NP_001116320.1	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 12	367					amino acid transport (GO:0006865)|cellular hyperosmotic response (GO:0071474)|cellular water homeostasis (GO:0009992)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|response to organic substance (GO:0010033)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)			AGCCTTGGGGAAGGCGATGAA	0.587																																					p.F367S		Atlas-SNP	.											.	SLC6A12	60	.	0			c.T1100C						PASS	.						107	96	100					12																	306024		2203	4300	6503	SO:0001583	missense	6539	exon11			TTGGGGAAGGCGA	L42300	CCDS8501.1	12p13	2013-07-19	2013-07-19		ENSG00000111181	ENSG00000111181		"Solute carriers"	11045	protein-coding gene	gene with protein product	"betaine/GABA transporter-1"	603080	"solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12"			7589472	Standard	NM_003044		Approved	BGT-1	uc009zdh.2	P48065	OTTHUMG00000090309	ENST00000428720.1:c.1100T>C	chr12.hg19:g.306024A>G	ENSP00000388184:p.Phe367Ser	116.0	0.0	.		85.0	24.0	.	NM_001122848	A0AV52|B2R992|D3DUN8	Missense_Mutation	SNP	ENST00000428720.1	hg19	CCDS8501.1	.	.	.	.	.	.	.	.	.	.	A	19.19	3.780522	0.70222	.	.	ENSG00000111181	ENST00000359674;ENST00000397296;ENST00000428720;ENST00000424061;ENST00000536824	T;T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24;-1.24	4.26	4.26	0.50523	.	0.067703	0.64402	D	0.000013	D	0.86644	0.5982	M	0.85777	2.775	0.44261	D	0.997113	D	0.58268	0.982	D	0.70935	0.971	D	0.87360	0.2343	10	0.87932	D	0	.	7.5395	0.27729	0.6532:0.0:0.0:0.3468	.	367	P48065	S6A12_HUMAN	S	367	ENSP00000352702:F367S;ENSP00000380464:F367S;ENSP00000388184:F367S;ENSP00000399136:F367S;ENSP00000444268:F367S	ENSP00000352702:F367S	F	-	2	0	SLC6A12	176285	1.000000	0.71417	0.987000	0.45799	0.802000	0.45316	6.483000	0.73617	1.782000	0.52362	0.391000	0.25812	TTC	.	.	.	none		0.587	SLC6A12-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206671.2	NM_003044		G	306024	A	G	306024	3	3	82	1	0	0	0	0	1	0	0	0	14688	246	9	3	768	3	SLC6A12	12	306024	Missense_Mutation	SNP	A	TCGA-B1-A47N-01A-11D-A25F-10		306024	133545871	24	5314											
GALNT9	50614	hgsc.bcm.edu	37	chr12	132834320	132834320	+	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	cagttgtagccatgggcggcGttcgcatactgctgcacctc	6	10	12	13	3	0	0	0	0	0	0	2	0	0	0	2	2	4	6	2	2	2	4	rs554022886		TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr12:132834320G>A	ENST00000328957.8	-	5	866	c.867C>T	c.(865-867)aaC>aaT	p.N289N	GALNT9_ENST00000535208.1_5'Flank|GALNT9_ENST00000535228.1_5'Flank	NM_001122636.1	NP_001116108.1	Q9HCQ5	GALT9_HUMAN	polypeptide N-acetylgalactosaminyltransferase 9	289					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)		CATGGGCGGCGTTCGCATACT	0.632													g|||	1	0.000199681	8e-04	0	5008	,	,		12187	0		0	False		,,,				2504	0				p.N289N	Colon(186;2147 2752 13553 41466)	Atlas-SNP	.											.	GALNT9	74	.	0			c.C867T						PASS	.						27	32	30					12																	132834320		692	1591	2283	SO:0001819	synonymous_variant	50614	exon5			GGCGGCGTTCGCA	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.867C>T	chr12.hg19:g.132834320G>A		95.0	0.0	.		72.0	18.0	.	NM_001122636	Q52LR8|Q6NT54|Q8NFR1	Silent	SNP	ENST00000328957.8	hg19																																																																																				.	.	.	none		0.632	GALNT9-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000402967.1	NM_001122636		A	132834320	G	A	132834320	2	1	82	1	0	0	0	0	0	0	0	1	6227	1136	40	1		1	GALNT9	12	132834320	Silent	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	132528296	132834320	1017575	25	5315											
GPR12	2835	hgsc.bcm.edu	37	chr13	27332981	27332981	+	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	tacacatcactgggcgagcgCgctctctgggcgagactgga	8	7	14	12	4	2	1	1	0	1	1	3	4	2	2	0	3	2	1	0	3	1	1			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr13:27332981C>T	ENST00000381436.2	-	1	1446	c.984G>A	c.(982-984)gcG>gcA	p.A328A	GPR12_ENST00000405846.3_Silent_p.A328A			P47775	GPR12_HUMAN	G protein-coupled receptor 12	328					cellular calcium ion homeostasis (GO:0006874)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|phosphatidylcholine binding (GO:0031210)			endometrium(7)|kidney(2)|large_intestine(6)|lung(14)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33	Colorectal(5;5.77e-05)	Breast(139;0.198)		Epithelial(112;9.37e-07)|OV - Ovarian serous cystadenocarcinoma(117;1.16e-06)|all cancers(112;8.31e-06)|GBM - Glioblastoma multiforme(144;0.00121)|Lung(94;0.111)|LUSC - Lung squamous cell carcinoma(192;0.184)		TGGGCGAGCGCGCTCTCTGGG	0.537																																					p.A328A		Atlas-SNP	.											.	GPR12	67	.	0			c.G984A						PASS	.						65	67	66					13																	27332981		2203	4300	6503	SO:0001819	synonymous_variant	2835	exon2			CGAGCGCGCTCTC	U18548	CCDS9319.1	13q12	2014-06-12			ENSG00000132975	ENSG00000132975		"GPCR / Class A : Orphans"	4466	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 84"	600752				8262253, 8530049	Standard	NM_005288		Approved	GPCR21, PPP1R84	uc010aal.3	P47775	OTTHUMG00000016620	ENST00000381436.2:c.984G>A	chr13.hg19:g.27332981C>T		155.0	0.0	.		127.0	56.0	.	NM_005288	Q5T8P3	Silent	SNP	ENST00000381436.2	hg19	CCDS9319.1																																																																																			.	.	.	none		0.537	GPR12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044257.2			T	27332981	C	T	27332981	2	4	82	1	0	0	0	0	0	0	0	1	6642	755	27	1		1	GPR12	13	27332981	Silent	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10		27332981	87836897	26	5316											
FRY	10129	hgsc.bcm.edu	37	chr13	32823745	32823745	+	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	cagggccatggccgtcacccGgagcacatcttccacttcct	7	8	9	17	2	2	0	1	0	1	0	4	1	4	1	5	3	1	1	5	3	0	2	rs372186855		TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr13:32823745G>T	ENST00000380250.3	+	49	7587	c.7091G>T	c.(7090-7092)cGg>cTg	p.R2364L		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	2364						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)		GCCGTCACCCGGAGCACATCT	0.542																																					p.R2364L		Atlas-SNP	.											.	FRY	312	.	0			c.G7091T						PASS	.						73	76	75					13																	32823745		2015	4173	6188	SO:0001583	missense	10129	exon49			TCACCCGGAGCAC	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.7091G>T	chr13.hg19:g.32823745G>T	ENSP00000369600:p.Arg2364Leu	67.0	0.0	.		77.0	4.0	.	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	hg19	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	G	35	5.453660	0.96223	.	.	ENSG00000073910	ENST00000380250;ENST00000380257;ENST00000380235	T	0.25085	1.82	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.32823	0.0842	L	0.54323	1.7	0.80722	D	1	P	0.46784	0.884	B	0.42214	0.38	T	0.02821	-1.1106	10	0.54805	T	0.06	.	20.6634	0.99662	0.0:0.0:1.0:0.0	.	2364	Q5TBA9	FRY_HUMAN	L	2364;1174;5	ENSP00000369600:R2364L	ENSP00000369567:R5L	R	+	2	0	FRY	31721745	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.894000	0.99253	0.655000	0.94253	CGG	.	.	.	alt		0.542	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		T	32823745	G	T	32823745	3	4	82	1	0	0	0	0	1	0	0	0	6070	1116	39	4	7285	4	FRY	13	32823745	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	5490764	32823745	82346133	27	5317											
PRPF39	55015	hgsc.bcm.edu	37	chr14	45564665	45564665	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgacgctgacagaaacagaaGcaaatttccctccagaatat	16	8	7	10	1	0	5	0	2	0	3	2	5	2	5	2	0	2	2	2	0	5	2			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr14:45564665G>A	ENST00000355765.6	+	2	393	c.223G>A	c.(223-225)Gca>Aca	p.A75T		NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	75					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						AGAAACAGAAGCAAATTTCCC	0.403																																					p.A75T		Atlas-SNP	.											.	PRPF39	46	.	0			c.G223A						PASS	.						46	47	46					14																	45564665		2031	4212	6243	SO:0001583	missense	55015	exon2			ACAGAAGCAAATT	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.223G>A	chr14.hg19:g.45564665G>A	ENSP00000348010:p.Ala75Thr	52.0	0.0	.		55.0	23.0	.	NM_017922	Q08AL1|Q08AL2|Q9NUU5	Missense_Mutation	SNP	ENST00000355765.6	hg19	CCDS9682.2	.	.	.	.	.	.	.	.	.	.	G	12.40	1.927796	0.34002	.	.	ENSG00000185246	ENST00000355765;ENST00000553605	T	0.46819	0.86	5.72	4.83	0.62350	.	.	.	.	.	T	0.32675	0.0837	N	0.20986	0.625	0.26211	N	0.979309	B	0.19817	0.039	B	0.23018	0.043	T	0.20538	-1.0272	9	0.15499	T	0.54	-21.2955	10.525	0.44943	0.1491:0.0:0.8509:0.0	.	75	Q86UA1	PRP39_HUMAN	T	75	ENSP00000348010:A75T	ENSP00000348010:A75T	A	+	1	0	PRPF39	44634415	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.367000	0.52350	1.429000	0.47314	0.591000	0.81541	GCA	.	.	.	none		0.403	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319683.2			A	45564665	G	A	45564665	3	1	82	1	0	0	0	0	1	0	0	0	12579	971	34	2	225	2	PRPF39	14	45564665	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10		45564665	61784875	28	5318											
SIN3A	25942	hgsc.bcm.edu	37	chr15	75673957	75673957	+	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	gatgtacttgctcatacctcTgcttccacagggtcatccga	8	12	8	13	1	3	0	2	0	1	0	5	2	5	0	3	1	4	3	3	1	2	4			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr15:75673957T>A	ENST00000394947.3	-	18	3599	c.3285A>T	c.(3283-3285)gcA>gcT	p.A1095A	SIN3A_ENST00000360439.4_Silent_p.A1095A|SIN3A_ENST00000394949.4_Silent_p.A1095A	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						CTCATACCTCTGCTTCCACAG	0.527																																					p.A1095A		Atlas-SNP	.											.	SIN3A	152	.	0			c.A3285T						PASS	.						227	191	203					15																	75673957		2197	4294	6491	SO:0001819	synonymous_variant	25942	exon18			TACCTCTGCTTCC	AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"SIN3 homolog A, transcription regulator (yeast)", "SIN3 transcription regulator homolog A (yeast)"			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.3285A>T	chr15.hg19:g.75673957T>A		152.0	0.0	.		170.0	77.0	.	NM_001145358		Silent	SNP	ENST00000394947.3	hg19	CCDS10279.1																																																																																			.	.	.	none		0.527	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477		A	75673957	T	A	75673957	2	1	82	1	0	0	0	0	0	0	0	1	14338	1567	55	5		5	SIN3A	15	75673957	Silent	SNP	T	TCGA-B1-A47N-01A-11D-A25F-10		75673957	26857435	29	5319			1	13		2	2	26	T		2.987995e-05
SIN3A	25942	hgsc.bcm.edu	37	chr15	75673982	75673982	+	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	ccacagggtcatccgaattcTcctcttctgtgtccagaagc	8	11	8	14	1	4	1	1	0	3	1	7	2	6	1	4	1	1	0	4	1	2	2			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr15:75673982T>A	ENST00000394947.3	-	18	3574	c.3260A>T	c.(3259-3261)gAg>gTg	p.E1087V	SIN3A_ENST00000360439.4_Missense_Mutation_p.E1087V|SIN3A_ENST00000394949.4_Missense_Mutation_p.E1087V	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						ATCCGAATTCTCCTCTTCTGT	0.502																																					p.E1087V		Atlas-SNP	.											.	SIN3A	152	.	0			c.A3260T						PASS	.						219	188	199					15																	75673982		2197	4294	6491	SO:0001583	missense	25942	exon18			GAATTCTCCTCTT	AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"SIN3 homolog A, transcription regulator (yeast)", "SIN3 transcription regulator homolog A (yeast)"			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.3260A>T	chr15.hg19:g.75673982T>A	ENSP00000378402:p.Glu1087Val	169.0	0.0	.		173.0	75.0	.	NM_001145358		Missense_Mutation	SNP	ENST00000394947.3	hg19	CCDS10279.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.186474	0.78789	.	.	ENSG00000169375	ENST00000394947;ENST00000394949;ENST00000360439	T;T;T	0.47528	0.84;0.84;0.84	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.47248	0.1435	L	0.61387	1.9	0.80722	D	1	B	0.28998	0.23	B	0.30716	0.119	T	0.41215	-0.9521	10	0.30078	T	0.28	-25.6466	14.6847	0.69042	0.0:0.0:0.0:1.0	.	1087	Q96ST3	SIN3A_HUMAN	V	1087	ENSP00000378402:E1087V;ENSP00000378403:E1087V;ENSP00000353622:E1087V	ENSP00000353622:E1087V	E	-	2	0	SIN3A	73461035	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.939000	0.87685	2.073000	0.62155	0.402000	0.26972	GAG	.	.	.	none		0.502	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477		A	75673982	T	A	75673982	3	1	82	1	0	0	0	0	1	0	0	0	14338	1551	54	5	577	5	SIN3A	15	75673982	Missense_Mutation	SNP	T	TCGA-B1-A47N-01A-11D-A25F-10	25	75673982	26857410	30	5320			1	13		2	2	26	T		2.987995e-05
FA2H	79152	hgsc.bcm.edu	37	chr16	74750468	74750468	+	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	agggaggctggcacagggggGaagaccaggcgggagccgtc	9	2	21	9	2	0	1	0	0	0	1	1	4	0	4	2	8	1	2	2	8	1	0			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr16:74750468G>C	ENST00000219368.3	-	6	885	c.816C>G	c.(814-816)ttC>ttG	p.F272L	FA2H_ENST00000544337.1_Missense_Mutation_p.F59L	NM_024306.4	NP_077282.3	Q7L5A8	FA2H_HUMAN	fatty acid 2-hydroxylase	272					cell death (GO:0008219)|central nervous system myelin maintenance (GO:0032286)|fatty acid biosynthetic process (GO:0006633)|lipid modification (GO:0030258)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of cell proliferation (GO:0042127)|regulation of hair cycle (GO:0042634)|sebaceous gland cell differentiation (GO:0001949)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	fatty acid alpha-hydroxylase activity (GO:0080132)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			endometrium(2)|large_intestine(4)|lung(3)|skin(1)	10						GCACAGGGGGGAAGACCAGGC	0.677																																					p.F272L		Atlas-SNP	.											.	FA2H	21	.	0			c.C816G						PASS	.						16	15	15					16																	74750468		2194	4297	6491	SO:0001583	missense	79152	exon6			AGGGGGGAAGACC	BC002679	CCDS10911.1	16q23	2013-03-04	2003-10-29	2003-10-31	ENSG00000103089	ENSG00000103089		"Fatty acid hydroxylase domain containing"	21197	protein-coding gene	gene with protein product	"fatty acid hydroxylase"	611026	"fatty acid hydroxylase domain containing 1", "spastic paraplegia 35 (autosomal recessive)"	FAXDC1, SPG35		20104589	Standard	NM_024306		Approved	FAAH, FLJ25287	uc002fde.2	Q7L5A8	OTTHUMG00000137603	ENST00000219368.3:c.816C>G	chr16.hg19:g.74750468G>C	ENSP00000219368:p.Phe272Leu	34.0	0.0	.		39.0	16.0	.	NM_024306	B7Z8T6|O75213|Q96DK1|Q9H1A5	Missense_Mutation	SNP	ENST00000219368.3	hg19	CCDS10911.1	.	.	.	.	.	.	.	.	.	.	g	23.5	4.426263	0.83667	.	.	ENSG00000103089	ENST00000219368;ENST00000544337	D;D	0.83506	-1.73;-1.73	5.07	3.07	0.35406	Fatty acid hydroxylase (1);	0.000000	0.85682	D	0.000000	D	0.89203	0.6648	M	0.75264	2.295	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.87214	0.2249	10	0.40728	T	0.16	0.1308	11.6853	0.51483	0.1462:0.0:0.8538:0.0	.	272;180	Q7L5A8;B2RDE6	FA2H_HUMAN;.	L	272;59	ENSP00000219368:F272L;ENSP00000442334:F59L	ENSP00000219368:F272L	F	-	3	2	FA2H	73307969	1.000000	0.71417	0.997000	0.53966	0.948000	0.59901	2.233000	0.43027	0.524000	0.28502	0.651000	0.88453	TTC	.	.	.	none		0.677	FA2H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269015.2	NM_024306		C	74750468	G	C	74750468	3	2	82	1	0	0	0	0	1	0	0	0	5356	1165	41	4	310	4	FA2H	16	74750468	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10		74750468	15604285	31	5321											
WDR81	124997	hgsc.bcm.edu	37	chr17	1630052	1630052	+	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	tggggctcctgcccttgcccCcgagcctcccctcatcccca	3	8	8	22	1	1	0	1	0	0	0	4	1	4	0	9	2	3	1	9	2	0	1			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr17:1630052C>T	ENST00000409644.1	+	1	1799	c.1799C>T	c.(1798-1800)cCc>cTc	p.P600L	WDR81_ENST00000446363.1_Intron|WDR81_ENST00000309182.5_Intron|WDR81_ENST00000419248.1_Intron|WDR81_ENST00000437219.2_Intron|RP11-961A15.1_ENST00000576540.1_RNA	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	600	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.				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)		GCCCTTGCCCCCGAGCCTCCC	0.657																																					p.P600L		Atlas-SNP	.											.	WDR81	180	.	0			c.C1799T						PASS	.						14	18	17					17																	1630052		692	1589	2281	SO:0001583	missense	124997	exon1			TTGCCCCCGAGCC	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.1799C>T	chr17.hg19:g.1630052C>T	ENSP00000386609:p.Pro600Leu	19.0	0.0	.		35.0	20.0	.	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Missense_Mutation	SNP	ENST00000409644.1	hg19	CCDS54062.1	.	.	.	.	.	.	.	.	.	.	C	5.306	0.241738	0.10077	.	.	ENSG00000167716	ENST00000409644	T	0.51574	0.7	5.43	5.43	0.79202	.	.	.	.	.	T	0.39545	0.1082	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.12528	-1.0544	6	0.09590	T	0.72	.	12.5648	0.56304	0.0:0.9236:0.0:0.0764	.	.	.	.	L	600	ENSP00000386609:P600L	ENSP00000386609:P600L	P	+	2	0	WDR81	1576802	0.524000	0.26282	0.970000	0.41538	0.006000	0.05464	4.407000	0.59754	2.546000	0.85860	0.462000	0.41574	CCC	.	.	.	none		0.657	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348		T	1630052	C	T	1630052	3	4	82	1	0	0	0	0	1	0	0	0	17342	623	22	2	1863	2	WDR81	17	1630052	Missense_Mutation	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10		1630052	79565158	32	5322											
MYBBP1A	10514	hgsc.bcm.edu	37	chr17	4445767	4445767	+	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	gaagtctctcacctgatgacGgggccgcaccgggcccgtga	7	6	14	14	4	2	3	1	3	1	0	3	4	2	3	4	3	0	1	4	3	1	0	rs200492249	byFrequency	TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr17:4445767G>T	ENST00000254718.4	-	22	3385	c.3079C>A	c.(3079-3081)Cgt>Agt	p.R1027S	MYBBP1A_ENST00000381556.2_Missense_Mutation_p.R1027S			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	1027					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						ACCTGATGACGGGGCCGCACC	0.627																																					p.R1027S		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.C3079A						PASS	.						69	80	76					17																	4445767		2203	4300	6503	SO:0001583	missense	10514	exon22			GATGACGGGGCCG	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.3079C>A	chr17.hg19:g.4445767G>T	ENSP00000254718:p.Arg1027Ser	116.0	0.0	.		149.0	48.0	.	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Missense_Mutation	SNP	ENST00000254718.4	hg19	CCDS11046.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.195223	0.38806	.	.	ENSG00000132382	ENST00000381556;ENST00000254718	T;T	0.67698	-0.28;-0.28	5.3	4.12	0.48240	Armadillo-type fold (1);	0.258408	0.43579	D	0.000546	T	0.68568	0.3015	M	0.65975	2.015	0.30663	N	0.754172	P;P	0.48407	0.854;0.91	B;P	0.49683	0.414;0.619	T	0.69591	-0.5104	10	0.38643	T	0.18	-19.6389	9.7224	0.40311	0.1107:0.0:0.8893:0.0	.	1027;1027	Q9BQG0;Q9BQG0-2	MBB1A_HUMAN;.	S	1027	ENSP00000370968:R1027S;ENSP00000254718:R1027S	ENSP00000254718:R1027S	R	-	1	0	MYBBP1A	4392516	1.000000	0.71417	0.995000	0.50966	0.009000	0.06853	2.897000	0.48664	2.473000	0.83533	0.561000	0.74099	CGT	.	G|0.999;A|0.001	.	alt		0.627	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520		T	4445767	G	T	4445767	3	4	82	1	0	0	0	0	1	0	0	0	10015	1116	39	4	967	4	MYBBP1A	17	4445767	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	2815715	4445767	76749443	33	5323											
TAF15	8148	hgsc.bcm.edu	37	chr17	34171711	34171755	+	In_Frame_Del	DEL	GGCTATGGAGGAGACCGAGGAGGTGGCTATGGAGGAGATCGAGGT	GGCTATGGAGGAGACCGAGGAGGTGGCTATGGAGGAGATCGAGGT	-																															atggtggggacagaggaggcGgctatggaggagaccgagga																								rs543739946|rs569473616|rs144910879|rs187380389|rs368600342|rs577544142|rs144917137|rs181978759	byFrequency	TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	GGCTATGGAGGAGACCGAGGAGGTGGCTATGGAGGAGATCGAGGT	GGCTATGGAGGAGACCGAGGAGGTGGCTATGGAGGAGATCGAGGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr17:34171711_34171755delGGCTATGGAGGAGACCGAGGAGGTGGCTATGGAGGAGATCGAGGT	ENST00000588240.1	+	15	1523_1567	c.1408_1452delGGCTATGGAGGAGACCGAGGAGGTGGCTATGGAGGAGATCGAGGT	c.(1408-1452)ggctatggaggagaccgaggaggtggctatggaggagatcgaggtdel	p.GYGGDRGGGYGGDRG485del	TAF15_ENST00000311979.3_In_Frame_Del_p.GYGGDRGGGYGGDRG482del|TAF15_ENST00000592237.1_Intron	NM_003487.3|NM_139215.2	NP_003478.1|NP_631961.1	Q16514	TAF12_HUMAN	TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa	0					chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of RNA biosynthetic process (GO:2001141)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)		TAF15/NR4A3(33)	lung(1)|ovary(1)|skin(2)|stomach(1)	5		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		cagaggaggcggctatggaggagaccgaggaggtggctatggaggagatcgaggtggctatggag	0.612			T	"TEC, CHN1, ZNF384"	"extraskeletal myxoid chondrosarcomas, ALL"																																p.469_484del		Pindel	.		Dom	yes		17	17q11.1-q11.2	8148	"TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa"		"L, M"	.	TAF15	46	.	0			c.1407_1451del						PASS	.		,	40,224,3996		2,0,36,14,196,1882					,	-3.9	0.1			9	54,332,7866		1,0,52,25,282,3766	no	codingComplex,codingComplex	TAF15	NM_139215.1,NM_003487.2	,	3,0,88,39,478,5648	A1A1,A1A2,A1R,A2A2,A2R,RR		4.6777,6.1972,5.195	,	,		94,556,11862				SO:0001651	inframe_deletion	8148	exon15			.	U51334	CCDS32623.1, CCDS59279.1	17q11.1-q11.2	2013-02-12	2002-08-29	2001-12-07		ENSG00000270647		"RNA binding motif (RRM) containing"	11547	protein-coding gene	gene with protein product		601574	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, N, 68kD (RNA-binding protein 56)"	TAF2N		8954779, 9795213	Standard	NM_003487		Approved	hTAFII68, RBP56, Npl3	uc002hkd.4	Q92804		ENST00000588240.1:c.1408_1452delGGCTATGGAGGAGACCGAGGAGGTGGCTATGGAGGAGATCGAGGT	chr17.hg19:g.34171711_34171755delGGCTATGGAGGAGACCGAGGAGGTGGCTATGGAGGAGATCGAGGT	ENSP00000466950:p.Gly485_Gly499del	53.0	0.0	.		68.0	10.0	0.147	NM_139215	D3DPM5|Q15775|Q5T077	In_Frame_Del	DEL	ENST00000588240.1	hg19	CCDS32623.1																																																																																			.	.	.	none		0.612	TAF15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449134.1	NM_139215		-	34171755	GGCTATGGAGGAGACCGAGGAGGTGGCTATGGAGGAGATCGAGGT	-	34171711	7	5	82	1	0	1	0	1	0	0	0	0	15530	1116	39	0	1466	0	TAF15	17	34171711	In_Frame_Del	DEL	GGCTATGGAGGAGACCGAGGAGGTGGCTATGGAGGAGATCGAGGT	TCGA-B1-A47N-01A-11D-A25F-10	29725944	34171711	47023499	34	5324											
PPM1E	22843	hgsc.bcm.edu	37	chr17	56833457	56833457	+	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	ggcggcggcgagccggagccGgaacccgaacccgaacccga	9	0	16	16	8	0	0	0	0	0	0	0	6	0	2	5	5	5	0	5	5	3	0	rs3834568|rs201186780|rs74256772	byFrequency	TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	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	.	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	chr17.hg19:g.56833457G>C		44.0	0.0	.		34.0	3.0	.	NM_014906	Q8N8J9|Q96DB8	Silent	SNP	ENST00000308249.2	hg19	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	82	1	0	0	0	0	0	0	0	1	12348	1103	39	4		4	PPM1E	17	56833457	Silent	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	22661746	56833457	24361753	35	5325											
SIN3B	23309	hgsc.bcm.edu	37	chr19	16977317	16977317	+	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	tcaagcagaacgacaccaagGccctgcgctccaagagcttg	12	5	10	14	2	1	2	1	0	0	2	2	3	2	2	3	1	4	3	3	1	4	1			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr19:16977317G>T	ENST00000248054.5	+	12	1777	c.1756G>T	c.(1756-1758)Gcc>Tcc	p.A586S	SIN3B_ENST00000595541.1_Missense_Mutation_p.A176S|SIN3B_ENST00000379803.1_Missense_Mutation_p.A618S					SIN3 transcription regulator family member B											endometrium(4)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26						CGACACCAAGGCCCTGCGCTC	0.602																																					p.A618S		Atlas-SNP	.											.	SIN3B	90	.	0			c.G1852T						PASS	.						147	105	119					19																	16977317		2203	4300	6503	SO:0001583	missense	23309	exon13			ACCAAGGCCCTGC	AB014600	CCDS32946.1, CCDS74308.1	19p13.12	2013-08-21	2013-08-21						19354	protein-coding gene	gene with protein product		607777	"SIN3 homolog B, transcription regulator (yeast)", "SIN3 transcription regulator homolog B (yeast)"			9734811	Standard	XM_005259832		Approved	KIAA0700	uc002ney.2	O75182		ENST00000248054.5:c.1756G>T	chr19.hg19:g.16977317G>T	ENSP00000248054:p.Ala586Ser	164.0	0.0	.		116.0	5.0	.	NM_015260		Missense_Mutation	SNP	ENST00000248054.5	hg19		.	.	.	.	.	.	.	.	.	.	G	32	5.177469	0.94846	.	.	ENSG00000127511	ENST00000379803;ENST00000248054	T;T	0.49720	0.81;0.77	4.96	4.96	0.65561	.	0.107077	0.64402	D	0.000006	T	0.49592	0.1566	L	0.49778	1.585	0.80722	D	1	P;P;P	0.49862	0.929;0.851;0.781	P;P;P	0.47102	0.537;0.525;0.459	T	0.41378	-0.9512	10	0.20046	T	0.44	-4.1143	18.1922	0.89810	0.0:0.0:1.0:0.0	.	176;586;618	B7Z392;O75182-2;O75182	.;.;SIN3B_HUMAN	S	618;586	ENSP00000369131:A618S;ENSP00000248054:A586S	ENSP00000248054:A586S	A	+	1	0	SIN3B	16838317	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.611000	0.98342	2.282000	0.76494	0.491000	0.48974	GCC	.	.	.	none		0.602	SIN3B-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000462846.1	NM_015260		T	16977317	G	T	16977317	3	4	82	1	0	0	0	0	1	0	0	0	14339	1203	42	4	1902	4	SIN3B	19	16977317	Missense_Mutation	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10		16977317	42151666	36	5326											
ZNF880	400713	hgsc.bcm.edu	37	chr19	52877551	52877551	+	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	attctttctttttttaaataGgaatctgtcttcctgacctg	8	20	5	8	0	4	1	0	1	4	0	5	2	5	2	2	1	0	0	2	1	4	8			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chr19:52877551G>A	ENST00000422689.2	+	3	154		c.e3-1		ZNF880_ENST00000597976.1_Splice_Site|ZNF880_ENST00000344085.5_Splice_Site|ZNF880_ENST00000600321.1_Splice_Site|ZNF880_ENST00000424032.2_Splice_Site	NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880						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						TTTTTAAATAGGAATCTGTCT	0.403																																					.		Atlas-SNP	.											.	ZNF880	45	.	0			c.140-1G>A						PASS	.						52	43	46					19																	52877551		692	1591	2283	SO:0001630	splice_region_variant	400713	exon3			TAAATAGGAATCT	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.140-1G>A	chr19.hg19:g.52877551G>A		58.0	0.0	.		78.0	11.0	.	NM_001145434	B4DNA6	Splice_Site	SNP	ENST00000422689.2	hg19	CCDS46164.1	.	.	.	.	.	.	.	.	.	.	g	4.728	0.135350	0.09032	.	.	ENSG00000221923	ENST00000424032;ENST00000344085;ENST00000422689	.	.	.	1.13	1.13	0.20643	.	.	.	.	.	.	.	.	.	.	.	0.23483	N	0.997585	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.6302	0.17506	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ZNF880	57569363	0.003000	0.15002	0.027000	0.17364	0.231000	0.25187	0.510000	0.22723	0.920000	0.36970	0.448000	0.29417	.	.	.	.	none		0.403	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	Intron	A	52877551	G	A	52877551	5	1	82	1	0	0	0	0	0	0	1	0	18209	1014	35	2	149	2	ZNF880	19	52877551	Splice_Site	SNP	G	TCGA-B1-A47N-01A-11D-A25F-10	35900234	52877551	6251432	37	5327											
TSPYL2	64061	hgsc.bcm.edu	37	chrX	53114044	53114044	+	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	aaggagttccagcgcaaccgCtcaggtaagtggcagtacca	12	6	12	11	2	1	0	1	0	0	0	2	1	2	1	3	3	3	6	3	3	4	3			TCGA-B1-A47N-01A-11D-A25F-10	TCGA-B1-A47N-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bd2cc59d-f5ce-46ed-beb0-4c80b24cbe71	2041c373-06a2-4ba8-b9f8-3c11c313e0db	g.chrX:53114044C>A	ENST00000375442.4	+	3	1125	c.993C>A	c.(991-993)cgC>cgA	p.R331R		NM_022117.3	NP_071400.1	Q9H2G4	TSYL2_HUMAN	TSPY-like 2	331					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						AGCGCAACCGCTCAGGTAAGT	0.498																																					p.R331R		Atlas-SNP	.											.	TSPYL2	53	.	0			c.C993A						PASS	.						105	85	92					X																	53114044		2203	4300	6503	SO:0001819	synonymous_variant	64061	exon3			CAACCGCTCAGGT	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.993C>A	chrX.hg19:g.53114044C>A		75.0	0.0	.		60.0	56.0	.	NM_022117	O94799|Q96DG7|Q9BZW6	Silent	SNP	ENST00000375442.4	hg19	CCDS14350.1																																																																																			.	.	.	none		0.498	TSPYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056718.1	NM_022117		A	53114044	C	A	53114044	2	1	82	1	0	0	0	0	0	0	0	1	16672	784	28	4		4	TSPYL2	23	53114044	Silent	SNP	C	TCGA-B1-A47N-01A-11D-A25F-10		53114044	102156516	38	5328											
EPHA8	2046	hgsc.bcm.edu	37	chr1	22902757	22902757	+	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	tccttccagcccatccacacGtaccaggtttgcaacgtcat	9	10	6	16	2	1	0	1	0	0	0	4	0	4	0	5	1	4	3	5	1	2	3			TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr1:22902757G>A	ENST00000166244.3	+	3	279	c.207G>A	c.(205-207)acG>acA	p.T69T	EPHA8_ENST00000538803.1_Silent_p.T69T|EPHA8_ENST00000374644.4_Silent_p.T69T	NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	69	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		CCATCCACACGTACCAGGTTT	0.607																																					p.T69T		Atlas-SNP	.											.	EPHA8	221	.	0			c.G207A						PASS	.						108	103	105					1																	22902757		2203	4300	6503	SO:0001819	synonymous_variant	2046	exon3			CCACACGTACCAG	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.207G>A	chr1.hg19:g.22902757G>A		301.0	0.0	.		234.0	51.0	.	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Silent	SNP	ENST00000166244.3	hg19	CCDS225.1																																																																																			.	.	.	none		0.607	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526		A	22902757	G	A	22902757	2	1	83	1	0	0	0	0	0	0	0	1	5175	1132	40	1		1	EPHA8	1	22902757	Silent	SNP	G	TCGA-B1-A47O-01A-11D-A25F-10		22902757	226347864	1	5329											
ERI3	79033	hgsc.bcm.edu	37	chr1	44778900	44778900	+	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	ggcttgaataatcccggtgaGctgaaaggaaagagaaatag	16	7	13	5	1	0	4	0	3	0	1	1	6	1	5	1	3	1	2	1	3	6	3			TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr1:44778900G>A	ENST00000372257.2	-	5	788	c.607C>T	c.(607-609)Ctc>Ttc	p.L203F	ERI3_ENST00000372259.5_Splice_Site_p.L88F|ERI3_ENST00000495828.1_5'UTR|ERI3_ENST00000537474.1_Splice_Site_p.L26F	NM_024066.1	NP_076971.1	O43414	ERI3_HUMAN	ERI1 exoribonuclease family member 3	203	Exonuclease.						exonuclease activity (GO:0004527)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(2)|lung(7)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						ATCCCGGTGAGCTGAAAGGAA	0.498																																					p.L203F		Atlas-SNP	.											.	ERI3	39	.	0			c.C607T						PASS	.						77	77	77					1																	44778900		2203	4300	6503	SO:0001630	splice_region_variant	79033	exon5			CGGTGAGCTGAAA	AF007157	CCDS30696.1	1p34.1	2009-10-07	2009-10-07	2008-12-16	ENSG00000117419	ENSG00000117419		"Enhanced RNAi three prime mRNA exonucleases"	17276	protein-coding gene	gene with protein product	"enhanced RNAi three prime mRNA exonuclease homolog 3 (C.elegans)", "exoribonuclease 3"	609917	"prion protein interacting protein"	PRNPIP			Standard	XM_005271184		Approved	FLJ22943, PINT1	uc001clt.3	O43414	OTTHUMG00000007637	ENST00000372257.2:c.607-1C>T	chr1.hg19:g.44778900G>A		139.0	0.0	.		113.0	27.0	.	NM_024066	B1AK98|Q5T2T7|Q5T2T9|Q5TG35|Q9BQA0|Q9UEB4	Missense_Mutation	SNP	ENST00000372257.2	hg19	CCDS30696.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.465812	0.84425	.	.	ENSG00000117419	ENST00000372257;ENST00000372259;ENST00000456170;ENST00000537474;ENST00000433471;ENST00000372253;ENST00000452396;ENST00000457571	T;T;T;T;T;T	0.19806	2.12;2.12;2.12;2.12;2.12;2.12	5.43	5.43	0.79202	Exonuclease (1);Exonuclease, RNase T/DNA polymerase III (1);Ribonuclease H-like (1);	0.167282	0.40908	D	0.000988	T	0.54951	0.1890	M	0.86502	2.82	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	0.60900	-0.7171	10	0.87932	D	0	.	19.4202	0.94719	0.0:0.0:1.0:0.0	.	201;125;203	F6UGJ8;B4DN03;O43414	.;.;ERI3_HUMAN	F	203;88;42;26;85;69;85;201	ENSP00000361331:L203F;ENSP00000361333:L88F;ENSP00000390710:L42F;ENSP00000438360:L26F;ENSP00000396764:L85F;ENSP00000412291:L201F	ENSP00000361327:L69F	L	-	1	0	ERI3	44551487	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	5.471000	0.66762	2.825000	0.97269	0.655000	0.94253	CTC	.	.	.	none		0.498	ERI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020243.1	NM_024066	Missense_Mutation	A	44778900	G	A	44778900	5	1	83	1	0	0	0	0	0	0	1	0	5231	985	34	2	426	2	ERI3	1	44778900	Splice_Site	SNP	G	TCGA-B1-A47O-01A-11D-A25F-10	21876143	44778900	204471721	2	5330											
KCNN3	3782	hgsc.bcm.edu	37	chr1	154680665	154680665	+	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	gcggtgagatgctccagcttCgactccaggctgccaatctg	7	9	12	13	2	1	1	0	1	1	1	4	3	3	1	3	2	3	3	3	2	1	1			TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr1:154680665C>T	ENST00000271915.4	-	8	2298	c.1983G>A	c.(1981-1983)tcG>tcA	p.S661S	KCNN3_ENST00000358505.2_Silent_p.S348S|KCNN3_ENST00000361147.4_Silent_p.S356S|KCNN3_ENST00000515643.1_5'UTR	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	666					potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	GCTCCAGCTTCGACTCCAGGC	0.567																																					p.S676S		Atlas-SNP	.											KCNN3,NS,carcinoma,0,1	KCNN3	141	.	0			c.G2028A						PASS	.						124	137	133					1																	154680665		2203	4300	6503	SO:0001819	synonymous_variant	3782	exon9			CAGCTTCGACTCC	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.1983G>A	chr1.hg19:g.154680665C>T		146.0	0.0	.		111.0	31.0	.	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Silent	SNP	ENST00000271915.4	hg19	CCDS30880.1																																																																																			.	.	.	none		0.567	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		T	154680665	C	T	154680665	2	4	83	1	0	0	0	0	0	0	0	1	8087	871	31	1		1	KCNN3	1	154680665	Silent	SNP	C	TCGA-B1-A47O-01A-11D-A25F-10	109901765	154680665	94569956	3	5331											
SULT1C4	27233	hgsc.bcm.edu	37	chr2	109003803	109003804	+	Frame_Shift_Ins	INS	-	-	CA																															ggagactggaagaaacacttINScaccgtggctcagaatgaga																										TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr2:109003803_109003804insCA	ENST00000272452.2	+	7	1150_1151	c.824_825insCA	c.(823-828)ttcaccfs	p.FT275fs	SULT1C4_ENST00000409309.3_Frame_Shift_Ins_p.FT200fs	NM_006588.2	NP_006579.2	O75897	ST1C4_HUMAN	sulfotransferase family, cytosolic, 1C, member 4	275					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	sulfotransferase activity (GO:0008146)			endometrium(1)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	12						AAGAAACACTTCACCGTGGCTC	0.431																																					p.F275fs		Atlas-Indel,Pindel	.											.	SULT1C4	41	.	0			c.824_825insCA						PASS	.																																			SO:0001589	frameshift_variant	27233	exon7			.	AF055584	CCDS2077.1	2q12.3	2008-09-04	2007-03-16	2007-03-16	ENSG00000198075	ENSG00000198075		"Sulfotransferases, cytosolic"	11457	protein-coding gene	gene with protein product		608357	"sulfotransferase family, cytosolic, 1C, member 2"	SULT1C2		10783263, 9852044	Standard	NM_006588		Approved	SULT1C	uc002tea.1	O75897	OTTHUMG00000130958	ENST00000272452.2:c.825_826dupCA	chr2.hg19:g.109003804_109003805dupCA	ENSP00000272452:p.Phe275fs	116.0	0.0	0		124.0	25.0	0.201613	NM_006588	Q069I8|Q08AS5|Q53S63	Frame_Shift_Ins	INS	ENST00000272452.2	hg19	CCDS2077.1																																																																																			.	.	.	none		0.431	SULT1C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253561.1	NM_006588		CA	109003804	-	CA	109003803	7	5	83	1	0	1	1	0	0	0	0	0	15391	1783	62	0	850	0	SULT1C4	2	109003803	Frame_Shift_Ins	INS	-	TCGA-B1-A47O-01A-11D-A25F-10		109003803	134195570	4	5332											
SCN2A	6326	hgsc.bcm.edu	37	chr2	166246020	166246020	+	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	ccattacgaccacgttgaaaCgcaaacaagaggaggtgtct	14	7	10	10	3	1	2	0	1	1	1	1	4	1	3	2	2	3	2	2	2	4	2	rs367833365		TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr2:166246020C>T	ENST00000375437.2	+	27	5994	c.5704C>T	c.(5704-5706)Cgc>Tgc	p.R1902C	SCN2A_ENST00000375427.2_Missense_Mutation_p.R1902C|SCN2A_ENST00000283256.6_Missense_Mutation_p.R1902C|SCN2A_ENST00000357398.3_Missense_Mutation_p.R1902C	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	1902			R -> T (associated with autism). {ECO:0000269|PubMed:12610651}.		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)	CACGTTGAAACGCAAACAAGA	0.433																																					p.R1902C		Atlas-SNP	.											.	SCN2A	589	.	0			c.C5704T	GRCh37	CM034570	SCN2A	M		PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	87	81	83		5704,5704,5704	5.9	1	2		83	0,8600		0,0,4300	no	missense,missense,missense	SCN2A	NM_001040142.1,NM_001040143.1,NM_021007.2	180,180,180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging	1902/2006,1902/2006,1902/2006	166246020	1,13005	2203	4300	6503	SO:0001583	missense	6326	exon26			TTGAAACGCAAAC	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.5704C>T	chr2.hg19:g.166246020C>T	ENSP00000364586:p.Arg1902Cys	212.0	0.0	.		205.0	39.0	.	NM_001040143	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	hg19	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	C	15.37	2.814541	0.50527	2.27E-4	0.0	ENSG00000136531	ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D	0.96745	-4.11;-4.11;-4.11;-4.11	5.87	5.87	0.94306	.	0.113909	0.37261	N	0.002173	D	0.98362	0.9456	M	0.90922	3.16	0.58432	D	0.999999	D;D	0.89917	0.994;1.0	P;D	0.87578	0.865;0.998	D	0.98727	1.0711	10	0.66056	D	0.02	.	13.6126	0.62088	0.2709:0.7291:0.0:0.0	.	1902;1902	Q99250-2;Q99250	.;SCN2A_HUMAN	C	1902	ENSP00000364586:R1902C;ENSP00000349973:R1902C;ENSP00000283256:R1902C;ENSP00000364576:R1902C	ENSP00000283256:R1902C	R	+	1	0	SCN2A	165954266	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	2.510000	0.45468	2.785000	0.95823	0.585000	0.79938	CGC	.	.	.	weak		0.433	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		T	166246020	C	T	166246020	3	4	83	1	0	0	0	0	1	0	0	0	13929	536	19	1	5902	1	SCN2A	2	166246020	Missense_Mutation	SNP	C	TCGA-B1-A47O-01A-11D-A25F-10	57242217	166246020	76953353	5	5333											
LRP2	4036	hgsc.bcm.edu	37	chr2	170003429	170003429	+	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	tccattcatccaggcagactCgattttaggttcctttcccc	7	14	6	14	1	1	1	1	0	0	1	6	2	5	1	5	2	0	2	5	2	1	5			TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr2:170003429C>T	ENST00000263816.3	-	69	12916	c.12631G>A	c.(12631-12633)Gag>Aag	p.E4211K		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	4211					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)"	CAGGCAGACTCGATTTTAGGT	0.458																																					p.E4211K		Atlas-SNP	.											.	LRP2	751	.	0			c.G12631A						PASS	.						83	63	70					2																	170003429		2203	4300	6503	SO:0001583	missense	4036	exon69			CAGACTCGATTTT		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.12631G>A	chr2.hg19:g.170003429C>T	ENSP00000263816:p.Glu4211Lys	200.0	0.0	.		195.0	42.0	.	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	hg19	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	36	5.742166	0.96873	.	.	ENSG00000081479	ENST00000263816	D	0.93604	-3.25	5.67	5.67	0.87782	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	D	0.97570	0.9204	M	0.91972	3.26	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.97877	1.0289	10	0.66056	D	0.02	.	19.7612	0.96319	0.0:1.0:0.0:0.0	.	4211	P98164	LRP2_HUMAN	K	4211	ENSP00000263816:E4211K	ENSP00000263816:E4211K	E	-	1	0	LRP2	169711675	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.818000	0.86416	2.670000	0.90874	0.655000	0.94253	GAG	.	.	.	none		0.458	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		T	170003429	C	T	170003429	3	4	83	1	0	0	0	0	1	0	0	0	8963	893	31	1	1380	1	LRP2	2	170003429	Missense_Mutation	SNP	C	TCGA-B1-A47O-01A-11D-A25F-10	3757409	170003429	73195944	6	5334											
TTN	7273	hgsc.bcm.edu	37	chr2	179473456	179473456	+	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	ttttgttactgaatatttgcAatgtctaagtgttgaagtga	11	18	9	3	0	1	3	0	3	1	0	1	3	1	3	0	0	2	3	0	0	6	7			TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr2:179473456A>T	ENST00000591111.1	-	224	47583	c.47359T>A	c.(47359-47361)Tgc>Agc	p.C15787S	TTN_ENST00000342992.6_Missense_Mutation_p.C14860S|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.C8488S|TTN_ENST00000460472.2_Missense_Mutation_p.C8363S|TTN_ENST00000589042.1_Missense_Mutation_p.C17428S|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.C8555S|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	15787	Fibronectin type-III 14. {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)			GAATATTTGCAATGTCTAAGT	0.398																																					p.C17428S		Atlas-SNP	.											.	TTN	18412	.	0			c.T52282A						PASS	.						116	109	111					2																	179473456		1874	4114	5988	SO:0001583	missense	7273	exon274			ATTTGCAATGTCT	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.47359T>A	chr2.hg19:g.179473456A>T	ENSP00000465570:p.Cys15787Ser	120.0	0.0	.		103.0	24.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	13.26	2.183832	0.38609	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.52295	0.67;0.67;0.67;0.67	5.72	5.72	0.89469	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.61590	0.2359	L	0.41124	1.26	0.54753	D	0.999988	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.998;0.998	T	0.64537	-0.6384	9	0.87932	D	0	.	15.9966	0.80256	1.0:0.0:0.0:0.0	.	8363;8488;8555;15787	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	S	14860;8363;8555;8488;8363	ENSP00000343764:C14860S;ENSP00000434586:C8363S;ENSP00000340554:C8555S;ENSP00000352154:C8488S	ENSP00000340554:C8555S	C	-	1	0	TTN	179181701	1.000000	0.71417	0.979000	0.43373	0.994000	0.84299	5.134000	0.64770	2.179000	0.69175	0.460000	0.39030	TGC	.	.	.	none		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179473456	A	T	179473456	3	4	83	1	0	0	0	0	1	0	0	0	16747	130	5	5	55767	5	TTN	2	179473456	Missense_Mutation	SNP	A	TCGA-B1-A47O-01A-11D-A25F-10	9470027	179473456	63725917	7	5335											
NSUN3	63899	hgsc.bcm.edu	37	chr3	93845254	93845254	+	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	gccaggaatgtgggctcttaGtgattccagataagggcaaa	12	9	13	7	0	1	2	0	1	1	1	2	3	2	3	2	3	0	2	2	3	4	3			TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr3:93845254G>T	ENST00000314622.4	+	6	1154	c.943G>T	c.(943-945)Gtg>Ttg	p.V315L		NM_022072.3	NP_071355.1	Q9H649	NSUN3_HUMAN	NOP2/Sun domain family, member 3	315							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|skin(1)	18						TGGGCTCTTAGTGATTCCAGA	0.463																																					p.V315L		Atlas-SNP	.											.	NSUN3	33	.	0			c.G943T						PASS	.						74	71	72					3																	93845254		2203	4300	6503	SO:0001583	missense	63899	exon6			CTCTTAGTGATTC	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.943G>T	chr3.hg19:g.93845254G>T	ENSP00000318986:p.Val315Leu	185.0	0.0	.		173.0	19.0	.	NM_022072	Q6PG41|Q8IXG9|Q9H6M2	Missense_Mutation	SNP	ENST00000314622.4	hg19	CCDS2927.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.523084	0.85600	.	.	ENSG00000178694	ENST00000314622	T	0.08720	3.06	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.34542	0.0901	M	0.81112	2.525	0.58432	D	0.999995	D	0.76494	0.999	D	0.78314	0.991	T	0.02477	-1.1153	10	0.72032	D	0.01	-17.5839	20.2789	0.98501	0.0:0.0:1.0:0.0	.	315	Q9H649	NSUN3_HUMAN	L	315	ENSP00000318986:V315L	ENSP00000318986:V315L	V	+	1	0	NSUN3	95327944	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	7.548000	0.82154	2.788000	0.95919	0.650000	0.86243	GTG	.	.	.	none		0.463	NSUN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352934.1	NM_022072		T	93845254	G	T	93845254	3	4	83	1	0	0	0	0	1	0	0	0	10686	1029	36	4	965	4	NSUN3	3	93845254	Missense_Mutation	SNP	G	TCGA-B1-A47O-01A-11D-A25F-10		93845254	104177176	8	5336											
DNAH8	1769	hgsc.bcm.edu	37	chr6	38781879	38781879	+	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	ttatttcctttataaaaagtGaagtacatcttgcaattcct	13	17	4	7	0	1	1	0	1	1	0	3	1	3	1	2	0	2	2	2	0	8	8			TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr6:38781879G>A	ENST00000359357.3	+	23	2910	c.2656G>A	c.(2656-2658)Gaa>Aaa	p.E886K	DNAH8_ENST00000449981.2_Missense_Mutation_p.E1103K|DNAH8_ENST00000441566.1_Missense_Mutation_p.E886K			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	886					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						TATAAAAAGTGAAGTACATCT	0.323																																					p.E1103K		Atlas-SNP	.											.	DNAH8	1239	.	0			c.G3307A						PASS	.						113	124	120					6																	38781879		2203	4300	6503	SO:0001583	missense	1769	exon25			AAAAGTGAAGTAC	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.2656G>A	chr6.hg19:g.38781879G>A	ENSP00000352312:p.Glu886Lys	130.0	0.0	.		118.0	5.0	.	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	G	16.25	3.071426	0.55646	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.57436	0.4;0.4;0.4	5.33	5.33	0.75918	.	0.128175	0.49916	D	0.000132	T	0.31702	0.0805	L	0.56769	1.78	0.48135	D	0.999592	B	0.16396	0.017	B	0.13407	0.009	T	0.28776	-1.0033	10	0.08599	T	0.76	.	16.803	0.85618	0.0:0.0:1.0:0.0	.	886	Q96JB1	DYH8_HUMAN	K	1091;1091;886;886	ENSP00000333363:E1091K;ENSP00000352312:E886K;ENSP00000402294:E886K	ENSP00000333363:E1091K	E	+	1	0	DNAH8	38889857	1.000000	0.71417	0.985000	0.45067	0.989000	0.77384	5.832000	0.69337	2.503000	0.84419	0.655000	0.94253	GAA	.	.	.	none		0.323	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		A	38781879	G	A	38781879	3	1	83	1	0	0	0	0	1	0	0	0	4609	1291	45	2	2738	2	DNAH8	6	38781879	Missense_Mutation	SNP	G	TCGA-B1-A47O-01A-11D-A25F-10		38781879	132333188	9	5337											
IQCE	23288	hgsc.bcm.edu	37	chr7	2645529	2645529	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagctctcctgtgccccgcgTtccgagccccatcgcccagg	4	7	11	19	4	1	0	0	0	1	0	4	2	2	0	7	1	3	2	7	1	0	1			TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr7:2645529T>C	ENST00000402050.2	+	20	1947	c.1763T>C	c.(1762-1764)gTt>gCt	p.V588A	IQCE_ENST00000404984.1_Missense_Mutation_p.V537A|IQCE_ENST00000325979.7_Missense_Mutation_p.V523A|IQCE_ENST00000438376.2_Missense_Mutation_p.V572A	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	588						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)		GTGCCCCGCGTTCCGAGCCCC	0.697																																					p.V588A		Atlas-SNP	.											.	IQCE	66	.	0			c.T1763C						PASS	.						26	33	31					7																	2645529		2083	4195	6278	SO:0001583	missense	23288	exon20			CCCGCGTTCCGAG	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.1763T>C	chr7.hg19:g.2645529T>C	ENSP00000385597:p.Val588Ala	160.0	0.0	.		53.0	8.0	.	NM_152558	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Missense_Mutation	SNP	ENST00000402050.2	hg19	CCDS43542.1	.	.	.	.	.	.	.	.	.	.	T	5.392	0.257572	0.10239	.	.	ENSG00000106012	ENST00000402050;ENST00000404984;ENST00000438376;ENST00000325979;ENST00000423196	T;T;T;T;T	0.29142	2.54;2.51;2.54;2.52;1.58	4.79	-5.48	0.02592	.	1.687250	0.03947	N	0.287950	T	0.17577	0.0422	L	0.32530	0.975	0.09310	N	1	P;P;B;P;B	0.37141	0.524;0.584;0.144;0.524;0.4	B;B;B;B;B	0.34418	0.095;0.182;0.035;0.095;0.121	T	0.18493	-1.0335	10	0.10377	T	0.69	-0.0383	7.0173	0.24895	0.0:0.2771:0.493:0.2299	.	523;572;588;588;572	B4DXN1;B4DDX4;Q6IPM2;B3KRY4;Q6IPM2-4	.;.;IQCE_HUMAN;.;.	A	588;537;572;523;168	ENSP00000385597:V588A;ENSP00000385945:V537A;ENSP00000396178:V572A;ENSP00000313772:V523A;ENSP00000405982:V168A	ENSP00000313772:V523A	V	+	2	0	IQCE	2612055	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.293000	0.08320	-0.613000	0.05694	0.459000	0.35465	GTT	.	.	.	none		0.697	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558		C	2645529	T	C	2645529	3	2	83	1	0	0	0	0	1	0	0	0	7813	1725	60	3	1841	3	IQCE	7	2645529	Missense_Mutation	SNP	T	TCGA-B1-A47O-01A-11D-A25F-10		2645529	156493134	10	5338											
PCLO	27445	hgsc.bcm.edu	37	chr7	82544315	82544315	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggcagaggatgatgcatgActaaaggaaacatctagagc	15	7	12	7	0	1	4	0	2	1	2	1	6	1	6	0	3	3	2	0	3	4	2			TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr7:82544315A>G	ENST00000333891.9	-	7	13324	c.12987T>C	c.(12985-12987)agT>agC	p.S4329S	PCLO_ENST00000423517.2_Silent_p.S4329S|PCLO_ENST00000437081.1_Silent_p.S1049S	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						ATGATGCATGACTAAAGGAAA	0.428																																					p.S4329S		Atlas-SNP	.											.	PCLO	1506	.	0			c.T12987C						PASS	.						81	78	79					7																	82544315		1889	4111	6000	SO:0001819	synonymous_variant	27445	exon7			TGCATGACTAAAG	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.12987T>C	chr7.hg19:g.82544315A>G		176.0	0.0	.		199.0	56.0	.	NM_014510		Silent	SNP	ENST00000333891.9	hg19	CCDS47630.1																																																																																			.	.	.	none		0.428	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		G	82544315	A	G	82544315	2	3	83	1	0	0	0	0	0	0	0	1	11590	272	10	3		3	PCLO	7	82544315	Silent	SNP	A	TCGA-B1-A47O-01A-11D-A25F-10	79898786	82544315	76594348	11	5339											
NDUFB6	4712	hgsc.bcm.edu	37	chr9	32571048	32571048	+	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	ctctttttgtataccccatgGacctggggggaaaaacacat	11	11	9	10	0	1	0	0	0	1	0	1	2	1	2	3	4	2	1	3	4	4	4			TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr9:32571048G>T	ENST00000379847.3	-	2	284	c.183C>A	c.(181-183)gtC>gtA	p.V61V	NDUFB6_ENST00000350021.2_Silent_p.V61V	NM_002493.4	NP_002484.1	O95139	NDUB6_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6, 17kDa	61					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|urinary_tract(1)	8			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00199)		ATACCCCATGGACCTGGGGGG	0.328																																					p.V61V		Atlas-SNP	.											.	NDUFB6	12	.	0			c.C183A						PASS	.						39	39	39					9																	32571048		2203	4289	6492	SO:0001819	synonymous_variant	4712	exon2			CCCATGGACCTGG	AF035840	CCDS6528.1, CCDS6529.1, CCDS75826.1	9p13.2	2011-07-04	2002-08-29		ENSG00000165264	ENSG00000165264		"Mitochondrial respiratory chain complex / Complex I"	7701	protein-coding gene	gene with protein product	"NADH-ubiquinone oxidoreductase beta subunit, 6", "NADH-ubiquinone oxidoreductase B17 subunit", "complex I, mitochondrial respiratory chain, B17 subunit"	603322	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6 (17kD, B17)"			9763677, 9760212	Standard	NM_002493		Approved	B17, CI	uc003zre.2	O95139	OTTHUMG00000019741	ENST00000379847.3:c.183C>A	chr9.hg19:g.32571048G>T		147.0	0.0	.		130.0	28.0	.	NM_182739	A8K0Y7|Q5VYT2|Q6IB84	Silent	SNP	ENST00000379847.3	hg19	CCDS6528.1																																																																																			.	.	.	none		0.328	NDUFB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052001.1	NM_002493		T	32571048	G	T	32571048	2	4	83	1	0	0	0	0	0	0	0	1	10292	1161	41	4		4	NDUFB6	9	32571048	Silent	SNP	G	TCGA-B1-A47O-01A-11D-A25F-10		32571048	108642383	12	5340											
SECISBP2	79048	hgsc.bcm.edu	37	chr9	91964729	91964729	+	Missense_Mutation	SNP	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	aactgatctccactccttcgGttgaggacaagtctgaagag	11	10	10	10	1	2	4	0	3	2	1	5	5	3	5	2	2	1	1	2	2	3	2			TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr9:91964729G>A	ENST00000375807.3	+	13	1848	c.1777G>A	c.(1777-1779)Gtt>Att	p.V593I	SECISBP2_ENST00000534113.2_Missense_Mutation_p.V525I|SECISBP2_ENST00000339901.4_Missense_Mutation_p.V520I	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	593					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						CACTCCTTCGGTTGAGGACAA	0.562																																					p.V593I		Atlas-SNP	.											.	SECISBP2	64	.	0			c.G1777A						PASS	.						149	126	134					9																	91964729		2203	4300	6503	SO:0001583	missense	79048	exon13			CCTTCGGTTGAGG	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.1777G>A	chr9.hg19:g.91964729G>A	ENSP00000364965:p.Val593Ile	192.0	0.0	.		179.0	31.0	.	NM_024077	F8W892|Q5HYY1|Q8IYC0|Q9H0A1	Missense_Mutation	SNP	ENST00000375807.3	hg19	CCDS6683.1	.	.	.	.	.	.	.	.	.	.	G	9.108	1.005789	0.19199	.	.	ENSG00000187742	ENST00000375807;ENST00000395669;ENST00000339901;ENST00000534113	T;T;T	0.72835	-0.69;-0.69;-0.69	4.41	2.53	0.30540	.	1.563310	0.03304	N	0.189460	T	0.68668	0.3026	L	0.54323	1.7	0.09310	N	1	B;B;B	0.20052	0.024;0.041;0.006	B;B;B	0.19946	0.012;0.027;0.012	T	0.48822	-0.9001	10	0.34782	T	0.22	-0.0032	9.8267	0.40916	0.086:0.1414:0.7726:0.0	.	600;520;593	Q59H19;Q96T21-2;Q96T21	.;.;SEBP2_HUMAN	I	593;599;520;525	ENSP00000364965:V593I;ENSP00000364959:V520I;ENSP00000436650:V525I	ENSP00000364959:V520I	V	+	1	0	SECISBP2	91154549	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.188000	0.17018	0.134000	0.18681	-0.797000	0.03246	GTT	.	.	.	none		0.562	SECISBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052990.3	NM_024077		A	91964729	G	A	91964729	3	1	83	1	0	0	0	0	1	0	0	0	14019	1261	44	2	1827	2	SECISBP2	9	91964729	Missense_Mutation	SNP	G	TCGA-B1-A47O-01A-11D-A25F-10	59393681	91964729	49248702	13	5341											
ERC1	23085	hgsc.bcm.edu	37	chr12	1372211	1372211	+	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	attttctaggacagtctccgTaagaaggatgacaggattga	13	11	11	6	1	2	3	0	2	2	1	3	6	2	6	1	3	0	1	1	3	3	5			TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr12:1372211T>A	ENST00000397203.2	+	14	2905	c.2499T>A	c.(2497-2499)cgT>cgA	p.R833R	ERC1_ENST00000589028.1_Silent_p.R833R|ERC1_ENST00000355446.5_Silent_p.R833R|ERC1_ENST00000543086.3_Silent_p.R805R|ERC1_ENST00000360905.4_Silent_p.R833R|ERC1_ENST00000546231.2_Silent_p.R837R			Q8IUD2	RB6I2_HUMAN	ELKS/RAB6-interacting/CAST family member 1	833					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)			ACAGTCTCCGTAAGAAGGATG	0.423																																					p.R833R		Atlas-SNP	.											.	ERC1	95	.	0			c.T2499A						PASS	.						75	70	72					12																	1372211		2203	4300	6503	SO:0001819	synonymous_variant	23085	exon14			TCTCCGTAAGAAG	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.2499T>A	chr12.hg19:g.1372211T>A		80.0	0.0	.		52.0	9.0	.	NM_178040	A2RU77|A7E295|D3DUP7|D3DUP8|Q6NVK2|Q8IUD3|Q8IUD4|Q8IUD5|Q8NAS1|Q9NXN5|Q9UIK7|Q9UPS1	Silent	SNP	ENST00000397203.2	hg19	CCDS8508.1																																																																																			.	.	.	none		0.423	ERC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398380.2	NM_015064		A	1372211	T	A	1372211	2	1	83	1	0	0	0	0	0	0	0	1	5212	1625	57	5		5	ERC1	12	1372211	Silent	SNP	T	TCGA-B1-A47O-01A-11D-A25F-10		1372211	132479684	14	5342											
GALNT6	11226	hgsc.bcm.edu	37	chr12	51757995	51757995	+	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	ggctccagtcaaagttgcctCggctatggactctgcccctc	6	10	10	15	1	2	0	1	0	1	0	5	1	3	1	4	3	2	3	4	3	2	2	rs138580901	byFrequency	TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr12:51757995C>G	ENST00000543196.2	-	5	1164	c.959G>C	c.(958-960)cGa>cCa	p.R320P	GALNT6_ENST00000356317.3_Missense_Mutation_p.R320P			Q8NCL4	GALT6_HUMAN	polypeptide N-acetylgalactosaminyltransferase 6	320					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(2)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						AAAGTTGCCTCGGCTATGGAC	0.552																																					p.R320P		Atlas-SNP	.											.	GALNT6	63	.	0			c.G959C						PASS	.						114	105	108					12																	51757995		2203	4300	6503	SO:0001583	missense	11226	exon6			TTGCCTCGGCTAT	Y08565	CCDS8813.1	12q13	2014-03-13	2014-03-13		ENSG00000139629	ENSG00000139629		"Glycosyltransferase family 2 domain containing"	4128	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 6"	605148	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6)"			10464263	Standard	NM_007210		Approved	GalNAc-T6	uc001ryl.1	Q8NCL4		ENST00000543196.2:c.959G>C	chr12.hg19:g.51757995C>G	ENSP00000444171:p.Arg320Pro	307.0	0.0	.		237.0	52.0	.	NM_007210	Q8IYH4|Q9H6G2|Q9UIV5	Missense_Mutation	SNP	ENST00000543196.2	hg19	CCDS8813.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.540572	0.85917	.	.	ENSG00000139629	ENST00000543196;ENST00000356317;ENST00000546163	T;T	0.61040	0.14;0.14	4.59	4.59	0.56863	Glycosyl transferase, family 2 (1);	0.414998	0.27720	N	0.018126	T	0.79930	0.4531	M	0.88105	2.93	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82669	-0.0343	10	0.56958	D	0.05	.	17.3609	0.87350	0.0:1.0:0.0:0.0	.	320	Q8NCL4	GALT6_HUMAN	P	320;320;301	ENSP00000444171:R320P;ENSP00000348668:R320P	ENSP00000348668:R320P	R	-	2	0	GALNT6	50044262	1.000000	0.71417	0.995000	0.50966	0.938000	0.57974	5.811000	0.69187	2.837000	0.97791	0.655000	0.94253	CGA	.	C|1.000;T|0.000	.	alt		0.552	GALNT6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469735.1	NM_007210		G	51757995	C	G	51757995	3	3	83	1	0	0	0	0	1	0	0	0	6224	884	31	4	937	4	GALNT6	12	51757995	Missense_Mutation	SNP	C	TCGA-B1-A47O-01A-11D-A25F-10	50385784	51757995	82093900	15	5343											
C12orf51	283450	hgsc.bcm.edu	37	chr12	112605266	112605266	+	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	cgtctgcccgaattgcaatcCccagcagctgccccaggaag	9	6	10	16	2	1	0	0	0	1	0	2	2	2	1	5	1	5	3	5	1	3	1			TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr12:112605266C>T	ENST00000430131.2	-	71	12268	c.11123G>A	c.(11122-11124)gGg>gAg	p.G3708E	HECTD4_ENST00000550722.1_Missense_Mutation_p.G3984E|HECTD4_ENST00000377560.5_Missense_Mutation_p.G3958E			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3708	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)										AATTGCAATCCCCAGCAGCTG	0.647																																					p.G3996E		Atlas-SNP	.											.	.	.	.	0			c.G11987A						PASS	.						48	55	53					12																	112605266		1986	4146	6132	SO:0001583	missense	283450	exon72			GCAATCCCCAGCA	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.11123G>A	chr12.hg19:g.112605266C>T	ENSP00000404379:p.Gly3708Glu	93.0	0.0	.		89.0	23.0	.	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	C	21.4	4.141592	0.77775	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722;ENST00000547085	T;T;T	0.60920	0.15;0.15;0.15	5.39	5.39	0.77823	HECT (4);	.	.	.	.	T	0.81583	0.4853	M	0.89840	3.065	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85365	0.1110	9	0.87932	D	0	.	19.1437	0.93457	0.0:1.0:0.0:0.0	.	3708	Q9Y4D8	K0614_HUMAN	E	3958;3708;3984;173	ENSP00000366783:G3958E;ENSP00000404379:G3708E;ENSP00000449784:G3984E	ENSP00000366783:G3958E	G	-	2	0	C12orf51	111089649	1.000000	0.71417	0.954000	0.39281	0.354000	0.29330	7.336000	0.79245	2.551000	0.86045	0.491000	0.48974	GGG	.	.	.	none		0.647	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		T	112605266	C	T	112605266	3	4	83	1	0	0	0	0	1	0	0	0	1698	623	22	2	887	2	C12orf51	12	112605266	Missense_Mutation	SNP	C	TCGA-B1-A47O-01A-11D-A25F-10	60847271	112605266	21246629	16	5344											
MTUS2	23281	hgsc.bcm.edu	37	chr13	29675028	29675028	+	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	ctggcggcatttggctttgtCcggagctccagcgtctcctc	3	12	12	14	3	1	0	0	0	1	0	5	1	3	1	3	4	2	3	3	4	0	2			TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr13:29675028C>T	ENST00000431530.3	+	3	2653	c.2595C>T	c.(2593-2595)gtC>gtT	p.V865V		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	855	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						TTGGCTTTGTCCGGAGCTCCA	0.622																																					p.V865V		Atlas-SNP	.											.	MTUS2	279	.	0			c.C2595T						PASS	.						9	10	10					13																	29675028		2018	4165	6183	SO:0001819	synonymous_variant	23281	exon3			CTTTGTCCGGAGC	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.2595C>T	chr13.hg19:g.29675028C>T		62.0	0.0	.		71.0	18.0	.	NM_001033602	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Silent	SNP	ENST00000431530.3	hg19	CCDS45022.1																																																																																			.	.	.	none		0.622	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270		T	29675028	C	T	29675028	2	4	83	1	0	0	0	0	0	0	0	1	9973	842	30	2		2	MTUS2	13	29675028	Silent	SNP	C	TCGA-B1-A47O-01A-11D-A25F-10		29675028	85494850	17	5345											
TRIP4	9325	hgsc.bcm.edu	37	chr15	64702014	64702014	+	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	aagaagaaaattcactagcaGagtatcatagcaggtaagtg	18	8	10	5	0	2	3	2	0	0	3	2	3	2	3	0	1	2	4	0	1	8	5			TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr15:64702014G>C	ENST00000261884.3	+	7	1090	c.1030G>C	c.(1030-1032)Gag>Cag	p.E344Q		NM_016213.4	NP_057297.2	Q15650	TRIP4_HUMAN	thyroid hormone receptor interactor 4	344					positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21						TTCACTAGCAGAGTATCATAG	0.433																																					p.E344Q		Atlas-SNP	.											.	TRIP4	43	.	0			c.G1030C						PASS	.						79	79	79					15																	64702014		2203	4300	6503	SO:0001583	missense	9325	exon7			CTAGCAGAGTATC	L40371	CCDS10194.1	15q22.1	2014-02-17			ENSG00000103671	ENSG00000103671		"-"	12310	protein-coding gene	gene with protein product	"zinc finger, C2HC5-type"	604501				7776974	Standard	NM_016213		Approved	HsT17391, ZC2HC5	uc002anm.3	Q15650	OTTHUMG00000133033	ENST00000261884.3:c.1030G>C	chr15.hg19:g.64702014G>C	ENSP00000261884:p.Glu344Gln	44.0	0.0	.		45.0	15.0	.	NM_016213	B2RAS0|Q96ED7|Q9UKH0	Missense_Mutation	SNP	ENST00000261884.3	hg19	CCDS10194.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.244397	0.59103	.	.	ENSG00000103671	ENST00000261884	.	.	.	5.81	5.81	0.92471	.	0.138874	0.64402	D	0.000005	T	0.78110	0.4232	M	0.80422	2.495	0.53005	D	0.999961	D	0.67145	0.996	P	0.57846	0.828	T	0.76710	-0.2859	9	0.38643	T	0.18	-24.7936	20.0734	0.97734	0.0:0.0:1.0:0.0	.	344	Q15650	TRIP4_HUMAN	Q	344	.	ENSP00000261884:E344Q	E	+	1	0	TRIP4	62489067	1.000000	0.71417	0.934000	0.37439	0.262000	0.26303	4.870000	0.63035	2.751000	0.94390	0.555000	0.69702	GAG	.	.	.	none		0.433	TRIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256635.2	NM_016213		C	64702014	G	C	64702014	3	2	83	1	0	0	0	0	1	0	0	0	16570	943	33	4	1056	4	TRIP4	15	64702014	Missense_Mutation	SNP	G	TCGA-B1-A47O-01A-11D-A25F-10		64702014	37829378	18	5346											
DNAH2	146754	hgsc.bcm.edu	37	chr17	7734797	7734797	+	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	ctgctagctctcgacccctcCcccctcaatgtggtccttct	4	12	6	19	1	3	0	1	0	2	0	6	1	5	0	6	1	2	2	6	1	2	2			TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr17:7734797C>G	ENST00000572933.1	+	81	14009	c.12549C>G	c.(12547-12549)tcC>tcG	p.S4183S	DNAH2_ENST00000389173.2_Silent_p.S4183S			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	4183					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)				TCGACCCCTCCCCCCTCAATG	0.547																																					p.S4183S		Atlas-SNP	.											.	DNAH2	498	.	0			c.C12549G						PASS	.						75	69	71					17																	7734797		2203	4300	6503	SO:0001819	synonymous_variant	146754	exon80			CCCCTCCCCCCTC	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.12549C>G	chr17.hg19:g.7734797C>G		138.0	0.0	.		133.0	33.0	.	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	hg19	CCDS32551.1																																																																																			.	.	.	none		0.547	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		G	7734797	C	G	7734797	2	3	83	1	0	0	0	0	0	0	0	1	4604	610	22	4		4	DNAH2	17	7734797	Silent	SNP	C	TCGA-B1-A47O-01A-11D-A25F-10		7734797	73460413	19	5347											
PIPOX	51268	hgsc.bcm.edu	37	chr17	27379969	27379969	+	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	tactgctgctgggaatgaaaGagaatcaagaattaaagaca	18	8	10	5	0	1	4	1	1	0	3	1	6	1	5	0	1	3	2	0	1	8	2	rs58011977	byFrequency	TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr17:27379969G>C	ENST00000323372.4	+	3	621	c.295G>C	c.(295-297)Gag>Cag	p.E99Q	PIPOX_ENST00000583215.1_3'UTR	NM_016518.2	NP_057602.2	Q9P0Z9	SOX_HUMAN	pipecolic acid oxidase	99					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)	GGGAATGAAAGAGAATCAAGA	0.448																																					p.E99Q		Atlas-SNP	.											.	PIPOX	42	.	0			c.G295C						PASS	.						77	74	75					17																	27379969		2203	4300	6503	SO:0001583	missense	51268	exon3			ATGAAAGAGAATC	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.295G>C	chr17.hg19:g.27379969G>C	ENSP00000317721:p.Glu99Gln	148.0	0.0	.		165.0	22.0	.	NM_016518	B3KNH0|Q96H28|Q9C070	Missense_Mutation	SNP	ENST00000323372.4	hg19	CCDS11248.1	.	.	.	.	.	.	.	.	.	.	G	7.939	0.742323	0.15642	.	.	ENSG00000179761	ENST00000323372;ENST00000419875	D	0.82984	-1.67	5.98	5.98	0.97165	FAD dependent oxidoreductase (1);	0.359343	0.34628	N	0.003812	D	0.84009	0.5378	L	0.46741	1.465	0.20074	N	0.999938	P	0.37594	0.601	P	0.45558	0.485	T	0.77993	-0.2378	10	0.48119	T	0.1	-19.736	17.9305	0.88996	0.0:0.0:1.0:0.0	.	99	Q9P0Z9	SOX_HUMAN	Q	99;30	ENSP00000317721:E99Q	ENSP00000317721:E99Q	E	+	1	0	PIPOX	24404095	0.321000	0.24625	0.962000	0.40283	0.014000	0.08584	2.932000	0.48940	2.837000	0.97791	0.591000	0.81541	GAG	.	G|0.999;A|0.001	.	alt		0.448	PIPOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255954.1	NM_016518		C	27379969	G	C	27379969	3	2	83	1	0	0	0	0	1	0	0	0	11950	943	33	4	305	4	PIPOX	17	27379969	Missense_Mutation	SNP	G	TCGA-B1-A47O-01A-11D-A25F-10	19645172	27379969	53815241	20	5348											
CETN1	1068	hgsc.bcm.edu	37	chr18	580595	580595	+	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	ccatgagagcgctgggcttcGaacccaggaaggaagagatg	12	5	15	9	2	0	2	0	1	0	2	1	7	0	4	2	3	2	2	2	3	3	1			TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr18:580595G>A	ENST00000327228.3	+	1	229	c.187G>A	c.(187-189)Gaa>Aaa	p.E63K		NM_004066.1	NP_004057.1	Q12798	CETN1_HUMAN	centrin, EF-hand protein, 1	63	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cellular response to heat (GO:0034605)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|photoreceptor connecting cilium (GO:0032391)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|calcium ion binding (GO:0005509)|nucleic acid binding (GO:0003676)	p.E63K(1)		breast(2)|cervix(1)|endometrium(3)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(2)	25						GCTGGGCTTCGAACCCAGGAA	0.552																																					p.E63K		Atlas-SNP	.											CETN1,NS,carcinoma,0,1	CETN1	48	.	1	Substitution - Missense(1)	lung(1)	c.G187A						PASS	.						77	59	65					18																	580595		2203	4300	6503	SO:0001583	missense	1068	exon1			GGCTTCGAACCCA	U03270	CCDS11820.1	18p11.32	2013-01-10			ENSG00000177143	ENSG00000177143		"EF-hand domain containing"	1866	protein-coding gene	gene with protein product		603187		CETN		8175926	Standard	NM_004066		Approved	CEN1	uc002kko.1	Q12798	OTTHUMG00000131471	ENST00000327228.3:c.187G>A	chr18.hg19:g.580595G>A	ENSP00000319052:p.Glu63Lys	89.0	0.0	.		83.0	25.0	.	NM_004066	B2R536	Missense_Mutation	SNP	ENST00000327228.3	hg19	CCDS11820.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.301757	0.81136	.	.	ENSG00000177143	ENST00000327228	T	0.37058	1.22	5.2	5.2	0.72013	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.46580	0.1400	N	0.21617	0.685	0.80722	D	1	D	0.76494	0.999	D	0.71870	0.975	T	0.46176	-0.9210	10	0.72032	D	0.01	.	16.6478	0.85181	0.0:0.0:1.0:0.0	.	63	Q12798	CETN1_HUMAN	K	63	ENSP00000319052:E63K	ENSP00000319052:E63K	E	+	1	0	CETN1	570595	1.000000	0.71417	0.887000	0.34795	0.129000	0.20672	4.687000	0.61708	2.882000	0.98803	0.655000	0.94253	GAA	.	.	.	none		0.552	CETN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254314.2	NM_004066		A	580595	G	A	580595	3	1	83	1	0	0	0	0	1	0	0	0	3276	1059	37	1	189	1	CETN1	18	580595	Missense_Mutation	SNP	G	TCGA-B1-A47O-01A-11D-A25F-10		580595	77496653	21	5349											
LPIN2	9663	hgsc.bcm.edu	37	chr18	2937962	2937962	+	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	tgtcctcactgggaattaccCgaaaatgagtattttctgat	11	14	8	8	1	2	2	1	2	1	0	3	4	3	3	2	1	1	1	2	1	5	4			TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr18:2937962C>A	ENST00000261596.4	-	7	1134	c.896G>T	c.(895-897)cGg>cTg	p.R299L		NM_014646.2	NP_055461.1	Q92539	LPIN2_HUMAN	lipin 2	299					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)		GGGAATTACCCGAAAATGAGT	0.413																																					p.R299L		Atlas-SNP	.											.	LPIN2	75	.	0			c.G896T						PASS	.						151	144	146					18																	2937962		2203	4300	6503	SO:0001583	missense	9663	exon7			ATTACCCGAAAAT	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.896G>T	chr18.hg19:g.2937962C>A	ENSP00000261596:p.Arg299Leu	93.0	0.0	.		100.0	4.0	.	NM_014646	A7MD25|D3DUH3	Missense_Mutation	SNP	ENST00000261596.4	hg19	CCDS11829.1	.	.	.	.	.	.	.	.	.	.	C	18.91	3.724085	0.68959	.	.	ENSG00000101577	ENST00000261596	T	0.81330	-1.48	5.86	5.86	0.93980	.	0.160462	0.56097	D	0.000036	T	0.79003	0.4373	M	0.70842	2.15	0.58432	D	0.999999	B	0.18166	0.026	B	0.19391	0.025	T	0.73720	-0.3894	10	0.07482	T	0.82	.	18.367	0.90394	0.0:1.0:0.0:0.0	.	299	Q92539	LPIN2_HUMAN	L	299	ENSP00000261596:R299L	ENSP00000261596:R299L	R	-	2	0	LPIN2	2927962	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.670000	0.74467	2.775000	0.95449	0.655000	0.94253	CGG	.	.	.	none		0.413	LPIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254363.2	NM_014646		A	2937962	C	A	2937962	3	1	83	1	0	0	0	0	1	0	0	0	8926	652	23	4	1850	4	LPIN2	18	2937962	Missense_Mutation	SNP	C	TCGA-B1-A47O-01A-11D-A25F-10	2357367	2937962	75139286	22	5350											
PAF1	55588	hgsc.bcm.edu	37	chr19	39879309	39879309	+	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	ctggttcccttcctcatccaTcatgcccctggttgggggaa	5	12	10	14	0	2	0	2	0	0	0	5	1	5	1	5	4	1	2	5	4	1	3			TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr19:39879309T>C	ENST00000599213.2	+	0	0				PAF1_ENST00000595564.1_Missense_Mutation_p.M240V|PAF1_ENST00000221265.3_Missense_Mutation_p.M250V|MED29_ENST00000594368.1_5'Flank|PAF1_ENST00000221266.7_Missense_Mutation_p.M217V|MED29_ENST00000315588.5_5'Flank			Q9NX70	MED29_HUMAN	mediator complex subunit 29						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mediator complex (GO:0016592)|nucleus (GO:0005634)				lung(2)|ovary(1)|pancreas(1)	4	all_cancers(60;7.82e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;1.88e-06)|Ovarian(47;0.0512)		Epithelial(26;1.04e-26)|all cancers(26;7.68e-24)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)			TCCTCATCCATCATGCCCCTG	0.532																																					p.M250V		Atlas-SNP	.											.	PAF1	43	.	0			c.A748G						PASS	.						102	88	93					19																	39879309		2203	4300	6503	SO:0001631	upstream_gene_variant	54623	exon10			CATCCATCATGCC	AL137304, AY729650	CCDS33021.1	19q13.2	2007-07-30	2007-07-30	2007-07-30		ENSG00000063322			23074	protein-coding gene	gene with protein product		612914	"intersex-like (Drosophila)"	IXL		15555573	Standard	NM_017592		Approved	DKFZp434H247	uc010xux.3	Q9NX70			chr19.hg19:g.39879309T>C	Exception_encountered	307.0	0.0	.		254.0	46.0	.	NM_019088	B4DNQ6|M0R2E4|Q5XX09|Q9NTF4	Missense_Mutation	SNP	ENST00000599213.2	hg19		.	.	.	.	.	.	.	.	.	.	T	10.70	1.423601	0.25639	.	.	ENSG00000006712	ENST00000221265;ENST00000221266;ENST00000416728	.	.	.	5.25	4.23	0.50019	.	0.151964	0.64402	D	0.000008	T	0.33673	0.0871	N	0.16862	0.45	0.58432	D	0.999997	B;B	0.27316	0.175;0.046	B;B	0.26094	0.058;0.066	T	0.08953	-1.0697	9	0.25751	T	0.34	-19.7403	9.6931	0.40141	0.1554:0.0:0.0:0.8446	.	217;250	F8W9Q2;Q8N7H5	.;PAF1_HUMAN	V	250;217;197	.	ENSP00000221265:M250V	M	-	1	0	PAF1	44571149	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.109000	0.77062	0.989000	0.38761	0.528000	0.53228	ATG	.	.	.	none		0.532	MED29-011	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000470870.1	XM_290829		C	39879309	T	C	39879309	1	2	83	0	1	0	0	0	0	0	0	0	11390	1435	50	3		3	PAF1	19	39879309	5'Flank	SNP	T	TCGA-B1-A47O-01A-11D-A25F-10		39879309	19249674	23	5351											
SPTBN4	57731	hgsc.bcm.edu	37	chr19	41063170	41063170	+	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	taagttcttcagtgacgcccGagagcttcagggacagattg	10	10	12	9	2	3	3	2	1	1	2	3	5	3	4	1	1	1	2	1	1	1	5	rs556623605		TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr19:41063170G>A	ENST00000352632.3	+	26	5617	c.5531G>A	c.(5530-5532)cGa>cAa	p.R1844Q	SPTBN4_ENST00000595535.1_Missense_Mutation_p.R1844Q|SPTBN4_ENST00000598249.1_Missense_Mutation_p.R1844Q|SPTBN4_ENST00000392023.1_Missense_Mutation_p.R520Q|SPTBN4_ENST00000338932.3_Missense_Mutation_p.R1844Q|SPTBN4_ENST00000392025.1_Missense_Mutation_p.R587Q			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	1844					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)			AGTGACGCCCGAGAGCTTCAG	0.662													G|||	1	0.000199681	0	0	5008	,	,		14986	0.001		0	False		,,,				2504	0				p.R1844Q		Atlas-SNP	.											.	SPTBN4	213	.	0			c.G5531A						PASS	.						26	31	29					19																	41063170		2202	4299	6501	SO:0001583	missense	57731	exon26			ACGCCCGAGAGCT	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.5531G>A	chr19.hg19:g.41063170G>A	ENSP00000263373:p.Arg1844Gln	84.0	0.0	.		38.0	8.0	.	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Missense_Mutation	SNP	ENST00000352632.3	hg19	CCDS12559.1	.	.	.	.	.	.	.	.	.	.	G	16.63	3.175439	0.57692	.	.	ENSG00000160460	ENST00000428507;ENST00000352632;ENST00000338932;ENST00000392025;ENST00000392023	T;T;T;T	0.34275	1.37;1.37;1.37;1.37	3.63	3.63	0.41609	.	0.000000	0.56097	D	0.000021	T	0.38026	0.1025	L	0.31752	0.955	0.32656	N	0.518776	P;P;D;D	0.64830	0.694;0.765;0.994;0.99	B;B;P;P	0.61397	0.117;0.149;0.888;0.853	T	0.37572	-0.9700	10	0.23891	T	0.37	.	8.599	0.33734	0.1104:0.0:0.8896:0.0	.	587;520;1844;1844	C9JY79;E9PGQ5;Q9H254;Q71S06	.;.;SPTN4_HUMAN;.	Q	1844;1844;1844;587;520	ENSP00000263373:R1844Q;ENSP00000340345:R1844Q;ENSP00000375879:R587Q;ENSP00000375877:R520Q	ENSP00000340345:R1844Q	R	+	2	0	SPTBN4	45755010	0.001000	0.12720	0.978000	0.43139	0.919000	0.55068	0.856000	0.27818	2.036000	0.60181	0.455000	0.32223	CGA	.	.	.	none		0.662	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2			A	41063170	G	A	41063170	3	1	83	1	0	0	0	0	1	0	0	0	15133	1058	37	1	5629	1	SPTBN4	19	41063170	Missense_Mutation	SNP	G	TCGA-B1-A47O-01A-11D-A25F-10	1183861	41063170	18065813	24	5352											
HRC	3270	hgsc.bcm.edu	37	chr19	49657889	49657889	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tactcagtggaggcctcctcTtcctcctcctcctcctcctc	3	13	5	20	0	2	0	1	0	1	0	10	1	9	1	8	2	1	0	8	2	1	2	rs57199624|rs147238387|rs551367394|rs542091249		TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr19:49657889T>C	ENST00000252825.4	-	1	792	c.606A>G	c.(604-606)gaA>gaG	p.E202E	HRC_ENST00000595625.1_Silent_p.E202E	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	202	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Glu-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		AGGcctcctcttcctcctcct	0.567																																					p.E202E	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.,1	HRC	85	.	0			c.A606G						PASS	.						122	91	101					19																	49657889		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			CTCCTCTTCCTCC		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.606A>G	chr19.hg19:g.49657889T>C		231.0	2.0	.		227.0	19.0	.	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	hg19	CCDS12759.1																																																																																			.	.	.	none		0.567	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		C	49657889	T	C	49657889	2	2	83	1	0	0	0	0	0	0	0	1	7359	1606	56	3		3	HRC	19	49657889	Silent	SNP	T	TCGA-B1-A47O-01A-11D-A25F-10	8594719	49657889	9471094	25	5353											
NLRP11	204801	hgsc.bcm.edu	37	chr19	56320200	56320200	+	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	tgaacactcaacttaagtgtCctcaggtgacagcagtaatc	13	10	8	10	0	2	2	2	2	0	0	4	2	3	2	1	1	3	2	1	1	4	2	rs16986626	byFrequency	TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr19:56320200C>G	ENST00000589093.1	-	3	1869	c.1776G>C	c.(1774-1776)agG>agC	p.R592S	NLRP11_ENST00000443188.1_Missense_Mutation_p.R592S|NLRP11_ENST00000360133.3_Missense_Mutation_p.R592S|NLRP11_ENST00000592953.1_Missense_Mutation_p.R493S|NLRP11_ENST00000589824.2_Missense_Mutation_p.R592S			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	592							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)		ACTTAAGTGTCCTCAGGTGAC	0.408																																					p.R592S		Atlas-SNP	.											.	NLRP11	139	.	0			c.G1776C						PASS	.						130	118	122					19																	56320200		2203	4300	6503	SO:0001583	missense	204801	exon5			AAGTGTCCTCAGG	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.1776G>C	chr19.hg19:g.56320200C>G	ENSP00000466285:p.Arg592Ser	128.0	0.0	.		138.0	31.0	.	NM_145007	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Missense_Mutation	SNP	ENST00000589093.1	hg19	CCDS12935.1	.	.	.	.	.	.	.	.	.	.	C	9.578	1.122803	0.20959	.	.	ENSG00000179873	ENST00000443188;ENST00000360133	T;T	0.53423	0.62;0.62	2.39	0.0904	0.14463	.	.	.	.	.	T	0.38983	0.1061	L	0.42245	1.32	0.80722	P	0.0	B;B	0.33345	0.286;0.409	B;B	0.40199	0.12;0.322	T	0.47129	-0.9141	8	0.56958	D	0.05	.	3.403	0.07331	0.0:0.5605:0.2737:0.1658	.	592;592	P59045;P59045-2	NAL11_HUMAN;.	S	592	ENSP00000409898:R592S;ENSP00000353251:R592S	ENSP00000353251:R592S	R	-	3	2	NLRP11	61012012	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.018000	0.13422	0.099000	0.17552	0.655000	0.94253	AGG	.	C|0.890;N|0.000	.	alt		0.408	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007		G	56320200	C	G	56320200	3	3	83	1	0	0	0	0	1	0	0	0	10480	854	30	4	1357	4	NLRP11	19	56320200	Missense_Mutation	SNP	C	TCGA-B1-A47O-01A-11D-A25F-10	6662311	56320200	2808783	26	5354											
ASIP	434	hgsc.bcm.edu	37	chr20	32856797	32856797	+	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	ccccggcgtttcccacgcagAaggaggcttcgatgaagaaa	11	6	12	12	4	0	3	0	1	0	2	2	5	1	4	3	3	0	3	3	3	3	2	rs538816237		TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr20:32856797A>G	ENST00000568305.1	+	4	425	c.223A>G	c.(223-225)Aag>Gag	p.K75E	RP4-785G19.5_ENST00000512005.1_RNA|ASIP_ENST00000374954.3_Splice_Site_p.K75E			P42127	ASIP_HUMAN	agouti signaling protein	75	Arg/Lys-rich (basic).				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						TCCCACGCAGAAGGAGGCTTC	0.697													A|||	1	0.000199681	0	0	5008	,	,		12806	0.001		0	False		,,,				2504	0				p.K75E		Atlas-SNP	.											.	ASIP	6	.	0			c.A223G						PASS	.						8	11	10					20																	32856797		2188	4282	6470	SO:0001630	splice_region_variant	434	exon3			ACGCAGAAGGAGG		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.223-1A>G	chr20.hg19:g.32856797A>G		81.0	0.0	.		39.0	8.0	.	NM_001672	Q3SXL2	Missense_Mutation	SNP	ENST00000568305.1	hg19	CCDS13232.1	.	.	.	.	.	.	.	.	.	.	A	15.14	2.744523	0.49151	.	.	ENSG00000101440	ENST00000374954	T	0.31769	1.48	4.61	4.61	0.57282	.	0.063957	0.64402	D	0.000013	T	0.48660	0.1512	M	0.82323	2.585	0.40299	D	0.978584	P	0.51240	0.943	P	0.54346	0.749	T	0.54970	-0.8213	9	.	.	.	.	10.3603	0.43989	1.0:0.0:0.0:0.0	.	75	P42127	ASIP_HUMAN	E	75	ENSP00000364092:K75E	.	K	+	1	0	ASIP	32320458	1.000000	0.71417	1.000000	0.80357	0.127000	0.20565	3.560000	0.53763	1.942000	0.56320	0.397000	0.26171	AAG	.	.	.	none		0.697	ASIP-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430541.1		Missense_Mutation	G	32856797	A	G	32856797	5	3	83	1	0	0	0	0	0	0	1	0	1043	260	9	3	233	3	ASIP	20	32856797	Splice_Site	SNP	A	TCGA-B1-A47O-01A-11D-A25F-10		32856797	30168723	27	5355											
CYTSA	23384	hgsc.bcm.edu	37	chr22	24720193	24720193	+	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	gtcaattttacgtaggtagaGgatgaataccgagccttcca	12	11	10	8	2	1	2	1	1	0	1	2	4	2	3	3	2	3	2	3	2	6	6			TCGA-B1-A47O-01A-11D-A25F-10	TCGA-B1-A47O-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ca2b9fe2-97e0-4d4f-afd7-a5acf638800f	c023a62c-e498-4e1e-be91-99cf6d7b0708	g.chr22:24720193G>T	ENST00000314328.9	+	6	2229	c.1944G>T	c.(1942-1944)gaG>gaT	p.E648D	SPECC1L_ENST00000437398.1_Missense_Mutation_p.E648D|SPECC1L-ADORA2A_ENST00000358654.2_Missense_Mutation_p.E648D|SPECC1L_ENST00000541492.1_Missense_Mutation_p.E648D|SPECC1L_ENST00000416735.1_3'UTR	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	648					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						CGTAGGTAGAGGATGAATACC	0.368																																					p.E648D		Atlas-SNP	.											.	SPECC1L	85	.	0			c.G1944T						PASS	.						102	105	104					22																	24720193		2203	4300	6503	SO:0001583	missense	23384	exon5			GGTAGAGGATGAA	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.1944G>T	chr22.hg19:g.24720193G>T	ENSP00000325785:p.Glu648Asp	80.0	0.0	.		86.0	4.0	.	NM_001145468	B7Z758|F5H1H6|O15081	Missense_Mutation	SNP	ENST00000314328.9	hg19	CCDS33619.1	.	.	.	.	.	.	.	.	.	.	G	12.62	1.992942	0.35131	.	.	ENSG00000100014	ENST00000398280;ENST00000437398;ENST00000421374;ENST00000314328;ENST00000541492	T;T;T;T	0.63580	-0.05;2.47;-0.05;2.95	5.42	-0.409	0.12378	.	0.099964	0.64402	D	0.000002	T	0.44871	0.1314	N	0.25890	0.77	0.39772	D	0.972172	B;B	0.24043	0.096;0.0	B;B	0.24006	0.05;0.001	T	0.27773	-1.0064	10	0.45353	T	0.12	-28.2528	10.7545	0.46228	0.5634:0.0:0.4366:0.0	.	648;648	F5H1H6;Q69YQ0	.;CYTSA_HUMAN	D	676;648;648;648;648	ENSP00000393363:E648D;ENSP00000405671:E648D;ENSP00000325785:E648D;ENSP00000439633:E648D	ENSP00000325785:E648D	E	+	3	2	SPECC1L	23050193	0.999000	0.42202	0.995000	0.50966	0.799000	0.45148	0.721000	0.25911	-0.091000	0.12440	-0.469000	0.05056	GAG	.	.	.	none		0.368	SPECC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319986.2	NM_015330		T	24720193	G	T	24720193	3	4	83	1	0	0	0	0	1	0	0	0	4211	991	35	4	1958	4	CYTSA	22	24720193	Missense_Mutation	SNP	G	TCGA-B1-A47O-01A-11D-A25F-10		24720193	26584373	28	5356											
SNIP1	79753	hgsc.bcm.edu	37	chr1	38005993	38005993	+	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	gttggtgtcctcaagaagtgCcccagaaagttcaaagcttg	11	10	11	9	0	2	2	2	0	0	2	3	2	3	2	3	1	2	3	3	1	4	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr1:38005993C>G	ENST00000296215.6	-	3	763	c.691G>C	c.(691-693)Gca>Cca	p.A231P	SNIP1_ENST00000468040.1_5'Flank	NM_024700.3	NP_078976.2	Q8TAD8	SNIP1_HUMAN	Smad nuclear interacting protein 1	231					I-kappaB kinase/NF-kappaB signaling (GO:0007249)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(2)|endometrium(1)|large_intestine(3)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(586;0.0393)				TCAAGAAGTGCCCCAGAAAGT	0.502																																					p.A231P		Atlas-SNP	.											.	SNIP1	44	.	0			c.G691C						PASS	.						66	69	68					1																	38005993		2203	4300	6503	SO:0001583	missense	79753	exon3			GAAGTGCCCCAGA		CCDS419.1	1p34.3	2010-07-06			ENSG00000163877	ENSG00000163877			30587	protein-coding gene	gene with protein product		608241				10887155, 15378006	Standard	NM_024700		Approved		uc001cbi.4	Q8TAD8	OTTHUMG00000004225	ENST00000296215.6:c.691G>C	chr1.hg19:g.38005993C>G	ENSP00000296215:p.Ala231Pro	113.0	0.0	.		118.0	63.0	.	NM_024700	Q96SP9|Q9H9T7	Missense_Mutation	SNP	ENST00000296215.6	hg19	CCDS419.1	.	.	.	.	.	.	.	.	.	.	C	32	5.162524	0.94727	.	.	ENSG00000163877	ENST00000296215;ENST00000436196	T	0.51071	0.72	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.73094	0.3543	M	0.87682	2.9	0.80722	D	1	D	0.69078	0.997	D	0.66602	0.945	T	0.72931	-0.4142	10	0.39692	T	0.17	-4.7851	20.1865	0.98220	0.0:1.0:0.0:0.0	.	231	Q8TAD8	SNIP1_HUMAN	P	231;215	ENSP00000296215:A231P	ENSP00000296215:A231P	A	-	1	0	SNIP1	37778580	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.440000	0.80464	2.775000	0.95449	0.655000	0.94253	GCA	.	.	.	none		0.502	SNIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012169.2	NM_024700		G	38005993	C	G	38005993	3	3	84	1	0	0	0	0	1	0	0	0	14861	739	26	4	507	4	SNIP1	1	38005993	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10		38005993	211244628	1	5357											
FCGR1B	2210	hgsc.bcm.edu	37	chr1	120927211	120927212	+	Frame_Shift_Del	DEL	GC	GC	-																															tttttgttcctgacatttcaGctcttcttctaaatgtctgt																										TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr1:120927211_120927212delGC	ENST00000369384.4	-	5	810_811	c.768_769delGC	c.(766-771)gagctgfs	p.EL256fs	RP11-439A17.10_ENST00000426275.1_RNA|FCGR1B_ENST00000472543.1_5'Flank|RP11-439A17.9_ENST00000457996.1_RNA|FCGR1B_ENST00000369383.4_Frame_Shift_Del_p.EL164fs	NM_001017986.3	NP_001017986.1	Q92637	FCGRB_HUMAN	Fc fragment of IgG, high affinity Ib, receptor (CD64)	256					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)|cytokine-mediated signaling pathway (GO:0019221)|Fc receptor signaling pathway (GO:0038093)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome membrane (GO:0031901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	immunoglobulin receptor activity (GO:0019763)			breast(1)|endometrium(1)|lung(2)	4	all_neural(166;0.181)	all_lung(203;7.27e-05)|Lung NSC(69;0.000389)|all_epithelial(167;0.068)		Lung(183;0.0327)|LUSC - Lung squamous cell carcinoma(189;0.19)	Intravenous Immunoglobulin(DB00028)	TGACATTTCAGCTCTTCTTCTA	0.465																																					p.257_257del		Atlas-INDEL	.											.	FCGR1B	14	.	0			c.769_770del						PASS	.																																			SO:0001589	frameshift_variant	2210	exon5			.		CCDS72844.1, CCDS72845.1, CCDS72846.1	1p11.2	2013-01-11	2005-02-02		ENSG00000198019	ENSG00000198019		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3614	protein-coding gene	gene with protein product		601502	"Fc fragment of IgG, high affinity Ib, receptor for (CD64)"			8697799, 9763663	Standard	NM_001017986		Approved	CD64b	uc001eip.3	Q92637	OTTHUMG00000040903	ENST00000369384.4:c.768_769delGC	chr1.hg19:g.120927211_120927212delGC	ENSP00000358391:p.Glu256fs	611.0	0.0	0		508.0	66.0	0.129921	NM_001017986	Q7KZ13|Q92638	Frame_Shift_Del	DEL	ENST00000369384.4	hg19	CCDS30821.1																																																																																			.	.	.	none		0.465	FCGR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098241.1			-	120927212	GC	-	120927211	7	5	84	1	0	1	0	1	0	0	0	0	5787	962	34	0	77	0	FCGR1B	1	120927211	Frame_Shift_Del	DEL	GC	TCGA-B1-A654-01A-11D-A31X-10	82921218	120927211	128323410	2	5358											
FCGR1A	2209	hgsc.bcm.edu	37	chr1	149762998	149762999	+	Frame_Shift_Del	DEL	GC	GC	-																															gacagacatttagaagaagaGctgaaatgtcaggaacaaaa																										TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr1:149762998_149762999delGC	ENST00000369168.4	+	6	1104_1105	c.1050_1051delGC	c.(1048-1053)gagctgfs	p.EL350fs	RP11-196G18.21_ENST00000420462.1_RNA|RP11-196G18.3_ENST00000428289.1_RNA|HIST2H2BF_ENST00000545683.1_Intron	NM_000566.3	NP_000557.1	P12314	FCGR1_HUMAN	Fc fragment of IgG, high affinity Ia, receptor (CD64)	350					antibody-dependent cellular cytotoxicity (GO:0001788)|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)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intracellular signal transduction (GO:0035556)|phagocytosis, engulfment (GO:0006911)|phagocytosis, recognition (GO:0006910)|positive regulation of phagocytosis (GO:0050766)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation of type III hypersensitivity (GO:0001805)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome membrane (GO:0031901)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	IgG receptor activity (GO:0019770)|receptor signaling protein activity (GO:0005057)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)	10	Breast(34;0.0124)|all_hematologic(923;0.127)				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)|Methyl aminolevulinate(DB00992)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Porfimer(DB00707)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	TAGAAGAAGAGCTGAAATGTCA	0.475																																					p.350_350del		Atlas-INDEL	.											.	FCGR1A	27	.	0			c.1049_1050del						PASS	.																																			SO:0001589	frameshift_variant	2209	exon6			.	BC032634	CCDS933.1	1q21.2-q21.3	2014-09-17	2005-02-02		ENSG00000150337	ENSG00000150337		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3613	protein-coding gene	gene with protein product		146760	"Fc fragment of IgG, high affinity Ia, receptor for (CD64)"			8697799, 9763663	Standard	NM_000566		Approved	CD64, CD64A	uc001esp.4	P12314	OTTHUMG00000012089	ENST00000369168.4:c.1050_1051delGC	chr1.hg19:g.149762998_149762999delGC	ENSP00000358165:p.Glu350fs	431.0	0.0	0		416.0	26.0	0.0625	NM_000566	P12315|Q5QNW7|Q92495|Q92663	Frame_Shift_Del	DEL	ENST00000369168.4	hg19	CCDS933.1																																																																																			.	.	.	none		0.475	FCGR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033446.1	NM_000566		-	149762999	GC	-	149762998	7	5	84	1	0	1	0	1	0	0	0	0	5786	962	34	0	1072	0	FCGR1A	1	149762998	Frame_Shift_Del	DEL	GC	TCGA-B1-A654-01A-11D-A31X-10	28835787	149762998	99487623	3	5359											
CRTC2	200186	hgsc.bcm.edu	37	chr1	153926765	153926765	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctctgggggaggagataagtAggcaggactatagggagagc	12	6	18	5	0	1	2	0	0	1	2	1	6	1	4	0	6	1	2	0	6	4	4			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr1:153926765A>G	ENST00000368633.1	-	4	527	c.400T>C	c.(400-402)Tac>Cac	p.Y134H	CRTC2_ENST00000368630.3_Intron|CRTC2_ENST00000476883.1_5'UTR	NM_181715.2	NP_859066.1	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2	134					gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|histone H3-K9 acetylation (GO:0043970)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cAMP response element binding protein binding (GO:0008140)			NS(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	27	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			GGAGATAAGTAGGCAGGACTA	0.512																																					p.Y134H		Atlas-SNP	.											.	CRTC2	58	.	0			c.T400C						PASS	.						61	54	56					1																	153926765		2203	4300	6503	SO:0001583	missense	200186	exon4			ATAAGTAGGCAGG	AY360172	CCDS30875.1	1q21.3	2008-02-05			ENSG00000160741	ENSG00000160741			27301	protein-coding gene	gene with protein product		608972				14506290, 14536081	Standard	NM_181715		Approved	TORC2	uc021pab.1	Q53ET0	OTTHUMG00000037156	ENST00000368633.1:c.400T>C	chr1.hg19:g.153926765A>G	ENSP00000357622:p.Tyr134His	70.0	0.0	.		46.0	16.0	.	NM_181715	Q6UUV8|Q7Z3X7|Q8N332	Missense_Mutation	SNP	ENST00000368633.1	hg19	CCDS30875.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.253357	0.80135	.	.	ENSG00000160741	ENST00000368633	T	0.38240	1.15	4.89	4.89	0.63831	.	0.000000	0.64402	D	0.000001	T	0.26702	0.0653	M	0.66297	2.02	0.40914	D	0.984258	P	0.38020	0.615	B	0.40134	0.32	T	0.16453	-1.0402	10	0.54805	T	0.06	-12.6013	10.82	0.46599	1.0:0.0:0.0:0.0	.	134	Q53ET0	CRTC2_HUMAN	H	134	ENSP00000357622:Y134H	ENSP00000357622:Y134H	Y	-	1	0	CRTC2	152193389	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	6.516000	0.73755	2.065000	0.61736	0.397000	0.26171	TAC	.	.	.	none		0.512	CRTC2-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090272.3	NM_181715		G	153926765	A	G	153926765	3	3	84	1	0	0	0	0	1	0	0	0	3902	420	15	3	1725	3	CRTC2	1	153926765	Missense_Mutation	SNP	A	TCGA-B1-A654-01A-11D-A31X-10	4163767	153926765	95323856	4	5360											
C1orf27	54953	hgsc.bcm.edu	37	chr1	186355194	186355194	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actttagaactggcaaatgaTtttcaaaatgccctgcgtag	13	12	8	8	1	1	2	1	1	0	1	1	2	1	2	1	1	3	2	1	1	6	5			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr1:186355194T>C	ENST00000287859.6	+	4	434	c.309T>C	c.(307-309)gaT>gaC	p.D103D	C1orf27_ENST00000432021.3_Silent_p.D103D|C1orf27_ENST00000419367.3_Intron|C1orf27_ENST00000367470.3_Silent_p.D103D	NM_017847.5	NP_060317.3	Q5SWX8	ODR4_HUMAN	chromosome 1 open reading frame 27	103						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						TGGCAAATGATTTTCAAAATG	0.289																																					p.D103D		Atlas-SNP	.											.	C1orf27	41	.	0			c.T309C						PASS	.						46	44	44					1																	186355194		1786	4058	5844	SO:0001819	synonymous_variant	54953	exon4			AAATGATTTTCAA	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.309T>C	chr1.hg19:g.186355194T>C		117.0	0.0	.		84.0	37.0	.	NM_001164245	B4DNY0|E9PFR7|Q19CC6|Q8WYB6|Q9BTS2|Q9H6A6|Q9NX06	Silent	SNP	ENST00000287859.6	hg19	CCDS53448.1																																																																																			.	.	.	none		0.289	C1orf27-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086352.2	NM_017847		C	186355194	T	C	186355194	2	2	84	1	0	0	0	0	0	0	0	1	2038	1490	52	3		3	C1orf27	1	186355194	Silent	SNP	T	TCGA-B1-A654-01A-11D-A31X-10	32428429	186355194	62895427	5	5361											
ERCC3	2071	hgsc.bcm.edu	37	chr2	128051097	128051097	+	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	gggcatgcttaccacccagaGgggcctggaggtgtggtcgt	6	8	17	10	1	0	1	0	0	0	1	1	2	0	2	3	6	2	2	3	6	1	1			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr2:128051097G>T	ENST00000285398.2	-	2	320	c.226C>A	c.(226-228)Ctc>Atc	p.L76I	ERCC3_ENST00000493187.2_Missense_Mutation_p.L12I	NM_000122.1	NP_000113.1	P19447	ERCC3_HUMAN	excision repair cross-complementation group 3	76					7-methylguanosine mRNA capping (GO:0006370)|apoptotic process (GO:0006915)|DNA repair (GO:0006281)|DNA topological change (GO:0006265)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA duplex unwinding (GO:0000717)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein localization (GO:0008104)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|response to UV (GO:0009411)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' DNA helicase activity (GO:0043138)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|damaged DNA binding (GO:0003684)|dATP binding (GO:0032564)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|peptide binding (GO:0042277)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	31	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.073)		ACCACCCAGAGGGGCCTGGAG	0.572			"Mis, S"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.L76I		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (B)	2	2q21	2071	"excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing)"		E	.	ERCC3	73	.	0			c.C226A						PASS	.						71	63	66					2																	128051097		2203	4300	6503	SO:0001583	missense	2071	exon2	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	CCCAGAGGGGCCT	M31899	CCDS2144.1	2q21	2014-09-17	2014-03-07		ENSG00000163161	ENSG00000163161		"General transcription factors", "General transcription factor IIH complex subunits"	3435	protein-coding gene	gene with protein product	"xeroderma pigmentosum group B complementing"	133510	"excision repair cross-complementing rodent repair deficiency, complementation group 3"			8202161	Standard	NM_000122		Approved	XPB, BTF2, RAD25, TFIIH, GTF2H	uc002toh.1	P19447	OTTHUMG00000131530	ENST00000285398.2:c.226C>A	chr2.hg19:g.128051097G>T	ENSP00000285398:p.Leu76Ile	59.0	0.0	.		51.0	18.0	.	NM_000122	Q53QM0	Missense_Mutation	SNP	ENST00000285398.2	hg19	CCDS2144.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.575903	0.86645	.	.	ENSG00000163161	ENST00000285398;ENST00000493187	T;T	0.77877	-1.13;-1.13	4.4	4.4	0.53042	.	0.000000	0.85682	D	0.000000	T	0.76695	0.4023	L	0.39020	1.185	0.80722	D	1	B;P	0.36465	0.177;0.554	P;P	0.45946	0.498;0.498	T	0.75303	-0.3365	10	0.33141	T	0.24	-17.9364	17.1634	0.86809	0.0:0.0:1.0:0.0	.	76;76	A8K359;P19447	.;ERCC3_HUMAN	I	76;12	ENSP00000285398:L76I;ENSP00000444796:L12I	ENSP00000285398:L76I	L	-	1	0	ERCC3	127767567	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	6.997000	0.76270	2.277000	0.76020	0.563000	0.77884	CTC	.	.	.	none		0.572	ERCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331028.1	NM_000122		T	128051097	G	T	128051097	3	4	84	1	0	0	0	0	1	0	0	0	5216	1000	35	4	2178	4	ERCC3	2	128051097	Missense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10		128051097	115148276	6	5362											
CHL1	10752	hgsc.bcm.edu	37	chr3	383612	383612	+	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	cagaattagaacacatcgaaCaagatgaaagagtatacatg	20	7	8	6	1	0	5	0	1	0	4	1	6	0	5	0	0	3	1	0	0	8	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr3:383612C>A	ENST00000256509.2	+	7	1168	c.526C>A	c.(526-528)Caa>Aaa	p.Q176K	CHL1_ENST00000397491.2_Missense_Mutation_p.Q176K	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	578	Glu-rich.|Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		ACACATCGAACAAGATGAAAG	0.378																																					p.Q176K		Atlas-SNP	.											.	CHL1	242	.	0			c.C526A						PASS	.						70	64	66					3																	383612		2203	4300	6503	SO:0001583	missense	10752	exon5			ATCGAACAAGATG	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.526C>A	chr3.hg19:g.383612C>A	ENSP00000256509:p.Gln176Lys	199.0	0.0	.		190.0	89.0	.	NM_001253388	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	hg19	CCDS2556.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.654162	0.88056	.	.	ENSG00000134121	ENST00000256509;ENST00000397491;ENST00000435603	T;T;T	0.60672	1.1;1.1;0.17	5.43	5.43	0.79202	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.74566	0.3733	L	0.61387	1.9	0.80722	D	1	D;D;D	0.71674	0.989;0.98;0.998	P;P;D	0.91635	0.87;0.746;0.999	T	0.76337	-0.2996	10	0.87932	D	0	.	17.7511	0.88434	0.0:1.0:0.0:0.0	.	176;176;176	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	K	176	ENSP00000256509:Q176K;ENSP00000380628:Q176K;ENSP00000397445:Q176K	ENSP00000256509:Q176K	Q	+	1	0	CHL1	358612	1.000000	0.71417	0.957000	0.39632	0.774000	0.43823	6.928000	0.75846	2.696000	0.92011	0.591000	0.81541	CAA	.	.	.	none		0.378	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614		A	383612	C	A	383612	3	1	84	1	0	0	0	0	1	0	0	0	3351	479	17	4	544	4	CHL1	3	383612	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10		383612	197638818	7	5363											
FYCO1	79443	hgsc.bcm.edu	37	chr3	46000087	46000087	+	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	0	0	0	0	0	0	0	0	0	acgtagttgttgcagcagtaGtaacagaagatgcggccaca	13	8	12	8	2	0	2	0	0	0	2	0	2	0	2	1	1	4	7	1	1	4	5			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr3:46000087G>C	ENST00000296137.2	-	13	3817	c.3612C>G	c.(3610-3612)taC>taG	p.Y1204*	FYCO1_ENST00000535325.1_Nonsense_Mutation_p.Y1204*|FYCO1_ENST00000438446.1_5'UTR	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	1204					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)		TGCAGCAGTAGTAACAGAAGA	0.547																																					p.Y1204X		Atlas-SNP	.											.	FYCO1	115	.	0			c.C3612G						PASS	.						72	70	71					3																	46000087		2203	4300	6503	SO:0001587	stop_gained	79443	exon13			GCAGTAGTAACAG	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.3612C>G	chr3.hg19:g.46000087G>C	ENSP00000296137:p.Tyr1204*	146.0	0.0	.		117.0	62.0	.	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Nonsense_Mutation	SNP	ENST00000296137.2	hg19	CCDS2734.1	.	.	.	.	.	.	.	.	.	.	G	46	12.162409	0.99642	.	.	ENSG00000163820	ENST00000296137;ENST00000535325	.	.	.	5.74	3.92	0.45320	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-19.7307	10.5363	0.45007	0.1343:0.0:0.8657:0.0	.	.	.	.	X	1204	.	.	Y	-	3	2	FYCO1	45975091	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.280000	0.51677	2.709000	0.92574	0.655000	0.94253	TAC	.	.	.	none		0.547	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513		C	46000087	G	C	46000087	4	2	84	1	0	0	0	0	0	1	0	0	6132	1024	36	4	848	4	FYCO1	3	46000087	Nonsense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	45616475	46000087	152022343	8	5364											
CELSR3	1951	hgsc.bcm.edu	37	chr3	48699894	48699894	+	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	ggacaaagagctaaggctccGccaccgatatgcgcccttgg	10	6	12	13	3	0	1	0	0	0	1	1	3	1	2	4	3	2	2	4	3	3	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr3:48699894G>A	ENST00000164024.4	-	1	454	c.174C>T	c.(172-174)ggC>ggT	p.G58G	RP11-148G20.1_ENST00000421275.1_RNA|CELSR3_ENST00000544264.1_Silent_p.G58G	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	58					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)		CTAAGGCTCCGCCACCGATAT	0.682																																					p.G58G		Atlas-SNP	.											.	CELSR3	237	.	0			c.C174T						PASS	.						21	26	25					3																	48699894		2117	4162	6279	SO:0001819	synonymous_variant	1951	exon1			GGCTCCGCCACCG	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.174C>T	chr3.hg19:g.48699894G>A		61.0	0.0	.		36.0	17.0	.	NM_001407	O75092	Silent	SNP	ENST00000164024.4	hg19	CCDS2775.1																																																																																			.	.	.	none		0.682	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		A	48699894	G	A	48699894	2	1	84	1	0	0	0	0	0	0	0	1	3225	1074	38	1		1	CELSR3	3	48699894	Silent	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	2699807	48699894	149322536	9	5365											
FRMD4B	23150	hgsc.bcm.edu	37	chr3	69230503	69230503	+	Missense_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	aatgtagtaactggaagacgGtggctcctgactctttgagt	10	12	12	7	1	1	3	0	2	1	1	2	4	2	4	1	3	1	3	1	3	4	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr3:69230503G>A	ENST00000398540.3	-	21	2481	c.2398C>T	c.(2398-2400)Ccg>Tcg	p.P800S	FRMD4B_ENST00000478263.1_Missense_Mutation_p.P452S|FRMD4B_ENST00000542259.1_Missense_Mutation_p.P746S	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	800					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)		CTGGAAGACGGTGGCTCCTGA	0.433																																					p.P800S		Atlas-SNP	.											.	FRMD4B	90	.	0			c.C2398T						PASS	.						73	72	73					3																	69230503		1939	4143	6082	SO:0001583	missense	23150	exon21			AAGACGGTGGCTC	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.2398C>T	chr3.hg19:g.69230503G>A	ENSP00000381549:p.Pro800Ser	72.0	0.0	.		102.0	6.0	.	NM_015123	Q8TAI3	Missense_Mutation	SNP	ENST00000398540.3	hg19	CCDS46863.1	.	.	.	.	.	.	.	.	.	.	G	13.15	2.152377	0.38021	.	.	ENSG00000114541	ENST00000398540;ENST00000542259;ENST00000478263	D;D	0.86956	-2.19;-2.18	5.83	4.95	0.65309	.	0.224065	0.47455	D	0.000237	D	0.84813	0.5555	M	0.63843	1.955	0.09310	N	1	B;P	0.42203	0.058;0.773	B;B	0.35114	0.022;0.196	T	0.79351	-0.1839	10	0.72032	D	0.01	-1.8047	16.2232	0.82269	0.0:0.0:0.8659:0.1341	.	644;800	B4DHD5;Q9Y2L6	.;FRM4B_HUMAN	S	800;746;452	ENSP00000381549:P800S;ENSP00000437658:P746S	ENSP00000381549:P800S	P	-	1	0	FRMD4B	69313193	0.959000	0.32827	0.066000	0.19879	0.545000	0.35147	2.106000	0.41835	1.441000	0.47550	-0.293000	0.09583	CCG	.	.	.	none		0.433	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1			A	69230503	G	A	69230503	3	1	84	1	0	0	0	0	1	0	0	0	6059	1261	44	2	718	2	FRMD4B	3	69230503	Missense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	20530609	69230503	128791927	10	5366											
SERPINI2	5276	hgsc.bcm.edu	37	chr3	167189524	167189526	+	In_Frame_Del	DEL	AAG	AAG	-																															gataaggaaacctcttgataAagatccactgcaaattcggt																										TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr3:167189524_167189526delAAG	ENST00000476257.1	-	3	395_397	c.97_99delCTT	c.(97-99)cttdel	p.L33del	SERPINI2_ENST00000465031.1_5'UTR|SERPINI2_ENST00000264677.4_In_Frame_Del_p.L33del|SERPINI2_ENST00000461846.1_In_Frame_Del_p.L33del|SERPINI2_ENST00000471111.1_In_Frame_Del_p.L33del			O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin), member 2	33					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						CCTCTTGATAAAGATCCACTGCA	0.384																																					p.43_44del		Atlas-INDEL	.											.	SERPINI2	85	.	0			c.128_130del						PASS	.																																			SO:0001651	inframe_deletion	5276	exon3			.	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.97_99delCTT	chr3.hg19:g.167189524_167189526delAAG	ENSP00000420621:p.Leu33del	89.0	0.0	0		75.0	35.0	0.466667	NM_001012303		In_Frame_Del	DEL	ENST00000476257.1	hg19	CCDS3200.1																																																																																			.	.	.	none		0.384	SERPINI2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350450.1	NM_006217		-	167189526	AAG	-	167189524	7	5	84	1	0	1	0	1	0	0	0	0	14132	1	1	0	1150	0	SERPINI2	3	167189524	In_Frame_Del	DEL	AAG	TCGA-B1-A654-01A-11D-A31X-10	97959021	167189524	30832906	11	5367											
ADD1	118	hgsc.bcm.edu	37	chr4	2930230	2930232	+	In_Frame_Del	DEL	AAG	AAG	-																															cgtcctttctgaagaagagcAagaagaagagtgactcctga																										TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr4:2930230_2930232delAAG	ENST00000398129.1	+	14	2214_2216	c.2194_2196delAAG	c.(2194-2196)aagdel	p.K734del	ADD1_ENST00000446856.1_In_Frame_Del_p.K734del|ADD1_ENST00000398123.2_3'UTR|ADD1_ENST00000398125.1_3'UTR|ADD1_ENST00000355842.3_3'UTR|ADD1_ENST00000513328.2_3'UTR|ADD1_ENST00000264758.7_In_Frame_Del_p.K765del|ADD1_ENST00000503455.2_3'UTR			P35611	ADDA_HUMAN	adducin 1 (alpha)	734	Interaction with calmodulin. {ECO:0000255}.				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)		GAAGAAGAGCAAGAAGAAGAGTG	0.616																																					p.762_763del	Esophageal Squamous(71;505 1201 20414 34538 37449)	Atlas-Indel,Pindel	.											.	ADD1	56	.	0			c.2286_2288del						PASS	.		,,,	2,4264		0,2,2131					,,,	5.2	1			63	0,8254		0,0,4127	no	utr-3,utr-3,coding,coding	ADD1	NM_176801.2,NM_014190.3,NM_014189.3,NM_001119.4	,,,	0,2,6258	A1A1,A1R,RR		0.0,0.0469,0.016	,,,	,,,		2,12518				SO:0001651	inframe_deletion	118	exon15			.	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.2194_2196delAAG	chr4.hg19:g.2930236_2930238delAAG	ENSP00000381197:p.Lys734del	157.0	0.0	0		117.0	50.0	0.42735	NM_014189	A2A3N8|A2A3P0|B4DI79|D3DVR3|D3DVR4|D3DVR5|Q13734|Q14729|Q16156|Q86XM2|Q9UJB6	In_Frame_Del	DEL	ENST00000398129.1	hg19	CCDS43205.1																																																																																			.	.	.	none		0.616	ADD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242840.1	NM_014189		-	2930232	AAG	-	2930230	7	5	84	1	0	1	0	1	0	0	0	0	304	131	5	0	2379	0	ADD1	4	2930230	In_Frame_Del	DEL	AAG	TCGA-B1-A654-01A-11D-A31X-10		2930230	188224046	12	5368											
AFAP1	60312	hgsc.bcm.edu	37	chr4	7783233	7783233	+	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	tagaggcctttctgtcagcaGgagagtagcgggcaaagatg	11	8	15	7	1	2	3	1	0	1	3	2	4	2	3	1	3	2	3	1	3	3	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr4:7783233G>T	ENST00000360265.4	-	12	1765				AFAP1_ENST00000358461.2_Intron|AFAP1_ENST00000420658.1_Missense_Mutation_p.P551H|AFAP1-AS1_ENST00000608442.1_RNA|AFAP1_ENST00000513842.1_5'UTR|AFAP1_ENST00000382543.3_Missense_Mutation_p.P551H			Q8N556	AFAP1_HUMAN	actin filament associated protein 1							cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(4)|stomach(2)	32						TCTGTCAGCAGGAGAGTAGCG	0.532																																					p.P551H		Atlas-SNP	.											.	AFAP1	93	.	0			c.C1652A						PASS	.						123	119	120					4																	7783233		692	1591	2283	SO:0001627	intron_variant	60312	exon13			TCAGCAGGAGAGT	AB209676	CCDS3397.1, CCDS47010.1	4p16	2014-02-12	2007-02-07		ENSG00000196526	ENSG00000196526		"Pleckstrin homology (PH) domain containing"	24017	protein-coding gene	gene with protein product		608252				14755689, 11641786, 11607843	Standard	NM_198595		Approved	AFAP-110, AFAP	uc011bwk.1	Q8N556	OTTHUMG00000125515	ENST00000360265.4:c.1531-2630C>A	chr4.hg19:g.7783233G>T		121.0	0.0	.		106.0	40.0	.	NM_001134647	A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Missense_Mutation	SNP	ENST00000360265.4	hg19	CCDS3397.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.848151	0.91277	.	.	ENSG00000196526	ENST00000420658;ENST00000382543	T;T	0.16597	2.33;2.33	5.8	5.8	0.92144	.	.	.	.	.	T	0.21427	0.0516	L	0.36672	1.1	0.80722	D	1	D	0.61697	0.99	P	0.45946	0.498	T	0.00287	-1.1846	9	0.45353	T	0.12	.	20.0706	0.97721	0.0:0.0:1.0:0.0	.	551	E9PDT7	.	H	551	ENSP00000410689:P551H;ENSP00000371983:P551H	ENSP00000371983:P551H	P	-	2	0	AFAP1	7834133	1.000000	0.71417	0.588000	0.28705	0.985000	0.73830	7.463000	0.80869	2.744000	0.94065	0.655000	0.94253	CCT	.	.	.	none		0.532	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2	NM_021638		T	7783233	G	T	7783233	1	4	84	0	1	0	0	0	0	0	0	0	353	1000	35	4		4	AFAP1	4	7783233	Intron	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	4853003	7783233	183371043	13	5369											
CTNND2	1501	hgsc.bcm.edu	37	chr5	10992734	10992734	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaggagtagggcctttgcCggtccctctcgatggttgaa	7	10	15	9	2	1	1	0	1	1	0	3	4	2	3	3	5	1	2	3	5	2	3	rs367931998		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr5:10992734C>T	ENST00000304623.8	-	19	3329	c.3140G>A	c.(3139-3141)cGg>cAg	p.R1047Q	CTNND2_ENST00000503622.1_Missense_Mutation_p.R710Q|CTNND2_ENST00000359640.2_Missense_Mutation_p.R989Q|CTNND2_ENST00000495388.2_5'UTR|CTNND2_ENST00000511377.1_Missense_Mutation_p.R956Q|CTNND2_ENST00000458100.2_Missense_Mutation_p.R614Q	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	1047					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						GGGCCTTTGCCGGTCCCTCTC	0.587																																					p.R1047Q		Atlas-SNP	.											CTNND2,mucosal,malignant_melanoma,0,1	CTNND2	289	.	0			c.G3140A						PASS	.						134	120	125					5																	10992734		2203	4300	6503	SO:0001583	missense	1501	exon19			CTTTGCCGGTCCC	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.3140G>A	chr5.hg19:g.10992734C>T	ENSP00000307134:p.Arg1047Gln	47.0	0.0	.		49.0	25.0	.	NM_001332	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Missense_Mutation	SNP	ENST00000304623.8	hg19	CCDS3881.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.691098	0.88735	.	.	ENSG00000169862	ENST00000304623;ENST00000359640;ENST00000511377;ENST00000538638;ENST00000458100;ENST00000503622	T;T;T;T;T	0.79554	-1.22;-1.28;-1.22;-1.25;-1.25	5.18	4.3	0.51218	.	0.063175	0.64402	D	0.000009	D	0.84497	0.5485	L	0.39245	1.2	0.80722	D	1	D;D;D	0.69078	0.997;0.997;0.993	D;D;P	0.70227	0.968;0.968;0.543	D	0.83914	0.0297	10	0.40728	T	0.16	-11.8165	14.9681	0.71210	0.1441:0.8559:0.0:0.0	.	710;639;1047	B4DRK2;B4DG58;Q9UQB3	.;.;CTND2_HUMAN	Q	1047;989;956;142;614;710	ENSP00000307134:R1047Q;ENSP00000352661:R989Q;ENSP00000426510:R956Q;ENSP00000391155:R614Q;ENSP00000426887:R710Q	ENSP00000307134:R1047Q	R	-	2	0	CTNND2	11045734	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.337000	0.79256	1.159000	0.42565	0.650000	0.86243	CGG	.	.	.	weak		0.587	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332		T	10992734	C	T	10992734	3	4	84	1	0	0	0	0	1	0	0	0	4022	652	23	1	553	1	CTNND2	5	10992734	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10		10992734	169922526	14	5370											
PCDHGC5	56097	hgsc.bcm.edu	37	chr5	140870632	140870633	+	Frame_Shift_Ins	INS	-	-	T																															tgcgtggctctcctactcacINStgttgccacagtccacagcc																										TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr5:140870632_140870633insT	ENST00000252087.1	+	1	1825_1826	c.1825_1826insT	c.(1825-1827)ctgfs	p.L609fs	PCDHGA8_ENST00000398604.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGC4_ENST00000306593.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_018929.2|NM_032403.2|NM_032407.1	NP_061752.1|NP_115779.1|NP_115783.1	Q9Y5F6	PCDGM_HUMAN	protocadherin gamma subfamily C, 5	609	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(4)|lung(10)|ovary(4)|prostate(1)|urinary_tract(2)	35			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCCTACTCACTGTTGCCACAG	0.619																																					p.L609fs		Atlas-Indel,Pindel	.											.	PCDHGC5	199	.	0			c.1825_1826insT						PASS	.																																			SO:0001589	frameshift_variant	56097	exon1			.	AF152526	CCDS4263.1, CCDS75350.1	5q31	2010-01-26			ENSG00000240764	ENSG00000240764		"Cadherins / Protocadherins : Clustered"	8718	other	protocadherin		606306				10380929	Standard	NM_018929		Approved	PCDH-GAMMA-C5	uc003lla.2	Q9Y5F6	OTTHUMG00000129624	ENST00000252087.1:c.1826dupT	chr5.hg19:g.140870633_140870633dupT	ENSP00000252087:p.Leu609fs	40.0	0.0	0		38.0	19.0	0.5	NM_018929	Q9Y5C2	Frame_Shift_Ins	INS	ENST00000252087.1	hg19	CCDS4263.1																																																																																			.	.	.	none		0.619	PCDHGC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251819.1	NM_018929		T	140870633	-	T	140870632	7	5	84	1	0	1	1	0	0	0	0	0	11578	564	20	0	1827	0	PCDHGC5	5	140870632	Frame_Shift_Ins	INS	-	TCGA-B1-A654-01A-11D-A31X-10	129877898	140870632	40044628	15	5371											
LARS	51520	hgsc.bcm.edu	37	chr5	145547749	145547751	+	In_Frame_Del	DEL	TCC	TCC	-																															ctgttttaacactggtttctTcctcttcctcttcttcatct																										TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr5:145547749_145547751delTCC	ENST00000394434.2	-	5	538_540	c.372_374delGGA	c.(370-375)gaggaa>gaa	p.124_125EE>E	LARS_ENST00000545646.1_Intron|LARS_ENST00000510191.1_In_Frame_Del_p.70_71EE>E|LARS_ENST00000511505.1_Intron|LARS_ENST00000274562.9_In_Frame_Del_p.97_98EE>E	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	124					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)	ACTGGTTTCTTCCTCTTCCTCTT	0.33																																					p.125_125del		Atlas-Indel,Pindel	.											.	LARS	100	.	0			c.373_375del						PASS	.																																			SO:0001651	inframe_deletion	51520	exon5			.	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.372_374delGGA	chr5.hg19:g.145547749_145547751delTCC	ENSP00000377954:p.Glu126del	105.0	0.0	0		88.0	28.0	0.318182	NM_020117	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	In_Frame_Del	DEL	ENST00000394434.2	hg19	CCDS34265.1																																																																																			.	.	.	none		0.33	LARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000373367.1	NM_020117		-	145547751	TCC	-	145547749	7	5	84	1	0	1	0	1	0	0	0	0	8641	1783	62	0	3268	0	LARS	5	145547749	In_Frame_Del	DEL	TCC	TCGA-B1-A654-01A-11D-A31X-10	4677117	145547749	35367511	16	5372											
MEOX2	4223	hgsc.bcm.edu	37	chr7	15725800	15725800	+	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	tgctgctgatggtggtgatgGtggtggtggtggtggtggtg	2	14	23	2	0	0	2	0	2	0	0	0	2	0	2	0	9	2	2	0	9	0	0	rs113582077	byFrequency	TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr7:15725800G>A	ENST00000262041.5	-	1	637	c.228C>T	c.(226-228)caC>caT	p.H76H	AC005550.5_ENST00000438923.1_lincRNA|AC005550.4_ENST00000442176.1_lincRNA	NM_005924.4	NP_005915.2	P50222	MEOX2_HUMAN	mesenchyme homeobox 2	76	Poly-His.				angiogenesis (GO:0001525)|blood circulation (GO:0008015)|limb development (GO:0060173)|multicellular organismal development (GO:0007275)|neuron death (GO:0070997)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle tissue development (GO:0007519)|somite specification (GO:0001757)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding (GO:0043565)	p.H80delH(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (126;0.0822)		ggtggtgatggtggtggtggt	0.612																																					p.H76H	Esophageal Squamous(140;197 1769 16409 18257 29929)	Atlas-SNP	.											.	MEOX2	68	.	1	Deletion - In frame(1)	stomach(1)	c.C228T						PASS	.						11	13	13					7																	15725800		2192	4293	6485	SO:0001819	synonymous_variant	4223	exon1			GTGATGGTGGTGG		CCDS34605.1	7p22.1-p21.3	2014-07-15	2005-12-22		ENSG00000106511	ENSG00000106511		"Homeoboxes / ANTP class : HOXL subclass"	7014	protein-coding gene	gene with protein product	"growth arrest-specific homeobox"	600535	"mesenchyme homeo box 2 (growth arrest-specific homeo box)", "mesenchyme homeobox 2 (growth arrest-specific homeo box)"	GAX		7713505	Standard	NM_005924		Approved	MOX2	uc003stc.3	P50222	OTTHUMG00000152390	ENST00000262041.5:c.228C>T	chr7.hg19:g.15725800G>A		11.0	0.0	.		35.0	9.0	.	NM_005924	B2R8I7|O75263|Q9UPL6	Silent	SNP	ENST00000262041.5	hg19	CCDS34605.1																																																																																			.	.	.	none		0.612	MEOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326058.2	NM_005924		A	15725800	G	A	15725800	2	1	84	1	0	0	0	0	0	0	0	1	9481	1252	44	2		2	MEOX2	7	15725800	Silent	SNP	G	TCGA-B1-A654-01A-11D-A31X-10		15725800	143412863	17	5373											
DFNA5	1687	hgsc.bcm.edu	37	chr7	24784199	24784199	+	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	acctctcggcagagtctctgAtgagctgctgcaaatccacc	9	9	9	14	1	2	3	0	2	2	1	5	3	3	3	3	1	3	4	3	1	1	0			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr7:24784199A>T	ENST00000342947.3	-	3	811	c.386T>A	c.(385-387)aTc>aAc	p.I129N	DFNA5_ENST00000545231.1_5'UTR|DFNA5_ENST00000409970.1_5'UTR|DFNA5_ENST00000409775.3_Missense_Mutation_p.I129N|DFNA5_ENST00000419307.1_5'UTR	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	129					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						AGAGTCTCTGATGAGCTGCTG	0.507																																					p.I129N	GBM(78;184 1250 20134 20900 23600)	Atlas-SNP	.											.	DFNA5	51	.	0			c.T386A						PASS	.						119	115	116					7																	24784199		2203	4300	6503	SO:0001583	missense	1687	exon3			TCTCTGATGAGCT	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.386T>A	chr7.hg19:g.24784199A>T	ENSP00000339587:p.Ile129Asn	70.0	0.0	.		66.0	12.0	.	NM_001127453	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Missense_Mutation	SNP	ENST00000342947.3	hg19	CCDS5389.1	.	.	.	.	.	.	.	.	.	.	A	17.33	3.361849	0.61403	.	.	ENSG00000105928	ENST00000342947;ENST00000409775	T;T	0.21932	1.98;1.98	5.59	5.59	0.84812	.	0.432748	0.26662	N	0.023150	T	0.42966	0.1226	M	0.67953	2.075	0.80722	D	1	D;D	0.61080	0.989;0.989	D;D	0.63283	0.913;0.913	T	0.22730	-1.0208	10	0.45353	T	0.12	-8.2661	15.7667	0.78131	1.0:0.0:0.0:0.0	.	129;129	A4FTY0;O60443	.;DFNA5_HUMAN	N	129	ENSP00000339587:I129N;ENSP00000386670:I129N	ENSP00000339587:I129N	I	-	2	0	DFNA5	24750724	1.000000	0.71417	0.742000	0.31022	0.252000	0.25951	5.678000	0.68153	2.138000	0.66242	0.528000	0.53228	ATC	.	.	.	none		0.507	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403		T	24784199	A	T	24784199	3	4	84	1	0	0	0	0	1	0	0	0	4456	333	12	5	1136	5	DFNA5	7	24784199	Missense_Mutation	SNP	A	TCGA-B1-A654-01A-11D-A31X-10	9058399	24784199	134354464	18	5374											
POR	5447	hgsc.bcm.edu	37	chr7	75615290	75615290	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacggctgccgccgctcggaTgaggactacctgtaccggga	7	7	14	13	5	0	1	0	1	0	0	1	4	0	4	4	4	4	3	4	4	3	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr7:75615290T>C	ENST00000461988.1	+	14	1824	c.1719T>C	c.(1717-1719)gaT>gaC	p.D573D	POR_ENST00000419840.1_Intron|POR_ENST00000450476.1_Silent_p.D472D|TMEM120A_ENST00000338761.4_RNA|TMEM120A_ENST00000493111.2_RNA|POR_ENST00000394893.1_Silent_p.D573D|POR_ENST00000439269.1_Silent_p.D311D|POR_ENST00000545601.1_Silent_p.D381D	NM_000941.2	NP_000932.3	P16435	NCPR_HUMAN	P450 (cytochrome) oxidoreductase	570					carnitine metabolic process (GO:0009437)|cellular organofluorine metabolic process (GO:0090346)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to peptide hormone stimulus (GO:0071375)|demethylation (GO:0070988)|fatty acid oxidation (GO:0019395)|flavonoid metabolic process (GO:0009812)|internal peptidyl-lysine acetylation (GO:0018393)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of lipase activity (GO:0060192)|nitrate catabolic process (GO:0043602)|nitric oxide catabolic process (GO:0046210)|oxidation-reduction process (GO:0055114)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|regulation of growth plate cartilage chondrocyte proliferation (GO:0003420)|response to drug (GO:0042493)|response to nutrient (GO:0007584)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|hydrolase activity (GO:0016787)|iron ion binding (GO:0005506)|iron-cytochrome-c reductase activity (GO:0047726)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric oxide dioxygenase activity (GO:0008941)			central_nervous_system(1)|endometrium(2)|kidney(2)|lung(3)|ovary(1)	9					Benzphetamine(DB00865)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Ethylmorphine(DB01466)|Flavin adenine dinucleotide(DB03147)|Lipoic Acid(DB00166)|Mitomycin(DB00305)|Nilutamide(DB00665)|Nitrofurantoin(DB00698)	GCCGCTCGGATGAGGACTACC	0.692																																					p.D573D		Atlas-SNP	.											.	POR	46	.	0			c.T1719C						PASS	.						11	17	15					7																	75615290		1973	4109	6082	SO:0001819	synonymous_variant	5447	exon14			CTCGGATGAGGAC	AF258341	CCDS5579.1	7q11.2	2006-12-05			ENSG00000127948	ENSG00000127948			9208	protein-coding gene	gene with protein product		124015				2516426	Standard	NM_000941		Approved	CYPOR, FLJ26468	uc003udy.3	P16435	OTTHUMG00000130413	ENST00000461988.1:c.1719T>C	chr7.hg19:g.75615290T>C		58.0	0.0	.		81.0	18.0	.	NM_000941	Q16455|Q197M5|Q8N181|Q9H3M8|Q9UDT3	Silent	SNP	ENST00000461988.1	hg19	CCDS5579.1	.	.	.	.	.	.	.	.	.	.	T	6.335	0.429939	0.11987	.	.	ENSG00000127948	ENST00000447222	.	.	.	3.59	-1.16	0.09678	.	.	.	.	.	.	.	.	.	.	.	0.41802	D	0.989923	.	.	.	.	.	.	.	.	.	.	.	.	.	-26.2896	4.2567	0.10721	0.1605:0.2767:0.0:0.5628	.	.	.	.	R	624	.	.	X	+	1	0	POR	75453226	0.000000	0.05858	0.885000	0.34714	0.753000	0.42808	-2.270000	0.01167	-0.213000	0.10094	-0.496000	0.04628	TGA	.	.	.	none		0.692	POR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252796.7	NM_000941		C	75615290	T	C	75615290	2	2	84	1	0	0	0	0	0	0	0	1	12264	1461	51	3		3	POR	7	75615290	Silent	SNP	T	TCGA-B1-A654-01A-11D-A31X-10	50831091	75615290	83523373	19	5375											
PTCD1	26024	hgsc.bcm.edu	37	chr7	99022430	99022430	+	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	ccactcaccttcatgtctgtGagaagctgtagaccgtcctt	8	12	8	13	1	3	2	2	1	1	2	4	3	4	2	4	0	1	2	4	0	2	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr7:99022430G>A	ENST00000292478.4	-	6	1975	c.1725C>T	c.(1723-1725)ctC>ctT	p.L575L	ATP5J2-PTCD1_ENST00000413834.1_Silent_p.L624L|PTCD1_ENST00000555673.1_Silent_p.L624L	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	575					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)			TCATGTCTGTGAGAAGCTGTA	0.612																																					p.L624L		Atlas-SNP	.											.	.	.	.	0			c.C1872T						PASS	.						52	53	53					7																	99022430		2203	4300	6503	SO:0001819	synonymous_variant	100526740	exon7			GTCTGTGAGAAGC	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.1725C>T	chr7.hg19:g.99022430G>A		35.0	0.0	.		30.0	9.0	.	NM_001198879	Q3ZB78|Q66K60|Q9UDV2	Silent	SNP	ENST00000292478.4	hg19	CCDS34691.1																																																																																			.	.	.	none		0.612	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1	NM_015545		A	99022430	G	A	99022430	2	1	84	1	0	0	0	0	0	0	0	1	12737	1277	45	2		2	PTCD1	7	99022430	Silent	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	23407140	99022430	60116233	20	5376											
CTSB	1508	hgsc.bcm.edu	37	chr8	11705226	11705226	+	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	tgtaggtcgggctgtagccaGgctcacagatcttgctacac	8	10	12	11	1	2	1	1	0	1	1	3	1	2	1	1	3	3	5	1	3	3	4			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr8:11705226G>T	ENST00000353047.6	-	7	891	c.638C>A	c.(637-639)cCt>cAt	p.P213H	CTSB_ENST00000415599.2_3'UTR|RP11-589N15.2_ENST00000602711.1_RNA|CTSB_ENST00000453527.2_Missense_Mutation_p.P213H|CTSB_ENST00000345125.3_Missense_Mutation_p.P213H|CTSB_ENST00000533455.1_Missense_Mutation_p.P213H|CTSB_ENST00000534510.1_Missense_Mutation_p.P213H|CTSB_ENST00000530640.2_Missense_Mutation_p.P213H|CTSB_ENST00000525076.1_5'Flank|CTSB_ENST00000531089.1_Missense_Mutation_p.P213H|CTSB_ENST00000434271.1_Missense_Mutation_p.P213H	NM_001908.3	NP_001899.1	P07858	CATB_HUMAN	cathepsin B	213					cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|decidualization (GO:0046697)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of apoptotic process (GO:0042981)|regulation of catalytic activity (GO:0050790)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|proteoglycan binding (GO:0043394)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(1)	16	all_epithelial(15;0.205)		STAD - Stomach adenocarcinoma(15;0.00546)	COAD - Colon adenocarcinoma(149;0.184)		GCTGTAGCCAGGCTCACAGAT	0.647																																					p.P213H		Atlas-SNP	.											.	CTSB	24	.	0			c.C638A						PASS	.						109	104	105					8																	11705226		2203	4300	6503	SO:0001583	missense	1508	exon9			TAGCCAGGCTCAC	M14221	CCDS5986.1	8p23.1	2012-10-02			ENSG00000164733	ENSG00000164733	3.4.22.1	"Cathepsins"	2527	protein-coding gene	gene with protein product		116810				8112600, 3463996	Standard	XM_006716244		Approved		uc003wuq.3	P07858	OTTHUMG00000090799	ENST00000353047.6:c.638C>A	chr8.hg19:g.11705226G>T	ENSP00000345672:p.Pro213His	62.0	0.0	.		53.0	24.0	.	NM_147780	B3KQR5|B3KRR5|Q503A6|Q96D87	Missense_Mutation	SNP	ENST00000353047.6	hg19	CCDS5986.1	.	.	.	.	.	.	.	.	.	.	G	14.30	2.493396	0.44352	.	.	ENSG00000164733	ENST00000434271;ENST00000540571;ENST00000353047;ENST00000530640;ENST00000531089;ENST00000453527;ENST00000345125;ENST00000533455;ENST00000534510;ENST00000541328	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	5.17	3.16	0.36331	Peptidase C1A, papain C-terminal (2);	0.662303	0.15592	N	0.254378	D	0.90765	0.7101	M	0.76838	2.35	0.45295	D	0.99829	D;P;P;D;D	0.60575	0.988;0.73;0.85;0.988;0.985	P;P;P;P;P	0.56163	0.752;0.512;0.512;0.723;0.793	D	0.90644	0.4577	10	0.52906	T	0.07	.	12.4013	0.55414	0.0:0.0:0.6427:0.3573	.	150;213;119;213;150	B3KUJ8;A8K2H4;B4DMY4;P07858;F5H2P9	.;.;.;CATB_HUMAN;.	H	213;150;213;213;213;213;213;213;213;119	ENSP00000415889:P213H;ENSP00000345672:P213H;ENSP00000435105:P213H;ENSP00000433215:P213H;ENSP00000409917:P213H;ENSP00000342070:P213H;ENSP00000432244:P213H;ENSP00000434217:P213H	ENSP00000342070:P213H	P	-	2	0	CTSB	11742635	0.137000	0.22531	0.501000	0.27601	0.244000	0.25665	2.483000	0.45233	2.397000	0.81536	0.561000	0.74099	CCT	.	.	.	none		0.647	CTSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207586.3	NM_147780		T	11705226	G	T	11705226	3	4	84	1	0	0	0	0	1	0	0	0	4032	1000	35	4	397	4	CTSB	8	11705226	Missense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10		11705226	134658796	21	5377											
DCAF4L2	138009	hgsc.bcm.edu	37	chr8	88885869	88885869	+	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	gtgcgggtatacccggagctCaggggtcgtcaggcctcgca	6	7	16	12	4	2	0	2	0	0	0	4	1	2	1	2	5	3	3	2	5	2	2			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr8:88885869C>G	ENST00000319675.3	-	1	427	c.331G>C	c.(331-333)Gag>Cag	p.E111Q		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	111										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						ACCCGGAGCTCAGGGGTCGTC	0.542																																					p.E111Q		Atlas-SNP	.											.	DCAF4L2	187	.	0			c.G331C						PASS	.						138	133	135					8																	88885869		2203	4300	6503	SO:0001583	missense	138009	exon1			GGAGCTCAGGGGT	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.331G>C	chr8.hg19:g.88885869C>G	ENSP00000316496:p.Glu111Gln	88.0	0.0	.		85.0	32.0	.	NM_152418		Missense_Mutation	SNP	ENST00000319675.3	hg19	CCDS6245.1	.	.	.	.	.	.	.	.	.	.	C	10.06	1.247732	0.22880	.	.	ENSG00000176566	ENST00000319675	T	0.61510	0.1	1.39	0.34	0.15985	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.699660	0.15847	N	0.241732	T	0.38480	0.1042	L	0.29908	0.895	0.09310	N	1	P	0.37330	0.59	B	0.33846	0.171	T	0.22452	-1.0216	10	0.72032	D	0.01	.	6.1683	0.20402	0.3004:0.6996:0.0:0.0	.	111	Q8NA75	DC4L2_HUMAN	Q	111	ENSP00000316496:E111Q	ENSP00000316496:E111Q	E	-	1	0	DCAF4L2	88954985	0.999000	0.42202	0.001000	0.08648	0.010000	0.07245	1.840000	0.39230	-0.115000	0.11915	0.467000	0.42956	GAG	.	.	.	none		0.542	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418		G	88885869	C	G	88885869	3	3	84	1	0	0	0	0	1	0	0	0	4274	835	29	4	860	4	DCAF4L2	8	88885869	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10	77180643	88885869	57478153	22	5378											
PHYHIPL	84457	hgsc.bcm.edu	37	chr10	60936661	60936661	+	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	ctcaacagccccaccagcccCtgtgaggaggtgatcaaaaa	13	5	9	14	0	2	2	2	2	0	0	2	3	2	3	5	2	3	0	5	2	3	0			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr10:60936661C>A	ENST00000373880.4	+	1	312	c.48C>A	c.(46-48)ccC>ccA	p.P16P	PHYHIPL_ENST00000373878.3_5'Flank|PHYHIPL_ENST00000433653.1_Silent_p.P16P	NM_032439.3	NP_115815.2	Q96FC7	PHIPL_HUMAN	phytanoyl-CoA 2-hydroxylase interacting protein-like	16						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						CCACCAGCCCCTGTGAGGAGG	0.627																																					p.P16P		Atlas-SNP	.											.	PHYHIPL	44	.	0			c.C48A						PASS	.						64	58	60					10																	60936661		2203	4300	6503	SO:0001819	synonymous_variant	84457	exon1			CAGCCCCTGTGAG	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.48C>A	chr10.hg19:g.60936661C>A		40.0	0.0	.		46.0	17.0	.	NM_032439	B7WP61|Q68DF3|Q6UXY3|Q8N3W3|Q96JM9|Q96NP7	Silent	SNP	ENST00000373880.4	hg19	CCDS7254.1																																																																																			.	.	.	none		0.627	PHYHIPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048156.1	NM_032439		A	60936661	C	A	60936661	2	1	84	1	0	0	0	0	0	0	0	1	11874	668	24	4		4	PHYHIPL	10	60936661	Silent	SNP	C	TCGA-B1-A654-01A-11D-A31X-10		60936661	74598086	23	5379											
MRPL11	65003	hgsc.bcm.edu	37	chr11	66204727	66204727	+	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	aaggtcaccaggcctgccacCtctttccctgggaggaagga	9	7	12	13	0	2	0	1	0	1	0	3	3	3	3	5	5	1	0	5	5	2	1			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr11:66204727C>G	ENST00000310999.7	-	4	414	c.321G>C	c.(319-321)gaG>gaC	p.E107D	MRPL11_ENST00000329819.4_Missense_Mutation_p.E107D|MRPL11_ENST00000524576.1_5'UTR|MRPL11_ENST00000430466.2_Missense_Mutation_p.E81D	NM_016050.3	NP_057134.1	Q9Y3B7	RM11_HUMAN	mitochondrial ribosomal protein L11	107					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(3)|lung(2)|ovary(1)|prostate(1)	7						GGCCTGCCACCTCTTTCCCTG	0.547																																					p.E107D		Atlas-SNP	.											.	MRPL11	25	.	0			c.G321C						PASS	.						82	76	78					11																	66204727		2200	4295	6495	SO:0001583	missense	65003	exon4			TGCCACCTCTTTC	AB051338	CCDS8139.1, CCDS8140.1, CCDS44655.1	11q13.2	2012-11-14			ENSG00000174547	ENSG00000174547		"Mitochondrial ribosomal proteins / large subunits"	14042	protein-coding gene	gene with protein product		611826					Standard	XR_247672		Approved		uc001ohz.4	Q9Y3B7	OTTHUMG00000167097	ENST00000310999.7:c.321G>C	chr11.hg19:g.66204727C>G	ENSP00000308897:p.Glu107Asp	38.0	0.0	.		41.0	22.0	.	NM_170739	A6NLT0|A8K219|Q32P46|Q96Q73	Missense_Mutation	SNP	ENST00000310999.7	hg19	CCDS8139.1	.	.	.	.	.	.	.	.	.	.	C	17.48	3.399495	0.62177	.	.	ENSG00000174547	ENST00000310999;ENST00000430466;ENST00000329819	.	.	.	5.79	1.92	0.25849	Ribosomal protein L11, C-terminal (3);	0.099158	0.64402	D	0.000002	T	0.61123	0.2322	L	0.45352	1.415	0.58432	D	0.999993	D;D;D	0.71674	0.993;0.995;0.998	D;D;D	0.71184	0.953;0.962;0.972	T	0.54649	-0.8262	9	0.27785	T	0.31	-33.3697	7.3258	0.26555	0.0:0.5948:0.0:0.4052	.	81;107;107	Q9Y3B7-2;Q9Y3B7;A6NLT0	.;RM11_HUMAN;.	D	107;81;107	.	ENSP00000308897:E107D	E	-	3	2	MRPL11	65961303	0.998000	0.40836	1.000000	0.80357	0.858000	0.48976	0.534000	0.23098	0.384000	0.24942	-0.123000	0.14984	GAG	.	.	.	none		0.547	MRPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393098.2	NM_016050		G	66204727	C	G	66204727	3	3	84	1	0	0	0	0	1	0	0	0	9783	680	24	4	342	4	MRPL11	11	66204727	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10		66204727	68801789	24	5380											
SRGAP1	57522	hgsc.bcm.edu	37	chr12	64377795	64377795	+	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	cggagatgcgagttcagcttCtccaggatctgcaagatttc	9	11	11	10	2	3	2	1	0	2	2	5	5	3	3	1	2	3	3	1	2	1	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr12:64377795C>T	ENST00000355086.3	+	2	660	c.136C>T	c.(136-138)Ctc>Ttc	p.L46F	SRGAP1_ENST00000543397.1_Missense_Mutation_p.L6F|SRGAP1_ENST00000357825.3_Missense_Mutation_p.L46F	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	46	F-BAR domain.|FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		AGTTCAGCTTCTCCAGGATCT	0.428																																					p.L46F		Atlas-SNP	.											.	SRGAP1	146	.	0			c.C136T						PASS	.						105	110	108					12																	64377795		2203	4300	6503	SO:0001583	missense	57522	exon2			CAGCTTCTCCAGG	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.136C>T	chr12.hg19:g.64377795C>T	ENSP00000347198:p.Leu46Phe	84.0	0.0	.		59.0	24.0	.	NM_020762	Q9H8A3|Q9P2P2	Missense_Mutation	SNP	ENST00000355086.3	hg19	CCDS8967.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.872961	0.91664	.	.	ENSG00000196935	ENST00000355086;ENST00000357825;ENST00000543397	T;T;T	0.24151	1.87;1.87;1.87	5.1	5.1	0.69264	Fps/Fes/Fer/CIP4 homology (3);	0.000000	0.31760	U	0.007120	T	0.53190	0.1781	M	0.74389	2.26	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.85130	0.996;0.994;0.997	T	0.52381	-0.8583	9	.	.	.	.	18.9008	0.92442	0.0:1.0:0.0:0.0	.	46;6;46	Q7Z6B7;G5EA48;Q7Z6B7-2	SRGP1_HUMAN;.;.	F	46;46;6	ENSP00000347198:L46F;ENSP00000350480:L46F;ENSP00000437948:L6F	.	L	+	1	0	SRGAP1	62664062	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	7.755000	0.85180	2.548000	0.85928	0.585000	0.79938	CTC	.	.	.	none		0.428	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1			T	64377795	C	T	64377795	3	4	84	1	0	0	0	0	1	0	0	0	15157	913	32	2	142	2	SRGAP1	12	64377795	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10		64377795	69474100	25	5381											
ARL1	400	hgsc.bcm.edu	37	chr12	101799660	101799660	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttctcccacttgtaatctgTacaaaattgtggtttttcct	8	18	5	10	0	2	0	0	0	2	0	4	0	3	0	2	1	1	3	2	1	4	7			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr12:101799660T>C	ENST00000261636.8	-	2	278	c.104A>G	c.(103-105)tAc>tGc	p.Y35C	ARL1_ENST00000536227.1_Missense_Mutation_p.Y18C|RP11-321F8.4_ENST00000547360.1_lincRNA|ARL1_ENST00000551828.1_Missense_Mutation_p.Y18C|ARL1_ENST00000549302.1_5'UTR|ARL1_ENST00000551688.1_Intron|ARL1_ENST00000539055.1_Intron|ARL1_ENST00000551671.1_Missense_Mutation_p.Y35C	NM_001177.4	NP_001168.1	P40616	ARL1_HUMAN	ADP-ribosylation factor-like 1	35					activation of phospholipase D activity (GO:0031584)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|GTP catabolic process (GO:0006184)|protein localization to Golgi apparatus (GO:0034067)|retrograde transport, endosome to Golgi (GO:0042147)|small GTPase mediated signal transduction (GO:0007264)|toxin metabolic process (GO:0009404)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	enzyme activator activity (GO:0008047)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			central_nervous_system(1)|upper_aerodigestive_tract(1)	2		Lung NSC(355;2.1e-05)|Breast(359;0.00015)|Myeloproliferative disorder(1001;0.163)		GBM - Glioblastoma multiforme(134;1.67e-09)|BRCA - Breast invasive adenocarcinoma(302;0.0125)		TTGTAATCTGTACAAAATTGT	0.368																																					p.Y35C		Atlas-SNP	.											.	ARL1	12	.	0			c.A104G						PASS	.						82	73	76					12																	101799660		1850	4074	5924	SO:0001583	missense	400	exon2			AATCTGTACAAAA	BX537387	CCDS44958.1, CCDS73510.1	12q23.3	2014-05-09						"ADP-ribosylation factors-like", "ADP-ribosylation factors"	692	protein-coding gene	gene with protein product		603425					Standard	XM_005268869		Approved	ARFL1	uc001tib.3	P40616	OTTHUMG00000170271	ENST00000261636.8:c.104A>G	chr12.hg19:g.101799660T>C	ENSP00000261636:p.Tyr35Cys	123.0	0.0	.		83.0	39.0	.	NM_001177	B4DWW1|P80417|Q53XB1	Missense_Mutation	SNP	ENST00000261636.8	hg19	CCDS44958.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.691681	0.88735	.	.	ENSG00000120805	ENST00000261636;ENST00000536227;ENST00000551828;ENST00000551671	D;D;D;D	0.82803	-1.65;-1.65;-1.65;-1.65	5.79	5.79	0.91817	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.95069	0.8403	H	0.98818	4.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	D	0.97048	0.9762	10	0.72032	D	0.01	-8.9448	16.1803	0.81892	0.0:0.0:0.0:1.0	.	35;35	F8VYN9;P40616	.;ARL1_HUMAN	C	35;18;18;35	ENSP00000261636:Y35C;ENSP00000441808:Y18C;ENSP00000448850:Y18C;ENSP00000448912:Y35C	ENSP00000261636:Y35C	Y	-	2	0	ARL1	100323791	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.930000	0.87610	2.229000	0.72834	0.524000	0.50904	TAC	.	.	.	none		0.368	ARL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408246.1	NM_001177		C	101799660	T	C	101799660	3	2	84	1	0	0	0	0	1	0	0	0	925	1638	57	3	461	3	ARL1	12	101799660	Missense_Mutation	SNP	T	TCGA-B1-A654-01A-11D-A31X-10	37421865	101799660	32052235	26	5382											
USP30	84749	hgsc.bcm.edu	37	chr12	109490532	109490532	+	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	tgaccgcggccgacagggccAtccagcgcttcctgcggacc	6	5	13	17	5	0	1	0	1	0	0	2	3	2	2	6	3	2	1	6	3	0	1			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr12:109490532A>T	ENST00000257548.5	+	1	142	c.49A>T	c.(49-51)Atc>Ttc	p.I17F	USP30_ENST00000392784.2_Intron|USP30-AS1_ENST00000478808.2_RNA	NM_032663.3	NP_116052.2	Q70CQ3	UBP30_HUMAN	ubiquitin specific peptidase 30	17					mitochondrial fusion (GO:0008053)|mitochondrion degradation (GO:0000422)|protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(7)|kidney(1)|large_intestine(1)|liver(2)|lung(11)|prostate(1)|skin(3)|stomach(2)	28						CGACAGGGCCATCCAGCGCTT	0.741																																					p.I17F		Atlas-SNP	.											.	USP30	48	.	0			c.A49T						PASS	.						6	7	7					12																	109490532		1633	3539	5172	SO:0001583	missense	84749	exon1			AGGGCCATCCAGC	BC022094	CCDS9123.2	12q23.3	2006-01-20	2005-08-08		ENSG00000135093	ENSG00000135093		"Ubiquitin-specific peptidases"	20065	protein-coding gene	gene with protein product		612492	"ubiquitin specific protease 30"			12838346	Standard	XM_005253962		Approved	MGC10702, FLJ40511	uc010sxi.2	Q70CQ3	OTTHUMG00000133613	ENST00000257548.5:c.49A>T	chr12.hg19:g.109490532A>T	ENSP00000257548:p.Ile17Phe	72.0	0.0	.		55.0	26.0	.	NM_032663	Q8WTU7|Q96JX4|Q9BSS3	Missense_Mutation	SNP	ENST00000257548.5	hg19	CCDS9123.2	.	.	.	.	.	.	.	.	.	.	A	20.9	4.071460	0.76301	.	.	ENSG00000135093	ENST00000257548;ENST00000536393	T	0.36699	1.24	4.83	-3.67	0.04476	.	0.525534	0.20286	N	0.095347	T	0.17746	0.0426	N	0.14661	0.345	0.36723	D	0.881283	B	0.02656	0.0	B	0.01281	0.0	T	0.03394	-1.1041	10	0.62326	D	0.03	-15.0275	9.4412	0.38670	0.2273:0.6458:0.0:0.1269	.	17	Q70CQ3	UBP30_HUMAN	F	17	ENSP00000257548:I17F	ENSP00000257548:I17F	I	+	1	0	USP30	107974915	0.830000	0.29337	0.983000	0.44433	0.992000	0.81027	-0.415000	0.07106	-0.293000	0.08986	0.482000	0.46254	ATC	.	.	.	none		0.741	USP30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257733.2	NM_032663		T	109490532	A	T	109490532	3	4	84	1	0	0	0	0	1	0	0	0	17073	217	8	5	51	5	USP30	12	109490532	Missense_Mutation	SNP	A	TCGA-B1-A654-01A-11D-A31X-10	7690872	109490532	24361363	27	5383											
BRCA2	90634	hgsc.bcm.edu	37	chr13	32972588	32972588	+	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	1	0	0	0	0	0	0	0	caaatacgaaacacccataaAgaaaaaagaactgaattctc	22	6	4	9	1	1	3	0	1	1	2	2	4	1	3	1	0	3	0	1	0	10	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr13:32972588A>C	ENST00000380130.2	-	0	3046				BRCA2_ENST00000544455.1_Missense_Mutation_p.K3313T|BRCA2_ENST00000380152.3_Missense_Mutation_p.K3313T	NM_052818.2	NP_438169.2	Q5TBK1	N42L1_HUMAN	NEDD4 binding protein 2-like 1											large_intestine(1)|lung(2)|ovary(1)|skin(1)	5		Lung SC(185;0.0262)		all cancers(112;6.3e-06)|Epithelial(112;3.51e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00607)|BRCA - Breast invasive adenocarcinoma(63;0.0171)		ACACCCATAAAGAAAAAAGAA	0.393																																					p.K3313T		Atlas-SNP	.											.	BRCA2	812	.	0			c.A9938C						PASS	.						69	72	71					13																	32972588		2203	4300	6503	SO:0001628	intergenic_variant	675	exon27			CCATAAAGAAAAA	U50527	CCDS9345.2, CCDS41877.1	13q13.1	2008-11-05			ENSG00000139597	ENSG00000139597			25037	protein-coding gene	gene with protein product	"hypothetical gene CG018"					8812419	Standard	NM_052818		Approved	CG018	uc001uuc.3	Q5TBK1	OTTHUMG00000016697		chr13.hg19:g.32972588A>C		104.0	0.0	.		125.0	51.0	.	NM_000059	A4QN21|Q5TBK0	Missense_Mutation	SNP	ENST00000380130.2	hg19	CCDS9345.2	.	.	.	.	.	.	.	.	.	.	A	16.59	3.166079	0.57476	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.00816	5.66;5.66	5.19	1.43	0.22495	.	0.585853	0.16656	N	0.205002	T	0.02688	0.0081	L	0.55834	1.745	0.29155	N	0.87815	D	0.71674	0.998	P	0.62560	0.904	T	0.30446	-0.9978	10	0.51188	T	0.08	.	8.9414	0.35731	0.7861:0.0:0.2139:0.0	.	3313	P51587	BRCA2_HUMAN	T	3313	ENSP00000369497:K3313T;ENSP00000439902:K3313T	ENSP00000369497:K3313T	K	+	2	0	BRCA2	31870588	0.216000	0.23585	0.108000	0.21378	0.601000	0.36947	2.044000	0.41241	0.111000	0.17947	0.383000	0.25322	AAG	.	.	.	none		0.393	N4BP2L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_052818		C	32972588	A	C	32972588	1	2	84	0	1	0	0	0	0	0	0	0	1501	72	3	5		5	BRCA2	13	32972588	IGR	SNP	A	TCGA-B1-A654-01A-11D-A31X-10		32972588	82197290	28	5384											
SPRY2	10253	hgsc.bcm.edu	37	chr13	80911824	80911824	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcgacccgttgccactcTgagctctggcctccatcagg	5	9	11	16	2	3	1	1	1	2	0	4	2	4	1	4	2	3	3	4	2	0	1			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr13:80911824T>C	ENST00000377102.1	-	2	994	c.17A>G	c.(16-18)cAg>cGg	p.Q6R	SPRY2_ENST00000540649.1_Missense_Mutation_p.Q6R|SPRY2_ENST00000377104.3_Missense_Mutation_p.Q6R			O43597	SPY2_HUMAN	sprouty homolog 2 (Drosophila)	6					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)		GTTGCCACTCTGAGCTCTGGC	0.602																																					p.Q6R		Atlas-SNP	.											.	SPRY2	28	.	0			c.A17G						PASS	.						36	39	38					13																	80911824		2203	4300	6503	SO:0001583	missense	10253	exon2			CCACTCTGAGCTC	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.17A>G	chr13.hg19:g.80911824T>C	ENSP00000366306:p.Gln6Arg	13.0	0.0	.		32.0	17.0	.	NM_005842	B2R9J9|Q5T6Z7	Missense_Mutation	SNP	ENST00000377102.1	hg19	CCDS9463.1	.	.	.	.	.	.	.	.	.	.	T	18.75	3.690500	0.68271	.	.	ENSG00000136158	ENST00000377104;ENST00000377102;ENST00000541655;ENST00000540649	T;T;T	0.57273	0.41;0.41;0.41	5.2	5.2	0.72013	.	0.258022	0.39687	N	0.001300	T	0.58380	0.2118	M	0.70275	2.135	0.58432	D	0.999996	P	0.51791	0.948	P	0.45610	0.487	T	0.66408	-0.5931	10	0.87932	D	0	2.2461	15.1453	0.72647	0.0:0.0:0.0:1.0	.	6	O43597	SPY2_HUMAN	R	6	ENSP00000366308:Q6R;ENSP00000366306:Q6R;ENSP00000439027:Q6R	ENSP00000366306:Q6R	Q	-	2	0	SPRY2	79809825	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.437000	0.80417	1.989000	0.58080	0.529000	0.55759	CAG	.	.	.	none		0.602	SPRY2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045387.1			C	80911824	T	C	80911824	3	2	84	1	0	0	0	0	1	0	0	0	15118	1580	55	3	934	3	SPRY2	13	80911824	Missense_Mutation	SNP	T	TCGA-B1-A654-01A-11D-A31X-10	47939236	80911824	34258054	29	5385											
ITPK1	3705	hgsc.bcm.edu	37	chr14	93408247	93408247	+	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	gaactcgctcacgccctcgtAgcctgggggtgggagagaga	8	6	16	11	3	1	2	1	0	0	2	3	5	1	2	2	3	2	2	2	3	2	1			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr14:93408247A>T	ENST00000267615.6	-	11	1077	c.904T>A	c.(904-906)Tac>Aac	p.Y302N	ITPK1_ENST00000556603.2_Missense_Mutation_p.Y302N|ITPK1_ENST00000354313.3_Intron|ITPK1_ENST00000555495.1_Missense_Mutation_p.Y183N			Q13572	ITPK1_HUMAN	inositol-tetrakisphosphate 1-kinase	302	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.				blood coagulation (GO:0007596)|dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|inositol trisphosphate metabolic process (GO:0032957)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|inositol tetrakisphosphate 1-kinase activity (GO:0047325)|inositol-1,3,4,5,6-pentakisphosphate 1-phosphatase activity (GO:0052825)|inositol-1,3,4,6-tetrakisphosphate 1-phosphatase activity (GO:0052831)|inositol-1,3,4,6-tetrakisphosphate 6-phosphatase activity (GO:0052830)|inositol-1,3,4-trisphosphate 5-kinase activity (GO:0052726)|inositol-1,3,4-trisphosphate 6-kinase activity (GO:0052725)|inositol-3,4,6-trisphosphate 1-kinase activity (GO:0052835)|isomerase activity (GO:0016853)|magnesium ion binding (GO:0000287)			endometrium(1)|large_intestine(3)|lung(6)|ovary(1)	11		all_cancers(154;0.077)|all_epithelial(191;0.247)		Epithelial(152;0.124)|all cancers(159;0.169)		ACGCCCTCGTAGCCTGGGGGT	0.652																																					p.Y302N		Atlas-SNP	.											.	ITPK1	53	.	0			c.T904A						PASS	.						19	15	17					14																	93408247		2087	4121	6208	SO:0001583	missense	3705	exon11			CCTCGTAGCCTGG	U51336	CCDS9907.1, CCDS45157.1	14q32.12	2012-08-16	2011-04-28		ENSG00000100605	ENSG00000100605	2.7.1.134		6177	protein-coding gene	gene with protein product		601838	"inositol 1,3,4-triphosphate 5/6 kinase"			8662638, 11042108	Standard	NM_014216		Approved		uc001ybh.3	Q13572	OTTHUMG00000171226	ENST00000267615.6:c.904T>A	chr14.hg19:g.93408247A>T	ENSP00000267615:p.Tyr302Asn	42.0	0.0	.		31.0	18.0	.	NM_001142593	Q9BTL6|Q9H2E7	Missense_Mutation	SNP	ENST00000267615.6	hg19	CCDS9907.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.272145	0.80469	.	.	ENSG00000100605	ENST00000405174;ENST00000556603;ENST00000555495;ENST00000267615;ENST00000311458	.	.	.	4.59	4.59	0.56863	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);	0.000000	0.85682	D	0.000000	T	0.79764	0.4502	M	0.84082	2.675	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.83445	0.0045	9	0.87932	D	0	-1.445	13.993	0.64378	1.0:0.0:0.0:0.0	.	302	Q13572	ITPK1_HUMAN	N	332;302;183;302;302	.	ENSP00000267615:Y302N	Y	-	1	0	ITPK1	92478000	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	8.912000	0.92726	1.717000	0.51406	0.460000	0.39030	TAC	.	.	.	none		0.652	ITPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412421.2	NM_014216		T	93408247	A	T	93408247	3	4	84	1	0	0	0	0	1	0	0	0	7923	420	15	5	392	5	ITPK1	14	93408247	Missense_Mutation	SNP	A	TCGA-B1-A654-01A-11D-A31X-10		93408247	13941293	30	5386											
WDR20	91833	hgsc.bcm.edu	37	chr14	102675840	102675840	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcagtctcaaatgctggcAgcaaaagcagtgtcatggac	13	7	11	10	0	2	0	2	0	1	0	3	1	2	1	0	2	4	5	0	2	3	0			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr14:102675840A>G	ENST00000342702.3	+	3	1364	c.1333A>G	c.(1333-1335)Agc>Ggc	p.S445G	WDR20_ENST00000424963.2_Missense_Mutation_p.S321G|WDR20_ENST00000499851.2_Missense_Mutation_p.S188G|WDR20_ENST00000454394.2_Missense_Mutation_p.S476G|WDR20_ENST00000299135.6_3'UTR|WDR20_ENST00000556807.1_Missense_Mutation_p.S384G|WDR20_ENST00000556511.2_Missense_Mutation_p.S384G|WDR20_ENST00000322340.5_Intron|WDR20_ENST00000335263.5_Missense_Mutation_p.S445G|WDR20_ENST00000545563.1_Missense_Mutation_p.S272G	NM_001242418.1|NM_144574.3	NP_001229347.1|NP_653175.2	Q8TBZ3	WDR20_HUMAN	WD repeat domain 20	445										breast(1)|large_intestine(2)|lung(4)|prostate(1)	8						AAATGCTGGCAGCAAAAGCAG	0.532											OREG0022939	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S476G		Atlas-SNP	.											.	WDR20	35	.	0			c.A1426G						PASS	.						101	103	102					14																	102675840		2203	4300	6503	SO:0001583	missense	91833	exon4			GCTGGCAGCAAAA	BC028387	CCDS9968.1, CCDS9969.1, CCDS9970.1, CCDS55942.1, CCDS55943.1, CCDS55944.1, CCDS55945.1	14q32.31	2013-01-09				ENSG00000140153		"WD repeat domain containing"	19667	protein-coding gene	gene with protein product							Standard	NM_181291		Approved	DMR, MGC33177, FLJ33659	uc010txu.2	Q8TBZ3		ENST00000342702.3:c.1333A>G	chr14.hg19:g.102675840A>G	ENSP00000341037:p.Ser445Gly	78.0	0.0	.	1368	73.0	31.0	.	NM_001242417	B4DN18|E7EUY8|F8W9S4|G3V2F8|G3V5R0|H0YJJ1|Q86TU2|Q8NCN7|Q8WXX2|Q9UF86	Missense_Mutation	SNP	ENST00000342702.3	hg19	CCDS9969.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.709|6.709	0.499566|0.499566	0.12762|0.12762	.|.	.|.	ENSG00000140153|ENSG00000140153	ENST00000556511|ENST00000335263;ENST00000299135;ENST00000424963;ENST00000342702;ENST00000556807;ENST00000499851;ENST00000454394;ENST00000401892;ENST00000545563	.|T;T;T;T;T;T;T	.|0.67698	.|-0.28;-0.28;-0.28;-0.28;-0.28;-0.28;-0.28	5.73|5.73	5.73|5.73	0.89815|0.89815	.|.	.|0.162599	.|0.64402	.|D	.|0.000002	T|T	0.56277|0.56277	0.1974|0.1974	L|L	0.32530|0.32530	0.975|0.975	0.80722|0.80722	D|D	1|1	.|B;B;B;B;B;B;B	.|0.24882	.|0.001;0.113;0.001;0.0;0.0;0.043;0.0	.|B;B;B;B;B;B;B	.|0.24006	.|0.001;0.05;0.001;0.0;0.002;0.027;0.002	T|T	0.52087|0.52087	-0.8622|-0.8622	5|10	.|0.19590	.|T	.|0.45	.|.	16.0225|16.0225	0.80509|0.80509	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|476;457;384;445;384;321;445	.|E7EUY8;Q5JPH5;G3V2F8;Q8TBZ3-2;F8W9S4;B3KR43;Q8TBZ3	.|.;.;.;.;.;.;WDR20_HUMAN	R|G	375|445;384;321;445;384;188;476;375;272	.|ENSP00000335434:S445G;ENSP00000395793:S321G;ENSP00000341037:S445G;ENSP00000450636:S384G;ENSP00000443641:S188G;ENSP00000406084:S476G;ENSP00000437927:S272G	.|ENSP00000299135:S384G	Q|S	+|+	2|1	0|0	WDR20|WDR20	101745593|101745593	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.951000|0.951000	0.60555|0.60555	7.099000|7.099000	0.76981|0.76981	2.198000|2.198000	0.70561|0.70561	0.533000|0.533000	0.62120|0.62120	CAG|AGC	.	.	.	none		0.532	WDR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414963.1	NM_181291		G	102675840	A	G	102675840	3	3	84	1	0	0	0	0	1	0	0	0	17292	188	7	3	1360	3	WDR20	14	102675840	Missense_Mutation	SNP	A	TCGA-B1-A654-01A-11D-A31X-10	9267593	102675840	4673700	31	5387											
GLCE	26035	hgsc.bcm.edu	37	chr15	69548696	69548696	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaaggctacaatgtggaagTccgagacagagtcaagtgca	14	7	13	7	1	1	3	1	1	0	2	2	5	2	4	1	2	2	2	1	2	5	1			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr15:69548696T>C	ENST00000261858.2	+	3	779	c.551T>C	c.(550-552)gTc>gCc	p.V184A	GLCE_ENST00000559420.2_Missense_Mutation_p.V120A	NM_015554.1	NP_056369.1	O94923	GLCE_HUMAN	glucuronic acid epimerase	184					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						AATGTGGAAGTCCGAGACAGA	0.428																																					p.V184A		Atlas-SNP	.											.	GLCE	48	.	0			c.T551C						PASS	.						101	101	101					15																	69548696		2200	4297	6497	SO:0001583	missense	26035	exon3			TGGAAGTCCGAGA	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.551T>C	chr15.hg19:g.69548696T>C	ENSP00000261858:p.Val184Ala	58.0	0.0	.		46.0	16.0	.	NM_015554	Q6GUQ2	Missense_Mutation	SNP	ENST00000261858.2	hg19	CCDS32277.1	.	.	.	.	.	.	.	.	.	.	T	16.89	3.246289	0.59103	.	.	ENSG00000138604	ENST00000261858	T	0.30714	1.52	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.36880	0.0983	M	0.79475	2.455	0.80722	D	1	B	0.22080	0.064	B	0.17722	0.019	T	0.20207	-1.0282	10	0.41790	T	0.15	-8.6789	14.1808	0.65574	0.0:0.0:0.0:1.0	.	184	O94923	GLCE_HUMAN	A	184	ENSP00000261858:V184A	ENSP00000261858:V184A	V	+	2	0	GLCE	67335750	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.831000	0.86748	2.084000	0.62774	0.533000	0.62120	GTC	.	.	.	none		0.428	GLCE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015554		C	69548696	T	C	69548696	3	2	84	1	0	0	0	0	1	0	0	0	6439	1667	58	3	553	3	GLCE	15	69548696	Missense_Mutation	SNP	T	TCGA-B1-A654-01A-11D-A31X-10		69548696	32982696	32	5388											
MYO9A	4649	hgsc.bcm.edu	37	chr15	72190184	72190184	+	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	gagagaggatggcctctctaCtctttgctttgactgatagg	8	13	12	8	0	2	3	0	2	2	1	3	6	2	4	1	3	2	1	1	3	2	4			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr15:72190184C>G	ENST00000356056.5	-	25	5132	c.4660G>C	c.(4660-4662)Gta>Cta	p.V1554L	MYO9A_ENST00000566885.1_Missense_Mutation_p.V1174L|MYO9A_ENST00000444904.1_Missense_Mutation_p.V1535L|MYO9A_ENST00000424560.1_Missense_Mutation_p.V1554L|MYO9A_ENST00000564571.1_Missense_Mutation_p.V1554L|MYO9A_ENST00000563542.1_5'UTR	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1554	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						GGCCTCTCTACTCTTTGCTTT	0.423																																					p.V1554L		Atlas-SNP	.											.	MYO9A	203	.	0			c.G4660C						PASS	.						76	66	70					15																	72190184		2199	4297	6496	SO:0001583	missense	4649	exon25			TCTCTACTCTTTG	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.4660G>C	chr15.hg19:g.72190184C>G	ENSP00000348349:p.Val1554Leu	76.0	0.0	.		93.0	42.0	.	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	hg19	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	C	10.20	1.285329	0.23478	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	D;D;D	0.83992	-1.79;-1.79;-1.79	5.92	1.58	0.23477	.	.	.	.	.	T	0.66597	0.2805	L	0.27053	0.805	0.09310	N	1	B;B;B	0.12013	0.001;0.005;0.001	B;B;B	0.08055	0.002;0.003;0.001	T	0.50583	-0.8811	9	0.30078	T	0.28	.	0.594	0.00733	0.2435:0.3197:0.1226:0.3143	.	1535;1554;1554	B2RTY4-2;B2RTY4-4;B2RTY4	.;.;MYO9A_HUMAN	L	1554;1554;1535	ENSP00000348349:V1554L;ENSP00000399162:V1554L;ENSP00000398250:V1535L	ENSP00000348349:V1554L	V	-	1	0	MYO9A	69977238	0.001000	0.12720	0.003000	0.11579	0.983000	0.72400	0.281000	0.18810	0.024000	0.15214	0.650000	0.86243	GTA	.	.	.	none		0.423	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		G	72190184	C	G	72190184	3	3	84	1	0	0	0	0	1	0	0	0	10091	565	20	4	3058	4	MYO9A	15	72190184	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10	2641488	72190184	30341208	33	5389											
TMEM202	338949	hgsc.bcm.edu	37	chr15	72698982	72698982	+	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	ggccttctttctcatctctgTctttaccatacttactggcc	5	17	5	14	0	4	0	1	0	4	0	6	0	4	0	3	2	3	0	3	2	3	6			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr15:72698982T>A	ENST00000341689.3	+	3	431	c.377T>A	c.(376-378)gTc>gAc	p.V126D	TMEM202_ENST00000567679.1_Missense_Mutation_p.S41T	NM_001080462.1	NP_001073931.1	A6NGA9	TM202_HUMAN	transmembrane protein 202	126						integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	18						CTCATCTCTGTCTTTACCATA	0.468																																					p.V126D		Atlas-SNP	.											.	TMEM202	40	.	0			c.T377A						PASS	.						180	160	167					15																	72698982		2199	4297	6496	SO:0001583	missense	338949	exon3			TCTCTGTCTTTAC		CCDS32287.1	15q24.1	2007-12-18				ENSG00000187806			33733	protein-coding gene	gene with protein product							Standard	NM_001080462		Approved	FLJ27523	uc002auq.3	A6NGA9		ENST00000341689.3:c.377T>A	chr15.hg19:g.72698982T>A	ENSP00000340212:p.Val126Asp	124.0	0.0	.		115.0	55.0	.	NM_001080462		Missense_Mutation	SNP	ENST00000341689.3	hg19	CCDS32287.1	.	.	.	.	.	.	.	.	.	.	T	12.61	1.990387	0.35131	.	.	ENSG00000187806	ENST00000341689	T	0.66815	-0.23	5.42	1.84	0.25277	.	1.663070	0.03249	N	0.181492	T	0.71459	0.3342	L	0.53249	1.67	0.09310	N	1	P	0.47191	0.891	P	0.51355	0.667	T	0.54214	-0.8327	10	0.87932	D	0	-26.7102	6.0845	0.19960	0.0:0.3095:0.0:0.6905	.	126	A6NGA9	TM202_HUMAN	D	126	ENSP00000340212:V126D	ENSP00000340212:V126D	V	+	2	0	TMEM202	70486036	0.002000	0.14202	0.000000	0.03702	0.006000	0.05464	0.033000	0.13754	0.514000	0.28300	0.533000	0.62120	GTC	.	.	.	none		0.468	TMEM202-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435756.1	NM_001080462		A	72698982	T	A	72698982	3	1	84	1	0	0	0	0	1	0	0	0	16139	1667	58	5	387	5	TMEM202	15	72698982	Missense_Mutation	SNP	T	TCGA-B1-A654-01A-11D-A31X-10	508798	72698982	29832410	34	5390											
SCAMP5	192683	hgsc.bcm.edu	37	chr15	75309011	75309011	+	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	gcgggggagccaccaactttGgcctcgcctttctctggctc	4	10	12	15	2	1	0	0	0	1	0	4	1	1	1	4	4	2	1	4	4	1	2			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr15:75309011G>T	ENST00000361900.6	+	5	421	c.214G>T	c.(214-216)Ggc>Tgc	p.G72C	SCAMP5_ENST00000545456.1_Intron|SCAMP5_ENST00000565923.1_3'UTR|SCAMP5_ENST00000562212.1_Missense_Mutation_p.G72C|SCAMP5_ENST00000425597.3_Missense_Mutation_p.G72C|SCAMP5_ENST00000568081.1_5'Flank	NM_001178111.1	NP_001171582.1	Q8TAC9	SCAM5_HUMAN	secretory carrier membrane protein 5	72					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						CACCAACTTTGGCCTCGCCTT	0.602																																					p.G72C		Atlas-SNP	.											.	SCAMP5	34	.	0			c.G214T						PASS	.						138	140	139					15																	75309011		2150	4256	6406	SO:0001583	missense	192683	exon5			AACTTTGGCCTCG	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.214G>T	chr15.hg19:g.75309011G>T	ENSP00000355387:p.Gly72Cys	47.0	0.0	.		39.0	17.0	.	NM_001178111	B3KPJ7|B7Z762|D3DW71|Q8N3M4	Missense_Mutation	SNP	ENST00000361900.6	hg19	CCDS45306.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.024083	0.93462	.	.	ENSG00000198794	ENST00000361900;ENST00000425597	T;T	0.20332	2.08;2.08	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.56381	0.1981	M	0.90977	3.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.68194	-0.5473	10	0.87932	D	0	-0.2016	17.294	0.87164	0.0:0.0:1.0:0.0	.	72;72	Q8TAC9-2;Q8TAC9	.;SCAM5_HUMAN	C	72	ENSP00000355387:G72C;ENSP00000406547:G72C	ENSP00000355387:G72C	G	+	1	0	SCAMP5	73096064	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.690000	0.98676	2.391000	0.81399	0.561000	0.74099	GGC	.	.	.	none		0.602	SCAMP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420015.2	NM_138967		T	75309011	G	T	75309011	3	4	84	1	0	0	0	0	1	0	0	0	13887	1348	47	4	224	4	SCAMP5	15	75309011	Missense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	2610029	75309011	27222381	35	5391											
RPS2	6187	hgsc.bcm.edu	37	chr16	2014483	2014484	+	In_Frame_Ins	INS	-	-	CGGCCT																															ccttgcctccgcgagctccgINScggcctcggccccggccccg																										TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr16:2014483_2014484insCGGCCT	ENST00000343262.4	-	2	199_200	c.143_144insAGGCCG	c.(142-144)cgc>cgAGGCCGc	p.48_48R>RGR	SNORA10_ENST00000384084.1_RNA|SNORA64_ENST00000384674.1_RNA|RPS2_ENST00000526522.1_In_Frame_Ins_p.48_48R>RGR|SNHG9_ENST00000459373.1_lincRNA|RNF151_ENST00000569714.1_5'Flank|RNF151_ENST00000321392.3_5'Flank|RPS2_ENST00000529806.1_In_Frame_Ins_p.48_48R>RGR|RNF151_ENST00000569210.2_5'Flank|RPS2_ENST00000530225.1_In_Frame_Ins_p.48_48R>RGR	NM_002952.3	NP_002943.2	P15880	RS2_HUMAN	ribosomal protein S2	48	Arg/Gly-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)|positive regulation of transferase activity (GO:0051347)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|urinary_tract(2)	7						CGCGAGCTCCGCGGCCTCGGCC	0.757																																					p.R48delinsRGR		Atlas-INDEL	.											.	RPS2	18	.	0			c.144_145insAGGCCG						PASS	.																																			SO:0001652	inframe_insertion	6187	exon2			.	AB007147	CCDS10452.1	16p13.3	2011-04-05			ENSG00000140988	ENSG00000140988		"S ribosomal proteins"	10404	protein-coding gene	gene with protein product		603624				9582194	Standard	NM_002952		Approved	LLREP3, S2	uc002cno.2	P15880	OTTHUMG00000128708	ENST00000343262.4:c.138_143dupAGGCCG	chr16.hg19:g.2014484_2014489dupCGGCCT	ENSP00000341885:p.GlyArg48dup	55.0	0.0	0		59.0	19.0	0.322034	NM_002952	B2R5G0|D3DU82|Q3MIB1	In_Frame_Ins	INS	ENST00000343262.4	hg19	CCDS10452.1																																																																																			.	.	.	none		0.757	RPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250613.2	NM_002952		CGGCCT	2014484	-	CGGCCT	2014483	7	5	84	1	0	1	1	0	0	0	0	0	13644	1074	38	0	761	0	RPS2	16	2014483	In_Frame_Ins	INS	-	TCGA-B1-A654-01A-11D-A31X-10		2014483	88340270	36	5392											
LCAT	3931	hgsc.bcm.edu	37	chr16	67976796	67976796	+	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	tgctgtccaggtactccacaGagtaggtcttgccaaagcca	10	9	10	12	0	1	1	0	0	1	1	3	1	3	1	4	2	4	3	4	2	3	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr16:67976796G>T	ENST00000264005.5	-	3	424	c.395C>A	c.(394-396)tCt>tAt	p.S132Y	CTC-479C5.17_ENST00000590594.1_lincRNA	NM_000229.1	NP_000220.1	P04180	LCAT_HUMAN	lecithin-cholesterol acyltransferase	132					cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|high-density lipoprotein particle remodeling (GO:0034375)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein metabolic process (GO:0042157)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|regulation of high-density lipoprotein particle assembly (GO:0090107)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle remodeling (GO:0034372)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)	apolipoprotein A-I binding (GO:0034186)|phosphatidylcholine-sterol O-acyltransferase activity (GO:0004607)			cervix(4)|endometrium(4)|large_intestine(1)|lung(6)|ovary(1)	16		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00418)|Epithelial(162;0.0183)|all cancers(182;0.12)		GTACTCCACAGAGTAGGTCTT	0.662																																					p.S132Y		Atlas-SNP	.											.	LCAT	31	.	0			c.C395A						PASS	.						62	68	66					16																	67976796		2198	4300	6498	SO:0001583	missense	3931	exon3			TCCACAGAGTAGG		CCDS10854.1	16q22.1	2012-10-02			ENSG00000213398	ENSG00000213398	2.3.1.43		6522	protein-coding gene	gene with protein product		606967					Standard	NM_000229		Approved		uc002euy.1	P04180	OTTHUMG00000137551	ENST00000264005.5:c.395C>A	chr16.hg19:g.67976796G>T	ENSP00000264005:p.Ser132Tyr	40.0	0.0	.		29.0	12.0	.	NM_000229	Q53XQ3	Missense_Mutation	SNP	ENST00000264005.5	hg19	CCDS10854.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.685825	0.88639	.	.	ENSG00000213398	ENST00000264005	D	0.97161	-4.27	5.98	5.98	0.97165	.	0.138327	0.49916	U	0.000130	D	0.98573	0.9523	M	0.91920	3.255	0.46654	D	0.999148	D	0.52996	0.957	P	0.59171	0.853	D	0.99257	1.0889	10	0.87932	D	0	-13.366	18.0148	0.89236	0.0:0.0:1.0:0.0	.	132	P04180	LCAT_HUMAN	Y	132	ENSP00000264005:S132Y	ENSP00000264005:S132Y	S	-	2	0	LCAT	66534297	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.289000	0.96061	2.861000	0.98227	0.650000	0.86243	TCT	.	.	.	none		0.662	LCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268885.3			T	67976796	G	T	67976796	3	4	84	1	0	0	0	0	1	0	0	0	8665	942	33	4	943	4	LCAT	16	67976796	Missense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	65962313	67976796	22377957	37	5393											
BCL6B	255877	hgsc.bcm.edu	37	chr17	6928020	6928031	+	In_Frame_Del	DEL	CAGCAGCAGCAG	CAGCAGCAGCAG	-																															cccagtggagacgaggcctcCagcagcagcagcagcagcag																								rs72254884|rs386385552		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	CAGCAGCAGCAG	CAGCAGCAGCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr17:6928020_6928031delCAGCAGCAGCAG	ENST00000293805.5	+	4	794_805	c.702_713delCAGCAGCAGCAG	c.(700-714)tccagcagcagcagc>tcc	p.234_238SSSSS>S		NM_181844.3	NP_862827	Q8N143	BCL6B_HUMAN	B-cell CLL/lymphoma 6, member B	234	Ser-rich.				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						ACGAGGCCTCcagcagcagcagcagcagcagc	0.59																																					p.234_238del		Pindel	.											.,22	BCL6B	85	.	0			c.701_712del						PASS	.																																			SO:0001651	inframe_deletion	255877	exon4			.	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.702_713delCAGCAGCAGCAG	chr17.hg19:g.6928020_6928031delCAGCAGCAGCAG	ENSP00000293805:p.Ser238_Ser241del	64.0	0.0	.		67.0	23.0	0.343	NM_181844	Q6PCB4	In_Frame_Del	DEL	ENST00000293805.5	hg19	CCDS42248.1																																																																																			.	.	.	alt		0.59	BCL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439455.2	NM_181844		-	6928031	CAGCAGCAGCAG	-	6928020	7	5	84	1	0	1	0	1	0	0	0	0	1377	581	21	0	712	0	BCL6B	17	6928020	In_Frame_Del	DEL	CAGCAGCAGCAG	TCGA-B1-A654-01A-11D-A31X-10		6928020	74267190	38	5394											
TMEM104	54868	hgsc.bcm.edu	37	chr17	72781730	72781730	+	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	cctcgtcctgctggtgttccTgggcttcatgaggtgagagg	4	12	15	10	1	1	2	1	2	0	1	4	3	3	2	3	4	1	3	3	4	0	2			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr17:72781730T>A	ENST00000335464.5	+	3	317	c.155T>A	c.(154-156)cTg>cAg	p.L52Q	TMEM104_ENST00000582330.1_Missense_Mutation_p.L52Q|TMEM104_ENST00000582773.1_Missense_Mutation_p.L52Q|TMEM104_ENST00000417024.2_Intron	NM_017728.3	NP_060198.3	Q8NE00	TM104_HUMAN	transmembrane protein 104	52						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)					CTGGTGTTCCTGGGCTTCATG	0.632																																					p.L52Q		Atlas-SNP	.											.	TMEM104	49	.	0			c.T155A						PASS	.						76	56	63					17																	72781730		2203	4300	6503	SO:0001583	missense	54868	exon3			TGTTCCTGGGCTT	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.155T>A	chr17.hg19:g.72781730T>A	ENSP00000334849:p.Leu52Gln	52.0	0.0	.		60.0	34.0	.	NM_017728	Q8TEU1|Q9NT56|Q9NXH1	Missense_Mutation	SNP	ENST00000335464.5	hg19	CCDS32723.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.482735	0.84747	.	.	ENSG00000109066	ENST00000335464	T	0.02498	4.27	4.98	4.98	0.66077	.	0.074254	0.53938	D	0.000043	T	0.16769	0.0403	M	0.84585	2.705	0.80722	D	1	D;D	0.76494	0.966;0.999	P;D	0.71656	0.869;0.974	T	0.00624	-1.1639	10	0.72032	D	0.01	-10.1576	14.642	0.68732	0.0:0.0:0.0:1.0	.	52;52	Q8NE00-2;Q8NE00	.;TM104_HUMAN	Q	52	ENSP00000334849:L52Q	ENSP00000334849:L52Q	L	+	2	0	TMEM104	70293325	1.000000	0.71417	1.000000	0.80357	0.785000	0.44390	7.568000	0.82369	1.872000	0.54250	0.260000	0.18958	CTG	.	.	.	none		0.632	TMEM104-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444442.1	NM_017728		A	72781730	T	A	72781730	3	1	84	1	0	0	0	0	1	0	0	0	16030	1580	55	5	161	5	TMEM104	17	72781730	Missense_Mutation	SNP	T	TCGA-B1-A654-01A-11D-A31X-10	65853710	72781730	8413480	39	5395											
ACSBG2	81616	hgsc.bcm.edu	37	chr19	6165945	6165945	+	Frame_Shift_Del	DEL	G	G	-																															gagcaggtcatcgagagccaGaaggcgaatcaatgcgcagt																										TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr19:6165945delG	ENST00000586696.1	+	7	933	c.657delG	c.(655-657)cagfs	p.Q219fs	ACSBG2_ENST00000252669.5_Frame_Shift_Del_p.Q219fs|ACSBG2_ENST00000591403.1_Frame_Shift_Del_p.Q219fs|ACSBG2_ENST00000588485.1_Frame_Shift_Del_p.Q32fs|ACSBG2_ENST00000588304.1_Frame_Shift_Del_p.Q169fs|ACSBG2_ENST00000591741.1_3'UTR			Q5FVE4	ACBG2_HUMAN	acyl-CoA synthetase bubblegum family member 2	219					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid metabolic process (GO:0001676)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(3)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TCGAGAGCCAGAAGGCGAATC	0.517											OREG0025194	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q219fs		Atlas-Indel,Pindel	.											.	ACSBG2	83	.	0			c.656delA						PASS	.						163	130	141					19																	6165945		2203	4300	6503	SO:0001589	frameshift_variant	81616	exon7			.		CCDS12159.1, CCDS74269.1	19p13.3	2012-10-02			ENSG00000130377	ENSG00000130377		"Acyl-CoA synthetase family"	24174	protein-coding gene	gene with protein product	"bubblegum related protein"	614363				11230166	Standard	XM_005259653		Approved	BGR, PRTD-NY3, DKFZp434K1635	uc002meh.1	Q5FVE4	OTTHUMG00000180754	ENST00000586696.1:c.657delG	chr19.hg19:g.6165945delG	ENSP00000465589:p.Gln219fs	70.0	0.0	0	632	56.0	18.0	0.321429	NM_030924	B3KSF2|Q6UWJ3|Q7Z5A0|Q8WW03|Q96M36|Q9BYZ3|Q9H0C4	Frame_Shift_Del	DEL	ENST00000586696.1	hg19	CCDS12159.1																																																																																			.	.	.	none		0.517	ACSBG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452898.1	NM_030924		-	6165945	G	-	6165945	7	5	84	1	0	1	0	1	0	0	0	0	174	933	33	0	679	0	ACSBG2	19	6165945	Frame_Shift_Del	DEL	G	TCGA-B1-A654-01A-11D-A31X-10		6165945	52963038	40	5396											
ACER1	125981	hgsc.bcm.edu	37	chr19	6312214	6312214	+	Missense_Mutation	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	ggggcatccatatgctatagCcactgcccaggagccacagg	10	6	12	13	0	0	0	0	0	0	0	1	1	1	1	4	4	4	2	4	4	3	3			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr19:6312214C>T	ENST00000301452.4	-	3	373	c.296G>A	c.(295-297)gGc>gAc	p.G99D		NM_133492.2	NP_597999.1	Q8TDN7	ACER1_HUMAN	alkaline ceramidase 1	99					cell differentiation (GO:0030154)|cellular response to calcium ion (GO:0071277)|ceramide catabolic process (GO:0046514)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)|regulation of lipid metabolic process (GO:0019216)|response to alkaline pH (GO:0010446)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ceramidase activity (GO:0017040)|dihydroceramidase activity (GO:0071633)			NS(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|pancreas(1)	15						TATGCTATAGCCACTGCCCAG	0.607																																					p.G99D		Atlas-SNP	.											.	ACER1	38	.	0			c.G296A						PASS	.						59	51	54					19																	6312214		2203	4300	6503	SO:0001583	missense	125981	exon3			CTATAGCCACTGC	AF347024	CCDS12161.1	19p13.3	2013-01-25	2008-12-19	2008-12-19	ENSG00000167769	ENSG00000167769	3.5.1.23	"Alkaline ceramidase"	18356	protein-coding gene	gene with protein product		613491	"N-acylsphingosine amidohydrolase (alkaline ceramidase) 3"	ASAH3		12783875	Standard	NM_133492		Approved		uc002mel.2	Q8TDN7		ENST00000301452.4:c.296G>A	chr19.hg19:g.6312214C>T	ENSP00000301452:p.Gly99Asp	87.0	0.0	.		68.0	24.0	.	NM_133492		Missense_Mutation	SNP	ENST00000301452.4	hg19	CCDS12161.1	.	.	.	.	.	.	.	.	.	.	C	8.699	0.909265	0.17833	.	.	ENSG00000167769	ENST00000301452	T	0.42900	0.96	5.13	0.47	0.16747	.	0.527539	0.21637	N	0.071397	T	0.37210	0.0995	M	0.73598	2.24	0.22851	N	0.998658	P	0.42518	0.782	B	0.39503	0.301	T	0.32561	-0.9902	10	0.72032	D	0.01	-15.663	4.4791	0.11759	0.278:0.5108:0.1345:0.0768	.	99	Q8TDN7	ACER1_HUMAN	D	99	ENSP00000301452:G99D	ENSP00000301452:G99D	G	-	2	0	ACER1	6263214	0.936000	0.31750	0.029000	0.17559	0.086000	0.17979	1.990000	0.40717	-0.045000	0.13468	-1.740000	0.00687	GGC	.	.	.	none		0.607	ACER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452982.1	NM_133492		T	6312214	C	T	6312214	3	4	84	1	0	0	0	0	1	0	0	0	138	739	26	2	514	2	ACER1	19	6312214	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10	146269	6312214	52816769	41	5397											
C21orf2	755	hgsc.bcm.edu	37	chr21	45750162	45750162	+	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	tgctgcacggcctccagcccCtctgcatccagctcccgcag	5	7	9	20	2	1	0	0	0	1	0	4	0	4	0	6	1	5	5	6	1	0	0			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr21:45750162C>A	ENST00000339818.4	-	7	897	c.690G>T	c.(688-690)gaG>gaT	p.E230D	C21orf2_ENST00000325223.7_Missense_Mutation_p.E229D|C21orf2_ENST00000397956.3_Missense_Mutation_p.E349D|C21orf2_ENST00000496321.1_5'UTR|AP001062.7_ENST00000448927.1_RNA|AP001062.8_ENST00000422357.1_RNA	NM_001271440.1|NM_004928.2	NP_001258369.1|NP_004919.1	O43822	CU002_HUMAN	chromosome 21 open reading frame 2	230					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)		CCTCCAGCCCCTCTGCATCCA	0.697																																					p.E349D		Atlas-SNP	.											.	C21orf2	10	.	0			c.G1047T						PASS	.						15	15	15					21																	45750162		2189	4284	6473	SO:0001583	missense	755	exon7			CAGCCCCTCTGCA	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.690G>T	chr21.hg19:g.45750162C>A	ENSP00000344566:p.Glu230Asp	46.0	0.0	.		55.0	23.0	.	NM_001271441	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Missense_Mutation	SNP	ENST00000339818.4	hg19	CCDS13709.1	.	.	.	.	.	.	.	.	.	.	C	18.28	3.589994	0.66105	.	.	ENSG00000160226	ENST00000339818;ENST00000397956;ENST00000325223	T;T;T	0.50813	1.46;0.73;1.47	5.13	3.29	0.37713	.	0.111298	0.64402	D	0.000014	T	0.57242	0.2040	M	0.69823	2.125	0.34719	D	0.728514	D;D;D;D	0.67145	0.986;0.996;0.976;0.986	P;P;P;P	0.58266	0.737;0.836;0.551;0.737	T	0.65747	-0.6093	10	0.29301	T	0.29	-28.6583	9.0929	0.36621	0.0:0.8222:0.0:0.1778	.	229;349;230;189	G5E952;Q8N5X6;O43822;O43822-2	.;.;CU002_HUMAN;.	D	230;349;229	ENSP00000344566:E230D;ENSP00000381047:E349D;ENSP00000317302:E229D	ENSP00000317302:E229D	E	-	3	2	C21orf2	44574590	1.000000	0.71417	0.986000	0.45419	0.343000	0.28985	2.457000	0.45005	1.153000	0.42468	0.655000	0.94253	GAG	.	.	.	none		0.697	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928		A	45750162	C	A	45750162	3	1	84	1	0	0	0	0	1	0	0	0	2125	680	24	4	84	4	C21orf2	21	45750162	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10		45750162	2379733	42	5398											
MN1	4330	hgsc.bcm.edu	37	chr22	28192976	28192976	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcccctgaggccccgacggCgcactcacccttcttgccac	5	6	9	21	4	2	1	1	1	1	0	2	2	2	1	6	2	1	1	6	2	0	2			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chr22:28192976C>T	ENST00000302326.4	-	1	4510	c.3556G>A	c.(3556-3558)Gcc>Acc	p.A1186T		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	1186					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						GCCCCGACGGCGCACTCACCC	0.647			T	ETV6	"AML, meningioma"																																p.A1186T		Atlas-SNP	.		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"L, O"	.	MN1	122	.	0			c.G3556A						PASS	.						18	20	19					22																	28192976		2099	4221	6320	SO:0001583	missense	4330	exon1			CGACGGCGCACTC	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.3556G>A	chr22.hg19:g.28192976C>T	ENSP00000304956:p.Ala1186Thr	26.0	0.0	.		35.0	16.0	.	NM_002430	A9Z1V9	Missense_Mutation	SNP	ENST00000302326.4	hg19	CCDS42998.1	.	.	.	.	.	.	.	.	.	.	C	16.84	3.233669	0.58886	.	.	ENSG00000169184	ENST00000302326	T	0.47869	0.83	5.04	1.75	0.24633	.	0.148707	0.45361	D	0.000368	T	0.22126	0.0533	N	0.08118	0	0.24692	N	0.993302	B	0.02656	0.0	B	0.06405	0.002	T	0.10132	-1.0643	10	0.37606	T	0.19	-5.5453	4.928	0.13903	0.0:0.5962:0.1578:0.2459	.	1186	Q10571	MN1_HUMAN	T	1186	ENSP00000304956:A1186T	ENSP00000304956:A1186T	A	-	1	0	MN1	26522976	0.758000	0.28405	0.850000	0.33497	0.970000	0.65996	0.490000	0.22403	0.512000	0.28257	0.456000	0.33151	GCC	.	.	.	none		0.647	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430		T	28192976	C	T	28192976	3	4	84	1	0	0	0	0	1	0	0	0	9680	768	27	1	414	1	MN1	22	28192976	Missense_Mutation	SNP	C	TCGA-B1-A654-01A-11D-A31X-10		28192976	23111590	43	5399											
MID1IP1	58526	hgsc.bcm.edu	37	chrX	38664368	38664368	+	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	acgatgttggcgtggaggtaGgcggcagtggcggctgcctg	5	8	20	8	4	0	0	0	0	0	0	0	2	0	1	1	7	1	4	1	7	1	2			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chrX:38664368G>T	ENST00000336949.6	+	2	1114	c.169G>T	c.(169-171)Ggc>Tgc	p.G57C	MID1IP1_ENST00000378474.3_Missense_Mutation_p.G57C|MID1IP1-AS1_ENST00000436893.1_RNA|MID1IP1_ENST00000457894.1_Missense_Mutation_p.G57C	NM_021242.4	NP_067065.1	Q9NPA3	M1IP1_HUMAN	MID1 interacting protein 1	57					lipid metabolic process (GO:0006629)|negative regulation of microtubule depolymerization (GO:0007026)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of ligase activity (GO:0051351)|protein polymerization (GO:0051258)|regulation of lipid biosynthetic process (GO:0046890)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				kidney(1)|large_intestine(3)|lung(2)|prostate(1)	7						CGTGGAGGTAGGCGGCAGTGG	0.662																																					p.G57C		Atlas-SNP	.											.	MID1IP1	12	.	0			c.G169T						PASS	.						42	33	37					X																	38664368		2202	4300	6502	SO:0001583	missense	58526	exon2			GAGGTAGGCGGCA		CCDS14249.1	Xp11.4	2012-02-23	2012-02-23		ENSG00000165175	ENSG00000165175			20715	protein-coding gene	gene with protein product	"gastrulation specific G12 homolog (zebrafish)"		"MID1 interacting protein 1 (gastrulation specific G12-like (zebrafish))"				Standard	NM_001098790		Approved	STRAIT11499, FLJ10386, MIG12, THRSPL, G12-like	uc010ngz.3	Q9NPA3	OTTHUMG00000024092	ENST00000336949.6:c.169G>T	chrX.hg19:g.38664368G>T	ENSP00000338706:p.Gly57Cys	151.0	0.0	.		151.0	74.0	.	NM_021242	D3DWB2	Missense_Mutation	SNP	ENST00000336949.6	hg19	CCDS14249.1	.	.	.	.	.	.	.	.	.	.	G	15.88	2.964421	0.53507	.	.	ENSG00000165175	ENST00000457894;ENST00000378474;ENST00000336949	.	.	.	4.84	1.05	0.20165	.	0.159061	0.29286	N	0.012584	T	0.43277	0.1240	L	0.40543	1.245	0.33031	D	0.530214	D	0.58620	0.983	P	0.51297	0.665	T	0.54589	-0.8271	9	0.59425	D	0.04	-14.4554	6.8616	0.24069	0.4221:0.0:0.5779:0.0	.	57	Q9NPA3	M1IP1_HUMAN	C	57	.	ENSP00000338706:G57C	G	+	1	0	MID1IP1	38549312	0.735000	0.28153	0.940000	0.37924	0.993000	0.82548	0.654000	0.24918	0.136000	0.18733	0.529000	0.55759	GGC	.	.	.	none		0.662	MID1IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060655.1			T	38664368	G	T	38664368	3	4	84	1	0	0	0	0	1	0	0	0	9584	1000	35	4	171	4	MID1IP1	23	38664368	Missense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10		38664368	116606192	44	5400											
RPA4	29935	hgsc.bcm.edu	37	chrX	96139635	96139635	+	Missense_Mutation	SNP	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	cgaggcccgacagtggtttgGtagagagaaagtcaagcagg	12	6	16	7	2	1	2	1	0	0	2	1	5	1	2	1	4	1	3	1	4	3	2			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chrX:96139635G>A	ENST00000373040.3	+	1	729	c.326G>A	c.(325-327)gGt>gAt	p.G109D	DIAPH2_ENST00000324765.8_Intron|DIAPH2_ENST00000355827.4_Intron|DIAPH2_ENST00000373049.4_Intron|DIAPH2_ENST00000373054.4_Intron|DIAPH2_ENST00000373061.3_Intron	NM_013347.4	NP_037479.1	Q13156	RFA4_HUMAN	replication protein A4, 30kDa	109					DNA damage checkpoint (GO:0000077)|DNA recombination (GO:0006310)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)	DNA replication factor A complex (GO:0005662)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	single-stranded DNA binding (GO:0003697)			endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)	13						CAGTGGTTTGGTAGAGAGAAA	0.463								Other identified genes with known or suspected DNA repair function																													p.G109D		Atlas-SNP	.											.	RPA4	29	.	0			c.G326A						PASS	.						101	87	92					X																	96139635		2203	4300	6503	SO:0001583	missense	29935	exon1			GGTTTGGTAGAGA	U24186	CCDS35345.1	Xq21	2010-04-09	2010-04-09		ENSG00000204086	ENSG00000204086			30305	protein-coding gene	gene with protein product		300767	"replication protein A4, 34kDa"			7760808	Standard	NM_013347		Approved	HSU24186	uc004efv.4	Q13156	OTTHUMG00000021987	ENST00000373040.3:c.326G>A	chrX.hg19:g.96139635G>A	ENSP00000362131:p.Gly109Asp	70.0	0.0	.		61.0	33.0	.	NM_013347	Q3SY03	Missense_Mutation	SNP	ENST00000373040.3	hg19	CCDS35345.1	.	.	.	.	.	.	.	.	.	.	G	0.245	-1.011087	0.02095	.	.	ENSG00000204086	ENST00000373040	T	0.37235	1.21	3.66	-0.387	0.12463	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);Nucleic acid binding, OB-fold, tRNA/helicase-type (1);	.	.	.	.	T	0.08313	0.0207	N	0.01086	-1.025	0.09310	N	1	B	0.25904	0.137	B	0.25759	0.063	T	0.29274	-1.0017	9	0.02654	T	1	-20.9474	2.3223	0.04214	0.1176:0.3079:0.405:0.1696	.	109	Q13156	RFA4_HUMAN	D	109	ENSP00000362131:G109D	ENSP00000362131:G109D	G	+	2	0	RPA4	96026291	0.001000	0.12720	0.000000	0.03702	0.019000	0.09904	0.691000	0.25467	-0.217000	0.10033	0.600000	0.82982	GGT	.	.	.	none		0.463	RPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057464.1	NM_013347		A	96139635	G	A	96139635	3	1	84	1	0	0	0	0	1	0	0	0	13552	1261	44	2	328	2	RPA4	23	96139635	Missense_Mutation	SNP	G	TCGA-B1-A654-01A-11D-A31X-10	57475267	96139635	59130925	45	5401											
RBMX2	51634	hgsc.bcm.edu	37	chrX	129546641	129546641	+	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	gagggaggcaagagaagaaaAgaccaggattagggacagag	18	2	17	4	0	0	4	0	0	0	4	0	9	0	7	1	4	0	1	1	4	5	1			TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	g.chrX:129546641A>T	ENST00000305536.6	+	6	852	c.788A>T	c.(787-789)aAg>aTg	p.K263M		NM_016024.2	NP_057108.2	Q9Y388	RBMX2_HUMAN	RNA binding motif protein, X-linked 2	263	Arg-rich.						nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(2)|large_intestine(1)|liver(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	19						AGAGAAGAAAAGACCAGGATT	0.527																																					p.K263M		Atlas-SNP	.											.	RBMX2	46	.	0			c.A788T						PASS	.						69	67	68					X																	129546641		1931	4135	6066	SO:0001583	missense	51634	exon6			AAGAAAAGACCAG	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.788A>T	chrX.hg19:g.129546641A>T	ENSP00000339090:p.Lys263Met	233.0	1.0	.		201.0	91.0	.	NM_016024	A8K9Z0|Q5JY82|Q9Y3I8	Missense_Mutation	SNP	ENST00000305536.6	hg19	CCDS43993.1	.	.	.	.	.	.	.	.	.	.	A	11.99	1.804392	0.31869	.	.	ENSG00000134597	ENST00000305536;ENST00000538614	T	0.14516	2.5	4.9	-0.267	0.12938	.	0.462561	0.21532	N	0.073035	T	0.12987	0.0315	L	0.29908	0.895	0.18873	N	0.999989	P	0.50943	0.94	P	0.50231	0.635	T	0.13019	-1.0525	10	0.66056	D	0.02	.	7.4457	0.27209	0.5412:0.0:0.4588:0.0	.	263	Q9Y388	RBMX2_HUMAN	M	263	ENSP00000339090:K263M	ENSP00000339090:K263M	K	+	2	0	RBMX2	129374322	0.289000	0.24334	0.029000	0.17559	0.223000	0.24884	0.054000	0.14205	-0.329000	0.08527	0.417000	0.27973	AAG	.	.	.	none		0.527	RBMX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058265.1	NM_016024		T	129546641	A	T	129546641	3	4	84	1	0	0	0	0	1	0	0	0	13165	72	3	5	810	5	RBMX2	23	129546641	Missense_Mutation	SNP	A	TCGA-B1-A654-01A-11D-A31X-10	33407006	129546641	25723919	46	5402											
ATP13A2	23400	hgsc.bcm.edu	37	chr1	17318334	17318334	+	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	cagcagccccaggaggctcaGgtctccttccacagtgtccc	7	7	10	17	0	2	0	1	0	1	0	5	1	4	1	5	3	2	2	5	3	0	1			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr1:17318334G>T	ENST00000326735.8	-	20	2179	c.2146C>A	c.(2146-2148)Ctg>Atg	p.L716M	ATP13A2_ENST00000452699.1_Missense_Mutation_p.L711M|RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000341676.5_Missense_Mutation_p.L711M			Q9NQ11	AT132_HUMAN	ATPase type 13A2	716					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		AGGAGGCTCAGGTCTCCTTCC	0.632																																					p.L716M		Atlas-SNP	.											.	ATP13A2	85	.	0			c.C2146A						PASS	.						68	65	66					1																	17318334		2203	4300	6503	SO:0001583	missense	23400	exon20			GGCTCAGGTCTCC	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"ATPases / P-type", "Parkinson disease"	30213	protein-coding gene	gene with protein product		610513	"Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.2146C>A	chr1.hg19:g.17318334G>T	ENSP00000327214:p.Leu716Met	91.0	0.0	.		64.0	18.0	.	NM_022089	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Missense_Mutation	SNP	ENST00000326735.8	hg19	CCDS175.1	.	.	.	.	.	.	.	.	.	.	G	11.38	1.621251	0.28889	.	.	ENSG00000159363	ENST00000326735;ENST00000341676;ENST00000452699;ENST00000503552	T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05	4.7	2.82	0.32997	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.199920	0.45606	D	0.000358	T	0.81451	0.4825	L	0.47190	1.495	0.37079	D	0.898894	D;D;D	0.69078	0.995;0.966;0.997	D;P;D	0.75020	0.985;0.756;0.971	T	0.80919	-0.1167	10	0.39692	T	0.17	-15.6307	9.9597	0.41688	0.1542:0.0:0.8458:0.0	.	711;711;716	Q5JXY1;Q6S9Z9;Q9NQ11	.;.;AT132_HUMAN	M	716;711;711;186	ENSP00000327214:L716M;ENSP00000341115:L711M;ENSP00000413307:L711M;ENSP00000421126:L186M	ENSP00000327214:L716M	L	-	1	2	ATP13A2	17190921	0.553000	0.26513	0.638000	0.29380	0.383000	0.30230	0.854000	0.27791	0.590000	0.29694	0.491000	0.48974	CTG	.	.	.	none		0.632	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089		T	17318334	G	T	17318334	3	4	85	1	0	0	0	0	1	0	0	0	1124	991	35	4	1672	4	ATP13A2	1	17318334	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10		17318334	231932287	1	5403											
RAP1GAP	5909	hgsc.bcm.edu	37	chr1	21936724	21936724	+	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	ggagtgttctcatcctggaaGaccacagccacgatgtcgtt	9	10	11	11	2	1	1	1	0	1	1	4	4	2	3	3	2	1	2	3	2	1	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr1:21936724G>C	ENST00000374765.4	-	14	1088	c.888C>G	c.(886-888)gtC>gtG	p.V296V	RAP1GAP_ENST00000374757.3_5'Flank|RAP1GAP_ENST00000542643.2_Silent_p.V296V|RAP1GAP_ENST00000374761.2_Silent_p.V327V|RAP1GAP_ENST00000374763.2_Silent_p.V296V|RAP1GAP_ENST00000290101.4_Silent_p.V360V	NM_002885.2	NP_002876.2	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein	296	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				GTP catabolic process (GO:0006184)|positive regulation of Rap GTPase activity (GO:0032854)|regulation of Ras GTPase activity (GO:0032318)|signal transduction (GO:0007165)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)|Rap GTPase activator activity (GO:0046582)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	17		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)		CATCCTGGAAGACCACAGCCA	0.637																																					p.V360V		Atlas-SNP	.											.	RAP1GAP	119	.	0			c.C1080G						PASS	.						112	87	96					1																	21936724		2203	4300	6503	SO:0001819	synonymous_variant	5909	exon14			CTGGAAGACCACA	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.888C>G	chr1.hg19:g.21936724G>C		156.0	0.0	.		191.0	52.0	.	NM_001145658	J3QSS6|O75062|Q5T3S9|Q5T3T4|Q7Z5S8|Q9UQ51	Silent	SNP	ENST00000374765.4	hg19	CCDS218.1																																																																																			.	.	.	none		0.637	RAP1GAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019759.2	NM_002885		C	21936724	G	C	21936724	2	2	85	1	0	0	0	0	0	0	0	1	13050	929	33	4		4	RAP1GAP	1	21936724	Silent	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	4618390	21936724	227313897	2	5404											
CSF3R	1441	hgsc.bcm.edu	37	chr1	36939407	36939408	+	In_Frame_Ins	INS	-	-	GTC																															ggtgggtaggtgggtctcagINSgtcctggctcccactggcag																								rs145989033		TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr1:36939407_36939408insGTC	ENST00000373106.1	-	5	989_990	c.442_443insGAC	c.(442-444)cct>cGACct	p.147_148insR	CSF3R_ENST00000418048.2_In_Frame_Ins_p.147_148insR|CSF3R_ENST00000361632.4_In_Frame_Ins_p.147_148insR|CSF3R_ENST00000373103.1_In_Frame_Ins_p.147_148insR|CSF3R_ENST00000331941.5_In_Frame_Ins_p.147_148insR|CSF3R_ENST00000487540.2_5'Flank|CSF3R_ENST00000440588.2_In_Frame_Ins_p.147_148insR|CSF3R_ENST00000338937.5_In_Frame_Ins_p.147_148insR|CSF3R_ENST00000373104.1_In_Frame_Ins_p.147_148insR	NM_000760.3	NP_000751.1	Q99062	CSF3R_HUMAN	colony stimulating factor 3 receptor (granulocyte)	147	Fibronectin type-III 1. {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)	GTGGGTCTCAGGTCCTGGCTCC	0.599																																					p.P148delinsRP		Atlas-Indel,Pindel	.											.	CSF3R	157	.	0			c.443_444insGAC						PASS	.																																			SO:0001652	inframe_insertion	1441	exon5			.	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.440_442dupGAC	chr1.hg19:g.36939408_36939410dupGTC	ENSP00000362198:p.Gly147_Pro148insArg	79.0	0.0	0		76.0	25.0	0.328947	NM_156039		In_Frame_Ins	INS	ENST00000373106.1	hg19	CCDS413.1																																																																																			.	.	.	none		0.599	CSF3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021997.2	NM_156039		GTC	36939408	-	GTC	36939407	7	5	85	1	0	1	1	0	0	0	0	0	3939	1000	35	0	2309	0	CSF3R	1	36939407	In_Frame_Ins	INS	-	TCGA-B1-A655-01A-11D-A31Z-10	15002683	36939407	212311214	3	5405											
RPS8	6202	hgsc.bcm.edu	37	chr1	45242407	45242407	+	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	gtaacaagaaataccgtgccCtgaggttggacgtggggaat	12	8	14	7	2	0	2	0	1	0	1	0	4	0	4	2	4	3	2	2	4	5	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr1:45242407C>G	ENST00000396651.3	+	3	332	c.172C>G	c.(172-174)Ctg>Gtg	p.L58V	SNORD46_ENST00000364043.1_RNA|SNORD38B_ENST00000384690.1_RNA|RPS8_ENST00000485390.1_3'UTR|RPS8_ENST00000372209.3_Intron|SNORD38A_ENST00000365161.1_RNA|SNORD55_ENST00000581525.1_RNA|RP11-269F19.2_ENST00000428791.1_RNA			P62241	RS8_HUMAN	ribosomal protein S8	58					cellular protein metabolic process (GO:0044267)|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)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(2)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)	10	Acute lymphoblastic leukemia(166;0.155)					ATACCGTGCCCTGAGGTTGGA	0.547																																					p.L58V		Atlas-SNP	.											.	RPS8	19	.	0			c.C172G						PASS	.						73	64	67					1																	45242407		2203	4300	6503	SO:0001583	missense	6202	exon3			CGTGCCCTGAGGT	BC070875	CCDS513.1	1p34.1-p32	2011-04-05			ENSG00000142937	ENSG00000142937		"S ribosomal proteins"	10441	protein-coding gene	gene with protein product		600357				8432552	Standard	NM_001012		Approved	S8	uc001cmi.3	P62241	OTTHUMG00000008494	ENST00000396651.3:c.172C>G	chr1.hg19:g.45242407C>G	ENSP00000379888:p.Leu58Val	38.0	0.0	.		30.0	13.0	.	NM_001012	P09058|Q6IRL7	Missense_Mutation	SNP	ENST00000396651.3	hg19	CCDS513.1	.	.	.	.	.	.	.	.	.	.	C	15.76	2.927456	0.52759	.	.	ENSG00000142937	ENST00000396651	T	0.37915	1.17	4.8	1.74	0.24563	.	0.000000	0.64402	D	0.000001	T	0.41003	0.1140	M	0.86953	2.85	0.80722	D	1	B	0.32101	0.356	B	0.31547	0.132	T	0.37619	-0.9698	10	0.87932	D	0	-24.8377	8.7594	0.34665	0.0:0.7558:0.0:0.2442	.	58	P62241	RS8_HUMAN	V	58	ENSP00000379888:L58V	ENSP00000379888:L58V	L	+	1	2	RPS8	45014994	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	2.400000	0.44504	0.166000	0.19597	0.655000	0.94253	CTG	.	.	.	none		0.547	RPS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023439.1	NM_001012		G	45242407	C	G	45242407	3	3	85	1	0	0	0	0	1	0	0	0	13674	680	24	4	182	4	RPS8	1	45242407	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	8303000	45242407	204008214	4	5406											
CYP4X1	260293	hgsc.bcm.edu	37	chr1	47489659	47489659	+	Frame_Shift_Del	DEL	A	A	-																															cacccactggttccttgggcAccagaaggtagatgggaggg																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr1:47489659delA	ENST00000371901.3	+	1	420	c.170delA	c.(169-171)cacfs	p.H57fs	CYP4X1_ENST00000538609.1_Intron	NM_178033.1	NP_828847.1	Q8N118	CP4X1_HUMAN	cytochrome P450, family 4, subfamily X, polypeptide 1	57						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	17						TTCCTTGGGCACCagaaggta	0.682																																					p.H57fs		Atlas-Indel,Pindel	.											.	CYP4X1	58	.	0			c.169delC						PASS	.						13	15	14					1																	47489659		2197	4293	6490	SO:0001589	frameshift_variant	260293	exon1			.	AK091806	CCDS544.1	1p33	2008-02-05			ENSG00000186377	ENSG00000186377		"Cytochrome P450s"	20244	protein-coding gene	gene with protein product		614999				12176035	Standard	NM_178033		Approved	MGC40051	uc001cqt.3	Q8N118	OTTHUMG00000008017	ENST00000371901.3:c.170delA	chr1.hg19:g.47489659delA	ENSP00000360968:p.His57fs	77.0	0.0	0		79.0	25.0	0.316456	NM_178033	G3V1U1|Q5VVE5|Q6ZN67|Q8NAZ3	Frame_Shift_Del	DEL	ENST00000371901.3	hg19	CCDS544.1																																																																																			.	.	.	none		0.682	CYP4X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022017.1	NM_178033		-	47489659	A	-	47489659	7	5	85	1	0	1	0	1	0	0	0	0	4195	159	6	0	172	0	CYP4X1	1	47489659	Frame_Shift_Del	DEL	A	TCGA-B1-A655-01A-11D-A31Z-10	2247252	47489659	201760962	5	5407											
AMPD1	270	hgsc.bcm.edu	37	chr1	115221050	115221050	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agattcttctctttggtgctAtagaccactctgtcagcatc	8	15	7	11	0	4	2	1	0	3	2	6	2	4	2	1	1	2	2	1	1	2	5			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr1:115221050A>G	ENST00000520113.2	-	8	1110	c.1095T>C	c.(1093-1095)taT>taC	p.Y365Y	AMPD1_ENST00000353928.6_Silent_p.Y332Y|AMPD1_ENST00000369538.3_Silent_p.Y361Y			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	365					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)	CTTTGGTGCTATAGACCACTC	0.408																																					p.Y365Y		Atlas-SNP	.											.	AMPD1	223	.	0			c.T1095C						PASS	.						160	155	157					1																	115221050		2203	4300	6503	SO:0001819	synonymous_variant	270	exon8			GGTGCTATAGACC	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.1095T>C	chr1.hg19:g.115221050A>G		76.0	0.0	.		86.0	30.0	.	NM_000036	A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Silent	SNP	ENST00000520113.2	hg19	CCDS876.2																																																																																			.	.	.	none		0.408	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4			G	115221050	A	G	115221050	2	3	85	1	0	0	0	0	0	0	0	1	585	456	16	3		3	AMPD1	1	115221050	Silent	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	67731391	115221050	134029571	6	5408											
MYT1L	23040	hgsc.bcm.edu	37	chr2	1805513	1805513	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcttccatctgggaattggaTtcatttagctccttgatttc	7	17	8	9	0	2	1	1	1	1	0	5	3	4	3	2	2	1	2	2	2	2	7			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:1805513T>C	ENST00000399161.2	-	23	3978	c.3231A>G	c.(3229-3231)gaA>gaG	p.E1077E	MYT1L_ENST00000428368.2_Silent_p.E1075E|MYT1L_ENST00000407844.1_Silent_p.E73E	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	1077					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)		GGGAATTGGATTCATTTAGCT	0.333																																					p.E1075E		Atlas-SNP	.											.	MYT1L	241	.	0			c.A3225G						PASS	.						232	228	229					2																	1805513		1805	4085	5890	SO:0001819	synonymous_variant	23040	exon23			ATTGGATTCATTT	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.3231A>G	chr2.hg19:g.1805513T>C		69.0	0.0	.		76.0	22.0	.	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Silent	SNP	ENST00000399161.2	hg19																																																																																				.	.	.	none		0.333	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		C	1805513	T	C	1805513	2	2	85	1	0	0	0	0	0	0	0	1	10114	1490	52	3		3	MYT1L	2	1805513	Silent	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10		1805513	241393860	7	5409											
SMC6	79677	hgsc.bcm.edu	37	chr2	17896324	17896324	+	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	ttctgggtcccgaagatgaaTgcaagctcctaaaagtgaga	13	9	11	8	1	1	3	0	2	1	2	3	5	3	3	2	1	2	2	2	1	5	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:17896324T>A	ENST00000448223.2	-	16	1803	c.1534A>T	c.(1534-1536)Att>Ttt	p.I512F	SMC6_ENST00000402989.1_Missense_Mutation_p.I512F|SMC6_ENST00000351948.4_Missense_Mutation_p.I512F|SMC6_ENST00000381272.4_Missense_Mutation_p.I538F	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	512	Flexible hinge.				cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					CGAAGATGAATGCAAGCTCCT	0.368																																					p.I512F		Atlas-SNP	.											.	SMC6	102	.	0			c.A1534T						PASS	.						71	74	73					2																	17896324		2203	4300	6503	SO:0001583	missense	79677	exon16			GATGAATGCAAGC	AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"Structural maintenance of chromosomes proteins"	20466	protein-coding gene	gene with protein product		609387	"SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.1534A>T	chr2.hg19:g.17896324T>A	ENSP00000404092:p.Ile512Phe	70.0	0.0	.		66.0	28.0	.	NM_001142286	A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Missense_Mutation	SNP	ENST00000448223.2	hg19	CCDS1690.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.349589	0.82132	.	.	ENSG00000163029	ENST00000448223;ENST00000351948;ENST00000381272;ENST00000402989;ENST00000446852	T;T;T;T;T	0.31247	2.1;2.1;1.62;2.1;1.5	6.16	6.16	0.99307	RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	T	0.54967	0.1891	M	0.74647	2.275	0.80722	D	1	D;D;D	0.71674	0.997;0.998;0.997	D;D;D	0.74674	0.961;0.984;0.977	T	0.57860	-0.7738	10	0.62326	D	0.03	.	13.2153	0.59856	0.0:0.0:0.1324:0.8676	.	538;538;512	C9JMN1;Q96SB8-2;Q96SB8	.;.;SMC6_HUMAN	F	512;512;538;512;538	ENSP00000404092:I512F;ENSP00000323439:I512F;ENSP00000370672:I538F;ENSP00000384539:I512F;ENSP00000408644:I538F	ENSP00000323439:I512F	I	-	1	0	SMC6	17759805	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.172000	0.65003	2.367000	0.80283	0.528000	0.53228	ATT	.	.	.	none		0.368	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207359.1	NM_024624		A	17896324	T	A	17896324	3	1	85	1	0	0	0	0	1	0	0	0	14800	1464	51	5	1793	5	SMC6	2	17896324	Missense_Mutation	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	16090811	17896324	225303049	8	5410											
RHOB	388	hgsc.bcm.edu	37	chr2	20647312	20647312	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatcgtgttcagtaaggacgAgttccccgaggtgtacgtgc	8	10	14	9	4	1	0	1	0	0	0	3	4	2	1	2	2	2	4	2	2	2	4			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:20647312A>G	ENST00000272233.4	+	1	478	c.86A>G	c.(85-87)gAg>gGg	p.E29G		NM_004040.2	NP_004031.1	P62745	RHOB_HUMAN	ras homolog family member B	29					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)	AGTAAGGACGAGTTCCCCGAG	0.662																																					p.E29G		Atlas-SNP	.											.	RHOB	18	.	0			c.A86G						PASS	.						121	120	120					2																	20647312		2203	4300	6503	SO:0001583	missense	388	exon1			AGGACGAGTTCCC		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.86A>G	chr2.hg19:g.20647312A>G	ENSP00000272233:p.Glu29Gly	66.0	0.0	.		85.0	26.0	.	NM_004040	B2R692|P01121|Q5U0H6|Q7RTN5|Q7RTR9|Q9CUV7	Missense_Mutation	SNP	ENST00000272233.4	hg19	CCDS1699.1	.	.	.	.	.	.	.	.	.	.	A	13.04	2.117942	0.37339	.	.	ENSG00000143878	ENST00000272233	T	0.78246	-1.16	5.74	4.56	0.56223	Small GTP-binding protein domain (1);	0.000000	0.85682	U	0.000000	T	0.76471	0.3992	L	0.58810	1.83	0.53688	D	0.999978	B	0.29716	0.255	B	0.35727	0.209	T	0.74559	-0.3625	10	0.56958	D	0.05	-19.0458	12.9321	0.58292	0.8645:0.1355:0.0:0.0	.	29	P62745	RHOB_HUMAN	G	29	ENSP00000272233:E29G	ENSP00000272233:E29G	E	+	2	0	RHOB	20510793	1.000000	0.71417	1.000000	0.80357	0.018000	0.09664	9.156000	0.94705	0.963000	0.38082	0.533000	0.62120	GAG	.	.	.	none		0.662	RHOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207500.1	NM_004040		G	20647312	A	G	20647312	3	3	85	1	0	0	0	0	1	0	0	0	13345	304	11	3	88	3	RHOB	2	20647312	Missense_Mutation	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	2750988	20647312	222552061	9	5411											
SLC5A6	8884	hgsc.bcm.edu	37	chr2	27427730	27427730	+	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	tggttcaccccgtataaggaGagcatcatgaagacaccccc	12	7	9	13	1	2	3	2	1	0	2	2	4	2	3	4	2	1	3	4	2	3	3	rs376306193		TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:27427730G>C	ENST00000310574.3	-	8	1277	c.804C>G	c.(802-804)ctC>ctG	p.L268L	SLC5A6_ENST00000461319.1_5'Flank|SLC5A6_ENST00000408041.1_Silent_p.L268L	NM_021095.2	NP_066918.2	Q9Y289	SC5A6_HUMAN	solute carrier family 5 (sodium/multivitamin and iodide cotransporter), member 6	268					biotin metabolic process (GO:0006768)|biotin transport (GO:0015878)|pantothenate metabolic process (GO:0015939)|pantothenate transmembrane transport (GO:0015887)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)			endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|ovary(3)|prostate(1)|skin(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Biotin(DB00121)|gabapentin enacarbil(DB08872)|Lipoic Acid(DB00166)	CGTATAAGGAGAGCATCATGA	0.587																																					p.L268L		Atlas-SNP	.											SLC5A6,NS,carcinoma,0,1	SLC5A6	63	.	0			c.C804G						PASS	.	G		0,4406		0,0,2203	103	95	98		804	-2.5	1	2		98	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SLC5A6	NM_021095.2		0,1,6502	CC,CG,GG		0.0116,0.0,0.0077		268/636	27427730	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8884	exon8			TAAGGAGAGCATC	AF069307	CCDS1740.1	2p23	2013-07-19	2013-07-19		ENSG00000138074	ENSG00000138074		"Solute carriers"	11041	protein-coding gene	gene with protein product		604024	"solute carrier family 5 (sodium-dependent vitamin transporter), member 6"			9516450, 10329687	Standard	NM_021095		Approved	SMVT	uc002rjd.3	Q9Y289	OTTHUMG00000097075	ENST00000310574.3:c.804C>G	chr2.hg19:g.27427730G>C		24.0	0.0	.		30.0	10.0	.	NM_021095	B2RB85|D6W549|Q969Y5	Silent	SNP	ENST00000310574.3	hg19	CCDS1740.1																																																																																			.	.	.	weak		0.587	SLC5A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214194.1	NM_021095		C	27427730	G	C	27427730	2	2	85	1	0	0	0	0	0	0	0	1	14682	929	33	4		4	SLC5A6	2	27427730	Silent	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	6780418	27427730	215771643	10	5412											
SMEK2	57223	hgsc.bcm.edu	37	chr2	55806886	55806886	+	Frame_Shift_Del	DEL	A	A	-																															catgcatacaatggttgtagAaaaaatttagaaattcactt																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:55806886delA	ENST00000345102.5	-	9	1698	c.1397delT	c.(1396-1398)ttcfs	p.F466fs	SMEK2_ENST00000272313.5_Frame_Shift_Del_p.F466fs|SMEK2_ENST00000407823.3_Frame_Shift_Del_p.F466fs	NM_001122964.1	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	466					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)			ATGGTTGTAGAAAAAATTTAG	0.303																																					p.F466fs		Atlas-Indel,Pindel	.											.	SMEK2	86	.	0			c.1398delC						PASS	.						76	80	79					2																	55806886		2203	4298	6501	SO:0001589	frameshift_variant	57223	exon9			.	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.1397delT	chr2.hg19:g.55806886delA	ENSP00000339769:p.Phe466fs	78.0	0.0	0		67.0	21.0	0.313433	NM_001122964	Q6P9B0|Q86XB8|Q9BQJ0|Q9BRK2|Q9H913|Q9P2G0	Frame_Shift_Del	DEL	ENST00000345102.5	hg19	CCDS46289.1																																																																																			.	.	.	none		0.303	SMEK2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251483.1	NM_020463		-	55806886	A	-	55806886	7	5	85	1	0	1	0	1	0	0	0	0	14807	246	9	0	1188	0	SMEK2	2	55806886	Frame_Shift_Del	DEL	A	TCGA-B1-A655-01A-11D-A31Z-10	28379156	55806886	187392487	11	5413											
INO80B	83444	hgsc.bcm.edu	37	chr2	74684908	74684908	+	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	cccgcacaggccaggcactcTgtagtcttcagtgctaccgc	7	8	10	16	2	3	0	1	0	2	0	3	0	3	0	3	2	2	4	3	2	2	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:74684908T>A	ENST00000233331.7	+	5	1082	c.988T>A	c.(988-990)Tgt>Agt	p.C330S	WBP1_ENST00000393972.3_5'Flank|WBP1_ENST00000233615.2_5'Flank|WBP1_ENST00000409737.1_5'Flank	NM_031288.3	NP_112578.2	Q9C086	IN80B_HUMAN	INO80 complex subunit B	330					chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Ino80 complex (GO:0031011)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	13						CCAGGCACTCTGTAGTCTTCA	0.682																																					p.C330S		Atlas-SNP	.											.	INO80B	37	.	0			c.T988A						PASS	.						18	20	19					2																	74684908		2117	4148	6265	SO:0001583	missense	83444	exon5			GCACTCTGTAGTC	AB054538	CCDS1942.2	2p13.1	2011-07-06	2008-08-07	2008-08-07	ENSG00000115274	ENSG00000115274		"Zinc fingers, HIT-type", "INO80 complex subunits"	13324	protein-coding gene	gene with protein product	"PAP-1 binding protein", "IES2 homolog (S. cerevisiae)"		"high mobility group AT-hook 1-like 4", "zinc finger, HIT type 4"	HMGA1L4, ZNHIT4		16230350	Standard	NM_031288		Approved	HMGIYL4, PAPA-1, hIes2, PAP-1BP, IES2	uc002slg.3	Q9C086	OTTHUMG00000129959	ENST00000233331.7:c.988T>A	chr2.hg19:g.74684908T>A	ENSP00000233331:p.Cys330Ser	21.0	0.0	.		25.0	8.0	.	NM_031288		Missense_Mutation	SNP	ENST00000233331.7	hg19	CCDS1942.2	.	.	.	.	.	.	.	.	.	.	T	27.9	4.869691	0.91587	.	.	ENSG00000115274	ENST00000233331	D	0.99042	-5.36	5.27	5.27	0.74061	Zinc finger, HIT-type (1);	0.000000	0.85682	D	0.000000	D	0.98927	0.9636	L	0.58354	1.805	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.87578	0.998;0.995;0.995	D	0.99671	1.0996	10	0.87932	D	0	-20.6182	13.1927	0.59719	0.0:0.0:0.0:1.0	.	348;315;330	B4DJ31;B4DJ22;Q9C086	.;.;IN80B_HUMAN	S	330	ENSP00000233331:C330S	ENSP00000233331:C330S	C	+	1	0	INO80B	74538416	1.000000	0.71417	0.996000	0.52242	0.864000	0.49448	5.346000	0.65992	2.211000	0.71520	0.459000	0.35465	TGT	.	.	.	none		0.682	INO80B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252223.2	NM_031288		A	74684908	T	A	74684908	3	1	85	1	0	0	0	0	1	0	0	0	7754	1580	55	5	1006	5	INO80B	2	74684908	Missense_Mutation	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	18878022	74684908	168514465	12	5414											
RPIA	22934	hgsc.bcm.edu	37	chr2	89037541	89037541	+	Missense_Mutation	SNP	T	T	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	tttatcttggactggaagttTgaccgggtacacaaatggag	11	12	12	6	1	1	1	0	1	1	0	1	4	1	4	1	4	1	2	1	4	4	5			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:89037541T>G	ENST00000283646.4	+	8	841	c.786T>G	c.(784-786)ttT>ttG	p.F262L		NM_144563.2	NP_653164.2	P49247	RPIA_HUMAN	ribose 5-phosphate isomerase A	262					carbohydrate metabolic process (GO:0005975)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|ribose phosphate metabolic process (GO:0019693)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	monosaccharide binding (GO:0048029)|ribose-5-phosphate isomerase activity (GO:0004751)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|skin(1)	18		Acute lymphoblastic leukemia(2;0.000456)|all_hematologic(2;0.00287)				ACTGGAAGTTTGACCGGGTAC	0.438																																					p.F262L		Atlas-SNP	.											.	RPIA	35	.	0			c.T786G						PASS	.						154	143	146					2																	89037541		1889	4125	6014	SO:0001583	missense	22934	exon8			GAAGTTTGACCGG	L35035	CCDS2004.2	2p11.2	2008-07-31	2008-07-31		ENSG00000153574	ENSG00000153574	5.3.1.6		10297	protein-coding gene	gene with protein product	"ribose 5-phosphate epimerase"	180430				7758956	Standard	NM_144563		Approved		uc002ste.3	P49247	OTTHUMG00000130333	ENST00000283646.4:c.786T>G	chr2.hg19:g.89037541T>G	ENSP00000283646:p.Phe262Leu	92.0	0.0	.		114.0	9.0	.	NM_144563	Q541P9|Q96BJ6	Missense_Mutation	SNP	ENST00000283646.4	hg19	CCDS2004.2	.	.	.	.	.	.	.	.	.	.	T	23.9	4.473758	0.84640	.	.	ENSG00000153574	ENST00000283646;ENST00000543560	T	0.76186	-1.0	5.55	1.74	0.24563	.	0.000000	0.85682	D	0.000000	T	0.82144	0.4973	M	0.70842	2.15	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.78321	-0.2249	10	0.42905	T	0.14	-10.0604	9.4754	0.38869	0.0:0.2052:0.0:0.7948	.	262	P49247	RPIA_HUMAN	L	262;128	ENSP00000283646:F262L	ENSP00000283646:F262L	F	+	3	2	RPIA	88818656	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.082000	0.30803	0.056000	0.16144	0.383000	0.25322	TTT	.	.	.	none		0.438	RPIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252683.2			G	89037541	T	G	89037541	3	3	85	1	0	0	0	0	1	0	0	0	13566	1809	63	5	816	5	RPIA	2	89037541	Missense_Mutation	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	14352633	89037541	154161832	13	5415											
FER1L5	90342	hgsc.bcm.edu	37	chr2	97368368	97368368	+	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	ggctggagaaggacatgcagAagacagacatccactaccac	15	4	11	11	0	0	4	0	0	0	4	1	6	1	5	2	3	2	2	2	3	3	1			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:97368368A>C	ENST00000457909.1	+	0	4790							A0AVI2	FR1L5_HUMAN	fer-1-like family member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(9)|large_intestine(9)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	38						GGACATGCAGAAGACAGACAT	0.602																																					p.K1799Q		Atlas-SNP	.											.	FER1L5	113	.	0			c.A5395C						PASS	.						39	45	43					2																	97368368		2131	4257	6388			90342	exon47			ATGCAGAAGACAG	BC126368		2q11.2	2014-06-27	2014-06-27		ENSG00000249715	ENSG00000249715			19044	protein-coding gene	gene with protein product			"fer-1-like 5 (C. elegans)"				Standard	XM_006712826		Approved	DKFZp434I0121	uc010fia.3	A0AVI2	OTTHUMG00000154929		chr2.hg19:g.97368368A>C		56.0	0.0	.		64.0	24.0	.	NM_001113382	Q17RH2|Q6ZU24	Missense_Mutation	SNP	ENST00000457909.1	hg19		.	.	.	.	.	.	.	.	.	.	A	12.29	1.894586	0.33442	.	.	ENSG00000214272	ENST00000414152;ENST00000436930;ENST00000397978	.	.	.	5.29	4.14	0.48551	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.139522	0.32068	U	0.006626	T	0.71256	0.3318	M	0.72576	2.205	.	.	.	D;D;D	0.71674	0.981;0.998;0.989	P;D;P	0.69479	0.77;0.964;0.885	T	0.79436	-0.1804	8	0.87932	D	0	-9.4277	10.0645	0.42295	0.9196:0.0:0.0804:0.0	.	507;1799;508	B7ZLI3;A0AVI2;A0AVI2-2	.;FR1L5_HUMAN;.	Q	1799;1803;508	.	ENSP00000442027:K508Q	K	+	1	0	FER1L5	96732095	0.999000	0.42202	1.000000	0.80357	0.680000	0.39746	2.466000	0.45084	0.865000	0.35603	0.459000	0.35465	AAG	.	.	.	none		0.602	FER1L5-001	KNOWN	basic|exp_conf	retained_intron	pseudogene	OTTHUMT00000339030.1	NM_001077400		C	97368368	A	C	97368368	1	2	85	0	1	0	0	0	0	0	0	0	5821	247	9	5		5	FER1L5	2	97368368	RNA	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	8330827	97368368	145831005	14	5416											
XIRP2	129446	hgsc.bcm.edu	37	chr2	168108259	168108259	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aatctggctgtgacttcaagCatgccccaccaacctatgag	11	9	8	13	0	2	2	1	2	1	0	2	2	2	2	4	1	3	2	4	1	4	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:168108259C>T	ENST00000409195.1	+	9	10446	c.10357C>T	c.(10357-10359)Cat>Tat	p.H3453Y	XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.H3231Y|XIRP2_ENST00000295237.9_Missense_Mutation_p.H3453Y|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	3278					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						TGACTTCAAGCATGCCCCACC	0.408																																					p.H3453Y		Atlas-SNP	.											.	XIRP2	914	.	0			c.C10357T						PASS	.						61	61	61					2																	168108259		1916	4139	6055	SO:0001583	missense	129446	exon9			TTCAAGCATGCCC	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.10357C>T	chr2.hg19:g.168108259C>T	ENSP00000386840:p.His3453Tyr	158.0	0.0	.		148.0	59.0	.	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	C	17.42	3.385682	0.61956	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.02916	4.12;4.12;4.11	6.16	5.29	0.74685	.	0.224814	0.46145	N	0.000309	T	0.14141	0.0342	M	0.71581	2.175	0.49483	D	0.99979	D;D;B	0.76494	0.999;0.999;0.368	D;D;B	0.80764	0.986;0.994;0.15	T	0.00213	-1.1913	10	0.87932	D	0	-12.9779	14.5412	0.67997	0.0:0.9292:0.0:0.0708	.	3278;3278;3231	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	Y	3453;3453;3231;867	ENSP00000386840:H3453Y;ENSP00000295237:H3453Y;ENSP00000387255:H3231Y	ENSP00000295237:H3453Y	H	+	1	0	XIRP2	167816505	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.228000	0.51270	1.628000	0.50416	-0.145000	0.13849	CAT	.	.	.	none		0.408	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		T	168108259	C	T	168108259	3	4	85	1	0	0	0	0	1	0	0	0	17442	710	25	2	10387	2	XIRP2	2	168108259	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	70739891	168108259	75091114	15	5417											
SLC25A12	8604	hgsc.bcm.edu	37	chr2	172700922	172700937	+	Frame_Shift_Del	DEL	CGGTTATGCCCAAAAT	CGGTTATGCCCAAAAT	-																															tgtagttaagatgcttcttcCggttatgcccaaaatgcagt																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	CGGTTATGCCCAAAAT	CGGTTATGCCCAAAAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:172700922_172700937delCGGTTATGCCCAAAAT	ENST00000422440.2	-	5	444_459	c.407_422delATTTTGGGCATAACCG	c.(406-423)cattttgggcataaccggfs	p.HFGHNR136fs	SLC25A12_ENST00000392592.4_Frame_Shift_Del_p.HFGHNR29fs|SLC25A12_ENST00000472748.1_5'UTR	NM_003705.4	NP_003696.2	O75746	CMC1_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 12	136	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				aspartate transport (GO:0015810)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|upper_aerodigestive_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)	ATGCTTCTTCCGGTTATGCCCAAAATGCAGTCGGAT	0.352																																					p.136_141del		Atlas-Indel,Pindel	.											.	SLC25A12	59	.	0			c.408_423del						PASS	.																																			SO:0001589	frameshift_variant	8604	exon5			.	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.407_422delATTTTGGGCATAACCG	chr2.hg19:g.172700922_172700937delCGGTTATGCCCAAAAT	ENSP00000388658:p.His136fs	109.0	0.0	0		101.0	13.0	0.128713	NM_003705	B3KR64|Q96AM8	Frame_Shift_Del	DEL	ENST00000422440.2	hg19	CCDS33327.1																																																																																			.	.	.	none		0.352	SLC25A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259010.2	NM_003705		-	172700937	CGGTTATGCCCAAAAT	-	172700922	7	5	85	1	0	1	0	1	0	0	0	0	14487	652	23	0	1670	0	SLC25A12	2	172700922	Frame_Shift_Del	DEL	CGGTTATGCCCAAAAT	TCGA-B1-A655-01A-11D-A31Z-10	4592663	172700922	70498451	16	5418											
TTN	7273	hgsc.bcm.edu	37	chr2	179577514	179577514	+	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	actttgtgatgtatctacatCgaacaactccagttcagcaa	13	12	6	10	1	2	1	1	1	1	0	4	2	3	1	1	0	4	3	1	0	5	4			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:179577514C>T	ENST00000591111.1	-	92	26511	c.26287G>A	c.(26287-26289)Gat>Aat	p.D8763N	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.D7836N|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.D9080N			Q8WZ42	TITIN_HUMAN	titin	12916	Ig-like 70.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTATCTACATCGAACAACTCC	0.418																																					p.D9080N		Atlas-SNP	.											.	TTN	18412	.	0			c.G27238A						PASS	.						88	84	85					2																	179577514		1928	4120	6048	SO:0001583	missense	7273	exon94			CTACATCGAACAA	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.26287G>A	chr2.hg19:g.179577514C>T	ENSP00000465570:p.Asp8763Asn	56.0	0.0	.		74.0	20.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.16	2.153386	0.38021	.	.	ENSG00000155657	ENST00000342992	T	0.38560	1.13	5.48	5.48	0.80851	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.23094	0.0558	N	0.03304	-0.355	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.08146	-1.0736	9	0.87932	D	0	.	12.9963	0.58648	0.0:0.9258:0.0:0.0742	.	8763	Q8WZ42	TITIN_HUMAN	N	7836	ENSP00000343764:D7836N	ENSP00000343764:D7836N	D	-	1	0	TTN	179285759	0.999000	0.42202	1.000000	0.80357	0.992000	0.81027	1.843000	0.39259	2.722000	0.93159	0.655000	0.94253	GAT	.	.	.	none		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179577514	C	T	179577514	3	4	85	1	0	0	0	0	1	0	0	0	16747	884	31	1	77367	1	TTN	2	179577514	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	6876592	179577514	63621859	17	5419											
FASTKD2	22868	hgsc.bcm.edu	37	chr2	207655323	207655323	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctatgtgtttccagatcTgcttattgtttgggttcaag	6	18	11	6	0	2	1	1	0	1	1	3	1	3	1	1	1	2	5	1	1	3	6			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:207655323T>C	ENST00000236980.6	+	11	2274	c.1926T>C	c.(1924-1926)tcT>tcC	p.S642S	FASTKD2_ENST00000402774.3_Silent_p.S642S|FASTKD2_ENST00000403094.3_Silent_p.S642S	NM_014929.3	NP_055744.2	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	642	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)|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)		TTTCCAGATCTGCTTATTGTT	0.363																																					p.S642S		Atlas-SNP	.											.	FASTKD2	49	.	0			c.T1926C						PASS	.						159	159	159					2																	207655323		2203	4300	6503	SO:0001819	synonymous_variant	22868	exon11			CAGATCTGCTTAT	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.1926T>C	chr2.hg19:g.207655323T>C		64.0	0.0	.		43.0	14.0	.	NM_001136193	Q9NVX6|Q9Y2H7	Silent	SNP	ENST00000236980.6	hg19	CCDS2371.1																																																																																			.	.	.	none		0.363	FASTKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256428.2	NM_014929		C	207655323	T	C	207655323	2	2	85	1	0	0	0	0	0	0	0	1	5693	1567	55	3		3	FASTKD2	2	207655323	Silent	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	28077809	207655323	35544050	18	5420											
LRRFIP1	9208	hgsc.bcm.edu	37	chr2	238666100	238666100	+	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	tgtctgttcctttcctcaggAaatccgacagctacagcaga	10	11	8	12	1	2	1	1	0	1	1	5	3	5	2	3	1	3	3	3	1	2	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr2:238666100A>T	ENST00000392000.4	+	9	864				LRRFIP1_ENST00000244815.5_Intron|LRRFIP1_ENST00000308482.9_Splice_Site_p.E378V|LRRFIP1_ENST00000289175.6_Intron	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1						innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|protein homodimerization activity (GO:0042803)			NS(1)|breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	29		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)		TTTCCTCAGGAAATCCGACAG	0.473																																					p.E378V		Atlas-SNP	.											.	LRRFIP1	171	.	0			c.A1133T						PASS	.						32	29	30					2																	238666100		1567	3579	5146	SO:0001627	intron_variant	9208	exon17			CTCAGGAAATCCG	AJ223075	CCDS2521.1, CCDS46551.1, CCDS46552.1, CCDS46553.1	2q37.3	2010-09-30			ENSG00000124831	ENSG00000124831			6702	protein-coding gene	gene with protein product	"GC-binding factor 2"	603256				9705290, 9525888, 16199883	Standard	NM_004735		Approved	FLAP-1, FLIIAP1, TRIP, GCF-2, HUFI-1	uc002vxe.3	Q32MZ4	OTTHUMG00000133339	ENST00000392000.4:c.747+1270A>T	chr2.hg19:g.238666100A>T		270.0	0.0	.		221.0	66.0	.	NM_001137550	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Missense_Mutation	SNP	ENST00000392000.4	hg19	CCDS46552.1	.	.	.	.	.	.	.	.	.	.	A	18.72	3.683862	0.68157	.	.	ENSG00000124831	ENST00000308482;ENST00000391999	T	0.53640	0.61	5.51	5.51	0.81932	.	.	.	.	.	T	0.51109	0.1655	M	0.75085	2.285	0.80722	D	1	B	0.32604	0.377	B	0.32465	0.146	T	0.57207	-0.7851	9	0.87932	D	0	.	14.8382	0.70201	1.0:0.0:0.0:0.0	.	378	E9PGZ2	.	V	378;368	ENSP00000310109:E378V	ENSP00000310109:E378V	E	+	2	0	LRRFIP1	238330839	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.546000	0.90661	2.097000	0.63578	0.533000	0.62120	GAA	.	.	.	none		0.473	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735		T	238666100	A	T	238666100	1	4	85	0	1	0	0	0	0	0	0	0	9034	260	9	5		5	LRRFIP1	2	238666100	Intron	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	31010777	238666100	4533273	19	5421											
ZNF167	55888	hgsc.bcm.edu	37	chr3	44612087	44612087	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catactggggagaaaccttaTgaatgcaatgagtgtggaga	14	9	13	5	0	0	4	0	2	0	2	0	6	0	4	1	3	3	1	1	3	5	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr3:44612087T>C	ENST00000273320.3	+	6	1914	c.1485T>C	c.(1483-1485)taT>taC	p.Y495Y	ZKSCAN7_ENST00000431636.1_Intron|ZKSCAN7_ENST00000341840.3_Intron|RP11-944L7.5_ENST00000419137.1_Intron|RP11-944L7.4_ENST00000457331.1_RNA|ZKSCAN7_ENST00000426540.1_Silent_p.Y495Y	NM_018651.2	NP_061121.2	Q9P0L1	ZKSC7_HUMAN	zinc finger with KRAB and SCAN domains 7	495					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										AGAAACCTTATGAATGCAATG	0.448																																					p.Y495Y		Atlas-SNP	.											.	.	.	.	0			c.T1485C						PASS	.						116	118	117					3																	44612087		2203	4300	6503	SO:0001819	synonymous_variant	55888	exon6			ACCTTATGAATGC	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.1485T>C	chr3.hg19:g.44612087T>C		88.0	0.0	.		91.0	9.0	.	NM_018651	A0PJV3|A8K5H0|Q6WL09|Q96FQ2	Silent	SNP	ENST00000273320.3	hg19	CCDS2715.1																																																																																			.	.	.	none		0.448	ZKSCAN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256752.4	NM_018651		C	44612087	T	C	44612087	2	2	85	1	0	0	0	0	0	0	0	1	17753	1471	51	3		3	ZNF167	3	44612087	Silent	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10		44612087	153410343	20	5422											
VPRBP	9730	hgsc.bcm.edu	37	chr3	51452313	51452313	+	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	cagtctgaatatcataaatcTttagagaagaagggatggga	16	10	11	4	0	3	3	1	1	2	2	3	6	3	5	0	2	0	0	0	2	7	4			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr3:51452313T>G	ENST00000335891.5	-	11	2266		c.e11-2					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)		ATCATAAATCTTTAGAGAAGA	0.373																																					.		Atlas-SNP	.											.	VPRBP	107	.	0			c.3442-2A>C						PASS	.						58	51	53					3																	51452313		1852	4108	5960	SO:0001630	splice_region_variant	9730	exon18			TAAATCTTTAGAG	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.2257-2A>C	chr3.hg19:g.51452313T>G		82.0	0.0	.		70.0	6.0	.	NM_001171904	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Splice_Site	SNP	ENST00000335891.5	hg19		.	.	.	.	.	.	.	.	.	.	T	25.0	4.587425	0.86851	.	.	ENSG00000145041	ENST00000423656;ENST00000335891	.	.	.	5.88	5.88	0.94601	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2997	0.82804	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	VPRBP	51427353	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.422000	0.80217	2.250000	0.74265	0.528000	0.53228	.	.	.	.	none		0.373	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014703	Intron	G	51452313	T	G	51452313	5	3	85	1	0	0	0	0	0	0	1	0	17197	1623	56	5	949	5	VPRBP	3	51452313	Splice_Site	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	6840226	51452313	146570117	21	5423											
MME	4311	hgsc.bcm.edu	37	chr3	154858036	154858036	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttctgtataacaagatgacAttggcccagatccaaaataa	16	10	6	9	0	1	3	0	1	1	2	2	3	2	3	2	1	1	1	2	1	6	5			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr3:154858036A>G	ENST00000460393.1	+	10	1032	c.912A>G	c.(910-912)acA>acG	p.T304T	MME_ENST00000462745.1_Silent_p.T304T|MME_ENST00000492661.1_Silent_p.T304T|MME_ENST00000360490.2_Silent_p.T304T|MME_ENST00000493237.1_Silent_p.T304T	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	304				T -> R (in Ref. 4; AAA51915). {ECO:0000305}.	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)	ACAAGATGACATTGGCCCAGA	0.323																																					p.T304T		Atlas-SNP	.											.	MME	133	.	0			c.A912G						PASS	.						74	69	71					3																	154858036		2203	4298	6501	SO:0001819	synonymous_variant	4311	exon10			GATGACATTGGCC		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.912A>G	chr3.hg19:g.154858036A>G		293.0	0.0	.		324.0	109.0	.	NM_007287	A8K6U6|D3DNJ9|Q3MIX4	Silent	SNP	ENST00000460393.1	hg19	CCDS3172.1																																																																																			.	.	.	none		0.323	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902		G	154858036	A	G	154858036	2	3	85	1	0	0	0	0	0	0	0	1	9652	204	8	3		3	MME	3	154858036	Silent	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	103405723	154858036	43164394	22	5424											
AFAP1	60312	hgsc.bcm.edu	37	chr4	7811366	7811366	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgggaacatcttcctcagcTgaggaggtctgctcgtctgt	6	12	13	10	1	4	1	1	1	3	0	6	3	5	3	1	3	3	2	1	3	1	1			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr4:7811366T>C	ENST00000360265.4	-	8	1263	c.1029A>G	c.(1027-1029)tcA>tcG	p.S343S	AFAP1_ENST00000420658.1_Silent_p.S343S|AFAP1_ENST00000382543.3_Silent_p.S343S|AFAP1_ENST00000358461.2_Silent_p.S343S			Q8N556	AFAP1_HUMAN	actin filament associated protein 1	343						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(4)|stomach(2)	32						CTTCCTCAGCTGAGGAGGTCT	0.537																																					p.S343S		Atlas-SNP	.											.	AFAP1	93	.	0			c.A1029G						PASS	.						145	115	125					4																	7811366		2203	4300	6503	SO:0001819	synonymous_variant	60312	exon9			CTCAGCTGAGGAG	AB209676	CCDS3397.1, CCDS47010.1	4p16	2014-02-12	2007-02-07		ENSG00000196526	ENSG00000196526		"Pleckstrin homology (PH) domain containing"	24017	protein-coding gene	gene with protein product		608252				14755689, 11641786, 11607843	Standard	NM_198595		Approved	AFAP-110, AFAP	uc011bwk.1	Q8N556	OTTHUMG00000125515	ENST00000360265.4:c.1029A>G	chr4.hg19:g.7811366T>C		50.0	0.0	.		55.0	18.0	.	NM_001134647	A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Silent	SNP	ENST00000360265.4	hg19	CCDS3397.1																																																																																			.	.	.	none		0.537	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2	NM_021638		C	7811366	T	C	7811366	2	2	85	1	0	0	0	0	0	0	0	1	353	1567	55	3		3	AFAP1	4	7811366	Silent	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10		7811366	183342910	23	5425											
GUF1	60558	hgsc.bcm.edu	37	chr4	44688034	44688034	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaggcaattattgaaagaaTccccccgtgagtatttggtg	11	12	10	8	1	1	3	1	2	0	1	2	3	2	3	3	2	0	2	3	2	5	4			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr4:44688034T>C	ENST00000281543.5	+	7	922	c.728T>C	c.(727-729)aTc>aCc	p.I243T	GUF1_ENST00000506793.1_3'UTR	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						ATTGAAAGAATCCCCCCGTGA	0.318																																					p.I243T		Atlas-SNP	.											.,1	GUF1	72	.	0			c.T728C						PASS	.						139	141	140					4																	44688034		2203	4298	6501	SO:0001583	missense	60558	exon7			AAAGAATCCCCCC		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.728T>C	chr4.hg19:g.44688034T>C	ENSP00000281543:p.Ile243Thr	40.0	0.0	.		42.0	11.0	.	NM_021927		Missense_Mutation	SNP	ENST00000281543.5	hg19	CCDS3468.1	.	.	.	.	.	.	.	.	.	.	T	19.13	3.768731	0.69878	.	.	ENSG00000151806	ENST00000281543	T	0.72615	-0.67	5.72	5.72	0.89469	Protein synthesis factor, GTP-binding (1);	0.045776	0.85682	D	0.000000	T	0.79082	0.4386	M	0.73430	2.235	0.80722	D	1	P	0.48834	0.916	P	0.51701	0.677	T	0.82159	-0.0595	10	0.87932	D	0	-21.9459	15.1683	0.72846	0.0:0.0:0.0:1.0	.	243	Q8N442	GUF1_HUMAN	T	243	ENSP00000281543:I243T	ENSP00000281543:I243T	I	+	2	0	GUF1	44382791	1.000000	0.71417	1.000000	0.80357	0.482000	0.33219	7.594000	0.82698	2.169000	0.68431	0.460000	0.39030	ATC	.	.	.	none		0.318	GUF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250469.3	NM_021927		C	44688034	T	C	44688034	3	2	85	1	0	0	0	0	1	0	0	0	6906	1435	50	3	754	3	GUF1	4	44688034	Missense_Mutation	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	36876668	44688034	146466242	24	5426											
PRDM8	56978	hgsc.bcm.edu	37	chr4	81123265	81123265	+	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	aagaccagcagcagcagcagCaggaggcacctttaggcccg	12	3	13	13	1	0	1	0	0	0	1	0	2	0	2	3	3	5	6	3	3	2	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr4:81123265C>G	ENST00000504452.1	+	8	1488	c.649C>G	c.(649-651)Cag>Gag	p.Q217E	PRDM8_ENST00000339711.4_Missense_Mutation_p.Q217E|PRDM8_ENST00000415738.2_Missense_Mutation_p.Q217E			Q9NQV8	PRDM8_HUMAN	PR domain containing 8	217	Gly-rich.|Poly-Gln.				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						gcagcagcagcagGAGGCACC	0.672											OREG0016246	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q217E		Atlas-SNP	.											.	PRDM8	44	.	0			c.C649G						PASS	.						18	24	22					4																	81123265		2023	4187	6210	SO:0001583	missense	56978	exon4			CAGCAGCAGGAGG	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.649C>G	chr4.hg19:g.81123265C>G	ENSP00000423985:p.Gln217Glu	80.0	0.0	.	1203	100.0	4.0	.	NM_001099403	A8K7X2|Q6IQ36	Missense_Mutation	SNP	ENST00000504452.1	hg19	CCDS43243.1	.	.	.	.	.	.	.	.	.	.	C	13.05	2.122577	0.37436	.	.	ENSG00000152784	ENST00000504452;ENST00000515013;ENST00000339711;ENST00000415738	T;T;T;T	0.63417	-0.04;0.54;-0.04;-0.04	4.66	4.66	0.58398	.	0.633514	0.14982	N	0.287212	T	0.46386	0.1390	N	0.24115	0.695	0.23889	N	0.996557	B	0.25105	0.118	B	0.24006	0.05	T	0.15263	-1.0443	10	0.02654	T	1	.	17.3364	0.87282	0.0:1.0:0.0:0.0	.	217	Q9NQV8	PRDM8_HUMAN	E	217	ENSP00000423985:Q217E;ENSP00000425149:Q217E;ENSP00000339764:Q217E;ENSP00000406998:Q217E	ENSP00000339764:Q217E	Q	+	1	0	PRDM8	81342289	0.010000	0.17322	0.510000	0.27712	0.511000	0.34104	1.329000	0.33770	2.420000	0.82092	0.313000	0.20887	CAG	.	.	.	none		0.672	PRDM8-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362793.1			G	81123265	C	G	81123265	3	3	85	1	0	0	0	0	1	0	0	0	12472	711	25	4	659	4	PRDM8	4	81123265	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	36435231	81123265	110031011	25	5427											
PKD2	5311	hgsc.bcm.edu	37	chr4	88996109	88996109	+	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	ggctgttggatggggtggccGaggtcagtagtcatgagctg	6	10	19	6	1	2	1	2	1	0	0	2	3	2	2	1	6	1	4	1	6	1	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr4:88996109G>C	ENST00000508588.1	+	9	1317	c.922G>C	c.(922-924)Gag>Cag	p.E308Q	PKD2_ENST00000237596.2_Missense_Mutation_p.E890Q|PKD2_ENST00000511337.1_3'UTR|PKD2_ENST00000502363.1_Missense_Mutation_p.E308Q			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)		TGGGGTGGCCGAGGTCAGTAG	0.468																																					p.E890Q		Atlas-SNP	.											.	PKD2	82	.	0			c.G2668C						PASS	.						138	108	118					4																	88996109		2203	4300	6503	SO:0001583	missense	5311	exon14			GTGGCCGAGGTCA	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.922G>C	chr4.hg19:g.88996109G>C	ENSP00000427131:p.Glu308Gln	113.0	0.0	.		87.0	18.0	.	NM_000297	Q8TB08|Q9P0T6|Q9Y3X8	Missense_Mutation	SNP	ENST00000508588.1	hg19		.	.	.	.	.	.	.	.	.	.	G	23.9	4.473075	0.84640	.	.	ENSG00000118762	ENST00000237596;ENST00000508588;ENST00000502363	T;D;D	0.92752	-0.39;-3.1;-3.1	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	D	0.95007	0.8384	L	0.54323	1.7	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.95429	0.8514	10	0.66056	D	0.02	-21.5133	18.3522	0.90342	0.0:0.0:1.0:0.0	.	890	Q13563	PKD2_HUMAN	Q	890;308;308	ENSP00000237596:E890Q;ENSP00000427131:E308Q;ENSP00000425289:E308Q	ENSP00000237596:E890Q	E	+	1	0	PKD2	89215133	1.000000	0.71417	0.985000	0.45067	0.635000	0.38103	9.576000	0.98192	2.318000	0.78349	0.650000	0.86243	GAG	.	.	.	none		0.468	PKD2-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000363253.2	NM_000297		C	88996109	G	C	88996109	3	2	85	1	0	0	0	0	1	0	0	0	11973	1059	37	4	2722	4	PKD2	4	88996109	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	7872844	88996109	102158167	26	5428											
DNAH5	1767	hgsc.bcm.edu	37	chr5	13839483	13839483	+	Missense_Mutation	SNP	A	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	acctgtctgtaagtggagttAttacaagcctgtcagtgcag	10	12	11	8	0	2	0	1	0	1	0	2	1	2	1	2	1	3	3	2	1	4	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr5:13839483A>C	ENST00000265104.4	-	35	5968	c.5864T>G	c.(5863-5865)aTa>aGa	p.I1955R		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1955	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)					AAGTGGAGTTATTACAAGCCT	0.418									Kartagener syndrome																												p.I1955R		Atlas-SNP	.											.	DNAH5	868	.	0			c.T5864G						PASS	.						126	129	128					5																	13839483		2203	4300	6503	SO:0001583	missense	1767	exon35	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GGAGTTATTACAA	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.5864T>G	chr5.hg19:g.13839483A>C	ENSP00000265104:p.Ile1955Arg	60.0	0.0	.		55.0	19.0	.	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	hg19	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.138855	0.77775	.	.	ENSG00000039139	ENST00000265104	T	0.14391	2.51	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.43678	0.1258	M	0.89163	3.01	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.53236	-0.8467	10	0.87932	D	0	.	13.8028	0.63212	1.0:0.0:0.0:0.0	.	1955	Q8TE73	DYH5_HUMAN	R	1955	ENSP00000265104:I1955R	ENSP00000265104:I1955R	I	-	2	0	DNAH5	13892483	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.307000	0.96226	1.870000	0.54199	0.533000	0.62120	ATA	.	.	.	none		0.418	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		C	13839483	A	C	13839483	3	2	85	1	0	0	0	0	1	0	0	0	4606	449	16	5	8190	5	DNAH5	5	13839483	Missense_Mutation	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10		13839483	167075777	27	5429											
AMACR	23600	hgsc.bcm.edu	37	chr5	33998825	33998825	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctgctgtcctgtaagtcgtAtagaaaggtgctccaccatc	9	12	9	11	1	1	1	0	0	1	1	5	1	3	1	3	1	2	4	3	1	4	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr5:33998825A>G	ENST00000335606.6	-	4	748	c.660T>C	c.(658-660)taT>taC	p.Y220Y	AMACR_ENST00000502637.1_Silent_p.Y205Y|AMACR_ENST00000512079.1_Silent_p.Y220Y|AMACR_ENST00000514195.1_5'UTR|RP11-1084J3.4_ENST00000382079.3_3'UTR|AMACR_ENST00000382072.2_Missense_Mutation_p.Y167H|AMACR_ENST00000382085.3_Silent_p.Y220Y|AMACR_ENST00000426255.2_Silent_p.Y220Y|AMACR_ENST00000382068.3_Missense_Mutation_p.Y167H|AMACR_ENST00000441713.2_Missense_Mutation_p.Y167H	NM_001167595.1|NM_014324.5	NP_001161067.1|NP_055139.4	Q9UHK6	AMACR_HUMAN	alpha-methylacyl-CoA racemase	220					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	alpha-methylacyl-CoA racemase activity (GO:0008111)|receptor binding (GO:0005102)			endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|stomach(1)|urinary_tract(1)	19						TGTAAGTCGTATAGAAAGGTG	0.458																																					p.Y167H		Atlas-SNP	.											.	AMACR	38	.	0			c.T499C						PASS	.						150	134	139					5																	33998825		2203	4300	6503	SO:0001819	synonymous_variant	23600	exon3			AGTCGTATAGAAA	AF047020	CCDS3902.1, CCDS3903.1, CCDS54836.1	5p13.2	2012-05-16			ENSG00000242110	ENSG00000242110	5.1.99.4		451	protein-coding gene	gene with protein product		604489				9307041	Standard	NM_014324		Approved	RACE	uc003jij.3	Q9UHK6	OTTHUMG00000090734	ENST00000335606.6:c.660T>C	chr5.hg19:g.33998825A>G		135.0	0.0	.		106.0	34.0	.	NM_203382	A5YM47|B8Y916|B8Y918|F8W9N1|O43673|Q3KT79|Q96GH1|Q9Y3Q1	Missense_Mutation	SNP	ENST00000335606.6	hg19	CCDS3902.1	.	.	.	.	.	.	.	.	.	.	A	11.20	1.568213	0.28003	.	.	ENSG00000242110	ENST00000382072;ENST00000441713	T;T	0.70164	-0.36;-0.46	5.34	0.947	0.19555	.	0.056699	0.64402	D	0.000001	T	0.45756	0.1358	.	.	.	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.14755	-1.0461	9	0.15499	T	0.54	-10.3866	8.1708	0.31254	0.5779:0.0:0.4221:0.0	.	167;167	Q6VRU4;Q9UHK6-4	.;.	H	167	ENSP00000371504:Y167H;ENSP00000403800:Y167H	ENSP00000371504:Y167H	Y	-	1	0	AMACR	34034582	0.996000	0.38824	0.997000	0.53966	0.411000	0.31082	0.457000	0.21875	0.241000	0.21283	-0.468000	0.05107	TAC	.	.	.	none		0.458	AMACR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207467.1	NM_014324		G	33998825	A	G	33998825	2	3	85	1	0	0	0	0	0	0	0	1	562	459	16	3		3	AMACR	5	33998825	Silent	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	20159342	33998825	146916435	28	5430											
ADAMTS6	11174	hgsc.bcm.edu	37	chr5	64766709	64766709	+	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	atcatgtttccactggggtcCatctttcccccaatattcta	8	15	5	13	0	3	0	1	0	2	0	6	0	6	0	4	2	0	1	4	2	3	5			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr5:64766709C>T	ENST00000536360.1	-	3	1171	c.358G>A	c.(358-360)Gga>Aga	p.G120R				Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 6	120						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)		CACTGGGGTCCATCTTTCCCC	0.373																																					p.G120R		Atlas-SNP	.											.	ADAMTS6	174	.	0			c.G358A						PASS	.						110	109	109					5																	64766709		2203	4300	6503	SO:0001583	missense	11174	exon3			GGGGTCCATCTTT	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.358G>A	chr5.hg19:g.64766709C>T	ENSP00000440995:p.Gly120Arg	77.0	0.0	.		84.0	22.0	.	NM_197941	Q59EX6|Q5IR87|Q5IR88|Q5IR89|Q68DL1	Missense_Mutation	SNP	ENST00000536360.1	hg19		.	.	.	.	.	.	.	.	.	.	C	25.7	4.664354	0.88251	.	.	ENSG00000049192	ENST00000381055;ENST00000261306;ENST00000464680;ENST00000536360	T;T;T	0.12039	2.72;2.72;2.72	5.78	5.78	0.91487	Peptidase M12B, propeptide (1);	0.000000	0.85682	D	0.000000	T	0.28830	0.0715	L	0.60455	1.87	0.80722	D	1	B	0.33857	0.429	P	0.47134	0.539	T	0.00599	-1.1651	10	0.28530	T	0.3	.	20.3754	0.98918	0.0:1.0:0.0:0.0	.	120	Q9UKP5	ATS6_HUMAN	R	120	ENSP00000370443:G120R;ENSP00000423551:G120R;ENSP00000440995:G120R	ENSP00000261306:G120R	G	-	1	0	ADAMTS6	64802465	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.112000	0.77086	2.894000	0.99253	0.591000	0.81541	GGA	.	.	.	none		0.373	ADAMTS6-201	KNOWN	basic	protein_coding	protein_coding		NM_197941		T	64766709	C	T	64766709	3	4	85	1	0	0	0	0	1	0	0	0	270	603	21	2	3087	2	ADAMTS6	5	64766709	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	30767884	64766709	116148551	29	5431											
PCDHGA5	56110	hgsc.bcm.edu	37	chr5	140745640	140745640	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggagctggcgcctcgctcCgcagaacctggctacctggt	5	8	14	14	3	0	1	0	0	0	1	2	2	1	2	4	4	3	4	4	4	2	1			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr5:140745640C>T	ENST00000518069.1	+	1	1743	c.1743C>T	c.(1741-1743)tcC>tcT	p.S581S	PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018918.2|NM_032054.1	NP_061741.1|NP_114443.1	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5	581	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)|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)			CGCCTCGCTCCGCAGAACCTG	0.627																																					p.S581S		Atlas-SNP	.											.	PCDHGA5	215	.	0			c.C1743T						PASS	.						97	108	105					5																	140745640		2203	4300	6503	SO:0001819	synonymous_variant	56110	exon1			TCGCTCCGCAGAA	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.1743C>T	chr5.hg19:g.140745640C>T		96.0	0.0	.		104.0	35.0	.	NM_032054	Q2M3F5|Q9Y5D2	Silent	SNP	ENST00000518069.1	hg19	CCDS54925.1																																																																																			.	.	.	none		0.627	PCDHGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374742.1	NM_018918		T	140745640	C	T	140745640	2	4	85	1	0	0	0	0	0	0	0	1	11564	639	23	1		1	PCDHGA5	5	140745640	Silent	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	75978931	140745640	40169620	30	5432											
UBTD2	92181	hgsc.bcm.edu	37	chr5	171661228	171661228	+	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	cttcaaggcatcccaaatctCtttccggccttcaaaagctg	10	11	6	14	1	3	0	2	0	1	0	6	0	5	0	3	2	1	2	3	2	4	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr5:171661228C>T	ENST00000393792.2	-	2	610	c.205G>A	c.(205-207)Gag>Aag	p.E69K		NM_152277.2	NP_689490.2	Q8WUN7	UBTD2_HUMAN	ubiquitin domain containing 2	69						cytoplasm (GO:0005737)				cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|prostate(1)|skin(1)	10	Renal(175;0.000159)|Lung NSC(126;0.00976)|all_lung(126;0.0156)	Medulloblastoma(196;0.00853)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TCCCAAATCTCTTTCCGGCCT	0.438																																					p.E69K		Atlas-SNP	.											UBTD2,colon,carcinoma,0,1	UBTD2	26	.	0			c.G205A						PASS	.						165	142	150					5																	171661228		2203	4300	6503	SO:0001583	missense	92181	exon2			AAATCTCTTTCCG	AF251700	CCDS4379.2	5q35.1	2008-10-30			ENSG00000168246	ENSG00000168246			24463	protein-coding gene	gene with protein product	"dendritic cell derived ubiquitin like protein"	610174				12507522	Standard	NM_152277		Approved	DC-UbP, MGC30022	uc003mbp.1	Q8WUN7	OTTHUMG00000130519	ENST00000393792.2:c.205G>A	chr5.hg19:g.171661228C>T	ENSP00000377381:p.Glu69Lys	100.0	0.0	.		93.0	32.0	.	NM_152277	Q8TDQ3	Missense_Mutation	SNP	ENST00000393792.2	hg19	CCDS4379.2	.	.	.	.	.	.	.	.	.	.	C	29.8	5.035386	0.93630	.	.	ENSG00000168246	ENST00000393792	T	0.64260	-0.09	5.51	5.51	0.81932	.	0.047322	0.85682	D	0.000000	D	0.84014	0.5379	M	0.93328	3.405	0.80722	D	1	D	0.54772	0.968	D	0.66847	0.947	D	0.87994	0.2751	10	0.87932	D	0	.	16.9267	0.86178	0.0:1.0:0.0:0.0	.	69	Q8WUN7	UBTD2_HUMAN	K	69	ENSP00000377381:E69K	ENSP00000377381:E69K	E	-	1	0	UBTD2	171593833	1.000000	0.71417	1.000000	0.80357	0.653000	0.38743	7.640000	0.83355	2.584000	0.87258	0.563000	0.77884	GAG	.	.	.	none		0.438	UBTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252936.1	NM_152277		T	171661228	C	T	171661228	3	4	85	1	0	0	0	0	1	0	0	0	16920	922	32	2	507	2	UBTD2	5	171661228	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	30915588	171661228	9254032	31	5433											
RGS14	10636	hgsc.bcm.edu	37	chr5	176798989	176798989	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctgcccgcccaagggccCagctccgaggagaccccacc	8	2	11	20	2	0	1	0	0	0	1	1	3	1	1	7	2	3	2	7	2	1	0			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr5:176798989C>T	ENST00000408923.3	+	15	1802	c.1614C>T	c.(1612-1614)ccC>ccT	p.P538P	RGS14_ENST00000506944.1_3'UTR	NM_006480.4	NP_006471.2	O43566	RGS14_HUMAN	regulator of G-protein signaling 14	538					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)			CCCAAGGGCCCAGCTCCGAGG	0.627																																					p.P538P	NSCLC(47;353 1896 28036)	Atlas-SNP	.											.	RGS14	34	.	0			c.C1614T						PASS	.						108	130	123					5																	176798989		2003	4169	6172	SO:0001819	synonymous_variant	10636	exon15			AGGGCCCAGCTCC	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.1614C>T	chr5.hg19:g.176798989C>T		60.0	0.0	.		44.0	18.0	.	NM_006480	O43565|Q506M1|Q6ZWA4|Q8TD62	Silent	SNP	ENST00000408923.3	hg19	CCDS43405.1	.	.	.	.	.	.	.	.	.	.	C	2.400	-0.337801	0.05278	.	.	ENSG00000169220	ENST00000511890	T	0.45276	0.9	4.52	1.21	0.21127	.	0.378652	0.25866	N	0.027786	T	0.45975	0.1369	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.44922	-0.9296	7	0.87932	D	0	-6.9952	11.7553	0.51872	0.4686:0.5314:0.0:0.0	.	.	.	.	L	409	ENSP00000422329:P409L	ENSP00000422329:P409L	P	+	2	0	RGS14	176731595	0.000000	0.05858	0.363000	0.25875	0.442000	0.32017	-0.925000	0.03992	0.463000	0.27118	0.644000	0.83932	CCA	.	.	.	none		0.627	RGS14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372676.1	NM_006480		T	176798989	C	T	176798989	2	4	85	1	0	0	0	0	0	0	0	1	13310	581	21	2		2	RGS14	5	176798989	Silent	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	5137761	176798989	4116271	32	5434											
HIST1H2BJ	8970	hgsc.bcm.edu	37	chr6	27100264	27100264	+	Missense_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	ggatctccctggaggtgatgGtcgagcgcttgttgtaatgc	6	12	15	8	2	1	1	0	1	1	0	3	4	1	3	1	4	2	3	1	4	1	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr6:27100264G>A	ENST00000607124.1	-	1	265	c.266C>T	c.(265-267)aCc>aTc	p.T89I	HIST1H2AG_ENST00000359193.2_5'Flank|HIST1H2BJ_ENST00000339812.2_Missense_Mutation_p.T89I|HIST1H2BJ_ENST00000541790.1_Missense_Mutation_p.T89I			P06899	H2B1J_HUMAN	histone cluster 1, H2bj	89					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						GGAGGTGATGGTCGAGCGCTT	0.602																																					p.T89I		Atlas-SNP	.											.	HIST1H2BJ	21	.	0			c.C266T						PASS	.						93	94	94					6																	27100264		2203	4297	6500	SO:0001583	missense	8970	exon1			GTGATGGTCGAGC	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.266C>T	chr6.hg19:g.27100264G>A	ENSP00000476136:p.Thr89Ile	62.0	0.0	.		33.0	12.0	.	NM_021058	B2R4J4|O60816	Missense_Mutation	SNP	ENST00000607124.1	hg19	CCDS4618.1	.	.	.	.	.	.	.	.	.	.	G	31	5.078432	0.94000	.	.	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	0.000487	T	0.67590	0.2909	M	0.93241	3.395	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.77512	-0.2560	10	0.87932	D	0	.	14.7851	0.69796	0.0:0.0:1.0:0.0	.	89	P06899	H2B1J_HUMAN	I	89	ENSP00000445633:T89I;ENSP00000342886:T89I	ENSP00000342886:T89I	T	-	2	0	HIST1H2BJ	27208243	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.903000	0.92573	2.268000	0.75426	0.585000	0.79938	ACC	.	.	.	none		0.602	HIST1H2BJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040138.2	NM_021058		A	27100264	G	A	27100264	3	1	85	1	0	0	0	0	1	0	0	0	7156	1261	44	2	118	2	HIST1H2BJ	6	27100264	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10		27100264	144014803	33	5435											
KCNK16	83795	hgsc.bcm.edu	37	chr6	39285639	39285639	+	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	ccctgtgcccaggtggttgaGgaagatcacgttaagcggga	9	8	15	9	2	1	2	1	1	0	1	1	4	1	4	2	4	2	2	2	4	2	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr6:39285639G>T	ENST00000373229.5	-	3	431	c.418C>A	c.(418-420)Ctc>Atc	p.L140I	KCNK16_ENST00000507712.1_Missense_Mutation_p.L75I|KCNK16_ENST00000437525.2_Missense_Mutation_p.L140I|KCNK16_ENST00000425054.2_Missense_Mutation_p.L140I|KCNK16_ENST00000373227.4_Missense_Mutation_p.L140I	NM_032115.3	NP_115491.1	Q96T55	KCNKG_HUMAN	potassium channel, subfamily K, member 16	140					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						AGGTGGTTGAGGAAGATCACG	0.592																																					p.L140I		Atlas-SNP	.											.	KCNK16	59	.	0			c.C418A						PASS	.						63	52	56					6																	39285639		2203	4300	6503	SO:0001583	missense	83795	exon3			GGTTGAGGAAGAT	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.418C>A	chr6.hg19:g.39285639G>T	ENSP00000362326:p.Leu140Ile	67.0	0.0	.		60.0	7.0	.	NM_001135106	B5TJL9|Q2M2N9|Q5TCF3|Q6X6Z3|Q6X6Z4|Q6X6Z5|Q9H591	Missense_Mutation	SNP	ENST00000373229.5	hg19	CCDS4843.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.504087	0.85176	.	.	ENSG00000095981	ENST00000373229;ENST00000425054;ENST00000507712;ENST00000373227;ENST00000437525	T;T;T;T;T	0.21734	1.99;1.99;1.99;1.99;1.99	5.65	4.78	0.61160	Ion transport 2 (1);	0.065126	0.64402	D	0.000007	T	0.26702	0.0653	L	0.41632	1.29	0.45979	D	0.998796	P;P;D;D	0.76494	0.939;0.707;0.986;0.999	P;P;P;D	0.77557	0.589;0.624;0.793;0.99	T	0.00599	-1.1651	10	0.39692	T	0.17	.	14.537	0.67969	0.0721:0.0:0.9279:0.0	.	140;140;140;140	B5TJL9;Q96T55-5;Q96T55-4;Q96T55	.;.;.;KCNKG_HUMAN	I	140;140;75;140;140	ENSP00000362326:L140I;ENSP00000391498:L140I;ENSP00000423842:L75I;ENSP00000362324:L140I;ENSP00000415375:L140I	ENSP00000362324:L140I	L	-	1	0	KCNK16	39393617	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.106000	0.64597	2.667000	0.90743	0.561000	0.74099	CTC	.	.	.	none		0.592	KCNK16-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040452.2	NM_032115		T	39285639	G	T	39285639	3	4	85	1	0	0	0	0	1	0	0	0	8070	1000	35	4	912	4	KCNK16	6	39285639	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	12185375	39285639	131829428	34	5436											
PRSS35	167681	hgsc.bcm.edu	37	chr6	84233613	84233613	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcacagctgtgaagctttcCacgggctgtagtggcattct	8	11	12	10	1	1	1	0	1	1	0	2	1	2	1	1	2	3	6	1	2	2	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr6:84233613C>T	ENST00000369700.3	+	2	630	c.453C>T	c.(451-453)tcC>tcT	p.S151S	PRSS35_ENST00000536636.1_Silent_p.S151S	NM_153362.2	NP_699193.2	Q8N3Z0	PRS35_HUMAN	protease, serine, 35	151	Peptidase S1.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(2)|large_intestine(12)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	32		all_cancers(76;0.000113)|Acute lymphoblastic leukemia(125;1.09e-08)|all_hematologic(105;3.12e-05)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0768)		TGAAGCTTTCCACGGGCTGTA	0.463																																					p.S151S		Atlas-SNP	.											.	PRSS35	60	.	0			c.C453T						PASS	.						101	100	101					6																	84233613		2203	4300	6503	SO:0001819	synonymous_variant	167681	exon2			GCTTTCCACGGGC	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.453C>T	chr6.hg19:g.84233613C>T		129.0	0.0	.		115.0	40.0	.	NM_153362	A8K7B3|Q9BQP6	Silent	SNP	ENST00000369700.3	hg19	CCDS4999.1																																																																																			.	.	.	none		0.463	PRSS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041352.1	NM_153362		T	84233613	C	T	84233613	2	4	85	1	0	0	0	0	0	0	0	1	12634	581	21	2		2	PRSS35	6	84233613	Silent	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	44947974	84233613	86881454	35	5437											
ENPP3	5169	hgsc.bcm.edu	37	chr6	132059234	132059234	+	Missense_Mutation	SNP	A	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	cacagaaagaaatggagtaaAtgtggttagtggaccaatat	17	9	11	4	0	0	2	0	0	0	2	0	4	0	4	1	3	0	2	1	3	7	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr6:132059234A>C	ENST00000414305.1	+	24	2559	c.2231A>C	c.(2230-2232)aAt>aCt	p.N744T	ENPP3_ENST00000358229.5_3'UTR|ENPP3_ENST00000357639.3_Missense_Mutation_p.N744T			O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 3	744	Nuclease.		N -> H (in dbSNP:rs36094194).		immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		AATGGAGTAAATGTGGTTAGT	0.303																																					p.N744T		Atlas-SNP	.											.	ENPP3	117	.	0			c.A2231C						PASS	.						114	125	121					6																	132059234		2203	4297	6500	SO:0001583	missense	5169	exon23			GAGTAAATGTGGT	AF005632	CCDS5148.1	6q22	2010-06-23			ENSG00000154269	ENSG00000154269	3.1.4.1, 3.6.1.9	"CD molecules"	3358	protein-coding gene	gene with protein product		602182		PDNP3		9344668	Standard	NM_005021		Approved	PD-IBETA, gp130RB13-6, B10, CD203c	uc003qcv.3	O14638	OTTHUMG00000016292	ENST00000414305.1:c.2231A>C	chr6.hg19:g.132059234A>C	ENSP00000406261:p.Asn744Thr	91.0	0.0	.		78.0	29.0	.	NM_005021	Q5JTL3	Missense_Mutation	SNP	ENST00000414305.1	hg19	CCDS5148.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.286561	0.80803	.	.	ENSG00000154269	ENST00000414305;ENST00000357639	T;T	0.69040	-0.37;-0.37	6.08	6.08	0.98989	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.196594	0.45867	D	0.000330	D	0.83036	0.5167	M	0.89534	3.04	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86746	0.1957	10	0.87932	D	0	-31.3676	16.6512	0.85203	1.0:0.0:0.0:0.0	.	744	O14638	ENPP3_HUMAN	T	744	ENSP00000406261:N744T;ENSP00000350265:N744T	ENSP00000350265:N744T	N	+	2	0	ENPP3	132100927	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.974000	0.88039	2.333000	0.79357	0.482000	0.46254	AAT	.	.	.	none		0.303	ENPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043627.2			C	132059234	A	C	132059234	3	2	85	1	0	0	0	0	1	0	0	0	5133	101	4	5	2321	5	ENPP3	6	132059234	Missense_Mutation	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	47825621	132059234	39055833	36	5438											
SNX9	51429	hgsc.bcm.edu	37	chr6	158358486	158358486	+	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	ccaaagaaagatctccatttCctgatggaatgtaatcacga	15	10	7	9	1	2	3	1	1	1	2	4	5	3	4	3	1	0	1	3	1	4	2	rs532553158		TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr6:158358486C>A	ENST00000392185.3	+	15	1635	c.1464C>A	c.(1462-1464)ttC>ttA	p.F488L		NM_016224.3	NP_057308.1	Q9Y5X1	SNX9_HUMAN	sorting nexin 9	488	BAR.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|lipid tube assembly (GO:0060988)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein oligomerization (GO:0032461)|receptor-mediated endocytosis (GO:0006898)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle membrane (GO:0030659)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	1-phosphatidylinositol binding (GO:0005545)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)	p.F488F(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	20		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)		ATCTCCATTTCCTGATGGAAT	0.378																																					p.F488L		Atlas-SNP	.											SNX9,head_neck,malignant_melanoma,0,1	SNX9	43	.	1	Substitution - coding silent(1)	skin(1)	c.C1464A						PASS	.						149	143	145					6																	158358486		2203	4300	6503	SO:0001583	missense	51429	exon15			CCATTTCCTGATG	AF121859	CCDS5253.1	6q25.1-q26	2008-05-22			ENSG00000130340	ENSG00000130340		"Sorting nexins"	14973	protein-coding gene	gene with protein product		605952				10531379, 17609109	Standard	NM_016224		Approved	SH3PX1, SDP1, SH3PXD3A	uc003qqv.1	Q9Y5X1	OTTHUMG00000015903	ENST00000392185.3:c.1464C>A	chr6.hg19:g.158358486C>A	ENSP00000376024:p.Phe488Leu	79.0	0.0	.		80.0	20.0	.	NM_016224	Q9BSI7|Q9BVM1|Q9UJH6|Q9UP20	Missense_Mutation	SNP	ENST00000392185.3	hg19	CCDS5253.1	.	.	.	.	.	.	.	.	.	.	C	18.01	3.528865	0.64860	.	.	ENSG00000130340	ENST00000539592;ENST00000392185;ENST00000252631	T	0.40476	1.03	5.39	2.61	0.31194	Sorting nexin protein, WASP-binding domain (1);	0.045544	0.85682	D	0.000000	T	0.20292	0.0488	L	0.43152	1.355	0.80722	D	1	P	0.52842	0.956	B	0.41619	0.361	T	0.03344	-1.1046	10	0.48119	T	0.1	-10.3916	8.3841	0.32491	0.0:0.6569:0.0:0.3431	.	488	Q9Y5X1	SNX9_HUMAN	L	488;488;288	ENSP00000376024:F488L	ENSP00000252631:F288L	F	+	3	2	SNX9	158278474	0.996000	0.38824	1.000000	0.80357	0.985000	0.73830	0.455000	0.21843	2.673000	0.90976	0.563000	0.77884	TTC	.	.	.	none		0.378	SNX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042856.1			A	158358486	C	A	158358486	3	1	85	1	0	0	0	0	1	0	0	0	14922	854	30	4	1522	4	SNX9	6	158358486	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	26299252	158358486	12756581	37	5439											
SCIN	85477	hgsc.bcm.edu	37	chr7	12680013	12680013	+	Frame_Shift_Del	DEL	T	T	-																															gagcctgttcacctactgagTttgttcaaagacaaaccgct																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr7:12680013delT	ENST00000297029.5	+	11	1553	c.1452delT	c.(1450-1452)agtfs	p.S484fs	SCIN_ENST00000519209.1_Frame_Shift_Del_p.S237fs|SCIN_ENST00000445618.2_Frame_Shift_Del_p.S237fs	NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	484	Ca(2+)-dependent actin binding.				actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	17				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		ACCTACTGAGTTTGTTCAAAG	0.453																																					p.S484fs		Atlas-Indel,Pindel	.											.	SCIN	105	.	0			c.1451delG						PASS	.						58	56	57					7																	12680013		1863	4100	5963	SO:0001589	frameshift_variant	85477	exon11			.	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.1452delT	chr7.hg19:g.12680013delT	ENSP00000297029:p.Ser484fs	59.0	0.0	0		51.0	17.0	0.333333	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Frame_Shift_Del	DEL	ENST00000297029.5	hg19	CCDS47545.1																																																																																			.	.	.	none		0.453	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128		-	12680013	T	-	12680013	7	5	85	1	0	1	0	1	0	0	0	0	13918	1722	60	0	1494	0	SCIN	7	12680013	Frame_Shift_Del	DEL	T	TCGA-B1-A655-01A-11D-A31Z-10		12680013	146458650	38	5440											
GCK	2645	hgsc.bcm.edu	37	chr7	44185276	44185276	+	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	cgcagtcggtggtcgagggtCgcagccccagcgtgctcagg	5	6	17	13	5	1	0	1	0	0	0	4	1	1	0	2	4	3	3	2	4	0	0			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr7:44185276C>G	ENST00000403799.3	-	9	1542	c.1073G>C	c.(1072-1074)cGa>cCa	p.R358P	GCK_ENST00000345378.2_Missense_Mutation_p.R359P|GCK_ENST00000395796.3_Missense_Mutation_p.R357P|GCK_ENST00000437084.1_Missense_Mutation_p.R341P	NM_000162.3	NP_000153.1	P35557	HXK4_HUMAN	glucokinase (hexokinase 4)	358	Hexokinase type-2.				calcium ion import (GO:0070509)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|cellular response to glucose starvation (GO:0042149)|cellular response to insulin stimulus (GO:0032869)|cellular response to leptin stimulus (GO:0044320)|detection of glucose (GO:0051594)|endocrine pancreas development (GO:0031018)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|NADP metabolic process (GO:0006739)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of gluconeogenesis (GO:0045721)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of insulin secretion (GO:0032024)|positive regulation of phosphorylation (GO:0042327)|regulation of glucose transport (GO:0010827)|regulation of glycolytic process (GO:0006110)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transport (GO:0043266)|second-messenger-mediated signaling (GO:0019932)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|secretory granule (GO:0030141)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|magnesium ion binding (GO:0000287)			central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(17)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	37						GGTCGAGGGTCGCAGCCCCAG	0.697																																					p.R359P		Atlas-SNP	.											.	GCK	125	.	0			c.G1076C						PASS	.						30	34	33					7																	44185276		2203	4299	6502	SO:0001583	missense	2645	exon9			GAGGGTCGCAGCC	AF041014	CCDS5479.1, CCDS5480.1, CCDS5481.1	7p15.3-p15.1	2008-02-07	2008-02-07		ENSG00000106633	ENSG00000106633	2.7.1.2, 2.7.1.1		4195	protein-coding gene	gene with protein product		138079	"maturity onset diabetes of the young 2"	MODY2		1740341, 1502186	Standard	NM_033507		Approved	HK4	uc003tkk.1	P35557	OTTHUMG00000022903	ENST00000403799.3:c.1073G>C	chr7.hg19:g.44185276C>G	ENSP00000384247:p.Arg358Pro	60.0	0.0	.		70.0	27.0	.	NM_033507	A4D2J2|A4D2J3|Q05810	Missense_Mutation	SNP	ENST00000403799.3	hg19	CCDS5479.1	.	.	.	.	.	.	.	.	.	.	C	11.13	1.547708	0.27652	.	.	ENSG00000106633	ENST00000336642;ENST00000403799;ENST00000395796;ENST00000345378;ENST00000437084	D;D;D;D;D	0.98044	-4.68;-4.68;-4.68;-4.68;-4.68	5.2	4.22	0.49857	Hexokinase, C-terminal (1);	0.488216	0.21760	N	0.069537	D	0.92961	0.7760	N	0.17248	0.465	0.36805	D	0.885564	B;B;B;B;B	0.32128	0.357;0.0;0.308;0.0;0.357	B;B;B;B;B	0.34536	0.094;0.001;0.185;0.003;0.094	D	0.91899	0.5530	10	0.34782	T	0.22	-12.1896	7.8212	0.29288	0.2196:0.6875:0.0:0.0928	.	358;359;357;341;358	P35557;P35557-2;P35557-3;C9JQD1;A7LFL1	HXK4_HUMAN;.;.;.;.	P	42;358;357;359;341	ENSP00000338009:R42P;ENSP00000384247:R358P;ENSP00000379142:R357P;ENSP00000223366:R359P;ENSP00000402840:R341P	ENSP00000338009:R42P	R	-	2	0	GCK	44151801	0.070000	0.21116	0.955000	0.39395	0.307000	0.27823	1.831000	0.39141	2.403000	0.81681	0.462000	0.41574	CGA	.	.	.	none		0.697	GCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251069.2			G	44185276	C	G	44185276	3	3	85	1	0	0	0	0	1	0	0	0	6300	884	31	4	332	4	GCK	7	44185276	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	31505263	44185276	114953387	39	5441											
POM121C	100101267	hgsc.bcm.edu	37	chr7	75070316	75070316	+	Missense_Mutation	SNP	A	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	tcttctctttgagggcactcAgtacagtctcctttgcacat	7	15	7	12	0	4	1	1	1	3	0	6	1	4	1	1	1	2	3	1	1	1	4			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr7:75070316A>C	ENST00000257665.5	-	3	868	c.869T>G	c.(868-870)cTg>cGg	p.L290R	POM121C_ENST00000453279.2_Missense_Mutation_p.L48R			A8CG34	P121C_HUMAN	POM121 transmembrane nucleoporin C	290	Pore side. {ECO:0000255}.|Required for targeting to the nucleus and nuclear pore complex.				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						GAGGGCACTCAGTACAGTCTC	0.438																																					p.L48R		Atlas-SNP	.											.	POM121C	46	.	0			c.T143G						PASS	.						141	153	149					7																	75070316		2203	4298	6501	SO:0001583	missense	100101267	exon5			GCACTCAGTACAG		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.869T>G	chr7.hg19:g.75070316A>C	ENSP00000257665:p.Leu290Arg	146.0	0.0	.		138.0	33.0	.	NM_001099415	O75115|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000257665.5	hg19		.	.	.	.	.	.	.	.	.	.	A	13.49	2.253891	0.39896	.	.	ENSG00000135213	ENST00000257665;ENST00000453279	T;T	0.39229	2.64;1.09	4.27	3.09	0.35607	.	0.499492	0.14888	N	0.292593	T	0.62233	0.2411	M	0.81497	2.545	0.44142	D	0.996934	D	0.89917	1.0	D	0.74674	0.984	T	0.60767	-0.7198	10	0.87932	D	0	.	8.0021	0.30304	0.8181:0.0:0.0:0.1819	.	290	A8CG34	P121C_HUMAN	R	290;48	ENSP00000257665:L290R;ENSP00000414208:L48R	ENSP00000257665:L290R	L	-	2	0	POM121C	74908252	1.000000	0.71417	0.998000	0.56505	0.211000	0.24417	6.656000	0.74396	0.601000	0.29879	-0.676000	0.03789	CTG	.	.	.	none		0.438	POM121C-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000343919.2	NM_001099415		C	75070316	A	C	75070316	3	2	85	1	0	0	0	0	1	0	0	0	12247	188	7	5	2864	5	POM121C	7	75070316	Missense_Mutation	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	30885040	75070316	84068347	40	5442											
LHFPL3	375612	hgsc.bcm.edu	37	chr7	103969251	103969251	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccggagccgccgccgctgcCgccgccgccgccgccgcgat	2	2	14	23	11	0	0	0	0	0	0	0	2	0	1	10	1	2	1	10	1	0	0			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr7:103969251C>T	ENST00000535008.1	+	1	148	c.24C>T	c.(22-24)gcC>gcT	p.A8A	LHFPL3_ENST00000543266.1_Silent_p.A8A|LHFPL3_ENST00000401970.2_5'UTR|LHFPL3_ENST00000424859.1_5'UTR			Q86UP9	LHPL3_HUMAN	lipoma HMGIC fusion partner-like 3	8						integral component of membrane (GO:0016021)		p.A8A(1)		kidney(1)|large_intestine(2)|lung(6)	9						ccgccgctgccgccgccgccg	0.721																																					p.A8A		Atlas-SNP	.											LHFPL3,NS,carcinoma,0,1	LHFPL3	24	.	1	Substitution - coding silent(1)	kidney(1)	c.C24T						PASS	.						11	14	13					7																	103969251		1949	4092	6041	SO:0001819	synonymous_variant	375612	exon1			CGCTGCCGCCGCC	AY260763		7q22.2	2006-06-13			ENSG00000187416	ENSG00000187416			6589	protein-coding gene	gene with protein product		609719	"lipoma HMGIC fusion partner-like 4"	LHFPL4		10329012	Standard	NM_199000		Approved		uc003vce.3	Q86UP9	OTTHUMG00000157273	ENST00000535008.1:c.24C>T	chr7.hg19:g.103969251C>T		29.0	1.0	.		37.0	2.0	.	NM_199000	A1L383|A4D0Q5	Silent	SNP	ENST00000535008.1	hg19																																																																																				.	.	.	none		0.721	LHFPL3-201	KNOWN	basic	protein_coding	protein_coding		NM_199000		T	103969251	C	T	103969251	2	4	85	1	0	0	0	0	0	0	0	1	8773	639	23	1		1	LHFPL3	7	103969251	Silent	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	28898935	103969251	55169412	41	5443											
MYOM2	9172	hgsc.bcm.edu	37	chr8	2020508	2020508	+	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	tcaccttcaggagggaaggcGagacggtcactctcaagtgc	10	7	13	11	2	4	1	4	0	1	1	5	4	4	3	1	4	1	0	1	4	2	1			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr8:2020508G>C	ENST00000262113.4	+	9	1018	c.877G>C	c.(877-879)Gag>Cag	p.E293Q	MYOM2_ENST00000523438.1_Intron	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	293	Ig-like C2-type 2.				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)		GAGGGAAGGCGAGACGGTCAC	0.602																																					p.E293Q		Atlas-SNP	.											MYOM2,NS,malignant_melanoma,0,2	MYOM2	251	.	0			c.G877C						PASS	.						85	70	75					8																	2020508		2203	4300	6503	SO:0001583	missense	9172	exon9			GAAGGCGAGACGG		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.877G>C	chr8.hg19:g.2020508G>C	ENSP00000262113:p.Glu293Gln	37.0	0.0	.		29.0	9.0	.	NM_003970	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	hg19	CCDS5957.1	.	.	.	.	.	.	.	.	.	.	G	17.83	3.485155	0.63962	.	.	ENSG00000036448	ENST00000262113	T	0.46063	0.88	5.13	4.25	0.50352	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.208574	0.40818	N	0.001006	T	0.46308	0.1386	M	0.63843	1.955	0.80722	D	1	B	0.29136	0.234	B	0.34180	0.177	T	0.50206	-0.8855	10	0.72032	D	0.01	.	15.6628	0.77203	0.0:0.1376:0.8624:0.0	.	293	P54296	MYOM2_HUMAN	Q	293	ENSP00000262113:E293Q	ENSP00000262113:E293Q	E	+	1	0	MYOM2	2007915	1.000000	0.71417	0.800000	0.32199	0.700000	0.40528	4.275000	0.58927	1.132000	0.42129	0.655000	0.94253	GAG	.	.	.	none		0.602	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970		C	2020508	G	C	2020508	3	2	85	1	0	0	0	0	1	0	0	0	10099	1059	37	4	907	4	MYOM2	8	2020508	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10		2020508	144343514	42	5444											
LOXL2	4017	hgsc.bcm.edu	37	chr8	23198538	23198538	+	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	tattgtatgtcctctccccaGggaagccaaacatgccgcag	10	9	9	13	1	1	0	0	0	1	0	3	1	2	1	5	1	3	2	5	1	4	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr8:23198538G>A	ENST00000389131.3	-	4	1079	c.710C>T	c.(709-711)cCt>cTt	p.P237L	RP11-177H13.2_ENST00000519692.1_RNA	NM_002318.2	NP_002309.1	Q9Y4K0	LOXL2_HUMAN	lysyl oxidase-like 2	237	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				aging (GO:0007568)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial to mesenchymal transition (GO:0001837)|histone modification (GO:0016570)|negative regulation of transcription, DNA-templated (GO:0045892)|oxidation-reduction process (GO:0055114)|positive regulation of chondrocyte differentiation (GO:0032332)|protein deamination (GO:0018277)|response to copper ion (GO:0046688)|response to hypoxia (GO:0001666)|sprouting angiogenesis (GO:0002040)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|chromosome (GO:0005694)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|electron carrier activity (GO:0009055)|methylated histone binding (GO:0035064)|oligosaccharide binding (GO:0070492)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)|transcription corepressor activity (GO:0003714)			breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(5)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(55;0.0453)|Breast(100;0.143)		Colorectal(74;0.0288)|COAD - Colon adenocarcinoma(73;0.096)		CCTCTCCCCAGGGAAGCCAAA	0.537																																					p.P237L		Atlas-SNP	.											.	LOXL2	97	.	0			c.C710T						PASS	.						163	132	142					8																	23198538		2203	4300	6503	SO:0001583	missense	4017	exon4			TCCCCAGGGAAGC	U89942	CCDS34864.1	8p21.3	2008-05-15				ENSG00000134013			6666	protein-coding gene	gene with protein product		606663				9722957	Standard	NM_002318		Approved	WS9-14	uc003xdh.1	Q9Y4K0		ENST00000389131.3:c.710C>T	chr8.hg19:g.23198538G>A	ENSP00000373783:p.Pro237Leu	45.0	0.0	.		45.0	15.0	.	NM_002318	B2R5Q0|Q53HV3|Q9BW70|Q9Y5Y8	Missense_Mutation	SNP	ENST00000389131.3	hg19	CCDS34864.1	.	.	.	.	.	.	.	.	.	.	G	19.94	3.920583	0.73213	.	.	ENSG00000134013	ENST00000389131	T	0.60424	0.19	5.83	5.83	0.93111	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.047123	0.85682	D	0.000000	T	0.78381	0.4274	M	0.83118	2.625	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.80636	-0.1294	10	0.72032	D	0.01	.	16.8345	0.85953	0.0:0.0:1.0:0.0	.	237	Q9Y4K0	LOXL2_HUMAN	L	237	ENSP00000373783:P237L	ENSP00000373783:P237L	P	-	2	0	LOXL2	23254483	1.000000	0.71417	0.975000	0.42487	0.192000	0.23643	9.751000	0.98889	2.750000	0.94351	0.655000	0.94253	CCT	.	.	.	none		0.537	LOXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375603.1			A	23198538	G	A	23198538	3	1	85	1	0	0	0	0	1	0	0	0	8907	1000	35	2	1658	2	LOXL2	8	23198538	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	21178030	23198538	123165484	43	5445											
EXOSC4	54512	hgsc.bcm.edu	37	chr8	145134932	145134932	+	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	accttcagcacaggtgagcgCaagcgacggccacatgggga	11	4	14	12	3	1	1	1	1	0	0	1	3	1	2	2	4	3	2	2	4	1	1			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr8:145134932C>T	ENST00000316052.5	+	2	361	c.258C>T	c.(256-258)cgC>cgT	p.R86R	GPAA1_ENST00000361036.6_5'Flank|EXOSC4_ENST00000525936.1_Intron|GPAA1_ENST00000355091.4_5'Flank|CTD-3065J16.9_ENST00000524499.1_RNA	NM_019037.2	NP_061910.1	Q9NPD3	EXOS4_HUMAN	exosome component 4	86					defense response to virus (GO:0051607)|DNA deamination (GO:0045006)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|maturation of 5.8S rRNA (GO:0000460)|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)|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)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	3'-5'-exoribonuclease activity (GO:0000175)|AU-rich element binding (GO:0017091)			lung(4)|prostate(1)|upper_aerodigestive_tract(2)	7	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;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.48e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CAGGTGAGCGCAAGCGACGGC	0.627																																					p.R86R		Atlas-SNP	.											EXOSC4,right_upper_lobe,carcinoma,0,1	EXOSC4	19	.	0			c.C258T						PASS	.						84	83	83					8																	145134932		2203	4300	6503	SO:0001819	synonymous_variant	54512	exon2			TGAGCGCAAGCGA	AF281133	CCDS6414.1	8q24.3	2004-03-26			ENSG00000178896	ENSG00000178896			18189	protein-coding gene	gene with protein product	"exosome component Rrp41"	606491				11110791	Standard	NM_019037		Approved	hRrp41p, FLJ20591, Rrp41p, RRP41, RRP41A, Ski6p, SKI6, p12A	uc003zau.3	Q9NPD3	OTTHUMG00000165437	ENST00000316052.5:c.258C>T	chr8.hg19:g.145134932C>T		86.0	0.0	.		118.0	40.0	.	NM_019037		Silent	SNP	ENST00000316052.5	hg19	CCDS6414.1																																																																																			.	.	.	none		0.627	EXOSC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384065.1	NM_019037		T	145134932	C	T	145134932	2	4	85	1	0	0	0	0	0	0	0	1	5319	697	25	2		2	EXOSC4	8	145134932	Silent	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	121936394	145134932	1229090	44	5446											
SLC39A4	55630	hgsc.bcm.edu	37	chr8	145640398	145640398	+	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	tgttgctggagctgatgaggGgcacagggtcccagctgctg	6	9	17	9	0	0	2	0	2	0	0	1	3	1	3	1	4	4	6	1	4	0	1	rs200044971		TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr8:145640398G>T	ENST00000301305.3	-	4	869	c.764C>A	c.(763-765)cCc>cAc	p.P255H	SLC39A4_ENST00000276833.5_Missense_Mutation_p.P230H|SLC39A4_ENST00000531013.1_5'Flank	NM_130849.2	NP_570901	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter), member 4	255					cellular response to zinc ion starvation (GO:0034224)|cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	14	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;1.12e-40)|all cancers(56;8.17e-36)|BRCA - Breast invasive adenocarcinoma(115;0.0407)|Colorectal(110;0.055)			GCTGATGAGGGGCACAGGGTC	0.672																																					p.P255H		Atlas-SNP	.											.	SLC39A4	54	.	0			c.C764A						PASS	.						40	45	43					8																	145640398		2203	4300	6503	SO:0001583	missense	55630	exon4			ATGAGGGGCACAG	AK025537	CCDS6424.1, CCDS43782.1	8q24.3	2013-05-22			ENSG00000147804	ENSG00000147804		"Solute carriers"	17129	protein-coding gene	gene with protein product		607059	"acrodermatitis enteropathica, zinc-deficiency type"	AEZ		12801924, 12659941, 14709598	Standard	NM_017767		Approved	ZIP4, AWMS2	uc003zcq.3	Q6P5W5		ENST00000301305.3:c.764C>A	chr8.hg19:g.145640398G>T	ENSP00000301305:p.Pro255His	32.0	0.0	.		38.0	15.0	.	NM_130849	Q7L5S5|Q9H6T8|Q9NXC4	Missense_Mutation	SNP	ENST00000301305.3	hg19	CCDS6424.1	.	.	.	.	.	.	.	.	.	.	G	15.50	2.850768	0.51270	.	.	ENSG00000147804	ENST00000276833;ENST00000301305;ENST00000526658	T;T;T	0.57436	0.4;0.4;0.4	5.0	-4.46	0.03536	.	3.799390	0.00575	N	0.000304	T	0.39989	0.1099	L	0.47716	1.5	0.09310	N	1	B;B	0.18461	0.028;0.028	B;B	0.16722	0.016;0.016	T	0.09662	-1.0664	10	0.38643	T	0.18	-5.3671	0.812	0.01095	0.3985:0.1207:0.2362:0.2446	.	255;230	Q6P5W5;A6NDY5	S39A4_HUMAN;.	H	230;255;161	ENSP00000276833:P230H;ENSP00000301305:P255H;ENSP00000434512:P161H	ENSP00000276833:P230H	P	-	2	0	SLC39A4	145611206	0.002000	0.14202	0.000000	0.03702	0.037000	0.13140	-0.570000	0.05895	-0.723000	0.04915	-0.320000	0.08662	CCC	.	G|0.998;A|0.002	.	alt		0.672	SLC39A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382688.1			T	145640398	G	T	145640398	3	4	85	1	0	0	0	0	1	0	0	0	14633	1232	43	4	1215	4	SLC39A4	8	145640398	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	505466	145640398	723624	45	5447											
C9orf93	203238	hgsc.bcm.edu	37	chr9	15729747	15729747	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcacagacaaaagaaggaacTagagctgcagtattctgaac	17	6	10	8	0	1	4	0	1	1	3	1	5	1	5	0	1	4	4	0	1	7	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr9:15729747T>C	ENST00000380701.3	+	16	2328	c.2000T>C	c.(1999-2001)cTa>cCa	p.L667P	CCDC171_ENST00000297641.3_Missense_Mutation_p.L667P	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	667																	AAGAAGGAACTAGAGCTGCAG	0.463																																					p.L667P		Atlas-SNP	.											.	.	.	.	0			c.T2000C						PASS	.						96	99	98					9																	15729747		2203	4299	6502	SO:0001583	missense	203238	exon16			AGGAACTAGAGCT	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.2000T>C	chr9.hg19:g.15729747T>C	ENSP00000370077:p.Leu667Pro	101.0	0.0	.		120.0	35.0	.	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Missense_Mutation	SNP	ENST00000380701.3	hg19	CCDS6481.1	.	.	.	.	.	.	.	.	.	.	T	16.14	3.037598	0.54896	.	.	ENSG00000164989	ENST00000297641;ENST00000380701	T;T	0.25912	1.77;1.77	5.61	5.61	0.85477	.	0.250009	0.33650	N	0.004693	T	0.39253	0.1071	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.76575	0.988;0.982;0.982	T	0.30563	-0.9974	10	0.72032	D	0.01	-6.1701	15.7924	0.78376	0.0:0.0:0.0:1.0	.	675;667;667	B7ZM22;Q6TFL3-3;Q6TFL3	.;.;CI093_HUMAN	P	667	ENSP00000297641:L667P;ENSP00000370077:L667P	ENSP00000297641:L667P	L	+	2	0	C9orf93	15719747	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	5.833000	0.69349	2.130000	0.65690	0.477000	0.44152	CTA	.	.	.	none		0.463	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550		C	15729747	T	C	15729747	3	2	85	1	0	0	0	0	1	0	0	0	2508	1522	53	3	2058	3	C9orf93	9	15729747	Missense_Mutation	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10		15729747	125483684	46	5448											
NPR2	4882	hgsc.bcm.edu	37	chr9	35792786	35792786	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgcgggtgctgtggcctcTggtttttcggctaagaatga	6	13	14	8	2	1	2	0	1	1	1	2	2	1	2	1	4	2	3	1	4	2	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr9:35792786T>C	ENST00000342694.2	+	1	636	c.381T>C	c.(379-381)tcT>tcC	p.S127S		NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2	127					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)	CTGTGGCCTCTGGTTTTTCGG	0.602																																					p.S127S		Atlas-SNP	.											.	NPR2	162	.	0			c.T381C						PASS	.						125	106	112					9																	35792786		2203	4300	6503	SO:0001819	synonymous_variant	4882	exon1			GGCCTCTGGTTTT	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.381T>C	chr9.hg19:g.35792786T>C		67.0	0.0	.		70.0	14.0	.	NM_003995	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Silent	SNP	ENST00000342694.2	hg19	CCDS6590.1																																																																																			.	.	.	none		0.602	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1			C	35792786	T	C	35792786	2	2	85	1	0	0	0	0	0	0	0	1	10602	1567	55	3		3	NPR2	9	35792786	Silent	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	20063039	35792786	105420645	47	5449											
NPR2	4882	hgsc.bcm.edu	37	chr9	35800822	35800822	+	Frame_Shift_Del	DEL	C	C	-																															tgtgcctttgacttggacgaCccatcctgtgataaaagtgg																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr9:35800822delC	ENST00000342694.2	+	6	1590	c.1335delC	c.(1333-1335)gacfs	p.D445fs		NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2	445					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)	ACTTGGACGACCCATCCTGTG	0.582																																					p.D445fs		Atlas-Indel,Pindel	.											.	NPR2	162	.	0			c.1334delA						PASS	.						126	103	111					9																	35800822		2203	4300	6503	SO:0001589	frameshift_variant	4882	exon6			.	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.1335delC	chr9.hg19:g.35800822delC	ENSP00000341083:p.Asp445fs	60.0	0.0	0		82.0	21.0	0.256098	NM_003995	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Frame_Shift_Del	DEL	ENST00000342694.2	hg19	CCDS6590.1																																																																																			.	.	.	none		0.582	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1			-	35800822	C	-	35800822	7	5	85	1	0	1	0	1	0	0	0	0	10602	506	18	0	1357	0	NPR2	9	35800822	Frame_Shift_Del	DEL	C	TCGA-B1-A655-01A-11D-A31Z-10	8036	35800822	105412609	48	5450											
OR1N2	138882	hgsc.bcm.edu	37	chr9	125315955	125315955	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgtgtgctgggtgctaacCaactgtcctgccctgatgca	6	11	13	11	0	0	1	0	1	0	0	1	1	1	1	3	2	6	3	3	2	2	1			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr9:125315955C>T	ENST00000373688.2	+	1	565	c.507C>T	c.(505-507)acC>acT	p.T169T		NM_001004457.1	NP_001004457.1	Q8NGR9	OR1N2_HUMAN	olfactory receptor, family 1, subfamily N, 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)			breast(2)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(3)	26						GGGTGCTAACCAACTGTCCTG	0.532																																					p.T169T		Atlas-SNP	.											.	OR1N2	51	.	0			c.C507T						PASS	.						141	123	129					9																	125315955		2203	4300	6503	SO:0001819	synonymous_variant	138882	exon1			GCTAACCAACTGT		CCDS35123.1	9q33.2	2013-09-20			ENSG00000171501	ENSG00000171501		"GPCR / Class A : Olfactory receptors"	15111	protein-coding gene	gene with protein product							Standard	NM_001004457		Approved		uc011lyx.2	Q8NGR9	OTTHUMG00000020607	ENST00000373688.2:c.507C>T	chr9.hg19:g.125315955C>T		44.0	0.0	.		48.0	19.0	.	NM_001004457	A3KFM2|B2RNY4|Q6IF17|Q96RA3	Silent	SNP	ENST00000373688.2	hg19	CCDS35123.1																																																																																			.	.	.	none		0.532	OR1N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053937.2			T	125315955	C	T	125315955	2	4	85	1	0	0	0	0	0	0	0	1	10977	581	21	2		2	OR1N2	9	125315955	Silent	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	89515133	125315955	15897476	49	5451											
MED27	9442	hgsc.bcm.edu	37	chr9	134889753	134889753	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggacaagagttgtgggctgAgcctttggtctacgtttggc	7	12	15	7	1	1	2	0	1	1	1	1	3	1	3	1	4	2	3	1	4	2	4			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr9:134889753A>G	ENST00000292035.5	-	3	513	c.450T>C	c.(448-450)gcT>gcC	p.A150A	MED27_ENST00000357028.2_Silent_p.A150A	NM_004269.3	NP_004260.2	Q6P2C8	MED27_HUMAN	mediator complex subunit 27	150					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)		TTGTGGGCTGAGCCTTTGGTC	0.428																																					p.A150A	Colon(41;784 923 6932 42329 52483)	Atlas-SNP	.											.	MED27	37	.	0			c.T450C						PASS	.						152	129	137					9																	134889753		2203	4300	6503	SO:0001819	synonymous_variant	9442	exon3			GGGCTGAGCCTTT	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.450T>C	chr9.hg19:g.134889753A>G		134.0	0.0	.		80.0	12.0	.	NM_001253881	O95401|Q4F964|Q5VTA4|Q5VTA5|Q9BU57|Q9NYR4|V9GYV9	Silent	SNP	ENST00000292035.5	hg19	CCDS6945.1																																																																																			.	.	.	none		0.428	MED27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054770.2	NM_004269		G	134889753	A	G	134889753	2	3	85	1	0	0	0	0	0	0	0	1	9452	291	11	3		3	MED27	9	134889753	Silent	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	9573798	134889753	6323678	50	5452											
GJD4	219770	hgsc.bcm.edu	37	chr10	35896876	35896876	+	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	ttttcggccggctacatcatCcacctcctcctccggaccct	5	11	6	19	3	1	0	1	0	0	0	6	1	5	1	7	3	1	1	7	3	1	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr10:35896876C>A	ENST00000321660.1	+	2	593	c.435C>A	c.(433-435)atC>atA	p.I145I	RP11-425A6.5_ENST00000609313.1_RNA	NM_153368.2	NP_699199.2	Q96KN9	CXD4_HUMAN	gap junction protein, delta 4, 40.1kDa	145					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						GCTACATCATCCACCTCCTCC	0.692																																					p.I145I		Atlas-SNP	.											.	GJD4	38	.	0			c.C435A						PASS	.						17	18	18					10																	35896876		2196	4293	6489	SO:0001819	synonymous_variant	219770	exon2			CATCATCCACCTC	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.435C>A	chr10.hg19:g.35896876C>A		19.0	0.0	.		23.0	8.0	.	NM_153368	Q8N2R7	Silent	SNP	ENST00000321660.1	hg19	CCDS7191.1																																																																																			.	.	.	none		0.692	GJD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047576.1	NM_153368		A	35896876	C	A	35896876	2	1	85	1	0	0	0	0	0	0	0	1	6426	845	30	4		4	GJD4	10	35896876	Silent	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10		35896876	99637871	51	5453											
ADAMTS14	140766	hgsc.bcm.edu	37	chr10	72513573	72513573	+	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	caggtgggtgacggaggagtGgggtgcctgcagccggagct	6	6	21	8	2	0	1	0	1	0	0	0	4	0	4	2	7	4	2	2	7	0	0			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr10:72513573G>T	ENST00000373207.1	+	19	2747	c.2747G>T	c.(2746-2748)tGg>tTg	p.W916L	ADAMTS14_ENST00000373208.1_Missense_Mutation_p.W919L	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	916	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				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						ACGGAGGAGTGGGGTGCCTGC	0.622																																					p.W919L		Atlas-SNP	.											.	ADAMTS14	148	.	0			c.G2756T						PASS	.						16	12	14					10																	72513573		2194	4295	6489	SO:0001583	missense	140766	exon19			AGGAGTGGGGTGC	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.2747G>T	chr10.hg19:g.72513573G>T	ENSP00000362303:p.Trp916Leu	43.0	0.0	.		39.0	8.0	.	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Missense_Mutation	SNP	ENST00000373207.1	hg19	CCDS7306.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.956346	0.73902	.	.	ENSG00000138316	ENST00000373208;ENST00000373207	T;T	0.74315	-0.83;-0.83	4.58	4.58	0.56647	.	0.000000	0.64402	D	0.000001	D	0.92195	0.7525	H	0.99325	4.515	0.58432	D	0.999995	D;D	0.89917	0.967;1.0	P;D	0.80764	0.897;0.994	D	0.95625	0.8684	10	0.87932	D	0	.	17.1757	0.86841	0.0:0.0:1.0:0.0	.	916;919	Q8WXS8;Q5T4G1	ATS14_HUMAN;.	L	919;916	ENSP00000362304:W919L;ENSP00000362303:W916L	ENSP00000362303:W916L	W	+	2	0	ADAMTS14	72183579	1.000000	0.71417	0.963000	0.40424	0.270000	0.26580	9.601000	0.98297	2.378000	0.81104	0.563000	0.77884	TGG	.	.	.	none		0.622	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722		T	72513573	G	T	72513573	3	4	85	1	0	0	0	0	1	0	0	0	259	1357	47	4	2830	4	ADAMTS14	10	72513573	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	36616697	72513573	63021174	52	5454											
C10orf11	83938	hgsc.bcm.edu	37	chr10	77818509	77818509	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacgagaggaggcgttggtcAgaggagtcttcatgaaggtg	11	8	17	5	2	3	3	2	1	1	2	3	6	3	5	0	5	1	1	0	5	2	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr10:77818509A>G	ENST00000372499.1	+	4	615	c.400A>G	c.(400-402)Aga>Gga	p.R134G	C10orf11_ENST00000593699.1_3'UTR	NM_032024.3	NP_114413.1	Q9H2I8	CJ011_HUMAN	chromosome 10 open reading frame 11	134	LRRCT.				melanocyte differentiation (GO:0030318)					endometrium(1)|large_intestine(4)|lung(4)|stomach(1)	10	Prostate(51;0.0095)|all_epithelial(25;0.0221)					GGCGTTGGTCAGAGGAGTCTT	0.488																																					p.R134G		Atlas-SNP	.											.	C10orf11	19	.	0			c.A400G						PASS	.						148	136	140					10																	77818509		2203	4300	6503	SO:0001583	missense	83938	exon4			TTGGTCAGAGGAG	AF267860	CCDS7351.1	10q22.3	2013-08-22			ENSG00000148655	ENSG00000148655			23405	protein-coding gene	gene with protein product	"oculocutaneous albinism 7, autosomal recessive"	614537				23395477	Standard	NM_032024		Approved	CDA017, OCA7	uc001jxi.3	Q9H2I8	OTTHUMG00000018532	ENST00000372499.1:c.400A>G	chr10.hg19:g.77818509A>G	ENSP00000361577:p.Arg134Gly	105.0	0.0	.		89.0	13.0	.	NM_032024	B1AVW6	Missense_Mutation	SNP	ENST00000372499.1	hg19	CCDS7351.1	.	.	.	.	.	.	.	.	.	.	A	18.82	3.704846	0.68615	.	.	ENSG00000148655	ENST00000354343;ENST00000372499	T	0.37235	1.21	5.66	4.46	0.54185	.	0.000000	0.85682	D	0.000000	T	0.51702	0.1690	M	0.83012	2.62	0.41798	D	0.989901	P	0.41313	0.745	P	0.49226	0.603	T	0.56974	-0.7890	10	0.46703	T	0.11	-22.7506	12.4457	0.55649	0.8601:0.1398:0.0:0.0	.	134	Q9H2I8	CJ011_HUMAN	G	162;134	ENSP00000361577:R134G	ENSP00000346310:R162G	R	+	1	2	C10orf11	77488515	0.984000	0.35163	1.000000	0.80357	0.977000	0.68977	2.280000	0.43443	2.164000	0.68074	0.533000	0.62120	AGA	.	.	.	none		0.488	C10orf11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048839.1	NM_032024		G	77818509	A	G	77818509	3	3	85	1	0	0	0	0	1	0	0	0	1584	180	7	3	414	3	C10orf11	10	77818509	Missense_Mutation	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	5304936	77818509	57716238	53	5455											
C10orf12	26148	hgsc.bcm.edu	37	chr10	98744160	98744160	+	Missense_Mutation	SNP	A	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	ggattcttagaaaatattccAatattcgaggaaagctcaga	16	11	8	6	1	2	2	1	0	1	2	4	5	3	4	1	2	1	1	1	2	7	6			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr10:98744160A>C	ENST00000286067.2	+	1	3120	c.3013A>C	c.(3013-3015)Aat>Cat	p.N1005H		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	1005										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)		AAAATATTCCAATATTCGAGG	0.453																																					p.N1005H		Atlas-SNP	.											.	C10orf12	94	.	0			c.A3013C						PASS	.						50	56	54					10																	98744160		2203	4300	6503	SO:0001583	missense	26148	exon1			TATTCCAATATTC	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.3013A>C	chr10.hg19:g.98744160A>C	ENSP00000286067:p.Asn1005His	49.0	0.0	.		60.0	21.0	.	NM_015652	Q9H945|Q9Y457	Missense_Mutation	SNP	ENST00000286067.2	hg19	CCDS7452.1	.	.	.	.	.	.	.	.	.	.	A	14.01	2.409208	0.42715	.	.	ENSG00000155640	ENST00000286067;ENST00000539886	T	0.11169	2.8	5.71	4.57	0.56435	.	0.273469	0.25106	U	0.033088	T	0.19005	0.0456	L	0.47716	1.5	0.34487	D	0.70458	D	0.55385	0.971	P	0.53224	0.721	T	0.18777	-1.0326	10	0.72032	D	0.01	-16.6286	12.7429	0.57264	0.7424:0.2576:0.0:0.0	.	1005	Q8N655	CJ012_HUMAN	H	1005;839	ENSP00000286067:N1005H	ENSP00000286067:N1005H	N	+	1	0	C10orf12	98734150	1.000000	0.71417	1.000000	0.80357	0.738000	0.42128	5.768000	0.68858	0.989000	0.38761	-0.313000	0.08912	AAT	.	.	.	none		0.453	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652		C	98744160	A	C	98744160	3	2	85	1	0	0	0	0	1	0	0	0	1591	130	5	5	3015	5	C10orf12	10	98744160	Missense_Mutation	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	20925651	98744160	36790587	54	5456											
ERLIN1	10613	hgsc.bcm.edu	37	chr10	101935785	101935785	+	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	ggattttattgaagattaagGtcttgtcataatctgcagta	12	16	9	4	0	3	2	1	1	2	1	3	3	3	3	0	2	1	2	0	2	5	7	rs369477049		TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr10:101935785G>C	ENST00000421367.2	-	5	3054	c.347C>G	c.(346-348)aCc>aGc	p.T116S	ERLIN1_ENST00000407654.3_Missense_Mutation_p.T116S	NM_001100626.1|NM_006459.3	NP_001094096.1|NP_006450.2	O75477	ERLN1_HUMAN	ER lipid raft associated 1	114					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)							Colorectal(252;0.234)		Epithelial(162;3.85e-10)|all cancers(201;3.25e-08)		GAAGATTAAGGTCTTGTCATA	0.393																																					p.T116S		Atlas-SNP	.											.	.	.	.	0			c.C347G						PASS	.						161	145	150					10																	101935785		2203	4300	6503	SO:0001583	missense	10613	exon5			ATTAAGGTCTTGT	AF064093	CCDS7487.2	10q24.31	2014-03-03	2007-01-26	2007-01-26	ENSG00000107566	ENSG00000107566			16947	protein-coding gene	gene with protein product	"Band_7 23-211 Keo4 (Interim) similar to C.elegans protein C42C1.9"	611604	"chromosome 10 open reading frame 69", "SPFH domain family, member 1"	C10orf69, SPFH1		11118313, 16835267, 24482476	Standard	NM_006459		Approved	KE04, Erlin-1, SPG62	uc001kqo.4	O75477	OTTHUMG00000018900	ENST00000421367.2:c.347C>G	chr10.hg19:g.101935785G>C	ENSP00000410964:p.Thr116Ser	95.0	0.0	.		97.0	35.0	.	NM_006459	B0QZ42|Q53HV0	Missense_Mutation	SNP	ENST00000421367.2	hg19	CCDS7487.2	.	.	.	.	.	.	.	.	.	.	G	16.19	3.053929	0.55218	.	.	ENSG00000107566	ENST00000421367;ENST00000407654;ENST00000370410;ENST00000370408	D;D;D	0.94417	-3.42;-3.42;-3.42	4.96	4.96	0.65561	.	0.114986	0.64402	U	0.000019	D	0.95020	0.8388	M	0.78456	2.415	0.58432	D	0.999999	B;B	0.29270	0.24;0.24	B;B	0.42959	0.403;0.403	D	0.92339	0.5880	10	0.09590	T	0.72	-17.5613	16.0678	0.80897	0.0:0.0:1.0:0.0	.	114;116	O75477;D3DR65	ERLN1_HUMAN;.	S	116;116;32;116	ENSP00000410964:T116S;ENSP00000384900:T116S;ENSP00000359436:T116S	ENSP00000359436:T116S	T	-	2	0	ERLIN1	101925775	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	9.771000	0.98977	2.456000	0.83038	0.561000	0.74099	ACC	.	.	.	none		0.393	ERLIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049840.2	NM_006459		C	101935785	G	C	101935785	3	2	85	1	0	0	0	0	1	0	0	0	5234	1261	44	4	727	4	ERLIN1	10	101935785	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	3191625	101935785	33598962	55	5457											
HIPK3	10114	hgsc.bcm.edu	37	chr11	33374883	33374883	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggcccacctgttagcctcTccgtgtacctcaagacctat	7	11	8	15	1	2	1	1	0	1	1	3	1	2	1	6	1	2	2	6	1	4	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr11:33374883T>C	ENST00000303296.4	+	17	3722	c.3417T>C	c.(3415-3417)tcT>tcC	p.S1139S	AL122015.1_ENST00000411202.1_RNA|HIPK3_ENST00000525975.1_Silent_p.S1118S|HIPK3_ENST00000379016.3_Silent_p.S1118S|HIPK3_ENST00000456517.1_Silent_p.S1118S	NM_005734.3	NP_005725.3	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3	1139					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						TGTTAGCCTCTCCGTGTACCT	0.517																																					p.S1139S		Atlas-SNP	.											.	HIPK3	92	.	0			c.T3417C						PASS	.						216	178	191					11																	33374883		2202	4298	6500	SO:0001819	synonymous_variant	10114	exon17			AGCCTCTCCGTGT	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.3417T>C	chr11.hg19:g.33374883T>C		125.0	0.0	.		112.0	31.0	.	NM_005734	O14632|Q2PBG4|Q2PBG5|Q92632|Q9HAS2	Silent	SNP	ENST00000303296.4	hg19	CCDS7884.1																																																																																			.	.	.	none		0.517	HIPK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255358.1	NM_005734		C	33374883	T	C	33374883	2	2	85	1	0	0	0	0	0	0	0	1	7125	1538	54	3		3	HIPK3	11	33374883	Silent	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10		33374883	101631633	56	5458											
KIAA0652	9776	hgsc.bcm.edu	37	chr11	46666907	46666907	+	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	agactgtccaagtgattgtcCaggctcggcttggtgaaaag	10	10	13	8	1	0	3	0	2	0	1	3	3	2	3	2	3	0	2	2	3	3	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr11:46666907C>T	ENST00000434074.1	+	3	777	c.88C>T	c.(88-90)Cag>Tag	p.Q30*	ATG13_ENST00000529655.1_Nonsense_Mutation_p.Q30*|ATG13_ENST00000528494.1_Nonsense_Mutation_p.Q30*|ATG13_ENST00000451945.1_Nonsense_Mutation_p.Q30*|ATG13_ENST00000359513.4_Nonsense_Mutation_p.Q30*|ATG13_ENST00000526508.1_Nonsense_Mutation_p.Q30*|ATG13_ENST00000312040.4_Nonsense_Mutation_p.Q30*|ATG13_ENST00000524625.1_Nonsense_Mutation_p.Q30*|ATG13_ENST00000530500.1_5'UTR	NM_001205120.1	NP_001192049.1	O75143	ATG13_HUMAN	autophagy related 13	30					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						AGTGATTGTCCAGGCTCGGCT	0.373																																					p.Q30X		Atlas-SNP	.											.	ATG13	60	.	0			c.C88T						PASS	.						95	90	91					11																	46666907		2201	4299	6500	SO:0001587	stop_gained	9776	exon4			ATTGTCCAGGCTC	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.88C>T	chr11.hg19:g.46666907C>T	ENSP00000400642:p.Gln30*	78.0	0.0	.		91.0	5.0	.	NM_001142673	B4DFI4|D3DQQ1|D3DQQ2|E9PQZ8|Q53EN6|Q9BRL3|Q9H8B0	Nonsense_Mutation	SNP	ENST00000434074.1	hg19	CCDS44582.1	.	.	.	.	.	.	.	.	.	.	C	37	6.442003	0.97568	.	.	ENSG00000175224	ENST00000395549;ENST00000434074;ENST00000312040;ENST00000451945;ENST00000529655;ENST00000533325;ENST00000526508;ENST00000524625;ENST00000359513;ENST00000528494;ENST00000526078	.	.	.	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-10.2057	19.4568	0.94895	0.0:1.0:0.0:0.0	.	.	.	.	X	30	.	ENSP00000310321:Q30X	Q	+	1	0	ATG13	46623483	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.103000	0.77014	2.832000	0.97577	0.655000	0.94253	CAG	.	.	.	none		0.373	ATG13-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390300.2	NM_014741		T	46666907	C	T	46666907	4	4	85	1	0	0	0	0	0	1	0	0	8195	595	21	2	94	2	KIAA0652	11	46666907	Nonsense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	13292024	46666907	88339609	57	5459											
PCNXL3	399909	hgsc.bcm.edu	37	chr11	65397996	65397996	+	Missense_Mutation	SNP	A	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	caagtacgtgctggagggctAtagcattagtgacaataatg	13	10	12	6	1	0	1	0	1	0	0	0	2	0	2	0	2	3	4	0	2	7	5			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr11:65397996A>C	ENST00000355703.3	+	27	4930	c.4391A>C	c.(4390-4392)tAt>tCt	p.Y1464S	PCNXL3_ENST00000531280.1_3'UTR	NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	1464						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						CTGGAGGGCTATAGCATTAGT	0.572																																					p.Y1464S		Atlas-SNP	.											.	PCNXL3	140	.	0			c.A4391C						PASS	.						86	92	90					11																	65397996		2116	4217	6333	SO:0001583	missense	399909	exon27			AGGGCTATAGCAT	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.4391A>C	chr11.hg19:g.65397996A>C	ENSP00000347931:p.Tyr1464Ser	135.0	0.0	.		122.0	41.0	.	NM_032223	Q6MZN8	Missense_Mutation	SNP	ENST00000355703.3	hg19	CCDS44650.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.559339	0.86335	.	.	ENSG00000197136	ENST00000355703	T	0.23552	1.9	5.02	5.02	0.67125	.	0.072055	0.56097	D	0.000021	T	0.55657	0.1934	M	0.88450	2.955	0.51767	D	0.999931	D;D	0.71674	0.982;0.998	D;D	0.73708	0.967;0.981	T	0.64516	-0.6389	10	0.87932	D	0	.	12.7937	0.57549	1.0:0.0:0.0:0.0	.	351;1464	Q9H6A9-3;Q9H6A9	.;PCX3_HUMAN	S	1464	ENSP00000347931:Y1464S	ENSP00000347931:Y1464S	Y	+	2	0	PCNXL3	65154572	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.753000	0.91637	2.131000	0.65755	0.529000	0.55759	TAT	.	.	.	none		0.572	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223		C	65397996	A	C	65397996	3	2	85	1	0	0	0	0	1	0	0	0	11600	449	16	5	4497	5	PCNXL3	11	65397996	Missense_Mutation	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	18731089	65397996	69608520	58	5460											
MRE11A	4361	hgsc.bcm.edu	37	chr11	94225958	94225958	+	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	aggtgcttacagtgcatctgCagtactcatttttatggtca	9	15	9	8	0	3	0	2	0	1	0	3	0	3	0	0	2	5	4	0	2	3	5			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr11:94225958C>A	ENST00000323929.3	-	2	232	c.10G>T	c.(10-12)Gca>Tca	p.A4S	ANKRD49_ENST00000544253.1_5'Flank|MRE11A_ENST00000407439.3_5'UTR|MRE11A_ENST00000393241.4_Missense_Mutation_p.A4S|MRE11A_ENST00000536144.1_5'UTR|ANKRD49_ENST00000540349.1_5'Flank|MRE11A_ENST00000323977.3_Missense_Mutation_p.A4S|ANKRD49_ENST00000544612.1_5'Flank|MRE11A_ENST00000540013.1_Missense_Mutation_p.A4S	NM_005591.3	NP_005582.1	P49959	MRE11_HUMAN	MRE11 meiotic recombination 11 homolog A (S. cerevisiae)	4					base-excision repair (GO:0006284)|cell proliferation (GO:0008283)|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)|double-strand break repair via nonhomologous end joining (GO:0006303)|innate immune response (GO:0045087)|intra-S DNA damage checkpoint (GO:0031573)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of DNA endoreduplication (GO:0032876)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair (GO:0006289)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of type I interferon production (GO:0032481)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|sister chromatid cohesion (GO:0007062)|synapsis (GO:0007129)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromatin (GO:0000785)|cytosol (GO:0005829)|Mre11 complex (GO:0030870)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|manganese ion binding (GO:0030145)|nuclease activity (GO:0004518)|protein C-terminus binding (GO:0008022)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			breast(5)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	29		Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824)				AGTGCATCTGCAGTACTCATT	0.423								Homologous recombination	Ataxia-Telangiectasia-Like Disorder																												p.A4S		Atlas-SNP	.											.	MRE11A	145	.	0			c.G10T						PASS	.						113	103	107					11																	94225958		2201	4298	6499	SO:0001583	missense	4361	exon2	Familial Cancer Database	ATLD	CATCTGCAGTACT	BC063458	CCDS8298.1, CCDS8299.1	11q21	2014-09-17	2001-11-28		ENSG00000020922	ENSG00000020922			7230	protein-coding gene	gene with protein product	"AT-like disease"	600814	"meiotic recombination (S. cerevisiae) 11 homolog A"	MRE11		8530104	Standard	XM_005274007		Approved	ATLD	uc001peu.2	P49959	OTTHUMG00000167780	ENST00000323929.3:c.10G>T	chr11.hg19:g.94225958C>A	ENSP00000325863:p.Ala4Ser	57.0	0.0	.		72.0	7.0	.	NM_005591	O43475	Missense_Mutation	SNP	ENST00000323929.3	hg19	CCDS8299.1	.	.	.	.	.	.	.	.	.	.	C	7.672	0.687277	0.14973	.	.	ENSG00000020922	ENST00000323929;ENST00000323977;ENST00000393241;ENST00000540013;ENST00000536754;ENST00000538923	T;T;T;T;T	0.76709	-0.84;-0.82;-0.84;-1.03;-1.04	5.01	-0.599	0.11645	.	0.961041	0.08657	N	0.913092	T	0.51109	0.1655	N	0.11255	0.115	0.23572	N	0.997382	B;B	0.06786	0.001;0.0	B;B	0.10450	0.005;0.002	T	0.30416	-0.9979	10	0.09843	T	0.71	.	2.2535	0.04049	0.1419:0.4157:0.2764:0.1661	.	4;4	P49959-2;P49959	.;MRE11_HUMAN	S	4	ENSP00000325863:A4S;ENSP00000326094:A4S;ENSP00000376933:A4S;ENSP00000440986:A4S;ENSP00000439511:A4S	ENSP00000325863:A4S	A	-	1	0	MRE11A	93865606	0.867000	0.29959	0.427000	0.26684	0.159000	0.22180	-0.223000	0.09177	-0.420000	0.07427	0.561000	0.74099	GCA	.	.	.	none		0.423	MRE11A-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396237.3	NM_005591		A	94225958	C	A	94225958	3	1	85	1	0	0	0	0	1	0	0	0	9766	710	25	4	2192	4	MRE11A	11	94225958	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	28827962	94225958	40780558	59	5461											
ASB8	140461	hgsc.bcm.edu	37	chr12	48543736	48543736	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acaagcctcatctttctctgCtgcatagtggagggctgttc	7	13	10	11	0	3	0	1	0	2	0	5	1	3	1	1	2	3	4	1	2	2	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr12:48543736C>T	ENST00000317697.3	-	4	449	c.280G>A	c.(280-282)Gca>Aca	p.A94T	ASB8_ENST00000535055.1_3'UTR|ASB8_ENST00000539528.1_3'UTR|ASB8_ENST00000537754.1_5'UTR|ASB8_ENST00000536549.1_Missense_Mutation_p.A94T|ASB8_ENST00000536953.1_3'UTR|ASB8_ENST00000536071.1_3'UTR	NM_024095.3	NP_077000.1	Q9H765	ASB8_HUMAN	ankyrin repeat and SOCS box containing 8	94					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(1)|kidney(2)|large_intestine(2)|lung(5)|soft_tissue(1)	11						TCTTTCTCTGCTGCATAGTGG	0.498																																					p.A94T		Atlas-SNP	.											.	ASB8	25	.	0			c.G280A						PASS	.						67	62	64					12																	48543736		2203	4300	6503	SO:0001583	missense	140461	exon4			TCTCTGCTGCATA	AK024908	CCDS8761.1	12q13.12	2013-01-10	2011-01-25			ENSG00000177981		"Ankyrin repeat domain containing"	17183	protein-coding gene	gene with protein product		615053	"ankyrin repeat and SOCS box-containing 8"			12076535	Standard	NM_024095		Approved	MGC5540, FLJ21255	uc001rrh.3	Q9H765		ENST00000317697.3:c.280G>A	chr12.hg19:g.48543736C>T	ENSP00000320893:p.Ala94Thr	59.0	0.0	.		83.0	26.0	.	NM_024095	A8K1P2|Q547Q2	Missense_Mutation	SNP	ENST00000317697.3	hg19	CCDS8761.1	.	.	.	.	.	.	.	.	.	.	C	32	5.172801	0.94807	.	.	ENSG00000177981	ENST00000317697;ENST00000536549;ENST00000446549;ENST00000539503;ENST00000545791;ENST00000540212	T;T;T;T;T	0.71934	-0.61;-0.61;-0.6;-0.37;-0.37	5.3	5.3	0.74995	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.81269	0.4787	L	0.49126	1.545	0.80722	D	1	D	0.71674	0.998	D	0.79108	0.992	T	0.81008	-0.1127	10	0.51188	T	0.08	-9.6125	18.938	0.92594	0.0:1.0:0.0:0.0	.	94	Q9H765	ASB8_HUMAN	T	94	ENSP00000320893:A94T;ENSP00000445622:A94T;ENSP00000444093:A94T;ENSP00000437769:A94T;ENSP00000442639:A94T	ENSP00000320893:A94T	A	-	1	0	ASB8	46830003	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.227000	0.78070	2.648000	0.89879	0.563000	0.77884	GCA	.	.	.	none		0.498	ASB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396497.1			T	48543736	C	T	48543736	3	4	85	1	0	0	0	0	1	0	0	0	1029	797	28	2	590	2	ASB8	12	48543736	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10		48543736	85308159	60	5462											
GALNT6	11226	hgsc.bcm.edu	37	chr12	51758036	51758036	+	Frame_Shift_Del	DEL	A	A	-																															tggacgggcttggcgaactcAaaagtattaaggtcgatggt																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr12:51758036delA	ENST00000543196.2	-	5	1123	c.918delT	c.(916-918)tttfs	p.F306fs	GALNT6_ENST00000356317.3_Frame_Shift_Del_p.F306fs			Q8NCL4	GALT6_HUMAN	polypeptide N-acetylgalactosaminyltransferase 6	306					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(2)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						TGGCGAACTCAAAAGTATTAA	0.577																																					p.E307fs		Atlas-Indel,Pindel	.											.	GALNT6	63	.	0			c.919delG						PASS	.						91	85	87					12																	51758036		2203	4300	6503	SO:0001589	frameshift_variant	11226	exon6			.	Y08565	CCDS8813.1	12q13	2014-03-13	2014-03-13		ENSG00000139629	ENSG00000139629		"Glycosyltransferase family 2 domain containing"	4128	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 6"	605148	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6)"			10464263	Standard	NM_007210		Approved	GalNAc-T6	uc001ryl.1	Q8NCL4		ENST00000543196.2:c.918delT	chr12.hg19:g.51758036delA	ENSP00000444171:p.Phe306fs	98.0	0.0	0		110.0	35.0	0.318182	NM_007210	Q8IYH4|Q9H6G2|Q9UIV5	Frame_Shift_Del	DEL	ENST00000543196.2	hg19	CCDS8813.1																																																																																			.	.	.	none		0.577	GALNT6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469735.1	NM_007210		-	51758036	A	-	51758036	7	5	85	1	0	1	0	1	0	0	0	0	6224	127	5	0	978	0	GALNT6	12	51758036	Frame_Shift_Del	DEL	A	TCGA-B1-A655-01A-11D-A31Z-10	3214300	51758036	82093859	61	5463											
ARHGAP5	394	hgsc.bcm.edu	37	chr14	32560648	32560648	+	Frame_Shift_Del	DEL	A	A	-																															caagcctaaaattattccctAtttggatgcttataaaacac																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr14:32560648delA	ENST00000345122.3	+	2	1088	c.773delA	c.(772-774)tatfs	p.Y258fs	ARHGAP5_ENST00000539826.2_Frame_Shift_Del_p.Y258fs|ARHGAP5_ENST00000432921.1_Frame_Shift_Del_p.Y258fs|ARHGAP5_ENST00000433497.1_Intron|ARHGAP5_ENST00000556611.1_Frame_Shift_Del_p.Y258fs|ARHGAP5_ENST00000396582.2_Intron	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	258					cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		ATTATTCCCTATTTGGATGCT	0.358																																					p.Y258fs	NSCLC(9;77 350 3443 29227 41353)	Atlas-Indel,Pindel	.											.	ARHGAP5	166	.	0			c.772delT						PASS	.						115	131	125					14																	32560648		2203	4299	6502	SO:0001589	frameshift_variant	394	exon2			.	U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"Rho GTPase activating proteins"	675	protein-coding gene	gene with protein product		602680	"growth factor independent 2"	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.773delA	chr14.hg19:g.32560648delA	ENSP00000371897:p.Tyr258fs	279.0	0.0	0		167.0	85.0	0.508982	NM_001030055	A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Frame_Shift_Del	DEL	ENST00000345122.3	hg19	CCDS32062.1																																																																																			.	.	.	none		0.358	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1	NM_001030055		-	32560648	A	-	32560648	7	5	85	1	0	1	0	1	0	0	0	0	886	449	16	0	775	0	ARHGAP5	14	32560648	Frame_Shift_Del	DEL	A	TCGA-B1-A655-01A-11D-A31Z-10		32560648	74788892	62	5464											
RGS6	9628	hgsc.bcm.edu	37	chr14	72939649	72939649	+	Frame_Shift_Del	DEL	C	C	-																															gaacgagccttttgggatgtCcacaggcctgtggtgagaaa																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr14:72939649delC	ENST00000553530.1	+	9	813	c.606delC	c.(604-606)gtcfs	p.V202fs	RGS6_ENST00000343854.6_Frame_Shift_Del_p.V202fs|RGS6_ENST00000402788.2_Frame_Shift_Del_p.V202fs|RGS6_ENST00000553690.1_3'UTR|RGS6_ENST00000434263.2_Frame_Shift_Del_p.V133fs|RGS6_ENST00000554782.1_Frame_Shift_Del_p.V63fs|RGS6_ENST00000555571.1_Frame_Shift_Del_p.V202fs|RGS6_ENST00000556437.1_Frame_Shift_Del_p.V202fs|RGS6_ENST00000406236.4_Frame_Shift_Del_p.V202fs|RGS6_ENST00000407322.4_Frame_Shift_Del_p.V202fs|RGS6_ENST00000355512.6_Frame_Shift_Del_p.V202fs|RGS6_ENST00000553525.1_Frame_Shift_Del_p.V202fs|RGS6_ENST00000404301.2_Frame_Shift_Del_p.V202fs	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	202					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)		TTTGGGATGTCCACAGGCCTG	0.373																																					p.V202fs	Ovarian(143;1926 2468 21071 48641)	Atlas-Indel,Pindel	.											.	RGS6	92	.	0			c.605delT						PASS	.						137	153	148					14																	72939649		2203	4300	6503	SO:0001589	frameshift_variant	9628	exon9			.	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.606delC	chr14.hg19:g.72939649delC	ENSP00000452331:p.Val202fs	197.0	0.0	0		150.0	70.0	0.466667	NM_001204424	C9JE95|F8W7W5|O75576|O75577|Q7Z4K3|Q7Z4K4|Q7Z4K5|Q7Z4K6|Q8TE13|Q8TE14|Q8TE15|Q8TE16|Q8TE17|Q8TE18|Q8TE19|Q8TE20|Q8TE21|Q8TE22|Q9UDS8|Q9UDT0|Q9Y245|Q9Y647	Frame_Shift_Del	DEL	ENST00000553530.1	hg19	CCDS9808.1																																																																																			.	.	.	none		0.373	RGS6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413033.2			-	72939649	C	-	72939649	7	5	85	1	0	1	0	1	0	0	0	0	13322	842	30	0	636	0	RGS6	14	72939649	Frame_Shift_Del	DEL	C	TCGA-B1-A655-01A-11D-A31Z-10	40379001	72939649	34409891	63	5465											
SERPINA12	145264	hgsc.bcm.edu	37	chr14	94964196	94964196	+	Missense_Mutation	SNP	A	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	catgggttttttgactgataAagtcattgatctgcttctga	9	17	9	6	0	3	4	1	4	2	0	3	4	3	4	0	1	1	2	0	1	2	6			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr14:94964196A>C	ENST00000341228.2	-	3	1334	c.539T>G	c.(538-540)tTt>tGt	p.F180C	SERPINA12_ENST00000556881.1_Missense_Mutation_p.F180C	NM_173850.2	NP_776249.1	Q8IW75	SPA12_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12	180					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	33				COAD - Colon adenocarcinoma(157;0.235)		TTGACTGATAAAGTCATTGAT	0.393																																					p.F180C		Atlas-SNP	.											.	SERPINA12	93	.	0			c.T539G						PASS	.						93	91	92					14																	94964196		2203	4300	6503	SO:0001583	missense	145264	exon3			CTGATAAAGTCAT	AY177692	CCDS9926.1	14q32.13	2014-02-21	2005-08-18		ENSG00000165953	ENSG00000165953		"Serine (or cysteine) peptidase inhibitors"	18359	protein-coding gene	gene with protein product			"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12"			24172014	Standard	NM_173850		Approved	OL-64, Vaspin	uc001ydj.3	Q8IW75	OTTHUMG00000171349	ENST00000341228.2:c.539T>G	chr14.hg19:g.94964196A>C	ENSP00000342109:p.Phe180Cys	130.0	0.0	.		82.0	39.0	.	NM_173850		Missense_Mutation	SNP	ENST00000341228.2	hg19	CCDS9926.1	.	.	.	.	.	.	.	.	.	.	A	10.99	1.508445	0.27036	.	.	ENSG00000165953	ENST00000556881;ENST00000341228	D;D	0.84589	-1.87;-1.87	5.49	4.34	0.51931	Serpin domain (3);	0.119433	0.38111	N	0.001802	D	0.87692	0.6241	L	0.46819	1.47	0.20196	N	0.99993	D	0.71674	0.998	P	0.61275	0.886	T	0.80627	-0.1298	10	0.87932	D	0	.	11.607	0.51037	0.1385:0.0:0.0:0.8615	.	180	Q8IW75	SPA12_HUMAN	C	180	ENSP00000451738:F180C;ENSP00000342109:F180C	ENSP00000342109:F180C	F	-	2	0	SERPINA12	94033949	0.995000	0.38212	0.009000	0.14445	0.037000	0.13140	3.607000	0.54102	0.903000	0.36546	-0.339000	0.08088	TTT	.	.	.	none		0.393	SERPINA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413097.1	NM_173850		C	94964196	A	C	94964196	3	2	85	1	0	0	0	0	1	0	0	0	14102	14	1	5	721	5	SERPINA12	14	94964196	Missense_Mutation	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	22024547	94964196	12385344	64	5466											
RASGRP1	10125	hgsc.bcm.edu	37	chr15	38798102	38798102	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catagatttcatcctcagtgTagtaaagatccagggataac	14	11	8	8	0	2	2	2	0	0	2	4	3	4	3	2	1	1	2	2	1	5	5			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr15:38798102T>C	ENST00000310803.5	-	10	1439	c.1262A>G	c.(1261-1263)tAc>tGc	p.Y421C	RASGRP1_ENST00000561180.1_Missense_Mutation_p.Y472C|RASGRP1_ENST00000450598.2_Missense_Mutation_p.Y421C|RP11-102L12.2_ENST00000560231.1_RNA|RASGRP1_ENST00000558164.1_Missense_Mutation_p.Y421C|RASGRP1_ENST00000539159.1_Missense_Mutation_p.Y373C|RASGRP1_ENST00000559830.1_Missense_Mutation_p.Y421C	NM_001128602.1|NM_005739.3	NP_001122074.1|NP_005730.2	O95267	GRP1_HUMAN	RAS guanyl releasing protein 1 (calcium and DAG-regulated)	421	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				activation of Rho GTPase activity (GO:0032862)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|platelet activation (GO:0030168)|Ras protein signal transduction (GO:0007265)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)|secretory granule localization (GO:0032252)|signal transduction (GO:0007165)|vesicle transport along microtubule (GO:0047496)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)		ATCCTCAGTGTAGTAAAGATC	0.448																																					p.Y421C		Atlas-SNP	.											.	RASGRP1	50	.	0			c.A1262G						PASS	.						75	74	74					15																	38798102		1892	4109	6001	SO:0001583	missense	10125	exon10			TCAGTGTAGTAAA	AF106071	CCDS45221.1, CCDS45222.1	15q15	2013-01-10				ENSG00000172575		"EF-hand domain containing"	9878	protein-coding gene	gene with protein product		603962				10087292, 9789079	Standard	NM_005739		Approved	CalDAG-GEFII, RASGRP	uc001zke.4	O95267		ENST00000310803.5:c.1262A>G	chr15.hg19:g.38798102T>C	ENSP00000310244:p.Tyr421Cys	68.0	0.0	.		68.0	25.0	.	NM_001128602	Q56CZ0|Q58G75|Q59HB1|Q5I3A8|Q6GV31|Q6NX39|Q7LDG6|Q9UI94|Q9UNN9	Missense_Mutation	SNP	ENST00000310803.5	hg19	CCDS45222.1	.	.	.	.	.	.	.	.	.	.	T	18.55	3.649116	0.67358	.	.	ENSG00000172575	ENST00000310803;ENST00000450598;ENST00000415523;ENST00000431814;ENST00000539159;ENST00000414708;ENST00000541438	T;T;T;T	0.50277	0.75;0.75;0.75;0.75	4.6	4.6	0.57074	Guanine-nucleotide dissociation stimulator CDC25 (3);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.69351	0.3101	M	0.79805	2.47	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;0.999;1.0	D;D;D;D	0.91635	0.999;0.976;0.989;0.995	T	0.74278	-0.3717	10	0.62326	D	0.03	-19.3572	14.1614	0.65450	0.0:0.0:0.0:1.0	.	421;421;421;421	C9JM27;C9JCE5;O95267;O95267-2	.;.;GRP1_HUMAN;.	C	421;421;421;421;373;421;421	ENSP00000310244:Y421C;ENSP00000388540:Y421C;ENSP00000444762:Y373C;ENSP00000413105:Y421C	ENSP00000310244:Y421C	Y	-	2	0	RASGRP1	36585394	1.000000	0.71417	0.998000	0.56505	0.724000	0.41520	7.525000	0.81892	1.909000	0.55274	0.533000	0.62120	TAC	.	.	.	none		0.448	RASGRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418223.1	NM_005739		C	38798102	T	C	38798102	3	2	85	1	0	0	0	0	1	0	0	0	13087	1638	57	3	1163	3	RASGRP1	15	38798102	Missense_Mutation	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10		38798102	63733290	65	5467											
DISP2	85455	hgsc.bcm.edu	37	chr15	40660678	40660678	+	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	acactggcgaccctctggacCctcgtagcaacagcagcctg	9	6	10	16	2	1	0	0	0	1	0	2	2	1	1	3	2	4	3	3	2	2	1	rs375551948		TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr15:40660678C>G	ENST00000267889.3	+	8	2452	c.2365C>G	c.(2365-2367)Cct>Gct	p.P789A	RP11-64K12.4_ENST00000558421.1_RNA	NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	789					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)		CCCTCTGGACCCTCGTAGCAA	0.687																																					p.P789A		Atlas-SNP	.											.	DISP2	86	.	0			c.C2365G						PASS	.						76	84	81					15																	40660678		2203	4300	6503	SO:0001583	missense	85455	exon8			CTGGACCCTCGTA	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.2365C>G	chr15.hg19:g.40660678C>G	ENSP00000267889:p.Pro789Ala	59.0	0.0	.		66.0	19.0	.	NM_033510	Q6AHW3|Q9C0C1	Missense_Mutation	SNP	ENST00000267889.3	hg19	CCDS10056.1	.	.	.	.	.	.	.	.	.	.	C	16.57	3.158992	0.57368	.	.	ENSG00000140323	ENST00000267889	T	0.30981	1.51	5.14	4.2	0.49525	.	0.052280	0.85682	D	0.000000	T	0.58119	0.2100	M	0.83483	2.645	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.63651	-0.6589	10	0.48119	T	0.1	-12.1506	14.8747	0.70485	0.1445:0.8555:0.0:0.0	.	789	A7MBM2	DISP2_HUMAN	A	789	ENSP00000267889:P789A	ENSP00000267889:P789A	P	+	1	0	DISP2	38447970	1.000000	0.71417	1.000000	0.80357	0.561000	0.35649	7.645000	0.83430	1.343000	0.45638	0.561000	0.74099	CCT	.	.	.	alt		0.687	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510		G	40660678	C	G	40660678	3	3	85	1	0	0	0	0	1	0	0	0	4542	623	22	4	2395	4	DISP2	15	40660678	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	1862576	40660678	61870714	66	5468											
MGA	23269	hgsc.bcm.edu	37	chr15	42005518	42005518	+	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	tggttgtacttgtttgaaaaGaaaagttgtacttgttaaag	13	16	10	2	0	0	2	0	1	0	1	0	2	0	2	0	1	2	6	0	1	8	8			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr15:42005518G>C	ENST00000570161.1	+	8	3254	c.3254G>C	c.(3253-3255)aGa>aCa	p.R1085T	MGA_ENST00000389936.4_Missense_Mutation_p.R1085T|MGA_ENST00000545763.1_Missense_Mutation_p.R1085T|MGA_ENST00000566586.1_Missense_Mutation_p.R1085T|MGA_ENST00000219905.7_Missense_Mutation_p.R1085T			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)	TGTTTGAAAAGAAAAGTTGTA	0.458																																					p.R1085T		Atlas-SNP	.											.	MGA	264	.	0			c.G3254C						PASS	.						98	94	96					15																	42005518		1937	4124	6061	SO:0001583	missense	23269	exon9			TGAAAAGAAAAGT	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.3254G>C	chr15.hg19:g.42005518G>C	ENSP00000457035:p.Arg1085Thr	106.0	0.0	.		80.0	24.0	.	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	hg19	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.245765	0.80024	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	T;T;T	0.17370	2.28;2.28;2.28	5.75	5.75	0.90469	.	0.177622	0.46758	D	0.000265	T	0.28433	0.0703	L	0.27053	0.805	0.35184	D	0.772759	D;D	0.76494	0.997;0.999	D;D	0.73708	0.981;0.931	T	0.25779	-1.0122	10	0.87932	D	0	.	13.1821	0.59660	0.0727:0.0:0.9273:0.0	.	1085;1085	F5H7K2;E7ENI0	.;.	T	1085	ENSP00000219905:R1085T;ENSP00000374586:R1085T;ENSP00000442467:R1085T	ENSP00000219905:R1085T	R	+	2	0	MGA	39792810	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.511000	0.53400	2.716000	0.92895	0.655000	0.94253	AGA	.	.	.	none		0.458	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		C	42005518	G	C	42005518	3	2	85	1	0	0	0	0	1	0	0	0	9547	942	33	4	3284	4	MGA	15	42005518	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	1344840	42005518	60525874	67	5469											
CEP152	22995	hgsc.bcm.edu	37	chr15	49074426	49074426	+	Splice_Site	DEL	C	C	-																															tgagccacctcttgtactgaCcctgcagaggaaagaaccat																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr15:49074426delC	ENST00000380950.2	-	11	1510	c.1323delG	c.(1321-1323)ggg>gg	p.G441fs	CEP152_ENST00000399334.3_Splice_Site_p.G441fs|CEP152_ENST00000325747.5_Splice_Site_p.G348fs|RP11-485O10.2_ENST00000558304.1_RNA	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	441					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		CTTGTACTGACCCTGCAGAGG	0.443																																					p.S442fs		Atlas-INDEL	.											.	CEP152	145	.	0			c.1324delT						PASS	.						86	82	83					15																	49074426		1973	4175	6148	SO:0001630	splice_region_variant	22995	exon11			.	AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"asterless"	613529	"microcephaly, primary autosomal recessive 4"	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.1322-1G>-	chr15.hg19:g.49074426delC		27.0	0.0	0		30.0	10.0	0.333333	NM_014985	E7ER66|Q17RV1|Q6NTA0	Frame_Shift_Del	DEL	ENST00000380950.2	hg19	CCDS58361.1																																																																																			.	.	.	none		0.443	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985	Frame_Shift_Del	-	49074426	C	-	49074426	8	5	85	1	0	1	0	1	0	0	1	0	3250	521	18	0	3705	0	CEP152	15	49074426	Splice_Site	DEL	C	TCGA-B1-A655-01A-11D-A31Z-10	7068908	49074426	53456966	68	5470											
ALPK3	57538	hgsc.bcm.edu	37	chr15	85400827	85400827	+	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	cccaggtccccggagctgtgAccctggcctcatagattccc	6	8	10	17	1	1	2	1	1	0	1	3	3	3	3	6	3	1	1	6	3	1	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr15:85400827A>T	ENST00000258888.5	+	6	3631	c.3464A>T	c.(3463-3465)gAc>gTc	p.D1155V		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1155					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)			CGGAGCTGTGACCCTGGCCTC	0.627																																					p.D1155V		Atlas-SNP	.											.	ALPK3	289	.	0			c.A3464T						PASS	.						42	49	47					15																	85400827		2203	4299	6502	SO:0001583	missense	57538	exon6			GCTGTGACCCTGG	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.3464A>T	chr15.hg19:g.85400827A>T	ENSP00000258888:p.Asp1155Val	64.0	0.0	.		62.0	19.0	.	NM_020778	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	hg19	CCDS10333.1	.	.	.	.	.	.	.	.	.	.	A	19.25	3.792367	0.70452	.	.	ENSG00000136383	ENST00000258888	T	0.68624	-0.34	5.17	5.17	0.71159	.	0.513935	0.19872	N	0.104179	T	0.72590	0.3479	L	0.32530	0.975	0.54753	D	0.999988	D	0.89917	1.0	D	0.85130	0.997	T	0.74607	-0.3609	10	0.72032	D	0.01	-24.6636	11.4077	0.49908	1.0:0.0:0.0:0.0	.	1155	Q96L96	ALPK3_HUMAN	V	1155	ENSP00000258888:D1155V	ENSP00000258888:D1155V	D	+	2	0	ALPK3	83201831	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	2.636000	0.46545	1.958000	0.56883	0.460000	0.39030	GAC	.	.	.	none		0.627	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778		T	85400827	A	T	85400827	3	4	85	1	0	0	0	0	1	0	0	0	546	275	10	5	3486	5	ALPK3	15	85400827	Missense_Mutation	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	36326401	85400827	17130565	69	5471											
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1268594	1268594	+	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	tggtgcctgcctcggcgcccCacccccgcccgctgcaggag	3	5	13	20	4	0	0	0	0	0	0	1	1	0	1	7	3	3	2	7	3	0	0			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr16:1268594C>A	ENST00000348261.5	+	33	6078	c.5830C>A	c.(5830-5832)Cac>Aac	p.H1944N	CACNA1H_ENST00000565831.1_Missense_Mutation_p.H1938N|CACNA1H_ENST00000358590.4_Missense_Mutation_p.H1938N	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)	CTCGGCGCCCCACCCCCGCCC	0.662																																					p.H1944N		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C5830A						PASS	.						14	17	16					16																	1268594		1988	4120	6108	SO:0001583	missense	8912	exon33			GCGCCCCACCCCC	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.5830C>A	chr16.hg19:g.1268594C>A	ENSP00000334198:p.His1944Asn	87.0	0.0	.		91.0	28.0	.	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	hg19	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	C	7.903	0.734914	0.15574	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.96554	-4.05;-3.99	3.75	1.55	0.23275	.	3.133360	0.01371	N	0.012566	D	0.90823	0.7118	N	0.22421	0.69	0.09310	N	1	B;B;B;B;B	0.30973	0.034;0.029;0.0;0.302;0.039	B;B;B;B;B	0.24006	0.023;0.021;0.0;0.05;0.015	D	0.84424	0.0573	10	0.27082	T	0.32	.	2.7944	0.05397	0.2401:0.5032:0.0:0.2567	.	690;679;685;1938;1944	A2SX38;A2SX35;A2SX37;O95180-2;O95180	.;.;.;.;CAC1H_HUMAN	N	1944;1938	ENSP00000334198:H1944N;ENSP00000351401:H1938N	ENSP00000334198:H1944N	H	+	1	0	CACNA1H	1208595	0.947000	0.32204	0.001000	0.08648	0.001000	0.01503	0.399000	0.20916	0.806000	0.34183	0.563000	0.77884	CAC	.	.	.	none		0.662	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		A	1268594	C	A	1268594	3	1	85	1	0	0	0	0	1	0	0	0	2547	594	21	4	5956	4	CACNA1H	16	1268594	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10		1268594	89086159	70	5472											
ZKSCAN2	342357	hgsc.bcm.edu	37	chr16	25266603	25266603	+	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	gagtggaggcttccaggttcCtcccgagacaccgccctggg	6	7	14	14	2	0	1	0	0	0	1	3	4	3	2	5	4	0	2	5	4	0	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr16:25266603C>G	ENST00000328086.7	-	2	1313	c.510G>C	c.(508-510)gaG>gaC	p.E170D		NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	170					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)		TTCCAGGTTCCTCCCGAGACA	0.622																																					p.E170D		Atlas-SNP	.											.	ZKSCAN2	90	.	0			c.G510C						PASS	.						88	78	82					16																	25266603		2197	4300	6497	SO:0001583	missense	342357	exon2			AGGTTCCTCCCGA	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.510G>C	chr16.hg19:g.25266603C>G	ENSP00000331626:p.Glu170Asp	43.0	0.0	.		46.0	12.0	.	NM_001012981	A1L3B4|Q6ZN77	Missense_Mutation	SNP	ENST00000328086.7	hg19	CCDS32410.1	.	.	.	.	.	.	.	.	.	.	C	14.86	2.660995	0.47572	.	.	ENSG00000155592	ENST00000328086;ENST00000536768	T	0.14766	2.48	5.3	-2.75	0.05914	.	0.376195	0.25654	N	0.029181	T	0.11495	0.0280	L	0.55743	1.74	0.29398	N	0.862144	B;B	0.20550	0.046;0.003	B;B	0.27608	0.081;0.005	T	0.11251	-1.0595	10	0.52906	T	0.07	-11.4516	6.0464	0.19762	0.0:0.4411:0.1273:0.4316	.	170;170	Q63HK3-2;Q63HK3	.;ZKSC2_HUMAN	D	170	ENSP00000331626:E170D	ENSP00000331626:E170D	E	-	3	2	ZKSCAN2	25174104	0.027000	0.19231	0.445000	0.26908	0.501000	0.33797	-1.330000	0.02675	-0.703000	0.05049	0.555000	0.69702	GAG	.	.	.	none		0.622	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981		G	25266603	C	G	25266603	3	3	85	1	0	0	0	0	1	0	0	0	17699	680	24	4	2417	4	ZKSCAN2	16	25266603	Missense_Mutation	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	23998009	25266603	65088150	71	5473											
TP53	7157	hgsc.bcm.edu	37	chr17	7578271	7578271	+	Missense_Mutation	SNP	T	T	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	ttccttccactcggataagaTgctgaggaggggccagacct	9	9	12	11	1	0	3	0	1	0	2	3	5	2	5	4	4	1	1	4	4	1	3			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr17:7578271T>G	ENST00000269305.4	-	6	767	c.578A>C	c.(577-579)cAt>cCt	p.H193P	TP53_ENST00000413465.2_Missense_Mutation_p.H193P|TP53_ENST00000455263.2_Missense_Mutation_p.H193P|TP53_ENST00000574684.1_Intron|TP53_ENST00000445888.2_Missense_Mutation_p.H193P|TP53_ENST00000359597.4_Missense_Mutation_p.H193P|TP53_ENST00000420246.2_Missense_Mutation_p.H193P	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	193	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		H -> D (in sporadic cancers; somatic mutation).|H -> L (in sporadic cancers; somatic mutation).|H -> N (in sporadic cancers; somatic mutation).|H -> P (in sporadic cancers; somatic mutation).|H -> Q (in sporadic cancers; somatic mutation).|H -> R (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7887414}.|H -> Y (in sporadic cancers; somatic mutation).|QH -> HN (in a sporadic cancer; somatic mutation).|QH -> HY (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.H193R(80)|p.H193L(42)|p.H193P(18)|p.0?(8)|p.?(6)|p.H61R(4)|p.H100R(4)|p.H100L(4)|p.H61L(4)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.H193fs*16(3)|p.P191fs*53(2)|p.H61P(2)|p.H100P(2)|p.A189fs*53(1)|p.P191fs*6(1)|p.H193_I195delHLI(1)|p.P59_E66>Q(1)|p.P191fs*15(1)|p.P98_E105>Q(1)|p.H193_I195>AP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TCGGATAAGATGCTGAGGAGG	0.562		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.H193P	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,0,1	TP53	33396	.	193	Substitution - Missense(160)|Whole gene deletion(8)|Complex - deletion inframe(6)|Unknown(6)|Deletion - In frame(5)|Deletion - Frameshift(4)|Insertion - Frameshift(3)|Complex - frameshift(1)	lung(36)|upper_aerodigestive_tract(26)|ovary(20)|breast(18)|oesophagus(14)|haematopoietic_and_lymphoid_tissue(12)|endometrium(12)|biliary_tract(10)|liver(9)|stomach(7)|central_nervous_system(6)|large_intestine(6)|urinary_tract(5)|skin(5)|bone(4)|pancreas(2)|prostate(1)	c.A578C	GRCh37	CM083194|CM951225	TP53	M		PASS	.						97	87	90					17																	7578271		2203	4300	6503	SO:0001583	missense	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ATAAGATGCTGAG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.578A>C	chr17.hg19:g.7578271T>G	ENSP00000269305:p.His193Pro	120.0	1.0	.		123.0	29.0	.	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	13.91	2.377907	0.42105	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99855	-7.2;-7.2;-7.2;-7.2;-7.2;-7.2;-7.2;-7.2	5.41	4.33	0.51752	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99840	0.9927	M	0.88906	2.99	0.58432	D	0.999998	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.97320	0.9943	10	0.87932	D	0	-29.0766	9.707	0.40222	0.0:0.0827:0.0:0.9173	.	154;193;193;100;193;193;193	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	P	193;193;193;193;193;193;182;100;61;100;61	ENSP00000410739:H193P;ENSP00000352610:H193P;ENSP00000269305:H193P;ENSP00000398846:H193P;ENSP00000391127:H193P;ENSP00000391478:H193P;ENSP00000425104:H61P;ENSP00000423862:H100P	ENSP00000269305:H193P	H	-	2	0	TP53	7518996	1.000000	0.71417	0.814000	0.32528	0.023000	0.10783	7.996000	0.88334	1.001000	0.39076	-0.256000	0.11100	CAT	.	.	.	none		0.562	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		G	7578271	T	G	7578271	3	3	85	1	0	0	0	0	1	0	0	0	16393	1464	51	5	716	5	TP53	17	7578271	Missense_Mutation	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10		7578271	73616939	72	5474											
STARD3	10948	hgsc.bcm.edu	37	chr17	37814678	37814685	+	Frame_Shift_Del	DEL	TGGCTACC	TGGCTACC	-																															ctgctcagcaaaggggcattTggctacctgctccccatcgt																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	TGGCTACC	TGGCTACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr17:37814678_37814685delTGGCTACC	ENST00000336308.5	+	6	668_675	c.450_457delTGGCTACC	c.(448-459)tttggctacctgfs	p.GYL151fs	STARD3_ENST00000544210.2_Frame_Shift_Del_p.LAT146fs|STARD3_ENST00000394250.4_Frame_Shift_Del_p.GYL133fs|STARD3_ENST00000578232.1_3'UTR|STARD3_ENST00000580611.1_Frame_Shift_Del_p.GYL125fs	NM_001165937.1|NM_006804.3	NP_001159409.1|NP_006795.3	Q14849	STAR3_HUMAN	StAR-related lipid transfer (START) domain containing 3	151	MENTAL. {ECO:0000255|PROSITE- ProRule:PRU00770}.				cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|mitochondrial transport (GO:0006839)|progesterone biosynthetic process (GO:0006701)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	cholesterol binding (GO:0015485)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|prostate(2)|stomach(1)	14	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;1.04e-44)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			AAGGGGCATTTGGCTACCTGCTCCCCAT	0.582																																					p.150_152del		Atlas-Indel,Pindel	.											.	STARD3	33	.	0			c.449_456del						PASS	.																																			SO:0001589	frameshift_variant	10948	exon6			.		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.450_457delTGGCTACC	chr17.hg19:g.37814678_37814685delTGGCTACC	ENSP00000337446:p.Gly151fs	46.0	0.0	0		50.0	14.0	0.28	NM_006804	A8MXA4|B4DUY1|F5H0G2|Q53Y53|Q96HM9	Frame_Shift_Del	DEL	ENST00000336308.5	hg19	CCDS11341.1																																																																																			.	.	.	none		0.582	STARD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256933.1			-	37814685	TGGCTACC	-	37814678	7	5	85	1	0	1	0	1	0	0	0	0	15269	1821	63	0	468	0	STARD3	17	37814678	Frame_Shift_Del	DEL	TGGCTACC	TCGA-B1-A655-01A-11D-A31Z-10	30236407	37814678	43380532	73	5475											
BRCA1	672	hgsc.bcm.edu	37	chr17	41203099	41203099	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctgtgggcatgttggtgaaGggcccatagcaacagatttc	9	10	13	9	0	0	2	0	1	0	1	1	2	0	2	2	3	2	3	2	3	3	3	rs273901762		TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr17:41203099G>A	ENST00000357654.3	-	20	5431	c.5313C>T	c.(5311-5313)ccC>ccT	p.P1771P	BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000352993.3_Silent_p.P629P|BRCA1_ENST00000309486.4_Silent_p.P1475P|BRCA1_ENST00000471181.2_Silent_p.P1792P|BRCA1_ENST00000346315.3_Silent_p.P1532P|BRCA1_ENST00000491747.2_Silent_p.P667P|BRCA1_ENST00000354071.3_Silent_p.P1506P|BRCA1_ENST00000591534.1_Silent_p.P262P|BRCA1_ENST00000586385.1_Silent_p.P81P|BRCA1_ENST00000351666.3_Silent_p.P588P|BRCA1_ENST00000493795.1_Silent_p.P1724P|BRCA1_ENST00000468300.1_Silent_p.P667P	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	1771	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.				androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		TGTTGGTGAAGGGCCCATAGC	0.478			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.P1792P		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.C5376T						PASS	.						70	69	69					17																	41203099		2203	4300	6503	SO:0001819	synonymous_variant	672	exon21	Familial Cancer Database		GGTGAAGGGCCCA	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.5313C>T	chr17.hg19:g.41203099G>A		53.0	0.0	.		63.0	24.0	.	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Silent	SNP	ENST00000357654.3	hg19	CCDS11453.1																																																																																			.	.	.	none		0.478	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		A	41203099	G	A	41203099	2	1	85	1	0	0	0	0	0	0	0	1	1500	987	35	2		2	BRCA1	17	41203099	Silent	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	3388421	41203099	39992111	74	5476											
HEATR6	63897	hgsc.bcm.edu	37	chr17	58121036	58121036	+	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	ttctggctgtgtctccagttGgtgcctggatgctgcccatg	3	14	13	11	0	2	0	0	0	2	0	3	1	2	1	3	3	3	3	3	3	0	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr17:58121036G>T	ENST00000184956.6	-	20	3450	c.3434C>A	c.(3433-3435)cCa>cAa	p.P1145Q	AC005702.4_ENST00000583144.1_RNA|MIR4737_ENST00000583979.1_RNA|HEATR6_ENST00000585976.1_Missense_Mutation_p.P1033Q|AC005702.2_ENST00000577558.1_RNA|AC005702.3_ENST00000582298.1_RNA|AC005702.1_ENST00000581326.1_RNA	NM_022070.4	NP_071353.4	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6	1145							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)			GTCTCCAGTTGGTGCCTGGAT	0.542																																					p.P1145Q		Atlas-SNP	.											.	HEATR6	98	.	0			c.C3434A						PASS	.						129	115	120					17																	58121036		2203	4300	6503	SO:0001583	missense	63897	exon20			CCAGTTGGTGCCT	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.3434C>A	chr17.hg19:g.58121036G>T	ENSP00000184956:p.Pro1145Gln	130.0	0.0	.		207.0	49.0	.	NM_022070	B3KXP3|Q6MZX1|Q6MZY2|Q8TDM9|Q9H6B3|Q9H6M7	Missense_Mutation	SNP	ENST00000184956.6	hg19	CCDS11623.1	.	.	.	.	.	.	.	.	.	.	G	0.083	-1.180886	0.01633	.	.	ENSG00000068097	ENST00000184956;ENST00000393017	T	0.64438	-0.1	4.96	0.0386	0.14201	Armadillo-type fold (1);	1.078860	0.07032	N	0.828585	T	0.32941	0.0846	N	0.03608	-0.345	0.09310	N	1	B;B	0.17268	0.021;0.0	B;B	0.13407	0.009;0.001	T	0.19451	-1.0305	10	0.20519	T	0.43	0.0678	3.9945	0.09551	0.5137:0.0:0.2773:0.209	.	880;1145	E7ESB9;Q6AI08	.;HEAT6_HUMAN	Q	1145;880	ENSP00000184956:P1145Q	ENSP00000184956:P1145Q	P	-	2	0	HEATR6	55475818	0.000000	0.05858	0.002000	0.10522	0.010000	0.07245	-0.029000	0.12329	0.348000	0.23949	-0.312000	0.09012	CCA	.	.	.	none		0.542	HEATR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449165.1	NM_022070		T	58121036	G	T	58121036	3	4	85	1	0	0	0	0	1	0	0	0	7040	1348	47	4	115	4	HEATR6	17	58121036	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	16917937	58121036	23074174	75	5477											
HELZ	9931	hgsc.bcm.edu	37	chr17	65162707	65162707	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagaggggtaatcgatttaaTtgaaactgaagttcaacctg	14	11	10	6	1	1	3	1	2	0	1	2	4	1	3	1	2	2	2	1	2	5	5			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr17:65162707T>C	ENST00000358691.5	-	15	1948	c.1782A>G	c.(1780-1782)caA>caG	p.Q594Q	HELZ_ENST00000580168.1_Silent_p.Q594Q	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	594						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)					ATCGATTTAATTGAAACTGAA	0.393																																					p.Q594Q		Atlas-SNP	.											.	HELZ	160	.	0			c.A1782G						PASS	.						104	96	98					17																	65162707		1858	4110	5968	SO:0001819	synonymous_variant	9931	exon15			ATTTAATTGAAAC	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.1782A>G	chr17.hg19:g.65162707T>C		85.0	0.0	.		117.0	9.0	.	NM_014877	I6L9H4	Silent	SNP	ENST00000358691.5	hg19	CCDS42374.1																																																																																			.	.	.	none		0.393	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		C	65162707	T	C	65162707	2	2	85	1	0	0	0	0	0	0	0	1	7056	1490	52	3		3	HELZ	17	65162707	Silent	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	7041671	65162707	16032503	76	5478											
FSCN2	25794	hgsc.bcm.edu	37	chr17	79496379	79496379	+	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	caccgctacgtctctgtgcgGcaaggtagggagggcacagg	8	6	16	11	3	1	0	0	0	1	0	2	1	1	1	1	5	2	4	1	5	3	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr17:79496379G>A	ENST00000417245.2	+	1	958	c.822G>A	c.(820-822)cgG>cgA	p.R274R	RP13-766D20.2_ENST00000442532.1_RNA|RP13-766D20.2_ENST00000430912.1_RNA|FSCN2_ENST00000334850.7_Silent_p.R274R	NM_001077182.2|NM_012418.3	NP_001070650.1|NP_036550.1	O14926	FSCN2_HUMAN	fascin actin-bundling protein 2, retinal	274					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)			TCTCTGTGCGGCAAGGTAGGG	0.647																																					p.R274R		Atlas-SNP	.											.	FSCN2	35	.	0			c.G822A						PASS	.						9	10	10					17																	79496379		2169	4246	6415	SO:0001819	synonymous_variant	25794	exon1			TGTGCGGCAAGGT	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.822G>A	chr17.hg19:g.79496379G>A		83.0	0.0	.		123.0	73.0	.	NM_001077182	A0AVC4|A8MRA6	Silent	SNP	ENST00000417245.2	hg19	CCDS45811.1																																																																																			.	.	.	none		0.647	FSCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394746.1	NM_012418		A	79496379	G	A	79496379	2	1	85	1	0	0	0	0	0	0	0	1	6075	1190	42	2		2	FSCN2	17	79496379	Silent	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	14333672	79496379	1698831	77	5479											
PCYT2	5833	hgsc.bcm.edu	37	chr17	79865647	79865647	+	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	ggggattccgccgccgactcAcctggctgctgtgatgggct	4	9	15	13	3	1	1	1	1	0	0	2	3	2	2	4	4	1	3	4	4	0	1			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr17:79865647A>G	ENST00000538936.2	-	5	601		c.e5+1		PCYT2_ENST00000538721.2_Splice_Site|PCYT2_ENST00000571105.1_Splice_Site|PCYT2_ENST00000570388.1_Splice_Site|PCYT2_ENST00000331285.3_Splice_Site|PCYT2_ENST00000570391.1_Splice_Site	NM_001256435.1|NM_002861.3	NP_001243364.1|NP_002852.1	Q99447	PCY2_HUMAN	phosphate cytidylyltransferase 2, ethanolamine						glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)	ethanolamine-phosphate cytidylyltransferase activity (GO:0004306)			breast(2)|endometrium(1)|lung(4)|ovary(1)	8	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)		Lamivudine(DB00709)	CCGCCGACTCACCTGGCTGCT	0.667																																					.		Atlas-SNP	.											.	PCYT2	23	.	0			c.258+2T>C						PASS	.						55	45	49					17																	79865647		2203	4300	6503	SO:0001630	splice_region_variant	5833	exon6			CGACTCACCTGGC	D84307	CCDS11791.1, CCDS54178.1, CCDS58610.1, CCDS62364.1	17q25.3	2008-07-18				ENSG00000185813			8756	protein-coding gene	gene with protein product		602679				9083101	Standard	XM_005256386		Approved	ET	uc002kch.2	Q99447		ENST00000538936.2:c.492+1T>C	chr17.hg19:g.79865647A>G		46.0	0.0	.		52.0	14.0	.	NM_001256435	B7Z7A5|B7ZAS0|F5H8B1|Q6IBM3|Q96G08	Splice_Site	SNP	ENST00000538936.2	hg19	CCDS11791.1	.	.	.	.	.	.	.	.	.	.	A	15.43	2.829822	0.50845	.	.	ENSG00000185813	ENST00000538721;ENST00000538936;ENST00000331285	.	.	.	4.34	4.34	0.51931	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2492	0.54589	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PCYT2	77458939	1.000000	0.71417	1.000000	0.80357	0.632000	0.37999	8.242000	0.89818	1.812000	0.52913	0.459000	0.35465	.	.	.	.	none		0.667	PCYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439939.1	NM_002861	Intron	G	79865647	A	G	79865647	5	3	85	1	0	0	0	0	0	0	1	0	11619	173	6	3	769	3	PCYT2	17	79865647	Splice_Site	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	369268	79865647	1329563	78	5480											
KCNG2	26251	hgsc.bcm.edu	37	chr18	77659162	77659162	+	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	aagtgcgccttcctgcgcgcGccactcaacatcattgacat	9	9	8	15	4	2	1	2	1	0	0	3	1	3	1	3	0	3	0	3	0	2	2	rs140841838		TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr18:77659162G>A	ENST00000316249.3	+	2	747	c.747G>A	c.(745-747)gcG>gcA	p.A249A	KCNG2_ENST00000590307.1_3'UTR	NM_012283.1	NP_036415.1	Q9UJ96	KCNG2_HUMAN	potassium voltage-gated channel, subfamily G, member 2	249					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of heart contraction (GO:0008016)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(2)|endometrium(4)|lung(7)|skin(1)|upper_aerodigestive_tract(4)	18		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;6.92e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0244)		TCCTGCGCGCGCCACTCAACA	0.677																																					p.A249A		Atlas-SNP	.											.	KCNG2	48	.	0			c.G747A						PASS	.	G		0,4404		0,0,2202	43	39	40		747	-3.4	0	18	dbSNP_134	40	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KCNG2	NM_012283.1		0,1,6501	AA,AG,GG		0.0116,0.0,0.0077		249/467	77659162	1,13003	2202	4300	6502	SO:0001819	synonymous_variant	26251	exon2			GCGCGCGCCACTC	AJ011021	CCDS12019.1	18q23	2011-07-05			ENSG00000178342	ENSG00000178342		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6249	protein-coding gene	gene with protein product		605696				10551266, 16382104	Standard	NM_012283		Approved	Kv6.2, KCNF2	uc010xfl.2	Q9UJ96	OTTHUMG00000044541	ENST00000316249.3:c.747G>A	chr18.hg19:g.77659162G>A		32.0	0.0	.		26.0	6.0	.	NM_012283		Silent	SNP	ENST00000316249.3	hg19	CCDS12019.1																																																																																			.	G|1.000;A|0.000	0.000	weak		0.677	KCNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103906.1	NM_012283		A	77659162	G	A	77659162	2	1	85	1	0	0	0	0	0	0	0	1	8035	1074	38	1		1	KCNG2	18	77659162	Silent	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10		77659162	418086	79	5481											
ICAM1	3383	hgsc.bcm.edu	37	chr19	10395839	10395839	+	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	tgtggtagcagccgcagtcaTaatgggcactgcaggcctca	9	8	13	11	1	2	0	2	0	0	0	2	0	2	0	2	3	3	5	2	3	2	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr19:10395839T>A	ENST00000264832.3	+	7	1800	c.1475T>A	c.(1474-1476)aTa>aAa	p.I492K	ICAM4_ENST00000380770.3_5'Flank|ICAM1_ENST00000423829.2_Missense_Mutation_p.I270K|ICAM4_ENST00000340992.4_5'Flank|ICAM4_ENST00000393717.2_5'Flank|CTD-2369P2.8_ENST00000589379.1_RNA|CTD-2369P2.5_ENST00000592893.1_RNA	NM_000201.2	NP_000192.2	P05362	ICAM1_HUMAN	intercellular adhesion molecule 1	492					adhesion of symbiont to host (GO:0044406)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell aging (GO:0007569)|cellular response to alkaloid (GO:0071312)|cellular response to glucose stimulus (GO:0071333)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nutrient levels (GO:0031669)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|establishment of endothelial barrier (GO:0061028)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|membrane to membrane docking (GO:0022614)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|ovarian follicle development (GO:0001541)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cellular extravasation (GO:0002693)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of vasoconstriction (GO:0045907)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of leukocyte mediated cytotoxicity (GO:0001910)|regulation of ruffle assembly (GO:1900027)|response to amino acid (GO:0043200)|response to amphetamine (GO:0001975)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to gonadotropin (GO:0034698)|response to ionizing radiation (GO:0010212)|response to organic cyclic compound (GO:0014070)|response to sulfur dioxide (GO:0010477)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)|T cell antigen processing and presentation (GO:0002457)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;2.81e-06)|all cancers(31;6.56e-06)		Hyaluronan(DB08818)|Natalizumab(DB00108)	GCCGCAGTCATAATGGGCACT	0.547																																					p.I492K		Atlas-SNP	.											.	ICAM1	32	.	0			c.T1475A						PASS	.						103	105	104					19																	10395839		2203	4300	6503	SO:0001583	missense	3383	exon7			CAGTCATAATGGG		CCDS12231.1	19p13.3-p13.2	2014-01-30	2008-07-18			ENSG00000090339		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Endogenous ligands"	5344	protein-coding gene	gene with protein product	"human rhinovirus receptor"	147840				2453850, 3871395	Standard	NM_000201		Approved	BB2, CD54	uc002mnq.2	P05362		ENST00000264832.3:c.1475T>A	chr19.hg19:g.10395839T>A	ENSP00000264832:p.Ile492Lys	67.0	0.0	.		83.0	29.0	.	NM_000201	B2R6M3|Q5NKV7|Q96B50	Missense_Mutation	SNP	ENST00000264832.3	hg19	CCDS12231.1	.	.	.	.	.	.	.	.	.	.	T	12.45	1.941110	0.34283	.	.	ENSG00000090339	ENST00000264832;ENST00000423829	T;T	0.05199	4.24;3.48	5.22	3.07	0.35406	.	4.242400	0.00744	N	0.001020	T	0.05593	0.0147	N	0.19112	0.55	0.09310	N	0.999997	B;B	0.27286	0.142;0.174	B;B	0.22880	0.042;0.028	T	0.29305	-1.0016	10	0.42905	T	0.14	-14.6127	4.9491	0.14004	0.1651:0.0921:0.0:0.7428	.	270;492	E7ESS4;P05362	.;ICAM1_HUMAN	K	492;270	ENSP00000264832:I492K;ENSP00000413124:I270K	ENSP00000264832:I492K	I	+	2	0	ICAM1	10256839	0.000000	0.05858	0.006000	0.13384	0.011000	0.07611	0.007000	0.13174	0.909000	0.36697	0.459000	0.35465	ATA	.	.	.	none		0.547	ICAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451207.1			A	10395839	T	A	10395839	3	1	85	1	0	0	0	0	1	0	0	0	7486	1406	49	5	1501	5	ICAM1	19	10395839	Missense_Mutation	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10		10395839	48733144	80	5482											
CACNA1A	773	hgsc.bcm.edu	37	chr19	13418985	13418985	+	Frame_Shift_Del	DEL	A	A	-																															cgaagacgacaatgaacaggAaaaggagaaacaacaggctg																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr19:13418985delA	ENST00000360228.5	-	14	1861	c.1862delT	c.(1861-1863)ttcfs	p.F621fs	CACNA1A_ENST00000573710.2_Frame_Shift_Del_p.F622fs	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	622					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)	AATGAACAGGAAAAGGAGAAA	0.542																																					p.F622fs		Atlas-Indel,Pindel	.											.	CACNA1A	715	.	0			c.1866delC						PASS	.						95	98	97					19																	13418985		2088	4230	6318	SO:0001589	frameshift_variant	773	exon14			.	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.1862delT	chr19.hg19:g.13418985delA	ENSP00000353362:p.Phe621fs	137.0	0.0	0		126.0	42.0	0.333333	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Frame_Shift_Del	DEL	ENST00000360228.5	hg19	CCDS45998.1																																																																																			.	.	.	none		0.542	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		-	13418985	A	-	13418985	7	5	85	1	0	1	0	1	0	0	0	0	2540	246	9	0	5905	0	CACNA1A	19	13418985	Frame_Shift_Del	DEL	A	TCGA-B1-A655-01A-11D-A31Z-10	3023146	13418985	45709998	81	5483											
PLEKHG2	64857	hgsc.bcm.edu	37	chr19	39913652	39913652	+	Missense_Mutation	SNP	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	ccgctgtgaaattcccgaagGttctcgccttcctagtctct	6	13	8	14	3	2	1	0	1	2	0	6	2	4	1	4	1	0	2	4	1	3	4			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr19:39913652G>A	ENST00000409794.3	+	18	2808	c.1958G>A	c.(1957-1959)gGt>gAt	p.G653D	CTB-60E11.4_ENST00000601124.1_lincRNA|PLEKHG2_ENST00000378550.1_Intron|PLEKHG2_ENST00000409797.2_Intron|PLEKHG2_ENST00000425673.1_Missense_Mutation_p.G624D|PLEKHG2_ENST00000458508.2_Missense_Mutation_p.G594D	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	653					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)			ATTCCCGAAGGTTCTCGCCTT	0.517																																					p.G653D		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.G1958A						PASS	.						95	100	98					19																	39913652		2203	4300	6503	SO:0001583	missense	64857	exon18			CCGAAGGTTCTCG	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.1958G>A	chr19.hg19:g.39913652G>A	ENSP00000386733:p.Gly653Asp	80.0	0.0	.		87.0	5.0	.	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	hg19	CCDS33022.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	2.825|2.825	-0.243916|-0.243916	0.05906|0.05906	.|.	.|.	ENSG00000090924|ENSG00000090924	ENST00000409794;ENST00000425673;ENST00000458508|ENST00000205135	T;T;T|.	0.69040|.	-0.25;-0.25;-0.37|.	3.44|3.44	0.133|0.133	0.14766|0.14766	.|.	1.062390|.	0.07458|.	N|.	0.900138|.	T|T	0.14830|0.14830	0.0358|0.0358	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B;B;B|.	0.30361|.	0.263;0.261;0.277|.	B;B;B|.	0.25987|.	0.065;0.044;0.043|.	T|T	0.26121|0.26121	-1.0112|-1.0112	10|5	0.46703|.	T|.	0.11|.	.|.	4.0591|4.0591	0.09831|0.09831	0.0:0.2305:0.195:0.5745|0.0:0.2305:0.195:0.5745	.|.	624;653;594|.	Q9H7P9-3;Q9H7P9;E7ESZ3|.	.;PKHG2_HUMAN;.|.	D|I	653;624;594|521	ENSP00000386733:G653D;ENSP00000392906:G624D;ENSP00000408857:G594D|.	ENSP00000386733:G653D|.	G|V	+|+	2|1	0|0	PLEKHG2|PLEKHG2	44605492|44605492	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.010000|0.010000	0.07245|0.07245	-0.226000|-0.226000	0.09139|0.09139	-0.034000|-0.034000	0.13713|0.13713	-0.467000|-0.467000	0.05162|0.05162	GGT|GTT	.	.	.	none		0.517	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835		A	39913652	G	A	39913652	3	1	85	1	0	0	0	0	1	0	0	0	12076	1261	44	2	2024	2	PLEKHG2	19	39913652	Missense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10	26494667	39913652	19215331	82	5484											
TRPM4	54795	hgsc.bcm.edu	37	chr19	49674876	49674876	+	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	gctcagctcccatgtctcctCgtggctggctcagggggagc	4	9	14	14	1	3	0	2	0	1	0	6	1	4	1	2	4	2	4	2	4	0	0			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr19:49674876C>T	ENST00000252826.5	+	8	1026	c.900C>T	c.(898-900)ctC>ctT	p.L300L	TRPM4_ENST00000427978.2_Silent_p.L300L|TRPM4_ENST00000601347.1_3'UTR|TRPM4_ENST00000355712.5_Silent_p.L17L	NM_017636.3	NP_060106.2	Q8TD43	TRPM4_HUMAN	transient receptor potential cation channel, subfamily M, member 4	300					calcium ion transmembrane transport (GO:0070588)|cardiac conduction (GO:0061337)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|protein sumoylation (GO:0016925)|regulation of membrane potential (GO:0042391)|regulation of T cell cytokine production (GO:0002724)|transmembrane transport (GO:0055085)|vasoconstriction (GO:0042310)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)			breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(18)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	49		all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15)		all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751)		CATGTCTCCTCGTGGCTGGCT	0.592																																					p.L300L		Atlas-SNP	.											TRPM4,NS,carcinoma,0,1	TRPM4	119	.	0			c.C900T						PASS	.						37	42	41					19																	49674876		2202	4300	6502	SO:0001819	synonymous_variant	54795	exon8			TCTCCTCGTGGCT	AK000048	CCDS33073.1, CCDS56098.1	19q13.3	2011-12-14				ENSG00000130529		"Voltage-gated ion channels / Transient receptor potential cation channels"	17993	protein-coding gene	gene with protein product		606936				11535825, 16382100	Standard	NM_017636		Approved	FLJ20041	uc002pmw.3	Q8TD43		ENST00000252826.5:c.900C>T	chr19.hg19:g.49674876C>T		66.0	0.0	.		72.0	23.0	.	NM_001195227	A2RU25|Q7Z5D9|Q96L84|Q9NXV1	Silent	SNP	ENST00000252826.5	hg19	CCDS33073.1																																																																																			.	.	.	none		0.592	TRPM4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465543.2	NM_017636		T	49674876	C	T	49674876	2	4	85	1	0	0	0	0	0	0	0	1	16600	871	31	1		1	TRPM4	19	49674876	Silent	SNP	C	TCGA-B1-A655-01A-11D-A31Z-10	9761224	49674876	9454107	83	5485											
ZNF175	7728	hgsc.bcm.edu	37	chr19	52091298	52091298	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaaagccttcacttctaagTctcaattcaaagagcatcag	14	10	7	10	0	5	1	4	0	2	1	6	2	5	2	1	1	2	1	1	1	4	4			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr19:52091298T>C	ENST00000262259.2	+	5	2072	c.1714T>C	c.(1714-1716)Tct>Cct	p.S572P	ZNF175_ENST00000436511.2_Intron	NM_007147.2	NP_009078.1	Q9Y473	ZN175_HUMAN	zinc finger protein 175	572					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)		CACTTCTAAGTCTCAATTCAA	0.453																																					p.S572P		Atlas-SNP	.											.	ZNF175	65	.	0			c.T1714C						PASS	.						87	85	86					19																	52091298		2203	4300	6503	SO:0001583	missense	7728	exon5			TCTAAGTCTCAAT	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.1714T>C	chr19.hg19:g.52091298T>C	ENSP00000262259:p.Ser572Pro	63.0	0.0	.		68.0	20.0	.	NM_007147	A8K9H2	Missense_Mutation	SNP	ENST00000262259.2	hg19	CCDS12837.1	.	.	.	.	.	.	.	.	.	.	T	13.83	2.354614	0.41700	.	.	ENSG00000105497	ENST00000262259	T	0.18657	2.2	2.18	1.09	0.20402	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36963	0.0986	M	0.78344	2.41	0.09310	N	0.999999	D	0.65815	0.995	P	0.57911	0.829	T	0.13255	-1.0516	9	0.72032	D	0.01	.	6.4454	0.21873	0.0:0.0:0.2498:0.7502	.	572	Q9Y473	ZN175_HUMAN	P	572	ENSP00000262259:S572P	ENSP00000262259:S572P	S	+	1	0	ZNF175	56783110	0.000000	0.05858	0.703000	0.30354	0.992000	0.81027	-0.482000	0.06544	0.258000	0.21686	0.533000	0.62120	TCT	.	.	.	none		0.453	ZNF175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396205.1	NM_007147		C	52091298	T	C	52091298	3	2	85	1	0	0	0	0	1	0	0	0	17757	1667	58	3	1728	3	ZNF175	19	52091298	Missense_Mutation	SNP	T	TCGA-B1-A655-01A-11D-A31Z-10	2416422	52091298	7037685	84	5486											
NFATC2	4773	hgsc.bcm.edu	37	chr20	50051812	50051813	+	Frame_Shift_Del	DEL	GC	GC	-																															ttttacaggtgtgcggatatGcttgttccgatattcaggga																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr20:50051812_50051813delGC	ENST00000396009.3	-	8	2163_2164	c.1944_1945delGC	c.(1942-1947)aagcatfs	p.H649fs	NFATC2_ENST00000610033.1_Frame_Shift_Del_p.H430fs|NFATC2_ENST00000371564.3_Frame_Shift_Del_p.H649fs|NFATC2_ENST00000609943.1_Frame_Shift_Del_p.H629fs|NFATC2_ENST00000609507.1_Frame_Shift_Del_p.H430fs|NFATC2_ENST00000414705.1_Frame_Shift_Del_p.H629fs	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	649					B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					GTGCGGATATGCTTGTTCCGAT	0.436																																					p.649_649del		Atlas-Indel,Pindel	.											.	NFATC2	112	.	0			c.1945_1946del						PASS	.																																			SO:0001589	frameshift_variant	4773	exon8			.	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.1944_1945delGC	chr20.hg19:g.50051812_50051813delGC	ENSP00000379330:p.His649fs	69.0	0.0	0		84.0	25.0	0.297619	NM_012340	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Frame_Shift_Del	DEL	ENST00000396009.3	hg19	CCDS13437.1																																																																																			.	.	.	none		0.436	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340		-	50051813	GC	-	50051812	7	5	85	1	0	1	0	1	0	0	0	0	10369	1319	46	0	892	0	NFATC2	20	50051812	Frame_Shift_Del	DEL	GC	TCGA-B1-A655-01A-11D-A31Z-10		50051812	12973708	85	5487											
BRWD1	54014	hgsc.bcm.edu	37	chr21	40665927	40665927	+	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	acaagcggccattatgtgttGaccaaatctttaccaaacag	14	10	7	10	1	1	1	0	1	1	0	1	1	1	1	3	1	3	1	3	1	5	4			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr21:40665927G>T	ENST00000333229.2	-	8	968	c.641C>A	c.(640-642)tCa>tAa	p.S214*	BRWD1_ENST00000342449.3_Nonsense_Mutation_p.S214*|BRWD1_ENST00000380800.3_Nonsense_Mutation_p.S214*	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	214					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)				ATTATGTGTTGACCAAATCTT	0.328																																					p.S214X	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.C641A						PASS	.						82	77	79					21																	40665927		2203	4300	6503	SO:0001587	stop_gained	54014	exon8			TGTGTTGACCAAA	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.641C>A	chr21.hg19:g.40665927G>T	ENSP00000330753:p.Ser214*	104.0	0.0	.		90.0	32.0	.	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Nonsense_Mutation	SNP	ENST00000333229.2	hg19	CCDS13662.1	.	.	.	.	.	.	.	.	.	.	G	37	6.060061	0.97246	.	.	ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800	.	.	.	5.12	4.18	0.49190	.	0.110931	0.39985	N	0.001212	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.83	15.0594	0.71939	0.0:0.1423:0.8577:0.0	.	.	.	.	X	214	.	ENSP00000330753:S214X	S	-	2	0	BRWD1	39587797	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.477000	0.73591	2.388000	0.81334	0.655000	0.94253	TCA	.	.	.	none		0.328	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		T	40665927	G	T	40665927	4	4	85	1	0	0	0	0	0	1	0	0	1527	1294	45	4	6700	4	BRWD1	21	40665927	Nonsense_Mutation	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10		40665927	7463968	86	5488											
RFPL3	10738	hgsc.bcm.edu	37	chr22	32754194	32754195	+	Missense_Mutation	DNP	TA	TA	AT																															gctgtcccgtctgctcagacTatctggaaaaaccaatgtcc																										TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	T|A	T|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chr22:32754194_32754195TA>AT	ENST00000249007.4	+	1	341_342	c.136_137TA>AT	c.(136-138)TAt>ATt	p.Y46I	RFPL3_ENST00000397468.1_Missense_Mutation_p.Y17I|RFPL3_ENST00000382088.3_Missense_Mutation_p.Y17I|RFPL3S_ENST00000461833.1_5'Flank	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	46							zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						CTGCTCAGACTATCTGGAAAAA	0.52																																					p.Y46N|p.Y46F		Atlas-SNP	.											.	RFPL3	91	.	0			c.T136A|c.A137T						PASS	.																																			SO:0001583	missense	10738	exon1			TCAGACTATCTGG|CAGACTATCTGGA	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	Exception_encountered	chr22.hg19:g.32754194_32754195delinsAT	ENSP00000249007:p.Tyr46Ile	134.0	0.0	.		149.0|150.0	40.0	.	NM_001098535	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Missense_Mutation	SNP	ENST00000249007.4	hg19	CCDS43011.1																																																																																			.	.	.	none		0.52	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604		AT	32754195	TA	AT	32754194	3	1	85	1	0	0	0	0	1	0	0	0	13268	1522	53	5	138	5	RFPL3	22	32754194	Missense_Mutation	DNP	TA	TCGA-B1-A655-01A-11D-A31Z-10		32754194	18550372	87	5489											
ERCC6L	54821	hgsc.bcm.edu	37	chrX	71427693	71427693	+	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	tcagatattttaaatcccaaGgctttttctcctggggtagc	9	15	8	9	0	2	1	1	0	1	1	4	1	3	1	2	3	1	2	2	3	5	6			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chrX:71427693G>T	ENST00000334463.3	-	2	1059	c.924C>A	c.(922-924)gcC>gcA	p.A308A	ERCC6L_ENST00000373657.1_Silent_p.A185A|PIN4_ENST00000423432.2_Intron	NM_017669.2	NP_060139.2	Q2NKX8	ERC6L_HUMAN	excision repair cross-complementation group 6-like	308					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)					TAAATCCCAAGGCTTTTTCTC	0.388																																					p.A308A		Atlas-SNP	.											.	ERCC6L	98	.	0			c.C924A						PASS	.						80	82	81					X																	71427693		2203	4299	6502	SO:0001819	synonymous_variant	54821	exon2			TCCCAAGGCTTTT	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.924C>A	chrX.hg19:g.71427693G>T		222.0	0.0	.		149.0	6.0	.	NM_017669	Q8NCI1|Q96H93|Q9NXQ8	Silent	SNP	ENST00000334463.3	hg19	CCDS35329.1																																																																																			.	.	.	none		0.388	ERCC6L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057174.2	NM_017669		T	71427693	G	T	71427693	2	4	85	1	0	0	0	0	0	0	0	1	5220	987	35	4		4	ERCC6L	23	71427693	Silent	SNP	G	TCGA-B1-A655-01A-11D-A31Z-10		71427693	83842867	88	5490											
TCEAL4	79921	hgsc.bcm.edu	37	chrX	102841991	102841991	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccaggaaagccaaaagaaaaActaataaggggctggctcat	18	5	10	8	0	1	1	1	0	0	1	1	2	1	2	2	4	2	2	2	4	7	2			TCGA-B1-A655-01A-11D-A31Z-10	TCGA-B1-A655-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10597e71-58d4-4013-97c4-efe9f0d395ea	4f069099-30a3-4559-b812-caa5ee9002f9	g.chrX:102841991A>G	ENST00000472745.1	+	3	940	c.388A>G	c.(388-390)Act>Gct	p.T130A	TCEAL4_ENST00000415568.2_Missense_Mutation_p.T130A|TCEAL4_ENST00000494801.1_Missense_Mutation_p.T130A|TCEAL4_ENST00000468024.1_Missense_Mutation_p.T130A|TCEAL4_ENST00000372629.4_Missense_Mutation_p.T273A|TCEAL4_ENST00000472484.1_Missense_Mutation_p.T130A			Q96EI5	TCAL4_HUMAN	transcription elongation factor A (SII)-like 4	130					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(2)|skin(2)	6						CAAAAGAAAAACTAATAAGGG	0.458																																					p.T130A		Atlas-SNP	.											.	TCEAL4	18	.	0			c.A388G						PASS	.						103	105	104					X																	102841991		2203	4300	6503	SO:0001583	missense	79921	exon3			AGAAAAACTAATA	AF314542	CCDS14510.2, CCDS76004.1	Xq22.2	2014-03-21			ENSG00000133142	ENSG00000133142			26121	protein-coding gene	gene with protein product						14702039, 16221301	Standard	XM_005262192		Approved	FLJ21174, WEX7	uc004ekn.3	Q96EI5	OTTHUMG00000022103	ENST00000472745.1:c.388A>G	chrX.hg19:g.102841991A>G	ENSP00000424314:p.Thr130Ala	259.0	0.0	.		166.0	74.0	.	NM_001006935	Q8WY12|Q9H2H1|Q9H775	Missense_Mutation	SNP	ENST00000472745.1	hg19	CCDS14510.2	.	.	.	.	.	.	.	.	.	.	A	16.75	3.208774	0.58343	.	.	ENSG00000133142	ENST00000372629;ENST00000468024;ENST00000472484;ENST00000415568;ENST00000414064;ENST00000472745;ENST00000494801	T;T;T;T;T;T	0.10288	2.89;2.89;2.89;2.89;2.89;2.89	3.99	2.8	0.32819	.	0.000000	0.48767	D	0.000161	T	0.24812	0.0602	M	0.74258	2.255	0.24242	N	0.995359	D	0.67145	0.996	P	0.62649	0.905	T	0.03296	-1.1051	10	0.56958	D	0.05	.	6.7545	0.23505	0.7622:0.2378:0.0:0.0	.	130	Q96EI5	TCAL4_HUMAN	A	273;130;130;130;101;130;130	ENSP00000361712:T273A;ENSP00000421857:T130A;ENSP00000421156:T130A;ENSP00000415564:T130A;ENSP00000424314:T130A;ENSP00000427494:T130A	ENSP00000361712:T273A	T	+	1	0	TCEAL4	102728647	1.000000	0.71417	0.931000	0.37212	0.715000	0.41141	1.685000	0.37659	0.692000	0.31613	0.352000	0.21897	ACT	.	.	.	none		0.458	TCEAL4-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252339.2	NM_024863		G	102841991	A	G	102841991	3	3	85	1	0	0	0	0	1	0	0	0	15685	43	2	3	390	3	TCEAL4	23	102841991	Missense_Mutation	SNP	A	TCGA-B1-A655-01A-11D-A31Z-10	31414298	102841991	52428569	89	5491											
GABRD	2563	hgsc.bcm.edu	37	chr1	1960690	1960690	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagccaggcggcggtgcccGccagggtgtctctaggtacg	5	7	16	13	4	2	0	1	0	1	0	3	0	2	0	3	5	3	1	3	5	2	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:1960690G>A	ENST00000378585.4	+	7	915	c.832G>A	c.(832-834)Gcc>Acc	p.A278T		NM_000815.4	NP_000806.2	O14764	GBRD_HUMAN	gamma-aminobutyric acid (GABA) A receptor, delta	278					signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			central_nervous_system(2)|endometrium(3)|kidney(2)|lung(8)|ovary(2)|prostate(1)|skin(2)	20	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;2.7e-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;2.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.17e-24)|GBM - Glioblastoma multiforme(42;9.56e-08)|Colorectal(212;4.12e-05)|COAD - Colon adenocarcinoma(227;0.000194)|Kidney(185;0.00231)|BRCA - Breast invasive adenocarcinoma(365;0.00441)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GGCGGTGCCCGCCAGGGTGTC	0.682																																					p.A278T		Atlas-SNP	.											.	GABRD	49	.	0			c.G832A						PASS	.						37	32	34					1																	1960690		2180	4269	6449	SO:0001583	missense	2563	exon7			GTGCCCGCCAGGG	BC033801	CCDS36.1	1p36.3	2012-06-22			ENSG00000187730	ENSG00000187730		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4084	protein-coding gene	gene with protein product	"GABA(A) receptor, delta"	137163				2176788, 10965146	Standard	NM_000815		Approved		uc001aip.2	O14764	OTTHUMG00000041064	ENST00000378585.4:c.832G>A	chr1.hg19:g.1960690G>A	ENSP00000367848:p.Ala278Thr	74.0	0.0	.		56.0	9.0	.	NM_000815	Q8N4N9	Missense_Mutation	SNP	ENST00000378585.4	hg19	CCDS36.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.624127	0.87560	.	.	ENSG00000187730	ENST00000378585	D	0.86164	-2.08	4.23	4.23	0.50019	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.95198	0.8443	H	0.94771	3.58	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.96541	0.9400	10	0.87932	D	0	-18.1939	16.1634	0.81734	0.0:0.0:1.0:0.0	.	278	O14764	GBRD_HUMAN	T	278	ENSP00000367848:A278T	ENSP00000367848:A278T	A	+	1	0	GABRD	1950550	1.000000	0.71417	0.998000	0.56505	0.588000	0.36517	9.302000	0.96175	2.367000	0.80283	0.655000	0.94253	GCC	.	.	.	none		0.682	GABRD-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098493.1	NM_000815		A	1960690	G	A	1960690	3	1	86	1	0	0	0	0	1	0	0	0	6176	1087	38	1	858	1	GABRD	1	1960690	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10		1960690	247289931	1	5492											
FGR	2268	hgsc.bcm.edu	37	chr1	27943445	27943445	+	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	agtagccgcccatgtccagtTtgcggatcttgtaatgcttc	7	13	10	11	2	1	0	0	0	1	0	3	1	2	1	3	1	3	4	3	1	2	5			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:27943445T>A	ENST00000374005.3	-	7	893	c.605A>T	c.(604-606)aAa>aTa	p.K202I	FGR_ENST00000399173.1_Missense_Mutation_p.K202I|FGR_ENST00000545953.1_Missense_Mutation_p.K136I|FGR_ENST00000374004.1_Missense_Mutation_p.K202I	NM_005248.2	NP_005239.1	P09769	FGR_HUMAN	FGR proto-oncogene, Src family tyrosine kinase	202	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				blood coagulation (GO:0007596)|defense response to Gram-positive bacterium (GO:0050830)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of innate immune response (GO:0045088)|regulation of phagocytosis (GO:0050764)|regulation of protein kinase activity (GO:0045859)|response to virus (GO:0009615)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|Fc-gamma receptor I complex binding (GO:0034988)|immunoglobulin receptor binding (GO:0034987)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphotyrosine binding (GO:0001784)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(4)	16		all_lung(284;2.05e-05)|Colorectal(325;3.46e-05)|Lung NSC(340;3.67e-05)|Renal(390;0.00121)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00244)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		CATGTCCAGTTTGCGGATCTT	0.562																																					p.K202I		Atlas-SNP	.											.	FGR	39	.	0			c.A605T						PASS	.						172	152	159					1																	27943445		2203	4300	6503	SO:0001583	missense	2268	exon7			TCCAGTTTGCGGA	BC064382	CCDS305.1	1p36.2-p36.1	2014-06-25	2014-06-25		ENSG00000000938	ENSG00000000938		"SH2 domain containing"	3697	protein-coding gene	gene with protein product		164940	"Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog", "v-fgr feline Gardner-Rasheed sarcoma viral oncogene homolog", "feline Gardner-Rasheed sarcoma viral oncogene homolog"	SRC2		3922831	Standard	NM_001042729		Approved	c-fgr, p55c-fgr	uc001bom.3	P09769	OTTHUMG00000003516	ENST00000374005.3:c.605A>T	chr1.hg19:g.27943445T>A	ENSP00000363117:p.Lys202Ile	199.0	0.0	.		139.0	29.0	.	NM_001042729	D3DPL7|Q9UIQ3	Missense_Mutation	SNP	ENST00000374005.3	hg19	CCDS305.1	.	.	.	.	.	.	.	.	.	.	T	16.35	3.098543	0.56183	.	.	ENSG00000000938	ENST00000374005;ENST00000545953;ENST00000399173;ENST00000374004;ENST00000374003;ENST00000457296	D;D;D;D;D;D	0.89415	-2.51;-2.51;-2.51;-2.51;-2.51;-2.51	4.38	4.38	0.52667	SH2 motif (5);	0.000000	0.56097	D	0.000024	D	0.90662	0.7071	M	0.81497	2.545	0.32422	N	0.549198	B	0.22080	0.064	B	0.36289	0.221	D	0.92358	0.5895	10	0.62326	D	0.03	.	13.1133	0.59285	0.0:0.0:0.0:1.0	.	202	P09769	FGR_HUMAN	I	202;136;202;202;202;202	ENSP00000363117:K202I;ENSP00000445302:K136I;ENSP00000382126:K202I;ENSP00000363116:K202I;ENSP00000363115:K202I;ENSP00000407670:K202I	ENSP00000363115:K202I	K	-	2	0	FGR	27816032	1.000000	0.71417	0.927000	0.36925	0.561000	0.35649	8.040000	0.89188	1.903000	0.55091	0.402000	0.26972	AAA	.	.	.	none		0.562	FGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009772.1	NM_005248		A	27943445	T	A	27943445	3	1	86	1	0	0	0	0	1	0	0	0	5881	1841	64	5	1012	5	FGR	1	27943445	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	25982755	27943445	221307176	2	5493											
MRPS15	64960	hgsc.bcm.edu	37	chr1	36921882	36921882	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caattcccagcccccagcatAtcttctcaaagacatcatag	13	9	4	15	0	3	1	2	0	2	1	5	1	4	1	3	0	2	1	3	0	4	4			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:36921882A>G	ENST00000373116.5	-	7	703	c.542T>C	c.(541-543)aTa>aCa	p.I181T	MRPS15_ENST00000488606.1_5'UTR	NM_031280.3	NP_112570.2	P82914	RT15_HUMAN	mitochondrial ribosomal protein S15	181					translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)	14		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CCCCCAGCATATCTTCTCAAA	0.498																																					p.I181T		Atlas-SNP	.											.	MRPS15	21	.	0			c.T542C						PASS	.						93	87	89					1																	36921882		2203	4300	6503	SO:0001583	missense	64960	exon7			CAGCATATCTTCT	AB049946	CCDS411.1	1p34.3	2012-09-13			ENSG00000116898	ENSG00000116898		"Mitochondrial ribosomal proteins / small subunits"	14504	protein-coding gene	gene with protein product		611979					Standard	NM_031280		Approved	FLJ11564	uc001cas.2	P82914	OTTHUMG00000008042	ENST00000373116.5:c.542T>C	chr1.hg19:g.36921882A>G	ENSP00000362208:p.Ile181Thr	67.0	0.0	.		72.0	22.0	.	NM_031280	B2RD82|Q9H2K1	Missense_Mutation	SNP	ENST00000373116.5	hg19	CCDS411.1	.	.	.	.	.	.	.	.	.	.	A	0.013	-1.615508	0.00828	.	.	ENSG00000116898	ENST00000373116	.	.	.	6.17	-2.05	0.07321	S15/NS1, RNA-binding (2);	0.501132	0.23960	N	0.042864	T	0.19846	0.0477	N	0.14661	0.345	0.09310	N	0.999999	B	0.09022	0.002	B	0.09377	0.004	T	0.29971	-0.9994	9	0.07813	T	0.8	-14.528	12.7078	0.57070	0.5586:0.0:0.4414:0.0	.	181	P82914	RT15_HUMAN	T	181	.	ENSP00000362208:I181T	I	-	2	0	MRPS15	36694469	0.606000	0.26949	0.007000	0.13788	0.015000	0.08874	1.243000	0.32767	-0.243000	0.09653	-0.899000	0.02877	ATA	.	.	.	none		0.498	MRPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022052.2	NM_031280		G	36921882	A	G	36921882	3	3	86	1	0	0	0	0	1	0	0	0	9832	449	16	3	239	3	MRPS15	1	36921882	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	8978437	36921882	212328739	3	5494											
BCAR3	8412	hgsc.bcm.edu	37	chr1	94033045	94033045	+	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	tgtttgggggaacacatgtgGactctgaagaataaggagta	13	10	14	4	0	1	2	0	1	1	1	1	5	1	5	0	4	1	2	0	4	5	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:94033045G>C	ENST00000370244.1	-	13	2378	c.2090C>G	c.(2089-2091)tCc>tGc	p.S697C	BCAR3_ENST00000260502.6_Missense_Mutation_p.S697C|BCAR3_ENST00000370247.3_Missense_Mutation_p.S606C|BCAR3_ENST00000370243.1_Missense_Mutation_p.S697C|BCAR3_ENST00000539242.1_Missense_Mutation_p.S373C	NM_001261408.1	NP_001248337.1	O75815	BCAR3_HUMAN	breast cancer anti-estrogen resistance 3	697	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)		AACACATGTGGACTCTGAAGA	0.463																																					p.S697C		Atlas-SNP	.											.	BCAR3	62	.	0			c.C2090G						PASS	.						103	107	105					1																	94033045		2203	4300	6503	SO:0001583	missense	8412	exon11			CATGTGGACTCTG	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.2090C>G	chr1.hg19:g.94033045G>C	ENSP00000359264:p.Ser697Cys	99.0	0.0	.		63.0	14.0	.	NM_001261409	D3DT43|Q5TEW3|Q6UW40|Q9BR50	Missense_Mutation	SNP	ENST00000370244.1	hg19	CCDS745.1	.	.	.	.	.	.	.	.	.	.	G	17.79	3.475298	0.63737	.	.	ENSG00000137936	ENST00000370247;ENST00000260502;ENST00000370244;ENST00000370243;ENST00000539242	T;T;T;T;T	0.34667	1.35;1.35;1.35;1.35;1.35	5.85	4.92	0.64577	Guanine-nucleotide dissociation stimulator CDC25 (3);Ras guanine nucleotide exchange factor, domain (1);	0.709965	0.14950	N	0.288969	T	0.26521	0.0648	L	0.53249	1.67	0.09310	N	1	P;P	0.52692	0.955;0.955	P;P	0.52598	0.703;0.703	T	0.12400	-1.0549	10	0.38643	T	0.18	-19.933	7.5531	0.27808	0.1189:0.0:0.7329:0.1482	.	697;606	O75815;Q5TEW3	BCAR3_HUMAN;.	C	606;697;697;697;373	ENSP00000359267:S606C;ENSP00000260502:S697C;ENSP00000359264:S697C;ENSP00000359263:S697C;ENSP00000441343:S373C	ENSP00000260502:S697C	S	-	2	0	BCAR3	93805633	1.000000	0.71417	0.201000	0.23476	0.452000	0.32318	3.862000	0.56009	1.434000	0.47414	0.655000	0.94253	TCC	.	.	.	none		0.463	BCAR3-003	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028420.1			C	94033045	G	C	94033045	3	2	86	1	0	0	0	0	1	0	0	0	1349	1174	41	4	395	4	BCAR3	1	94033045	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	57111163	94033045	155217576	4	5495											
GON4L	54856	hgsc.bcm.edu	37	chr1	155734744	155734744	+	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	ggcatatcaataagtgatacAtattactgagtccacgaaat	16	11	7	7	1	1	2	1	2	0	0	2	3	2	2	1	1	2	1	1	1	7	5			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:155734744A>G	ENST00000368331.1	-	21	4522				GON4L_ENST00000471341.1_5'UTR|GON4L_ENST00000437809.1_Intron|GON4L_ENST00000361040.5_Missense_Mutation_p.M1507T|GON4L_ENST00000271883.5_Intron	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)						regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					TAAGTGATACATATTACTGAG	0.398																																					p.M1507T		Atlas-SNP	.											.	GON4L	392	.	0			c.T4520C						PASS	.						84	76	78					1																	155734744		2203	4300	6503	SO:0001627	intron_variant	54856	exon21			TGATACATATTAC	AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"gon-4 homolog (C.elegans)"	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.4473+46T>C	chr1.hg19:g.155734744A>G		299.0	0.0	.		303.0	86.0	.	NM_032292	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Missense_Mutation	SNP	ENST00000368331.1	hg19		.	.	.	.	.	.	.	.	.	.	A	10.67	1.416623	0.25552	.	.	ENSG00000116580	ENST00000361040	T	0.11277	2.79	4.47	-0.731	0.11151	.	.	.	.	.	T	0.01489	0.0048	N	0.08118	0	0.09310	N	1	B	0.13594	0.008	B	0.11329	0.006	T	0.46693	-0.9173	9	0.87932	D	0	.	4.9844	0.14182	0.5165:0.3159:0.1676:0.0	.	1507	Q3T8J9-2	.	T	1507	ENSP00000354322:M1507T	ENSP00000354322:M1507T	M	-	2	0	GON4L	154001368	0.000000	0.05858	0.000000	0.03702	0.121000	0.20230	-0.744000	0.04839	-0.308000	0.08792	0.378000	0.23410	ATG	.	.	.	none		0.398	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292		G	155734744	A	G	155734744	1	3	86	0	1	0	0	0	0	0	0	0	6579	217	8	3		3	GON4L	1	155734744	Intron	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	61701699	155734744	93515877	5	5496											
GORAB	92344	hgsc.bcm.edu	37	chr1	170508438	170508438	+	Missense_Mutation	SNP	A	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	ccttgtagagcaaagccaaaAacttgggcttcaagatggat	14	9	10	8	0	1	2	1	0	0	2	1	3	1	3	2	2	3	3	2	2	5	4			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:170508438A>C	ENST00000367763.3	+	2	244	c.224A>C	c.(223-225)aAa>aCa	p.K75T	GORAB_ENST00000367762.1_Missense_Mutation_p.K75T|GORAB_ENST00000465717.1_3'UTR	NM_152281.2	NP_689494.2	Q5T7V8	GORAB_HUMAN	golgin, RAB6-interacting	75						cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)				endometrium(2)|large_intestine(3)|liver(2)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	17						CAAAGCCAAAAACTTGGGCTT	0.443																																					p.K75T		Atlas-SNP	.											.	GORAB	41	.	0			c.A224C						PASS	.						107	102	104					1																	170508438		2203	4300	6503	SO:0001583	missense	92344	exon2			GCCAAAAACTTGG	AK021814	CCDS1289.1, CCDS53428.1	1q24.2	2009-02-13	2009-02-13	2009-02-13	ENSG00000120370	ENSG00000120370			25676	protein-coding gene	gene with protein product	"gerodermia osteodysplastica"	607983	"SCY1-like 1 binding protein 1"	SCYL1BP1		12783284, 15781263, 18997784	Standard	NM_152281		Approved	FLJ11752, NTKL-BP1, GO	uc001gha.2	Q5T7V8	OTTHUMG00000035228	ENST00000367763.3:c.224A>C	chr1.hg19:g.170508438A>C	ENSP00000356737:p.Lys75Thr	164.0	0.0	.		149.0	39.0	.	NM_152281	Q49A22|Q6P1P9|Q9HAE6|Q9Y350	Missense_Mutation	SNP	ENST00000367763.3	hg19	CCDS1289.1	.	.	.	.	.	.	.	.	.	.	A	16.66	3.186138	0.57909	.	.	ENSG00000120370	ENST00000367763;ENST00000367762	T;T	0.63580	-0.05;-0.05	5.49	4.37	0.52481	.	0.297450	0.41194	D	0.000932	T	0.62307	0.2417	M	0.70275	2.135	0.32365	N	0.556672	D	0.71674	0.998	D	0.66351	0.943	T	0.66268	-0.5966	10	0.56958	D	0.05	-12.6953	6.2817	0.21011	0.7838:0.0:0.0755:0.1408	.	75	Q5T7V8	GORAB_HUMAN	T	75	ENSP00000356737:K75T;ENSP00000356736:K75T	ENSP00000356736:K75T	K	+	2	0	GORAB	168775062	1.000000	0.71417	1.000000	0.80357	0.654000	0.38779	2.106000	0.41835	0.919000	0.36945	0.528000	0.53228	AAA	.	.	.	none		0.443	GORAB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085226.1	NM_152281		C	170508438	A	C	170508438	3	2	86	1	0	0	0	0	1	0	0	0	6581	14	1	5	230	5	GORAB	1	170508438	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	14773694	170508438	78742183	6	5497											
PRDX6	9588	hgsc.bcm.edu	37	chr1	173454533	173454534	+	Frame_Shift_Ins	INS	-	-	AAAAAAA																															caattgtgaagagcccacagINSaaaagttaccttttcccatc																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:173454533_173454534insAAAAAAA	ENST00000340385.5	+	3	418_419	c.286_287insAAAAAAA	c.(286-288)gaafs	p.-96fs	PRDX6_ENST00000470017.1_3'UTR	NM_004905.2	NP_004896.1	P30041	PRDX6_HUMAN	peroxiredoxin 6						hydrogen peroxide catabolic process (GO:0042744)|phospholipid catabolic process (GO:0009395)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|membrane (GO:0016020)	antioxidant activity (GO:0016209)|glutathione peroxidase activity (GO:0004602)|peroxiredoxin activity (GO:0051920)|phospholipase A2 activity (GO:0004623)	p.E96*(1)		NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	12						AGAGCCCACAGAAAAGTTACCT	0.441																																					p.E96fs		Atlas-Indel,Pindel	.											PRDX6,bladder,carcinoma,0,2	PRDX6	20	.	1	Substitution - Nonsense(1)	urinary_tract(1)	c.286_287insAAAAAAA						PASS	.																																			SO:0001589	frameshift_variant	9588	exon3			.	D14662	CCDS1307.1	1q24.1	2008-02-05			ENSG00000117592	ENSG00000117592			16753	protein-coding gene	gene with protein product		602316				11233154	Standard	NM_004905		Approved	AOP2, KIAA0106, 1-Cys, NSGPx, PRX, aiPLA2, MGC46173, p29	uc001giy.1	P30041	OTTHUMG00000034804	Exception_encountered	chr1.hg19:g.173454533_173454534insAAAAAAA	ENSP00000342026:p.Glu96fs	152.0	0.0	0		134.0	10.0	0.0746269	NM_004905	A8JZY7|P32077|Q5TAH4|Q5ZEZ8	Frame_Shift_Ins	INS	ENST00000340385.5	hg19	CCDS1307.1																																																																																			.	.	.	none		0.441	PRDX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084222.1	NM_004905		AAAAAAA	173454534	-	AAAAAAA	173454533	7	5	86	1	0	1	1	0	0	0	0	0	12479	943	33	0	296	0	PRDX6	1	173454533	Frame_Shift_Ins	INS	-	TCGA-B1-A656-01A-11D-A31X-10	2946095	173454533	75796088	7	5498											
LGTN	1939	hgsc.bcm.edu	37	chr1	206767112	206767112	+	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	cactgagtatgggtccagacCataggcctccaagttccgga	10	8	11	12	1	0	2	0	1	0	1	3	3	3	3	5	3	0	2	5	3	3	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:206767112C>T	ENST00000271764.2	-	14	1748	c.1540G>A	c.(1540-1542)Ggt>Agt	p.G514S	EIF2D_ENST00000472709.2_Intron|EIF2D_ENST00000367114.3_Missense_Mutation_p.G390S	NM_006893.2	NP_008824.2	P41214	EIF2D_HUMAN	eukaryotic translation initiation factor 2D	514	SUI1. {ECO:0000255|PROSITE- ProRule:PRU00200}.				formation of translation preinitiation complex (GO:0001731)|intracellular protein transport (GO:0006886)|IRES-dependent translational initiation (GO:0002192)|ribosome disassembly (GO:0032790)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	receptor activity (GO:0004872)|translation initiation factor activity (GO:0003743)			autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	23						GGGTCCAGACCATAGGCCTCC	0.622																																					p.G514S		Atlas-SNP	.											.	EIF2D	42	.	0			c.G1540A						PASS	.						59	53	55					1																	206767112		2203	4300	6503	SO:0001583	missense	1939	exon14			CCAGACCATAGGC	BC001585	CCDS1465.1, CCDS55680.1	1q32.1	2014-05-06	2011-01-19	2011-01-19	ENSG00000143486	ENSG00000143486			6583	protein-coding gene	gene with protein product		613709				20566627	Standard	NM_001201478		Approved	LGTN	uc001heh.2	P41214	OTTHUMG00000184619	ENST00000271764.2:c.1540G>A	chr1.hg19:g.206767112C>T	ENSP00000271764:p.Gly514Ser	45.0	0.0	.		37.0	8.0	.	NM_006893	Q5SY40|Q8IXV3|Q96DG3|Q96TG7|Q9NR27|Q9NSN0|Q9NV18|Q9NZ21	Missense_Mutation	SNP	ENST00000271764.2	hg19	CCDS1465.1	.	.	.	.	.	.	.	.	.	.	C	35	5.545011	0.96488	.	.	ENSG00000143486	ENST00000367114;ENST00000271764	T;T	0.31510	1.49;1.49	5.68	5.68	0.88126	Translation initiation factor SUI1 (3);	0.000000	0.85682	D	0.000000	T	0.55273	0.1910	M	0.72479	2.2	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;0.976	T	0.44050	-0.9353	10	0.21540	T	0.41	-19.8057	18.7742	0.91904	0.0:1.0:0.0:0.0	.	390;514	P41214-2;P41214	.;EIF2D_HUMAN	S	390;514	ENSP00000356081:G390S;ENSP00000271764:G514S	ENSP00000271764:G514S	G	-	1	0	EIF2D	204833735	1.000000	0.71417	0.991000	0.47740	0.995000	0.86356	7.586000	0.82596	2.676000	0.91093	0.563000	0.77884	GGT	.	.	.	none		0.622	EIF2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088475.1	NM_006893		T	206767112	C	T	206767112	3	4	86	1	0	0	0	0	1	0	0	0	8767	594	21	2	222	2	LGTN	1	206767112	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	33312579	206767112	42483509	8	5499											
TP53BP2	7159	hgsc.bcm.edu	37	chr1	223983631	223983631	+	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	ggtgggtatggagggtactcCtccaggtacacatcaagcac	10	8	13	10	0	1	0	1	0	0	0	3	1	3	1	2	5	3	4	2	5	4	3	rs376978247		TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:223983631C>A	ENST00000343537.7	-	13	2901	c.2610G>T	c.(2608-2610)gaG>gaT	p.E870D	TP53BP2_ENST00000498843.1_5'UTR|TP53BP2_ENST00000391878.2_Missense_Mutation_p.E741D|TP53BP2_ENST00000391879.2_Missense_Mutation_p.E103D	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	864	Pro-rich.				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)		GAGGGTACTCCTCCAGGTACA	0.572																																					p.E870D		Atlas-SNP	.											.	TP53BP2	144	.	0			c.G2610T						PASS	.						104	105	105					1																	223983631		2203	4300	6503	SO:0001583	missense	7159	exon13			GTACTCCTCCAGG	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.2610G>T	chr1.hg19:g.223983631C>A	ENSP00000341957:p.Glu870Asp	81.0	0.0	.		72.0	19.0	.	NM_001031685	B4DG66|Q12892|Q86X75|Q96KQ3	Missense_Mutation	SNP	ENST00000343537.7	hg19	CCDS44319.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.85|16.85	3.235801|3.235801	0.58886|0.58886	.|.	.|.	ENSG00000143514|ENSG00000143514	ENST00000391878;ENST00000343537;ENST00000391879|ENST00000494100	T;T;T|.	0.54279|.	0.68;0.85;0.58|.	5.55|5.55	3.32|3.32	0.38043|0.38043	Src homology-3 domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.60702|.	0.2289|.	L|L	0.60455|0.60455	1.87|1.87	0.80722|0.80722	D|D	1|1	D;D|.	0.69078|.	0.997;0.997|.	D;D|.	0.72625|.	0.978;0.978|.	T|.	0.54938|.	-0.8218|.	10|.	0.34782|.	T|.	0.22|.	.|.	9.5862|9.5862	0.39517|0.39517	0.0:0.7192:0.0:0.2808|0.0:0.7192:0.0:0.2808	.|.	870;864|.	B4DG66;Q13625|.	.;ASPP2_HUMAN|.	D|X	741;870;103|204	ENSP00000375750:E741D;ENSP00000341957:E870D;ENSP00000375751:E103D|.	ENSP00000341957:E870D|.	E|G	-|-	3|1	2|0	TP53BP2|TP53BP2	222050254|222050254	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.740000|0.740000	0.42216|0.42216	1.205000|1.205000	0.32308|0.32308	0.441000|0.441000	0.26529|0.26529	0.563000|0.563000	0.77884|0.77884	GAG|GGA	.	.	.	none		0.572	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3	NM_001031685, NM_005426		A	223983631	C	A	223983631	3	1	86	1	0	0	0	0	1	0	0	0	16396	680	24	4	818	4	TP53BP2	1	223983631	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	17216519	223983631	25266990	9	5500											
PARP1	142	hgsc.bcm.edu	37	chr1	226555997	226555999	+	In_Frame_Del	DEL	GAG	GAG	-																															ttgagagatccaggatctgaGagtcgctgctgccctgagac																								rs369734863		TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr1:226555997_226555999delGAG	ENST00000366794.5	-	16	2321_2323	c.2178_2180delCTC	c.(2176-2181)gactct>gat	p.S727del	PARP1_ENST00000490921.1_5'UTR	NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	727	PARP alpha-helical. {ECO:0000255|PROSITE- ProRule:PRU00398}.				base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		CAGGATCTGAGAGTCGCTGCTGC	0.562								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																													p.727_727del		Atlas-Indel,Pindel	.											.	PARP1	100	.	0			c.2179_2181del						PASS	.																																			SO:0001651	inframe_deletion	142	exon16			.	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.2178_2180delCTC	chr1.hg19:g.226555997_226555999delGAG	ENSP00000355759:p.Ser727del	76.0	0.0	0		66.0	17.0	0.257576	NM_001618	B1ANJ4|Q8IUZ9	In_Frame_Del	DEL	ENST00000366794.5	hg19	CCDS1554.1																																																																																			.	.	.	none		0.562	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618		-	226555999	GAG	-	226555997	7	5	86	1	0	1	0	1	0	0	0	0	11461	942	33	0	896	0	PARP1	1	226555997	In_Frame_Del	DEL	GAG	TCGA-B1-A656-01A-11D-A31X-10	2572366	226555997	22694624	10	5501											
MYCN	4613	hgsc.bcm.edu	37	chr2	16082258	16082258	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gacctcgagtttgactcgctAcagccctgcttctacccgga	7	10	9	15	3	1	1	0	1	1	0	3	4	1	2	3	1	4	3	3	1	2	4			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr2:16082258A>G	ENST00000281043.3	+	2	369	c.72A>G	c.(70-72)ctA>ctG	p.L24L	MYCNOS_ENST00000419083.1_RNA|MYCNOS_ENST00000453400.1_RNA|MYCNOS_ENST00000420452.1_RNA|MYCNOS_ENST00000439180.1_RNA|MYCNOS_ENST00000448719.1_RNA	NM_005378.4	NP_005369.2	P04198	MYCN_HUMAN	v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog	24					branching morphogenesis of an epithelial tube (GO:0048754)|cartilage condensation (GO:0001502)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|lung development (GO:0030324)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|positive regulation of cell death (GO:0010942)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin (GO:0000785)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	31	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)			TTGACTCGCTACAGCCCTGCT	0.642			A		neuroblastoma																																p.L24L		Atlas-SNP	.		Dom	yes		2	2p24.1	4613	"v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)"		O	.	MYCN	63	.	0			c.A72G						PASS	.						54	56	56					2																	16082258		2203	4300	6503	SO:0001819	synonymous_variant	4613	exon2			CTCGCTACAGCCC	BC002712	CCDS1687.1	2p24.3	2013-08-14	2013-07-09		ENSG00000134323	ENSG00000134323		"Basic helix-loop-helix proteins"	7559	protein-coding gene	gene with protein product		164840		NMYC			Standard	XM_006711886		Approved	bHLHe37, N-myc, MYCNOT	uc002rci.3	P04198	OTTHUMG00000039579	ENST00000281043.3:c.72A>G	chr2.hg19:g.16082258A>G		264.0	0.0	.		216.0	58.0	.	NM_005378	Q53XS5|Q6LDT9	Silent	SNP	ENST00000281043.3	hg19	CCDS1687.1																																																																																			.	.	.	none		0.642	MYCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095469.2	NM_005378		G	16082258	A	G	16082258	2	3	86	1	0	0	0	0	0	0	0	1	10028	378	14	3		3	MYCN	2	16082258	Silent	SNP	A	TCGA-B1-A656-01A-11D-A31X-10		16082258	227117115	11	5502											
DPY30	84661	hgsc.bcm.edu	37	chr2	32264491	32264491	+	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	atccacggcctcctgataccTgcgtttgtccctccagcatc	6	11	7	17	2	0	1	0	1	0	0	5	1	4	1	6	1	3	2	6	1	1	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr2:32264491T>A	ENST00000342166.5	-	2	150	c.35A>T	c.(34-36)cAg>cTg	p.Q12L	DPY30_ENST00000295066.3_Splice_Site_p.Q12L			Q9C005	DPY30_HUMAN	dpy-30 homolog (C. elegans)	12					endosomal transport (GO:0016197)|histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			large_intestine(2)	2	Acute lymphoblastic leukemia(172;0.155)					TCCTGATACCTGCGTTTGTCC	0.567																																					p.Q12L		Atlas-SNP	.											.	DPY30	6	.	0			c.A35T						PASS	.						104	103	103					2																	32264491		2203	4300	6503	SO:0001630	splice_region_variant	84661	exon2			GATACCTGCGTTT		CCDS1777.1	2p22.3	2013-09-09			ENSG00000162961	ENSG00000162961			24590	protein-coding gene	gene with protein product		612032				12477932	Standard	XM_006712117		Approved	Saf19, HDPY-30, Cps25	uc002roa.1	Q9C005	OTTHUMG00000128457	ENST00000342166.5:c.36+1A>T	chr2.hg19:g.32264491T>A		117.0	0.0	.		103.0	29.0	.	NM_032574	D6W578	Missense_Mutation	SNP	ENST00000342166.5	hg19	CCDS1777.1	.	.	.	.	.	.	.	.	.	.	T	13.66	2.302365	0.40694	.	.	ENSG00000162961	ENST00000342166;ENST00000295066	.	.	.	5.92	3.54	0.40534	.	0.158879	0.56097	D	0.000023	T	0.44498	0.1296	.	.	.	0.41659	D	0.989174	B	0.14438	0.01	B	0.10450	0.005	T	0.45264	-0.9273	8	0.48119	T	0.1	-14.8864	9.1274	0.36824	0.0:0.0721:0.136:0.7919	.	12	Q9C005	DPY30_HUMAN	L	12	.	ENSP00000295066:Q12L	Q	-	2	0	DPY30	32117995	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	2.804000	0.47931	2.274000	0.75844	0.533000	0.62120	CAG	.	.	.	none		0.567	DPY30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250255.2	NM_032574	Missense_Mutation	A	32264491	T	A	32264491	5	1	86	1	0	0	0	0	0	0	1	0	4746	1594	55	5	280	5	DPY30	2	32264491	Splice_Site	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	16182233	32264491	210934882	12	5503											
EPAS1	2034	hgsc.bcm.edu	37	chr2	46607787	46607787	+	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	ggccgtcggggatcagcgcaCagagttcttgggagcagcgc	7	6	17	11	4	2	1	1	0	1	1	3	3	2	3	1	4	3	3	1	4	0	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr2:46607787C>G	ENST00000263734.3	+	12	2486	c.1976C>G	c.(1975-1977)aCa>aGa	p.T659R		NM_001430.4	NP_001421.2	Q99814	EPAS1_HUMAN	endothelial PAS domain protein 1	659					angiogenesis (GO:0001525)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|erythrocyte differentiation (GO:0030218)|lung development (GO:0030324)|mitochondrion organization (GO:0007005)|myoblast fate commitment (GO:0048625)|norepinephrine metabolic process (GO:0042415)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart rate (GO:0002027)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|surfactant homeostasis (GO:0043129)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|histone acetyltransferase binding (GO:0035035)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	LUSC - Lung squamous cell carcinoma(58;0.151)			GATCAGCGCACAGAGTTCTTG	0.592																																					p.T659R		Atlas-SNP	.											.	EPAS1	83	.	0			c.C1976G						PASS	.						71	83	79					2																	46607787		2199	4290	6489	SO:0001583	missense	2034	exon12			AGCGCACAGAGTT	U81984	CCDS1825.1	2p21-p16	2013-05-21			ENSG00000116016	ENSG00000116016		"Basic helix-loop-helix proteins"	3374	protein-coding gene	gene with protein product	"HIF-1 alpha-like factor"	603349				9000051, 9079689, 18378852	Standard	NM_001430		Approved	MOP2, PASD2, HIF2A, HLF, bHLHe73	uc002ruv.3	Q99814	OTTHUMG00000128818	ENST00000263734.3:c.1976C>G	chr2.hg19:g.46607787C>G	ENSP00000263734:p.Thr659Arg	90.0	0.0	.		76.0	17.0	.	NM_001430	Q86VA2|Q99630	Missense_Mutation	SNP	ENST00000263734.3	hg19	CCDS1825.1	.	.	.	.	.	.	.	.	.	.	C	9.602	1.128965	0.21041	.	.	ENSG00000116016	ENST00000263734	T	0.46451	0.87	4.89	3.08	0.35506	.	1.373260	0.04589	N	0.396496	T	0.30823	0.0777	N	0.22421	0.69	0.09310	N	1	B	0.23316	0.083	B	0.25405	0.06	T	0.26155	-1.0111	10	0.24483	T	0.36	.	6.4229	0.21754	0.1452:0.7017:0.0:0.1531	.	659	Q99814	EPAS1_HUMAN	R	659	ENSP00000263734:T659R	ENSP00000263734:T659R	T	+	2	0	EPAS1	46461291	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	1.108000	0.31123	0.480000	0.27534	-0.237000	0.12165	ACA	.	.	.	none		0.592	EPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250752.2	NM_001430		G	46607787	C	G	46607787	3	3	86	1	0	0	0	0	1	0	0	0	5152	478	17	4	2022	4	EPAS1	2	46607787	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	14343296	46607787	196591586	13	5504											
REV1	51455	hgsc.bcm.edu	37	chr2	100019396	100019397	+	Frame_Shift_Ins	INS	-	-	A																															tcatgttttagaaacccatcINSaattaacttctggggactgc																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr2:100019396_100019397insA	ENST00000258428.3	-	20	3567_3568	c.3339_3340insT	c.(3337-3342)attgatfs	p.D1114fs	REV1_ENST00000393445.3_Frame_Shift_Ins_p.D1113fs|REV1_ENST00000465835.1_5'Flank|RP11-527J8.1_ENST00000608144.1_RNA	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	1114					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						AGAAACCCATCAATTAACTTCT	0.421								Direct reversal of damage																													p.D1114_G1115delinsX		Atlas-Indel,Pindel	.											.	REV1	100	.	0			c.3340_3341insT						PASS	.																																			SO:0001589	frameshift_variant	51455	exon20			.	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.3340dupT	chr2.hg19:g.100019398_100019398dupA	ENSP00000258428:p.Asp1114fs	124.0	0.0	0		98.0	27.0	0.27551	NM_016316	O95941|Q53SI7|Q9C0J4|Q9NUP2	Frame_Shift_Ins	INS	ENST00000258428.3	hg19	CCDS2045.1																																																																																			.	.	.	none		0.421	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316		A	100019397	-	A	100019396	7	5	86	1	0	1	1	0	0	0	0	0	13252	826	29	0	431	0	REV1	2	100019396	Frame_Shift_Ins	INS	-	TCGA-B1-A656-01A-11D-A31X-10	53411609	100019396	143179977	14	5505											
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125175092	125175092	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actcagtgagagcccgatttGttcgctttgtgcccctggaa	7	12	11	11	2	1	1	1	1	0	1	2	4	1	2	3	1	2	2	3	1	1	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr2:125175092G>A	ENST00000431078.1	+	4	818	c.454G>A	c.(454-456)Gtt>Att	p.V152I		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	152	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				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)		AGCCCGATTTGTTCGCTTTGT	0.498																																					p.V152I		Atlas-SNP	.											CNTNAP5,NS,haematopoietic_neoplasm,0,1	CNTNAP5	405	.	0			c.G454A						PASS	.						96	100	99					2																	125175092		1990	4172	6162	SO:0001583	missense	129684	exon4			CGATTTGTTCGCT	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.454G>A	chr2.hg19:g.125175092G>A	ENSP00000399013:p.Val152Ile	122.0	1.0	.		125.0	41.0	.	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	hg19	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	G	15.92	2.974606	0.53720	.	.	ENSG00000155052	ENST00000431078	D	0.97642	-4.47	6.17	-6.25	0.02039	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.767069	0.11093	N	0.600490	D	0.90116	0.6912	N	0.16656	0.425	0.29732	N	0.837787	B	0.02656	0.0	B	0.10450	0.005	T	0.79266	-0.1874	10	0.20046	T	0.44	.	9.7379	0.40399	0.4913:0.3858:0.1229:0.0	.	152	Q8WYK1	CNTP5_HUMAN	I	152	ENSP00000399013:V152I	ENSP00000399013:V152I	V	+	1	0	CNTNAP5	124891562	0.005000	0.15991	0.001000	0.08648	0.952000	0.60782	0.076000	0.14712	-1.035000	0.03291	0.655000	0.94253	GTT	.	.	.	none		0.498	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			A	125175092	G	A	125175092	3	1	86	1	0	0	0	0	1	0	0	0	3652	1377	48	2	468	2	CNTNAP5	2	125175092	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	25155696	125175092	118024281	15	5506											
ALS2	57679	hgsc.bcm.edu	37	chr2	202572610	202572610	+	Frame_Shift_Del	DEL	G	G	-																															accctggctctggtgattcaGatcgggaatctgacttccca																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr2:202572610delG	ENST00000264276.6	-	28	4757	c.4385delC	c.(4384-4386)tctfs	p.S1462fs	ALS2_ENST00000457679.2_3'UTR	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	1462					behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						TGGTGATTCAGATCGGGAATC	0.488																																					p.S1462fs		Atlas-INDEL	.											.	ALS2	172	.	0			c.4386delT						PASS	.						75	72	73					2																	202572610		1869	4110	5979	SO:0001589	frameshift_variant	57679	exon28			.	AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"Rho guanine nucleotide exchange factors"	443	protein-coding gene	gene with protein product	"alsin"	606352	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.4385delC	chr2.hg19:g.202572610delG	ENSP00000264276:p.Ser1462fs	328.0	0.0	0		256.0	24.0	0.09375	NM_020919	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Frame_Shift_Del	DEL	ENST00000264276.6	hg19	CCDS42800.1																																																																																			.	.	.	none		0.488	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919		-	202572610	G	-	202572610	7	5	86	1	0	1	0	1	0	0	0	0	550	942	33	0	616	0	ALS2	2	202572610	Frame_Shift_Del	DEL	G	TCGA-B1-A656-01A-11D-A31X-10	77397518	202572610	40626763	16	5507	60	2									
ALS2	57679	hgsc.bcm.edu	37	chr2	202572613	202572623	+	Frame_Shift_Del	DEL	CGGGAATCTGA	CGGGAATCTGA	-																															ctggctctggtgattcagatCgggaatctgacttcccagtg																								rs374047961		TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	CGGGAATCTGA	CGGGAATCTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr2:202572613_202572623delCGGGAATCTGA	ENST00000264276.6	-	28	4744_4754	c.4372_4382delTCAGATTCCCG	c.(4372-4383)tcagattcccgafs	p.SDSR1458fs	ALS2_ENST00000457679.2_3'UTR	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	1458					behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)	p.R1461Q(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						TGATTCAGATCGGGAATCTGACTTCCCAGTG	0.488																																					p.1458_1461del		Atlas-INDEL	.											.	ALS2	172	.	1	Substitution - Missense(1)	endometrium(1)	c.4373_4383del						PASS	.																																			SO:0001589	frameshift_variant	57679	exon28			.	AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"Rho guanine nucleotide exchange factors"	443	protein-coding gene	gene with protein product	"alsin"	606352	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.4372_4382delTCAGATTCCCG	chr2.hg19:g.202572613_202572623delCGGGAATCTGA	ENSP00000264276:p.Ser1458fs	329.0	0.0	0		251.0	22.0	0.0876494	NM_020919	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Frame_Shift_Del	DEL	ENST00000264276.6	hg19	CCDS42800.1																																																																																			.	.	.	none		0.488	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919		-	202572623	CGGGAATCTGA	-	202572613	7	5	86	1	0	1	0	1	0	0	0	0	550	884	31	0	619	0	ALS2	2	202572613	Frame_Shift_Del	DEL	CGGGAATCTGA	TCGA-B1-A656-01A-11D-A31X-10	3	202572613	40626760	17	5508	60	2									
NEU2	4759	hgsc.bcm.edu	37	chr2	233898967	233898967	+	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	aagtcacggagcaacagcagCtgcagaccagggccaatgtg	13	4	13	11	1	1	1	1	0	0	1	1	2	1	2	2	2	5	4	2	2	3	0			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr2:233898967C>T	ENST00000233840.3	+	2	343	c.343C>T	c.(343-345)Ctg>Ttg	p.L115L		NM_005383.2	NP_005374.2	Q9Y3R4	NEUR2_HUMAN	sialidase 2 (cytosolic sialidase)	115					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)	GCAACAGCAGCTGCAGACCAG	0.627																																					p.L115L		Atlas-SNP	.											.	NEU2	42	.	0			c.C343T						PASS	.						89	72	78					2																	233898967		2203	4300	6503	SO:0001819	synonymous_variant	4759	exon2			CAGCAGCTGCAGA	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.343C>T	chr2.hg19:g.233898967C>T		111.0	0.0	.		64.0	14.0	.	NM_005383	Q3KNW4|Q6NTB4	Silent	SNP	ENST00000233840.3	hg19	CCDS2501.1																																																																																			.	.	.	none		0.627	NEU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257053.2	NM_005383		T	233898967	C	T	233898967	2	4	86	1	0	0	0	0	0	0	0	1	10349	796	28	2		2	NEU2	2	233898967	Silent	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	31326354	233898967	9300406	18	5509											
MTMR14	64419	hgsc.bcm.edu	37	chr3	9724894	9724896	+	In_Frame_Del	DEL	CCT	CCT	-																															gtgcaacaaacacaaaactaCctgaagctgctgctttcctt																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr3:9724894_9724896delCCT	ENST00000296003.4	+	10	1052_1054	c.930_932delCCT	c.(928-933)tacctg>tag	p.310_311YL>*	MTMR14_ENST00000351233.5_In_Frame_Del_p.310_311YL>*|MTMR14_ENST00000420925.1_In_Frame_Del_p.64_65YL>*|MTMR14_ENST00000353332.5_In_Frame_Del_p.310_311YL>*	NM_001077525.2	NP_001070993.1	Q8NCE2	MTMRE_HUMAN	myotubularin related protein 14	310					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)					CACAAAACTACCTGAAGCTGCTG	0.429																																					p.310_311del		Atlas-INDEL	.											.	MTMR14	43	.	0			c.929_931del						PASS	.																																			SO:0001651	inframe_deletion	64419	exon10			.	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.930_932delCCT	chr3.hg19:g.9724894_9724896delCCT	ENSP00000296003:p.Tyr310_Leu311delins*	289.0	0.0	0		141.0	71.0	0.503546	NM_001077525	Q0JTH5|Q0JU83|Q6PIZ4|Q6QE21|Q86VK9|Q8IYK1|Q8TCM7|Q9H6C0	In_Frame_Del	DEL	ENST00000296003.4	hg19	CCDS43043.1																																																																																			.	.	.	none		0.429	MTMR14-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338435.1	NM_022485		-	9724896	CCT	-	9724894	7	5	86	1	0	1	0	1	0	0	0	0	9949	518	18	0	968	0	MTMR14	3	9724894	In_Frame_Del	DEL	CCT	TCGA-B1-A656-01A-11D-A31X-10		9724894	188297536	19	5510	61	2									
MTMR14	64419	hgsc.bcm.edu	37	chr3	9724897	9724898	+	Frame_Shift_Ins	INS	-	-	A																															aacaaacacaaaactacctgINSaagctgctgctttccttagt																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr3:9724897_9724898insA	ENST00000296003.4	+	10	1055_1056	c.933_934insA	c.(934-936)aagfs	p.K312fs	MTMR14_ENST00000351233.5_Frame_Shift_Ins_p.K312fs|MTMR14_ENST00000420925.1_Frame_Shift_Ins_p.K66fs|MTMR14_ENST00000353332.5_Frame_Shift_Ins_p.K312fs	NM_001077525.2	NP_001070993.1	Q8NCE2	MTMRE_HUMAN	myotubularin related protein 14	312					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)					AAAACTACCTGAAGCTGCTGCT	0.431																																					p.L311fs		Atlas-INDEL	.											.	MTMR14	43	.	0			c.933_934insA						PASS	.																																			SO:0001589	frameshift_variant	64419	exon10			.	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.935dupA	chr3.hg19:g.9724899_9724899dupA	ENSP00000296003:p.Lys312fs	291.0	0.0	0		143.0	67.0	0.468531	NM_001077525	Q0JTH5|Q0JU83|Q6PIZ4|Q6QE21|Q86VK9|Q8IYK1|Q8TCM7|Q9H6C0	Frame_Shift_Ins	INS	ENST00000296003.4	hg19	CCDS43043.1																																																																																			.	.	.	none		0.431	MTMR14-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338435.1	NM_022485		A	9724898	-	A	9724897	7	5	86	1	0	1	1	0	0	0	0	0	9949	1277	45	0	971	0	MTMR14	3	9724897	Frame_Shift_Ins	INS	-	TCGA-B1-A656-01A-11D-A31X-10	3	9724897	188297533	20	5511	61	2									
HDAC11	79885	hgsc.bcm.edu	37	chr3	13525052	13525052	+	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	gtgcacacgaggcgctatctTaatgagctcaaggtacagga	12	8	12	9	2	2	1	1	1	1	0	2	3	2	2	0	3	3	4	0	3	4	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr3:13525052T>G	ENST00000295757.3	+	3	423	c.240T>G	c.(238-240)ctT>ctG	p.L80L	HDAC11_ENST00000446613.2_Intron|HDAC11_ENST00000405025.1_Silent_p.L52L|HDAC11_ENST00000404040.1_Silent_p.L80L|HDAC11_ENST00000433119.1_Silent_p.L52L|HDAC11_ENST00000402271.1_Silent_p.L80L|HDAC11_ENST00000402259.1_Intron|HDAC11_ENST00000437379.2_Silent_p.L52L|HDAC11_ENST00000404548.1_Silent_p.L80L|HDAC11_ENST00000522202.1_Silent_p.L52L	NM_024827.3	NP_079103.2	Q96DB2	HDA11_HUMAN	histone deacetylase 11	80	Histone deacetylase.				chromatin modification (GO:0016568)|histone deacetylation (GO:0016575)|oligodendrocyte development (GO:0014003)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone deacetylase activity (GO:0004407)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|transcription factor binding (GO:0008134)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(4)|prostate(3)	13						GGCGCTATCTTAATGAGCTCA	0.647																																					p.L80L		Atlas-SNP	.											.	HDAC11	39	.	0			c.T240G						PASS	.						63	72	69					3																	13525052		2203	4300	6503	SO:0001819	synonymous_variant	79885	exon3			CTATCTTAATGAG	AK025426	CCDS2615.1, CCDS46760.1	3p25.1	2008-07-18			ENSG00000163517	ENSG00000163517	3.5.1.98		19086	protein-coding gene	gene with protein product		607226				11948178	Standard	NM_001136041		Approved		uc003bxy.3	Q96DB2	OTTHUMG00000129800	ENST00000295757.3:c.240T>G	chr3.hg19:g.13525052T>G		180.0	0.0	.		105.0	65.0	.	NM_024827	B4DDK1|Q9H6I7|Q9H6X3|Q9NTC9	Silent	SNP	ENST00000295757.3	hg19	CCDS2615.1																																																																																			.	.	.	none		0.647	HDAC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252028.5	NM_024827		G	13525052	T	G	13525052	2	3	86	1	0	0	0	0	0	0	0	1	7013	1741	61	5		5	HDAC11	3	13525052	Silent	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	3800155	13525052	184497378	21	5512											
TRAK1	22906	hgsc.bcm.edu	37	chr3	42218379	42218379	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgtcactcggcttcttgaGgaggtaagtgctccagggga	7	10	15	9	1	2	1	1	1	1	0	4	3	3	3	1	5	1	4	1	5	1	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr3:42218379G>A	ENST00000327628.5	+	3	760	c.360G>A	c.(358-360)gaG>gaA	p.E120E	TRAK1_ENST00000449246.1_Silent_p.E46E|TRAK1_ENST00000487159.1_3'UTR|TRAK1_ENST00000341421.3_Silent_p.E62E|TRAK1_ENST00000396175.1_Silent_p.E62E	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	120	HAP1 N-terminal.				endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						GGCTTCTTGAGGAGGTAAGTG	0.388																																					p.E120E	GBM(44;195 884 22595 31865 41850)	Atlas-SNP	.											TRAK1_ENST00000543338,NS,carcinoma,0,3	TRAK1	188	.	0			c.G360A						PASS	.						157	164	162					3																	42218379		2203	4300	6503	SO:0001819	synonymous_variant	22906	exon3			TCTTGAGGAGGTA		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.360G>A	chr3.hg19:g.42218379G>A		126.0	0.0	.		82.0	39.0	.	NM_001265608	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Silent	SNP	ENST00000327628.5	hg19	CCDS43072.1																																																																																			.	.	.	none		0.388	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965		A	42218379	G	A	42218379	2	1	86	1	0	0	0	0	0	0	0	1	16461	991	35	2		2	TRAK1	3	42218379	Silent	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	28693327	42218379	155804051	22	5513											
SNRK	54861	hgsc.bcm.edu	37	chr3	43388848	43388848	+	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	taggcagtcatggccaaccaAaattgatgtaccccaggacc	13	7	9	12	0	1	1	1	1	0	0	1	2	1	2	5	3	2	2	5	3	5	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr3:43388848A>T	ENST00000296088.7	+	7	1401	c.1097A>T	c.(1096-1098)aAa>aTa	p.K366I	RP11-188P20.3_ENST00000607513.1_RNA|SNRK_ENST00000454177.1_Missense_Mutation_p.K366I|SNRK_ENST00000437827.1_Missense_Mutation_p.K160I|SNRK_ENST00000429705.2_Missense_Mutation_p.K366I|SNRK-AS1_ENST00000422681.1_RNA	NM_017719.4	NP_060189.3			SNF related kinase											breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(5)|prostate(1)|skin(2)|stomach(1)	27				KIRC - Kidney renal clear cell carcinoma(284;0.0636)|Kidney(284;0.0792)		TGGCCAACCAAAATTGATGTA	0.483																																					p.K366I		Atlas-SNP	.											.	SNRK	118	.	0			c.A1097T						PASS	.						104	110	108					3																	43388848		1980	4155	6135	SO:0001583	missense	54861	exon7			CAACCAAAATTGA	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.1097A>T	chr3.hg19:g.43388848A>T	ENSP00000296088:p.Lys366Ile	55.0	0.0	.		27.0	16.0	.	NM_017719		Missense_Mutation	SNP	ENST00000296088.7	hg19	CCDS43075.1	.	.	.	.	.	.	.	.	.	.	A	14.78	2.636679	0.47049	.	.	ENSG00000163788	ENST00000454177;ENST00000429705;ENST00000296088;ENST00000437827	T;T;T;T	0.66460	-0.21;-0.21;-0.21;2.71	5.07	3.91	0.45181	.	0.175030	0.49305	N	0.000150	T	0.48960	0.1529	N	0.19112	0.55	0.49687	D	0.999812	B	0.23735	0.09	B	0.21360	0.034	T	0.49244	-0.8960	10	0.42905	T	0.14	.	10.4529	0.44533	0.9229:0.0:0.0771:0.0	.	366	Q9NRH2	SNRK_HUMAN	I	366;366;366;160	ENSP00000401246:K366I;ENSP00000411375:K366I;ENSP00000296088:K366I;ENSP00000409516:K160I	ENSP00000296088:K366I	K	+	2	0	SNRK	43363852	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.731000	0.68554	2.049000	0.60858	0.533000	0.62120	AAA	.	.	.	none		0.483	SNRK-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344325.1	NM_017719		T	43388848	A	T	43388848	3	4	86	1	0	0	0	0	1	0	0	0	14864	14	1	5	1115	5	SNRK	3	43388848	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	1170469	43388848	154633582	23	5514											
SETD2	29072	hgsc.bcm.edu	37	chr3	47165390	47165391	+	Frame_Shift_Ins	INS	-	-	A																															gcttctaaagattctggtacINSaattataattggtggttctt																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr3:47165390_47165391insA	ENST00000409792.3	-	3	777_778	c.735_736insT	c.(733-738)attgtafs	p.V246fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	246	Pro-rich.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		GATTCTGGTACAATTATAATTG	0.381			"N, F, S, Mis"		clear cell renal carcinoma																																p.V246fs		Atlas-Indel,Pindel	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.736_737insT						PASS	.																																			SO:0001589	frameshift_variant	29072	exon3			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.736dupT	chr3.hg19:g.47165392_47165392dupA	ENSP00000386759:p.Val246fs	72.0	0.0	0		52.0	30.0	0.576923	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Ins	INS	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.	.	none		0.381	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		A	47165391	-	A	47165390	7	5	86	1	0	1	1	0	0	0	0	0	14144	478	17	0	7034	0	SETD2	3	47165390	Frame_Shift_Ins	INS	-	TCGA-B1-A656-01A-11D-A31X-10	3776542	47165390	150857040	24	5515											
SH3TC1	54436	hgsc.bcm.edu	37	chr4	8230146	8230146	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggcagtggggctggccaacTtcggggccctgtgcctgcat	5	8	16	12	1	0	0	0	0	0	0	1	0	0	0	3	6	3	3	3	6	1	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr4:8230146T>C	ENST00000245105.3	+	12	2792	c.2725T>C	c.(2725-2727)Ttc>Ctc	p.F909L	SH3TC1_ENST00000539824.1_Missense_Mutation_p.F833L	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	909										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						GCTGGCCAACTTCGGGGCCCT	0.706																																					p.F909L	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											.	SH3TC1	105	.	0			c.T2725C						PASS	.						32	39	37					4																	8230146		2202	4298	6500	SO:0001583	missense	54436	exon12			GCCAACTTCGGGG	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.2725T>C	chr4.hg19:g.8230146T>C	ENSP00000245105:p.Phe909Leu	73.0	0.0	.		82.0	24.0	.	NM_018986	Q4W5G5	Missense_Mutation	SNP	ENST00000245105.3	hg19	CCDS3399.1	.	.	.	.	.	.	.	.	.	.	T	3.669	-0.067891	0.07228	.	.	ENSG00000125089	ENST00000382516;ENST00000245105;ENST00000539824;ENST00000535265	T;T	0.56103	0.48;0.48	4.63	0.869	0.19096	Tetratricopeptide-like helical (1);	0.456640	0.23165	N	0.051183	T	0.31765	0.0807	L	0.29908	0.895	0.32645	N	0.520198	B	0.21225	0.053	B	0.25759	0.063	T	0.40327	-0.9569	10	0.02654	T	1	-12.4248	8.0727	0.30699	0.0:0.2424:0.0:0.7576	.	909	Q8TE82	S3TC1_HUMAN	L	647;909;833;738	ENSP00000245105:F909L;ENSP00000441045:F833L	ENSP00000245105:F909L	F	+	1	0	SH3TC1	8281046	1.000000	0.71417	0.984000	0.44739	0.251000	0.25915	1.897000	0.39799	0.167000	0.19631	0.459000	0.35465	TTC	.	.	.	none		0.706	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986		C	8230146	T	C	8230146	3	2	86	1	0	0	0	0	1	0	0	0	14274	1609	56	3	2767	3	SH3TC1	4	8230146	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10		8230146	182924130	25	5516											
NPFFR2	10886	hgsc.bcm.edu	37	chr4	73012854	73012854	+	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	taccgagtgagactcaactcCcagaataaaaccagtccagt	15	7	7	12	1	1	2	1	1	0	2	3	4	3	2	4	0	3	0	4	0	5	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr4:73012854C>G	ENST00000308744.6	+	4	992	c.894C>G	c.(892-894)tcC>tcG	p.S298S	NPFFR2_ENST00000395999.1_Silent_p.S199S|NPFFR2_ENST00000344413.5_3'UTR|NPFFR2_ENST00000506359.1_3'UTR|NPFFR2_ENST00000358749.3_Silent_p.S196S	NM_004885.2	NP_004876.2	Q9Y5X5	NPFF2_HUMAN	neuropeptide FF receptor 2	298					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)			GACTCAACTCCCAGAATAAAA	0.443																																					p.S298S		Atlas-SNP	.											.	NPFFR2	98	.	0			c.C894G						PASS	.						121	117	119					4																	73012854		2203	4300	6503	SO:0001819	synonymous_variant	10886	exon4			CAACTCCCAGAAT	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.894C>G	chr4.hg19:g.73012854C>G		82.0	0.0	.		58.0	15.0	.	NM_004885	Q96RV1|Q9NR49	Silent	SNP	ENST00000308744.6	hg19	CCDS3551.1																																																																																			.	.	.	none		0.443	NPFFR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252170.2	NM_004885		G	73012854	C	G	73012854	2	3	86	1	0	0	0	0	0	0	0	1	10585	610	22	4		4	NPFFR2	4	73012854	Silent	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	64782708	73012854	118141422	26	5517											
FAM13A	10144	hgsc.bcm.edu	37	chr4	89658657	89658657	+	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	agaaggaagcagtttcgcccTcgataattggctgcagcaaa	13	8	11	9	2	0	1	0	0	0	1	2	3	0	2	1	2	3	5	1	2	4	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr4:89658657T>A	ENST00000264344.5	-	21	2819	c.2612A>T	c.(2611-2613)gAg>gTg	p.E871V	FAM13A_ENST00000513837.1_Missense_Mutation_p.E517V|FAM13A_ENST00000511976.1_Missense_Mutation_p.E457V|FAM13A_ENST00000508369.1_Missense_Mutation_p.E545V|FAM13A_ENST00000395002.2_Intron|FAM13A_ENST00000503556.1_Missense_Mutation_p.E531V	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	871					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						AGTTTCGCCCTCGATAATTGG	0.542																																					p.E871V		Atlas-SNP	.											.	FAM13A	181	.	0			c.A2612T						PASS	.						103	100	101					4																	89658657		2203	4300	6503	SO:0001583	missense	10144	exon21			TCGCCCTCGATAA	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.2612A>T	chr4.hg19:g.89658657T>A	ENSP00000264344:p.Glu871Val	115.0	0.0	.		85.0	24.0	.	NM_014883	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Missense_Mutation	SNP	ENST00000264344.5	hg19	CCDS34029.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.640552	0.87859	.	.	ENSG00000138640	ENST00000264344;ENST00000503556;ENST00000511976;ENST00000508369;ENST00000513837	T;T;T;T;T	0.51817	1.33;0.69;0.77;0.7;0.71	4.84	4.84	0.62591	.	0.109676	0.64402	D	0.000010	T	0.66636	0.2809	M	0.71036	2.16	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;0.999	D;D;D;D;D	0.71870	0.974;0.975;0.963;0.974;0.974	T	0.71377	-0.4611	10	0.87932	D	0	.	14.5853	0.68320	0.0:0.0:0.0:1.0	.	517;457;871;531;545	O94988-6;E9PGM7;O94988;O94988-5;O94988-1	.;.;FA13A_HUMAN;.;.	V	871;531;457;545;517	ENSP00000264344:E871V;ENSP00000427189:E531V;ENSP00000421914:E457V;ENSP00000421562:E545V;ENSP00000423252:E517V	ENSP00000264344:E871V	E	-	2	0	FAM13A	89877680	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.507000	0.81676	2.023000	0.59567	0.477000	0.44152	GAG	.	.	.	none		0.542	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1			A	89658657	T	A	89658657	3	1	86	1	0	0	0	0	1	0	0	0	5456	1551	54	5	475	5	FAM13A	4	89658657	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	16645803	89658657	101495619	27	5518											
KIAA0922	23240	hgsc.bcm.edu	37	chr4	154542029	154542029	+	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	aaggggtgttgctccagtctCaaggtgcgtaattcttacta	9	13	11	8	1	2	0	1	0	2	0	4	0	3	0	1	3	3	3	1	3	5	5			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr4:154542029C>A	ENST00000409663.3	+	27	3738	c.3686C>A	c.(3685-3687)tCa>tAa	p.S1229*	KIAA0922_ENST00000409959.3_Nonsense_Mutation_p.S1230*|KIAA0922_ENST00000440693.1_Nonsense_Mutation_p.S1146*	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	1229						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)				GCTCCAGTCTCAAGGTGCGTA	0.303																																					p.S1230X		Atlas-SNP	.											.	KIAA0922	214	.	0			c.C3689A						PASS	.						94	112	106					4																	154542029		2203	4300	6503	SO:0001587	stop_gained	23240	exon27			CAGTCTCAAGGTG	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.3686C>A	chr4.hg19:g.154542029C>A	ENSP00000386574:p.Ser1229*	671.0	0.0	.		651.0	188.0	.	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Nonsense_Mutation	SNP	ENST00000409663.3	hg19	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	C	40	7.923983	0.98563	.	.	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	.	.	.	5.5	3.61	0.41365	.	1.125250	0.06486	N	0.733676	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	0.0653	9.2055	0.37287	0.0:0.8085:0.0:0.1915	.	.	.	.	X	1229;1146;1230;1007	.	ENSP00000240487:S1007X	S	+	2	0	KIAA0922	154761479	0.021000	0.18746	0.003000	0.11579	0.003000	0.03518	1.282000	0.33226	0.532000	0.28657	0.563000	0.77884	TCA	.	.	.	none		0.303	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196		A	154542029	C	A	154542029	4	1	86	1	0	0	0	0	0	1	0	0	8208	838	29	4	3795	4	KIAA0922	4	154542029	Nonsense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	64883372	154542029	36612247	28	5519											
F2R	2149	hgsc.bcm.edu	37	chr5	76029290	76029290	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaatggatacctgctctagtAacctgaataacagcatatac	16	10	6	9	0	1	1	0	1	1	0	1	2	1	2	2	1	6	3	2	1	8	6			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr5:76029290A>G	ENST00000319211.4	+	2	1505	c.1240A>G	c.(1240-1242)Aac>Gac	p.N414D		NM_001992.3	NP_001983.2	P25116	PAR1_HUMAN	coagulation factor II (thrombin) receptor	414					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)	CTGCTCTAGTAACCTGAATAA	0.388																																					p.N414D		Atlas-SNP	.											.	F2R	58	.	0			c.A1240G						PASS	.						69	74	72					5																	76029290		2200	4300	6500	SO:0001583	missense	2149	exon2			TCTAGTAACCTGA	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.1240A>G	chr5.hg19:g.76029290A>G	ENSP00000321326:p.Asn414Asp	143.0	0.0	.		121.0	21.0	.	NM_001992	Q53XV0|Q96RF7|Q9BUN4	Missense_Mutation	SNP	ENST00000319211.4	hg19	CCDS4032.1	.	.	.	.	.	.	.	.	.	.	A	14.69	2.610635	0.46527	.	.	ENSG00000181104	ENST00000319211	T	0.75938	-0.98	4.79	1.18	0.20946	.	0.606938	0.17367	N	0.176834	T	0.67477	0.2897	L	0.59436	1.845	0.29406	N	0.861551	P	0.35433	0.501	B	0.32864	0.154	T	0.59968	-0.7354	10	0.34782	T	0.22	-19.7943	13.2149	0.59854	0.7302:0.2698:0.0:0.0	.	414	P25116	PAR1_HUMAN	D	414	ENSP00000321326:N414D	ENSP00000321326:N414D	N	+	1	0	F2R	76065046	0.204000	0.23447	0.988000	0.46212	0.977000	0.68977	0.936000	0.28938	0.110000	0.17919	0.379000	0.24179	AAC	.	.	.	none		0.388	F2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254068.2			G	76029290	A	G	76029290	3	3	86	1	0	0	0	0	1	0	0	0	5345	362	13	3	1246	3	F2R	5	76029290	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10		76029290	104885970	29	5520											
AFF4	27125	hgsc.bcm.edu	37	chr5	132224787	132224791	+	Frame_Shift_Del	DEL	GCTTT	GCTTT	-																															tcacctgtcatcaaagacaaGctttgttctccgaggcttag																								rs370588988		TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	GCTTT	GCTTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr5:132224787_132224791delGCTTT	ENST00000265343.5	-	14	3091_3095	c.2712_2716delAAAGC	c.(2710-2718)acaaagcttfs	p.KL905fs		NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	905					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)			TCAAAGACAAGCTTTGTTCTCCGAG	0.351																																					p.905_906del	Ovarian(126;889 1733 2942 10745 11605)	Pindel	.											.	AFF4	120	.	0			c.2713_2717del						PASS	.																																			SO:0001589	frameshift_variant	27125	exon14			.	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.2712_2716delAAAGC	chr5.hg19:g.132224787_132224791delGCTTT	ENSP00000265343:p.Lys905fs	429.0	0.0	.		459.0	23.0	0.050	NM_014423	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Frame_Shift_Del	DEL	ENST00000265343.5	hg19	CCDS4164.1																																																																																			.	.	.	none		0.351	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133049.1	NM_014423		-	132224791	GCTTT	-	132224787	7	5	86	1	0	1	0	1	0	0	0	0	359	971	34	0	807	0	AFF4	5	132224787	Frame_Shift_Del	DEL	GCTTT	TCGA-B1-A656-01A-11D-A31X-10	56195497	132224787	48690473	30	5521											
TMEM173	340061	hgsc.bcm.edu	37	chr5	138855862	138855862	+	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	ggtctcaagagaaatccgtgCggagagggaggggcttttcc	9	8	16	8	2	1	2	1	0	1	2	4	5	3	3	2	5	1	1	2	5	2	2	rs117897081	byFrequency	TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr5:138855862C>T	ENST00000330794.4	-	8	1457	c.1124G>A	c.(1123-1125)cGc>cAc	p.R375H	TMEM173_ENST00000511850.1_5'Flank	NM_198282.2	NP_938023.1	Q86WV6	STING_HUMAN	transmembrane protein 173	375	C-terminal tail (CTT).				activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	cyclic-di-GMP binding (GO:0035438)|cyclic-GMP-AMP binding (GO:0061507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|lung(6)|upper_aerodigestive_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GAAATCCGTGCGGAGAGGGAG	0.597																																					p.R375H		Atlas-SNP	.											.	TMEM173	19	.	0			c.G1124A						PASS	.						44	44	44					5																	138855862		2203	4300	6503	SO:0001583	missense	340061	exon8			TCCGTGCGGAGAG		CCDS4215.1	5q31.2	2009-11-06			ENSG00000184584	ENSG00000184584			27962	protein-coding gene	gene with protein product		612374				12477932	Standard	XM_005268445		Approved	FLJ38577, NET23	uc003lep.3	Q86WV6	OTTHUMG00000129239	ENST00000330794.4:c.1124G>A	chr5.hg19:g.138855862C>T	ENSP00000331288:p.Arg375His	105.0	0.0	.		90.0	38.0	.	NM_198282	A8K3P6|B6EB35|D6RBX0|D6RE01|D6RID9	Missense_Mutation	SNP	ENST00000330794.4	hg19	CCDS4215.1	.	.	.	.	.	.	.	.	.	.	C	13.97	2.395533	0.42512	.	.	ENSG00000184584	ENST00000330794	T	0.30448	1.53	5.36	3.48	0.39840	.	0.070055	0.53938	N	0.000050	T	0.36744	0.0978	M	0.70595	2.14	0.35562	D	0.804743	D	0.60160	0.987	P	0.50537	0.643	T	0.49532	-0.8930	10	0.42905	T	0.14	-17.9707	5.749	0.18136	0.1568:0.6785:0.0:0.1647	.	375	Q86WV6	TM173_HUMAN	H	375	ENSP00000331288:R375H	ENSP00000331288:R375H	R	-	2	0	TMEM173	138836046	0.671000	0.27521	0.933000	0.37362	0.148000	0.21650	0.972000	0.29409	1.268000	0.44264	-0.369000	0.07265	CGC	.	C|0.995;A|0.005	.	alt		0.597	TMEM173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251338.1	NM_198282		T	138855862	C	T	138855862	3	4	86	1	0	0	0	0	1	0	0	0	16101	768	27	1	19	1	TMEM173	5	138855862	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	6631075	138855862	42059398	31	5522											
UNC5A	90249	hgsc.bcm.edu	37	chr5	176305475	176305475	+	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	tcctctctgcatccccatcaGgagatccccttttatcacat	8	13	4	16	0	3	1	2	0	1	1	7	2	6	1	5	1	1	1	5	1	1	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr5:176305475G>A	ENST00000329542.4	+	13	2293		c.e13-1		UNC5A_ENST00000261961.3_Splice_Site	NM_133369.2	NP_588610.2	Q6ZN44	UNC5A_HUMAN	unc-5 homolog A (C. elegans)						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)		p.?(1)		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)			ATCCCCATCAGGAGATCCCCT	0.612																																					.		Atlas-SNP	.											UNC5A,NS,carcinoma,0,1	UNC5A	76	.	1	Unknown(1)	kidney(1)	c.2020-1G>A						PASS	.						89	83	85					5																	176305475		2203	4300	6503	SO:0001630	splice_region_variant	90249	exon13			CCATCAGGAGATC	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.2020-1G>A	chr5.hg19:g.176305475G>A		115.0	0.0	.		110.0	24.0	.	NM_133369	B2RXE6|Q8TF26|Q96GP4	Splice_Site	SNP	ENST00000329542.4	hg19	CCDS34299.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.275028	0.80580	.	.	ENSG00000113763	ENST00000329542;ENST00000261961	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.176	0.89761	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UNC5A	176238081	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	9.860000	0.99555	2.641000	0.89580	0.491000	0.48974	.	.	.	.	none		0.612	UNC5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372166.1	XM_030300	Intron	A	176305475	G	A	176305475	5	1	86	1	0	0	0	0	0	0	1	0	17003	1014	35	2	2069	2	UNC5A	5	176305475	Splice_Site	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	37449613	176305475	4609785	32	5523											
COL19A1	1310	hgsc.bcm.edu	37	chr6	70646796	70646796	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccagtgccagtgcattccAaacaaggtatgctagtttta	12	11	9	9	0	0	0	0	0	0	0	1	1	1	0	3	1	4	4	3	1	5	5			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr6:70646796A>G	ENST00000322773.4	+	8	969	c.867A>G	c.(865-867)ccA>ccG	p.P289P		NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	289					cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						AGTGCATTCCAAACAAGGTAT	0.448																																					p.P289P		Atlas-SNP	.											.	COL19A1	232	.	0			c.A867G						PASS	.						145	136	139					6																	70646796		2203	4300	6503	SO:0001819	synonymous_variant	1310	exon8			CATTCCAAACAAG		CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"Collagens"	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.867A>G	chr6.hg19:g.70646796A>G		122.0	0.0	.		102.0	28.0	.	NM_001858	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Silent	SNP	ENST00000322773.4	hg19	CCDS4970.1																																																																																			.	.	.	none		0.448	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1			G	70646796	A	G	70646796	2	3	86	1	0	0	0	0	0	0	0	1	3678	117	5	3		3	COL19A1	6	70646796	Silent	SNP	A	TCGA-B1-A656-01A-11D-A31X-10		70646796	100468271	33	5524											
LIMK1	3984	hgsc.bcm.edu	37	chr7	73535230	73535230	+	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	tgtactggacagatcatcggGcgggtgaacgcagaccctga	10	7	14	10	3	1	4	1	2	0	2	2	5	1	5	1	3	2	2	1	3	2	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr7:73535230G>A	ENST00000336180.2	+	15	1683	c.1632G>A	c.(1630-1632)ggG>ggA	p.G544G	LIMK1_ENST00000418310.1_Silent_p.G574G|LIMK1_ENST00000538333.3_Silent_p.G510G	NM_002314.3	NP_002305.1	P53667	LIMK1_HUMAN	LIM domain kinase 1	544	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|nervous system development (GO:0007399)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of axon extension (GO:0045773)|positive regulation of stress fiber assembly (GO:0051496)|protein phosphorylation (GO:0006468)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)	ATP binding (GO:0005524)|heat shock protein binding (GO:0031072)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21		Lung NSC(55;0.137)			Dabrafenib(DB08912)	AGATCATCGGGCGGGTGAACG	0.647																																					p.G544G		Atlas-SNP	.											.	LIMK1	55	.	0			c.G1632A						PASS	.						86	82	84					7																	73535230		2203	4300	6503	SO:0001819	synonymous_variant	3984	exon15			CATCGGGCGGGTG	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.1632G>A	chr7.hg19:g.73535230G>A		135.0	0.0	.		126.0	6.0	.	NM_002314	B7Z6I8|D3DXF4|D3DXF5|O15283|Q15820|Q15821|Q75MU3|Q9Y5Q1	Silent	SNP	ENST00000336180.2	hg19	CCDS5563.1																																																																																			.	.	.	none		0.647	LIMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252335.2	NM_002314		A	73535230	G	A	73535230	2	1	86	1	0	0	0	0	0	0	0	1	8808	1190	42	2		2	LIMK1	7	73535230	Silent	SNP	G	TCGA-B1-A656-01A-11D-A31X-10		73535230	85603433	34	5525											
SRRT	51593	hgsc.bcm.edu	37	chr7	100485704	100485704	+	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	caggactcccctacccacacCagactccccagggcctgatg	9	5	8	19	0	0	2	0	1	0	1	2	3	2	3	7	2	1	0	7	2	1	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr7:100485704C>A	ENST00000347433.4	+	18	2526	c.2368C>A	c.(2368-2370)Cag>Aag	p.Q790K	SRRT_ENST00000457580.2_Missense_Mutation_p.Q786K|SRRT_ENST00000388793.4_Missense_Mutation_p.Q789K|SRRT_ENST00000432932.1_Missense_Mutation_p.Q785K			Q9BXP5	SRRT_HUMAN	serrate, RNA effector molecule	790	Pro-rich.				cell proliferation (GO:0008283)|neuronal stem cell maintenance (GO:0097150)|primary miRNA processing (GO:0031053)|regulation of transcription, DNA-templated (GO:0006355)|response to arsenic-containing substance (GO:0046685)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						CTACCCACACCAGACTCCCCA	0.612																																					p.Q790K		Atlas-SNP	.											.	SRRT	108	.	0			c.C2368A						PASS	.						52	56	55					7																	100485704		2203	4300	6503	SO:0001583	missense	51593	exon18			CCACACCAGACTC		CCDS34709.1, CCDS47665.1, CCDS47666.1, CCDS47667.1	7q21	2014-04-14	2014-04-14		ENSG00000087087	ENSG00000087087			24101	protein-coding gene	gene with protein product	"arsenite resistance protein"	614469	"serrate RNA effector molecule homolog (Arabidopsis)"			11239002, 11230166	Standard	NM_015908		Approved	Asr2, serrate, ARS2	uc003uwy.2	Q9BXP5	OTTHUMG00000157031	ENST00000347433.4:c.2368C>A	chr7.hg19:g.100485704C>A	ENSP00000314491:p.Gln790Lys	157.0	0.0	.		148.0	69.0	.	NM_015908	A4D2E5|A4D2E6|A6NK22|B4DJL4|B4DZA6|O95808|Q32MI4|Q6NT74|Q8TDQ5|Q9BWP6|Q9BXP4|Q9Y4S4	Missense_Mutation	SNP	ENST00000347433.4	hg19	CCDS34709.1	.	.	.	.	.	.	.	.	.	.	C	16.78	3.217920	0.58560	.	.	ENSG00000087087	ENST00000457580;ENST00000388793;ENST00000342198;ENST00000432932;ENST00000347433;ENST00000448764;ENST00000445337	.	.	.	4.91	4.91	0.64330	Arsenite-resistance protein 2 (1);	0.000000	0.85682	D	0.000000	T	0.50446	0.1616	N	0.08118	0	0.51767	D	0.999935	B;P;P;D	0.53885	0.206;0.954;0.954;0.963	B;D;D;D	0.71414	0.058;0.954;0.954;0.973	T	0.46789	-0.9166	9	0.15952	T	0.53	.	15.6172	0.76775	0.0:1.0:0.0:0.0	.	789;785;786;790	Q9BXP5-3;Q9BXP5-4;Q9BXP5-2;Q9BXP5	.;.;.;SRRT_HUMAN	K	786;789;155;785;790;420;67	.	ENSP00000344670:Q155K	Q	+	1	0	SRRT	100323640	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.964000	0.63701	2.545000	0.85829	0.484000	0.47621	CAG	.	.	.	none		0.612	SRRT-004	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347168.1	NM_015908		A	100485704	C	A	100485704	3	1	86	1	0	0	0	0	1	0	0	0	15184	595	21	4	2434	4	SRRT	7	100485704	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	26950474	100485704	58652959	35	5526											
CDHR3	222256	hgsc.bcm.edu	37	chr7	105673047	105673047	+	Frame_Shift_Del	DEL	G	G	-																															tgggctgaggatgctggtctGggttccagaaatgagggtgg																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr7:105673047delG	ENST00000317716.9	+	19	2642	c.2562delG	c.(2560-2562)ctgfs	p.L854fs	CDHR3_ENST00000478080.1_Frame_Shift_Del_p.L766fs|CDHR3_ENST00000343407.5_3'UTR|CDHR3_ENST00000542731.1_Frame_Shift_Del_p.L854fs	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	854					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						ATGCTGGTCTGGGTTCCAGAA	0.552																																					p.L854fs		Atlas-Indel,Pindel	.											.	CDHR3	153	.	0			c.2561delT						PASS	.						68	76	73					7																	105673047		2097	4220	6317	SO:0001589	frameshift_variant	222256	exon19			.	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.2562delG	chr7.hg19:g.105673047delG	ENSP00000325954:p.Leu854fs	175.0	0.0	0		170.0	37.0	0.217647	NM_152750	Q8TCI7	Frame_Shift_Del	DEL	ENST00000317716.9	hg19	CCDS47684.1																																																																																			.	.	.	none		0.552	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750		-	105673047	G	-	105673047	7	5	86	1	0	1	0	1	0	0	0	0	3122	1335	47	0	2636	0	CDHR3	7	105673047	Frame_Shift_Del	DEL	G	TCGA-B1-A656-01A-11D-A31X-10	5187343	105673047	53465616	36	5527											
DLD	1738	hgsc.bcm.edu	37	chr7	107556127	107556127	+	Frame_Shift_Del	DEL	A	A	-																															gctaccaagaagtcagatggAaaaattgatgtttcgtaagt																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr7:107556127delA	ENST00000205402.5	+	9	1142	c.861delA	c.(859-861)ggafs	p.G287fs	DLD_ENST00000537148.1_Frame_Shift_Del_p.G188fs|DLD_ENST00000440410.1_Frame_Shift_Del_p.G264fs|DLD_ENST00000437604.2_Frame_Shift_Del_p.G239fs	NM_000108.3	NP_000099.2	P09622	DLDH_HUMAN	dihydrolipoamide dehydrogenase	287					branched-chain amino acid catabolic process (GO:0009083)|cell redox homeostasis (GO:0045454)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|gastrulation (GO:0007369)|lysine catabolic process (GO:0006554)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|proteolysis (GO:0006508)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of membrane potential (GO:0042391)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|tricarboxylic acid cycle (GO:0006099)	acrosomal matrix (GO:0043159)|cilium (GO:0005929)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dihydrolipoyl dehydrogenase activity (GO:0004148)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(1)|lung(10)|prostate(1)	20					Flavin adenine dinucleotide(DB03147)	AGTCAGATGGAAAAATTGATG	0.308																																					p.G287fs		Atlas-INDEL	.											.	DLD	72	.	0			c.860delG						PASS	.						52	54	54					7																	107556127		2203	4300	6503	SO:0001589	frameshift_variant	1738	exon9			.	AB209703	CCDS5749.1	7q31-q32	2006-05-22	2006-05-22		ENSG00000091140	ENSG00000091140	1.8.1.4		2898	protein-coding gene	gene with protein product	"E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex"	238331	"dihydrolipoamide dehydrogenase (E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex)"	LAD, GCSL			Standard	NM_000108		Approved	DLDH	uc003vet.3	P09622	OTTHUMG00000154813	ENST00000205402.5:c.861delA	chr7.hg19:g.107556127delA	ENSP00000205402:p.Gly287fs	127.0	0.0	0		125.0	14.0	0.112	NM_000108	B2R5X0|B4DHG0|B4DT69|Q14131|Q14167|Q59EV8|Q8WTS4	Frame_Shift_Del	DEL	ENST00000205402.5	hg19	CCDS5749.1																																																																																			.	.	.	none		0.308	DLD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337194.3	NM_000108		-	107556127	A	-	107556127	7	5	86	1	0	1	0	1	0	0	0	0	4553	233	9	0	895	0	DLD	7	107556127	Frame_Shift_Del	DEL	A	TCGA-B1-A656-01A-11D-A31X-10	1883080	107556127	51582536	37	5528	62	2									
DLD	1738	hgsc.bcm.edu	37	chr7	107556131	107556131	+	Frame_Shift_Del	DEL	A	A	-																															ccaagaagtcagatggaaaaAttgatgtttcgtaagtatac																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr7:107556131delA	ENST00000205402.5	+	9	1146	c.865delA	c.(865-867)attfs	p.I289fs	DLD_ENST00000537148.1_Frame_Shift_Del_p.I190fs|DLD_ENST00000440410.1_Frame_Shift_Del_p.I266fs|DLD_ENST00000437604.2_Frame_Shift_Del_p.I241fs	NM_000108.3	NP_000099.2	P09622	DLDH_HUMAN	dihydrolipoamide dehydrogenase	289					branched-chain amino acid catabolic process (GO:0009083)|cell redox homeostasis (GO:0045454)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|gastrulation (GO:0007369)|lysine catabolic process (GO:0006554)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|proteolysis (GO:0006508)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of membrane potential (GO:0042391)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|tricarboxylic acid cycle (GO:0006099)	acrosomal matrix (GO:0043159)|cilium (GO:0005929)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dihydrolipoyl dehydrogenase activity (GO:0004148)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(1)|lung(10)|prostate(1)	20					Flavin adenine dinucleotide(DB03147)	AGATGGAAAAATTGATGTTTC	0.323																																					p.K288fs		Pindel	.											.	DLD	72	.	0			c.864delA						PASS	.						52	54	53					7																	107556131		2203	4300	6503	SO:0001589	frameshift_variant	1738	exon9			.	AB209703	CCDS5749.1	7q31-q32	2006-05-22	2006-05-22		ENSG00000091140	ENSG00000091140	1.8.1.4		2898	protein-coding gene	gene with protein product	"E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex"	238331	"dihydrolipoamide dehydrogenase (E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex)"	LAD, GCSL			Standard	NM_000108		Approved	DLDH	uc003vet.3	P09622	OTTHUMG00000154813	ENST00000205402.5:c.865delA	chr7.hg19:g.107556131delA	ENSP00000205402:p.Ile289fs	116.0	0.0	.		122.0	12.0	0.098	NM_000108	B2R5X0|B4DHG0|B4DT69|Q14131|Q14167|Q59EV8|Q8WTS4	Frame_Shift_Del	DEL	ENST00000205402.5	hg19	CCDS5749.1																																																																																			.	.	.	none		0.323	DLD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337194.3	NM_000108		-	107556131	A	-	107556131	7	5	86	1	0	1	0	1	0	0	0	0	4553	101	4	0	899	0	DLD	7	107556131	Frame_Shift_Del	DEL	A	TCGA-B1-A656-01A-11D-A31X-10	4	107556131	51582532	38	5529	62	2									
ANK1	286	hgsc.bcm.edu	37	chr8	41551436	41551436	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caatgacgctgcaaagcaggCgcaggctggtggtgtctccc	8	7	14	12	2	1	1	0	1	1	0	2	1	1	1	1	4	2	5	1	4	2	0			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr8:41551436C>T	ENST00000347528.4	-	29	3595	c.3512G>A	c.(3511-3513)cGc>cAc	p.R1171H	ANK1_ENST00000396945.1_Missense_Mutation_p.R1171H|ANK1_ENST00000265709.8_Missense_Mutation_p.R1212H|ANK1_ENST00000379758.2_Missense_Mutation_p.R1171H|ANK1_ENST00000396942.1_Missense_Mutation_p.R1171H|ANK1_ENST00000289734.7_Missense_Mutation_p.R1171H|ANK1_ENST00000352337.4_Missense_Mutation_p.R1171H	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	1171	ZU5 2. {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)	p.R1171H(1)		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)			GCAAAGCAGGCGCAGGCTGGT	0.647																																					p.R1212H		Atlas-SNP	.											ANK1,caecum,carcinoma,0,1	ANK1	497	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3635A						PASS	.						31	28	29					8																	41551436		2203	4300	6503	SO:0001583	missense	286	exon30			AGCAGGCGCAGGC	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.3512G>A	chr8.hg19:g.41551436C>T	ENSP00000339620:p.Arg1171His	176.0	0.0	.		161.0	37.0	.	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Missense_Mutation	SNP	ENST00000347528.4	hg19	CCDS6119.1	.	.	.	.	.	.	.	.	.	.	C	35	5.421819	0.96111	.	.	ENSG00000029534	ENST00000347528;ENST00000289734;ENST00000379758;ENST00000396945;ENST00000396942;ENST00000352337;ENST00000265709;ENST00000358820	T;T;T;T;T;T;T	0.73469	-0.72;-0.72;-0.69;-0.68;-0.69;-0.67;-0.75	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	D	0.87018	0.6073	M	0.80183	2.485	0.80722	D	1	D;D;D;P;D;D	0.89917	0.988;0.996;0.994;0.914;0.988;1.0	D;P;P;P;D;D	0.73708	0.91;0.821;0.677;0.498;0.91;0.981	D	0.88810	0.3291	10	0.87932	D	0	.	18.7318	0.91738	0.0:1.0:0.0:0.0	.	1212;1171;1171;1171;1171;487	P16157-21;P16157-4;P16157;P16157-5;P16157-3;B3KX39	.;.;ANK1_HUMAN;.;.;.	H	1171;1171;1171;1171;1171;1171;1212;1171	ENSP00000339620:R1171H;ENSP00000289734:R1171H;ENSP00000369082:R1171H;ENSP00000380149:R1171H;ENSP00000380147:R1171H;ENSP00000309131:R1171H;ENSP00000265709:R1212H	ENSP00000265709:R1212H	R	-	2	0	ANK1	41670593	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.794000	0.85869	2.493000	0.84123	0.313000	0.20887	CGC	.	.	.	none		0.647	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		T	41551436	C	T	41551436	3	4	86	1	0	0	0	0	1	0	0	0	620	768	27	1	2515	1	ANK1	8	41551436	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10		41551436	104812586	39	5530											
SLC20A2	6575	hgsc.bcm.edu	37	chr8	42302170	42302170	+	Frame_Shift_Del	DEL	T	T	-																															taaaaggcccatacctgttaTtttcctccgcatccacggac																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr8:42302170delT	ENST00000342228.3	-	6	1093	c.724delA	c.(724-726)atafs	p.I242fs	SLC20A2_ENST00000520262.1_Frame_Shift_Del_p.I242fs|SLC20A2_ENST00000520179.1_Frame_Shift_Del_p.I242fs	NM_006749.4	NP_006740.1	Q08357	S20A2_HUMAN	solute carrier family 20 (phosphate transporter), member 2	242					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)			ATACCTGTTATTTTCCTCCGC	0.463																																					p.I242fs		Atlas-Indel,Pindel	.											.	SLC20A2	64	.	0			c.725delT						PASS	.						137	120	126					8																	42302170		2203	4300	6503	SO:0001589	frameshift_variant	6575	exon6			.		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.724delA	chr8.hg19:g.42302170delT	ENSP00000340465:p.Ile242fs	124.0	0.0	0		126.0	42.0	0.333333	NM_001257180		Frame_Shift_Del	DEL	ENST00000342228.3	hg19	CCDS6132.1																																																																																			.	.	.	none		0.463	SLC20A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377578.1			-	42302170	T	-	42302170	7	5	86	1	0	1	0	1	0	0	0	0	14452	1493	52	0	1258	0	SLC20A2	8	42302170	Frame_Shift_Del	DEL	T	TCGA-B1-A656-01A-11D-A31X-10	750734	42302170	104061852	40	5531											
RFX3	5991	hgsc.bcm.edu	37	chr9	3271084	3271084	+	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	gccacaatttttctatcaggCtaaattgaagattcacaaca	15	12	5	9	0	3	2	2	1	1	1	3	2	3	2	1	1	1	1	1	1	6	6			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr9:3271084C>G	ENST00000382004.3	-	11	1432	c.1121G>C	c.(1120-1122)aGc>aCc	p.S374T	RFX3_ENST00000358730.2_Missense_Mutation_p.S374T|RFX3_ENST00000302303.1_Missense_Mutation_p.S374T	NM_001282116.1|NM_134428.1	NP_001269045.1|NP_602304.1	P48380	RFX3_HUMAN	regulatory factor X, 3 (influences HLA class II expression)	374					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)		TTCTATCAGGCTAAATTGAAG	0.388																																					p.S374T		Atlas-SNP	.											.	RFX3	156	.	0			c.G1121C						PASS	.						166	152	156					9																	3271084		2203	4300	6503	SO:0001583	missense	5991	exon11			ATCAGGCTAAATT	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.1121G>C	chr9.hg19:g.3271084C>G	ENSP00000371434:p.Ser374Thr	111.0	0.0	.		122.0	35.0	.	NM_134428	A8K0H5|D3DRH8|D3DRH9|Q5JTL7|Q5JTL8|Q6NW13|Q8WTU4|Q95HL5|Q95HL6	Missense_Mutation	SNP	ENST00000382004.3	hg19	CCDS6449.1	.	.	.	.	.	.	.	.	.	.	c	5.417	0.262094	0.10239	.	.	ENSG00000080298	ENST00000382004;ENST00000358730;ENST00000302303	T;T;T	0.08102	3.13;3.13;3.13	5.76	4.85	0.62838	.	0.039316	0.85682	D	0.000000	T	0.03695	0.0105	N	0.04508	-0.205	0.48632	D	0.999686	B;B;B	0.09022	0.002;0.0;0.002	B;B;B	0.12156	0.007;0.007;0.004	T	0.43877	-0.9364	10	0.09338	T	0.73	-10.837	11.3803	0.49752	0.0:0.8614:0.0:0.1386	.	374;374;374	P48380-3;P48380-2;P48380	.;.;RFX3_HUMAN	T	374	ENSP00000371434:S374T;ENSP00000351574:S374T;ENSP00000303847:S374T	ENSP00000303847:S374T	S	-	2	0	RFX3	3261084	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.760000	0.55235	2.738000	0.93877	0.645000	0.84053	AGC	.	.	.	none		0.388	RFX3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051545.1	NM_002919		G	3271084	C	G	3271084	3	3	86	1	0	0	0	0	1	0	0	0	13277	797	28	4	1316	4	RFX3	9	3271084	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10		3271084	137942347	41	5532											
SLC24A2	25769	hgsc.bcm.edu	37	chr9	19516367	19516367	+	Frame_Shift_Del	DEL	A	A	-																															gccactggctggaatctgtgAatgacggtgtacaggagcca																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr9:19516367delA	ENST00000341998.2	-	10	1831	c.1770delT	c.(1768-1770)attfs	p.I590fs	SLC24A2_ENST00000286344.3_Frame_Shift_Del_p.I573fs	NM_001193288.2|NM_020344.3	NP_001180217.1|NP_065077.1	Q9UI40	NCKX2_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	590					cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)	cadmium ion binding (GO:0046870)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium, potassium:sodium antiporter activity (GO:0008273)|manganese ion binding (GO:0030145)|nickel cation binding (GO:0016151)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|symporter activity (GO:0015293)			endometrium(3)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)		GGAATCTGTGAATGACGGTGT	0.547																																					p.H591fs		Atlas-Indel,Pindel	.											.	SLC24A2	93	.	0			c.1771delC						PASS	.						47	44	45					9																	19516367		2203	4300	6503	SO:0001589	frameshift_variant	25769	exon10			.	AF097366	CCDS6493.1, CCDS55297.1	9p22.1	2013-05-22			ENSG00000155886	ENSG00000155886		"Solute carriers"	10976	protein-coding gene	gene with protein product		609838				10662833	Standard	NM_020344		Approved	NCKX2	uc003zoa.2	Q9UI40	OTTHUMG00000019646	ENST00000341998.2:c.1770delT	chr9.hg19:g.19516367delA	ENSP00000344801:p.Ile590fs	97.0	0.0	0		86.0	29.0	0.337209	NM_020344	B7ZLL8|Q9NTN5|Q9NZQ4	Frame_Shift_Del	DEL	ENST00000341998.2	hg19	CCDS6493.1																																																																																			.	.	.	none		0.547	SLC24A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051866.2	NM_020344		-	19516367	A	-	19516367	7	5	86	1	0	1	0	1	0	0	0	0	14479	242	9	0	219	0	SLC24A2	9	19516367	Frame_Shift_Del	DEL	A	TCGA-B1-A656-01A-11D-A31X-10	16245283	19516367	121697064	42	5533											
STXBP1	6812	hgsc.bcm.edu	37	chr9	130438137	130438137	+	Missense_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	agatcaaggaccctatgcgaGccatcgtccccattctgctg	9	9	9	14	2	2	1	1	0	1	1	4	3	3	2	4	1	3	1	4	1	2	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr9:130438137G>A	ENST00000373299.1	+	14	1280	c.1165G>A	c.(1165-1167)Gcc>Acc	p.A389T	STXBP1_ENST00000373302.3_Missense_Mutation_p.A389T|STXBP1_ENST00000481942.1_3'UTR	NM_001032221.3	NP_001027392.1	P61764	STXB1_HUMAN	syntaxin binding protein 1	389					axon target recognition (GO:0007412)|energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|long term synaptic depression (GO:0060292)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|protein stabilization (GO:0050821)|protein transport (GO:0015031)|regulation of insulin secretion (GO:0050796)|regulation of SNARE complex assembly (GO:0035542)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|regulation of synaptic vesicle priming (GO:0010807)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|SNARE binding (GO:0000149)|syntaxin binding (GO:0019905)|syntaxin-1 binding (GO:0017075)			breast(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|skin(2)	23						CCCTATGCGAGCCATCGTCCC	0.507																																					p.A389T		Atlas-SNP	.											.	STXBP1	99	.	0			c.G1165A						PASS	.						157	112	127					9																	130438137		2203	4300	6503	SO:0001583	missense	6812	exon14			ATGCGAGCCATCG	AF004563	CCDS6874.1, CCDS35146.1	9q34.1	2008-07-21			ENSG00000136854	ENSG00000136854			11444	protein-coding gene	gene with protein product	"syntaxin-binding protein 1"	602926				9545644	Standard	NM_001032221		Approved	hUNC18, MUNC18-1, UNC18, rbSec1	uc004brk.2	P61764	OTTHUMG00000020713	ENST00000373299.1:c.1165G>A	chr9.hg19:g.130438137G>A	ENSP00000362396:p.Ala389Thr	123.0	0.0	.		92.0	22.0	.	NM_001032221	B1AM97|Q28208|Q62759|Q64320|Q96TG8	Missense_Mutation	SNP	ENST00000373299.1	hg19	CCDS35146.1	.	.	.	.	.	.	.	.	.	.	G	14.01	2.406455	0.42715	.	.	ENSG00000136854	ENST00000535154;ENST00000373302;ENST00000541198;ENST00000373299	T;T	0.80033	-1.33;-1.33	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.62913	0.2467	N	0.04203	-0.255	0.58432	D	0.999998	B;B	0.14012	0.009;0.008	B;B	0.18263	0.021;0.012	T	0.59369	-0.7467	10	0.13108	T	0.6	-12.1555	17.491	0.87703	0.0:0.0:1.0:0.0	.	389;389	P61764;P61764-2	STXB1_HUMAN;.	T	343;389;221;389	ENSP00000362399:A389T;ENSP00000362396:A389T	ENSP00000362396:A389T	A	+	1	0	STXBP1	129477958	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.669000	0.68081	2.793000	0.96121	0.655000	0.94253	GCC	.	.	.	none		0.507	STXBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054229.1	NM_003165		A	130438137	G	A	130438137	3	1	86	1	0	0	0	0	1	0	0	0	15364	971	34	2	1219	2	STXBP1	9	130438137	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	110921770	130438137	10775294	43	5534											
ASB6	140459	hgsc.bcm.edu	37	chr9	132400146	132400146	+	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	gtcgggcagaggcagggcttTgaccttcacatccacaggcc	8	7	13	13	1	1	2	1	1	0	1	3	2	2	2	3	4	0	3	3	4	0	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr9:132400146T>A	ENST00000277458.4	-	6	1354	c.1189A>T	c.(1189-1191)Aaa>Taa	p.K397*	RP11-483H20.4_ENST00000455074.1_RNA|ASB6_ENST00000277459.4_3'UTR|ASB6_ENST00000450050.2_Nonsense_Mutation_p.K318*	NM_017873.3	NP_060343.1	Q9NWX5	ASB6_HUMAN	ankyrin repeat and SOCS box containing 6	397	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				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)				GGCAGGGCTTTGACCTTCACA	0.607																																					p.K397X		Atlas-SNP	.											.	ASB6	31	.	0			c.A1189T						PASS	.						66	63	64					9																	132400146		2203	4300	6503	SO:0001587	stop_gained	140459	exon6			GGGCTTTGACCTT		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.1189A>T	chr9.hg19:g.132400146T>A	ENSP00000277458:p.Lys397*	47.0	0.0	.		29.0	9.0	.	NM_017873	Q5SZB7|Q9BV15	Nonsense_Mutation	SNP	ENST00000277458.4	hg19	CCDS6924.1	.	.	.	.	.	.	.	.	.	.	T	37	6.123362	0.97305	.	.	ENSG00000148331	ENST00000277458;ENST00000450050	.	.	.	4.95	0.937	0.19494	.	0.300887	0.39759	N	0.001264	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.0669	11.7516	0.51852	0.0:0.0:0.4323:0.5677	.	.	.	.	X	397;318	.	ENSP00000277458:K397X	K	-	1	0	ASB6	131439967	0.998000	0.40836	0.854000	0.33618	0.993000	0.82548	1.584000	0.36589	-0.003000	0.14444	0.379000	0.24179	AAA	.	.	.	none		0.607	ASB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054594.1	NM_017873		A	132400146	T	A	132400146	4	1	86	1	0	0	0	0	0	1	0	0	1027	1821	63	5	80	5	ASB6	9	132400146	Nonsense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	1962009	132400146	8813285	44	5535											
ALOX5	240	hgsc.bcm.edu	37	chr10	45936826	45936826	+	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	cgtgagattcaccattgcaaTcaacaccaaggcccgtgagc	12	7	9	13	2	2	2	2	2	0	1	2	3	2	2	3	1	3	1	3	1	3	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr10:45936826T>A	ENST00000374391.2	+	9	1273	c.1220T>A	c.(1219-1221)aTc>aAc	p.I407N	ALOX5_ENST00000542434.1_Missense_Mutation_p.I407N	NM_000698.3|NM_001256153.1	NP_000689.1|NP_001243082.1	P09917	LOX5_HUMAN	arachidonate 5-lipoxygenase	407	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|leukotriene production involved in inflammatory response (GO:0002540)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular space (GO:0005615)|nuclear envelope (GO:0005635)|nuclear envelope lumen (GO:0005641)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)	arachidonate 5-lipoxygenase activity (GO:0004051)|iron ion binding (GO:0005506)			breast(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Lung SC(717;0.0257)			Aminosalicylic Acid(DB00233)|Balsalazide(DB01014)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Masoprocol(DB00179)|Meclofenamic acid(DB00939)|Mesalazine(DB00244)|Minocycline(DB01017)|Montelukast(DB00471)|Sulfasalazine(DB00795)|Vitamin E(DB00163)|Zileuton(DB00744)	ACCATTGCAATCAACACCAAG	0.627																																					p.I407N		Atlas-SNP	.											.	ALOX5	88	.	0			c.T1220A						PASS	.						180	169	173					10																	45936826		2203	4300	6503	SO:0001583	missense	240	exon9			TTGCAATCAACAC	J03571	CCDS7212.1, CCDS58078.1	10q11.2	2008-03-18			ENSG00000012779	ENSG00000012779	1.13.11.34	"Arachidonate lipoxygenases"	435	protein-coding gene	gene with protein product		152390				2565035	Standard	NM_001256153		Approved	5-LOX	uc001jce.4	P09917	OTTHUMG00000018081	ENST00000374391.2:c.1220T>A	chr10.hg19:g.45936826T>A	ENSP00000363512:p.Ile407Asn	94.0	0.0	.		67.0	24.0	.	NM_000698	B7ZLS0|E5FPY5|E5FPY7|E5FPY8|Q5JQ14	Missense_Mutation	SNP	ENST00000374391.2	hg19	CCDS7212.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.185478	0.78677	.	.	ENSG00000012779	ENST00000542434;ENST00000374391	D;D	0.94000	-3.33;-3.33	5.45	5.45	0.79879	Lipoxygenase, C-terminal (3);	0.047406	0.85682	D	0.000000	D	0.97399	0.9149	M	0.93197	3.39	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.989;0.995	D	0.98292	1.0514	10	0.87932	D	0	-34.9933	13.4602	0.61223	0.0:0.0:0.0:1.0	.	407;407;407	B7ZLS0;E5FPY8;P09917	.;.;LOX5_HUMAN	N	407	ENSP00000437634:I407N;ENSP00000363512:I407N	ENSP00000363512:I407N	I	+	2	0	ALOX5	45256832	1.000000	0.71417	1.000000	0.80357	0.638000	0.38207	7.996000	0.88334	2.054000	0.61138	0.533000	0.62120	ATC	.	.	.	none		0.627	ALOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047780.1			A	45936826	T	A	45936826	3	1	86	1	0	0	0	0	1	0	0	0	540	1435	50	5	1254	5	ALOX5	10	45936826	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10		45936826	89597921	45	5536											
NCOA4	8031	hgsc.bcm.edu	37	chr10	51585173	51585173	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtgatgagaattgtgagaaGgaggctctgtataagtggct	11	12	15	3	0	1	3	0	3	1	2	1	6	1	4	0	3	0	3	0	3	4	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr10:51585173G>A	ENST00000443446.1	+	8	1501	c.1272G>A	c.(1270-1272)aaG>aaA	p.K424K	NCOA4_ENST00000374087.4_Silent_p.K424K|NCOA4_ENST00000438493.1_Silent_p.K440K|NCOA4_ENST00000430396.2_Silent_p.K324K|NCOA4_ENST00000452682.1_Silent_p.K440K|NCOA4_ENST00000414907.2_Silent_p.K258K|NCOA4_ENST00000344348.6_Silent_p.K424K|NCOA4_ENST00000374082.1_Silent_p.K424K	NM_001145262.1	NP_001138734.1	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4	424					androgen receptor signaling pathway (GO:0030521)|male gonad development (GO:0008584)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|skin(1)	5						ATTGTGAGAAGGAGGCTCTGT	0.478			T	RET	papillary thyroid																																p.K440K		Atlas-SNP	.		Dom	yes		10	10q11.2	8031	nuclear receptor coactivator 4 - PTC3 (ELE1)		E	.	NCOA4	58	.	0			c.G1320A						PASS	.						70	75	73					10																	51585173		2203	4300	6503	SO:0001819	synonymous_variant	8031	exon9			TGAGAAGGAGGCT	L49399	CCDS73092.1, CCDS73093.1, CCDS73094.1	10q11.2	2014-04-10			ENSG00000138293	ENSG00000266412			7671	protein-coding gene	gene with protein product	"RET-activating gene ELE1"	601984				8290261, 8643607, 24695223	Standard	NM_001145260		Approved	ARA70, RFG, ELE1, PTC3, DKFZp762E1112	uc009xon.3	Q13772	OTTHUMG00000188314	ENST00000443446.1:c.1272G>A	chr10.hg19:g.51585173G>A		175.0	0.0	.		151.0	47.0	.	NM_001145261	A8K8W5|B4E260|E9PAV7|J3KQN8|Q14239	Silent	SNP	ENST00000443446.1	hg19	CCDS7237.1																																																																																			.	.	.	none		0.478	NCOA4-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048052.1	NM_005437		A	51585173	G	A	51585173	2	1	86	1	0	0	0	0	0	0	0	1	10238	991	35	2		2	NCOA4	10	51585173	Silent	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	5648347	51585173	83949574	46	5537											
NUDT13	25961	hgsc.bcm.edu	37	chr10	74879906	74879906	+	Missense_Mutation	SNP	A	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	aatacctggccccccggcacAgcctgttaggtaagtccaga	10	7	10	14	1	0	1	0	0	0	1	1	1	1	1	6	3	2	3	6	3	4	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr10:74879906A>C	ENST00000357321.4	+	3	332	c.214A>C	c.(214-216)Agc>Cgc	p.S72R	NUDT13_ENST00000544879.1_5'UTR|NUDT13_ENST00000488223.1_3'UTR|NUDT13_ENST00000372997.3_Missense_Mutation_p.S72R|NUDT13_ENST00000537969.1_5'UTR|NUDT13_ENST00000349051.5_Missense_Mutation_p.S72R	NM_001283016.1|NM_015901.4	NP_001269945.1|NP_056985.3			nudix (nucleoside diphosphate linked moiety X)-type motif 13											large_intestine(2)|lung(5)	7	Prostate(51;0.0119)					CCCCCGGCACAGCCTGTTAGG	0.498																																					p.S72R		Atlas-SNP	.											.	NUDT13	16	.	0			c.A214C						PASS	.						55	56	56					10																	74879906		2203	4300	6503	SO:0001583	missense	25961	exon3			CGGCACAGCCTGT	AL050114	CCDS31220.1, CCDS60551.1, CCDS60552.1, CCDS60553.1, CCDS73148.1	10q22.3	2014-04-24			ENSG00000166321	ENSG00000166321		"Nudix motif containing"	18827	protein-coding gene	gene with protein product		609233				15164054	Standard	NM_001283019		Approved	DKFZp586P2219	uc001jtj.3	Q86X67	OTTHUMG00000018453	ENST00000357321.4:c.214A>C	chr10.hg19:g.74879906A>C	ENSP00000349874:p.Ser72Arg	78.0	0.0	.		52.0	17.0	.	NM_015901		Missense_Mutation	SNP	ENST00000357321.4	hg19	CCDS31220.1	.	.	.	.	.	.	.	.	.	.	A	12.27	1.887191	0.33348	.	.	ENSG00000166321	ENST00000357321;ENST00000349051;ENST00000372997	T;T;T	0.32515	1.45;1.45;1.45	5.63	5.63	0.86233	NADH pyrophosphatase-like, N-terminal (1);	0.319618	0.40302	N	0.001140	T	0.25419	0.0618	L	0.38531	1.155	0.80722	D	1	B;B;B	0.33755	0.424;0.045;0.079	B;B;B	0.29942	0.109;0.102;0.092	T	0.03453	-1.1035	10	0.35671	T	0.21	.	15.0175	0.71597	1.0:0.0:0.0:0.0	.	72;72;72	Q86X67-2;Q5SQM6;Q86X67	.;.;NUD13_HUMAN	R	72	ENSP00000349874:S72R;ENSP00000335326:S72R;ENSP00000362088:S72R	ENSP00000335326:S72R	S	+	1	0	NUDT13	74549912	0.996000	0.38824	0.776000	0.31678	0.176000	0.22953	3.633000	0.54295	2.148000	0.66965	0.533000	0.62120	AGC	.	.	.	none		0.498	NUDT13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048614.1	NM_015901		C	74879906	A	C	74879906	3	2	86	1	0	0	0	0	1	0	0	0	10736	188	7	5	220	5	NUDT13	10	74879906	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	23294733	74879906	60654841	47	5538											
ZMIZ1	57178	hgsc.bcm.edu	37	chr10	80968102	80968102	+	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	ctttcccacagcacttacagAatcctgccaacttccacaat	12	10	3	16	0	0	1	0	0	0	1	3	1	3	1	4	0	4	1	4	0	4	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr10:80968102A>T	ENST00000334512.5	+	6	642	c.70A>T	c.(70-72)Aat>Tat	p.N24Y		NM_020338.3	NP_065071.1	Q9ULJ6	ZMIZ1_HUMAN	zinc finger, MIZ-type containing 1	24					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)			GCACTTACAGAATCCTGCCAA	0.622																																					p.N24Y		Atlas-SNP	.											.	ZMIZ1	101	.	0			c.A70T						PASS	.						68	56	60					10																	80968102		2203	4300	6503	SO:0001583	missense	57178	exon6			TTACAGAATCCTG	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.70A>T	chr10.hg19:g.80968102A>T	ENSP00000334474:p.Asn24Tyr	70.0	0.0	.		63.0	16.0	.	NM_020338	Q5JSH9|Q7Z7E6	Missense_Mutation	SNP	ENST00000334512.5	hg19	CCDS7357.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.022073	0.75275	.	.	ENSG00000108175	ENST00000334512;ENST00000394592	T	0.34667	1.35	5.23	4.1	0.47936	.	.	.	.	.	T	0.52645	0.1747	L	0.60455	1.87	0.80722	D	1	D;D	0.65815	0.995;0.993	D;P	0.72982	0.979;0.885	T	0.52793	-0.8528	9	0.87932	D	0	-6.037	9.9202	0.41459	0.9182:0.0:0.0818:0.0	.	24;24	Q9ULJ6;A0JLS3	ZMIZ1_HUMAN;.	Y	24	ENSP00000334474:N24Y	ENSP00000334474:N24Y	N	+	1	0	ZMIZ1	80638108	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	8.717000	0.91425	0.846000	0.35142	0.379000	0.24179	AAT	.	.	.	none		0.622	ZMIZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048944.2	NM_020338		T	80968102	A	T	80968102	3	4	86	1	0	0	0	0	1	0	0	0	17708	246	9	5	76	5	ZMIZ1	10	80968102	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	6088196	80968102	54566645	48	5539											
SORCS1	114815	hgsc.bcm.edu	37	chr10	108371744	108371744	+	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	tccgggttgtagtcatccagGtttggagaaaaggacaagcg	11	9	14	7	2	1	1	1	0	0	1	3	3	3	2	2	4	1	3	2	4	4	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr10:108371744G>T	ENST00000263054.6	-	22	2965	c.2958C>A	c.(2956-2958)aaC>aaA	p.N986K	SORCS1_ENST00000369698.1_Missense_Mutation_p.N521K|SORCS1_ENST00000478809.2_5'UTR|SORCS1_ENST00000344440.6_Missense_Mutation_p.N986K	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	986					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)		AGTCATCCAGGTTTGGAGAAA	0.463																																					p.N986K		Atlas-SNP	.											.	SORCS1	534	.	0			c.C2958A						PASS	.						113	103	106					10																	108371744		2203	4300	6503	SO:0001583	missense	114815	exon22			ATCCAGGTTTGGA	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.2958C>A	chr10.hg19:g.108371744G>T	ENSP00000263054:p.Asn986Lys	161.0	0.0	.		158.0	44.0	.	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	hg19	CCDS7559.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.41|19.41	3.822407|3.822407	0.71028|0.71028	.|.	.|.	ENSG00000108018|ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440|ENST00000452214	T;T;T|.	0.24908|.	1.83;2.4;2.4|.	5.4|5.4	4.49|4.49	0.54785|0.54785	.|.	0.048600|.	0.85682|.	D|.	0.000000|.	T|T	0.73869|0.73869	0.3642|0.3642	M|M	0.80183|0.80183	2.485|2.485	0.44359|0.44359	D|D	0.997259|0.997259	D;D;D;D;D|.	0.58620|.	0.972;0.983;0.983;0.972;0.983|.	P;P;P;P;P|.	0.62298|.	0.797;0.9;0.9;0.797;0.9|.	T|T	0.75391|0.75391	-0.3334|-0.3334	9|5	.|.	.|.	.|.	-33.8428|-33.8428	11.7072|11.7072	0.51603|0.51603	0.1432:0.0:0.8568:0.0|0.1432:0.0:0.8568:0.0	.|.	986;986;986;986;986|.	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2|.	.;.;.;SORC1_HUMAN;.|.	K|N	521;986;986|1	ENSP00000358712:N521K;ENSP00000263054:N986K;ENSP00000345964:N986K|.	.|.	N|T	-|-	3|2	2|0	SORCS1|SORCS1	108361734|108361734	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.681000|1.681000	0.37618|0.37618	1.406000|1.406000	0.46857|0.46857	0.650000|0.650000	0.86243|0.86243	AAC|ACC	.	.	.	none		0.463	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		T	108371744	G	T	108371744	3	4	86	1	0	0	0	0	1	0	0	0	14943	1252	44	4	802	4	SORCS1	10	108371744	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	27403642	108371744	27163003	49	5540											
OR5P2	120065	hgsc.bcm.edu	37	chr11	7818418	7818420	+	Missense_Mutation	TNP	TGG	TGG	AAT																															aagaggatgactcgaaggatTggatcatctgttaagcccaa																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T|G|G	T|G|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr11:7818418_7818420TGG>AAT	ENST00000329434.2	-	1	100_102	c.70_72CCA>ATT	c.(70-72)CCA>ATT	p.P24I	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	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)|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)		CTCGAAGGATTGGATCATCTGTT	0.429																																					p.P24P|p.P24L|p.P24T		Atlas-SNP	.											.	OR5P2	68	.	0			c.A72T|c.C71T|c.C70A						PASS	.																																			SO:0001583	missense	120065	exon1			AAGGATTGGATCA|AGGATTGGATCAT|GGATTGGATCATC	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.70_72CCA>ATT	chr11.hg19:g.7818418TGG>AAT	ENSP00000331823:p.Pro24Ile	68.0|67.0|67.0	0.0	.		63.0|62.0|61.0	15.0	.	NM_153444	Q3MIS8	Silent|Missense_Mutation|Missense_Mutation	SNP	ENST00000329434.2	hg19	CCDS7782.1																																																																																			.	.	.	none		0.429	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444		AAT	7818420	TGG	AAT	7818418	3	1	86	1	0	0	0	0	1	0	0	0	11185	1799	63	5	900	5	OR5P2	11	7818418	Missense_Mutation	TNP	TGG	TCGA-B1-A656-01A-11D-A31X-10		7818418	127188098	50	5541											
LGR4	55366	hgsc.bcm.edu	37	chr11	27402259	27402259	+	Splice_Site	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	gaggattatcatacaaatgtCtgtgaaaatatccaaaaaaa	20	10	6	5	0	2	1	1	1	1	0	3	3	3	2	1	1	1	0	1	1	9	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr11:27402259C>G	ENST00000379214.4	-	9	1274		c.e9-1		LGR4_ENST00000389858.4_Splice_Site	NM_018490.2	NP_060960.2	Q9BXB1	LGR4_HUMAN	leucine-rich repeat containing G protein-coupled receptor 4						bone mineralization (GO:0030282)|bone remodeling (GO:0046849)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cell differentiation involved in metanephros development (GO:0072202)|epithelial cell proliferation (GO:0050673)|innate immune response (GO:0045087)|male genitalia development (GO:0030539)|metanephric glomerulus development (GO:0072224)|metanephric nephron tubule morphogenesis (GO:0072282)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(10)|ovary(1)	32						ATACAAATGTCTGTGAAAATA	0.299																																					.		Atlas-SNP	.											.	LGR4	87	.	0			c.831-1G>C						PASS	.						49	52	51					11																	27402259		2201	4289	6490	SO:0001630	splice_region_variant	55366	exon10			AAATGTCTGTGAA	AF257182	CCDS31449.1	11p14-p13	2012-08-21	2011-01-25	2004-11-12	ENSG00000205213	ENSG00000205213		"GPCR / Class A : Orphans"	13299	protein-coding gene	gene with protein product		606666	"G protein-coupled receptor 48", "leucine-rich repeat-containing G protein-coupled receptor 4"	GPR48		10894923	Standard	NM_018490		Approved		uc001mrj.4	Q9BXB1	OTTHUMG00000133508	ENST00000379214.4:c.831-1G>C	chr11.hg19:g.27402259C>G		232.0	0.0	.		223.0	73.0	.	NM_018490	A6NCH3|G5E9B3|Q8N537|Q9NYD1	Splice_Site	SNP	ENST00000379214.4	hg19	CCDS31449.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.067334	0.76301	.	.	ENSG00000205213	ENST00000379214;ENST00000389858	.	.	.	5.51	5.51	0.81932	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.7788	0.96409	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	LGR4	27358835	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.487000	0.81328	2.749000	0.94314	0.460000	0.39030	.	.	.	.	none		0.299	LGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257467.1	NM_018490	Intron	G	27402259	C	G	27402259	5	3	86	1	0	0	0	0	0	0	1	0	8763	927	32	4	2065	4	LGR4	11	27402259	Splice_Site	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	19583841	27402259	107604257	51	5542											
PLCB3	5331	hgsc.bcm.edu	37	chr11	64034708	64034708	+	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	gtcttgtggctgggcagcagCaggtcctgcaacagctggca	7	8	15	11	0	1	0	0	0	1	0	2	0	2	0	1	4	5	7	1	4	1	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr11:64034708C>T	ENST00000540288.1	+	30	3569	c.3466C>T	c.(3466-3468)Cag>Tag	p.Q1156*	PLCB3_ENST00000279230.6_Nonsense_Mutation_p.Q1156*|PLCB3_ENST00000325234.5_Nonsense_Mutation_p.Q1089*	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	1156					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						TGGGCAGCAGCAGGTCCTGCA	0.672																																					p.Q1156X		Atlas-SNP	.											.	PLCB3	103	.	0			c.C3466T						PASS	.						19	18	18					11																	64034708		1955	3784	5739	SO:0001587	stop_gained	5331	exon30			CAGCAGCAGGTCC	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.3466C>T	chr11.hg19:g.64034708C>T	ENSP00000443631:p.Gln1156*	138.0	0.0	.		101.0	30.0	.	NM_000932	A5PKZ6|G5E960|Q8N1A4	Nonsense_Mutation	SNP	ENST00000540288.1	hg19	CCDS8064.1	.	.	.	.	.	.	.	.	.	.	C	39	7.682014	0.98431	.	.	ENSG00000149782	ENST00000279230;ENST00000540288;ENST00000325234	.	.	.	4.42	4.42	0.53409	.	0.339854	0.29830	N	0.011090	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	.	11.0366	0.47804	0.0:0.6842:0.3158:0.0	.	.	.	.	X	1156;1156;1089	.	ENSP00000279230:Q1156X	Q	+	1	0	PLCB3	63791284	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.151000	0.58105	2.297000	0.77311	0.561000	0.74099	CAG	.	.	.	none		0.672	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1			T	64034708	C	T	64034708	4	4	86	1	0	0	0	0	0	1	0	0	12036	711	25	2	3584	2	PLCB3	11	64034708	Nonsense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	36632449	64034708	70971808	52	5543											
NAALADL1	10004	hgsc.bcm.edu	37	chr11	64813975	64813975	+	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	aaggctgtgtggtaggtgggGtagatcctggctgaagtctt	7	12	17	5	0	1	2	0	1	1	1	2	2	2	2	1	6	0	4	1	6	4	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr11:64813975G>A	ENST00000358658.3	-	14	1650	c.1623C>T	c.(1621-1623)taC>taT	p.Y541Y	NAALADL1_ENST00000340252.4_Silent_p.Y592Y|NAALADL1_ENST00000355369.2_Intron|NAALADL1_ENST00000526799.1_5'UTR|NAALADL1_ENST00000528884.1_Intron|NAALADL1_ENST00000355721.3_Silent_p.Y500Y|NAALADL1_ENST00000339885.2_Missense_Mutation_p.T511I|NAALADL1_ENST00000356632.3_Silent_p.Y506Y	NM_005468.2	NP_005459.2	Q9UQQ1	NALDL_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 1	541	NAALADase.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	29						GGTAGGTGGGGTAGATCCTGG	0.552																																					p.Y541Y		Atlas-SNP	.											.	NAALADL1	58	.	0			c.C1623T						PASS	.						130	109	116					11																	64813975		2201	4297	6498	SO:0001819	synonymous_variant	10004	exon14			GGTGGGGTAGATC	AF010141	CCDS31604.1	11q12	2011-08-16			ENSG00000168060	ENSG00000168060			23536	protein-coding gene	gene with protein product	"ileal peptidase I100"	602640				10085079	Standard	NM_005468		Approved		uc001ocn.3	Q9UQQ1	OTTHUMG00000165595	ENST00000358658.3:c.1623C>T	chr11.hg19:g.64813975G>A		184.0	0.0	.		138.0	31.0	.	NM_005468	C9J8A1|C9J964|C9JL35|C9JSN0|O43176	Silent	SNP	ENST00000358658.3	hg19	CCDS31604.1	.	.	.	.	.	.	.	.	.	.	G	18.25	3.583064	0.65992	.	.	ENSG00000168060	ENST00000339885	T	0.48522	0.81	5.53	4.63	0.57726	.	.	.	.	.	T	0.49609	0.1567	.	.	.	0.26194	N	0.979542	.	.	.	.	.	.	T	0.48317	-0.9046	6	0.87932	D	0	-29.7051	8.5374	0.33371	0.1733:0.0:0.8267:0.0	.	.	.	.	I	511	ENSP00000340111:T511I	ENSP00000340111:T511I	T	-	2	0	NAALADL1	64570551	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.241000	0.51376	1.370000	0.46153	0.561000	0.74099	ACC	.	.	.	none		0.552	NAALADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385162.1	NM_005468		A	64813975	G	A	64813975	2	1	86	1	0	0	0	0	0	0	0	1	10136	1256	44	2		2	NAALADL1	11	64813975	Silent	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	779267	64813975	70192541	53	5544											
CLPB	81570	hgsc.bcm.edu	37	chr11	72145214	72145214	+	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	tggggaccccgttccagctgTcctgtcctgggagtgtttct	3	13	13	12	1	1	0	0	0	1	0	4	2	4	2	5	3	1	3	5	3	0	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr11:72145214T>A	ENST00000294053.3	-	1	478	c.305A>T	c.(304-306)gAc>gTc	p.D102V	CLPB_ENST00000538039.1_Missense_Mutation_p.D102V|CLPB_ENST00000437826.2_Silent_p.G21G|CLPB_ENST00000543042.1_5'UTR|CLPB_ENST00000542555.1_5'Flank|CLPB_ENST00000340729.5_Missense_Mutation_p.D102V|CLPB_ENST00000445069.2_Intron	NM_001258394.1|NM_030813.4	NP_001245323.1|NP_110440.1	Q9H078	CLPB_HUMAN	ClpB caseinolytic peptidase B homolog (E. coli)	102					cellular response to heat (GO:0034605)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	19						GTTCCAGCTGTCCTGTCCTGG	0.662											OREG0021194	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D102V		Atlas-SNP	.											.	CLPB	45	.	0			c.A305T						PASS	.						45	49	47					11																	72145214		2200	4292	6492	SO:0001583	missense	81570	exon1			CAGCTGTCCTGTC	BC006404	CCDS8215.1, CCDS58152.1, CCDS58153.1, CCDS58154.1	11q13.4	2013-01-10			ENSG00000162129	ENSG00000162129		"Ankyrin repeat domain containing"	30664	protein-coding gene	gene with protein product	"suppressor of potassium transport defect 3"					11230166, 7835694	Standard	NM_030813		Approved	HSP78, SKD3, FLJ13152	uc010rqy.3	Q9H078	OTTHUMG00000167902	ENST00000294053.3:c.305A>T	chr11.hg19:g.72145214T>A	ENSP00000294053:p.Asp102Val	96.0	0.0	.	1135	69.0	15.0	.	NM_001258392	B4DXJ7|B4DXP7|E7EWN6|F8W7P6|Q8ND11|Q9H8Y0	Missense_Mutation	SNP	ENST00000294053.3	hg19	CCDS8215.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.964448	0.53507	.	.	ENSG00000162129	ENST00000294053;ENST00000538039;ENST00000340729	T;T;T	0.69175	1.9;1.08;-0.38	5.04	2.43	0.29744	.	0.289184	0.26286	N	0.025253	T	0.45856	0.1363	N	0.14661	0.345	0.80722	D	1	P;B;P	0.37955	0.514;0.437;0.612	B;B;B	0.38880	0.284;0.189;0.203	T	0.43637	-0.9379	10	0.72032	D	0.01	-12.7372	5.6906	0.17827	0.1674:0.0:0.1731:0.6594	.	102;102;102	F8W7P6;Q9H078-2;Q9H078	.;.;CLPB_HUMAN	V	102	ENSP00000294053:D102V;ENSP00000441518:D102V;ENSP00000340385:D102V	ENSP00000294053:D102V	D	-	2	0	CLPB	71822862	1.000000	0.71417	1.000000	0.80357	0.867000	0.49689	1.637000	0.37155	0.808000	0.34231	0.533000	0.62120	GAC	.	.	.	none		0.662	CLPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396889.1	NM_030813		A	72145214	T	A	72145214	3	1	86	1	0	0	0	0	1	0	0	0	3553	1667	58	5	1886	5	CLPB	11	72145214	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	7331239	72145214	62861302	54	5545											
KCNE3	10008	hgsc.bcm.edu	37	chr11	74168349	74168350	+	Missense_Mutation	DNP	TT	TT	AA																															catgataggggtcactacgcTtgtccactttgcgggagcgg																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr11:74168349_74168350TT>AA	ENST00000310128.4	-	3	678_679	c.259_260AA>TT	c.(259-261)AAg>TTg	p.K87L	KCNE3_ENST00000525550.1_Missense_Mutation_p.K87L|RP11-702H23.4_ENST00000533008.1_RNA|RP11-702H23.6_ENST00000530510.1_RNA	NM_005472.4	NP_005463.1	Q9Y6H6	KCNE3_HUMAN	potassium voltage-gated channel, Isk-related family, member 3	87					regulation of potassium ion transport (GO:0043266)	integral component of membrane (GO:0016021)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			cervix(1)|large_intestine(1)|lung(1)|ovary(1)	4	Breast(11;2.86e-06)					GTCACTACGCTTGTCCACTTTG	0.495																																					p.K87M|p.K87X		Atlas-SNP	.											.	KCNE3	7	.	0			c.A260T|c.A259T						PASS	.																																			SO:0001583	missense	10008	exon3			CTACGCTTGTCCA|TACGCTTGTCCAC	AF076531	CCDS8232.1	11q13.4	2014-09-17				ENSG00000175538		"Potassium channels"	6243	protein-coding gene	gene with protein product		604433				10219239	Standard	NM_005472		Approved	MiRP2, HOKPP	uc001ovc.3	Q9Y6H6		ENST00000310128.4:c.259_260delinsAA	chr11.hg19:g.74168349_74168350delinsAA	ENSP00000310557:p.Lys87Leu	119.0|120.0	0.0	.		87.0	19.0	.	NM_005472		Missense_Mutation|Nonsense_Mutation	SNP	ENST00000310128.4	hg19	CCDS8232.1																																																																																			.	.	.	none		0.495	KCNE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385531.1	NM_005472		AA	74168350	TT	AA	74168349	3	1	86	1	0	0	0	0	1	0	0	0	8031	1609	56	5	55	5	KCNE3	11	74168349	Missense_Mutation	DNP	TT	TCGA-B1-A656-01A-11D-A31X-10	2023135	74168349	60838167	55	5546											
FZD4	8322	hgsc.bcm.edu	37	chr11	86663362	86663362	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttctgtggtgggaatttgcTgcagttcagactctctggcc	5	14	13	9	0	3	1	1	0	2	1	4	2	3	2	1	3	2	4	1	3	1	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr11:86663362T>C	ENST00000531380.1	-	2	741	c.436A>G	c.(436-438)Agc>Ggc	p.S146G	PRSS23_ENST00000533902.2_3'UTR	NM_012193.3	NP_036325.2	Q9ULV1	FZD4_HUMAN	frizzled class receptor 4	146	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|cerebellum vasculature morphogenesis (GO:0061301)|extracellular matrix-cell signaling (GO:0035426)|locomotion involved in locomotory behavior (GO:0031987)|negative regulation of cell-substrate adhesion (GO:0010812)|neuron differentiation (GO:0030182)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal blood vessel morphogenesis (GO:0061304)|sensory perception of sound (GO:0007605)|substrate adhesion-dependent cell spreading (GO:0034446)|vasculogenesis (GO:0001570)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(1)|kidney(1)|large_intestine(3)|lung(9)|prostate(6)|skin(1)	21		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GGGAATTTGCTGCAGTTCAGA	0.557																																					p.S146G		Atlas-SNP	.											.	FZD4	52	.	0			c.A436G						PASS	.						91	94	93					11																	86663362		2201	4299	6500	SO:0001583	missense	8322	exon2			ATTTGCTGCAGTT	AB032417	CCDS8279.1	11q14-q21	2014-01-29	2014-01-29			ENSG00000174804		"GPCR / Class F : Frizzled receptors", "CD molecules"	4042	protein-coding gene	gene with protein product		604579	"frizzled (Drosophila) homolog 4", "exudative vitreoretinopathy 1", "frizzled homolog 4 (Drosophila)", "frizzled 4, seven transmembrane spanning receptor", "frizzled family receptor 4"	EVR1		10544037, 15024691	Standard	NM_012193		Approved	CD344	uc001pce.3	Q9ULV1		ENST00000531380.1:c.436A>G	chr11.hg19:g.86663362T>C	ENSP00000434034:p.Ser146Gly	146.0	0.0	.		101.0	20.0	.	NM_012193	A8K9Q3|Q14C97|Q6S9E4	Missense_Mutation	SNP	ENST00000531380.1	hg19	CCDS8279.1	.	.	.	.	.	.	.	.	.	.	T	15.71	2.915066	0.52546	.	.	ENSG00000174804	ENST00000531380	T	0.80393	-1.37	5.82	5.82	0.92795	Frizzled domain (5);	0.000000	0.85682	D	0.000000	D	0.82426	0.5034	M	0.77712	2.385	0.58432	D	0.999999	B	0.25441	0.126	B	0.32289	0.143	T	0.79037	-0.1967	9	.	.	.	.	16.1832	0.81925	0.0:0.0:0.0:1.0	.	146	Q9ULV1	FZD4_HUMAN	G	146	ENSP00000434034:S146G	.	S	-	1	0	FZD4	86341010	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.221000	0.58574	2.228000	0.72767	0.533000	0.62120	AGC	.	.	.	none		0.557	FZD4-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393818.2	NM_012193		C	86663362	T	C	86663362	3	2	86	1	0	0	0	0	1	0	0	0	6139	1580	55	3	1181	3	FZD4	11	86663362	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	12495013	86663362	48343154	56	5547											
PLCZ1	89869	hgsc.bcm.edu	37	chr12	18876363	18876364	+	Frame_Shift_Ins	INS	-	-	T																															ttgctaaaagaattttccggINSttttcagaatatgtgttgaa																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr12:18876363_18876364insT	ENST00000266505.7	-	4	511_512	c.248_249insA	c.(247-249)aacfs	p.N83fs	PLCZ1_ENST00000447925.2_Frame_Shift_Ins_p.N81fs|RP11-361I14.2_ENST00000536931.1_RNA|PLCZ1_ENST00000539875.1_Intron|PLCZ1_ENST00000435379.1_Intron					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)					GAATTTTCCGGTTTTCAGAATA	0.332																																					p.N83fs		Pindel	.											.	PLCZ1	107	.	0			c.249_250insA						PASS	.																																			SO:0001589	frameshift_variant	89869	exon4			.	AY035866	CCDS8680.1	12p13.31	2013-01-10			ENSG00000139151	ENSG00000139151	3.1.4.11	"EF-hand domain containing"	19218	protein-coding gene	gene with protein product		608075				12117804	Standard	NM_033123		Approved	NYD-SP27, PLCzeta	uc021qvx.2	Q86YW0	OTTHUMG00000168937	ENST00000266505.7:c.249dupA	chr12.hg19:g.18876367_18876367dupT	ENSP00000266505:p.Asn83fs	108.0	0.0	.		171.0	46.0	0.269	NM_033123		Frame_Shift_Ins	INS	ENST00000266505.7	hg19	CCDS8680.1																																																																																			.	.	.	none		0.332	PLCZ1-001	KNOWN	NAGNAG_splice_site|non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401667.3	NM_033123		T	18876364	-	T	18876363	7	5	86	1	0	1	1	0	0	0	0	0	12051	1252	44	0	1625	0	PLCZ1	12	18876363	Frame_Shift_Ins	INS	-	TCGA-B1-A656-01A-11D-A31X-10		18876363	114975532	57	5548											
C12orf40	283461	hgsc.bcm.edu	37	chr12	40076521	40076521	+	Frame_Shift_Del	DEL	A	A	-																															tacattactgaaaaacactcAatacagcatatttgggggaa																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr12:40076521delA	ENST00000324616.5	+	8	949	c.795delA	c.(793-795)tcafs	p.S265fs	C12orf40_ENST00000398716.1_Frame_Shift_Del_p.S188fs|C12orf40_ENST00000405531.3_Frame_Shift_Del_p.S265fs	NM_001031748.2	NP_001026918.2	Q86WS4	CL040_HUMAN	chromosome 12 open reading frame 40	265										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						AAAAACACTCAATACAGCATA	0.353																																					p.S265X		Atlas-Indel,Pindel	.											.	C12orf40	118	.	0			c.794delC						PASS	.						133	134	134					12																	40076521		1841	4086	5927	SO:0001589	frameshift_variant	283461	exon8			.	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.795delA	chr12.hg19:g.40076521delA	ENSP00000317671:p.Ser265fs	120.0	0.0	0		154.0	36.0	0.233766	NM_001031748	B7WNU1|Q8IXY6|Q8N818|V9HW02	Frame_Shift_Del	DEL	ENST00000324616.5	hg19	CCDS41770.1																																																																																			.	.	.	none		0.353	C12orf40-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257664.2	NM_173599		-	40076521	A	-	40076521	7	5	86	1	0	1	0	1	0	0	0	0	1688	117	5	0	825	0	C12orf40	12	40076521	Frame_Shift_Del	DEL	A	TCGA-B1-A656-01A-11D-A31X-10	21200158	40076521	93775374	58	5549											
LRIG3	121227	hgsc.bcm.edu	37	chr12	59268266	59268266	+	Missense_Mutation	SNP	T	T	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	cacatttcccttcaaatacaTagggcctgtggatcccaaaa	13	10	6	12	0	1	0	1	0	0	0	3	1	3	1	3	2	1	0	3	2	5	4			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr12:59268266T>G	ENST00000320743.3	-	17	3071	c.2785A>C	c.(2785-2787)Atg>Ctg	p.M929L	LRIG3_ENST00000379141.4_Missense_Mutation_p.M869L	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	929					otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)			LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			TTCAAATACATAGGGCCTGTG	0.428			T	ROS1	NSCLC																																p.M929L		Atlas-SNP	.		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	.	LRIG3	120	.	0			c.A2785C						PASS	.						148	135	139					12																	59268266		2203	4300	6503	SO:0001583	missense	121227	exon17			AATACATAGGGCC	AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"Immunoglobulin superfamily / I-set domain containing"	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.2785A>C	chr12.hg19:g.59268266T>G	ENSP00000326759:p.Met929Leu	146.0	0.0	.		130.0	48.0	.	NM_153377	Q6UXL7|Q8NC72	Missense_Mutation	SNP	ENST00000320743.3	hg19	CCDS8960.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	4.815|4.815	0.151595|0.151595	0.09185|0.09185	.|.	.|.	ENSG00000139263|ENSG00000139263	ENST00000379141;ENST00000320743|ENST00000550825	T;T|.	0.54479|.	0.62;0.57|.	6.03|6.03	5.14|5.14	0.70334|0.70334	.|.	0.517740|.	0.14462|.	N|.	0.318092|.	T|T	0.19366|0.19366	0.0465|0.0465	N|N	0.12182|0.12182	0.205|0.205	0.18873|0.18873	N|N	0.999984|0.999984	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.16453|0.16453	-1.0402|-1.0402	9|5	.|.	.|.	.|.	.|.	4.6325|4.6325	0.12509|0.12509	0.2843:0.5306:0.0:0.1851|0.2843:0.5306:0.0:0.1851	.|.	869;929|.	Q6UXM1-2;Q6UXM1|.	.;LRIG3_HUMAN|.	L|S	869;929|30	ENSP00000368436:M869L;ENSP00000326759:M929L|.	.|.	M|Y	-|-	1|2	0|0	LRIG3|LRIG3	57554533|57554533	0.449000|0.449000	0.25689|0.25689	0.998000|0.998000	0.56505|0.56505	0.018000|0.018000	0.09664|0.09664	0.724000|0.724000	0.25954|0.25954	1.568000|1.568000	0.49683|0.49683	-0.132000|-0.132000	0.14878|0.14878	ATG|TAT	.	.	.	none		0.428	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377		G	59268266	T	G	59268266	3	3	86	1	0	0	0	0	1	0	0	0	8953	1406	49	5	586	5	LRIG3	12	59268266	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	19191745	59268266	74583629	59	5550											
GPN3	51184	hgsc.bcm.edu	37	chr12	110902939	110902939	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acggagtagttgaagtgttcTgctgctggatccaggtttac	8	13	13	7	1	1	1	0	1	1	0	2	3	2	3	1	3	3	6	1	3	3	5			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr12:110902939T>C	ENST00000228827.3	-	2	191	c.129A>G	c.(127-129)gcA>gcG	p.A43A	GPN3_ENST00000537466.2_Silent_p.A53A|GPN3_ENST00000552180.1_5'UTR|GPN3_ENST00000543199.1_Silent_p.A82A	NM_016301.3	NP_057385.3			GPN-loop GTPase 3											endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|urinary_tract(1)	8						TGAAGTGTTCTGCTGCTGGAT	0.547																																					p.A82A		Atlas-SNP	.											.	GPN3	37	.	0			c.A246G						PASS	.						190	151	164					12																	110902939		2203	4300	6503	SO:0001819	synonymous_variant	51184	exon2			GTGTTCTGCTGCT	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.129A>G	chr12.hg19:g.110902939T>C		111.0	0.0	.		106.0	18.0	.	NM_001164372		Silent	SNP	ENST00000228827.3	hg19	CCDS9147.1																																																																																			.	.	.	none		0.547	GPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404607.1	NM_016301		C	110902939	T	C	110902939	2	2	86	1	0	0	0	0	0	0	0	1	6626	1567	55	3		3	GPN3	12	110902939	Silent	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	51634673	110902939	22948956	60	5551											
FAM155A	728215	hgsc.bcm.edu	37	chr13	108518698	108518698	+	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	ccgctgcctctgctgctgctGctgctgctgctgctgccgct	0	12	12	17	2	1	0	0	0	1	0	1	0	1	0	3	0	10	10	3	0	0	0			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr13:108518698G>T	ENST00000375915.2	-	1	385	c.247C>A	c.(247-249)Cag>Aag	p.Q83K		NM_001080396.2	NP_001073865.1	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A	83	Poly-Gln.					integral component of membrane (GO:0016021)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						tgctgctgctgctgctgctgc	0.706																																					p.Q83K		Atlas-SNP	.											.	FAM155A	82	.	0			c.C247A						PASS	.						16	22	20					13																	108518698		1929	3762	5691	SO:0001583	missense	728215	exon1			GCTGCTGCTGCTG	L10374	CCDS32006.1	13q33.3	2008-04-15			ENSG00000204442	ENSG00000204442			33877	protein-coding gene	gene with protein product							Standard	NM_001080396		Approved		uc001vql.3	B1AL88	OTTHUMG00000017326	ENST00000375915.2:c.247C>A	chr13.hg19:g.108518698G>T	ENSP00000365080:p.Gln83Lys	16.0	0.0	.		28.0	5.0	.	NM_001080396	B2RUV1|B7Z334	Missense_Mutation	SNP	ENST00000375915.2	hg19	CCDS32006.1	.	.	.	.	.	.	.	.	.	.	G	10.92	1.487166	0.26686	.	.	ENSG00000204442	ENST00000375915	T	0.62364	0.03	4.45	4.45	0.53987	Armadillo-like helical (1);	0.715687	0.11618	N	0.546038	T	0.55146	0.1902	L	0.43923	1.385	0.25117	N	0.990675	B	0.13594	0.008	B	0.13407	0.009	T	0.45308	-0.9270	10	0.36615	T	0.2	.	12.5709	0.56337	0.0:0.0:1.0:0.0	.	83	B1AL88	F155A_HUMAN	K	83	ENSP00000365080:Q83K	ENSP00000365080:Q83K	Q	-	1	0	FAM155A	107316699	1.000000	0.71417	0.893000	0.35052	0.674000	0.39518	4.577000	0.60922	2.027000	0.59764	0.561000	0.74099	CAG	.	.	.	none		0.706	FAM155A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045736.2	NM_001080396		T	108518698	G	T	108518698	3	4	86	1	0	0	0	0	1	0	0	0	5469	1328	46	4	1141	4	FAM155A	13	108518698	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10		108518698	6651180	61	5552											
MCF2L	23263	hgsc.bcm.edu	37	chr13	113719317	113719318	+	Frame_Shift_Ins	INS	-	-	G																															cagtccttcgggaccgagctINSggctgaaacagagctgccca																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr13:113719317_113719318insG	ENST00000375608.3	+	8	822_823	c.764_765insG	c.(763-768)ctggctfs	p.A256fs	MCF2L_ENST00000421756.1_Frame_Shift_Ins_p.A230fs|MCF2L_ENST00000423482.2_Frame_Shift_Ins_p.A224fs|MCF2L_ENST00000375604.2_Frame_Shift_Ins_p.A283fs|MCF2L_ENST00000397030.1_Frame_Shift_Ins_p.A259fs|MCF2L_ENST00000434480.2_Frame_Shift_Ins_p.A232fs|MCF2L_ENST00000535094.2_Frame_Shift_Ins_p.A226fs|MCF2L_ENST00000442652.2_Frame_Shift_Ins_p.A256fs|MCF2L_ENST00000375597.4_Frame_Shift_Ins_p.A224fs|MCF2L_ENST00000375601.3_Frame_Shift_Ins_p.A230fs			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	256					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)				GGGACCGAGCTGGCTGAAACAG	0.564																																					p.L225fs		Atlas-Indel,Pindel	.											.	MCF2L	182	.	0			c.674_675insG						PASS	.																																			SO:0001589	frameshift_variant	23263	exon7			.	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.766dupG	chr13.hg19:g.113719319_113719319dupG	ENSP00000364758:p.Ala256fs	106.0	0.0	0		76.0	16.0	0.210526	NM_001112732	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Frame_Shift_Ins	INS	ENST00000375608.3	hg19																																																																																				.	.	.	none		0.564	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4			G	113719318	-	G	113719317	7	5	86	1	0	1	1	0	0	0	0	0	9386	1580	55	0	966	0	MCF2L	13	113719317	Frame_Shift_Ins	INS	-	TCGA-B1-A656-01A-11D-A31X-10	5200619	113719317	1450561	62	5553											
THBS1	7057	hgsc.bcm.edu	37	chr15	39877738	39877738	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccaatgccacagttcctgAtggagaatgctgtcctcgct	8	11	9	13	1	0	2	0	1	0	1	4	3	3	2	4	1	2	3	4	1	2	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr15:39877738A>G	ENST00000260356.5	+	7	1259	c.1094A>G	c.(1093-1095)gAt>gGt	p.D365G		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	365	VWFC. {ECO:0000255|PROSITE- ProRule:PRU00220}.				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)		ACAGTTCCTGATGGAGAATGC	0.507																																					p.D365G		Atlas-SNP	.											.	THBS1	106	.	0			c.A1094G						PASS	.						218	152	174					15																	39877738		2200	4297	6497	SO:0001583	missense	7057	exon7			TTCCTGATGGAGA		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.1094A>G	chr15.hg19:g.39877738A>G	ENSP00000260356:p.Asp365Gly	35.0	0.0	.		34.0	7.0	.	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	hg19	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	A	31	5.103828	0.94245	.	.	ENSG00000137801	ENST00000260356	T	0.65364	-0.15	5.86	5.86	0.93980	von Willebrand factor, type C (4);	0.000000	0.34676	N	0.003775	T	0.77751	0.4177	M	0.69463	2.115	0.58432	D	0.999998	D	0.76494	0.999	D	0.85130	0.997	T	0.79640	-0.1719	10	0.66056	D	0.02	-17.1145	15.4256	0.75048	1.0:0.0:0.0:0.0	.	365	P07996	TSP1_HUMAN	G	365	ENSP00000260356:D365G	ENSP00000260356:D365G	D	+	2	0	THBS1	37665030	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	9.339000	0.96797	2.237000	0.73441	0.533000	0.62120	GAT	.	.	.	none		0.507	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		G	39877738	A	G	39877738	3	3	86	1	0	0	0	0	1	0	0	0	15865	333	12	3	1116	3	THBS1	15	39877738	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10		39877738	62653654	63	5554											
SPINT1	6692	hgsc.bcm.edu	37	chr15	41136856	41136856	+	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	cggcctccagggcacccaggCcgggccaccgcccgcgcccc	4	1	13	23	5	0	0	0	0	0	0	1	0	1	0	9	4	0	1	9	4	0	0			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr15:41136856C>A	ENST00000344051.4	+	2	338	c.104C>A	c.(103-105)gCc>gAc	p.A35D	SPINT1_ENST00000562057.1_Missense_Mutation_p.A35D|SPINT1_ENST00000431806.1_Missense_Mutation_p.A35D|RP11-532F12.5_ENST00000568419.1_RNA|RP11-532F12.5_ENST00000565315.1_RNA|RP11-532F12.5_ENST00000564302.1_RNA|RP11-532F12.5_ENST00000568525.1_RNA			O43278	SPIT1_HUMAN	serine peptidase inhibitor, Kunitz type 1	35					branching involved in labyrinthine layer morphogenesis (GO:0060670)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|placenta blood vessel development (GO:0060674)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	16		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		GGCACCCAGGCCGGGCCACCG	0.761																																					p.A35D		Atlas-SNP	.											.	SPINT1	28	.	0			c.C104A						PASS	.						6	8	8					15																	41136856		2067	4058	6125	SO:0001583	missense	6692	exon2			CCCAGGCCGGGCC		CCDS10067.1, CCDS45231.1	15q13.3	2008-02-05	2005-08-17		ENSG00000166145	ENSG00000166145			11246	protein-coding gene	gene with protein product		605123	"serine protease inhibitor, Kunitz type 1"				Standard	XM_006720657		Approved	HAI, MANSC2	uc001zna.3	O43278	OTTHUMG00000130068	ENST00000344051.4:c.104C>A	chr15.hg19:g.41136856C>A	ENSP00000342098:p.Ala35Asp	15.0	0.0	.		77.0	23.0	.	NM_181642	Q7Z7D2	Missense_Mutation	SNP	ENST00000344051.4	hg19	CCDS10067.1	.	.	.	.	.	.	.	.	.	.	C	18.06	3.538187	0.65085	.	.	ENSG00000166145	ENST00000344051;ENST00000431806	D;D	0.95656	-3.76;-3.77	5.02	3.07	0.35406	.	0.452065	0.24688	N	0.036402	D	0.89591	0.6759	N	0.08118	0	0.09310	N	1	P;P;P	0.48162	0.906;0.9;0.906	B;P;P	0.49999	0.425;0.628;0.521	T	0.82341	-0.0505	10	0.29301	T	0.29	-21.5589	6.2982	0.21097	0.0:0.7099:0.1902:0.1	.	35;35;35	B2RBU9;O43278-2;O43278	.;.;SPIT1_HUMAN	D	35	ENSP00000342098:A35D;ENSP00000409935:A35D	ENSP00000342098:A35D	A	+	2	0	SPINT1	38924148	0.876000	0.30132	0.328000	0.25416	0.002000	0.02628	3.594000	0.54008	1.206000	0.43276	0.563000	0.77884	GCC	.	.	.	none		0.761	SPINT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252359.2	NM_003710		A	41136856	C	A	41136856	3	1	86	1	0	0	0	0	1	0	0	0	15080	739	26	4	106	4	SPINT1	15	41136856	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	1259118	41136856	61394536	64	5555											
LRRC57	255252	hgsc.bcm.edu	37	chr15	42837381	42837381	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggatgctctggggaagcatgCtgagctcaagacaattctct	10	10	12	9	0	3	2	1	1	2	1	4	4	3	4	0	3	4	4	0	3	3	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr15:42837381C>T	ENST00000323443.2	-	4	939	c.572G>A	c.(571-573)aGc>aAc	p.S191N	LRRC57_ENST00000563454.1_Missense_Mutation_p.S191N|LRRC57_ENST00000397130.3_Missense_Mutation_p.S191N			Q8N9N7	LRC57_HUMAN	leucine rich repeat containing 57	191						extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|lung(5)|prostate(1)	8		all_cancers(109;1.99e-12)|all_epithelial(112;5.11e-11)|Lung NSC(122;4.53e-07)|all_lung(180;1.64e-06)|Melanoma(134;0.0262)		GBM - Glioblastoma multiforme(94;6.87e-07)		GGGAAGCATGCTGAGCTCAAG	0.423																																					p.S191N		Atlas-SNP	.											.	LRRC57	20	.	0			c.G572A						PASS	.						99	94	96					15																	42837381		2203	4299	6502	SO:0001583	missense	255252	exon5			AGCATGCTGAGCT	AK094891	CCDS10089.1	15q15.1	2006-02-13			ENSG00000180979	ENSG00000180979			26719	protein-coding gene	gene with protein product							Standard	NM_153260		Approved	FLJ36812	uc001zqc.3	Q8N9N7	OTTHUMG00000130679	ENST00000323443.2:c.572G>A	chr15.hg19:g.42837381C>T	ENSP00000326817:p.Ser191Asn	85.0	0.0	.		74.0	26.0	.	NM_153260	Q7Z2Z6|Q8N1T6	Missense_Mutation	SNP	ENST00000323443.2	hg19	CCDS10089.1	.	.	.	.	.	.	.	.	.	.	C	16.88	3.243740	0.58995	.	.	ENSG00000180979	ENST00000323443;ENST00000397130	T;T	0.46451	0.87;0.87	5.36	4.43	0.53597	.	0.131595	0.64402	D	0.000001	T	0.32763	0.0840	L	0.33339	1.005	0.54753	D	0.999984	B	0.11235	0.004	B	0.09377	0.004	T	0.08126	-1.0737	10	0.34782	T	0.22	.	14.3053	0.66380	0.0:0.9273:0.0:0.0727	.	191	Q8N9N7	LRC57_HUMAN	N	191	ENSP00000326817:S191N;ENSP00000380319:S191N	ENSP00000326817:S191N	S	-	2	0	LRRC57	40624673	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.969000	0.49232	2.520000	0.84964	0.557000	0.71058	AGC	.	.	.	none		0.423	LRRC57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253174.1	NM_153260		T	42837381	C	T	42837381	3	4	86	1	0	0	0	0	1	0	0	0	9020	797	28	2	155	2	LRRC57	15	42837381	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	1700525	42837381	59694011	65	5556											
SHC4	399694	hgsc.bcm.edu	37	chr15	49148178	49148178	+	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	acaacttttcacactgtatgGggcagtaagccatttgttcc	10	13	8	10	0	1	0	1	0	0	0	2	0	2	0	2	2	2	4	2	2	3	6			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr15:49148178G>T	ENST00000332408.4	-	8	1642	c.1214C>A	c.(1213-1215)cCc>cAc	p.P405H	SHC4_ENST00000396535.3_Missense_Mutation_p.P162H|SHC4_ENST00000537958.1_Missense_Mutation_p.P119H	NM_203349.3	NP_976224.3	Q6S5L8	SHC4_HUMAN	SHC (Src homology 2 domain containing) family, member 4	405	CH1.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of cell proliferation (GO:0008284)|regulation of gene expression (GO:0010468)|stem cell differentiation (GO:0048863)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(2)|large_intestine(8)|lung(11)|ovary(3)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	29		all_lung(180;0.00466)		all cancers(107;9.4e-08)|GBM - Glioblastoma multiforme(94;5.94e-07)		ACACTGTATGGGGCAGTAAGC	0.408																																					p.P405H		Atlas-SNP	.											.	SHC4	70	.	0			c.C1214A						PASS	.						140	128	132					15																	49148178		2197	4294	6491	SO:0001583	missense	399694	exon8			TGTATGGGGCAGT	AY358250	CCDS10130.1	15q21.1-q21.2	2013-02-14			ENSG00000185634	ENSG00000185634		"SH2 domain containing"	16743	protein-coding gene	gene with protein product	"rai-like protein"						Standard	NM_203349		Approved	RaLP	uc001zxb.1	Q6S5L8	OTTHUMG00000131513	ENST00000332408.4:c.1214C>A	chr15.hg19:g.49148178G>T	ENSP00000329668:p.Pro405His	145.0	0.0	.		117.0	28.0	.	NM_203349	Q6UXQ3|Q8IYW3	Missense_Mutation	SNP	ENST00000332408.4	hg19	CCDS10130.1	.	.	.	.	.	.	.	.	.	.	G	17.07	3.293981	0.60086	.	.	ENSG00000185634	ENST00000332408;ENST00000396535;ENST00000537958	T;T;T	0.31769	3.48;1.48;1.5	5.03	5.03	0.67393	.	0.200639	0.36134	N	0.002762	T	0.44435	0.1293	L	0.43923	1.385	0.46521	D	0.999085	P;D	0.69078	0.575;0.997	B;P	0.60886	0.211;0.88	T	0.31194	-0.9952	10	0.59425	D	0.04	-10.6953	15.38	0.74648	0.0:0.0:1.0:0.0	.	162;405	Q6S5L8-2;Q6S5L8	.;SHC4_HUMAN	H	405;162;119	ENSP00000329668:P405H;ENSP00000379786:P162H;ENSP00000443300:P119H	ENSP00000329668:P405H	P	-	2	0	SHC4	46935470	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.871000	0.69628	2.612000	0.88384	0.655000	0.94253	CCC	.	.	.	none		0.408	SHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254371.1	NM_203349		T	49148178	G	T	49148178	3	4	86	1	0	0	0	0	1	0	0	0	14286	1232	43	4	698	4	SHC4	15	49148178	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	6310797	49148178	53383214	66	5557											
FBXL22	283807	hgsc.bcm.edu	37	chr15	63889797	63889797	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacaacttcctcctgggccCggcactccgcagcctctcca	6	7	9	19	2	1	0	0	0	1	0	5	1	4	1	6	3	2	2	6	3	1	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr15:63889797C>T	ENST00000360587.2	+	1	246	c.206C>T	c.(205-207)cCg>cTg	p.P69L	USP3-AS1_ENST00000561256.1_RNA|USP3-AS1_ENST00000558831.1_RNA|USP3-AS1_ENST00000561191.1_RNA|USP3-AS1_ENST00000559737.1_RNA|FBXL22_ENST00000534939.1_Missense_Mutation_p.P69L|USP3-AS1_ENST00000560962.1_RNA|USP3-AS1_ENST00000559861.1_RNA|USP3-AS1_ENST00000560622.1_RNA|FBXL22_ENST00000539570.3_Missense_Mutation_p.P63L	NM_203373.2	NP_976307.2	Q6P050	FXL22_HUMAN	F-box and leucine-rich repeat protein 22	69					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				lung(4)	4						CTCCTGGGCCCGGCACTCCGC	0.617																																					p.P69L		Atlas-SNP	.											.	FBXL22	4	.	0			c.C206T						PASS	.						47	38	41					15																	63889797		2203	4300	6503	SO:0001583	missense	283807	exon1			TGGGCCCGGCACT	BC065833	CCDS10187.1, CCDS10187.2	15q22.1	2012-04-05			ENSG00000197361	ENSG00000197361		"F-boxes / Leucine-rich repeats"	27537	protein-coding gene	gene with protein product		609088				12477932	Standard	NM_203373		Approved	Fbl22, FLJ39626	uc002amn.4	Q6P050	OTTHUMG00000132905	ENST00000360587.2:c.206C>T	chr15.hg19:g.63889797C>T	ENSP00000353794:p.Pro69Leu	58.0	0.0	.		25.0	6.0	.	NM_203373		Missense_Mutation	SNP	ENST00000360587.2	hg19	CCDS10187.2	.	.	.	.	.	.	.	.	.	.	C	27.1	4.799631	0.90538	.	.	ENSG00000197361	ENST00000360587;ENST00000539570	T;T	0.38722	1.12;1.12	5.72	5.72	0.89469	.	0.183522	0.48767	D	0.000162	T	0.58352	0.2116	L	0.48642	1.525	0.58432	D	0.999999	D	0.76494	0.999	D	0.63957	0.92	T	0.58940	-0.7547	10	0.87932	D	0	-2.5763	18.8613	0.92273	0.0:1.0:0.0:0.0	.	63	Q6P050	FXL22_HUMAN	L	69;63	ENSP00000353794:P69L;ENSP00000442112:P63L	ENSP00000353794:P69L	P	+	2	0	FBXL22	61676850	1.000000	0.71417	0.959000	0.39883	0.594000	0.36715	7.583000	0.82559	2.699000	0.92147	0.563000	0.77884	CCG	.	.	.	none		0.617	FBXL22-001	KNOWN	downstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256412.4	NM_203373		T	63889797	C	T	63889797	3	4	86	1	0	0	0	0	1	0	0	0	5726	652	23	1	190	1	FBXL22	15	63889797	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	14741619	63889797	38641595	67	5558											
LARP6	55323	hgsc.bcm.edu	37	chr15	71128826	71128826	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcacgctcgttctcaccTccacttgcagtggtgccact	5	12	7	17	2	2	0	2	0	1	0	6	0	4	0	4	1	2	3	4	1	0	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr15:71128826T>C	ENST00000299213.8	-	2	289	c.219A>G	c.(217-219)ggA>ggG	p.G73G		NM_018357.2	NP_060827.2	Q9BRS8	LARP6_HUMAN	La ribonucleoprotein domain family, member 6	73					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						CGTTCTCACCTCCACTTGCAG	0.522																																					p.G73G		Atlas-SNP	.											.	LARP6	43	.	0			c.A219G						PASS	.						70	72	71					15																	71128826		2199	4297	6496	SO:0001819	synonymous_variant	55323	exon2			CTCACCTCCACTT	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.219A>G	chr15.hg19:g.71128826T>C		81.0	0.0	.		70.0	24.0	.	NM_018357	Q5XKE4|Q8N3N2|Q9NUR0	Silent	SNP	ENST00000299213.8	hg19	CCDS32281.1																																																																																			.	.	.	none		0.522	LARP6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417197.2	NM_018357		C	71128826	T	C	71128826	2	2	86	1	0	0	0	0	0	0	0	1	8639	1538	54	3		3	LARP6	15	71128826	Silent	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	7239029	71128826	31402566	68	5559											
NTRK3	4916	hgsc.bcm.edu	37	chr15	88680721	88680721	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctggctgttgagcttggccTccccctgctcctgccagagc	3	11	11	16	0	1	2	0	1	1	1	3	2	3	2	5	2	4	4	5	2	0	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr15:88680721T>C	ENST00000360948.2	-	6	697	c.536A>G	c.(535-537)gAg>gGg	p.E179G	NTRK3_ENST00000357724.2_Missense_Mutation_p.E179G|NTRK3_ENST00000558676.1_Missense_Mutation_p.E179G|NTRK3_ENST00000557856.1_Missense_Mutation_p.E179G|NTRK3_ENST00000355254.2_Missense_Mutation_p.E179G|NTRK3_ENST00000540489.2_Missense_Mutation_p.E179G|NTRK3_ENST00000394480.2_Missense_Mutation_p.E179G|NTRK3_ENST00000317501.3_Missense_Mutation_p.E179G|NTRK3_ENST00000542733.2_Missense_Mutation_p.E81G	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	179	LRRCT.				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)			GAGCTTGGCCTCCCCCTGCTC	0.567			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)																											p.E179G		Atlas-SNP	.		Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	.	NTRK3	587	.	0			c.A536G						PASS	.						124	94	104					15																	88680721		2201	4299	6500	SO:0001583	missense	4916	exon7			TTGGCCTCCCCCT	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.536A>G	chr15.hg19:g.88680721T>C	ENSP00000354207:p.Glu179Gly	56.0	0.0	.		41.0	4.0	.	NM_001243101	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	hg19	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	T	16.79	3.219821	0.58560	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254;ENST00000542733;ENST00000540489;ENST00000317501	D;D;D;D;D;D;D	0.89875	-2.58;-2.58;-2.58;-2.58;-2.58;-2.58;-2.58	5.71	5.71	0.89125	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.92331	0.7567	L	0.51422	1.61	0.58432	D	0.999993	D;D;P;D;D;P	0.76494	0.999;0.999;0.47;0.999;0.998;0.47	D;D;B;D;D;B	0.81914	0.995;0.986;0.244;0.995;0.993;0.244	D	0.91792	0.5444	10	0.40728	T	0.16	.	15.1854	0.72996	0.0:0.0:0.0:1.0	.	81;179;179;179;179;179	B7Z7U4;E9PG56;B7Z4C5;Q96CY4;Q16288-3;Q16288	.;.;.;.;.;NTRK3_HUMAN	G	179;179;179;179;81;179;179	ENSP00000377990:E179G;ENSP00000354207:E179G;ENSP00000350356:E179G;ENSP00000347397:E179G;ENSP00000437773:E81G;ENSP00000444673:E179G;ENSP00000318328:E179G	ENSP00000318328:E179G	E	-	2	0	NTRK3	86481725	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.723000	0.68492	2.171000	0.68590	0.528000	0.53228	GAG	.	.	.	none		0.567	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				C	88680721	T	C	88680721	3	2	86	1	0	0	0	0	1	0	0	0	10715	1551	54	3	2301	3	NTRK3	15	88680721	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	17551895	88680721	13850671	69	5560											
PARN	5073	hgsc.bcm.edu	37	chr16	14678281	14678281	+	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	atgtgttgttaatgatatccTgcaaaccacgaagcaaagaa	16	10	8	7	1	0	2	0	1	0	1	1	3	1	2	2	0	3	4	2	0	6	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr16:14678281T>C	ENST00000437198.2	-	16	1147		c.e16-2		PARN_ENST00000539279.1_Splice_Site|PARN_ENST00000420015.2_Splice_Site|PARN_ENST00000341484.7_Splice_Site	NM_001134477.2|NM_002582.3	NP_001127949.1|NP_002573.1	O95453	PARN_HUMAN	poly(A)-specific ribonuclease						female gamete generation (GO:0007292)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA metabolic process (GO:0016070)|RNA modification (GO:0009451)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|nuclease activity (GO:0004518)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(A)-specific ribonuclease activity (GO:0004535)|protein kinase binding (GO:0019901)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|urinary_tract(1)	21						AATGATATCCTGCAAACCACG	0.383																																					.		Atlas-SNP	.											.	PARN	72	.	0			c.868-2A>G						PASS	.						52	50	51					16																	14678281		1825	4081	5906	SO:0001630	splice_region_variant	5073	exon16			ATATCCTGCAAAC	AJ005698	CCDS45419.1, CCDS45420.1, CCDS58425.1	16p13	2014-08-08	2011-07-07		ENSG00000140694	ENSG00000140694	3.1.13.4		8609	protein-coding gene	gene with protein product	"deadenylation nuclease"	604212	"poly(A)-specific ribonuclease (deadenylation nuclease)"			10640832	Standard	NM_002582		Approved	DAN	uc010uzd.2	O95453	OTTHUMG00000173199	ENST00000437198.2:c.1006-2A>G	chr16.hg19:g.14678281T>C		95.0	0.0	.		60.0	22.0	.	NM_001242992	B2RCB3|B4DDG8|B4DWR4|B4E1H6	Splice_Site	SNP	ENST00000437198.2	hg19	CCDS45419.1	.	.	.	.	.	.	.	.	.	.	T	19.70	3.876641	0.72180	.	.	ENSG00000140694	ENST00000437198;ENST00000341484;ENST00000420015;ENST00000539279	.	.	.	5.75	5.75	0.90469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9377	0.70970	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PARN	14585782	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	6.627000	0.74258	2.198000	0.70561	0.456000	0.33151	.	.	.	.	none		0.383	PARN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422383.1	NM_002582	Intron	C	14678281	T	C	14678281	5	2	86	1	0	0	0	0	0	0	1	0	11460	1594	55	3	951	3	PARN	16	14678281	Splice_Site	SNP	T	TCGA-B1-A656-01A-11D-A31X-10		14678281	75676472	70	5561											
ACSM2A	123876	hgsc.bcm.edu	37	chr16	20489950	20489950	+	Missense_Mutation	SNP	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	cggcacagaaggagacattgGcatcagggtcaaacccatca	14	5	11	11	1	3	2	3	0	0	2	3	3	3	2	1	4	1	2	1	4	2	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr16:20489950G>A	ENST00000573854.1	+	10	1346	c.1232G>A	c.(1231-1233)gGc>gAc	p.G411D	ACSM2A_ENST00000396104.2_Missense_Mutation_p.G411D|ACSM2A_ENST00000575690.1_Missense_Mutation_p.G411D|ACSM2A_ENST00000219054.6_Missense_Mutation_p.G411D|ACSM2A_ENST00000575558.1_3'UTR|ACSM2A_ENST00000417235.2_Missense_Mutation_p.G332D|ACSM2A_ENST00000536134.1_Missense_Mutation_p.G183D	NM_001010845.2	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member 2A	411					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						GGAGACATTGGCATCAGGGTC	0.527																																					p.G411D		Atlas-SNP	.											.	ACSM2A	120	.	0			c.G1232A						PASS	.						103	87	92					16																	20489950		2203	4297	6500	SO:0001583	missense	123876	exon11			ACATTGGCATCAG	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.1232G>A	chr16.hg19:g.20489950G>A	ENSP00000459451:p.Gly411Asp	89.0	0.0	.		67.0	24.0	.	NM_001010845	B3KTT9|O75202	Missense_Mutation	SNP	ENST00000573854.1	hg19	CCDS32401.1	.	.	.	.	.	.	.	.	.	.	G	9.906	1.208165	0.22205	.	.	ENSG00000183747	ENST00000417235;ENST00000219054;ENST00000536134;ENST00000396104	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	3.33	0.71	0.18157	AMP-dependent synthetase/ligase (1);	0.312022	0.23048	N	0.052540	T	0.57975	0.2090	M	0.68952	2.095	0.20638	N	0.99987	D;D	0.76494	0.999;0.999	D;D	0.74674	0.977;0.984	T	0.52313	-0.8592	10	0.87932	D	0	-4.1522	11.8873	0.52610	0.0:0.6828:0.3172:0.0	.	332;411	B7Z8R0;Q08AH3	.;ACS2A_HUMAN	D	332;411;183;411	ENSP00000392169:G332D;ENSP00000219054:G411D;ENSP00000445082:G183D;ENSP00000379411:G411D	ENSP00000219054:G411D	G	+	2	0	ACSM2A	20397451	0.419000	0.25449	0.008000	0.14137	0.141000	0.21300	0.682000	0.25335	0.408000	0.25621	0.289000	0.19496	GGC	.	.	.	none		0.527	ACSM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436764.1	NM_001010845		A	20489950	G	A	20489950	3	1	86	1	0	0	0	0	1	0	0	0	183	1203	42	2	1266	2	ACSM2A	16	20489950	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	5811669	20489950	69864803	71	5562											
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24801321	24801321	+	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	taccactgaaatgactggacCaaataacactactaacttta	17	10	4	10	0	0	2	0	2	0	0	0	3	0	3	2	1	4	0	2	1	7	6			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr16:24801321C>G	ENST00000395799.3	+	6	1487	c.1358C>G	c.(1357-1359)cCa>cGa	p.P453R	TNRC6A_ENST00000315183.7_Missense_Mutation_p.P453R	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	453	Interaction with argonaute family proteins.|Sufficient for interaction with AGO1, AGO3 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)	p.P453Q(1)		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)		ATGACTGGACCAAATAACACT	0.438																																					p.P453R		Atlas-SNP	.											TNRC6A,NS,carcinoma,0,1	TNRC6A	171	.	1	Substitution - Missense(1)	lung(1)	c.C1358G						PASS	.						58	56	57					16																	24801321		2197	4300	6497	SO:0001583	missense	27327	exon6			CTGGACCAAATAA	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.1358C>G	chr16.hg19:g.24801321C>G	ENSP00000379144:p.Pro453Arg	106.0	0.0	.		102.0	25.0	.	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	hg19	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	C	16.88	3.243926	0.58995	.	.	ENSG00000090905	ENST00000315183;ENST00000395799	T;T	0.44881	0.91;1.02	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.67069	0.2854	M	0.69823	2.125	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.989;0.999;0.998	T	0.67138	-0.5746	10	0.72032	D	0.01	-7.5051	20.3594	0.98849	0.0:1.0:0.0:0.0	.	200;453;453	Q8NDV7-2;Q8NDV7-6;Q8NDV7	.;.;TNR6A_HUMAN	R	453	ENSP00000326900:P453R;ENSP00000379144:P453R	ENSP00000326900:P453R	P	+	2	0	TNRC6A	24708822	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.247000	0.78257	2.816000	0.96949	0.563000	0.77884	CCA	.	.	.	none		0.438	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		G	24801321	C	G	24801321	3	3	86	1	0	0	0	0	1	0	0	0	16352	594	21	4	1380	4	TNRC6A	16	24801321	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	4311371	24801321	65553432	72	5563											
PYDC1	260434	hgsc.bcm.edu	37	chr16	31228204	31228204	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttgtcggtgaggtccacgAtatctagctgcccgagcgcg	6	9	14	12	5	1	1	0	1	1	0	3	3	2	1	2	2	3	2	2	2	2	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr16:31228204A>G	ENST00000302964.3	-	1	476	c.146T>C	c.(145-147)aTc>aCc	p.I49T	TRIM72_ENST00000322122.3_Intron|PYDC1_ENST00000568383.1_5'Flank	NM_152901.2	NP_690865.1	Q8WXC3	PYDC1_HUMAN	PYD (pyrin domain) containing 1	49	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				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						GAGGTCCACGATATCTAGCTG	0.652																																					p.I49T		Atlas-SNP	.											.	PYDC1	7	.	0			c.T146C						PASS	.						68	61	63					16																	31228204		2197	4300	6497	SO:0001583	missense	260434	exon1			TCCACGATATCTA		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	ENST00000302964.3:c.146T>C	chr16.hg19:g.31228204A>G	ENSP00000304336:p.Ile49Thr	172.0	0.0	.		98.0	23.0	.	NM_152901	B2R8L4|Q8NFP8	Missense_Mutation	SNP	ENST00000302964.3	hg19	CCDS10710.1	.	.	.	.	.	.	.	.	.	.	A	10.48	1.362629	0.24684	.	.	ENSG00000169900	ENST00000302964	T	0.45276	0.9	4.3	0.865	0.19074	Pyrin (2);DEATH-like (2);	2.187950	0.03117	U	0.163273	T	0.29355	0.0731	.	.	.	0.09310	N	1	P	0.42296	0.775	B	0.40864	0.342	T	0.18209	-1.0344	9	0.18710	T	0.47	.	5.5097	0.16874	0.124:0.4356:0.4404:0.0	.	49	Q8WXC3	PYDC1_HUMAN	T	49	ENSP00000304336:I49T	ENSP00000304336:I49T	I	-	2	0	PYDC1	31135705	0.000000	0.05858	0.000000	0.03702	0.091000	0.18340	-0.903000	0.04084	0.401000	0.25424	-0.415000	0.06103	ATC	.	.	.	none		0.652	PYDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255543.2	NM_152901		G	31228204	A	G	31228204	3	3	86	1	0	0	0	0	1	0	0	0	12871	333	12	3	127	3	PYDC1	16	31228204	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	6426883	31228204	59126549	73	5564											
N4BP1	9683	hgsc.bcm.edu	37	chr16	48576974	48576974	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaagatctctgagctggcatGggcaggttctgctggagact	8	10	15	8	0	2	3	0	1	2	2	3	5	2	3	0	4	2	5	0	4	1	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr16:48576974G>A	ENST00000262384.3	-	7	2768	c.2532C>T	c.(2530-2532)ccC>ccT	p.P844P	N4BP1_ENST00000565423.1_5'UTR	NM_153029.3	NP_694574.3	O75113	N4BP1_HUMAN	NEDD4 binding protein 1	844					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)				GAGCTGGCATGGGCAGGTTCT	0.577																																					p.P844P		Atlas-SNP	.											.	N4BP1	121	.	0			c.C2532T						PASS	.						53	52	53					16																	48576974		1974	4170	6144	SO:0001819	synonymous_variant	9683	exon7			TGGCATGGGCAGG	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.2532C>T	chr16.hg19:g.48576974G>A		76.0	0.0	.		68.0	9.0	.	NM_153029	A7MD49|Q2YDX1	Silent	SNP	ENST00000262384.3	hg19	CCDS45479.1																																																																																			.	.	.	none		0.577	N4BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429920.1	NM_014664		A	48576974	G	A	48576974	2	1	86	1	0	0	0	0	0	0	0	1	10116	1335	47	2		2	N4BP1	16	48576974	Silent	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	17348770	48576974	41777779	74	5565											
HS3ST3A1	9955	hgsc.bcm.edu	37	chr17	13504436	13504436	+	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	agagggcactggccgggcccGgaggggccatcctagccgga	7	3	18	13	3	0	1	0	0	0	1	1	3	1	3	5	7	1	1	5	7	1	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr17:13504436G>T	ENST00000284110.1	-	1	808	c.11C>A	c.(10-12)cCg>cAg	p.P4Q		NM_006042.1	NP_006033.1	Q9Y663	HS3SA_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1	4					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 3 activity (GO:0033872)|sulfotransferase activity (GO:0008146)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_lung(20;0.114)		UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		GGCCGGGCCCGGAGGGGCCAT	0.711																																					p.P4Q		Atlas-SNP	.											.	HS3ST3A1	39	.	0			c.C11A						PASS	.						21	21	21					17																	13504436		2176	4264	6440	SO:0001583	missense	9955	exon1			GGGCCCGGAGGGG	AF105376	CCDS11165.1	17p12	2007-04-02			ENSG00000153976	ENSG00000153976	2.8.2.23	"Sulfotransferases, membrane-bound"	5196	protein-coding gene	gene with protein product		604057				9988767	Standard	NM_006042		Approved	3OST3A1, 30ST3A1	uc002gob.1	Q9Y663	OTTHUMG00000058768	ENST00000284110.1:c.11C>A	chr17.hg19:g.13504436G>T	ENSP00000284110:p.Pro4Gln	66.0	0.0	.		67.0	15.0	.	NM_006042	A8K7N2	Missense_Mutation	SNP	ENST00000284110.1	hg19	CCDS11165.1	.	.	.	.	.	.	.	.	.	.	G	11.91	1.778371	0.31502	.	.	ENSG00000153976	ENST00000284110	T	0.50548	0.74	2.79	-0.456	0.12190	.	0.327925	0.15205	U	0.274780	T	0.30854	0.0778	N	0.24115	0.695	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.05632	-1.0873	10	0.66056	D	0.02	.	9.3973	0.38410	0.3961:0.0:0.6039:0.0	.	4	Q9Y663	HS3SA_HUMAN	Q	4	ENSP00000284110:P4Q	ENSP00000284110:P4Q	P	-	2	0	HS3ST3A1	13445161	0.000000	0.05858	0.792000	0.32020	0.729000	0.41735	-0.271000	0.08572	-0.327000	0.08551	-1.119000	0.02030	CCG	.	.	.	none		0.711	HS3ST3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129952.1	NM_006042		T	13504436	G	T	13504436	3	4	86	1	0	0	0	0	1	0	0	0	7372	1116	39	4	1217	4	HS3ST3A1	17	13504436	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10		13504436	67690774	75	5566											
ZNF830	91603	hgsc.bcm.edu	37	chr17	33288777	33288777	+	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	actccggttaagagcgagctCctgtggcagactcacgtcct	8	9	11	13	3	1	2	1	0	0	2	4	3	4	2	3	2	2	3	3	2	1	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr17:33288777C>A	ENST00000361952.3	+	1	229	c.192C>A	c.(190-192)ctC>ctA	p.L64L	CCT6B_ENST00000436961.3_5'Flank|CCT6B_ENST00000314144.5_5'Flank|CCT6B_ENST00000421975.3_5'Flank	NM_052857.3	NP_443089.3	Q96NB3	ZN830_HUMAN	zinc finger protein 830	64					blastocyst growth (GO:0001832)|mitotic nuclear division (GO:0007067)|nuclear cell cycle DNA replication (GO:0033260)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|large_intestine(1)|liver(2)|lung(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Ovarian(249;0.17)				AGAGCGAGCTCCTGTGGCAGA	0.582																																					p.L64L		Atlas-SNP	.											.	ZNF830	26	.	0			c.C192A						PASS	.						93	90	91					17																	33288777		2203	4300	6503	SO:0001819	synonymous_variant	91603	exon1			CGAGCTCCTGTGG	AK055707	CCDS32618.1	17q12	2013-10-23	2008-03-25	2008-03-25	ENSG00000198783	ENSG00000198783			28291	protein-coding gene	gene with protein product	"orphan maintenance of genome 1"		"coiled-coil domain containing 16"	CCDC16		23066043	Standard	NM_052857		Approved	MGC20398, OMCG1	uc002hih.4	Q96NB3	OTTHUMG00000179771	ENST00000361952.3:c.192C>A	chr17.hg19:g.33288777C>A		117.0	0.0	.		128.0	53.0	.	NM_052857	Q96F60|Q96GZ5|Q9BU38	Silent	SNP	ENST00000361952.3	hg19	CCDS32618.1																																																																																			.	.	.	none		0.582	ZNF830-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448018.1	NM_052857		A	33288777	C	A	33288777	2	1	86	1	0	0	0	0	0	0	0	1	18196	842	30	4		4	ZNF830	17	33288777	Silent	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	19784341	33288777	47906433	76	5567											
GGNBP2	79893	hgsc.bcm.edu	37	chr17	34934557	34934557	+	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	gaacgacacatacatgtttgCtgtgaaacagacttcattgc	13	11	8	9	1	1	2	1	1	0	1	1	4	1	2	0	0	5	2	0	0	3	4			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr17:34934557C>T	ENST00000304718.4	+	7	1102	c.786C>T	c.(784-786)tgC>tgT	p.C262C		NM_024835.3	NP_079111.1	Q9H3C7	GGNB2_HUMAN	gametogenetin binding protein 2	262					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)		p.C262C(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)	38		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		TACATGTTTGCTGTGAAACAG	0.463																																					p.C262C		Atlas-SNP	.											GGNBP2,NS,carcinoma,0,1	GGNBP2	72	.	1	Substitution - coding silent(1)	lung(1)	c.C786T						PASS	.						216	194	201					17																	34934557		2203	4300	6503	SO:0001819	synonymous_variant	79893	exon7			TGTTTGCTGTGAA	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.786C>T	chr17.hg19:g.34934557C>T		131.0	0.0	.		108.0	24.0	.	NM_024835	B2RPK7|Q96T90|Q9GZR8|Q9H767	Silent	SNP	ENST00000304718.4	hg19	CCDS11314.1																																																																																			.	.	.	none		0.463	GGNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256684.2	NM_024835		T	34934557	C	T	34934557	2	4	86	1	0	0	0	0	0	0	0	1	6366	805	28	2		2	GGNBP2	17	34934557	Silent	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	1645780	34934557	46260653	77	5568											
RPRML	388394	hgsc.bcm.edu	37	chr17	45056083	45056083	+	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	tgcaccagaaagttgatcatGctctcggacttgatgagcag	11	10	11	9	1	2	4	1	3	1	1	3	5	2	5	1	1	3	4	1	1	1	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr17:45056083G>T	ENST00000322329.3	-	1	531	c.291C>A	c.(289-291)agC>agA	p.S97R	LRRC37A17P_ENST00000570478.1_RNA|RP11-156P1.2_ENST00000571841.1_Intron|GOSR2_ENST00000439730.2_Intron	NM_203400.4	NP_981945.1	Q8N4K4	RPRML_HUMAN	reprimo-like	97						integral component of membrane (GO:0016021)				lung(1)	1						AGTTGATCATGCTCTCGGACT	0.652																																					p.S97R		Atlas-SNP	.											.	RPRML	2	.	0			c.C291A						PASS	.						34	32	33					17																	45056083		2201	4300	6501	SO:0001583	missense	388394	exon1			GATCATGCTCTCG	BC033942	CCDS11508.1	17q21.32	2006-09-26				ENSG00000179673			32422	protein-coding gene	gene with protein product							Standard	NM_203400		Approved	MGC43894	uc002ilb.3	Q8N4K4		ENST00000322329.3:c.291C>A	chr17.hg19:g.45056083G>T	ENSP00000318032:p.Ser97Arg	106.0	0.0	.		102.0	28.0	.	NM_203400		Missense_Mutation	SNP	ENST00000322329.3	hg19	CCDS11508.1	.	.	.	.	.	.	.	.	.	.	G	17.66	3.444031	0.63067	.	.	ENSG00000179673	ENST00000322329	.	.	.	3.72	2.72	0.32119	.	0.000000	0.85682	D	0.000000	T	0.66655	0.2811	L	0.52573	1.65	0.58432	D	0.999997	D	0.76494	0.999	D	0.72075	0.976	T	0.65561	-0.6138	9	0.52906	T	0.07	-8.687	10.3405	0.43875	0.103:0.0:0.897:0.0	.	97	Q8N4K4	RPRML_HUMAN	R	97	.	ENSP00000318032:S97R	S	-	3	2	RPRML	42411082	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.546000	0.45778	0.727000	0.32360	0.313000	0.20887	AGC	.	.	.	none		0.652	RPRML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440919.1	NM_203400		T	45056083	G	T	45056083	3	4	86	1	0	0	0	0	1	0	0	0	13632	1310	46	4	75	4	RPRML	17	45056083	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	10121526	45056083	36139127	78	5569											
HOXB4	3214	hgsc.bcm.edu	37	chr17	46655633	46655634	+	In_Frame_Ins	INS	-	-	CTT																															tattcctcgcatggagggaaINScttggggtcgacatagtttg																										TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr17:46655633_46655634insCTT	ENST00000332503.5	-	1	1839_1840	c.48_49insAAG	c.(46-51)aagttc>aagAAGttc	p.16_17insK	HOXB3_ENST00000472863.1_Intron|MIR10A_ENST00000385043.1_RNA|HOXB3_ENST00000489475.1_Intron|HOXB3_ENST00000498678.1_Intron|HOXB3_ENST00000460160.1_Intron|HOXB-AS3_ENST00000465846.2_RNA|HOXB3_ENST00000465120.3_Intron|HOXB3_ENST00000552000.2_Intron|HOXB3_ENST00000476342.1_Intron	NM_024015.4	NP_076920.1	P17483	HXB4_HUMAN	homeobox B4	16	Pro-rich (part of the transcriptional activation domain).				anterior/posterior pattern specification (GO:0009952)|bone marrow development (GO:0048539)|cell proliferation (GO:0008283)|definitive hemopoiesis (GO:0060216)|embryonic skeletal system morphogenesis (GO:0048704)|hematopoietic stem cell differentiation (GO:0060218)|morphogenesis of an epithelial sheet (GO:0002011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|somatic stem cell division (GO:0048103)|spleen development (GO:0048536)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|urinary_tract(2)	9						CATGGAGGGAACTTGGGGTCGA	0.5																																					p.F17delinsKF		Pindel	.											.	HOXB4	16	.	0			c.49_50insAAG						PASS	.																																			SO:0001652	inframe_insertion	3214	exon1			.		CCDS11529.1	17q21.32	2011-06-20	2005-12-22		ENSG00000182742	ENSG00000182742		"Homeoboxes / ANTP class : HOXL subclass"	5115	protein-coding gene	gene with protein product		142965	"homeo box B4"	HOX2, HOX2F		1973146, 1358459	Standard	NM_024015		Approved		uc002inp.3	P17483	OTTHUMG00000159920	ENST00000332503.5:c.46_48dupAAG	chr17.hg19:g.46655634_46655636dupCTT	ENSP00000328928:p.Lys16_Lys16dup	166.0	0.0	.		188.0	36.0	0.191	NM_024015	Q9NTA0	In_Frame_Ins	INS	ENST00000332503.5	hg19	CCDS11529.1																																																																																			.	.	.	none		0.5	HOXB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358259.2			CTT	46655634	-	CTT	46655633	7	5	86	1	0	1	1	0	0	0	0	0	7310	43	2	0	714	0	HOXB4	17	46655633	In_Frame_Ins	INS	-	TCGA-B1-A656-01A-11D-A31X-10	1599550	46655633	34539577	79	5570											
CEP192	55125	hgsc.bcm.edu	37	chr18	13055803	13055803	+	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	atatcaccagcgagttgagtAccacaattattcaaggcagt	14	10	8	9	1	2	1	2	1	0	0	2	2	2	1	2	1	2	3	2	1	5	5			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr18:13055803A>T	ENST00000325971.8	+	17	3019	c.1426A>T	c.(1426-1428)Acc>Tcc	p.T476S	CEP192_ENST00000506447.1_Missense_Mutation_p.T1072S|CEP192_ENST00000430049.2_Missense_Mutation_p.T597S			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	476					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						CGAGTTGAGTACCACAATTAT	0.368																																					p.T1072S		Atlas-SNP	.											.	CEP192	340	.	0			c.A3214T						PASS	.						57	57	57					18																	13055803		2203	4300	6503	SO:0001583	missense	55125	exon19			TTGAGTACCACAA	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.1426A>T	chr18.hg19:g.13055803A>T	ENSP00000317156:p.Thr476Ser	67.0	0.0	.		42.0	14.0	.	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	hg19		.	.	.	.	.	.	.	.	.	.	A	19.71	3.878317	0.72294	.	.	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	T;T;T	0.21031	2.03;2.03;2.03	4.5	4.5	0.54988	.	0.111905	0.39687	N	0.001284	T	0.22704	0.0548	L	0.39397	1.21	0.42538	D	0.993064	B;B;P	0.43973	0.291;0.291;0.823	B;B;P	0.44477	0.214;0.214;0.451	T	0.02307	-1.1179	10	0.44086	T	0.13	-5.7927	14.1063	0.65091	1.0:0.0:0.0:0.0	.	597;1072;476	C9JT09;E9PF99;Q8TEP8	.;.;CE192_HUMAN	S	1072;476;476;597	ENSP00000427550:T1072S;ENSP00000317156:T476S;ENSP00000389190:T597S	ENSP00000317156:T476S	T	+	1	0	CEP192	13045803	1.000000	0.71417	0.998000	0.56505	0.797000	0.45037	6.760000	0.74939	1.790000	0.52503	0.460000	0.39030	ACC	.	.	.	none		0.368	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142		T	13055803	A	T	13055803	3	4	86	1	0	0	0	0	1	0	0	0	3253	391	14	5	3284	5	CEP192	18	13055803	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10		13055803	65021445	80	5571											
PHLPP1	23239	hgsc.bcm.edu	37	chr18	60384475	60384475	+	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	ggactcggagattggctgccTcatccgcttctatgcaggta	7	11	12	11	2	2	1	1	0	1	1	4	3	3	2	2	4	2	4	2	4	2	4			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr18:60384475T>A	ENST00000262719.5	+	1	1793	c.1559T>A	c.(1558-1560)cTc>cAc	p.L520H	PHLPP1_ENST00000400316.4_Missense_Mutation_p.L8H			O60346	PHLP1_HUMAN	PH domain and leucine rich repeat protein phosphatase 1	520					apoptotic process (GO:0006915)|entrainment of circadian clock (GO:0009649)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			endometrium(2)|kidney(2)|lung(13)	17						ATTGGCTGCCTCATCCGCTTC	0.537																																					p.L520H		Atlas-SNP	.											.	PHLPP1	164	.	0			c.T1559A						PASS	.						76	88	84					18																	60384475		2032	4181	6213	SO:0001583	missense	23239	exon1			GCTGCCTCATCCG	AB011178	CCDS45881.1, CCDS45881.2	18q21.32	2013-01-11	2009-05-26	2009-05-26	ENSG00000081913	ENSG00000081913		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent", "Pleckstrin homology (PH) domain containing"	20610	protein-coding gene	gene with protein product		609396	"pleckstrin homology domain containing, family E (with leucine rich repeats) member 1", "PH domain and leucine rich repeat protein phosphatase"	PLEKHE1, PHLPP		10570941, 15808505	Standard	NM_194449		Approved	KIAA0606, SCOP	uc021ule.1	O60346	OTTHUMG00000150629	ENST00000262719.5:c.1559T>A	chr18.hg19:g.60384475T>A	ENSP00000262719:p.Leu520His	80.0	0.0	.		46.0	16.0	.	NM_194449	A1A4F5|Q641Q7|Q6P4C4|Q6PJI6|Q86TN6|Q96FK2|Q9NUY1	Missense_Mutation	SNP	ENST00000262719.5	hg19	CCDS45881.2	.	.	.	.	.	.	.	.	.	.	T	21.9	4.221833	0.79464	.	.	ENSG00000081913	ENST00000400316;ENST00000262719	T;T	0.35605	1.52;1.3	3.91	3.91	0.45181	.	.	.	.	.	T	0.49932	0.1586	L	0.43923	1.385	0.45272	D	0.998273	D	0.89917	1.0	D	0.87578	0.998	T	0.51498	-0.8698	9	0.66056	D	0.02	-10.6803	11.9254	0.52817	0.0:0.0:0.0:1.0	.	520	O60346	PHLP1_HUMAN	H	8;520	ENSP00000383170:L8H;ENSP00000262719:L520H	ENSP00000262719:L520H	L	+	2	0	PHLPP1	58535455	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.650000	0.74368	1.653000	0.50694	0.454000	0.30748	CTC	.	.	.	none		0.537	PHLPP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319249.2	NM_194449		A	60384475	T	A	60384475	3	1	86	1	0	0	0	0	1	0	0	0	11861	1551	54	5	1561	5	PHLPP1	18	60384475	Missense_Mutation	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	47328672	60384475	17692773	81	5572											
FEM1A	55527	hgsc.bcm.edu	37	chr19	4792820	4792820	+	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	aaacgagatctgcttggggcCcttaaacactggaggcgggc	10	7	14	10	2	1	1	0	0	1	1	1	3	1	2	1	5	3	1	1	5	3	2			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:4792820C>A	ENST00000269856.3	+	1	1093	c.954C>A	c.(952-954)gcC>gcA	p.A318A	AC005523.2_ENST00000601192.1_RNA|AC005523.2_ENST00000596170.1_RNA|AC005523.3_ENST00000598782.1_lincRNA	NM_018708.2	NP_061178.1	Q9BSK4	FEM1A_HUMAN	fem-1 homolog a (C. elegans)	318					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)		TGCTTGGGGCCCTTAAACACT	0.597																																					p.A318A		Atlas-SNP	.											.	FEM1A	41	.	0			c.C954A						PASS	.						47	51	50					19																	4792820		2203	4299	6502	SO:0001819	synonymous_variant	55527	exon1			TGGGGCCCTTAAA	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.954C>A	chr19.hg19:g.4792820C>A		159.0	0.0	.		108.0	32.0	.	NM_018708	B2RDI3|Q711P8|Q9NPN7|Q9NPW8	Silent	SNP	ENST00000269856.3	hg19	CCDS12135.1																																																																																			.	.	.	none		0.597	FEM1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459000.1			A	4792820	C	A	4792820	2	1	86	1	0	0	0	0	0	0	0	1	5816	610	22	4		4	FEM1A	19	4792820	Silent	SNP	C	TCGA-B1-A656-01A-11D-A31X-10		4792820	54336163	82	5573											
ZNF558	148156	hgsc.bcm.edu	37	chr19	8922694	8922694	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttcgtgctgaagactttaaAacactgattacattcattga	13	15	6	7	1	1	4	1	3	0	1	2	4	1	4	0	0	3	1	0	0	4	6			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:8922694A>G	ENST00000601372.1	-	10	1183	c.472T>C	c.(472-474)Ttt>Ctt	p.F158L	ZNF558_ENST00000301475.1_Missense_Mutation_p.F158L|ZNF558_ENST00000444186.2_Missense_Mutation_p.F87L			Q96NG5	ZN558_HUMAN	zinc finger protein 558	158					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	15						AAGACTTTAAAACACTGATTA	0.338																																					p.F158L		Atlas-SNP	.											.	ZNF558	43	.	0			c.T472C						PASS	.						42	38	40					19																	8922694		2203	4300	6503	SO:0001583	missense	148156	exon6			CTTTAAAACACTG	AK055494	CCDS12208.1	19p13.2	2013-09-20			ENSG00000167785	ENSG00000167785		"Zinc fingers, C2H2-type", "-"	26422	protein-coding gene	gene with protein product							Standard	NM_144693		Approved	FLJ30932	uc002mkn.1	Q96NG5	OTTHUMG00000182196	ENST00000601372.1:c.472T>C	chr19.hg19:g.8922694A>G	ENSP00000471277:p.Phe158Leu	84.0	0.0	.		72.0	9.0	.	NM_144693	A8K5F0|B7Z798	Missense_Mutation	SNP	ENST00000601372.1	hg19	CCDS12208.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.492197	0.84962	.	.	ENSG00000167785	ENST00000301475;ENST00000444186	T;T	0.07216	3.21;3.21	5.07	4.0	0.46444	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.44688	D	0.000434	T	0.04137	0.0115	N	0.12182	0.205	0.34332	D	0.687801	P	0.39250	0.665	B	0.30716	0.119	T	0.30208	-0.9986	10	0.72032	D	0.01	-19.1944	8.9778	0.35946	0.7058:0.2942:0.0:0.0	.	158	Q96NG5	ZN558_HUMAN	L	158;87	ENSP00000301475:F158L;ENSP00000410703:F87L	ENSP00000301475:F158L	F	-	1	0	ZNF558	8783694	0.975000	0.34042	0.999000	0.59377	0.988000	0.76386	1.844000	0.39269	2.128000	0.65567	0.482000	0.46254	TTT	.	.	.	none		0.338	ZNF558-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459955.2	NM_144693		G	8922694	A	G	8922694	3	3	86	1	0	0	0	0	1	0	0	0	18001	14	1	3	740	3	ZNF558	19	8922694	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	4129874	8922694	50206289	83	5574											
ZNF426	79088	hgsc.bcm.edu	37	chr19	9639297	9639297	+	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	cacattgtttacactcatagGgtttttctccagtgtggatt	8	17	8	8	0	2	0	1	0	1	0	3	1	2	1	1	2	1	2	1	2	2	7			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:9639297G>A	ENST00000535489.1	-	6	1760	c.1424C>T	c.(1423-1425)cCc>cTc	p.P475L	ZNF426_ENST00000593003.1_Missense_Mutation_p.P437L|ZNF426_ENST00000253115.2_Missense_Mutation_p.P475L			Q9BUY5	ZN426_HUMAN	zinc finger protein 426	475					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20						ACACTCATAGGGTTTTTCTCC	0.428																																					p.P475L		Atlas-SNP	.											.	ZNF426	56	.	0			c.C1424T						PASS	.						95	93	94					19																	9639297		2203	4300	6503	SO:0001583	missense	79088	exon8			TCATAGGGTTTTT	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.1424C>T	chr19.hg19:g.9639297G>A	ENSP00000439017:p.Pro475Leu	147.0	0.0	.		114.0	29.0	.	NM_024106	B3KTL2	Missense_Mutation	SNP	ENST00000535489.1	hg19	CCDS12215.1	.	.	.	.	.	.	.	.	.	.	G	17.19	3.326242	0.60743	.	.	ENSG00000130818	ENST00000545189;ENST00000253115;ENST00000535489	T;T	0.17054	2.3;2.3	1.52	1.52	0.23074	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36717	0.0977	M	0.74546	2.27	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77557	0.99;0.99	T	0.24012	-1.0172	9	0.72032	D	0.01	.	8.9649	0.35869	0.0:0.0:1.0:0.0	.	462;475	Q59EH4;Q9BUY5	.;ZN426_HUMAN	L	462;475;475	ENSP00000253115:P475L;ENSP00000439017:P475L	ENSP00000253115:P475L	P	-	2	0	ZNF426	9500297	0.426000	0.25506	0.005000	0.12908	0.100000	0.18952	1.495000	0.35627	1.133000	0.42147	0.563000	0.77884	CCC	.	.	.	none		0.428	ZNF426-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449905.1	NM_024106		A	9639297	G	A	9639297	3	1	86	1	0	0	0	0	1	0	0	0	17912	1232	43	2	244	2	ZNF426	19	9639297	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	716603	9639297	49489686	84	5575											
ICAM3	3385	hgsc.bcm.edu	37	chr19	10444569	10444569	+	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	ggttcttcccccattgcttcTgtcggctgcatagacgtgag	5	13	11	12	2	2	2	0	1	2	1	4	2	3	2	2	2	2	4	2	2	1	5	rs369252388		TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:10444569T>A	ENST00000160262.5	-	7	1816	c.1608A>T	c.(1606-1608)acA>acT	p.T536T	RAVER1_ENST00000293677.6_5'Flank|ICAM3_ENST00000589261.1_Silent_p.T459T	NM_002162.3	NP_002153.2	P32942	ICAM3_HUMAN	intercellular adhesion molecule 3	536					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)			CCATTGCTTCTGTCGGCTGCA	0.567																																					p.T536T		Atlas-SNP	.											.	ICAM3	29	.	0			c.A1608T						PASS	.	T		0,4406		0,0,2203	180	166	171		1608	-8.7	0	19		171	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ICAM3	NM_002162.3		0,1,6502	AA,AT,TT		0.0116,0.0,0.0077		536/548	10444569	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	3385	exon7			TGCTTCTGTCGGC		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.1608A>T	chr19.hg19:g.10444569T>A		162.0	0.0	.		121.0	24.0	.	NM_002162	Q6PD68	Silent	SNP	ENST00000160262.5	hg19	CCDS12235.1																																																																																			.	.	.	weak		0.567	ICAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451234.1			A	10444569	T	A	10444569	2	1	86	1	0	0	0	0	0	0	0	1	7488	1567	55	5		5	ICAM3	19	10444569	Silent	SNP	T	TCGA-B1-A656-01A-11D-A31X-10	805272	10444569	48684414	85	5576											
CYP4F3	4051	hgsc.bcm.edu	37	chr19	15752256	15752256	+	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	tgagcctgtcctcgctgggcCtttggccaatggcagcatcc	5	10	12	14	1	0	1	0	1	0	0	3	1	2	1	5	3	2	3	5	3	1	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:15752256C>G	ENST00000221307.8	+	2	78	c.31C>G	c.(31-33)Ctt>Gtt	p.L11V	CYP4F3_ENST00000585846.1_Missense_Mutation_p.L11V|CYP4F3_ENST00000591058.1_Missense_Mutation_p.L11V|CYP4F3_ENST00000586182.2_Missense_Mutation_p.L11V	NM_000896.2	NP_000887.2	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 3	11					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						CTCGCTGGGCCTTTGGCCAAT	0.652																																					p.L11V		Atlas-SNP	.											.	CYP4F3	69	.	0			c.C31G						PASS	.						56	56	56					19																	15752256		2203	4300	6503	SO:0001583	missense	4051	exon2			CTGGGCCTTTGGC	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.31C>G	chr19.hg19:g.15752256C>G	ENSP00000221307:p.Leu11Val	84.0	0.0	.		64.0	16.0	.	NM_001199209	B7Z8Z3|O60634|Q5U740	Missense_Mutation	SNP	ENST00000221307.8	hg19	CCDS12332.1	.	.	.	.	.	.	.	.	.	.	.	12.16	1.854157	0.32791	.	.	ENSG00000186529	ENST00000221307	D	0.93426	-3.22	3.73	2.65	0.31530	.	0.298234	0.22742	U	0.056184	D	0.92450	0.7603	M	0.73598	2.24	0.09310	N	1	P;P	0.38420	0.63;0.63	B;B	0.43082	0.317;0.407	D	0.85130	0.0974	10	0.42905	T	0.14	.	8.5276	0.33315	0.2301:0.7698:0.0:0.0	.	11;11	B7Z8Z3;Q08477	.;CP4F3_HUMAN	V	11	ENSP00000221307:L11V	ENSP00000221307:L11V	L	+	1	0	CYP4F3	15613256	0.000000	0.05858	0.002000	0.10522	0.028000	0.11728	-0.157000	0.10085	0.504000	0.28082	0.411000	0.27672	CTT	.	.	.	none		0.652	CYP4F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460819.3	NM_000896		G	15752256	C	G	15752256	3	3	86	1	0	0	0	0	1	0	0	0	4192	681	24	4	33	4	CYP4F3	19	15752256	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	5307687	15752256	43376727	86	5577											
ZNF506	440515	hgsc.bcm.edu	37	chr19	19905760	19905760	+	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	ccacattcctcacatttgtaGggtttctctccagtatgaat	9	15	6	11	0	2	1	1	1	1	0	5	1	4	1	3	1	0	3	3	1	3	5			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:19905760G>C	ENST00000540806.2	-	4	1024	c.936C>G	c.(934-936)ccC>ccG	p.P312P	ZNF506_ENST00000450683.2_Silent_p.P280P|CTC-559E9.6_ENST00000589657.1_RNA|CTC-559E9.4_ENST00000590274.1_lincRNA|CTC-559E9.6_ENST00000591884.1_RNA|ZNF506_ENST00000443905.2_Silent_p.P312P|ZNF506_ENST00000587461.1_Intron			Q5JVG8	ZN506_HUMAN	zinc finger protein 506	312					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						CACATTTGTAGGGTTTCTCTC	0.373																																					p.P312P		Atlas-SNP	.											.	ZNF506	36	.	0			c.C936G						PASS	.						55	59	57					19																	19905760		2197	4300	6497	SO:0001819	synonymous_variant	440515	exon4			TTTGTAGGGTTTC	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.936C>G	chr19.hg19:g.19905760G>C		36.0	0.0	.		39.0	10.0	.	NM_001099269	B3KTH6	Silent	SNP	ENST00000540806.2	hg19	CCDS42531.1																																																																																			.	.	.	none		0.373	ZNF506-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460794.1	XM_036218		C	19905760	G	C	19905760	2	2	86	1	0	0	0	0	0	0	0	1	17964	987	35	4		4	ZNF506	19	19905760	Silent	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	4153504	19905760	39223223	87	5578											
CYP2F1	1572	hgsc.bcm.edu	37	chr19	41627458	41627458	+	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	gcttcgactatgatgatgagCgtctgctcaccattatccgc	8	12	9	12	3	2	3	1	3	1	0	4	4	3	3	2	0	2	2	2	0	2	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:41627458C>T	ENST00000331105.2	+	5	652	c.580C>T	c.(580-582)Cgt>Tgt	p.R194C		NM_000774.3	NP_000765.2	P24903	CP2F1_HUMAN	cytochrome P450, family 2, subfamily F, polypeptide 1	194					naphthalene metabolic process (GO:0018931)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|trichloroethylene metabolic process (GO:0018979)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(11)|ovary(2)|skin(2)	29						TGATGATGAGCGTCTGCTCAC	0.562																																					p.R194C		Atlas-SNP	.											.	CYP2F1	60	.	0			c.C580T						PASS	.						113	115	115					19																	41627458		2181	4299	6480	SO:0001583	missense	1572	exon5			GATGAGCGTCTGC	J02906	CCDS12572.1	19q13.1-q13.2	2008-02-05	2003-01-14		ENSG00000197446	ENSG00000197446		"Cytochrome P450s"	2632	protein-coding gene	gene with protein product		124070	"cytochrome P450, subfamily IIF, polypeptide 1"	CYP2F			Standard	NM_000774		Approved		uc002opu.1	P24903	OTTHUMG00000167412	ENST00000331105.2:c.580C>T	chr19.hg19:g.41627458C>T	ENSP00000333534:p.Arg194Cys	69.0	0.0	.		43.0	13.0	.	NM_000774	A7KAU6|A7KAU7|A7KAU8|A7KAU9|A7KAV0|Q32MN5|Q8WWJ2	Missense_Mutation	SNP	ENST00000331105.2	hg19	CCDS12572.1	.	.	.	.	.	.	.	.	.	.	c	10.84	1.464169	0.26335	.	.	ENSG00000197446	ENST00000331105	T	0.69435	-0.4	2.87	2.87	0.33458	.	0.714608	0.13306	U	0.397870	T	0.79052	0.4381	M	0.79475	2.455	0.34749	D	0.731557	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.983	T	0.82147	-0.0601	10	0.72032	D	0.01	.	7.7914	0.29123	0.0:0.7393:0.2607:0.0	.	194;194	Q32MN5;P24903	.;CP2F1_HUMAN	C	194	ENSP00000333534:R194C	ENSP00000333534:R194C	R	+	1	0	CYP2F1	46319298	0.000000	0.05858	0.113000	0.21522	0.208000	0.24298	-0.348000	0.07740	1.461000	0.47929	0.064000	0.15345	CGT	.	.	.	none		0.562	CYP2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394527.2			T	41627458	C	T	41627458	3	4	86	1	0	0	0	0	1	0	0	0	4173	768	27	1	594	1	CYP2F1	19	41627458	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	21721698	41627458	17501525	88	5579											
PSG9	5678	hgsc.bcm.edu	37	chr19	43772079	43772079	+	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	aatatactgtttctcttccaCtgtatgcaggcccatatata	11	15	5	10	0	1	0	0	0	1	0	3	0	2	0	2	1	2	3	2	1	7	8			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:43772079C>T	ENST00000270077.3	-	2	383	c.287G>A	c.(286-288)aGt>aAt	p.S96N	PSG9_ENST00000418820.2_Missense_Mutation_p.S96N|PSG9_ENST00000593948.1_Missense_Mutation_p.S96N|PSG9_ENST00000443718.3_Missense_Mutation_p.S96N|PSG9_ENST00000291752.5_Missense_Mutation_p.S96N|PSG9_ENST00000596730.1_Missense_Mutation_p.S96N|PSG9_ENST00000244293.7_Missense_Mutation_p.S96N	NM_002784.3	NP_002775.3	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	96	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Prostate(69;0.00682)				TTCTCTTCCACTGTATGCAGG	0.428																																					p.S96N		Atlas-SNP	.											.	PSG9	77	.	0			c.G287A						PASS	.						250	239	243					19																	43772079		2203	4300	6503	SO:0001583	missense	5678	exon2			CTTCCACTGTATG	M34481	CCDS12618.1	19q13.2	2013-01-29			ENSG00000183668	ENSG00000183668		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9526	protein-coding gene	gene with protein product		176398		PSG11		7806221	Standard	XM_005259076		Approved	PSGII	uc002owd.4	Q00887	OTTHUMG00000182826	ENST00000270077.3:c.287G>A	chr19.hg19:g.43772079C>T	ENSP00000270077:p.Ser96Asn	171.0	0.0	.		149.0	44.0	.	NM_002784	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000270077.3	hg19	CCDS12618.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	10.79|10.79	1.448341|1.448341	0.26074|0.26074	.|.	.|.	ENSG00000183668|ENSG00000183668	ENST00000270077;ENST00000291752;ENST00000443718;ENST00000435220;ENST00000244293|ENST00000418820	T;T;T;T|.	0.69175|.	-0.38;-0.38;-0.38;-0.38|.	1.56|1.56	-1.3|-1.3	0.09259|0.09259	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);|.	.|.	.|.	.|.	.|.	T|T	0.65249|0.65249	0.2673|0.2673	M|M	0.93507|0.93507	3.425|3.425	0.09310|0.09310	N|N	1|1	P;P;D;P;B;B|.	0.53885|.	0.729;0.904;0.963;0.872;0.056;0.184|.	P;D;D;P;B;B|.	0.67231|.	0.826;0.921;0.95;0.686;0.272;0.393|.	T|T	0.59873|0.59873	-0.7372|-0.7372	9|5	0.54805|.	T|.	0.06|.	.|.	7.098|7.098	0.25321|0.25321	0.0:0.4456:0.5544:0.0|0.0:0.4456:0.5544:0.0	.|.	96;45;96;96;96;96|.	E7EW65;Q15225;Q15227;G3XAA7;Q6LEU7;Q00887|.	.;.;.;.;.;PSG9_HUMAN|.	N|M	96;96;96;57;96|83	ENSP00000270077:S96N;ENSP00000291752:S96N;ENSP00000396753:S96N;ENSP00000244293:S96N|.	ENSP00000244293:S96N|.	S|V	-|-	2|1	0|0	PSG9|PSG9	48463919|48463919	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.052000|0.052000	0.14988|0.14988	-0.107000|-0.107000	0.10873|0.10873	-0.216000|-0.216000	0.10048|0.10048	-0.876000|-0.876000	0.02978|0.02978	AGT|GTG	.	.	.	none		0.428	PSG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323065.1	NM_002784		T	43772079	C	T	43772079	3	4	86	1	0	0	0	0	1	0	0	0	12672	565	20	2	1013	2	PSG9	19	43772079	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	2144621	43772079	15356904	89	5580											
ZNF836	162962	hgsc.bcm.edu	37	chr19	52660313	52660313	+	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	ccctaatgtgtgttttctcaAgttgggtgggtaatgacagc	8	14	12	7	0	1	1	1	1	1	0	2	1	1	1	1	2	1	3	1	2	3	5	rs186568049		TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:52660313A>T	ENST00000322146.8	-	5	1144	c.623T>A	c.(622-624)cTt>cAt	p.L208H	CTC-471J1.8_ENST00000594362.1_RNA|ZNF836_ENST00000597252.1_Missense_Mutation_p.L208H	NM_001102657.1	NP_001096127.1	Q6ZNA1	ZN836_HUMAN	zinc finger protein 836	208					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|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						TGTTTTCTCAAGTTGGGTGGG	0.373																																					p.L208H		Atlas-SNP	.											.	ZNF836	158	.	0			c.T623A						PASS	.						66	64	65					19																	52660313		1911	4155	6066	SO:0001583	missense	162962	exon5			TTCTCAAGTTGGG	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.623T>A	chr19.hg19:g.52660313A>T	ENSP00000325038:p.Leu208His	180.0	0.0	.		177.0	48.0	.	NM_001102657		Missense_Mutation	SNP	ENST00000322146.8	hg19	CCDS46162.1	.	.	.	.	.	.	.	.	.	.	A	0.030	-1.337491	0.01287	.	.	ENSG00000196267	ENST00000322146;ENST00000396443	T	0.06371	3.31	1.8	-0.761	0.11038	.	.	.	.	.	T	0.02380	0.0073	N	0.08118	0	0.09310	N	1	P	0.50943	0.94	B	0.43783	0.431	T	0.13737	-1.0498	9	0.02654	T	1	.	2.5139	0.04663	0.2469:0.1649:0.0:0.5882	.	208	Q6ZNA1	ZN836_HUMAN	H	208;6	ENSP00000325038:L208H	ENSP00000325038:L208H	L	-	2	0	ZNF836	57352125	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	0.440000	0.21592	-0.496000	0.06650	-1.328000	0.01277	CTT	.	A|1.000;C|0.000	.	alt		0.373	ZNF836-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462456.1	NM_001102657		T	52660313	A	T	52660313	3	4	86	1	0	0	0	0	1	0	0	0	18199	72	3	5	2189	5	ZNF836	19	52660313	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	8888234	52660313	6468670	90	5581											
ZIM2	23619	hgsc.bcm.edu	37	chr19	57286732	57286732	+	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	tgccttcctggggatcctttCctagaggatcctttgattgt	5	16	10	10	0	0	2	0	1	0	1	4	4	4	4	5	3	1	0	5	3	1	5			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr19:57286732C>T	ENST00000391708.3	-	12	1450	c.908G>A	c.(907-909)gGa>gAa	p.G303E	ZIM2_ENST00000601070.1_Missense_Mutation_p.G303E|AC006115.3_ENST00000594400.1_RNA|ZIM2_ENST00000599935.1_Missense_Mutation_p.G303E|ZIM2_ENST00000221722.5_Missense_Mutation_p.G303E|ZIM2_ENST00000593711.1_Missense_Mutation_p.G303E|AC006115.3_ENST00000597946.1_RNA|AC006115.3_ENST00000595954.1_RNA	NM_001146326.1|NM_001146327.1	NP_001139798.1|NP_001139799.1	Q9NZV7	ZIM2_HUMAN	zinc finger, imprinted 2	303					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			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)		GGGATCCTTTCCTAGAGGATC	0.453																																					p.G303E		Atlas-SNP	.											.	ZIM2	511	.	0			c.G908A						PASS	.						119	114	116					19																	57286732		2203	4300	6503	SO:0001583	missense	23619	exon11			TCCTTTCCTAGAG	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.908G>A	chr19.hg19:g.57286732C>T	ENSP00000375589:p.Gly303Glu	112.0	0.0	.		88.0	21.0	.	NM_015363	Q2M3K1	Missense_Mutation	SNP	ENST00000391708.3	hg19	CCDS33123.1	.	.	.	.	.	.	.	.	.	.	C	15.06	2.720643	0.48728	.	.	ENSG00000198300	ENST00000391708;ENST00000221722	T;T	0.04317	3.65;3.65	3.89	0.45	0.16624	.	.	.	.	.	T	0.03220	0.0094	N	0.24115	0.695	.	.	.	B	0.21606	0.058	B	0.20184	0.028	T	0.37911	-0.9685	8	0.49607	T	0.09	.	2.8917	0.05678	0.3745:0.3962:0.0:0.2293	.	303	Q9NZV7	ZIM2_HUMAN	E	303	ENSP00000375589:G303E;ENSP00000221722:G303E	ENSP00000221722:G303E	G	-	2	0	ZIM2	61978544	0.000000	0.05858	0.131000	0.22000	0.731000	0.41821	-0.337000	0.07852	0.176000	0.19873	0.655000	0.94253	GGA	.	.	.	none		0.453	ZIM2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416094.2			T	57286732	C	T	57286732	3	4	86	1	0	0	0	0	1	0	0	0	17696	855	30	2	679	2	ZIM2	19	57286732	Missense_Mutation	SNP	C	TCGA-B1-A656-01A-11D-A31X-10	4626419	57286732	1842251	91	5582											
TIAM1	7074	hgsc.bcm.edu	37	chr21	32639267	32639267	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ataaaactcgtgctctacatGttgactttctgcgtttccca	9	15	6	11	2	2	1	0	1	2	0	4	1	3	1	1	0	4	3	1	0	3	5			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chr21:32639267G>A	ENST00000286827.3	-	5	493	c.22C>T	c.(22-24)Cat>Tat	p.H8Y	TIAM1_ENST00000541036.1_Missense_Mutation_p.H8Y|TIAM1_ENST00000469412.1_Intron	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	8					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						TGCTCTACATGTTGACTTTCT	0.527																																					p.H8Y		Atlas-SNP	.											.	TIAM1	522	.	0			c.C22T						PASS	.						54	56	55					21																	32639267		2203	4300	6503	SO:0001583	missense	7074	exon5			CTACATGTTGACT		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.22C>T	chr21.hg19:g.32639267G>A	ENSP00000286827:p.His8Tyr	50.0	0.0	.		24.0	7.0	.	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	hg19	CCDS13609.1	.	.	.	.	.	.	.	.	.	.	G	13.84	2.358038	0.41801	.	.	ENSG00000156299	ENST00000286827;ENST00000541036;ENST00000455508	T;T	0.39056	1.1;1.1	5.08	2.64	0.31445	.	0.211502	0.47852	D	0.000203	T	0.23611	0.0571	N	0.08118	0	0.21147	N	0.999772	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.22521	-1.0214	10	0.87932	D	0	.	11.7355	0.51763	0.0:0.0:0.3141:0.6859	.	8;8;8	F5GZ53;B7ZLR6;Q13009	.;.;TIAM1_HUMAN	Y	8	ENSP00000286827:H8Y;ENSP00000441570:H8Y	ENSP00000286827:H8Y	H	-	1	0	TIAM1	31561138	1.000000	0.71417	0.978000	0.43139	0.974000	0.67602	5.772000	0.68889	0.251000	0.21505	0.460000	0.39030	CAT	.	.	.	none		0.527	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		A	32639267	G	A	32639267	3	1	86	1	0	0	0	0	1	0	0	0	15902	1377	48	2	4853	2	TIAM1	21	32639267	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10		32639267	15490628	92	5583											
ASMTL	8623	hgsc.bcm.edu	37	chrX	1540611	1540611	+	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	tgctggtttgttccctctcgGatggcaaactccaggtatgt	6	14	11	10	1	1	0	0	0	1	0	4	1	3	1	2	4	2	5	2	4	2	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chrX:1540611G>C	ENST00000381317.3	-	9	1217	c.1185C>G	c.(1183-1185)atC>atG	p.I395M	ASMTL_ENST00000381333.4_Missense_Mutation_p.I379M|ASMTL_ENST00000416733.2_Missense_Mutation_p.I319M|ASMTL_ENST00000534940.1_Missense_Mutation_p.I337M	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	395	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)				TTCCCTCTCGGATGGCAAACT	0.537																																					p.I395M		Atlas-SNP	.											.	ASMTL	56	.	0			c.C1185G						PASS	.						267	279	275					X																	1540611		2010	4172	6182	SO:0001583	missense	8623	exon9			CTCTCGGATGGCA	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.1185C>G	chrX.hg19:g.1540611G>C	ENSP00000370718:p.Ile395Met	561.0	1.0	.		288.0	119.0	.	NM_004192	B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	Missense_Mutation	SNP	ENST00000381317.3	hg19	CCDS43917.1	.	.	.	.	.	.	.	.	.	.	g	11.19	1.566957	0.28003	.	.	ENSG00000169093	ENST00000416733;ENST00000534940;ENST00000381333;ENST00000381317	T;T;T;T	0.26223	1.75;1.75;1.75;1.75	1.58	-3.16	0.05217	O-methyltransferase, family 2 (1);	0.083070	0.47093	U	0.000252	T	0.24275	0.0588	L	0.38175	1.15	0.09310	N	1	D;D;D	0.60575	0.979;0.988;0.979	P;P;P	0.55713	0.782;0.666;0.582	T	0.14643	-1.0465	10	0.87932	D	0	.	5.5218	0.16938	0.2398:0.184:0.5763:0.0	.	319;379;395	E7ER97;O95671-2;O95671	.;.;ASML_HUMAN	M	319;337;379;395	ENSP00000410578:I319M;ENSP00000446410:I337M;ENSP00000370734:I379M;ENSP00000370718:I395M	ENSP00000370718:I395M	I	-	3	3	ASMTL	1500611	0.986000	0.35501	0.006000	0.13384	0.132000	0.20833	-0.099000	0.11007	-0.451000	0.07097	0.100000	0.15512	ATC	.	.	.	alt		0.537	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192		C	1540611	G	C	1540611	3	2	86	1	0	0	0	0	1	0	0	0	1046	1164	41	4	700	4	ASMTL	23	1540611	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10		1540611	153729949	93	5584											
ACOT9	23597	hgsc.bcm.edu	37	chrX	23723161	23723161	+	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	tcaacaggtttctgaaacatGatgtcatctactgctaccac	12	12	6	11	0	4	2	2	2	2	0	4	2	4	2	1	1	5	2	1	1	4	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chrX:23723161G>A	ENST00000336430.7	-	13	1160	c.1029C>T	c.(1027-1029)atC>atT	p.I343I	ACOT9_ENST00000379295.1_Silent_p.I283I|ACOT9_ENST00000379303.5_Silent_p.I352I	NM_001033583.2	NP_001028755.2	Q9Y305	ACOT9_HUMAN	acyl-CoA thioesterase 9	343					acyl-CoA metabolic process (GO:0006637)	mitochondrion (GO:0005739)	acetyl-CoA hydrolase activity (GO:0003986)|carboxylic ester hydrolase activity (GO:0052689)			breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(4)|pancreas(1)|skin(1)	15						TCTGAAACATGATGTCATCTA	0.403																																					p.I352I		Atlas-SNP	.											.	ACOT9	33	.	0			c.C1056T						PASS	.						120	109	113					X																	23723161		2203	4300	6503	SO:0001819	synonymous_variant	23597	exon14			AAACATGATGTCA	AF132950	CCDS35216.1, CCDS43924.1	Xp22.11	2008-02-05			ENSG00000123130	ENSG00000123130		"Acyl CoA thioesterases"	17152	protein-coding gene	gene with protein product		300862				10383425, 10810093, 16103133, 16940157	Standard	XM_005274471		Approved	CGI-16, MT-ACT48, ACATE2	uc004dao.3	Q9Y305	OTTHUMG00000021257	ENST00000336430.7:c.1029C>T	chrX.hg19:g.23723161G>A		166.0	0.0	.		161.0	100.0	.	NM_001037171	B3KNC9|B7ZM94	Silent	SNP	ENST00000336430.7	hg19	CCDS35216.1																																																																																			.	.	.	none		0.403	ACOT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056065.1	NM_012332		A	23723161	G	A	23723161	2	1	86	1	0	0	0	0	0	0	0	1	157	1280	45	2		2	ACOT9	23	23723161	Silent	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	22182550	23723161	131547399	94	5585											
AR	367	hgsc.bcm.edu	37	chrX	66765167	66765167	+	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	tttgctgctgctgcagcagcAgcagcagcagcagcagcagc	9	6	13	13	0	0	0	0	0	0	0	0	0	0	0	0	0	13	12	0	0	0	1			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chrX:66765167A>T	ENST00000374690.3	+	1	703	c.179A>T	c.(178-180)cAg>cTg	p.Q60L	AR_ENST00000396044.3_Missense_Mutation_p.Q60L|AR_ENST00000504326.1_Missense_Mutation_p.Q60L|AR_ENST00000513847.1_3'UTR	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	60	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)	CTgcagcagcagcagcagcag	0.677									Androgen Insensitivity Syndrome																												p.Q60L		Atlas-SNP	.											.	AR	249	.	0			c.A179T	GRCh37	CI994028	AR	I		PASS	.						6	9	8					X																	66765167		1971	3901	5872	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	AGCAGCAGCAGCA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.179A>T	chrX.hg19:g.66765167A>T	ENSP00000363822:p.Gln60Leu	72.0	0.0	.		77.0	7.0	.	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	11.27	1.588228	0.28357	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.57436	0.4;0.4;0.4	.	.	.	.	1.241110	0.06210	N	0.684797	T	0.29288	0.0729	N	0.19112	0.55	0.09310	N	0.999999	P;P;.	0.36048	0.534;0.534;.	B;B;.	0.29862	0.08;0.108;.	T	0.11494	-1.0585	8	0.12103	T	0.63	.	.	.	.	.	60;60;58	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	L	60	ENSP00000363822:Q60L;ENSP00000421155:Q60L;ENSP00000379359:Q60L	ENSP00000363822:Q60L	Q	+	2	0	AR	66681892	0.997000	0.39634	0.860000	0.33809	0.513000	0.34164	1.220000	0.32491	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	66765167	A	T	66765167	3	4	86	1	0	0	0	0	1	0	0	0	836	188	7	5	181	5	AR	23	66765167	Missense_Mutation	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	43042006	66765167	88505393	95	5586											
ZMAT1	84460	hgsc.bcm.edu	37	chrX	101152941	101152941	+	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	cccacatagtgagactgagcAataagtggagagctaaacat	16	7	10	8	0	0	3	0	2	0	2	0	5	0	3	1	1	3	2	1	1	5	3			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chrX:101152941A>T	ENST00000372782.3	-	5	452	c.405T>A	c.(403-405)atT>atA	p.I135I	ZMAT1_ENST00000458570.1_5'UTR|ZMAT1_ENST00000540921.1_Silent_p.I135I	NM_001011657.3	NP_001011657	Q5H9K5	ZMAT1_HUMAN	zinc finger, matrin-type 1	135						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22						GAGACTGAGCAATAAGTGGAG	0.403																																					p.I135I		Atlas-SNP	.											.	ZMAT1	143	.	0			c.T405A						PASS	.						157	124	135					X																	101152941		2203	4300	6503	SO:0001819	synonymous_variant	84460	exon5			CTGAGCAATAAGT	Z69304	CCDS35348.1	Xq21	2012-10-05	2010-09-15		ENSG00000166432	ENSG00000166432		"Zinc fingers, matrin-type"	29377	protein-coding gene	gene with protein product							Standard	NM_001011657		Approved	KIAA1789	uc011mrl.2	Q5H9K5	OTTHUMG00000022044	ENST00000372782.3:c.405T>A	chrX.hg19:g.101152941A>T		86.0	0.0	.		76.0	36.0	.	NM_001011657	Q8NDS3|Q96JN6	Silent	SNP	ENST00000372782.3	hg19	CCDS35348.1																																																																																			.	.	.	none		0.403	ZMAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057598.1			T	101152941	A	T	101152941	2	4	86	1	0	0	0	0	0	0	0	1	17703	126	5	5		5	ZMAT1	23	101152941	Silent	SNP	A	TCGA-B1-A656-01A-11D-A31X-10	34387774	101152941	54117619	96	5587											
PNCK	139728	hgsc.bcm.edu	37	chrX	152937048	152937048	+	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	cggtgcctagcatgttcccaGcctggattttggagagtcca	7	11	12	11	1	0	1	0	0	0	1	2	3	2	2	4	3	3	2	4	3	1	4			TCGA-B1-A656-01A-11D-A31X-10	TCGA-B1-A656-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ac9225b-09f2-40d9-8d53-3287fa4779b7	1b3cf7d6-8f3d-472a-958f-0e800ef04ce3	g.chrX:152937048G>C	ENST00000370150.1	-	6	672	c.494C>G	c.(493-495)gCt>gGt	p.A165G	PNCK_ENST00000393831.2_Missense_Mutation_p.A165G|PNCK_ENST00000340888.3_Missense_Mutation_p.A165G|PNCK_ENST00000475172.1_5'UTR|PNCK_ENST00000370145.4_Missense_Mutation_p.A182G|PNCK_ENST00000447676.2_Missense_Mutation_p.A248G|PNCK_ENST00000370142.1_Missense_Mutation_p.A165G			Q6P2M8	KCC1B_HUMAN	pregnancy up-regulated nonubiquitous CaM kinase	165	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			breast(2)|lung(3)|skin(1)	6	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CATGTTCCCAGCCTGGATTTT	0.602																																					p.A248G		Atlas-SNP	.											.	PNCK	70	.	0			c.C743G						PASS	.						121	112	115					X																	152937048		2203	4300	6503	SO:0001583	missense	139728	exon6			TTCCCAGCCTGGA	BC033746	CCDS35503.2, CCDS48189.1	Xq28	2013-10-14	2013-10-14		ENSG00000130822	ENSG00000130822			13415	protein-coding gene	gene with protein product		300680	"pregnancy upregulated non-ubiquitously expressed CaM kinase", "pregnancy up-regulated non-ubiquitously expressed CaM kinase"			12477932	Standard	NM_001039582		Approved	MGC45419, CaMK1b	uc011myu.2	Q6P2M8	OTTHUMG00000024216	ENST00000370150.1:c.494C>G	chrX.hg19:g.152937048G>C	ENSP00000359169:p.Ala165Gly	101.0	0.0	.		66.0	39.0	.	NM_001039582	B4DJR8|B4E1A6|B7WPG0|D3DWU7|Q8N4R0	Missense_Mutation	SNP	ENST00000370150.1	hg19		.	.	.	.	.	.	.	.	.	.	g	7.308	0.614372	0.14129	.	.	ENSG00000130822	ENST00000340888;ENST00000370150;ENST00000393831;ENST00000370142;ENST00000370145;ENST00000447676;ENST00000439087;ENST00000422811	T;T;T;T;T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17;-0.17;-0.17;-0.17;-0.17	4.91	3.95	0.45737	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.215813	0.29579	N	0.011742	T	0.32734	0.0839	N	0.01789	-0.72	0.28784	N	0.899677	B;B;B;B	0.28350	0.001;0.208;0.026;0.026	B;B;B;B	0.22152	0.01;0.038;0.022;0.022	T	0.31586	-0.9938	10	0.49607	T	0.09	-9.2523	10.6054	0.45392	0.0:0.0:0.689:0.311	.	192;248;182;165	B4DJG4;Q6P2M8-5;B4E1A6;Q6P2M8	.;.;.;KCC1B_HUMAN	G	165;165;165;165;182;248;165;165	ENSP00000340586:A165G;ENSP00000359169:A165G;ENSP00000377417:A165G;ENSP00000359161:A165G;ENSP00000359164:A182G;ENSP00000405950:A248G;ENSP00000415770:A165G;ENSP00000391772:A165G	ENSP00000340586:A165G	A	-	2	0	PNCK	152590242	0.291000	0.24352	0.998000	0.56505	0.864000	0.49448	3.237000	0.51344	2.005000	0.58758	0.529000	0.55759	GCT	.	.	.	none		0.602	PNCK-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000061044.2	NM_198452		C	152937048	G	C	152937048	3	2	86	1	0	0	0	0	1	0	0	0	12152	971	34	4	561	4	PNCK	23	152937048	Missense_Mutation	SNP	G	TCGA-B1-A656-01A-11D-A31X-10	51784107	152937048	2333512	97	5588											
AMY1A	276	hgsc.bcm.edu	37	chr1	104199090	104199090	+	Frame_Shift_Del	DEL	T	T	-																															gctcttgaatgtgagcgataTttagctcccaagggatttgg																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:104199090delT	ENST00000370083.4	+	2	358	c.138delT	c.(136-138)tatfs	p.Y46fs		NM_001008221.1|NM_004038.3	NP_001008222.1|NP_004029.2	P04745	AMY1_HUMAN	amylase, alpha 1A (salivary)	46					carbohydrate metabolic process (GO:0005975)|digestion (GO:0007586)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|metal ion binding (GO:0046872)						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)		GTGAGCGATATTTAGCTCCCA	0.413																																					p.Y46fs	Pancreas(131;743 2392 43382 44986)	Atlas-INDEL	.											.	AMY1C	11	.	0			c.137delA						PASS	.																																			SO:0001589	frameshift_variant	278	exon2			.		CCDS30782.1	1p21	2012-10-02	2007-05-03		ENSG00000237763	ENSG00000237763	3.2.1.1		474	protein-coding gene	gene with protein product		104700	"amylase, alpha 1A; salivary"	AMY1			Standard	XM_005270755		Approved		uc001duv.3	P04745	OTTHUMG00000011020	ENST00000370083.4:c.138delT	chr1.hg19:g.104199090delT	ENSP00000359100:p.Tyr46fs	774.0	0.0	0		648.0	55.0	0.0848765	NM_001008219	A6NJS5|A8K8H6|Q13763|Q5T083	Frame_Shift_Del	DEL	ENST00000370083.4	hg19	CCDS30782.1																																																																																			.	.	.	none		0.413	AMY1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030304.2	NM_001008221		-	104199090	T	-	104199090	7	5	87	1	0	1	0	1	0	0	0	0	591	1500	52	0	140	0	AMY1A	1	104199090	Frame_Shift_Del	DEL	T	TCGA-B1-A657-01A-11D-A31X-10		104199090	145051531	1	5589											
AMY1A	277	hgsc.bcm.edu	37	chr1	104238120	104238120	+	Frame_Shift_Del	DEL	C	C	-																															ccctccaaatcccttgggagCtaaatatcgctcacattcaa																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:104238120delC	ENST00000330330.5	-	2	436	c.142delG	c.(142-144)gctfs	p.A48fs	AMY1B_ENST00000370080.3_Frame_Shift_Del_p.A48fs|AMY1B_ENST00000464691.1_5'Flank	NM_001008218.1	NP_001008219.1	P04745	AMY1_HUMAN	amylase, alpha 1B (salivary)	48					carbohydrate metabolic process (GO:0005975)|digestion (GO:0007586)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|metal ion binding (GO:0046872)			large_intestine(1)|lung(1)	2		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)		CCCTTGGGAGCTAAATATCGC	0.408																																					p.A48fs		Atlas-INDEL	.											.	AMY1C	11	.	0			c.143delC						PASS	.						1	1	1					1																	104238120		4	8	12	SO:0001589	frameshift_variant	278	exon2			.		CCDS30783.1	1p21	2012-10-02	2007-05-03		ENSG00000174876	ENSG00000174876	3.2.1.1		475	protein-coding gene	gene with protein product		104701	"amylase, alpha 1B; salivary"	AMY1			Standard	XM_005270758		Approved			P04745	OTTHUMG00000011021	ENST00000330330.5:c.142delG	chr1.hg19:g.104238120delC	ENSP00000330484:p.Ala48fs	731.0	0.0	0		639.0	48.0	0.0751174	NM_001008219	A6NJS5|A8K8H6|Q13763|Q5T083	Frame_Shift_Del	DEL	ENST00000330330.5	hg19	CCDS30783.1																																																																																			.	.	.	none		0.408	AMY1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030309.1	NM_001008218		-	104238120	C	-	104238120	7	5	87	1	0	1	0	1	0	0	0	0	591	797	28	0	3009	0	AMY1A	1	104238120	Frame_Shift_Del	DEL	C	TCGA-B1-A657-01A-11D-A31X-10	39030	104238120	145012501	2	5590											
AMY1A	278	hgsc.bcm.edu	37	chr1	104293229	104293229	+	Frame_Shift_Del	DEL	T	T	-																															gctcttgaatgtgagcgataTttagctcccaagggatttgg																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:104293229delT	ENST00000370079.3	+	1	202	c.138delT	c.(136-138)tatfs	p.Y46fs		NM_001008219.1	NP_001008220.1	P04745	AMY1_HUMAN	amylase, alpha 1C (salivary)	46					carbohydrate metabolic process (GO:0005975)|digestion (GO:0007586)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|metal ion binding (GO:0046872)			lung(5)|skin(3)	8		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)		GTGAGCGATATTTAGCTCCCA	0.413																																					p.Y46fs		Atlas-INDEL	.											.	AMY1C	11	.	0			c.137delA						PASS	.						1	1	1					1																	104293229		232	481	713	SO:0001589	frameshift_variant	278	exon2			.		CCDS30784.1	1p21	2012-10-02	2007-05-03		ENSG00000187733	ENSG00000187733	3.2.1.1		476	protein-coding gene	gene with protein product		104702	"amylase, alpha 1C; salivary"	AMY1			Standard	XM_005270761		Approved			P04745	OTTHUMG00000011045	ENST00000370079.3:c.138delT	chr1.hg19:g.104293229delT	ENSP00000359096:p.Tyr46fs	784.0	0.0	0		629.0	57.0	0.09062	NM_001008219	A6NJS5|A8K8H6|Q13763|Q5T083	Frame_Shift_Del	DEL	ENST00000370079.3	hg19	CCDS30784.1																																																																																			.	.	.	none		0.413	AMY1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030375.1	NM_001008219		-	104293229	T	-	104293229	7	5	87	1	0	1	0	1	0	0	0	0	591	1500	52	0	3292	0	AMY1A	1	104293229	Frame_Shift_Del	DEL	T	TCGA-B1-A657-01A-11D-A31X-10	55109	104293229	144957392	3	5591											
DENND4B	9909	hgsc.bcm.edu	37	chr1	153916546	153916546	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacacaccccagctcaacgAgggggggcttgtcacggccc	8	4	13	16	2	2	0	2	0	0	0	2	1	2	0	3	4	2	3	3	4	1	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:153916546A>G	ENST00000361217.4	-	2	723	c.305T>C	c.(304-306)cTc>cCc	p.L102P		NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	102	MABP. {ECO:0000255|PROSITE- ProRule:PRU00831}.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CAGCTCAACGAGGGGGGGCTT	0.632																																					p.L102P		Atlas-SNP	.											.	DENND4B	210	.	0			c.T305C						PASS	.						28	32	31					1																	153916546		1905	4105	6010	SO:0001583	missense	9909	exon2			TCAACGAGGGGGG	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"DENN/MADD domain containing"	29044	protein-coding gene	gene with protein product			"KIAA0476"	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.305T>C	chr1.hg19:g.153916546A>G	ENSP00000354597:p.Leu102Pro	109.0	0.0	.		72.0	17.0	.	NM_014856	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	hg19	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.314898	0.81358	.	.	ENSG00000198837	ENST00000361217;ENST00000368646	T;T	0.29655	1.56;1.56	4.7	4.7	0.59300	MABP domain (1);	.	.	.	.	T	0.34164	0.0888	L	0.52126	1.63	0.80722	D	1	D	0.64830	0.994	P	0.59288	0.855	T	0.19451	-1.0305	9	0.87932	D	0	-8.3452	13.2712	0.60161	1.0:0.0:0.0:0.0	.	102	O75064	DEN4B_HUMAN	P	102;113	ENSP00000354597:L102P;ENSP00000357635:L113P	ENSP00000354597:L102P	L	-	2	0	DENND4B	152183170	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	8.903000	0.92573	1.964000	0.57103	0.379000	0.24179	CTC	.	.	.	none		0.632	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806		G	153916546	A	G	153916546	3	3	87	1	0	0	0	0	1	0	0	0	4436	304	11	3	4293	3	DENND4B	1	153916546	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	49623317	153916546	95334075	4	5592											
THBS3	7059	hgsc.bcm.edu	37	chr1	155175049	155175049	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcgcccatcagccaggccCgcttgctgtaggttcacggc	5	8	13	15	3	2	0	2	0	0	0	2	0	2	0	3	3	3	4	3	3	1	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:155175049C>T	ENST00000368378.3	-	3	365	c.345G>A	c.(343-345)gcG>gcA	p.A115A	THBS3_ENST00000486260.1_5'UTR|RP11-263K19.4_ENST00000430312.1_RNA|RP11-263K19.4_ENST00000422665.1_RNA|THBS3_ENST00000541990.1_5'UTR|RP11-263K19.4_ENST00000453136.1_RNA|THBS3_ENST00000457183.2_Intron	NM_001252607.1|NM_007112.4	NP_001239536.1|NP_009043.1	P49746	TSP3_HUMAN	thrombospondin 3	115	Laminin G-like.				bone trabecula formation (GO:0060346)|cell-matrix adhesion (GO:0007160)|growth plate cartilage development (GO:0003417)|ossification involved in bone maturation (GO:0043931)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.A115A(1)		breast(6)|endometrium(4)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(3)	48	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CAGCCAGGCCCGCTTGCTGTA	0.627																																					p.A115A		Atlas-SNP	.											.	THBS3	70	.	1	Substitution - coding silent(1)	lung(1)	c.G345A						PASS	.						100	82	88					1																	155175049		2203	4300	6503	SO:0001819	synonymous_variant	7059	exon3			CAGGCCCGCTTGC	L38969	CCDS1099.1, CCDS58034.1, CCDS72937.1	1q21	2008-02-05			ENSG00000169231	ENSG00000169231			11787	protein-coding gene	gene with protein product		188062				1601886	Standard	NM_007112		Approved		uc001fix.3	P49746	OTTHUMG00000035710	ENST00000368378.3:c.345G>A	chr1.hg19:g.155175049C>T		66.0	0.0	.		55.0	13.0	.	NM_007112	B1AVR8|B4DQ20|Q8WV34	Silent	SNP	ENST00000368378.3	hg19	CCDS1099.1																																																																																			.	.	.	none		0.627	THBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086856.1	NM_007112		T	155175049	C	T	155175049	2	4	87	1	0	0	0	0	0	0	0	1	15867	639	23	1		1	THBS3	1	155175049	Silent	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	1258503	155175049	94075572	5	5593											
C1orf112	55732	hgsc.bcm.edu	37	chr1	169798424	169798424	+	Frame_Shift_Del	DEL	T	T	-																															gatatctctactcaaagccgTtttctacagttttgagcagt																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:169798424delT	ENST00000286031.6	+	13	1848	c.1148delT	c.(1147-1149)gttfs	p.V383fs	C1orf112_ENST00000413811.2_Frame_Shift_Del_p.F311fs|C1orf112_ENST00000359326.4_Frame_Shift_Del_p.V383fs|C1orf112_ENST00000498289.1_3'UTR	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	383										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)					CTCAAAGCCGTTTTCTACAGT	0.368																																					p.V383fs		Atlas-Indel,Pindel	.											C1orf112,NS,carcinoma,0,3	C1orf112	74	.	0			c.1147delG						PASS	.						133	130	131					1																	169798424		2203	4300	6503	SO:0001589	frameshift_variant	55732	exon13			.	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.1148delT	chr1.hg19:g.169798424delT	ENSP00000286031:p.Val383fs	143.0	0.0	0		111.0	29.0	0.261261	NM_018186	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Frame_Shift_Del	DEL	ENST00000286031.6	hg19	CCDS1285.1																																																																																			.	.	.	none		0.368	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186		-	169798424	T	-	169798424	7	5	87	1	0	1	0	1	0	0	0	0	1987	1725	60	0	1190	0	C1orf112	1	169798424	Frame_Shift_Del	DEL	T	TCGA-B1-A657-01A-11D-A31X-10	14623375	169798424	79452197	6	5594											
C1orf14	81626	hgsc.bcm.edu	37	chr1	182922005	182922005	+	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	ggcagcaggggctcctccgcCgccgccgccgccgcctctcc	2	4	13	22	6	1	0	0	0	1	0	4	0	3	0	9	3	1	3	9	3	0	0			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:182922005C>G	ENST00000367547.3	-	1	500	c.264G>C	c.(262-264)gcG>gcC	p.A88A	SHCBP1L_ENST00000488956.1_5'UTR|SHCBP1L_ENST00000423786.1_5'Flank	NM_030933.2	NP_112195.2	Q9BZQ2	SHP1L_HUMAN	SHC SH2-domain binding protein 1-like	160										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|pancreas(1)|prostate(1)|skin(2)	15						GCTCCTccgccgccgccgccg	0.746																																					p.A88A		Atlas-SNP	.											.	SHCBP1L	64	.	0			c.G264C						PASS	.						5	6	6					1																	182922005		2140	4210	6350	SO:0001819	synonymous_variant	81626	exon1			CTCCGCCGCCGCC	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.264G>C	chr1.hg19:g.182922005C>G		35.0	0.0	.		43.0	18.0	.	NM_030933	Q4G195|Q9BZQ3|Q9H2B6	Silent	SNP	ENST00000367547.3	hg19	CCDS30955.1																																																																																			.	.	.	none		0.746	SHCBP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085956.1	NM_030933		G	182922005	C	G	182922005	2	3	87	1	0	0	0	0	0	0	0	1	2002	639	23	4		4	C1orf14	1	182922005	Silent	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	13123581	182922005	66328616	7	5595											
F13B	2165	hgsc.bcm.edu	37	chr1	197020002	197020002	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaggagatgtgcacattccTttagattctgcaaaaataag	14	11	10	6	0	1	2	0	0	1	2	2	4	2	3	1	2	2	2	1	2	4	5			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:197020002T>C	ENST00000367412.1	-	10	1606	c.1563A>G	c.(1561-1563)aaA>aaG	p.K521K	F13B_ENST00000490002.1_5'Flank	NM_001994.2	NP_001985.2	P05160	F13B_HUMAN	coagulation factor XIII, B polypeptide	521					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						TGCACATTCCTTTAGATTCTG	0.348																																					p.K521K		Atlas-SNP	.											.,1	F13B	137	.	0			c.A1563G						PASS	.						85	85	85					1																	197020002		2203	4300	6503	SO:0001819	synonymous_variant	2165	exon10			CATTCCTTTAGAT	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.1563A>G	chr1.hg19:g.197020002T>C		102.0	0.0	.		68.0	27.0	.	NM_001994	A8K3E5|Q5VYL5	Silent	SNP	ENST00000367412.1	hg19	CCDS1388.1																																																																																			.	.	.	none		0.348	F13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088821.2	NM_001994		C	197020002	T	C	197020002	2	2	87	1	0	0	0	0	0	0	0	1	5343	1606	56	3		3	F13B	1	197020002	Silent	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	14097997	197020002	52230619	8	5596											
PPP1R15B	84919	hgsc.bcm.edu	37	chr1	204379052	204379052	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaattctggcagcagtctgAattgttgctgtaaagttctg	10	14	10	7	0	3	1	0	1	3	0	3	1	3	1	0	1	2	6	0	1	4	5			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:204379052A>G	ENST00000367188.4	-	1	1867	c.1488T>C	c.(1486-1488)atT>atC	p.I496I	RP11-739N20.2_ENST00000443515.1_RNA	NM_032833.3	NP_116222.3	Q5SWA1	PR15B_HUMAN	protein phosphatase 1, regulatory subunit 15B	496					ER overload response (GO:0006983)|regulation of translation (GO:0006417)|response to hydrogen peroxide (GO:0042542)	protein phosphatase type 1 complex (GO:0000164)	protein serine/threonine phosphatase activity (GO:0004722)			breast(3)|cervix(1)|kidney(4)|large_intestine(3)|lung(16)|ovary(1)|pancreas(2)|skin(1)|urinary_tract(3)	34	all_cancers(21;0.0032)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.179)|all_epithelial(62;0.193)|Prostate(682;0.227)		all cancers(3;1.14e-29)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.139)			CAGCAGTCTGAATTGTTGCTG	0.458																																					p.I496I		Atlas-SNP	.											.	PPP1R15B	67	.	0			c.T1488C						PASS	.						73	78	76					1																	204379052		2203	4300	6503	SO:0001819	synonymous_variant	84919	exon1			AGTCTGAATTGTT	AK027650	CCDS1445.1	1q32.1	2012-04-17	2011-10-04		ENSG00000158615	ENSG00000158615		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14951	protein-coding gene	gene with protein product		613257	"protein phosphatase 1, regulatory (inhibitor) subunit 15B"			11948623	Standard	XM_005245551		Approved	FLJ14744	uc001hav.4	Q5SWA1	OTTHUMG00000036105	ENST00000367188.4:c.1488T>C	chr1.hg19:g.204379052A>G		81.0	0.0	.		72.0	23.0	.	NM_032833	Q53GQ4|Q658M2|Q6P156|Q96SN1	Silent	SNP	ENST00000367188.4	hg19	CCDS1445.1																																																																																			.	.	.	none		0.458	PPP1R15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087974.1	NM_032833		G	204379052	A	G	204379052	2	3	87	1	0	0	0	0	0	0	0	1	12374	242	9	3		3	PPP1R15B	1	204379052	Silent	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	7359050	204379052	44871569	9	5597											
PARP1	142	hgsc.bcm.edu	37	chr1	226570817	226570817	+	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	ccgccacggaggcgctggttTctggggggaatatacggtcc	6	8	16	11	4	1	0	0	0	1	0	2	2	2	2	3	7	1	2	3	7	3	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:226570817T>A	ENST00000366794.5	-	8	1222	c.1079A>T	c.(1078-1080)gAa>gTa	p.E360V		NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	360					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)		GGCGCTGGTTTCTGGGGGGAA	0.507								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																													p.E360V		Atlas-SNP	.											.	PARP1	100	.	0			c.A1079T						PASS	.						111	139	129					1																	226570817		2203	4300	6503	SO:0001583	missense	142	exon8			CTGGTTTCTGGGG	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.1079A>T	chr1.hg19:g.226570817T>A	ENSP00000355759:p.Glu360Val	142.0	0.0	.		96.0	40.0	.	NM_001618	B1ANJ4|Q8IUZ9	Missense_Mutation	SNP	ENST00000366794.5	hg19	CCDS1554.1	.	.	.	.	.	.	.	.	.	.	T	11.05	1.525131	0.27299	.	.	ENSG00000143799	ENST00000366794	T	0.09723	2.95	5.26	5.26	0.73747	.	0.049169	0.85682	D	0.000000	T	0.05731	0.0150	N	0.08118	0	0.80722	D	1	B	0.06786	0.001	B	0.09377	0.004	T	0.38090	-0.9677	10	0.32370	T	0.25	.	9.4103	0.38487	0.0:0.0804:0.0:0.9196	.	360	P09874	PARP1_HUMAN	V	360	ENSP00000355759:E360V	ENSP00000355759:E360V	E	-	2	0	PARP1	224637440	0.994000	0.37717	0.177000	0.23020	0.267000	0.26476	3.623000	0.54224	1.977000	0.57605	0.454000	0.30748	GAA	.	.	.	none		0.507	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618		A	226570817	T	A	226570817	3	1	87	1	0	0	0	0	1	0	0	0	11461	1783	62	5	2029	5	PARP1	1	226570817	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	22191765	226570817	22679804	10	5598											
C1orf96	126731	hgsc.bcm.edu	37	chr1	229461075	229461076	+	Frame_Shift_Del	DEL	AG	AG	-																															ctgttcttctccacatccacAgagtgagctcgctgcctttg																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:229461075_229461076delAG	ENST00000366687.1	-	3	770_771	c.719_720delCT	c.(718-720)tctfs	p.S240fs	CCSAP_ENST00000483092.1_5'UTR|RP4-803J11.2_ENST00000418348.1_RNA|CCSAP_ENST00000366686.1_Frame_Shift_Del_p.S126fs|CCSAP_ENST00000284617.2_Frame_Shift_Del_p.S240fs			Q6IQ19	CCSAP_HUMAN	centriole, cilia and spindle-associated protein	240					multicellular organismal development (GO:0007275)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|regulation of embryonic development (GO:0045995)	axon (GO:0030424)|axoneme (GO:0005930)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cilium (GO:0005929)|spindle (GO:0005819)											CCACATCCACAGAGTGAGCTCG	0.441																																					p.240_241del		Atlas-Indel,Pindel	.											.	.	.	.	0			c.720_721del						PASS	.																																			SO:0001589	frameshift_variant	126731	exon4			.	BC071609	CCDS1577.1	1q42.13	2012-06-19	2012-06-19	2012-06-19	ENSG00000154429	ENSG00000154429			29578	protein-coding gene	gene with protein product	"centriole and spindle-associated protein"		"chromosome 1 open reading frame 96"	C1orf96		22493317	Standard	NM_145257		Approved	FLJ41471, CSAP	uc001htl.4	Q6IQ19	OTTHUMG00000037663	ENST00000366687.1:c.719_720delCT	chr1.hg19:g.229461077_229461078delAG	ENSP00000355648:p.Ser240fs	125.0	0.0	0		101.0	28.0	0.277228	NM_145257	A8K5X2|Q6P9G2|Q6ZW85|Q8IXU1|Q96BM2	Frame_Shift_Del	DEL	ENST00000366687.1	hg19	CCDS1577.1																																																																																			.	.	.	none		0.441	CCSAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091839.1	NM_145257		-	229461076	AG	-	229461075	7	5	87	1	0	1	0	1	0	0	0	0	2075	175	7	0	96	0	C1orf96	1	229461075	Frame_Shift_Del	DEL	AG	TCGA-B1-A657-01A-11D-A31X-10	2890258	229461075	19789546	11	5599											
ARID4B	51742	hgsc.bcm.edu	37	chr1	235345203	235345203	+	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	attactgccactacttggaaAttctgcttttctgtcattga	9	17	6	9	0	3	1	1	1	2	0	3	2	3	2	1	1	4	1	1	1	3	7			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:235345203A>T	ENST00000264183.3	-	20	3528	c.3031T>A	c.(3031-3033)Ttt>Att	p.F1011I	ARID4B_ENST00000366603.2_Missense_Mutation_p.F1011I|ARID4B_ENST00000494543.1_5'Flank|ARID4B_ENST00000349213.3_Missense_Mutation_p.F925I	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	1011					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)			CTACTTGGAAATTCTGCTTTT	0.438																																					p.F1011I		Atlas-SNP	.											.	ARID4B	142	.	0			c.T3031A						PASS	.						116	121	119					1																	235345203		2203	4300	6503	SO:0001583	missense	51742	exon20			TTGGAAATTCTGC	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.3031T>A	chr1.hg19:g.235345203A>T	ENSP00000264183:p.Phe1011Ile	104.0	0.0	.		77.0	24.0	.	NM_016374	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	Missense_Mutation	SNP	ENST00000264183.3	hg19	CCDS31061.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.17|18.17	3.563590|3.563590	0.65651|0.65651	.|.	.|.	ENSG00000054267|ENSG00000054267	ENST00000391856;ENST00000349213;ENST00000366603;ENST00000264183|ENST00000444620	T;T;T|.	0.23552|.	1.9;1.95;1.95|.	5.18|5.18	4.03|4.03	0.46877|0.46877	.|.	0.359358|.	0.32785|.	N|.	0.005655|.	T|T	0.47303|0.47303	0.1438|0.1438	N|N	0.19112|0.19112	0.55|0.55	0.53688|0.53688	D|D	0.999971|0.999971	D;D;D;D|.	0.67145|.	0.996;0.992;0.996;0.987|.	D;D;D;D|.	0.77557|.	0.99;0.974;0.99;0.942|.	T|T	0.33085|0.33085	-0.9882|-0.9882	10|5	0.25751|.	T|.	0.34|.	-11.9576|-11.9576	12.1739|12.1739	0.54173|0.54173	0.8568:0.1432:0.0:0.0|0.8568:0.1432:0.0:0.0	.|.	692;1011;925;1011|.	Q4LE39-4;Q4LE39-3;Q4LE39-2;Q4LE39|.	.;.;.;ARI4B_HUMAN|.	I|K	1011;925;1011;1011|410	ENSP00000264184:F925I;ENSP00000355562:F1011I;ENSP00000264183:F1011I|.	ENSP00000264183:F1011I|.	F|N	-|-	1|3	0|2	ARID4B|ARID4B	233411826|233411826	1.000000|1.000000	0.71417|0.71417	0.989000|0.989000	0.46669|0.46669	0.991000|0.991000	0.79684|0.79684	5.361000|5.361000	0.66092|0.66092	0.956000|0.956000	0.37904|0.37904	0.477000|0.477000	0.44152|0.44152	TTT|AAT	.	.	.	none		0.438	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374		T	235345203	A	T	235345203	3	4	87	1	0	0	0	0	1	0	0	0	920	101	4	5	927	5	ARID4B	1	235345203	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	5884128	235345203	13905418	12	5600											
FMN2	56776	hgsc.bcm.edu	37	chr1	240371139	240371139	+	Silent	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	cttcccggagcgggcataccCcctcctccccctcttcccgg	3	8	8	22	3	1	0	0	0	1	0	5	1	5	1	7	3	2	1	7	3	1	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr1:240371139C>T	ENST00000319653.9	+	5	3257	c.3027C>T	c.(3025-3027)ccC>ccT	p.P1009P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1009	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	0.731																																					p.P1009P		Atlas-SNP	.											.	FMN2	451	.	0			c.C3027T						PASS	.																																			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.3027C>T	chr1.hg19:g.240371139C>T		87.0	0.0	.		81.0	5.0	.	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	hg19	CCDS31069.2																																																																																			.	.	.	none		0.731	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		T	240371139	C	T	240371139	2	4	87	1	0	0	0	0	0	0	0	1	5957	610	22	2		2	FMN2	1	240371139	Silent	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	5025936	240371139	8879482	13	5601											
ARID5A	10865	hgsc.bcm.edu	37	chr2	97215160	97215160	+	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	tcatgaaggagcgacacacgCccatcgagagggtgccccat	11	5	12	13	3	1	2	1	1	0	1	2	5	1	3	3	2	2	0	3	2	1	0			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr2:97215160C>A	ENST00000357485.3	+	3	301	c.223C>A	c.(223-225)Ccc>Acc	p.P75T	ARID5A_ENST00000454558.2_Missense_Mutation_p.P7T	NM_212481.1	NP_997646.1	Q03989	ARI5A_HUMAN	AT rich interactive domain 5A (MRF1-like)	75	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				chondrocyte differentiation (GO:0002062)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)|skin(1)|urinary_tract(2)	14						GCGACACACGCCCATCGAGAG	0.697																																					p.P75T		Atlas-SNP	.											.	ARID5A	31	.	0			c.C223A						PASS	.						97	90	92					2																	97215160		2203	4300	6503	SO:0001583	missense	10865	exon3			CACACGCCCATCG	M62324	CCDS33251.1	2p11.1	2013-02-07			ENSG00000196843	ENSG00000196843		"-"	17361	protein-coding gene	gene with protein product	"modulator recognition factor 1"	611583				8649988	Standard	NM_212481		Approved	MRF-1, RP11-363D14	uc002swe.3	Q03989	OTTHUMG00000155229	ENST00000357485.3:c.223C>A	chr2.hg19:g.97215160C>A	ENSP00000350078:p.Pro75Thr	111.0	0.0	.		127.0	72.0	.	NM_212481	Q6NX37	Missense_Mutation	SNP	ENST00000357485.3	hg19	CCDS33251.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.586158	0.86851	.	.	ENSG00000196843	ENST00000357485;ENST00000359765;ENST00000454558	T;T	0.64085	-0.08;-0.08	5.07	5.07	0.68467	ARID/BRIGHT DNA-binding domain (5);	0.000000	0.64402	D	0.000002	T	0.77274	0.4106	M	0.75777	2.31	0.51233	D	0.999918	D	0.58970	0.984	D	0.69307	0.963	T	0.79401	-0.1819	10	0.72032	D	0.01	-21.3112	13.8159	0.63292	0.0:1.0:0.0:0.0	.	75	Q03989	ARI5A_HUMAN	T	75;75;7	ENSP00000350078:P75T;ENSP00000400785:P7T	ENSP00000350078:P75T	P	+	1	0	ARID5A	96578887	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.160000	0.58164	2.653000	0.90120	0.561000	0.74099	CCC	.	.	.	none		0.697	ARID5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338888.2	NM_212481		A	97215160	C	A	97215160	3	1	87	1	0	0	0	0	1	0	0	0	921	739	26	4	233	4	ARID5A	2	97215160	Missense_Mutation	SNP	C	TCGA-B1-A657-01A-11D-A31X-10		97215160	145984213	14	5602											
TTN	7273	hgsc.bcm.edu	37	chr2	179431535	179431535	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cactcttagacgcaaatctgTaatgcggcgtttattacatt	11	14	7	9	3	2	1	0	0	2	1	2	1	2	1	0	1	2	3	0	1	5	6			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr2:179431535T>C	ENST00000591111.1	-	276	74625	c.74401A>G	c.(74401-74403)Aca>Gca	p.T24801A	TTN_ENST00000342992.6_Missense_Mutation_p.T23874A|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T17569A|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.T26442A|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T17502A|TTN_ENST00000460472.2_Missense_Mutation_p.T17377A|TTN-AS1_ENST00000592600.1_RNA			Q8WZ42	TITIN_HUMAN	titin	24801	Fibronectin type-III 80. {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)			CGCAAATCTGTAATGCGGCGT	0.428																																					p.T26442A		Atlas-SNP	.											.	TTN	18412	.	0			c.A79324G						PASS	.						71	70	70					2																	179431535		1854	4108	5962	SO:0001583	missense	7273	exon326			AATCTGTAATGCG	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.74401A>G	chr2.hg19:g.179431535T>C	ENSP00000465570:p.Thr24801Ala	58.0	0.0	.		60.0	42.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	12.10	1.835271	0.32421	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.58940	0.3;0.3;0.3;0.3	5.75	4.57	0.56435	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.56543	0.1992	L	0.41415	1.275	0.58432	D	0.999992	D;D;D;D	0.56746	0.977;0.977;0.977;0.958	P;P;P;P	0.49192	0.602;0.602;0.602;0.506	T	0.60073	-0.7334	9	0.87932	D	0	.	13.2067	0.59800	0.0:0.0:0.1326:0.8674	.	17377;17502;17569;24801	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	A	23874;17377;17569;17502;17375	ENSP00000343764:T23874A;ENSP00000434586:T17377A;ENSP00000340554:T17569A;ENSP00000352154:T17502A	ENSP00000340554:T17569A	T	-	1	0	TTN	179139781	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.040000	0.89188	0.965000	0.38133	0.459000	0.35465	ACA	.	.	.	none		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179431535	T	C	179431535	3	2	87	1	0	0	0	0	1	0	0	0	16747	1638	57	3	28803	3	TTN	2	179431535	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	82216375	179431535	63767838	15	5603											
PPARG	5468	hgsc.bcm.edu	37	chr3	12447397	12447397	+	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	atagccatcaggtttgggcgGatgccacaggccgagaagga	11	6	15	9	2	1	1	1	0	0	1	1	4	1	3	3	5	2	1	3	5	2	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr3:12447397G>C	ENST00000287820.6	+	5	757	c.636G>C	c.(634-636)cgG>cgC	p.R212R	PPARG_ENST00000309576.6_Silent_p.R184R|PPARG_ENST00000397015.2_Silent_p.R184R|PPARG_ENST00000539812.1_Silent_p.R182R|PPARG_ENST00000397026.2_Silent_p.R190R|PPARG_ENST00000397012.2_Silent_p.R184R|PPARG_ENST00000397000.1_Silent_p.R184R|PPARG_ENST00000397010.2_Silent_p.R184R	NM_015869.4	NP_056953.2	P37231	PPARG_HUMAN	peroxisome proliferator-activated receptor gamma	212	Interaction with FAM120B. {ECO:0000250}.				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)	GGTTTGGGCGGATGCCACAGG	0.542			T	PAX8	follicular thyroid		"Insulin resistance ; lipodystrophy, familial partial L;diabetes mellitus, insulin-resistantI, with acanthosis nigricans and hypertension"																														p.R212R		Atlas-SNP	.		Dom	yes		3	3p25	5468	"peroxisome proliferative activated receptor, gamma"	yes	E	.	PPARG	49	.	0			c.G636C						PASS	.						66	65	65					3																	12447397		2203	4300	6503	SO:0001819	synonymous_variant	5468	exon5			TGGGCGGATGCCA	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.636G>C	chr3.hg19:g.12447397G>C		62.0	0.0	.		83.0	5.0	.	NM_015869	A8K3G6|B5BUA1|O00684|O00710|O14515|Q0QJH8|Q15178|Q15179|Q15180|Q15832|Q86U60|Q96J12	Silent	SNP	ENST00000287820.6	hg19	CCDS2609.1																																																																																			.	.	.	none		0.542	PPARG-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251979.2	NM_005037		C	12447397	G	C	12447397	2	2	87	1	0	0	0	0	0	0	0	1	12306	1161	41	4		4	PPARG	3	12447397	Silent	SNP	G	TCGA-B1-A657-01A-11D-A31X-10		12447397	185575033	16	5604											
DLEC1	9940	hgsc.bcm.edu	37	chr3	38101279	38101280	+	In_Frame_Ins	INS	-	-	CAT																															acagcgagttgctacggaaaINScatcatttgatctccccaga																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr3:38101279_38101280insCAT	ENST00000308059.6	+	3	630_631	c.609_610insCAT	c.(610-612)cat>CATcat	p.204_204H>HH	DLEC1_ENST00000452631.2_In_Frame_Ins_p.204_204H>HH|DLEC1_ENST00000346219.3_In_Frame_Ins_p.204_204H>HH					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)		TGCTACGGAAACATCATTTGAT	0.465																																					p.K203delinsKH		Atlas-Indel,Pindel	.											.	DLEC1	278	.	0			c.609_610insCAT						PASS	.																																			SO:0001652	inframe_insertion	9940	exon3			.	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.613_615dupCAT	chr3.hg19:g.38101283_38101285dupCAT	ENSP00000308597:p.His205dup	60.0	0.0	0		91.0	39.0	0.428571	NM_007335		In_Frame_Ins	INS	ENST00000308059.6	hg19	CCDS2672.2																																																																																			.	.	.	none		0.465	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		CAT	38101280	-	CAT	38101279	7	5	87	1	0	1	1	0	0	0	0	0	4554	40	2	0	619	0	DLEC1	3	38101279	In_Frame_Ins	INS	-	TCGA-B1-A657-01A-11D-A31X-10	25653882	38101279	159921151	17	5605											
LIMD1	8994	hgsc.bcm.edu	37	chr3	45714309	45714327	+	Splice_Site	DEL	ACAAGTAAGAAGGGATGGG	ACAAGTAAGAAGGGATGGG	-																															ctactgtgtccgagattaccAcaagtaagaagggatgggag																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	ACAAGTAAGAAGGGATGGG	ACAAGTAAGAAGGGATGGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr3:45714309_45714327delACAAGTAAGAAGGGATGGG	ENST00000273317.4	+	5	1790_1793	c.1769_1772delACAAGTAAGAAGGGATGGG	c.(1768-1773)cacaag>cg	p.HK590fs	LIMD1_ENST00000465039.1_3'UTR|LIMD1_ENST00000440097.1_Splice_Site_p.HK590fs	NM_014240.2	NP_055055.1	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1	590	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.|Necessary for nuclear localization.				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)		CGAGATTACCACAAGTAAGAAGGGATGGGAGCAGACAGG	0.53																																					p.590_591del		Pindel	.											.	LIMD1	34	.	0			c.1768_1772del						PASS	.																																			SO:0001630	splice_region_variant	8994	exon5			.	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.1772+1ACAAGTAAGAAGGGATGGG>-	chr3.hg19:g.45714309_45714327delACAAGTAAGAAGGGATGGG		54.0	0.0	.		59.0	10.0	0.169	NM_014240	Q17RQ1|Q9BQQ9|Q9NQ47	Frame_Shift_Del	DEL	ENST00000273317.4	hg19	CCDS2729.1																																																																																			.	.	.	none		0.53	LIMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257327.1	NM_014240	Frame_Shift_Del	-	45714327	ACAAGTAAGAAGGGATGGG	-	45714309	8	5	87	1	0	1	0	1	0	0	1	0	8805	159	6	0	1787	0	LIMD1	3	45714309	Splice_Site	DEL	ACAAGTAAGAAGGGATGGG	TCGA-B1-A657-01A-11D-A31X-10	7613030	45714309	152308121	18	5606											
DAG1	1605	hgsc.bcm.edu	37	chr3	49547996	49547996	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctgtgggcctctcgctgcTgctgcccctctcggggagga	2	10	15	14	2	3	0	0	0	3	0	5	2	3	2	3	4	3	3	3	4	0	0			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr3:49547996T>C	ENST00000539901.1	+	2	587	c.29T>C	c.(28-30)cTg>cCg	p.L10P	DAG1_ENST00000515359.2_Missense_Mutation_p.L10P|DAG1_ENST00000538711.1_Missense_Mutation_p.L10P|DAG1_ENST00000479935.1_3'UTR|DAG1_ENST00000541308.1_Missense_Mutation_p.L10P|DAG1_ENST00000545947.1_Missense_Mutation_p.L10P|DAG1_ENST00000308775.2_Missense_Mutation_p.L10P	NM_001177644.2	NP_001171115	Q14118	DAG1_HUMAN	dystroglycan 1 (dystrophin-associated glycoprotein 1)	10					basement membrane organization (GO:0071711)|branching involved in salivary gland morphogenesis (GO:0060445)|calcium-dependent cell-matrix adhesion (GO:0016340)|commissural neuron axon guidance (GO:0071679)|cytoskeletal anchoring at plasma membrane (GO:0007016)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|microtubule anchoring (GO:0034453)|modulation by virus of host morphology or physiology (GO:0019048)|morphogenesis of an epithelial sheet (GO:0002011)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell migration (GO:0030336)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase B signaling (GO:0051898)|nerve maturation (GO:0021682)|NLS-bearing protein import into nucleus (GO:0006607)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell outer membrane (GO:0009279)|cell-cell adherens junction (GO:0005913)|contractile ring (GO:0070938)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystroglycan complex (GO:0016011)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|node of Ranvier (GO:0033268)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|alpha-actinin binding (GO:0051393)|calcium ion binding (GO:0005509)|laminin-1 binding (GO:0043237)|SH2 domain binding (GO:0042169)|structural constituent of muscle (GO:0008307)|tubulin binding (GO:0015631)|vinculin binding (GO:0017166)|virus receptor activity (GO:0001618)			NS(1)|autonomic_ganglia(2)|breast(2)|endometrium(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	23				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.00241)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		CTCTCGCTGCTGCTGCCCCTC	0.577																																					p.L10P		Atlas-SNP	.											.	DAG1	60	.	0			c.T29C						PASS	.						85	84	84					3																	49547996		2203	4300	6503	SO:0001583	missense	1605	exon3			CGCTGCTGCTGCC	L19711	CCDS2799.1	3p21	2014-09-17			ENSG00000173402	ENSG00000173402			2666	protein-coding gene	gene with protein product	"alpha-dystroglycan", "dystrophin-associated glycoprotein-1", "beta-dystroglycan"	128239				7774920, 1741056	Standard	NM_001177643		Approved	A3a, 156DAG, AGRNR, DAG	uc021wyd.1	Q14118	OTTHUMG00000156869	ENST00000539901.1:c.29T>C	chr3.hg19:g.49547996T>C	ENSP00000439334:p.Leu10Pro	48.0	0.0	.		60.0	13.0	.	NM_001177642	A8K6M7|Q969J9	Missense_Mutation	SNP	ENST00000539901.1	hg19	CCDS2799.1	.	.	.	.	.	.	.	.	.	.	T	8.905	0.957260	0.18507	.	.	ENSG00000173402	ENST00000515359;ENST00000421560;ENST00000308775;ENST00000545947;ENST00000541308;ENST00000539901;ENST00000538711;ENST00000418588;ENST00000431960;ENST00000452317;ENST00000435508;ENST00000452060;ENST00000428779;ENST00000419218	T;T;T;T;T;T;T;T;T;T;T;T;T	0.60797	0.78;0.77;0.78;0.78;0.78;0.78;0.78;0.75;0.76;0.16;0.64;0.74;0.76	5.85	4.7	0.59300	.	0.080454	0.51477	N	0.000097	T	0.42086	0.1187	L	0.29908	0.895	0.53688	D	0.999978	B	0.02656	0.0	B	0.01281	0.0	T	0.31138	-0.9954	10	0.52906	T	0.07	-6.6126	6.3137	0.21178	0.1406:0.0754:0.0:0.784	.	10	Q14118	DAG1_HUMAN	P	10	ENSP00000440705:L10P;ENSP00000412067:L10P;ENSP00000312435:L10P;ENSP00000442600:L10P;ENSP00000440590:L10P;ENSP00000439334:L10P;ENSP00000438421:L10P;ENSP00000405859:L10P;ENSP00000388833:L10P;ENSP00000387859:L10P;ENSP00000415321:L10P;ENSP00000410145:L10P;ENSP00000401382:L10P	ENSP00000312435:L10P	L	+	2	0	DAG1	49523000	0.990000	0.36364	1.000000	0.80357	0.095000	0.18619	1.145000	0.31577	1.044000	0.40200	0.455000	0.32223	CTG	.	.	.	none		0.577	DAG1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346326.1			C	49547996	T	C	49547996	3	2	87	1	0	0	0	0	1	0	0	0	4227	1580	55	3	31	3	DAG1	3	49547996	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	3833687	49547996	148474434	19	5607											
MBNL1	4154	hgsc.bcm.edu	37	chr3	152163262	152163262	+	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	gcacatttgcaagccaagatCaaggctgcccaataccaggt	13	7	9	12	0	1	1	1	0	0	1	1	1	1	1	3	2	4	3	3	2	5	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr3:152163262C>T	ENST00000463374.1	+	4	1252	c.741C>T	c.(739-741)atC>atT	p.I247I	MBNL1_ENST00000357472.3_Silent_p.I247I|MBNL1_ENST00000324196.5_Silent_p.I247I|MBNL1_ENST00000492948.1_Silent_p.I247I|MBNL1_ENST00000485910.1_Silent_p.I179I|MBNL1_ENST00000355460.2_Silent_p.I247I|MBNL1_ENST00000498502.1_Silent_p.I247I|MBNL1_ENST00000282486.6_Silent_p.I247I|MBNL1_ENST00000545754.1_Silent_p.I179I|MBNL1_ENST00000324210.5_Silent_p.I247I|MBNL1_ENST00000485509.1_Silent_p.I247I|MBNL1_ENST00000282488.7_Silent_p.I179I|MBNL1_ENST00000493459.1_Silent_p.I190I	NM_207293.1	NP_997176.1	Q9NR56	MBNL1_HUMAN	muscleblind-like splicing regulator 1	247					alternative mRNA splicing, via spliceosome (GO:0000380)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|mRNA splice site selection (GO:0006376)|myoblast differentiation (GO:0045445)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|skeletal muscle tissue development (GO:0007519)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			AAGCCAAGATCAAGGCTGCCC	0.507																																					p.I247I		Atlas-SNP	.											.	MBNL1	100	.	0			c.C741T						PASS	.						101	100	101					3																	152163262		2203	4300	6503	SO:0001819	synonymous_variant	4154	exon5			CAAGATCAAGGCT	Y13829	CCDS3163.1, CCDS3164.1, CCDS3165.1, CCDS3166.1, CCDS3167.1, CCDS3168.1, CCDS54656.1	3q25	2013-01-18	2012-02-23	2003-03-14	ENSG00000152601	ENSG00000152601		"Zinc fingers, CCCH-type domain containing"	6923	protein-coding gene	gene with protein product		606516	"muscleblind (Drosophila)-like", "muscleblind-like (Drosophila)"	MBNL			Standard	NM_021038		Approved	KIAA0428, EXP42, EXP40, EXP35, EXP	uc003ezm.3	Q9NR56	OTTHUMG00000159163	ENST00000463374.1:c.741C>T	chr3.hg19:g.152163262C>T		118.0	0.0	.		145.0	37.0	.	NM_207292	E9PBW7|O43311|O43797|Q86UV8|Q86UV9|Q96P92|Q96RE3	Silent	SNP	ENST00000463374.1	hg19	CCDS3165.1	.	.	.	.	.	.	.	.	.	.	C	9.846	1.192282	0.21954	.	.	ENSG00000152601	ENST00000464596	.	.	.	5.42	4.54	0.55810	.	.	.	.	.	T	0.69762	0.3147	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68727	-0.5332	4	.	.	.	-15.5766	13.8836	0.63696	0.0:0.927:0.0:0.073	.	.	.	.	L	246	.	.	S	+	2	0	MBNL1	153645952	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.700000	0.37815	1.284000	0.44531	0.655000	0.94253	TCA	.	.	.	none		0.507	MBNL1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353604.1	NM_021038		T	152163262	C	T	152163262	2	4	87	1	0	0	0	0	0	0	0	1	9360	816	29	2		2	MBNL1	3	152163262	Silent	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	102615266	152163262	45859168	20	5608											
USP13	8975	hgsc.bcm.edu	37	chr3	179462840	179462840	+	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	ctttcacccagatgaactgaTcgcttatgaactaacgagaa	14	10	7	10	2	1	5	1	3	0	2	2	6	1	5	1	0	3	1	1	0	5	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr3:179462840T>A	ENST00000263966.3	+	13	2015	c.1544T>A	c.(1543-1545)aTc>aAc	p.I515N	USP13_ENST00000496897.1_Missense_Mutation_p.I450N|USP13_ENST00000482333.1_3'UTR	NM_003940.2	NP_003931.2	Q92995	UBP13_HUMAN	ubiquitin specific peptidase 13 (isopeptidase T-3)	515	USP.				autophagy (GO:0006914)|cell proliferation (GO:0008283)|melanocyte differentiation (GO:0030318)|protein K63-linked deubiquitination (GO:0070536)|protein stabilization (GO:0050821)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	46	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			GATGAACTGATCGCTTATGAA	0.478																																					p.I515N		Atlas-SNP	.											.	USP13	117	.	0			c.T1544A						PASS	.						120	113	115					3																	179462840		2203	4300	6503	SO:0001583	missense	8975	exon13			AACTGATCGCTTA	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.1544T>A	chr3.hg19:g.179462840T>A	ENSP00000263966:p.Ile515Asn	117.0	0.0	.		158.0	65.0	.	NM_003940	A8K2S3|B4DYF3|D3DNS2|Q96B25	Missense_Mutation	SNP	ENST00000263966.3	hg19	CCDS3235.1	.	.	.	.	.	.	.	.	.	.	T	11.23	1.576799	0.28092	.	.	ENSG00000058056	ENST00000263966;ENST00000496897;ENST00000497155	T;T	0.13778	2.56;2.57	5.22	5.22	0.72569	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.145148	0.48286	D	0.000197	T	0.14056	0.0340	N	0.26042	0.785	0.58432	D	0.999993	P;B	0.38335	0.627;0.244	P;B	0.44422	0.449;0.281	T	0.16247	-1.0409	10	0.17832	T	0.49	-17.5512	15.1067	0.72326	0.0:0.0:0.0:1.0	.	515;515	Q92995;A8K2S3	UBP13_HUMAN;.	N	515;450;161	ENSP00000263966:I515N;ENSP00000417146:I450N	ENSP00000263966:I515N	I	+	2	0	USP13	180945534	1.000000	0.71417	0.955000	0.39395	0.938000	0.57974	6.035000	0.70940	1.966000	0.57179	0.533000	0.62120	ATC	.	.	.	none		0.478	USP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349617.1			A	179462840	T	A	179462840	3	1	87	1	0	0	0	0	1	0	0	0	17056	1435	50	5	1594	5	USP13	3	179462840	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	27299578	179462840	18559590	21	5609											
DLG1	1739	hgsc.bcm.edu	37	chr3	196888577	196888577	+	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	aggacagggatcacagggacAgtgggaggagagggaagaac	15	2	19	5	0	1	2	1	0	0	2	1	8	1	7	0	6	1	0	0	6	2	0			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr3:196888577A>T	ENST00000419354.1	-	6	802	c.516T>A	c.(514-516)acT>acA	p.T172T	DLG1_ENST00000346964.2_Silent_p.T172T|DLG1_ENST00000452595.1_Intron|DLG1_ENST00000422288.1_Intron|DLG1_ENST00000448528.2_Silent_p.T172T|DLG1_ENST00000450955.1_Intron|DLG1_ENST00000357674.4_Intron|DLG1_ENST00000392382.2_Intron|DLG1_ENST00000314062.3_Intron|DLG1_ENST00000443183.1_Intron			Q12959	DLG1_HUMAN	discs, large homolog 1 (Drosophila)	172	Interaction with SH3 domains.				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)		TCACAGGGACAGTGGGAGGAG	0.388																																					p.T172T		Atlas-SNP	.											.	DLG1	120	.	0			c.T516A						PASS	.						71	75	74					3																	196888577		2203	4300	6503	SO:0001819	synonymous_variant	1739	exon6			AGGGACAGTGGGA	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.516T>A	chr3.hg19:g.196888577A>T		381.0	0.0	.		398.0	99.0	.	NM_001098424	A5YKK7|B4DGU1|B4DGZ8|B7ZMM0|B9EIQ5|D3DXB8|D3DXB9|E7EWL7|E9PG21|Q12958	Silent	SNP	ENST00000419354.1	hg19	CCDS43194.1																																																																																			.	.	.	none		0.388	DLG1-008	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258170.2	NM_004087		T	196888577	A	T	196888577	2	4	87	1	0	0	0	0	0	0	0	1	4556	175	7	5		5	DLG1	3	196888577	Silent	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	17425737	196888577	1133853	22	5610											
CLNK	116449	hgsc.bcm.edu	37	chr4	10522421	10522421	+	Missense_Mutation	SNP	T	T	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	gaaagtgctcttacctctgtTttgcacactgtggttgcttg	6	16	10	9	0	2	0	0	0	2	0	2	1	2	0	1	1	4	5	1	1	2	5			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr4:10522421T>G	ENST00000226951.6	-	15	1005	c.766A>C	c.(766-768)Aac>Cac	p.N256H		NM_052964.2	NP_443196.2	Q7Z7G1	CLNK_HUMAN	cytokine-dependent hematopoietic cell linker	256					immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|positive regulation of signal transduction (GO:0009967)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	intracellular (GO:0005622)	SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(1)	17						TTACCTCTGTTTTGCACACTG	0.373																																					p.N256H	GBM(87;402 1286 6949 13902 35851)	Atlas-SNP	.											.	CLNK	85	.	0			c.A766C						PASS	.						140	125	129					4																	10522421		1858	4107	5965	SO:0001583	missense	116449	exon15			CTCTGTTTTGCAC	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.766A>C	chr4.hg19:g.10522421T>G	ENSP00000226951:p.Asn256His	137.0	0.0	.		104.0	35.0	.	NM_052964	Q05C27|Q9P2U9	Missense_Mutation	SNP	ENST00000226951.6	hg19	CCDS47024.1	.	.	.	.	.	.	.	.	.	.	T	8.569	0.879522	0.17467	.	.	ENSG00000109684	ENST00000226951;ENST00000429087	T	0.23552	1.9	3.58	2.44	0.29823	.	1.529250	0.03878	N	0.276734	T	0.19565	0.0470	N	0.24115	0.695	0.34150	D	0.667466	B	0.26876	0.162	B	0.30855	0.121	T	0.34179	-0.9839	10	0.46703	T	0.11	-4.8736	3.7403	0.08527	0.0:0.2405:0.0:0.7595	.	256	Q7Z7G1	CLNK_HUMAN	H	256;220	ENSP00000226951:N256H	ENSP00000226951:N256H	N	-	1	0	CLNK	10131519	0.030000	0.19436	0.584000	0.28653	0.521000	0.34408	0.593000	0.23999	0.761000	0.33130	0.379000	0.24179	AAC	.	.	.	none		0.373	CLNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359047.1	NM_052964		G	10522421	T	G	10522421	3	3	87	1	0	0	0	0	1	0	0	0	3549	1841	64	5	540	5	CLNK	4	10522421	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10		10522421	180631855	23	5611											
USP46	64854	hgsc.bcm.edu	37	chr4	53492228	53492228	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcattggtaagcgttcccTgaaaaatctcatggacccag	11	12	8	10	1	2	1	2	1	1	0	4	2	3	2	2	2	1	2	2	2	3	4			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr4:53492228T>C	ENST00000441222.3	-	4	702	c.518A>G	c.(517-519)cAg>cGg	p.Q173R	USP46_ENST00000508499.1_Missense_Mutation_p.Q166R|USP46_ENST00000451218.2_Missense_Mutation_p.Q146R	NM_022832.3	NP_073743.2	P62068	UBP46_HUMAN	ubiquitin specific peptidase 46	173	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)			AAGCGTTCCCTGAAAAATCTC	0.383																																					p.Q173R		Atlas-SNP	.											.	USP46	38	.	0			c.A518G						PASS	.						123	117	119					4																	53492228		1869	4137	6006	SO:0001583	missense	64854	exon4			GTTCCCTGAAAAA	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.518A>G	chr4.hg19:g.53492228T>C	ENSP00000407818:p.Gln173Arg	224.0	0.0	.		202.0	64.0	.	NM_022832	B7Z3Y7|B7Z675|B7Z7S3|G8ACC7|Q80V95|Q9H7U4|Q9H9T8	Missense_Mutation	SNP	ENST00000441222.3	hg19	CCDS47053.1	.	.	.	.	.	.	.	.	.	.	T	15.86	2.958840	0.53400	.	.	ENSG00000109189	ENST00000441222;ENST00000451218;ENST00000508499	T;T;T	0.31247	1.5;1.5;1.5	5.08	5.08	0.68730	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.64402	D	0.000018	T	0.33818	0.0876	M	0.67953	2.075	0.80722	D	1	B;B;B;B	0.18610	0.02;0.011;0.029;0.01	B;B;B;B	0.29077	0.059;0.059;0.098;0.025	T	0.13872	-1.0493	10	0.12430	T	0.62	-17.1457	14.345	0.66654	0.0:0.0:0.0:1.0	.	57;161;173;166	P62068-2;P62068-4;P62068;P62068-3	.;.;UBP46_HUMAN;.	R	173;146;166	ENSP00000407818:Q173R;ENSP00000390102:Q146R;ENSP00000423244:Q166R	ENSP00000407818:Q173R	Q	-	2	0	USP46	53186985	1.000000	0.71417	1.000000	0.80357	0.639000	0.38242	6.263000	0.72521	2.046000	0.60703	0.528000	0.53228	CAG	.	.	.	none		0.383	USP46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361516.2	NM_022832		C	53492228	T	C	53492228	3	2	87	1	0	0	0	0	1	0	0	0	17089	1580	55	3	606	3	USP46	4	53492228	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	42969807	53492228	137662048	24	5612											
EXOC1	55763	hgsc.bcm.edu	37	chr4	56759888	56759888	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtggaccctgcttctttccTaagtactacattgggaaatg	9	14	9	9	0	1	0	0	0	1	0	2	2	2	2	2	2	3	2	2	2	4	6			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr4:56759888T>C	ENST00000381295.2	+	15	2243	c.1895T>C	c.(1894-1896)cTa>cCa	p.L632P	EXOC1_ENST00000349598.6_Missense_Mutation_p.L617P|EXOC1_ENST00000346134.7_Missense_Mutation_p.L632P	NM_001024924.1	NP_001020095.1	Q9NV70	EXOC1_HUMAN	exocyst complex component 1	632					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)					GCTTCTTTCCTAAGTACTACA	0.343																																					p.L632P		Atlas-SNP	.											.	EXOC1	103	.	0			c.T1895C						PASS	.						95	89	91					4																	56759888		2203	4300	6503	SO:0001583	missense	55763	exon15			CTTTCCTAAGTAC	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.1895T>C	chr4.hg19:g.56759888T>C	ENSP00000370695:p.Leu632Pro	141.0	0.0	.		121.0	40.0	.	NM_018261	Q504V4|Q8WUE7|Q96T15|Q9NZE4	Missense_Mutation	SNP	ENST00000381295.2	hg19	CCDS3502.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.097917	0.76870	.	.	ENSG00000090989	ENST00000381295;ENST00000346134;ENST00000349598	.	.	.	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.80529	0.4640	M	0.80422	2.495	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.85130	0.952;0.997	T	0.83349	-0.0004	9	0.87932	D	0	.	16.0821	0.81012	0.0:0.0:0.0:1.0	.	617;632	Q9NV70-2;Q9NV70	.;EXOC1_HUMAN	P	632;632;617	.	ENSP00000326514:L632P	L	+	2	0	EXOC1	56454645	1.000000	0.71417	0.150000	0.22450	0.970000	0.65996	7.698000	0.84413	2.200000	0.70718	0.460000	0.39030	CTA	.	.	.	none		0.343	EXOC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361799.1	NM_018261		C	56759888	T	C	56759888	3	2	87	1	0	0	0	0	1	0	0	0	5303	1522	53	3	1949	3	EXOC1	4	56759888	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	3267660	56759888	134394388	25	5613											
CDKL2	8999	hgsc.bcm.edu	37	chr4	76521462	76521462	+	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	cattaatgttataaatgcctGatggggaatgtctgttcggt	10	15	11	5	1	1	1	0	1	1	0	2	2	1	2	1	3	1	2	1	3	5	4			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr4:76521462G>T	ENST00000429927.2	-	10	2088	c.1385C>A	c.(1384-1386)tCa>tAa	p.S462*	CDKL2_ENST00000307465.4_Nonsense_Mutation_p.S462*	NM_003948.3	NP_003939.1	Q92772	CDKL2_HUMAN	cyclin-dependent kinase-like 2 (CDC2-related kinase)	462					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)			ATAAATGCCTGATGGGGAATG	0.328																																					p.S462X		Atlas-SNP	.											.	CDKL2	58	.	0			c.C1385A						PASS	.						175	163	167					4																	76521462		2203	4300	6503	SO:0001587	stop_gained	8999	exon10			ATGCCTGATGGGG	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.1385C>A	chr4.hg19:g.76521462G>T	ENSP00000412365:p.Ser462*	132.0	0.0	.		101.0	5.0	.	NM_003948	B2R695	Nonsense_Mutation	SNP	ENST00000429927.2	hg19	CCDS3570.1	.	.	.	.	.	.	.	.	.	.	G	42	9.585214	0.99211	.	.	ENSG00000138769	ENST00000429927;ENST00000307465	.	.	.	4.98	4.98	0.66077	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.3084	11.0954	0.48141	0.0:0.0:0.8156:0.1844	.	.	.	.	X	462	.	ENSP00000306340:S462X	S	-	2	0	CDKL2	76740486	1.000000	0.71417	0.996000	0.52242	0.796000	0.44982	2.209000	0.42806	2.738000	0.93877	0.655000	0.94253	TCA	.	.	.	none		0.328	CDKL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252409.2	NM_003948		T	76521462	G	T	76521462	4	4	87	1	0	0	0	0	0	1	0	0	3156	1294	45	4	104	4	CDKL2	4	76521462	Nonsense_Mutation	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	19761574	76521462	114632814	26	5614											
ANTXR2	118429	hgsc.bcm.edu	37	chr4	80976344	80976344	+	Frame_Shift_Del	DEL	C	C	-																															ggacaccaacacaataaacaCtagccccaagtgacctggat																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr4:80976344delC	ENST00000307333.7	-	6	517	c.515delG	c.(514-516)agtfs	p.S172fs	ANTXR2_ENST00000295465.4_Frame_Shift_Del_p.S172fs|ANTXR2_ENST00000403729.2_Frame_Shift_Del_p.S172fs|ANTXR2_ENST00000346652.6_Frame_Shift_Del_p.S172fs|ANTXR2_ENST00000404191.1_Frame_Shift_Del_p.S95fs	NM_001145794.1	NP_001139266.1	P58335	ANTR2_HUMAN	anthrax toxin receptor 2	172	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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						ACAATAAACACTAGCCCCAAG	0.383									Juvenile Hyaline Fibromatosis																												p.S172fs		Atlas-Indel,Pindel	.											.	ANTXR2	97	.	0			c.516delT						PASS	.						75	67	69					4																	80976344		1845	4088	5933	SO:0001589	frameshift_variant	118429	exon6	Familial Cancer Database	incl. Infantile Systemic Hyalinosis	.	AY040326	CCDS47085.1, CCDS47086.1, CCDS68733.1	4q21.3	2004-01-15			ENSG00000163297	ENSG00000163297			21732	protein-coding gene	gene with protein product	"capillary morphogenesis protein 2"	608041				11683410, 12700348	Standard	NM_058172		Approved	CMG2, CMG-2, FLJ31074	uc003hlz.4	P58335	OTTHUMG00000151982	ENST00000307333.7:c.515delG	chr4.hg19:g.80976344delC	ENSP00000306185:p.Ser172fs	147.0	0.0	0		127.0	42.0	0.330709	NM_001145794	Q4W5H6|Q59E98|Q5JPE9|Q86UI1|Q8N4J8|Q8NB13|Q96NC7	Frame_Shift_Del	DEL	ENST00000307333.7	hg19	CCDS47086.1																																																																																			.	.	.	none		0.383	ANTXR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324663.1	NM_058172		-	80976344	C	-	80976344	7	5	87	1	0	1	0	1	0	0	0	0	712	565	20	0	1041	0	ANTXR2	4	80976344	Frame_Shift_Del	DEL	C	TCGA-B1-A657-01A-11D-A31X-10	4454882	80976344	110177932	27	5615											
ZNF474	133923	hgsc.bcm.edu	37	chr5	121487756	121487756	+	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	tcaccattctaaagaacccaCtttccttatcaaccaagctg	13	11	3	14	0	3	1	2	0	1	1	4	1	4	1	4	0	3	1	4	0	6	4			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr5:121487756C>A	ENST00000296600.4	+	2	454	c.71C>A	c.(70-72)aCt>aAt	p.T24N	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	24							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)		AAAGAACCCACTTTCCTTATC	0.378																																					p.T24N		Atlas-SNP	.											.	ZNF474	43	.	0			c.C71A						PASS	.						84	89	88					5																	121487756		2203	4300	6503	SO:0001583	missense	133923	exon2			AACCCACTTTCCT	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.71C>A	chr5.hg19:g.121487756C>A	ENSP00000296600:p.Thr24Asn	140.0	0.0	.		98.0	25.0	.	NM_207317	A8K4M0|Q96M07	Missense_Mutation	SNP	ENST00000296600.4	hg19	CCDS4130.1	.	.	.	.	.	.	.	.	.	.	C	12.95	2.091741	0.36952	.	.	ENSG00000164185	ENST00000296600;ENST00000504912;ENST00000505843	T	0.52526	0.66	5.05	5.05	0.67936	.	0.714933	0.11261	U	0.582526	T	0.47985	0.1475	L	0.32530	0.975	0.30368	N	0.783168	D	0.54601	0.967	P	0.52823	0.71	T	0.35051	-0.9804	10	0.31617	T	0.26	-19.2224	10.871	0.46883	0.0:0.9131:0.0:0.0869	.	24	Q6S9Z5	ZN474_HUMAN	N	24	ENSP00000296600:T24N	ENSP00000296600:T24N	T	+	2	0	ZNF474	121515655	0.887000	0.30362	1.000000	0.80357	0.931000	0.56810	1.121000	0.31283	2.624000	0.88883	0.655000	0.94253	ACT	.	.	.	none		0.378	ZNF474-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250883.2	NM_207317		A	121487756	C	A	121487756	3	1	87	1	0	0	0	0	1	0	0	0	17944	565	20	4	73	4	ZNF474	5	121487756	Missense_Mutation	SNP	C	TCGA-B1-A657-01A-11D-A31X-10		121487756	59427504	28	5616											
NKX2-5	1482	hgsc.bcm.edu	37	chr5	172660100	172660100	+	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	cgccgctccagctcatagacCtgcgcctgcgagaagagcac	9	5	11	16	4	1	3	1	0	0	3	2	4	2	3	4	0	4	3	4	0	2	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr5:172660100C>A	ENST00000329198.4	-	2	720	c.447G>T	c.(445-447)caG>caT	p.Q149H	NKX2-5_ENST00000521848.1_3'UTR|NKX2-5_ENST00000424406.2_3'UTR	NM_001166175.1|NM_001166176.1|NM_004387.3	NP_001159647.1|NP_001159648.1|NP_004378.1	P52952	NKX25_HUMAN	NK2 homeobox 5	149					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)			GCTCATAGACCTGCGCCTGCG	0.687																																					p.Q149H	Esophageal Squamous(72;810 1219 2387 13420 44943)	Atlas-SNP	.											.	NKX2-5	42	.	0			c.G447T						PASS	.						14	12	13					5																	172660100		2202	4297	6499	SO:0001583	missense	1482	exon2			ATAGACCTGCGCC	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.447G>T	chr5.hg19:g.172660100C>A	ENSP00000327758:p.Gln149His	60.0	0.0	.		74.0	22.0	.	NM_004387	A8K3K0|B4DNB6|E9PBU6	Missense_Mutation	SNP	ENST00000329198.4	hg19	CCDS4387.1	.	.	.	.	.	.	.	.	.	.	C	19.43	3.825180	0.71143	.	.	ENSG00000183072	ENST00000329198	D	0.98044	-4.68	4.21	0.675	0.17952	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.49916	D	0.000124	D	0.98950	0.9643	H	0.97564	4.03	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98290	1.0513	10	0.87932	D	0	.	9.3001	0.37840	0.0:0.6233:0.0:0.3767	.	149	P52952	NKX25_HUMAN	H	149	ENSP00000327758:Q149H	ENSP00000327758:Q149H	Q	-	3	2	NKX2-5	172592706	0.997000	0.39634	0.999000	0.59377	0.962000	0.63368	0.536000	0.23129	0.002000	0.14630	0.462000	0.41574	CAG	.	.	.	none		0.687	NKX2-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252942.2			A	172660100	C	A	172660100	3	1	87	1	0	0	0	0	1	0	0	0	10460	680	24	4	531	4	NKX2-5	5	172660100	Missense_Mutation	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	51172344	172660100	8255160	29	5617											
FGFR4	2264	hgsc.bcm.edu	37	chr5	176520385	176520385	+	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	agcctgactccagcaggcagAaccaagtctcccactttgca	11	7	8	15	0	1	2	0	1	1	1	3	2	2	2	4	1	4	3	4	1	2	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr5:176520385A>G	ENST00000292408.4	+	10	1496				FGFR4_ENST00000393637.1_Silent_p.R370R|FGFR4_ENST00000292410.3_Silent_p.R370R|FGFR4_ENST00000393648.2_Intron|FGFR4_ENST00000502906.1_Intron	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4						alveolar secondary septum development (GO:0061144)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphate ion homeostasis (GO:0055062)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of proteolysis (GO:0045862)|protein autophosphorylation (GO:0046777)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cholesterol homeostasis (GO:2000188)|regulation of extracellular matrix disassembly (GO:0010715)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Palifermin(DB00039)|Ponatinib(DB08901)	CAGCAGGCAGAACCAAGTCTC	0.642										TSP Lung(9;0.080)																											p.R370R		Atlas-SNP	.											.	FGFR4	174	.	0			c.A1110G						PASS	.						77	80	79					5																	176520385		2203	4300	6503	SO:0001627	intron_variant	2264	exon8			AGGCAGAACCAAG	AF202063	CCDS4410.1, CCDS4411.1	5q35.2	2013-09-19			ENSG00000160867	ENSG00000160867		"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3691	protein-coding gene	gene with protein product		134935					Standard	XM_005265837		Approved	JTK2, CD334	uc003mfm.3	P22455	OTTHUMG00000151523	ENST00000292408.4:c.1252-22A>G	chr5.hg19:g.176520385A>G		97.0	0.0	.		87.0	37.0	.	NM_022963	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Silent	SNP	ENST00000292408.4	hg19	CCDS4410.1																																																																																			.	.	.	none		0.642	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1			G	176520385	A	G	176520385	1	3	87	0	1	0	0	0	0	0	0	0	5875	243	9	3		3	FGFR4	5	176520385	Intron	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	3860285	176520385	4394875	30	5618											
DNAH8	1769	hgsc.bcm.edu	37	chr6	38863980	38863980	+	Missense_Mutation	SNP	A	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	cctgaagactctgtgtttgaAgtacccaaaatatatgaatt	14	13	7	7	0	1	4	0	3	1	1	1	4	1	4	2	0	1	2	2	0	8	5			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr6:38863980A>C	ENST00000359357.3	+	58	8522	c.8268A>C	c.(8266-8268)gaA>gaC	p.E2756D	DNAH8_ENST00000449981.2_Missense_Mutation_p.E2973D|DNAH8_ENST00000441566.1_Missense_Mutation_p.E2720D			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2756					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						CTGTGTTTGAAGTACCCAAAA	0.408																																					p.E2973D		Atlas-SNP	.											.	DNAH8	1239	.	0			c.A8919C						PASS	.						111	103	105					6																	38863980		2203	4300	6503	SO:0001583	missense	1769	exon60			GTTTGAAGTACCC	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.8268A>C	chr6.hg19:g.38863980A>C	ENSP00000352312:p.Glu2756Asp	143.0	0.0	.		100.0	23.0	.	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	A	11.73	1.726071	0.30593	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T;T	0.29142	1.58;1.75;1.75;1.72	5.36	4.19	0.49359	.	0.050135	0.85682	D	0.000000	T	0.09730	0.0239	L	0.41710	1.295	0.53688	D	0.99997	B	0.11235	0.004	B	0.15052	0.012	T	0.07849	-1.0751	10	0.34782	T	0.22	.	4.8304	0.13437	0.7142:0.0:0.1479:0.1378	.	2756	Q96JB1	DYH8_HUMAN	D	2961;2961;2756;2720	ENSP00000415331:E2961D;ENSP00000333363:E2961D;ENSP00000352312:E2756D;ENSP00000402294:E2720D	ENSP00000333363:E2961D	E	+	3	2	DNAH8	38971958	0.986000	0.35501	0.985000	0.45067	0.950000	0.60333	0.446000	0.21694	0.975000	0.38392	0.482000	0.46254	GAA	.	.	.	none		0.408	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		C	38863980	A	C	38863980	3	2	87	1	0	0	0	0	1	0	0	0	4609	69	3	5	8490	5	DNAH8	6	38863980	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10		38863980	132251087	31	5619											
GCLC	2729	hgsc.bcm.edu	37	chr6	53380907	53380907	+	Splice_Site	SNP	C	C	T																															caacacaaagccatactcacCtgaagcgagggtgcttgttt																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr6:53380907C>T	ENST00000229416.6	-	4	1043	c.560G>A	c.(559-561)aGt>aAt	p.S187N	GCLC_ENST00000514004.1_Splice_Site_p.S187N	NM_001197115.1|NM_001498.3	NP_001184044.1|NP_001489.1	P48506	GSH1_HUMAN	glutamate-cysteine ligase, catalytic subunit	187					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)	CCATACTCACCTGAAGCGAGG	0.468																																					p.S187N		Atlas-SNP	.											.	GCLC	58	.	0			c.G560A						PASS	.						125	118	120					6																	53380907		2203	4300	6503	SO:0001630	splice_region_variant	2729	exon4			ACTCACCTGAAGC	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.560+1G>A	chr6.hg19:g.53380907C>T		88.0	0.0	.		65.0	15.0	.	NM_001498	Q14399	Missense_Mutation	SNP	ENST00000229416.6	hg19	CCDS4952.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.532099	0.85812	.	.	ENSG00000001084	ENST00000229416;ENST00000514004;ENST00000514933	T;T;T	0.54479	0.57;0.57;0.57	5.26	5.26	0.73747	.	0.072360	0.85682	D	0.000000	T	0.43322	0.1242	M	0.68593	2.085	0.80722	D	1	P	0.45531	0.86	B	0.39503	0.301	T	0.47983	-0.9074	9	.	.	.	-14.2666	19.2221	0.93801	0.0:1.0:0.0:0.0	.	187	P48506	GSH1_HUMAN	N	187;187;134	ENSP00000229416:S187N;ENSP00000421908:S187N;ENSP00000423615:S134N	.	S	-	2	0	GCLC	53488866	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.776000	0.85560	2.622000	0.88805	0.561000	0.74099	AGT	.	.	.	none		0.468	GCLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359710.2		Missense_Mutation	T	53380907	C	T	53380907	5	4	87	1	0	0	0	0	0	0	1	0	6302	695	24	2	1405	2	GCLC	6	53380907	Splice_Site	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	14516927	53380907	117734160	32	5620	63	2									
GCLC	2729	hgsc.bcm.edu	37	chr6	53380911	53380911	+	Missense_Mutation	SNP	A	A	G																															acaaagccatactcacctgaAgcgagggtgcttgtttattg																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr6:53380911A>G	ENST00000229416.6	-	4	1039	c.556T>C	c.(556-558)Ttc>Ctc	p.F186L	GCLC_ENST00000514004.1_Missense_Mutation_p.F186L	NM_001197115.1|NM_001498.3	NP_001184044.1|NP_001489.1	P48506	GSH1_HUMAN	glutamate-cysteine ligase, catalytic subunit	186					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)	ACTCACCTGAAGCGAGGGTGC	0.473																																					p.F186L		Atlas-SNP	.											.	GCLC	58	.	0			c.T556C						PASS	.						125	118	121					6																	53380911		2203	4300	6503	SO:0001583	missense	2729	exon4			ACCTGAAGCGAGG	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.556T>C	chr6.hg19:g.53380911A>G	ENSP00000229416:p.Phe186Leu	89.0	0.0	.		67.0	16.0	.	NM_001498	Q14399	Missense_Mutation	SNP	ENST00000229416.6	hg19	CCDS4952.1	.	.	.	.	.	.	.	.	.	.	A	34	5.408603	0.96051	.	.	ENSG00000001084	ENST00000229416;ENST00000514004;ENST00000514933	T;T;T	0.76578	-1.03;0.25;-1.03	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	D	0.90642	0.7065	H	0.96080	3.765	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.93595	0.6925	10	0.87932	D	0	.	15.6543	0.77121	1.0:0.0:0.0:0.0	.	186	P48506	GSH1_HUMAN	L	186;186;133	ENSP00000229416:F186L;ENSP00000421908:F186L;ENSP00000423615:F133L	ENSP00000229416:F186L	F	-	1	0	GCLC	53488870	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.287000	0.95975	2.164000	0.68074	0.459000	0.35465	TTC	.	.	.	none		0.473	GCLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359710.2			G	53380911	A	G	53380911	3	3	87	1	0	0	0	0	1	0	0	0	6302	72	3	3	1409	3	GCLC	6	53380911	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	4	53380911	117734156	33	5621	63	2									
FAM135A	57579	hgsc.bcm.edu	37	chr6	71236101	71236101	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtactatgaagaaacagattAttcagctttggatggaacaa	16	11	9	5	0	1	3	1	1	0	2	1	5	1	5	0	2	4	2	0	2	7	5			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr6:71236101A>G	ENST00000418814.2	+	15	3928	c.3314A>G	c.(3313-3315)tAt>tGt	p.Y1105C	FAM135A_ENST00000361499.3_Missense_Mutation_p.Y909C|FAM135A_ENST00000505769.1_Missense_Mutation_p.Y685C|FAM135A_ENST00000457062.2_Missense_Mutation_p.Y892C|FAM135A_ENST00000505868.1_Missense_Mutation_p.Y1105C|FAM135A_ENST00000370479.3_Missense_Mutation_p.Y892C	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	1105										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						GAAACAGATTATTCAGCTTTG	0.348																																					p.Y1105C		Atlas-SNP	.											.	FAM135A	181	.	0			c.A3314G						PASS	.						84	91	88					6																	71236101		2203	4300	6503	SO:0001583	missense	57579	exon13			CAGATTATTCAGC	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.3314A>G	chr6.hg19:g.71236101A>G	ENSP00000410768:p.Tyr1105Cys	186.0	0.0	.		159.0	48.0	.	NM_001162529	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Missense_Mutation	SNP	ENST00000418814.2	hg19	CCDS55028.1	.	.	.	.	.	.	.	.	.	.	A	3.081	-0.188920	0.06299	.	.	ENSG00000082269	ENST00000418814;ENST00000370479;ENST00000505769;ENST00000457062;ENST00000361499;ENST00000505868	T;T;T;T;T;T	0.23552	2.22;2.22;1.9;2.22;2.22;2.2	5.9	2.09	0.27110	.	0.582275	0.19653	N	0.109143	T	0.06050	0.0157	L	0.40543	1.245	0.09310	N	1	B;B;B;B	0.09022	0.0;0.0;0.0;0.002	B;B;B;B	0.06405	0.002;0.001;0.001;0.002	T	0.35773	-0.9775	10	0.38643	T	0.18	.	3.5522	0.07851	0.6563:0.1354:0.0711:0.1372	.	1105;1105;909;892	Q9P2D6-4;Q9P2D6;Q9P2D6-2;Q9P2D6-3	.;F135A_HUMAN;.;.	C	1105;892;685;892;909;1105	ENSP00000410768:Y1105C;ENSP00000359510:Y892C;ENSP00000423785:Y685C;ENSP00000409201:Y892C;ENSP00000354913:Y909C;ENSP00000423307:Y1105C	ENSP00000354913:Y909C	Y	+	2	0	FAM135A	71292822	0.798000	0.28890	0.004000	0.12327	0.251000	0.25915	1.664000	0.37439	0.115000	0.18071	0.533000	0.62120	TAT	.	.	.	none		0.348	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819		G	71236101	A	G	71236101	3	3	87	1	0	0	0	0	1	0	0	0	5452	449	16	3	3442	3	FAM135A	6	71236101	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	17855190	71236101	99878966	34	5622											
FAM20C	56975	hgsc.bcm.edu	37	chr7	193541	193541	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagaaactgccgcccgcggcCgagccggccgagcgcgcctt	6	3	15	17	8	0	1	0	0	0	1	0	4	0	1	6	2	4	0	6	2	1	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr7:193541C>T	ENST00000313766.5	+	1	573	c.342C>T	c.(340-342)gcC>gcT	p.A114A	AC093627.12_ENST00000467050.1_RNA	NM_020223.3	NP_064608.2	Q8IXL6	DMP4_HUMAN	family with sequence similarity 20, member C	114					dentinogenesis (GO:0097187)|enamel mineralization (GO:0070166)|odontoblast differentiation (GO:0071895)|osteoclast maturation (GO:0036179)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|protein phosphorylation (GO:0006468)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of phosphorus metabolic process (GO:0051174)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|lung(2)|urinary_tract(1)	4		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.57e-17)|Epithelial(4;1.26e-16)|all cancers(6;4.79e-14)		CGCCCGCGGCCGAGCCGGCCG	0.741																																					p.A114A		Atlas-SNP	.											.	FAM20C	18	.	0			c.C342T						PASS	.						1	1	1					7																	193541		632	1547	2179	SO:0001819	synonymous_variant	56975	exon1			CGCGGCCGAGCCG	BC040074	CCDS47522.1	7p22.3	2012-11-29			ENSG00000177706	ENSG00000177706			22140	protein-coding gene	gene with protein product	"dentin matrix protein 4"	611061				17369251, 17924334	Standard	NM_020223		Approved	IMAGE:4942737, DKFZp547D065, DMP4	uc003sip.3	Q8IXL6	OTTHUMG00000151401	ENST00000313766.5:c.342C>T	chr7.hg19:g.193541C>T		21.0	0.0	.		40.0	23.0	.	NM_020223	A4D2Q5|L8B5W8|Q5I0W9|Q7Z4I0|Q9NPT2	Silent	SNP	ENST00000313766.5	hg19	CCDS47522.1																																																																																			.	.	.	none		0.741	FAM20C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322476.2	NM_020223		T	193541	C	T	193541	2	4	87	1	0	0	0	0	0	0	0	1	5543	639	23	1		1	FAM20C	7	193541	Silent	SNP	C	TCGA-B1-A657-01A-11D-A31X-10		193541	158945122	35	5623			1	14		2	2	21	N	T_C	5.232973e-05
FAM20C	56975	hgsc.bcm.edu	37	chr7	193561	193561	+	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	cgagccggccgagcgcgcctTgcgggggcgggatcccggcg	3	3	20	15	9	0	0	0	0	0	0	1	3	1	1	4	5	3	0	4	5	0	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr7:193561T>A	ENST00000313766.5	+	1	593	c.362T>A	c.(361-363)tTg>tAg	p.L121*	AC093627.12_ENST00000467050.1_RNA	NM_020223.3	NP_064608.2	Q8IXL6	DMP4_HUMAN	family with sequence similarity 20, member C	121					dentinogenesis (GO:0097187)|enamel mineralization (GO:0070166)|odontoblast differentiation (GO:0071895)|osteoclast maturation (GO:0036179)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|protein phosphorylation (GO:0006468)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of phosphorus metabolic process (GO:0051174)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|lung(2)|urinary_tract(1)	4		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.57e-17)|Epithelial(4;1.26e-16)|all cancers(6;4.79e-14)		GAGCGCGCCTTGCGGGGGCGG	0.766																																					p.L121X		Atlas-SNP	.											.	FAM20C	18	.	0			c.T362A						PASS	.						1	1	1					7																	193561		742	1670	2412	SO:0001587	stop_gained	56975	exon1			GCGCCTTGCGGGG	BC040074	CCDS47522.1	7p22.3	2012-11-29			ENSG00000177706	ENSG00000177706			22140	protein-coding gene	gene with protein product	"dentin matrix protein 4"	611061				17369251, 17924334	Standard	NM_020223		Approved	IMAGE:4942737, DKFZp547D065, DMP4	uc003sip.3	Q8IXL6	OTTHUMG00000151401	ENST00000313766.5:c.362T>A	chr7.hg19:g.193561T>A	ENSP00000322323:p.Leu121*	13.0	0.0	.		26.0	14.0	.	NM_020223	A4D2Q5|L8B5W8|Q5I0W9|Q7Z4I0|Q9NPT2	Nonsense_Mutation	SNP	ENST00000313766.5	hg19	CCDS47522.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.498085	0.85069	.	.	ENSG00000177706	ENST00000313766	.	.	.	4.45	-5.01	0.02991	.	3.462960	0.02171	U	0.059669	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	.	5.991	0.19460	0.0:0.2449:0.3819:0.3732	.	.	.	.	X	121	.	ENSP00000322323:L121X	L	+	2	0	FAM20C	288644	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	-0.083000	0.11286	-0.496000	0.06650	0.459000	0.35465	TTG	.	.	.	none		0.766	FAM20C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322476.2	NM_020223		A	193561	T	A	193561	4	1	87	1	0	0	0	0	0	1	0	0	5543	1821	63	5	364	5	FAM20C	7	193561	Nonsense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	20	193561	158945102	36	5624			1	14		2	2	21	N	T_C	5.232973e-05
THSD7A	221981	hgsc.bcm.edu	37	chr7	11582721	11582721	+	Missense_Mutation	SNP	A	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	agggataggtccagtgcataAttttaagtccattggctttg	10	14	11	6	0	0	0	0	0	0	0	2	1	2	1	2	3	1	2	2	3	3	6			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr7:11582721A>C	ENST00000423059.4	-	5	1728	c.1477T>G	c.(1477-1479)Tta>Gta	p.L493V		NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	493	TSP type-1 4. {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)		CCAGTGCATAATTTTAAGTCC	0.383										HNSCC(18;0.044)																											p.L493V		Atlas-SNP	.											.	THSD7A	219	.	0			c.T1477G						PASS	.						127	122	124					7																	11582721		1872	4098	5970	SO:0001583	missense	221981	exon5			TGCATAATTTTAA		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.1477T>G	chr7.hg19:g.11582721A>C	ENSP00000406482:p.Leu493Val	170.0	0.0	.		166.0	75.0	.	NM_015204		Missense_Mutation	SNP	ENST00000423059.4	hg19	CCDS47543.1	.	.	.	.	.	.	.	.	.	.	A	15.74	2.921725	0.52653	.	.	ENSG00000005108	ENST00000262042;ENST00000423059	T	0.60920	0.15	5.78	4.61	0.57282	.	0.197404	0.43110	D	0.000620	T	0.64735	0.2625	M	0.76574	2.34	0.45307	D	0.998302	P	0.45594	0.862	P	0.52109	0.69	T	0.61613	-0.7027	10	0.21540	T	0.41	.	10.5833	0.45267	0.8816:0.0:0.1184:0.0	.	493	Q9UPZ6	THS7A_HUMAN	V	493	ENSP00000406482:L493V	ENSP00000262042:L493V	L	-	1	2	THSD7A	11549246	0.998000	0.40836	0.998000	0.56505	0.944000	0.59088	3.710000	0.54860	2.333000	0.79357	0.482000	0.46254	TTA	.	.	.	none		0.383	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		C	11582721	A	C	11582721	3	2	87	1	0	0	0	0	1	0	0	0	15891	98	4	5	3588	5	THSD7A	7	11582721	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	11389160	11582721	147555942	37	5625											
TMED4	222068	hgsc.bcm.edu	37	chr7	44621390	44621390	+	Missense_Mutation	SNP	T	T	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	cgagggcaggaagacctcctTctgcttatcccacatctggg	8	9	11	13	1	2	1	0	0	2	1	4	3	4	2	3	3	1	2	3	3	2	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr7:44621390T>G	ENST00000457408.2	-	2	245	c.193A>C	c.(193-195)Aag>Cag	p.K65Q	TMED4_ENST00000444131.2_5'UTR|TMED4_ENST00000481238.1_Missense_Mutation_p.K65Q|TMED4_ENST00000289577.5_Missense_Mutation_p.K65Q	NM_182547.2	NP_872353.2	Q7Z7H5	TMED4_HUMAN	transmembrane emp24 protein transport domain containing 4	65	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein transport (GO:0015031)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	signal transducer activity (GO:0004871)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)	6						AAGACCTCCTTCTGCTTATCC	0.657																																					p.K65Q		Atlas-SNP	.											.	TMED4	13	.	0			c.A193C						PASS	.						99	100	100					7																	44621390		2203	4300	6503	SO:0001583	missense	222068	exon2			CCTCCTTCTGCTT	BC035467	CCDS5493.1	7p13	2004-12-21			ENSG00000158604	ENSG00000158604			22301	protein-coding gene	gene with protein product		612038				12761501	Standard	NM_182547		Approved	HNLF	uc003tli.3	Q7Z7H5	OTTHUMG00000129210	ENST00000457408.2:c.193A>C	chr7.hg19:g.44621390T>G	ENSP00000404042:p.Lys65Gln	108.0	0.0	.		115.0	49.0	.	NM_182547	A4D2K8|B4DFJ4|Q56VW3|Q7Z432|Q8N2P6	Missense_Mutation	SNP	ENST00000457408.2	hg19	CCDS5493.1	.	.	.	.	.	.	.	.	.	.	T	15.37	2.812640	0.50527	.	.	ENSG00000158604	ENST00000457408;ENST00000289577;ENST00000481238	T;T;T	0.46819	2.22;0.86;1.46	5.36	5.36	0.76844	GOLD (2);	0.227073	0.44285	D	0.000478	T	0.24353	0.0590	N	0.04018	-0.295	0.31797	N	0.628865	B;B	0.14438	0.01;0.007	B;B	0.19666	0.022;0.026	T	0.19192	-1.0313	10	0.27785	T	0.31	-9.1229	8.6427	0.33987	0.17:0.0:0.0:0.83	.	65;65	Q7Z7H5-3;Q7Z7H5	.;TMED4_HUMAN	Q	65	ENSP00000404042:K65Q;ENSP00000289577:K65Q;ENSP00000417443:K65Q	ENSP00000289577:K65Q	K	-	1	0	TMED4	44587915	0.974000	0.33945	1.000000	0.80357	0.998000	0.95712	1.146000	0.31589	2.246000	0.74042	0.533000	0.62120	AAG	.	.	.	none		0.657	TMED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251290.1	NM_182547		G	44621390	T	G	44621390	3	3	87	1	0	0	0	0	1	0	0	0	16018	1792	62	5	506	5	TMED4	7	44621390	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	33038669	44621390	114517273	38	5626											
PNPLA8	50640	hgsc.bcm.edu	37	chr7	108154603	108154603	+	Frame_Shift_Del	DEL	T	T	-																															attaccttgacagccactccTtttccttcaggaaattctag																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr7:108154603delT	ENST00000422087.1	-	5	1597	c.1191delA	c.(1189-1191)aaafs	p.K397fs	PNPLA8_ENST00000453144.1_Frame_Shift_Del_p.K297fs|PNPLA8_ENST00000257694.8_Frame_Shift_Del_p.K397fs|PNPLA8_ENST00000483879.1_Intron|PNPLA8_ENST00000426128.2_Frame_Shift_Del_p.K397fs|PNPLA8_ENST00000388728.5_Frame_Shift_Del_p.K397fs|PNPLA8_ENST00000436062.1_Frame_Shift_Del_p.K397fs	NM_015723.3	NP_056538.1	Q9NP80	PLPL8_HUMAN	patatin-like phospholipase domain containing 8	397					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						CAGCCACTCCTTTTCCTTCAG	0.353																																					p.G398fs		Atlas-Indel,Pindel	.											.	PNPLA8	82	.	0			c.1192delG						PASS	.						189	210	203					7																	108154603		2203	4300	6503	SO:0001589	frameshift_variant	50640	exon3			.	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.1191delA	chr7.hg19:g.108154603delT	ENSP00000410804:p.Lys397fs	89.0	0.0	0		106.0	23.0	0.216981	NM_001256008	A4D0S1|C9JZI4|O95035|Q8N3I3|Q9H7T5|Q9NR17|Q9NUN2|Q9NZ79	Frame_Shift_Del	DEL	ENST00000422087.1	hg19	CCDS34733.1																																																																																			.	.	.	none		0.353	PNPLA8-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337475.1	NM_015723		-	108154603	T	-	108154603	7	5	87	1	0	1	0	1	0	0	0	0	12178	1606	56	0	1189	0	PNPLA8	7	108154603	Frame_Shift_Del	DEL	T	TCGA-B1-A657-01A-11D-A31X-10	63533213	108154603	50984060	39	5627											
CHCHD3	54927	hgsc.bcm.edu	37	chr7	132570441	132570442	+	Frame_Shift_Ins	INS	-	-	G																															cctctcctccagtctagccaINSgctgttctttgtagaatgca																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr7:132570441_132570442insG	ENST00000262570.5	-	5	577_578	c.433_434insC	c.(433-435)ctgfs	p.L145fs	CHCHD3_ENST00000476546.1_5'UTR|CHCHD3_ENST00000448878.1_Frame_Shift_Ins_p.L150fs	NM_017812.2	NP_060282.1	Q9NX63	MIC19_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 3	145					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						CAGTCTAGCCAGCTGTTCTTTG	0.332																																					p.L145fs		Atlas-Indel,Pindel	.											.	CHCHD3	21	.	0			c.434_435insC						PASS	.																																			SO:0001589	frameshift_variant	54927	exon5			.	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.434dupC	chr7.hg19:g.132570442_132570442dupG	ENSP00000262570:p.Leu145fs	89.0	0.0	0		65.0	15.0	0.230769	NM_017812		Frame_Shift_Ins	INS	ENST00000262570.5	hg19	CCDS5828.1																																																																																			.	.	.	none		0.332	CHCHD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000338899.1	NM_017812		G	132570442	-	G	132570441	7	5	87	1	0	1	1	0	0	0	0	0	3319	188	7	0	265	0	CHCHD3	7	132570441	Frame_Shift_Ins	INS	-	TCGA-B1-A657-01A-11D-A31X-10	24415838	132570441	26568222	40	5628											
XRCC2	7516	hgsc.bcm.edu	37	chr7	152345944	152345944	+	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	gtcgtcgagaggcatgagaaGgttcttctgatgagctcgag	9	10	15	7	3	2	4	0	3	2	2	5	7	2	4	0	2	1	3	0	2	1	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr7:152345944G>T	ENST00000359321.1	-	3	711	c.626C>A	c.(625-627)cCt>cAt	p.P209H	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	209					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)		GGCATGAGAAGGTTCTTCTGA	0.453								Homologous recombination																													p.P209H		Atlas-SNP	.											.	XRCC2	30	.	0			c.C626A						PASS	.						180	179	180					7																	152345944		2203	4300	6503	SO:0001583	missense	7516	exon3			TGAGAAGGTTCTT	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.626C>A	chr7.hg19:g.152345944G>T	ENSP00000352271:p.Pro209His	78.0	0.0	.		90.0	17.0	.	NM_005431	B2R925	Missense_Mutation	SNP	ENST00000359321.1	hg19	CCDS5933.1	.	.	.	.	.	.	.	.	.	.	G	3.744	-0.053028	0.07362	.	.	ENSG00000196584	ENST00000359321	T	0.59364	0.27	5.06	5.06	0.68205	.	0.796894	0.11753	N	0.532874	T	0.49098	0.1537	L	0.36672	1.1	0.09310	N	1	B	0.19331	0.035	B	0.21708	0.036	T	0.38134	-0.9675	10	0.45353	T	0.12	-11.3151	10.9302	0.47213	0.0958:0.0:0.9042:0.0	.	209	O43543	XRCC2_HUMAN	H	209	ENSP00000352271:P209H	ENSP00000352271:P209H	P	-	2	0	XRCC2	151976877	0.216000	0.23585	0.036000	0.18154	0.024000	0.10985	2.673000	0.46858	2.353000	0.79882	0.467000	0.42956	CCT	.	.	.	none		0.453	XRCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322783.1	NM_005431		T	152345944	G	T	152345944	3	4	87	1	0	0	0	0	1	0	0	0	17465	1000	35	4	220	4	XRCC2	7	152345944	Missense_Mutation	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	19775503	152345944	6792719	41	5629											
WDR67	93594	hgsc.bcm.edu	37	chr8	124154514	124154514	+	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	tttcctaggtgattaaagaaAatttggcaaaggctgaacaa	16	11	9	5	0	0	3	0	2	0	1	1	3	1	3	1	3	1	2	1	3	8	4	rs144810574	byFrequency	TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr8:124154514A>T	ENST00000287380.1	+	19	2743	c.2653A>T	c.(2653-2655)Aat>Tat	p.N885Y	TBC1D31_ENST00000309336.3_Intron|TBC1D31_ENST00000378080.2_Intron|TBC1D31_ENST00000522420.1_Missense_Mutation_p.N780Y|TBC1D31_ENST00000327098.5_Intron|TBC1D31_ENST00000521676.1_Missense_Mutation_p.N762Y|TBC1D31_ENST00000518805.1_Missense_Mutation_p.N439Y	NM_145647.3	NP_663622.2	Q96DN5	TBC31_HUMAN	TBC1 domain family, member 31	885						centrosome (GO:0005813)	Rab GTPase activator activity (GO:0005097)										GATTAAAGAAAATTTGGCAAA	0.338																																					p.N885Y		Atlas-SNP	.											.	WDR67	97	.	0			c.A2653T						PASS	.						51	48	49					8																	124154514		2203	4300	6503	SO:0001583	missense	93594	exon19			AAAGAAAATTTGG	AK094612	CCDS6338.1, CCDS47916.1	8q24.13	2013-07-10	2013-07-10	2013-07-10	ENSG00000156787	ENSG00000156787		"WD repeat domain containing"	30888	protein-coding gene	gene with protein product			"WD repeat domain 67"	WDR67		12477932	Standard	NM_001145088		Approved	MGC21654, Gm85	uc003ypp.2	Q96DN5	OTTHUMG00000165081	ENST00000287380.1:c.2653A>T	chr8.hg19:g.124154514A>T	ENSP00000287380:p.Asn885Tyr	405.0	1.0	.		349.0	107.0	.	NM_145647	B7ZL19|Q2M2J9|Q3MIR6|Q8TBP9	Missense_Mutation	SNP	ENST00000287380.1	hg19	CCDS6338.1	.	.	.	.	.	.	.	.	.	.	A	10.88	1.474411	0.26423	.	.	ENSG00000156787	ENST00000287380;ENST00000522420;ENST00000521676;ENST00000518805	D;D;D;D	0.86230	-2.09;-2.09;-2.09;-2.09	5.36	4.15	0.48705	.	0.359706	0.32120	N	0.006559	T	0.80199	0.4579	L	0.29908	0.895	0.58432	D	0.999994	P;B	0.42785	0.79;0.0	B;B	0.41723	0.365;0.001	T	0.81892	-0.0724	10	0.72032	D	0.01	-12.8896	9.5604	0.39366	0.7375:0.0:0.0:0.2625	.	780;885	E7ERK7;Q96DN5	.;WDR67_HUMAN	Y	885;780;762;439	ENSP00000287380:N885Y;ENSP00000429334:N780Y;ENSP00000430628:N762Y;ENSP00000429494:N439Y	ENSP00000287380:N885Y	N	+	1	0	WDR67	124223695	0.899000	0.30636	0.992000	0.48379	0.716000	0.41182	1.826000	0.39092	2.046000	0.60703	0.386000	0.25728	AAT	.	A|0.999;C|0.001	.	alt		0.338	TBC1D31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381721.1	NM_145647		T	124154514	A	T	124154514	3	4	87	1	0	0	0	0	1	0	0	0	17330	14	1	5	2727	5	WDR67	8	124154514	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10		124154514	22209508	42	5630											
COL22A1	169044	hgsc.bcm.edu	37	chr8	139707081	139707081	+	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	agactcaccggttccccaggCaggcctggatcgcccttctc	6	8	10	17	2	2	1	1	0	1	1	5	2	3	2	5	4	0	2	5	4	0	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr8:139707081C>A	ENST00000303045.6	-	33	3080	c.2634G>T	c.(2632-2634)ctG>ctT	p.L878L	COL22A1_ENST00000435777.1_Silent_p.L878L|COL22A1_ENST00000341807.4_5'UTR	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	878	Collagen-like 7.|Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GTTCCCCAGGCAGGCCTGGAT	0.607										HNSCC(7;0.00092)																											p.L878L		Atlas-SNP	.											.	COL22A1	390	.	0			c.G2634T						PASS	.						104	98	100					8																	139707081		2203	4300	6503	SO:0001819	synonymous_variant	169044	exon33			CCCAGGCAGGCCT	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.2634G>T	chr8.hg19:g.139707081C>A		69.0	0.0	.		54.0	16.0	.	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Silent	SNP	ENST00000303045.6	hg19	CCDS6376.1																																																																																			.	.	.	none		0.607	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		A	139707081	C	A	139707081	2	1	87	1	0	0	0	0	0	0	0	1	3683	697	25	4		4	COL22A1	8	139707081	Silent	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	15552567	139707081	6656941	43	5631											
SCRIB	23513	hgsc.bcm.edu	37	chr8	144892982	144892982	+	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	aggctcccctgctgcccagcAtcctctgcagcaggtgagcg	6	7	12	16	1	1	1	0	1	1	0	3	1	3	1	4	2	6	5	4	2	0	0			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr8:144892982A>T	ENST00000320476.3	-	12	1284	c.1278T>A	c.(1276-1278)gaT>gaA	p.D426E	SCRIB_ENST00000356994.2_Missense_Mutation_p.D426E|MIR937_ENST00000401271.1_RNA|SCRIB_ENST00000377533.3_Missense_Mutation_p.D345E	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	426	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)			GCTGCCCAGCATCCTCTGCAG	0.662																																					p.D426E	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.T1278A						PASS	.						24	25	25					8																	144892982		2202	4298	6500	SO:0001583	missense	23513	exon12			CCCAGCATCCTCT	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.1278T>A	chr8.hg19:g.144892982A>T	ENSP00000322938:p.Asp426Glu	28.0	0.0	.		21.0	6.0	.	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Missense_Mutation	SNP	ENST00000320476.3	hg19	CCDS6411.1	.	.	.	.	.	.	.	.	.	.	A	15.84	2.951040	0.53186	.	.	ENSG00000180900	ENST00000356994;ENST00000320476;ENST00000377533	T;T;T	0.76448	-1.02;-1.02;-1.02	3.91	-5.87	0.02297	.	.	.	.	.	T	0.37972	0.1023	N	0.02011	-0.69	0.19775	N	0.999951	B;B	0.06786	0.001;0.0	B;B	0.06405	0.001;0.002	T	0.40683	-0.9550	9	0.06365	T	0.9	.	0.624	0.00783	0.3145:0.12:0.3208:0.2448	.	426;426	Q14160;Q14160-3	SCRIB_HUMAN;.	E	426;426;345	ENSP00000349486:D426E;ENSP00000322938:D426E;ENSP00000366756:D345E	ENSP00000322938:D426E	D	-	3	2	SCRIB	144964970	0.000000	0.05858	0.001000	0.08648	0.733000	0.41908	-0.296000	0.08287	-1.858000	0.01158	-0.464000	0.05259	GAT	.	.	.	none		0.662	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356		T	144892982	A	T	144892982	3	4	87	1	0	0	0	0	1	0	0	0	13950	214	8	5	3793	5	SCRIB	8	144892982	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	5185901	144892982	1471040	44	5632											
SHB	6461	hgsc.bcm.edu	37	chr9	37919918	37919918	+	Frame_Shift_Del	DEL	C	C	-																															agtggatgacttccgggacaCtgtcgaacggagggctgttc																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr9:37919918delC	ENST00000377707.3	-	6	1995	c.1430delG	c.(1429-1431)agtfs	p.S477fs	RP11-613M10.9_ENST00000540557.1_Intron	NM_003028.2	NP_003019.2	Q15464	SHB_HUMAN	Src homology 2 domain containing adaptor protein B	477	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(2)|endometrium(4)|lung(1)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)	11		all_epithelial(88;0.122)		GBM - Glioblastoma multiforme(29;3.27e-05)|Lung(182;0.0658)		TTCCGGGACACTGTCGAACGG	0.517																																					p.S477fs		Atlas-Indel,Pindel	.											.	SHB	31	.	0			c.1431delT						PASS	.						145	154	151					9																	37919918		2044	4183	6227	SO:0001589	frameshift_variant	6461	exon6			.		CCDS43806.1	9p13.2	2013-09-23	2005-05-24		ENSG00000107338	ENSG00000107338		"SH2 domain containing"	10838	protein-coding gene	gene with protein product		600314	"SHB adaptor protein (a Src homology 2 protein)", "SHB (Src homology 2 domain containing) adaptor protein B"			7713524	Standard	NM_003028		Approved		uc004aax.3	Q15464	OTTHUMG00000019936	ENST00000377707.3:c.1430delG	chr9.hg19:g.37919918delC	ENSP00000366936:p.Ser477fs	150.0	0.0	0		140.0	35.0	0.25	NM_003028	B9EGM0|D3DRQ5|Q504U5|Q5VUM8	Frame_Shift_Del	DEL	ENST00000377707.3	hg19	CCDS43806.1																																																																																			.	.	.	none		0.517	SHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052490.1			-	37919918	C	-	37919918	7	5	87	1	0	1	0	1	0	0	0	0	14281	565	20	0	103	0	SHB	9	37919918	Frame_Shift_Del	DEL	C	TCGA-B1-A657-01A-11D-A31X-10		37919918	103293513	45	5633											
C9orf86	55684	hgsc.bcm.edu	37	chr9	139734263	139734263	+	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	tcagactgaagaatgactcgGacctcttcgggctggggctg	8	9	14	10	2	2	4	1	2	1	2	4	5	2	5	1	4	0	2	1	4	2	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr9:139734263G>A	ENST00000311502.7	+	13	2112	c.1876G>A	c.(1876-1878)Gac>Aac	p.D626N	RABL6_ENST00000357466.2_Intron|RABL6_ENST00000371675.3_Missense_Mutation_p.D511N|RABL6_ENST00000432842.2_3'UTR|RABL6_ENST00000371663.4_Missense_Mutation_p.D627N			Q3YEC7	RABL6_HUMAN	RAB, member RAS oncogene family-like 6	626					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)										GAATGACTCGGACCTCTTCGG	0.657																																					p.D627N		Atlas-SNP	.											.	.	.	.	0			c.G1879A						PASS	.						29	35	33					9																	139734263		1894	4100	5994	SO:0001583	missense	55684	exon13			GACTCGGACCTCT	AK094382	CCDS48058.1, CCDS55352.1, CCDS55353.1	9q34.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000196642	ENSG00000196642			24703	protein-coding gene	gene with protein product	"Rab-like protein 1", "partner of ARF"	610615	"chromosome 9 open reading frame 86"	C9orf86		14702039, 16582619, 17962191, 19433581	Standard	NM_024718		Approved	FLJ10101, FLJ13045, pp8875, bA216L13.9, Parf, RBEL1	uc004cjj.1	Q3YEC7	OTTHUMG00000020947	ENST00000311502.7:c.1876G>A	chr9.hg19:g.139734263G>A	ENSP00000311134:p.Asp626Asn	33.0	0.0	.		49.0	18.0	.	NM_001173988	A8QVZ7|A8QVZ8|C6K8I4|C6K8I5|Q4F968|Q5T5R7|Q8IWK1|Q8TCL4|Q8WU94|Q96SR8|Q9BU21|Q9H935	Missense_Mutation	SNP	ENST00000311502.7	hg19	CCDS48058.1	.	.	.	.	.	.	.	.	.	.	.	19.33	3.807620	0.70797	.	.	ENSG00000196642	ENST00000371663;ENST00000311502;ENST00000371675;ENST00000435930	T;T;T;T	0.80909	-1.11;-1.14;-1.13;-1.43	4.72	4.72	0.59763	.	0.000000	0.85682	D	0.000000	D	0.88930	0.6571	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;0.996	D	0.90196	0.4253	10	0.66056	D	0.02	-24.3311	15.167	0.72837	0.0:0.0:1.0:0.0	.	420;627;626	B1AMX5;Q3YEC7-2;Q3YEC7	.;.;PARF_HUMAN	N	627;626;511;420	ENSP00000360727:D627N;ENSP00000311134:D626N;ENSP00000360740:D511N;ENSP00000408442:D420N	ENSP00000311134:D626N	D	+	1	0	C9orf86	138854084	1.000000	0.71417	0.511000	0.27724	0.034000	0.12701	7.931000	0.87625	2.162000	0.67917	0.561000	0.74099	GAC	.	.	.	none		0.657	RABL6-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055141.4	NM_024718		A	139734263	G	A	139734263	3	1	87	1	0	0	0	0	1	0	0	0	2504	1174	41	2	2173	2	C9orf86	9	139734263	Missense_Mutation	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	101814345	139734263	1479168	46	5634											
PTEN	5728	hgsc.bcm.edu	37	chr10	89692845	89692845	+	Frame_Shift_Del	DEL	A	A	-																															cttttgtgaagatcttgaccAatggctaagtgaagatgaca																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr10:89692845delA	ENST00000371953.3	+	5	1686	c.329delA	c.(328-330)caafs	p.Q110fs		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	110	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.R55fs*1(5)|p.?(5)|p.Y27fs*1(2)|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)		GATCTTGACCAATGGCTAAGT	0.398		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.Q110fs		Atlas-Indel,Pindel	.	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,0,6	PTEN	3652	.	50	Whole gene deletion(37)|Deletion - Frameshift(8)|Unknown(5)	prostate(16)|central_nervous_system(11)|skin(6)|lung(5)|haematopoietic_and_lymphoid_tissue(4)|breast(3)|ovary(3)|soft_tissue(1)|urinary_tract(1)	c.328delC						PASS	.						127	117	121					10																	89692845		2203	4297	6500	SO:0001589	frameshift_variant	5728	exon5	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.329delA	chr10.hg19:g.89692845delA	ENSP00000361021:p.Gln110fs	229.0	0.0	0		224.0	59.0	0.263393	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Frame_Shift_Del	DEL	ENST00000371953.3	hg19	CCDS31238.1																																																																																			.	.	.	none		0.398	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		-	89692845	A	-	89692845	7	5	87	1	0	1	0	1	0	0	0	0	12748	130	5	0	347	0	PTEN	10	89692845	Frame_Shift_Del	DEL	A	TCGA-B1-A657-01A-11D-A31X-10		89692845	45841902	47	5635											
SYCE1	93426	hgsc.bcm.edu	37	chr10	135372389	135372390	+	Missense_Mutation	DNP	AG	AG	TT																															cggctctcttacgcgagtccAgttccttctgcagggcctca																										TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr10:135372389_135372390AG>TT	ENST00000343131.5	-	4	366_367	c.262_263CT>AA	c.(262-264)CTg>AAg	p.L88K	SYCE1_ENST00000368517.3_Missense_Mutation_p.L52K|SYCE1_ENST00000432597.2_Missense_Mutation_p.L52K|SPRN_ENST00000541506.1_Intron	NM_001143764.1	NP_001137236.1	Q8N0S2	SYCE1_HUMAN	synaptonemal complex central element protein 1	88					synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|stomach(3)|urinary_tract(1)	19		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		ACGCGAGTCCAGTTCCTTCTGC	0.53																																					p.L88Q|p.L88M		Atlas-SNP	.											.	SYCE1	81	.	0			c.T263A|c.C262A						PASS	.																																			SO:0001583	missense	93426	exon4			GAGTCCAGTTCCT|AGTCCAGTTCCTT	AY027808	CCDS7687.1, CCDS44500.1, CCDS44501.1	10q26.3	2009-03-12	2005-09-27	2005-09-27	ENSG00000171772	ENSG00000171772			28852	protein-coding gene	gene with protein product	"cancer/testis antigen 76"	611486	"chromosome 10 open reading frame 94"	C10orf94		11829491	Standard	NM_130784		Approved	bA108K14.6, CT76	uc001lno.2	Q8N0S2	OTTHUMG00000019321	ENST00000343131.5:c.262_263delinsTT	chr10.hg19:g.135372389_135372390delinsTT	ENSP00000341282:p.Leu88Lys	59.0|60.0	0.0	.		72.0	21.0|22.0	.	NM_001143763	B2RC80|Q9BWU3|Q9BWU4	Missense_Mutation	SNP	ENST00000343131.5	hg19	CCDS44501.1																																																																																			.	.	.	none		0.53	SYCE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_201564		TT	135372390	AG	TT	135372389	3	4	87	1	0	0	0	0	1	0	0	0	15440	188	7	5	875	5	SYCE1	10	135372389	Missense_Mutation	DNP	AG	TCGA-B1-A657-01A-11D-A31X-10	45679544	135372389	162358	48	5636											
DAK	26007	hgsc.bcm.edu	37	chr11	61111339	61111339	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcccttagatgctgaaaccActgcagcagcctggcctaac	10	8	9	14	0	0	2	0	1	0	1	0	2	0	2	4	1	7	3	4	1	3	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr11:61111339A>G	ENST00000394900.3	+	12	1223	c.994A>G	c.(994-996)Act>Gct	p.T332A		NM_015533.3	NP_056348.2	Q3LXA3	DHAK_HUMAN	dihydroxyacetone kinase 2 homolog (S. cerevisiae)	332	DhaK. {ECO:0000255|PROSITE- ProRule:PRU00814}.				carbohydrate phosphorylation (GO:0046835)|cellular carbohydrate metabolic process (GO:0044262)|glycerol metabolic process (GO:0006071)|innate immune response (GO:0045087)|regulation of innate immune response (GO:0045088)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|FAD-AMP lyase (cyclizing) activity (GO:0034012)|glycerone kinase activity (GO:0004371)|metal ion binding (GO:0046872)|triokinase activity (GO:0050354)			NS(1)|breast(3)|endometrium(3)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	23						TGCTGAAACCACTGCAGCAGC	0.627																																					p.T332A		Atlas-SNP	.											.	DAK	52	.	0			c.A994G						PASS	.						88	95	93					11																	61111339		2203	4299	6502	SO:0001583	missense	26007	exon12			GAAACCACTGCAG		CCDS8003.1	11q12.2	2009-11-06	2006-04-04		ENSG00000149476	ENSG00000149476			24552	protein-coding gene	gene with protein product		615844	"dihydroxyacetone kinase 2 homolog (yeast)"				Standard	XM_005273898		Approved	DKFZP586B1621, NET45	uc001nre.3	Q3LXA3	OTTHUMG00000168076	ENST00000394900.3:c.994A>G	chr11.hg19:g.61111339A>G	ENSP00000378360:p.Thr332Ala	44.0	0.0	.		53.0	16.0	.	NM_015533	Q2L9C1|Q53EQ9|Q9BVA7|Q9H895	Missense_Mutation	SNP	ENST00000394900.3	hg19	CCDS8003.1	.	.	.	.	.	.	.	.	.	.	A	9.592	1.126311	0.20959	.	.	ENSG00000149476	ENST00000394900;ENST00000529479	T;T	0.29142	1.58;1.58	5.84	3.45	0.39498	Dak kinase (2);	0.410578	0.28219	N	0.016157	T	0.18045	0.0433	N	0.25957	0.775	0.19575	N	0.999969	B;B	0.11235	0.004;0.0	B;B	0.16289	0.015;0.005	T	0.21280	-1.0250	10	0.25106	T	0.35	-6.7353	5.6557	0.17640	0.6665:0.0:0.0707:0.2628	.	332;332	Q2L9C1;Q3LXA3	.;DHAK_HUMAN	A	332;331	ENSP00000378360:T332A;ENSP00000432539:T331A	ENSP00000378360:T332A	T	+	1	0	DAK	60867915	0.984000	0.35163	0.040000	0.18447	0.922000	0.55478	3.052000	0.49893	0.443000	0.26582	0.533000	0.62120	ACT	.	.	.	none		0.627	DAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394425.4	NM_015533		G	61111339	A	G	61111339	3	3	87	1	0	0	0	0	1	0	0	0	4230	159	6	3	1036	3	DAK	11	61111339	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10		61111339	73895177	49	5637											
CCDC87	55231	hgsc.bcm.edu	37	chr11	66359427	66359427	+	Missense_Mutation	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	caactgcttcagatcctcagCcacgatgagcccagtcagct	10	8	8	15	1	3	2	3	1	0	1	4	3	4	2	3	0	5	2	3	0	1	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr11:66359427C>T	ENST00000333861.3	-	1	1127	c.1060G>A	c.(1060-1062)Gct>Act	p.A354T	CCS_ENST00000310190.4_5'Flank|CCS_ENST00000533244.1_5'Flank	NM_018219.2	NP_060689.2	Q9NVE4	CCD87_HUMAN	coiled-coil domain containing 87	354					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						AGATCCTCAGCCACGATGAGC	0.587																																					p.A354T		Atlas-SNP	.											.	CCDC87	83	.	0			c.G1060A						PASS	.						49	55	53					11																	66359427		2200	4295	6495	SO:0001583	missense	55231	exon1			CCTCAGCCACGAT	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.1060G>A	chr11.hg19:g.66359427C>T	ENSP00000328487:p.Ala354Thr	54.0	0.0	.		69.0	29.0	.	NM_018219	Q8NE76	Missense_Mutation	SNP	ENST00000333861.3	hg19	CCDS8145.1	.	.	.	.	.	.	.	.	.	.	C	13.95	2.390249	0.42410	.	.	ENSG00000182791	ENST00000333861	T	0.32753	1.44	5.3	1.08	0.20341	.	0.256314	0.25159	N	0.032698	T	0.24353	0.0590	M	0.67953	2.075	0.31044	N	0.715953	B	0.27882	0.192	B	0.21151	0.033	T	0.13150	-1.0520	10	0.44086	T	0.13	.	3.6025	0.08030	0.1848:0.5359:0.0:0.2793	.	354	Q9NVE4	CCD87_HUMAN	T	354	ENSP00000328487:A354T	ENSP00000328487:A354T	A	-	1	0	CCDC87	66116003	0.993000	0.37304	0.982000	0.44146	0.282000	0.26991	0.720000	0.25896	0.395000	0.25257	-0.251000	0.11542	GCT	.	.	.	none		0.587	CCDC87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393825.1	NM_018219		T	66359427	C	T	66359427	3	4	87	1	0	0	0	0	1	0	0	0	2864	739	26	2	1493	2	CCDC87	11	66359427	Missense_Mutation	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	5248088	66359427	68647089	50	5638											
ANKRD13D	338692	hgsc.bcm.edu	37	chr11	67058950	67058950	+	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	gctctggtttctcttaggccCccgatttctacgttgagatg	5	15	10	11	2	3	1	0	1	3	1	4	3	3	1	2	2	1	3	2	2	2	5	rs373999660		TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr11:67058950C>A	ENST00000447274.2	+	4	1269	c.94C>A	c.(94-96)Ccc>Acc	p.P32T	ANKRD13D_ENST00000514166.1_Missense_Mutation_p.P32T|ANKRD13D_ENST00000308440.6_Missense_Mutation_p.P32T|ANKRD13D_ENST00000511455.2_Missense_Mutation_p.P119T			Q6ZTN6	AN13D_HUMAN	ankyrin repeat domain 13 family, member D	32						endosome (GO:0005768)|plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			CTCTTAGGCCCCCGATTTCTA	0.627																																					p.P119T		Atlas-SNP	.											.	ANKRD13D	71	.	0			c.C355A						PASS	.						58	61	60					11																	67058950		2200	4295	6495	SO:0001583	missense	338692	exon4			TAGGCCCCCGATT	AK027313	CCDS31616.1, CCDS31616.2	11q13.2	2013-01-11		2005-08-09	ENSG00000172932	ENSG00000172932		"Ankyrin repeat domain containing"	27880	protein-coding gene	gene with protein product		615126					Standard	NM_207354		Approved		uc001okd.2	Q6ZTN6	OTTHUMG00000162929	ENST00000447274.2:c.94C>A	chr11.hg19:g.67058950C>A	ENSP00000402616:p.Pro32Thr	54.0	0.0	.		36.0	10.0	.	NM_207354	D6RCN6|Q0VAK0|Q0VGC3|Q6ZVD0|Q86SU1	Missense_Mutation	SNP	ENST00000447274.2	hg19		.	.	.	.	.	.	.	.	.	.	C	14.41	2.526001	0.44969	.	.	ENSG00000172932	ENST00000447274;ENST00000511455;ENST00000308440;ENST00000514166	T;T;T;T	0.35048	1.33;1.49;1.33;1.33	3.95	3.02	0.34903	.	0.093915	0.45361	D	0.000371	T	0.45538	0.1347	M	0.67397	2.05	0.45108	D	0.998126	P;D	0.59357	0.887;0.985	B;P	0.53809	0.441;0.735	T	0.44862	-0.9300	10	0.66056	D	0.02	-20.8257	8.6108	0.33801	0.0:0.7549:0.157:0.0882	.	119;32	Q6ZTN6-3;Q6ZTN6	.;AN13D_HUMAN	T	32;119;32;32	ENSP00000402616:P32T;ENSP00000427130:P119T;ENSP00000310874:P32T;ENSP00000444404:P32T	ENSP00000310874:P32T	P	+	1	0	ANKRD13D	66815526	0.007000	0.16637	0.972000	0.41901	0.271000	0.26615	1.546000	0.36179	1.014000	0.39417	0.561000	0.74099	CCC	.	.	.	alt		0.627	ANKRD13D-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000371067.2	NM_207354		A	67058950	C	A	67058950	3	1	87	1	0	0	0	0	1	0	0	0	644	623	22	4	369	4	ANKRD13D	11	67058950	Missense_Mutation	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	699523	67058950	67947566	51	5639											
PITPNM1	9600	hgsc.bcm.edu	37	chr11	67267651	67267651	+	Silent	SNP	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	ggggaggcatctgggcctggGggggcctcaggcccatcggg	4	5	21	11	1	2	0	1	0	1	0	3	1	2	1	3	9	0	1	3	9	0	0			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr11:67267651G>A	ENST00000534749.1	-	5	1070	c.882C>T	c.(880-882)ccC>ccT	p.P294P	PITPNM1_ENST00000356404.3_Silent_p.P294P|PITPNM1_ENST00000436757.2_Silent_p.P294P			O00562	PITM1_HUMAN	phosphatidylinositol transfer protein, membrane-associated 1	294					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						CTGGGCCTGGGGGGGCCTCAG	0.692																																					p.P294P	GBM(28;144 709 4607 5525)	Atlas-SNP	.											.	PITPNM1	84	.	0			c.C882T						PASS	.						25	31	29					11																	67267651		2171	4250	6421	SO:0001819	synonymous_variant	9600	exon6			GCCTGGGGGGGCC	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.882C>T	chr11.hg19:g.67267651G>A		13.0	0.0	.		23.0	11.0	.	NM_001130848	A6NME4|Q6T7X3|Q8TBN3|Q9BZ73	Silent	SNP	ENST00000534749.1	hg19	CCDS31620.1																																																																																			.	.	.	none		0.692	PITPNM1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395520.1	NM_004910		A	67267651	G	A	67267651	2	1	87	1	0	0	0	0	0	0	0	1	11957	1219	43	2		2	PITPNM1	11	67267651	Silent	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	208701	67267651	67738865	52	5640											
LASS5	91012	hgsc.bcm.edu	37	chr12	50529605	50529605	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccgctgatacttggcataaTtggccagtttggctgcctgg	6	12	13	10	1	0	1	0	1	0	0	0	1	0	1	3	4	2	4	3	4	2	5			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr12:50529605T>C	ENST00000317551.6	-	8	906	c.782A>G	c.(781-783)aAt>aGt	p.N261S	CERS5_ENST00000422340.2_Missense_Mutation_p.N203S	NM_147190.2	NP_671723.1	Q8N5B7	CERS5_HUMAN	ceramide synthase 5	261	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)										CTTGGCATAATTGGCCAGTTT	0.428																																					p.N261S		Atlas-SNP	.											.	.	.	.	0			c.A782G						PASS	.						92	88	89					12																	50529605		2203	4300	6503	SO:0001583	missense	91012	exon8			GCATAATTGGCCA		CCDS8801.1, CCDS61120.1	12q13.12	2014-09-04	2011-07-08	2011-07-08	ENSG00000139624			"Homeoboxes / CERS class"	23749	protein-coding gene	gene with protein product		615335	"LAG1 longevity assurance homolog 5 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 5"	LASS5			Standard	NM_147190		Approved	Trh4, MGC45411, FLJ25304	uc001rwd.4	Q8N5B7	OTTHUMG00000169819	ENST00000317551.6:c.782A>G	chr12.hg19:g.50529605T>C	ENSP00000325485:p.Asn261Ser	107.0	0.0	.		87.0	20.0	.	NM_147190	B4DV54	Missense_Mutation	SNP	ENST00000317551.6	hg19	CCDS8801.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.79|15.79	2.936979|2.936979	0.52972|0.52972	.|.	.|.	ENSG00000139624|ENSG00000139624	ENST00000550547;ENST00000547800|ENST00000551005;ENST00000317551;ENST00000422340	.|D;D;D	.|0.84660	.|-1.88;-1.88;-1.88	4.7|4.7	4.7|4.7	0.59300|0.59300	.|TRAM/LAG1/CLN8 homology domain (3);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.86239|0.86239	0.5885|0.5885	L|L	0.58101|0.58101	1.795|1.795	0.58432|0.58432	D|D	0.999999|0.999999	.|P;B;P	.|0.40794	.|0.688;0.198;0.729	.|P;B;P	.|0.47346	.|0.491;0.14;0.544	D|D	0.86223|0.86223	0.1632|0.1632	5|10	.|0.42905	.|T	.|0.14	-12.9936|-12.9936	14.6573|14.6573	0.68844|0.68844	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|203;261;180	.|B4DV54;Q8N5B7;F8W0U5	.|.;CERS5_HUMAN;.	V|S	63;165|180;261;203	.|ENSP00000447556:N180S;ENSP00000325485:N261S;ENSP00000389050:N203S	.|ENSP00000325485:N261S	I|N	-|-	1|2	0|0	CERS5|CERS5	48815872|48815872	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	7.868000|7.868000	0.87116|0.87116	2.099000|2.099000	0.63709|0.63709	0.533000|0.533000	0.62120|0.62120	ATT|AAT	.	.	.	none		0.428	CERS5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406069.3	NM_147190		C	50529605	T	C	50529605	3	2	87	1	0	0	0	0	1	0	0	0	8649	1493	52	3	408	3	LASS5	12	50529605	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10		50529605	83322290	53	5641											
SIRT4	23409	hgsc.bcm.edu	37	chr12	120750516	120750517	+	Frame_Shift_Del	DEL	AA	AA	-																															tgtgcacaagcgtgtaaaagAagccgactccctcttggtgg																								rs16950058|rs201277474	byFrequency	TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr12:120750516_120750517delAA	ENST00000202967.4	+	3	814_815	c.755_756delAA	c.(754-756)gaafs	p.E252fs	RNU6-1088P_ENST00000516850.1_RNA|SIRT4_ENST00000537892.1_3'UTR	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)					CGTGTAAAAGAAGCCGACTCCC	0.525																																					p.252_252del		Atlas-INDEL	.											.	SIRT4	29	.	0			c.754_755del						PASS	.																																			SO:0001589	frameshift_variant	23409	exon3			.	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.755_756delAA	chr12.hg19:g.120750516_120750517delAA	ENSP00000202967:p.Glu252fs	146.0	0.0	0		104.0	29.0	0.278846	NM_012240		Frame_Shift_Del	DEL	ENST00000202967.4	hg19	CCDS9194.1																																																																																			.	.	.	none		0.525	SIRT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402003.1	NM_012240		-	120750517	AA	-	120750516	7	5	87	1	0	1	0	1	0	0	0	0	14353	246	9	0	761	0	SIRT4	12	120750516	Frame_Shift_Del	DEL	AA	TCGA-B1-A657-01A-11D-A31X-10	70220911	120750516	13101379	54	5642											
GSX1	219409	hgsc.bcm.edu	37	chr13	28367053	28367053	+	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	ggccccccgggccgcccgcgCtgcctctactcaaggcttcc	3	6	11	21	4	2	0	1	0	1	0	3	0	3	0	7	3	2	2	7	3	2	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr13:28367053C>T	ENST00000302945.2	+	1	274	c.226C>T	c.(226-228)Ctg>Ttg	p.L76L		NM_145657.1	NP_663632.1	Q9H4S2	GSX1_HUMAN	GS homeobox 1	76					adenohypophysis development (GO:0021984)|hypothalamus development (GO:0021854)|neuron fate commitment (GO:0048663)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spinal cord association neuron differentiation (GO:0021527)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)	4		Lung SC(185;0.0161)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	GBM - Glioblastoma multiforme(144;0.0402)|all cancers(112;0.0404)|OV - Ovarian serous cystadenocarcinoma(117;0.197)		gccgcccgcgcTGCCTCTACT	0.741																																					p.L76L		Atlas-SNP	.											.	GSX1	20	.	0			c.C226T						PASS	.						2	3	3					13																	28367053		1552	3186	4738	SO:0001819	synonymous_variant	219409	exon1			CCCGCGCTGCCTC	AB044157	CCDS9326.1	13q12.2	2012-03-09		2007-07-26	ENSG00000169840	ENSG00000169840		"Homeoboxes / ANTP class : HOXL subclass"	20374	protein-coding gene	gene with protein product				GSH1			Standard	NM_145657		Approved	Gsh-1	uc001urr.1	Q9H4S2	OTTHUMG00000016637	ENST00000302945.2:c.226C>T	chr13.hg19:g.28367053C>T		11.0	0.0	.		16.0	4.0	.	NM_145657	Q9UD62	Silent	SNP	ENST00000302945.2	hg19	CCDS9326.1																																																																																			.	.	.	none		0.741	GSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044309.2	NM_145657		T	28367053	C	T	28367053	2	4	87	1	0	0	0	0	0	0	0	1	6856	796	28	2		2	GSX1	13	28367053	Silent	SNP	C	TCGA-B1-A657-01A-11D-A31X-10		28367053	86802825	55	5643											
NBEA	26960	hgsc.bcm.edu	37	chr13	35758158	35758158	+	Missense_Mutation	SNP	T	T	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	tccaagtttgaaccatggatTccttgccaagttaattcctg	10	14	7	10	0	0	1	0	1	0	0	3	2	3	2	5	1	2	2	5	1	4	5			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr13:35758158T>G	ENST00000400445.3	+	30	5411	c.4877T>G	c.(4876-4878)tTc>tGc	p.F1626C	NBEA_ENST00000540320.1_Missense_Mutation_p.F1626C|NBEA_ENST00000379939.2_Missense_Mutation_p.F1623C|NBEA_ENST00000310336.4_Missense_Mutation_p.F1626C	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1626					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)		AACCATGGATTCCTTGCCAAG	0.413																																					p.F1626C		Atlas-SNP	.											.	NBEA	340	.	0			c.T4877G						PASS	.						122	110	113					13																	35758158		1890	4124	6014	SO:0001583	missense	26960	exon30			ATGGATTCCTTGC	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.4877T>G	chr13.hg19:g.35758158T>G	ENSP00000383295:p.Phe1626Cys	89.0	0.0	.		102.0	32.0	.	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	T	14.31	2.497854	0.44455	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	T;T;T;T	0.50277	0.76;0.75;0.75;0.76	5.82	5.82	0.92795	.	0.290400	0.35291	N	0.003313	T	0.31796	0.0808	N	0.08118	0	0.80722	D	1	B	0.27732	0.187	B	0.30855	0.121	T	0.19745	-1.0296	10	0.45353	T	0.12	.	14.7488	0.69508	0.0:0.0:0.0:1.0	.	1623	Q5T321	.	C	1626;1626;1623;1626	ENSP00000440951:F1626C;ENSP00000383295:F1626C;ENSP00000369271:F1623C;ENSP00000308534:F1626C	ENSP00000308534:F1626C	F	+	2	0	NBEA	34656158	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.896000	0.63222	2.222000	0.72286	0.383000	0.25322	TTC	.	.	.	none		0.413	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		G	35758158	T	G	35758158	3	3	87	1	0	0	0	0	1	0	0	0	10194	1783	62	5	4995	5	NBEA	13	35758158	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	7391105	35758158	79411720	56	5644											
IRS2	8660	hgsc.bcm.edu	37	chr13	110436093	110436093	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgaccgcgtcgctgggggAcacgttgaggtagtccccgt	5	8	17	11	5	0	2	0	2	0	0	2	3	1	3	3	4	0	3	3	4	1	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr13:110436093A>G	ENST00000375856.3	-	1	2822	c.2308T>C	c.(2308-2310)Tcc>Ccc	p.S770P		NM_003749.2	NP_003740.2	Q9Y4H2	IRS2_HUMAN	insulin receptor substrate 2	770					brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular response to glucose stimulus (GO:0071333)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid homeostasis (GO:0055088)|mammary gland development (GO:0030879)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of kinase activity (GO:0033673)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mesenchymal cell proliferation (GO:0002053)|regulation of lipid metabolic process (GO:0019216)|response to glucose (GO:0009749)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	19	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)			TCGCTGGGGGACACGTTGAGG	0.682																																					p.S770P	Melanoma(100;613 2409 40847)	Atlas-SNP	.											IRS2,colon,carcinoma,0,1	IRS2	44	.	0			c.T2308C						PASS	.						20	13	15					13																	110436093		2115	4168	6283	SO:0001583	missense	8660	exon1			TGGGGGACACGTT	AB000732	CCDS9510.1	13q34	2013-01-10			ENSG00000185950	ENSG00000185950		"Pleckstrin homology (PH) domain containing"	6126	protein-coding gene	gene with protein product		600797				9312143	Standard	NM_003749		Approved		uc001vqv.3	Q9Y4H2	OTTHUMG00000017338	ENST00000375856.3:c.2308T>C	chr13.hg19:g.110436093A>G	ENSP00000365016:p.Ser770Pro	33.0	0.0	.		49.0	2.0	.	NM_003749	Q96RR2|Q9BZG0|Q9Y6I5	Missense_Mutation	SNP	ENST00000375856.3	hg19	CCDS9510.1	.	.	.	.	.	.	.	.	.	.	A	13.36	2.213503	0.39102	.	.	ENSG00000185950	ENST00000375856	T	0.22336	1.96	4.34	4.34	0.51931	.	0.000000	0.85682	D	0.000000	T	0.47967	0.1474	M	0.80746	2.51	0.58432	D	0.999993	D	0.76494	0.999	D	0.83275	0.996	T	0.54629	-0.8265	10	0.72032	D	0.01	-21.3465	13.69	0.62539	1.0:0.0:0.0:0.0	.	770	Q9Y4H2	IRS2_HUMAN	P	770	ENSP00000365016:S770P	ENSP00000365016:S770P	S	-	1	0	IRS2	109234094	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	4.780000	0.62382	1.821000	0.53095	0.448000	0.29417	TCC	.	.	.	none		0.682	IRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045755.1	NM_003749		G	110436093	A	G	110436093	3	3	87	1	0	0	0	0	1	0	0	0	7848	275	10	3	1716	3	IRS2	13	110436093	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	74677935	110436093	4733785	57	5645											
GPR137C	283554	hgsc.bcm.edu	37	chr14	53099007	53099007	+	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	aaagtccatttaattatggcTgggataatctttcagataag	14	14	8	5	0	2	1	1	0	1	1	3	2	3	2	1	2	0	1	1	2	5	6			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr14:53099007T>A	ENST00000321662.6	+	4	847	c.847T>A	c.(847-849)Tgg>Agg	p.W283R		NM_001099652.1	NP_001093122.1	Q8N3F9	G137C_HUMAN	G protein-coupled receptor 137C	283						integral component of membrane (GO:0016021)				NS(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	8	Breast(41;0.0716)					TAATTATGGCTGGGATAATCT	0.378																																					p.W283R		Atlas-SNP	.											.	GPR137C	24	.	0			c.T847A						PASS	.						125	122	123					14																	53099007		1858	4099	5957	SO:0001583	missense	283554	exon4			TATGGCTGGGATA	BX647179	CCDS45106.1	14q22.1	2012-08-10				ENSG00000180998			25445	protein-coding gene	gene with protein product							Standard	NM_001099652		Approved	DKFZp762F0713, TM7SF1L2	uc001wzu.4	Q8N3F9		ENST00000321662.6:c.847T>A	chr14.hg19:g.53099007T>A	ENSP00000315106:p.Trp283Arg	166.0	0.0	.		126.0	24.0	.	NM_001099652	Q86SM2	Missense_Mutation	SNP	ENST00000321662.6	hg19	CCDS45106.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.1|25.1	4.606362|4.606362	0.87157|0.87157	.|.	.|.	ENSG00000180998|ENSG00000180998	ENST00000542169|ENST00000321662	.|T	.|0.62498	.|0.02	5.58|5.58	5.58|5.58	0.84498|0.84498	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.77942|0.77942	0.4206|0.4206	M|M	0.68952|0.68952	2.095|2.095	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.999;0.999	T|T	0.80360|0.80360	-0.1415|-0.1415	5|10	.|0.87932	.|D	.|0	-12.2616|-12.2616	16.0439|16.0439	0.80704|0.80704	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|283;112	.|Q8N3F9;B3KW22	.|G137C_HUMAN;.	Q|R	252|283	.|ENSP00000315106:W283R	.|ENSP00000315106:W283R	L|W	+|+	2|1	0|0	GPR137C|GPR137C	52168757|52168757	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.499000|7.499000	0.81566|0.81566	2.250000|2.250000	0.74265|0.74265	0.482000|0.482000	0.46254|0.46254	CTG|TGG	.	.	.	none		0.378	GPR137C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411685.1	XM_290615		A	53099007	T	A	53099007	3	1	87	1	0	0	0	0	1	0	0	0	6654	1580	55	5	861	5	GPR137C	14	53099007	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10		53099007	54250533	58	5646											
DNAJC17	55192	hgsc.bcm.edu	37	chr15	41099608	41099608	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcaatgcctagcagcgcgtAcaggtccatctgtaagagct	10	9	10	12	2	2	1	1	0	1	1	3	1	3	1	2	1	5	4	2	1	4	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr15:41099608A>G	ENST00000220496.4	-	1	67	c.37T>C	c.(37-39)Tac>Cac	p.Y13H	ZFYVE19_ENST00000299173.10_5'Flank|ZFYVE19_ENST00000336455.5_Missense_Mutation_p.Y41C|ZFYVE19_ENST00000355341.4_5'UTR|ZFYVE19_ENST00000564258.1_5'UTR|ZFYVE19_ENST00000570108.1_Missense_Mutation_p.Y41C	NM_018163.2	NP_060633.1	Q9NVM6	DJC17_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 17	13	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				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)		AGCAGCGCGTACAGGTCCATC	0.577																																					p.Y41C		Atlas-SNP	.											.	ZFYVE19	31	.	0			c.A122G						PASS	.						180	134	150					15																	41099608		2203	4300	6503	SO:0001583	missense	84936	exon1			GCGCGTACAGGTC	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.37T>C	chr15.hg19:g.41099608A>G	ENSP00000220496:p.Tyr13His	127.0	0.0	.		155.0	43.0	.	NM_032850		Missense_Mutation	SNP	ENST00000220496.4	hg19	CCDS10065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	27.8|27.8	4.859778|4.859778	0.91433|0.91433	.|.	.|.	ENSG00000166140|ENSG00000104129	ENST00000336455|ENST00000220496	T|T	0.27402|0.58940	1.67|0.3	5.35|5.35	5.35|5.35	0.76521|0.76521	.|Heat shock protein DnaJ, N-terminal (5);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.81730|0.81730	0.4884|0.4884	M|M	0.94063|0.94063	3.49|3.49	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.87578	.|0.998	D|D	0.86513|0.86513	0.1811|0.1811	8|10	0.87932|0.87932	D|D	0|0	.|.	14.7373|14.7373	0.69424|0.69424	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|13	.|Q9NVM6	.|DJC17_HUMAN	C|H	41|13	ENSP00000337824:Y41C|ENSP00000220496:Y13H	ENSP00000337824:Y41C|ENSP00000220496:Y13H	Y|Y	+|-	2|1	0|0	ZFYVE19|DNAJC17	38886900|38886900	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	5.383000|5.383000	0.66219|0.66219	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	TAC|TAC	.	.	.	none		0.577	DNAJC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252356.2	NM_018163		G	41099608	A	G	41099608	3	3	87	1	0	0	0	0	1	0	0	0	4638	391	14	3	921	3	DNAJC17	15	41099608	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10		41099608	61431784	59	5647											
MFAP1	4236	hgsc.bcm.edu	37	chr15	44105507	44105507	+	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	gcttcctgctccagctccttCtgtttcaatgcttcggcttc	3	16	7	15	1	2	0	1	0	1	0	7	0	5	0	3	1	3	6	3	1	1	5			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr15:44105507C>T	ENST00000267812.3	-	5	898	c.666G>A	c.(664-666)caG>caA	p.Q222Q		NM_005926.2	NP_005917.2	P55081	MFAP1_HUMAN	microfibrillar-associated protein 1	222					extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|microfibril (GO:0001527)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|lung(6)|skin(2)|upper_aerodigestive_tract(3)	15		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.33e-07)		CCAGCTCCTTCTGTTTCAATG	0.488																																					p.Q222Q		Atlas-SNP	.											.	MFAP1	36	.	0			c.G666A						PASS	.						350	297	315					15																	44105507		2198	4298	6496	SO:0001819	synonymous_variant	4236	exon5			CTCCTTCTGTTTC		CCDS10105.1	15q15-q21	2014-05-20			ENSG00000140259	ENSG00000140259			7032	protein-coding gene	gene with protein product		600215				7835894	Standard	NM_005926		Approved		uc001zth.1	P55081	OTTHUMG00000060145	ENST00000267812.3:c.666G>A	chr15.hg19:g.44105507C>T		74.0	0.0	.		74.0	23.0	.	NM_005926	Q86TG6	Silent	SNP	ENST00000267812.3	hg19	CCDS10105.1																																																																																			.	.	.	none		0.488	MFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133491.2	NM_005926		T	44105507	C	T	44105507	2	4	87	1	0	0	0	0	0	0	0	1	9520	912	32	2		2	MFAP1	15	44105507	Silent	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	3005899	44105507	58425885	60	5648											
PIF1	80119	hgsc.bcm.edu	37	chr15	65114469	65114469	+	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	aggggttcctacttacctgcAaaggcatggagggtggtgcc	8	9	15	9	0	0	0	0	0	0	0	1	1	1	1	3	6	4	3	3	6	3	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr15:65114469A>T	ENST00000268043.4	-	4	907	c.813T>A	c.(811-813)ttT>ttA	p.F271L	PIF1_ENST00000333425.6_Missense_Mutation_p.F271L|PIF1_ENST00000559239.1_Missense_Mutation_p.F271L					PIF1 5'-to-3' DNA helicase											kidney(1)|lung(1)	2						ACTTACCTGCAAAGGCATGGA	0.612																																					p.F271L		Atlas-SNP	.											.	PIF1	43	.	0			c.T813A						PASS	.						60	64	63					15																	65114469		2202	4299	6501	SO:0001583	missense	80119	exon4			ACCTGCAAAGGCA	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.813T>A	chr15.hg19:g.65114469A>T	ENSP00000268043:p.Phe271Leu	48.0	0.0	.		45.0	10.0	.	NM_025049		Missense_Mutation	SNP	ENST00000268043.4	hg19	CCDS10195.2	.	.	.	.	.	.	.	.	.	.	A	24.6	4.553832	0.86231	.	.	ENSG00000140451	ENST00000268043;ENST00000333425	T;T	0.52295	0.67;0.67	4.98	2.66	0.31614	.	0.100402	0.64402	D	0.000001	T	0.54711	0.1875	L	0.48174	1.505	0.80722	D	1	D	0.58970	0.984	D	0.64877	0.93	T	0.50725	-0.8794	10	0.54805	T	0.06	-11.173	7.9896	0.30233	0.8322:0.0:0.1678:0.0	.	271	Q9H611	PIF1_HUMAN	L	271	ENSP00000268043:F271L;ENSP00000328174:F271L	ENSP00000268043:F271L	F	-	3	2	PIF1	62901522	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.558000	0.36309	0.336000	0.23639	0.533000	0.62120	TTT	.	.	.	none		0.612	PIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256533.1	NM_025049		T	65114469	A	T	65114469	3	4	87	1	0	0	0	0	1	0	0	0	11890	127	5	5	1152	5	PIF1	15	65114469	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	21008962	65114469	37416923	61	5649											
NEO1	4756	hgsc.bcm.edu	37	chr15	73581573	73581573	+	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	tgccctttgactcccagccaCcccagcgtaagtagaagcat	10	8	8	15	1	0	2	0	1	0	1	1	2	1	2	5	0	4	3	5	0	3	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr15:73581573C>A	ENST00000339362.5	+	26	4183	c.3736C>A	c.(3736-3738)Ccc>Acc	p.P1246T	NEO1_ENST00000560262.1_Missense_Mutation_p.P1246T|NEO1_ENST00000261908.6_Missense_Mutation_p.P1246T|NEO1_ENST00000558964.1_Missense_Mutation_p.P1235T			Q92859	NEO1_HUMAN	neogenin 1	1246					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|iron ion homeostasis (GO:0055072)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						CTCCCAGCCACCCCAGCGTAA	0.458																																					p.P1246T		Atlas-SNP	.											.	NEO1	102	.	0			c.C3736A						PASS	.						154	102	119					15																	73581573		2198	4297	6495	SO:0001583	missense	4756	exon25			CAGCCACCCCAGC	U61262	CCDS10247.1, CCDS53957.1, CCDS58378.1	15q22.3-q23	2014-06-20	2010-06-24		ENSG00000067141	ENSG00000067141		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7754	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 2"	601907	"neogenin (chicken) homolog 1"			9121761	Standard	NM_002499		Approved	NGN, HsT17534, IGDCC2, NTN1R2	uc002avm.4	Q92859	OTTHUMG00000133509	ENST00000339362.5:c.3736C>A	chr15.hg19:g.73581573C>A	ENSP00000341198:p.Pro1246Thr	70.0	0.0	.		73.0	32.0	.	NM_001172623	B7ZKM9|B7ZKN0|O00340|Q17RX1	Missense_Mutation	SNP	ENST00000339362.5	hg19	CCDS10247.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.713733	0.89112	.	.	ENSG00000067141	ENST00000339362;ENST00000379842;ENST00000261908	T;T	0.45276	0.9;0.9	5.48	5.48	0.80851	Neogenin, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.61640	0.2363	M	0.62723	1.935	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;0.999;0.999	D;D;D;D	0.75484	0.986;0.968;0.98;0.98	T	0.53627	-0.8412	10	0.17832	T	0.49	-12.2116	19.387	0.94560	0.0:1.0:0.0:0.0	.	1246;1235;957;1246	B7ZKM9;B7ZKN0;E7EUX3;Q92859	.;.;.;NEO1_HUMAN	T	1246;957;1246	ENSP00000341198:P1246T;ENSP00000261908:P1246T	ENSP00000261908:P1246T	P	+	1	0	NEO1	71368626	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.463000	0.80869	2.572000	0.86782	0.655000	0.94253	CCC	.	.	.	none		0.458	NEO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257472.2	NM_002499		A	73581573	C	A	73581573	3	1	87	1	0	0	0	0	1	0	0	0	10343	507	18	4	3834	4	NEO1	15	73581573	Missense_Mutation	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	8467104	73581573	28949819	62	5650											
PML	5371	hgsc.bcm.edu	37	chr15	74325643	74325643	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccaggcccagcacctccaaGgcagtctcaccaccccacct	9	4	6	22	0	1	0	1	0	1	0	3	0	2	0	8	2	1	2	8	2	1	0			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr15:74325643G>A	ENST00000268058.3	+	6	1641	c.1545G>A	c.(1543-1545)aaG>aaA	p.K515K	PML_ENST00000563500.1_Silent_p.K467K|PML_ENST00000359928.4_Intron|PML_ENST00000564428.1_Silent_p.K467K|PML_ENST00000569477.1_Silent_p.K515K|PML_ENST00000435786.2_Silent_p.K515K|PML_ENST00000268059.6_Silent_p.K515K|PML_ENST00000395135.3_Silent_p.K515K|PML_ENST00000565898.1_Silent_p.K467K|PML_ENST00000436891.3_Silent_p.K515K|PML_ENST00000567543.1_Intron|PML_ENST00000569965.1_Silent_p.K515K|PML_ENST00000354026.6_Silent_p.K467K|PML_ENST00000395132.2_Intron	NM_033238.2	NP_150241.2	P29590	PML_HUMAN	promyelocytic leukemia	515	Interaction with PER2.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to interleukin-4 (GO:0071353)|cellular senescence (GO:0090398)|circadian regulation of gene expression (GO:0032922)|common-partner SMAD protein phosphorylation (GO:0007182)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|entrainment of circadian clock by photoperiod (GO:0043153)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|maintenance of protein location in nucleus (GO:0051457)|myeloid cell differentiation (GO:0030099)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation in response to oxidative stress (GO:0032938)|negative regulation of viral release from host cell (GO:1902187)|PML body organization (GO:0030578)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of histone deacetylation (GO:0031065)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)|regulation of calcium ion transport into cytosol (GO:0010522)|regulation of circadian rhythm (GO:0042752)|regulation of double-strand break repair (GO:2000779)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of protein phosphorylation (GO:0001932)|regulation of transcription, DNA-templated (GO:0006355)|response to cytokine (GO:0034097)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|retinoic acid receptor signaling pathway (GO:0048384)|SMAD protein import into nucleus (GO:0007184)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	cobalt ion binding (GO:0050897)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|SUMO binding (GO:0032183)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	31						GCACCTCCAAGGCAGTCTCAC	0.652			T	"RARA, PAX5"	"APL, ALL"																																p.K515K		Atlas-SNP	.		Dom	yes		15	15q22	5371	promyelocytic leukemia		L	.	PML	169	.	0			c.G1545A						PASS	.						62	58	60					15																	74325643		2198	4297	6495	SO:0001819	synonymous_variant	5371	exon6			CTCCAAGGCAGTC	AB208950	CCDS10255.1, CCDS10256.1, CCDS10257.1, CCDS10258.1, CCDS45297.1, CCDS45298.1, CCDS45299.1, CCDS45300.1, CCDS58386.1	15q24.1	2011-04-21			ENSG00000140464	ENSG00000140464		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	9113	protein-coding gene	gene with protein product		102578					Standard	NM_033244		Approved	MYL, TRIM19, RNF71	uc002awv.3	P29590	OTTHUMG00000137607	ENST00000268058.3:c.1545G>A	chr15.hg19:g.74325643G>A		92.0	0.0	.		85.0	21.0	.	NM_033244	E9PBR7|P29591|P29592|P29593|Q00755|Q15959|Q59FP9|Q8WUA0|Q96S41|Q9BPW2|Q9BWP7|Q9BZX6|Q9BZX7|Q9BZX8|Q9BZX9|Q9BZY0|Q9BZY2|Q9BZY3	Silent	SNP	ENST00000268058.3	hg19	CCDS10255.1																																																																																			.	.	.	none		0.652	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269021.3	NM_002675		A	74325643	G	A	74325643	2	1	87	1	0	0	0	0	0	0	0	1	12142	991	35	2		2	PML	15	74325643	Silent	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	744070	74325643	28205749	63	5651											
SLC28A1	9154	hgsc.bcm.edu	37	chr15	85476453	85476453	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctctccaagctggtctacccGgaggtggaggagtccaagtt	8	9	13	11	1	2	0	0	0	2	0	4	3	3	3	3	5	2	2	3	5	3	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr15:85476453G>A	ENST00000286749.3	+	12	1251	c.1161G>A	c.(1159-1161)ccG>ccA	p.P387P	SLC28A1_ENST00000394573.1_Silent_p.P387P|SLC28A1_ENST00000537624.1_Silent_p.P387P|SLC28A1_ENST00000538177.1_Intron|SLC28A1_ENST00000537216.1_Silent_p.P387P			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	387					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)	TGGTCTACCCGGAGGTGGAGG	0.572																																					p.P387P		Atlas-SNP	.											.	SLC28A1	118	.	0			c.G1161A						PASS	.						132	113	119					15																	85476453		2203	4299	6502	SO:0001819	synonymous_variant	9154	exon13			CTACCCGGAGGTG	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.1161G>A	chr15.hg19:g.85476453G>A		76.0	0.0	.		56.0	17.0	.	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Silent	SNP	ENST00000286749.3	hg19	CCDS10334.1																																																																																			.	.	.	none		0.572	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2			A	85476453	G	A	85476453	2	1	87	1	0	0	0	0	0	0	0	1	14544	1103	39	1		1	SLC28A1	15	85476453	Silent	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	11150810	85476453	17054939	64	5652											
ZNF597	146434	hgsc.bcm.edu	37	chr16	3487293	3487293	+	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	agaaagtgtgttggttcctaAatattcagagagttctacta	13	14	9	5	0	2	2	1	0	1	2	3	3	3	2	1	1	1	3	1	1	6	8			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr16:3487293A>T	ENST00000301744.4	-	4	641	c.406T>A	c.(406-408)Tta>Ata	p.L136I		NM_152457.1	NP_689670.1	Q96LX8	ZN597_HUMAN	zinc finger protein 597	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(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	13						TTGGTTCCTAAATATTCAGAG	0.403																																					p.L136I		Atlas-SNP	.											.	ZNF597	41	.	0			c.T406A						PASS	.						133	137	136					16																	3487293		2197	4300	6497	SO:0001583	missense	146434	exon4			TTCCTAAATATTC	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.406T>A	chr16.hg19:g.3487293A>T	ENSP00000301744:p.Leu136Ile	201.0	0.0	.		208.0	123.0	.	NM_152457		Missense_Mutation	SNP	ENST00000301744.4	hg19	CCDS10505.1	.	.	.	.	.	.	.	.	.	.	A	5.442	0.266748	0.10294	.	.	ENSG00000167981	ENST00000301744	T	0.06849	3.25	4.91	2.52	0.30459	.	0.000000	0.36101	N	0.002790	T	0.05593	0.0147	L	0.41236	1.265	0.09310	N	1	P	0.47350	0.894	B	0.39935	0.314	T	0.31251	-0.9950	10	0.22706	T	0.39	-1.0026	3.965	0.09428	0.7202:0.0:0.0973:0.1825	.	136	Q96LX8	ZN597_HUMAN	I	136	ENSP00000301744:L136I	ENSP00000301744:L136I	L	-	1	2	ZNF597	3427294	0.067000	0.21026	0.811000	0.32455	0.229000	0.25112	0.918000	0.28678	0.994000	0.38892	0.533000	0.62120	TTA	.	.	.	none		0.403	ZNF597-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251511.2	NM_152457		T	3487293	A	T	3487293	3	4	87	1	0	0	0	0	1	0	0	0	18039	11	1	5	872	5	ZNF597	16	3487293	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10		3487293	86867460	65	5653											
ZNF646	9726	hgsc.bcm.edu	37	chr16	31092685	31092685	+	Silent	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	gagcggcccttccgctgcacCcagtgcgggcgctcctaccg	4	6	13	18	5	0	0	0	0	0	0	2	1	2	0	5	2	4	3	5	2	1	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr16:31092685C>T	ENST00000394979.2	+	1	5463	c.5040C>T	c.(5038-5040)acC>acT	p.T1680T	ZNF646_ENST00000300850.5_Silent_p.T1680T			O15015	ZN646_HUMAN	zinc finger protein 646	1680					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						TCCGCTGCACCCAGTGCGGGC	0.652																																					p.T1680T		Atlas-SNP	.											.	ZNF646	133	.	0			c.C5040T						PASS	.						68	80	76					16																	31092685		2197	4300	6497	SO:0001819	synonymous_variant	9726	exon2			CTGCACCCAGTGC	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.5040C>T	chr16.hg19:g.31092685C>T		92.0	0.0	.		112.0	19.0	.	NM_014699	Q8IVD8	Silent	SNP	ENST00000394979.2	hg19																																																																																				.	.	.	none		0.652	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699		T	31092685	C	T	31092685	2	4	87	1	0	0	0	0	0	0	0	1	18074	610	22	2		2	ZNF646	16	31092685	Silent	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	27605392	31092685	59262068	66	5654											
ITGAM	3684	hgsc.bcm.edu	37	chr16	31335987	31335987	+	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	cttagaattgcatcgaggacCcagtgagccccattgtgctg	9	10	11	11	1	0	2	0	1	0	1	1	4	0	3	3	1	3	2	3	1	2	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr16:31335987C>A	ENST00000287497.8	+	18	2248	c.2173C>A	c.(2173-2175)Cca>Aca	p.P725T	ITGAM_ENST00000544665.3_Missense_Mutation_p.P726T			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	725					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)			endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						CATCGAGGACCCAGTGAGCCC	0.602																																					p.P726T		Atlas-SNP	.											.	ITGAM	137	.	0			c.C2176A						PASS	.						49	51	50					16																	31335987		1980	4148	6128	SO:0001583	missense	3684	exon18			GAGGACCCAGTGA	J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"CD molecules", "Complement system", "Integrins"	6149	protein-coding gene	gene with protein product		120980	"integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.2173C>A	chr16.hg19:g.31335987C>A	ENSP00000287497:p.Pro725Thr	109.0	0.0	.		140.0	17.0	.	NM_001145808	Q4VAK0|Q4VAK1|Q4VAK2	Missense_Mutation	SNP	ENST00000287497.8	hg19	CCDS45470.1	.	.	.	.	.	.	.	.	.	.	C	5.122	0.208084	0.09704	.	.	ENSG00000169896	ENST00000544665;ENST00000287497	T;T	0.42513	0.97;0.97	4.64	-0.352	0.12598	Integrin alpha-2 (1);	.	.	.	.	T	0.16599	0.0399	N	0.11427	0.14	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.12156	0.007;0.004;0.004	T	0.28586	-1.0039	9	0.07030	T	0.85	.	3.2574	0.06836	0.4401:0.1772:0.0:0.3826	.	131;725;725	B3KXM6;Q4VAK1;P11215	.;.;ITAM_HUMAN	T	726;725	ENSP00000441691:P726T;ENSP00000287497:P725T	ENSP00000287497:P725T	P	+	1	0	ITGAM	31243488	0.534000	0.26362	0.001000	0.08648	0.001000	0.01503	0.014000	0.13333	-0.004000	0.14419	-1.364000	0.01208	CCA	.	.	.	none		0.602	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632		A	31335987	C	A	31335987	3	1	87	1	0	0	0	0	1	0	0	0	7894	623	22	4	2246	4	ITGAM	16	31335987	Missense_Mutation	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	243302	31335987	59018766	67	5655											
CLEC18A	348174	hgsc.bcm.edu	37	chr16	69988283	69988283	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctcaagccagggcagcccTctgtggaaccccaaccccga	9	4	11	17	1	2	0	1	0	1	0	2	2	2	1	6	3	4	2	6	3	3	0			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr16:69988283T>C	ENST00000288040.6	+	3	450	c.263T>C	c.(262-264)cTc>cCc	p.L88P	CLEC18A_ENST00000568461.1_Missense_Mutation_p.L88P|CLEC18A_ENST00000449317.2_Missense_Mutation_p.L88P|CLEC18A_ENST00000393701.2_Missense_Mutation_p.L88P	NM_001136214.2	NP_001129686.1	A5D8T8	CL18A_HUMAN	C-type lectin domain family 18, member A	88	SCP.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(2)|lung(1)|skin(1)	5						AGGGCAGCCCTCTGTGGAACC	0.662																																					p.L88P		Atlas-SNP	.											.	CLEC18A	9	.	0			c.T263C						PASS	.						54	49	51					16																	69988283		2198	4300	6498	SO:0001583	missense	348174	exon4			CAGCCCTCTGTGG	AF428259	CCDS10886.1	16q22.1	2010-04-27	2009-03-10	2009-03-10		ENSG00000157322		"C-type lectin domain containing"	30388	protein-coding gene	gene with protein product	"mannose receptor-like"					12975309	Standard	NM_001136214		Approved	MRCL	uc010vlo.3	A5D8T8		ENST00000288040.6:c.263T>C	chr16.hg19:g.69988283T>C	ENSP00000288040:p.Leu88Pro	309.0	1.0	.		396.0	181.0	.	NM_001271197	A8K1G9|Q6DCB3|Q7Z5K9|Q96HH2	Missense_Mutation	SNP	ENST00000288040.6	hg19	CCDS10886.1	.	.	.	.	.	.	.	.	.	.	.	9.120	1.008658	0.19199	.	.	ENSG00000157322	ENST00000393701;ENST00000539957;ENST00000449317;ENST00000288040	T;T;T	0.07908	3.15;3.15;3.15	1.97	1.97	0.26223	CAP domain (3);	0.922111	0.09270	N	0.825284	T	0.07999	0.0200	L	0.47190	1.495	0.52501	D	0.999956	B;B;B	0.19331	0.035;0.004;0.003	B;B;B	0.17098	0.017;0.007;0.006	T	0.17137	-1.0379	9	.	.	.	.	5.9927	0.19476	0.0:0.0:0.0:1.0	.	88;88;88	B4DPF2;A5D8T8;F8W692	.;CL18A_HUMAN;.	P	88	ENSP00000377304:L88P;ENSP00000413990:L88P;ENSP00000288040:L88P	.	L	+	2	0	CLEC18A	68545784	0.004000	0.15560	0.898000	0.35279	0.442000	0.32017	0.109000	0.15417	1.168000	0.42723	0.155000	0.16302	CTC	.	.	.	none		0.662	CLEC18A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268955.2	NM_182619		C	69988283	T	C	69988283	3	2	87	1	0	0	0	0	1	0	0	0	3504	1551	54	3	273	3	CLEC18A	16	69988283	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	38652296	69988283	20366470	68	5656											
ZFHX3	463	hgsc.bcm.edu	37	chr16	72984405	72984405	+	Missense_Mutation	SNP	A	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	tggcctcgtgcctggagttgAccgtgtgcagccgcagcttc	4	10	14	13	3	0	1	0	1	0	0	2	2	0	2	4	2	4	4	4	2	0	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr16:72984405A>C	ENST00000268489.5	-	3	3851	c.3179T>G	c.(3178-3180)gTc>gGc	p.V1060G	ZFHX3_ENST00000397992.5_Missense_Mutation_p.V146G	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	1060					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)				CCTGGAGTTGACCGTGTGCAG	0.602																																					p.V1060G		Atlas-SNP	.											.	ZFHX3	404	.	0			c.T3179G						PASS	.						70	59	63					16																	72984405		2198	4300	6498	SO:0001583	missense	463	exon3			GAGTTGACCGTGT	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.3179T>G	chr16.hg19:g.72984405A>C	ENSP00000268489:p.Val1060Gly	59.0	0.0	.		72.0	37.0	.	NM_006885	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	hg19	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	A	15.80	2.939889	0.52972	.	.	ENSG00000140836	ENST00000268489;ENST00000397992	T;T	0.49432	0.78;0.78	5.31	4.22	0.49857	Zinc finger, C2H2-like (1);	0.148255	0.30464	N	0.009580	T	0.42449	0.1203	N	0.19112	0.55	0.80722	D	1	P	0.48640	0.913	P	0.51918	0.684	T	0.25606	-1.0127	10	0.41790	T	0.15	.	11.0251	0.47741	0.927:0.0:0.073:0.0	.	1060	Q15911	ZFHX3_HUMAN	G	1060;146	ENSP00000268489:V1060G;ENSP00000438926:V146G	ENSP00000268489:V1060G	V	-	2	0	ZFHX3	71541906	1.000000	0.71417	0.999000	0.59377	0.974000	0.67602	5.860000	0.69546	0.859000	0.35456	0.528000	0.53228	GTC	.	.	.	none		0.602	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		C	72984405	A	C	72984405	3	2	87	1	0	0	0	0	1	0	0	0	17646	275	10	5	7964	5	ZFHX3	16	72984405	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	2996122	72984405	17370348	69	5657											
JPH3	57338	hgsc.bcm.edu	37	chr16	87678517	87678517	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcagaacatcctcgtcggcGgcaagcgcaagaacctcatc	12	5	10	14	4	1	2	1	0	0	2	5	2	2	2	2	2	4	3	2	2	4	0			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr16:87678517G>A	ENST00000284262.2	+	2	1278	c.1036G>A	c.(1036-1038)Ggc>Agc	p.G346S		NM_020655.2	NP_065706.2	Q8WXH2	JPH3_HUMAN	junctophilin 3	346					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)		CCTCGTCGGCGGCAAGCGCAA	0.677																																					p.G346S		Atlas-SNP	.											.	JPH3	95	.	0			c.G1036A						PASS	.						45	54	51					16																	87678517		2197	4300	6497	SO:0001583	missense	57338	exon2			GTCGGCGGCAAGC	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.1036G>A	chr16.hg19:g.87678517G>A	ENSP00000284262:p.Gly346Ser	47.0	0.0	.		71.0	29.0	.	NM_020655	D3DUN2|Q8N471|Q9HDC3|Q9HDC4	Missense_Mutation	SNP	ENST00000284262.2	hg19	CCDS10962.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.531280	0.85706	.	.	ENSG00000154118	ENST00000537256;ENST00000284262	T	0.45668	0.89	4.56	4.56	0.56223	.	0.050973	0.85682	D	0.000000	T	0.37919	0.1021	L	0.46157	1.445	0.80722	D	1	P	0.42941	0.794	B	0.38562	0.276	T	0.29088	-1.0023	10	0.37606	T	0.19	.	16.3368	0.83067	0.0:0.0:1.0:0.0	.	346	Q8WXH2	JPH3_HUMAN	S	209;346	ENSP00000284262:G346S	ENSP00000284262:G346S	G	+	1	0	JPH3	86236018	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	9.580000	0.98207	2.098000	0.63641	0.561000	0.74099	GGC	.	.	.	none		0.677	JPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269108.2			A	87678517	G	A	87678517	3	1	87	1	0	0	0	0	1	0	0	0	7969	1116	39	1	1042	1	JPH3	16	87678517	Missense_Mutation	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	14694112	87678517	2676236	70	5658											
KLHL11	55175	hgsc.bcm.edu	37	chr17	40010765	40010765	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgctatagagcttcccttTgacttctgttagtccaaaag	11	14	7	9	0	1	2	0	1	1	1	3	2	3	2	2	0	2	3	2	0	6	6			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr17:40010765T>C	ENST00000319121.3	-	2	1414	c.1354A>G	c.(1354-1356)Aaa>Gaa	p.K452E		NM_018143.1	NP_060613.1	Q9NVR0	KLH11_HUMAN	kelch-like family member 11	452										NS(2)|breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	17		Breast(137;0.00156)				AGCTTCCCTTTGACTTCTGTT	0.373																																					p.K452E		Atlas-SNP	.											.	KLHL11	44	.	0			c.A1354G						PASS	.						122	125	124					17																	40010765		2203	4300	6503	SO:0001583	missense	55175	exon2			TCCCTTTGACTTC		CCDS11411.1	17q21	2013-01-30	2013-01-30		ENSG00000178502	ENSG00000178502		"Kelch-like", "BTB/POZ domain containing"	19008	protein-coding gene	gene with protein product			"kelch-like 11 (Drosophila)"				Standard	NM_018143		Approved	FLJ10572	uc002hyf.1	Q9NVR0	OTTHUMG00000133506	ENST00000319121.3:c.1354A>G	chr17.hg19:g.40010765T>C	ENSP00000314608:p.Lys452Glu	206.0	0.0	.		214.0	96.0	.	NM_018143		Missense_Mutation	SNP	ENST00000319121.3	hg19	CCDS11411.1	.	.	.	.	.	.	.	.	.	.	T	11.41	1.630131	0.28978	.	.	ENSG00000178502	ENST00000319121;ENST00000540254	T	0.77358	-1.09	4.73	3.62	0.41486	Galactose oxidase, beta-propeller (1);	0.051953	0.85682	D	0.000000	T	0.64616	0.2614	L	0.37507	1.11	0.53688	D	0.999976	B	0.06786	0.001	B	0.11329	0.006	T	0.54721	-0.8251	10	0.08179	T	0.78	3.0205	11.6837	0.51472	0.0:0.0:0.1485:0.8515	.	452	Q9NVR0	KLH11_HUMAN	E	452;315	ENSP00000314608:K452E	ENSP00000314608:K452E	K	-	1	0	KLHL11	37264291	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	4.582000	0.60957	0.901000	0.36495	0.477000	0.44152	AAA	.	.	.	none		0.373	KLHL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257464.2	NM_018143		C	40010765	T	C	40010765	3	2	87	1	0	0	0	0	1	0	0	0	8374	1821	63	3	776	3	KLHL11	17	40010765	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10		40010765	41184445	71	5659											
KIF18B	146909	hgsc.bcm.edu	37	chr17	43009571	43009571	+	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	gggagctctggggtgcagggCtggctgggagggtggggtgg	3	7	26	5	0	1	0	0	0	1	0	1	2	1	2	0	10	2	4	0	10	0	0			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr17:43009571C>T	ENST00000593135.1	-	10	1339	c.1242G>A	c.(1240-1242)caG>caA	p.Q414Q	KIF18B_ENST00000438933.2_Silent_p.Q426Q|KIF18B_ENST00000339151.4_Silent_p.Q426Q|KIF18B_ENST00000590129.1_Silent_p.Q435Q|KIF18B_ENST00000587309.1_Silent_p.Q426Q	NM_001265577.1	NP_001252506.1	Q86Y91	KI18B_HUMAN	kinesin family member 18B	435	Pro-rich.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|regulation of cell division (GO:0051302)	astral microtubule (GO:0000235)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule plus-end (GO:0035371)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	21		Prostate(33;0.155)				GGGTGCAGGGCTGGCTGGGAG	0.657																																					p.Q426Q		Atlas-SNP	.											.	KIF18B	63	.	0			c.G1278A						PASS	.						18	21	20					17																	43009571		1898	4102	6000	SO:0001819	synonymous_variant	146909	exon10			GCAGGGCTGGCTG		CCDS45709.1, CCDS58555.1, CCDS45709.2	17q21.31	2014-09-04			ENSG00000186185			"Kinesins"	27102	protein-coding gene	gene with protein product		614570				16084724	Standard	NM_001264573		Approved		uc010wjh.3	Q86Y91	OTTHUMG00000179867	ENST00000593135.1:c.1242G>A	chr17.hg19:g.43009571C>T		33.0	0.0	.		51.0	8.0	.	NM_001264573	A6NJI2|B7ZM49|B9EGM8|D5L6I1	Silent	SNP	ENST00000593135.1	hg19	CCDS45709.2																																																																																			.	.	.	none		0.657	KIF18B-001	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000448724.1	NM_001080443		T	43009571	C	T	43009571	2	4	87	1	0	0	0	0	0	0	0	1	8288	796	28	2		2	KIF18B	17	43009571	Silent	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	2998806	43009571	38185639	72	5660											
TLK2	11011	hgsc.bcm.edu	37	chr17	60663585	60663585	+	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	gagaaaaaggagaattaccaCaagtaagtgatacttgagtg	18	8	11	4	0	0	4	0	2	0	2	0	6	0	4	1	1	2	1	1	1	7	4			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr17:60663585C>A	ENST00000326270.9	+	17	1792	c.1524C>A	c.(1522-1524)caC>caA	p.H508Q	TLK2_ENST00000542523.1_Missense_Mutation_p.H454Q|TLK2_ENST00000582809.1_Missense_Mutation_p.H337Q|TLK2_ENST00000346027.5_Missense_Mutation_p.H486Q|TLK2_ENST00000343388.7_Missense_Mutation_p.H454Q	NM_001284333.1	NP_001271262.1	Q86UE8	TLK2_HUMAN	tousled-like kinase 2	508	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|negative regulation of autophagy (GO:0010507)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	intermediate filament (GO:0005882)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(4)|large_intestine(6)|liver(2)|lung(10)|prostate(1)|stomach(1)|urinary_tract(1)	39						AGAATTACCACAAGTAAGTGA	0.328																																					p.H486Q		Atlas-SNP	.											.	TLK2	223	.	0			c.C1458A						PASS	.						33	34	33					17																	60663585		2202	4297	6499	SO:0001583	missense	11011	exon16			TTACCACAAGTAA	AB004884	CCDS11633.1, CCDS45753.1, CCDS62283.1	17q23	2008-07-18							11842	protein-coding gene	gene with protein product		608439				9427565, 10523312	Standard	NM_006852		Approved	PKU-ALPHA, MGC44450	uc002izz.4	Q86UE8		ENST00000326270.9:c.1524C>A	chr17.hg19:g.60663585C>A	ENSP00000316512:p.His508Gln	737.0	1.0	.		639.0	311.0	.	NM_006852	D3DU07|Q9UKI7|Q9Y4F7	Missense_Mutation	SNP	ENST00000326270.9	hg19		.	.	.	.	.	.	.	.	.	.	C	8.052	0.766147	0.15983	.	.	ENSG00000146872	ENST00000346027;ENST00000343388;ENST00000326270;ENST00000542523	T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1	5.45	3.48	0.39840	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	0.62841	0.2461	N	0.26042	0.785	0.80722	D	1	D;B;B;B	0.69078	0.997;0.005;0.028;0.157	D;B;B;B	0.66351	0.943;0.037;0.064;0.166	T	0.62044	-0.6937	10	0.54805	T	0.06	-0.8054	8.4022	0.32592	0.0:0.7596:0.0:0.2404	.	508;454;486;486	Q86UE8;Q86UE8-3;Q86UE8-2;D3DU05	TLK2_HUMAN;.;.;.	Q	486;454;508;454	ENSP00000275780:H486Q;ENSP00000340800:H454Q;ENSP00000316512:H508Q;ENSP00000442311:H454Q	ENSP00000316512:H508Q	H	+	3	2	TLK2	58017317	1.000000	0.71417	1.000000	0.80357	0.119000	0.20118	5.818000	0.69236	0.688000	0.31529	-0.251000	0.11542	CAC	.	.	.	none		0.328	TLK2-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000445140.1	NM_006852		A	60663585	C	A	60663585	3	1	87	1	0	0	0	0	1	0	0	0	15956	477	17	4	1516	4	TLK2	17	60663585	Missense_Mutation	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	17654014	60663585	20531625	73	5661											
LPIN2	9663	hgsc.bcm.edu	37	chr18	2939488	2939488	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accctagtaccttggtggacTctgggaatccgccccacgtc	7	9	10	15	2	1	0	0	0	1	0	3	2	2	2	5	3	1	1	5	3	3	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr18:2939488T>C	ENST00000261596.4	-	6	1050	c.812A>G	c.(811-813)gAg>gGg	p.E271G		NM_014646.2	NP_055461.1	Q92539	LPIN2_HUMAN	lipin 2	271					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)		CTTGGTGGACTCTGGGAATCC	0.493																																					p.E271G		Atlas-SNP	.											.	LPIN2	75	.	0			c.A812G						PASS	.						125	117	120					18																	2939488		2203	4300	6503	SO:0001583	missense	9663	exon6			GTGGACTCTGGGA	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.812A>G	chr18.hg19:g.2939488T>C	ENSP00000261596:p.Glu271Gly	42.0	0.0	.		42.0	16.0	.	NM_014646	A7MD25|D3DUH3	Missense_Mutation	SNP	ENST00000261596.4	hg19	CCDS11829.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.103696	0.76983	.	.	ENSG00000101577	ENST00000261596	T	0.81247	-1.47	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	D	0.87337	0.6152	M	0.70595	2.14	0.80722	D	1	D	0.62365	0.991	P	0.60012	0.867	D	0.86664	0.1906	10	0.38643	T	0.18	-35.667	16.2194	0.82247	0.0:0.0:0.0:1.0	.	271	Q92539	LPIN2_HUMAN	G	271	ENSP00000261596:E271G	ENSP00000261596:E271G	E	-	2	0	LPIN2	2929488	1.000000	0.71417	1.000000	0.80357	0.537000	0.34900	7.649000	0.83500	2.234000	0.73211	0.528000	0.53228	GAG	.	.	.	none		0.493	LPIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254363.2	NM_014646		C	2939488	T	C	2939488	3	2	87	1	0	0	0	0	1	0	0	0	8926	1551	54	3	1938	3	LPIN2	18	2939488	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10		2939488	75137760	74	5662											
C18orf34	374864	hgsc.bcm.edu	37	chr18	30992013	30992013	+	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	acctatattggtttgatcatCtctagtggaagaagaggaaa	14	12	10	5	0	2	3	1	1	1	2	3	5	2	5	1	3	0	1	1	3	6	5			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr18:30992013C>T	ENST00000383096.3	-	3	222	c.40G>A	c.(40-42)Gat>Aat	p.D14N	CCDC178_ENST00000406524.2_Missense_Mutation_p.D14N|CCDC178_ENST00000579947.1_Missense_Mutation_p.D14N|CCDC178_ENST00000583930.1_Missense_Mutation_p.D14N|CCDC178_ENST00000402325.1_Missense_Mutation_p.D14N|CCDC178_ENST00000579916.1_Missense_Mutation_p.D14N|CCDC178_ENST00000403303.1_Missense_Mutation_p.D14N|CCDC178_ENST00000300227.8_Missense_Mutation_p.D14N			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	14																	GTTTGATCATCTCTAGTGGAA	0.274																																					p.D14N		Atlas-SNP	.											.	.	.	.	0			c.G40A						PASS	.						43	45	44					18																	30992013		2201	4293	6494	SO:0001583	missense	374864	exon2			GATCATCTCTAGT	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.40G>A	chr18.hg19:g.30992013C>T	ENSP00000372576:p.Asp14Asn	552.0	1.0	.		432.0	150.0	.	NM_001105528	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Missense_Mutation	SNP	ENST00000383096.3	hg19	CCDS42424.1	.	.	.	.	.	.	.	.	.	.	C	4.876	0.162801	0.09287	.	.	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524;ENST00000402325;ENST00000399177	T;T;T;T;T;T	0.49432	2.37;2.37;2.37;2.35;2.36;0.78	3.45	1.65	0.23941	.	.	.	.	.	T	0.30262	0.0759	N	0.22421	0.69	0.09310	N	1	B;B;B;B;B	0.25609	0.13;0.13;0.13;0.13;0.13	B;B;B;B;B	0.24269	0.052;0.032;0.052;0.052;0.052	T	0.20605	-1.0270	9	0.48119	T	0.1	0.1645	5.6192	0.17448	0.0:0.7486:0.0:0.2514	.	14;14;14;14;14	F8W7A7;A1L4G8;B5MD75;Q5BJE1-2;Q5BJE1	.;.;.;.;CR034_HUMAN	N	14	ENSP00000385591:D14N;ENSP00000372576:D14N;ENSP00000300227:D14N;ENSP00000385867:D14N;ENSP00000385234:D14N;ENSP00000382130:D14N	ENSP00000300227:D14N	D	-	1	0	C18orf34	29246011	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-0.323000	0.07997	0.464000	0.27142	0.655000	0.94253	GAT	.	.	.	none		0.274	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995		T	30992013	C	T	30992013	3	4	87	1	0	0	0	0	1	0	0	0	1904	913	32	2	2647	2	C18orf34	18	30992013	Missense_Mutation	SNP	C	TCGA-B1-A657-01A-11D-A31X-10	28052525	30992013	47085235	75	5663											
FBN3	84467	hgsc.bcm.edu	37	chr19	8183905	8183905	+	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	tcccttgcacactcgtccacGtctgaaggtttgtgtggaaa	8	12	10	11	2	1	1	0	1	1	0	4	2	3	2	2	2	1	2	2	2	2	2			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr19:8183905G>A	ENST00000600128.1	-	26	3627	c.3213C>T	c.(3211-3213)gaC>gaT	p.D1071D	FBN3_ENST00000270509.2_Splice_Site_p.D1071D|FBN3_ENST00000601739.1_Splice_Site_p.D1071D			Q75N90	FBN3_HUMAN	fibrillin 3	1071	EGF-like 14; 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						ACTCGTCCACGTCTGAAGGTT	0.617																																					p.D1071D		Atlas-SNP	.											.	FBN3	300	.	0			c.C3213T						PASS	.						66	52	57					19																	8183905		2203	4300	6503	SO:0001630	splice_region_variant	84467	exon25			GTCCACGTCTGAA		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.3212-1C>T	chr19.hg19:g.8183905G>A		32.0	0.0	.		28.0	12.0	.	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	hg19	CCDS12196.1																																																																																			.	.	.	none		0.617	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	Silent	A	8183905	G	A	8183905	5	1	87	1	0	0	0	0	0	0	1	0	5711	1159	40	1	5372	1	FBN3	19	8183905	Splice_Site	SNP	G	TCGA-B1-A657-01A-11D-A31X-10		8183905	50945078	76	5664											
PRDX2	7001	hgsc.bcm.edu	37	chr19	12911694	12911694	+	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	taggacctgagggtgtgagcTtagctgcaacctccctcttt	7	12	11	11	0	1	2	0	2	1	0	2	3	2	3	3	2	4	3	3	2	3	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr19:12911694T>C	ENST00000301522.2	-	3	386				PRDX2_ENST00000334482.5_Intron|PRDX2_ENST00000435703.1_Missense_Mutation_p.K98R|CTD-2659N19.10_ENST00000585496.1_RNA	NM_005809.4	NP_005800.3	P32119	PRDX2_HUMAN	peroxiredoxin 2						cellular response to oxidative stress (GO:0034599)|hydrogen peroxide catabolic process (GO:0042744)|negative regulation of apoptotic process (GO:0043066)|negative regulation of neuron apoptotic process (GO:0043524)|regulation of apoptotic process (GO:0042981)|removal of superoxide radicals (GO:0019430)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	antioxidant activity (GO:0016209)|thioredoxin peroxidase activity (GO:0008379)			endometrium(1)|large_intestine(1)|lung(1)|prostate(1)	4						gggtgtgagcttagctgcaac	0.572																																					p.K98R		Atlas-SNP	.											.	PRDX2	20	.	0			c.A293G						PASS	.						48	45	46					19																	12911694		2197	4296	6493	SO:0001627	intron_variant	7001	exon3			GTGAGCTTAGCTG		CCDS12281.1	19p13.2	2008-07-17			ENSG00000167815	ENSG00000167815			9353	protein-coding gene	gene with protein product	"thioredoxin-dependent peroxide reductase 1", "thiol-specific antioxidant 1", "natural killer-enhancing factor B", "thioredoxin peroxidase 1", "torin"	600538		TDPX1		7607688	Standard	NM_005809		Approved	PRP, NKEFB, TSA, PRXII, PRX2, MGC4104	uc002mvd.4	P32119	OTTHUMG00000134285	ENST00000301522.2:c.257+35A>G	chr19.hg19:g.12911694T>C		99.0	0.0	.		76.0	22.0	.	NM_181738	A8K0C0|P31945|P32118|P35701|Q6FHG4|Q92763|Q9UC23	Missense_Mutation	SNP	ENST00000301522.2	hg19	CCDS12281.1	.	.	.	.	.	.	.	.	.	.	T	11.47	1.649424	0.29336	.	.	ENSG00000167815	ENST00000435703	T	0.45668	0.89	3.3	-6.61	0.01818	.	.	.	.	.	T	0.25344	0.0616	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.30001	-0.9993	8	0.87932	D	0	.	5.1763	0.15137	0.0:0.3936:0.2769:0.3294	.	98	A8K0C0	.	R	98	ENSP00000408905:K98R	ENSP00000408905:K98R	K	-	2	0	PRDX2	12772694	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-0.583000	0.05807	-1.609000	0.01585	0.379000	0.24179	AAG	.	.	.	none		0.572	PRDX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258950.2	NM_005809		C	12911694	T	C	12911694	1	2	87	0	1	0	0	0	0	0	0	0	12475	1609	56	3		3	PRDX2	19	12911694	Intron	SNP	T	TCGA-B1-A657-01A-11D-A31X-10	4727789	12911694	46217289	77	5665											
FBXO46	23403	hgsc.bcm.edu	37	chr19	46215777	46215777	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcatccgccctggccagcAggaactccacgttgctgggg	6	7	12	16	2	1	0	1	0	0	0	3	1	3	1	5	4	3	3	5	4	1	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr19:46215777A>G	ENST00000317683.3	-	2	1110	c.977T>C	c.(976-978)cTg>cCg	p.L326P		NM_001080469.1	NP_001073938.1	Q6PJ61	FBX46_HUMAN	F-box protein 46	326										breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(2)|skin(1)	15		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00568)|GBM - Glioblastoma multiforme(486;0.0844)|Epithelial(262;0.201)		CCTGGCCAGCAGGAACTCCAC	0.697																																					p.L326P		Atlas-SNP	.											.	FBXO46	34	.	0			c.T977C						PASS	.						24	27	26					19																	46215777		1982	4149	6131	SO:0001583	missense	23403	exon2			GCCAGCAGGAACT	BC021978	CCDS46116.1	19q13.3	2008-02-05	2004-06-15	2004-06-16		ENSG00000177051		"F-boxes /  "other""	25069	protein-coding gene	gene with protein product		609117	"F-box only protein 34-like"	FBXO34L		9585442	Standard	NM_001080469		Approved	20D7-FC4, Fbx46	uc002pcz.3	Q6PJ61		ENST00000317683.3:c.977T>C	chr19.hg19:g.46215777A>G	ENSP00000410007:p.Leu326Pro	74.0	0.0	.		96.0	27.0	.	NM_001080469		Missense_Mutation	SNP	ENST00000317683.3	hg19	CCDS46116.1	.	.	.	.	.	.	.	.	.	.	A	14.80	2.643535	0.47258	.	.	ENSG00000177051	ENST00000317683	.	.	.	4.39	4.39	0.52855	.	.	.	.	.	T	0.52789	0.1756	N	0.14661	0.345	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.51204	-0.8735	8	0.30078	T	0.28	-6.761	11.5914	0.50947	1.0:0.0:0.0:0.0	.	326	Q6PJ61	FBX46_HUMAN	P	326	.	ENSP00000410007:L326P	L	-	2	0	FBXO46	50907617	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	5.008000	0.63991	1.851000	0.53745	0.460000	0.39030	CTG	.	.	.	none		0.697	FBXO46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459661.1	XM_371179		G	46215777	A	G	46215777	3	3	87	1	0	0	0	0	1	0	0	0	5762	188	7	3	838	3	FBXO46	19	46215777	Missense_Mutation	SNP	A	TCGA-B1-A657-01A-11D-A31X-10	33304083	46215777	12913206	78	5666											
DEFB118	117285	hgsc.bcm.edu	37	chr20	29960794	29960794	+	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	ccaatgaagaccacaggcgaGttcctgcgacatctcccaca	12	6	8	15	2	1	2	0	1	1	1	3	4	2	2	4	1	1	1	4	1	2	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr20:29960794G>T	ENST00000253381.2	+	2	226	c.193G>T	c.(193-195)Gtt>Ttt	p.V65F		NM_054112.2	NP_473453.1	Q96PH6	DB118_HUMAN	defensin, beta 118	65					cell-matrix adhesion (GO:0007160)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)				breast(1)|endometrium(1)|lung(7)|ovary(3)|pancreas(1)|prostate(1)	14	all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			CCACAGGCGAGTTCCTGCGAC	0.443																																					p.V65F		Atlas-SNP	.											.	DEFB118	30	.	0			c.G193T						PASS	.						155	137	143					20																	29960794		2203	4300	6503	SO:0001583	missense	117285	exon2			AGGCGAGTTCCTG	AF347073	CCDS13177.1	20q11.21	2008-02-01	2002-05-09	2002-05-10	ENSG00000131068	ENSG00000131068		"Defensins, beta"	16196	protein-coding gene	gene with protein product		607650	"chromosome 20 open reading frame 63"	C20orf63		11564719, 15033915	Standard	NM_054112		Approved	dJ1018D12.3, DEFB-18, ESC42	uc002wvr.3	Q96PH6	OTTHUMG00000032161	ENST00000253381.2:c.193G>T	chr20.hg19:g.29960794G>T	ENSP00000253381:p.Val65Phe	144.0	0.0	.		109.0	30.0	.	NM_054112	Q17RC4|Q8N691|Q9NUH0	Missense_Mutation	SNP	ENST00000253381.2	hg19	CCDS13177.1	.	.	.	.	.	.	.	.	.	.	G	2.822	-0.244584	0.05906	.	.	ENSG00000131068	ENST00000253381	T	0.07908	3.15	3.19	-6.39	0.01951	.	7.214320	0.00397	N	0.000047	T	0.04588	0.0125	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.35201	-0.9798	10	0.15066	T	0.55	-0.7743	3.7626	0.08610	0.1823:0.2329:0.4708:0.114	.	65	Q96PH6	DB118_HUMAN	F	65	ENSP00000253381:V65F	ENSP00000253381:V65F	V	+	1	0	DEFB118	29424455	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.760000	0.00786	-2.810000	0.00348	-2.435000	0.00213	GTT	.	.	.	none		0.443	DEFB118-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078501.2	NM_054112		T	29960794	G	T	29960794	3	4	87	1	0	0	0	0	1	0	0	0	4408	1029	36	4	199	4	DEFB118	20	29960794	Missense_Mutation	SNP	G	TCGA-B1-A657-01A-11D-A31X-10		29960794	33064726	79	5667											
TPX2	22974	hgsc.bcm.edu	37	chr20	30388879	30388879	+	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	attctccactcgattccactGctaaactcagctgtgagctg	9	12	7	13	1	2	1	1	1	1	0	5	2	3	1	2	0	4	3	2	0	2	3			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr20:30388879G>T	ENST00000300403.6	+	18	2768	c.2240G>T	c.(2239-2241)tGc>tTc	p.C747F	TPX2_ENST00000340513.4_Missense_Mutation_p.C783F	NM_012112.4	NP_036244.2	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated	747					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)			CGATTCCACTGCTAAACTCAG	0.512																																					p.C747F		Atlas-SNP	.											.	TPX2	61	.	0			c.G2240T						PASS	.						123	105	111					20																	30388879		2203	4300	6503	SO:0001583	missense	22974	exon18			TCCACTGCTAAAC	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.2240G>T	chr20.hg19:g.30388879G>T	ENSP00000300403:p.Cys747Phe	103.0	0.0	.		67.0	23.0	.	NM_012112	Q9H1R4|Q9NRA3|Q9UFN9|Q9UL00|Q9Y2M1	Missense_Mutation	SNP	ENST00000300403.6	hg19	CCDS13190.1	.	.	.	.	.	.	.	.	.	.	G	17.86	3.492479	0.64074	.	.	ENSG00000088325	ENST00000300403;ENST00000340513	T	0.37058	1.22	5.28	5.28	0.74379	.	0.110708	0.64402	D	0.000005	T	0.59169	0.2174	M	0.63428	1.95	0.43021	D	0.994579	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.994	T	0.61307	-0.7089	10	0.87932	D	0	.	18.0758	0.89426	0.0:0.0:1.0:0.0	.	783;747	Q96RR5;Q9ULW0	.;TPX2_HUMAN	F	747;783	ENSP00000341145:C783F	ENSP00000300403:C747F	C	+	2	0	TPX2	29852540	1.000000	0.71417	1.000000	0.80357	0.692000	0.40212	3.773000	0.55333	2.745000	0.94114	0.655000	0.94253	TGC	.	.	.	none		0.512	TPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078569.2			T	30388879	G	T	30388879	3	4	87	1	0	0	0	0	1	0	0	0	16444	1319	46	4	2302	4	TPX2	20	30388879	Missense_Mutation	SNP	G	TCGA-B1-A657-01A-11D-A31X-10	428085	30388879	32636641	80	5668											
SUSD2	56241	hgsc.bcm.edu	37	chr22	24579518	24579518	+	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	actcctccgggcaagtgcacTgtgtgtcacctctgctctat	6	12	9	14	1	3	0	1	0	2	0	5	0	5	0	3	1	2	3	3	1	2	1			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chr22:24579518T>A	ENST00000358321.3	+	3	604	c.343T>A	c.(343-345)Tgt>Agt	p.C115S		NM_019601.3	NP_062547.1	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2	115					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						GCAAGTGCACTGTGTGTCACC	0.632																																					p.C115S		Atlas-SNP	.											.	SUSD2	68	.	0			c.T343A						PASS	.						130	114	119					22																	24579518		2203	4300	6503	SO:0001583	missense	56241	exon3			GTGCACTGTGTGT	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.343T>A	chr22.hg19:g.24579518T>A	ENSP00000351075:p.Cys115Ser	54.0	0.0	.		46.0	19.0	.	NM_019601	Q9H5Y6	Missense_Mutation	SNP	ENST00000358321.3	hg19	CCDS13824.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.185964	0.78789	.	.	ENSG00000099994	ENST00000358321	D	0.84873	-1.91	3.5	3.5	0.40072	.	0.000000	0.85682	D	0.000000	D	0.90511	0.7027	M	0.78637	2.42	0.50467	D	0.999877	D	0.71674	0.998	D	0.78314	0.991	D	0.90662	0.4591	10	0.87932	D	0	-25.3814	8.8392	0.35131	0.0:0.0:0.0:1.0	.	115	Q9UGT4	SUSD2_HUMAN	S	115	ENSP00000351075:C115S	ENSP00000351075:C115S	C	+	1	0	SUSD2	22909518	1.000000	0.71417	0.993000	0.49108	0.923000	0.55619	6.119000	0.71590	1.859000	0.53934	0.369000	0.22263	TGT	.	.	.	none		0.632	SUSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320088.1	NM_019601		A	24579518	T	A	24579518	3	1	87	1	0	0	0	0	1	0	0	0	15420	1580	55	5	353	5	SUSD2	22	24579518	Missense_Mutation	SNP	T	TCGA-B1-A657-01A-11D-A31X-10		24579518	26725048	81	5669											
SNX12	29934	hgsc.bcm.edu	37	chrX	70280928	70280928	+	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	ctcctcttgcaggaacatgtGtaggcagcgttcattctgag	8	12	11	10	1	3	1	1	1	2	0	4	2	4	2	1	2	3	4	1	2	2	4			TCGA-B1-A657-01A-11D-A31X-10	TCGA-B1-A657-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c22d5cb0-397b-480a-97ae-4bf07e07c1f0	86a94d68-d695-416e-a19a-d1f1d0952902	g.chrX:70280928G>T	ENST00000374274.3	-	4	543	c.427C>A	c.(427-429)Cac>Aac	p.H143N	SNX12_ENST00000465030.1_5'UTR|SNX12_ENST00000276105.3_Missense_Mutation_p.H139N	NM_001256185.1|NM_001256188.1|NM_013346.3	NP_001243114.1|NP_001243117.1|NP_037478.2	Q9UMY4	SNX12_HUMAN	sorting nexin 12	143	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				intracellular protein transport (GO:0006886)|negative regulation of early endosome to late endosome transport (GO:2000642)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein processing (GO:0010955)|negative regulation of protein transport (GO:0051224)|regulation of endocytosis (GO:0030100)	early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	enzyme binding (GO:0019899)|phosphatidylinositol binding (GO:0035091)	p.H143Y(1)		endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	8	Renal(35;0.156)					AGGAACATGTGTAGGCAGCGT	0.517																																					p.H143N		Atlas-SNP	.											.	SNX12	18	.	1	Substitution - Missense(1)	lung(1)	c.C427A						PASS	.						104	78	87					X																	70280928		2203	4300	6503	SO:0001583	missense	29934	exon5			ACATGTGTAGGCA	AF171229	CCDS14405.1, CCDS59169.1	Xq13.1	2008-03-11			ENSG00000147164	ENSG00000147164		"Sorting nexins"	14976	protein-coding gene	gene with protein product		300883					Standard	NM_013346		Approved		uc004dyr.2	Q9UMY4	OTTHUMG00000021786	ENST00000374274.3:c.427C>A	chrX.hg19:g.70280928G>T	ENSP00000363392:p.His143Asn	47.0	0.0	.		47.0	32.0	.	NM_001256185	F8W8K5|Q8WUG9	Missense_Mutation	SNP	ENST00000374274.3	hg19	CCDS14405.1	.	.	.	.	.	.	.	.	.	.	G	14.99	2.698895	0.48307	.	.	ENSG00000147164	ENST00000374274;ENST00000276105	T;T	0.39787	1.06;1.06	5.25	5.25	0.73442	.	0.208471	0.50627	D	0.000112	T	0.66557	0.2801	M	0.79926	2.475	0.80722	D	1	D	0.71674	0.998	D	0.83275	0.996	T	0.66964	-0.5790	10	0.38643	T	0.18	-19.7041	16.8073	0.85709	0.0:0.0:1.0:0.0	.	143	Q3SYF1	.	N	143;139	ENSP00000363392:H143N;ENSP00000276105:H139N	ENSP00000276105:H139N	H	-	1	0	SNX12	70197653	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	9.653000	0.98506	2.434000	0.82447	0.594000	0.82650	CAC	.	.	.	none		0.517	SNX12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057094.1	NM_013346		T	70280928	G	T	70280928	3	4	87	1	0	0	0	0	1	0	0	0	14896	1377	48	4	65	4	SNX12	23	70280928	Missense_Mutation	SNP	G	TCGA-B1-A657-01A-11D-A31X-10		70280928	84989632	82	5670											
AMY2B	280	hgsc.bcm.edu	37	chr1	104122036	104122036	+	Missense_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	gcacaggcattaaaatctacGtttctgacgatggcaaagct	13	10	9	9	2	2	1	0	1	2	0	2	2	2	1	0	2	2	5	0	2	4	3	rs143243690	byFrequency	TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr1:104122036G>A	ENST00000361355.4	+	12	2066	c.1450G>A	c.(1450-1452)Gtt>Att	p.V484I	AMY2B_ENST00000491397.1_3'UTR	NM_020978.3	NP_066188.1	P19961	AMY2B_HUMAN	amylase, alpha 2B (pancreatic)	484					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)		TAAAATCTACGTTTCTGACGA	0.323													.|||	2	0.000399361	0	0	5008	,	,		17291	0		0.001	False		,,,				2504	0.001				p.V484I		Atlas-SNP	.											.	AMY2B	80	.	0			c.G1450A						PASS	.	G	ILE/VAL	0,4406		0,0,2203	227	235	232		1450	2.2	0.2	1	dbSNP_134	232	1,8599	1.2+/-3.3	0,1,4299	no	missense	AMY2B	NM_020978.3	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	484/512	104122036	1,13005	2203	4300	6503	SO:0001583	missense	280	exon12			ATCTACGTTTCTG	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.1450G>A	chr1.hg19:g.104122036G>A	ENSP00000354610:p.Val484Ile	735.0	1.0	.		1115.0	198.0	.	NM_020978	B3KTI1|B3KXB7|D3DT76|Q9UBH3	Missense_Mutation	SNP	ENST00000361355.4	hg19	CCDS782.1	.	.	.	.	.	.	.	.	.	.	G	8.662	0.900711	0.17686	0.0	1.16E-4	ENSG00000240038	ENST00000361355	T	0.78595	-1.19	4.14	2.25	0.28309	Alpha-amylase, C-terminal all beta (2);Glycosyl hydrolase, family 13, all-beta (1);	0.067775	0.64402	N	0.000017	T	0.74168	0.3681	H	0.95884	3.735	0.48040	D	0.999579	B	0.22346	0.068	B	0.20184	0.028	T	0.72577	-0.4251	10	0.56958	D	0.05	.	8.6944	0.34287	0.2605:0.0:0.7395:0.0	.	484	P19961	AMY2B_HUMAN	I	484	ENSP00000354610:V484I	ENSP00000354610:V484I	V	+	1	0	AMY2B	103923559	1.000000	0.71417	0.165000	0.22776	0.168000	0.22595	4.103000	0.57783	0.339000	0.23719	-0.224000	0.12420	GTT	.	G|1.000;A|0.000	0.000	weak		0.323	AMY2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030318.1	NM_020978		A	104122036	G	A	104122036	3	1	88	1	0	0	0	0	1	0	0	0	595	1145	40	1	1488	1	AMY2B	1	104122036	Missense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08		104122036	145128585	1	5671											
LRIG2	9860	hgsc.bcm.edu	37	chr1	113616063	113616063	+	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	cctaggcgtcccggaggagcAgttgctggggtgtcgatcta	6	9	16	10	3	1	0	0	0	1	0	3	3	2	2	2	5	2	3	2	5	2	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr1:113616063A>T	ENST00000361127.5	+	1	233	c.35A>T	c.(34-36)cAg>cTg	p.Q12L	RP11-31F15.2_ENST00000421157.1_lincRNA	NM_014813.1	NP_055628.1	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like domains 2	12					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)		CCGGAGGAGCAGTTGCTGGGG	0.642											OREG0013684	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q12L		Atlas-SNP	.											.	LRIG2	67	.	0			c.A35T						PASS	.						109	125	120					1																	113616063		2203	4300	6503	SO:0001583	missense	9860	exon1			AGGAGCAGTTGCT	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.35A>T	chr1.hg19:g.113616063A>T	ENSP00000355396:p.Gln12Leu	320.0	0.0	.	1451	352.0	123.0	.	NM_014813	Q9NSN2	Missense_Mutation	SNP	ENST00000361127.5	hg19	CCDS30808.1	.	.	.	.	.	.	.	.	.	.	A	9.612	1.131598	0.21041	.	.	ENSG00000198799	ENST00000361127	T	0.60920	0.15	4.86	-2.01	0.07410	.	0.866104	0.09769	N	0.758205	T	0.10637	0.0260	N	0.08118	0	0.21220	N	0.99976	B	0.02656	0.0	B	0.01281	0.0	T	0.18335	-1.0340	10	0.35671	T	0.21	.	0.3463	0.00342	0.1887:0.2563:0.2382:0.3168	.	12	O94898	LRIG2_HUMAN	L	12	ENSP00000355396:Q12L	ENSP00000355396:Q12L	Q	+	2	0	LRIG2	113417586	0.910000	0.30920	0.987000	0.45799	0.031000	0.12232	-0.515000	0.06290	-0.294000	0.08973	-0.290000	0.09829	CAG	.	.	.	none		0.642	LRIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033549.2	NM_014813		T	113616063	A	T	113616063	3	4	88	1	0	0	0	0	1	0	0	0	8952	188	7	5	37	5	LRIG2	1	113616063	Missense_Mutation	SNP	A	TCGA-B3-3925-01A-01D-1458-08	9494027	113616063	135634558	2	5672											
KIAA0907	22889	hgsc.bcm.edu	37	chr1	155899153	155899153	+	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	gagttgatactgcagccccaCtaagtcggctgatctaaaaa	13	9	9	10	1	1	2	0	2	1	0	2	3	1	2	2	1	3	3	2	1	5	4			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr1:155899153C>G	ENST00000368321.3	-	4	421	c.398G>C	c.(397-399)aGt>aCt	p.S133T	KIAA0907_ENST00000482337.1_5'UTR|KIAA0907_ENST00000368320.3_Missense_Mutation_p.S133T|KIAA0907_ENST00000368319.3_Missense_Mutation_p.S133T	NM_014949.2	NP_055764.2	Q7Z7F0	K0907_HUMAN	KIAA0907	133							RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|urinary_tract(1)	21	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;8.82e-06)			TGCAGCCCCACTAAGTCGGCT	0.408																																					p.S133T		Atlas-SNP	.											.	KIAA0907	58	.	0			c.G398C						PASS	.						126	119	122					1																	155899153		2203	4300	6503	SO:0001583	missense	22889	exon4			GCCCCACTAAGTC	BC062637	CCDS30885.1	1q22	2012-11-30			ENSG00000132680	ENSG00000132680			29145	protein-coding gene	gene with protein product						10048485	Standard	NM_014949		Approved	BLOM7	uc001fmi.1	Q7Z7F0	OTTHUMG00000014103	ENST00000368321.3:c.398G>C	chr1.hg19:g.155899153C>G	ENSP00000357304:p.Ser133Thr	88.0	0.0	.		139.0	52.0	.	NM_014949	O94981|Q7L7Q2|Q7Z7E9|Q8TBQ0	Missense_Mutation	SNP	ENST00000368321.3	hg19	CCDS30885.1	.	.	.	.	.	.	.	.	.	.	C	18.00	3.524402	0.64747	.	.	ENSG00000132680	ENST00000368321;ENST00000368320;ENST00000368319	T;T;T	0.34859	1.34;1.34;1.34	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.20129	0.0484	N	0.16790	0.44	0.80722	D	1	P;P;P;P;P;B	0.50819	0.873;0.939;0.873;0.884;0.682;0.336	P;P;B;P;B;B	0.52646	0.541;0.699;0.439;0.705;0.303;0.395	T	0.01720	-1.1288	10	0.08179	T	0.78	-11.4646	17.2104	0.86929	0.0:1.0:0.0:0.0	.	133;133;133;133;133;133	D3DVA4;Q7Z7F0-4;A8K1I7;Q7Z7F0-3;Q7Z7F0-2;Q7Z7F0	.;.;.;.;.;K0907_HUMAN	T	133	ENSP00000357304:S133T;ENSP00000357303:S133T;ENSP00000357302:S133T	ENSP00000357302:S133T	S	-	2	0	KIAA0907	154165777	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.105000	0.77031	2.831000	0.97527	0.650000	0.86243	AGT	.	.	.	none		0.408	KIAA0907-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039583.1	NM_014949		G	155899153	C	G	155899153	3	3	88	1	0	0	0	0	1	0	0	0	8206	565	20	4	1490	4	KIAA0907	1	155899153	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08	42283090	155899153	93351468	3	5673											
USF1	7391	hgsc.bcm.edu	37	chr1	161011569	161011569	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctggggaagtaagtatagTgcgtctcagcagctgtcccc	8	10	13	10	1	1	0	1	0	1	0	3	1	2	1	2	2	4	5	2	2	4	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr1:161011569T>C	ENST00000368021.3	-	6	548	c.344A>G	c.(343-345)cAc>cGc	p.H115R	F11R_ENST00000289779.3_5'Flank|TSTD1_ENST00000423014.2_5'Flank|TSTD1_ENST00000368024.1_5'Flank|USF1_ENST00000368020.1_Missense_Mutation_p.H115R|USF1_ENST00000435396.1_Missense_Mutation_p.H56R|TSTD1_ENST00000368023.3_5'Flank|TSTD1_ENST00000318289.10_5'Flank|USF1_ENST00000368019.1_Missense_Mutation_p.H115R	NM_007122.3	NP_009053.1	P22415	USF1_HUMAN	upstream transcription factor 1	115					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)			GTAAGTATAGTGCGTCTCAGC	0.572											OREG0013936	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H115R		Atlas-SNP	.											.	USF1	29	.	0			c.A344G						PASS	.						95	87	90					1																	161011569		2203	4300	6503	SO:0001583	missense	7391	exon6			GTATAGTGCGTCT	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.344A>G	chr1.hg19:g.161011569T>C	ENSP00000357000:p.His115Arg	123.0	0.0	.	1813	141.0	13.0	.	NM_001276373	B2RBZ4|Q5SY46|Q7Z5Y1	Missense_Mutation	SNP	ENST00000368021.3	hg19	CCDS1214.1	.	.	.	.	.	.	.	.	.	.	T	5.051	0.195050	0.09599	.	.	ENSG00000158773	ENST00000368020;ENST00000368021;ENST00000435396;ENST00000368019;ENST00000534633	D;D;D;D	0.91740	-2.9;-2.9;-2.85;-2.89	5.23	5.23	0.72850	.	0.048337	0.85682	D	0.000000	T	0.72614	0.3482	N	0.19112	0.55	0.42447	D	0.992738	B	0.11235	0.004	B	0.09377	0.004	T	0.67480	-0.5660	10	0.02654	T	1	-18.6648	13.1223	0.59334	0.0:0.0:0.0:1.0	.	115	P22415	USF1_HUMAN	R	115;115;56;115;56	ENSP00000356999:H115R;ENSP00000357000:H115R;ENSP00000390109:H56R;ENSP00000356998:H115R	ENSP00000356998:H115R	H	-	2	0	USF1	159278193	0.992000	0.36948	0.993000	0.49108	0.996000	0.88848	1.041000	0.30291	2.194000	0.70268	0.533000	0.62120	CAC	.	.	.	none		0.572	USF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077050.1	NM_007122		C	161011569	T	C	161011569	3	2	88	1	0	0	0	0	1	0	0	0	17044	1696	59	3	612	3	USF1	1	161011569	Missense_Mutation	SNP	T	TCGA-B3-3925-01A-01D-1458-08	5112416	161011569	88239052	4	5674											
IMMT	10989	hgsc.bcm.edu	37	chr2	86371415	86371415	+	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	tctggctgcacctgagtggtTcctattcctacggcgctggc	4	12	12	13	2	1	1	0	1	1	0	3	1	3	1	3	4	2	4	3	4	2	4			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr2:86371415T>G	ENST00000410111.3	-	15	2640	c.2253A>C	c.(2251-2253)ggA>ggC	p.G751G	IMMT_ENST00000442664.2_Silent_p.G750G|IMMT_ENST00000409051.2_Silent_p.G704G|IMMT_ENST00000449247.2_Silent_p.G740G|IMMT_ENST00000254636.5_Silent_p.G652G	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	751					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						CCTGAGTGGTTCCTATTCCTA	0.478																																					p.G751G		Atlas-SNP	.											.	IMMT	65	.	0			c.A2253C						PASS	.						68	66	67					2																	86371415		1922	4128	6050	SO:0001819	synonymous_variant	10989	exon15			AGTGGTTCCTATT	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.2253A>C	chr2.hg19:g.86371415T>G		94.0	0.0	.		101.0	40.0	.	NM_006839	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Silent	SNP	ENST00000410111.3	hg19	CCDS46355.1	.	.	.	.	.	.	.	.	.	.	T	7.004	0.555382	0.13436	.	.	ENSG00000132305	ENST00000419070	.	.	.	5.3	-1.19	0.09585	.	.	.	.	.	T	0.52058	0.1711	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44329	-0.9335	4	.	.	.	-22.8427	7.6657	0.28430	0.0:0.4268:0.1243:0.4489	.	.	.	.	H	606	.	.	N	-	1	0	IMMT	86224926	0.864000	0.29904	0.998000	0.56505	0.905000	0.53344	-0.251000	0.08818	-0.076000	0.12775	-0.256000	0.11100	AAC	.	.	.	none		0.478	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839		G	86371415	T	G	86371415	2	3	88	1	0	0	0	0	0	0	0	1	7725	1770	62	5		5	IMMT	2	86371415	Silent	SNP	T	TCGA-B3-3925-01A-01D-1458-08		86371415	156827958	5	5675											
VWC2L	402117	hgsc.bcm.edu	37	chr2	215440518	215440518	+	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	ctgctcagtgttcgaaacgtGaatgccaaggcaagcagact	12	8	11	10	2	1	2	1	1	0	1	2	3	1	2	1	1	4	4	1	1	4	1			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr2:215440518G>T	ENST00000312504.5	+	4	1445	c.643G>T	c.(643-645)Gaa>Taa	p.E215*	VWC2L_ENST00000427124.1_3'UTR|AC107218.3_ENST00000437883.1_RNA|AC107218.3_ENST00000412896.1_RNA	NM_001080500.2	NP_001073969.1	B2RUY7	VWC2L_HUMAN	von Willebrand factor C domain containing protein 2-like	215					negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of neuron differentiation (GO:0045666)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|synapse (GO:0045202)				breast(1)|endometrium(1)|large_intestine(3)|lung(10)|prostate(1)	16						TTCGAAACGTGAATGCCAAGG	0.458																																					p.E215X		Atlas-SNP	.											.	VWC2L	40	.	0			c.G643T						PASS	.						225	220	221					2																	215440518		2026	4199	6225	SO:0001587	stop_gained	402117	exon4			AAACGTGAATGCC	AB374231	CCDS46509.1	2q34-q35	2011-01-25	2011-01-25		ENSG00000174453	ENSG00000174453			37203	protein-coding gene	gene with protein product			"von Willebrand factor C domain-containing protein 2-like"				Standard	NM_001080500		Approved		uc002vet.2	B2RUY7	OTTHUMG00000154811	ENST00000312504.5:c.643G>T	chr2.hg19:g.215440518G>T	ENSP00000308976:p.Glu215*	211.0	0.0	.		305.0	93.0	.	NM_001080500	A6NC69|B2RUW7|B7X8X1	Nonsense_Mutation	SNP	ENST00000312504.5	hg19	CCDS46509.1	.	.	.	.	.	.	.	.	.	.	G	44	10.583132	0.99432	.	.	ENSG00000174453	ENST00000312504	.	.	.	5.58	5.58	0.84498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	-3.3711	19.5796	0.95461	0.0:0.0:1.0:0.0	.	.	.	.	X	215	.	ENSP00000308976:E215X	E	+	1	0	VWC2L	215148763	1.000000	0.71417	0.997000	0.53966	0.999000	0.98932	9.476000	0.97823	2.624000	0.88883	0.655000	0.94253	GAA	.	.	.	none		0.458	VWC2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337175.1	NM_001080500		T	215440518	G	T	215440518	4	4	88	1	0	0	0	0	0	1	0	0	17256	1291	45	4	653	4	VWC2L	2	215440518	Nonsense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08	129069103	215440518	27758855	6	5676											
GIGYF2	26058	hgsc.bcm.edu	37	chr2	233681733	233681734	+	Frame_Shift_Ins	INS	-	-	AGGAAAC																															aggaagaagaacttgcccgaINSaggaaacaggtatgtatctg																										TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr2:233681733_233681734insAGGAAAC	ENST00000409547.1	+	22	2672_2673	c.2361_2362insAGGAAAC	c.(2362-2364)aggfs	p.-790fs	GIGYF2_ENST00000409196.3_Frame_Shift_Ins_p.-784fs|GIGYF2_ENST00000452341.2_Frame_Shift_Ins_p.-621fs|GIGYF2_ENST00000373566.3_Frame_Shift_Ins_p.-812fs|GIGYF2_ENST00000409480.1_Frame_Shift_Ins_p.-812fs|GIGYF2_ENST00000373563.4_Frame_Shift_Ins_p.-790fs|GIGYF2_ENST00000409451.3_Frame_Shift_Ins_p.-811fs	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2						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)		AACTTGCCCGAAGGAAACAGGT	0.47																																					p.R808fs		Atlas-INDEL	.											.	GIGYF2	288	.	0			c.2424_2425insAGGAAAC						PASS	.																																			SO:0001589	frameshift_variant	26058	exon22			.	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.2362_2368dupAGGAAAC	chr2.hg19:g.233681734_233681740dupAGGAAAC	ENSP00000386537:p.Gln790fs	261.0	0.0	0		323.0	45.0	0.139319	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Frame_Shift_Ins	INS	ENST00000409547.1	hg19	CCDS33401.1																																																																																			.	.	.	none		0.47	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		AGGAAAC	233681734	-	AGGAAAC	233681733	7	5	88	1	0	1	1	0	0	0	0	0	6385	233	9	0	2501	0	GIGYF2	2	233681733	Frame_Shift_Ins	INS	-	TCGA-B3-3925-01A-01D-1458-08	18241215	233681733	9517640	7	5677											
OGG1	4968	hgsc.bcm.edu	37	chr3	9798226	9798227	+	Frame_Shift_Ins	INS	-	-	AA																															tggatgtccatatgtggcacINSattgcccaacgtgactacag																										TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr3:9798226_9798227insAA	ENST00000344629.7	+	5	1162_1163	c.819_820insAA	c.(820-822)attfs	p.I274fs	OGG1_ENST00000339511.5_Frame_Shift_Ins_p.I274fs|OGG1_ENST00000302036.7_Frame_Shift_Ins_p.I274fs|OGG1_ENST00000302008.8_Frame_Shift_Ins_p.I274fs|OGG1_ENST00000349503.5_Intron|OGG1_ENST00000449570.2_Frame_Shift_Ins_p.I274fs|OGG1_ENST00000302003.7_Frame_Shift_Ins_p.I274fs|OGG1_ENST00000383826.5_Intron			O15527	OGG1_HUMAN	8-oxoguanine DNA glycosylase	274					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)					ATATGTGGCACATTGCCCAACG	0.599								Base excision repair (BER), DNA glycosylases																													p.H273fs		Atlas-INDEL	.											.	OGG1	57	.	0			c.819_820insAA						PASS	.																																			SO:0001589	frameshift_variant	4968	exon5			.	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	Exception_encountered	chr3.hg19:g.9798226_9798227insAA	ENSP00000342851:p.Ile274fs	80.0	0.0	0		86.0	28.0	0.325581	NM_016821	A8K1E3|O00390|O00670|O00705|O14876|O95488|P78554|Q9BW42|Q9UIK0|Q9UIK1|Q9UIK2|Q9UL34|Q9Y2C0|Q9Y2C1|Q9Y6C3|Q9Y6C4	Frame_Shift_Ins	INS	ENST00000344629.7	hg19	CCDS2581.1																																																																																			.	.	.	none		0.599	OGG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214223.2	NM_016821		AA	9798227	-	AA	9798226	7	5	88	1	0	1	1	0	0	0	0	0	10852	477	17	0	837	0	OGG1	3	9798226	Frame_Shift_Ins	INS	-	TCGA-B3-3925-01A-01D-1458-08		9798226	188224204	8	5678	64	2									
OGG1	4968	hgsc.bcm.edu	37	chr3	9798228	9798228	+	Missense_Mutation	SNP	T	T	A																															ggatgtccatatgtggcacaTtgcccaacgtgactacagct																										TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr3:9798228T>A	ENST00000344629.7	+	5	1164	c.821T>A	c.(820-822)aTt>aAt	p.I274N	OGG1_ENST00000339511.5_Missense_Mutation_p.I274N|OGG1_ENST00000302036.7_Missense_Mutation_p.I274N|OGG1_ENST00000302008.8_Missense_Mutation_p.I274N|OGG1_ENST00000349503.5_Intron|OGG1_ENST00000449570.2_Missense_Mutation_p.I274N|OGG1_ENST00000302003.7_Missense_Mutation_p.I274N|OGG1_ENST00000383826.5_Intron			O15527	OGG1_HUMAN	8-oxoguanine DNA glycosylase	274					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)					ATGTGGCACATTGCCCAACGT	0.602								Base excision repair (BER), DNA glycosylases																													p.I274N		Atlas-SNP	.											.	OGG1	57	.	0			c.T821A						PASS	.						81	78	79					3																	9798228		2203	4300	6503	SO:0001583	missense	4968	exon5			GGCACATTGCCCA	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.821T>A	chr3.hg19:g.9798228T>A	ENSP00000342851:p.Ile274Asn	77.0	0.0	.		79.0	31.0	.	NM_016819	A8K1E3|O00390|O00670|O00705|O14876|O95488|P78554|Q9BW42|Q9UIK0|Q9UIK1|Q9UIK2|Q9UL34|Q9Y2C0|Q9Y2C1|Q9Y6C3|Q9Y6C4	Missense_Mutation	SNP	ENST00000344629.7	hg19	CCDS2581.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.74|17.74	3.464569|3.464569	0.63513|0.63513	.|.	.|.	ENSG00000114026|ENSG00000114026	ENST00000302003;ENST00000344629;ENST00000302036;ENST00000339511;ENST00000449570;ENST00000302008|ENST00000441094;ENST00000416333	D;D;D;D;D;D|.	0.88046|.	-2.33;-2.33;-2.33;-2.33;-2.33;-2.33|.	5.43|5.43	5.43|5.43	0.79202|0.79202	HhH-GPD domain (2);DNA glycosylase (1);Helix-turn-helix, base-excision DNA repair, C-terminal (1);|.	0.044994|.	0.85682|.	D|.	0.000000|.	D|D	0.87124|0.87124	0.6099|0.6099	H|H	0.95745|0.95745	3.715|3.715	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D;D;D|.	0.97110|.	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0|.	D|D	0.91042|0.91042	0.4872|0.4872	10|5	0.87932|.	D|.	0|.	-15.1918|-15.1918	15.7624|15.7624	0.78096|0.78096	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	274;274;274;274;274;274;274;274|.	E5KPN1;O15527-3;E5KPM5;E5KPM7;E5KPM9;E5KPN0;O15527;O15527-2|.	.;.;.;.;.;.;OGG1_HUMAN;.|.	N|M	274|172;41	ENSP00000305584:I274N;ENSP00000342851:I274N;ENSP00000306561:I274N;ENSP00000345520:I274N;ENSP00000403598:I274N;ENSP00000305527:I274N|.	ENSP00000305584:I274N|.	I|L	+|+	2|1	0|2	OGG1|OGG1	9773228|9773228	1.000000|1.000000	0.71417|0.71417	0.970000|0.970000	0.41538|0.41538	0.135000|0.135000	0.20990|0.20990	7.054000|7.054000	0.76649|0.76649	2.176000|2.176000	0.68965|0.68965	0.533000|0.533000	0.62120|0.62120	ATT|TTG	.	.	.	none		0.602	OGG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214223.2	NM_016821		A	9798228	T	A	9798228	3	1	88	1	0	0	0	0	1	0	0	0	10852	1493	52	5	839	5	OGG1	3	9798228	Missense_Mutation	SNP	T	TCGA-B3-3925-01A-01D-1458-08	2	9798228	188224202	9	5679	64	2									
RAF1	5894	hgsc.bcm.edu	37	chr3	12633229	12633229	+	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	cagaacagccacctcattccTgaaggcctggaattgctctg	10	9	9	13	0	2	2	1	1	1	1	3	3	3	3	4	2	3	1	4	2	3	2	rs368807126		TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr3:12633229T>A	ENST00000251849.4	-	11	1610	c.1171A>T	c.(1171-1173)Agg>Tgg	p.R391W	RAF1_ENST00000542177.1_Missense_Mutation_p.R310W|RAF1_ENST00000442415.2_Missense_Mutation_p.R411W|RAF1_ENST00000534997.1_Missense_Mutation_p.R176W	NM_002880.3	NP_002871.1	P04049	RAF1_HUMAN	Raf-1 proto-oncogene, serine/threonine kinase	391	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)	ACCTCATTCCTGAAGGCCTGG	0.507			T	SRGAP3	pilocytic astrocytoma				Noonan syndrome																												p.R391W		Atlas-SNP	.		Dom	yes		3	3p25	5894	v-raf-1 murine leukemia viral oncogene homolog 1		M	.	RAF1	66	.	0			c.A1171T						PASS	.	T	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	110	99	103		1171	4	1	3		103	0,8600		0,0,4300	no	missense	RAF1	NM_002880.3	101	0,1,6502	AA,AT,TT		0.0,0.0227,0.0077	probably-damaging	391/649	12633229	1,13005	2203	4300	6503	SO:0001583	missense	5894	exon11	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	CATTCCTGAAGGC	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.1171A>T	chr3.hg19:g.12633229T>A	ENSP00000251849:p.Arg391Trp	77.0	0.0	.		102.0	31.0	.	NM_002880	B0LPH8|B2R5N3|Q15278|Q9UC20	Missense_Mutation	SNP	ENST00000251849.4	hg19	CCDS2612.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.216060	0.79352	2.27E-4	0.0	ENSG00000132155	ENST00000251849;ENST00000442415;ENST00000432427;ENST00000534997;ENST00000542177	D;D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66;-1.66	5.15	3.96	0.45880	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.84419	0.5468	L	0.28192	0.835	0.80722	D	1	D;D;D	0.71674	0.994;0.994;0.998	D;D;D	0.77557	0.99;0.985;0.99	D	0.85467	0.1170	10	0.87932	D	0	.	11.796	0.52100	0.0:0.0:0.2774:0.7226	.	310;176;391	B4E0X2;B4E1N6;P04049	.;.;RAF1_HUMAN	W	391;411;270;176;310	ENSP00000251849:R391W;ENSP00000401888:R411W;ENSP00000398591:R270W;ENSP00000441186:R176W;ENSP00000443567:R310W	ENSP00000251849:R391W	R	-	1	2	RAF1	12608229	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.865000	0.56033	1.047000	0.40274	0.533000	0.62120	AGG	.	.	.	weak		0.507	RAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252015.2	NM_002880		A	12633229	T	A	12633229	3	1	88	1	0	0	0	0	1	0	0	0	13015	1579	55	5	803	5	RAF1	3	12633229	Missense_Mutation	SNP	T	TCGA-B3-3925-01A-01D-1458-08	2835001	12633229	185389201	10	5680											
TOP2B	7155	hgsc.bcm.edu	37	chr3	25646332	25646332	+	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	tgaaaaaacagaagcagaatCttcttcattactgtcaaatt	17	12	5	7	0	4	3	2	1	2	2	4	3	4	3	0	0	3	1	0	0	7	4			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr3:25646332C>A	ENST00000264331.4	-	33	4407	c.4408G>T	c.(4408-4410)Gat>Tat	p.D1470Y	TOP2B_ENST00000542520.1_Missense_Mutation_p.D322Y|TOP2B_ENST00000540199.1_Missense_Mutation_p.D322Y|TOP2B_ENST00000435706.2_Missense_Mutation_p.D1465Y	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	1470					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)	p.D1465Y(1)		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)	GAAGCAGAATCTTCTTCATTA	0.313																																					p.D1465Y		Atlas-SNP	.											TOP2B,rectum,carcinoma,0,1	TOP2B	98	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4393T						PASS	.						118	110	112					3																	25646332		1811	4068	5879	SO:0001583	missense	7155	exon33			CAGAATCTTCTTC	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.4408G>T	chr3.hg19:g.25646332C>A	ENSP00000264331:p.Asp1470Tyr	82.0	1.0	.		142.0	54.0	.	NM_001068	Q13600|Q9UMG8|Q9UQP8	Missense_Mutation	SNP	ENST00000264331.4	hg19		.	.	.	.	.	.	.	.	.	.	C	19.71	3.878740	0.72294	.	.	ENSG00000077097	ENST00000542520;ENST00000435706;ENST00000264331;ENST00000540199	T;T;T;T	0.49720	0.77;0.85;0.85;0.77	5.48	5.48	0.80851	.	0.262894	0.42964	D	0.000636	T	0.51261	0.1664	N	0.08118	0	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.995;0.996	T	0.61744	-0.7000	10	0.66056	D	0.02	-20.2424	17.9046	0.88914	0.0:1.0:0.0:0.0	.	1470;1465	Q02880;Q02880-2	TOP2B_HUMAN;.	Y	322;1465;1470;322	ENSP00000446023:D322Y;ENSP00000396704:D1465Y;ENSP00000264331:D1470Y;ENSP00000437352:D322Y	ENSP00000264331:D1470Y	D	-	1	0	TOP2B	25621336	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.225000	0.65294	2.722000	0.93159	0.563000	0.77884	GAT	.	.	.	none		0.313	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				A	25646332	C	A	25646332	3	1	88	1	0	0	0	0	1	0	0	0	16378	913	32	4	488	4	TOP2B	3	25646332	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08	13013103	25646332	172376098	11	5681											
SCN10A	6336	hgsc.bcm.edu	37	chr3	38835251	38835251	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccggtgtgtgctgtagaacGgatctagatcctccaggggc	7	9	14	11	2	1	2	0	0	1	2	3	3	3	3	3	4	2	2	3	4	3	2	rs140609990		TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr3:38835251G>A	ENST00000449082.2	-	1	250	c.251C>T	c.(250-252)cCg>cTg	p.P84L		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	84					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)	GCTGTAGAACGGATCTAGATC	0.572													G|||	1	0.000199681	8e-04	0	5008	,	,		12896	0		0	False		,,,				2504	0				p.P84L		Atlas-SNP	.											.	SCN10A	359	.	0			c.C251T						PASS	.	G	LEU/PRO	6,4400	9.9+/-24.2	0,6,2197	154	158	157		251	5.2	1	3	dbSNP_134	157	0,8600		0,0,4300	yes	missense	SCN10A	NM_006514.2	98	0,6,6497	AA,AG,GG		0.0,0.1362,0.0461	possibly-damaging	84/1957	38835251	6,13000	2203	4300	6503	SO:0001583	missense	6336	exon1			TAGAACGGATCTA	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.251C>T	chr3.hg19:g.38835251G>A	ENSP00000390600:p.Pro84Leu	212.0	0.0	.		316.0	94.0	.	NM_006514	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	hg19	CCDS33736.1	.	.	.	.	.	.	.	.	.	.	G	14.95	2.689442	0.48097	0.001362	0.0	ENSG00000185313	ENST00000449082	D	0.96856	-4.15	5.19	5.19	0.71726	.	0.170309	0.52532	D	0.000066	D	0.96842	0.8969	M	0.91612	3.225	0.52501	D	0.999956	D	0.54601	0.967	B	0.41135	0.348	D	0.98036	1.0379	10	0.87932	D	0	.	18.9136	0.92496	0.0:0.0:1.0:0.0	.	84	Q9Y5Y9	SCNAA_HUMAN	L	84	ENSP00000390600:P84L	ENSP00000390600:P84L	P	-	2	0	SCN10A	38810255	1.000000	0.71417	0.997000	0.53966	0.163000	0.22366	9.575000	0.98187	2.704000	0.92352	0.563000	0.77884	CCG	.	G|1.000;A|0.000	0.000	weak		0.572	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		A	38835251	G	A	38835251	3	1	88	1	0	0	0	0	1	0	0	0	13925	1116	39	1	5727	1	SCN10A	3	38835251	Missense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08	13188919	38835251	159187179	12	5682											
ATP6V1A	523	hgsc.bcm.edu	37	chr3	113503595	113503595	+	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	tggaattgtcagtgagaactCgcttatcaaacacaaaatca	16	10	7	8	1	3	1	3	1	0	1	4	3	3	2	0	1	2	1	0	1	6	2			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr3:113503595C>G	ENST00000273398.3	+	5	587	c.479C>G	c.(478-480)tCg>tGg	p.S160W	ATP6V1A_ENST00000538620.1_Missense_Mutation_p.S127W	NM_001690.3	NP_001681.2	P38606	VATA_HUMAN	ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A	160					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus (GO:0005902)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	ATP binding (GO:0005524)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Alendronate(DB00630)|Etidronic acid(DB01077)|Tiludronate(DB01133)	AGTGAGAACTCGCTTATCAAA	0.368																																					p.S160W		Atlas-SNP	.											.	ATP6V1A	71	.	0			c.C479G						PASS	.						121	116	118					3																	113503595		2203	4300	6503	SO:0001583	missense	523	exon5			AGAACTCGCTTAT	L09235	CCDS2976.1	3q13.31	2010-04-21	2002-08-29	2003-04-25	ENSG00000114573	ENSG00000114573	3.6.3.14	"ATPases / V-type"	851	protein-coding gene	gene with protein product		607027	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), alpha polypeptide, 70kD, isoform 1"	VPP2, ATP6A1, ATP6V1A1		8463241	Standard	NM_001690		Approved	Vma1, VA68	uc003eao.3	P38606	OTTHUMG00000159295	ENST00000273398.3:c.479C>G	chr3.hg19:g.113503595C>G	ENSP00000273398:p.Ser160Trp	125.0	0.0	.		171.0	58.0	.	NM_001690	B2RBR8|B7Z1R5|D3DN75|Q53YD9|Q96DY6|Q9UHY3	Missense_Mutation	SNP	ENST00000273398.3	hg19	CCDS2976.1	.	.	.	.	.	.	.	.	.	.	C	18.49	3.634753	0.67130	.	.	ENSG00000114573	ENST00000273398;ENST00000538620;ENST00000496747;ENST00000475322	D;T	0.86956	-2.19;-1.41	6.07	5.2	0.72013	.	0.000000	0.85682	D	0.000000	D	0.92502	0.7619	M	0.78916	2.43	0.80722	D	1	D	0.64830	0.994	P	0.61397	0.888	D	0.93432	0.6786	10	0.87932	D	0	-10.5657	15.5979	0.76602	0.0:0.9341:0.0:0.0659	.	160	P38606	VATA_HUMAN	W	160;127;127;160	ENSP00000273398:S160W;ENSP00000439874:S127W	ENSP00000273398:S160W	S	+	2	0	ATP6V1A	114986285	1.000000	0.71417	0.905000	0.35620	0.616000	0.37450	7.253000	0.78320	1.578000	0.49821	0.655000	0.94253	TCG	.	.	.	none		0.368	ATP6V1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354457.1	NM_001690		G	113503595	C	G	113503595	3	3	88	1	0	0	0	0	1	0	0	0	1177	893	31	4	493	4	ATP6V1A	3	113503595	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08	74668344	113503595	84518835	13	5683											
RUFY3	22902	hgsc.bcm.edu	37	chr4	71659564	71659564	+	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	caaccggctcttcaaacaggActttggagacaagatcaaca	15	7	8	11	1	3	2	2	0	1	2	3	4	3	3	1	3	3	1	1	3	4	2			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr4:71659564A>G	ENST00000226328.4	+	0	4233				RUFY3_ENST00000502653.1_Missense_Mutation_p.D414G|RUFY3_ENST00000381006.3_Missense_Mutation_p.D467G	NM_014961.3	NP_055776.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3						negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)				endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			TTCAAACAGGACTTTGGAGAC	0.527																																					p.D467G		Atlas-SNP	.											.	RUFY3	61	.	0			c.A1400G						PASS	.						52	48	50					4																	71659564		2203	4300	6503	SO:0001628	intergenic_variant	22902	exon13			AACAGGACTTTGG	AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189		"Zinc fingers, FYVE domain containing"	30285	protein-coding gene	gene with protein product	"single axon-related 1"	611194				17439943	Standard	NM_001130709		Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910		chr4.hg19:g.71659564A>G		83.0	0.0	.		99.0	34.0	.	NM_001037442	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	Missense_Mutation	SNP	ENST00000226328.4	hg19	CCDS3547.1	.	.	.	.	.	.	.	.	.	.	A	18.32	3.597113	0.66332	.	.	ENSG00000018189	ENST00000381006;ENST00000502653	T;T	0.08720	3.06;3.06	5.87	5.87	0.94306	.	0.237818	0.42294	D	0.000726	T	0.10508	0.0257	.	.	.	0.80722	D	1	B	0.31548	0.328	B	0.31101	0.124	T	0.04900	-1.0919	9	0.51188	T	0.08	-8.0298	16.2631	0.82557	1.0:0.0:0.0:0.0	.	467	Q7L099-3	.	G	467;414	ENSP00000370394:D467G;ENSP00000425400:D414G	ENSP00000370394:D467G	D	+	2	0	RUFY3	71878428	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.930000	0.92872	2.239000	0.73571	0.528000	0.53228	GAC	.	.	.	none		0.527	RUFY3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252161.2	NM_014961		G	71659564	A	G	71659564	1	3	88	0	1	0	0	0	0	0	0	0	13753	275	10	3		3	RUFY3	4	71659564	IGR	SNP	A	TCGA-B3-3925-01A-01D-1458-08		71659564	119494712	14	5684											
TIGD2	166815	hgsc.bcm.edu	37	chr4	90035227	90035227	+	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	cagtgttggatgcaatttatGaagtgtcaagagcttggaac	12	12	12	5	0	1	2	1	1	0	1	1	4	1	4	0	2	3	3	0	2	5	4			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr4:90035227G>T	ENST00000317005.2	+	1	1260	c.1102G>T	c.(1102-1104)Gaa>Taa	p.E368*	RP11-84C13.1_ENST00000603357.1_lincRNA|FAM13A_ENST00000502459.1_5'Flank	NM_145715.2	NP_663761.1	Q4W5G0	TIGD2_HUMAN	tigger transposable element derived 2	368	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)		TGCAATTTATGAAGTGTCAAG	0.363																																					p.E368X		Atlas-SNP	.											.	TIGD2	36	.	0			c.G1102T						PASS	.						81	80	80					4																	90035227		2203	4300	6503	SO:0001587	stop_gained	166815	exon1			ATTTATGAAGTGT	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.1102G>T	chr4.hg19:g.90035227G>T	ENSP00000317170:p.Glu368*	54.0	0.0	.		103.0	31.0	.	NM_145715		Nonsense_Mutation	SNP	ENST00000317005.2	hg19	CCDS3633.1	.	.	.	.	.	.	.	.	.	.	G	35	5.519555	0.96416	.	.	ENSG00000180346	ENST00000317005	.	.	.	4.36	3.47	0.39725	.	0.000000	0.43110	D	0.000607	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	-9.209	6.0713	0.19891	0.1044:0.193:0.7026:0.0	.	.	.	.	X	368	.	ENSP00000317170:E368X	E	+	1	0	TIGD2	90254250	1.000000	0.71417	0.996000	0.52242	0.956000	0.61745	2.543000	0.45752	2.264000	0.75181	0.460000	0.39030	GAA	.	.	.	none		0.363	TIGD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253545.2	NM_145715		T	90035227	G	T	90035227	4	4	88	1	0	0	0	0	0	1	0	0	15908	1291	45	4	1104	4	TIGD2	4	90035227	Nonsense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08	18375663	90035227	101119049	15	5685											
PCDH18	54510	hgsc.bcm.edu	37	chr4	138450855	138450855	+	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	ttgagtgactggtgactgttGtgactctgccggctgcccat	5	13	13	10	1	1	4	0	4	1	0	1	4	1	4	2	2	2	2	2	2	0	2			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr4:138450855G>A	ENST00000344876.4	-	1	2774	c.2388C>T	c.(2386-2388)caC>caT	p.H796H	PCDH18_ENST00000507846.1_Silent_p.H576H|PCDH18_ENST00000510305.1_Silent_p.H7H|PCDH18_ENST00000511115.1_Intron|PCDH18_ENST00000412923.2_Silent_p.H796H	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	796					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)					GGTGACTGTTGTGACTCTGCC	0.498																																					p.H796H		Atlas-SNP	.											.	PCDH18	229	.	0			c.C2388T						PASS	.						125	109	114					4																	138450855		2203	4300	6503	SO:0001819	synonymous_variant	54510	exon1			ACTGTTGTGACTC	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.2388C>T	chr4.hg19:g.138450855G>A		69.0	0.0	.		97.0	44.0	.	NM_019035	A8K7K3|B7ZKT1|Q52LS2	Silent	SNP	ENST00000344876.4	hg19	CCDS34064.1																																																																																			.	.	.	none		0.498	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		A	138450855	G	A	138450855	2	1	88	1	0	0	0	0	0	0	0	1	11520	1368	48	2		2	PCDH18	4	138450855	Silent	SNP	G	TCGA-B3-3925-01A-01D-1458-08	48415628	138450855	52703421	16	5686											
ABCE1	6059	hgsc.bcm.edu	37	chr4	146041306	146041306	+	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	ggtgatgctgggggaaaatgGtaagttttctgttttgtgat	8	16	15	2	0	1	2	0	2	1	0	1	3	1	3	0	4	1	4	0	4	3	5			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr4:146041306G>A	ENST00000296577.4	+	11	1659		c.e11+1		ABCE1_ENST00000502803.1_Splice_Site|OTUD4_ENST00000455611.2_Intron	NM_001040876.1|NM_002940.2	NP_001035809.1|NP_002931.2	P61221	ABCE1_HUMAN	ATP-binding cassette, sub-family E (OABP), member 1						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)					GGGGAAAATGGTAAGTTTTCT	0.313																																					.		Atlas-SNP	.											.	ABCE1	47	.	0			c.1144+1G>A						PASS	.						66	72	70					4																	146041306		2203	4296	6499	SO:0001630	splice_region_variant	6059	exon11			AAAATGGTAAGTT	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.1144+1G>A	chr4.hg19:g.146041306G>A		62.0	0.0	.		95.0	33.0	.	NM_002940	O88793|Q13181|Q13864|Q6NR76|Q96AL0|Q96B10|Q99K66	Splice_Site	SNP	ENST00000296577.4	hg19	CCDS34071.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.276838	0.80580	.	.	ENSG00000164163	ENST00000296577	.	.	.	5.31	5.31	0.75309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.3284	0.94273	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ABCE1	146260756	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	9.869000	0.99810	2.623000	0.88846	0.555000	0.69702	.	.	.	.	none		0.313	ABCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365104.1	NM_002940	Intron	A	146041306	G	A	146041306	5	1	88	1	0	0	0	0	0	0	1	0	64	1275	44	2	1183	2	ABCE1	4	146041306	Splice_Site	SNP	G	TCGA-B3-3925-01A-01D-1458-08	7590451	146041306	45112970	17	5687											
DDR1	780	hgsc.bcm.edu	37	chr6	30857025	30857025	+	Missense_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	cctggtgccccgcagggtcgGtgtttcccaaggaggaggag	6	7	17	11	2	0	0	0	0	0	0	2	3	1	3	4	6	1	2	4	6	1	1			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr6:30857025G>A	ENST00000324771.8	+	6	783	c.235G>A	c.(235-237)Gtg>Atg	p.V79M	DDR1_ENST00000454612.2_Missense_Mutation_p.V79M|DDR1_ENST00000418800.2_Missense_Mutation_p.V79M|DDR1_ENST00000376568.3_Missense_Mutation_p.V79M|DDR1_ENST00000513240.1_Missense_Mutation_p.V79M|DDR1_ENST00000452441.1_Missense_Mutation_p.V79M|DDR1_ENST00000508312.1_Missense_Mutation_p.V97M|MIR4640_ENST00000581824.1_RNA|DDR1_ENST00000376575.3_Missense_Mutation_p.V79M|DDR1_ENST00000376567.2_Missense_Mutation_p.V79M|DDR1_ENST00000376570.4_Missense_Mutation_p.V79M|DDR1_ENST00000446312.1_Missense_Mutation_p.V79M|DDR1_ENST00000361741.4_5'Flank|DDR1_ENST00000376569.3_Missense_Mutation_p.V79M			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	79	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				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)	CGCAGGGTCGGTGTTTCCCAA	0.647																																					p.V97M		Atlas-SNP	.											.	DDR1	213	.	0			c.G289A						PASS	.						174	186	181					6																	30857025		1511	2709	4220	SO:0001583	missense	780	exon4			GGGTCGGTGTTTC	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.235G>A	chr6.hg19:g.30857025G>A	ENSP00000318217:p.Val79Met	384.0	0.0	.		482.0	150.0	.	NM_001202523	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Missense_Mutation	SNP	ENST00000324771.8	hg19	CCDS34385.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.45|16.45	3.125934|3.125934	0.56721|0.56721	.|.	.|.	ENSG00000204580|ENSG00000204580	ENST00000424544|ENST00000505066;ENST00000460944;ENST00000324771;ENST00000505534;ENST00000508317;ENST00000418800;ENST00000509639;ENST00000454612;ENST00000437124;ENST00000396342;ENST00000512694;ENST00000515233;ENST00000515881;ENST00000376569;ENST00000511510;ENST00000376575;ENST00000376570;ENST00000446312;ENST00000504927;ENST00000428153;ENST00000376568;ENST00000452441;ENST00000508312;ENST00000512336;ENST00000421124;ENST00000512725;ENST00000504679;ENST00000503495;ENST00000376567;ENST00000513240	.|D;D;D;D;D;D;D;D;D;D;D;D;T;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	.|0.98987	.|-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;0.66;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3;-5.3	4.84|4.84	4.84|4.84	0.62591|0.62591	.|Coagulation factor 5/8 C-terminal type domain (4);Galactose-binding domain-like (1);	.|0.156961	.|0.41396	.|D	.|0.000884	D|D	0.98729|0.98729	0.9573|0.9573	M|M	0.67517|0.67517	2.055|2.055	0.20563|0.20563	N|N	0.99989|0.99989	.|D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D	.|0.97110	.|0.973;0.984;0.998;0.976;1.0	D|D	0.95690|0.95690	0.8739|0.8739	5|10	.|0.87932	.|D	.|0	.|.	11.2046|11.2046	0.48762|0.48762	0.0:0.1855:0.8145:0.0|0.0:0.1855:0.8145:0.0	.|.	.|79;105;97;79;79	.|Q08345-4;B7Z3A2;B7Z2K0;Q08345-5;Q08345	.|.;.;.;.;DDR1_HUMAN	D|M	62|79;79;79;79;79;79;79;79;79;79;79;79;79;79;79;79;79;79;79;79;79;79;97;79;79;79;79;105;79;79	.|ENSP00000421189:V79M;ENSP00000426420:V79M;ENSP00000318217:V79M;ENSP00000420833:V79M;ENSP00000427369:V79M;ENSP00000407699:V79M;ENSP00000422331:V79M;ENSP00000406091:V79M;ENSP00000394273:V79M;ENSP00000379631:V79M;ENSP00000426229:V79M;ENSP00000422467:V79M;ENSP00000423492:V79M;ENSP00000365753:V79M;ENSP00000425113:V79M;ENSP00000365759:V79M;ENSP00000365754:V79M;ENSP00000405998:V79M;ENSP00000427597:V79M;ENSP00000390593:V79M;ENSP00000365752:V79M;ENSP00000405039:V79M;ENSP00000422442:V97M;ENSP00000421719:V79M;ENSP00000409682:V79M;ENSP00000422108:V79M;ENSP00000423906:V79M;ENSP00000423749:V105M;ENSP00000365751:V79M;ENSP00000427552:V79M	.|ENSP00000318217:V79M	G|V	+|+	2|1	0|0	DDR1|DDR1	30965004|30965004	1.000000|1.000000	0.71417|0.71417	0.415000|0.415000	0.26534|0.26534	0.938000|0.938000	0.57974|0.57974	4.107000|4.107000	0.57811|0.57811	2.509000|2.509000	0.84616|0.84616	0.305000|0.305000	0.20034|0.20034	GGT|GTG	.	.	.	none		0.647	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994		A	30857025	G	A	30857025	3	1	88	1	0	0	0	0	1	0	0	0	4338	1261	44	2	245	2	DDR1	6	30857025	Missense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08		30857025	140258042	18	5688											
PREP	5550	hgsc.bcm.edu	37	chr6	105825364	105825364	+	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	acactgctcaagaaatggcaCagtaatcttattctgggcct	12	11	8	10	0	3	1	1	0	2	1	3	1	3	1	1	2	1	3	1	2	4	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr6:105825364C>G	ENST00000369110.3	-	3	343	c.151G>C	c.(151-153)Gtg>Ctg	p.V51L		NM_002726.4	NP_002717.3	P48147	PPCE_HUMAN	prolyl endopeptidase	51					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)	p.V51L(1)		breast(1)|endometrium(2)|large_intestine(7)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)	AGAAATGGCACAGTAATCTTA	0.353																																					p.V51L		Atlas-SNP	.											PREP,NS,carcinoma,0,1	PREP	65	.	1	Substitution - Missense(1)	lung(1)	c.G151C						PASS	.						95	93	94					6																	105825364		2203	4300	6503	SO:0001583	missense	5550	exon3			ATGGCACAGTAAT		CCDS5053.1	6q22	2008-02-05			ENSG00000085377	ENSG00000085377	3.4.21.26		9358	protein-coding gene	gene with protein product		600400				7959018	Standard	NM_002726		Approved		uc003prc.3	P48147	OTTHUMG00000015297	ENST00000369110.3:c.151G>C	chr6.hg19:g.105825364C>G	ENSP00000358106:p.Val51Leu	100.0	0.0	.		173.0	62.0	.	NM_002726	Q8N6D4	Missense_Mutation	SNP	ENST00000369110.3	hg19	CCDS5053.1	.	.	.	.	.	.	.	.	.	.	C	12.02	1.812019	0.32053	.	.	ENSG00000085377	ENST00000369110	T	0.44881	0.91	5.76	4.89	0.63831	Peptidase S9A/B/C, oligopeptidase, N-terminal beta-propeller (2);	0.241940	0.41823	D	0.000804	T	0.07098	0.0180	N	0.01352	-0.895	0.39317	D	0.965174	B	0.02656	0.0	B	0.01281	0.0	T	0.15065	-1.0450	10	0.25751	T	0.34	-16.8555	10.4377	0.44445	0.0:0.8553:0.0:0.1447	.	51	P48147	PPCE_HUMAN	L	51	ENSP00000358106:V51L	ENSP00000358106:V51L	V	-	1	0	PREP	105932057	0.730000	0.28100	0.982000	0.44146	0.979000	0.70002	1.374000	0.34283	2.700000	0.92200	0.650000	0.86243	GTG	.	.	.	none		0.353	PREP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041658.1			G	105825364	C	G	105825364	3	3	88	1	0	0	0	0	1	0	0	0	12484	478	17	4	2033	4	PREP	6	105825364	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08	74968339	105825364	65289703	19	5689											
ROS1	6098	hgsc.bcm.edu	37	chr6	117622147	117622147	+	Missense_Mutation	SNP	T	T	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	tcaaacttaccttcaaagctTtcatttatgactccactgtt	11	16	3	11	0	3	1	3	1	0	0	4	1	4	1	2	0	3	2	2	0	4	6			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr6:117622147T>G	ENST00000368508.3	-	42	6921	c.6723A>C	c.(6721-6723)gaA>gaC	p.E2241D	RN7SKP18_ENST00000516005.1_RNA|RN7SKP51_ENST00000410781.1_RNA|ROS1_ENST00000368507.3_Missense_Mutation_p.E2235D	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	2241					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)		CTTCAAAGCTTTCATTTATGA	0.333			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																p.E2241D		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	.	ROS1	728	.	0			c.A6723C						PASS	.						77	74	75					6																	117622147		2203	4300	6503	SO:0001583	missense	6098	exon42			AAAGCTTTCATTT	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.6723A>C	chr6.hg19:g.117622147T>G	ENSP00000357494:p.Glu2241Asp	76.0	0.0	.		109.0	38.0	.	NM_002944	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	hg19	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	T	11.69	1.713310	0.30413	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	T;T	0.71341	-0.56;-0.56	4.98	1.37	0.22104	.	0.267889	0.32190	N	0.006450	T	0.30823	0.0777	L	0.27053	0.805	0.23174	N	0.998172	B	0.24963	0.115	B	0.20577	0.03	T	0.18871	-1.0323	10	0.30854	T	0.27	.	7.4549	0.27261	0.0:0.2549:0.0:0.7451	.	2241	P08922	ROS1_HUMAN	D	2241;2235	ENSP00000357494:E2241D;ENSP00000357493:E2235D	ENSP00000357493:E2235D	E	-	3	2	ROS1	117728840	0.999000	0.42202	0.996000	0.52242	0.448000	0.32197	0.295000	0.19065	0.439000	0.26476	0.459000	0.35465	GAA	.	.	.	none		0.333	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			G	117622147	T	G	117622147	3	3	88	1	0	0	0	0	1	0	0	0	13544	1838	64	5	328	5	ROS1	6	117622147	Missense_Mutation	SNP	T	TCGA-B3-3925-01A-01D-1458-08	11796783	117622147	53492920	20	5690											
POLM	27434	hgsc.bcm.edu	37	chr7	44121926	44121926	+	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	ccggcggctgcgacccatgcGaggctcgaccaggtagatgg	7	5	16	13	5	0	1	0	0	0	1	1	4	0	1	3	5	2	3	3	5	1	1	rs375526665		TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr7:44121926G>T	ENST00000242248.5	-	1	213	c.112C>A	c.(112-114)Cgc>Agc	p.R38S	POLM_ENST00000335195.6_Missense_Mutation_p.R38S|POLM_ENST00000395831.3_Missense_Mutation_p.R38S	NM_013284.2	NP_037416.1	Q9NP87	DPOLM_HUMAN	polymerase (DNA directed), mu	38	BRCT. {ECO:0000255|PROSITE- ProRule:PRU00033}.				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						CGACCCATGCGAGGCTCGACC	0.751								DNA polymerases (catalytic subunits)																													p.R38S		Atlas-SNP	.											.	POLM	50	.	0			c.C112A						PASS	.	G	SER/ARG	1,4241		0,1,2120	6	8	7		112	4.4	0.8	7		7	0,8326		0,0,4163	no	missense	POLM	NM_013284.2	110	0,1,6283	TT,TG,GG		0.0,0.0236,0.0080	possibly-damaging	38/495	44121926	1,12567	2121	4163	6284	SO:0001583	missense	27434	exon1			CCATGCGAGGCTC	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.112C>A	chr7.hg19:g.44121926G>T	ENSP00000242248:p.Arg38Ser	14.0	0.0	.		22.0	7.0	.	NM_013284	D3DVK4|Q6P5X8|Q86WQ9	Missense_Mutation	SNP	ENST00000242248.5	hg19	CCDS34625.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.451233	0.84209	2.36E-4	0.0	ENSG00000122678	ENST00000335195;ENST00000242248;ENST00000395831;ENST00000414235;ENST00000452049	T;T;T;T;T	0.36699	2.24;2.54;1.55;1.24;1.24	5.31	4.41	0.53225	BRCT (3);	0.108961	0.64402	D	0.000019	T	0.51143	0.1657	M	0.61703	1.905	0.40282	D	0.978403	P;D;D;D;P;P	0.62365	0.638;0.959;0.991;0.976;0.894;0.819	B;P;P;P;P;B	0.59948	0.162;0.796;0.866;0.813;0.591;0.439	T	0.55515	-0.8129	10	0.72032	D	0.01	-27.4319	11.1603	0.48512	0.0:0.0:0.8158:0.1842	.	38;38;38;38;38;38	B4DG75;Q6PIY2;Q9H980;Q86WQ9;Q6P5X8;Q9NP87	.;.;.;.;.;DPOLM_HUMAN	S	38	ENSP00000335141:R38S;ENSP00000242248:R38S;ENSP00000379174:R38S;ENSP00000390899:R38S;ENSP00000399244:R38S	ENSP00000242248:R38S	R	-	1	0	POLM	44088451	0.981000	0.34729	0.836000	0.33094	0.795000	0.44927	1.385000	0.34408	1.202000	0.43218	0.561000	0.74099	CGC	.	.	.	weak		0.751	POLM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339594.1	NM_013284		T	44121926	G	T	44121926	3	4	88	1	0	0	0	0	1	0	0	0	12213	1058	37	4	1416	4	POLM	7	44121926	Missense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08		44121926	115016737	21	5691											
ASB15	142685	hgsc.bcm.edu	37	chr7	123264837	123264837	+	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	gtcgctgccgagtatggtcaCtgtgacgtgttagaacatct	8	12	12	9	3	2	2	1	1	1	1	3	3	2	2	1	1	2	3	1	1	3	2			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr7:123264837C>A	ENST00000451558.1	+	10	1187	c.666C>A	c.(664-666)caC>caA	p.H222Q	ASB15_ENST00000434204.1_Missense_Mutation_p.H222Q|ASB15_ENST00000451215.1_Missense_Mutation_p.H222Q|RP11-390E23.3_ENST00000451016.1_RNA|RP11-390E23.3_ENST00000429396.1_RNA|ASB15_ENST00000540573.1_Missense_Mutation_p.H222Q|RP11-390E23.3_ENST00000418409.1_RNA|ASB15_ENST00000275699.3_Missense_Mutation_p.H222Q|RP11-390E23.3_ENST00000440504.1_RNA|RP11-390E23.3_ENST00000422401.1_RNA			Q8WXK1	ASB15_HUMAN	ankyrin repeat and SOCS box containing 15	222					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|kidney(1)|large_intestine(1)|lung(6)|skin(3)	12						AGTATGGTCACTGTGACGTGT	0.468											OREG0018282	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H222Q		Atlas-SNP	.											.	ASB15	94	.	0			c.C666A						PASS	.						132	95	107					7																	123264837		2203	4300	6503	SO:0001583	missense	142685	exon6			TGGTCACTGTGAC	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.666C>A	chr7.hg19:g.123264837C>A	ENSP00000397655:p.His222Gln	61.0	0.0	.	1525	83.0	35.0	.	NM_080928	Q3ZCP3|Q3ZCP5|Q68D37	Missense_Mutation	SNP	ENST00000451558.1	hg19	CCDS34742.1	.	.	.	.	.	.	.	.	.	.	C	12.02	1.811718	0.32053	.	.	ENSG00000146809	ENST00000451558;ENST00000434204;ENST00000451215;ENST00000540573;ENST00000542545;ENST00000447789;ENST00000275699	T;T;T;T;T;T	0.65549	-0.1;-0.1;-0.1;-0.1;-0.16;-0.1	5.36	5.36	0.76844	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.67154	0.2863	L	0.33792	1.035	0.58432	D	0.999999	D	0.54601	0.967	P	0.58391	0.838	T	0.60924	-0.7166	10	0.22706	T	0.39	-7.5108	19.4438	0.94838	0.0:1.0:0.0:0.0	.	222	Q8WXK1	ASB15_HUMAN	Q	222;222;222;222;11;222;222	ENSP00000397655:H222Q;ENSP00000390963:H222Q;ENSP00000416433:H222Q;ENSP00000438643:H222Q;ENSP00000401166:H222Q;ENSP00000275699:H222Q	ENSP00000275699:H222Q	H	+	3	2	ASB15	123052073	0.988000	0.35896	1.000000	0.80357	0.235000	0.25334	1.161000	0.31773	2.674000	0.91012	0.491000	0.48974	CAC	.	.	.	none		0.468	ASB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347493.1			A	123264837	C	A	123264837	3	1	88	1	0	0	0	0	1	0	0	0	1019	564	20	4	684	4	ASB15	7	123264837	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08	79142911	123264837	35873826	22	5692											
MGAM	8972	hgsc.bcm.edu	37	chr7	141800677	141800677	+	Missense_Mutation	SNP	T	T	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	ggctggctcttctgggatgaTgggcaaagcattggtgagta	8	11	16	6	0	2	2	0	2	2	0	2	3	2	3	0	5	1	5	0	5	2	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr7:141800677T>G	ENST00000549489.2	+	45	5357	c.5262T>G	c.(5260-5262)gaT>gaG	p.D1754E	MGAM_ENST00000475668.2_Missense_Mutation_p.D2650E	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1754	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)	TCTGGGATGATGGGCAAAGCA	0.502																																					p.D1754E		Atlas-SNP	.											.	MGAM	767	.	0			c.T5262G						PASS	.						86	86	86					7																	141800677		1981	4153	6134	SO:0001583	missense	8972	exon45			GGATGATGGGCAA	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.5262T>G	chr7.hg19:g.141800677T>G	ENSP00000447378:p.Asp1754Glu	32.0	0.0	.		52.0	26.0	.	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	hg19	CCDS47727.1	.	.	.	.	.	.	.	.	.	.	T	18.11	3.550375	0.65311	.	.	ENSG00000257335	ENST00000549489;ENST00000475668	D	0.96265	-3.96	4.83	1.2	0.21068	.	.	.	.	.	D	0.97343	0.9131	M	0.89414	3.03	0.24431	N	0.994574	D	0.55172	0.97	P	0.56823	0.807	D	0.92205	0.5771	9	0.87932	D	0	.	7.7862	0.29093	0.0:0.3312:0.0:0.6688	.	1754	O43451	MGA_HUMAN	E	1754;2651	ENSP00000447378:D1754E	ENSP00000373973:D1754E	D	+	3	2	MGAM	141447146	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	0.614000	0.24314	0.058000	0.16222	-0.269000	0.10298	GAT	.	.	.	none		0.502	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			G	141800677	T	G	141800677	3	3	88	1	0	0	0	0	1	0	0	0	9548	1461	51	5	5436	5	MGAM	7	141800677	Missense_Mutation	SNP	T	TCGA-B3-3925-01A-01D-1458-08	18535840	141800677	17337986	23	5693											
SNTB1	6641	hgsc.bcm.edu	37	chr8	121587444	121587444	+	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	aaccagggctggtttccactGtttcttgctctcccctggca	5	13	9	14	0	2	0	0	0	2	0	4	0	3	0	4	3	2	5	4	3	1	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr8:121587444G>A	ENST00000395601.3	-	5	1432	c.1018C>T	c.(1018-1020)Cag>Tag	p.Q340*	SNTB1_ENST00000517992.1_Nonsense_Mutation_p.Q340*|SNTB1_ENST00000519177.1_5'UTR	NM_021021.3	NP_066301.1	Q13884	SNTB1_HUMAN	syntrophin, beta 1 (dystrophin-associated protein A1, 59kDa, basic component 1)	340	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				muscle contraction (GO:0006936)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|focal adhesion (GO:0005925)|protein complex (GO:0043234)|synapse (GO:0045202)				NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|prostate(2)|skin(6)	24	Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)		STAD - Stomach adenocarcinoma(47;0.00503)			GGTTTCCACTGTTTCTTGCTC	0.483																																					p.Q340X		Atlas-SNP	.											.	SNTB1	54	.	0			c.C1018T						PASS	.						149	139	142					8																	121587444		2203	4300	6503	SO:0001587	stop_gained	6641	exon4			TCCACTGTTTCTT	AF028828	CCDS6334.1	8q23-q24	2013-01-10	2002-08-29		ENSG00000172164	ENSG00000172164		"Pleckstrin homology (PH) domain containing"	11168	protein-coding gene	gene with protein product	"tax interaction protein 43"	600026	"syntrophin, beta 1 (dystrophin-associated protein A1, 59kD, basic component 1)"	SNT2B1		8183929, 9482110	Standard	NM_021021		Approved	59-DAP, A1B, BSYN2, TIP-43, SNT2	uc010mdg.3	Q13884	OTTHUMG00000165041	ENST00000395601.3:c.1018C>T	chr8.hg19:g.121587444G>A	ENSP00000378965:p.Gln340*	170.0	0.0	.		219.0	62.0	.	NM_021021	A8K9E0|O14912|Q4KMG8	Nonsense_Mutation	SNP	ENST00000395601.3	hg19	CCDS6334.1	.	.	.	.	.	.	.	.	.	.	G	40	8.420009	0.98803	.	.	ENSG00000172164	ENST00000395601;ENST00000517992	.	.	.	6.01	5.11	0.69529	.	0.476872	0.25380	N	0.031082	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.7345	0.85444	0.0:0.0:0.8703:0.1297	.	.	.	.	X	340	.	ENSP00000378965:Q340X	Q	-	1	0	SNTB1	121656625	1.000000	0.71417	0.999000	0.59377	0.901000	0.52897	6.995000	0.76257	2.861000	0.98227	0.650000	0.86243	CAG	.	.	.	none		0.483	SNTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381535.1	NM_021021		A	121587444	G	A	121587444	4	1	88	1	0	0	0	0	0	1	0	0	14885	1386	48	2	614	2	SNTB1	8	121587444	Nonsense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08		121587444	24776578	24	5694											
C10orf12	26148	hgsc.bcm.edu	37	chr10	98741324	98741326	+	In_Frame_Del	DEL	TTT	TTT	-																															actgctgacaaagagaatacTttacagtgtccaaaaacacc																										TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	TTT	TTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr10:98741324_98741326delTTT	ENST00000286067.2	+	1	284_286	c.177_179delTTT	c.(175-180)acttta>aca	p.L60del		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	60										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)		AAGAGAATACTTTACAGTGTCCA	0.404																																					p.59_60del		Atlas-INDEL	.											.	C10orf12	94	.	0			c.176_178del						PASS	.																																			SO:0001651	inframe_deletion	26148	exon1			.	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.177_179delTTT	chr10.hg19:g.98741324_98741326delTTT	ENSP00000286067:p.Leu60del	79.0	0.0	0		108.0	37.0	0.342593	NM_015652	Q9H945|Q9Y457	In_Frame_Del	DEL	ENST00000286067.2	hg19	CCDS7452.1																																																																																			.	.	.	none		0.404	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652		-	98741326	TTT	-	98741324	7	5	88	1	0	1	0	1	0	0	0	0	1591	1596	56	0	179	0	C10orf12	10	98741324	In_Frame_Del	DEL	TTT	TCGA-B3-3925-01A-01D-1458-08		98741324	36793423	25	5695											
COL17A1	1308	hgsc.bcm.edu	37	chr10	105793764	105793764	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagatctccagcaaagtcAgctcccaatagtccgccatt	11	9	6	15	1	2	1	1	0	1	1	6	1	5	1	5	0	2	2	5	0	3	2			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr10:105793764A>G	ENST00000353479.5	-	52	4385	c.4095T>C	c.(4093-4095)gcT>gcC	p.A1365A	COL17A1_ENST00000369733.3_Silent_p.A1283A	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	1365	Triple-helical region.				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|hemidesmosome (GO:0030056)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				NS(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|liver(1)|lung(22)|ovary(5)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	62		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		CAGCAAAGTCAGCTCCCAATA	0.587																																					p.A1365A		Atlas-SNP	.											.	COL17A1	149	.	0			c.T4095C						PASS	.						109	106	107					10																	105793764		2203	4300	6503	SO:0001819	synonymous_variant	1308	exon52			AAAGTCAGCTCCC	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.4095T>C	chr10.hg19:g.105793764A>G		122.0	0.0	.		140.0	42.0	.	NM_000494	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Silent	SNP	ENST00000353479.5	hg19	CCDS7554.1																																																																																			.	.	.	none		0.587	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494		G	105793764	A	G	105793764	2	3	88	1	0	0	0	0	0	0	0	1	3676	175	7	3		3	COL17A1	10	105793764	Silent	SNP	A	TCGA-B3-3925-01A-01D-1458-08	7052440	105793764	29740983	26	5696											
PTPRE	5791	hgsc.bcm.edu	37	chr10	129859261	129859261	+	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	attccctgttcagactacatCaatgcttcctacatagatgt	11	14	5	11	0	2	2	2	0	0	2	4	2	4	2	2	0	3	2	2	0	4	6			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr10:129859261C>A	ENST00000254667.3	+	8	849	c.570C>A	c.(568-570)atC>atA	p.I190I	PTPRE_ENST00000419012.2_Silent_p.I190I|PTPRE_ENST00000430713.2_3'UTR|PTPRE_ENST00000306042.5_Silent_p.I132I	NM_006504.4	NP_006495.1	P23469	PTPRE_HUMAN	protein tyrosine phosphatase, receptor type, E	190	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of insulin receptor signaling pathway (GO:0046627)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of mast cell activation (GO:0033003)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	22		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)			Alendronate(DB00630)	CAGACTACATCAATGCTTCCT	0.483																																					p.I190I	Colon(52;977 1184 20575 41685)	Atlas-SNP	.											.	PTPRE	132	.	0			c.C570A						PASS	.						175	160	165					10																	129859261		2203	4300	6503	SO:0001819	synonymous_variant	5791	exon8			CTACATCAATGCT	AF406557	CCDS7657.1, CCDS7658.1	10q26	2011-06-09			ENSG00000132334	ENSG00000132334		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"	9669	protein-coding gene	gene with protein product		600926				8595895	Standard	NM_130435		Approved	PTPE	uc001lkb.3	P23469	OTTHUMG00000019254	ENST00000254667.3:c.570C>A	chr10.hg19:g.129859261C>A		87.0	0.0	.		109.0	38.0	.	NM_006504	Q13345|Q5VWH3|Q5VWH4|Q96KQ6	Silent	SNP	ENST00000254667.3	hg19	CCDS7657.1																																																																																			.	.	.	none		0.483	PTPRE-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050990.1			A	129859261	C	A	129859261	2	1	88	1	0	0	0	0	0	0	0	1	12813	816	29	4		4	PTPRE	10	129859261	Silent	SNP	C	TCGA-B3-3925-01A-01D-1458-08	24065497	129859261	5675486	27	5697											
PAOX	196743	hgsc.bcm.edu	37	chr10	135193909	135193909	+	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	ctggaatgctgtgtgagcggCacccacagcatggacctggt	8	8	14	11	1	0	1	0	1	0	0	0	3	0	3	2	4	3	3	2	4	1	0			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr10:135193909C>T	ENST00000278060.5	+	2	671	c.588C>T	c.(586-588)ggC>ggT	p.G196G	PAOX_ENST00000368539.4_Intron|PAOX_ENST00000368535.2_3'UTR|PAOX_ENST00000480071.2_Silent_p.G196G|PAOX_ENST00000357296.3_Silent_p.G196G|AL360181.1_ENST00000597657.1_5'Flank	NM_152911.2	NP_690875.1	Q6QHF9	PAOX_HUMAN	polyamine oxidase (exo-N4-amino)	334					cellular nitrogen compound metabolic process (GO:0034641)|oxidation-reduction process (GO:0055114)|polyamine biosynthetic process (GO:0006596)|polyamine catabolic process (GO:0006598)|polyamine metabolic process (GO:0006595)|positive regulation of spermidine biosynthetic process (GO:1901307)|putrescine biosynthetic process (GO:0009446)|putrescine catabolic process (GO:0009447)|small molecule metabolic process (GO:0044281)|spermidine catabolic process (GO:0046203)|spermine catabolic process (GO:0046208)|xenobiotic metabolic process (GO:0006805)	peroxisomal matrix (GO:0005782)	N(1),N(12)-diacetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity (GO:0052899)|N1-acetylspermidine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity (GO:0052904)|N1-acetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity (GO:0052903)|polyamine oxidase activity (GO:0046592)|receptor binding (GO:0005102)|spermidine:oxygen oxidoreductase (3-aminopropanal-forming) activity (GO:0052902)|spermine:oxygen oxidoreductase (spermidine-forming) activity (GO:0052901)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|urinary_tract(2)	23		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;4.39e-07)|OV - Ovarian serous cystadenocarcinoma(35;1.21e-06)|Epithelial(32;1.94e-06)		GTGTGAGCGGCACCCACAGCA	0.622																																					p.G196G		Atlas-SNP	.											.	PAOX	82	.	0			c.C588T						PASS	.						33	36	35					10																	135193909		2202	4299	6501	SO:0001819	synonymous_variant	196743	exon2			GAGCGGCACCCAC	BC032778	CCDS7682.1, CCDS7683.1, CCDS7684.1	10q26.3	2003-11-13			ENSG00000148832	ENSG00000148832			20837	protein-coding gene	gene with protein product		615853				12660232	Standard	NM_207127		Approved	PAO	uc001lmv.3	Q6QHF9	OTTHUMG00000019318	ENST00000278060.5:c.588C>T	chr10.hg19:g.135193909C>T		73.0	0.0	.		83.0	7.0	.	NM_207128	D3DXI6|Q5VWY0|Q6QHF5|Q6QHF6|Q6QHF7|Q6QHF8|Q6QHG0|Q6QHG1|Q6QHG2|Q6QHG3|Q6QHG4|Q6QHG5|Q6QHG6|Q86WP9|Q8N555|Q8NCX3	Silent	SNP	ENST00000278060.5	hg19	CCDS7683.1																																																																																			.	.	.	none		0.622	PAOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051146.2	NM_152911		T	135193909	C	T	135193909	2	4	88	1	0	0	0	0	0	0	0	1	11430	697	25	2		2	PAOX	10	135193909	Silent	SNP	C	TCGA-B3-3925-01A-01D-1458-08	5334648	135193909	340838	28	5698											
GYS2	2998	hgsc.bcm.edu	37	chr12	21757442	21757442	+	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	ccaagcaacttcaaagagcaGtaactcctccacaggaagtt	15	7	7	12	0	1	1	1	0	0	1	3	2	3	2	3	1	4	4	3	1	5	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr12:21757442G>T	ENST00000261195.2	-	1	339	c.85C>A	c.(85-87)Ctg>Atg	p.L29M		NM_021957.3	NP_068776.2	P54840	GYS2_HUMAN	glycogen synthase 2 (liver)	29					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						TCAAAGAGCAGTAACTCCTCC	0.493																																					p.L29M	Colon(149;9 1820 3690 10544 50424)	Atlas-SNP	.											.	GYS2	110	.	0			c.C85A						PASS	.						117	114	115					12																	21757442		2203	4299	6502	SO:0001583	missense	2998	exon1			AGAGCAGTAACTC		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.85C>A	chr12.hg19:g.21757442G>T	ENSP00000261195:p.Leu29Met	207.0	0.0	.		346.0	175.0	.	NM_021957	A0AVD8	Missense_Mutation	SNP	ENST00000261195.2	hg19	CCDS8690.1	.	.	.	.	.	.	.	.	.	.	G	15.54	2.864428	0.51482	.	.	ENSG00000111713	ENST00000261195	T	0.66638	-0.22	5.28	2.44	0.29823	.	0.076400	0.53938	D	0.000050	T	0.52964	0.1767	N	0.19112	0.55	0.34049	D	0.655926	P	0.52577	0.954	P	0.48166	0.569	T	0.61584	-0.7033	10	0.46703	T	0.11	-15.2558	7.1986	0.25868	0.35:0.0:0.65:0.0	.	29	P54840	GYS2_HUMAN	M	29	ENSP00000261195:L29M	ENSP00000261195:L29M	L	-	1	2	GYS2	21648709	0.646000	0.27295	0.229000	0.23960	0.989000	0.77384	0.796000	0.26986	0.361000	0.24292	0.655000	0.94253	CTG	.	.	.	none		0.493	GYS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402396.1	NM_021957		T	21757442	G	T	21757442	3	4	88	1	0	0	0	0	1	0	0	0	6920	1020	36	4	2090	4	GYS2	12	21757442	Missense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08		21757442	112094453	29	5699											
TSFM	25895	hgsc.bcm.edu	37	chr12	58177005	58177005	+	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	catgaagctgcggcggaaaaCaggctactcctttgtaaatt	12	10	10	9	2	0	1	0	1	0	0	1	2	1	2	1	3	4	3	1	3	6	4			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr12:58177005C>T	ENST00000300209.8	+	0	2563				TSFM_ENST00000454289.3_Missense_Mutation_p.T57I|RP11-571M6.15_ENST00000471530.1_Nonsense_Mutation_p.Q72*|TSFM_ENST00000350762.5_5'UTR|RP11-571M6.15_ENST00000553083.1_3'UTR|TSFM_ENST00000540550.1_Missense_Mutation_p.T57I|TSFM_ENST00000550559.1_Missense_Mutation_p.T57I|TSFM_ENST00000497617.1_3'UTR|TSFM_ENST00000548851.1_Missense_Mutation_p.T57I|TSFM_ENST00000543727.1_Missense_Mutation_p.T57I|TSFM_ENST00000323833.8_Missense_Mutation_p.T57I	NM_015433.2	NP_056248.2	Q96AZ1	MT21B_HUMAN	methyltransferase like 21B							cytoplasm (GO:0005737)|intracellular (GO:0005622)	methyltransferase activity (GO:0008168)			endometrium(1)|lung(1)	2						CGGCGGAAAACAGGCTACTCC	0.582											OREG0021954	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T57I		Atlas-SNP	.											.	TSFM	26	.	0			c.C170T						PASS	.						100	110	107					12																	58177005		2203	4300	6503	SO:0001628	intergenic_variant	10102	exon2			GGAAAACAGGCTA	AL050100, AF455816	CCDS8957.1, CCDS31848.1	12q14.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000123427	ENSG00000123427			24936	protein-coding gene	gene with protein product		615258	"family with sequence similarity 119, member B"	FAM119B		12477932	Standard	NM_015433		Approved	DKFZP586D0919	uc001sqg.3	Q96AZ1	OTTHUMG00000170459		chr12.hg19:g.58177005C>T		215.0	0.0	.	1028	337.0	96.0	.	NM_005726	Q9H749|Q9Y3W2	Missense_Mutation	SNP	ENST00000300209.8	hg19	CCDS8957.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.599184	0.87055	.	.	ENSG00000123297	ENST00000454289;ENST00000543727;ENST00000540550;ENST00000323833;ENST00000550559;ENST00000548851;ENST00000434359;ENST00000457189	.	.	.	5.29	5.29	0.74685	Translation elongation factor Ts, conserved site (1);Ubiquitin-associated/translation elongation factor EF1B, N-terminal (1);UBA-like (1);	0.000000	0.85682	D	0.000000	D	0.89784	0.6815	H	0.97103	3.94	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	0.92805	0.6259	9	0.87932	D	0	.	17.8551	0.88760	0.0:1.0:0.0:0.0	.	57;57;57	B4E391;P43897;P43897-2	.;EFTS_HUMAN;.	I	57;57;57;57;57;57;7;7	.	ENSP00000313877:T57I	T	+	2	0	TSFM	56463272	1.000000	0.71417	0.991000	0.47740	0.509000	0.34042	6.612000	0.74187	2.753000	0.94483	0.462000	0.41574	ACA	.	.	.	none		0.582	METTL21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409268.1	NM_015433		T	58177005	C	T	58177005	1	4	88	0	1	0	0	0	0	0	0	0	16627	478	17	2		2	TSFM	12	58177005	IGR	SNP	C	TCGA-B3-3925-01A-01D-1458-08	36419563	58177005	75674890	30	5700											
CCDC63	160762	hgsc.bcm.edu	37	chr12	111321841	111321841	+	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	tttcctttcctagctctcaaGgcaaagaagcatgtcaagaa	13	11	7	10	0	2	2	2	0	1	2	5	2	4	2	2	1	2	3	2	1	6	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr12:111321841G>C	ENST00000308208.5	+	8	1103	c.861G>C	c.(859-861)aaG>aaC	p.K287N	CCDC63_ENST00000545036.1_Missense_Mutation_p.K247N|CCDC63_ENST00000552694.1_Missense_Mutation_p.K208N	NM_152591.1	NP_689804.1	Q8NA47	CCD63_HUMAN	coiled-coil domain containing 63	287										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						TAGCTCTCAAGGCAAAGAAGC	0.502																																					p.K287N		Atlas-SNP	.											.	CCDC63	89	.	0			c.G861C						PASS	.						129	129	129					12																	111321841		2203	4300	6503	SO:0001583	missense	160762	exon8			TCTCAAGGCAAAG	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.861G>C	chr12.hg19:g.111321841G>C	ENSP00000312399:p.Lys287Asn	170.0	0.0	.		296.0	144.0	.	NM_152591	B4DY03|Q0P603|Q6P2E1	Missense_Mutation	SNP	ENST00000308208.5	hg19	CCDS9151.1	.	.	.	.	.	.	.	.	.	.	G	13.24	2.177145	0.38413	.	.	ENSG00000173093	ENST00000545036;ENST00000308208;ENST00000552694	T;T;T	0.21734	1.99;1.99;1.99	5.68	4.78	0.61160	.	0.332758	0.32357	N	0.006214	T	0.45836	0.1362	M	0.83012	2.62	0.33081	D	0.536687	D	0.71674	0.998	D	0.66351	0.943	T	0.64296	-0.6441	10	0.66056	D	0.02	.	10.8325	0.46669	0.089:0.0:0.911:0.0	.	287	Q8NA47	CCD63_HUMAN	N	247;287;208	ENSP00000445881:K247N;ENSP00000312399:K287N;ENSP00000450217:K208N	ENSP00000312399:K287N	K	+	3	2	CCDC63	109806224	0.905000	0.30787	0.841000	0.33234	0.034000	0.12701	1.260000	0.32968	1.383000	0.46405	0.655000	0.94253	AAG	.	.	.	none		0.502	CCDC63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404673.2	NM_152591		C	111321841	G	C	111321841	3	2	88	1	0	0	0	0	1	0	0	0	2836	991	35	4	887	4	CCDC63	12	111321841	Missense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08	53144836	111321841	22530054	31	5701											
ANAPC5	51433	hgsc.bcm.edu	37	chr12	121746455	121746458	+	Frame_Shift_Del	DEL	TTCT	TTCT	-																															agtcaacctttgcaaaatagTtcttggcttcattgaggttc																								rs146935401		TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	TTCT	TTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr12:121746455_121746458delTTCT	ENST00000261819.3	-	17	2214_2217	c.2093_2096delAGAA	c.(2092-2097)aagaacfs	p.KN698fs	ANAPC5_ENST00000344395.4_Frame_Shift_Del_p.KN586fs|ANAPC5_ENST00000441917.2_Frame_Shift_Del_p.KN586fs|ANAPC5_ENST00000535482.1_Frame_Shift_Del_p.KN364fs|ANAPC5_ENST00000544314.1_5'UTR|ANAPC5_ENST00000541887.1_Frame_Shift_Del_p.KN685fs	NM_016237.4	NP_057321.2	Q9UJX4	APC5_HUMAN	anaphase promoting complex subunit 5	698					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)			breast(6)|endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(3)	31	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TGCAAAATAGTTCTTGGCTTCATT	0.49																																					p.698_699del		Atlas-INDEL	.											.	ANAPC5	60	.	0			c.2094_2097del						PASS	.																																			SO:0001589	frameshift_variant	51433	exon17			.	AF191339	CCDS9220.1, CCDS45000.1	12q24.31	2014-08-12			ENSG00000089053	ENSG00000089053		"Anaphase promoting complex subunits"	15713	protein-coding gene	gene with protein product		606948				9469815	Standard	NM_016237		Approved	APC5	uc001uag.3	Q9UJX4	OTTHUMG00000169157	ENST00000261819.3:c.2093_2096delAGAA	chr12.hg19:g.121746455_121746458delTTCT	ENSP00000261819:p.Lys698fs	220.0	0.0	0		299.0	132.0	0.441472	NM_016237	E9PFB2|Q8N4H7|Q9BQD4	Frame_Shift_Del	DEL	ENST00000261819.3	hg19	CCDS9220.1																																																																																			.	.	.	none		0.49	ANAPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402582.1			-	121746458	TTCT	-	121746455	7	5	88	1	0	1	0	1	0	0	0	0	605	1725	60	0	175	0	ANAPC5	12	121746455	Frame_Shift_Del	DEL	TTCT	TCGA-B3-3925-01A-01D-1458-08	10424614	121746455	12105440	32	5702											
MYH7	4625	hgsc.bcm.edu	37	chr14	23886422	23886422	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccagggactcctcataggCgttcttgagtttgaagagct	8	13	11	9	1	2	3	1	2	1	1	4	4	4	4	2	2	1	3	2	2	2	5			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr14:23886422C>T	ENST00000355349.3	-	32	4621	c.4459G>A	c.(4459-4461)Gcc>Acc	p.A1487T	CTD-2201G16.1_ENST00000557368.1_RNA|MIR208B_ENST00000401172.1_RNA	NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1487					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		TCCTCATAGGCGTTCTTGAGT	0.597																																					p.A1487T		Atlas-SNP	.											.	MYH7	349	.	0			c.G4459A						PASS	.						118	124	122					14																	23886422		2203	4300	6503	SO:0001583	missense	4625	exon32			CATAGGCGTTCTT	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.4459G>A	chr14.hg19:g.23886422C>T	ENSP00000347507:p.Ala1487Thr	234.0	0.0	.		257.0	77.0	.	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	hg19	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.374149	0.82573	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	T	0.78364	-1.17	5.27	5.27	0.74061	Myosin tail (1);	.	.	.	.	D	0.84000	0.5376	M	0.81942	2.565	0.39473	D	0.967754	P	0.43662	0.814	P	0.50440	0.641	D	0.86199	0.1617	9	0.59425	D	0.04	.	13.987	0.64341	0.1513:0.8487:0.0:0.0	.	1487	P12883	MYH7_HUMAN	T	1487;1492	ENSP00000347507:A1487T	ENSP00000347507:A1487T	A	-	1	0	MYH7	22956262	0.987000	0.35691	0.998000	0.56505	0.982000	0.71751	2.764000	0.47613	2.746000	0.94184	0.591000	0.81541	GCC	.	.	.	none		0.597	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		T	23886422	C	T	23886422	3	4	88	1	0	0	0	0	1	0	0	0	10046	768	27	1	1384	1	MYH7	14	23886422	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08		23886422	83463118	33	5703											
PLCB2	5330	hgsc.bcm.edu	37	chr15	40594160	40594160	+	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	gggtgcagatccactcacttTgcctttggggaggtggcagg	6	10	16	9	0	1	1	1	0	0	1	2	2	2	2	2	6	2	2	2	6	0	2			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr15:40594160T>A	ENST00000260402.3	-	7	829	c.580A>T	c.(580-582)Aaa>Taa	p.K194*	PLCB2_ENST00000456256.2_Nonsense_Mutation_p.K194*|PLCB2-AS1_ENST00000559520.1_RNA|PLCB2_ENST00000543785.2_Nonsense_Mutation_p.K194*|PLCB2_ENST00000557821.1_Nonsense_Mutation_p.K194*	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	194					activation of phospholipase C activity (GO:0007202)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|sensory perception of bitter taste (GO:0050913)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(3)	39		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		CCACTCACTTTGCCTTTGGGG	0.582																																					p.K194X		Atlas-SNP	.											.	PLCB2	177	.	0			c.A580T						PASS	.						43	46	45					15																	40594160		2018	4185	6203	SO:0001587	stop_gained	5330	exon7			TCACTTTGCCTTT		CCDS42020.1, CCDS61591.1, CCDS61592.1, CCDS73704.1	15q15.1	2012-01-23			ENSG00000137841	ENSG00000137841	3.1.4.11		9055	protein-coding gene	gene with protein product		604114				1644792, 9925923	Standard	XM_005254448		Approved	FLJ38135	uc001zld.3	Q00722	OTTHUMG00000172412	ENST00000260402.3:c.580A>T	chr15.hg19:g.40594160T>A	ENSP00000260402:p.Lys194*	99.0	0.0	.		72.0	21.0	.	NM_004573	A8K6J2|B9EGH5	Nonsense_Mutation	SNP	ENST00000260402.3	hg19	CCDS42020.1	.	.	.	.	.	.	.	.	.	.	T	37	6.183272	0.97357	.	.	ENSG00000137841	ENST00000260402;ENST00000456256;ENST00000543785	.	.	.	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.9216	0.70843	0.0:0.0:0.0:1.0	.	.	.	.	X	194	.	ENSP00000260402:K194X	K	-	1	0	PLCB2	38381452	1.000000	0.71417	1.000000	0.80357	0.792000	0.44763	4.795000	0.62489	2.185000	0.69588	0.454000	0.30748	AAA	.	.	.	none		0.582	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1			A	40594160	T	A	40594160	4	1	88	1	0	0	0	0	0	1	0	0	12035	1821	63	5	3081	5	PLCB2	15	40594160	Nonsense_Mutation	SNP	T	TCGA-B3-3925-01A-01D-1458-08		40594160	61937232	34	5704											
GLDN	342035	hgsc.bcm.edu	37	chr15	51693835	51693835	+	Missense_Mutation	SNP	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	tcagccctcacttctgaatgGcagttacacgttcatccacc	9	11	6	15	1	4	1	3	1	1	0	5	1	5	1	3	1	2	3	3	1	2	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr15:51693835G>A	ENST00000335449.6	+	9	1129	c.1073G>A	c.(1072-1074)gGc>gAc	p.G358D	GLDN_ENST00000396399.2_Missense_Mutation_p.G234D	NM_181789.2	NP_861454.2	Q6ZMI3	GLDN_HUMAN	gliomedin	358	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|microvillus organization (GO:0032528)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19				all cancers(107;0.00194)|GBM - Glioblastoma multiforme(94;0.00942)		CTTCTGAATGGCAGTTACACG	0.483											OREG0023125	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G358D		Atlas-SNP	.											.	GLDN	54	.	0			c.G1073A						PASS	.						267	204	226					15																	51693835		2196	4293	6489	SO:0001583	missense	342035	exon9			TGAATGGCAGTTA	AY358144	CCDS10140.2	15q15.3	2008-02-05	2005-10-06	2005-10-06	ENSG00000186417	ENSG00000186417			29514	protein-coding gene	gene with protein product		608603	"collomin"	COLM		16039564, 12642876	Standard	XM_005254338		Approved	CRG-L2, CLOM, colmedin, UNC-112	uc002aba.3	Q6ZMI3	OTTHUMG00000131746	ENST00000335449.6:c.1073G>A	chr15.hg19:g.51693835G>A	ENSP00000335196:p.Gly358Asp	176.0	0.0	.	979	197.0	76.0	.	NM_181789	Q6UXZ7|Q7Z359	Missense_Mutation	SNP	ENST00000335449.6	hg19	CCDS10140.2	.	.	.	.	.	.	.	.	.	.	G	4.101	0.016804	0.07959	.	.	ENSG00000186417	ENST00000335449;ENST00000396399;ENST00000537339	D;D	0.88431	-2.38;-2.38	5.71	3.4	0.38934	Olfactomedin-like (3);	0.890672	0.09441	N	0.801780	T	0.77274	0.4106	N	0.14661	0.345	0.20638	N	0.999872	B	0.13594	0.008	B	0.16289	0.015	T	0.61855	-0.6977	10	0.12103	T	0.63	.	7.3269	0.26560	0.359:0.0:0.641:0.0	.	358	Q6ZMI3	GLDN_HUMAN	D	358;234;234	ENSP00000335196:G358D;ENSP00000379681:G234D	ENSP00000335196:G358D	G	+	2	0	GLDN	49481127	0.992000	0.36948	0.561000	0.28357	0.921000	0.55340	1.691000	0.37721	1.316000	0.45131	0.655000	0.94253	GGC	.	.	.	none		0.483	GLDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254667.2	NM_181789		A	51693835	G	A	51693835	3	1	88	1	0	0	0	0	1	0	0	0	6441	1203	42	2	1107	2	GLDN	15	51693835	Missense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08	11099675	51693835	50837557	35	5705											
VPS13C	54832	hgsc.bcm.edu	37	chr15	62221845	62221845	+	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	acactggcacatacatacagCttgtcaagaacagcatcaat	16	8	6	11	0	2	1	2	0	0	1	2	1	2	1	0	1	5	3	0	1	5	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr15:62221845C>G	ENST00000261517.5	-	51	6214	c.6141G>C	c.(6139-6141)aaG>aaC	p.K2047N	VPS13C_ENST00000249837.3_Missense_Mutation_p.K2004N|VPS13C_ENST00000395896.4_Missense_Mutation_p.K2047N|VPS13C_ENST00000395898.3_Missense_Mutation_p.K2004N	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						ATACATACAGCTTGTCAAGAA	0.368																																					p.K2047N		Atlas-SNP	.											.	VPS13C	506	.	0			c.G6141C						PASS	.						192	162	172					15																	62221845		2203	4300	6503	SO:0001583	missense	54832	exon51			ATACAGCTTGTCA	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.6141G>C	chr15.hg19:g.62221845C>G	ENSP00000261517:p.Lys2047Asn	76.0	0.0	.		82.0	30.0	.	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	hg19	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.069131	0.76301	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T;T	0.46451	0.87;0.87;1.04;1.03	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.51449	0.1675	M	0.71581	2.175	0.80722	D	1	P;P;P;B	0.40794	0.544;0.729;0.544;0.409	B;B;B;B	0.44044	0.176;0.439;0.34;0.336	T	0.51601	-0.8685	10	0.37606	T	0.19	.	18.867	0.92296	0.0:1.0:0.0:0.0	.	2004;2047;2004;2047	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	N	2004;2047;2047;2047	ENSP00000249837:K2004N;ENSP00000261517:K2047N;ENSP00000379233:K2047N;ENSP00000379235:K2047N	ENSP00000249837:K2004N	K	-	3	2	VPS13C	60009137	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	2.197000	0.42696	2.442000	0.82660	0.655000	0.94253	AAG	.	.	.	none		0.368	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		G	62221845	C	G	62221845	3	3	88	1	0	0	0	0	1	0	0	0	17203	796	28	4	5288	4	VPS13C	15	62221845	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08	10528010	62221845	40309547	36	5706											
MYO9A	4649	hgsc.bcm.edu	37	chr15	72192125	72192125	+	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	ttccctgtaggctttccatcTtgcttgtatgcaaatagcag	8	15	8	10	0	1	0	0	0	1	0	3	0	3	0	2	1	3	6	2	1	4	7			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr15:72192125T>G	ENST00000356056.5	-	24	3845	c.3373A>C	c.(3373-3375)Aga>Cga	p.R1125R	MYO9A_ENST00000563542.1_5'UTR|MYO9A_ENST00000444904.1_Silent_p.R1106R|MYO9A_ENST00000566885.1_Silent_p.R745R|MYO9A_ENST00000564571.1_Silent_p.R1125R|MYO9A_ENST00000424560.1_Silent_p.R1125R	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1125	IQ 4. {ECO:0000255|PROSITE- ProRule:PRU00116}.|Neck or regulatory domain.				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						GCTTTCCATCTTGCTTGTATG	0.438																																					p.R1125R		Atlas-SNP	.											.	MYO9A	203	.	0			c.A3373C						PASS	.						85	81	82					15																	72192125		2199	4297	6496	SO:0001819	synonymous_variant	4649	exon24			TCCATCTTGCTTG	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.3373A>C	chr15.hg19:g.72192125T>G		97.0	0.0	.		123.0	46.0	.	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Silent	SNP	ENST00000356056.5	hg19	CCDS10239.1																																																																																			.	.	.	none		0.438	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		G	72192125	T	G	72192125	2	3	88	1	0	0	0	0	0	0	0	1	10091	1617	56	5		5	MYO9A	15	72192125	Silent	SNP	T	TCGA-B3-3925-01A-01D-1458-08	9970280	72192125	30339267	37	5707											
BTBD12	84464	hgsc.bcm.edu	37	chr16	3641173	3641173	+	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	tcctcctcttcatctgcccaCattgacctcaagagttcctg	7	13	5	16	0	4	2	2	1	2	1	7	2	7	2	5	0	1	1	5	0	1	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr16:3641173C>G	ENST00000294008.3	-	12	3106	c.2466G>C	c.(2464-2466)atG>atC	p.M822I		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	822	Glu-rich.|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						CATCTGCCCACATTGACCTCA	0.468								Direct reversal of damage																													p.M822I		Atlas-SNP	.											.	SLX4	173	.	0			c.G2466C						PASS	.						165	176	172					16																	3641173		2197	4300	6497	SO:0001583	missense	84464	exon12			TGCCCACATTGAC	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.2466G>C	chr16.hg19:g.3641173C>G	ENSP00000294008:p.Met822Ile	247.0	0.0	.		291.0	79.0	.	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	hg19	CCDS10506.2	.	.	.	.	.	.	.	.	.	.	C	18.93	3.727924	0.69074	.	.	ENSG00000188827	ENST00000294008	T	0.01347	4.99	5.57	5.57	0.84162	.	0.430257	0.24894	N	0.034741	T	0.02304	0.0071	L	0.47190	1.495	0.28137	N	0.92995	B	0.30406	0.278	B	0.24155	0.051	T	0.37267	-0.9713	10	0.45353	T	0.12	.	18.5351	0.91008	0.0:1.0:0.0:0.0	.	822	Q8IY92	SLX4_HUMAN	I	822	ENSP00000294008:M822I	ENSP00000294008:M822I	M	-	3	0	SLX4	3581174	1.000000	0.71417	0.995000	0.50966	0.993000	0.82548	3.184000	0.50926	2.619000	0.88677	0.561000	0.74099	ATG	.	.	.	none		0.468	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444		G	3641173	C	G	3641173	3	3	88	1	0	0	0	0	1	0	0	0	1542	478	17	4	3054	4	BTBD12	16	3641173	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08		3641173	86713580	38	5708											
SRCAP	10847	hgsc.bcm.edu	37	chr16	30732089	30732089	+	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	cagtggtggtggtgaacaacCcacgggcgcccctgggccct	6	6	15	14	2	0	1	0	1	0	0	0	1	0	1	4	5	2	0	4	5	2	0			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr16:30732089C>A	ENST00000262518.4	+	20	3428	c.3043C>A	c.(3043-3045)Cca>Aca	p.P1015T	SRCAP_ENST00000395059.2_Missense_Mutation_p.P1015T|SRCAP_ENST00000344771.4_Missense_Mutation_p.P1015T	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1015	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)			GGTGAACAACCCACGGGCGCC	0.602																																					p.P1015T		Atlas-SNP	.											.	SRCAP	298	.	0			c.C3043A						PASS	.						65	74	71					16																	30732089		2197	4300	6497	SO:0001583	missense	10847	exon20			AACAACCCACGGG	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.3043C>A	chr16.hg19:g.30732089C>A	ENSP00000262518:p.Pro1015Thr	223.0	0.0	.		275.0	93.0	.	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	hg19	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	C	15.07	2.724931	0.48833	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.91631	-2.88;-2.81;-2.85	5.25	5.25	0.73442	.	0.000000	0.50627	D	0.000110	D	0.90219	0.6942	N	0.14661	0.345	0.41912	D	0.990471	D;D;D	0.76494	0.999;0.999;0.997	D;D;P	0.67382	0.934;0.951;0.895	D	0.87595	0.2493	10	0.25106	T	0.35	-10.7491	11.2203	0.48851	0.0:0.9156:0.0:0.0844	.	1015;1015;1015	Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2	.;.;SRCAP_HUMAN	T	1015	ENSP00000262518:P1015T;ENSP00000378499:P1015T;ENSP00000343042:P1015T	ENSP00000262518:P1015T	P	+	1	0	SRCAP	30639590	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	4.640000	0.61368	2.729000	0.93468	0.557000	0.71058	CCA	.	.	.	none		0.602	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		A	30732089	C	A	30732089	3	1	88	1	0	0	0	0	1	0	0	0	15147	623	22	4	3113	4	SRCAP	16	30732089	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08	27090916	30732089	59622664	39	5709											
ZZEF1	23140	hgsc.bcm.edu	37	chr17	3953114	3953114	+	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	gatcttctaggctcgagtccCcatctggcaatacacccagc	9	9	8	15	1	3	0	0	0	3	0	5	2	4	0	3	2	2	2	3	2	3	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr17:3953114C>T	ENST00000381638.2	-	37	6027	c.5903G>A	c.(5902-5904)gGg>gAg	p.G1968E		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	1968							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						GCTCGAGTCCCCATCTGGCAA	0.498																																					p.G1968E		Atlas-SNP	.											.	ZZEF1	195	.	0			c.G5903A						PASS	.						97	92	94					17																	3953114		2203	4300	6503	SO:0001583	missense	23140	exon37			GAGTCCCCATCTG	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.5903G>A	chr17.hg19:g.3953114C>T	ENSP00000371051:p.Gly1968Glu	111.0	0.0	.		170.0	54.0	.	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Missense_Mutation	SNP	ENST00000381638.2	hg19	CCDS11043.1	.	.	.	.	.	.	.	.	.	.	C	16.80	3.222545	0.58668	.	.	ENSG00000074755	ENST00000381638	T	0.20881	2.04	5.33	4.35	0.52113	.	0.334072	0.36555	N	0.002540	T	0.21427	0.0516	N	0.19112	0.55	0.40921	D	0.984313	D;D	0.59767	0.962;0.986	P;P	0.54174	0.744;0.738	T	0.00888	-1.1526	10	0.49607	T	0.09	-17.7018	10.7443	0.46170	0.0:0.9108:0.0:0.0892	.	1968;1968	O43149-2;O43149	.;ZZEF1_HUMAN	E	1968	ENSP00000371051:G1968E	ENSP00000371051:G1968E	G	-	2	0	ZZEF1	3899863	0.864000	0.29904	0.970000	0.41538	0.425000	0.31504	1.732000	0.38146	2.672000	0.90937	0.508000	0.49915	GGG	.	.	.	none		0.498	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		T	3953114	C	T	3953114	3	4	88	1	0	0	0	0	1	0	0	0	18267	623	22	2	3058	2	ZZEF1	17	3953114	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08		3953114	77242096	40	5710											
QRICH2	84074	hgsc.bcm.edu	37	chr17	74283337	74283337	+	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	tggcagccttgcccctgtctTggctctccctcaactcggcc	3	11	9	18	1	3	0	1	0	2	0	5	0	3	0	5	3	3	2	5	3	1	2			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr17:74283337T>A	ENST00000262765.5	-	7	3628	c.3449A>T	c.(3448-3450)cAa>cTa	p.Q1150L		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	1150										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						GCCCCTGTCTTGGCTCTCCCT	0.567																																					p.Q1150L		Atlas-SNP	.											.	QRICH2	143	.	0			c.A3449T						PASS	.						128	104	112					17																	74283337		2203	4300	6503	SO:0001583	missense	84074	exon7			CTGTCTTGGCTCT	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.3449A>T	chr17.hg19:g.74283337T>A	ENSP00000262765:p.Gln1150Leu	74.0	0.0	.		118.0	31.0	.	NM_032134	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	hg19	CCDS32741.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.420700	0.83559	.	.	ENSG00000129646	ENST00000262765;ENST00000447564;ENST00000301613	T;T	0.63580	1.79;-0.05	4.89	4.89	0.63831	.	.	.	.	.	T	0.67906	0.2943	L	0.34521	1.04	0.32374	N	0.555436	D;D	0.71674	0.998;0.998	D;D	0.66351	0.943;0.943	T	0.73704	-0.3899	9	0.52906	T	0.07	-7.7869	12.7966	0.57562	0.0:0.0:0.0:1.0	.	1150;1150	B5MD94;Q9H0J4	.;QRIC2_HUMAN	L	1150;158;1150	ENSP00000262765:Q1150L;ENSP00000394461:Q158L	ENSP00000262765:Q1150L	Q	-	2	0	QRICH2	71794932	1.000000	0.71417	0.985000	0.45067	0.931000	0.56810	4.519000	0.60517	1.836000	0.53414	0.454000	0.30748	CAA	.	.	.	none		0.567	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134		A	74283337	T	A	74283337	3	1	88	1	0	0	0	0	1	0	0	0	12893	1812	63	5	1594	5	QRICH2	17	74283337	Missense_Mutation	SNP	T	TCGA-B3-3925-01A-01D-1458-08	70330223	74283337	6911873	41	5711											
TBCD	6904	hgsc.bcm.edu	37	chr17	80888515	80888515	+	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	ttgaggacaaccttctgaatGagaggtgagtggtgtctctt	9	13	13	6	0	2	4	0	4	2	1	3	6	2	5	1	3	1	0	1	3	2	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr17:80888515G>C	ENST00000355528.4	+	33	3239	c.3109G>C	c.(3109-3111)Gag>Cag	p.E1037Q	TBCD_ENST00000539345.2_Missense_Mutation_p.E1037Q	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	1037					'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)			CCTTCTGAATGAGAGGTGAGT	0.597																																					p.E1037Q		Atlas-SNP	.											.	TBCD	94	.	0			c.G3109C						PASS	.						92	89	90					17																	80888515		2024	4185	6209	SO:0001583	missense	6904	exon33			CTGAATGAGAGGT	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.3109G>C	chr17.hg19:g.80888515G>C	ENSP00000347719:p.Glu1037Gln	60.0	0.0	.		106.0	27.0	.	NM_005993	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Missense_Mutation	SNP	ENST00000355528.4	hg19	CCDS45818.1	.	.	.	.	.	.	.	.	.	.	G	11.82	1.751852	0.31046	.	.	ENSG00000141556	ENST00000355528;ENST00000334614;ENST00000539345	T	0.35236	1.32	4.63	2.48	0.30137	Armadillo-like helical (1);Armadillo-type fold (1);Tubulin-specific chaperone D, C-terminal (1);	0.128907	0.50627	D	0.000107	T	0.27731	0.0682	L	0.42245	1.32	0.80722	D	1	P;P;P	0.41313	0.745;0.601;0.709	B;B;B	0.41946	0.27;0.307;0.371	T	0.02632	-1.1131	9	.	.	.	.	5.3369	0.15963	0.113:0.2093:0.6777:0.0	.	814;1037;1037	F8WC00;Q9BTW9;Q9BTW9-4	.;TBCD_HUMAN;.	Q	1037;788;29	ENSP00000347719:E1037Q	.	E	+	1	0	TBCD	78481804	1.000000	0.71417	0.852000	0.33557	0.360000	0.29518	3.799000	0.55529	0.939000	0.37446	0.591000	0.81541	GAG	.	.	.	none		0.597	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993		C	80888515	G	C	80888515	3	2	88	1	0	0	0	0	1	0	0	0	15645	1291	45	4	3239	4	TBCD	17	80888515	Missense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08	6605178	80888515	306695	42	5712											
HDHD2	84064	hgsc.bcm.edu	37	chr18	44662721	44662721	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atagcttgccttttaagagcTtcctgtgcgcctggcacagc	7	12	10	12	1	0	1	0	0	0	1	1	1	1	1	3	1	5	3	3	1	2	5			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr18:44662721T>C	ENST00000300605.6	-	2	242	c.90A>G	c.(88-90)gaA>gaG	p.E30E	HDHD2_ENST00000587841.1_Intron|IER3IP1_ENST00000588705.1_3'UTR	NM_032124.4	NP_115500.1	Q9H0R4	HDHD2_HUMAN	haloacid dehalogenase-like hydrolase domain containing 2	30						extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)			kidney(2)|large_intestine(2)|lung(1)|skin(1)	6						TTTTAAGAGCTTCCTGTGCGC	0.463																																					p.E30E		Atlas-SNP	.											.	HDHD2	12	.	0			c.A90G						PASS	.						99	82	88					18																	44662721		2203	4300	6503	SO:0001819	synonymous_variant	84064	exon2			AAGAGCTTCCTGT	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.90A>G	chr18.hg19:g.44662721T>C		159.0	0.0	.		221.0	83.0	.	NM_032124	A8K7T3|Q96NV4	Silent	SNP	ENST00000300605.6	hg19	CCDS32829.1																																																																																			.	.	.	none		0.463	HDHD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450668.2	NM_032124		C	44662721	T	C	44662721	2	2	88	1	0	0	0	0	0	0	0	1	7030	1606	56	3		3	HDHD2	18	44662721	Silent	SNP	T	TCGA-B3-3925-01A-01D-1458-08		44662721	33414527	43	5713											
MYO5B	4645	hgsc.bcm.edu	37	chr18	47500737	47500737	+	Silent	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	tacccatagatgtccaggacCccgatgaaggagtgctgctt	10	9	11	11	1	0	2	0	1	0	1	1	5	1	4	4	2	3	2	4	2	3	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr18:47500737C>T	ENST00000285039.7	-	10	1604	c.1305G>A	c.(1303-1305)ggG>ggA	p.G435G		NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	435	Myosin motor.		G -> R (in DIAR2). {ECO:0000269|PubMed:20186687}.		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)		TGTCCAGGACCCCGATGAAGG	0.582																																					p.G435G		Atlas-SNP	.											.	MYO5B	178	.	0			c.G1305A						PASS	.						98	108	104					18																	47500737		2136	4239	6375	SO:0001819	synonymous_variant	4645	exon10			CAGGACCCCGATG	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.1305G>A	chr18.hg19:g.47500737C>T		108.0	0.0	.		92.0	35.0	.	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Silent	SNP	ENST00000285039.7	hg19	CCDS42436.1																																																																																			.	.	.	none		0.582	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2			T	47500737	C	T	47500737	2	4	88	1	0	0	0	0	0	0	0	1	10086	610	22	2		2	MYO5B	18	47500737	Silent	SNP	C	TCGA-B3-3925-01A-01D-1458-08	2838016	47500737	30576511	44	5714											
RAB27B	5874	hgsc.bcm.edu	37	chr18	52555227	52555230	+	Splice_Site	DEL	CCAA	CCAA	-																															catctgctttcttttcaaggCcaactgcaagcaaatgctta																										TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	CCAA	CCAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr18:52555227_52555230delCCAA	ENST00000262094.5	+	5	866_869	c.345_348delCCAA	c.(343-348)agccaa>ag	p.SQ115fs	RAB27B_ENST00000586594.1_3'UTR|RP11-839G9.1_ENST00000588466.1_RNA	NM_004163.4	NP_004154.2	O00194	RB27B_HUMAN	RAB27B, member RAS oncogene family	115					multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|multivesicular body membrane (GO:0032585)|trans-Golgi network transport vesicle (GO:0030140)|zymogen granule membrane (GO:0042589)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|protein domain specific binding (GO:0019904)			large_intestine(3)|lung(3)|skin(1)	7				Colorectal(16;0.0273)|READ - Rectum adenocarcinoma(59;0.219)		CTTTTCAAGGCCAACTGCAAGCAA	0.402																																					p.115_116del		Atlas-INDEL	.											.	RAB27B	24	.	0			c.344_347del						PASS	.																																			SO:0001630	splice_region_variant	5874	exon5			.	U57093	CCDS11958.1	18q21.2	2006-12-18			ENSG00000041353	ENSG00000041353		"RAB, member RAS oncogene"	9767	protein-coding gene	gene with protein product		603869				9066979	Standard	NM_004163		Approved		uc002lfr.3	O00194	OTTHUMG00000132710	ENST00000262094.5:c.344-1CCAA>-	chr18.hg19:g.52555227_52555230delCCAA		131.0	0.0	0		199.0	39.0	0.19598	NM_004163	B2RAB0|Q9BZB6	Frame_Shift_Del	DEL	ENST00000262094.5	hg19	CCDS11958.1																																																																																			.	.	.	none		0.402	RAB27B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256008.3	NM_004163	Frame_Shift_Del	-	52555230	CCAA	-	52555227	8	5	88	1	0	1	0	1	0	0	1	0	12928	753	26	0	359	0	RAB27B	18	52555227	Splice_Site	DEL	CCAA	TCGA-B3-3925-01A-01D-1458-08	5054490	52555227	25522021	45	5715											
RFX2	5990	hgsc.bcm.edu	37	chr19	6013026	6013026	+	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	tggtgcatgggctgctgccgCatggccatgtactgcgtgtc	4	11	15	11	2	0	0	0	0	0	0	1	0	0	0	2	3	5	5	2	3	1	1			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr19:6013026C>T	ENST00000303657.5	-	8	1019	c.870G>A	c.(868-870)atG>atA	p.M290I	RFX2_ENST00000359161.3_Missense_Mutation_p.M290I|CTC-232P5.1_ENST00000587836.1_RNA|RFX2_ENST00000592546.1_Missense_Mutation_p.M265I	NM_000635.3	NP_000626.2	P48378	RFX2_HUMAN	regulatory factor X, 2 (influences HLA class II expression)	290					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						GCTGCTGCCGCATGGCCATGT	0.617																																					p.M290I	Colon(38;171 817 19800 47433 48051)	Atlas-SNP	.											.	RFX2	60	.	0			c.G870A						PASS	.						104	104	104					19																	6013026		2203	4300	6503	SO:0001583	missense	5990	exon8			CTGCCGCATGGCC		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.870G>A	chr19.hg19:g.6013026C>T	ENSP00000306335:p.Met290Ile	279.0	0.0	.		320.0	119.0	.	NM_000635	A8K581|B3KNC4|Q6IQ44|Q8SNA2	Missense_Mutation	SNP	ENST00000303657.5	hg19	CCDS12157.1	.	.	.	.	.	.	.	.	.	.	C	17.54	3.414320	0.62511	.	.	ENSG00000087903	ENST00000303657;ENST00000359161;ENST00000537791	T	0.65364	-0.15	4.99	4.99	0.66335	.	0.038993	0.85682	D	0.000000	T	0.57359	0.2048	L	0.60845	1.875	0.80722	D	1	B;B	0.13594	0.008;0.005	B;B	0.17722	0.019;0.013	T	0.57341	-0.7828	10	0.51188	T	0.08	-34.5934	10.8416	0.46720	0.0:0.9125:0.0:0.0875	.	265;290	P48378-2;P48378	.;RFX2_HUMAN	I	290;265;77	ENSP00000306335:M290I	ENSP00000306335:M290I	M	-	3	0	RFX2	5964026	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.796000	0.62496	2.473000	0.83533	0.557000	0.71058	ATG	.	.	.	none		0.617	RFX2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452687.1	NM_000635		T	6013026	C	T	6013026	3	4	88	1	0	0	0	0	1	0	0	0	13276	710	25	2	1345	2	RFX2	19	6013026	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08		6013026	53115957	46	5716											
GIPR	2696	hgsc.bcm.edu	37	chr19	46184876	46184876	+	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	gggcagggcttcctggtcagCgtcctctactgcttcatcaa	6	11	11	13	1	4	0	3	0	1	0	6	0	6	0	2	3	3	3	2	3	2	3	rs529800464		TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr19:46184876C>G	ENST00000590918.1	+	13	1266	c.1167C>G	c.(1165-1167)agC>agG	p.S389R	GIPR_ENST00000263281.3_Missense_Mutation_p.S389R|GIPR_ENST00000304207.8_Missense_Mutation_p.S353R	NM_000164.2	NP_000155.1	P48546	GIPR_HUMAN	gastric inhibitory polypeptide receptor	389					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)		TCCTGGTCAGCGTCCTCTACT	0.677																																					p.S389R		Atlas-SNP	.											.	GIPR	36	.	0			c.C1167G						PASS	.						35	40	38					19																	46184876		2203	4300	6503	SO:0001583	missense	2696	exon13			GGTCAGCGTCCTC		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.1167C>G	chr19.hg19:g.46184876C>G	ENSP00000467494:p.Ser389Arg	96.0	0.0	.		99.0	30.0	.	NM_000164	B7WP14|B7ZKQ0|Q14401|Q16400|Q52M04|Q9UPI1	Missense_Mutation	SNP	ENST00000590918.1	hg19	CCDS12671.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.160957	0.78226	.	.	ENSG00000010310	ENST00000263281;ENST00000304207	T;T	0.58940	0.3;1.18	4.81	2.65	0.31530	GPCR, family 2-like (1);GPCR, family 2, secretin-like, conserved site (1);	0.209202	0.33959	N	0.004388	T	0.68842	0.3045	M	0.65677	2.01	0.35843	D	0.826177	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.73380	0.98;0.953;0.971	T	0.73898	-0.3837	10	0.87932	D	0	.	7.5841	0.27982	0.0:0.8105:0.0:0.1895	.	353;389;389	B7WP14;P48546;P48546-2	.;GIPR_HUMAN;.	R	389;353	ENSP00000263281:S389R;ENSP00000305321:S353R	ENSP00000263281:S389R	S	+	3	2	GIPR	50876716	0.911000	0.30947	0.991000	0.47740	0.988000	0.76386	0.947000	0.29082	0.609000	0.30018	0.561000	0.74099	AGC	.	.	.	none		0.677	GIPR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459640.1			G	46184876	C	G	46184876	3	3	88	1	0	0	0	0	1	0	0	0	6402	767	27	4	1213	4	GIPR	19	46184876	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08	40171850	46184876	12944107	47	5717											
SIGLEC9	27180	hgsc.bcm.edu	37	chr19	51633170	51633170	+	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	gcccctgactgaaccttgggCagaagacagtcccccagacc	10	5	10	16	0	0	5	0	2	0	3	1	5	1	5	6	1	1	1	6	1	2	1			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr19:51633170C>G	ENST00000250360.3	+	7	1293	c.1226C>G	c.(1225-1227)gCa>gGa	p.A409G	SIGLEC9_ENST00000440804.3_Intron	NM_014441.2	NP_055256.1	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	409					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)		GAACCTTGGGCAGAAGACAGT	0.602																																					p.A409G		Atlas-SNP	.											.	SIGLEC9	85	.	0			c.C1226G						PASS	.						72	77	75					19																	51633170		2203	4300	6503	SO:0001583	missense	27180	exon7			CTTGGGCAGAAGA	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.1226C>G	chr19.hg19:g.51633170C>G	ENSP00000250360:p.Ala409Gly	141.0	0.0	.		142.0	38.0	.	NM_014441	Q6GTU4|Q9BYI9	Missense_Mutation	SNP	ENST00000250360.3	hg19	CCDS12825.1	.	.	.	.	.	.	.	.	.	.	.	2.098	-0.406818	0.04832	.	.	ENSG00000129450	ENST00000250360	T	0.11277	2.79	1.96	-1.87	0.07737	.	.	.	.	.	T	0.08403	0.0209	M	0.63843	1.955	0.09310	N	1	P	0.35174	0.488	B	0.32211	0.142	T	0.31916	-0.9926	9	0.22109	T	0.4	.	2.1117	0.03704	0.2511:0.4132:0.0:0.3357	.	409	Q9Y336	SIGL9_HUMAN	G	409	ENSP00000250360:A409G	ENSP00000250360:A409G	A	+	2	0	SIGLEC9	56324982	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.824000	0.01708	-0.341000	0.08376	-0.346000	0.07831	GCA	.	.	.	none		0.602	SIGLEC9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464224.1	NM_014441		G	51633170	C	G	51633170	3	3	88	1	0	0	0	0	1	0	0	0	14328	710	25	4	1252	4	SIGLEC9	19	51633170	Missense_Mutation	SNP	C	TCGA-B3-3925-01A-01D-1458-08	5448294	51633170	7495813	48	5718											
CD40	958	hgsc.bcm.edu	37	chr20	44757638	44757638	+	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	gccaaccggtcacccaggagGatggcaaagagagtcgcatc	12	4	13	12	2	1	1	1	0	0	1	3	4	1	3	3	4	1	2	3	4	2	0			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr20:44757638G>C	ENST00000372285.3	+	9	865	c.793G>C	c.(793-795)Gat>Cat	p.D265H	CD40_ENST00000489304.1_3'UTR|CD40_ENST00000372276.3_3'UTR	NM_001250.4	NP_001241.1	P25942	TNR5_HUMAN	CD40 molecule, TNF receptor superfamily member 5	265					B cell proliferation (GO:0042100)|cellular calcium ion homeostasis (GO:0006874)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|inflammatory response (GO:0006954)|platelet activation (GO:0030168)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|protein complex assembly (GO:0006461)|regulation of immune response (GO:0050776)|regulation of immunoglobulin secretion (GO:0051023)	CD40 receptor complex (GO:0035631)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|enzyme binding (GO:0019899)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10		Myeloproliferative disorder(115;0.0122)				CACCCAGGAGGATGGCAAAGA	0.582									Immune Deficiency with Hyper-IgM																												p.D265H		Atlas-SNP	.											.	CD40	33	.	0			c.G793C						PASS	.						94	86	89					20																	44757638		2203	4300	6503	SO:0001583	missense	958	exon9	Familial Cancer Database	Hypogammaglobulinemia with Hyper-IgM, HIGM type I-V, XLHIGM	CAGGAGGATGGCA	X60592	CCDS13393.1, CCDS13394.1	20q12-q13.2	2014-09-17	2006-03-28	2005-01-14	ENSG00000101017	ENSG00000101017		"Tumor necrosis factor receptor superfamily", "CD molecules"	11919	protein-coding gene	gene with protein product		109535	"tumor necrosis factor receptor superfamily, member 5"	TNFRSF5		7687385, 2998589	Standard	XM_005260617		Approved	p50, Bp50	uc002xrg.1	P25942	OTTHUMG00000033053	ENST00000372285.3:c.793G>C	chr20.hg19:g.44757638G>C	ENSP00000361359:p.Asp265His	120.0	0.0	.		208.0	43.0	.	NM_001250	E1P5S9|Q53GN5|Q5JY15|Q5U007|Q7M4Q8|Q86YK5|Q9BYU0	Missense_Mutation	SNP	ENST00000372285.3	hg19	CCDS13393.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.14|19.14	3.769455|3.769455	0.69992|0.69992	.|.	.|.	ENSG00000101017|ENSG00000101017	ENST00000372285|ENST00000372278	T|.	0.75050|.	-0.9|.	4.61|4.61	4.61|4.61	0.57282|0.57282	.|.	2.083250|.	0.02069|.	N|.	0.051393|.	T|T	0.72078|0.72078	0.3416|0.3416	L|L	0.61218|0.61218	1.895|1.895	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|T	0.75792|0.75792	-0.3193|-0.3193	10|6	0.48119|0.87932	T|D	0.1|0	-17.99|-17.99	14.7536|14.7536	0.69546|0.69546	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	265|.	P25942|.	TNR5_HUMAN|.	H|S	265|214	ENSP00000361359:D265H|.	ENSP00000361359:D265H|ENSP00000361352:R214S	D|R	+|+	1|3	0|2	CD40|CD40	44191045|44191045	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.759000|0.759000	0.43091|0.43091	5.327000|5.327000	0.65881|0.65881	2.375000|2.375000	0.81037|0.81037	0.491000|0.491000	0.48974|0.48974	GAT|AGG	.	.	.	none		0.582	CD40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080376.1	NM_001250		C	44757638	G	C	44757638	3	2	88	1	0	0	0	0	1	0	0	0	3017	1174	41	4	827	4	CD40	20	44757638	Missense_Mutation	SNP	G	TCGA-B3-3925-01A-01D-1458-08		44757638	18267882	49	5719											
ZNFX1	57169	hgsc.bcm.edu	37	chr20	47887763	47887763	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctggcgatccattttggagcTacaagccttccgaagaacct	10	10	9	12	2	0	1	0	0	0	1	2	4	2	2	4	2	4	1	4	2	4	4			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr20:47887763T>C	ENST00000396105.1	-	3	832	c.586A>G	c.(586-588)Agc>Ggc	p.S196G	ZNFX1_ENST00000371754.4_Missense_Mutation_p.S196G|ZNFX1_ENST00000371752.1_Missense_Mutation_p.S196G	NM_021035.2	NP_066363.1	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	196							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(8)|kidney(7)|large_intestine(15)|liver(1)|lung(17)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	60			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			ATTTTGGAGCTACAAGCCTTC	0.448																																					p.S196G		Atlas-SNP	.											.	ZNFX1	194	.	0			c.A586G						PASS	.						122	125	124					20																	47887763		2203	4300	6503	SO:0001583	missense	57169	exon3			TGGAGCTACAAGC	AK022641	CCDS13417.1	20q13.13	2014-02-12			ENSG00000124201	ENSG00000124201			29271	protein-coding gene	gene with protein product						10718198	Standard	NM_021035		Approved	KIAA1404, FLJ11277	uc002xui.3	Q9P2E3	OTTHUMG00000032696	ENST00000396105.1:c.586A>G	chr20.hg19:g.47887763T>C	ENSP00000379412:p.Ser196Gly	183.0	0.0	.		306.0	151.0	.	NM_021035	Q9BQM7|Q9BQM8|Q9H8C1|Q9H9S2|Q9NUM1|Q9NWW1	Missense_Mutation	SNP	ENST00000396105.1	hg19	CCDS13417.1	.	.	.	.	.	.	.	.	.	.	T	9.975	1.226419	0.22542	.	.	ENSG00000124201	ENST00000396106;ENST00000371754;ENST00000371752;ENST00000396105;ENST00000371744	D;D;D;T	0.86865	-1.89;-2.18;-2.18;-0.82	5.86	5.86	0.93980	.	0.260907	0.49916	D	0.000128	T	0.81564	0.4849	L	0.45581	1.43	0.25150	N	0.990437	B	0.13145	0.007	B	0.10450	0.005	T	0.66590	-0.5885	10	0.21540	T	0.41	-21.586	10.261	0.43427	0.0:0.0774:0.0:0.9226	.	196	Q9P2E3	ZNFX1_HUMAN	G	196	ENSP00000360819:S196G;ENSP00000360817:S196G;ENSP00000379412:S196G;ENSP00000360809:S196G	ENSP00000360809:S196G	S	-	1	0	ZNFX1	47321170	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	1.608000	0.36847	2.241000	0.73720	0.533000	0.62120	AGC	.	.	.	none		0.448	ZNFX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079647.2	NM_021035		C	47887763	T	C	47887763	3	2	88	1	0	0	0	0	1	0	0	0	18217	1522	53	3	5218	3	ZNFX1	20	47887763	Missense_Mutation	SNP	T	TCGA-B3-3925-01A-01D-1458-08	3130125	47887763	15137757	50	5720											
GNAZ	2781	hgsc.bcm.edu	37	chr22	23438484	23438484	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcaccttcaagatggtggAcgtgggggggcagaggtcag	8	7	18	8	1	3	2	3	0	0	2	3	3	3	3	1	6	0	2	1	6	1	1			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr22:23438484A>G	ENST00000248996.4	+	2	1268	c.602A>G	c.(601-603)gAc>gGc	p.D201G	RTDR1_ENST00000216036.4_Intron	NM_002073.2	NP_002064.1	P19086	GNAZ_HUMAN	guanine nucleotide binding protein (G protein), alpha z polypeptide	201					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|receptor signaling protein activity (GO:0005057)|signal transducer activity (GO:0004871)			endometrium(3)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(5)|urinary_tract(1)	19	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.166)		AAGATGGTGGACGTGGGGGGG	0.567																																					p.D201G		Atlas-SNP	.											GNAZ,NS,carcinoma,-1,1	GNAZ	45	.	0			c.A602G						PASS	.						131	136	135					22																	23438484		2203	4300	6503	SO:0001583	missense	2781	exon2			TGGTGGACGTGGG		CCDS13804.1	22q11.1-q11.2	2008-06-10			ENSG00000128266	ENSG00000128266			4395	protein-coding gene	gene with protein product		139160				2115889	Standard	NM_002073		Approved		uc002zwu.1	P19086	OTTHUMG00000150611	ENST00000248996.4:c.602A>G	chr22.hg19:g.23438484A>G	ENSP00000248996:p.Asp201Gly	247.0	1.0	.		228.0	69.0	.	NM_002073	B2R6C1|Q4QRJ6	Missense_Mutation	SNP	ENST00000248996.4	hg19	CCDS13804.1	.	.	.	.	.	.	.	.	.	.	A	13.88	2.367786	0.42003	.	.	ENSG00000128266	ENST00000248996;ENST00000456059	D	0.95656	-3.77	4.7	2.53	0.30540	.	0.000000	0.85682	D	0.000000	D	0.96386	0.8821	H	0.98577	4.27	0.80722	D	1	B	0.10296	0.003	B	0.08055	0.003	D	0.92468	0.5983	10	0.87932	D	0	.	6.794	0.23715	0.7665:0.1527:0.0808:0.0	.	201	P19086	GNAZ_HUMAN	G	201;149	ENSP00000248996:D201G	ENSP00000248996:D201G	D	+	2	0	GNAZ	21768484	1.000000	0.71417	0.650000	0.29550	0.158000	0.22134	9.084000	0.94076	0.268000	0.21939	-0.313000	0.08912	GAC	.	.	.	none		0.567	GNAZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319073.1	NM_002073		G	23438484	A	G	23438484	3	3	88	1	0	0	0	0	1	0	0	0	6521	275	10	3	604	3	GNAZ	22	23438484	Missense_Mutation	SNP	A	TCGA-B3-3925-01A-01D-1458-08		23438484	27866082	51	5721											
CABIN1	23523	hgsc.bcm.edu	37	chr22	24447425	24447425	+	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	ctgaaacttgtgcagcccatTcctttcttcacgtaggttgt	7	15	8	11	1	2	1	1	1	1	0	3	1	3	1	2	1	3	3	2	1	2	6			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr22:24447425T>A	ENST00000398319.2	+	8	1180	c.795T>A	c.(793-795)atT>atA	p.I265I	CABIN1_ENST00000263119.5_Silent_p.I265I|CABIN1_ENST00000405822.2_Intron	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	265					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						TGCAGCCCATTCCTTTCTTCA	0.577																																					p.I265I		Atlas-SNP	.											.	CABIN1	153	.	0			c.T795A						PASS	.						100	85	90					22																	24447425		2203	4300	6503	SO:0001819	synonymous_variant	23523	exon8			GCCCATTCCTTTC	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.795T>A	chr22.hg19:g.24447425T>A		58.0	0.0	.		56.0	24.0	.	NM_001199281	G5E9F3|Q6PHY0|Q9Y460	Silent	SNP	ENST00000398319.2	hg19	CCDS13823.1																																																																																			.	.	.	none		0.577	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295		A	24447425	T	A	24447425	2	1	88	1	0	0	0	0	0	0	0	1	2530	1771	62	5		5	CABIN1	22	24447425	Silent	SNP	T	TCGA-B3-3925-01A-01D-1458-08	1008941	24447425	26857141	52	5722											
DEPDC5	9681	hgsc.bcm.edu	37	chr22	32193641	32193641	+	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	cttcacttctcgtaaccattAaaaaactcttcatccagtat	13	14	2	12	1	4	0	2	0	2	0	6	0	5	0	2	0	2	2	2	0	5	6			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr22:32193641A>T	ENST00000382112.3	+	12	893	c.823A>T	c.(823-825)Aaa>Taa	p.K275*	DEPDC5_ENST00000400242.3_Nonsense_Mutation_p.K275*|DEPDC5_ENST00000535622.1_Nonsense_Mutation_p.K275*|DEPDC5_ENST00000382111.2_Nonsense_Mutation_p.K275*|DEPDC5_ENST00000400246.1_Nonsense_Mutation_p.K275*|DEPDC5_ENST00000536766.1_Nonsense_Mutation_p.K247*|DEPDC5_ENST00000400248.2_Nonsense_Mutation_p.K275*|DEPDC5_ENST00000382105.2_Nonsense_Mutation_p.K275*|DEPDC5_ENST00000266091.3_Nonsense_Mutation_p.K275*|DEPDC5_ENST00000400249.2_Nonsense_Mutation_p.K275*	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	275					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						CGTAACCATTAAAAAACTCTT	0.438																																					p.K275X		Atlas-SNP	.											.	DEPDC5	266	.	0			c.A823T						PASS	.						83	84	84					22																	32193641		1902	4127	6029	SO:0001587	stop_gained	9681	exon13			ACCATTAAAAAAC	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.823A>T	chr22.hg19:g.32193641A>T	ENSP00000371546:p.Lys275*	58.0	0.0	.		69.0	28.0	.	NM_001242897	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Nonsense_Mutation	SNP	ENST00000382112.3	hg19	CCDS46692.1	.	.	.	.	.	.	.	.	.	.	A	38	6.793795	0.97841	.	.	ENSG00000100150	ENST00000535622;ENST00000536766;ENST00000400242;ENST00000266091;ENST00000400249;ENST00000382109;ENST00000400246;ENST00000382105;ENST00000382112;ENST00000382111;ENST00000400248	.	.	.	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.9647	0.64202	1.0:0.0:0.0:0.0	.	.	.	.	X	275;247;275;275;275;275;275;275;275;275;275	.	ENSP00000266091:K275X	K	+	1	0	DEPDC5	30523641	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.097000	0.94193	1.921000	0.55644	0.443000	0.29094	AAA	.	.	.	none		0.438	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662		T	32193641	A	T	32193641	4	4	88	1	0	0	0	0	0	1	0	0	4444	363	13	5	869	5	DEPDC5	22	32193641	Nonsense_Mutation	SNP	A	TCGA-B3-3925-01A-01D-1458-08	7746216	32193641	19110925	53	5723											
SOX10	6663	hgsc.bcm.edu	37	chr22	38374016	38374016	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggggcactccgcctcgccCtgggcggccttcccgttctt	1	9	12	19	5	1	0	0	0	1	0	4	0	3	0	6	4	0	2	6	4	0	3			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chr22:38374016C>T	ENST00000396884.2	-	3	837	c.555G>A	c.(553-555)caG>caA	p.Q185Q	SOX10_ENST00000470555.1_5'Flank|SOX10_ENST00000360880.2_Silent_p.Q185Q|POLR2F_ENST00000407936.1_Intron|POLR2F_ENST00000405557.1_Intron	NM_006941.3	NP_008872.1	P56693	SOX10_HUMAN	SRY (sex determining region Y)-box 10	185					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)					CCGCCTCGCCCTGGGCGGCCT	0.682																																					p.Q185Q	Melanoma(39;342 1098 6220 32775 40068)|GBM(21;140 497 5227 16059 19275)	Atlas-SNP	.											.	SOX10	48	.	0			c.G555A						PASS	.						30	30	30					22																	38374016		2202	4300	6502	SO:0001819	synonymous_variant	6663	exon3			CTCGCCCTGGGCG		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.555G>A	chr22.hg19:g.38374016C>T		65.0	0.0	.		67.0	19.0	.	NM_006941	B4DV62|Q6FHW7	Silent	SNP	ENST00000396884.2	hg19	CCDS13964.1	.	.	.	.	.	.	.	.	.	.	C	0.065	-1.215656	0.01542	.	.	ENSG00000100146	ENST00000446929	.	.	.	4.24	0.707	0.18139	.	.	.	.	.	T	0.50531	0.1621	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34329	-0.9833	4	.	.	.	.	4.6565	0.12620	0.1228:0.6075:0.12:0.1497	.	.	.	.	K	62	.	.	R	-	2	0	SOX10	36703962	1.000000	0.71417	0.997000	0.53966	0.009000	0.06853	2.108000	0.41854	-0.014000	0.14175	-1.644000	0.00765	AGG	.	.	.	none		0.682	SOX10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313875.1	NM_006941		T	38374016	C	T	38374016	2	4	88	1	0	0	0	0	0	0	0	1	14954	680	24	2		2	SOX10	22	38374016	Silent	SNP	C	TCGA-B3-3925-01A-01D-1458-08	6180375	38374016	12930550	54	5724											
MXRA5	25878	hgsc.bcm.edu	37	chrX	3238719	3238719	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatgggagaggaattgttgtActtgataatcttggagttgt	11	15	13	2	0	1	2	0	1	1	1	1	5	1	4	0	3	1	3	0	3	4	7			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chrX:3238719A>G	ENST00000217939.6	-	5	5161	c.5007T>C	c.(5005-5007)agT>agC	p.S1669S		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	1669						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)				GAATTGTTGTACTTGATAATC	0.438																																					p.S1669S		Atlas-SNP	.											.	MXRA5	815	.	0			c.T5007C						PASS	.						171	162	165					X																	3238719		2203	4300	6503	SO:0001819	synonymous_variant	25878	exon5			TGTTGTACTTGAT	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.5007T>C	chrX.hg19:g.3238719A>G		221.0	0.0	.		292.0	220.0	.	NM_015419	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	hg19	CCDS14124.1																																																																																			.	.	.	none		0.438	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		G	3238719	A	G	3238719	2	3	88	1	0	0	0	0	0	0	0	1	10010	388	14	3		3	MXRA5	23	3238719	Silent	SNP	A	TCGA-B3-3925-01A-01D-1458-08		3238719	152031841	55	5725											
CTPS2	56474	hgsc.bcm.edu	37	chrX	16685795	16685795	+	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	tcgaacttacctttcaagttAaggcagtttcttgcaaactc	11	14	6	10	1	2	0	1	0	1	0	4	1	2	0	1	1	4	4	1	1	5	5			TCGA-B3-3925-01A-01D-1458-08	TCGA-B3-3925-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5bb6b194-3bad-4d65-8345-c5a0161b4a0f	acd62c81-b9cd-47ac-b708-52546a54aa37	g.chrX:16685795A>C	ENST00000443824.1	-	12	1985	c.1242T>G	c.(1240-1242)ctT>ctG	p.L414L	CTPS2_ENST00000380241.3_Silent_p.L414L|CTPS2_ENST00000359276.4_Silent_p.L414L	NM_001144002.1	NP_001137474.1	Q9NRF8	PYRG2_HUMAN	CTP synthase 2	414	Glutamine amidotransferase type-1. {ECO:0000255|PROSITE-ProRule:PRU00605}.				'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)					CTTTCAAGTTAAGGCAGTTTC	0.323																																					p.L414L		Atlas-SNP	.											.	CTPS2	49	.	0			c.T1242G						PASS	.						104	95	98					X																	16685795		2203	4300	6503	SO:0001819	synonymous_variant	56474	exon12			CAAGTTAAGGCAG	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.1242T>G	chrX.hg19:g.16685795A>C		67.0	0.0	.		85.0	58.0	.	NM_001144002	B3KWM2|Q9BRI0|Q9H809|Q9H8K9	Silent	SNP	ENST00000443824.1	hg19	CCDS14175.1	.	.	.	.	.	.	.	.	.	.	A	8.285	0.816447	0.16607	.	.	ENSG00000047230	ENST00000455276	.	.	.	5.47	-4.64	0.03349	.	0.000000	0.64402	D	0.000015	.	.	.	.	.	.	0.44862	D	0.997874	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-19.4425	9.4054	0.38457	0.1945:0.5966:0.0:0.2089	.	.	.	.	X	36	.	ENSP00000400431:L36X	L	-	2	0	CTPS2	16595716	0.000000	0.05858	0.699000	0.30290	0.941000	0.58515	-1.673000	0.01951	-0.843000	0.04189	0.486000	0.48141	TTA	.	.	.	none		0.323	CTPS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055906.1	NM_019857		C	16685795	A	C	16685795	2	2	88	1	0	0	0	0	0	0	0	1	4025	349	13	5		5	CTPS2	23	16685795	Silent	SNP	A	TCGA-B3-3925-01A-01D-1458-08	13447076	16685795	138584765	56	5726											
ALK	238	hgsc.bcm.edu	37	chr2	29432730	29432730	+	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	gacaggtcaagaggcagtttCtggcagcaatgtctctggga	10	9	14	8	0	3	1	1	0	2	1	4	3	3	2	0	4	1	4	0	4	2	1			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr2:29432730C>G	ENST00000389048.3	-	25	4664	c.3758G>C	c.(3757-3759)aGa>aCa	p.R1253T	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1253	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)	GAGGCAGTTTCTGGCAGCAAT	0.493			"T, Mis, A"	"NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"	"ALCL, NSCLC, Neuroblastoma"	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.R1253T		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	.	ALK	533	.	0			c.G3758C						PASS	.						105	107	106					2																	29432730		2203	4300	6503	SO:0001583	missense	238	exon25	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	CAGTTTCTGGCAG	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.3758G>C	chr2.hg19:g.29432730C>G	ENSP00000373700:p.Arg1253Thr	98.0	0.0	.		105.0	16.0	.	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	hg19	CCDS33172.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.983743	0.93044	.	.	ENSG00000171094	ENST00000389048	D	0.87571	-2.27	5.2	5.2	0.72013	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.53938	D	0.000057	D	0.95468	0.8528	H	0.94385	3.53	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96698	0.9516	9	.	.	.	.	17.5154	0.87771	0.0:1.0:0.0:0.0	.	1253	Q9UM73	ALK_HUMAN	T	1253	ENSP00000373700:R1253T	.	R	-	2	0	ALK	29286234	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	7.462000	0.80851	2.418000	0.82041	0.655000	0.94253	AGA	.	.	.	none		0.493	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		G	29432730	C	G	29432730	3	3	89	1	0	0	0	0	1	0	0	0	525	913	32	4	1124	4	ALK	2	29432730	Missense_Mutation	SNP	C	TCGA-B3-3926-01A-01D-1252-08		29432730	213766643	1	5727											
PLXND1	23129	hgsc.bcm.edu	37	chr3	129284750	129284750	+	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	ctgtcgcgcaccgcaaagtcCttctgctgctccagcgcgtg	5	9	11	16	5	1	0	0	0	1	0	4	0	3	0	3	0	3	4	3	0	1	1			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr3:129284750C>A	ENST00000324093.4	-	24	4480	c.4302G>T	c.(4300-4302)aaG>aaT	p.K1434N	PLXND1_ENST00000393239.1_Missense_Mutation_p.K1434N	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1434					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						CCGCAAAGTCCTTCTGCTGCT	0.587																																					p.K1434N	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.G4302T						PASS	.						107	90	96					3																	129284750		2203	4300	6503	SO:0001583	missense	23129	exon24			AAAGTCCTTCTGC	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.4302G>T	chr3.hg19:g.129284750C>A	ENSP00000317128:p.Lys1434Asn	69.0	0.0	.		117.0	15.0	.	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	hg19	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	C	16.25	3.069256	0.55539	.	.	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.12879	2.64;2.64	4.86	2.99	0.34606	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.106561	0.64402	D	0.000006	T	0.28400	0.0702	L	0.59436	1.845	0.53005	D	0.999968	P;D	0.76494	0.643;0.999	B;D	0.71184	0.315;0.972	T	0.01448	-1.1352	10	0.87932	D	0	.	8.6019	0.33749	0.0:0.7443:0.0:0.2557	.	29;1434	B4DRU3;Q9Y4D7	.;PLXD1_HUMAN	N	1434	ENSP00000317128:K1434N;ENSP00000376931:K1434N	ENSP00000317128:K1434N	K	-	3	2	PLXND1	130767440	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	0.849000	0.27723	0.973000	0.38340	0.563000	0.77884	AAG	.	.	.	none		0.587	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103		A	129284750	C	A	129284750	3	1	89	1	0	0	0	0	1	0	0	0	12134	680	24	4	1527	4	PLXND1	3	129284750	Missense_Mutation	SNP	C	TCGA-B3-3926-01A-01D-1252-08		129284750	68737680	2	5728											
RBAK	57786	hgsc.bcm.edu	37	chr7	5105227	5105227	+	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	acgtacttgatgtggaaaatCtctgaagtcagatctcaatt	13	13	8	7	1	3	3	2	2	2	1	5	4	3	4	0	1	1	1	0	1	5	3			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr7:5105227C>T	ENST00000353796.3	+	6	2464	c.2140C>T	c.(2140-2142)Ctc>Ttc	p.L714F	RBAK_ENST00000396912.1_Missense_Mutation_p.L714F|RBAK-RBAKDN_ENST00000396904.2_Intron|RBAK-RBAKDN_ENST00000407184.1_Intron	NM_001204456.1	NP_001191385.1	Q9NYW8	RBAK_HUMAN	RB-associated KRAB zinc finger	714	Interaction with AR.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.L714I(1)		NS(1)|kidney(1)|large_intestine(2)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	10		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0916)|OV - Ovarian serous cystadenocarcinoma(56;2.44e-14)		TGTGGAAAATCTCTGAAGTCA	0.373																																					p.L714F		Atlas-SNP	.											RBAK_ENST00000396912,colon,carcinoma,0,1	RBAK	82	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2140T						PASS	.						38	41	40					7																	5105227		2116	4249	6365	SO:0001583	missense	57786	exon6			GAAAATCTCTGAA	AF226869	CCDS5337.1	7p22.1	2013-01-08			ENSG00000146587	ENSG00000146587		"Zinc fingers, C2H2-type", "-"	17680	protein-coding gene	gene with protein product		608191					Standard	NM_021163		Approved	ZNF769	uc003sns.1	Q9NYW8	OTTHUMG00000121155	ENST00000353796.3:c.2140C>T	chr7.hg19:g.5105227C>T	ENSP00000275423:p.Leu714Phe	89.0	0.0	.		56.0	15.0	.	NM_001204456	A6NDF2|A8KAK4|B2RN44|B9EGS1|F8W6M7	Missense_Mutation	SNP	ENST00000353796.3	hg19	CCDS5337.1	.	.	.	.	.	.	.	.	.	.	C	10.71	1.428124	0.25726	.	.	ENSG00000146587	ENST00000353796;ENST00000396912	T;T	0.07688	3.17;3.17	3.63	2.74	0.32292	.	0.328508	0.22348	N	0.061256	T	0.06188	0.0160	N	0.08118	0	0.30907	N	0.729093	P	0.51240	0.943	P	0.49799	0.622	T	0.35076	-0.9803	8	.	.	.	.	9.2279	0.37418	0.0:0.8873:0.0:0.1127	.	714	Q9NYW8	RBAK_HUMAN	F	714	ENSP00000275423:L714F;ENSP00000380120:L714F	.	L	+	1	0	RBAK	5071753	0.000000	0.05858	0.637000	0.29366	0.480000	0.33159	0.225000	0.17757	1.089000	0.41292	0.455000	0.32223	CTC	.	.	.	none		0.373	RBAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241640.2	NM_021163		T	5105227	C	T	5105227	3	4	89	1	0	0	0	0	1	0	0	0	13113	913	32	2	2154	2	RBAK	7	5105227	Missense_Mutation	SNP	C	TCGA-B3-3926-01A-01D-1252-08		5105227	154033436	3	5729											
EPDR1	54749	hgsc.bcm.edu	37	chr7	37960767	37960767	+	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	acgacgggctcaaccagcgcGtgcgggtgctggacgagagg	8	4	18	11	6	1	1	1	0	0	1	1	4	1	2	1	4	4	2	1	4	1	0			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr7:37960767G>T	ENST00000199448.4	+	1	605	c.226G>T	c.(226-228)Gtg>Ttg	p.V76L	EPDR1_ENST00000559325.1_Missense_Mutation_p.V196L|EPDR1_ENST00000425345.1_5'Flank|EPDR1_ENST00000476620.1_Intron|EPDR1_ENST00000423717.1_Missense_Mutation_p.V76L	NM_017549.4	NP_060019.2	Q9UM22	EPDR1_HUMAN	ependymin related 1	76					cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|large_intestine(2)|lung(9)|ovary(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	22						CAACCAGCGCGTGCGGGTGCT	0.706																																					p.V76L		Atlas-SNP	.											.	EPDR1	48	.	0			c.G226T						PASS	.						15	16	16					7																	37960767		2107	4126	6233	SO:0001583	missense	54749	exon1			CAGCGCGTGCGGG	BC018299	CCDS5454.1, CCDS5454.2, CCDS59051.1, CCDS59052.1	7p14.1	2013-07-31	2013-07-31		ENSG00000086289	ENSG00000086289			17572	protein-coding gene	gene with protein product			"ependymin related protein 1 (zebrafish)"			11749721, 11248421	Standard	NM_001242946		Approved	MERP-1, MERP1, UCC1, EPDR	uc003tfp.4	Q9UM22	OTTHUMG00000102187	ENST00000199448.4:c.226G>T	chr7.hg19:g.37960767G>T	ENSP00000199448:p.Val76Leu	83.0	0.0	.		135.0	18.0	.	NM_001242946	A8K4C0|C9JYS3|Q06BL0|Q99M77	Missense_Mutation	SNP	ENST00000199448.4	hg19	CCDS5454.2	.	.	.	.	.	.	.	.	.	.	G	11.76	1.733873	0.30684	.	.	ENSG00000086289	ENST00000199448;ENST00000423717	.	.	.	4.04	1.93	0.25924	.	0.478080	0.21214	N	0.078255	T	0.40473	0.1118	L	0.42686	1.345	0.80722	D	1	B	0.16603	0.018	B	0.09377	0.004	T	0.14392	-1.0474	9	0.21014	T	0.42	-17.3655	3.9195	0.09237	0.2427:0.1958:0.5615:0.0	.	196	A4D1W8	.	L	196;170	.	ENSP00000199448:V196L	V	+	1	0	EPDR1	37927292	0.988000	0.35896	1.000000	0.80357	0.959000	0.62525	0.596000	0.24044	0.866000	0.35629	0.313000	0.20887	GTG	.	.	.	none		0.706	EPDR1-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220037.3	NM_017549		T	37960767	G	T	37960767	3	4	89	1	0	0	0	0	1	0	0	0	5165	1145	40	4	588	4	EPDR1	7	37960767	Missense_Mutation	SNP	G	TCGA-B3-3926-01A-01D-1252-08	32855540	37960767	121177896	4	5730											
SAV1	60485	hgsc.bcm.edu	37	chr14	51132122	51132129	+	Frame_Shift_Del	DEL	CTAGACTT	CTAGACTT	-																															atactctctagggacatctgCtagacttctggcaagataag																										TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	CTAGACTT	CTAGACTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr14:51132122_51132129delCTAGACTT	ENST00000324679.4	-	2	666_673	c.303_310delAAGTCTAG	c.(301-312)agaagtctagcafs	p.RSLA101fs	RP11-248J18.2_ENST00000602954.1_RNA	NM_021818.3	NP_068590.1	Q9H4B6	SAV1_HUMAN	salvador family WW domain containing protein 1	101					hair follicle development (GO:0001942)|hippo signaling (GO:0035329)|intestinal epithelial cell differentiation (GO:0060575)|keratinocyte differentiation (GO:0030216)|lung epithelial cell differentiation (GO:0060487)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of epithelial cell proliferation (GO:0050680)|positive regulation of apoptotic process (GO:0043065)|regulation of stem cell maintenance (GO:2000036)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)				breast(1)|kidney(2)|lung(2)|prostate(1)	6	all_epithelial(31;0.000611)|Breast(41;0.0333)					GGGACATCTGCTAGACTTCTGGCAAGAT	0.385																																					p.102_104del		Atlas-INDEL	.											.	SAV1	18	.	0			c.304_311del						PASS	.																																			SO:0001589	frameshift_variant	60485	exon2			.	AK023071	CCDS9701.1	14q13-q23	2014-04-14	2014-04-14		ENSG00000151748	ENSG00000151748			17795	protein-coding gene	gene with protein product	"WW domain-containing adaptor 45"	607203	"salvador homolog 1 (Drosophila)"			12202036, 11027580	Standard	NM_021818		Approved	WW45, WWP4, salvador	uc001wyh.2	Q9H4B6	OTTHUMG00000140293	ENST00000324679.4:c.303_310delAAGTCTAG	chr14.hg19:g.51132122_51132129delCTAGACTT	ENSP00000324729:p.Arg101fs	59.0	0.0	0		50.0	13.0	0.26	NM_021818	A8K4B8|D3DSB6|Q6IA58|Q9H949|Q9HAK9	Frame_Shift_Del	DEL	ENST00000324679.4	hg19	CCDS9701.1																																																																																			.	.	.	none		0.385	SAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276879.1			-	51132129	CTAGACTT	-	51132122	7	5	89	1	0	1	0	1	0	0	0	0	13869	797	28	0	857	0	SAV1	14	51132122	Frame_Shift_Del	DEL	CTAGACTT	TCGA-B3-3926-01A-01D-1252-08		51132122	56217418	5	5731											
MRC2	9902	hgsc.bcm.edu	37	chr17	60766323	60766323	+	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	atctgccagaagggcacgggTatgtgtcaccagtcacctgg	9	8	13	11	1	3	1	2	0	1	1	3	1	3	1	3	3	1	2	3	3	2	1			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr17:60766323T>C	ENST00000303375.5	+	23	3736		c.e23+2		MRC2_ENST00000580916.1_Splice_Site|MRC2_ENST00000446119.2_Splice_Site	NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2						collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						AGGGCACGGGTATGTGTCACC	0.642																																					.		Atlas-SNP	.											.	MRC2	126	.	0			c.3334+2T>C						PASS	.						42	35	37					17																	60766323		2203	4300	6503	SO:0001630	splice_region_variant	9902	exon23			CACGGGTATGTGT	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.3334+2T>C	chr17.hg19:g.60766323T>C		54.0	0.0	.		81.0	14.0	.	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Splice_Site	SNP	ENST00000303375.5	hg19	CCDS11634.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.155893	0.78114	.	.	ENSG00000011028	ENST00000303375;ENST00000446119	.	.	.	4.73	4.73	0.59995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3771	0.66886	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	MRC2	58120055	1.000000	0.71417	0.863000	0.33907	0.565000	0.35776	5.032000	0.64140	1.978000	0.57642	0.459000	0.35465	.	.	.	.	none		0.642	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1		Intron	C	60766323	T	C	60766323	5	2	89	1	0	0	0	0	0	0	1	0	9765	1652	57	3	3426	3	MRC2	17	60766323	Splice_Site	SNP	T	TCGA-B3-3926-01A-01D-1252-08		60766323	20428887	6	5732											
ACSBG2	81616	hgsc.bcm.edu	37	chr19	6177264	6177264	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtggattgcaggagcagtgAcaaaggactttaaactgaca	14	8	12	7	1	0	2	0	2	0	0	0	5	0	5	0	3	3	2	0	3	3	3			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr19:6177264A>G	ENST00000586696.1	+	8	1039	c.763A>G	c.(763-765)Aca>Gca	p.T255A	ACSBG2_ENST00000591403.1_Missense_Mutation_p.T255A|ACSBG2_ENST00000252669.5_Missense_Mutation_p.T255A|ACSBG2_ENST00000588485.1_Missense_Mutation_p.T68A|ACSBG2_ENST00000591741.1_3'UTR|ACSBG2_ENST00000588304.1_Missense_Mutation_p.T205A			Q5FVE4	ACBG2_HUMAN	acyl-CoA synthetase bubblegum family member 2	255					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid metabolic process (GO:0001676)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)	p.T255A(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(3)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						AGGAGCAGTGACAAAGGACTT	0.423																																					p.T255A		Atlas-SNP	.											ACSBG2,NS,carcinoma,0,1	ACSBG2	83	.	1	Substitution - Missense(1)	endometrium(1)	c.A763G						PASS	.						100	71	81					19																	6177264		2203	4300	6503	SO:0001583	missense	81616	exon8			GCAGTGACAAAGG		CCDS12159.1, CCDS74269.1	19p13.3	2012-10-02			ENSG00000130377	ENSG00000130377		"Acyl-CoA synthetase family"	24174	protein-coding gene	gene with protein product	"bubblegum related protein"	614363				11230166	Standard	XM_005259653		Approved	BGR, PRTD-NY3, DKFZp434K1635	uc002meh.1	Q5FVE4	OTTHUMG00000180754	ENST00000586696.1:c.763A>G	chr19.hg19:g.6177264A>G	ENSP00000465589:p.Thr255Ala	84.0	0.0	.		67.0	3.0	.	NM_030924	B3KSF2|Q6UWJ3|Q7Z5A0|Q8WW03|Q96M36|Q9BYZ3|Q9H0C4	Missense_Mutation	SNP	ENST00000586696.1	hg19	CCDS12159.1	.	.	.	.	.	.	.	.	.	.	A	0.181	-1.062649	0.01950	.	.	ENSG00000130377	ENST00000252669	T	0.39997	1.05	4.48	-5.64	0.02466	AMP-dependent synthetase/ligase (1);	1.364350	0.05348	N	0.531310	T	0.10937	0.0267	N	0.01640	-0.785	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.25328	-1.0135	10	0.05351	T	0.99	-3.1473	3.0878	0.06284	0.1441:0.0988:0.3567:0.4004	.	255;255	B4DYU1;Q5FVE4	.;ACBG2_HUMAN	A	255	ENSP00000252669:T255A	ENSP00000252669:T255A	T	+	1	0	ACSBG2	6128264	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	0.149000	0.16243	-0.740000	0.04803	-0.902000	0.02854	ACA	.	.	.	none		0.423	ACSBG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452898.1	NM_030924		G	6177264	A	G	6177264	3	3	89	1	0	0	0	0	1	0	0	0	174	275	10	3	789	3	ACSBG2	19	6177264	Missense_Mutation	SNP	A	TCGA-B3-3926-01A-01D-1252-08		6177264	52951719	7	5733											
UBA52	7311	hgsc.bcm.edu	37	chr19	18685757	18685757	+	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	gccagcttgcccagaaatacAactgcgacaagatgatctgc	13	7	9	12	1	1	3	0	1	1	2	1	4	1	3	2	0	6	1	2	0	4	2			TCGA-B3-3926-01A-01D-1252-08	TCGA-B3-3926-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	814dbddd-9703-4c92-b179-428d00b907bf	cc643b5f-d509-4216-928c-5f6ec8b526e2	g.chr19:18685757A>T	ENST00000442744.2	+	4	326	c.268A>T	c.(268-270)Aac>Tac	p.N90Y	UBA52_ENST00000598780.1_Missense_Mutation_p.N90Y|UBA52_ENST00000595683.1_Missense_Mutation_p.N90Y|UBA52_ENST00000599595.1_Missense_Mutation_p.N90Y|UBA52_ENST00000596304.1_Missense_Mutation_p.N90Y|UBA52_ENST00000430157.2_Missense_Mutation_p.N90Y|CRLF1_ENST00000594325.1_Intron|UBA52_ENST00000595158.1_Missense_Mutation_p.N90Y|UBA52_ENST00000596273.1_Missense_Mutation_p.N90Y|UBA52_ENST00000599551.1_Missense_Mutation_p.N90Y|UBA52_ENST00000597451.1_Missense_Mutation_p.N90Y	NM_001033930.1	NP_001029102.1	P62987	RL40_HUMAN	ubiquitin A-52 residue ribosomal protein fusion product 1	90					activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|viral transcription (GO:0019083)|virion assembly (GO:0019068)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|ribosome (GO:0005840)	structural constituent of ribosome (GO:0003735)			endometrium(1)|large_intestine(2)	3						CCAGAAATACAACTGCGACAA	0.612																																					p.N90Y		Atlas-SNP	.											.	UBA52	6	.	0			c.A268T						PASS	.						46	42	43					19																	18685757		2203	4300	6503	SO:0001583	missense	7311	exon4			AAATACAACTGCG		CCDS12382.1	19p13.1-p12	2011-04-06			ENSG00000221983	ENSG00000221983		"L ribosomal proteins"	12458	protein-coding gene	gene with protein product	"ribosomal protein L40", "ubiquitin-52 amino acid fusion protein", "ubiquitin carboxyl extension protein 52", "60S ribosomal protein L40", "ubiquitin-CEP52"	191321				8188300	Standard	XM_005260051		Approved	RPL40, CEP52, HUBCEP52, MGC57125, MGC126879, MGC126881, L40	uc002njs.3	P62987		ENST00000442744.2:c.268A>T	chr19.hg19:g.18685757A>T	ENSP00000388107:p.Asn90Tyr	77.0	0.0	.		128.0	13.0	.	NM_001033930	P02248|P02249|P02250|P14793|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Missense_Mutation	SNP	ENST00000442744.2	hg19	CCDS12382.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.273436	0.80580	.	.	ENSG00000221983	ENST00000442744;ENST00000430157	T;T	0.45668	0.89;0.89	4.52	4.52	0.55395	.	0.000000	0.85682	D	0.000000	T	0.67822	0.2934	M	0.93197	3.39	0.58432	D	0.99999	D	0.59767	0.986	P	0.59424	0.857	T	0.76822	-0.2817	10	0.87932	D	0	-2.438	11.7658	0.51930	1.0:0.0:0.0:0.0	.	90	P62987	RL40_HUMAN	Y	90	ENSP00000388107:N90Y;ENSP00000396910:N90Y	ENSP00000396910:N90Y	N	+	1	0	UBA52	18546757	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.564000	0.60830	1.667000	0.50832	0.379000	0.24179	AAC	.	.	.	none		0.612	UBA52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465117.2	NM_003333		T	18685757	A	T	18685757	3	4	89	1	0	0	0	0	1	0	0	0	16843	130	5	5	278	5	UBA52	19	18685757	Missense_Mutation	SNP	A	TCGA-B3-3926-01A-01D-1252-08	12508493	18685757	40443226	8	5734											
ATP1A1	476	hgsc.bcm.edu	37	chr1	116941400	116941400	+	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	ctttgcctcaattgtgactgGagtagaggaaggtgagagct	10	11	14	6	0	1	3	1	2	0	2	1	6	1	5	1	3	2	2	1	3	3	3	rs11540954		TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr1:116941400G>C	ENST00000295598.5	+	16	2534	c.2282G>C	c.(2281-2283)gGa>gCa	p.G761A	ATP1A1_ENST00000369496.4_Missense_Mutation_p.G730A|ATP1A1_ENST00000537345.1_Missense_Mutation_p.G761A	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	761					ATP biosynthetic process (GO:0006754)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|membrane hyperpolarization (GO:0060081)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of glucocorticoid biosynthetic process (GO:0031947)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart contraction (GO:0045823)|positive regulation of striated muscle contraction (GO:0045989)|potassium ion import (GO:0010107)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of sodium ion transport (GO:0002028)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|chaperone binding (GO:0051087)|phosphatase activity (GO:0016791)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(2)|breast(2)|cervix(3)|endometrium(2)|kidney(5)|large_intestine(9)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Ciclopirox(DB01188)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Ethacrynic acid(DB00903)|Hydroflumethiazide(DB00774)|Ouabain(DB01092)|Trichlormethiazide(DB01021)	ATTGTGACTGGAGTAGAGGAA	0.438																																					p.G761A		Atlas-SNP	.											.	ATP1A1	87	.	0			c.G2282C						PASS	.						138	136	136					1																	116941400		2203	4300	6503	SO:0001583	missense	476	exon16			TGACTGGAGTAGA	D00099	CCDS887.1, CCDS53351.1, CCDS53352.1	1p13	2012-10-22			ENSG00000163399	ENSG00000163399	3.6.3.9	"ATPases / P-type"	799	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-1", "sodium pump subunit alpha-1", "sodium-potassium ATPase catalytic subunit alpha-1"	182310					Standard	NM_000701		Approved		uc001ege.3	P05023	OTTHUMG00000012109	ENST00000295598.5:c.2282G>C	chr1.hg19:g.116941400G>C	ENSP00000295598:p.Gly761Ala	180.0	0.0	.		178.0	56.0	.	NM_000701	B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Missense_Mutation	SNP	ENST00000295598.5	hg19	CCDS887.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.988230	0.93106	.	.	ENSG00000163399	ENST00000295598;ENST00000537345;ENST00000369496	D;D;D	0.91577	-2.87;-2.87;-2.86	5.23	5.23	0.72850	HAD-like domain (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.88937	0.6573	N	0.11106	0.095	0.80722	D	1	D;D	0.65815	0.995;0.992	D;D	0.70227	0.968;0.929	D	0.91640	0.5326	10	0.66056	D	0.02	.	19.0012	0.92834	0.0:0.0:1.0:0.0	rs11540954	761;761	F5H3A1;P05023	.;AT1A1_HUMAN	A	761;761;730	ENSP00000295598:G761A;ENSP00000445306:G761A;ENSP00000358508:G730A	ENSP00000295598:G761A	G	+	2	0	ATP1A1	116742923	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.657000	0.98554	2.718000	0.92993	0.655000	0.94253	GGA	.	.	.	weak		0.438	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5	NM_001160233		C	116941400	G	C	116941400	3	2	90	1	0	0	0	0	1	0	0	0	1128	1174	41	4	2360	4	ATP1A1	1	116941400	Missense_Mutation	SNP	G	TCGA-B3-4103-01A-01D-1458-08		116941400	132309221	1	5735											
ATP1B1	481	hgsc.bcm.edu	37	chr1	169096584	169096584	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taaatgatgaaacttatggcTacaaagagggcaaaccgtgc	16	8	10	7	1	0	3	0	2	0	1	0	3	0	3	1	2	4	2	1	2	7	3			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr1:169096584T>C	ENST00000367816.1	+	5	1034	c.505T>C	c.(505-507)Tac>Cac	p.Y169H	ATP1B1_ENST00000367815.4_Missense_Mutation_p.Y169H|ATP1B1_ENST00000367813.3_Missense_Mutation_p.Y161H|ATP1B1_ENST00000499679.3_Missense_Mutation_p.Y113H			P05026	AT1B1_HUMAN	ATPase, Na+/K+ transporting, beta 1 polypeptide	169					blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular potassium ion homeostasis (GO:0030007)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|leukocyte migration (GO:0050900)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|positive regulation of ATP catabolic process (GO:1903291)|positive regulation of ATPase activity (GO:0032781)|positive regulation of calcium:sodium antiporter activity (GO:1903281)|positive regulation of potassium ion import (GO:1903288)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of sodium ion export from cell (GO:1903278)|potassium ion import (GO:0010107)|protein localization to plasma membrane (GO:0072659)|protein stabilization (GO:0050821)|protein transport into plasma membrane raft (GO:0044861)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression (GO:0010468)|relaxation of cardiac muscle (GO:0055119)|response to hypoxia (GO:0001666)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|vesicle (GO:0031982)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|MHC class II protein complex binding (GO:0023026)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	14	all_hematologic(923;0.208)					AACTTATGGCTACAAAGAGGG	0.388																																					p.Y169H		Atlas-SNP	.											.	ATP1B1	29	.	0			c.T505C						PASS	.						104	101	102					1																	169096584		2203	4300	6503	SO:0001583	missense	481	exon4			TATGGCTACAAAG	U16799	CCDS1276.1	1q24.2	2012-10-22			ENSG00000143153	ENSG00000143153		"ATPases / P-type"	804	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit beta-1", "sodium pump subunit beta-1", "sodium-potassium ATPase subunit beta 1 (non-catalytic)"	182330		ATP1B			Standard	NM_001677		Approved		uc001gfr.1	P05026	OTTHUMG00000034590	ENST00000367816.1:c.505T>C	chr1.hg19:g.169096584T>C	ENSP00000356790:p.Tyr169His	167.0	0.0	.		188.0	58.0	.	NM_001677	Q5TGZ3	Missense_Mutation	SNP	ENST00000367816.1	hg19	CCDS1276.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.574319	0.86542	.	.	ENSG00000143153	ENST00000367816;ENST00000367815;ENST00000499679;ENST00000367813	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	6.02	6.02	0.97574	.	0.049448	0.85682	D	0.000000	T	0.72087	0.3417	M	0.92738	3.34	0.42584	D	0.993227	D	0.76494	0.999	D	0.76071	0.987	T	0.80130	-0.1511	9	0.87932	D	0	-19.3541	16.5446	0.84426	0.0:0.0:0.0:1.0	.	169	P05026	AT1B1_HUMAN	H	169;169;113;161	ENSP00000356790:Y169H;ENSP00000356789:Y169H;ENSP00000423450:Y113H;ENSP00000356787:Y161H	ENSP00000356787:Y161H	Y	+	1	0	ATP1B1	167363208	1.000000	0.71417	1.000000	0.80357	0.643000	0.38383	7.388000	0.79795	2.311000	0.77944	0.533000	0.62120	TAC	.	.	.	none		0.388	ATP1B1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083696.1			C	169096584	T	C	169096584	3	2	90	1	0	0	0	0	1	0	0	0	1132	1522	53	3	519	3	ATP1B1	1	169096584	Missense_Mutation	SNP	T	TCGA-B3-4103-01A-01D-1458-08	52155184	169096584	80154037	2	5736											
SELE	6401	hgsc.bcm.edu	37	chr1	169698749	169698749	+	Frame_Shift_Del	DEL	T	T	-																															ggttgtgttccatgggaagcTtccagggttttggaaacatt																										TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr1:169698749delT	ENST00000333360.7	-	6	920	c.781delA	c.(781-783)agcfs	p.S261fs	C1orf112_ENST00000498289.1_Intron|SELE_ENST00000367775.1_Frame_Shift_Del_p.S199fs|SELE_ENST00000367779.4_Frame_Shift_Del_p.S261fs|SELE_ENST00000367780.4_Frame_Shift_Del_p.S199fs|SELE_ENST00000367782.4_Frame_Shift_Del_p.S261fs|SELE_ENST00000367774.1_Frame_Shift_Del_p.S261fs|SELE_ENST00000367777.1_Frame_Shift_Del_p.S261fs|SELE_ENST00000367776.1_Frame_Shift_Del_p.S261fs|SELE_ENST00000367781.4_Frame_Shift_Del_p.S261fs	NM_000450.2	NP_000441.2	P16581	LYAM2_HUMAN	selectin E	261	Sushi 2. {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)	p.S261G(1)		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)	CATGGGAAGCTTCCAGGGTTT	0.448																																					p.S261fs		Atlas-INDEL	.											.	SELE	84	.	1	Substitution - Missense(1)	lung(1)	c.782delG						PASS	.						137	130	132					1																	169698749		2203	4300	6503	SO:0001589	frameshift_variant	6401	exon6			.	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.781delA	chr1.hg19:g.169698749delT	ENSP00000331736:p.Ser261fs	235.0	0.0	0		250.0	97.0	0.388	NM_000450	A2RRD6|P16111	Frame_Shift_Del	DEL	ENST00000333360.7	hg19	CCDS1283.1																																																																																			.	.	.	none		0.448	SELE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084333.1	NM_000450		-	169698749	T	-	169698749	7	5	90	1	0	1	0	1	0	0	0	0	14026	1609	56	0	1083	0	SELE	1	169698749	Frame_Shift_Del	DEL	T	TCGA-B3-4103-01A-01D-1458-08	602165	169698749	79551872	3	5737											
CEP350	9857	hgsc.bcm.edu	37	chr1	179965912	179965912	+	Frame_Shift_Del	DEL	A	A	-																															accagcaattgatgcattgcAaaattctgaatgtttgatta																										TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr1:179965912delA	ENST00000367607.3	+	6	1038	c.620delA	c.(619-621)caafs	p.Q207fs		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	207					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						GATGCATTGCAAAATTCTGAA	0.378																																					p.Q207fs		Atlas-INDEL	.											.	CEP350	418	.	0			c.619delC						PASS	.						78	73	75					1																	179965912		2203	4300	6503	SO:0001589	frameshift_variant	9857	exon6			.	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.620delA	chr1.hg19:g.179965912delA	ENSP00000356579:p.Gln207fs	44.0	0.0	0		55.0	12.0	0.218182	NM_014810	O75068|Q8TDK3|Q8WY20	Frame_Shift_Del	DEL	ENST00000367607.3	hg19	CCDS1336.1																																																																																			.	.	.	none		0.378	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		-	179965912	A	-	179965912	7	5	90	1	0	1	0	1	0	0	0	0	3256	130	5	0	638	0	CEP350	1	179965912	Frame_Shift_Del	DEL	A	TCGA-B3-4103-01A-01D-1458-08	10267163	179965912	69284709	4	5738											
GOLT1A	127845	hgsc.bcm.edu	37	chr1	204183026	204183026	+	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	ttactctgccattcggtgatGgagatcatgccgcactcagc	8	11	10	12	2	3	2	2	1	1	1	4	3	3	2	2	2	4	1	2	2	1	2			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr1:204183026G>T	ENST00000308302.3	-	1	194	c.9C>A	c.(7-9)tcC>tcA	p.S3S		NM_198447.1	NP_940849.1			golgi transport 1A											kidney(1)|lung(2)|urinary_tract(1)	4	all_cancers(21;0.0165)|Breast(84;0.179)|all_epithelial(62;0.242)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.244)			ATTCGGTGATGGAGATCATGC	0.642																																					p.S3S		Atlas-SNP	.											.	GOLT1A	15	.	0			c.C9A						PASS	.						68	53	58					1																	204183026		2203	4300	6503	SO:0001819	synonymous_variant	127845	exon1			GGTGATGGAGATC	BC058832	CCDS1443.1	1q32.1	2010-06-24	2010-06-24		ENSG00000174567	ENSG00000174567			24766	protein-coding gene	gene with protein product			"golgi transport 1 homolog A (S. cerevisiae)"			12477932	Standard	NM_198447		Approved	FLJ42654, CGI-141, YMR292W, GOT1, MGC62027	uc001has.1	Q6ZVE7	OTTHUMG00000036056	ENST00000308302.3:c.9C>A	chr1.hg19:g.204183026G>T		42.0	0.0	.		50.0	11.0	.	NM_198447		Silent	SNP	ENST00000308302.3	hg19	CCDS1443.1																																																																																			.	.	.	none		0.642	GOLT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087887.1	NM_198447		T	204183026	G	T	204183026	2	4	90	1	0	0	0	0	0	0	0	1	6577	1335	47	4		4	GOLT1A	1	204183026	Silent	SNP	G	TCGA-B3-4103-01A-01D-1458-08	24217114	204183026	45067595	5	5739											
GRHL1	29841	hgsc.bcm.edu	37	chr2	10101557	10101557	+	Missense_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	cagagaccttcaaggaaggcGttcaggaggtaaggaaacaa	16	5	13	7	1	2	1	2	0	0	1	2	5	2	4	1	5	1	2	1	5	5	3	rs140278187		TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr2:10101557G>A	ENST00000324907.9	+	4	797	c.661G>A	c.(661-663)Gtt>Att	p.V221I	GRHL1_ENST00000405379.2_Missense_Mutation_p.V221I|GRHL1_ENST00000324883.5_Silent_p.A57A	NM_198182.2	NP_937825.2	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1 (Drosophila)	221					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)		CAAGGAAGGCGTTCAGGAGGT	0.463													G|||	1	0.000199681	0	0	5008	,	,		19940	0		0.001	False		,,,				2504	0				p.V221I		Atlas-SNP	.											.	GRHL1	95	.	0			c.G661A						PASS	.	G	ILE/VAL	0,4406		0,0,2203	77	76	76		661	4.6	1	2	dbSNP_134	76	6,8594	5.0+/-18.6	0,6,4294	yes	missense	GRHL1	NM_198182.2	29	0,6,6497	AA,AG,GG		0.0698,0.0,0.0461	benign	221/619	10101557	6,13000	2203	4300	6503	SO:0001583	missense	29841	exon4			GAAGGCGTTCAGG	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.661G>A	chr2.hg19:g.10101557G>A	ENSP00000324693:p.Val221Ile	154.0	0.0	.		170.0	54.0	.	NM_198182	A6NLA4|B2R7E4|B5MEC2|Q53T93|Q6NWN7|Q6NWN8|Q6NWN9|Q8NI33	Missense_Mutation	SNP	ENST00000324907.9	hg19	CCDS33144.2	.	.	.	.	.	.	.	.	.	.	G	13.48	2.248540	0.39797	0.0	6.98E-4	ENSG00000134317	ENST00000405379;ENST00000324907	T;T	0.11604	2.76;2.76	5.5	4.63	0.57726	.	0.205183	0.45361	D	0.000378	T	0.07369	0.0186	N	0.08118	0	0.80722	D	1	P	0.39520	0.676	B	0.41666	0.363	T	0.47394	-0.9121	10	0.23302	T	0.38	.	14.5094	0.67774	0.0707:0.0:0.9293:0.0	.	221	Q9NZI5	GRHL1_HUMAN	I	221	ENSP00000384209:V221I;ENSP00000324693:V221I	ENSP00000324693:V221I	V	+	1	0	GRHL1	10019008	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.852000	0.55934	1.337000	0.45525	-0.244000	0.11960	GTT	.	G|1.000;A|0.000	0.000	weak		0.463	GRHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323543.2	NM_014552		A	10101557	G	A	10101557	3	1	90	1	0	0	0	0	1	0	0	0	6770	1145	40	1	675	1	GRHL1	2	10101557	Missense_Mutation	SNP	G	TCGA-B3-4103-01A-01D-1458-08		10101557	233097816	6	5740											
TMEM37	6344	hgsc.bcm.edu	37	chr2	120194829	120194829	+	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	0	0	0	0	0	0	0	caagtgggtcatgggttccaTcctcctcctggtgtctttcg	4	14	11	12	1	2	0	1	0	1	0	7	0	6	0	4	3	0	1	4	3	1	2			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr2:120194829T>C	ENST00000019103.5	-	0	1865				TMEM37_ENST00000409826.1_Missense_Mutation_p.I141T|TMEM37_ENST00000465296.1_3'UTR|TMEM37_ENST00000306406.4_Missense_Mutation_p.I129T	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)	ATGGGTTCCATCCTCCTCCTG	0.567																																					p.I129T		Atlas-SNP	.											.	TMEM37	40	.	0			c.T386C						PASS	.						178	170	172					2																	120194829		2203	4300	6503	SO:0001628	intergenic_variant	140738	exon2			GTTCCATCCTCCT		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		chr2.hg19:g.120194829T>C		464.0	0.0	.		471.0	126.0	.	NM_183240	Q12961|Q13213|Q53T00	Missense_Mutation	SNP	ENST00000019103.5	hg19	CCDS2127.1	.	.	.	.	.	.	.	.	.	.	T	0.231	-1.020958	0.02061	.	.	ENSG00000171227	ENST00000409826;ENST00000306406	.	.	.	4.97	-0.356	0.12583	.	1.570890	0.03832	N	0.269166	T	0.20129	0.0484	N	0.16478	0.41	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.11542	-1.0583	9	0.28530	T	0.3	-15.3671	1.4103	0.02290	0.1454:0.1645:0.1419:0.5481	.	129	Q8WXS4	CCGL_HUMAN	T	141;129	.	ENSP00000303148:I129T	I	+	2	0	TMEM37	119911299	0.156000	0.22821	0.071000	0.20095	0.017000	0.09413	0.523000	0.22925	-0.194000	0.10399	0.533000	0.62120	ATC	.	.	.	none		0.567	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2			C	120194829	T	C	120194829	1	2	90	0	1	0	0	0	0	0	0	0	16170	1435	50	3		3	TMEM37	2	120194829	IGR	SNP	T	TCGA-B3-4103-01A-01D-1458-08	110093272	120194829	123004544	7	5741											
KCNH7	90134	hgsc.bcm.edu	37	chr2	163241347	163241347	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcatcatcaatggaggagAtgaaagatgaggatctgctt	13	11	12	5	0	4	4	3	2	1	2	4	7	4	6	0	3	1	2	0	3	2	2			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr2:163241347A>G	ENST00000332142.5	-	13	2912	c.2813T>C	c.(2812-2814)aTc>aCc	p.I938T		NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	938					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)	AATGGAGGAGATGAAAGATGA	0.408																																					p.I938T	GBM(196;1492 2208 17507 24132 45496)	Atlas-SNP	.											.	KCNH7	378	.	0			c.T2813C						PASS	.						242	233	236					2																	163241347		2203	4300	6503	SO:0001583	missense	90134	exon13			GAGGAGATGAAAG	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.2813T>C	chr2.hg19:g.163241347A>G	ENSP00000331727:p.Ile938Thr	459.0	1.0	.		437.0	141.0	.	NM_033272	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Missense_Mutation	SNP	ENST00000332142.5	hg19	CCDS2219.1	.	.	.	.	.	.	.	.	.	.	A	8.070	0.770061	0.15983	.	.	ENSG00000184611	ENST00000332142	D	0.98474	-4.95	5.6	4.45	0.53987	.	0.526834	0.21408	N	0.075025	D	0.92446	0.7602	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	D	0.88732	0.3237	10	0.10636	T	0.68	.	9.6489	0.39886	0.9219:0.0:0.0781:0.0	.	938	Q9NS40	KCNH7_HUMAN	T	938	ENSP00000331727:I938T	ENSP00000331727:I938T	I	-	2	0	KCNH7	162949593	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.587000	0.53957	2.141000	0.66446	0.533000	0.62120	ATC	.	.	.	none		0.408	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1	NM_033272		G	163241347	A	G	163241347	3	3	90	1	0	0	0	0	1	0	0	0	8044	333	12	3	793	3	KCNH7	2	163241347	Missense_Mutation	SNP	A	TCGA-B3-4103-01A-01D-1458-08	43046518	163241347	79958026	8	5742											
ITGB5	3693	hgsc.bcm.edu	37	chr3	124515613	124515614	+	Nonsense_Mutation	DNP	CC	CC	AT																															ccgcagggcaaacacatgctCcgtgtgtctgctgggacagc																										TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr3:124515613_124515614CC>AT	ENST00000296181.4	-	10	1610_1611	c.1314_1315GG>AT	c.(1312-1317)acGGag>acATag	p.E439*		NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	439					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|epithelial cell-cell adhesion (GO:0090136)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alphav-beta5 complex (GO:0034684)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	30				GBM - Glioblastoma multiforme(114;0.163)		AACACATGCTCCGTGTGTCTGC	0.609																																					p.E439X|p.T438T		Atlas-SNP	.											.	ITGB5	66	.	0			c.G1315T|c.G1314A						PASS	.																																			SO:0001587	stop_gained	3693	exon10			CATGCTCCGTGTG|ATGCTCCGTGTGT	J05633	CCDS3030.1	3q21.2	2010-03-23			ENSG00000082781	ENSG00000082781		"Integrins"	6160	protein-coding gene	gene with protein product		147561				2211615	Standard	NM_002213		Approved		uc003eho.3	P18084	OTTHUMG00000159432	ENST00000296181.4:c.1314_1315delinsAT	chr3.hg19:g.124515613_124515614delinsAT	ENSP00000296181:p.Glu439*	73.0	0.0	.		89.0|91.0	22.0|24.0	.	NM_002213	B0LPF8|B2RD70	Nonsense_Mutation|Silent	SNP	ENST00000296181.4	hg19	CCDS3030.1																																																																																			.	.	.	none		0.609	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3	NM_002213		AT	124515614	CC	AT	124515613	4	1	90	1	0	0	0	0	0	1	0	0	7905	864	30	4	1108	4	ITGB5	3	124515613	Nonsense_Mutation	DNP	CC	TCGA-B3-4103-01A-01D-1458-08		124515613	73506817	9	5743											
PCYT1A	5130	hgsc.bcm.edu	37	chr3	195974373	195974373	+	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	aagcctttgaagttgtgtgtGagctcatcactgcaaactgg	10	12	11	8	0	2	2	2	2	0	0	2	2	2	2	1	1	4	3	1	1	3	2			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr3:195974373G>A	ENST00000292823.2	-	6	523	c.351C>T	c.(349-351)ctC>ctT	p.L117L	PCYT1A_ENST00000431016.1_Silent_p.L117L|PCYT1A_ENST00000491544.1_5'UTR|PCYT1A_ENST00000419333.1_Silent_p.L117L	NM_005017.2	NP_005008.2	P49585	PCY1A_HUMAN	phosphate cytidylyltransferase 1, choline, alpha	117					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|glycogen granule (GO:0042587)	choline-phosphate cytidylyltransferase activity (GO:0004105)|lipid binding (GO:0008289)			cervix(1)|endometrium(3)|large_intestine(8)|lung(5)|ovary(1)	18	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.28e-24)|all cancers(36;1.01e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00259)	Choline(DB00122)|Lamivudine(DB00709)	AGTTGTGTGTGAGCTCATCAC	0.527																																					p.L117L		Atlas-SNP	.											.	PCYT1A	34	.	0			c.C351T						PASS	.						171	138	149					3																	195974373		2203	4300	6503	SO:0001819	synonymous_variant	5130	exon6			GTGTGTGAGCTCA	L28957	CCDS3315.1	3q29	2010-07-19	2005-09-05		ENSG00000161217	ENSG00000161217	2.7.7.15		8754	protein-coding gene	gene with protein product	"phosphate cytidylyltransferase 1, choline, alpha isoform"	123695	"phosphate cytidylyltransferase 1, choline, alpha isoform"	PCYT1		7918629	Standard	NM_005017		Approved	CT, CTPCT	uc003fwg.3	P49585	OTTHUMG00000155670	ENST00000292823.2:c.351C>T	chr3.hg19:g.195974373G>A		170.0	0.0	.		245.0	63.0	.	NM_005017	A9LYK9|D3DXB1|Q86Y88	Silent	SNP	ENST00000292823.2	hg19	CCDS3315.1																																																																																			.	.	.	none		0.527	PCYT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341147.1	NM_005017		A	195974373	G	A	195974373	2	1	90	1	0	0	0	0	0	0	0	1	11617	1277	45	2		2	PCYT1A	3	195974373	Silent	SNP	G	TCGA-B3-4103-01A-01D-1458-08	71458760	195974373	2048057	10	5744											
LRRC33	375387	hgsc.bcm.edu	37	chr3	196387840	196387840	+	Silent	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	aatcagatctcactttgtccCctgccagctgcctcggaccg	7	10	8	16	2	2	1	2	0	1	1	5	2	3	2	5	1	3	1	5	1	1	1			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr3:196387840C>T	ENST00000328557.4	+	3	1529	c.1326C>T	c.(1324-1326)ccC>ccT	p.P442P		NM_198565.1	NP_940967.1	Q86YC3	NRROS_HUMAN	negative regulator of reactive oxygen species	442					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|superoxide metabolic process (GO:0006801)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											CACTTTGTCCCCTGCCAGCTG	0.592																																					p.P442P		Atlas-SNP	.											.	LRRC33	91	.	0			c.C1326T						PASS	.						144	148	147					3																	196387840		2203	4300	6503	SO:0001819	synonymous_variant	375387	exon3			TTGTCCCCTGCCA	AY358322	CCDS3319.1	3q29	2013-07-02	2013-07-02	2013-07-02	ENSG00000174004	ENSG00000174004			24613	protein-coding gene	gene with protein product		615322	"leucine rich repeat containing 33"	LRRC33		12975309	Standard	NM_198565		Approved	UNQ3030, ELLP3030, MGC50789, GARPL1	uc003fwv.3	Q86YC3	OTTHUMG00000155569	ENST00000328557.4:c.1326C>T	chr3.hg19:g.196387840C>T		439.0	1.0	.		489.0	202.0	.	NM_198565		Silent	SNP	ENST00000328557.4	hg19	CCDS3319.1																																																																																			.	.	.	none		0.592	NRROS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340676.1	NM_198565		T	196387840	C	T	196387840	2	4	90	1	0	0	0	0	0	0	0	1	8995	610	22	2		2	LRRC33	3	196387840	Silent	SNP	C	TCGA-B3-4103-01A-01D-1458-08	413467	196387840	1634590	11	5745											
CLOCK	9575	hgsc.bcm.edu	37	chr4	56301654	56301654	+	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	ctgagttgctgctgttgctgAgactgatgttgctggtgatg	5	15	15	6	0	0	4	0	4	0	1	0	5	0	4	0	1	4	7	0	1	0	3			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr4:56301654A>T	ENST00000309964.4	-	22	2719	c.2469T>A	c.(2467-2469)tcT>tcA	p.S823S	CLOCK_ENST00000513440.1_Silent_p.S823S|CLOCK_ENST00000381322.1_Silent_p.S823S	NM_004898.3	NP_004889.1	O15516	CLOCK_HUMAN	clock circadian regulator	823	Interaction with NR3C1. {ECO:0000250|UniProtKB:O08785}.|Poly-Gln.				cellular response to ionizing radiation (GO:0071479)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|DNA damage checkpoint (GO:0000077)|histone acetylation (GO:0016573)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of transcription, DNA-templated (GO:0045892)|photoperiodism (GO:0009648)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|chromosome (GO:0005694)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|histone acetyltransferase activity (GO:0004402)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(8)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(11;0.00335)|Glioma(25;0.08)|all_epithelial(27;0.0992)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0107)			GCTGTTGCTGAGACTGATGTT	0.527																																					p.S823S		Atlas-SNP	.											.	CLOCK	81	.	0			c.T2469A						PASS	.						273	230	244					4																	56301654		2203	4300	6503	SO:0001819	synonymous_variant	9575	exon23			TTGCTGAGACTGA	AF011568	CCDS3500.1	4q12	2012-12-07	2012-12-07		ENSG00000134852	ENSG00000134852		"Chromatin-modifying enzymes / K-acetyltransferases", "Basic helix-loop-helix proteins"	2082	protein-coding gene	gene with protein product		601851	"clock (mouse) homolog", "clock homolog (mouse)"			10198158	Standard	NM_001267843		Approved	KIAA0334, KAT13D, bHLHe8	uc003hba.2	O15516	OTTHUMG00000102141	ENST00000309964.4:c.2469T>A	chr4.hg19:g.56301654A>T		205.0	0.0	.		195.0	62.0	.	NM_004898	A0AV01|A2I2N9|O14516|Q9UIT8	Silent	SNP	ENST00000309964.4	hg19	CCDS3500.1																																																																																			.	.	.	none		0.527	CLOCK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361993.2	NM_004898		T	56301654	A	T	56301654	2	4	90	1	0	0	0	0	0	0	0	1	3551	291	11	5		5	CLOCK	4	56301654	Silent	SNP	A	TCGA-B3-4103-01A-01D-1458-08		56301654	134852622	12	5746											
UGT2B7	7364	hgsc.bcm.edu	37	chr4	69978199	69978199	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaagagaatgttatgaaattAtcaagaattcaacatgatca	20	11	6	4	0	3	4	3	2	0	2	3	5	3	4	0	0	1	1	0	0	8	3			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr4:69978199A>G	ENST00000305231.7	+	6	1381	c.1335A>G	c.(1333-1335)ttA>ttG	p.L445L	UGT2B7_ENST00000508661.1_3'UTR|UGT2B7_ENST00000509763.1_3'UTR	NM_001074.2	NP_001065.2	P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	445					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)	TTATGAAATTATCAAGAATTC	0.393																																					p.L445L		Atlas-SNP	.											.	UGT2B7	79	.	0			c.A1335G						PASS	.						66	70	69					4																	69978199		2203	4300	6503	SO:0001819	synonymous_variant	7364	exon6			GAAATTATCAAGA	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.1335A>G	chr4.hg19:g.69978199A>G		203.0	0.0	.		252.0	66.0	.	NM_001074	B2R810|Q6GTW0	Silent	SNP	ENST00000305231.7	hg19	CCDS3526.1																																																																																			.	.	.	none		0.393	UGT2B7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251560.1	NM_001074		G	69978199	A	G	69978199	2	3	90	1	0	0	0	0	0	0	0	1	16974	446	16	3		3	UGT2B7	4	69978199	Silent	SNP	A	TCGA-B3-4103-01A-01D-1458-08	13676545	69978199	121176077	13	5747											
ARHGAP24	83478	hgsc.bcm.edu	37	chr4	86921691	86921691	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcctccatgatgaactggAtcaggagaggaaaaagttca	15	7	12	7	0	2	3	2	2	0	1	3	7	3	5	2	3	2	1	2	3	3	1			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr4:86921691A>G	ENST00000395184.1	+	10	2529	c.2063A>G	c.(2062-2064)gAt>gGt	p.D688G	RP13-514E23.2_ENST00000610225.1_RNA|ARHGAP24_ENST00000395183.2_Missense_Mutation_p.D593G|ARHGAP24_ENST00000264343.4_Missense_Mutation_p.D595G	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	688					activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)			breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		GATGAACTGGATCAGGAGAGG	0.448																																					p.D688G		Atlas-SNP	.											.	ARHGAP24	116	.	0			c.A2063G						PASS	.						71	73	72					4																	86921691		2203	4300	6503	SO:0001583	missense	83478	exon10			AACTGGATCAGGA	AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	25361	protein-coding gene	gene with protein product		610586				11230166, 15254788	Standard	NM_001042669		Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.2063A>G	chr4.hg19:g.86921691A>G	ENSP00000378611:p.Asp688Gly	151.0	0.0	.		129.0	53.0	.	NM_001025616	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	Missense_Mutation	SNP	ENST00000395184.1	hg19	CCDS34025.1	.	.	.	.	.	.	.	.	.	.	A	27.8	4.865537	0.91511	.	.	ENSG00000138639	ENST00000395184;ENST00000395183;ENST00000514229;ENST00000264343	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.57095	0.2030	L	0.54323	1.7	0.80722	D	1	D;D;P	0.69078	0.959;0.997;0.877	P;P;B	0.60117	0.637;0.869;0.339	T	0.60439	-0.7263	10	0.87932	D	0	.	16.002	0.80301	1.0:0.0:0.0:0.0	.	593;595;688	Q8N264-3;Q8N264-2;Q8N264	.;.;RHG24_HUMAN	G	688;593;603;595	ENSP00000378611:D688G;ENSP00000378610:D593G;ENSP00000425589:D603G;ENSP00000264343:D595G	ENSP00000264343:D595G	D	+	2	0	ARHGAP24	87140715	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.248000	0.95456	2.241000	0.73720	0.533000	0.62120	GAT	.	.	.	none		0.448	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252815.2	NM_031305		G	86921691	A	G	86921691	3	3	90	1	0	0	0	0	1	0	0	0	873	333	12	3	2213	3	ARHGAP24	4	86921691	Missense_Mutation	SNP	A	TCGA-B3-4103-01A-01D-1458-08	16943492	86921691	104232585	14	5748											
SEMA5A	9037	hgsc.bcm.edu	37	chr5	9226981	9226981	+	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	ggcacaaaaagaagccatacCgagcggttggtgcagacagg	14	4	14	9	2	0	2	0	0	0	2	0	3	0	2	2	4	4	3	2	4	4	2	rs141767878		TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr5:9226981C>T	ENST00000382496.5	-	7	1097	c.432G>A	c.(430-432)tcG>tcA	p.S144S		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	144	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				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						GAAGCCATACCGAGCGGTTGG	0.438																																					p.S144S		Atlas-SNP	.											.	SEMA5A	236	.	0			c.G432A						PASS	.	C		0,4406		0,0,2203	56	60	58		432	4.1	1	5	dbSNP_134	58	1,8599	1.2+/-3.3	0,1,4299	yes	coding-synonymous-near-splice	SEMA5A	NM_003966.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		144/1075	9226981	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	9037	exon7			CCATACCGAGCGG	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.432+1G>A	chr5.hg19:g.9226981C>T		161.0	0.0	.		117.0	6.0	.	NM_003966	D3DTC6|O60408|Q1RLL9	Silent	SNP	ENST00000382496.5	hg19	CCDS3875.1	.	.	.	.	.	.	.	.	.	.	C	13.82	2.352056	0.41700	0.0	1.16E-4	ENSG00000112902	ENST00000514923	.	.	.	4.93	4.05	0.47172	.	.	.	.	.	T	0.62708	0.2450	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60826	-0.7186	4	.	.	.	.	11.7678	0.51941	0.0:0.823:0.177:0.0	.	.	.	.	I	92	.	.	V	-	1	0	SEMA5A	9279981	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	3.490000	0.53245	1.185000	0.42971	0.655000	0.94253	GTT	.	C|1.000;T|0.000	0.000	weak		0.438	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2		Silent	T	9226981	C	T	9226981	5	4	90	1	0	0	0	0	0	0	1	0	14050	666	23	1	2860	1	SEMA5A	5	9226981	Splice_Site	SNP	C	TCGA-B3-4103-01A-01D-1458-08		9226981	171688279	15	5749											
ADAMTS19	171019	hgsc.bcm.edu	37	chr5	128956361	128956361	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcgtgtgctgatggtcttcAtatcatgtctggtgaatgga	8	15	12	6	1	4	2	2	2	2	0	5	3	4	3	0	3	1	1	0	3	2	2			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr5:128956361A>G	ENST00000274487.4	+	9	1656	c.1511A>G	c.(1510-1512)cAt>cGt	p.H504R	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	504	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)		GATGGTCTTCATATCATGTCT	0.373																																					p.H504R		Atlas-SNP	.											ADAMTS19,caecum,carcinoma,0,1	ADAMTS19	216	.	0			c.A1511G						PASS	.						167	153	157					5																	128956361		2203	4300	6503	SO:0001583	missense	171019	exon9			GTCTTCATATCAT	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.1511A>G	chr5.hg19:g.128956361A>G	ENSP00000274487:p.His504Arg	229.0	0.0	.		282.0	12.0	.	NM_133638		Missense_Mutation	SNP	ENST00000274487.4	hg19	CCDS4146.1	.	.	.	.	.	.	.	.	.	.	A	19.79	3.893486	0.72639	.	.	ENSG00000145808	ENST00000274487	T	0.62639	0.01	4.51	4.51	0.55191	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.64402	D	0.000001	T	0.73140	0.3549	L	0.49126	1.545	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	T	0.72459	-0.4287	9	.	.	.	.	14.8814	0.70537	1.0:0.0:0.0:0.0	.	504	Q8TE59	ATS19_HUMAN	R	504	ENSP00000274487:H504R	.	H	+	2	0	ADAMTS19	128984260	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.916000	0.87491	2.246000	0.74042	0.533000	0.62120	CAT	.	.	.	none		0.373	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		G	128956361	A	G	128956361	3	3	90	1	0	0	0	0	1	0	0	0	264	217	8	3	1545	3	ADAMTS19	5	128956361	Missense_Mutation	SNP	A	TCGA-B3-4103-01A-01D-1458-08	119729380	128956361	51958899	16	5750											
GABRG2	2566	hgsc.bcm.edu	37	chr5	161576298	161576298	+	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	cggaaaccaagcaaggacaaAgataaaaagaagaaaaaccc	24	1	8	8	1	0	3	0	0	0	3	0	5	0	5	2	2	3	1	2	2	10	1			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr5:161576298A>T	ENST00000361925.4	+	8	1327	c.1107A>T	c.(1105-1107)aaA>aaT	p.K369N	GABRG2_ENST00000393933.4_Missense_Mutation_p.K274N|GABRG2_ENST00000356592.3_Missense_Mutation_p.K369N|GABRG2_ENST00000414552.2_Missense_Mutation_p.K409N			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	369					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GCAAGGACAAAGATAAAAAGA	0.373																																					p.K409N		Atlas-SNP	.											.	GABRG2	142	.	0			c.A1227T						PASS	.						118	102	107					5																	161576298		2203	4300	6503	SO:0001583	missense	2566	exon9			GGACAAAGATAAA		CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4087	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma 2"	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.1107A>T	chr5.hg19:g.161576298A>T	ENSP00000354651:p.Lys369Asn	158.0	0.0	.		178.0	57.0	.	NM_198903	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Missense_Mutation	SNP	ENST00000361925.4	hg19	CCDS4358.1	.	.	.	.	.	.	.	.	.	.	A	14.77	2.633505	0.47049	.	.	ENSG00000113327	ENST00000356592;ENST00000414552;ENST00000361925;ENST00000393933	D;D;D;D	0.86865	-2.18;-2.18;-2.15;-2.15	5.61	0.527	0.17084	Neurotransmitter-gated ion-channel transmembrane domain (2);	1.305790	0.04797	N	0.432698	D	0.85535	0.5719	M	0.68317	2.08	0.48511	D	0.999667	B;B;B	0.14438	0.01;0.007;0.01	B;B;B	0.23852	0.02;0.049;0.049	T	0.70916	-0.4742	10	0.56958	D	0.05	.	5.4602	0.16612	0.5861:0.1356:0.2784:0.0	.	409;369;369	F5HB82;P18507;P18507-2	.;GBRG2_HUMAN;.	N	369;409;369;274	ENSP00000349000:K369N;ENSP00000410732:K409N;ENSP00000354651:K369N;ENSP00000377510:K274N	ENSP00000349000:K369N	K	+	3	2	GABRG2	161508876	1.000000	0.71417	0.996000	0.52242	0.970000	0.65996	3.143000	0.50608	-0.128000	0.11641	-0.263000	0.10527	AAA	.	.	.	none		0.373	GABRG2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252706.1			T	161576298	A	T	161576298	3	4	90	1	0	0	0	0	1	0	0	0	6179	69	3	5	1261	5	GABRG2	5	161576298	Missense_Mutation	SNP	A	TCGA-B3-4103-01A-01D-1458-08	32619937	161576298	19338962	17	5751											
FAM135A	57579	hgsc.bcm.edu	37	chr6	71234676	71234676	+	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	cgatagtgaaattacacaaaTggaacacaatctggcatcca	17	8	7	9	1	1	1	0	1	1	0	2	3	2	2	1	2	2	1	1	2	6	2			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr6:71234676T>A	ENST00000418814.2	+	15	2503	c.1889T>A	c.(1888-1890)aTg>aAg	p.M630K	FAM135A_ENST00000457062.2_Missense_Mutation_p.M417K|FAM135A_ENST00000505868.1_Missense_Mutation_p.M630K|FAM135A_ENST00000505769.1_Missense_Mutation_p.M434K|FAM135A_ENST00000370479.3_Missense_Mutation_p.M417K|FAM135A_ENST00000361499.3_Missense_Mutation_p.M434K	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	630										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						ATTACACAAATGGAACACAAT	0.393																																					p.M630K		Atlas-SNP	.											.	FAM135A	181	.	0			c.T1889A						PASS	.						70	64	66					6																	71234676		2203	4299	6502	SO:0001583	missense	57579	exon13			CACAAATGGAACA	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.1889T>A	chr6.hg19:g.71234676T>A	ENSP00000410768:p.Met630Lys	143.0	0.0	.		127.0	52.0	.	NM_001162529	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Missense_Mutation	SNP	ENST00000418814.2	hg19	CCDS55028.1	.	.	.	.	.	.	.	.	.	.	T	10.84	1.464055	0.26335	.	.	ENSG00000082269	ENST00000418814;ENST00000370479;ENST00000505769;ENST00000457062;ENST00000361499;ENST00000505868	T;T;T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16;-1.16;-1.16	5.87	3.5	0.40072	.	0.419502	0.28453	N	0.015293	T	0.28928	0.0718	N	0.08118	0	0.27751	N	0.944159	B;B;B;B	0.15473	0.013;0.008;0.011;0.013	B;B;B;B	0.20577	0.03;0.008;0.019;0.03	T	0.27571	-1.0070	10	0.06494	T	0.89	.	8.0899	0.30795	0.0:0.2862:0.0:0.7138	.	630;630;434;417	Q9P2D6-4;Q9P2D6;Q9P2D6-2;Q9P2D6-3	.;F135A_HUMAN;.;.	K	630;417;434;417;434;630	ENSP00000410768:M630K;ENSP00000359510:M417K;ENSP00000423785:M434K;ENSP00000409201:M417K;ENSP00000354913:M434K;ENSP00000423307:M630K	ENSP00000354913:M434K	M	+	2	0	FAM135A	71291397	0.983000	0.35010	0.999000	0.59377	0.962000	0.63368	0.518000	0.22847	0.576000	0.29452	0.533000	0.62120	ATG	.	.	.	none		0.393	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819		A	71234676	T	A	71234676	3	1	90	1	0	0	0	0	1	0	0	0	5452	1464	51	5	2017	5	FAM135A	6	71234676	Missense_Mutation	SNP	T	TCGA-B3-4103-01A-01D-1458-08		71234676	99880391	18	5752											
CTTNBP2	83992	hgsc.bcm.edu	37	chr7	117364734	117364734	+	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	caagtgttataactggaaacTatggataaagggaaacttcc	16	10	9	6	0	0	0	0	0	0	0	1	3	1	3	1	3	3	1	1	3	8	5			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr7:117364734T>A	ENST00000160373.3	-	19	4405	c.4314A>T	c.(4312-4314)atA>atT	p.I1438I		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1438					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)		AACTGGAAACTATGGATAAAG	0.438																																					p.I1438I		Atlas-SNP	.											.	CTTNBP2	200	.	0			c.A4314T						PASS	.						106	96	100					7																	117364734		2203	4300	6503	SO:0001819	synonymous_variant	83992	exon19			GGAAACTATGGAT		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.4314A>T	chr7.hg19:g.117364734T>A		147.0	0.0	.		187.0	53.0	.	NM_033427	O43389|Q7LG11|Q9C0A5	Silent	SNP	ENST00000160373.3	hg19	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	T	2.995	-0.207314	0.06180	.	.	ENSG00000077063	ENST00000446636	.	.	.	5.45	-4.08	0.03963	.	.	.	.	.	T	0.38532	0.1044	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37934	-0.9684	4	.	.	.	-1.618	1.9951	0.03455	0.2862:0.4031:0.1445:0.1662	.	.	.	.	C	926	.	.	S	-	1	0	CTTNBP2	117151970	0.378000	0.25114	0.285000	0.24819	0.253000	0.25986	-0.307000	0.08167	-0.488000	0.06726	-0.408000	0.06270	AGT	.	.	.	none		0.438	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		A	117364734	T	A	117364734	2	1	90	1	0	0	0	0	0	0	0	1	4047	1512	53	5		5	CTTNBP2	7	117364734	Silent	SNP	T	TCGA-B3-4103-01A-01D-1458-08		117364734	41773929	19	5753											
ARF5	381	hgsc.bcm.edu	37	chr7	127229193	127229193	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaaactgaagttgggggagAttgtcaccaccatcccaacc	13	7	9	12	0	1	2	1	1	0	1	2	3	2	2	4	2	2	1	4	2	3	2			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr7:127229193A>G	ENST00000000233.5	+	2	278	c.124A>G	c.(124-126)Att>Gtt	p.I42V	ARF5_ENST00000467281.1_3'UTR|GCC1_ENST00000497650.1_Intron	NM_001662.3	NP_001653.1	P84085	ARF5_HUMAN	ADP-ribosylation factor 5	42					GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			cervix(2)|kidney(1)|lung(10)|ovary(1)	14						GTTGGGGGAGATTGTCACCAC	0.632											OREG0018287	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I42V		Atlas-SNP	.											.	ARF5	20	.	0			c.A124G						PASS	.						84	77	79					7																	127229193		2203	4300	6503	SO:0001583	missense	381	exon2			GGGGAGATTGTCA		CCDS34745.1	7q31.3	2008-07-18			ENSG00000004059	ENSG00000004059		"ADP-ribosylation factors"	658	protein-coding gene	gene with protein product		103188				1993656	Standard	NM_001662		Approved		uc003vmb.2	P84085	OTTHUMG00000023246	ENST00000000233.5:c.124A>G	chr7.hg19:g.127229193A>G	ENSP00000000233:p.Ile42Val	99.0	0.0	.	1555	117.0	46.0	.	NM_001662	P26437	Missense_Mutation	SNP	ENST00000000233.5	hg19	CCDS34745.1	.	.	.	.	.	.	.	.	.	.	a	17.35	3.367076	0.61513	.	.	ENSG00000004059	ENST00000000233;ENST00000415666	D;D	0.81821	-1.54;-1.54	5.19	3.96	0.45880	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.56572	0.1994	N	0.03050	-0.425	0.44635	D	0.997619	B;B	0.10296	0.003;0.003	B;B	0.16289	0.015;0.015	T	0.53746	-0.8395	10	0.29301	T	0.29	-8.2547	9.1237	0.36801	0.8363:0.0:0.0:0.1636	.	42;42	A4D0Z3;P84085	.;ARF5_HUMAN	V	42	ENSP00000000233:I42V;ENSP00000412701:I42V	ENSP00000000233:I42V	I	+	1	0	ARF5	127016429	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.106000	0.77039	1.962000	0.57031	0.444000	0.29173	ATT	.	.	.	none		0.632	ARF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059567.2	NM_001662		G	127229193	A	G	127229193	3	3	90	1	0	0	0	0	1	0	0	0	847	333	12	3	130	3	ARF5	7	127229193	Missense_Mutation	SNP	A	TCGA-B3-4103-01A-01D-1458-08	9864459	127229193	31909470	20	5754											
ABRA	137735	hgsc.bcm.edu	37	chr8	107782408	107782408	+	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	cctccccgctttccttttcgCccggagccatgctgcccacc	3	10	7	21	3	0	0	0	0	0	0	3	1	2	1	8	1	3	2	8	1	0	3			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr8:107782408C>A	ENST00000311955.3	-	1	65	c.11G>T	c.(10-12)gGc>gTc	p.G4V		NM_139166.4	NP_631905.1			actin-binding Rho activating protein											breast(1)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|prostate(2)	27			OV - Ovarian serous cystadenocarcinoma(57;3.83e-09)			TTCCTTTTCGCCCGGAGCCAT	0.597																																					p.G4V		Atlas-SNP	.											.	ABRA	57	.	0			c.G11T						PASS	.						33	37	35					8																	107782408		2202	4295	6497	SO:0001583	missense	137735	exon1			TTTTCGCCCGGAG	AF503617	CCDS6305.1	8q23.1	2012-02-06			ENSG00000174429	ENSG00000174429			30655	protein-coding gene	gene with protein product	"striated muscle activator of Rho-dependent signaling"	609747				11983702	Standard	NM_139166		Approved	STARS	uc003ymm.4	Q8N0Z2	OTTHUMG00000164809	ENST00000311955.3:c.11G>T	chr8.hg19:g.107782408C>A	ENSP00000311436:p.Gly4Val	110.0	0.0	.		125.0	27.0	.	NM_139166		Missense_Mutation	SNP	ENST00000311955.3	hg19	CCDS6305.1	.	.	.	.	.	.	.	.	.	.	C	13.23	2.174542	0.38413	.	.	ENSG00000174429	ENST00000311955	.	.	.	5.66	3.63	0.41609	.	0.510379	0.22113	N	0.064446	T	0.45796	0.1360	L	0.44542	1.39	0.53005	D	0.999964	P	0.42203	0.773	P	0.45712	0.491	T	0.45948	-0.9226	9	0.59425	D	0.04	-3.5289	4.2762	0.10809	0.0:0.5455:0.0:0.4545	.	4	Q8N0Z2	ABRA_HUMAN	V	4	.	ENSP00000311436:G4V	G	-	2	0	ABRA	107851584	1.000000	0.71417	0.870000	0.34147	0.314000	0.28054	1.867000	0.39499	1.377000	0.46286	0.655000	0.94253	GGC	.	.	.	none		0.597	ABRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380416.1	NM_139166		A	107782408	C	A	107782408	3	1	90	1	0	0	0	0	1	0	0	0	100	739	26	4	1142	4	ABRA	8	107782408	Missense_Mutation	SNP	C	TCGA-B3-4103-01A-01D-1458-08		107782408	38581614	21	5755											
MRPL13	28998	hgsc.bcm.edu	37	chr8	121455496	121455496	+	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	tagcagcaagtttgccaggtGgctgcattttcccatctaag	9	12	10	10	0	1	0	0	0	1	0	2	0	2	0	2	2	4	5	2	2	3	5			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr8:121455496G>A	ENST00000306185.3	-	2	371	c.80C>T	c.(79-81)cCa>cTa	p.P27L	MTBP_ENST00000305949.1_5'Flank	NM_014078.5	NP_054797.2	Q9BYD1	RM13_HUMAN	mitochondrial ribosomal protein L13	27					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrial ribosome (GO:0005761)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	6	Lung NSC(37;1.69e-07)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			TTTGCCAGGTGGCTGCATTTT	0.373																																					p.P27L		Atlas-SNP	.											.	MRPL13	18	.	0			c.C80T						PASS	.						123	118	120					8																	121455496		2203	4300	6503	SO:0001583	missense	28998	exon2			CCAGGTGGCTGCA	AB049640	CCDS6332.1	8q22.1-q22.3	2012-09-13			ENSG00000172172	ENSG00000172172		"Mitochondrial ribosomal proteins / large subunits"	14278	protein-coding gene	gene with protein product		610200				11543634	Standard	NM_014078		Approved	L13, RPL13, L13mt, RPML13, L13A	uc003ypa.3	Q9BYD1	OTTHUMG00000165039	ENST00000306185.3:c.80C>T	chr8.hg19:g.121455496G>A	ENSP00000306548:p.Pro27Leu	178.0	0.0	.		194.0	62.0	.	NM_014078	B2R4R8|Q9UI04	Missense_Mutation	SNP	ENST00000306185.3	hg19	CCDS6332.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.607489	0.87157	.	.	ENSG00000172172	ENST00000306185;ENST00000518918	.	.	.	5.65	5.65	0.86999	Ribosomal protein L13 domain (2);	0.000000	0.85682	D	0.000000	D	0.83280	0.5220	M	0.80508	2.5	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82942	-0.0207	9	0.45353	T	0.12	-0.4573	19.3324	0.94297	0.0:0.0:1.0:0.0	.	27	Q9BYD1	RM13_HUMAN	L	27;3	.	ENSP00000306548:P27L	P	-	2	0	MRPL13	121524677	1.000000	0.71417	0.998000	0.56505	0.884000	0.51177	9.102000	0.94226	2.663000	0.90544	0.542000	0.68232	CCA	.	.	.	none		0.373	MRPL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381523.1	NM_014078		A	121455496	G	A	121455496	3	1	90	1	0	0	0	0	1	0	0	0	9785	1348	47	2	480	2	MRPL13	8	121455496	Missense_Mutation	SNP	G	TCGA-B3-4103-01A-01D-1458-08	13673088	121455496	24908526	22	5756											
CYHR1	50626	hgsc.bcm.edu	37	chr8	145690192	145690192	+	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	ctcagccccagtgtactcacCtcggctgtgctcacggctgc	5	9	10	17	2	3	0	3	0	0	0	4	0	3	0	3	2	4	4	3	2	1	1			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr8:145690192C>G	ENST00000438911.2	-	1	226	c.93G>C	c.(91-93)gaG>gaC	p.E31D	CYHR1_ENST00000424149.2_Splice_Site_p.E31D|KIFC2_ENST00000301331.5_5'Flank|CYHR1_ENST00000306145.5_Splice_Site_p.E31D|CYHR1_ENST00000530374.1_5'Flank|KIFC2_ENST00000301332.2_5'Flank|CTD-2517M22.16_ENST00000525461.1_RNA|CYHR1_ENST00000403000.2_Splice_Site_p.E31D	NM_138496.1	NP_612505.1	Q6ZMK1	CYHR1_HUMAN	cysteine/histidine-rich 1	31						cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)	zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|lung(3)|ovary(2)	7	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)			GTGTACTCACCTCGGCTGTGC	0.627																																					p.E31D		Atlas-SNP	.											.	CYHR1	39	.	0			c.G93C						PASS	.						37	38	38					8																	145690192		2197	4298	6495	SO:0001630	splice_region_variant	50626	exon2			ACTCACCTCGGCT	AB007965	CCDS6426.1, CCDS47943.1	8q24	2004-12-07	2005-07-24		ENSG00000187954	ENSG00000187954			17806	protein-coding gene	gene with protein product			"cysteine and histidine rich 1"			10745073	Standard	NM_138496		Approved	CHRP, KIAA0496, MGC13010	uc003zcv.2	Q6ZMK1	OTTHUMG00000165171	ENST00000438911.2:c.93+1G>C	chr8.hg19:g.145690192C>G		38.0	0.0	.		51.0	18.0	.	NM_032687	B3KSX0|D3DWM3|Q9BSF6|Q9BSU6	Missense_Mutation	SNP	ENST00000438911.2	hg19	CCDS47943.1	.	.	.	.	.	.	.	.	.	.	c	17.42	3.385251	0.61956	.	.	ENSG00000187954	ENST00000438911;ENST00000526887;ENST00000403000;ENST00000424149;ENST00000306145;ENST00000533764;ENST00000530637	T;T;T;T;T;T;T	0.43688	0.94;1.65;0.94;0.94;0.94;0.94;0.94	4.22	4.22	0.49857	.	0.251507	0.25386	U	0.031059	T	0.24736	0.0600	N	0.08118	0	0.09310	N	0.999991	B;B	0.21606	0.058;0.0	B;B	0.19391	0.025;0.001	T	0.27297	-1.0078	10	0.72032	D	0.01	.	12.4423	0.55631	0.0:1.0:0.0:0.0	.	31;31	Q6ZMK1-3;Q6ZMK1	.;CYHR1_HUMAN	D	31	ENSP00000387426:E31D;ENSP00000434470:E31D;ENSP00000385962:E31D;ENSP00000414647:E31D;ENSP00000304826:E31D;ENSP00000432902:E31D;ENSP00000434642:E31D	ENSP00000304826:E31D	E	-	3	2	CYHR1	145661000	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	2.359000	0.44142	2.074000	0.62210	0.556000	0.70494	GAG	.	.	.	none		0.627	CYHR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000382438.1	NM_032687	Missense_Mutation	G	145690192	C	G	145690192	5	3	90	1	0	0	0	0	0	0	1	0	4142	695	24	4	1348	4	CYHR1	8	145690192	Splice_Site	SNP	C	TCGA-B3-4103-01A-01D-1458-08	24234696	145690192	673830	23	5757											
TNFSF8	944	hgsc.bcm.edu	37	chr9	117666220	117666220	+	Missense_Mutation	SNP	A	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	agagaaactgttcagtctgaAttactgtataagaagatgga	16	11	10	4	0	2	4	1	1	1	3	2	6	2	5	0	1	2	2	0	1	6	4			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr9:117666220A>C	ENST00000223795.2	-	4	809	c.696T>G	c.(694-696)aaT>aaG	p.N232K	TNFSF8_ENST00000474301.1_Intron	NM_001244.3	NP_001235.1	P32971	TNFL8_HUMAN	tumor necrosis factor (ligand) superfamily, member 8	232					apoptotic process (GO:0006915)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor binding (GO:0005102)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(3)|urinary_tract(1)	12						TTCAGTCTGAATTACTGTATA	0.408																																					p.N232K		Atlas-SNP	.											.	TNFSF8	34	.	0			c.T696G						PASS	.						165	157	159					9																	117666220		2203	4300	6503	SO:0001583	missense	944	exon4			GTCTGAATTACTG	L09753	CCDS6810.1, CCDS75884.1	9q33	2008-02-05			ENSG00000106952	ENSG00000106952		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11938	protein-coding gene	gene with protein product		603875		CD30LG		8391931, 9349718	Standard	NM_001244		Approved	CD153	uc004bji.2	P32971	OTTHUMG00000021025	ENST00000223795.2:c.696T>G	chr9.hg19:g.117666220A>C	ENSP00000223795:p.Asn232Lys	266.0	0.0	.		273.0	82.0	.	NM_001244	O43404	Missense_Mutation	SNP	ENST00000223795.2	hg19	CCDS6810.1	.	.	.	.	.	.	.	.	.	.	A	10.09	1.255547	0.22965	.	.	ENSG00000106952	ENST00000223795	.	.	.	5.78	2.21	0.28008	.	0.916415	0.09426	N	0.803692	T	0.18130	0.0435	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.23048	-1.0199	9	0.48119	T	0.1	-0.0101	4.7061	0.12849	0.6059:0.1526:0.2415:0.0	.	232	P32971	TNFL8_HUMAN	K	232	.	ENSP00000223795:N232K	N	-	3	2	TNFSF8	116706041	0.167000	0.22975	0.531000	0.27976	0.664000	0.39144	0.394000	0.20834	0.135000	0.18707	-0.256000	0.11100	AAT	.	.	.	none		0.408	TNFSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055464.1			C	117666220	A	C	117666220	3	2	90	1	0	0	0	0	1	0	0	0	16323	98	4	5	12	5	TNFSF8	9	117666220	Missense_Mutation	SNP	A	TCGA-B3-4103-01A-01D-1458-08		117666220	23547211	24	5758											
TNKS2	80351	hgsc.bcm.edu	37	chr10	93593686	93593686	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcatctacaaacctgccgccTactcctgagctatgggtgtg	8	11	9	13	1	2	1	1	1	1	0	3	1	3	1	4	1	5	1	4	1	4	3			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr10:93593686T>C	ENST00000371627.4	+	12	1731	c.1352T>C	c.(1351-1353)cTa>cCa	p.L451P		NM_025235.3	NP_079511.1	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2	451					multicellular organism growth (GO:0035264)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein polyubiquitination (GO:0000209)|regulation of multicellular organism growth (GO:0040014)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			biliary_tract(1)|breast(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	48		Colorectal(252;0.162)				ACCTGCCGCCTACTCCTGAGC	0.413																																					p.L451P		Atlas-SNP	.											.	TNKS2	103	.	0			c.T1352C						PASS	.						148	131	137					10																	93593686		2203	4300	6503	SO:0001583	missense	80351	exon12			GCCGCCTACTCCT	AF342982	CCDS7417.1	10q23.3	2013-01-10			ENSG00000107854	ENSG00000107854		"Poly (ADP-ribose) polymerases", "Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	15677	protein-coding gene	gene with protein product		607128					Standard	NM_025235		Approved	TNKL, TANK2, PARP-5b, PARP-5c, PARP5B, PARP5C, pART6	uc001khp.3	Q9H2K2	OTTHUMG00000018747	ENST00000371627.4:c.1352T>C	chr10.hg19:g.93593686T>C	ENSP00000360689:p.Leu451Pro	225.0	0.0	.		240.0	79.0	.	NM_025235	B2RBD3|Q9H8F2|Q9HAS4	Missense_Mutation	SNP	ENST00000371627.4	hg19	CCDS7417.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.715685	0.89112	.	.	ENSG00000107854	ENST00000371627	T	0.70164	-0.46	5.83	5.83	0.93111	Ankyrin repeat-containing domain (3);	0.000000	0.47093	D	0.000247	D	0.86489	0.5945	M	0.94142	3.5	0.80722	D	1	D	0.69078	0.997	D	0.70227	0.968	D	0.89940	0.4072	10	0.62326	D	0.03	.	16.1968	0.82036	0.0:0.0:0.0:1.0	.	451	Q9H2K2	TNKS2_HUMAN	P	451	ENSP00000360689:L451P	ENSP00000360689:L451P	L	+	2	0	TNKS2	93583666	1.000000	0.71417	0.975000	0.42487	0.983000	0.72400	8.040000	0.89188	2.225000	0.72522	0.533000	0.62120	CTA	.	.	.	none		0.413	TNKS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049374.1	NM_025235		C	93593686	T	C	93593686	3	2	90	1	0	0	0	0	1	0	0	0	16333	1522	53	3	1398	3	TNKS2	10	93593686	Missense_Mutation	SNP	T	TCGA-B3-4103-01A-01D-1458-08		93593686	41941061	25	5759											
ITPRIP	85450	hgsc.bcm.edu	37	chr10	106075425	106075425	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgaggccctgcaagggggCgccccccagcccaggcagct	6	3	16	16	1	0	1	0	1	0	0	0	1	0	1	5	5	3	3	5	5	1	0			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr10:106075425C>T	ENST00000337478.1	-	2	556	c.385G>A	c.(385-387)Gcc>Acc	p.A129T	ITPRIP_ENST00000278071.2_Missense_Mutation_p.A129T|ITPRIP_ENST00000358187.2_Missense_Mutation_p.A129T|RP11-127L20.5_ENST00000472915.2_RNA	NM_001272013.1	NP_001258942.1	Q8IWB1	IPRI_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein	129						membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(9)|upper_aerodigestive_tract(1)	20						TGCAAGGGGGCGCCCCCCAGC	0.692																																					p.A129T		Atlas-SNP	.											.	ITPRIP	44	.	0			c.G385A						PASS	.						35	41	39					10																	106075425		2203	4298	6501	SO:0001583	missense	85450	exon2			AGGGGGCGCCCCC	AB051541	CCDS7557.1	10q25.1	2011-04-28	2011-04-28	2008-08-11	ENSG00000148841	ENSG00000148841			29370	protein-coding gene	gene with protein product			"KIAA1754", "inositol 1,4,5-triphosphate receptor interacting protein"	KIAA1754		11214970, 16990268	Standard	NM_001272012		Approved	bA127L20.2, DANGER	uc001kye.4	Q8IWB1	OTTHUMG00000019003	ENST00000337478.1:c.385G>A	chr10.hg19:g.106075425C>T	ENSP00000337178:p.Ala129Thr	167.0	0.0	.		179.0	76.0	.	NM_001272013	D3DRA5|Q5JU17|Q96MS8|Q9C0A9	Missense_Mutation	SNP	ENST00000337478.1	hg19	CCDS7557.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.730767	0.00687	.	.	ENSG00000148841	ENST00000337478;ENST00000278071;ENST00000358187	T;T;T	0.22134	1.97;1.97;1.97	5.68	-5.02	0.02982	.	1.189030	0.05773	N	0.607175	T	0.10551	0.0258	N	0.13043	0.29	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.39563	-0.9608	10	0.12430	T	0.62	-5.7595	10.1192	0.42609	0.0857:0.426:0.0:0.4883	.	129	Q8IWB1	IPRI_HUMAN	T	129	ENSP00000337178:A129T;ENSP00000278071:A129T;ENSP00000350915:A129T	ENSP00000278071:A129T	A	-	1	0	ITPRIP	106065415	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-0.312000	0.08113	-1.181000	0.02730	-1.119000	0.02030	GCC	.	.	.	none		0.692	ITPRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050204.1	NM_033397		T	106075425	C	T	106075425	3	4	90	1	0	0	0	0	1	0	0	0	7930	768	27	1	1262	1	ITPRIP	10	106075425	Missense_Mutation	SNP	C	TCGA-B3-4103-01A-01D-1458-08	12481739	106075425	29459322	26	5760											
MRGPRX1	259249	hgsc.bcm.edu	37	chr11	18955994	18955994	+	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	gctcggtgctcacggcactcAgaaagctcaggcctgcaaag	10	6	12	13	2	3	1	3	0	0	1	4	1	3	1	1	3	3	5	1	3	2	0			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr11:18955994A>T	ENST00000302797.3	-	1	562	c.338T>A	c.(337-339)cTg>cAg	p.L113Q	MRGPRX1_ENST00000526914.1_5'UTR|RP11-583F24.8_ENST00000528646.1_RNA	NM_147199.3	NP_671732.3	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	113					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						CACGGCACTCAGAAAGCTCAG	0.542																																					p.L113Q		Atlas-SNP	.											.	MRGPRX1	84	.	0			c.T338A						PASS	.						100	96	98					11																	18955994		2194	4286	6480	SO:0001583	missense	259249	exon1			GCACTCAGAAAGC		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.338T>A	chr11.hg19:g.18955994A>T	ENSP00000305766:p.Leu113Gln	157.0	0.0	.		153.0	7.0	.	NM_147199	Q4V9L2|Q8TDD8|Q8TDD9	Missense_Mutation	SNP	ENST00000302797.3	hg19	CCDS7846.1	.	.	.	.	.	.	.	.	.	.	.	16.41	3.114997	0.56505	.	.	ENSG00000170255	ENST00000302797	D	0.81579	-1.51	2.28	2.28	0.28536	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000078	D	0.91199	0.7227	H	0.95982	3.75	0.29298	N	0.868908	D	0.89917	1.0	D	0.91635	0.999	D	0.85057	0.0932	10	0.87932	D	0	.	8.4333	0.32771	1.0:0.0:0.0:0.0	.	113	Q96LB2	MRGX1_HUMAN	Q	113	ENSP00000305766:L113Q	ENSP00000305766:L113Q	L	-	2	0	MRGPRX1	18912570	0.996000	0.38824	0.008000	0.14137	0.026000	0.11368	7.327000	0.79147	1.292000	0.44672	0.402000	0.26972	CTG	.	.	.	none		0.542	MRGPRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369913.1	NM_147199		T	18955994	A	T	18955994	3	4	90	1	0	0	0	0	1	0	0	0	9773	188	7	5	634	5	MRGPRX1	11	18955994	Missense_Mutation	SNP	A	TCGA-B3-4103-01A-01D-1458-08		18955994	116050522	27	5761											
ABCG4	64137	hgsc.bcm.edu	37	chr11	119027678	119027678	+	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	tatggctgagaagaagagcaGccctgagaagaacgaggtcc	14	5	14	8	1	0	5	0	2	0	5	1	8	1	5	2	2	3	2	2	2	5	1			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr11:119027678G>T	ENST00000449422.2	+	9	1210	c.1022G>T	c.(1021-1023)aGc>aTc	p.S341I	ABCG4_ENST00000531739.1_Missense_Mutation_p.S341I|AP002956.1_ENST00000599663.1_Intron|ABCG4_ENST00000307417.3_Missense_Mutation_p.S341I	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	341					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)		AAGAAGAGCAGCCCTGAGAAG	0.607																																					p.S341I		Atlas-SNP	.											.	ABCG4	77	.	0			c.G1022T						PASS	.						180	164	170					11																	119027678		2200	4295	6495	SO:0001583	missense	64137	exon9			AGAGCAGCCCTGA	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.1022G>T	chr11.hg19:g.119027678G>T	ENSP00000406874:p.Ser341Ile	253.0	0.0	.		220.0	75.0	.	NM_022169	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Missense_Mutation	SNP	ENST00000449422.2	hg19	CCDS8415.1	.	.	.	.	.	.	.	.	.	.	G	16.00	2.998773	0.54147	.	.	ENSG00000172350	ENST00000307417;ENST00000449422;ENST00000531739;ENST00000534402	D;D;D;T	0.87412	-2.25;-2.25;-2.25;0.85	5.65	3.69	0.42338	.	0.573919	0.21547	N	0.072794	T	0.78660	0.4318	L	0.35854	1.095	0.36220	D	0.851913	B	0.13594	0.008	B	0.13407	0.009	T	0.75360	-0.3345	10	0.38643	T	0.18	-8.3485	6.2254	0.20706	0.071:0.1345:0.6546:0.1398	.	341	Q9H172	ABCG4_HUMAN	I	341;341;341;19	ENSP00000304111:S341I;ENSP00000406874:S341I;ENSP00000434318:S341I;ENSP00000434571:S19I	ENSP00000304111:S341I	S	+	2	0	ABCG4	118532888	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.327000	0.43858	1.359000	0.45940	0.655000	0.94253	AGC	.	.	.	none		0.607	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169		T	119027678	G	T	119027678	3	4	90	1	0	0	0	0	1	0	0	0	70	971	34	4	1052	4	ABCG4	11	119027678	Missense_Mutation	SNP	G	TCGA-B3-4103-01A-01D-1458-08	100071684	119027678	15978838	28	5762											
WDR66	144406	hgsc.bcm.edu	37	chr12	122413567	122413567	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttttgtcatgagagcaatTggcttttacccatctgaaga	10	14	8	9	0	2	3	1	2	1	2	2	4	2	3	2	1	2	2	2	1	3	5			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr12:122413567T>C	ENST00000288912.4	+	19	3836	c.2982T>C	c.(2980-2982)atT>atC	p.I994I		NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	994							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)		TGAGAGCAATTGGCTTTTACC	0.438																																					p.I994I	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											.	WDR66	143	.	0			c.T2982C						PASS	.						119	111	113					12																	122413567		1915	4145	6060	SO:0001819	synonymous_variant	144406	exon19			AGCAATTGGCTTT	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.2982T>C	chr12.hg19:g.122413567T>C		184.0	0.0	.		141.0	49.0	.	NM_144668	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Silent	SNP	ENST00000288912.4	hg19	CCDS41853.1																																																																																			.	.	.	none		0.438	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668		C	122413567	T	C	122413567	2	2	90	1	0	0	0	0	0	0	0	1	17329	1800	63	3		3	WDR66	12	122413567	Silent	SNP	T	TCGA-B3-4103-01A-01D-1458-08		122413567	11438328	29	5763											
FRMD6	122786	hgsc.bcm.edu	37	chr14	52182105	52182105	+	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	cggaagctcatatactacacGgggtgccccatgcgctccag	9	7	11	14	3	1	0	1	0	0	0	2	1	2	1	3	3	5	2	3	3	4	3			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr14:52182105G>T	ENST00000344768.5	+	10	1108	c.912G>T	c.(910-912)acG>acT	p.T304T	FRMD6_ENST00000395718.2_Silent_p.T296T|FRMD6_ENST00000553556.1_5'Flank|FRMD6_ENST00000554167.1_Silent_p.T227T|FRMD6_ENST00000356218.4_Silent_p.T296T			Q96NE9	FRMD6_HUMAN	FERM domain containing 6	304	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				apical constriction (GO:0003383)|cellular protein localization (GO:0034613)|regulation of actin filament-based process (GO:0032970)	apical junction complex (GO:0043296)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_epithelial(31;0.0163)|Breast(41;0.089)					TATACTACACGGGGTGCCCCA	0.507																																					p.T304T		Atlas-SNP	.											.	FRMD6	100	.	0			c.G912T						PASS	.						62	65	64					14																	52182105		2203	4300	6503	SO:0001819	synonymous_variant	122786	exon10			CTACACGGGGTGC	BI465118	CCDS9704.1, CCDS58318.1, CCDS58319.1	14q22.1	2011-06-22	2005-07-20	2005-07-20	ENSG00000139926	ENSG00000139926			19839	protein-coding gene	gene with protein product	"expanded homolog"	614555	"chromosome 14 open reading frame 31"	C14orf31			Standard	NM_152330		Approved	MGC17921, willin, EX1	uc001wzd.3	Q96NE9	OTTHUMG00000140294	ENST00000344768.5:c.912G>T	chr14.hg19:g.52182105G>T		153.0	0.0	.		156.0	13.0	.	NM_001267046	D3DSB9|Q5HYF2|Q8N2X1|Q8WUH7	Silent	SNP	ENST00000344768.5	hg19	CCDS58318.1																																																																																			.	.	.	none		0.507	FRMD6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276881.1	NM_152330		T	52182105	G	T	52182105	2	4	90	1	0	0	0	0	0	0	0	1	6061	1103	39	4		4	FRMD6	14	52182105	Silent	SNP	G	TCGA-B3-4103-01A-01D-1458-08		52182105	55167435	30	5764											
ANGEL1	23357	hgsc.bcm.edu	37	chr14	77274402	77274411	+	Frame_Shift_Del	DEL	GAGTGAACTG	GAGTGAACTG	-																															caggatgttataagacatcaGagtgaactggaactgagggc																								rs138394702	byFrequency	TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	GAGTGAACTG	GAGTGAACTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr14:77274402_77274411delGAGTGAACTG	ENST00000251089.2	-	3	842_851	c.730_739delCAGTTCACTC	c.(730-741)cagttcactctgfs	p.QFTL244fs	ANGEL1_ENST00000554941.1_5'Flank	NM_015305.3	NP_056120.2	Q9UNK9	ANGE1_HUMAN	angel homolog 1 (Drosophila)	244										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	22			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0285)		TAAGACATCAGAGTGAACTGGAACTGAGGG	0.505																																					p.244_247del		Atlas-INDEL	.											.	ANGEL1	63	.	0			c.731_740del						PASS	.																																			SO:0001589	frameshift_variant	23357	exon3			.	AF111169	CCDS9852.1	14q24.3	2014-06-17		2005-08-04	ENSG00000013523	ENSG00000013523			19961	protein-coding gene	gene with protein product				KIAA0759		11943475	Standard	NM_015305		Approved	Ccr4e	uc001xsv.3	Q9UNK9	OTTHUMG00000171494	ENST00000251089.2:c.730_739delCAGTTCACTC	chr14.hg19:g.77274402_77274411delGAGTGAACTG	ENSP00000251089:p.Gln244fs	121.0	0.0	0		121.0	26.0	0.214876	NM_015305	B4DWL7|O94859|Q8NCS9	Frame_Shift_Del	DEL	ENST00000251089.2	hg19	CCDS9852.1																																																																																			.	.	.	none		0.505	ANGEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413712.2	NM_015305		-	77274411	GAGTGAACTG	-	77274402	7	5	90	1	0	1	0	1	0	0	0	0	608	933	33	0	1305	0	ANGEL1	14	77274402	Frame_Shift_Del	DEL	GAGTGAACTG	TCGA-B3-4103-01A-01D-1458-08	25092297	77274402	30075138	31	5765											
TMC3	342125	hgsc.bcm.edu	37	chr15	81648105	81648105	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctcctgttcttccaatataGcttcctttaagaaaaataca	13	15	3	10	0	2	1	0	0	2	1	5	1	4	1	3	0	2	2	3	0	7	8			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr15:81648105G>A	ENST00000359440.5	-	9	1031	c.896C>T	c.(895-897)gCt>gTt	p.A299V	RP11-761I4.3_ENST00000560851.1_RNA|RP11-761I4.3_ENST00000559781.1_RNA|TMC3_ENST00000558726.1_Missense_Mutation_p.A299V	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						TTCCAATATAGCTTCCTTTAA	0.284																																					p.A299V		Atlas-SNP	.											.	TMC3	112	.	0			c.C896T						PASS	.						120	114	116					15																	81648105		1789	4056	5845	SO:0001583	missense	342125	exon9			AATATAGCTTCCT	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.896C>T	chr15.hg19:g.81648105G>A	ENSP00000352413:p.Ala299Val	89.0	0.0	.		112.0	35.0	.	NM_001080532		Missense_Mutation	SNP	ENST00000359440.5	hg19	CCDS45324.1	.	.	.	.	.	.	.	.	.	.	G	15.67	2.901887	0.52227	.	.	ENSG00000188869	ENST00000359440	T	0.21191	2.02	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.37183	0.0994	L	0.54965	1.715	0.58432	D	0.999997	D;D	0.58970	0.984;0.973	P;P	0.56514	0.785;0.8	T	0.15037	-1.0451	10	0.72032	D	0.01	-13.4261	16.9402	0.86216	0.0:0.0:1.0:0.0	.	299;299	Q7Z5M5-2;Q7Z5M5	.;TMC3_HUMAN	V	299	ENSP00000352413:A299V	ENSP00000352413:A299V	A	-	2	0	TMC3	79435160	1.000000	0.71417	0.925000	0.36789	0.111000	0.19643	6.165000	0.71891	2.408000	0.81797	0.555000	0.69702	GCT	.	.	.	none		0.284	TMC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417795.3	NM_181841		A	81648105	G	A	81648105	3	1	90	1	0	0	0	0	1	0	0	0	15998	971	34	2	2462	2	TMC3	15	81648105	Missense_Mutation	SNP	G	TCGA-B3-4103-01A-01D-1458-08		81648105	20883287	32	5766											
ADAMTS17	170691	hgsc.bcm.edu	37	chr15	100657190	100657190	+	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	cgcatgttctacactggcacCcgggcagtgtgtgcctccag	6	9	12	14	2	1	0	0	0	1	0	2	0	2	0	3	2	2	4	3	2	1	2			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr15:100657190C>T	ENST00000268070.4	-	13	1855	c.1750G>A	c.(1750-1752)Ggt>Agt	p.G584S		NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	584	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)	50	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		ACACTGGCACCCGGGCAGTGT	0.632																																					p.G584S		Atlas-SNP	.											.	ADAMTS17	127	.	0			c.G1750A						PASS	.						39	33	35					15																	100657190		2203	4300	6503	SO:0001583	missense	170691	exon13			TGGCACCCGGGCA	AJ315735	CCDS10383.1	15q24	2014-01-28	2005-08-19		ENSG00000140470	ENSG00000140470		"ADAM metallopeptidases with thrombospondin type 1 motif"	17109	protein-coding gene	gene with protein product		607511	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17"			11867212	Standard	NM_139057		Approved	FLJ32769, FLJ16363	uc002bvv.1	Q8TE56	OTTHUMG00000149867	ENST00000268070.4:c.1750G>A	chr15.hg19:g.100657190C>T	ENSP00000268070:p.Gly584Ser	65.0	0.0	.		50.0	20.0	.	NM_139057	Q2I7G4|Q6ZN75	Missense_Mutation	SNP	ENST00000268070.4	hg19	CCDS10383.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.259132	0.80246	.	.	ENSG00000140470	ENST00000268070;ENST00000378898	T	0.60672	0.17	5.18	5.18	0.71444	.	0.141210	0.47852	D	0.000203	T	0.69459	0.3113	M	0.88450	2.955	0.54753	D	0.999987	P;B	0.38473	0.633;0.251	B;B	0.40375	0.327;0.108	T	0.77120	-0.2705	10	0.87932	D	0	.	18.7048	0.91633	0.0:1.0:0.0:0.0	.	341;584	Q8TE56-2;Q8TE56	.;ATS17_HUMAN	S	584;341	ENSP00000268070:G584S	ENSP00000268070:G584S	G	-	1	0	ADAMTS17	98474713	0.870000	0.30015	0.451000	0.26982	0.858000	0.48976	2.708000	0.47152	2.419000	0.82065	0.655000	0.94253	GGT	.	.	.	none		0.632	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1	NM_139057		T	100657190	C	T	100657190	3	4	90	1	0	0	0	0	1	0	0	0	262	623	22	2	1577	2	ADAMTS17	15	100657190	Missense_Mutation	SNP	C	TCGA-B3-4103-01A-01D-1458-08	19009085	100657190	1874202	33	5767											
IFT140	9742	hgsc.bcm.edu	37	chr16	1608090	1608090	+	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	ggacaccatctgagggatgtGgtggcacccaggctccacct	8	7	13	13	0	1	1	0	1	1	0	2	3	2	3	4	5	0	2	4	5	0	0			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr16:1608090G>T	ENST00000426508.2	-	19	2608	c.2245C>A	c.(2245-2247)Cac>Aac	p.H749N	IFT140_ENST00000439987.2_5'UTR	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	749					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)				TGAGGGATGTGGTGGCACCCA	0.552																																					p.H749N		Atlas-SNP	.											.	IFT140	128	.	0			c.C2245A						PASS	.						149	145	146					16																	1608090		2199	4300	6499	SO:0001583	missense	9742	exon19			GGATGTGGTGGCA	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.2245C>A	chr16.hg19:g.1608090G>T	ENSP00000406012:p.His749Asn	421.0	1.0	.		568.0	163.0	.	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Missense_Mutation	SNP	ENST00000426508.2	hg19	CCDS10439.1	.	.	.	.	.	.	.	.	.	.	G	9.526	1.109524	0.20714	.	.	ENSG00000187535	ENST00000397417;ENST00000426508;ENST00000439987	T	0.41400	1.0	5.0	-3.73	0.04398	.	0.869820	0.10298	N	0.691510	T	0.15912	0.0383	N	0.08118	0	0.09310	N	1	B;B	0.23735	0.017;0.09	B;B	0.26416	0.021;0.069	T	0.23048	-1.0199	10	0.17832	T	0.49	.	1.4862	0.02447	0.393:0.097:0.2946:0.2155	.	749;474	Q96RY7;B4DR58	IF140_HUMAN;.	N	749	ENSP00000406012:H749N	ENSP00000380562:H749N	H	-	1	0	IFT140	1548091	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	-0.055000	0.11807	-1.123000	0.02940	0.563000	0.77884	CAC	.	.	.	none		0.552	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714		T	1608090	G	T	1608090	3	4	90	1	0	0	0	0	1	0	0	0	7563	1348	47	4	2195	4	IFT140	16	1608090	Missense_Mutation	SNP	G	TCGA-B3-4103-01A-01D-1458-08		1608090	88746663	34	5768											
ASGR1	432	hgsc.bcm.edu	37	chr17	7081872	7081872	+	Missense_Mutation	SNP	T	T	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	gatgctgaaggtcttgatacTccttggtcatgatagggctg	8	13	13	7	0	2	3	1	3	1	0	3	4	3	3	1	3	2	2	1	3	3	4			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr17:7081872T>G	ENST00000269299.3	-	2	410	c.11A>C	c.(10-12)gAg>gCg	p.E4A	ASGR1_ENST00000380920.4_5'Flank|ASGR1_ENST00000572879.1_5'Flank|ASGR1_ENST00000574388.1_Missense_Mutation_p.E4A	NM_001197216.2|NM_001671.4	NP_001184145.1|NP_001662.1	P07306	ASGR1_HUMAN	asialoglycoprotein receptor 1	4					cellular response to extracellular stimulus (GO:0031668)|receptor-mediated endocytosis (GO:0006898)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	asialoglycoprotein receptor activity (GO:0004873)|carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)|urinary_tract(1)	10						GTCTTGATACTCCTTGGTCAT	0.577																																					p.E4A		Atlas-SNP	.											.	ASGR1	20	.	0			c.A11C						PASS	.						129	90	103					17																	7081872		2203	4300	6503	SO:0001583	missense	432	exon2			TGATACTCCTTGG		CCDS11089.1, CCDS56017.1	17p13-p11	2011-08-30			ENSG00000141505	ENSG00000141505		"C-type lectin domain containing"	742	protein-coding gene	gene with protein product		108360					Standard	NM_001671		Approved	CLEC4H1	uc002ges.4	P07306	OTTHUMG00000102159	ENST00000269299.3:c.11A>C	chr17.hg19:g.7081872T>G	ENSP00000269299:p.Glu4Ala	92.0	0.0	.		124.0	60.0	.	NM_001671	I3L1X1	Missense_Mutation	SNP	ENST00000269299.3	hg19	CCDS11089.1	.	.	.	.	.	.	.	.	.	.	T	14.43	2.533519	0.45073	.	.	ENSG00000141505	ENST00000269299;ENST00000380920	T	0.01015	5.44	4.43	4.43	0.53597	.	0.332135	0.21660	N	0.071026	T	0.00724	0.0024	N	0.14661	0.345	0.80722	D	1	B	0.30741	0.293	B	0.22386	0.039	T	0.73212	-0.4054	10	0.32370	T	0.25	.	10.0445	0.42177	0.0:0.0:0.0:1.0	.	4	P07306	ASGR1_HUMAN	A	4	ENSP00000269299:E4A	ENSP00000269299:E4A	E	-	2	0	ASGR1	7022596	0.996000	0.38824	0.991000	0.47740	0.852000	0.48524	3.429000	0.52800	1.875000	0.54330	0.449000	0.29647	GAG	.	.	.	none		0.577	ASGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220004.3	NM_001671		G	7081872	T	G	7081872	3	3	90	1	0	0	0	0	1	0	0	0	1039	1551	54	5	896	5	ASGR1	17	7081872	Missense_Mutation	SNP	T	TCGA-B3-4103-01A-01D-1458-08		7081872	74113338	35	5769											
PFAS	5198	hgsc.bcm.edu	37	chr17	8170542	8170542	+	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	ctttcccaaagcctccgtgcCccgtgagcctggtgagggag	6	8	13	14	2	0	2	0	2	0	0	2	3	2	3	6	2	3	0	6	2	1	1			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr17:8170542C>T	ENST00000314666.6	+	24	3297	c.3164C>T	c.(3163-3165)cCc>cTc	p.P1055L	PFAS_ENST00000545834.1_Missense_Mutation_p.P631L	NM_012393.2	NP_036525.1	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	1055					'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)	GCCTCCGTGCCCCGTGAGCCT	0.677																																					p.P1055L		Atlas-SNP	.											.	PFAS	91	.	0			c.C3164T						PASS	.						18	17	17					17																	8170542		2201	4299	6500	SO:0001583	missense	5198	exon24			CCGTGCCCCGTGA	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.3164C>T	chr17.hg19:g.8170542C>T	ENSP00000313490:p.Pro1055Leu	21.0	0.0	.		44.0	13.0	.	NM_012393	A6H8V8	Missense_Mutation	SNP	ENST00000314666.6	hg19	CCDS11136.1	.	.	.	.	.	.	.	.	.	.	C	6.971	0.549059	0.13312	.	.	ENSG00000178921	ENST00000545834;ENST00000314666;ENST00000546020	T;T	0.33216	1.42;2.17	5.57	4.6	0.57074	AIR synthase-related protein, C-terminal (1);	0.289920	0.33959	N	0.004381	T	0.20495	0.0493	N	0.22421	0.69	0.48452	D	0.999654	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.04509	-1.0946	10	0.87932	D	0	-5.7605	8.6639	0.34110	0.0:0.8278:0.0:0.1722	.	1055;1055	A8K8N7;O15067	.;PUR4_HUMAN	L	631;1055;464	ENSP00000441706:P631L;ENSP00000313490:P1055L	ENSP00000313490:P1055L	P	+	2	0	PFAS	8111267	0.561000	0.26578	0.827000	0.32855	0.173000	0.22820	1.670000	0.37502	1.368000	0.46115	0.655000	0.94253	CCC	.	.	.	none		0.677	PFAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226994.2			T	8170542	C	T	8170542	3	4	90	1	0	0	0	0	1	0	0	0	11761	623	22	2	3254	2	PFAS	17	8170542	Missense_Mutation	SNP	C	TCGA-B3-4103-01A-01D-1458-08	1088670	8170542	73024668	36	5770											
PIPOX	51268	hgsc.bcm.edu	37	chr17	27370356	27370357	+	Splice_Site	INS	-	-	G																															aggatcctcctgctggagcaINSggtactgtgtcccttctgca																										TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr17:27370356_27370357insG	ENST00000323372.4	+	1	439_440	c.113_114insG	c.(112-117)cagttc>caGgttc	p.F39fs	PIPOX_ENST00000583215.1_Intron	NM_016518.2	NP_057602.2	Q9P0Z9	SOX_HUMAN	pipecolic acid oxidase	39					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)	CTGCTGGAGCAGGTACTGTGTC	0.584																																					p.Q38fs		Atlas-INDEL	.											.	PIPOX	42	.	0			c.113_114insG						PASS	.																																			SO:0001630	splice_region_variant	51268	exon1			.	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.114+1->G	chr17.hg19:g.27370358_27370358dupG		91.0	0.0	0		156.0	78.0	0.5	NM_016518	B3KNH0|Q96H28|Q9C070	Frame_Shift_Ins	INS	ENST00000323372.4	hg19	CCDS11248.1																																																																																			.	.	.	none		0.584	PIPOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255954.1	NM_016518	Frame_Shift_Ins	G	27370357	-	G	27370356	8	5	90	1	0	1	1	0	0	0	1	0	11950	202	7	0	115	0	PIPOX	17	27370356	Splice_Site	INS	-	TCGA-B3-4103-01A-01D-1458-08	19199814	27370356	53824854	37	5771											
ACE	1636	hgsc.bcm.edu	37	chr17	61562641	61562641	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccagcaagtttgtggaggaaTatgaccggacatcccaggtg	11	8	13	9	1	0	1	0	1	0	0	1	4	1	4	3	4	1	2	3	4	3	2			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr17:61562641T>C	ENST00000290866.4	+	13	1990	c.1966T>C	c.(1966-1968)Tat>Cat	p.Y656H	ACE_ENST00000577647.1_Missense_Mutation_p.Y82H|ACE_ENST00000428043.1_Missense_Mutation_p.Y656H|ACE_ENST00000490216.2_Missense_Mutation_p.Y82H|ACE_ENST00000421982.2_5'UTR|ACE_ENST00000290863.6_Missense_Mutation_p.Y82H|ACE_ENST00000413513.3_Missense_Mutation_p.Y82H	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	656	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)	TGTGGAGGAATATGACCGGAC	0.552																																					p.Y656H		Atlas-SNP	.											.	ACE	187	.	0			c.T1966C						PASS	.						165	123	137					17																	61562641		2203	4300	6503	SO:0001583	missense	1636	exon13			GAGGAATATGACC	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.1966T>C	chr17.hg19:g.61562641T>C	ENSP00000290866:p.Tyr656His	91.0	0.0	.		111.0	52.0	.	NM_000789	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Missense_Mutation	SNP	ENST00000290866.4	hg19	CCDS11637.1	.	.	.	.	.	.	.	.	.	.	T	14.19	2.460662	0.43736	.	.	ENSG00000159640	ENST00000290866;ENST00000428043;ENST00000290863;ENST00000413513	T;T;T;T	0.48836	0.8;0.8;0.8;0.8	5.09	5.09	0.68999	.	0.060975	0.64402	D	0.000002	T	0.71031	0.3292	M	0.86864	2.845	0.80722	D	1	D;D;P;D	0.76494	0.971;0.998;0.881;0.999	P;D;P;D	0.85130	0.887;0.997;0.843;0.994	T	0.75584	-0.3267	10	0.54805	T	0.06	-20.9481	12.3936	0.55373	0.0:0.0:0.0:1.0	.	82;656;82;656	B4DXI3;P12821-2;P12821-3;P12821	.;.;.;ACE_HUMAN	H	656;656;82;82	ENSP00000290866:Y656H;ENSP00000397593:Y656H;ENSP00000290863:Y82H;ENSP00000392247:Y82H	ENSP00000290863:Y82H	Y	+	1	0	ACE	58916373	1.000000	0.71417	1.000000	0.80357	0.861000	0.49209	4.885000	0.63142	1.919000	0.55581	0.379000	0.24179	TAT	.	.	.	none		0.552	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2			C	61562641	T	C	61562641	3	2	90	1	0	0	0	0	1	0	0	0	136	1406	49	3	2219	3	ACE	17	61562641	Missense_Mutation	SNP	T	TCGA-B3-4103-01A-01D-1458-08	34192285	61562641	19632569	38	5772											
DAZAP1	26528	hgsc.bcm.edu	37	chr19	1428875	1428875	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agctgagcctcgggacagcaAgagccaagcgccgggacagc	11	2	15	13	3	0	2	0	1	0	1	1	4	0	4	3	2	6	2	3	2	2	0			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr19:1428875A>G	ENST00000233078.4	+	8	742	c.581A>G	c.(580-582)aAg>aGg	p.K194R	DAZAP1_ENST00000586579.1_3'UTR|DAZAP1_ENST00000336761.6_Missense_Mutation_p.K194R	NM_018959.2	NP_061832.2	Q96EP5	DAZP1_HUMAN	DAZ associated protein 1	194					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)		CGGGACAGCAAGAGCCAAGCG	0.657																																					p.K194R		Atlas-SNP	.											.	DAZAP1	52	.	0			c.A581G						PASS	.						37	46	43					19																	1428875		2203	4300	6503	SO:0001583	missense	26528	exon8			ACAGCAAGAGCCA		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.581A>G	chr19.hg19:g.1428875A>G	ENSP00000233078:p.Lys194Arg	80.0	0.0	.		87.0	26.0	.	NM_018959	Q96MJ3|Q9NRR9	Missense_Mutation	SNP	ENST00000233078.4	hg19	CCDS12065.1	.	.	.	.	.	.	.	.	.	.	A	15.03	2.711305	0.48517	.	.	ENSG00000071626	ENST00000233078;ENST00000336761	T;T	0.73363	-0.74;-0.74	5.03	5.03	0.67393	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	T	0.74891	0.3776	N	0.24115	0.695	0.80722	D	1	P;B;B	0.46578	0.88;0.073;0.119	P;B;B	0.62184	0.899;0.014;0.031	T	0.71573	-0.4552	10	0.22109	T	0.4	.	13.948	0.64099	1.0:0.0:0.0:0.0	.	261;194;194	Q5IRN4;Q96EP5;Q96EP5-2	.;DAZP1_HUMAN;.	R	194	ENSP00000233078:K194R;ENSP00000337132:K194R	ENSP00000233078:K194R	K	+	2	0	DAZAP1	1379875	1.000000	0.71417	0.983000	0.44433	0.941000	0.58515	6.547000	0.73892	1.906000	0.55180	0.459000	0.35465	AAG	.	.	.	none		0.657	DAZAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449522.3	NM_170711		G	1428875	A	G	1428875	3	3	90	1	0	0	0	0	1	0	0	0	4246	72	3	3	611	3	DAZAP1	19	1428875	Missense_Mutation	SNP	A	TCGA-B3-4103-01A-01D-1458-08		1428875	57700108	39	5773											
EEF2	1938	hgsc.bcm.edu	37	chr19	3979985	3979985	+	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	cgtcttcaccaggaactggtCcacgcccacgaggcccacaa	10	5	9	17	3	2	0	1	0	1	0	3	2	3	1	4	3	1	0	4	3	2	1			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr19:3979985C>T	ENST00000309311.6	-	10	1514	c.1426G>A	c.(1426-1428)Gac>Aac	p.D476N	SNORD37_ENST00000384048.1_RNA	NM_001961.3	NP_001952.1	P13639	EF2_HUMAN	eukaryotic translation elongation factor 2	476					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)		AGGAACTGGTCCACGCCCACG	0.592																																					p.D476N	Colon(165;1804 1908 4071 6587 18799)	Atlas-SNP	.											.	EEF2	57	.	0			c.G1426A						PASS	.						69	57	61					19																	3979985		2203	4300	6503	SO:0001583	missense	1938	exon10			ACTGGTCCACGCC	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.1426G>A	chr19.hg19:g.3979985C>T	ENSP00000307940:p.Asp476Asn	85.0	0.0	.		76.0	23.0	.	NM_001961	B2RMP5|D6W618|Q58J86	Missense_Mutation	SNP	ENST00000309311.6	hg19	CCDS12117.1	.	.	.	.	.	.	.	.	.	.	C	35	5.492373	0.96339	.	.	ENSG00000167658	ENST00000543343;ENST00000309311	D	0.82255	-1.59	5.45	5.45	0.79879	Translation elongation factor EFTu/EF1A, domain 2 (1);Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.000000	0.85682	D	0.000000	D	0.95239	0.8456	H	0.98965	4.385	0.80722	D	1	D	0.69078	0.997	D	0.83275	0.996	D	0.97201	0.9864	10	0.87932	D	0	-55.7781	18.2479	0.89993	0.0:1.0:0.0:0.0	.	476	P13639	EF2_HUMAN	N	476	ENSP00000307940:D476N	ENSP00000307940:D476N	D	-	1	0	EEF2	3930985	1.000000	0.71417	0.999000	0.59377	0.932000	0.56968	7.773000	0.85462	2.555000	0.86185	0.561000	0.74099	GAC	.	.	.	none		0.592	EEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457615.2	NM_001961		T	3979985	C	T	3979985	3	4	90	1	0	0	0	0	1	0	0	0	4931	855	30	2	1174	2	EEF2	19	3979985	Missense_Mutation	SNP	C	TCGA-B3-4103-01A-01D-1458-08	2551110	3979985	55148998	40	5774											
FBN3	84467	hgsc.bcm.edu	37	chr19	8182139	8182139	+	Frame_Shift_Del	DEL	T	T	-																															cagtgttaatacagtgcacgTcacacccaccattctggacc																										TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr19:8182139delT	ENST00000600128.1	-	28	3914	c.3500delA	c.(3499-3501)gacfs	p.D1167fs	FBN3_ENST00000601739.1_Frame_Shift_Del_p.D1167fs|FBN3_ENST00000270509.2_Frame_Shift_Del_p.D1167fs			Q75N90	FBN3_HUMAN	fibrillin 3	1167	EGF-like 16; 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						ACAGTGCACGTCACACCCACC	0.637																																					p.D1167fs		Atlas-INDEL	.											.	FBN3	300	.	0			c.3501delC						PASS	.						82	67	72					19																	8182139		2203	4300	6503	SO:0001589	frameshift_variant	84467	exon27			.		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.3500delA	chr19.hg19:g.8182139delT	ENSP00000470498:p.Asp1167fs	86.0	0.0	0		62.0	14.0	0.225806	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Frame_Shift_Del	DEL	ENST00000600128.1	hg19	CCDS12196.1																																																																																			.	.	.	none		0.637	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		-	8182139	T	-	8182139	7	5	90	1	0	1	0	1	0	0	0	0	5711	1667	58	0	5077	0	FBN3	19	8182139	Frame_Shift_Del	DEL	T	TCGA-B3-4103-01A-01D-1458-08	4202154	8182139	50946844	41	5775											
EIF3G	8666	hgsc.bcm.edu	37	chr19	10230530	10230530	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actcactcaaagtctccagtAggcatcgcaaaaagtattct	14	10	6	11	1	4	0	2	0	2	0	6	0	4	0	1	1	0	4	1	1	5	3			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr19:10230530A>G	ENST00000253108.4	-	1	48	c.6T>C	c.(4-6)ccT>ccC	p.P2P	EIF3G_ENST00000587168.1_5'Flank	NM_003755.3	NP_003746.2			eukaryotic translation initiation factor 3, subunit G											central_nervous_system(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(20;3.53e-09)|Epithelial(33;4.91e-06)|all cancers(31;1.1e-05)			AGTCTCCAGTAGGCATCGCAA	0.642											OREG0025231	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P2P	Colon(124;1100 1638 3822 4510 4876)	Atlas-SNP	.											.	EIF3G	16	.	0			c.T6C						PASS	.						57	60	59					19																	10230530		2203	4300	6503	SO:0001819	synonymous_variant	8666	exon1			TCCAGTAGGCATC	U96074	CCDS12227.1	19p13.2	2013-02-12	2007-07-27	2007-07-27		ENSG00000130811		"RNA binding motif (RRM) containing"	3274	protein-coding gene	gene with protein product		603913	"eukaryotic translation initiation factor 3, subunit 4 delta, 44kDa"	EIF3S4		9822659	Standard	NM_003755		Approved	eIF3-delta, eIF3-p44, eIF3g	uc002mnd.3	O75821		ENST00000253108.4:c.6T>C	chr19.hg19:g.10230530A>G		120.0	0.0	.	663	114.0	27.0	.	NM_003755		Silent	SNP	ENST00000253108.4	hg19	CCDS12227.1																																																																																			.	.	.	none		0.642	EIF3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451144.1			G	10230530	A	G	10230530	2	3	90	1	0	0	0	0	0	0	0	1	5019	407	15	3		3	EIF3G	19	10230530	Silent	SNP	A	TCGA-B3-4103-01A-01D-1458-08	2048391	10230530	48898453	42	5776											
ZNF627	199692	hgsc.bcm.edu	37	chr19	11728624	11728624	+	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	gtcgatccacttactttcgaGtacatgaaaaaattcatact	14	13	5	9	2	1	1	1	1	0	0	4	3	2	1	1	0	3	1	1	0	6	5			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr19:11728624G>T	ENST00000361113.5	+	4	1514	c.1306G>T	c.(1306-1308)Gta>Tta	p.V436L	ZNF627_ENST00000588174.1_3'UTR	NM_145295.3	NP_660338.1	Q7L945	ZN627_HUMAN	zinc finger protein 627	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)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14						TTACTTTCGAGTACATGAAAA	0.423																																					p.V436L	Melanoma(112;173 1614 10731 17751 23322)	Atlas-SNP	.											.	ZNF627	43	.	0			c.G1306T						PASS	.						55	59	57					19																	11728624		2198	4297	6495	SO:0001583	missense	199692	exon4			TTTCGAGTACATG	AK074846	CCDS42502.1	19p13.2	2013-01-08				ENSG00000198551		"Zinc fingers, C2H2-type", "-"	30570	protein-coding gene	gene with protein product		612248				12477932	Standard	NM_145295		Approved	FLJ90365	uc002msk.2	Q7L945		ENST00000361113.5:c.1306G>T	chr19.hg19:g.11728624G>T	ENSP00000354414:p.Val436Leu	186.0	0.0	.		149.0	38.0	.	NM_145295	O14846|Q4KMP9|Q6NT81|Q9BRG4	Missense_Mutation	SNP	ENST00000361113.5	hg19	CCDS42502.1	.	.	.	.	.	.	.	.	.	.	g	3.954	-0.011756	0.07727	.	.	ENSG00000198551	ENST00000361113	T	0.07908	3.15	1.43	-2.1	0.07210	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04588	0.0125	N	0.25825	0.765	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44345	-0.9334	9	0.23302	T	0.38	.	3.0288	0.06099	0.5661:0.2481:0.1857:0.0	.	436	Q7L945	ZN627_HUMAN	L	436	ENSP00000354414:V436L	ENSP00000354414:V436L	V	+	1	0	ZNF627	11589624	0.000000	0.05858	0.000000	0.03702	0.781000	0.44180	-2.946000	0.00680	-0.450000	0.07107	-0.670000	0.03821	GTA	.	.	.	none		0.423	ZNF627-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458875.1	NM_145295		T	11728624	G	T	11728624	3	4	90	1	0	0	0	0	1	0	0	0	18063	1029	36	4	1320	4	ZNF627	19	11728624	Missense_Mutation	SNP	G	TCGA-B3-4103-01A-01D-1458-08	1498094	11728624	47400359	43	5777											
SLC5A3	6526	hgsc.bcm.edu	37	chr21	35467607	35467607	+	Missense_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	atctaatagaagcaccgtgaGtggatacttcctggcggggc	10	9	13	9	2	1	2	0	1	1	1	2	3	2	3	2	4	2	1	2	4	4	4			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr21:35467607G>A	ENST00000381151.3	+	2	622	c.110G>A	c.(109-111)aGt>aAt	p.S37N	AP000320.7_ENST00000362077.4_RNA|MRPS6_ENST00000399312.2_Intron|SLC5A3_ENST00000608209.1_Missense_Mutation_p.S37N			P53794	SC5A3_HUMAN	solute carrier family 5 (sodium/myo-inositol cotransporter), member 3	37					inositol metabolic process (GO:0006020)|peripheral nervous system development (GO:0007422)|regulation of respiratory gaseous exchange (GO:0043576)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	myo-inositol:sodium symporter activity (GO:0005367)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	20						AGCACCGTGAGTGGATACTTC	0.488																																					p.S37N		Atlas-SNP	.											.	SLC5A3	52	.	0			c.G110A						PASS	.						169	168	169					21																	35467607		2203	4300	6503	SO:0001583	missense	6526	exon2			CCGTGAGTGGATA		CCDS33549.1	21q22.11	2013-05-22	2008-09-02		ENSG00000198743	ENSG00000198743		"Solute carriers"	11038	protein-coding gene	gene with protein product		600444	"solute carrier family 5 (inositol transporter), member 3"			7789985	Standard	NM_006933		Approved	SMIT, SMIT1	uc002yto.3	P53794	OTTHUMG00000065821	ENST00000381151.3:c.110G>A	chr21.hg19:g.35467607G>A	ENSP00000370543:p.Ser37Asn	265.0	0.0	.		308.0	107.0	.	NM_006933	O43489	Missense_Mutation	SNP	ENST00000381151.3	hg19	CCDS33549.1	.	.	.	.	.	.	.	.	.	.	G	14.33	2.502590	0.44455	.	.	ENSG00000198743	ENST00000381151	D	0.86497	-2.13	6.09	6.09	0.99107	.	0.000000	0.85682	D	0.000000	D	0.84252	0.5431	L	0.42487	1.325	0.52099	D	0.999947	B	0.27286	0.174	B	0.20767	0.031	T	0.80355	-0.1417	10	0.56958	D	0.05	.	19.2541	0.93938	0.0:0.0:1.0:0.0	.	37	P53794	SC5A3_HUMAN	N	37	ENSP00000370543:S37N	ENSP00000370543:S37N	S	+	2	0	SLC5A3	34389477	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.594000	0.98254	2.898000	0.99336	0.596000	0.82720	AGT	.	.	.	none		0.488	SLC5A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000141037.1			A	35467607	G	A	35467607	3	1	90	1	0	0	0	0	1	0	0	0	14679	1029	36	2	112	2	SLC5A3	21	35467607	Missense_Mutation	SNP	G	TCGA-B3-4103-01A-01D-1458-08		35467607	12662288	44	5778											
SUSD2	56241	hgsc.bcm.edu	37	chr22	24581140	24581140	+	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	ttccgagaggaccctgtggcCtgggcacgaactcagtgcca	8	7	13	13	2	1	1	1	0	0	1	2	4	2	2	4	3	2	1	4	3	1	1			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr22:24581140C>A	ENST00000358321.3	+	6	1122	c.861C>A	c.(859-861)gcC>gcA	p.A287A		NM_019601.3	NP_062547.1	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2	287	AMOP. {ECO:0000255|PROSITE- ProRule:PRU00347}.				immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	26						ACCCTGTGGCCTGGGCACGAA	0.662																																					p.A287A		Atlas-SNP	.											.	SUSD2	68	.	0			c.C861A						PASS	.						29	30	30					22																	24581140		2203	4299	6502	SO:0001819	synonymous_variant	56241	exon6			TGTGGCCTGGGCA	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.861C>A	chr22.hg19:g.24581140C>A		79.0	0.0	.		69.0	21.0	.	NM_019601	Q9H5Y6	Silent	SNP	ENST00000358321.3	hg19	CCDS13824.1																																																																																			.	.	.	none		0.662	SUSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320088.1	NM_019601		A	24581140	C	A	24581140	2	1	90	1	0	0	0	0	0	0	0	1	15420	668	24	4		4	SUSD2	22	24581140	Silent	SNP	C	TCGA-B3-4103-01A-01D-1458-08		24581140	26723426	45	5779											
EP300	2033	hgsc.bcm.edu	37	chr22	41574679	41574681	+	In_Frame_Del	DEL	CCC	CCC	-																															ctccacggccacagtcccagCccccccactccagtccttcc																										TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	CCC	CCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr22:41574679_41574681delCCC	ENST00000263253.7	+	31	8183_8185	c.6964_6966delCCC	c.(6964-6966)cccdel	p.P2323del	RP1-85F18.6_ENST00000415054.1_RNA|RP1-85F18.5_ENST00000420537.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	2323					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						ACAGTCCCAGCCCCCCCACTCCA	0.616			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.2321_2322del		Atlas-INDEL	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300	367	.	0			c.6963_6965del						PASS	.																																			SO:0001651	inframe_deletion	2033	exon31	Familial Cancer Database	Broad Thumb-Hallux syndrome	.	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.6964_6966delCCC	chr22.hg19:g.41574682_41574684delCCC	ENSP00000263253:p.Pro2323del	135.0	0.0	0		146.0	38.0	0.260274	NM_001429	B1AKC2	In_Frame_Del	DEL	ENST00000263253.7	hg19	CCDS14010.1																																																																																			.	.	.	none		0.616	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		-	41574681	CCC	-	41574679	7	5	90	1	0	1	0	1	0	0	0	0	5150	739	26	0	7086	0	EP300	22	41574679	In_Frame_Del	DEL	CCC	TCGA-B3-4103-01A-01D-1458-08	16993539	41574679	9729887	46	5780											
TTLL1	25809	hgsc.bcm.edu	37	chr22	43442517	43442517	+	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	atgttgagggtgtcattaatCaggttgtacttgaggattcg	9	15	13	4	1	2	2	2	2	0	0	3	3	2	3	0	3	1	3	0	3	2	6			TCGA-B3-4103-01A-01D-1458-08	TCGA-B3-4103-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	62fba643-8f61-4d98-afe1-fbfeca74cdfa	3fbd8531-47c5-4f07-9928-0b4e7cd5aad5	g.chr22:43442517C>G	ENST00000266254.7	-	10	1281	c.1041G>C	c.(1039-1041)ctG>ctC	p.L347L	TTLL1_ENST00000331018.7_Silent_p.L318L|AL022476.2_ENST00000443063.1_RNA	NM_012263.4	NP_036395.1	O95922	TTLL1_HUMAN	tubulin tyrosine ligase-like family, member 1	347	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)		TGTCATTAATCAGGTTGTACT	0.512																																					p.L347L		Atlas-SNP	.											.	TTLL1	41	.	0			c.G1041C						PASS	.						365	313	331					22																	43442517		2203	4300	6503	SO:0001819	synonymous_variant	25809	exon10			ATTAATCAGGTTG	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.1041G>C	chr22.hg19:g.43442517C>G		317.0	0.0	.		301.0	13.0	.	NM_012263	B2RDS7|Q9BR27|Q9NRS9|Q9UMU0	Silent	SNP	ENST00000266254.7	hg19	CCDS14043.1	.	.	.	.	.	.	.	.	.	.	C	3.860	-0.030135	0.07543	.	.	ENSG00000100271	ENST00000495814	.	.	.	5.41	0.463	0.16700	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.2216	0.15371	0.1717:0.307:0.4416:0.0796	.	.	.	.	S	273	.	.	X	-	2	2	TTLL1	41772461	0.997000	0.39634	0.466000	0.27168	0.403000	0.30841	0.331000	0.19733	0.219000	0.20840	0.555000	0.69702	TGA	.	.	.	none		0.512	TTLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319659.1	NM_012263		G	43442517	C	G	43442517	2	3	90	1	0	0	0	0	0	0	0	1	16734	813	29	4		4	TTLL1	22	43442517	Silent	SNP	C	TCGA-B3-4103-01A-01D-1458-08	1867838	43442517	7862049	47	5781											
CCNL2	81669	hgsc.bcm.edu	37	chr1	1334456	1334456	+	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	agctcgcagcccaccacgcgGaggtcggtctctgtgtcggt	5	8	14	14	5	1	0	0	0	1	0	5	1	1	1	2	4	2	2	2	4	0	0	rs374243154		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:1334456G>A	ENST00000400809.3	-	1	236	c.231C>T	c.(229-231)ctC>ctT	p.L77L	RP4-758J18.2_ENST00000444362.1_5'Flank|MRPL20_ENST00000493287.1_5'Flank|CCNL2_ENST00000408918.4_Silent_p.L77L|RP4-758J18.2_ENST00000448629.2_5'Flank|CCNL2_ENST00000408952.5_5'Flank|RP4-758J18.2_ENST00000576232.1_5'Flank	NM_030937.4	NP_112199.2	Q96S94	CCNL2_HUMAN	cyclin L2	77					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(3)|ovary(2)|prostate(2)	13	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.03e-36)|OV - Ovarian serous cystadenocarcinoma(86;4.17e-22)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.0023)|BRCA - Breast invasive adenocarcinoma(365;0.00465)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.146)		CCACCACGCGGAGGTCGGTCT	0.692																																					p.L77L		Atlas-SNP	.											.	CCNL2	54	.	0			c.C231T						PASS	.	G	,	0,4404		0,0,2202	52	43	46		231,231	0.9	0.1	1		46	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous	CCNL2	NM_001039577.3,NM_030937.4	,	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	,	77/227,77/521	1334456	1,13003	2202	4300	6502	SO:0001819	synonymous_variant	81669	exon1			CACGCGGAGGTCG	AF251294	CCDS30557.1, CCDS30558.1	1p36.33	2014-07-03			ENSG00000221978	ENSG00000221978			20570	protein-coding gene	gene with protein product	"cyclin S"	613482	"cyclin M"	CCNM		14725631	Standard	NM_030937		Approved	ania-6b, PCEE, SB138, HLA-ISO, CCNS	uc001afi.2	Q96S94	OTTHUMG00000002917	ENST00000400809.3:c.231C>T	chr1.hg19:g.1334456G>A		46.0	0.0	.		47.0	16.0	.	NM_030937	A8K8A3|B1B152|Q5T2N5|Q5T2N6|Q6IQ12|Q7Z4Z8|Q8N3C9|Q8N3D5|Q8NHE3|Q8TEL0|Q96B00	Silent	SNP	ENST00000400809.3	hg19	CCDS30557.1																																																																																			.	.	.	none		0.692	CCNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008146.2	NM_030937		A	1334456	G	A	1334456	2	1	91	1	0	0	0	0	0	0	0	1	2934	1161	41	2		2	CCNL2	1	1334456	Silent	SNP	G	TCGA-B3-4104-01A-01D-1458-08		1334456	247916165	1	5782											
CCNL2	81669	hgsc.bcm.edu	37	chr1	1334592	1334592	+	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	ccccgatcagcaccccctgcGaccctgagggtgcgccccca	6	4	10	21	3	1	1	1	1	0	0	1	3	1	1	7	1	3	1	7	1	0	0			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:1334592G>A	ENST00000400809.3	-	1	100	c.95C>T	c.(94-96)tCg>tTg	p.S32L	RP4-758J18.2_ENST00000444362.1_5'Flank|MRPL20_ENST00000493287.1_5'Flank|CCNL2_ENST00000408918.4_Missense_Mutation_p.S32L|RP4-758J18.2_ENST00000448629.2_5'Flank|CCNL2_ENST00000408952.5_5'Flank|RP4-758J18.2_ENST00000576232.1_5'Flank	NM_030937.4	NP_112199.2	Q96S94	CCNL2_HUMAN	cyclin L2	32					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(3)|ovary(2)|prostate(2)	13	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.03e-36)|OV - Ovarian serous cystadenocarcinoma(86;4.17e-22)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.0023)|BRCA - Breast invasive adenocarcinoma(365;0.00465)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.146)		CACCCCCTGCGACCCTGAGGG	0.711																																					p.S32L		Atlas-SNP	.											.	CCNL2	54	.	0			c.C95T						PASS	.						39	35	36					1																	1334592		2202	4300	6502	SO:0001583	missense	81669	exon1			CCCTGCGACCCTG	AF251294	CCDS30557.1, CCDS30558.1	1p36.33	2014-07-03			ENSG00000221978	ENSG00000221978			20570	protein-coding gene	gene with protein product	"cyclin S"	613482	"cyclin M"	CCNM		14725631	Standard	NM_030937		Approved	ania-6b, PCEE, SB138, HLA-ISO, CCNS	uc001afi.2	Q96S94	OTTHUMG00000002917	ENST00000400809.3:c.95C>T	chr1.hg19:g.1334592G>A	ENSP00000383611:p.Ser32Leu	49.0	0.0	.		63.0	28.0	.	NM_030937	A8K8A3|B1B152|Q5T2N5|Q5T2N6|Q6IQ12|Q7Z4Z8|Q8N3C9|Q8N3D5|Q8NHE3|Q8TEL0|Q96B00	Missense_Mutation	SNP	ENST00000400809.3	hg19	CCDS30557.1	.	.	.	.	.	.	.	.	.	.	G	9.593	1.126618	0.20959	.	.	ENSG00000221978	ENST00000400809;ENST00000408918	T;T	0.45668	1.45;0.89	2.66	1.69	0.24217	.	0.620701	0.13809	N	0.361266	T	0.34571	0.0902	L	0.50333	1.59	0.45762	D	0.998651	B;B;B;B	0.25390	0.076;0.038;0.076;0.125	B;B;B;B	0.16722	0.012;0.016;0.007;0.016	T	0.18461	-1.0336	10	0.48119	T	0.1	.	9.3386	0.38065	0.0:0.2214:0.7786:0.0	.	32;32;32;32	F2Z3J5;C9J148;Q96S94;Q96S94-2	.;.;CCNL2_HUMAN;.	L	32	ENSP00000383611:S32L;ENSP00000386158:S32L	ENSP00000383611:S32L	S	-	2	0	CCNL2	1324455	0.139000	0.22563	0.041000	0.18516	0.007000	0.05969	3.167000	0.50793	0.644000	0.30656	0.591000	0.81541	TCG	.	.	.	none		0.711	CCNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008146.2	NM_030937		A	1334592	G	A	1334592	3	1	91	1	0	0	0	0	1	0	0	0	2934	1059	37	1	1537	1	CCNL2	1	1334592	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	136	1334592	247916029	2	5783											
PLEKHG5	57449	hgsc.bcm.edu	37	chr1	6528353	6528353	+	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	agggtggaggggaaggaactCgtggggactctggggcccga	8	5	21	7	2	1	0	0	0	1	0	2	5	1	4	1	9	1	0	1	9	2	0			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:6528353C>T	ENST00000400915.3	-	21	2777	c.2711G>A	c.(2710-2712)cGa>cAa	p.R904Q	PLEKHG5_ENST00000377725.1_Missense_Mutation_p.R848Q|PLEKHG5_ENST00000377748.1_Missense_Mutation_p.R925Q|PLEKHG5_ENST00000537245.1_Missense_Mutation_p.R927Q|PLEKHG5_ENST00000377740.3_Intron|PLEKHG5_ENST00000377732.1_Missense_Mutation_p.R885Q|TNFRSF25_ENST00000461703.2_5'Flank|PLEKHG5_ENST00000535355.1_Missense_Mutation_p.R917Q|TNFRSF25_ENST00000348333.3_5'Flank|PLEKHG5_ENST00000544978.1_Missense_Mutation_p.R848Q|TNFRSF25_ENST00000351959.5_5'Flank|PLEKHG5_ENST00000400913.1_Missense_Mutation_p.R848Q|TNFRSF25_ENST00000356876.3_5'Flank|PLEKHG5_ENST00000340850.5_Missense_Mutation_p.R848Q|TNFRSF25_ENST00000377782.3_5'Flank|TNFRSF25_ENST00000351748.3_5'Flank|PLEKHG5_ENST00000377737.2_Missense_Mutation_p.R848Q|PLEKHG5_ENST00000377728.3_Missense_Mutation_p.R848Q	NM_001042663.1	NP_001036128.1	O94827	PKHG5_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 5	904					apoptotic signaling pathway (GO:0097190)|endothelial cell chemotaxis (GO:0035767)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			liver(1)	1	Ovarian(185;0.02)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;5.51e-35)|GBM - Glioblastoma multiforme(13;3.57e-27)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419)		GGAAGGAACTCGTGGGGACTC	0.662																																					p.R927Q		Atlas-SNP	.											.	PLEKHG5	66	.	0			c.G2780A						PASS	.						13	15	14					1																	6528353		2184	4290	6474	SO:0001583	missense	57449	exon21			GGAACTCGTGGGG	AK024676	CCDS79.1, CCDS41240.1, CCDS41241.1, CCDS57967.1, CCDS57968.1, CCDS57969.1	1p36.31	2014-09-17		2005-08-09	ENSG00000171680	ENSG00000171680		"Pleckstrin homology (PH) domain containing"	29105	protein-coding gene	gene with protein product	"synectin-binding guanine exchange factor"	611101				17564964	Standard	NM_001042663		Approved	KIAA0720, Syx, GEF720, Tech	uc010nzr.1	O94827	OTTHUMG00000000905	ENST00000400915.3:c.2711G>A	chr1.hg19:g.6528353C>T	ENSP00000383706:p.Arg904Gln	25.0	0.0	.		18.0	8.0	.	NM_001265592	B3KU07|B7Z2M3|B7Z5X2|F5GZ21|F5H1I0|Q5SY17|Q5T8W5|Q5T8W9|Q6ZNM0|Q7Z436|Q86YD8|Q96BS1	Missense_Mutation	SNP	ENST00000400915.3	hg19	CCDS41241.1	.	.	.	.	.	.	.	.	.	.	C	0.669	-0.802826	0.02841	.	.	ENSG00000171680	ENST00000377748;ENST00000340850;ENST00000400913;ENST00000400915;ENST00000377732;ENST00000377728;ENST00000377725;ENST00000535355;ENST00000377737;ENST00000535966;ENST00000537245;ENST00000544978	T;T;T;T;T;T;T;T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1;-0.1;-0.1;-0.1;-0.1;-0.1;-0.1;-0.1	4.88	-8.23	0.01033	.	0.885603	0.10069	N	0.719935	T	0.21921	0.0528	N	0.02539	-0.55	0.09310	N	1	B;B;B;B	0.13594	0.008;0.0;0.008;0.002	B;B;B;B	0.04013	0.001;0.0;0.001;0.0	T	0.25984	-1.0116	10	0.11182	T	0.66	-0.2459	2.6352	0.04956	0.1692:0.3187:0.354:0.158	.	917;848;925;904	F5GZ21;O94827-4;O94827-2;O94827	.;.;.;PKHG5_HUMAN	Q	925;848;848;904;885;848;848;917;848;754;927;848	ENSP00000366977:R925Q;ENSP00000344570:R848Q;ENSP00000383704:R848Q;ENSP00000383706:R904Q;ENSP00000366961:R885Q;ENSP00000366957:R848Q;ENSP00000366954:R848Q;ENSP00000441445:R917Q;ENSP00000366966:R848Q;ENSP00000439625:R927Q;ENSP00000437710:R848Q	ENSP00000344570:R848Q	R	-	2	0	PLEKHG5	6450940	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-1.455000	0.02379	-1.208000	0.02634	-2.049000	0.00408	CGA	.	.	.	none		0.662	PLEKHG5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002631.1	NM_020631		T	6528353	C	T	6528353	3	4	91	1	0	0	0	0	1	0	0	0	12080	884	31	1	485	1	PLEKHG5	1	6528353	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	5193761	6528353	242722268	3	5784											
THRAP3	9967	hgsc.bcm.edu	37	chr1	36748232	36748232	+	Missense_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	aagatctgcatcaagatctcGttctcgttcattttcgaagt	10	15	7	9	3	5	2	2	0	3	2	8	3	5	2	0	0	1	3	0	0	3	4	rs148045717		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:36748232G>A	ENST00000354618.5	+	3	292	c.68G>A	c.(67-69)cGt>cAt	p.R23H	THRAP3_ENST00000469141.2_Missense_Mutation_p.R23H	NM_005119.3	NP_005110.2	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	23	Arg-rich.|Required for mRNA splicing activation.|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)				TCAAGATCTCGTTCTCGTTCA	0.453			T	USP6	aneurysmal bone cysts																																p.R23H	Pancreas(129;785 1795 20938 23278 32581)	Atlas-SNP	.		Dom	yes		1	1p34.3	9967	thyroid hormone receptor associated protein 3 (TRAP150)		M	THRAP3,NS,malignant_melanoma,+1,1	THRAP3	93	.	0			c.G68A						PASS	.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	124	110	114		68	5.8	1	1	dbSNP_134	114	0,8600		0,0,4300	no	missense	THRAP3	NM_005119.3	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	23/956	36748232	1,13005	2203	4300	6503	SO:0001583	missense	9967	exon3			GATCTCGTTCTCG	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.68G>A	chr1.hg19:g.36748232G>A	ENSP00000346634:p.Arg23His	91.0	0.0	.		182.0	82.0	.	NM_005119	D3DPS5|Q5VTK6	Missense_Mutation	SNP	ENST00000354618.5	hg19	CCDS405.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.031760	0.93575	2.27E-4	0.0	ENSG00000054118	ENST00000354618;ENST00000469141;ENST00000478853	T;T	0.14766	2.48;2.48	5.76	5.76	0.90799	.	0.000000	0.64402	D	0.000001	T	0.36082	0.0954	L	0.55481	1.735	0.58432	D	0.999997	D	0.89917	1.0	D	0.85130	0.997	T	0.00986	-1.1490	10	0.72032	D	0.01	-8.0853	19.3309	0.94288	0.0:0.0:1.0:0.0	.	23	Q9Y2W1	TR150_HUMAN	H	23	ENSP00000346634:R23H;ENSP00000433825:R23H	ENSP00000346634:R23H	R	+	2	0	THRAP3	36520819	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.473000	0.60196	2.880000	0.98712	0.650000	0.86243	CGT	.	G|1.000;A|0.000	0.000	weak		0.453	THRAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021688.2	NM_005119		A	36748232	G	A	36748232	3	1	91	1	0	0	0	0	1	0	0	0	15886	1145	40	1	70	1	THRAP3	1	36748232	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	30219879	36748232	212502389	4	5785											
MACF1	23499	hgsc.bcm.edu	37	chr1	39910503	39910503	+	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	cagcagtaagatggaagaaaGaaaggtacagtgtatgatcc	17	7	12	5	0	0	4	0	1	0	3	1	5	1	5	1	2	2	4	1	2	6	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:39910503G>C	ENST00000372915.3	+	79	19385	c.19298G>C	c.(19297-19299)aGa>aCa	p.R6433T	MACF1_ENST00000361689.2_Missense_Mutation_p.R4475T|MACF1_ENST00000545844.1_Missense_Mutation_p.R4475T|MACF1_ENST00000567887.1_Missense_Mutation_p.R6571T|MACF1_ENST00000317713.7_Missense_Mutation_p.R4475T|MACF1_ENST00000289893.4_Missense_Mutation_p.R4977T|MACF1_ENST00000539005.1_Missense_Mutation_p.R4345T|MACF1_ENST00000564288.1_Missense_Mutation_p.R6534T			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	6433					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)			ATGGAAGAAAGAAAGGTACAG	0.418																																					p.R4475T		Atlas-SNP	.											.	MACF1	909	.	0			c.G13424C						PASS	.						105	96	99					1																	39910503		2203	4300	6503	SO:0001583	missense	23499	exon77			AAGAAAGAAAGGT	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.19298G>C	chr1.hg19:g.39910503G>C	ENSP00000362006:p.Arg6433Thr	83.0	0.0	.		109.0	49.0	.	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	34|34	5.305218|5.305218	0.95601|0.95601	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000372925|ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893	.|T;T;T;T;T;T	.|0.60920	.|0.15;0.15;0.15;0.15;0.15;0.15	6.16|6.16	6.16|6.16	0.99307|0.99307	.|.	.|0.000000	.|0.64402	.|D	.|0.000002	T|T	0.80824|0.80824	0.4697|0.4697	M|M	0.85299|0.85299	2.745|2.745	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.85130	.|0.997;0.997	T|T	0.81662|0.81662	-0.0831|-0.0831	5|10	.|0.87932	.|D	.|0	.|.	20.8598|20.8598	0.99761|0.99761	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|6433;4475	.|Q9UPN3;F8W8Q1	.|MACF1_HUMAN;.	N|T	3478|4475;6433;4475;4475;4345;4977	.|ENSP00000439537:R4475T;ENSP00000362006:R6433T;ENSP00000354573:R4475T;ENSP00000313438:R4475T;ENSP00000444364:R4345T;ENSP00000289893:R4977T	.|ENSP00000289893:R4977T	K|R	+|+	3|2	2|0	MACF1|MACF1	39683090|39683090	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.831000|7.831000	0.86748|0.86748	2.937000|2.937000	0.99478|0.99478	0.650000|0.650000	0.86243|0.86243	AAG|AGA	.	.	.	none		0.418	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		C	39910503	G	C	39910503	3	2	91	1	0	0	0	0	1	0	0	0	9151	942	33	4	19877	4	MACF1	1	39910503	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	3162271	39910503	209340118	5	5786											
ATP1A1	476	hgsc.bcm.edu	37	chr1	116931284	116931284	+	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	cccttgtgattcgaaatggtGagaaaatgagcataaatgcg	14	10	11	6	2	0	3	0	3	0	1	1	5	0	3	1	1	2	1	1	1	5	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:116931284G>A	ENST00000295598.5	+	6	778	c.526G>A	c.(526-528)Gag>Aag	p.E176K	ATP1A1_ENST00000537345.1_Missense_Mutation_p.E176K|ATP1A1_ENST00000369496.4_Missense_Mutation_p.E145K	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	176					ATP biosynthetic process (GO:0006754)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|membrane hyperpolarization (GO:0060081)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of glucocorticoid biosynthetic process (GO:0031947)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart contraction (GO:0045823)|positive regulation of striated muscle contraction (GO:0045989)|potassium ion import (GO:0010107)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of sodium ion transport (GO:0002028)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|chaperone binding (GO:0051087)|phosphatase activity (GO:0016791)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(2)|breast(2)|cervix(3)|endometrium(2)|kidney(5)|large_intestine(9)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Ciclopirox(DB01188)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Ethacrynic acid(DB00903)|Hydroflumethiazide(DB00774)|Ouabain(DB01092)|Trichlormethiazide(DB01021)	TCGAAATGGTGAGAAAATGAG	0.398																																					p.E176K		Atlas-SNP	.											.	ATP1A1	87	.	0			c.G526A						PASS	.						99	104	102					1																	116931284		2203	4300	6503	SO:0001583	missense	476	exon6			AATGGTGAGAAAA	D00099	CCDS887.1, CCDS53351.1, CCDS53352.1	1p13	2012-10-22			ENSG00000163399	ENSG00000163399	3.6.3.9	"ATPases / P-type"	799	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-1", "sodium pump subunit alpha-1", "sodium-potassium ATPase catalytic subunit alpha-1"	182310					Standard	NM_000701		Approved		uc001ege.3	P05023	OTTHUMG00000012109	ENST00000295598.5:c.526G>A	chr1.hg19:g.116931284G>A	ENSP00000295598:p.Glu176Lys	175.0	0.0	.		251.0	98.0	.	NM_000701	B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Missense_Mutation	SNP	ENST00000295598.5	hg19	CCDS887.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.528363	0.85706	.	.	ENSG00000163399	ENST00000295598;ENST00000537345;ENST00000339159;ENST00000369496	D;D;D	0.90069	-2.61;-2.61;-2.61	5.17	5.17	0.71159	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.048596	0.85682	D	0.000000	T	0.77671	0.4165	N	0.05351	-0.065	0.80722	D	1	B;B	0.25904	0.044;0.137	B;B	0.38803	0.124;0.282	T	0.75300	-0.3366	10	0.33940	T	0.23	.	18.8482	0.92215	0.0:0.0:1.0:0.0	.	176;176	F5H3A1;P05023	.;AT1A1_HUMAN	K	176;176;175;145	ENSP00000295598:E176K;ENSP00000445306:E176K;ENSP00000358508:E145K	ENSP00000295598:E176K	E	+	1	0	ATP1A1	116732807	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	9.657000	0.98554	2.676000	0.91093	0.655000	0.94253	GAG	.	.	.	none		0.398	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5	NM_001160233		A	116931284	G	A	116931284	3	1	91	1	0	0	0	0	1	0	0	0	1128	1291	45	2	564	2	ATP1A1	1	116931284	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	77020781	116931284	132319337	6	5787											
TDRD10	126668	hgsc.bcm.edu	37	chr1	154493835	154493835	+	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	ctgggctccatgcagaaagtGacacttgcaatccaggagct	11	8	11	11	0	0	2	0	1	0	1	2	3	2	3	2	2	3	4	2	2	2	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:154493835G>A	ENST00000368480.3	+	6	334	c.249G>A	c.(247-249)gtG>gtA	p.V83V	TDRD10_ENST00000368482.4_Silent_p.V83V			Q5VZ19	TDR10_HUMAN	tudor domain containing 10	83	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			TGCAGAAAGTGACACTTGCAA	0.502																																					p.V83V		Atlas-SNP	.											.	TDRD10	48	.	0			c.G249A						PASS	.						139	147	144					1																	154493835		2203	4300	6503	SO:0001819	synonymous_variant	126668	exon6			GAAAGTGACACTT	AL713777	CCDS30878.2, CCDS41406.1	1q21.3	2013-02-12			ENSG00000163239	ENSG00000163239		"Tudor domain containing", "RNA binding motif (RRM) containing"	25316	protein-coding gene	gene with protein product						12975309	Standard	NM_182499		Approved	DKFZp434M202	uc009wow.3	Q5VZ19	OTTHUMG00000037264	ENST00000368480.3:c.249G>A	chr1.hg19:g.154493835G>A		311.0	0.0	.		368.0	35.0	.	NM_182499	A4FU09|B0QZ53|B4DXV4|Q3ZCP1|Q3ZCS7|Q5SXY7|Q6UXV2|Q8TCN3	Silent	SNP	ENST00000368480.3	hg19	CCDS41406.1																																																																																			.	.	.	none		0.502	TDRD10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090700.2	NM_182499		A	154493835	G	A	154493835	2	1	91	1	0	0	0	0	0	0	0	1	15743	1277	45	2		2	TDRD10	1	154493835	Silent	SNP	G	TCGA-B3-4104-01A-01D-1458-08	37562551	154493835	94756786	7	5788											
LRRN2	10446	hgsc.bcm.edu	37	chr1	204587907	204587907	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacctcacggaccgggaggCgctggaggtccggaggctcc	6	4	17	14	4	1	0	1	0	0	0	3	4	3	4	4	7	0	3	4	7	0	0	rs371946869		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:204587907C>T	ENST00000367175.1	-	1	3426	c.1214G>A	c.(1213-1215)cGc>cAc	p.R405H	LRRN2_ENST00000496057.1_5'Flank|LRRN2_ENST00000367177.3_Missense_Mutation_p.R405H|LRRN2_ENST00000367176.3_Missense_Mutation_p.R405H|RP11-430C7.4_ENST00000453895.1_RNA			O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2	405	LRRCT.				cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|liver(1)|lung(22)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			GACCGGGAGGCGCTGGAGGTC	0.662													C|||	1	0.000199681	0	0	5008	,	,		16007	0		0	False		,,,				2504	0.001				p.R405H		Atlas-SNP	.											.	LRRN2	81	.	0			c.G1214A						PASS	.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	41	46	44		1214,1214	4.6	1	1		44	2,8598	1.2+/-3.3	0,2,4298	no	missense,missense	LRRN2	NM_006338.2,NM_201630.1	29,29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign,benign	405/714,405/714	204587907	2,13004	2203	4300	6503	SO:0001583	missense	10446	exon3			GGGAGGCGCTGGA	AF030435	CCDS1448.1	1q32.1	2013-01-11	2007-01-31	2007-01-31	ENSG00000170382	ENSG00000170382		"Immunoglobulin superfamily / I-set domain containing"	16914	protein-coding gene	gene with protein product	"leucine rich and ankyrin repeats 1", "fibronectin type III, immunoglobulin and leucine rich repeat domain 7"	605492	"leucine rich repeat neuronal 5"	LRRN5		9662332	Standard	NM_006338		Approved	GAC1, LRANK1, FIGLER7	uc001hbf.1	O75325	OTTHUMG00000035989	ENST00000367175.1:c.1214G>A	chr1.hg19:g.204587907C>T	ENSP00000356143:p.Arg405His	140.0	0.0	.		116.0	8.0	.	NM_006338	B2R624|Q5T0Y0|Q6UXM0|Q8N182	Missense_Mutation	SNP	ENST00000367175.1	hg19	CCDS1448.1	.	.	.	.	.	.	.	.	.	.	C	12.88	2.070520	0.36566	0.0	2.33E-4	ENSG00000170382	ENST00000367176;ENST00000367177;ENST00000367175	T;T;T	0.59502	0.26;0.26;0.26	5.69	4.59	0.56863	Cysteine-rich flanking region, C-terminal (1);	0.159801	0.29767	N	0.011250	T	0.36580	0.0972	N	0.08118	0	0.37294	D	0.90841	B	0.17465	0.022	B	0.09377	0.004	T	0.40059	-0.9583	10	0.66056	D	0.02	.	11.5883	0.50931	0.0:0.7898:0.1305:0.0797	.	405	O75325	LRRN2_HUMAN	H	405	ENSP00000356144:R405H;ENSP00000356145:R405H;ENSP00000356143:R405H	ENSP00000356143:R405H	R	-	2	0	LRRN2	202854530	0.939000	0.31865	1.000000	0.80357	0.940000	0.58332	1.848000	0.39309	2.684000	0.91462	0.557000	0.71058	CGC	.	.	.	none		0.662	LRRN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089894.1	NM_006338		T	204587907	C	T	204587907	3	4	91	1	0	0	0	0	1	0	0	0	9042	768	27	1	931	1	LRRN2	1	204587907	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	50094072	204587907	44662714	8	5789											
SLC26A9	115019	hgsc.bcm.edu	37	chr1	205888030	205888030	+	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	ctgggcaaagaggactgcgtCatgtatgctgggaaagacgt	11	8	15	7	2	1	2	1	0	0	2	1	4	1	4	0	3	2	3	0	3	3	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr1:205888030C>T	ENST00000367135.3	-	19	2307	c.2194G>A	c.(2194-2196)Gac>Aac	p.D732N	SLC26A9_ENST00000340781.4_Missense_Mutation_p.D732N|SLC26A9_ENST00000367134.2_Missense_Mutation_p.D732N	NM_052934.3	NP_443166.1	Q7LBE3	S26A9_HUMAN	solute carrier family 26 (anion exchanger), member 9	732	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				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)			AGGACTGCGTCATGTATGCTG	0.517											OREG0014164	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D732N		Atlas-SNP	.											.	SLC26A9	176	.	0			c.G2194A						PASS	.						310	292	298					1																	205888030		2203	4300	6503	SO:0001583	missense	115019	exon19			CTGCGTCATGTAT	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.2194G>A	chr1.hg19:g.205888030C>T	ENSP00000356103:p.Asp732Asn	502.0	2.0	.	2155	646.0	307.0	.	NM_134325	A7E2V6|B1AVM8|B1AVM9|B7ZKK2|Q96PK9|Q96RN0	Missense_Mutation	SNP	ENST00000367135.3	hg19	CCDS30990.1	.	.	.	.	.	.	.	.	.	.	C	17.83	3.484381	0.63962	.	.	ENSG00000174502	ENST00000340781;ENST00000367135;ENST00000367134	D;D;D	0.90069	-2.61;-2.61;-2.61	5.2	5.2	0.72013	Sulphate transporter/antisigma-factor antagonist STAS (3);	0.000000	0.85682	D	0.000000	D	0.95137	0.8424	M	0.84948	2.725	0.54753	D	0.999984	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.95535	0.8607	10	0.72032	D	0.01	.	18.7233	0.91704	0.0:1.0:0.0:0.0	.	732;732	Q7LBE3;B1AVM8	S26A9_HUMAN;.	N	732	ENSP00000341682:D732N;ENSP00000356103:D732N;ENSP00000356102:D732N	ENSP00000341682:D732N	D	-	1	0	SLC26A9	204154653	1.000000	0.71417	0.271000	0.24616	0.102000	0.19082	6.298000	0.72763	2.584000	0.87258	0.563000	0.77884	GAC	.	.	.	none		0.517	SLC26A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087742.1	NM_052934		T	205888030	C	T	205888030	3	4	91	1	0	0	0	0	1	0	0	0	14537	826	29	2	489	2	SLC26A9	1	205888030	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	1300123	205888030	43362591	9	5790											
ETAA1	54465	hgsc.bcm.edu	37	chr2	67631299	67631299	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttattcaagacgaaattcaAaattgtatagttacatctaa	17	14	5	5	1	3	1	2	0	1	1	3	2	3	1	0	0	1	3	0	0	9	8			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr2:67631299A>G	ENST00000272342.5	+	5	1615	c.1485A>G	c.(1483-1485)caA>caG	p.Q495Q	ETAA1_ENST00000462772.1_Intron	NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	495						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						ACGAAATTCAAAATTGTATAG	0.279																																					p.Q495Q		Atlas-SNP	.											.	ETAA1	88	.	0			c.A1485G						PASS	.						20	22	22					2																	67631299		2126	4252	6378	SO:0001819	synonymous_variant	54465	exon5			AATTCAAAATTGT	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.1485A>G	chr2.hg19:g.67631299A>G		51.0	0.0	.		89.0	44.0	.	NM_019002	Q05BT7|Q53SC4	Silent	SNP	ENST00000272342.5	hg19	CCDS1882.1																																																																																			.	.	.	none		0.279	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1	NM_019002		G	67631299	A	G	67631299	2	3	91	1	0	0	0	0	0	0	0	1	5269	11	1	3		3	ETAA1	2	67631299	Silent	SNP	A	TCGA-B3-4104-01A-01D-1458-08		67631299	175568074	10	5791											
CCDC108	255101	hgsc.bcm.edu	37	chr2	219886640	219886640	+	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	cacattcccaaaggccagctCcttttcctttgcctggaggc	7	11	8	15	0	0	0	0	0	0	0	3	1	3	1	5	3	2	1	5	3	1	4			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr2:219886640C>T	ENST00000341552.5	-	18	3075	c.2992G>A	c.(2992-2994)Gag>Aag	p.E998K	CCDC108_ENST00000441968.1_Missense_Mutation_p.E998K|CCDC108_ENST00000453220.1_Missense_Mutation_p.E998K	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	998						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)		AAGGCCAGCTCCTTTTCCTTT	0.597																																					p.E998K		Atlas-SNP	.											.	CCDC108	208	.	0			c.G2992A						PASS	.						103	108	106					2																	219886640		2203	4300	6503	SO:0001583	missense	255101	exon18			CCAGCTCCTTTTC	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.2992G>A	chr2.hg19:g.219886640C>T	ENSP00000340776:p.Glu998Lys	279.0	0.0	.		159.0	90.0	.	NM_194302	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Missense_Mutation	SNP	ENST00000341552.5	hg19	CCDS2430.2	.	.	.	.	.	.	.	.	.	.	C	9.157	1.017735	0.19355	.	.	ENSG00000181378	ENST00000341552;ENST00000441968;ENST00000453220	T;T;T	0.05199	3.48;3.48;3.48	4.89	3.11	0.35812	.	0.308243	0.23081	N	0.052148	T	0.08626	0.0214	M	0.67953	2.075	0.27209	N	0.959953	P	0.35656	0.514	B	0.37650	0.255	T	0.20107	-1.0285	10	0.12103	T	0.63	-17.3902	10.4801	0.44689	0.0:0.5718:0.3504:0.0778	.	998	Q6ZU64	CC108_HUMAN	K	998	ENSP00000340776:E998K;ENSP00000413377:E998K;ENSP00000409117:E998K	ENSP00000340776:E998K	E	-	1	0	CCDC108	219594884	0.378000	0.25114	0.953000	0.39169	0.255000	0.26057	0.327000	0.19663	0.289000	0.22422	-1.886000	0.00541	GAG	.	.	.	none		0.597	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302		T	219886640	C	T	219886640	3	4	91	1	0	0	0	0	1	0	0	0	2745	864	30	2	2857	2	CCDC108	2	219886640	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	152255341	219886640	23312733	11	5792											
EFHB	151651	hgsc.bcm.edu	37	chr3	19925989	19925989	+	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	cttggtctcagaagtgtccgGagagtcttttctgtgcttcc	5	15	11	10	1	3	2	1	0	3	2	6	3	5	2	2	2	1	1	2	2	1	4			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr3:19925989G>C	ENST00000295824.9	-	11	2213	c.2052C>G	c.(2050-2052)ctC>ctG	p.L684L	EFHB_ENST00000344838.4_Silent_p.L554L	NM_144715.3	NP_653316.3	Q8N7U6	EFHB_HUMAN	EF-hand domain family, member B	684							calcium ion binding (GO:0005509)			breast(2)|endometrium(4)|kidney(1)|lung(17)|prostate(1)|urinary_tract(1)	26						GAAGTGTCCGGAGAGTCTTTT	0.393																																					p.L684L		Atlas-SNP	.											.	EFHB	186	.	0			c.C2052G						PASS	.						126	130	128					3																	19925989		2203	4300	6503	SO:0001819	synonymous_variant	151651	exon11			TGTCCGGAGAGTC	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.2052C>G	chr3.hg19:g.19925989G>C		129.0	0.0	.		190.0	85.0	.	NM_144715	A6ND25|A8MPR3|Q6ZWK9|Q8IV58|Q96LQ6	Silent	SNP	ENST00000295824.9	hg19	CCDS33715.2																																																																																			.	.	.	none		0.393	EFHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318673.2	NM_144715		C	19925989	G	C	19925989	2	2	91	1	0	0	0	0	0	0	0	1	4947	1161	41	4		4	EFHB	3	19925989	Silent	SNP	G	TCGA-B3-4104-01A-01D-1458-08		19925989	178096441	12	5793											
COL6A6	131873	hgsc.bcm.edu	37	chr3	130287049	130287049	+	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	ttggtgtagtccagttcagcGacatcaataaggaagagttt	12	12	11	6	1	2	1	2	0	0	1	3	3	3	2	1	2	1	3	1	2	4	5			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr3:130287049G>A	ENST00000358511.6	+	5	2033	c.2002G>A	c.(2002-2004)Gac>Aac	p.D668N	COL6A6_ENST00000453409.2_Missense_Mutation_p.D668N	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	668	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)		p.D668N(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						CCAGTTCAGCGACATCAATAA	0.423																																					p.D668N		Atlas-SNP	.											COL6A6,colon,carcinoma,0,1	COL6A6	497	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2002A						PASS	.						178	173	175					3																	130287049		1922	4127	6049	SO:0001583	missense	131873	exon5			TTCAGCGACATCA	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.2002G>A	chr3.hg19:g.130287049G>A	ENSP00000351310:p.Asp668Asn	239.0	0.0	.		330.0	152.0	.	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	hg19	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	G	4.358	0.066002	0.08388	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.79749	-1.3;-1.3	5.53	-3.41	0.04839	von Willebrand factor, type A (3);	0.427722	0.21922	N	0.067159	T	0.71307	0.3324	L	0.50993	1.605	0.09310	N	1	B	0.18461	0.028	B	0.13407	0.009	T	0.58335	-0.7654	10	0.38643	T	0.18	.	13.4535	0.61184	0.0599:0.6662:0.1805:0.0934	.	668	A6NMZ7	CO6A6_HUMAN	N	668	ENSP00000351310:D668N;ENSP00000399236:D668N	ENSP00000351310:D668N	D	+	1	0	COL6A6	131769739	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.129000	0.10515	-0.601000	0.05783	0.655000	0.94253	GAC	.	.	.	none		0.423	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		A	130287049	G	A	130287049	3	1	91	1	0	0	0	0	1	0	0	0	3705	1058	37	1	2020	1	COL6A6	3	130287049	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	110361060	130287049	67735381	13	5794											
FGFR3	2261	hgsc.bcm.edu	37	chr4	1803568	1803568	+	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	atctgcccccacagagcgctCcccgcaccggcccatcctgc	6	5	8	22	3	1	1	0	0	1	1	3	1	3	1	7	1	3	2	7	1	0	0	rs121913483		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr4:1803568C>G	ENST00000260795.2	+	6	848	c.746C>G	c.(745-747)tCc>tGc	p.S249C	FGFR3_ENST00000440486.2_Missense_Mutation_p.S249C|FGFR3_ENST00000412135.2_Missense_Mutation_p.S249C|FGFR3_ENST00000340107.4_Missense_Mutation_p.S249C|FGFR3_ENST00000474521.1_3'UTR|FGFR3_ENST00000481110.2_Missense_Mutation_p.S249C|FGFR3_ENST00000352904.1_Missense_Mutation_p.S249C			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	249			S -> C (in KERSEB, bladder cancer, cervical cancer and TD1). {ECO:0000269|PubMed:10360402, ECO:0000269|PubMed:10471491, ECO:0000269|PubMed:15772091, ECO:0000269|PubMed:8589699, ECO:0000269|PubMed:8845844}.		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)	p.S249C(1204)|p.R248_S249del(1)		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)	ACAGAGCGCTCCCCGCACCGG	0.736		1	"Mis, T"	"IGH@, ETV6"	"bladder, MM, T-cell lymphoma"		"Hypochondroplasia, Thanatophoric dysplasia"		Saethre-Chotzen syndrome;Muenke syndrome																												p.S249C		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"L, E"	FGFR3_ENST00000340107,bladder,carcinoma,0,1251	FGFR3	3320	.	1205	Substitution - Missense(1204)|Deletion - In frame(1)	urinary_tract(1168)|skin(27)|cervix(5)|lung(4)|upper_aerodigestive_tract(1)	c.C746G	GRCh37	CM950470	FGFR3	M	rs121913483	PASS	.						13	16	15					4																	1803568		2180	4267	6447	SO:0001583	missense	2261	exon7	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	AGCGCTCCCCGCA	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.746C>G	chr4.hg19:g.1803568C>G	ENSP00000260795:p.Ser249Cys	44.0	1.0	.		32.0	14.0	.	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Missense_Mutation	SNP	ENST00000260795.2	hg19	CCDS3353.1	.	.	.	.	.	.	.	.	.	.	c	18.75	3.690127	0.68271	.	.	ENSG00000068078	ENST00000481110;ENST00000340107;ENST00000440486;ENST00000412135;ENST00000260795;ENST00000352904;ENST00000507588	D;T;T;T;T;T;T	0.82081	-1.57;-1.35;-1.33;-1.33;-1.33;-1.33;-1.32	3.94	3.94	0.45596	.	0.000000	0.85682	D	0.000000	D	0.92808	0.7713	M	0.92412	3.305	0.30597	A	0.239052	D;D;D;D;D;D	0.89917	0.998;0.997;1.0;1.0;1.0;1.0	P;D;D;D;D;D	0.80764	0.906;0.978;0.983;0.994;0.968;0.993	D	0.94822	0.7988	9	0.72032	D	0.01	.	16.2883	0.82736	0.0:1.0:0.0:0.0	.	212;249;249;249;249;249	Q8NI15;P22607-2;P22607-4;P22607-3;P22607;F8W9L4	.;.;.;.;FGFR3_HUMAN;.	C	249;249;249;249;249;249;69	ENSP00000420533:S249C;ENSP00000339824:S249C;ENSP00000414914:S249C;ENSP00000412903:S249C;ENSP00000260795:S249C;ENSP00000231803:S249C;ENSP00000427289:S69C	ENSP00000260795:S249C	S	+	2	0	FGFR3	1773366	1.000000	0.71417	1.000000	0.80357	0.445000	0.32107	7.424000	0.80242	1.903000	0.55091	0.436000	0.28706	TCC	.	.	.	weak		0.736	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142		G	1803568	C	G	1803568	3	3	91	1	0	0	0	0	1	0	0	0	5874	855	30	4	768	4	FGFR3	4	1803568	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08		1803568	189350708	14	5795											
UNC5C	8633	hgsc.bcm.edu	37	chr4	96127913	96127913	+	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	gggcccacagctcaccacagGggtcaaaagtgtctgagagt	11	6	13	11	0	3	1	2	1	1	1	3	2	3	1	2	3	1	1	2	3	2	0			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr4:96127913G>T	ENST00000453304.1	-	11	2116	c.1768C>A	c.(1768-1770)Cct>Act	p.P590T		NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	590	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)	p.P590T(1)		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)		CTCACCACAGGGGTCAAAAGT	0.537																																					p.P590T		Atlas-SNP	.											UNC5C,NS,carcinoma,0,1	UNC5C	141	.	1	Substitution - Missense(1)	lung(1)	c.C1768A						PASS	.						50	49	50					4																	96127913		2203	4300	6503	SO:0001583	missense	8633	exon11			CCACAGGGGTCAA	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.1768C>A	chr4.hg19:g.96127913G>T	ENSP00000406022:p.Pro590Thr	87.0	0.0	.		106.0	20.0	.	NM_003728	Q8IUT0	Missense_Mutation	SNP	ENST00000453304.1	hg19	CCDS3643.1	.	.	.	.	.	.	.	.	.	.	G	17.77	3.471684	0.63737	.	.	ENSG00000182168	ENST00000453304;ENST00000331502;ENST00000513796	T;T	0.56103	0.48;0.48	5.28	5.28	0.74379	ZU5 (3);	0.000000	0.85682	D	0.000000	T	0.71804	0.3383	M	0.90977	3.165	0.80722	D	1	P;B	0.49559	0.925;0.055	P;B	0.49561	0.615;0.021	T	0.80127	-0.1512	10	0.87932	D	0	.	19.2637	0.93979	0.0:0.0:1.0:0.0	.	590;590	A8K385;O95185	.;UNC5C_HUMAN	T	590;549;609	ENSP00000406022:P590T;ENSP00000426924:P609T	ENSP00000328673:P549T	P	-	1	0	UNC5C	96346936	1.000000	0.71417	0.971000	0.41717	0.843000	0.47879	7.884000	0.87274	2.611000	0.88343	0.563000	0.77884	CCT	.	.	.	none		0.537	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728		T	96127913	G	T	96127913	3	4	91	1	0	0	0	0	1	0	0	0	17005	1232	43	4	1051	4	UNC5C	4	96127913	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	94324345	96127913	95026363	15	5796											
PCDHGA3	56112	hgsc.bcm.edu	37	chr5	140725009	140725009	+	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	aaacaaccccagaggagcctCcatcttctcagtgacagccc	12	6	7	16	0	2	2	1	1	2	1	4	3	3	3	5	1	4	0	5	1	2	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr5:140725009C>T	ENST00000253812.6	+	1	1409	c.1409C>T	c.(1408-1410)tCc>tTc	p.S470F	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	470	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)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGAGGAGCCTCCATCTTCTCA	0.547																																					p.S470F		Atlas-SNP	.											.	PCDHGA3	246	.	0			c.C1409T						PASS	.						116	132	127					5																	140725009		2135	4271	6406	SO:0001583	missense	56112	exon1			GAGCCTCCATCTT	AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"Cadherins / Protocadherins : Clustered"	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.1409C>T	chr5.hg19:g.140725009C>T	ENSP00000253812:p.Ser470Phe	231.0	0.0	.		308.0	143.0	.	NM_032011	Q9Y5D4	Missense_Mutation	SNP	ENST00000253812.6	hg19	CCDS47290.1	.	.	.	.	.	.	.	.	.	.	.	15.45	2.838553	0.51057	.	.	ENSG00000254245	ENST00000253812	T	0.02709	4.19	5.36	4.5	0.54988	Cadherin (3);Cadherin-like (1);	0.000000	0.33199	U	0.005170	T	0.09468	0.0233	M	0.64997	1.995	0.27060	N	0.963586	P;P	0.49358	0.734;0.923	P;P	0.56648	0.485;0.803	T	0.01566	-1.1323	10	0.72032	D	0.01	.	11.5922	0.50951	0.0:0.8506:0.0:0.1494	.	470;470	Q9Y5H0-2;Q9Y5H0	.;PCDG3_HUMAN	F	470	ENSP00000253812:S470F	ENSP00000253812:S470F	S	+	2	0	PCDHGA3	140705193	0.021000	0.18746	1.000000	0.80357	0.953000	0.61014	1.432000	0.34936	1.399000	0.46721	0.563000	0.77884	TCC	.	.	.	none		0.547	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916		T	140725009	C	T	140725009	3	4	91	1	0	0	0	0	1	0	0	0	11562	855	30	2	1411	2	PCDHGA3	5	140725009	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08		140725009	40190251	16	5797											
CLINT1	9685	hgsc.bcm.edu	37	chr5	157240138	157240138	+	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	tctttgttcttctttgctttCtttcgctcttcacgaagcct	3	21	5	12	2	6	0	1	0	5	0	7	1	6	0	1	0	2	3	1	0	1	7			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr5:157240138C>G	ENST00000411809.2	-	5	654	c.450G>C	c.(448-450)aaG>aaC	p.K150N	CLINT1_ENST00000296951.5_Missense_Mutation_p.K132N|CLINT1_ENST00000523908.1_Missense_Mutation_p.K150N|CLINT1_ENST00000523094.1_Missense_Mutation_p.K132N|CLINT1_ENST00000530742.1_Missense_Mutation_p.K132N	NM_014666.3	NP_055481.1	Q14677	EPN4_HUMAN	clathrin interactor 1	150					clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)	clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|lipid binding (GO:0008289)			breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|urinary_tract(1)	21	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)			TCTTTGCTTTCTTTCGCTCTT	0.423																																					p.K150N	Colon(22;427 587 2170 6147 14291)	Atlas-SNP	.											.	CLINT1	86	.	0			c.G450C						PASS	.						217	207	210					5																	157240138		1913	4128	6041	SO:0001583	missense	9685	exon5			TGCTTTCTTTCGC	AF434813	CCDS47330.1, CCDS56388.1, CCDS56389.1	5q33.3	2006-06-13			ENSG00000113282	ENSG00000113282			23186	protein-coding gene	gene with protein product		607265				12213833, 12429846	Standard	NM_014666		Approved	ENTH, KIAA0171, EPNR, CLINT	uc011ddv.2	Q14677	OTTHUMG00000163527	ENST00000411809.2:c.450G>C	chr5.hg19:g.157240138C>G	ENSP00000388340:p.Lys150Asn	125.0	0.0	.		168.0	83.0	.	NM_014666	B7Z6F8|D3DQJ6|Q8NAF1|Q96E05	Missense_Mutation	SNP	ENST00000411809.2	hg19	CCDS47330.1	.	.	.	.	.	.	.	.	.	.	C	17.00	3.275997	0.59649	.	.	ENSG00000113282	ENST00000523094;ENST00000530742;ENST00000411809;ENST00000296951;ENST00000523908	T;T;T;T;T	0.54279	0.6;0.6;0.6;0.6;0.58	5.88	4.05	0.47172	ENTH/VHS (1);	0.085100	0.85682	D	0.000000	T	0.67608	0.2911	M	0.75884	2.315	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.80764	0.994;0.989	T	0.64689	-0.6348	10	0.33141	T	0.24	-15.7865	9.2432	0.37509	0.0:0.7587:0.0:0.2413	.	150;150	B7Z6F8;Q14677	.;EPN4_HUMAN	N	132;132;150;132;150	ENSP00000429345:K132N;ENSP00000433419:K132N;ENSP00000388340:K150N;ENSP00000296951:K132N;ENSP00000429824:K150N	ENSP00000296951:K132N	K	-	3	2	CLINT1	157172716	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.312000	0.33574	0.753000	0.32945	0.655000	0.94253	AAG	.	.	.	none		0.423	CLINT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374001.1	NM_014666		G	157240138	C	G	157240138	3	3	91	1	0	0	0	0	1	0	0	0	3533	912	32	4	1459	4	CLINT1	5	157240138	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	16515129	157240138	23675122	17	5798											
OR14J1	442191	hgsc.bcm.edu	37	chr6	29274483	29274483	+	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	gactatggtcaatttgacttCaatgagtggattccttctta	10	16	8	7	0	3	2	2	2	1	0	4	4	4	3	1	2	0	0	1	2	4	6			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr6:29274483C>T	ENST00000377160.2	+	1	81	c.17C>T	c.(16-18)tCa>tTa	p.S6L		NM_030946.1	NP_112208.1	Q9UGF5	O14J1_HUMAN	olfactory receptor, family 14, subfamily J, member 1	6						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(3)|lung(8)|ovary(2)|upper_aerodigestive_tract(2)	17						AATTTGACTTCAATGAGTGGA	0.403																																					p.S6L		Atlas-SNP	.											.	OR14J1	43	.	0			c.C17T						PASS	.						178	185	182					6																	29274483		1511	2709	4220	SO:0001583	missense	442191	exon1			TGACTTCAATGAG		CCDS34362.1	6p21.3	2012-08-09	2008-04-02	2008-04-02	ENSG00000204695	ENSG00000204695		"GPCR / Class A : Olfactory receptors"	13971	protein-coding gene	gene with protein product			"olfactory receptor, family 5, subfamily U, member 1"	OR5U1			Standard	NM_030946		Approved	hs6M1-28	uc011dln.2	Q9UGF5	OTTHUMG00000031184	ENST00000377160.2:c.17C>T	chr6.hg19:g.29274483C>T	ENSP00000366365:p.Ser6Leu	258.0	0.0	.		408.0	159.0	.	NM_030946	A2BEC2|B0V078|Q5ST27	Missense_Mutation	SNP	ENST00000377160.2	hg19	CCDS34362.1	.	.	.	.	.	.	.	.	.	.	C	7.344	0.621483	0.14193	.	.	ENSG00000204695	ENST00000377160	T	0.00522	6.84	4.73	1.88	0.25563	.	0.481890	0.15328	N	0.268184	T	0.00073	0.0002	N	0.05414	-0.055	0.09310	N	1	B	0.25441	0.126	B	0.24701	0.055	T	0.08911	-1.0699	10	0.27785	T	0.31	.	4.4271	0.11509	0.1483:0.4819:0.288:0.0819	.	6	Q9UGF5	O14J1_HUMAN	L	6	ENSP00000366365:S6L	ENSP00000366365:S6L	S	+	2	0	OR14J1	29382462	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-2.295000	0.01143	0.263000	0.21812	0.655000	0.94253	TCA	.	.	.	none		0.403	OR14J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076362.2			T	29274483	C	T	29274483	3	4	91	1	0	0	0	0	1	0	0	0	10955	838	29	2	19	2	OR14J1	6	29274483	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08		29274483	141840584	18	5799											
BRD2	6046	hgsc.bcm.edu	37	chr6	32945959	32945959	+	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	cagggtccaatatccaagccCaagaggaaaagagagaaaaa	20	3	10	8	0	0	3	0	0	0	3	2	5	2	4	3	2	1	0	3	2	8	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr6:32945959C>G	ENST00000374825.4	+	10	3336	c.1635C>G	c.(1633-1635)ccC>ccG	p.P545P	BRD2_ENST00000449085.2_Silent_p.P498P|BRD2_ENST00000374831.4_Silent_p.P545P|BRD2_ENST00000443797.2_Silent_p.P425P|BRD2_ENST00000395289.2_Silent_p.P545P|BRD2_ENST00000395287.1_Silent_p.P545P	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	545	Arg/Lys-rich (highly basic).				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						TATCCAAGCCCAAGAGGAAAA	0.463																																					p.P545P		Atlas-SNP	.											.	BRD2	70	.	0			c.C1635G						PASS	.						38	46	43					6																	32945959		1508	2708	4216	SO:0001819	synonymous_variant	6046	exon10			CAAGCCCAAGAGG	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.1635C>G	chr6.hg19:g.32945959C>G		99.0	0.0	.		91.0	36.0	.	NM_005104	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Silent	SNP	ENST00000374825.4	hg19	CCDS4762.1	.	.	.	.	.	.	.	.	.	.	C	10.41	1.342233	0.24339	.	.	ENSG00000204256	ENST00000449025	T	0.31247	1.5	5.35	-3.94	0.04130	.	0.000000	0.49916	D	0.000124	T	0.08403	0.0209	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.14924	-1.0455	7	0.18710	T	0.47	-14.208	4.8892	0.13719	0.4611:0.1625:0.0:0.3764	.	.	.	.	R	551	ENSP00000409613:P551R	ENSP00000409613:P551R	P	+	2	0	BRD2	33053937	0.103000	0.21917	0.943000	0.38184	0.899000	0.52679	-0.561000	0.05957	-0.702000	0.05056	-0.272000	0.10252	CCA	.	.	.	none		0.463	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2			G	32945959	C	G	32945959	2	3	91	1	0	0	0	0	0	0	0	1	1504	581	21	4		4	BRD2	6	32945959	Silent	SNP	C	TCGA-B3-4104-01A-01D-1458-08	3671476	32945959	138169108	19	5800											
BRD2	6046	hgsc.bcm.edu	37	chr6	32947799	32947799	+	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	ggagccctctttacgtgattCaaacccagaagagattgaga	13	9	10	9	1	2	4	1	2	1	3	2	7	2	5	2	1	3	0	2	1	3	4			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr6:32947799C>G	ENST00000374825.4	+	11	3737	c.2036C>G	c.(2035-2037)tCa>tGa	p.S679*	BRD2_ENST00000449085.2_Nonsense_Mutation_p.S632*|BRD2_ENST00000374831.4_Nonsense_Mutation_p.S679*|BRD2_ENST00000443797.2_Nonsense_Mutation_p.S559*|BRD2_ENST00000395289.2_Nonsense_Mutation_p.S714*|BRD2_ENST00000395287.1_Nonsense_Mutation_p.S714*	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	679	NET. {ECO:0000255|PROSITE- ProRule:PRU00857}.				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						TTACGTGATTCAAACCCAGAA	0.498																																					p.S714X		Atlas-SNP	.											.	BRD2	70	.	0			c.C2141G						PASS	.						65	64	64					6																	32947799		1511	2709	4220	SO:0001587	stop_gained	6046	exon11			GTGATTCAAACCC	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.2036C>G	chr6.hg19:g.32947799C>G	ENSP00000363958:p.Ser679*	72.0	0.0	.		105.0	44.0	.	NM_001199455	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Nonsense_Mutation	SNP	ENST00000374825.4	hg19	CCDS4762.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	52|52	19.743137|19.743137	0.99923|0.99923	.|.	.|.	ENSG00000204256|ENSG00000204256	ENST00000449025|ENST00000374825;ENST00000374831;ENST00000395289;ENST00000443797;ENST00000395287;ENST00000449085	.|.	.|.	.|.	5.51|5.51	5.51|5.51	0.81932|0.81932	.|.	.|0.000000	.|0.41605	.|D	.|0.000858	T|.	0.70055|.	0.3180|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.70457|.	-0.4866|.	3|.	.|0.52906	.|T	.|0.07	-14.2571|-14.2571	16.9633|16.9633	0.86278|0.86278	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	E|X	685|679;679;714;559;714;632	.|.	.|ENSP00000363958:S679X	Q|S	+|+	1|2	0|0	BRD2|BRD2	33055777|33055777	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.637000|7.637000	0.83313|0.83313	2.873000|2.873000	0.98535|0.98535	0.643000|0.643000	0.83706|0.83706	CAA|TCA	.	.	.	none		0.498	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2			G	32947799	C	G	32947799	4	3	91	1	0	0	0	0	0	1	0	0	1504	838	29	4	2074	4	BRD2	6	32947799	Nonsense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	1840	32947799	138167268	20	5801											
SMPD2	6610	hgsc.bcm.edu	37	chr6	109763791	109763791	+	Frame_Shift_Del	DEL	C	C	-																															aggacatctacctagcacatCgtgtggcccaagcttgggaa																								rs534167199		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr6:109763791delC	ENST00000258052.3	+	6	813	c.454delC	c.(454-456)cgtfs	p.R152fs	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)	152					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)	p.R152C(1)		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)		CCTAGCACATCGTGTGGCCCA	0.537																																					p.H151fs		Atlas-INDEL	.											.	SMPD2	25	.	1	Substitution - Missense(1)	endometrium(1)	c.453delT						PASS	.						169	147	154					6																	109763791		2203	4300	6503	SO:0001589	frameshift_variant	6610	exon6			.	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.454delC	chr6.hg19:g.109763791delC	ENSP00000258052:p.Arg152fs	205.0	0.0	0		259.0	117.0	0.451737	NM_003080	Q5TED1|Q9BWR3	Frame_Shift_Del	DEL	ENST00000258052.3	hg19	CCDS5075.1																																																																																			.	.	.	none		0.537	SMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041755.1			-	109763791	C	-	109763791	7	5	91	1	0	1	0	1	0	0	0	0	14818	884	31	0	476	0	SMPD2	6	109763791	Frame_Shift_Del	DEL	C	TCGA-B3-4104-01A-01D-1458-08	76815992	109763791	61351276	21	5802											
CHRM2	1129	hgsc.bcm.edu	37	chr7	136700056	136700056	+	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	atgatgattgcagctgcctgGgtcctctctttcatcctctg	5	15	9	12	0	3	2	1	2	2	0	6	2	5	2	3	1	3	2	3	1	0	2			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr7:136700056G>T	ENST00000445907.2	+	3	972	c.444G>T	c.(442-444)tgG>tgT	p.W148C	CHRM2_ENST00000402486.3_Missense_Mutation_p.W148C|hsa-mir-490_ENST00000593789.1_RNA|CHRM2_ENST00000453373.1_Missense_Mutation_p.W148C|hsa-mir-490_ENST00000439694.1_RNA|hsa-mir-490_ENST00000598184.1_RNA|hsa-mir-490_ENST00000597642.1_RNA|hsa-mir-490_ENST00000592183.1_RNA|CHRM2_ENST00000320658.5_Missense_Mutation_p.W148C|CHRM2_ENST00000401861.1_Missense_Mutation_p.W148C|CHRM2_ENST00000397608.3_Missense_Mutation_p.W148C|hsa-mir-490_ENST00000425981.2_RNA|hsa-mir-490_ENST00000586239.1_RNA	NM_001006627.1|NM_001006629.1	NP_001006628.1|NP_001006630.1	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	148					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|nervous system development (GO:0007399)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|regulation of heart contraction (GO:0008016)|response to virus (GO:0009615)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(13)|liver(1)|lung(29)|ovary(4)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	68					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Bethanechol(DB01019)|Brompheniramine(DB00835)|Carbachol(DB00411)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Dimetindene(DB08801)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxacurium chloride(DB01135)|Doxepin(DB01142)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Rocuronium(DB00728)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	CAGCTGCCTGGGTCCTCTCTT	0.488																																					p.W148C		Atlas-SNP	.											.	CHRM2	167	.	0			c.G444T						PASS	.						66	68	68					7																	136700056		2203	4300	6503	SO:0001583	missense	1129	exon3			TGCCTGGGTCCTC		CCDS5843.1	7q35-q36	2014-09-17			ENSG00000181072	ENSG00000181072		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1951	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 2"	118493					Standard	NM_000739		Approved		uc003vtl.1	P08172	OTTHUMG00000155658	ENST00000445907.2:c.444G>T	chr7.hg19:g.136700056G>T	ENSP00000399745:p.Trp148Cys	120.0	0.0	.		145.0	26.0	.	NM_001006632	Q4VBK6|Q9P1X9	Missense_Mutation	SNP	ENST00000445907.2	hg19	CCDS5843.1	.	.	.	.	.	.	.	.	.	.	G	18.18	3.567740	0.65651	.	.	ENSG00000181072	ENST00000445907;ENST00000453373;ENST00000320658;ENST00000397608;ENST00000402486;ENST00000401861	D;D;D;D;D;D	0.88818	-2.43;-2.43;-2.43;-2.43;-2.43;-2.43	5.65	5.65	0.86999	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.97340	0.9130	H	0.99156	4.45	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98748	1.0719	10	0.87932	D	0	-1.0967	19.7244	0.96157	0.0:0.0:1.0:0.0	.	148	P08172	ACM2_HUMAN	C	148	ENSP00000399745:W148C;ENSP00000415386:W148C;ENSP00000319984:W148C;ENSP00000380733:W148C;ENSP00000384937:W148C;ENSP00000384401:W148C	ENSP00000319984:W148C	W	+	3	0	CHRM2	136350596	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.807000	0.99171	2.659000	0.90383	0.655000	0.94253	TGG	.	.	.	none		0.488	CHRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341010.1			T	136700056	G	T	136700056	3	4	91	1	0	0	0	0	1	0	0	0	3379	1241	43	4	446	4	CHRM2	7	136700056	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08		136700056	22438607	22	5803											
MLL3	58508	hgsc.bcm.edu	37	chr7	151879016	151879016	+	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	gcccaaggatttgggaaattGatctgtcatcacaggcctag	11	10	11	9	0	3	1	2	1	1	0	3	3	3	3	2	3	0	0	2	3	3	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr7:151879016G>A	ENST00000262189.6	-	36	6147	c.5929C>T	c.(5929-5931)Caa>Taa	p.Q1977*	KMT2C_ENST00000355193.2_Nonsense_Mutation_p.Q1977*	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1977	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)										TTGGGAAATTGATCTGTCATC	0.458																																					p.Q1977X		Atlas-SNP	.											MLL3_ENST00000355193,NS,carcinoma,0,2	MLL3	1564	.	0			c.C5929T						PASS	.						215	223	220					7																	151879016		2203	4300	6503	SO:0001587	stop_gained	58508	exon36			GAAATTGATCTGT	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.5929C>T	chr7.hg19:g.151879016G>A	ENSP00000262189:p.Gln1977*	536.0	0.0	.		722.0	115.0	.	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Nonsense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	G	47	13.696566	0.99758	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	.	.	.	5.37	4.49	0.54785	.	0.000000	0.42420	U	0.000717	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.3796	0.44104	0.1499:0.0:0.8501:0.0	.	.	.	.	X	1977	.	ENSP00000262189:Q1977X	Q	-	1	0	MLL3	151509949	1.000000	0.71417	0.139000	0.22197	0.959000	0.62525	6.683000	0.74533	1.289000	0.44618	0.558000	0.71614	CAA	.	.	.	none		0.458	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			A	151879016	G	A	151879016	4	1	91	1	0	0	0	0	0	1	0	0	9629	1299	45	2	8902	2	MLL3	7	151879016	Nonsense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	15178960	151879016	7259647	23	5804											
ERLIN2	11160	hgsc.bcm.edu	37	chr8	37597912	37597912	+	Missense_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	cctgctgacttcgaccagcgGccctggtttccatctcatgc	5	11	9	16	2	1	1	1	1	1	0	4	2	2	1	4	2	3	2	4	2	0	2			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr8:37597912G>A	ENST00000276461.5	+	3	204	c.137G>A	c.(136-138)gGc>gAc	p.G46D	ERLIN2_ENST00000397228.2_Missense_Mutation_p.G46D|ERLIN2_ENST00000523107.1_Missense_Mutation_p.G46D|ERLIN2_ENST00000519638.1_Missense_Mutation_p.G46D|ERLIN2_ENST00000523887.1_Missense_Mutation_p.G46D|RP11-863K10.7_ENST00000330539.1_5'Flank|ERLIN2_ENST00000518586.1_Missense_Mutation_p.G46D|ERLIN2_ENST00000335171.6_Missense_Mutation_p.G46D	NM_007175.6	NP_009106.1	O94905	ERLN2_HUMAN	ER lipid raft associated 2	46					cell death (GO:0008219)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)				NS(1)|large_intestine(1)|lung(5)	7		Lung NSC(58;0.174)	BRCA - Breast invasive adenocarcinoma(5;6.14e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			TCGACCAGCGGCCCTGGTTTC	0.537																																					p.G46D		Atlas-SNP	.											.	ERLIN2	27	.	0			c.G137A						PASS	.						228	199	208					8																	37597912		2203	4300	6503	SO:0001583	missense	11160	exon3			CCAGCGGCCCTGG	AY358108	CCDS6095.1, CCDS34879.1	8p11.2	2012-11-23	2007-01-26	2007-01-26	ENSG00000147475	ENSG00000147475			1356	protein-coding gene	gene with protein product		611605	"chromosome 8 open reading frame 2", "SPFH domain family, member 2"	C8orf2, SPFH2, Erlin-2		10449903, 15897872, 16835267	Standard	NM_007175		Approved	NET32, SPG18	uc003xke.4	O94905	OTTHUMG00000164005	ENST00000276461.5:c.137G>A	chr8.hg19:g.37597912G>A	ENSP00000276461:p.Gly46Asp	415.0	0.0	.		521.0	25.0	.	NM_001003791	A0JLQ1|A8K5S9|B4DM38|D3DSW0|Q6NW21|Q86VS6|Q86W49	Missense_Mutation	SNP	ENST00000276461.5	hg19	CCDS6095.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.263471	0.80358	.	.	ENSG00000147475	ENST00000397228;ENST00000523887;ENST00000276461;ENST00000518586;ENST00000335171;ENST00000521644;ENST00000519638	D;D;D;D;D;D;D	0.94457	-3.43;-3.43;-3.43;-3.43;-3.43;-3.43;-3.43	5.91	5.91	0.95273	.	0.088984	0.85682	D	0.000000	D	0.95204	0.8445	L	0.45137	1.4	0.80722	D	1	D;B;B	0.58620	0.983;0.257;0.009	P;B;B	0.57502	0.822;0.162;0.029	D	0.94048	0.7315	10	0.37606	T	0.19	-17.7147	19.29	0.94095	0.0:0.0:1.0:0.0	.	46;46;46	O94905;O94905-3;O94905-2	ERLN2_HUMAN;.;.	D	46	ENSP00000380405:G46D;ENSP00000429903:G46D;ENSP00000276461:G46D;ENSP00000427847:G46D;ENSP00000335220:G46D;ENSP00000429621:G46D;ENSP00000428112:G46D	ENSP00000276461:G46D	G	+	2	0	ERLIN2	37717070	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.379000	0.97198	2.799000	0.96334	0.650000	0.86243	GGC	.	.	.	none		0.537	ERLIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376712.2	NM_007175		A	37597912	G	A	37597912	3	1	91	1	0	0	0	0	1	0	0	0	5235	1203	42	2	143	2	ERLIN2	8	37597912	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08		37597912	108766110	24	5805											
ST18	9705	hgsc.bcm.edu	37	chr8	53028901	53028901	+	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	cttagacctgccagctctttCagcagactttcattgttctg	7	15	7	12	0	4	2	2	0	2	2	4	2	4	2	2	0	3	3	2	0	1	5			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr8:53028901C>T	ENST00000276480.7	-	25	3620	c.2937G>A	c.(2935-2937)ctG>ctA	p.L979L		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	979					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				CCAGCTCTTTCAGCAGACTTT	0.433																																					p.L979L		Atlas-SNP	.											.	ST18	212	.	0			c.G2937A						PASS	.						232	167	189					8																	53028901		2203	4300	6503	SO:0001819	synonymous_variant	9705	exon25			CTCTTTCAGCAGA	AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"Zinc fingers, C2HC-type containing"	18695	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 3"		"zinc finger protein 387", "suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.2937G>A	chr8.hg19:g.53028901C>T		139.0	0.0	.		175.0	69.0	.	NM_014682	Q17RY1	Silent	SNP	ENST00000276480.7	hg19	CCDS6149.1																																																																																			.	.	.	none		0.433	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1			T	53028901	C	T	53028901	2	4	91	1	0	0	0	0	0	0	0	1	15224	813	29	2		2	ST18	8	53028901	Silent	SNP	C	TCGA-B3-4104-01A-01D-1458-08	15430989	53028901	93335121	25	5806											
TYRP1	7306	hgsc.bcm.edu	37	chr9	12704628	12704628	+	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	gggacaaacccatttgtctcCaaatgatcctatttttgtcc	10	14	6	11	0	1	1	0	1	1	0	4	2	3	2	4	1	1	0	4	1	3	4			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr9:12704628C>A	ENST00000388918.5	+	6	1313	c.1184C>A	c.(1183-1185)cCa>cAa	p.P395Q	TYRP1_ENST00000381136.2_Missense_Mutation_p.P105Q|TYRP1_ENST00000381137.2_Missense_Mutation_p.P104Q|RP11-3L8.3_ENST00000417638.1_RNA	NM_000550.2	NP_000541.1	P17643	TYRP1_HUMAN	tyrosinase-related protein 1	395				PN -> SQ (in Ref. 7; CAA35820). {ECO:0000305}.	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)		CATTTGTCTCCAAATGATCCT	0.443									Oculocutaneous Albinism																												p.P395Q		Atlas-SNP	.											.	TYRP1	60	.	0			c.C1184A						PASS	.						122	105	111					9																	12704628		2203	4300	6503	SO:0001583	missense	7306	exon6	Familial Cancer Database		TGTCTCCAAATGA	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.1184C>A	chr9.hg19:g.12704628C>A	ENSP00000373570:p.Pro395Gln	188.0	0.0	.		380.0	111.0	.	NM_000550	P78468|P78469|Q13721|Q15679	Missense_Mutation	SNP	ENST00000388918.5	hg19	CCDS34990.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.173865	0.78452	.	.	ENSG00000107165	ENST00000381137;ENST00000388918;ENST00000381136	D;D;D	0.99089	-5.41;-5.41;-5.41	5.5	5.5	0.81552	Tyrosinase (1);Uncharacterised domain, di-copper centre (2);	0.000000	0.85682	D	0.000000	D	0.99468	0.9811	M	0.91768	3.24	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98693	1.0697	10	0.72032	D	0.01	-20.7972	19.7537	0.96281	0.0:1.0:0.0:0.0	.	395	P17643	TYRP1_HUMAN	Q	104;395;105	ENSP00000370529:P104Q;ENSP00000373570:P395Q;ENSP00000370528:P105Q	ENSP00000370528:P105Q	P	+	2	0	TYRP1	12694628	1.000000	0.71417	0.999000	0.59377	0.634000	0.38068	7.370000	0.79589	2.736000	0.93811	0.591000	0.81541	CCA	.	.	.	none		0.443	TYRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055502.3	NM_000550		A	12704628	C	A	12704628	3	1	91	1	0	0	0	0	1	0	0	0	16828	594	21	4	1202	4	TYRP1	9	12704628	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08		12704628	128508803	26	5807											
C9orf24	84688	hgsc.bcm.edu	37	chr9	34397497	34397497	+	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	cccaccaatctcccacttacCggagtcagaaacttgttggc	10	9	7	15	1	2	1	1	0	1	1	3	2	2	2	4	2	2	1	4	2	3	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr9:34397497C>T	ENST00000297623.2	-	1	333	c.135G>A	c.(133-135)ccG>ccA	p.P45P		NM_032596.3	NP_115985.2	Q8NCR6	SMRP1_HUMAN	chromosome 9 open reading frame 24	45					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)		TCCCACTTACCGGAGTCAGAA	0.522																																					p.P45P		Atlas-SNP	.											.	C9orf24	15	.	0			c.G135A						PASS	.						125	117	120					9																	34397497		2203	4300	6503	SO:0001630	splice_region_variant	84688	exon1			ACTTACCGGAGTC	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.135+1G>A	chr9.hg19:g.34397497C>T		215.0	0.0	.		308.0	87.0	.	NM_032596	Q5T598|Q5T599|Q5T5A0|Q8N9G4|Q96KD1|Q96LN1	Silent	SNP	ENST00000297623.2	hg19	CCDS6554.1	.	.	.	.	.	.	.	.	.	.	C	14.01	2.408871	0.42715	.	.	ENSG00000164972	ENST00000444429	.	.	.	5.44	4.53	0.55603	.	.	.	.	.	T	0.61739	0.2371	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59721	-0.7401	4	.	.	.	-0.9559	10.3744	0.44073	0.0:0.9067:0.0:0.0933	.	.	.	.	R	11	.	.	G	-	1	0	C9orf24	34387497	0.988000	0.35896	0.992000	0.48379	0.887000	0.51463	2.922000	0.48860	1.271000	0.44313	0.467000	0.42956	GGG	.	.	.	none		0.522	C9orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001098.3	NM_147169	Silent	T	34397497	C	T	34397497	5	4	91	1	0	0	0	0	0	0	1	0	2477	666	23	1	787	1	C9orf24	9	34397497	Splice_Site	SNP	C	TCGA-B3-4104-01A-01D-1458-08	21692869	34397497	106815934	27	5808											
ALDH1B1	219	hgsc.bcm.edu	37	chr9	38396007	38396007	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcagcccgggaagccttcCgcctggggtccccatggcgc	6	5	14	16	3	0	0	0	0	0	0	2	1	2	1	6	4	3	1	6	4	2	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr9:38396007C>T	ENST00000377698.3	+	2	415	c.262C>T	c.(262-264)Cgc>Tgc	p.R88C		NM_000692.4	NP_000683.3	P30837	AL1B1_HUMAN	aldehyde dehydrogenase 1 family, member B1	88					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)		GGAAGCCTTCCGCCTGGGGTC	0.677																																					p.R88C		Atlas-SNP	.											.	ALDH1B1	50	.	0			c.C262T						PASS	.						62	67	65					9																	38396007		2203	4300	6503	SO:0001583	missense	219	exon2			GCCTTCCGCCTGG	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.262C>T	chr9.hg19:g.38396007C>T	ENSP00000366927:p.Arg88Cys	221.0	0.0	.		313.0	22.0	.	NM_000692	B2R8F0|Q8WX76|Q9BV45	Missense_Mutation	SNP	ENST00000377698.3	hg19	CCDS6615.1	.	.	.	.	.	.	.	.	.	.	C	13.05	2.121727	0.37436	.	.	ENSG00000137124	ENST00000377698	T	0.77358	-1.09	5.61	2.7	0.31948	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.373330	0.22798	N	0.055518	T	0.71443	0.3340	M	0.67625	2.065	0.43377	D	0.995473	B	0.14012	0.009	B	0.18561	0.022	T	0.68349	-0.5432	10	0.87932	D	0	.	4.9629	0.14076	0.2807:0.5588:0.0:0.1605	.	88	P30837	AL1B1_HUMAN	C	88	ENSP00000366927:R88C	ENSP00000366927:R88C	R	+	1	0	ALDH1B1	38386007	0.002000	0.14202	0.982000	0.44146	0.995000	0.86356	-0.376000	0.07465	0.750000	0.32877	0.655000	0.94253	CGC	.	.	.	none		0.677	ALDH1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052492.1			T	38396007	C	T	38396007	3	4	91	1	0	0	0	0	1	0	0	0	493	652	23	1	264	1	ALDH1B1	9	38396007	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	3998510	38396007	102817424	28	5809											
NEBL	10529	hgsc.bcm.edu	37	chr10	21309109	21309109	+	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	ggtgtatctgccaccgtggtGaaggactgcttcgggtagtg	6	11	16	8	2	1	1	0	1	1	0	2	2	1	2	2	4	2	3	2	4	3	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr10:21309109G>A	ENST00000417816.2	-	3	539	c.186C>T	c.(184-186)ttC>ttT	p.F62F	NEBL_ENST00000377159.4_Silent_p.F28F	NM_001173484.1|NM_213569.2	NP_001166955.1|NP_998734.1	O76041	NEBL_HUMAN	nebulette	107					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						CCACCGTGGTGAAGGACTGCT	0.413																																					p.F62F		Atlas-SNP	.											.	NEBL	199	.	0			c.C186T						PASS	.						103	97	99					10																	21309109		2203	4300	6503	SO:0001819	synonymous_variant	10529	exon3			CGTGGTGAAGGAC	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.186C>T	chr10.hg19:g.21309109G>A		153.0	0.0	.		193.0	11.0	.	NM_001173484	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Silent	SNP	ENST00000417816.2	hg19	CCDS7133.1																																																																																			.	.	.	none		0.413	NEBL-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047112.1	NM_006393		A	21309109	G	A	21309109	2	1	91	1	0	0	0	0	0	0	0	1	10310	1281	45	2		2	NEBL	10	21309109	Silent	SNP	G	TCGA-B3-4104-01A-01D-1458-08		21309109	114225638	29	5810											
SGMS1	259230	hgsc.bcm.edu	37	chr10	52071078	52071078	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccgtgtggccgctgtacagaTagtccccacacatgttgtga	8	10	11	12	2	0	2	0	1	0	1	1	2	1	2	4	1	1	3	4	1	2	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr10:52071078T>C	ENST00000361781.2	-	9	1798	c.839A>G	c.(838-840)tAt>tGt	p.Y280C	SGMS1_ENST00000429490.1_Missense_Mutation_p.Y111C	NM_147156.3	NP_671512.1	Q86VZ5	SMS1_HUMAN	sphingomyelin synthase 1	286					apoptotic process (GO:0006915)|cell growth (GO:0016049)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|Golgi trans cisterna (GO:0000138)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ceramide cholinephosphotransferase activity (GO:0047493)|kinase activity (GO:0016301)|sphingomyelin synthase activity (GO:0033188)			endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16						GCTGTACAGATAGTCCCCACA	0.453																																					p.Y280C		Atlas-SNP	.											.	SGMS1	40	.	0			c.A839G						PASS	.						141	105	117					10																	52071078		2203	4300	6503	SO:0001583	missense	259230	exon9			TACAGATAGTCCC	AY280959	CCDS7240.1	10q11.2	2013-01-10	2007-03-16	2007-03-16	ENSG00000198964	ENSG00000198964	2.7.8.27	"Sterile alpha motif (SAM) domain containing"	29799	protein-coding gene	gene with protein product		611573	"transmembrane protein 23"	TMEM23		11841947, 14976195	Standard	NM_147156		Approved	MOB, MGC17342, SMS1	uc001jje.3	Q86VZ5	OTTHUMG00000018231	ENST00000361781.2:c.839A>G	chr10.hg19:g.52071078T>C	ENSP00000354829:p.Tyr280Cys	113.0	0.0	.		129.0	57.0	.	NM_147156	Q68U43|Q6EKK0|Q75SP1	Missense_Mutation	SNP	ENST00000361781.2	hg19	CCDS7240.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.171766	0.78452	.	.	ENSG00000198964	ENST00000412547;ENST00000361781;ENST00000429490	T	0.53206	0.63	5.87	4.68	0.58851	.	0.056539	0.64402	D	0.000001	T	0.65974	0.2743	M	0.73430	2.235	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.76575	0.968;0.988	T	0.69548	-0.5116	10	0.87932	D	0	-23.9233	11.1732	0.48584	0.1378:0.0:0.0:0.8622	.	111;286	B4DJU2;Q86VZ5	.;SMS1_HUMAN	C	80;280;111	ENSP00000354829:Y280C	ENSP00000354829:Y280C	Y	-	2	0	SGMS1	51741084	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.058000	0.64300	2.371000	0.80710	0.533000	0.62120	TAT	.	.	.	none		0.453	SGMS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048074.2	NM_147156		C	52071078	T	C	52071078	3	2	91	1	0	0	0	0	1	0	0	0	14227	1406	49	3	414	3	SGMS1	10	52071078	Missense_Mutation	SNP	T	TCGA-B3-4104-01A-01D-1458-08	30761969	52071078	83463669	30	5811											
IDE	3416	hgsc.bcm.edu	37	chr10	94297234	94297234	+	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	atattctcgcttgtcttcagGagacttggtaatgtgatttc	8	17	9	7	1	3	2	1	1	2	1	5	3	3	2	0	2	0	2	0	2	2	7			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr10:94297234G>C	ENST00000265986.6	-	2	228	c.172C>G	c.(172-174)Cct>Gct	p.P58A		NM_004969.3	NP_004960.2	P14735	IDE_HUMAN	insulin-degrading enzyme	58					beta-amyloid metabolic process (GO:0050435)|bradykinin catabolic process (GO:0010815)|determination of adult lifespan (GO:0008340)|hormone catabolic process (GO:0042447)|insulin catabolic process (GO:1901143)|insulin metabolic process (GO:1901142)|insulin receptor signaling pathway (GO:0008286)|negative regulation of proteolysis (GO:0045861)|positive regulation of protein oligomerization (GO:0032461)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|ubiquitin homeostasis (GO:0010992)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|beta-amyloid binding (GO:0001540)|beta-endorphin binding (GO:0031626)|glycoprotein binding (GO:0001948)|insulin binding (GO:0043559)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|urinary_tract(2)	33					"""Insulin(DB00071)|Bacitracin(DB00626)|Insulin Regular(DB00030)"	TTGTCTTCAGGAGACTTGGTA	0.388																																					p.P58A		Atlas-SNP	.											.	IDE	77	.	0			c.C172G						PASS	.						216	192	200					10																	94297234		2203	4300	6503	SO:0001583	missense	3416	exon2			CTTCAGGAGACTT	M21188	CCDS7421.1, CCDS53554.1	10q23-q25	2007-03-27			ENSG00000119912	ENSG00000119912			5381	protein-coding gene	gene with protein product	"insulysin"	146680				2293021	Standard	NM_004969		Approved		uc001kia.3	P14735	OTTHUMG00000018759	ENST00000265986.6:c.172C>G	chr10.hg19:g.94297234G>C	ENSP00000265986:p.Pro58Ala	166.0	0.0	.		210.0	85.0	.	NM_004969	B2R721|B7ZAU2|D3DR35|Q5T5N2	Missense_Mutation	SNP	ENST00000265986.6	hg19	CCDS7421.1	.	.	.	.	.	.	.	.	.	.	G	10.72	1.430602	0.25726	.	.	ENSG00000119912	ENST00000265986;ENST00000436178	T;T	0.30448	1.53;1.53	5.58	5.58	0.84498	Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.056903	0.64402	D	0.000001	T	0.20659	0.0497	N	0.14661	0.345	0.80722	D	1	B	0.13145	0.007	B	0.14578	0.011	T	0.09228	-1.0684	10	0.10902	T	0.67	-4.7075	19.5704	0.95409	0.0:0.0:1.0:0.0	.	58	P14735	IDE_HUMAN	A	58;44	ENSP00000265986:P58A;ENSP00000408850:P44A	ENSP00000265986:P58A	P	-	1	0	IDE	94287214	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.325000	0.96381	2.624000	0.88883	0.655000	0.94253	CCT	.	.	.	none		0.388	IDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049393.1	NM_004969		C	94297234	G	C	94297234	3	2	91	1	0	0	0	0	1	0	0	0	7500	1174	41	4	2983	4	IDE	10	94297234	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	42226156	94297234	41237513	31	5812											
RIC8A	60626	hgsc.bcm.edu	37	chr11	209483	209483	+	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	tgtcatctggctgcagagtgTccgaatcctgtcccgggacc	6	10	12	13	2	2	1	1	0	1	1	5	3	5	2	4	2	1	2	4	2	1	0			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr11:209483T>A	ENST00000526104.1	+	3	1553	c.209T>A	c.(208-210)gTc>gAc	p.V70D	RIC8A_ENST00000325207.5_Missense_Mutation_p.V70D|BET1L_ENST00000529614.2_5'Flank|BET1L_ENST00000325147.9_5'Flank|RIC8A_ENST00000527696.1_Missense_Mutation_p.V64D|BET1L_ENST00000332865.6_5'Flank|BET1L_ENST00000486280.1_5'Flank|BET1L_ENST00000382762.3_5'Flank|BET1L_ENST00000410108.1_5'Flank			Q9NPQ8	RIC8A_HUMAN	RIC8 guanine nucleotide exchange factor A	70					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)		CTGCAGAGTGTCCGAATCCTG	0.642																																					p.V70D		Atlas-SNP	.											.	RIC8A	45	.	0			c.T209A						PASS	.						83	79	80					11																	209483		2203	4300	6503	SO:0001583	missense	60626	exon3			AGAGTGTCCGAAT	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.209T>A	chr11.hg19:g.209483T>A	ENSP00000432008:p.Val70Asp	142.0	0.0	.		107.0	23.0	.	NM_021932	Q0P508|Q2T9J1|Q7Z352|Q96EZ1|Q96SZ2|Q9H064|Q9H5H3|Q9H9E7	Missense_Mutation	SNP	ENST00000526104.1	hg19		.	.	.	.	.	.	.	.	.	.	T	31	5.086235	0.94100	.	.	ENSG00000177963	ENST00000526104;ENST00000325207;ENST00000531209;ENST00000528357;ENST00000530889;ENST00000527696	T;T;T;T	0.53423	0.7;0.7;0.62;0.7	4.32	4.32	0.51571	Armadillo-type fold (1);	0.242015	0.40302	N	0.001130	T	0.54983	0.1892	L	0.39898	1.24	0.53688	D	0.999973	D;P;P	0.58620	0.983;0.904;0.951	P;P;P	0.59761	0.807;0.863;0.784	T	0.59621	-0.7420	10	0.87932	D	0	-12.0203	13.3635	0.60669	0.0:0.0:0.0:1.0	.	64;70;70	Q9NPQ8-2;Q9NPQ8;Q9NPQ8-3	.;RIC8A_HUMAN;.	D	70;70;70;46;74;64	ENSP00000432008:V70D;ENSP00000325941:V70D;ENSP00000433968:V74D;ENSP00000434833:V64D	ENSP00000325941:V70D	V	+	2	0	RIC8A	199483	1.000000	0.71417	0.975000	0.42487	0.986000	0.74619	7.525000	0.81892	1.906000	0.55180	0.459000	0.35465	GTC	.	.	.	none		0.642	RIC8A-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000384761.1	NM_021932		A	209483	T	A	209483	3	1	91	1	0	0	0	0	1	0	0	0	13368	1667	58	5	219	5	RIC8A	11	209483	Missense_Mutation	SNP	T	TCGA-B3-4104-01A-01D-1458-08		209483	134797033	32	5813											
APLNR	187	hgsc.bcm.edu	37	chr11	57004337	57004337	+	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	aaacacggtccagagcaccaGaccgttgcccgtggtgccca	10	5	11	15	3	0	2	0	0	0	2	1	2	1	2	5	2	4	2	5	2	1	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr11:57004337G>C	ENST00000606794.1	-	1	338	c.142C>G	c.(142-144)Ctg>Gtg	p.L48V		NM_005161.4	NP_005152.1	P35414	APJ_HUMAN	apelin receptor	48					G-protein coupled receptor signaling pathway (GO:0007186)|gastrulation (GO:0007369)|heart development (GO:0007507)|regulation of body fluid levels (GO:0050878)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						CAGAGCACCAGACCGTTGCCC	0.592																																					p.L48V		Atlas-SNP	.											.	APLNR	62	.	0			c.C142G						PASS	.						75	72	73					11																	57004337		2201	4296	6497	SO:0001583	missense	187	exon1			GCACCAGACCGTT	U03642	CCDS7950.1	11q12.1	2012-08-08	2008-05-12	2008-05-12	ENSG00000134817	ENSG00000134817			339	protein-coding gene	gene with protein product	"APJ (apelin) receptor"	600052	"angiotensin II receptor-like 1"	AGTRL1		8294032, 14622440	Standard	NM_005161		Approved	FLJ90771, APJ, APJR	uc001njo.3	P35414	OTTHUMG00000167021	ENST00000606794.1:c.142C>G	chr11.hg19:g.57004337G>C	ENSP00000475344:p.Leu48Val	181.0	0.0	.		149.0	70.0	.	NM_005161		Missense_Mutation	SNP	ENST00000606794.1	hg19	CCDS7950.1	.	.	.	.	.	.	.	.	.	.	G	12.76	2.034103	0.35893	.	.	ENSG00000134817	ENST00000257254;ENST00000444275	T	0.77098	-1.07	5.25	4.13	0.48395	GPCR, rhodopsin-like superfamily (1);	0.088434	0.47455	D	0.000235	T	0.71417	0.3337	L	0.35593	1.075	0.37382	D	0.912064	P	0.43231	0.801	P	0.45610	0.487	T	0.74506	-0.3643	10	0.36615	T	0.2	-13.9545	12.6969	0.57010	0.0931:0.0:0.9069:0.0	.	48	P35414	APJ_HUMAN	V	48;13	ENSP00000257254:L48V	ENSP00000257254:L48V	L	-	1	2	APLNR	56760913	0.027000	0.19231	1.000000	0.80357	0.995000	0.86356	0.324000	0.19610	2.460000	0.83146	0.561000	0.74099	CTG	.	.	.	none		0.592	APLNR-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470575.1	NM_005161		C	57004337	G	C	57004337	3	2	91	1	0	0	0	0	1	0	0	0	777	933	33	4	1004	4	APLNR	11	57004337	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	56794854	57004337	78002179	33	5814											
MS4A15	219995	hgsc.bcm.edu	37	chr11	60540926	60540926	+	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	ggcctttgctgggacagccaTtctgctcatggattttggtg	5	14	13	9	0	2	0	1	0	1	0	2	2	2	2	2	4	3	2	2	4	0	4			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr11:60540926T>A	ENST00000405633.3	+	5	546	c.467T>A	c.(466-468)aTt>aAt	p.I156N	MS4A15_ENST00000528170.1_Missense_Mutation_p.I115N|MS4A15_ENST00000337911.4_Missense_Mutation_p.I63N	NM_001098835.1	NP_001092305.1	Q8N5U1	M4A15_HUMAN	membrane-spanning 4-domains, subfamily A, member 15	156						integral component of membrane (GO:0016021)				breast(1)|large_intestine(2)|lung(3)	6						GGGACAGCCATTCTGCTCATG	0.572																																					p.I156N		Atlas-SNP	.											.	MS4A15	37	.	0			c.T467A						PASS	.						101	82	89					11																	60540926		2203	4300	6503	SO:0001583	missense	219995	exon5			CAGCCATTCTGCT	AY584608	CCDS7991.1, CCDS44617.1, CCDS60802.1	11q12.2	2008-03-25							28573	protein-coding gene	gene with protein product							Standard	NM_001098835		Approved		uc009ynf.1	Q8N5U1		ENST00000405633.3:c.467T>A	chr11.hg19:g.60540926T>A	ENSP00000386022:p.Ile156Asn	71.0	0.0	.		70.0	39.0	.	NM_001098835	A9UJY6|A9UJY7|F2Z2J5	Missense_Mutation	SNP	ENST00000405633.3	hg19	CCDS44617.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.159477	0.78226	.	.	ENSG00000166961	ENST00000528170;ENST00000337911;ENST00000405633	T;T;T	0.02763	4.17;4.17;4.17	4.73	4.73	0.59995	.	0.564419	0.18877	N	0.128670	T	0.12433	0.0302	M	0.82132	2.575	0.32907	D	0.514004	D;D	0.61080	0.98;0.989	P;P	0.60345	0.873;0.837	T	0.06006	-1.0851	10	0.87932	D	0	-4.8067	10.6302	0.45532	0.0:0.0:0.0:1.0	.	115;156	F2Z2J5;Q8N5U1	.;M4A15_HUMAN	N	115;63;156	ENSP00000434165:I115N;ENSP00000338692:I63N;ENSP00000386022:I156N	ENSP00000338692:I63N	I	+	2	0	MS4A15	60297502	0.968000	0.33430	0.979000	0.43373	0.987000	0.75469	2.143000	0.42187	1.772000	0.52199	0.454000	0.30748	ATT	.	.	.	none		0.572	MS4A15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395618.1			A	60540926	T	A	60540926	3	1	91	1	0	0	0	0	1	0	0	0	9866	1493	52	5	481	5	MS4A15	11	60540926	Missense_Mutation	SNP	T	TCGA-B3-4104-01A-01D-1458-08	3536589	60540926	74465590	34	5815											
VWCE	220001	hgsc.bcm.edu	37	chr11	61026184	61026184	+	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	ccccccgagaagcccccactGggggctgctgggggccaggg	5	3	17	16	1	0	1	0	0	0	1	0	2	0	1	6	5	2	2	6	5	1	0			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr11:61026184G>A	ENST00000335613.5	-	20	3217	c.2831C>T	c.(2830-2832)cCa>cTa	p.P944L	VWCE_ENST00000535710.1_Missense_Mutation_p.P409L	NM_152718.2	NP_689931.2	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	944						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						AGCCCCCACTGGGGGCTGCTG	0.662																																					p.P944L		Atlas-SNP	.											.	VWCE	84	.	0			c.C2831T						PASS	.						32	41	38					11																	61026184		2181	4260	6441	SO:0001583	missense	220001	exon20			CCCACTGGGGGCT	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.2831C>T	chr11.hg19:g.61026184G>A	ENSP00000334186:p.Pro944Leu	224.0	0.0	.		178.0	55.0	.	NM_152718	A5PKV0|Q7Z7L6|Q86WK8	Missense_Mutation	SNP	ENST00000335613.5	hg19	CCDS8002.1	.	.	.	.	.	.	.	.	.	.	G	7.159	0.585335	0.13749	.	.	ENSG00000167992	ENST00000335613;ENST00000535710	T;T	0.68025	-0.3;3.56	4.57	2.7	0.31948	.	1.078380	0.07367	N	0.885042	T	0.43545	0.1252	N	0.03115	-0.41	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33007	-0.9885	10	0.48119	T	0.1	.	7.595	0.28044	0.2008:0.0:0.7992:0.0	.	944	Q96DN2	VWCE_HUMAN	L	944;409	ENSP00000334186:P944L;ENSP00000442570:P409L	ENSP00000334186:P944L	P	-	2	0	VWCE	60782760	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	1.128000	0.31369	0.478000	0.27488	-0.254000	0.11334	CCA	.	.	.	none		0.662	VWCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398811.1	NM_152718		A	61026184	G	A	61026184	3	1	91	1	0	0	0	0	1	0	0	0	17257	1348	47	2	40	2	VWCE	11	61026184	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	485258	61026184	73980332	35	5816											
CORO1B	57175	hgsc.bcm.edu	37	chr11	67207603	67207603	+	Frame_Shift_Del	DEL	C	C	-																															tcttaccgggcgatctcgcaCttgctgacctccaggccccg																										TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr11:67207603delC	ENST00000341356.5	-	8	1103	c.993delG	c.(991-993)aagfs	p.K331fs	CORO1B_ENST00000539724.1_Intron|CORO1B_ENST00000393893.1_Frame_Shift_Del_p.K331fs|PTPRCAP_ENST00000326294.3_5'Flank	NM_020441.2	NP_065174.1	Q9BR76	COR1B_HUMAN	coronin, actin binding protein, 1B	331					actin cytoskeleton organization (GO:0030036)|actin filament branching (GO:0090135)|actin filament bundle assembly (GO:0051017)|cell migration (GO:0016477)|endothelial cell chemotaxis (GO:0035767)|negative regulation of Arp2/3 complex-mediated actin nucleation (GO:0034316)|positive regulation of lamellipodium morphogenesis (GO:2000394)|protein localization to cell leading edge (GO:1902463)|ruffle organization (GO:0031529)|wound healing (GO:0042060)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|Arp2/3 complex binding (GO:0071933)|identical protein binding (GO:0042802)			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	13			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			CGATCTCGCACTTGCTGACCT	0.622																																					p.C332fs		Atlas-INDEL	.											.	CORO1B	30	.	0			c.994delT						PASS	.						65	67	66					11																	67207603		2200	4295	6495	SO:0001589	frameshift_variant	57175	exon8			.	AK000860	CCDS8164.1	11q13.1	2013-01-10	2001-11-28		ENSG00000172725	ENSG00000172725		"Coronins", "WD repeat domain containing"	2253	protein-coding gene	gene with protein product		609849	"coronin, actin-binding protein, 1B"			9778037	Standard	NM_001018070		Approved	coronin-2	uc001olk.1	Q9BR76	OTTHUMG00000167775	ENST00000341356.5:c.993delG	chr11.hg19:g.67207603delC	ENSP00000340211:p.Lys331fs	172.0	0.0	0		139.0	65.0	0.467626	NM_020441	B2RD45	Frame_Shift_Del	DEL	ENST00000341356.5	hg19	CCDS8164.1																																																																																			.	.	.	none		0.622	CORO1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396220.1	NM_020441		-	67207603	C	-	67207603	7	5	91	1	0	1	0	1	0	0	0	0	3756	564	20	0	492	0	CORO1B	11	67207603	Frame_Shift_Del	DEL	C	TCGA-B3-4104-01A-01D-1458-08	6181419	67207603	67798913	36	5817											
STARD10	10809	hgsc.bcm.edu	37	chr11	72470333	72470333	+	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	gcgggcgatgtcaaaagtctCaatgacgttgctgtcccatt	9	11	11	10	3	2	1	2	1	1	0	4	2	3	1	1	1	1	2	1	1	3	2			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr11:72470333C>G	ENST00000334805.6	-	3	1220	c.301G>C	c.(301-303)Gag>Cag	p.E101Q	STARD10_ENST00000538437.1_5'UTR|STARD10_ENST00000538536.1_Missense_Mutation_p.E55Q|STARD10_ENST00000545082.1_Missense_Mutation_p.E72Q|STARD10_ENST00000543304.1_Missense_Mutation_p.E101Q|ARAP1_ENST00000359373.5_Intron	NM_006645.2	NP_006636.2	Q9Y365	PCTL_HUMAN	StAR-related lipid transfer (START) domain containing 10	101	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				bile acid secretion (GO:0032782)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)	cytosol (GO:0005829)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|microvillus (GO:0005902)	lipid binding (GO:0008289)			endometrium(4)|large_intestine(1)|lung(2)|prostate(1)	8			BRCA - Breast invasive adenocarcinoma(5;7.08e-07)			TCAAAAGTCTCAATGACGTTG	0.562																																					p.E101Q		Atlas-SNP	.											.	STARD10	25	.	0			c.G301C						PASS	.						138	143	141					11																	72470333		2184	4279	6463	SO:0001583	missense	10809	exon3			AAGTCTCAATGAC	AF039696	CCDS41688.1	11q13	2011-09-12	2007-08-16	2003-02-07		ENSG00000214530		"StAR-related lipid transfer (START) domain containing"	10666	protein-coding gene	gene with protein product			"serologically defined colon cancer antigen 28", "START domain containing 10"	SDCCAG28		9610721	Standard	NM_006645		Approved	NY-CO-28, CGI-52, PCTP2	uc001otb.3	Q9Y365		ENST00000334805.6:c.301G>C	chr11.hg19:g.72470333C>G	ENSP00000335247:p.Glu101Gln	128.0	0.0	.		127.0	64.0	.	NM_006645	O60532	Missense_Mutation	SNP	ENST00000334805.6	hg19	CCDS41688.1	.	.	.	.	.	.	.	.	.	.	C	36	5.751817	0.96890	.	.	ENSG00000214530	ENST00000537351;ENST00000543304;ENST00000334805;ENST00000538536;ENST00000545082;ENST00000544767;ENST00000537947;ENST00000536728;ENST00000542989;ENST00000546314;ENST00000539138;ENST00000535054	T;T;T;T;T;T;T;T;T;T;D;T	0.85088	1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;-1.94;0.81	5.95	5.95	0.96441	Lipid-binding START (3);START-like domain (1);	0.062950	0.64402	U	0.000008	D	0.91126	0.7206	M	0.79805	2.47	0.58432	D	0.999995	P;P	0.52316	0.94;0.952	P;P	0.57720	0.591;0.826	D	0.88905	0.3355	10	0.28530	T	0.3	-28.7367	17.8792	0.88835	0.0:1.0:0.0:0.0	.	55;101	F5GY11;Q9Y365	.;PCTL_HUMAN	Q	8;101;101;55;72;32;101;32;101;101;72;55	ENSP00000445708:E8Q;ENSP00000438792:E101Q;ENSP00000335247:E101Q;ENSP00000440016:E55Q;ENSP00000443548:E72Q;ENSP00000438357:E32Q;ENSP00000445657:E101Q;ENSP00000442414:E32Q;ENSP00000443597:E101Q;ENSP00000445886:E101Q;ENSP00000441589:E72Q;ENSP00000440924:E55Q	ENSP00000335247:E101Q	E	-	1	0	STARD10	72147981	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.825000	0.97269	0.655000	0.94253	GAG	.	.	.	none		0.562	STARD10-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397254.1			G	72470333	C	G	72470333	3	3	91	1	0	0	0	0	1	0	0	0	15267	835	29	4	594	4	STARD10	11	72470333	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	5262730	72470333	62536183	37	5818											
ARRB1	408	hgsc.bcm.edu	37	chr11	74985127	74985127	+	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	caggtcctcacagggtgctaGaggccaagttcgtgtcttcg	7	10	13	11	2	2	1	1	0	1	1	5	1	3	1	2	3	1	2	2	3	2	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr11:74985127G>C	ENST00000420843.2	-	11	1002	c.905C>G	c.(904-906)tCt>tGt	p.S302C	ARRB1_ENST00000393505.4_Missense_Mutation_p.S302C|ARRB1_ENST00000360025.3_Missense_Mutation_p.S302C	NM_004041.4	NP_004032.2	P49407	ARRB1_HUMAN	arrestin, beta 1	302					activation of MAPK activity (GO:0000187)|apoptotic DNA fragmentation (GO:0006309)|blood coagulation (GO:0007596)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor internalization (GO:0002031)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of GTPase activity (GO:0034260)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein ubiquitination (GO:0031397)|Notch signaling pathway (GO:0007219)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of GTPase activity (GO:0043547)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H4 acetylation (GO:0090240)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-Golgi vesicle-mediated transport (GO:0006892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|stress fiber assembly (GO:0043149)|transcription from RNA polymerase II promoter (GO:0006366)	basolateral plasma membrane (GO:0016323)|chromatin (GO:0000785)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|pseudopodium (GO:0031143)	angiotensin receptor binding (GO:0031701)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|enzyme inhibitor activity (GO:0004857)|GTPase activator activity (GO:0005096)|insulin-like growth factor receptor binding (GO:0005159)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|large_intestine(2)|lung(4)|prostate(1)	11						CAGGGTGCTAGAGGCCAAGTT	0.602																																					p.S302C		Atlas-SNP	.											.	ARRB1	37	.	0			c.C905G						PASS	.						263	213	230					11																	74985127		2200	4293	6493	SO:0001583	missense	408	exon11			GTGCTAGAGGCCA	BC003636	CCDS31640.1, CCDS44684.1	11q13	2008-12-11			ENSG00000137486	ENSG00000137486			711	protein-coding gene	gene with protein product	"arrestin 2"	107940		ARR1		8486659	Standard	NM_004041		Approved		uc001owe.2	P49407	OTTHUMG00000165444	ENST00000420843.2:c.905C>G	chr11.hg19:g.74985127G>C	ENSP00000409581:p.Ser302Cys	382.0	0.0	.		366.0	162.0	.	NM_020251	B6V9G8|O75625|O75630|Q2PP20|Q9BTK8	Missense_Mutation	SNP	ENST00000420843.2	hg19	CCDS44684.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.125072	0.77436	.	.	ENSG00000137486	ENST00000420843;ENST00000393505;ENST00000360025	T;T;T	0.19250	2.16;2.16;2.16	4.51	4.51	0.55191	Immunoglobulin E-set (1);Arrestin, C-terminal (1);Arrestin-like, C-terminal (1);	0.000000	0.64402	D	0.000002	T	0.50633	0.1627	M	0.87827	2.91	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.71870	0.933;0.975	T	0.60712	-0.7209	10	0.72032	D	0.01	-10.6596	14.7321	0.69388	0.0:0.0:1.0:0.0	.	302;302	P49407-2;P49407	.;ARRB1_HUMAN	C	302	ENSP00000409581:S302C;ENSP00000377141:S302C;ENSP00000353124:S302C	ENSP00000353124:S302C	S	-	2	0	ARRB1	74662775	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	9.770000	0.98971	2.058000	0.61347	0.462000	0.41574	TCT	.	.	.	none		0.602	ARRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384092.3	NM_004041		C	74985127	G	C	74985127	3	2	91	1	0	0	0	0	1	0	0	0	980	942	33	4	375	4	ARRB1	11	74985127	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	2514794	74985127	60021389	38	5819											
RAPGEF3	10411	hgsc.bcm.edu	37	chr12	48142257	48142257	+	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	ctgttgggtcatgagcactgGaatctggtcccatggcctcc	6	11	12	12	0	2	1	1	1	1	0	4	2	4	2	3	4	1	2	3	4	1	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr12:48142257G>A	ENST00000449771.2	-	12	1311	c.1223C>T	c.(1222-1224)tCc>tTc	p.S408F	RAPGEF3_ENST00000389212.3_Missense_Mutation_p.S408F|RAPGEF3_ENST00000405493.2_Missense_Mutation_p.S366F|RAPGEF3_ENST00000549151.1_Missense_Mutation_p.S366F|RAPGEF3_ENST00000171000.4_Missense_Mutation_p.S366F|RAPGEF3_ENST00000395358.3_Missense_Mutation_p.S408F|RAPGEF3_ENST00000548919.1_Missense_Mutation_p.S366F			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	408	Interaction with PDE3B.|N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				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)		ATGAGCACTGGAATCTGGTCC	0.547																																					p.S408F		Atlas-SNP	.											.	RAPGEF3	98	.	0			c.C1223T						PASS	.						131	109	117					12																	48142257		2203	4300	6503	SO:0001583	missense	10411	exon12			GCACTGGAATCTG	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.1223C>T	chr12.hg19:g.48142257G>A	ENSP00000395708:p.Ser408Phe	87.0	0.0	.		82.0	30.0	.	NM_001098531	A8K2G5|E7EQC8|O95634|Q8WVN0	Missense_Mutation	SNP	ENST00000449771.2	hg19	CCDS41775.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.512216	0.85389	.	.	ENSG00000079337	ENST00000405493;ENST00000449771;ENST00000541821;ENST00000549151;ENST00000171000;ENST00000389211;ENST00000389212;ENST00000397089;ENST00000548919;ENST00000395358	T;T;T;T;T;T;T	0.71579	-0.39;-0.4;-0.39;-0.39;-0.4;-0.58;-0.49	5.16	5.16	0.70880	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (3);	0.662303	0.13744	N	0.365734	T	0.80210	0.4581	L	0.44542	1.39	0.58432	D	0.999999	D;D	0.89917	0.992;1.0	D;D	0.77557	0.937;0.99	T	0.79320	-0.1852	10	0.59425	D	0.04	.	16.511	0.84284	0.0:0.0:1.0:0.0	.	420;408	B7Z5J6;O95398	.;RPGF3_HUMAN	F	366;408;55;366;366;366;408;420;366;408	ENSP00000384521:S366F;ENSP00000395708:S408F;ENSP00000448619:S366F;ENSP00000171000:S366F;ENSP00000373864:S408F;ENSP00000448480:S366F;ENSP00000378764:S408F	ENSP00000171000:S366F	S	-	2	0	RAPGEF3	46428524	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.309000	0.78937	2.588000	0.87417	0.650000	0.86243	TCC	.	.	.	none		0.547	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1	NM_006105		A	48142257	G	A	48142257	3	1	91	1	0	0	0	0	1	0	0	0	13058	1174	41	2	1616	2	RAPGEF3	12	48142257	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08		48142257	85709638	39	5820											
MLL2	8085	hgsc.bcm.edu	37	chr12	49425839	49425839	+	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	ctgtagctgctgctgctgctGaggacttaagtgccgcagct	6	11	13	11	1	0	1	0	1	0	0	0	2	0	2	1	1	7	8	1	1	2	2			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr12:49425839G>A	ENST00000301067.7	-	39	12648	c.12649C>T	c.(12649-12651)Cag>Tag	p.Q4217*		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	4217	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)										TGCTGCTGCTGAGGACTTAAG	0.622																																					p.Q4217X		Atlas-SNP	.											.	MLL2	1173	.	0			c.C12649T						PASS	.						29	33	32					12																	49425839		2083	4219	6302	SO:0001587	stop_gained	8085	exon39			GCTGCTGAGGACT	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.12649C>T	chr12.hg19:g.49425839G>A	ENSP00000301067:p.Gln4217*	96.0	0.0	.		81.0	36.0	.	NM_003482	O14687	Nonsense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	53	20.787619	0.99934	.	.	ENSG00000167548	ENST00000301067	.	.	.	4.89	4.89	0.63831	.	0.000000	0.34531	N	0.003897	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.7009	0.88294	0.0:0.0:1.0:0.0	.	.	.	.	X	4217	.	ENSP00000301067:Q4217X	Q	-	1	0	MLL2	47712106	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	6.491000	0.73649	2.662000	0.90505	0.655000	0.94253	CAG	.	.	.	none		0.622	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49425839	G	A	49425839	4	1	91	1	0	0	0	0	0	1	0	0	9628	1299	45	2	4028	2	MLL2	12	49425839	Nonsense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	1283582	49425839	84426056	40	5821											
MLL2	8085	hgsc.bcm.edu	37	chr12	49426526	49426526	+	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	ttgctgctgctgttgttgctGaggagacagtaaagttcgac	8	13	13	7	1	0	2	0	1	0	1	1	4	0	2	0	1	4	8	0	1	2	5			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr12:49426526G>A	ENST00000301067.7	-	39	11961	c.11962C>T	c.(11962-11964)Cag>Tag	p.Q3988*	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3988	Gln-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.Q3718*(1)									TGTTGTTGCTGAGGAGACAGT	0.532																																					p.Q3988X		Atlas-SNP	.											MLL2,NS,lymphoid_neoplasm,0,1	MLL2	1173	.	1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C11962T						PASS	.						64	70	68					12																	49426526		2196	4296	6492	SO:0001587	stop_gained	8085	exon39			GTTGCTGAGGAGA	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.11962C>T	chr12.hg19:g.49426526G>A	ENSP00000301067:p.Gln3988*	42.0	0.0	.		31.0	13.0	.	NM_003482	O14687	Nonsense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	50	17.079656	0.99878	.	.	ENSG00000167548	ENST00000301067	.	.	.	4.88	4.88	0.63580	.	0.000000	0.34652	N	0.003786	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.6695	0.88212	0.0:0.0:1.0:0.0	.	.	.	.	X	3988	.	ENSP00000301067:Q3988X	Q	-	1	0	MLL2	47712793	0.997000	0.39634	1.000000	0.80357	0.099000	0.18886	3.213000	0.51153	2.643000	0.89663	0.655000	0.94253	CAG	.	.	.	none		0.532	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49426526	G	A	49426526	4	1	91	1	0	0	0	0	0	1	0	0	9628	1299	45	2	4715	2	MLL2	12	49426526	Nonsense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	687	49426526	84425369	41	5822											
INSM2	84684	hgsc.bcm.edu	37	chr14	36005048	36005048	+	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	attttctcgtgcaagcactgCccgtccactttttttagctc	6	16	6	13	2	1	0	0	0	1	0	4	0	2	0	2	0	4	3	2	0	2	6			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr14:36005048C>T	ENST00000307169.3	+	1	1801	c.1590C>T	c.(1588-1590)tgC>tgT	p.C530C		NM_032594.3	NP_115983.3	Q96T92	INSM2_HUMAN	insulinoma-associated 2	530					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	10	Breast(36;0.122)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(9;2.16e-07)|Lung(238;2.63e-07)|Epithelial(34;0.00145)|all cancers(34;0.00452)	GBM - Glioblastoma multiforme(112;0.0223)		GCAAGCACTGCCCGTCCACTT	0.627																																					p.C530C		Atlas-SNP	.											.	INSM2	39	.	0			c.C1590T						PASS	.						31	34	33					14																	36005048		2200	4297	6497	SO:0001819	synonymous_variant	84684	exon1			GCACTGCCCGTCC	AF260323	CCDS9657.1	14q13.1	2013-01-08			ENSG00000168348	ENSG00000168348		"Zinc fingers, C2H2-type"	17539	protein-coding gene	gene with protein product	"mlt 1"	614027					Standard	NM_032594		Approved	IA-6	uc001wth.1	Q96T92	OTTHUMG00000140223	ENST00000307169.3:c.1590C>T	chr14.hg19:g.36005048C>T		133.0	0.0	.		116.0	23.0	.	NM_032594	A1L432|J9Y024|Q8N8K7|Q96Q84	Silent	SNP	ENST00000307169.3	hg19	CCDS9657.1																																																																																			.	.	.	none		0.627	INSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276686.1			T	36005048	C	T	36005048	2	4	91	1	0	0	0	0	0	0	0	1	7779	747	26	2		2	INSM2	14	36005048	Silent	SNP	C	TCGA-B3-4104-01A-01D-1458-08		36005048	71344492	42	5823											
FKBP3	2287	hgsc.bcm.edu	37	chr14	45603575	45603575	+	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	atctgaaccgtgttcctgcaGaaacttgataatgtccttct	10	14	7	10	1	2	3	0	2	2	1	4	3	4	3	3	0	3	2	3	0	3	4			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr14:45603575G>A	ENST00000216330.3	-	2	495	c.85C>T	c.(85-87)Ctg>Ttg	p.L29L	FKBP3_ENST00000396062.3_Silent_p.L29L|FANCM_ENST00000542564.2_5'Flank|FANCM_ENST00000267430.5_5'Flank|FANCM_ENST00000556036.1_5'Flank			Q00688	FKBP3_HUMAN	FK506 binding protein 3, 25kDa	29					chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)			NS(1)|biliary_tract(1)|endometrium(1)|large_intestine(2)|lung(6)|skin(1)	12						TGTTCCTGCAGAAACTTGATA	0.652																																					p.L29L		Atlas-SNP	.											.	FKBP3	21	.	0			c.C85T						PASS	.						85	76	79					14																	45603575		2203	4300	6503	SO:0001819	synonymous_variant	2287	exon1			CCTGCAGAAACTT	M96256	CCDS9683.1	14q21.2	2008-08-11	2002-08-29		ENSG00000100442	ENSG00000100442			3719	protein-coding gene	gene with protein product		186947	"FK506-binding protein 3 (25kD)"			1374240, 1532945	Standard	NM_002013		Approved	FKBP-25, PPIase	uc010tqf.2	Q00688	OTTHUMG00000140267	ENST00000216330.3:c.85C>T	chr14.hg19:g.45603575G>A		215.0	0.0	.		161.0	59.0	.	NM_002013	B2R4Q9|Q14317	Silent	SNP	ENST00000216330.3	hg19	CCDS9683.1																																																																																			.	.	.	none		0.652	FKBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276796.1	NM_002013		A	45603575	G	A	45603575	2	1	91	1	0	0	0	0	0	0	0	1	5916	933	33	2		2	FKBP3	14	45603575	Silent	SNP	G	TCGA-B3-4104-01A-01D-1458-08	9598527	45603575	61745965	43	5824											
ZFP36L1	677	hgsc.bcm.edu	37	chr14	69256349	69256349	+	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	tggctgctgctggagctgctCaggtagccctcctggtccga	4	10	14	13	1	1	0	1	0	0	0	3	2	3	1	3	4	5	6	3	4	1	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr14:69256349C>G	ENST00000439696.2	-	2	1219	c.918G>C	c.(916-918)ctG>ctC	p.L306L	ZFP36L1_ENST00000336440.3_Silent_p.L306L|ZFP36L1_ENST00000555997.1_3'UTR	NM_001244701.1|NM_004926.3	NP_001231630.1|NP_004917.2	Q07352	TISB_HUMAN	ZFP36 ring finger protein-like 1	306					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)		TGGAGCTGCTCAGGTAGCCCT	0.597											OREG0022753	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L375L		Atlas-SNP	.											.	ZFP36L1	47	.	0			c.G1125C						PASS	.						71	79	76					14																	69256349		2203	4300	6503	SO:0001819	synonymous_variant	677	exon3			GCTGCTCAGGTAG	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.918G>C	chr14.hg19:g.69256349C>G		229.0	0.0	.	1113	196.0	81.0	.	NM_001244701	Q13851	Silent	SNP	ENST00000439696.2	hg19	CCDS9791.1																																																																																			.	.	.	none		0.597	ZFP36L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413227.1			G	69256349	C	G	69256349	2	3	91	1	0	0	0	0	0	0	0	1	17658	813	29	4		4	ZFP36L1	14	69256349	Silent	SNP	C	TCGA-B3-4104-01A-01D-1458-08	23652774	69256349	38093191	44	5825											
MLH3	27030	hgsc.bcm.edu	37	chr14	75514890	75514890	+	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	aagagctatgttccaggaaaGattttttatgtttctcattt	11	18	7	5	0	1	2	1	0	1	2	3	3	2	3	1	1	1	3	1	1	4	7			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr14:75514890G>C	ENST00000556740.1	-	1	1504	c.1469C>G	c.(1468-1470)tCt>tGt	p.S490C	MLH3_ENST00000544985.1_5'Flank|MLH3_ENST00000555671.1_5'Flank|MLH3_ENST00000238662.7_Missense_Mutation_p.S490C|MLH3_ENST00000556257.1_Missense_Mutation_p.S490C|MLH3_ENST00000380968.2_De_novo_Start_OutOfFrame|MLH3_ENST00000355774.2_Missense_Mutation_p.S490C			Q9UHC1	MLH3_HUMAN	mutL homolog 3	490					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)	p.S490Y(2)		breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		TTCCAGGAAAGATTTTTTATG	0.378								Mismatch excision repair (MMR)																													p.S490C		Atlas-SNP	.											MLH3,NS,carcinoma,0,1	MLH3	200	.	2	Substitution - Missense(2)	lung(2)	c.C1469G						PASS	.						90	97	95					14																	75514890		2203	4299	6502	SO:0001583	missense	27030	exon2			AGGAAAGATTTTT	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)"			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.1469C>G	chr14.hg19:g.75514890G>C	ENSP00000452316:p.Ser490Cys	223.0	0.0	.		358.0	134.0	.	NM_014381	P49751|Q56DK9|Q9P292|Q9UHC0	Missense_Mutation	SNP	ENST00000556740.1	hg19	CCDS32123.1	.	.	.	.	.	.	.	.	.	.	G	6.646	0.487760	0.12641	.	.	ENSG00000119684	ENST00000355774;ENST00000238662;ENST00000556257;ENST00000556740	D;D;D;D	0.83506	-1.63;-1.67;-1.73;-1.63	5.34	-0.28	0.12886	.	1.749140	0.02828	N	0.126415	T	0.81786	0.4896	L	0.56769	1.78	0.09310	N	0.999996	P;P	0.48503	0.911;0.761	P;B	0.47162	0.54;0.24	T	0.65705	-0.6103	10	0.54805	T	0.06	0.3633	2.4863	0.04600	0.2139:0.342:0.3276:0.1165	.	490;490	Q9UHC1-2;Q9UHC1	.;MLH3_HUMAN	C	490	ENSP00000348020:S490C;ENSP00000238662:S490C;ENSP00000451540:S490C;ENSP00000452316:S490C	ENSP00000238662:S490C	S	-	2	0	MLH3	74584643	0.000000	0.05858	0.121000	0.21740	0.448000	0.32197	0.167000	0.16602	-0.075000	0.12798	-0.291000	0.09656	TCT	.	.	.	none		0.378	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		C	75514890	G	C	75514890	3	2	91	1	0	0	0	0	1	0	0	0	9625	942	33	4	2940	4	MLH3	14	75514890	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	6258541	75514890	31834650	45	5826											
GABRB3	2562	hgsc.bcm.edu	37	chr15	26793190	26793190	+	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	agttgtcaaaggatattgctGaattcctggtatcgccaatg	11	13	10	7	1	1	1	1	1	0	0	3	2	2	2	2	2	1	3	2	2	5	5			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr15:26793190G>C	ENST00000311550.5	-	9	1283	c.1172C>G	c.(1171-1173)tCa>tGa	p.S391*	GABRB3_ENST00000545868.1_Nonsense_Mutation_p.S306*|GABRB3_ENST00000299267.4_Nonsense_Mutation_p.S391*|GABRB3_ENST00000400188.3_Nonsense_Mutation_p.S320*|GABRB3_ENST00000541819.2_Nonsense_Mutation_p.S447*	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	391					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)	GGATATTGCTGAATTCCTGGT	0.493																																					p.S391X		Atlas-SNP	.											.	GABRB3	338	.	0			c.C1172G						PASS	.						123	114	117					15																	26793190		2203	4300	6503	SO:0001587	stop_gained	2562	exon9			ATTGCTGAATTCC		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.1172C>G	chr15.hg19:g.26793190G>C	ENSP00000308725:p.Ser391*	245.0	0.0	.		273.0	125.0	.	NM_021912	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Nonsense_Mutation	SNP	ENST00000311550.5	hg19	CCDS10019.1	.	.	.	.	.	.	.	.	.	.	G	32	5.176507	0.94846	.	.	ENSG00000166206	ENST00000311550;ENST00000541819;ENST00000299267;ENST00000400188;ENST00000545868	.	.	.	5.82	4.9	0.64082	.	0.597023	0.16989	N	0.191371	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	.	13.4207	0.60996	0.0746:0.0:0.9254:0.0	.	.	.	.	X	391;447;391;320;306	.	ENSP00000299267:S391X	S	-	2	0	GABRB3	24344283	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.681000	0.61663	2.752000	0.94435	0.655000	0.94253	TCA	.	.	.	none		0.493	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2			C	26793190	G	C	26793190	4	2	91	1	0	0	0	0	0	1	0	0	6175	1294	45	4	253	4	GABRB3	15	26793190	Nonsense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08		26793190	75738202	46	5827											
DMXL2	23312	hgsc.bcm.edu	37	chr15	51857284	51857284	+	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	ttaaatacaattgctaaataCcttgaggatcccatgctaag	15	12	6	8	0	0	1	0	1	0	0	1	2	1	2	2	1	4	2	2	1	8	7			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr15:51857284C>A	ENST00000251076.5	-	4	652		c.e4+1		DMXL2_ENST00000449909.3_Splice_Site|DMXL2_ENST00000560421.1_Splice_Site|DMXL2_ENST00000543779.2_Splice_Site	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2							cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		TTGCTAAATACCTTGAGGATC	0.294																																					.		Atlas-SNP	.											.	DMXL2	262	.	0			c.364+1G>T						PASS	.						26	26	26					15																	51857284		2194	4290	6484	SO:0001630	splice_region_variant	23312	exon5			TAAATACCTTGAG	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.364+1G>T	chr15.hg19:g.51857284C>A		31.0	0.0	.		55.0	24.0	.	NM_015263	B2RTR3|B7ZMH3|F5GWF1|O94938	Splice_Site	SNP	ENST00000251076.5	hg19	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.052647	0.75960	.	.	ENSG00000104093	ENST00000251076;ENST00000543779;ENST00000449909	.	.	.	4.9	4.9	0.64082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4422	0.90670	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DMXL2	49644576	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	6.430000	0.73391	2.419000	0.82065	0.655000	0.94253	.	.	.	.	none		0.294	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263	Intron	A	51857284	C	A	51857284	5	1	91	1	0	0	0	0	0	0	1	0	4597	521	18	4	8908	4	DMXL2	15	51857284	Splice_Site	SNP	C	TCGA-B3-4104-01A-01D-1458-08	25064094	51857284	50674108	47	5828											
CX3CL1	6376	hgsc.bcm.edu	37	chr16	57413597	57413597	+	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	cacgtgcagcaagatgacatCaaagatacctgtagctttgc	13	9	9	10	1	1	3	1	1	0	2	1	3	1	3	1	0	5	4	1	0	4	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr16:57413597C>T	ENST00000006053.6	+	2	233	c.122C>T	c.(121-123)tCa>tTa	p.S41L	CX3CL1_ENST00000563383.1_Missense_Mutation_p.S47L|CX3CL1_ENST00000565912.1_Missense_Mutation_p.S3L|CX3CL1_ENST00000564948.1_Intron	NM_002996.3	NP_002987.1	P78423	X3CL1_HUMAN	chemokine (C-X3-C motif) ligand 1	41	Chemokine.				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						AAGATGACATCAAAGATACCT	0.517																																					p.S41L		Atlas-SNP	.											.	CX3CL1	27	.	0			c.C122T						PASS	.						180	130	147					16																	57413597		2198	4300	6498	SO:0001583	missense	6376	exon2			TGACATCAAAGAT	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.122C>T	chr16.hg19:g.57413597C>T	ENSP00000006053:p.Ser41Leu	108.0	0.0	.		109.0	6.0	.	NM_002996	O00672	Missense_Mutation	SNP	ENST00000006053.6	hg19	CCDS10779.1	.	.	.	.	.	.	.	.	.	.	C	10.24	1.296655	0.23650	.	.	ENSG00000006210	ENST00000006053	T	0.05199	3.48	3.0	0.929	0.19449	Chemokine interleukin-8-like domain (3);	2.900500	0.01491	N	0.017077	T	0.10551	0.0258	L	0.55103	1.725	0.09310	N	1	B	0.29862	0.259	B	0.35114	0.196	T	0.36744	-0.9735	10	0.87932	D	0	-27.7552	5.6639	0.17684	0.2253:0.5558:0.2189:0.0	.	41	P78423	X3CL1_HUMAN	L	41	ENSP00000006053:S41L	ENSP00000006053:S41L	S	+	2	0	CX3CL1	55971098	0.000000	0.05858	0.004000	0.12327	0.044000	0.14063	-1.476000	0.02333	0.302000	0.22762	0.460000	0.39030	TCA	.	.	.	none		0.517	CX3CL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257345.3	NM_002996		T	57413597	C	T	57413597	3	4	91	1	0	0	0	0	1	0	0	0	4076	838	29	2	128	2	CX3CL1	16	57413597	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08		57413597	32941156	48	5829											
WDR59	79726	hgsc.bcm.edu	37	chr16	74990405	74990405	+	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	atagtgtgcaaagctgtcatGaggattccactgcacagctc	11	10	10	10	0	1	1	1	1	0	0	3	2	2	2	1	1	4	4	1	1	2	2			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr16:74990405G>A	ENST00000262144.6	-	3	338	c.208C>T	c.(208-210)Cat>Tat	p.H70Y	WDR59_ENST00000562331.1_5'UTR	NM_030581.3	NP_085058.3	Q6PJI9	WDR59_HUMAN	WD repeat domain 59	70										breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)	27						AAGCTGTCATGAGGATTCCAC	0.468																																					p.H70Y		Atlas-SNP	.											.	WDR59	66	.	0			c.C208T						PASS	.						106	94	98					16																	74990405		2198	4300	6498	SO:0001583	missense	79726	exon3			TGTCATGAGGATT	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.208C>T	chr16.hg19:g.74990405G>A	ENSP00000262144:p.His70Tyr	94.0	0.0	.		123.0	42.0	.	NM_030581	B3KRC3|Q71RE7|Q96PW5|Q9BSW6|Q9HA43	Missense_Mutation	SNP	ENST00000262144.6	hg19	CCDS32488.1	.	.	.	.	.	.	.	.	.	.	G	35	5.427353	0.96131	.	.	ENSG00000103091	ENST00000262144;ENST00000536050	T	0.70282	-0.47	6.17	6.17	0.99709	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.83119	0.5185	M	0.78049	2.395	0.80722	D	1	D;D	0.67145	0.996;0.993	D;D	0.75484	0.986;0.968	T	0.76072	-0.3093	10	0.06236	T	0.91	-22.0166	20.8794	0.99867	0.0:0.0:1.0:0.0	.	70;70	Q6PJI9-2;Q6PJI9	.;WDR59_HUMAN	Y	70;49	ENSP00000262144:H70Y	ENSP00000262144:H70Y	H	-	1	0	WDR59	73547906	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.410000	0.97335	2.941000	0.99782	0.655000	0.94253	CAT	.	.	.	none		0.468	WDR59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410601.3	NM_030581		A	74990405	G	A	74990405	3	1	91	1	0	0	0	0	1	0	0	0	17320	1290	45	2	2812	2	WDR59	16	74990405	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	17576808	74990405	15364348	49	5830											
ZDHHC7	55625	hgsc.bcm.edu	37	chr16	85010706	85010706	+	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	gagaacaaagcttaccgtctCgtcgttgcatatggagtgga	11	10	12	8	3	1	1	0	0	1	1	3	4	1	3	1	2	4	3	1	2	4	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr16:85010706C>T	ENST00000313732.4	-	7	1097	c.745G>A	c.(745-747)Gag>Aag	p.E249K	ZDHHC7_ENST00000564466.1_Missense_Mutation_p.E286K|ZDHHC7_ENST00000569488.1_5'Flank	NM_017740.2	NP_060210.2	Q9NXF8	ZDHC7_HUMAN	zinc finger, DHHC-type containing 7	249					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						CTTACCGTCTCGTCGTTGCAT	0.448																																					p.E286K		Atlas-SNP	.											.	ZDHHC7	55	.	0			c.G856A						PASS	.						162	149	153					16																	85010706		2199	4300	6499	SO:0001583	missense	55625	exon8			CCGTCTCGTCGTT	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.745G>A	chr16.hg19:g.85010706C>T	ENSP00000315604:p.Glu249Lys	223.0	0.0	.		285.0	130.0	.	NM_001145548	D3DUM1|Q8WV42|Q9NVD8	Missense_Mutation	SNP	ENST00000313732.4	hg19	CCDS10950.1	.	.	.	.	.	.	.	.	.	.	C	36	5.726803	0.96847	.	.	ENSG00000153786	ENST00000313732;ENST00000344861	T;T	0.23552	1.9;1.9	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.47395	0.1443	L	0.57130	1.785	0.80722	D	1	P;D	0.71674	0.943;0.998	P;P	0.62184	0.674;0.899	T	0.26677	-1.0096	10	0.54805	T	0.06	-14.3722	19.2167	0.93781	0.0:1.0:0.0:0.0	.	286;249	Q9NXF8-2;Q9NXF8	.;ZDHC7_HUMAN	K	249;286	ENSP00000315604:E249K;ENSP00000341681:E286K	ENSP00000315604:E249K	E	-	1	0	ZDHHC7	83568207	1.000000	0.71417	0.981000	0.43875	0.844000	0.47949	7.666000	0.83877	2.784000	0.95788	0.655000	0.94253	GAG	.	.	.	none		0.448	ZDHHC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269087.1	NM_017740		T	85010706	C	T	85010706	3	4	91	1	0	0	0	0	1	0	0	0	17632	893	31	1	189	1	ZDHHC7	16	85010706	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	10020301	85010706	5344047	50	5831											
ITGAE	3682	hgsc.bcm.edu	37	chr17	3659152	3659152	+	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	ggatctgagcactgaagccaAtctgtgccagctggtagtga	10	9	13	9	0	2	3	0	3	2	0	2	4	2	4	2	2	4	3	2	2	3	1	rs376670383		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr17:3659152A>T	ENST00000263087.4	-	11	1309	c.1211T>A	c.(1210-1212)aTt>aAt	p.I404N		NM_002208.4	NP_002199.3	P38570	ITAE_HUMAN	integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)	404					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)		ACTGAAGCCAATCTGTGCCAG	0.592																																					p.I404N	NSCLC(182;635 2928 8995 38788)	Atlas-SNP	.											.	ITGAE	96	.	0			c.T1211A						PASS	.						93	58	70					17																	3659152		2203	4300	6503	SO:0001583	missense	3682	exon11			AAGCCAATCTGTG	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.1211T>A	chr17.hg19:g.3659152A>T	ENSP00000263087:p.Ile404Asn	8.0	0.0	.		15.0	8.0	.	NM_002208	Q17RS6|Q9NZU9	Missense_Mutation	SNP	ENST00000263087.4	hg19	CCDS32531.1	.	.	.	.	.	.	.	.	.	.	A	9.577	1.122528	0.20877	.	.	ENSG00000083457	ENST00000263087	T	0.58358	0.34	4.49	2.07	0.26955	.	.	.	.	.	T	0.41143	0.1146	L	0.51422	1.61	0.22571	N	0.998974	P	0.34462	0.454	B	0.29785	0.107	T	0.28744	-1.0034	9	0.51188	T	0.08	.	5.4982	0.16815	0.6409:0.0:0.3591:0.0	.	404	P38570	ITAE_HUMAN	N	404	ENSP00000263087:I404N	ENSP00000263087:I404N	I	-	2	0	ITGAE	3605901	0.002000	0.14202	0.605000	0.28930	0.320000	0.28249	0.698000	0.25571	0.284000	0.22305	0.421000	0.28195	ATT	.	.	.	alt		0.592	ITGAE-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438169.1	NM_002208		T	3659152	A	T	3659152	3	4	91	1	0	0	0	0	1	0	0	0	7892	101	4	5	2412	5	ITGAE	17	3659152	Missense_Mutation	SNP	A	TCGA-B3-4104-01A-01D-1458-08		3659152	77536058	51	5832											
TP53	7157	hgsc.bcm.edu	37	chr17	7579415	7579415	+	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	ggacagaagatgacaggggcCaggagggggctggtgcaggg	10	3	22	6	0	0	3	0	1	0	2	0	5	0	5	1	8	1	2	1	8	1	0			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr17:7579415C>T	ENST00000269305.4	-	4	461	c.272G>A	c.(271-273)tGg>tAg	p.W91*	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Nonsense_Mutation_p.W91*|TP53_ENST00000455263.2_Nonsense_Mutation_p.W91*|TP53_ENST00000413465.2_Nonsense_Mutation_p.W91*|TP53_ENST00000420246.2_Nonsense_Mutation_p.W91*|TP53_ENST00000445888.2_Nonsense_Mutation_p.W91*	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	91	Interaction with WWOX.		W -> C (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.W91*(7)|p.G59fs*23(3)|p.V73fs*9(1)|p.D48fs*55(1)|p.A88fs*52(1)|p.W91fs*13(1)|p.P87fs*54(1)|p.P13fs*18(1)|p.S33fs*23(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGACAGGGGCCAGGAGGGGGC	0.632		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.W91X	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000455263,NS,carcinoma,+1,10	TP53	33396	.	25	Deletion - Frameshift(10)|Whole gene deletion(8)|Substitution - Nonsense(7)	lung(7)|upper_aerodigestive_tract(4)|bone(4)|central_nervous_system(3)|breast(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)|prostate(1)|liver(1)	c.G272A						PASS	.						44	50	48					17																	7579415		2202	4299	6501	SO:0001587	stop_gained	7157	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AGGGGCCAGGAGG	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.272G>A	chr17.hg19:g.7579415C>T	ENSP00000269305:p.Trp91*	128.0	0.0	.		143.0	23.0	.	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	19.89	3.911071	0.72983	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591	.	.	.	4.08	4.08	0.47627	.	0.425160	0.22616	N	0.057766	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-8.1711	14.5887	0.68347	0.0:1.0:0.0:0.0	.	.	.	.	X	91	.	ENSP00000269305:W91X	W	-	2	0	TP53	7520140	0.997000	0.39634	0.998000	0.56505	0.633000	0.38033	-0.143000	0.10296	2.561000	0.86390	0.561000	0.74099	TGG	.	.	.	none		0.632	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		T	7579415	C	T	7579415	4	4	91	1	0	0	0	0	0	1	0	0	16393	595	21	2	1030	2	TP53	17	7579415	Nonsense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	3920263	7579415	73615795	52	5833											
KRT13	3860	hgsc.bcm.edu	37	chr17	39659037	39659037	+	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	ctgaatcatggcagtgttggTagacacctccttgttcagct	8	13	10	10	0	2	2	2	1	0	1	3	2	3	2	2	2	1	5	2	2	2	4			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr17:39659037T>A	ENST00000246635.3	-	5	971	c.925A>T	c.(925-927)Acc>Tcc	p.T309S	AC019349.5_ENST00000411759.1_RNA|KRT13_ENST00000587544.1_Missense_Mutation_p.T309S|KRT13_ENST00000587118.1_5'Flank|KRT13_ENST00000336861.3_Missense_Mutation_p.T309S	NM_153490.2	NP_705694	P13646	K1C13_HUMAN	keratin 13	309	Coil 2.|Rod.				cellular response to retinoic acid (GO:0071300)|cytoskeleton organization (GO:0007010)|response to radiation (GO:0009314)|tongue morphogenesis (GO:0043587)	extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			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)				GCAGTGTTGGTAGACACCTCC	0.577																																					p.T309S		Atlas-SNP	.											.	KRT13	72	.	0			c.A925T						PASS	.						216	195	202					17																	39659037		2203	4300	6503	SO:0001583	missense	3860	exon5			TGTTGGTAGACAC		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.925A>T	chr17.hg19:g.39659037T>A	ENSP00000246635:p.Thr309Ser	456.0	0.0	.		447.0	195.0	.	NM_002274	Q53G54|Q6AZK5|Q8N240	Missense_Mutation	SNP	ENST00000246635.3	hg19	CCDS11396.1	.	.	.	.	.	.	.	.	.	.	T	0.668	-0.803036	0.02841	.	.	ENSG00000171401	ENST00000246635;ENST00000336861;ENST00000157775	T;T	0.76968	-1.06;-1.06	4.45	-3.03	0.05429	Filament (1);	0.306290	0.23211	N	0.050674	T	0.51058	0.1652	N	0.05124	-0.11	0.09310	N	1	B;B;B;B	0.15719	0.014;0.008;0.006;0.008	B;B;B;B	0.28305	0.053;0.088;0.03;0.088	T	0.47446	-0.9117	10	0.02654	T	1	.	12.9134	0.58192	0.301:0.0:0.0:0.699	.	297;309;309;309	P13646-2;A1A4E9;P13646-3;P13646	.;.;.;K1C13_HUMAN	S	309;309;297	ENSP00000246635:T309S;ENSP00000336604:T309S	ENSP00000157775:T297S	T	-	1	0	KRT13	36912563	0.000000	0.05858	0.056000	0.19401	0.751000	0.42716	-0.832000	0.04400	-0.336000	0.08438	0.391000	0.25812	ACC	.	.	.	none		0.577	KRT13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257297.1	NM_153490		A	39659037	T	A	39659037	3	1	91	1	0	0	0	0	1	0	0	0	8457	1638	57	5	467	5	KRT13	17	39659037	Missense_Mutation	SNP	T	TCGA-B3-4104-01A-01D-1458-08	32079622	39659037	41536173	53	5834											
DBF4B	80174	hgsc.bcm.edu	37	chr17	42828063	42828063	+	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	tgtgtgagtgccacaaccctCctgccggccttgcccaaggg	6	8	12	15	1	0	1	0	1	0	0	1	1	1	1	6	2	4	0	6	2	2	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr17:42828063C>T	ENST00000315005.3	+	14	1428	c.1290C>T	c.(1288-1290)ctC>ctT	p.L430L	DBF4B_ENST00000393547.2_Intron	NM_145663.2	NP_663696.1	Q8NFT6	DBF4B_HUMAN	DBF4 zinc finger B	430					cell cycle (GO:0007049)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of protein kinase activity (GO:0045860)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|lung(5)	7		Prostate(33;0.0322)				CCACAACCCTCCTGCCGGCCT	0.617																																					p.L430L		Atlas-SNP	.											.	DBF4B	66	.	0			c.C1290T						PASS	.						56	52	53					17																	42828063		2203	4300	6503	SO:0001819	synonymous_variant	80174	exon14			AACCCTCCTGCCG	AF465820	CCDS11485.1, CCDS45706.1, CCDS45706.2	17q21.31	2014-02-17	2014-02-17		ENSG00000161692	ENSG00000161692		"Zinc fingers, DBF-type"	17883	protein-coding gene	gene with protein product	"chiffon homolog B (Drosophila)", "zinc finger, DBF-type containing 1B"	611661	"DBF4 homolog B (S. cerevisiae)"			15668232	Standard	NM_145663		Approved	FLJ13087, DRF1, ASKL1, chifb, ZDBF1B	uc002ihf.3	Q8NFT6	OTTHUMG00000165717	ENST00000315005.3:c.1290C>T	chr17.hg19:g.42828063C>T		132.0	0.0	.		131.0	59.0	.	NM_145663	D3DX56|Q8TEX0|Q96B19|Q9H912	Silent	SNP	ENST00000315005.3	hg19	CCDS11485.1																																																																																			.	.	.	none		0.617	DBF4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385930.1	NM_025104		T	42828063	C	T	42828063	2	4	91	1	0	0	0	0	0	0	0	1	4251	842	30	2		2	DBF4B	17	42828063	Silent	SNP	C	TCGA-B3-4104-01A-01D-1458-08	3169026	42828063	38367147	54	5835											
EPN3	55040	hgsc.bcm.edu	37	chr17	48615544	48615544	+	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	tggccctcgccatgagccgtGaggaggcagagaaggtgagg	9	5	18	9	2	0	4	0	3	0	1	1	6	0	5	3	5	1	1	3	5	1	0			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr17:48615544G>A	ENST00000268933.3	+	3	1246	c.667G>A	c.(667-669)Gag>Aag	p.E223K	EPN3_ENST00000537145.1_Missense_Mutation_p.E278K|RP11-94C24.8_ENST00000513017.1_RNA|EPN3_ENST00000541226.1_Missense_Mutation_p.E167K	NM_017957.2	NP_060427.2	Q9H201	EPN3_HUMAN	epsin 3	223						clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;2.88e-09)			CATGAGCCGTGAGGAGGCAGA	0.667																																					p.E223K		Atlas-SNP	.											.	EPN3	32	.	0			c.G667A						PASS	.						47	38	41					17																	48615544		2203	4300	6503	SO:0001583	missense	55040	exon3			AGCCGTGAGGAGG	AF324241	CCDS11570.1	17q21.33	2008-07-18				ENSG00000049283			18235	protein-coding gene	gene with protein product		607264				10951261, 11359770	Standard	NM_017957		Approved	FLJ20778, MGC129899	uc002ira.4	Q9H201		ENST00000268933.3:c.667G>A	chr17.hg19:g.48615544G>A	ENSP00000268933:p.Glu223Lys	63.0	0.0	.		43.0	29.0	.	NM_017957	A8K6J3|A8KAB2|Q9BVN6|Q9NWK2	Missense_Mutation	SNP	ENST00000268933.3	hg19	CCDS11570.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.925509	0.92319	.	.	ENSG00000049283	ENST00000268933;ENST00000442715;ENST00000537145;ENST00000541226;ENST00000411703	T;T;T	0.58060	2.08;1.24;0.36	4.54	4.54	0.55810	Ubiquitin interacting motif (3);	0.062476	0.64402	D	0.000007	T	0.73434	0.3586	M	0.79805	2.47	0.58432	D	0.999991	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.87578	0.997;0.998;0.992	T	0.74408	-0.3675	10	0.35671	T	0.21	-20.981	17.345	0.87308	0.0:0.0:1.0:0.0	.	278;278;223	B4DK18;F6QWW5;Q9H201	.;.;EPN3_HUMAN	K	223;278;278;167;223	ENSP00000268933:E223K;ENSP00000439512:E278K;ENSP00000440540:E167K	ENSP00000268933:E223K	E	+	1	0	EPN3	45970543	1.000000	0.71417	0.861000	0.33841	0.595000	0.36748	9.783000	0.99037	2.247000	0.74100	0.456000	0.33151	GAG	.	.	.	none		0.667	EPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367573.1	NM_017957		A	48615544	G	A	48615544	3	1	91	1	0	0	0	0	1	0	0	0	5189	1291	45	2	673	2	EPN3	17	48615544	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	5787481	48615544	32579666	55	5836											
EPN3	55040	hgsc.bcm.edu	37	chr17	48616322	48616322	+	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	ctgagccggcaggagcacgaGaaggtagtgggccgagcccg	9	3	18	11	4	0	2	0	1	0	1	0	5	0	3	3	4	3	3	3	4	2	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr17:48616322G>C	ENST00000268933.3	+	4	1338	c.759G>C	c.(757-759)gaG>gaC	p.E253D	EPN3_ENST00000537145.1_Intron|RP11-94C24.8_ENST00000513017.1_RNA|EPN3_ENST00000541226.1_Intron	NM_017957.2	NP_060427.2	Q9H201	EPN3_HUMAN	epsin 3	253						clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;2.88e-09)			AGGAGCACGAGAAGGTAGTGG	0.687																																					p.E253D		Atlas-SNP	.											.	EPN3	32	.	0			c.G759C						PASS	.						24	24	24					17																	48616322		2201	4299	6500	SO:0001583	missense	55040	exon4			GCACGAGAAGGTA	AF324241	CCDS11570.1	17q21.33	2008-07-18				ENSG00000049283			18235	protein-coding gene	gene with protein product		607264				10951261, 11359770	Standard	NM_017957		Approved	FLJ20778, MGC129899	uc002ira.4	Q9H201		ENST00000268933.3:c.759G>C	chr17.hg19:g.48616322G>C	ENSP00000268933:p.Glu253Asp	48.0	0.0	.		24.0	11.0	.	NM_017957	A8K6J3|A8KAB2|Q9BVN6|Q9NWK2	Missense_Mutation	SNP	ENST00000268933.3	hg19	CCDS11570.1	.	.	.	.	.	.	.	.	.	.	G	13.33	2.204206	0.38905	.	.	ENSG00000049283	ENST00000268933;ENST00000411703	T	0.15256	2.44	4.5	3.51	0.40186	Ubiquitin interacting motif (2);	0.319926	0.29668	N	0.011504	T	0.12944	0.0314	L	0.42245	1.32	0.80722	D	1	B	0.12630	0.006	B	0.13407	0.009	T	0.07309	-1.0779	10	0.11794	T	0.64	.	9.5827	0.39497	0.0:0.1552:0.684:0.1609	.	253	Q9H201	EPN3_HUMAN	D	253	ENSP00000268933:E253D	ENSP00000268933:E253D	E	+	3	2	EPN3	45971321	1.000000	0.71417	0.999000	0.59377	0.801000	0.45260	4.211000	0.58507	1.001000	0.39076	0.313000	0.20887	GAG	.	.	.	none		0.687	EPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367573.1	NM_017957		C	48616322	G	C	48616322	3	2	91	1	0	0	0	0	1	0	0	0	5189	933	33	4	769	4	EPN3	17	48616322	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	778	48616322	32578888	56	5837											
SPATA20	64847	hgsc.bcm.edu	37	chr17	48628090	48628090	+	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	ccggaggcttctatagcgcaGaagatgcagactcgccccca	10	6	11	14	3	1	3	0	0	1	3	2	4	1	4	3	2	2	3	3	2	3	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr17:48628090G>A	ENST00000356488.4	+	10	1230	c.1147G>A	c.(1147-1149)Gaa>Aaa	p.E383K	SPATA20_ENST00000393244.3_Missense_Mutation_p.E339K|SPATA20_ENST00000511937.1_3'UTR|SPATA20_ENST00000006658.6_Missense_Mutation_p.E399K	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	383					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)			CTATAGCGCAGAAGATGCAGA	0.672											OREG0024568	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E399K		Atlas-SNP	.											.	SPATA20	59	.	0			c.G1195A						PASS	.						47	58	54					17																	48628090		2203	4299	6502	SO:0001583	missense	64847	exon11			AGCGCAGAAGATG		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.1147G>A	chr17.hg19:g.48628090G>A	ENSP00000348878:p.Glu383Lys	323.0	1.0	.	119	450.0	205.0	.	NM_022827	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Missense_Mutation	SNP	ENST00000356488.4	hg19	CCDS58563.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.393663	0.83011	.	.	ENSG00000006282	ENST00000006658;ENST00000356488;ENST00000393244	T;T;T	0.30981	1.51;1.51;1.51	5.64	5.64	0.86602	Six-hairpin glycosidase (1);Six-hairpin glycosidase-like (1);	0.000000	0.85682	D	0.000000	T	0.68137	0.2968	H	0.95187	3.635	0.80722	D	1	D;D	0.76494	0.999;0.99	D;D	0.77557	0.99;0.964	T	0.77907	-0.2412	10	0.72032	D	0.01	-3.9451	16.6877	0.85314	0.0:0.1292:0.8708:0.0	.	383;399	Q8TB22;Q8TB22-2	SPT20_HUMAN;.	K	399;383;339	ENSP00000006658:E399K;ENSP00000348878:E383K;ENSP00000376935:E339K	ENSP00000006658:E399K	E	+	1	0	SPATA20	45983089	1.000000	0.71417	0.953000	0.39169	0.342000	0.28953	7.988000	0.88194	2.664000	0.90586	0.655000	0.94253	GAA	.	.	.	none		0.672	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827		A	48628090	G	A	48628090	3	1	91	1	0	0	0	0	1	0	0	0	15018	943	33	2	1237	2	SPATA20	17	48628090	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	11768	48628090	32567120	57	5838											
SPATA20	64847	hgsc.bcm.edu	37	chr17	48628385	48628385	+	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	aagggggagctgcagggccaGaatgtgctgaccgtccggta	9	6	17	9	2	0	2	0	1	0	1	1	3	1	3	3	4	3	4	3	4	3	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr17:48628385G>A	ENST00000356488.4	+	11	1445	c.1362G>A	c.(1360-1362)caG>caA	p.Q454Q	SPATA20_ENST00000393244.3_Silent_p.Q410Q|SPATA20_ENST00000511937.1_3'UTR|SPATA20_ENST00000006658.6_Silent_p.Q470Q	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	454					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)			TGCAGGGCCAGAATGTGCTGA	0.637											OREG0024568	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q470Q		Atlas-SNP	.											.	SPATA20	59	.	0			c.G1410A						PASS	.						37	42	40					17																	48628385		2203	4300	6503	SO:0001819	synonymous_variant	64847	exon12			GGGCCAGAATGTG		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.1362G>A	chr17.hg19:g.48628385G>A		100.0	0.0	.	119	145.0	67.0	.	NM_022827	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Silent	SNP	ENST00000356488.4	hg19	CCDS58563.1																																																																																			.	.	.	none		0.637	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827		A	48628385	G	A	48628385	2	1	91	1	0	0	0	0	0	0	0	1	15018	933	33	2		2	SPATA20	17	48628385	Silent	SNP	G	TCGA-B3-4104-01A-01D-1458-08	295	48628385	32566825	58	5839											
TEX2	55852	hgsc.bcm.edu	37	chr17	62238165	62238165	+	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	atatatagccccttacccttCtttgccaatttctccaacct	9	15	2	15	0	2	0	0	0	2	0	3	0	2	0	6	0	4	0	6	0	6	7			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr17:62238165C>G	ENST00000583097.1	-	8	2972	c.2800G>C	c.(2800-2802)Gaa>Caa	p.E934Q	TEX2_ENST00000258991.3_Missense_Mutation_p.E941Q|TEX2_ENST00000584379.1_Missense_Mutation_p.E934Q			Q8IWB9	TEX2_HUMAN	testis expressed 2	934					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)		CCTTACCCTTCTTTGCCAATT	0.463																																					p.E941Q		Atlas-SNP	.											.	TEX2	89	.	0			c.G2821C						PASS	.						176	187	183					17																	62238165		2203	4300	6503	SO:0001583	missense	55852	exon8			ACCCTTCTTTGCC	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.2800G>C	chr17.hg19:g.62238165C>G	ENSP00000462665:p.Glu934Gln	408.0	0.0	.		1011.0	701.0	.	NM_018469	Q6AHZ5|Q8N3L0|Q9C0C5	Missense_Mutation	SNP	ENST00000583097.1	hg19		.	.	.	.	.	.	.	.	.	.	C	16.25	3.069164	0.55539	.	.	ENSG00000136478	ENST00000258991	T	0.50548	0.74	5.84	5.84	0.93424	.	0.096119	0.64402	D	0.000001	T	0.67711	0.2922	M	0.68952	2.095	0.80722	D	1	D;D	0.69078	0.997;0.962	D;P	0.65010	0.931;0.756	T	0.66464	-0.5917	10	0.52906	T	0.07	.	20.1386	0.98045	0.0:1.0:0.0:0.0	.	941;934	Q8IWB9-2;Q8IWB9	.;TEX2_HUMAN	Q	941	ENSP00000258991:E941Q	ENSP00000258991:E941Q	E	-	1	0	TEX2	59591897	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.767000	0.95098	0.561000	0.74099	GAA	.	.	.	none		0.463	TEX2-003	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000443745.1	NM_018469		G	62238165	C	G	62238165	3	3	91	1	0	0	0	0	1	0	0	0	15793	922	32	4	603	4	TEX2	17	62238165	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	13609780	62238165	18957045	59	5840											
SLC38A10	124565	hgsc.bcm.edu	37	chr17	79249777	79249777	+	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	cgagggtcttacctgctgctCacacagcagcgtgctcaggg	7	8	13	13	2	3	0	2	0	1	0	3	1	3	0	1	2	6	4	1	2	1	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr17:79249777C>T	ENST00000374759.3	-	8	1287	c.904G>A	c.(904-906)Gag>Aag	p.E302K	SLC38A10_ENST00000288439.5_Missense_Mutation_p.E302K|SLC38A10_ENST00000546352.1_5'UTR	NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	302					amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			ACCTGCTGCTCACACAGCAGC	0.597																																					p.E302K		Atlas-SNP	.											.	SLC38A10	133	.	0			c.G904A						PASS	.						91	87	88					17																	79249777		2203	4300	6503	SO:0001583	missense	124565	exon8			GCTGCTCACACAG	BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637		"Solute carriers"	28237	protein-coding gene	gene with protein product							Standard	XM_005257019		Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.904G>A	chr17.hg19:g.79249777C>T	ENSP00000363891:p.Glu302Lys	249.0	0.0	.		361.0	77.0	.	NM_001037984	Q6ZRC5|Q8NA99|Q96C66	Missense_Mutation	SNP	ENST00000374759.3	hg19	CCDS42397.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.510735	0.85389	.	.	ENSG00000157637	ENST00000374759;ENST00000288439	T;T	0.02216	4.39;4.39	4.88	4.88	0.63580	.	0.239727	0.41396	D	0.000893	T	0.05456	0.0144	N	0.16567	0.415	0.58432	D	0.999998	B;D	0.89917	0.178;1.0	B;D	0.85130	0.054;0.997	T	0.65307	-0.6200	10	0.16420	T	0.52	-37.9351	17.6417	0.88138	0.0:1.0:0.0:0.0	.	302;302	Q9HBR0-2;Q9HBR0	.;S38AA_HUMAN	K	302	ENSP00000363891:E302K;ENSP00000288439:E302K	ENSP00000288439:E302K	E	-	1	0	SLC38A10	76864372	1.000000	0.71417	0.929000	0.37066	0.845000	0.48019	7.379000	0.79691	2.244000	0.73946	0.655000	0.94253	GAG	.	.	.	none		0.597	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	NM_138570		T	79249777	C	T	79249777	3	4	91	1	0	0	0	0	1	0	0	0	14615	835	29	2	2769	2	SLC38A10	17	79249777	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	17011612	79249777	1945433	60	5841											
DSC2	1824	hgsc.bcm.edu	37	chr18	28660162	28660162	+	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	catgcgaacagtctgtattgGagggttacactcagggccct	9	10	12	10	1	2	0	1	0	1	0	2	2	2	1	1	3	3	2	1	3	3	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr18:28660162G>C	ENST00000280904.6	-	10	1863	c.1420C>G	c.(1420-1422)Cca>Gca	p.P474A	DSC2_ENST00000251081.6_Missense_Mutation_p.P474A	NM_024422.3	NP_077740.1	Q02487	DSC2_HUMAN	desmocollin 2	474	Cadherin 4. {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)			GTCTGTATTGGAGGGTTACAC	0.443																																					p.P474A		Atlas-SNP	.											.	DSC2	168	.	0			c.C1420G						PASS	.						195	167	177					18																	28660162		2203	4300	6503	SO:0001583	missense	1824	exon10			GTATTGGAGGGTT	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.1420C>G	chr18.hg19:g.28660162G>C	ENSP00000280904:p.Pro474Ala	265.0	0.0	.		427.0	225.0	.	NM_024422		Missense_Mutation	SNP	ENST00000280904.6	hg19	CCDS11892.1	.	.	.	.	.	.	.	.	.	.	G	5.668	0.307878	0.10733	.	.	ENSG00000134755	ENST00000251081;ENST00000280904;ENST00000438199;ENST00000399347	T;T	0.60548	0.18;0.18	5.92	-2.13	0.07144	Cadherin (3);Cadherin-like (1);	2.202610	0.03087	N	0.159213	T	0.31199	0.0789	N	0.11673	0.155	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.15052	0.005;0.012	T	0.20672	-1.0268	10	0.06365	T	0.9	.	4.1607	0.10282	0.1425:0.4668:0.1934:0.1973	.	474;474	Q02487;Q02487-2	DSC2_HUMAN;.	A	474;474;240;487	ENSP00000251081:P474A;ENSP00000280904:P474A	ENSP00000251081:P474A	P	-	1	0	DSC2	26914160	0.000000	0.05858	0.000000	0.03702	0.251000	0.25915	-0.336000	0.07863	-0.382000	0.07870	-0.150000	0.13652	CCA	.	.	.	none		0.443	DSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254943.1	NM_004949		C	28660162	G	C	28660162	3	2	91	1	0	0	0	0	1	0	0	0	4768	1174	41	4	1353	4	DSC2	18	28660162	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08		28660162	49417086	61	5842											
C19orf21	126353	hgsc.bcm.edu	37	chr19	757669	757669	+	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	aacaagccccacctggccaaCgggcacgtggttcccatcaa	11	5	9	16	2	1	0	1	0	0	0	2	0	2	0	5	3	3	2	5	3	4	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr19:757669C>T	ENST00000215582.6	+	2	826	c.723C>T	c.(721-723)aaC>aaT	p.N241N		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	241					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											ACCTGGCCAACGGGCACGTGG	0.672																																					p.N241N		Atlas-SNP	.											C19orf21,colon,carcinoma,+1,1	C19orf21	56	.	0			c.C723T						PASS	.						24	27	26					19																	757669		2203	4300	6503	SO:0001819	synonymous_variant	126353	exon2			GGCCAACGGGCAC	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.723C>T	chr19.hg19:g.757669C>T		53.0	0.0	.		59.0	29.0	.	NM_173481		Silent	SNP	ENST00000215582.6	hg19	CCDS12042.1																																																																																			.	.	.	none		0.672	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481		T	757669	C	T	757669	2	4	91	1	0	0	0	0	0	0	0	1	1915	535	19	1		1	C19orf21	19	757669	Silent	SNP	C	TCGA-B3-4104-01A-01D-1458-08		757669	58371314	62	5843											
PIK3R2	5296	hgsc.bcm.edu	37	chr19	18279617	18279617	+	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	gtgggcaagatcaaccgcacGcaggcagaggagatgctgag	12	4	16	9	2	1	4	1	1	0	3	1	5	1	4	1	3	2	5	1	3	2	0			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr19:18279617G>A	ENST00000593731.1	+	15	2450	c.1890G>A	c.(1888-1890)acG>acA	p.T630T	PIK3R2_ENST00000222254.8_Silent_p.T630T			O00459	P85B_HUMAN	phosphoinositide-3-kinase, regulatory subunit 2 (beta)	630	SH2 2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	phosphatidylinositol 3-kinase regulator activity (GO:0035014)|receptor tyrosine kinase binding (GO:0030971)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(3)|pancreas(1)|stomach(1)	24					Isoprenaline(DB01064)	TCAACCGCACGCAGGCAGAGG	0.657											OREG0025359	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T630T		Atlas-SNP	.											.	PIK3R2	48	.	0			c.G1890A						PASS	.						75	48	57					19																	18279617		2203	4300	6503	SO:0001819	synonymous_variant	5296	exon15			CCGCACGCAGGCA		CCDS12371.1	19p13.11	2013-03-28	2008-02-04		ENSG00000105647	ENSG00000105647		"SH2 domain containing"	8980	protein-coding gene	gene with protein product		603157				1314371	Standard	NM_005027		Approved	P85B, p85	uc002nia.2	O00459	OTTHUMG00000183383	ENST00000593731.1:c.1890G>A	chr19.hg19:g.18279617G>A		65.0	0.0	.	724	48.0	21.0	.	NM_005027	Q5EAT5|Q9UPH9	Silent	SNP	ENST00000593731.1	hg19	CCDS12371.1																																																																																			.	.	.	none		0.657	PIK3R2-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000466386.2	NM_005027		A	18279617	G	A	18279617	2	1	91	1	0	0	0	0	0	0	0	1	11926	1074	38	1		1	PIK3R2	19	18279617	Silent	SNP	G	TCGA-B3-4104-01A-01D-1458-08	17521948	18279617	40849366	63	5844											
PRR12	57479	hgsc.bcm.edu	37	chr19	50099849	50099849	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtccactacggggcaggcGccaaggagctgggggccttc	6	7	16	12	2	0	0	0	0	0	0	2	1	1	1	3	6	2	2	3	6	2	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr19:50099849G>A	ENST00000418929.2	+	4	2269	c.2257G>A	c.(2257-2259)Gcc>Acc	p.A753T		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	0							DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		CGGGGCAGGCGCCAAGGAGCT	0.692																																					p.A753T		Atlas-SNP	.											PRR12_ENST00000418929,NS,carcinoma,0,1	PRR12	157	.	0			c.G2257A						PASS	.						9	11	10					19																	50099849		1883	4040	5923	SO:0001583	missense	57479	exon4			GCAGGCGCCAAGG	AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"KIAA1205"	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.2257G>A	chr19.hg19:g.50099849G>A	ENSP00000394510:p.Ala753Thr	42.0	0.0	.		18.0	6.0	.	NM_020719	E9PB06|Q8N4J6	Missense_Mutation	SNP	ENST00000418929.2	hg19	CCDS46143.1	.	.	.	.	.	.	.	.	.	.	G	7.112	0.576277	0.13686	.	.	ENSG00000126464	ENST00000418929	.	.	.	3.56	3.56	0.40772	.	.	.	.	.	T	0.33177	0.0854	.	.	.	0.26879	N	0.967589	D	0.61080	0.989	P	0.48552	0.581	T	0.06516	-1.0822	7	0.23891	T	0.37	.	10.6184	0.45465	0.0:0.197:0.803:0.0	.	753	Q9ULL5-3	.	T	753	.	ENSP00000394510:A753T	A	+	1	0	PRR12	54791661	0.998000	0.40836	1.000000	0.80357	0.271000	0.26615	1.743000	0.38258	2.001000	0.58596	0.313000	0.20887	GCC	.	.	.	none		0.692	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719		A	50099849	G	A	50099849	3	1	91	1	0	0	0	0	1	0	0	0	12594	1087	38	1	2271	1	PRR12	19	50099849	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	31820232	50099849	9029134	64	5845											
CPXM1	56265	hgsc.bcm.edu	37	chr20	2775058	2775058	+	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	tcccctggggtcagcagacgCcaataatccccgccccacgc	8	5	9	19	3	1	1	1	0	0	1	3	1	3	1	7	2	1	1	7	2	2	1			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr20:2775058C>A	ENST00000380605.2	-	14	2047	c.1983G>T	c.(1981-1983)tgG>tgT	p.W661C		NM_001184699.1|NM_019609.4	NP_001171628.1|NP_062555.1	Q96SM3	CPXM1_HUMAN	carboxypeptidase X (M14 family), member 1	661					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						TCAGCAGACGCCAATAATCCC	0.597																																					p.W661C		Atlas-SNP	.											.	CPXM1	107	.	0			c.G1983T						PASS	.						56	55	55					20																	2775058		2203	4300	6503	SO:0001583	missense	56265	exon14			CAGACGCCAATAA	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.1983G>T	chr20.hg19:g.2775058C>A	ENSP00000369979:p.Trp661Cys	128.0	0.0	.		106.0	24.0	.	NM_019609	Q6P4G8|Q6UW65|Q9NUB5	Missense_Mutation	SNP	ENST00000380605.2	hg19	CCDS13033.1	.	.	.	.	.	.	.	.	.	.	c	21.1	4.099189	0.76983	.	.	ENSG00000088882	ENST00000380605;ENST00000421947	T	0.41758	0.99	5.12	5.12	0.69794	Peptidase M14, carboxypeptidase A (1);Carboxypeptidase-like, regulatory domain (1);Carboxypeptidase, regulatory domain (1);	0.000000	0.85682	D	0.000000	T	0.76399	0.3982	H	0.97103	3.94	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84208	0.0454	10	0.87932	D	0	-16.2562	16.4323	0.83853	0.0:1.0:0.0:0.0	.	661	Q96SM3	CPXM1_HUMAN	C	661;357	ENSP00000369979:W661C	ENSP00000369979:W661C	W	-	3	0	CPXM1	2723058	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	7.560000	0.82277	2.821000	0.97095	0.651000	0.88453	TGG	.	.	.	none		0.597	CPXM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077643.2	NM_019609		A	2775058	C	A	2775058	3	1	91	1	0	0	0	0	1	0	0	0	3839	740	26	4	225	4	CPXM1	20	2775058	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08		2775058	60250462	65	5846											
CTCFL	140690	hgsc.bcm.edu	37	chr20	56090811	56090811	+	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	gtttcagcttgtaggtatctCtgctggcatagctgcactgg	6	14	12	9	0	2	0	1	0	1	0	3	0	2	0	0	3	4	8	0	3	3	5			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr20:56090811C>G	ENST00000608263.1	-	5	1800	c.1139G>C	c.(1138-1140)aGa>aCa	p.R380T	CTCFL_ENST00000608425.1_Missense_Mutation_p.R380T|CTCFL_ENST00000608903.1_Missense_Mutation_p.R118T|CTCFL_ENST00000429804.3_Missense_Mutation_p.R380T|CTCFL_ENST00000422869.2_Missense_Mutation_p.R380T|CTCFL_ENST00000371196.2_Missense_Mutation_p.R380T|CTCFL_ENST00000502686.2_Missense_Mutation_p.R118T|CTCFL_ENST00000243914.3_Missense_Mutation_p.R380T|CTCFL_ENST00000433949.3_Missense_Mutation_p.R175T|CTCFL_ENST00000423479.3_Missense_Mutation_p.R380T|CTCFL_ENST00000608440.1_Missense_Mutation_p.R380T|CTCFL_ENST00000539382.1_Missense_Mutation_p.R175T|CTCFL_ENST00000432255.2_Intron|CTCFL_ENST00000609232.1_Missense_Mutation_p.R380T|CTCFL_ENST00000608858.1_5'UTR	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	380					cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			GTAGGTATCTCTGCTGGCATA	0.483																																					p.R380T		Atlas-SNP	.											.	CTCFL	97	.	0			c.G1139C						PASS	.						175	165	169					20																	56090811		2203	4300	6503	SO:0001583	missense	140690	exon5			GTATCTCTGCTGG		CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"Zinc fingers, C2H2-type"	16234	protein-coding gene	gene with protein product	"cancer/testis antigen 27"	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.1139G>C	chr20.hg19:g.56090811C>G	ENSP00000476783:p.Arg380Thr	338.0	0.0	.		573.0	253.0	.	NM_001269044	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Missense_Mutation	SNP	ENST00000608263.1	hg19	CCDS13459.1	.	.	.	.	.	.	.	.	.	.	C	12.42	1.933464	0.34096	.	.	ENSG00000124092	ENST00000423479;ENST00000243914;ENST00000371196;ENST00000429804;ENST00000433949;ENST00000502686;ENST00000422109;ENST00000426658;ENST00000539382;ENST00000422869	T;T;T;T;T;T;T;T;T;T	0.27557	2.51;2.51;2.51;1.66;2.51;2.51;1.66;2.51;2.51;2.51	5.24	0.214	0.15249	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.465807	0.17788	N	0.161995	T	0.20700	0.0498	N	0.16016	0.355	0.35738	D	0.818477	B;P;B;P;P	0.43231	0.016;0.801;0.056;0.801;0.801	B;B;B;P;P	0.49012	0.038;0.412;0.088;0.598;0.598	T	0.18398	-1.0338	10	0.12103	T	0.63	-30.8232	9.21	0.37313	0.0:0.5082:0.0:0.4918	.	380;380;380;380;380	A6XGM9;A6XGM2;E7EUE3;A6XGL8;Q8NI51	.;.;.;.;CTCFL_HUMAN	T	380;380;380;380;380;118;380;380;175;380	ENSP00000415579:R380T;ENSP00000243914:R380T;ENSP00000360239:R380T;ENSP00000415329:R380T;ENSP00000392034:R380T;ENSP00000437999:R118T;ENSP00000413713:R380T;ENSP00000403369:R380T;ENSP00000439998:R175T;ENSP00000399061:R380T	ENSP00000243914:R380T	R	-	2	0	CTCFL	55524217	0.986000	0.35501	0.791000	0.31998	0.533000	0.34776	0.574000	0.23714	0.045000	0.15804	-0.312000	0.09012	AGA	.	.	.	none		0.483	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618		G	56090811	C	G	56090811	3	3	91	1	0	0	0	0	1	0	0	0	4003	913	32	4	876	4	CTCFL	20	56090811	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08	53315753	56090811	6934709	66	5847											
ZBTB46	140685	hgsc.bcm.edu	37	chr20	62407208	62407208	+	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	tggggtgaggggagggcccaGatagctggcttctcctccca	6	8	16	11	0	1	2	0	1	1	1	3	3	2	3	3	6	1	2	3	6	1	2			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr20:62407208G>A	ENST00000245663.4	-	3	1195	c.1045C>T	c.(1045-1047)Ctg>Ttg	p.L349L	ZBTB46_ENST00000302995.2_Silent_p.L349L|ZBTB46_ENST00000395104.1_Silent_p.L349L	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	349					negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					GGAGGGCCCAGATAGCTGGCT	0.662																																					p.L349L		Atlas-SNP	.											.	ZBTB46	72	.	0			c.C1045T						PASS	.						56	58	57					20																	62407208		2203	4300	6503	SO:0001819	synonymous_variant	140685	exon3			GGCCCAGATAGCT	AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16094	protein-coding gene	gene with protein product	"BTB-ZF protein expressed in effector lymphocytes"	614639	"BTB (POZ) domain containing 4"	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.1045C>T	chr20.hg19:g.62407208G>A		176.0	0.0	.		208.0	99.0	.	NM_025224	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Silent	SNP	ENST00000245663.4	hg19	CCDS13538.1																																																																																			.	.	.	none		0.662	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224		A	62407208	G	A	62407208	2	1	91	1	0	0	0	0	0	0	0	1	17559	933	33	2		2	ZBTB46	20	62407208	Silent	SNP	G	TCGA-B3-4104-01A-01D-1458-08	6316397	62407208	618312	67	5848											
PICK1	9463	hgsc.bcm.edu	37	chr22	38470965	38470965	+	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	ctgcgggatgccgacgtcttCcccatcgaggtagacctggc	6	8	13	14	4	1	1	0	0	1	1	3	4	2	2	4	3	2	1	4	3	1	2			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr22:38470965C>G	ENST00000404072.3	+	13	1421	c.1074C>G	c.(1072-1074)ttC>ttG	p.F358L	RP5-1039K5.13_ENST00000445483.1_RNA|PICK1_ENST00000356976.3_Missense_Mutation_p.F358L	NM_001039583.1|NM_001039584.1	NP_001034672.1|NP_001034673.1	Q9NRD5	PICK1_HUMAN	protein interacting with PRKCA 1	358					ATP catabolic process (GO:0006200)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|dendritic spine maintenance (GO:0097062)|dendritic spine organization (GO:0097061)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|glial cell development (GO:0021782)|long term synaptic depression (GO:0060292)|monoamine transport (GO:0015844)|negative regulation of Arp2/3 complex-mediated actin nucleation (GO:0034316)|neuronal ion channel clustering (GO:0045161)|positive regulation of receptor internalization (GO:0002092)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|protein targeting (GO:0006605)|receptor clustering (GO:0043113)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endocytic vesicle membrane (GO:0030666)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	actin filament binding (GO:0051015)|Arp2/3 complex binding (GO:0071933)|ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein kinase C binding (GO:0005080)|receptor binding (GO:0005102)			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13	Melanoma(58;0.045)					CCGACGTCTTCCCCATCGAGG	0.607																																					p.F358L		Atlas-SNP	.											.	PICK1	30	.	0			c.C1074G						PASS	.						106	74	85					22																	38470965		2203	4300	6503	SO:0001583	missense	9463	exon13			CGTCTTCCCCATC	AL049654	CCDS13965.1	22q13.1	2006-02-14	2006-02-14	2006-02-14	ENSG00000100151	ENSG00000100151			9394	protein-coding gene	gene with protein product		605926	"protein kinase C, alpha binding protein", "protein interacting with PRKCA"	PRKCABP		10340301, 10591208	Standard	XM_006724377		Approved	dJ1039K5, MGC15204	uc003aus.3	Q9NRD5	OTTHUMG00000151159	ENST00000404072.3:c.1074C>G	chr22.hg19:g.38470965C>G	ENSP00000385205:p.Phe358Leu	83.0	0.0	.		66.0	25.0	.	NM_012407	B3KS52|O95906	Missense_Mutation	SNP	ENST00000404072.3	hg19	CCDS13965.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.273750	0.80580	.	.	ENSG00000100151	ENST00000404072;ENST00000356976	T;T	0.37411	1.2;1.2	4.33	3.21	0.36854	.	0.047493	0.85682	N	0.000000	T	0.55800	0.1943	M	0.81497	2.545	0.58432	D	0.999998	D	0.63880	0.993	D	0.68192	0.956	T	0.59726	-0.7400	10	0.72032	D	0.01	-17.1105	8.2306	0.31595	0.0:0.7398:0.162:0.0982	.	358	Q9NRD5	PICK1_HUMAN	L	358	ENSP00000385205:F358L;ENSP00000349465:F358L	ENSP00000349465:F358L	F	+	3	2	PICK1	36800911	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	2.142000	0.42177	2.124000	0.65301	0.561000	0.74099	TTC	.	.	.	none		0.607	PICK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321569.2	NM_012407		G	38470965	C	G	38470965	3	3	91	1	0	0	0	0	1	0	0	0	11888	854	30	4	1120	4	PICK1	22	38470965	Missense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08		38470965	12833601	68	5849											
MKL1	57591	hgsc.bcm.edu	37	chr22	40814967	40814967	+	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	tcacgaggatctgcagtggcGaggcctgcagggtcagctgc	7	7	16	11	2	3	0	2	0	1	0	3	3	3	1	1	4	4	3	1	4	0	0	rs199908950		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr22:40814967G>A	ENST00000355630.3	-	12	2065	c.1475C>T	c.(1474-1476)tCg>tTg	p.S492L	MKL1_ENST00000396617.3_Missense_Mutation_p.S492L|MKL1_ENST00000402042.1_Missense_Mutation_p.S442L|MKL1_ENST00000407029.1_Missense_Mutation_p.S492L	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	492					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						CTGCAGTGGCGAGGCCTGCAG	0.677			T	RBM15	acute megakaryocytic leukemia																																p.S492L		Atlas-SNP	.		Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	.	MKL1	69	.	0			c.C1475T						PASS	.						29	30	30					22																	40814967		2200	4299	6499	SO:0001583	missense	57591	exon12			AGTGGCGAGGCCT	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.1475C>T	chr22.hg19:g.40814967G>A	ENSP00000347847:p.Ser492Leu	77.0	0.0	.		68.0	11.0	.	NM_020831	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Missense_Mutation	SNP	ENST00000355630.3	hg19	CCDS14003.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.036393	0.75617	.	.	ENSG00000196588	ENST00000355630;ENST00000396617;ENST00000402042;ENST00000407029	T;T;T;T	0.69040	-0.29;-0.37;-0.36;-0.29	5.15	5.15	0.70609	.	0.061993	0.64402	D	0.000003	D	0.86163	0.5867	M	0.92367	3.3	0.52099	D	0.999946	B;D;D	0.76494	0.255;0.999;0.999	B;D;D	0.72625	0.024;0.978;0.978	D	0.88893	0.3347	10	0.62326	D	0.03	-16.568	18.819	0.92089	0.0:0.0:1.0:0.0	.	442;492;492	B0QY83;E7ER32;Q969V6	.;.;MKL1_HUMAN	L	492;492;442;492	ENSP00000347847:S492L;ENSP00000379861:S492L;ENSP00000385584:S442L;ENSP00000385835:S492L	ENSP00000347847:S492L	S	-	2	0	MKL1	39144913	1.000000	0.71417	0.515000	0.27774	0.937000	0.57800	6.783000	0.75078	2.676000	0.91093	0.591000	0.81541	TCG	.	G|0.999;A|0.001	0.001	weak		0.677	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831		A	40814967	G	A	40814967	3	1	91	1	0	0	0	0	1	0	0	0	9608	1059	37	1	1336	1	MKL1	22	40814967	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	2344002	40814967	10489599	69	5850											
PARVB	29780	hgsc.bcm.edu	37	chr22	44564537	44564537	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gttctttacaacctgttcacCaagtacaagaacgtggagtg	12	11	9	9	1	2	1	1	0	1	1	2	2	2	2	2	1	4	3	2	1	6	5			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr22:44564537C>T	ENST00000338758.7	+	13	1137	c.1074C>T	c.(1072-1074)acC>acT	p.T358T	PARVB_ENST00000406477.3_Silent_p.T391T|PARVB_ENST00000404989.1_Silent_p.T321T	NM_013327.4	NP_037459.2	Q9HBI1	PARVB_HUMAN	parvin, beta	358	CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin cytoskeleton reorganization (GO:0031532)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell projection assembly (GO:0030031)|establishment or maintenance of cell polarity regulating cell shape (GO:0071963)|lamellipodium assembly (GO:0030032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(3)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Ovarian(80;0.0246)|all_neural(38;0.0423)				ACCTGTTCACCAAGTACAAGA	0.552																																					p.T391T		Atlas-SNP	.											.	PARVB	44	.	0			c.C1173T						PASS	.						99	92	94					22																	44564537		2203	4300	6503	SO:0001819	synonymous_variant	29780	exon14			GTTCACCAAGTAC	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.1074C>T	chr22.hg19:g.44564537C>T		103.0	0.0	.		117.0	13.0	.	NM_001003828	B0QYM8|B0QYN1|B2R9X6|Q5TGJ5|Q86X93|Q96PN1|Q9NSP7|Q9UGT3|Q9Y368|Q9Y3L6|Q9Y3L7	Silent	SNP	ENST00000338758.7	hg19	CCDS14056.1																																																																																			.	.	.	none		0.552	PARVB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319518.2	NM_001003828		T	44564537	C	T	44564537	2	4	91	1	0	0	0	0	0	0	0	1	11476	581	21	2		2	PARVB	22	44564537	Silent	SNP	C	TCGA-B3-4104-01A-01D-1458-08	3749570	44564537	6740029	70	5851											
CELSR1	9620	hgsc.bcm.edu	37	chr22	46930992	46930992	+	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	tcctcattcagacgaagctcGtaggtgggctgcgtgaacac	9	9	12	11	3	2	2	2	1	0	1	4	3	3	2	1	2	3	3	1	2	3	2	rs529594359		TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chr22:46930992G>A	ENST00000262738.3	-	1	2075	c.2076C>T	c.(2074-2076)taC>taT	p.Y692Y	CELSR1_ENST00000497509.1_5'Flank|CELSR1_ENST00000395964.1_Silent_p.Y692Y	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	692	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		GACGAAGCTCGTAGGTGGGCT	0.642													G|||	1	0.000199681	8e-04	0	5008	,	,		18477	0		0	False		,,,				2504	0				p.Y692Y		Atlas-SNP	.											.	CELSR1	242	.	0			c.C2076T						PASS	.						44	28	34					22																	46930992		2201	4298	6499	SO:0001819	synonymous_variant	9620	exon1			AAGCTCGTAGGTG	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.2076C>T	chr22.hg19:g.46930992G>A		52.0	0.0	.		48.0	13.0	.	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	hg19	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	G	3.230	-0.157692	0.06544	.	.	ENSG00000075275	ENST00000454637	.	.	.	4.51	1.53	0.23141	.	.	.	.	.	T	0.55689	0.1936	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48479	-0.9032	4	.	.	.	.	8.3078	0.32053	0.4017:0.0:0.5983:0.0	.	.	.	.	M	67	.	.	T	-	2	0	CELSR1	45309656	0.873000	0.30073	0.986000	0.45419	0.599000	0.36880	-0.092000	0.11129	0.459000	0.27016	0.305000	0.20034	ACG	.	.	.	none		0.642	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		A	46930992	G	A	46930992	2	1	91	1	0	0	0	0	0	0	0	1	3223	1140	40	1		1	CELSR1	22	46930992	Silent	SNP	G	TCGA-B3-4104-01A-01D-1458-08	2366455	46930992	4373574	71	5852											
STAG2	10735	hgsc.bcm.edu	37	chrX	123176469	123176469	+	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	tgcagaactctgagataattCgaaaaatgactgaagaattc	17	10	8	6	1	1	5	0	3	1	3	3	7	1	5	0	0	2	1	0	0	6	3			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chrX:123176469C>T	ENST00000371160.1	+	7	726	c.436C>T	c.(436-438)Cga>Tga	p.R146*	STAG2_ENST00000371157.3_Nonsense_Mutation_p.R146*|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000371144.3_Nonsense_Mutation_p.R146*|STAG2_ENST00000371145.3_Nonsense_Mutation_p.R146*|STAG2_ENST00000354548.5_Nonsense_Mutation_p.R77*|STAG2_ENST00000218089.9_Nonsense_Mutation_p.R146*	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	146					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						TGAGATAATTCGAAAAATGAC	0.284																																					p.R146X		Atlas-SNP	.											.	STAG2	309	.	0			c.C436T						PASS	.						79	75	76					X																	123176469		2203	4300	6503	SO:0001587	stop_gained	10735	exon7			ATAATTCGAAAAA	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.436C>T	chrX.hg19:g.123176469C>T	ENSP00000360202:p.Arg146*	63.0	0.0	.		98.0	85.0	.	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Nonsense_Mutation	SNP	ENST00000371160.1	hg19	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.683809	0.88639	.	.	ENSG00000101972	ENST00000218089;ENST00000455404;ENST00000354548;ENST00000371160;ENST00000435103;ENST00000371157;ENST00000371145;ENST00000371144;ENST00000428941;ENST00000435215	.	.	.	5.74	4.86	0.63082	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-21.2847	12.9796	0.58555	0.2934:0.7066:0.0:0.0	.	.	.	.	X	146;146;77;146;146;146;146;146;146;146	.	ENSP00000218089:R146X	R	+	1	2	STAG2	123004150	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	1.312000	0.33574	1.156000	0.42514	0.522000	0.50473	CGA	.	.	.	none		0.284	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		T	123176469	C	T	123176469	4	4	91	1	0	0	0	0	0	1	0	0	15255	876	31	1	454	1	STAG2	23	123176469	Nonsense_Mutation	SNP	C	TCGA-B3-4104-01A-01D-1458-08		123176469	32094091	72	5853											
IL9R	3581	hgsc.bcm.edu	37	chrX	155232601	155232601	+	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	ggagagtgaggccctgaggcGagacatgggcacctggctcc	8	5	17	11	1	0	4	0	2	0	2	1	6	1	4	3	5	0	2	3	5	0	0			TCGA-B3-4104-01A-01D-1458-08	TCGA-B3-4104-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	368382d0-ad7f-4735-b04a-e806d2a2d9a4	23886794-9d4c-4511-82ee-830db88796d5	g.chrX:155232601G>A	ENST00000244174.5	+	2	238	c.59G>A	c.(58-60)cGa>cAa	p.R20Q	IL9R_ENST00000540897.1_Missense_Mutation_p.R57Q|IL9R_ENST00000369423.2_Missense_Mutation_p.R67Q|IL9R_ENST00000424344.3_5'UTR	NM_002186.2	NP_002177.2	Q01113	IL9R_HUMAN	interleukin 9 receptor	20					cell proliferation (GO:0008283)|positive regulation of cell growth (GO:0030307)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	interleukin-9 receptor activity (GO:0004919)			NS(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(12)|upper_aerodigestive_tract(1)	23	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					GCCCTGAGGCGAGACATGGGC	0.612																																					p.R67Q		Atlas-SNP	.											.	IL9R	73	.	0			c.G200A						PASS	.	G	GLN/ARG	1,4405		0,1,2202	164	163	163		59	-2.3	0	X		163	0,8592		0,0,4296	no	missense	IL9R	NM_002186.2	43	0,1,6498	AA,AG,GG		0.0,0.0227,0.0077	benign	20/522	155232601	1,12997	2203	4296	6499	SO:0001583	missense	3581	exon3			TGAGGCGAGACAT	M84747	CCDS14771.4, CCDS59180.1	Xq28 and Yq12	2008-02-05			ENSG00000124334	ENSG00000124334		"Pseudoautosomal regions / PAR2", "Interleukins and interleukin receptors", "CD molecules"	6030	protein-coding gene	gene with protein product		300007				1376929, 8666384	Standard	NM_002186		Approved	CD129	uc004fnv.1	Q01113	OTTHUMG00000022720	ENST00000244174.5:c.59G>A	chrX.hg19:g.155232601G>A	ENSP00000244174:p.Arg20Gln	282.0	1.0	.		236.0	84.0	.	NM_176786	B9ZVT0|Q14634|Q8WWU1|Q96TF0	Missense_Mutation	SNP	ENST00000244174.5	hg19	CCDS14771.4	.	.	.	.	.	.	.	.	.	.	g	5.676	0.309355	0.10733	2.27E-4	0.0	ENSG00000124334	ENST00000244174;ENST00000369423;ENST00000540897	T;T;T	0.22743	2.98;1.94;1.94	1.18	-2.35	0.06684	.	4.396220	0.00735	N	0.000961	T	0.09512	0.0234	.	.	.	0.09310	N	1	B;B	0.28419	0.021;0.211	B;B	0.10450	0.002;0.005	T	0.11324	-1.0592	9	0.13108	T	0.6	-13.6917	3.8243	0.08848	0.2084:0.4817:0.3099:0.0	.	20;67	Q01113;B9ZVT0	IL9R_HUMAN;.	Q	20;67;57	ENSP00000244174:R20Q;ENSP00000358431:R67Q;ENSP00000438112:R57Q	ENSP00000244174:R20Q	R	+	2	0	IL9R	154885795	0.000000	0.05858	0.000000	0.03702	0.739000	0.42172	-0.677000	0.05215	-1.521000	0.01771	-0.733000	0.03571	CGA	.	.	.	weak		0.612	IL9R-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058981.1	NM_002186		A	155232601	G	A	155232601	3	1	91	1	0	0	0	0	1	0	0	0	7715	1058	37	1	65	1	IL9R	23	155232601	Missense_Mutation	SNP	G	TCGA-B3-4104-01A-01D-1458-08	32056132	155232601	37959	73	5854											
S100PBP	64766	hgsc.bcm.edu	37	chr1	33292114	33292114	+	Frame_Shift_Del	DEL	A	A	-																															ccattaaacagacgctctgtActagaaaagaatcttataaa																										TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr1:33292114delA	ENST00000373475.5	+	3	668	c.414delA	c.(412-414)gtafs	p.V138fs	S100PBP_ENST00000398243.3_Frame_Shift_Del_p.V138fs|S100PBP_ENST00000356689.3_3'UTR|S100PBP_ENST00000373476.1_Frame_Shift_Del_p.V138fs	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)				GACGCTCTGTACTAGAAAAGA	0.413																																					p.V138fs		Atlas-INDEL	.											S100PBP,colon,carcinoma,0,1	S100PBP	31	.	0			c.413delT						PASS	.						55	56	56					1																	33292114		2203	4300	6503	SO:0001589	frameshift_variant	64766	exon3			.	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.414delA	chr1.hg19:g.33292114delA	ENSP00000362574:p.Val138fs	100.0	0.0	0		70.0	16.0	0.228571	NM_001256121		Frame_Shift_Del	DEL	ENST00000373475.5	hg19	CCDS30666.1																																																																																			.	.	.	none		0.413	S100PBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011266.1	NM_022753		-	33292114	A	-	33292114	7	5	92	1	0	1	0	1	0	0	0	0	13804	378	14	0	416	0	S100PBP	1	33292114	Frame_Shift_Del	DEL	A	TCGA-B3-8121-01A-21D-2396-08		33292114	215958507	1	5855											
ATP5F1	515	hgsc.bcm.edu	37	chr1	112002161	112002161	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtaaagaatcgcctggactAtcatatatctgtgcagaaca	15	10	8	8	1	2	2	1	0	1	2	3	3	2	3	1	1	2	2	1	1	7	4	rs201457142		TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr1:112002161A>G	ENST00000369722.3	+	6	1202	c.596A>G	c.(595-597)tAt>tGt	p.Y199C	ATP5F1_ENST00000483994.1_Missense_Mutation_p.Y138C|ATP5F1_ENST00000369721.4_3'UTR	NM_001688.4	NP_001679.2	P24539	AT5F1_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit B1	199					ATP catabolic process (GO:0006200)|ATP synthesis coupled proton transport (GO:0015986)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) (GO:0000276)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	hydrogen ion transmembrane transporter activity (GO:0015078)|transmembrane transporter activity (GO:0022857)			breast(1)|cervix(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	8		all_cancers(81;8.16e-06)|all_epithelial(167;5.63e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|Colorectal(144;0.0296)|all cancers(265;0.0488)|Epithelial(280;0.0732)|COAD - Colon adenocarcinoma(174;0.114)|LUSC - Lung squamous cell carcinoma(189;0.135)		CGCCTGGACTATCATATATCT	0.418													A|||	1	0.000199681	8e-04	0	5008	,	,		19484	0		0	False		,,,				2504	0				p.Y199C		Atlas-SNP	.											.	ATP5F1	20	.	0			c.A596G						PASS	.	A	CYS/TYR	1,4405	2.1+/-5.4	0,1,2202	79	85	83		596	4.8	1	1		83	1,8599		0,1,4299	no	missense	ATP5F1	NM_001688.4	194	0,2,6501	GG,GA,AA		0.0116,0.0227,0.0154	probably-damaging	199/257	112002161	2,13004	2203	4300	6503	SO:0001583	missense	515	exon6			TGGACTATCATAT	X60221	CCDS836.1	1p13.2	2012-10-12	2010-06-11		ENSG00000116459	ENSG00000116459		"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	840	protein-coding gene	gene with protein product		603270	"ATP synthase, H+ transporting, mitochondrial F0 complex, subunit b, isoform 1", "ATP synthase, H+ transporting, mitochondrial F0 complex, subunit B1"			1831354	Standard	XM_005270929		Approved		uc001ebc.3	P24539	OTTHUMG00000011745	ENST00000369722.3:c.596A>G	chr1.hg19:g.112002161A>G	ENSP00000358737:p.Tyr199Cys	73.0	0.0	.		50.0	7.0	.	NM_001688	Q9BQ68|Q9BRU8	Missense_Mutation	SNP	ENST00000369722.3	hg19	CCDS836.1	.	.	.	.	.	.	.	.	.	.	A	16.68	3.189998	0.58017	2.27E-4	1.16E-4	ENSG00000116459	ENST00000369722;ENST00000483994	T;T	0.38887	1.11;1.11	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.62950	0.2470	M	0.89095	3.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.71178	-0.4669	10	0.59425	D	0.04	.	14.394	0.66999	1.0:0.0:0.0:0.0	.	199;199	Q08ET0;P24539	.;AT5F1_HUMAN	C	199;138	ENSP00000358737:Y199C;ENSP00000420366:Y138C	ENSP00000358737:Y199C	Y	+	2	0	ATP5F1	111803684	1.000000	0.71417	0.998000	0.56505	0.208000	0.24298	8.489000	0.90461	1.956000	0.56807	0.383000	0.25322	TAT	.	A|0.999;G|0.001	0.001	weak		0.418	ATP5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032455.1	NM_001688		G	112002161	A	G	112002161	3	3	92	1	0	0	0	0	1	0	0	0	1152	449	16	3	618	3	ATP5F1	1	112002161	Missense_Mutation	SNP	A	TCGA-B3-8121-01A-21D-2396-08	78710047	112002161	137248460	2	5856											
SLC16A1	6566	hgsc.bcm.edu	37	chr1	113460277	113460277	+	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	tagggttaagtccaggaactGattaattgtttggaagactg	12	13	12	4	0	0	2	0	1	0	1	1	4	1	4	1	3	1	2	1	3	5	5			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr1:113460277G>A	ENST00000538576.1	-	4	1582	c.751C>T	c.(751-753)Cag>Tag	p.Q251*	SLC16A1_ENST00000369626.3_Nonsense_Mutation_p.Q251*|SLC16A1_ENST00000433570.4_Nonsense_Mutation_p.Q251*	NM_001166496.1	NP_001159968.1	P53985	MOT1_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 1	251					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)	TCCAGGAACTGATTAATTGTT	0.388																																					p.Q251X		Atlas-SNP	.											.	SLC16A1	61	.	0			c.C751T						PASS	.						101	103	103					1																	113460277		2203	4300	6503	SO:0001587	stop_gained	6566	exon4			GGAACTGATTAAT	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.751C>T	chr1.hg19:g.113460277G>A	ENSP00000441065:p.Gln251*	156.0	0.0	.		86.0	17.0	.	NM_001166496	Q49A45|Q5T8R6|Q9NSJ9	Nonsense_Mutation	SNP	ENST00000538576.1	hg19	CCDS858.1	.	.	.	.	.	.	.	.	.	.	G	18.51	3.639199	0.67244	.	.	ENSG00000155380	ENST00000369626;ENST00000538576;ENST00000458229;ENST00000433570;ENST00000443580	.	.	.	5.74	-3.2	0.05156	.	0.477590	0.27223	N	0.020353	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.6817	0.91548	0.0:0.0:0.6596:0.3404	.	.	.	.	X	251	.	ENSP00000358640:Q251X	Q	-	1	0	SLC16A1	113261800	0.997000	0.39634	0.183000	0.23137	0.253000	0.25986	1.851000	0.39338	-0.739000	0.04809	-0.457000	0.05445	CAG	.	.	.	none		0.388	SLC16A1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033539.1	NM_003051		A	113460277	G	A	113460277	4	1	92	1	0	0	0	0	0	1	0	0	14415	1299	45	2	759	2	SLC16A1	1	113460277	Nonsense_Mutation	SNP	G	TCGA-B3-8121-01A-21D-2396-08	1458116	113460277	135790344	3	5857											
SNAPIN	23557	hgsc.bcm.edu	37	chr1	153631989	153631989	+	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	acccctatgttaagaagctaCttaatgcccggcgacgcgtt	10	10	9	12	4	0	1	0	0	0	1	0	2	0	1	3	1	3	3	3	1	5	5			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr1:153631989C>G	ENST00000368685.5	+	3	346	c.256C>G	c.(256-258)Ctt>Gtt	p.L86V	SNAPIN_ENST00000478558.1_3'UTR|ILF2_ENST00000480213.1_5'Flank	NM_012437.5	NP_036569.1	O95295	SNAPN_HUMAN	SNAP-associated protein	86	Interaction with TOR1A.				anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|endosome to lysosome transport (GO:0008333)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|negative regulation of neuron projection development (GO:0010977)|neuron projection development (GO:0031175)|neurotransmitter secretion (GO:0007269)|positive regulation of late endosome to lysosome transport (GO:1902824)|regulation of protein binding (GO:0043393)|synaptic vesicle exocytosis (GO:0016079)|synaptic vesicle fusion to presynaptic membrane (GO:0031629)|synaptic vesicle maturation (GO:0016188)|synaptic vesicle transport (GO:0048489)|terminal button organization (GO:0072553)|viral process (GO:0016032)	BLOC-1 complex (GO:0031083)|cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)|secretory granule (GO:0030141)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	SNARE binding (GO:0000149)			lung(3)	3	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)			TAAGAAGCTACTTAATGCCCG	0.443																																					p.L86V		Atlas-SNP	.											.	SNAPIN	6	.	0			c.C256G						PASS	.						147	146	146					1																	153631989		2203	4300	6503	SO:0001583	missense	23557	exon3			AAGCTACTTAATG	AF086837	CCDS1049.1	1q22	2013-09-27		2007-11-14	ENSG00000143553	ENSG00000143553		"Biogenesis of lysosomal organelles complex-1 subunits"	17145	protein-coding gene	gene with protein product	"snapin", "SNAP-25-binding protein", "biogenesis of lysosomal organelles complex-1, subunit 7"	607007		SNAPAP		10195194, 12659861	Standard	NM_012437		Approved	BLOC1S7	uc001fcq.4	O95295	OTTHUMG00000037086	ENST00000368685.5:c.256C>G	chr1.hg19:g.153631989C>G	ENSP00000357674:p.Leu86Val	148.0	0.0	.		95.0	14.0	.	NM_012437	D3DV56|Q5SXU8	Missense_Mutation	SNP	ENST00000368685.5	hg19	CCDS1049.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.734669	0.48939	.	.	ENSG00000143553	ENST00000368685	T	0.46451	0.87	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.19685	0.0473	L	0.39245	1.2	0.49582	D	0.999803	B	0.28998	0.23	B	0.20955	0.032	T	0.03364	-1.1044	10	0.15066	T	0.55	-16.4091	17.2626	0.87075	0.0:1.0:0.0:0.0	.	86	O95295	SNAPN_HUMAN	V	86	ENSP00000357674:L86V	ENSP00000357674:L86V	L	+	1	0	SNAPIN	151898613	0.999000	0.42202	0.961000	0.40146	0.986000	0.74619	4.168000	0.58216	2.941000	0.99782	0.655000	0.94253	CTT	.	.	.	none		0.443	SNAPIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090036.1	NM_012437		G	153631989	C	G	153631989	3	3	92	1	0	0	0	0	1	0	0	0	14852	565	20	4	266	4	SNAPIN	1	153631989	Missense_Mutation	SNP	C	TCGA-B3-8121-01A-21D-2396-08	40171712	153631989	95618632	4	5858											
NLRC4	58484	hgsc.bcm.edu	37	chr2	32475306	32475307	+	Missense_Mutation	DNP	GC	GC	CT																															tatggctttcagaatttcttGctcagtggtgtttttcacac																										TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr2:32475306_32475307GC>CT	ENST00000404025.2	-	5	2114_2115	c.1626_1627GC>AG	c.(1624-1629)gaGCaa>gaAGaa	p.Q543E	NLRC4_ENST00000342905.6_Intron|NLRC4_ENST00000360906.5_Missense_Mutation_p.Q543E|NLRC4_ENST00000402280.1_Missense_Mutation_p.Q543E			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	543					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)					AGAATTTCTTGCTCAGTGGTGT	0.446																																					p.Q543E|p.E542E		Atlas-SNP	.											.	NLRC4	165	.	0			c.C1627G|c.G1626A						PASS	.																																			SO:0001583	missense	58484	exon4			TTTCTTGCTCAGT|TTCTTGCTCAGTG	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.1626_1627delinsCT	chr2.hg19:g.32475306_32475307delinsCT	ENSP00000385090:p.Gln543Glu	164.0|163.0	0.0	.		105.0|106.0	21.0	.	NM_001199138	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Missense_Mutation|Silent	SNP	ENST00000404025.2	hg19	CCDS33174.1																																																																																			.	.	.	none		0.446	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209		CT	32475307	GC	CT	32475306	3	2	92	1	0	0	0	0	1	0	0	0	10476	1328	46	4	1471	4	NLRC4	2	32475306	Missense_Mutation	DNP	GC	TCGA-B3-8121-01A-21D-2396-08		32475306	210724067	5	5859											
HAT1	8520	hgsc.bcm.edu	37	chr2	172848182	172848182	+	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	atgaaccaaatagaaataagCatgcaacatgaacagctgga	20	6	8	7	0	0	3	0	2	0	1	0	4	0	4	1	1	6	3	1	1	7	2			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr2:172848182C>A	ENST00000264108.4	+	11	1212	c.1176C>A	c.(1174-1176)agC>agA	p.S392R	SLC25A12_ENST00000472748.1_Intron|HAT1_ENST00000392584.1_Missense_Mutation_p.S307R	NM_003642.3	NP_003633.1	O14929	HAT1_HUMAN	histone acetyltransferase 1	392					chromatin organization (GO:0006325)|chromatin silencing at telomere (GO:0006348)|DNA packaging (GO:0006323)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4 acetylation (GO:0043967)|internal protein amino acid acetylation (GO:0006475)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	H4 histone acetyltransferase activity (GO:0010485)|histone acetyltransferase activity (GO:0004402)			breast(1)|kidney(1)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|prostate(1)	19			OV - Ovarian serous cystadenocarcinoma(117;0.216)			TAGAAATAAGCATGCAACATG	0.388																																					p.S392R		Atlas-SNP	.											HAT1,NS,carcinoma,0,1	HAT1	40	.	0			c.C1176A						PASS	.						112	112	112					2																	172848182		2203	4300	6503	SO:0001583	missense	8520	exon11			AATAAGCATGCAA	AF030424	CCDS2245.1	2q31.2-q33.1	2011-07-01			ENSG00000128708	ENSG00000128708	2.3.1.48	"Chromatin-modifying enzymes / K-acetyltransferases"	4821	protein-coding gene	gene with protein product		603053				9427644	Standard	NM_003642		Approved	KAT1	uc002uhi.3	O14929	OTTHUMG00000132282	ENST00000264108.4:c.1176C>A	chr2.hg19:g.172848182C>A	ENSP00000264108:p.Ser392Arg	77.0	0.0	.		55.0	3.0	.	NM_003642	Q49A44|Q53QF0|Q53SU4|Q6P594|Q8WWB9	Missense_Mutation	SNP	ENST00000264108.4	hg19	CCDS2245.1	.	.	.	.	.	.	.	.	.	.	C	3.309	-0.141123	0.06669	.	.	ENSG00000128708	ENST00000392584;ENST00000264108	.	.	.	5.94	3.11	0.35812	.	0.224777	0.53938	D	0.000049	T	0.40423	0.1116	L	0.38175	1.15	0.32521	N	0.536232	B	0.02656	0.0	B	0.04013	0.001	T	0.45220	-0.9276	9	0.87932	D	0	-6.6111	8.5772	0.33605	0.0:0.7345:0.127:0.1386	.	392	O14929	HAT1_HUMAN	R	307;392	.	ENSP00000264108:S392R	S	+	3	2	HAT1	172556428	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.923000	0.28757	0.370000	0.24538	0.591000	0.81541	AGC	.	.	.	none		0.388	HAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255377.1	NM_003642		A	172848182	C	A	172848182	3	1	92	1	0	0	0	0	1	0	0	0	6971	709	25	4	1218	4	HAT1	2	172848182	Missense_Mutation	SNP	C	TCGA-B3-8121-01A-21D-2396-08	140372876	172848182	70351191	6	5860											
ZNF142	7701	hgsc.bcm.edu	37	chr2	219510938	219510938	+	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	atgtgcacacggaggtagtgCttccacttggtgacatagcc	9	10	12	10	1	0	1	0	1	0	0	1	2	1	2	2	3	3	3	2	3	2	4			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr2:219510938C>A	ENST00000449707.1	-	7	1828	c.1407G>T	c.(1405-1407)aaG>aaT	p.K469N	ZNF142_ENST00000411696.2_Missense_Mutation_p.K469N	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	469					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(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)		GGAGGTAGTGCTTCCACTTGG	0.517																																					p.K469N	Colon(170;867 1942 8995 15834 18053)	Atlas-SNP	.											.	ZNF142	190	.	0			c.G1407T						PASS	.						226	220	222					2																	219510938		2153	4245	6398	SO:0001583	missense	7701	exon7			GTAGTGCTTCCAC	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.1407G>T	chr2.hg19:g.219510938C>A	ENSP00000408643:p.Lys469Asn	134.0	0.0	.		139.0	32.0	.	NM_001105537	Q92510	Missense_Mutation	SNP	ENST00000449707.1	hg19	CCDS42817.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.188772	0.78789	.	.	ENSG00000115568	ENST00000449707;ENST00000411696	T;T	0.54071	0.59;0.59	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	0.85682	D	0.000000	T	0.62684	0.2448	L	0.41906	1.305	0.42919	D	0.994282	D;D	0.89917	1.0;0.999	D;D	0.85130	0.996;0.997	T	0.62978	-0.6739	10	0.54805	T	0.06	-14.9575	12.26	0.54645	0.0:0.9228:0.0:0.0772	.	469;306	P52746;A8MWU9	ZN142_HUMAN;.	N	469	ENSP00000408643:K469N;ENSP00000398798:K469N	ENSP00000398798:K469N	K	-	3	2	ZNF142	219219182	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.173000	0.50839	2.709000	0.92574	0.561000	0.74099	AAG	.	.	.	none		0.517	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081		A	219510938	C	A	219510938	3	1	92	1	0	0	0	0	1	0	0	0	17743	796	28	4	3672	4	ZNF142	2	219510938	Missense_Mutation	SNP	C	TCGA-B3-8121-01A-21D-2396-08	46662756	219510938	23688435	7	5861											
ADAMTS16	170690	hgsc.bcm.edu	37	chr5	5235247	5235247	+	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	cagtgtgccgagcacaacagCagacgattcagagggcggca	12	4	14	11	3	1	2	1	0	0	2	1	4	1	2	1	2	4	3	1	2	1	1			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr5:5235247C>G	ENST00000274181.7	+	13	2109	c.1971C>G	c.(1969-1971)agC>agG	p.S657R	ADAMTS16_ENST00000513709.1_3'UTR	NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	657	Cys-rich.				branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						AGCACAACAGCAGACGATTCA	0.512																																					p.S657R		Atlas-SNP	.											.	ADAMTS16	543	.	0			c.C1971G						PASS	.						76	80	79					5																	5235247		1950	4152	6102	SO:0001583	missense	170690	exon13			CAACAGCAGACGA	AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536		"ADAM metallopeptidases with thrombospondin type 1 motif"	17108	protein-coding gene	gene with protein product		607510	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16"			11867212	Standard	NM_139056		Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.1971C>G	chr5.hg19:g.5235247C>G	ENSP00000274181:p.Ser657Arg	97.0	0.0	.		124.0	16.0	.	NM_139056	C6G490|Q8IVE2	Missense_Mutation	SNP	ENST00000274181.7	hg19	CCDS43299.1	.	.	.	.	.	.	.	.	.	.	C	10.26	1.302320	0.23736	.	.	ENSG00000145536	ENST00000274181;ENST00000536857	T	0.63580	-0.05	4.57	3.68	0.42216	.	0.198340	0.50627	D	0.000116	T	0.56702	0.2003	M	0.62016	1.91	0.80722	D	1	P;B	0.50710	0.938;0.296	B;B	0.41860	0.368;0.292	T	0.58825	-0.7568	10	0.33940	T	0.23	.	11.2853	0.49218	0.0:0.908:0.0:0.092	.	657;657	Q8TE57;Q8TE57-2	ATS16_HUMAN;.	R	657	ENSP00000274181:S657R	ENSP00000274181:S657R	S	+	3	2	ADAMTS16	5288247	1.000000	0.71417	0.100000	0.21137	0.015000	0.08874	2.587000	0.46128	2.270000	0.75569	0.655000	0.94253	AGC	.	.	.	none		0.512	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056		G	5235247	C	G	5235247	3	3	92	1	0	0	0	0	1	0	0	0	261	709	25	4	2021	4	ADAMTS16	5	5235247	Missense_Mutation	SNP	C	TCGA-B3-8121-01A-21D-2396-08		5235247	175680013	8	5862											
VCAN	1462	hgsc.bcm.edu	37	chr5	82850838	82850838	+	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	gtttgagcatgacttccgttGgactgatggcagcacactgg	8	11	13	9	1	0	3	0	3	0	0	1	4	1	4	1	3	2	5	1	3	0	3			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr5:82850838G>A	ENST00000265077.3	+	12	10281	c.9716G>A	c.(9715-9717)tGg>tAg	p.W3239*	VCAN_ENST00000502527.2_Nonsense_Mutation_p.W498*|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000342785.4_Nonsense_Mutation_p.W1485*|VCAN_ENST00000512590.2_Nonsense_Mutation_p.W1437*|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000343200.5_Nonsense_Mutation_p.W2252*	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	3239	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				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)	p.W3239S(1)		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)	GACTTCCGTTGGACTGATGGC	0.443																																					p.W3239X		Atlas-SNP	.											VCAN,NS,carcinoma,0,1	VCAN	498	.	1	Substitution - Missense(1)	lung(1)	c.G9716A						PASS	.						236	192	207					5																	82850838		2203	4300	6503	SO:0001587	stop_gained	1462	exon12			TCCGTTGGACTGA	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.9716G>A	chr5.hg19:g.82850838G>A	ENSP00000265077:p.Trp3239*	89.0	0.0	.		79.0	13.0	.	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Nonsense_Mutation	SNP	ENST00000265077.3	hg19	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	G	48	13.927085	0.99770	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000342785;ENST00000512590;ENST00000502527	.	.	.	5.81	5.81	0.92471	.	0.000000	0.56097	D	0.000028	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.089	0.97809	0.0:0.0:1.0:0.0	.	.	.	.	X	3239;2252;1485;1437;498	.	ENSP00000265077:W3239X	W	+	2	0	VCAN	82886594	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	9.756000	0.98918	2.752000	0.94435	0.557000	0.71058	TGG	.	.	.	none		0.443	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		A	82850838	G	A	82850838	4	1	92	1	0	0	0	0	0	1	0	0	17150	1357	47	2	9758	2	VCAN	5	82850838	Nonsense_Mutation	SNP	G	TCGA-B3-8121-01A-21D-2396-08	77615591	82850838	98064422	9	5863											
HIST1H4B	8366	hgsc.bcm.edu	37	chr6	26027471	26027471	+	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	acctttaccgcctttgccgcGaccagacatgtctaaccagc	9	9	7	16	3	1	1	0	0	1	1	1	2	1	1	6	0	4	0	6	0	2	4			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr6:26027471G>C	ENST00000377364.3	-	1	9	c.10C>G	c.(10-12)Cgc>Ggc	p.R4G		NM_003544.2	NP_003535.1	P62805	H4_HUMAN	histone cluster 1, H4b	4					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						CCTTTGCCGCGACCAGACATG	0.512																																					p.R4G		Atlas-SNP	.											HIST1H4B,NS,carcinoma,0,1	HIST1H4B	27	.	0			c.C10G						PASS	.						49	47	47					6																	26027471		2203	4300	6503	SO:0001583	missense	8366	exon1			TGCCGCGACCAGA	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.10C>G	chr6.hg19:g.26027471G>C	ENSP00000366581:p.Arg4Gly	95.0	0.0	.		104.0	16.0	.	NM_003544	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000377364.3	hg19	CCDS4572.1	.	.	.	.	.	.	.	.	.	.	g	12.98	2.099423	0.37048	.	.	ENSG00000124529	ENST00000377364	.	.	.	4.56	3.6	0.41247	.	0.000000	0.47852	U	0.000206	T	0.42988	0.1227	.	.	.	0.29320	N	0.867408	.	.	.	.	.	.	T	0.30592	-0.9973	6	0.72032	D	0.01	.	13.1415	0.59438	0.0:0.0:0.7636:0.2364	.	.	.	.	G	4	.	ENSP00000366581:R4G	R	-	1	0	HIST1H4B	26135450	0.573000	0.26676	0.167000	0.22817	0.033000	0.12548	0.731000	0.26058	2.454000	0.82982	0.563000	0.77884	CGC	.	.	.	none		0.512	HIST1H4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040079.2	NM_003544		C	26027471	G	C	26027471	3	2	92	1	0	0	0	0	1	0	0	0	7173	1058	37	4	305	4	HIST1H4B	6	26027471	Missense_Mutation	SNP	G	TCGA-B3-8121-01A-21D-2396-08		26027471	145087596	10	5864											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51924820	51924820	+	Missense_Mutation	SNP	A	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	tatttgtctctggagccacaAagaacccactgagccgtgct	10	10	9	12	1	1	2	0	1	1	1	2	3	1	3	3	1	4	1	3	1	3	2	rs143341567		TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr6:51924820A>C	ENST00000371117.3	-	15	1414	c.1139T>G	c.(1138-1140)tTt>tGt	p.F380C	AL590391.1_ENST00000408630.2_RNA|PKHD1_ENST00000340994.4_Missense_Mutation_p.F380C	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	380					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)					TGGAGCCACAAAGAACCCACT	0.443																																					p.F380C		Atlas-SNP	.											.	PKHD1	927	.	0			c.T1139G						PASS	.						85	77	80					6																	51924820		2203	4300	6503	SO:0001583	missense	5314	exon15			GCCACAAAGAACC	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.1139T>G	chr6.hg19:g.51924820A>C	ENSP00000360158:p.Phe380Cys	121.0	0.0	.		67.0	18.0	.	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.110642	0.77210	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	T;T	0.76968	-1.06;-1.06	5.46	5.46	0.80206	.	0.000000	0.64402	D	0.000001	D	0.85617	0.5738	M	0.78049	2.395	0.38168	D	0.939231	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.88299	0.2948	10	0.87932	D	0	.	15.0065	0.71516	1.0:0.0:0.0:0.0	.	380;380	P08F94-2;P08F94	.;PKHD1_HUMAN	C	380	ENSP00000360158:F380C;ENSP00000341097:F380C	ENSP00000341097:F380C	F	-	2	0	PKHD1	52032779	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.103000	0.71492	2.195000	0.70347	0.528000	0.53228	TTT	.	A|1.000;G|0.000	.	alt		0.443	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		C	51924820	A	C	51924820	3	2	92	1	0	0	0	0	1	0	0	0	11978	14	1	5	11336	5	PKHD1	6	51924820	Missense_Mutation	SNP	A	TCGA-B3-8121-01A-21D-2396-08	25897349	51924820	119190247	11	5865											
KCNQ5	56479	hgsc.bcm.edu	37	chr6	73905126	73905126	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctcagcttgcctcatgtcAaactgaaataagttcttcat	11	13	5	12	0	5	1	4	1	1	0	5	1	5	1	2	0	3	2	2	0	3	4			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr6:73905126A>G	ENST00000370398.1	+	14	2897	c.2788A>G	c.(2788-2790)Aaa>Gaa	p.K930E	KCNQ5_ENST00000355635.3_Missense_Mutation_p.K931E|KCNQ5_ENST00000355194.4_Missense_Mutation_p.K930E|KCNQ5_ENST00000414165.2_Missense_Mutation_p.K820E|KCNQ5_ENST00000342056.2_Missense_Mutation_p.K949E|KCNQ5_ENST00000403813.2_Missense_Mutation_p.K921E|KCNQ5_ENST00000402622.2_Missense_Mutation_p.K940E	NM_019842.3	NP_062816.2	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 5	930					protein complex assembly (GO:0006461)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|cervix(1)|endometrium(6)|kidney(7)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	57		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)	Ezogabine(DB04953)	GCCTCATGTCAAACTGAAATA	0.408																																					p.K949E	GBM(142;1375 1859 14391 23261 44706)	Atlas-SNP	.											.	KCNQ5	153	.	0			c.A2845G						PASS	.						64	65	65					6																	73905126		2203	4300	6503	SO:0001583	missense	56479	exon15			CATGTCAAACTGA	AF202977	CCDS4976.1, CCDS55034.1	6q14	2012-07-05			ENSG00000185760	ENSG00000185760		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6299	protein-coding gene	gene with protein product		607357				10787416, 10816588, 16382104	Standard	NM_019842		Approved	Kv7.5	uc011dyh.2	Q9NR82	OTTHUMG00000015020	ENST00000370398.1:c.2788A>G	chr6.hg19:g.73905126A>G	ENSP00000359425:p.Lys930Glu	122.0	0.0	.		112.0	17.0	.	NM_001160133	A6NKT6|A6PVT6|A8MSQ5|B4DS33|B5MC83|B7ZL37|F5GZV0|Q17RE1|Q5VVP3|Q86W40|Q9NRN0|Q9NYA6	Missense_Mutation	SNP	ENST00000370398.1	hg19	CCDS4976.1	.	.	.	.	.	.	.	.	.	.	A	14.61	2.587561	0.46110	.	.	ENSG00000185760	ENST00000342056;ENST00000451840;ENST00000355194;ENST00000370398;ENST00000402622;ENST00000355635;ENST00000403813;ENST00000414165	D;D;D;D;D;D;D	0.99429	-5.66;-5.66;-5.66;-5.66;-5.67;-5.7;-5.89	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	D	0.98698	0.9563	N	0.24115	0.695	0.24539	N	0.994073	D;P;B;P;B	0.61697	0.99;0.792;0.017;0.525;0.435	D;B;B;B;B	0.72982	0.979;0.254;0.021;0.117;0.078	D	0.96550	0.9407	10	0.62326	D	0.03	.	16.4622	0.84064	1.0:0.0:0.0:0.0	.	820;940;949;921;930	F5GZV0;Q9NR82-3;A6PVT6;Q9NR82-2;Q9NR82	.;.;.;.;KCNQ5_HUMAN	E	949;949;930;930;940;931;921;820	ENSP00000345055:K949E;ENSP00000347326:K930E;ENSP00000359425:K930E;ENSP00000385501:K940E;ENSP00000347853:K931E;ENSP00000384453:K921E;ENSP00000409861:K820E	ENSP00000345055:K949E	K	+	1	0	KCNQ5	73961847	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.654000	0.67974	2.289000	0.77006	0.533000	0.62120	AAA	.	.	.	none		0.408	KCNQ5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041198.3	NM_019842		G	73905126	A	G	73905126	3	3	92	1	0	0	0	0	1	0	0	0	8093	131	5	3	2903	3	KCNQ5	6	73905126	Missense_Mutation	SNP	A	TCGA-B3-8121-01A-21D-2396-08	21980306	73905126	97209941	12	5866											
RARS2	57038	hgsc.bcm.edu	37	chr6	88231239	88231239	+	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	cgatctatagcagctgcaagAtctctgaaacaaagtggcca	14	8	9	10	1	2	2	0	1	2	1	3	3	2	2	1	1	4	3	1	1	5	2			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr6:88231239A>T	ENST00000369536.5	-	12	1023	c.978T>A	c.(976-978)gaT>gaA	p.D326E	RARS2_ENST00000497828.1_5'Flank	NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	326					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)		CAGCTGCAAGATCTCTGAAAC	0.323																																					p.D326E		Atlas-SNP	.											.	RARS2	61	.	0			c.T978A						PASS	.						83	83	83					6																	88231239		2203	4300	6503	SO:0001583	missense	57038	exon12			TGCAAGATCTCTG	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.978T>A	chr6.hg19:g.88231239A>T	ENSP00000358549:p.Asp326Glu	64.0	0.0	.		33.0	8.0	.	NM_020320	B2RDT7|Q96FU5|Q9H8K8	Missense_Mutation	SNP	ENST00000369536.5	hg19	CCDS5011.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.219539	0.79464	.	.	ENSG00000146282	ENST00000369536	D	0.82081	-1.57	5.83	-1.0	0.10196	Arginyl-tRNA synthetase, class Ia, core (2);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	D	0.90335	0.6976	H	0.95712	3.71	0.58432	D	0.999996	D	0.71674	0.998	D	0.80764	0.994	D	0.90743	0.4651	10	0.87932	D	0	.	11.7636	0.51918	0.557:0.0:0.443:0.0	.	326	Q5T160	SYRM_HUMAN	E	326	ENSP00000358549:D326E	ENSP00000358549:D326E	D	-	3	2	RARS2	88287958	0.984000	0.35163	0.987000	0.45799	0.993000	0.82548	0.740000	0.26188	-0.395000	0.07715	0.533000	0.62120	GAT	.	.	.	none		0.323	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320		T	88231239	A	T	88231239	3	4	92	1	0	0	0	0	1	0	0	0	13072	330	12	5	794	5	RARS2	6	88231239	Missense_Mutation	SNP	A	TCGA-B3-8121-01A-21D-2396-08	14326113	88231239	82883828	13	5867											
IGFBP1	3484	hgsc.bcm.edu	37	chr7	45932569	45932569	+	Frame_Shift_Del	DEL	C	C	-																															gtctttgcagtgtgagacatCcatggatggagaggcgggac																										TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr7:45932569delC	ENST00000275525.3	+	4	955	c.659delC	c.(658-660)tccfs	p.S220fs	IGFBP1_ENST00000457280.1_Frame_Shift_Del_p.S218fs|IGFBP1_ENST00000468955.1_Frame_Shift_Del_p.S177fs	NM_000596.2	NP_000587.1	P08833	IBP1_HUMAN	insulin-like growth factor binding protein 1	220	Thyroglobulin type-1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|insulin receptor signaling pathway (GO:0008286)|positive regulation of cell growth (GO:0030307)|signal transduction (GO:0007165)|tissue regeneration (GO:0042246)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	insulin-like growth factor binding (GO:0005520)			large_intestine(2)|lung(4)	6						TGTGAGACATCCATGGATGGA	0.547																																					p.S220fs		Atlas-INDEL	.											.	IGFBP1	19	.	0			c.658delT						PASS	.						84	79	81					7																	45932569		2203	4300	6503	SO:0001589	frameshift_variant	3484	exon4			.		CCDS5504.1	7p12.3	2014-09-16			ENSG00000146678	ENSG00000146678			5469	protein-coding gene	gene with protein product	"placental protein 12", "amniotic fluid binding protein", "alpha-pregnancy-associated endometrial globulin", "growth hormone independent-binding protein", "binding protein-28", "binding protein-26", "binding protein-25", "IGF-binding protein 1"	146730		IBP1		2461294	Standard	NM_000596		Approved	IGF-BP25, AFBP, hIGFBP-1, PP12	uc003tnp.3	P08833	OTTHUMG00000152343	ENST00000275525.3:c.659delC	chr7.hg19:g.45932569delC	ENSP00000275525:p.Ser220fs	101.0	0.0	0		119.0	11.0	0.092437	NM_000596	A4D2F4|D3DVL9|Q8IYP5	Frame_Shift_Del	DEL	ENST00000275525.3	hg19	CCDS5504.1																																																																																			.	.	.	none		0.547	IGFBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251355.2	NM_000596		-	45932569	C	-	45932569	7	5	92	1	0	1	0	1	0	0	0	0	7585	855	30	0	673	0	IGFBP1	7	45932569	Frame_Shift_Del	DEL	C	TCGA-B3-8121-01A-21D-2396-08		45932569	113206094	14	5868											
TRIP6	7205	hgsc.bcm.edu	37	chr7	100465513	100465514	+	Frame_Shift_Ins	INS	-	-	C																															caccccagggtcaatttttgINScccccttccatctgagcagt																										TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr7:100465513_100465514insC	ENST00000200457.4	+	2	500_501	c.140_141insC	c.(139-144)tgccccfs	p.CP47fs		NM_003302.2	NP_003293.2	Q15654	TRIP6_HUMAN	thyroid hormone receptor interactor 6	47					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)					GTCAATTTTTGCCCCCTTCCAT	0.624																																					p.C47fs		Atlas-INDEL	.											.	TRIP6	45	.	0			c.140_141insC						PASS	.																																			SO:0001589	frameshift_variant	7205	exon2			.	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.145dupC	chr7.hg19:g.100465518_100465518dupC	ENSP00000200457:p.Cys47fs	265.0	0.0	0		335.0	81.0	0.241791	NM_003302	A4D2E7|F2ZC07|F2ZC08|O15170|O15275|Q9BTB2|Q9BUE5|Q9BXP3|Q9UNT4	Frame_Shift_Ins	INS	ENST00000200457.4	hg19	CCDS5708.1																																																																																			.	.	.	none		0.624	TRIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347151.2	NM_003302		C	100465514	-	C	100465513	7	5	92	1	0	1	1	0	0	0	0	0	16571	1319	46	0	146	0	TRIP6	7	100465513	Frame_Shift_Ins	INS	-	TCGA-B3-8121-01A-21D-2396-08	54532944	100465513	58673150	15	5869											
CAPRIN2	65981	hgsc.bcm.edu	37	chr12	30888129	30888129	+	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	cttctctgggccttcttttgCgcttttagtagctgttaaaa	6	18	8	9	1	2	0	0	0	2	0	3	0	2	0	1	1	2	4	1	1	4	8	rs145888176		TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr12:30888129C>T	ENST00000395805.2	-	4	1129	c.582G>A	c.(580-582)gcG>gcA	p.A194A	CAPRIN2_ENST00000417045.1_Silent_p.A194A|CAPRIN2_ENST00000538387.1_5'Flank|CAPRIN2_ENST00000298892.5_Silent_p.A194A|CAPRIN2_ENST00000308433.5_5'UTR|CAPRIN2_ENST00000251071.5_Silent_p.A194A	NM_001206856.1	NP_001193785.1			caprin family member 2									p.A194A(1)		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)					CCTTCTTTTGCGCTTTTAGTA	0.378																																					p.A194A		Atlas-SNP	.											CAPRIN2,NS,carcinoma,0,1	CAPRIN2	109	.	1	Substitution - coding silent(1)	lung(1)	c.G582A						PASS	.	C	,,,	0,4406		0,0,2203	127	123	125		582,582,582,582	-5.3	1	12	dbSNP_134	125	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CAPRIN2	NM_001002259.1,NM_001206856.1,NM_023925.3,NM_032156.3	,,,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,,,	194/1128,194/906,194/1078,194/961	30888129	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	65981	exon4			CTTTTGCGCTTTT	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.582G>A	chr12.hg19:g.30888129C>T		171.0	0.0	.		91.0	5.0	.	NM_023925		Silent	SNP	ENST00000395805.2	hg19	CCDS55816.1																																																																																			.	C|1.000;T|0.000	0.000	weak		0.378	CAPRIN2-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403322.2	NM_023925		T	30888129	C	T	30888129	2	4	92	1	0	0	0	0	0	0	0	1	2638	755	27	1		1	CAPRIN2	12	30888129	Silent	SNP	C	TCGA-B3-8121-01A-21D-2396-08		30888129	102963766	16	5870											
GIT2	9815	hgsc.bcm.edu	37	chr12	110385121	110385127	+	Frame_Shift_Del	DEL	TGGGAGA	TGGGAGA	-																															gggcggctcgcttctcccatTgggagatatggtttctgacc																								rs185965842	byFrequency	TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	TGGGAGA	TGGGAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr12:110385121_110385127delTGGGAGA	ENST00000355312.3	-	15	1574_1580	c.1575_1581delTCTCCCA	c.(1573-1581)tatctcccafs	p.YLP525fs	GIT2_ENST00000338373.5_Intron|GIT2_ENST00000551209.1_Frame_Shift_Del_p.YLP474fs|GIT2_ENST00000361006.5_Frame_Shift_Del_p.YLP525fs|GIT2_ENST00000553118.1_Intron|GIT2_ENST00000356259.4_Intron|GIT2_ENST00000354574.4_Frame_Shift_Del_p.YLP477fs|GIT2_ENST00000547815.1_3'UTR|GIT2_ENST00000457474.2_Frame_Shift_Del_p.YLP477fs|GIT2_ENST00000343646.5_Frame_Shift_Del_p.YLP445fs|TCHP_ENST00000550780.1_Intron|GIT2_ENST00000360185.4_Frame_Shift_Del_p.YLP475fs	NM_057169.3	NP_476510.1	Q14161	GIT2_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 2	525					behavioral response to pain (GO:0048266)|regulation of ARF GTPase activity (GO:0032312)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.L526I(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(8)|skin(4)	27						CTTCTCCCATTGGGAGATATGGTTTCT	0.57																																					p.526_528del		Atlas-INDEL	.											.	GIT2	81	.	1	Substitution - Missense(1)	large_intestine(1)	c.1576_1582del						PASS	.																																			SO:0001589	frameshift_variant	9815	exon15			.	AF124491	CCDS9138.1, CCDS9139.1, CCDS44968.1, CCDS44969.1, CCDS55884.1	12q24.1	2013-01-10	2008-09-05			ENSG00000139436		"ADP-ribosylation factor GTPase activating proteins", "Ankyrin repeat domain containing"	4273	protein-coding gene	gene with protein product		608564	"G protein-coupled receptor kinase interactor 2"			9826657, 10896954	Standard	NM_139201		Approved	KIAA0148	uc001tps.2	Q14161	OTTHUMG00000169313	ENST00000355312.3:c.1575_1581delTCTCCCA	chr12.hg19:g.110385121_110385127delTGGGAGA	ENSP00000347464:p.Tyr525fs	92.0	0.0	0		110.0	15.0	0.136364	NM_001135214	Q86U59|Q96CI2|Q9BV91|Q9Y5V2	Frame_Shift_Del	DEL	ENST00000355312.3	hg19	CCDS9138.1																																																																																			.	.	.	none		0.57	GIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403407.1	NM_057169		-	110385127	TGGGAGA	-	110385121	7	5	92	1	0	1	0	1	0	0	0	0	6404	1799	63	0	722	0	GIT2	12	110385121	Frame_Shift_Del	DEL	TGGGAGA	TCGA-B3-8121-01A-21D-2396-08	79496992	110385121	23466774	17	5871											
RAN	5901	hgsc.bcm.edu	37	chr12	131359114	131359114	+	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	agtgtgccatcataatgtttGatgtaacatcgagagttact	12	14	9	6	1	1	2	1	1	0	1	2	3	1	2	1	0	3	3	1	0	3	4			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr12:131359114G>A	ENST00000543796.1	+	5	529	c.271G>A	c.(271-273)Gat>Aat	p.D91N	RAN_ENST00000254675.3_Missense_Mutation_p.D3N|RAN_ENST00000392367.3_Missense_Mutation_p.D108N|RAN_ENST00000392369.2_Missense_Mutation_p.D91N|RAN_ENST00000541630.1_Missense_Mutation_p.D3N			P62826	RAN_HUMAN	RAN, member RAS oncogene family	91					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)		CATAATGTTTGATGTAACATC	0.413																																					p.D91N		Atlas-SNP	.											.	RAN	18	.	0			c.G271A						PASS	.						122	103	109					12																	131359114		2203	4300	6503	SO:0001583	missense	5901	exon5			ATGTTTGATGTAA	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.271G>A	chr12.hg19:g.131359114G>A	ENSP00000446215:p.Asp91Asn	95.0	0.0	.		50.0	9.0	.	NM_006325	A8K3Z8|P17080|P28746|P28747|Q6IPB2|Q86V08|Q8NI90|Q9CSP3|Q9CWI7|Q9CZA2|Q9UDJ5|Q9UEU9	Missense_Mutation	SNP	ENST00000543796.1	hg19	CCDS9271.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.769269	0.90020	.	.	ENSG00000132341	ENST00000543796;ENST00000448750;ENST00000541630;ENST00000392369;ENST00000254675;ENST00000535090;ENST00000392367	D;D;D;D;D;D;D	0.86694	-2.16;-2.16;-2.16;-2.16;-2.16;-2.16;-2.16	3.93	3.93	0.45458	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.95465	0.8527	H	0.96720	3.87	0.80722	D	1	D;D	0.55800	0.973;0.973	D;D	0.68192	0.956;0.956	D	0.97181	0.9851	10	0.87932	D	0	-17.8637	15.3182	0.74099	0.0:0.0:1.0:0.0	.	91;91	A8K3Z8;P62826	.;RAN_HUMAN	N	91;109;3;91;3;87;108	ENSP00000446215:D91N;ENSP00000396127:D109N;ENSP00000441210:D3N;ENSP00000376176:D91N;ENSP00000254675:D3N;ENSP00000444042:D87N;ENSP00000376174:D108N	ENSP00000254675:D3N	D	+	1	0	RAN	129925067	1.000000	0.71417	0.974000	0.42286	0.827000	0.46813	9.335000	0.96500	1.906000	0.55180	0.561000	0.74099	GAT	.	.	.	none		0.413	RAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259441.2	NM_006325		A	131359114	G	A	131359114	3	1	92	1	0	0	0	0	1	0	0	0	13037	1290	45	2	285	2	RAN	12	131359114	Missense_Mutation	SNP	G	TCGA-B3-8121-01A-21D-2396-08	20973993	131359114	2492781	18	5872											
TJP1	7082	hgsc.bcm.edu	37	chr15	30008820	30008820	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtgaaatagcttactttgaAgaataactagaaaaatttga	18	12	8	3	0	0	5	0	3	0	2	0	5	0	5	0	1	3	1	0	1	9	6			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr15:30008820A>G	ENST00000346128.6	-	23	4671	c.4197T>C	c.(4195-4197)tcT>tcC	p.S1399S	TJP1_ENST00000400011.2_Silent_p.S1323S|TJP1_ENST00000356107.6_Silent_p.S1399S|TJP1_ENST00000545208.2_Silent_p.S1319S	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	1399					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)		CTTACTTTGAAGAATAACTAG	0.368																																					p.S1399S	Melanoma(77;681 1843 6309 6570)	Atlas-SNP	.											.	TJP1	140	.	0			c.T4197C						PASS	.						60	61	61					15																	30008820		1812	4085	5897	SO:0001819	synonymous_variant	7082	exon23			CTTTGAAGAATAA		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.4197T>C	chr15.hg19:g.30008820A>G		81.0	0.0	.		54.0	7.0	.	NM_003257	B4E3K1|Q2NKP3|Q4ZGJ6	Silent	SNP	ENST00000346128.6	hg19	CCDS42007.1																																																																																			.	.	.	none		0.368	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		G	30008820	A	G	30008820	2	3	92	1	0	0	0	0	0	0	0	1	15941	59	3	3		3	TJP1	15	30008820	Silent	SNP	A	TCGA-B3-8121-01A-21D-2396-08		30008820	72522572	19	5873											
TJP1	7082	hgsc.bcm.edu	37	chr15	30065529	30065529	+	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	gaggattatctcgtccaccaGatattgcaattccaaatcca	13	11	6	11	1	1	1	0	0	1	1	5	3	4	2	4	1	1	1	4	1	4	4			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr15:30065529G>T	ENST00000346128.6	-	3	590	c.116C>A	c.(115-117)tCt>tAt	p.S39Y	TJP1_ENST00000400011.2_Missense_Mutation_p.S43Y|TJP1_ENST00000495972.2_Missense_Mutation_p.S39Y|TJP1_ENST00000356107.6_Missense_Mutation_p.S39Y|TJP1_ENST00000545208.2_Missense_Mutation_p.S39Y	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	39	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)		TCGTCCACCAGATATTGCAAT	0.363																																					p.S39Y	Melanoma(77;681 1843 6309 6570)	Atlas-SNP	.											.	TJP1	140	.	0			c.C116A						PASS	.						136	121	126					15																	30065529		1874	4102	5976	SO:0001583	missense	7082	exon3			CCACCAGATATTG		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.116C>A	chr15.hg19:g.30065529G>T	ENSP00000281537:p.Ser39Tyr	148.0	0.0	.		108.0	19.0	.	NM_175610	B4E3K1|Q2NKP3|Q4ZGJ6	Missense_Mutation	SNP	ENST00000346128.6	hg19	CCDS42007.1	.	.	.	.	.	.	.	.	.	.	G	19.61	3.859179	0.71834	.	.	ENSG00000104067	ENST00000346128;ENST00000400011;ENST00000545208;ENST00000400007;ENST00000356107	T;T;T;T	0.29655	1.56;1.56;1.56;1.56	5.5	5.5	0.81552	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.66509	0.2796	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	0.999;0.999;0.999;0.998	T	0.73291	-0.4029	9	.	.	.	.	19.7625	0.96325	0.0:0.0:1.0:0.0	.	32;39;39;43	A9CQZ8;Q07157-2;Q07157;G5E9E7	.;.;ZO1_HUMAN;.	Y	39;43;39;39;39	ENSP00000281537:S39Y;ENSP00000382890:S43Y;ENSP00000441202:S39Y;ENSP00000348416:S39Y	.	S	-	2	0	TJP1	27852821	1.000000	0.71417	0.999000	0.59377	0.256000	0.26092	9.715000	0.98748	2.749000	0.94314	0.585000	0.79938	TCT	.	.	.	none		0.363	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		T	30065529	G	T	30065529	3	4	92	1	0	0	0	0	1	0	0	0	15941	942	33	4	5234	4	TJP1	15	30065529	Missense_Mutation	SNP	G	TCGA-B3-8121-01A-21D-2396-08	56709	30065529	72465863	20	5874											
EFCAB3	146779	hgsc.bcm.edu	37	chr17	60484528	60484528	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaataaaggagcctttgcaTttctttgaggattatttttt	11	18	8	4	0	1	2	0	1	1	1	1	4	1	4	1	2	2	1	1	2	4	8			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr17:60484528T>C	ENST00000305286.3	+	8	900	c.822T>C	c.(820-822)caT>caC	p.H274H	EFCAB3_ENST00000450662.2_Silent_p.H326H	NM_173503.3	NP_775774.1	Q8N7B9	EFCB3_HUMAN	EF-hand calcium binding domain 3	274							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)			AGCCTTTGCATTTCTTTGAGG	0.358																																					p.H326H		Atlas-SNP	.											.	EFCAB3	71	.	0			c.T978C						PASS	.						80	82	81					17																	60484528		2203	4300	6503	SO:0001819	synonymous_variant	146779	exon10			TTTGCATTTCTTT	AK098684	CCDS11632.1, CCDS45751.1	17q23.3	2013-01-10			ENSG00000172421	ENSG00000172421		"EF-hand domain containing"	26379	protein-coding gene	gene with protein product						12477932	Standard	NM_173503		Approved	FLJ25818	uc010wpc.2	Q8N7B9	OTTHUMG00000179175	ENST00000305286.3:c.822T>C	chr17.hg19:g.60484528T>C		92.0	0.0	.		74.0	7.0	.	NM_001144933	J3KQM8	Silent	SNP	ENST00000305286.3	hg19	CCDS11632.1																																																																																			.	.	.	none		0.358	EFCAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379114.1	NM_173503		C	60484528	T	C	60484528	2	2	92	1	0	0	0	0	0	0	0	1	4937	1490	52	3		3	EFCAB3	17	60484528	Silent	SNP	T	TCGA-B3-8121-01A-21D-2396-08		60484528	20710682	21	5875											
KLHL14	57565	hgsc.bcm.edu	37	chr18	30350134	30350134	+	Missense_Mutation	SNP	A	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	cacgttggccgtgtagaggtActcgagcaccaggcgcagcc	8	6	14	13	4	0	1	0	0	0	1	1	2	0	1	3	3	3	5	3	3	2	3			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr18:30350134A>C	ENST00000359358.4	-	2	859	c.421T>G	c.(421-423)Tac>Gac	p.Y141D	AC012123.1_ENST00000426194.1_Intron|KLHL14_ENST00000358095.4_Missense_Mutation_p.Y141D	NM_020805.1	NP_065856.1	Q9P2G3	KLH14_HUMAN	kelch-like family member 14	141	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						GTGTAGAGGTACTCGAGCACC	0.642																																					p.Y141D		Atlas-SNP	.											.	KLHL14	92	.	0			c.T421G						PASS	.						99	99	99					18																	30350134		2203	4300	6503	SO:0001583	missense	57565	exon2			AGAGGTACTCGAG	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.421T>G	chr18.hg19:g.30350134A>C	ENSP00000352314:p.Tyr141Asp	216.0	0.0	.		268.0	50.0	.	NM_020805	A6NNW1|B4DHA0|Q8WU41	Missense_Mutation	SNP	ENST00000359358.4	hg19	CCDS32813.1	.	.	.	.	.	.	.	.	.	.	A	9.978	1.227338	0.22542	.	.	ENSG00000197705	ENST00000359358;ENST00000358095	T;T	0.71222	-0.55;-0.55	4.34	4.34	0.51931	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.134366	0.51477	D	0.000081	T	0.78660	0.4318	L	0.48362	1.52	0.80722	D	1	D	0.63880	0.993	D	0.81914	0.995	T	0.80876	-0.1186	10	0.87932	D	0	.	13.0081	0.58717	1.0:0.0:0.0:0.0	.	141	Q9P2G3	KLH14_HUMAN	D	141	ENSP00000352314:Y141D;ENSP00000350808:Y141D	ENSP00000350808:Y141D	Y	-	1	0	KLHL14	28604132	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.006000	0.70724	1.738000	0.51689	0.377000	0.23210	TAC	.	.	.	none		0.642	KLHL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448376.1			C	30350134	A	C	30350134	3	2	92	1	0	0	0	0	1	0	0	0	8377	391	14	5	1497	5	KLHL14	18	30350134	Missense_Mutation	SNP	A	TCGA-B3-8121-01A-21D-2396-08		30350134	47727114	22	5876											
ATP5A1	498	hgsc.bcm.edu	37	chr18	43671697	43671697	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttctgcttgaacattcctcAgcccatgtacgcgggcaata	9	11	8	13	2	2	1	1	1	1	0	3	1	3	1	2	1	4	3	2	1	4	5			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr18:43671697A>G	ENST00000398752.6	-	3	381	c.260T>C	c.(259-261)cTg>cCg	p.L87P	ATP5A1_ENST00000593152.2_Missense_Mutation_p.L37P|ATP5A1_ENST00000591267.1_5'Flank|ATP5A1_ENST00000282050.2_Missense_Mutation_p.L87P|ATP5A1_ENST00000590665.1_Missense_Mutation_p.L87P	NM_001001935.2|NM_004046.5	NP_001001935.1|NP_004037.1	P25705	ATPA_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle	87					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular metabolic process (GO:0044237)|embryo development (GO:0009790)|lipid metabolic process (GO:0006629)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|negative regulation of endothelial cell proliferation (GO:0001937)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting ATP synthase complex, catalytic core F(1) (GO:0045261)	ATP binding (GO:0005524)|MHC class I protein binding (GO:0042288)|poly(A) RNA binding (GO:0044822)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)			breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|skin(1)|urinary_tract(1)	22						AACATTCCTCAGCCCATGTAC	0.388																																					p.L87P		Atlas-SNP	.											.	ATP5A1	52	.	0			c.T260C						PASS	.						100	98	98					18																	43671697		2203	4300	6503	SO:0001583	missense	498	exon3			TTCCTCAGCCCAT	D14710	CCDS11927.1, CCDS58620.1, CCDS59315.1	18q21	2012-10-12	2006-01-13		ENSG00000152234	ENSG00000152234	3.6.1.14	"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	823	protein-coding gene	gene with protein product		164360	"ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 2, non-cardiac muscle-like 2", "ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscle"	ATP5AL2, ATPM		1830491	Standard	NM_001257334		Approved	ATP5A, hATP1, OMR, ORM	uc002lbr.2	P25705	OTTHUMG00000132637	ENST00000398752.6:c.260T>C	chr18.hg19:g.43671697A>G	ENSP00000381736:p.Leu87Pro	134.0	0.0	.		103.0	25.0	.	NM_004046	A8K092|B4DY56|K7ENP3|Q53XX6|Q8IXV2|Q96FB4|Q96HW2|Q96IR6|Q9BTV8	Missense_Mutation	SNP	ENST00000398752.6	hg19	CCDS11927.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.527021	0.85706	.	.	ENSG00000152234	ENST00000282050;ENST00000398752;ENST00000542290	D;D	0.88354	-2.37;-2.37	5.24	5.24	0.73138	ATPase, F1/A1 complex, alpha subunit, N-terminal (1);ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal (1);ATPase, F1/A1 complex, alpha/beta subunit, N-terminal (1);	0.147149	0.47852	D	0.000217	D	0.96873	0.8979	H	0.98996	4.395	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.98545	1.0634	10	0.87932	D	0	-17.4309	15.1468	0.72662	1.0:0.0:0.0:0.0	.	87	P25705	ATPA_HUMAN	P	87;87;37	ENSP00000282050:L87P;ENSP00000381736:L87P	ENSP00000282050:L87P	L	-	2	0	ATP5A1	41925695	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	9.176000	0.94839	1.975000	0.57531	0.533000	0.62120	CTG	.	.	.	none		0.388	ATP5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255884.1	NM_004046		G	43671697	A	G	43671697	3	3	92	1	0	0	0	0	1	0	0	0	1147	188	7	3	1441	3	ATP5A1	18	43671697	Missense_Mutation	SNP	A	TCGA-B3-8121-01A-21D-2396-08	13321563	43671697	34405551	23	5877											
ANKRD27	84079	hgsc.bcm.edu	37	chr19	33132944	33132944	+	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	acaaacctctctggcttggaGactgtgtaatgagctgcacc	10	10	10	11	0	1	2	0	1	1	1	2	3	1	2	2	2	3	4	2	2	2	2			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr19:33132944G>A	ENST00000306065.4	-	10	1048	c.890C>T	c.(889-891)tCt>tTt	p.S297F	ANKRD27_ENST00000587352.1_Missense_Mutation_p.S297F	NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	297	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)					CTGGCTTGGAGACTGTGTAAT	0.493																																					p.S297F		Atlas-SNP	.											.	ANKRD27	86	.	0			c.C890T						PASS	.						149	138	142					19																	33132944		2203	4300	6503	SO:0001583	missense	84079	exon10			CTTGGAGACTGTG	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.890C>T	chr19.hg19:g.33132944G>A	ENSP00000304292:p.Ser297Phe	214.0	0.0	.		199.0	53.0	.	NM_032139	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Missense_Mutation	SNP	ENST00000306065.4	hg19	CCDS32986.1	.	.	.	.	.	.	.	.	.	.	G	9.152	1.016485	0.19355	.	.	ENSG00000105186	ENST00000306065	T	0.31247	1.5	5.43	5.43	0.79202	Vacuolar sorting protein 9, subgroup (1);Vacuolar sorting protein 9 (2);	0.000000	0.64402	D	0.000017	T	0.40222	0.1108	M	0.72118	2.19	0.53005	D	0.999961	B	0.23058	0.079	B	0.28638	0.092	T	0.23904	-1.0175	10	0.44086	T	0.13	-22.3055	19.253	0.93933	0.0:0.0:1.0:0.0	.	297	Q96NW4	ANR27_HUMAN	F	297	ENSP00000304292:S297F	ENSP00000304292:S297F	S	-	2	0	ANKRD27	37824784	1.000000	0.71417	1.000000	0.80357	0.678000	0.39670	5.388000	0.66249	2.551000	0.86045	0.563000	0.77884	TCT	.	.	.	none		0.493	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1	NM_032139		A	33132944	G	A	33132944	3	1	92	1	0	0	0	0	1	0	0	0	655	942	33	2	2342	2	ANKRD27	19	33132944	Missense_Mutation	SNP	G	TCGA-B3-8121-01A-21D-2396-08		33132944	25996039	24	5878											
LILRA5	353514	hgsc.bcm.edu	37	chr19	54819027	54819027	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgacggactgaggttatcaGctgctcctgaaaatcaaaac	13	9	10	9	1	2	3	2	3	0	0	3	4	3	4	1	2	3	3	1	2	5	1			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr19:54819027G>A	ENST00000301219.3	-	6	838	c.719C>T	c.(718-720)gCt>gTt	p.A240V	AC008984.2_ENST00000507363.1_RNA|LILRA5_ENST00000346508.3_Missense_Mutation_p.A228V	NM_021250.2	NP_067073.1	A6NI73	LIRA5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 5	240					innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GAGGTTATCAGCTGCTCCTGA	0.517																																					p.A240V		Atlas-SNP	.											.	LILRA5	49	.	0			c.C719T						PASS	.						83	76	78					19																	54819027		2203	4300	6503	SO:0001583	missense	353514	exon6			TTATCAGCTGCTC	AF212842	CCDS12888.1, CCDS12889.1	19q13.4	2013-01-11	2005-05-13	2005-05-13	ENSG00000187116	ENSG00000187116		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	16309	protein-coding gene	gene with protein product		606047		LILRB7		10941842	Standard	NM_181986		Approved	ILT11, LIR9, CD85, CD85f	uc002qfe.3	A6NI73	OTTHUMG00000065357	ENST00000301219.3:c.719C>T	chr19.hg19:g.54819027G>A	ENSP00000301219:p.Ala240Val	69.0	0.0	.		66.0	13.0	.	NM_021250	A6NHI3	Missense_Mutation	SNP	ENST00000301219.3	hg19	CCDS12888.1	.	.	.	.	.	.	.	.	.	.	G	10.56	1.383828	0.25031	.	.	ENSG00000187116	ENST00000301219;ENST00000346508	T;T	0.00502	7.02;6.95	2.31	2.31	0.28768	.	.	.	.	.	T	0.00608	0.0020	M	0.62154	1.92	0.21386	N	0.999702	B;B	0.25048	0.117;0.014	B;B	0.31946	0.138;0.01	T	0.37103	-0.9720	9	0.38643	T	0.18	.	8.1667	0.31230	0.0:0.0:1.0:0.0	.	228;240	A6NI73-2;A6NI73	.;LIRA5_HUMAN	V	240;228	ENSP00000301219:A240V;ENSP00000302948:A228V	ENSP00000301219:A240V	A	-	2	0	LILRA5	59510839	0.000000	0.05858	0.004000	0.12327	0.073000	0.16967	0.233000	0.17911	1.603000	0.50134	0.536000	0.68110	GCT	.	.	.	none		0.517	LILRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140231.1	NM_181985		A	54819027	G	A	54819027	3	1	92	1	0	0	0	0	1	0	0	0	8795	971	34	2	188	2	LILRA5	19	54819027	Missense_Mutation	SNP	G	TCGA-B3-8121-01A-21D-2396-08	21686083	54819027	4309956	25	5879											
ZNF341	84905	hgsc.bcm.edu	37	chr20	32345059	32345060	+	Frame_Shift_Ins	INS	-	-	C																															aaaccccgccgcccccatgaINSccagcgccaccgggggcacg																										TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr20:32345059_32345060insC	ENST00000375200.1	+	6	1212_1213	c.847_848insC	c.(847-849)accfs	p.T283fs	ZNF341_ENST00000342427.2_Frame_Shift_Ins_p.T283fs	NM_001282933.1	NP_001269862.1	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	283					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						CGCCCCCATGACCAGCGCCACC	0.629																																					p.T283fs		Atlas-INDEL	.											.	ZNF341	73	.	0			c.847_848insC						PASS	.																																			SO:0001589	frameshift_variant	84905	exon6			.	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.849dupC	chr20.hg19:g.32345061_32345061dupC	ENSP00000364346:p.Thr283fs	318.0	0.0	0		414.0	128.0	0.309179	NM_032819	A2RUF4|B2RXE5|B7ZM09|Q5JXM8|Q96ST5	Frame_Shift_Ins	INS	ENST00000375200.1	hg19																																																																																				.	.	.	none		0.629	ZNF341-201	KNOWN	basic	protein_coding	protein_coding				C	32345060	-	C	32345059	7	5	92	1	0	1	1	0	0	0	0	0	17869	275	10	0	869	0	ZNF341	20	32345059	Frame_Shift_Ins	INS	-	TCGA-B3-8121-01A-21D-2396-08		32345059	30680461	26	5880											
NUP50	10762	hgsc.bcm.edu	37	chr22	45574449	45574449	+	Frame_Shift_Del	DEL	T	T	-																															tgaaacacagtctccttcccTttttggctcaacaaaattac																										TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chr22:45574449delT	ENST00000347635.4	+	5	1137	c.671delT	c.(670-672)cttfs	p.L224fs	NUP50_ENST00000396096.2_Frame_Shift_Del_p.L196fs|NUP50_ENST00000425733.2_5'UTR|NUP50_ENST00000407019.2_Frame_Shift_Del_p.L196fs|CTA-268H5.12_ENST00000610217.1_RNA	NM_007172.3	NP_009103.2	Q9UKX7	NUP50_HUMAN	nucleoporin 50kDa	224	5 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)|intracellular transport (GO:0046907)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	9		Ovarian(80;0.00965)|all_neural(38;0.0244)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		TCTCCTTCCCTTTTTGGCTCA	0.408																																					p.L224fs		Atlas-INDEL	.											.	NUP50	24	.	0			c.670delC						PASS	.						40	41	40					22																	45574449		2203	4300	6503	SO:0001589	frameshift_variant	10762	exon5			.	AF107840	CCDS14062.1, CCDS14063.1	22q13.3	2007-01-22	2002-08-29		ENSG00000093000	ENSG00000093000			8065	protein-coding gene	gene with protein product		604646	"nucleoporin 50kD"	NPAP60L		10449902	Standard	XM_005261312		Approved		uc003bfr.3	Q9UKX7	OTTHUMG00000151265	ENST00000347635.4:c.671delT	chr22.hg19:g.45574449delT	ENSP00000345895:p.Leu224fs	106.0	0.0	0		83.0	11.0	0.13253	NM_007172	B1AHA4|B2RB15|O75644|Q8N6V5|Q9NPM9|Q9NPR6|Q9P1K5	Frame_Shift_Del	DEL	ENST00000347635.4	hg19	CCDS14062.1																																																																																			.	.	.	none		0.408	NUP50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321993.2			-	45574449	T	-	45574449	7	5	92	1	0	1	0	1	0	0	0	0	10773	1609	56	0	685	0	NUP50	22	45574449	Frame_Shift_Del	DEL	T	TCGA-B3-8121-01A-21D-2396-08		45574449	5730117	27	5881											
HUWE1	10075	hgsc.bcm.edu	37	chrX	53589174	53589174	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttcctgagtgtgctcctcCtcatcctcagggtccaggat	5	13	9	14	0	3	1	2	1	1	0	8	2	8	2	5	2	1	1	5	2	0	1			TCGA-B3-8121-01A-21D-2396-08	TCGA-B3-8121-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef96a344-c871-4819-aada-dd93a5c7ca7d	5e9a09f1-d8de-4b72-99a8-ec2dad680376	g.chrX:53589174C>T	ENST00000342160.3	-	53	7693	c.7236G>A	c.(7234-7236)gaG>gaA	p.E2412E	HUWE1_ENST00000262854.6_Silent_p.E2412E			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	2412	Glu-rich.				base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)	p.E2275D(1)		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						TGTGCTCCTCCTCATCCTCAG	0.498																																					p.E2412E		Atlas-SNP	.											.	HUWE1	724	.	1	Substitution - Missense(1)	breast(1)	c.G7236A						PASS	.						138	86	104					X																	53589174		2203	4300	6503	SO:0001819	synonymous_variant	10075	exon54			CTCCTCCTCATCC	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.7236G>A	chrX.hg19:g.53589174C>T		59.0	0.0	.		57.0	16.0	.	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Silent	SNP	ENST00000342160.3	hg19	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	C	2.473	-0.321458	0.05386	.	.	ENSG00000086758	ENST00000427052	.	.	.	4.93	4.05	0.47172	.	.	.	.	.	T	0.57592	0.2064	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55082	-0.8196	4	.	.	.	.	8.1437	0.31100	0.0:0.8128:0.0:0.1872	.	.	.	.	R	1446	.	.	G	-	1	0	HUWE1	53605899	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.451000	0.35145	2.164000	0.68074	0.513000	0.50165	GGA	.	.	.	none		0.498	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		T	53589174	C	T	53589174	2	4	92	1	0	0	0	0	0	0	0	1	7468	680	24	2		2	HUWE1	23	53589174	Silent	SNP	C	TCGA-B3-8121-01A-21D-2396-08		53589174	101681386	28	5882											
PHC2	1912	hgsc.bcm.edu	37	chr1	33790580	33790580	+	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	agcagcagggcttgcccgtcGatttcctgggcacggaattc	7	9	13	12	3	0	0	0	0	0	0	3	2	1	1	2	3	3	4	2	3	1	3	rs370770593		TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr1:33790580G>C	ENST00000257118.5	-	14	2516	c.2463C>G	c.(2461-2463)atC>atG	p.I821M	PHC2_ENST00000485928.1_5'UTR|PHC2_ENST00000373422.3_Missense_Mutation_p.I427M|PHC2_ENST00000431992.1_Missense_Mutation_p.I792M|PHC2_ENST00000419414.2_Missense_Mutation_p.I822M|RP11-415J8.3_ENST00000588828.1_RNA|RP11-415J8.3_ENST00000587696.1_RNA|PHC2_ENST00000373418.3_Missense_Mutation_p.I286M|RP11-415J8.3_ENST00000457957.2_RNA	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)	821	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				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)				CTTGCCCGTCGATTTCCTGGG	0.602																																					p.I821M		Atlas-SNP	.											PHC2,NS,carcinoma,0,1	PHC2	78	.	0			c.C2463G						PASS	.						64	57	59					1																	33790580		2203	4300	6503	SO:0001583	missense	1912	exon14			CCCGTCGATTTCC	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.2463C>G	chr1.hg19:g.33790580G>C	ENSP00000257118:p.Ile821Met	52.0	0.0	.		44.0	17.0	.	NM_198040	A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	Missense_Mutation	SNP	ENST00000257118.5	hg19	CCDS378.1	.	.	.	.	.	.	.	.	.	.	G	11.89	1.774537	0.31411	.	.	ENSG00000134686	ENST00000431992;ENST00000257118;ENST00000373422;ENST00000373418;ENST00000307890;ENST00000419414	T;T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01;-0.01	5.73	-2.29	0.06805	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.79969	0.4538	M	0.93978	3.48	0.80722	D	1	D;D;D	0.63880	0.993;0.993;0.993	D;D;D	0.66351	0.943;0.909;0.943	T	0.81627	-0.0847	10	0.87932	D	0	-18.6041	12.5999	0.56491	0.6063:0.0:0.3937:0.0	.	822;793;821	A8KA40;B7ZLY0;Q8IXK0	.;.;PHC2_HUMAN	M	792;821;427;286;397;822	ENSP00000389436:I792M;ENSP00000257118:I821M;ENSP00000362521:I427M;ENSP00000362517:I286M;ENSP00000391440:I822M	ENSP00000257118:I821M	I	-	3	3	PHC2	33563167	0.002000	0.14202	0.497000	0.27552	0.479000	0.33129	-1.250000	0.02885	-0.720000	0.04935	-1.814000	0.00607	ATC	.	.	.	none		0.602	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000011895.1	NM_198040		C	33790580	G	C	33790580	3	2	93	1	0	0	0	0	1	0	0	0	11824	1048	37	4	117	4	PHC2	1	33790580	Missense_Mutation	SNP	G	TCGA-B3-A6W5-01A-12D-A33Q-10		33790580	215460041	1	5883											
ZNF691	51058	hgsc.bcm.edu	37	chr1	43316674	43316674	+	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	ccagaaccacacctgcctgaGgaaggggaagggggtaagcc	12	3	15	11	0	0	2	0	1	0	1	0	4	0	4	5	5	3	1	5	5	4	1			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr1:43316674G>T	ENST00000372506.1	+	4	385	c.45G>T	c.(43-45)gaG>gaT	p.E15D	ZNF691_ENST00000372502.1_Missense_Mutation_p.E37D|ZNF691_ENST00000372508.3_Missense_Mutation_p.E15D|ZNF691_ENST00000372504.1_Missense_Mutation_p.E37D|ZNF691_ENST00000397044.3_Missense_Mutation_p.E46D|ZNF691_ENST00000372507.1_Missense_Mutation_p.E15D	NM_001242739.1	NP_001229668.1	Q5VV52	ZN691_HUMAN	zinc finger protein 691	46						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)				ACCTGCCTGAGGAAGGGGAAG	0.547																																					p.E46D		Atlas-SNP	.											.	ZNF691	30	.	0			c.G138T						PASS	.						75	75	75					1																	43316674		2203	4300	6503	SO:0001583	missense	51058	exon4			GCCTGAGGAAGGG		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.45G>T	chr1.hg19:g.43316674G>T	ENSP00000361584:p.Glu15Asp	124.0	0.0	.		89.0	4.0	.	NM_001242739	A8MXP6|B4DJR7|O95878|Q9NWE8	Missense_Mutation	SNP	ENST00000372506.1	hg19	CCDS476.1	.	.	.	.	.	.	.	.	.	.	G	15.82	2.946137	0.53079	.	.	ENSG00000164011	ENST00000372508;ENST00000372507;ENST00000372506;ENST00000397044;ENST00000372504;ENST00000397034;ENST00000372503;ENST00000372502	T;T;T;T;T;T;T	0.09630	3.03;3.03;3.03;2.96;2.97;4.42;2.97	5.58	3.66	0.41972	.	0.220360	0.32593	N	0.005885	T	0.07954	0.0199	N	0.19112	0.55	0.35419	D	0.793114	B;B	0.16603	0.007;0.018	B;B	0.16722	0.016;0.016	T	0.11991	-1.0565	10	0.59425	D	0.04	-16.8708	10.9839	0.47510	0.0:0.1404:0.7137:0.1459	.	46;46	B4DJR7;Q5VV52	.;ZN691_HUMAN	D	15;15;15;46;37;46;46;37	ENSP00000361586:E15D;ENSP00000361585:E15D;ENSP00000361584:E15D;ENSP00000380237:E46D;ENSP00000361582:E37D;ENSP00000380228:E46D;ENSP00000361580:E37D	ENSP00000361580:E37D	E	+	3	2	ZNF691	43089261	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.991000	0.40727	0.789000	0.33779	0.655000	0.94253	GAG	.	.	.	none		0.547	ZNF691-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020192.1	NM_015911		T	43316674	G	T	43316674	3	4	93	1	0	0	0	0	1	0	0	0	18108	991	35	4	47	4	ZNF691	1	43316674	Missense_Mutation	SNP	G	TCGA-B3-A6W5-01A-12D-A33Q-10	9526094	43316674	205933947	2	5884											
PTPRF	5792	hgsc.bcm.edu	37	chr1	44035436	44035436	+	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	acgagcaacggccgcatcaaGcagctgcgttcaggtgagca	11	5	13	12	4	2	1	2	1	0	0	2	2	2	1	1	2	6	6	1	2	2	1			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr1:44035436G>T	ENST00000359947.4	+	6	895	c.555G>T	c.(553-555)aaG>aaT	p.K185N	PTPRF_ENST00000438120.1_Missense_Mutation_p.K185N|PTPRF_ENST00000372413.3_Missense_Mutation_p.K185N|PTPRF_ENST00000372414.3_Missense_Mutation_p.K185N	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	185	Ig-like C2-type 2.				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)				GCCGCATCAAGCAGCTGCGTT	0.587																																					p.K185N		Atlas-SNP	.											.	PTPRF	172	.	0			c.G555T						PASS	.						40	39	39					1																	44035436		2203	4300	6503	SO:0001583	missense	5792	exon6			CATCAAGCAGCTG	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.555G>T	chr1.hg19:g.44035436G>T	ENSP00000353030:p.Lys185Asn	74.0	0.0	.		40.0	14.0	.	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Missense_Mutation	SNP	ENST00000359947.4	hg19	CCDS489.2	.	.	.	.	.	.	.	.	.	.	G	19.86	3.906136	0.72868	.	.	ENSG00000142949	ENST00000359947;ENST00000438120;ENST00000372414;ENST00000372413;ENST00000437607	T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29	4.82	0.168	0.15012	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.35805	N	0.002976	T	0.64638	0.2616	N	0.20610	0.595	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.997	D;D;D;D	0.91635	0.997;0.995;0.999;0.94	T	0.59716	-0.7402	10	0.37606	T	0.19	.	9.6408	0.39837	0.3951:0.0:0.6049:0.0	.	185;185;185;185	Q5T020;P10586-2;P10586;Q5T019	.;.;PTPRF_HUMAN;.	N	185	ENSP00000353030:K185N;ENSP00000398822:K185N;ENSP00000361491:K185N;ENSP00000361490:K185N;ENSP00000413306:K185N	ENSP00000353030:K185N	K	+	3	2	PTPRF	43808023	0.982000	0.34865	1.000000	0.80357	0.993000	0.82548	0.295000	0.19065	0.060000	0.16281	0.561000	0.74099	AAG	.	.	.	none		0.587	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1			T	44035436	G	T	44035436	3	4	93	1	0	0	0	0	1	0	0	0	12814	962	34	4	569	4	PTPRF	1	44035436	Missense_Mutation	SNP	G	TCGA-B3-A6W5-01A-12D-A33Q-10	718762	44035436	205215185	3	5885											
CELSR2	1952	hgsc.bcm.edu	37	chr1	109801145	109801145	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcatcacgctgcgcctggaGgacatgtcacccgagcgctt	8	7	12	14	4	2	0	2	0	0	0	2	3	2	2	2	2	3	3	2	2	0	1			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr1:109801145G>A	ENST00000271332.3	+	2	3463	c.3402G>A	c.(3400-3402)gaG>gaA	p.E1134E		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	1134	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		TGCGCCTGGAGGACATGTCAC	0.647																																					p.E1134E	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.G3402A						PASS	.						42	36	38					1																	109801145		2203	4300	6503	SO:0001819	synonymous_variant	1952	exon2			CCTGGAGGACATG	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.3402G>A	chr1.hg19:g.109801145G>A		128.0	0.0	.		130.0	43.0	.	NM_001408	Q5T2Y7|Q92566	Silent	SNP	ENST00000271332.3	hg19	CCDS796.1																																																																																			.	.	.	none		0.647	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		A	109801145	G	A	109801145	2	1	93	1	0	0	0	0	0	0	0	1	3224	991	35	2		2	CELSR2	1	109801145	Silent	SNP	G	TCGA-B3-A6W5-01A-12D-A33Q-10	65765709	109801145	139449476	4	5886											
PTPN22	26191	hgsc.bcm.edu	37	chr1	114397574	114397574	+	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	tgtcatcctcttggtaacaaCgtacatcccagatgagctca	11	11	7	12	1	3	2	2	1	1	1	5	2	5	2	2	1	4	3	2	1	3	3			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr1:114397574C>T	ENST00000359785.5	-	8	773	c.638G>A	c.(637-639)cGt>cAt	p.R213H	PTPN22_ENST00000538253.1_Intron|AP4B1-AS1_ENST00000419536.1_RNA|PTPN22_ENST00000525799.1_Intron|PTPN22_ENST00000528414.1_Missense_Mutation_p.R213H|PTPN22_ENST00000460620.1_Intron|PTPN22_ENST00000420377.2_Missense_Mutation_p.R213H|PTPN22_ENST00000534519.1_5'Flank	NM_001193431.1|NM_015967.5	NP_001180360.1|NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	213	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of T cell activation (GO:0050868)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphoanandamide dephosphorylation (GO:0035644)|protein dephosphorylation (GO:0006470)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of innate immune response (GO:0045088)|regulation of natural killer cell proliferation (GO:0032817)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	kinase binding (GO:0019900)|protein tyrosine phosphatase activity (GO:0004725)|SH3 domain binding (GO:0017124)			NS(1)|breast(1)|kidney(3)|large_intestine(4)|lung(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTGGTAACAACGTACATCCCA	0.408																																					p.R213H		Atlas-SNP	.											.	PTPN22	90	.	0			c.G638A						PASS	.						178	156	163					1																	114397574		2203	4300	6503	SO:0001583	missense	26191	exon8			TAACAACGTACAT	AF001846	CCDS863.1, CCDS864.1, CCDS864.2	1p13.2	2011-06-09	2005-02-02		ENSG00000134242	ENSG00000134242		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9652	protein-coding gene	gene with protein product		600716	"protein tyrosine phosphatase, non-receptor type 8"	PTPN8		10068674, 1373816	Standard	NM_015967		Approved	Lyp, Lyp1, Lyp2	uc001eds.3	Q9Y2R2	OTTHUMG00000011936	ENST00000359785.5:c.638G>A	chr1.hg19:g.114397574C>T	ENSP00000352833:p.Arg213His	80.0	0.0	.		84.0	43.0	.	NM_001193431	A0N0K6|B1ALC8|D4NZ71|E9PLD8|E9PPI1|O95063|O95064|Q6IPX8|Q8WVM1	Missense_Mutation	SNP	ENST00000359785.5	hg19	CCDS863.1	.	.	.	.	.	.	.	.	.	.	C	35	5.473320	0.96274	.	.	ENSG00000134242	ENST00000359785;ENST00000528414;ENST00000420377;ENST00000354605	D;D;D	0.84516	-1.86;-1.86;-1.86	6.16	6.16	0.99307	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.85682	D	0.000000	D	0.91563	0.7335	M	0.72353	2.195	0.80722	D	1	D;D;D;D	0.89917	0.983;1.0;1.0;1.0	P;D;D;D	0.97110	0.835;1.0;0.994;0.994	D	0.91177	0.4973	10	0.87932	D	0	.	19.6313	0.95704	0.0:1.0:0.0:0.0	.	213;213;213;213	E9PMT0;E9PLD8;G5E984;Q9Y2R2	.;.;.;PTN22_HUMAN	H	213	ENSP00000352833:R213H;ENSP00000435176:R213H;ENSP00000388229:R213H	ENSP00000346621:R213H	R	-	2	0	PTPN22	114199097	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	4.496000	0.60360	2.937000	0.99478	0.650000	0.86243	CGT	.	.	.	none		0.408	PTPN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033015.1	NM_015967		T	114397574	C	T	114397574	3	4	93	1	0	0	0	0	1	0	0	0	12800	536	19	1	1864	1	PTPN22	1	114397574	Missense_Mutation	SNP	C	TCGA-B3-A6W5-01A-12D-A33Q-10	4596429	114397574	134853047	5	5887											
SYCP1	6847	hgsc.bcm.edu	37	chr1	115453123	115453123	+	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	gtcttctccaagccagagagGtttgtttaaggaaacatttt	11	14	9	7	0	2	1	0	0	2	1	3	3	2	2	2	2	2	2	2	2	3	6			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr1:115453123G>A	ENST00000369522.3	+	17	1665		c.e17+1		SYCP1_ENST00000369518.1_Splice_Site	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1						chiasma assembly (GO:0051026)|lateral element assembly (GO:0051878)|meiotic DNA repair synthesis (GO:0000711)|reciprocal meiotic recombination (GO:0007131)|regulation of protein localization (GO:0032880)|sperm chromatin condensation (GO:0035092)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|male germ cell nucleus (GO:0001673)|transverse filament (GO:0000802)	DNA binding (GO:0003677)		RGS22/SYCP1(2)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGCCAGAGAGGTTTGTTTAAG	0.259																																					.		Atlas-SNP	.											.	SYCP1	149	.	0			c.1425+1G>A						PASS	.						40	46	44					1																	115453123		2199	4290	6489	SO:0001630	splice_region_variant	6847	exon17			AGAGAGGTTTGTT	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.1425+1G>A	chr1.hg19:g.115453123G>A		337.0	1.0	.		262.0	87.0	.	NM_003176	O14963|Q5VXJ6	Splice_Site	SNP	ENST00000369522.3	hg19	CCDS879.1	.	.	.	.	.	.	.	.	.	.	G	17.09	3.300500	0.60195	.	.	ENSG00000198765	ENST00000369522;ENST00000536734;ENST00000455987;ENST00000369518	.	.	.	4.96	4.96	0.65561	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0505	0.64732	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SYCP1	115254646	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	5.024000	0.64090	2.440000	0.82611	0.467000	0.42956	.	.	.	.	none		0.259	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176	Intron	A	115453123	G	A	115453123	5	1	93	1	0	0	0	0	0	0	1	0	15443	1275	44	2	1488	2	SYCP1	1	115453123	Splice_Site	SNP	G	TCGA-B3-A6W5-01A-12D-A33Q-10	1055549	115453123	133797498	6	5888											
ADCY10	55811	hgsc.bcm.edu	37	chr1	167829047	167829047	+	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	acccacagatgctcttaccaGcttcaagatcttcataaaca	14	10	4	13	0	4	2	2	0	2	2	4	2	4	2	2	0	4	2	2	0	4	4			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr1:167829047G>T	ENST00000367851.4	-	16	2078	c.1894C>A	c.(1894-1896)Ctg>Atg	p.L632M	ADCY10_ENST00000545172.1_Missense_Mutation_p.L479M|ADCY10_ENST00000367848.1_Missense_Mutation_p.L540M	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	632					cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						GCTCTTACCAGCTTCAAGATC	0.423																																					p.L632M		Atlas-SNP	.											.	ADCY10	175	.	0			c.C1894A						PASS	.						205	216	212					1																	167829047		2203	4300	6503	SO:0001583	missense	55811	exon16			TTACCAGCTTCAA	AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	4.6.1.1	"Adenylate cyclases"	21285	protein-coding gene	gene with protein product	"soluble adenylyl cyclase", "Hypercalciuria, absorptive, 2"	605205					Standard	XM_006711449		Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.1894C>A	chr1.hg19:g.167829047G>T	ENSP00000356825:p.Leu632Met	69.0	0.0	.		66.0	4.0	.	NM_018417	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Missense_Mutation	SNP	ENST00000367851.4	hg19	CCDS1265.1	.	.	.	.	.	.	.	.	.	.	G	10.72	1.429730	0.25726	.	.	ENSG00000143199	ENST00000545172;ENST00000367851;ENST00000367848	T;T;T	0.66280	-0.2;-0.2;-0.2	5.4	2.21	0.28008	.	0.644144	0.15119	N	0.279490	T	0.20292	0.0488	N	0.08118	0	0.20307	N	0.999911	B;B;B	0.19583	0.037;0.037;0.022	B;B;B	0.14023	0.01;0.01;0.004	T	0.04041	-1.0982	9	0.48119	T	0.1	-6.5051	8.477	0.33018	0.0:0.1476:0.549:0.3034	.	479;540;632	F5GWS5;Q96PN6-2;Q96PN6	.;.;ADCYA_HUMAN	M	479;632;540	ENSP00000441992:L479M;ENSP00000356825:L632M;ENSP00000356822:L540M	ENSP00000356822:L540M	L	-	1	2	ADCY10	166095671	0.936000	0.31750	1.000000	0.80357	0.434000	0.31775	0.414000	0.21164	0.701000	0.31803	0.655000	0.94253	CTG	.	.	.	none		0.423	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417		T	167829047	G	T	167829047	3	4	93	1	0	0	0	0	1	0	0	0	293	962	34	4	3010	4	ADCY10	1	167829047	Missense_Mutation	SNP	G	TCGA-B3-A6W5-01A-12D-A33Q-10	52375924	167829047	81421574	7	5889											
RAB3GAP2	25782	hgsc.bcm.edu	37	chr1	220345388	220345388	+	Missense_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	aatcccaggtctcatcgatgGccactatagggataggagaa	13	8	11	9	1	1	1	1	0	1	1	4	4	2	2	2	4	0	0	2	4	5	3			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr1:220345388G>A	ENST00000358951.2	-	23	2536	c.2420C>T	c.(2419-2421)gCc>gTc	p.A807V		NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN	RAB3 GTPase activating protein subunit 2 (non-catalytic)	807					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)		CTCATCGATGGCCACTATAGG	0.423																																					p.A807V		Atlas-SNP	.											.	RAB3GAP2	120	.	0			c.C2420T						PASS	.						45	44	44					1																	220345388		2203	4300	6503	SO:0001583	missense	25782	exon23			TCGATGGCCACTA	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.2420C>T	chr1.hg19:g.220345388G>A	ENSP00000351832:p.Ala807Val	169.0	0.0	.		172.0	46.0	.	NM_012414	A6H8V0|O75872|Q9HAB0|Q9UFJ7|Q9UQ15	Missense_Mutation	SNP	ENST00000358951.2	hg19	CCDS31028.1	.	.	.	.	.	.	.	.	.	.	G	16.90	3.250887	0.59212	.	.	ENSG00000118873	ENST00000358951	T	0.32753	1.44	5.71	5.71	0.89125	.	0.048492	0.85682	D	0.000000	T	0.40932	0.1137	L	0.31065	0.9	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	T	0.05500	-1.0881	10	0.02654	T	1	.	19.8635	0.96793	0.0:0.0:1.0:0.0	.	807	Q9H2M9	RBGPR_HUMAN	V	807	ENSP00000351832:A807V	ENSP00000351832:A807V	A	-	2	0	RAB3GAP2	218412011	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.901000	0.92560	2.700000	0.92200	0.650000	0.86243	GCC	.	.	.	none		0.423	RAB3GAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090205.2	NM_012414		A	220345388	G	A	220345388	3	1	93	1	0	0	0	0	1	0	0	0	12949	1203	42	2	1813	2	RAB3GAP2	1	220345388	Missense_Mutation	SNP	G	TCGA-B3-A6W5-01A-12D-A33Q-10	52516341	220345388	28905233	8	5890											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228468061	228468061	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggccggcgccacacgctggtActgaagagcatccagcgggc	8	4	15	14	4	0	2	0	1	0	1	1	2	1	2	3	4	3	3	3	4	2	1			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr1:228468061A>G	ENST00000422127.1	+	29	7889	c.7845A>G	c.(7843-7845)gtA>gtG	p.V2615V	OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000570156.2_Silent_p.V3044V|OBSCN_ENST00000359599.6_Silent_p.V1462V|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.V2615V	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2615	Ig-like 25.				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)				ACACGCTGGTACTGAAGAGCA	0.632																																					p.V3044V		Atlas-SNP	.											.	OBSCN	2142	.	0			c.A9132G						PASS	.						35	41	39					1																	228468061		2126	4221	6347	SO:0001819	synonymous_variant	84033	exon34			GCTGGTACTGAAG	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.7845A>G	chr1.hg19:g.228468061A>G		71.0	0.0	.		50.0	19.0	.	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	hg19	CCDS58065.1																																																																																			.	.	.	none		0.632	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		G	228468061	A	G	228468061	2	3	93	1	0	0	0	0	0	0	0	1	10819	378	14	3		3	OBSCN	1	228468061	Silent	SNP	A	TCGA-B3-A6W5-01A-12D-A33Q-10	8122673	228468061	20782560	9	5891											
SNRNP200	23020	hgsc.bcm.edu	37	chr2	96950320	96950340	+	Splice_Site	DEL	ATACCTGGCGGGCAGAGGAGG	ATACCTGGCGGGCAGAGGAGG	-																															cttctcgtaccagtccatgtAtacctggcgggcagaggagg																								rs372471318|rs376605359|rs190395367|rs143898031	byFrequency	TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	ATACCTGGCGGGCAGAGGAGG	ATACCTGGCGGGCAGAGGAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr2:96950320_96950340delATACCTGGCGGGCAGAGGAGG	ENST00000323853.5	-	31	4242_4245	c.4165_4168delCCTCCTCTGCCCGCCAGGTAT	c.(4165-4170)cctcct>ct	p.PP1389del	SNRNP200_ENST00000349783.5_Intron	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	1389	Helicase ATP-binding 2. {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)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						CAGTCCATGTATACCTGGCGGGCAGAGGAGGGAGGCAGAAC	0.529																																					p.1389_1390del		Atlas-Indel,Pindel	.											.	SNRNP200	195	.	0			c.4165_4169del						PASS	.																																			SO:0001630	splice_region_variant	23020	exon31			.	AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 200 KD"	601664	"activating signal cointegrator 1 complex subunit 3-like 1", "retinitis pigmentosa 33 (autosomal dominant)"	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.4165-1CCTCCTCTGCCCGCCAGGTAT>-	chr2.hg19:g.96950320_96950340delATACCTGGCGGGCAGAGGAGG		51.0	0.0	0		42.0	16.0	0.380952	NM_014014	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Frame_Shift_Del	DEL	ENST00000323853.5	hg19	CCDS2020.1																																																																																			.	.	.	none		0.529	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252846.2	NM_014014	In_Frame_Del	-	96950340	ATACCTGGCGGGCAGAGGAGG	-	96950320	8	5	93	1	0	1	0	1	0	0	1	0	14865	449	16	0	2302	0	SNRNP200	2	96950320	Splice_Site	DEL	ATACCTGGCGGGCAGAGGAGG	TCGA-B3-A6W5-01A-12D-A33Q-10		96950320	146249053	10	5892											
LMAN2L	81562	hgsc.bcm.edu	37	chr2	97400231	97400231	+	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	tgtccatggattttgaagtgCacctgcaactcccagtctct	8	13	8	12	0	1	1	0	1	1	0	4	2	3	2	3	1	3	2	3	1	2	2	rs199689213		TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr2:97400231C>T	ENST00000264963.4	-	3	361	c.339G>A	c.(337-339)gtG>gtA	p.V113V	LMAN2L_ENST00000377079.4_Silent_p.V113V|LMAN2L_ENST00000537039.1_5'UTR|LMAN2L_ENST00000534882.1_5'UTR|LMAN2L_ENST00000426463.2_5'UTR	NM_030805.3	NP_110432.1	Q9H0V9	LMA2L_HUMAN	lectin, mannose-binding 2-like	113	L-type lectin-like. {ECO:0000255|PROSITE- ProRule:PRU00658}.				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						TTTTGAAGTGCACCTGCAACT	0.478													C|||	1	0.000199681	0	0	5008	,	,		21277	0		0	False		,,,				2504	0.001				p.V113V		Atlas-SNP	.											.	LMAN2L	27	.	0			c.G339A						PASS	.						193	171	178					2																	97400231		2203	4300	6503	SO:0001819	synonymous_variant	81562	exon3			GAAGTGCACCTGC	AL136617	CCDS2023.1, CCDS46365.1	2q11.1	2008-02-05			ENSG00000114988	ENSG00000114988			19263	protein-coding gene	gene with protein product		609552				12609988	Standard	NM_001142292		Approved	DKFZp564L2423, VIPL	uc002swv.3	Q9H0V9	OTTHUMG00000130453	ENST00000264963.4:c.339G>A	chr2.hg19:g.97400231C>T		57.0	0.0	.		71.0	43.0	.	NM_030805	B4DSH3|D3DXH6|Q53GV3|Q53S67|Q63HN6|Q8NBQ6|Q9BQ14	Silent	SNP	ENST00000264963.4	hg19	CCDS2023.1																																																																																			.	C|0.999;T|0.001	0.001	weak		0.478	LMAN2L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252844.1	NM_030805		T	97400231	C	T	97400231	2	4	93	1	0	0	0	0	0	0	0	1	8846	697	25	2		2	LMAN2L	2	97400231	Silent	SNP	C	TCGA-B3-A6W5-01A-12D-A33Q-10	449911	97400231	145799142	11	5893											
FN1	2335	hgsc.bcm.edu	37	chr2	216269139	216269139	+	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	aaagactccagtggctttggGgctctcttggttgcccttta	6	14	11	10	0	1	1	0	0	1	1	3	1	2	1	2	4	1	3	2	4	2	5			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr2:216269139G>A	ENST00000359671.1	-	20	3491	c.3226C>T	c.(3226-3228)Ccc>Tcc	p.P1076S	FN1_ENST00000345488.5_Missense_Mutation_p.P1076S|FN1_ENST00000432072.2_Missense_Mutation_p.P1076S|FN1_ENST00000354785.4_Missense_Mutation_p.P1076S|FN1_ENST00000336916.4_Missense_Mutation_p.P1076S|FN1_ENST00000357867.4_Missense_Mutation_p.P1076S|FN1_ENST00000346544.3_Missense_Mutation_p.P1076S|FN1_ENST00000357009.2_Missense_Mutation_p.P1076S|FN1_ENST00000446046.1_Missense_Mutation_p.P1076S|FN1_ENST00000443816.1_Missense_Mutation_p.P1076S|FN1_ENST00000356005.4_Missense_Mutation_p.P1076S|FN1_ENST00000323926.6_Missense_Mutation_p.P1076S|FN1_ENST00000421182.1_Missense_Mutation_p.P1076S			P02751	FINC_HUMAN	fibronectin 1	1076	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316, ECO:0000255|PROSITE-ProRule:PRU00478, ECO:0000255|PROSITE-ProRule:PRU00479}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	GTGGCTTTGGGGCTCTCTTGG	0.443																																					p.P1076S		Atlas-SNP	.											.	FN1	521	.	0			c.C3226T						PASS	.						96	92	93					2																	216269139		2203	4300	6503	SO:0001583	missense	2335	exon20			CTTTGGGGCTCTC		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.3226C>T	chr2.hg19:g.216269139G>A	ENSP00000352696:p.Pro1076Ser	95.0	0.0	.		112.0	32.0	.	NM_212476	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	hg19		.	.	.	.	.	.	.	.	.	.	G	15.97	2.989242	0.53934	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005	T;T;T;T;T;T;T;T;T;T;T;T;T	0.59364	0.27;0.27;0.27;0.27;0.27;0.27;0.27;0.27;0.27;0.27;0.27;0.27;0.27	5.83	5.83	0.93111	.	0.090164	0.46758	D	0.000261	T	0.61800	0.2376	N	0.25647	0.755	0.37259	D	0.906904	P;B;B;P;P;B;P;D;D;B	0.76494	0.925;0.03;0.028;0.925;0.891;0.055;0.792;0.998;0.999;0.338	P;B;B;P;P;B;P;D;D;B	0.87578	0.79;0.062;0.054;0.661;0.688;0.089;0.507;0.998;0.998;0.287	T	0.65861	-0.6065	10	0.48119	T	0.1	.	9.6598	0.39947	0.0:0.233:0.5644:0.2026	.	1076;1076;1076;1076;1076;1076;1076;1076;1076;1076	P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.	S	1076	ENSP00000394423:P1076S;ENSP00000323534:P1076S;ENSP00000338200:P1076S;ENSP00000350534:P1076S;ENSP00000346839:P1076S;ENSP00000352696:P1076S;ENSP00000265312:P1076S;ENSP00000273049:P1076S;ENSP00000349509:P1076S;ENSP00000410422:P1076S;ENSP00000415018:P1076S;ENSP00000399538:P1076S;ENSP00000348285:P1076S	ENSP00000265313:P1076S	P	-	1	0	FN1	215977384	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.440000	0.35024	2.770000	0.95276	0.655000	0.94253	CCC	.	.	.	none		0.443	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		A	216269139	G	A	216269139	3	1	93	1	0	0	0	0	1	0	0	0	5969	1232	43	2	4315	2	FN1	2	216269139	Missense_Mutation	SNP	G	TCGA-B3-A6W5-01A-12D-A33Q-10	118868908	216269139	26930234	12	5894											
COL4A3	1285	hgsc.bcm.edu	37	chr2	228172490	228172490	+	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	ggagacagtggatcacctgcAacctggacaacgagaggctt	12	6	13	10	1	1	2	1	0	0	2	1	6	1	4	2	4	3	2	2	4	2	1			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr2:228172490A>C	ENST00000396578.3	+	48	4479	c.4317A>C	c.(4315-4317)gcA>gcC	p.A1439A	AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000433324.1_RNA|AC097662.2_ENST00000439598.2_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	1439	Epitope recognized by Goodpasture antibodies.				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)		GATCACCTGCAACCTGGACAA	0.473																																					p.A1439A		Atlas-SNP	.											.	COL4A3	293	.	0			c.A4317C						PASS	.						114	112	113					2																	228172490		1987	4165	6152	SO:0001819	synonymous_variant	1285	exon48			ACCTGCAACCTGG		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.4317A>C	chr2.hg19:g.228172490A>C		290.0	0.0	.		293.0	168.0	.	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Silent	SNP	ENST00000396578.3	hg19	CCDS42829.1																																																																																			.	.	.	none		0.473	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091		C	228172490	A	C	228172490	2	2	93	1	0	0	0	0	0	0	0	1	3693	117	5	5		5	COL4A3	2	228172490	Silent	SNP	A	TCGA-B3-A6W5-01A-12D-A33Q-10	11903351	228172490	15026883	13	5895											
SH3TC1	54436	hgsc.bcm.edu	37	chr4	8238155	8238155	+	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	tagcactcagcatcaccctgGgtaagccccctgagcccctg	8	7	9	17	0	2	1	2	1	0	0	2	1	2	1	5	1	4	3	5	1	2	2	rs546239040		TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr4:8238155G>C	ENST00000245105.3	+	16	3623	c.3556G>C	c.(3556-3558)Ggg>Cgg	p.G1186R	SH3TC1_ENST00000539824.1_Splice_Site_p.G1110R	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	1186										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						CATCACCCTGGGTAAGCCCCC	0.647																																					p.G1186R	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											.	SH3TC1	105	.	0			c.G3556C						PASS	.						28	25	26					4																	8238155		2043	3933	5976	SO:0001630	splice_region_variant	54436	exon16			ACCCTGGGTAAGC	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.3556+1G>C	chr4.hg19:g.8238155G>C		225.0	0.0	.		154.0	58.0	.	NM_018986	Q4W5G5	Missense_Mutation	SNP	ENST00000245105.3	hg19	CCDS3399.1	.	.	.	.	.	.	.	.	.	.	G	17.02	3.282626	0.59867	.	.	ENSG00000125089	ENST00000245105;ENST00000539824;ENST00000535265	T;T	0.79352	-1.0;-1.26	3.71	3.71	0.42584	Tetratricopeptide-like helical (1);	0.000000	0.64402	D	0.000001	D	0.87265	0.6134	M	0.78049	2.395	0.58432	D	0.999994	D	0.89917	1.0	D	0.81914	0.995	D	0.89430	0.3716	10	0.87932	D	0	-34.6905	15.0602	0.71947	0.0:0.0:1.0:0.0	.	1186	Q8TE82	S3TC1_HUMAN	R	1186;1110;1015	ENSP00000245105:G1186R;ENSP00000441045:G1110R	ENSP00000245105:G1186R	G	+	1	0	SH3TC1	8289055	1.000000	0.71417	0.995000	0.50966	0.242000	0.25591	7.799000	0.85936	2.108000	0.64289	0.555000	0.69702	GGG	.	.	.	none		0.647	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986	Missense_Mutation	C	8238155	G	C	8238155	5	2	93	1	0	0	0	0	0	0	1	0	14274	1246	43	4	3614	4	SH3TC1	4	8238155	Splice_Site	SNP	G	TCGA-B3-A6W5-01A-12D-A33Q-10		8238155	182916121	14	5896											
ARHGAP24	83478	hgsc.bcm.edu	37	chr4	86491717	86491717	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggagaacaatgactccaCggagaacccccaacaaggcc	15	2	11	13	1	0	3	0	1	0	2	1	6	1	4	4	4	3	0	4	4	5	0	rs377269441	byFrequency	TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr4:86491717C>T	ENST00000395184.1	+	2	489	c.23C>T	c.(22-24)aCg>aTg	p.T8M	ARHGAP24_ENST00000506421.1_3'UTR|ARHGAP24_ENST00000503995.1_Missense_Mutation_p.T8M	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	8					activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)			breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		AATGACTCCACGGAGAACCCC	0.473													C|||	3	0.000599042	0.0023	0	5008	,	,		17976	0		0	False		,,,				2504	0				p.T8M		Atlas-SNP	.											.	ARHGAP24	116	.	0			c.C23T						PASS	.	C	MET/THR	2,4404	4.2+/-10.8	0,2,2201	71	63	66		23	-1.1	0	4		66	1,8599	1.2+/-3.3	0,1,4299	no	missense	ARHGAP24	NM_001025616.2	81	0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231	benign	8/749	86491717	3,13003	2203	4300	6503	SO:0001583	missense	83478	exon2			ACTCCACGGAGAA	AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	25361	protein-coding gene	gene with protein product		610586				11230166, 15254788	Standard	NM_001042669		Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.23C>T	chr4.hg19:g.86491717C>T	ENSP00000378611:p.Thr8Met	74.0	0.0	.		60.0	26.0	.	NM_001025616	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	Missense_Mutation	SNP	ENST00000395184.1	hg19	CCDS34025.1	.	.	.	.	.	.	.	.	.	.	C	12.05	1.821481	0.32237	4.54E-4	1.16E-4	ENSG00000138639	ENST00000395184;ENST00000503995	T;T	0.13307	2.84;2.6	5.81	-1.08	0.09936	Pleckstrin homology-type (1);	1.720280	0.02385	N	0.079112	T	0.05960	0.0155	N	0.02011	-0.69	0.09310	N	1	B;B;B	0.13145	0.0;0.0;0.007	B;B;B	0.09377	0.001;0.001;0.004	T	0.34079	-0.9843	10	0.33141	T	0.24	.	7.8497	0.29446	0.0:0.3655:0.118:0.5164	.	8;8;153	Q8N264;Q8N264-4;Q8N264-5	RHG24_HUMAN;.;.	M	8	ENSP00000378611:T8M;ENSP00000423206:T8M	ENSP00000378611:T8M	T	+	2	0	ARHGAP24	86710741	0.000000	0.05858	0.000000	0.03702	0.979000	0.70002	-0.748000	0.04818	-0.625000	0.05604	0.655000	0.94253	ACG	.	.	.	weak		0.473	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252815.2	NM_031305		T	86491717	C	T	86491717	3	4	93	1	0	0	0	0	1	0	0	0	873	536	19	1	25	1	ARHGAP24	4	86491717	Missense_Mutation	SNP	C	TCGA-B3-A6W5-01A-12D-A33Q-10	78253562	86491717	104662559	15	5897											
CD180	4064	hgsc.bcm.edu	37	chr5	66479374	66479374	+	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	actttgtggagcattaatgtGtaagcgggtaaatgccaaat	13	12	11	5	1	0	0	0	0	0	0	0	1	0	1	1	2	3	3	1	2	5	4			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr5:66479374G>T	ENST00000256447.4	-	3	1454	c.1297C>A	c.(1297-1299)Cac>Aac	p.H433N	CTD-2306M10.1_ENST00000602471.1_lincRNA	NM_005582.2	NP_005573.2	Q99467	CD180_HUMAN	CD180 molecule	433					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)		GCATTAATGTGTAAGCGGGTA	0.453																																					p.H433N		Atlas-SNP	.											.	CD180	78	.	0			c.C1297A						PASS	.						175	182	179					5																	66479374		2203	4300	6503	SO:0001583	missense	4064	exon3			TAATGTGTAAGCG	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.1297C>A	chr5.hg19:g.66479374G>T	ENSP00000256447:p.His433Asn	92.0	0.0	.		78.0	28.0	.	NM_005582	B2R7Z7|Q32MM5	Missense_Mutation	SNP	ENST00000256447.4	hg19	CCDS3992.1	.	.	.	.	.	.	.	.	.	.	G	0.265	-0.997055	0.02145	.	.	ENSG00000134061	ENST00000256447	T	0.56941	0.43	4.81	1.92	0.25849	.	0.981481	0.08336	N	0.961541	T	0.34077	0.0885	L	0.27975	0.815	0.09310	N	1	B	0.25235	0.121	B	0.23018	0.043	T	0.25257	-1.0137	10	0.16420	T	0.52	.	4.3619	0.11206	0.0748:0.1263:0.41:0.3888	.	433	Q99467	CD180_HUMAN	N	433	ENSP00000256447:H433N	ENSP00000256447:H433N	H	-	1	0	CD180	66515130	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-0.155000	0.10115	0.185000	0.20105	0.563000	0.77884	CAC	.	.	.	none		0.453	CD180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253973.2	NM_005582		T	66479374	G	T	66479374	3	4	93	1	0	0	0	0	1	0	0	0	2974	1377	48	4	692	4	CD180	5	66479374	Missense_Mutation	SNP	G	TCGA-B3-A6W5-01A-12D-A33Q-10		66479374	114435886	16	5898											
KDM3B	51780	hgsc.bcm.edu	37	chr5	137728920	137728920	+	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	gctgaagcaatctggagagcCcttcctgcaggatgggtcat	9	9	13	10	0	2	2	1	1	1	1	3	4	3	3	2	3	3	3	2	3	2	1			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr5:137728920C>T	ENST00000314358.5	+	9	2890	c.2690C>T	c.(2689-2691)cCc>cTc	p.P897L	KDM3B_ENST00000394866.1_Missense_Mutation_p.P553L|KDM3B_ENST00000542866.1_5'UTR	NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	897					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						TCTGGAGAGCCCTTCCTGCAG	0.512																																					p.P897L		Atlas-SNP	.											.	KDM3B	177	.	0			c.C2690T						PASS	.						127	114	118					5																	137728920		2203	4300	6503	SO:0001583	missense	51780	exon9			GAGAGCCCTTCCT	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.2690C>T	chr5.hg19:g.137728920C>T	ENSP00000326563:p.Pro897Leu	95.0	0.0	.		78.0	41.0	.	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Missense_Mutation	SNP	ENST00000314358.5	hg19	CCDS34242.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.382255	0.82792	.	.	ENSG00000120733	ENST00000314358;ENST00000545151;ENST00000394866	T;T	0.70045	0.14;-0.45	6.08	6.08	0.98989	.	0.210265	0.51477	D	0.000095	T	0.62780	0.2456	N	0.22421	0.69	0.80722	D	1	P;B	0.46512	0.879;0.374	P;B	0.45998	0.5;0.084	T	0.63919	-0.6528	10	0.51188	T	0.08	-18.7842	20.2751	0.98485	0.0:1.0:0.0:0.0	.	553;897	Q7LBC6-2;Q7LBC6	.;KDM3B_HUMAN	L	897;687;553	ENSP00000326563:P897L;ENSP00000378335:P553L	ENSP00000326563:P897L	P	+	2	0	KDM3B	137756819	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.818000	0.86416	2.890000	0.99128	0.655000	0.94253	CCC	.	.	.	none		0.512	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604		T	137728920	C	T	137728920	3	4	93	1	0	0	0	0	1	0	0	0	8134	623	22	2	2724	2	KDM3B	5	137728920	Missense_Mutation	SNP	C	TCGA-B3-A6W5-01A-12D-A33Q-10	71249546	137728920	43186340	17	5899											
WWC1	23286	hgsc.bcm.edu	37	chr5	167881045	167881045	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggtggaggaggaggagggAgaagaggatgttttcaccga	12	6	20	3	1	1	2	1	0	0	2	1	10	1	7	1	7	0	1	1	7	1	2	rs201870717|rs116415672	byFrequency	TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr5:167881045A>G	ENST00000265293.4	+	18	3100	c.2598A>G	c.(2596-2598)ggA>ggG	p.G866G	WWC1_ENST00000522140.1_3'UTR|WWC1_ENST00000521089.1_Silent_p.G866G	NM_001161661.1|NM_001161662.1|NM_015238.2	NP_001155133.1|NP_001155134.1|NP_056053.1	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	866	Glu-rich.|Interaction with histone H3.				cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|hippo signaling (GO:0035329)|negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of MAPK cascade (GO:0043410)|regulation of hippo signaling (GO:0035330)|regulation of intracellular transport (GO:0032386)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(1)|skin(4)	43	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		aggaggagggagaagaggaTG	0.542																																					p.G866G		Atlas-SNP	.											.	WWC1	98	.	0			c.A2598G						PASS	.						119	113	115					5																	167881045		2202	4300	6502	SO:0001819	synonymous_variant	23286	exon18			GGAGGGAGAAGAG	AF506799	CCDS4366.1, CCDS54945.1	5q34	2014-06-13	2006-11-09		ENSG00000113645	ENSG00000113645		"WW, C2 and coiled-coil domain containing"	29435	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 168"	610533	"WW, C2 and coiled-coil domain containing 1"			10048485, 12559952	Standard	NM_001161661		Approved	KIBRA, KIAA0869, PPP1R168	uc011den.2	Q8IX03	OTTHUMG00000130408	ENST00000265293.4:c.2598A>G	chr5.hg19:g.167881045A>G		78.0	0.0	.		74.0	18.0	.	NM_015238	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Silent	SNP	ENST00000265293.4	hg19	CCDS4366.1	.	.	.	.	.	.	.	.	.	.	A	4.385	0.071000	0.08436	.	.	ENSG00000113645	ENST00000393895;ENST00000524228	.	.	.	4.51	0.519	0.17035	.	.	.	.	.	T	0.41834	0.1176	.	.	.	0.54753	D	0.99998	.	.	.	.	.	.	T	0.20840	-1.0263	4	.	.	.	.	1.5039	0.02482	0.5457:0.1811:0.099:0.1742	.	.	.	.	G	828;643	.	.	R	+	1	2	WWC1	167813623	0.495000	0.26051	0.050000	0.19076	0.001000	0.01503	0.164000	0.16542	-0.074000	0.12820	-0.499000	0.04595	AGA	.	.	.	weak		0.542	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238		G	167881045	A	G	167881045	2	3	93	1	0	0	0	0	0	0	0	1	17423	291	11	3		3	WWC1	5	167881045	Silent	SNP	A	TCGA-B3-A6W5-01A-12D-A33Q-10	30152125	167881045	13034215	18	5900											
C6orf167	253714	hgsc.bcm.edu	37	chr6	97702477	97702477	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atcaaacttgtaaaatgatgCtacatgagtaataatccacc	17	11	5	8	0	1	2	1	2	0	0	2	2	2	2	2	0	3	3	2	0	6	5			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr6:97702477C>T	ENST00000275053.4	-	10	1340	c.1075G>A	c.(1075-1077)Gca>Aca	p.A359T	MMS22L_ENST00000369251.2_Missense_Mutation_p.A359T	NM_198468.2	NP_940870.2	Q6ZRQ5	MMS22_HUMAN	MMS22-like, DNA repair protein	359					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						TAAAATGATGCTACATGAGTA	0.333																																					p.A359T		Atlas-SNP	.											.	MMS22L	102	.	0			c.G1075A						PASS	.						116	116	116					6																	97702477		2203	4300	6503	SO:0001583	missense	253714	exon10			ATGATGCTACATG		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.1075G>A	chr6.hg19:g.97702477C>T	ENSP00000275053:p.Ala359Thr	112.0	0.0	.		63.0	24.0	.	NM_198468	D6R9Y8|D6RBQ4|E1P529|Q5THT2|Q68CQ6|Q68D32	Missense_Mutation	SNP	ENST00000275053.4	hg19	CCDS5039.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.768632	0.90020	.	.	ENSG00000146263	ENST00000275053;ENST00000369251;ENST00000510018;ENST00000482634	T;T;T;T	0.51574	0.7;0.7;0.7;0.7	5.09	5.09	0.68999	.	0.237263	0.35067	N	0.003479	T	0.58708	0.2141	M	0.69823	2.125	0.51482	D	0.999929	D;D	0.67145	0.996;0.981	P;P	0.61800	0.894;0.715	T	0.64228	-0.6457	10	0.72032	D	0.01	-5.7806	16.6752	0.85277	0.0:1.0:0.0:0.0	.	359;359	E2QRD4;Q6ZRQ5	.;MMS22_HUMAN	T	359;359;247;51	ENSP00000275053:A359T;ENSP00000358254:A359T;ENSP00000427288:A247T;ENSP00000421225:A51T	ENSP00000275053:A359T	A	-	1	0	MMS22L	97809198	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.404000	0.66344	2.364000	0.80123	0.655000	0.94253	GCA	.	.	.	none		0.333	MMS22L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041573.3	NM_198468		T	97702477	C	T	97702477	3	4	93	1	0	0	0	0	1	0	0	0	2344	797	28	2	2720	2	C6orf167	6	97702477	Missense_Mutation	SNP	C	TCGA-B3-A6W5-01A-12D-A33Q-10		97702477	73412590	19	5901											
TTYH3	80727	hgsc.bcm.edu	37	chr7	2671817	2671817	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtcagctacgcggcgcccTggtgggtgagcctcctgcac	4	7	16	14	3	1	1	1	1	0	0	2	1	2	1	3	4	4	2	3	4	1	1			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr7:2671817T>C	ENST00000258796.7	+	1	233	c.28T>C	c.(28-30)Tgg>Cgg	p.W10R	TTYH3_ENST00000407643.1_Missense_Mutation_p.W10R	NM_025250.2	NP_079526.1	Q9C0H2	TTYH3_HUMAN	tweety family member 3	10					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|intracellular calcium activated chloride channel activity (GO:0005229)			kidney(1)|large_intestine(3)|lung(9)|prostate(2)|upper_aerodigestive_tract(2)	17		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.04e-14)		CGCGGCGCCCTGGTGGGTGAG	0.751																																					p.W10R		Atlas-SNP	.											.	TTYH3	36	.	0			c.T28C						PASS	.						7	9	8					7																	2671817		2139	4188	6327	SO:0001583	missense	80727	exon1			GCGCCCTGGTGGG		CCDS34588.1	7p22	2013-09-02	2013-09-02		ENSG00000136295	ENSG00000136295			22222	protein-coding gene	gene with protein product		608919	"tweety homolog 3 (Drosophila)"				Standard	NM_025250		Approved	KIAA1691	uc003smp.3	Q9C0H2	OTTHUMG00000152050	ENST00000258796.7:c.28T>C	chr7.hg19:g.2671817T>C	ENSP00000258796:p.Trp10Arg	61.0	0.0	.		72.0	28.0	.	NM_025250	A4D201|B7WP98|Q6L749|Q6ZVG3|Q8TEG6	Missense_Mutation	SNP	ENST00000258796.7	hg19	CCDS34588.1	.	.	.	.	.	.	.	.	.	.	T	14.47	2.544055	0.45280	.	.	ENSG00000136295	ENST00000258796;ENST00000407643	T;T	0.10382	2.89;2.88	4.09	2.9	0.33743	.	0.164594	0.43919	U	0.000511	T	0.27559	0.0677	M	0.74881	2.28	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.00862	-1.1536	10	0.36615	T	0.2	.	8.2175	0.31521	0.1789:0.0:0.0:0.8211	.	10	Q9C0H2	TTYH3_HUMAN	R	10	ENSP00000258796:W10R;ENSP00000385316:W10R	ENSP00000258796:W10R	W	+	1	0	TTYH3	2638343	0.969000	0.33509	1.000000	0.80357	0.546000	0.35178	1.685000	0.37659	0.544000	0.28883	0.260000	0.18958	TGG	.	.	.	none		0.751	TTYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325082.2	XM_166523		C	2671817	T	C	2671817	3	2	93	1	0	0	0	0	1	0	0	0	16753	1580	55	3	30	3	TTYH3	7	2671817	Missense_Mutation	SNP	T	TCGA-B3-A6W5-01A-12D-A33Q-10		2671817	156466846	20	5902											
KCTD7	154881	hgsc.bcm.edu	37	chr7	66103373	66103373	+	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	acatgcagccactgaagggcGagaaggtgcgccaagcgttt	11	6	14	10	3	0	2	0	1	0	1	0	3	0	2	2	2	4	2	2	2	3	1			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr7:66103373G>A	ENST00000275532.3	+	3	632	c.448G>A	c.(448-450)Gag>Aag	p.E150K	KCTD7_ENST00000443322.1_Missense_Mutation_p.E150K	NM_001167961.2|NM_153033.4	NP_001161433.1|NP_694578.1	Q96MP8	KCTD7_HUMAN	potassium channel tetramerization domain containing 7	150					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						ACTGAAGGGCGAGAAGGTGCG	0.597																																					p.E150K		Atlas-SNP	.											.	KCTD7	26	.	0			c.G448A						PASS	.						89	76	80					7																	66103373		2203	4300	6503	SO:0001583	missense	154881	exon3			AAGGGCGAGAAGG	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.448G>A	chr7.hg19:g.66103373G>A	ENSP00000275532:p.Glu150Lys	147.0	0.0	.		224.0	60.0	.	NM_001167961	A4D2M4|Q8IVR0	Missense_Mutation	SNP	ENST00000275532.3	hg19	CCDS5534.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	25.2|25.2	4.608515|4.608515	0.87258|0.87258	.|.	.|.	ENSG00000243335|ENSG00000243335	ENST00000275532;ENST00000443322|ENST00000449064	T;T|.	0.66460|.	-0.21;-0.21|.	5.93|5.93	5.93|5.93	0.95920|0.95920	.|.	.|0.467978	.|0.15967	.|N	.|0.235981	T|T	0.75766|0.75766	0.3894|0.3894	L|L	0.61218|0.61218	1.895|1.895	0.80722|0.80722	D|D	1|1	P|.	0.43412|.	0.806|.	B|.	0.41202|.	0.35|.	T|T	0.74166|0.74166	-0.3753|-0.3753	9|7	0.42905|0.56958	T|D	0.14|0.05	.|.	19.3421|19.3421	0.94347|0.94347	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	150|.	Q96MP8|.	KCTD7_HUMAN|.	K|Q	150|93	ENSP00000275532:E150K;ENSP00000411624:E150K|.	ENSP00000275532:E150K|ENSP00000388463:R93Q	E|R	+|+	1|2	0|0	KCTD7|KCTD7	65740808|65740808	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	9.152000|9.152000	0.94680|0.94680	2.826000|2.826000	0.97356|0.97356	0.655000|0.655000	0.94253|0.94253	GAG|CGA	.	.	.	none		0.597	KCTD7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251733.2	NM_153033		A	66103373	G	A	66103373	3	1	93	1	0	0	0	0	1	0	0	0	8121	1059	37	1	458	1	KCTD7	7	66103373	Missense_Mutation	SNP	G	TCGA-B3-A6W5-01A-12D-A33Q-10	63431556	66103373	93035290	21	5903											
PAXIP1	22976	hgsc.bcm.edu	37	chr7	154760427	154760427	+	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	ggaactgctgctgcagggcaTgctgctgctgaaagggctgg	7	8	17	9	0	0	1	0	1	0	0	0	2	0	2	0	4	7	8	0	4	2	0			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr7:154760427T>A	ENST00000404141.1	-	7	1638	c.1484A>T	c.(1483-1485)cAt>cTt	p.H495L	PAXIP1_ENST00000397192.1_Missense_Mutation_p.H495L|PAXIP1_ENST00000473219.1_5'UTR			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	495	Gln-rich.			Missing (in Ref. 4; AAB91434). {ECO:0000305}.	adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		ctgcagggcatgctgctgctg	0.602																																					p.H495L		Atlas-SNP	.											.	PAXIP1	150	.	0			c.A1484T						PASS	.						31	36	34					7																	154760427		1789	3250	5039	SO:0001583	missense	22976	exon7			AGGGCATGCTGCT	U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"PAX transcription activation domain interacting protein 1 like"	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.1484A>T	chr7.hg19:g.154760427T>A	ENSP00000384048:p.His495Leu	25.0	0.0	.		31.0	13.0	.	NM_007349	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Missense_Mutation	SNP	ENST00000404141.1	hg19	CCDS47753.1	.	.	.	.	.	.	.	.	.	.	T	15.10	2.732484	0.48939	.	.	ENSG00000157212	ENST00000404141;ENST00000397192;ENST00000323199	D;D	0.89746	-2.56;-2.56	4.81	4.81	0.61882	.	0.000000	0.45867	U	0.000323	T	0.80253	0.4589	L	0.29908	0.895	0.39697	D	0.971138	B;B;B;B	0.33238	0.18;0.403;0.403;0.18	B;B;B;B	0.28232	0.04;0.087;0.087;0.04	T	0.77803	-0.2451	10	0.10377	T	0.69	-8.3358	14.0572	0.64776	0.0:0.0:0.0:1.0	.	448;404;461;495	B4DEQ6;Q6ZW49-3;Q6ZW49-1;Q6ZW49	.;.;.;PAXI1_HUMAN	L	495;495;448	ENSP00000384048:H495L;ENSP00000380376:H495L	ENSP00000319149:H448L	H	-	2	0	PAXIP1	154391360	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	3.606000	0.54095	1.796000	0.52611	0.528000	0.53228	CAT	.	.	.	none		0.602	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349		A	154760427	T	A	154760427	3	1	93	1	0	0	0	0	1	0	0	0	11494	1464	51	5	1785	5	PAXIP1	7	154760427	Missense_Mutation	SNP	T	TCGA-B3-A6W5-01A-12D-A33Q-10	88657054	154760427	4378236	22	5904											
NCOA2	10499	hgsc.bcm.edu	37	chr8	71040937	71040937	+	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	ggtgccatcgaagaacagacCtgctgtgcttggaggcgatg	9	8	15	9	2	0	2	0	0	0	2	1	5	0	3	2	3	4	2	2	3	2	1			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr8:71040937C>T	ENST00000452400.2	-	17	3784	c.3603G>A	c.(3601-3603)caG>caA	p.Q1201Q	NCOA2_ENST00000267974.4_Splice_Site_p.Q289Q	NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	1201					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)			AAGAACAGACCTGCTGTGCTT	0.562			T	"RUNXBP2, HEY1"	"AML, Chondrosarcoma"																																p.Q1201Q		Atlas-SNP	.		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	.	NCOA2	147	.	0			c.G3603A						PASS	.						98	100	100					8																	71040937		2043	4181	6224	SO:0001630	splice_region_variant	10499	exon17			ACAGACCTGCTGT	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.3603+1G>A	chr8.hg19:g.71040937C>T		45.0	0.0	.		26.0	9.0	.	NM_006540	Q14CD2	Silent	SNP	ENST00000452400.2	hg19	CCDS47872.1	.	.	.	.	.	.	.	.	.	.	C	16.05	3.012869	0.54468	.	.	ENSG00000140396	ENST00000518363	.	.	.	5.89	5.89	0.94794	.	.	.	.	.	T	0.74989	0.3789	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72191	-0.4365	4	.	.	.	.	18.4423	0.90671	0.0:1.0:0.0:0.0	.	.	.	.	K	302	.	.	R	-	2	0	NCOA2	71203491	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	6.981000	0.76166	2.793000	0.96121	0.655000	0.94253	AGA	.	.	.	none		0.562	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1		Silent	T	71040937	C	T	71040937	5	4	93	1	0	0	0	0	0	0	1	0	10236	695	24	2	819	2	NCOA2	8	71040937	Splice_Site	SNP	C	TCGA-B3-A6W5-01A-12D-A33Q-10		71040937	75323085	23	5905											
ZNF462	58499	hgsc.bcm.edu	37	chr9	109736499	109736500	+	Frame_Shift_Del	DEL	CC	CC	-																															gatcttcgctgtcctctctgCctctatcacaccaaatacaa																										TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr9:109736499_109736500delCC	ENST00000277225.5	+	9	7066_7067	c.6777_6778delCC	c.(6775-6780)tgcctcfs	p.L2260fs	ZNF462_ENST00000457913.1_Frame_Shift_Del_p.L2320fs|ZNF462_ENST00000441147.2_Frame_Shift_Del_p.L1166fs|ZNF462_ENST00000542028.1_Frame_Shift_Del_p.L217fs|RP11-508N12.2_ENST00000439901.1_RNA			Q96JM2	ZN462_HUMAN	zinc finger protein 462	2260					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						GTCCTCTCTGCCTCTATCACAC	0.53																																					p.2259_2259del		Atlas-Indel,Pindel	.											.	ZNF462	322	.	0			c.6776_6777del						PASS	.																																			SO:0001589	frameshift_variant	58499	exon9			.	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.6777_6778delCC	chr9.hg19:g.109736499_109736500delCC	ENSP00000277225:p.Leu2260fs	84.0	0.0	0		66.0	11.0	0.166667	NM_021224	Q5T0T4|Q8N408	Frame_Shift_Del	DEL	ENST00000277225.5	hg19	CCDS35096.1																																																																																			.	.	.	none		0.53	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224		-	109736500	CC	-	109736499	7	5	93	1	0	1	0	1	0	0	0	0	17938	747	26	0	6807	0	ZNF462	9	109736499	Frame_Shift_Del	DEL	CC	TCGA-B3-A6W5-01A-12D-A33Q-10		109736499	31476932	24	5906											
SC5DL	6309	hgsc.bcm.edu	37	chr11	121174116	121174116	+	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	actccgtgttgcagattactAtttttttacaccatacgtgt	9	17	6	9	2	0	1	0	0	0	1	1	1	1	1	2	0	4	2	2	0	4	8			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr11:121174116A>T	ENST00000392789.2	+	2	269	c.32A>T	c.(31-33)tAt>tTt	p.Y11F	SC5D_ENST00000534230.1_Missense_Mutation_p.Y11F|SC5D_ENST00000264027.4_Missense_Mutation_p.Y11F	NM_001024956.2	NP_001020127.1	O75845	SC5D_HUMAN	sterol-C5-desaturase	11					cholesterol biosynthetic process (GO:0006695)|cholesterol biosynthetic process via lathosterol (GO:0033490)|fatty acid biosynthetic process (GO:0006633)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	C-5 sterol desaturase activity (GO:0000248)|iron ion binding (GO:0005506)|lathosterol oxidase activity (GO:0050046)										GCAGATTACTATTTTTTTACA	0.383																																					p.Y11F		Atlas-SNP	.											.	.	.	.	0			c.A32T						PASS	.						159	144	149					11																	121174116		2203	4299	6502	SO:0001583	missense	6309	exon2			ATTACTATTTTTT		CCDS8435.1	11q23.3	2013-03-04	2013-03-04	2013-03-04	ENSG00000109929	ENSG00000109929	1.14.21.6	"Fatty acid hydroxylase domain containing"	10547	protein-coding gene	gene with protein product	"lathosterol oxidase"	602286	"sterol-C5-desaturase (fungal ERG3, delta-5-desaturase)-like", "sterol-C5-desaturase (ERG3 delta-5-desaturase homolog, fungal)-like", "sterol-C5-desaturase (ERG3 delta-5-desaturase homolog, S. cerevisiae)-like"	SC5DL		8976377	Standard	NM_006918		Approved		uc001pxu.3	O75845	OTTHUMG00000166068	ENST00000392789.2:c.32A>T	chr11.hg19:g.121174116A>T	ENSP00000376539:p.Tyr11Phe	83.0	0.0	.		58.0	20.0	.	NM_001024956	O00119|Q6GTM5|Q9UK15	Missense_Mutation	SNP	ENST00000392789.2	hg19	CCDS8435.1	.	.	.	.	.	.	.	.	.	.	A	14.53	2.562520	0.45694	.	.	ENSG00000109929	ENST00000264027;ENST00000527762;ENST00000534230;ENST00000392789	D;D;D;D	0.86627	-1.76;-1.77;-2.15;-1.76	6.01	4.87	0.63330	.	0.112103	0.64402	D	0.000006	D	0.85440	0.5697	M	0.74881	2.28	0.32097	N	0.59109	B;P;P	0.45348	0.027;0.704;0.856	B;B;B	0.41440	0.027;0.221;0.357	D	0.85106	0.0960	10	0.27082	T	0.32	-11.9118	10.2655	0.43452	0.7368:0.0:0.0:0.2632	.	11;11;11	O75845;E9PQ91;E9PPW5	SC5D_HUMAN;.;.	F	11	ENSP00000264027:Y11F;ENSP00000436290:Y11F;ENSP00000432550:Y11F;ENSP00000376539:Y11F	ENSP00000264027:Y11F	Y	+	2	0	SC5DL	120679326	1.000000	0.71417	0.224000	0.23877	0.434000	0.31775	6.037000	0.70956	1.080000	0.41073	0.528000	0.53228	TAT	.	.	.	none		0.383	SC5D-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387702.1	NM_001024956		T	121174116	A	T	121174116	3	4	93	1	0	0	0	0	1	0	0	0	13879	449	16	5	34	5	SC5DL	11	121174116	Missense_Mutation	SNP	A	TCGA-B3-A6W5-01A-12D-A33Q-10		121174116	13832400	25	5907											
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-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	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,0,2	KRT3	65	.	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	chr12.hg19:g.53183951C>T	ENSP00000413479:p.Gly588Ser	25.0	0.0	.		36.0	4.0	.	NM_057088	A6NIS2|Q701L8	Missense_Mutation	SNP	ENST00000417996.2	hg19	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	93	1	0	0	0	0	1	0	0	0	8473	652	23	1	128	1	KRT3	12	53183951	Missense_Mutation	SNP	C	TCGA-B3-A6W5-01A-12D-A33Q-10		53183951	80667944	26	5908											
C13orf39	196541	hgsc.bcm.edu	37	chr13	103343200	103343200	+	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	ctccgtaactctctatggatTcctggatgacaatctccttt	8	15	6	12	1	2	1	0	1	2	0	6	3	4	3	3	2	1	1	3	2	3	4			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr13:103343200T>A	ENST00000267273.6	-	2	250	c.245A>T	c.(244-246)gAa>gTa	p.E82V		NM_001010977.1	NP_001010977.1	Q5VZV1	MT21C_HUMAN	methyltransferase like 21C	82					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						CTCTATGGATTCCTGGATGAC	0.463																																					p.E82V		Atlas-SNP	.											.	METTL21C	23	.	0			c.A245T						PASS	.						158	134	142					13																	103343200		2203	4300	6503	SO:0001583	missense	196541	exon2			ATGGATTCCTGGA		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.245A>T	chr13.hg19:g.103343200T>A	ENSP00000267273:p.Glu82Val	129.0	0.0	.		115.0	55.0	.	NM_001010977		Missense_Mutation	SNP	ENST00000267273.6	hg19	CCDS32003.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.898708	0.91962	.	.	ENSG00000139780	ENST00000267273	T	0.08008	3.14	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.36524	0.0970	M	0.88512	2.96	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.30090	-0.9990	10	0.66056	D	0.02	-13.0518	15.9872	0.80168	0.0:0.0:0.0:1.0	.	82	Q5VZV1	MT21C_HUMAN	V	82	ENSP00000267273:E82V	ENSP00000267273:E82V	E	-	2	0	METTL21C	102141201	1.000000	0.71417	0.632000	0.29296	0.950000	0.60333	7.423000	0.80229	2.367000	0.80283	0.528000	0.53228	GAA	.	.	.	none		0.463	METTL21C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045682.2	NM_001010977		A	103343200	T	A	103343200	3	1	93	1	0	0	0	0	1	0	0	0	1734	1783	62	5	561	5	C13orf39	13	103343200	Missense_Mutation	SNP	T	TCGA-B3-A6W5-01A-12D-A33Q-10		103343200	11826678	27	5909											
NTRK3	4916	hgsc.bcm.edu	37	chr15	88576204	88576204	+	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	cggcatccagtgacgagggcGtggtgatgccgtggttgatg	6	9	18	8	4	0	3	0	3	0	0	1	4	1	3	2	4	1	2	2	4	0	1			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr15:88576204G>T	ENST00000360948.2	-	13	1630	c.1469C>A	c.(1468-1470)aCg>aAg	p.T490K	NTRK3_ENST00000558306.1_5'UTR|NTRK3_ENST00000557856.1_Missense_Mutation_p.T482K|NTRK3_ENST00000540489.2_Missense_Mutation_p.T490K|NTRK3_ENST00000542733.2_Missense_Mutation_p.T392K|NTRK3_ENST00000558676.1_Missense_Mutation_p.T482K|NTRK3_ENST00000355254.2_Missense_Mutation_p.T490K|NTRK3_ENST00000394480.2_Missense_Mutation_p.T490K|NTRK3_ENST00000357724.2_Missense_Mutation_p.T482K|NTRK3_ENST00000317501.3_Missense_Mutation_p.T490K	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	490					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)			TGACGAGGGCGTGGTGATGCC	0.607			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)																											p.T490K		Atlas-SNP	.		Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	.	NTRK3	587	.	0			c.C1469A						PASS	.						101	63	76					15																	88576204		2201	4299	6500	SO:0001583	missense	4916	exon14			GAGGGCGTGGTGA	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.1469C>A	chr15.hg19:g.88576204G>T	ENSP00000354207:p.Thr490Lys	36.0	0.0	.		34.0	12.0	.	NM_001012338	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	hg19	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.990206	0.74589	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254;ENST00000542733;ENST00000540489;ENST00000317501	T;T;T;T;T;T;T	0.74209	-0.82;-0.78;-0.74;-0.82;-0.72;-0.05;-0.05	4.91	3.96	0.45880	.	0.049576	0.85682	D	0.000000	T	0.74245	0.3691	L	0.55213	1.73	0.58432	D	0.999999	P;P;P;D;P;D	0.55800	0.605;0.91;0.873;0.973;0.904;0.964	B;B;P;P;P;P	0.49528	0.205;0.298;0.535;0.47;0.493;0.614	T	0.76471	-0.2947	10	0.72032	D	0.01	.	11.0307	0.47772	0.0945:0.0:0.9055:0.0	.	392;482;482;490;490;490	B7Z7U4;E9PG56;B7Z4C5;Q96CY4;Q16288-3;Q16288	.;.;.;.;.;NTRK3_HUMAN	K	490;490;482;490;392;490;490	ENSP00000377990:T490K;ENSP00000354207:T490K;ENSP00000350356:T482K;ENSP00000347397:T490K;ENSP00000437773:T392K;ENSP00000444673:T490K;ENSP00000318328:T490K	ENSP00000318328:T490K	T	-	2	0	NTRK3	86377208	1.000000	0.71417	0.758000	0.31321	0.749000	0.42624	3.300000	0.51834	1.209000	0.43321	0.650000	0.86243	ACG	.	.	.	none		0.607	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				T	88576204	G	T	88576204	3	4	93	1	0	0	0	0	1	0	0	0	10715	1145	40	4	1340	4	NTRK3	15	88576204	Missense_Mutation	SNP	G	TCGA-B3-A6W5-01A-12D-A33Q-10		88576204	13955188	28	5910											
RECQL5	9400	hgsc.bcm.edu	37	chr17	73654500	73654500	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccggccagactcctggtagtAcccagccatagacttggcaa	10	7	10	14	1	0	2	0	0	0	2	1	2	1	2	5	3	2	3	5	3	4	4			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr17:73654500A>G	ENST00000317905.5	-	7	1186	c.1027T>C	c.(1027-1029)Tac>Cac	p.Y343H	RECQL5_ENST00000423245.2_Missense_Mutation_p.Y316H|RECQL5_ENST00000420326.2_Missense_Mutation_p.Y343H|RECQL5_ENST00000340830.5_Missense_Mutation_p.Y343H|RECQL5_ENST00000584999.1_Missense_Mutation_p.Y343H	NM_004259.6	NP_004250.4	O94762	RECQ5_HUMAN	RecQ protein-like 5	343	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)			TCCTGGTAGTACCCAGCCATA	0.547								Other identified genes with known or suspected DNA repair function																													p.Y343H		Atlas-SNP	.											.	RECQL5	77	.	0			c.T1027C						PASS	.						115	117	116					17																	73654500		2203	4300	6503	SO:0001583	missense	9400	exon7			GGTAGTACCCAGC	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.1027T>C	chr17.hg19:g.73654500A>G	ENSP00000317636:p.Tyr343His	68.0	0.0	.		73.0	24.0	.	NM_001003715	Q9H0B1|Q9P1W7|Q9UNC8	Missense_Mutation	SNP	ENST00000317905.5	hg19	CCDS42380.1	.	.	.	.	.	.	.	.	.	.	A	15.21	2.766636	0.49574	.	.	ENSG00000108469	ENST00000423245;ENST00000317905;ENST00000420326;ENST00000340830	T;T;T	0.80480	-1.38;-1.38;-1.38	5.84	5.84	0.93424	Helicase, C-terminal (3);	0.059843	0.64402	D	0.000001	D	0.93776	0.8010	H	0.97852	4.09	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.998	D	0.95965	0.8965	10	0.87932	D	0	-12.8087	16.2108	0.82158	1.0:0.0:0.0:0.0	.	343;316;343	O94762;Q6P4G0;O94762-3	RECQ5_HUMAN;.;.	H	343	ENSP00000317636:Y343H;ENSP00000414933:Y343H;ENSP00000341983:Y343H	ENSP00000317636:Y343H	Y	-	1	0	RECQL5	71166095	1.000000	0.71417	0.981000	0.43875	0.775000	0.43874	9.339000	0.96797	2.232000	0.73038	0.533000	0.62120	TAC	.	.	.	none		0.547	RECQL5-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448207.1	NM_004259		G	73654500	A	G	73654500	3	3	93	1	0	0	0	0	1	0	0	0	13216	391	14	3	2091	3	RECQL5	17	73654500	Missense_Mutation	SNP	A	TCGA-B3-A6W5-01A-12D-A33Q-10		73654500	7540710	29	5911											
ZNF257	113835	hgsc.bcm.edu	37	chr19	22272080	22272084	+	Frame_Shift_Del	DEL	ACTGG	ACTGG	-																															ctcaacataagataattcatActggagagaaaccctacaaa																								rs368738613		TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	ACTGG	ACTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr19:22272080_22272084delACTGG	ENST00000594947.1	+	4	1672_1676	c.1528_1532delACTGG	c.(1528-1533)actggafs	p.TG510fs		NM_033468.2	NP_258429.2	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	510					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)				GATAATTCATACTGGAGAGAAACCC	0.39																																					p.509_511del		Atlas-Indel,Pindel	.											.	ZNF257	156	.	0			c.1527_1531del						PASS	.																																			SO:0001589	frameshift_variant	113835	exon4			.	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.1528_1532delACTGG	chr19.hg19:g.22272080_22272084delACTGG	ENSP00000470209:p.Thr510fs	73.0	0.0	0		66.0	19.0	0.287879	NM_033468	B3KPS4|E9PG34|Q8NE34	Frame_Shift_Del	DEL	ENST00000594947.1	hg19	CCDS46030.1																																																																																			.	.	.	none		0.39	ZNF257-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464382.1			-	22272084	ACTGG	-	22272080	7	5	93	1	0	1	0	1	0	0	0	0	17812	391	14	0	1542	0	ZNF257	19	22272080	Frame_Shift_Del	DEL	ACTGG	TCGA-B3-A6W5-01A-12D-A33Q-10		22272080	36856903	30	5912											
CEACAM3	1084	hgsc.bcm.edu	37	chr19	42314872	42314872	+	Missense_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	ctccctccctgtccacagatGtcccctctctccactgccca	5	10	4	22	0	1	1	0	0	1	1	7	1	6	1	7	0	1	0	7	0	0	0			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr19:42314872G>A	ENST00000357396.3	+	6	871	c.630G>A	c.(628-630)atG>atA	p.M210I	CEACAM3_ENST00000221999.4_Missense_Mutation_p.V193I|CEACAM3_ENST00000344550.4_Missense_Mutation_p.V193I	NM_001815.2	NP_001806.2	P40198	CEAM3_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 3	210						integral component of membrane (GO:0016021)				endometrium(2)|kidney(4)|large_intestine(1)|lung(4)|prostate(3)|skin(4)|stomach(1)	19						GTCCACAGATGTCCCCTCTCT	0.577																																					p.M210I		Atlas-SNP	.											.	CEACAM3	37	.	0			c.G630A						PASS	.						96	83	88					19																	42314872		2203	4300	6503	SO:0001583	missense	1084	exon6			ACAGATGTCCCCT	E03349	CCDS12586.2, CCDS62685.1	19q13.2	2013-01-11			ENSG00000170956	ENSG00000170956		"CD molecules", "Immunoglobulin superfamily / V-set domain containing"	1815	protein-coding gene	gene with protein product		609142		CGM1			Standard	NM_001815		Approved	CD66d	uc002orn.2	P40198	OTTHUMG00000150142	ENST00000357396.3:c.630G>A	chr19.hg19:g.42314872G>A	ENSP00000349971:p.Met210Ile	93.0	0.0	.		48.0	19.0	.	NM_001815	G5E978|Q3KPH9	Missense_Mutation	SNP	ENST00000357396.3	hg19	CCDS12586.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.335|0.335	-0.954094|-0.954094	0.02285|0.02285	.|.	.|.	ENSG00000170956|ENSG00000170956	ENST00000357396|ENST00000221999;ENST00000344550	T|T;T	0.01113|0.01165	5.32|5.24;5.24	2.13|2.13	-4.26|-4.26	0.03755|0.03755	.|.	.|.	.|.	.|.	.|.	T|T	0.00815|0.00815	0.0027|0.0027	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	1|1	B|B	0.13594|0.31174	0.008|0.311	B|B	0.15052|0.23716	0.012|0.048	T|T	0.43718|0.43718	-0.9374|-0.9374	8|9	.|0.59425	.|D	.|0.04	.|.	1.0806|1.0806	0.01642|0.01642	0.2181:0.1802:0.4221:0.1797|0.2181:0.1802:0.4221:0.1797	.|.	210|193	P40198|G5E978	CEAM3_HUMAN|.	I|I	210|193	ENSP00000349971:M210I|ENSP00000221999:V193I;ENSP00000341725:V193I	.|ENSP00000221999:V193I	M|V	+|+	3|1	0|0	CEACAM3|CEACAM3	47006712|47006712	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-1.916000|-1.916000	0.01576|0.01576	-1.442000|-1.442000	0.01955|0.01955	-1.295000|-1.295000	0.01343|0.01343	ATG|GTC	.	.	.	none		0.577	CEACAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316509.2	NM_001815		A	42314872	G	A	42314872	3	1	93	1	0	0	0	0	1	0	0	0	3195	1377	48	2	652	2	CEACAM3	19	42314872	Missense_Mutation	SNP	G	TCGA-B3-A6W5-01A-12D-A33Q-10	20042792	42314872	16814111	31	5913											
ADAMTS1	9510	hgsc.bcm.edu	37	chr21	28213400	28213400	+	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	ggtccaggttggaaagcattGacgccatcatgtgggaatcc	10	9	13	9	1	1	1	1	1	0	0	3	3	3	3	3	4	1	2	3	4	2	2			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr21:28213400G>A	ENST00000284984.3	-	4	1749	c.1295C>T	c.(1294-1296)tCa>tTa	p.S432L		NM_006988.3	NP_008919.3	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 1	432	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)		GGAAAGCATTGACGCCATCAT	0.483																																					p.S432L		Atlas-SNP	.											.	ADAMTS1	131	.	0			c.C1295T						PASS	.						219	161	181					21																	28213400		2203	4300	6503	SO:0001583	missense	9510	exon4			AGCATTGACGCCA	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.1295C>T	chr21.hg19:g.28213400G>A	ENSP00000284984:p.Ser432Leu	109.0	0.0	.		88.0	35.0	.	NM_006988	D3DSD5|Q9NSJ8|Q9P2K0|Q9UH83|Q9UP80	Missense_Mutation	SNP	ENST00000284984.3	hg19	CCDS33524.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.767069	0.90020	.	.	ENSG00000154734	ENST00000284984;ENST00000517777	T;D	0.87179	3.86;-2.22	5.35	5.35	0.76521	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	.	.	.	.	D	0.92724	0.7687	M	0.68317	2.08	0.80722	D	1	D	0.64830	0.994	D	0.67725	0.953	D	0.92773	0.6234	9	0.87932	D	0	.	19.6142	0.95626	0.0:0.0:1.0:0.0	.	432	Q9UHI8	ATS1_HUMAN	L	432;170	ENSP00000284984:S432L;ENSP00000429557:S170L	ENSP00000284984:S432L	S	-	2	0	ADAMTS1	27135271	1.000000	0.71417	0.358000	0.25811	0.795000	0.44927	9.208000	0.95075	2.941000	0.99782	0.655000	0.94253	TCA	.	.	.	none		0.483	ADAMTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171650.2			A	28213400	G	A	28213400	3	1	93	1	0	0	0	0	1	0	0	0	255	1294	45	2	1632	2	ADAMTS1	21	28213400	Missense_Mutation	SNP	G	TCGA-B3-A6W5-01A-12D-A33Q-10		28213400	19916495	32	5914											
KCNJ15	3772	hgsc.bcm.edu	37	chr21	39671219	39671219	+	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	atcggcatgtccagcaccccCctggtgaagcacactgctgg	8	7	11	15	1	0	1	0	1	0	0	2	1	1	1	4	3	3	4	4	3	1	0			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr21:39671219C>A	ENST00000328656.4	+	4	339	c.36C>A	c.(34-36)ccC>ccA	p.P12P	KCNJ15_ENST00000398938.2_Silent_p.P12P|KCNJ15_ENST00000398934.1_Silent_p.P12P|KCNJ15_ENST00000398932.1_Silent_p.P12P|KCNJ15_ENST00000398930.1_Silent_p.P12P	NM_001276437.1|NM_001276438.1|NM_001276439.1|NM_002243.3	NP_001263366.1|NP_001263367.1|NP_001263368.1|NP_002234.2	Q99712	KCJ15_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 15	12					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	24					Yohimbine(DB01392)	CCAGCACCCCCCTGGTGAAGC	0.527																																					p.D12E		Atlas-SNP	.											.	KCNJ15	43	.	0			c.C36A						PASS	.						56	52	53					21																	39671219		2203	4300	6503	SO:0001819	synonymous_variant	3772	exon3			CACCCCCCTGGTG	Y10745	CCDS13656.1	21q22.2	2011-07-05			ENSG00000157551	ENSG00000157551		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6261	protein-coding gene	gene with protein product		602106				9299242, 8995301, 16382105	Standard	NM_170736		Approved	Kir4.2, Kir1.3, IRKK	uc002ywx.4	Q99712	OTTHUMG00000090609	ENST00000328656.4:c.36C>A	chr21.hg19:g.39671219C>A		155.0	0.0	.		116.0	39.0	.	NM_170736	D3DSH5|O00564|Q96L28|Q99446	Missense_Mutation	SNP	ENST00000328656.4	hg19	CCDS13656.1																																																																																			.	.	.	none		0.527	KCNJ15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207181.2	NM_002243		A	39671219	C	A	39671219	2	1	93	1	0	0	0	0	0	0	0	1	8056	610	22	4		4	KCNJ15	21	39671219	Silent	SNP	C	TCGA-B3-A6W5-01A-12D-A33Q-10	11457819	39671219	8458676	33	5915											
PSMG1	8624	hgsc.bcm.edu	37	chr21	40555300	40555300	+	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	ttcaccacctctccgaagaaCgtggccgccatagccgcccc	8	6	8	19	4	2	1	1	0	1	1	3	2	2	1	8	1	2	0	8	1	3	2			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr21:40555300C>T	ENST00000331573.3	-	1	477	c.12G>A	c.(10-12)acG>acA	p.T4T	PSMG1_ENST00000380900.2_Silent_p.T4T|AF129408.17_ENST00000608767.1_RNA	NM_001261824.1|NM_003720.3	NP_001248753.1|NP_003711.1	O95456	PSMG1_HUMAN	proteasome (prosome, macropain) assembly chaperone 1	4				T -> S (in Ref. 3; CAG46650). {ECO:0000305}.	cerebellar granule cell precursor proliferation (GO:0021930)|proteasome assembly (GO:0043248)|proteasome core complex assembly (GO:0080129)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(2)	8		Prostate(19;8.44e-08)				CTCCGAAGAACGTGGCCGCCA	0.721																																					p.T4T		Atlas-SNP	.											.	PSMG1	11	.	0			c.G12A						PASS	.						11	9	10					21																	40555300		2170	4244	6414	SO:0001819	synonymous_variant	8624	exon1			GAAGAACGTGGCC	AJ006291	CCDS13660.1, CCDS13661.1	21q22.3	2007-10-23	2007-10-23	2007-10-23	ENSG00000183527	ENSG00000183527			3043	protein-coding gene	gene with protein product		605296	"Down syndrome critical region gene 2"	DSCR2		10872820, 17189198	Standard	NM_003720		Approved	c21-LRP, LRPC21, PAC1	uc002yxi.4	O95456	OTTHUMG00000066034	ENST00000331573.3:c.12G>A	chr21.hg19:g.40555300C>T		24.0	0.0	.		32.0	14.0	.	NM_203433	B5BUN2|Q6FHA3|Q6FHD3|Q6S713	Silent	SNP	ENST00000331573.3	hg19	CCDS13660.1																																																																																			.	.	.	none		0.721	PSMG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141404.2	NM_003720		T	40555300	C	T	40555300	2	4	93	1	0	0	0	0	0	0	0	1	12721	523	19	1		1	PSMG1	21	40555300	Silent	SNP	C	TCGA-B3-A6W5-01A-12D-A33Q-10	884081	40555300	7574595	34	5916											
SREBF2	6721	hgsc.bcm.edu	37	chr22	42274013	42274013	+	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	ctggtaaatggtgtgattgtCctgagcgtctttgtgaagct	7	15	13	6	1	1	3	0	3	1	0	2	3	2	3	1	2	2	2	1	2	3	3			TCGA-B3-A6W5-01A-12D-A33Q-10	TCGA-B3-A6W5-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec2328b7-a0f9-49c8-b4e9-a58bbe773253	2943c0fb-d6d4-4cfb-af57-36d91e6005ba	g.chr22:42274013C>T	ENST00000361204.4	+	9	1813	c.1647C>T	c.(1645-1647)gtC>gtT	p.V549V		NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	549					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						GTGTGATTGTCCTGAGCGTCT	0.557																																					p.V549V		Atlas-SNP	.											.	SREBF2	99	.	0			c.C1647T						PASS	.						158	149	152					22																	42274013		2203	4300	6503	SO:0001819	synonymous_variant	6721	exon9			GATTGTCCTGAGC	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.1647C>T	chr22.hg19:g.42274013C>T		78.0	0.0	.		55.0	21.0	.	NM_004599	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Silent	SNP	ENST00000361204.4	hg19	CCDS14023.1																																																																																			.	.	.	none		0.557	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599		T	42274013	C	T	42274013	2	4	93	1	0	0	0	0	0	0	0	1	15154	842	30	2		2	SREBF2	22	42274013	Silent	SNP	C	TCGA-B3-A6W5-01A-12D-A33Q-10		42274013	9030553	35	5917											
MTOR	2475	hgsc.bcm.edu	37	chr1	11273603	11273603	+	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	atgatcgtgctctgaattgaGgtgttcatgacccagaattc	10	13	10	8	1	2	5	1	4	1	1	4	5	2	5	1	1	1	2	1	1	2	3			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr1:11273603G>C	ENST00000361445.4	-	21	3214	c.3138C>G	c.(3136-3138)acC>acG	p.T1046T		NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	1046					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)	TCTGAATTGAGGTGTTCATGA	0.458																																					p.T1046T		Atlas-SNP	.											.	MTOR	327	.	0			c.C3138G						PASS	.						97	98	98					1																	11273603		2203	4300	6503	SO:0001819	synonymous_variant	2475	exon21			AATTGAGGTGTTC	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.3138C>G	chr1.hg19:g.11273603G>C		129.0	0.0	.		187.0	71.0	.	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Silent	SNP	ENST00000361445.4	hg19	CCDS127.1																																																																																			.	.	.	none		0.458	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		C	11273603	G	C	11273603	2	2	94	1	0	0	0	0	0	0	0	1	9961	987	35	4		4	MTOR	1	11273603	Silent	SNP	G	TCGA-B9-4113-01A-01D-1252-08		11273603	237977018	1	5918											
UBR4	23352	hgsc.bcm.edu	37	chr1	19490300	19490300	+	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	ttcagtttttcaactacattCttctgtgacaggtatttctt	8	20	5	8	0	5	1	2	1	3	0	5	1	5	1	0	1	2	2	0	1	3	9			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr1:19490300C>G	ENST00000375254.3	-	34	4749	c.4722G>C	c.(4720-4722)aaG>aaC	p.K1574N	UBR4_ENST00000375226.2_Missense_Mutation_p.K1574N|UBR4_ENST00000375267.2_Missense_Mutation_p.K1574N|UBR4_ENST00000375217.2_Missense_Mutation_p.K1574N	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	1574					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)		CAACTACATTCTTCTGTGACA	0.403																																					p.K1574N		Atlas-SNP	.											.	UBR4	415	.	0			c.G4722C						PASS	.						191	172	178					1																	19490300		2203	4300	6503	SO:0001583	missense	23352	exon34			TACATTCTTCTGT	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.4722G>C	chr1.hg19:g.19490300C>G	ENSP00000364403:p.Lys1574Asn	214.0	0.0	.		175.0	70.0	.	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	hg19	CCDS189.1	.	.	.	.	.	.	.	.	.	.	C	18.79	3.698108	0.68386	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000417040;ENST00000419533	T;T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23;-0.15	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.73273	0.3566	L	0.39898	1.24	0.80722	D	1	D	0.57899	0.981	D	0.67231	0.95	T	0.73040	-0.4108	10	0.49607	T	0.09	.	12.9635	0.58472	0.0:0.9263:0.0:0.0737	.	1574	Q5T4S7	UBR4_HUMAN	N	1574;1574;1574;1574;284;790	ENSP00000364403:K1574N;ENSP00000364416:K1574N;ENSP00000364365:K1574N;ENSP00000364374:K1574N;ENSP00000404897:K284N	ENSP00000364365:K1574N	K	-	3	2	UBR4	19362887	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.411000	0.59781	2.674000	0.91012	0.655000	0.94253	AAG	.	.	.	none		0.403	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		G	19490300	C	G	19490300	3	3	94	1	0	0	0	0	1	0	0	0	16916	912	32	4	11121	4	UBR4	1	19490300	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	8216697	19490300	229760321	2	5919											
EPHA8	2046	hgsc.bcm.edu	37	chr1	22927186	22927186	+	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	cccatccgctggacggccccAgaggccatcgccttccgcac	6	5	10	20	4	0	1	0	0	0	1	3	2	2	2	7	3	0	2	7	3	0	1			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr1:22927186A>T	ENST00000166244.3	+	14	2493	c.2421A>T	c.(2419-2421)ccA>ccT	p.P807P		NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	807	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GGACGGCCCCAGAGGCCATCG	0.682																																					p.P807P		Atlas-SNP	.											.	EPHA8	221	.	0			c.A2421T						PASS	.						58	61	60					1																	22927186		2203	4299	6502	SO:0001819	synonymous_variant	2046	exon14			GGCCCCAGAGGCC	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.2421A>T	chr1.hg19:g.22927186A>T		249.0	0.0	.		225.0	82.0	.	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Silent	SNP	ENST00000166244.3	hg19	CCDS225.1																																																																																			.	.	.	none		0.682	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526		T	22927186	A	T	22927186	2	4	94	1	0	0	0	0	0	0	0	1	5175	175	7	5		5	EPHA8	1	22927186	Silent	SNP	A	TCGA-B9-4113-01A-01D-1252-08	3436886	22927186	226323435	3	5920											
ZMYM6	9204	hgsc.bcm.edu	37	chr1	35457962	35457962	+	Frame_Shift_Del	DEL	T	T	-																															gaagattgggaagatggaaaTttcatagcatcttcctgtgt																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr1:35457962delT	ENST00000357182.4	-	15	2246	c.2019delA	c.(2017-2019)aaafs	p.K673fs	ZMYM6_ENST00000487874.1_Frame_Shift_Del_p.K673fs|ZMYM6_ENST00000373340.2_Frame_Shift_Del_p.K673fs|ZMYM6_ENST00000493328.1_5'UTR	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6	673					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)				AAGATGGAAATTTCATAGCAT	0.383																																					p.F674fs		Atlas-INDEL	.											.	ZMYM6	110	.	0			c.2020delT						PASS	.						150	142	145					1																	35457962		2203	4300	6503	SO:0001589	frameshift_variant	9204	exon15			.	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.2019delA	chr1.hg19:g.35457962delT	ENSP00000349708:p.Lys673fs	196.0	0.0	0		165.0	54.0	0.327273	NM_007167	B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	Frame_Shift_Del	DEL	ENST00000357182.4	hg19	CCDS387.2																																																																																			.	.	.	none		0.383	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011999.1	NM_007167		-	35457962	T	-	35457962	7	5	94	1	0	1	0	1	0	0	0	0	17716	1490	52	0	1966	0	ZMYM6	1	35457962	Frame_Shift_Del	DEL	T	TCGA-B9-4113-01A-01D-1252-08	12530776	35457962	213792659	4	5921											
MCOLN3	55283	hgsc.bcm.edu	37	chr1	85487988	85487988	+	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	gtggaattccttacgttgtaCtttgcaaagaaaccgaggta	12	12	10	7	2	0	1	0	0	0	1	1	3	1	2	2	2	4	4	2	2	6	6	rs375444573		TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr1:85487988C>A	ENST00000370589.2	-	10	1243	c.1191G>T	c.(1189-1191)aaG>aaT	p.K397N	MCOLN3_ENST00000474447.1_5'UTR|MCOLN3_ENST00000341115.4_Missense_Mutation_p.K341N|WDR63_ENST00000370596.1_Intron	NM_018298.10	NP_060768.8	Q8TDD5	MCLN3_HUMAN	mucolipin 3	397					auditory receptor cell differentiation (GO:0042491)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|locomotory behavior (GO:0007626)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(6)|kidney(3)|large_intestine(9)|lung(12)|prostate(3)|skin(1)	34				all cancers(265;0.00957)|Epithelial(280;0.0254)		TTACGTTGTACTTTGCAAAGA	0.433																																					p.K397N		Atlas-SNP	.											.	MCOLN3	74	.	0			c.G1191T						PASS	.						85	78	81					1																	85487988		2203	4300	6503	SO:0001583	missense	55283	exon10			GTTGTACTTTGCA	AF475085	CCDS701.1, CCDS58009.1	1p22.3	2011-12-16			ENSG00000055732	ENSG00000055732		"Voltage-gated ion channels / Transient receptor potential cation channels"	13358	protein-coding gene	gene with protein product		607400				16382100	Standard	NM_018298		Approved	TRPML3, FLJ11006, TRP-ML3	uc001dkp.3	Q8TDD5	OTTHUMG00000009955	ENST00000370589.2:c.1191G>T	chr1.hg19:g.85487988C>A	ENSP00000359621:p.Lys397Asn	27.0	0.0	.		52.0	19.0	.	NM_018298	Q5T4H5|Q5T4H6|Q9NV09	Missense_Mutation	SNP	ENST00000370589.2	hg19	CCDS701.1	.	.	.	.	.	.	.	.	.	.	C	13.71	2.319843	0.41096	.	.	ENSG00000055732	ENST00000370589;ENST00000302814;ENST00000370588;ENST00000341115	T;T	0.69926	-0.44;-0.44	5.74	4.78	0.61160	Polycystin cation channel, PKD1/PKD2 (1);	0.088648	0.85682	D	0.000000	T	0.40645	0.1125	L	0.41710	1.295	0.48830	D	0.999718	B;B	0.27625	0.076;0.183	B;B	0.29077	0.043;0.098	T	0.42949	-0.9421	10	0.41790	T	0.15	-17.9811	9.0071	0.36117	0.0:0.7676:0.0:0.2324	.	341;397	Q8TDD5-2;Q8TDD5	.;MCLN3_HUMAN	N	397;397;341;341	ENSP00000359621:K397N;ENSP00000342698:K341N	ENSP00000304843:K397N	K	-	3	2	MCOLN3	85260576	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	1.405000	0.34635	1.307000	0.44944	0.655000	0.94253	AAG	.	.	.	none		0.433	MCOLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027569.2	NM_018298		A	85487988	C	A	85487988	3	1	94	1	0	0	0	0	1	0	0	0	9404	564	20	4	486	4	MCOLN3	1	85487988	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	50030026	85487988	163762633	5	5922											
CD46	4179	hgsc.bcm.edu	37	chr1	207940508	207940508	+	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	tgtctgtgacagtaacagtaCttgggatcccccagttccaa	10	11	9	11	0	1	1	0	1	1	0	3	2	3	2	3	1	2	3	3	1	3	4			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr1:207940508C>A	ENST00000358170.2	+	6	980	c.824C>A	c.(823-825)aCt>aAt	p.T275N	CD46_ENST00000361067.1_Missense_Mutation_p.T275N|CD46_ENST00000354848.1_Missense_Mutation_p.T275N|CD46_ENST00000322875.4_Missense_Mutation_p.T275N|CD46_ENST00000322918.5_Missense_Mutation_p.T275N|CD46_ENST00000469535.1_3'UTR|CD46_ENST00000367042.1_Missense_Mutation_p.T275N|CD46_ENST00000441839.2_Missense_Mutation_p.T275N|CD46_ENST00000480003.1_Missense_Mutation_p.T275N|CD46_ENST00000367047.1_Missense_Mutation_p.T212N|CD46_ENST00000360212.2_Missense_Mutation_p.T275N|CD46_ENST00000367041.1_Missense_Mutation_p.T275N|CD46_ENST00000357714.1_Missense_Mutation_p.T275N	NM_002389.4	NP_002380.3	P15529	MCP_HUMAN	CD46 molecule, complement regulatory protein	275	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adaptive immune response (GO:0002250)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|interleukin-10 production (GO:0032613)|negative regulation of complement activation (GO:0045916)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transforming growth factor beta production (GO:0071636)|proteolysis (GO:0006508)|regulation of complement activation (GO:0030449)|regulation of Notch signaling pathway (GO:0008593)|sequestering of extracellular ligand from receptor (GO:0035581)|single fertilization (GO:0007338)|T cell mediated immunity (GO:0002456)|viral process (GO:0016032)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|inner acrosomal membrane (GO:0002079)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cadherin binding (GO:0045296)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	19						AGTAACAGTACTTGGGATCCC	0.358																																					p.T275N		Atlas-SNP	.											.	CD46	34	.	0			c.C824A						PASS	.						110	105	107					1																	207940508		2203	4300	6503	SO:0001583	missense	4179	exon6			ACAGTACTTGGGA	BC030594	CCDS1479.1, CCDS1480.1, CCDS1481.1, CCDS1482.1, CCDS1484.1, CCDS1485.1, CCDS31008.1, CCDS31009.1	1q32	2014-09-17	2006-03-28	2006-02-09	ENSG00000117335	ENSG00000117335		"CD molecules", "Complement system"	6953	protein-coding gene	gene with protein product		120920	"antigen identified by monoclonal antibody TRA-2-10", "membrane cofactor protein (CD46, trophoblast-lymphocyte cross-reactive antigen)", "CD46 antigen, complement regulatory protein"	MIC10, MCP		7929741	Standard	NM_002389		Approved	TRA2.10, MGC26544, TLX	uc001hgj.3	P15529	OTTHUMG00000036397	ENST00000358170.2:c.824C>A	chr1.hg19:g.207940508C>A	ENSP00000350893:p.Thr275Asn	80.0	0.0	.		60.0	23.0	.	NM_172352	A0T1T0|A0T1T1|A0T1T2|Q15429|Q53GV9|Q5HY94|Q5VWS6|Q5VWS7|Q5VWS8|Q5VWS9|Q5VWT0|Q5VWT1|Q5VWT2|Q6N0A1|Q7Z3R5|Q9NNW2|Q9NNW3|Q9NNW4|Q9UCJ4	Missense_Mutation	SNP	ENST00000358170.2	hg19	CCDS1485.1	.	.	.	.	.	.	.	.	.	.	C	16.51	3.142222	0.57044	.	.	ENSG00000117335	ENST00000358170;ENST00000354848;ENST00000322918;ENST00000367042;ENST00000367041;ENST00000357714;ENST00000322875;ENST00000367047;ENST00000441839;ENST00000361067;ENST00000360212;ENST00000480003	T;T;T;T;T;T;T;T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18	5.05	-4.14	0.03892	Complement control module (2);Sushi/SCR/CCP (3);	1.003600	0.08033	N	0.993895	T	0.68815	0.3042	M	0.69463	2.115	0.09310	N	1	P;B;D;P;B;D;B;D;P;P;P;D;D;D	0.63880	0.582;0.253;0.993;0.582;0.253;0.969;0.395;0.979;0.582;0.836;0.582;0.961;0.961;0.975	B;B;P;B;B;D;B;P;B;B;B;D;D;D	0.75020	0.2;0.141;0.869;0.2;0.141;0.974;0.227;0.831;0.2;0.32;0.2;0.961;0.961;0.985	T	0.60647	-0.7222	10	0.72032	D	0.01	.	1.9531	0.03370	0.4968:0.2102:0.1229:0.1701	.	275;275;275;275;275;275;275;275;275;275;275;275;275;275	P15529-4;P15529-5;P15529-14;P15529-3;P15529-12;P15529-13;P15529-2;P15529-11;P15529-7;P15529-9;P15529-15;P15529-6;P15529-8;P15529	.;.;.;.;.;.;.;.;.;.;.;.;.;MCP_HUMAN	N	275;275;275;275;275;275;275;212;275;275;275;275	ENSP00000350893:T275N;ENSP00000346912:T275N;ENSP00000314664:T275N;ENSP00000356009:T275N;ENSP00000356008:T275N;ENSP00000350346:T275N;ENSP00000313875:T275N;ENSP00000356014:T212N;ENSP00000413543:T275N;ENSP00000354358:T275N;ENSP00000353342:T275N;ENSP00000418471:T275N	ENSP00000313875:T275N	T	+	2	0	CD46	206007131	0.000000	0.05858	0.000000	0.03702	0.077000	0.17291	-0.614000	0.05604	-0.469000	0.06911	0.655000	0.94253	ACT	.	.	.	none		0.358	CD46-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000088588.3	NM_172361		A	207940508	C	A	207940508	3	1	94	1	0	0	0	0	1	0	0	0	3020	565	20	4	846	4	CD46	1	207940508	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	122452520	207940508	41310113	6	5923											
RBM34	23029	hgsc.bcm.edu	37	chr1	235318245	235318245	+	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	caacaaacacagttctctcaTtctttaatctctcttcttct	10	17	1	13	0	7	0	1	0	6	0	9	0	7	0	0	0	2	1	0	0	3	6			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr1:235318245T>A	ENST00000408888.3	-	4	778	c.548A>T	c.(547-549)aAt>aTt	p.N183I	RBM34_ENST00000366606.3_Missense_Mutation_p.N178I			P42696	RBM34_HUMAN	RNA binding motif protein 34	183						nucleolus (GO:0005730)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)	1	Ovarian(103;0.0398)	all_cancers(173;0.177)|Prostate(94;0.0166)	OV - Ovarian serous cystadenocarcinoma(106;5.43e-05)|Epithelial(3;0.000121)			AGTTCTCTCATTCTTTAATCT	0.328																																					p.N183I		Atlas-SNP	.											.	RBM34	41	.	0			c.A548T						PASS	.						159	139	145					1																	235318245		1826	4086	5912	SO:0001583	missense	23029	exon4			CTCTCATTCTTTA		CCDS41477.1, CCDS41477.2	1q42.3	2013-02-12			ENSG00000188739	ENSG00000188739		"RNA binding motif (RRM) containing"	28965	protein-coding gene	gene with protein product						7788527, 15134903	Standard	NM_015014		Approved	KIAA0117	uc001hwn.3	P42696	OTTHUMG00000039620	ENST00000408888.3:c.548A>T	chr1.hg19:g.235318245T>A	ENSP00000386226:p.Asn183Ile	288.0	0.0	.		266.0	90.0	.	NM_001161533	A8K8J7|Q8N2Z8|Q9H5A1	Missense_Mutation	SNP	ENST00000408888.3	hg19	CCDS41477.2	.	.	.	.	.	.	.	.	.	.	T	18.53	3.643590	0.67244	.	.	ENSG00000188739	ENST00000408888;ENST00000366606;ENST00000447801	T;T;T	0.75154	-0.91;-0.91;0.96	5.87	5.87	0.94306	Nucleotide-binding, alpha-beta plait (1);	0.236119	0.48767	D	0.000162	D	0.85225	0.5648	M	0.76328	2.33	0.80722	D	1	D;B	0.89917	1.0;0.431	D;B	0.81914	0.995;0.186	D	0.85305	0.1075	10	0.45353	T	0.12	-17.2719	14.8054	0.69952	0.0:0.0:0.0:1.0	.	183;183	P42696-2;P42696	.;RBM34_HUMAN	I	183;178;181	ENSP00000386226:N183I;ENSP00000355565:N178I;ENSP00000400000:N181I	ENSP00000355565:N178I	N	-	2	0	RBM34	233384868	0.999000	0.42202	0.998000	0.56505	0.918000	0.54935	4.345000	0.59360	2.371000	0.80710	0.533000	0.62120	AAT	.	.	.	none		0.328	RBM34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100146.1	NM_015014		A	235318245	T	A	235318245	3	1	94	1	0	0	0	0	1	0	0	0	13144	1493	52	5	797	5	RBM34	1	235318245	Missense_Mutation	SNP	T	TCGA-B9-4113-01A-01D-1252-08	27377737	235318245	13932376	7	5924											
HADHA	3030	hgsc.bcm.edu	37	chr2	26459821	26459821	+	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	atttcattcataacttctgaGaactctgaatgtagctcttt	11	17	5	8	0	5	2	2	2	3	1	5	3	5	2	0	0	3	2	0	0	4	6			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr2:26459821G>C	ENST00000380649.3	-	4	345	c.216C>G	c.(214-216)ttC>ttG	p.F72L	HADHA_ENST00000461025.1_5'Flank|HADHA_ENST00000457468.2_Intron	NM_000182.4	NP_000173.2	P40939	ECHA_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit	72					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acetyltransferase activity (GO:0003985)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)			autonomic_ganglia(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(4)|skin(1)	30	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TAACTTCTGAGAACTCTGAAT	0.403																																					p.F72L		Atlas-SNP	.											.	HADHA	87	.	0			c.C216G						PASS	.						102	99	100					2																	26459821		2203	4300	6503	SO:0001583	missense	3030	exon4			TTCTGAGAACTCT	D16480	CCDS1721.1	2p23	2014-09-17	2010-04-30		ENSG00000084754	ENSG00000084754	1.1.1.211, 4.2.1.17		4801	protein-coding gene	gene with protein product	"gastrin-binding protein", "long-chain-3-hydroxyacyl-CoA dehydrogenase", "long-chain 2-enoyl-CoA hydratase", "mitochondrial trifunctional protein, alpha subunit"	600890	"hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit"			9605857, 7918661	Standard	NM_000182		Approved	GBP, LCEH, LCHAD, MTPA	uc002rgy.3	P40939	OTTHUMG00000096979	ENST00000380649.3:c.216C>G	chr2.hg19:g.26459821G>C	ENSP00000370023:p.Phe72Leu	180.0	0.0	.		246.0	82.0	.	NM_000182	B2R7L4|B4DYP2|Q16679|Q53T69|Q53TA2|Q96GT7|Q9UQC5	Missense_Mutation	SNP	ENST00000380649.3	hg19	CCDS1721.1	.	.	.	.	.	.	.	.	.	.	G	5.697	0.313101	0.10789	.	.	ENSG00000084754	ENST00000380649	T	0.57907	0.37	5.78	1.36	0.22044	Crotonase, core (1);	0.277100	0.45126	N	0.000390	T	0.26011	0.0634	N	0.12831	0.26	0.80722	D	1	B	0.02656	0.0	B	0.11329	0.006	T	0.07790	-1.0754	10	0.07990	T	0.79	-24.6945	7.1425	0.25564	0.2509:0.1413:0.6078:0.0	.	72	P40939	ECHA_HUMAN	L	72	ENSP00000370023:F72L	ENSP00000370023:F72L	F	-	3	2	HADHA	26313325	0.026000	0.19158	0.266000	0.24541	0.047000	0.14425	0.239000	0.18023	0.351000	0.24027	0.591000	0.81541	TTC	.	.	.	none		0.403	HADHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214051.1	NM_000182		C	26459821	G	C	26459821	3	2	94	1	0	0	0	0	1	0	0	0	6950	933	33	4	2143	4	HADHA	2	26459821	Missense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08		26459821	216739552	8	5925											
GTF3C2	2976	hgsc.bcm.edu	37	chr2	27565919	27565920	+	Frame_Shift_Ins	INS	-	-	TGGCCTTT																															gatggaggattaggctgttgINSgggccttttggggccttttc																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr2:27565919_27565920insTGGCCTTT	ENST00000359541.2	-	3	771_772	c.342_343insAAAGGCCA	c.(340-345)ccccaafs	p.Q115fs	GTF3C2_ENST00000264720.3_Frame_Shift_Ins_p.Q115fs|AC109828.1_ENST00000588707.1_RNA|AC109828.1_ENST00000590383.1_RNA|AC109828.1_ENST00000589232.1_RNA|AC109828.1_ENST00000589853.1_RNA			Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide 2, beta 110kDa	115					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)				central_nervous_system(4)|endometrium(6)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	38	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTAGGCTGTTGGGGCCTTTTGG	0.535																																					p.P115fs		Atlas-INDEL	.											GTF3C2,NS,malignant_melanoma,0,1	GTF3C2	73	.	0			c.343_344insAAAGGCCA						PASS	.																																			SO:0001589	frameshift_variant	2976	exon3			.	D13636	CCDS1749.1	2p23.3	2013-01-10	2002-08-29		ENSG00000115207	ENSG00000115207		"General transcription factors", "WD repeat domain containing"	4665	protein-coding gene	gene with protein product		604883	"general transcription factor IIIC, polypeptide 2 (beta subunit, 110kD)"			7729686	Standard	NM_001521		Approved	KIAA0011, TFIIIC110	uc002rjw.2	Q8WUA4	OTTHUMG00000097785	ENST00000359541.2:c.342_343insAAAGGCCA	chr2.hg19:g.27565919_27565920insTGGCCTTT	ENSP00000352536:p.Gln115fs	332.0	0.0	0		225.0	28.0	0.124444	NM_001035521	D6W557|Q16632|Q9BWI7	Frame_Shift_Ins	INS	ENST00000359541.2	hg19	CCDS1749.1																																																																																			.	.	.	none		0.535	GTF3C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215028.2			TGGCCTTT	27565920	-	TGGCCTTT	27565919	7	5	94	1	0	1	1	0	0	0	0	0	6880	1357	47	0	2460	0	GTF3C2	2	27565919	Frame_Shift_Ins	INS	-	TCGA-B9-4113-01A-01D-1252-08	1106098	27565919	215633454	9	5926	65	3									
GTF3C2	2976	hgsc.bcm.edu	37	chr2	27565920	27565920	+	Silent	SNP	G	G	T																															gatggaggattaggctgttgGggccttttggggccttttcg																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr2:27565920G>T	ENST00000359541.2	-	3	771	c.342C>A	c.(340-342)ccC>ccA	p.P114P	GTF3C2_ENST00000264720.3_Silent_p.P114P|AC109828.1_ENST00000588707.1_RNA|AC109828.1_ENST00000590383.1_RNA|AC109828.1_ENST00000589232.1_RNA|AC109828.1_ENST00000589853.1_RNA			Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide 2, beta 110kDa	114					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)				central_nervous_system(4)|endometrium(6)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	38	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TAGGCTGTTGGGGCCTTTTGG	0.537																																					p.V114V		Atlas-SNP	.											.	GTF3C2	73	.	0			c.T342A						PASS	.						94	89	91					2																	27565920		2203	4300	6503	SO:0001819	synonymous_variant	2976	exon4			CTGTTGGGGCCTT	D13636	CCDS1749.1	2p23.3	2013-01-10	2002-08-29		ENSG00000115207	ENSG00000115207		"General transcription factors", "WD repeat domain containing"	4665	protein-coding gene	gene with protein product		604883	"general transcription factor IIIC, polypeptide 2 (beta subunit, 110kD)"			7729686	Standard	NM_001521		Approved	KIAA0011, TFIIIC110	uc002rjw.2	Q8WUA4	OTTHUMG00000097785	ENST00000359541.2:c.342C>A	chr2.hg19:g.27565920G>T		331.0	1.0	.		227.0	78.0	.	NM_001521	D6W557|Q16632|Q9BWI7	Silent	SNP	ENST00000359541.2	hg19	CCDS1749.1																																																																																			.	.	.	none		0.537	GTF3C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215028.2			T	27565920	G	T	27565920	2	4	94	1	0	0	0	0	0	0	0	1	6880	1219	43	4		4	GTF3C2	2	27565920	Silent	SNP	G	TCGA-B9-4113-01A-01D-1252-08	1	27565920	215633453	10	5927	65	3									
GTF3C2	2976	hgsc.bcm.edu	37	chr2	27565929	27565930	+	Frame_Shift_Del	DEL	GG	GG	-																															ttaggctgttggggccttttGgggccttttcgtgtcctacc																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr2:27565929_27565930delGG	ENST00000359541.2	-	3	761_762	c.332_333delCC	c.(331-333)cccfs	p.P111fs	GTF3C2_ENST00000264720.3_Frame_Shift_Del_p.P111fs|AC109828.1_ENST00000588707.1_RNA|AC109828.1_ENST00000590383.1_RNA|AC109828.1_ENST00000589232.1_RNA|AC109828.1_ENST00000589853.1_RNA			Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide 2, beta 110kDa	111					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)				central_nervous_system(4)|endometrium(6)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	38	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGGGCCTTTTGGGGCCTTTTCG	0.525																																					p.111_112del		Atlas-INDEL	.											GTF3C2,NS,carcinoma,0,1	GTF3C2	73	.	0			c.333_334del						PASS	.																																			SO:0001589	frameshift_variant	2976	exon3			.	D13636	CCDS1749.1	2p23.3	2013-01-10	2002-08-29		ENSG00000115207	ENSG00000115207		"General transcription factors", "WD repeat domain containing"	4665	protein-coding gene	gene with protein product		604883	"general transcription factor IIIC, polypeptide 2 (beta subunit, 110kD)"			7729686	Standard	NM_001521		Approved	KIAA0011, TFIIIC110	uc002rjw.2	Q8WUA4	OTTHUMG00000097785	ENST00000359541.2:c.332_333delCC	chr2.hg19:g.27565931_27565932delGG	ENSP00000352536:p.Pro111fs	316.0	0.0	0		232.0	15.0	0.0646552	NM_001035521	D6W557|Q16632|Q9BWI7	Frame_Shift_Del	DEL	ENST00000359541.2	hg19	CCDS1749.1																																																																																			.	.	.	none		0.525	GTF3C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215028.2			-	27565930	GG	-	27565929	7	5	94	1	0	1	0	1	0	0	0	0	6880	1335	47	0	2470	0	GTF3C2	2	27565929	Frame_Shift_Del	DEL	GG	TCGA-B9-4113-01A-01D-1252-08	9	27565929	215633444	11	5928	65	3									
HAAO	23498	hgsc.bcm.edu	37	chr2	42994588	42994588	+	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	gcaagagggtcaccccagggGcttcttgcaggcagggtcct	7	7	15	12	0	2	1	1	0	1	1	3	1	3	1	3	5	1	4	3	5	1	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr2:42994588G>C	ENST00000294973.6	-	10	905	c.850C>G	c.(850-852)Ccc>Gcc	p.P284A		NM_012205.2	NP_036337.2			3-hydroxyanthranilate 3,4-dioxygenase											breast(2)|cervix(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|urinary_tract(2)	11						CACCCCAGGGGCTTCTTGCAG	0.617																																					p.P284A		Atlas-SNP	.											.	HAAO	26	.	0			c.C850G						PASS	.						38	38	38					2																	42994588		2203	4300	6503	SO:0001583	missense	23498	exon10			CCAGGGGCTTCTT	Z29481	CCDS33187.1	2p	2008-02-05			ENSG00000162882	ENSG00000162882	1.13.11.6		4796	protein-coding gene	gene with protein product		604521				7514594	Standard	NM_012205		Approved		uc002rst.4	P46952	OTTHUMG00000152348	ENST00000294973.6:c.850C>G	chr2.hg19:g.42994588G>C	ENSP00000294973:p.Pro284Ala	61.0	0.0	.		67.0	11.0	.	NM_012205		Missense_Mutation	SNP	ENST00000294973.6	hg19	CCDS33187.1	.	.	.	.	.	.	.	.	.	.	g	10.57	1.385999	0.25031	.	.	ENSG00000162882	ENST00000294973	T	0.30182	1.54	4.83	1.94	0.25998	.	0.156970	0.42682	N	0.000678	T	0.24275	0.0588	L	0.55743	1.74	0.45791	D	0.998671	B	0.06786	0.001	B	0.01281	0.0	T	0.06320	-1.0833	10	0.44086	T	0.13	.	5.3274	0.15915	0.1974:0.1834:0.6193:0.0	.	284	P46952	3HAO_HUMAN	A	284	ENSP00000294973:P284A	ENSP00000294973:P284A	P	-	1	0	HAAO	42848092	0.924000	0.31332	0.996000	0.52242	0.700000	0.40528	1.053000	0.30442	0.449000	0.26747	0.550000	0.68814	CCC	.	.	.	none		0.617	HAAO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325948.2			C	42994588	G	C	42994588	3	2	94	1	0	0	0	0	1	0	0	0	6944	1203	42	4	14	4	HAAO	2	42994588	Missense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08	15428659	42994588	200204785	12	5929											
BIN1	274	hgsc.bcm.edu	37	chr2	127818193	127818193	+	Intron	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	tgttcttctttctgcgcagcCgcgaaaacagtttacttttc	7	16	7	11	3	3	0	0	0	3	0	4	1	3	0	1	0	4	3	1	0	3	7	rs117721706	byFrequency	TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr2:127818193C>G	ENST00000316724.5	-	11	1269				BIN1_ENST00000466111.1_Intron|BIN1_ENST00000346226.3_Intron|BIN1_ENST00000348750.4_Intron|BIN1_ENST00000393041.3_Intron|BIN1_ENST00000259238.4_Missense_Mutation_p.R263P|BIN1_ENST00000357970.3_Intron|BIN1_ENST00000352848.3_Missense_Mutation_p.R263P|BIN1_ENST00000393040.3_Intron|BIN1_ENST00000376113.2_Missense_Mutation_p.R263P|BIN1_ENST00000351659.3_Intron|BIN1_ENST00000409400.1_Intron	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1						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)		TCTGCGCAGCCGCGAAAACAG	0.632																																					p.R263P		Atlas-SNP	.											.	BIN1	85	.	0			c.G788C						PASS	.						120	112	114					2																	127818193		2203	4300	6503	SO:0001627	intron_variant	274	exon10			CGCAGCCGCGAAA	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.858-1462G>C	chr2.hg19:g.127818193C>G		183.0	0.0	.		143.0	47.0	.	NM_139346	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Missense_Mutation	SNP	ENST00000316724.5	hg19	CCDS2138.1	.	.	.	.	.	.	.	.	.	.	C	17.43	3.387780	0.61956	.	.	ENSG00000136717	ENST00000376113;ENST00000259238;ENST00000352848	T;T;T	0.56611	0.45;0.47;0.53	4.72	4.72	0.59763	.	.	.	.	.	T	0.68559	0.3014	.	.	.	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.998	D;D;D	0.75484	0.986;0.986;0.986	T	0.66031	-0.6024	8	0.29301	T	0.29	.	14.976	0.71273	0.0:1.0:0.0:0.0	.	263;263;263	O00499-8;O00499-11;O00499-10	.;.;.	P	263	ENSP00000365281:R263P;ENSP00000259238:R263P;ENSP00000315284:R263P	ENSP00000259238:R263P	R	-	2	0	BIN1	127534663	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.415000	0.52700	2.337000	0.79520	0.561000	0.74099	CGG	.	C|0.992;T|0.008	.	alt		0.632	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343		G	127818193	C	G	127818193	1	3	94	0	1	0	0	0	0	0	0	0	1432	652	23	4		4	BIN1	2	127818193	Intron	SNP	C	TCGA-B9-4113-01A-01D-1252-08	84823605	127818193	115381180	13	5930											
XRCC5	7520	hgsc.bcm.edu	37	chr2	216981563	216981564	+	Frame_Shift_Ins	INS	-	-	C																															ccaggttctcaacaggctgaINSctgtatcctttttctgccag																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr2:216981563_216981564insC	ENST00000392133.3	+	5	778_779	c.317_318insC	c.(316-321)gacttcfs	p.F107fs	XRCC5_ENST00000392132.2_Frame_Shift_Ins_p.F107fs			P13010	XRCC5_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)	107					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)		CAACAGGCTGACTGTATCCTTT	0.421								Non-homologous end-joining																													p.D106fs		Atlas-INDEL	.											.	XRCC5	64	.	0			c.317_318insC						PASS	.																																			SO:0001589	frameshift_variant	7520	exon3			.	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.318dupC	chr2.hg19:g.216981564_216981564dupC	ENSP00000375978:p.Phe107fs	96.0	0.0	0		75.0	24.0	0.32	NM_021141	A8K3X5|Q0Z7V0|Q4VBQ5|Q53HH7|Q7M4N0|Q9UCQ0|Q9UCQ1	Frame_Shift_Ins	INS	ENST00000392133.3	hg19	CCDS2402.1																																																																																			.	.	.	none		0.421	XRCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256675.3	NM_021141		C	216981564	-	C	216981563	7	5	94	1	0	1	1	0	0	0	0	0	17468	275	10	0	327	0	XRCC5	2	216981563	Frame_Shift_Ins	INS	-	TCGA-B9-4113-01A-01D-1252-08	89163370	216981563	26217810	14	5931											
TRNT1	51095	hgsc.bcm.edu	37	chr3	3189651	3189651	+	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	gaagtaccaaggagagcactGtctcctaaaggaaatgcagc	15	6	11	9	0	1	1	0	0	1	1	2	4	1	2	2	2	4	3	2	2	6	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr3:3189651G>C	ENST00000251607.6	+	8	1220	c.1118G>C	c.(1117-1119)tGt>tCt	p.C373S	TRNT1_ENST00000280591.6_Missense_Mutation_p.C353S	NM_182916.2	NP_886552	Q96Q11	TRNT1_HUMAN	tRNA nucleotidyl transferase, CCA-adding, 1	373					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)		GGAGAGCACTGTCTCCTAAAG	0.438																																					p.C373S		Atlas-SNP	.											.	TRNT1	34	.	0			c.G1118C						PASS	.						118	110	113					3																	3189651		2203	4300	6503	SO:0001583	missense	51095	exon8			AGCACTGTCTCCT	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.1118G>C	chr3.hg19:g.3189651G>C	ENSP00000251607:p.Cys373Ser	38.0	0.0	.		20.0	8.0	.	NM_182916	A8K2Z6|B7WP13|C9JKA2|Q8ND57|Q9BS97|Q9Y362	Missense_Mutation	SNP	ENST00000251607.6	hg19	CCDS2561.2	.	.	.	.	.	.	.	.	.	.	G	9.399	1.077394	0.20227	.	.	ENSG00000072756	ENST00000251607;ENST00000280591	T;T	0.39229	1.09;1.11	5.24	2.0	0.26442	.	1.262890	0.05220	N	0.508422	T	0.22085	0.0532	N	0.08118	0	0.09310	N	0.999992	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.19910	-1.0291	10	0.17832	T	0.49	-3.7877	5.7122	0.17941	0.1687:0.3466:0.4847:0.0	.	353;373	Q96Q11-2;Q96Q11	.;TRNT1_HUMAN	S	373;353	ENSP00000251607:C373S;ENSP00000280591:C353S	ENSP00000251607:C373S	C	+	2	0	TRNT1	3164651	0.026000	0.19158	0.010000	0.14722	0.971000	0.66376	2.269000	0.43346	1.168000	0.42723	0.655000	0.94253	TGT	.	.	.	none		0.438	TRNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337616.1			C	3189651	G	C	3189651	3	2	94	1	0	0	0	0	1	0	0	0	16585	1377	48	4	1144	4	TRNT1	3	3189651	Missense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08		3189651	194832779	15	5932											
OSBPL10	114884	hgsc.bcm.edu	37	chr3	31774841	31774841	+	Missense_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	ggctgatggcaaagagccaaGtgtcccatttttcagctgct	9	11	11	10	0	1	2	1	1	0	1	2	2	2	2	2	2	3	4	2	2	2	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr3:31774841G>A	ENST00000396556.2	-	6	1125	c.1003C>T	c.(1003-1005)Ctt>Ttt	p.L335F	OSBPL10_ENST00000467647.1_5'UTR|OSBPL10_ENST00000438237.2_Missense_Mutation_p.L271F	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	335					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)		AAAGAGCCAAGTGTCCCATTT	0.473																																					p.L335F		Atlas-SNP	.											.	OSBPL10	160	.	0			c.C1003T						PASS	.						166	156	159					3																	31774841		2203	4300	6503	SO:0001583	missense	114884	exon6			AGCCAAGTGTCCC	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.1003C>T	chr3.hg19:g.31774841G>A	ENSP00000379804:p.Leu335Phe	318.0	0.0	.		285.0	80.0	.	NM_017784	B4E212|Q9BTU5	Missense_Mutation	SNP	ENST00000396556.2	hg19	CCDS2651.1	.	.	.	.	.	.	.	.	.	.	G	13.60	2.285363	0.40394	.	.	ENSG00000144645	ENST00000396556;ENST00000438237;ENST00000428241	T;T;T	0.52983	1.87;2.22;0.64	5.66	2.21	0.28008	.	0.326770	0.33075	N	0.005319	T	0.41328	0.1154	M	0.68952	2.095	0.45076	D	0.998091	B;B;B	0.19445	0.036;0.005;0.001	B;B;B	0.15870	0.014;0.005;0.005	T	0.30621	-0.9972	10	0.52906	T	0.07	-1.9596	6.3688	0.21469	0.2078:0.138:0.6542:0.0	.	271;335;103	B4E212;Q9BXB5;Q59ED9	.;OSB10_HUMAN;.	F	335;271;143	ENSP00000379804:L335F;ENSP00000406124:L271F;ENSP00000399200:L143F	ENSP00000379804:L335F	L	-	1	0	OSBPL10	31749845	0.602000	0.26916	0.675000	0.29917	0.982000	0.71751	0.776000	0.26704	0.470000	0.27294	0.555000	0.69702	CTT	.	.	.	none		0.473	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2			A	31774841	G	A	31774841	3	1	94	1	0	0	0	0	1	0	0	0	11282	1029	36	2	1319	2	OSBPL10	3	31774841	Missense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08	28585190	31774841	166247589	16	5933											
ATR	545	hgsc.bcm.edu	37	chr3	142274792	142274792	+	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	cagacagaagcttttagttgAgaagatgaacattcatgttg	14	12	10	5	0	1	5	1	2	0	4	1	6	1	5	0	0	2	3	0	0	4	5			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr3:142274792A>T	ENST00000350721.4	-	10	2389	c.2268T>A	c.(2266-2268)tcT>tcA	p.S756S	ATR_ENST00000383101.3_Silent_p.S692S	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	756					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						CTTTTAGTTGAGAAGATGAAC	0.368								Other conserved DNA damage response genes																													p.S756S		Atlas-SNP	.											.	ATR	285	.	0			c.T2268A						PASS	.						118	119	119					3																	142274792		2203	4300	6503	SO:0001819	synonymous_variant	545	exon10			TAGTTGAGAAGAT	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.2268T>A	chr3.hg19:g.142274792A>T		178.0	0.0	.		128.0	42.0	.	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Silent	SNP	ENST00000350721.4	hg19	CCDS3124.1																																																																																			.	.	.	none		0.368	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		T	142274792	A	T	142274792	2	4	94	1	0	0	0	0	0	0	0	1	1204	291	11	5		5	ATR	3	142274792	Silent	SNP	A	TCGA-B9-4113-01A-01D-1252-08	110499951	142274792	55747638	17	5934											
SLC26A1	10861	hgsc.bcm.edu	37	chr4	985220	985220	+	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	gctgcagcccggccagcaatGagtaggcgatggcctgcggc	7	5	16	13	3	0	1	0	1	0	0	0	2	0	1	3	4	4	4	3	4	2	1			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr4:985220G>A	ENST00000361661.2	-	3	649	c.272C>T	c.(271-273)tCa>tTa	p.S91L	SLC26A1_ENST00000513138.1_5'Flank|SLC26A1_ENST00000398520.2_Missense_Mutation_p.S91L|IDUA_ENST00000247933.4_Intron|SLC26A1_ENST00000398516.2_Missense_Mutation_p.S91L|IDUA_ENST00000453894.1_Intron	NM_213613.2	NP_998778.1	Q9H2B4	S26A1_HUMAN	solute carrier family 26 (anion exchanger), member 1	91					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|chloride transport (GO:0006821)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|oxalate transport (GO:0019532)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|chloride transmembrane transporter activity (GO:0015108)|oxalate transmembrane transporter activity (GO:0019531)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(1)|endometrium(4)|pancreas(1)|prostate(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GGCCAGCAATGAGTAGGCGAT	0.632																																					p.S91L		Atlas-SNP	.											.	SLC26A1	44	.	0			c.C272T						PASS	.						105	99	101					4																	985220		2203	4300	6503	SO:0001583	missense	10861	exon2			AGCAATGAGTAGG	AF297659	CCDS33933.1, CCDS33934.1	4p16.3	2013-07-18	2013-07-18		ENSG00000145217	ENSG00000145217		"Solute carriers"	10993	protein-coding gene	gene with protein product		610130	"solute carrier family 26 (sulfate transporter), member 1"				Standard	NM_213613		Approved	SAT-1, EDM4	uc003gcc.3	Q9H2B4	OTTHUMG00000160003	ENST00000361661.2:c.272C>T	chr4.hg19:g.985220G>A	ENSP00000354721:p.Ser91Leu	257.0	0.0	.		228.0	82.0	.	NM_022042	A8K9N2|Q7Z5R3|Q96BK0	Missense_Mutation	SNP	ENST00000361661.2	hg19	CCDS33934.1	.	.	.	.	.	.	.	.	.	.	G	18.15	3.559905	0.65538	.	.	ENSG00000145217	ENST00000398520;ENST00000361661;ENST00000398516	D;D;D	0.92495	-3.05;-3.05;-3.05	5.18	5.18	0.71444	.	0.226096	0.46758	D	0.000276	D	0.96993	0.9018	M	0.93763	3.455	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.72338	0.977;0.969	D	0.98001	1.0360	10	0.87932	D	0	.	16.1549	0.81657	0.0:0.0:1.0:0.0	.	91;91	Q9H2B4;Q96BK0	S26A1_HUMAN;.	L	91	ENSP00000381532:S91L;ENSP00000354721:S91L;ENSP00000381528:S91L	ENSP00000354721:S91L	S	-	2	0	SLC26A1	975220	0.998000	0.40836	0.985000	0.45067	0.336000	0.28762	2.673000	0.46858	2.402000	0.81655	0.313000	0.20887	TCA	.	.	.	none		0.632	SLC26A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358783.1	NM_022042, NM_134425		A	985220	G	A	985220	3	1	94	1	0	0	0	0	1	0	0	0	14527	1294	45	2	1944	2	SLC26A1	4	985220	Missense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08		985220	190169056	18	5935											
ACOX3	8310	hgsc.bcm.edu	37	chr4	8417674	8417674	+	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	tctccaaggacagatcggctCcaggggaacgagcgaaaaga	14	4	13	10	3	1	2	0	0	1	2	4	6	2	4	2	4	2	1	2	4	4	0			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr4:8417674C>T	ENST00000356406.5	-	3	274	c.197G>A	c.(196-198)gGa>gAa	p.G66E	ACOX3_ENST00000413009.2_Missense_Mutation_p.G66E|ACOX3_ENST00000503233.1_Missense_Mutation_p.G66E	NM_003501.2	NP_003492.2	O15254	ACOX3_HUMAN	acyl-CoA oxidase 3, pristanoyl	66					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(17)|prostate(1)|skin(3)|stomach(1)	42						CAGATCGGCTCCAGGGGAACG	0.483																																					p.G66E		Atlas-SNP	.											.	ACOX3	70	.	0			c.G197A						PASS	.						71	67	68					4																	8417674		2203	4300	6503	SO:0001583	missense	8310	exon3			TCGGCTCCAGGGG	Y11411	CCDS3401.1, CCDS47017.1	4p15.3	2010-04-30	2010-04-30		ENSG00000087008	ENSG00000087008	1.3.3.6		121	protein-coding gene	gene with protein product		603402	"acyl-Coenzyme A oxidase 3, pristanoyl"			9271077	Standard	NM_003501		Approved		uc003glc.4	O15254	OTTHUMG00000090509	ENST00000356406.5:c.197G>A	chr4.hg19:g.8417674C>T	ENSP00000348775:p.Gly66Glu	231.0	0.0	.		197.0	74.0	.	NM_001101667	Q96AJ8	Missense_Mutation	SNP	ENST00000356406.5	hg19	CCDS3401.1	.	.	.	.	.	.	.	.	.	.	C	9.453	1.091143	0.20471	.	.	ENSG00000087008	ENST00000413009;ENST00000356406;ENST00000503233	T;T;T	0.41758	0.99;0.99;0.99	5.39	-0.535	0.11879	Acyl-CoA dehydrogenase/oxidase (1);	0.611319	0.16430	N	0.214753	T	0.21509	0.0518	L	0.31664	0.95	0.38700	D	0.952962	B;B	0.16166	0.016;0.01	B;B	0.17433	0.018;0.005	T	0.33007	-0.9885	10	0.02654	T	1	-6.3195	6.2369	0.20768	0.0:0.5193:0.1203:0.3604	.	66;66	O15254-2;O15254	.;ACOX3_HUMAN	E	66	ENSP00000413994:G66E;ENSP00000348775:G66E;ENSP00000421625:G66E	ENSP00000348775:G66E	G	-	2	0	ACOX3	8468574	0.730000	0.28100	0.000000	0.03702	0.001000	0.01503	1.878000	0.39608	-0.212000	0.10109	-0.145000	0.13849	GGA	.	.	.	none		0.483	ACOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206997.4			T	8417674	C	T	8417674	3	4	94	1	0	0	0	0	1	0	0	0	160	855	30	2	1969	2	ACOX3	4	8417674	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	7432454	8417674	182736602	19	5936											
AASDH	132949	hgsc.bcm.edu	37	chr4	57248668	57248668	+	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	tttgttttttttcaacaaggAtatactttagattacatttt	11	22	4	4	0	1	1	1	0	0	1	1	2	1	2	0	1	3	1	0	1	6	12			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr4:57248668A>T	ENST00000205214.6	-	3	506	c.326T>A	c.(325-327)aTc>aAc	p.I109N	AASDH_ENST00000451613.1_Missense_Mutation_p.I109N|AASDH_ENST00000434343.2_5'UTR|AASDH_ENST00000513376.1_Missense_Mutation_p.I9N|AASDH_ENST00000502617.1_Missense_Mutation_p.I109N|AASDH_ENST00000510762.1_Intron|AASDH_ENST00000602986.1_Intron	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	109					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				TTCAACAAGGATATACTTTAG	0.323																																					p.I109N		Atlas-SNP	.											.	AASDH	101	.	0			c.T326A						PASS	.						47	48	48					4																	57248668		2203	4300	6503	SO:0001583	missense	132949	exon3			ACAAGGATATACT	AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"Acyl-CoA synthetase family"	23993	protein-coding gene	gene with protein product	"acyl-CoA synthetase family member 4"	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.326T>A	chr4.hg19:g.57248668A>T	ENSP00000205214:p.Ile109Asn	72.0	0.0	.		45.0	16.0	.	NM_181806	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Missense_Mutation	SNP	ENST00000205214.6	hg19	CCDS3504.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.611899	0.87258	.	.	ENSG00000157426	ENST00000205214;ENST00000513376;ENST00000451613;ENST00000502617	T;T;T;T	0.66638	0.83;-0.22;0.83;0.83	5.88	5.88	0.94601	AMP-dependent synthetase/ligase (1);	0.289492	0.43919	D	0.000514	T	0.81093	0.4751	M	0.78049	2.395	0.25673	N	0.985874	D;D;D;D	0.65815	0.989;0.991;0.995;0.991	P;D;P;P	0.63957	0.87;0.92;0.902;0.873	T	0.76408	-0.2970	10	0.87932	D	0	-4.2072	15.9439	0.79779	1.0:0.0:0.0:0.0	.	109;109;109;109	Q4L235-4;B4E2K0;Q4L235-3;Q4L235	.;.;.;ACSF4_HUMAN	N	109;9;109;109	ENSP00000205214:I109N;ENSP00000423760:I9N;ENSP00000409656:I109N;ENSP00000421171:I109N	ENSP00000205214:I109N	I	-	2	0	AASDH	56943425	1.000000	0.71417	0.864000	0.33941	0.979000	0.70002	6.594000	0.74104	2.250000	0.74265	0.533000	0.62120	ATC	.	.	.	none		0.323	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806		T	57248668	A	T	57248668	3	4	94	1	0	0	0	0	1	0	0	0	22	333	12	5	3022	5	AASDH	4	57248668	Missense_Mutation	SNP	A	TCGA-B9-4113-01A-01D-1252-08	48830994	57248668	133905608	20	5937											
ABCG2	9429	hgsc.bcm.edu	37	chr4	89039327	89039327	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cataagtcttcctgaggccaAtaaggtgaggctatcaaaca	14	9	9	9	0	2	2	1	2	1	0	3	2	3	2	2	3	1	1	2	3	5	4			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr4:89039327A>G	ENST00000237612.3	-	7	1320	c.775T>C	c.(775-777)Ttg>Ctg	p.L259L	ABCG2_ENST00000515655.1_Silent_p.L259L	NM_004827.2	NP_004818.2	Q9UNQ0	ABCG2_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 2 (Junior blood group)	259	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular iron ion homeostasis (GO:0006879)|drug export (GO:0046618)|drug transmembrane transport (GO:0006855)|embryonic process involved in female pregnancy (GO:0060136)|heme transport (GO:0015886)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(13)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Afatinib(DB08916)|Apixaban(DB06605)|Buprenorphine(DB00921)|Cabazitaxel(DB06772)|Carboplatin(DB00958)|Cisplatin(DB00515)|Cladribine(DB00242)|Clofarabine(DB00631)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gefitinib(DB00317)|Glyburide(DB01016)|Hesperetin(DB01094)|Hydrocortisone(DB00741)|Imatinib(DB00619)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Methotrexate(DB00563)|Mitoxantrone(DB01204)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Nilotinib(DB04868)|Nitrofurantoin(DB00698)|Novobiocin(DB01051)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Prazosin(DB00457)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Teniposide(DB00444)|Teriflunomide(DB08880)|Testosterone(DB00624)|Topotecan(DB01030)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vincristine(DB00541)|Vismodegib(DB08828)|Zafirlukast(DB00549)|Zidovudine(DB00495)	CCTGAGGCCAATAAGGTGAGG	0.433																																					p.L259L		Atlas-SNP	.											.	ABCG2	151	.	0			c.T775C						PASS	.						127	115	119					4																	89039327		2203	4300	6503	SO:0001819	synonymous_variant	9429	exon7			AGGCCAATAAGGT	AF103796	CCDS3628.1, CCDS58910.1	4q22.1	2014-08-27	2014-08-27		ENSG00000118777	ENSG00000118777		"CD molecules", "ATP binding cassette transporters / subfamily G"	74	protein-coding gene	gene with protein product		603756	"ATP-binding cassette, sub-family G (WHITE), member 2"			8894702, 9861027	Standard	NM_001257386		Approved	EST157481, MXR, BCRP, ABCP, CD338	uc003hrg.3	Q9UNQ0	OTTHUMG00000130601	ENST00000237612.3:c.775T>C	chr4.hg19:g.89039327A>G		99.0	0.0	.		86.0	32.0	.	NM_004827	A0A1W3|A8K1T5|O95374|Q4W5I3|Q53ZQ1|Q569L4|Q5YLG4|Q86V64|Q8IX16|Q96LD6|Q96TA8|Q9BY73|Q9NUS0	Silent	SNP	ENST00000237612.3	hg19	CCDS3628.1																																																																																			.	.	.	none		0.433	ABCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253051.1	NM_004827		G	89039327	A	G	89039327	2	3	94	1	0	0	0	0	0	0	0	1	69	98	4	3		3	ABCG2	4	89039327	Silent	SNP	A	TCGA-B9-4113-01A-01D-1252-08	31790659	89039327	102114949	21	5938											
NDST4	64579	hgsc.bcm.edu	37	chr4	115767018	115767018	+	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	ctgtctgaggggtcaatgagGatggtgatgatcttggcttt	7	14	15	5	0	3	4	1	4	2	0	3	5	3	5	0	5	0	1	0	5	1	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr4:115767018G>A	ENST00000264363.2	-	10	2754	c.2076C>T	c.(2074-2076)atC>atT	p.I692I		NM_022569.1	NP_072091.1	Q9H3R1	NDST4_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 4	692	Heparan sulfate N-sulfotransferase 4.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(43)|ovary(1)|prostate(7)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	81		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)		GGTCAATGAGGATGGTGATGA	0.433																																					p.I692I		Atlas-SNP	.											.	NDST4	193	.	0			c.C2076T						PASS	.						135	126	129					4																	115767018		2203	4300	6503	SO:0001819	synonymous_variant	64579	exon10			AATGAGGATGGTG	AB036429	CCDS3706.1	4q26	2008-02-05			ENSG00000138653	ENSG00000138653		"Sulfotransferases, membrane-bound"	20779	protein-coding gene	gene with protein product		615039				11087757	Standard	NM_022569		Approved		uc003ibu.3	Q9H3R1	OTTHUMG00000132916	ENST00000264363.2:c.2076C>T	chr4.hg19:g.115767018G>A		135.0	0.0	.		128.0	51.0	.	NM_022569	Q2KHM8	Silent	SNP	ENST00000264363.2	hg19	CCDS3706.1																																																																																			.	.	.	none		0.433	NDST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256427.1	NM_022569		A	115767018	G	A	115767018	2	1	94	1	0	0	0	0	0	0	0	1	10265	1164	41	2		2	NDST4	4	115767018	Silent	SNP	G	TCGA-B9-4113-01A-01D-1252-08	26727691	115767018	75387258	22	5939											
ASB5	140458	hgsc.bcm.edu	37	chr4	177136796	177136796	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtaacgttggcagctggagTtgtgggataaggtgcaatct	10	11	15	5	1	1	0	0	0	1	0	1	2	1	2	0	4	3	6	0	4	3	4			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr4:177136796T>C	ENST00000296525.3	-	7	1058	c.945A>G	c.(943-945)caA>caG	p.Q315Q	ASB5_ENST00000512254.1_Silent_p.Q262Q	NM_080874.3	NP_543150.1	Q8WWX0	ASB5_HUMAN	ankyrin repeat and SOCS box containing 5	315	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					endometrium(2)|kidney(1)|large_intestine(9)|lung(18)|prostate(2)|skin(2)	34		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.13e-20)|Epithelial(43;9.94e-18)|OV - Ovarian serous cystadenocarcinoma(60;2e-09)|GBM - Glioblastoma multiforme(59;0.000254)|STAD - Stomach adenocarcinoma(60;0.000653)|LUSC - Lung squamous cell carcinoma(193;0.0393)		GCAGCTGGAGTTGTGGGATAA	0.368																																					p.Q315Q		Atlas-SNP	.											.	ASB5	88	.	0			c.A945G						PASS	.						119	109	113					4																	177136796		2203	4300	6503	SO:0001819	synonymous_variant	140458	exon7			CTGGAGTTGTGGG	AY057053	CCDS3827.1	4q34.1	2013-01-10	2011-01-25		ENSG00000164122	ENSG00000164122		"Ankyrin repeat domain containing"	17180	protein-coding gene	gene with protein product		615050	"ankyrin repeat and SOCS box-containing 5"				Standard	NM_080874		Approved		uc003iuq.2	Q8WWX0	OTTHUMG00000160793	ENST00000296525.3:c.945A>G	chr4.hg19:g.177136796T>C		68.0	0.0	.		56.0	16.0	.	NM_080874	Q8N7B5	Silent	SNP	ENST00000296525.3	hg19	CCDS3827.1																																																																																			.	.	.	none		0.368	ASB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362344.1			C	177136796	T	C	177136796	2	2	94	1	0	0	0	0	0	0	0	1	1026	1722	60	3		3	ASB5	4	177136796	Silent	SNP	T	TCGA-B9-4113-01A-01D-1252-08	61369778	177136796	14017480	23	5940											
FAM149A	25854	hgsc.bcm.edu	37	chr4	187077186	187077186	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttgaacaaaaaccagctcAgcccggtaggaaatggcgca	14	6	10	11	2	2	1	1	1	1	0	2	2	2	2	2	3	4	3	2	3	5	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr4:187077186A>G	ENST00000356371.5	+	7	1289	c.1289A>G	c.(1288-1290)cAg>cGg	p.Q430R	FAM149A_ENST00000503432.1_Missense_Mutation_p.Q139R|FAM149A_ENST00000514829.1_3'UTR|FAM149A_ENST00000502970.1_Missense_Mutation_p.Q139R|FAM149A_ENST00000227065.4_Missense_Mutation_p.Q139R|FAM149A_ENST00000514153.1_Missense_Mutation_p.Q139R|FAM149A_ENST00000389354.5_Missense_Mutation_p.Q139R			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	430										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)		AAACCAGCTCAGCCCGGTAGG	0.433																																					p.Q139R		Atlas-SNP	.											.	FAM149A	52	.	0			c.A416G						PASS	.						103	96	98					4																	187077186		2203	4300	6503	SO:0001583	missense	25854	exon6			CAGCTCAGCCCGG	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.1289A>G	chr4.hg19:g.187077186A>G	ENSP00000348732:p.Gln430Arg	132.0	0.0	.		114.0	41.0	.	NM_001006655	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	Missense_Mutation	SNP	ENST00000356371.5	hg19		.	.	.	.	.	.	.	.	.	.	A	8.579	0.881917	0.17467	.	.	ENSG00000109794	ENST00000503432;ENST00000356371;ENST00000227065;ENST00000502970;ENST00000514153;ENST00000389354	T;T;T;T;T;T	0.11169	2.81;2.8;2.81;2.81;2.81;2.81	5.46	-10.9	0.00192	.	1.583490	0.03252	N	0.182041	T	0.03263	0.0095	N	0.08118	0	0.09310	N	1	B;B;B	0.09022	0.001;0.002;0.001	B;B;B	0.08055	0.002;0.003;0.001	T	0.34004	-0.9846	10	0.12766	T	0.61	0.1667	2.1131	0.03708	0.3:0.2092:0.3344:0.1565	.	430;430;139	A5PLN7-3;A5PLN7;B4DHZ9	.;F149A_HUMAN;.	R	139;430;139;139;139;139	ENSP00000426835:Q139R;ENSP00000348732:Q430R;ENSP00000227065:Q139R;ENSP00000427155:Q139R;ENSP00000424380:Q139R;ENSP00000374005:Q139R	ENSP00000227065:Q139R	Q	+	2	0	FAM149A	187314180	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.206000	0.03011	-1.534000	0.01743	-0.343000	0.07986	CAG	.	.	.	none		0.433	FAM149A-201	KNOWN	basic	protein_coding	protein_coding		NM_001006655		G	187077186	A	G	187077186	3	3	94	1	0	0	0	0	1	0	0	0	5459	188	7	3	430	3	FAM149A	4	187077186	Missense_Mutation	SNP	A	TCGA-B9-4113-01A-01D-1252-08	9940390	187077186	4077090	24	5941											
LIFR	3977	hgsc.bcm.edu	37	chr5	38504185	38504185	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttaacagctgttgaattaaTatccttcactttgaatgaag	13	16	6	6	0	1	3	1	3	0	0	2	3	2	3	1	0	2	2	1	0	6	7			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr5:38504185T>C	ENST00000263409.4	-	10	1492	c.1330A>G	c.(1330-1332)Att>Gtt	p.I444V	LIFR_ENST00000453190.2_Missense_Mutation_p.I444V|LIFR_ENST00000503088.1_5'UTR	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	444	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)					GTTGAATTAATATCCTTCACT	0.269			T	PLAG1	salivary adenoma																																p.I444V	Melanoma(13;4 730 6426 9861 34751)	Atlas-SNP	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	.	LIFR	348	.	0			c.A1330G						PASS	.						54	59	58					5																	38504185		2201	4295	6496	SO:0001583	missense	3977	exon10			AATTAATATCCTT	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.1330A>G	chr5.hg19:g.38504185T>C	ENSP00000263409:p.Ile444Val	66.0	0.0	.		57.0	18.0	.	NM_002310	Q6LCD9	Missense_Mutation	SNP	ENST00000263409.4	hg19	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	T	3.712	-0.059335	0.07317	.	.	ENSG00000113594	ENST00000263409;ENST00000453190	T;T	0.56103	0.48;0.48	5.65	-2.44	0.06502	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.807977	0.11218	N	0.587055	T	0.34164	0.0888	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30534	-0.9975	10	0.11794	T	0.64	-5.8891	11.1796	0.48620	0.0:0.4564:0.0:0.5436	.	444	P42702	LIFR_HUMAN	V	444	ENSP00000263409:I444V;ENSP00000398368:I444V	ENSP00000263409:I444V	I	-	1	0	LIFR	38539942	0.638000	0.27225	0.525000	0.27900	0.996000	0.88848	0.083000	0.14871	-0.426000	0.07360	0.528000	0.53228	ATT	.	.	.	none		0.269	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310		C	38504185	T	C	38504185	3	2	94	1	0	0	0	0	1	0	0	0	8787	1406	49	3	2007	3	LIFR	5	38504185	Missense_Mutation	SNP	T	TCGA-B9-4113-01A-01D-1252-08		38504185	142411075	25	5942											
PCDHGA4	56111	hgsc.bcm.edu	37	chr5	140735217	140735218	+	Frame_Shift_Ins	INS	-	-	G																															aaaatgaaaatcctggggcaINSagatttcctcttcctgaagc																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr5:140735217_140735218insG	ENST00000571252.1	+	1	450_451	c.450_451insG	c.(451-453)agafs	p.R151fs	PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	151	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)			ATCCTGGGGCAAGATTTCCTCT	0.45																																					p.A150fs		Atlas-INDEL	.											.	PCDHGA4	150	.	0			c.450_451insG						PASS	.																																			SO:0001589	frameshift_variant	56111	exon1			.	AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		Exception_encountered	chr5.hg19:g.140735217_140735218insG	ENSP00000458570:p.Arg151fs	110.0	0.0	0		77.0	22.0	0.285714	NM_032053	Q9Y5D3	Frame_Shift_Ins	INS	ENST00000571252.1	hg19	CCDS58979.1																																																																																			.	.	.	none		0.45	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917		G	140735218	-	G	140735217	7	5	94	1	0	1	1	0	0	0	0	0	11563	117	5	0	452	0	PCDHGA4	5	140735217	Frame_Shift_Ins	INS	-	TCGA-B9-4113-01A-01D-1252-08	102231032	140735217	40180043	26	5943											
SLC36A3	285641	hgsc.bcm.edu	37	chr5	150660717	150660717	+	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	gtgaagaagatgccgatagaGtacatcagcttgactgactg	13	9	12	7	1	1	6	1	3	0	3	1	7	1	6	1	0	3	2	1	0	4	3			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr5:150660717G>T	ENST00000335230.3	-	9	1413	c.1002C>A	c.(1000-1002)taC>taA	p.Y334*	SLC36A3_ENST00000377713.3_Nonsense_Mutation_p.Y375*	NM_181774.3	NP_861439.3	Q495N2	S36A3_HUMAN	solute carrier family 36, member 3	334						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	21		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGCCGATAGAGTACATCAGCT	0.522																																					p.Y375X		Atlas-SNP	.											.	SLC36A3	54	.	0			c.C1125A						PASS	.						222	171	188					5																	150660717		2203	4300	6503	SO:0001587	stop_gained	285641	exon10			GATAGAGTACATC	AY162215	CCDS4314.1, CCDS47316.1	5q33.1	2013-07-17	2013-07-17		ENSG00000186334	ENSG00000186334		"Solute carriers"	19659	protein-coding gene	gene with protein product		608332				12809675	Standard	NM_181774		Approved	PAT3, TRAMD2, tramdorin2	uc003ltw.2	Q495N2	OTTHUMG00000130128	ENST00000335230.3:c.1002C>A	chr5.hg19:g.150660717G>T	ENSP00000334750:p.Tyr334*	186.0	0.0	.		198.0	75.0	.	NM_001145017	Q495N3|Q6ZMU7|Q6ZRU4|Q7Z6B4	Nonsense_Mutation	SNP	ENST00000335230.3	hg19	CCDS4314.1	.	.	.	.	.	.	.	.	.	.	G	39	7.569738	0.98365	.	.	ENSG00000186334	ENST00000335230;ENST00000377713	.	.	.	4.06	1.12	0.20585	.	0.196500	0.45361	D	0.000367	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-21.071	7.6369	0.28272	0.4739:0.0:0.5261:0.0	.	.	.	.	X	334;375	.	ENSP00000334750:Y334X	Y	-	3	2	SLC36A3	150640910	1.000000	0.71417	0.967000	0.41034	0.964000	0.63967	1.720000	0.38022	0.092000	0.17331	0.561000	0.74099	TAC	.	.	.	none		0.522	SLC36A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252436.1	NM_181774		T	150660717	G	T	150660717	4	4	94	1	0	0	0	0	0	1	0	0	14608	1024	36	4	418	4	SLC36A3	5	150660717	Nonsense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08	9925500	150660717	30254543	27	5944											
RGS14	10636	hgsc.bcm.edu	37	chr5	176797996	176797996	+	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	ctgcagcccattctggagaaGcacggcttgagcccgctaga	9	7	12	13	2	1	3	0	1	1	2	1	4	1	3	2	2	4	4	2	2	2	3			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr5:176797996G>T	ENST00000408923.3	+	11	1406	c.1218G>T	c.(1216-1218)aaG>aaT	p.K406N		NM_006480.4	NP_006471.2	O43566	RGS14_HUMAN	regulator of G-protein signaling 14	406	Necessary for interaction with RABGEF1. {ECO:0000250}.|RBD 2. {ECO:0000255|PROSITE- ProRule:PRU00262}.				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)			TTCTGGAGAAGCACGGCTTGA	0.751																																					p.K406N	NSCLC(47;353 1896 28036)	Atlas-SNP	.											.	RGS14	34	.	0			c.G1218T						PASS	.						10	12	11					5																	176797996		1750	3841	5591	SO:0001583	missense	10636	exon11			GGAGAAGCACGGC	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.1218G>T	chr5.hg19:g.176797996G>T	ENSP00000386229:p.Lys406Asn	72.0	0.0	.		49.0	16.0	.	NM_006480	O43565|Q506M1|Q6ZWA4|Q8TD62	Missense_Mutation	SNP	ENST00000408923.3	hg19	CCDS43405.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.43|13.43	2.234827|2.234827	0.39498|0.39498	.|.	.|.	ENSG00000169220|ENSG00000169220	ENST00000408923;ENST00000336477|ENST00000511890	T|.	0.63417|.	-0.04|.	4.96|4.96	2.0|2.0	0.26442|0.26442	Raf-like Ras-binding (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.61060|0.61060	0.2317|0.2317	M|M	0.71206|0.71206	2.165|2.165	0.42256|0.42256	D|D	0.991993|0.991993	D;D;D|.	0.89917|.	1.0;1.0;0.995|.	D;D;D|.	0.97110|.	1.0;0.999;0.951|.	T|T	0.57940|0.57940	-0.7724|-0.7724	10|5	0.87932|.	D|.	0|.	-28.6256|-28.6256	5.8726|5.8726	0.18812|0.18812	0.3015:0.0:0.5635:0.135|0.3015:0.0:0.5635:0.135	.|.	177;254;406|.	B3KUX0;O43566-5;O43566|.	.;.;RGS14_HUMAN|.	N|I	406;187|277	ENSP00000386229:K406N|.	ENSP00000336864:K187N|.	K|S	+|+	3|2	2|0	RGS14|RGS14	176730602|176730602	1.000000|1.000000	0.71417|0.71417	0.972000|0.972000	0.41901|0.41901	0.033000|0.033000	0.12548|0.12548	1.059000|1.059000	0.30517|0.30517	0.704000|0.704000	0.31869|0.31869	-0.225000|-0.225000	0.12378|0.12378	AAG|AGC	.	.	.	none		0.751	RGS14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372676.1	NM_006480		T	176797996	G	T	176797996	3	4	94	1	0	0	0	0	1	0	0	0	13310	962	34	4	1260	4	RGS14	5	176797996	Missense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08	26137279	176797996	4117264	28	5945											
OR11A1	26531	hgsc.bcm.edu	37	chr6	29395381	29395381	+	Missense_Mutation	SNP	T	T	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	agaagccaaggaggacaaatTcagtaatagtttcgtttcct	14	11	9	7	1	1	1	1	0	0	1	3	3	2	3	2	2	1	3	2	2	5	5			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr6:29395381T>G	ENST00000377149.1	-	5	510	c.38A>C	c.(37-39)gAa>gCa	p.E13A	OR11A1_ENST00000377148.1_Missense_Mutation_p.E13A|OR5V1_ENST00000377154.1_Intron|OR11A1_ENST00000377147.2_Missense_Mutation_p.E13A			Q9GZK7	O11A1_HUMAN	olfactory receptor, family 11, subfamily A, member 1	13						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|large_intestine(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	19						GAGGACAAATTCAGTAATAGT	0.398																																					p.E13A		Atlas-SNP	.											.	OR11A1	30	.	0			c.A38C						PASS	.						67	65	66					6																	29395381		1509	2709	4218	SO:0001583	missense	26531	exon1			ACAAATTCAGTAA		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.38A>C	chr6.hg19:g.29395381T>G	ENSP00000366354:p.Glu13Ala	130.0	0.0	.		98.0	34.0	.	NM_013937	A2BF33|A6NFQ3|B0S7T2|Q5ST16|Q9GZK8	Missense_Mutation	SNP	ENST00000377149.1	hg19	CCDS34363.1	.	.	.	.	.	.	.	.	.	.	T	16.42	3.118839	0.56505	.	.	ENSG00000204694	ENST00000377148;ENST00000377149;ENST00000377147	T;T;T	0.01119	5.31;5.31;5.31	3.66	2.48	0.30137	.	0.000000	0.33290	U	0.005076	T	0.00998	0.0033	M	0.88512	2.96	0.09310	N	1	P	0.34977	0.478	B	0.38327	0.271	T	0.41928	-0.9481	10	0.54805	T	0.06	-0.4728	5.5487	0.17079	0.0:0.2499:0.0:0.7501	.	13	Q9GZK7	O11A1_HUMAN	A	13	ENSP00000366353:E13A;ENSP00000366354:E13A;ENSP00000366352:E13A	ENSP00000366352:E13A	E	-	2	0	OR11A1	29503360	0.004000	0.15560	0.093000	0.20910	0.716000	0.41182	0.571000	0.23669	0.465000	0.27167	0.327000	0.21459	GAA	.	.	.	none		0.398	OR11A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000193778.1			G	29395381	T	G	29395381	3	3	94	1	0	0	0	0	1	0	0	0	10931	1783	62	5	913	5	OR11A1	6	29395381	Missense_Mutation	SNP	T	TCGA-B9-4113-01A-01D-1252-08		29395381	141719686	29	5946											
HECA	51696	hgsc.bcm.edu	37	chr6	139495590	139495590	+	Frame_Shift_Del	DEL	A	A	-																															ttcacaagatcatctgcatcAagtgtaagtcacggtgggat																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr6:139495590delA	ENST00000367658.2	+	3	1666	c.1381delA	c.(1381-1383)aagfs	p.K461fs	RP1-225E12.2_ENST00000588638.1_RNA|RP1-225E12.2_ENST00000587577.1_RNA|RP1-225E12.2_ENST00000588529.1_RNA|RP1-225E12.3_ENST00000585874.1_RNA|RP1-225E12.2_ENST00000586266.1_RNA|RP1-225E12.2_ENST00000591102.1_RNA|RP1-225E12.2_ENST00000415194.2_RNA|RP1-225E12.2_ENST00000585447.1_RNA|RP1-225E12.2_ENST00000590679.1_RNA|RP1-225E12.2_ENST00000589192.1_RNA|RP1-225E12.2_ENST00000590219.1_RNA|RP1-225E12.2_ENST00000586229.1_RNA	NM_016217.2	NP_057301.1	Q9UBI9	HDC_HUMAN	headcase homolog (Drosophila)	461					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)		CATCTGCATCAAGTGTAAGTC	0.547																																					p.I460fs		Atlas-INDEL	.											.	HECA	45	.	0			c.1380delC						PASS	.						234	198	210					6																	139495590		2203	4300	6503	SO:0001589	frameshift_variant	51696	exon3			.	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.1381delA	chr6.hg19:g.139495590delA	ENSP00000356630:p.Lys461fs	156.0	0.0	0		180.0	59.0	0.327778	NM_016217		Frame_Shift_Del	DEL	ENST00000367658.2	hg19	CCDS5194.1																																																																																			.	.	.	none		0.547	HECA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042456.1	NM_016217		-	139495590	A	-	139495590	7	5	94	1	0	1	0	1	0	0	0	0	7045	131	5	0	1391	0	HECA	6	139495590	Frame_Shift_Del	DEL	A	TCGA-B9-4113-01A-01D-1252-08	110100209	139495590	31619477	30	5947											
SEPT7	989	hgsc.bcm.edu	37	chr7	35912377	35912377	+	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	gcagtggataatagtaattgGtaagaagggtttgtcctcac	12	12	12	5	0	1	1	1	0	0	1	2	2	2	2	1	3	0	4	1	3	5	6			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr7:35912377G>A	ENST00000435235.1	+	4	650		c.e4+1		SEPT7_ENST00000475109.1_Splice_Site|SEPT7_ENST00000399035.3_Splice_Site|SEPT7_ENST00000494488.2_Splice_Site|SEPT7_ENST00000469679.2_Splice_Site|SEPT7_ENST00000350320.6_Splice_Site|SEPT7_ENST00000399034.2_Splice_Site			Q16181	SEPT7_HUMAN	septin 7						cilium morphogenesis (GO:0060271)|cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein heterooligomerization (GO:0051291)|regulation of embryonic cell shape (GO:0016476)	actin cytoskeleton (GO:0015629)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|septin complex (GO:0031105)|stress fiber (GO:0001725)	GTP binding (GO:0005525)|identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)	14						ATAGTAATTGGTAAGAAGGGT	0.388																																					.		Atlas-SNP	.											.	SEPT7	24	.	0			c.374+1G>A						PASS	.						134	127	129					7																	35912377		1851	4091	5942	SO:0001630	splice_region_variant	989	exon4			TAATTGGTAAGAA	S72008	CCDS75582.1	7p14.2	2013-01-21	2005-01-11	2005-01-12	ENSG00000122545	ENSG00000122545		"Septins"	1717	protein-coding gene	gene with protein product		603151	"CDC10 cell division cycle 10 homolog (S. cerevisiae)"	CDC10		8037772	Standard	NM_001788		Approved	CDC3, SEPT7A	uc011kau.2	Q16181	OTTHUMG00000155063	ENST00000435235.1:c.218+1G>A	chr7.hg19:g.35912377G>A		34.0	0.0	.		35.0	13.0	.	NM_001011553	Q52M76|Q6NX50	Splice_Site	SNP	ENST00000435235.1	hg19		.	.	.	.	.	.	.	.	.	.	g	24.0	4.477060	0.84640	.	.	ENSG00000122545	ENST00000435235;ENST00000399034;ENST00000350320;ENST00000469679;ENST00000399035;ENST00000537785;ENST00000493670;ENST00000494488	.	.	.	4.7	4.7	0.59300	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.0851	0.89455	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SEPT7	35878902	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.695000	0.98691	2.338000	0.79540	0.574000	0.79327	.	.	.	.	none		0.388	SEPT7-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000338285.1	NM_001788	Intron	A	35912377	G	A	35912377	5	1	94	1	0	0	0	0	0	0	1	0	14082	1275	44	2	390	2	SEPT7	7	35912377	Splice_Site	SNP	G	TCGA-B9-4113-01A-01D-1252-08		35912377	123226286	31	5948											
PRKRIP1	79706	hgsc.bcm.edu	37	chr7	102040095	102040096	+	Splice_Site	DNP	GG	GG	AA																															atggatgccatggctgagaaGgtcagtgagccagaaggctg																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr7:102040095_102040096GG>AA	ENST00000496391.1	+	7	1616	c.306_306GG>AA	c.(304-306)aaGG>aaAAg	p.K102K	PRKRIP1_ENST00000482465.1_3'UTR|PRKRIP1_ENST00000354783.4_Splice_Site_p.K64K|PRKRIP1_ENST00000462601.1_Splice_Site_p.K45K|PRKRIP1_ENST00000397912.3_Splice_Site_p.K102K			Q9H875	PKRI1_HUMAN	PRKR interacting protein 1 (IL11 inducible)	102	Required for RNA-binding. {ECO:0000250}.				negative regulation of phosphorylation (GO:0042326)|negative regulation of protein kinase activity (GO:0006469)|renal system process (GO:0003014)	extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	double-stranded RNA binding (GO:0003725)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)			endometrium(1)|lung(4)|ovary(1)	6						TGGCTGAGAAGGTCAGTGAGCC	0.554																																					p.K102K|.		Atlas-SNP	.											.	PRKRIP1	25	.	0			c.G306A|c.306+1G>A						PASS	.																																			SO:0001630	splice_region_variant	79706	exon3			TGAGAAGGTCAGT|GAGAAGGTCAGTG	AK023964	CCDS34714.1	7q22.1	2013-01-09			ENSG00000128563	ENSG00000128563		"Zinc fingers, C2H2-type", "-"	21894	protein-coding gene	gene with protein product	"likely ortholog of mouse C114 dsRNA-binding protein", "KRAB box domain containing 3"					12679338	Standard	NM_024653		Approved	C114, FLJ13902, KRBOX3	uc003uzh.2	Q9H875	OTTHUMG00000157717	Exception_encountered	chr7.hg19:g.102040095_102040096delinsAA		224.0|223.0	0.0	.		366.0|360.0	147.0	.	NM_024653	B4DGM2|Q8NDM6|Q96CF8	Silent|Splice_Site	SNP	ENST00000496391.1	hg19	CCDS34714.1																																																																																			.	.	.	none		0.554	PRKRIP1-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349489.1	NM_024653	Silent	AA	102040096	GG	AA	102040095	5	1	94	1	0	0	0	0	0	0	1	0	12535	1014	35	2	316	2	PRKRIP1	7	102040095	Splice_Site	DNP	GG	TCGA-B9-4113-01A-01D-1252-08	66127718	102040095	57098568	32	5949											
ZNF777	27153	hgsc.bcm.edu	37	chr7	149129443	149129443	+	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	tggctgaagctgctgtcgcaCtcggggcacttgtagggctt	5	11	15	10	2	0	1	0	1	0	0	2	1	0	1	0	4	2	7	0	4	2	3			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr7:149129443C>T	ENST00000247930.4	-	6	2243	c.1920G>A	c.(1918-1920)gaG>gaA	p.E640E		NM_015694.2	NP_056509.2	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	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)			large_intestine(5)|lung(17)|ovary(1)|skin(2)|urinary_tract(1)	26	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			TGCTGTCGCACTCGGGGCACT	0.652																																					p.E640E		Atlas-SNP	.											.	ZNF777	63	.	0			c.G1920A						PASS	.						90	106	100					7																	149129443		2182	4272	6454	SO:0001819	synonymous_variant	27153	exon6			GTCGCACTCGGGG	AB033111	CCDS43675.1	7q36.1	2013-01-08			ENSG00000196453	ENSG00000196453		"Zinc fingers, C2H2-type", "-"	22213	protein-coding gene	gene with protein product							Standard	NM_015694		Approved	KIAA1285	uc003wfv.3	Q9ULD5	OTTHUMG00000158967	ENST00000247930.4:c.1920G>A	chr7.hg19:g.149129443C>T		366.0	1.0	.		515.0	202.0	.	NM_015694	Q8N2R2|Q8N659	Silent	SNP	ENST00000247930.4	hg19	CCDS43675.1																																																																																			.	.	.	none		0.652	ZNF777-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352708.1	NM_015694		T	149129443	C	T	149129443	2	4	94	1	0	0	0	0	0	0	0	1	18162	564	20	2		2	ZNF777	7	149129443	Silent	SNP	C	TCGA-B9-4113-01A-01D-1252-08	47089348	149129443	10009220	33	5950											
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77776650	77776650	+	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	cacctcaggggttcaaacctCactacccacagaaagttgtt	12	9	7	13	0	3	1	3	0	0	1	3	1	3	1	3	2	2	3	3	2	3	4			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr8:77776650C>A	ENST00000521891.2	+	11	11148	c.10700C>A	c.(10699-10701)tCa>tAa	p.S3567*	ZFHX4_ENST00000050961.6_Nonsense_Mutation_p.S3518*|ZFHX4_ENST00000518282.1_Nonsense_Mutation_p.S3541*|ZFHX4_ENST00000455469.2_Nonsense_Mutation_p.S3522*	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	3518					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)			GTTCAAACCTCACTACCCACA	0.493										HNSCC(33;0.089)																											p.S3567X		Atlas-SNP	.											.	ZFHX4	878	.	0			c.C10700A						PASS	.						85	86	86					8																	77776650		2128	4274	6402	SO:0001587	stop_gained	79776	exon11			AAACCTCACTACC		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.10700C>A	chr8.hg19:g.77776650C>A	ENSP00000430497:p.Ser3567*	51.0	0.0	.		106.0	5.0	.	NM_024721	G3V138|Q18PS0|Q6ZN20	Nonsense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	C	52	19.301884	0.99917	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	.	.	.	4.36	4.36	0.52297	.	0.000000	0.36628	U	0.002492	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.448	0.87584	0.0:1.0:0.0:0.0	.	.	.	.	X	3567;3551;3522;3518;3541	.	ENSP00000050961:S3518X	S	+	2	0	ZFHX4	77939205	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.563000	0.82314	2.435000	0.82474	0.650000	0.86243	TCA	.	.	.	none		0.493	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		A	77776650	C	A	77776650	4	1	94	1	0	0	0	0	0	1	0	0	17647	838	29	4	10738	4	ZFHX4	8	77776650	Nonsense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08		77776650	68587372	34	5951											
COL5A1	1289	hgsc.bcm.edu	37	chr9	137593045	137593045	+	Frame_Shift_Del	DEL	A	A	-																															gaattgctctcagcgtccacAagaaaaatgtcaccttgatc																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr9:137593045delA	ENST00000371817.3	+	4	934	c.520delA	c.(520-522)aagfs	p.K175fs	COL5A1_ENST00000464187.1_3'UTR	NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	175	Laminin G-like.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CAGCGTCCACAAGAAAAATGT	0.478																																					p.H173fs		Atlas-INDEL	.											.	COL5A1	323	.	0			c.519delC						PASS	.						132	100	111					9																	137593045		2203	4298	6501	SO:0001589	frameshift_variant	1289	exon4			.	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"Collagens"	2209	protein-coding gene	gene with protein product	"alpha 1 type V collagen"	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.520delA	chr9.hg19:g.137593045delA	ENSP00000360882:p.Lys175fs	89.0	0.0	0		78.0	28.0	0.358974	NM_000093	Q15094|Q5SUX4	Frame_Shift_Del	DEL	ENST00000371817.3	hg19	CCDS6982.1																																																																																			.	.	.	none		0.478	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		-	137593045	A	-	137593045	7	5	94	1	0	1	0	1	0	0	0	0	3698	131	5	0	534	0	COL5A1	9	137593045	Frame_Shift_Del	DEL	A	TCGA-B9-4113-01A-01D-1252-08		137593045	3620386	35	5952											
ECD	11319	hgsc.bcm.edu	37	chr10	74896486	74896486	+	Missense_Mutation	SNP	T	T	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	tggttcctagtggtgaaactTttgctgatgcaggtgtgtgc	6	15	14	6	0	0	2	0	2	0	0	1	2	1	2	1	3	4	3	1	3	2	4			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr10:74896486T>G	ENST00000372979.4	-	13	1886	c.1680A>C	c.(1678-1680)aaA>aaC	p.K560N	ECD_ENST00000454759.2_Missense_Mutation_p.K517N|ECD_ENST00000430082.2_Missense_Mutation_p.K593N	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	560					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)					TGGTGAAACTTTTGCTGATGC	0.418																																					p.K593N		Atlas-SNP	.											.	ECD	50	.	0			c.A1779C						PASS	.						221	194	203					10																	74896486		2203	4300	6503	SO:0001583	missense	11319	exon14			GAAACTTTTGCTG	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.1680A>C	chr10.hg19:g.74896486T>G	ENSP00000362070:p.Lys560Asn	225.0	0.0	.		179.0	75.0	.	NM_001135752	C9JX46|E9PAW8	Missense_Mutation	SNP	ENST00000372979.4	hg19	CCDS7321.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.034517	0.75617	.	.	ENSG00000122882	ENST00000372979;ENST00000430082;ENST00000454759	T;T;T	0.19669	2.13;2.13;2.13	5.66	3.37	0.38596	.	0.091325	0.85682	D	0.000000	T	0.34048	0.0884	M	0.64997	1.995	0.47037	D	0.999297	D;D;P	0.60575	0.978;0.988;0.51	P;P;P	0.60286	0.872;0.872;0.493	T	0.03597	-1.1021	10	0.40728	T	0.16	-2.9522	7.962	0.30076	0.0:0.1669:0.0:0.8331	.	517;593;560	E9PAW8;C9JX46;O95905	.;.;SGT1_HUMAN	N	560;593;517	ENSP00000362070:K560N;ENSP00000401566:K593N;ENSP00000395786:K517N	ENSP00000362070:K560N	K	-	3	2	ECD	74566492	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	1.537000	0.36083	0.981000	0.38548	0.533000	0.62120	AAA	.	.	.	none		0.418	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265		G	74896486	T	G	74896486	3	3	94	1	0	0	0	0	1	0	0	0	4890	1838	64	5	262	5	ECD	10	74896486	Missense_Mutation	SNP	T	TCGA-B9-4113-01A-01D-1252-08		74896486	60638261	36	5953											
COX15	1355	hgsc.bcm.edu	37	chr10	101491791	101491791	+	Missense_Mutation	SNP	A	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	caaggccctcaacggcggaaAgagcaatcgctgcatactga	13	5	11	12	3	1	2	1	1	0	1	2	3	1	3	1	3	4	3	1	3	5	1			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr10:101491791A>C	ENST00000016171.5	-	1	66	c.16T>G	c.(16-18)Ttt>Gtt	p.F6V	CUTC_ENST00000493385.1_Intron|CUTC_ENST00000370476.5_5'Flank|COX15_ENST00000370483.5_Missense_Mutation_p.F6V			Q7KZN9	COX15_HUMAN	cytochrome c oxidase assembly homolog 15 (yeast)	6					cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)|oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)			endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	13		Colorectal(252;0.234)		Epithelial(162;3.08e-10)|all cancers(201;2.43e-08)		AACGGCGGAAAGAGCAATCGC	0.607																																					p.F6V		Atlas-SNP	.											.	COX15	25	.	0			c.T16G						PASS	.						48	36	40					10																	101491791		2203	4300	6503	SO:0001583	missense	1355	exon1			GCGGAAAGAGCAA	AF044323	CCDS7481.1, CCDS7482.1	10q24	2014-09-17	2012-10-15		ENSG00000014919	ENSG00000014919		"Mitochondrial respiratory chain complex assembly factors"	2263	protein-coding gene	gene with protein product		603646	"COX15 (yeast) homolog, cytochrome c oxidase assembly protein", "COX15 homolog, cytochrome c oxidase assembly protein (yeast)"			9878253	Standard	NM_078470		Approved		uc001kqb.4	Q7KZN9	OTTHUMG00000018893	ENST00000016171.5:c.16T>G	chr10.hg19:g.101491791A>C	ENSP00000016171:p.Phe6Val	56.0	0.0	.		56.0	18.0	.	NM_078470	A8K6I9|O60556|O75878|Q5TD00|Q5TD01|Q7Z3Q3|Q9NTN0	Missense_Mutation	SNP	ENST00000016171.5	hg19	CCDS7482.1	.	.	.	.	.	.	.	.	.	.	A	6.792	0.515219	0.12944	.	.	ENSG00000014919	ENST00000370483;ENST00000016171	.	.	.	4.58	0.265	0.15612	.	0.865040	0.09787	N	0.755882	T	0.23054	0.0557	N	0.19112	0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.21621	-1.0240	9	0.27785	T	0.31	1.4857	3.7279	0.08481	0.4456:0.2267:0.3277:0.0	.	6;6	Q7KZN9-2;Q7KZN9	.;COX15_HUMAN	V	6	.	ENSP00000016171:F6V	F	-	1	0	COX15	101481781	0.005000	0.15991	0.002000	0.10522	0.186000	0.23388	-0.083000	0.11286	-0.100000	0.12241	0.454000	0.30748	TTT	.	.	.	none		0.607	COX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049818.1	NP_510870		C	101491791	A	C	101491791	3	2	94	1	0	0	0	0	1	0	0	0	3766	72	3	5	1322	5	COX15	10	101491791	Missense_Mutation	SNP	A	TCGA-B9-4113-01A-01D-1252-08	26595305	101491791	34042956	37	5954											
E2F8	79733	hgsc.bcm.edu	37	chr11	19251275	19251275	+	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	tggtgcacaccgttgggctcAggccttggggtggcgtcaca	5	9	16	11	2	2	0	2	0	0	0	2	0	2	0	2	6	1	3	2	6	0	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr11:19251275A>T	ENST00000527884.1	-	10	1851	c.1619T>A	c.(1618-1620)cTg>cAg	p.L540Q	RP11-428C19.4_ENST00000527978.1_RNA|E2F8_ENST00000250024.4_Missense_Mutation_p.L540Q	NM_001256371.1|NM_001256372.1	NP_001243300.1|NP_001243301.1	A0AVK6	E2F8_HUMAN	E2F transcription factor 8	540					cell cycle comprising mitosis without cytokinesis (GO:0033301)|chorionic trophoblast cell differentiation (GO:0060718)|hepatocyte differentiation (GO:0070365)|negative regulation of cytokinesis (GO:0032466)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|RNA polymerase II core promoter 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)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CGTTGGGCTCAGGCCTTGGGG	0.582																																					p.L540Q		Atlas-SNP	.											.	E2F8	84	.	0			c.T1619A						PASS	.						116	110	112					11																	19251275		2199	4293	6492	SO:0001583	missense	79733	exon10			GGGCTCAGGCCTT		CCDS7849.1	11p15	2008-02-05			ENSG00000129173	ENSG00000129173			24727	protein-coding gene	gene with protein product		612047				15722552	Standard	NM_024680		Approved	FLJ23311	uc001mpo.2	A0AVK6	OTTHUMG00000166102	ENST00000527884.1:c.1619T>A	chr11.hg19:g.19251275A>T	ENSP00000434199:p.Leu540Gln	448.0	0.0	.		410.0	146.0	.	NM_001256372	A8K9H3|Q2VPJ3|Q3C1U6|Q5BKY4|Q8N340|Q9H5M0	Missense_Mutation	SNP	ENST00000527884.1	hg19	CCDS7849.1	.	.	.	.	.	.	.	.	.	.	A	13.34	2.208327	0.39003	.	.	ENSG00000129173	ENST00000527884;ENST00000396159;ENST00000250024	T;T	0.19669	2.13;2.13	5.63	3.22	0.36961	.	0.443233	0.22737	N	0.056245	T	0.17323	0.0416	M	0.62723	1.935	0.38602	D	0.950684	P	0.37955	0.612	B	0.34722	0.188	T	0.13737	-1.0498	10	0.66056	D	0.02	-1.4647	1.4873	0.02450	0.4262:0.2981:0.1324:0.1433	.	540	A0AVK6	E2F8_HUMAN	Q	540	ENSP00000434199:L540Q;ENSP00000250024:L540Q	ENSP00000250024:L540Q	L	-	2	0	E2F8	19207851	0.981000	0.34729	1.000000	0.80357	0.949000	0.60115	1.281000	0.33214	0.376000	0.24707	0.533000	0.62120	CTG	.	.	.	none		0.582	E2F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387830.1	NM_024680		T	19251275	A	T	19251275	3	4	94	1	0	0	0	0	1	0	0	0	4875	188	7	5	1000	5	E2F8	11	19251275	Missense_Mutation	SNP	A	TCGA-B9-4113-01A-01D-1252-08		19251275	115755241	38	5955											
QSER1	79832	hgsc.bcm.edu	37	chr11	32954930	32954930	+	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	gccacaagcatctcttgagtCatcaacccaaaggctatctg	12	9	7	13	0	4	1	2	1	2	0	5	1	4	1	2	1	2	2	2	1	4	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr11:32954930C>A	ENST00000399302.2	+	4	2074	c.1739C>A	c.(1738-1740)tCa>tAa	p.S580*	QSER1_ENST00000527788.1_Nonsense_Mutation_p.S341*	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	580										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)					TCTCTTGAGTCATCAACCCAA	0.398																																					p.S580X		Atlas-SNP	.											.	QSER1	153	.	0			c.C1739A						PASS	.						82	77	79					11																	32954930		1869	4115	5984	SO:0001587	stop_gained	79832	exon4			TTGAGTCATCAAC	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.1739C>A	chr11.hg19:g.32954930C>A	ENSP00000382241:p.Ser580*	47.0	0.0	.		48.0	14.0	.	NM_001076786	Q6ZU30|Q6ZUR5	Nonsense_Mutation	SNP	ENST00000399302.2	hg19	CCDS41631.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.281137	0.80692	.	.	ENSG00000060749	ENST00000399302;ENST00000078652;ENST00000527788	.	.	.	5.01	5.01	0.66863	.	0.480260	0.19152	N	0.121422	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.6645	0.91485	0.0:1.0:0.0:0.0	.	.	.	.	X	580;341;341	.	ENSP00000078652:S341X	S	+	2	0	QSER1	32911506	0.999000	0.42202	0.049000	0.19019	0.007000	0.05969	5.597000	0.67577	2.496000	0.84212	0.591000	0.81541	TCA	.	.	.	none		0.398	QSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388448.1	NM_024774		A	32954930	C	A	32954930	4	1	94	1	0	0	0	0	0	1	0	0	12895	838	29	4	1745	4	QSER1	11	32954930	Nonsense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	13703655	32954930	102051586	39	5956											
MADD	8567	hgsc.bcm.edu	37	chr11	47304129	47304129	+	Missense_Mutation	SNP	T	T	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	gtactttggggaatggatccTtaaccccaccaactatgcct	10	11	8	12	0	0	0	0	0	0	0	1	2	1	2	5	3	4	1	5	3	5	4			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr11:47304129T>G	ENST00000311027.5	+	9	1832	c.1667T>G	c.(1666-1668)cTt>cGt	p.L556R	MADD_ENST00000407859.3_Missense_Mutation_p.L556R|MADD_ENST00000402192.2_Missense_Mutation_p.L556R|MADD_ENST00000395336.3_Missense_Mutation_p.L556R|MADD_ENST00000402799.1_Missense_Mutation_p.L556R|MADD_ENST00000406482.1_Missense_Mutation_p.L556R|MADD_ENST00000342922.4_Missense_Mutation_p.L556R|MADD_ENST00000489415.1_3'UTR|MADD_ENST00000349238.3_Missense_Mutation_p.L556R|MADD_ENST00000395344.3_Missense_Mutation_p.L556R	NM_003682.3	NP_003673.3			MAP-kinase activating death domain											breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		GAATGGATCCTTAACCCCACC	0.537																																					p.L556R		Atlas-SNP	.											.	MADD	172	.	0			c.T1667G						PASS	.						69	53	58					11																	47304129		2201	4298	6499	SO:0001583	missense	8567	exon9			GGATCCTTAACCC	AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"DENN/MADD domain containing"	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.1667T>G	chr11.hg19:g.47304129T>G	ENSP00000310933:p.Leu556Arg	138.0	0.0	.		137.0	50.0	.	NM_130474		Missense_Mutation	SNP	ENST00000311027.5	hg19	CCDS7930.1	.	.	.	.	.	.	.	.	.	.	T	29.5	5.010292	0.93346	.	.	ENSG00000110514	ENST00000342922;ENST00000395342;ENST00000402799;ENST00000406482;ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395344;ENST00000395336;ENST00000402192	T;T;T;T;T;T;T;T;T	0.08896	3.16;3.05;3.05;3.14;3.15;3.04;3.06;3.15;3.16	5.77	5.77	0.91146	dDENN (1);	0.000000	0.85682	D	0.000000	T	0.28797	0.0714	M	0.65975	2.015	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;0.999;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D	0.91635	0.995;0.997;0.998;0.991;0.991;0.991;0.997;0.999;0.999;0.999	T	0.00686	-1.1610	10	0.87932	D	0	-13.2301	16.383	0.83481	0.0:0.0:0.0:1.0	.	556;556;556;556;556;556;556;556;556;556	B5MEE5;A8K8S7;Q8WXG6-7;F8W9P9;Q8WXG6-6;Q8WXG6-5;Q8WXG6-2;Q8WXG6-4;Q8WXG6;Q8WXG6-3	.;.;.;.;.;.;.;.;MADD_HUMAN;.	R	556	ENSP00000343902:L556R;ENSP00000385585:L556R;ENSP00000384435:L556R;ENSP00000304505:L556R;ENSP00000310933:L556R;ENSP00000384204:L556R;ENSP00000378753:L556R;ENSP00000378745:L556R;ENSP00000384287:L556R	ENSP00000310933:L556R	L	+	2	0	MADD	47260705	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	7.628000	0.83189	2.326000	0.78906	0.533000	0.62120	CTT	.	.	.	none		0.537	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1			G	47304129	T	G	47304129	3	3	94	1	0	0	0	0	1	0	0	0	9159	1609	56	5	1697	5	MADD	11	47304129	Missense_Mutation	SNP	T	TCGA-B9-4113-01A-01D-1252-08	14349199	47304129	87702387	40	5957											
A2ML1	144568	hgsc.bcm.edu	37	chr12	9006738	9006738	+	Frame_Shift_Del	DEL	A	A	-																															tctcaggtcacattaactttActattagtacaaagattctg																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr12:9006738delA	ENST00000299698.7	+	21	2785	c.2605delA	c.(2605-2607)actfs	p.T869fs	A2ML1_ENST00000539547.1_Frame_Shift_Del_p.T378fs	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						CATTAACTTTACTATTAGTAC	0.468																																					p.F868fs		Atlas-INDEL	.											.	A2ML1	199	.	0			c.2604delT						PASS	.						55	56	56					12																	9006738		1864	4095	5959	SO:0001589	frameshift_variant	144568	exon21			.	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.2605delA	chr12.hg19:g.9006738delA	ENSP00000299698:p.Thr869fs	75.0	0.0	0		134.0	72.0	0.537313	NM_144670		Frame_Shift_Del	DEL	ENST00000299698.7	hg19	CCDS8596.2																																																																																			.	.	.	none		0.468	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670		-	9006738	A	-	9006738	7	5	94	1	0	1	0	1	0	0	0	0	5	391	14	0	2687	0	A2ML1	12	9006738	Frame_Shift_Del	DEL	A	TCGA-B9-4113-01A-01D-1252-08		9006738	124845157	41	5958											
PIK3C2G	5288	hgsc.bcm.edu	37	chr12	18658292	18658292	+	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	cattcatcctgggagtatgtGaccgtcacaatgataatatc	12	12	8	9	1	2	2	2	2	0	0	4	3	3	3	2	1	0	1	2	1	4	4			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr12:18658292G>A	ENST00000266497.5	+	22	3135	c.3097G>A	c.(3097-3099)Gac>Aac	p.D1033N	PIK3C2G_ENST00000433979.1_Missense_Mutation_p.D1033N|PIK3C2G_ENST00000538779.1_Missense_Mutation_p.D1074N			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	1033	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)				GGGAGTATGTGACCGTCACAA	0.393																																					p.D1033N		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.G3097A						PASS	.						129	112	117					12																	18658292		1934	4151	6085	SO:0001583	missense	5288	exon23			GTATGTGACCGTC	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.3097G>A	chr12.hg19:g.18658292G>A	ENSP00000266497:p.Asp1033Asn	16.0	0.0	.		11.0	7.0	.	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	hg19	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.018323	0.93404	.	.	ENSG00000139144	ENST00000433979;ENST00000266497;ENST00000538779	D;D;D	0.94897	-3.55;-3.55;-3.55	4.47	4.47	0.54385	Protein kinase-like domain (1);Phosphatidylinositol 3/4-kinase, conserved site (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.127925	0.51477	D	0.000089	D	0.98105	0.9375	H	0.95043	3.615	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98863	1.0763	10	0.87932	D	0	-20.5375	17.403	0.87465	0.0:0.0:1.0:0.0	.	1073;1074;1033	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	N	1033;1033;1074	ENSP00000404845:D1033N;ENSP00000266497:D1033N;ENSP00000445381:D1074N	ENSP00000266497:D1033N	D	+	1	0	PIK3C2G	18549559	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.524000	0.98036	2.771000	0.95319	0.650000	0.86243	GAC	.	.	.	none		0.393	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570		A	18658292	G	A	18658292	3	1	94	1	0	0	0	0	1	0	0	0	11918	1290	45	2	3183	2	PIK3C2G	12	18658292	Missense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08	9651554	18658292	115193603	42	5959											
PDZRN4	29951	hgsc.bcm.edu	37	chr12	41585335	41585335	+	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	gattcaatattataggaggtCgaccaaatcaggtaaaacac	17	9	8	7	1	2	0	2	0	0	0	3	3	2	1	1	3	1	1	1	3	7	5			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr12:41585335C>T	ENST00000402685.2	+	2	732	c.724C>T	c.(724-726)Cga>Tga	p.R242*		NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	242	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.						ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				TATAGGAGGTCGACCAAATCA	0.303																																					p.R242X		Atlas-SNP	.											.	PDZRN4	346	.	0			c.C724T						PASS	.						97	90	92					12																	41585335		1568	3576	5144	SO:0001587	stop_gained	29951	exon2			GGAGGTCGACCAA	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.724C>T	chr12.hg19:g.41585335C>T	ENSP00000384197:p.Arg242*	56.0	0.0	.		105.0	34.0	.	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Nonsense_Mutation	SNP	ENST00000402685.2	hg19	CCDS53777.1	.	.	.	.	.	.	.	.	.	.	C	37	6.538183	0.97646	.	.	ENSG00000165966	ENST00000402685	.	.	.	4.48	2.64	0.31445	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.2118	0.37322	0.0:0.8273:0.0:0.1727	.	.	.	.	X	242	.	ENSP00000384197:R242X	R	+	1	2	PDZRN4	39871602	0.791000	0.28800	0.992000	0.48379	0.995000	0.86356	1.196000	0.32198	0.591000	0.29711	0.563000	0.77884	CGA	.	.	.	none		0.303	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377		T	41585335	C	T	41585335	4	4	94	1	0	0	0	0	0	1	0	0	11717	876	31	1	730	1	PDZRN4	12	41585335	Nonsense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	22927043	41585335	92266560	43	5960											
ACAD10	80724	hgsc.bcm.edu	37	chr12	112184083	112184083	+	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	tgggcacgtccctgtatgccCccgaggtaccttctttaaag	7	11	10	13	2	1	0	0	0	1	0	2	1	2	0	4	2	2	3	4	2	4	5			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr12:112184083C>A	ENST00000313698.4	+	14	2406	c.2251C>A	c.(2251-2253)Ccc>Acc	p.P751T	ACAD10_ENST00000392636.2_Missense_Mutation_p.P353T|ACAD10_ENST00000455480.2_Missense_Mutation_p.P782T|ACAD10_ENST00000413681.3_3'UTR	NM_025247.5	NP_079523.3	Q6JQN1	ACD10_HUMAN	acyl-CoA dehydrogenase family, member 10	751						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						CCTGTATGCCCCCGAGGTACC	0.473																																					p.P782T		Atlas-SNP	.											.	ACAD10	93	.	0			c.C2344A						PASS	.						106	103	104					12																	112184083		2203	4300	6503	SO:0001583	missense	80724	exon15			TATGCCCCCGAGG	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.2251C>A	chr12.hg19:g.112184083C>A	ENSP00000325137:p.Pro751Thr	265.0	0.0	.		339.0	89.0	.	NM_001136538	G3XAJ0|Q8N828|Q8NAP2|Q96BX5	Missense_Mutation	SNP	ENST00000313698.4	hg19	CCDS31903.1	.	.	.	.	.	.	.	.	.	.	C	17.52	3.408994	0.62399	.	.	ENSG00000111271	ENST00000392636;ENST00000413681;ENST00000455480;ENST00000515283;ENST00000313698	D;D;D	0.99660	-6.32;-6.32;-6.32	5.29	3.43	0.39272	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, N-terminal (1);Acyl-CoA dehydrogenase/oxidase, N-terminal (1);	0.378699	0.25436	N	0.030684	D	0.99629	0.9864	H	0.97732	4.065	0.80722	D	1	D;B;B	0.53462	0.96;0.209;0.298	P;B;B	0.57057	0.812;0.396;0.141	D	0.98657	1.0682	10	0.87932	D	0	.	9.228	0.37418	0.1463:0.776:0.0:0.0777	.	782;751;751	G3XAJ0;Q6JQN1;Q6JQN1-2	.;ACD10_HUMAN;.	T	353;751;782;144;751	ENSP00000376411:P353T;ENSP00000389813:P782T;ENSP00000325137:P751T	ENSP00000325137:P751T	P	+	1	0	ACAD10	110668466	0.071000	0.21146	0.012000	0.15200	0.965000	0.64279	1.166000	0.31834	0.708000	0.31955	0.561000	0.74099	CCC	.	.	.	none		0.473	ACAD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368307.1	NM_025247		A	112184083	C	A	112184083	3	1	94	1	0	0	0	0	1	0	0	0	108	623	22	4	2398	4	ACAD10	12	112184083	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	70598748	112184083	21667812	44	5961											
TMEM132D	121256	hgsc.bcm.edu	37	chr12	130184819	130184819	+	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	tctcggaaagcaaagaccctCaggcacggcagcttctcccc	10	6	9	16	2	3	1	1	0	2	1	5	2	3	2	3	3	2	4	3	3	2	1			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr12:130184819C>G	ENST00000422113.2	-	2	830	c.504G>C	c.(502-504)ctG>ctC	p.L168L	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	168					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)		CAAAGACCCTCAGGCACGGCA	0.662																																					p.L168L		Atlas-SNP	.											.	TMEM132D	299	.	0			c.G504C						PASS	.						18	20	20					12																	130184819		2203	4299	6502	SO:0001819	synonymous_variant	121256	exon2			GACCCTCAGGCAC	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.504G>C	chr12.hg19:g.130184819C>G		96.0	0.0	.		103.0	57.0	.	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Silent	SNP	ENST00000422113.2	hg19	CCDS9266.1																																																																																			.	.	.	none		0.662	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		G	130184819	C	G	130184819	2	3	94	1	0	0	0	0	0	0	0	1	16059	813	29	4		4	TMEM132D	12	130184819	Silent	SNP	C	TCGA-B9-4113-01A-01D-1252-08	18000736	130184819	3667076	45	5962											
SLC46A3	283537	hgsc.bcm.edu	37	chr13	29287510	29287510	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctggaatggaaaggcaaaatAgcaaagcaaacagagccaaa	21	3	10	7	0	0	1	0	0	0	1	0	3	0	3	1	3	4	3	1	3	8	1			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr13:29287510A>G	ENST00000266943.6	-	3	736	c.367T>C	c.(367-369)Tat>Cat	p.Y123H	SLC46A3_ENST00000380814.4_Missense_Mutation_p.Y123H	NM_001135919.1|NM_181785.3	NP_001129391.1|NP_861450.1	Q7Z3Q1	S46A3_HUMAN	solute carrier family 46, member 3	123					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(2)|prostate(1)|skin(1)	15		Lung SC(185;0.0367)		all cancers(112;0.159)		AAGGCAAAATAGCAAAGCAAA	0.408																																					p.Y123H		Atlas-SNP	.											.	SLC46A3	86	.	0			c.T367C						PASS	.						74	67	69					13																	29287510		2203	4300	6503	SO:0001583	missense	283537	exon3			CAAAATAGCAAAG		CCDS9332.1, CCDS45021.1	13q12.3	2013-05-22	2007-03-29		ENSG00000139508	ENSG00000139508		"Solute carriers"	27501	protein-coding gene	gene with protein product							Standard	NM_001135919		Approved	DKFZp686A1775, FLJ42613	uc001usj.3	Q7Z3Q1	OTTHUMG00000016650	ENST00000266943.6:c.367T>C	chr13.hg19:g.29287510A>G	ENSP00000266943:p.Tyr123His	68.0	0.0	.		54.0	13.0	.	NM_181785	Q3ZCV8|Q6NUK5|Q6P9B3|Q6ZVG5|Q96QA1	Missense_Mutation	SNP	ENST00000266943.6	hg19	CCDS9332.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.182467	0.78677	.	.	ENSG00000139508	ENST00000266943;ENST00000380814	T;T	0.80994	-1.44;-1.44	6.17	5.0	0.66597	Major facilitator superfamily domain, general substrate transporter (1);	0.059964	0.64402	D	0.000002	D	0.88123	0.6352	M	0.74881	2.28	0.42496	D	0.992918	D;B;B	0.89917	1.0;0.36;0.413	D;B;B	0.79784	0.993;0.139;0.219	D	0.87590	0.2490	10	0.42905	T	0.14	-22.8055	12.1889	0.54257	0.9341:0.0:0.0659:0.0	.	48;123;123	B5MEH0;Q7Z3Q1-2;Q7Z3Q1	.;.;S46A3_HUMAN	H	123	ENSP00000266943:Y123H;ENSP00000370192:Y123H	ENSP00000266943:Y123H	Y	-	1	0	SLC46A3	28185510	1.000000	0.71417	0.981000	0.43875	0.958000	0.62258	6.725000	0.74752	1.160000	0.42584	0.533000	0.62120	TAT	.	.	.	none		0.408	SLC46A3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276111.1	NM_181785		G	29287510	A	G	29287510	3	3	94	1	0	0	0	0	1	0	0	0	14659	420	15	3	1048	3	SLC46A3	13	29287510	Missense_Mutation	SNP	A	TCGA-B9-4113-01A-01D-1252-08		29287510	85882368	46	5963											
ATP7B	540	hgsc.bcm.edu	37	chr13	52548108	52548108	+	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	tcaaatcccatgtcttctatAgcagctctgagttcttctgg	8	15	7	11	0	6	1	1	1	5	0	7	1	7	1	1	1	2	3	1	1	3	5			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr13:52548108A>T	ENST00000242839.4	-	2	1404	c.1248T>A	c.(1246-1248)gcT>gcA	p.A416A	ATP7B_ENST00000482841.1_5'UTR|ATP7B_ENST00000542656.1_Silent_p.A384A|ATP7B_ENST00000448424.2_Silent_p.A416A|ATP7B_ENST00000344297.5_Silent_p.A416A|ATP7B_ENST00000400370.3_Silent_p.A416A|ATP7B_ENST00000400366.3_Silent_p.A305A|ATP7B_ENST00000418097.2_Silent_p.A416A	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	416	HMA 4. {ECO:0000255|PROSITE- ProRule:PRU00280}.				cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	TGTCTTCTATAGCAGCTCTGA	0.458									Wilson disease																												p.A416A		Atlas-SNP	.											.	ATP7B	123	.	0			c.T1248A						PASS	.						100	98	98					13																	52548108		1934	4142	6076	SO:0001819	synonymous_variant	540	exon2	Familial Cancer Database		TTCTATAGCAGCT	U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"ATPases / P-type"	870	protein-coding gene	gene with protein product	"Wilson disease", "copper pump 2", "copper-transporting ATPase 2"	606882	"ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.1248T>A	chr13.hg19:g.52548108A>T		201.0	0.0	.		245.0	90.0	.	NM_000053	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Silent	SNP	ENST00000242839.4	hg19	CCDS41892.1																																																																																			.	.	.	none		0.458	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053		T	52548108	A	T	52548108	2	4	94	1	0	0	0	0	0	0	0	1	1191	407	15	5		5	ATP7B	13	52548108	Silent	SNP	A	TCGA-B9-4113-01A-01D-1252-08	23260598	52548108	62621770	47	5964											
RNF219	79596	hgsc.bcm.edu	37	chr13	79190506	79190506	+	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	acaacagtcccaaaatcctgTctttggggaagaaaaacatt	16	9	7	9	0	1	1	0	0	1	1	3	2	3	2	2	2	2	0	2	2	6	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr13:79190506T>A	ENST00000282003.6	-	6	1448	c.1390A>T	c.(1390-1392)Aca>Tca	p.T464S	RNF219-AS1_ENST00000606429.1_RNA|RNF219-AS1_ENST00000560209.2_RNA|RNF219-AS1_ENST00000560584.2_RNA	NM_024546.3	NP_078822.3	Q5W0B1	RN219_HUMAN	ring finger protein 219	464	Ser-rich.						zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|liver(1)|lung(11)|prostate(1)|skin(1)	32		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.0414)		CAAAATCCTGTCTTTGGGGAA	0.333																																					p.T464S		Atlas-SNP	.											.	RNF219	94	.	0			c.A1390T						PASS	.						38	40	39					13																	79190506		2203	4298	6501	SO:0001583	missense	79596	exon6			ATCCTGTCTTTGG	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.1390A>T	chr13.hg19:g.79190506T>A	ENSP00000282003:p.Thr464Ser	34.0	0.0	.		58.0	25.0	.	NM_024546	B2RN99|Q8TBY2|Q9H0T2|Q9H8M0	Missense_Mutation	SNP	ENST00000282003.6	hg19	CCDS31997.1	.	.	.	.	.	.	.	.	.	.	T	12.02	1.813748	0.32053	.	.	ENSG00000152193	ENST00000282003	T	0.13778	2.56	5.86	3.32	0.38043	.	0.182284	0.39475	N	0.001352	T	0.03959	0.0111	N	0.03608	-0.345	0.26073	N	0.9812	B	0.10296	0.003	B	0.08055	0.003	T	0.36841	-0.9731	10	0.10902	T	0.67	-12.2367	1.5693	0.02612	0.3186:0.0903:0.1164:0.4747	.	464	Q5W0B1	RN219_HUMAN	S	464	ENSP00000282003:T464S	ENSP00000282003:T464S	T	-	1	0	RNF219	78088507	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	1.424000	0.34848	1.050000	0.40346	0.533000	0.62120	ACA	.	.	.	none		0.333	RNF219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045363.1	NM_024546		A	79190506	T	A	79190506	3	1	94	1	0	0	0	0	1	0	0	0	13495	1667	58	5	794	5	RNF219	13	79190506	Missense_Mutation	SNP	T	TCGA-B9-4113-01A-01D-1252-08	26642398	79190506	35979372	48	5965											
SDR39U1	23351	hgsc.bcm.edu	37	chr14	24910963	24910963	+	IGR	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	gcaattgggtggtctctaggCggctgccgattacctctttt	5	14	12	10	2	2	0	0	0	2	0	3	1	2	0	2	4	2	2	2	4	3	5			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr14:24910963C>G	ENST00000251343.5	+	0	6225				SDR39U1_ENST00000399390.1_5'Flank|SDR39U1_ENST00000555365.1_5'UTR|SDR39U1_ENST00000554698.1_Intron|SDR39U1_ENST00000538105.2_Intron|SDR39U1_ENST00000399395.3_Missense_Mutation_p.R82P|SDR39U1_ENST00000555561.1_5'Flank|SDR39U1_ENST00000553930.1_5'UTR			O15037	KHNYN_HUMAN	KH and NYN domain containing								RNA binding (GO:0003723)			kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(3)	24						GGTCTCTAGGCGGCTGCCGAT	0.498																																					p.R82P		Atlas-SNP	.											SDR39U1,colon,carcinoma,0,1	SDR39U1	19	.	0			c.G245C						PASS	.						48	39	42					14																	24910963		1856	4091	5947	SO:0001628	intergenic_variant	56948	exon4			TCTAGGCGGCTGC	AB002321	CCDS32058.1	14q11.2	2010-11-23	2009-10-14	2009-10-14	ENSG00000100441	ENSG00000100441			20166	protein-coding gene	gene with protein product			"KIAA0323"	KIAA0323		17114934	Standard	NM_015299		Approved		uc001wph.4	O15037			chr14.hg19:g.24910963C>G		84.0	0.0	.		74.0	6.0	.	NM_020195	Q86TZ6|Q8IUQ2|Q96BA9	Missense_Mutation	SNP	ENST00000251343.5	hg19	CCDS32058.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.024548	0.93518	.	.	ENSG00000100445	ENST00000399395;ENST00000336353	D	0.93426	-3.22	5.46	5.46	0.80206	NAD(P)-binding domain (1);	0.222455	0.46145	D	0.000301	D	0.96972	0.9011	M	0.84585	2.705	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97373	0.9977	10	0.87932	D	0	-11.9991	17.1594	0.86800	0.0:1.0:0.0:0.0	.	82;108	Q9NRG7-2;Q9NRG7	.;D39U1_HUMAN	P	82;108	ENSP00000382327:R82P	ENSP00000336854:R108P	R	-	2	0	SDR39U1	23980803	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.215000	0.77966	2.714000	0.92807	0.655000	0.94253	CGC	.	.	.	none		0.498	KHNYN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412928.1			G	24910963	C	G	24910963	1	3	94	0	1	0	0	0	0	0	0	0	13985	768	27	4		4	SDR39U1	14	24910963	IGR	SNP	C	TCGA-B9-4113-01A-01D-1252-08		24910963	82438577	49	5966											
SPINT1	6692	hgsc.bcm.edu	37	chr15	41146021	41146021	+	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	gtttatggaggctgcttgggCaacaagaacaactaccttcg	11	10	11	9	1	0	1	0	0	0	1	1	2	0	2	1	3	5	4	1	3	6	5			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr15:41146021C>T	ENST00000344051.4	+	5	1089	c.855C>T	c.(853-855)ggC>ggT	p.G285G	SPINT1_ENST00000562057.1_Silent_p.G285G|SPINT1_ENST00000431806.1_Silent_p.G285G			O43278	SPIT1_HUMAN	serine peptidase inhibitor, Kunitz type 1	285	BPTI/Kunitz inhibitor 1. {ECO:0000255|PROSITE-ProRule:PRU00031}.				branching involved in labyrinthine layer morphogenesis (GO:0060670)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|placenta blood vessel development (GO:0060674)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	16		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		GCTGCTTGGGCAACAAGAACA	0.572																																					p.G285G		Atlas-SNP	.											.	SPINT1	28	.	0			c.C855T						PASS	.						120	128	125					15																	41146021		2203	4300	6503	SO:0001819	synonymous_variant	6692	exon5			CTTGGGCAACAAG		CCDS10067.1, CCDS45231.1	15q13.3	2008-02-05	2005-08-17		ENSG00000166145	ENSG00000166145			11246	protein-coding gene	gene with protein product		605123	"serine protease inhibitor, Kunitz type 1"				Standard	XM_006720657		Approved	HAI, MANSC2	uc001zna.3	O43278	OTTHUMG00000130068	ENST00000344051.4:c.855C>T	chr15.hg19:g.41146021C>T		391.0	0.0	.		317.0	106.0	.	NM_181642	Q7Z7D2	Silent	SNP	ENST00000344051.4	hg19	CCDS10067.1																																																																																			.	.	.	none		0.572	SPINT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252359.2	NM_003710		T	41146021	C	T	41146021	2	4	94	1	0	0	0	0	0	0	0	1	15080	697	25	2		2	SPINT1	15	41146021	Silent	SNP	C	TCGA-B9-4113-01A-01D-1252-08		41146021	61385371	50	5967											
TP53BP1	7158	hgsc.bcm.edu	37	chr15	43724401	43724401	+	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	tgttctctcacctggctatgGagcgactctgtatcatcccc	6	13	8	14	1	4	0	2	0	2	0	6	2	5	1	3	2	1	3	3	2	2	3			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr15:43724401G>A	ENST00000263801.3	-	17	3903	c.3651C>T	c.(3649-3651)ctC>ctT	p.L1217L	TP53BP1_ENST00000450115.2_Silent_p.L1222L|TP53BP1_ENST00000382039.3_Silent_p.L1222L|TP53BP1_ENST00000382044.4_Silent_p.L1222L	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	1217					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)		CCTGGCTATGGAGCGACTCTG	0.483								Other conserved DNA damage response genes																													p.L1222L		Atlas-SNP	.											.	TP53BP1	157	.	0			c.C3666T						PASS	.						137	112	121					15																	43724401		2201	4298	6499	SO:0001819	synonymous_variant	7158	exon17			GCTATGGAGCGAC	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.3651C>T	chr15.hg19:g.43724401G>A		48.0	0.0	.		37.0	13.0	.	NM_001141980	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Silent	SNP	ENST00000263801.3	hg19	CCDS10096.1																																																																																			.	.	.	none		0.483	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			A	43724401	G	A	43724401	2	1	94	1	0	0	0	0	0	0	0	1	16395	1161	41	2		2	TP53BP1	15	43724401	Silent	SNP	G	TCGA-B9-4113-01A-01D-1252-08	2578380	43724401	58806991	51	5968											
CGNL1	84952	hgsc.bcm.edu	37	chr15	57730838	57730838	+	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	cccggccaaatctggtgtgaCagctattcgtttatgcagct	8	12	10	11	2	1	1	0	1	1	0	2	1	1	1	2	2	3	4	2	2	3	4			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr15:57730838C>G	ENST00000281282.5	+	2	719	c.641C>G	c.(640-642)aCa>aGa	p.T214R		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	214	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)		TCTGGTGTGACAGCTATTCGT	0.517																																					p.T214R		Atlas-SNP	.											.	CGNL1	125	.	0			c.C641G						PASS	.						132	132	132					15																	57730838		2192	4292	6484	SO:0001583	missense	84952	exon3			GTGTGACAGCTAT	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.641C>G	chr15.hg19:g.57730838C>G	ENSP00000281282:p.Thr214Arg	625.0	1.0	.		467.0	169.0	.	NM_001252335	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Missense_Mutation	SNP	ENST00000281282.5	hg19	CCDS10161.1	.	.	.	.	.	.	.	.	.	.	C	5.347	0.249277	0.10130	.	.	ENSG00000128849	ENST00000281282	T	0.76968	-1.06	4.98	4.04	0.47022	.	0.178508	0.26851	N	0.022178	T	0.70124	0.3188	L	0.51422	1.61	0.30026	N	0.813928	B	0.27625	0.183	B	0.19666	0.026	T	0.69495	-0.5130	10	0.56958	D	0.05	-12.3608	10.9213	0.47167	0.4244:0.5756:0.0:0.0	.	214	Q0VF96	CGNL1_HUMAN	R	214	ENSP00000281282:T214R	ENSP00000281282:T214R	T	+	2	0	CGNL1	55518130	0.432000	0.25554	0.389000	0.26208	0.182000	0.23217	1.535000	0.36061	1.275000	0.44379	0.650000	0.86243	ACA	.	.	.	none		0.517	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866		G	57730838	C	G	57730838	3	3	94	1	0	0	0	0	1	0	0	0	3306	478	17	4	643	4	CGNL1	15	57730838	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	14006437	57730838	44800554	52	5969											
MCTP2	55784	hgsc.bcm.edu	37	chr15	94841734	94841734	+	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	tcctacacctcggtgcccagCagtctgtccactgcagggat	7	9	10	15	1	1	0	0	0	1	0	4	1	3	1	4	2	4	2	4	2	1	1			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr15:94841734C>T	ENST00000357742.4	+	1	240	c.240C>T	c.(238-240)agC>agT	p.S80S	MCTP2_ENST00000543482.1_Silent_p.S80S|MCTP2_ENST00000331706.4_5'UTR|MCTP2_ENST00000451018.3_Silent_p.S80S	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	80					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)			CGGTGCCCAGCAGTCTGTCCA	0.587																																					p.S80S		Atlas-SNP	.											.	MCTP2	122	.	0			c.C240T						PASS	.						60	62	62					15																	94841734		2197	4298	6495	SO:0001819	synonymous_variant	55784	exon1			GCCCAGCAGTCTG	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.240C>T	chr15.hg19:g.94841734C>T		359.0	0.0	.		261.0	80.0	.	NM_001159643	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Silent	SNP	ENST00000357742.4	hg19	CCDS32338.1																																																																																			.	.	.	none		0.587	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349		T	94841734	C	T	94841734	2	4	94	1	0	0	0	0	0	0	0	1	9408	709	25	2		2	MCTP2	15	94841734	Silent	SNP	C	TCGA-B9-4113-01A-01D-1252-08	37110896	94841734	7689658	53	5970											
ATAD5	79915	hgsc.bcm.edu	37	chr17	29220728	29220728	+	Missense_Mutation	SNP	T	T	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	gccagagacaaaggaaacaaTccagagacaaagaaatctat	21	4	8	8	0	1	3	0	0	1	3	2	6	2	4	2	1	1	0	2	1	6	1			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr17:29220728T>G	ENST00000321990.4	+	21	5235	c.4857T>G	c.(4855-4857)aaT>aaG	p.N1619K		NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1619					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)				AAGGAAACAATCCAGAGACAA	0.393																																					p.N1619K		Atlas-SNP	.											.	ATAD5	150	.	0			c.T4857G						PASS	.						82	91	88					17																	29220728		2203	4300	6503	SO:0001583	missense	79915	exon21			AAACAATCCAGAG		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.4857T>G	chr17.hg19:g.29220728T>G	ENSP00000313171:p.Asn1619Lys	120.0	0.0	.		126.0	28.0	.	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	hg19	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.522716	0.00149	.	.	ENSG00000176208	ENST00000321990	T	0.06218	3.33	4.7	-1.39	0.08997	.	7.549810	0.00481	N	0.000125	T	0.04998	0.0134	L	0.39898	1.24	0.09310	N	1	B	0.15473	0.013	B	0.08055	0.003	T	0.32025	-0.9922	10	0.07325	T	0.83	.	2.0379	0.03544	0.2113:0.3553:0.099:0.3344	.	1619	Q96QE3	ATAD5_HUMAN	K	1619	ENSP00000313171:N1619K	ENSP00000313171:N1619K	N	+	3	2	ATAD5	26244854	0.000000	0.05858	0.027000	0.17364	0.126000	0.20510	-1.140000	0.03210	-0.300000	0.08895	-0.326000	0.08463	AAT	.	.	.	none		0.393	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		G	29220728	T	G	29220728	3	3	94	1	0	0	0	0	1	0	0	0	1076	1432	50	5	4939	5	ATAD5	17	29220728	Missense_Mutation	SNP	T	TCGA-B9-4113-01A-01D-1252-08		29220728	51974482	54	5971											
TANC2	26115	hgsc.bcm.edu	37	chr17	61466867	61466867	+	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	atgctgcagcagcagggtacCtgagcattgtggtgctgctg	7	10	15	9	0	0	1	0	1	0	0	0	1	0	1	1	2	8	8	1	2	1	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr17:61466867C>A	ENST00000424789.2	+	15	2795	c.2791C>A	c.(2791-2793)Ctg>Atg	p.L931M	RP11-269G24.3_ENST00000583552.1_RNA|AC015923.1_ENST00000431604.1_RNA|TANC2_ENST00000389520.4_Missense_Mutation_p.L931M	NM_025185.3	NP_079461.2	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	931					in utero embryonic development (GO:0001701)					breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|upper_aerodigestive_tract(3)	44						AGCAGGGTACCTGAGCATTGT	0.537																																					p.L931M		Atlas-SNP	.											.	TANC2	266	.	0			c.C2791A						PASS	.						31	31	31					17																	61466867		2010	4178	6188	SO:0001583	missense	26115	exon15			GGGTACCTGAGCA	AB032974	CCDS45754.1	17q23.3	2013-01-11				ENSG00000170921		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30212	protein-coding gene	gene with protein product	"rolling pebbles homolog B (Drosophila)"	615047					Standard	NM_025185		Approved	DKFZP564D166, FLJ10215, FLJ11824, KIAA1148, KIAA1636, rols, ROLSA	uc002jal.4	Q9HCD6		ENST00000424789.2:c.2791C>A	chr17.hg19:g.61466867C>A	ENSP00000387593:p.Leu931Met	29.0	0.0	.		57.0	28.0	.	NM_025185	Q9HAC3|Q9NW88|Q9NXY9|Q9ULS2	Missense_Mutation	SNP	ENST00000424789.2	hg19	CCDS45754.1	.	.	.	.	.	.	.	.	.	.	C	8.463	0.855695	0.17106	.	.	ENSG00000170921	ENST00000389520;ENST00000424789	T;T	0.68765	-0.35;-0.35	5.17	5.17	0.71159	Ankyrin repeat-containing domain (4);	0.063998	0.64402	D	0.000005	T	0.62998	0.2474	L	0.50333	1.59	0.51767	D	0.999933	B;B;B	0.28128	0.082;0.118;0.201	B;B;B	0.31390	0.036;0.091;0.129	T	0.58989	-0.7538	10	0.14656	T	0.56	.	18.698	0.91610	0.0:1.0:0.0:0.0	.	931;841;931	Q9HCD6-2;D3DU10;Q9HCD6	.;.;TANC2_HUMAN	M	931	ENSP00000374171:L931M;ENSP00000387593:L931M	ENSP00000374171:L931M	L	+	1	2	TANC2	58820599	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.060000	0.57477	2.401000	0.81631	0.555000	0.69702	CTG	.	.	.	none		0.537	TANC2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444765.1			A	61466867	C	A	61466867	3	1	94	1	0	0	0	0	1	0	0	0	15557	680	24	4	2849	4	TANC2	17	61466867	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	32246139	61466867	19728343	55	5972											
PTPRM	5797	hgsc.bcm.edu	37	chr18	7567846	7567846	+	Frame_Shift_Del	DEL	T	T	-																															cttgggacttgcctggcgacTttggccggacttttgctaac																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr18:7567846delT	ENST00000332175.8	+	1	1067	c.30delT	c.(28-30)actfs	p.T10fs	PTPRM_ENST00000580170.1_Frame_Shift_Del_p.T10fs|PTPRM_ENST00000400060.4_Frame_Shift_Del_p.T10fs	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	10					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)				GCCTGGCGACTTTGGCCGGAC	0.766																																					p.T10fs		Atlas-INDEL	.											.	PTPRM	185	.	0			c.29delC						PASS	.						56	56	56					18																	7567846		2203	4300	6503	SO:0001589	frameshift_variant	5797	exon1			.	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.30delT	chr18.hg19:g.7567846delT	ENSP00000331418:p.Thr10fs	172.0	0.0	0		129.0	46.0	0.356589	NM_001105244	A7MBN1|D3DUH8|J3QL11	Frame_Shift_Del	DEL	ENST00000332175.8	hg19	CCDS11840.1																																																																																			.	.	.	none		0.766	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			-	7567846	T	-	7567846	7	5	94	1	0	1	0	1	0	0	0	0	12819	1596	56	0	32	0	PTPRM	18	7567846	Frame_Shift_Del	DEL	T	TCGA-B9-4113-01A-01D-1252-08		7567846	70509402	56	5973											
SALL3	27164	hgsc.bcm.edu	37	chr18	76754972	76754972	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgcaagagcgcgttggaaaTccactaccgcagccatacta	12	8	9	12	3	0	1	0	0	0	1	1	2	1	2	3	1	5	3	3	1	5	5			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr18:76754972T>C	ENST00000537592.2	+	2	2981	c.2981T>C	c.(2980-2982)aTc>aCc	p.I994T	SALL3_ENST00000536229.3_Intron|SALL3_ENST00000575389.2_Intron	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	994					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)		GCGTTGGAAATCCACTACCGC	0.562																																					p.I994T		Atlas-SNP	.											.	SALL3	162	.	0			c.T2981C						PASS	.						61	61	61					18																	76754972		2203	4300	6503	SO:0001583	missense	27164	exon2			TGGAAATCCACTA	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.2981T>C	chr18.hg19:g.76754972T>C	ENSP00000441823:p.Ile994Thr	148.0	0.0	.		86.0	33.0	.	NM_171999	Q9UGH1	Missense_Mutation	SNP	ENST00000537592.2	hg19	CCDS12013.1	.	.	.	.	.	.	.	.	.	.	T	12.28	1.890593	0.33348	.	.	ENSG00000256463	ENST00000537592	T	0.07114	3.22	5.15	5.15	0.70609	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49305	D	0.000142	T	0.10809	0.0264	N	0.12637	0.245	0.80722	D	1	P	0.50819	0.939	P	0.53988	0.739	T	0.22695	-1.0209	10	0.56958	D	0.05	-22.1664	14.9958	0.71431	0.0:0.0:0.0:1.0	.	994	Q9BXA9	SALL3_HUMAN	T	994	ENSP00000441823:I994T	ENSP00000299466:I994T	I	+	2	0	SALL3	74855960	1.000000	0.71417	0.961000	0.40146	0.689000	0.40095	4.390000	0.59646	1.943000	0.56356	0.379000	0.24179	ATC	.	.	.	none		0.562	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999		C	76754972	T	C	76754972	3	2	94	1	0	0	0	0	1	0	0	0	13825	1435	50	3	2987	3	SALL3	18	76754972	Missense_Mutation	SNP	T	TCGA-B9-4113-01A-01D-1252-08	69187126	76754972	1322276	57	5974											
DOT1L	84444	hgsc.bcm.edu	37	chr19	2191111	2191111	+	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	caaccactcggtgaccgaccCcgagaagctcaacaactacg	13	4	8	16	4	1	2	1	1	0	1	2	4	1	2	4	1	5	1	4	1	5	1			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr19:2191111C>G	ENST00000398665.3	+	5	401	c.365C>G	c.(364-366)cCc>cGc	p.P122R		NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	122	DOT1. {ECO:0000255|PROSITE- ProRule:PRU00902}.				histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTGACCGACCCCGAGAAGCTC	0.602																																					p.P122R		Atlas-SNP	.											.	DOT1L	205	.	0			c.C365G						PASS	.						70	80	77					19																	2191111		2112	4210	6322	SO:0001583	missense	84444	exon5			CCGACCCCGAGAA	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.365C>G	chr19.hg19:g.2191111C>G	ENSP00000381657:p.Pro122Arg	122.0	0.0	.		116.0	41.0	.	NM_032482	O60379|Q96JL1	Missense_Mutation	SNP	ENST00000398665.3	hg19	CCDS42460.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.003702	0.93287	.	.	ENSG00000104885	ENST00000398665;ENST00000221482;ENST00000452696	T;T	0.23754	1.89;1.89	4.75	4.75	0.60458	.	0.053872	0.85682	D	0.000000	T	0.58552	0.2130	M	0.88105	2.93	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.68800	-0.5313	10	0.87932	D	0	-14.6108	16.8009	0.85614	0.0:1.0:0.0:0.0	.	122	Q8TEK3-2	.	R	122;122;98	ENSP00000381657:P122R;ENSP00000404284:P98R	ENSP00000221482:P122R	P	+	2	0	DOT1L	2142111	1.000000	0.71417	0.943000	0.38184	0.962000	0.63368	7.246000	0.78247	2.193000	0.70182	0.555000	0.69702	CCC	.	.	.	none		0.602	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482		G	2191111	C	G	2191111	3	3	94	1	0	0	0	0	1	0	0	0	4711	623	22	4	383	4	DOT1L	19	2191111	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08		2191111	56937872	58	5975											
CASP14	23581	hgsc.bcm.edu	37	chr19	15164633	15164633	+	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	ttcgtggtactcatggctcaCgggagggaaggcttcctcaa	8	10	13	10	2	3	0	3	0	0	0	5	2	4	2	1	5	1	3	1	5	3	3			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr19:15164633C>T	ENST00000427043.3	+	4	575	c.267C>T	c.(265-267)caC>caT	p.H89H	CASP14_ENST00000221740.1_Silent_p.H89H|AC004699.1_ENST00000411269.1_RNA	NM_012114.2	NP_036246.1	P31944	CASPE_HUMAN	caspase 14, apoptosis-related cysteine peptidase	89					cornification (GO:0070268)|epidermis development (GO:0008544)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinization (GO:0031424)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(3)	26						TCATGGCTCACGGGAGGGAAG	0.552																																					p.H89H		Atlas-SNP	.											.	CASP14	44	.	0			c.C267T						PASS	.						95	83	87					19																	15164633		2203	4300	6503	SO:0001819	synonymous_variant	23581	exon4			GGCTCACGGGAGG		CCDS12323.1	19p13.1	2008-07-16	2005-08-17			ENSG00000105141			1502	protein-coding gene	gene with protein product	"apoptosis-related cysteine protease"	605848	"caspase 14, apoptosis-related cysteine protease"			10203698, 9792675	Standard	NM_012114		Approved	MICE, MGC119078, MGC119079	uc010dzv.2	P31944		ENST00000427043.3:c.267C>T	chr19.hg19:g.15164633C>T		281.0	0.0	.		244.0	35.0	.	NM_012114	O95823|Q3SYC9	Silent	SNP	ENST00000427043.3	hg19	CCDS12323.1																																																																																			.	.	.	none		0.552	CASP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465663.1	NM_012114		T	15164633	C	T	15164633	2	4	94	1	0	0	0	0	0	0	0	1	2672	535	19	1		1	CASP14	19	15164633	Silent	SNP	C	TCGA-B9-4113-01A-01D-1252-08	12973522	15164633	43964350	59	5976											
NWD1	284434	hgsc.bcm.edu	37	chr19	16918705	16918705	+	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	ccttttacactcagctgcccGagaccctctccagcgtggcc	6	9	8	18	2	2	1	1	0	1	1	3	2	2	1	5	1	4	1	5	1	1	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr19:16918705G>A	ENST00000552788.1	+	16	4045	c.4045G>A	c.(4045-4047)Gag>Aag	p.E1349K	NWD1_ENST00000549814.1_Missense_Mutation_p.E1307K|NWD1_ENST00000523826.1_Missense_Mutation_p.E1143K|NWD1_ENST00000379808.3_Missense_Mutation_p.E1349K|NWD1_ENST00000524140.2_Missense_Mutation_p.E1349K|NWD1_ENST00000339803.6_Missense_Mutation_p.E1214K			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	1349							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						TCAGCTGCCCGAGACCCTCTC	0.567																																					p.E1349K		Atlas-SNP	.											.	NWD1	303	.	0			c.G4045A						PASS	.						152	131	138					19																	16918705		2203	4300	6503	SO:0001583	missense	284434	exon18			CTGCCCGAGACCC	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.4045G>A	chr19.hg19:g.16918705G>A	ENSP00000447224:p.Glu1349Lys	475.0	0.0	.		404.0	153.0	.	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	hg19		.	.	.	.	.	.	.	.	.	.	G	12.61	1.989439	0.35131	.	.	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.57907	0.45;0.44;0.45;0.37;0.43;0.44	4.95	3.91	0.45181	WD40 repeat-like-containing domain (1);	0.427481	0.20913	N	0.083440	T	0.24509	0.0594	L	0.27053	0.805	0.09310	N	1	P;B;B	0.45078	0.85;0.145;0.089	B;B;B	0.25140	0.058;0.039;0.017	T	0.14952	-1.0454	10	0.09843	T	0.71	-19.7004	6.6582	0.22998	0.1992:0.0:0.8008:0.0	.	1349;1349;1214	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	K	1214;1349;1307;1349;1143;1349;1214	ENSP00000428579:E1349K;ENSP00000447548:E1307K;ENSP00000369136:E1349K;ENSP00000428955:E1143K;ENSP00000447224:E1349K;ENSP00000340159:E1214K	ENSP00000340159:E1214K	E	+	1	0	NWD1	16779705	0.274000	0.24191	0.991000	0.47740	0.505000	0.33919	1.839000	0.39220	2.282000	0.76494	0.655000	0.94253	GAG	.	.	.	none		0.567	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525		A	16918705	G	A	16918705	3	1	94	1	0	0	0	0	1	0	0	0	10788	1059	37	1	3694	1	NWD1	19	16918705	Missense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08	1754072	16918705	42210278	60	5977											
ZNF285	26974	hgsc.bcm.edu	37	chr19	44896570	44896570	+	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	caggtttatctgggctttatCcaatagtgccagctcttcct	7	15	8	11	0	2	0	0	0	2	0	4	0	4	0	3	2	2	3	3	2	4	6	rs144077949	byFrequency	TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr19:44896570C>G	ENST00000330997.4	-	3	140	c.76G>C	c.(76-78)Gat>Cat	p.D26H	ZNF285_ENST00000591679.1_Missense_Mutation_p.D33H|CTC-512J12.4_ENST00000588655.1_RNA|CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000544719.2_Missense_Mutation_p.D26H	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	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)|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						TGGGCTTTATCCAATAGTGCC	0.453																																					p.D26H		Atlas-SNP	.											.	ZNF285	86	.	0			c.G76C						PASS	.						149	132	138					19																	44896570		2203	4300	6503	SO:0001583	missense	26974	exon3			CTTTATCCAATAG	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.76G>C	chr19.hg19:g.44896570C>G	ENSP00000333595:p.Asp26His	67.0	0.0	.		74.0	33.0	.	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Missense_Mutation	SNP	ENST00000330997.4	hg19	CCDS12638.1	.	.	.	.	.	.	.	.	.	.	C	17.50	3.405340	0.62288	.	.	ENSG00000062370	ENST00000544719;ENST00000330997	T;T	0.06142	3.34;4.17	3.07	1.89	0.25635	Krueppel-associated box (4);	.	.	.	.	T	0.23054	0.0557	M	0.88310	2.945	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.74674	0.984;0.984	T	0.09640	-1.0665	9	0.87932	D	0	.	3.2985	0.06974	0.2577:0.5999:0.0:0.1424	.	50;26	B7ZLR9;Q96NJ3	.;ZN285_HUMAN	H	49;26	ENSP00000439431:D49H;ENSP00000333595:D26H	ENSP00000333595:D26H	D	-	1	0	ZNF285	49588410	0.829000	0.29322	0.154000	0.22540	0.897000	0.52465	1.205000	0.32308	1.738000	0.51689	0.449000	0.29647	GAT	.	C|0.997;T|0.003	.	alt		0.453	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354		G	44896570	C	G	44896570	3	3	94	1	0	0	0	0	1	0	0	0	17834	855	30	4	1704	4	ZNF285	19	44896570	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	27977865	44896570	14232413	61	5978											
ZNF665	79788	hgsc.bcm.edu	37	chr19	53669370	53669370	+	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	agcccttctatcacgttgagCtcttctaccagggagatttt	8	14	8	11	1	4	2	1	1	3	1	4	3	4	2	2	1	3	2	2	1	2	7			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr19:53669370C>G	ENST00000600412.1	-	2	293	c.178G>C	c.(178-180)Gct>Cct	p.A60P	ZNF665_ENST00000396424.3_Missense_Mutation_p.A125P|CTD-2245F17.2_ENST00000600257.1_RNA			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	60					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		TCACGTTGAGCTCTTCTACCA	0.388																																					p.A125P		Atlas-SNP	.											.	ZNF665	136	.	0			c.G373C						PASS	.						118	124	122					19																	53669370		2073	4226	6299	SO:0001583	missense	79788	exon4			GTTGAGCTCTTCT		CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"Zinc fingers, C2H2-type", "-"	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.178G>C	chr19.hg19:g.53669370C>G	ENSP00000469154:p.Ala60Pro	271.0	0.0	.		196.0	64.0	.	NM_024733	A8K5T8	Missense_Mutation	SNP	ENST00000600412.1	hg19		.	.	.	.	.	.	.	.	.	.	C	7.108	0.575466	0.13623	.	.	ENSG00000197497	ENST00000396424	T	0.08370	3.1	2.4	-0.298	0.12814	.	.	.	.	.	T	0.04588	0.0125	N	0.17082	0.46	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.44267	-0.9339	9	0.24483	T	0.36	.	6.4255	0.21768	0.1793:0.4658:0.3549:0.0	.	125	Q9H7R5-2	.	P	125	ENSP00000379702:A125P	ENSP00000379702:A125P	A	-	1	0	ZNF665	58361182	0.000000	0.05858	0.003000	0.11579	0.034000	0.12701	0.042000	0.13949	0.315000	0.23110	0.543000	0.68304	GCT	.	.	.	none		0.388	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733		G	53669370	C	G	53669370	3	3	94	1	0	0	0	0	1	0	0	0	18085	797	28	4	1667	4	ZNF665	19	53669370	Missense_Mutation	SNP	C	TCGA-B9-4113-01A-01D-1252-08	8772800	53669370	5459613	62	5979											
PRIC285	85441	hgsc.bcm.edu	37	chr20	62193087	62193087	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcttcagctccatccttcTcaggagcagtcctgagggta	7	10	12	12	0	2	1	2	1	1	0	6	2	5	2	3	3	2	4	3	3	1	3			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr20:62193087T>C	ENST00000467148.1	-	12	6772	c.6703A>G	c.(6703-6705)Aga>Gga	p.R2235G	HELZ2_ENST00000427522.2_Missense_Mutation_p.R1666G	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2235	Interaction with THRAP3.				cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										TCCATCCTTCTCAGGAGCAGT	0.667																																					p.R2235G		Atlas-SNP	.											.	.	.	.	0			c.A6703G						PASS	.						28	28	28					20																	62193087		2195	4295	6490	SO:0001583	missense	85441	exon13			TCCTTCTCAGGAG	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.6703A>G	chr20.hg19:g.62193087T>C	ENSP00000417401:p.Arg2235Gly	88.0	0.0	.		63.0	23.0	.	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	hg19	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	T	8.870	0.949007	0.18356	.	.	ENSG00000130589	ENST00000427522;ENST00000467148	D;D	0.81821	-1.54;-1.54	2.96	1.78	0.24846	ATPase, AAA+ type, core (1);	1.202560	0.05584	N	0.573417	T	0.76772	0.4034	L	0.41124	1.26	0.29383	N	0.863141	B;B	0.29270	0.24;0.122	B;B	0.39027	0.288;0.19	T	0.68161	-0.5482	10	0.66056	D	0.02	-9.3242	4.3793	0.11286	0.0:0.1118:0.2045:0.6837	.	2235;1666	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	G	1666;2235	ENSP00000393257:R1666G;ENSP00000417401:R2235G	ENSP00000393257:R1666G	R	-	1	2	RP4-697K14.7	61663531	0.466000	0.25823	0.958000	0.39756	0.288000	0.27193	0.564000	0.23563	0.497000	0.27926	0.402000	0.26972	AGA	.	.	.	none		0.667	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		C	62193087	T	C	62193087	3	2	94	1	0	0	0	0	1	0	0	0	12495	1559	54	3	1278	3	PRIC285	20	62193087	Missense_Mutation	SNP	T	TCGA-B9-4113-01A-01D-1252-08		62193087	832433	63	5980											
LSS	4047	hgsc.bcm.edu	37	chr21	47626684	47626684	+	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	gatttctcatgttcagcagcTgaaatcacagagagcaccct	12	10	8	11	0	3	2	3	1	1	1	4	4	3	2	1	0	3	4	1	0	1	2			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr21:47626684T>G	ENST00000397728.3	-	16	1546		c.e16-2		LSS_ENST00000522411.1_Splice_Site|LSS_ENST00000356396.4_Splice_Site|LSS_ENST00000457828.2_Splice_Site	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)						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)					GTTCAGCAGCTGAAATCACAG	0.582																																					.	Pancreas(114;955 2313 34923 50507)	Atlas-SNP	.											.	LSS	50	.	0			c.1468-2A>C						PASS	.						71	60	64					21																	47626684		2203	4300	6503	SO:0001630	splice_region_variant	4047	exon17			AGCAGCTGAAATC	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.1468-2A>C	chr21.hg19:g.47626684T>G		175.0	0.0	.		154.0	59.0	.	NM_001001438	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Splice_Site	SNP	ENST00000397728.3	hg19	CCDS13733.1	.	.	.	.	.	.	.	.	.	.	T	14.90	2.674567	0.47781	.	.	ENSG00000160285	ENST00000356396;ENST00000457828;ENST00000397728;ENST00000522411	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4665	0.75406	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	LSS	46451112	1.000000	0.71417	0.974000	0.42286	0.221000	0.24807	7.752000	0.85141	2.206000	0.71126	0.533000	0.62120	.	.	.	.	none		0.582	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2		Intron	G	47626684	T	G	47626684	5	3	94	1	0	0	0	0	0	0	1	0	9072	1594	55	5	760	5	LSS	21	47626684	Splice_Site	SNP	T	TCGA-B9-4113-01A-01D-1252-08		47626684	503211	64	5981											
TOP3B	8940	hgsc.bcm.edu	37	chr22	22319734	22319735	+	In_Frame_Ins	INS	-	-	TTG																															cttggccttttctttcctgcINSttgtggcctccacctggaag																										TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr22:22319734_22319735insTTG	ENST00000398793.2	-	9	1299_1300	c.865_866insCAA	c.(865-867)agc>aCAAgc	p.288_289insT	TOP3B_ENST00000413067.2_In_Frame_Ins_p.17_18insT|TOP3B_ENST00000357179.5_In_Frame_Ins_p.288_289insT	NM_003935.3	NP_003926.1	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	288					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)		TTCTTTCCTGCTTGTGGCCTCC	0.535																																					p.S289delinsTS		Atlas-INDEL	.											.	TOP3B	107	.	0			c.866_867insCAA						PASS	.																																			SO:0001652	inframe_insertion	8940	exon9			.	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.863_865dupCAA	chr22.hg19:g.22319735_22319737dupTTG	ENSP00000381773:p.Thr288_Thr288dup	68.0	0.0	0		55.0	14.0	0.254545	NM_003935	A0M8Q3|Q9BUP5	In_Frame_Ins	INS	ENST00000398793.2	hg19	CCDS13797.1																																																																																			.	.	.	none		0.535	TOP3B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320251.1	NM_003935		TTG	22319735	-	TTG	22319734	7	5	94	1	0	1	1	0	0	0	0	0	16380	797	28	0	1762	0	TOP3B	22	22319734	In_Frame_Ins	INS	-	TCGA-B9-4113-01A-01D-1252-08		22319734	28984832	65	5982											
CYP2D6	1565	hgsc.bcm.edu	37	chr22	42523507	42523516	+	Frame_Shift_Del	DEL	AGGGGGACGA	AGGGGGACGA	-																															atgtcatatgggtcacacccAgggggacgatgtccccaaag																								rs149686350|rs61745683	byFrequency	TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	AGGGGGACGA	AGGGGGACGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chr22:42523507_42523516delAGGGGGACGA	ENST00000360608.5	-	7	1220_1229	c.1106_1115delTCGTCCCCCT	c.(1105-1116)atcgtccccctgfs	p.IVPL369fs	CYP2D6_ENST00000389970.3_Frame_Shift_Del_p.IVPL369fs|CYP2D6_ENST00000359033.4_Frame_Shift_Del_p.IVPL318fs|NDUFA6-AS1_ENST00000595777.1_RNA|NDUFA6-AS1_ENST00000536447.2_RNA|NDUFA6-AS1_ENST00000610250.1_RNA|NDUFA6-AS1_ENST00000451451.1_RNA|NDUFA6-AS1_ENST00000600968.1_RNA|NDUFA6-AS1_ENST00000434834.1_RNA|NDUFA6-AS1_ENST00000417327.1_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|NDUFA6-AS1_ENST00000439129.1_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	369			I -> T (in allele CYP2D6*26).		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)	p.I318I(1)|p.I369I(1)		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)	GGTCACACCCAGGGGGACGATGTCCCCAAA	0.624																																					p.369_372del		Atlas-INDEL	.											.	CYP2D6	104	.	2	Substitution - coding silent(2)	urinary_tract(2)	c.1107_1116del						PASS	.																																			SO:0001589	frameshift_variant	1565	exon7			.	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.1106_1115delTCGTCCCCCT	chr22.hg19:g.42523507_42523516delAGGGGGACGA	ENSP00000353820:p.Ile369fs	205.0	0.0	0		147.0	14.0	0.0952381	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Frame_Shift_Del	DEL	ENST00000360608.5	hg19	CCDS46721.1																																																																																			.	.	.	none		0.624	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1			-	42523516	AGGGGGACGA	-	42523507	7	5	94	1	0	1	0	1	0	0	0	0	4171	188	7	0	390	0	CYP2D6	22	42523507	Frame_Shift_Del	DEL	AGGGGGACGA	TCGA-B9-4113-01A-01D-1252-08	20203773	42523507	8781059	66	5983											
LONRF3	79836	hgsc.bcm.edu	37	chrX	118109101	118109101	+	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	agaaagtcccgcaaggcgagGcgctggcgccggcgcccccg	7	2	16	16	7	0	1	0	0	0	1	1	2	1	1	4	4	0	2	4	4	2	0			TCGA-B9-4113-01A-01D-1252-08	TCGA-B9-4113-11A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	527ea66a-fb9e-4308-b49d-48226ac05304	881301ff-ec26-46fd-834f-93d9b3ec8da0	g.chrX:118109101G>T	ENST00000371628.3	+	1	389	c.358G>T	c.(358-360)Gcg>Tcg	p.A120S	LONRF3_ENST00000422289.2_5'Flank|LONRF3_ENST00000304778.7_Missense_Mutation_p.A120S	NM_001031855.1	NP_001027026.1	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger 3	120							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						GCAAGGCGAGGCGCTGGCGCC	0.731																																					p.A120S		Atlas-SNP	.											.	LONRF3	138	.	0			c.G358T						PASS	.						2	3	3					X																	118109101		1637	3395	5032	SO:0001583	missense	79836	exon1			GGCGAGGCGCTGG	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.358G>T	chrX.hg19:g.118109101G>T	ENSP00000360690:p.Ala120Ser	7.0	0.0	.		8.0	7.0	.	NM_001031855	Q5JPN6|Q8NB00|Q9H647	Missense_Mutation	SNP	ENST00000371628.3	hg19	CCDS35374.1	.	.	.	.	.	.	.	.	.	.	G	3.593	-0.083174	0.07141	.	.	ENSG00000175556	ENST00000365713;ENST00000304778;ENST00000371628	T;T;T	0.80738	-1.41;-1.41;-1.17	4.27	3.38	0.38709	.	1.631660	0.03606	N	0.234137	T	0.65544	0.2701	N	0.08118	0	0.80722	D	1	B;B	0.23249	0.082;0.062	B;B	0.24394	0.053;0.024	T	0.41052	-0.9530	10	0.09590	T	0.72	-3.3969	10.5187	0.44905	0.0:0.1987:0.8013:0.0	.	120;120	Q496Y0-2;Q496Y0	.;LONF3_HUMAN	S	120	ENSP00000360691:A120S;ENSP00000307732:A120S;ENSP00000360690:A120S	ENSP00000307732:A120S	A	+	1	0	LONRF3	117993129	0.999000	0.42202	0.063000	0.19743	0.011000	0.07611	1.162000	0.31786	0.786000	0.33708	0.529000	0.55759	GCG	.	.	.	none		0.731	LONRF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355124.2	NM_024778		T	118109101	G	T	118109101	3	4	94	1	0	0	0	0	1	0	0	0	8903	1203	42	4	360	4	LONRF3	23	118109101	Missense_Mutation	SNP	G	TCGA-B9-4113-01A-01D-1252-08		118109101	37161459	67	5984											
ZYG11B	79699	hgsc.bcm.edu	37	chr1	53236935	53236935	+	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	cctggtgctgaattcattaaCtctctccctcgaggatcctt	7	14	7	13	1	2	1	1	1	1	0	6	3	4	2	3	2	2	1	3	2	2	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr1:53236935C>A	ENST00000294353.6	+	3	585	c.440C>A	c.(439-441)aCt>aAt	p.T147N	ZYG11B_ENST00000443756.2_Missense_Mutation_p.T147N|ZYG11B_ENST00000545132.1_Missense_Mutation_p.T147N	NM_024646.2	NP_078922.1	Q9C0D3	ZY11B_HUMAN	zyg-11 family member B, cell cycle regulator	147										breast(1)|endometrium(1)|kidney(6)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	30						AATTCATTAACTCTCTCCCTC	0.478																																					p.T147N		Atlas-SNP	.											.	ZYG11B	61	.	0			c.C440A						PASS	.						97	94	95					1																	53236935		2203	4300	6503	SO:0001583	missense	79699	exon3			CATTAACTCTCTC	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.440C>A	chr1.hg19:g.53236935C>A	ENSP00000294353:p.Thr147Asn	169.0	0.0	.		73.0	24.0	.	NM_024646	Q8N2X3|Q9H8L8	Missense_Mutation	SNP	ENST00000294353.6	hg19	CCDS30717.1	.	.	.	.	.	.	.	.	.	.	C	15.14	2.745282	0.49151	.	.	ENSG00000162378	ENST00000443756;ENST00000545132;ENST00000294353	T;T;T	0.07021	3.23;3.23;3.23	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.09686	0.0238	L	0.38175	1.15	0.58432	D	0.999994	B;B	0.24258	0.1;0.027	B;B	0.22753	0.041;0.013	T	0.24977	-1.0145	10	0.23891	T	0.37	.	19.6182	0.95643	0.0:1.0:0.0:0.0	.	147;147	B4DK95;Q9C0D3	.;ZY11B_HUMAN	N	147	ENSP00000400522:T147N;ENSP00000441315:T147N;ENSP00000294353:T147N	ENSP00000294353:T147N	T	+	2	0	ZYG11B	53009523	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.662000	0.68032	2.653000	0.90120	0.650000	0.86243	ACT	.	.	.	none		0.478	ZYG11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024749.1	NM_024646		A	53236935	C	A	53236935	3	1	95	1	0	0	0	0	1	0	0	0	18265	565	20	4	450	4	ZYG11B	1	53236935	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08		53236935	196013686	1	5985											
SGIP1	84251	hgsc.bcm.edu	37	chr1	67138996	67138996	+	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	agatgacactacggcccttgCtcctctctttggcccaccac	7	10	7	17	1	1	2	0	1	1	1	3	2	2	2	4	2	2	1	4	2	1	3	rs142151342		TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr1:67138996C>A	ENST00000371037.4	+	12	670	c.593C>A	c.(592-594)gCt>gAt	p.A198D	SGIP1_ENST00000371035.3_Missense_Mutation_p.A155D|SGIP1_ENST00000371036.3_Missense_Mutation_p.A165D|SGIP1_ENST00000468286.1_3'UTR|SGIP1_ENST00000371039.1_Missense_Mutation_p.A166D|AL139147.1_ENST00000502413.2_Intron|SGIP1_ENST00000237247.6_Missense_Mutation_p.A202D	NM_032291.2	NP_115667.2	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting protein 1	198	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						ACGGCCCTTGCTCCTCTCTTT	0.363																																					p.A198D		Atlas-SNP	.											.	SGIP1	272	.	0			c.C593A						PASS	.						177	185	183					1																	67138996		2203	4300	6503	SO:0001583	missense	84251	exon12			CCCTTGCTCCTCT	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.593C>A	chr1.hg19:g.67138996C>A	ENSP00000360076:p.Ala198Asp	620.0	0.0	.		301.0	95.0	.	NM_032291	A6NL81|A6NLD1|Q4LE32|Q5VYE2|Q5VYE3|Q5VYE4|Q68D76|Q6MZY6|Q8IWC2	Missense_Mutation	SNP	ENST00000371037.4	hg19	CCDS30744.1	.	.	.	.	.	.	.	.	.	.	C	13.76	2.332511	0.41297	.	.	ENSG00000118473	ENST00000237247;ENST00000371039;ENST00000424320;ENST00000371035;ENST00000371038;ENST00000407289;ENST00000371036;ENST00000371037	T;T;T;T;T;T	0.03330	3.97;3.97;3.97;3.97;3.97;3.97	5.73	5.73	0.89815	.	0.171335	0.52532	D	0.000074	T	0.04003	0.0112	N	0.17474	0.49	0.35690	D	0.814803	D	0.71674	0.998	D	0.76071	0.987	T	0.59736	-0.7398	10	0.11485	T	0.65	-18.8968	18.4621	0.90743	0.0:1.0:0.0:0.0	.	198	Q9BQI5	SGIP1_HUMAN	D	202;166;190;155;201;201;165;198	ENSP00000237247:A202D;ENSP00000360078:A166D;ENSP00000410439:A190D;ENSP00000360074:A155D;ENSP00000360075:A165D;ENSP00000360076:A198D	ENSP00000237247:A202D	A	+	2	0	SGIP1	66911584	0.996000	0.38824	1.000000	0.80357	0.595000	0.36748	4.773000	0.62331	2.718000	0.92993	0.650000	0.86243	GCT	.	C|1.000;G|0.000	.	alt		0.363	SGIP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025395.4	NM_032291		A	67138996	C	A	67138996	3	1	95	1	0	0	0	0	1	0	0	0	14219	797	28	4	639	4	SGIP1	1	67138996	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	13902061	67138996	182111625	2	5986											
BCAR3	8412	hgsc.bcm.edu	37	chr1	94054731	94054731	+	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	tggaagatgatggcgccactCtgctgggagatgggccggcg	7	7	18	9	3	1	3	0	1	1	2	1	5	1	4	2	5	1	1	2	5	1	0			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr1:94054731C>T	ENST00000370244.1	-	7	1020	c.732G>A	c.(730-732)caG>caA	p.Q244Q	BCAR3_ENST00000260502.6_Silent_p.Q244Q|BCAR3_ENST00000370247.3_Silent_p.Q153Q|BCAR3_ENST00000370243.1_Silent_p.Q244Q	NM_001261408.1	NP_001248337.1	O75815	BCAR3_HUMAN	breast cancer anti-estrogen resistance 3	244	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				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)		TGGCGCCACTCTGCTGGGAGA	0.667																																					p.Q244Q		Atlas-SNP	.											.	BCAR3	62	.	0			c.G732A						PASS	.						30	30	30					1																	94054731		2203	4300	6503	SO:0001819	synonymous_variant	8412	exon5			GCCACTCTGCTGG	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.732G>A	chr1.hg19:g.94054731C>T		61.0	0.0	.		94.0	35.0	.	NM_001261409	D3DT43|Q5TEW3|Q6UW40|Q9BR50	Silent	SNP	ENST00000370244.1	hg19	CCDS745.1																																																																																			.	.	.	none		0.667	BCAR3-003	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028420.1			T	94054731	C	T	94054731	2	4	95	1	0	0	0	0	0	0	0	1	1349	912	32	2		2	BCAR3	1	94054731	Silent	SNP	C	TCGA-B9-4114-01A-01D-1252-08	26915735	94054731	155195890	3	5987											
ATP1A1	476	hgsc.bcm.edu	37	chr1	116931576	116931576	+	Missense_Mutation	SNP	A	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	accccagactaggtctccagAtttcacaaatgaaaaccccc	14	7	5	15	0	2	3	1	1	1	2	3	3	2	3	5	1	1	0	5	1	4	2			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr1:116931576A>C	ENST00000295598.5	+	7	941	c.689A>C	c.(688-690)gAt>gCt	p.D230A	ATP1A1_ENST00000369496.4_Missense_Mutation_p.D199A|ATP1A1_ENST00000537345.1_Missense_Mutation_p.D230A|ATP1A1_ENST00000491156.1_3'UTR	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	230					ATP biosynthetic process (GO:0006754)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|membrane hyperpolarization (GO:0060081)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of glucocorticoid biosynthetic process (GO:0031947)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart contraction (GO:0045823)|positive regulation of striated muscle contraction (GO:0045989)|potassium ion import (GO:0010107)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of sodium ion transport (GO:0002028)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|chaperone binding (GO:0051087)|phosphatase activity (GO:0016791)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(2)|breast(2)|cervix(3)|endometrium(2)|kidney(5)|large_intestine(9)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Ciclopirox(DB01188)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Ethacrynic acid(DB00903)|Hydroflumethiazide(DB00774)|Ouabain(DB01092)|Trichlormethiazide(DB01021)	AGGTCTCCAGATTTCACAAAT	0.453																																					p.D230A		Atlas-SNP	.											.	ATP1A1	87	.	0			c.A689C						PASS	.						86	90	89					1																	116931576		2203	4300	6503	SO:0001583	missense	476	exon7			CTCCAGATTTCAC	D00099	CCDS887.1, CCDS53351.1, CCDS53352.1	1p13	2012-10-22			ENSG00000163399	ENSG00000163399	3.6.3.9	"ATPases / P-type"	799	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-1", "sodium pump subunit alpha-1", "sodium-potassium ATPase catalytic subunit alpha-1"	182310					Standard	NM_000701		Approved		uc001ege.3	P05023	OTTHUMG00000012109	ENST00000295598.5:c.689A>C	chr1.hg19:g.116931576A>C	ENSP00000295598:p.Asp230Ala	193.0	0.0	.		89.0	38.0	.	NM_001160233	B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Missense_Mutation	SNP	ENST00000295598.5	hg19	CCDS887.1	.	.	.	.	.	.	.	.	.	.	A	18.67	3.674536	0.67928	.	.	ENSG00000163399	ENST00000295598;ENST00000537345;ENST00000339159;ENST00000369496	D;D;D	0.90197	-2.63;-2.63;-2.63	5.14	5.14	0.70334	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	T	0.82098	0.4963	L	0.41027	1.25	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.81493	-0.0908	10	0.87932	D	0	.	15.1179	0.72419	1.0:0.0:0.0:0.0	.	230;230	F5H3A1;P05023	.;AT1A1_HUMAN	A	230;230;229;199	ENSP00000295598:D230A;ENSP00000445306:D230A;ENSP00000358508:D199A	ENSP00000295598:D230A	D	+	2	0	ATP1A1	116733099	1.000000	0.71417	0.971000	0.41717	0.988000	0.76386	9.139000	0.94554	2.165000	0.68154	0.533000	0.62120	GAT	.	.	.	none		0.453	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5	NM_001160233		C	116931576	A	C	116931576	3	2	95	1	0	0	0	0	1	0	0	0	1128	333	12	5	731	5	ATP1A1	1	116931576	Missense_Mutation	SNP	A	TCGA-B9-4114-01A-01D-1252-08	22876845	116931576	132319045	4	5988											
CELF3	11189	hgsc.bcm.edu	37	chr1	151678722	151678722	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctctttgctgctgctgctgTtgctgctgctgctgctgctg	0	17	12	12	0	1	0	0	0	1	0	2	0	1	0	0	0	10	11	0	0	0	2			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr1:151678722T>C	ENST00000290583.4	-	10	1897	c.1104A>G	c.(1102-1104)caA>caG	p.Q368Q	CELF3_ENST00000392706.3_Silent_p.Q163Q|RP11-98D18.1_ENST00000457548.1_RNA|CELF3_ENST00000290585.4_Silent_p.Q318Q|CELF3_ENST00000470688.1_5'UTR	NM_001172648.1|NM_007185.4	NP_001166119.1|NP_009116.3	Q5SZQ8	CELF3_HUMAN	CUGBP, Elav-like family member 3	368	Gln-rich.				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	21						gctgctgctgttgctgctgct	0.657																																					p.Q368Q		Atlas-SNP	.											CELF3,caecum,carcinoma,0,1	CELF3	49	.	0			c.A1104G						PASS	.						19	20	20					1																	151678722		2200	4297	6497	SO:0001819	synonymous_variant	11189	exon10			CTGCTGTTGCTGC	U80759	CCDS1002.1, CCDS53367.1	1q21	2013-02-12	2010-02-19	2010-02-19	ENSG00000159409	ENSG00000159409		"Trinucleotide (CAG) repeat containing", "RNA binding motif (RRM) containing"	11967	protein-coding gene	gene with protein product	"expanded repeat domain, CAG/CTG 4", "CAG repeat domain", "CUG-BP and ETR-3 like factor 3"	612678	"trinucleotide repeat containing 4"	TNRC4		9225980	Standard	XM_005244859		Approved	CAGH4, BRUNOL1, ERDA4, MGC57297	uc001eys.2	Q5SZQ8	OTTHUMG00000013064	ENST00000290583.4:c.1104A>G	chr1.hg19:g.151678722T>C		13.0	0.0	.		35.0	3.0	.	NM_007185	B7ZKK6|O15414|Q499Y6|Q5SZQ7|Q6NVK0|Q8IZ98|Q9BZC2|Q9HB30	Silent	SNP	ENST00000290583.4	hg19	CCDS1002.1	.	.	.	.	.	.	.	.	.	.	.	4.938	0.174339	0.09391	.	.	ENSG00000159409	ENST00000420342	.	.	.	3.25	1.39	0.22231	.	.	.	.	.	T	0.36496	0.0969	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.19943	-1.0290	4	.	.	.	-0.0118	5.4728	0.16680	0.0:0.7409:0.0:0.2591	.	.	.	.	S	369	.	.	N	-	2	0	CELF3	149945346	0.076000	0.21285	1.000000	0.80357	0.644000	0.38419	-0.812000	0.04496	0.416000	0.25844	-0.389000	0.06534	AAC	.	.	.	none		0.657	CELF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036663.2	NM_007185		C	151678722	T	C	151678722	2	2	95	1	0	0	0	0	0	0	0	1	3219	1722	60	3		3	CELF3	1	151678722	Silent	SNP	T	TCGA-B9-4114-01A-01D-1252-08	34747146	151678722	97571899	5	5989											
PGLYRP3	114771	hgsc.bcm.edu	37	chr1	153279661	153279661	+	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	0	0	0	0	0	0	0	0	0	gggagctggtctgtgatgatGtaggccacaggcagggtcag	8	8	18	7	0	2	2	1	2	1	0	2	3	2	3	1	5	1	3	1	5	1	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr1:153279661G>C	ENST00000290722.1	-	2	190	c.138C>G	c.(136-138)taC>taG	p.Y46*		NM_052891.1	NP_443123.1	Q96LB9	PGRP3_HUMAN	peptidoglycan recognition protein 3	46					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(1)|liver(1)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	28	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CTGTGATGATGTAGGCCACAG	0.622																																					p.Y46X		Atlas-SNP	.											.	PGLYRP3	55	.	0			c.C138G						PASS	.						53	47	49					1																	153279661		2203	4300	6503	SO:0001587	stop_gained	114771	exon2			GATGATGTAGGCC	AY035376	CCDS1035.1	1q21	2008-02-05			ENSG00000159527	ENSG00000159527			30014	protein-coding gene	gene with protein product	"peptidoglycan recognition protein I alpha precursor"	608197				11461926	Standard	NM_052891		Approved	PGRPIA, PGLYRPIalpha, PGRP-Ialpha	uc001fbn.1	Q96LB9	OTTHUMG00000014044	ENST00000290722.1:c.138C>G	chr1.hg19:g.153279661G>C	ENSP00000290722:p.Tyr46*	42.0	0.0	.		74.0	23.0	.	NM_052891	A1A4U8|Q5SY65	Nonsense_Mutation	SNP	ENST00000290722.1	hg19	CCDS1035.1	.	.	.	.	.	.	.	.	.	.	G	14.60	2.582950	0.46006	.	.	ENSG00000159527	ENST00000290722	.	.	.	4.06	-2.35	0.06684	.	0.381500	0.19389	N	0.115444	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.6165	8.7113	0.34385	0.4751:0.0:0.5249:0.0	.	.	.	.	X	46	.	ENSP00000290722:Y46X	Y	-	3	2	PGLYRP3	151546285	0.000000	0.05858	0.045000	0.18777	0.020000	0.10135	-0.301000	0.08232	-0.603000	0.05767	-0.137000	0.14449	TAC	.	.	.	none		0.622	PGLYRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039488.1	NM_052891		C	153279661	G	C	153279661	4	2	95	1	0	0	0	0	0	1	0	0	11802	1372	48	4	911	4	PGLYRP3	1	153279661	Nonsense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	1600939	153279661	95970960	6	5990											
IRF2BP2	359948	hgsc.bcm.edu	37	chr1	234743056	234743058	+	In_Frame_Del	DEL	AGC	AGC	-																															gctttgtctggagcaagggaAgcagaacttgtgcgaaggga																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	AGC	AGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr1:234743056_234743058delAGC	ENST00000366609.3	-	2	1619_1621	c.1589_1591delGCT	c.(1588-1593)tgcttc>ttc	p.C530del	RP4-781K5.2_ENST00000436039.1_RNA|IRF2BP2_ENST00000366610.3_In_Frame_Del_p.C514del|IRF2BP2_ENST00000491430.1_5'UTR	NM_182972.2	NP_892017.2	Q7Z5L9	I2BP2_HUMAN	interferon regulatory factor 2 binding protein 2	530	Cys-rich.				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)			GAGCAAGGGAAGCAGAACTTGTG	0.586																																					p.530_531del		Atlas-INDEL	.											.	IRF2BP2	37	.	0			c.1590_1592del						PASS	.																																			SO:0001651	inframe_deletion	359948	exon2			.	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.1589_1591delGCT	chr1.hg19:g.234743056_234743058delAGC	ENSP00000355568:p.Cys530del	217.0	0.0	0		313.0	74.0	0.236422	NM_182972	B1AM35|B1AM36|Q6P083|Q7Z5L8|Q8N351|Q8WUH8	In_Frame_Del	DEL	ENST00000366609.3	hg19	CCDS1602.1																																																																																			.	.	.	none		0.586	IRF2BP2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000092705.1	NM_182972		-	234743058	AGC	-	234743056	7	5	95	1	0	1	0	1	0	0	0	0	7837	72	3	0	176	0	IRF2BP2	1	234743056	In_Frame_Del	DEL	AGC	TCGA-B9-4114-01A-01D-1252-08	81463395	234743056	14507565	7	5991											
CAPN13	92291	hgsc.bcm.edu	37	chr2	30955349	30955349	+	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	gaagcagaccaggctggggaAgctgaccctgccgacgctgt	9	5	15	12	2	0	2	0	1	0	1	0	5	0	3	3	3	3	4	3	3	2	0			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr2:30955349A>T	ENST00000295055.8	-	20	2058	c.1882T>A	c.(1882-1884)Ttc>Atc	p.F628I	CAPN13_ENST00000534090.2_Missense_Mutation_p.F628I	NM_144575.2	NP_653176.2	Q6MZZ7	CAN13_HUMAN	calpain 13	628					proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	30	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					AGGCTGGGGAAGCTGACCCTG	0.597																																					p.F628I		Atlas-SNP	.											.	CAPN13	70	.	0			c.T1882A						PASS	.						27	31	30					2																	30955349		2106	4221	6327	SO:0001583	missense	92291	exon20			TGGGGAAGCTGAC		CCDS46252.1	2p22-p21	2008-02-05			ENSG00000162949	ENSG00000162949			16663	protein-coding gene	gene with protein product		610228				11675017	Standard	NM_144575		Approved	FLJ23523	uc021vfm.1	Q6MZZ7	OTTHUMG00000152053	ENST00000295055.8:c.1882T>A	chr2.hg19:g.30955349A>T	ENSP00000295055:p.Phe628Ile	33.0	0.0	.		52.0	13.0	.	NM_144575	Q17RF0|Q580X1|Q8TE80	Missense_Mutation	SNP	ENST00000295055.8	hg19	CCDS46252.1	.	.	.	.	.	.	.	.	.	.	a	26.8	4.772877	0.90108	.	.	ENSG00000162949	ENST00000295055;ENST00000534090	T;T	0.35789	1.29;1.29	5.5	5.5	0.81552	EF-hand-like domain (1);	0.051382	0.85682	D	0.000000	T	0.63414	0.2509	M	0.87038	2.855	0.43787	D	0.996328	D	0.89917	1.0	D	0.68621	0.959	T	0.70539	-0.4844	10	0.87932	D	0	.	13.1283	0.59368	1.0:0.0:0.0:0.0	.	628	Q6MZZ7	CAN13_HUMAN	I	628	ENSP00000295055:F628I;ENSP00000431298:F628I	ENSP00000295055:F628I	F	-	1	0	CAPN13	30808853	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.047000	0.64232	2.094000	0.63399	0.529000	0.55759	TTC	.	.	.	none		0.597	CAPN13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325101.2	NM_144575		T	30955349	A	T	30955349	3	4	95	1	0	0	0	0	1	0	0	0	2628	72	3	5	139	5	CAPN13	2	30955349	Missense_Mutation	SNP	A	TCGA-B9-4114-01A-01D-1252-08		30955349	212244024	8	5992											
TRAK2	66008	hgsc.bcm.edu	37	chr2	202262967	202262967	+	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	gataagctaaaggactcattGaaccgaagaggtgtagaaca	17	7	11	6	1	1	3	1	1	0	2	1	6	1	4	1	2	3	2	1	2	7	4	rs201579398		TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr2:202262967G>A	ENST00000332624.3	-	6	1019	c.591C>T	c.(589-591)ttC>ttT	p.F197F	TRAK2_ENST00000430254.1_Silent_p.F197F	NM_015049.2	NP_055864.2	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2	197	HAP1 N-terminal.				protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GABA receptor binding (GO:0050811)|receptor binding (GO:0005102)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	23						AGGACTCATTGAACCGAAGAG	0.438																																					p.F197F		Atlas-SNP	.											.	TRAK2	62	.	0			c.C591T						PASS	.	G		0,4406		0,0,2203	128	123	125		591	4.9	1	2		125	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TRAK2	NM_015049.2		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		197/915	202262967	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	66008	exon6			CTCATTGAACCGA	AB038951	CCDS2347.1	2q33.1	2012-03-05	2005-12-13	2005-12-13	ENSG00000115993	ENSG00000115993			13206	protein-coding gene	gene with protein product	"gamma-aminobutyric acid(A) receptor-interacting factor", "milton homolog 2 (Drosophila)", "O-linked N-acetylglucosamine transferase interacting protein 98"	607334	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 3"	ALS2CR3		11161814, 16380713, 20230862	Standard	NM_015049		Approved	CALS-C, KIAA0549, GRIF-1, OIP98, MILT2	uc002uyb.4	O60296	OTTHUMG00000132822	ENST00000332624.3:c.591C>T	chr2.hg19:g.202262967G>A		230.0	0.0	.		17.0	9.0	.	NM_015049	E7EV21|Q8WVH7|Q96NS2|Q9C0K5|Q9C0K6	Silent	SNP	ENST00000332624.3	hg19	CCDS2347.1																																																																																			.	G|0.999;A|0.001	0.001	weak		0.438	TRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256284.3	NM_015049		A	202262967	G	A	202262967	2	1	95	1	0	0	0	0	0	0	0	1	16462	1281	45	2		2	TRAK2	2	202262967	Silent	SNP	G	TCGA-B9-4114-01A-01D-1252-08	171307618	202262967	40936406	9	5993											
SP140	11262	hgsc.bcm.edu	37	chr2	231177371	231177371	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaatttcaaggaagtgtttgCtattcaggaaacaaatggga	15	11	11	4	0	2	0	2	0	0	0	2	4	2	3	0	3	2	2	0	3	6	4			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr2:231177371C>T	ENST00000392045.3	+	27	2690	c.2576C>T	c.(2575-2577)gCt>gTt	p.A859V	SP140_ENST00000417495.3_Missense_Mutation_p.A745V|SP140_ENST00000420434.3_Missense_Mutation_p.A832V|SP140_ENST00000343805.6_Missense_Mutation_p.A799V|SP140_ENST00000486687.2_Intron|SP140_ENST00000350136.5_Missense_Mutation_p.A728V	NM_007237.4	NP_009168.4	Q13342	SP140_HUMAN	SP140 nuclear body protein	859					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)		GAAGTGTTTGCTATTCAGGAA	0.393																																					p.A859V		Atlas-SNP	.											.	SP140	121	.	0			c.C2576T						PASS	.						157	145	149					2																	231177371		1872	4114	5986	SO:0001583	missense	11262	exon27			TGTTTGCTATTCA	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.2576C>T	chr2.hg19:g.231177371C>T	ENSP00000375899:p.Ala859Val	232.0	0.0	.		152.0	46.0	.	NM_007237	E7ESH9|E7EUR5|E9PFJ6|Q0VGE5|Q13341|Q3KR17|Q4ZG66|Q53TG1|Q6NSG4|Q92881|Q96TG3	Missense_Mutation	SNP	ENST00000392045.3	hg19	CCDS42831.1	.	.	.	.	.	.	.	.	.	.	C	17.17	3.321189	0.60634	.	.	ENSG00000079263	ENST00000350136;ENST00000392045;ENST00000417495;ENST00000343805;ENST00000420434	T;T;T;T	0.45668	0.89;0.89;0.89;0.89	3.48	2.5	0.30297	Bromodomain (3);	.	.	.	.	T	0.57562	0.2062	M	0.68952	2.095	0.23645	N	0.997215	D;P;D;D	0.64830	0.993;0.956;0.992;0.994	D;B;P;P	0.72625	0.978;0.39;0.708;0.663	T	0.38499	-0.9658	9	0.87932	D	0	-5.2094	7.4406	0.27181	0.2583:0.7417:0.0:0.0	.	832;745;799;859	E7EUR5;E7ESH9;E9PFJ6;Q13342	.;.;.;LY10_HUMAN	V	728;859;745;799;832	ENSP00000345846:A728V;ENSP00000375899:A859V;ENSP00000342096:A799V;ENSP00000398210:A832V	ENSP00000342096:A799V	A	+	2	0	SP140	230885615	0.425000	0.25498	0.936000	0.37596	0.918000	0.54935	0.202000	0.17295	1.966000	0.57179	0.462000	0.41574	GCT	.	.	.	none		0.393	SP140-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000332015.1	NM_007237		T	231177371	C	T	231177371	3	4	95	1	0	0	0	0	1	0	0	0	14975	797	28	2	2799	2	SP140	2	231177371	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	28914404	231177371	12022002	10	5994											
IFT57	55081	hgsc.bcm.edu	37	chr3	107937434	107937434	+	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	ttcttcagcgaagcaatcaaGaacatagcatacatgttctc	14	11	6	10	1	4	1	2	0	2	1	5	2	4	1	0	0	5	3	0	0	6	5			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr3:107937434G>C	ENST00000264538.3	-	3	689	c.442C>G	c.(442-444)Ctt>Gtt	p.L148V		NM_018010.3	NP_060480.1	Q9NWB7	IFT57_HUMAN	intraflagellar transport 57	148					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cilium assembly (GO:0042384)|heart looping (GO:0001947)|intraciliary transport (GO:0042073)|left/right pattern formation (GO:0060972)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|dendrite terminus (GO:0044292)|Golgi apparatus (GO:0005794)|intraciliary transport particle B (GO:0030992)|photoreceptor connecting cilium (GO:0032391)	DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	14			OV - Ovarian serous cystadenocarcinoma(3;0.0428)|Epithelial(53;0.246)			AAGCAATCAAGAACATAGCAT	0.343																																					p.L148V		Atlas-SNP	.											.	IFT57	44	.	0			c.C442G						PASS	.						73	74	73					3																	107937434		2203	4299	6502	SO:0001583	missense	55081	exon3			AATCAAGAACATA	AK001009	CCDS2951.1	3q13.13	2014-07-03	2014-07-03	2005-11-02	ENSG00000114446	ENSG00000114446		"Intraflagellar transport homologs"	17367	protein-coding gene	gene with protein product		606621	"estrogen-related receptor beta like 1", "intraflagellar transport 57 homolog (Chlamydomonas)"	ESRRBL1			Standard	NM_018010		Approved	FLJ10147, HIPPI, MHS4R2	uc003dwx.4	Q9NWB7	OTTHUMG00000159223	ENST00000264538.3:c.442C>G	chr3.hg19:g.107937434G>C	ENSP00000264538:p.Leu148Val	200.0	0.0	.		47.0	7.0	.	NM_018010	Q96DA9	Missense_Mutation	SNP	ENST00000264538.3	hg19	CCDS2951.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.034317	0.75617	.	.	ENSG00000114446	ENST00000264538	.	.	.	5.99	5.12	0.69794	.	0.000000	0.85682	D	0.000000	D	0.84584	0.5504	M	0.90977	3.165	0.80722	D	1	D	0.76494	0.999	D	0.71656	0.974	D	0.87397	0.2367	9	0.51188	T	0.08	.	15.0869	0.72162	0.0674:0.0:0.9326:0.0	.	148	Q9NWB7	IFT57_HUMAN	V	148	.	ENSP00000264538:L148V	L	-	1	0	IFT57	109420124	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.875000	0.69660	1.540000	0.49301	0.655000	0.94253	CTT	.	.	.	none		0.343	IFT57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353918.1	NM_018010		C	107937434	G	C	107937434	3	2	95	1	0	0	0	0	1	0	0	0	7569	942	33	4	883	4	IFT57	3	107937434	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08		107937434	90084996	11	5995											
PVRL3	25945	hgsc.bcm.edu	37	chr3	110852638	110852638	+	Missense_Mutation	SNP	T	T	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	tgccacgatcattgctagtgTagtgggtggggctctcttca	6	13	13	9	1	3	0	2	0	1	0	4	1	3	0	1	3	2	3	1	3	2	4	rs537220727		TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr3:110852638T>G	ENST00000485303.1	+	6	1501	c.1226T>G	c.(1225-1227)gTa>gGa	p.V409G	PVRL3_ENST00000493615.1_Intron|PVRL3_ENST00000319792.3_3'UTR	NM_001243286.1|NM_015480.2	NP_001230215.1|NP_056295.1	Q9NQS3	PVRL3_HUMAN	poliovirus receptor-related 3	409					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|fertilization (GO:0009566)|homophilic cell adhesion (GO:0007156)|lens morphogenesis in camera-type eye (GO:0002089)|retina morphogenesis in camera-type eye (GO:0060042)|single organismal cell-cell adhesion (GO:0016337)	apical junction complex (GO:0043296)|cell-cell adherens junction (GO:0005913)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	cell adhesion molecule binding (GO:0050839)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(3)	19						ATTGCTAGTGTAGTGGGTGGG	0.438																																					p.V409G		Atlas-SNP	.											PVRL3,colon,carcinoma,0,1	PVRL3	78	.	0			c.T1226G						PASS	.						174	171	172					3																	110852638		2203	4300	6503	SO:0001583	missense	25945	exon6			CTAGTGTAGTGGG	AF282874	CCDS2957.1, CCDS58842.1, CCDS58843.1	3q13	2013-01-29			ENSG00000177707	ENSG00000177707		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17664	protein-coding gene	gene with protein product		607147				11024295	Standard	NM_015480		Approved	nectin-3, PPR3, PVRR3, DKFZP566B0846, CDw113, CD113	uc003dxt.2	Q9NQS3	OTTHUMG00000159239	ENST00000485303.1:c.1226T>G	chr3.hg19:g.110852638T>G	ENSP00000418070:p.Val409Gly	354.0	1.0	.		38.0	3.0	.	NM_015480	E9PFR0|Q6NVZ3|Q8NC05|Q8WVU4|Q9BVA9|Q9Y412	Missense_Mutation	SNP	ENST00000485303.1	hg19	CCDS2957.1	.	.	.	.	.	.	.	.	.	.	T	10.21	1.287793	0.23478	.	.	ENSG00000177707	ENST00000485303	T	0.19532	2.14	5.76	4.63	0.57726	Cytochrome c1, transmembrane anchor, C-terminal (1);	0.108700	0.64402	D	0.000009	T	0.15522	0.0374	L	0.38175	1.15	0.80722	D	1	B	0.27229	0.172	B	0.22386	0.039	T	0.05632	-1.0873	10	0.87932	D	0	.	7.2403	0.26092	0.0:0.1282:0.0:0.8717	.	409	Q9NQS3	PVRL3_HUMAN	G	409	ENSP00000418070:V409G	ENSP00000418070:V409G	V	+	2	0	PVRL3	112335328	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.306000	0.51881	2.206000	0.71126	0.383000	0.25322	GTA	.	.	.	none		0.438	PVRL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354045.1	NM_015480		G	110852638	T	G	110852638	3	3	95	1	0	0	0	0	1	0	0	0	12854	1638	57	5	1248	5	PVRL3	3	110852638	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08	2915204	110852638	87169792	12	5996											
RARRES1	5918	hgsc.bcm.edu	37	chr3	158422600	158422600	+	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	ccactgcctcacactagtgaGctgtgccaagtagtagtgtg	9	10	11	11	0	1	1	1	1	0	0	1	1	1	1	3	0	3	3	3	0	4	3	rs140091959		TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr3:158422600G>C	ENST00000237696.5	-	4	932	c.652C>G	c.(652-654)Ctc>Gtc	p.L218V	RARRES1_ENST00000498640.1_5'UTR|RARRES1_ENST00000479756.1_Missense_Mutation_p.L218V	NM_206963.1	NP_996846.1	P49788	TIG1_HUMAN	retinoic acid receptor responder (tazarotene induced) 1	218					negative regulation of cell proliferation (GO:0008285)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)	9			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)		Tretinoin(DB00755)	ACACTAGTGAGCTGTGCCAAG	0.443																																					p.L218V		Atlas-SNP	.											.	RARRES1	22	.	0			c.C652G						PASS	.						114	102	106					3																	158422600		2203	4300	6503	SO:0001583	missense	5918	exon4			TAGTGAGCTGTGC	U27185	CCDS3184.1, CCDS54665.1	3q25.32	2013-07-29			ENSG00000118849	ENSG00000118849			9867	protein-coding gene	gene with protein product	"latexin-like"	605090				8601727, 9270552	Standard	NM_002888		Approved	TIG1, LXNL	uc003fci.3	P49788	OTTHUMG00000158834	ENST00000237696.5:c.652C>G	chr3.hg19:g.158422600G>C	ENSP00000237696:p.Leu218Val	94.0	0.0	.		44.0	11.0	.	NM_206963	Q8N1D7	Missense_Mutation	SNP	ENST00000237696.5	hg19	CCDS3184.1	.	.	.	.	.	.	.	.	.	.	-	6.185	0.402312	0.11696	.	.	ENSG00000118849	ENST00000237696;ENST00000479756	T;T	0.26660	1.72;1.72	5.2	2.23	0.28157	.	0.201181	0.42821	D	0.000657	T	0.17408	0.0418	L	0.33485	1.01	0.23969	N	0.996317	B;B	0.29136	0.234;0.036	B;B	0.32289	0.143;0.021	T	0.19484	-1.0304	10	0.23891	T	0.37	.	8.0807	0.30744	0.0:0.1549:0.525:0.3201	.	218;218	P49788-2;P49788	.;TIG1_HUMAN	V	218	ENSP00000237696:L218V;ENSP00000418556:L218V	ENSP00000237696:L218V	L	-	1	0	RARRES1	159905294	0.982000	0.34865	0.467000	0.27180	0.899000	0.52679	0.162000	0.16501	0.572000	0.29383	0.387000	0.25754	CTC	.	G|0.999;A|0.001	.	alt		0.443	RARRES1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352358.1			C	158422600	G	C	158422600	3	2	95	1	0	0	0	0	1	0	0	0	13068	971	34	4	259	4	RARRES1	3	158422600	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	47569962	158422600	39599830	13	5997											
EVC	2121	hgsc.bcm.edu	37	chr4	5721079	5721079	+	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	aagagagaagtgcagatgtcGaaggacaaggaagctgttga	16	6	15	4	1	0	4	0	1	0	3	1	8	0	6	0	2	2	3	0	2	5	1	rs373072919		TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr4:5721079G>A	ENST00000264956.6	+	2	463	c.279G>A	c.(277-279)tcG>tcA	p.S93S	EVC_ENST00000509451.1_Silent_p.S93S|EVC_ENST00000382674.2_Silent_p.S93S	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	93					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)				TGCAGATGTCGAAGGACAAGG	0.512																																					p.S93S		Atlas-SNP	.											.	EVC	90	.	0			c.G279A						PASS	.	G		0,4406		0,0,2203	251	241	245		279	-5.8	0	4		245	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	EVC	NM_153717.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		93/993	5721079	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2121	exon2			GATGTCGAAGGAC	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.279G>A	chr4.hg19:g.5721079G>A		266.0	0.0	.		431.0	178.0	.	NM_153717		Silent	SNP	ENST00000264956.6	hg19	CCDS3383.1																																																																																			.	.	.	weak		0.512	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1			A	5721079	G	A	5721079	2	1	95	1	0	0	0	0	0	0	0	1	5287	1045	37	1		1	EVC	4	5721079	Silent	SNP	G	TCGA-B9-4114-01A-01D-1252-08		5721079	185433197	14	5998											
KCTD8	386617	hgsc.bcm.edu	37	chr4	44449785	44449785	+	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	tcggggtcgcggctctcgttGagcgtgtccccgaagacctc	4	9	14	14	6	1	2	0	1	1	1	6	3	2	2	3	3	1	2	3	3	1	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr4:44449785G>A	ENST00000360029.3	-	1	1039	c.756C>T	c.(754-756)ctC>ctT	p.L252L	AC131951.1_ENST00000584757.1_RNA	NM_198353.2	NP_938167.1	Q6ZWB6	KCTD8_HUMAN	potassium channel tetramerization domain containing 8	252					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						GGCTCTCGTTGAGCGTGTCCC	0.657										HNSCC(17;0.042)																											p.L252L		Atlas-SNP	.											.	KCTD8	96	.	0			c.C756T						PASS	.						40	34	36					4																	44449785		2203	4300	6503	SO:0001819	synonymous_variant	386617	exon1			CTCGTTGAGCGTG	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.756C>T	chr4.hg19:g.44449785G>A		59.0	0.0	.		126.0	51.0	.	NM_198353	A2RU39	Silent	SNP	ENST00000360029.3	hg19	CCDS3467.1																																																																																			.	.	.	none		0.657	KCTD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216868.1			A	44449785	G	A	44449785	2	1	95	1	0	0	0	0	0	0	0	1	8122	1277	45	2		2	KCTD8	4	44449785	Silent	SNP	G	TCGA-B9-4114-01A-01D-1252-08	38728706	44449785	146704491	15	5999											
LNX1	84708	hgsc.bcm.edu	37	chr4	54343092	54343092	+	Missense_Mutation	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	tcttttcaataatgccactgCctcactccggctgacctctg	7	13	6	15	1	4	1	2	1	2	0	5	1	5	1	4	1	2	1	4	1	2	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr4:54343092C>T	ENST00000263925.7	-	9	2034	c.1720G>A	c.(1720-1722)Gca>Aca	p.A574T	LNX1_ENST00000306888.2_Missense_Mutation_p.A478T|FIP1L1_ENST00000507166.1_Intron	NM_001126328.2	NP_001119800.1	Q8TBB1	LNX1_HUMAN	ligand of numb-protein X 1, E3 ubiquitin protein ligase	574	PDZ 3. {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)			AATGCCACTGCCTCACTCCGG	0.488																																					p.A574T		Atlas-SNP	.											.	LNX1	139	.	0			c.G1720A						PASS	.						166	166	166					4																	54343092		2203	4300	6503	SO:0001583	missense	84708	exon9			CCACTGCCTCACT	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.1720G>A	chr4.hg19:g.54343092C>T	ENSP00000263925:p.Ala574Thr	308.0	0.0	.		274.0	46.0	.	NM_001126328	Q4W5K7|Q8N4C2|Q96MJ7|Q9BY20	Missense_Mutation	SNP	ENST00000263925.7	hg19	CCDS47057.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.304671	0.81136	.	.	ENSG00000072201	ENST00000306888;ENST00000538207;ENST00000263925	T;T	0.51574	0.7;0.7	5.16	5.16	0.70880	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.76435	0.3987	M	0.91510	3.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.82024	-0.0662	10	0.87932	D	0	.	18.8374	0.92168	0.0:1.0:0.0:0.0	.	574;478	Q8TBB1;Q8TBB1-2	LNX1_HUMAN;.	T	478;412;574	ENSP00000302879:A478T;ENSP00000263925:A574T	ENSP00000263925:A574T	A	-	1	0	LNX1	54037849	1.000000	0.71417	0.998000	0.56505	0.311000	0.27955	6.748000	0.74877	2.687000	0.91594	0.561000	0.74099	GCA	.	.	.	none		0.488	LNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219934.2			T	54343092	C	T	54343092	3	4	95	1	0	0	0	0	1	0	0	0	8872	739	26	2	478	2	LNX1	4	54343092	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	9893307	54343092	136811184	16	6000											
AGPAT9	84803	hgsc.bcm.edu	37	chr4	84457815	84457815	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgggaagatcctttccaccTggctgacgctggttctcggc	5	10	12	14	3	1	2	0	1	1	1	4	3	3	3	4	4	0	3	4	4	1	2			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr4:84457815T>C	ENST00000395226.2	+	2	258	c.40T>C	c.(40-42)Tgg>Cgg	p.W14R	AGPAT9_ENST00000264409.4_Missense_Mutation_p.W14R	NM_001256421.1	NP_001243350.1	Q53EU6	GPAT3_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 9	14					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|regulation of TOR signaling (GO:0032006)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(3)	13		Hepatocellular(203;0.114)				CCTTTCCACCTGGCTGACGCT	0.582																																					p.W14R		Atlas-SNP	.											.	AGPAT9	41	.	0			c.T40C						PASS	.						88	69	75					4																	84457815		2203	4300	6503	SO:0001583	missense	84803	exon2			TCCACCTGGCTGA	AK055749	CCDS3606.1	4q21.23	2014-02-13	2008-01-29		ENSG00000138678	ENSG00000138678	2.3.1.15	"1-acylglycerol-3-phosphate O-acyltransferases"	28157	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, theta"	610958	"1-acylglycerol-3-phosphate O-acyltransferase 9 (lysophosphatidic acid acyltransferase, theta)"			12975309	Standard	NM_001256421		Approved	MGC11324, LPAAT-theta, MAG1, HMFN0839	uc003how.4	Q53EU6	OTTHUMG00000130431	ENST00000395226.2:c.40T>C	chr4.hg19:g.84457815T>C	ENSP00000378651:p.Trp14Arg	80.0	0.0	.		214.0	44.0	.	NM_001256421	Q68CJ4|Q6GPI6|Q96NA3	Missense_Mutation	SNP	ENST00000395226.2	hg19	CCDS3606.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.459554	0.84317	.	.	ENSG00000138678	ENST00000395226;ENST00000264409	T;T	0.48201	0.82;0.82	4.68	4.68	0.58851	.	0.000000	0.85682	D	0.000000	T	0.64405	0.2595	M	0.86028	2.79	0.47374	D	0.999407	D	0.58970	0.984	P	0.54372	0.75	T	0.71341	-0.4622	10	0.59425	D	0.04	-8.2831	13.1799	0.59649	0.0:0.0:0.0:1.0	.	14	Q53EU6	GPAT3_HUMAN	R	14	ENSP00000378651:W14R;ENSP00000264409:W14R	ENSP00000264409:W14R	W	+	1	0	AGPAT9	84676839	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	3.587000	0.53957	1.760000	0.52011	0.374000	0.22700	TGG	.	.	.	none		0.582	AGPAT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252821.3	NM_032717		C	84457815	T	C	84457815	3	2	95	1	0	0	0	0	1	0	0	0	392	1580	55	3	42	3	AGPAT9	4	84457815	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08	30114723	84457815	106696461	17	6001											
SEMA5A	9037	hgsc.bcm.edu	37	chr5	9119220	9119220	+	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	ccacaggtagtgctgcagggAgaccacgaggtccagggagt	10	5	16	10	1	0	1	0	0	0	1	1	4	1	2	3	4	2	3	3	4	1	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr5:9119220A>T	ENST00000382496.5	-	15	2480	c.1815T>A	c.(1813-1815)tcT>tcA	p.S605S		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	605	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						TGCTGCAGGGAGACCACGAGG	0.652																																					p.S605S		Atlas-SNP	.											.	SEMA5A	236	.	0			c.T1815A						PASS	.						57	51	53					5																	9119220		2203	4300	6503	SO:0001819	synonymous_variant	9037	exon15			GCAGGGAGACCAC	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.1815T>A	chr5.hg19:g.9119220A>T		38.0	0.0	.		79.0	20.0	.	NM_003966	D3DTC6|O60408|Q1RLL9	Silent	SNP	ENST00000382496.5	hg19	CCDS3875.1																																																																																			.	.	.	none		0.652	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2			T	9119220	A	T	9119220	2	4	95	1	0	0	0	0	0	0	0	1	14050	291	11	5		5	SEMA5A	5	9119220	Silent	SNP	A	TCGA-B9-4114-01A-01D-1252-08		9119220	171796040	18	6002											
RAI14	26064	hgsc.bcm.edu	37	chr5	34757668	34757668	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctcggcaagaagggggcCagtgccaccaaacacgacag	12	3	13	13	2	0	1	0	0	0	1	1	2	0	1	3	3	3	2	3	3	3	0			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr5:34757668C>T	ENST00000265109.3	+	3	419	c.132C>T	c.(130-132)gcC>gcT	p.A44A	RAI14_ENST00000503673.1_Silent_p.A44A|RAI14_ENST00000515799.1_Silent_p.A47A|RAI14_ENST00000512629.1_Silent_p.A44A|RAI14_ENST00000506376.1_Silent_p.A36A|RAI14_ENST00000428746.2_Silent_p.A44A|RAI14_ENST00000397449.1_Silent_p.A37A|RAI14_ENST00000507276.1_3'UTR	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	44			A -> T (in dbSNP:rs17521570).			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)					AGAAGGGGGCCAGTGCCACCA	0.542																																					p.A47A		Atlas-SNP	.											.	RAI14	100	.	0			c.C141T						PASS	.						74	71	72					5																	34757668		2203	4300	6503	SO:0001819	synonymous_variant	26064	exon5			GGGGGCCAGTGCC	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.132C>T	chr5.hg19:g.34757668C>T		137.0	0.0	.		155.0	28.0	.	NM_001145525	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Silent	SNP	ENST00000265109.3	hg19	CCDS34142.1																																																																																			.	.	.	none		0.542	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577		T	34757668	C	T	34757668	2	4	95	1	0	0	0	0	0	0	0	1	13021	581	21	2		2	RAI14	5	34757668	Silent	SNP	C	TCGA-B9-4114-01A-01D-1252-08	25638448	34757668	146157592	19	6003											
PARP8	79668	hgsc.bcm.edu	37	chr5	50123848	50123848	+	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	accagccaaagaatccaattTtagagctgctaaaaaactct	17	9	5	10	0	1	2	0	0	1	2	2	2	2	2	3	0	4	2	3	0	7	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr5:50123848T>A	ENST00000281631.5	+	20	2206	c.2048T>A	c.(2047-2049)tTt>tAt	p.F683Y	PARP8_ENST00000505697.2_Missense_Mutation_p.F683Y|PARP8_ENST00000514067.2_Missense_Mutation_p.F641Y|PARP8_ENST00000505554.1_Missense_Mutation_p.F662Y|PARP8_ENST00000511363.2_3'UTR|PARP8_ENST00000514342.2_Missense_Mutation_p.F394Y|PARP8_ENST00000503750.2_Missense_Mutation_p.F641Y	NM_001178056.1|NM_024615.3	NP_001171527.1|NP_078891.2	Q8N3A8	PARP8_HUMAN	poly (ADP-ribose) polymerase family, member 8	683	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.					intracellular (GO:0005622)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Lung NSC(810;0.0305)|Breast(144;0.222)				GAATCCAATTTTAGAGCTGCT	0.383																																					p.F683Y		Atlas-SNP	.											.	PARP8	93	.	0			c.T2048A						PASS	.						127	124	125					5																	50123848		2203	4300	6503	SO:0001583	missense	79668	exon21			CCAATTTTAGAGC	AL834477	CCDS3954.1, CCDS54849.1	5q11.2	2010-02-16			ENSG00000151883	ENSG00000151883		"Poly (ADP-ribose) polymerases"	26124	protein-coding gene	gene with protein product						15273990	Standard	NM_001178055		Approved	FLJ21308, pART16	uc003joo.3	Q8N3A8	OTTHUMG00000096969	ENST00000281631.5:c.2048T>A	chr5.hg19:g.50123848T>A	ENSP00000281631:p.Phe683Tyr	217.0	0.0	.		125.0	41.0	.	NM_001178055	Q3KRB7|Q6DHZ1|Q9H754	Missense_Mutation	SNP	ENST00000281631.5	hg19	CCDS3954.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.379826	0.82682	.	.	ENSG00000151883	ENST00000505697;ENST00000503750;ENST00000514342;ENST00000281631;ENST00000514067;ENST00000505554;ENST00000503561;ENST00000423185	T;T;T;T;T;T	0.18502	2.21;2.21;2.21;2.21;2.21;2.21	5.7	5.7	0.88788	Poly(ADP-ribose) polymerase, catalytic domain (2);	0.059647	0.64402	D	0.000002	T	0.34193	0.0889	L	0.48935	1.535	0.54753	D	0.99998	D;P;P	0.53619	0.961;0.954;0.891	P;D;P	0.66351	0.492;0.943;0.492	T	0.01382	-1.1369	9	.	.	.	-16.5844	15.9599	0.79923	0.0:0.0:0.0:1.0	.	575;641;683	B4DQ81;Q8N3A8-2;Q8N3A8	.;.;PARP8_HUMAN	Y	683;641;394;683;641;662;394;394	ENSP00000422217:F683Y;ENSP00000440851:F641Y;ENSP00000439022:F394Y;ENSP00000281631:F683Y;ENSP00000424814:F641Y;ENSP00000423946:F662Y	.	F	+	2	0	PARP8	50159605	1.000000	0.71417	0.997000	0.53966	0.999000	0.98932	8.036000	0.88901	2.153000	0.67306	0.533000	0.62120	TTT	.	.	.	none		0.383	PARP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214035.3	NM_024615		A	50123848	T	A	50123848	3	1	95	1	0	0	0	0	1	0	0	0	11472	1841	64	5	2126	5	PARP8	5	50123848	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08	15366180	50123848	130791412	20	6004											
NR2F1	7025	hgsc.bcm.edu	37	chr5	92929424	92929424	+	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	gctgcgcaccgtgtcctcctCcgtcatcgagcagctcttct	4	11	9	17	4	3	0	1	0	2	0	7	1	6	0	4	0	3	4	4	0	0	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr5:92929424C>A	ENST00000327111.3	+	3	2835	c.1148C>A	c.(1147-1149)tCc>tAc	p.S383Y	NR2F1_ENST00000506162.1_3'UTR	NM_005654.4	NP_005645.1	P10589	COT1_HUMAN	nuclear receptor subfamily 2, group F, member 1	383					cerebral cortex regionalization (GO:0021796)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|retinoic acid-responsive element binding (GO:0044323)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(4)|large_intestine(6)|lung(2)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	21		all_cancers(142;1.62e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0416)|all cancers(79;9.57e-18)		GTGTCCTCCTCCGTCATCGAG	0.582																																					p.S383Y		Atlas-SNP	.											.	NR2F1	56	.	0			c.C1148A						PASS	.						123	118	120					5																	92929424		2203	4300	6503	SO:0001583	missense	7025	exon3			CCTCCTCCGTCAT	BC004154	CCDS4068.1	5q14	2013-01-16			ENSG00000175745	ENSG00000175745		"Nuclear hormone receptors"	7975	protein-coding gene	gene with protein product		132890		ERBAL3, TFCOUP1		8530078	Standard	NM_005654		Approved	EAR-3, COUP-TFI, TCFCOUP1, SVP44	uc003kkj.3	P10589	OTTHUMG00000119079	ENST00000327111.3:c.1148C>A	chr5.hg19:g.92929424C>A	ENSP00000325819:p.Ser383Tyr	292.0	0.0	.		414.0	121.0	.	NM_005654		Missense_Mutation	SNP	ENST00000327111.3	hg19	CCDS4068.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.607237	0.87157	.	.	ENSG00000175745	ENST00000327111	D	0.96856	-4.15	6.17	6.17	0.99709	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (1);	0.000000	0.85682	D	0.000000	D	0.96482	0.8852	L	0.52206	1.635	0.80722	D	1	P	0.48294	0.908	P	0.50490	0.642	D	0.96365	0.9269	10	0.87932	D	0	.	20.4898	0.99202	0.0:1.0:0.0:0.0	.	383	P10589	COT1_HUMAN	Y	383	ENSP00000325819:S383Y	ENSP00000325819:S383Y	S	+	2	0	NR2F1	92955180	1.000000	0.71417	0.974000	0.42286	0.983000	0.72400	6.074000	0.71253	2.941000	0.99782	0.655000	0.94253	TCC	.	.	.	none		0.582	NR2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239293.2	NM_005654		A	92929424	C	A	92929424	3	1	95	1	0	0	0	0	1	0	0	0	10634	855	30	4	1158	4	NR2F1	5	92929424	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	42805576	92929424	87985836	21	6005											
POU5F2	134187	hgsc.bcm.edu	37	chr5	93076682	93076682	+	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	tccattttgcataagcccagAaggttctctgcttccacttc	8	14	6	13	0	1	1	0	0	1	1	5	1	3	1	3	1	3	3	3	1	2	6			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr5:93076682A>T	ENST00000510627.4	-	1	661	c.588T>A	c.(586-588)ctT>ctA	p.L196L	FAM172A_ENST00000395965.3_Intron|FAM172A_ENST00000505869.1_Intron|POU5F2_ENST00000606183.1_5'UTR|FAM172A_ENST00000509163.1_Intron|FAM172A_ENST00000509739.1_Intron|RP11-185E12.2_ENST00000606528.1_RNA	NM_153216.1	NP_694948.1	Q8N7G0	PO5F2_HUMAN	POU domain class 5, transcription factor 2	196					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)						all_cancers(142;3.87e-05)|all_epithelial(76;4.59e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0415)|all cancers(79;2.03e-19)		ATAAGCCCAGAAGGTTCTCTG	0.542																																					p.L196L		Atlas-SNP	.											.	POU5F2	10	.	0			c.T588A						PASS	.						107	107	107					5																	93076682		2115	4250	6365	SO:0001819	synonymous_variant	134187	exon1			GCCCAGAAGGTTC		CCDS59489.1	5q15	2011-06-20				ENSG00000248483		"Homeoboxes / POU class"	26367	protein-coding gene	gene with protein product						7908264	Standard	NM_153216		Approved	SPRM-1, FLJ25680	uc003kkl.1	Q8N7G0		ENST00000510627.4:c.588T>A	chr5.hg19:g.93076682A>T		166.0	0.0	.		208.0	66.0	.	NM_153216	Q15169|Q6MZL7|Q8N748	Silent	SNP	ENST00000510627.4	hg19	CCDS59489.1																																																																																			.	.	.	none		0.542	POU5F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369873.5	NM_153216		T	93076682	A	T	93076682	2	4	95	1	0	0	0	0	0	0	0	1	12290	233	9	5		5	POU5F2	5	93076682	Silent	SNP	A	TCGA-B9-4114-01A-01D-1252-08	147258	93076682	87838578	22	6006											
FNIP1	96459	hgsc.bcm.edu	37	chr5	131042155	131042155	+	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	ttgtttggctgcgtcgccaaCgtcgctggtagctgctggca	4	12	14	11	4	0	0	0	0	0	0	2	0	0	0	1	3	4	7	1	3	2	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr5:131042155C>A	ENST00000510461.1	-	9	958	c.863G>T	c.(862-864)cGt>cTt	p.R288L	FNIP1_ENST00000511848.1_Missense_Mutation_p.R288L|CTC-432M15.3_ENST00000514667.1_Intron|FNIP1_ENST00000307968.7_Missense_Mutation_p.R260L|FNIP1_ENST00000307954.8_Missense_Mutation_p.R243L	NM_133372.2	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1	288					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)		GCGTCGCCAACGTCGCTGGTA	0.453																																					p.R288L		Atlas-SNP	.											.	FNIP1	104	.	0			c.G863T						PASS	.						100	93	96					5																	131042155		2203	4300	6503	SO:0001583	missense	96459	exon9			CGCCAACGTCGCT	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.863G>T	chr5.hg19:g.131042155C>A	ENSP00000421985:p.Arg288Leu	201.0	0.0	.		68.0	15.0	.	NM_133372	D6RJH5|Q86T47|Q9BUT0	Missense_Mutation	SNP	ENST00000510461.1	hg19	CCDS34227.1	.	.	.	.	.	.	.	.	.	.	C	36	5.709610	0.96821	.	.	ENSG00000217128	ENST00000307968;ENST00000307954;ENST00000544351;ENST00000510461;ENST00000511848	T;T;T;T	0.47528	1.83;1.67;1.57;0.84	5.6	5.6	0.85130	.	.	.	.	.	T	0.73473	0.3591	M	0.83012	2.62	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;1.0;1.0	D;D;D;D	0.91635	0.998;0.994;0.998;0.999	T	0.76340	-0.2995	9	0.87932	D	0	-7.1358	19.9737	0.97296	0.0:1.0:0.0:0.0	.	288;288;260;288	A8K8V8;Q8TF40-2;Q8TF40-3;Q8TF40	.;.;.;FNIP1_HUMAN	L	260;243;48;288;288	ENSP00000309266:R260L;ENSP00000310453:R243L;ENSP00000421985:R288L;ENSP00000425619:R288L	ENSP00000310453:R243L	R	-	2	0	FNIP1	131070054	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	7.776000	0.85560	2.793000	0.96121	0.591000	0.81541	CGT	.	.	.	none		0.453	FNIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370077.1	NM_133372		A	131042155	C	A	131042155	3	1	95	1	0	0	0	0	1	0	0	0	5982	536	19	4	2677	4	FNIP1	5	131042155	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	37965473	131042155	49873105	23	6007											
PCDHGA12	26025	hgsc.bcm.edu	37	chr5	140811171	140811177	+	Frame_Shift_Del	DEL	GGTATGT	GGTATGT	-																															ggaagtgaggtattccttccGgtatgtggacgacaaggcgg																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	GGTATGT	GGTATGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr5:140811171_140811177delGGTATGT	ENST00000252085.3	+	1	987_993	c.845_851delGGTATGT	c.(844-852)cggtatgtgfs	p.RYV282fs	PCDHGB7_ENST00000398594.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA8_ENST00000398604.2_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	282	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)|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)			TATTCCTTCCGGTATGTGGACGACAAG	0.522																																					p.282_284del		Atlas-INDEL	.											.	PCDHGA12	271	.	0			c.844_850del						PASS	.																																			SO:0001589	frameshift_variant	26025	exon1			.	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.845_851delGGTATGT	chr5.hg19:g.140811171_140811177delGGTATGT	ENSP00000252085:p.Arg282fs	177.0	0.0	0		254.0	63.0	0.248031	NM_032094	O15100|Q6UW70|Q9Y5D7	Frame_Shift_Del	DEL	ENST00000252085.3	hg19	CCDS4260.1																																																																																			.	.	.	none		0.522	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735		-	140811177	GGTATGT	-	140811171	7	5	95	1	0	1	0	1	0	0	0	0	11560	1116	39	0	847	0	PCDHGA12	5	140811171	Frame_Shift_Del	DEL	GGTATGT	TCGA-B9-4114-01A-01D-1252-08	9769016	140811171	40104089	24	6008											
HLA-DQA2	3118	hgsc.bcm.edu	37	chr6	32713781	32713781	+	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	ttacctcaccttcctcccttCtgctgatgagatttatgact	7	16	5	13	0	2	3	1	3	1	1	4	4	4	3	4	0	2	1	4	0	2	5			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr6:32713781C>T	ENST00000374940.3	+	3	647	c.545C>T	c.(544-546)tCt>tTt	p.S182F		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	182	Alpha-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)|immune response (GO:0006955)|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)|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)			endometrium(2)|large_intestine(3)|lung(7)|skin(1)	13					"""Insulin(DB00071)"	TTCCTCCCTTCTGCTGATGAG	0.502																																					p.S182F		Atlas-SNP	.											.	HLA-DQA2	27	.	0			c.C545T						PASS	.						191	211	204					6																	32713781		1511	2707	4218	SO:0001583	missense	3118	exon3			TCCCTTCTGCTGA		CCDS4753.1	6p21.3	2013-01-11			ENSG00000237541	ENSG00000237541		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4943	protein-coding gene	gene with protein product		613503		HLA-DXA			Standard	NM_020056		Approved		uc003obx.3	P01906	OTTHUMG00000031108	ENST00000374940.3:c.545C>T	chr6.hg19:g.32713781C>T	ENSP00000364076:p.Ser182Phe	417.0	1.0	.		286.0	92.0	.	NM_020056	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	Missense_Mutation	SNP	ENST00000374940.3	hg19	CCDS4753.1	.	.	.	.	.	.	.	.	.	.	.	13.77	2.336406	0.41398	.	.	ENSG00000237541	ENST00000374940	T	0.03152	4.03	3.06	2.06	0.26882	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.585185	0.16577	U	0.208364	T	0.10035	0.0246	M	0.89478	3.035	0.30030	N	0.813521	D	0.89917	1.0	D	0.97110	1.0	T	0.01553	-1.1326	10	0.66056	D	0.02	.	7.1176	0.25424	0.4092:0.5908:0.0:0.0	.	182	P01906	DQA2_HUMAN	F	182	ENSP00000364076:S182F	ENSP00000364076:S182F	S	+	2	0	HLA-DQA2	32821759	0.009000	0.17119	0.999000	0.59377	0.758000	0.43043	0.626000	0.24492	1.700000	0.51204	0.174000	0.16983	TCT	.	.	.	none		0.502	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076179.2	NM_020056		T	32713781	C	T	32713781	3	4	95	1	0	0	0	0	1	0	0	0	7212	913	32	2	555	2	HLA-DQA2	6	32713781	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08		32713781	138401286	25	6009											
LEMD2	221496	hgsc.bcm.edu	37	chr6	33748926	33748926	+	Missense_Mutation	SNP	A	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	tctggatttccacactcaaaAttacctaggagaaaaaaaac	18	9	5	9	0	2	1	1	0	1	1	3	3	3	2	2	2	2	0	2	2	8	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr6:33748926A>C	ENST00000293760.5	-	4	877	c.858T>G	c.(856-858)aaT>aaG	p.N286K	LEMD2_ENST00000508327.1_5'UTR|LEMD2_ENST00000502643.1_5'UTR	NM_181336.3	NP_851853.1	Q8NC56	LEMD2_HUMAN	LEM domain containing 2	286					negative regulation of MAPK cascade (GO:0043409)|skeletal muscle cell differentiation (GO:0035914)	integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|nuclear membrane (GO:0031965)				central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(2)|pancreas(1)	9						CACACTCAAAATTACCTAGGA	0.368																																					p.N286K		Atlas-SNP	.											.	LEMD2	20	.	0			c.T858G						PASS	.						74	68	70					6																	33748926		2203	4300	6503	SO:0001583	missense	221496	exon4			CTCAAAATTACCT		CCDS4785.1, CCDS47411.1	6p21.31	2009-11-06			ENSG00000161904	ENSG00000161904			21244	protein-coding gene	gene with protein product						12477932	Standard	NM_001143944		Approved	dJ482C21.1, NET25	uc011drm.2	Q8NC56	OTTHUMG00000014535	ENST00000293760.5:c.858T>G	chr6.hg19:g.33748926A>C	ENSP00000293760:p.Asn286Lys	115.0	0.0	.		152.0	49.0	.	NM_181336	B4DVH5|E7EVT2|Q5T972|Q5T974	Missense_Mutation	SNP	ENST00000293760.5	hg19	CCDS4785.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.71|19.71	3.877584|3.877584	0.72294|0.72294	.|.	.|.	ENSG00000161904|ENSG00000161904	ENST00000442696|ENST00000293760	.|.	.|.	.|.	5.65|5.65	3.27|3.27	0.37495|0.37495	.|Inner nuclear membrane protein MAN1 (1);	.|0.000000	.|0.64402	.|D	.|0.000001	T|T	0.33876|0.33876	0.0878|0.0878	L|L	0.35414|0.35414	1.06|1.06	0.80722|0.80722	D|D	1|1	.|D	.|0.71674	.|0.998	.|D	.|0.64595	.|0.927	T|T	0.40664|0.40664	-0.9551|-0.9551	5|9	.|0.06099	.|T	.|0.92	-4.6423|-4.6423	8.5956|8.5956	0.33714|0.33714	0.8505:0.0:0.1495:0.0|0.8505:0.0:0.1495:0.0	.|.	.|286	.|Q8NC56	.|LEMD2_HUMAN	S|K	152|286	.|.	.|ENSP00000293760:N286K	I|N	-|-	2|3	0|2	LEMD2|LEMD2	33856904|33856904	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	2.063000|2.063000	0.41423|0.41423	0.432000|0.432000	0.26286|0.26286	0.533000|0.533000	0.62120|0.62120	ATT|AAT	.	.	.	none		0.368	LEMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040209.3	XM_166338		C	33748926	A	C	33748926	3	2	95	1	0	0	0	0	1	0	0	0	8727	98	4	5	677	5	LEMD2	6	33748926	Missense_Mutation	SNP	A	TCGA-B9-4114-01A-01D-1252-08	1035145	33748926	137366141	26	6010											
TTBK1	84630	hgsc.bcm.edu	37	chr6	43251695	43251695	+	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	gctcggagccctcaggctcaCtgtcggccaaagagcggtgg	7	6	15	13	3	2	1	2	0	0	1	4	2	2	2	2	5	2	2	2	5	1	0			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr6:43251695C>A	ENST00000259750.4	+	14	3300	c.3217C>A	c.(3217-3219)Ctg>Atg	p.L1073M		NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	1073					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)			CTCAGGCTCACTGTCGGCCAA	0.687																																					p.L1073M		Atlas-SNP	.											.	TTBK1	124	.	0			c.C3217A						PASS	.						18	19	18					6																	43251695		2183	4238	6421	SO:0001583	missense	84630	exon14			GGCTCACTGTCGG	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.3217C>A	chr6.hg19:g.43251695C>A	ENSP00000259750:p.Leu1073Met	85.0	0.0	.		121.0	46.0	.	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Missense_Mutation	SNP	ENST00000259750.4	hg19	CCDS34455.1	.	.	.	.	.	.	.	.	.	.	C	12.46	1.945410	0.34377	.	.	ENSG00000146216	ENST00000259750	T	0.55413	0.52	5.02	3.14	0.36123	.	0.348022	0.23768	N	0.044741	T	0.27349	0.0671	L	0.36672	1.1	0.80722	D	1	B	0.19200	0.034	B	0.14023	0.01	T	0.30736	-0.9968	10	0.56958	D	0.05	.	11.2746	0.49159	0.1311:0.7259:0.143:0.0	.	1073	Q5TCY1	TTBK1_HUMAN	M	1073	ENSP00000259750:L1073M	ENSP00000259750:L1073M	L	+	1	2	TTBK1	43359673	0.733000	0.28132	0.999000	0.59377	0.950000	0.60333	1.377000	0.34317	2.326000	0.78906	0.455000	0.32223	CTG	.	.	.	none		0.687	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3			A	43251695	C	A	43251695	3	1	95	1	0	0	0	0	1	0	0	0	16688	564	20	4	3267	4	TTBK1	6	43251695	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	9502769	43251695	127863372	27	6011											
ROS1	6098	hgsc.bcm.edu	37	chr6	117746764	117746764	+	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	gcaccacagaaatccataggCagccaagagttgcaaaattg	16	6	9	10	0	0	2	0	0	0	2	1	2	1	2	3	1	2	4	3	1	5	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr6:117746764C>G	ENST00000368508.3	-	1	254	c.56G>C	c.(55-57)tGc>tCc	p.C19S	GOPC_ENST00000467125.1_Intron|ROS1_ENST00000368507.3_Missense_Mutation_p.C19S	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	19					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)		AATCCATAGGCAGCCAAGAGT	0.388			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																p.C19S		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	.	ROS1	728	.	0			c.G56C						PASS	.						120	119	119					6																	117746764		2203	4300	6503	SO:0001583	missense	6098	exon1			CATAGGCAGCCAA	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.56G>C	chr6.hg19:g.117746764C>G	ENSP00000357494:p.Cys19Ser	287.0	0.0	.		135.0	41.0	.	NM_002944	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	hg19	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	C	13.17	2.155746	0.38021	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	T;T	0.70631	-0.5;-0.5	5.11	2.22	0.28083	.	0.273852	0.26757	N	0.022646	T	0.41766	0.1173	L	0.51422	1.61	0.80722	D	1	B	0.14438	0.01	B	0.06405	0.002	T	0.42649	-0.9439	10	0.62326	D	0.03	.	3.545	0.07826	0.175:0.5642:0.1691:0.0917	.	19	P08922	ROS1_HUMAN	S	19	ENSP00000357494:C19S;ENSP00000357493:C19S	ENSP00000357493:C19S	C	-	2	0	ROS1	117853457	0.849000	0.29639	0.992000	0.48379	0.875000	0.50365	0.358000	0.20216	0.366000	0.24427	0.655000	0.94253	TGC	.	.	.	none		0.388	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			G	117746764	C	G	117746764	3	3	95	1	0	0	0	0	1	0	0	0	13544	710	25	4	7159	4	ROS1	6	117746764	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	74495069	117746764	53368303	28	6012											
TMEM184A	202915	hgsc.bcm.edu	37	chr7	1590513	1590513	+	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	ctggtggtctccgaggaggaGgaggctgagccaggagtcga	8	6	19	8	2	1	1	0	1	1	0	3	7	1	5	2	7	1	1	2	7	0	0			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr7:1590513G>A	ENST00000297477.5	-	3	641	c.325C>T	c.(325-327)Ctc>Ttc	p.L109F		NM_001097620.1	NP_001091089.1	Q6ZMB5	T184A_HUMAN	transmembrane protein 184A	109					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)		CCGAGGAGGAGGAGGCTGAGC	0.632																																					p.L109F		Atlas-SNP	.											.	TMEM184A	35	.	0			c.C325T						PASS	.						88	97	94					7																	1590513		2203	4300	6503	SO:0001583	missense	202915	exon3			GGAGGAGGAGGCT		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.325C>T	chr7.hg19:g.1590513G>A	ENSP00000297477:p.Leu109Phe	120.0	0.0	.		200.0	47.0	.	NM_001097620	Q8TBQ6	Missense_Mutation	SNP	ENST00000297477.5	hg19	CCDS43537.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.153532	0.78114	.	.	ENSG00000164855	ENST00000297477;ENST00000319010;ENST00000414730;ENST00000441933;ENST00000431208	T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74	5.15	5.15	0.70609	.	0.000000	0.64402	U	0.000001	T	0.52677	0.1749	M	0.70787	2.145	0.80722	D	1	P	0.36599	0.56	B	0.41813	0.367	T	0.56450	-0.7977	10	0.51188	T	0.08	-14.3095	12.9955	0.58644	0.0782:0.0:0.9218:0.0	.	109	Q6ZMB5	T184A_HUMAN	F	109	ENSP00000297477:L109F;ENSP00000325945:L109F;ENSP00000398382:L109F;ENSP00000389092:L109F;ENSP00000403499:L109F	ENSP00000297477:L109F	L	-	1	0	TMEM184A	1557039	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.819000	0.86621	2.396000	0.81511	0.407000	0.27541	CTC	.	.	.	none		0.632	TMEM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239229.4	NM_152689		A	1590513	G	A	1590513	3	1	95	1	0	0	0	0	1	0	0	0	16116	1000	35	2	944	2	TMEM184A	7	1590513	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08		1590513	157548150	29	6013											
TFR2	7036	hgsc.bcm.edu	37	chr7	100228607	100228607	+	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	gccgcagtcgtggcccggggCccaggtgataaggggagcct	6	5	18	12	3	0	1	0	1	0	0	1	2	0	2	4	6	1	1	4	6	1	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr7:100228607C>T	ENST00000462107.1	-	10	1462	c.1175G>A	c.(1174-1176)gGc>gAc	p.G392D	TFR2_ENST00000544242.1_5'UTR|TFR2_ENST00000223051.3_Missense_Mutation_p.G392D|TFR2_ENST00000431692.1_Silent_p.G306G			Q9UP52	TFR2_HUMAN	transferrin receptor 2	392					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)	TGGCCCGGGGCCCAGGTGATA	0.612																																					p.G392D		Atlas-SNP	.											.	TFR2	53	.	0			c.G1175A						PASS	.						35	34	35					7																	100228607		2203	4300	6503	SO:0001583	missense	7036	exon9			CCGGGGCCCAGGT	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.1175G>A	chr7.hg19:g.100228607C>T	ENSP00000420525:p.Gly392Asp	34.0	0.0	.		83.0	23.0	.	NM_003227	A6NGM7|O75422|Q1HE13|Q9HA99|Q9NX67	Missense_Mutation	SNP	ENST00000462107.1	hg19	CCDS34707.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.012638	0.75161	.	.	ENSG00000106327	ENST00000223051;ENST00000462107	T;T	0.52983	0.64;0.64	4.74	4.74	0.60224	.	0.144170	0.45867	D	0.000322	T	0.70684	0.3252	M	0.91768	3.24	0.80722	D	1	D	0.69078	0.997	D	0.64042	0.921	T	0.73943	-0.3823	10	0.34782	T	0.22	-26.2357	13.0917	0.59169	0.0:1.0:0.0:0.0	.	392	Q9UP52	TFR2_HUMAN	D	392	ENSP00000223051:G392D;ENSP00000420525:G392D	ENSP00000223051:G392D	G	-	2	0	TFR2	100066543	1.000000	0.71417	1.000000	0.80357	0.667000	0.39255	1.935000	0.40173	2.470000	0.83445	0.561000	0.74099	GGC	.	.	.	none		0.612	TFR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356392.3	NM_003227		T	100228607	C	T	100228607	3	4	95	1	0	0	0	0	1	0	0	0	15823	739	26	2	1270	2	TFR2	7	100228607	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	98638094	100228607	58910056	30	6014											
LOC441294	441294	hgsc.bcm.edu	37	chr7	143270908	143270908	+	Frame_Shift_Del	DEL	T	T	-																															gaaatggaatccagtagaaaTgatgccaaagatgatcttgg																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr7:143270908delT	ENST00000420911.2	+	1	2015	c.1998delT	c.(1996-1998)aatfs	p.N666fs	RNU6-162P_ENST00000516228.1_RNA	NM_001008747.1	NP_001008747.1	A4D2H0	CTGEF_HUMAN	CTAGE family, member 15	666						integral component of membrane (GO:0016021)											CCAGTAGAAATGATGCCAAAG	0.418																																					p.N666fs		Atlas-INDEL	.											.	.	.	.	0			c.1997delA						PASS	.																																			SO:0001589	frameshift_variant	441294	exon1			.		CCDS64788.1	7q35	2013-02-25	2013-02-25	2013-02-25	ENSG00000176227	ENSG00000271079			37295	protein-coding gene	gene with protein product			"CTAGE family, member 15, pseudogene"	CTAGE15P			Standard	NM_001008747		Approved		uc011kth.3	A4D2H0	OTTHUMG00000153233	ENST00000420911.2:c.1998delT	chr7.hg19:g.143270908delT	ENSP00000474204:p.Asn666fs	578.0	0.0	0		260.0	27.0	0.103846	NM_001008747	A6H8Z8	Frame_Shift_Del	DEL	ENST00000420911.2	hg19																																																																																				.	.	.	none		0.418	CTAGE15-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000330280.2	NM_001008747		-	143270908	T	-	143270908	7	5	95	1	0	1	0	1	0	0	0	0	8887	1461	51	0	2000	0	LOC441294	7	143270908	Frame_Shift_Del	DEL	T	TCGA-B9-4114-01A-01D-1252-08	43042301	143270908	15867755	31	6015											
CTAGE6P	340307	hgsc.bcm.edu	37	chr7	143452754	143452754	+	Frame_Shift_Del	DEL	A	A	-																															ccaagatcatctttggcatcAtttctactggattccatttc																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr7:143452754delA	ENST00000470691.2	-	1	2035	c.1998delT	c.(1996-1998)aatfs	p.N666fs	RNU6-267P_ENST00000516714.1_RNA	NM_178561.4	NP_848656.2	Q86UF2	CTGE6_HUMAN	CTAGE family, member 6	666						integral component of membrane (GO:0016021)						Melanoma(164;0.0903)					CTTTGGCATCATTTCTACTGG	0.418																																					p.D667fs		Atlas-INDEL	.											.	.	.	.	0			c.1999delG						PASS	.																																			SO:0001589	frameshift_variant	340307	exon1			.	BC043153	CCDS64790.1	7q35	2013-05-22	2013-02-25	2013-02-25	ENSG00000271321	ENSG00000271321			28644	protein-coding gene	gene with protein product			"CTAGE family, member 6, pseudogene"	CTAGE6P		12477932	Standard	NM_178561		Approved	MGC41943	uc003wdk.4	Q86UF2	OTTHUMG00000157770	ENST00000470691.2:c.1998delT	chr7.hg19:g.143452754delA	ENSP00000474388:p.Asn666fs	599.0	0.0	0		266.0	32.0	0.120301	NM_178561	A4FU29|Q3ZCM5	Frame_Shift_Del	DEL	ENST00000470691.2	hg19																																																																																				.	.	.	none		0.418	CTAGE6-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349580.2	NM_178561		-	143452754	A	-	143452754	7	5	95	1	0	1	0	1	0	0	0	0	3997	214	8	0	339	0	CTAGE6P	7	143452754	Frame_Shift_Del	DEL	A	TCGA-B9-4114-01A-01D-1252-08	181846	143452754	15685909	32	6016											
MLL3	58508	hgsc.bcm.edu	37	chr7	151882674	151882674	+	Missense_Mutation	SNP	T	T	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	ctctttcttgtgagcttgctTttctccacaatttggcaatt	6	19	6	10	0	3	1	0	1	3	0	4	1	3	1	1	1	2	3	1	1	2	7			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr7:151882674T>G	ENST00000262189.6	-	34	5269	c.5051A>C	c.(5050-5052)aAa>aCa	p.K1684T	KMT2C_ENST00000355193.2_Missense_Mutation_p.K1684T	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1684					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)										TGAGCTTGCTTTTCTCCACAA	0.343																																					p.K1684T		Atlas-SNP	.											.	MLL3	1564	.	0			c.A5051C						PASS	.						142	123	130					7																	151882674		2202	4300	6502	SO:0001583	missense	58508	exon34			CTTGCTTTTCTCC	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.5051A>C	chr7.hg19:g.151882674T>G	ENSP00000262189:p.Lys1684Thr	206.0	0.0	.		131.0	13.0	.	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	T	17.93	3.508980	0.64410	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.93604	-3.25;-3.25	5.03	5.03	0.67393	High mobility group, HMG1/HMG2 (1);	0.000000	0.49305	D	0.000155	D	0.94496	0.8228	L	0.38175	1.15	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	D	0.94705	0.7887	10	0.51188	T	0.08	.	14.7869	0.69810	0.0:0.0:0.0:1.0	.	1684;745	Q8NEZ4;Q8NEZ4-2	MLL3_HUMAN;.	T	1684	ENSP00000262189:K1684T;ENSP00000347325:K1684T	ENSP00000262189:K1684T	K	-	2	0	MLL3	151513607	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.888000	0.87302	1.889000	0.54706	0.523000	0.50628	AAA	.	.	.	none		0.343	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			G	151882674	T	G	151882674	3	3	95	1	0	0	0	0	1	0	0	0	9629	1841	64	5	9788	5	MLL3	7	151882674	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08	8429920	151882674	7255989	33	6017											
AGPAT5	55326	hgsc.bcm.edu	37	chr8	6614714	6614714	+	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	gaattttatgagtcaccagaTccagaaagaagaaaaagatt	19	9	8	5	0	1	6	1	1	0	5	2	7	2	6	2	0	0	0	2	0	6	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr8:6614714T>A	ENST00000285518.6	+	8	1212	c.900T>A	c.(898-900)gaT>gaA	p.D300E		NM_018361.3	NP_060831.2	Q9NUQ2	PLCE_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 5	300					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|hematopoietic progenitor cell differentiation (GO:0002244)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)		AGPAT5/MCPH1(2)	endometrium(2)|kidney(2)|large_intestine(4)|lung(3)	11			STAD - Stomach adenocarcinoma(24;0.0578)	READ - Rectum adenocarcinoma(644;0.156)|COAD - Colon adenocarcinoma(149;0.191)		AGTCACCAGATCCAGAAAGAA	0.323																																					p.D300E		Atlas-SNP	.											.	AGPAT5	31	.	0			c.T900A						PASS	.						44	45	45					8																	6614714		2203	4300	6503	SO:0001583	missense	55326	exon8			ACCAGATCCAGAA	AF375789	CCDS34796.1	8p23.1	2013-02-05	2013-02-05		ENSG00000155189	ENSG00000155189	2.3.1.51	"1-acylglycerol-3-phosphate O-acyltransferases"	20886	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, epsilon"	614796	"1-acylglycerol-3-phosphate O-acyltransferase 5 (lysophosphatidic acid acyltransferase, epsilon)"				Standard	NM_018361		Approved	FLJ11210, LPAAT-e, LPAAT-epsilon	uc003wqo.3	Q9NUQ2	OTTHUMG00000163656	ENST00000285518.6:c.900T>A	chr8.hg19:g.6614714T>A	ENSP00000285518:p.Asp300Glu	91.0	0.0	.		15.0	8.0	.	NM_018361	Q8IZ47|Q9BQG4	Missense_Mutation	SNP	ENST00000285518.6	hg19	CCDS34796.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.60|19.60	3.858531|3.858531	0.71834|0.71834	.|.	.|.	ENSG00000155189|ENSG00000155189	ENST00000285518|ENST00000518327	T|.	0.62232|.	0.04|.	6.04|6.04	2.42|2.42	0.29668|0.29668	.|.	0.087594|.	0.85682|.	D|.	0.000000|.	T|T	0.62624|0.62624	0.2443|0.2443	M|M	0.72576|0.72576	2.205|2.205	0.53005|0.53005	D|D	0.999968|0.999968	P|.	0.37663|.	0.604|.	B|.	0.34779|.	0.189|.	T|T	0.56932|0.56932	-0.7897|-0.7897	10|5	0.09843|.	T|.	0.71|.	-7.4458|-7.4458	7.7568|7.7568	0.28930|0.28930	0.0:0.3185:0.0:0.6815|0.0:0.3185:0.0:0.6815	.|.	300|.	Q9NUQ2|.	PLCE_HUMAN|.	E|N	300|117	ENSP00000285518:D300E|.	ENSP00000285518:D300E|.	D|I	+|+	3|2	2|0	AGPAT5|AGPAT5	6602122|6602122	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	1.618000|1.618000	0.36954|0.36954	0.190000|0.190000	0.20209|0.20209	0.459000|0.459000	0.35465|0.35465	GAT|ATC	.	.	.	none		0.323	AGPAT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374684.1	NM_018361		A	6614714	T	A	6614714	3	1	95	1	0	0	0	0	1	0	0	0	390	1432	50	5	930	5	AGPAT5	8	6614714	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08		6614714	139749308	34	6018											
TNKS	8658	hgsc.bcm.edu	37	chr8	9413684	9413684	+	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	gggatccgcccgacaggcccCgatccccggacccggttgac	6	4	13	18	5	0	1	0	1	0	0	2	5	2	3	7	4	0	1	7	4	0	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr8:9413684C>G	ENST00000310430.6	+	1	261	c.235C>G	c.(235-237)Cga>Gga	p.R79G	RP11-375N15.2_ENST00000607598.1_RNA|TNKS_ENST00000520408.1_Missense_Mutation_p.R79G|TNKS_ENST00000522110.1_Missense_Mutation_p.R79G	NM_003747.2	NP_003738.2	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	79					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.R79*(2)		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)		CGACAGGCCCCGATCCCCGGA	0.701																																					p.R79G		Atlas-SNP	.											TNKS_ENST00000310430,NS,carcinoma,-1,2	TNKS	198	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C235G						PASS	.						23	26	25					8																	9413684		2202	4299	6501	SO:0001583	missense	8658	exon1			AGGCCCCGATCCC	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.235C>G	chr8.hg19:g.9413684C>G	ENSP00000311579:p.Arg79Gly	75.0	0.0	.		103.0	27.0	.	NM_003747	O95272|Q4G0F2	Missense_Mutation	SNP	ENST00000310430.6	hg19	CCDS5974.1	.	.	.	.	.	.	.	.	.	.	C	13.78	2.337846	0.41398	.	.	ENSG00000173273	ENST00000520408;ENST00000310430;ENST00000522110	T;T	0.62788	0.0;0.05	4.84	2.01	0.26516	.	0.123149	0.33457	N	0.004900	T	0.41096	0.1144	N	0.19112	0.55	0.26334	N	0.977462	B;B	0.17038	0.006;0.02	B;B	0.12837	0.008;0.008	T	0.28618	-1.0038	10	0.51188	T	0.08	.	5.6253	0.17478	0.3245:0.5507:0.0:0.1248	.	79;79	E7EWY6;O95271	.;TNKS1_HUMAN	G	79	ENSP00000428299:R79G;ENSP00000311579:R79G	ENSP00000311579:R79G	R	+	1	2	TNKS	9451094	0.020000	0.18652	0.999000	0.59377	0.985000	0.73830	0.272000	0.18644	0.719000	0.32188	-0.169000	0.13324	CGA	.	.	.	none		0.701	TNKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206935.1	NM_003747		G	9413684	C	G	9413684	3	3	95	1	0	0	0	0	1	0	0	0	16331	644	23	4	237	4	TNKS	8	9413684	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	2798970	9413684	136950338	35	6019											
KIAA1967	57805	hgsc.bcm.edu	37	chr8	22464154	22464154	+	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	gcgggtcttcactggtattgTtaccagcttgcatgactact	7	14	10	10	1	2	1	1	1	1	0	2	1	2	1	1	2	4	4	1	2	3	6			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr8:22464154T>A	ENST00000308511.4	+	4	434	c.185T>A	c.(184-186)gTt>gAt	p.V62D	CCAR2_ENST00000520861.1_5'Flank|CCAR2_ENST00000389279.3_Missense_Mutation_p.V62D|CCAR2_ENST00000521301.1_Missense_Mutation_p.V62D			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	62					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)										ACTGGTATTGTTACCAGCTTG	0.463																																					p.V62D		Atlas-SNP	.											.	KIAA1967	72	.	0			c.T185A						PASS	.						154	131	139					8																	22464154		2203	4300	6503	SO:0001583	missense	57805	exon4			GTATTGTTACCAG	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.185T>A	chr8.hg19:g.22464154T>A	ENSP00000310670:p.Val62Asp	109.0	0.0	.		159.0	51.0	.	NM_021174	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Missense_Mutation	SNP	ENST00000308511.4	hg19	CCDS34863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.9|24.9	4.584955|4.584955	0.86748|0.86748	.|.	.|.	ENSG00000158941|ENSG00000158941	ENST00000523801;ENST00000518989|ENST00000308511;ENST00000521301;ENST00000389279;ENST00000521837;ENST00000523349	.|T;T	.|0.61040	.|0.14;0.14	5.87|5.87	5.87|5.87	0.94306|0.94306	.|.	.|0.000000	.|0.64402	.|D	.|0.000004	.|T	.|0.76905	.|0.4053	M|M	0.80982|0.80982	2.52|2.52	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.85130	.|0.997	.|T	.|0.80108	.|-0.1520	.|10	.|0.87932	.|D	.|0	-21.0092|-21.0092	14.0962|14.0962	0.65023|0.65023	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|62	.|Q8N163	.|K1967_HUMAN	X|D	69;14|62	.|ENSP00000310670:V62D;ENSP00000373930:V62D	.|ENSP00000310670:V62D	C|V	+|+	3|2	2|0	KIAA1967|KIAA1967	22520099|22520099	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	6.291000|6.291000	0.72719|0.72719	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	TGT|GTT	.	.	.	none		0.463	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174		A	22464154	T	A	22464154	3	1	95	1	0	0	0	0	1	0	0	0	8272	1725	60	5	195	5	KIAA1967	8	22464154	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08	13050470	22464154	123899868	36	6020											
KCNS2	3788	hgsc.bcm.edu	37	chr8	99441267	99441267	+	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	cctacaccattgaaaaggagGagaacgagggcctggccacc	13	4	12	12	1	0	2	0	1	0	1	0	5	0	3	5	4	2	0	5	4	4	2			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr8:99441267G>T	ENST00000287042.4	+	2	1410	c.1060G>T	c.(1060-1062)Gag>Tag	p.E354*	KCNS2_ENST00000521839.1_Nonsense_Mutation_p.E354*	NM_020697.2	NP_065748.1	Q9ULS6	KCNS2_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 2	354					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			autonomic_ganglia(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	31	Breast(36;2.4e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.0448)			TGAAAAGGAGGAGAACGAGGG	0.577																																					p.E354X	Pancreas(138;844 2489 9202 24627)	Atlas-SNP	.											.	KCNS2	93	.	0			c.G1060T						PASS	.						89	80	83					8																	99441267		2203	4300	6503	SO:0001587	stop_gained	3788	exon2			AAGGAGGAGAACG	AB032970	CCDS6279.1	8q22	2011-07-05			ENSG00000156486	ENSG00000156486		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6301	protein-coding gene	gene with protein product		602906				9305895, 16382104	Standard	NM_020697		Approved	Kv9.2	uc003yin.3	Q9ULS6	OTTHUMG00000044337	ENST00000287042.4:c.1060G>T	chr8.hg19:g.99441267G>T	ENSP00000287042:p.Glu354*	148.0	0.0	.		202.0	51.0	.	NM_020697	A8KAN1	Nonsense_Mutation	SNP	ENST00000287042.4	hg19	CCDS6279.1	.	.	.	.	.	.	.	.	.	.	G	40	8.203350	0.98704	.	.	ENSG00000156486	ENST00000287042;ENST00000521839	.	.	.	5.91	5.91	0.95273	.	0.158483	0.56097	D	0.000029	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	20.3052	0.98627	0.0:0.0:1.0:0.0	.	.	.	.	X	354	.	ENSP00000287042:E354X	E	+	1	0	KCNS2	99510443	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	9.869000	0.99810	2.808000	0.96608	0.655000	0.94253	GAG	.	.	.	none		0.577	KCNS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103134.1	NM_020697		T	99441267	G	T	99441267	4	4	95	1	0	0	0	0	0	1	0	0	8096	1175	41	4	1062	4	KCNS2	8	99441267	Nonsense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	76977113	99441267	46922755	37	6021											
FAM135B	51059	hgsc.bcm.edu	37	chr8	139164000	139164000	+	Silent	SNP	G	G	T																															acattcaagtctttaggcatGccctttggggtttcctcaag																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr8:139164000G>T	ENST00000395297.1	-	13	2888	c.2718C>A	c.(2716-2718)ggC>ggA	p.G906G		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	906										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)			CTTTAGGCATGCCCTTTGGGG	0.458										HNSCC(54;0.14)																											p.G906G		Atlas-SNP	.											.	FAM135B	423	.	0			c.C2718A						PASS	.						128	126	127					8																	139164000		2203	4300	6503	SO:0001819	synonymous_variant	51059	exon13			AGGCATGCCCTTT	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.2718C>A	chr8.hg19:g.139164000G>T		307.0	0.0	.		335.0	98.0	.	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Silent	SNP	ENST00000395297.1	hg19	CCDS6375.2																																																																																			.	.	.	none		0.458	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		T	139164000	G	T	139164000	2	4	95	1	0	0	0	0	0	0	0	1	5453	1306	46	4		4	FAM135B	8	139164000	Silent	SNP	G	TCGA-B9-4114-01A-01D-1252-08	39722733	139164000	7200022	38	6022	66	2									
FAM135B	51059	hgsc.bcm.edu	37	chr8	139164004	139164004	+	Missense_Mutation	SNP	T	T	C																															tcaagtctttaggcatgcccTttggggtttcctcaagtgct																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr8:139164004T>C	ENST00000395297.1	-	13	2884	c.2714A>G	c.(2713-2715)aAg>aGg	p.K905R		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	905										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)			AGGCATGCCCTTTGGGGTTTC	0.468										HNSCC(54;0.14)																											p.K905R		Atlas-SNP	.											.	FAM135B	423	.	0			c.A2714G						PASS	.						125	124	124					8																	139164004		2203	4300	6503	SO:0001583	missense	51059	exon13			ATGCCCTTTGGGG	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.2714A>G	chr8.hg19:g.139164004T>C	ENSP00000378710:p.Lys905Arg	310.0	0.0	.		338.0	94.0	.	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	hg19	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	T	15.06	2.721538	0.48728	.	.	ENSG00000147724	ENST00000395297	T	0.16597	2.33	5.33	4.15	0.48705	.	0.392353	0.28031	N	0.016877	T	0.19127	0.0459	L	0.32530	0.975	0.09310	N	1	P;P;B	0.51351	0.944;0.728;0.164	P;B;B	0.50617	0.646;0.343;0.04	T	0.04017	-1.0984	10	0.46703	T	0.11	-11.8381	9.5929	0.39557	0.1559:0.0:0.0:0.8441	.	905;905;905	Q49AJ0-3;Q49AJ0-4;Q49AJ0	.;.;F135B_HUMAN	R	905	ENSP00000378710:K905R	ENSP00000276737:K905R	K	-	2	0	FAM135B	139233186	0.652000	0.27349	0.013000	0.15412	0.286000	0.27126	4.148000	0.58085	0.833000	0.34828	0.533000	0.62120	AAG	.	.	.	none		0.468	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		C	139164004	T	C	139164004	3	2	95	1	0	0	0	0	1	0	0	0	5453	1609	56	3	1538	3	FAM135B	8	139164004	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08	4	139164004	7200018	39	6023	66	2									
UNC13B	10497	hgsc.bcm.edu	37	chr9	35375163	35375163	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggcaggaatcacttctgcaAtggctacacgcacttctctt	10	11	8	12	1	3	0	1	0	2	0	4	1	3	1	0	3	2	4	0	3	3	4			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr9:35375163A>G	ENST00000378495.3	+	13	1555	c.1333A>G	c.(1333-1335)Atg>Gtg	p.M445V	UNC13B_ENST00000378496.4_Missense_Mutation_p.M445V|UNC13B_ENST00000396787.1_Missense_Mutation_p.M457V	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	445					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)			CACTTCTGCAATGGCTACACG	0.537																																					p.M445V		Atlas-SNP	.											.	UNC13B	153	.	0			c.A1333G						PASS	.						240	213	222					9																	35375163		2203	4300	6503	SO:0001583	missense	10497	exon13			TCTGCAATGGCTA	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.1333A>G	chr9.hg19:g.35375163A>G	ENSP00000367756:p.Met445Val	447.0	1.0	.		369.0	223.0	.	NM_006377	Q5VYM8	Missense_Mutation	SNP	ENST00000378495.3	hg19	CCDS6579.1	.	.	.	.	.	.	.	.	.	.	A	12.32	1.903474	0.33628	.	.	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496;ENST00000535471	T;T;T	0.61040	0.14;0.14;0.14	5.81	3.16	0.36331	.	0.084309	0.85682	D	0.000000	T	0.40932	0.1137	L	0.28504	0.86	0.45295	D	0.998291	B;B	0.23806	0.091;0.03	B;B	0.24006	0.05;0.019	T	0.17228	-1.0376	10	0.26408	T	0.33	-19.0987	8.125	0.30992	0.6561:0.1107:0.0:0.2332	.	445;445	F8W8M9;O14795	.;UN13B_HUMAN	V	457;445;445;32	ENSP00000380006:M457V;ENSP00000367756:M445V;ENSP00000367757:M445V	ENSP00000367756:M445V	M	+	1	0	UNC13B	35365163	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.969000	0.56816	1.010000	0.39314	0.482000	0.46254	ATG	.	.	.	none		0.537	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377		G	35375163	A	G	35375163	3	3	95	1	0	0	0	0	1	0	0	0	16997	101	4	3	1383	3	UNC13B	9	35375163	Missense_Mutation	SNP	A	TCGA-B9-4114-01A-01D-1252-08		35375163	105838268	40	6024											
ABL1	25	hgsc.bcm.edu	37	chr9	133748371	133748371	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggtgctgctgtacatggcCactcagatctcgtcagccat	7	11	11	12	1	3	1	2	0	1	1	4	1	3	1	2	2	4	3	2	2	1	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr9:133748371C>T	ENST00000318560.5	+	6	1413	c.1032C>T	c.(1030-1032)gcC>gcT	p.A344A		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	344	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	TGTACATGGCCACTCAGATCT	0.577			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"																																p.A363A		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.C1089T						PASS	.						73	59	64					9																	133748371		2203	4300	6503	SO:0001819	synonymous_variant	25	exon6			CATGGCCACTCAG	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.1032C>T	chr9.hg19:g.133748371C>T		137.0	0.0	.		143.0	90.0	.	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	hg19	CCDS35166.1																																																																																			.	.	.	none		0.577	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		T	133748371	C	T	133748371	2	4	95	1	0	0	0	0	0	0	0	1	92	581	21	2		2	ABL1	9	133748371	Silent	SNP	C	TCGA-B9-4114-01A-01D-1252-08	98373208	133748371	7465060	41	6025											
ARMC4	55130	hgsc.bcm.edu	37	chr10	28257893	28257893	+	Frame_Shift_Del	DEL	T	T	-																															tgtgaaacagatggtcttggTttttcaagttttcctgtgtg																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr10:28257893delT	ENST00000305242.5	-	9	1289	c.1197delA	c.(1195-1197)aaafs	p.K399fs	ARMC4_ENST00000537576.1_Frame_Shift_Del_p.K91fs|ARMC4_ENST00000545014.1_Intron|ARMC4_ENST00000480504.1_5'UTR|ARMC4_ENST00000239715.3_Frame_Shift_Del_p.K256fs	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	399					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						ATGGTCTTGGTTTTTCAAGTT	0.398																																					p.P400fs		Atlas-INDEL	.											.	ARMC4	177	.	0			c.1198delC						PASS	.						4	3	3					10																	28257893		1579	3445	5024	SO:0001589	frameshift_variant	55130	exon9			.	AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"Armadillo repeat containing"	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.1197delA	chr10.hg19:g.28257893delT	ENSP00000306410:p.Lys399fs	513.0	0.0	0		177.0	24.0	0.135593	NM_018076	A8K906|B7Z7I1|Q9H0C0	Frame_Shift_Del	DEL	ENST00000305242.5	hg19	CCDS7157.1																																																																																			.	.	.	none		0.398	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1	NM_018076		-	28257893	T	-	28257893	7	5	95	1	0	1	0	1	0	0	0	0	953	1722	60	0	1985	0	ARMC4	10	28257893	Frame_Shift_Del	DEL	T	TCGA-B9-4114-01A-01D-1252-08		28257893	107276854	42	6026											
NODAL	4838	hgsc.bcm.edu	37	chr10	72195424	72195424	+	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	ctaccctggacatctgcttcTccagggccccagggtgcttc	5	10	10	16	0	2	0	0	0	2	0	4	1	2	1	4	3	3	2	4	3	1	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr10:72195424T>A	ENST00000287139.3	-	2	508	c.509A>T	c.(508-510)gAg>gTg	p.E170V	AC022532.1_ENST00000420338.2_Missense_Mutation_p.L124H	NM_018055.4	NP_060525.3	Q96S42	NODAL_HUMAN	nodal growth differentiation factor	170					axial mesodermal cell fate specification (GO:0048327)|brain development (GO:0007420)|cell migration involved in gastrulation (GO:0042074)|digestive tract morphogenesis (GO:0048546)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic pattern specification (GO:0009880)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|endodermal cell differentiation (GO:0035987)|epiblast cell-extraembryonic ectoderm cell signaling involved in anterior/posterior axis specification (GO:0060802)|floor plate morphogenesis (GO:0033505)|formation of anatomical boundary (GO:0048859)|growth (GO:0040007)|heart looping (GO:0001947)|inhibition of neuroepithelial cell differentiation (GO:0002085)|left lung morphogenesis (GO:0060460)|liver development (GO:0001889)|maternal placenta development (GO:0001893)|maternal process involved in parturition (GO:0060137)|mesendoderm development (GO:0048382)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of chorionic trophoblast cell proliferation (GO:1901383)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of trophoblast cell migration (GO:1901164)|neural fold formation (GO:0001842)|nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900164)|placenta development (GO:0001890)|polarity specification of proximal/distal axis (GO:0010085)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900224)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of gastrulation (GO:0010470)|regulation of stem cell maintenance (GO:2000036)|SMAD protein signal transduction (GO:0060395)|stem cell maintenance (GO:0019827)|transforming growth factor beta receptor signaling pathway involved in primitive streak formation (GO:0090010)|trophectodermal cellular morphogenesis (GO:0001831)|vasculature development (GO:0001944)	extracellular space (GO:0005615)	morphogen activity (GO:0016015)|type I activin receptor binding (GO:0070698)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(2)	15						CATCTGCTTCTCCAGGGCCCC	0.602																																					p.E170V		Atlas-SNP	.											.	NODAL	32	.	0			c.A509T						PASS	.						37	37	37					10																	72195424		2203	4300	6503	SO:0001583	missense	4838	exon2			TGCTTCTCCAGGG	BC033585	CCDS7304.1	10q22.1	2012-12-07	2012-12-07		ENSG00000156574	ENSG00000156574			7865	protein-coding gene	gene with protein product		601265	"nodal, mouse, homolog", "nodal homolog (mouse)"			9354794	Standard	NM_018055		Approved		uc001jrc.2	Q96S42	OTTHUMG00000018408	ENST00000287139.3:c.509A>T	chr10.hg19:g.72195424T>A	ENSP00000287139:p.Glu170Val	74.0	0.0	.		122.0	38.0	.	NM_018055	Q2M3A5|Q8N4V3	Missense_Mutation	SNP	ENST00000287139.3	hg19	CCDS7304.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.27|14.27	2.486027|2.486027	0.44147|0.44147	.|.	.|.	ENSG00000156574|ENSG00000197604	ENST00000287139;ENST00000414871|ENST00000420338	D;D|.	0.85339|.	-1.97;-1.94|.	5.99|5.99	1.14|1.14	0.20703|0.20703	.|.	0.737242|.	0.13941|.	N|.	0.352164|.	T|T	0.39306|0.39306	0.1073|0.1073	L|L	0.56769|0.56769	1.78|1.78	0.28250|0.28250	N|N	0.925313|0.925313	B|.	0.17268|.	0.021|.	B|.	0.22880|.	0.042|.	T|T	0.46233|0.46233	-0.9206|-0.9206	10|6	0.31617|0.87932	T|D	0.26|0	.|.	1.0685|1.0685	0.01616|0.01616	0.1347:0.2379:0.2788:0.3486|0.1347:0.2379:0.2788:0.3486	.|.	170|.	Q96S42|.	NODAL_HUMAN|.	V|H	170;115|124	ENSP00000287139:E170V;ENSP00000394468:E115V|.	ENSP00000287139:E170V|ENSP00000411125:L124H	E|L	-|+	2|2	0|0	NODAL|AC022532.1	71865430|71865430	0.001000|0.001000	0.12720|0.12720	0.956000|0.956000	0.39512|0.39512	0.792000|0.792000	0.44763|0.44763	0.801000|0.801000	0.27055|0.27055	0.162000|0.162000	0.19483|0.19483	0.533000|0.533000	0.62120|0.62120	GAG|CTC	.	.	.	none		0.602	NODAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048511.1	NM_018055		A	72195424	T	A	72195424	3	1	95	1	0	0	0	0	1	0	0	0	10525	1551	54	5	542	5	NODAL	10	72195424	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08	43937531	72195424	63339323	43	6027											
NOLC1	9221	hgsc.bcm.edu	37	chr10	103917239	103917239	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgggaaggctgcagccaaagCatcagagagtagcagcagtg	13	5	15	8	0	1	1	1	0	0	1	1	3	1	2	1	2	5	6	1	2	3	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr10:103917239C>T	ENST00000605788.1	+	4	603	c.368C>T	c.(367-369)gCa>gTa	p.A123V	NOLC1_ENST00000603742.1_5'UTR|NOLC1_ENST00000405356.1_Missense_Mutation_p.A123V|NOLC1_ENST00000488254.2_Missense_Mutation_p.A124V	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	123	11 X 12 AA approximate repeats of an acidic serine cluster.				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)		GCAGCCAAAGCATCAGAGAGT	0.512																																					p.A123V		Atlas-SNP	.											.	NOLC1	61	.	0			c.C368T						PASS	.						68	65	66					10																	103917239		2203	4300	6503	SO:0001583	missense	9221	exon4			CCAAAGCATCAGA	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.368C>T	chr10.hg19:g.103917239C>T	ENSP00000474710:p.Ala123Val	95.0	0.0	.		75.0	21.0	.	NM_004741	Q15030|Q5VV70|Q9BUV3	Missense_Mutation	SNP	ENST00000605788.1	hg19	CCDS7530.1	.	.	.	.	.	.	.	.	.	.	C	12.57	1.978454	0.34942	.	.	ENSG00000166197	ENST00000405356;ENST00000370007	T	0.43294	0.95	5.52	5.52	0.82312	.	0.307617	0.28589	N	0.014814	T	0.47967	0.1474	M	0.78801	2.425	0.28217	N	0.926698	P;P;P	0.42296	0.775;0.775;0.666	B;B;B	0.42282	0.382;0.382;0.212	T	0.57207	-0.7851	10	0.66056	D	0.02	-13.6615	11.8733	0.52534	0.272:0.728:0.0:0.0	.	124;123;123	Q14978-3;Q14978-2;Q14978	.;.;NOLC1_HUMAN	V	123	ENSP00000385410:A123V	ENSP00000359024:A123V	A	+	2	0	NOLC1	103907229	0.977000	0.34250	0.998000	0.56505	0.422000	0.31414	2.072000	0.41510	2.620000	0.88729	0.655000	0.94253	GCA	.	.	.	none		0.512	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741		T	103917239	C	T	103917239	3	4	95	1	0	0	0	0	1	0	0	0	10536	710	25	2	382	2	NOLC1	10	103917239	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	31721815	103917239	31617508	44	6028											
BRSK2	9024	hgsc.bcm.edu	37	chr11	1466623	1466623	+	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	atcgaccccgacgtgctggaCagcatgcactcactgggctg	8	7	12	14	3	1	0	1	0	0	0	2	3	1	1	2	2	3	4	2	2	0	0			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr11:1466623C>T	ENST00000528841.1	+	10	1296	c.912C>T	c.(910-912)gaC>gaT	p.D304D	BRSK2_ENST00000382179.1_Silent_p.D350D|BRSK2_ENST00000308230.5_Silent_p.D304D|BRSK2_ENST00000531197.1_Silent_p.D304D|BRSK2_ENST00000526678.1_Silent_p.D304D|BRSK2_ENST00000308219.9_Silent_p.D304D|BRSK2_ENST00000528710.1_Silent_p.D244D|BRSK2_ENST00000544817.1_5'UTR			Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2	304	UBA.				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)		ACGTGCTGGACAGCATGCACT	0.667																																					p.D350D		Atlas-SNP	.											.	BRSK2	97	.	0			c.C1050T						PASS	.						34	42	39					11																	1466623		2132	4245	6377	SO:0001819	synonymous_variant	9024	exon10			GCTGGACAGCATG	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.912C>T	chr11.hg19:g.1466623C>T		43.0	0.0	.		58.0	24.0	.	NM_001256630	B3KVE9|E9PLM7|O60843|O95099|Q5J5B4|Q6ZMQ4|Q8TB60	Silent	SNP	ENST00000528841.1	hg19	CCDS58107.1																																																																																			.	.	.	none		0.667	BRSK2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393033.1	NM_003957		T	1466623	C	T	1466623	2	4	95	1	0	0	0	0	0	0	0	1	1526	477	17	2		2	BRSK2	11	1466623	Silent	SNP	C	TCGA-B9-4114-01A-01D-1252-08		1466623	133539893	45	6029											
EIF3M	493860	hgsc.bcm.edu	37	chr11	32623898	32623898	+	3'UTR	SNP	A	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	cacttaatgcctggaaacaaAatctgaacaaagtgaaaaac	20	7	6	8	0	1	2	0	2	1	0	1	3	1	3	1	1	4	0	1	1	8	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr11:32623898A>T	ENST00000335185.5	-	0	3742				EIF3M_ENST00000531120.1_Missense_Mutation_p.N360Y|EIF3M_ENST00000524896.1_Missense_Mutation_p.N228Y	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)					CTGGAAACAAAATCTGAACAA	0.328																																					p.N360Y		Atlas-SNP	.											.	EIF3M	37	.	0			c.A1078T						PASS	.						93	93	93					11																	32623898		2202	4298	6500	SO:0001624	3_prime_UTR_variant	10480	exon11			AAACAAAATCTGA	AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279	ENST00000335185.5:c.*459T>A	chr11.hg19:g.32623898A>T		173.0	0.0	.		22.0	10.0	.	NM_006360	Q6P5Q7|Q6ZMW0|Q86WE7	Missense_Mutation	SNP	ENST00000335185.5	hg19	CCDS41630.1	.	.	.	.	.	.	.	.	.	.	A	17.70	3.454889	0.63290	.	.	ENSG00000149100	ENST00000531120;ENST00000524896;ENST00000526267	T;T;T	0.51325	1.26;0.72;0.71	5.7	5.7	0.88788	.	0.042254	0.85682	D	0.000000	T	0.62889	0.2465	M	0.82056	2.57	0.80722	D	1	D;D	0.61697	0.97;0.99	P;P	0.51615	0.675;0.675	T	0.69986	-0.4996	10	0.87932	D	0	-19.1647	15.9644	0.79956	1.0:0.0:0.0:0.0	.	228;360	B4E2Q4;Q7L2H7	.;EIF3M_HUMAN	Y	360;228;213	ENSP00000436049:N360Y;ENSP00000436787:N228Y;ENSP00000432139:N213Y	ENSP00000436787:N228Y	N	+	1	0	EIF3M	32580474	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.302000	0.89953	2.172000	0.68678	0.460000	0.39030	AAT	.	.	.	none		0.328	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391		T	32623898	A	T	32623898	1	4	95	0	1	0	0	0	0	0	0	0	5025	14	1	5		5	EIF3M	11	32623898	3'UTR	SNP	A	TCGA-B9-4114-01A-01D-1252-08	31157275	32623898	102382618	46	6030											
TMX2	51075	hgsc.bcm.edu	37	chr11	57480106	57480106	+	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	aaaagatggcggtcttggcaCctctaattgctctcgtgtat	9	13	10	9	2	3	1	0	0	3	1	4	1	3	1	1	3	1	3	1	3	4	4			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr11:57480106C>A	ENST00000278422.4	+	1	28	c.16C>A	c.(16-18)Cct>Act	p.P6T	TMX2-CTNND1_ENST00000528395.1_Missense_Mutation_p.P6T|TMX2_ENST00000378312.4_Missense_Mutation_p.P6T|MED19_ENST00000337672.2_5'Flank|MED19_ENST00000431606.2_5'Flank	NM_015959.3	NP_057043.1	Q9Y320	TMX2_HUMAN	thioredoxin-related transmembrane protein 2	6					cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|urinary_tract(2)	12						GGTCTTGGCACCTCTAATTGC	0.592																																					p.P6T		Atlas-SNP	.											.	TMX2	29	.	0			c.C16A						PASS	.						70	57	61					11																	57480106		2201	4296	6497	SO:0001583	missense	51075	exon1			TTGGCACCTCTAA	AF132965	CCDS7967.1, CCDS44601.1	11q12.1	2012-09-20	2009-02-23	2009-02-23	ENSG00000213593	ENSG00000213593		"Protein disulfide isomerases"	30739	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 12"		"thioredoxin domain containing 14"	TXNDC14		12670024	Standard	NM_015959		Approved	PDIA12	uc001nlc.2	Q9Y320	OTTHUMG00000167200	ENST00000278422.4:c.16C>A	chr11.hg19:g.57480106C>A	ENSP00000278422:p.Pro6Thr	59.0	0.0	.		76.0	27.0	.	NM_015959	B7Z4R4|Q53G73|Q561W0|Q5J7Q7|Q8NBP9|Q9H3L1	Missense_Mutation	SNP	ENST00000278422.4	hg19	CCDS7967.1	.	.	.	.	.	.	.	.	.	.	C	18.57	3.651806	0.67472	.	.	ENSG00000213593	ENST00000378312;ENST00000278422	T	0.53857	0.6	5.98	5.98	0.97165	.	0.128810	0.53938	U	0.000057	T	0.64349	0.2590	L	0.43152	1.355	0.58432	D	0.999993	D;D	0.67145	0.996;0.985	P;P	0.58266	0.836;0.756	T	0.63919	-0.6528	10	0.66056	D	0.02	-4.5842	20.0512	0.97629	0.0:1.0:0.0:0.0	.	6;6	Q9Y320-2;Q9Y320	.;TMX2_HUMAN	T	6	ENSP00000367562:P6T	ENSP00000436274:P6T	P	+	1	0	TMX2	57236682	0.999000	0.42202	0.427000	0.26684	0.277000	0.26821	4.548000	0.60718	2.847000	0.97988	0.591000	0.81541	CCT	.	.	.	none		0.592	TMX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393708.1	NM_015959		A	57480106	C	A	57480106	3	1	95	1	0	0	0	0	1	0	0	0	16279	507	18	4	18	4	TMX2	11	57480106	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	24856208	57480106	77526410	47	6031											
FAU	740	hgsc.bcm.edu	37	chr11	64889268	64889268	+	5'Flank	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	aaggtgtgtagctcctgggcGcggacaaagagctgcatatt	10	9	14	8	2	0	1	0	0	0	1	1	2	1	2	1	3	3	4	1	3	4	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr11:64889268G>T	ENST00000279242.2	+	0	0				MRPL49_ENST00000534078.1_5'Flank|FAU_ENST00000531743.1_Silent_p.R6R|MRPL49_ENST00000526171.1_5'Flank|FAU_ENST00000529639.1_Silent_p.R6R|FAU_ENST00000525297.1_Silent_p.R6R|FAU_ENST00000279259.3_Silent_p.R6R|MRPL49_ENST00000531705.1_5'Flank|FAU_ENST00000527548.1_Silent_p.R6R|FAU_ENST00000434372.2_Silent_p.R6R|FAU_ENST00000529259.1_Silent_p.R6R	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						GCTCCTGGGCGCGGACAAAGA	0.532																																					p.R6R		Atlas-SNP	.											.	FAU	17	.	0			c.C18A						PASS	.						71	64	66					11																	64889268		2201	4297	6498	SO:0001631	upstream_gene_variant	2197	exon2			CTGGGCGCGGACA		CCDS8096.1	11q13.1	2012-11-14	2001-10-16	2001-10-19	ENSG00000149792	ENSG00000149792		"Mitochondrial ribosomal proteins / large subunits"	1176	protein-coding gene	gene with protein product	"neighbor of FAU", "next to FAU"	606866	"chromosome 11 open reading frame 4"	C11orf4		8786148	Standard	NM_004927		Approved	NOF, NOF1, L49mt	uc001oda.2	Q13405	OTTHUMG00000165608		chr11.hg19:g.64889268G>T	Exception_encountered	110.0	0.0	.		160.0	39.0	.	NM_001997	B2R4G6	Silent	SNP	ENST00000279242.2	hg19	CCDS8096.1																																																																																			.	.	.	none		0.532	MRPL49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385293.1	NM_004927		T	64889268	G	T	64889268	1	4	95	0	1	0	0	0	0	0	0	0	5701	1074	38	4		4	FAU	11	64889268	5'Flank	SNP	G	TCGA-B9-4114-01A-01D-1252-08	7409162	64889268	70117248	48	6032											
SIK2	23235	hgsc.bcm.edu	37	chr11	111590501	111590501	+	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	ctctcccctggcgtttaggtCaatggctgtctgcttgaccc	4	13	10	14	1	3	1	1	1	2	0	4	1	3	1	3	3	1	3	3	3	2	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr11:111590501C>T	ENST00000304987.3	+	10	1442	c.1269C>T	c.(1267-1269)gtC>gtT	p.V423V	SIK2_ENST00000533868.1_3'UTR	NM_015191.1	NP_056006.1	Q9H0K1	SIK2_HUMAN	salt-inducible kinase 2	423					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						GCGTTTAGGTCAATGGCTGTC	0.517																																					p.V423V		Atlas-SNP	.											.	SIK2	89	.	0			c.C1269T						PASS	.						45	30	35					11																	111590501		2201	4297	6498	SO:0001819	synonymous_variant	23235	exon10			TTAGGTCAATGGC	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.1269C>T	chr11.hg19:g.111590501C>T		45.0	0.0	.		59.0	21.0	.	NM_015191	A8K5B8|B0YJ94|O94878|Q17RV0|Q6AZE2|Q76N03|Q8NCV7|Q96CZ8	Silent	SNP	ENST00000304987.3	hg19	CCDS8347.1																																																																																			.	.	.	none		0.517	SIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319352.3	NM_015191		T	111590501	C	T	111590501	2	4	95	1	0	0	0	0	0	0	0	1	14331	813	29	2		2	SIK2	11	111590501	Silent	SNP	C	TCGA-B9-4114-01A-01D-1252-08	46701233	111590501	23416015	49	6033											
OAF	220323	hgsc.bcm.edu	37	chr11	120097580	120097581	+	Missense_Mutation	DNP	AC	AC	CA																															tcggggtctggagcatctgcAcatggatgtcgctgtcaact																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr11:120097580_120097581AC>CA	ENST00000328965.4	+	3	935_936	c.422_423AC>CA	c.(421-423)cAC>cCA	p.H141P	OAF_ENST00000531220.1_Missense_Mutation_p.H25P	NM_178507.2	NP_848602.1	Q86UD1	OAF_HUMAN	OAF homolog (Drosophila)	141						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)		GAGCATCTGCACATGGATGTCG	0.619																																					p.H141P|p.H141Q		Atlas-SNP	.											.	OAF	12	.	0			c.A422C|c.C423A						PASS	.																																			SO:0001583	missense	220323	exon3			ATCTGCACATGGA|TCTGCACATGGAT	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	Exception_encountered	chr11.hg19:g.120097580_120097581delinsCA	ENSP00000332613:p.His141Pro	142.0|139.0	0.0	.		182.0|183.0	60.0|57.0	.	NM_178507		Missense_Mutation	SNP	ENST00000328965.4	hg19	CCDS8430.1																																																																																			.	.	.	none		0.619	OAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388036.2	NM_178507		CA	120097581	AC	CA	120097580	3	2	95	1	0	0	0	0	1	0	0	0	10805	159	6	5	432	5	OAF	11	120097580	Missense_Mutation	DNP	AC	TCGA-B9-4114-01A-01D-1252-08	8507079	120097580	14908936	50	6034											
SMARCC2	6601	hgsc.bcm.edu	37	chr12	56558312	56558312	+	Missense_Mutation	SNP	T	T	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	gtggtgatgcccatgcaggtTaggaggagcggggaggttaa	9	8	19	5	1	0	1	0	1	0	0	0	4	0	4	1	7	3	3	1	7	2	2			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr12:56558312T>G	ENST00000267064.4	-	27	3429	c.3343A>C	c.(3343-3345)Aac>Cac	p.N1115H	SMARCC2_ENST00000347471.4_Intron|SMARCC2_ENST00000394023.3_Intron|SMARCC2_ENST00000550164.1_Missense_Mutation_p.N1146H|RP11-977G19.5_ENST00000553176.1_RNA	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	1115	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)			CCATGCAGGTTAGGAGGAGCG	0.592																																					p.N1115H		Atlas-SNP	.											.	SMARCC2	212	.	0			c.A3343C						PASS	.						114	95	101					12																	56558312		2203	4300	6503	SO:0001583	missense	6601	exon27			GCAGGTTAGGAGG	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.3343A>C	chr12.hg19:g.56558312T>G	ENSP00000267064:p.Asn1115His	123.0	0.0	.		259.0	113.0	.	NM_003075	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Missense_Mutation	SNP	ENST00000267064.4	hg19	CCDS8907.1	.	.	.	.	.	.	.	.	.	.	T	14.73	2.622273	0.46840	.	.	ENSG00000139613	ENST00000550164;ENST00000267064	T;T	0.47528	0.85;0.84	5.28	4.1	0.47936	.	1.132090	0.06439	N	0.725536	T	0.33498	0.0865	N	0.14661	0.345	0.27631	N	0.948035	B	0.09022	0.002	B	0.04013	0.001	T	0.23833	-1.0177	9	.	.	.	-9.2359	11.5054	0.50463	0.0:0.0:0.1507:0.8493	.	1115	Q8TAQ2	SMRC2_HUMAN	H	1146;1115	ENSP00000449396:N1146H;ENSP00000267064:N1115H	.	N	-	1	0	SMARCC2	54844579	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.575000	0.36493	0.921000	0.36994	0.460000	0.39030	AAC	.	.	.	none		0.592	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1			G	56558312	T	G	56558312	3	3	95	1	0	0	0	0	1	0	0	0	14789	1754	61	5	309	5	SMARCC2	12	56558312	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08		56558312	77293583	51	6035											
GLI1	2735	hgsc.bcm.edu	37	chr12	57861143	57861143	+	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	ggtgccggaagtcatactcaCgcctcgaaaacctgaagacg	12	6	11	12	4	2	2	2	1	0	1	3	4	2	3	3	2	3	0	3	2	5	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr12:57861143C>A	ENST00000228682.2	+	9	1031	c.940C>A	c.(940-942)Cgc>Agc	p.R314S	GLI1_ENST00000546141.1_Missense_Mutation_p.R273S|GLI1_ENST00000543426.1_Missense_Mutation_p.R186S	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	314					cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			GTCATACTCACGCCTCGAAAA	0.542																																					p.R314S	Pancreas(157;841 1936 10503 41495 50368)	Atlas-SNP	.											GLI1,NS,carcinoma,-1,1	GLI1	141	.	0			c.C940A						PASS	.						109	96	101					12																	57861143		2203	4300	6503	SO:0001583	missense	2735	exon9			TACTCACGCCTCG		CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"Zinc fingers, C2H2-type"	4317	protein-coding gene	gene with protein product		165220	"glioma-associated oncogene homolog 1 (zinc finger protein)", "glioma-associated oncogene family zinc finger 1"	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.940C>A	chr12.hg19:g.57861143C>A	ENSP00000228682:p.Arg314Ser	123.0	0.0	.		190.0	38.0	.	NM_005269	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Missense_Mutation	SNP	ENST00000228682.2	hg19	CCDS8940.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.759669	0.89932	.	.	ENSG00000111087	ENST00000543426;ENST00000228682;ENST00000546141;ENST00000528467;ENST00000443131	T;T;T;T	0.39406	1.08;1.08;1.08;1.08	4.64	3.69	0.42338	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.53938	D	0.000056	T	0.49098	0.1537	N	0.21448	0.665	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.53906	-0.8372	10	0.87932	D	0	.	13.7621	0.62973	0.1541:0.8459:0.0:0.0	.	314	P08151	GLI1_HUMAN	S	186;314;273;273;186	ENSP00000437607:R186S;ENSP00000228682:R314S;ENSP00000441006:R273S;ENSP00000434408:R273S	ENSP00000228682:R314S	R	+	1	0	GLI1	56147410	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	3.744000	0.55112	2.575000	0.86900	0.563000	0.77884	CGC	.	.	.	none		0.542	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269		A	57861143	C	A	57861143	3	1	95	1	0	0	0	0	1	0	0	0	6444	536	19	4	970	4	GLI1	12	57861143	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	1302831	57861143	75990752	52	6036											
C12orf66	144577	hgsc.bcm.edu	37	chr12	64615826	64615826	+	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	aggctgtgatagaccttctcGgccgcggccaggtgcgccaa	7	7	14	13	4	1	2	0	1	1	1	2	2	1	2	4	4	1	1	4	4	2	2			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr12:64615826G>C	ENST00000398055.3	-	1	245	c.192C>G	c.(190-192)gcC>gcG	p.A64A	C12orf66_ENST00000544871.1_Intron|RPS11P6_ENST00000535684.1_RNA|C12orf66_ENST00000540673.1_5'UTR|C12orf66_ENST00000311915.8_Silent_p.A64A	NM_152440.4	NP_689653	Q96MD2	CL066_HUMAN	chromosome 12 open reading frame 66	64										central_nervous_system(1)|large_intestine(1)|lung(2)|ovary(1)	5						AGACCTTCTCGGCCGCGGCCA	0.637																																					p.A64A		Atlas-SNP	.											.	C12orf66	28	.	0			c.C192G						PASS	.						26	30	29					12																	64615826		1954	4127	6081	SO:0001819	synonymous_variant	144577	exon1			CTTCTCGGCCGCG		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.192C>G	chr12.hg19:g.64615826G>C		36.0	0.0	.		60.0	18.0	.	NM_152440	C9JX54|Q8IYA0	Silent	SNP	ENST00000398055.3	hg19	CCDS41803.1																																																																																			.	.	.	none		0.637	C12orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400921.1	NM_152440		C	64615826	G	C	64615826	2	2	95	1	0	0	0	0	0	0	0	1	1711	1103	39	4		4	C12orf66	12	64615826	Silent	SNP	G	TCGA-B9-4114-01A-01D-1252-08	6754683	64615826	69236069	53	6037											
MYO1H	283446	hgsc.bcm.edu	37	chr12	109834319	109834319	+	Frame_Shift_Del	DEL	A	A	-																															ttctcgagtattttgcagtgAcctgcccaatgacccagtca																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr12:109834319delA	ENST00000431443.2	+	3	373	c.373delA	c.(373-375)accfs	p.T125fs	MYO1H_ENST00000310903.5_Frame_Shift_Del_p.T125fs	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	125	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						TTTTGCAGTGACCTGCCCAAT	0.498																																					p.V124fs		Atlas-INDEL	.											.	MYO1H	98	.	0			c.372delG						PASS	.						71	71	71					12																	109834319		1896	4123	6019	SO:0001589	frameshift_variant	283446	exon3			.		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.373delA	chr12.hg19:g.109834319delA	ENSP00000444076:p.Thr125fs	100.0	0.0	0		135.0	21.0	0.155556	NM_001101421	F5H3C6	Frame_Shift_Del	DEL	ENST00000431443.2	hg19																																																																																				.	.	.	none		0.498	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597		-	109834319	A	-	109834319	7	5	95	1	0	1	0	1	0	0	0	0	10082	275	10	0	383	0	MYO1H	12	109834319	Frame_Shift_Del	DEL	A	TCGA-B9-4114-01A-01D-1252-08	45218493	109834319	24017576	54	6038											
PEBP1	5037	hgsc.bcm.edu	37	chr12	118577333	118577333	+	Missense_Mutation	SNP	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	agtcctctccgattatgtggGctcggggcctcccaagggca	6	9	13	13	2	1	0	0	0	1	0	5	1	3	0	4	4	0	2	4	4	2	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr12:118577333G>A	ENST00000261313.2	+	3	675	c.323G>A	c.(322-324)gGc>gAc	p.G108D	PEBP1_ENST00000542939.1_3'UTR	NM_002567.2	NP_002558.1	P30086	PEBP1_HUMAN	phosphatidylethanolamine binding protein 1	108	Interaction with RAF1.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|phosphatidylethanolamine binding (GO:0008429)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|serine-type endopeptidase inhibitor activity (GO:0004867)			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GATTATGTGGGCTCGGGGCCT	0.522																																					p.G108D	NSCLC(44;94 1357 12187 49467)	Atlas-SNP	.											.	PEBP1	13	.	0			c.G323A						PASS	.						123	110	115					12																	118577333		2203	4300	6503	SO:0001583	missense	5037	exon3			ATGTGGGCTCGGG	X85033	CCDS9187.1	12q24	2009-06-16	2006-02-16	2006-02-16	ENSG00000089220	ENSG00000089220			8630	protein-coding gene	gene with protein product	"Raf kinase inhibitory protein", "hippocampal cholinergic neurostimulating peptide"	604591	"prostatic binding protein"	PBP		15782137	Standard	NM_002567		Approved	RKIP, HCNP, PEBP	uc001twu.1	P30086	OTTHUMG00000168860	ENST00000261313.2:c.323G>A	chr12.hg19:g.118577333G>A	ENSP00000261313:p.Gly108Asp	193.0	0.0	.		249.0	101.0	.	NM_002567	B2R4S1	Missense_Mutation	SNP	ENST00000261313.2	hg19	CCDS9187.1	.	.	.	.	.	.	.	.	.	.	G	34	5.318256	0.95682	.	.	ENSG00000089220	ENST00000261313;ENST00000418769	T	0.56776	0.44	5.43	5.43	0.79202	.	0.047800	0.85682	D	0.000000	D	0.82751	0.5105	H	0.96805	3.885	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.85130	0.997;0.994	D	0.88070	0.2800	10	0.59425	D	0.04	.	19.2412	0.93883	0.0:0.0:1.0:0.0	.	108;108	B4DRT4;P30086	.;PEBP1_HUMAN	D	108	ENSP00000261313:G108D	ENSP00000261313:G108D	G	+	2	0	PEBP1	117061716	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	9.447000	0.97595	2.543000	0.85770	0.563000	0.77884	GGC	.	.	.	none		0.522	PEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401405.1	NM_002567		A	118577333	G	A	118577333	3	1	95	1	0	0	0	0	1	0	0	0	11720	1203	42	2	333	2	PEBP1	12	118577333	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	8743014	118577333	15274562	55	6039											
ZCCHC8	55596	hgsc.bcm.edu	37	chr12	122964832	122964833	+	Frame_Shift_Ins	INS	-	-	A																															ttattctgttgtatttctccINSaacttctgtttccccatcag																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr12:122964832_122964833insA	ENST00000336229.4	-	11	1174_1175	c.1044_1045insT	c.(1042-1047)gttggafs	p.G349fs	ZCCHC8_ENST00000538116.1_5'Flank|ZCCHC8_ENST00000543897.1_Frame_Shift_Ins_p.G111fs|ZCCHC8_ENST00000536306.1_Frame_Shift_Ins_p.G111fs	NM_017612.3	NP_060082.2	Q6NZY4	ZCHC8_HUMAN	zinc finger, CCHC domain containing 8	349					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)		TGTATTTCTCCAACTTCTGTTT	0.371																																					p.G349fs		Atlas-INDEL	.											.	ZCCHC8	56	.	0			c.1045_1046insT						PASS	.																																			SO:0001589	frameshift_variant	55596	exon11			.	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.1045dupT	chr12.hg19:g.122964834_122964834dupA	ENSP00000337313:p.Gly349fs	44.0	0.0	0		59.0	26.0	0.440678	NM_017612	Q7L2P6|Q8N2K5|Q96SK7|Q9NSS2|Q9NSS3	Frame_Shift_Ins	INS	ENST00000336229.4	hg19																																																																																				.	.	.	none		0.371	ZCCHC8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017612		A	122964833	-	A	122964832	7	5	95	1	0	1	1	0	0	0	0	0	17606	603	21	0	1094	0	ZCCHC8	12	122964832	Frame_Shift_Ins	INS	-	TCGA-B9-4114-01A-01D-1252-08	4387499	122964832	10887063	56	6040											
ITM2B	9445	hgsc.bcm.edu	37	chr13	48830432	48830433	+	In_Frame_Ins	INS	-	-	CAA																															aagaaaatattaaaatctttINSgaagaagaagaagttgaatt																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr13:48830432_48830433insCAA	ENST00000378565.5	+	3	569_570	c.366_367insCAA	c.(367-369)gaa>CAAgaa	p.122_123insQ	ITM2B_ENST00000378549.5_Intron	NM_021999.4	NP_068839.1	Q9Y287	ITM2B_HUMAN	integral membrane protein 2B	122	Necessary for interaction with APP and inhibitor effects on APP processing.				extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|nervous system development (GO:0007399)	endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle membrane (GO:0030660)|integral component of organelle membrane (GO:0031301)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|beta-amyloid binding (GO:0001540)			endometrium(1)|large_intestine(2)|lung(3)	6		all_cancers(8;2.2e-31)|all_epithelial(8;6.77e-15)|all_lung(13;9.67e-07)|all_hematologic(8;9.72e-06)|Lung NSC(96;8.3e-05)|Breast(56;0.000141)|Acute lymphoblastic leukemia(8;0.00045)|Prostate(109;0.000669)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;1.97e-06)		TTAAAATCTTTGAAGAAGAAGA	0.401																																					p.F122delinsFQ		Atlas-INDEL	.											.	ITM2B	24	.	0			c.366_367insCAA						PASS	.																																			SO:0001652	inframe_insertion	9445	exon3			.	AF092128	CCDS9409.1	13q14.2	2012-10-10			ENSG00000136156	ENSG00000136156		"BRICHOS domain containing"	6174	protein-coding gene	gene with protein product	"BRICHOS domain containing 2B"	603904				9795190	Standard	NM_021999		Approved	BRI, E25B, E3-16, BRICD2B	uc001vbz.3	Q9Y287	OTTHUMG00000016894	Exception_encountered	chr13.hg19:g.48830432_48830433insCAA	ENSP00000367828:p.Phe122_Glu123insGln	161.0	0.0	0		82.0	26.0	0.317073	NM_021999	Q5W0A3|Q96B24|Q9NYH1	In_Frame_Ins	INS	ENST00000378565.5	hg19	CCDS9409.1																																																																																			.	.	.	none		0.401	ITM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044870.3	NM_021999		CAA	48830433	-	CAA	48830432	7	5	95	1	0	1	1	0	0	0	0	0	7920	1809	63	0	376	0	ITM2B	13	48830432	In_Frame_Ins	INS	-	TCGA-B9-4114-01A-01D-1252-08		48830432	66339446	57	6041											
RNF31	55072	hgsc.bcm.edu	37	chr14	24617213	24617213	+	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	ctacctcaacaccctgtccaCggctctgaacatcctggaga	10	8	7	16	1	2	2	1	1	1	1	4	3	4	2	4	2	3	1	4	2	3	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr14:24617213C>G	ENST00000324103.6	+	2	541	c.221C>G	c.(220-222)aCg>aGg	p.T74R	RNF31_ENST00000559275.1_5'UTR|RNF31_ENST00000382687.3_5'Flank|PSME2_ENST00000216802.5_5'Flank|PSME2_ENST00000560410.1_5'Flank|PSME2_ENST00000471700.2_5'Flank|RNF31_ENST00000557878.1_3'UTR	NM_017999.4	NP_060469.4	Q96EP0	RNF31_HUMAN	ring finger protein 31	74	Polyubiquitin-binding.				CD40 signaling pathway (GO:0023035)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein linear polyubiquitination (GO:0097039)|protein polyubiquitination (GO:0000209)|T cell receptor signaling pathway (GO:0050852)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|LUBAC complex (GO:0071797)	ligase activity (GO:0016874)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(4)|skin(2)|soft_tissue(1)	39				GBM - Glioblastoma multiforme(265;0.00861)		ACCCTGTCCACGGCTCTGAAC	0.607																																					p.T74R		Atlas-SNP	.											.	RNF31	95	.	0			c.C221G						PASS	.						80	85	83					14																	24617213		2063	4198	6261	SO:0001583	missense	55072	exon2			TGTCCACGGCTCT	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.221C>G	chr14.hg19:g.24617213C>G	ENSP00000315112:p.Thr74Arg	127.0	0.0	.		176.0	55.0	.	NM_017999	A0A962|Q86VI2|Q8TEI0|Q96GB4|Q96NF1|Q9H5F1|Q9NWD2	Missense_Mutation	SNP	ENST00000324103.6	hg19	CCDS41931.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.498171	0.85069	.	.	ENSG00000092098	ENST00000324103	T	0.47869	0.83	5.31	5.31	0.75309	PUB domain (1);	0.130527	0.51477	D	0.000093	T	0.61135	0.2323	L	0.44542	1.39	0.80722	D	1	D	0.89917	1.0	D	0.70716	0.97	T	0.55730	-0.8095	9	.	.	.	-13.9514	17.9131	0.88940	0.0:1.0:0.0:0.0	.	74	Q96EP0	RNF31_HUMAN	R	74	ENSP00000315112:T74R	.	T	+	2	0	RNF31	23687053	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.011000	0.64011	2.779000	0.95612	0.655000	0.94253	ACG	.	.	.	none		0.607	RNF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071921.3	NM_017999		G	24617213	C	G	24617213	3	3	95	1	0	0	0	0	1	0	0	0	13500	536	19	4	227	4	RNF31	14	24617213	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08		24617213	82732327	58	6042											
KIAA0391	9692	hgsc.bcm.edu	37	chr14	35593087	35593087	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagactttagaacctagaggTtacagtcttctcatccgggg	11	11	10	9	1	2	3	1	0	2	3	4	3	3	3	2	3	2	1	2	3	5	5			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr14:35593087T>C	ENST00000557565.1	+	2	1017	c.636T>C	c.(634-636)ggT>ggC	p.G212G	PPP2R3C_ENST00000261475.5_5'Flank|KIAA0391_ENST00000604948.1_Silent_p.G117G|KIAA0391_ENST00000534898.4_Silent_p.G212G|PPP2R3C_ENST00000555644.1_5'Flank|KIAA0391_ENST00000603588.1_Intron|KIAA0391_ENST00000605870.1_Intron|KIAA0391_ENST00000603544.1_Silent_p.G212G|KIAA0391_ENST00000321130.10_Silent_p.G212G|KIAA0391_ENST00000250377.7_Silent_p.G117G	NM_001282234.1	NP_001269163.1	O15091	MRRP3_HUMAN	KIAA0391	212					tRNA processing (GO:0008033)	mitochondrion (GO:0005739)				central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	14	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)		AACCTAGAGGTTACAGTCTTC	0.358																																					p.G212G		Atlas-SNP	.											.	KIAA0391	35	.	0			c.T636C						PASS	.						49	50	49					14																	35593087		2203	4300	6503	SO:0001819	synonymous_variant	9692	exon2			TAGAGGTTACAGT	AB002389	CCDS32063.1, CCDS58312.1, CCDS58313.1, CCDS58314.1	14q13.2	2013-06-18			ENSG00000100890	ENSG00000100890			19958	protein-coding gene	gene with protein product	"mitochondrial RNase P subunit 3", "proteinaceous RNase P"	609947				9205841, 18984158	Standard	NM_001256678		Approved	MRPP3, PRORP	uc001wsy.2	O15091		ENST00000557565.1:c.636T>C	chr14.hg19:g.35593087T>C		146.0	0.0	.		69.0	4.0	.	NM_014672	B4DXD9|B4E0S8|B4E211|C4AM93|D3DS99|D3DSA1|Q86SZ4|Q86YB5|Q8N5L5	Silent	SNP	ENST00000557565.1	hg19	CCDS32063.1																																																																																			.	.	.	none		0.358	KIAA0391-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000411280.1	NM_014672		C	35593087	T	C	35593087	2	2	95	1	0	0	0	0	0	0	0	1	8179	1712	60	3		3	KIAA0391	14	35593087	Silent	SNP	T	TCGA-B9-4114-01A-01D-1252-08	10975874	35593087	71756453	59	6043											
FAM179B	23116	hgsc.bcm.edu	37	chr14	45433529	45433529	+	Frame_Shift_Del	DEL	C	C	-																															cacgtgagggatagcatgcaCatttatggatcttacagccc																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr14:45433529delC	ENST00000361577.3	+	1	2119	c.1905delC	c.(1903-1905)cacfs	p.H635fs	KLHL28_ENST00000553817.1_Intron|FAM179B_ENST00000382233.2_Frame_Shift_Del_p.H635fs|FAM179B_ENST00000361462.2_Frame_Shift_Del_p.H635fs|KLHL28_ENST00000396128.4_5'Flank	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	635										endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						ATAGCATGCACATTTATGGAT	0.453																																					p.H635fs		Atlas-INDEL	.											.	FAM179B	115	.	0			c.1904delA						PASS	.						98	86	90					14																	45433529		2203	4300	6503	SO:0001589	frameshift_variant	23116	exon1			.	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.1905delC	chr14.hg19:g.45433529delC	ENSP00000355045:p.His635fs	114.0	0.0	0		59.0	19.0	0.322034	NM_015091	Q68D66|Q6PG27	Frame_Shift_Del	DEL	ENST00000361577.3	hg19	CCDS9681.1																																																																																			.	.	.	none		0.453	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781		-	45433529	C	-	45433529	7	5	95	1	0	1	0	1	0	0	0	0	5510	477	17	0	1907	0	FAM179B	14	45433529	Frame_Shift_Del	DEL	C	TCGA-B9-4114-01A-01D-1252-08	9840442	45433529	61916011	60	6044											
SERPINA1	5265	hgsc.bcm.edu	37	chr14	94849213	94849213	+	Missense_Mutation	SNP	T	T	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	tgagggtacggaggagttccTggaagccttcatggatctga	9	10	15	7	1	2	2	1	2	1	0	3	6	3	6	2	5	2	2	2	5	2	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr14:94849213T>G	ENST00000448921.1	-	4	934	c.362A>C	c.(361-363)cAg>cCg	p.Q121P	SERPINA1_ENST00000449399.3_Missense_Mutation_p.Q121P|SERPINA1_ENST00000404814.4_Missense_Mutation_p.Q121P|SERPINA1_ENST00000437397.1_Missense_Mutation_p.Q121P|SERPINA1_ENST00000393087.4_Missense_Mutation_p.Q121P|SERPINA1_ENST00000393088.4_Missense_Mutation_p.Q121P|SERPINA1_ENST00000440909.1_Missense_Mutation_p.Q121P|SERPINA1_ENST00000355814.4_Missense_Mutation_p.Q121P|SERPINA1_ENST00000402629.1_Missense_Mutation_p.Q121P|SERPINA1_ENST00000555289.1_5'Flank	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	121					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)		GAGGAGTTCCTGGAAGCCTTC	0.572																																					p.Q121P		Atlas-SNP	.											.	SERPINA1	51	.	0			c.A362C						PASS	.						57	56	57					14																	94849213		2203	4300	6503	SO:0001583	missense	5265	exon4			AGTTCCTGGAAGC	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.362A>C	chr14.hg19:g.94849213T>G	ENSP00000416066:p.Gln121Pro	101.0	0.0	.		122.0	29.0	.	NM_001127701	A6PX14|B2RDQ8|Q0PVP5|Q13672|Q53XB8|Q5U0M1|Q7M4R2|Q86U18|Q86U19|Q96BF9|Q96ES1|Q9P1P0|Q9UCE6|Q9UCM3	Missense_Mutation	SNP	ENST00000448921.1	hg19	CCDS9925.1	.	.	.	.	.	.	.	.	.	.	T	14.75	2.629267	0.46944	.	.	ENSG00000197249	ENST00000440909;ENST00000448921;ENST00000437397;ENST00000355814;ENST00000393087;ENST00000393088;ENST00000404814;ENST00000449399;ENST00000402629;ENST00000554720;ENST00000556091;ENST00000557492	D;D;D;D;D;D;D;D;D;T;D;D	0.88431	-2.38;-2.38;-2.38;-2.38;-2.38;-2.38;-2.38;-2.38;-2.38;-0.96;-1.72;-1.72	5.8	-0.59	0.11679	Serpin domain (3);	0.589490	0.16883	N	0.195601	D	0.91472	0.7308	M	0.90082	3.085	0.21020	N	0.999801	B;B	0.25486	0.127;0.091	B;B	0.41946	0.136;0.371	D	0.87168	0.2219	10	0.72032	D	0.01	.	7.1129	0.25401	0.0:0.3182:0.1125:0.5693	.	121;121	P01009-2;P01009	.;A1AT_HUMAN	P	121;121;121;121;121;121;121;121;121;35;121;121	ENSP00000390299:Q121P;ENSP00000416066:Q121P;ENSP00000408474:Q121P;ENSP00000348068:Q121P;ENSP00000376802:Q121P;ENSP00000376803:Q121P;ENSP00000385960:Q121P;ENSP00000416354:Q121P;ENSP00000386094:Q121P;ENSP00000450561:Q35P;ENSP00000452169:Q121P;ENSP00000452452:Q121P	ENSP00000348068:Q121P	Q	-	2	0	SERPINA1	93918966	0.002000	0.14202	0.075000	0.20258	0.907000	0.53573	-0.082000	0.11304	-0.099000	0.12263	-0.379000	0.06801	CAG	.	.	.	none		0.572	SERPINA1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317768.2	NM_001002235		G	94849213	T	G	94849213	3	3	95	1	0	0	0	0	1	0	0	0	14099	1580	55	5	910	5	SERPINA1	14	94849213	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08	49415684	94849213	12500327	61	6045											
WDR20	91833	hgsc.bcm.edu	37	chr14	102675938	102675938	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagaggcaccacgagaaagaTcacaagcgaaatcatagcat	18	4	10	9	2	2	3	2	0	0	3	2	6	2	3	1	1	2	2	1	1	4	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr14:102675938T>C	ENST00000342702.3	+	3	1462	c.1431T>C	c.(1429-1431)gaT>gaC	p.D477D	WDR20_ENST00000335263.5_Silent_p.D477D|WDR20_ENST00000499851.2_Silent_p.D220D|WDR20_ENST00000322340.5_Intron|WDR20_ENST00000556511.2_Silent_p.D416D|WDR20_ENST00000454394.2_Silent_p.D508D|WDR20_ENST00000545563.1_Silent_p.D304D|WDR20_ENST00000299135.6_3'UTR|WDR20_ENST00000556807.1_Silent_p.D416D|WDR20_ENST00000424963.2_Silent_p.D353D	NM_001242418.1|NM_144574.3	NP_001229347.1|NP_653175.2	Q8TBZ3	WDR20_HUMAN	WD repeat domain 20	477										breast(1)|large_intestine(2)|lung(4)|prostate(1)	8						ACGAGAAAGATCACAAGCGAA	0.473											OREG0022939	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D508D		Atlas-SNP	.											.	WDR20	35	.	0			c.T1524C						PASS	.						114	105	108					14																	102675938		2203	4300	6503	SO:0001819	synonymous_variant	91833	exon4			GAAAGATCACAAG	BC028387	CCDS9968.1, CCDS9969.1, CCDS9970.1, CCDS55942.1, CCDS55943.1, CCDS55944.1, CCDS55945.1	14q32.31	2013-01-09				ENSG00000140153		"WD repeat domain containing"	19667	protein-coding gene	gene with protein product							Standard	NM_181291		Approved	DMR, MGC33177, FLJ33659	uc010txu.2	Q8TBZ3		ENST00000342702.3:c.1431T>C	chr14.hg19:g.102675938T>C		204.0	0.0	.	1368	239.0	78.0	.	NM_001242417	B4DN18|E7EUY8|F8W9S4|G3V2F8|G3V5R0|H0YJJ1|Q86TU2|Q8NCN7|Q8WXX2|Q9UF86	Silent	SNP	ENST00000342702.3	hg19	CCDS9969.1	.	.	.	.	.	.	.	.	.	.	T	3.721	-0.057478	0.07317	.	.	ENSG00000140153	ENST00000556511	.	.	.	5.73	-3.12	0.05282	.	.	.	.	.	T	0.63604	0.2525	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63093	-0.6714	4	.	.	.	.	14.198	0.65684	0.0:0.4331:0.0:0.5669	.	.	.	.	P	408	.	.	S	+	1	0	WDR20	101745691	0.985000	0.35326	0.982000	0.44146	0.999000	0.98932	0.241000	0.18065	-0.454000	0.07066	0.533000	0.62120	TCA	.	.	.	none		0.473	WDR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414963.1	NM_181291		C	102675938	T	C	102675938	2	2	95	1	0	0	0	0	0	0	0	1	17292	1432	50	3		3	WDR20	14	102675938	Silent	SNP	T	TCGA-B9-4114-01A-01D-1252-08	7826725	102675938	4673602	62	6046											
PLCB2	5330	hgsc.bcm.edu	37	chr15	40590557	40590557	+	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	cctggcggtacatctcagccGaggagaggcctgagaactgg	9	6	15	11	2	1	2	1	1	1	2	2	5	1	2	3	5	3	1	3	5	2	1	rs201305253	byFrequency	TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr15:40590557G>A	ENST00000260402.3	-	11	1271	c.1022C>T	c.(1021-1023)tCg>tTg	p.S341L	PLCB2_ENST00000456256.2_Missense_Mutation_p.S341L|PLCB2-AS1_ENST00000559520.1_RNA|PLCB2_ENST00000557821.1_Missense_Mutation_p.S341L	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	341	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				activation of phospholipase C activity (GO:0007202)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|sensory perception of bitter taste (GO:0050913)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(3)	39		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		CATCTCAGCCGAGGAGAGGCC	0.627													G|||	2	0.000399361	8e-04	0	5008	,	,		20598	0		0	False		,,,				2504	0.001				p.S341L		Atlas-SNP	.											.	PLCB2	177	.	0			c.C1022T						PASS	.						33	36	35					15																	40590557		2082	4236	6318	SO:0001583	missense	5330	exon11			TCAGCCGAGGAGA		CCDS42020.1, CCDS61591.1, CCDS61592.1, CCDS73704.1	15q15.1	2012-01-23			ENSG00000137841	ENSG00000137841	3.1.4.11		9055	protein-coding gene	gene with protein product		604114				1644792, 9925923	Standard	XM_005254448		Approved	FLJ38135	uc001zld.3	Q00722	OTTHUMG00000172412	ENST00000260402.3:c.1022C>T	chr15.hg19:g.40590557G>A	ENSP00000260402:p.Ser341Leu	100.0	0.0	.		125.0	31.0	.	NM_004573	A8K6J2|B9EGH5	Missense_Mutation	SNP	ENST00000260402.3	hg19	CCDS42020.1	.	.	.	.	.	.	.	.	.	.	G	32	5.183791	0.94885	.	.	ENSG00000137841	ENST00000260402;ENST00000456256	T;T	0.59772	0.24;0.24	4.38	4.38	0.52667	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3);	0.136952	0.50627	D	0.000108	D	0.83151	0.5192	H	0.95712	3.71	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.999;0.952;0.997	D	0.88893	0.3347	10	0.87932	D	0	.	17.4798	0.87670	0.0:0.0:1.0:0.0	.	341;341;341	B9EGH5;Q00722-2;Q00722	.;.;PLCB2_HUMAN	L	341	ENSP00000260402:S341L;ENSP00000411991:S341L	ENSP00000260402:S341L	S	-	2	0	PLCB2	38377849	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.657000	0.98554	2.438000	0.82558	0.563000	0.77884	TCG	.	G|0.999;A|0.001	0.001	weak		0.627	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1			A	40590557	G	A	40590557	3	1	95	1	0	0	0	0	1	0	0	0	12035	1059	37	1	2623	1	PLCB2	15	40590557	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08		40590557	61940835	63	6047											
ANKDD1A	348094	hgsc.bcm.edu	37	chr15	65239709	65239709	+	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	gcagctccgttctgtgctgtGgcggctggcctccaggtatc	3	11	14	13	2	1	0	0	0	1	0	4	0	3	0	3	4	2	6	3	4	1	2			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr15:65239709G>T	ENST00000380230.3	+	13	1276	c.1247G>T	c.(1246-1248)tGg>tTg	p.W416L	ANKDD1A_ENST00000395720.1_Missense_Mutation_p.W416L|ANKDD1A_ENST00000357698.3_Missense_Mutation_p.W384L|ANKDD1A_ENST00000395723.1_Missense_Mutation_p.W293L	NM_182703.3	NP_874362.3	Q495B1	AKD1A_HUMAN	ankyrin repeat and death domain containing 1A	416	Death. {ECO:0000255|PROSITE- ProRule:PRU00064}.				signal transduction (GO:0007165)					NS(1)|endometrium(1)|large_intestine(10)|liver(2)|lung(4)|ovary(1)|prostate(2)	21						TCTGTGCTGTGGCGGCTGGCC	0.597																																					p.W416L		Atlas-SNP	.											.	ANKDD1A	47	.	0			c.G1247T						PASS	.						45	40	42					15																	65239709		2202	4299	6501	SO:0001583	missense	348094	exon13			TGCTGTGGCGGCT		CCDS10197.2	15q22.31	2013-01-10	2006-02-16		ENSG00000166839	ENSG00000166839		"Ankyrin repeat domain containing"	28002	protein-coding gene	gene with protein product						12477932	Standard	NM_182703		Approved	FLJ25870	uc002aoa.3	Q495B1	OTTHUMG00000133051	ENST00000380230.3:c.1247G>T	chr15.hg19:g.65239709G>T	ENSP00000369579:p.Trp416Leu	53.0	0.0	.		65.0	22.0	.	NM_182703	Q495B2|Q495B3|Q8N7A0|Q8NBS5	Missense_Mutation	SNP	ENST00000380230.3	hg19	CCDS10197.2	.	.	.	.	.	.	.	.	.	.	G	23.9	4.469077	0.84533	.	.	ENSG00000166839	ENST00000380230;ENST00000357698;ENST00000395720;ENST00000395723	D;D;D;D	0.84070	-1.8;-1.8;-1.8;-1.8	4.63	4.63	0.57726	Death (1);DEATH-like (1);	0.000000	0.64402	D	0.000017	D	0.85758	0.5771	M	0.78637	2.42	0.80722	D	1	P	0.45283	0.855	P	0.48524	0.58	D	0.83545	0.0098	10	0.16420	T	0.52	-16.8697	16.2408	0.82408	0.0:0.0:1.0:0.0	.	416	Q495B1	AKD1A_HUMAN	L	416;384;416;293	ENSP00000369579:W416L;ENSP00000350329:W384L;ENSP00000379070:W416L;ENSP00000379073:W293L	ENSP00000350329:W384L	W	+	2	0	ANKDD1A	63026762	1.000000	0.71417	0.995000	0.50966	0.848000	0.48234	9.170000	0.94795	2.423000	0.82170	0.655000	0.94253	TGG	.	.	.	none		0.597	ANKDD1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256705.2	NM_182703		T	65239709	G	T	65239709	3	4	95	1	0	0	0	0	1	0	0	0	624	1357	47	4	1297	4	ANKDD1A	15	65239709	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	24649152	65239709	37291683	64	6048											
ISLR2	57611	hgsc.bcm.edu	37	chr15	74425252	74425252	+	Frame_Shift_Del	DEL	G	G	-																															cggaaggactgcctgccaacGtgacgacgcttagtctgtcc																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr15:74425252delG	ENST00000361742.3	+	4	926	c.157delG	c.(157-159)gtgfs	p.V53fs	ISLR2_ENST00000435464.1_Frame_Shift_Del_p.V53fs|ISLR2_ENST00000565159.1_Frame_Shift_Del_p.V53fs|ISLR2_ENST00000453268.2_Frame_Shift_Del_p.V53fs|ISLR2_ENST00000419208.1_Frame_Shift_Del_p.V53fs|ISLR2_ENST00000561975.1_Intron|ISLR2_ENST00000445793.1_Frame_Shift_Del_p.V53fs|ISLR2_ENST00000565540.1_Frame_Shift_Del_p.V53fs	NM_001130136.1|NM_020851.2	NP_001123608.1|NP_065902.1	Q6UXK2	ISLR2_HUMAN	immunoglobulin superfamily containing leucine-rich repeat 2	53					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						GCCTGCCAACGTGACGACGCT	0.632																																					p.N52fs		Atlas-INDEL	.											ISLR2,colon,carcinoma,0,1	ISLR2	78	.	0			c.156delC						PASS	.						82	68	73					15																	74425252		2198	4297	6495	SO:0001589	frameshift_variant	57611	exon4			.		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.157delG	chr15.hg19:g.74425252delG	ENSP00000355402:p.Val53fs	171.0	0.0	0		234.0	76.0	0.324786	NM_001130136	A8K352|Q9P263	Frame_Shift_Del	DEL	ENST00000361742.3	hg19	CCDS10259.1																																																																																			.	.	.	none		0.632	ISLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269046.1	NM_020851		-	74425252	G	-	74425252	7	5	95	1	0	1	0	1	0	0	0	0	7866	1145	40	0	159	0	ISLR2	15	74425252	Frame_Shift_Del	DEL	G	TCGA-B9-4114-01A-01D-1252-08	9185543	74425252	28106140	65	6049											
FAM154B	283726	hgsc.bcm.edu	37	chr15	82574679	82574679	+	Missense_Mutation	SNP	A	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	tcgccttgattatatacctcAtcagcttgaactcaagtttg	10	15	6	10	1	3	2	3	2	0	0	4	2	3	2	2	0	3	2	2	0	5	6			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr15:82574679A>C	ENST00000339465.5	+	3	542	c.473A>C	c.(472-474)cAt>cCt	p.H158P	FAM154B_ENST00000427381.2_Missense_Mutation_p.H143P|FAM154B_ENST00000565501.1_3'UTR	NM_001008226.1	NP_001008227.1	Q658L1	F154B_HUMAN	family with sequence similarity 154, member B	158										autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(2)	19						TATATACCTCATCAGCTTGAA	0.433																																					p.H158P		Atlas-SNP	.											.	FAM154B	50	.	0			c.A473C						PASS	.						112	111	111					15																	82574679		2203	4300	6503	SO:0001583	missense	283726	exon3			TACCTCATCAGCT	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.473A>C	chr15.hg19:g.82574679A>C	ENSP00000340445:p.His158Pro	370.0	0.0	.		51.0	9.0	.	NM_001008226	B4E2M2	Missense_Mutation	SNP	ENST00000339465.5	hg19	CCDS32310.1	.	.	.	.	.	.	.	.	.	.	A	19.09	3.760509	0.69763	.	.	ENSG00000188659	ENST00000339465;ENST00000427381	T;T	0.14391	2.51;2.51	3.9	3.9	0.45041	.	0.144157	0.45126	D	0.000381	T	0.35219	0.0924	M	0.77103	2.36	0.51012	D	0.999907	D;D	0.67145	0.996;0.992	D;D	0.69824	0.966;0.953	T	0.12142	-1.0559	10	0.37606	T	0.19	-13.415	13.1531	0.59500	1.0:0.0:0.0:0.0	.	143;158	B4E2M2;Q658L1	.;F154B_HUMAN	P	158;143	ENSP00000340445:H158P;ENSP00000403743:H143P	ENSP00000340445:H158P	H	+	2	0	FAM154B	80361734	0.998000	0.40836	0.633000	0.29310	0.980000	0.70556	4.775000	0.62346	1.751000	0.51876	0.438000	0.28831	CAT	.	.	.	none		0.433	FAM154B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419644.1	NM_001008226		C	82574679	A	C	82574679	3	2	95	1	0	0	0	0	1	0	0	0	5468	217	8	5	483	5	FAM154B	15	82574679	Missense_Mutation	SNP	A	TCGA-B9-4114-01A-01D-1252-08	8149427	82574679	19956713	66	6050											
LINS1	55180	hgsc.bcm.edu	37	chr15	101114034	101114034	+	Frame_Shift_Del	DEL	C	C	-																															acagacagtgtcttcaacaaCcccgaattcacagcttgcaa																										TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr15:101114034delC	ENST00000314742.8	-	5	1266	c.1044delG	c.(1042-1044)gggfs	p.G348fs	LINS_ENST00000559149.1_5'UTR|LINS_ENST00000561308.1_Frame_Shift_Del_p.G348fs|LINS_ENST00000560133.1_Frame_Shift_Del_p.G229fs	NM_001040616.2	NP_001035706	Q8NG48	LINES_HUMAN	lines homolog (Drosophila)	348										central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(4)	21						TCTTCAACAACCCCGAATTCA	0.448																																					p.L349fs		Atlas-INDEL	.											.	LINS	62	.	0			c.1045delT						PASS	.			0,4264		0,0,2132	146	133	137			2.5	0.1	15		137	2,8252		0,2,4125	no	frameshift	LINS	NM_001040616.2		0,2,6257	A1A1,A1R,RR		0.0242,0.0,0.016			101114034	2,12516	2203	4300	6503	SO:0001589	frameshift_variant	55180	exon5			.	AK095448	CCDS10385.1	15q26.3	2010-09-08	2010-09-08	2010-09-08	ENSG00000140471	ENSG00000140471			30922	protein-coding gene	gene with protein product		610350	"lines homolog 1 (Drosophila)"	LINS1		12119551, 8889548	Standard	NM_001040616		Approved	WINS1	uc002bwg.3	Q8NG48	OTTHUMG00000149865	ENST00000314742.8:c.1044delG	chr15.hg19:g.101114034delC	ENSP00000318423:p.Gly348fs	281.0	0.0	0		213.0	57.0	0.267606	NM_001040616	Q96FW2|Q9NVQ3	Frame_Shift_Del	DEL	ENST00000314742.8	hg19	CCDS10385.1																																																																																			.	.	.	none		0.448	LINS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313592.1	NM_018148		-	101114034	C	-	101114034	7	5	95	1	0	1	0	1	0	0	0	0	8825	494	18	0	1241	0	LINS1	15	101114034	Frame_Shift_Del	DEL	C	TCGA-B9-4114-01A-01D-1252-08	18539355	101114034	1417358	67	6051											
PALB2	79728	hgsc.bcm.edu	37	chr16	23646407	23646407	+	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	tgggcccagcgggagagctgActttagttaatgagagaagt	11	9	15	6	1	0	4	0	2	0	2	0	6	0	4	1	2	2	2	1	2	3	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr16:23646407A>T	ENST00000261584.4	-	4	1612	c.1460T>A	c.(1459-1461)gTc>gAc	p.V487D		NM_024675.3	NP_078951.2	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2	487	DNA-binding (with the preference D loop > dsDNA > ssDNA).				DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|inner cell mass cell proliferation (GO:0001833)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|post-anal tail morphogenesis (GO:0036342)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(3)	55				GBM - Glioblastoma multiforme(48;0.0167)		GGGAGAGCTGACTTTAGTTAA	0.458			"F, N, Mis"			"Wilms tumor, medulloblastoma, AML ,breast"		Involved in tolerance or repair of DNA crosslinks																													p.V487D		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.T1460A						PASS	.						131	131	131					16																	23646407		2197	4300	6497	SO:0001583	missense	79728	exon4			GAGCTGACTTTAG		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.1460T>A	chr16.hg19:g.23646407A>T	ENSP00000261584:p.Val487Asp	403.0	0.0	.		179.0	89.0	.	NM_024675	A6NIE1|Q8N7Y6|Q8ND31|Q9H6W1	Missense_Mutation	SNP	ENST00000261584.4	hg19	CCDS32406.1	.	.	.	.	.	.	.	.	.	.	A	10.89	1.479867	0.26511	.	.	ENSG00000083093	ENST00000261584	T	0.15603	2.41	5.67	1.89	0.25635	.	0.327339	0.25935	N	0.027358	T	0.28267	0.0698	M	0.63428	1.95	0.19775	N	0.999954	D	0.67145	0.996	P	0.62298	0.9	T	0.04693	-1.0933	10	0.59425	D	0.04	-1.5018	4.5066	0.11891	0.6154:0.2179:0.1667:0.0	.	487	Q86YC2	PALB2_HUMAN	D	487	ENSP00000261584:V487D	ENSP00000261584:V487D	V	-	2	0	PALB2	23553908	0.059000	0.20769	0.013000	0.15412	0.188000	0.23474	1.278000	0.33179	0.529000	0.28599	0.533000	0.62120	GTC	.	.	.	none		0.458	PALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435287.2	NM_024675		T	23646407	A	T	23646407	3	4	95	1	0	0	0	0	1	0	0	0	11413	275	10	5	2140	5	PALB2	16	23646407	Missense_Mutation	SNP	A	TCGA-B9-4114-01A-01D-1252-08		23646407	66708346	68	6052											
CYB5D1	124637	hgsc.bcm.edu	37	chr17	7762716	7762716	+	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	ccaggtgggggttctggagtCcatatgggaaatcctacacc	9	9	13	10	0	1	0	0	0	1	0	3	2	3	2	4	5	1	1	4	5	3	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr17:7762716C>T	ENST00000332439.4	+	4	625	c.473C>T	c.(472-474)tCc>tTc	p.S158F	LSMD1_ENST00000335155.5_5'Flank|LSMD1_ENST00000575071.1_5'Flank|LSMD1_ENST00000576384.1_5'Flank|LSMD1_ENST00000575208.1_5'Flank|LSMD1_ENST00000333775.5_5'Flank|CYB5D1_ENST00000571846.1_Intron|CYB5D1_ENST00000570446.1_Missense_Mutation_p.S30F|LSMD1_ENST00000575771.1_5'Flank|LSMD1_ENST00000576861.1_Intron|LSMD1_ENST00000570555.1_Intron	NM_144607.4	NP_653208.2	Q6P9G0	CB5D1_HUMAN	cytochrome b5 domain containing 1	158							heme binding (GO:0020037)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(2)|skin(2)	6		all_cancers(10;0.11)|Prostate(122;0.219)				GTTCTGGAGTCCATATGGGAA	0.502																																					p.S158F		Atlas-SNP	.											.	CYB5D1	16	.	0			c.C473T						PASS	.						47	45	46					17																	7762716		2203	4300	6503	SO:0001583	missense	124637	exon4			TGGAGTCCATATG	AK057061	CCDS11123.1	17p13.1	2006-01-12	2006-01-12						26516	protein-coding gene	gene with protein product						12477932	Standard	NM_144607		Approved	FLJ32499	uc002gjb.4	Q6P9G0		ENST00000332439.4:c.473C>T	chr17.hg19:g.7762716C>T	ENSP00000331479:p.Ser158Phe	107.0	0.0	.		111.0	24.0	.	NM_144607	D3DTQ8|Q96DM7	Missense_Mutation	SNP	ENST00000332439.4	hg19	CCDS11123.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.968751	0.74131	.	.	ENSG00000182224	ENST00000332439	T	0.45668	0.89	5.27	5.27	0.74061	.	0.155423	0.42821	D	0.000659	T	0.40372	0.1114	M	0.64997	1.995	0.50467	D	0.999875	B	0.31910	0.346	B	0.26864	0.074	T	0.42447	-0.9451	10	0.72032	D	0.01	-23.6807	13.3117	0.60384	0.1589:0.841:0.0:0.0	.	158	Q6P9G0	CB5D1_HUMAN	F	158	ENSP00000331479:S158F	ENSP00000331479:S158F	S	+	2	0	CYB5D1	7703441	0.999000	0.42202	0.979000	0.43373	0.882000	0.50991	4.339000	0.59322	2.449000	0.82847	0.462000	0.41574	TCC	.	.	.	none		0.502	CYB5D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440841.1	NM_144607		T	7762716	C	T	7762716	3	4	95	1	0	0	0	0	1	0	0	0	4126	855	30	2	487	2	CYB5D1	17	7762716	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08		7762716	73432494	69	6053											
ERBB2	2064	hgsc.bcm.edu	37	chr17	37876080	37876080	+	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	agggctgccccgccgagcagAgagccaggttggcctggacc	7	4	16	14	2	0	1	0	0	0	1	0	4	0	2	6	4	3	3	6	4	0	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr17:37876080A>C	ENST00000269571.5	+	16	2098	c.1939A>C	c.(1939-1941)Aga>Cga	p.R647R	ERBB2_ENST00000584450.1_Silent_p.R647R|ERBB2_ENST00000584601.1_Silent_p.R617R|ERBB2_ENST00000406381.2_Silent_p.R617R|ERBB2_ENST00000540147.1_Silent_p.R617R|ERBB2_ENST00000541774.1_Silent_p.R632R|ERBB2_ENST00000445658.2_Silent_p.R371R			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	647					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)	CGCCGAGCAGAGAGCCAGGTT	0.597		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)																											p.R647R		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.A1939C						PASS	.						153	131	138					17																	37876080		2203	4300	6503	SO:0001819	synonymous_variant	2064	exon16			GAGCAGAGAGCCA	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.1939A>C	chr17.hg19:g.37876080A>C		243.0	0.0	.		471.0	93.0	.	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Silent	SNP	ENST00000269571.5	hg19	CCDS32642.1																																																																																			.	.	.	none		0.597	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			C	37876080	A	C	37876080	2	2	95	1	0	0	0	0	0	0	0	1	5208	296	11	5		5	ERBB2	17	37876080	Silent	SNP	A	TCGA-B9-4114-01A-01D-1252-08	30113364	37876080	43319130	70	6054											
ATXN7L3	56970	hgsc.bcm.edu	37	chr17	42275086	42275086	+	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	gaccaggtccgcgtatatctCctgagcgatggcctgggccc	6	8	13	14	3	1	1	0	1	1	0	3	3	2	1	5	3	1	1	5	3	2	2			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr17:42275086C>A	ENST00000454077.2	-	2	63	c.64G>T	c.(64-66)Gag>Tag	p.E22*	ATXN7L3_ENST00000593073.1_Intron|ATXN7L3_ENST00000389384.4_Nonsense_Mutation_p.E22*|CTB-175E5.7_ENST00000586560.1_RNA	NM_020218.1	NP_064603.1			ataxin 7-like 3											kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(2)	12		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.113)		GCGTATATCTCCTGAGCGATG	0.577																																					p.E22X		Atlas-SNP	.											.	ATXN7L3	31	.	0			c.G64T						PASS	.						96	95	96					17																	42275086		1985	4163	6148	SO:0001587	stop_gained	56970	exon2			ATATCTCCTGAGC	AK056002	CCDS42345.1, CCDS45697.1	17q21	2010-03-10			ENSG00000087152	ENSG00000087152			25416	protein-coding gene	gene with protein product						15115762	Standard	NM_001098833		Approved	DKFZp761G2113	uc002ifz.3	Q14CW9		ENST00000454077.2:c.64G>T	chr17.hg19:g.42275086C>A	ENSP00000397259:p.Glu22*	159.0	0.0	.		328.0	58.0	.	NM_020218		Nonsense_Mutation	SNP	ENST00000454077.2	hg19	CCDS45697.1	.	.	.	.	.	.	.	.	.	.	C	17.71	3.456493	0.63401	.	.	ENSG00000087152	ENST00000454077;ENST00000389384	.	.	.	4.47	4.47	0.54385	.	0.064498	0.64402	U	0.000011	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	.	14.0541	0.64756	0.0:1.0:0.0:0.0	.	.	.	.	X	22	.	ENSP00000374035:E22X	E	-	1	0	ATXN7L3	39630612	1.000000	0.71417	1.000000	0.80357	0.174000	0.22865	7.490000	0.81461	2.010000	0.58986	0.655000	0.94253	GAG	.	.	.	none		0.577	ATXN7L3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457724.1			A	42275086	C	A	42275086	4	1	95	1	0	0	0	0	0	1	0	0	1218	864	30	4	1044	4	ATXN7L3	17	42275086	Nonsense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	4399006	42275086	38920124	71	6055											
ABCA6	23460	hgsc.bcm.edu	37	chr17	67108373	67108373	+	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	tttcaaaaacatagaagaacCtgcacacttcagtctcccat	15	10	4	12	0	3	2	2	0	1	2	4	2	3	2	2	0	3	1	2	0	5	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr17:67108373C>T	ENST00000284425.2	-	16	2257	c.2083G>A	c.(2083-2085)Ggt>Agt	p.G695S		NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	695	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)					ATAGAAGAACCTGCACACTTC	0.368																																					p.G695S		Atlas-SNP	.											ABCA6,middle_lobe,carcinoma,0,1	ABCA6	210	.	0			c.G2083A						PASS	.						156	164	162					17																	67108373		2203	4300	6503	SO:0001583	missense	23460	exon16			AAGAACCTGCACA	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.2083G>A	chr17.hg19:g.67108373C>T	ENSP00000284425:p.Gly695Ser	548.0	0.0	.		63.0	28.0	.	NM_080284	Q6NSH9|Q8N856|Q8WWZ6	Missense_Mutation	SNP	ENST00000284425.2	hg19	CCDS11683.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.599754	0.87055	.	.	ENSG00000154262	ENST00000284425	T	0.80393	-1.37	4.65	4.65	0.58169	ABC transporter-like (1);	0.116516	0.38058	N	0.001826	D	0.94308	0.8171	H	0.99261	4.49	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96675	0.9499	10	0.87932	D	0	.	17.0385	0.86483	0.0:1.0:0.0:0.0	.	695	Q8N139	ABCA6_HUMAN	S	695	ENSP00000284425:G695S	ENSP00000284425:G695S	G	-	1	0	ABCA6	64619968	1.000000	0.71417	1.000000	0.80357	0.685000	0.39939	6.512000	0.73737	2.568000	0.86640	0.655000	0.94253	GGT	.	.	.	none		0.368	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284		T	67108373	C	T	67108373	3	4	95	1	0	0	0	0	1	0	0	0	36	681	24	2	2866	2	ABCA6	17	67108373	Missense_Mutation	SNP	C	TCGA-B9-4114-01A-01D-1252-08	24833287	67108373	14086837	72	6056											
SPHK1	8877	hgsc.bcm.edu	37	chr17	74382029	74382029	+	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	cccgtggccccctagtggtcGgttgcggacgtggcctcttt	2	11	14	14	4	1	0	0	0	1	0	2	1	1	1	4	5	1	1	4	5	1	3			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr17:74382029G>A	ENST00000545180.1	+	5	819				SPHK1_ENST00000323374.4_Intron|SPHK1_ENST00000392496.3_Intron|SPHK1_ENST00000592299.1_Intron|SPHK1_ENST00000590959.1_Missense_Mutation_p.G6S			Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1						'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)	CCTAGTGGTCGGTTGCGGACG	0.667											OREG0024750	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G6S	GBM(90;966 1307 27369 33775 44498)	Atlas-SNP	.											.	SPHK1	24	.	0			c.G16A						PASS	.						23	24	24					17																	74382029		1923	4109	6032	SO:0001627	intron_variant	8877	exon3			GTGGTCGGTTGCG	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.11-37G>A	chr17.hg19:g.74382029G>A		23.0	0.0	.	1152	38.0	19.0	.	NM_021972	Q8N632|Q96GK1|Q9HD92|Q9NY70|Q9NYL3	Missense_Mutation	SNP	ENST00000545180.1	hg19	CCDS45785.1																																																																																			.	.	.	none		0.667	SPHK1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450113.1	NM_182965, NM_021972		A	74382029	G	A	74382029	1	1	95	0	1	0	0	0	0	0	0	0	15058	1116	39	1		1	SPHK1	17	74382029	Intron	SNP	G	TCGA-B9-4114-01A-01D-1252-08	7273656	74382029	6813181	73	6057											
PRKCSH	5589	hgsc.bcm.edu	37	chr19	11558373	11558373	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaggaggaggaggaggaggaAgaagaggctgaagaagagga	17	1	22	1	0	0	5	0	1	0	4	0	13	0	12	0	8	0	1	0	8	4	0			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr19:11558373A>G	ENST00000589838.1	+	10	969	c.969A>G	c.(967-969)gaA>gaG	p.E323E	PRKCSH_ENST00000412601.1_Silent_p.E323E|PRKCSH_ENST00000591462.1_Silent_p.E323E|PRKCSH_ENST00000587327.1_Silent_p.E323E|PRKCSH_ENST00000592741.1_Silent_p.E323E|PRKCSH_ENST00000252455.2_Silent_p.E323E			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	323	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)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(3)	19						aggaggaggaagaagaggctg	0.642																																					p.E323E		Atlas-SNP	.											PRKCSH,colon,carcinoma,0,1	PRKCSH	55	.	0			c.A969G						PASS	.																																			SO:0001819	synonymous_variant	5589	exon11			GGAGGAAGAAGAG		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.969A>G	chr19.hg19:g.11558373A>G		43.0	0.0	.		52.0	5.0	.	NM_001001329	A8K318|Q96BU9|Q96D06|Q9P0W9	Silent	SNP	ENST00000589838.1	hg19	CCDS32911.1																																																																																			.	.	.	none		0.642	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1			G	11558373	A	G	11558373	2	3	95	1	0	0	0	0	0	0	0	1	12526	69	3	3		3	PRKCSH	19	11558373	Silent	SNP	A	TCGA-B9-4114-01A-01D-1252-08		11558373	47570610	74	6058											
ATP4A	495	hgsc.bcm.edu	37	chr19	36050918	36050918	+	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	ccacccccgacgccagcgatGcgatgcgcccaatgatggtg	8	5	12	16	5	0	1	0	1	0	0	0	4	0	1	5	1	3	0	5	1	1	0			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr19:36050918G>T	ENST00000262623.3	-	7	873	c.845C>A	c.(844-846)gCa>gAa	p.A282E		NM_000704.2	NP_000695.2	P20648	ATP4A_HUMAN	ATPase, H+/K+ exchanging, alpha polypeptide	282					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|ion transmembrane transport (GO:0034220)|pH reduction (GO:0045851)|regulation of proton transport (GO:0010155)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|magnesium ion binding (GO:0000287)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(26)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	53	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)	CGCCAGCGATGCGATGCGCCC	0.647																																					p.A282E		Atlas-SNP	.											.	ATP4A	123	.	0			c.C845A						PASS	.						96	73	81					19																	36050918		2203	4300	6503	SO:0001583	missense	495	exon7			AGCGATGCGATGC		CCDS12467.1	19q13.1	2010-04-20			ENSG00000105675	ENSG00000105675	3.6.3.10	"ATPases / P-type"	819	protein-coding gene	gene with protein product	"gastric H,K-ATPase alpha subunit", "H(+)-K(+)-ATPase alpha subunit", "proton pump"	137216				1330887	Standard	NM_000704		Approved	ATP6A	uc002oal.1	P20648	OTTHUMG00000048106	ENST00000262623.3:c.845C>A	chr19.hg19:g.36050918G>T	ENSP00000262623:p.Ala282Glu	167.0	0.0	.		257.0	72.0	.	NM_000704	O00738	Missense_Mutation	SNP	ENST00000262623.3	hg19	CCDS12467.1	.	.	.	.	.	.	.	.	.	.	G	16.50	3.140434	0.56936	.	.	ENSG00000105675	ENST00000262623	D	0.92495	-3.05	3.94	3.94	0.45596	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.077790	0.48767	D	0.000178	D	0.96324	0.8801	M	0.91920	3.255	0.80722	D	1	D	0.57899	0.981	D	0.66196	0.942	D	0.97050	0.9763	10	0.87932	D	0	.	13.8309	0.63380	0.0:0.0:1.0:0.0	.	282	P20648	ATP4A_HUMAN	E	282	ENSP00000262623:A282E	ENSP00000262623:A282E	A	-	2	0	ATP4A	40742758	1.000000	0.71417	0.276000	0.24689	0.038000	0.13279	9.600000	0.98282	2.203000	0.70933	0.561000	0.74099	GCA	.	.	.	none		0.647	ATP4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109470.2	NM_000704		T	36050918	G	T	36050918	3	4	95	1	0	0	0	0	1	0	0	0	1145	1319	46	4	2326	4	ATP4A	19	36050918	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08	24492545	36050918	23078065	75	6059											
UBOX5	22888	hgsc.bcm.edu	37	chr20	3090943	3090943	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggaggcacattcggggcccaGgatgctcccaggctgctctg	6	7	15	13	1	1	0	0	0	1	0	3	2	2	2	2	6	2	4	2	6	0	1			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr20:3090943G>A	ENST00000217173.2	-	5	1906	c.1435C>T	c.(1435-1437)Ctg>Ttg	p.L479L	UBOX5_ENST00000348031.2_Silent_p.L425L|UBOX5-AS1_ENST00000454019.1_RNA|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						TCGGGGCCCAGGATGCTCCCA	0.587																																					p.P477L		Atlas-SNP	.											.	UBOX5	47	.	0			c.C1430T						PASS	.						60	69	66					20																	3090943		2203	4300	6503	SO:0001819	synonymous_variant	22888	exon5			GGCCCAGGATGCT	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.1435C>T	chr20.hg19:g.3090943G>A		165.0	0.0	.		253.0	97.0	.	NM_001267584		Missense_Mutation	SNP	ENST00000217173.2	hg19	CCDS13046.1																																																																																			.	.	.	none		0.587	UBOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077706.2	NM_014948		A	3090943	G	A	3090943	2	1	95	1	0	0	0	0	0	0	0	1	16906	991	35	2		2	UBOX5	20	3090943	Silent	SNP	G	TCGA-B9-4114-01A-01D-1252-08		3090943	59934577	76	6060											
ZSWIM1	90204	hgsc.bcm.edu	37	chr20	44512145	44512145	+	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	gggcctgtgtgcccagaacaAtcatgctccctcagacacca	10	7	9	15	0	2	2	2	0	0	2	3	2	3	2	4	1	3	1	4	1	2	0			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr20:44512145A>T	ENST00000372523.1	+	2	1009	c.914A>T	c.(913-915)aAt>aTt	p.N305I	ZSWIM1_ENST00000372520.1_Missense_Mutation_p.N305I	NM_080603.4	NP_542170.3	Q9BR11	ZSWM1_HUMAN	zinc finger, SWIM-type containing 1	305						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)				GCCCAGAACAATCATGCTCCC	0.542																																					p.N305I		Atlas-SNP	.											.	ZSWIM1	35	.	0			c.A914T						PASS	.						106	100	102					20																	44512145		2203	4300	6503	SO:0001583	missense	90204	exon2			AGAACAATCATGC	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.914A>T	chr20.hg19:g.44512145A>T	ENSP00000361601:p.Asn305Ile	207.0	0.0	.		330.0	103.0	.	NM_080603	Q5JZH2|Q9BR12|Q9BV30	Missense_Mutation	SNP	ENST00000372523.1	hg19	CCDS13382.2	.	.	.	.	.	.	.	.	.	.	A	1.890	-0.455649	0.04540	.	.	ENSG00000168612	ENST00000372523;ENST00000372520	T;T	0.23754	1.89;1.89	5.03	-5.13	0.02884	.	1.279150	0.05647	U	0.584537	T	0.15565	0.0375	N	0.19112	0.55	0.09310	N	1	B	0.33379	0.41	B	0.29440	0.102	T	0.20538	-1.0272	10	0.37606	T	0.19	-6.9614	13.0392	0.58889	0.2965:0.0964:0.607:0.0	.	305	Q9BR11	ZSWM1_HUMAN	I	305	ENSP00000361601:N305I;ENSP00000361598:N305I	ENSP00000361598:N305I	N	+	2	0	ZSWIM1	43945552	0.000000	0.05858	0.000000	0.03702	0.097000	0.18754	-3.302000	0.00520	-0.994000	0.03463	-0.256000	0.11100	AAT	.	.	.	none		0.542	ZSWIM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157064.2	NM_080603		T	44512145	A	T	44512145	3	4	95	1	0	0	0	0	1	0	0	0	18252	101	4	5	916	5	ZSWIM1	20	44512145	Missense_Mutation	SNP	A	TCGA-B9-4114-01A-01D-1252-08	41421202	44512145	18513375	77	6061											
GRAMD4	23151	hgsc.bcm.edu	37	chr22	47068788	47068788	+	Missense_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	cattgatttcatctttaaacGctgcccgaggctgcgcgcca	8	11	9	13	4	2	1	1	1	1	0	2	2	2	1	2	1	3	2	2	1	2	4	rs371794625		TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chr22:47068788G>A	ENST00000406902.1	+	14	1346	c.1133G>A	c.(1132-1134)cGc>cAc	p.R378H	GRAMD4_ENST00000361034.3_Missense_Mutation_p.R378H|GRAMD4_ENST00000408031.1_5'Flank			Q6IC98	GRAM4_HUMAN	GRAM domain containing 4	378					apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)	12		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|BRCA - Breast invasive adenocarcinoma(115;0.166)		ATCTTTAAACGCTGCCCGAGG	0.577													G|||	1	0.000199681	8e-04	0	5008	,	,		16350	0		0	False		,,,				2504	0				p.R378H		Atlas-SNP	.											.	GRAMD4	53	.	0			c.G1133A						PASS	.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	71	68	69		1133	4.6	1	22		69	0,8600		0,0,4300	no	missense	GRAMD4	NM_015124.3	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	378/579	47068788	1,13005	2203	4300	6503	SO:0001583	missense	23151	exon13			TTAAACGCTGCCC		CCDS33672.1	22q13.31	2008-03-03			ENSG00000075240	ENSG00000075240			29113	protein-coding gene	gene with protein product	"death-inducing-protein"	613691				15565177	Standard	NM_015124		Approved	KIAA0767, DIP	uc003bhx.3	Q6IC98	OTTHUMG00000150402	ENST00000406902.1:c.1133G>A	chr22.hg19:g.47068788G>A	ENSP00000385689:p.Arg378His	77.0	0.0	.		117.0	42.0	.	NM_015124	A9IN51|A9IN57|Q68EN0|Q9UGE6|Q9Y4B9	Missense_Mutation	SNP	ENST00000406902.1	hg19	CCDS33672.1	.	.	.	.	.	.	.	.	.	.	g	29.5	5.010183	0.93346	2.27E-4	0.0	ENSG00000075240	ENST00000406902;ENST00000361034	T;T	0.45276	0.9;0.9	4.63	4.63	0.57726	.	0.079168	0.49916	D	0.000133	T	0.51466	0.1676	L	0.48642	1.525	0.53688	D	0.99997	D	0.71674	0.998	P	0.56216	0.794	T	0.56177	-0.8022	10	0.87932	D	0	-22.1761	15.3516	0.74393	0.0:0.0:1.0:0.0	.	378	Q6IC98	GRAM4_HUMAN	H	378	ENSP00000385689:R378H;ENSP00000354313:R378H	ENSP00000354313:R378H	R	+	2	0	GRAMD4	45447452	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	8.900000	0.92551	2.294000	0.77228	0.563000	0.77884	CGC	.	.	.	weak		0.577	GRAMD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317969.1	NM_015124		A	47068788	G	A	47068788	3	1	95	1	0	0	0	0	1	0	0	0	6759	1087	38	1	1183	1	GRAMD4	22	47068788	Missense_Mutation	SNP	G	TCGA-B9-4114-01A-01D-1252-08		47068788	4235778	78	6062											
TBL1X	6907	hgsc.bcm.edu	37	chrX	9652170	9652170	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctagtgccaccggccgcccTcatctccattctccagaagg	7	8	9	17	2	3	1	1	0	2	1	5	1	3	1	6	2	1	1	6	2	2	2			TCGA-B9-4114-01A-01D-1252-08	TCGA-B9-4114-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cc2df365-fa55-4871-8e93-807b85a7e7d0	4acde02c-30d6-41f7-9fb2-b689951809b9	g.chrX:9652170T>C	ENST00000217964.7	+	6	939	c.299T>C	c.(298-300)cTc>cCc	p.L100P	TBL1X_ENST00000424279.1_Missense_Mutation_p.L49P|TBL1X_ENST00000407597.2_Missense_Mutation_p.L100P|TBL1X_ENST00000536365.1_Missense_Mutation_p.L49P|TBL1X_ENST00000380961.1_Missense_Mutation_p.L49P	NM_005647.3	NP_005638.1	O60907	TBL1X_HUMAN	transducin (beta)-like 1X-linked	100	F-box-like.				canonical Wnt signaling pathway (GO:0060070)|cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|histone binding (GO:0042393)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|cervix(1)|endometrium(5)|large_intestine(7)|lung(2)|ovary(1)|skin(2)	20		Hepatocellular(5;0.000888)				CCGGCCGCCCTCATCTCCATT	0.582																																					p.L100P		Atlas-SNP	.											.	TBL1X	103	.	0			c.T299C						PASS	.						94	71	79					X																	9652170		2203	4300	6503	SO:0001583	missense	6907	exon6			CCGCCCTCATCTC	Y12781	CCDS14133.1, CCDS48078.1	Xp22.3	2013-01-10	2002-05-22	2002-05-24	ENSG00000101849	ENSG00000101849		"WD repeat domain containing"	11585	protein-coding gene	gene with protein product		300196	"transducin (beta)-like 1"	TBL1		10330347	Standard	NM_005647		Approved	EBI	uc004csr.3	O60907	OTTHUMG00000021117	ENST00000217964.7:c.299T>C	chrX.hg19:g.9652170T>C	ENSP00000217964:p.Leu100Pro	65.0	0.0	.		91.0	4.0	.	NM_001139466	A8K044|A8K4J7|Q86UY2	Missense_Mutation	SNP	ENST00000217964.7	hg19	CCDS14133.1	.	.	.	.	.	.	.	.	.	.	T	19.16	3.774447	0.70107	.	.	ENSG00000101849	ENST00000407597;ENST00000424279;ENST00000536365;ENST00000380961;ENST00000415293;ENST00000217964	D;D;D;D;D	0.88896	-2.44;-2.11;-2.11;-2.11;-2.44	4.43	4.43	0.53597	.	0.000000	0.64402	D	0.000001	D	0.95217	0.8449	M	0.91300	3.195	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.95982	0.8978	10	0.87932	D	0	.	13.2538	0.60066	0.0:0.0:0.0:1.0	.	63;100	Q59F53;O60907	.;TBL1X_HUMAN	P	100;49;49;49;49;100	ENSP00000385988:L100P;ENSP00000394097:L49P;ENSP00000445317:L49P;ENSP00000370348:L49P;ENSP00000217964:L100P	ENSP00000217964:L100P	L	+	2	0	TBL1X	9612170	1.000000	0.71417	0.987000	0.45799	0.486000	0.33341	7.492000	0.81482	1.570000	0.49709	0.437000	0.28790	CTC	.	.	.	none		0.582	TBL1X-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055709.1	NM_005647		C	9652170	T	C	9652170	3	2	95	1	0	0	0	0	1	0	0	0	15651	1551	54	3	309	3	TBL1X	23	9652170	Missense_Mutation	SNP	T	TCGA-B9-4114-01A-01D-1252-08		9652170	145618390	79	6063											
PIGV	55650	hgsc.bcm.edu	37	chr1	27121059	27121059	+	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	ttgtttgccctcctgacattCagtgccatggggcagctgga	6	12	12	11	0	1	1	1	1	0	0	2	2	2	2	3	3	3	3	3	3	0	3			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr1:27121059C>T	ENST00000374145.1	+	3	1216	c.534C>T	c.(532-534)ttC>ttT	p.F178F	PIGV_ENST00000449950.2_Intron|PIGV_ENST00000078527.4_Silent_p.F178F	NM_001202554.1	NP_001189483.1	Q9NUD9	PIGV_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class V	178					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)			NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	14		all_cancers(24;3.93e-26)|all_epithelial(13;3.96e-23)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.26e-54)|Epithelial(14;2.85e-53)|OV - Ovarian serous cystadenocarcinoma(117;1.91e-30)|Colorectal(126;1.31e-09)|COAD - Colon adenocarcinoma(152;3.45e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000504)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.0222)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.153)|LUSC - Lung squamous cell carcinoma(448;0.227)		TCCTGACATTCAGTGCCATGG	0.562																																					p.F178F		Atlas-SNP	.											.	PIGV	47	.	0			c.C534T						PASS	.						79	78	78					1																	27121059		2203	4300	6503	SO:0001819	synonymous_variant	55650	exon3			GACATTCAGTGCC	AK000484	CCDS287.1	1p36.11	2013-02-26	2006-06-28		ENSG00000060642	ENSG00000060642		"Dolichyl D-mannosyl phosphate dependent mannosyltransferases", "Phosphatidylinositol glycan anchor biosynthesis"	26031	protein-coding gene	gene with protein product	"GPI mannosyltransferase 2", "dol-P-Man dependent GPI mannosyltransferase"	610274	"phosphatidylinositol glycan, class V"			15623507	Standard	NM_017837		Approved	FLJ20477	uc001bmz.3	Q9NUD9	OTTHUMG00000004005	ENST00000374145.1:c.534C>T	chr1.hg19:g.27121059C>T		116.0	0.0	.		180.0	57.0	.	NM_001202554	D3DPL2|Q5JYG7|Q5JYG8|Q5JYG9|Q9NX26	Silent	SNP	ENST00000374145.1	hg19	CCDS287.1																																																																																			.	.	.	none		0.562	PIGV-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011441.1	NM_017837		T	27121059	C	T	27121059	2	4	96	1	0	0	0	0	0	0	0	1	11908	825	29	2		2	PIGV	1	27121059	Silent	SNP	C	TCGA-B9-4115-01A-01D-1252-08		27121059	222129562	1	6064											
SLC9A1	6548	hgsc.bcm.edu	37	chr1	27428600	27428600	+	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	ggcaggatgcgctcggaaggCagggacttggggtggatgtt	7	8	20	6	2	0	0	0	0	0	0	1	4	0	4	0	8	1	4	0	8	1	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr1:27428600C>T	ENST00000263980.3	-	9	2417	c.1842G>A	c.(1840-1842)ctG>ctA	p.L614L	SLC9A1_ENST00000490329.1_5'Flank|SLC9A1_ENST00000545949.1_Silent_p.L275L	NM_003047.4	NP_003038.2	P19634	SL9A1_HUMAN	solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1	614					carbohydrate metabolic process (GO:0005975)|cardiac muscle cell differentiation (GO:0055007)|cell growth (GO:0016049)|cellular response to acidic pH (GO:0071468)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|hydrogen ion transmembrane transport (GO:1902600)|ion transport (GO:0006811)|negative regulation of apoptotic process (GO:0043066)|neuron death (GO:0070997)|positive regulation of action potential (GO:0045760)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial membrane permeability (GO:0035794)|protein oligomerization (GO:0051259)|regulation of intracellular pH (GO:0051453)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of the force of heart contraction (GO:0002026)|response to acidic pH (GO:0010447)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|sodium ion export (GO:0071436)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|sodium:proton antiporter activity (GO:0015385)|solute:proton antiporter activity (GO:0015299)			central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;2.19e-50)|OV - Ovarian serous cystadenocarcinoma(117;1.8e-29)|Colorectal(126;7.61e-09)|COAD - Colon adenocarcinoma(152;9.32e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000521)|KIRC - Kidney renal clear cell carcinoma(1967;0.00079)|STAD - Stomach adenocarcinoma(196;0.00125)|READ - Rectum adenocarcinoma(331;0.046)	Amiloride(DB00594)	GCTCGGAAGGCAGGGACTTGG	0.582																																					p.L614L		Atlas-SNP	.											.	SLC9A1	68	.	0			c.G1842A						PASS	.						136	126	129					1																	27428600		2203	4300	6503	SO:0001819	synonymous_variant	6548	exon9			GGAAGGCAGGGAC	M81768	CCDS295.1	1p36.1-p35	2014-06-13	2012-03-22		ENSG00000090020	ENSG00000090020		"Solute carriers"	11071	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 143"	107310	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 1 (antiporter, Na+/H+, amiloride sensitive)", "solute carrier family 9 (sodium/hydrogen exchanger), member 1"	APNH, NHE1		8283968	Standard	NM_003047		Approved	PPP1R143	uc001bnm.4	P19634	OTTHUMG00000004271	ENST00000263980.3:c.1842G>A	chr1.hg19:g.27428600C>T		166.0	0.0	.		270.0	74.0	.	NM_003047	B1ALD6|D3DPL4|Q96EM2	Silent	SNP	ENST00000263980.3	hg19	CCDS295.1																																																																																			.	.	.	none		0.582	SLC9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012336.2	NM_003047		T	27428600	C	T	27428600	2	4	96	1	0	0	0	0	0	0	0	1	14722	697	25	2		2	SLC9A1	1	27428600	Silent	SNP	C	TCGA-B9-4115-01A-01D-1252-08	307541	27428600	221822021	2	6065											
MACF1	23499	hgsc.bcm.edu	37	chr1	39907695	39907695	+	Missense_Mutation	SNP	T	T	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	cctgttggcactgacctcaaTactgttaaagatcagttaaa	13	12	7	9	0	2	2	2	1	0	1	2	2	2	2	2	1	1	4	2	1	6	4			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr1:39907695T>G	ENST00000372915.3	+	74	18528	c.18441T>G	c.(18439-18441)aaT>aaG	p.N6147K	MACF1_ENST00000289893.4_Missense_Mutation_p.N4691K|MACF1_ENST00000361689.2_Missense_Mutation_p.N4189K|MACF1_ENST00000539005.1_Missense_Mutation_p.N4059K|MACF1_ENST00000317713.7_Missense_Mutation_p.N4189K|MACF1_ENST00000567887.1_Missense_Mutation_p.N6285K|MACF1_ENST00000564288.1_Missense_Mutation_p.N6248K|MACF1_ENST00000545844.1_Missense_Mutation_p.N4189K			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	6147					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)			CTGACCTCAATACTGTTAAAG	0.353																																					p.N4189K		Atlas-SNP	.											.	MACF1	909	.	0			c.T12567G						PASS	.						118	110	113					1																	39907695		2203	4300	6503	SO:0001583	missense	23499	exon72			CCTCAATACTGTT	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.18441T>G	chr1.hg19:g.39907695T>G	ENSP00000362006:p.Asn6147Lys	217.0	0.0	.		45.0	12.0	.	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.72|16.72	3.201648|3.201648	0.58234|0.58234	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893|ENST00000372925	T;T;T;T;T;T|.	0.48836|.	0.8;0.8;0.8;0.8;0.8;0.8|.	5.62|5.62	4.71|4.71	0.59529|0.59529	.|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.33990|0.33990	0.0882|0.0882	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	D;P|.	0.55605|.	0.972;0.843|.	P;P|.	0.55455|.	0.776;0.62|.	T|T	0.14727|0.14727	-1.0462|-1.0462	10|5	0.32370|.	T|.	0.25|.	.|.	9.9927|9.9927	0.41881|0.41881	0.0:0.8446:0.0:0.1554|0.0:0.8446:0.0:0.1554	.|.	6147;4189|.	Q9UPN3;F8W8Q1|.	MACF1_HUMAN;.|.	K|D	4189;6147;4189;4189;4059;4691|3193	ENSP00000439537:N4189K;ENSP00000362006:N6147K;ENSP00000354573:N4189K;ENSP00000313438:N4189K;ENSP00000444364:N4059K;ENSP00000289893:N4691K|.	ENSP00000289893:N4691K|.	N|Y	+|+	3|1	2|0	MACF1|MACF1	39680282|39680282	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	2.512000|2.512000	0.45485|0.45485	1.352000|1.352000	0.45808|0.45808	-0.366000|-0.366000	0.07423|0.07423	AAT|TAC	.	.	.	none		0.353	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		G	39907695	T	G	39907695	3	3	96	1	0	0	0	0	1	0	0	0	9151	1403	49	5	19000	5	MACF1	1	39907695	Missense_Mutation	SNP	T	TCGA-B9-4115-01A-01D-1252-08	12479095	39907695	209342926	3	6066											
MCOLN3	55283	hgsc.bcm.edu	37	chr1	85491700	85491700	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataatcataatgtaccatccAttgacaaattccatttgatc	15	14	3	9	0	1	2	1	2	0	0	4	2	3	2	3	0	1	1	3	0	4	6			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr1:85491700A>G	ENST00000370589.2	-	9	1069	c.1017T>C	c.(1015-1017)aaT>aaC	p.N339N	MCOLN3_ENST00000370587.1_3'UTR|MCOLN3_ENST00000474447.1_5'Flank|MCOLN3_ENST00000341115.4_Silent_p.N283N|WDR63_ENST00000370596.1_Intron	NM_018298.10	NP_060768.8	Q8TDD5	MCLN3_HUMAN	mucolipin 3	339					auditory receptor cell differentiation (GO:0042491)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|locomotory behavior (GO:0007626)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(6)|kidney(3)|large_intestine(9)|lung(12)|prostate(3)|skin(1)	34				all cancers(265;0.00957)|Epithelial(280;0.0254)		TGTACCATCCATTGACAAATT	0.333																																					p.N339N		Atlas-SNP	.											.	MCOLN3	74	.	0			c.T1017C						PASS	.						57	56	56					1																	85491700		2203	4300	6503	SO:0001819	synonymous_variant	55283	exon9			CCATCCATTGACA	AF475085	CCDS701.1, CCDS58009.1	1p22.3	2011-12-16			ENSG00000055732	ENSG00000055732		"Voltage-gated ion channels / Transient receptor potential cation channels"	13358	protein-coding gene	gene with protein product		607400				16382100	Standard	NM_018298		Approved	TRPML3, FLJ11006, TRP-ML3	uc001dkp.3	Q8TDD5	OTTHUMG00000009955	ENST00000370589.2:c.1017T>C	chr1.hg19:g.85491700A>G		64.0	0.0	.		40.0	13.0	.	NM_018298	Q5T4H5|Q5T4H6|Q9NV09	Silent	SNP	ENST00000370589.2	hg19	CCDS701.1																																																																																			.	.	.	none		0.333	MCOLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027569.2	NM_018298		G	85491700	A	G	85491700	2	3	96	1	0	0	0	0	0	0	0	1	9404	214	8	3		3	MCOLN3	1	85491700	Silent	SNP	A	TCGA-B9-4115-01A-01D-1252-08	45584005	85491700	163758921	4	6067											
ATP1A2	477	hgsc.bcm.edu	37	chr1	160105304	160105304	+	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	gacattggcattgccatgggCatctctggctctgacgtctc	6	12	11	12	1	3	1	0	1	3	0	5	2	3	1	1	3	1	3	1	3	0	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr1:160105304C>A	ENST00000361216.3	+	16	2285	c.2196C>A	c.(2194-2196)ggC>ggA	p.G732G	ATP1A2_ENST00000392233.3_Silent_p.G732G	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	732					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)			TTGCCATGGGCATCTCTGGCT	0.602																																					p.G732G		Atlas-SNP	.											.	ATP1A2	167	.	0			c.C2196A						PASS	.						169	125	140					1																	160105304		2203	4300	6503	SO:0001819	synonymous_variant	477	exon16			CATGGGCATCTCT	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.2196C>A	chr1.hg19:g.160105304C>A		142.0	0.0	.		246.0	97.0	.	NM_000702	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Silent	SNP	ENST00000361216.3	hg19	CCDS1196.1	.	.	.	.	.	.	.	.	.	.	C	5.352	0.250270	0.10130	.	.	ENSG00000018625	ENST00000447527	.	.	.	4.31	2.27	0.28462	.	.	.	.	.	T	0.32406	0.0828	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.19844	-1.0293	4	.	.	.	.	4.575	0.12228	0.1513:0.6098:0.1479:0.091	.	.	.	.	E	443	.	.	A	+	2	0	ATP1A2	158371928	0.489000	0.26004	1.000000	0.80357	0.433000	0.31745	-0.303000	0.08210	1.154000	0.42482	0.561000	0.74099	GCA	.	.	.	none		0.602	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702		A	160105304	C	A	160105304	2	1	96	1	0	0	0	0	0	0	0	1	1129	697	25	4		4	ATP1A2	1	160105304	Silent	SNP	C	TCGA-B9-4115-01A-01D-1252-08	74613604	160105304	89145317	5	6068											
IRF6	3664	hgsc.bcm.edu	37	chr1	209964089	209964089	+	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	tgggaatttgacctgctccaGgctgacgggaccaaagagct	10	8	13	10	1	0	3	0	2	0	1	1	5	1	5	3	3	2	3	3	3	2	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr1:209964089G>C	ENST00000367021.3	-	7	983	c.811C>G	c.(811-813)Ctg>Gtg	p.L271V	IRF6_ENST00000542854.1_Missense_Mutation_p.L176V	NM_006147.3	NP_006138.1	O14896	IRF6_HUMAN	interferon regulatory factor 6	271					cell cycle arrest (GO:0007050)|cell development (GO:0048468)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell proliferation (GO:0008285)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|large_intestine(4)|lung(12)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	28				OV - Ovarian serous cystadenocarcinoma(81;0.0351)		ACCTGCTCCAGGCTGACGGGA	0.572										HNSCC(57;0.16)																											p.L271V		Atlas-SNP	.											.	IRF6	65	.	0			c.C811G						PASS	.						80	76	77					1																	209964089		2203	4300	6503	SO:0001583	missense	3664	exon7			GCTCCAGGCTGAC	AL022398	CCDS1492.1, CCDS55681.1	1q32.2-q32.3	2011-02-10			ENSG00000117595	ENSG00000117595			6121	protein-coding gene	gene with protein product		607199	"Van der Woude syndrome"	VWS, LPS		12219090	Standard	NM_006147		Approved	OFC6, VWS1	uc001hhq.2	O14896	OTTHUMG00000036521	ENST00000367021.3:c.811C>G	chr1.hg19:g.209964089G>C	ENSP00000355988:p.Leu271Val	229.0	0.0	.		167.0	71.0	.	NM_006147	B4DLE2|D3DT90|F5GWX8|G0ZTL0	Missense_Mutation	SNP	ENST00000367021.3	hg19	CCDS1492.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.139845	0.77775	.	.	ENSG00000117595	ENST00000367021;ENST00000542854;ENST00000456314	D;D;D	0.95788	-3.57;-3.57;-3.81	6.17	5.26	0.73747	SMAD domain-like (1);SMAD/FHA domain (1);Interferon regulatory factor-3 (1);	0.000000	0.85682	D	0.000000	D	0.95557	0.8556	L	0.39397	1.21	0.58432	D	0.999995	D	0.89917	1.0	D	0.91635	0.999	D	0.93440	0.6793	9	.	.	.	.	9.4637	0.38800	0.1513:0.0:0.8487:0.0	.	271	O14896	IRF6_HUMAN	V	271;176;271	ENSP00000355988:L271V;ENSP00000440532:L176V;ENSP00000403855:L271V	.	L	-	1	2	IRF6	208030712	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.122000	0.57910	2.941000	0.99782	0.655000	0.94253	CTG	.	.	.	none		0.572	IRF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088827.1	NM_006147		C	209964089	G	C	209964089	3	2	96	1	0	0	0	0	1	0	0	0	7841	991	35	4	604	4	IRF6	1	209964089	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08	49858785	209964089	39286532	6	6069											
PRKCE	5581	hgsc.bcm.edu	37	chr2	45879507	45879507	+	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	tctttcacgatgcccccataGgctacgacgacttcgtggcc	7	10	9	15	4	2	0	1	0	1	0	3	3	2	0	3	2	2	1	3	2	2	4			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr2:45879507G>C	ENST00000306156.3	+	1	595	c.268G>C	c.(268-270)Ggc>Cgc	p.G90R		NM_005400.2	NP_005391.1	Q02156	KPCE_HUMAN	protein kinase C, epsilon	90	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|cellular response to ethanol (GO:0071361)|cellular response to hypoxia (GO:0071456)|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)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|locomotory exploration behavior (GO:0035641)|macrophage activation involved in immune response (GO:0002281)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cellular glucuronidation (GO:2001031)|positive regulation of cytokinesis (GO:0032467)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of insulin secretion (GO:0032024)|positive regulation of lipid catabolic process (GO:0050996)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|release of sequestered calcium ion into cytosol (GO:0051209)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|TRAM-dependent toll-like receptor 4 signaling pathway (GO:0035669)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|ethanol binding (GO:0035276)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|receptor activator activity (GO:0030546)|signal transducer activity (GO:0004871)		MBOAT2/PRKCE(2)	breast(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(13)|ovary(3)|upper_aerodigestive_tract(2)	34		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)		Tamoxifen(DB00675)	TGCCCCCATAGGCTACGACGA	0.622																																					p.G90R		Atlas-SNP	.											.	PRKCE	58	.	0			c.G268C						PASS	.						64	54	57					2																	45879507		2203	4300	6503	SO:0001583	missense	5581	exon1			CCCATAGGCTACG		CCDS1824.1	2p21	2009-07-10			ENSG00000171132	ENSG00000171132	2.7.11.1		9401	protein-coding gene	gene with protein product		176975				1382605, 7877991	Standard	NM_005400		Approved		uc002rut.3	Q02156	OTTHUMG00000128817	ENST00000306156.3:c.268G>C	chr2.hg19:g.45879507G>C	ENSP00000306124:p.Gly90Arg	53.0	0.0	.		98.0	43.0	.	NM_005400	B0LPH7|Q32MQ3|Q53SL4|Q53SM5|Q9UE81	Missense_Mutation	SNP	ENST00000306156.3	hg19	CCDS1824.1	.	.	.	.	.	.	.	.	.	.	G	34	5.307076	0.95629	.	.	ENSG00000171132	ENST00000421201;ENST00000306156	T;T	0.71461	-0.57;-0.57	4.95	4.95	0.65309	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.062205	0.64402	D	0.000006	D	0.84629	0.5514	M	0.86651	2.83	0.80722	D	1	D	0.67145	0.996	D	0.68943	0.961	T	0.83162	-0.0098	10	0.16896	T	0.51	.	18.1985	0.89830	0.0:0.0:1.0:0.0	.	90	Q02156	KPCE_HUMAN	R	90	ENSP00000394574:G90R;ENSP00000306124:G90R	ENSP00000306124:G90R	G	+	1	0	PRKCE	45733011	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.802000	0.99131	2.270000	0.75569	0.561000	0.74099	GGC	.	.	.	none		0.622	PRKCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250751.2			C	45879507	G	C	45879507	3	2	96	1	0	0	0	0	1	0	0	0	12521	1000	35	4	270	4	PRKCE	2	45879507	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08		45879507	197319866	7	6070											
REV1	51455	hgsc.bcm.edu	37	chr2	100019166	100019166	+	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	catcattgaattcaacagctCcagctagattgggtgctgga	11	11	10	9	0	2	2	2	1	0	1	3	3	3	3	1	2	4	3	1	2	3	4			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr2:100019166C>T	ENST00000258428.3	-	21	3710	c.3482G>A	c.(3481-3483)gGa>gAa	p.G1161E	RP11-527J8.1_ENST00000608144.1_RNA|REV1_ENST00000465835.1_5'Flank|REV1_ENST00000393445.3_Missense_Mutation_p.G1160E	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	1161	Protein interaction domain; mediates interaction with DNA polymerase zeta.				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						TTCAACAGCTCCAGCTAGATT	0.493								Direct reversal of damage																													p.G1161E		Atlas-SNP	.											.	REV1	100	.	0			c.G3482A						PASS	.						99	97	98					2																	100019166		2203	4300	6503	SO:0001583	missense	51455	exon21			ACAGCTCCAGCTA	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.3482G>A	chr2.hg19:g.100019166C>T	ENSP00000258428:p.Gly1161Glu	198.0	0.0	.		123.0	51.0	.	NM_016316	O95941|Q53SI7|Q9C0J4|Q9NUP2	Missense_Mutation	SNP	ENST00000258428.3	hg19	CCDS2045.1	.	.	.	.	.	.	.	.	.	.	C	33	5.204692	0.95033	.	.	ENSG00000135945	ENST00000393445;ENST00000258428	T;T	0.38077	1.16;1.16	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.64046	0.2563	M	0.74881	2.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.63906	-0.6531	10	0.66056	D	0.02	.	20.3854	0.98941	0.0:1.0:0.0:0.0	.	1161;1160	Q9UBZ9;Q9UBZ9-2	REV1_HUMAN;.	E	1160;1161	ENSP00000377091:G1160E;ENSP00000258428:G1161E	ENSP00000258428:G1161E	G	-	2	0	REV1	99385598	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.844000	0.75390	2.825000	0.97269	0.655000	0.94253	GGA	.	.	.	none		0.493	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316		T	100019166	C	T	100019166	3	4	96	1	0	0	0	0	1	0	0	0	13252	855	30	2	285	2	REV1	2	100019166	Missense_Mutation	SNP	C	TCGA-B9-4115-01A-01D-1252-08	54139659	100019166	143180207	8	6071											
NUP210	23225	hgsc.bcm.edu	37	chr3	13415370	13415370	+	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	gaagttcccactgccaccgtGggcctgcggaggaaaagcca	10	5	13	13	2	0	0	0	0	0	0	1	3	1	2	5	3	3	1	5	3	3	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr3:13415370G>A	ENST00000254508.5	-	12	1517	c.1435C>T	c.(1435-1437)Cac>Tac	p.H479Y		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	479					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)					CTGCCACCGTGGGCCTGCGGA	0.592																																					p.H479Y		Atlas-SNP	.											.	NUP210	182	.	0			c.C1435T						PASS	.						87	65	72					3																	13415370		2203	4300	6503	SO:0001583	missense	23225	exon12			CACCGTGGGCCTG	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.1435C>T	chr3.hg19:g.13415370G>A	ENSP00000254508:p.His479Tyr	40.0	0.0	.		65.0	25.0	.	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	hg19	CCDS33704.1	.	.	.	.	.	.	.	.	.	.	G	11.47	1.647580	0.29246	.	.	ENSG00000132182	ENST00000254508	T	0.41400	1.0	5.8	3.99	0.46301	Invasin/intimin cell-adhesion (1);	0.386148	0.30003	N	0.010650	T	0.31918	0.0812	L	0.57536	1.79	0.37940	D	0.932281	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.001	T	0.21999	-1.0229	10	0.02654	T	1	.	8.5233	0.33289	0.1373:0.1281:0.7346:0.0	.	479;479	Q8TEM1-2;Q8TEM1	.;PO210_HUMAN	Y	479	ENSP00000254508:H479Y	ENSP00000254508:H479Y	H	-	1	0	NUP210	13390370	0.997000	0.39634	0.794000	0.32065	0.780000	0.44128	2.395000	0.44459	0.784000	0.33661	0.655000	0.94253	CAC	.	.	.	none		0.592	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923		A	13415370	G	A	13415370	3	1	96	1	0	0	0	0	1	0	0	0	10767	1348	47	2	4344	2	NUP210	3	13415370	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08		13415370	184607060	9	6072											
TRANK1	9881	hgsc.bcm.edu	37	chr3	36873055	36873055	+	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	tccacagggtccaaacagagCaggcggtttagtctgacctc	10	8	11	12	1	1	2	0	1	1	1	4	2	3	2	3	3	2	2	3	3	2	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr3:36873055C>T	ENST00000429976.2	-	21	8134	c.7887G>A	c.(7885-7887)ctG>ctA	p.L2629L	TRANK1_ENST00000428977.2_Silent_p.L2079L|TRANK1_ENST00000301807.6_Silent_p.L2079L	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	2629							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						CCAAACAGAGCAGGCGGTTTA	0.532																																					p.L2629L		Atlas-SNP	.											.	TRANK1	398	.	0			c.G7887A						PASS	.						60	62	61					3																	36873055		2004	4167	6171	SO:0001819	synonymous_variant	9881	exon21			ACAGAGCAGGCGG	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.7887G>A	chr3.hg19:g.36873055C>T		49.0	0.0	.		85.0	32.0	.	NM_014831	Q8N8K0	Silent	SNP	ENST00000429976.2	hg19	CCDS46789.2																																																																																			.	.	.	none		0.532	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		T	36873055	C	T	36873055	2	4	96	1	0	0	0	0	0	0	0	1	16466	697	25	2		2	TRANK1	3	36873055	Silent	SNP	C	TCGA-B9-4115-01A-01D-1252-08	23457685	36873055	161149375	10	6073											
ACAA1	30	hgsc.bcm.edu	37	chr3	38178134	38178134	+	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	cagattcacgtccttgagaaCcgcggtcatgactgccgaga	10	8	11	12	4	2	4	2	2	0	3	3	6	3	4	3	1	2	0	3	1	1	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr3:38178134C>G	ENST00000333167.8	-	2	386	c.214G>C	c.(214-216)Gtt>Ctt	p.V72L	MYD88_ENST00000417037.2_5'Flank|ACAA1_ENST00000301810.7_Missense_Mutation_p.V72L|ACAA1_ENST00000444607.2_Missense_Mutation_p.V72L|MYD88_ENST00000443433.2_5'Flank|ACAA1_ENST00000544624.1_5'UTR|MYD88_ENST00000396334.3_5'Flank|ACAA1_ENST00000450296.1_Missense_Mutation_p.V72L|MYD88_ENST00000424893.1_5'Flank|MYD88_ENST00000495303.1_5'Flank	NM_001607.3	NP_001598.1	P09110	THIK_HUMAN	acetyl-CoA acyltransferase 1	72					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)		TCCTTGAGAACCGCGGTCATG	0.642																																					p.V72L		Atlas-SNP	.											.	ACAA1	32	.	0			c.G214C						PASS	.						53	47	49					3																	38178134		2203	4300	6503	SO:0001583	missense	30	exon2			TGAGAACCGCGGT	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.214G>C	chr3.hg19:g.38178134C>G	ENSP00000333664:p.Val72Leu	60.0	0.0	.		94.0	28.0	.	NM_001130410	G5E935|Q96CA6	Missense_Mutation	SNP	ENST00000333167.8	hg19	CCDS2673.1	.	.	.	.	.	.	.	.	.	.	C	17.65	3.442786	0.63067	.	.	ENSG00000060971	ENST00000333167;ENST00000301810;ENST00000450296;ENST00000358122;ENST00000444607	D;D;D;D	0.93604	-2.13;-2.13;-3.25;-2.13	4.85	4.85	0.62838	Thiolase-like, subgroup (1);Thiolase, N-terminal (1);Thiolase-like (1);	0.212850	0.38605	N	0.001627	D	0.87164	0.6109	N	0.17278	0.47	0.80722	D	1	B;B;B;B	0.18863	0.001;0.003;0.031;0.0	B;B;B;B	0.17979	0.003;0.02;0.019;0.004	T	0.82806	-0.0275	10	0.14656	T	0.56	-17.5296	17.9617	0.89087	0.0:1.0:0.0:0.0	.	4;72;72;72	F5GXL8;C9JDE9;G5E935;P09110	.;.;.;THIK_HUMAN	L	72;72;72;4;72	ENSP00000333664:V72L;ENSP00000301810:V72L;ENSP00000395183:V72L;ENSP00000391918:V72L	ENSP00000301810:V72L	V	-	1	0	ACAA1	38153138	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.483000	0.60264	2.230000	0.72887	0.655000	0.94253	GTT	.	.	.	none		0.642	ACAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342980.1	NM_001607		G	38178134	C	G	38178134	3	3	96	1	0	0	0	0	1	0	0	0	104	507	18	4	1104	4	ACAA1	3	38178134	Missense_Mutation	SNP	C	TCGA-B9-4115-01A-01D-1252-08	1305079	38178134	159844296	11	6074											
CTBP1	1487	hgsc.bcm.edu	37	chr4	1232016	1232016	+	Frame_Shift_Del	DEL	A	A	-																															tgcgcgtcgcagaaggccacAgtggccacgtccttcaggat																										TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr4:1232016delA	ENST00000290921.6	-	2	331	c.150delT	c.(148-150)actfs	p.T50fs	CTBP1_ENST00000510568.1_Frame_Shift_Del_p.T39fs|CTBP1_ENST00000382952.3_Frame_Shift_Del_p.T39fs|CTBP1_ENST00000515690.1_5'UTR	NM_001328.2	NP_001319.1	Q13363	CTBP1_HUMAN	C-terminal binding protein 1	50	Interaction with GLIS2 1. {ECO:0000250}.				Golgi organization (GO:0007030)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone acetylation (GO:0035067)|negative regulation of histone H4 acetylation (GO:0090241)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone deacetylation (GO:0031065)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|regulation of transcription by chromatin organization (GO:0034401)|viral genome replication (GO:0019079)|white fat cell differentiation (GO:0050872)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|urinary_tract(1)	8			OV - Ovarian serous cystadenocarcinoma(23;0.00818)	Colorectal(103;0.2)		AGAAGGCCACAGTGGCCACGT	0.657																																					p.V51fs		Atlas-INDEL	.											.	CTBP1	30	.	0			c.151delG						PASS	.						69	66	67					4																	1232016		2202	4298	6500	SO:0001589	frameshift_variant	1487	exon2			.	U37408	CCDS3348.1, CCDS43203.1	4p16	2008-02-05			ENSG00000159692	ENSG00000159692			2494	protein-coding gene	gene with protein product	"brefeldin A-ribosylated substrate"	602618				9479502	Standard	XM_005272261		Approved	BARS	uc003gcv.1	Q13363	OTTHUMG00000089259	ENST00000290921.6:c.150delT	chr4.hg19:g.1232016delA	ENSP00000290921:p.Thr50fs	164.0	0.0	0		275.0	80.0	0.290909	NM_001328	Q4W5N3|Q7Z2Q5	Frame_Shift_Del	DEL	ENST00000290921.6	hg19	CCDS3348.1																																																																																			.	.	.	none		0.657	CTBP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000202938.1	NM_001328		-	1232016	A	-	1232016	7	5	96	1	0	1	0	1	0	0	0	0	3999	175	7	0	1204	0	CTBP1	4	1232016	Frame_Shift_Del	DEL	A	TCGA-B9-4115-01A-01D-1252-08		1232016	189922260	12	6075											
HPSE	10855	hgsc.bcm.edu	37	chr4	84243394	84243394	+	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	tggttgacttgagattgccaGtaacttctctcttcaaaggt	9	15	9	8	0	3	2	1	2	2	1	4	3	3	2	1	2	2	2	1	2	2	6			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr4:84243394G>A	ENST00000405413.2	-	3	487	c.351C>T	c.(349-351)taC>taT	p.Y117Y	HPSE_ENST00000512196.1_Silent_p.Y117Y|HPSE_ENST00000311412.5_Silent_p.Y117Y|HPSE_ENST00000513463.1_Silent_p.Y117Y	NM_006665.5	NP_006656.2	Q9Y251	HPSE_HUMAN	heparanase	117					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)	GAGATTGCCAGTAACTTCTCT	0.403																																					p.Y117Y		Atlas-SNP	.											.	HPSE	55	.	0			c.C351T						PASS	.						85	87	86					4																	84243394		2203	4300	6503	SO:0001819	synonymous_variant	10855	exon2			TTGCCAGTAACTT	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.351C>T	chr4.hg19:g.84243394G>A		166.0	0.0	.		56.0	24.0	.	NM_001199830	A9JIG7|C7F7I3|C7F7I4|E9PCA9|E9PGR1|Q53GE5|Q9UL39	Silent	SNP	ENST00000405413.2	hg19	CCDS3602.1																																																																																			.	.	.	none		0.403	HPSE-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252812.2	NM_006665		A	84243394	G	A	84243394	2	1	96	1	0	0	0	0	0	0	0	1	7351	1024	36	2		2	HPSE	4	84243394	Silent	SNP	G	TCGA-B9-4115-01A-01D-1252-08	83011378	84243394	106910882	13	6076											
FAM198B	51313	hgsc.bcm.edu	37	chr4	159092402	159092402	+	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	cccaagtagatggcacacgcAgtgcccagcagaaggtttct	11	7	11	12	1	1	2	0	0	1	2	1	2	1	2	2	2	2	5	2	2	3	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr4:159092402A>T	ENST00000296530.8	-	2	747	c.126T>A	c.(124-126)acT>acA	p.T42T	RP11-597D13.9_ENST00000505532.1_RNA|FAM198B_ENST00000393807.5_Silent_p.T42T|RP11-597D13.9_ENST00000514381.1_RNA|FAM198B_ENST00000592057.1_Silent_p.T42T|FAM198B_ENST00000589306.1_Intron|RP11-597D13.9_ENST00000503611.1_RNA|RP11-597D13.9_ENST00000509463.1_RNA|FAM198B_ENST00000585682.1_Silent_p.T42T	NM_016613.6	NP_057697.2	Q6UWH4	F198B_HUMAN	family with sequence similarity 198, member B	42						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						TGGCACACGCAGTGCCCAGCA	0.637																																					p.T42T		Atlas-SNP	.											.	FAM198B	134	.	0			c.T126A						PASS	.						42	44	43					4																	159092402		2202	4299	6501	SO:0001819	synonymous_variant	51313	exon2			ACACGCAGTGCCC		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.126T>A	chr4.hg19:g.159092402A>T		172.0	0.0	.		301.0	115.0	.	NM_016613	Q498Z3|Q6IAF9|Q6ZMF2|Q86XL0	Silent	SNP	ENST00000296530.8	hg19	CCDS3798.1																																																																																			.	.	.	none		0.637	FAM198B-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365230.1	NM_001031700, NM_016613		T	159092402	A	T	159092402	2	4	96	1	0	0	0	0	0	0	0	1	5533	175	7	5		5	FAM198B	4	159092402	Silent	SNP	A	TCGA-B9-4115-01A-01D-1252-08	74849008	159092402	32061874	14	6077											
FAM173B	134145	hgsc.bcm.edu	37	chr5	10249973	10249973	+	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	agccgctccagcctcacctcCtcctccctccatcgcgagat	6	8	6	21	3	1	1	1	0	0	1	7	2	6	1	8	0	2	1	8	0	0	0			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr5:10249973C>T	ENST00000511437.1	-	1	25	c.13G>A	c.(13-15)Gga>Aga	p.G5R	CCT5_ENST00000506600.1_5'Flank|FAM173B_ENST00000510052.1_5'UTR|CTD-2256P15.1_ENST00000509915.1_RNA|CCT5_ENST00000515390.1_5'Flank|CCT5_ENST00000280326.4_5'Flank|CCT5_ENST00000515676.1_5'Flank|CCT5_ENST00000503026.1_5'Flank|FAM173B_ENST00000280330.8_5'UTR|FAM173B_ENST00000510047.1_Missense_Mutation_p.G5R	NM_199133.3	NP_954584.2	Q6P4H8	F173B_HUMAN	family with sequence similarity 173, member B	5						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	16						GCCTCACCTCCTCCTCCCTCC	0.532																																					p.G5R		Atlas-SNP	.											.	FAM173B	24	.	0			c.G13A						PASS	.						21	28	26					5																	10249973		1815	4066	5881	SO:0001583	missense	134145	exon1			CACCTCCTCCTCC		CCDS43301.1, CCDS58942.1	5p15.2	2008-08-08			ENSG00000150756	ENSG00000150756			27029	protein-coding gene	gene with protein product						12477932	Standard	NM_199133		Approved		uc003jeo.3	Q6P4H8	OTTHUMG00000161771	ENST00000511437.1:c.13G>A	chr5.hg19:g.10249973C>T	ENSP00000422338:p.Gly5Arg	116.0	0.0	.		122.0	45.0	.	NM_199133	B4DT41|B4DXK2|E9PBZ4	Missense_Mutation	SNP	ENST00000511437.1	hg19	CCDS43301.1	.	.	.	.	.	.	.	.	.	.	C	15.01	2.707244	0.48412	.	.	ENSG00000150756	ENST00000511437;ENST00000510047	T;T	0.19250	2.16;2.23	4.76	4.76	0.60689	.	2.684740	0.03150	N	0.167810	T	0.32823	0.0842	L	0.34521	1.04	0.30467	N	0.773718	P;P	0.50943	0.94;0.901	P;P	0.51615	0.675;0.476	T	0.30001	-0.9993	10	0.87932	D	0	.	13.2821	0.60222	0.0:1.0:0.0:0.0	.	5;5	E9PBZ4;Q6P4H8	.;F173B_HUMAN	R	5	ENSP00000422338:G5R;ENSP00000420876:G5R	ENSP00000424210:G5R	G	-	1	0	FAM173B	10302973	0.990000	0.36364	0.880000	0.34516	0.780000	0.44128	0.276000	0.18716	2.166000	0.68216	0.561000	0.74099	GGA	.	.	.	none		0.532	FAM173B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000366048.2	NM_199133		T	10249973	C	T	10249973	3	4	96	1	0	0	0	0	1	0	0	0	5498	690	24	2	708	2	FAM173B	5	10249973	Missense_Mutation	SNP	C	TCGA-B9-4115-01A-01D-1252-08		10249973	170665287	15	6078											
MAST4	375449	hgsc.bcm.edu	37	chr5	66438012	66438022	+	Frame_Shift_Del	DEL	AGGCAGAATTT	AGGCAGAATTT	-																															gaacagtttgctgagacagaAggcagaatttattccccaac																										TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	AGGCAGAATTT	AGGCAGAATTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr5:66438012_66438022delAGGCAGAATTT	ENST00000403625.2	+	20	2859_2869	c.2564_2574delAGGCAGAATTT	c.(2563-2574)aaggcagaatttfs	p.KAEF855fs	MAST4_ENST00000261569.7_Frame_Shift_Del_p.KAEF661fs|MAST4_ENST00000403666.1_Frame_Shift_Del_p.KAEF666fs|MAST4_ENST00000405643.1_Frame_Shift_Del_p.KAEF676fs|MAST4_ENST00000404260.3_Frame_Shift_Del_p.KAEF858fs	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	858	AGC-kinase C-terminal.					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)		CTGAGACAGAAGGCAGAATTTATTCCCCAAC	0.403																																					p.855_858del		Atlas-INDEL	.											.	MAST4	218	.	0			c.2563_2573del						PASS	.																																			SO:0001589	frameshift_variant	375449	exon20			.	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.2564_2574delAGGCAGAATTT	chr5.hg19:g.66438012_66438022delAGGCAGAATTT	ENSP00000385727:p.Lys855fs	271.0	0.0	0		41.0	16.0	0.390244	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Frame_Shift_Del	DEL	ENST00000403625.2	hg19	CCDS54861.1																																																																																			.	.	.	none		0.403	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			-	66438022	AGGCAGAATTT	-	66438012	7	5	96	1	0	1	0	1	0	0	0	0	9334	72	3	0	2772	0	MAST4	5	66438012	Frame_Shift_Del	DEL	AGGCAGAATTT	TCGA-B9-4115-01A-01D-1252-08	56188039	66438012	114477248	16	6079											
RGNEF	64283	hgsc.bcm.edu	37	chr5	73163796	73163796	+	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	ctggaaggagggagactgtgGgacaggtccatccattgtcc	9	8	15	9	0	0	1	0	0	0	1	3	5	3	4	3	5	0	0	3	5	1	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr5:73163796G>C	ENST00000426542.2	+	18	2268	c.2248G>C	c.(2248-2250)Gga>Cga	p.G750R	ARHGEF28_ENST00000545377.1_Missense_Mutation_p.G750R|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.G750R|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.G750R|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.G437R|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.G750R|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.G750R			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	750					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)	p.G750R(4)									GGAGACTGTGGGACAGGTCCA	0.522																																					p.G750R		Atlas-SNP	.											NP_001073948_1,NS,carcinoma,0,2	.	.	.	4	Substitution - Missense(4)	lung(4)	c.G2248C						PASS	.						104	99	101					5																	73163796		1962	4159	6121	SO:0001583	missense	64283	exon19			ACTGTGGGACAGG		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.2248G>C	chr5.hg19:g.73163796G>C	ENSP00000412175:p.Gly750Arg	81.0	0.0	.		33.0	12.0	.	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	hg19	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	G	2.497	-0.316052	0.05422	.	.	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799	T;T;T;T;T;T;T	0.10192	3.16;3.16;3.15;2.9;3.16;3.15;3.0	5.67	4.72	0.59763	.	.	.	.	.	T	0.10208	0.0250	L	0.44542	1.39	0.09310	N	1	B;B;B;P	0.36282	0.014;0.027;0.015;0.546	B;B;B;B	0.36244	0.005;0.005;0.019;0.22	T	0.18209	-1.0344	9	0.20519	T	0.43	.	10.1606	0.42849	0.0:0.175:0.6902:0.1348	.	437;750;750;750	B5MDA3;Q8N1W1;E9PC75;Q8N1W1-4	.;RGNEF_HUMAN;.;.	R	750;750;750;750;750;750;437	ENSP00000296794:G750R;ENSP00000441913:G750R;ENSP00000441436:G750R;ENSP00000287898:G750R;ENSP00000411459:G750R;ENSP00000412175:G750R;ENSP00000296799:G437R	ENSP00000287898:G750R	G	+	1	0	RP11-428C6.1	73199552	0.004000	0.15560	0.021000	0.16686	0.002000	0.02628	1.469000	0.35343	2.671000	0.90904	0.585000	0.79938	GGA	.	.	.	none		0.522	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			C	73163796	G	C	73163796	3	2	96	1	0	0	0	0	1	0	0	0	13296	1233	43	4	2318	4	RGNEF	5	73163796	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08	6725784	73163796	107751464	17	6080											
SHROOM1	134549	hgsc.bcm.edu	37	chr5	132160478	132160478	+	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	tgctctggggtaactctgcaGgatacatcaccgcagcctct	8	10	10	13	1	4	0	1	0	3	0	4	1	4	1	2	3	5	4	2	3	2	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr5:132160478G>T	ENST00000378679.3	-	6	1874	c.1070C>A	c.(1069-1071)cCt>cAt	p.P357H	SHROOM1_ENST00000319854.3_Missense_Mutation_p.P357H|SHROOM1_ENST00000378676.1_Intron|SHROOM1_ENST00000488072.1_5'Flank	NM_001172700.1	NP_001166171.1	Q2M3G4	SHRM1_HUMAN	shroom family member 1	357					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)			TAACTCTGCAGGATACATCAC	0.567																																					p.P357H		Atlas-SNP	.											.	SHROOM1	35	.	0			c.C1070A						PASS	.						60	62	61					5																	132160478		2203	4300	6503	SO:0001583	missense	134549	exon3			TCTGCAGGATACA	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.1070C>A	chr5.hg19:g.132160478G>T	ENSP00000367950:p.Pro357His	110.0	0.0	.		204.0	78.0	.	NM_133456	B7WP40|B7ZL01|Q8TDP0|Q8TF41	Missense_Mutation	SNP	ENST00000378679.3	hg19	CCDS54902.1	.	.	.	.	.	.	.	.	.	.	G	9.923	1.212785	0.22289	.	.	ENSG00000164403	ENST00000378679;ENST00000319854	T;T	0.24350	1.86;1.86	3.93	3.06	0.35304	.	0.509864	0.20038	N	0.100569	T	0.18130	0.0435	L	0.27053	0.805	0.19300	N	0.999977	B;B	0.27498	0.18;0.113	B;B	0.29176	0.099;0.046	T	0.19976	-1.0289	10	0.72032	D	0.01	-3.8793	9.1379	0.36886	0.0:0.0:0.7829:0.2171	.	357;357	Q2M3G4-2;Q2M3G4	.;SHRM1_HUMAN	H	357	ENSP00000367950:P357H;ENSP00000324245:P357H	ENSP00000324245:P357H	P	-	2	0	SHROOM1	132188377	0.141000	0.22595	0.029000	0.17559	0.002000	0.02628	1.458000	0.35223	1.222000	0.43521	-0.268000	0.10319	CCT	.	.	.	none		0.567	SHROOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133033.1	NM_133456		T	132160478	G	T	132160478	3	4	96	1	0	0	0	0	1	0	0	0	14306	1000	35	4	1508	4	SHROOM1	5	132160478	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08	58996682	132160478	48754782	18	6081											
SEC24A	10802	hgsc.bcm.edu	37	chr5	134002687	134002687	+	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	ttcagctgtcaaccaagaagGtaagtgaaccaagaaacaaa	19	6	8	8	0	2	3	2	1	0	2	2	3	2	3	2	1	4	2	2	1	8	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr5:134002687G>A	ENST00000398844.2	+	3	1027		c.e3+1		SEC24A_ENST00000322887.4_Splice_Site	NM_021982.2	NP_068817.1	O95486	SC24A_HUMAN	SEC24 family member A						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of protein secretion (GO:0050714)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045714)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	36			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AACCAAGAAGGTAAGTGAACC	0.438																																					.		Atlas-SNP	.											.	SEC24A	77	.	0			c.739+1G>A						PASS	.						40	39	39					5																	134002687		1833	4087	5920	SO:0001630	splice_region_variant	10802	exon3			AAGAAGGTAAGTG	AJ131244	CCDS43363.1, CCDS58967.1	5q31.1	2013-10-21	2013-10-21		ENSG00000113615	ENSG00000113615			10703	protein-coding gene	gene with protein product		607183	"SEC24 (S. cerevisiae) related gene family, member A", "SEC24 family, member A (S. cerevisiae)"			10075675, 10329445	Standard	NM_021982		Approved		uc003kzs.3	O95486	OTTHUMG00000163064	ENST00000398844.2:c.739+1G>A	chr5.hg19:g.134002687G>A		99.0	0.0	.		137.0	50.0	.	NM_001252231	A8MVW3|Q8WUV2|Q96GP7	Splice_Site	SNP	ENST00000398844.2	hg19	CCDS43363.1	.	.	.	.	.	.	.	.	.	.	G	17.08	3.297202	0.60086	.	.	ENSG00000113615	ENST00000398844;ENST00000322887	.	.	.	4.94	4.94	0.65067	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.7049	0.85369	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SEC24A	134030586	1.000000	0.71417	1.000000	0.80357	0.712000	0.41017	5.912000	0.69948	2.428000	0.82296	0.603000	0.83216	.	.	.	.	none		0.438	SEC24A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371563.1		Intron	A	134002687	G	A	134002687	5	1	96	1	0	0	0	0	0	0	1	0	14007	1275	44	2	750	2	SEC24A	5	134002687	Splice_Site	SNP	G	TCGA-B9-4115-01A-01D-1252-08	1842209	134002687	46912573	19	6082											
SPOCK1	6695	hgsc.bcm.edu	37	chr5	136834142	136834142	+	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	gtcattgtctaggaaattgcCgtggttggggcccgcgcctc	5	11	14	11	3	2	0	1	0	1	0	3	1	2	1	3	4	1	1	3	4	2	4	rs200001053		TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr5:136834142C>A	ENST00000394945.1	-	2	275	c.106G>T	c.(106-108)Ggc>Tgc	p.G36C	SPOCK1_ENST00000282223.7_Missense_Mutation_p.G36C	NM_004598.3	NP_004589.1	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1	36					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)			AGGAAATTGCCGTGGTTGGGG	0.682																																					p.G36C		Atlas-SNP	.											.	SPOCK1	58	.	0			c.G106T						PASS	.						22	21	21					5																	136834142		2203	4299	6502	SO:0001583	missense	6695	exon2			AATTGCCGTGGTT	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.106G>T	chr5.hg19:g.136834142C>A	ENSP00000378401:p.Gly36Cys	37.0	0.0	.		56.0	17.0	.	NM_004598	B3KSW3|Q59EW0|Q8N630|Q9UCL8	Missense_Mutation	SNP	ENST00000394945.1	hg19	CCDS4191.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.179946	0.78564	.	.	ENSG00000152377	ENST00000394945;ENST00000282223;ENST00000505690	T;T;T	0.55588	0.54;0.54;0.51	3.66	2.77	0.32553	.	0.371240	0.21081	N	0.080484	T	0.58509	0.2127	L	0.56199	1.76	0.25077	N	0.990954	D	0.62365	0.991	P	0.55965	0.788	T	0.51576	-0.8688	10	0.66056	D	0.02	.	9.9319	0.41528	0.204:0.796:0.0:0.0	.	36	Q08629	TICN1_HUMAN	C	36	ENSP00000378401:G36C;ENSP00000282223:G36C;ENSP00000424517:G36C	ENSP00000282223:G36C	G	-	1	0	SPOCK1	136862041	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.898000	0.63238	0.626000	0.30322	0.462000	0.41574	GGC	.	C|1.000;G|0.000	.	alt		0.682	SPOCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251222.1	NM_004598		A	136834142	C	A	136834142	3	1	96	1	0	0	0	0	1	0	0	0	15091	652	23	4	1253	4	SPOCK1	5	136834142	Missense_Mutation	SNP	C	TCGA-B9-4115-01A-01D-1252-08	2831455	136834142	44081118	20	6083											
HIST1H2AD	3013	hgsc.bcm.edu	37	chr6	26199108	26199109	+	Frame_Shift_Del	DEL	CA	CA	-																															cttggccttgtggtgactctCagtcttcttggggagcagta																										TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	CA	CA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr6:26199108_26199109delCA	ENST00000341023.1	-	1	362_363	c.363_364delTG	c.(361-366)actgagfs	p.E122fs	HIST1H2BF_ENST00000359985.1_5'Flank|HIST1H3D_ENST00000356476.2_5'Flank|HIST1H3D_ENST00000377831.5_5'UTR	NM_021065.2	NP_066409.1	P20671	H2A1D_HUMAN	histone cluster 1, H2ad	122						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6		all_hematologic(11;0.196)				TGGTGACTCTCAGTCTTCTTGG	0.485																																					p.122_122del		Atlas-INDEL	.											.	HIST1H2AD	20	.	0			c.364_365del						PASS	.																																			SO:0001589	frameshift_variant	3013	exon1			.	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.363_364delTG	chr6.hg19:g.26199108_26199109delCA	ENSP00000341094:p.Glu122fs	194.0	0.0	0		285.0	27.0	0.0947368	NM_021065	A0PK91|P57754|Q6FGY6	Frame_Shift_Del	DEL	ENST00000341023.1	hg19	CCDS4591.1																																																																																			.	.	.	none		0.485	HIST1H2AD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040100.1	NM_021065		-	26199109	CA	-	26199108	7	5	96	1	0	1	0	1	0	0	0	0	7138	835	29	0	32	0	HIST1H2AD	6	26199108	Frame_Shift_Del	DEL	CA	TCGA-B9-4115-01A-01D-1252-08		26199108	144915959	21	6084											
BTN3A2	11118	hgsc.bcm.edu	37	chr6	26370805	26370805	+	Frame_Shift_Del	DEL	A	A	-																															aaattccctcctcggcctggAaaagacagccagcatttcca																										TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr6:26370805delA	ENST00000356386.2	+	5	877	c.689delA	c.(688-690)gaafs	p.E230fs	BTN3A2_ENST00000527422.1_Frame_Shift_Del_p.E230fs|BTN3A2_ENST00000377708.2_Frame_Shift_Del_p.E230fs|BTN3A2_ENST00000508906.2_Frame_Shift_Del_p.E188fs|BTN3A2_ENST00000396934.3_Frame_Shift_Del_p.E207fs|BTN3A2_ENST00000532994.1_3'UTR|BTN3A2_ENST00000396948.1_Frame_Shift_Del_p.E230fs	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	230					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						CTCGGCCTGGAAAAGACAGCC	0.522																																					p.E230fs		Atlas-INDEL	.											.	BTN3A2	44	.	0			c.688delG						PASS	.						105	103	103					6																	26370805		2203	4300	6503	SO:0001589	frameshift_variant	11118	exon5			.	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.689delA	chr6.hg19:g.26370805delA	ENSP00000348751:p.Glu230fs	253.0	0.0	0		196.0	70.0	0.357143	NM_007047	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Frame_Shift_Del	DEL	ENST00000356386.2	hg19	CCDS4605.1																																																																																			.	.	.	none		0.522	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2			-	26370805	A	-	26370805	7	5	96	1	0	1	0	1	0	0	0	0	1565	246	9	0	699	0	BTN3A2	6	26370805	Frame_Shift_Del	DEL	A	TCGA-B9-4115-01A-01D-1252-08	171697	26370805	144744262	22	6085											
KIF6	221458	hgsc.bcm.edu	37	chr6	39313488	39313488	+	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	ccacagacctgtcttccagtGgggtgctggtgctgctctgt	4	12	13	12	0	2	1	0	0	2	1	3	1	3	1	3	3	3	3	3	3	0	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr6:39313488G>T	ENST00000287152.7	-	21	2403	c.2309C>A	c.(2308-2310)cCa>cAa	p.P770Q	KIF6_ENST00000538893.1_Missense_Mutation_p.P714Q|KIF6_ENST00000373215.3_Missense_Mutation_p.P753Q|KIF6_ENST00000394362.1_Missense_Mutation_p.P204Q|KIF6_ENST00000373216.3_Missense_Mutation_p.P753Q|KIF6_ENST00000373213.4_Missense_Mutation_p.P609Q|KIF6_ENST00000541946.1_Missense_Mutation_p.P221Q|KIF6_ENST00000229913.5_Missense_Mutation_p.P221Q	NM_145027.4	NP_659464.3	Q6ZMV9	KIF6_HUMAN	kinesin family member 6	770					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						GTCTTCCAGTGGGGTGCTGGT	0.557																																					p.P770Q		Atlas-SNP	.											.	KIF6	233	.	0			c.C2309A						PASS	.						124	107	113					6																	39313488		2203	4300	6503	SO:0001583	missense	221458	exon21			TCCAGTGGGGTGC	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.2309C>A	chr6.hg19:g.39313488G>T	ENSP00000287152:p.Pro770Gln	53.0	0.0	.		67.0	29.0	.	NM_145027	Q2MDE3|Q2MDE4|Q5T8J6|Q6ZWE3|Q86T87|Q8WTV4	Missense_Mutation	SNP	ENST00000287152.7	hg19	CCDS4844.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.700|6.700	0.497738|0.497738	0.12762|0.12762	.|.	.|.	ENSG00000164627|ENSG00000164627	ENST00000458470|ENST00000287152;ENST00000394362;ENST00000373216;ENST00000373213;ENST00000229913;ENST00000373215;ENST00000538893;ENST00000541946	.|T;T;T;T;T;T;T;T	.|0.71222	.|-0.49;1.51;-0.53;-0.31;1.53;-0.49;-0.55;1.49	4.12|4.12	-1.35|-1.35	0.09114|0.09114	.|.	.|.	.|.	.|.	.|.	T|T	0.11665|0.11665	0.0284|0.0284	N|N	0.01352|0.01352	-0.895|-0.895	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.26195	.|0.09;0.09;0.144;0.054	.|B;B;B;B	.|0.29440	.|0.048;0.03;0.102;0.022	T|T	0.20940|0.20940	-1.0260|-1.0260	5|9	.|0.09084	.|T	.|0.74	.|.	1.384|1.384	0.02236|0.02236	0.1966:0.3047:0.3385:0.1602|0.1966:0.3047:0.3385:0.1602	.|.	.|753;714;753;770	.|E7EUN7;F6VGH2;Q6ZMV9-3;Q6ZMV9	.|.;.;.;KIF6_HUMAN	N|Q	645|770;204;753;609;221;753;714;221	.|ENSP00000287152:P770Q;ENSP00000377889:P204Q;ENSP00000362312:P753Q;ENSP00000362309:P609Q;ENSP00000229913:P221Q;ENSP00000362311:P753Q;ENSP00000441435:P714Q;ENSP00000439064:P221Q	.|ENSP00000229913:P221Q	H|P	-|-	1|2	0|0	KIF6|KIF6	39421466|39421466	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.191000|0.191000	0.23601|0.23601	-1.263000|-1.263000	0.02850|0.02850	-0.421000|-0.421000	0.07416|0.07416	0.563000|0.563000	0.77884|0.77884	CAC|CCA	.	.	.	none		0.557	KIF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040455.2	NM_145027		T	39313488	G	T	39313488	3	4	96	1	0	0	0	0	1	0	0	0	8315	1348	47	4	147	4	KIF6	6	39313488	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08	12942683	39313488	131801579	23	6086											
NR2E1	7101	hgsc.bcm.edu	37	chr6	108499383	108499383	+	Missense_Mutation	SNP	T	T	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	aatcagctgccagacttctcTtcatgagcatcaagtgggct	10	11	9	11	0	4	2	3	1	1	1	5	2	4	2	1	1	3	3	1	1	2	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr6:108499383T>G	ENST00000368986.4	+	5	1288	c.580T>G	c.(580-582)Ttc>Gtc	p.F194V	NR2E1_ENST00000368983.3_Missense_Mutation_p.F231V	NM_003269.3	NP_003260.1	Q9Y466	NR2E1_HUMAN	nuclear receptor subfamily 2, group E, member 1	194	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)		CAGACTTCTCTTCATGAGCAT	0.527																																					p.F194V		Atlas-SNP	.											.	NR2E1	57	.	0			c.T580G						PASS	.						123	104	110					6																	108499383		2203	4300	6503	SO:0001583	missense	7101	exon5			CTTCTCTTCATGA	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.580T>G	chr6.hg19:g.108499383T>G	ENSP00000357982:p.Phe194Val	181.0	0.0	.		79.0	29.0	.	NM_003269	Q6ZMP8	Missense_Mutation	SNP	ENST00000368986.4	hg19	CCDS5063.1	.	.	.	.	.	.	.	.	.	.	T	31	5.077084	0.94000	.	.	ENSG00000112333	ENST00000368986;ENST00000368983	T;T	0.50813	0.73;0.73	5.6	5.6	0.85130	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.043698	0.85682	D	0.000000	T	0.30070	0.0753	N	0.26092	0.79	0.80722	D	1	P	0.46621	0.881	P	0.48089	0.566	T	0.07009	-1.0795	10	0.30854	T	0.27	.	14.0221	0.64563	0.0:0.0:0.0:1.0	.	194	Q9Y466	NR2E1_HUMAN	V	194;231	ENSP00000357982:F194V;ENSP00000357979:F231V	ENSP00000357979:F231V	F	+	1	0	NR2E1	108606076	1.000000	0.71417	0.970000	0.41538	0.957000	0.61999	7.698000	0.84413	2.134000	0.65973	0.528000	0.53228	TTC	.	.	.	none		0.527	NR2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041712.2			G	108499383	T	G	108499383	3	3	96	1	0	0	0	0	1	0	0	0	10632	1609	56	5	598	5	NR2E1	6	108499383	Missense_Mutation	SNP	T	TCGA-B9-4115-01A-01D-1252-08	69185895	108499383	62615684	24	6087											
HIPK2	28996	hgsc.bcm.edu	37	chr7	139299101	139299101	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccgggcacaaatctgggctgTtcctgtctgcaggggcatgc	6	9	14	12	1	2	0	0	0	2	0	3	0	3	0	2	4	2	5	2	4	1	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr7:139299101T>C	ENST00000406875.3	-	8	2015	c.1921A>G	c.(1921-1923)Aca>Gca	p.T641A	HIPK2_ENST00000428878.2_Missense_Mutation_p.T614A|HIPK2_ENST00000342645.6_Missense_Mutation_p.T641A	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	641	Interaction with SKI and SMAD1.				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)			breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					ATCTGGGCTGTTCCTGTCTGC	0.597																																					p.T641A		Atlas-SNP	.											.	HIPK2	192	.	0			c.A1921G						PASS	.						47	54	52					7																	139299101		1956	4149	6105	SO:0001583	missense	28996	exon8			GGGCTGTTCCTGT	AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"homeodomain-interacting protein kinase 2"			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.1921A>G	chr7.hg19:g.139299101T>C	ENSP00000385571:p.Thr641Ala	39.0	0.0	.		107.0	46.0	.	NM_022740	Q75MR7|Q8WWI4|Q9H2Y1	Missense_Mutation	SNP	ENST00000406875.3	hg19		.	.	.	.	.	.	.	.	.	.	T	12.91	2.079694	0.36662	.	.	ENSG00000064393	ENST00000406875;ENST00000428878;ENST00000342645	T;T;T	0.50277	0.75;0.8;0.78	5.39	2.9	0.33743	.	.	.	.	.	T	0.33847	0.0877	.	.	.	0.43667	D	0.996098	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.06481	-1.0824	8	0.27785	T	0.31	.	9.7368	0.40392	0.0:0.1461:0.0:0.8539	.	641;614	Q9H2X6;Q9H2X6-3	HIPK2_HUMAN;.	A	641;614;641	ENSP00000385571:T641A;ENSP00000413724:T614A;ENSP00000343108:T641A	ENSP00000343108:T641A	T	-	1	0	HIPK2	138949641	1.000000	0.71417	0.996000	0.52242	0.984000	0.73092	0.813000	0.27225	0.383000	0.24910	0.460000	0.39030	ACA	.	.	.	none		0.597	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740		C	139299101	T	C	139299101	3	2	96	1	0	0	0	0	1	0	0	0	7124	1725	60	3	1707	3	HIPK2	7	139299101	Missense_Mutation	SNP	T	TCGA-B9-4115-01A-01D-1252-08		139299101	19839562	25	6088											
AMAC1L2	83650	hgsc.bcm.edu	37	chr8	11188719	11188719	+	Missense_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	ccagcgctgccagccctctgGtgccaccaatggcctgctgg	5	7	12	17	1	1	0	0	0	1	0	1	0	1	0	6	3	5	2	6	3	1	0			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr8:11188719G>A	ENST00000382435.4	+	1	323	c.104G>A	c.(103-105)gGt>gAt	p.G35D		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	35						integral component of membrane (GO:0016021)		p.G35D(1)									CAGCCCTCTGGTGCCACCAAT	0.682																																					p.G35D		Atlas-SNP	.											AMAC1L2,NS,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	endometrium(1)	c.G104A						PASS	.																																			SO:0001583	missense	83650	exon1			CCTCTGGTGCCAC	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"Solute carriers"	15546	protein-coding gene	gene with protein product		615199	"acyl-malonyl condensing enzyme 1-like 2"	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.104G>A	chr8.hg19:g.11188719G>A	ENSP00000371872:p.Gly35Asp	118.0	1.0	.		273.0	14.0	.	NM_054028	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	hg19	CCDS5980.1	.	.	.	.	.	.	.	.	.	.	A	0.007	-1.973298	0.00452	.	.	ENSG00000177710	ENST00000382435	T	0.23348	1.91	0.34	0.34	0.15985	.	0.293668	0.23411	N	0.048476	T	0.06280	0.0162	N	0.02539	-0.55	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.28267	-1.0049	9	0.09084	T	0.74	0.0032	.	.	.	.	35	Q96KT7	S35G5_HUMAN	D	35	ENSP00000371872:G35D	ENSP00000371872:G35D	G	+	2	0	SLC35G5	11226129	0.973000	0.33851	0.352000	0.25734	0.047000	0.14425	0.142000	0.16096	-1.532000	0.01747	-2.047000	0.00414	GGT	.	.	.	none		0.682	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028		A	11188719	G	A	11188719	3	1	96	1	0	0	0	0	1	0	0	0	560	1261	44	2	106	2	AMAC1L2	8	11188719	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08		11188719	135175303	26	6089											
FGFR1	2260	hgsc.bcm.edu	37	chr8	38271216	38271216	+	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	ggcagggctcctcgggcagcGgctcatgagagaagacggaa	10	4	17	10	3	1	3	1	1	0	2	3	5	2	4	1	5	1	4	1	5	2	0	rs377620009		TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr8:38271216G>T	ENST00000447712.2	-	18	3340	c.2399C>A	c.(2398-2400)cCg>cAg	p.P800Q	FGFR1_ENST00000532791.1_Missense_Mutation_p.P798Q|FGFR1_ENST00000397108.4_Missense_Mutation_p.P798Q|FGFR1_ENST00000425967.3_Missense_Mutation_p.P831Q|FGFR1_ENST00000326324.6_Missense_Mutation_p.P709Q|FGFR1_ENST00000397113.2_Missense_Mutation_p.P798Q|FGFR1_ENST00000397091.5_Missense_Mutation_p.P798Q|FGFR1_ENST00000356207.5_Missense_Mutation_p.P711Q|FGFR1_ENST00000341462.5_Missense_Mutation_p.P800Q|FGFR1_ENST00000335922.5_Missense_Mutation_p.P790Q|FGFR1_ENST00000397103.1_Missense_Mutation_p.P711Q	NM_001174063.1|NM_015850.3|NM_023110.2	NP_001167534.1|NP_056934.2|NP_075598.2	P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1	800					angiogenesis (GO:0001525)|auditory receptor cell development (GO:0060117)|axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell maturation (GO:0048469)|cell migration (GO:0016477)|chondrocyte differentiation (GO:0002062)|chordate embryonic development (GO:0043009)|embryonic limb morphogenesis (GO:0030326)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lung-associated mesenchyme development (GO:0060484)|MAPK cascade (GO:0000165)|mesenchymal cell differentiation (GO:0048762)|midbrain development (GO:0030901)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|outer ear morphogenesis (GO:0042473)|paraxial mesoderm development (GO:0048339)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)|regulation of cell differentiation (GO:0045595)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of lateral mesodermal cell fate specification (GO:0048378)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ventricular zone neuroblast division (GO:0021847)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)		FGFR1/ZNF703(2)	breast(2)|central_nervous_system(7)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	50	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	CTCGGGCAGCGGCTCATGAGA	0.662		1	T	"BCR, FOP, ZNF198, CEP1"	"MPD, NHL"		"Pfeiffer syndrome, Kallman syndrome"																														p.P831Q	Melanoma(146;1153 1840 21453 21841 43625)	Atlas-SNP	.		Dom	yes		8	8p11.2-p11.1	2260	fibroblast growth factor receptor 1	yes	L	Q7Z2S2_HUMAN,NS,carcinoma,0,4	FGFR1	284	.	0			c.C2492A						PASS	.						21	28	26					8																	38271216		2059	4189	6248	SO:0001583	missense	2260	exon19			GGCAGCGGCTCAT	M34185	CCDS6107.2, CCDS43730.1, CCDS43731.1, CCDS43732.1, CCDS55221.1, CCDS55222.1, CCDS55223.1	8p11.23-p11.22	2014-04-03	2008-08-01		ENSG00000077782	ENSG00000077782	2.7.10.1	"CD molecules", "Immunoglobulin superfamily / I-set domain containing"	3688	protein-coding gene	gene with protein product	"Pfeiffer syndrome"	136350	"fms-related tyrosine kinase 2"	FLT2, KAL2		2162671	Standard	NM_015850		Approved	H2, H3, H4, H5, CEK, FLG, BFGFR, N-SAM, CD331	uc011lbu.2	P11362	OTTHUMG00000147366	ENST00000447712.2:c.2399C>A	chr8.hg19:g.38271216G>T	ENSP00000400162:p.Pro800Gln	40.0	0.0	.		50.0	3.0	.	NM_001174067	A8K6T9|A8K8V5|C1KBH8|P17049|Q02063|Q02065|Q14306|Q14307|Q53H63|Q59H40|Q5BJG2|Q8N685|Q9UD50|Q9UDF0|Q9UDF1|Q9UDF2	Missense_Mutation	SNP	ENST00000447712.2	hg19	CCDS6107.2	.	.	.	.	.	.	.	.	.	.	G	25.9	4.689014	0.88735	.	.	ENSG00000077782	ENST00000397091;ENST00000425967;ENST00000447712;ENST00000341462;ENST00000532791;ENST00000397113;ENST00000356207;ENST00000335922;ENST00000326324;ENST00000397103;ENST00000397108	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	5.53	5.53	0.82687	.	0.101061	0.64402	D	0.000002	D	0.86389	0.5921	M	0.76574	2.34	0.58432	D	0.999997	D;D;D;D;D	0.71674	0.996;0.996;0.994;0.998;0.996	D;D;P;D;D	0.70487	0.956;0.956;0.905;0.969;0.956	D	0.87462	0.2408	10	0.87932	D	0	.	19.4585	0.94906	0.0:0.0:1.0:0.0	.	709;709;800;790;798	P11362-14;P11362-4;P11362;P11362-20;P11362-2	.;.;FGFR1_HUMAN;.;.	Q	798;831;800;800;798;798;711;790;709;711;798	ENSP00000380280:P798Q;ENSP00000393312:P831Q;ENSP00000400162:P800Q;ENSP00000340636:P800Q;ENSP00000432972:P798Q;ENSP00000380302:P798Q;ENSP00000348537:P711Q;ENSP00000337247:P790Q;ENSP00000327229:P709Q;ENSP00000380292:P711Q;ENSP00000380297:P798Q	ENSP00000327229:P709Q	P	-	2	0	FGFR1	38390373	1.000000	0.71417	0.955000	0.39395	0.952000	0.60782	7.781000	0.85668	2.602000	0.87976	0.655000	0.94253	CCG	.	.	.	alt		0.662	FGFR1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	38271216	G	T	38271216	3	4	96	1	0	0	0	0	1	0	0	0	5870	1116	39	4	73	4	FGFR1	8	38271216	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08	27082497	38271216	108092806	27	6090											
TYRP1	7306	hgsc.bcm.edu	37	chr9	12694339	12694339	+	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	acaactgtgggacgtgccgtCctggctggagaggagctgcc	7	7	16	11	2	0	1	0	0	0	1	1	4	1	3	3	4	4	2	3	4	1	0			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr9:12694339C>G	ENST00000388918.5	+	2	472	c.343C>G	c.(343-345)Cct>Gct	p.P115A	TYRP1_ENST00000381137.2_5'UTR|TYRP1_ENST00000381136.2_5'Flank	NM_000550.2	NP_000541.1	P17643	TYRP1_HUMAN	tyrosinase-related protein 1	115					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)		GACGTGCCGTCCTGGCTGGAG	0.507									Oculocutaneous Albinism																												p.P115A		Atlas-SNP	.											.	TYRP1	60	.	0			c.C343G						PASS	.						35	33	34					9																	12694339		2203	4300	6503	SO:0001583	missense	7306	exon2	Familial Cancer Database		TGCCGTCCTGGCT	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.343C>G	chr9.hg19:g.12694339C>G	ENSP00000373570:p.Pro115Ala	63.0	0.0	.		48.0	14.0	.	NM_000550	P78468|P78469|Q13721|Q15679	Missense_Mutation	SNP	ENST00000388918.5	hg19	CCDS34990.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.937217	0.52972	.	.	ENSG00000107165	ENST00000388918	D	0.98926	-5.24	5.5	5.5	0.81552	Uncharacterised domain, di-copper centre (2);	0.097920	0.64402	D	0.000001	D	0.97324	0.9125	L	0.55834	1.745	0.80722	D	1	B	0.10296	0.003	B	0.14578	0.011	D	0.95286	0.8390	9	.	.	.	-1.287	19.7727	0.96373	0.0:1.0:0.0:0.0	.	115	P17643	TYRP1_HUMAN	A	115	ENSP00000373570:P115A	.	P	+	1	0	TYRP1	12684339	0.998000	0.40836	1.000000	0.80357	0.744000	0.42396	3.774000	0.55341	2.758000	0.94735	0.563000	0.77884	CCT	.	.	.	none		0.507	TYRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055502.3	NM_000550		G	12694339	C	G	12694339	3	3	96	1	0	0	0	0	1	0	0	0	16828	855	30	4	345	4	TYRP1	9	12694339	Missense_Mutation	SNP	C	TCGA-B9-4115-01A-01D-1252-08		12694339	128519092	28	6091											
KIF12	113220	hgsc.bcm.edu	37	chr9	116859620	116859620	+	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	cagggcctccagactcccaaAttccaccacccgcagctgct	9	6	7	19	1	0	1	0	0	0	1	3	1	3	1	6	1	2	3	6	1	1	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr9:116859620A>T	ENST00000374118.3	-	4	430	c.193T>A	c.(193-195)Ttt>Att	p.F65I	KIF12_ENST00000473174.1_Intron	NM_138424.1	NP_612433.1	Q96FN5	KIF12_HUMAN	kinesin family member 12	198	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	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(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	17						AGACTCCCAAATTCCACCACC	0.602																																					p.F65I		Atlas-SNP	.											.	KIF12	35	.	0			c.T193A						PASS	.						41	43	43					9																	116859620		2203	4300	6503	SO:0001583	missense	113220	exon4			TCCCAAATTCCAC	BC010626	CCDS6801.1	9q33.1	2008-02-05			ENSG00000136883	ENSG00000136883		"Kinesins"	21495	protein-coding gene	gene with protein product		611278					Standard	NM_138424		Approved		uc004bif.3	Q96FN5	OTTHUMG00000020533	ENST00000374118.3:c.193T>A	chr9.hg19:g.116859620A>T	ENSP00000363232:p.Phe65Ile	71.0	0.0	.		92.0	32.0	.	NM_138424	Q5TBE0	Missense_Mutation	SNP	ENST00000374118.3	hg19	CCDS6801.1	.	.	.	.	.	.	.	.	.	.	A	6.945	0.544191	0.13312	.	.	ENSG00000136883	ENST00000374118;ENST00000259410	T	0.70045	-0.45	5.5	0.00987	0.14080	Kinesin, motor domain (4);	0.463632	0.22239	N	0.062709	T	0.33000	0.0848	N	0.01817	-0.705	0.23906	N	0.996504	B	0.10296	0.003	B	0.15484	0.013	T	0.21245	-1.0251	10	0.52906	T	0.07	.	4.5522	0.12117	0.4767:0.0:0.0832:0.4401	.	198	Q96FN5	KIF12_HUMAN	I	65;198	ENSP00000363232:F65I	ENSP00000259410:F198I	F	-	1	0	KIF12	115899441	0.889000	0.30405	0.842000	0.33263	0.054000	0.15201	1.421000	0.34815	-0.251000	0.09542	-0.451000	0.05528	TTT	.	.	.	none		0.602	KIF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053751.1	NM_138424		T	116859620	A	T	116859620	3	4	96	1	0	0	0	0	1	0	0	0	8280	101	4	5	1400	5	KIF12	9	116859620	Missense_Mutation	SNP	A	TCGA-B9-4115-01A-01D-1252-08	104165281	116859620	24353811	29	6092											
METTL10	399818	hgsc.bcm.edu	37	chr10	126477651	126477651	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatttccagttccaatatcAagcactgaagcatccagtgg	12	10	7	12	0	1	1	1	1	0	0	4	1	4	1	4	1	2	3	4	1	4	3			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr10:126477651A>G	ENST00000368836.2	-	3	288	c.252T>C	c.(250-252)ctT>ctC	p.L84L	RP11-12J10.3_ENST00000494792.1_Missense_Mutation_p.L49S	NM_212554.2	NP_997719.2	Q5JPI9	MET10_HUMAN	methyltransferase like 10	84							methyltransferase activity (GO:0008168)			endometrium(1)|large_intestine(2)|lung(1)|urinary_tract(1)	5		all_lung(145;0.0186)|Lung NSC(174;0.0295)|all_neural(114;0.116)|Colorectal(57;0.172)		Colorectal(40;0.101)|COAD - Colon adenocarcinoma(40;0.111)		TTCCAATATCAAGCACTGAAG	0.348																																					p.L84L		Atlas-SNP	.											.	METTL10	16	.	0			c.T252C						PASS	.						172	152	159					10																	126477651		2203	4300	6503	SO:0001819	synonymous_variant	399818	exon3			AATATCAAGCACT		CCDS31307.1	10q26.13	2010-01-15			ENSG00000203791	ENSG00000203791			33787	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 138"	C10orf138			Standard	NM_212554		Approved	Em:AC068896.3	uc001lhy.1	Q5JPI9	OTTHUMG00000019217	ENST00000368836.2:c.252T>C	chr10.hg19:g.126477651A>G		182.0	0.0	.		110.0	39.0	.	NM_212554	A8MPY7	Silent	SNP	ENST00000368836.2	hg19	CCDS31307.1																																																																																			.	.	.	none		0.348	METTL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050884.1	NM_212554		G	126477651	A	G	126477651	2	3	96	1	0	0	0	0	0	0	0	1	9501	117	5	3		3	METTL10	10	126477651	Silent	SNP	A	TCGA-B9-4115-01A-01D-1252-08		126477651	9057096	30	6093											
OSBPL5	114879	hgsc.bcm.edu	37	chr11	3143300	3143300	+	Frame_Shift_Del	DEL	T	T	-																															gctgccgtgtggcgcgcttcTtctcctgccggtagttctcc																										TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr11:3143300delT	ENST00000263650.7	-	5	488	c.329delA	c.(328-330)aagfs	p.K111fs	OSBPL5_ENST00000525498.1_Frame_Shift_Del_p.K63fs|OSBPL5_ENST00000348039.5_Frame_Shift_Del_p.K111fs|OSBPL5_ENST00000389989.3_Frame_Shift_Del_p.K111fs|OSBPL5_ENST00000542243.1_Frame_Shift_Del_p.E26fs	NM_020896.3	NP_065947.1	Q9H0X9	OSBL5_HUMAN	oxysterol binding protein-like 5	111					cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|Golgi to plasma membrane transport (GO:0006893)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|oxysterol binding (GO:0008142)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	25		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		GGCGCGCTTCTTCTCCTGCCG	0.687																																					p.K110fs		Atlas-INDEL	.											.	OSBPL5	78	.	0			c.330delG						PASS	.						43	34	37					11																	3143300		2191	4291	6482	SO:0001589	frameshift_variant	114879	exon5			.	AF392453	CCDS31343.1, CCDS31344.1	11p15.4	2013-01-10			ENSG00000021762	ENSG00000021762		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16392	protein-coding gene	gene with protein product		606733					Standard	NM_145638		Approved	KIAA1534, ORP5	uc001lxk.2	Q9H0X9	OTTHUMG00000011702	ENST00000263650.7:c.329delA	chr11.hg19:g.3143300delT	ENSP00000263650:p.Lys111fs	9.0	0.0	0		25.0	11.0	0.44	NM_145638	A6NDP0|A6NJS8|Q54A90|Q8N596|Q9BZB0|Q9P1Z4	Frame_Shift_Del	DEL	ENST00000263650.7	hg19	CCDS31344.1																																																																																			.	.	.	none		0.687	OSBPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032332.2			-	3143300	T	-	3143300	7	5	96	1	0	1	0	1	0	0	0	0	11287	1609	56	0	2382	0	OSBPL5	11	3143300	Frame_Shift_Del	DEL	T	TCGA-B9-4115-01A-01D-1252-08		3143300	131863216	31	6094											
OTUB1	55611	hgsc.bcm.edu	37	chr11	63756155	63756155	+	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	cagaaccctctggtgtcagaGcggctggagctctcggtcct	6	9	13	13	2	3	2	1	0	2	2	5	3	4	3	2	4	3	2	2	4	1	0			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr11:63756155G>T	ENST00000538426.1	+	3	194	c.150G>T	c.(148-150)gaG>gaT	p.E50D	OTUB1_ENST00000536443.1_3'UTR|OTUB1_ENST00000422031.2_Missense_Mutation_p.E87D|OTUB1_ENST00000541478.1_Intron|OTUB1_ENST00000543004.1_Missense_Mutation_p.E59D|OTUB1_ENST00000428192.2_Missense_Mutation_p.E50D|OTUB1_ENST00000543988.1_Missense_Mutation_p.E20D|OTUB1_ENST00000535715.1_Missense_Mutation_p.E50D	NM_017670.2	NP_060140.2	Q96FW1	OTUB1_HUMAN	OTU deubiquitinase, ubiquitin aldehyde binding 1	50					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|immune system process (GO:0002376)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein K48-linked deubiquitination (GO:0071108)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	NEDD8-specific protease activity (GO:0019784)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)	6						TGGTGTCAGAGCGGCTGGAGC	0.537																																					p.E50D		Atlas-SNP	.											.	OTUB1	19	.	0			c.G150T						PASS	.						114	116	115					11																	63756155		2201	4297	6498	SO:0001583	missense	55611	exon3			GTCAGAGCGGCTG	AY177200	CCDS8055.1	11q13.1	2014-02-24	2014-02-24			ENSG00000167770		"OTU domain containing"	23077	protein-coding gene	gene with protein product		608337	"OTU domain, ubiquitin aldehyde binding 1"			12704427, 19383985	Standard	NM_017670		Approved	FLJ20113, FLJ40710	uc001nyf.1	Q96FW1		ENST00000538426.1:c.150G>T	chr11.hg19:g.63756155G>T	ENSP00000444357:p.Glu50Asp	346.0	0.0	.		515.0	141.0	.	NM_017670	Q32Q78|Q96II3|Q9NXQ4|Q9P0B8	Missense_Mutation	SNP	ENST00000538426.1	hg19	CCDS8055.1	.	.	.	.	.	.	.	.	.	.	G	8.534	0.871741	0.17322	.	.	ENSG00000167770	ENST00000535715;ENST00000428192;ENST00000422031;ENST00000538426;ENST00000543004;ENST00000543988	T;T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85;0.85	5.49	5.49	0.81192	.	.	.	.	.	T	0.29491	0.0735	N	0.17248	0.465	0.35424	D	0.793481	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.29971	-0.9994	9	0.15952	T	0.53	.	10.7288	0.46085	0.0876:0.0:0.9124:0.0	.	87;50	B4DPD5;Q96FW1	.;OTUB1_HUMAN	D	50;50;87;50;59;20	ENSP00000440211:E50D;ENSP00000402551:E50D;ENSP00000416973:E87D;ENSP00000444357:E50D;ENSP00000437453:E59D;ENSP00000441328:E20D	ENSP00000416973:E87D	E	+	3	2	OTUB1	63512731	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	1.546000	0.36179	2.753000	0.94483	0.591000	0.81541	GAG	.	.	.	none		0.537	OTUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396277.1	NM_017670		T	63756155	G	T	63756155	3	4	96	1	0	0	0	0	1	0	0	0	11318	962	34	4	160	4	OTUB1	11	63756155	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08	60612855	63756155	71250361	32	6095											
IGSF9B	22997	hgsc.bcm.edu	37	chr11	133814179	133814179	+	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	tactgctggtccagcatgagCactttgcactcataccagcc	9	10	8	14	0	1	1	1	1	0	0	2	1	2	1	3	1	7	4	3	1	2	3			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr11:133814179C>A	ENST00000321016.8	-	3	575	c.345G>T	c.(343-345)gtG>gtT	p.V115V	IGSF9B_ENST00000533871.2_Silent_p.V115V			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	115	Ig-like 1.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		CCAGCATGAGCACTTTGCACT	0.577																																					p.V115V		Atlas-SNP	.											.	IGSF9B	290	.	0			c.G345T						PASS	.						108	116	113					11																	133814179		2103	4231	6334	SO:0001819	synonymous_variant	22997	exon3			CATGAGCACTTTG	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.345G>T	chr11.hg19:g.133814179C>A		59.0	0.0	.		67.0	32.0	.	NM_014987	G5EA26	Silent	SNP	ENST00000321016.8	hg19																																																																																				.	.	.	none		0.577	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		A	133814179	C	A	133814179	2	1	96	1	0	0	0	0	0	0	0	1	7613	697	25	4		4	IGSF9B	11	133814179	Silent	SNP	C	TCGA-B9-4115-01A-01D-1252-08	70058024	133814179	1192337	33	6096											
ATP11A	23250	hgsc.bcm.edu	37	chr13	113516824	113516825	+	Missense_Mutation	DNP	GC	GC	AG																															cgctcctgggactgtttgacGcactggtgttcttctttggt																								rs140812688		TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr13:113516824_113516825GC>AG	ENST00000487903.1	+	25	3014_3015	c.2926_2927GC>AG	c.(2926-2928)GCa>AGa	p.A976R	ATP11A_ENST00000375645.3_Missense_Mutation_p.A976R|ATP11A_ENST00000375630.2_Missense_Mutation_p.A976R|ATP11A_ENST00000283558.8_Missense_Mutation_p.A976R			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	976					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)				ACTGTTTGACGCACTGGTGTTC	0.535																																					p.A976T|p.A976G		Atlas-SNP	.											.	ATP11A	225	.	0			c.G2926A|c.C2927G						PASS	.																																			SO:0001583	missense	23250	exon25			TTTGACGCACTGG|TTGACGCACTGGT	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	Exception_encountered	chr13.hg19:g.113516824_113516825delinsAG	ENSP00000420387:p.Ala976Arg	86.0	0.0	.		92.0	38.0	.	NM_032189	Q5VXT2	Missense_Mutation	SNP	ENST00000487903.1	hg19	CCDS32011.1																																																																																			.	G|1.000;A|0.000|.	0.000|.	weak|none		0.535	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205		AG	113516825	GC	AG	113516824	3	1	96	1	0	0	0	0	1	0	0	0	1119	1087	38	1	3024	1	ATP11A	13	113516824	Missense_Mutation	DNP	GC	TCGA-B9-4115-01A-01D-1252-08		113516824	1653054	34	6097											
ZFYVE26	23503	hgsc.bcm.edu	37	chr14	68282659	68282659	+	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	cttctgcgaagcagcttcctCttttccaaatggatgattca	9	14	7	11	1	3	1	1	1	2	0	5	3	5	2	2	1	3	2	2	1	2	5			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr14:68282659C>A	ENST00000347230.4	-	2	160	c.22G>T	c.(22-24)Gag>Tag	p.E8*	ZFYVE26_ENST00000555452.1_Nonsense_Mutation_p.E8*	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	8					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)		GCAGCTTCCTCTTTTCCAAAT	0.478																																					p.E8X		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.G22T						PASS	.						30	30	30					14																	68282659		2203	4300	6503	SO:0001587	stop_gained	23503	exon2			CTTCCTCTTTTCC	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.22G>T	chr14.hg19:g.68282659C>A	ENSP00000251119:p.Glu8*	56.0	0.0	.		64.0	24.0	.	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Nonsense_Mutation	SNP	ENST00000347230.4	hg19	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	C	37	6.195059	0.97367	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	.	.	.	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-20.4213	20.2576	0.98430	0.0:1.0:0.0:0.0	.	.	.	.	X	8	.	ENSP00000251119:E8X	E	-	1	0	ZFYVE26	67352412	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.200000	0.72118	2.783000	0.95769	0.655000	0.94253	GAG	.	.	.	none		0.478	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		A	68282659	C	A	68282659	4	1	96	1	0	0	0	0	0	1	0	0	17680	922	32	4	7761	4	ZFYVE26	14	68282659	Nonsense_Mutation	SNP	C	TCGA-B9-4115-01A-01D-1252-08		68282659	39066881	35	6098											
DICER1	23405	hgsc.bcm.edu	37	chr14	95556880	95556880	+	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	ttagctttgaggcttcggagGgctcttcttgctgctgcaga	5	14	13	9	1	2	2	0	1	2	1	3	3	2	3	0	3	4	6	0	3	1	5			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr14:95556880G>T	ENST00000526495.1	-	29	6015	c.5724C>A	c.(5722-5724)gcC>gcA	p.A1908A	DICER1_ENST00000343455.3_Silent_p.A1908A|DICER1_ENST00000541352.1_3'UTR|DICER1_ENST00000527416.2_5'UTR|DICER1_ENST00000393063.1_Silent_p.A1908A|DICER1_ENST00000556045.1_Silent_p.A806A|DICER1_ENST00000527414.1_Silent_p.A1908A			Q9UPY3	DICER_HUMAN	dicer 1, ribonuclease type III	1908	DRBM. {ECO:0000255|PROSITE- ProRule:PRU00266}.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac muscle cell development (GO:0055013)|cerebral cortex development (GO:0021987)|defense response to virus (GO:0051607)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|hair follicle cell proliferation (GO:0071335)|hair follicle morphogenesis (GO:0031069)|inner ear receptor cell development (GO:0060119)|intestinal epithelial cell development (GO:0060576)|lung development (GO:0030324)|mRNA stabilization (GO:0048255)|multicellular organism growth (GO:0035264)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|olfactory bulb interneuron differentiation (GO:0021889)|peripheral nervous system myelin formation (GO:0032290)|positive regulation of gene expression (GO:0010628)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of myelination (GO:0031643)|positive regulation of Schwann cell differentiation (GO:0014040)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|production of siRNA involved in RNA interference (GO:0030422)|regulation of cell cycle (GO:0051726)|regulation of enamel mineralization (GO:0070173)|regulation of neuron differentiation (GO:0045664)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of viral genome replication (GO:0045069)|reproductive structure development (GO:0048608)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|spinal cord motor neuron differentiation (GO:0021522)|spindle assembly (GO:0051225)|spleen development (GO:0048536)|stem cell maintenance (GO:0019827)|targeting of mRNA for destruction involved in RNA interference (GO:0030423)|zygote asymmetric cell division (GO:0010070)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|growth cone (GO:0030426)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|ribonuclease III activity (GO:0004525)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(13)|kidney(3)|large_intestine(10)|lung(33)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	75		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		GGCTTCGGAGGGCTCTTCTTG	0.413			"Mis F, N"		"sex cord-stromal tumour, TGCT, embryonal rhadomyosarcoma"	pleuropulmonary blastoma			Familial Multinodular Goiter ;DICER 1 syndrome																												p.A1908A		Atlas-SNP	.	yes	Rec	yes	Familial Pleuropulmonary Blastoma	14	14q32.13	23405	"dicer 1, ribonuclease type III "		"E, M, O"	.	DICER1	181	.	0			c.C5724A						PASS	.						187	186	187					14																	95556880		2203	4300	6503	SO:0001819	synonymous_variant	23405	exon28	Familial Cancer Database	Adolescent Multinodular Goiter, incl. Multinodular Euthyroid Goiter & Non-Medullary Thyroid Cancer;incl. Pleuropulmonary Blastoma, Familial ; Cystic Nephroma, Familial	TCGGAGGGCTCTT	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.5724C>A	chr14.hg19:g.95556880G>T		468.0	0.0	.		95.0	36.0	.	NM_030621	A7E2D3|B3KRG4|E0AD28|O95943|Q9UQ02	Silent	SNP	ENST00000526495.1	hg19	CCDS9931.1																																																																																			.	.	.	none		0.413	DICER1-004	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387997.1			T	95556880	G	T	95556880	2	4	96	1	0	0	0	0	0	0	0	1	4523	1219	43	4		4	DICER1	14	95556880	Silent	SNP	G	TCGA-B9-4115-01A-01D-1252-08	27274221	95556880	11792660	36	6099											
SIVA1	10572	hgsc.bcm.edu	37	chr14	105222013	105222013	+	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	ggggcccaggcctacctggaCcacgtgtgggatgaaggctg	7	6	17	11	1	0	1	0	1	0	0	0	3	0	3	4	6	1	1	4	6	2	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr14:105222013C>T	ENST00000329967.6	+	2	267	c.165C>T	c.(163-165)gaC>gaT	p.D55D	SIVA1_ENST00000347067.5_Intron	NM_006427.3	NP_006418.2	O15304	SIVA_HUMAN	SIVA1, apoptosis-inducing factor	55	Interaction with BCL2L1 isoform Bcl-x(L) and inhibition of BCL2L1 anti-apoptotic activity.				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)		CCTACCTGGACCACGTGTGGG	0.607																																					p.D55D		Atlas-SNP	.											.	SIVA1	12	.	0			c.C165T						PASS	.						92	88	89					14																	105222013		2203	4300	6503	SO:0001819	synonymous_variant	10572	exon2			CCTGGACCACGTG	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.165C>T	chr14.hg19:g.105222013C>T		228.0	0.0	.		314.0	98.0	.	NM_006427	Q96P98|Q9UPD6	Silent	SNP	ENST00000329967.6	hg19	CCDS9992.1	.	.	.	.	.	.	.	.	.	.	C	3.241	-0.155408	0.06544	.	.	ENSG00000184990	ENST00000556195	.	.	.	4.89	3.01	0.34805	.	.	.	.	.	T	0.55641	0.1933	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50499	-0.8821	4	.	.	.	-28.3879	7.3185	0.26513	0.0:0.783:0.0:0.217	.	.	.	.	I	73	.	.	T	+	2	0	SIVA1	104293058	0.105000	0.21958	0.720000	0.30636	0.302000	0.27658	0.003000	0.13083	1.027000	0.39758	0.462000	0.41574	ACC	.	.	.	none		0.607	SIVA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410541.1	NM_006427		T	105222013	C	T	105222013	2	4	96	1	0	0	0	0	0	0	0	1	14358	506	18	2		2	SIVA1	14	105222013	Silent	SNP	C	TCGA-B9-4115-01A-01D-1252-08	9665133	105222013	2127527	37	6100											
KIAA0430	9665	hgsc.bcm.edu	37	chr16	15716936	15716936	+	Frame_Shift_Del	DEL	A	A	-																															tgctcgaatttgcaatgttgAaagcaagcggggatgctctg																										TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr16:15716936delA	ENST00000396368.3	-	11	2521	c.2315delT	c.(2314-2316)ttcfs	p.F772fs	KIAA0430_ENST00000602337.1_Frame_Shift_Del_p.F769fs|KIAA0430_ENST00000540441.2_Intron|KIAA0430_ENST00000548025.1_Frame_Shift_Del_p.F769fs|KIAA0430_ENST00000344181.3_Frame_Shift_Del_p.F441fs|KIAA0430_ENST00000551742.1_Frame_Shift_Del_p.F772fs	NM_001184998.1|NM_001184999.1|NM_014647.3	NP_001171927.1|NP_001171928.1|NP_055462.2	Q9Y4F3	MARF1_HUMAN	KIAA0430	772					double-strand break repair (GO:0006302)|female meiotic division (GO:0007143)|negative regulation of phosphatase activity (GO:0010923)|oogenesis (GO:0048477)|regulation of gene expression (GO:0010468)	membrane (GO:0016020)|peroxisome (GO:0005777)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(4)|endometrium(8)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(5)|skin(1)	40						TGCAATGTTGAAAGCAAGCGG	0.408																																					p.F772fs		Atlas-INDEL	.											.	KIAA0430	154	.	0			c.2316delC						PASS	.						91	88	89					16																	15716936		1865	4105	5970	SO:0001589	frameshift_variant	9665	exon11			.	AB007890	CCDS10562.2, CCDS53990.1, CCDS55991.1	16p13.11	2013-01-11			ENSG00000166783	ENSG00000166783		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	29562	protein-coding gene	gene with protein product	"limkain b1", "protein phosphatase 1, regulatory subunit 34", "meiosis arrest female 1"	614593				9455477, 10493829, 15932519, 22442484, 23090997	Standard	NM_014647		Approved	LKAP, PPP1R34, Marf1	uc010uzw.2	Q9Y4F3	OTTHUMG00000129884	ENST00000396368.3:c.2315delT	chr16.hg19:g.15716936delA	ENSP00000379654:p.Phe772fs	253.0	0.0	0		195.0	63.0	0.323077	NM_001184998	A8MSK2|B2RNX2|B4DYY9|B7ZMG1|B7ZMG2|F8VV09|Q6P1R6|Q8WYR2|Q9Y4J9	Frame_Shift_Del	DEL	ENST00000396368.3	hg19	CCDS10562.2																																																																																			.	.	.	none		0.408	KIAA0430-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252131.2	NM_014647		-	15716936	A	-	15716936	7	5	96	1	0	1	0	1	0	0	0	0	8184	246	9	0	2981	0	KIAA0430	16	15716936	Frame_Shift_Del	DEL	A	TCGA-B9-4115-01A-01D-1252-08		15716936	74637817	38	6101											
CES8	283848	hgsc.bcm.edu	37	chr16	67038037	67038037	+	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	ggtgtggtgatcccagatgaCcctttggtgctcctgaccca	6	11	12	12	0	0	4	0	3	0	1	2	4	2	4	4	3	1	1	4	3	0	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr16:67038037C>A	ENST00000326686.5	+	9	990	c.990C>A	c.(988-990)gaC>gaA	p.D330E	CES4A_ENST00000535696.1_Missense_Mutation_p.D236E|CES4A_ENST00000398354.1_Missense_Mutation_p.D330E|CES4A_ENST00000338718.4_Missense_Mutation_p.D353E|CES4A_ENST00000540579.1_Missense_Mutation_p.D232E|CES4A_ENST00000540947.2_Missense_Mutation_p.D330E|CES4A_ENST00000541479.1_Missense_Mutation_p.D353E			Q5XG92	EST4A_HUMAN	carboxylesterase 4A	330						extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)			large_intestine(2)|liver(2)|lung(4)|ovary(1)	9						TCCCAGATGACCCTTTGGTGC	0.512																																					p.D330E		Atlas-SNP	.											.	CES4A	24	.	0			c.C990A						PASS	.						232	229	230					16																	67038037		2041	4186	6227	SO:0001583	missense	283848	exon9			AGATGACCCTTTG	AK094783	CCDS42174.1, CCDS42174.2, CCDS54024.1, CCDS54025.1, CCDS42174.3	16q22.1	2011-10-25	2010-10-12	2010-10-12	ENSG00000172824	ENSG00000172824		"Carboxylesterases"	26741	protein-coding gene	gene with protein product			"carboxylesterase 8 (putative)"	CES8		12975309, 17364878, 20931200	Standard	NM_001190201		Approved	FLJ37464	uc010vix.2	Q5XG92		ENST00000326686.5:c.990C>A	chr16.hg19:g.67038037C>A	ENSP00000314145:p.Asp330Glu	284.0	0.0	.		399.0	143.0	.	NM_173815	A8KAJ6|B7Z349|B7Z3L2|B7Z6R3|Q6UX55|Q8N9F4	Missense_Mutation	SNP	ENST00000326686.5	hg19		.	.	.	.	.	.	.	.	.	.	c	1.498	-0.552834	0.03996	.	.	ENSG00000172824	ENST00000540947;ENST00000541479;ENST00000338718;ENST00000398354;ENST00000326686;ENST00000538199;ENST00000540579;ENST00000535696	T;T;T;T;T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24;-0.24;-0.24;-0.24;-0.24	4.63	0.0898	0.14460	Carboxylesterase, type B (1);	0.569501	0.15610	N	0.253409	T	0.52773	0.1755	L	0.41415	1.275	0.09310	N	1	B;B;B;B	0.19331	0.023;0.004;0.02;0.035	B;B;B;B	0.28305	0.022;0.004;0.088;0.021	T	0.45977	-0.9224	10	0.49607	T	0.09	.	4.644	0.12563	0.0:0.4819:0.153:0.3651	.	236;353;330;353	Q5XG92-7;F8WEE9;Q5XG92;F5H5S4	.;.;EST4A_HUMAN;.	E	330;353;353;330;330;293;232;236	ENSP00000444052:D330E;ENSP00000443175:D353E;ENSP00000340714:D353E;ENSP00000381397:D330E;ENSP00000314145:D330E;ENSP00000441103:D293E;ENSP00000441907:D232E;ENSP00000441644:D236E	ENSP00000314145:D330E	D	+	3	2	CES4A	65595538	0.000000	0.05858	0.009000	0.14445	0.083000	0.17756	-0.546000	0.06062	-0.221000	0.09973	0.486000	0.48141	GAC	.	.	.	none		0.512	CES4A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173815		A	67038037	C	A	67038037	3	1	96	1	0	0	0	0	1	0	0	0	3275	506	18	4	1105	4	CES8	16	67038037	Missense_Mutation	SNP	C	TCGA-B9-4115-01A-01D-1252-08	51321101	67038037	23316716	39	6102											
MYST2	11143	hgsc.bcm.edu	37	chr17	47869250	47869250	+	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	ggatctatggtattacagagGaatgcaggcagtagttcaga	13	10	13	5	0	2	2	1	0	1	2	2	4	2	4	0	4	2	5	0	4	5	5			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr17:47869250G>T	ENST00000259021.4	+	2	298	c.18G>T	c.(16-18)agG>agT	p.R6S	KAT7_ENST00000509773.1_Missense_Mutation_p.R6S|FAM117A_ENST00000514018.1_5'Flank|KAT7_ENST00000503935.2_5'UTR|KAT7_ENST00000510819.1_Missense_Mutation_p.R6S|KAT7_ENST00000424009.2_Missense_Mutation_p.R6S|KAT7_ENST00000435742.2_5'UTR|KAT7_ENST00000454930.2_Missense_Mutation_p.R6S	NM_007067.4	NP_008998.1	O95251	KAT7_HUMAN	K(lysine) acetyltransferase 7	6					chromatin organization (GO:0006325)|DNA replication (GO:0006260)|histone H3 acetylation (GO:0043966)|histone H4-K12 acetylation (GO:0043983)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TATTACAGAGGAATGCAGGCA	0.423																																					p.R6S		Atlas-SNP	.											.	.	.	.	0			c.G18T						PASS	.						148	136	140					17																	47869250		2203	4300	6503	SO:0001583	missense	11143	exon2			ACAGAGGAATGCA	AF074606	CCDS11554.1, CCDS56035.1, CCDS56036.1, CCDS56037.1, CCDS56038.1	17q21.32	2013-01-10	2011-07-21	2011-07-21	ENSG00000136504	ENSG00000136504	2.3.1.48	"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing"	17016	protein-coding gene	gene with protein product	"histone acetyltransferase binding to ORC1"	609880	"MYST histone acetyltransferase 2"	MYST2		10438470, 10930412	Standard	NM_001199155		Approved	HBOA, HBO1, ZC2HC7	uc002ipm.3	O95251	OTTHUMG00000161770	ENST00000259021.4:c.18G>T	chr17.hg19:g.47869250G>T	ENSP00000259021:p.Arg6Ser	322.0	0.0	.		434.0	102.0	.	NM_001199158	B3KN74|B4DF85|B4DFB4|B4DFE0|B4DGY4|E7ER15|G5E9K7	Missense_Mutation	SNP	ENST00000259021.4	hg19	CCDS11554.1	.	.	.	.	.	.	.	.	.	.	G	15.49	2.848691	0.51164	.	.	ENSG00000136504	ENST00000259021;ENST00000454930;ENST00000509773;ENST00000510819;ENST00000424009	.	.	.	5.6	2.52	0.30459	.	0.093201	0.64402	D	0.000001	T	0.63189	0.2490	L	0.48642	1.525	0.80722	D	1	D;D;D;B;P	0.54601	0.967;0.967;0.967;0.421;0.557	P;P;P;B;B	0.60789	0.879;0.879;0.879;0.058;0.124	T	0.62144	-0.6916	9	0.87932	D	0	-16.1716	9.2677	0.37652	0.3015:0.0:0.6985:0.0	.	6;6;6;6;6	B4DFE0;B4DFB4;E7ER15;O95251;G5E9K7	.;.;.;KAT7_HUMAN;.	S	6	.	ENSP00000259021:R6S	R	+	3	2	KAT7	45224249	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	1.877000	0.39598	0.295000	0.22570	-0.137000	0.14449	AGG	.	.	.	none		0.423	KAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366032.1	NM_007067		T	47869250	G	T	47869250	3	4	96	1	0	0	0	0	1	0	0	0	10110	1165	41	4	24	4	MYST2	17	47869250	Missense_Mutation	SNP	G	TCGA-B9-4115-01A-01D-1252-08		47869250	33325960	40	6103											
CEP192	55125	hgsc.bcm.edu	37	chr18	13049324	13049324	+	Frame_Shift_Del	DEL	T	T	-																															agaaaacacagcagctattgTttatgttgaaaatggagaga																										TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr18:13049324delT	ENST00000325971.8	+	14	2339	c.746delT	c.(745-747)gttfs	p.V249fs	CEP192_ENST00000506447.1_Frame_Shift_Del_p.V845fs|CEP192_ENST00000430049.2_Frame_Shift_Del_p.V370fs			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	249					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						GCAGCTATTGTTTATGTTGAA	0.383																																					p.V845fs		Atlas-INDEL	.											.	CEP192	340	.	0			c.2533delG						PASS	.						100	95	97					18																	13049324		2203	4300	6503	SO:0001589	frameshift_variant	55125	exon16			.	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.746delT	chr18.hg19:g.13049324delT	ENSP00000317156:p.Val249fs	249.0	0.0	0		61.0	19.0	0.311475	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Frame_Shift_Del	DEL	ENST00000325971.8	hg19																																																																																				.	.	.	none		0.383	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142		-	13049324	T	-	13049324	7	5	96	1	0	1	0	1	0	0	0	0	3253	1725	60	0	2592	0	CEP192	18	13049324	Frame_Shift_Del	DEL	T	TCGA-B9-4115-01A-01D-1252-08		13049324	65027924	41	6104											
COX7A1	1346	hgsc.bcm.edu	37	chr19	36642400	36642402	+	In_Frame_Del	DEL	TGT	TGT	-																															cattgtcactcggtacaggaTgttgtcaacgatgccgccct																								rs375983153		TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr19:36642400_36642402delTGT	ENST00000292907.3	-	3	610_612	c.149_151delACA	c.(148-153)aacatc>atc	p.N50del	COX7A1_ENST00000437291.2_5'UTR	NM_001864.2	NP_001855.1	P24310	CX7A1_HUMAN	cytochrome c oxidase subunit VIIa polypeptide 1 (muscle)	50					generation of precursor metabolites and energy (GO:0006091)|hydrogen ion transmembrane transport (GO:1902600)	integral component of membrane (GO:0016021)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)			endometrium(2)|large_intestine(1)	3	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			CGGTACAGGATGTTGTCAACGAT	0.626																																					p.50_51del		Atlas-INDEL	.											.	COX7A1	9	.	0			c.150_152del						PASS	.																																			SO:0001651	inframe_deletion	1346	exon3			.	BC002757	CCDS12490.1	19q13.1	2011-07-04			ENSG00000161281	ENSG00000161281	1.9.3.1	"Mitochondrial respiratory chain complex / Complex IV"	2287	protein-coding gene	gene with protein product		123995		COX7A		1327965, 2550906	Standard	NM_001864		Approved	COX7AH	uc002odm.1	P24310	OTTHUMG00000048144	ENST00000292907.3:c.149_151delACA	chr19.hg19:g.36642403_36642405delTGT	ENSP00000292907:p.Asn50del	194.0	0.0	0		242.0	64.0	0.264463	NM_001864		In_Frame_Del	DEL	ENST00000292907.3	hg19	CCDS12490.1																																																																																			.	.	.	none		0.626	COX7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109545.2	NM_001864		-	36642402	TGT	-	36642400	7	5	96	1	0	1	0	1	0	0	0	0	3781	1464	51	0	96	0	COX7A1	19	36642400	In_Frame_Del	DEL	TGT	TCGA-B9-4115-01A-01D-1252-08		36642400	22486583	42	6105											
ITPKC	80271	hgsc.bcm.edu	37	chr19	41223385	41223385	+	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	cccaagcaaaagacggagccAgacaggtccagcctccggac	13	2	11	15	2	0	2	0	0	0	2	2	4	2	4	5	3	3	1	5	3	3	0			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr19:41223385A>T	ENST00000263370.2	+	1	378	c.345A>T	c.(343-345)ccA>ccT	p.P115P	ADCK4_ENST00000243583.6_5'Flank|ADCK4_ENST00000450541.1_5'Flank|ADCK4_ENST00000324464.3_5'Flank	NM_025194.2	NP_079470.1	Q96DU7	IP3KC_HUMAN	inositol-trisphosphate 3-kinase C	115					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)			AGACGGAGCCAGACAGGTCCA	0.597																																					p.P115P		Atlas-SNP	.											.	ITPKC	36	.	0			c.A345T						PASS	.						51	58	56					19																	41223385		2202	4300	6502	SO:0001819	synonymous_variant	80271	exon1			GGAGCCAGACAGG	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.345A>T	chr19.hg19:g.41223385A>T		139.0	0.0	.		201.0	65.0	.	NM_025194	Q9UE25|Q9Y475	Silent	SNP	ENST00000263370.2	hg19	CCDS12563.1																																																																																			.	.	.	none		0.597	ITPKC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463104.1	NM_025194		T	41223385	A	T	41223385	2	4	96	1	0	0	0	0	0	0	0	1	7926	175	7	5		5	ITPKC	19	41223385	Silent	SNP	A	TCGA-B9-4115-01A-01D-1252-08	4580985	41223385	17905598	43	6106											
ERF	2077	hgsc.bcm.edu	37	chr19	42752789	42752790	+	In_Frame_Ins	INS	-	-	AAA																															cccacccccttcgaggcgacINSagtcttcactccagcgccgc																										TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr19:42752789_42752790insAAA	ENST00000222329.4	-	4	1631_1632	c.1474_1475insTTT	c.(1474-1476)tgt>tTTTgt	p.491_492insF	ERF_ENST00000595941.1_5'Flank|AC006486.9_ENST00000594664.1_Intron|ERF_ENST00000440177.2_In_Frame_Ins_p.416_417insF	NM_006494.2	NP_006485.2	P50548	ERF_HUMAN	Ets2 repressor factor	491					cell cycle (GO:0007049)|cell differentiation (GO:0030154)|chorio-allantoic fusion (GO:0060710)|ectodermal cell differentiation (GO:0010668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|trophoblast giant cell differentiation (GO:0060707)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	17		Prostate(69;0.00682)				TTCGAGGCGACAGTCTTCACTC	0.698																																					p.C492delinsFC		Atlas-INDEL	.											.	ERF	47	.	0			c.1475_1476insTTT						PASS	.																																			SO:0001652	inframe_insertion	2077	exon4			.	U58535	CCDS12600.1	19q13	2008-07-16				ENSG00000105722			3444	protein-coding gene	gene with protein product	"Ets2 repressor factor"	611888				7588608, 9192842	Standard	XM_005258644		Approved	PE-2, PE2	uc002ote.4	P50548		ENST00000222329.4:c.1474_1475insTTT	chr19.hg19:g.42752789_42752790insAAA	ENSP00000222329:p.Asp491_Cys492insPhe	190.0	0.0	0		249.0	60.0	0.240964	NM_006494	B2RAP1|B7Z4R0|Q59G38|Q9UPI7	In_Frame_Ins	INS	ENST00000222329.4	hg19	CCDS12600.1																																																																																			.	.	.	none		0.698	ERF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463684.1	NM_006494		AAA	42752790	-	AAA	42752789	7	5	96	1	0	1	1	0	0	0	0	0	5223	478	17	0	175	0	ERF	19	42752789	In_Frame_Ins	INS	-	TCGA-B9-4115-01A-01D-1252-08	1529404	42752789	16376194	44	6107											
ALDH16A1	126133	hgsc.bcm.edu	37	chr19	49971767	49971767	+	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	ccgccctggcctacggcaacActgtggtcatggtgcccagt	6	8	12	15	2	1	0	1	0	0	0	1	0	1	0	4	4	3	1	4	4	2	1			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr19:49971767A>T	ENST00000293350.4	+	15	2231	c.2068A>T	c.(2068-2070)Act>Tct	p.T690S	ALDH16A1_ENST00000433981.2_Missense_Mutation_p.T525S|ALDH16A1_ENST00000540132.1_Missense_Mutation_p.T527S|ALDH16A1_ENST00000455361.2_Missense_Mutation_p.T639S|CTD-3148I10.9_ENST00000599536.1_Intron	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	690						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)		CTACGGCAACACTGTGGTCAT	0.687																																					p.T690S		Atlas-SNP	.											.	ALDH16A1	54	.	0			c.A2068T						PASS	.						123	129	127					19																	49971767		2203	4300	6503	SO:0001583	missense	126133	exon15			GGCAACACTGTGG	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.2068A>T	chr19.hg19:g.49971767A>T	ENSP00000293350:p.Thr690Ser	345.0	0.0	.		542.0	197.0	.	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Missense_Mutation	SNP	ENST00000293350.4	hg19	CCDS12766.1	.	.	.	.	.	.	.	.	.	.	A	3.550	-0.091783	0.07053	.	.	ENSG00000161618	ENST00000293350;ENST00000455361;ENST00000540132;ENST00000433981	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	4.37	-5.8	0.02347	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.561034	0.18181	N	0.149153	T	0.53899	0.1825	N	0.20845	0.615	0.09310	N	1	B;B;B	0.13145	0.003;0.007;0.004	B;B;B	0.17098	0.007;0.012;0.017	T	0.46748	-0.9169	10	0.13108	T	0.6	-7.5334	9.9685	0.41738	0.1664:0.0:0.7061:0.1275	.	527;639;690	F5H4B6;B4DLQ1;Q8IZ83	.;.;A16A1_HUMAN	S	690;639;527;525	ENSP00000293350:T690S;ENSP00000410142:T639S;ENSP00000445088:T527S;ENSP00000398675:T525S	ENSP00000293350:T690S	T	+	1	0	ALDH16A1	54663579	0.000000	0.05858	0.003000	0.11579	0.071000	0.16799	-0.795000	0.04580	-0.972000	0.03559	0.397000	0.26171	ACT	.	.	.	none		0.687	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329		T	49971767	A	T	49971767	3	4	96	1	0	0	0	0	1	0	0	0	488	159	6	5	2126	5	ALDH16A1	19	49971767	Missense_Mutation	SNP	A	TCGA-B9-4115-01A-01D-1252-08	7218978	49971767	9157216	45	6108											
ZNF134	7693	hgsc.bcm.edu	37	chr19	58131703	58131703	+	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	gatgaacaccagggtacacaCcatggactgaaacttcacac	15	6	8	12	0	1	2	1	2	0	0	1	4	1	3	2	2	3	1	2	2	3	2			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chr19:58131703C>A	ENST00000396161.5	+	3	526	c.216C>A	c.(214-216)caC>caA	p.H72Q	ZNF134_ENST00000597975.1_3'UTR	NM_003435.3	NP_003426.3	P52741	ZN134_HUMAN	zinc finger protein 134	72					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(3)|prostate(1)	11		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		AGGGTACACACCATGGACTGA	0.493																																					p.H72Q		Atlas-SNP	.											.	ZNF134	34	.	0			c.C216A						PASS	.						108	104	105					19																	58131703		2041	4225	6266	SO:0001583	missense	7693	exon3			TACACACCATGGA	U09412	CCDS42638.1	19q13.4	2013-01-08	2006-06-13			ENSG00000213762		"Zinc fingers, C2H2-type"	12918	protein-coding gene	gene with protein product		604076	"zinc finger protein 134 (clone pHZ-15)"			7557990	Standard	NM_003435		Approved	pHZ-15	uc002qpn.2	P52741		ENST00000396161.5:c.216C>A	chr19.hg19:g.58131703C>A	ENSP00000379464:p.His72Gln	293.0	1.0	.		82.0	29.0	.	NM_003435	Q9Y4B2	Missense_Mutation	SNP	ENST00000396161.5	hg19	CCDS42638.1	.	.	.	.	.	.	.	.	.	.	C	13.72	2.322492	0.41096	.	.	ENSG00000213762	ENST00000418193;ENST00000396161	T	0.66995	-0.24	4.05	0.456	0.16655	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.63153	0.2487	M	0.81682	2.555	0.09310	N	1	B	0.30211	0.273	B	0.28638	0.092	T	0.58719	-0.7587	9	0.87932	D	0	.	5.1641	0.15077	0.163:0.6473:0.0:0.1897	.	72	P52741	ZN134_HUMAN	Q	139;72	ENSP00000379464:H72Q	ENSP00000379464:H72Q	H	+	3	2	ZNF134	62823515	0.000000	0.05858	0.000000	0.03702	0.967000	0.64934	0.316000	0.19469	0.092000	0.17331	0.655000	0.94253	CAC	.	.	.	none		0.493	ZNF134-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466808.1	NM_003435		A	58131703	C	A	58131703	3	1	96	1	0	0	0	0	1	0	0	0	17736	506	18	4	222	4	ZNF134	19	58131703	Missense_Mutation	SNP	C	TCGA-B9-4115-01A-01D-1252-08	8159936	58131703	997280	46	6109											
HTATSF1	27336	hgsc.bcm.edu	37	chrX	135594033	135594033	+	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	tgagaagttgtttgatgaggAggaagattccagtgagaagt	13	11	15	2	0	0	5	0	4	0	3	1	9	1	7	1	2	0	2	1	2	3	3			TCGA-B9-4115-01A-01D-1252-08	TCGA-B9-4115-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c21a098-a845-4933-9153-f44ea58bb752	50da5c23-8dd6-49bd-8316-9d1438d89ee8	g.chrX:135594033A>T	ENST00000218364.4	+	9	2303	c.2129A>T	c.(2128-2130)gAg>gTg	p.E710V	HTATSF1_ENST00000535601.1_Missense_Mutation_p.E710V	NM_014500.4	NP_055315.2	O43719	HTSF1_HUMAN	HIV-1 Tat specific factor 1	710	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)					TTTGATGAGGAGGAAGATTCC	0.458																																					p.E710V		Atlas-SNP	.											.	HTATSF1	66	.	0			c.A2129T						PASS	.						221	193	203					X																	135594033		2203	4300	6503	SO:0001583	missense	27336	exon10			ATGAGGAGGAAGA	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.2129A>T	chrX.hg19:g.135594033A>T	ENSP00000218364:p.Glu710Val	131.0	1.0	.		17.0	14.0	.	NM_001163280	D3DWG9|Q59G06|Q99730	Missense_Mutation	SNP	ENST00000218364.4	hg19	CCDS14657.1	.	.	.	.	.	.	.	.	.	.	A	9.409	1.080079	0.20309	.	.	ENSG00000102241	ENST00000535601;ENST00000218364;ENST00000415377	T;T	0.34667	1.35;1.35	2.64	2.64	0.31445	.	.	.	.	.	T	0.21227	0.0511	N	0.14661	0.345	0.09310	N	1	P	0.42757	0.789	B	0.38655	0.278	T	0.08006	-1.0743	9	0.87932	D	0	-2.0207	8.2917	0.31960	1.0:0.0:0.0:0.0	.	710	O43719	HTSF1_HUMAN	V	710;710;676	ENSP00000442699:E710V;ENSP00000218364:E710V	ENSP00000218364:E710V	E	+	2	0	HTATSF1	135421699	0.836000	0.29430	0.004000	0.12327	0.938000	0.57974	2.165000	0.42396	1.296000	0.44742	0.235000	0.17854	GAG	.	.	.	none		0.458	HTATSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058497.1	NM_014500		T	135594033	A	T	135594033	3	4	96	1	0	0	0	0	1	0	0	0	7440	304	11	5	2163	5	HTATSF1	23	135594033	Missense_Mutation	SNP	A	TCGA-B9-4115-01A-01D-1252-08		135594033	19676527	47	6110											
CA6	765	hgsc.bcm.edu	37	chr1	9009376	9009376	+	Frame_Shift_Del	DEL	A	A	-																															ctaccccgcctgtgggggccAgagacagtcgcctatcaacc																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr1:9009376delA	ENST00000377443.2	+	2	138	c.134delA	c.(133-135)cagfs	p.Q45fs	CA6_ENST00000377436.3_Frame_Shift_Del_p.Q45fs|CA6_ENST00000377442.2_Intron|CA6_ENST00000480186.3_Frame_Shift_Del_p.Q45fs|CA6_ENST00000476083.1_Intron	NM_001215.3	NP_001206.2	P23280	CAH6_HUMAN	carbonic anhydrase VI	45					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)	TGTGGGGGCCAGAGACAGTCG	0.602																																					p.Q45fs		Atlas-INDEL	.											.	CA6	47	.	0			c.133delC						PASS	.						44	42	43					1																	9009376		2203	4300	6503	SO:0001589	frameshift_variant	765	exon2			.	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.134delA	chr1.hg19:g.9009376delA	ENSP00000366662:p.Gln45fs	80.0	0.0	0		153.0	59.0	0.385621	NM_001270500	E7EMQ1|Q5FBW3|Q5FC00|Q96QX8|Q9UF03	Frame_Shift_Del	DEL	ENST00000377443.2	hg19	CCDS30578.1																																																																																			.	.	.	none		0.602	CA6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000004911.1			-	9009376	A	-	9009376	7	5	97	1	0	1	0	1	0	0	0	0	2523	188	7	0	140	0	CA6	1	9009376	Frame_Shift_Del	DEL	A	TCGA-B9-4116-01A-01D-1252-08		9009376	240241245	1	6111											
CLCN6	1185	hgsc.bcm.edu	37	chr1	11888206	11888206	+	Missense_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	cttcaccctcaacttcttccGttctgggattcagtttggaa	7	15	7	12	1	5	0	3	0	2	0	6	2	6	2	2	2	1	2	2	2	2	6			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr1:11888206G>A	ENST00000346436.6	+	11	936	c.884G>A	c.(883-885)cGt>cAt	p.R295H	CLCN6_ENST00000376492.3_3'UTR|CLCN6_ENST00000376496.3_Missense_Mutation_p.R295H|CLCN6_ENST00000376487.3_Missense_Mutation_p.R273H|CLCN6_ENST00000312413.6_Missense_Mutation_p.R295H	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6	295					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)		AACTTCTTCCGTTCTGGGATT	0.483																																					p.R295H		Atlas-SNP	.											.	CLCN6	77	.	0			c.G884A						PASS	.						224	231	229					1																	11888206		2203	4300	6503	SO:0001583	missense	1185	exon11			TCTTCCGTTCTGG	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.884G>A	chr1.hg19:g.11888206G>A	ENSP00000234488:p.Arg295His	636.0	0.0	.		990.0	54.0	.	NM_001286	A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Missense_Mutation	SNP	ENST00000346436.6	hg19	CCDS138.1	.	.	.	.	.	.	.	.	.	.	G	35	5.415466	0.96092	.	.	ENSG00000011021	ENST00000312413;ENST00000346436;ENST00000376487;ENST00000376496;ENST00000376492	D;D;D;D	0.94232	-3.36;-3.38;-3.38;-3.38	5.06	5.06	0.68205	Chloride channel, core (2);	0.048615	0.85682	D	0.000000	D	0.96046	0.8712	.	.	.	0.80722	D	1	D;D;D	0.76494	0.989;0.999;0.992	P;P;P	0.60117	0.459;0.869;0.594	D	0.96294	0.9216	9	0.66056	D	0.02	-10.0688	17.6173	0.88071	0.0:0.0:1.0:0.0	.	273;295;295	F8W9R3;P51797-3;P51797	.;.;CLCN6_HUMAN	H	295;295;273;295;295	ENSP00000308367:R295H;ENSP00000234488:R295H;ENSP00000365670:R273H;ENSP00000365679:R295H	ENSP00000308367:R295H	R	+	2	0	CLCN6	11810793	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.263000	0.95617	2.625000	0.88918	0.655000	0.94253	CGT	.	.	.	none		0.483	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	NM_001286		A	11888206	G	A	11888206	3	1	97	1	0	0	0	0	1	0	0	0	3469	1145	40	1	936	1	CLCN6	1	11888206	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	2878830	11888206	237362415	2	6112											
FGR	2268	hgsc.bcm.edu	37	chr1	27943508	27943508	+	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	cccagtcccggatggacaggGagtaggcacctgtggagagg	9	5	17	10	1	0	1	0	0	0	1	1	5	1	4	3	6	0	2	3	6	1	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr1:27943508G>A	ENST00000374005.3	-	7	830	c.542C>T	c.(541-543)tCc>tTc	p.S181F	FGR_ENST00000374004.1_Missense_Mutation_p.S181F|FGR_ENST00000399173.1_Missense_Mutation_p.S181F|FGR_ENST00000545953.1_Missense_Mutation_p.S115F	NM_005248.2	NP_005239.1	P09769	FGR_HUMAN	FGR proto-oncogene, Src family tyrosine kinase	181	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				blood coagulation (GO:0007596)|defense response to Gram-positive bacterium (GO:0050830)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of innate immune response (GO:0045088)|regulation of phagocytosis (GO:0050764)|regulation of protein kinase activity (GO:0045859)|response to virus (GO:0009615)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|Fc-gamma receptor I complex binding (GO:0034988)|immunoglobulin receptor binding (GO:0034987)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphotyrosine binding (GO:0001784)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(4)	16		all_lung(284;2.05e-05)|Colorectal(325;3.46e-05)|Lung NSC(340;3.67e-05)|Renal(390;0.00121)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00244)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		GATGGACAGGGAGTAGGCACC	0.567																																					p.S181F		Atlas-SNP	.											.	FGR	39	.	0			c.C542T						PASS	.						103	96	99					1																	27943508		2203	4300	6503	SO:0001583	missense	2268	exon7			GACAGGGAGTAGG	BC064382	CCDS305.1	1p36.2-p36.1	2014-06-25	2014-06-25		ENSG00000000938	ENSG00000000938		"SH2 domain containing"	3697	protein-coding gene	gene with protein product		164940	"Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog", "v-fgr feline Gardner-Rasheed sarcoma viral oncogene homolog", "feline Gardner-Rasheed sarcoma viral oncogene homolog"	SRC2		3922831	Standard	NM_001042729		Approved	c-fgr, p55c-fgr	uc001bom.3	P09769	OTTHUMG00000003516	ENST00000374005.3:c.542C>T	chr1.hg19:g.27943508G>A	ENSP00000363117:p.Ser181Phe	183.0	0.0	.		225.0	128.0	.	NM_001042729	D3DPL7|Q9UIQ3	Missense_Mutation	SNP	ENST00000374005.3	hg19	CCDS305.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.328135	0.81690	.	.	ENSG00000000938	ENST00000374005;ENST00000545953;ENST00000399173;ENST00000374004;ENST00000374003;ENST00000457296	D;D;D;D;D;D	0.89552	-2.53;-2.53;-2.53;-2.53;-2.53;-2.53	4.38	4.38	0.52667	SH2 motif (5);	0.000000	0.56097	D	0.000031	D	0.95079	0.8406	H	0.98199	4.17	0.50813	D	0.999899	D	0.57571	0.98	P	0.50754	0.649	D	0.97122	0.9812	10	0.87932	D	0	.	16.3789	0.83431	0.0:0.0:1.0:0.0	.	181	P09769	FGR_HUMAN	F	181;115;181;181;181;181	ENSP00000363117:S181F;ENSP00000445302:S115F;ENSP00000382126:S181F;ENSP00000363116:S181F;ENSP00000363115:S181F;ENSP00000407670:S181F	ENSP00000363115:S181F	S	-	2	0	FGR	27816095	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	5.670000	0.68088	2.348000	0.79779	0.491000	0.48974	TCC	.	.	.	none		0.567	FGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009772.1	NM_005248		A	27943508	G	A	27943508	3	1	97	1	0	0	0	0	1	0	0	0	5881	1174	41	2	1075	2	FGR	1	27943508	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	16055302	27943508	221307113	3	6113											
PABPC4	8761	hgsc.bcm.edu	37	chr1	40038242	40038242	+	Frame_Shift_Del	DEL	G	G	-																															atcacatcaaagttcatggtGtccaaagcccgctcagctgt																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr1:40038242delG	ENST00000372857.3	-	2	1002	c.210delC	c.(208-210)gacfs	p.D70fs	PABPC4_ENST00000372862.3_Frame_Shift_Del_p.D70fs|RP11-69E11.8_ENST00000415255.1_RNA|PABPC4_ENST00000529216.1_5'Flank|PABPC4_ENST00000372858.3_Frame_Shift_Del_p.D70fs|PABPC4_ENST00000372856.3_Frame_Shift_Del_p.D70fs	NM_003819.3	NP_003810.1	Q13310	PABP4_HUMAN	poly(A) binding protein, cytoplasmic 4 (inducible form)	70	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				blood coagulation (GO:0007596)|RNA catabolic process (GO:0006401)|RNA processing (GO:0006396)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|prostate(1)|skin(3)	21	Lung NSC(20;1.55e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.89e-18)|Epithelial(16;6.17e-17)|all cancers(16;1.18e-15)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			AGTTCATGGTGTCCAAAGCCC	0.468																																					p.T71fs		Atlas-INDEL	.											.	PABPC4	56	.	0			c.211delA						PASS	.						83	77	79					1																	40038242		2203	4300	6503	SO:0001589	frameshift_variant	8761	exon2			.	U33818	CCDS438.1, CCDS44114.1, CCDS44115.1	1p34.2	2013-02-12	2001-11-28		ENSG00000090621	ENSG00000090621		"RNA binding motif (RRM) containing"	8557	protein-coding gene	gene with protein product		603407	"poly(A)-binding protein, cytoplasmic 4 (inducible form)"			10543404	Standard	NM_001135653		Approved	iPABP, APP-1	uc001cdl.2	Q13310	OTTHUMG00000009097	ENST00000372857.3:c.210delC	chr1.hg19:g.40038242delG	ENSP00000361948:p.Asp70fs	179.0	0.0	0		117.0	34.0	0.290598	NM_001135653	B1ANQ8|Q4VC03|Q6P0N3	Frame_Shift_Del	DEL	ENST00000372857.3	hg19	CCDS438.1																																																																																			.	.	.	none		0.468	PABPC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025220.1	NM_001135653		-	40038242	G	-	40038242	7	5	97	1	0	1	0	1	0	0	0	0	11373	1368	48	0	1828	0	PABPC4	1	40038242	Frame_Shift_Del	DEL	G	TCGA-B9-4116-01A-01D-1252-08	12094734	40038242	209212379	4	6114	67	2									
PABPC4	8761	hgsc.bcm.edu	37	chr1	40038244	40038244	+	Missense_Mutation	SNP	C	C	A																															cacatcaaagttcatggtgtCcaaagcccgctcagctgtaa																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr1:40038244C>A	ENST00000372857.3	-	2	1000	c.208G>T	c.(208-210)Gac>Tac	p.D70Y	PABPC4_ENST00000372862.3_Missense_Mutation_p.D70Y|RP11-69E11.8_ENST00000415255.1_RNA|PABPC4_ENST00000529216.1_5'Flank|PABPC4_ENST00000372858.3_Missense_Mutation_p.D70Y|PABPC4_ENST00000372856.3_Missense_Mutation_p.D70Y	NM_003819.3	NP_003810.1	Q13310	PABP4_HUMAN	poly(A) binding protein, cytoplasmic 4 (inducible form)	70	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				blood coagulation (GO:0007596)|RNA catabolic process (GO:0006401)|RNA processing (GO:0006396)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|prostate(1)|skin(3)	21	Lung NSC(20;1.55e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.89e-18)|Epithelial(16;6.17e-17)|all cancers(16;1.18e-15)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			TTCATGGTGTCCAAAGCCCGC	0.463																																					p.D70Y		Atlas-SNP	.											.	PABPC4	56	.	0			c.G208T						PASS	.						81	75	77					1																	40038244		2203	4300	6503	SO:0001583	missense	8761	exon2			TGGTGTCCAAAGC	U33818	CCDS438.1, CCDS44114.1, CCDS44115.1	1p34.2	2013-02-12	2001-11-28		ENSG00000090621	ENSG00000090621		"RNA binding motif (RRM) containing"	8557	protein-coding gene	gene with protein product		603407	"poly(A)-binding protein, cytoplasmic 4 (inducible form)"			10543404	Standard	NM_001135653		Approved	iPABP, APP-1	uc001cdl.2	Q13310	OTTHUMG00000009097	ENST00000372857.3:c.208G>T	chr1.hg19:g.40038244C>A	ENSP00000361948:p.Asp70Tyr	177.0	0.0	.		118.0	35.0	.	NM_001135653	B1ANQ8|Q4VC03|Q6P0N3	Missense_Mutation	SNP	ENST00000372857.3	hg19	CCDS438.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.994504	0.93167	.	.	ENSG00000090621	ENST00000372862;ENST00000372858;ENST00000372857;ENST00000372856;ENST00000451091	T;T;T;T;T	0.18016	2.24;2.24;2.24;2.24;2.24	5.69	5.69	0.88448	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.38692	0.1050	L	0.46157	1.445	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.998	D;D;D	0.76575	0.964;0.988;0.924	T	0.05649	-1.0872	10	0.87932	D	0	.	19.8057	0.96531	0.0:1.0:0.0:0.0	.	70;70;70	Q13310;Q13310-2;Q4VC03	PABP4_HUMAN;.;.	Y	70	ENSP00000361953:D70Y;ENSP00000361949:D70Y;ENSP00000361948:D70Y;ENSP00000361947:D70Y;ENSP00000406675:D70Y	ENSP00000361947:D70Y	D	-	1	0	PABPC4	39810831	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.705000	0.84606	2.682000	0.91365	0.655000	0.94253	GAC	.	.	.	none		0.463	PABPC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025220.1	NM_001135653		A	40038244	C	A	40038244	3	1	97	1	0	0	0	0	1	0	0	0	11373	855	30	4	1830	4	PABPC4	1	40038244	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08	2	40038244	209212377	5	6115	67	2									
CACNA1S	779	hgsc.bcm.edu	37	chr1	201039482	201039482	+	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	cagctgcagctcagccagggGacgtggtcgggggctcagcg	6	5	18	12	3	2	0	2	0	0	0	3	1	2	1	1	5	5	4	1	5	0	0			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr1:201039482G>A	ENST00000362061.3	-	17	2504	c.2278C>T	c.(2278-2280)Ccc>Tcc	p.P760S	CACNA1S_ENST00000367338.3_Missense_Mutation_p.P760S	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	760					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)	TCAGCCAGGGGACGTGGTCGG	0.587																																					p.P760S		Atlas-SNP	.											.	CACNA1S	249	.	0			c.C2278T						PASS	.						70	75	73					1																	201039482		2203	4300	6503	SO:0001583	missense	779	exon17			CCAGGGGACGTGG	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.2278C>T	chr1.hg19:g.201039482G>A	ENSP00000355192:p.Pro760Ser	250.0	0.0	.		385.0	121.0	.	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	hg19	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	G	16.37	3.105070	0.56291	.	.	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.95821	-3.82;-3.73	4.18	4.18	0.49190	.	0.000000	0.85682	D	0.000000	D	0.97492	0.9179	M	0.79805	2.47	0.58432	D	0.999995	D	0.89917	1.0	D	0.91635	0.999	D	0.97283	0.9919	10	0.37606	T	0.19	.	16.8708	0.86040	0.0:0.0:1.0:0.0	.	760	Q13698	CAC1S_HUMAN	S	760	ENSP00000355192:P760S;ENSP00000356307:P760S	ENSP00000355192:P760S	P	-	1	0	CACNA1S	199306105	1.000000	0.71417	0.292000	0.24919	0.289000	0.27227	7.945000	0.87732	2.032000	0.59987	0.643000	0.83706	CCC	.	.	.	none		0.587	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		A	201039482	G	A	201039482	3	1	97	1	0	0	0	0	1	0	0	0	2549	1174	41	2	3455	2	CACNA1S	1	201039482	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	161001238	201039482	48211139	6	6116											
MYCN	4613	hgsc.bcm.edu	37	chr2	16086058	16086058	+	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	gggaccacgtgccggagttgGtaaagaatgagaaggccgcc	11	5	16	9	3	0	2	0	1	0	2	0	5	0	4	4	4	1	2	4	4	4	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr2:16086058G>C	ENST00000281043.3	+	3	1531	c.1234G>C	c.(1234-1236)Gta>Cta	p.V412L		NM_005378.4	NP_005369.2	P04198	MYCN_HUMAN	v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog	412	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				branching morphogenesis of an epithelial tube (GO:0048754)|cartilage condensation (GO:0001502)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|lung development (GO:0030324)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|positive regulation of cell death (GO:0010942)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin (GO:0000785)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	31	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)			GCCGGAGTTGGTAAAGAATGA	0.572			A		neuroblastoma																																p.V412L		Atlas-SNP	.		Dom	yes		2	2p24.1	4613	"v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)"		O	.	MYCN	63	.	0			c.G1234C						PASS	.						90	100	97					2																	16086058		2203	4300	6503	SO:0001583	missense	4613	exon3			GAGTTGGTAAAGA	BC002712	CCDS1687.1	2p24.3	2013-08-14	2013-07-09		ENSG00000134323	ENSG00000134323		"Basic helix-loop-helix proteins"	7559	protein-coding gene	gene with protein product		164840		NMYC			Standard	XM_006711886		Approved	bHLHe37, N-myc, MYCNOT	uc002rci.3	P04198	OTTHUMG00000039579	ENST00000281043.3:c.1234G>C	chr2.hg19:g.16086058G>C	ENSP00000281043:p.Val412Leu	304.0	0.0	.		496.0	163.0	.	NM_005378	Q53XS5|Q6LDT9	Missense_Mutation	SNP	ENST00000281043.3	hg19	CCDS1687.1	.	.	.	.	.	.	.	.	.	.	G	15.87	2.959315	0.53400	.	.	ENSG00000134323	ENST00000281043;ENST00000426211	D	0.97976	-4.64	5.14	4.26	0.50523	Helix-loop-helix DNA-binding (5);	0.515918	0.19319	N	0.117200	D	0.94535	0.8240	L	0.27053	0.805	0.39651	D	0.970461	P	0.40144	0.704	B	0.40864	0.342	D	0.93971	0.7249	10	0.56958	D	0.05	-13.1384	10.2421	0.43319	0.1524:0.0:0.8476:0.0	.	412	P04198	MYCN_HUMAN	L	412;330	ENSP00000281043:V412L	ENSP00000281043:V412L	V	+	1	0	MYCN	16003509	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	4.154000	0.58125	1.331000	0.45412	-0.192000	0.12808	GTA	.	.	.	none		0.572	MYCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095469.2	NM_005378		C	16086058	G	C	16086058	3	2	97	1	0	0	0	0	1	0	0	0	10028	1261	44	4	1240	4	MYCN	2	16086058	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08		16086058	227113315	7	6117											
LCLAT1	253558	hgsc.bcm.edu	37	chr2	30863165	30863173	+	In_Frame_Del	DEL	GAAGAGAAA	GAAGAGAAA	-																															tctggtgccacaaacggtggGaagagaaagaagagaggctg																								rs200693287|rs150085223	byFrequency	TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	GAAGAGAAA	GAAGAGAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr2:30863165_30863173delGAAGAGAAA	ENST00000309052.4	+	7	1134_1142	c.925_933delGAAGAGAAA	c.(925-933)gaagagaaadel	p.EEK309del	LCLAT1_ENST00000540623.1_In_Frame_Del_p.EEK271del|LCLAT1_ENST00000491680.2_3'UTR|LCLAT1_ENST00000379509.3_In_Frame_Del_p.EEK271del	NM_182551.3	NP_872357.2	Q6UWP7	LCLT1_HUMAN	lysocardiolipin acyltransferase 1	309					cardiolipin acyl-chain remodeling (GO:0035965)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|multicellular organismal development (GO:0007275)|phosphatidic acid biosynthetic process (GO:0006654)|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)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)	19						CAAACGGTGGGAAGAGAAAGAAGAGAGGC	0.498																																					p.308_311del		Atlas-INDEL	.											.	LCLAT1	51	.	0			c.924_932del						PASS	.																																			SO:0001651	inframe_deletion	253558	exon7			.	AK095284	CCDS1772.1, CCDS42670.1	2p23.1	2008-12-15	2008-12-15	2008-12-15	ENSG00000172954	ENSG00000172954			26756	protein-coding gene	gene with protein product		614241	"lysocardiolipin acyltransferase"	LYCAT		18931347, 15152008, 16620771, 17675553	Standard	NM_001002257		Approved	FLJ37965, ALCAT1, AGPAT8	uc002rnl.3	Q6UWP7	OTTHUMG00000099349	ENST00000309052.4:c.925_933delGAAGAGAAA	chr2.hg19:g.30863165_30863173delGAAGAGAAA	ENSP00000310551:p.Glu309_Lys311del	220.0	0.0	0		186.0	23.0	0.123656	NM_182551	A6H8Z7|Q8N1Q7	In_Frame_Del	DEL	ENST00000309052.4	hg19	CCDS1772.1																																																																																			.	.	.	none		0.498	LCLAT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000216780.1	NM_182551		-	30863173	GAAGAGAAA	-	30863165	7	5	97	1	0	1	0	1	0	0	0	0	8684	1175	41	0	947	0	LCLAT1	2	30863165	In_Frame_Del	DEL	GAAGAGAAA	TCGA-B9-4116-01A-01D-1252-08	14777107	30863165	212336208	8	6118											
MAT2A	4144	hgsc.bcm.edu	37	chr2	85769094	85769097	+	Splice_Site	DEL	AAGT	AAGT	-																															acgccctgattctaaaactcAagtaagtgatgatcataaag																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	AAGT	AAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr2:85769094_85769097delAAGT	ENST00000306434.3	+	5	671_672	c.548_549delAAGT	c.(547-549)caa>c	p.Q183fs	MAT2A_ENST00000490878.1_3'UTR|MAT2A_ENST00000409017.1_Splice_Site_p.Q120fs	NM_005911.5	NP_005902.1	P31153	METK2_HUMAN	methionine adenosyltransferase II, alpha	183					cellular nitrogen compound metabolic process (GO:0034641)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|methionine adenosyltransferase complex (GO:0048269)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methionine adenosyltransferase activity (GO:0004478)			breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	9					L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	TCTAAAACTCAAGTAAGTGATGAT	0.382																																					p.183_183del		Atlas-INDEL	.											.	MAT2A	23	.	0			c.547_549del						PASS	.																																			SO:0001630	splice_region_variant	4144	exon5			.		CCDS1977.1	2p11.2	2008-06-03			ENSG00000168906	ENSG00000168906			6904	protein-coding gene	gene with protein product		601468				1426236, 9703951	Standard	NM_005911		Approved	SAMS2, MATA2, MATII	uc002spr.3	P31153	OTTHUMG00000130174	ENST00000306434.3:c.549+1AAGT>-	chr2.hg19:g.85769098_85769101delAAGT		153.0	0.0	0		52.0	13.0	0.25	NM_005911	A8K511|B4DN45|D6W5L1|Q53SP5	In_Frame_Del	DEL	ENST00000306434.3	hg19	CCDS1977.1																																																																																			.	.	.	none		0.382	MAT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252491.2	NM_005911	Frame_Shift_Del	-	85769097	AAGT	-	85769094	8	5	97	1	0	1	0	1	0	0	1	0	9337	144	5	0	566	0	MAT2A	2	85769094	Splice_Site	DEL	AAGT	TCGA-B9-4116-01A-01D-1252-08	54905929	85769094	157430279	9	6119											
FAM128A	653784	hgsc.bcm.edu	37	chr2	132249519	132249520	+	Frame_Shift_Ins	INS	-	-	A																															ggggctcgctcgctagcctcINStgcccggcacacatggactt																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr2:132249519_132249520insA	ENST00000309451.6	-	2	293_294	c.248_249insT	c.(247-249)cagfs	p.Q83fs	AC093838.4_ENST00000438378.2_RNA|MZT2A_ENST00000410036.2_5'UTR|MIR4784_ENST00000579560.1_RNA	NM_001085365.1	NP_001078834.1	Q6P582	MZT2A_HUMAN	mitotic spindle organizing protein 2A	83						centrosome (GO:0005813)|gamma-tubulin ring complex (GO:0008274)|spindle (GO:0005819)				breast(1)|lung(1)	2						TCGCTAGCCTCTGCCCGGCACA	0.703																																					p.Q83fs		Atlas-INDEL	.											.	MZT2A	6	.	0			c.249_250insT						PASS	.																																			SO:0001589	frameshift_variant	653784	exon2			.	BC018206	CCDS42758.1	2q21.1	2013-10-11	2010-07-22	2010-07-22	ENSG00000173272	ENSG00000173272			33187	protein-coding gene	gene with protein product	"mitotic-spindle organizing protein associated with a ring of gamma-tubulin 2A"	613449	"family with sequence similarity 128, member A"	FAM128A		20360068	Standard	NM_001085365		Approved	MOZART2A	uc002tsw.4	Q6P582	OTTHUMG00000153606	ENST00000309451.6:c.248_249insT	chr2.hg19:g.132249519_132249520insA	ENSP00000311500:p.Gln83fs	38.0	0.0	0		49.0	17.0	0.346939	NM_001085365	Q3SWV8|Q8WVB2	Frame_Shift_Ins	INS	ENST00000309451.6	hg19	CCDS42758.1																																																																																			.	.	.	none		0.703	MZT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331811.2			A	132249520	-	A	132249519	7	5	97	1	0	1	1	0	0	0	0	0	5438	912	32	0	235	0	FAM128A	2	132249519	Frame_Shift_Ins	INS	-	TCGA-B9-4116-01A-01D-1252-08	46480425	132249519	110949854	10	6120											
C2orf80	389073	hgsc.bcm.edu	37	chr2	209045533	209045533	+	Missense_Mutation	SNP	A	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	taaagacttcctcaatcgggAtactgttctgttaaacaaca	14	12	6	9	1	2	1	1	0	1	1	4	2	3	2	1	1	3	2	1	1	7	5			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr2:209045533A>C	ENST00000341287.4	-	6	497	c.302T>G	c.(301-303)aTc>aGc	p.I101S	C2orf80_ENST00000453017.1_Missense_Mutation_p.I101S|C2orf80_ENST00000451346.1_Missense_Mutation_p.I82S	NM_001099334.2	NP_001092804	Q0P641	CB080_HUMAN	chromosome 2 open reading frame 80	101										endometrium(2)|large_intestine(3)|lung(6)|skin(2)	13						CTCAATCGGGATACTGTTCTG	0.363																																					p.I101S		Atlas-SNP	.											.	C2orf80	19	.	0			c.T302G						PASS	.						98	92	94					2																	209045533		1810	4083	5893	SO:0001583	missense	389073	exon6			ATCGGGATACTGT	AC016697, AW136505, BC035737	CCDS42809.1	2q33.3	2013-10-31			ENSG00000188674	ENSG00000188674			34352	protein-coding gene	gene with protein product	"gonad development associated 1"	615536				22080834, 24055526	Standard	NM_001099334		Approved	LOC389073, GONDA1	uc002vcr.3	Q0P641	OTTHUMG00000154751	ENST00000341287.4:c.302T>G	chr2.hg19:g.209045533A>C	ENSP00000343171:p.Ile101Ser	133.0	0.0	.		86.0	26.0	.	NM_001099334	A6NKZ3	Missense_Mutation	SNP	ENST00000341287.4	hg19	CCDS42809.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.20|14.20	2.465820|2.465820	0.43839|0.43839	.|.	.|.	ENSG00000188674|ENSG00000188674	ENST00000451342;ENST00000341287;ENST00000451346;ENST00000453017;ENST00000423952|ENST00000428015	T;T;T;T;T|.	0.54866|.	1.04;1.51;1.46;0.55;1.02|.	4.67|4.67	3.47|3.47	0.39725|0.39725	.|.	0.384012|.	0.22416|.	N|.	0.060357|.	T|.	0.33381|.	0.0861|.	L|L	0.32530|0.32530	0.975|0.975	0.28843|0.28843	N|N	0.896464|0.896464	B|.	0.29646|.	0.253|.	B|.	0.33799|.	0.17|.	T|.	0.22068|.	-1.0227|.	10|.	0.87932|.	D|.	0|.	-4.0257|-4.0257	7.2927|7.2927	0.26374|0.26374	0.8979:0.0:0.1021:0.0|0.8979:0.0:0.1021:0.0	.|.	101|.	Q0P641|.	CB080_HUMAN|.	S|X	26;101;82;101;14|52	ENSP00000389385:I26S;ENSP00000343171:I101S;ENSP00000405393:I82S;ENSP00000397144:I101S;ENSP00000413016:I14S|.	ENSP00000343171:I101S|.	I|Y	-|-	2|3	0|2	C2orf80|C2orf80	208753778|208753778	1.000000|1.000000	0.71417|0.71417	0.937000|0.937000	0.37676|0.37676	0.941000|0.941000	0.58515|0.58515	2.253000|2.253000	0.43205|0.43205	0.883000|0.883000	0.36040|0.36040	0.455000|0.455000	0.32223|0.32223	ATC|TAT	.	.	.	none		0.363	C2orf80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336931.1	NM_001099334		C	209045533	A	C	209045533	3	2	97	1	0	0	0	0	1	0	0	0	2199	333	12	5	295	5	C2orf80	2	209045533	Missense_Mutation	SNP	A	TCGA-B9-4116-01A-01D-1252-08	76796014	209045533	34153840	11	6121											
MON1A	84315	hgsc.bcm.edu	37	chr3	49946456	49946456	+	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	acacattcccatcaataggtGaggggcgtgagaatgaagag	14	7	13	7	1	1	4	1	3	0	2	2	5	2	4	1	3	0	0	1	3	4	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr3:49946456G>A	ENST00000417270.1	-	7	2376	c.1683C>T	c.(1681-1683)ctC>ctT	p.L561L	MON1A_ENST00000483022.1_5'Flank|CTD-2330K9.3_ENST00000419183.1_Intron|MON1A_ENST00000455683.2_Silent_p.L488L|MON1A_ENST00000296473.3_Silent_p.L650L			Q86VX9	MON1A_HUMAN	MON1 secretory trafficking family member A	553										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)	13				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		ATCAATAGGTGAGGGGCGTGA	0.607																																					p.L650L		Atlas-SNP	.											.	MON1A	41	.	0			c.C1950T						PASS	.						48	43	45					3																	49946456		2203	4300	6503	SO:0001819	synonymous_variant	84315	exon6			ATAGGTGAGGGGC	AK074404	CCDS2808.2, CCDS46830.1	3p21.31	2013-08-21	2013-08-21		ENSG00000164077	ENSG00000164077			28207	protein-coding gene	gene with protein product		611464	"MON1 homolog A (yeast)"			12477932	Standard	NM_032355		Approved	MGC13272, SAND1	uc003cxz.3	Q86VX9	OTTHUMG00000156737	ENST00000417270.1:c.1683C>T	chr3.hg19:g.49946456G>A		68.0	0.0	.		126.0	38.0	.	NM_032355	B2RDQ1|G5E9N1|Q8NAV7|Q9BRF3	Silent	SNP	ENST00000417270.1	hg19																																																																																				.	.	.	none		0.607	MON1A-005	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000345538.2	NM_032355		A	49946456	G	A	49946456	2	1	97	1	0	0	0	0	0	0	0	1	9705	1277	45	2		2	MON1A	3	49946456	Silent	SNP	G	TCGA-B9-4116-01A-01D-1252-08		49946456	148075974	12	6122											
TMF1	7110	hgsc.bcm.edu	37	chr3	69096707	69096707	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcagtgggtataactaaTgtttcatttacttcttcaga	10	17	6	8	0	4	1	3	0	1	1	5	1	5	1	1	1	2	2	1	1	4	8			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr3:69096707T>C	ENST00000398559.2	-	2	1365	c.1149A>G	c.(1147-1149)acA>acG	p.T383T	MIR3136_ENST00000583498.1_RNA|CTD-2013N24.2_ENST00000596732.1_RNA|CTD-2013N24.2_ENST00000598783.1_RNA|CTD-2013N24.2_ENST00000601735.1_RNA|CTD-2013N24.2_ENST00000595925.1_RNA|TMF1_ENST00000543976.1_Silent_p.T383T|CTD-2013N24.2_ENST00000596274.1_RNA|CTD-2013N24.2_ENST00000596523.1_RNA|CTD-2013N24.2_ENST00000597950.1_RNA|CTD-2013N24.2_ENST00000482368.2_RNA			P82094	TMF1_HUMAN	TATA element modulatory factor 1	383					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)		GTATAACTAATGTTTCATTTA	0.383																																					p.T383T		Atlas-SNP	.											.	TMF1	77	.	0			c.A1149G						PASS	.						129	121	123					3																	69096707		1871	4109	5980	SO:0001819	synonymous_variant	7110	exon2			AACTAATGTTTCA		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.1149A>G	chr3.hg19:g.69096707T>C		229.0	0.0	.		106.0	42.0	.	NM_007114	B7ZLJ2|Q17R87|Q59GK0	Silent	SNP	ENST00000398559.2	hg19	CCDS43105.1																																																																																			.	.	.	none		0.383	TMF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352106.1	NM_007114		C	69096707	T	C	69096707	2	2	97	1	0	0	0	0	0	0	0	1	16240	1451	51	3		3	TMF1	3	69096707	Silent	SNP	T	TCGA-B9-4116-01A-01D-1252-08	19150251	69096707	128925723	13	6123											
ZBTB11	27107	hgsc.bcm.edu	37	chr3	101370247	101370247	+	Missense_Mutation	SNP	T	T	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	tcttgaggaccactgctttcTtgttcctgcatgcctgctgt	4	16	9	12	0	2	1	0	1	2	0	3	2	3	2	3	1	4	4	3	1	0	4	rs374150569		TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr3:101370247T>G	ENST00000312938.4	-	11	3505	c.2925A>C	c.(2923-2925)caA>caC	p.Q975H		NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	975					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						CACTGCTTTCTTGTTCCTGCA	0.448																																					p.Q975H		Atlas-SNP	.											.	ZBTB11	77	.	0			c.A2925C						PASS	.						202	171	181					3																	101370247		2203	4300	6503	SO:0001583	missense	27107	exon11			GCTTTCTTGTTCC	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.2925A>C	chr3.hg19:g.101370247T>G	ENSP00000326200:p.Gln975His	421.0	1.0	.		258.0	75.0	.	NM_014415	Q2NKP9	Missense_Mutation	SNP	ENST00000312938.4	hg19	CCDS2943.1	.	.	.	.	.	.	.	.	.	.	T	18.57	3.652999	0.67472	.	.	ENSG00000066422	ENST00000312938	T	0.12672	2.66	5.49	-2.58	0.06228	.	0.060521	0.64402	D	0.000003	T	0.10252	0.0251	N	0.24115	0.695	0.80722	D	1	D	0.62365	0.991	P	0.51999	0.687	T	0.20874	-1.0262	10	0.02654	T	1	-14.7598	12.7952	0.57556	0.0:0.4538:0.0:0.5462	.	975	O95625	ZBT11_HUMAN	H	975	ENSP00000326200:Q975H	ENSP00000326200:Q975H	Q	-	3	2	ZBTB11	102852937	0.931000	0.31567	0.982000	0.44146	0.882000	0.50991	-0.067000	0.11579	-0.456000	0.07043	0.454000	0.30748	CAA	.	.	.	alt		0.448	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415		G	101370247	T	G	101370247	3	3	97	1	0	0	0	0	1	0	0	0	17536	1606	56	5	240	5	ZBTB11	3	101370247	Missense_Mutation	SNP	T	TCGA-B9-4116-01A-01D-1252-08	32273540	101370247	96652183	14	6124											
PVRL3	25945	hgsc.bcm.edu	37	chr3	110830989	110830989	+	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	1	0	0	0	0	0	0	0	0	accataacacagatttcatgGgagaagatacatggcaaaag	18	7	9	7	0	1	3	1	0	0	3	1	4	1	3	1	2	2	1	1	2	5	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr3:110830989G>A	ENST00000485303.1	+	2	548	c.273G>A	c.(271-273)tgG>tgA	p.W91*	PVRL3_ENST00000493615.1_Nonsense_Mutation_p.W68*|PVRL3_ENST00000488016.1_3'UTR|PVRL3_ENST00000319792.3_Nonsense_Mutation_p.W91*	NM_001243286.1|NM_015480.2	NP_001230215.1|NP_056295.1	Q9NQS3	PVRL3_HUMAN	poliovirus receptor-related 3	91	Ig-like V-type.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|fertilization (GO:0009566)|homophilic cell adhesion (GO:0007156)|lens morphogenesis in camera-type eye (GO:0002089)|retina morphogenesis in camera-type eye (GO:0060042)|single organismal cell-cell adhesion (GO:0016337)	apical junction complex (GO:0043296)|cell-cell adherens junction (GO:0005913)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	cell adhesion molecule binding (GO:0050839)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(3)	19						AGATTTCATGGGAGAAGATAC	0.378																																					p.W91X		Atlas-SNP	.											.	PVRL3	78	.	0			c.G273A						PASS	.						79	75	77					3																	110830989		2203	4300	6503	SO:0001587	stop_gained	25945	exon2			TTCATGGGAGAAG	AF282874	CCDS2957.1, CCDS58842.1, CCDS58843.1	3q13	2013-01-29			ENSG00000177707	ENSG00000177707		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17664	protein-coding gene	gene with protein product		607147				11024295	Standard	NM_015480		Approved	nectin-3, PPR3, PVRR3, DKFZP566B0846, CDw113, CD113	uc003dxt.2	Q9NQS3	OTTHUMG00000159239	ENST00000485303.1:c.273G>A	chr3.hg19:g.110830989G>A	ENSP00000418070:p.Trp91*	178.0	0.0	.		13.0	4.0	.	NM_001243286	E9PFR0|Q6NVZ3|Q8NC05|Q8WVU4|Q9BVA9|Q9Y412	Nonsense_Mutation	SNP	ENST00000485303.1	hg19	CCDS2957.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.619371|5.619371	0.96649|0.96649	.|.	.|.	ENSG00000177707|ENSG00000177707	ENST00000486596|ENST00000461477;ENST00000485303;ENST00000319792;ENST00000493615;ENST00000481766	.|.	.|.	.|.	5.84|5.84	5.84|5.84	0.93424|0.93424	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.45875|.	0.1364|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.38001|.	-0.9681|.	3|.	.|0.02654	.|T	.|1	.|.	17.649|17.649	0.88157|0.88157	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	R|X	91|44;91;91;68;76	.|.	.|ENSP00000321514:W91X	G|W	+|+	1|3	0|0	PVRL3|PVRL3	112313679|112313679	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	8.517000|8.517000	0.90555|0.90555	2.760000|2.760000	0.94817|0.94817	0.655000|0.655000	0.94253|0.94253	GGA|TGG	.	.	.	none		0.378	PVRL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354045.1	NM_015480		A	110830989	G	A	110830989	4	1	97	1	0	0	0	0	0	1	0	0	12854	1241	43	2	279	2	PVRL3	3	110830989	Nonsense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	9460742	110830989	87191441	15	6125											
C3orf17	25871	hgsc.bcm.edu	37	chr3	112736366	112736368	+	In_Frame_Del	DEL	CAT	CAT	-																															gtaaaggactgcacataacaCatctgtttctgcatctaagg																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	CAT	CAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr3:112736366_112736368delCAT	ENST00000314400.5	-	2	379_381	c.188_190delATG	c.(187-192)gatgtg>gtg	p.D63del	RP11-572M11.4_ENST00000467342.1_RNA|RP11-572M11.4_ENST00000460707.1_RNA|C3orf17_ENST00000383675.2_In_Frame_Del_p.D63del|C3orf17_ENST00000393857.2_Intron|RP11-572M11.4_ENST00000470313.1_RNA|RP11-572M11.4_ENST00000496389.1_RNA	NM_015412.3	NP_056227.2	Q6NW34	CC017_HUMAN	chromosome 3 open reading frame 17	63					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						GCACATAACACATCTGTTTCTGC	0.478																																					p.63_64del		Atlas-INDEL	.											.	C3orf17	37	.	0			c.189_191del						PASS	.																																			SO:0001651	inframe_deletion	25871	exon2			.	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.188_190delATG	chr3.hg19:g.112736366_112736368delCAT	ENSP00000320251:p.Asp63del	162.0	0.0	0		86.0	23.0	0.267442	NM_015412	D3DN69|Q68DM6|Q9H7U0|Q9UFM4	In_Frame_Del	DEL	ENST00000314400.5	hg19	CCDS33824.1																																																																																			.	.	.	none		0.478	C3orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354405.3	NM_015412		-	112736368	CAT	-	112736366	7	5	97	1	0	1	0	1	0	0	0	0	2212	478	17	0	1545	0	C3orf17	3	112736366	In_Frame_Del	DEL	CAT	TCGA-B9-4116-01A-01D-1252-08	1905377	112736366	85286064	16	6126											
PIGZ	80235	hgsc.bcm.edu	37	chr3	196675120	196675120	+	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	ccagcagccacaatgcctccAagaagccagctgcgccaccg	11	3	9	18	2	0	1	0	0	0	1	1	1	1	1	7	0	6	2	7	0	3	0			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr3:196675120A>T	ENST00000412723.1	-	3	794	c.648T>A	c.(646-648)ctT>ctA	p.L216L	PIGZ_ENST00000443835.1_3'UTR	NM_025163.2	NP_079439.2	Q86VD9	PIGZ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Z	216					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)		CAATGCCTCCAAGAAGCCAGC	0.637																																					p.L216L		Atlas-SNP	.											.	PIGZ	34	.	0			c.T648A						PASS	.						59	67	64					3																	196675120		2203	4299	6502	SO:0001819	synonymous_variant	80235	exon3			GCCTCCAAGAAGC	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.648T>A	chr3.hg19:g.196675120A>T		139.0	0.0	.		271.0	114.0	.	NM_025163	Q9H9G6	Silent	SNP	ENST00000412723.1	hg19	CCDS3324.1																																																																																			.	.	.	none		0.637	PIGZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340486.2	NM_025163		T	196675120	A	T	196675120	2	4	97	1	0	0	0	0	0	0	0	1	11912	117	5	5		5	PIGZ	3	196675120	Silent	SNP	A	TCGA-B9-4116-01A-01D-1252-08	83938754	196675120	1347310	17	6127											
RFC1	5981	hgsc.bcm.edu	37	chr4	39325032	39325032	+	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	tcatcttcatgcaactgcctCtccagctgtaaaatgtgtca	10	13	6	12	0	5	0	3	0	2	0	6	0	5	0	2	0	4	3	2	0	3	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr4:39325032C>T	ENST00000381897.1	-	7	781	c.648G>A	c.(646-648)gaG>gaA	p.E216E	RFC1_ENST00000418436.1_5'UTR|RFC1_ENST00000349703.2_Silent_p.E216E	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	216					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						GCAACTGCCTCTCCAGCTGTA	0.373																																					p.E216E	Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)	Atlas-SNP	.											.	RFC1	114	.	0			c.G648A						PASS	.						149	124	132					4																	39325032		2203	4300	6503	SO:0001819	synonymous_variant	5981	exon7			CTGCCTCTCCAGC	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.648G>A	chr4.hg19:g.39325032C>T		169.0	0.0	.		33.0	12.0	.	NM_002913	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Silent	SNP	ENST00000381897.1	hg19	CCDS56329.1																																																																																			.	.	.	none		0.373	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913		T	39325032	C	T	39325032	2	4	97	1	0	0	0	0	0	0	0	1	13257	912	32	2		2	RFC1	4	39325032	Silent	SNP	C	TCGA-B9-4116-01A-01D-1252-08		39325032	151829244	18	6128											
UGT2B7	7364	hgsc.bcm.edu	37	chr4	69968643	69968643	+	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	aattgcatcagccctggcccAgatcccacaaaaggtaagat	14	7	8	12	0	1	2	1	0	0	2	2	2	2	2	3	2	2	2	3	2	4	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr4:69968643A>T	ENST00000508661.1	+	3	1016	c.989A>T	c.(988-990)cAg>cTg	p.Q330L	UGT2B7_ENST00000305231.7_Missense_Mutation_p.Q330L|UGT2B7_ENST00000509763.1_3'UTR			P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	330					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)	GCCCTGGCCCAGATCCCACAA	0.428																																					p.Q330L		Atlas-SNP	.											.	UGT2B7	79	.	0			c.A989T						PASS	.						173	167	169					4																	69968643		2203	4300	6503	SO:0001583	missense	7364	exon3			TGGCCCAGATCCC	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.989A>T	chr4.hg19:g.69968643A>T	ENSP00000427659:p.Gln330Leu	438.0	0.0	.		51.0	17.0	.	NM_001074	B2R810|Q6GTW0	Missense_Mutation	SNP	ENST00000508661.1	hg19		.	.	.	.	.	.	.	.	.	.	A	7.768	0.706788	0.15239	.	.	ENSG00000171234	ENST00000502942;ENST00000305231;ENST00000508661	T;T;T	0.61158	0.13;0.13;0.13	3.0	1.8	0.24995	.	0.000000	0.64402	U	0.000001	T	0.75125	0.3807	M	0.93898	3.47	0.22961	N	0.998502	P;P	0.47545	0.875;0.897	P;P	0.59424	0.857;0.657	T	0.66097	-0.6008	9	.	.	.	.	6.2555	0.20872	0.8699:0.0:0.1301:0.0	.	330;330	E9PBP8;P16662	.;UD2B7_HUMAN	L	81;330;330	ENSP00000426206:Q81L;ENSP00000304811:Q330L;ENSP00000427659:Q330L	.	Q	+	2	0	UGT2B7	70003232	1.000000	0.71417	0.097000	0.21041	0.105000	0.19272	6.429000	0.73387	0.370000	0.24538	0.477000	0.44152	CAG	.	.	.	none		0.428	UGT2B7-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000362103.1	NM_001074		T	69968643	A	T	69968643	3	4	97	1	0	0	0	0	1	0	0	0	16974	188	7	5	999	5	UGT2B7	4	69968643	Missense_Mutation	SNP	A	TCGA-B9-4116-01A-01D-1252-08	30643611	69968643	121185633	19	6129											
ANTXR2	118429	hgsc.bcm.edu	37	chr4	80992809	80992809	+	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	tatttgccacactcccagacCtgaaagatgaaattgaactg	14	10	7	10	0	0	5	0	3	0	2	1	5	1	5	3	0	2	0	3	0	4	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr4:80992809C>A	ENST00000307333.7	-	2	155		c.e2-1		ANTXR2_ENST00000295465.4_Splice_Site|ANTXR2_ENST00000346652.6_Splice_Site|ANTXR2_ENST00000403729.2_Splice_Site|ANTXR2_ENST00000404191.1_Splice_Site	NM_001145794.1	NP_001139266.1	P58335	ANTR2_HUMAN	anthrax toxin receptor 2						reproductive process (GO:0022414)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)	13						ACTCCCAGACCTGAAAGATGA	0.383									Juvenile Hyaline Fibromatosis																												.		Atlas-SNP	.											.	ANTXR2	97	.	0			c.153-1G>T						PASS	.						71	71	71					4																	80992809		1839	4093	5932	SO:0001630	splice_region_variant	118429	exon3	Familial Cancer Database	incl. Infantile Systemic Hyalinosis	CCAGACCTGAAAG	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.153-1G>T	chr4.hg19:g.80992809C>A		112.0	0.0	.		79.0	21.0	.	NM_058172	Q4W5H6|Q59E98|Q5JPE9|Q86UI1|Q8N4J8|Q8NB13|Q96NC7	Splice_Site	SNP	ENST00000307333.7	hg19	CCDS47086.1	.	.	.	.	.	.	.	.	.	.	C	15.41	2.826045	0.50739	.	.	ENSG00000163297	ENST00000403729;ENST00000346652;ENST00000307333;ENST00000295465	.	.	.	5.61	5.61	0.85477	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5222	0.84320	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ANTXR2	81211833	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	5.415000	0.66411	2.642000	0.89623	0.563000	0.77884	.	.	.	.	none		0.383	ANTXR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324663.1	NM_058172	Intron	A	80992809	C	A	80992809	5	1	97	1	0	0	0	0	0	0	1	0	712	695	24	4	1420	4	ANTXR2	4	80992809	Splice_Site	SNP	C	TCGA-B9-4116-01A-01D-1252-08	11024166	80992809	110161467	20	6130											
C4orf37	285555	hgsc.bcm.edu	37	chr4	98865112	98865112	+	Missense_Mutation	SNP	T	T	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	cagcatatttgttagtcaagTtaggtaattcatcagaaatt	14	15	7	5	0	3	1	3	0	0	1	3	1	3	1	0	1	1	4	0	1	6	7			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr4:98865112T>G	ENST00000295268.3	-	8	1069	c.980A>C	c.(979-981)aAc>aCc	p.N327T		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	327																	GTTAGTCAAGTTAGGTAATTC	0.323																																					p.N327T		Atlas-SNP	.											.	.	.	.	0			c.A980C						PASS	.						130	127	128					4																	98865112		2203	4300	6503	SO:0001583	missense	285555	exon8			GTCAAGTTAGGTA	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.980A>C	chr4.hg19:g.98865112T>G	ENSP00000295268:p.Asn327Thr	329.0	0.0	.		29.0	9.0	.	NM_174952		Missense_Mutation	SNP	ENST00000295268.3	hg19	CCDS3645.1	.	.	.	.	.	.	.	.	.	.	T	4.606	0.112544	0.08831	.	.	ENSG00000163116	ENST00000522676;ENST00000295268	T;T	0.48201	0.82;2.71	4.0	4.0	0.46444	.	1.315340	0.04739	N	0.422540	T	0.38878	0.1057	L	0.29908	0.895	0.25587	N	0.986734	B	0.33694	0.421	B	0.29862	0.108	T	0.32375	-0.9909	10	0.59425	D	0.04	-9.3556	9.6357	0.39806	0.0:0.0:0.0:1.0	.	327	Q8N412	CD037_HUMAN	T	41;327	ENSP00000428346:N41T;ENSP00000295268:N327T	ENSP00000295268:N327T	N	-	2	0	C4orf37	99084135	0.997000	0.39634	0.663000	0.29738	0.803000	0.45373	2.716000	0.47219	2.041000	0.60428	0.456000	0.33151	AAC	.	.	.	none		0.323	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952		G	98865112	T	G	98865112	3	3	97	1	0	0	0	0	1	0	0	0	2269	1725	60	5	415	5	C4orf37	4	98865112	Missense_Mutation	SNP	T	TCGA-B9-4116-01A-01D-1252-08	17872303	98865112	92289164	21	6131											
NPY2R	4887	hgsc.bcm.edu	37	chr4	156136059	156136059	+	Missense_Mutation	SNP	T	T	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	ctccacttttgccaatccccTtctctatggctggatgaaca	8	13	6	14	0	1	1	0	1	1	0	4	2	3	2	4	2	2	1	4	2	3	4			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr4:156136059T>G	ENST00000329476.3	+	2	1457	c.968T>G	c.(967-969)cTt>cGt	p.L323R	NPY2R_ENST00000506608.1_Missense_Mutation_p.L323R	NM_000910.2	NP_000901.1	P49146	NPY2R_HUMAN	neuropeptide Y receptor Y2	323					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)	GCCAATCCCCTTCTCTATGGC	0.527																																					p.L323R		Atlas-SNP	.											.	NPY2R	87	.	0			c.T968G						PASS	.						116	97	103					4																	156136059		2203	4300	6503	SO:0001583	missense	4887	exon2			ATCCCCTTCTCTA	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.968T>G	chr4.hg19:g.156136059T>G	ENSP00000332591:p.Leu323Arg	159.0	0.0	.		247.0	84.0	.	NM_000910	Q13281|Q13457|Q4W5G7|Q6AZZ6|Q9UE67	Missense_Mutation	SNP	ENST00000329476.3	hg19	CCDS3791.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.979528	0.74360	.	.	ENSG00000185149	ENST00000329476;ENST00000506608	T;T	0.56275	0.47;0.47	5.74	5.74	0.90152	GPCR, rhodopsin-like superfamily (1);	0.285408	0.32970	N	0.005436	T	0.78342	0.4268	M	0.93939	3.475	0.80722	D	1	P	0.51240	0.943	D	0.63113	0.911	D	0.84029	0.0358	10	0.72032	D	0.01	.	15.2138	0.73247	0.0:0.0:0.0:1.0	.	323	P49146	NPY2R_HUMAN	R	323	ENSP00000332591:L323R;ENSP00000426366:L323R	ENSP00000332591:L323R	L	+	2	0	NPY2R	156355509	0.998000	0.40836	0.885000	0.34714	0.928000	0.56348	8.040000	0.89188	2.189000	0.69895	0.523000	0.50628	CTT	.	.	.	none		0.527	NPY2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365128.1	NM_000910		G	156136059	T	G	156136059	3	3	97	1	0	0	0	0	1	0	0	0	10616	1609	56	5	970	5	NPY2R	4	156136059	Missense_Mutation	SNP	T	TCGA-B9-4116-01A-01D-1252-08	57270947	156136059	35018217	22	6132											
CDH9	1007	hgsc.bcm.edu	37	chr5	26906161	26906161	+	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	tcccatctggccacccatgtCtttggcctgtataacaacct	8	12	6	15	0	2	0	0	0	2	0	3	0	3	0	5	2	2	1	5	2	3	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr5:26906161C>T	ENST00000231021.4	-	5	890	c.718G>A	c.(718-720)Gac>Aac	p.D240N		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	240	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D240N(1)		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						CCACCCATGTCTTTGGCCTGT	0.448																																					p.D240N	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											CDH9,NS,carcinoma,0,4	CDH9	305	.	1	Substitution - Missense(1)	lung(1)	c.G718A						PASS	.						232	208	216					5																	26906161		2203	4300	6503	SO:0001583	missense	1007	exon5			CCATGTCTTTGGC	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.718G>A	chr5.hg19:g.26906161C>T	ENSP00000231021:p.Asp240Asn	282.0	0.0	.		54.0	12.0	.	NM_016279	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	hg19	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	C	35	5.553655	0.96501	.	.	ENSG00000113100	ENST00000231021	T	0.79940	-1.32	5.6	5.6	0.85130	Cadherin (5);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.92548	0.7633	M	0.93939	3.475	0.80722	D	1	D	0.76494	0.999	D	0.76575	0.988	D	0.93866	0.7158	9	.	.	.	.	18.5289	0.90984	0.0:1.0:0.0:0.0	.	240	Q9ULB4	CADH9_HUMAN	N	240	ENSP00000231021:D240N	.	D	-	1	0	CDH9	26941918	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.750000	0.85110	2.802000	0.96397	0.650000	0.86243	GAC	.	.	.	none		0.448	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		T	26906161	C	T	26906161	3	4	97	1	0	0	0	0	1	0	0	0	3119	913	32	2	1683	2	CDH9	5	26906161	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08		26906161	154009099	23	6133											
ANKHD1	54882	hgsc.bcm.edu	37	chr5	139908303	139908303	+	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	gggactgttttaccctcagaGtctgctggactagctactgc	7	12	11	11	0	2	1	1	0	1	1	2	3	2	3	1	2	5	3	1	2	3	4			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr5:139908303G>C	ENST00000360839.2	+	29	5926	c.5772G>C	c.(5770-5772)gaG>gaC	p.E1924D	ANKHD1_ENST00000544120.1_Missense_Mutation_p.E307D|SNORD45_ENST00000363181.1_RNA|ANKHD1-EIF4EBP3_ENST00000532219.1_Missense_Mutation_p.E1924D|ANKHD1_ENST00000297183.6_Missense_Mutation_p.E1924D	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	1924						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)			TACCCTCAGAGTCTGCTGGAC	0.488																																					p.E1924D		Atlas-SNP	.											ANKHD1-EIF4EBP3,NS,carcinoma,0,2	ANKHD1	233	.	0			c.G5772C						PASS	.						81	77	78					5																	139908303		2203	4300	6503	SO:0001583	missense	54882	exon29			CTCAGAGTCTGCT	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.5772G>C	chr5.hg19:g.139908303G>C	ENSP00000354085:p.Glu1924Asp	159.0	0.0	.		54.0	4.0	.	NM_017747	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Missense_Mutation	SNP	ENST00000360839.2	hg19	CCDS4225.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.835|9.835	1.189371|1.189371	0.21954|0.21954	.|.	.|.	ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996|ENSG00000131503	ENST00000360839;ENST00000297183;ENST00000253810;ENST00000431508;ENST00000536646;ENST00000433049;ENST00000544120;ENST00000532219|ENST00000435794;ENST00000432301	T;T;T;T;T;T|.	0.65916|.	-0.14;-0.18;1.89;1.89;1.48;-0.18|.	4.98|4.98	1.47|1.47	0.22746|0.22746	.|.	0.238205|.	0.41396|.	D|.	0.000887|.	T|T	0.33789|0.33789	0.0875|0.0875	L|L	0.34521|0.34521	1.04|1.04	0.25479|0.25479	N|N	0.987752|0.987752	B;P;B;P;B;B|.	0.42409|.	0.184;0.779;0.28;0.462;0.231;0.231|.	B;B;B;B;B;B|.	0.35510|.	0.055;0.204;0.118;0.121;0.054;0.054|.	T|T	0.25152|0.25152	-1.0140|-1.0140	10|5	0.19590|.	T|.	0.45|.	.|.	8.8813|8.8813	0.35376|0.35376	0.3024:0.0:0.6976:0.0|0.3024:0.0:0.6976:0.0	.|.	307;354;307;1924;1924;1924|.	Q8IWG5;Q9H059;F6WFL0;E9PF56;Q8IWZ2;Q8IWZ3|.	.;.;.;.;.;ANKH1_HUMAN|.	D|L	1924;1924;1924;580;359;446;307;1924|415;375	ENSP00000354085:E1924D;ENSP00000297183:E1924D;ENSP00000393204:E580D;ENSP00000390034:E446D;ENSP00000437687:E307D;ENSP00000432016:E1924D|.	ENSP00000432016:E1924D|.	E|V	+|+	3|1	2|0	ANKHD1-EIF4EBP3;ANKHD1|ANKHD1	139888487|139888487	0.997000|0.997000	0.39634|0.39634	0.996000|0.996000	0.52242|0.52242	0.985000|0.985000	0.73830|0.73830	0.224000|0.224000	0.17738|0.17738	0.419000|0.419000	0.25927|0.25927	0.650000|0.650000	0.86243|0.86243	GAG|GTC	.	.	.	none		0.488	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		C	139908303	G	C	139908303	3	2	97	1	0	0	0	0	1	0	0	0	628	1020	36	4	5992	4	ANKHD1	5	139908303	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	113002142	139908303	41006957	24	6134											
MED7	9443	hgsc.bcm.edu	37	chr5	156565887	156565887	+	Missense_Mutation	SNP	T	T	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	atcagcatccattggttcagTttttactctcattcctgctt	7	18	5	11	0	3	0	3	0	1	0	6	0	5	0	2	1	3	4	2	1	1	7			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr5:156565887T>G	ENST00000286317.5	-	2	937	c.556A>C	c.(556-558)Act>Cct	p.T186P	MED7_ENST00000420343.1_Missense_Mutation_p.T186P	NM_004270.4	NP_004261.1	O43513	MED7_HUMAN	mediator complex subunit 7	186					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)			ATTGGTTCAGTTTTTACTCTC	0.373																																					p.T186P		Atlas-SNP	.											.	MED7	18	.	0			c.A556C						PASS	.						170	159	163					5																	156565887		2203	4300	6503	SO:0001583	missense	9443	exon2			GTTCAGTTTTTAC	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.556A>C	chr5.hg19:g.156565887T>G	ENSP00000286317:p.Thr186Pro	267.0	0.0	.		121.0	45.0	.	NM_001100816		Missense_Mutation	SNP	ENST00000286317.5	hg19	CCDS4334.1	.	.	.	.	.	.	.	.	.	.	T	13.62	2.291433	0.40494	.	.	ENSG00000155868	ENST00000286317;ENST00000420343;ENST00000524289	.	.	.	5.81	1.99	0.26369	.	0.426120	0.27048	N	0.021196	T	0.36248	0.0960	L	0.52573	1.65	0.35094	D	0.764574	P	0.45634	0.863	B	0.41271	0.352	T	0.40327	-0.9569	9	0.27082	T	0.32	-13.3431	5.9577	0.19283	0.1123:0.1921:0.0:0.6956	.	186	O43513	MED7_HUMAN	P	186	.	ENSP00000286317:T186P	T	-	1	0	MED7	156498465	0.995000	0.38212	0.985000	0.45067	0.991000	0.79684	0.479000	0.22228	0.098000	0.17522	0.533000	0.62120	ACT	.	.	.	none		0.373	MED7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252567.2	NM_004270		G	156565887	T	G	156565887	3	3	97	1	0	0	0	0	1	0	0	0	9459	1725	60	5	149	5	MED7	5	156565887	Missense_Mutation	SNP	T	TCGA-B9-4116-01A-01D-1252-08	16657584	156565887	24349373	25	6135											
SLC22A16	85413	hgsc.bcm.edu	37	chr6	110757106	110757106	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaagataaatgaggccaaatGctgccccgatggcaaatttt	15	9	9	8	1	0	2	0	1	0	1	0	3	0	2	3	2	2	2	3	2	5	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr6:110757106G>A	ENST00000368919.3	-	6	1436	c.1370C>T	c.(1369-1371)gCa>gTa	p.A457V	SLC22A16_ENST00000330550.4_Missense_Mutation_p.A423V|SLC22A16_ENST00000439654.1_Missense_Mutation_p.A457V	NM_033125.3	NP_149116.2	Q86VW1	S22AG_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 16	457					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)	GAGGCCAAATGCTGCCCCGAT	0.363																																					p.A457V		Atlas-SNP	.											.	SLC22A16	81	.	0			c.C1370T						PASS	.						102	99	100					6																	110757106		2203	4300	6503	SO:0001583	missense	85413	exon6			CCAAATGCTGCCC		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.1370C>T	chr6.hg19:g.110757106G>A	ENSP00000357915:p.Ala457Val	185.0	0.0	.		125.0	39.0	.	NM_033125	O14567|Q5JXM1|Q8IUG8|Q8IZD5|Q96M90|Q96RU0	Missense_Mutation	SNP	ENST00000368919.3	hg19	CCDS5084.1	.	.	.	.	.	.	.	.	.	.	G	16.34	3.095193	0.56075	.	.	ENSG00000004809	ENST00000368919;ENST00000451557;ENST00000330550;ENST00000439654	D;D;D;D	0.90133	-2.62;-2.62;-2.62;-2.62	4.75	0.519	0.17035	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.355691	0.31809	N	0.007039	T	0.81814	0.4902	L	0.56124	1.755	0.80722	D	1	B;B	0.31413	0.322;0.275	B;B	0.37550	0.253;0.164	T	0.76924	-0.2779	10	0.72032	D	0.01	.	8.3956	0.32555	0.3527:0.0:0.6473:0.0	.	457;423	Q86VW1;Q86VW1-2	S22AG_HUMAN;.	V	457;374;423;457	ENSP00000357915:A457V;ENSP00000395642:A374V;ENSP00000328583:A423V;ENSP00000408799:A457V	ENSP00000328583:A423V	A	-	2	0	SLC22A16	110863799	0.999000	0.42202	0.000000	0.03702	0.591000	0.36615	2.826000	0.48104	-0.101000	0.12219	-0.339000	0.08088	GCA	.	.	.	none		0.363	SLC22A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043428.1	NM_033125		A	110757106	G	A	110757106	3	1	97	1	0	0	0	0	1	0	0	0	14460	1319	46	2	375	2	SLC22A16	6	110757106	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08		110757106	60357961	26	6136											
SYNJ2	8871	hgsc.bcm.edu	37	chr6	158449969	158449969	+	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	tcgggggtgttctatttctcAtggccaaacgatgggtctcg	6	13	13	9	3	3	0	1	0	3	0	6	1	3	0	1	4	1	1	1	4	2	3	rs140060886		TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr6:158449969A>T	ENST00000355585.4	+	3	471	c.396A>T	c.(394-396)tcA>tcT	p.S132S	SYNJ2_ENST00000449859.2_Silent_p.S81S|SYNJ2_ENST00000367122.2_Silent_p.S132S|SYNJ2_ENST00000367121.3_Silent_p.S132S	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	132	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	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)		TCTATTTCTCATGGCCAAACG	0.542																																					p.S132S		Atlas-SNP	.											.	SYNJ2	111	.	0			c.A396T						PASS	.						66	67	66					6																	158449969		2203	4300	6503	SO:0001819	synonymous_variant	8871	exon3			TTTCTCATGGCCA	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.396A>T	chr6.hg19:g.158449969A>T		133.0	0.0	.		235.0	70.0	.	NM_003898	Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	Silent	SNP	ENST00000355585.4	hg19	CCDS5254.1	.	.	.	.	.	.	.	.	.	.	A	4.185	0.032976	0.08101	.	.	ENSG00000078269	ENST00000367113	.	.	.	4.62	-9.25	0.00666	.	.	.	.	.	T	0.35219	0.0924	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68868	-0.5295	4	.	.	.	.	9.0699	0.36486	0.2544:0.577:0.1011:0.0675	.	.	.	.	L	107	.	.	H	+	2	0	SYNJ2	158369957	0.008000	0.16893	0.903000	0.35520	0.321000	0.28281	-1.071000	0.03437	1.946000	0.56461	0.533000	0.62120	CAT	.	A|1.000;G|0.000	.	alt		0.542	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2			T	158449969	A	T	158449969	2	4	97	1	0	0	0	0	0	0	0	1	15465	204	8	5		5	SYNJ2	6	158449969	Silent	SNP	A	TCGA-B9-4116-01A-01D-1252-08	47692863	158449969	12665098	27	6137											
NOD1	10392	hgsc.bcm.edu	37	chr7	30475651	30475651	+	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	cgtgttctgctgcagggcccTcgcaaggctctttcctcctt	3	13	10	15	2	2	0	0	0	2	0	5	0	4	0	3	2	2	5	3	2	1	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr7:30475651T>A	ENST00000222823.4	-	11	3109	c.2584A>T	c.(2584-2586)Agg>Tgg	p.R862W		NM_006092.2	NP_006083.1	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain containing 1	862					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						TGCAGGGCCCTCGCAAGGCTC	0.443																																					p.R862W		Atlas-SNP	.											.	NOD1	79	.	0			c.A2584T						PASS	.						129	106	114					7																	30475651		2203	4300	6503	SO:0001583	missense	10392	exon11			GGGCCCTCGCAAG	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.2584A>T	chr7.hg19:g.30475651T>A	ENSP00000222823:p.Arg862Trp	123.0	0.0	.		173.0	52.0	.	NM_006092	B4DTU3|Q549U4|Q8IWF5	Missense_Mutation	SNP	ENST00000222823.4	hg19	CCDS5427.1	.	.	.	.	.	.	.	.	.	.	T	8.038	0.763254	0.15914	.	.	ENSG00000106100	ENST00000222823	T	0.55052	0.54	5.12	-1.83	0.07833	.	0.871180	0.09788	N	0.755710	T	0.39145	0.1067	L	0.49126	1.545	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.36866	-0.9730	10	0.62326	D	0.03	.	1.2857	0.02050	0.1549:0.2137:0.3025:0.3289	.	862	Q9Y239	NOD1_HUMAN	W	862	ENSP00000222823:R862W	ENSP00000222823:R862W	R	-	1	2	NOD1	30442176	0.008000	0.16893	0.000000	0.03702	0.092000	0.18411	0.609000	0.24238	-0.810000	0.04375	-0.313000	0.08912	AGG	.	.	.	none		0.443	NOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250443.2			A	30475651	T	A	30475651	3	1	97	1	0	0	0	0	1	0	0	0	10523	1550	54	5	293	5	NOD1	7	30475651	Missense_Mutation	SNP	T	TCGA-B9-4116-01A-01D-1252-08		30475651	128663012	28	6138											
EIF4H	7458	hgsc.bcm.edu	37	chr7	73601993	73601993	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagccagaaggagttgcccAcagagcccccctacacagca	12	4	10	15	0	0	2	0	0	0	2	0	3	0	3	5	1	5	3	5	1	3	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr7:73601993A>G	ENST00000265753.8	+	2	251	c.112A>G	c.(112-114)Aca>Gca	p.T38A	EIF4H_ENST00000353999.6_Missense_Mutation_p.T38A|EIF4H_ENST00000495187.1_3'UTR	NM_022170.1	NP_071496.1	Q15056	IF4H_HUMAN	eukaryotic translation initiation factor 4H	38					cellular protein metabolic process (GO:0044267)|developmental growth (GO:0048589)|gene expression (GO:0010467)|regulation of translational initiation (GO:0006446)|sexual reproduction (GO:0019953)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(1)|lung(2)|prostate(1)	4						GGAGTTGCCCACAGAGCCCCC	0.527																																					p.T38A		Atlas-SNP	.											.	EIF4H	19	.	0			c.A112G						PASS	.						93	91	92					7																	73601993		2203	4297	6500	SO:0001583	missense	7458	exon2			TTGCCCACAGAGC		CCDS5564.1, CCDS5565.1	7q11.23	2013-02-12	2006-11-27	2006-11-27	ENSG00000106682	ENSG00000106682		"RNA binding motif (RRM) containing"	12741	protein-coding gene	gene with protein product		603431	"Williams-Beuren syndrome chromosome region 1"	WBSCR1		9516461, 15078951	Standard	NM_022170		Approved	WSCR1, KIAA0038	uc003uad.1	Q15056	OTTHUMG00000023025	ENST00000265753.8:c.112A>G	chr7.hg19:g.73601993A>G	ENSP00000265753:p.Thr38Ala	296.0	0.0	.		422.0	133.0	.	NM_022170	A8K3R1|D3DXF6|D3DXF8	Missense_Mutation	SNP	ENST00000265753.8	hg19	CCDS5564.1	.	.	.	.	.	.	.	.	.	.	A	16.19	3.053342	0.55218	.	.	ENSG00000106682	ENST00000265753;ENST00000353999	T;T	0.74002	-0.8;-0.8	5.05	5.05	0.67936	Nucleotide-binding, alpha-beta plait (1);	0.118143	0.64402	D	0.000020	T	0.72020	0.3409	L	0.55990	1.75	0.54753	D	0.999988	B;B;B;B	0.20368	0.012;0.012;0.044;0.006	B;B;B;B	0.28916	0.096;0.096;0.047;0.054	T	0.70310	-0.4907	10	0.49607	T	0.09	-15.2629	13.9042	0.63823	1.0:0.0:0.0:0.0	.	38;38;38;38	B4DMV6;Q75MU2;Q15056-2;Q15056	.;.;.;IF4H_HUMAN	A	38	ENSP00000265753:T38A;ENSP00000265754:T38A	ENSP00000265753:T38A	T	+	1	0	EIF4H	73239929	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.887000	0.63156	2.029000	0.59856	0.379000	0.24179	ACA	.	.	.	none		0.527	EIF4H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252375.2	NM_022170		G	73601993	A	G	73601993	3	3	97	1	0	0	0	0	1	0	0	0	5041	159	6	3	118	3	EIF4H	7	73601993	Missense_Mutation	SNP	A	TCGA-B9-4116-01A-01D-1252-08	43126342	73601993	85536670	29	6139											
POR	5447	hgsc.bcm.edu	37	chr7	75615481	75615481	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccacccttggccccaggtctAcgtccagcacctgctaaagc	8	7	8	18	1	1	0	0	0	1	0	2	0	2	0	6	2	4	2	6	2	3	3	rs72557954		TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr7:75615481A>G	ENST00000461988.1	+	15	1925	c.1820A>G	c.(1819-1821)tAc>tGc	p.Y607C	TMEM120A_ENST00000338761.4_RNA|TMEM120A_ENST00000493111.2_RNA|POR_ENST00000450476.1_Missense_Mutation_p.Y506C|POR_ENST00000419840.1_Intron|POR_ENST00000439269.1_Missense_Mutation_p.Y345C|POR_ENST00000545601.1_Missense_Mutation_p.Y415C|POR_ENST00000394893.1_Missense_Mutation_p.Y607C	NM_000941.2	NP_000932.3	P16435	NCPR_HUMAN	P450 (cytochrome) oxidoreductase	604					carnitine metabolic process (GO:0009437)|cellular organofluorine metabolic process (GO:0090346)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to peptide hormone stimulus (GO:0071375)|demethylation (GO:0070988)|fatty acid oxidation (GO:0019395)|flavonoid metabolic process (GO:0009812)|internal peptidyl-lysine acetylation (GO:0018393)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of lipase activity (GO:0060192)|nitrate catabolic process (GO:0043602)|nitric oxide catabolic process (GO:0046210)|oxidation-reduction process (GO:0055114)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|regulation of growth plate cartilage chondrocyte proliferation (GO:0003420)|response to drug (GO:0042493)|response to nutrient (GO:0007584)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|hydrolase activity (GO:0016787)|iron ion binding (GO:0005506)|iron-cytochrome-c reductase activity (GO:0047726)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric oxide dioxygenase activity (GO:0008941)			central_nervous_system(1)|endometrium(2)|kidney(2)|lung(3)|ovary(1)	9					Benzphetamine(DB00865)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Ethylmorphine(DB01466)|Flavin adenine dinucleotide(DB03147)|Lipoic Acid(DB00166)|Mitomycin(DB00305)|Nilutamide(DB00665)|Nitrofurantoin(DB00698)	CCCCAGGTCTACGTCCAGCAC	0.632																																					p.Y607C		Atlas-SNP	.											.	POR	46	.	0			c.A1820G	GRCh37	CM087168	POR	M	rs72557954	PASS	.						43	56	52					7																	75615481		2106	4224	6330	SO:0001583	missense	5447	exon15			AGGTCTACGTCCA	AF258341	CCDS5579.1	7q11.2	2006-12-05			ENSG00000127948	ENSG00000127948			9208	protein-coding gene	gene with protein product		124015				2516426	Standard	NM_000941		Approved	CYPOR, FLJ26468	uc003udy.3	P16435	OTTHUMG00000130413	ENST00000461988.1:c.1820A>G	chr7.hg19:g.75615481A>G	ENSP00000419970:p.Tyr607Cys	28.0	0.0	.		41.0	19.0	.	NM_000941	Q16455|Q197M5|Q8N181|Q9H3M8|Q9UDT3	Missense_Mutation	SNP	ENST00000461988.1	hg19	CCDS5579.1	.	.	.	.	.	.	.	.	.	.	A	11.75	1.731367	0.30684	.	.	ENSG00000127948	ENST00000461988;ENST00000394893;ENST00000545601;ENST00000450476;ENST00000439269	D;D;D;D;D	0.82081	-1.57;-1.57;-1.57;-1.57;-1.57	3.59	3.59	0.41128	Oxidoreductase FAD/NAD(P)-binding (1);Flavoprotein pyridine nucleotide cytochrome reductase (1);	0.127712	0.53938	D	0.000041	D	0.94512	0.8233	H	0.99336	4.52	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.95784	0.8819	10	0.87932	D	0	-33.1823	12.3556	0.55174	1.0:0.0:0.0:0.0	.	604;506;415;613	P16435;E7EVY7;F5H468;Q59ED7	NCPR_HUMAN;.;.;.	C	607;607;415;506;345	ENSP00000419970:Y607C;ENSP00000378355:Y607C;ENSP00000446149:Y415C;ENSP00000416572:Y506C;ENSP00000412490:Y345C	ENSP00000378355:Y607C	Y	+	2	0	POR	75453417	1.000000	0.71417	0.956000	0.39512	0.099000	0.18886	5.702000	0.68332	1.863000	0.54032	0.459000	0.35465	TAC	.	A|0.999;G|0.001	0.001	weak		0.632	POR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252796.7	NM_000941		G	75615481	A	G	75615481	3	3	97	1	0	0	0	0	1	0	0	0	12264	391	14	3	1874	3	POR	7	75615481	Missense_Mutation	SNP	A	TCGA-B9-4116-01A-01D-1252-08	2013488	75615481	83523182	30	6140											
BAIAP2L1	55971	hgsc.bcm.edu	37	chr7	97933661	97933661	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctattctcagacaagttcacGgtgctgatgcttctcactgg	8	13	9	11	1	3	2	3	1	2	1	5	2	3	2	0	2	2	3	0	2	2	4	rs555687728		TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr7:97933661G>A	ENST00000005260.8	-	12	1484	c.1269C>T	c.(1267-1269)acC>acT	p.T423T		NM_018842.4	NP_061330.2	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1	423					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)	p.T423T(1)		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)			ACAAGTTCACGGTGCTGATGC	0.537													G|||	1	0.000199681	0	0	5008	,	,		18777	0		0	False		,,,				2504	0.001				p.T423T		Atlas-SNP	.											BAIAP2L1,NS,carcinoma,0,1	BAIAP2L1	61	.	1	Substitution - coding silent(1)	breast(1)	c.C1269T						PASS	.						119	99	105					7																	97933661		2203	4300	6503	SO:0001819	synonymous_variant	55971	exon12			GTTCACGGTGCTG	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.1269C>T	chr7.hg19:g.97933661G>A		99.0	0.0	.		245.0	50.0	.	NM_018842	A4D268|Q75L21|Q75L22|Q96CV4|Q9H5F5|Q9Y2M8	Silent	SNP	ENST00000005260.8	hg19	CCDS34687.1																																																																																			.	.	.	none		0.537	BAIAP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334681.1	NM_018842		A	97933661	G	A	97933661	2	1	97	1	0	0	0	0	0	0	0	1	1302	1103	39	1		1	BAIAP2L1	7	97933661	Silent	SNP	G	TCGA-B9-4116-01A-01D-1252-08	22318180	97933661	61205002	31	6141											
ANKRD7	56311	hgsc.bcm.edu	37	chr7	117879989	117879989	+	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	acccacaattcactgcgagcCatggaaagaagaaacatgct	16	6	8	11	1	1	2	1	0	0	2	1	4	1	3	2	1	4	1	2	1	4	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr7:117879989C>A	ENST00000265224.4	+	6	894	c.739C>A	c.(739-741)Cat>Aat	p.H247N	ANKRD7_ENST00000357099.4_Missense_Mutation_p.H267N|ANKRD7_ENST00000433239.1_Missense_Mutation_p.H194N|ANKRD7_ENST00000417525.1_Silent_p.A192A|ANKRD7_ENST00000477532.1_3'UTR	NM_019644.3	NP_062618.2	Q92527	ANKR7_HUMAN	ankyrin repeat domain 7	247					male gonad development (GO:0008584)	nucleus (GO:0005634)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)	29						CACTGCGAGCCATGGAAAGAA	0.338																																					p.H247N		Atlas-SNP	.											.	ANKRD7	44	.	0			c.C739A						PASS	.						95	90	92					7																	117879989		1874	4112	5986	SO:0001583	missense	56311	exon6			GCGAGCCATGGAA	D78334	CCDS43638.1	7q31	2013-01-10			ENSG00000106013	ENSG00000106013		"Ankyrin repeat domain containing"	18588	protein-coding gene	gene with protein product	"testis-specific ankyrin motif containing protein"	610731				8812458	Standard	NM_019644		Approved	TSA806	uc003vji.3	Q92527	OTTHUMG00000156960	ENST00000265224.4:c.739C>A	chr7.hg19:g.117879989C>A	ENSP00000265224:p.His247Asn	88.0	0.0	.		221.0	31.0	.	NM_019644	B4DYF5|Q96QN1|Q9UDM3	Missense_Mutation	SNP	ENST00000265224.4	hg19	CCDS43638.1	.	.	.	.	.	.	.	.	.	.	C	8.240	0.806672	0.16467	.	.	ENSG00000106013	ENST00000357099;ENST00000265224;ENST00000433239	T;T;T	0.39787	1.07;1.18;1.06	3.96	-7.92	0.01160	.	7.917730	0.01487	U	0.016939	T	0.22551	0.0544	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08722	-1.0708	10	0.42905	T	0.14	-2.3393	0.7429	0.00977	0.3457:0.1668:0.1118:0.3758	.	247	Q92527	ANKR7_HUMAN	N	267;247;194	ENSP00000349612:H267N;ENSP00000265224:H247N;ENSP00000388473:H194N	ENSP00000265224:H247N	H	+	1	0	ANKRD7	117667225	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	-0.364000	0.07583	-2.334000	0.00630	-2.920000	0.00090	CAT	.	.	.	none		0.338	ANKRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346826.1	NM_001077708		A	117879989	C	A	117879989	3	1	97	1	0	0	0	0	1	0	0	0	686	594	21	4	761	4	ANKRD7	7	117879989	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08	19946328	117879989	41258674	32	6142											
PRKAG2	51422	hgsc.bcm.edu	37	chr7	151262972	151262972	+	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	ggctttggcatatcagacatCtaaacggaagataaacgcaa	16	8	9	8	2	2	2	1	0	1	2	2	3	2	3	0	3	2	3	0	3	7	4			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr7:151262972C>T	ENST00000287878.4	-	12	1738		c.e12-1		PRKAG2_ENST00000492843.1_Splice_Site|PRKAG2_ENST00000433631.2_Splice_Site|PRKAG2_ENST00000418337.2_Splice_Site|PRKAG2_ENST00000392801.2_Splice_Site	NM_016203.3	NP_057287.2	Q9UGJ0	AAKG2_HUMAN	protein kinase, AMP-activated, gamma 2 non-catalytic subunit						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)	TATCAGACATCTAAACGGAAG	0.418																																					.		Atlas-SNP	.											.	PRKAG2	86	.	0			c.1234-1G>A						PASS	.						168	137	147					7																	151262972		2203	4300	6503	SO:0001630	splice_region_variant	51422	exon13			AGACATCTAAACG	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.1234-1G>A	chr7.hg19:g.151262972C>T		151.0	0.0	.		87.0	31.0	.	NM_016203	Q53Y07|Q6NUI0|Q75MP4|Q9NUZ9|Q9UDN8|Q9ULX8	Splice_Site	SNP	ENST00000287878.4	hg19	CCDS5928.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.459439	0.84317	.	.	ENSG00000106617	ENST00000418337;ENST00000287878;ENST00000492843;ENST00000433631;ENST00000392801	.	.	.	6.06	6.06	0.98353	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.609	0.95594	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PRKAG2	150893905	1.000000	0.71417	1.000000	0.80357	0.802000	0.45316	7.538000	0.82048	2.882000	0.98803	0.655000	0.94253	.	.	.	.	none		0.418	PRKAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348440.2	NM_016203	Intron	T	151262972	C	T	151262972	5	4	97	1	0	0	0	0	0	0	1	0	12511	927	32	2	496	2	PRKAG2	7	151262972	Splice_Site	SNP	C	TCGA-B9-4116-01A-01D-1252-08	33382983	151262972	7875691	33	6143											
FAM84B	157638	hgsc.bcm.edu	37	chr8	127569250	127569250	+	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	tacggcccagtgcgggtactGagcctgcgacacgaactcca	9	6	12	14	4	0	1	0	1	0	0	1	3	1	1	3	2	6	1	3	2	3	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr8:127569250G>C	ENST00000304916.3	-	2	840	c.385C>G	c.(385-387)Cag>Gag	p.Q129E	RP11-89K10.1_ENST00000519880.1_RNA|RP11-89K10.1_ENST00000520512.1_RNA|RP11-103H7.5_ENST00000524320.1_RNA|FAM84B_ENST00000517458.1_5'Flank|RP11-89K10.1_ENST00000517773.1_RNA	NM_174911.4	NP_777571.1	Q96KN1	FA84B_HUMAN	family with sequence similarity 84, member B	129						cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	5	Ovarian(5;9.43e-05)|Esophageal squamous(12;0.0012)|Hepatocellular(40;0.128)|Myeloproliferative disorder(2;0.135)		STAD - Stomach adenocarcinoma(47;0.000556)|Colorectal(2;0.0102)|Lung(2;0.0136)|READ - Rectum adenocarcinoma(2;0.0723)			TGCGGGTACTGAGCCTGCGAC	0.637																																					p.Q129E		Atlas-SNP	.											.	FAM84B	19	.	0			c.C385G						PASS	.						27	29	29					8																	127569250		2202	4299	6501	SO:0001583	missense	157638	exon2			GGTACTGAGCCTG	AJ417849	CCDS6358.1	8q24.13	2006-02-09				ENSG00000168672			24166	protein-coding gene	gene with protein product	"breast cancer membrane-associated protein 101", "neurological/sensory 2"	609483				12477722	Standard	NM_174911		Approved	BCMP101, NSE2	uc003yrz.2	Q96KN1		ENST00000304916.3:c.385C>G	chr8.hg19:g.127569250G>C	ENSP00000302578:p.Gln129Glu	109.0	0.0	.		156.0	43.0	.	NM_174911		Missense_Mutation	SNP	ENST00000304916.3	hg19	CCDS6358.1	.	.	.	.	.	.	.	.	.	.	G	14.26	2.480872	0.44044	.	.	ENSG00000168672	ENST00000304916	T	0.03152	4.03	4.81	4.81	0.61882	.	0.057812	0.64402	D	0.000001	T	0.14270	0.0345	M	0.63428	1.95	0.51767	D	0.999933	D	0.71674	0.998	D	0.67725	0.953	T	0.06215	-1.0839	10	0.27785	T	0.31	-11.9573	16.8556	0.86005	0.0:0.0:1.0:0.0	.	129	Q96KN1	FA84B_HUMAN	E	129	ENSP00000302578:Q129E	ENSP00000302578:Q129E	Q	-	1	0	FAM84B	127638432	1.000000	0.71417	0.977000	0.42913	0.005000	0.04900	7.807000	0.86032	2.181000	0.69327	0.467000	0.42956	CAG	.	.	.	none		0.637	FAM84B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381487.1	NM_174911		C	127569250	G	C	127569250	3	2	97	1	0	0	0	0	1	0	0	0	5649	1299	45	4	551	4	FAM84B	8	127569250	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08		127569250	18794772	34	6144											
C9orf79	286234	hgsc.bcm.edu	37	chr9	90501484	90501484	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaaggatgtgcagaagacCgggttcaggagctccggaag	12	5	17	7	2	1	2	1	0	0	2	2	6	2	6	2	5	2	3	2	5	3	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr9:90501484C>T	ENST00000325643.5	+	4	2148	c.2082C>T	c.(2080-2082)acC>acT	p.T694T		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	694					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TGCAGAAGACCGGGTTCAGGA	0.612																																					p.T694T		Atlas-SNP	.											.	.	.	.	0			c.C2082T						PASS	.						54	69	64					9																	90501484		2203	4300	6503	SO:0001819	synonymous_variant	286234	exon4			GAAGACCGGGTTC	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.2082C>T	chr9.hg19:g.90501484C>T		160.0	0.0	.		234.0	65.0	.	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Silent	SNP	ENST00000325643.5	hg19	CCDS6676.1																																																																																			.	.	.	none		0.612	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828		T	90501484	C	T	90501484	2	4	97	1	0	0	0	0	0	0	0	1	2499	639	23	1		1	C9orf79	9	90501484	Silent	SNP	C	TCGA-B9-4116-01A-01D-1252-08		90501484	50711947	35	6145											
NUP214	8021	hgsc.bcm.edu	37	chr9	134010301	134010301	+	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	gtagaaaaaagaagaaaagcAcccagagatatttgtgaact	20	7	9	5	0	0	5	0	1	0	4	0	6	0	5	1	0	2	2	1	0	9	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr9:134010301A>T	ENST00000359428.5	+	8	992	c.848A>T	c.(847-849)cAc>cTc	p.H283L	RP11-544A12.4_ENST00000587264.1_RNA|RP11-544A12.4_ENST00000587408.1_RNA|RP11-544A12.4_ENST00000589667.1_RNA|RP11-544A12.4_ENST00000586290.1_RNA|NUP214_ENST00000411637.2_Missense_Mutation_p.H283L|RP11-544A12.4_ENST00000589540.1_RNA|RP11-544A12.4_ENST00000415391.2_RNA|RP11-544A12.4_ENST00000588378.1_RNA|NUP214_ENST00000451030.1_Missense_Mutation_p.H283L|RP11-544A12.4_ENST00000590461.1_RNA			P35658	NU214_HUMAN	nucleoporin 214kDa	283	Seven-bladed beta propeller.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		GAAGAAAAGCACCCAGAGATA	0.378			T	"DEK, SET, ABL1"	"AML, T-ALL"																																p.H283L	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.A848T						PASS	.						69	67	67					9																	134010301		2203	4300	6503	SO:0001583	missense	8021	exon8			AAAAGCACCCAGA	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.848A>T	chr9.hg19:g.134010301A>T	ENSP00000352400:p.His283Leu	111.0	0.0	.		57.0	17.0	.	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	hg19	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	A	19.58	3.855209	0.71719	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375	D;D;D	0.93488	-3.23;-3.23;-3.23	5.69	3.32	0.38043	WD40/YVTN repeat-like-containing domain (1);	0.000000	0.43110	D	0.000603	T	0.80954	0.4723	N	0.08118	0	0.31118	N	0.709181	B;B	0.33022	0.202;0.394	B;B	0.32022	0.099;0.139	T	0.75227	-0.3392	10	0.23891	T	0.37	-11.0116	3.1676	0.06541	0.5712:0.2182:0.2105:0.0	.	283;283	P35658-4;P35658	.;NU214_HUMAN	L	283	ENSP00000352400:H283L;ENSP00000396576:H283L;ENSP00000405014:H283L	ENSP00000352400:H283L	H	+	2	0	NUP214	133000122	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.069000	0.50026	0.950000	0.37743	0.528000	0.53228	CAC	.	.	.	none		0.378	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		T	134010301	A	T	134010301	3	4	97	1	0	0	0	0	1	0	0	0	10769	159	6	5	878	5	NUP214	9	134010301	Missense_Mutation	SNP	A	TCGA-B9-4116-01A-01D-1252-08	43508817	134010301	7203130	36	6146											
SEC16A	9919	hgsc.bcm.edu	37	chr9	139369195	139369195	+	Frame_Shift_Del	DEL	G	G	-																															ccacacttgtgcttccagcaGggctattagcaaatccggga																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr9:139369195delG	ENST00000371706.3	-	1	2372	c.2339delC	c.(2338-2340)cctfs	p.P780fs	SEC16A_ENST00000431893.2_Frame_Shift_Del_p.P780fs|SEC16A_ENST00000290037.6_Frame_Shift_Del_p.P780fs|SEC16A_ENST00000313050.7_Frame_Shift_Del_p.P958fs			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	780					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)		GCTTCCAGCAGGGCTATTAGC	0.507																																					p.P958fs		Atlas-INDEL	.											.	SEC16A	249	.	0			c.2874delT						PASS	.						65	64	64					9																	139369195		1939	4138	6077	SO:0001589	frameshift_variant	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.2339delC	chr9.hg19:g.139369195delG	ENSP00000360771:p.Pro780fs	104.0	0.0	0		213.0	76.0	0.356808	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Frame_Shift_Del	DEL	ENST00000371706.3	hg19																																																																																				.	.	.	none		0.507	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459		-	139369195	G	-	139369195	7	5	97	1	0	1	0	1	0	0	0	0	13999	1000	35	0	4320	0	SEC16A	9	139369195	Frame_Shift_Del	DEL	G	TCGA-B9-4116-01A-01D-1252-08	5358894	139369195	1844236	37	6147											
FAM45A	404636	hgsc.bcm.edu	37	chr10	120879873	120879873	+	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	acattgtatctcagtttggaAtggaaactgttatcttacac	12	15	7	7	0	2	0	1	0	2	0	3	2	2	2	0	2	2	3	0	2	5	5			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr10:120879873A>T	ENST00000361432.2	+	5	528	c.502A>T	c.(502-504)Atg>Ttg	p.M168L	FAM45A_ENST00000489988.1_3'UTR|FAM45A_ENST00000535029.1_Intron|FAM45A_ENST00000544016.1_Missense_Mutation_p.M17L	NM_207009.2	NP_996892.1	Q8TCE6	FA45A_HUMAN	family with sequence similarity 45, member A	168										breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(2)|urinary_tract(1)	14		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0293)		TCAGTTTGGAATGGAAACTGT	0.343																																					p.M168L		Atlas-SNP	.											.	FAM45A	30	.	0			c.A502T						PASS	.						87	84	85					10																	120879873		2203	4300	6503	SO:0001583	missense	404636	exon5			TTTGGAATGGAAA	AF168713	CCDS7609.1	10q25	2008-09-04			ENSG00000119979	ENSG00000119979			31793	protein-coding gene	gene with protein product							Standard	NM_207009		Approved			Q8TCE6	OTTHUMG00000019143	ENST00000361432.2:c.502A>T	chr10.hg19:g.120879873A>T	ENSP00000354688:p.Met168Leu	121.0	0.0	.		137.0	42.0	.	NM_207009	B1AMV6|B4DDC3|D3DRC8|Q9NXW4	Missense_Mutation	SNP	ENST00000361432.2	hg19	CCDS7609.1	.	.	.	.	.	.	.	.	.	.	A	8.904	0.957092	0.18507	.	.	ENSG00000119979	ENST00000546291;ENST00000361432;ENST00000544016	.	.	.	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.51719	0.1691	L	0.42245	1.32	0.58432	D	0.999999	B;B;B;B	0.22414	0.051;0.069;0.01;0.051	B;B;B;B	0.24701	0.055;0.04;0.022;0.037	T	0.48625	-0.9019	9	0.02654	T	1	.	15.0195	0.71617	1.0:0.0:0.0:0.0	.	95;17;160;168	B4DNL9;B4DMU4;Q8TCE6-2;Q8TCE6	.;.;.;FA45A_HUMAN	L	168;168;17	.	ENSP00000354688:M168L	M	+	1	0	FAM45A	120869863	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.380000	0.90149	2.285000	0.76669	0.533000	0.62120	ATG	.	.	.	none		0.343	FAM45A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050623.1	NM_207009		T	120879873	A	T	120879873	3	4	97	1	0	0	0	0	1	0	0	0	5571	101	4	5	520	5	FAM45A	10	120879873	Missense_Mutation	SNP	A	TCGA-B9-4116-01A-01D-1252-08		120879873	14654874	38	6148											
LRRC4C	57689	hgsc.bcm.edu	37	chr11	40136626	40136630	+	Frame_Shift_Del	DEL	AGCAC	AGCAC	-																															aatttaacgtaccatcactgAgcacagctatccgcactttg																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	AGCAC	AGCAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr11:40136626_40136630delAGCAC	ENST00000278198.2	-	2	3176_3180	c.1213_1217delGTGCT	c.(1213-1218)gtgctcfs	p.VL405fs	LRRC4C_ENST00000528697.1_Frame_Shift_Del_p.VL405fs|LRRC4C_ENST00000530763.1_Frame_Shift_Del_p.VL405fs|LRRC4C_ENST00000527150.1_Frame_Shift_Del_p.VL405fs			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	405	Ig-like C2-type.				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)				ACCATCACTGAGCACAGCTATCCGC	0.454																																					p.405_406del		Atlas-INDEL	.											LRRC4C,NS,carcinoma,0,1	LRRC4C	190	.	0			c.1214_1218del						PASS	.																																			SO:0001589	frameshift_variant	57689	exon5			.	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.1213_1217delGTGCT	chr11.hg19:g.40136626_40136630delAGCAC	ENSP00000278198:p.Val405fs	484.0	0.0	0		222.0	50.0	0.225225	NM_020929	A8K0T1|Q7L0N3	Frame_Shift_Del	DEL	ENST00000278198.2	hg19	CCDS31464.1																																																																																			.	.	.	none		0.454	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929		-	40136630	AGCAC	-	40136626	7	5	97	1	0	1	0	1	0	0	0	0	9015	304	11	0	709	0	LRRC4C	11	40136626	Frame_Shift_Del	DEL	AGCAC	TCGA-B9-4116-01A-01D-1252-08		40136626	94869890	39	6149											
TRIM48	79097	hgsc.bcm.edu	37	chr11	55032729	55032729	+	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	gctctgtttgctgtgctccaGctctcaggagcaccggtatc	5	12	11	13	1	2	0	1	0	2	0	5	1	3	1	2	2	4	7	2	2	1	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr11:55032729G>T	ENST00000417545.2	+	2	484	c.398G>T	c.(397-399)aGc>aTc	p.S133I		NM_024114.3	NP_077019.2	Q8IWZ4	TRI48_HUMAN	tripartite motif containing 48	117						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(13)|lung(19)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						CTGTGCTCCAGCTCTCAGGAG	0.507																																					p.S133I		Atlas-SNP	.											.	TRIM48	149	.	0			c.G398T						PASS	.						53	49	50					11																	55032729		2190	4261	6451	SO:0001583	missense	79097	exon2			GCTCCAGCTCTCA	AF521869	CCDS7947.2	11q12	2013-01-09	2011-01-25		ENSG00000150244	ENSG00000150244		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19021	protein-coding gene	gene with protein product			"tripartite motif-containing 48"				Standard	NM_024114		Approved	RNF101	uc010rid.2	Q8IWZ4	OTTHUMG00000157011	ENST00000417545.2:c.398G>T	chr11.hg19:g.55032729G>T	ENSP00000402414:p.Ser133Ile	54.0	0.0	.		16.0	8.0	.	NM_024114	Q9BUW4	Missense_Mutation	SNP	ENST00000417545.2	hg19	CCDS7947.2	.	.	.	.	.	.	.	.	.	.	g	7.071	0.568353	0.13560	.	.	ENSG00000150244	ENST00000417545	T	0.42900	0.96	0.596	-1.19	0.09585	Zinc finger, B-box (3);	.	.	.	.	T	0.36524	0.0970	N	0.20610	0.595	0.09310	N	1	P	0.49961	0.93	P	0.57009	0.811	T	0.23797	-1.0178	9	0.62326	D	0.03	.	4.2471	0.10677	0.7213:0.0:0.2787:0.0	.	117	Q8IWZ4	TRI48_HUMAN	I	133	ENSP00000402414:S133I	ENSP00000402414:S133I	S	+	2	0	TRIM48	54789305	0.000000	0.05858	0.045000	0.18777	0.232000	0.25224	-0.139000	0.10358	-0.425000	0.07371	-0.506000	0.04501	AGC	.	.	.	none		0.507	TRIM48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347088.1			T	55032729	G	T	55032729	3	4	97	1	0	0	0	0	1	0	0	0	16535	971	34	4	404	4	TRIM48	11	55032729	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	14896103	55032729	79973787	40	6150											
COX8A	1351	hgsc.bcm.edu	37	chr11	63743765	63743765	+	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	gcgggctggatcctgtcacaCctggagacctacaggaggcc	8	6	14	13	1	1	1	1	0	0	1	2	4	2	3	4	5	1	1	4	5	1	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr11:63743765C>G	ENST00000314133.3	+	2	257	c.183C>G	c.(181-183)caC>caG	p.H61Q	AP000721.4_ENST00000535431.1_Intron	NM_004074.2	NP_004065.1	P10176	COX8A_HUMAN	cytochrome c oxidase subunit VIIIA (ubiquitous)	61					cellular metabolic process (GO:0044237)|generation of precursor metabolites and energy (GO:0006091)|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)	cytochrome-c oxidase activity (GO:0004129)										TCCTGTCACACCTGGAGACCT	0.587																																					p.H61Q		Atlas-SNP	.											.	COX8A	6	.	0			c.C183G						PASS	.						200	160	173					11																	63743765		2201	4297	6498	SO:0001583	missense	1351	exon2			GTCACACCTGGAG	J04823	CCDS8054.1	11q12-q13	2011-07-04	2010-04-27	2004-03-24	ENSG00000176340	ENSG00000176340	1.9.3.1	"Mitochondrial respiratory chain complex / Complex IV"	2294	protein-coding gene	gene with protein product		123870	"cytochrome c oxidase subunit VIII", "cytochrome c oxidase subunit 8A (ubiquitous)"	COX8		2543673, 2847943	Standard	NM_004074		Approved	COX8-2, COX8L, VIII-L, COX, VIII	uc001nye.3	P10176	OTTHUMG00000167785	ENST00000314133.3:c.183C>G	chr11.hg19:g.63743765C>G	ENSP00000321260:p.His61Gln	314.0	0.0	.		522.0	139.0	.	NM_004074	P15955	Missense_Mutation	SNP	ENST00000314133.3	hg19	CCDS8054.1	.	.	.	.	.	.	.	.	.	.	C	17.58	3.425954	0.62733	.	.	ENSG00000176340	ENST00000314133	.	.	.	5.75	3.88	0.44766	Cytochrome c oxidase subunit VIII/photosystem I reaction centre subunit IX (1);	0.064498	0.64402	D	0.000010	T	0.47002	0.1422	.	.	.	0.34757	D	0.732368	B	0.33940	0.433	B	0.37091	0.241	T	0.59337	-0.7473	8	0.87932	D	0	-8.3625	8.2466	0.31693	0.0:0.7603:0.1565:0.0832	.	61	P10176	COX8A_HUMAN	Q	61	.	ENSP00000321260:H61Q	H	+	3	2	COX8A	63500341	0.967000	0.33354	0.996000	0.52242	0.629000	0.37895	0.650000	0.24858	0.774000	0.33427	0.655000	0.94253	CAC	.	.	.	none		0.587	COX8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396273.1	NM_004074		G	63743765	C	G	63743765	3	3	97	1	0	0	0	0	1	0	0	0	3787	506	18	4	189	4	COX8A	11	63743765	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08	8711036	63743765	71262751	41	6151											
SCYL1	57410	hgsc.bcm.edu	37	chr11	65305494	65305494	+	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	1	0	0	0	0	0	0	0	0	gagtccgactggagcagctgGgaagctgagggctcctggga	8	6	18	9	1	0	1	0	1	0	0	2	6	2	4	2	4	3	4	2	4	1	0			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr11:65305494G>A	ENST00000270176.5	+	16	2165	c.2088G>A	c.(2086-2088)tgG>tgA	p.W696*	SCYL1_ENST00000524944.1_Nonsense_Mutation_p.W696*|SCYL1_ENST00000527009.1_Nonsense_Mutation_p.W553*|SCYL1_ENST00000420247.2_Nonsense_Mutation_p.W679*|SCYL1_ENST00000525364.1_Nonsense_Mutation_p.W695*|SCYL1_ENST00000533862.1_Missense_Mutation_p.G684E|SCYL1_ENST00000534462.1_3'UTR|SCYL1_ENST00000279270.6_Nonsense_Mutation_p.W696*	NM_020680.3	NP_065731.3	Q96KG9	NTKL_HUMAN	SCY1-like 1 (S. cerevisiae)	696					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						GGAGCAGCTGGGAAGCTGAGG	0.637																																					p.W696X		Atlas-SNP	.											.	SCYL1	76	.	0			c.G2088A						PASS	.						34	36	35					11																	65305494		1905	4127	6032	SO:0001587	stop_gained	57410	exon16			CAGCTGGGAAGCT	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.2088G>A	chr11.hg19:g.65305494G>A	ENSP00000270176:p.Trp696*	35.0	0.0	.		45.0	18.0	.	NM_020680	A6NJF1|Q96G50|Q96KG8|Q96KH1|Q9HAW5|Q9HBL3|Q9NR53	Nonsense_Mutation	SNP	ENST00000270176.5	hg19	CCDS41672.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.30|12.30	1.897578|1.897578	0.33535|0.33535	.|.	.|.	ENSG00000142186|ENSG00000142186	ENST00000533862|ENST00000270176;ENST00000525364;ENST00000420247;ENST00000279270;ENST00000524944;ENST00000527009;ENST00000528545	T|.	0.12774|.	2.65|.	4.3|4.3	4.3|4.3	0.51218|0.51218	.|.	.|0.000000	.|0.50627	.|D	.|0.000105	T|.	0.43612|.	0.1255|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	B|.	0.22746|.	0.074|.	B|.	0.20955|.	0.032|.	T|.	0.48375|.	-0.9041|.	7|.	0.05436|0.11485	T|T	0.98|0.65	.|.	12.6154|12.6154	0.56573|0.56573	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	684|.	Q96KG9-6|.	.|.	E|X	684|696;695;679;696;696;553;168	ENSP00000437254:G684E|.	ENSP00000437254:G684E|ENSP00000270176:W696X	G|W	+|+	2|3	0|0	SCYL1|SCYL1	65062070|65062070	1.000000|1.000000	0.71417|0.71417	0.987000|0.987000	0.45799|0.45799	0.319000|0.319000	0.28217|0.28217	6.160000|6.160000	0.71862|0.71862	2.126000|2.126000	0.65437|0.65437	0.561000|0.561000	0.74099|0.74099	GGG|TGG	.	.	.	none		0.637	SCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389159.2	NM_020680		A	65305494	G	A	65305494	4	1	97	1	0	0	0	0	0	1	0	0	13960	1241	43	2	2150	2	SCYL1	11	65305494	Nonsense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	1561729	65305494	69701022	42	6152											
FGF3	2248	hgsc.bcm.edu	37	chr11	69625463	69625464	+	Frame_Shift_Ins	INS	-	-	T																															actcgcactcggcgctgtagINStgctcctgcggggatgagat																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr11:69625463_69625464insT	ENST00000334134.2	-	3	419_420	c.329_330insA	c.(328-330)cacfs	p.H110fs		NM_005247.2	NP_005238.1	P11487	FGF3_HUMAN	fibroblast growth factor 3	110					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)			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)			CGGCGCTGTAGTGCTCCTGCGG	0.639																																					p.H110fs		Atlas-INDEL	.											.	FGF3	27	.	0			c.330_331insA						PASS	.																																			SO:0001589	frameshift_variant	2248	exon3			.		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.330dupA	chr11.hg19:g.69625464_69625464dupT	ENSP00000334122:p.His110fs	132.0	0.0	0		174.0	54.0	0.310345	NM_005247	Q0VG69	Frame_Shift_Ins	INS	ENST00000334134.2	hg19	CCDS8195.1																																																																																			.	.	.	none		0.639	FGF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396835.1	NM_005247		T	69625464	-	T	69625463	7	5	97	1	0	1	1	0	0	0	0	0	5860	1020	36	0	393	0	FGF3	11	69625463	Frame_Shift_Ins	INS	-	TCGA-B9-4116-01A-01D-1252-08	4319969	69625463	65381053	43	6153											
IGSF9B	22997	hgsc.bcm.edu	37	chr11	133805658	133805658	+	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	gcaccctcagcttcaggtcgCtgcaaagcggcatggggaca	9	6	13	13	2	2	0	2	0	0	0	3	1	2	1	1	4	3	5	1	4	1	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr11:133805658C>T	ENST00000321016.8	-	7	1052		c.e7-1		IGSF9B_ENST00000533871.2_Splice_Site			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B						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)		CTTCAGGTCGCTGCAAAGCGG	0.617																																					.		Atlas-SNP	.											.	IGSF9B	290	.	0			c.822-1G>A						PASS	.						20	24	22					11																	133805658		2117	4221	6338	SO:0001630	splice_region_variant	22997	exon8			AGGTCGCTGCAAA	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.822-1G>A	chr11.hg19:g.133805658C>T		63.0	0.0	.		60.0	32.0	.	NM_014987	G5EA26	Splice_Site	SNP	ENST00000321016.8	hg19		.	.	.	.	.	.	.	.	.	.	C	33	5.219946	0.95139	.	.	ENSG00000080854	ENST00000321016;ENST00000533871;ENST00000527648	.	.	.	5.18	5.18	0.71444	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.0502	0.93039	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	IGSF9B	133310868	1.000000	0.71417	0.166000	0.22797	0.790000	0.44656	5.713000	0.68415	2.560000	0.86352	0.561000	0.74099	.	.	.	.	none		0.617	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	Intron	T	133805658	C	T	133805658	5	4	97	1	0	0	0	0	0	0	1	0	7613	811	28	2	3280	2	IGSF9B	11	133805658	Splice_Site	SNP	C	TCGA-B9-4116-01A-01D-1252-08	64180195	133805658	1200858	44	6154											
ITGA7	3679	hgsc.bcm.edu	37	chr12	56096870	56096870	+	Frame_Shift_Del	DEL	T	T	-																															ccactctgtagcagtcagtcTcctccaggctcaacgggcaa																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr12:56096870delT	ENST00000555728.1	-	2	327	c.299delA	c.(298-300)gagfs	p.E100fs	ITGA7_ENST00000347027.6_Frame_Shift_Del_p.E100fs|ITGA7_ENST00000257879.6_Frame_Shift_Del_p.E100fs|ITGA7_ENST00000257880.7_Frame_Shift_Del_p.E100fs|ITGA7_ENST00000394230.2_Frame_Shift_Del_p.E100fs|ITGA7_ENST00000452168.2_Intron|ITGA7_ENST00000394229.2_Frame_Shift_Del_p.E100fs|ITGA7_ENST00000553804.1_Frame_Shift_Del_p.E100fs			Q13683	ITA7_HUMAN	integrin, alpha 7	100					blood vessel morphogenesis (GO:0048514)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|regulation of cell shape (GO:0008360)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integrin alpha7-beta1 complex (GO:0034677)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(16)|ovary(2)|prostate(2)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						GCAGTCAGTCTCCTCCAGGCT	0.642																																					p.E100fs		Atlas-INDEL	.											.	ITGA7	194	.	0			c.300delG						PASS	.						106	96	99					12																	56096870		2203	4300	6503	SO:0001589	frameshift_variant	3679	exon2			.		CCDS8888.1, CCDS44914.1, CCDS55832.1	12q13	2014-09-17				ENSG00000135424		"Integrins"	6143	protein-coding gene	gene with protein product		600536				7607681	Standard	NM_002206		Approved		uc001shh.3	Q13683		ENST00000555728.1:c.299delA	chr12.hg19:g.56096870delT	ENSP00000452387:p.Glu100fs	250.0	0.0	0		363.0	130.0	0.358127	NM_002206	B4E3U0|C9JMD3|C9JMZ6|O43197|Q86W93|Q9NY89|Q9UET0|Q9UEV2	Frame_Shift_Del	DEL	ENST00000555728.1	hg19																																																																																				.	.	.	none		0.642	ITGA7-014	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000410138.1	NM_002206		-	56096870	T	-	56096870	7	5	97	1	0	1	0	1	0	0	0	0	7888	1551	54	0	3388	0	ITGA7	12	56096870	Frame_Shift_Del	DEL	T	TCGA-B9-4116-01A-01D-1252-08		56096870	77755025	45	6155											
PPFIA2	8499	hgsc.bcm.edu	37	chr12	81661720	81661720	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgtgttggaatctgtaataAtaaagctaagctgctgtagt	12	14	10	5	0	1	0	0	0	1	0	1	1	1	1	0	1	3	6	0	1	7	6			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr12:81661720A>G	ENST00000549396.1	-	29	3617	c.3457T>C	c.(3457-3459)Tta>Cta	p.L1153L	PPFIA2_ENST00000545296.2_Intron|PPFIA2_ENST00000407050.4_Silent_p.L1052L|PPFIA2_ENST00000541570.2_Silent_p.L689L|PPFIA2_ENST00000550359.2_Silent_p.L1000L|PPFIA2_ENST00000552948.1_Silent_p.L1132L|PPFIA2_ENST00000443686.3_Silent_p.L1048L|RP11-121G22.3_ENST00000549161.1_lincRNA|PPFIA2_ENST00000549325.1_Silent_p.L1138L|PPFIA2_ENST00000541017.1_Silent_p.L339L|PPFIA2_ENST00000548586.1_Silent_p.L1147L|PPFIA2_ENST00000550584.2_Silent_p.L1153L|PPFIA2_ENST00000333447.7_Silent_p.L1141L	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	1153	SAM 3. {ECO:0000255|PROSITE- ProRule:PRU00184}.				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						ATCTGTAATAATAAAGCTAAG	0.363																																					p.L1153L		Atlas-SNP	.											.	PPFIA2	207	.	0			c.T3457C						PASS	.						68	66	67					12																	81661720		1846	4101	5947	SO:0001819	synonymous_variant	8499	exon28			GTAATAATAAAGC	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.3457T>C	chr12.hg19:g.81661720A>G		33.0	0.0	.		32.0	8.0	.	NM_001220473	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Silent	SNP	ENST00000549396.1	hg19	CCDS55857.1																																																																																			.	.	.	none		0.363	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1			G	81661720	A	G	81661720	2	3	97	1	0	0	0	0	0	0	0	1	12317	98	4	3		3	PPFIA2	12	81661720	Silent	SNP	A	TCGA-B9-4116-01A-01D-1252-08	25564850	81661720	52190175	46	6156											
KIAA1033	23325	hgsc.bcm.edu	37	chr12	105512257	105512259	+	In_Frame_Del	DEL	GTG	GTG	-																															ttgttacgaggtgctatgaaGtggtgatgaacgtagtccac																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	GTG	GTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr12:105512257_105512259delGTG	ENST00000332180.5	+	7	556_558	c.469_471delGTG	c.(469-471)gtgdel	p.V158del		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						GTGCTATGAAGTGGTGATGAACG	0.34																																					p.156_157del		Atlas-INDEL	.											.	KIAA1033	83	.	0			c.468_470del						PASS	.																																			SO:0001651	inframe_deletion	23325	exon7			.	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.469_471delGTG	chr12.hg19:g.105512260_105512262delGTG	ENSP00000328062:p.Val158del	194.0	0.0	0		36.0	11.0	0.305556	NM_015275		In_Frame_Del	DEL	ENST00000332180.5	hg19	CCDS41826.1																																																																																			.	.	.	none		0.34	KIAA1033-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406138.4	NM_015275		-	105512259	GTG	-	105512257	7	5	97	1	0	1	0	1	0	0	0	0	8213	1029	36	0	495	0	KIAA1033	12	105512257	In_Frame_Del	DEL	GTG	TCGA-B9-4116-01A-01D-1252-08	23850537	105512257	28339638	47	6157											
ZNF10	7556	hgsc.bcm.edu	37	chr12	133732280	133732280	+	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	cagagagacatttgaggcaaGtggcattcacccaaaagaaa	17	6	10	8	0	1	4	1	1	0	3	1	5	1	4	1	2	0	2	1	2	4	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr12:133732280G>C	ENST00000248211.6	+	5	670	c.448G>C	c.(448-450)Gtg>Ctg	p.V150L	ZNF10_ENST00000402932.2_Intron|ZNF268_ENST00000416488.1_Intron|CTD-2140B24.4_ENST00000540096.2_Intron|ZNF10_ENST00000426665.2_Missense_Mutation_p.V150L	NM_015394.4	NP_056209.2	P21506	ZNF10_HUMAN	zinc finger protein 10	150				Missing (in Ref. 1). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|prostate(1)|skin(5)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.00948)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		TTTGAGGCAAGTGGCATTCAC	0.428																																					p.V150L		Atlas-SNP	.											.	ZNF10	58	.	0			c.G448C						PASS	.						110	106	107					12																	133732280		2203	4300	6503	SO:0001583	missense	7556	exon5			AGGCAAGTGGCAT	X52332, BC024182	CCDS9283.1	12q24.33	2013-01-08	2005-05-22		ENSG00000256223	ENSG00000256223		"Zinc fingers, C2H2-type", "-"	12879	protein-coding gene	gene with protein product		194538	"zinc finger protein 10 (KOX 1)"			7865130, 8262519	Standard	NM_015394		Approved	KOX1	uc001ulq.3	P21506	OTTHUMG00000167944	ENST00000248211.6:c.448G>C	chr12.hg19:g.133732280G>C	ENSP00000248211:p.Val150Leu	148.0	0.0	.		43.0	10.0	.	NM_015394	B2RBS1|Q8TC91	Missense_Mutation	SNP	ENST00000248211.6	hg19	CCDS9283.1	.	.	.	.	.	.	.	.	.	.	G	13.56	2.273178	0.40194	.	.	ENSG00000256223	ENST00000248211;ENST00000426665;ENST00000537119	T;T;T	0.05447	3.44;3.44;4.56	4.44	4.44	0.53790	.	0.698949	0.11773	N	0.530882	T	0.04137	0.0115	N	0.16708	0.43	0.80722	D	1	P	0.34662	0.462	B	0.31614	0.133	T	0.51252	-0.8729	9	.	.	.	.	8.5148	0.33239	0.1041:0.0:0.8959:0.0	.	150	P21506	ZNF10_HUMAN	L	150;150;108	ENSP00000248211:V150L;ENSP00000393814:V150L;ENSP00000437397:V108L	.	V	+	1	0	ZNF10	132242353	0.671000	0.27521	1.000000	0.80357	0.991000	0.79684	1.986000	0.40677	2.460000	0.83146	0.655000	0.94253	GTG	.	.	.	none		0.428	ZNF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397182.1	NM_015394		C	133732280	G	C	133732280	3	2	97	1	0	0	0	0	1	0	0	0	17724	1029	36	4	462	4	ZNF10	12	133732280	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	28220023	133732280	119615	48	6158											
IL17D	53342	hgsc.bcm.edu	37	chr13	21295994	21295994	+	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	cccgtgggctgcacctgcgtCcccgagccggagaaggacgc	6	4	15	16	5	0	1	0	0	0	1	1	4	1	2	5	3	3	2	5	3	1	0	rs372465901		TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr13:21295994C>T	ENST00000304920.3	+	3	618	c.510C>T	c.(508-510)gtC>gtT	p.V170V		NM_138284.1	NP_612141.1	Q8TAD2	IL17D_HUMAN	interleukin 17D	170					inflammatory response (GO:0006954)	extracellular space (GO:0005615)				endometrium(1)|skin(1)	2		all_cancers(29;9.63e-24)|all_epithelial(30;1.09e-19)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000301)|Epithelial(112;0.000633)|OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Lung(94;0.0154)|LUSC - Lung squamous cell carcinoma(192;0.0414)		GCACCTGCGTCCCCGAGCCGG	0.706																																					p.V170V		Atlas-SNP	.											.	IL17D	4	.	0			c.C510T						PASS	.						39	39	39					13																	21295994		2190	4279	6469	SO:0001819	synonymous_variant	53342	exon3			CTGCGTCCCCGAG	AY078238	CCDS9292.1	13q11	2008-07-18			ENSG00000172458	ENSG00000172458		"Interleukins and interleukin receptors"	5984	protein-coding gene	gene with protein product	"interleukin 27"	607587				12097364	Standard	NM_138284		Approved	IL-22, IL-27, IL-17D, IL27, FLJ30846	uc001unm.3	Q8TAD2	OTTHUMG00000016521	ENST00000304920.3:c.510C>T	chr13.hg19:g.21295994C>T		104.0	0.0	.		209.0	72.0	.	NM_138284	B1AM69	Silent	SNP	ENST00000304920.3	hg19	CCDS9292.1																																																																																			.	.	.	alt		0.706	IL17D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044087.1	NM_138284		T	21295994	C	T	21295994	2	4	97	1	0	0	0	0	0	0	0	1	7644	842	30	2		2	IL17D	13	21295994	Silent	SNP	C	TCGA-B9-4116-01A-01D-1252-08		21295994	93873884	49	6159											
IGF1R	3480	hgsc.bcm.edu	37	chr15	99465632	99465632	+	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	ctgggctgcagcgcctccaaCttcgtctttgcaaggactat	7	11	10	13	2	1	0	0	0	1	0	3	1	2	1	2	2	4	3	2	2	3	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr15:99465632C>A	ENST00000268035.6	+	11	3068	c.2457C>A	c.(2455-2457)aaC>aaA	p.N819K	IGF1R_ENST00000558762.1_Missense_Mutation_p.N819K	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	819	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"	GCGCCTCCAACTTCGTCTTTG	0.517																																					p.N819K		Atlas-SNP	.											.	IGF1R	147	.	0			c.C2457A						PASS	.						105	102	103					15																	99465632		2197	4297	6494	SO:0001583	missense	3480	exon11			CTCCAACTTCGTC	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"CD molecules", "Fibronectin type III domain containing"	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.2457C>A	chr15.hg19:g.99465632C>A	ENSP00000268035:p.Asn819Lys	209.0	0.0	.		350.0	122.0	.	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Missense_Mutation	SNP	ENST00000268035.6	hg19	CCDS10378.1	.	.	.	.	.	.	.	.	.	.	C	14.97	2.695512	0.48202	.	.	ENSG00000140443	ENST00000268035	T	0.68624	-0.34	5.5	4.59	0.56863	Immunoglobulin-like fold (1);	0.086755	0.47455	N	0.000239	T	0.57169	0.2035	L	0.44542	1.39	0.50171	D	0.999854	B;B	0.33964	0.434;0.18	B;B	0.34489	0.184;0.109	T	0.58747	-0.7582	10	0.54805	T	0.06	.	9.3354	0.38047	0.1455:0.7829:0.0:0.0716	.	819;819	C9J5X1;P08069	.;IGF1R_HUMAN	K	819	ENSP00000268035:N819K	ENSP00000268035:N819K	N	+	3	2	IGF1R	97283155	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	1.087000	0.30865	1.319000	0.45190	-0.127000	0.14921	AAC	.	.	.	none		0.517	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875		A	99465632	C	A	99465632	3	1	97	1	0	0	0	0	1	0	0	0	7578	564	20	4	2499	4	IGF1R	15	99465632	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08		99465632	3065760	50	6160											
MKL2	57496	hgsc.bcm.edu	37	chr16	14346228	14346228	+	Missense_Mutation	SNP	T	T	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	tttatttgacacagcctagtTcacccccgccaccccagcaa	10	9	5	17	1	1	1	1	1	0	0	1	1	1	1	6	0	2	2	6	0	3	5			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr16:14346228T>G	ENST00000341243.5	+	13	2539	c.2539T>G	c.(2539-2541)Tca>Gca	p.S847A	MKL2_ENST00000574045.1_Missense_Mutation_p.S808A|MKL2_ENST00000318282.5_Missense_Mutation_p.S808A|MKL2_ENST00000571589.1_Missense_Mutation_p.S858A			Q9ULH7	MKL2_HUMAN	MKL/myocardin-like 2	847					blood vessel morphogenesis (GO:0048514)|cardiac muscle tissue development (GO:0048738)|embryonic organ development (GO:0048568)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|muscle organ development (GO:0007517)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(6)|liver(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						ACAGCCTAGTTCACCCCCGCC	0.522																																					p.S808A		Atlas-SNP	.											.	MKL2	103	.	0			c.T2422G						PASS	.						111	107	108					16																	14346228		2197	4300	6497	SO:0001583	missense	57496	exon15			CCTAGTTCACCCC	AB033069	CCDS32391.1	16p13.12	2012-11-29			ENSG00000186260	ENSG00000186260			29819	protein-coding gene	gene with protein product		609463				10574462	Standard	NM_014048		Approved	MRTF-B, FLJ31823	uc002dcg.3	Q9ULH7	OTTHUMG00000177379	ENST00000341243.5:c.2539T>G	chr16.hg19:g.14346228T>G	ENSP00000345841:p.Ser847Ala	208.0	0.0	.		246.0	70.0	.	NM_014048	A6ND53|B4DGT8|Q68CT1|Q6UB16|Q86WW2|Q8N226	Missense_Mutation	SNP	ENST00000341243.5	hg19		.	.	.	.	.	.	.	.	.	.	T	15.37	2.812492	0.50527	.	.	ENSG00000186260	ENST00000318282;ENST00000341243	.	.	.	5.98	4.89	0.63831	.	0.443487	0.25106	N	0.033091	T	0.29882	0.0747	L	0.41710	1.295	0.20563	N	0.999886	B;B	0.19583	0.022;0.037	B;B	0.15052	0.005;0.012	T	0.19353	-1.0308	9	0.22706	T	0.39	-7.812	6.5315	0.22330	0.1376:0.0725:0.0:0.7899	.	858;808	B4DGT8;Q9ULH7-4	.;.	A	808;847	.	ENSP00000339086:S808A	S	+	1	0	MKL2	14253729	1.000000	0.71417	0.041000	0.18516	0.317000	0.28152	4.265000	0.58865	1.089000	0.41292	-0.250000	0.11733	TCA	.	.	.	none		0.522	MKL2-202	KNOWN	basic	protein_coding	protein_coding		NM_014048		G	14346228	T	G	14346228	3	3	97	1	0	0	0	0	1	0	0	0	9609	1783	62	5	2472	5	MKL2	16	14346228	Missense_Mutation	SNP	T	TCGA-B9-4116-01A-01D-1252-08		14346228	76008525	51	6161											
BFAR	51283	hgsc.bcm.edu	37	chr16	14755800	14755800	+	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	tatacgccctcaagagctccCccaggctgagtctgctctac	8	9	8	16	1	3	2	1	1	2	1	4	2	4	2	3	1	4	3	3	1	4	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr16:14755800C>G	ENST00000261658.2	+	6	1112	c.835C>G	c.(835-837)Ccc>Gcc	p.P279A	BFAR_ENST00000563971.1_Missense_Mutation_p.P154A|BFAR_ENST00000426842.2_Missense_Mutation_p.P151A	NM_016561.2	NP_057645.1	Q9NZS9	BFAR_HUMAN	bifunctional apoptosis regulator	279					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						CAAGAGCTCCCCCAGGCTGAG	0.567																																					p.P279A		Atlas-SNP	.											.	BFAR	38	.	0			c.C835G						PASS	.						222	192	202					16																	14755800		2197	4300	6497	SO:0001583	missense	51283	exon6			AGCTCCCCCAGGC	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.835C>G	chr16.hg19:g.14755800C>G	ENSP00000261658:p.Pro279Ala	325.0	0.0	.		478.0	175.0	.	NM_016561	A8K4Z9|B4DUT0|D3DUG8	Missense_Mutation	SNP	ENST00000261658.2	hg19	CCDS10554.1	.	.	.	.	.	.	.	.	.	.	C	18.00	3.524396	0.64747	.	.	ENSG00000103429	ENST00000261658;ENST00000426842	T;T	0.55760	2.85;0.5	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.62950	0.2470	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.85130	0.991;0.997;0.996	T	0.67142	-0.5745	10	0.87932	D	0	.	18.1703	0.89743	0.0:1.0:0.0:0.0	.	151;279;279	B4DUT0;B2R9R6;Q9NZS9	.;.;BFAR_HUMAN	A	279;151	ENSP00000261658:P279A;ENSP00000400634:P151A	ENSP00000261658:P279A	P	+	1	0	BFAR	14663301	1.000000	0.71417	0.584000	0.28653	0.249000	0.25844	7.391000	0.79828	2.513000	0.84729	0.655000	0.94253	CCC	.	.	.	none		0.567	BFAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252088.1	NM_016561		G	14755800	C	G	14755800	3	3	97	1	0	0	0	0	1	0	0	0	1414	623	22	4	853	4	BFAR	16	14755800	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08	409572	14755800	75598953	52	6162											
GPRC5B	51704	hgsc.bcm.edu	37	chr16	19884048	19884048	+	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	gacacgtactgagggaggagGtccagcccacagcctcggga	10	4	15	12	2	0	1	0	1	0	0	2	5	1	4	3	4	3	1	3	4	1	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr16:19884048G>A	ENST00000300571.2	-	2	311	c.120C>T	c.(118-120)gaC>gaT	p.D40D	GPRC5B_ENST00000537135.1_Silent_p.D66D|GPRC5B_ENST00000535671.1_Silent_p.D40D|GPRC5B_ENST00000569847.1_Silent_p.D40D|GPRC5B_ENST00000569479.1_Silent_p.D40D	NM_016235.1	NP_057319.1	Q9NZH0	GPC5B_HUMAN	G protein-coupled receptor, class C, group 5, member B	40					glucose homeostasis (GO:0042593)|locomotory behavior (GO:0007626)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein tyrosine kinase activity (GO:0061098)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|G-protein coupled receptor binding (GO:0001664)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						GAGGGAGGAGGTCCAGCCCAC	0.637																																					p.D40D		Atlas-SNP	.											.	GPRC5B	54	.	0			c.C120T						PASS	.						50	51	51					16																	19884048		2197	4300	6497	SO:0001819	synonymous_variant	51704	exon2			GAGGAGGTCCAGC	AF202640	CCDS10581.1	16p12	2014-01-30	2014-01-30		ENSG00000167191	ENSG00000167191		"GPCR / Class C : Orphans"	13308	protein-coding gene	gene with protein product		605948	"G protein-coupled receptor, family C, group 1, member B", "G protein-coupled receptor, family C, group 5, member B"			10493829, 10783259	Standard	XM_005255357		Approved	RAIG-2	uc002dgt.3	Q9NZH0	OTTHUMG00000131460	ENST00000300571.2:c.120C>T	chr16.hg19:g.19884048G>A		115.0	0.0	.		207.0	82.0	.	NM_016235	D2DFB0|O75205|Q8NBZ8	Silent	SNP	ENST00000300571.2	hg19	CCDS10581.1																																																																																			.	.	.	none		0.637	GPRC5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254285.1			A	19884048	G	A	19884048	2	1	97	1	0	0	0	0	0	0	0	1	6732	1252	44	2		2	GPRC5B	16	19884048	Silent	SNP	G	TCGA-B9-4116-01A-01D-1252-08	5128248	19884048	70470705	53	6163											
BCL7C	9274	hgsc.bcm.edu	37	chr16	30899187	30899187	+	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	ggacaggcaggccggcttctCaggggtcaggggcatttggg	6	7	19	9	1	2	0	2	0	1	0	3	1	2	1	1	9	0	3	1	9	0	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr16:30899187C>T	ENST00000215115.4	-	6	1668	c.653G>A	c.(652-654)tGa>tAa	p.*218*	AC106782.20_ENST00000572471.1_RNA|MIR4519_ENST00000564901.1_RNA|MIR4519_ENST00000570025.1_RNA|BCL7C_ENST00000380317.4_Intron|MIR4519_ENST00000565573.1_RNA	NM_004765.2	NP_004756.2	Q8WUZ0	BCL7C_HUMAN	B-cell CLL/lymphoma 7C	0					apoptotic process (GO:0006915)			p.*218L(1)		large_intestine(1)|lung(3)|prostate(1)|skin(1)	6			Colorectal(24;0.198)			GCCGGCTTCTCAGGGGTCAGG	0.592																																					p.X218X		Atlas-SNP	.											.	BCL7C	30	.	1	Nonstop extension(1)	lung(1)	c.G653A						PASS	.						81	107	98					16																	30899187		2196	4300	6496	SO:0001819	synonymous_variant	9274	exon6			GCTTCTCAGGGGT	AJ223980	CCDS10693.1, CCDS67012.1	16p11	2012-11-19			ENSG00000099385	ENSG00000099385			1006	protein-coding gene	gene with protein product		605847				9931421	Standard	NM_004765		Approved		uc002dzv.3	Q8WUZ0	OTTHUMG00000177719	ENST00000215115.4:c.653G>A	chr16.hg19:g.30899187C>T		404.0	0.0	.		677.0	259.0	.	NM_004765	O43770|Q6PD89	Silent	SNP	ENST00000215115.4	hg19	CCDS10693.1																																																																																			.	.	.	none		0.592	BCL7C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255547.3	NM_004765		T	30899187	C	T	30899187	2	4	97	1	0	0	0	0	0	0	0	1	1380	837	29	2		2	BCL7C	16	30899187	Silent	SNP	C	TCGA-B9-4116-01A-01D-1252-08	11015139	30899187	59455566	54	6164											
ZNF423	23090	hgsc.bcm.edu	37	chr16	49671278	49671278	+	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	tcggccttggacttcttgctGtgggccagtggaatgttctt	4	15	13	9	1	2	0	0	0	2	0	3	2	2	2	2	4	1	2	2	4	1	5			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr16:49671278G>T	ENST00000561648.1	-	4	1838	c.1785C>A	c.(1783-1785)caC>caA	p.H595Q	ZNF423_ENST00000563137.2_Missense_Mutation_p.H535Q|ZNF423_ENST00000535559.1_Missense_Mutation_p.H478Q|ZNF423_ENST00000562520.1_Missense_Mutation_p.H535Q|ZNF423_ENST00000562871.1_Missense_Mutation_p.H535Q|ZNF423_ENST00000262383.2_Missense_Mutation_p.H595Q|ZNF423_ENST00000567169.1_Missense_Mutation_p.H478Q	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	595					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)				ACTTCTTGCTGTGGGCCAGTG	0.572																																					p.H595Q		Atlas-SNP	.											.	ZNF423	463	.	0			c.C1785A						PASS	.						127	100	109					16																	49671278		2198	4300	6498	SO:0001583	missense	23090	exon4			CTTGCTGTGGGCC	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.1785C>A	chr16.hg19:g.49671278G>T	ENSP00000455426:p.His595Gln	150.0	0.0	.		318.0	99.0	.	NM_015069	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	hg19	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	G	8.424	0.846973	0.17034	.	.	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.08634	3.07;3.14	4.78	2.8	0.32819	.	0.047718	0.85682	D	0.000000	T	0.05273	0.0140	N	0.24115	0.695	0.37616	D	0.921121	B	0.26120	0.142	B	0.24394	0.053	T	0.43702	-0.9375	9	.	.	.	.	8.2567	0.31760	0.2436:0.0:0.7564:0.0	.	595	Q2M1K9	ZN423_HUMAN	Q	595;478	ENSP00000262383:H595Q;ENSP00000442321:H478Q	.	H	-	3	2	ZNF423	48228779	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.823000	0.55715	0.439000	0.26476	0.561000	0.74099	CAC	.	.	.	none		0.572	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		T	49671278	G	T	49671278	3	4	97	1	0	0	0	0	1	0	0	0	17910	1368	48	4	2089	4	ZNF423	16	49671278	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	18772091	49671278	40683475	55	6165											
BBS2	583	hgsc.bcm.edu	37	chr16	56531663	56531663	+	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	gcattccctcaccttaactaGcacctttcgtaattcctcaa	10	13	3	15	1	2	0	2	0	0	0	5	0	4	0	4	0	2	3	4	0	4	6			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr16:56531663G>A	ENST00000245157.5	-	14	2209	c.1789C>T	c.(1789-1791)Cta>Tta	p.L597L	BBS2_ENST00000568104.1_Intron	NM_031885.3	NP_114091	Q9BXC9	BBS2_HUMAN	Bardet-Biedl syndrome 2	597					adult behavior (GO:0030534)|artery smooth muscle contraction (GO:0014824)|brain morphogenesis (GO:0048854)|cartilage development (GO:0051216)|cerebral cortex development (GO:0021987)|cilium morphogenesis (GO:0060271)|fat cell differentiation (GO:0045444)|Golgi to plasma membrane protein transport (GO:0043001)|hippocampus development (GO:0021766)|melanosome transport (GO:0032402)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|positive regulation of multicellular organism growth (GO:0040018)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|sperm axoneme assembly (GO:0007288)|striatum development (GO:0021756)|vasodilation (GO:0042311)|visual perception (GO:0007601)	BBSome (GO:0034464)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)	26						ACCTTAACTAGCACCTTTCGT	0.373									Bardet-Biedl syndrome																												p.L597L		Atlas-SNP	.											.	BBS2	67	.	0			c.C1789T						PASS	.						141	133	136					16																	56531663		2198	4300	6498	SO:0001819	synonymous_variant	583	exon14	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	TAACTAGCACCTT	AF342736	CCDS32451.1	16q21	2013-01-08				ENSG00000125124			967	protein-coding gene	gene with protein product		606151		BBS		11285252	Standard	NM_031885		Approved		uc002ejd.2	Q9BXC9		ENST00000245157.5:c.1789C>T	chr16.hg19:g.56531663G>A		282.0	0.0	.		75.0	31.0	.	NM_031885	Q96CM0|Q96SN9	Silent	SNP	ENST00000245157.5	hg19	CCDS32451.1																																																																																			.	.	.	none		0.373	BBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434386.2	NM_031885		A	56531663	G	A	56531663	2	1	97	1	0	0	0	0	0	0	0	1	1338	962	34	2		2	BBS2	16	56531663	Silent	SNP	G	TCGA-B9-4116-01A-01D-1252-08	6860385	56531663	33823090	56	6166											
ZC3H18	124245	hgsc.bcm.edu	37	chr16	88653023	88653023	+	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	ttcaggatgatgacctggaaGaaggtgaagtgaaggacccc	13	7	14	7	0	1	5	1	4	0	1	1	8	1	8	3	4	0	0	3	4	4	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr16:88653023G>T	ENST00000301011.5	+	3	819	c.619G>T	c.(619-621)Gaa>Taa	p.E207*	ZC3H18_ENST00000452588.2_Nonsense_Mutation_p.E207*	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	207						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)		TGACCTGGAAGAAGGTGAAGT	0.542																																					p.E207X	Ovarian(121;375 2276 20373 38669)	Atlas-SNP	.											.	ZC3H18	90	.	0			c.G619T						PASS	.						136	105	116					16																	88653023		2198	4300	6498	SO:0001587	stop_gained	124245	exon3			CTGGAAGAAGGTG	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.619G>T	chr16.hg19:g.88653023G>T	ENSP00000301011:p.Glu207*	93.0	0.0	.		166.0	40.0	.	NM_144604	Q96DG4|Q96MP7	Nonsense_Mutation	SNP	ENST00000301011.5	hg19	CCDS10967.1	.	.	.	.	.	.	.	.	.	.	G	41	8.860379	0.98980	.	.	ENSG00000158545	ENST00000301011;ENST00000289509;ENST00000452588;ENST00000545404	.	.	.	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-25.7045	18.3833	0.90457	0.0:0.0:1.0:0.0	.	.	.	.	X	207;207;207;90	.	ENSP00000289509:E207X	E	+	1	0	ZC3H18	87180524	1.000000	0.71417	0.978000	0.43139	0.763000	0.43281	9.161000	0.94739	2.350000	0.79820	0.462000	0.41574	GAA	.	.	.	none		0.542	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1	NM_144604		T	88653023	G	T	88653023	4	4	97	1	0	0	0	0	0	1	0	0	17580	943	33	4	625	4	ZC3H18	16	88653023	Nonsense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	32121360	88653023	1701730	57	6167											
MINK1	100130311	hgsc.bcm.edu	37	chr17	4800540	4800540	+	5'Flank	SNP	T	T	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	tctgggggcagcagccaagtTtacttcatgactctgaaccg	9	10	11	11	1	3	2	1	2	2	0	3	2	3	2	2	2	4	3	2	2	3	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr17:4800540T>G	ENST00000381365.3	+	0	0				C17orf107_ENST00000521575.1_5'Flank|MINK1_ENST00000453408.3_Silent_p.V1299V|MINK1_ENST00000355280.6_Silent_p.V1319V|MINK1_ENST00000347992.7_Silent_p.V1290V	NM_001145536.1	NP_001139008.1	Q6ZR85	CQ107_HUMAN	chromosome 17 open reading frame 107											endometrium(2)	2						GCAGCCAAGTTTACTTCATGA	0.612																																					p.V1319V		Atlas-SNP	.											.	MINK1	110	.	0			c.T3957G						PASS	.						71	73	72					17																	4800540		1933	4140	6073	SO:0001631	upstream_gene_variant	50488	exon32			CCAAGTTTACTTC	AK128415	CCDS45591.1	17p13.2	2009-09-30			ENSG00000205710	ENSG00000205710			37238	protein-coding gene	gene with protein product							Standard	NM_001145536		Approved		uc002fzl.3	Q6ZR85	OTTHUMG00000164838		chr17.hg19:g.4800540T>G	Exception_encountered	72.0	0.0	.		96.0	26.0	.	NM_153827		Silent	SNP	ENST00000381365.3	hg19	CCDS45591.1																																																																																			.	.	.	none		0.612	C17orf107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380556.1	NM_001145536		G	4800540	T	G	4800540	1	3	97	0	1	0	0	0	0	0	0	0	9594	1828	64	5		5	MINK1	17	4800540	5'Flank	SNP	T	TCGA-B9-4116-01A-01D-1252-08		4800540	76394670	58	6168											
SLC16A13	201232	hgsc.bcm.edu	37	chr17	6942168	6942169	+	In_Frame_Ins	INS	-	-	ATA																															gcctgggactgttgcagatgINSatagagagcatcggggggct																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr17:6942168_6942169insATA	ENST00000308027.6	+	3	1349_1350	c.1041_1042insATA	c.(1042-1044)ata>ATAata	p.348_348I>II		NM_201566.2	NP_963860.1	Q7RTY0	MOT13_HUMAN	solute carrier family 16, member 13	348						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						TGTTGCAGATGATAGAGAGCAT	0.589																																					p.M347delinsMI		Atlas-INDEL	.											.	SLC16A13	28	.	0			c.1041_1042insATA						PASS	.																																			SO:0001652	inframe_insertion	201232	exon3			.	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.1042_1044dupATA	chr17.hg19:g.6942169_6942171dupATA	ENSP00000309751:p.Ile348dup	309.0	0.0	0		467.0	118.0	0.252677	NM_201566	A3KMG3|A5PKU5|Q2VP92	In_Frame_Ins	INS	ENST00000308027.6	hg19	CCDS11085.1																																																																																			.	.	.	none		0.589	SLC16A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219923.2			ATA	6942169	-	ATA	6942168	7	5	97	1	0	1	1	0	0	0	0	0	14419	1290	45	0	1051	0	SLC16A13	17	6942168	In_Frame_Ins	INS	-	TCGA-B9-4116-01A-01D-1252-08	2141628	6942168	74253042	59	6169											
YBX2	51087	hgsc.bcm.edu	37	chr17	7193332	7193332	+	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	gcggggggactcgctcatctCcctgctgttggtgcccctcc	2	10	13	16	2	2	0	1	0	1	0	5	1	3	1	4	4	2	3	4	4	0	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr17:7193332C>A	ENST00000007699.5	-	6	866	c.803G>T	c.(802-804)gGa>gTa	p.G268V	YBX2_ENST00000570627.1_5'Flank	NM_015982.3	NP_057066.2	Q9Y2T7	YBOX2_HUMAN	Y box binding protein 2	268	Pro-rich.|Required for mRNA-binding.				mRNA stabilization (GO:0048255)|negative regulation of binding (GO:0051100)|negative regulation of translation (GO:0017148)|oocyte development (GO:0048599)|regulation of transcription, DNA-templated (GO:0006355)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|translational attenuation (GO:0009386)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|polysome (GO:0005844)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lipid binding (GO:0008289)|mRNA 3'-UTR binding (GO:0003730)|ribonucleoprotein complex binding (GO:0043021)|translation regulator activity (GO:0045182)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|skin(3)	12						TCGCTCATCTCCCTGCTGTTG	0.632																																					p.G268V		Atlas-SNP	.											.	YBX2	28	.	0			c.G803T						PASS	.						52	55	54					17																	7193332		2203	4300	6503	SO:0001583	missense	51087	exon6			TCATCTCCCTGCT	AF096834	CCDS11098.1	17p13.1	2013-12-20			ENSG00000006047	ENSG00000006047			17948	protein-coding gene	gene with protein product		611447				10100484, 9780336	Standard	NM_015982		Approved	MSY2, CSDA3	uc002gfq.2	Q9Y2T7	OTTHUMG00000177992	ENST00000007699.5:c.803G>T	chr17.hg19:g.7193332C>A	ENSP00000007699:p.Gly268Val	151.0	0.0	.		274.0	112.0	.	NM_015982	D3DTP1|Q8N4P0	Missense_Mutation	SNP	ENST00000007699.5	hg19	CCDS11098.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.845908	0.51164	.	.	ENSG00000006047	ENST00000007699	T	0.29142	1.58	5.34	5.34	0.76211	.	0.251035	0.34750	N	0.003707	T	0.52370	0.1730	M	0.62723	1.935	0.53688	D	0.999978	D	0.89917	1.0	D	0.74023	0.982	T	0.52426	-0.8577	10	0.72032	D	0.01	-13.9828	14.9276	0.70890	0.0:1.0:0.0:0.0	.	268	Q9Y2T7	YBOX2_HUMAN	V	268	ENSP00000007699:G268V	ENSP00000007699:G268V	G	-	2	0	YBX2	7134056	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	2.987000	0.49378	2.689000	0.91719	0.462000	0.41574	GGA	.	.	.	none		0.632	YBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440172.2	NM_015982		A	7193332	C	A	7193332	3	1	97	1	0	0	0	0	1	0	0	0	17482	855	30	4	303	4	YBX2	17	7193332	Missense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08	251164	7193332	74001878	60	6170											
SPEM1	374768	hgsc.bcm.edu	37	chr17	7324267	7324267	+	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	aagcagagttctcctgcagtCcatcttcggtgcaccatgga	9	10	10	12	1	2	1	0	0	2	1	5	2	3	2	3	2	3	4	3	2	1	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr17:7324267C>A	ENST00000323675.3	+	3	298	c.273C>A	c.(271-273)gtC>gtA	p.V91V	RP11-104H15.7_ENST00000575310.1_RNA	NM_199339.2	NP_955371.2	Q8N4L4	SPEM1_HUMAN	spermatid maturation 1	91					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)				CTCCTGCAGTCCATCTTCGGT	0.597																																					p.V91V		Atlas-SNP	.											.	SPEM1	41	.	0			c.C273A						PASS	.						112	120	117					17																	7324267		2106	4203	6309	SO:0001819	synonymous_variant	374768	exon3			TGCAGTCCATCTT	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.273C>A	chr17.hg19:g.7324267C>A		176.0	0.0	.		335.0	133.0	.	NM_199339		Silent	SNP	ENST00000323675.3	hg19	CCDS42254.1																																																																																			.	.	.	none		0.597	SPEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440932.1	NM_199339		A	7324267	C	A	7324267	2	1	97	1	0	0	0	0	0	0	0	1	15049	842	30	4		4	SPEM1	17	7324267	Silent	SNP	C	TCGA-B9-4116-01A-01D-1252-08	130935	7324267	73870943	61	6171											
NCOR1	9611	hgsc.bcm.edu	37	chr17	15964734	15964734	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagctactagaagagtctgaActttgagagccacgttccct	11	10	9	11	1	1	4	0	2	1	3	2	5	2	4	2	0	4	2	2	0	4	4			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr17:15964734A>G	ENST00000268712.3	-	37	6119	c.5862T>C	c.(5860-5862)agT>agC	p.S1954S	NCOR1_ENST00000395851.1_Intron|NCOR1_ENST00000395857.3_Silent_p.S538S	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1954	Interaction with C1D. {ECO:0000250}.|Poly-Ser.				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)		AAGAGTCTGAACTTTGAGAGC	0.428																																					p.S1954S		Atlas-SNP	.											.	NCOR1	240	.	0			c.T5862C						PASS	.						219	200	206					17																	15964734		2203	4300	6503	SO:0001819	synonymous_variant	9611	exon37			GTCTGAACTTTGA	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.5862T>C	chr17.hg19:g.15964734A>G		367.0	0.0	.		325.0	87.0	.	NM_006311	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Silent	SNP	ENST00000268712.3	hg19	CCDS11175.1																																																																																			.	.	.	none		0.428	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		G	15964734	A	G	15964734	2	3	97	1	0	0	0	0	0	0	0	1	10242	40	2	3		3	NCOR1	17	15964734	Silent	SNP	A	TCGA-B9-4116-01A-01D-1252-08	8640467	15964734	65230476	62	6172											
PLEKHH3	79990	hgsc.bcm.edu	37	chr17	40821477	40821477	+	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	ctgcaggaggagctggctctCtcccaccctcaaggccaggg	7	6	13	15	0	2	0	1	0	1	0	4	2	3	2	3	5	2	3	3	5	1	0			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr17:40821477C>A	ENST00000591022.1	-	12	2563	c.2176G>T	c.(2176-2178)Gag>Tag	p.E726*	PLEKHH3_ENST00000456950.2_5'UTR|PLEKHH3_ENST00000293349.6_Nonsense_Mutation_p.E723*|PLEKHH3_ENST00000412503.1_Nonsense_Mutation_p.E549*	NM_024927.4	NP_079203	Q7Z736	PKHH3_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 3	726	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|skin(2)	13		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.14)		AGCTGGCTCTCTCCCACCCTC	0.622																																					p.E726X		Atlas-SNP	.											.	PLEKHH3	49	.	0			c.G2176T						PASS	.						20	23	22					17																	40821477		2202	4300	6502	SO:0001587	stop_gained	79990	exon12			GGCTCTCTCCCAC	BC052978	CCDS11434.1	17q21.2	2013-01-11				ENSG00000068137		"Pleckstrin homology (PH) domain containing"	26105	protein-coding gene	gene with protein product						12477932	Standard	NM_024927		Approved	FLJ21019	uc002iau.3	Q7Z736		ENST00000591022.1:c.2176G>T	chr17.hg19:g.40821477C>A	ENSP00000468678:p.Glu726*	68.0	0.0	.		114.0	48.0	.	NM_024927	C9JQ76|Q59H20|Q96B28|Q9H7D6|Q9NT18	Nonsense_Mutation	SNP	ENST00000591022.1	hg19	CCDS11434.1	.	.	.	.	.	.	.	.	.	.	C	41	8.827108	0.98968	.	.	ENSG00000068137	ENST00000293349;ENST00000412503	.	.	.	4.43	4.43	0.53597	.	0.336296	0.21518	N	0.073272	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	-10.0927	16.1774	0.81862	0.0:1.0:0.0:0.0	.	.	.	.	X	726;549	.	ENSP00000293349:E726X	E	-	1	0	PLEKHH3	38075003	0.999000	0.42202	0.997000	0.53966	0.955000	0.61496	3.927000	0.56499	2.465000	0.83290	0.655000	0.94253	GAG	.	.	.	none		0.622	PLEKHH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452332.1	NM_024927		A	40821477	C	A	40821477	4	1	97	1	0	0	0	0	0	1	0	0	12085	922	32	4	213	4	PLEKHH3	17	40821477	Nonsense_Mutation	SNP	C	TCGA-B9-4116-01A-01D-1252-08	24856743	40821477	40373733	63	6173											
TIMM44	10469	hgsc.bcm.edu	37	chr19	8002997	8002997	+	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	tttttatactttctttcattTctttgtttttggctaattct	5	27	3	6	0	4	0	1	0	3	0	4	0	4	0	0	1	1	2	0	1	3	12			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr19:8002997T>A	ENST00000270538.3	-	3	495	c.227A>T	c.(226-228)gAa>gTa	p.E76V		NM_006351.3	NP_006342.2	O43615	TIM44_HUMAN	translocase of inner mitochondrial membrane 44 homolog (yeast)	76					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO:0015450)			NS(1)|endometrium(3)|kidney(3)|large_intestine(2)|liver(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	17						TTCTTTCATTTCTTTGTTTTT	0.393																																					p.E76V		Atlas-SNP	.											.	TIMM44	47	.	0			c.A227T						PASS	.						194	192	193					19																	8002997		2203	4300	6503	SO:0001583	missense	10469	exon3			TTCATTTCTTTGT	AF026030	CCDS12192.1	19p13.3-p13.2	2008-07-04				ENSG00000104980			17316	protein-coding gene	gene with protein product		605058				10848612, 10339406	Standard	NM_006351		Approved	TIM44	uc002miz.3	O43615		ENST00000270538.3:c.227A>T	chr19.hg19:g.8002997T>A	ENSP00000270538:p.Glu76Val	319.0	0.0	.		485.0	164.0	.	NM_006351	A8K0R9|D6W664|Q8N193	Missense_Mutation	SNP	ENST00000270538.3	hg19	CCDS12192.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.629496	0.87660	.	.	ENSG00000104980	ENST00000270538	D	0.87491	-2.26	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	D	0.93625	0.7964	M	0.85777	2.775	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.94461	0.7676	10	0.87932	D	0	-30.5113	13.3329	0.60500	0.0:0.0:0.0:1.0	.	76	O43615	TIM44_HUMAN	V	76	ENSP00000270538:E76V	ENSP00000270538:E76V	E	-	2	0	TIMM44	7908997	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.452000	0.80683	2.047000	0.60756	0.528000	0.53228	GAA	.	.	.	none		0.393	TIMM44-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461596.3			A	8002997	T	A	8002997	3	1	97	1	0	0	0	0	1	0	0	0	15924	1783	62	5	1175	5	TIMM44	19	8002997	Missense_Mutation	SNP	T	TCGA-B9-4116-01A-01D-1252-08		8002997	51125986	64	6174											
RAB11B	9230	hgsc.bcm.edu	37	chr19	8468330	8468331	+	Frame_Shift_Del	DEL	CA	CA	-																															cgtgtcacagaaacagatcgCagaccgcgctgcccacgacg																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	CA	CA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr19:8468330_8468331delCA	ENST00000328024.6	+	5	763_764	c.545_546delCA	c.(544-546)gcafs	p.A182fs		NM_004218.3	NP_004209.2	Q15907	RB11B_HUMAN	RAB11B, member RAS oncogene family	182					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						AAACAGATCGCAGACCGCGCTG	0.653																																					p.182_182del		Atlas-INDEL	.											.	RAB11B	15	.	0			c.544_545del						PASS	.																																			SO:0001589	frameshift_variant	9230	exon5			.	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.545_546delCA	chr19.hg19:g.8468330_8468331delCA	ENSP00000333547:p.Ala182fs	178.0	0.0	0		255.0	75.0	0.294118	NM_004218	A5YM50|B2R7I4|B4DMK0|D6W671|Q2YDT2|Q5U0I1|Q6FHR0|Q6FI42|Q8NI07	Frame_Shift_Del	DEL	ENST00000328024.6	hg19	CCDS12201.1																																																																																			.	.	.	none		0.653	RAB11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460343.2	NM_004218		-	8468331	CA	-	8468330	7	5	97	1	0	1	0	1	0	0	0	0	12905	710	25	0	563	0	RAB11B	19	8468330	Frame_Shift_Del	DEL	CA	TCGA-B9-4116-01A-01D-1252-08	465333	8468330	50660653	65	6175											
OR7E24	26648	hgsc.bcm.edu	37	chr19	9362275	9362275	+	Missense_Mutation	SNP	T	T	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	tgattatgttacagctcaccTgcttcaaggatgtggacatt	10	14	9	8	0	2	1	2	1	0	0	2	3	2	3	1	2	3	3	1	2	3	4			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr19:9362275T>G	ENST00000456448.1	+	1	670	c.556T>G	c.(556-558)Tgc>Ggc	p.C186G		NM_001079935.1	NP_001073404.1	Q6IFN5	O7E24_HUMAN	olfactory receptor, family 7, subfamily E, member 24	186						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)	16						ACAGCTCACCTGCTTCAAGGA	0.403																																					p.C186G		Atlas-SNP	.											.	OR7E24	48	.	0			c.T556G						PASS	.						96	100	99					19																	9362275		2015	4185	6200	SO:0001583	missense	26648	exon1			CTCACCTGCTTCA	Y10529	CCDS45955.1	19p13.2	2012-08-09	2004-03-04	2004-03-05		ENSG00000237521		"GPCR / Class A : Olfactory receptors"	8396	protein-coding gene	gene with protein product			"olfactory receptor, family 7, subfamily E, member 24 pseudogene"	OR7E24P		9268701	Standard	NM_001079935		Approved	OR19-8, HSHT2, OR7E24Q	uc002mlb.1	Q6IFN5		ENST00000456448.1:c.556T>G	chr19.hg19:g.9362275T>G	ENSP00000387523:p.Cys186Gly	107.0	0.0	.		47.0	12.0	.	NM_001079935	B9EJD9|Q9UPJ1	Missense_Mutation	SNP	ENST00000456448.1	hg19	CCDS45955.1	.	.	.	.	.	.	.	.	.	.	t	10.40	1.340959	0.24339	.	.	ENSG00000237521	ENST00000456448	T	0.00224	8.51	2.21	-0.132	0.13489	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00241	0.0007	L	0.53249	1.67	0.09310	N	1	D	0.52996	0.957	P	0.50490	0.642	T	0.48614	-0.9020	9	0.87932	D	0	.	6.5019	0.22174	0.0:0.4011:0.0:0.5989	.	186	Q6IFN5	O7E24_HUMAN	G	186	ENSP00000387523:C186G	ENSP00000387523:C186G	C	+	1	0	OR7E24	9223275	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	1.214000	0.32419	-0.264000	0.09365	-0.483000	0.04790	TGC	.	.	.	none		0.403	OR7E24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449006.1			G	9362275	T	G	9362275	3	3	97	1	0	0	0	0	1	0	0	0	11228	1580	55	5	558	5	OR7E24	19	9362275	Missense_Mutation	SNP	T	TCGA-B9-4116-01A-01D-1252-08	893945	9362275	49766708	66	6176											
UPF1	5976	hgsc.bcm.edu	37	chr19	18963808	18963808	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctcagactcaagataacAtcactgtcaggtgggacctg	11	9	11	10	0	4	2	4	0	0	2	4	3	4	3	1	2	2	1	1	2	2	1			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr19:18963808A>G	ENST00000599848.1	+	7	1194	c.985A>G	c.(985-987)Atc>Gtc	p.I329V	UPF1_ENST00000262803.5_Missense_Mutation_p.I329V			Q92900	RENT1_HUMAN	UPF1 regulator of nonsense transcripts homolog (yeast)	329	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						TCAAGATAACATCACTGTCAG	0.537																																					p.I329V		Atlas-SNP	.											.	UPF1	88	.	0			c.A985G						PASS	.						131	115	120					19																	18963808		2203	4300	6503	SO:0001583	missense	5976	exon7			GATAACATCACTG	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.985A>G	chr19.hg19:g.18963808A>G	ENSP00000470142:p.Ile329Val	231.0	0.0	.		287.0	92.0	.	NM_002911	O00239|O43343|Q86Z25|Q92842	Missense_Mutation	SNP	ENST00000599848.1	hg19		.	.	.	.	.	.	.	.	.	.	A	11.03	1.518996	0.27211	.	.	ENSG00000005007	ENST00000262803	D	0.88975	-2.45	4.16	4.16	0.48862	.	0.052684	0.64402	D	0.000001	T	0.79052	0.4381	N	0.16903	0.455	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.12156	0.003;0.007	T	0.72077	-0.4399	10	0.18276	T	0.48	-35.3027	12.395	0.55380	1.0:0.0:0.0:0.0	.	329;329	Q92900;Q92900-2	RENT1_HUMAN;.	V	329	ENSP00000262803:I329V	ENSP00000262803:I329V	I	+	1	0	UPF1	18824808	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.925000	0.92832	1.534000	0.49203	0.438000	0.28831	ATC	.	.	.	none		0.537	UPF1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464684.1	NM_002911		G	18963808	A	G	18963808	3	3	97	1	0	0	0	0	1	0	0	0	17015	217	8	3	1011	3	UPF1	19	18963808	Missense_Mutation	SNP	A	TCGA-B9-4116-01A-01D-1252-08	9601533	18963808	40165175	67	6177											
HSD17B14	51171	hgsc.bcm.edu	37	chr19	49316535	49316535	+	Missense_Mutation	SNP	A	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	gcagttcaatgcccgtgcagAagttggcttcggaggccagg	8	8	15	10	2	1	1	1	0	0	1	2	2	1	2	2	4	2	5	2	4	2	3			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr19:49316535A>C	ENST00000263278.4	-	9	976	c.710T>G	c.(709-711)tTc>tGc	p.F237C	BCAT2_ENST00000597011.1_5'Flank|BCAT2_ENST00000402551.1_5'Flank|BCAT2_ENST00000598162.1_5'Flank|BCAT2_ENST00000545387.2_5'Flank|BCAT2_ENST00000316273.6_5'Flank|BCAT2_ENST00000601496.1_5'Flank|HSD17B14_ENST00000599157.1_Missense_Mutation_p.F213C|BCAT2_ENST00000599246.1_5'Flank	NM_016246.2	NP_057330.2	Q9BPX1	DHB14_HUMAN	hydroxysteroid (17-beta) dehydrogenase 14	237					steroid catabolic process (GO:0006706)	cytosol (GO:0005829)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			large_intestine(3)|lung(1)|skin(1)	5		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;0.000341)|all cancers(93;0.000764)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.0346)		GCCCGTGCAGAAGTTGGCTTC	0.677																																					p.F237C		Atlas-SNP	.											.	HSD17B14	25	.	0			c.T710G						PASS	.						24	22	23					19																	49316535		2201	4294	6495	SO:0001583	missense	51171	exon9			GTGCAGAAGTTGG	AF126781	CCDS12736.1	19q13.33	2011-09-14	2006-11-22	2006-11-22		ENSG00000087076		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	23238	protein-coding gene	gene with protein product	"retinal short-chain dehydrogenase/reductase 3", "short chain dehydrogenase/reductase family 47C, member 1"	612832	"dehydrogenase/reductase (SDR family) member 10"	DHRS10		10800688, 17067289, 19027726	Standard	XM_005258969		Approved	retSDR3, SDR47C1	uc002pkv.1	Q9BPX1		ENST00000263278.4:c.710T>G	chr19.hg19:g.49316535A>C	ENSP00000263278:p.Phe237Cys	18.0	0.0	.		46.0	22.0	.	NM_016246	Q9UKU3	Missense_Mutation	SNP	ENST00000263278.4	hg19	CCDS12736.1	.	.	.	.	.	.	.	.	.	.	A	14.03	2.414225	0.42817	.	.	ENSG00000087076	ENST00000263278	T	0.25250	1.81	4.54	4.54	0.55810	NAD(P)-binding domain (1);	0.056642	0.64402	D	0.000001	T	0.48732	0.1516	M	0.70787	2.145	0.48571	D	0.99967	D	0.89917	1.0	D	0.97110	1.0	T	0.51888	-0.8648	10	0.72032	D	0.01	.	12.4586	0.55718	1.0:0.0:0.0:0.0	.	237	Q9BPX1	DHB14_HUMAN	C	237	ENSP00000263278:F237C	ENSP00000263278:F237C	F	-	2	0	HSD17B14	54008347	1.000000	0.71417	0.995000	0.50966	0.070000	0.16714	4.249000	0.58766	1.991000	0.58162	0.379000	0.24179	TTC	.	.	.	none		0.677	HSD17B14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466212.1	NM_016246		C	49316535	A	C	49316535	3	2	97	1	0	0	0	0	1	0	0	0	7390	246	9	5	106	5	HSD17B14	19	49316535	Missense_Mutation	SNP	A	TCGA-B9-4116-01A-01D-1252-08	30352727	49316535	9812448	68	6178											
NKX2-4	644524	hgsc.bcm.edu	37	chr20	21376576	21376576	+	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	gtcctgccatagagcaggttGgcgcccaggacgccgccgct	6	6	14	15	4	0	1	0	0	0	1	1	2	1	2	5	3	2	3	5	3	1	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr20:21376576G>T	ENST00000351817.4	-	2	1666	c.1038C>A	c.(1036-1038)gcC>gcA	p.A346A	RP11-227D2.3_ENST00000552439.1_RNA|RP11-227D2.3_ENST00000419666.2_RNA	NM_033176.1	NP_149416.1	Q9H2Z4	NKX24_HUMAN	NK2 homeobox 4	346					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			lung(2)|upper_aerodigestive_tract(1)	3						AGAGCAGGTTGGCGCCCAGGA	0.736																																					p.A346A		Atlas-SNP	.											.	NKX2-4	7	.	0			c.C1038A						PASS	.						18	19	18					20																	21376576		1266	2943	4209	SO:0001819	synonymous_variant	644524	exon2			CAGGTTGGCGCCC		CCDS42855.1	20p11.22	2012-03-09	2007-07-09	2002-10-04	ENSG00000125816	ENSG00000125816		"Homeoboxes / ANTP class : NKL subclass"	7837	protein-coding gene	gene with protein product		607808	"NK-2 (Drosophila) homolog D", "NK2 transcription factor related, locus 4 (Drosophila)"	NKX2D		1346742, 10818213	Standard	NM_033176		Approved	NKX2.4	uc010gcz.3	Q9H2Z4	OTTHUMG00000032022	ENST00000351817.4:c.1038C>A	chr20.hg19:g.21376576G>T		63.0	0.0	.		105.0	30.0	.	NM_033176	Q5VZV8	Silent	SNP	ENST00000351817.4	hg19	CCDS42855.1																																																																																			.	.	.	none		0.736	NKX2-4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078270.2			T	21376576	G	T	21376576	2	4	97	1	0	0	0	0	0	0	0	1	10459	1335	47	4		4	NKX2-4	20	21376576	Silent	SNP	G	TCGA-B9-4116-01A-01D-1252-08		21376576	41648944	69	6179											
CEP250	11190	hgsc.bcm.edu	37	chr20	34091451	34091451	+	Frame_Shift_Del	DEL	A	A	-																															tccatgaactccaggagctcAaagaccagctggagcagcag																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr20:34091451delA	ENST00000397527.1	+	30	5974	c.5254delA	c.(5254-5256)aaafs	p.K1752fs	CEP250_ENST00000342580.4_Frame_Shift_Del_p.K1696fs	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	1752	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)			CCAGGAGCTCAAAGACCAGCT	0.577																																					p.L1751fs		Atlas-INDEL	.											.	CEP250	141	.	0			c.5253delC						PASS	.						81	80	80					20																	34091451		2203	4300	6503	SO:0001589	frameshift_variant	11190	exon30			.	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.5254delA	chr20.hg19:g.34091451delA	ENSP00000380661:p.Lys1752fs	166.0	0.0	0		311.0	105.0	0.337621	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Frame_Shift_Del	DEL	ENST00000397527.1	hg19	CCDS13255.1																																																																																			.	.	.	none		0.577	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		-	34091451	A	-	34091451	7	5	97	1	0	1	0	1	0	0	0	0	3254	131	5	0	5360	0	CEP250	20	34091451	Frame_Shift_Del	DEL	A	TCGA-B9-4116-01A-01D-1252-08	12714875	34091451	28934069	70	6180											
ACTR5	79913	hgsc.bcm.edu	37	chr20	37400319	37400319	+	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	aagagtatgaagaaaagggaGgagagtacctcaaggagcac	18	4	14	5	0	1	4	1	1	0	3	1	7	1	6	1	3	2	3	1	3	7	2			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr20:37400319G>C	ENST00000243903.4	+	9	1721	c.1684G>C	c.(1684-1686)Gga>Cga	p.G562R		NM_024855.3	NP_079131.3	Q9H9F9	ARP5_HUMAN	ARP5 actin-related protein 5 homolog (yeast)	562					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)				AGAAAAGGGAGGAGAGTACCT	0.557																																					p.G562R		Atlas-SNP	.											.	ACTR5	44	.	0			c.G1684C						PASS	.						108	88	94					20																	37400319		2203	4300	6503	SO:0001583	missense	79913	exon9			AAGGGAGGAGAGT	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.1684G>C	chr20.hg19:g.37400319G>C	ENSP00000243903:p.Gly562Arg	123.0	0.0	.		187.0	75.0	.	NM_024855	Q86WF7|Q8IUY5|Q8N724|Q9BRN0|Q9BVB7	Missense_Mutation	SNP	ENST00000243903.4	hg19	CCDS13308.1	.	.	.	.	.	.	.	.	.	.	G	32	5.160871	0.94727	.	.	ENSG00000101442	ENST00000243903	T	0.07688	3.17	6.05	6.05	0.98169	.	0.000000	0.85682	D	0.000000	T	0.31263	0.0791	M	0.66439	2.03	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.00166	-1.1966	10	0.87932	D	0	-21.9656	20.6086	0.99469	0.0:0.0:1.0:0.0	.	562	Q9H9F9	ARP5_HUMAN	R	562	ENSP00000243903:G562R	ENSP00000243903:G562R	G	+	1	0	ACTR5	36833733	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.960000	0.93117	2.880000	0.98712	0.655000	0.94253	GGA	.	.	.	none		0.557	ACTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079205.2	NM_024855		C	37400319	G	C	37400319	3	2	97	1	0	0	0	0	1	0	0	0	215	1001	35	4	1718	4	ACTR5	20	37400319	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	3308868	37400319	25625201	71	6181											
ZNFX1	57169	hgsc.bcm.edu	37	chr20	47864026	47864027	+	Missense_Mutation	DNP	GT	GT	AG																															ccattgcggcacttgaaccaGtgaccacgaggataacctat																										TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G|T	G|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chr20:47864026_47864027GT>AG	ENST00000396105.1	-	14	5780_5781	c.5534_5535AC>CT	c.(5533-5535)cAC>cCT	p.H1845P	ZNFX1_ENST00000371754.4_Intron|ZNFX1_ENST00000371752.1_Missense_Mutation_p.H1845P|ZNFX1_ENST00000469991.1_5'Flank	NM_021035.2	NP_066363.1	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	1845							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(8)|kidney(7)|large_intestine(15)|liver(1)|lung(17)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	60			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			ACTTGAACCAGTGACCACGAGG	0.545																																					p.H1845H|p.H1845P		Atlas-SNP	.											.	ZNFX1	194	.	0			c.C5535T|c.A5534C						PASS	.																																			SO:0001583	missense	57169	exon14			GAACCAGTGACCA|AACCAGTGACCAC	AK022641	CCDS13417.1	20q13.13	2014-02-12			ENSG00000124201	ENSG00000124201			29271	protein-coding gene	gene with protein product						10718198	Standard	NM_021035		Approved	KIAA1404, FLJ11277	uc002xui.3	Q9P2E3	OTTHUMG00000032696	ENST00000396105.1:c.5534_5535delinsAG	chr20.hg19:g.47864026_47864027delinsAG	ENSP00000379412:p.His1845Pro	142.0	0.0	.		225.0|229.0	81.0|85.0	.	NM_021035	Q9BQM7|Q9BQM8|Q9H8C1|Q9H9S2|Q9NUM1|Q9NWW1	Silent|Missense_Mutation	SNP	ENST00000396105.1	hg19	CCDS13417.1																																																																																			.	.	.	none		0.545	ZNFX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079647.2	NM_021035		AG	47864027	GT	AG	47864026	3	1	97	1	0	0	0	0	1	0	0	0	18217	1020	36	2	225	2	ZNFX1	20	47864026	Missense_Mutation	DNP	GT	TCGA-B9-4116-01A-01D-1252-08	10463707	47864026	15161494	72	6182											
ZRSR2	8233	hgsc.bcm.edu	37	chrX	15841260	15841260	+	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	cggagccggagccggagccgCaggagccgccgcagccggag	7	0	19	15	7	0	0	0	0	0	0	0	5	0	5	6	5	5	2	6	5	0	0			TCGA-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	g.chrX:15841260C>G	ENST00000307771.7	+	11	1368	c.1344C>G	c.(1342-1344)cgC>cgG	p.R448R		NM_005089.3	NP_005080.1	Q15696	U2AFM_HUMAN	zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2	448	Arg/Ser-rich (RS domain).				mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	U12-type spliceosomal complex (GO:0005689)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|pre-mRNA 3'-splice site binding (GO:0030628)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(38)|kidney(1)|large_intestine(2)|ovary(2)	48	Hepatocellular(33;0.183)					gccggagccgCAGGAGCCGCC	0.647			"F, S, Mis"		"MDS, CLL"																																p.R448R	NSCLC(197;1631 3042 5741 31152)	Atlas-SNP	.		Rec	yes		X	Xp22.1	8233	"zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2"		L	.	ZRSR2	78	.	0			c.C1344G						PASS	.						7	9	9					X																	15841260		1924	3790	5714	SO:0001819	synonymous_variant	8233	exon11			GAGCCGCAGGAGC	BC050451	CCDS14172.1	Xp22.1	2014-09-17	2006-09-26	2006-09-26	ENSG00000169249	ENSG00000169249		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	23019	protein-coding gene	gene with protein product		300028	"U2(RNU2) small nuclear RNA auxiliary factor 1-like 2", "U2 small nuclear RNA auxiliary factor 1-like 2"	U2AF1L2		8586425, 9237760, 15146077	Standard	NM_005089		Approved	U2AF1-RS2, URP	uc004cxg.4	Q15696	OTTHUMG00000021184	ENST00000307771.7:c.1344C>G	chrX.hg19:g.15841260C>G		31.0	0.0	.		50.0	5.0	.	NM_005089	Q14D69	Silent	SNP	ENST00000307771.7	hg19	CCDS14172.1																																																																																			.	.	.	none		0.647	ZRSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055889.1	NM_005089		G	15841260	C	G	15841260	2	3	97	1	0	0	0	0	0	0	0	1	18237	697	25	4		4	ZRSR2	23	15841260	Silent	SNP	C	TCGA-B9-4116-01A-01D-1252-08		15841260	139429300	73	6183											
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-B9-4116-01A-01D-1252-08	TCGA-B9-4116-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	847c8d58-eb11-487b-bc85-d58a4d47fae7	21d19fa5-2fc4-4abc-8810-947be94de078	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	chrX.hg19:g.50350751G>C	ENSP00000289292:p.Gln1131Glu	55.0	0.0	.		101.0	5.0	.	NM_020717	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	hg19	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	97	1	0	0	0	0	1	0	0	0	14309	1386	48	4	1106	4	SHROOM4	23	50350751	Missense_Mutation	SNP	G	TCGA-B9-4116-01A-01D-1252-08	34509491	50350751	104919809	74	6184											
SCMH1	22955	hgsc.bcm.edu	37	chr1	41579112	41579113	+	Frame_Shift_Ins	INS	-	-	G																															gaacctccccaatagtggctINSgggcaaatgaaatgagggtt																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:41579112_41579113insG	ENST00000326197.7	-	7	856_857	c.557_558insC	c.(556-558)ccafs	p.P186fs	SCMH1_ENST00000402904.2_Frame_Shift_Ins_p.P186fs|SCMH1_ENST00000372597.1_Frame_Shift_Ins_p.P139fs|SCMH1_ENST00000337495.5_Frame_Shift_Ins_p.P196fs|SCMH1_ENST00000456518.2_Intron|SCMH1_ENST00000397171.2_Frame_Shift_Ins_p.P125fs|SCMH1_ENST00000397174.2_Frame_Shift_Ins_p.P166fs|SCMH1_ENST00000361191.5_Frame_Shift_Ins_p.P125fs|SCMH1_ENST00000372595.1_Frame_Shift_Ins_p.P125fs|SCMH1_ENST00000361705.3_Frame_Shift_Ins_p.P139fs|SCMH1_ENST00000372596.1_Frame_Shift_Ins_p.P125fs					sex comb on midleg homolog 1 (Drosophila)											breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(2)|pancreas(2)|upper_aerodigestive_tract(1)	15	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162)	Myeloproliferative disorder(586;0.0393)				CAATAGTGGCTGGGCAAATGAA	0.53																																					p.P196fs		Atlas-INDEL	.											.	SCMH1	120	.	0			c.588_589insC						PASS	.																																			SO:0001589	frameshift_variant	22955	exon8			.	AF149045	CCDS461.1, CCDS30688.1, CCDS53301.1, CCDS53302.1, CCDS53303.1, CCDS53304.1	1p34	2013-01-10			ENSG00000010803	ENSG00000010803		"Sterile alpha motif (SAM) domain containing"	19003	protein-coding gene	gene with protein product						10524249	Standard	NM_012236		Approved	Scml3	uc001cgs.3	Q96GD3	OTTHUMG00000005720	ENST00000326197.7:c.558dupC	chr1.hg19:g.41579115_41579115dupG	ENSP00000318094:p.Pro186fs	55.0	0.0	0		107.0	20.0	0.186916	NM_001172219		Frame_Shift_Ins	INS	ENST00000326197.7	hg19	CCDS30688.1																																																																																			.	.	.	none		0.53	SCMH1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015656.1			G	41579113	-	G	41579112	7	5	98	1	0	1	1	0	0	0	0	0	13921	1567	55	0	1460	0	SCMH1	1	41579112	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08		41579112	207671509	1	6185											
OR2M7	391196	hgsc.bcm.edu	37	chr1	248487257	248487257	+	Missense_Mutation	SNP	A	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	caacagggaaaacaagcattActatacagcagatgaaaata	21	6	7	7	0	0	2	0	1	0	1	0	3	0	3	0	1	6	2	0	1	10	4	rs144715512		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr1:248487257A>C	ENST00000317965.2	-	1	642	c.614T>G	c.(613-615)gTa>gGa	p.V205G		NM_001004691.1	NP_001004691.1	Q8NG81	OR2M7_HUMAN	olfactory receptor, family 2, subfamily M, member 7	205						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(6)|large_intestine(3)|lung(29)|skin(3)	42	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			AACAAGCATTACTATACAGCA	0.433																																					p.V205G		Atlas-SNP	.											OR2M7,NS,carcinoma,0,1	OR2M7	84	.	0			c.T614G						PASS	.						287	275	279					1																	248487257		2203	4300	6503	SO:0001583	missense	391196	exon1			AGCATTACTATAC	BK004486	CCDS31111.1	1q44	2012-08-09			ENSG00000177186	ENSG00000177186		"GPCR / Class A : Olfactory receptors"	19594	protein-coding gene	gene with protein product							Standard	NM_001004691		Approved		uc010pzk.2	Q8NG81	OTTHUMG00000040461	ENST00000317965.2:c.614T>G	chr1.hg19:g.248487257A>C	ENSP00000324557:p.Val205Gly	299.0	1.0	.		50.0	2.0	.	NM_001004691	B2RNL0|Q6IEX6	Missense_Mutation	SNP	ENST00000317965.2	hg19	CCDS31111.1	.	.	.	.	.	.	.	.	.	.	A	8.086	0.773543	0.16051	.	.	ENSG00000177186	ENST00000317965	T	0.39229	1.09	1.55	0.00354	0.14055	GPCR, rhodopsin-like superfamily (1);	1.653810	0.04603	U	0.398866	T	0.34948	0.0915	L	0.45285	1.41	0.09310	N	1	B	0.15719	0.014	B	0.26770	0.073	T	0.43750	-0.9372	10	0.72032	D	0.01	.	2.386	0.04365	0.5781:0.0:0.1782:0.2437	.	205	Q8NG81	OR2M7_HUMAN	G	205	ENSP00000324557:V205G	ENSP00000324557:V205G	V	-	2	0	OR2M7	246553880	0.000000	0.05858	0.061000	0.19648	0.178000	0.23041	0.670000	0.25157	0.708000	0.31955	0.163000	0.16589	GTA	.	A|1.000;G|0.000	.	alt		0.433	OR2M7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097357.1	NM_001004691		C	248487257	A	C	248487257	3	2	98	1	0	0	0	0	1	0	0	0	11021	391	14	5	327	5	OR2M7	1	248487257	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	206908145	248487257	763364	2	6186											
TMEM214	54867	hgsc.bcm.edu	37	chr2	27259433	27259433	+	Missense_Mutation	SNP	T	T	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	gggccctgggtcaagcaggtTttgccaacctcaccgaggga	8	7	14	12	1	2	0	2	0	0	0	2	2	2	1	4	4	3	2	4	4	2	2	rs564964647		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:27259433T>G	ENST00000238788.9	+	6	861	c.799T>G	c.(799-801)Ttt>Gtt	p.F267V	TMEM214_ENST00000404032.3_Missense_Mutation_p.F222V	NM_017727.4	NP_060197.4	Q6NUQ4	TM214_HUMAN	transmembrane protein 214	267					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						TCAAGCAGGTTTTGCCAACCT	0.567																																					p.F267V		Atlas-SNP	.											.	TMEM214	41	.	0			c.T799G						PASS	.						103	103	103					2																	27259433		1943	4141	6084	SO:0001583	missense	54867	exon6			GCAGGTTTTGCCA		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.799T>G	chr2.hg19:g.27259433T>G	ENSP00000238788:p.Phe267Val	124.0	0.0	.		611.0	177.0	.	NM_017727	A6NNF2|B3KUI9|B5MCD8|D6W547|Q53SW1|Q69YH4|Q8NC45|Q8WZ37|Q9NXH2	Missense_Mutation	SNP	ENST00000238788.9	hg19	CCDS42664.1	.	.	.	.	.	.	.	.	.	.	T	27.9	4.873746	0.91664	.	.	ENSG00000119777	ENST00000238788;ENST00000404032;ENST00000537397	T;T	0.52295	0.67;0.67	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.63861	0.2547	M	0.74258	2.255	0.80722	D	1	D;P	0.56746	0.977;0.917	P;P	0.57679	0.794;0.825	T	0.65417	-0.6173	10	0.42905	T	0.14	-14.1771	15.3509	0.74384	0.0:0.0:0.0:1.0	.	222;267	Q6NUQ4-2;Q6NUQ4	.;TM214_HUMAN	V	267;222;9	ENSP00000238788:F267V;ENSP00000384417:F222V	ENSP00000238788:F267V	F	+	1	0	TMEM214	27112937	1.000000	0.71417	0.436000	0.26797	0.968000	0.65278	7.508000	0.81686	2.128000	0.65567	0.459000	0.35465	TTT	.	.	.	none		0.567	TMEM214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324748.1	NM_017727		G	27259433	T	G	27259433	3	3	98	1	0	0	0	0	1	0	0	0	16149	1841	64	5	821	5	TMEM214	2	27259433	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08		27259433	215939940	3	6187											
CGREF1	10669	hgsc.bcm.edu	37	chr2	27327221	27327221	+	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	gcaggattaacactgtcatcGtcaaaggtaacatccttcct	12	11	7	11	1	2	0	2	0	0	0	5	1	4	1	2	2	2	2	2	2	3	3	rs112618911		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:27327221G>T	ENST00000260595.5	-	2	306	c.14C>A	c.(13-15)aCg>aAg	p.T5K	CGREF1_ENST00000452318.2_Intron|CGREF1_ENST00000405600.1_Missense_Mutation_p.T5K|CGREF1_ENST00000402394.1_Missense_Mutation_p.T5K|CGREF1_ENST00000312734.4_Missense_Mutation_p.T5K|CGREF1_ENST00000404694.3_Missense_Mutation_p.T127K|CGREF1_ENST00000402550.1_Missense_Mutation_p.T5K			Q99674	CGRE1_HUMAN	cell growth regulator with EF-hand domain 1	5					cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			kidney(1)|lung(4)|ovary(1)|prostate(2)|skin(1)|soft_tissue(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CACTGTCATCGTCAAAGGTAA	0.567																																					p.T5K		Atlas-SNP	.											.	CGREF1	31	.	0			c.C14A						PASS	.						67	59	62					2																	27327221		2203	4300	6503	SO:0001583	missense	10669	exon2			GTCATCGTCAAAG	BC034764	CCDS33162.1, CCDS33162.2, CCDS54339.1	2p23.3	2013-01-10			ENSG00000138028	ENSG00000138028		"EF-hand domain containing"	16962	protein-coding gene	gene with protein product		606137				8968090	Standard	NM_006569		Approved	CGR11	uc002riq.3	Q99674	OTTHUMG00000152009	ENST00000260595.5:c.14C>A	chr2.hg19:g.27327221G>T	ENSP00000260595:p.Thr5Lys	37.0	0.0	.		149.0	38.0	.	NM_001166239	A6NHV7|B4DXY8|B5MCB7|B5MCC9|B5MCP5|E7EU99|Q8N4B7	Missense_Mutation	SNP	ENST00000260595.5	hg19		.	.	.	.	.	.	.	.	.	.	A	13.14	2.147472	0.37923	.	.	ENSG00000138028	ENST00000402550;ENST00000402394;ENST00000405600;ENST00000389521;ENST00000312734;ENST00000404694;ENST00000260595	T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5	4.73	-7.65	0.01281	.	1.833840	0.02770	N	0.119586	T	0.16300	0.0392	N	0.12182	0.205	0.09310	N	1	B;B;B	0.10296	0.002;0.002;0.003	B;B;B	0.06405	0.002;0.002;0.002	T	0.20638	-1.0269	10	0.44086	T	0.13	-10.5345	8.4971	0.33134	0.1308:0.0:0.5748:0.2945	.	127;5;5	B5MCC9;B5MCP5;Q99674	.;.;CGRE1_HUMAN	K	5;5;5;5;5;127;5	ENSP00000385452:T5K;ENSP00000386113:T5K;ENSP00000324025:T5K;ENSP00000385574:T127K;ENSP00000260595:T5K	ENSP00000260595:T5K	T	-	2	0	CGREF1	27180725	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.719000	0.04974	-2.518000	0.00499	-1.007000	0.02485	ACG	.	G|0.998;A|0.002	.	alt		0.567	CGREF1-201	KNOWN	basic	protein_coding	protein_coding		NM_006569		T	27327221	G	T	27327221	3	4	98	1	0	0	0	0	1	0	0	0	3307	1145	40	4	1154	4	CGREF1	2	27327221	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	67788	27327221	215872152	4	6188											
CEBPZ	10153	hgsc.bcm.edu	37	chr2	37454852	37454852	+	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	catcaccagtctgggaataaGggtatgccctattcacacct	11	10	8	12	0	3	0	2	0	1	0	3	1	3	1	3	2	1	1	3	2	4	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:37454852G>A	ENST00000234170.5	-	2	1629	c.1484C>T	c.(1483-1485)cCt>cTt	p.P495L		NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	495					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)				CTGGGAATAAGGGTATGCCCT	0.368																																					p.P495L		Atlas-SNP	.											.	CEBPZ	68	.	0			c.C1484T						PASS	.						83	79	80					2																	37454852		2203	4300	6503	SO:0001583	missense	10153	exon2			GAATAAGGGTATG	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.1484C>T	chr2.hg19:g.37454852G>A	ENSP00000234170:p.Pro495Leu	69.0	0.0	.		34.0	20.0	.	NM_005760	Q8NE75	Missense_Mutation	SNP	ENST00000234170.5	hg19	CCDS1787.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.952289	0.73787	.	.	ENSG00000115816	ENST00000234170;ENST00000545744	T	0.24538	1.85	5.59	5.59	0.84812	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.64494	0.2603	M	0.93898	3.47	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74247	-0.3727	10	0.87932	D	0	.	19.6055	0.95580	0.0:0.0:1.0:0.0	.	495	Q03701	CEBPZ_HUMAN	L	495	ENSP00000234170:P495L	ENSP00000234170:P495L	P	-	2	0	CEBPZ	37308356	1.000000	0.71417	1.000000	0.80357	0.726000	0.41606	9.296000	0.96104	2.631000	0.89168	0.650000	0.86243	CCT	.	.	.	none		0.368	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760		A	37454852	G	A	37454852	3	1	98	1	0	0	0	0	1	0	0	0	3206	1000	35	2	1740	2	CEBPZ	2	37454852	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	10127631	37454852	205744521	5	6189											
GPR45	11250	hgsc.bcm.edu	37	chr2	105858582	105858582	+	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	ctgtccctctgctgcatgccCttcaccgccgtcaccctcat	4	11	6	20	2	4	0	3	0	1	0	5	0	5	0	5	0	3	2	5	0	0	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:105858582C>G	ENST00000258456.1	+	1	383	c.267C>G	c.(265-267)ccC>ccG	p.P89P		NM_007227.3	NP_009158.3	Q9Y5Y3	GPR45_HUMAN	G protein-coupled receptor 45	89						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	28						GCTGCATGCCCTTCACCGCCG	0.627																																					p.P89P		Atlas-SNP	.											.	GPR45	73	.	0			c.C267G						PASS	.						125	115	118					2																	105858582		2203	4300	6503	SO:0001819	synonymous_variant	11250	exon1			CATGCCCTTCACC	AF118266	CCDS2066.1	2q11.1-q12	2012-08-21			ENSG00000135973	ENSG00000135973		"GPCR / Class A : Orphans"	4503	protein-coding gene	gene with protein product		604838				10036181	Standard	NM_007227		Approved	PSP24, PSP24A	uc002tco.1	Q9Y5Y3	OTTHUMG00000130805	ENST00000258456.1:c.267C>G	chr2.hg19:g.105858582C>G		151.0	0.0	.		527.0	245.0	.	NM_007227	Q6NWS4|Q6NXU6	Silent	SNP	ENST00000258456.1	hg19	CCDS2066.1																																																																																			.	.	.	none		0.627	GPR45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253348.1	NM_007227		G	105858582	C	G	105858582	2	3	98	1	0	0	0	0	0	0	0	1	6703	668	24	4		4	GPR45	2	105858582	Silent	SNP	C	TCGA-B9-4117-01A-01D-1252-08	68403730	105858582	137340791	6	6190											
TFCP2L1	29842	hgsc.bcm.edu	37	chr2	122042681	122042681	+	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	cgggctgcgtgtgccagaagAgcatggctggaactcccagc	8	6	15	12	2	0	2	0	0	0	2	1	3	1	3	2	3	5	3	2	3	2	0			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:122042681A>T	ENST00000263707.5	-	1	102	c.5T>A	c.(4-6)cTc>cAc	p.L2H		NM_014553.2	NP_055368.1	Q9NZI6	TF2L1_HUMAN	transcription factor CP2-like 1	2	Mediate transcriptional repression.				cell morphogenesis (GO:0000902)|cytoplasm organization (GO:0007028)|determination of adult lifespan (GO:0008340)|epithelial cell maturation (GO:0002070)|female pregnancy (GO:0007565)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of growth (GO:0045927)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|salivary gland development (GO:0007431)|steroid biosynthetic process (GO:0006694)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(4)|large_intestine(5)|lung(7)|ovary(1)|pancreas(2)|skin(1)|stomach(1)	22	Renal(3;0.01)					GTGCCAGAAGAGCATGGCTGG	0.756																																					p.L2H		Atlas-SNP	.											.	TFCP2L1	54	.	0			c.T5A						PASS	.						17	16	16					2																	122042681		2192	4286	6478	SO:0001583	missense	29842	exon1			CAGAAGAGCATGG	AF198488	CCDS2134.1	2q14	2008-02-05			ENSG00000115112	ENSG00000115112			17925	protein-coding gene	gene with protein product		609785				10644752, 11073954	Standard	NM_014553		Approved	LBP-9, CRTR1	uc002tmx.3	Q9NZI6	OTTHUMG00000131443	ENST00000263707.5:c.5T>A	chr2.hg19:g.122042681A>T	ENSP00000263707:p.Leu2His	14.0	0.0	.		31.0	19.0	.	NM_014553	Q4ZG43	Missense_Mutation	SNP	ENST00000263707.5	hg19	CCDS2134.1	.	.	.	.	.	.	.	.	.	.	a	17.41	3.381885	0.61845	.	.	ENSG00000115112	ENST00000263707	T	0.26373	1.74	4.1	4.1	0.47936	.	0.097761	0.43747	U	0.000539	T	0.39835	0.1093	L	0.38175	1.15	0.58432	D	0.999999	D;D	0.89917	1.0;0.988	D;P	0.87578	0.998;0.832	T	0.29518	-1.0009	10	0.87932	D	0	.	12.7432	0.57266	1.0:0.0:0.0:0.0	.	2;2	Q5JV87;Q9NZI6	.;TF2L1_HUMAN	H	2	ENSP00000263707:L2H	ENSP00000263707:L2H	L	-	2	0	TFCP2L1	121759151	1.000000	0.71417	1.000000	0.80357	0.009000	0.06853	6.622000	0.74233	1.467000	0.48044	0.398000	0.26397	CTC	.	.	.	none		0.756	TFCP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338539.1	NM_014553		T	122042681	A	T	122042681	3	4	98	1	0	0	0	0	1	0	0	0	15808	304	11	5	1494	5	TFCP2L1	2	122042681	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	16184099	122042681	121156692	7	6191											
ALS2	57679	hgsc.bcm.edu	37	chr2	202626257	202626257	+	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	ctcctcgccacacgccaactGtaaaatcctgactgctaaca	12	8	5	16	2	0	1	0	1	0	0	3	1	2	1	4	0	3	2	4	0	4	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr2:202626257G>A	ENST00000264276.6	-	4	832	c.460C>T	c.(460-462)Cag>Tag	p.Q154*	ALS2_ENST00000496244.1_5'UTR|ALS2_ENST00000467448.1_Nonsense_Mutation_p.Q154*	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	154					behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						CACGCCAACTGTAAAATCCTG	0.522																																					p.Q154X		Atlas-SNP	.											.	ALS2	172	.	0			c.C460T						PASS	.						79	79	79					2																	202626257		2073	4196	6269	SO:0001587	stop_gained	57679	exon4			CCAACTGTAAAAT	AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"Rho guanine nucleotide exchange factors"	443	protein-coding gene	gene with protein product	"alsin"	606352	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.460C>T	chr2.hg19:g.202626257G>A	ENSP00000264276:p.Gln154*	50.0	0.0	.		121.0	55.0	.	NM_001135745	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Nonsense_Mutation	SNP	ENST00000264276.6	hg19	CCDS42800.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.582281	0.86748	.	.	ENSG00000003393	ENST00000264276;ENST00000467448	.	.	.	6.17	6.17	0.99709	.	0.056382	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	.	.	.	X	154	.	ENSP00000264276:Q154X	Q	-	1	0	ALS2	202334502	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	5.405000	0.66351	2.941000	0.99782	0.655000	0.94253	CAG	.	.	.	none		0.522	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919		A	202626257	G	A	202626257	4	1	98	1	0	0	0	0	0	1	0	0	550	1386	48	2	4715	2	ALS2	2	202626257	Nonsense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	80583576	202626257	40573116	8	6192											
CIDEC	63924	hgsc.bcm.edu	37	chr3	9911862	9911862	+	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	cctcacctgttctgatggggGctgccatttctgccccttct	3	14	9	15	0	4	1	1	1	3	0	4	1	4	1	5	2	2	2	5	2	0	3	rs201802471|rs368273807		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr3:9911862G>C	ENST00000336832.2	-	4	491	c.352C>G	c.(352-354)Ccc>Gcc	p.P118A	CIDEC_ENST00000383817.1_Intron|CIDEC_ENST00000423850.1_Missense_Mutation_p.P44A|CIDEC_ENST00000455015.1_Missense_Mutation_p.P44A|CIDEC_ENST00000430427.1_Missense_Mutation_p.P128A|CIDEC_ENST00000443115.1_Intron	NM_001199552.1|NM_001199623.1|NM_022094.3	NP_001186481.1|NP_001186552.1|NP_071377.2	Q96AQ7	CIDEC_HUMAN	cell death-inducing DFFA-like effector c	118	CIDE-N. {ECO:0000255|PROSITE- ProRule:PRU00447}.				apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|lipid particle organization (GO:0034389)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|lipid particle (GO:0005811)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(1)|lung(2)|ovary(1)|skin(1)	8	Medulloblastoma(99;0.227)					TCTGATGGGGGCTGCCATTTC	0.542																																					p.P131A		Atlas-SNP	.											.,1	CIDEC	22	.	0			c.C391G						PASS	.						70	72	72					3																	9911862		2203	4300	6503	SO:0001583	missense	63924	exon4			ATGGGGGCTGCCA		CCDS2587.1, CCDS56239.1, CCDS74897.1	3p25	2004-07-26			ENSG00000187288	ENSG00000187288			24229	protein-coding gene	gene with protein product		612120				12429024	Standard	NM_001199623		Approved	CIDE-3, FLJ20871, Fsp27	uc021wsw.1	Q96AQ7	OTTHUMG00000128522	ENST00000336832.2:c.352C>G	chr3.hg19:g.9911862G>C	ENSP00000338642:p.Pro118Ala	114.0	0.0	.		367.0	90.0	.	NM_001199623	C9JMN7|Q67DW9|Q9GZY9	Missense_Mutation	SNP	ENST00000336832.2	hg19	CCDS2587.1	.	.	.	.	.	.	.	.	.	.	G	13.53	2.265024	0.40095	.	.	ENSG00000187288	ENST00000336832;ENST00000455015;ENST00000423850;ENST00000430427	T;T;T;T	0.47869	0.83;0.83;0.83;0.83	5.78	1.72	0.24424	Caspase-activated nuclease CIDE-N (2);	0.213000	0.49916	N	0.000130	T	0.47040	0.1424	M	0.71036	2.16	0.80722	D	1	B;B	0.33528	0.034;0.416	B;B	0.40506	0.026;0.331	T	0.33701	-0.9858	10	0.51188	T	0.08	-13.7547	5.8544	0.18712	0.2576:0.1378:0.6046:0.0	.	118;128	Q96AQ7;C9JMN7	CIDEC_HUMAN;.	A	118;44;44;128	ENSP00000338642:P118A;ENSP00000392975:P44A;ENSP00000400649:P44A;ENSP00000408631:P128A	ENSP00000338642:P118A	P	-	1	0	CIDEC	9886862	0.940000	0.31905	0.348000	0.25681	0.967000	0.64934	1.716000	0.37981	0.025000	0.15241	0.461000	0.40582	CCC	.	G|0.999;C|0.001	0.001	weak		0.542	CIDEC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250334.1	NM_022094		C	9911862	G	C	9911862	3	2	98	1	0	0	0	0	1	0	0	0	3429	1203	42	4	376	4	CIDEC	3	9911862	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08		9911862	188110568	9	6193											
DTX3L	151636	hgsc.bcm.edu	37	chr3	122283388	122283388	+	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	gctctaagtcctcgggcggcGgggagtgcacggtcagcacc	6	6	16	13	4	2	0	1	0	1	0	4	1	3	1	2	5	2	3	2	5	1	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr3:122283388G>T	ENST00000296161.4	+	1	304	c.115G>T	c.(115-117)Ggg>Tgg	p.G39W	DTX3L_ENST00000383661.3_Missense_Mutation_p.G39W|PARP9_ENST00000462315.1_5'Flank|PARP9_ENST00000360356.2_5'UTR|PARP9_ENST00000492382.1_5'Flank|PARP9_ENST00000471785.1_5'Flank|PARP9_ENST00000477522.2_5'UTR	NM_138287.3	NP_612144.1	Q8TDB6	DTX3L_HUMAN	deltex 3 like, E3 ubiquitin ligase	39					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)		CTCGGGCGGCGGGGAGTGCAC	0.672																																					p.G39W		Atlas-SNP	.											.	DTX3L	59	.	0			c.G115T						PASS	.						48	57	54					3																	122283388		2203	4299	6502	SO:0001583	missense	151636	exon1			GGCGGCGGGGAGT		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.115G>T	chr3.hg19:g.122283388G>T	ENSP00000296161:p.Gly39Trp	115.0	0.0	.		365.0	62.0	.	NM_138287	B3KWH6|Q53ZZ3|Q5MJP7	Missense_Mutation	SNP	ENST00000296161.4	hg19	CCDS3015.1	.	.	.	.	.	.	.	.	.	.	G	16.54	3.152626	0.57259	.	.	ENSG00000163840	ENST00000296161;ENST00000383661	T;T	0.69040	0.13;-0.37	4.59	4.59	0.56863	.	0.000000	0.47455	D	0.000228	T	0.81749	0.4888	M	0.80982	2.52	0.37919	D	0.931622	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.86218	0.1629	10	0.87932	D	0	-25.6532	14.2431	0.65971	0.0:0.0:1.0:0.0	.	39;39	Q8TDB6-2;Q8TDB6	.;DTX3L_HUMAN	W	39	ENSP00000296161:G39W;ENSP00000373157:G39W	ENSP00000296161:G39W	G	+	1	0	DTX3L	123766078	1.000000	0.71417	1.000000	0.80357	0.039000	0.13416	5.884000	0.69729	2.342000	0.79632	0.655000	0.94253	GGG	.	.	.	none		0.672	DTX3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355966.1	NM_138287		T	122283388	G	T	122283388	3	4	98	1	0	0	0	0	1	0	0	0	4798	1116	39	4	117	4	DTX3L	3	122283388	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	112371526	122283388	75739042	10	6194											
FAM43A	131583	hgsc.bcm.edu	37	chr3	194408136	194408136	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctctaccagacgtcggccaAcgcgctggcggaatttaaac	10	7	11	13	5	1	1	0	0	1	1	2	2	1	2	2	3	3	2	2	3	5	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr3:194408136A>G	ENST00000329759.4	+	1	1515	c.581A>G	c.(580-582)aAc>aGc	p.N194S		NM_153690.4	NP_710157.2	Q8N2R8	FA43A_HUMAN	family with sequence similarity 43, member A	194										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)		ACGTCGGCCAACGCGCTGGCG	0.672																																					p.N194S		Atlas-SNP	.											.	FAM43A	24	.	0			c.A581G						PASS	.						5	4	4					3																	194408136		2020	3974	5994	SO:0001583	missense	131583	exon1			CGGCCAACGCGCT	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.581A>G	chr3.hg19:g.194408136A>G	ENSP00000371397:p.Asn194Ser	0.0	0.0	.		24.0	5.0	.	NM_153690	A3KME2|Q8IXP4|Q8WZ07	Missense_Mutation	SNP	ENST00000329759.4	hg19	CCDS33923.1	.	.	.	.	.	.	.	.	.	.	A	8.875	0.950325	0.18431	.	.	ENSG00000185112	ENST00000329759	T	0.62364	0.03	5.07	3.85	0.44370	Pleckstrin homology-type (1);	0.222998	0.44688	D	0.000422	T	0.40119	0.1104	N	0.13098	0.295	0.31328	N	0.685214	B	0.33171	0.4	B	0.33960	0.173	T	0.40403	-0.9565	10	0.07644	T	0.81	-38.1095	12.0384	0.53438	0.8111:0.1889:0.0:0.0	.	194	Q8N2R8	FA43A_HUMAN	S	194	ENSP00000371397:N194S	ENSP00000371397:N194S	N	+	2	0	FAM43A	195889425	0.999000	0.42202	1.000000	0.80357	0.903000	0.53119	3.528000	0.53524	1.913000	0.55393	0.379000	0.24179	AAC	.	.	.	none		0.672	FAM43A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342734.1	NM_153690		G	194408136	A	G	194408136	3	3	98	1	0	0	0	0	1	0	0	0	5569	43	2	3	583	3	FAM43A	3	194408136	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08	72124748	194408136	3614294	11	6195											
PDCD6	10016	hgsc.bcm.edu	37	chr5	311485	311485	+	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	gacgggggcagattgccttcGacgacttcatccagggctgc	7	8	14	12	3	1	1	1	0	0	1	3	4	2	1	2	3	2	2	2	3	0	3	rs368897410		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr5:311485G>A	ENST00000264933.4	+	5	545	c.445G>A	c.(445-447)Gac>Aac	p.D149N	AHRR_ENST00000512529.1_Intron|AHRR_ENST00000505113.1_Intron|PDCD6_ENST00000511482.1_3'UTR|PDCD6_ENST00000505221.1_Intron|PDCD6_ENST00000507528.1_Missense_Mutation_p.D147N|AHRR_ENST00000316418.5_Intron	NM_001267556.1|NM_001267558.1|NM_013232.3	NP_001254485.1|NP_001254487.1|NP_037364.1	O75340	PDCD6_HUMAN	programmed cell death 6	149	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|cellular response to heat (GO:0034605)|intracellular protein transport (GO:0006886)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|proteolysis (GO:0006508)|response to calcium ion (GO:0051592)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	binding, bridging (GO:0060090)|calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|calcium-dependent protein binding (GO:0048306)|protein dimerization activity (GO:0046983)			breast(2)|endometrium(1)|large_intestine(4)|lung(1)	8			Epithelial(17;0.00193)|OV - Ovarian serous cystadenocarcinoma(19;0.00489)|all cancers(22;0.00511)|Lung(60;0.113)			GATTGCCTTCGACGACTTCAT	0.582																																					p.D149N		Atlas-SNP	.											.	PDCD6	24	.	0			c.G445A						PASS	.	G	,ASN/ASP,	1,4405	2.1+/-5.4	0,1,2202	92	76	81		,445,	5.7	0.9	5		81	0,8600		0,0,4300	no	intron,missense,intron	PDCD6,AHRR	NM_001242412.1,NM_013232.3,NM_020731.4	,23,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,probably-damaging,	,149/192,	311485	1,13005	2203	4300	6503	SO:0001583	missense	10016	exon5			GCCTTCGACGACT	AF035606	CCDS3854.1, CCDS58940.1, CCDS58941.1, CCDS75222.1, CCDS75223.1	5p15.33	2013-01-10			ENSG00000249915	ENSG00000249915		"EF-hand domain containing"	8765	protein-coding gene	gene with protein product	"apoptosis-linked gene-2"	601057				8560270	Standard	NM_013232		Approved	ALG-2, PEF1B	uc003jat.1	O75340	OTTHUMG00000090283	ENST00000264933.4:c.445G>A	chr5.hg19:g.311485G>A	ENSP00000264933:p.Asp149Asn	37.0	0.0	.		163.0	44.0	.	NM_013232	B2RD16|E7ESR3|Q2YDC2|Q5TZS0	Missense_Mutation	SNP	ENST00000264933.4	hg19	CCDS3854.1	.	.	.	.	.	.	.	.	.	.	g	36	5.640171	0.96693	2.27E-4	0.0	ENSG00000249915	ENST00000264933;ENST00000507528;ENST00000507473	T;T;T	0.79141	1.36;1.36;-1.24	5.72	5.72	0.89469	EF-hand-like domain (1);	.	.	.	.	D	0.88789	0.6532	M	0.82132	2.575	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.995;0.997	D	0.89735	0.3929	9	0.87932	D	0	.	17.3651	0.87362	0.0:0.0:1.0:0.0	.	147;149	Q2YDC2;O75340	.;PDCD6_HUMAN	N	149;147;62	ENSP00000264933:D149N;ENSP00000423815:D147N;ENSP00000425370:D62N	ENSP00000264933:D149N	D	+	1	0	PDCD6	364485	1.000000	0.71417	0.914000	0.36105	0.835000	0.47333	9.347000	0.97059	2.692000	0.91855	0.655000	0.94253	GAC	.	.	.	weak		0.582	PDCD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206609.2	NM_013232		A	311485	G	A	311485	3	1	98	1	0	0	0	0	1	0	0	0	11630	1058	37	1	463	1	PDCD6	5	311485	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08		311485	180603775	12	6196											
NSUN2	54888	hgsc.bcm.edu	37	chr5	6616902	6616902	+	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	caatagggtttagtgaacacGtggaatacaccatccttcca	13	10	8	10	1	0	1	0	1	0	0	2	2	2	2	3	2	2	1	3	2	6	5	rs138724893		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr5:6616902G>T	ENST00000264670.6	-	9	1270	c.959C>A	c.(958-960)aCg>aAg	p.T320K	NSUN2_ENST00000539938.1_Missense_Mutation_p.T84K|NSUN2_ENST00000506139.1_Missense_Mutation_p.T285K	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	320					mitotic nuclear division (GO:0007067)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|tRNA (cytosine-5-)-methyltransferase activity (GO:0016428)|tRNA binding (GO:0000049)	p.T320M(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	41						TAGTGAACACGTGGAATACAC	0.468																																					p.T320K		Atlas-SNP	.											NSUN2,NS,carcinoma,0,1	NSUN2	82	.	1	Substitution - Missense(1)	prostate(1)	c.C959A						PASS	.						151	133	139					5																	6616902		2203	4300	6503	SO:0001583	missense	54888	exon9			GAACACGTGGAAT	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.959C>A	chr5.hg19:g.6616902G>T	ENSP00000264670:p.Thr320Lys	68.0	0.0	.		86.0	38.0	.	NM_017755	A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Missense_Mutation	SNP	ENST00000264670.6	hg19	CCDS3869.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.517699	0.85495	.	.	ENSG00000037474	ENST00000264670;ENST00000539938;ENST00000506139	T;T;T	0.26810	1.71;1.71;1.71	5.56	4.69	0.59074	Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p (1);	0.092104	0.85682	D	0.000000	T	0.70133	0.3189	H	0.99507	4.6	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.84435	0.0579	10	0.87932	D	0	-41.0989	14.8419	0.70233	0.0693:0.0:0.9307:0.0	.	285;320	B4DQW2;Q08J23	.;NSUN2_HUMAN	K	320;84;285	ENSP00000264670:T320K;ENSP00000444338:T84K;ENSP00000420957:T285K	ENSP00000264670:T320K	T	-	2	0	NSUN2	6669902	1.000000	0.71417	0.047000	0.18901	0.855000	0.48748	8.772000	0.91757	1.498000	0.48600	0.650000	0.86243	ACG	.	G|1.000;A|0.000	.	alt		0.468	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755		T	6616902	G	T	6616902	3	4	98	1	0	0	0	0	1	0	0	0	10685	1145	40	4	1388	4	NSUN2	5	6616902	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	6305417	6616902	174298358	13	6197											
MEGF10	84466	hgsc.bcm.edu	37	chr5	126753406	126753406	+	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	gtaatgagacatgttctcctGgattctacggggaagcttgc	9	12	12	8	1	2	1	0	1	2	1	3	4	2	3	1	3	3	3	1	3	3	5			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr5:126753406G>A	ENST00000274473.6	+	11	1474	c.1207G>A	c.(1207-1209)Gga>Aga	p.G403R	MEGF10_ENST00000508365.1_Missense_Mutation_p.G403R|MEGF10_ENST00000503335.2_Missense_Mutation_p.G403R|MEGF10_ENST00000418761.2_Missense_Mutation_p.G403R	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10	403	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)		ATGTTCTCCTGGATTCTACGG	0.532																																					p.G403R		Atlas-SNP	.											.	MEGF10	152	.	0			c.G1207A						PASS	.						121	103	109					5																	126753406		2203	4300	6503	SO:0001583	missense	84466	exon11			TCTCCTGGATTCT	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.1207G>A	chr5.hg19:g.126753406G>A	ENSP00000274473:p.Gly403Arg	45.0	0.0	.		106.0	49.0	.	NM_032446	Q68DE5|Q8WUL3	Missense_Mutation	SNP	ENST00000274473.6	hg19	CCDS4142.1	.	.	.	.	.	.	.	.	.	.	G	33	5.226760	0.95173	.	.	ENSG00000145794	ENST00000503335;ENST00000508365;ENST00000418761;ENST00000274473	T;T;T;T	0.72394	-0.65;-0.65;-0.65;-0.65	5.69	5.69	0.88448	EGF-like, laminin (2);	0.000000	0.64402	D	0.000001	D	0.89392	0.6702	H	0.95816	3.725	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	D	0.90450	0.4438	10	0.44086	T	0.13	-11.0125	19.8251	0.96614	0.0:0.0:1.0:0.0	.	403;403	Q96KG7-2;Q96KG7	.;MEG10_HUMAN	R	403	ENSP00000423354:G403R;ENSP00000423195:G403R;ENSP00000416284:G403R;ENSP00000274473:G403R	ENSP00000274473:G403R	G	+	1	0	MEGF10	126781305	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.864000	0.99589	2.692000	0.91855	0.655000	0.94253	GGA	.	.	.	none		0.532	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446		A	126753406	G	A	126753406	3	1	98	1	0	0	0	0	1	0	0	0	9467	1349	47	2	1241	2	MEGF10	5	126753406	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	120136504	126753406	54161854	14	6198											
FLT4	2324	hgsc.bcm.edu	37	chr5	180052935	180052936	+	Frame_Shift_Ins	INS	-	-	G																															ccactggatgctgagaggcaINSggggcaccccgtaggccgtg																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr5:180052935_180052936insG	ENST00000261937.6	-	10	1432_1433	c.1354_1355insC	c.(1354-1356)ctgfs	p.L452fs	FLT4_ENST00000393347.3_Frame_Shift_Ins_p.L452fs|FLT4_ENST00000424276.2_5'UTR|FLT4_ENST00000502649.1_Frame_Shift_Ins_p.L452fs	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	452	Ig-like C2-type 5.				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)	GCTGAGAGGCAGGGGCACCCCG	0.649																																					p.L452fs	Colon(97;1075 1466 27033 27547 35871)	Atlas-INDEL	.											.	FLT4	356	.	0			c.1355_1356insC						PASS	.																																			SO:0001589	frameshift_variant	2324	exon10			.	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.1355dupC	chr5.hg19:g.180052939_180052939dupG	ENSP00000261937:p.Leu452fs	69.0	0.0	0		323.0	30.0	0.0928793	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Frame_Shift_Ins	INS	ENST00000261937.6	hg19	CCDS4457.1																																																																																			.	.	.	none		0.649	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4			G	180052936	-	G	180052935	7	5	98	1	0	1	1	0	0	0	0	0	5951	188	7	0	2828	0	FLT4	5	180052935	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	53299529	180052935	862325	15	6199											
TFAP2A	7020	hgsc.bcm.edu	37	chr6	10398708	10398708	+	Missense_Mutation	SNP	T	T	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	cgttgttgtccgtgtggctgTtggggttgttgctgaggtac	2	16	17	6	2	0	1	0	1	0	0	1	1	1	1	1	4	2	8	1	4	1	6	rs201591227		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr6:10398708T>G	ENST00000482890.1	-	8	1608	c.1256A>C	c.(1255-1257)aAc>aCc	p.N419T	TFAP2A_ENST00000319516.4_Missense_Mutation_p.N415T|TFAP2A_ENST00000379604.2_Missense_Mutation_p.N419T|TFAP2A_ENST00000379608.3_Missense_Mutation_p.N413T|TFAP2A_ENST00000379613.3_Missense_Mutation_p.N421T|TFAP2A_ENST00000497266.1_5'Flank			P05549	AP2A_HUMAN	transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha)	419					anterior neuropore closure (GO:0021506)|basement membrane organization (GO:0071711)|bone morphogenesis (GO:0060349)|cellular response to iron ion (GO:0071281)|cornea development in camera-type eye (GO:0061303)|embryonic body morphogenesis (GO:0010172)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|embryonic pattern specification (GO:0009880)|epidermis morphogenesis (GO:0048730)|eyelid development in camera-type eye (GO:0061029)|face morphogenesis (GO:0060325)|forebrain neuron development (GO:0021884)|inner ear morphogenesis (GO:0042472)|keratinocyte development (GO:0003334)|kidney development (GO:0001822)|lens induction in camera-type eye (GO:0060235)|metanephric nephron development (GO:0072210)|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 neuron apoptotic process (GO:0043524)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|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)|neural crest cell development (GO:0014032)|oculomotor nerve formation (GO:0021623)|optic cup structural organization (GO:0003409)|optic vesicle morphogenesis (GO:0003404)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of tooth mineralization (GO:0070172)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell differentiation (GO:0045595)|regulation of neuron differentiation (GO:0045664)|retina layer formation (GO:0010842)|sensory perception of sound (GO:0007605)|sympathetic nervous system development (GO:0048485)|transcription from RNA polymerase II promoter (GO:0006366)|trigeminal nerve development (GO:0021559)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|protein dimerization activity (GO:0046983)|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 (GO:0000982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II 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)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)	13	Breast(50;0.0427)|Ovarian(93;0.0991)	all_hematologic(90;0.107)				CGTGTGGCTGTTGGGGTTGTT	0.622																																					p.N419T		Atlas-SNP	.											.	TFAP2A	129	.	0			c.A1256C						PASS	.						317	330	326					6																	10398708		2203	4300	6503	SO:0001583	missense	7020	exon7			TGGCTGTTGGGGT	X52611	CCDS4510.1, CCDS34337.1, CCDS43422.1	6p24.3	2013-09-19	2001-11-28		ENSG00000137203	ENSG00000137203			11742	protein-coding gene	gene with protein product		107580	"transcription factor AP-2 alpha (activating enhancer-binding protein 2 alpha)"	TFAP2, AP2TF		1916817, 3063603	Standard	NM_001032280		Approved	AP-2	uc003myr.3	P05549	OTTHUMG00000014235	ENST00000482890.1:c.1256A>C	chr6.hg19:g.10398708T>G	ENSP00000418541:p.Asn419Thr	715.0	1.0	.		1832.0	626.0	.	NM_003220	Q13777|Q5TAV5|Q8N1C6	Missense_Mutation	SNP	ENST00000482890.1	hg19	CCDS4510.1	.	.	.	.	.	.	.	.	.	.	T	12.06	1.825513	0.32237	.	.	ENSG00000137203	ENST00000379613;ENST00000379604;ENST00000319516;ENST00000379608;ENST00000482890	D;D;D;D;D	0.97114	-4.25;-4.25;-4.25;-4.25;-4.25	5.41	5.41	0.78517	.	0.042320	0.85682	D	0.000000	D	0.97247	0.9100	L	0.55481	1.735	0.80722	D	1	D;D;D	0.71674	0.993;0.983;0.998	D;P;D	0.83275	0.968;0.829;0.996	D	0.96866	0.9636	10	0.34782	T	0.22	-13.6146	15.4442	0.75216	0.0:0.0:0.0:1.0	.	415;419;413	Q5TAV5;P05549;Q8N1C6	.;AP2A_HUMAN;.	T	421;419;415;413;419	ENSP00000368933:N421T;ENSP00000368924:N419T;ENSP00000316516:N415T;ENSP00000368928:N413T;ENSP00000418541:N419T	ENSP00000316516:N415T	N	-	2	0	TFAP2A	10506694	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.249000	0.58766	2.048000	0.60808	0.533000	0.62120	AAC	.	.	.	weak		0.622	TFAP2A-007	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353619.2	NM_003220		G	10398708	T	G	10398708	3	3	98	1	0	0	0	0	1	0	0	0	15799	1725	60	5	61	5	TFAP2A	6	10398708	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08		10398708	160716359	16	6200											
CAP2	10486	hgsc.bcm.edu	37	chr6	17507928	17507928	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gacgctgccaccttttacacTaacagggtcttaaaggacta	12	10	8	11	1	1	0	0	0	1	0	1	2	1	1	2	2	3	1	2	2	5	5			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr6:17507928T>C	ENST00000229922.2	+	6	1033	c.501T>C	c.(499-501)acT>acC	p.T167T	CAP2_ENST00000489374.1_Intron|CAP2_ENST00000493172.1_Intron|CAP2_ENST00000465994.1_Intron|CAP2_ENST00000378990.2_Silent_p.T141T	NM_006366.2	NP_006357.1	P40123	CAP2_HUMAN	CAP, adenylate cyclase-associated protein, 2 (yeast)	167					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)			CCTTTTACACTAACAGGGTCT	0.413																																					p.T167T		Atlas-SNP	.											.	CAP2	61	.	0			c.T501C						PASS	.						138	124	129					6																	17507928		2203	4300	6503	SO:0001819	synonymous_variant	10486	exon6			TTACACTAACAGG	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.501T>C	chr6.hg19:g.17507928T>C		143.0	0.0	.		132.0	50.0	.	NM_006366	B2R5Y3|B7Z1C4|B7Z214|Q6IAY2	Silent	SNP	ENST00000229922.2	hg19	CCDS4539.1																																																																																			.	.	.	none		0.413	CAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039952.2			C	17507928	T	C	17507928	2	2	98	1	0	0	0	0	0	0	0	1	2622	1509	53	3		3	CAP2	6	17507928	Silent	SNP	T	TCGA-B9-4117-01A-01D-1252-08	7109220	17507928	153607139	17	6201											
HIST1H1C	3006	hgsc.bcm.edu	37	chr6	26056427	26056427	+	Missense_Mutation	SNP	T	T	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	gaccaagtttgatacggctgTtgtttttctccacatcatag	9	15	8	9	1	2	1	1	1	1	0	3	2	2	1	2	1	1	4	2	1	3	6	rs182693914		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr6:26056427T>G	ENST00000343677.2	-	1	272	c.230A>C	c.(229-231)aAc>aCc	p.N77T		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	77	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						GATACGGCTGTTGTTTTTCTC	0.527																																					p.N77T		Atlas-SNP	.											HIST1H1C,NS,carcinoma,0,1	HIST1H1C	80	.	0			c.A230C						PASS	.						106	111	109					6																	26056427		2203	4300	6503	SO:0001583	missense	3006	exon1			CGGCTGTTGTTTT	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.230A>C	chr6.hg19:g.26056427T>G	ENSP00000339566:p.Asn77Thr	162.0	2.0	.		476.0	201.0	.	NM_005319	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	hg19	CCDS4577.1	.	.	.	.	.	.	.	.	.	.	T	18.74	3.688031	0.68271	.	.	ENSG00000187837	ENST00000343677	T	0.08984	3.03	5.63	5.63	0.86233	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.152097	0.56097	D	0.000023	T	0.24275	0.0588	M	0.85945	2.785	0.80722	D	1	D	0.64830	0.994	D	0.71870	0.975	T	0.02617	-1.1133	10	0.66056	D	0.02	-32.5039	15.3144	0.74062	0.0:0.0:0.0:1.0	.	77	P16403	H12_HUMAN	T	77	ENSP00000339566:N77T	ENSP00000339566:N77T	N	-	2	0	HIST1H1C	26164406	1.000000	0.71417	1.000000	0.80357	0.303000	0.27691	6.087000	0.71362	2.271000	0.75665	0.533000	0.62120	AAC	.	.	.	weak		0.527	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319		G	26056427	T	G	26056427	3	3	98	1	0	0	0	0	1	0	0	0	7131	1725	60	5	415	5	HIST1H1C	6	26056427	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	8548499	26056427	145058640	18	6202											
URGCP	55665	hgsc.bcm.edu	37	chr7	43916495	43916495	+	Frame_Shift_Del	DEL	C	C	-																															ccagtgcccggaagccgtcgCcctgtttctccatctgggct																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr7:43916495delC	ENST00000453200.1	-	6	3060	c.2567delG	c.(2566-2568)ggcfs	p.G856fs	URGCP_ENST00000443736.1_Frame_Shift_Del_p.G813fs|URGCP_ENST00000402306.3_Frame_Shift_Del_p.G847fs|URGCP_ENST00000497914.1_5'UTR|URGCP_ENST00000336086.6_Frame_Shift_Del_p.G813fs|URGCP-MRPS24_ENST00000603700.1_Intron|URGCP_ENST00000447717.3_Frame_Shift_Del_p.G813fs|URGCP_ENST00000223341.7_Frame_Shift_Del_p.G813fs			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	856	VLIG-type G.				cell cycle (GO:0007049)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|liver(1)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GAAGCCGTCGCCCTGTTTCTC	0.637																																					p.G856fs		Atlas-INDEL	.											.	URGCP	170	.	0			c.2568delC						PASS	.						29	31	30					7																	43916495		1994	4175	6169	SO:0001589	frameshift_variant	55665	exon6			.		CCDS43572.1, CCDS47577.1, CCDS47578.1	7p13	2010-02-17			ENSG00000106608	ENSG00000106608			30890	protein-coding gene	gene with protein product	"up-regulated gene 4"	610337				10819331, 12082552	Standard	NM_017920		Approved	URG4, KIAA1507, FLJ20654, DKFZp666G166, DKFZp686O0457	uc003tiw.3	Q8TCY9	OTTHUMG00000155245	ENST00000453200.1:c.2567delG	chr7.hg19:g.43916495delC	ENSP00000396918:p.Gly856fs	42.0	0.0	0		167.0	39.0	0.233533	NM_001077663	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Frame_Shift_Del	DEL	ENST00000453200.1	hg19	CCDS47578.1																																																																																			.	.	.	none		0.637	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664		-	43916495	C	-	43916495	7	5	98	1	0	1	0	1	0	0	0	0	17038	739	26	0	232	0	URGCP	7	43916495	Frame_Shift_Del	DEL	C	TCGA-B9-4117-01A-01D-1252-08		43916495	115222168	19	6203											
CAV2	858	hgsc.bcm.edu	37	chr7	116140377	116140377	+	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	cctttgacaaagtgtggatcTgcagccatgccctctttgaa	9	12	9	11	0	2	2	0	2	2	0	2	3	2	3	3	1	3	1	3	1	2	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr7:116140377T>A	ENST00000222693.4	+	2	606	c.214T>A	c.(214-216)Tgc>Agc	p.C72S	AC002066.1_ENST00000446355.2_RNA|CAV2_ENST00000393480.2_Missense_Mutation_p.C72S|CAV2_ENST00000343213.2_Intron|CAV2_ENST00000462876.1_3'UTR	NM_001206747.1|NM_001206748.1|NM_001233.4	NP_001193676.1|NP_001193677.1|NP_001224.1	P51636	CAV2_HUMAN	caveolin 2	72					caveola assembly (GO:0070836)|endoplasmic reticulum organization (GO:0007029)|mitochondrion organization (GO:0007005)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of endothelial cell proliferation (GO:0001938)|protein oligomerization (GO:0051259)|regulation of mitosis (GO:0007088)|skeletal muscle fiber development (GO:0048741)|synaptic transmission (GO:0007268)|vesicle docking (GO:0048278)|vesicle fusion (GO:0006906)|vesicle organization (GO:0016050)	acrosomal membrane (GO:0002080)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lipid particle (GO:0005811)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|transport vesicle (GO:0030133)	D1 dopamine receptor binding (GO:0031748)|protein homodimerization activity (GO:0042803)			large_intestine(1)|lung(1)|skin(1)	3	all_epithelial(6;1.53e-06)|Lung NSC(10;0.00592)|all_lung(10;0.00642)		STAD - Stomach adenocarcinoma(10;0.00878)			AGTGTGGATCTGCAGCCATGC	0.542																																					p.C72S		Atlas-SNP	.											.	CAV2	10	.	0			c.T214A						PASS	.						169	138	149					7																	116140377		2203	4300	6503	SO:0001583	missense	858	exon2			TGGATCTGCAGCC	AF035752	CCDS5765.1, CCDS5766.1	7q31	2006-02-09			ENSG00000105971	ENSG00000105971			1528	protein-coding gene	gene with protein product		601048				8552590, 10087206	Standard	NM_001233		Approved	CAV	uc003vid.3	P51636	OTTHUMG00000023414	ENST00000222693.4:c.214T>A	chr7.hg19:g.116140377T>A	ENSP00000222693:p.Cys72Ser	69.0	0.0	.		348.0	92.0	.	NM_001233	A4D0U2|Q9UGM7	Missense_Mutation	SNP	ENST00000222693.4	hg19	CCDS5766.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.420268	0.83559	.	.	ENSG00000105971	ENST00000222693;ENST00000393480	D;D	0.92249	-3.0;-3.0	4.6	4.6	0.57074	.	0.193833	0.56097	D	0.000032	D	0.93213	0.7838	M	0.85197	2.74	0.39643	D	0.970342	P	0.35656	0.514	B	0.41135	0.348	D	0.93194	0.6586	10	0.36615	T	0.2	-15.4697	14.2879	0.66258	0.0:0.0:0.0:1.0	.	72	P51636	CAV2_HUMAN	S	72	ENSP00000222693:C72S;ENSP00000377120:C72S	ENSP00000222693:C72S	C	+	1	0	CAV2	115927613	0.972000	0.33761	1.000000	0.80357	0.995000	0.86356	1.530000	0.36007	1.828000	0.53243	0.460000	0.39030	TGC	.	.	.	none		0.542	CAV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059735.4	NM_001233		A	116140377	T	A	116140377	3	1	98	1	0	0	0	0	1	0	0	0	2696	1580	55	5	220	5	CAV2	7	116140377	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	72223882	116140377	42998286	20	6204											
DPYSL2	1808	hgsc.bcm.edu	37	chr8	26505196	26505196	+	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	gtggctgtgaccagcaccaaTgcagccaaagtcttcaacct	11	8	9	13	0	2	1	1	1	1	0	2	1	2	1	4	1	4	3	4	1	3	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr8:26505196T>A	ENST00000311151.5	+	11	1573	c.1161T>A	c.(1159-1161)aaT>aaA	p.N387K	DPYSL2_ENST00000521913.1_Missense_Mutation_p.N351K|DPYSL2_ENST00000523027.1_Missense_Mutation_p.N351K	NM_001386.5	NP_001377.1	Q16555	DPYL2_HUMAN	dihydropyrimidinase-like 2	387					axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|olfactory bulb development (GO:0021772)|positive regulation of glutamate secretion (GO:0014049)|pyrimidine nucleobase catabolic process (GO:0006208)|regulation of neuron differentiation (GO:0045664)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|spinal cord development (GO:0021510)|synaptic vesicle transport (GO:0048489)	axon (GO:0030424)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	dihydropyrimidinase activity (GO:0004157)			breast(1)|endometrium(5)|large_intestine(8)|lung(3)|prostate(1)|skin(1)|stomach(1)	20		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)		CCAGCACCAATGCAGCCAAAG	0.552																																					p.N492K		Atlas-SNP	.											.	DPYSL2	49	.	0			c.T1476A						PASS	.						133	121	125					8																	26505196		2203	4300	6503	SO:0001583	missense	1808	exon11			CACCAATGCAGCC	D78013	CCDS6051.1, CCDS59096.1	8p22-p21	2011-09-28			ENSG00000092964	ENSG00000092964			3014	protein-coding gene	gene with protein product		602463				8973361	Standard	NM_001197293		Approved	DRP-2, DHPRP2, CRMP2, DRP2	uc003xfa.3	Q16555	OTTHUMG00000099439	ENST00000311151.5:c.1161T>A	chr8.hg19:g.26505196T>A	ENSP00000309539:p.Asn387Lys	106.0	0.0	.		190.0	118.0	.	NM_001197293	A8K5H2|B4DR31|D3DSS7|O00424	Missense_Mutation	SNP	ENST00000311151.5	hg19	CCDS6051.1	.	.	.	.	.	.	.	.	.	.	T	19.82	3.898016	0.72639	.	.	ENSG00000092964	ENST00000545637;ENST00000521913;ENST00000311151;ENST00000522745;ENST00000523027	D;D;D;D	0.92595	-3.07;-3.07;-3.07;-3.07	5.22	-6.76	0.01732	Amidohydrolase 1 (1);Metal-dependent hydrolase, composite domain (1);	0.000000	0.85682	D	0.000000	D	0.96144	0.8743	M	0.92367	3.3	0.53688	D	0.999974	D;P	0.76494	0.999;0.835	D;B	0.83275	0.996;0.269	D	0.94988	0.8132	10	0.66056	D	0.02	-27.4582	18.9516	0.92643	0.0:0.601:0.0:0.399	.	387;443	Q16555;Q59GB4	DPYL2_HUMAN;.	K	26;351;387;387;351	ENSP00000427985:N351K;ENSP00000309539:N387K;ENSP00000428909:N387K;ENSP00000431117:N351K	ENSP00000309539:N387K	N	+	3	2	DPYSL2	26561113	0.000000	0.05858	0.783000	0.31826	0.973000	0.67179	-2.232000	0.01205	-1.277000	0.02411	-1.098000	0.02139	AAT	.	.	.	none		0.552	DPYSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216904.3	NM_001386		A	26505196	T	A	26505196	3	1	98	1	0	0	0	0	1	0	0	0	4749	1461	51	5	1203	5	DPYSL2	8	26505196	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08		26505196	119858826	21	6205											
TLN1	7094	hgsc.bcm.edu	37	chr9	35711016	35711016	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcagggcgttatcacactcCttctggccgggtgcctgctg	4	10	13	14	3	2	0	1	0	1	0	3	0	3	0	3	3	2	3	3	3	1	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr9:35711016C>T	ENST00000314888.9	-	31	4436	c.4083G>A	c.(4081-4083)aaG>aaA	p.K1361K	TLN1_ENST00000540444.1_Silent_p.K1361K	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1361	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)			TATCACACTCCTTCTGGCCGG	0.532																																					p.K1361K		Atlas-SNP	.											.	TLN1	185	.	0			c.G4083A						PASS	.						107	94	98					9																	35711016		2203	4300	6503	SO:0001819	synonymous_variant	7094	exon31			ACACTCCTTCTGG	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.4083G>A	chr9.hg19:g.35711016C>T		49.0	0.0	.		184.0	49.0	.	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Silent	SNP	ENST00000314888.9	hg19	CCDS35009.1																																																																																			.	.	.	none		0.532	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		T	35711016	C	T	35711016	2	4	98	1	0	0	0	0	0	0	0	1	15959	680	24	2		2	TLN1	9	35711016	Silent	SNP	C	TCGA-B9-4117-01A-01D-1252-08		35711016	105502415	22	6206											
ZCCHC6	79670	hgsc.bcm.edu	37	chr9	88940291	88940291	+	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	gggccaatccttcaattcccGagataccaattctttgacac	11	11	6	13	1	2	2	1	1	1	1	4	3	4	2	4	1	1	0	4	1	4	5			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr9:88940291G>C	ENST00000375963.3	-	12	1919	c.1747C>G	c.(1747-1749)Cgg>Ggg	p.R583G	ZCCHC6_ENST00000375961.2_Missense_Mutation_p.R583G|ZCCHC6_ENST00000277141.6_5'UTR|ZCCHC6_ENST00000375960.2_Missense_Mutation_p.R460G|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	583	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						TTCAATTCCCGAGATACCAAT	0.403																																					p.R583G		Atlas-SNP	.											.	ZCCHC6	105	.	0			c.C1747G						PASS	.						101	98	99					9																	88940291		2203	4300	6503	SO:0001583	missense	79670	exon12			ATTCCCGAGATAC	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.1747C>G	chr9.hg19:g.88940291G>C	ENSP00000365130:p.Arg583Gly	81.0	0.0	.		34.0	12.0	.	NM_024617	Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	Missense_Mutation	SNP	ENST00000375963.3	hg19	CCDS35057.1	.	.	.	.	.	.	.	.	.	.	G	18.25	3.583577	0.65992	.	.	ENSG00000083223	ENST00000375960;ENST00000375961;ENST00000375963	T;T;T	0.78707	-1.2;-1.2;-1.2	5.1	5.1	0.69264	PAP/25A-associated (1);	0.000000	0.85682	D	0.000000	D	0.87358	0.6157	M	0.76838	2.35	0.54753	D	0.999989	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.88322	0.2963	10	0.72032	D	0.01	-11.8038	13.6554	0.62336	0.0:0.0:0.8455:0.1544	.	460;583	Q5VYS8-4;Q5VYS8	.;TUT7_HUMAN	G	460;583;583	ENSP00000365127:R460G;ENSP00000365128:R583G;ENSP00000365130:R583G	ENSP00000365127:R460G	R	-	1	2	ZCCHC6	88130111	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.937000	0.56575	2.658000	0.90341	0.650000	0.86243	CGG	.	.	.	none		0.403	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1	NM_024617		C	88940291	G	C	88940291	3	2	98	1	0	0	0	0	1	0	0	0	17604	1057	37	4	2804	4	ZCCHC6	9	88940291	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	53229275	88940291	52273140	23	6207											
ANK3	288	hgsc.bcm.edu	37	chr10	61819138	61819138	+	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	taacccaccagttactcttcGagcttgagcgcaggactcta	10	10	8	13	2	2	1	0	1	2	0	3	3	2	2	2	1	4	3	2	1	3	5			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr10:61819138G>C	ENST00000280772.2	-	41	12837	c.12646C>G	c.(12646-12648)Cga>Gga	p.R4216G	RP11-388P9.2_ENST00000414383.1_RNA|ANK3_ENST00000355288.2_Missense_Mutation_p.R840G|ANK3_ENST00000503366.1_Missense_Mutation_p.R1707G|ANK3_ENST00000373827.2_Missense_Mutation_p.R1700G	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	4216					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						GTTACTCTTCGAGCTTGAGCG	0.408																																					p.R4216G		Atlas-SNP	.											ANK3_ENST00000355288,colon,carcinoma,0,2	ANK3	703	.	0			c.C12646G						PASS	.						201	175	184					10																	61819138		2203	4300	6503	SO:0001583	missense	288	exon41			CTCTTCGAGCTTG	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.12646C>G	chr10.hg19:g.61819138G>C	ENSP00000280772:p.Arg4216Gly	139.0	0.0	.		39.0	2.0	.	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	hg19	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	G	13.70	2.315261	0.40996	.	.	ENSG00000151150	ENST00000280772;ENST00000373827;ENST00000373820;ENST00000355288;ENST00000503366;ENST00000395299;ENST00000373817	T;T;T;T;T	0.79352	-0.67;-1.26;0.38;-0.38;-1.22	5.56	4.65	0.58169	.	0.000000	0.30329	U	0.009875	T	0.73783	0.3631	L	0.29908	0.895	0.80722	D	1	P;P;P;P;B;P;D	0.58268	0.889;0.543;0.889;0.945;0.447;0.543;0.982	B;B;B;P;B;B;P	0.49752	0.301;0.162;0.394;0.597;0.307;0.162;0.621	T	0.77464	-0.2578	10	0.72032	D	0.01	.	13.835	0.63404	0.0733:0.0:0.9267:0.0	.	1707;840;1700;4216;941;840;239	E9PE32;A8KA62;Q5CZH9;Q12955;F5GXK0;B1AQT2;B1AQT0	.;.;.;ANK3_HUMAN;.;.;.	G	4216;1700;298;840;1707;1686;941	ENSP00000280772:R4216G;ENSP00000362933:R1700G;ENSP00000362926:R298G;ENSP00000347436:R840G;ENSP00000425236:R1707G	ENSP00000280772:R4216G	R	-	1	2	ANK3	61489144	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	7.006000	0.76329	2.623000	0.88846	0.455000	0.32223	CGA	.	.	.	none		0.408	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		C	61819138	G	C	61819138	3	2	98	1	0	0	0	0	1	0	0	0	622	1066	37	4	499	4	ANK3	10	61819138	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08		61819138	73715609	24	6208											
SEC31B	25956	hgsc.bcm.edu	37	chr10	102255181	102255181	+	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	cccaatctgtaagatgatgtCtctttagagtggagggtagc	10	12	12	7	0	2	3	0	1	2	2	3	4	2	4	1	2	1	2	1	2	4	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr10:102255181C>G	ENST00000370345.3	-	19	2530	c.2433G>C	c.(2431-2433)gaG>gaC	p.E811D	SEC31B_ENST00000494350.1_5'Flank	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	811					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)		AAGATGATGTCTCTTTAGAGT	0.488																																					p.E811D		Atlas-SNP	.											.	SEC31B	84	.	0			c.G2433C						PASS	.						69	61	63					10																	102255181		2203	4300	6503	SO:0001583	missense	25956	exon19			TGATGTCTCTTTA	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.2433G>C	chr10.hg19:g.102255181C>G	ENSP00000359370:p.Glu811Asp	40.0	0.0	.		33.0	17.0	.	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Missense_Mutation	SNP	ENST00000370345.3	hg19	CCDS7495.1	.	.	.	.	.	.	.	.	.	.	C	12.40	1.927568	0.34002	.	.	ENSG00000075826	ENST00000370345	T	0.51325	0.71	5.76	-1.7	0.08159	.	0.960732	0.08733	N	0.901781	T	0.18676	0.0448	N	0.08118	0	0.09310	N	0.999998	B;B	0.32893	0.017;0.389	B;B	0.25987	0.006;0.065	T	0.13308	-1.0514	10	0.33141	T	0.24	-8.994	0.6819	0.00876	0.1758:0.2806:0.2804:0.2633	.	810;811	Q9NQW1-5;Q9NQW1	.;SC31B_HUMAN	D	811	ENSP00000359370:E811D	ENSP00000359370:E811D	E	-	3	2	SEC31B	102245171	.	.	0.335000	0.25508	0.480000	0.33159	.	.	-0.009000	0.14296	0.561000	0.74099	GAG	.	.	.	none		0.488	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490		G	102255181	C	G	102255181	3	3	98	1	0	0	0	0	1	0	0	0	14012	912	32	4	1138	4	SEC31B	10	102255181	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08	40436043	102255181	33279566	25	6209											
DCLRE1A	9937	hgsc.bcm.edu	37	chr10	115608965	115608965	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctacatctctttttttgAcgctgtgacctctcactaga	7	18	5	11	1	3	3	1	2	3	1	5	3	3	3	1	0	1	1	1	0	2	6			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr10:115608965A>G	ENST00000361384.2	-	2	2816	c.1899T>C	c.(1897-1899)cgT>cgC	p.R633R	DCLRE1A_ENST00000369305.1_Silent_p.R633R	NM_014881.3	NP_055696.3	Q6PJP8	DCR1A_HUMAN	DNA cross-link repair 1A	633					mitotic nuclear division (GO:0007067)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(2)|urinary_tract(1)	31				Epithelial(162;0.0157)|all cancers(201;0.0171)		TCTTTTTTTGACGCTGTGACC	0.368								Other identified genes with known or suspected DNA repair function																													p.R633R		Atlas-SNP	.											.	DCLRE1A	80	.	0			c.T1899C						PASS	.						162	164	163					10																	115608965		2203	4300	6503	SO:0001819	synonymous_variant	9937	exon2			TTTTTGACGCTGT		CCDS7584.1	10q25.1	2010-06-24	2010-06-24		ENSG00000198924	ENSG00000198924			17660	protein-coding gene	gene with protein product	"PSO2 homolog (S. cerevisiae)"	609682	"DNA cross-link repair 1A (PSO2 homolog, S. cerevisiae)"			9806498, 17804464	Standard	NM_014881		Approved	SNM1, PSO2, KIAA0086, hSNM1	uc031pxf.1	Q6PJP8	OTTHUMG00000019077	ENST00000361384.2:c.1899T>C	chr10.hg19:g.115608965A>G		145.0	0.0	.		225.0	84.0	.	NM_014881	D3DRC1|Q14701|Q6P5Y3|Q6PKL4	Silent	SNP	ENST00000361384.2	hg19	CCDS7584.1																																																																																			.	.	.	none		0.368	DCLRE1A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050444.1	NM_014881		G	115608965	A	G	115608965	2	3	98	1	0	0	0	0	0	0	0	1	4296	262	10	3		3	DCLRE1A	10	115608965	Silent	SNP	A	TCGA-B9-4117-01A-01D-1252-08	13353784	115608965	19925782	26	6210											
SLC43A3	29015	hgsc.bcm.edu	37	chr11	57188512	57188512	+	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	acagagtgatgatggtcgaaCggtgttggccaaataggttc	11	10	14	6	2	0	3	0	2	0	1	2	4	0	3	1	4	1	2	1	4	3	3	rs148055054		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr11:57188512C>T	ENST00000395123.2	-	7	768	c.464G>A	c.(463-465)cGt>cAt	p.R155H	SLC43A3_ENST00000528098.1_5'UTR|SLC43A3_ENST00000395124.1_Missense_Mutation_p.R155H|SLC43A3_ENST00000533524.1_Missense_Mutation_p.R168H|SLC43A3_ENST00000529554.1_Missense_Mutation_p.R155H|SLC43A3_ENST00000352187.1_Missense_Mutation_p.R155H	NM_001278201.1|NM_014096.2	NP_001265130.1|NP_054815.2	Q8NBI5	S43A3_HUMAN	solute carrier family 43, member 3	155					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	27						GATGGTCGAACGGTGTTGGCC	0.448																																					p.R155H		Atlas-SNP	.											.	SLC43A3	54	.	0			c.G464A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG	1,4401	2.1+/-5.4	0,1,2200	156	128	138		464,464,464	5.8	1	11	dbSNP_134	138	0,8592		0,0,4296	no	missense,missense,missense	SLC43A3	NM_014096.2,NM_017611.2,NM_199329.1	29,29,29	0,1,6496	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging	155/492,155/492,155/492	57188512	1,12993	2201	4296	6497	SO:0001583	missense	29015	exon7			GTCGAACGGTGTT	AL157431	CCDS7956.1, CCDS60784.1	11q11	2013-05-22			ENSG00000134802	ENSG00000134802		"Solute carriers"	17466	protein-coding gene	gene with protein product	"likely ortholog of mouse embryonic epithelial gene 1"					7531438, 11704567	Standard	NM_017611		Approved	SEEEG-1, Eeg1, DKFZp762A227, FOAP-13, PRO1659	uc001nki.3	Q8NBI5	OTTHUMG00000167113	ENST00000395123.2:c.464G>A	chr11.hg19:g.57188512C>T	ENSP00000378555:p.Arg155His	63.0	0.0	.		91.0	35.0	.	NM_017611	B4DNR8|E7EQD2|Q9NSS4	Missense_Mutation	SNP	ENST00000395123.2	hg19	CCDS7956.1	.	.	.	.	.	.	.	.	.	.	C	35	5.465074	0.96257	2.27E-4	0.0	ENSG00000134802	ENST00000395123;ENST00000395124;ENST00000352187;ENST00000529554;ENST00000533524;ENST00000530005;ENST00000529113;ENST00000525474	T;T;T;T;T;T;D;D	0.84146	-0.35;-0.35;-0.35;-0.35;-0.35;-0.46;-1.81;-1.81	5.85	5.85	0.93711	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.93468	0.7916	M	0.87180	2.865	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.997;0.998	D	0.93715	0.7027	10	0.62326	D	0.03	-17.6544	17.9537	0.89062	0.0:1.0:0.0:0.0	.	155;168;155;155	B4DV87;E7EQD2;Q8NBI5;A8K2X6	.;.;S43A3_HUMAN;.	H	155;155;155;155;168;155;102;155	ENSP00000378555:R155H;ENSP00000378556:R155H;ENSP00000337561:R155H;ENSP00000436254:R155H;ENSP00000434515:R168H;ENSP00000435893:R155H;ENSP00000434293:R102H;ENSP00000436055:R155H	ENSP00000337561:R155H	R	-	2	0	SLC43A3	56945088	1.000000	0.71417	0.993000	0.49108	0.945000	0.59286	6.437000	0.73421	2.782000	0.95742	0.655000	0.94253	CGT	.	C|1.000;T|0.000	0.000	weak		0.448	SLC43A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393057.1	NM_017611		T	57188512	C	T	57188512	3	4	98	1	0	0	0	0	1	0	0	0	14647	536	19	1	1043	1	SLC43A3	11	57188512	Missense_Mutation	SNP	C	TCGA-B9-4117-01A-01D-1252-08		57188512	77818004	27	6211											
TMPRSS13	84000	hgsc.bcm.edu	37	chr11	117789447	117789447	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtcccagctggagatgccTgggctggagatgcctgggct	5	9	17	10	0	0	2	0	0	0	2	1	4	1	2	3	4	3	3	3	4	0	0			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr11:117789447T>C	ENST00000430170.2	-	2	215	c.128A>G	c.(127-129)cAg>cGg	p.Q43R	TMPRSS13_ENST00000528626.1_Missense_Mutation_p.Q43R|TMPRSS13_ENST00000524993.1_Missense_Mutation_p.Q43R|TMPRSS13_ENST00000445164.2_Missense_Mutation_p.Q43R|TMPRSS13_ENST00000526090.1_Missense_Mutation_p.Q43R	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	43	13 X 5 AA repeats of A-S-P-A-[GLQR].|4 X 5 AA repeats of T-P-P-G-R.|Ala-rich.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		TGGAGATGCCTGGGCTGGAGA	0.662																																					p.Q43R		Atlas-SNP	.											.	TMPRSS13	75	.	0			c.A128G						PASS	.						42	49	47					11																	117789447		1901	4116	6017	SO:0001583	missense	84000	exon2			GATGCCTGGGCTG	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.128A>G	chr11.hg19:g.117789447T>C	ENSP00000387702:p.Gln43Arg	60.0	0.0	.		280.0	12.0	.	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Missense_Mutation	SNP	ENST00000430170.2	hg19	CCDS58185.1	.	.	.	.	.	.	.	.	.	.	T	4.646	0.120139	0.08881	.	.	ENSG00000137747	ENST00000528626;ENST00000336500;ENST00000524993;ENST00000430170;ENST00000445164;ENST00000526090	D;D;D;D;D	0.87650	-2.28;-2.24;-2.25;-2.24;-2.14	2.41	-1.65	0.08291	.	.	.	.	.	T	0.73466	0.3590	N	0.19112	0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.57906	-0.7730	9	0.33141	T	0.24	.	5.582	0.17254	0.0:0.5323:0.0:0.4677	.	43;43	Q9BYE2-4;E9PRA0	.;.	R	43	ENSP00000435813:Q43R;ENSP00000434279:Q43R;ENSP00000387702:Q43R;ENSP00000394114:Q43R;ENSP00000436502:Q43R	ENSP00000337113:Q43R	Q	-	2	0	TMPRSS13	117294657	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.101000	0.00604	-0.033000	0.13736	-0.271000	0.10264	CAG	.	.	.	none		0.662	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046		C	117789447	T	C	117789447	3	2	98	1	0	0	0	0	1	0	0	0	16257	1580	55	3	1623	3	TMPRSS13	11	117789447	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	60600935	117789447	17217069	28	6212											
ST3GAL4	6484	hgsc.bcm.edu	37	chr11	126276866	126276866	+	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	ttcccatcccagagaagaagGagccgtgcctccagggtgag	10	6	13	12	1	0	3	0	1	0	2	3	5	3	4	5	2	2	0	5	2	2	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr11:126276866G>C	ENST00000526727.1	+	3	504	c.130G>C	c.(130-132)Gag>Cag	p.E44Q	ST3GAL4_ENST00000526756.1_3'UTR|ST3GAL4_ENST00000444328.2_Missense_Mutation_p.E44Q|ST3GAL4_ENST00000532243.1_Missense_Mutation_p.E43Q|ST3GAL4_ENST00000392669.2_Missense_Mutation_p.E44Q|ST3GAL4_ENST00000530591.1_Missense_Mutation_p.E40Q|ST3GAL4_ENST00000356132.4_Missense_Mutation_p.E44Q|ST3GAL4_ENST00000227495.6_Missense_Mutation_p.E40Q|ST3GAL4_ENST00000449406.2_Missense_Mutation_p.E33Q|ST3GAL4_ENST00000534083.1_Missense_Mutation_p.E44Q|ST3GAL4_ENST00000534457.1_Missense_Mutation_p.E39Q			Q11206	SIA4C_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	44					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836)|monosialoganglioside sialyltransferase activity (GO:0047288)			endometrium(1)|large_intestine(2)|lung(5)|stomach(1)	9	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.138)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0767)		AGAGAAGAAGGAGCCGTGCCT	0.547																																					p.E44Q		Atlas-SNP	.											.	ST3GAL4	25	.	0			c.G130C						PASS	.						85	86	86					11																	126276866		2201	4298	6499	SO:0001583	missense	6484	exon4			AAGAAGGAGCCGT	X74570	CCDS8474.1, CCDS58193.1, CCDS58194.1	11q23-q24	2013-03-01	2003-01-14	2005-02-07	ENSG00000110080	ENSG00000110080	2.4.99.4	"Sialyltransferases"	10864	protein-coding gene	gene with protein product	"ST3Gal IV"	104240	"sialyltransferase 4C (beta-galactosidase alpha-2,3-sialytransferase)"	CGS23, SIAT4, NANTA3, SIAT4C		8557707, 8288606	Standard	NM_006278		Approved	STZ, SAT3, FLJ11867	uc001qds.3	Q11206	OTTHUMG00000165830	ENST00000526727.1:c.130G>C	chr11.hg19:g.126276866G>C	ENSP00000436047:p.Glu44Gln	94.0	0.0	.		419.0	165.0	.	NM_001254757	A8K6B2|O60497|Q8N6A6|Q8NFG7|Q96QQ9	Missense_Mutation	SNP	ENST00000526727.1	hg19	CCDS58193.1	.	.	.	.	.	.	.	.	.	.	G	13.82	2.349790	0.41599	.	.	ENSG00000110080	ENST00000227495;ENST00000444328;ENST00000356132;ENST00000530591;ENST00000534083;ENST00000526311;ENST00000528858;ENST00000534452;ENST00000392669;ENST00000526727;ENST00000449406;ENST00000532243;ENST00000534457	T;T;T;T;T;T;T;T;T;T;T	0.43688	0.94;0.94;0.97;0.94;0.94;0.94;0.94;0.94;0.95;0.94;0.94	5.4	3.42	0.39159	.	0.741690	0.13270	N	0.400600	T	0.28234	0.0697	L	0.50333	1.59	0.09310	N	1	P;P;P	0.49559	0.925;0.454;0.454	B;B;B	0.37346	0.247;0.105;0.105	T	0.09530	-1.0670	10	0.13470	T	0.59	.	6.0778	0.19925	0.1787:0.1907:0.6306:0.0	.	25;40;44	Q9HAA9;Q6IBE6;Q11206	.;.;SIA4C_HUMAN	Q	40;44;44;40;44;44;44;44;44;44;33;43;39	ENSP00000227495:E40Q;ENSP00000394354:E44Q;ENSP00000348451:E44Q;ENSP00000433989:E40Q;ENSP00000433318:E44Q;ENSP00000432424:E44Q;ENSP00000376437:E44Q;ENSP00000436047:E44Q;ENSP00000399444:E33Q;ENSP00000434349:E43Q;ENSP00000434668:E39Q	ENSP00000227495:E40Q	E	+	1	0	ST3GAL4	125782076	0.018000	0.18449	0.992000	0.48379	0.963000	0.63663	1.290000	0.33319	2.527000	0.85204	0.561000	0.74099	GAG	.	.	.	none		0.547	ST3GAL4-003	PUTATIVE	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386470.1	NM_006278		C	126276866	G	C	126276866	3	2	98	1	0	0	0	0	1	0	0	0	15229	1175	41	4	128	4	ST3GAL4	11	126276866	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	8487419	126276866	8729650	29	6213											
MYBPC1	4604	hgsc.bcm.edu	37	chr12	102038482	102038482	+	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	cctgcatatcaggttgacaaAggaggcagagtgaggtttgt	11	10	14	6	0	1	3	1	2	0	1	1	4	1	4	1	4	1	4	1	4	2	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr12:102038482A>T	ENST00000550270.1	+	10	798	c.798A>T	c.(796-798)aaA>aaT	p.K266N	MYBPC1_ENST00000551300.1_Missense_Mutation_p.K167N|MYBPC1_ENST00000361466.2_Missense_Mutation_p.K291N|MYBPC1_ENST00000550501.1_Intron|RP11-755O11.2_ENST00000552081.1_RNA|MYBPC1_ENST00000553190.1_Missense_Mutation_p.K266N|MYBPC1_ENST00000392934.3_Missense_Mutation_p.K253N|RP11-755O11.2_ENST00000547027.1_RNA|MYBPC1_ENST00000547509.1_Missense_Mutation_p.K252N|MYBPC1_ENST00000452455.2_Missense_Mutation_p.K266N|MYBPC1_ENST00000441232.1_Missense_Mutation_p.K266N|MYBPC1_ENST00000545503.2_Missense_Mutation_p.K266N|MYBPC1_ENST00000549145.1_Missense_Mutation_p.K279N|MYBPC1_ENST00000360610.2_Missense_Mutation_p.K266N|MYBPC1_ENST00000361685.2_Missense_Mutation_p.K291N|MYBPC1_ENST00000536007.1_Missense_Mutation_p.K247N|MYBPC1_ENST00000547405.1_Missense_Mutation_p.K240N|MYBPC1_ENST00000541119.1_Missense_Mutation_p.K254N			Q00872	MYPC1_HUMAN	myosin binding protein C, slow type	266	Ig-like C2-type 2.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myofibril (GO:0030016)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	57						AGGTTGACAAAGGAGGCAGAG	0.368																																					p.K291N		Atlas-SNP	.											.	MYBPC1	235	.	0			c.A873T						PASS	.						86	82	83					12																	102038482		2203	4300	6503	SO:0001583	missense	4604	exon12			TGACAAAGGAGGC		CCDS9083.1, CCDS9084.1, CCDS9085.1, CCDS55877.1, CCDS58268.1, CCDS58269.1, CCDS58270.1, CCDS58271.1, CCDS58272.1, CCDS58273.1	12q23.2	2013-02-11	2001-11-28		ENSG00000196091	ENSG00000196091		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7549	protein-coding gene	gene with protein product		160794	"myosin-binding protein C, slow-type"			8375400, 16918501	Standard	NM_002465		Approved		uc010svs.2	Q00872	OTTHUMG00000170274	ENST00000550270.1:c.798A>T	chr12.hg19:g.102038482A>T	ENSP00000449702:p.Lys266Asn	40.0	0.0	.		65.0	18.0	.	NM_206819	B4DKR5|B7Z8G8|B7ZL02|B7ZL09|B7ZL10|E7ESM5|E7EWS6|G3XAE8|Q15497|Q17RR7|Q569K7|Q86T48|Q86TC8|Q8N3L2	Missense_Mutation	SNP	ENST00000550270.1	hg19	CCDS9085.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.395297	0.83011	.	.	ENSG00000196091	ENST00000547405;ENST00000452455;ENST00000441232;ENST00000360610;ENST00000392934;ENST00000547509;ENST00000361685;ENST00000549145;ENST00000553190;ENST00000540770;ENST00000545503;ENST00000536007;ENST00000541119;ENST00000361466;ENST00000551300;ENST00000550270	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98;0.98	5.8	5.8	0.92144	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.000000	0.56097	D	0.000037	T	0.69806	0.3152	M	0.87328	2.875	0.80722	D	1	P;D;D;D;D;P;D;D;P;D;D	0.89917	0.623;1.0;0.999;1.0;0.999;0.623;0.999;1.0;0.863;0.999;0.999	P;D;D;D;D;P;D;D;P;D;D	0.91635	0.499;0.999;0.993;0.999;0.998;0.627;0.998;0.999;0.614;0.998;0.999	T	0.75926	-0.3145	10	0.87932	D	0	.	15.8202	0.78633	1.0:0.0:0.0:0.0	.	247;254;266;266;253;240;266;266;291;291;279	B7ZL02;B7ZL10;E7EWS6;B7ZL09;E7ESM5;Q17RR7;Q00872-3;Q00872;G3XAE8;Q00872-2;F8VZY0	.;.;.;.;.;.;.;MYPC1_HUMAN;.;.;.	N	240;266;266;266;253;252;291;279;266;291;266;247;254;291;167;266	ENSP00000448175:K240N;ENSP00000400908:K266N;ENSP00000388989:K266N;ENSP00000353822:K266N;ENSP00000376665:K253N;ENSP00000447362:K252N;ENSP00000354845:K291N;ENSP00000447660:K279N;ENSP00000447900:K266N;ENSP00000440034:K266N;ENSP00000446128:K247N;ENSP00000442847:K254N;ENSP00000354849:K291N;ENSP00000447116:K167N;ENSP00000449702:K266N	ENSP00000353822:K266N	K	+	3	2	MYBPC1	100562613	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.038000	0.64177	2.212000	0.71576	0.533000	0.62120	AAA	.	.	.	none		0.368	MYBPC1-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000408806.1			T	102038482	A	T	102038482	3	4	98	1	0	0	0	0	1	0	0	0	10018	69	3	5	919	5	MYBPC1	12	102038482	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08		102038482	31813413	30	6214											
ACAD10	80724	hgsc.bcm.edu	37	chr12	112174685	112174685	+	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	gaatccctgctgcagaggagTatttcaggatgtactgtctc	9	12	11	9	0	2	1	1	0	1	1	4	4	3	3	1	2	3	4	1	2	3	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr12:112174685T>A	ENST00000313698.4	+	12	1746	c.1591T>A	c.(1591-1593)Tat>Aat	p.Y531N	ACAD10_ENST00000455480.2_Missense_Mutation_p.Y562N|ACAD10_ENST00000549590.1_Missense_Mutation_p.Y531N|ACAD10_ENST00000392636.2_Missense_Mutation_p.Y133N|ACAD10_ENST00000413681.3_3'UTR	NM_025247.5	NP_079523.3	Q6JQN1	ACD10_HUMAN	acyl-CoA dehydrogenase family, member 10	531						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						TGCAGAGGAGTATTTCAGGAT	0.502																																					p.Y562N		Atlas-SNP	.											.	ACAD10	93	.	0			c.T1684A						PASS	.						124	112	116					12																	112174685		2203	4300	6503	SO:0001583	missense	80724	exon13			GAGGAGTATTTCA	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.1591T>A	chr12.hg19:g.112174685T>A	ENSP00000325137:p.Tyr531Asn	44.0	0.0	.		132.0	50.0	.	NM_001136538	G3XAJ0|Q8N828|Q8NAP2|Q96BX5	Missense_Mutation	SNP	ENST00000313698.4	hg19	CCDS31903.1	.	.	.	.	.	.	.	.	.	.	T	19.30	3.801553	0.70682	.	.	ENSG00000111271	ENST00000392636;ENST00000413681;ENST00000549590;ENST00000455480;ENST00000313698	T;T;T;T	0.30448	1.53;1.53;1.53;1.53	5.29	4.14	0.48551	Protein kinase-like domain (1);	0.289517	0.34133	N	0.004238	T	0.61887	0.2383	M	0.92880	3.355	0.37403	D	0.912927	D;D;D	0.89917	0.997;0.999;1.0	P;D;D	0.91635	0.879;0.957;0.999	T	0.72020	-0.4416	10	0.66056	D	0.02	.	10.4594	0.44570	0.0:0.0776:0.0:0.9224	.	562;531;531	G3XAJ0;Q6JQN1;Q6JQN1-2	.;ACD10_HUMAN;.	N	133;531;531;562;531	ENSP00000376411:Y133N;ENSP00000446959:Y531N;ENSP00000389813:Y562N;ENSP00000325137:Y531N	ENSP00000325137:Y531N	Y	+	1	0	ACAD10	110659068	0.972000	0.33761	0.981000	0.43875	0.974000	0.67602	1.626000	0.37039	0.863000	0.35553	0.459000	0.35465	TAT	.	.	.	none		0.502	ACAD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368307.1	NM_025247		A	112174685	T	A	112174685	3	1	98	1	0	0	0	0	1	0	0	0	108	1638	57	5	1730	5	ACAD10	12	112174685	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	10136203	112174685	21677210	31	6215											
EP400	57634	hgsc.bcm.edu	37	chr12	132551479	132551479	+	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	gcccatgaacgtcgcggggaTcagcgtggcgatcggtcagc	7	6	16	12	6	2	1	2	1	0	0	4	3	2	2	1	4	3	0	1	4	1	0			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr12:132551479T>A	ENST00000333577.4	+	50	8931	c.8822T>A	c.(8821-8823)aTc>aAc	p.I2941N	EP400_ENST00000330386.6_Missense_Mutation_p.I2824N|EP400_ENST00000332482.4_Missense_Mutation_p.I2868N|EP400_ENST00000389562.2_Missense_Mutation_p.I2904N|EP400_ENST00000389561.2_Missense_Mutation_p.I2905N			Q96L91	EP400_HUMAN	E1A binding protein p400	2941					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)		GTCGCGGGGATCAGCGTGGCG	0.687																																					p.I2905N		Atlas-SNP	.											.	EP400	370	.	0			c.T8714A						PASS	.						29	29	29					12																	132551479		2203	4299	6502	SO:0001583	missense	57634	exon49			CGGGGATCAGCGT	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.8822T>A	chr12.hg19:g.132551479T>A	ENSP00000333602:p.Ile2941Asn	47.0	0.0	.		89.0	35.0	.	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	hg19		.	.	.	.	.	.	.	.	.	.	T	18.43	3.621758	0.66787	.	.	ENSG00000183495	ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000541296	D;D;D;D;D	0.92545	-3.06;-3.05;-2.99;-3.01;-3.02	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	D	0.93112	0.7807	L	0.34521	1.04	0.44899	D	0.997913	D;D;D;D	0.89917	0.992;1.0;1.0;1.0	D;D;D;D	0.87578	0.976;0.998;0.998;0.998	D	0.92827	0.6277	10	0.40728	T	0.16	.	14.4084	0.67099	0.0:0.0:0.0:1.0	.	2941;2905;2824;2904	Q96L91;Q96L91-2;Q96L91-4;Q96L91-5	EP400_HUMAN;.;.;.	N	2941;2905;2904;2868;2824;2905	ENSP00000333602:I2941N;ENSP00000374212:I2905N;ENSP00000374213:I2904N;ENSP00000331737:I2868N;ENSP00000330620:I2824N	ENSP00000330620:I2824N	I	+	2	0	EP400	131117432	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.698000	0.84413	1.817000	0.53016	0.454000	0.30748	ATC	.	.	.	none		0.687	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		A	132551479	T	A	132551479	3	1	98	1	0	0	0	0	1	0	0	0	5151	1435	50	5	8901	5	EP400	12	132551479	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	20376794	132551479	1300416	32	6216											
IFT88	8100	hgsc.bcm.edu	37	chr13	21189985	21189985	+	Missense_Mutation	SNP	T	T	G																															tgcaaaactcattgctcctgTaattgaaacatcttttgctg																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr13:21189985T>G	ENST00000319980.6	+	16	1520	c.1193T>G	c.(1192-1194)gTa>gGa	p.V398G	IFT88_ENST00000382778.4_Missense_Mutation_p.V398G|IFT88_ENST00000351808.5_Missense_Mutation_p.V389G|IFT88_ENST00000461115.1_3'UTR|IFT88_ENST00000537103.1_Missense_Mutation_p.V370G	NM_175605.3	NP_783195.2	Q13099	IFT88_HUMAN	intraflagellar transport 88	398					anterior/posterior pattern specification (GO:0009952)|cardiac muscle cell differentiation (GO:0055007)|cardiac septum morphogenesis (GO:0060411)|cilium morphogenesis (GO:0060271)|cochlea development (GO:0090102)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|embryonic digit morphogenesis (GO:0042733)|epidermal stem cell homeostasis (GO:0036334)|epidermis development (GO:0008544)|epithelial cell morphogenesis (GO:0003382)|eye development (GO:0001654)|forebrain morphogenesis (GO:0048853)|heart formation (GO:0060914)|inner ear receptor stereocilium organization (GO:0060122)|kidney development (GO:0001822)|liver development (GO:0001889)|lung vasculature development (GO:0060426)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|protein localization (GO:0008104)|regulation of autophagic vacuole assembly (GO:2000785)|regulation of cilium assembly (GO:1902017)|regulation of fat cell differentiation (GO:0045598)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of protein processing (GO:0070613)|regulation of smoothened signaling pathway (GO:0008589)|response to fluid shear stress (GO:0034405)|smoothened signaling pathway (GO:0007224)|sperm axoneme assembly (GO:0007288)|spermatid nucleus elongation (GO:0007290)|spinal cord dorsal/ventral patterning (GO:0021513)|telencephalon development (GO:0021537)	acrosomal membrane (GO:0002080)|apical part of cell (GO:0045177)|axonemal basal plate (GO:0097541)|centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|kinocilium (GO:0060091)|motile cilium (GO:0031514)|motile primary cilium (GO:0031512)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	27		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)		ATTGCTCCTGTAATTGAAACA	0.279																																					p.V398G		Atlas-SNP	.											.	IFT88	83	.	0			c.T1193G						PASS	.						81	91	87					13																	21189985		2203	4295	6498	SO:0001583	missense	8100	exon16			CTCCTGTAATTGA	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.1193T>G	chr13.hg19:g.21189985T>G	ENSP00000323580:p.Val398Gly	62.0	0.0	.		181.0	63.0	.	NM_175605	A2A491|B4DUS2|Q5SZJ6|Q8N719	Missense_Mutation	SNP	ENST00000319980.6	hg19	CCDS31944.1	.	.	.	.	.	.	.	.	.	.	T	19.63	3.863350	0.71949	.	.	ENSG00000032742	ENST00000382778;ENST00000389374;ENST00000351808;ENST00000319980;ENST00000537103	T;T;T;T	0.35789	1.31;1.29;1.29;1.31	5.59	3.19	0.36642	.	0.122813	0.56097	D	0.000035	T	0.34978	0.0916	M	0.74647	2.275	0.80722	D	1	B;P;P;B	0.37985	0.433;0.594;0.613;0.104	B;B;B;B	0.36845	0.234;0.164;0.197;0.058	T	0.22765	-1.0207	10	0.66056	D	0.02	-16.2168	6.1242	0.20170	0.0:0.3259:0.0:0.6741	.	370;398;196;398	F5H6C2;E7EW86;Q6MZX0;Q13099	.;.;.;IFT88_HUMAN	G	398;261;389;398;370	ENSP00000372228:V398G;ENSP00000261632:V389G;ENSP00000323580:V398G;ENSP00000437719:V370G	ENSP00000323580:V398G	V	+	2	0	IFT88	20087985	0.997000	0.39634	0.988000	0.46212	0.997000	0.91878	2.622000	0.46427	0.942000	0.37525	0.528000	0.53228	GTA	.	.	.	none		0.279	IFT88-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044075.3	NM_006531		G	21189985	T	G	21189985	3	3	98	1	0	0	0	0	1	0	0	0	7573	1638	57	5	1247	5	IFT88	13	21189985	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08		21189985	93979893	33	6217	68	2									
IFT88	8100	hgsc.bcm.edu	37	chr13	21189988	21189988	+	Missense_Mutation	SNP	T	T	A																															aaaactcattgctcctgtaaTtgaaacatcttttgctgcag																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr13:21189988T>A	ENST00000319980.6	+	16	1523	c.1196T>A	c.(1195-1197)aTt>aAt	p.I399N	IFT88_ENST00000382778.4_Missense_Mutation_p.I399N|IFT88_ENST00000351808.5_Missense_Mutation_p.I390N|IFT88_ENST00000461115.1_3'UTR|IFT88_ENST00000537103.1_Missense_Mutation_p.I371N	NM_175605.3	NP_783195.2	Q13099	IFT88_HUMAN	intraflagellar transport 88	399					anterior/posterior pattern specification (GO:0009952)|cardiac muscle cell differentiation (GO:0055007)|cardiac septum morphogenesis (GO:0060411)|cilium morphogenesis (GO:0060271)|cochlea development (GO:0090102)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|embryonic digit morphogenesis (GO:0042733)|epidermal stem cell homeostasis (GO:0036334)|epidermis development (GO:0008544)|epithelial cell morphogenesis (GO:0003382)|eye development (GO:0001654)|forebrain morphogenesis (GO:0048853)|heart formation (GO:0060914)|inner ear receptor stereocilium organization (GO:0060122)|kidney development (GO:0001822)|liver development (GO:0001889)|lung vasculature development (GO:0060426)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|protein localization (GO:0008104)|regulation of autophagic vacuole assembly (GO:2000785)|regulation of cilium assembly (GO:1902017)|regulation of fat cell differentiation (GO:0045598)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of protein processing (GO:0070613)|regulation of smoothened signaling pathway (GO:0008589)|response to fluid shear stress (GO:0034405)|smoothened signaling pathway (GO:0007224)|sperm axoneme assembly (GO:0007288)|spermatid nucleus elongation (GO:0007290)|spinal cord dorsal/ventral patterning (GO:0021513)|telencephalon development (GO:0021537)	acrosomal membrane (GO:0002080)|apical part of cell (GO:0045177)|axonemal basal plate (GO:0097541)|centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|kinocilium (GO:0060091)|motile cilium (GO:0031514)|motile primary cilium (GO:0031512)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	27		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)		GCTCCTGTAATTGAAACATCT	0.279																																					p.I399N		Atlas-SNP	.											.	IFT88	83	.	0			c.T1196A						PASS	.						81	90	87					13																	21189988		2203	4293	6496	SO:0001583	missense	8100	exon16			CTGTAATTGAAAC	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.1196T>A	chr13.hg19:g.21189988T>A	ENSP00000323580:p.Ile399Asn	61.0	0.0	.		180.0	60.0	.	NM_175605	A2A491|B4DUS2|Q5SZJ6|Q8N719	Missense_Mutation	SNP	ENST00000319980.6	hg19	CCDS31944.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.408083	0.83340	.	.	ENSG00000032742	ENST00000382778;ENST00000389374;ENST00000351808;ENST00000319980;ENST00000537103	T;T;T;T	0.40756	1.03;1.02;1.02;1.04	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.69717	0.3142	M	0.88105	2.93	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;1.0;0.998	D;D;D;D	0.79784	0.986;0.979;0.993;0.991	T	0.76564	-0.2913	10	0.87932	D	0	-20.545	14.7446	0.69480	0.0:0.0:0.0:1.0	.	371;399;197;399	F5H6C2;E7EW86;Q6MZX0;Q13099	.;.;.;IFT88_HUMAN	N	399;262;390;399;371	ENSP00000372228:I399N;ENSP00000261632:I390N;ENSP00000323580:I399N;ENSP00000437719:I371N	ENSP00000323580:I399N	I	+	2	0	IFT88	20087988	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	7.260000	0.78391	2.121000	0.65114	0.528000	0.53228	ATT	.	.	.	none		0.279	IFT88-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044075.3	NM_006531		A	21189988	T	A	21189988	3	1	98	1	0	0	0	0	1	0	0	0	7573	1493	52	5	1250	5	IFT88	13	21189988	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	3	21189988	93979890	34	6218	68	2									
CLMN	79789	hgsc.bcm.edu	37	chr14	95669398	95669398	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggagtccaggtctggcataTagccctctggctcttcgaga	7	11	12	11	1	3	1	0	0	3	1	5	3	4	2	2	4	1	2	2	4	2	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr14:95669398T>C	ENST00000298912.4	-	9	2401	c.2288A>G	c.(2287-2289)tAt>tGt	p.Y763C		NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	763					negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		GTCTGGCATATAGCCCTCTGG	0.567																																					p.Y763C		Atlas-SNP	.											.	CLMN	103	.	0			c.A2288G						PASS	.						38	39	39					14																	95669398		2203	4300	6503	SO:0001583	missense	79789	exon9			GGCATATAGCCCT	AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.2288A>G	chr14.hg19:g.95669398T>C	ENSP00000298912:p.Tyr763Cys	20.0	0.0	.		206.0	84.0	.	NM_024734	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Missense_Mutation	SNP	ENST00000298912.4	hg19	CCDS9933.1	.	.	.	.	.	.	.	.	.	.	T	9.014	0.983104	0.18889	.	.	ENSG00000165959	ENST00000298912	D	0.92647	-3.08	5.22	-4.75	0.03239	.	0.879712	0.09454	N	0.800049	D	0.83718	0.5315	L	0.39397	1.21	0.09310	N	1	B	0.12630	0.006	B	0.08055	0.003	T	0.68055	-0.5510	10	0.40728	T	0.16	.	3.381	0.07255	0.1129:0.3809:0.1154:0.3907	.	763	Q96JQ2	CLMN_HUMAN	C	763	ENSP00000298912:Y763C	ENSP00000298912:Y763C	Y	-	2	0	CLMN	94739151	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.163000	0.03138	-0.982000	0.03515	-1.236000	0.01555	TAT	.	.	.	none		0.567	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2			C	95669398	T	C	95669398	3	2	98	1	0	0	0	0	1	0	0	0	3544	1406	49	3	740	3	CLMN	14	95669398	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08		95669398	11680142	35	6219											
FBXO22	26263	hgsc.bcm.edu	37	chr15	76196905	76196905	+	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	gcgtaacctggatctccgcaGgcctggcggaggccggccac	6	5	15	15	4	1	0	0	0	1	0	2	2	1	2	5	6	1	2	5	6	1	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr15:76196905G>A	ENST00000308275.3	+	2	319	c.214G>A	c.(214-216)Ggc>Agc	p.G72S	FBXO22_ENST00000565131.1_3'UTR|FBXO22_ENST00000453211.2_Missense_Mutation_p.G72S|FBXO22_ENST00000540507.1_Intron	NM_147188.2	NP_671717.1	Q8NEZ5	FBX22_HUMAN	F-box protein 22	72					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						GATCTCCGCAGGCCTGGCGGA	0.602																																					p.G72S		Atlas-SNP	.											.	FBXO22	60	.	0			c.G214A						PASS	.						108	101	103					15																	76196905		2197	4294	6491	SO:0001583	missense	26263	exon2			TCCGCAGGCCTGG	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.214G>A	chr15.hg19:g.76196905G>A	ENSP00000307833:p.Gly72Ser	129.0	0.0	.		305.0	92.0	.	NM_012170	Q0D2P8|Q6PIL5|Q8IXW3|Q9H824|Q9UKC0	Missense_Mutation	SNP	ENST00000308275.3	hg19	CCDS10287.1	.	.	.	.	.	.	.	.	.	.	G	6.702	0.498156	0.12762	.	.	ENSG00000167196	ENST00000308275;ENST00000453211	.	.	.	3.51	0.501	0.16925	.	0.746536	0.11012	N	0.609403	T	0.13841	0.0335	N	0.03608	-0.345	0.09310	N	0.999993	B;B	0.09022	0.0;0.002	B;B	0.08055	0.001;0.003	T	0.33599	-0.9862	9	0.12103	T	0.63	-1.7367	7.3984	0.26950	0.0987:0.332:0.5694:0.0	.	72;72	Q8NEZ5;Q8NEZ5-3	FBX22_HUMAN;.	S	72	.	ENSP00000307833:G72S	G	+	1	0	FBXO22	73983960	0.001000	0.12720	0.002000	0.10522	0.591000	0.36615	0.233000	0.17911	0.106000	0.17784	0.563000	0.77884	GGC	.	.	.	none		0.602	FBXO22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286477.2	NM_147188		A	76196905	G	A	76196905	3	1	98	1	0	0	0	0	1	0	0	0	5741	1000	35	2	220	2	FBXO22	15	76196905	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08		76196905	26334487	36	6220											
CREBBP	1387	hgsc.bcm.edu	37	chr16	3808859	3808859	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttatgaattaacttactggaAttccgaggagctggggatct	11	13	11	6	1	1	1	0	1	1	0	2	5	2	4	1	4	3	1	1	4	5	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr16:3808859A>G	ENST00000262367.5	-	17	4174	c.3365T>C	c.(3364-3366)aTt>aCt	p.I1122T	CREBBP_ENST00000382070.3_Missense_Mutation_p.I1084T	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1122	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)		ACTTACTGGAATTCCGAGGAG	0.438			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.I1122T		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.T3365C						PASS	.						69	68	68					16																	3808859		2197	4300	6497	SO:0001583	missense	1387	exon17			ACTGGAATTCCGA	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.3365T>C	chr16.hg19:g.3808859A>G	ENSP00000262367:p.Ile1122Thr	64.0	0.0	.		62.0	14.0	.	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	hg19	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	A	14.55	2.568041	0.45798	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	T;T	0.19532	2.14;2.14	5.05	5.05	0.67936	Bromodomain (6);Bromodomain, conserved site (1);	0.000000	0.64402	D	0.000001	T	0.54303	0.1850	M	0.89534	3.04	0.80722	D	1	D;D	0.59767	0.986;0.986	D;D	0.97110	1.0;1.0	T	0.64952	-0.6286	10	0.72032	D	0.01	-13.4551	15.0885	0.72174	1.0:0.0:0.0:0.0	.	1152;1122	Q4LE28;Q92793	.;CBP_HUMAN	T	1122;1152;1084	ENSP00000262367:I1122T;ENSP00000371502:I1084T	ENSP00000262367:I1122T	I	-	2	0	CREBBP	3748860	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	9.067000	0.93955	2.022000	0.59522	0.459000	0.35465	ATT	.	.	.	none		0.438	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		G	3808859	A	G	3808859	3	3	98	1	0	0	0	0	1	0	0	0	3863	101	4	3	4023	3	CREBBP	16	3808859	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08		3808859	86545894	37	6221											
HERPUD1	9709	hgsc.bcm.edu	37	chr16	56970652	56970652	+	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	aatcggggacagtatcctgaGgattcctcaagtgatggttt	10	12	12	7	1	1	2	1	2	0	0	4	4	3	4	2	4	0	2	2	4	3	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr16:56970652G>T	ENST00000439977.2	+	4	551	c.354G>T	c.(352-354)gaG>gaT	p.E118D	HERPUD1_ENST00000379792.2_Missense_Mutation_p.E93D|HERPUD1_ENST00000344114.4_Missense_Mutation_p.E117D|HERPUD1_ENST00000570273.1_3'UTR|HERPUD1_ENST00000300302.5_Missense_Mutation_p.E117D	NM_001010989.1|NM_014685.2	NP_001010989.1|NP_055500.1	Q15011	HERP1_HUMAN	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	118					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of protein binding (GO:0032092)|regulation of protein ubiquitination (GO:0031396)|response to unfolded protein (GO:0006986)|ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|stomach(1)	11						AGTATCCTGAGGATTCCTCAA	0.443			T	ERG	prostate																																p.E118D		Atlas-SNP	.		Dom	yes		16	16q12.2-q13	9709	"homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1"		E	.	HERPUD1	28	.	0			c.G354T						PASS	.						142	131	135					16																	56970652		2198	4300	6498	SO:0001583	missense	9709	exon4			TCCTGAGGATTCC	AB034989	CCDS10771.1, CCDS45492.1	16q13	2008-05-14			ENSG00000051108	ENSG00000051108			13744	protein-coding gene	gene with protein product		608070				10922362, 10708769	Standard	NM_001010989		Approved	KIAA0025, Mif1, HERP, SUP	uc002eke.2	Q15011	OTTHUMG00000133276	ENST00000439977.2:c.354G>T	chr16.hg19:g.56970652G>T	ENSP00000409555:p.Glu118Asp	85.0	0.0	.		77.0	41.0	.	NM_014685	E9PGD1|O60644|Q6IAN8|Q96D92	Missense_Mutation	SNP	ENST00000439977.2	hg19	CCDS10771.1	.	.	.	.	.	.	.	.	.	.	G	11.41	1.631353	0.28978	.	.	ENSG00000051108	ENST00000439977;ENST00000379792;ENST00000300302;ENST00000344114	T;T	0.44881	1.51;0.91	6.16	3.15	0.36227	.	0.708796	0.14867	N	0.293775	T	0.20577	0.0495	N	0.08118	0	0.26730	N	0.970611	B;B;B;B;B;B	0.20988	0.017;0.008;0.033;0.0;0.05;0.029	B;B;B;B;B;B	0.19666	0.008;0.026;0.022;0.0;0.019;0.009	T	0.21552	-1.0242	10	0.14656	T	0.56	-20.3489	8.8344	0.35104	0.2378:0.0:0.7622:0.0	.	118;117;118;93;117;118	B4E3N8;Q15011-3;A4UAE9;E9PGD1;Q15011-2;Q15011	.;.;.;.;.;HERP1_HUMAN	D	117;93;118;117	ENSP00000369118:E93D;ENSP00000340931:E117D	ENSP00000300302:E118D	E	+	3	2	HERPUD1	55528153	1.000000	0.71417	0.999000	0.59377	0.979000	0.70002	0.509000	0.22707	0.939000	0.37446	0.650000	0.86243	GAG	.	.	.	none		0.443	HERPUD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257056.5			T	56970652	G	T	56970652	3	4	98	1	0	0	0	0	1	0	0	0	7070	991	35	4	368	4	HERPUD1	16	56970652	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	53161793	56970652	33384101	38	6222											
ZFHX3	463	hgsc.bcm.edu	37	chr16	72984698	72984698	+	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	cgctccacgttcatgtgcagGcccagcatgtccaggttgtc	6	10	11	14	2	1	0	1	0	0	0	4	0	3	0	3	2	2	5	3	2	0	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr16:72984698G>A	ENST00000268489.5	-	3	3558	c.2886C>T	c.(2884-2886)ggC>ggT	p.G962G	ZFHX3_ENST00000397992.5_Silent_p.G48G	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	962					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)				TCATGTGCAGGCCCAGCATGT	0.607																																					p.G962G		Atlas-SNP	.											.	ZFHX3	404	.	0			c.C2886T						PASS	.						106	90	96					16																	72984698		2198	4300	6498	SO:0001819	synonymous_variant	463	exon3			GTGCAGGCCCAGC	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.2886C>T	chr16.hg19:g.72984698G>A		38.0	0.0	.		260.0	65.0	.	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	hg19	CCDS10908.1																																																																																			.	.	.	none		0.607	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		A	72984698	G	A	72984698	2	1	98	1	0	0	0	0	0	0	0	1	17646	1190	42	2		2	ZFHX3	16	72984698	Silent	SNP	G	TCGA-B9-4117-01A-01D-1252-08	16014046	72984698	17370055	39	6223											
USP6	9098	hgsc.bcm.edu	37	chr17	5042939	5042939	+	Missense_Mutation	SNP	A	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	cccaggaggaccagctggccAcctgctggcaggctgaacac	9	4	13	15	0	0	1	0	1	0	0	0	3	0	3	4	5	3	4	4	5	1	0			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:5042939A>C	ENST00000574788.1	+	22	3698	c.1468A>C	c.(1468-1470)Acc>Ccc	p.T490P	USP6_ENST00000332776.4_Missense_Mutation_p.T490P|USP6_ENST00000304328.5_Missense_Mutation_p.T173P|USP6_ENST00000250066.6_Missense_Mutation_p.T490P			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	490					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						CCAGCTGGCCACCTGCTGGCA	0.607			T	"COL1A1, CDH11, ZNF9, OMD"	aneurysmal bone cysts																																p.T490P		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	.	USP6	213	.	0			c.A1468C						PASS	.						44	48	47					17																	5042939		2203	4300	6503	SO:0001583	missense	9098	exon14			CTGGCCACCTGCT	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.1468A>C	chr17.hg19:g.5042939A>C	ENSP00000460380:p.Thr490Pro	66.0	0.0	.		325.0	20.0	.	NM_004505	Q15634|Q86WP6|Q8IWT4	Missense_Mutation	SNP	ENST00000574788.1	hg19	CCDS11069.2	.	.	.	.	.	.	.	.	.	.	A	0.016	-1.512750	0.00975	.	.	ENSG00000129204	ENST00000332776;ENST00000250066;ENST00000304328	T;T;T	0.13901	2.55;3.03;2.73	0.0465	0.0465	0.14256	.	0.094876	0.64402	D	0.000001	T	0.09423	0.0232	N	0.08118	0	0.09310	N	1	P;P	0.47106	0.89;0.797	P;B	0.52554	0.702;0.321	T	0.20773	-1.0265	9	0.38643	T	0.18	.	.	.	.	.	173;490	P35125-2;P35125	.;UBP6_HUMAN	P	490;490;173	ENSP00000328010:T490P;ENSP00000250066:T490P;ENSP00000305473:T173P	ENSP00000250066:T490P	T	+	1	0	USP6	4983663	0.933000	0.31639	0.264000	0.24511	0.260000	0.26232	-0.165000	0.09968	0.115000	0.18071	0.113000	0.15668	ACC	.	.	.	none		0.607	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505		C	5042939	A	C	5042939	3	2	98	1	0	0	0	0	1	0	0	0	17098	159	6	5	1518	5	USP6	17	5042939	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08		5042939	76152271	40	6224											
PER1	5187	hgsc.bcm.edu	37	chr17	8047043	8047043	+	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	gggaagggggtagtggctggTggggtgggccagggggtgga	5	6	27	3	0	0	0	0	0	0	0	0	2	0	2	1	11	0	2	1	11	2	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:8047043T>G	ENST00000317276.4	-	19	2850	c.2613A>C	c.(2611-2613)ccA>ccC	p.P871P	PER1_ENST00000581082.1_Silent_p.P848P|PER1_ENST00000578089.1_5'UTR	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	871	Pro-rich.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						TAGTGGCTGGTGGGGTGGGCC	0.672			T	ETV6	"AML, CMML"			Other conserved DNA damage response genes																													p.P871P		Atlas-SNP	.		Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	PER1,NS,carcinoma,0,1	PER1	104	.	0			c.A2613C						PASS	.						9	11	10					17																	8047043		2183	4270	6453	SO:0001819	synonymous_variant	5187	exon19			GGCTGGTGGGGTG	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.2613A>C	chr17.hg19:g.8047043T>G		11.0	1.0	.		52.0	29.0	.	NM_002616	B2RPA8|B4DI49|D3DTR3	Silent	SNP	ENST00000317276.4	hg19	CCDS11131.1																																																																																			.	.	.	none		0.672	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2			G	8047043	T	G	8047043	2	3	98	1	0	0	0	0	0	0	0	1	11736	1683	59	5		5	PER1	17	8047043	Silent	SNP	T	TCGA-B9-4117-01A-01D-1252-08	3004104	8047043	73148167	41	6225											
TMEM132E	124842	hgsc.bcm.edu	37	chr17	32964849	32964850	+	Frame_Shift_Ins	INS	-	-	C																															gggtgttcctgggcaacgggINScagccgctgcgggtgcaagg																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:32964849_32964850insC	ENST00000321639.5	+	10	2881_2882	c.2553_2554insC	c.(2554-2556)cagfs	p.Q852fs		NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	852						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57				BRCA - Breast invasive adenocarcinoma(366;0.231)		TGGGCAACGGGCAGCCGCTGCG	0.673																																					p.G851fs		Atlas-INDEL	.											.	TMEM132E	122	.	0			c.2553_2554insC						PASS	.																																			SO:0001589	frameshift_variant	124842	exon10			.	BN000149	CCDS11283.1	17q12	2012-11-01			ENSG00000181291	ENSG00000181291			26991	protein-coding gene	gene with protein product							Standard	NM_207313		Approved		uc002hif.3	Q6IEE7	OTTHUMG00000132927	ENST00000321639.5:c.2554dupC	chr17.hg19:g.32964850_32964850dupC	ENSP00000316532:p.Gln852fs	69.0	0.0	0		347.0	19.0	0.054755	NM_207313	Q8WUF4|Q8WVA5	Frame_Shift_Ins	INS	ENST00000321639.5	hg19	CCDS11283.1																																																																																			.	.	.	none		0.673	TMEM132E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256440.2	NM_207313		C	32964850	-	C	32964849	7	5	98	1	0	1	1	0	0	0	0	0	16060	1190	42	0	2591	0	TMEM132E	17	32964849	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	24917806	32964849	48230361	42	6226											
KRTAP4-2	85291	hgsc.bcm.edu	37	chr17	39334233	39334233	+	Missense_Mutation	SNP	T	T	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	ggtctggcagcagctggggcTgcagcaggtgggctggcagc	5	6	20	10	0	1	0	0	0	1	0	1	0	1	0	0	7	5	8	0	7	0	0	rs560495299	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:39334233T>G	ENST00000377726.2	-	1	227	c.184A>C	c.(184-186)Agc>Cgc	p.S62R		NM_033062.3	NP_149051	Q9BYR5	KRA42_HUMAN	keratin associated protein 4-2	62	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)			CAGCTGGGGCTGCAGCAGGTG	0.657													T|||	17	0.00339457	0.0023	0.0014	5008	,	,		17958	0.0099		0	False		,,,				2504	0.0031				p.S62R		Atlas-SNP	.											.	KRTAP4-2	93	.	0			c.A184C						PASS	.						40	46	44					17																	39334233		2201	4298	6499	SO:0001583	missense	85291	exon1			TGGGGCTGCAGCA	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.184A>C	chr17.hg19:g.39334233T>G	ENSP00000366955:p.Ser62Arg	123.0	0.0	.		477.0	30.0	.	NM_033062	A0JP64	Missense_Mutation	SNP	ENST00000377726.2	hg19	CCDS11384.1	.	.	.	.	.	.	.	.	.	.	.	0.738	-0.777466	0.02929	.	.	ENSG00000244537	ENST00000377726;ENST00000458321	T	0.00603	6.28	4.67	-1.59	0.08453	.	1.674050	0.04249	N	0.338307	T	0.00178	0.0005	N	0.00011	-3.005	0.09310	N	1	B	0.16802	0.019	B	0.20955	0.032	T	0.51608	-0.8684	10	0.12766	T	0.61	.	14.1242	0.65210	0.0:0.0:0.3626:0.6374	.	62	Q9BYR5	KRA42_HUMAN	R	62;179	ENSP00000366955:S62R	ENSP00000366955:S62R	S	-	1	0	KRTAP4-2	36587759	0.000000	0.05858	0.001000	0.08648	0.119000	0.20118	-2.321000	0.01119	-0.438000	0.07232	-1.986000	0.00452	AGC	.	.	.	none		0.657	KRTAP4-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257305.1			G	39334233	T	G	39334233	3	3	98	1	0	0	0	0	1	0	0	0	8558	1580	55	5	230	5	KRTAP4-2	17	39334233	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	6369384	39334233	41860977	43	6227											
KRTAP4-1	85285	hgsc.bcm.edu	37	chr17	39340878	39340878	+	Missense_Mutation	SNP	T	T	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	gcagctggacacaccacagcTggggcggcaggtggtctgac	8	5	16	12	1	1	1	0	1	1	0	1	2	1	2	1	6	2	4	1	6	0	0			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:39340878T>G	ENST00000398472.1	-	1	716	c.229A>C	c.(229-231)Agc>Cgc	p.S77R				Q9BYQ7	KRA41_HUMAN	keratin associated protein 4-1	77	18 X 5 AA repeats of C-C-[GRQC]-[SPT]- [VSTL].					keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	5		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			ACACCACAGCTGGGGCGGCAG	0.642																																					p.S77R		Atlas-SNP	.											.	KRTAP4-1	58	.	0			c.A229C						PASS	.						21	25	24					17																	39340878		2070	4197	6267	SO:0001583	missense	85285	exon1			CACAGCTGGGGCG	AC006070		17q21.2	2013-06-25			ENSG00000198443	ENSG00000198443		"Keratin associated proteins"	18907	protein-coding gene	gene with protein product			"keratin associated protein 4-10"	KRTAP4-10		11279113	Standard	NM_033060		Approved	KAP4.1, KAP4.10	uc002hwe.4	Q9BYQ7	OTTHUMG00000132081	ENST00000398472.1:c.229A>C	chr17.hg19:g.39340878T>G	ENSP00000381489:p.Ser77Arg	104.0	0.0	.		197.0	9.0	.	NM_033060	A8MWS7|Q3SYF2	Missense_Mutation	SNP	ENST00000398472.1	hg19		.	.	.	.	.	.	.	.	.	.	T	13.90	2.375762	0.42105	.	.	ENSG00000244537;ENSG00000198443;ENSG00000198443	ENST00000458321;ENST00000398472;ENST00000334190	T	0.00737	5.76	5.02	2.28	0.28536	.	.	.	.	.	T	0.00637	0.0021	.	.	.	0.25986	N	0.98232	B	0.21905	0.062	B	0.15870	0.014	T	0.49322	-0.8952	8	0.59425	D	0.04	.	1.9461	0.03357	0.2357:0.2353:0.0:0.5289	.	77	Q9BYQ7	KRA41_HUMAN	R	73;77;77	ENSP00000381489:S77R	ENSP00000335483:S77R	S	-	1	0	KRTAP4-2;KRTAP4-1	36594404	0.742000	0.28228	1.000000	0.80357	0.970000	0.65996	0.669000	0.25142	1.854000	0.53819	0.482000	0.46254	AGC	.	.	.	none		0.642	KRTAP4-1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255108.1	NM_033060		G	39340878	T	G	39340878	3	3	98	1	0	0	0	0	1	0	0	0	8555	1580	55	5	162	5	KRTAP4-1	17	39340878	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	6645	39340878	41854332	44	6228											
GHDC	84514	hgsc.bcm.edu	37	chr17	40344945	40344945	+	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	tgcagagaggcctccccaagGtcctggtttgaggtcggggg	6	8	17	10	1	0	2	0	1	0	1	3	3	2	2	4	6	1	2	4	6	1	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:40344945G>T	ENST00000301671.8	-	3	807	c.366C>A	c.(364-366)gaC>gaA	p.D122E	GHDC_ENST00000436923.2_Missense_Mutation_p.D122E|GHDC_ENST00000428494.2_Intron|GHDC_ENST00000587427.1_Missense_Mutation_p.D122E|GHDC_ENST00000414034.3_Missense_Mutation_p.D122E|GHDC_ENST00000593209.1_Missense_Mutation_p.D122E|GHDC_ENST00000590520.1_5'Flank			Q8N2G8	GHDC_HUMAN	GH3 domain containing	122						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		all_cancers(22;0.000229)|Breast(137;0.00104)|all_epithelial(22;0.00304)		BRCA - Breast invasive adenocarcinoma(366;0.124)		CCTCCCCAAGGTCCTGGTTTG	0.607																																					p.D122E		Atlas-SNP	.											.	GHDC	63	.	0			c.C366A						PASS	.						105	118	113					17																	40344945		2203	4300	6503	SO:0001583	missense	84514	exon4			CCCAAGGTCCTGG	AF316997, BC011056	CCDS11422.1, CCDS45682.1	17q21.2	2006-08-02				ENSG00000167925			24438	protein-coding gene	gene with protein product		608587				11161808, 11735219	Standard	NR_024573		Approved	LGP1	uc002hzf.4	Q8N2G8		ENST00000301671.8:c.366C>A	chr17.hg19:g.40344945G>T	ENSP00000301671:p.Asp122Glu	144.0	0.0	.		674.0	230.0	.	NM_001142623	B4DQS4|E9PDB5|Q9BXM6	Missense_Mutation	SNP	ENST00000301671.8	hg19	CCDS11422.1	.	.	.	.	.	.	.	.	.	.	G	0.862	-0.734923	0.03111	.	.	ENSG00000167925	ENST00000393854;ENST00000414034;ENST00000301671;ENST00000436923	.	.	.	4.61	1.41	0.22369	.	1.247040	0.05644	N	0.583915	T	0.19886	0.0478	N	0.14661	0.345	0.09310	N	1	B;B	0.26400	0.148;0.009	B;B	0.24394	0.053;0.007	T	0.25082	-1.0142	9	0.18276	T	0.48	-0.018	4.8152	0.13363	0.1998:0.1781:0.6221:0.0	.	122;122	Q8N2G8-2;Q8N2G8	.;GHDC_HUMAN	E	66;122;122;122	.	ENSP00000301671:D122E	D	-	3	2	GHDC	37598471	0.000000	0.05858	0.002000	0.10522	0.094000	0.18550	0.158000	0.16422	0.544000	0.28883	0.561000	0.74099	GAC	.	.	.	none		0.607	GHDC-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449794.1	NM_032484		T	40344945	G	T	40344945	3	4	98	1	0	0	0	0	1	0	0	0	6376	1252	44	4	1343	4	GHDC	17	40344945	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	1004067	40344945	40850265	45	6229											
ITGB4	3691	hgsc.bcm.edu	37	chr17	73732406	73732406	+	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	tggccactgtgagtgtggccGctgccactgccaccagcagt	6	8	13	14	1	0	1	0	1	0	0	0	1	0	1	5	2	3	2	5	2	0	0	rs201929789		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr17:73732406G>C	ENST00000200181.3	+	15	1986	c.1799G>C	c.(1798-1800)cGc>cCc	p.R600P	ITGB4_ENST00000579662.1_Missense_Mutation_p.R600P|ITGB4_ENST00000450894.3_Missense_Mutation_p.R600P|ITGB4_ENST00000339591.3_Missense_Mutation_p.R600P|ITGB4_ENST00000449880.2_Missense_Mutation_p.R600P|ITGB4_ENST00000584558.1_3'UTR	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	600	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)			GAGTGTGGCCGCTGCCACTGC	0.632																																					p.R600P		Atlas-SNP	.											ITGB4,colon,carcinoma,0,1	ITGB4	165	.	0			c.G1799C						PASS	.						65	69	67					17																	73732406		2203	4300	6503	SO:0001583	missense	3691	exon15			GTGGCCGCTGCCA		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.1799G>C	chr17.hg19:g.73732406G>C	ENSP00000200181:p.Arg600Pro	123.0	0.0	.		385.0	151.0	.	NM_001005731	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	ENST00000200181.3	hg19	CCDS11727.1	.	.	.	.	.	.	.	.	.	.	G	13.70	2.314176	0.40996	.	.	ENSG00000132470	ENST00000450894;ENST00000200181;ENST00000339591;ENST00000449880	D;D;D	0.94862	-3.54;-3.54;-3.54	4.6	4.6	0.57074	.	0.067612	0.64402	D	0.000010	D	0.97222	0.9092	M	0.83774	2.66	0.58432	D	0.999999	D;D;D;D;D	0.89917	0.999;0.999;1.0;1.0;1.0	D;D;D;D;D	0.79784	0.916;0.961;0.993;0.985;0.985	D	0.98032	1.0377	10	0.72032	D	0.01	.	16.4661	0.84079	0.0:0.0:1.0:0.0	.	560;600;600;600;600	B4E3N0;P16144-5;P16144-3;A0AVL6;P16144	.;.;.;.;ITB4_HUMAN	P	516;600;600;600	ENSP00000200181:R600P;ENSP00000344079:R600P;ENSP00000400217:R600P	ENSP00000200181:R600P	R	+	2	0	ITGB4	71244001	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.642000	0.67888	2.095000	0.63458	0.558000	0.71614	CGC	.	G|0.998;C|0.002	0.002	weak		0.632	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			C	73732406	G	C	73732406	3	2	98	1	0	0	0	0	1	0	0	0	7904	1087	38	4	1853	4	ITGB4	17	73732406	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	33387461	73732406	7462804	46	6230											
FAM108A1	81926	hgsc.bcm.edu	37	chr19	1881347	1881347	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggctgtactggaagtcggcAcgctccgtcaggtgcagctt	6	10	14	11	3	1	0	1	0	0	0	3	1	2	1	1	4	3	6	1	4	2	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:1881347A>G	ENST00000292577.7	-	2	652	c.219T>C	c.(217-219)cgT>cgC	p.R73R	ABHD17A_ENST00000250974.9_Silent_p.R73R|ABHD17A_ENST00000590661.1_Silent_p.R73R	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)										GGAAGTCGGCACGCTCCGTCA	0.716																																					p.R73R		Atlas-SNP	.											FAM108A1,NS,carcinoma,0,1	FAM108A1	29	.	0			c.T219C						PASS	.						19	22	21					19																	1881347		2188	4262	6450	SO:0001819	synonymous_variant	81926	exon2			GTCGGCACGCTCC	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.219T>C	chr19.hg19:g.1881347A>G		75.0	0.0	.		190.0	8.0	.	NM_031213	A8K0G8|D6W5Z9|Q6PJU2|Q8WUH9|Q9BWL0|Q9H7Q9	Silent	SNP	ENST00000292577.7	hg19	CCDS45902.1																																																																																			.	.	.	none		0.716	ABHD17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415556.2	NM_031213		G	1881347	A	G	1881347	2	3	98	1	0	0	0	0	0	0	0	1	5395	146	6	3		3	FAM108A1	19	1881347	Silent	SNP	A	TCGA-B9-4117-01A-01D-1252-08		1881347	57247636	47	6231											
PLEKHJ1	55111	hgsc.bcm.edu	37	chr19	2234038	2234038	+	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	ttcgttcctgtagaagatgaGgcttctccgcatgaactcgt	8	13	10	10	3	1	4	0	2	1	2	5	4	2	4	2	1	1	4	2	1	3	4			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:2234038G>T	ENST00000589097.1	-	6	1456	c.343C>A	c.(343-345)Ctc>Atc	p.L115I	PLEKHJ1_ENST00000589791.1_5'UTR|PLEKHJ1_ENST00000587394.2_Missense_Mutation_p.L115I|PLEKHJ1_ENST00000586608.2_Missense_Mutation_p.L116I|PLEKHJ1_ENST00000591099.2_Silent_p.A84A|SF3A2_ENST00000221494.5_5'Flank|PLEKHJ1_ENST00000587962.2_Missense_Mutation_p.L115I|PLEKHJ1_ENST00000326631.2_Missense_Mutation_p.L115I|MIR1227_ENST00000408484.1_RNA			Q9NW61	PKHJ1_HUMAN	pleckstrin homology domain containing, family J member 1	115										endometrium(1)|kidney(1)	2				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)		TAGAAGATGAGGCTTCTCCGC	0.642																																					p.L115I		Atlas-SNP	.											.	PLEKHJ1	7	.	0			c.C343A						PASS	.						119	107	111					19																	2234038		2203	4300	6503	SO:0001583	missense	55111	exon5			AGATGAGGCTTCT	AK001159	CCDS12083.1, CCDS74251.1	19p13.3	2013-01-10				ENSG00000104886		"Pleckstrin homology (PH) domain containing"	18211	protein-coding gene	gene with protein product	"guanine nucleotide releasing protein x"					11602354	Standard	XM_006722784		Approved	FLJ10297	uc002lvf.1	Q9NW61		ENST00000589097.1:c.343C>A	chr19.hg19:g.2234038G>T	ENSP00000465391:p.Leu115Ile	176.0	0.0	.		567.0	185.0	.	NM_018049	B3KUQ9|D6W604	Missense_Mutation	SNP	ENST00000589097.1	hg19	CCDS12083.1	.	.	.	.	.	.	.	.	.	.	G	12.10	1.836779	0.32421	.	.	ENSG00000104886	ENST00000326631	.	.	.	4.05	2.94	0.34122	.	0.176721	0.36591	N	0.002508	T	0.28234	0.0697	L	0.32530	0.975	0.42701	D	0.993613	P	0.42692	0.787	B	0.33121	0.158	T	0.06881	-1.0802	9	0.33940	T	0.23	-16.6324	7.7627	0.28961	0.0916:0.0:0.7474:0.161	.	115	Q9NW61	PKHJ1_HUMAN	I	115	.	ENSP00000318075:L115I	L	-	1	0	PLEKHJ1	2185038	1.000000	0.71417	0.983000	0.44433	0.410000	0.31052	5.117000	0.64667	1.788000	0.52465	0.561000	0.74099	CTC	.	.	.	none		0.642	PLEKHJ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451255.1	NM_018049		T	2234038	G	T	2234038	3	4	98	1	0	0	0	0	1	0	0	0	12086	1000	35	4	114	4	PLEKHJ1	19	2234038	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	352691	2234038	56894945	48	6232											
KDM4B	23030	hgsc.bcm.edu	37	chr19	5131903	5131903	+	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	tgttgtgtgtttcaggcaccGtccacattttccaaattgaa	9	15	8	9	1	1	1	1	1	0	0	3	1	3	1	3	1	0	3	3	1	2	5	rs544835411		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:5131903G>C	ENST00000159111.4	+	13	2009	c.1791G>C	c.(1789-1791)ccG>ccC	p.P597P	KDM4B_ENST00000536461.1_Silent_p.P631P	NM_015015.2	NP_055830	O94953	KDM4B_HUMAN	lysine (K)-specific demethylase 4B	597					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(1)|liver(1)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						TTCAGGCACCGTCCACATTTT	0.652																																					p.P597P		Atlas-SNP	.											.	KDM4B	120	.	0			c.G1791C						PASS	.						36	39	38					19																	5131903		2201	4299	6500	SO:0001819	synonymous_variant	23030	exon13			GGCACCGTCCACA	AB020683	CCDS12138.1	19p13.3	2013-01-23	2009-04-06	2009-04-06		ENSG00000127663		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	29136	protein-coding gene	gene with protein product	"tudor domain containing 14B"	609765	"jumonji domain containing 2B"	JMJD2B		10048485, 15138608	Standard	NM_015015		Approved	KIAA0876, TDRD14B	uc002mbq.4	O94953		ENST00000159111.4:c.1791G>C	chr19.hg19:g.5131903G>C		31.0	0.0	.		89.0	20.0	.	NM_015015	B9EGN8|D6W631|O75274|Q6P3R5|Q9P1V1|Q9UF40	Silent	SNP	ENST00000159111.4	hg19	CCDS12138.1																																																																																			.	.	.	none		0.652	KDM4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450558.1	NM_015015		C	5131903	G	C	5131903	2	2	98	1	0	0	0	0	0	0	0	1	8136	1132	40	4		4	KDM4B	19	5131903	Silent	SNP	G	TCGA-B9-4117-01A-01D-1252-08	2897865	5131903	53997080	49	6233											
MRI1	81576	hgsc.bcm.edu	37	chr19	13875777	13875777	+	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	ggaccgggactcgccgcgctCgtggccttcgtgcgcgacaa	5	6	15	15	8	0	0	0	0	0	0	3	3	0	2	3	3	1	1	3	3	1	1	rs558173579	byFrequency	TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:13875777C>T	ENST00000586600.1	+	0	1922				MRI1_ENST00000319545.8_Silent_p.L75L|MRI1_ENST00000040663.6_Silent_p.L75L			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)			TCGCCGCGCTCGTGGCCTTCG	0.756													C|||	13	0.00259585	0.0098	0	5008	,	,		6863	0		0	False		,,,				2504	0				p.L75L		Atlas-SNP	.											.	MRI1	35	.	0			c.C225T						PASS	.						4	5	4					19																	13875777		1806	3486	5292	SO:0001628	intergenic_variant	84245	exon2			CGCGCTCGTGGCC	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			chr19.hg19:g.13875777C>T		0.0	0.0	.		8.0	6.0	.	NM_001031727	Q9BQ72	Silent	SNP	ENST00000586600.1	hg19	CCDS12296.1																																																																																			.	.	.	none		0.756	CCDC130-001	KNOWN	alternative_5_UTR|upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453216.2	NM_030818		T	13875777	C	T	13875777	1	4	98	0	1	0	0	0	0	0	0	0	9777	871	31	1		1	MRI1	19	13875777	IGR	SNP	C	TCGA-B9-4117-01A-01D-1252-08	8743874	13875777	45253206	50	6234											
UBA2	10054	hgsc.bcm.edu	37	chr19	34921484	34921484	+	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	ggtttatgcatttgtagattGatctggatactattgatgta	10	18	10	3	0	1	3	0	2	1	1	1	4	1	4	0	2	2	4	0	2	5	9			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:34921484G>C	ENST00000246548.4	+	2	212	c.142G>C	c.(142-144)Gat>Cat	p.D48H	UBA2_ENST00000439527.2_5'UTR|CTD-2588C8.8_ENST00000592220.1_RNA	NM_005499.2	NP_005490.1	Q9UBT2	SAE2_HUMAN	ubiquitin-like modifier activating enzyme 2	48					cellular protein metabolic process (GO:0044267)|positive regulation of catalytic activity (GO:0043085)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)|SMT3-dependent protein catabolic process (GO:0019950)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|SUMO activating enzyme complex (GO:0031510)	ATP binding (GO:0005524)|enzyme activator activity (GO:0008047)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|SUMO activating enzyme activity (GO:0019948)			breast(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	20	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			TTTGTAGATTGATCTGGATAC	0.358																																					p.D48H		Atlas-SNP	.											.	UBA2	53	.	0			c.G142C						PASS	.						185	170	175					19																	34921484		2203	4300	6503	SO:0001583	missense	10054	exon2			TAGATTGATCTGG	BC003153	CCDS12439.1	19q13.11	2008-02-05	2007-11-30	2007-11-30		ENSG00000126261		"Ubiquitin-like modifier activating enzymes"	30661	protein-coding gene	gene with protein product	"UBA2, ubiquitin-activating enzyme E1 homolog (yeast)"	613295	"SUMO1 activating enzyme subunit 2"	SAE2		10187858, 9920803	Standard	NM_005499		Approved	FLJ13058, HRIHFB2115, ARX	uc002nvk.3	Q9UBT2		ENST00000246548.4:c.142G>C	chr19.hg19:g.34921484G>C	ENSP00000246548:p.Asp48His	95.0	0.0	.		152.0	52.0	.	NM_005499	B3KWB9|O95605|Q59H87|Q6IBP6|Q9NTJ1|Q9UED2	Missense_Mutation	SNP	ENST00000246548.4	hg19	CCDS12439.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.624070	0.87560	.	.	ENSG00000126261	ENST00000246548	D	0.84442	-1.85	5.22	5.22	0.72569	UBA/THIF-type NAD/FAD binding fold (1);Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.100210	0.64402	D	0.000001	D	0.96565	0.8879	H	0.99937	4.99	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	D	0.98698	1.0699	10	0.87932	D	0	-19.2256	17.8923	0.88876	0.0:0.0:1.0:0.0	.	48	Q9UBT2	SAE2_HUMAN	H	48	ENSP00000246548:D48H	ENSP00000246548:D48H	D	+	1	0	UBA2	39613324	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.953000	0.93041	2.603000	0.88011	0.563000	0.77884	GAT	.	.	.	none		0.358	UBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459257.3	NM_005499		C	34921484	G	C	34921484	3	2	98	1	0	0	0	0	1	0	0	0	16840	1290	45	4	148	4	UBA2	19	34921484	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	21045707	34921484	24207499	51	6235											
RYR1	6261	hgsc.bcm.edu	37	chr19	39039030	39039030	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gactacgtaacggatccccgTggcctcatctccaagaagga	11	7	10	13	3	2	1	1	0	1	1	4	4	3	3	4	3	2	1	4	3	4	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:39039030T>C	ENST00000359596.3	+	89	12252	c.12252T>C	c.(12250-12252)cgT>cgC	p.R4084R	RYR1_ENST00000360985.3_Silent_p.R4079R|RYR1_ENST00000355481.4_Silent_p.R4079R			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4084					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)	CGGATCCCCGTGGCCTCATCT	0.557																																					p.R4084R		Atlas-SNP	.											.	RYR1	708	.	0			c.T12252C						PASS	.						132	113	119					19																	39039030		2203	4300	6503	SO:0001819	synonymous_variant	6261	exon89			TCCCCGTGGCCTC	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.12252T>C	chr19.hg19:g.39039030T>C		99.0	0.0	.		299.0	101.0	.	NM_000540	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	hg19	CCDS33011.1																																																																																			.	.	.	none		0.557	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			C	39039030	T	C	39039030	2	2	98	1	0	0	0	0	0	0	0	1	13781	1683	59	3		3	RYR1	19	39039030	Silent	SNP	T	TCGA-B9-4117-01A-01D-1252-08	4117546	39039030	20089953	52	6236											
FCGBP	8857	hgsc.bcm.edu	37	chr19	40366038	40366038	+	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	cagtactcacgacagaagtcCggccgcctccactcgccgag	9	5	10	17	5	1	1	1	0	0	1	4	3	3	1	5	1	1	1	5	1	2	1			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:40366038C>G	ENST00000221347.6	-	30	14203	c.14196G>C	c.(14194-14196)ccG>ccC	p.P4732P		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4732						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)			GACAGAAGTCCGGCCGCCTCC	0.647																																					p.P4732P		Atlas-SNP	.											.	FCGBP	416	.	0			c.G14196C						PASS	.																																			SO:0001819	synonymous_variant	8857	exon30			GAAGTCCGGCCGC	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.14196G>C	chr19.hg19:g.40366038C>G		164.0	0.0	.		205.0	59.0	.	NM_003890	O95784	Silent	SNP	ENST00000221347.6	hg19	CCDS12546.1																																																																																			.	.	.	none		0.647	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		G	40366038	C	G	40366038	2	3	98	1	0	0	0	0	0	0	0	1	5785	639	23	4		4	FCGBP	19	40366038	Silent	SNP	C	TCGA-B9-4117-01A-01D-1252-08	1327008	40366038	18762945	53	6237											
NUCB1	4924	hgsc.bcm.edu	37	chr19	49422348	49422348	+	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	gcgggagatggaggaggagcGactgcgcatgcgggagcatg	9	4	21	7	4	0	1	0	0	0	1	0	7	0	5	0	5	4	2	0	5	0	0			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:49422348G>A	ENST00000405315.4	+	9	1212	c.878G>A	c.(877-879)cGa>cAa	p.R293Q	NUCB1_ENST00000485798.1_Intron|NUCB1_ENST00000263273.5_Missense_Mutation_p.R293Q|NUCB1-AS1_ENST00000416432.1_RNA|NUCB1_ENST00000407032.1_Missense_Mutation_p.R293Q	NM_006184.5	NP_006175.2	Q02818	NUCB1_HUMAN	nucleobindin 1	293	Binds to GNAI2 and GNAI3. {ECO:0000250}.|EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.					endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			cervix(1)|endometrium(4)|large_intestine(4)|lung(8)	17		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000171)|all cancers(93;0.000333)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0244)		GAGGAGGAGCGACTGCGCATG	0.612																																					p.R293Q		Atlas-SNP	.											.	NUCB1	44	.	0			c.G878A						PASS	.						56	58	58					19																	49422348		2203	4300	6503	SO:0001583	missense	4924	exon9			AGGAGCGACTGCG	BC002356	CCDS12740.1	19q13.33	2013-01-10			ENSG00000104805	ENSG00000104805		"EF-hand domain containing"	8043	protein-coding gene	gene with protein product		601323				8661046	Standard	NM_006184		Approved	NUC, Calnuc	uc002plb.4	Q02818	OTTHUMG00000152514	ENST00000405315.4:c.878G>A	chr19.hg19:g.49422348G>A	ENSP00000385923:p.Arg293Gln	39.0	0.0	.		126.0	43.0	.	NM_006184	B2RD64|Q15838|Q7Z4J7|Q9BUR1	Missense_Mutation	SNP	ENST00000405315.4	hg19	CCDS12740.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.875643|5.875643	0.97055|0.97055	.|.	.|.	ENSG00000104805|ENSG00000104805	ENST00000424608|ENST00000405315;ENST00000407032;ENST00000263273	.|T;T;T	.|0.71698	.|-0.59;-0.59;-0.59	5.01|5.01	5.01|5.01	0.66863|0.66863	.|EF-hand-like domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.81437|0.81437	0.4822|0.4822	M|M	0.64630|0.64630	1.985|1.985	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.72982	.|0.979;0.979	T|T	0.80596|0.80596	-0.1312|-0.1312	5|10	.|0.40728	.|T	.|0.16	.|.	16.1855|16.1855	0.81948|0.81948	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|293;293	.|Q02818;Q53GX6	.|NUCB1_HUMAN;.	N|Q	263|293	.|ENSP00000385923:R293Q;ENSP00000385211:R293Q;ENSP00000263273:R293Q	.|ENSP00000263273:R293Q	D|R	+|+	1|2	0|0	NUCB1|NUCB1	54114160|54114160	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	9.177000|9.177000	0.94849|0.94849	2.514000|2.514000	0.84764|0.84764	0.591000|0.591000	0.81541|0.81541	GAC|CGA	.	.	.	none		0.612	NUCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326545.2	NM_006184		A	49422348	G	A	49422348	3	1	98	1	0	0	0	0	1	0	0	0	10725	1058	37	1	908	1	NUCB1	19	49422348	Missense_Mutation	SNP	G	TCGA-B9-4117-01A-01D-1252-08	9056310	49422348	9706635	54	6238											
ZNF665	79788	hgsc.bcm.edu	37	chr19	53668284	53668284	+	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	tttaccacattcatcacactTgtaaggtttctctccagaat	11	15	4	11	0	3	1	2	0	1	1	5	1	4	1	2	1	1	2	2	1	3	6			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:53668284T>A	ENST00000600412.1	-	2	1379	c.1264A>T	c.(1264-1266)Aag>Tag	p.K422*	CTD-2245F17.2_ENST00000600257.1_RNA|ZNF665_ENST00000396424.3_Nonsense_Mutation_p.K487*			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	422					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		TCATCACACTTGTAAGGTTTC	0.413																																					p.K487X		Atlas-SNP	.											.	ZNF665	136	.	0			c.A1459T						PASS	.						91	95	93					19																	53668284		2203	4300	6503	SO:0001587	stop_gained	79788	exon4			CACACTTGTAAGG		CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"Zinc fingers, C2H2-type", "-"	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.1264A>T	chr19.hg19:g.53668284T>A	ENSP00000469154:p.Lys422*	88.0	0.0	.		217.0	68.0	.	NM_024733	A8K5T8	Nonsense_Mutation	SNP	ENST00000600412.1	hg19		.	.	.	.	.	.	.	.	.	.	T	17.85	3.490740	0.64074	.	.	ENSG00000197497	ENST00000396424	.	.	.	2.18	1.14	0.20703	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.3597	0.21420	0.0:0.1475:0.0:0.8525	.	.	.	.	X	487	.	ENSP00000379702:K487X	K	-	1	0	ZNF665	58360096	0.000000	0.05858	0.027000	0.17364	0.049000	0.14656	-2.447000	0.01010	1.001000	0.39076	0.358000	0.22013	AAG	.	.	.	none		0.413	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733		A	53668284	T	A	53668284	4	1	98	1	0	0	0	0	0	1	0	0	18085	1821	63	5	581	5	ZNF665	19	53668284	Nonsense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	4245936	53668284	5460699	55	6239											
LILRB2	10288	hgsc.bcm.edu	37	chr19	54783677	54783677	+	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	agcaccagggggtcactgagCtcagaccaccgagcgcggct	9	4	14	14	3	2	2	2	1	0	1	2	3	2	2	3	3	3	3	3	3	0	0			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:54783677C>T	ENST00000391749.4	-	4	595	c.324G>A	c.(322-324)gaG>gaA	p.E108E	LILRB2_ENST00000314446.5_Silent_p.E108E|LILRB2_ENST00000391746.1_Silent_p.E108E|LILRB2_ENST00000434421.1_5'UTR|LILRB2_ENST00000471216.1_5'Flank|LILRB2_ENST00000391748.1_Silent_p.E108E|MIR4752_ENST00000579672.1_RNA	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	108	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)		GGTCACTGAGCTCAGACCACC	0.602																																					p.E108E		Atlas-SNP	.											.	LILRB2	94	.	0			c.G324A						PASS	.						105	105	105					19																	54783677		2203	4300	6503	SO:0001819	synonymous_variant	10288	exon4			ACTGAGCTCAGAC	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.324G>A	chr19.hg19:g.54783677C>T		101.0	0.0	.		359.0	108.0	.	NM_005874	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Silent	SNP	ENST00000391749.4	hg19	CCDS12886.1																																																																																			.	.	.	none		0.602	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1			T	54783677	C	T	54783677	2	4	98	1	0	0	0	0	0	0	0	1	8798	796	28	2		2	LILRB2	19	54783677	Silent	SNP	C	TCGA-B9-4117-01A-01D-1252-08	1115393	54783677	4345306	56	6240											
ZNF71	58491	hgsc.bcm.edu	37	chr19	57133670	57133670	+	Missense_Mutation	SNP	T	T	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	gcaaggccttcagccagagcTcctacctcatccagcaccag	10	6	8	17	0	2	1	2	0	0	1	4	1	4	1	6	1	4	3	6	1	2	2	rs575219516		TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr19:57133670T>G	ENST00000328070.6	+	3	1249	c.1015T>G	c.(1015-1017)Tcc>Gcc	p.S339A		NM_021216.4	NP_067039.1	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	339					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S339A(1)		endometrium(3)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	26				GBM - Glioblastoma multiforme(193;0.062)|Lung(386;0.0681)|LUSC - Lung squamous cell carcinoma(496;0.18)		CAGCCAGAGCTCCTACCTCAT	0.632													.|||	1	0.000199681	0	0.0014	5008	,	,		21342	0		0	False		,,,				2504	0				p.S339A		Atlas-SNP	.											ZNF71,NS,carcinoma,0,1	ZNF71	69	.	1	Substitution - Missense(1)	endometrium(1)	c.T1015G						PASS	.						87	80	82					19																	57133670		2203	4300	6503	SO:0001583	missense	58491	exon3			CAGAGCTCCTACC	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.1015T>G	chr19.hg19:g.57133670T>G	ENSP00000328245:p.Ser339Ala	127.0	0.0	.		180.0	9.0	.	NM_021216	Q15919|Q9UC09|Q9UQD3	Missense_Mutation	SNP	ENST00000328070.6	hg19	CCDS12947.1	.	.	.	.	.	.	.	.	.	.	T	11.73	1.726062	0.30593	.	.	ENSG00000197951	ENST00000328070	T	0.35421	1.31	3.76	1.4	0.22301	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.34135	0.0887	M	0.69358	2.11	0.09310	N	1	B	0.21452	0.056	B	0.15052	0.012	T	0.27157	-1.0082	9	0.44086	T	0.13	.	8.5519	0.33458	0.0:0.0:0.3775:0.6225	.	339	Q9NQZ8	ZNF71_HUMAN	A	339	ENSP00000328245:S339A	ENSP00000328245:S339A	S	+	1	0	ZNF71	61825482	0.000000	0.05858	0.996000	0.52242	0.982000	0.71751	-3.336000	0.00507	0.480000	0.27534	0.459000	0.35465	TCC	.	.	.	none		0.632	ZNF71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459798.2	NM_021216		G	57133670	T	G	57133670	3	3	98	1	0	0	0	0	1	0	0	0	18126	1551	54	5	1017	5	ZNF71	19	57133670	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	2349993	57133670	1995313	57	6241											
AHCY	191	hgsc.bcm.edu	37	chr20	32868894	32868914	+	In_Frame_Del	DEL	CTGGGCTTGCTTCTCAGTTAG	CTGGGCTTGCTTCTCAGTTAG	-																															tcacaggacatgcccaggtaCtgggcttgcttctcagttag																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	CTGGGCTTGCTTCTCAGTTAG	CTGGGCTTGCTTCTCAGTTAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr20:32868894_32868914delCTGGGCTTGCTTCTCAGTTAG	ENST00000217426.2	-	10	1302_1322	c.1225_1245delCTAACTGAGAAGCAAGCCCAG	c.(1225-1245)ctaactgagaagcaagcccagdel	p.LTEKQAQ409del	RP4-785G19.5_ENST00000512005.1_RNA|AHCY_ENST00000538132.1_In_Frame_Del_p.LTEKQAQ381del|CTD-3216D2.5_ENST00000609218.1_RNA	NM_000687.2	NP_000678.1	P23526	SAHH_HUMAN	adenosylhomocysteinase	409					cellular nitrogen compound metabolic process (GO:0034641)|chronic inflammatory response to antigenic stimulus (GO:0002439)|circadian sleep/wake cycle (GO:0042745)|homocysteine biosynthetic process (GO:0071268)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|S-adenosylhomocysteine catabolic process (GO:0019510)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|nucleus (GO:0005634)	adenosylhomocysteinase activity (GO:0004013)|adenyl nucleotide binding (GO:0030554)|NAD binding (GO:0051287)			endometrium(6)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						TGCCCAGGTACTGGGCTTGCTTCTCAGTTAGCTTGGTCAAC	0.566																																					p.409_416del		Atlas-INDEL	.											.	AHCY	43	.	0			c.1226_1246del						PASS	.																																			SO:0001651	inframe_deletion	191	exon10			.	M61832	CCDS13233.1, CCDS54457.1	20q11.22	2009-06-12	2009-06-12		ENSG00000101444	ENSG00000101444	3.3.1.1		343	protein-coding gene	gene with protein product		180960	"S-adenosylhomocysteine hydrolase"			7079734, 6580258	Standard	NM_001161766		Approved	SAHH	uc002xai.3	P23526	OTTHUMG00000140098	ENST00000217426.2:c.1225_1245delCTAACTGAGAAGCAAGCCCAG	chr20.hg19:g.32868894_32868914delCTGGGCTTGCTTCTCAGTTAG	ENSP00000217426:p.Leu409_Gln415del	44.0	0.0	0		104.0	26.0	0.25	NM_000687	A8K307|B3KUN3|E1P5P2|F5H737|Q96A36	In_Frame_Del	DEL	ENST00000217426.2	hg19	CCDS13233.1																																																																																			.	.	.	none		0.566	AHCY-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078773.2	NM_000687		-	32868914	CTGGGCTTGCTTCTCAGTTAG	-	32868894	7	5	98	1	0	1	0	1	0	0	0	0	409	564	20	0	57	0	AHCY	20	32868894	In_Frame_Del	DEL	CTGGGCTTGCTTCTCAGTTAG	TCGA-B9-4117-01A-01D-1252-08		32868894	30156626	58	6242											
CTCFL	140690	hgsc.bcm.edu	37	chr20	56098886	56098887	+	Frame_Shift_Ins	INS	-	-	C																															tgctgcaggctctgccggggINScccttcctcaagccacagca																										TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr20:56098886_56098887insC	ENST00000608263.1	-	1	1036_1037	c.375_376insG	c.(373-378)gggcccfs	p.P126fs	CTCFL_ENST00000423479.3_Frame_Shift_Ins_p.P126fs|CTCFL_ENST00000539382.1_Intron|CTCFL_ENST00000371196.2_Frame_Shift_Ins_p.P126fs|CTCFL_ENST00000422869.2_Frame_Shift_Ins_p.P126fs|CTCFL_ENST00000502686.2_Intron|CTCFL_ENST00000608158.1_Frame_Shift_Ins_p.P126fs|CTCFL_ENST00000608440.1_Frame_Shift_Ins_p.P126fs|CTCFL_ENST00000432255.2_Frame_Shift_Ins_p.P126fs|CTCFL_ENST00000609232.1_Frame_Shift_Ins_p.P126fs|CTCFL_ENST00000243914.3_Frame_Shift_Ins_p.P126fs|CTCFL_ENST00000429804.3_Frame_Shift_Ins_p.P126fs|CTCFL_ENST00000608425.1_Frame_Shift_Ins_p.P126fs|CTCFL_ENST00000608903.1_Intron|CTCFL_ENST00000608858.1_Intron|CTCFL_ENST00000481655.2_Frame_Shift_Ins_p.P126fs|CTCFL_ENST00000433949.3_Intron	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	126					cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			CTCTGCCGGGGCCCTTCCTCAA	0.579																																					p.P126fs		Atlas-INDEL	.											.	CTCFL	97	.	0			c.376_377insG						PASS	.																																			SO:0001589	frameshift_variant	140690	exon1			.		CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"Zinc fingers, C2H2-type"	16234	protein-coding gene	gene with protein product	"cancer/testis antigen 27"	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.376dupG	chr20.hg19:g.56098889_56098889dupC	ENSP00000476783:p.Pro126fs	119.0	0.0	0		415.0	24.0	0.0578313	NM_001269044	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Frame_Shift_Ins	INS	ENST00000608263.1	hg19	CCDS13459.1																																																																																			.	.	.	none		0.579	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618		C	56098887	-	C	56098886	7	5	98	1	0	1	1	0	0	0	0	0	4003	1203	42	0	1655	0	CTCFL	20	56098886	Frame_Shift_Ins	INS	-	TCGA-B9-4117-01A-01D-1252-08	23229992	56098886	6926634	59	6243											
NF2	4771	hgsc.bcm.edu	37	chr22	30000103	30000103	+	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	gatggagttcaattgcgaggTaaccggccggcagccccgac	9	6	14	12	4	1	0	1	0	0	0	1	4	1	1	4	4	3	3	4	4	2	3			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chr22:30000103T>G	ENST00000338641.4	+	1	555		c.e1+2		NF2_ENST00000361452.4_Splice_Site|NF2_ENST00000353887.4_Splice_Site|NF2_ENST00000413209.2_Splice_Site|NF2_ENST00000334961.7_Splice_Site|NF2_ENST00000397789.3_Splice_Site|NF2_ENST00000403999.3_Splice_Site|NF2_ENST00000361166.4_Splice_Site|NF2_ENST00000347330.5_Splice_Site|NF2_ENST00000403435.1_Splice_Site|NF2_ENST00000361676.4_Splice_Site	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)						actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(1)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						AATTGCGAGGTAACCGGCCGG	0.562			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																												.		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	.	NF2	1312	.	1	Unknown(1)	lung(1)	c.114+2T>G						PASS	.						35	25	29					22																	30000103		2202	4299	6501	SO:0001630	splice_region_variant	4771	exon1	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	GCGAGGTAACCGG	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"A-kinase anchor proteins"	7773	protein-coding gene	gene with protein product	"moesin-ezrin-radixin like", "schwannomin"	607379	"neurofibromin 2 (bilateral acoustic neuroma)"			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.114+2T>G	chr22.hg19:g.30000103T>G		7.0	0.0	.		17.0	15.0	.	NM_016418	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Splice_Site	SNP	ENST00000338641.4	hg19	CCDS13861.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.472138	0.84533	.	.	ENSG00000186575	ENST00000413209;ENST00000347330;ENST00000338641;ENST00000403435;ENST00000361452;ENST00000397822;ENST00000403999;ENST00000334961;ENST00000353887;ENST00000397789;ENST00000361676;ENST00000361166	.	.	.	5.37	5.37	0.77165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0321	0.71717	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	NF2	28330103	1.000000	0.71417	0.999000	0.59377	0.979000	0.70002	5.795000	0.69074	2.034000	0.60081	0.459000	0.35465	.	.	.	.	none		0.562	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268	Intron	G	30000103	T	G	30000103	5	3	98	1	0	0	0	0	0	0	1	0	10364	1652	57	5	118	5	NF2	22	30000103	Splice_Site	SNP	T	TCGA-B9-4117-01A-01D-1252-08		30000103	21304463	60	6244											
MAOA	4128	hgsc.bcm.edu	37	chrX	43590945	43590945	+	Missense_Mutation	SNP	A	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	cttgtgtgtgttttagtgcaAatacgtaattaatgcgatcc	10	16	9	6	2	0	0	0	0	0	0	1	1	1	0	1	0	3	3	1	0	5	6			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:43590945A>C	ENST00000338702.3	+	8	923	c.800A>C	c.(799-801)aAa>aCa	p.K267T	MAOA_ENST00000542639.1_Missense_Mutation_p.K134T	NM_000240.3	NP_000231.1	P21397	AOFA_HUMAN	monoamine oxidase A	267					cellular biogenic amine metabolic process (GO:0006576)|dopamine catabolic process (GO:0042420)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	primary amine oxidase activity (GO:0008131)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	18					Almotriptan(DB00918)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Minaprine(DB00805)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Naratriptan(DB00952)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Riboflavin(DB00140)|Rizatriptan(DB00953)|Selegiline(DB01037)|Sertraline(DB01104)|Sumatriptan(DB00669)|Testosterone(DB00624)|Tranylcypromine(DB00752)|Zolmitriptan(DB00315)|Zonisamide(DB00909)	TTTTAGTGCAAATACGTAATT	0.418																																					p.K267T		Atlas-SNP	.											.	MAOA	48	.	0			c.A800C						PASS	.						110	82	92					X																	43590945		2203	4300	6503	SO:0001583	missense	4128	exon8			AGTGCAAATACGT		CCDS14260.1, CCDS59163.1	Xp11.4-p11.3	2008-02-05			ENSG00000189221	ENSG00000189221	1.4.3.4		6833	protein-coding gene	gene with protein product		309850					Standard	NM_000240		Approved		uc004dfy.4	P21397	OTTHUMG00000021387	ENST00000338702.3:c.800A>C	chrX.hg19:g.43590945A>C	ENSP00000340684:p.Lys267Thr	82.0	0.0	.		95.0	30.0	.	NM_000240	B4DF46|Q16426	Missense_Mutation	SNP	ENST00000338702.3	hg19	CCDS14260.1	.	.	.	.	.	.	.	.	.	.	A	10.50	1.367611	0.24771	.	.	ENSG00000189221	ENST00000338702;ENST00000542639	D;D	0.92699	-3.09;-3.09	5.81	-4.19	0.03835	Amine oxidase (1);	0.452762	0.27682	N	0.018281	D	0.92280	0.7551	M	0.86420	2.815	0.40067	D	0.975962	B	0.20887	0.049	B	0.28991	0.097	T	0.76729	-0.2852	10	0.72032	D	0.01	.	16.9162	0.86152	0.7596:0.0:0.2404:0.0	.	267	P21397	AOFA_HUMAN	T	267;134	ENSP00000340684:K267T;ENSP00000440846:K134T	ENSP00000340684:K267T	K	+	2	0	MAOA	43475889	0.137000	0.22531	0.008000	0.14137	0.362000	0.29581	-0.156000	0.10100	-1.760000	0.01312	-0.488000	0.04728	AAA	.	.	.	none		0.418	MAOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056300.1	NM_000240		C	43590945	A	C	43590945	3	2	98	1	0	0	0	0	1	0	0	0	9232	14	1	5	830	5	MAOA	23	43590945	Missense_Mutation	SNP	A	TCGA-B9-4117-01A-01D-1252-08		43590945	111679615	61	6245											
NOX1	27035	hgsc.bcm.edu	37	chrX	100099033	100099033	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgcaggctctttgccaaagTccgagggccacataagaaaa	13	6	11	11	2	1	1	0	0	1	1	2	2	2	1	3	2	1	2	3	2	4	2			TCGA-B9-4117-01A-01D-1252-08	TCGA-B9-4117-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	022fd0e9-aeef-4d27-a58a-66acca664e1d	1dfccb8c-84c0-4831-983e-08d93bf00ad4	g.chrX:100099033T>C	ENST00000372966.3	-	13	1808	c.1603A>G	c.(1603-1605)Act>Gct	p.T535A	NOX1_ENST00000217885.5_Missense_Mutation_p.T486A|NOX1_ENST00000372964.1_Intron|NOX1_ENST00000372960.4_Missense_Mutation_p.T498A	NM_007052.4|NM_013955.2	NP_008983.2|NP_039249.1	Q9Y5S8	NOX1_HUMAN	NADPH oxidase 1	535	Interaction with NOXO1.				angiogenesis (GO:0001525)|cell migration (GO:0016477)|cellular response to hyperoxia (GO:0071455)|cellular stress response to acidic pH (GO:1990451)|extracellular matrix organization (GO:0030198)|hydrogen peroxide metabolic process (GO:0042743)|inflammatory response (GO:0006954)|intracellular pH elevation (GO:0051454)|NADP metabolic process (GO:0006739)|oxidation-reduction process (GO:0055114)|oxygen metabolic process (GO:0072592)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of JNK cascade (GO:0046330)|positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902177)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation vascular endothelial growth factor production (GO:0010575)|proton transport (GO:0015992)|regulation of blood pressure (GO:0008217)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|respiratory burst (GO:0045730)|signal transduction (GO:0007165)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|early endosome (GO:0005769)|integral component of membrane (GO:0016021)|invadopodium membrane (GO:0071438)|NADPH oxidase complex (GO:0043020)	metal ion binding (GO:0046872)|NADP binding (GO:0050661)|Rac GTPase binding (GO:0048365)|superoxide-generating NADPH oxidase activity (GO:0016175)|voltage-gated proton channel activity (GO:0030171)			cervix(1)|lung(3)|ovary(1)|skin(2)	7						TTTGCCAAAGTCCGAGGGCCA	0.433																																					p.T535A		Atlas-SNP	.											.	NOX1	79	.	0			c.A1603G						PASS	.						65	51	55					X																	100099033		2202	4299	6501	SO:0001583	missense	27035	exon13			CCAAAGTCCGAGG	AF127763	CCDS14474.1, CCDS14475.1, CCDS65298.1	Xq22	2008-08-01			ENSG00000007952	ENSG00000007952			7889	protein-coding gene	gene with protein product	"mitogenic oxidase (pyridine nucleotide-dependent superoxide-generating)", "NADPH oxidase homolog-1", "NADPH oxidase 1 variant NOH-1L"	300225				10485709, 10615049	Standard	NM_007052		Approved	NOH1, NOH-1, MOX1, GP91-2	uc004egj.3	Q9Y5S8	OTTHUMG00000022007	ENST00000372966.3:c.1603A>G	chrX.hg19:g.100099033T>C	ENSP00000362057:p.Thr535Ala	20.0	0.0	.		34.0	13.0	.	NM_007052	A8K836|O95691|Q2PP02	Missense_Mutation	SNP	ENST00000372966.3	hg19	CCDS14474.1	.	.	.	.	.	.	.	.	.	.	t	0.927	-0.714078	0.03206	.	.	ENSG00000007952	ENST00000372966;ENST00000217885;ENST00000372960	D;T;D	0.94650	-3.48;0.09;-3.48	5.09	-0.337	0.12654	Ferric reductase, NAD binding (1);	0.458064	0.22296	N	0.061923	T	0.70456	0.3226	N	0.00277	-1.72	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	0.70938	-0.4736	10	0.02654	T	1	-0.2036	5.1658	0.15084	0.0:0.3874:0.3302:0.2825	.	498;486;535	A6NGA6;Q9Y5S8-3;Q9Y5S8	.;.;NOX1_HUMAN	A	535;486;498	ENSP00000362057:T535A;ENSP00000217885:T486A;ENSP00000362051:T498A	ENSP00000217885:T486A	T	-	1	0	NOX1	99985689	0.000000	0.05858	0.000000	0.03702	0.904000	0.53231	0.069000	0.14552	-0.326000	0.08564	0.483000	0.47432	ACT	.	.	.	none		0.433	NOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057495.1	NM_007052		C	100099033	T	C	100099033	3	2	98	1	0	0	0	0	1	0	0	0	10563	1667	58	3	95	3	NOX1	23	100099033	Missense_Mutation	SNP	T	TCGA-B9-4117-01A-01D-1252-08	56508088	100099033	55171527	62	6246											
ECE1	1889	hgsc.bcm.edu	37	chr1	21585300	21585300	+	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	gtgtcctggaagttgtccttGgcccagggacctgtgatgtt	5	13	14	9	0	0	1	0	1	0	0	2	3	2	3	4	3	0	2	4	3	1	3			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr1:21585300G>T	ENST00000374893.6	-	6	722	c.648C>A	c.(646-648)gcC>gcA	p.A216A	ECE1_ENST00000357071.4_Silent_p.A204A|ECE1_ENST00000264205.6_Silent_p.A213A|ECE1_ENST00000415912.2_Silent_p.A200A|ECE1_ENST00000436918.2_Silent_p.A216A|ECE1_ENST00000528294.1_5'Flank	NM_001397.2	NP_001388.1	P42892	ECE1_HUMAN	endothelin converting enzyme 1	216					bradykinin catabolic process (GO:0010815)|calcitonin catabolic process (GO:0010816)|ear development (GO:0043583)|embryonic digit morphogenesis (GO:0042733)|endothelin maturation (GO:0034959)|heart development (GO:0007507)|hormone catabolic process (GO:0042447)|peptide hormone processing (GO:0016486)|pharyngeal system development (GO:0060037)|positive regulation of receptor recycling (GO:0001921)|protein processing (GO:0016485)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|substance P catabolic process (GO:0010814)	early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intrinsic component of endosome membrane (GO:0031302)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)|Weibel-Palade body (GO:0033093)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)			endometrium(5)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	25		Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206)		AGTTGTCCTTGGCCCAGGGAC	0.597																																					p.A216A		Atlas-SNP	.											.	ECE1	76	.	0			c.C648A						PASS	.						156	119	132					1																	21585300		2203	4300	6503	SO:0001819	synonymous_variant	1889	exon6			GTCCTTGGCCCAG	D49471	CCDS215.1, CCDS44081.1, CCDS44082.1, CCDS44083.1	1p36.1	2008-02-05			ENSG00000117298	ENSG00000117298			3146	protein-coding gene	gene with protein product		600423		ECE		7805846, 7864876, 17592116	Standard	NM_001397		Approved		uc001bei.2	P42892	OTTHUMG00000002625	ENST00000374893.6:c.648C>A	chr1.hg19:g.21585300G>T		106.0	0.0	.		106.0	35.0	.	NM_001397	A8K3P1|B4E291|Q14217|Q17RN5|Q2Z2K8|Q58GE7|Q5THM5|Q5THM7|Q5THM8|Q9UJQ6|Q9UPF4|Q9UPM4|Q9Y501	Silent	SNP	ENST00000374893.6	hg19	CCDS215.1																																																																																			.	.	.	none		0.597	ECE1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007470.2	NM_001397		T	21585300	G	T	21585300	2	4	99	1	0	0	0	0	0	0	0	1	4891	1335	47	4		4	ECE1	1	21585300	Silent	SNP	G	TCGA-B9-4617-01A-01D-1252-08		21585300	227665321	1	6247											
KCNC4	3749	hgsc.bcm.edu	37	chr1	110768796	110768796	+	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	tgcgccgatggtagtgtccgGaaaggtatggcttcccaagc	8	9	14	10	3	0	0	0	0	0	0	2	2	2	1	3	4	2	3	3	4	4	3			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr1:110768796G>A	ENST00000369787.3	+	3	1842	c.1815G>A	c.(1813-1815)cgG>cgA	p.R605R	KCNC4_ENST00000413138.3_Silent_p.R605R|KCNC4_ENST00000412512.2_Intron|KCNC4_ENST00000438661.2_Silent_p.R605R	NM_004978.4	NP_004969.2	Q03721	KCNC4_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 4	605					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)		GTAGTGTCCGGAAAGGTATGG	0.642																																					p.R605R		Atlas-SNP	.											.	KCNC4	113	.	0			c.G1815A						PASS	.						50	56	54					1																	110768796		2203	4300	6503	SO:0001819	synonymous_variant	3749	exon3			TGTCCGGAAAGGT	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.1815G>A	chr1.hg19:g.110768796G>A		70.0	0.0	.		96.0	37.0	.	NM_001039574	Q3MIM4|Q5TBI6	Silent	SNP	ENST00000369787.3	hg19	CCDS821.1																																																																																			.	.	.	none		0.642	KCNC4-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052146.2	NM_001039574		A	110768796	G	A	110768796	2	1	99	1	0	0	0	0	0	0	0	1	8024	1161	41	2		2	KCNC4	1	110768796	Silent	SNP	G	TCGA-B9-4617-01A-01D-1252-08	89183496	110768796	138481825	2	6248											
ITLN2	142683	hgsc.bcm.edu	37	chr1	160924190	160924190	+	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	catttacctgcactgcacccActggtggccacagagaagaa	12	7	9	13	0	0	2	0	0	0	2	0	3	0	2	3	2	3	2	3	2	3	2	rs145856391		TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr1:160924190A>T	ENST00000368029.3	-	2	123	c.66T>A	c.(64-66)agT>agA	p.S22R		NM_080878.2	NP_543154.1	Q8WWU7	ITLN2_HUMAN	intelectin 2	22						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)			CACTGCACCCACTGGTGGCCA	0.552											OREG0013934	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S22R		Atlas-SNP	.											.	ITLN2	35	.	0			c.T66A						PASS	.						101	93	96					1																	160924190		2201	4298	6499	SO:0001583	missense	142683	exon2			GCACCCACTGGTG	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.66T>A	chr1.hg19:g.160924190A>T	ENSP00000357008:p.Ser22Arg	16.0	0.0	.	1812	10.0	6.0	.	NM_080878	Q17RR2|Q5VYI0	Missense_Mutation	SNP	ENST00000368029.3	hg19	CCDS1212.1	.	.	.	.	.	.	.	.	.	.	A	0.005	-2.158971	0.00321	.	.	ENSG00000158764	ENST00000368029	T	0.17691	2.26	3.74	0.0268	0.14151	.	1.672490	0.04351	N	0.355594	T	0.01627	0.0052	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.38265	-0.9669	10	0.12103	T	0.63	-0.4519	0.7369	0.00967	0.343:0.1034:0.1768:0.3767	.	22;22	A6NI51;Q8WWU7	.;ITLN2_HUMAN	R	22	ENSP00000357008:S22R	ENSP00000357008:S22R	S	-	3	2	ITLN2	159190814	0.000000	0.05858	0.010000	0.14722	0.002000	0.02628	-0.072000	0.11486	-0.250000	0.09555	-2.614000	0.00158	AGT	.	A|1.000;G|0.000	.	alt		0.552	ITLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071465.1	NM_080878		T	160924190	A	T	160924190	3	4	99	1	0	0	0	0	1	0	0	0	7918	156	6	5	939	5	ITLN2	1	160924190	Missense_Mutation	SNP	A	TCGA-B9-4617-01A-01D-1252-08	50155394	160924190	88326431	3	6249											
NIT1	4817	hgsc.bcm.edu	37	chr1	161090544	161090544	+	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	tctatggcaatctgggtcacCcactgtcttaagacttgact	9	13	8	11	0	4	2	1	1	3	1	4	2	4	2	1	2	0	1	1	2	3	3			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr1:161090544C>A	ENST00000368009.2	+	7	1049	c.973C>A	c.(973-975)Cca>Aca	p.P325T	DEDD_ENST00000489249.1_5'Flank|NIT1_ENST00000392190.5_Missense_Mutation_p.P289T|NIT1_ENST00000368008.1_Intron|PFDN2_ENST00000368010.3_5'Flank|PFDN2_ENST00000468311.1_5'Flank|NIT1_ENST00000368007.4_Missense_Mutation_p.P310T	NM_005600.2	NP_005591.1	Q86X76	NIT1_HUMAN	nitrilase 1	325					nitrogen compound metabolic process (GO:0006807)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	nitrilase activity (GO:0000257)			NS(1)|breast(2)|endometrium(2)|large_intestine(3)|lung(3)|prostate(1)	12	all_cancers(52;3.39e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			TCTGGGTCACCCACTGTCTTA	0.567																																					p.P325T		Atlas-SNP	.											.	NIT1	41	.	0			c.C973A						PASS	.						50	44	46					1																	161090544		2202	4299	6501	SO:0001583	missense	4817	exon7			GGTCACCCACTGT	AF069984	CCDS1218.1, CCDS53401.1, CCDS53402.1, CCDS53403.1	1q21-q22	2008-05-14			ENSG00000158793	ENSG00000158793			7828	protein-coding gene	gene with protein product		604618				9671749	Standard	NM_005600		Approved		uc001fxv.2	Q86X76	OTTHUMG00000031473	ENST00000368009.2:c.973C>A	chr1.hg19:g.161090544C>A	ENSP00000356988:p.Pro325Thr	110.0	0.0	.		85.0	33.0	.	NM_005600	B1AQP3|D3DVF4|O76091	Missense_Mutation	SNP	ENST00000368009.2	hg19	CCDS1218.1	.	.	.	.	.	.	.	.	.	.	C	11.86	1.763738	0.31228	.	.	ENSG00000158793	ENST00000368009;ENST00000368007;ENST00000392190	T;T;T	0.78481	-1.16;-1.18;-1.13	4.9	4.9	0.64082	.	0.347201	0.28365	N	0.015606	T	0.69070	0.3070	N	0.08118	0	0.35810	D	0.823791	D;P	0.89917	1.0;0.61	D;B	0.83275	0.996;0.262	T	0.75687	-0.3231	10	0.45353	T	0.12	-10.3808	13.4666	0.61258	0.0:1.0:0.0:0.0	.	310;325	Q86X76-4;Q86X76	.;NIT1_HUMAN	T	325;310;289	ENSP00000356988:P325T;ENSP00000356986:P310T;ENSP00000376028:P289T	ENSP00000356986:P310T	P	+	1	0	NIT1	159357168	0.046000	0.20272	0.938000	0.37757	0.597000	0.36814	1.708000	0.37899	2.551000	0.86045	0.563000	0.77884	CCA	.	.	.	none		0.567	NIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077060.1			A	161090544	C	A	161090544	3	1	99	1	0	0	0	0	1	0	0	0	10440	623	22	4	1056	4	NIT1	1	161090544	Missense_Mutation	SNP	C	TCGA-B9-4617-01A-01D-1252-08	166354	161090544	88160077	4	6250											
LTBP1	4052	hgsc.bcm.edu	37	chr2	33622241	33622241	+	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	agttacaggctgaggaatgcGgcatcctcaatggatgtgaa	12	9	13	7	1	1	2	1	2	0	0	2	4	2	4	1	4	2	3	1	4	4	1			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr2:33622241G>T	ENST00000404816.2	+	33	5229	c.4876G>T	c.(4876-4878)Ggc>Tgc	p.G1626C	LTBP1_ENST00000390003.4_Missense_Mutation_p.G1301C|LTBP1_ENST00000418533.2_Missense_Mutation_p.G1258C|LTBP1_ENST00000404525.1_Missense_Mutation_p.G1247C|LTBP1_ENST00000402934.1_Missense_Mutation_p.G1245C|LTBP1_ENST00000354476.3_Missense_Mutation_p.G1627C|LTBP1_ENST00000407925.1_Missense_Mutation_p.G1300C|LTBP1_ENST00000272273.5_Missense_Mutation_p.G524C			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1626	EGF-like 17. {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)				TGAGGAATGCGGCATCCTCAA	0.453																																					p.G1626C		Atlas-SNP	.											LTBP1,NS,carcinoma,0,1	LTBP1	317	.	0			c.G4876T						PASS	.						166	152	157					2																	33622241		2203	4300	6503	SO:0001583	missense	4052	exon33			GAATGCGGCATCC		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.4876G>T	chr2.hg19:g.33622241G>T	ENSP00000386043:p.Gly1626Cys	80.0	0.0	.		69.0	3.0	.	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	hg19	CCDS33177.2	.	.	.	.	.	.	.	.	.	.	G	28.4	4.920839	0.92249	.	.	ENSG00000049323	ENST00000404816;ENST00000354476;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925;ENST00000272273	D;D;D;D;D;D;D;D	0.87571	-2.27;-2.27;-2.27;-2.27;-2.27;-2.27;-2.27;-2.27	5.49	5.49	0.81192	Matrix fibril-associated (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.93779	0.8011	M	0.78916	2.43	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.93794	0.7095	9	0.66056	D	0.02	.	19.7433	0.96241	0.0:0.0:1.0:0.0	.	524;1626;1258;1247;1300;1301;1627	E7EUU6;Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4	.;LTBP1_HUMAN;.;.;.;.;.	C	1626;1627;1301;1258;1245;1247;1300;524	ENSP00000386043:G1626C;ENSP00000346467:G1627C;ENSP00000374653:G1301C;ENSP00000393057:G1258C;ENSP00000384373:G1245C;ENSP00000385359:G1247C;ENSP00000384091:G1300C;ENSP00000272273:G524C	ENSP00000272273:G524C	G	+	1	0	LTBP1	33475745	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.813000	0.99286	2.733000	0.93635	0.655000	0.94253	GGC	.	.	.	none		0.453	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		T	33622241	G	T	33622241	3	4	99	1	0	0	0	0	1	0	0	0	9080	1116	39	4	5061	4	LTBP1	2	33622241	Missense_Mutation	SNP	G	TCGA-B9-4617-01A-01D-1252-08		33622241	209577132	5	6251											
C2orf78	388960	hgsc.bcm.edu	37	chr2	74043217	74043217	+	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	aaaagacccttaaaaagcccCgaagctccctaggcatgcac	15	5	7	14	1	0	1	0	0	0	1	1	2	1	1	4	1	3	3	4	1	7	2			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr2:74043217C>A	ENST00000409561.1	+	3	1988	c.1867C>A	c.(1867-1869)Cga>Aga	p.R623R		NM_001080474.1	NP_001073943.1	A6NCI8	CB078_HUMAN	chromosome 2 open reading frame 78	623										cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|soft_tissue(1)|urinary_tract(1)	34						TAAAAAGCCCCGAAGCTCCCT	0.453																																					p.R623R		Atlas-SNP	.											.	C2orf78	150	.	0			c.C1867A						PASS	.						72	69	70					2																	74043217		1840	4088	5928	SO:0001819	synonymous_variant	388960	exon3			AAGCCCCGAAGCT	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.1867C>A	chr2.hg19:g.74043217C>A		109.0	0.0	.		97.0	4.0	.	NM_001080474		Silent	SNP	ENST00000409561.1	hg19	CCDS46338.1																																																																																			.	.	.	none		0.453	C2orf78-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000328083.1	NM_001080474		A	74043217	C	A	74043217	2	1	99	1	0	0	0	0	0	0	0	1	2197	644	23	4		4	C2orf78	2	74043217	Silent	SNP	C	TCGA-B9-4617-01A-01D-1252-08	40420976	74043217	169156156	6	6252											
DARS	1615	hgsc.bcm.edu	37	chr2	136680361	136680361	+	Missense_Mutation	SNP	A	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	gccaaaatcttacctggtccAatagagaaaaccttctcaaa	16	9	5	11	0	2	1	1	0	2	1	4	2	3	1	4	1	2	0	4	1	8	3			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr2:136680361A>C	ENST00000264161.4	-	9	1019	c.804T>G	c.(802-804)atT>atG	p.I268M	DARS_ENST00000537273.1_Missense_Mutation_p.I168M	NM_001349.2	NP_001340.2	P14868	SYDC_HUMAN	aspartyl-tRNA synthetase	268					aspartyl-tRNA aminoacylation (GO:0006422)|gene expression (GO:0010467)|protein complex assembly (GO:0006461)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacylase activity (GO:0004046)|aspartate-tRNA ligase activity (GO:0004815)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(2)	15				BRCA - Breast invasive adenocarcinoma(221;0.168)	L-Aspartic Acid(DB00128)	TACCTGGTCCAATAGAGAAAA	0.308																																					p.I268M		Atlas-SNP	.											.	DARS	44	.	0			c.T804G						PASS	.						81	81	81					2																	136680361		2203	4300	6503	SO:0001583	missense	1615	exon9			TGGTCCAATAGAG	J05032	CCDS2180.1	2q21.3	2011-07-01			ENSG00000115866	ENSG00000115866	6.1.1.12	"Aminoacyl tRNA synthetases / Class II"	2678	protein-coding gene	gene with protein product	"aspartate tRNA ligase 1, cytoplasmic"	603084				2674137	Standard	NM_001349		Approved		uc002tux.1	P14868	OTTHUMG00000131741	ENST00000264161.4:c.804T>G	chr2.hg19:g.136680361A>C	ENSP00000264161:p.Ile268Met	159.0	0.0	.		170.0	78.0	.	NM_001349	A8K3J2|D3DP77|Q2TNI3|Q32Q69|Q53HV4|Q53YC5|Q68CR9|Q9BW52	Missense_Mutation	SNP	ENST00000264161.4	hg19	CCDS2180.1	.	.	.	.	.	.	.	.	.	.	A	18.86	3.714290	0.68730	.	.	ENSG00000115866	ENST00000264161;ENST00000537273	D;D	0.84730	-1.89;-1.89	5.71	5.71	0.89125	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (D/K/N) (1);	0.105460	0.64402	D	0.000004	D	0.94820	0.8327	H	0.96547	3.84	0.53688	D	0.999978	D	0.58970	0.984	D	0.70227	0.968	D	0.96332	0.9244	10	0.87932	D	0	-18.2315	15.9798	0.80097	1.0:0.0:0.0:0.0	.	268	P14868	SYDC_HUMAN	M	268;168	ENSP00000264161:I268M;ENSP00000444192:I168M	ENSP00000264161:I268M	I	-	3	3	DARS	136396831	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.221000	0.42917	2.169000	0.68431	0.477000	0.44152	ATT	.	.	.	none		0.308	DARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254660.5	NM_001349		C	136680361	A	C	136680361	3	2	99	1	0	0	0	0	1	0	0	0	4243	126	5	5	733	5	DARS	2	136680361	Missense_Mutation	SNP	A	TCGA-B9-4617-01A-01D-1252-08	62637144	136680361	106519012	7	6253											
PPIG	9360	hgsc.bcm.edu	37	chr2	170460568	170460568	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccatgggaataaaggttcAacgtcctcgatgtttttttg	10	14	10	7	2	1	0	1	0	0	0	3	2	2	1	2	2	2	2	2	2	4	5			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr2:170460568A>G	ENST00000260970.3	+	3	237	c.17A>G	c.(16-18)cAa>cGa	p.Q6R	PPIG_ENST00000409714.3_Missense_Mutation_p.Q6R|PPIG_ENST00000448752.2_Missense_Mutation_p.Q6R|PPIG_ENST00000462903.1_Missense_Mutation_p.Q6R	NM_004792.2	NP_004783.2	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G (cyclophilin G)	6					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)	ATAAAGGTTCAACGTCCTCGA	0.308																																					p.Q6R		Atlas-SNP	.											.	PPIG	100	.	0			c.A17G						PASS	.						95	97	96					2																	170460568		2203	4300	6503	SO:0001583	missense	9360	exon3			AGGTTCAACGTCC	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.17A>G	chr2.hg19:g.170460568A>G	ENSP00000260970:p.Gln6Arg	113.0	0.0	.		127.0	46.0	.	NM_004792	D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9	Missense_Mutation	SNP	ENST00000260970.3	hg19	CCDS2235.1	.	.	.	.	.	.	.	.	.	.	A	15.51	2.854084	0.51270	.	.	ENSG00000138398	ENST00000260970;ENST00000530133;ENST00000409714;ENST00000462903;ENST00000448752;ENST00000418888;ENST00000414307	T;T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01;1.01	5.19	4.0	0.46444	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (1);Cyclophilin-like (1);	0.066333	0.64402	D	0.000008	T	0.35393	0.0930	N	0.17800	0.525	0.43403	D	0.995537	B;B;B;P	0.35107	0.149;0.149;0.444;0.484	B;B;B;B	0.43623	0.058;0.058;0.425;0.407	T	0.16600	-1.0397	10	0.41790	T	0.15	-4.8499	12.2535	0.54611	0.8577:0.1423:0.0:0.0	.	6;6;6;6	E9PG73;Q2NKQ6;Q13427-2;Q13427	.;.;.;PPIG_HUMAN	R	6	ENSP00000260970:Q6R;ENSP00000386245:Q6R;ENSP00000435987:Q6R;ENSP00000407083:Q6R;ENSP00000394202:Q6R;ENSP00000402222:Q6R	ENSP00000260970:Q6R	Q	+	2	0	PPIG	170168814	1.000000	0.71417	0.991000	0.47740	0.962000	0.63368	4.391000	0.59652	0.887000	0.36136	0.459000	0.35465	CAA	.	.	.	none		0.308	PPIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255264.2			G	170460568	A	G	170460568	3	3	99	1	0	0	0	0	1	0	0	0	12334	130	5	3	19	3	PPIG	2	170460568	Missense_Mutation	SNP	A	TCGA-B9-4617-01A-01D-1252-08	33780207	170460568	72738805	8	6254											
ZAK	51776	hgsc.bcm.edu	37	chr2	174097114	174097114	+	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	aaacaacattacagggaagcGgctgctgctgctggaggaag	13	6	14	8	1	0	0	0	0	0	0	0	3	0	3	0	4	7	4	0	4	5	1			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr2:174097114G>T	ENST00000375213.3	+	14	1208	c.1130G>T	c.(1129-1131)cGg>cTg	p.R377L	MLTK_ENST00000409176.2_Missense_Mutation_p.R377L|MLK7-AS1_ENST00000422703.1_RNA|MLK7-AS1_ENST00000423106.2_RNA	NM_016653.2	NP_057737.2	Q9NYL2	MLTK_HUMAN		377	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell death (GO:0008219)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|DNA damage checkpoint (GO:0000077)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|response to radiation (GO:0009314)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)										ACAGGGAAGCGGCTGCTGCTG	0.428																																					p.R377L		Atlas-SNP	.											.	ZAK	62	.	0			c.G1130T						PASS	.						156	157	157					2																	174097114		1971	4169	6140	SO:0001583	missense	0	exon14			GGAAGCGGCTGCT																												ENST00000375213.3:c.1130G>T	chr2.hg19:g.174097114G>T	ENSP00000364361:p.Arg377Leu	348.0	0.0	.		330.0	160.0	.	NM_016653	B3KPG2|Q53SX1|Q580W8|Q59GY5|Q86YW8|Q9HCC4|Q9HCC5|Q9HDD2|Q9NYE9	Missense_Mutation	SNP	ENST00000375213.3	hg19	CCDS42777.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.682483	0.88542	.	.	ENSG00000091436	ENST00000409176;ENST00000375213	T;T	0.47528	0.84;0.84	5.8	5.8	0.92144	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.051262	0.64402	D	0.000001	T	0.56485	0.1988	L	0.41573	1.285	0.80722	D	1	D	0.56287	0.975	P	0.58520	0.84	T	0.57585	-0.7786	10	0.87932	D	0	.	15.1807	0.72956	0.069:0.0:0.931:0.0	.	377	Q9NYL2	MLTK_HUMAN	L	377	ENSP00000387259:R377L;ENSP00000364361:R377L	ENSP00000364361:R377L	R	+	2	0	AC013461.1	173805360	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.414000	0.66405	2.736000	0.93811	0.643000	0.83706	CGG	.	.	.	none		0.428	MLTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255401.1			T	174097114	G	T	174097114	3	4	99	1	0	0	0	0	1	0	0	0	17524	1116	39	4	1565	4	ZAK	2	174097114	Missense_Mutation	SNP	G	TCGA-B9-4617-01A-01D-1252-08	3636546	174097114	69102259	9	6255											
GLS	2744	hgsc.bcm.edu	37	chr2	191827660	191827660	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacacctcaaggagattctgAcaacgggaaggaaaatcaaa	18	5	9	9	1	3	2	2	1	1	1	3	5	3	4	1	3	1	0	1	3	6	1			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr2:191827660A>G	ENST00000320717.3	+	18	2216	c.1958A>G	c.(1957-1959)gAc>gGc	p.D653G	GLS_ENST00000409428.1_Missense_Mutation_p.D158G	NM_014905.4	NP_055720.3	O94925	GLSK_HUMAN	glutaminase	653					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)	GGAGATTCTGACAACGGGAAG	0.378																																					p.D653G		Atlas-SNP	.											.	GLS	47	.	0			c.A1958G						PASS	.						100	94	96					2																	191827660		2203	4300	6503	SO:0001583	missense	2744	exon18			ATTCTGACAACGG	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.1958A>G	chr2.hg19:g.191827660A>G	ENSP00000317379:p.Asp653Gly	117.0	0.0	.		119.0	50.0	.	NM_014905	Q9UL05|Q9UL06|Q9UL07|Q9UN40	Missense_Mutation	SNP	ENST00000320717.3	hg19	CCDS2308.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.749|6.749	0.506930|0.506930	0.12883|0.12883	.|.	.|.	ENSG00000115419|ENSG00000115419	ENST00000320717;ENST00000409428|ENST00000412247	T;T|.	0.52295|.	0.99;0.67|.	5.34|5.34	2.91|2.91	0.33838|0.33838	.|.	0.568432|.	0.20287|.	N|.	0.095338|.	T|T	0.22244|0.22244	0.0536|0.0536	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	0.999999|0.999999	B;B|.	0.15930|.	0.015;0.015|.	B;B|.	0.15870|.	0.014;0.014|.	T|T	0.21861|0.21861	-1.0233|-1.0233	10|6	0.23302|0.19147	T|T	0.38|0.46	-10.5512|-10.5512	9.8019|9.8019	0.40770|0.40770	0.7963:0.0:0.2037:0.0|0.7963:0.0:0.2037:0.0	.|.	653;653|.	A8K132;O94925|.	.;GLSK_HUMAN|.	G|A	653;158|153	ENSP00000317379:D653G;ENSP00000387177:D158G|.	ENSP00000317379:D653G|ENSP00000403329:T153A	D|T	+|+	2|1	0|0	GLS|GLS	191535905|191535905	0.329000|0.329000	0.24696|0.24696	0.798000|0.798000	0.32154|0.32154	0.981000|0.981000	0.71138|0.71138	2.092000|2.092000	0.41700|0.41700	1.036000|1.036000	0.39998|0.39998	0.533000|0.533000	0.62120|0.62120	GAC|ACA	.	.	.	none		0.378	GLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255999.2			G	191827660	A	G	191827660	3	3	99	1	0	0	0	0	1	0	0	0	6470	275	10	3	2028	3	GLS	2	191827660	Missense_Mutation	SNP	A	TCGA-B9-4617-01A-01D-1252-08	17730546	191827660	51371713	10	6256											
CYP20A1	57404	hgsc.bcm.edu	37	chr2	204154489	204154489	+	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	aaaaatttttttaaaacagaTattgtcagcatgtgctttgt	14	17	6	4	0	1	1	1	0	0	1	1	1	1	1	0	0	3	2	0	0	5	7			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr2:204154489T>C	ENST00000356079.4	+	10	1096	c.973T>C	c.(973-975)Tat>Cat	p.Y325H	CYP20A1_ENST00000429815.2_Splice_Site_p.Y333H|CYP20A1_ENST00000461371.1_3'UTR	NM_177538.2	NP_803882.1	Q6UW02	CP20A_HUMAN	cytochrome P450, family 20, subfamily A, polypeptide 1	325						integral component of membrane (GO:0016021)|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)			cervix(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	11						TTAAAACAGATATTGTCAGCA	0.328																																					p.Y325H		Atlas-SNP	.											.	CYP20A1	40	.	0			c.T973C						PASS	.						46	46	46					2																	204154489		2203	4300	6503	SO:0001630	splice_region_variant	57404	exon10			AACAGATATTGTC	AK021770	CCDS2357.1	2q33	2008-02-05			ENSG00000119004	ENSG00000119004		"Cytochrome P450s"	20576	protein-coding gene	gene with protein product							Standard	NM_177538		Approved	CYP-M	uc002uzv.4	Q6UW02	OTTHUMG00000132854	ENST00000356079.4:c.972-1T>C	chr2.hg19:g.204154489T>C		153.0	0.0	.		132.0	60.0	.	NM_177538	Q4ZG61|Q8N4Q8|Q8WWA9|Q9HC04	Missense_Mutation	SNP	ENST00000356079.4	hg19	CCDS2357.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.045301	0.75846	.	.	ENSG00000119004	ENST00000356079;ENST00000421618;ENST00000429815	T;T	0.76186	-1.0;-1.0	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.87569	0.6210	M	0.84433	2.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.89608	0.3839	10	0.87932	D	0	-12.683	15.831	0.78752	0.0:0.0:0.0:1.0	.	333;325	E9PHG5;Q6UW02	.;CP20A_HUMAN	H	325;298;333	ENSP00000348380:Y325H;ENSP00000407860:Y333H	ENSP00000348380:Y325H	Y	+	1	0	CYP20A1	203862734	1.000000	0.71417	0.984000	0.44739	0.845000	0.48019	6.587000	0.74071	2.154000	0.67381	0.473000	0.43528	TAT	.	.	.	none		0.328	CYP20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256328.3	NM_020674	Missense_Mutation	C	204154489	T	C	204154489	5	2	99	1	0	0	0	0	0	0	1	0	4154	1420	49	3	1011	3	CYP20A1	2	204154489	Splice_Site	SNP	T	TCGA-B9-4617-01A-01D-1252-08	12326829	204154489	39044884	11	6257											
HDLBP	3069	hgsc.bcm.edu	37	chr2	242170343	242170343	+	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	tcttttcgtaccctgtgatgGtaatttggtcctggggctaa	6	16	11	8	1	1	1	0	1	1	0	3	1	2	1	2	4	1	3	2	4	3	6			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr2:242170343G>C	ENST00000391975.1	-	25	3532	c.3305C>G	c.(3304-3306)aCc>aGc	p.T1102S	HDLBP_ENST00000427183.2_Missense_Mutation_p.T1069S|HDLBP_ENST00000310931.4_Missense_Mutation_p.T1102S|HDLBP_ENST00000391976.2_Missense_Mutation_p.T1102S	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	1102	KH 13. {ECO:0000255|PROSITE- ProRule:PRU00117}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)	cytoplasm (GO:0005737)|high-density lipoprotein particle (GO:0034364)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)			breast(7)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		CCCTGTGATGGTAATTTGGTC	0.527																																					p.T1102S		Atlas-SNP	.											.	HDLBP	118	.	0			c.C3305G						PASS	.						109	94	99					2																	242170343		2203	4300	6503	SO:0001583	missense	3069	exon25			GTGATGGTAATTT		CCDS2547.1, CCDS58760.1	2q37.3	2008-07-18	2008-07-18		ENSG00000115677	ENSG00000115677			4857	protein-coding gene	gene with protein product		142695	"vigilin"	VGL		1318310, 8390966	Standard	NM_005336		Approved	HBP	uc002waz.3	Q00341	OTTHUMG00000133391	ENST00000391975.1:c.3305C>G	chr2.hg19:g.242170343G>C	ENSP00000375836:p.Thr1102Ser	109.0	0.0	.		99.0	42.0	.	NM_005336	B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Missense_Mutation	SNP	ENST00000391975.1	hg19	CCDS2547.1	.	.	.	.	.	.	.	.	.	.	G	13.15	2.150608	0.37923	.	.	ENSG00000115677	ENST00000391975;ENST00000391976;ENST00000310931;ENST00000427183	T;T;T;T	0.33216	1.42;1.42;1.42;1.42	5.53	4.66	0.58398	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.092124	0.85682	D	0.000000	T	0.30293	0.0760	L	0.52266	1.64	0.54753	D	0.999981	B;B	0.31318	0.319;0.16	B;B	0.39465	0.236;0.3	T	0.04333	-1.0959	10	0.12103	T	0.63	-51.7385	10.7199	0.46034	0.1453:0.0:0.8547:0.0	.	1069;1102	E7EM71;Q00341	.;VIGLN_HUMAN	S	1102;1102;1102;1069	ENSP00000375836:T1102S;ENSP00000375837:T1102S;ENSP00000312042:T1102S;ENSP00000399139:T1069S	ENSP00000312042:T1102S	T	-	2	0	HDLBP	241819016	1.000000	0.71417	1.000000	0.80357	0.289000	0.27227	6.493000	0.73658	1.352000	0.45808	-0.156000	0.13503	ACC	.	.	.	none		0.527	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	NM_203346		C	242170343	G	C	242170343	3	2	99	1	0	0	0	0	1	0	0	0	7032	1261	44	4	517	4	HDLBP	2	242170343	Missense_Mutation	SNP	G	TCGA-B9-4617-01A-01D-1252-08	38015854	242170343	1029030	12	6258											
ZNF501	115560	hgsc.bcm.edu	37	chr3	44776081	44776081	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatgtgtgcagtgaatgtggAagttgtttccgtaaacagtc	10	14	12	5	1	0	1	0	1	0	0	2	2	1	2	1	1	2	4	1	1	5	4			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr3:44776081A>G	ENST00000396048.2	+	3	605	c.168A>G	c.(166-168)ggA>ggG	p.G56G		NM_001258280.1|NM_145044.3	NP_001245209.1|NP_659481.2	Q96CX3	ZN501_HUMAN	zinc finger protein 501	56					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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)		GTGAATGTGGAAGTTGTTTCC	0.403																																					p.G56G		Atlas-SNP	.											ZNF501,NS,neuroblastoma,0,1	ZNF501	27	.	0			c.A168G						PASS	.						94	107	103					3																	44776081		2188	4293	6481	SO:0001819	synonymous_variant	115560	exon3			ATGTGGAAGTTGT	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.168A>G	chr3.hg19:g.44776081A>G		128.0	0.0	.		200.0	62.0	.	NM_001258280	B4DLY7|Q96NU9	Silent	SNP	ENST00000396048.2	hg19	CCDS2720.2																																																																																			.	.	.	none		0.403	ZNF501-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256654.4	NM_145044		G	44776081	A	G	44776081	2	3	99	1	0	0	0	0	0	0	0	1	17961	233	9	3		3	ZNF501	3	44776081	Silent	SNP	A	TCGA-B9-4617-01A-01D-1252-08		44776081	153246349	13	6259											
RUVBL1	8607	hgsc.bcm.edu	37	chr3	127831784	127831784	+	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	ctgtcttcttgatctcagttGagtaaacttcactccccacc	8	14	5	14	0	4	2	2	2	3	0	6	2	5	2	3	0	1	2	3	0	2	5			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr3:127831784G>A	ENST00000322623.5	-	3	407	c.308C>T	c.(307-309)tCa>tTa	p.S103L	RUVBL1_ENST00000417360.1_Missense_Mutation_p.S103L|RUVBL1_ENST00000464873.1_Missense_Mutation_p.S43L	NM_003707.2	NP_003698.1	Q9Y265	RUVB1_HUMAN	RuvB-like AAA ATPase 1	103					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Ino80 complex (GO:0031011)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)			endometrium(1)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26				GBM - Glioblastoma multiforme(114;0.181)		GATCTCAGTTGAGTAAACTTC	0.502																																					p.S103L		Atlas-SNP	.											.	RUVBL1	38	.	0			c.C308T						PASS	.						154	141	146					3																	127831784		2203	4300	6503	SO:0001583	missense	8607	exon3			TCAGTTGAGTAAA	AF070735	CCDS3047.1	3q21	2013-09-12	2013-09-12		ENSG00000175792	ENSG00000175792		"INO80 complex subunits", "ATPases / AAA-type"	10474	protein-coding gene	gene with protein product	"pontin", "INO80 complex subunit H"	603449	"RuvB (E coli homolog)-like 1", "RuvB-like 1 (E. coli)", "RuvB-like AAA ATPase"			9774387, 9588198	Standard	NM_003707		Approved	TIP49, NMP238, RVB1, TIP49a, Pontin52, ECP54, TIH1, Rvb1, INO80H	uc003ekh.3	Q9Y265	OTTHUMG00000159658	ENST00000322623.5:c.308C>T	chr3.hg19:g.127831784G>A	ENSP00000318297:p.Ser103Leu	193.0	0.0	.		255.0	91.0	.	NM_003707	B2R5S0|P82276|Q1KMR0|Q53HK5|Q53HL7|Q53Y27|Q9BSX9	Missense_Mutation	SNP	ENST00000322623.5	hg19	CCDS3047.1	.	.	.	.	.	.	.	.	.	.	G	35	5.572289	0.96553	.	.	ENSG00000175792	ENST00000464873;ENST00000322623;ENST00000417360	T;T;T	0.74209	-0.82;-0.5;-0.06	5.79	5.79	0.91817	TIP49, C-terminal (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.92140	0.7508	H	0.98577	4.27	0.80722	D	1	D;D;P	0.63046	0.992;0.983;0.884	P;D;P	0.69142	0.897;0.962;0.766	D	0.94607	0.7801	10	0.87932	D	0	-15.933	20.0349	0.97554	0.0:0.0:1.0:0.0	.	103;103;43	Q9Y265-2;Q9Y265;E7ETR0	.;RUVB1_HUMAN;.	L	43;103;103	ENSP00000420738:S43L;ENSP00000318297:S103L;ENSP00000393755:S103L	ENSP00000318297:S103L	S	-	2	0	RUVBL1	129314474	1.000000	0.71417	0.963000	0.40424	0.881000	0.50899	9.869000	0.99810	2.735000	0.93741	0.591000	0.81541	TCA	.	.	.	none		0.502	RUVBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356728.2			A	127831784	G	A	127831784	3	1	99	1	0	0	0	0	1	0	0	0	13765	1294	45	2	1098	2	RUVBL1	3	127831784	Missense_Mutation	SNP	G	TCGA-B9-4617-01A-01D-1252-08	83055703	127831784	70190646	14	6260											
WDFY3	23001	hgsc.bcm.edu	37	chr4	85630153	85630153	+	Frame_Shift_Del	DEL	A	A	-																															ccaaagtgttcaaatgcatcAaatattggaagttgctgatt																										TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr4:85630153delA	ENST00000295888.4	-	53	8533	c.8126delT	c.(8125-8127)ttgfs	p.L2709fs	WDFY3_ENST00000322366.6_Frame_Shift_Del_p.L2692fs	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	2709	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.|Interaction with SQSTM1.|Sufficient for translocalization to p62 bodies/ALIS.				aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		CAAATGCATCAAATATTGGAA	0.343																																					p.L2709fs		Atlas-INDEL	.											.	WDFY3	314	.	0			c.8127delG						PASS	.						111	114	113					4																	85630153		2203	4300	6503	SO:0001589	frameshift_variant	23001	exon53			.	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.8126delT	chr4.hg19:g.85630153delA	ENSP00000295888:p.Leu2709fs	233.0	0.0	0		210.0	92.0	0.438095	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Frame_Shift_Del	DEL	ENST00000295888.4	hg19	CCDS3609.1																																																																																			.	.	.	none		0.343	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		-	85630153	A	-	85630153	7	5	99	1	0	1	0	1	0	0	0	0	17282	131	5	0	2518	0	WDFY3	4	85630153	Frame_Shift_Del	DEL	A	TCGA-B9-4617-01A-01D-1252-08		85630153	105524123	15	6261											
MCCC2	64087	hgsc.bcm.edu	37	chr5	70931074	70931075	+	Splice_Site	INS	-	-	TA																															gagctttgatgtccgagaggINStatgtgaaagtggaactgtg																										TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr5:70931074_70931075insTA	ENST00000340941.6	+	10	1128		c.e10+1		MCCC2_ENST00000510895.2_3'UTR|MCCC2_ENST00000323375.8_Splice_Site|MCCC2_ENST00000509358.2_Splice_Site	NM_022132.4	NP_071415.1	Q9HCC0	MCCB_HUMAN	methylcrotonoyl-CoA carboxylase 2 (beta)						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)	TGTCCGAGAGGTATGTGAAAGT	0.406																																					.		Atlas-INDEL	.											.	MCCC2	47	.	0			c.999+1->TA						PASS	.																																			SO:0001630	splice_region_variant	64087	exon10			.	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.999+1->TA	chr5.hg19:g.70931075_70931076dupTA		175.0	0.0	0		115.0	48.0	0.417391	NM_022132	A6NIY9|Q96C27|Q9Y4L7	Splice_Site	INS	ENST00000340941.6	hg19	CCDS34184.1																																																																																			.	.	.	none		0.406	MCCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369243.4		Intron	TA	70931075	-	TA	70931074	8	5	99	1	0	1	1	0	0	0	1	0	9382	1275	44	0	1038	0	MCCC2	5	70931074	Splice_Site	INS	-	TCGA-B9-4617-01A-01D-1252-08		70931074	109984186	16	6262											
PCDH1	5097	hgsc.bcm.edu	37	chr5	141233645	141233645	+	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	cttggccgtctgggcagatgCcggtgtggctgcgggtggga	3	9	20	9	3	1	1	0	0	1	1	1	2	1	2	2	6	2	2	2	6	0	1			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr5:141233645C>G	ENST00000287008.3	-	5	3823	c.3676G>C	c.(3676-3678)Gca>Cca	p.A1226P	PCDH1_ENST00000503492.1_3'UTR	NM_032420.2	NP_115796.2	Q08174	PCDH1_HUMAN	protocadherin 1	0					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)		TGGGCAGATGCCGGTGTGGCT	0.667																																					p.A1226P	Ovarian(132;1609 1739 4190 14731 45037)	Atlas-SNP	.											PCDH1,NS,carcinoma,0,1	PCDH1	119	.	0			c.G3676C						PASS	.						24	31	29					5																	141233645		2203	4300	6503	SO:0001583	missense	5097	exon5			CAGATGCCGGTGT	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	ENST00000287008.3:c.3676G>C	chr5.hg19:g.141233645C>G	ENSP00000287008:p.Ala1226Pro	46.0	0.0	.		39.0	21.0	.	NM_032420	Q8IUP2	Missense_Mutation	SNP	ENST00000287008.3	hg19	CCDS4267.1	.	.	.	.	.	.	.	.	.	.	C	7.872	0.728354	0.15507	.	.	ENSG00000156453	ENST00000287008	T	0.53640	0.61	3.89	3.89	0.44902	.	.	.	.	.	T	0.28863	0.0716	N	0.14661	0.345	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.08554	-1.0716	9	0.34782	T	0.22	.	9.8085	0.40808	0.0:0.7904:0.2096:0.0	.	1226	Q08174-2	.	P	1226	ENSP00000287008:A1226P	ENSP00000287008:A1226P	A	-	1	0	PCDH1	141213829	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	2.372000	0.44257	2.457000	0.83068	0.462000	0.41574	GCA	.	.	.	none		0.667	PCDH1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320587.2	NM_032420		G	141233645	C	G	141233645	3	3	99	1	0	0	0	0	1	0	0	0	11513	739	26	4	41	4	PCDH1	5	141233645	Missense_Mutation	SNP	C	TCGA-B9-4617-01A-01D-1252-08	70302571	141233645	39681615	17	6263											
SLIT3	6586	hgsc.bcm.edu	37	chr5	168135045	168135045	+	Frame_Shift_Del	DEL	T	T	-																															cctgggtgcatgtcccgttaTtcttgcacgggctggagagg																										TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr5:168135045delT	ENST00000519560.1	-	26	3199	c.2780delA	c.(2779-2781)aatfs	p.N928fs	SLIT3_ENST00000404867.3_Frame_Shift_Del_p.N928fs|CTC-558O2.1_ENST00000522615.1_RNA|CTC-558O2.1_ENST00000521870.1_RNA|SLIT3_ENST00000332966.8_Frame_Shift_Del_p.N935fs	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	928	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TGTCCCGTTATTCTTGCACGG	0.592																																					p.N934fs	Ovarian(29;311 847 10864 17279 24903)	Atlas-INDEL	.											.	SLIT3	224	.	0			c.2802delT						PASS	.						157	113	128					5																	168135045		2203	4300	6503	SO:0001589	frameshift_variant	6586	exon26			.	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.2780delA	chr5.hg19:g.168135045delT	ENSP00000430333:p.Asn928fs	117.0	0.0	0		100.0	48.0	0.48	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Frame_Shift_Del	DEL	ENST00000519560.1	hg19	CCDS4369.1																																																																																			.	.	.	none		0.592	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062		-	168135045	T	-	168135045	7	5	99	1	0	1	0	1	0	0	0	0	14754	1493	52	0	1835	0	SLIT3	5	168135045	Frame_Shift_Del	DEL	T	TCGA-B9-4617-01A-01D-1252-08	26901400	168135045	12780215	18	6264											
SNRNP48	154007	hgsc.bcm.edu	37	chr6	7601644	7601644	+	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	tgatctaactcaagctgatcGtcttgccctctatgatttcg	8	15	7	11	2	4	3	1	3	3	0	6	3	4	3	1	0	3	1	1	0	3	4	rs143226311	byFrequency	TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr6:7601644G>C	ENST00000342415.5	+	5	541	c.482G>C	c.(481-483)cGt>cCt	p.R161P		NM_152551.3	NP_689764.3	Q6IEG0	SNR48_HUMAN	small nuclear ribonucleoprotein 48kDa (U11/U12)	161					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	U12-type spliceosomal complex (GO:0005689)	metal ion binding (GO:0046872)			kidney(2)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	10						CAAGCTGATCGTCTTGCCCTC	0.368																																					p.R161P		Atlas-SNP	.											.	SNRNP48	32	.	0			c.G482C						PASS	.						116	112	114					6																	7601644		2203	4300	6503	SO:0001583	missense	154007	exon5			CTGATCGTCTTGC	AK056796	CCDS4502.1	6p24.3	2011-10-11	2008-10-29	2008-10-29	ENSG00000168566	ENSG00000168566			21368	protein-coding gene	gene with protein product	"U11/U12 snRNP 48K"		"chromosome 6 open reading frame 151"	C6orf151		15146077	Standard	XR_427825		Approved	FLJ32234, dJ512B11.2, dJ336K20B.1	uc003mxr.3	Q6IEG0	OTTHUMG00000014213	ENST00000342415.5:c.482G>C	chr6.hg19:g.7601644G>C	ENSP00000339834:p.Arg161Pro	228.0	0.0	.		174.0	63.0	.	NM_152551	A8K8P4|Q14C91|Q5T339|Q5THM1|Q5THM2|Q96MK1	Missense_Mutation	SNP	ENST00000342415.5	hg19	CCDS4502.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.334843	0.81801	.	.	ENSG00000168566	ENST00000342415	T	0.50548	0.74	5.95	5.08	0.68730	.	0.000000	0.85682	D	0.000000	T	0.62962	0.2471	M	0.82323	2.585	0.54753	D	0.999982	D	0.89917	1.0	D	0.85130	0.997	T	0.70916	-0.4742	10	0.87932	D	0	-15.5175	12.6775	0.56903	0.0793:0.0:0.9207:0.0	.	161	Q6IEG0	SNR48_HUMAN	P	161	ENSP00000339834:R161P	ENSP00000339834:R161P	R	+	2	0	SNRNP48	7546643	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	8.383000	0.90157	1.520000	0.48965	0.491000	0.48974	CGT	.	G|1.000;A|0.000	.	alt		0.368	SNRNP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039787.3	NM_152551		C	7601644	G	C	7601644	3	2	99	1	0	0	0	0	1	0	0	0	14870	1145	40	4	500	4	SNRNP48	6	7601644	Missense_Mutation	SNP	G	TCGA-B9-4617-01A-01D-1252-08		7601644	163513423	19	6265											
OR2B3	442184	hgsc.bcm.edu	37	chr6	29054989	29054989	+	Missense_Mutation	SNP	T	T	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	atctgagaagccaagtagtaTaaactcttttggggagctct	12	12	10	7	0	3	1	0	1	3	1	3	3	3	2	1	2	3	3	1	2	6	5	rs139090624		TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr6:29054989T>G	ENST00000377173.2	-	1	101	c.37A>C	c.(37-39)Ata>Cta	p.I13L		NM_001005226.2	NP_001005226.1	O76000	OR2B3_HUMAN	olfactory receptor, family 2, subfamily B, member 3	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(1)|kidney(2)|lung(17)|prostate(1)|skin(2)	24						CCAAGTAGTATAAACTCTTTT	0.373																																					p.I13L		Atlas-SNP	.											.	OR2B3	44	.	0			c.A37C						PASS	.						67	67	67					6																	29054989		2203	4300	6503	SO:0001583	missense	442184	exon1			GTAGTATAAACTC		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.37A>C	chr6.hg19:g.29054989T>G	ENSP00000366378:p.Ile13Leu	102.0	0.0	.		107.0	45.0	.	NM_001005226	B0UYQ1|Q5ST41|Q96R13	Missense_Mutation	SNP	ENST00000377173.2	hg19	CCDS34358.1	.	.	.	.	.	.	.	.	.	.	T	5.503	0.277866	0.10403	.	.	ENSG00000204703	ENST00000377173	T	0.00873	5.59	3.37	2.19	0.27852	.	0.523945	0.15199	U	0.275147	T	0.00412	0.0013	L	0.50993	1.605	0.09310	N	1	B	0.22003	0.063	B	0.23716	0.048	T	0.46775	-0.9167	10	0.42905	T	0.14	.	5.2242	0.15385	0.0:0.104:0.3105:0.5855	.	13	O76000	OR2B3_HUMAN	L	13	ENSP00000366378:I13L	ENSP00000366378:I13L	I	-	1	0	OR2B3	29162968	0.045000	0.20229	0.611000	0.29010	0.205000	0.24178	-0.114000	0.10757	0.370000	0.24538	-0.396000	0.06452	ATA	.	T|1.000;C|0.000	.	alt		0.373	OR2B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076469.2			G	29054989	T	G	29054989	3	3	99	1	0	0	0	0	1	0	0	0	10997	1406	49	5	908	5	OR2B3	6	29054989	Missense_Mutation	SNP	T	TCGA-B9-4617-01A-01D-1252-08	21453345	29054989	142060078	20	6266											
CDK13	8621	hgsc.bcm.edu	37	chr7	40127807	40127807	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggcatgactgatgatgttTccacaattaaagcccccagg	11	10	10	10	0	0	3	0	3	0	0	1	3	1	3	3	2	1	2	3	2	3	2			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr7:40127807T>C	ENST00000181839.4	+	12	3717	c.3112T>C	c.(3112-3114)Tcc>Ccc	p.S1038P	CDK13_ENST00000340829.5_Missense_Mutation_p.S1038P	NM_003718.4|NM_031267.3	NP_003709.3|NP_112557.2	Q14004	CDK13_HUMAN	cyclin-dependent kinase 13	1038					alternative mRNA splicing, via spliceosome (GO:0000380)|hemopoiesis (GO:0030097)|multicellular organismal development (GO:0007275)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|positive regulation of cell proliferation (GO:0008284)|regulation of mitosis (GO:0007088)|viral process (GO:0016032)	cyclin K-CDK13 complex (GO:0002945)|extracellular space (GO:0005615)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(2)|prostate(2)|skin(5)|stomach(2)|urinary_tract(1)	49						TGATGATGTTTCCACAATTAA	0.453																																					p.S1038P		Atlas-SNP	.											.	CDK13	114	.	0			c.T3112C						PASS	.						90	87	88					7																	40127807		2203	4300	6503	SO:0001583	missense	8621	exon12			GATGTTTCCACAA	M80629	CCDS5461.1, CCDS5462.1	7p14.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000065883	ENSG00000065883		"Cyclin-dependent kinases"	1733	protein-coding gene	gene with protein product	"cholinesterase-related cell division controller"	603309	"cell division cycle 2-like 5 (cholinesterase-related cell division controller)"	CDC2L5		1731328, 19884882	Standard	NM_003718		Approved	CHED, CDC2L, KIAA1791	uc003thh.4	Q14004	OTTHUMG00000023726	ENST00000181839.4:c.3112T>C	chr7.hg19:g.40127807T>C	ENSP00000181839:p.Ser1038Pro	105.0	0.0	.		208.0	97.0	.	NM_003718	Q53G78|Q6DKQ9|Q75MH4|Q75MH5|Q96JN4|Q9H4A0|Q9H4A1|Q9UDR4	Missense_Mutation	SNP	ENST00000181839.4	hg19	CCDS5461.1	.	.	.	.	.	.	.	.	.	.	T	8.629	0.893231	0.17613	.	.	ENSG00000065883	ENST00000181839;ENST00000340829	T;T	0.34472	1.36;1.36	5.56	5.56	0.83823	.	.	.	.	.	T	0.21347	0.0514	N	0.04090	-0.28	0.28827	N	0.897359	P;B	0.41265	0.744;0.069	B;B	0.44044	0.439;0.014	T	0.05162	-1.0902	8	.	.	.	-7.2605	9.3088	0.37891	0.2509:0.0:0.0:0.7491	.	1038;1038	Q14004-2;Q14004	.;CDK13_HUMAN	P	1038	ENSP00000181839:S1038P;ENSP00000340557:S1038P	.	S	+	1	0	CDK13	40094332	1.000000	0.71417	1.000000	0.80357	0.728000	0.41692	3.739000	0.55075	2.250000	0.74265	0.477000	0.44152	TCC	.	.	.	none		0.453	CDK13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250726.2	NM_003718		C	40127807	T	C	40127807	3	2	99	1	0	0	0	0	1	0	0	0	3131	1783	62	3	3158	3	CDK13	7	40127807	Missense_Mutation	SNP	T	TCGA-B9-4617-01A-01D-1252-08		40127807	119010856	21	6267											
CUX1	1523	hgsc.bcm.edu	37	chr7	101837159	101837159	+	Missense_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	agtttgcaccgtccgagggcGctgggacacaggtacgtgtc	7	8	15	11	4	0	0	0	0	0	0	2	2	1	1	2	3	2	4	2	3	1	2			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr7:101837159G>A	ENST00000292535.7	+	13	1152	c.1114G>A	c.(1114-1116)Gct>Act	p.A372T	CUX1_ENST00000547394.2_Missense_Mutation_p.A367T|CUX1_ENST00000425244.2_Missense_Mutation_p.A337T|CUX1_ENST00000556210.1_Missense_Mutation_p.A372T|CUX1_ENST00000292538.4_Missense_Mutation_p.A383T|CUX1_ENST00000393824.3_Missense_Mutation_p.A344T|CUX1_ENST00000550008.2_Missense_Mutation_p.A372T|SNORA48_ENST00000517015.1_RNA|CUX1_ENST00000437600.4_Missense_Mutation_p.A381T|CUX1_ENST00000360264.3_Missense_Mutation_p.A383T|CUX1_ENST00000549414.2_Missense_Mutation_p.A372T|CUX1_ENST00000560541.1_3'UTR|CUX1_ENST00000546411.2_Missense_Mutation_p.A372T	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	372					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						GTCCGAGGGCGCTGGGACACA	0.517																																					p.A383T		Atlas-SNP	.											.	CUX1	253	.	0			c.G1147A						PASS	.						81	68	73					7																	101837159		2203	4300	6503	SO:0001583	missense	1523	exon13			GAGGGCGCTGGGA	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.1114G>A	chr7.hg19:g.101837159G>A	ENSP00000292535:p.Ala372Thr	84.0	0.0	.		100.0	58.0	.	NM_001202543	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000292535.7	hg19	CCDS5721.1	.	.	.	.	.	.	.	.	.	.	G	16.57	3.161274	0.57368	.	.	ENSG00000257923	ENST00000292538;ENST00000547394;ENST00000360264;ENST00000425244;ENST00000437600;ENST00000292535;ENST00000549414;ENST00000550008;ENST00000546411;ENST00000556210	T;T;T;T;T;T;T;T;T;T	0.60797	1.36;1.36;0.17;1.35;1.36;0.17;0.18;0.18;0.16;0.16	5.71	3.92	0.45320	.	0.260144	0.32918	N	0.005499	T	0.28433	0.0703	N	0.04018	-0.295	0.45318	D	0.998318	B;B;B;B;B;B;B	0.32071	0.021;0.004;0.01;0.355;0.017;0.103;0.007	B;B;B;B;B;B;B	0.24006	0.004;0.001;0.005;0.05;0.007;0.017;0.004	T	0.08534	-1.0717	10	0.42905	T	0.14	-7.0079	5.9431	0.19203	0.1559:0.0:0.5972:0.2469	.	344;372;337;367;381;383;383	B4DZZ2;P39880;B3KV79;G3V1Z6;Q13948-2;Q13948;P39880-3	.;CUX1_HUMAN;.;.;.;CASP_HUMAN;.	T	383;367;383;337;381;372;372;372;372;372	ENSP00000292538:A383T;ENSP00000449371:A367T;ENSP00000353401:A383T;ENSP00000409745:A337T;ENSP00000414091:A381T;ENSP00000292535:A372T;ENSP00000446630:A372T;ENSP00000447373:A372T;ENSP00000450125:A372T;ENSP00000451558:A372T	ENSP00000292535:A372T	A	+	1	0	CUX1	101623879	0.969000	0.33509	0.996000	0.52242	0.920000	0.55202	1.299000	0.33424	0.775000	0.33450	0.561000	0.74099	GCT	.	.	.	none		0.517	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913		A	101837159	G	A	101837159	3	1	99	1	0	0	0	0	1	0	0	0	4066	1087	38	1	1231	1	CUX1	7	101837159	Missense_Mutation	SNP	G	TCGA-B9-4617-01A-01D-1252-08	61709352	101837159	57301504	22	6268											
SLC13A1	6561	hgsc.bcm.edu	37	chr7	122774491	122774491	+	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	ctaggaaaagccactgaagcCagatccaggataagagtaga	17	5	11	8	0	0	4	0	1	0	3	1	6	1	6	3	2	2	1	3	2	6	3			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr7:122774491C>G	ENST00000194130.2	-	8	944	c.905G>C	c.(904-906)tGg>tCg	p.W302S	SLC13A1_ENST00000539873.1_3'UTR	NM_022444.3	NP_071889.2	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 1	302					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)	CCACTGAAGCCAGATCCAGGA	0.418																																					p.W302S		Atlas-SNP	.											.	SLC13A1	110	.	0			c.G905C						PASS	.						126	107	114					7																	122774491		2203	4300	6503	SO:0001583	missense	6561	exon8			TGAAGCCAGATCC		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.905G>C	chr7.hg19:g.122774491C>G	ENSP00000194130:p.Trp302Ser	88.0	0.0	.		156.0	72.0	.	NM_022444	Q9H5Z0	Missense_Mutation	SNP	ENST00000194130.2	hg19	CCDS5786.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.154544	0.78114	.	.	ENSG00000081800	ENST00000194130	T	0.02974	4.09	6.04	6.04	0.98038	.	0.106696	0.64402	D	0.000001	T	0.17109	0.0411	M	0.79343	2.45	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.00002	-1.2618	10	0.72032	D	0.01	-10.0465	18.0887	0.89466	0.0:1.0:0.0:0.0	.	302;302	A4D0X1;Q9BZW2	.;S13A1_HUMAN	S	302	ENSP00000194130:W302S	ENSP00000194130:W302S	W	-	2	0	SLC13A1	122561727	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.962000	0.70364	2.873000	0.98535	0.563000	0.77884	TGG	.	.	.	none		0.418	SLC13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347404.1	NM_022444		G	122774491	C	G	122774491	3	3	99	1	0	0	0	0	1	0	0	0	14404	595	21	4	914	4	SLC13A1	7	122774491	Missense_Mutation	SNP	C	TCGA-B9-4617-01A-01D-1252-08	20937332	122774491	36364172	23	6269											
ALDOB	229	hgsc.bcm.edu	37	chr9	104190767	104190770	+	Frame_Shift_Del	DEL	TTTG	TTTG	-																															ttaccttgaatggtggtttcTttgtttgttcctgcaagagg																								rs387906225		TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	TTTG	TTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr9:104190767_104190770delTTTG	ENST00000374855.4	-	4	484_487	c.360_363delCAAA	c.(358-363)aacaaafs	p.NK120fs	ALDOB_ENST00000468981.3_Intron	NM_000035.3	NP_000026.2	P05062	ALDOB_HUMAN	aldolase B, fructose-bisphosphate	120			Missing (in HFI). {ECO:0000269|PubMed:15532022}.		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)				TGGTGGTTTCTTTGTTTGTTCCTG	0.402																																					p.121_122del		Atlas-INDEL	.											.	ALDOB	69	.	0			c.361_364del	GRCh37	CD900270	ALDOB	D		PASS	.			0,4264		0,0,2132						5.9	1			251	1,8253		0,1,4126	no	frameshift	ALDOB	NM_000035.3		0,1,6258	A1A1,A1R,RR		0.0121,0.0,0.0080				1,12517				SO:0001589	frameshift_variant	229	exon4			.	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.360_363delCAAA	chr9.hg19:g.104190771_104190774delTTTG	ENSP00000363988:p.Asn120fs	335.0	0.0	0		283.0	104.0	0.367491	NM_000035	Q13741|Q13742|Q5T7D6	Frame_Shift_Del	DEL	ENST00000374855.4	hg19	CCDS6756.1																																																																																			.	.	.	none		0.402	ALDOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053434.2			-	104190770	TTTG	-	104190767	7	5	99	1	0	1	0	1	0	0	0	0	508	1606	56	0	755	0	ALDOB	9	104190767	Frame_Shift_Del	DEL	TTTG	TCGA-B9-4617-01A-01D-1252-08		104190767	37022664	24	6270											
MYST4	23522	hgsc.bcm.edu	37	chr10	76602897	76602897	+	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	tttcctaagtcagccaagggGtctagaggatcatgtaatga	12	11	11	7	0	3	2	2	1	1	1	4	3	4	3	2	3	1	1	2	3	4	4	rs569038847	byFrequency	TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr10:76602897G>T	ENST00000287239.4	+	3	771	c.282G>T	c.(280-282)ggG>ggT	p.G94G	KAT6B_ENST00000372724.1_Silent_p.G94G|KAT6B_ENST00000372711.1_Silent_p.G94G|KAT6B_ENST00000372725.1_Silent_p.G94G|KAT6B_ENST00000372714.1_Silent_p.G94G	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	94					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										CAGCCAAGGGGTCTAGAGGAT	0.473																																					p.G94G		Atlas-SNP	.											.	.	.	.	0			c.G282T						PASS	.						110	115	114					10																	76602897		2203	4300	6503	SO:0001819	synonymous_variant	23522	exon3			CAAGGGGTCTAGA	AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.282G>T	chr10.hg19:g.76602897G>T		347.0	0.0	.		467.0	142.0	.	NM_001256469	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Silent	SNP	ENST00000287239.4	hg19	CCDS7345.1																																																																																			.	.	.	none		0.473	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		T	76602897	G	T	76602897	2	4	99	1	0	0	0	0	0	0	0	1	10112	1248	44	4		4	MYST4	10	76602897	Silent	SNP	G	TCGA-B9-4617-01A-01D-1252-08		76602897	58931850	25	6271											
LRP4	4038	hgsc.bcm.edu	37	chr11	46897384	46897384	+	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	ggcatcggcccatagcagttGggagctggccttgtccacag	7	8	14	12	1	0	0	0	0	0	0	2	1	1	1	3	4	2	4	3	4	1	3			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr11:46897384G>A	ENST00000378623.1	-	26	3912	c.3670C>T	c.(3670-3672)Caa>Taa	p.Q1224*	LRP4-AS1_ENST00000531719.1_RNA|LRP4-AS1_ENST00000502049.2_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1224					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)		CATAGCAGTTGGGAGCTGGCC	0.602																																					p.Q1224X		Atlas-SNP	.											.	LRP4	160	.	0			c.C3670T						PASS	.						117	87	97					11																	46897384		2201	4299	6500	SO:0001587	stop_gained	4038	exon26			GCAGTTGGGAGCT	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.3670C>T	chr11.hg19:g.46897384G>A	ENSP00000367888:p.Gln1224*	108.0	0.0	.		101.0	40.0	.	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Nonsense_Mutation	SNP	ENST00000378623.1	hg19	CCDS31478.1	.	.	.	.	.	.	.	.	.	.	G	43	10.368400	0.99392	.	.	ENSG00000134569	ENST00000378623	.	.	.	5.71	5.71	0.89125	.	0.058544	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.23302	T	0.38	.	19.8574	0.96764	0.0:0.0:1.0:0.0	.	.	.	.	X	1224	.	ENSP00000367888:Q1224X	Q	-	1	0	LRP4	46853960	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.670000	0.83925	2.704000	0.92352	0.555000	0.69702	CAA	.	.	.	none		0.602	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334		A	46897384	G	A	46897384	4	1	99	1	0	0	0	0	0	1	0	0	8966	1357	47	2	2099	2	LRP4	11	46897384	Nonsense_Mutation	SNP	G	TCGA-B9-4617-01A-01D-1252-08		46897384	88109132	26	6272											
OR5I1	10798	hgsc.bcm.edu	37	chr11	55703836	55703836	+	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	ttggaaaacctaatagaataAactcagtgaccaacgtgtag	17	9	8	7	1	1	2	1	1	0	1	1	3	1	3	2	1	3	1	2	1	9	5			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr11:55703836A>T	ENST00000301532.3	-	1	40	c.41T>A	c.(40-42)tTt>tAt	p.F14Y		NM_006637.1	NP_006628.1	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I, member 1	14					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						TAATAGAATAAACTCAGTGAC	0.358																																					p.F14Y		Atlas-SNP	.											.	OR5I1	110	.	0			c.T41A						PASS	.						50	49	49					11																	55703836		2201	4293	6494	SO:0001583	missense	10798	exon1			AGAATAAACTCAG	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.41T>A	chr11.hg19:g.55703836A>T	ENSP00000301532:p.Phe14Tyr	88.0	0.0	.		85.0	34.0	.	NM_006637	Q6IEU4	Missense_Mutation	SNP	ENST00000301532.3	hg19	CCDS7949.1	.	.	.	.	.	.	.	.	.	.	A	16.89	3.246108	0.59103	.	.	ENSG00000167825	ENST00000301532	T	0.04360	3.64	5.05	5.05	0.67936	.	0.000000	0.48767	D	0.000175	T	0.27027	0.0662	M	0.92412	3.305	0.35686	D	0.814491	D	0.63880	0.993	D	0.67548	0.952	T	0.50566	-0.8813	10	0.72032	D	0.01	.	13.0502	0.58950	1.0:0.0:0.0:0.0	.	14	Q13606	OR5I1_HUMAN	Y	14	ENSP00000301532:F14Y	ENSP00000301532:F14Y	F	-	2	0	OR5I1	55460412	1.000000	0.71417	0.960000	0.40013	0.238000	0.25445	8.249000	0.89833	2.020000	0.59435	0.519000	0.50382	TTT	.	.	.	none		0.358	OR5I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391528.1	NM_006637		T	55703836	A	T	55703836	3	4	99	1	0	0	0	0	1	0	0	0	11171	14	1	5	906	5	OR5I1	11	55703836	Missense_Mutation	SNP	A	TCGA-B9-4617-01A-01D-1252-08	8806452	55703836	79302680	27	6273											
RBM4	5936	hgsc.bcm.edu	37	chr11	66411450	66411450	+	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	cggagccccctgcgtcgcgcTacagccccagtccccactgt	5	6	10	20	4	0	0	0	0	0	0	2	1	1	1	6	1	4	1	6	1	1	1			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr11:66411450T>A	ENST00000409406.1	+	2	1719	c.942T>A	c.(940-942)gcT>gcA	p.A314A	RBM14-RBM4_ENST00000412278.2_Silent_p.A289A|RBM4_ENST00000398692.4_Intron|RBM4_ENST00000578778.1_Intron|RBM4_ENST00000506523.2_Intron|RBM4_ENST00000408993.2_Silent_p.A314A|RBM4_ENST00000515838.2_3'UTR|RBM4_ENST00000530235.1_Intron|RBM4_ENST00000310092.7_Silent_p.A314A|RBM4_ENST00000514361.3_Silent_p.A289A|RBM14-RBM4_ENST00000500635.2_Intron|RBM4_ENST00000503028.2_Silent_p.A314A|RBM4_ENST00000396053.4_Intron			Q9BWF3	RBM4_HUMAN	RNA binding motif protein 4	314	Interaction with TNPO3.				cap-independent translational initiation (GO:0002190)|cell differentiation (GO:0030154)|circadian regulation of translation (GO:0097167)|entrainment of circadian clock by photoperiod (GO:0043153)|IRES-dependent translational initiation (GO:0002192)|mRNA processing (GO:0006397)|negative regulation of translation (GO:0017148)|negative regulation of translation in response to stress (GO:0032055)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of nucleocytoplasmic transport (GO:0046822)|response to arsenic-containing substance (GO:0046685)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|stress-activated MAPK cascade (GO:0051403)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	miRNA binding (GO:0035198)|mRNA 3'-UTR binding (GO:0003730)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA intronic binding (GO:0097157)|pre-mRNA intronic pyrimidine-rich binding (GO:0097158)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(4)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13				Lung(977;0.0112)|LUSC - Lung squamous cell carcinoma(976;0.0266)		TGCGTCGCGCTACAGCCCCAG	0.617																																					p.A314A		Atlas-SNP	.											.	RBM4	34	.	0			c.T942A						PASS	.						47	52	50					11																	66411450		2091	4236	6327	SO:0001819	synonymous_variant	5936	exon3			TCGCGCTACAGCC	U89505	CCDS41676.1, CCDS55776.1, CCDS55777.1	11q13	2013-02-12			ENSG00000173933	ENSG00000173933		"Zinc fingers, CCHC domain containing", "RNA binding motif (RRM) containing"	9901	protein-coding gene	gene with protein product		602571				9169144, 16260624	Standard	NM_002896		Approved	LARK, RBM4A, ZCRB3A, ZCCHC21		Q9BWF3	OTTHUMG00000154171	ENST00000409406.1:c.942T>A	chr11.hg19:g.66411450T>A		136.0	0.0	.		161.0	59.0	.	NM_002896	B3KUN0|B4E1U0|E7EQS3|O02916|Q4VC48|Q6P1P2|Q8WU85	Silent	SNP	ENST00000409406.1	hg19	CCDS41676.1																																																																																			.	.	.	none		0.617	RBM4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334212.1	NM_002896		A	66411450	T	A	66411450	2	1	99	1	0	0	0	0	0	0	0	1	13147	1509	53	5		5	RBM4	11	66411450	Silent	SNP	T	TCGA-B9-4617-01A-01D-1252-08	10707614	66411450	68595066	28	6274											
PCF11	51585	hgsc.bcm.edu	37	chr11	82877725	82877725	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaagttccaagtctgccaaaAgatggaaatctggttgggaa	15	9	11	6	0	2	1	0	0	2	1	3	3	3	3	2	3	1	2	2	3	6	2			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr11:82877725A>G	ENST00000298281.4	+	5	2238	c.1786A>G	c.(1786-1788)Aga>Gga	p.R596G		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	596					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)		p.R695R(1)|p.R596R(1)		cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						GTCTGCCAAAAGATGGAAATC	0.348																																					p.R596G		Atlas-SNP	.											PCF11_ENST00000298281,bladder,carcinoma,0,2	PCF11	220	.	2	Substitution - coding silent(2)	urinary_tract(2)	c.A1786G						PASS	.						73	75	74					11																	82877725		1759	3852	5611	SO:0001583	missense	51585	exon5			GCCAAAAGATGGA	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.1786A>G	chr11.hg19:g.82877725A>G	ENSP00000298281:p.Arg596Gly	166.0	0.0	.		154.0	72.0	.	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	hg19	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	A	15.47	2.844048	0.51164	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.68903	0.49;-0.36;-0.17	6.07	-0.732	0.11147	.	0.000000	0.64402	D	0.000005	T	0.71099	0.3300	L	0.34521	1.04	0.41136	D	0.985927	D;D	0.76494	0.999;0.999	D;D	0.78314	0.991;0.991	T	0.67280	-0.5710	9	.	.	.	.	17.6867	0.88258	0.3868:0.6132:0.0:0.0	.	596;596	E9PQ01;O94913	.;PCF11_HUMAN	G	596	ENSP00000298281:R596G;ENSP00000434540:R596G;ENSP00000431567:R596G	.	R	+	1	2	PCF11	82555373	0.996000	0.38824	0.972000	0.41901	0.993000	0.82548	0.572000	0.23684	-0.360000	0.08138	-0.316000	0.08728	AGA	.	.	.	none		0.348	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		G	82877725	A	G	82877725	3	3	99	1	0	0	0	0	1	0	0	0	11580	64	3	3	1804	3	PCF11	11	82877725	Missense_Mutation	SNP	A	TCGA-B9-4617-01A-01D-1252-08	16466275	82877725	52128791	29	6275											
C11orf65	160140	hgsc.bcm.edu	37	chr11	108276173	108276173	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tacatttgcctcatccactcTatttttctaagttttctttt	7	22	2	10	0	4	0	1	0	3	0	5	0	5	0	2	0	2	1	2	0	3	10			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr11:108276173T>C	ENST00000529391.1	-	5	552	c.543A>G	c.(541-543)atA>atG	p.I181M	C11orf65_ENST00000525729.1_Missense_Mutation_p.I132M|C11orf65_ENST00000393084.1_Missense_Mutation_p.I181M|C11orf65_ENST00000526725.1_5'UTR			Q8NCR3	CK065_HUMAN	chromosome 11 open reading frame 65	181										endometrium(1)|large_intestine(3)|lung(4)|ovary(2)	10		all_cancers(61;1.38e-11)|all_epithelial(67;3.16e-07)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;8.21e-06)|BRCA - Breast invasive adenocarcinoma(274;1.01e-05)|all cancers(92;0.000189)|Colorectal(284;0.114)|OV - Ovarian serous cystadenocarcinoma(223;0.144)		TCATCCACTCTATTTTTCTAA	0.338																																					p.I181M		Atlas-SNP	.											.	C11orf65	29	.	0			c.A543G						PASS	.						126	123	124					11																	108276173		2200	4298	6498	SO:0001583	missense	160140	exon6			CCACTCTATTTTT	BC059411	CCDS8340.1	11q22.3	2012-05-30			ENSG00000166323	ENSG00000166323			28519	protein-coding gene	gene with protein product						12477932	Standard	NM_152587		Approved	MGC33948	uc001pkh.3	Q8NCR3	OTTHUMG00000166489	ENST00000529391.1:c.543A>G	chr11.hg19:g.108276173T>C	ENSP00000436400:p.Ile181Met	98.0	0.0	.		107.0	49.0	.	NM_152587	B4DZU4|Q6PCA8	Missense_Mutation	SNP	ENST00000529391.1	hg19	CCDS8340.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.26|15.26	2.780994|2.780994	0.49891|0.49891	.|.	.|.	ENSG00000166323|ENSG00000166323	ENST00000525729;ENST00000529391;ENST00000393084;ENST00000533583|ENST00000524755	T;T;T;T|.	0.34859|.	1.34;1.34;1.34;1.34|.	5.18|5.18	2.62|2.62	0.31277|0.31277	.|.	0.055200|.	0.64402|.	D|.	0.000002|.	T|.	0.50051|.	0.1593|.	M|M	0.68593|0.68593	2.085|2.085	0.31954|0.31954	N|N	0.609249|0.609249	D;D|.	0.67145|.	0.971;0.996|.	P;D|.	0.67548|.	0.839;0.952|.	T|.	0.56619|.	-0.7949|.	10|.	0.62326|.	D|.	0.03|.	-23.4088|-23.4088	5.4186|5.4186	0.16388|0.16388	0.3028:0.0:0.1462:0.551|0.3028:0.0:0.1462:0.551	.|.	132;181|.	B4DZU4;Q8NCR3|.	.;CK065_HUMAN|.	M|W	132;181;181;163|13	ENSP00000433395:I132M;ENSP00000436400:I181M;ENSP00000376799:I181M;ENSP00000434500:I163M|.	ENSP00000376799:I181M|.	I|X	-|-	3|2	3|0	C11orf65|C11orf65	107781383|107781383	0.996000|0.996000	0.38824|0.38824	1.000000|1.000000	0.80357|0.80357	0.960000|0.960000	0.62799|0.62799	0.888000|0.888000	0.28268|0.28268	0.865000|0.865000	0.35603|0.35603	0.460000|0.460000	0.39030|0.39030	ATA|TAG	.	.	.	none		0.338	C11orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390010.3	NM_152587		C	108276173	T	C	108276173	3	2	99	1	0	0	0	0	1	0	0	0	1657	1512	53	3	414	3	C11orf65	11	108276173	Missense_Mutation	SNP	T	TCGA-B9-4617-01A-01D-1252-08	25398448	108276173	26730343	30	6276											
PRH1	5554	hgsc.bcm.edu	37	chr12	11035282	11035282	+	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	gctcctcatctaggaactgcTcagagtctcctccatctgtg	7	12	8	14	0	5	1	2	0	3	1	8	2	7	2	3	1	2	2	3	1	2	1			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr12:11035282T>A	ENST00000428168.2	-	3	153	c.116A>T	c.(115-117)gAg>gTg	p.E39V	PRR4_ENST00000536668.1_5'UTR	NM_006250.3	NP_006241.2	P02810	PRPC_HUMAN	proline-rich protein HaeIII subfamily 1	39	Inhibits hydroxyapatite formation, binds to hydroxyapatite and calcium.					extracellular space (GO:0005615)				endometrium(1)|kidney(1)|lung(2)|upper_aerodigestive_tract(1)	5				BRCA - Breast invasive adenocarcinoma(232;0.245)		TAGGAACTGCTCAGAGTCTCC	0.547																																					p.E39V		Atlas-SNP	.											.	PRH1	17	.	0			c.A116T						PASS	.						82	49	60					12																	11035282		2200	4286	6486	SO:0001583	missense	5554	exon3			AACTGCTCAGAGT			12p13.2	2013-05-10			ENSG00000231887	ENSG00000231887			9366	protein-coding gene	gene with protein product		168730				3009472	Standard	NM_001291314		Approved	Pa	uc021qvf.1	P02810		ENST00000428168.2:c.116A>T	chr12.hg19:g.11035282T>A	ENSP00000412436:p.Glu39Val	244.0	0.0	.		311.0	80.0	.	NM_006250	A2VCM0|A3KN66|A5D902|B2RMW2|Q4VBP2|Q53XA2|Q6P2F6	Missense_Mutation	SNP	ENST00000428168.2	hg19		.	.	.	.	.	.	.	.	.	.	T	9.894	1.205135	0.22205	.	.	ENSG00000231887	ENST00000428168	T	0.15487	2.42	1.5	-1.61	0.08399	.	.	.	.	.	T	0.15696	0.0378	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.30475	-0.9977	6	0.59425	D	0.04	.	4.6309	0.12500	0.0:0.3995:0.0:0.6005	.	.	.	.	V	39	ENSP00000412436:E39V	ENSP00000412436:E39V	E	-	2	0	PRH1	10926549	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.486000	0.02312	-0.466000	0.06943	0.459000	0.35465	GAG	.	.	.	none		0.547	PRH1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_006250		A	11035282	T	A	11035282	3	1	99	1	0	0	0	0	1	0	0	0	12492	1551	54	5	392	5	PRH1	12	11035282	Missense_Mutation	SNP	T	TCGA-B9-4617-01A-01D-1252-08		11035282	122816613	31	6277											
LRP6	4040	hgsc.bcm.edu	37	chr12	12317326	12317326	+	Missense_Mutation	SNP	T	T	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	attgtttgtttccagagaaaTtcgtctgatatctgctctcc	8	17	7	9	1	3	2	0	1	3	1	6	3	4	2	2	0	1	3	2	0	2	5			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr12:12317326T>G	ENST00000261349.4	-	9	2009	c.1933A>C	c.(1933-1935)Att>Ctt	p.I645L	LRP6_ENST00000543091.1_Missense_Mutation_p.I645L	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	645	Beta-propeller 3.				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)				TCCAGAGAAATTCGTCTGATA	0.418																																					p.I645L		Atlas-SNP	.											.	LRP6	170	.	0			c.A1933C						PASS	.						105	104	104					12																	12317326		2203	4300	6503	SO:0001583	missense	4040	exon9			GAGAAATTCGTCT	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.1933A>C	chr12.hg19:g.12317326T>G	ENSP00000261349:p.Ile645Leu	172.0	0.0	.		238.0	82.0	.	NM_002336	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	hg19	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	T	25.8	4.672125	0.88348	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.91180	-2.8;-2.8	5.65	5.65	0.86999	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000008	D	0.94228	0.8147	L	0.60455	1.87	0.80722	D	1	P;B	0.40066	0.701;0.236	D;P	0.64877	0.93;0.578	D	0.92901	0.6339	10	0.33940	T	0.23	.	16.1778	0.81874	0.0:0.0:0.0:1.0	.	645;645	F5H7J9;O75581	.;LRP6_HUMAN	L	645	ENSP00000261349:I645L;ENSP00000442472:I645L	ENSP00000261349:I645L	I	-	1	0	LRP6	12208593	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.222000	0.72249	2.279000	0.76181	0.533000	0.62120	ATT	.	.	.	none		0.418	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			G	12317326	T	G	12317326	3	3	99	1	0	0	0	0	1	0	0	0	8969	1493	52	5	2968	5	LRP6	12	12317326	Missense_Mutation	SNP	T	TCGA-B9-4617-01A-01D-1252-08	1282044	12317326	121534569	32	6278											
KRT85	3891	hgsc.bcm.edu	37	chr12	52756665	52756665	+	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	ttggcattctcaatctcggcCgtcagcctctggatcatgcg	6	12	10	13	3	5	0	3	0	3	0	7	1	5	1	2	3	2	1	2	3	1	2	rs1621938	byFrequency	TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr12:52756665C>G	ENST00000257901.3	-	6	1125	c.1050G>C	c.(1048-1050)acG>acC	p.T350T	KRT85_ENST00000544265.1_Silent_p.T138T	NM_002283.3	NP_002274.1	P78386	KRT85_HUMAN	keratin 85	350	Coil 2.|Rod.				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)		CAATCTCGGCCGTCAGCCTCT	0.587																																					p.T350T		Atlas-SNP	.											KRT85,caecum,carcinoma,0,1	KRT85	78	.	0			c.G1050C						PASS	.						147	120	129					12																	52756665		2203	4300	6503	SO:0001819	synonymous_variant	3891	exon6			CTCGGCCGTCAGC	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.1050G>C	chr12.hg19:g.52756665C>G		144.0	1.0	.		199.0	67.0	.	NM_002283	Q9NSB1	Silent	SNP	ENST00000257901.3	hg19	CCDS8824.1																																																																																			.	C|0.975;T|0.025	.	alt		0.587	KRT85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405184.1	NM_002283		G	52756665	C	G	52756665	2	3	99	1	0	0	0	0	0	0	0	1	8506	639	23	4		4	KRT85	12	52756665	Silent	SNP	C	TCGA-B9-4617-01A-01D-1252-08	40439339	52756665	81095230	33	6279											
DDX55	57696	hgsc.bcm.edu	37	chr12	124093348	124093348	+	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	tggtgttggatgaggcagacAgacttctggacatggggttt	8	12	16	5	0	1	3	0	1	1	2	1	5	1	5	0	6	0	3	0	6	0	3			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr12:124093348A>T	ENST00000238146.4	+	6	573	c.523A>T	c.(523-525)Aga>Tga	p.R175*	DDX55_ENST00000538744.1_Nonsense_Mutation_p.R175*	NM_020936.1	NP_065987.1	Q8NHQ9	DDX55_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	175	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)		TGAGGCAGACAGACTTCTGGA	0.537																																					p.R175X		Atlas-SNP	.											.	DDX55	51	.	0			c.A523T						PASS	.						140	127	132					12																	124093348		2203	4300	6503	SO:0001587	stop_gained	57696	exon6			GCAGACAGACTTC	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.523A>T	chr12.hg19:g.124093348A>T	ENSP00000238146:p.Arg175*	81.0	0.0	.		136.0	85.0	.	NM_020936	Q658L6|Q8IYH0|Q9HCH7	Nonsense_Mutation	SNP	ENST00000238146.4	hg19	CCDS9251.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.529924	0.85706	.	.	ENSG00000111364	ENST00000238146;ENST00000538449;ENST00000538744	.	.	.	5.56	0.428	0.16499	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-35.4688	10.2464	0.43343	0.5084:0.4032:0.0:0.0884	.	.	.	.	X	175	.	ENSP00000238146:R175X	R	+	1	2	DDX55	122659301	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	1.558000	0.36309	0.084000	0.17077	0.460000	0.39030	AGA	.	.	.	none		0.537	DDX55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400616.2			T	124093348	A	T	124093348	4	4	99	1	0	0	0	0	0	1	0	0	4375	180	7	5	545	5	DDX55	12	124093348	Nonsense_Mutation	SNP	A	TCGA-B9-4617-01A-01D-1252-08	71336683	124093348	9758547	34	6280											
FLJ10357	55701	hgsc.bcm.edu	37	chr14	21546590	21546590	+	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	ggcagatccccggctgacggCactgcagagggatggggggg	7	4	20	10	2	0	3	0	1	0	2	1	4	1	4	2	7	1	4	2	7	0	0			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr14:21546590C>G	ENST00000298694.4	+	10	2316	c.2189C>G	c.(2188-2190)gCa>gGa	p.A730G	ARHGEF40_ENST00000298693.3_Missense_Mutation_p.A730G			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	730						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						CGGCTGACGGCACTGCAGAGG	0.632																																					p.A730G		Atlas-SNP	.											.	ARHGEF40	84	.	0			c.C2189G						PASS	.						58	61	60					14																	21546590		2203	4300	6503	SO:0001583	missense	55701	exon10			TGACGGCACTGCA		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.2189C>G	chr14.hg19:g.21546590C>G	ENSP00000298694:p.Ala730Gly	238.0	0.0	.		168.0	44.0	.	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Missense_Mutation	SNP	ENST00000298694.4	hg19	CCDS32041.1	.	.	.	.	.	.	.	.	.	.	C	11.27	1.587748	0.28268	.	.	ENSG00000165801	ENST00000298694;ENST00000298693	T;T	0.02323	4.4;4.34	4.47	-0.131	0.13494	.	0.432236	0.19670	N	0.108771	T	0.01523	0.0049	N	0.14661	0.345	0.09310	N	1	B;B	0.22541	0.058;0.071	B;B	0.24155	0.051;0.048	T	0.47736	-0.9094	10	0.20046	T	0.44	.	3.5884	0.07979	0.4355:0.3333:0.0:0.2312	.	730;730	Q8TER5-4;Q8TER5	.;ARH40_HUMAN	G	730	ENSP00000298694:A730G;ENSP00000298693:A730G	ENSP00000298693:A730G	A	+	2	0	ARHGEF40	20616430	0.001000	0.12720	0.020000	0.16555	0.990000	0.78478	0.130000	0.15850	0.110000	0.17919	0.462000	0.41574	GCA	.	.	.	none		0.632	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1			G	21546590	C	G	21546590	3	3	99	1	0	0	0	0	1	0	0	0	5933	710	25	4	2227	4	FLJ10357	14	21546590	Missense_Mutation	SNP	C	TCGA-B9-4617-01A-01D-1252-08		21546590	85802950	35	6281											
ACIN1	22985	hgsc.bcm.edu	37	chr14	23564436	23564436	+	Missense_Mutation	SNP	A	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	ctgccatactctacccctcgAttaccactcagaactccccg	9	9	4	19	2	2	1	1	0	1	1	4	2	3	1	6	0	5	0	6	0	4	3			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr14:23564436A>C	ENST00000262710.1	-	1	387	c.60T>G	c.(58-60)aaT>aaG	p.N20K	ACIN1_ENST00000457657.1_Missense_Mutation_p.N20K|ACIN1_ENST00000605057.1_5'Flank|ACIN1_ENST00000555053.1_Missense_Mutation_p.N20K|C14orf119_ENST00000554203.1_5'Flank|C14orf119_ENST00000319074.4_5'UTR	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	20					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)		CTACCCCTCGATTACCACTCA	0.592																																					p.N20K		Atlas-SNP	.											.	ACIN1	147	.	0			c.T60G						PASS	.						98	98	98					14																	23564436		2203	4300	6503	SO:0001583	missense	22985	exon1			CCCTCGATTACCA	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.60T>G	chr14.hg19:g.23564436A>C	ENSP00000262710:p.Asn20Lys	240.0	0.0	.		196.0	90.0	.	NM_001164814	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Missense_Mutation	SNP	ENST00000262710.1	hg19	CCDS9587.1	.	.	.	.	.	.	.	.	.	.	A	19.37	3.814723	0.70912	.	.	ENSG00000100813	ENST00000262710;ENST00000457657;ENST00000555053	T;T;T	0.19806	2.36;2.12;2.36	5.45	4.3	0.51218	.	0.000000	0.38548	N	0.001657	T	0.15782	0.0380	N	0.08118	0	0.80722	D	1	P;P	0.48162	0.906;0.849	P;B	0.49192	0.602;0.398	T	0.04165	-1.0972	10	0.87932	D	0	-12.5512	10.7996	0.46480	0.8313:0.1687:0.0:0.0	.	20;20	G3V3M7;Q9UKV3	.;ACINU_HUMAN	K	20	ENSP00000262710:N20K;ENSP00000405677:N20K;ENSP00000451328:N20K	ENSP00000262710:N20K	N	-	3	2	ACIN1	22634276	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.665000	0.25083	2.288000	0.76882	0.482000	0.46254	AAT	.	.	.	none		0.592	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977		C	23564436	A	C	23564436	3	2	99	1	0	0	0	0	1	0	0	0	142	330	12	5	4188	5	ACIN1	14	23564436	Missense_Mutation	SNP	A	TCGA-B9-4617-01A-01D-1252-08	2017846	23564436	83785104	36	6282											
REC8	79711	hgsc.bcm.edu	37	chr14	24648037	24648037	+	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	gacccattgtgcccagccacCcccaaaagccctcaggcgag	10	4	9	18	1	1	0	1	0	0	0	1	2	1	0	6	1	3	0	6	1	2	1			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr14:24648037C>T	ENST00000354464.6	-	0	3646				REC8_ENST00000311457.3_Missense_Mutation_p.P372L|REC8_ENST00000559919.1_Missense_Mutation_p.P372L	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4						DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		GCCCAGCCACCCCCAAAAGCC	0.587																																					p.P372L		Atlas-SNP	.											.	REC8	47	.	0			c.C1115T						PASS	.						146	162	157					14																	24648037		1917	4120	6037	SO:0001628	intergenic_variant	9985	exon14			AGCCACCCCCAAA	AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"Importins"	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801		chr14.hg19:g.24648037C>T		450.0	0.0	.		448.0	185.0	.	NM_001048205	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Missense_Mutation	SNP	ENST00000354464.6	hg19	CCDS9616.1	.	.	.	.	.	.	.	.	.	.	C	17.63	3.436138	0.62955	.	.	ENSG00000100918	ENST00000311457;ENST00000447460	T	0.25085	1.82	5.18	4.29	0.51040	.	0.233366	0.37348	N	0.002138	T	0.19248	0.0462	L	0.34521	1.04	0.35201	D	0.774243	B;B	0.20887	0.049;0.029	B;B	0.20577	0.03;0.013	T	0.15178	-1.0446	10	0.40728	T	0.16	-11.8468	9.8882	0.41274	0.0:0.9069:0.0:0.0931	.	356;373	O95072-2;O95072	.;REC8_HUMAN	L	372;355	ENSP00000308699:P372L	ENSP00000308699:P372L	P	+	2	0	REC8	23717877	0.253000	0.23982	0.233000	0.24025	0.042000	0.13812	1.235000	0.32671	1.403000	0.46800	0.462000	0.41574	CCC	.	.	.	none		0.587	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658		T	24648037	C	T	24648037	1	4	99	0	1	0	0	0	0	0	0	0	13212	623	22	2		2	REC8	14	24648037	IGR	SNP	C	TCGA-B9-4617-01A-01D-1252-08	1083601	24648037	82701503	37	6283											
AKAP6	9472	hgsc.bcm.edu	37	chr14	33291241	33291241	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatgggagatgcagttaacGtgttaaagcaaaaatttaca	18	10	9	4	1	0	1	0	0	0	1	0	2	0	1	0	1	4	4	0	1	7	4	rs376840822		TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr14:33291241G>A	ENST00000280979.4	+	13	4392	c.4222G>A	c.(4222-4224)Gtg>Atg	p.V1408M	AKAP6_ENST00000557272.1_Intron	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	1408					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)		TGCAGTTAACGTGTTAAAGCA	0.438																																					p.V1408M	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.G4222A						PASS	.						72	70	71					14																	33291241		2203	4300	6503	SO:0001583	missense	9472	exon13			GTTAACGTGTTAA	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.4222G>A	chr14.hg19:g.33291241G>A	ENSP00000280979:p.Val1408Met	127.0	0.0	.		121.0	50.0	.	NM_004274	A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	hg19	CCDS9644.1	.	.	.	.	.	.	.	.	.	.	G	4.459	0.084949	0.08583	.	.	ENSG00000151320	ENST00000280979	T	0.07327	3.2	5.6	-2.53	0.06326	.	1.038410	0.07611	N	0.925352	T	0.06645	0.0170	L	0.27053	0.805	0.09310	N	1	B	0.23735	0.09	B	0.15870	0.014	T	0.39440	-0.9614	10	0.45353	T	0.12	0.19	11.7736	0.51972	0.494:0.0:0.506:0.0	.	1408	Q13023	AKAP6_HUMAN	M	1408	ENSP00000280979:V1408M	ENSP00000280979:V1408M	V	+	1	0	AKAP6	32360992	0.022000	0.18835	0.000000	0.03702	0.813000	0.45954	0.177000	0.16801	-0.393000	0.07739	-0.253000	0.11424	GTG	.	.	.	alt		0.438	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274		A	33291241	G	A	33291241	3	1	99	1	0	0	0	0	1	0	0	0	455	1145	40	1	4268	1	AKAP6	14	33291241	Missense_Mutation	SNP	G	TCGA-B9-4617-01A-01D-1252-08	8643204	33291241	74058299	38	6284											
ZC3H7A	29066	hgsc.bcm.edu	37	chr16	11859408	11859408	+	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	ttgaacacagtaaggttaatCtttccattgccgccaaagaa	14	11	7	9	1	1	2	0	1	1	1	2	2	2	2	3	1	2	2	3	1	5	5			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr16:11859408C>A	ENST00000396516.2	-	13	1853	c.1656G>T	c.(1654-1656)aaG>aaT	p.K552N	ZC3H7A_ENST00000355758.4_Missense_Mutation_p.K552N			Q8IWR0	Z3H7A_HUMAN	zinc finger CCCH-type containing 7A	552						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						TAAGGTTAATCTTTCCATTGC	0.453																																					p.K552N		Atlas-SNP	.											.	ZC3H7A	72	.	0			c.G1656T						PASS	.						95	95	95					16																	11859408		2197	4300	6497	SO:0001583	missense	29066	exon14			GTTAATCTTTCCA	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.1656G>T	chr16.hg19:g.11859408C>A	ENSP00000379773:p.Lys552Asn	186.0	0.0	.		246.0	72.0	.	NM_014153	D3DUG5|Q9NPE9	Missense_Mutation	SNP	ENST00000396516.2	hg19	CCDS10550.1	.	.	.	.	.	.	.	.	.	.	C	12.82	2.052633	0.36181	.	.	ENSG00000122299	ENST00000355758;ENST00000396516	T;T	0.11063	2.81;2.81	5.81	4.85	0.62838	.	0.088461	0.85682	D	0.000000	T	0.11665	0.0284	L	0.49126	1.545	0.80722	D	1	B;B	0.19445	0.036;0.001	B;B	0.20577	0.03;0.003	T	0.02933	-1.1092	10	0.49607	T	0.09	.	10.5495	0.45079	0.0:0.8534:0.0:0.1466	.	273;552	Q9NXC8;Q8IWR0	.;Z3H7A_HUMAN	N	552	ENSP00000347999:K552N;ENSP00000379773:K552N	ENSP00000347999:K552N	K	-	3	2	ZC3H7A	11766909	0.997000	0.39634	0.962000	0.40283	0.488000	0.33401	1.255000	0.32909	2.736000	0.93811	0.655000	0.94253	AAG	.	.	.	none		0.453	ZC3H7A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437066.1	NM_014153		A	11859408	C	A	11859408	3	1	99	1	0	0	0	0	1	0	0	0	17584	912	32	4	1299	4	ZC3H7A	16	11859408	Missense_Mutation	SNP	C	TCGA-B9-4617-01A-01D-1252-08		11859408	78495345	39	6285											
ABCC12	94160	hgsc.bcm.edu	37	chr16	48173154	48173154	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaaaaggcgtacgccgcacAaaagaccattaggatcggga	16	4	12	9	4	0	1	0	0	0	1	1	4	0	3	2	3	1	2	2	3	6	2			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr16:48173154A>G	ENST00000311303.3	-	5	1096	c.751T>C	c.(751-753)Tgt>Cgt	p.C251R	ABCC12_ENST00000448542.1_Missense_Mutation_p.C251R|ABCC12_ENST00000416054.1_Missense_Mutation_p.C251R	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	251	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)				TACGCCGCACAAAAGACCATT	0.483																																					p.C251R		Atlas-SNP	.											.	ABCC12	190	.	0			c.T751C						PASS	.						122	111	115					16																	48173154		2201	4300	6501	SO:0001583	missense	94160	exon5			CCGCACAAAAGAC	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.751T>C	chr16.hg19:g.48173154A>G	ENSP00000311030:p.Cys251Arg	174.0	0.0	.		238.0	67.0	.	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Missense_Mutation	SNP	ENST00000311303.3	hg19	CCDS10730.1	.	.	.	.	.	.	.	.	.	.	A	13.91	2.376652	0.42105	.	.	ENSG00000140798	ENST00000311303;ENST00000448542;ENST00000416054	D;D;D	0.90004	-2.6;-2.6;-2.6	5.88	5.88	0.94601	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.93161	0.7822	M	0.71581	2.175	0.80722	D	1	D;P	0.76494	0.999;0.942	D;P	0.80764	0.994;0.82	D	0.93294	0.6671	10	0.59425	D	0.04	.	11.3056	0.49334	0.8477:0.1522:0.0:0.0	.	251;251	Q96J65-2;Q96J65	.;MRP9_HUMAN	R	251	ENSP00000311030:C251R;ENSP00000401855:C251R;ENSP00000413046:C251R	ENSP00000311030:C251R	C	-	1	0	ABCC12	46730655	0.999000	0.42202	0.890000	0.34922	0.048000	0.14542	4.352000	0.59404	2.239000	0.73571	0.533000	0.62120	TGT	.	.	.	none		0.483	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226		G	48173154	A	G	48173154	3	3	99	1	0	0	0	0	1	0	0	0	52	130	5	3	3428	3	ABCC12	16	48173154	Missense_Mutation	SNP	A	TCGA-B9-4617-01A-01D-1252-08	36313746	48173154	42181599	40	6286											
LRRC50	123872	hgsc.bcm.edu	37	chr16	84203896	84203896	+	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	ttaaaggagaggatggagatCgagagccagaggggaccctc	13	5	16	7	1	0	4	0	0	0	4	2	9	0	6	2	5	1	0	2	5	2	1	rs375641621		TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr16:84203896C>G	ENST00000378553.5	+	8	1586	c.1462C>G	c.(1462-1464)Cga>Gga	p.R488G	DNAAF1_ENST00000563818.1_3'UTR	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	488	Pro-rich.				axonemal dynein complex assembly (GO:0070286)|cilium morphogenesis (GO:0060271)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|left/right pattern formation (GO:0060972)|lung development (GO:0030324)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|regulation of cilium beat frequency (GO:0003356)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dynein binding (GO:0045502)			NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						GGATGGAGATCGAGAGCCAGA	0.597																																					p.R488G		Atlas-SNP	.											.	DNAAF1	81	.	0			c.C1462G						PASS	.						41	40	40					16																	84203896		2200	4300	6500	SO:0001583	missense	123872	exon8			GGAGATCGAGAGC	BC024009	CCDS10943.2	16q24.1	2012-05-03	2011-06-09	2011-06-09	ENSG00000154099	ENSG00000154099			30539	protein-coding gene	gene with protein product	"outer row dynein assembly 7 homolog (Chlamydomonas)"	613190	"leucine rich repeat containing 50"	LRRC50		19944405	Standard	NM_178452		Approved	FLJ25330, ODA7, CILD13	uc002fhl.4	Q8NEP3	OTTHUMG00000128517	ENST00000378553.5:c.1462C>G	chr16.hg19:g.84203896C>G	ENSP00000367815:p.Arg488Gly	85.0	0.0	.		139.0	6.0	.	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Missense_Mutation	SNP	ENST00000378553.5	hg19	CCDS10943.2	.	.	.	.	.	.	.	.	.	.	C	1.384	-0.582571	0.03827	.	.	ENSG00000154099	ENST00000378553	T	0.26957	1.7	1.35	-0.756	0.11057	.	.	.	.	.	T	0.07683	0.0193	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	0.38373	-0.9664	9	0.22109	T	0.4	.	7.0593	0.25117	0.0:0.4357:0.5643:0.0	.	252;488	Q8NEP3-2;Q8NEP3	.;DAAF1_HUMAN	G	488	ENSP00000367815:R488G	ENSP00000367815:R488G	R	+	1	2	DNAAF1	82761397	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.340000	0.19892	-0.207000	0.10187	-1.719000	0.00708	CGA	.	.	.	alt		0.597	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452		G	84203896	C	G	84203896	3	3	99	1	0	0	0	0	1	0	0	0	9016	876	31	4	1492	4	LRRC50	16	84203896	Missense_Mutation	SNP	C	TCGA-B9-4617-01A-01D-1252-08	36030742	84203896	6150857	41	6287											
RNMTL1	55178	hgsc.bcm.edu	37	chr17	694912	694912	+	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	tcgggtctatgtggctgacaActgtggcctttatgcccagg	6	12	13	10	1	1	1	0	1	1	0	2	1	1	1	2	4	2	1	2	4	3	3			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr17:694912A>T	ENST00000304478.4	+	4	972	c.866A>T	c.(865-867)aAc>aTc	p.N289I	RP11-676J12.8_ENST00000574560.1_RNA	NM_018146.2	NP_060616.1			RNA methyltransferase like 1											breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (25;0.0219)		GTGGCTGACAACTGTGGCCTT	0.498																																					p.N289I		Atlas-SNP	.											.	RNMTL1	25	.	0			c.A866T						PASS	.						115	105	108					17																	694912		2203	4300	6503	SO:0001583	missense	55178	exon4			CTGACAACTGTGG	AF177344	CCDS10997.1	17p13.3	2008-02-05			ENSG00000171861	ENSG00000171861			18485	protein-coding gene	gene with protein product		612600				12296377	Standard	NM_018146		Approved	FLJ10581, HC90	uc002frw.3	Q9HC36	OTTHUMG00000090285	ENST00000304478.4:c.866A>T	chr17.hg19:g.694912A>T	ENSP00000306080:p.Asn289Ile	349.0	1.0	.		365.0	202.0	.	NM_018146		Missense_Mutation	SNP	ENST00000304478.4	hg19	CCDS10997.1	.	.	.	.	.	.	.	.	.	.	A	19.72	3.879315	0.72294	.	.	ENSG00000171861	ENST00000304478	T	0.28255	1.62	5.59	5.59	0.84812	tRNA/rRNA methyltransferase, SpoU (1);	0.131490	0.64402	D	0.000001	T	0.51839	0.1698	M	0.67625	2.065	0.58432	D	0.999999	D	0.71674	0.998	D	0.75484	0.986	T	0.45789	-0.9237	10	0.25106	T	0.35	-36.3731	14.5694	0.68202	1.0:0.0:0.0:0.0	.	289	Q9HC36	RMTL1_HUMAN	I	289	ENSP00000306080:N289I	ENSP00000306080:N289I	N	+	2	0	RNMTL1	641662	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	3.177000	0.50871	2.120000	0.65058	0.482000	0.46254	AAC	.	.	.	none		0.498	RNMTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206611.1	NM_018146		T	694912	A	T	694912	3	4	99	1	0	0	0	0	1	0	0	0	13520	43	2	5	880	5	RNMTL1	17	694912	Missense_Mutation	SNP	A	TCGA-B9-4617-01A-01D-1252-08		694912	80500298	42	6288											
NEURL4	84461	hgsc.bcm.edu	37	chr17	7230249	7230249	+	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	cctgccggtggggagctcagGttcacattcaggagccctcc	6	8	13	14	1	3	0	3	0	0	0	4	2	4	2	4	5	3	2	4	5	0	2			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr17:7230249G>A	ENST00000399464.2	-	4	888	c.873C>T	c.(871-873)aaC>aaT	p.N291N	NEURL4_ENST00000570460.1_Silent_p.N269N|NEURL4_ENST00000315614.7_Silent_p.N291N	NM_032442.2	NP_115818.2	Q96JN8	NEUL4_HUMAN	neuralized E3 ubiquitin protein ligase 4	291						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						GGGAGCTCAGGTTCACATTCA	0.562																																					p.N291N		Atlas-SNP	.											.	NEURL4	192	.	0			c.C873T						PASS	.						77	81	80					17																	7230249		2036	4185	6221	SO:0001819	synonymous_variant	84461	exon4			GCTCAGGTTCACA		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.873C>T	chr17.hg19:g.7230249G>A		154.0	0.0	.		210.0	116.0	.	NM_001005408	Q6GPI8|Q96IU9|Q9H0B0	Silent	SNP	ENST00000399464.2	hg19	CCDS42251.1																																																																																			.	.	.	none		0.562	NEURL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255434.2	NM_032442		A	7230249	G	A	7230249	2	1	99	1	0	0	0	0	0	0	0	1	10354	1252	44	2		2	NEURL4	17	7230249	Silent	SNP	G	TCGA-B9-4617-01A-01D-1252-08	6535337	7230249	73964961	43	6289											
HLF	3131	hgsc.bcm.edu	37	chr17	53398135	53398135	+	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	atccgggcctcgttcctggaGaaggagaactcggccctccg	7	7	13	14	4	0	2	0	0	0	2	5	4	3	2	5	4	1	1	5	4	2	1			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr17:53398135G>A	ENST00000226067.5	+	4	1256	c.783G>A	c.(781-783)gaG>gaA	p.E261E	HLF_ENST00000573945.1_Silent_p.E176E|HLF_ENST00000430986.2_Silent_p.E176E|HLF_ENST00000575307.1_3'UTR|HLF_ENST00000575345.1_Silent_p.E176E	NM_002126.4	NP_002117.1	Q16534	HLF_HUMAN	hepatic leukemia factor	261	bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				multicellular organismal development (GO:0007275)|rhythmic process (GO:0048511)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|ovary(2)	3						CGTTCCTGGAGAAGGAGAACT	0.617			T	TCF3	ALL																																p.E261E		Atlas-SNP	.		Dom	yes		17	17q22	3131	hepatic leukemia factor		L	.	HLF	39	.	0			c.G783A						PASS	.						28	32	31					17																	53398135		2202	4298	6500	SO:0001819	synonymous_variant	3131	exon4			CCTGGAGAAGGAG		CCDS11585.1	17q22	2011-05-19			ENSG00000108924	ENSG00000108924			4977	protein-coding gene	gene with protein product		142385				1386162	Standard	XM_005257269		Approved	MGC33822	uc002iug.1	Q16534		ENST00000226067.5:c.783G>A	chr17.hg19:g.53398135G>A		61.0	0.0	.		82.0	26.0	.	NM_002126	A8K1X8|Q6FHS9	Silent	SNP	ENST00000226067.5	hg19	CCDS11585.1																																																																																			.	.	.	none		0.617	HLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439185.1	NM_002126		A	53398135	G	A	53398135	2	1	99	1	0	0	0	0	0	0	0	1	7221	933	33	2		2	HLF	17	53398135	Silent	SNP	G	TCGA-B9-4617-01A-01D-1252-08	46167886	53398135	27797075	44	6290											
GNA13	10672	hgsc.bcm.edu	37	chr17	63049838	63049838	+	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	ctctcgagcatcaaccagcaCcctcatacctttgtttaaaa	12	11	4	14	1	3	0	2	0	1	0	4	1	3	0	3	0	4	3	3	0	4	4			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr17:63049838C>A	ENST00000439174.2	-	2	537	c.292G>T	c.(292-294)Gtg>Ttg	p.V98L	RP11-583F2.5_ENST00000581796.1_RNA|GNA13_ENST00000541118.1_Missense_Mutation_p.V3L	NM_006572.4	NP_006563.2	Q14344	GNA13_HUMAN	guanine nucleotide binding protein (G protein), alpha 13	98					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						TCAACCAGCACCCTCATACCT	0.383																																					p.V98L		Atlas-SNP	.											.	GNA13	69	.	0			c.G292T						PASS	.						115	115	115					17																	63049838		2203	4300	6503	SO:0001583	missense	10672	exon2			CCAGCACCCTCAT	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.292G>T	chr17.hg19:g.63049838C>A	ENSP00000400717:p.Val98Leu	301.0	0.0	.		361.0	195.0	.	NM_006572	B2R977|B7Z7R0|F5H1G8|Q8TD70	Missense_Mutation	SNP	ENST00000439174.2	hg19	CCDS11661.1	.	.	.	.	.	.	.	.	.	.	C	32	5.149213	0.94645	.	.	ENSG00000120063	ENST00000439174;ENST00000541118;ENST00000239138	D;D	0.87729	-2.29;-2.29	5.28	5.28	0.74379	G protein alpha subunit, helical insertion (2);	0.059604	0.64402	D	0.000003	D	0.86176	0.5870	L	0.59436	1.845	0.80722	D	1	P	0.36125	0.538	B	0.34590	0.186	D	0.87418	0.2380	10	0.87932	D	0	.	18.9394	0.92600	0.0:1.0:0.0:0.0	.	98	Q14344	GNA13_HUMAN	L	98;3;73	ENSP00000400717:V98L;ENSP00000439647:V3L	ENSP00000239138:V73L	V	-	1	0	GNA13	60480300	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.487000	0.81328	2.455000	0.83008	0.655000	0.94253	GTG	.	.	.	none		0.383	GNA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445720.1	NM_006572		A	63049838	C	A	63049838	3	1	99	1	0	0	0	0	1	0	0	0	6508	507	18	4	853	4	GNA13	17	63049838	Missense_Mutation	SNP	C	TCGA-B9-4617-01A-01D-1252-08	9651703	63049838	18145372	45	6291											
KIAA0802	23255	hgsc.bcm.edu	37	chr18	8825493	8825493	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcagaccatcagtgtgggcTtgcagactgaagccctgcgt	8	10	12	11	1	2	3	2	1	0	2	2	3	2	3	2	1	3	2	2	1	1	2			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr18:8825493T>C	ENST00000306329.11	+	13	4942	c.4942T>C	c.(4942-4944)Ttg>Ctg	p.L1648L	SOGA2_ENST00000518815.1_Silent_p.L654L|SOGA2_ENST00000400050.3_Silent_p.L1288L|SOGA2_ENST00000306285.7_Silent_p.L654L|SOGA2_ENST00000359865.3_Silent_p.L1329L|SOGA2_ENST00000517570.1_Silent_p.L1288L																							CAGTGTGGGCTTGCAGACTGA	0.637																																					p.L1329L		Atlas-SNP	.											CCDC165,NS,carcinoma,0,1	.	.	.	0			c.T3985C						PASS	.						33	33	33					18																	8825493		2203	4300	6503	SO:0001819	synonymous_variant	23255	exon15			GTGGGCTTGCAGA																												ENST00000306329.11:c.4942T>C	chr18.hg19:g.8825493T>C		75.0	0.0	.		66.0	3.0	.	NM_015210		Silent	SNP	ENST00000306329.11	hg19																																																																																				.	.	.	none		0.637	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1			C	8825493	T	C	8825493	2	2	99	1	0	0	0	0	0	0	0	1	8201	1606	56	3		3	KIAA0802	18	8825493	Silent	SNP	T	TCGA-B9-4617-01A-01D-1252-08		8825493	69251755	46	6292											
CSNK2A1	1457	hgsc.bcm.edu	37	chr20	467041	467041	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgacatcatattggcgctgcTgacgggcgtactgccccctg	6	10	12	13	3	1	2	1	2	0	0	1	2	1	2	2	2	3	3	2	2	2	3			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chr20:467041T>C	ENST00000217244.3	-	13	1414	c.1039A>G	c.(1039-1041)Agc>Ggc	p.S347G	CSNK2A1_ENST00000400227.3_Missense_Mutation_p.S347G|CSNK2A1_ENST00000349736.5_Missense_Mutation_p.S347G|CSNK2A1_ENST00000400217.2_Missense_Mutation_p.S211G	NM_177559.2	NP_808227.1	P68400	CSK21_HUMAN	casein kinase 2, alpha 1 polypeptide	347					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)			TTGGCGCTGCTGACGGGCGTA	0.428																																					p.S347G		Atlas-SNP	.											.	CSNK2A1	36	.	0			c.A1039G						PASS	.						87	84	85					20																	467041		2203	4300	6503	SO:0001583	missense	1457	exon12			CGCTGCTGACGGG	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.1039A>G	chr20.hg19:g.467041T>C	ENSP00000217244:p.Ser347Gly	165.0	0.0	.		143.0	34.0	.	NM_001895	B4DYS6|D3DVV8|P19138|P20426|Q14013|Q5U065	Missense_Mutation	SNP	ENST00000217244.3	hg19	CCDS13003.1	.	.	.	.	.	.	.	.	.	.	t	16.92	3.254163	0.59212	.	.	ENSG00000101266	ENST00000400227;ENST00000349736;ENST00000217244;ENST00000381973;ENST00000400217	T;T;T;T	0.63417	0.35;0.34;0.34;-0.04	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.46756	0.1409	N	0.19112	0.55	0.58432	D	0.999999	B	0.06786	0.001	B	0.04013	0.001	T	0.36939	-0.9727	10	0.27785	T	0.31	-15.3796	14.2224	0.65836	0.0:0.0:0.0:1.0	.	347	P68400	CSK21_HUMAN	G	347;347;347;347;211	ENSP00000383086:S347G;ENSP00000339247:S347G;ENSP00000217244:S347G;ENSP00000383076:S211G	ENSP00000217244:S347G	S	-	1	0	CSNK2A1	415041	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.400000	0.79949	2.207000	0.71202	0.478000	0.44815	AGC	.	.	.	none		0.428	CSNK2A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077466.1	NM_001895		C	467041	T	C	467041	3	2	99	1	0	0	0	0	1	0	0	0	3959	1580	55	3	144	3	CSNK2A1	20	467041	Missense_Mutation	SNP	T	TCGA-B9-4617-01A-01D-1252-08		467041	62558479	47	6293											
MAGEB4	4115	hgsc.bcm.edu	37	chrX	30261219	30261219	+	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	gagcccggcccagagttgcaGccaggcgtggcactacagcc	8	4	14	15	2	0	1	0	0	0	1	0	2	0	1	4	3	5	3	4	3	1	2			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chrX:30261219G>T	ENST00000378982.2	+	1	1163	c.967G>T	c.(967-969)Gcc>Tcc	p.A323S	MAGEB1_ENST00000397550.1_5'Flank|MAGEB1_ENST00000378981.3_5'Flank	NM_002367.3	NP_002358.1	O15481	MAGB4_HUMAN	melanoma antigen family B, 4	323										breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27						CAGAGTTGCAGCCAGGCGTGG	0.522																																					p.A323S		Atlas-SNP	.											.	MAGEB4	75	.	0			c.G967T						PASS	.						48	44	45					X																	30261219		2202	4300	6502	SO:0001583	missense	4115	exon1			GTTGCAGCCAGGC		CCDS14221.1	Xp21.3	2009-03-17			ENSG00000120289	ENSG00000120289			6811	protein-coding gene	gene with protein product	"melanoma-associated antigen B4", "cancer/testis antigen family 3, member 6"	300153				9441743	Standard	NM_002367		Approved	MGC33144, CT3.6	uc004dcb.3	O15481	OTTHUMG00000021321	ENST00000378982.2:c.967G>T	chrX.hg19:g.30261219G>T	ENSP00000368266:p.Ala323Ser	57.0	0.0	.		26.0	23.0	.	NM_002367	B2R9G0|Q6FHH4|Q8IZ00	Missense_Mutation	SNP	ENST00000378982.2	hg19	CCDS14221.1	.	.	.	.	.	.	.	.	.	.	G	11.79	1.743265	0.30865	.	.	ENSG00000120289	ENST00000378982	T	0.01821	4.62	2.95	1.12	0.20585	.	1.311600	0.06398	U	0.718346	T	0.02888	0.0086	M	0.61703	1.905	0.09310	N	1	P	0.48834	0.916	B	0.42522	0.39	T	0.43032	-0.9416	10	0.51188	T	0.08	.	3.6067	0.08045	0.1562:0.2589:0.5849:0.0	.	323	O15481	MAGB4_HUMAN	S	323	ENSP00000368266:A323S	ENSP00000368266:A323S	A	+	1	0	MAGEB4	30171140	0.000000	0.05858	0.001000	0.08648	0.373000	0.29922	-0.156000	0.10100	0.167000	0.19631	0.600000	0.82982	GCC	.	.	.	none		0.522	MAGEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056159.1	NM_002367		T	30261219	G	T	30261219	3	4	99	1	0	0	0	0	1	0	0	0	9185	971	34	4	969	4	MAGEB4	23	30261219	Missense_Mutation	SNP	G	TCGA-B9-4617-01A-01D-1252-08		30261219	125009341	48	6294											
DMD	1756	hgsc.bcm.edu	37	chrX	32867885	32867885	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcgaggaggtctaggaggCgcctcccatcctgtaggtca	7	9	13	12	2	2	0	1	0	1	0	5	3	4	2	3	5	0	1	3	5	2	3			TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chrX:32867885C>T	ENST00000357033.4	-	3	352	c.146G>A	c.(145-147)cGc>cAc	p.R49H	DMD_ENST00000288447.4_Missense_Mutation_p.R41H|snoU13_ENST00000459244.1_RNA|DMD_ENST00000378677.2_Missense_Mutation_p.R45H	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	49	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.		Missing (in BMD).		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)				GTCTAGGAGGCGCCTCCCATC	0.393																																					p.R49H		Atlas-SNP	.											.	DMD	2127	.	0			c.G146A						PASS	.						89	85	86					X																	32867885		2202	4300	6502	SO:0001583	missense	1756	exon3			AGGAGGCGCCTCC	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.146G>A	chrX.hg19:g.32867885C>T	ENSP00000354923:p.Arg49His	118.0	0.0	.		98.0	8.0	.	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.580687	0.86748	.	.	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000288447;ENST00000447523	D;D;D;D	0.94931	-3.56;-3.56;-3.56;-3.56	5.63	4.76	0.60689	Calponin homology domain (5);	0.490245	0.13997	U	0.348381	D	0.95856	0.8651	M	0.62266	1.93	0.80722	D	1	D;D;P;D	0.71674	0.998;0.994;0.884;0.995	P;P;B;P	0.61874	0.895;0.78;0.439;0.86	D	0.94777	0.7950	10	0.54805	T	0.06	.	11.8557	0.52435	0.0:0.9123:0.0:0.0877	.	41;41;49;45	Q4G0X0;P11532-4;P11532;E9PDN5	.;.;DMD_HUMAN;.	H	41;45;49;49;41;12	ENSP00000367948:R45H;ENSP00000354923:R49H;ENSP00000288447:R41H;ENSP00000395904:R12H	ENSP00000288447:R41H	R	-	2	0	DMD	32777806	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.592000	0.46171	2.346000	0.79739	0.600000	0.82982	CGC	.	.	.	none		0.393	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		T	32867885	C	T	32867885	3	4	99	1	0	0	0	0	1	0	0	0	4582	768	27	1	11462	1	DMD	23	32867885	Missense_Mutation	SNP	C	TCGA-B9-4617-01A-01D-1252-08	2606666	32867885	122402675	49	6295											
XPNPEP2	7512	hgsc.bcm.edu	37	chrX	128885748	128885749	+	Frame_Shift_Del	DEL	TC	TC	-																															caaccttcgagccagtgacaTcccctataaccccttcttct																										TCGA-B9-4617-01A-01D-1252-08	TCGA-B9-4617-10A-01D-1252-08	TC	TC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aed3977e-c899-4a95-b26a-957bdbd865a6	513c77a4-6151-4d55-9b91-4b9923b7d895	g.chrX:128885748_128885749delTC	ENST00000371106.3	+	9	959_960	c.767_768delTC	c.(766-768)atcfs	p.I256fs		NM_003399.5	NP_003390.4	O43895	XPP2_HUMAN	X-prolyl aminopeptidase (aminopeptidase P) 2, membrane-bound	256						anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			endometrium(3)|kidney(3)|large_intestine(5)|liver(1)|lung(20)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	37						GCCAGTGACATCCCCTATAACC	0.441																																					p.256_256del		Atlas-INDEL	.											.	XPNPEP2	84	.	0			c.766_767del						PASS	.																																			SO:0001589	frameshift_variant	7512	exon9			.	U90724	CCDS14613.1	Xq25	2008-02-05			ENSG00000122121	ENSG00000122121	3.4.11.9		12823	protein-coding gene	gene with protein product		300145				9375790, 9628831	Standard	NM_003399		Approved		uc004eut.1	O43895	OTTHUMG00000022373	ENST00000371106.3:c.767_768delTC	chrX.hg19:g.128885748_128885749delTC	ENSP00000360147:p.Ile256fs	377.0	0.0	0		282.0	234.0	0.829787	NM_003399	A0AV16|O75994	Frame_Shift_Del	DEL	ENST00000371106.3	hg19	CCDS14613.1																																																																																			.	.	.	none		0.441	XPNPEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058210.1	NM_003399		-	128885749	TC	-	128885748	7	5	99	1	0	1	0	1	0	0	0	0	17455	1435	50	0	801	0	XPNPEP2	23	128885748	Frame_Shift_Del	DEL	TC	TCGA-B9-4617-01A-01D-1252-08	96017863	128885748	26384812	50	6296											
ARHGEF10L	55160	hgsc.bcm.edu	37	chr1	18023596	18023596	+	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	gcacacctcccgggcccgctGctctccatgcgggagccggc	4	5	13	19	4	1	0	0	0	1	0	3	1	2	1	5	3	3	3	5	3	0	0			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr1:18023596G>A	ENST00000361221.3	+	29	3720	c.3561G>A	c.(3559-3561)ctG>ctA	p.L1187L	ARHGEF10L_ENST00000452522.1_Silent_p.L1148L|ARHGEF10L_ENST00000469726.1_3'UTR|ARHGEF10L_ENST00000375408.3_Silent_p.L960L|ARHGEF10L_ENST00000167825.4_Silent_p.L890L|ARHGEF10L_ENST00000375415.1_Silent_p.L1148L	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	1187						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		CGGGCCCGCTGCTCTCCATGC	0.677																																					p.L1187L		Atlas-SNP	.											.	ARHGEF10L	219	.	0			c.G3561A						PASS	.						13	14	14					1																	18023596		2189	4283	6472	SO:0001819	synonymous_variant	55160	exon29			CCCGCTGCTCTCC	AB046846	CCDS182.1, CCDS30617.1	1p36.13	2011-11-16			ENSG00000074964	ENSG00000074964		"Rho guanine nucleotide exchange factors"	25540	protein-coding gene	gene with protein product	"GrinchGEF"	612494				10997877, 16112081	Standard	XM_005245923		Approved	FLJ10521, KIAA1626	uc001ban.3	Q9HCE6	OTTHUMG00000002514	ENST00000361221.3:c.3561G>A	chr1.hg19:g.18023596G>A		25.0	0.0	.		25.0	12.0	.	NM_018125	B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Silent	SNP	ENST00000361221.3	hg19	CCDS182.1																																																																																			.	.	.	none		0.677	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	NM_018125		A	18023596	G	A	18023596	2	1	100	1	0	0	0	0	0	0	0	1	895	1306	46	2		2	ARHGEF10L	1	18023596	Silent	SNP	G	TCGA-B9-5155-01A-01D-1589-08		18023596	231227025	1	6297											
TMCO4	255104	hgsc.bcm.edu	37	chr1	20063898	20063898	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catctcctgcagacagaagtAgatgactctggctcccaggc	10	8	10	13	0	2	4	0	1	2	3	4	4	3	4	2	2	1	3	2	2	2	1			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr1:20063898A>G	ENST00000294543.6	-	13	1472	c.1231T>C	c.(1231-1233)Tac>Cac	p.Y411H	TMCO4_ENST00000489814.1_5'UTR|TMCO4_ENST00000375122.2_Missense_Mutation_p.Y371H|TMCO4_ENST00000375127.1_Missense_Mutation_p.Y411H	NM_181719.4	NP_859070.3	Q5TGY1	TMCO4_HUMAN	transmembrane and coiled-coil domains 4	411						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)		AGACAGAAGTAGATGACTCTG	0.512																																					p.Y411H		Atlas-SNP	.											.	TMCO4	46	.	0			c.T1231C						PASS	.						122	116	118					1																	20063898		2203	4300	6503	SO:0001583	missense	255104	exon13			AGAAGTAGATGAC		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.1231T>C	chr1.hg19:g.20063898A>G	ENSP00000294543:p.Tyr411His	113.0	0.0	.		160.0	91.0	.	NM_181719	Q5TGY2|Q6MZN5|Q7Z6K6|Q9UQP4|Q9Y3K1	Missense_Mutation	SNP	ENST00000294543.6	hg19	CCDS198.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.679476	0.88542	.	.	ENSG00000162542	ENST00000294543;ENST00000375127;ENST00000375122	T;T;T	0.55588	0.51;0.51;0.51	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.70422	0.3222	M	0.70903	2.155	0.52501	D	0.999959	D	0.65815	0.995	D	0.73708	0.981	T	0.74124	-0.3766	10	0.87932	D	0	-10.3943	13.6373	0.62229	1.0:0.0:0.0:0.0	.	411	Q5TGY1	TMCO4_HUMAN	H	411;411;371	ENSP00000294543:Y411H;ENSP00000364269:Y411H;ENSP00000364264:Y371H	ENSP00000294543:Y411H	Y	-	1	0	TMCO4	19936485	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.389000	0.90172	2.172000	0.68678	0.533000	0.62120	TAC	.	.	.	none		0.512	TMCO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007658.1	NM_181719		G	20063898	A	G	20063898	3	3	100	1	0	0	0	0	1	0	0	0	16010	420	15	3	689	3	TMCO4	1	20063898	Missense_Mutation	SNP	A	TCGA-B9-5155-01A-01D-1589-08	2040302	20063898	229186723	2	6298											
TAL1	6886	hgsc.bcm.edu	37	chr1	47685450	47685450	+	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	caggatggaggctgcgggccGtgtgtttgggcgcgggctcc	3	8	20	10	4	0	0	0	0	0	0	1	2	1	2	2	6	1	3	2	6	0	1	rs536520955	byFrequency	TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr1:47685450G>T	ENST00000294339.3	-	4	1514	c.938C>A	c.(937-939)aCg>aAg	p.T313K	TAL1_ENST00000371884.2_Missense_Mutation_p.T313K|TAL1_ENST00000459729.1_5'UTR|TAL1_ENST00000371883.3_Missense_Mutation_p.T315K	NM_003189.2	NP_003180.1	P17542	TAL1_HUMAN	T-cell acute lymphocytic leukemia 1	313					angiogenesis (GO:0001525)|astrocyte fate commitment (GO:0060018)|basophil differentiation (GO:0030221)|cell fate commitment (GO:0045165)|definitive hemopoiesis (GO:0060216)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|erythrocyte maturation (GO:0043249)|hemangioblast cell differentiation (GO:0060217)|hematopoietic stem cell differentiation (GO:0060218)|hemopoiesis (GO:0030097)|locomotory behavior (GO:0007626)|megakaryocyte development (GO:0035855)|megakaryocyte differentiation (GO:0030219)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|platelet formation (GO:0030220)|positive regulation of cell division (GO:0051781)|positive regulation of chromatin assembly or disassembly (GO:0045799)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell proliferation (GO:0042127)|regulation of mast cell differentiation (GO:0060375)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spinal cord association neuron differentiation (GO:0021527)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|E-box binding (GO:0070888)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			haematopoietic_and_lymphoid_tissue(1)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	15						GCTGCGGGCCGTGTGTTTGGG	0.687			T	"TRD@, SIL"	lymphoblastic leukemia/biphasic																																p.T313K		Atlas-SNP	.		Dom	yes		1	1p32	6886	T-cell acute lymphocytic leukemia 1 (SCL)		L	.	TAL1	31	.	0			c.C938A						PASS	.						24	29	27					1																	47685450		2193	4294	6487	SO:0001583	missense	6886	exon4			CGGGCCGTGTGTT	M29038	CCDS547.1	1p32	2013-05-21	2001-12-04		ENSG00000162367	ENSG00000162367		"Basic helix-loop-helix proteins"	11556	protein-coding gene	gene with protein product		187040		TCL5		2740341	Standard	NM_001287347		Approved	SCL, bHLHa17	uc009vyq.2	P17542	OTTHUMG00000007847	ENST00000294339.3:c.938C>A	chr1.hg19:g.47685450G>T	ENSP00000294339:p.Thr313Lys	53.0	0.0	.		74.0	38.0	.	NM_003189	D3DQ24	Missense_Mutation	SNP	ENST00000294339.3	hg19	CCDS547.1	.	.	.	.	.	.	.	.	.	.	G	16.31	3.086069	0.55861	.	.	ENSG00000162367	ENST00000371884;ENST00000371883;ENST00000294339	D;D;D	0.97404	-4.37;-4.37;-4.37	5.05	5.05	0.67936	.	0.348037	0.26518	N	0.023921	D	0.91583	0.7341	N	0.14661	0.345	0.30052	N	0.811637	P	0.38827	0.649	B	0.32090	0.14	D	0.89725	0.3922	10	0.39692	T	0.17	.	14.0701	0.64854	0.0:0.1508:0.8492:0.0	.	313	P17542	TAL1_HUMAN	K	313;315;313	ENSP00000360951:T313K;ENSP00000360950:T315K;ENSP00000294339:T313K	ENSP00000294339:T313K	T	-	2	0	TAL1	47458037	0.955000	0.32602	0.909000	0.35828	0.555000	0.35460	4.030000	0.57260	2.363000	0.80096	0.478000	0.44815	ACG	.	.	.	none		0.687	TAL1-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021640.1	NM_003189		T	47685450	G	T	47685450	3	4	100	1	0	0	0	0	1	0	0	0	15553	1145	40	4	61	4	TAL1	1	47685450	Missense_Mutation	SNP	G	TCGA-B9-5155-01A-01D-1589-08	27621552	47685450	201565171	3	6299											
SYDE2	84144	hgsc.bcm.edu	37	chr1	85656155	85656155	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaagagtttgtagcgttacaTaccacatatgtacagtactc	13	12	8	8	1	0	1	0	0	0	1	1	2	0	1	1	0	5	5	1	0	7	7			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr1:85656155T>C	ENST00000341460.5	-	2	1075	c.1026A>G	c.(1024-1026)gtA>gtG	p.V342V		NM_032184.1	NP_115560.1	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	342					activation of Rho GTPase activity (GO:0032862)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	20				all cancers(265;0.0126)|Epithelial(280;0.0336)		TAGCGTTACATACCACATATG	0.353																																					p.V342V		Atlas-SNP	.											.	SYDE2	135	.	0			c.A1026G						PASS	.						153	141	145					1																	85656155		1928	4133	6061	SO:0001819	synonymous_variant	84144	exon2			GTTACATACCACA	AL834286	CCDS44169.1	1p22.3	2008-02-05		2005-08-09	ENSG00000097096	ENSG00000097096			25841	protein-coding gene	gene with protein product							Standard	NM_032184		Approved	FLJ13815	uc009wcm.3	Q5VT97	OTTHUMG00000009956	ENST00000341460.5:c.1026A>G	chr1.hg19:g.85656155T>C		63.0	0.0	.		74.0	35.0	.	NM_032184	Q5VT96|Q8NDB8|Q9H8A6	Silent	SNP	ENST00000341460.5	hg19	CCDS44169.1																																																																																			.	.	.	none		0.353	SYDE2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127989.2			C	85656155	T	C	85656155	2	2	100	1	0	0	0	0	0	0	0	1	15448	1393	49	3		3	SYDE2	1	85656155	Silent	SNP	T	TCGA-B9-5155-01A-01D-1589-08	37970705	85656155	163594466	4	6300											
HS2ST1	9653	hgsc.bcm.edu	37	chr1	87569257	87569257	+	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	ggtttttcaggggtgctactGaactctatcgcacaggtata	9	13	11	8	1	2	1	1	1	1	0	3	1	2	1	0	4	3	4	0	4	5	6			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr1:87569257G>A	ENST00000370550.5	+	6	1192	c.829G>A	c.(829-831)Gaa>Aaa	p.E277K	RP5-1052I5.2_ENST00000370548.2_Missense_Mutation_p.E251K|HS2ST1_ENST00000356813.4_Missense_Mutation_p.E251K	NM_012262.3	NP_036394.1	Q7LGA3	HS2ST_HUMAN	heparan sulfate 2-O-sulfotransferase 1	277					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	sulfotransferase activity (GO:0008146)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)	9		Lung NSC(277;0.153)		all cancers(265;0.00699)|Epithelial(280;0.0261)		GGGTGCTACTGAACTCTATCG	0.363																																					p.E277K		Atlas-SNP	.											.	HS2ST1	43	.	0			c.G829A						PASS	.						102	102	102					1																	87569257		2203	4300	6503	SO:0001583	missense	9653	exon6			GCTACTGAACTCT	AB007917	CCDS711.1, CCDS44171.1	1p22.3	2008-02-05			ENSG00000153936	ENSG00000153936		"Sulfotransferases, membrane-bound"	5193	protein-coding gene	gene with protein product		604844				9455484	Standard	NM_012262		Approved	KIAA0448	uc010osk.2	Q7LGA3	OTTHUMG00000010255	ENST00000370550.5:c.829G>A	chr1.hg19:g.87569257G>A	ENSP00000359581:p.Glu277Lys	239.0	1.0	.		239.0	106.0	.	NM_012262	D3DT22|O75036|Q32NB5|Q8TAC5|Q9H441|Q9NUJ9	Missense_Mutation	SNP	ENST00000370550.5	hg19	CCDS711.1	.	.	.	.	.	.	.	.	.	.	G	18.73	3.686327	0.68157	.	.	ENSG00000153936	ENST00000370550;ENST00000370548;ENST00000356813	T;T;T	0.73789	-0.78;-0.78;-0.78	5.55	5.55	0.83447	.	0.045925	0.85682	D	0.000000	T	0.44932	0.1317	N	0.13272	0.32	0.80722	D	1	B;B	0.20887	0.007;0.049	B;B	0.15484	0.013;0.011	T	0.47222	-0.9134	10	0.14252	T	0.57	-17.3525	19.5161	0.95165	0.0:0.0:1.0:0.0	.	277;251	Q7LGA3;Q7LGA3-2	HS2ST_HUMAN;.	K	277;251;251	ENSP00000359581:E277K;ENSP00000359579:E251K;ENSP00000349268:E251K	ENSP00000349268:E251K	E	+	1	0	HS2ST1	87341845	1.000000	0.71417	0.863000	0.33907	0.974000	0.67602	9.869000	0.99810	2.605000	0.88082	0.467000	0.42956	GAA	.	.	.	none		0.363	HS2ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028279.2	NM_012262		A	87569257	G	A	87569257	3	1	100	1	0	0	0	0	1	0	0	0	7369	1291	45	2	855	2	HS2ST1	1	87569257	Missense_Mutation	SNP	G	TCGA-B9-5155-01A-01D-1589-08	1913102	87569257	161681364	5	6301											
LRRC8C	84230	hgsc.bcm.edu	37	chr1	90179254	90179254	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gactttgcttttatgcttcaTatgatagatcagtatgaccc	10	16	7	8	0	2	3	2	2	0	1	2	4	2	3	1	0	2	3	1	0	4	7			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr1:90179254T>C	ENST00000370454.4	+	3	1380	c.1125T>C	c.(1123-1125)caT>caC	p.H375H	RP11-302M6.4_ENST00000370453.5_Intron|LRRC8C_ENST00000479252.1_Intron	NM_032270.4	NP_115646	Q8TDW0	LRC8C_HUMAN	leucine rich repeat containing 8 family, member C	375					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)		TTATGCTTCATATGATAGATC	0.373																																					p.H375H		Atlas-SNP	.											.	LRRC8C	73	.	0			c.T1125C						PASS	.						52	53	52					1																	90179254		2203	4300	6503	SO:0001819	synonymous_variant	84230	exon3			GCTTCATATGATA		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.1125T>C	chr1.hg19:g.90179254T>C		93.0	0.0	.		102.0	36.0	.	NM_032270	B3KXS9|Q29RV6|Q9H075	Silent	SNP	ENST00000370454.4	hg19	CCDS725.1																																																																																			.	.	.	none		0.373	LRRC8C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028435.2	NM_032270		C	90179254	T	C	90179254	2	2	100	1	0	0	0	0	0	0	0	1	9030	1403	49	3		3	LRRC8C	1	90179254	Silent	SNP	T	TCGA-B9-5155-01A-01D-1589-08	2609997	90179254	159071367	6	6302											
BTBD8	284697	hgsc.bcm.edu	37	chr1	92612759	92612759	+	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	tgttcccagaacattgacgtCtatactagaatgcctgatta	12	13	7	9	1	1	4	0	2	1	2	2	4	2	4	2	0	3	1	2	0	6	6			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr1:92612759C>G	ENST00000342818.3	+	8	1189	c.953C>G	c.(952-954)tCt>tGt	p.S318C	BTBD8_ENST00000540648.1_3'UTR	NM_183242.3	NP_899065.2	Q5XKL5	BTBD8_HUMAN	BTB (POZ) domain containing 8	318						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)		ACATTGACGTCTATACTAGAA	0.323																																					p.S318C		Atlas-SNP	.											.	BTBD8	32	.	0			c.C953G						PASS	.						172	167	168					1																	92612759		2203	4300	6503	SO:0001583	missense	284697	exon8			TGACGTCTATACT	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.953C>G	chr1.hg19:g.92612759C>G	ENSP00000343686:p.Ser318Cys	146.0	0.0	.		163.0	70.0	.	NM_183242	Q6V9S5	Missense_Mutation	SNP	ENST00000342818.3	hg19	CCDS737.1	.	.	.	.	.	.	.	.	.	.	C	14.43	2.533918	0.45073	.	.	ENSG00000189195	ENST00000342818	T	0.66099	-0.19	5.49	5.49	0.81192	.	0.352773	0.24511	N	0.037898	T	0.58104	0.2099	L	0.43152	1.355	0.80722	D	1	D	0.57257	0.979	P	0.50231	0.635	T	0.61387	-0.7073	10	0.59425	D	0.04	-6.2864	18.5235	0.90962	0.0:1.0:0.0:0.0	.	318	Q5XKL5	BTBD8_HUMAN	C	318	ENSP00000343686:S318C	ENSP00000343686:S318C	S	+	2	0	BTBD8	92385347	0.230000	0.23740	0.025000	0.17156	0.257000	0.26127	2.777000	0.47717	2.753000	0.94483	0.557000	0.71058	TCT	.	.	.	none		0.323	BTBD8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028372.1	NM_183242		G	92612759	C	G	92612759	3	3	100	1	0	0	0	0	1	0	0	0	1549	913	32	4	983	4	BTBD8	1	92612759	Missense_Mutation	SNP	C	TCGA-B9-5155-01A-01D-1589-08	2433505	92612759	156637862	7	6303											
CCDC19	25790	hgsc.bcm.edu	37	chr1	159846354	159846354	+	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	ggcccctcctaccgaagaatCctctcgaactcatcccggtc	8	8	7	18	3	2	1	1	0	1	1	7	3	5	1	6	2	2	0	6	2	4	1			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr1:159846354C>A	ENST00000368099.4	-	10	1408	c.1344G>T	c.(1342-1344)agG>agT	p.R448S	CCDC19_ENST00000426543.2_Missense_Mutation_p.R363S|CCDC19_ENST00000476696.1_5'UTR	NM_012337.2	NP_036469.2														endometrium(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	26	all_hematologic(112;0.0597)		BRCA - Breast invasive adenocarcinoma(70;0.151)			ACCGAAGAATCCTCTCGAACT	0.527																																					p.R448S		Atlas-SNP	.											.	CCDC19	79	.	0			c.G1344T						PASS	.						81	77	79					1																	159846354		2203	4300	6503	SO:0001583	missense	25790	exon10			AAGAATCCTCTCG																												ENST00000368099.4:c.1344G>T	chr1.hg19:g.159846354C>A	ENSP00000357079:p.Arg448Ser	36.0	0.0	.		36.0	19.0	.	NM_012337		Missense_Mutation	SNP	ENST00000368099.4	hg19	CCDS30914.1	.	.	.	.	.	.	.	.	.	.	c	19.82	3.899092	0.72754	.	.	ENSG00000213085	ENST00000368099;ENST00000426543	T;T	0.11385	2.78;2.78	5.16	5.16	0.70880	.	0.148017	0.64402	D	0.000016	T	0.11239	0.0274	M	0.82823	2.61	0.47905	D	0.999549	B	0.31752	0.338	B	0.39617	0.305	T	0.01583	-1.1319	9	.	.	.	-16.358	10.0537	0.42233	0.0:0.9081:0.0:0.0919	.	448	Q9UL16	CCD19_HUMAN	S	448;363	ENSP00000357079:R448S;ENSP00000403044:R363S	.	R	-	3	2	CCDC19	158112978	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.145000	0.31577	2.571000	0.86741	0.486000	0.48141	AGG	.	.	.	none		0.527	CCDC19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085979.1			A	159846354	C	A	159846354	3	1	100	1	0	0	0	0	1	0	0	0	2797	854	30	4	323	4	CCDC19	1	159846354	Missense_Mutation	SNP	C	TCGA-B9-5155-01A-01D-1589-08	67233595	159846354	89404267	8	6304											
USF1	7391	hgsc.bcm.edu	37	chr1	161011449	161011449	+	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	gcaatatctcaccagtgccaGgaggggtcgcctgccccagc	8	6	12	15	1	1	0	1	0	1	0	3	1	1	1	5	3	3	1	5	3	2	1			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr1:161011449G>A	ENST00000368021.3	-	6	668	c.464C>T	c.(463-465)cCt>cTt	p.P155L	USF1_ENST00000435396.1_Missense_Mutation_p.P96L|F11R_ENST00000289779.3_5'Flank|TSTD1_ENST00000318289.10_5'Flank|TSTD1_ENST00000368024.1_5'Flank|USF1_ENST00000368019.1_Intron|USF1_ENST00000368020.1_Missense_Mutation_p.P155L|TSTD1_ENST00000466967.1_5'Flank|TSTD1_ENST00000368023.3_5'Flank|TSTD1_ENST00000423014.2_5'Flank	NM_007122.3	NP_009053.1	P22415	USF1_HUMAN	upstream transcription factor 1	155					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)			ACCAGTGCCAGGAGGGGTCGC	0.582											OREG0013936	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P155L		Atlas-SNP	.											.	USF1	29	.	0			c.C464T						PASS	.						52	51	52					1																	161011449		2203	4300	6503	SO:0001583	missense	7391	exon6			GTGCCAGGAGGGG	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.464C>T	chr1.hg19:g.161011449G>A	ENSP00000357000:p.Pro155Leu	67.0	0.0	.	1813	77.0	25.0	.	NM_001276373	B2RBZ4|Q5SY46|Q7Z5Y1	Missense_Mutation	SNP	ENST00000368021.3	hg19	CCDS1214.1	.	.	.	.	.	.	.	.	.	.	G	15.30	2.792171	0.50102	.	.	ENSG00000158773	ENST00000368020;ENST00000368021;ENST00000435396;ENST00000534633	D;D;D	0.92911	-3.11;-3.11;-3.13	5.02	4.11	0.48088	.	0.265359	0.39020	N	0.001485	T	0.73289	0.3568	N	0.08118	0	0.48135	D	0.99959	B	0.02656	0.0	B	0.01281	0.0	T	0.71133	-0.4681	10	0.44086	T	0.13	-11.2539	11.3156	0.49390	0.088:0.0:0.912:0.0	.	155	P22415	USF1_HUMAN	L	155;155;96;96	ENSP00000356999:P155L;ENSP00000357000:P155L;ENSP00000390109:P96L	ENSP00000356999:P155L	P	-	2	0	USF1	159278073	1.000000	0.71417	0.978000	0.43139	0.995000	0.86356	6.370000	0.73114	1.345000	0.45676	0.655000	0.94253	CCT	.	.	.	none		0.582	USF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077050.1	NM_007122		A	161011449	G	A	161011449	3	1	100	1	0	0	0	0	1	0	0	0	17044	1000	35	2	492	2	USF1	1	161011449	Missense_Mutation	SNP	G	TCGA-B9-5155-01A-01D-1589-08	1165095	161011449	88239172	9	6305											
NIT1	4817	hgsc.bcm.edu	37	chr1	161090529	161090529	+	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	accgcaggcctgacctctatGgcaatctgggtcacccactg	8	8	10	15	1	3	1	1	1	2	0	3	1	3	1	4	3	0	2	4	3	2	1			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr1:161090529G>C	ENST00000368009.2	+	7	1034	c.958G>C	c.(958-960)Ggc>Cgc	p.G320R	DEDD_ENST00000489249.1_5'Flank|NIT1_ENST00000368008.1_Intron|PFDN2_ENST00000468311.1_5'Flank|NIT1_ENST00000392190.5_Missense_Mutation_p.G284R|NIT1_ENST00000368007.4_Missense_Mutation_p.G305R|PFDN2_ENST00000368010.3_5'Flank	NM_005600.2	NP_005591.1	Q86X76	NIT1_HUMAN	nitrilase 1	320	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				nitrogen compound metabolic process (GO:0006807)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	nitrilase activity (GO:0000257)			NS(1)|breast(2)|endometrium(2)|large_intestine(3)|lung(3)|prostate(1)	12	all_cancers(52;3.39e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			TGACCTCTATGGCAATCTGGG	0.577																																					p.G320R		Atlas-SNP	.											.	NIT1	41	.	0			c.G958C						PASS	.						53	47	49					1																	161090529		2203	4300	6503	SO:0001583	missense	4817	exon7			CTCTATGGCAATC	AF069984	CCDS1218.1, CCDS53401.1, CCDS53402.1, CCDS53403.1	1q21-q22	2008-05-14			ENSG00000158793	ENSG00000158793			7828	protein-coding gene	gene with protein product		604618				9671749	Standard	NM_005600		Approved		uc001fxv.2	Q86X76	OTTHUMG00000031473	ENST00000368009.2:c.958G>C	chr1.hg19:g.161090529G>C	ENSP00000356988:p.Gly320Arg	75.0	0.0	.		81.0	30.0	.	NM_005600	B1AQP3|D3DVF4|O76091	Missense_Mutation	SNP	ENST00000368009.2	hg19	CCDS1218.1	.	.	.	.	.	.	.	.	.	.	G	14.99	2.700065	0.48307	.	.	ENSG00000158793	ENST00000368009;ENST00000368007;ENST00000392190	D;D;D	0.85629	-2.01;-2.01;-2.01	4.9	4.9	0.64082	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (2);	0.180864	0.48767	D	0.000178	D	0.85383	0.5684	L	0.37697	1.125	0.35101	D	0.765216	D;D	0.67145	0.995;0.996	D;D	0.67900	0.954;0.926	D	0.86846	0.2020	10	0.54805	T	0.06	-6.5407	15.6362	0.76953	0.0:0.0:1.0:0.0	.	305;320	Q86X76-4;Q86X76	.;NIT1_HUMAN	R	320;305;284	ENSP00000356988:G320R;ENSP00000356986:G305R;ENSP00000376028:G284R	ENSP00000356986:G305R	G	+	1	0	NIT1	159357153	0.997000	0.39634	0.996000	0.52242	0.646000	0.38490	2.400000	0.44504	2.551000	0.86045	0.563000	0.77884	GGC	.	.	.	none		0.577	NIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077060.1			C	161090529	G	C	161090529	3	2	100	1	0	0	0	0	1	0	0	0	10440	1348	47	4	1041	4	NIT1	1	161090529	Missense_Mutation	SNP	G	TCGA-B9-5155-01A-01D-1589-08	79080	161090529	88160092	10	6306											
BAT2L2	23215	hgsc.bcm.edu	37	chr1	171553267	171553267	+	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	ttcctatattgtatgaacatCaactggggcaggcatcagga	12	11	10	8	0	2	1	2	1	0	0	3	2	3	2	1	4	2	3	1	4	5	5			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr1:171553267C>T	ENST00000338920.4	+	29	7813	c.7576C>T	c.(7576-7578)Caa>Taa	p.Q2526*	PRRC2C_ENST00000426496.2_Nonsense_Mutation_p.Q2461*|PRRC2C_ENST00000367742.3_Nonsense_Mutation_p.Q2528*|PRRC2C_ENST00000392078.3_Nonsense_Mutation_p.Q2528*	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	2526	Gln-rich.				hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										GTATGAACATCAACTGGGGCA	0.478																																					p.Q2526X		Atlas-SNP	.											.	.	.	.	0			c.C7576T						PASS	.						199	195	197					1																	171553267		2203	4300	6503	SO:0001587	stop_gained	23215	exon29			GAACATCAACTGG	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.7576C>T	chr1.hg19:g.171553267C>T	ENSP00000343629:p.Gln2526*	266.0	0.0	.		339.0	150.0	.	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Nonsense_Mutation	SNP	ENST00000338920.4	hg19	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	C	50	16.839304	0.99873	.	.	ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080	.	.	.	6.16	6.16	0.99307	.	0.000000	0.43260	D	0.000582	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	.	.	.	X	2528;2480;2461;2528;2526;2283	.	ENSP00000343629:Q2526X	Q	+	1	0	PRRC2C	169819891	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.356000	0.79445	2.937000	0.99478	0.650000	0.86243	CAA	.	.	.	none		0.478	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		T	171553267	C	T	171553267	4	4	100	1	0	0	0	0	0	1	0	0	1321	827	29	2	7686	2	BAT2L2	1	171553267	Nonsense_Mutation	SNP	C	TCGA-B9-5155-01A-01D-1589-08	10462738	171553267	77697354	11	6307											
C1orf125	126859	hgsc.bcm.edu	37	chr1	179503894	179503894	+	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	aaatagagccagacaggcagAggagaagtttgaagatgcat	17	6	13	5	0	0	6	0	1	0	5	0	7	0	6	1	2	2	3	1	2	4	2	rs531976426	byFrequency	TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr1:179503894A>T	ENST00000367618.3	+	25	3215	c.2828A>T	c.(2827-2829)gAg>gTg	p.E943V		NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	943	Glu-rich.									NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						AGACAGGCAGAGGAGAAGTTT	0.338																																					p.E943V		Atlas-SNP	.											.	AXDND1	142	.	0			c.A2828T						PASS	.						68	70	69					1																	179503894		2203	4300	6503	SO:0001583	missense	126859	exon25			AGGCAGAGGAGAA	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.2828A>T	chr1.hg19:g.179503894A>T	ENSP00000356590:p.Glu943Val	140.0	0.0	.		128.0	52.0	.	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Missense_Mutation	SNP	ENST00000367618.3	hg19	CCDS30948.1	.	.	.	.	.	.	.	.	.	.	A	13.11	2.139365	0.37728	.	.	ENSG00000162779	ENST00000367618;ENST00000360322;ENST00000434088	T;T	0.34275	1.37;1.37	4.89	4.89	0.63831	.	0.000000	0.64402	D	0.000001	T	0.47838	0.1467	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.49532	-0.8930	10	0.87932	D	0	-4.2767	12.2781	0.54749	1.0:0.0:0.0:0.0	.	827;943	E9PCJ4;Q5T1B0	.;AXDN1_HUMAN	V	943;827;803	ENSP00000356590:E943V;ENSP00000391716:E803V	ENSP00000353471:E827V	E	+	2	0	AXDND1	177770517	1.000000	0.71417	1.000000	0.80357	0.510000	0.34073	3.729000	0.54999	2.179000	0.69175	0.482000	0.46254	GAG	.	.	.	none		0.338	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696		T	179503894	A	T	179503894	3	4	100	1	0	0	0	0	1	0	0	0	1995	304	11	5	2922	5	C1orf125	1	179503894	Missense_Mutation	SNP	A	TCGA-B9-5155-01A-01D-1589-08	7950627	179503894	69746727	12	6308											
TDRD5	163589	hgsc.bcm.edu	37	chr1	179609125	179609129	+	Frame_Shift_Del	DEL	GTGTT	GTGTT	-																															ttgagaaacaggaagttgaaGtgttctacccagactttgga																										TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	GTGTT	GTGTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr1:179609125_179609129delGTGTT	ENST00000367614.1	+	10	2031_2035	c.1672_1676delGTGTT	c.(1672-1677)gtgttcfs	p.VF558fs	TDRD5_ENST00000444136.1_Frame_Shift_Del_p.VF558fs|TDRD5_ENST00000294848.8_Frame_Shift_Del_p.VF558fs	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	558	Tudor. {ECO:0000255|PROSITE- ProRule:PRU00211}.				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						GGAAGTTGAAGTGTTCTACCCAGAC	0.395																																					p.557_559del		Atlas-INDEL	.											.	TDRD5	149	.	0			c.1671_1675del						PASS	.																																			SO:0001589	frameshift_variant	163589	exon10			.	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.1672_1676delGTGTT	chr1.hg19:g.179609125_179609129delGTGTT	ENSP00000356586:p.Val558fs	306.0	0.0	0		268.0	75.0	0.279851	NM_001199085	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Frame_Shift_Del	DEL	ENST00000367614.1	hg19	CCDS1332.1																																																																																			.	.	.	none		0.395	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		-	179609129	GTGTT	-	179609125	7	5	100	1	0	1	0	1	0	0	0	0	15745	1029	36	0	1706	0	TDRD5	1	179609125	Frame_Shift_Del	DEL	GTGTT	TCGA-B9-5155-01A-01D-1589-08	105231	179609125	69641496	13	6309											
CAPN9	10753	hgsc.bcm.edu	37	chr1	230907780	230907780	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaagcttccgaggccagagAatcgagctcatccgaatccg	11	7	11	12	4	1	1	1	0	0	1	5	5	4	1	4	1	2	3	4	1	3	2			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr1:230907780A>G	ENST00000271971.2	+	7	923	c.810A>G	c.(808-810)agA>agG	p.R270R	CAPN9_ENST00000366666.2_Silent_p.R207R|RP11-99J16__A.2_ENST00000412344.1_RNA|CAPN9_ENST00000354537.1_Silent_p.R270R	NM_006615.2	NP_006606.1	O14815	CAN9_HUMAN	calpain 9	270	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				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)				GAGGCCAGAGAATCGAGCTCA	0.537																																					p.R270R		Atlas-SNP	.											.	CAPN9	116	.	0			c.A810G						PASS	.						88	84	85					1																	230907780		2203	4300	6503	SO:0001819	synonymous_variant	10753	exon7			CCAGAGAATCGAG	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.810A>G	chr1.hg19:g.230907780A>G		145.0	0.0	.		133.0	57.0	.	NM_006615	B1APS1|B1AQI0|Q9NS74	Silent	SNP	ENST00000271971.2	hg19	CCDS1586.1																																																																																			.	.	.	none		0.537	CAPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092179.1	NM_006615		G	230907780	A	G	230907780	2	3	100	1	0	0	0	0	0	0	0	1	2634	243	9	3		3	CAPN9	1	230907780	Silent	SNP	A	TCGA-B9-5155-01A-01D-1589-08	51298655	230907780	18342841	14	6310											
PGBD2	267002	hgsc.bcm.edu	37	chr1	249211266	249211267	+	Frame_Shift_Ins	INS	-	-	A																															atttcattgttaatgaaaccINSaatcgttatgcttggcagaa																										TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr1:249211266_249211267insA	ENST00000329291.5	+	3	630_631	c.483_484insA	c.(484-486)aatfs	p.N162fs	PGBD2_ENST00000462488.1_Intron|PGBD2_ENST00000355360.4_Intron|PGBD2_ENST00000539153.1_Frame_Shift_Ins_p.N159fs	NM_170725.2	NP_733843.1	Q6P3X8	PGBD2_HUMAN	piggyBac transposable element derived 2	162										NS(1)|endometrium(3)|lung(6)|ovary(1)|skin(3)	14	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.012)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			TTAATGAAACCAATCGTTATGC	0.376																																					p.T161fs		Atlas-INDEL	.											.	PGBD2	103	.	0			c.483_484insA						PASS	.																																			SO:0001589	frameshift_variant	267002	exon3			.	AF229602	CCDS31128.1, CCDS31129.1	1q	2008-02-05			ENSG00000185220	ENSG00000185220			19399	protein-coding gene	gene with protein product							Standard	XM_005270333		Approved		uc001ifh.3	Q6P3X8	OTTHUMG00000040424	ENST00000329291.5:c.485dupA	chr1.hg19:g.249211268_249211268dupA	ENSP00000331643:p.Asn162fs	213.0	0.0	0		241.0	105.0	0.435685	NM_170725	B3KVR8|Q6MZF8	Frame_Shift_Ins	INS	ENST00000329291.5	hg19	CCDS31128.1																																																																																			.	.	.	none		0.376	PGBD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000097318.1			A	249211267	-	A	249211266	7	5	100	1	0	1	1	0	0	0	0	0	11788	581	21	0	489	0	PGBD2	1	249211266	Frame_Shift_Ins	INS	-	TCGA-B9-5155-01A-01D-1589-08	18303486	249211266	39355	15	6311											
ATAD2B	54454	hgsc.bcm.edu	37	chr2	24046400	24046400	+	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	tccgcagtgcaatcagggcgGcttcagtgcacagggccttg	7	8	14	12	2	2	0	2	0	0	0	3	0	3	0	2	3	2	4	2	3	1	2			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr2:24046400G>C	ENST00000238789.5	-	16	2202	c.1859C>G	c.(1858-1860)gCc>gGc	p.A620G	ATAD2B_ENST00000474583.1_5'UTR	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	620						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AATCAGGGCGGCTTCAGTGCA	0.468																																					p.A620G		Atlas-SNP	.											.	ATAD2B	110	.	0			c.C1859G						PASS	.						77	74	75					2																	24046400		1978	4160	6138	SO:0001583	missense	54454	exon16			AGGGCGGCTTCAG	AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"ATPases / AAA-type"	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.1859C>G	chr2.hg19:g.24046400G>C	ENSP00000238789:p.Ala620Gly	64.0	0.0	.		67.0	31.0	.	NM_001242338	B9ZVQ5|Q6ZNA6|Q8N9E7	Missense_Mutation	SNP	ENST00000238789.5	hg19	CCDS46227.1	.	.	.	.	.	.	.	.	.	.	G	31	5.060927	0.93846	.	.	ENSG00000119778	ENST00000238789;ENST00000458510	D;D	0.96396	-4.0;-3.74	5.21	5.21	0.72293	.	.	.	.	.	D	0.98280	0.9430	M	0.85099	2.735	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.99150	1.0858	9	0.87932	D	0	.	19.1413	0.93446	0.0:0.0:1.0:0.0	.	620	Q9ULI0	ATD2B_HUMAN	G	620;58	ENSP00000238789:A620G;ENSP00000392764:A58G	ENSP00000238789:A620G	A	-	2	0	ATAD2B	23899904	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.790000	0.99075	2.609000	0.88269	0.655000	0.94253	GCC	.	.	.	none		0.468	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552		C	24046400	G	C	24046400	3	2	100	1	0	0	0	0	1	0	0	0	1072	1203	42	4	2569	4	ATAD2B	2	24046400	Missense_Mutation	SNP	G	TCGA-B9-5155-01A-01D-1589-08		24046400	219152973	16	6312											
C2orf44	80304	hgsc.bcm.edu	37	chr2	24262142	24262142	+	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	atgctggacagcgagtagaaCaggtgtatcatctgcaacag	13	8	12	8	1	2	1	1	0	1	1	2	3	2	2	0	2	5	4	0	2	4	2			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr2:24262142C>A	ENST00000295148.4	-	2	280	c.223G>T	c.(223-225)Gtt>Ttt	p.V75F	C2orf44_ENST00000406895.3_Missense_Mutation_p.V75F	NM_025203.2	NP_079479.1	Q9H6R7	CB044_HUMAN	chromosome 2 open reading frame 44	75									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)					GCGAGTAGAACAGGTGTATCA	0.517			T	ALK	NSCLC																																p.V75F		Atlas-SNP	.		Dom	yes		2	2p23.3	80304	chromosome 2 open reading frame 44		E	.	C2orf44	56	.	0			c.G223T						PASS	.						113	100	104					2																	24262142		2203	4300	6503	SO:0001583	missense	80304	exon2			GTAGAACAGGTGT	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.223G>T	chr2.hg19:g.24262142C>A	ENSP00000295148:p.Val75Phe	49.0	0.0	.		66.0	30.0	.	NM_025203	D6W532|Q8IYK0|Q9HBP5	Missense_Mutation	SNP	ENST00000295148.4	hg19	CCDS1705.1	.	.	.	.	.	.	.	.	.	.	C	7.466	0.645750	0.14451	.	.	ENSG00000163026	ENST00000295148;ENST00000406895;ENST00000443232	T;T;T	0.51071	3.45;3.45;0.72	5.24	-5.89	0.02282	.	0.374860	0.32218	N	0.006412	T	0.16428	0.0395	N	0.08118	0	0.09310	N	0.999998	P;P	0.34546	0.456;0.456	B;B	0.27076	0.076;0.076	T	0.11060	-1.0603	10	0.87932	D	0	-0.5627	4.2048	0.10483	0.0901:0.4263:0.0883:0.3952	.	75;75	Q9H6R7-2;Q9H6R7	.;CB044_HUMAN	F	75	ENSP00000295148:V75F;ENSP00000385816:V75F;ENSP00000413426:V75F	ENSP00000295148:V75F	V	-	1	0	C2orf44	24115646	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.157000	0.16402	-1.253000	0.02488	-0.890000	0.02929	GTT	.	.	.	none		0.517	C2orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246825.1	NM_025203		A	24262142	C	A	24262142	3	1	100	1	0	0	0	0	1	0	0	0	2170	478	17	4	1954	4	C2orf44	2	24262142	Missense_Mutation	SNP	C	TCGA-B9-5155-01A-01D-1589-08	215742	24262142	218937231	17	6313											
ASPRV1	151516	hgsc.bcm.edu	37	chr2	70188627	70188627	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaagaagagaaacccacagAgcagtgtcggcgcaatcacg	15	3	11	12	3	1	3	1	0	0	3	2	4	1	3	2	1	2	2	2	1	4	0			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr2:70188627A>G	ENST00000320256.4	-	1	770	c.194T>C	c.(193-195)cTc>cCc	p.L65P	PCBP1-AS1_ENST00000457076.1_RNA|PCBP1-AS1_ENST00000418564.1_RNA|PCBP1-AS1_ENST00000596259.1_RNA|PCBP1-AS1_ENST00000415222.1_RNA|PCBP1-AS1_ENST00000413436.1_RNA|PCBP1-AS1_ENST00000419542.1_RNA|PCBP1-AS1_ENST00000435880.2_RNA	NM_152792.2	NP_690005.2			aspartic peptidase, retroviral-like 1											endometrium(3)|large_intestine(4)|lung(6)|ovary(1)	14						AAACCCACAGAGCAGTGTCGG	0.657																																					p.L65P		Atlas-SNP	.											.	ASPRV1	41	.	0			c.T194C						PASS	.						41	39	39					2																	70188627		2203	4300	6503	SO:0001583	missense	151516	exon1			CCACAGAGCAGTG	AK055994	CCDS1897.1	2p13.3	2008-02-20			ENSG00000244617	ENSG00000244617			26321	protein-coding gene	gene with protein product	"Skin ASpartic Protease"	611765				16098038, 16565508	Standard	NM_152792		Approved	Taps, SASPase, FLJ25084	uc002sfz.4	Q53RT3	OTTHUMG00000129647	ENST00000320256.4:c.194T>C	chr2.hg19:g.70188627A>G	ENSP00000315383:p.Leu65Pro	60.0	0.0	.		58.0	24.0	.	NM_152792		Missense_Mutation	SNP	ENST00000320256.4	hg19	CCDS1897.1	.	.	.	.	.	.	.	.	.	.	A	15.92	2.974023	0.53720	.	.	ENSG00000244617	ENST00000320256	T	0.57273	0.41	5.79	4.57	0.56435	.	0.521020	0.14392	N	0.322440	T	0.52008	0.1708	N	0.24115	0.695	0.50813	D	0.999891	D	0.58970	0.984	P	0.57371	0.819	T	0.53472	-0.8434	10	0.87932	D	0	-8.9663	9.3054	0.37872	0.819:0.181:0.0:0.0	.	65	Q53RT3	APRV1_HUMAN	P	65	ENSP00000315383:L65P	ENSP00000315383:L65P	L	-	2	0	ASPRV1	70042131	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.247000	0.58750	2.207000	0.71202	0.533000	0.62120	CTC	.	.	.	none		0.657	ASPRV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334161.1	NM_152792		G	70188627	A	G	70188627	3	3	100	1	0	0	0	0	1	0	0	0	1058	304	11	3	841	3	ASPRV1	2	70188627	Missense_Mutation	SNP	A	TCGA-B9-5155-01A-01D-1589-08	45926485	70188627	173010746	18	6314											
SPOPL	339745	hgsc.bcm.edu	37	chr2	139318408	139318408	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	taaatgatttagaccctgaaGtttttaaagaaatgatgaga	17	13	8	3	0	0	6	0	4	0	3	0	7	0	6	1	0	0	1	1	0	7	6			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr2:139318408G>A	ENST00000280098.4	+	8	1127	c.748G>A	c.(748-750)Gtt>Att	p.V250I		NM_001001664.2	NP_001001664.1	Q6IQ16	SPOPL_HUMAN	speckle-type POZ protein-like	250	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				negative regulation of protein ubiquitination (GO:0031397)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nucleus (GO:0005634)				breast(2)|cervix(2)|endometrium(2)|large_intestine(2)|lung(11)|skin(2)	21				BRCA - Breast invasive adenocarcinoma(221;0.0296)		AGACCCTGAAGTTTTTAAAGA	0.328																																					p.V250I		Atlas-SNP	.											.	SPOPL	54	.	0			c.G748A						PASS	.						72	76	75					2																	139318408		2203	4300	6503	SO:0001583	missense	339745	exon8			CCTGAAGTTTTTA		CCDS33298.1	2q22.1	2013-01-09			ENSG00000144228	ENSG00000144228		"BTB/POZ domain containing"	27934	protein-coding gene	gene with protein product	"HIB homolog 2", "roadkill homolog 2"						Standard	NM_001001664		Approved	BTBD33	uc002tvh.3	Q6IQ16	OTTHUMG00000153635	ENST00000280098.4:c.748G>A	chr2.hg19:g.139318408G>A	ENSP00000280098:p.Val250Ile	101.0	0.0	.		118.0	58.0	.	NM_001001664		Missense_Mutation	SNP	ENST00000280098.4	hg19	CCDS33298.1	.	.	.	.	.	.	.	.	.	.	G	34	5.402843	0.96030	.	.	ENSG00000144228	ENST00000280098	T	0.68331	-0.32	5.24	5.24	0.73138	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.77705	0.4170	L	0.59912	1.85	0.80722	D	1	D	0.56968	0.978	P	0.60682	0.878	T	0.76165	-0.3059	9	.	.	.	-16.2686	19.1816	0.93625	0.0:0.0:1.0:0.0	.	250	Q6IQ16	SPOPL_HUMAN	I	250	ENSP00000280098:V250I	.	V	+	1	0	SPOPL	139034878	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.813000	0.99286	2.601000	0.87937	0.655000	0.94253	GTT	.	.	.	none		0.328	SPOPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331897.1			A	139318408	G	A	139318408	3	1	100	1	0	0	0	0	1	0	0	0	15097	1029	36	2	774	2	SPOPL	2	139318408	Missense_Mutation	SNP	G	TCGA-B9-5155-01A-01D-1589-08	69129781	139318408	103880965	19	6315											
PKP4	8502	hgsc.bcm.edu	37	chr2	159537000	159537001	+	Frame_Shift_Ins	INS	-	-	T																															agaactttgatgcatacagaINSttgtatttgcagtctcctca																										TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr2:159537000_159537001insT	ENST00000389759.3	+	22	3502_3503	c.3390_3391insT	c.(3391-3393)ttgfs	p.L1131fs	PKP4_ENST00000389757.3_Frame_Shift_Ins_p.L1088fs|AC005042.4_ENST00000342892.4_RNA|AC005042.4_ENST00000442666.1_RNA	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	1131					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						ATGCATACAGATTGTATTTGCA	0.351										HNSCC(62;0.18)																											p.R1130fs		Atlas-INDEL	.											.	PKP4	133	.	0			c.3390_3391insT						PASS	.																																			SO:0001589	frameshift_variant	8502	exon22			.	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.3392dupT	chr2.hg19:g.159537002_159537002dupT	ENSP00000374409:p.Leu1131fs	138.0	0.0	0		173.0	88.0	0.508671	NM_003628	Q86W91	Frame_Shift_Ins	INS	ENST00000389759.3	hg19	CCDS33305.1																																																																																			.	.	.	none		0.351	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1			T	159537001	-	T	159537000	7	5	100	1	0	1	1	0	0	0	0	0	11994	330	12	0	3472	0	PKP4	2	159537000	Frame_Shift_Ins	INS	-	TCGA-B9-5155-01A-01D-1589-08	20218592	159537000	83662373	20	6316											
CCDC141	285025	hgsc.bcm.edu	37	chr2	179701991	179701991	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actcatcatgctctctggatGttcagcactgattctgtgta	8	15	8	10	0	5	1	3	1	2	0	6	2	5	2	0	1	2	4	0	1	1	3			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr2:179701991G>A	ENST00000420890.2	-	23	4072	c.3955C>T	c.(3955-3957)Cat>Tat	p.H1319Y	CCDC141_ENST00000480419.1_5'UTR|CCDC141_ENST00000295723.5_Missense_Mutation_p.H744Y	NM_173648.3	NP_775919.3	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	1319										NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(37)|ovary(8)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)	78			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			CTCTCTGGATGTTCAGCACTG	0.493																																					p.H1319Y		Atlas-SNP	.											.	CCDC141	362	.	0			c.C3955T						PASS	.						121	105	110					2																	179701991		2203	4300	6503	SO:0001583	missense	285025	exon23			CTGGATGTTCAGC	AK096821		2q31.2	2013-01-14			ENSG00000163492	ENSG00000163492		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26821	protein-coding gene	gene with protein product	"coiled-coil protein associated with myosin II and DISC1"					20956536	Standard	NM_173648		Approved	FLJ39502, CAMDI	uc002une.2	Q6ZP82	OTTHUMG00000132578	ENST00000420890.2:c.3955C>T	chr2.hg19:g.179701991G>A	ENSP00000395995:p.His1319Tyr	77.0	0.0	.		91.0	37.0	.	NM_173648	H7C0P1|J3KNW6|Q8N8H3	Missense_Mutation	SNP	ENST00000420890.2	hg19		.	.	.	.	.	.	.	.	.	.	G	0.081	-1.183772	0.01620	.	.	ENSG00000163492	ENST00000420890;ENST00000343876;ENST00000295723	T;T;T	0.44083	0.93;1.53;1.53	5.71	4.83	0.62350	.	1.233450	0.05438	N	0.547098	T	0.31167	0.0788	N	0.22421	0.69	0.09310	N	1	P;P	0.48503	0.61;0.911	B;B	0.41813	0.26;0.367	T	0.03306	-1.1050	10	0.07482	T	0.82	0.9855	10.9382	0.47257	0.1512:0.0:0.8488:0.0	.	744;744	Q6ZP82;Q6ZP82-2	CC141_HUMAN;.	Y	1319;763;744	ENSP00000395995:H1319Y;ENSP00000344627:H763Y;ENSP00000295723:H744Y	ENSP00000295723:H744Y	H	-	1	0	CCDC141	179410236	0.771000	0.28555	0.016000	0.15963	0.438000	0.31896	2.406000	0.44557	1.387000	0.46486	0.655000	0.94253	CAT	.	.	.	none		0.493	CCDC141-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173648		A	179701991	G	A	179701991	3	1	100	1	0	0	0	0	1	0	0	0	2777	1377	48	2	401	2	CCDC141	2	179701991	Missense_Mutation	SNP	G	TCGA-B9-5155-01A-01D-1589-08	20164991	179701991	63497382	21	6317											
DOCK10	55619	hgsc.bcm.edu	37	chr2	225670917	225670917	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttgatagctgtctggcttTgaaatcctccattggtgctt	6	17	10	8	0	1	2	0	2	1	0	3	2	3	2	2	2	2	4	2	2	2	5			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr2:225670917T>C	ENST00000258390.7	-	34	3807	c.3740A>G	c.(3739-3741)cAa>cGa	p.Q1247R	DOCK10_ENST00000409592.3_Missense_Mutation_p.Q1241R	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1247					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)		TGTCTGGCTTTGAAATCCTCC	0.363																																					p.Q1247R		Atlas-SNP	.											.	DOCK10	308	.	0			c.A3740G						PASS	.						142	140	140					2																	225670917		1854	4089	5943	SO:0001583	missense	55619	exon34			TGGCTTTGAAATC	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.3740A>G	chr2.hg19:g.225670917T>C	ENSP00000258390:p.Gln1247Arg	52.0	0.0	.		58.0	28.0	.	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	hg19	CCDS46528.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	1.613|1.613	-0.523497|-0.523497	0.04141|0.04141	.|.	.|.	ENSG00000135905|ENSG00000135905	ENST00000422684|ENST00000409592;ENST00000258390	.|T;T	.|0.21361	.|2.01;2.01	5.85|5.85	1.96|1.96	0.26148|0.26148	.|.	.|0.628162	.|0.17934	.|N	.|0.157066	T|T	0.18215|0.18215	0.0437|0.0437	L|L	0.54323|0.54323	1.7|1.7	0.28864|0.28864	N|N	0.895366|0.895366	.|B;B	.|0.25955	.|0.112;0.138	.|B;B	.|0.18561	.|0.022;0.013	T|T	0.25293|0.25293	-1.0136|-1.0136	5|10	.|0.10902	.|T	.|0.67	.|.	13.4531|13.4531	0.61182|0.61182	0.0:0.0:0.3725:0.6275|0.0:0.0:0.3725:0.6275	.|.	.|1247;1241	.|Q96BY6;B3FL70	.|DOC10_HUMAN;.	E|R	138|1241;1247	.|ENSP00000386694:Q1241R;ENSP00000258390:Q1247R	.|ENSP00000258390:Q1247R	K|Q	-|-	1|2	0|0	DOCK10|DOCK10	225379161|225379161	0.680000|0.680000	0.27605|0.27605	0.279000|0.279000	0.24732|0.24732	0.344000|0.344000	0.29017|0.29017	0.810000|0.810000	0.27183|0.27183	0.089000|0.089000	0.17243|0.17243	-0.291000|-0.291000	0.09656|0.09656	AAA|CAA	.	.	.	none		0.363	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			C	225670917	T	C	225670917	3	2	100	1	0	0	0	0	1	0	0	0	4687	1812	63	3	2912	3	DOCK10	2	225670917	Missense_Mutation	SNP	T	TCGA-B9-5155-01A-01D-1589-08	45968926	225670917	17528456	22	6318											
COL6A3	1293	hgsc.bcm.edu	37	chr2	238262001	238262001	+	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	cacctgtgcacctctggtccCctgctctccctcaaagcccg	5	9	7	20	1	3	0	1	0	2	0	5	0	4	0	6	1	3	2	6	1	1	0	rs138588234		TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr2:238262001C>G	ENST00000295550.4	-	25	7125	c.6673G>C	c.(6673-6675)Ggg>Cgg	p.G2225R	COL6A3_ENST00000346358.4_Missense_Mutation_p.G2025R|COL6A3_ENST00000353578.4_Missense_Mutation_p.G2019R|COL6A3_ENST00000347401.3_Missense_Mutation_p.G2024R|COL6A3_ENST00000472056.1_Missense_Mutation_p.G1618R|COL6A3_ENST00000409809.1_Missense_Mutation_p.G2019R	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2225	Collagen-like 3.|Triple-helical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.G2225R(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)		CCTCTGGTCCCCTGCTCTCCC	0.507																																					p.G2225R		Atlas-SNP	.											COL6A3,arm,malignant_melanoma,0,1	COL6A3	608	.	1	Substitution - Missense(1)	skin(1)	c.G6673C						PASS	.						71	63	66					2																	238262001		2203	4300	6503	SO:0001583	missense	1293	exon25			TGGTCCCCTGCTC	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.6673G>C	chr2.hg19:g.238262001C>G	ENSP00000295550:p.Gly2225Arg	52.0	0.0	.		81.0	0.0	.	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	12.84	2.058734	0.36277	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.99637	-6.29;-6.29;-6.29;-6.29;-6.29;-6.29	5.21	5.21	0.72293	.	0.000000	0.51477	D	0.000089	D	0.99796	0.9913	H	0.97315	3.98	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;1.0;0.999	D	0.96877	0.9643	10	0.87932	D	0	.	16.9555	0.86258	0.0:1.0:0.0:0.0	.	1618;1618;2019;2225	E9PFQ6;B7ZMJ7;P12111-2;P12111	.;.;.;CO6A3_HUMAN	R	2225;2024;2019;1618;2019;2025	ENSP00000295550:G2225R;ENSP00000315609:G2024R;ENSP00000315873:G2019R;ENSP00000418285:G1618R;ENSP00000386844:G2019R;ENSP00000295546:G2025R	ENSP00000295550:G2225R	G	-	1	0	COL6A3	237926740	1.000000	0.71417	1.000000	0.80357	0.724000	0.41520	5.391000	0.66266	2.429000	0.82318	0.655000	0.94253	GGG	.	.	.	alt		0.507	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		G	238262001	C	G	238262001	3	3	100	1	0	0	0	0	1	0	0	0	3703	623	22	4	2940	4	COL6A3	2	238262001	Missense_Mutation	SNP	C	TCGA-B9-5155-01A-01D-1589-08	12591084	238262001	4937372	23	6319											
GADL1	339896	hgsc.bcm.edu	37	chr3	30819676	30819676	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttacttattacttaccaaatTaagttttgcccagaactcgg	12	15	5	9	1	0	1	0	0	0	1	1	1	0	1	2	1	5	1	2	1	7	7			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr3:30819676T>C	ENST00000282538.5	-	14	1537	c.1387A>G	c.(1387-1389)Aat>Gat	p.N463D	GADL1_ENST00000498387.1_5'UTR	NM_207359.2	NP_997242.2	Q6ZQY3	GADL1_HUMAN	glutamate decarboxylase-like 1	463					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						CTTACCAAATTAAGTTTTGCC	0.368																																					p.N463D		Atlas-SNP	.											.	GADL1	91	.	0			c.A1387G						PASS	.						69	74	72					3																	30819676		2203	4300	6503	SO:0001583	missense	339896	exon14			CCAAATTAAGTTT	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.1387A>G	chr3.hg19:g.30819676T>C	ENSP00000282538:p.Asn463Asp	107.0	0.0	.		173.0	45.0	.	NM_207359		Missense_Mutation	SNP	ENST00000282538.5	hg19	CCDS2649.2	.	.	.	.	.	.	.	.	.	.	T	10.90	1.481092	0.26598	.	.	ENSG00000144644	ENST00000282538	T	0.35973	1.28	6.02	-3.37	0.04898	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.641607	0.16112	N	0.229060	T	0.17704	0.0425	N	0.05230	-0.09	0.09310	N	0.999995	B	0.02656	0.0	B	0.04013	0.001	T	0.20672	-1.0268	10	0.07990	T	0.79	-15.4742	21.8233	0.99961	0.0:0.0:0.7797:0.2203	.	463	Q6ZQY3	GADL1_HUMAN	D	463	ENSP00000282538:N463D	ENSP00000282538:N463D	N	-	1	0	GADL1	30794680	0.310000	0.24527	0.388000	0.26195	0.995000	0.86356	0.409000	0.21082	-0.824000	0.04295	0.533000	0.62120	AAT	.	.	.	none		0.368	GADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253106.2	NM_207359		C	30819676	T	C	30819676	3	2	100	1	0	0	0	0	1	0	0	0	6192	1754	61	3	186	3	GADL1	3	30819676	Missense_Mutation	SNP	T	TCGA-B9-5155-01A-01D-1589-08		30819676	167202754	24	6320											
SETD2	29072	hgsc.bcm.edu	37	chr3	47158197	47158197	+	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	catctttagaaagaggtgtaCactcacactgcattcgctta	12	12	7	10	1	2	2	1	0	1	2	3	2	2	2	0	1	2	3	0	1	4	5			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr3:47158197C>G	ENST00000409792.3	-	4	4544	c.4502G>C	c.(4501-4503)tGt>tCt	p.C1501S		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1501	AWS. {ECO:0000255|PROSITE- ProRule:PRU00562}.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		AAGAGGTGTACACTCACACTG	0.318			"N, F, S, Mis"		clear cell renal carcinoma																																p.C1501S		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	SETD2_ENST00000409792,NS,carcinoma,-1,6	SETD2	721	.	0			c.G4502C						PASS	.						114	110	111					3																	47158197		2203	4300	6503	SO:0001583	missense	29072	exon4			GGTGTACACTCAC	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4502G>C	chr3.hg19:g.47158197C>G	ENSP00000386759:p.Cys1501Ser	113.0	0.0	.		188.0	106.0	.	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	C	29.1	4.973314	0.92919	.	.	ENSG00000181555	ENST00000451092;ENST00000543224;ENST00000409792	D	0.85411	-1.98	5.93	5.93	0.95920	AWS (2);	0.000000	0.64402	D	0.000007	D	0.95538	0.8550	H	0.96691	3.865	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.77004	0.989;0.989	D	0.96291	0.9214	10	0.87932	D	0	.	20.3495	0.98807	0.0:1.0:0.0:0.0	.	1501;1501	F2Z317;Q9BYW2	.;SETD2_HUMAN	S	1501	ENSP00000386759:C1501S	ENSP00000386759:C1501S	C	-	2	0	SETD2	47133201	1.000000	0.71417	0.994000	0.49952	0.997000	0.91878	7.794000	0.85869	2.814000	0.96858	0.591000	0.81541	TGT	.	.	.	none		0.318	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		G	47158197	C	G	47158197	3	3	100	1	0	0	0	0	1	0	0	0	14144	478	17	4	3264	4	SETD2	3	47158197	Missense_Mutation	SNP	C	TCGA-B9-5155-01A-01D-1589-08	16338521	47158197	150864233	25	6321											
USP19	10869	hgsc.bcm.edu	37	chr3	49149414	49149414	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcaggtacactgaccaggaAggggtagccaatgttctcag	11	7	14	9	0	1	1	1	1	1	0	2	2	1	2	2	5	2	4	2	5	4	3			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr3:49149414A>G	ENST00000398888.2	-	19	2842	c.2524T>C	c.(2524-2526)Ttc>Ctc	p.F842L	USP19_ENST00000398892.3_Missense_Mutation_p.F882L|USP19_ENST00000417901.1_Missense_Mutation_p.F945L|USP19_ENST00000434032.2_Missense_Mutation_p.F943L|USP19_ENST00000398896.1_Missense_Mutation_p.F650L|USP19_ENST00000398898.2_Missense_Mutation_p.F882L|USP19_ENST00000453664.1_Missense_Mutation_p.F933L	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	842	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)		CTGACCAGGAAGGGGTAGCCA	0.587																																					p.F945L		Atlas-SNP	.											.	USP19	158	.	0			c.T2833C						PASS	.						81	87	85					3																	49149414		2103	4217	6320	SO:0001583	missense	10869	exon20			CCAGGAAGGGGTA	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.2524T>C	chr3.hg19:g.49149414A>G	ENSP00000381863:p.Phe842Leu	47.0	0.0	.		97.0	39.0	.	NM_001199161	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Missense_Mutation	SNP	ENST00000398888.2	hg19	CCDS43090.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.360831	0.82353	.	.	ENSG00000172046	ENST00000398896;ENST00000398898;ENST00000417901;ENST00000453664;ENST00000398892;ENST00000398888;ENST00000434032	T;T;T;T;T;T;T	0.21031	2.07;2.04;2.14;2.13;2.03;2.17;2.12	5.94	5.94	0.96194	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.407146	0.28895	N	0.013785	T	0.34571	0.0902	L	0.35593	1.075	0.80722	D	1	P;P;P;D;B	0.63046	0.767;0.767;0.602;0.992;0.149	B;B;B;D;B	0.76071	0.34;0.34;0.25;0.987;0.093	T	0.03922	-1.0992	10	0.18276	T	0.48	-26.8203	16.3979	0.83621	1.0:0.0:0.0:0.0	.	943;933;842;882;650	E9PEG8;E7EN22;O94966;B5MEG5;E7ESU0	.;.;UBP19_HUMAN;.;.	L	650;882;945;933;882;842;943	ENSP00000381870:F650L;ENSP00000381872:F882L;ENSP00000395260:F945L;ENSP00000400090:F933L;ENSP00000381867:F882L;ENSP00000381863:F842L;ENSP00000401197:F943L	ENSP00000381863:F842L	F	-	1	0	USP19	49124418	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.978000	0.93450	2.279000	0.76181	0.459000	0.35465	TTC	.	.	.	none		0.587	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677		G	49149414	A	G	49149414	3	3	100	1	0	0	0	0	1	0	0	0	17062	72	3	3	1464	3	USP19	3	49149414	Missense_Mutation	SNP	A	TCGA-B9-5155-01A-01D-1589-08	1991217	49149414	148873016	26	6322											
ACOX2	8309	hgsc.bcm.edu	37	chr3	58514651	58514651	+	Missense_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	gaaagagtttctgctgttgtGtctggtagtccaggaccttt	7	15	12	7	0	2	1	0	0	2	1	3	3	3	2	2	2	1	4	2	2	2	4			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr3:58514651G>A	ENST00000302819.5	-	9	1316	c.1025C>T	c.(1024-1026)aCa>aTa	p.T342I	ACOX2_ENST00000459701.2_Missense_Mutation_p.T328I	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	342					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)		CTGCTGTTGTGTCTGGTAGTC	0.507																																					p.T342I		Atlas-SNP	.											.	ACOX2	53	.	0			c.C1025T						PASS	.						138	131	133					3																	58514651		2203	4300	6503	SO:0001583	missense	8309	exon9			TGTTGTGTCTGGT	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.1025C>T	chr3.hg19:g.58514651G>A	ENSP00000307697:p.Thr342Ile	66.0	0.0	.		115.0	48.0	.	NM_003500	A6NF16|B2R8U5	Missense_Mutation	SNP	ENST00000302819.5	hg19	CCDS33775.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.376899	0.82682	.	.	ENSG00000168306	ENST00000459701;ENST00000302819	T;T	0.70869	-0.52;-0.52	4.94	4.94	0.65067	Acyl-CoA dehydrogenase/oxidase C-terminal (2);	0.000000	0.64402	D	0.000001	D	0.85927	0.5811	M	0.85197	2.74	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	D	0.87969	0.2735	10	0.87932	D	0	-28.2004	18.3225	0.90243	0.0:0.0:1.0:0.0	.	342	Q99424	ACOX2_HUMAN	I	328;342	ENSP00000418562:T328I;ENSP00000307697:T342I	ENSP00000307697:T342I	T	-	2	0	ACOX2	58489691	1.000000	0.71417	0.965000	0.40720	0.808000	0.45660	8.509000	0.90529	2.728000	0.93425	0.561000	0.74099	ACA	.	.	.	none		0.507	ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1			A	58514651	G	A	58514651	3	1	100	1	0	0	0	0	1	0	0	0	159	1377	48	2	1048	2	ACOX2	3	58514651	Missense_Mutation	SNP	G	TCGA-B9-5155-01A-01D-1589-08	9365237	58514651	139507779	27	6323											
IQCB1	9657	hgsc.bcm.edu	37	chr3	121500645	121500645	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagttcaactcggcgtgcaTcagtgagttcttggagtcct	7	13	11	10	2	4	1	3	1	1	0	6	2	5	2	1	2	2	3	1	2	1	3			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr3:121500645T>C	ENST00000310864.6	-	13	1569	c.1355A>G	c.(1354-1356)gAt>gGt	p.D452G	IQCB1_ENST00000349820.6_Missense_Mutation_p.D319G	NM_001023570.2	NP_001018864.2	Q15051	IQCB1_HUMAN	IQ motif containing B1	452					cilium assembly (GO:0042384)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)	calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)			NS(1)|biliary_tract(1)|breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(11)|prostate(1)|skin(1)	30				GBM - Glioblastoma multiforme(114;0.0983)		TCGGCGTGCATCAGTGAGTTC	0.408																																					p.D452G		Atlas-SNP	.											.	IQCB1	50	.	0			c.A1355G						PASS	.						151	141	145					3																	121500645		2203	4300	6503	SO:0001583	missense	9657	exon13			CGTGCATCAGTGA	D25278	CCDS33836.1, CCDS33837.1	3q21.1	2014-01-28	2004-09-02		ENSG00000173226	ENSG00000173226			28949	protein-coding gene	gene with protein product	"nephrocystin-5"	609237	"IQ calmodulin-binding motif containing 1"			15723066	Standard	NM_001023571		Approved	KIAA0036, NPHP5, SLSN5	uc010hre.1	Q15051	OTTHUMG00000128677	ENST00000310864.6:c.1355A>G	chr3.hg19:g.121500645T>C	ENSP00000311505:p.Asp452Gly	165.0	0.0	.		259.0	153.0	.	NM_001023570	Q3KS08|Q3KS09|Q5DKQ7|Q8NI79|Q9BS08	Missense_Mutation	SNP	ENST00000310864.6	hg19	CCDS33837.1	.	.	.	.	.	.	.	.	.	.	T	18.84	3.710100	0.68730	.	.	ENSG00000173226	ENST00000310864;ENST00000349820	T;T	0.79141	-1.24;-1.24	4.61	4.61	0.57282	.	0.000000	0.85682	D	0.000000	D	0.85204	0.5643	M	0.66939	2.045	0.52501	D	0.999953	D;D	0.89917	0.993;1.0	D;D	0.87578	0.971;0.998	D	0.86234	0.1639	10	0.72032	D	0.01	-13.185	10.5952	0.45333	0.0:0.0:0.0:1.0	.	452;319	Q15051;Q15051-2	IQCB1_HUMAN;.	G	452;319	ENSP00000311505:D452G;ENSP00000323756:D319G	ENSP00000311505:D452G	D	-	2	0	IQCB1	122983335	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	3.446000	0.52928	2.062000	0.61559	0.482000	0.46254	GAT	.	.	.	none		0.408	IQCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250573.1	NM_014642		C	121500645	T	C	121500645	3	2	100	1	0	0	0	0	1	0	0	0	7810	1435	50	3	453	3	IQCB1	3	121500645	Missense_Mutation	SNP	T	TCGA-B9-5155-01A-01D-1589-08	62985994	121500645	76521785	28	6324											
MBNL1	4154	hgsc.bcm.edu	37	chr3	152165476	152165476	+	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	tgaaaaaaccaacggtgccaCcgcagtctttaacactggta	14	8	8	11	2	1	1	0	1	1	0	1	1	1	1	3	2	4	2	3	2	6	3			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr3:152165476C>A	ENST00000463374.1	+	6	1440	c.929C>A	c.(928-930)aCc>aAc	p.T310N	Y_RNA_ENST00000364347.1_RNA|MBNL1_ENST00000357472.3_Missense_Mutation_p.T292N|MBNL1_ENST00000282488.7_Missense_Mutation_p.T224N|MBNL1_ENST00000282486.6_Missense_Mutation_p.T310N|MBNL1_ENST00000492948.1_Missense_Mutation_p.T292N|MBNL1_ENST00000498502.1_Missense_Mutation_p.T310N|MBNL1_ENST00000493459.1_Missense_Mutation_p.T253N|MBNL1_ENST00000485910.1_Missense_Mutation_p.T224N|MBNL1_ENST00000545754.1_Missense_Mutation_p.T224N|MBNL1_ENST00000324210.5_Missense_Mutation_p.T292N|MBNL1_ENST00000485509.1_Intron|MBNL1_ENST00000355460.2_Missense_Mutation_p.T292N|MBNL1_ENST00000324196.5_Intron	NM_207293.1	NP_997176.1	Q9NR56	MBNL1_HUMAN	muscleblind-like splicing regulator 1	310					alternative mRNA splicing, via spliceosome (GO:0000380)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|mRNA splice site selection (GO:0006376)|myoblast differentiation (GO:0045445)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|skeletal muscle tissue development (GO:0007519)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			AACGGTGCCACCGCAGTCTTT	0.453																																					p.T310N		Atlas-SNP	.											.	MBNL1	100	.	0			c.C929A						PASS	.						97	95	95					3																	152165476		2203	4300	6503	SO:0001583	missense	4154	exon6			GTGCCACCGCAGT	Y13829	CCDS3163.1, CCDS3164.1, CCDS3165.1, CCDS3166.1, CCDS3167.1, CCDS3168.1, CCDS54656.1	3q25	2013-01-18	2012-02-23	2003-03-14	ENSG00000152601	ENSG00000152601		"Zinc fingers, CCCH-type domain containing"	6923	protein-coding gene	gene with protein product		606516	"muscleblind (Drosophila)-like", "muscleblind-like (Drosophila)"	MBNL			Standard	NM_021038		Approved	KIAA0428, EXP42, EXP40, EXP35, EXP	uc003ezm.3	Q9NR56	OTTHUMG00000159163	ENST00000463374.1:c.929C>A	chr3.hg19:g.152165476C>A	ENSP00000418108:p.Thr310Asn	160.0	0.0	.		146.0	6.0	.	NM_207293	E9PBW7|O43311|O43797|Q86UV8|Q86UV9|Q96P92|Q96RE3	Missense_Mutation	SNP	ENST00000463374.1	hg19	CCDS3165.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.64|17.64	3.440834|3.440834	0.63067|0.63067	.|.	.|.	ENSG00000152601|ENSG00000152601	ENST00000464596|ENST00000282486;ENST00000282488;ENST00000355460;ENST00000493459;ENST00000324210;ENST00000498502;ENST00000545754;ENST00000357472;ENST00000485910;ENST00000463374;ENST00000465907;ENST00000492948	.|.	.|.	.|.	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.75072|0.75072	0.3800|0.3800	M|M	0.62723|0.62723	1.935|1.935	0.80722|0.80722	D|D	1|1	.|D;B;P;P;P;P;P	.|0.58970	.|0.984;0.371;0.57;0.923;0.612;0.954;0.847	.|P;B;B;P;B;P;P	.|0.59703	.|0.862;0.149;0.36;0.461;0.197;0.662;0.662	T|T	0.73701|0.73701	-0.3900|-0.3900	5|9	.|0.41790	.|T	.|0.15	.|.	19.4004|19.4004	0.94627|0.94627	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|224;224;310;292;253;292;292	.|Q9NR56-3;Q96RE3;Q9NR56;Q86UV8;Q86VM6;Q9NR56-2;Q96P92	.|.;.;MBNL1_HUMAN;.;.;.;.	T|N	291|310;224;292;253;292;310;224;292;224;310;224;292	.|.	.|ENSP00000282486:T310N	P|T	+|+	1|2	0|0	MBNL1|MBNL1	153648166|153648166	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.518000|7.518000	0.81795|0.81795	2.577000|2.577000	0.86979|0.86979	0.655000|0.655000	0.94253|0.94253	CCG|ACC	.	.	.	none		0.453	MBNL1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353604.1	NM_021038		A	152165476	C	A	152165476	3	1	100	1	0	0	0	0	1	0	0	0	9360	507	18	4	951	4	MBNL1	3	152165476	Missense_Mutation	SNP	C	TCGA-B9-5155-01A-01D-1589-08	30664831	152165476	45856954	29	6325											
RAB28	9364	hgsc.bcm.edu	37	chr4	13481115	13481115	+	Frame_Shift_Del	DEL	A	A	-																															gtttgtttgtactgtttcccAaaagtttcttgagcaaaaca																										TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr4:13481115delA	ENST00000330852.5	-	2	325	c.111delT	c.(109-111)tttfs	p.F37fs	RAB28_ENST00000338176.4_Frame_Shift_Del_p.F37fs|RAB28_ENST00000288723.4_Frame_Shift_Del_p.F37fs	NM_001017979.2	NP_001017979.1	P51157	RAB28_HUMAN	RAB28, member RAS oncogene family	37					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	ciliary basal body (GO:0036064)|ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	8						ACTGTTTCCCAAAAGTTTCTT	0.308																																					p.G38fs		Atlas-INDEL	.											.	RAB28	56	.	0			c.112delG						PASS	.						69	70	70					4																	13481115		2203	4292	6495	SO:0001589	frameshift_variant	9364	exon2			.	X94703	CCDS3409.1, CCDS33961.1, CCDS54741.1	4p16.1	2014-04-24			ENSG00000157869	ENSG00000157869		"RAB, member RAS oncogene"	9768	protein-coding gene	gene with protein product		612994				8647132	Standard	NM_004249		Approved		uc003gmu.2	P51157	OTTHUMG00000090543	ENST00000330852.5:c.111delT	chr4.hg19:g.13481115delA	ENSP00000328551:p.Phe37fs	69.0	0.0	0		97.0	40.0	0.412371	NM_004249	G8JLC5|Q8IYR8|Q8NI05	Frame_Shift_Del	DEL	ENST00000330852.5	hg19	CCDS33961.1																																																																																			.	.	.	none		0.308	RAB28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207068.2	NM_001017979		-	13481115	A	-	13481115	7	5	100	1	0	1	0	1	0	0	0	0	12929	127	5	0	718	0	RAB28	4	13481115	Frame_Shift_Del	DEL	A	TCGA-B9-5155-01A-01D-1589-08		13481115	177673161	30	6326											
WDR19	57728	hgsc.bcm.edu	37	chr4	39196261	39196261	+	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	tttataatcatcagacatctCgaaagattcctgtccttggt	11	15	6	9	1	3	2	2	0	1	2	6	3	5	2	2	1	0	0	2	1	3	5			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr4:39196261C>G	ENST00000399820.3	+	5	542	c.388C>G	c.(388-390)Cga>Gga	p.R130G	WDR19_ENST00000288634.7_Intron|WDR19_ENST00000506503.1_Missense_Mutation_p.R130G	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	130					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						TCAGACATCTCGAAAGATTCC	0.403																																					p.R130G		Atlas-SNP	.											.	WDR19	96	.	0			c.C388G						PASS	.						94	86	88					4																	39196261		1834	4094	5928	SO:0001583	missense	57728	exon5			ACATCTCGAAAGA	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.388C>G	chr4.hg19:g.39196261C>G	ENSP00000382717:p.Arg130Gly	34.0	0.0	.		35.0	5.0	.	NM_025132	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Missense_Mutation	SNP	ENST00000399820.3	hg19	CCDS47042.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.986458	0.74589	.	.	ENSG00000157796	ENST00000399820;ENST00000509560;ENST00000506503;ENST00000399836	T;T;T	0.30714	3.42;1.52;3.42	5.58	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	T	0.62780	0.2456	M	0.89785	3.06	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74348	0.983;0.979	T	0.69720	-0.5069	10	0.51188	T	0.08	-8.1952	17.1715	0.86832	0.1347:0.8653:0.0:0.0	.	130;130	Q8NEZ3;D6R9P6	WDR19_HUMAN;.	G	130;71;130;129	ENSP00000382717:R130G;ENSP00000426918:R71G;ENSP00000423491:R130G	ENSP00000382717:R130G	R	+	1	2	WDR19	38872656	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.725000	0.68507	2.604000	0.88044	0.655000	0.94253	CGA	.	.	.	none		0.403	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1			G	39196261	C	G	39196261	3	3	100	1	0	0	0	0	1	0	0	0	17291	876	31	4	406	4	WDR19	4	39196261	Missense_Mutation	SNP	C	TCGA-B9-5155-01A-01D-1589-08	25715146	39196261	151958015	31	6327											
ARSJ	79642	hgsc.bcm.edu	37	chr4	114823444	114823444	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgtgcttatccacaagtaaCacctgaatggcaagttgaac	13	11	8	9	0	0	2	0	2	0	0	1	2	1	2	2	1	3	4	2	1	6	4			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr4:114823444C>T	ENST00000315366.7	-	2	2652	c.1786G>A	c.(1786-1788)Gtt>Att	p.V596I	ARSJ_ENST00000541197.1_Intron	NM_024590.3	NP_078866.3	Q5FYB0	ARSJ_HUMAN	arylsulfatase family, member J	596				STCHSGVTCG -> KPANLAR (in Ref. 2; CAJ18095 and 3; AAQ89010). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	21		Ovarian(17;0.0035)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00194)		CCACAAGTAACACCTGAATGG	0.363																																					p.V596I		Atlas-SNP	.											.	ARSJ	55	.	0			c.G1786A						PASS	.						73	68	69					4																	114823444		1876	4106	5982	SO:0001583	missense	79642	exon2			AAGTAACACCTGA		CCDS43264.1	4q26	2013-02-14	2006-03-07		ENSG00000180801	ENSG00000180801		"Arylsulfatase family"	26286	protein-coding gene	gene with protein product		610010	"arylsulfatase J"			12975309, 16174644	Standard	NM_024590		Approved	FLJ23548	uc003ibq.1	Q5FYB0	OTTHUMG00000161067	ENST00000315366.7:c.1786G>A	chr4.hg19:g.114823444C>T	ENSP00000320219:p.Val596Ile	68.0	0.0	.		78.0	33.0	.	NM_024590	A2RUG0|B7ZM45|Q1HA39|Q5FWE4|Q6UWT9	Missense_Mutation	SNP	ENST00000315366.7	hg19	CCDS43264.1	.	.	.	.	.	.	.	.	.	.	C	10.17	1.275258	0.23307	.	.	ENSG00000180801	ENST00000315366;ENST00000545965	D	0.96967	-4.19	5.4	-1.33	0.09172	.	9.916930	0.00447	U	0.000097	D	0.89424	0.6711	N	0.08118	0	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.82550	-0.0401	10	0.33141	T	0.24	.	4.2183	0.10545	0.1145:0.2273:0.4949:0.1632	.	596	Q5FYB0	ARSJ_HUMAN	I	596;165	ENSP00000320219:V596I	ENSP00000320219:V596I	V	-	1	0	ARSJ	115042893	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.114000	0.15520	0.004000	0.14682	-0.165000	0.13383	GTT	.	.	.	none		0.363	ARSJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363650.1	NM_024590		T	114823444	C	T	114823444	3	4	100	1	0	0	0	0	1	0	0	0	995	478	17	2	17	2	ARSJ	4	114823444	Missense_Mutation	SNP	C	TCGA-B9-5155-01A-01D-1589-08	75627183	114823444	76330832	32	6328											
SLC45A2	51151	hgsc.bcm.edu	37	chr5	33982376	33982376	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtagtggaggcccttctccTtgtcctgatgggagcagaca	7	10	14	10	0	1	2	0	1	1	1	3	4	2	4	3	4	1	2	3	4	1	3			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr5:33982376T>C	ENST00000296589.4	-	2	673	c.527A>G	c.(526-528)aAg>aGg	p.K176R	SLC45A2_ENST00000382102.3_Missense_Mutation_p.K176R|SLC45A2_ENST00000342059.3_Intron|SLC45A2_ENST00000509381.1_Missense_Mutation_p.K176R|SLC45A2_ENST00000345083.5_Missense_Mutation_p.K176R	NM_016180.3	NP_057264	Q9UMX9	S45A2_HUMAN	solute carrier family 45, member 2	176					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						GCCCTTCTCCTTGTCCTGATG	0.493																																					p.K176R	Ovarian(31;380 859 8490 22203 49048)	Atlas-SNP	.											.	SLC45A2	100	.	0			c.A527G						PASS	.						107	103	104					5																	33982376		2203	4300	6503	SO:0001583	missense	51151	exon2			TTCTCCTTGTCCT	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.527A>G	chr5.hg19:g.33982376T>C	ENSP00000296589:p.Lys176Arg	67.0	0.0	.		72.0	22.0	.	NM_016180	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000296589.4	hg19	CCDS3901.1	.	.	.	.	.	.	.	.	.	.	T	19.40	3.821212	0.71028	.	.	ENSG00000164175	ENST00000296589;ENST00000382102;ENST00000509381;ENST00000345083	T;T;D;T	0.91521	-0.69;-0.69;-2.86;-0.69	5.2	4.0	0.46444	Major facilitator superfamily domain, general substrate transporter (1);	0.072278	0.85682	D	0.000000	D	0.86176	0.5870	L	0.60067	1.865	0.58432	D	0.999997	P;B;B	0.41498	0.752;0.198;0.096	B;B;B	0.40659	0.336;0.155;0.115	T	0.82741	-0.0307	10	0.02654	T	1	-13.0181	11.4541	0.50171	0.1351:0.0:0.0:0.8649	.	176;176;176	D6RGY6;Q9UMX9-4;Q9UMX9	.;.;S45A2_HUMAN	R	176	ENSP00000296589:K176R;ENSP00000371534:K176R;ENSP00000421100:K176R;ENSP00000340444:K176R	ENSP00000296589:K176R	K	-	2	0	SLC45A2	34018133	1.000000	0.71417	0.998000	0.56505	0.952000	0.60782	4.064000	0.57506	0.888000	0.36160	0.450000	0.29827	AAG	.	.	.	none		0.493	SLC45A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207443.2	NM_016180		C	33982376	T	C	33982376	3	2	100	1	0	0	0	0	1	0	0	0	14654	1609	56	3	1104	3	SLC45A2	5	33982376	Missense_Mutation	SNP	T	TCGA-B9-5155-01A-01D-1589-08		33982376	146932884	33	6329											
PAIP1	10605	hgsc.bcm.edu	37	chr5	43555937	43555937	+	Frame_Shift_Del	DEL	A	A	-																															aaagggtgtacttactgtgtAactggaagaataacctgaag																										TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr5:43555937delA	ENST00000306846.3	-	2	662	c.430delT	c.(430-432)tacfs	p.Y144fs	PAIP1_ENST00000514514.1_Frame_Shift_Del_p.Y65fs|PAIP1_ENST00000436644.2_Frame_Shift_Del_p.Y65fs|PAIP1_ENST00000338972.4_Frame_Shift_Del_p.Y32fs	NM_006451.4|NM_182789.3	NP_006442.2|NP_877590.1	Q9H074	PAIP1_HUMAN	poly(A) binding protein interacting protein 1	144					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	RNA binding (GO:0003723)|translation activator activity (GO:0008494)			endometrium(2)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Lung NSC(6;2.07e-05)					CTTACTGTGTAACTGGAAGAA	0.403																																					p.Y144fs		Atlas-INDEL	.											.	PAIP1	46	.	0			c.431delA						PASS	.						115	125	121					5																	43555937		2203	4300	6503	SO:0001589	frameshift_variant	10605	exon2			.	AF013758	CCDS3947.1, CCDS3948.1, CCDS47204.1	5p12	2008-02-05			ENSG00000172239	ENSG00000172239			16945	protein-coding gene	gene with protein product		605184				9548260, 11230166	Standard	NM_006451		Approved		uc003job.3	Q9H074	OTTHUMG00000096960	ENST00000306846.3:c.430delT	chr5.hg19:g.43555937delA	ENSP00000302768:p.Tyr144fs	234.0	0.0	0		305.0	121.0	0.396721	NM_006451	A6NKV8|O60455|Q96B61|Q9BS63	Frame_Shift_Del	DEL	ENST00000306846.3	hg19	CCDS3947.1																																																																																			.	.	.	none		0.403	PAIP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214024.1	NM_006451		-	43555937	A	-	43555937	7	5	100	1	0	1	0	1	0	0	0	0	11403	362	13	0	1049	0	PAIP1	5	43555937	Frame_Shift_Del	DEL	A	TCGA-B9-5155-01A-01D-1589-08	9573561	43555937	137359323	34	6330											
PPIP5K2	23262	hgsc.bcm.edu	37	chr5	102503901	102503901	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccctgacatatatgactgtAtaaaatatgatgtccagcat	14	13	6	8	0	0	3	0	3	0	0	2	3	2	3	2	0	1	2	2	0	6	5			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr5:102503901A>G	ENST00000358359.3	+	19	2697	c.2188A>G	c.(2188-2190)Ata>Gta	p.I730V	PPIP5K2_ENST00000414217.1_Missense_Mutation_p.I730V|PPIP5K2_ENST00000513500.1_3'UTR|PPIP5K2_ENST00000321521.9_Missense_Mutation_p.I730V	NM_001276277.1	NP_001263206.1	O43314	VIP2_HUMAN	diphosphoinositol pentakisphosphate kinase 2	730					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						ATATGACTGTATAAAATATGA	0.333																																					p.I730V		Atlas-SNP	.											.	PPIP5K2	98	.	0			c.A2188G						PASS	.						102	112	109					5																	102503901		2202	4289	6491	SO:0001583	missense	23262	exon18			GACTGTATAAAAT	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.2188A>G	chr5.hg19:g.102503901A>G	ENSP00000351126:p.Ile730Val	229.0	0.0	.		257.0	117.0	.	NM_015216	A1NI53|A6NGS8|Q8TB50	Missense_Mutation	SNP	ENST00000358359.3	hg19		.	.	.	.	.	.	.	.	.	.	A	10.45	1.354908	0.24512	.	.	ENSG00000145725	ENST00000321521;ENST00000358359;ENST00000451606;ENST00000414217;ENST00000509597	T;T;T;T	0.30182	1.54;1.54;1.54;1.54	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.19485	0.0468	N	0.10972	0.075	0.52501	D	0.999953	B;B;B	0.23185	0.062;0.029;0.081	B;B;B	0.33960	0.173;0.06;0.1	T	0.14337	-1.0476	10	0.27082	T	0.32	.	10.3029	0.43663	0.9261:0.0:0.0739:0.0	.	730;730;730	E9PGM8;O43314-2;O43314	.;.;VIP2_HUMAN	V	730;730;730;730;4	ENSP00000313070:I730V;ENSP00000351126:I730V;ENSP00000416016:I730V;ENSP00000424948:I4V	ENSP00000313070:I730V	I	+	1	0	PPIP5K2	102531800	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.118000	0.64673	2.218000	0.71995	0.377000	0.23210	ATA	.	.	.	none		0.333	PPIP5K2-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000370487.1	NM_015216		G	102503901	A	G	102503901	3	3	100	1	0	0	0	0	1	0	0	0	12343	449	16	3	2258	3	PPIP5K2	5	102503901	Missense_Mutation	SNP	A	TCGA-B9-5155-01A-01D-1589-08	58947964	102503901	78411359	35	6331											
SRP19	6728	hgsc.bcm.edu	37	chr5	112200371	112200371	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgtccaatacagaggcagAgtccgggtccagctcaaaca	13	6	11	11	1	1	2	1	0	0	2	4	3	4	2	3	2	3	2	3	2	3	1			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr5:112200371A>G	ENST00000505459.1	+	4	398	c.243A>G	c.(241-243)agA>agG	p.R81R	CTC-487M23.8_ENST00000506997.1_Intron|SRP19_ENST00000515463.1_Missense_Mutation_p.E56G|CTC-487M23.8_ENST00000512790.1_3'UTR|CTC-554D6.1_ENST00000520401.1_3'UTR|SRP19_ENST00000282999.3_Silent_p.R81R	NM_001204193.1|NM_003135.2	NP_001191122.1|NP_003126.1	P09132	SRP19_HUMAN	signal recognition particle 19kDa	81					cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|large_intestine(1)	3		all_cancers(142;0.00328)|all_epithelial(76;6.39e-05)|Prostate(80;0.00174)|Colorectal(10;0.00372)|Ovarian(225;0.156)		Epithelial(69;1.7e-09)|OV - Ovarian serous cystadenocarcinoma(64;1.17e-08)|all cancers(49;3.96e-07)|Colorectal(14;0.0056)|COAD - Colon adenocarcinoma(37;0.0104)		ACAGAGGCAGAGTCCGGGTCC	0.408																																					p.E56G		Atlas-SNP	.											.	SRP19	12	.	0			c.A167G						PASS	.						94	96	95					5																	112200371		2202	4300	6502	SO:0001819	synonymous_variant	6728	exon3			AGGCAGAGTCCGG		CCDS4108.1, CCDS56375.1, CCDS56376.1, CCDS75286.1	5q21-q22	2008-07-18	2002-08-29		ENSG00000153037	ENSG00000153037			11300	protein-coding gene	gene with protein product		182175	"signal recognition particle 19kD"			2460823	Standard	NM_003135		Approved		uc011cvu.2	P09132	OTTHUMG00000128805	ENST00000505459.1:c.243A>G	chr5.hg19:g.112200371A>G		99.0	0.0	.		105.0	46.0	.	NM_001204196	B2R4E9|D6RCQ5|Q05D77|Q96FG6	Missense_Mutation	SNP	ENST00000505459.1	hg19	CCDS4108.1	.	.	.	.	.	.	.	.	.	.	A	12.12	1.841718	0.32513	.	.	ENSG00000153037	ENST00000515463	.	.	.	5.81	2.02	0.26589	.	.	.	.	.	T	0.38585	0.1046	.	.	.	0.22511	N	0.999035	.	.	.	.	.	.	T	0.36383	-0.9750	5	0.87932	D	0	3.1809	4.3944	0.11356	0.6417:0.0:0.2229:0.1354	.	.	.	.	G	56	.	ENSP00000425562:E56G	E	+	2	0	SRP19	112228270	0.997000	0.39634	1.000000	0.80357	0.994000	0.84299	0.495000	0.22483	0.107000	0.17824	0.454000	0.30748	GAG	.	.	.	none		0.408	SRP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250737.3	NM_003135		G	112200371	A	G	112200371	2	3	100	1	0	0	0	0	0	0	0	1	15166	301	11	3		3	SRP19	5	112200371	Silent	SNP	A	TCGA-B9-5155-01A-01D-1589-08	9696470	112200371	68714889	36	6332											
FOXF2	2295	hgsc.bcm.edu	37	chr6	1390675	1390675	+	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	tcatcaagctgcctaagggcCtcgggcggcccggcaagggc	7	5	15	14	3	2	0	2	0	0	0	3	0	2	0	3	5	2	2	3	5	3	1			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr6:1390675C>G	ENST00000259806.1	+	1	607	c.493C>G	c.(493-495)Ctc>Gtc	p.L165V		NM_001452.1	NP_001443.1	Q12947	FOXF2_HUMAN	forkhead box F2	165					embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digestive tract development (GO:0048566)|epithelial to mesenchymal transition (GO:0001837)|establishment of planar polarity of embryonic epithelium (GO:0042249)|extracellular matrix organization (GO:0030198)|genitalia development (GO:0048806)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	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)			large_intestine(2)|lung(5)|prostate(1)	8	Ovarian(93;0.0733)	all_lung(73;0.0713)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.095)		GCCTAAGGGCCTCGGGCGGCC	0.682																																					p.L165V		Atlas-SNP	.											.	FOXF2	28	.	0			c.C493G						PASS	.						47	56	53					6																	1390675		2202	4300	6502	SO:0001583	missense	2295	exon1			AAGGGCCTCGGGC	U13220	CCDS4472.1	6p25.3	2008-04-10			ENSG00000137273	ENSG00000137273		"Forkhead boxes"	3810	protein-coding gene	gene with protein product		603250		FKHL6		9799607, 7957066	Standard	NM_001452		Approved	FREAC2	uc003mtm.3	Q12947	OTTHUMG00000016243	ENST00000259806.1:c.493C>G	chr6.hg19:g.1390675C>G	ENSP00000259806:p.Leu165Val	155.0	0.0	.		162.0	66.0	.	NM_001452	Q5TGJ1|Q9UQ85	Missense_Mutation	SNP	ENST00000259806.1	hg19	CCDS4472.1	.	.	.	.	.	.	.	.	.	.	C	18.65	3.669525	0.67814	.	.	ENSG00000137273	ENST00000259806	D	0.95377	-3.69	4.53	2.67	0.31697	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.64402	D	0.000003	D	0.85767	0.5773	N	0.10916	0.065	0.50632	D	0.999889	P	0.46064	0.872	P	0.51918	0.684	T	0.82733	-0.0311	10	0.17832	T	0.49	.	7.1657	0.25689	0.2936:0.6205:0.0:0.0859	.	165	Q12947	FOXF2_HUMAN	V	165	ENSP00000259806:L165V	ENSP00000259806:L165V	L	+	1	0	FOXF2	1335674	0.998000	0.40836	0.997000	0.53966	0.974000	0.67602	3.613000	0.54152	0.901000	0.36495	0.536000	0.68110	CTC	.	.	.	none		0.682	FOXF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043558.1			G	1390675	C	G	1390675	3	3	100	1	0	0	0	0	1	0	0	0	6013	681	24	4	495	4	FOXF2	6	1390675	Missense_Mutation	SNP	C	TCGA-B9-5155-01A-01D-1589-08		1390675	169724392	37	6333											
GMPR	2766	hgsc.bcm.edu	37	chr6	16254914	16254914	+	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	caatgggtattcagaacattTtgtggaattcgtgaaacttg	12	14	10	5	1	1	2	1	1	0	1	2	3	1	3	0	2	2	1	0	2	5	6			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr6:16254914T>A	ENST00000259727.4	+	4	527	c.413T>A	c.(412-414)tTt>tAt	p.F138Y		NM_006877.3	NP_006868.3	P36959	GMPR1_HUMAN	guanosine monophosphate reductase	138					nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to cold (GO:0009409)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|GMP reductase complex (GO:1902560)	GMP reductase activity (GO:0003920)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	20	Breast(50;0.0427)|Ovarian(93;0.103)	all_hematologic(90;0.0895)				TCAGAACATTTTGTGGAATTC	0.443																																					p.F138Y		Atlas-SNP	.											.	GMPR	44	.	0			c.T413A						PASS	.						198	185	190					6																	16254914		2203	4300	6503	SO:0001583	missense	2766	exon4			AACATTTTGTGGA		CCDS4537.1	6p23	2009-07-10			ENSG00000137198	ENSG00000137198	1.7.1.7		4376	protein-coding gene	gene with protein product		139265				2194676	Standard	NM_006877		Approved		uc003nbs.3	P36959	OTTHUMG00000014302	ENST00000259727.4:c.413T>A	chr6.hg19:g.16254914T>A	ENSP00000259727:p.Phe138Tyr	169.0	0.0	.		199.0	94.0	.	NM_006877	Q96HQ6	Missense_Mutation	SNP	ENST00000259727.4	hg19	CCDS4537.1	.	.	.	.	.	.	.	.	.	.	T	33	5.251862	0.95336	.	.	ENSG00000137198	ENST00000259727	T	0.78595	-1.19	5.65	5.65	0.86999	Aldolase-type TIM barrel (1);IMP dehydrogenase/GMP reductase (1);	0.000000	0.85682	D	0.000000	D	0.89125	0.6626	H	0.95611	3.695	0.80722	D	1	P	0.46784	0.884	P	0.58391	0.838	D	0.92062	0.5657	10	0.87932	D	0	5.8785	15.8909	0.79296	0.0:0.0:0.0:1.0	.	138	P36959	GMPR1_HUMAN	Y	138	ENSP00000259727:F138Y	ENSP00000259727:F138Y	F	+	2	0	GMPR	16362893	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.680000	0.84062	2.146000	0.66826	0.533000	0.62120	TTT	.	.	.	none		0.443	GMPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039942.2			A	16254914	T	A	16254914	3	1	100	1	0	0	0	0	1	0	0	0	6503	1841	64	5	427	5	GMPR	6	16254914	Missense_Mutation	SNP	T	TCGA-B9-5155-01A-01D-1589-08	14864239	16254914	154860153	38	6334											
RBM24	221662	hgsc.bcm.edu	37	chr6	17292212	17292212	+	Silent	SNP	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	gcaggatatgttactgctggGggctatggctacgcagtcca	8	10	14	9	1	0	0	0	0	0	0	1	1	1	1	1	4	3	6	1	4	4	4			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr6:17292212G>A	ENST00000379052.5	+	4	809	c.573G>A	c.(571-573)ggG>ggA	p.G191G	RBM24_ENST00000425446.2_Silent_p.G133G|RBM24_ENST00000318204.5_Silent_p.G146G|RBM24_ENST00000508508.1_3'UTR	NM_001143942.1	NP_001137414.1	Q9BX46	RBM24_HUMAN	RNA binding motif protein 24	191	Ala-rich.				cell differentiation (GO:0030154)|regulation of mRNA stability (GO:0043488)|regulation of myotube differentiation (GO:0010830)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)			endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(1)	13	Breast(50;0.0615)|Ovarian(93;0.0733)	all_hematologic(90;0.062)	all cancers(50;0.131)|Epithelial(50;0.15)			TTACTGCTGGGGGCTATGGCT	0.642																																					p.G191G		Atlas-SNP	.											.	RBM24	40	.	0			c.G573A						PASS	.						16	17	16					6																	17292212		2195	4295	6490	SO:0001819	synonymous_variant	221662	exon4			TGCTGGGGGCTAT	BC040928	CCDS4538.1, CCDS47378.1, CCDS47379.1	6p22.3	2013-02-12	2004-04-23	2004-04-23	ENSG00000112183	ENSG00000112183		"RNA binding motif (RRM) containing"	21539	protein-coding gene	gene with protein product			"RNA-binding region (RNP1, RRM) containing 6"	RNPC6			Standard	NM_153020		Approved	FLJ30829, dJ259A10.1	uc003nbz.4	Q9BX46	OTTHUMG00000014306	ENST00000379052.5:c.573G>A	chr6.hg19:g.17292212G>A		31.0	0.0	.		30.0	10.0	.	NM_001143942	E9PAY4|Q6QDA4|Q8N9D3|Q96NI3	Silent	SNP	ENST00000379052.5	hg19	CCDS47378.1	.	.	.	.	.	.	.	.	.	.	G	1.218	-0.627857	0.03610	.	.	ENSG00000112183	ENST00000503965	T	0.24723	1.84	5.66	1.6	0.23607	.	0.052843	0.64402	D	0.000001	T	0.08537	0.0212	.	.	.	0.80722	D	1	B;B	0.17667	0.023;0.023	B;B	0.18871	0.023;0.023	T	0.09862	-1.0655	9	0.32370	T	0.25	-31.6851	11.5655	0.50802	0.0677:0.4891:0.4432:0.0	.	90;105	B7Z6B4;B7Z6B7	.;.	E	156	ENSP00000421971:G156E	ENSP00000421971:G156E	G	+	2	0	RBM24	17400191	0.982000	0.34865	0.998000	0.56505	0.622000	0.37654	0.135000	0.15952	0.303000	0.22785	0.655000	0.94253	GGG	.	.	.	none		0.642	RBM24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039946.2	NM_153020		A	17292212	G	A	17292212	2	1	100	1	0	0	0	0	0	0	0	1	13137	1219	43	2		2	RBM24	6	17292212	Silent	SNP	G	TCGA-B9-5155-01A-01D-1589-08	1037298	17292212	153822855	39	6335											
DDX43	55510	hgsc.bcm.edu	37	chr6	74119027	74119027	+	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	tttgaaccccagataatgaaGattttgttagatgtgcgccc	11	13	9	8	1	0	5	0	2	0	3	0	5	0	5	3	0	2	1	3	0	4	5			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr6:74119027G>A	ENST00000370336.4	+	10	1394	c.1236G>A	c.(1234-1236)aaG>aaA	p.K412K	DDX43_ENST00000479773.1_3'UTR	NM_018665.2	NP_061135.2	Q9NXZ2	DDX43_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43	412	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				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						AGATAATGAAGATTTTGTTAG	0.393																																					p.K412K		Atlas-SNP	.											.	DDX43	69	.	0			c.G1236A						PASS	.						216	203	207					6																	74119027		2203	4300	6503	SO:0001819	synonymous_variant	55510	exon10			AATGAAGATTTTG		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.1236G>A	chr6.hg19:g.74119027G>A		203.0	0.0	.		204.0	102.0	.	NM_018665	B4E0C8|Q6NXR1	Silent	SNP	ENST00000370336.4	hg19	CCDS4977.1																																																																																			.	.	.	none		0.393	DDX43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041219.3	NM_018665		A	74119027	G	A	74119027	2	1	100	1	0	0	0	0	0	0	0	1	4365	933	33	2		2	DDX43	6	74119027	Silent	SNP	G	TCGA-B9-5155-01A-01D-1589-08	56826815	74119027	96996040	40	6336											
AMD1	262	hgsc.bcm.edu	37	chr6	111213404	111213404	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggacgtatgaattctgactgTtggtatgtttaatgcaattt	10	17	10	4	1	1	2	0	2	1	0	1	3	1	3	0	2	1	5	0	2	5	7			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr6:111213404T>C	ENST00000368885.3	+	5	804	c.468T>C	c.(466-468)tgT>tgC	p.C156C	AMD1_ENST00000451850.2_Intron|AMD1_ENST00000368882.3_Silent_p.C8C|AMD1_ENST00000368876.1_Silent_p.C87C|AMD1_ENST00000368877.5_Silent_p.C127C	NM_001634.4	NP_001625.2	P17707	DCAM_HUMAN	adenosylmethionine decarboxylase 1	156					cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|S-adenosylmethioninamine biosynthetic process (GO:0006557)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)|spermine biosynthetic process (GO:0006597)	cytosol (GO:0005829)	adenosylmethionine decarboxylase activity (GO:0004014)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(2)	8		all_cancers(87;3.83e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0209)		OV - Ovarian serous cystadenocarcinoma(136;0.0522)|Epithelial(106;0.111)|all cancers(137;0.143)	S-Adenosylmethionine(DB00118)	ATTCTGACTGTTGGTATGTTT	0.308																																					p.C156C		Atlas-SNP	.											.	AMD1	23	.	0			c.T468C						PASS	.						309	287	294					6																	111213404		2203	4300	6503	SO:0001819	synonymous_variant	262	exon5			TGACTGTTGGTAT	M88006	CCDS5086.1, CCDS75504.1, CCDS75505.1	6q21	2014-05-13			ENSG00000123505	ENSG00000123505	4.1.1.50		457	protein-coding gene	gene with protein product		180980	"S-adenosylmethionine decarboxylase 1"				Standard	NM_001634		Approved	SAMDC	uc003puk.1	P17707	OTTHUMG00000015369	ENST00000368885.3:c.468T>C	chr6.hg19:g.111213404T>C		308.0	0.0	.		337.0	170.0	.	NM_001634	E1P5F7|Q5VXN4|Q5VXN6|Q9BWK4	Silent	SNP	ENST00000368885.3	hg19	CCDS5086.1																																																																																			.	.	.	none		0.308	AMD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041816.1			C	111213404	T	C	111213404	2	2	100	1	0	0	0	0	0	0	0	1	566	1731	60	3		3	AMD1	6	111213404	Silent	SNP	T	TCGA-B9-5155-01A-01D-1589-08	37094377	111213404	59901663	41	6337											
SLC2A12	154091	hgsc.bcm.edu	37	chr6	134350343	134350343	+	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	ttgcaattgcttgcaaaactCccaagggaatcacaagacca	15	8	7	11	0	1	1	1	0	0	1	2	2	2	2	2	1	4	3	2	1	6	3			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr6:134350343C>A	ENST00000275230.5	-	2	775	c.620G>T	c.(619-621)gGa>gTa	p.G207V		NM_145176.2	NP_660159.1	Q8TD20	GTR12_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 12	207					glucose transport (GO:0015758)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			NS(1)|breast(1)|large_intestine(6)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	17	Breast(56;0.214)|Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0101)|GBM - Glioblastoma multiforme(68;0.0123)		TTGCAAAACTCCCAAGGGAAT	0.428																																					p.G207V	Melanoma(122;1663 1672 14489 35294 41228)	Atlas-SNP	.											.	SLC2A12	43	.	0			c.G620T						PASS	.						88	89	89					6																	134350343		2203	4300	6503	SO:0001583	missense	154091	exon2			AAAACTCCCAAGG	AL035699	CCDS5169.1	6q23.2	2013-05-22			ENSG00000146411	ENSG00000146411		"Solute carriers"	18067	protein-coding gene	gene with protein product		610372				11780753, 11832379	Standard	XM_006715349		Approved	GLUT12, GLUT8	uc003qem.1	Q8TD20	OTTHUMG00000015611	ENST00000275230.5:c.620G>T	chr6.hg19:g.134350343C>A	ENSP00000275230:p.Gly207Val	119.0	0.0	.		155.0	9.0	.	NM_145176	B3KV17|Q7Z6U3|Q96MR8	Missense_Mutation	SNP	ENST00000275230.5	hg19	CCDS5169.1	.	.	.	.	.	.	.	.	.	.	C	17.59	3.427056	0.62733	.	.	ENSG00000146411	ENST00000275230	T	0.74315	-0.83	5.4	5.4	0.78164	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.054326	0.85682	D	0.000000	T	0.75295	0.3830	L	0.52011	1.625	0.80722	D	1	D	0.52996	0.957	P	0.58172	0.834	T	0.77621	-0.2519	10	0.59425	D	0.04	-13.7225	14.7476	0.69499	0.0:0.8556:0.1444:0.0	.	207	Q8TD20	GTR12_HUMAN	V	207	ENSP00000275230:G207V	ENSP00000275230:G207V	G	-	2	0	SLC2A12	134392036	1.000000	0.71417	0.991000	0.47740	0.961000	0.63080	6.163000	0.71880	2.542000	0.85734	0.467000	0.42956	GGA	.	.	.	none		0.428	SLC2A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042302.1			A	134350343	C	A	134350343	3	1	100	1	0	0	0	0	1	0	0	0	14554	855	30	4	1249	4	SLC2A12	6	134350343	Missense_Mutation	SNP	C	TCGA-B9-5155-01A-01D-1589-08	23136939	134350343	36764724	42	6338											
DYNC1I1	1780	hgsc.bcm.edu	37	chr7	95668696	95668696	+	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	ttctcacctgtttgtcacatCatcatttgactggactgtca	8	16	6	11	0	5	1	5	1	1	0	6	2	5	2	1	1	0	1	1	1	0	3			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr7:95668696C>T	ENST00000324972.6	+	14	1716	c.1523C>T	c.(1522-1524)tCa>tTa	p.S508L	DYNC1I1_ENST00000497626.1_3'UTR|DYNC1I1_ENST00000359388.4_Missense_Mutation_p.S471L|DYNC1I1_ENST00000457059.1_Missense_Mutation_p.S491L|DYNC1I1_ENST00000537881.1_Missense_Mutation_p.S471L|DYNC1I1_ENST00000437599.1_Missense_Mutation_p.S488L|DYNC1I1_ENST00000447467.2_Missense_Mutation_p.S491L	NM_004411.4	NP_004402.1	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	508					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)			TTTGTCACATCATCATTTGAC	0.448																																					p.S508L		Atlas-SNP	.											.	DYNC1I1	111	.	0			c.C1523T						PASS	.						127	114	118					7																	95668696		2203	4300	6503	SO:0001583	missense	1780	exon14			TCACATCATCATT	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.1523C>T	chr7.hg19:g.95668696C>T	ENSP00000320130:p.Ser508Leu	118.0	0.0	.		184.0	123.0	.	NM_004411	B4DME3|F5H050|G5E9K1|Q8TBF7|Q9Y2X1	Missense_Mutation	SNP	ENST00000324972.6	hg19	CCDS5644.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.849383	0.91277	.	.	ENSG00000158560	ENST00000447467;ENST00000324972;ENST00000537881;ENST00000437599;ENST00000359388;ENST00000457059	T;T;T;T;T;T	0.62105	0.05;0.05;0.05;0.05;0.05;0.05	4.27	4.27	0.50696	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	0.85936	0.5813	H	0.96805	3.885	0.80722	D	1	D;D;D;D;D	0.76494	0.998;0.998;0.998;0.998;0.999	D;D;D;D;D	0.79784	0.993;0.988;0.988;0.993;0.988	D	0.90105	0.4187	10	0.54805	T	0.06	-8.2427	18.0108	0.89222	0.0:1.0:0.0:0.0	.	491;488;491;508;471	Q7Z6M0;G5E9K1;O14576-2;O14576;O14576-3	.;.;.;DC1I1_HUMAN;.	L	491;508;471;488;471;491	ENSP00000392337:S491L;ENSP00000320130:S508L;ENSP00000438377:S471L;ENSP00000398118:S488L;ENSP00000352348:S471L;ENSP00000412444:S491L	ENSP00000320130:S508L	S	+	2	0	DYNC1I1	95506632	1.000000	0.71417	0.936000	0.37596	0.939000	0.58152	7.609000	0.82925	2.666000	0.90696	0.557000	0.71058	TCA	.	.	.	none		0.448	DYNC1I1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333432.1	NM_004411		T	95668696	C	T	95668696	3	4	100	1	0	0	0	0	1	0	0	0	4844	838	29	2	1573	2	DYNC1I1	7	95668696	Missense_Mutation	SNP	C	TCGA-B9-5155-01A-01D-1589-08		95668696	63469967	43	6339											
DLX5	1749	hgsc.bcm.edu	37	chr7	96651541	96651541	+	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	ggcggccagctcggcgcgttCcggcaaggcgaggtactgag	6	5	18	12	6	0	1	0	1	0	0	2	2	1	1	2	6	2	4	2	6	2	2	rs376488297		TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr7:96651541C>G	ENST00000222598.4	-	2	969	c.496G>C	c.(496-498)Gaa>Caa	p.E166Q	DLX5_ENST00000486603.2_Missense_Mutation_p.E166Q|DLX5_ENST00000493764.1_5'UTR	NM_005221.5	NP_005212.1	P56178	DLX5_HUMAN	distal-less homeobox 5	166					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)					TCGGCGCGTTCCGGCAAGGCG	0.542																																					p.E166Q		Atlas-SNP	.											.	DLX5	52	.	0			c.G496C						PASS	.						101	102	101					7																	96651541		2203	4300	6503	SO:0001583	missense	1749	exon2			CGCGTTCCGGCAA		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.496G>C	chr7.hg19:g.96651541C>G	ENSP00000222598:p.Glu166Gln	231.0	0.0	.		296.0	59.0	.	NM_005221	B7Z4P3|Q9UPL1	Missense_Mutation	SNP	ENST00000222598.4	hg19	CCDS5647.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.931253	0.92389	.	.	ENSG00000105880	ENST00000222598	D	0.96200	-3.94	5.41	5.41	0.78517	Homeobox, eukaryotic (1);Homeodomain-related (1);Helix-turn-helix motif, lambda-like repressor (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.96815	0.8960	L	0.47078	1.49	0.80722	D	1	D;D	0.71674	0.966;0.998	P;D	0.76575	0.789;0.988	D	0.97186	0.9854	10	0.87932	D	0	-9.535	18.9868	0.92773	0.0:1.0:0.0:0.0	.	166;166	B7Z4P3;P56178	.;DLX5_HUMAN	Q	166	ENSP00000222598:E166Q	ENSP00000222598:E166Q	E	-	1	0	DLX5	96489477	1.000000	0.71417	0.968000	0.41197	0.708000	0.40852	7.582000	0.82546	2.816000	0.96949	0.563000	0.77884	GAA	.	.	.	alt		0.542	DLX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334371.2			G	96651541	C	G	96651541	3	3	100	1	0	0	0	0	1	0	0	0	4576	864	30	4	381	4	DLX5	7	96651541	Missense_Mutation	SNP	C	TCGA-B9-5155-01A-01D-1589-08	982845	96651541	62487122	44	6340											
STAG3	10734	hgsc.bcm.edu	37	chr7	99800113	99800113	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcatttacagatagagcggcTacaccagcggcgccgcctcc	9	7	10	15	4	1	2	1	0	0	2	2	2	2	2	4	2	4	1	4	2	3	4			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr7:99800113T>C	ENST00000426455.1	+	25	3007	c.2600T>C	c.(2599-2601)cTa>cCa	p.L867P	GATS_ENST00000436886.2_3'UTR|GATS_ENST00000543273.1_RNA|STAG3_ENST00000317296.5_Missense_Mutation_p.L867P|STAG3_ENST00000394018.2_Missense_Mutation_p.L809P|STAG3_ENST00000440830.1_3'UTR	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	867					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ATAGAGCGGCTACACCAGCGG	0.512																																					p.L867P		Atlas-SNP	.											.	STAG3	121	.	0			c.T2600C						PASS	.						106	113	110					7																	99800113		2203	4300	6503	SO:0001583	missense	10734	exon25			AGCGGCTACACCA	AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.2600T>C	chr7.hg19:g.99800113T>C	ENSP00000400359:p.Leu867Pro	254.0	0.0	.		382.0	242.0	.	NM_012447	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Missense_Mutation	SNP	ENST00000426455.1	hg19	CCDS34703.1	.	.	.	.	.	.	.	.	.	.	.	20.4	3.986379	0.74589	.	.	ENSG00000066923	ENST00000426455;ENST00000394018;ENST00000317296	T;T;T	0.33865	1.39;1.42;1.39	5.03	5.03	0.67393	.	0.000000	0.39544	N	0.001333	T	0.61148	0.2324	M	0.81497	2.545	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.87578	0.997;0.998;0.976	T	0.66658	-0.5868	10	0.87932	D	0	-8.8042	12.7629	0.57374	0.0:0.0:0.0:1.0	.	809;867;867	B4DZ10;D6W5U7;Q9UJ98	.;.;STAG3_HUMAN	P	867;809;867	ENSP00000400359:L867P;ENSP00000377586:L809P;ENSP00000319318:L867P	ENSP00000319318:L867P	L	+	2	0	STAG3	99638049	0.998000	0.40836	0.999000	0.59377	0.806000	0.45545	7.178000	0.77657	2.122000	0.65172	0.460000	0.39030	CTA	.	.	.	none		0.512	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447		C	99800113	T	C	99800113	3	2	100	1	0	0	0	0	1	0	0	0	15256	1522	53	3	2694	3	STAG3	7	99800113	Missense_Mutation	SNP	T	TCGA-B9-5155-01A-01D-1589-08	3148572	99800113	59338550	45	6341											
PSMC2	5701	hgsc.bcm.edu	37	chr7	103002482	103002482	+	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	cagtttgccaagtttgtggtGgaccttagtgatcaggtggc	7	13	14	7	0	1	1	1	1	0	0	1	2	1	2	2	4	1	2	2	4	2	3			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr7:103002482G>T	ENST00000435765.1	+	6	780	c.369G>T	c.(367-369)gtG>gtT	p.V123V	SLC26A5_ENST00000356767.4_Intron|PSMC2_ENST00000292644.3_Silent_p.V123V|PSMC2_ENST00000544811.1_5'UTR|SLC26A5_ENST00000339444.6_Intron|SLC26A5_ENST00000393735.2_Intron	NM_002803.3	NP_002794.1	P35998	PRS7_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 2	123					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|osteoblast differentiation (GO:0001649)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	21						AGTTTGTGGTGGACCTTAGTG	0.383																																					p.V123V		Atlas-SNP	.											.	PSMC2	38	.	0			c.G369T						PASS	.						156	143	148					7																	103002482		2203	4300	6503	SO:0001819	synonymous_variant	5701	exon5			TGTGGTGGACCTT	D11094	CCDS5731.1	7q22.1-q22.3	2010-04-21			ENSG00000161057	ENSG00000161057		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9548	protein-coding gene	gene with protein product	"proteasome 26S subunit, ATPase, 2", "mammalian suppressor of sgv-1 of yeast", "protease 26S subunit 7", "putative protein product of Nbla10058"	154365				9473509, 1377363	Standard	NM_002803		Approved	MSS1, S7, Nbla10058	uc003vbs.3	P35998	OTTHUMG00000157206	ENST00000435765.1:c.369G>T	chr7.hg19:g.103002482G>T		102.0	0.0	.		170.0	60.0	.	NM_001204453	A4D0Q1|B7Z5E2|Q3LIA5|Q9UDI3	Silent	SNP	ENST00000435765.1	hg19	CCDS5731.1																																																																																			.	.	.	none		0.383	PSMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347922.1	NM_002803		T	103002482	G	T	103002482	2	4	100	1	0	0	0	0	0	0	0	1	12696	1335	47	4		4	PSMC2	7	103002482	Silent	SNP	G	TCGA-B9-5155-01A-01D-1589-08	3202369	103002482	56136181	46	6342											
WEE2	494551	hgsc.bcm.edu	37	chr7	141408685	141408685	+	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	cttcgagccaaaccccagagAagggtgaagtgcaggattca	13	6	12	10	1	1	2	1	1	0	1	2	5	1	3	3	2	3	1	3	2	3	2			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr7:141408685A>T	ENST00000397541.2	+	1	533	c.127A>T	c.(127-129)Aag>Tag	p.K43*	WEE2-AS1_ENST00000459753.1_RNA|WEE2-AS1_ENST00000465110.1_RNA|WEE2-AS1_ENST00000462383.1_RNA|WEE2-AS1_ENST00000478332.1_RNA|WEE2-AS1_ENST00000488785.1_RNA|WEE2-AS1_ENST00000471512.1_RNA|WEE2-AS1_ENST00000495800.1_RNA	NM_001105558.1	NP_001099028.1	P0C1S8	WEE2_HUMAN	WEE1 homolog 2 (S. pombe)	43					female meiotic division (GO:0007143)|female pronucleus assembly (GO:0035038)|mitotic nuclear division (GO:0007067)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of oocyte maturation (GO:1900194)|regulation of meiosis I (GO:0060631)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(2)|stomach(1)	31	Melanoma(164;0.0171)					AACCCCAGAGAAGGGTGAAGT	0.473																																					p.K43X		Atlas-SNP	.											.	WEE2	59	.	0			c.A127T						PASS	.						167	168	167					7																	141408685		1953	4139	6092	SO:0001587	stop_gained	494551	exon1			CCAGAGAAGGGTG	AK131218	CCDS43660.1	7q32	2008-07-02			ENSG00000214102	ENSG00000214102			19684	protein-coding gene	gene with protein product		614084					Standard	NM_001105558		Approved	FLJ16107	uc003vwn.2	P0C1S8	OTTHUMG00000157536	ENST00000397541.2:c.127A>T	chr7.hg19:g.141408685A>T	ENSP00000380675:p.Lys43*	265.0	0.0	.		341.0	193.0	.	NM_001105558		Nonsense_Mutation	SNP	ENST00000397541.2	hg19	CCDS43660.1	.	.	.	.	.	.	.	.	.	.	a	36	5.620662	0.96660	.	.	ENSG00000214102	ENST00000397541	.	.	.	4.78	-2.3	0.06785	.	1.588760	0.04251	U	0.338596	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.0729	2.105	0.03688	0.4246:0.2574:0.07:0.2479	.	.	.	.	X	43	.	ENSP00000380675:K43X	K	+	1	0	WEE2	141055154	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	0.169000	0.16641	-0.353000	0.08224	-0.255000	0.11280	AAG	.	.	.	none		0.473	WEE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349091.1	NM_001105558		T	141408685	A	T	141408685	4	4	100	1	0	0	0	0	0	1	0	0	17357	247	9	5	129	5	WEE2	7	141408685	Nonsense_Mutation	SNP	A	TCGA-B9-5155-01A-01D-1589-08	38406203	141408685	17729978	47	6343											
MYST3	7994	hgsc.bcm.edu	37	chr8	41794928	41794928	+	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	tcctcctcttcttcatcgatCtcaaacgtgggttctaatct	7	16	5	13	2	6	0	2	0	5	0	10	1	8	0	2	1	1	1	2	1	2	4			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr8:41794928C>A	ENST00000396930.3	-	17	3741	c.3198G>T	c.(3196-3198)gaG>gaT	p.E1066D	KAT6A_ENST00000265713.2_Missense_Mutation_p.E1066D|KAT6A_ENST00000406337.1_Missense_Mutation_p.E1066D	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1066					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)										CTTCATCGATCTCAAACGTGG	0.433																																					p.E1066D		Atlas-SNP	.											.	.	.	.	0			c.G3198T						PASS	.						125	120	122					8																	41794928		2203	4300	6503	SO:0001583	missense	7994	exon17			ATCGATCTCAAAC	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.3198G>T	chr8.hg19:g.41794928C>A	ENSP00000380136:p.Glu1066Asp	175.0	0.0	.		157.0	64.0	.	NM_001099412	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	hg19	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	C	13.09	2.132187	0.37630	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930;ENST00000418721	T;T;T	0.62105	0.05;0.05;0.05	5.63	-1.75	0.08031	.	0.000000	0.64402	D	0.000004	T	0.64271	0.2583	M	0.63843	1.955	0.26390	N	0.976585	D	0.67145	0.996	P	0.54759	0.76	T	0.62812	-0.6775	10	0.24483	T	0.36	-25.1078	12.5465	0.56203	0.0:0.464:0.0:0.536	.	1066	Q92794	KAT6A_HUMAN	D	1066;1066;1066;646	ENSP00000265713:E1066D;ENSP00000385888:E1066D;ENSP00000380136:E1066D	ENSP00000265713:E1066D	E	-	3	2	KAT6A	41914085	0.998000	0.40836	0.955000	0.39395	0.909000	0.53808	0.458000	0.21892	-0.247000	0.09597	0.650000	0.86243	GAG	.	.	.	none		0.433	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		A	41794928	C	A	41794928	3	1	100	1	0	0	0	0	1	0	0	0	10111	912	32	4	2824	4	MYST3	8	41794928	Missense_Mutation	SNP	C	TCGA-B9-5155-01A-01D-1589-08		41794928	104569094	48	6344											
HAS2	3037	hgsc.bcm.edu	37	chr8	122627047	122627047	+	Frame_Shift_Del	DEL	C	C	-																															tgcatagcccaggctcagcaCccggttcgtgagatgcctgt																										TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr8:122627047delC	ENST00000303924.4	-	4	1498	c.961delG	c.(961-963)gtgfs	p.V321fs		NM_005328.2	NP_005319.1	Q92819	HYAS2_HUMAN	hyaluronan synthase 2	321					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)			AGGCTCAGCACCCGGTTCGTG	0.453																																					p.V321fs		Atlas-INDEL	.											.	HAS2	87	.	0			c.962delT						PASS	.						143	136	138					8																	122627047		2203	4300	6503	SO:0001589	frameshift_variant	3037	exon4			.	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.961delG	chr8.hg19:g.122627047delC	ENSP00000306991:p.Val321fs	196.0	0.0	0		241.0	116.0	0.481328	NM_005328	Q32MM3	Frame_Shift_Del	DEL	ENST00000303924.4	hg19	CCDS6335.1																																																																																			.	.	.	none		0.453	HAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381150.2	NM_005328		-	122627047	C	-	122627047	7	5	100	1	0	1	0	1	0	0	0	0	6969	507	18	0	701	0	HAS2	8	122627047	Frame_Shift_Del	DEL	C	TCGA-B9-5155-01A-01D-1589-08	80832119	122627047	23736975	49	6345											
SLURP1	57152	hgsc.bcm.edu	37	chr8	143822661	143822661	+	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	cacaggagctggagcaggagCgggtcaccacggggctctgg	8	4	18	11	2	2	0	1	0	1	0	2	3	2	3	1	7	3	3	1	7	0	0			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr8:143822661C>A	ENST00000246515.1	-	3	237	c.212G>T	c.(211-213)cGc>cTc	p.R71L		NM_020427.2	NP_065160.1	P55000	SLUR1_HUMAN	secreted LY6/PLAUR domain containing 1	71	UPAR/Ly6.		R -> H (in MDM; reduced expression of the protein). {ECO:0000269|PubMed:17008884}.		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)					GGAGCAGGAGCGGGTCACCAC	0.657																																					p.R71L		Atlas-SNP	.											SLURP1,NS,carcinoma,0,1	SLURP1	16	.	0			c.G212T	GRCh37	CM070268	SLURP1	M		PASS	.						55	53	54					8																	143822661		2202	4296	6498	SO:0001583	missense	57152	exon3			CAGGAGCGGGTCA	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.212G>T	chr8.hg19:g.143822661C>A	ENSP00000246515:p.Arg71Leu	23.0	0.0	.		36.0	2.0	.	NM_020427	Q53YJ6|Q6PUA6|Q92483	Missense_Mutation	SNP	ENST00000246515.1	hg19	CCDS6387.1	.	.	.	.	.	.	.	.	.	.	C	17.36	3.370708	0.61624	.	.	ENSG00000126233	ENST00000246515	T	0.73897	-0.79	3.76	1.84	0.25277	Ly-6 antigen / uPA receptor -like (1);CD59 antigen (1);	0.390066	0.17436	N	0.174313	T	0.73536	0.3599	M	0.67953	2.075	0.29005	N	0.887223	P	0.49090	0.919	P	0.49421	0.61	T	0.67945	-0.5539	10	0.72032	D	0.01	.	4.8794	0.13672	0.0:0.6546:0.2207:0.1247	.	71	P55000	SLUR1_HUMAN	L	71	ENSP00000246515:R71L	ENSP00000246515:R71L	R	-	2	0	SLURP1	143819663	0.028000	0.19301	0.813000	0.32504	0.624000	0.37722	0.103000	0.15292	0.321000	0.23259	0.448000	0.29417	CGC	.	.	.	none		0.657	SLURP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379741.1	NM_020427		A	143822661	C	A	143822661	3	1	100	1	0	0	0	0	1	0	0	0	14769	768	27	4	103	4	SLURP1	8	143822661	Missense_Mutation	SNP	C	TCGA-B9-5155-01A-01D-1589-08	21195614	143822661	2541361	50	6346											
PRSS3	5646	hgsc.bcm.edu	37	chr9	33797829	33797829	+	Missense_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	gcctgccctgcccatcagccGcatccaggtgagactgggag	7	6	13	15	1	1	1	1	1	0	1	2	3	2	2	5	2	3	1	5	2	0	0	rs138654302		TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr9:33797829G>A	ENST00000361005.5	+	3	374	c.374G>A	c.(373-375)cGc>cAc	p.R125H	PRSS3_ENST00000429677.3_Missense_Mutation_p.R61H|RP11-133O22.6_ENST00000454429.2_RNA|PRSS3_ENST00000342836.4_Missense_Mutation_p.R82H|PRSS3_ENST00000379405.3_Missense_Mutation_p.R68H	NM_007343.3	NP_031369	P35030	TRY3_HUMAN	protease, serine, 3	125	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)			CCCATCAGCCGCATCCAGGTG	0.577																																					p.R125H		Atlas-SNP	.											PRSS3_ENST00000361005,NS,carcinoma,0,2	PRSS3	79	.	0			c.G374A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	109	100	103		245,182,203,374	-1	0.9	9	dbSNP_134	103	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	PRSS3	NM_001197097.2,NM_001197098.1,NM_002771.3,NM_007343.3	29,29,29,29	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	benign,benign,benign,benign	82/262,61/241,68/248,125/305	33797829	2,13004	2203	4300	6503	SO:0001583	missense	5646	exon3			TCAGCCGCATCCA		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.374G>A	chr9.hg19:g.33797829G>A	ENSP00000354280:p.Arg125His	94.0	1.0	.		131.0	41.0	.	NM_007343	A8CED1|A8CED3|A9Z1Y4|E7ES07|F8W7P3|P15951|Q15665|Q5VXV0|Q6ISJ4|Q9UQV3	Missense_Mutation	SNP	ENST00000361005.5	hg19	CCDS47958.1	.	.	.	.	.	.	.	.	.	.	G	8.689	0.906916	0.17833	2.27E-4	1.16E-4	ENSG00000010438	ENST00000361005;ENST00000457896;ENST00000342836;ENST00000429677;ENST00000379405	D;D;D;D;D	0.88896	-2.44;-2.44;-2.44;-2.44;-2.44	3.38	-1.0	0.10196	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.193106	0.56097	N	0.000021	T	0.80210	0.4581	L	0.35644	1.08	0.39352	D	0.965773	B;B;B	0.21520	0.006;0.057;0.006	B;B;B	0.20184	0.009;0.028;0.007	T	0.66532	-0.5900	10	0.40728	T	0.16	.	8.2506	0.31715	0.4318:0.0:0.5682:0.0	.	68;125;82	P35030-3;P35030;P35030-4	.;TRY3_HUMAN;.	H	125;80;82;61;68	ENSP00000354280:R125H;ENSP00000401249:R80H;ENSP00000340889:R82H;ENSP00000401828:R61H;ENSP00000368715:R68H	ENSP00000340889:R82H	R	+	2	0	PRSS3	33787829	0.962000	0.33011	0.872000	0.34217	0.074000	0.17049	2.182000	0.42556	-0.172000	0.10779	-0.671000	0.03813	CGC	.	G|1.000;A|0.000	0.000	weak		0.577	PRSS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052121.1	NM_002771		A	33797829	G	A	33797829	3	1	100	1	0	0	0	0	1	0	0	0	12632	1087	38	1	428	1	PRSS3	9	33797829	Missense_Mutation	SNP	G	TCGA-B9-5155-01A-01D-1589-08		33797829	107415602	51	6347											
CCIN	881	hgsc.bcm.edu	37	chr9	36169599	36169599	+	Missense_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	actgggacatggccctgagtGtggacaaccacgtcttcttt	8	11	11	11	1	2	1	0	1	2	0	2	3	2	3	2	3	1	0	2	3	1	2			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr9:36169599G>A	ENST00000335119.2	+	1	211	c.100G>A	c.(100-102)Gtg>Atg	p.V34M		NM_005893.2	NP_005884.2	Q13939	CALI_HUMAN	calicin	34	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				breast(3)|endometrium(2)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(4)	21			STAD - Stomach adenocarcinoma(86;0.228)			GGCCCTGAGTGTGGACAACCA	0.502																																					p.V34M		Atlas-SNP	.											.	CCIN	56	.	0			c.G100A						PASS	.						164	154	157					9																	36169599		2203	4300	6503	SO:0001583	missense	881	exon1			CTGAGTGTGGACA	Z46967	CCDS6599.1	9p13.1	2013-10-02			ENSG00000185972	ENSG00000185972		"BTB/POZ domain containing"	1568	protein-coding gene	gene with protein product		603960				7641791	Standard	NM_005893		Approved	KBTBD14, BTBD20	uc003zzb.4	Q13939	OTTHUMG00000019901	ENST00000335119.2:c.100G>A	chr9.hg19:g.36169599G>A	ENSP00000334996:p.Val34Met	67.0	0.0	.		101.0	10.0	.	NM_005893	Q9BXG7	Missense_Mutation	SNP	ENST00000335119.2	hg19	CCDS6599.1	.	.	.	.	.	.	.	.	.	.	G	15.93	2.977645	0.53720	.	.	ENSG00000185972	ENST00000335119	T	0.77750	-1.12	5.69	5.69	0.88448	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.50627	D	0.000116	D	0.90508	0.7026	M	0.92367	3.3	0.36717	D	0.880964	D	0.67145	0.996	D	0.81914	0.995	D	0.94029	0.7299	10	0.87932	D	0	.	15.3016	0.73955	0.0:0.0:1.0:0.0	.	34	Q13939	CALI_HUMAN	M	34	ENSP00000334996:V34M	ENSP00000334996:V34M	V	+	1	0	CCIN	36159599	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	5.496000	0.66918	2.690000	0.91761	0.561000	0.74099	GTG	.	.	.	none		0.502	CCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052418.1	NM_005893		A	36169599	G	A	36169599	3	1	100	1	0	0	0	0	1	0	0	0	2880	1377	48	2	102	2	CCIN	9	36169599	Missense_Mutation	SNP	G	TCGA-B9-5155-01A-01D-1589-08	2371770	36169599	105043832	52	6348											
PTCH1	5727	hgsc.bcm.edu	37	chr9	98229471	98229471	+	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	tcttccaacatgacatacttCacgttactgaaactcctgtg	11	13	5	12	1	2	2	1	2	1	0	4	2	4	2	2	0	4	1	2	0	4	4			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr9:98229471C>A	ENST00000331920.6	-	15	2786	c.2487G>T	c.(2485-2487)gtG>gtT	p.V829V	PTCH1_ENST00000375274.2_Silent_p.V828V|PTCH1_ENST00000418258.1_Silent_p.V678V|PTCH1_ENST00000429896.2_Silent_p.V678V|PTCH1_ENST00000421141.1_Silent_p.V678V|PTCH1_ENST00000430669.2_Silent_p.V763V|PTCH1_ENST00000437951.1_Silent_p.V763V	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	829			V -> M (in squamous cell carcinoma). {ECO:0000269|PubMed:11286632}.		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)				TGACATACTTCACGTTACTGA	0.448																																					p.V829V		Atlas-SNP	.											.	PTCH1	1850	.	0			c.G2487T						PASS	.						168	154	159					9																	98229471		2203	4300	6503	SO:0001819	synonymous_variant	5727	exon15			ATACTTCACGTTA	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.2487G>T	chr9.hg19:g.98229471C>A		118.0	0.0	.		152.0	64.0	.	NM_000264	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	ENST00000331920.6	hg19	CCDS6714.1																																																																																			.	.	.	none		0.448	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		A	98229471	C	A	98229471	2	1	100	1	0	0	0	0	0	0	0	1	12740	813	29	4		4	PTCH1	9	98229471	Silent	SNP	C	TCGA-B9-5155-01A-01D-1589-08	62059872	98229471	42983960	53	6349											
C9orf125	84302	hgsc.bcm.edu	37	chr9	104238602	104238602	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attccaggatccgcatgggcTctggattgatgtagtgctgg	7	12	14	8	1	1	1	0	1	1	0	3	3	3	3	2	4	1	4	2	4	1	3			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr9:104238602T>C	ENST00000374851.1	-	4	1920	c.773A>G	c.(772-774)gAg>gGg	p.E258G	RP11-490D19.6_ENST00000450109.1_RNA|TMEM246_ENST00000374847.1_Missense_Mutation_p.E258G|RP11-490D19.6_ENST00000424154.1_RNA|RP11-490D19.6_ENST00000425734.1_RNA|TMEM246_ENST00000374848.3_Missense_Mutation_p.E258G|RP11-490D19.6_ENST00000431507.1_RNA			Q9BRR3	TM246_HUMAN	transmembrane protein 246	258						integral component of membrane (GO:0016021)											CCGCATGGGCTCTGGATTGAT	0.557																																					p.E258G		Atlas-SNP	.											.	.	.	.	0			c.A773G						PASS	.						88	89	89					9																	104238602		2203	4300	6503	SO:0001583	missense	84302	exon2			ATGGGCTCTGGAT	BC006115	CCDS6757.1	9q31.1	2012-04-02	2012-04-02	2012-04-02	ENSG00000165152	ENSG00000165152			28180	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 125"	C9orf125		12477932	Standard	NM_032342		Approved	MGC12992	uc004bbm.3	Q9BRR3	OTTHUMG00000020381	ENST00000374851.1:c.773A>G	chr9.hg19:g.104238602T>C	ENSP00000363984:p.Glu258Gly	152.0	0.0	.		159.0	72.0	.	NM_032342	Q49AQ4	Missense_Mutation	SNP	ENST00000374851.1	hg19	CCDS6757.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.277935	0.80692	.	.	ENSG00000165152	ENST00000374848;ENST00000374847;ENST00000374851	.	.	.	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.76849	0.4045	M	0.62723	1.935	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.78863	-0.2036	9	0.66056	D	0.02	-17.5086	15.1322	0.72533	0.0:0.0:0.0:1.0	.	258	Q9BRR3	CI125_HUMAN	G	258	.	ENSP00000363980:E258G	E	-	2	0	C9orf125	103278423	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.770000	0.85390	2.177000	0.69029	0.455000	0.32223	GAG	.	.	.	none		0.557	TMEM246-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053444.1	NM_032342		C	104238602	T	C	104238602	3	2	100	1	0	0	0	0	1	0	0	0	2456	1551	54	3	442	3	C9orf125	9	104238602	Missense_Mutation	SNP	T	TCGA-B9-5155-01A-01D-1589-08	6009131	104238602	36974829	54	6350											
C5	727	hgsc.bcm.edu	37	chr9	123742457	123742457	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcatacgcagaaatggccaAtgtaaaggtgctctgggctg	12	8	13	8	1	1	1	0	0	1	1	1	1	1	1	1	3	3	5	1	3	5	2			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr9:123742457A>G	ENST00000223642.1	-	28	3591	c.3562T>C	c.(3562-3564)Ttg>Ctg	p.L1188L		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	1188					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)	GAAATGGCCAATGTAAAGGTG	0.413																																					p.L1188L		Atlas-SNP	.											.	C5	124	.	0			c.T3562C						PASS	.						141	139	140					9																	123742457		2203	4300	6503	SO:0001819	synonymous_variant	727	exon28			TGGCCAATGTAAA	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.3562T>C	chr9.hg19:g.123742457A>G		93.0	0.0	.		103.0	42.0	.	NM_001735	Q14CJ0|Q27I61	Silent	SNP	ENST00000223642.1	hg19	CCDS6826.1																																																																																			.	.	.	none		0.413	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735		G	123742457	A	G	123742457	2	3	100	1	0	0	0	0	0	0	0	1	2282	98	4	3		3	C5	9	123742457	Silent	SNP	A	TCGA-B9-5155-01A-01D-1589-08	19503855	123742457	17470974	55	6351											
BRD3	8019	hgsc.bcm.edu	37	chr9	136915699	136915699	+	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	gacagaggacacggccgccaCttgctgtgtaccttcaagac	10	7	11	13	2	1	2	1	0	0	2	1	4	1	3	3	2	2	2	3	2	2	3			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr9:136915699C>G	ENST00000303407.7	-	5	696	c.511G>C	c.(511-513)Gtg>Ctg	p.V171L	BRD3_ENST00000357885.2_Missense_Mutation_p.V171L|BRD3_ENST00000371834.2_Missense_Mutation_p.V171L	NM_007371.3	NP_031397.1	Q15059	BRD3_HUMAN	bromodomain containing 3	171					chromatin modification (GO:0016568)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)		BRD3/C15orf55(3)	kidney(1)|skin(1)|stomach(4)	6				OV - Ovarian serous cystadenocarcinoma(145;1.43e-08)|Epithelial(140;8.41e-08)|all cancers(34;5.21e-07)		ACGGCCGCCACTTGCTGTGTA	0.607			T	C15orf55	lethal midline carcinoma of young people																																p.V171L		Atlas-SNP	.		Dom	yes		9	9q34	8019	bromodomain containing 3		E	.	BRD3	82	.	0			c.G511C						PASS	.						29	37	34					9																	136915699		2202	4299	6501	SO:0001583	missense	8019	exon5			CCGCCACTTGCTG		CCDS6980.1	9q34	2010-12-23	2002-01-14		ENSG00000169925	ENSG00000169925			1104	protein-coding gene	gene with protein product	"RING3-like"	601541	"bromodomain-containing 3"			7584044, 8781126	Standard	NM_007371		Approved	RING3L, ORFX, KIAA0043	uc004cew.3	Q15059	OTTHUMG00000021004	ENST00000303407.7:c.511G>C	chr9.hg19:g.136915699C>G	ENSP00000305918:p.Val171Leu	76.0	0.0	.		69.0	34.0	.	NM_007371	B1APD9|Q4G5Y3|Q5T1R7|Q8N5M3|Q92645	Missense_Mutation	SNP	ENST00000303407.7	hg19	CCDS6980.1	.	.	.	.	.	.	.	.	.	.	C	15.02	2.710248	0.48517	.	.	ENSG00000169925	ENST00000303407;ENST00000371834;ENST00000357885	T;T;T	0.46451	0.87;0.87;0.87	4.97	4.06	0.47325	.	0.269386	0.30528	N	0.009440	T	0.40791	0.1131	M	0.68952	2.095	0.31270	N	0.691828	B;B	0.12013	0.005;0.0	B;B	0.12837	0.008;0.001	T	0.43861	-0.9365	10	0.25106	T	0.35	-32.3956	13.0826	0.59121	0.0:0.9204:0.0:0.0796	.	171;171	Q15059-2;Q15059	.;BRD3_HUMAN	L	171	ENSP00000305918:V171L;ENSP00000360900:V171L;ENSP00000350557:V171L	ENSP00000305918:V171L	V	-	1	0	BRD3	135905520	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.505000	0.53356	1.182000	0.42928	0.561000	0.74099	GTG	.	.	.	none		0.607	BRD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055390.4	NM_007371		G	136915699	C	G	136915699	3	3	100	1	0	0	0	0	1	0	0	0	1505	565	20	4	1701	4	BRD3	9	136915699	Missense_Mutation	SNP	C	TCGA-B9-5155-01A-01D-1589-08	13173242	136915699	4297732	56	6352											
KLF6	1316	hgsc.bcm.edu	37	chr10	3823844	3823844	+	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	ggcactgacctgtgtgcgtcCgctggtgtgctttcaagtgg	4	12	15	10	2	1	1	1	1	0	0	2	1	2	1	2	3	2	3	2	3	1	1			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr10:3823844C>A	ENST00000497571.1	-	2	925	c.665G>T	c.(664-666)cGg>cTg	p.R222L	KLF6_ENST00000542957.1_Missense_Mutation_p.R222L|KLF6_ENST00000469435.1_Missense_Mutation_p.R222L|KLF6_ENST00000173785.4_Intron	NM_001160124.1|NM_001300.5	NP_001153596.1|NP_001291.3	Q99612	KLF6_HUMAN	Kruppel-like factor 6	222					B cell differentiation (GO:0030183)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(3)|endometrium(1)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16				Colorectal(1;0.238)		TGTGTGCGTCCGCTGGTGTGC	0.677											OREG0019980	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R222L		Atlas-SNP	.											.	KLF6	38	.	0			c.G665T						PASS	.						45	39	41					10																	3823844		2203	4300	6503	SO:0001583	missense	1316	exon2			TGCGTCCGCTGGT	U51869	CCDS7060.1, CCDS53490.1	10p15	2013-01-08	2004-11-29	2004-12-01	ENSG00000067082	ENSG00000067082		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	2235	protein-coding gene	gene with protein product	"GC-rich binding factor"	602053	"core promoter element binding protein"	BCD1, ST12, COPEB		9503030, 9685731	Standard	NM_001300		Approved	CPBP, GBF, Zf9, PAC1	uc001iha.3	Q99612	OTTHUMG00000017567	ENST00000497571.1:c.665G>T	chr10.hg19:g.3823844C>A	ENSP00000419923:p.Arg222Leu	38.0	0.0	.	614	35.0	20.0	.	NM_001160125	B2RE86|B4DDN0|D3DRR1|F5H3M5|Q5VUT7|Q5VUT8|Q9BT79	Missense_Mutation	SNP	ENST00000497571.1	hg19	CCDS7060.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.729162	0.89390	.	.	ENSG00000067082	ENST00000497571;ENST00000542957;ENST00000469435	T;T;T	0.78595	1.82;-1.19;-1.19	4.88	4.88	0.63580	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	0.85745	0.5768	L	0.54908	1.71	0.80722	D	1	D;D;P	0.89917	1.0;1.0;0.738	D;D;B	0.91635	0.999;0.999;0.359	D	0.87437	0.2392	10	0.87932	D	0	.	17.05	0.86516	0.0:1.0:0.0:0.0	.	222;222;222	F5H3M5;Q99612-2;Q99612	.;.;KLF6_HUMAN	L	222	ENSP00000419923:R222L;ENSP00000445301:R222L;ENSP00000419079:R222L	ENSP00000419079:R222L	R	-	2	0	KLF6	3813844	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.711000	0.84669	2.253000	0.74438	0.462000	0.41574	CGG	.	.	.	none		0.677	KLF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046495.1			A	3823844	C	A	3823844	3	1	100	1	0	0	0	0	1	0	0	0	8357	652	23	4	198	4	KLF6	10	3823844	Missense_Mutation	SNP	C	TCGA-B9-5155-01A-01D-1589-08		3823844	131710903	57	6353											
C10orf140	387640	hgsc.bcm.edu	37	chr10	21804183	21804183	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atccccatctctcccaataaTgagtgatggtggacaaggaa	13	9	9	10	0	1	2	0	2	1	0	4	4	3	4	3	3	0	0	3	3	4	1			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr10:21804183T>C	ENST00000449193.2	-	4	4821	c.2569A>G	c.(2569-2571)Att>Gtt	p.I857V	SKIDA1_ENST00000444772.3_Missense_Mutation_p.I778V	NM_207371.3	NP_997254.3	Q1XH10	SKDA1_HUMAN	SKI/DACH domain containing 1	776						nucleus (GO:0005634)											CTCCCAATAATGAGTGATGGT	0.438																																					p.I857V		Atlas-SNP	.											.	.	.	.	0			c.A2569G						PASS	.						114	105	108					10																	21804183		1886	4112	5998	SO:0001583	missense	387640	exon4			CAATAATGAGTGA	AK131456	CCDS44363.1	10p12.31	2012-06-13	2012-06-13	2012-06-13	ENSG00000180592	ENSG00000180592			32697	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 140"	C10orf140			Standard	NM_207371		Approved	FLJ45187	uc021pnx.1	Q1XH10	OTTHUMG00000017797	ENST00000449193.2:c.2569A>G	chr10.hg19:g.21804183T>C	ENSP00000410041:p.Ile857Val	47.0	0.0	.		54.0	27.0	.	NM_207371	B1ANA5|Q6ZMX4|Q8N3C3	Missense_Mutation	SNP	ENST00000449193.2	hg19	CCDS44363.1	.	.	.	.	.	.	.	.	.	.	T	1.949	-0.441669	0.04604	.	.	ENSG00000180592	ENST00000449193;ENST00000444772	.	.	.	5.64	4.51	0.55191	.	0.181152	0.48286	D	0.000183	T	0.21761	0.0524	N	0.12182	0.205	0.28344	N	0.9212	B	0.18741	0.03	B	0.13407	0.009	T	0.18053	-1.0349	9	0.11485	T	0.65	-2.0894	9.6526	0.39906	0.0:0.1404:0.0:0.8596	.	857	E9PAX1	.	V	857;778	.	ENSP00000442432:I778V	I	-	1	0	C10orf140	21844189	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.252000	0.43196	1.081000	0.41110	0.533000	0.62120	ATT	.	.	.	none		0.438	SKIDA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286950.2	NM_207371		C	21804183	T	C	21804183	3	2	100	1	0	0	0	0	1	0	0	0	1597	1464	51	3	161	3	C10orf140	10	21804183	Missense_Mutation	SNP	T	TCGA-B9-5155-01A-01D-1589-08	17980339	21804183	113730564	58	6354											
KIAA1217	56243	hgsc.bcm.edu	37	chr10	24762791	24762791	+	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	cgctcactataatgcccacgGcccccctcacaccatgcagc	9	6	6	20	2	2	0	2	0	0	0	2	0	2	0	5	1	3	2	5	1	2	2			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr10:24762791G>C	ENST00000376454.3	+	6	1511	c.1481G>C	c.(1480-1482)gGc>gCc	p.G494A	KIAA1217_ENST00000376451.2_Missense_Mutation_p.G212A|KIAA1217_ENST00000430453.2_Missense_Mutation_p.G415A|KIAA1217_ENST00000458595.1_Missense_Mutation_p.G494A|KIAA1217_ENST00000376452.3_Missense_Mutation_p.G494A|KIAA1217_ENST00000396446.1_Missense_Mutation_p.G212A|KIAA1217_ENST00000376462.1_Missense_Mutation_p.G414A|KIAA1217_ENST00000396445.1_Missense_Mutation_p.G212A|KIAA1217_ENST00000307544.6_Missense_Mutation_p.G212A	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	494					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						AATGCCCACGGCCCCCCTCAC	0.577																																					p.G494A		Atlas-SNP	.											.	KIAA1217	235	.	0			c.G1481C						PASS	.						91	81	84					10																	24762791		2203	4300	6503	SO:0001583	missense	56243	exon6			CCCACGGCCCCCC	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.1481G>C	chr10.hg19:g.24762791G>C	ENSP00000365637:p.Gly494Ala	143.0	0.0	.		132.0	55.0	.	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Missense_Mutation	SNP	ENST00000376454.3	hg19	CCDS31165.1	.	.	.	.	.	.	.	.	.	.	G	3.550	-0.091916	0.07053	.	.	ENSG00000120549	ENST00000376462;ENST00000376456;ENST00000458595;ENST00000442879;ENST00000376454;ENST00000376452;ENST00000438429;ENST00000430453;ENST00000307544;ENST00000450158;ENST00000396445;ENST00000376451;ENST00000396446	T;T;T;T;T;T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68	5.44	4.46	0.54185	.	0.426273	0.28312	N	0.015814	T	0.57286	0.2043	L	0.55481	1.735	0.30862	N	0.733437	B;B;P;B;P;P;D;B	0.89917	0.418;0.349;0.787;0.168;0.787;0.787;1.0;0.417	B;B;B;B;B;B;D;B	0.76071	0.107;0.05;0.228;0.107;0.228;0.228;0.987;0.124	T	0.52162	-0.8612	10	0.12103	T	0.63	.	10.9169	0.47142	0.0:0.0:0.5812:0.4187	.	494;494;212;212;212;212;494;494	Q5T5P2-7;A6NLF3;Q5T5P2-4;Q5T5P2-8;Q5T5P2-3;Q5T5P2-6;Q5T5P2;Q5T5P2-2	.;.;.;.;.;.;SKT_HUMAN;.	A	414;494;494;212;494;494;344;415;212;212;212;212;212	ENSP00000365645:G414A;ENSP00000365639:G494A;ENSP00000392625:G494A;ENSP00000365637:G494A;ENSP00000365635:G494A;ENSP00000404798:G344A;ENSP00000389680:G415A;ENSP00000302343:G212A;ENSP00000379722:G212A;ENSP00000365634:G212A;ENSP00000379723:G212A	ENSP00000302343:G212A	G	+	2	0	KIAA1217	24802797	0.645000	0.27286	0.447000	0.26932	0.176000	0.22953	3.691000	0.54720	2.561000	0.86390	0.655000	0.94253	GGC	.	.	.	none		0.577	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		C	24762791	G	C	24762791	3	2	100	1	0	0	0	0	1	0	0	0	8223	1203	42	4	1503	4	KIAA1217	10	24762791	Missense_Mutation	SNP	G	TCGA-B9-5155-01A-01D-1589-08	2958608	24762791	110771956	59	6355											
HERC4	26091	hgsc.bcm.edu	37	chr10	69714847	69714847	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attcaatcactgggagaaaaAgagaggagacattctgcctg	15	8	11	7	0	3	3	2	0	1	3	3	6	3	3	1	2	1	0	1	2	3	2			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr10:69714847A>G	ENST00000395198.3	-	19	2337	c.2090T>C	c.(2089-2091)cTt>cCt	p.L697P	HERC4_ENST00000412272.2_Missense_Mutation_p.L697P|HERC4_ENST00000395187.2_3'UTR|HERC4_ENST00000480158.1_5'UTR|HERC4_ENST00000277817.6_Missense_Mutation_p.L587P|HERC4_ENST00000373700.4_Missense_Mutation_p.L689P	NM_022079.2	NP_071362.1	Q5GLZ8	HERC4_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 4	697					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						TGGGAGAAAAAGAGAGGAGAC	0.393																																					p.L697P		Atlas-SNP	.											.	HERC4	78	.	0			c.T2090C						PASS	.						102	97	99					10																	69714847		2203	4300	6503	SO:0001583	missense	26091	exon19			AGAAAAAGAGAGG	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.2090T>C	chr10.hg19:g.69714847A>G	ENSP00000378624:p.Leu697Pro	91.0	0.0	.		98.0	28.0	.	NM_022079	Q5GC98|Q5GC99|Q5GCA0|Q8IXP9|Q9HCH9	Missense_Mutation	SNP	ENST00000395198.3	hg19	CCDS41533.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.155772	0.78114	.	.	ENSG00000148634	ENST00000277817;ENST00000412272;ENST00000395198;ENST00000373700	T;T;T;T	0.54279	0.84;0.58;0.6;0.62	5.69	5.69	0.88448	.	0.200034	0.41294	D	0.000909	T	0.61999	0.2392	L	0.45352	1.415	0.80722	D	1	P;D;P;P;P	0.54397	0.955;0.966;0.885;0.937;0.897	P;P;P;P;P	0.62649	0.66;0.905;0.571;0.771;0.594	T	0.64715	-0.6342	10	0.72032	D	0.01	.	11.8771	0.52554	0.8544:0.1456:0.0:0.0	.	697;587;547;689;697	Q5GLZ8-3;Q5GLZ8-6;Q5VXS9;Q5GLZ8-2;Q5GLZ8	.;.;.;.;HERC4_HUMAN	P	587;697;697;689	ENSP00000277817:L587P;ENSP00000416504:L697P;ENSP00000378624:L697P;ENSP00000362804:L689P	ENSP00000277817:L587P	L	-	2	0	HERC4	69384853	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.194000	0.77789	2.168000	0.68352	0.533000	0.62120	CTT	.	.	.	none		0.393	HERC4-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359262.1	NM_015601		G	69714847	A	G	69714847	3	3	100	1	0	0	0	0	1	0	0	0	7067	72	3	3	1115	3	HERC4	10	69714847	Missense_Mutation	SNP	A	TCGA-B9-5155-01A-01D-1589-08	44952056	69714847	65819900	60	6356											
CCAR1	55749	hgsc.bcm.edu	37	chr10	70513756	70513756	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tactgcaatttttatgtaatGcacagagaagtagagtcctt	13	14	8	6	0	0	2	0	0	0	2	1	3	1	2	1	0	3	4	1	0	6	7			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr10:70513756G>A	ENST00000265872.6	+	11	1385	c.1266G>A	c.(1264-1266)atG>atA	p.M422I	SNORD98_ENST00000408255.1_RNA|CCAR1_ENST00000535016.1_Missense_Mutation_p.M407I|CCAR1_ENST00000543719.1_Missense_Mutation_p.M407I	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	422					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						TTTATGTAATGCACAGAGAAG	0.378																																					p.M422I		Atlas-SNP	.											.	CCAR1	118	.	0			c.G1266A						PASS	.						137	138	138					10																	70513756		2203	4300	6503	SO:0001583	missense	55749	exon11			TGTAATGCACAGA	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.1266G>A	chr10.hg19:g.70513756G>A	ENSP00000265872:p.Met422Ile	171.0	0.0	.		183.0	82.0	.	NM_018237	A0JLT7|A1L4P7|A8K9D4|B4DNP8|B4DRK8|Q32NE3|Q5EBM3|Q5VUP6|Q6PIZ0|Q6X935|Q9H8N4|Q9NVA7|Q9NVQ0|Q9NWM6	Missense_Mutation	SNP	ENST00000265872.6	hg19	CCDS7282.1	.	.	.	.	.	.	.	.	.	.	G	17.95	3.514342	0.64522	.	.	ENSG00000060339	ENST00000265872;ENST00000535016;ENST00000543719;ENST00000539539;ENST00000543225;ENST00000536012	T;T;T;T;T;T	0.23348	1.91;1.91;1.91;1.92;1.93;1.92	5.95	5.95	0.96441	.	0.041894	0.85682	D	0.000000	T	0.26011	0.0634	L	0.50333	1.59	0.50467	D	0.999877	B;P;B	0.35844	0.048;0.524;0.088	B;B;B	0.28849	0.025;0.095;0.05	T	0.02167	-1.1202	10	0.25751	T	0.34	-13.4805	20.3886	0.98946	0.0:0.0:1.0:0.0	.	407;422;396	Q8IX12-2;Q8IX12;F5H2E6	.;CCAR1_HUMAN;.	I	422;407;407;407;396;227	ENSP00000265872:M422I;ENSP00000441820:M407I;ENSP00000445254:M407I;ENSP00000439252:M407I;ENSP00000438610:M396I;ENSP00000439642:M227I	ENSP00000265872:M422I	M	+	3	0	CCAR1	70183762	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.600000	0.74132	2.810000	0.96702	0.650000	0.86243	ATG	.	.	.	none		0.378	CCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048356.2	NM_018237		A	70513756	G	A	70513756	3	1	100	1	0	0	0	0	1	0	0	0	2732	1319	46	2	1304	2	CCAR1	10	70513756	Missense_Mutation	SNP	G	TCGA-B9-5155-01A-01D-1589-08	798909	70513756	65020991	61	6357											
POLR3A	11128	hgsc.bcm.edu	37	chr10	79745045	79745045	+	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	tcatctgggtgcctggctcaCcaatgctctgggcacacaga	8	9	11	13	0	4	1	2	0	2	1	4	1	4	1	2	3	2	3	2	3	1	0			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr10:79745045C>T	ENST00000372371.3	-	24	3262	c.3125G>A	c.(3124-3126)gGt>gAt	p.G1042D		NM_007055.3	NP_008986.2	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa	1042					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)			GCCTGGCTCACCAATGCTCTG	0.537																																					p.G1042D		Atlas-SNP	.											.	POLR3A	104	.	0			c.G3125A						PASS	.						124	122	123					10																	79745045		2203	4300	6503	SO:0001583	missense	11128	exon24			GGCTCACCAATGC	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.3125G>A	chr10.hg19:g.79745045C>T	ENSP00000361446:p.Gly1042Asp	196.0	0.0	.		200.0	75.0	.	NM_007055	Q8IW34|Q8TCW5	Missense_Mutation	SNP	ENST00000372371.3	hg19	CCDS7354.1	.	.	.	.	.	.	.	.	.	.	C	33	5.197516	0.94960	.	.	ENSG00000148606	ENST00000372371	D	0.87491	-2.26	5.95	5.95	0.96441	RNA polymerase Rpb1, domain 5 (1);	0.000000	0.85682	D	0.000000	D	0.96405	0.8827	H	0.97516	4.02	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.97111	0.9804	9	.	.	.	-13.79	20.3802	0.98930	0.0:1.0:0.0:0.0	.	1042	O14802	RPC1_HUMAN	D	1042	ENSP00000361446:G1042D	.	G	-	2	0	POLR3A	79415051	1.000000	0.71417	0.942000	0.38095	0.985000	0.73830	7.336000	0.79245	2.822000	0.97130	0.563000	0.77884	GGT	.	.	.	none		0.537	POLR3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048923.1	NM_007055		T	79745045	C	T	79745045	3	4	100	1	0	0	0	0	1	0	0	0	12235	507	18	2	1079	2	POLR3A	10	79745045	Missense_Mutation	SNP	C	TCGA-B9-5155-01A-01D-1589-08	9231289	79745045	55789702	62	6358											
SLC5A12	159963	hgsc.bcm.edu	37	chr11	26720065	26720065	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatgatccagagacccagcAagttaaaatacaaggcacta	18	6	8	9	0	0	2	0	1	0	1	1	4	1	2	2	1	2	3	2	1	7	3			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr11:26720065A>G	ENST00000396005.3	-	7	1148	c.839T>C	c.(838-840)tTg>tCg	p.L280S	SLC5A12_ENST00000280467.6_Missense_Mutation_p.L280S	NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	280					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						GAGACCCAGCAAGTTAAAATA	0.438																																					p.L280S		Atlas-SNP	.											.	SLC5A12	134	.	0			c.T839C						PASS	.						113	103	106					11																	26720065		2203	4299	6502	SO:0001583	missense	159963	exon7			CCCAGCAAGTTAA	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.839T>C	chr11.hg19:g.26720065A>G	ENSP00000379326:p.Leu280Ser	43.0	0.0	.		57.0	35.0	.	NM_178498	Q86UC7	Missense_Mutation	SNP	ENST00000396005.3	hg19	CCDS7860.2	.	.	.	.	.	.	.	.	.	.	A	17.57	3.423743	0.62733	.	.	ENSG00000148942	ENST00000396005;ENST00000280467;ENST00000533617	D;D;D	0.89415	-2.51;-2.51;-2.51	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000002	D	0.94059	0.8096	M	0.75150	2.29	0.54753	D	0.999984	B;D	0.89917	0.22;1.0	B;D	0.87578	0.217;0.998	D	0.93413	0.6770	10	0.40728	T	0.16	.	16.6277	0.84984	1.0:0.0:0.0:0.0	.	280;280	Q1EHB4-2;Q1EHB4	.;SC5AC_HUMAN	S	280;280;92	ENSP00000379326:L280S;ENSP00000280467:L280S;ENSP00000435053:L92S	ENSP00000280467:L280S	L	-	2	0	SLC5A12	26676641	1.000000	0.71417	0.914000	0.36105	0.771000	0.43674	9.154000	0.94694	2.330000	0.79161	0.528000	0.53228	TTG	.	.	.	none		0.438	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498		G	26720065	A	G	26720065	3	3	100	1	0	0	0	0	1	0	0	0	14677	131	5	3	1053	3	SLC5A12	11	26720065	Missense_Mutation	SNP	A	TCGA-B9-5155-01A-01D-1589-08		26720065	108286451	63	6359											
CAPRIN1	4076	hgsc.bcm.edu	37	chr11	34118752	34118752	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctaaattttaggaggatatgAtggttaccgcccttcattct	10	15	8	8	1	2	1	1	1	1	0	2	3	2	3	2	3	1	1	2	3	5	7			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr11:34118752A>G	ENST00000341394.4	+	17	2099	c.1910A>G	c.(1909-1911)gAt>gGt	p.D637G	CAPRIN1_ENST00000530820.1_Missense_Mutation_p.D637G|CAPRIN1_ENST00000533657.1_3'UTR|CAPRIN1_ENST00000389645.3_Missense_Mutation_p.D637G|CAPRIN1_ENST00000529307.1_Missense_Mutation_p.D556G|CAPRIN1_ENST00000532820.1_Missense_Mutation_p.D637G	NM_005898.4	NP_005889.3	Q14444	CAPR1_HUMAN	cell cycle associated protein 1	637					negative regulation of translation (GO:0017148)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)	18		Acute lymphoblastic leukemia(5;0.00045)|all_hematologic(20;0.0016)				GGAGGATATGATGGTTACCGC	0.368																																					p.D637G		Atlas-SNP	.											.	CAPRIN1	110	.	0			c.A1910G						PASS	.						93	92	92					11																	34118752		2202	4298	6500	SO:0001583	missense	4076	exon17			GATATGATGGTTA	BC001731	CCDS31453.1, CCDS31454.1	11p13	2010-08-03	2007-03-27	2007-03-27	ENSG00000135387	ENSG00000135387			6743	protein-coding gene	gene with protein product	"cytoplasmic activation/proliferation-associated protein-1"	601178	"membrane component, chromosome 11, surface marker 1", "GPI-anchored membrane protein 1"	M11S1, GPIAP1		7657653, 16177067, 17210633, 14764709, 15471883	Standard	NM_005898		Approved	caprin-1, RNG105	uc001mvh.1	Q14444	OTTHUMG00000166248	ENST00000341394.4:c.1910A>G	chr11.hg19:g.34118752A>G	ENSP00000340329:p.Asp637Gly	105.0	0.0	.		97.0	45.0	.	NM_203364	A6NMY7|D3DR06|Q15074|Q6IMN4|Q6IMN7|Q9BV09	Missense_Mutation	SNP	ENST00000341394.4	hg19	CCDS31453.1	.	.	.	.	.	.	.	.	.	.	A	28.8	4.954141	0.92726	.	.	ENSG00000135387	ENST00000341394;ENST00000389645;ENST00000532820;ENST00000530820;ENST00000529307	T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54	6.17	6.17	0.99709	.	0.090003	0.85682	D	0.000000	T	0.56659	0.2000	M	0.74258	2.255	0.58432	D	0.999993	D;D	0.71674	0.998;0.996	D;D	0.71870	0.975;0.924	T	0.57087	-0.7871	10	0.51188	T	0.08	-10.4721	16.8222	0.85835	1.0:0.0:0.0:0.0	.	637;637	Q14444;Q14444-2	CAPR1_HUMAN;.	G	637;637;637;637;556	ENSP00000340329:D637G;ENSP00000374296:D637G;ENSP00000434150:D637G;ENSP00000434204:D637G;ENSP00000431581:D556G	ENSP00000340329:D637G	D	+	2	0	CAPRIN1	34075328	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.962000	0.93254	2.371000	0.80710	0.533000	0.62120	GAT	.	.	.	none		0.368	CAPRIN1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000388680.2	NM_005898		G	34118752	A	G	34118752	3	3	100	1	0	0	0	0	1	0	0	0	2637	333	12	3	1972	3	CAPRIN1	11	34118752	Missense_Mutation	SNP	A	TCGA-B9-5155-01A-01D-1589-08	7398687	34118752	100887764	64	6360											
FOLH1	2346	hgsc.bcm.edu	37	chr11	49175458	49175458	+	Frame_Shift_Del	DEL	T	T	-																															aagcaatttctgtaaaattcTttactgcagaaaaaagtgaa																										TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr11:49175458delT	ENST00000256999.2	-	17	2170	c.1910delA	c.(1909-1911)aagfs	p.K637fs	FOLH1_ENST00000340334.7_Frame_Shift_Del_p.K622fs|FOLH1_ENST00000356696.3_Frame_Shift_Del_p.K637fs|FOLH1_ENST00000533034.1_Frame_Shift_Del_p.K622fs|FOLH1_ENST00000343844.4_Frame_Shift_Del_p.K329fs	NM_004476.1	NP_004467.1	Q04609	FOLH1_HUMAN	folate hydrolase (prostate-specific membrane antigen) 1	637					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)	TGTAAAATTCTTTACTGCAGA	0.338																																					p.K637fs		Atlas-INDEL	.											.	FOLH1	141	.	0			c.1911delG						PASS	.						84	86	85					11																	49175458		2200	4296	6496	SO:0001589	frameshift_variant	2346	exon17			.	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.1910delA	chr11.hg19:g.49175458delT	ENSP00000256999:p.Lys637fs	95.0	0.0	0		108.0	44.0	0.407407	NM_004476	A4UU12|A9CB79|B7Z312|B7Z343|D3DQS5|E9PDX8|O43748|Q16305|Q541A4|Q8TAY3|Q9NP15|Q9NYE2|Q9P1P8	Frame_Shift_Del	DEL	ENST00000256999.2	hg19	CCDS7946.1																																																																																			.	.	.	none		0.338	FOLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390896.1	NM_004476		-	49175458	T	-	49175458	7	5	100	1	0	1	0	1	0	0	0	0	5986	1609	56	0	354	0	FOLH1	11	49175458	Frame_Shift_Del	DEL	T	TCGA-B9-5155-01A-01D-1589-08	15056706	49175458	85831058	65	6361											
C11orf82	220042	hgsc.bcm.edu	37	chr11	82642927	82642927	+	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	ctgtcattgactacttccatCaacttttgcagacttttaat	10	17	4	10	0	2	2	2	1	0	1	3	2	3	2	1	0	3	1	1	0	3	7			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr11:82642927C>A	ENST00000533655.1	+	6	759	c.547C>A	c.(547-549)Caa>Aaa	p.Q183K	C11orf82_ENST00000528759.1_3'UTR|C11orf82_ENST00000525361.1_Intron|C11orf82_ENST00000430323.2_Missense_Mutation_p.Q183K|C11orf82_ENST00000533750.1_3'UTR|C11orf82_ENST00000525388.1_3'UTR|C11orf82_ENST00000329143.3_5'UTR	NM_145018.3	NP_659455.3	Q8IXT1	DDIAS_HUMAN		183					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)		p.Q183E(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	33						CTACTTCCATCAACTTTTGCA	0.418																																					p.Q183K		Atlas-SNP	.											C11orf82,NS,carcinoma,0,1	C11orf82	71	.	1	Substitution - Missense(1)	lung(1)	c.C547A						PASS	.						177	179	178					11																	82642927		2203	4300	6503	SO:0001583	missense	220042	exon6			TTCCATCAACTTT																												ENST00000533655.1:c.547C>A	chr11.hg19:g.82642927C>A	ENSP00000435421:p.Gln183Lys	284.0	1.0	.		257.0	95.0	.	NM_145018	Q96LK6|Q9H856	Missense_Mutation	SNP	ENST00000533655.1	hg19	CCDS8263.1	.	.	.	.	.	.	.	.	.	.	C	6.456	0.452276	0.12283	.	.	ENSG00000165490	ENST00000430323;ENST00000533655	T;T	0.14640	2.49;2.49	5.45	5.45	0.79879	.	0.357786	0.25127	N	0.032927	T	0.16599	0.0399	L	0.56769	1.78	0.80722	D	1	P	0.39282	0.666	B	0.33339	0.162	T	0.03103	-1.1072	9	.	.	.	.	19.289	0.94090	0.0:1.0:0.0:0.0	.	183	Q8IXT1	NOXIN_HUMAN	K	183	ENSP00000414687:Q183K;ENSP00000435421:Q183K	.	Q	+	1	0	C11orf82	82320575	0.908000	0.30866	0.511000	0.27724	0.134000	0.20937	3.767000	0.55288	2.567000	0.86603	0.563000	0.77884	CAA	.	.	.	none		0.418	C11orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391936.1			A	82642927	C	A	82642927	3	1	100	1	0	0	0	0	1	0	0	0	1667	827	29	4	561	4	C11orf82	11	82642927	Missense_Mutation	SNP	C	TCGA-B9-5155-01A-01D-1589-08	33467469	82642927	52363589	66	6362											
MRE11A	4361	hgsc.bcm.edu	37	chr11	94224022	94224022	+	Missense_Mutation	SNP	A	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	attttcctgggcaagtcttaAaatttcatcgagtgttacaa	12	15	7	7	1	2	0	1	0	1	0	4	1	3	0	1	1	1	2	1	1	5	5			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr11:94224022A>C	ENST00000323929.3	-	3	352	c.130T>G	c.(130-132)Tta>Gta	p.L44V	MRE11A_ENST00000536144.1_5'UTR|MRE11A_ENST00000540013.1_Missense_Mutation_p.L44V|MRE11A_ENST00000393241.4_Missense_Mutation_p.L44V|ANKRD49_ENST00000544612.1_5'Flank|MRE11A_ENST00000323977.3_Missense_Mutation_p.L44V|MRE11A_ENST00000407439.3_Missense_Mutation_p.L47V	NM_005591.3	NP_005582.1	P49959	MRE11_HUMAN	MRE11 meiotic recombination 11 homolog A (S. cerevisiae)	44					base-excision repair (GO:0006284)|cell proliferation (GO:0008283)|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)|double-strand break repair via nonhomologous end joining (GO:0006303)|innate immune response (GO:0045087)|intra-S DNA damage checkpoint (GO:0031573)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of DNA endoreduplication (GO:0032876)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair (GO:0006289)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of type I interferon production (GO:0032481)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|sister chromatid cohesion (GO:0007062)|synapsis (GO:0007129)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromatin (GO:0000785)|cytosol (GO:0005829)|Mre11 complex (GO:0030870)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|manganese ion binding (GO:0030145)|nuclease activity (GO:0004518)|protein C-terminus binding (GO:0008022)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			breast(5)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	29		Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824)				GCAAGTCTTAAAATTTCATCG	0.333								Homologous recombination	Ataxia-Telangiectasia-Like Disorder																												p.L44V		Atlas-SNP	.											.	MRE11A	145	.	0			c.T130G						PASS	.						140	138	139					11																	94224022		2201	4298	6499	SO:0001583	missense	4361	exon3	Familial Cancer Database	ATLD	GTCTTAAAATTTC	BC063458	CCDS8298.1, CCDS8299.1	11q21	2014-09-17	2001-11-28		ENSG00000020922	ENSG00000020922			7230	protein-coding gene	gene with protein product	"AT-like disease"	600814	"meiotic recombination (S. cerevisiae) 11 homolog A"	MRE11		8530104	Standard	XM_005274007		Approved	ATLD	uc001peu.2	P49959	OTTHUMG00000167780	ENST00000323929.3:c.130T>G	chr11.hg19:g.94224022A>C	ENSP00000325863:p.Leu44Val	154.0	0.0	.		174.0	65.0	.	NM_005591	O43475	Missense_Mutation	SNP	ENST00000323929.3	hg19	CCDS8299.1	.	.	.	.	.	.	.	.	.	.	A	17.80	3.477531	0.63849	.	.	ENSG00000020922	ENST00000323929;ENST00000407439;ENST00000323977;ENST00000393241;ENST00000540013;ENST00000536754;ENST00000538923	D;D;D;D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66;-1.66;-1.66;-1.66	4.46	3.34	0.38264	Metallophosphoesterase domain (1);	0.075606	0.53938	D	0.000060	D	0.86674	0.5989	M	0.63843	1.955	0.54753	D	0.999985	D;D;D	0.58268	0.982;0.957;0.981	D;P;D	0.69654	0.965;0.904;0.925	D	0.85303	0.1074	10	0.46703	T	0.11	-6.346	7.1552	0.25632	0.7509:0.0:0.2491:0.0	.	47;44;44	B3KTC7;P49959-2;P49959	.;.;MRE11_HUMAN	V	44;47;44;44;44;44;44	ENSP00000325863:L44V;ENSP00000385614:L47V;ENSP00000326094:L44V;ENSP00000376933:L44V;ENSP00000440986:L44V;ENSP00000439511:L44V;ENSP00000442809:L44V	ENSP00000325863:L44V	L	-	1	2	MRE11A	93863670	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	3.003000	0.49505	1.651000	0.50673	0.379000	0.24179	TTA	.	.	.	none		0.333	MRE11A-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396237.3	NM_005591		C	94224022	A	C	94224022	3	2	100	1	0	0	0	0	1	0	0	0	9766	11	1	5	2068	5	MRE11A	11	94224022	Missense_Mutation	SNP	A	TCGA-B9-5155-01A-01D-1589-08	11581095	94224022	40782494	67	6363											
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103124155	103124155	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgaggttaactttactacaaCaagaagtggattacgagggc	14	10	11	6	1	0	2	0	1	0	1	0	4	0	3	0	3	5	1	0	3	7	5			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr11:103124155C>T	ENST00000375735.2	+	66	10328	c.10184C>T	c.(10183-10185)aCa>aTa	p.T3395I	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.T3402I	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3395	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)		TTTACTACAACAAGAAGTGGA	0.363																																					p.T3402I		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.C10205T						PASS	.						103	98	100					11																	103124155		1815	4086	5901	SO:0001583	missense	79659	exon67			CTACAACAAGAAG	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.10184C>T	chr11.hg19:g.103124155C>T	ENSP00000364887:p.Thr3395Ile	95.0	0.0	.		116.0	35.0	.	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	C	28.7	4.945803	0.92593	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.29142	1.58;1.58	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.72771	0.3502	H	0.97611	4.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.995;0.996	T	0.82168	-0.0591	10	0.87932	D	0	.	20.3334	0.98727	0.0:1.0:0.0:0.0	.	3395;3402	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	I	3395;3402	ENSP00000364887:T3395I;ENSP00000381167:T3402I	ENSP00000364887:T3395I	T	+	2	0	DYNC2H1	102629365	1.000000	0.71417	0.990000	0.47175	0.992000	0.81027	6.057000	0.71119	2.818000	0.97014	0.591000	0.81541	ACA	.	.	.	none		0.363	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		T	103124155	C	T	103124155	3	4	100	1	0	0	0	0	1	0	0	0	4848	478	17	2	10471	2	DYNC2H1	11	103124155	Missense_Mutation	SNP	C	TCGA-B9-5155-01A-01D-1589-08	8900133	103124155	31882361	68	6364											
IL10RA	3587	hgsc.bcm.edu	37	chr11	117869597	117869597	+	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	ggctttggcagcaccaagccAtccctgcagactgaagagcc	10	6	11	14	0	0	3	0	1	0	2	1	3	1	3	4	2	4	4	4	2	2	1			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr11:117869597A>T	ENST00000227752.3	+	7	1098	c.978A>T	c.(976-978)ccA>ccT	p.P326P	IL10RA_ENST00000541785.1_Silent_p.P306P|IL10RA_ENST00000533700.1_3'UTR|IL10RA_ENST00000545409.1_Silent_p.P177P	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	326					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)		GCACCAAGCCATCCCTGCAGA	0.612																																					p.P326P		Atlas-SNP	.											.	IL10RA	46	.	0			c.A978T						PASS	.						89	75	80					11																	117869597		2200	4296	6496	SO:0001819	synonymous_variant	3587	exon7			CAAGCCATCCCTG	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.978A>T	chr11.hg19:g.117869597A>T		96.0	0.0	.		86.0	31.0	.	NM_001558	A8K6I0|B0YJ27	Silent	SNP	ENST00000227752.3	hg19	CCDS8388.1																																																																																			.	.	.	none		0.612	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1			T	117869597	A	T	117869597	2	4	100	1	0	0	0	0	0	0	0	1	7627	204	8	5		5	IL10RA	11	117869597	Silent	SNP	A	TCGA-B9-5155-01A-01D-1589-08	14745442	117869597	17136919	69	6365											
HSPA8	3312	hgsc.bcm.edu	37	chr11	122930940	122930940	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgacgctgagagtcattaaAgtaagctggcactgtgacca	12	9	11	9	1	1	3	1	3	0	1	1	4	1	3	1	1	1	4	1	1	3	2			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr11:122930940A>G	ENST00000532636.1	-	4	567	c.448T>C	c.(448-450)Ttt>Ctt	p.F150L	HSPA8_ENST00000227378.3_Missense_Mutation_p.F150L|HSPA8_ENST00000526110.1_Intron|SNORD14C_ENST00000365382.1_RNA|HSPA8_ENST00000534319.1_5'UTR|SNORD14D_ENST00000384390.1_RNA|HSPA8_ENST00000453788.2_Missense_Mutation_p.F150L|HSPA8_ENST00000526862.1_5'Flank|HSPA8_ENST00000533540.1_Intron|SNORD14E_ENST00000364009.1_RNA|HSPA8_ENST00000534624.1_Missense_Mutation_p.F150L			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	150					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)		GAGTCATTAAAGTAAGCTGGC	0.403																																					p.F150L	Colon(21;486 594 5900 6733 14272)	Atlas-SNP	.											.	HSPA8	168	.	0			c.T448C						PASS	.						71	68	69					11																	122930940		2202	4299	6501	SO:0001583	missense	3312	exon4			CATTAAAGTAAGC	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.448T>C	chr11.hg19:g.122930940A>G	ENSP00000437125:p.Phe150Leu	109.0	0.0	.		109.0	47.0	.	NM_006597	Q9H3R6	Missense_Mutation	SNP	ENST00000532636.1	hg19	CCDS8440.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.939342	0.73557	.	.	ENSG00000109971	ENST00000532636;ENST00000534624;ENST00000453788;ENST00000227378;ENST00000528292;ENST00000525463;ENST00000525624;ENST00000534567;ENST00000527387;ENST00000532182	T;T;T;T;T;T;T;T;T;T	0.01947	4.54;4.54;4.54;4.54;4.54;4.54;4.54;4.54;4.54;4.54	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.13884	0.0336	H	0.99783	4.775	0.80722	D	1	B;B;P;P;B	0.35923	0.014;0.106;0.528;0.472;0.106	B;B;B;B;B	0.35413	0.06;0.202;0.128;0.078;0.202	T	0.21348	-1.0248	10	0.72032	D	0.01	-23.667	14.7286	0.69362	1.0:0.0:0.0:0.0	.	150;150;150;150;150	B4DTX2;Q53GZ6;E7ET08;P11142-2;P11142	.;.;.;.;HSP7C_HUMAN	L	150;150;150;150;90;109;150;150;150;150	ENSP00000437125:F150L;ENSP00000432083:F150L;ENSP00000404372:F150L;ENSP00000227378:F150L;ENSP00000432884:F90L;ENSP00000436762:F109L;ENSP00000435154:F150L;ENSP00000431641:F150L;ENSP00000436183:F150L;ENSP00000434415:F150L	ENSP00000227378:F150L	F	-	1	0	HSPA8	122436150	1.000000	0.71417	0.668000	0.29813	0.342000	0.28953	9.203000	0.95033	1.919000	0.55581	0.459000	0.35465	TTT	.	.	.	none		0.403	HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1			G	122930940	A	G	122930940	3	3	100	1	0	0	0	0	1	0	0	0	7423	72	3	3	1516	3	HSPA8	11	122930940	Missense_Mutation	SNP	A	TCGA-B9-5155-01A-01D-1589-08	5061343	122930940	12075576	70	6366											
ERC1	23085	hgsc.bcm.edu	37	chr12	1219488	1219488	+	Missense_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	gcaaatggaagtgtatcggaGccattctaaatttatgaaaa	16	11	9	5	1	1	1	0	1	1	0	2	3	1	3	1	2	1	2	1	2	8	5			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr12:1219488G>A	ENST00000397203.2	+	5	1698	c.1292G>A	c.(1291-1293)aGc>aAc	p.S431N	ERC1_ENST00000355446.5_Missense_Mutation_p.S431N|ERC1_ENST00000546231.2_Missense_Mutation_p.S431N|ERC1_ENST00000589028.1_Missense_Mutation_p.S431N|ERC1_ENST00000536573.2_3'UTR|ERC1_ENST00000543086.3_Missense_Mutation_p.S431N|ERC1_ENST00000360905.4_Missense_Mutation_p.S431N			Q8IUD2	RB6I2_HUMAN	ELKS/RAB6-interacting/CAST family member 1	431					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)			GTGTATCGGAGCCATTCTAAA	0.353																																					p.S431N		Atlas-SNP	.											.	ERC1	95	.	0			c.G1292A						PASS	.						102	105	104					12																	1219488		2203	4300	6503	SO:0001583	missense	23085	exon5			ATCGGAGCCATTC	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.1292G>A	chr12.hg19:g.1219488G>A	ENSP00000380386:p.Ser431Asn	71.0	0.0	.		110.0	50.0	.	NM_178039	A2RU77|A7E295|D3DUP7|D3DUP8|Q6NVK2|Q8IUD3|Q8IUD4|Q8IUD5|Q8NAS1|Q9NXN5|Q9UIK7|Q9UPS1	Missense_Mutation	SNP	ENST00000397203.2	hg19	CCDS8508.1	.	.	.	.	.	.	.	.	.	.	G	15.77	2.931718	0.52866	.	.	ENSG00000082805	ENST00000347735;ENST00000397203;ENST00000454194;ENST00000537890;ENST00000543086;ENST00000542302;ENST00000546231;ENST00000355446;ENST00000360905;ENST00000440394;ENST00000538971;ENST00000536573	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	5.93	5.93	0.95920	.	0.037884	0.85682	D	0.000000	T	0.43545	0.1252	L	0.28400	0.85	0.52099	D	0.999949	B;B;B;B;B	0.24721	0.016;0.032;0.027;0.035;0.11	B;B;B;B;B	0.33392	0.017;0.073;0.018;0.025;0.163	T	0.18935	-1.0321	10	0.20046	T	0.44	-11.7406	20.3938	0.98981	0.0:0.0:1.0:0.0	.	207;68;431;431;431	F5H327;F5GZU8;Q8IUD2-2;Q8IUD2-3;Q8IUD2	.;.;.;.;RB6I2_HUMAN	N	431;431;431;431;431;431;431;431;431;431;207;68	ENSP00000340054:S431N;ENSP00000380386:S431N;ENSP00000438546:S431N;ENSP00000445336:S431N;ENSP00000442739:S431N;ENSP00000347621:S431N;ENSP00000354158:S431N;ENSP00000410064:S431N	ENSP00000340054:S431N	S	+	2	0	ERC1	1089749	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.536000	0.60636	2.831000	0.97527	0.585000	0.79938	AGC	.	.	.	none		0.353	ERC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398380.2	NM_015064		A	1219488	G	A	1219488	3	1	100	1	0	0	0	0	1	0	0	0	5212	971	34	2	1306	2	ERC1	12	1219488	Missense_Mutation	SNP	G	TCGA-B9-5155-01A-01D-1589-08		1219488	132632407	71	6367											
CASC1	55259	hgsc.bcm.edu	37	chr12	25308273	25308273	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaatttagtttcctgtttcAatttctctgcttcaggaaaa	10	17	6	8	0	3	0	2	0	1	0	5	1	4	1	1	1	1	4	1	1	5	6			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr12:25308273A>G	ENST00000320267.9	-	4	335	c.254T>C	c.(253-255)tTg>tCg	p.L85S	CASC1_ENST00000545133.1_Missense_Mutation_p.L26S|CASC1_ENST00000354189.5_Missense_Mutation_p.L149S|CASC1_ENST00000395990.2_Missense_Mutation_p.L45S|CASC1_ENST00000557684.1_5'UTR|CASC1_ENST00000537577.1_5'UTR|CASC1_ENST00000395987.3_Missense_Mutation_p.L91S	NM_001082973.1	NP_001076442	Q6TDU7	CASC1_HUMAN	cancer susceptibility candidate 1	85	Glu-rich.									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)			TTCCTGTTTCAATTTCTCTGC	0.368																																					p.L149S		Atlas-SNP	.											.	CASC1	146	.	0			c.T446C						PASS	.						109	110	109					12																	25308273		2203	4296	6499	SO:0001583	missense	55259	exon5			TGTTTCAATTTCT	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.254T>C	chr12.hg19:g.25308273A>G	ENSP00000313141:p.Leu85Ser	71.0	0.0	.		78.0	31.0	.	NM_001082972	B4DNP2|F5H6T6|Q17RL2|Q4G171|Q5U5K5|Q9NV50	Missense_Mutation	SNP	ENST00000320267.9	hg19	CCDS41762.1	.	.	.	.	.	.	.	.	.	.	A	12.00	1.805347	0.31961	.	.	ENSG00000118307	ENST00000354189;ENST00000395987;ENST00000320267;ENST00000395990;ENST00000395992;ENST00000545133;ENST00000389246;ENST00000554347	T;T;T;T;T;T	0.26518	1.73;2.24;2.24;2.24;2.24;2.24	5.23	2.62	0.31277	.	0.255560	0.34223	N	0.004152	T	0.15912	0.0383	L	0.40543	1.245	0.80722	D	1	B;P;P;P	0.43352	0.418;0.804;0.483;0.763	B;B;B;B	0.38225	0.121;0.268;0.084;0.173	T	0.05068	-1.0908	10	0.25751	T	0.34	-7.1998	4.8547	0.13554	0.5806:0.2448:0.0:0.1745	.	26;149;85;91	F5H6T6;Q6TDU7-3;Q6TDU7;F8W8F9	.;.;CASC1_HUMAN;.	S	149;91;85;45;91;26;45;45	ENSP00000346126:L149S;ENSP00000379310:L91S;ENSP00000313141:L85S;ENSP00000379313:L45S;ENSP00000437373:L26S;ENSP00000451232:L45S	ENSP00000313141:L85S	L	-	2	0	CASC1	25199540	1.000000	0.71417	0.706000	0.30403	0.919000	0.55068	2.273000	0.43381	0.896000	0.36366	0.523000	0.50628	TTG	.	.	.	none		0.368	CASC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316761.1	NM_018272		G	25308273	A	G	25308273	3	3	100	1	0	0	0	0	1	0	0	0	2662	131	5	3	1944	3	CASC1	12	25308273	Missense_Mutation	SNP	A	TCGA-B9-5155-01A-01D-1589-08	24088785	25308273	108543622	72	6368											
DIP2B	57609	hgsc.bcm.edu	37	chr12	51138542	51138542	+	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	tcatcccgatcaactccagaGgagagaagcagaggatgcac	14	5	11	11	1	2	3	2	0	0	3	4	7	4	5	2	2	3	2	2	2	2	0			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr12:51138542G>T	ENST00000301180.5	+	38	4685	c.4651G>T	c.(4651-4653)Gga>Tga	p.G1551*	Y_RNA_ENST00000363558.1_RNA	NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	1551						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						CAACTCCAGAGGAGAGAAGCA	0.537																																					p.G1551X		Atlas-SNP	.											.	DIP2B	167	.	0			c.G4651T						PASS	.						138	112	121					12																	51138542		2203	4300	6503	SO:0001587	stop_gained	57609	exon38			TCCAGAGGAGAGA	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.4651G>T	chr12.hg19:g.51138542G>T	ENSP00000301180:p.Gly1551*	58.0	0.0	.		89.0	50.0	.	NM_173602	Q6B011|Q8N1L5|Q8NB38	Nonsense_Mutation	SNP	ENST00000301180.5	hg19	CCDS31799.1	.	.	.	.	.	.	.	.	.	.	G	42	9.552953	0.99202	.	.	ENSG00000066084	ENST00000301180	.	.	.	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-14.1606	19.7069	0.96076	0.0:0.0:1.0:0.0	.	.	.	.	X	1551	.	ENSP00000301180:G1551X	G	+	1	0	DIP2B	49424809	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.601000	0.98297	2.894000	0.99253	0.591000	0.81541	GGA	.	.	.	none		0.537	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602		T	51138542	G	T	51138542	4	4	100	1	0	0	0	0	0	1	0	0	4530	1001	35	4	4801	4	DIP2B	12	51138542	Nonsense_Mutation	SNP	G	TCGA-B9-5155-01A-01D-1589-08	25830269	51138542	82713353	73	6369											
PARP4	143	hgsc.bcm.edu	37	chr13	25009395	25009395	+	Frame_Shift_Del	DEL	G	G	-																															atagtggttcagttgctgttGgtttacatgactctgtccaa																								rs551694088		TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr13:25009395delG	ENST00000381989.3	-	31	3989	c.3884delC	c.(3883-3885)ccafs	p.P1295fs		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1295					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)		AGTTGCTGTTGGTTTACATGA	0.428																																					p.P1295fs		Atlas-INDEL	.											.	PARP4	142	.	0			c.3885delA						PASS	.						100	104	103					13																	25009395		2203	4300	6503	SO:0001589	frameshift_variant	143	exon31			.	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.3884delC	chr13.hg19:g.25009395delG	ENSP00000371419:p.Pro1295fs	137.0	0.0	0		129.0	54.0	0.418605	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Frame_Shift_Del	DEL	ENST00000381989.3	hg19	CCDS9307.1																																																																																			.	.	.	none		0.428	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437		-	25009395	G	-	25009395	7	5	100	1	0	1	0	1	0	0	0	0	11470	1348	47	0	1306	0	PARP4	13	25009395	Frame_Shift_Del	DEL	G	TCGA-B9-5155-01A-01D-1589-08		25009395	90160483	74	6370											
LRCH1	23143	hgsc.bcm.edu	37	chr13	47269134	47269134	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agagcagatggtctccattcGgaatttatgaactataaggc	13	11	10	7	1	1	3	0	1	1	2	3	4	1	4	1	3	2	1	1	3	5	5	rs201892262		TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr13:47269134G>A	ENST00000389798.3	+	9	1424	c.1227G>A	c.(1225-1227)tcG>tcA	p.S409S	LRCH1_ENST00000311191.6_Silent_p.S409S|LRCH1_ENST00000389797.3_Silent_p.S409S	NM_015116.2	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 1	409										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)		GTCTCCATTCGGAATTTATGA	0.403																																					p.S409S		Atlas-SNP	.											.	LRCH1	104	.	0			c.G1227A						PASS	.	G	,,	0,4406		0,0,2203	153	161	158		1227,1227,1227	-10.2	0	13		158	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	LRCH1	NM_001164211.1,NM_001164213.1,NM_015116.2	,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,	409/764,409/697,409/729	47269134	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23143	exon9			CCATTCGGAATTT	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.1227G>A	chr13.hg19:g.47269134G>A		211.0	0.0	.		177.0	86.0	.	NM_015116	B7ZLL5|F8W6F0|Q17R43|Q2KHR1|Q5TBU9|Q7Z5F6|Q7Z5F7	Silent	SNP	ENST00000389798.3	hg19	CCDS31972.1																																																																																			.	G|0.999;A|0.001	0.001	weak		0.403	LRCH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044824.2	NM_015116		A	47269134	G	A	47269134	2	1	100	1	0	0	0	0	0	0	0	1	8939	1103	39	1		1	LRCH1	13	47269134	Silent	SNP	G	TCGA-B9-5155-01A-01D-1589-08	22259739	47269134	67900744	75	6371											
COCH	1690	hgsc.bcm.edu	37	chr14	31348144	31348144	+	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	gatggtctgcttctttcacaGtaactagtaggtataattat	11	16	8	6	0	3	0	1	0	2	0	3	1	3	0	0	2	2	4	0	2	6	8			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr14:31348144G>T	ENST00000396618.3	+	5	423	c.367G>T	c.(367-369)Gta>Tta	p.V123L	COCH_ENST00000216361.4_Missense_Mutation_p.V123L|COCH_ENST00000460581.2_Missense_Mutation_p.V11L|RP11-829H16.3_ENST00000555108.1_RNA|COCH_ENST00000475087.1_Missense_Mutation_p.V123L|COCH_ENST00000382493.4_5'Flank	NM_004086.2	NP_004077.1	O43405	COCH_HUMAN	cochlin	123					defense response to bacterium (GO:0042742)|positive regulation of innate immune response (GO:0045089)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|pancreas(1)|skin(3)	19	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.00645)		TTCTTTCACAGTAACTAGTAG	0.403																																					p.V123L		Atlas-SNP	.											.	COCH	54	.	0			c.G367T						PASS	.						153	144	147					14																	31348144		2203	4300	6503	SO:0001583	missense	1690	exon5			TTCACAGTAACTA		CCDS9640.1	14q11.2-q13	2013-05-01	2013-05-01		ENSG00000100473	ENSG00000100473			2180	protein-coding gene	gene with protein product		603196	"coagulation factor C (Limulus polyphemus homolog); cochlin", "coagulation factor C homolog, cochlin (Limulus polyphemus)"	DFNA31, DFNA9		9806553	Standard	NM_004086		Approved	COCH-5B2	uc001wqp.2	O43405	OTTHUMG00000029432	ENST00000396618.3:c.367G>T	chr14.hg19:g.31348144G>T	ENSP00000379862:p.Val123Leu	171.0	0.0	.		171.0	77.0	.	NM_004086	A8K9K9|D3DS84|Q96IU6	Missense_Mutation	SNP	ENST00000396618.3	hg19	CCDS9640.1	.	.	.	.	.	.	.	.	.	.	G	15.49	2.849750	0.51270	.	.	ENSG00000100473	ENST00000216361;ENST00000396618;ENST00000475087;ENST00000556908;ENST00000460581;ENST00000542225	D;D;D;D;T	0.88818	-2.43;-2.43;-2.43;-2.43;-0.19	5.87	4.97	0.65823	LCCL (2);	0.117297	0.56097	D	0.000021	T	0.81861	0.4912	L	0.27053	0.805	0.80722	D	1	B;B	0.12013	0.005;0.005	B;B	0.10450	0.005;0.005	T	0.76735	-0.2850	10	0.42905	T	0.14	-12.1146	12.3896	0.55350	0.0779:0.0:0.9221:0.0	.	123;123	Q96IU6;O43405	.;COCH_HUMAN	L	123;123;123;107;11;11	ENSP00000216361:V123L;ENSP00000379862:V123L;ENSP00000451528:V123L;ENSP00000452541:V107L;ENSP00000451713:V11L	ENSP00000216361:V123L	V	+	1	0	COCH	30417895	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.223000	0.51231	2.785000	0.95823	0.655000	0.94253	GTA	.	.	.	none		0.403	COCH-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276608.1	NM_004086		T	31348144	G	T	31348144	3	4	100	1	0	0	0	0	1	0	0	0	3658	1029	36	4	381	4	COCH	14	31348144	Missense_Mutation	SNP	G	TCGA-B9-5155-01A-01D-1589-08		31348144	76001396	76	6372											
C14orf105	55195	hgsc.bcm.edu	37	chr14	57938247	57938247	+	Missense_Mutation	SNP	T	T	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	catgtttccattttgccaatTttccagggacagtagttatt	9	17	7	8	0	0	0	0	0	0	0	2	1	2	1	3	1	1	3	3	1	3	8			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr14:57938247T>G	ENST00000216445.3	-	6	853	c.717A>C	c.(715-717)aaA>aaC	p.K239N	C14orf105_ENST00000422976.2_Missense_Mutation_p.K279N|C14orf105_ENST00000534126.1_Missense_Mutation_p.K238N	NM_001283057.1|NM_018168.2	NP_001269986.1|NP_060638.2	Q9NVL8	CN105_HUMAN	chromosome 14 open reading frame 105	239										breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)	11						TTTTGCCAATTTTCCAGGGAC	0.393																																					p.K239N		Atlas-SNP	.											.	C14orf105	26	.	0			c.A717C						PASS	.						80	70	74					14																	57938247		2203	4300	6503	SO:0001583	missense	55195	exon6			GCCAATTTTCCAG	AK001512	CCDS9730.1, CCDS61458.1, CCDS61459.1	14q22.2	2012-09-25			ENSG00000100557	ENSG00000100557			20189	protein-coding gene	gene with protein product							Standard	XM_005267806		Approved	FLJ10650	uc001xcy.2	Q9NVL8	OTTHUMG00000140317	ENST00000216445.3:c.717A>C	chr14.hg19:g.57938247T>G	ENSP00000216445:p.Lys239Asn	60.0	0.0	.		54.0	27.0	.	NM_018168	Q53G04	Missense_Mutation	SNP	ENST00000216445.3	hg19	CCDS9730.1	.	.	.	.	.	.	.	.	.	.	T	15.71	2.914840	0.52546	.	.	ENSG00000100557	ENST00000216445;ENST00000422976;ENST00000534126	T;T;T	0.52057	0.68;0.68;0.68	5.29	2.57	0.30868	.	0.316033	0.28453	N	0.015295	T	0.48978	0.1530	M	0.63428	1.95	0.09310	N	0.999998	P;P;P;P	0.51351	0.703;0.703;0.944;0.944	B;B;P;P	0.52957	0.136;0.136;0.714;0.714	T	0.34825	-0.9813	10	0.40728	T	0.16	-18.2156	3.672	0.08277	0.0:0.1387:0.2192:0.6421	.	279;279;238;239	B7ZL43;F5GWJ3;E9PSE9;Q9NVL8	.;.;.;CN105_HUMAN	N	239;279;238	ENSP00000216445:K239N;ENSP00000392368:K279N;ENSP00000434003:K238N	ENSP00000216445:K239N	K	-	3	2	C14orf105	57008000	0.946000	0.32159	0.071000	0.20095	0.052000	0.14988	0.795000	0.26972	0.916000	0.36871	0.528000	0.53228	AAA	.	.	.	none		0.393	C14orf105-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276921.2	NM_018168		G	57938247	T	G	57938247	3	3	100	1	0	0	0	0	1	0	0	0	1739	1838	64	5	177	5	C14orf105	14	57938247	Missense_Mutation	SNP	T	TCGA-B9-5155-01A-01D-1589-08	26590103	57938247	49411293	77	6373											
DPF3	8110	hgsc.bcm.edu	37	chr14	73137911	73137911	+	Intron	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	ggcgtcctcgacaggagcgaGgctcttccaaatcgtcctca	8	8	11	14	4	2	0	1	0	1	0	7	3	5	1	3	3	1	1	3	3	1	1			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr14:73137911G>C	ENST00000556509.1	-	8	871				DPF3_ENST00000546183.1_Missense_Mutation_p.P346R|DPF3_ENST00000557704.1_5'UTR|DPF3_ENST00000541685.1_Missense_Mutation_p.P336R	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)		ACAGGAGCGAGGCTCTTCCAA	0.572																																					p.P336R		Atlas-SNP	.											.	DPF3	117	.	0			c.C1007G						PASS	.						68	73	71					14																	73137911		2163	4247	6410	SO:0001627	intron_variant	8110	exon9			GAGCGAGGCTCTT	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+3036C>G	chr14.hg19:g.73137911G>C		43.0	0.0	.		64.0	19.0	.	NM_012074	A8MSI3|B7Z276|F5H575|Q32UJ0|Q6P9E6|Q6ZT41|Q9H7Y5	Missense_Mutation	SNP	ENST00000556509.1	hg19		.	.	.	.	.	.	.	.	.	.	G	18.64	3.667377	0.67814	.	.	ENSG00000205683	ENST00000541685;ENST00000546183	T;T	0.69926	-0.41;-0.44	5.79	5.79	0.91817	.	.	.	.	.	T	0.60130	0.2245	N	0.19112	0.55	0.32437	N	0.547203	P;P	0.43701	0.815;0.815	B;B	0.42522	0.39;0.39	T	0.69910	-0.5017	9	0.87932	D	0	.	20.04	0.97581	0.0:0.0:1.0:0.0	.	346;336	F5H575;Q92784-2	.;.	R	336;346	ENSP00000441640:P336R;ENSP00000444662:P346R	ENSP00000381791:P391R	P	-	2	0	DPF3	72207664	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.568000	0.60857	2.733000	0.93635	0.655000	0.94253	CCT	.	.	.	none		0.572	DPF3-004	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000413152.2			C	73137911	G	C	73137911	1	2	100	0	1	0	0	0	0	0	0	0	4720	1000	35	4		4	DPF3	14	73137911	Intron	SNP	G	TCGA-B9-5155-01A-01D-1589-08	15199664	73137911	34211629	78	6374											
SERPINA3	12	hgsc.bcm.edu	37	chr14	95081284	95081284	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccgaggcctttgccactgActttcaggactcagctgcag	7	10	10	14	1	2	1	2	1	0	0	3	3	3	2	3	2	3	2	3	2	0	2			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr14:95081284A>G	ENST00000467132.1	+	2	1654	c.506A>G	c.(505-507)gAc>gGc	p.D169G	RP11-986E7.7_ENST00000553947.1_3'UTR|SERPINA3_ENST00000482740.1_5'Flank|SERPINA3_ENST00000393080.4_Missense_Mutation_p.D169G|SERPINA3_ENST00000393078.3_Missense_Mutation_p.D169G			P01011	AACT_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3	169					acute-phase response (GO:0006953)|inflammatory response (GO:0006954)|maintenance of gastrointestinal epithelium (GO:0030277)|negative regulation of endopeptidase activity (GO:0010951)|regulation of lipid metabolic process (GO:0019216)|regulation of proteolysis (GO:0030162)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	DNA binding (GO:0003677)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(17)|ovary(2)|pancreas(1)|skin(3)|stomach(1)	40		all_cancers(154;0.0525)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.212)|Epithelial(152;0.228)		TTTGCCACTGACTTTCAGGAC	0.502																																					p.D169G		Atlas-SNP	.											.	SERPINA3	78	.	0			c.A506G						PASS	.						92	86	88					14																	95081284		2203	4300	6503	SO:0001583	missense	12	exon2			CCACTGACTTTCA	K01500	CCDS32150.1	14q32.1	2014-06-03	2005-08-18		ENSG00000196136	ENSG00000196136		"Serine (or cysteine) peptidase inhibitors"	16	protein-coding gene	gene with protein product		107280	"alpha-1-antichymotrypsin", "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3"	AACT		3260956, 24172014	Standard	NM_001085		Approved	ACT, alpha-1-antichymotrypsin	uc001ydp.3	P01011	OTTHUMG00000029851	ENST00000467132.1:c.506A>G	chr14.hg19:g.95081284A>G	ENSP00000450540:p.Asp169Gly	61.0	0.0	.		79.0	39.0	.	NM_001085	B3KVQ7|Q13703|Q2TU87|Q2TU88|Q59GP9|Q6LBY8|Q6LDT7|Q6NSC9|Q8N177|Q96DW8|Q9UC47|Q9UNU9	Missense_Mutation	SNP	ENST00000467132.1	hg19	CCDS32150.1	.	.	.	.	.	.	.	.	.	.	A	16.28	3.077587	0.55753	.	.	ENSG00000196136	ENST00000553947;ENST00000393078;ENST00000393080;ENST00000555820;ENST00000467132	D;D;D;D	0.88975	-2.45;-2.45;-2.45;-2.45	5.13	5.13	0.70059	Serpin domain (3);	0.523027	0.19106	N	0.122568	D	0.94568	0.8250	M	0.89287	3.02	0.45676	D	0.99859	D;D	0.63880	0.984;0.993	P;P	0.62089	0.896;0.898	D	0.95248	0.8357	10	0.72032	D	0.01	.	14.4161	0.67151	1.0:0.0:0.0:0.0	.	169;194	P01011;G3V5I3	AACT_HUMAN;.	G	194;169;169;169;169	ENSP00000452367:D194G;ENSP00000376793:D169G;ENSP00000376795:D169G;ENSP00000450540:D169G	ENSP00000376793:D169G	D	+	2	0	SERPINA3	94151037	0.969000	0.33509	0.201000	0.23476	0.040000	0.13550	3.607000	0.54102	2.046000	0.60703	0.459000	0.35465	GAC	.	.	.	none		0.502	SERPINA3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268080.3	NM_001085		G	95081284	A	G	95081284	3	3	100	1	0	0	0	0	1	0	0	0	14103	275	10	3	508	3	SERPINA3	14	95081284	Missense_Mutation	SNP	A	TCGA-B9-5155-01A-01D-1589-08	21943373	95081284	12268256	79	6375											
JAG2	3714	hgsc.bcm.edu	37	chr14	105621904	105621904	+	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	cggcggcacactcacctgcaCtccccaggcacggtgcatcc	7	5	10	19	3	1	0	1	0	0	0	3	0	3	0	4	4	2	4	4	4	0	0			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr14:105621904C>T	ENST00000331782.3	-	5	1186	c.783G>A	c.(781-783)gaG>gaA	p.E261E	RP11-44N21.4_ENST00000548203.1_RNA|JAG2_ENST00000347004.2_Silent_p.E261E	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	261	EGF-like 1. {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)		CTCACCTGCACTCCCCAGGCA	0.632																																					p.E261E		Atlas-SNP	.											.	JAG2	69	.	0			c.G783A						PASS	.						99	103	101					14																	105621904		2203	4300	6503	SO:0001819	synonymous_variant	3714	exon5			CCTGCACTCCCCA	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.783G>A	chr14.hg19:g.105621904C>T		123.0	0.0	.		155.0	78.0	.	NM_145159	Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Silent	SNP	ENST00000331782.3	hg19	CCDS9998.1																																																																																			.	.	.	none		0.632	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2			T	105621904	C	T	105621904	2	4	100	1	0	0	0	0	0	0	0	1	7942	564	20	2		2	JAG2	14	105621904	Silent	SNP	C	TCGA-B9-5155-01A-01D-1589-08	10540620	105621904	1727636	80	6376											
RAB8B	51762	hgsc.bcm.edu	37	chr15	63548782	63548782	+	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	aaagacaagtgtcaaaagaaAgaggggagaaggtaaatgtg	20	5	14	2	0	1	4	1	0	0	4	1	5	1	4	0	3	0	1	0	3	8	1	rs202115341		TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr15:63548782A>T	ENST00000321437.4	+	5	559	c.403A>T	c.(403-405)Aga>Tga	p.R135*	RAB8B_ENST00000448330.2_Nonsense_Mutation_p.R135*	NM_016530.2	NP_057614.1	Q92930	RAB8B_HUMAN	RAB8B, member RAS oncogene family	135					adherens junction organization (GO:0034332)|antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|positive regulation of cell projection organization (GO:0031346)|positive regulation of corticotropin secretion (GO:0051461)|protein import into peroxisome membrane (GO:0045046)|small GTPase mediated signal transduction (GO:0007264)	cell tip (GO:0051286)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|receptor binding (GO:0005102)			kidney(3)|large_intestine(2)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	9						GTCAAAAGAAAGAGGGGAGAA	0.343																																					p.R135X		Atlas-SNP	.											.	RAB8B	23	.	0			c.A403T						PASS	.						100	95	97					15																	63548782		2203	4300	6503	SO:0001587	stop_gained	51762	exon5			AAAGAAAGAGGGG	AL833365	CCDS10183.1	15q22	2008-11-18			ENSG00000166128	ENSG00000166128		"RAB, member RAS oncogene"	30273	protein-coding gene	gene with protein product		613532				9030196, 18772196	Standard	XM_006720569		Approved		uc002alz.3	Q92930	OTTHUMG00000132862	ENST00000321437.4:c.403A>T	chr15.hg19:g.63548782A>T	ENSP00000312734:p.Arg135*	86.0	0.0	.		84.0	42.0	.	NM_016530	Q5JPC4|Q9P293	Nonsense_Mutation	SNP	ENST00000321437.4	hg19	CCDS10183.1	.	.	.	.	.	.	.	.	.	.	A	20.5	3.996156	0.74703	.	.	ENSG00000166128	ENST00000321437;ENST00000448330	.	.	.	5.61	5.61	0.85477	.	0.079005	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09843	T	0.71	.	14.9901	0.71381	1.0:0.0:0.0:0.0	.	.	.	.	X	135	.	ENSP00000312734:R135X	R	+	1	2	RAB8B	61335835	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.066000	0.71185	2.131000	0.65755	0.533000	0.62120	AGA	.	A|1.000;G|0.000	.	alt		0.343	RAB8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256336.1	NM_016530		T	63548782	A	T	63548782	4	4	100	1	0	0	0	0	0	1	0	0	12970	64	3	5	421	5	RAB8B	15	63548782	Nonsense_Mutation	SNP	A	TCGA-B9-5155-01A-01D-1589-08		63548782	38982610	81	6377											
HERC1	8925	hgsc.bcm.edu	37	chr15	63953965	63953965	+	Missense_Mutation	SNP	T	T	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	aaggtacctttcagaacttgTtgacttagatttggtcttca	10	16	8	7	0	3	3	2	1	1	2	3	3	3	3	1	2	2	2	1	2	4	7			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr15:63953965T>G	ENST00000443617.2	-	45	9244	c.9157A>C	c.(9157-9159)Aca>Cca	p.T3053P		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	3053					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						TCAGAACTTGTTGACTTAGAT	0.448																																					p.T3053P		Atlas-SNP	.											.	HERC1	624	.	0			c.A9157C						PASS	.						158	146	150					15																	63953965		1961	4150	6111	SO:0001583	missense	8925	exon45			AACTTGTTGACTT	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.9157A>C	chr15.hg19:g.63953965T>G	ENSP00000390158:p.Thr3053Pro	120.0	0.0	.		134.0	53.0	.	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	T	11.66	1.706292	0.30232	.	.	ENSG00000103657	ENST00000443617	T	0.24538	1.85	5.92	0.624	0.17659	.	0.249806	0.33631	U	0.004712	T	0.11024	0.0269	N	0.10809	0.05	0.41003	D	0.984949	B	0.02656	0.0	B	0.01281	0.0	T	0.09487	-1.0672	10	0.48119	T	0.1	.	5.1239	0.14875	0.1861:0.2447:0.0:0.5692	.	3053	Q15751	HERC1_HUMAN	P	3053	ENSP00000390158:T3053P	ENSP00000390158:T3053P	T	-	1	0	HERC1	61741018	0.938000	0.31826	0.970000	0.41538	0.987000	0.75469	1.624000	0.37018	0.136000	0.18733	0.528000	0.53228	ACA	.	.	.	none		0.448	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		G	63953965	T	G	63953965	3	3	100	1	0	0	0	0	1	0	0	0	7064	1725	60	5	5564	5	HERC1	15	63953965	Missense_Mutation	SNP	T	TCGA-B9-5155-01A-01D-1589-08	405183	63953965	38577427	82	6378											
BNC1	646	hgsc.bcm.edu	37	chr15	83935687	83935687	+	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	aacacactgaagagccggtcCagtaggatttttaggcgaac	13	8	11	9	2	0	2	0	1	0	1	1	4	1	3	2	3	3	1	2	3	5	4			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr15:83935687C>A	ENST00000345382.2	-	3	421	c.336G>T	c.(334-336)ctG>ctT	p.L112L	RP11-382A20.4_ENST00000565495.1_RNA|BNC1_ENST00000569704.1_Silent_p.L105L	NM_001717.3	NP_001708.3	Q01954	BNC1_HUMAN	basonuclin 1	112					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						AGAGCCGGTCCAGTAGGATTT	0.507																																					p.L112L		Atlas-SNP	.											.	BNC1	149	.	0			c.G336T						PASS	.						121	113	115					15																	83935687		2203	4300	6503	SO:0001819	synonymous_variant	646	exon3			CCGGTCCAGTAGG	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.336G>T	chr15.hg19:g.83935687C>A		115.0	0.0	.		155.0	78.0	.	NM_001717	Q15840	Silent	SNP	ENST00000345382.2	hg19	CCDS10324.1																																																																																			.	.	.	none		0.507	BNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304006.1	NM_001717		A	83935687	C	A	83935687	2	1	100	1	0	0	0	0	0	0	0	1	1474	581	21	4		4	BNC1	15	83935687	Silent	SNP	C	TCGA-B9-5155-01A-01D-1589-08	19981722	83935687	18595705	83	6379											
MFGE8	4240	hgsc.bcm.edu	37	chr15	89449052	89449053	+	Frame_Shift_Ins	INS	-	-	AA																															tgtggcagctcgtggggtacINSaatctcacgtactgagcctc																										TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr15:89449052_89449053insAA	ENST00000566497.1	-	5	681_682	c.620_621insTT	c.(619-621)ttgfs	p.L207fs	MFGE8_ENST00000539437.1_Frame_Shift_Ins_p.L199fs|MFGE8_ENST00000542878.1_Frame_Shift_Ins_p.L163fs|MFGE8_ENST00000268150.8_Frame_Shift_Ins_p.L207fs|MFGE8_ENST00000559997.1_Intron|MFGE8_ENST00000268151.7_Frame_Shift_Ins_p.L207fs			Q08431	MFGM_HUMAN	milk fat globule-EGF factor 8 protein	207	F5/8 type C 1. {ECO:0000255|PROSITE- ProRule:PRU00081}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|phagocytosis, engulfment (GO:0006911)|phagocytosis, recognition (GO:0006910)|positive regulation of apoptotic cell clearance (GO:2000427)|single fertilization (GO:0007338)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|vesicle (GO:0031982)	phosphatidylethanolamine binding (GO:0008429)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	22	Lung NSC(78;0.0392)|all_lung(78;0.077)					TCGTGGGGTACAATCTCACGTA	0.584																																					p.L207fs		Atlas-INDEL	.											.	MFGE8	60	.	0			c.621_622insTT						PASS	.																																			SO:0001589	frameshift_variant	4240	exon5			.	U58516	CCDS10347.1, CCDS45345.1	15q25	2009-03-25			ENSG00000140545	ENSG00000140545			7036	protein-coding gene	gene with protein product	"sperm surface protein hP47"	602281	"sperm associated antigen 10"	SPAG10		9027496, 19204935	Standard	NM_005928		Approved	SED1, EDIL1, BA46, OAcGD3S, HsT19888, MFG-E8, hP47	uc002bng.4	Q08431	OTTHUMG00000148682	ENST00000566497.1:c.619_620dupTT	chr15.hg19:g.89449053_89449054dupAA	ENSP00000456281:p.Leu207fs	137.0	0.0	0		186.0	70.0	0.376344	NM_001114614	B2R6M7|Q53FU9|Q7Z3D2|Q9BTL9	Frame_Shift_Ins	INS	ENST00000566497.1	hg19	CCDS10347.1																																																																																			.	.	.	none		0.584	MFGE8-015	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000432804.1	NM_005928		AA	89449053	-	AA	89449052	7	5	100	1	0	1	1	0	0	0	0	0	9527	477	17	0	558	0	MFGE8	15	89449052	Frame_Shift_Ins	INS	-	TCGA-B9-5155-01A-01D-1589-08	5513365	89449052	13082340	84	6380											
LINS1	55180	hgsc.bcm.edu	37	chr15	101114203	101114205	+	In_Frame_Del	DEL	TGA	TGA	-																															ccttccttttaacaaaagccTgaataggccaggtaataact																										TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr15:101114203_101114205delTGA	ENST00000314742.8	-	5	1095_1097	c.873_875delTCA	c.(871-876)attcag>atg	p.291_292IQ>M	LINS_ENST00000560133.1_In_Frame_Del_p.172_173IQ>M|LINS_ENST00000559149.1_5'UTR|LINS_ENST00000561308.1_In_Frame_Del_p.291_292IQ>M	NM_001040616.2	NP_001035706	Q8NG48	LINES_HUMAN	lines homolog (Drosophila)	291										central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(4)	21						AACAAAAGCCTGAATAGGCCAGG	0.429																																					p.292_292del		Atlas-INDEL	.											.	LINS	62	.	0			c.874_876del						PASS	.																																			SO:0001651	inframe_deletion	55180	exon5			.	AK095448	CCDS10385.1	15q26.3	2010-09-08	2010-09-08	2010-09-08	ENSG00000140471	ENSG00000140471			30922	protein-coding gene	gene with protein product		610350	"lines homolog 1 (Drosophila)"	LINS1		12119551, 8889548	Standard	NM_001040616		Approved	WINS1	uc002bwg.3	Q8NG48	OTTHUMG00000149865	ENST00000314742.8:c.873_875delTCA	chr15.hg19:g.101114203_101114205delTGA	ENSP00000318423:p.Ile291_Gln292delinsMet	59.0	0.0	0		67.0	27.0	0.402985	NM_001040616	Q96FW2|Q9NVQ3	In_Frame_Del	DEL	ENST00000314742.8	hg19	CCDS10385.1																																																																																			.	.	.	none		0.429	LINS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313592.1	NM_018148		-	101114205	TGA	-	101114203	7	5	100	1	0	1	0	1	0	0	0	0	8825	1580	55	0	1410	0	LINS1	15	101114203	In_Frame_Del	DEL	TGA	TCGA-B9-5155-01A-01D-1589-08	11665151	101114203	1417189	85	6381											
SMCR8	140775	hgsc.bcm.edu	37	chr17	18220177	18220177	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcctgaccagtcagattgaTagagcacttctaaaacaaca	15	9	6	11	0	2	4	1	2	1	2	3	4	3	4	2	0	3	1	2	0	4	4			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr17:18220177T>C	ENST00000406438.3	+	1	1554	c.1074T>C	c.(1072-1074)gaT>gaC	p.D358D	TOP3A_ENST00000321105.5_5'Flank|TOP3A_ENST00000542570.1_5'Flank|TOP3A_ENST00000582230.1_5'Flank	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	358						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						GTCAGATTGATAGAGCACTTC	0.443																																					p.D358D		Atlas-SNP	.											.	SMCR8	62	.	0			c.T1074C						PASS	.						93	90	91					17																	18220177		2203	4300	6503	SO:0001819	synonymous_variant	140775	exon1			GATTGATAGAGCA	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.1074T>C	chr17.hg19:g.18220177T>C		90.0	0.0	.		158.0	50.0	.	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Silent	SNP	ENST00000406438.3	hg19	CCDS11195.2																																																																																			.	.	.	none		0.443	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775		C	18220177	T	C	18220177	2	2	100	1	0	0	0	0	0	0	0	1	14805	1403	49	3		3	SMCR8	17	18220177	Silent	SNP	T	TCGA-B9-5155-01A-01D-1589-08		18220177	62975033	86	6382											
KIAA0100	9703	hgsc.bcm.edu	37	chr17	26943748	26943748	+	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	aagaactggtgtgtcagctgGatggtgagaggcaccacatt	11	9	14	7	0	1	2	1	1	0	2	1	4	1	3	1	4	2	2	1	4	2	1			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr17:26943748G>C	ENST00000528896.2	-	35	6119	c.6045C>G	c.(6043-6045)atC>atG	p.I2015M	SPAG5-AS1_ENST00000554154.1_RNA|SGK494_ENST00000301037.5_5'Flank|SPAG5-AS1_ENST00000414744.1_RNA|SPAG5-AS1_ENST00000424210.1_RNA|RP11-192H23.4_ENST00000577790.1_5'Flank|KIAA0100_ENST00000544884.1_Missense_Mutation_p.I1872M|RP11-192H23.4_ENST00000534850.1_5'Flank|SGK494_ENST00000469832.3_5'Flank|KIAA0100_ENST00000579924.2_5'UTR|KIAA0100_ENST00000389003.3_Missense_Mutation_p.I1872M	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	2015						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)					GTGTCAGCTGGATGGTGAGAG	0.418																																					p.I2015M		Atlas-SNP	.											.	KIAA0100	175	.	0			c.C6045G						PASS	.						91	90	90					17																	26943748		2203	4300	6503	SO:0001583	missense	9703	exon35			CAGCTGGATGGTG	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.6045C>G	chr17.hg19:g.26943748G>C	ENSP00000436773:p.Ile2015Met	89.0	0.0	.		157.0	98.0	.	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	hg19	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	G	16.14	3.038680	0.55003	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	T;T	0.56611	0.45;0.45	5.87	4.9	0.64082	FMP27,  C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.71126	0.3303	M	0.75615	2.305	0.58432	D	0.999996	D	0.89917	1.0	D	0.91635	0.999	T	0.74968	-0.3483	10	0.87932	D	0	.	12.8127	0.57649	0.1357:0.0:0.8643:0.0	.	2015	Q14667	K0100_HUMAN	M	2015;1985;2015;1872	ENSP00000436773:I2015M;ENSP00000446443:I1872M	ENSP00000005905:I2015M	I	-	3	3	KIAA0100	23967875	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.779000	0.55379	1.482000	0.48325	0.561000	0.74099	ATC	.	.	.	none		0.418	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		C	26943748	G	C	26943748	3	2	100	1	0	0	0	0	1	0	0	0	8161	1164	41	4	682	4	KIAA0100	17	26943748	Missense_Mutation	SNP	G	TCGA-B9-5155-01A-01D-1589-08	8723571	26943748	54251462	87	6383											
SSH2	85464	hgsc.bcm.edu	37	chr17	27959406	27959406	+	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	atcacttttcccttttggtgCtaggtctgccacagaagaat	9	14	8	10	0	2	2	1	0	1	2	3	2	3	2	2	2	2	1	2	2	3	5			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr17:27959406C>G	ENST00000269033.3	-	15	2876	c.2725G>C	c.(2725-2727)Gca>Cca	p.A909P	SSH2_ENST00000540801.1_Missense_Mutation_p.A936P|RP11-68I3.2_ENST00000581474.1_RNA	NM_001282129.1|NM_033389.2	NP_001269058.1|NP_203747.2	Q76I76	SSH2_HUMAN	slingshot protein phosphatase 2	909					actin cytoskeleton organization (GO:0030036)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)		SSH2/SUZ12(2)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CCTTTTGGTGCTAGGTCTGCC	0.488																																					p.A909P		Atlas-SNP	.											.	SSH2	107	.	0			c.G2725C						PASS	.						198	211	206					17																	27959406		2203	4300	6503	SO:0001583	missense	85464	exon15			TTGGTGCTAGGTC	AB072359	CCDS11253.1, CCDS74024.1	17q11.2	2013-03-05	2013-03-05		ENSG00000141298	ENSG00000141298		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"	30580	protein-coding gene	gene with protein product		606779	"slingshot homolog 2 (Drosophila)"			11832213, 11214970	Standard	XM_005258059		Approved	KIAA1725	uc002heo.1	Q76I76	OTTHUMG00000132752	ENST00000269033.3:c.2725G>C	chr17.hg19:g.27959406C>G	ENSP00000269033:p.Ala909Pro	401.0	0.0	.		614.0	355.0	.	NM_033389	Q8TDB5|Q8WYL1|Q8WYL2|Q96F40|Q96H36|Q9C0D8	Missense_Mutation	SNP	ENST00000269033.3	hg19	CCDS11253.1	.	.	.	.	.	.	.	.	.	.	C	11.09	1.535294	0.27475	.	.	ENSG00000141298	ENST00000269033;ENST00000540801	T;T	0.10288	2.89;2.89	5.97	2.62	0.31277	.	1.241560	0.05233	N	0.510668	T	0.13415	0.0325	L	0.54323	1.7	0.09310	N	1	P;P	0.46220	0.874;0.8	P;B	0.44990	0.466;0.276	T	0.21075	-1.0256	10	0.34782	T	0.22	-0.0415	1.9181	0.03301	0.1384:0.4444:0.1353:0.2819	.	936;909	F5H527;Q76I76	.;SSH2_HUMAN	P	909;936	ENSP00000269033:A909P;ENSP00000444743:A936P	ENSP00000269033:A909P	A	-	1	0	SSH2	24983532	0.015000	0.18098	0.385000	0.26158	0.507000	0.33981	0.589000	0.23939	0.853000	0.35312	-0.245000	0.11935	GCA	.	.	.	none		0.488	SSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256116.1	NM_033389		G	27959406	C	G	27959406	3	3	100	1	0	0	0	0	1	0	0	0	15197	797	28	4	1550	4	SSH2	17	27959406	Missense_Mutation	SNP	C	TCGA-B9-5155-01A-01D-1589-08	1015658	27959406	53235804	88	6384											
ZNF830	91603	hgsc.bcm.edu	37	chr17	33289325	33289325	+	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	aaacaccgcggaagcgttacCggaaggtttttttgacgacc	11	9	11	10	5	0	1	0	1	0	0	0	4	0	3	3	3	3	2	3	3	4	4			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr17:33289325C>G	ENST00000361952.3	+	1	777	c.740C>G	c.(739-741)cCg>cGg	p.P247R	CCT6B_ENST00000436961.3_5'Flank|CCT6B_ENST00000421975.3_5'Flank|CCT6B_ENST00000314144.5_5'Flank	NM_052857.3	NP_443089.3	Q96NB3	ZN830_HUMAN	zinc finger protein 830	247					blastocyst growth (GO:0001832)|mitotic nuclear division (GO:0007067)|nuclear cell cycle DNA replication (GO:0033260)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|large_intestine(1)|liver(2)|lung(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Ovarian(249;0.17)				GAAGCGTTACCGGAAGGTTTT	0.463																																					p.P247R		Atlas-SNP	.											.	ZNF830	26	.	0			c.C740G						PASS	.						60	58	59					17																	33289325		2203	4300	6503	SO:0001583	missense	91603	exon1			CGTTACCGGAAGG	AK055707	CCDS32618.1	17q12	2013-10-23	2008-03-25	2008-03-25	ENSG00000198783	ENSG00000198783			28291	protein-coding gene	gene with protein product	"orphan maintenance of genome 1"		"coiled-coil domain containing 16"	CCDC16		23066043	Standard	NM_052857		Approved	MGC20398, OMCG1	uc002hih.4	Q96NB3	OTTHUMG00000179771	ENST00000361952.3:c.740C>G	chr17.hg19:g.33289325C>G	ENSP00000354518:p.Pro247Arg	62.0	0.0	.		90.0	55.0	.	NM_052857	Q96F60|Q96GZ5|Q9BU38	Missense_Mutation	SNP	ENST00000361952.3	hg19	CCDS32618.1	.	.	.	.	.	.	.	.	.	.	C	19.09	3.760549	0.69763	.	.	ENSG00000198783	ENST00000361952	D	0.83837	-1.77	5.98	5.02	0.67125	.	0.000000	0.85682	D	0.000000	D	0.91233	0.7237	M	0.86502	2.82	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92053	0.5650	10	0.72032	D	0.01	-15.6542	11.0329	0.47783	0.0:0.9152:0.0:0.0848	.	247	Q96NB3	ZN830_HUMAN	R	247	ENSP00000354518:P247R	ENSP00000354518:P247R	P	+	2	0	ZNF830	30313438	1.000000	0.71417	0.991000	0.47740	0.997000	0.91878	6.618000	0.74214	1.552000	0.49463	0.591000	0.81541	CCG	.	.	.	none		0.463	ZNF830-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448018.1	NM_052857		G	33289325	C	G	33289325	3	3	100	1	0	0	0	0	1	0	0	0	18196	652	23	4	742	4	ZNF830	17	33289325	Missense_Mutation	SNP	C	TCGA-B9-5155-01A-01D-1589-08	5329919	33289325	47905885	89	6385											
LIG3	3980	hgsc.bcm.edu	37	chr17	33310454	33310454	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtaccacattaaatgcatgTttgagaaactagagcgggcc	13	9	11	8	1	0	2	0	1	0	2	0	3	0	2	2	2	4	3	2	2	5	4			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr17:33310454T>C	ENST00000378526.4	+	2	563	c.430T>C	c.(430-432)Ttt>Ctt	p.F144L	LIG3_ENST00000586407.1_Intron|LIG3_ENST00000262327.5_Missense_Mutation_p.F144L	NM_013975.3	NP_039269.2	P49916	DNLI3_HUMAN	ligase III, DNA, ATP-dependent	144					base-excision repair (GO:0006284)|base-excision repair, DNA ligation (GO:0006288)|DNA biosynthetic process (GO:0071897)|DNA repair (GO:0006281)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitochondrial DNA repair (GO:0043504)|negative regulation of DNA recombination (GO:0045910)|nucleotide-excision repair (GO:0006289)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(8)|lung(9)|ovary(3)|pancreas(2)|prostate(1)|skin(3)|stomach(1)	31		Ovarian(249;0.17)			Bleomycin(DB00290)	TAAATGCATGTTTGAGAAACT	0.488								Other BER factors																													p.F144L		Atlas-SNP	.											.	LIG3	164	.	0			c.T430C						PASS	.						51	50	50					17																	33310454		2203	4300	6503	SO:0001583	missense	3980	exon2			TGCATGTTTGAGA		CCDS11284.2, CCDS11285.2	17q11.2-q12	2008-10-29			ENSG00000005156	ENSG00000005156			6600	protein-coding gene	gene with protein product		600940	"ligase II, DNA, ATP-dependent"	LIG2		7760816	Standard	NM_002311		Approved		uc002hik.2	P49916	OTTHUMG00000128519	ENST00000378526.4:c.430T>C	chr17.hg19:g.33310454T>C	ENSP00000367787:p.Phe144Leu	22.0	0.0	.		66.0	42.0	.	NM_013975	Q16714|Q6NVK3	Missense_Mutation	SNP	ENST00000378526.4	hg19	CCDS11284.2	.	.	.	.	.	.	.	.	.	.	T	35	5.433129	0.96150	.	.	ENSG00000005156	ENST00000378526;ENST00000262327	T;T	0.28255	1.62;1.62	5.84	5.84	0.93424	Zinc finger, PARP-type (3);	0.000000	0.85682	D	0.000000	T	0.53818	0.1820	M	0.62209	1.925	0.80722	D	1	D;D;D;D	0.89917	0.998;0.998;0.989;1.0	D;D;D;D	0.97110	0.99;0.99;0.984;1.0	T	0.55768	-0.8089	10	0.72032	D	0.01	-10.3188	15.397	0.74805	0.0:0.0:0.0:1.0	.	144;144;144;144	E5KLB5;P49916;E5KLB6;Q96DF0	.;DNLI3_HUMAN;.;.	L	144	ENSP00000367787:F144L;ENSP00000262327:F144L	ENSP00000262327:F144L	F	+	1	0	LIG3	30334567	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.845000	0.86875	2.243000	0.73865	0.533000	0.62120	TTT	.	.	.	none		0.488	LIG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250330.3	NM_013975		C	33310454	T	C	33310454	3	2	100	1	0	0	0	0	1	0	0	0	8789	1725	60	3	432	3	LIG3	17	33310454	Missense_Mutation	SNP	T	TCGA-B9-5155-01A-01D-1589-08	21129	33310454	47884756	90	6386											
AMAC1	146861	hgsc.bcm.edu	37	chr17	33520712	33520712	+	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	gaacgatagaccagaagcctCagggacagcgccaggcctcc	12	3	12	14	2	1	2	1	0	0	2	2	5	2	3	5	2	3	0	5	2	3	1			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr17:33520712C>T	ENST00000297307.5	-	1	700	c.615G>A	c.(613-615)ctG>ctA	p.L205L	RP11-799D4.2_ENST00000590144.1_RNA	NM_152462.2	NP_689675.1	Q8N808	S35G3_HUMAN	solute carrier family 35, member G3	205						integral component of membrane (GO:0016021)											CCAGAAGCCTCAGGGACAGCG	0.627																																					p.L205L		Atlas-SNP	.											.	.	.	.	0			c.G615A						PASS	.						91	98	96					17																	33520712		2203	4300	6503	SO:0001819	synonymous_variant	146861	exon1			AAGCCTCAGGGAC	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.615G>A	chr17.hg19:g.33520712C>T		173.0	0.0	.		240.0	168.0	.	NM_152462	B9EGE9	Silent	SNP	ENST00000297307.5	hg19	CCDS11293.1																																																																																			.	.	.	none		0.627	SLC35G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256445.2	NM_152462		T	33520712	C	T	33520712	2	4	100	1	0	0	0	0	0	0	0	1	559	813	29	2		2	AMAC1	17	33520712	Silent	SNP	C	TCGA-B9-5155-01A-01D-1589-08	210258	33520712	47674498	91	6387											
STK11	6794	hgsc.bcm.edu	37	chr19	1220439	1220439	+	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	gcattgtgcacaaggacatcAagccggggaacctgctgctc	10	7	12	12	1	1	0	1	0	0	0	2	2	1	2	2	3	5	4	2	3	3	1			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr19:1220439A>T	ENST00000326873.7	+	4	1705	c.532A>T	c.(532-534)Aag>Tag	p.K178*		NM_000455.4	NP_000446.1	Q15831	STK11_HUMAN	serine/threonine kinase 11	178	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.?(4)|p.K178fs*86(1)		biliary_tract(1)|breast(3)|cervix(35)|gastrointestinal_tract_(site_indeterminate)(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|liver(1)|lung(219)|oesophagus(1)|ovary(4)|pancreas(6)|prostate(2)|skin(15)|small_intestine(1)|stomach(9)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	328		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18)		CAAGGACATCAAGCCGGGGAA	0.662		14	"D, Mis, N, F, S"		"NSCLC, pancreatic"	"jejunal harmartoma, ovarian, testicular, pancreatic"			Peutz-Jeghers syndrome	TSP Lung(3;<1E-08)																											p.K178X		Atlas-SNP	.	yes	Rec	yes	Peutz-Jeghers syndrome	19	19p13.3	6794	serine/threonine kinase 11 gene (LKB1)		"E, M, O"	.	STK11	410	.	29	Whole gene deletion(20)|Deletion - Frameshift(5)|Unknown(4)	cervix(15)|lung(9)|oesophagus(1)|ovary(1)|prostate(1)|kidney(1)|pancreas(1)	c.A532T						PASS	.						44	52	49					19																	1220439		2098	4239	6337	SO:0001587	stop_gained	6794	exon4	Familial Cancer Database	PJS, Hamartous Intestinal Polyposis	GACATCAAGCCGG	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.532A>T	chr19.hg19:g.1220439A>T	ENSP00000324856:p.Lys178*	21.0	0.0	.		18.0	9.0	.	NM_000455	B2RBX7|E7EW76	Nonsense_Mutation	SNP	ENST00000326873.7	hg19	CCDS45896.1	.	.	.	.	.	.	.	.	.	.	A	47	13.228355	0.99728	.	.	ENSG00000118046	ENST00000326873;ENST00000405031	.	.	.	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-49.8258	14.9586	0.71138	1.0:0.0:0.0:0.0	.	.	.	.	X	178	.	ENSP00000324856:K178X	K	+	1	0	STK11	1171439	1.000000	0.71417	1.000000	0.80357	0.416000	0.31233	9.209000	0.95087	2.135000	0.66039	0.459000	0.35465	AAG	.	.	.	none		0.662	STK11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449839.3	NM_000455		T	1220439	A	T	1220439	4	4	100	1	0	0	0	0	0	1	0	0	15299	131	5	5	546	5	STK11	19	1220439	Nonsense_Mutation	SNP	A	TCGA-B9-5155-01A-01D-1589-08		1220439	57908544	92	6388											
EPS15L1	58513	hgsc.bcm.edu	37	chr19	16513268	16513268	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgggcctcctggcggcttTcatgcagctgggaaagtttg	5	12	15	9	1	1	0	1	0	0	0	2	1	2	1	2	4	2	4	2	4	1	2			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr19:16513268T>C	ENST00000248070.6	-	16	1794	c.1655A>G	c.(1654-1656)gAa>gGa	p.E552G	EPS15L1_ENST00000594975.1_Missense_Mutation_p.E552G|EPS15L1_ENST00000455140.2_Missense_Mutation_p.E552G|EPS15L1_ENST00000597937.1_Missense_Mutation_p.E552G|EPS15L1_ENST00000602009.1_Missense_Mutation_p.E398G|EPS15L1_ENST00000535753.2_Missense_Mutation_p.E552G	NM_021235.2	NP_067058.1	Q9UBC2	EP15R_HUMAN	epidermal growth factor receptor pathway substrate 15-like 1	552					endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	clathrin coat of coated pit (GO:0030132)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(4)|skin(2)	30						CTGGCGGCTTTCATGCAGCTG	0.537																																					p.E552G		Atlas-SNP	.											.	EPS15L1	81	.	0			c.A1655G						PASS	.						56	56	56					19																	16513268		2203	4300	6503	SO:0001583	missense	58513	exon16			CGGCTTTCATGCA	AF110265	CCDS32944.1, CCDS58653.1, CCDS58654.1, CCDS59363.1	19p13.12	2013-01-10				ENSG00000127527		"EF-hand domain containing"	24634	protein-coding gene	gene with protein product							Standard	NM_001258374		Approved	eps15R	uc002ndx.4	Q9UBC2		ENST00000248070.6:c.1655A>G	chr19.hg19:g.16513268T>C	ENSP00000248070:p.Glu552Gly	68.0	0.0	.		115.0	51.0	.	NM_021235	A2RRF3|A5PL29|B4DKA3	Missense_Mutation	SNP	ENST00000248070.6	hg19	CCDS32944.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.595745	0.86953	.	.	ENSG00000127527	ENST00000455140;ENST00000248070;ENST00000535753	D;T;T	0.87966	-2.32;1.65;1.24	5.5	5.5	0.81552	.	0.053238	0.64402	D	0.000001	D	0.89093	0.6617	L	0.52011	1.625	0.58432	D	0.999994	D;D;P;P;P;P	0.62365	0.991;0.975;0.952;0.952;0.955;0.913	P;P;P;P;P;P	0.58970	0.849;0.77;0.606;0.606;0.606;0.702	D	0.87153	0.2210	10	0.27785	T	0.31	.	12.9903	0.58614	0.0:0.0:0.0:1.0	.	552;552;551;552;552;552	A8K5P4;A5PL29;A5PKY0;A2RRF3;Q9UBC2;G3V0H2	.;.;.;.;EP15R_HUMAN;.	G	552	ENSP00000393313:E552G;ENSP00000248070:E552G;ENSP00000440103:E552G	ENSP00000248070:E552G	E	-	2	0	EPS15L1	16374268	1.000000	0.71417	0.763000	0.31416	0.892000	0.51952	7.218000	0.77991	2.096000	0.63516	0.533000	0.62120	GAA	.	.	.	none		0.537	EPS15L1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461040.1	NM_021235		C	16513268	T	C	16513268	3	2	100	1	0	0	0	0	1	0	0	0	5195	1783	62	3	971	3	EPS15L1	19	16513268	Missense_Mutation	SNP	T	TCGA-B9-5155-01A-01D-1589-08	15292829	16513268	42615715	93	6389											
ZNF676	163223	hgsc.bcm.edu	37	chr19	22363129	22363129	+	Missense_Mutation	SNP	A	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	aattctcttgtgtttagtaaAgcttgaggaccaggtgaagg	11	13	12	5	0	1	2	0	2	1	0	2	3	1	3	1	3	1	3	1	3	5	6			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr19:22363129A>C	ENST00000397121.2	-	3	1707	c.1390T>G	c.(1390-1392)Ttt>Gtt	p.F464V		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	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)			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)				TGTTTAGTAAAGCTTGAGGAC	0.413																																					p.F464V		Atlas-SNP	.											.	ZNF676	146	.	0			c.T1390G						PASS	.						126	131	129					19																	22363129		2157	4266	6423	SO:0001583	missense	163223	exon3			TAGTAAAGCTTGA	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.1390T>G	chr19.hg19:g.22363129A>C	ENSP00000380310:p.Phe464Val	255.0	0.0	.		248.0	103.0	.	NM_001001411	A8MVX5	Missense_Mutation	SNP	ENST00000397121.2	hg19	CCDS42539.1	.	.	.	.	.	.	.	.	.	.	.	2.545	-0.305325	0.05495	.	.	ENSG00000196109	ENST00000397121	T	0.18338	2.22	0.149	-0.298	0.12814	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07908	0.0198	N	0.11673	0.155	0.09310	N	1	B	0.27951	0.195	B	0.24394	0.053	T	0.27262	-1.0079	9	0.72032	D	0.01	.	4.6797	0.12729	0.3583:0.0:0.6417:0.0	.	464	Q8N7Q3	ZN676_HUMAN	V	464	ENSP00000380310:F464V	ENSP00000380310:F464V	F	-	1	0	ZNF676	22154969	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.610000	0.05629	-1.346000	0.02211	-1.381000	0.01174	TTT	.	.	.	none		0.413	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411		C	22363129	A	C	22363129	3	2	100	1	0	0	0	0	1	0	0	0	18095	72	3	5	380	5	ZNF676	19	22363129	Missense_Mutation	SNP	A	TCGA-B9-5155-01A-01D-1589-08	5849861	22363129	36765854	94	6390											
ZNF416	55659	hgsc.bcm.edu	37	chr19	58083736	58083736	+	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	aatccagtgtgaattttctgGtgttcaacgagggtatagct	10	14	11	6	1	2	1	1	1	1	0	3	2	3	1	1	2	2	3	1	2	5	5			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr19:58083736G>C	ENST00000196489.3	-	4	1758	c.1536C>G	c.(1534-1536)caC>caG	p.H512Q		NM_017879.1	NP_060349.1	Q9BWM5	ZN416_HUMAN	zinc finger protein 416	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)			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)		GAATTTTCTGGTGTTCAACGA	0.438																																					p.H512Q		Atlas-SNP	.											.	ZNF416	50	.	0			c.C1536G						PASS	.						99	99	99					19																	58083736		2203	4300	6503	SO:0001583	missense	55659	exon4			TTTCTGGTGTTCA	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.1536C>G	chr19.hg19:g.58083736G>C	ENSP00000196489:p.His512Gln	137.0	0.0	.		140.0	65.0	.	NM_017879	Q9NWW8	Missense_Mutation	SNP	ENST00000196489.3	hg19	CCDS12954.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.017774	0.75161	.	.	ENSG00000083817	ENST00000196489;ENST00000359489;ENST00000428052	D	0.86865	-2.18	3.58	1.43	0.22495	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.93776	0.8010	M	0.93808	3.46	0.29684	N	0.841443	D	0.89917	1.0	D	0.91635	0.999	D	0.86737	0.1952	9	0.72032	D	0.01	.	6.7993	0.23742	0.3194:0.0:0.6806:0.0	.	512	Q9BWM5	ZN416_HUMAN	Q	512;415;410	ENSP00000196489:H512Q	ENSP00000196489:H512Q	H	-	3	2	ZNF416	62775548	0.022000	0.18835	0.039000	0.18376	0.939000	0.58152	0.165000	0.16564	0.838000	0.34948	0.655000	0.94253	CAC	.	.	.	none		0.438	ZNF416-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466787.1	NM_017879		C	58083736	G	C	58083736	3	2	100	1	0	0	0	0	1	0	0	0	17905	1252	44	4	252	4	ZNF416	19	58083736	Missense_Mutation	SNP	G	TCGA-B9-5155-01A-01D-1589-08	35720607	58083736	1045247	95	6391			1	15		2	2	30	N	G_A	9.554818e-05
ZNF416	55659	hgsc.bcm.edu	37	chr19	58083765	58083765	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagggtatagctttgtctaaAaaatttcccacattcactgc	12	13	7	9	0	2	0	1	0	1	0	3	1	3	0	1	1	2	2	1	1	5	6			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr19:58083765A>G	ENST00000196489.3	-	4	1729	c.1507T>C	c.(1507-1509)Ttt>Ctt	p.F503L		NM_017879.1	NP_060349.1	Q9BWM5	ZN416_HUMAN	zinc finger protein 416	503					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)		CTTTGTCTAAAAAATTTCCCA	0.418																																					p.F503L		Atlas-SNP	.											.	ZNF416	50	.	0			c.T1507C						PASS	.						80	81	81					19																	58083765		2203	4300	6503	SO:0001583	missense	55659	exon4			GTCTAAAAAATTT	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.1507T>C	chr19.hg19:g.58083765A>G	ENSP00000196489:p.Phe503Leu	124.0	0.0	.		138.0	64.0	.	NM_017879	Q9NWW8	Missense_Mutation	SNP	ENST00000196489.3	hg19	CCDS12954.1	.	.	.	.	.	.	.	.	.	.	A	35	5.419811	0.96111	.	.	ENSG00000083817	ENST00000196489;ENST00000359489;ENST00000428052	T	0.46063	0.88	3.48	3.48	0.39840	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.64594	0.2612	M	0.82517	2.595	0.41420	D	0.987799	D	0.89917	1.0	D	0.91635	0.999	T	0.70605	-0.4826	9	0.87932	D	0	.	11.3666	0.49675	1.0:0.0:0.0:0.0	.	503	Q9BWM5	ZN416_HUMAN	L	503;406;401	ENSP00000196489:F503L	ENSP00000196489:F503L	F	-	1	0	ZNF416	62775577	1.000000	0.71417	0.060000	0.19600	0.888000	0.51559	5.931000	0.70113	1.577000	0.49804	0.533000	0.62120	TTT	.	.	.	none		0.418	ZNF416-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466787.1	NM_017879		G	58083765	A	G	58083765	3	3	100	1	0	0	0	0	1	0	0	0	17905	14	1	3	281	3	ZNF416	19	58083765	Missense_Mutation	SNP	A	TCGA-B9-5155-01A-01D-1589-08	29	58083765	1045218	96	6392			1	15		2	2	30	N	G_A	9.554818e-05
REM1	28954	hgsc.bcm.edu	37	chr20	30064536	30064536	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggagtggggaagaccagcttGgccagcctctttgcagggaa	9	7	16	9	0	1	1	0	0	1	1	1	4	1	4	3	5	3	2	3	5	2	2			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr20:30064536G>A	ENST00000201979.2	+	2	581	c.288G>A	c.(286-288)ttG>ttA	p.L96L	DEFB124_ENST00000481595.1_5'UTR	NM_014012.4	NP_054731.2	O75628	REM1_HUMAN	RAS (RAD and GEM)-like GTP-binding 1	96					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)			kidney(3)|large_intestine(3)|lung(14)|pancreas(2)|upper_aerodigestive_tract(1)	23	all_cancers(5;0.000119)|Lung NSC(7;1.32e-05)|all_lung(7;2.14e-05)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			AGACCAGCTTGGCCAGCCTCT	0.582																																					p.L96L		Atlas-SNP	.											.	REM1	54	.	0			c.G288A						PASS	.						41	38	39					20																	30064536		2203	4300	6503	SO:0001819	synonymous_variant	28954	exon2			CAGCTTGGCCAGC	AF152863	CCDS13181.1	20q11.21	2014-05-09	2004-04-14	2004-04-16	ENSG00000088320	ENSG00000088320			15922	protein-coding gene	gene with protein product	"GTPase GES"	610388	"RAS (RAD and GEM)-like GTP-binding"	REM		10831614, 14623965	Standard	NM_014012		Approved	GES	uc002wwa.3	O75628	OTTHUMG00000032168	ENST00000201979.2:c.288G>A	chr20.hg19:g.30064536G>A		43.0	0.0	.		47.0	27.0	.	NM_014012	E1P5L1|Q5TZR7|Q5TZR8|Q9NP57	Silent	SNP	ENST00000201979.2	hg19	CCDS13181.1																																																																																			.	.	.	none		0.582	REM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078508.2	NM_014012		A	30064536	G	A	30064536	2	1	100	1	0	0	0	0	0	0	0	1	13235	1339	47	2		2	REM1	20	30064536	Silent	SNP	G	TCGA-B9-5155-01A-01D-1589-08		30064536	32960984	97	6393											
PIGU	128869	hgsc.bcm.edu	37	chr20	33163023	33163023	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggaacagacgatgatgatgCaggtgaggacaaagatgttt	14	8	15	4	1	0	5	0	3	0	2	0	8	0	7	0	3	2	2	0	3	2	1			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr20:33163023C>T	ENST00000374820.2	-	10	1039	c.1019G>A	c.(1018-1020)tGc>tAc	p.C340Y	PIGU_ENST00000452740.2_Missense_Mutation_p.C360Y			Q9H490	PIGU_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class U	360					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|regulation of JAK-STAT cascade (GO:0046425)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	9						GATGATGATGCAGGTGAGGAC	0.512																																					p.C360Y		Atlas-SNP	.											.	PIGU	35	.	0			c.G1079A						PASS	.						181	141	155					20																	33163023		2203	4300	6503	SO:0001583	missense	128869	exon11			ATGATGCAGGTGA	AL118520	CCDS13239.1	20q11.22	2013-02-26	2006-11-07	2006-11-07	ENSG00000101464	ENSG00000101464		"Phosphatidylinositol glycan anchor biosynthesis"	15791	protein-coding gene	gene with protein product	"GPI transamidase subunit"	608528	"CDC91 (cell division cycle 91, S. cerevisiae, homolog)-like 1", "CDC91 cell division cycle 91-like 1 (S. cerevisiae)"	CDC91L1		12802054, 15034568	Standard	NM_080476		Approved	bA346K17.2, GAB1	uc002xas.3	Q9H490	OTTHUMG00000032304	ENST00000374820.2:c.1019G>A	chr20.hg19:g.33163023C>T	ENSP00000363953:p.Cys340Tyr	59.0	0.0	.		47.0	19.0	.	NM_080476	Q7Z489|Q8N2F2	Missense_Mutation	SNP	ENST00000374820.2	hg19		.	.	.	.	.	.	.	.	.	.	C	24.8	4.572584	0.86542	.	.	ENSG00000101464	ENST00000217446;ENST00000374820;ENST00000452740;ENST00000438215	.	.	.	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.76695	0.4023	M	0.70595	2.14	0.80722	D	1	D;D;D	0.76494	0.999;0.997;0.997	D;D;D	0.87578	0.998;0.991;0.995	T	0.70121	-0.4959	9	0.09084	T	0.74	-16.1694	19.1929	0.93674	0.0:1.0:0.0:0.0	.	360;340;360	E7EVL4;Q9H490-2;Q9H490	.;.;PIGU_HUMAN	Y	360;340;360;106	.	ENSP00000217446:C360Y	C	-	2	0	PIGU	32626684	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	5.845000	0.69437	2.711000	0.92665	0.655000	0.94253	TGC	.	.	.	none		0.512	PIGU-201	KNOWN	basic	protein_coding	protein_coding		NM_080476		T	33163023	C	T	33163023	3	4	100	1	0	0	0	0	1	0	0	0	11907	710	25	2	236	2	PIGU	20	33163023	Missense_Mutation	SNP	C	TCGA-B9-5155-01A-01D-1589-08	3098487	33163023	29862497	98	6394											
TSHZ2	128553	hgsc.bcm.edu	37	chr20	51871026	51871026	+	Frame_Shift_Del	DEL	T	T	-																															acaggatcttttgcagattcTttttcttctcagaagaacgc																										TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr20:51871026delT	ENST00000371497.5	+	2	1916	c.1029delT	c.(1027-1029)tctfs	p.S343fs	TSHZ2_ENST00000603338.2_Frame_Shift_Del_p.S340fs|RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000329613.6_Frame_Shift_Del_p.S340fs	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	343					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)			TTGCAGATTCTTTTTCTTCTC	0.493																																					p.S343fs		Atlas-INDEL	.											.	TSHZ2	209	.	0			c.1028delC						PASS	.						78	86	83					20																	51871026		2203	4300	6503	SO:0001589	frameshift_variant	128553	exon2			.	AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	13010	protein-coding gene	gene with protein product		614118	"chromosome 20 open reading frame 17", "zinc finger protein 218", "teashirt family zinc finger 2"	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.1029delT	chr20.hg19:g.51871026delT	ENSP00000360552:p.Ser343fs	154.0	0.0	0		222.0	105.0	0.472973	NM_173485	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Frame_Shift_Del	DEL	ENST00000371497.5	hg19	CCDS33490.1																																																																																			.	.	.	none		0.493	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485		-	51871026	T	-	51871026	7	5	100	1	0	1	0	1	0	0	0	0	16636	1596	56	0	1035	0	TSHZ2	20	51871026	Frame_Shift_Del	DEL	T	TCGA-B9-5155-01A-01D-1589-08	18708003	51871026	11154494	99	6395											
CSTF1	1477	hgsc.bcm.edu	37	chr20	54974310	54974310	+	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	gacggtgctgaagtttgttcTgccattttttccaaaaattc	9	16	8	8	1	1	1	0	1	1	0	3	2	2	1	2	1	2	3	2	1	3	6			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr20:54974310T>A	ENST00000217109.4	+	5	1285	c.933T>A	c.(931-933)tcT>tcA	p.S311S	CSTF1_ENST00000493039.1_3'UTR	NM_001033521.1|NM_001324.2	NP_001028693.1|NP_001315.1	Q05048	CSTF1_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 1, 50kDa	311					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	15			Colorectal(105;0.202)			AAGTTTGTTCTGCCATTTTTT	0.398																																					p.S311S		Atlas-SNP	.											.	CSTF1	29	.	0			c.T933A						PASS	.						123	113	117					20																	54974310		2203	4300	6503	SO:0001819	synonymous_variant	1477	exon5			TTGTTCTGCCATT		CCDS13452.1	20q13.31	2013-01-10	2002-08-29		ENSG00000101138	ENSG00000101138		"WD repeat domain containing"	2483	protein-coding gene	gene with protein product		600369	"cleavage stimulation factor, 3' pre-RNA, subunit 1, 50kD"			1358884, 11257228	Standard	NM_001033521		Approved		uc002xxl.1	Q05048	OTTHUMG00000032791	ENST00000217109.4:c.933T>A	chr20.hg19:g.54974310T>A		137.0	0.0	.		134.0	61.0	.	NM_001033522	Q5QPD8	Silent	SNP	ENST00000217109.4	hg19	CCDS13452.1																																																																																			.	.	.	none		0.398	CSTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079794.2	NM_001033521		A	54974310	T	A	54974310	2	1	100	1	0	0	0	0	0	0	0	1	3985	1567	55	5		5	CSTF1	20	54974310	Silent	SNP	T	TCGA-B9-5155-01A-01D-1589-08	3103284	54974310	8051210	100	6396											
KCNJ15	3772	hgsc.bcm.edu	37	chr21	39671714	39671714	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaaaaagcgggctgagacCatcaagttcagccactgtgc	12	6	10	13	1	2	1	2	1	0	1	2	2	2	1	3	1	3	2	3	1	3	1			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr21:39671714C>T	ENST00000328656.4	+	4	834	c.531C>T	c.(529-531)acC>acT	p.T177T	KCNJ15_ENST00000398938.2_Silent_p.T177T|KCNJ15_ENST00000398930.1_Silent_p.T177T|KCNJ15_ENST00000398934.1_Silent_p.T177T|KCNJ15_ENST00000398932.1_Silent_p.T177T	NM_001276437.1|NM_001276438.1|NM_001276439.1|NM_002243.3	NP_001263366.1|NP_001263367.1|NP_001263368.1|NP_002234.2	Q99712	KCJ15_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 15	177					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	24					Yohimbine(DB01392)	GGGCTGAGACCATCAAGTTCA	0.507																																					p.E177D		Atlas-SNP	.											.	KCNJ15	43	.	0			c.A531T						PASS	.						65	62	63					21																	39671714		2203	4300	6503	SO:0001819	synonymous_variant	3772	exon4			TGAGACCATCAAG	Y10745	CCDS13656.1	21q22.2	2011-07-05			ENSG00000157551	ENSG00000157551		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6261	protein-coding gene	gene with protein product		602106				9299242, 8995301, 16382105	Standard	NM_170736		Approved	Kir4.2, Kir1.3, IRKK	uc002ywx.4	Q99712	OTTHUMG00000090609	ENST00000328656.4:c.531C>T	chr21.hg19:g.39671714C>T		74.0	0.0	.		70.0	26.0	.	NM_002243	D3DSH5|O00564|Q96L28|Q99446	Missense_Mutation	SNP	ENST00000328656.4	hg19	CCDS13656.1																																																																																			.	.	.	none		0.507	KCNJ15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207181.2	NM_002243		T	39671714	C	T	39671714	2	4	100	1	0	0	0	0	0	0	0	1	8056	581	21	2		2	KCNJ15	21	39671714	Silent	SNP	C	TCGA-B9-5155-01A-01D-1589-08		39671714	8458181	101	6397											
CCDC157	550631	hgsc.bcm.edu	37	chr22	30771620	30771620	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccaatcaatgctgtccaaaAtccgggaagtggcccagcag	12	7	10	12	1	1	0	1	0	0	0	4	1	4	1	4	2	2	2	4	2	5	0			TCGA-B9-5155-01A-01D-1589-08	TCGA-B9-5155-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9ca1b195-86fe-4597-933d-93903a61f676	d8826711-1c53-40c3-b444-2c9614f49b6f	g.chr22:30771620A>G	ENST00000405659.1	+	10	2534	c.1825A>G	c.(1825-1827)Atc>Gtc	p.I609V	CCDC157_ENST00000338306.3_Missense_Mutation_p.I609V|RP1-130H16.16_ENST00000332468.4_RNA			Q569K6	CC157_HUMAN	coiled-coil domain containing 157	609										central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(1)	15						GCTGTCCAAAATCCGGGAAGT	0.612																																					p.I609V		Atlas-SNP	.											.	CCDC157	86	.	0			c.A1825G						PASS	.						49	47	48					22																	30771620		2203	4300	6503	SO:0001583	missense	550631	exon10			TCCAAAATCCGGG	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.1825A>G	chr22.hg19:g.30771620A>G	ENSP00000385357:p.Ile609Val	40.0	0.0	.		50.0	4.0	.	NM_001017437	Q0VD76|Q9BYA4	Missense_Mutation	SNP	ENST00000405659.1	hg19	CCDS33632.2	.	.	.	.	.	.	.	.	.	.	A	15.73	2.921236	0.52653	.	.	ENSG00000187860	ENST00000405659;ENST00000338306	T;T	0.77098	-1.07;-1.07	5.24	2.99	0.34606	.	0.148034	0.46145	D	0.000309	T	0.59851	0.2224	L	0.41236	1.265	0.80722	D	1	P	0.37731	0.607	B	0.30782	0.12	T	0.56547	-0.7961	10	0.26408	T	0.33	-23.0767	5.0133	0.14324	0.6607:0.1879:0.1514:0.0	.	609	Q569K6	CC157_HUMAN	V	609	ENSP00000385357:I609V;ENSP00000343087:I609V	ENSP00000343087:I609V	I	+	1	0	CCDC157	29101620	0.715000	0.27946	0.993000	0.49108	0.936000	0.57629	0.528000	0.23002	1.981000	0.57761	0.533000	0.62120	ATC	.	.	.	none		0.612	CCDC157-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320936.1	NM_001017437		G	30771620	A	G	30771620	3	3	100	1	0	0	0	0	1	0	0	0	2791	101	4	3	1855	3	CCDC157	22	30771620	Missense_Mutation	SNP	A	TCGA-B9-5155-01A-01D-1589-08		30771620	20532946	102	6398											
TAS1R2	80834	hgsc.bcm.edu	37	chr1	19166252	19166252	+	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	aagaggtccacgatggtgacCagcaccccgctgtaggcaga	11	5	13	12	2	0	3	0	1	0	2	1	4	1	3	4	3	1	4	4	3	2	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr1:19166252C>G	ENST00000375371.3	-	6	2382	c.2361G>C	c.(2359-2361)ctG>ctC	p.L787L		NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	787					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)	CGATGGTGACCAGCACCCCGC	0.567																																					p.L787L		Atlas-SNP	.											.	TAS1R2	134	.	0			c.G2361C						PASS	.						125	94	105					1																	19166252		2203	4300	6503	SO:0001819	synonymous_variant	80834	exon6			GGTGACCAGCACC		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.2361G>C	chr1.hg19:g.19166252C>G		50.0	0.0	.		37.0	16.0	.	NM_152232	Q5TZ19	Silent	SNP	ENST00000375371.3	hg19	CCDS187.1																																																																																			.	.	.	none		0.567	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1			G	19166252	C	G	19166252	2	3	101	1	0	0	0	0	0	0	0	1	15575	581	21	4		4	TAS1R2	1	19166252	Silent	SNP	C	TCGA-B9-5156-01A-01D-1589-08		19166252	230084369	1	6399											
EIF2C1	26523	hgsc.bcm.edu	37	chr1	36354062	36354062	+	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	ctgccccccctgcagcaggtGttccaggcacctcgccggcc	4	6	11	20	2	0	0	0	0	0	0	2	0	1	0	7	3	3	4	7	3	0	1	rs79428335		TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr1:36354062G>A	ENST00000373204.4	+	2	273	c.60G>A	c.(58-60)gtG>gtA	p.V20V	AGO1_ENST00000373206.1_5'UTR	NM_012199.2	NP_036331.1	Q9UL18	AGO1_HUMAN	argonaute RISC catalytic component 1	20					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)										TGCAGCAGGTGTTCCAGGCAC	0.562																																					p.V20V		Atlas-SNP	.											.	.	.	.	0			c.G60A						PASS	.						73	70	71					1																	36354062		2203	4300	6503	SO:0001819	synonymous_variant	26523	exon2			GCAGGTGTTCCAG	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.60G>A	chr1.hg19:g.36354062G>A		124.0	0.0	.		107.0	30.0	.	NM_012199	Q5TA57|Q6P4S0	Silent	SNP	ENST00000373204.4	hg19	CCDS398.1																																																																																			.	.	.	alt		0.562	AGO1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019337.3			A	36354062	G	A	36354062	2	1	101	1	0	0	0	0	0	0	0	1	5007	1364	48	2		2	EIF2C1	1	36354062	Silent	SNP	G	TCGA-B9-5156-01A-01D-1589-08	17187810	36354062	212896559	2	6400											
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144915498	144915498	+	Frame_Shift_Del	DEL	T	T	-																															aagcaggccttgaatctccaTttcatgttccagcacttgtt																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr1:144915498delT	ENST00000369354.3	-	14	2116	c.1927delA	c.(1927-1929)atgfs	p.M643fs	PDE4DIP_ENST00000313382.9_Frame_Shift_Del_p.M709fs|PDE4DIP_ENST00000369359.4_Frame_Shift_Del_p.M780fs|PDE4DIP_ENST00000530740.1_Frame_Shift_Del_p.M780fs|PDE4DIP_ENST00000313431.9_Frame_Shift_Del_p.M806fs|PDE4DIP_ENST00000369351.3_Frame_Shift_Del_p.M643fs|PDE4DIP_ENST00000479408.2_Frame_Shift_Del_p.M430fs|PDE4DIP_ENST00000529945.1_Frame_Shift_Del_p.M806fs|PDE4DIP_ENST00000369349.3_Frame_Shift_Del_p.M643fs|PDE4DIP_ENST00000369356.4_Frame_Shift_Del_p.M643fs			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	643				M -> V (in Ref. 4; CAD91152). {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)		TGAATCTCCATTTCATGTTCC	0.468			T	PDGFRB	MPD																																p.M806fs		Atlas-INDEL	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.2417delT						PASS	.						319	290	300					1																	144915498		2203	4296	6499	SO:0001589	frameshift_variant	9659	exon10			.	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.1927delA	chr1.hg19:g.144915498delT	ENSP00000358360:p.Met643fs	452.0	0.0	0		447.0	85.0	0.190157	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Frame_Shift_Del	DEL	ENST00000369354.3	hg19	CCDS30824.1																																																																																			.	.	.	none		0.468	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		-	144915498	T	-	144915498	7	5	101	1	0	1	0	1	0	0	0	0	11650	1493	52	0	5247	0	PDE4DIP	1	144915498	Frame_Shift_Del	DEL	T	TCGA-B9-5156-01A-01D-1589-08	108561436	144915498	104335123	3	6401											
RPRD2	23248	hgsc.bcm.edu	37	chr1	150390094	150390094	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatatccccaccgtttgaaTctcttttaccttgccaatga	9	14	5	13	1	1	2	0	2	1	0	3	2	2	2	5	0	2	2	5	0	4	5			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr1:150390094T>C	ENST00000369068.4	+	2	232	c.228T>C	c.(226-228)aaT>aaC	p.N76N	RPRD2_ENST00000539519.1_Silent_p.N76N|RPRD2_ENST00000369067.3_Silent_p.N76N|RPRD2_ENST00000401000.4_Silent_p.N76N|RPRD2_ENST00000492220.1_3'UTR	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	76	CID. {ECO:0000255|PROSITE- ProRule:PRU00724}.					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						ACCGTTTGAATCTCTTTTACC	0.363																																					p.N76N		Atlas-SNP	.											.	RPRD2	189	.	0			c.T228C						PASS	.						231	217	221					1																	150390094		1865	4102	5967	SO:0001819	synonymous_variant	23248	exon2			TTTGAATCTCTTT	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.228T>C	chr1.hg19:g.150390094T>C		298.0	0.0	.		284.0	97.0	.	NM_015203	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Silent	SNP	ENST00000369068.4	hg19	CCDS44216.1																																																																																			.	.	.	none		0.363	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203		C	150390094	T	C	150390094	2	2	101	1	0	0	0	0	0	0	0	1	13630	1432	50	3		3	RPRD2	1	150390094	Silent	SNP	T	TCGA-B9-5156-01A-01D-1589-08	5474596	150390094	98860527	4	6402											
SLC9A11	284525	hgsc.bcm.edu	37	chr1	173545857	173545857	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagaatctaaattcagtcctAcagcggctaaggcaagagtg	15	8	10	8	1	2	2	1	0	1	2	3	2	3	2	1	2	2	2	1	2	7	4			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr1:173545857A>G	ENST00000367714.3	-	8	1267	c.845T>C	c.(844-846)gTa>gCa	p.V282A	SLC9C2_ENST00000536496.1_Missense_Mutation_p.V180A|RP3-436N22.3_ENST00000431459.1_RNA|SLC9C2_ENST00000466087.1_5'UTR	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	282					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										ATTCAGTCCTACAGCGGCTAA	0.368																																					p.V282A		Atlas-SNP	.											SLC9A11,colon,carcinoma,0,1	.	.	.	0			c.T845C						PASS	.						68	68	68					1																	173545857		2203	4300	6503	SO:0001583	missense	284525	exon8			AGTCCTACAGCGG	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.845T>C	chr1.hg19:g.173545857A>G	ENSP00000356687:p.Val282Ala	67.0	0.0	.		59.0	3.0	.	NM_178527	Q86UF3	Missense_Mutation	SNP	ENST00000367714.3	hg19	CCDS1308.1	.	.	.	.	.	.	.	.	.	.	A	13.60	2.285972	0.40394	.	.	ENSG00000162753	ENST00000367714;ENST00000536496	T;T	0.06687	3.27;3.27	5.48	4.36	0.52297	Cation/H+ exchanger (1);	0.426381	0.19800	N	0.105771	T	0.02727	0.0082	L	0.50333	1.59	0.09310	N	1	B	0.18166	0.026	B	0.23275	0.045	T	0.42548	-0.9445	10	0.23302	T	0.38	-14.6781	8.1183	0.30957	0.9095:0.0:0.0905:0.0	.	282	Q5TAH2	S9A11_HUMAN	A	282;180	ENSP00000356687:V282A;ENSP00000445437:V180A	ENSP00000356687:V282A	V	-	2	0	SLC9A11	171812480	0.049000	0.20398	0.097000	0.21041	0.518000	0.34316	4.102000	0.57776	0.925000	0.37094	-0.250000	0.11733	GTA	.	.	.	none		0.368	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527		G	173545857	A	G	173545857	3	3	101	1	0	0	0	0	1	0	0	0	14724	391	14	3	2613	3	SLC9A11	1	173545857	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	23155763	173545857	75704764	5	6403											
HMCN1	83872	hgsc.bcm.edu	37	chr1	186158954	186158954	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctacagtgccaatgggaccAttgaatatcagaccacattc	13	9	7	12	0	1	2	1	1	0	1	2	3	1	3	4	1	2	0	4	1	4	4			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr1:186158954A>G	ENST00000271588.4	+	107	17081	c.16852A>G	c.(16852-16854)Att>Gtt	p.I5618V	HMCN1_ENST00000367492.2_Missense_Mutation_p.I5501V	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5618					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						CAATGGGACCATTGAATATCA	0.448																																					p.I5618V		Atlas-SNP	.											.	HMCN1	797	.	0			c.A16852G						PASS	.						122	111	115					1																	186158954		2203	4300	6503	SO:0001583	missense	83872	exon107			GGGACCATTGAAT	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.16852A>G	chr1.hg19:g.186158954A>G	ENSP00000271588:p.Ile5618Val	119.0	0.0	.		115.0	31.0	.	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	A	5.555	0.287307	0.10513	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.62364	0.03;0.03	5.91	-0.414	0.12359	.	0.153154	0.56097	N	0.000026	T	0.40670	0.1126	N	0.20986	0.625	0.23896	N	0.996533	B	0.06786	0.001	B	0.06405	0.002	T	0.20538	-1.0272	10	0.45353	T	0.12	.	6.395	0.21607	0.5367:0.2325:0.2308:0.0	.	5618	Q96RW7	HMCN1_HUMAN	V	5618;5501	ENSP00000271588:I5618V;ENSP00000356462:I5501V	ENSP00000271588:I5618V	I	+	1	0	HMCN1	184425577	1.000000	0.71417	0.994000	0.49952	0.983000	0.72400	2.129000	0.42055	-0.086000	0.12550	0.533000	0.62120	ATT	.	.	.	none		0.448	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		G	186158954	A	G	186158954	3	3	101	1	0	0	0	0	1	0	0	0	7227	217	8	3	17278	3	HMCN1	1	186158954	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	12613097	186158954	63091667	6	6404											
LRRN2	10446	hgsc.bcm.edu	37	chr1	204588079	204588079	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtctgctggtgcaaggcacTgagagcgttgttgttgagca	7	11	15	8	2	1	2	0	2	1	1	1	3	1	2	0	2	4	7	0	2	1	3			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr1:204588079T>C	ENST00000367175.1	-	1	3254	c.1042A>G	c.(1042-1044)Agt>Ggt	p.S348G	RP11-430C7.4_ENST00000453895.1_RNA|LRRN2_ENST00000496057.1_5'Flank|LRRN2_ENST00000367177.3_Missense_Mutation_p.S348G|LRRN2_ENST00000367176.3_Missense_Mutation_p.S348G			O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2	348					cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|liver(1)|lung(22)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			TGCAAGGCACTGAGAGCGTTG	0.617																																					p.S348G		Atlas-SNP	.											.	LRRN2	81	.	0			c.A1042G						PASS	.						66	59	62					1																	204588079		2203	4300	6503	SO:0001583	missense	10446	exon3			AGGCACTGAGAGC	AF030435	CCDS1448.1	1q32.1	2013-01-11	2007-01-31	2007-01-31	ENSG00000170382	ENSG00000170382		"Immunoglobulin superfamily / I-set domain containing"	16914	protein-coding gene	gene with protein product	"leucine rich and ankyrin repeats 1", "fibronectin type III, immunoglobulin and leucine rich repeat domain 7"	605492	"leucine rich repeat neuronal 5"	LRRN5		9662332	Standard	NM_006338		Approved	GAC1, LRANK1, FIGLER7	uc001hbf.1	O75325	OTTHUMG00000035989	ENST00000367175.1:c.1042A>G	chr1.hg19:g.204588079T>C	ENSP00000356143:p.Ser348Gly	45.0	0.0	.		37.0	10.0	.	NM_006338	B2R624|Q5T0Y0|Q6UXM0|Q8N182	Missense_Mutation	SNP	ENST00000367175.1	hg19	CCDS1448.1	.	.	.	.	.	.	.	.	.	.	T	15.96	2.988226	0.53934	.	.	ENSG00000170382	ENST00000367176;ENST00000367177;ENST00000367175	T;T;T	0.58797	0.31;0.31;0.31	5.69	5.69	0.88448	.	0.000000	0.50627	D	0.000109	T	0.74030	0.3663	M	0.68952	2.095	0.49213	D	0.999765	D	0.76494	0.999	D	0.74023	0.982	T	0.76394	-0.2975	10	0.62326	D	0.03	.	15.6141	0.76750	0.0:0.0:0.0:1.0	.	348	O75325	LRRN2_HUMAN	G	348	ENSP00000356144:S348G;ENSP00000356145:S348G;ENSP00000356143:S348G	ENSP00000356143:S348G	S	-	1	0	LRRN2	202854702	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.287000	0.72671	2.171000	0.68590	0.460000	0.39030	AGT	.	.	.	none		0.617	LRRN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089894.1	NM_006338		C	204588079	T	C	204588079	3	2	101	1	0	0	0	0	1	0	0	0	9042	1580	55	3	1103	3	LRRN2	1	204588079	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08	18429125	204588079	44662542	7	6405											
URB2	9816	hgsc.bcm.edu	37	chr1	229771856	229771856	+	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	gggcccctccacggtactctCtgcatgcctcctggagctgc	4	9	11	17	1	1	0	0	0	1	0	4	1	3	1	5	3	5	3	5	3	1	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr1:229771856C>T	ENST00000258243.2	+	4	1632	c.1496C>T	c.(1495-1497)tCt>tTt	p.S499F		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	499						aggresome (GO:0016235)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.S499F(1)		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						ACGGTACTCTCTGCATGCCTC	0.577																																					p.S499F		Atlas-SNP	.											URB2,NS,carcinoma,0,2	URB2	152	.	1	Substitution - Missense(1)	lung(1)	c.C1496T						PASS	.						113	118	116					1																	229771856		2203	4300	6503	SO:0001583	missense	9816	exon4			TACTCTCTGCATG	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.1496C>T	chr1.hg19:g.229771856C>T	ENSP00000258243:p.Ser499Phe	199.0	0.0	.		174.0	57.0	.	NM_014777	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	hg19	CCDS31052.1	.	.	.	.	.	.	.	.	.	.	C	4.911	0.169357	0.09339	.	.	ENSG00000135763	ENST00000258243	T	0.33216	1.42	5.35	0.996	0.19844	.	1.134710	0.06163	N	0.676348	T	0.23094	0.0558	L	0.34521	1.04	0.09310	N	1	B	0.33448	0.412	B	0.27887	0.084	T	0.24261	-1.0165	9	.	.	.	0.0631	11.0794	0.48051	0.0671:0.3671:0.5657:0.0	.	499	Q14146	URB2_HUMAN	F	499	ENSP00000258243:S499F	.	S	+	2	0	URB2	227838479	0.357000	0.24938	0.001000	0.08648	0.004000	0.04260	1.775000	0.38584	0.327000	0.23409	-0.153000	0.13522	TCT	.	.	.	none		0.577	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777		T	229771856	C	T	229771856	3	4	101	1	0	0	0	0	1	0	0	0	17037	913	32	2	1506	2	URB2	1	229771856	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08	25183777	229771856	19478765	8	6406											
CPSF3	51692	hgsc.bcm.edu	37	chr2	9570989	9570994	+	In_Frame_Del	DEL	TTCTGA	TTCTGA	-																															gctatttatagatggcttctTtctgattatgtcaaagttag																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	TTCTGA	TTCTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr2:9570989_9570994delTTCTGA	ENST00000238112.3	+	4	527_532	c.321_326delTTCTGA	c.(319-327)ctttctgat>ctt	p.SD108del	CPSF3_ENST00000460593.1_In_Frame_Del_p.SD71del	NM_016207.3	NP_057291.1	Q9UKF6	CPSF3_HUMAN	cleavage and polyadenylation specific factor 3, 73kDa	108					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)|ribonucleoprotein complex (GO:0030529)	5'-3' exonuclease activity (GO:0008409)|endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;2.39e-25)|all_epithelial(98;8.75e-19)|Lung NSC(108;2.38e-06)|Ovarian(717;0.0308)		all cancers(51;2.2e-40)|Epithelial(75;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(76;4.35e-21)|STAD - Stomach adenocarcinoma(1183;0.00644)		GATGGCTTCTTTCTGATTATGTCAAA	0.35																																					p.107_109del	Colon(194;1259 2048 3845 5218 19985)	Atlas-INDEL	.											.	CPSF3	63	.	0			c.320_325del						PASS	.																																			SO:0001651	inframe_deletion	51692	exon4			.	AF171877	CCDS1664.1	2p25.1	2009-01-06	2002-08-29		ENSG00000119203	ENSG00000119203			2326	protein-coding gene	gene with protein product		606029	"cleavage and polyadenylation specific factor 3, 73kD subunit"			8929409	Standard	NM_016207		Approved	CPSF-73, CPSF73, YSH1	uc002qzo.2	Q9UKF6	OTTHUMG00000090415	ENST00000238112.3:c.321_326delTTCTGA	chr2.hg19:g.9570989_9570994delTTCTGA	ENSP00000238112:p.Ser108_Asp109del	124.0	0.0	0		133.0	41.0	0.308271	NM_016207	O14769|Q53RS2|Q96F36	In_Frame_Del	DEL	ENST00000238112.3	hg19	CCDS1664.1																																																																																			.	.	.	none		0.35	CPSF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206843.1	NM_016207		-	9570994	TTCTGA	-	9570989	7	5	101	1	0	1	0	1	0	0	0	0	3828	1828	64	0	335	0	CPSF3	2	9570989	In_Frame_Del	DEL	TTCTGA	TCGA-B9-5156-01A-01D-1589-08		9570989	233628384	9	6407											
SLC3A1	6519	hgsc.bcm.edu	37	chr2	44507998	44507998	+	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	ccatttttggaacgatggaaGattttgagaatctggttgca	11	14	11	5	1	1	2	0	1	1	2	1	6	1	4	1	3	2	2	1	3	3	5			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr2:44507998G>T	ENST00000260649.6	+	2	650	c.574G>T	c.(574-576)Gat>Tat	p.D192Y	SLC3A1_ENST00000409229.3_Missense_Mutation_p.D192Y|SLC3A1_ENST00000410056.3_Missense_Mutation_p.D192Y|SLC3A1_ENST00000409741.1_Missense_Mutation_p.D192Y|SLC3A1_ENST00000409387.1_Missense_Mutation_p.D192Y	NM_000341.3	NP_000332.2	Q07837	SLC31_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 1	192					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|basic amino acid transport (GO:0015802)|carbohydrate metabolic process (GO:0005975)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|vacuolar membrane (GO:0005774)	amino acid transmembrane transporter activity (GO:0015171)|basic amino acid transmembrane transporter activity (GO:0015174)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|L-cystine transmembrane transporter activity (GO:0015184)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(3)	26		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			L-Cystine(DB00138)	AACGATGGAAGATTTTGAGAA	0.373																																					p.D192Y		Atlas-SNP	.											.	SLC3A1	62	.	0			c.G574T						PASS	.						111	107	108					2																	44507998		2203	4300	6503	SO:0001583	missense	6519	exon2			ATGGAAGATTTTG		CCDS1819.1	2p16.3	2013-07-19	2013-07-19		ENSG00000138079	ENSG00000138079		"Solute carriers"	11025	protein-coding gene	gene with protein product		104614	"solute carrier family 3 (cystine, dibasic and neutral amino acid transporters, activator of cystine, dibasic and neutral amino acid transport), member 1"			8486766, 9186880	Standard	NM_000341		Approved	CSNU1, D2H, RBAT, ATR1, NBAT	uc002ruc.4	Q07837	OTTHUMG00000128759	ENST00000260649.6:c.574G>T	chr2.hg19:g.44507998G>T	ENSP00000260649:p.Asp192Tyr	147.0	0.0	.		125.0	37.0	.	NM_000341	A8K0S1|O00658|Q15295|Q4J6B4|Q4J6B5|Q4J6B6|Q4J6B7|Q4J6B8|Q4J6B9|Q52M92|Q52M94	Missense_Mutation	SNP	ENST00000260649.6	hg19	CCDS1819.1	.	.	.	.	.	.	.	.	.	.	G	18.16	3.563097	0.65538	.	.	ENSG00000138079	ENST00000260649;ENST00000409387;ENST00000540334;ENST00000410056;ENST00000409741;ENST00000409229;ENST00000541289	D;D;D;D;D	0.99758	-6.65;-6.65;-5.38;-6.65;-6.65	4.74	3.86	0.44501	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);	0.054412	0.64402	D	0.000001	D	0.99862	0.9935	H	0.98256	4.185	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	0.81914	0.995;0.995;0.995;0.988;0.984	D	0.96726	0.9536	10	0.87932	D	0	-14.6276	13.4464	0.61144	0.0768:0.0:0.9232:0.0	.	192;192;192;192;192	Q07837;B8ZZK1;Q4J6B5;Q4J6B6;Q4J6B8	SLC31_HUMAN;.;.;.;.	Y	192;192;128;192;192;192;192	ENSP00000260649:D192Y;ENSP00000387308:D192Y;ENSP00000387337:D192Y;ENSP00000386954:D192Y;ENSP00000386620:D192Y	ENSP00000260649:D192Y	D	+	1	0	SLC3A1	44361502	1.000000	0.71417	0.989000	0.46669	0.730000	0.41778	7.381000	0.79718	1.110000	0.41699	0.655000	0.94253	GAT	.	.	.	none		0.373	SLC3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250676.1	NM_000341		T	44507998	G	T	44507998	3	4	101	1	0	0	0	0	1	0	0	0	14639	942	33	4	580	4	SLC3A1	2	44507998	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08	34937009	44507998	198691375	10	6408											
PNPT1	87178	hgsc.bcm.edu	37	chr2	55908004	55908004	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acttaccgccattaattgctAggacatcaggctcatttaca	12	12	6	11	1	2	0	2	0	0	0	2	1	2	1	2	2	3	2	2	2	4	6			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr2:55908004A>G	ENST00000447944.2	-	6	589	c.503T>C	c.(502-504)cTa>cCa	p.L168P		NM_033109.3	NP_149100.2	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	168					cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA polyadenylation (GO:0097222)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA 5'-end processing (GO:0000964)|mitochondrial RNA catabolic process (GO:0000957)|mitochondrion morphogenesis (GO:0070584)|mitotic cell cycle arrest (GO:0071850)|mRNA catabolic process (GO:0006402)|negative regulation of growth (GO:0045926)|nuclear polyadenylation-dependent mRNA catabolic process (GO:0071042)|positive regulation of miRNA catabolic process (GO:2000627)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|positive regulation of mRNA catabolic process (GO:0061014)|protein homooligomerization (GO:0051260)|protein homotrimerization (GO:0070207)|regulation of cellular respiration (GO:0043457)|regulation of cellular senescence (GO:2000772)|RNA catabolic process (GO:0006401)|RNA import into mitochondrion (GO:0035927)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA polyadenylation (GO:0043631)|rRNA import into mitochondrion (GO:0035928)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrial degradosome (GO:0045025)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	3'-5'-exoribonuclease activity (GO:0000175)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|polyribonucleotide nucleotidyltransferase activity (GO:0004654)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			ATTAATTGCTAGGACATCAGG	0.313																																					p.L168P		Atlas-SNP	.											.	PNPT1	68	.	0			c.T503C						PASS	.						57	60	59					2																	55908004		2203	4299	6502	SO:0001583	missense	87178	exon6			ATTGCTAGGACAT	BC053660	CCDS1856.1	2p15	2013-01-08			ENSG00000138035	ENSG00000138035			23166	protein-coding gene	gene with protein product	"polynucleotide phosphorylase", "3'-5' RNA exonuclease"	610316	"deafness, autosomal recessive 70"	DFNB70		12419256	Standard	NM_033109		Approved	PNPase, OLD35, old-35	uc002rzf.3	Q8TCS8	OTTHUMG00000129335	ENST00000447944.2:c.503T>C	chr2.hg19:g.55908004A>G	ENSP00000400646:p.Leu168Pro	123.0	0.0	.		78.0	23.0	.	NM_033109	Q53SU0|Q68CN1|Q7Z7D1|Q8IWX1|Q96T05|Q9BRU3|Q9BVX0	Missense_Mutation	SNP	ENST00000447944.2	hg19	CCDS1856.1	.	.	.	.	.	.	.	.	.	.	A	19.89	3.910089	0.72983	.	.	ENSG00000138035	ENST00000447944	T	0.68025	-0.3	5.24	5.24	0.73138	Ribosomal protein S5 domain 2-type fold (1);Exoribonuclease, phosphorolytic domain 1 (1);	0.000000	0.64402	D	0.000001	T	0.79470	0.4451	M	0.67625	2.065	0.80722	D	1	D	0.67145	0.996	D	0.77004	0.989	T	0.78602	-0.2140	10	0.36615	T	0.2	-15.1193	15.4288	0.75075	1.0:0.0:0.0:0.0	.	168	Q8TCS8	PNPT1_HUMAN	P	168	ENSP00000400646:L168P	ENSP00000260604:L168P	L	-	2	0	PNPT1	55761508	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	8.590000	0.90821	2.107000	0.64212	0.383000	0.25322	CTA	.	.	.	none		0.313	PNPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251481.2	NM_033109		G	55908004	A	G	55908004	3	3	101	1	0	0	0	0	1	0	0	0	12180	420	15	3	1940	3	PNPT1	2	55908004	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	11400006	55908004	187291369	11	6409											
FANCL	55120	hgsc.bcm.edu	37	chr2	58431304	58431304	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgattaaatgctctctaccAgaagcatcttctgcttttaa	11	15	6	9	0	3	2	0	1	3	1	4	2	3	2	1	0	4	3	1	0	5	5			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr2:58431304A>G	ENST00000233741.4	-	6	468	c.432T>C	c.(430-432)tcT>tcC	p.S144S	FANCL_ENST00000403295.3_Silent_p.S144S|FANCL_ENST00000540646.1_Intron|FANCL_ENST00000402135.3_Silent_p.S144S|FANCL_ENST00000403676.1_Silent_p.S27S	NM_018062.3	NP_060532.2	Q9NW38	FANCL_HUMAN	Fanconi anemia, complementation group L	144	UBC-RWD region (URD).		S -> F (in dbSNP:rs36059257).		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						GCTCTCTACCAGAAGCATCTT	0.408								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.S144S		Atlas-SNP	.											.	FANCL	35	.	0			c.T432C						PASS	.						137	133	135					2																	58431304		2203	4300	6503	SO:0001819	synonymous_variant	55120	exon6	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TCTACCAGAAGCA	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.432T>C	chr2.hg19:g.58431304A>G		197.0	0.0	.		166.0	45.0	.	NM_018062	Q6GU60	Silent	SNP	ENST00000233741.4	hg19	CCDS1860.1	.	.	.	.	.	.	.	.	.	.	A	11.14	1.550764	0.27739	.	.	ENSG00000115392	ENST00000427708	.	.	.	6.03	1.08	0.20341	.	.	.	.	.	T	0.55784	0.1942	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47045	-0.9147	4	.	.	.	-18.6795	8.6392	0.33968	0.7171:0.0:0.2829:0.0	.	.	.	.	R	144	.	.	W	-	1	0	FANCL	58284808	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.352000	0.44080	0.161000	0.19458	0.533000	0.62120	TGG	.	.	.	none		0.408	FANCL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251497.1	NM_018062		G	58431304	A	G	58431304	2	3	101	1	0	0	0	0	0	0	0	1	5677	175	7	3		3	FANCL	2	58431304	Silent	SNP	A	TCGA-B9-5156-01A-01D-1589-08	2523300	58431304	184768069	12	6410											
THNSL2	55258	hgsc.bcm.edu	37	chr2	88482283	88482283	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcagtgaaccgcaatgacAtcatccacaggactgtccag	12	7	10	12	1	1	2	1	2	0	0	3	3	3	3	3	2	1	2	3	2	2	0			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr2:88482283A>G	ENST00000324166.5	+	5	2559	c.868A>G	c.(868-870)Atc>Gtc	p.I290V	THNSL2_ENST00000343544.4_Missense_Mutation_p.I290V|THNSL2_ENST00000402102.1_Missense_Mutation_p.I290V|THNSL2_ENST00000449349.1_Intron|THNSL2_ENST00000377254.3_Missense_Mutation_p.I290V|THNSL2_ENST00000496844.1_3'UTR|THNSL2_ENST00000358591.2_Missense_Mutation_p.I290V	NM_018271.4	NP_060741.3	Q86YJ6	THNS2_HUMAN	threonine synthase-like 2 (S. cerevisiae)	290					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						CCGCAATGACATCATCCACAG	0.512																																					p.I290V		Atlas-SNP	.											.	THNSL2	66	.	0			c.A868G						PASS	.						93	89	90					2																	88482283		2203	4300	6503	SO:0001583	missense	55258	exon5			AATGACATCATCC		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.868A>G	chr2.hg19:g.88482283A>G	ENSP00000327323:p.Ile290Val	103.0	0.0	.		88.0	27.0	.	NM_018271	B3KTB1|B5MDX8|B7WPF8|D9ZZB8|Q6P2M7|Q6PI27|Q9NV54	Missense_Mutation	SNP	ENST00000324166.5	hg19	CCDS2002.2	.	.	.	.	.	.	.	.	.	.	A	27.0	4.789980	0.90367	.	.	ENSG00000144115	ENST00000358591;ENST00000377254;ENST00000402102;ENST00000544063;ENST00000343544;ENST00000324166	T;T;T;T;T	0.11385	2.78;2.78;2.78;2.78;2.78	5.81	5.81	0.92471	Threonine synthase (1);Pyridoxal phosphate-dependent enzyme, beta subunit (2);	0.000000	0.85682	D	0.000000	T	0.20495	0.0493	L	0.37561	1.115	0.49389	D	0.999788	D;D;D	0.62365	0.991;0.987;0.979	P;P;P	0.59703	0.844;0.862;0.784	T	0.00701	-1.1603	10	0.38643	T	0.18	.	15.3313	0.74215	1.0:0.0:0.0:0.0	.	132;290;290	A8K0C1;Q86YJ6;Q86YJ6-2	.;THNS2_HUMAN;.	V	290;290;290;132;290;290	ENSP00000351402:I290V;ENSP00000366464:I290V;ENSP00000384475:I290V;ENSP00000339563:I290V;ENSP00000327323:I290V	ENSP00000327323:I290V	I	+	1	0	THNSL2	88263398	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.322000	0.90000	2.219000	0.72066	0.533000	0.62120	ATC	.	.	.	none		0.512	THNSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252662.1	NM_018271		G	88482283	A	G	88482283	3	3	101	1	0	0	0	0	1	0	0	0	15875	217	8	3	886	3	THNSL2	2	88482283	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	30050979	88482283	154717090	13	6411											
TRIM43	129868	hgsc.bcm.edu	37	chr2	96260855	96260855	+	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	agattcaagaaaatcagagaAatctatatgaggagggaaga	20	7	11	3	0	3	5	2	1	1	4	3	8	3	7	0	2	0	0	0	2	7	3			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr2:96260855A>T	ENST00000272395.2	+	3	605	c.469A>T	c.(469-471)Aat>Tat	p.N157Y		NM_001164464.1|NM_138800.1	NP_001157936.1|NP_620155.1	Q96BQ3	TRI43_HUMAN	tripartite motif containing 43	157						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(1)|large_intestine(3)|lung(7)|ovary(1)	12						AAATCAGAGAAATCTATATGA	0.403																																					p.N157Y		Atlas-SNP	.											.	TRIM43	51	.	0			c.A469T						PASS	.						58	56	56					2																	96260855		2203	4299	6502	SO:0001583	missense	129868	exon3			CAGAGAAATCTAT	BK000505	CCDS2015.1	2q11	2014-02-17	2011-01-25		ENSG00000144015	ENSG00000144015		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19015	protein-coding gene	gene with protein product			"tripartite motif-containing 43"				Standard	NM_138800		Approved	TRIM43A	uc002suv.3	Q96BQ3	OTTHUMG00000130401	ENST00000272395.2:c.469A>T	chr2.hg19:g.96260855A>T	ENSP00000272395:p.Asn157Tyr	66.0	0.0	.		46.0	14.0	.	NM_138800	Q53TJ7	Missense_Mutation	SNP	ENST00000272395.2	hg19	CCDS2015.1	.	.	.	.	.	.	.	.	.	.	.	11.90	1.776990	0.31411	.	.	ENSG00000144015	ENST00000272395	T	0.06608	3.28	0.911	0.911	0.19343	.	.	.	.	.	T	0.12178	0.0296	L	0.59436	1.845	0.09310	N	1	D	0.89917	1.0	D	0.77557	0.99	T	0.17137	-1.0379	9	0.02654	T	1	-3.9711	4.1749	0.10348	1.0:0.0:0.0:0.0	.	157	Q96BQ3	TRI43_HUMAN	Y	157	ENSP00000272395:N157Y	ENSP00000272395:N157Y	N	+	1	0	TRIM43	95624582	0.197000	0.23362	0.060000	0.19600	0.268000	0.26511	0.953000	0.29162	0.680000	0.31366	0.308000	0.20428	AAT	.	.	.	none		0.403	TRIM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252784.1	NM_138800		T	96260855	A	T	96260855	3	4	101	1	0	0	0	0	1	0	0	0	16530	14	1	5	475	5	TRIM43	2	96260855	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	7778572	96260855	146938518	14	6412											
DARS	1615	hgsc.bcm.edu	37	chr2	136673870	136673871	+	Frame_Shift_Ins	INS	-	-	A																															cttcacaatattctagtcttINSagagttggctccaaaaattt																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr2:136673870_136673871insA	ENST00000264161.4	-	11	1246_1247	c.1031_1032insT	c.(1030-1032)ctafs	p.L344fs	DARS_ENST00000537273.1_Frame_Shift_Ins_p.L244fs	NM_001349.2	NP_001340.2	P14868	SYDC_HUMAN	aspartyl-tRNA synthetase	344					aspartyl-tRNA aminoacylation (GO:0006422)|gene expression (GO:0010467)|protein complex assembly (GO:0006461)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacylase activity (GO:0004046)|aspartate-tRNA ligase activity (GO:0004815)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(2)	15				BRCA - Breast invasive adenocarcinoma(221;0.168)	L-Aspartic Acid(DB00128)	ATTCTAGTCTTAGAGTTGGCTC	0.366																																					p.L344fs		Atlas-INDEL	.											.	DARS	44	.	0			c.1032_1033insT						PASS	.																																			SO:0001589	frameshift_variant	1615	exon11			.	J05032	CCDS2180.1	2q21.3	2011-07-01			ENSG00000115866	ENSG00000115866	6.1.1.12	"Aminoacyl tRNA synthetases / Class II"	2678	protein-coding gene	gene with protein product	"aspartate tRNA ligase 1, cytoplasmic"	603084				2674137	Standard	NM_001349		Approved		uc002tux.1	P14868	OTTHUMG00000131741	ENST00000264161.4:c.1032dupT	chr2.hg19:g.136673871_136673871dupA	ENSP00000264161:p.Leu344fs	149.0	0.0	0		153.0	48.0	0.313726	NM_001349	A8K3J2|D3DP77|Q2TNI3|Q32Q69|Q53HV4|Q53YC5|Q68CR9|Q9BW52	Frame_Shift_Ins	INS	ENST00000264161.4	hg19	CCDS2180.1																																																																																			.	.	.	none		0.366	DARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254660.5	NM_001349		A	136673871	-	A	136673870	7	5	101	1	0	1	1	0	0	0	0	0	4243	1741	61	0	497	0	DARS	2	136673870	Frame_Shift_Ins	INS	-	TCGA-B9-5156-01A-01D-1589-08	40413015	136673870	106525503	15	6413											
ZEB2	9839	hgsc.bcm.edu	37	chr2	145156027	145156027	+	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	ctggtctggactggtggcatGaaagtagcagggggaaatgc	10	8	17	6	0	1	1	0	1	1	0	1	3	1	3	0	6	2	3	0	6	3	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr2:145156027G>A	ENST00000558170.2	-	8	3911	c.2727C>T	c.(2725-2727)ttC>ttT	p.F909F	ZEB2_ENST00000539609.3_Silent_p.F885F|ZEB2_ENST00000409487.3_Silent_p.F909F|ZEB2_ENST00000303660.4_Silent_p.F909F	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2	909					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)		CTGGTGGCATGAAAGTAGCAG	0.498																																					p.F909F	Melanoma(33;1235 1264 5755 16332)	Atlas-SNP	.											.	ZEB2	218	.	0			c.C2727T						PASS	.						176	170	172					2																	145156027		2203	4300	6503	SO:0001819	synonymous_variant	9839	exon8			TGGCATGAAAGTA	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.2727C>T	chr2.hg19:g.145156027G>A		240.0	0.0	.		172.0	60.0	.	NM_014795	A0JP09|B7Z2P2|F5H814|Q9UED1	Silent	SNP	ENST00000558170.2	hg19	CCDS2186.1																																																																																			.	.	.	none		0.498	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	NM_014795		A	145156027	G	A	145156027	2	1	101	1	0	0	0	0	0	0	0	1	17636	1281	45	2		2	ZEB2	2	145156027	Silent	SNP	G	TCGA-B9-5156-01A-01D-1589-08	8482157	145156027	98043346	16	6414											
CD302	9936	hgsc.bcm.edu	37	chr2	160637446	160637446	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catctgggcctttccattgcTttttcaaagtatccagtata	9	16	6	10	0	2	0	1	0	1	0	4	0	4	0	3	1	1	3	3	1	4	7			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr2:160637446T>C	ENST00000259053.4	-	3	285	c.242A>G	c.(241-243)aAg>aGg	p.K81R	CD302_ENST00000429078.2_Missense_Mutation_p.K81R|CD302_ENST00000480212.1_5'UTR|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.K1666R|LY75_ENST00000554112.1_Missense_Mutation_p.K1722R|LY75_ENST00000553424.1_Missense_Mutation_p.K1666R|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.K1722R	NM_001198764.1|NM_014880.4	NP_001185693.1|NP_055695.2	Q8IX05	CD302_HUMAN	CD302 molecule	81	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				phagocytosis (GO:0006909)	cell cortex (GO:0005938)|filopodium (GO:0030175)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|prostate(1)|skin(1)	11						TTTCCATTGCTTTTTCAAAGT	0.338																																					p.K1722R		Atlas-SNP	.											.	.	.	.	0			c.A5165G						PASS	.						153	141	145					2																	160637446		2203	4300	6503	SO:0001583	missense	100526664	exon36			CATTGCTTTTTCA	AY314007	CCDS33308.1, CCDS56139.1, CCDS74595.1	2q24.2	2011-08-30	2006-03-28		ENSG00000241399	ENSG00000241399		"CD molecules", "C-type lectin domain containing"	30843	protein-coding gene	gene with protein product	"C-type lectin domain family 13, member A"	612246	"CD302 antigen"			7584026, 7584028	Standard	NM_014880		Approved	DCL-1, KIAA0022, BIMLEC, CLEC13A		Q8IX05	OTTHUMG00000154080	ENST00000259053.4:c.242A>G	chr2.hg19:g.160637446T>C	ENSP00000259053:p.Lys81Arg	116.0	0.0	.		103.0	27.0	.	NM_001198759	A8K5G4|B4E2T9|Q15009	Missense_Mutation	SNP	ENST00000259053.4	hg19	CCDS33308.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.151609	0.78001	.	.	ENSG00000241399;ENSG00000241399;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000259053;ENST00000429078;ENST00000554112;ENST00000553424;ENST00000504764;ENST00000505052	T;T;T;T;T;T	0.08370	3.1;3.1;3.1;3.1;3.1;3.1	5.21	3.98	0.46160	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.222293	0.36854	N	0.002374	T	0.14874	0.0359	L	0.51422	1.61	0.21445	N	0.99969	P;B;P;D	0.58620	0.901;0.386;0.642;0.983	P;B;B;P	0.57324	0.702;0.178;0.178;0.818	T	0.09100	-1.0690	10	0.19590	T	0.45	-28.4385	10.1369	0.42712	0.0:0.0:0.3327:0.6673	.	81;1666;1722;81	B4E2T9;O60449-3;O60449-2;Q8IX05	.;.;.;CD302_HUMAN	R	81;81;1722;1666;1722;1666	ENSP00000259053:K81R;ENSP00000394301:K81R;ENSP00000451511:K1722R;ENSP00000451446:K1666R;ENSP00000423463:K1722R;ENSP00000421035:K1666R	ENSP00000259053:K81R	K	-	2	0	LY75;CD302;LY75-CD302	160345692	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.111000	0.31159	2.097000	0.63578	0.533000	0.62120	AAG	.	.	.	none		0.338	CD302-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333760.1	NM_014880		C	160637446	T	C	160637446	3	2	101	1	0	0	0	0	1	0	0	0	3005	1609	56	3	472	3	CD302	2	160637446	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08	15481419	160637446	82561927	17	6415											
UBR3	130507	hgsc.bcm.edu	37	chr2	170843265	170843265	+	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	gtggcccctcctctgaagatCgacctactggattagttgta	8	12	10	11	1	1	2	0	1	1	1	3	4	2	3	4	2	1	2	4	2	4	4			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr2:170843265C>G	ENST00000272793.5	+	25	3795	c.3745C>G	c.(3745-3747)Cga>Gga	p.R1249G	UBR3_ENST00000392631.1_Missense_Mutation_p.R70G|UBR3_ENST00000418381.1_Missense_Mutation_p.R1249G			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	1249					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						CTCTGAAGATCGACCTACTGG	0.408																																					p.R1249G		Atlas-SNP	.											UBR3_ENST00000272793,NS,carcinoma,0,2	UBR3	182	.	0			c.C3745G						PASS	.						109	108	108					2																	170843265		2203	4300	6503	SO:0001583	missense	130507	exon25			GAAGATCGACCTA	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.3745C>G	chr2.hg19:g.170843265C>G	ENSP00000272793:p.Arg1249Gly	135.0	0.0	.		103.0	29.0	.	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Missense_Mutation	SNP	ENST00000272793.5	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.13|17.13	3.312099|3.312099	0.60414|0.60414	.|.	.|.	ENSG00000144357|ENSG00000144357	ENST00000392632|ENST00000272793;ENST00000442603;ENST00000418381;ENST00000392631	.|T;T;T	.|0.57907	.|0.37;0.37;0.89	5.27|5.27	3.38|3.38	0.38709|0.38709	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.67748|0.67748	0.2926|0.2926	M|M	0.71581|0.71581	2.175|2.175	0.32414|0.32414	N|N	0.550296|0.550296	.|D;D;D	.|0.67145	.|0.993;0.996;0.987	.|D;D;D	.|0.79108	.|0.982;0.992;0.953	T|T	0.71481|0.71481	-0.4580|-0.4580	5|10	.|0.20519	.|T	.|0.43	.|.	13.7422|13.7422	0.62855|0.62855	0.4588:0.5412:0.0:0.0|0.4588:0.5412:0.0:0.0	.|.	.|1249;70;1249	.|Q6ZT12;Q6ZT12-2;E7EVK3	.|UBR3_HUMAN;.;.	M|G	306|1249;1249;1249;70	.|ENSP00000272793:R1249G;ENSP00000396068:R1249G;ENSP00000376408:R70G	.|ENSP00000272793:R1249G	I|R	+|+	3|1	3|2	UBR3|UBR3	170551511|170551511	0.662000|0.662000	0.27439|0.27439	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	1.024000|1.024000	0.30077|0.30077	0.530000|0.530000	0.28619|0.28619	0.585000|0.585000	0.79938|0.79938	ATC|CGA	.	.	.	none		0.408	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070		G	170843265	C	G	170843265	3	3	101	1	0	0	0	0	1	0	0	0	16915	876	31	4	3843	4	UBR3	2	170843265	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08	10205819	170843265	72356108	18	6416											
EXOSC7	23016	hgsc.bcm.edu	37	chr3	45038724	45038724	+	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	gtcctcgggagcactgctggGttctctatgtggatgtgctg	4	13	15	9	1	1	0	0	0	1	0	4	2	2	2	1	3	3	4	1	3	1	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr3:45038724G>C	ENST00000265564.7	+	4	448	c.400G>C	c.(400-402)Gtt>Ctt	p.V134L	EXOSC7_ENST00000461361.1_3'UTR	NM_015004.3	NP_055819.2	Q15024	EXOS7_HUMAN	exosome component 7	134					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 catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|RNA binding (GO:0003723)			endometrium(3)|large_intestine(1)|lung(3)	7				BRCA - Breast invasive adenocarcinoma(193;0.00911)|KIRC - Kidney renal clear cell carcinoma(197;0.0509)|Kidney(197;0.064)		GCACTGCTGGGTTCTCTATGT	0.468																																					p.V134L		Atlas-SNP	.											.	EXOSC7	19	.	0			c.G400C						PASS	.						128	118	121					3																	45038724		2203	4300	6503	SO:0001583	missense	23016	exon4			TGCTGGGTTCTCT	BC012831	CCDS2725.1	3p21.32	2010-05-07			ENSG00000075914	ENSG00000075914	3.1.13.-		28112	protein-coding gene	gene with protein product		606488				11719186, 11812149	Standard	NR_023353		Approved	hRrp42p, Rrp42p, RRP42, EAP1, KIAA0116, p8	uc003coi.2	Q15024	OTTHUMG00000133095	ENST00000265564.7:c.400G>C	chr3.hg19:g.45038724G>C	ENSP00000265564:p.Val134Leu	85.0	0.0	.		101.0	44.0	.	NM_015004	Q96E72	Missense_Mutation	SNP	ENST00000265564.7	hg19	CCDS2725.1	.	.	.	.	.	.	.	.	.	.	G	14.56	2.573110	0.45902	.	.	ENSG00000075914	ENST00000265564	T	0.62232	0.04	5.71	-7.06	0.01568	Ribosomal protein S5 domain 2-type fold (1);Exoribonuclease, phosphorolytic domain 1 (1);	0.510215	0.21639	N	0.071362	T	0.55940	0.1952	M	0.67625	2.065	0.49130	D	0.999757	B;B	0.09022	0.002;0.002	B;B	0.16289	0.015;0.015	T	0.26643	-1.0097	10	0.30078	T	0.28	-1.5027	19.6631	0.95882	0.2416:0.0:0.7584:0.0	.	134;134	B2RDZ9;Q15024	.;EXOS7_HUMAN	L	134	ENSP00000265564:V134L	ENSP00000265564:V134L	V	+	1	0	EXOSC7	45013728	0.981000	0.34729	0.040000	0.18447	0.953000	0.61014	0.073000	0.14640	-1.400000	0.02061	-0.224000	0.12420	GTT	.	.	.	none		0.468	EXOSC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256754.2	NM_015004		C	45038724	G	C	45038724	3	2	101	1	0	0	0	0	1	0	0	0	5321	1261	44	4	414	4	EXOSC7	3	45038724	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08		45038724	152983706	19	6417											
BOC	91653	hgsc.bcm.edu	37	chr3	112991328	112991328	+	Missense_Mutation	SNP	A	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	tcatcgtcaccaaaggccagAgtctcattctggagtgtgtg	9	11	11	10	1	4	1	3	0	2	1	6	2	4	2	2	2	0	0	2	2	1	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr3:112991328A>C	ENST00000495514.1	+	7	1443	c.739A>C	c.(739-741)Agt>Cgt	p.S247R	BOC_ENST00000355385.3_Missense_Mutation_p.S247R|BOC_ENST00000273395.4_Missense_Mutation_p.S247R			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	247	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			CAAAGGCCAGAGTCTCATTCT	0.617																																					p.S247R		Atlas-SNP	.											.	BOC	139	.	0			c.A739C						PASS	.						164	157	159					3																	112991328		2203	4300	6503	SO:0001583	missense	91653	exon7			GGCCAGAGTCTCA	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.739A>C	chr3.hg19:g.112991328A>C	ENSP00000418663:p.Ser247Arg	261.0	0.0	.		318.0	73.0	.	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Missense_Mutation	SNP	ENST00000495514.1	hg19	CCDS2971.1	.	.	.	.	.	.	.	.	.	.	A	16.39	3.110475	0.56398	.	.	ENSG00000144857	ENST00000495514;ENST00000273395;ENST00000355385	T;T;T	0.69685	-0.42;-0.42;-0.42	5.93	5.93	0.95920	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.043438	0.85682	D	0.000000	T	0.60932	0.2307	L	0.41573	1.285	0.50313	D	0.999862	B;B	0.16603	0.014;0.018	B;B	0.21360	0.033;0.034	T	0.56275	-0.8006	10	0.44086	T	0.13	.	16.3797	0.83452	1.0:0.0:0.0:0.0	.	247;247	Q9BWV1-3;Q9BWV1	.;BOC_HUMAN	R	247	ENSP00000418663:S247R;ENSP00000273395:S247R;ENSP00000347546:S247R	ENSP00000273395:S247R	S	+	1	0	BOC	114474018	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.474000	0.73578	2.271000	0.75665	0.533000	0.62120	AGT	.	.	.	none		0.617	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254		C	112991328	A	C	112991328	3	2	101	1	0	0	0	0	1	0	0	0	1481	304	11	5	757	5	BOC	3	112991328	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	67952604	112991328	85031102	20	6418											
RPN1	6184	hgsc.bcm.edu	37	chr3	128348859	128348859	+	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	tgtaatgggtcttccacccgCcaaagagagggaagcgaggc	11	6	14	10	2	1	1	0	0	1	1	2	4	2	2	3	3	1	1	3	3	3	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr3:128348859C>T	ENST00000296255.3	-	5	1019	c.971G>A	c.(970-972)gGc>gAc	p.G324D	RPN1_ENST00000490166.1_5'Flank|RPN1_ENST00000497289.1_Missense_Mutation_p.G152D	NM_002950.3	NP_002941.1	P04843	RPN1_HUMAN	ribophorin I	324					cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|gene expression (GO:0010467)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)|rough endoplasmic reticulum (GO:0005791)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)|poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(2)|stomach(2)	13				GBM - Glioblastoma multiforme(114;0.189)		CTTCCACCCGCCAAAGAGAGG	0.458			T	EVI1	AML																																p.G324D		Atlas-SNP	.		Dom	yes		3	3q21.3-q25.2	6184	ribophorin I		L	.	RPN1	39	.	0			c.G971A						PASS	.						76	74	74					3																	128348859		2203	4300	6503	SO:0001583	missense	6184	exon5			CACCCGCCAAAGA		CCDS3051.1	3q21.3	2013-03-06			ENSG00000163902	ENSG00000163902			10381	protein-coding gene	gene with protein product	"oligosaccharyltransferase 1 homolog (S. cerevisiae)", "oligosaccharyltransferase complex subunit (non-catalytic)"	180470					Standard	NM_002950		Approved	OST1	uc003ekr.1	P04843	OTTHUMG00000159691	ENST00000296255.3:c.971G>A	chr3.hg19:g.128348859C>T	ENSP00000296255:p.Gly324Asp	68.0	0.0	.		87.0	41.0	.	NM_002950	B2R5Z0|D3DNB6|Q68DT1	Missense_Mutation	SNP	ENST00000296255.3	hg19	CCDS3051.1	.	.	.	.	.	.	.	.	.	.	C	32	5.165154	0.94768	.	.	ENSG00000163902	ENST00000296255;ENST00000497289;ENST00000537139;ENST00000545956	.	.	.	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	D	0.87051	0.6081	M	0.93678	3.445	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90352	0.4367	9	0.87932	D	0	-19.9225	19.0082	0.92861	0.0:1.0:0.0:0.0	.	324	P04843	RPN1_HUMAN	D	324;152;95;298	.	ENSP00000296255:G324D	G	-	2	0	RPN1	129831549	1.000000	0.71417	0.920000	0.36463	0.991000	0.79684	7.380000	0.79704	2.487000	0.83934	0.591000	0.81541	GGC	.	.	.	none		0.458	RPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356934.2	NM_002950		T	128348859	C	T	128348859	3	4	101	1	0	0	0	0	1	0	0	0	13620	739	26	2	876	2	RPN1	3	128348859	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08	15357531	128348859	69673571	21	6419											
ATR	545	hgsc.bcm.edu	37	chr3	142268491	142268491	+	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	gcttgctttggcagcaagatCaggtagtagaacttgtaatg	11	12	12	6	0	1	2	1	0	0	2	1	2	1	2	0	2	3	7	0	2	5	6			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr3:142268491C>A	ENST00000350721.4	-	15	3122	c.3001G>T	c.(3001-3003)Gat>Tat	p.D1001Y	ATR_ENST00000383101.3_Missense_Mutation_p.D937Y	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1001					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						GCAGCAAGATCAGGTAGTAGA	0.348								Other conserved DNA damage response genes																													p.D1001Y		Atlas-SNP	.											.	ATR	285	.	0			c.G3001T						PASS	.						50	51	51					3																	142268491		2203	4299	6502	SO:0001583	missense	545	exon15			CAAGATCAGGTAG	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.3001G>T	chr3.hg19:g.142268491C>A	ENSP00000343741:p.Asp1001Tyr	64.0	0.0	.		82.0	37.0	.	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	hg19	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	C	4.829	0.154136	0.09236	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.63417	-0.04;-0.04	5.59	5.59	0.84812	Armadillo-like helical (1);Armadillo-type fold (1);	0.062472	0.64402	D	0.000004	T	0.34919	0.0914	N	0.02539	-0.55	0.43453	D	0.995646	B	0.06786	0.001	B	0.08055	0.003	T	0.41466	-0.9507	10	0.02654	T	1	-18.3072	17.7702	0.88489	0.0:1.0:0.0:0.0	.	1001	Q13535	ATR_HUMAN	Y	1001;937	ENSP00000343741:D1001Y;ENSP00000372581:D937Y	ENSP00000343741:D1001Y	D	-	1	0	ATR	143751181	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.835000	0.69368	2.635000	0.89317	0.655000	0.94253	GAT	.	.	.	none		0.348	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		A	142268491	C	A	142268491	3	1	101	1	0	0	0	0	1	0	0	0	1204	826	29	4	5065	4	ATR	3	142268491	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08	13919632	142268491	55753939	22	6420											
SH3TC1	54436	hgsc.bcm.edu	37	chr4	8229750	8229752	+	In_Frame_Del	DEL	ACC	ACC	-																															ggcaagcgctggcctccctgAccccgggcacaggccaggcg																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	ACC	ACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr4:8229750_8229752delACC	ENST00000245105.3	+	12	2396_2398	c.2329_2331delACC	c.(2329-2331)accdel	p.T777del	SH3TC1_ENST00000539824.1_In_Frame_Del_p.T701del	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	777										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						GGCCTCCCTGACCCCGGGCACAG	0.685																																					p.776_777del	NSCLC(145;2298 2623 35616 37297)	Atlas-INDEL	.											.	SH3TC1	105	.	0			c.2328_2330del						PASS	.																																			SO:0001651	inframe_deletion	54436	exon12			.	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.2329_2331delACC	chr4.hg19:g.8229750_8229752delACC	ENSP00000245105:p.Thr777del	43.0	0.0	0		49.0	12.0	0.244898	NM_018986	Q4W5G5	In_Frame_Del	DEL	ENST00000245105.3	hg19	CCDS3399.1																																																																																			.	.	.	none		0.685	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986		-	8229752	ACC	-	8229750	7	5	101	1	0	1	0	1	0	0	0	0	14274	275	10	0	2371	0	SH3TC1	4	8229750	In_Frame_Del	DEL	ACC	TCGA-B9-5156-01A-01D-1589-08		8229750	182924526	23	6421											
FBXL5	26234	hgsc.bcm.edu	37	chr4	15640266	15640266	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgcaatcactttctttttaaTatccttaagctcttcatagg	10	18	4	9	0	4	0	2	0	2	0	5	0	5	0	1	1	2	2	1	1	5	8			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr4:15640266T>C	ENST00000341285.3	-	4	572	c.448A>G	c.(448-450)Att>Gtt	p.I150V	FBXL5_ENST00000382358.4_Missense_Mutation_p.I24V|FBXL5_ENST00000412094.2_Missense_Mutation_p.I133V	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	150	Hemerythrin-like.				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						TTCTTTTTAATATCCTTAAGC	0.368																																					p.I150V		Atlas-SNP	.											.	FBXL5	52	.	0			c.A448G						PASS	.						76	67	70					4																	15640266		2201	4299	6500	SO:0001583	missense	26234	exon4			TTTTAATATCCTT	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.448A>G	chr4.hg19:g.15640266T>C	ENSP00000344866:p.Ile150Val	73.0	0.0	.		65.0	21.0	.	NM_001193534	A8MSK4|B4DIB5|Q4W5A8|Q8NHP3|Q9NXN2|Q9P0I0|Q9P0X5|Q9UJT7|Q9UKC8	Missense_Mutation	SNP	ENST00000341285.3	hg19	CCDS3415.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	31|31	5.081114|5.081114	0.94050|0.94050	.|.	.|.	ENSG00000118564|ENSG00000118564	ENST00000341285;ENST00000412094;ENST00000382358;ENST00000512066;ENST00000503196;ENST00000509314|ENST00000513163	T;T;T|.	0.38722|.	1.18;1.17;1.12|.	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.59169|0.59169	0.2174|0.2174	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	P;P|.	0.51791|.	0.948;0.913|.	D;P|.	0.67103|.	0.949;0.891|.	T|T	0.55431|0.55431	-0.8142|-0.8142	10|5	0.72032|.	D|.	0.01|.	-22.925|-22.925	16.1306|16.1306	0.81436|0.81436	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	133;150|.	Q9UKA1-2;Q9UKA1|.	.;FBXL5_HUMAN|.	V|C	150;133;24;112;95;95|70	ENSP00000344866:I150V;ENSP00000408679:I133V;ENSP00000371795:I24V|.	ENSP00000344866:I150V|.	I|Y	-|-	1|2	0|0	FBXL5|FBXL5	15249364|15249364	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	8.034000|8.034000	0.88864|0.88864	2.209000|2.209000	0.71365|0.71365	0.528000|0.528000	0.53228|0.53228	ATT|TAT	.	.	.	none		0.368	FBXL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214235.2			C	15640266	T	C	15640266	3	2	101	1	0	0	0	0	1	0	0	0	5729	1406	49	3	1659	3	FBXL5	4	15640266	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08	7410516	15640266	175514010	24	6422											
GC	2638	hgsc.bcm.edu	37	chr4	72620174	72620174	+	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	ttctgaataatctgcacataGttcttgtcccttgtcaatga	10	16	6	9	0	4	2	1	2	3	0	5	2	5	2	1	0	1	2	1	0	4	6			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr4:72620174G>A	ENST00000273951.8	-	10	1559	c.1216C>T	c.(1216-1218)Cta>Tta	p.L406L	GC_ENST00000503472.1_5'UTR|GC_ENST00000504199.1_Silent_p.L425L|GC_ENST00000513476.1_Silent_p.L406L	NM_000583.3|NM_001204306.1	NP_000574.2|NP_001191235.1	P02774	VTDB_HUMAN	group-specific component (vitamin D binding protein)	406	Albumin 3. {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)	TCTGCACATAGTTCTTGTCCC	0.308																																					p.L425L		Atlas-SNP	.											.	GC	132	.	0			c.C1273T						PASS	.						77	76	76					4																	72620174		2203	4300	6503	SO:0001819	synonymous_variant	2638	exon11			CACATAGTTCTTG	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.1216C>T	chr4.hg19:g.72620174G>A		45.0	0.0	.		54.0	16.0	.	NM_001204307	B4DPP2|D6RAK8|Q16309|Q16310|Q53F31|Q6GTG1	Silent	SNP	ENST00000273951.8	hg19	CCDS3550.1																																																																																			.	.	.	none		0.308	GC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252167.2			A	72620174	G	A	72620174	2	1	101	1	0	0	0	0	0	0	0	1	6289	1020	36	2		2	GC	4	72620174	Silent	SNP	G	TCGA-B9-5156-01A-01D-1589-08	56979908	72620174	118534102	25	6423											
CENPE	1062	hgsc.bcm.edu	37	chr4	104041471	104041471	+	Frame_Shift_Del	DEL	T	T	-																															ctttagcttcatgcagtgaaTtttccagctctcgaattttc																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr4:104041471delT	ENST00000265148.3	-	44	7252	c.7163delA	c.(7162-7164)aatfs	p.N2388fs	CENPE_ENST00000380026.3_Frame_Shift_Del_p.N2267fs	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	2388	Kinetochore-binding domain.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)			NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		ATGCAGTGAATTTTCCAGCTC	0.333																																					p.N2388fs		Atlas-INDEL	.											.	CENPE	253	.	0			c.7164delT						PASS	.						106	90	96					4																	104041471		2202	4296	6498	SO:0001589	frameshift_variant	1062	exon44			.	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.7163delA	chr4.hg19:g.104041471delT	ENSP00000265148:p.Asn2388fs	68.0	0.0	0		62.0	18.0	0.290323	NM_001813	A6NKY9|A8K2U7|Q4LE75	Frame_Shift_Del	DEL	ENST00000265148.3	hg19	CCDS34042.1																																																																																			.	.	.	none		0.333	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				-	104041471	T	-	104041471	7	5	101	1	0	1	0	1	0	0	0	0	3232	1493	52	0	966	0	CENPE	4	104041471	Frame_Shift_Del	DEL	T	TCGA-B9-5156-01A-01D-1589-08	31421297	104041471	87112805	26	6424											
LRBA	987	hgsc.bcm.edu	37	chr4	151827133	151827134	+	Frame_Shift_Ins	INS	-	-	T																															actgctctgctaacatgagaINStttggaagactgcaaaaaaa																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr4:151827133_151827134insT	ENST00000357115.3	-	13	1854_1855	c.1611_1612insA	c.(1609-1614)aaatctfs	p.S538fs	LRBA_ENST00000535741.1_Frame_Shift_Ins_p.S538fs|LRBA_ENST00000510413.1_Frame_Shift_Ins_p.S538fs|LRBA_ENST00000507224.1_Frame_Shift_Ins_p.S538fs	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	538						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)					CTAACATGAGATTTGGAAGACT	0.396																																					p.S538fs		Atlas-INDEL	.											.	LRBA	253	.	0			c.1612_1613insA						PASS	.																																			SO:0001589	frameshift_variant	987	exon13			.	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.1612dupA	chr4.hg19:g.151827136_151827136dupT	ENSP00000349629:p.Ser538fs	78.0	0.0	0		67.0	27.0	0.402985	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Frame_Shift_Ins	INS	ENST00000357115.3	hg19	CCDS3773.1																																																																																			.	.	.	none		0.396	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			T	151827134	-	T	151827133	7	5	101	1	0	1	1	0	0	0	0	0	8938	333	12	0	7163	0	LRBA	4	151827133	Frame_Shift_Ins	INS	-	TCGA-B9-5156-01A-01D-1589-08	47785662	151827133	39327143	27	6425											
TERT	7015	hgsc.bcm.edu	37	chr5	1282605	1282605	+	Missense_Mutation	SNP	T	T	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	gtagaaaaagagcctgttctTttgaaacgtggtctccgtga	11	12	11	7	2	2	4	0	2	2	2	3	4	2	4	2	1	2	2	2	1	4	4			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr5:1282605T>G	ENST00000310581.5	-	3	1765	c.1708A>C	c.(1708-1710)Aag>Cag	p.K570Q	TERT_ENST00000508104.2_Missense_Mutation_p.K570Q|TERT_ENST00000334602.6_Missense_Mutation_p.K570Q|TERT_ENST00000296820.5_Missense_Mutation_p.K570Q	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	telomerase reverse transcriptase	570			K -> N (in AA susceptibility; abolishes telomerase catalytic activity but no effect on binding to TERC). {ECO:0000269|PubMed:16990594, ECO:0000269|PubMed:19760749}.		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)	AGCCTGTTCTTTTGAAACGTG	0.517									TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis																												p.K570Q		Atlas-SNP	.											.	TERT	2594	.	0			c.A1708C						PASS	.						119	114	116					5																	1282605		2203	4300	6503	SO:0001583	missense	7015	exon3	Familial Cancer Database	;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	TGTTCTTTTGAAA	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.1708A>C	chr5.hg19:g.1282605T>G	ENSP00000309572:p.Lys570Gln	79.0	0.0	.		51.0	13.0	.	NM_001193376	O14783|Q2XS35|Q8N6C3|Q8NG38|Q8NG46	Missense_Mutation	SNP	ENST00000310581.5	hg19	CCDS3861.2	.	.	.	.	.	.	.	.	.	.	T	15.08	2.727919	0.48833	.	.	ENSG00000164362	ENST00000310581;ENST00000296820;ENST00000334602;ENST00000508104	D;D;D;D	0.86497	-2.13;-2.13;-2.13;-2.13	4.64	3.42	0.39159	Telomerase ribonucleoprotein complex - RNA-binding domain (2);	0.049349	0.85682	D	0.000000	D	0.93969	0.8069	M	0.92026	3.265	0.49213	D	0.999767	D;D;D	0.89917	0.998;1.0;0.999	D;D;D	0.97110	0.952;1.0;0.972	D	0.93578	0.6910	10	0.72032	D	0.01	-0.3505	11.0502	0.47882	0.0:0.0:0.1562:0.8438	.	570;570;570	O14746-3;O14746;Q8NG38	.;TERT_HUMAN;.	Q	570	ENSP00000309572:K570Q;ENSP00000296820:K570Q;ENSP00000334346:K570Q;ENSP00000426042:K570Q	ENSP00000296820:K570Q	K	-	1	0	TERT	1335605	1.000000	0.71417	0.999000	0.59377	0.854000	0.48673	2.991000	0.49409	0.585000	0.29608	0.379000	0.24179	AAG	.	.	.	none		0.517	TERT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206729.2			G	1282605	T	G	1282605	3	3	101	1	0	0	0	0	1	0	0	0	15776	1850	64	5	1746	5	TERT	5	1282605	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08		1282605	179632655	28	6426											
CDH6	1004	hgsc.bcm.edu	37	chr5	31323226	31323226	+	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	gaaaatgacacggaccccacTgccccgccatacgactcctt	11	6	7	17	3	0	1	0	1	0	0	1	4	1	2	6	1	2	0	6	1	3	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr5:31323226T>G	ENST00000265071.2	+	12	2449	c.2184T>G	c.(2182-2184)acT>acG	p.T728T		NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	728					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CGGACCCCACTGCCCCGCCAT	0.557																																					p.T728T		Atlas-SNP	.											.	CDH6	175	.	0			c.T2184G						PASS	.						42	43	42					5																	31323226		2203	4300	6503	SO:0001819	synonymous_variant	1004	exon12			CCCCACTGCCCCG	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.2184T>G	chr5.hg19:g.31323226T>G		39.0	0.0	.		34.0	5.0	.	NM_004932	A8K5H5|Q9BWS0	Silent	SNP	ENST00000265071.2	hg19	CCDS3894.1																																																																																			.	.	.	none		0.557	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207355.2	NM_004932		G	31323226	T	G	31323226	2	3	101	1	0	0	0	0	0	0	0	1	3116	1567	55	5		5	CDH6	5	31323226	Silent	SNP	T	TCGA-B9-5156-01A-01D-1589-08	30040621	31323226	149592034	29	6427											
TRIM36	55521	hgsc.bcm.edu	37	chr5	114515696	114515696	+	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	cctttagctatcaattccatGatgtagccaaattcactcat	12	14	4	11	0	3	1	3	1	0	0	4	1	4	1	3	0	2	2	3	0	5	6			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr5:114515696G>A	ENST00000282369.3	-	1	160	c.39C>T	c.(37-39)atC>atT	p.I13I	TRIM36_ENST00000379617.2_Silent_p.I13I|TRIM36_ENST00000514154.1_5'UTR|TRIM36_ENST00000379618.2_Silent_p.I13I	NM_018700.3	NP_061170.2	Q9NQ86	TRI36_HUMAN	tripartite motif containing 36	13					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)		TCAATTCCATGATGTAGCCAA	0.577																																					p.I13I		Atlas-SNP	.											.	TRIM36	126	.	0			c.C39T						PASS	.						116	117	117					5																	114515696		2202	4300	6502	SO:0001819	synonymous_variant	55521	exon1			TTCCATGATGTAG	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.39C>T	chr5.hg19:g.114515696G>A		162.0	0.0	.		137.0	47.0	.	NM_001017397	A1L3Z1|A6NDD0|B7Z3V4|B7ZAV7|E9PFI8|Q0P5Z9	Silent	SNP	ENST00000282369.3	hg19	CCDS4115.1																																																																																			.	.	.	none		0.577	TRIM36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250854.2	NM_018700		A	114515696	G	A	114515696	2	1	101	1	0	0	0	0	0	0	0	1	16522	1280	45	2		2	TRIM36	5	114515696	Silent	SNP	G	TCGA-B9-5156-01A-01D-1589-08	83192470	114515696	66399564	30	6428											
PCDHGA1	56114	hgsc.bcm.edu	37	chr5	140712438	140712438	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtctgctacaggcttcgggAggcggcttagcgagcatgcc	6	8	15	12	4	1	0	0	0	1	0	2	2	1	1	1	4	5	4	1	4	2	3			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr5:140712438A>G	ENST00000517417.1	+	1	2187	c.2187A>G	c.(2185-2187)ggA>ggG	p.G729G	PCDHGA1_ENST00000378105.3_Silent_p.G729G	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	729					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)			AGGCTTCGGGAGGCGGCTTAG	0.662																																					p.G729G		Atlas-SNP	.											PCDHGA1_ENST00000517417,colon,carcinoma,0,2	PCDHGA1	397	.	0			c.A2187G						PASS	.						64	69	68					5																	140712438		2203	4300	6503	SO:0001819	synonymous_variant	56114	exon1			TTCGGGAGGCGGC	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.2187A>G	chr5.hg19:g.140712438A>G		91.0	0.0	.		98.0	37.0	.	NM_018912	Q2M273|Q9Y5D6	Silent	SNP	ENST00000517417.1	hg19	CCDS54922.1																																																																																			.	.	.	none		0.662	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		G	140712438	A	G	140712438	2	3	101	1	0	0	0	0	0	0	0	1	11557	291	11	3		3	PCDHGA1	5	140712438	Silent	SNP	A	TCGA-B9-5156-01A-01D-1589-08	26196742	140712438	40202822	31	6429											
LARS	51520	hgsc.bcm.edu	37	chr5	145506033	145506033	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatggcatgactttcttcaTgtatttcttcagttctggca	9	17	7	8	0	5	1	2	1	3	0	5	1	5	1	0	2	0	4	0	2	2	6			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr5:145506033T>C	ENST00000394434.2	-	28	3122	c.2956A>G	c.(2956-2958)Atg>Gtg	p.M986V	LARS_ENST00000274562.9_Missense_Mutation_p.M959V|LARS_ENST00000545646.1_Missense_Mutation_p.M940V|LARS_ENST00000510191.1_Missense_Mutation_p.M932V	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	986					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)	ACTTTCTTCATGTATTTCTTC	0.428																																					p.M986V		Atlas-SNP	.											.	LARS	100	.	0			c.A2956G						PASS	.						202	156	171					5																	145506033		2202	4300	6502	SO:0001583	missense	51520	exon28			TCTTCATGTATTT	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.2956A>G	chr5.hg19:g.145506033T>C	ENSP00000377954:p.Met986Val	112.0	0.0	.		86.0	24.0	.	NM_020117	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	Missense_Mutation	SNP	ENST00000394434.2	hg19	CCDS34265.1	.	.	.	.	.	.	.	.	.	.	T	13.98	2.399675	0.42512	.	.	ENSG00000133706	ENST00000394434;ENST00000545646;ENST00000540713;ENST00000510191;ENST00000274562	T;T;T;T	0.63913	-0.06;-0.06;-0.06;-0.07	5.17	5.17	0.71159	Aminoacyl-tRNA synthetase, class 1a, anticodon-binding (1);	0.037152	0.85682	D	0.000000	T	0.66157	0.2761	M	0.86864	2.845	0.80722	D	1	B;P;B	0.38335	0.007;0.627;0.001	B;B;B	0.36030	0.007;0.216;0.007	T	0.68401	-0.5418	10	0.25751	T	0.34	.	15.1805	0.72952	0.0:0.0:0.0:1.0	.	959;940;986	B4DER1;F5H698;Q9P2J5	.;.;SYLC_HUMAN	V	986;940;295;932;959	ENSP00000377954:M986V;ENSP00000437791:M940V;ENSP00000426005:M932V;ENSP00000274562:M959V	ENSP00000274562:M959V	M	-	1	0	LARS	145486226	1.000000	0.71417	0.937000	0.37676	0.899000	0.52679	5.892000	0.69790	2.178000	0.69098	0.455000	0.32223	ATG	.	.	.	none		0.428	LARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000373367.1	NM_020117		C	145506033	T	C	145506033	3	2	101	1	0	0	0	0	1	0	0	0	8641	1464	51	3	594	3	LARS	5	145506033	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08	4793595	145506033	35409227	32	6430											
PDGFRB	5159	hgsc.bcm.edu	37	chr5	149511592	149511592	+	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	cctcagcatcctcatggaagGcccgcatggtgtagtggcca	8	8	12	13	1	2	0	2	0	0	0	3	1	3	1	4	4	1	3	4	4	2	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr5:149511592G>T	ENST00000261799.4	-	8	1662	c.1193C>A	c.(1192-1194)gCc>gAc	p.A398D		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	398	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)	CTCATGGAAGGCCCGCATGGT	0.607			T	"ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"	"MPD, AML, CMML, CML"																																p.A398D		Atlas-SNP	.		Dom	yes		5	5q31-q32	5159	"platelet-derived growth factor receptor, beta polypeptide"		L	.	PDGFRB	142	.	0			c.C1193A						PASS	.						129	106	114					5																	149511592		2203	4300	6503	SO:0001583	missense	5159	exon8			TGGAAGGCCCGCA	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.1193C>A	chr5.hg19:g.149511592G>T	ENSP00000261799:p.Ala398Asp	98.0	0.0	.		53.0	11.0	.	NM_002609	B5A957|Q8N5L4	Missense_Mutation	SNP	ENST00000261799.4	hg19	CCDS4303.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.318803	0.81469	.	.	ENSG00000113721	ENST00000261799;ENST00000544453	T	0.76968	-1.06	5.52	4.65	0.58169	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.000000	0.52532	D	0.000079	D	0.86908	0.6046	M	0.79805	2.47	0.41506	D	0.988315	D;D	0.89917	0.992;1.0	D;D	0.77004	0.959;0.989	D	0.88006	0.2759	10	0.87932	D	0	.	10.3808	0.44110	0.1488:0.0:0.8512:0.0	.	398;398	A8KAM8;P09619	.;PGFRB_HUMAN	D	398;68	ENSP00000261799:A398D	ENSP00000261799:A398D	A	-	2	0	PDGFRB	149491785	1.000000	0.71417	0.995000	0.50966	0.994000	0.84299	4.122000	0.57910	1.325000	0.45301	0.655000	0.94253	GCC	.	.	.	none		0.607	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609		T	149511592	G	T	149511592	3	4	101	1	0	0	0	0	1	0	0	0	11669	1203	42	4	2191	4	PDGFRB	5	149511592	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08	4005559	149511592	31403668	33	6431											
SLC34A1	6569	hgsc.bcm.edu	37	chr5	176824798	176824800	+	In_Frame_Del	DEL	CTT	CTT	-																															ctgcagattgccctctgtcaCttcttcttcaacatctcggg																								rs387907506		TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr5:176824798_176824800delCTT	ENST00000324417.5	+	13	1522_1524	c.1431_1433delCTT	c.(1429-1434)cacttc>cac	p.F480del	SLC34A1_ENST00000513614.1_3'UTR	NM_003052.4	NP_003043.3	Q06495	NPT2A_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 1	480					arsenate ion transmembrane transport (GO:1901684)|bone remodeling (GO:0046849)|cellular response to metal ion (GO:0071248)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to staurosporine (GO:0072734)|dentinogenesis (GO:0097187)|gentamycin metabolic process (GO:1901128)|glycoprotein metabolic process (GO:0009100)|indole metabolic process (GO:0042431)|ion transport (GO:0006811)|kidney development (GO:0001822)|ossification (GO:0001503)|phosphate ion homeostasis (GO:0055062)|phosphate ion transport (GO:0006817)|positive regulation of membrane potential (GO:0045838)|positive regulation of phosphate transmembrane transport (GO:2000187)|positive regulation of sodium-dependent phosphate transport (GO:2000120)|protein homooligomerization (GO:0051260)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to growth hormone (GO:0060416)|response to lead ion (GO:0010288)|response to magnesium ion (GO:0032026)|response to mercury ion (GO:0046689)|response to potassium ion (GO:0035864)|response to thyroid hormone (GO:0097066)|response to vitamin A (GO:0033189)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|tricarboxylic acid metabolic process (GO:0072350)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|membrane-bounded vesicle (GO:0031988)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|symporter activity (GO:0015293)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCCTCTGTCACTTCTTCTTCAAC	0.616																																					p.477_478del		Atlas-INDEL	.											.	SLC34A1	73	.	0			c.1430_1432del						PASS	.																																			SO:0001651	inframe_deletion	6569	exon13			.	L13258	CCDS4418.1, CCDS54953.1	5q35.3	2013-07-17	2013-07-17		ENSG00000131183	ENSG00000131183		"Solute carriers"	11019	protein-coding gene	gene with protein product	"sodium/phosphate co-transporter", "solute carrier family 17 (sodium phosphate), member 2", "Na+-phosphate cotransporter type II"	182309	"solute carrier family 34 (sodium phosphate), member 1"	NPT2, SLC17A2		8327470, 8693007	Standard	NM_003052		Approved	NAPI-3, NPTIIa, SLC11	uc003mgk.4	Q06495	OTTHUMG00000130857	ENST00000324417.5:c.1431_1433delCTT	chr5.hg19:g.176824804_176824806delCTT	ENSP00000321424:p.Phe480del	136.0	0.0	0		118.0	26.0	0.220339	NM_003052	B4DPE3	In_Frame_Del	DEL	ENST00000324417.5	hg19	CCDS4418.1																																																																																			.	.	.	none		0.616	SLC34A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253431.1	NM_003052		-	176824800	CTT	-	176824798	7	5	101	1	0	1	0	1	0	0	0	0	14580	564	20	0	1568	0	SLC34A1	5	176824798	In_Frame_Del	DEL	CTT	TCGA-B9-5156-01A-01D-1589-08	27313206	176824798	4090462	34	6432											
PRPF4B	8899	hgsc.bcm.edu	37	chr6	4032504	4032504	+	Missense_Mutation	SNP	A	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	agaaggcgatctcaagagaaAattggtaaggccagatctcc	15	7	11	8	1	2	3	1	0	2	3	4	5	2	3	2	3	0	1	2	3	5	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr6:4032504A>C	ENST00000337659.6	+	2	853	c.753A>C	c.(751-753)aaA>aaC	p.K251N	PRPF4B_ENST00000538861.1_Missense_Mutation_p.K237N	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN	pre-mRNA processing factor 4B	251	Arg/Lys-rich (basic).				mRNA splicing, via spliceosome (GO:0000398)|protein phosphorylation (GO:0006468)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|chromosome (GO:0005694)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(3)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	22	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				CTCAAGAGAAAATTGGTAAGG	0.343																																					p.K251N		Atlas-SNP	.											.	PRPF4B	140	.	0			c.A753C						PASS	.						123	134	131					6																	4032504		2203	4300	6503	SO:0001583	missense	8899	exon2			AGAGAAAATTGGT	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.753A>C	chr6.hg19:g.4032504A>C	ENSP00000337194:p.Lys251Asn	216.0	0.0	.		188.0	79.0	.	NM_003913	A8K5C9|Q5D0F6|Q5TAY8|Q8IVC3|Q8TDP2|Q96QT7|Q9UEE6	Missense_Mutation	SNP	ENST00000337659.6	hg19	CCDS4488.1	.	.	.	.	.	.	.	.	.	.	A	16.00	2.997406	0.54147	.	.	ENSG00000112739	ENST00000337659;ENST00000538861	T;T	0.67865	-0.29;-0.29	5.61	-1.1	0.09872	.	0.000000	0.85682	D	0.000000	T	0.28699	0.0711	L	0.36672	1.1	0.32528	N	0.535323	P	0.43477	0.808	B	0.33960	0.173	T	0.13255	-1.0516	10	0.32370	T	0.25	.	10.743	0.46164	0.6402:0.0:0.3598:0.0	.	251	Q13523	PRP4B_HUMAN	N	251;237	ENSP00000337194:K251N;ENSP00000439331:K237N	ENSP00000337194:K251N	K	+	3	2	PRPF4B	3977503	0.997000	0.39634	0.223000	0.23860	0.955000	0.61496	1.838000	0.39211	-0.329000	0.08527	0.533000	0.62120	AAA	.	.	.	none		0.343	PRPF4B-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314018.2			C	4032504	A	C	4032504	3	2	101	1	0	0	0	0	1	0	0	0	12583	11	1	5	759	5	PRPF4B	6	4032504	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08		4032504	167082563	35	6433											
MUC21	394263	hgsc.bcm.edu	37	chr6	30954340	30954340	+	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	ctgagtccagcacaccctccAgtggggccagcacagccacc	9	4	10	18	0	0	1	0	1	0	0	2	1	2	1	6	2	3	2	6	2	0	0			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr6:30954340A>T	ENST00000376296.3	+	2	629	c.388A>T	c.(388-390)Agt>Tgt	p.S130C	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	130	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						CACACCCTCCAGTGGGGCCAG	0.607																																					p.S130C		Atlas-SNP	.											.	MUC21	98	.	0			c.A388T						PASS	.						164	155	158					6																	30954340		2203	4300	6503	SO:0001583	missense	394263	exon2			CCCTCCAGTGGGG	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.388A>T	chr6.hg19:g.30954340A>T	ENSP00000365473:p.Ser130Cys	255.0	0.0	.		249.0	57.0	.	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	hg19	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	A	9.389	1.074974	0.20227	.	.	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.03301	3.98	3.34	-1.87	0.07737	.	.	.	.	.	T	0.01092	0.0036	N	0.24115	0.695	0.09310	N	1	D	0.53619	0.961	P	0.47162	0.54	T	0.47433	-0.9118	8	.	.	.	.	4.8046	0.13314	0.3103:0.0:0.5043:0.1854	.	130	Q5SSG8	MUC21_HUMAN	C	130	ENSP00000365473:S130C	.	S	+	1	0	MUC21	31062319	0.007000	0.16637	0.000000	0.03702	0.014000	0.08584	1.200000	0.32247	-0.218000	0.10018	-0.425000	0.05940	AGT	.	.	.	none		0.607	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909		T	30954340	A	T	30954340	3	4	101	1	0	0	0	0	1	0	0	0	9984	188	7	5	394	5	MUC21	6	30954340	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	26921836	30954340	140160727	36	6434											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51889440	51889440	+	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	gggcagatgaggcccaccctCtgatgcagtcatagcctctg	8	8	12	13	0	3	3	1	2	2	1	3	3	3	3	3	2	2	2	3	2	1	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr6:51889440C>G	ENST00000371117.3	-	32	5443	c.5168G>C	c.(5167-5169)aGa>aCa	p.R1723T	PKHD1_ENST00000340994.4_Missense_Mutation_p.R1723T	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1723	IPT/TIG 12; 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)					GGCCCACCCTCTGATGCAGTC	0.532																																					p.R1723T		Atlas-SNP	.											.	PKHD1	927	.	0			c.G5168C						PASS	.						87	86	86					6																	51889440		2203	4300	6503	SO:0001583	missense	5314	exon32			CACCCTCTGATGC	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.5168G>C	chr6.hg19:g.51889440C>G	ENSP00000360158:p.Arg1723Thr	114.0	0.0	.		97.0	28.0	.	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	16.25	3.071085	0.55646	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.87256	-2.05;-2.23	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	D	0.91543	0.7329	M	0.66939	2.045	0.35080	D	0.763272	D;D	0.76494	0.99;0.999	D;D	0.77557	0.96;0.99	D	0.91115	0.4925	10	0.45353	T	0.12	.	18.6881	0.91573	0.0:1.0:0.0:0.0	.	1723;1723	P08F94-2;P08F94	.;PKHD1_HUMAN	T	1723	ENSP00000360158:R1723T;ENSP00000341097:R1723T	ENSP00000341097:R1723T	R	-	2	0	PKHD1	51997399	1.000000	0.71417	0.878000	0.34440	0.146000	0.21551	5.086000	0.64474	2.659000	0.90383	0.650000	0.86243	AGA	.	.	.	none		0.532	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		G	51889440	C	G	51889440	3	3	101	1	0	0	0	0	1	0	0	0	11978	913	32	4	7239	4	PKHD1	6	51889440	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08	20935100	51889440	119225627	37	6435											
LIMK1	3984	hgsc.bcm.edu	37	chr7	73530183	73530183	+	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	tggcgcgtctcatggtggacGagaagactcagcctgagggc	8	7	16	10	3	2	3	2	1	1	2	3	5	2	4	1	4	1	0	1	4	1	0			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr7:73530183G>A	ENST00000336180.2	+	13	1513	c.1462G>A	c.(1462-1464)Gag>Aag	p.E488K	LIMK1_ENST00000538333.3_Missense_Mutation_p.E454K|LIMK1_ENST00000418310.1_Missense_Mutation_p.E518K	NM_002314.3	NP_002305.1	P53667	LIMK1_HUMAN	LIM domain kinase 1	488	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|nervous system development (GO:0007399)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of axon extension (GO:0045773)|positive regulation of stress fiber assembly (GO:0051496)|protein phosphorylation (GO:0006468)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)	ATP binding (GO:0005524)|heat shock protein binding (GO:0031072)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21		Lung NSC(55;0.137)			Dabrafenib(DB08912)	CATGGTGGACGAGAAGACTCA	0.607																																					p.E488K		Atlas-SNP	.											.	LIMK1	55	.	0			c.G1462A						PASS	.						101	83	89					7																	73530183		2203	4300	6503	SO:0001583	missense	3984	exon13			GTGGACGAGAAGA	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.1462G>A	chr7.hg19:g.73530183G>A	ENSP00000336740:p.Glu488Lys	70.0	0.0	.		76.0	22.0	.	NM_002314	B7Z6I8|D3DXF4|D3DXF5|O15283|Q15820|Q15821|Q75MU3|Q9Y5Q1	Missense_Mutation	SNP	ENST00000336180.2	hg19	CCDS5563.1	.	.	.	.	.	.	.	.	.	.	g	14.48	2.547545	0.45383	.	.	ENSG00000106683	ENST00000418310;ENST00000419043;ENST00000336180;ENST00000538333	T;T;T	0.62232	0.04;0.04;0.04	5.25	3.45	0.39498	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.210321	0.48767	D	0.000162	T	0.43942	0.1270	N	0.17345	0.48	0.50813	D	0.999895	P;P	0.48834	0.543;0.916	B;B	0.42386	0.364;0.386	T	0.28427	-1.0044	10	0.39692	T	0.17	-19.111	8.804	0.34927	0.0834:0.1523:0.7643:0.0	.	454;488	B7Z6I8;P53667	.;LIMK1_HUMAN	K	518;488;488;454	ENSP00000409717:E518K;ENSP00000336740:E488K;ENSP00000444452:E454K	ENSP00000336740:E488K	E	+	1	0	LIMK1	73168119	1.000000	0.71417	0.039000	0.18376	0.059000	0.15707	7.647000	0.83462	0.627000	0.30340	-0.240000	0.12126	GAG	.	.	.	none		0.607	LIMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252335.2	NM_002314		A	73530183	G	A	73530183	3	1	101	1	0	0	0	0	1	0	0	0	8808	1059	37	1	1512	1	LIMK1	7	73530183	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08		73530183	85608480	38	6436											
STYXL1	51657	hgsc.bcm.edu	37	chr7	75633079	75633079	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaggaacgctccttaccaaTgaagtgacacatgtggcgta	13	8	10	10	2	0	2	0	2	0	0	1	3	1	3	2	2	2	2	2	2	6	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr7:75633079T>C	ENST00000248600.1	-	7	1036	c.694A>G	c.(694-696)Att>Gtt	p.I232V	STYXL1_ENST00000359697.3_Missense_Mutation_p.I232V|STYXL1_ENST00000451157.1_Missense_Mutation_p.I232V|STYXL1_ENST00000340062.5_Missense_Mutation_p.I136V|STYXL1_ENST00000360591.3_3'UTR|STYXL1_ENST00000431581.1_Missense_Mutation_p.I232V	NM_016086.2	NP_057170.1	Q9Y6J8	STYL1_HUMAN	serine/threonine/tyrosine interacting-like 1	232	Tyrosine-protein phosphatase.				intracellular signal transduction (GO:0035556)|protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	10						TCCTTACCAATGAAGTGACAC	0.537																																					p.I232V		Atlas-SNP	.											.	STYXL1	35	.	0			c.A694G						PASS	.						113	87	96					7																	75633079		2203	4300	6503	SO:0001583	missense	51657	exon7			TACCAATGAAGTG	AF069762	CCDS5580.1	7q11.23	2011-06-09	2005-09-22	2005-09-22	ENSG00000127952	ENSG00000127952		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	18165	protein-coding gene	gene with protein product			"dual specificity phosphatase 24 (putative)"	DUSP24		9757831	Standard	NM_016086		Approved	MK-STYX	uc003uel.3	Q9Y6J8	OTTHUMG00000130459	ENST00000248600.1:c.694A>G	chr7.hg19:g.75633079T>C	ENSP00000248600:p.Ile232Val	73.0	0.0	.		80.0	47.0	.	NM_016086	Q9UBP1|Q9UK06|Q9UK07|Q9UKG2|Q9UKG3	Missense_Mutation	SNP	ENST00000248600.1	hg19	CCDS5580.1	.	.	.	.	.	.	.	.	.	.	T	10.43	1.347287	0.24426	.	.	ENSG00000127952	ENST00000248600;ENST00000359697;ENST00000340062;ENST00000404050;ENST00000431581;ENST00000454618;ENST00000451157	D;D;D;D;T;D	0.88124	-2.34;-2.34;-2.34;-2.34;0.0;-2.34	3.74	-3.86	0.04230	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.287194	0.36374	N	0.002630	T	0.79435	0.4445	L	0.52823	1.66	0.80722	D	1	B;B;B;B;B;B	0.33748	0.423;0.172;0.096;0.01;0.087;0.086	B;B;B;B;B;B	0.32805	0.153;0.133;0.081;0.007;0.12;0.124	T	0.66212	-0.5980	10	0.62326	D	0.03	.	8.0828	0.30754	0.0:0.0993:0.6291:0.2716	.	232;232;232;136;232;136	Q9Y6J8-3;C9J4H0;Q9Y6J8-2;Q9Y6J8-4;Q9Y6J8;Q7Z3H6	.;.;.;.;STYL1_HUMAN;.	V	232;232;136;232;232;187;232	ENSP00000248600:I232V;ENSP00000352726:I232V;ENSP00000343383:I136V;ENSP00000392221:I232V;ENSP00000406073:I187V;ENSP00000411812:I232V	ENSP00000248600:I232V	I	-	1	0	STYXL1	75471015	0.998000	0.40836	0.219000	0.23793	0.709000	0.40893	0.666000	0.25097	-0.708000	0.05015	0.460000	0.39030	ATT	.	.	.	none		0.537	STYXL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344825.1	NM_016086		C	75633079	T	C	75633079	3	2	101	1	0	0	0	0	1	0	0	0	15373	1464	51	3	259	3	STYXL1	7	75633079	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08	2102896	75633079	83505584	39	6437											
STYXL1	51657	hgsc.bcm.edu	37	chr7	75643205	75643205	+	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	tggctgcttgaggcacaagaTctgagagtggagaccaaaga	13	7	14	7	0	1	5	0	2	1	4	1	7	1	5	1	3	1	3	1	3	2	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr7:75643205T>C	ENST00000248600.1	-	5	650	c.308A>G	c.(307-309)gAt>gGt	p.D103G	STYXL1_ENST00000359697.3_Splice_Site_p.D103G|STYXL1_ENST00000451157.1_Splice_Site_p.D103G|STYXL1_ENST00000340062.5_Intron|STYXL1_ENST00000460184.2_5'UTR|STYXL1_ENST00000360591.3_Intron|STYXL1_ENST00000431581.1_Splice_Site_p.D103G	NM_016086.2	NP_057170.1	Q9Y6J8	STYL1_HUMAN	serine/threonine/tyrosine interacting-like 1	103	Rhodanese.				intracellular signal transduction (GO:0035556)|protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	10						AGGCACAAGATCTGAGAGTGG	0.498																																					p.D103G		Atlas-SNP	.											.	STYXL1	35	.	0			c.A308G						PASS	.						125	109	114					7																	75643205		2203	4300	6503	SO:0001630	splice_region_variant	51657	exon5			ACAAGATCTGAGA	AF069762	CCDS5580.1	7q11.23	2011-06-09	2005-09-22	2005-09-22	ENSG00000127952	ENSG00000127952		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	18165	protein-coding gene	gene with protein product			"dual specificity phosphatase 24 (putative)"	DUSP24		9757831	Standard	NM_016086		Approved	MK-STYX	uc003uel.3	Q9Y6J8	OTTHUMG00000130459	ENST00000248600.1:c.308-1A>G	chr7.hg19:g.75643205T>C		165.0	0.0	.		189.0	89.0	.	NM_016086	Q9UBP1|Q9UK06|Q9UK07|Q9UKG2|Q9UKG3	Missense_Mutation	SNP	ENST00000248600.1	hg19	CCDS5580.1	.	.	.	.	.	.	.	.	.	.	T	9.558	1.117639	0.20877	.	.	ENSG00000127952	ENST00000248600;ENST00000359697;ENST00000404050;ENST00000431581;ENST00000454618;ENST00000451157	T;T;T;T	0.26660	1.72;1.72;1.72;1.72	5.26	-5.09	0.02920	Rhodanese-like (4);	2.770220	0.00966	N	0.003162	T	0.14787	0.0357	N	0.16478	0.41	0.26750	N	0.970228	B;B;B	0.10296	0.003;0.001;0.002	B;B;B	0.11329	0.006;0.001;0.003	T	0.18209	-1.0344	10	0.22706	T	0.39	.	7.9066	0.29765	0.1461:0.5762:0.0:0.2777	.	103;103;103	C9J4H0;Q9Y6J8-2;Q9Y6J8	.;.;STYL1_HUMAN	G	103;103;103;103;58;103	ENSP00000248600:D103G;ENSP00000352726:D103G;ENSP00000392221:D103G;ENSP00000411812:D103G	ENSP00000248600:D103G	D	-	2	0	STYXL1	75481141	0.053000	0.20554	0.002000	0.10522	0.015000	0.08874	-0.109000	0.10840	-0.873000	0.04032	0.454000	0.30748	GAT	.	.	.	none		0.498	STYXL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344825.1	NM_016086	Missense_Mutation	C	75643205	T	C	75643205	5	2	101	1	0	0	0	0	0	0	1	0	15373	1449	50	3	653	3	STYXL1	7	75643205	Splice_Site	SNP	T	TCGA-B9-5156-01A-01D-1589-08	10126	75643205	83495458	40	6438											
ZNF3	7551	hgsc.bcm.edu	37	chr7	99669265	99669266	+	Frame_Shift_Ins	INS	-	-	C																															attacattcatagggtttctINScccccgtgtggatcctccga																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr7:99669265_99669266insC	ENST00000424697.1	-	6	1147_1148	c.841_842insG	c.(841-843)gagfs	p.E281fs	ZNF3_ENST00000413658.2_Intron|ZNF3_ENST00000303915.6_Frame_Shift_Ins_p.E281fs|ZNF3_ENST00000299667.4_Frame_Shift_Ins_p.E281fs	NM_001278284.1|NM_001278287.1|NM_001278290.1|NM_001278291.1|NM_001278292.1|NM_032924.3	NP_001265213.1|NP_001265216.1|NP_001265219.1|NP_001265220.1|NP_001265221.1|NP_116313.3	P17036	ZNF3_HUMAN	zinc finger protein 3	281					cell differentiation (GO:0030154)|leukocyte activation (GO:0045321)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	25	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)	Ovarian(593;2.06e-05)|Myeloproliferative disorder(862;0.0122)|Breast(660;0.029)	STAD - Stomach adenocarcinoma(171;0.129)			ATAGGGTTTCTCCCCCGTGTGG	0.515																																					p.E281fs		Atlas-INDEL	.											.	ZNF3	54	.	0			c.842_843insG						PASS	.																																			SO:0001589	frameshift_variant	7551	exon6			.	AF027136	CCDS43618.1, CCDS43619.1	7q22.1	2013-01-08	2006-05-05					"Zinc fingers, C2H2-type", "-"	13089	protein-coding gene	gene with protein product		194510	"zinc finger protein 3 (A8-51)"				Standard	NM_032924		Approved	A8-51, KOX25, PP838, FLJ20216, HF.12, Zfp113	uc003usr.4	P17036		ENST00000424697.1:c.842dupG	chr7.hg19:g.99669270_99669270dupC	ENSP00000415358:p.Glu281fs	83.0	0.0	0		113.0	28.0	0.247788	NM_032924	D6W5U0|P13683|Q9HBR4|Q9NNX8|Q9NXJ1|Q9UC15|Q9UC16	Frame_Shift_Ins	INS	ENST00000424697.1	hg19	CCDS43619.1																																																																																			.	.	.	none		0.515	ZNF3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336247.3	NM_017715		C	99669266	-	C	99669265	7	5	101	1	0	1	1	0	0	0	0	0	17841	1551	54	0	631	0	ZNF3	7	99669265	Frame_Shift_Ins	INS	-	TCGA-B9-5156-01A-01D-1589-08	24026060	99669265	59469398	41	6439											
ZNF786	136051	hgsc.bcm.edu	37	chr7	148767681	148767681	+	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	cacaggcaaagggcctctcgGgcctgtggatgcgctggtgc	6	7	16	12	2	1	0	0	0	1	0	2	1	1	1	2	5	2	2	2	5	1	0			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr7:148767681G>T	ENST00000491431.1	-	4	2247	c.2183C>A	c.(2182-2184)cCc>cAc	p.P728H	ZNF786_ENST00000451334.3_Missense_Mutation_p.P691H|ZNF786_ENST00000316286.9_Missense_Mutation_p.P642H	NM_152411.3	NP_689624.2	Q8N393	ZN786_HUMAN	zinc finger protein 786	728					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|cervix(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(2)	26	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			GGGCCTCTCGGGCCTGTGGAT	0.567																																					p.P728H		Atlas-SNP	.											.	ZNF786	69	.	0			c.C2183A						PASS	.						131	135	133					7																	148767681		2045	4211	6256	SO:0001583	missense	136051	exon4			CTCTCGGGCCTGT	AK095701, AL834510	CCDS47738.1	7q36.1	2013-01-08			ENSG00000197362	ENSG00000197362		"Zinc fingers, C2H2-type", "-"	21806	protein-coding gene	gene with protein product							Standard	NM_152411		Approved	DKFZp762I137	uc003wfh.2	Q8N393	OTTHUMG00000158975	ENST00000491431.1:c.2183C>A	chr7.hg19:g.148767681G>T	ENSP00000417470:p.Pro728His	241.0	1.0	.		297.0	138.0	.	NM_152411	A1A568|B4DMI1	Missense_Mutation	SNP	ENST00000491431.1	hg19	CCDS47738.1	.	.	.	.	.	.	.	.	.	.	G	14.92	2.678888	0.47886	.	.	ENSG00000197362	ENST00000316286;ENST00000491431;ENST00000451334	T;T;T	0.19394	2.15;2.15;2.15	4.62	3.7	0.42460	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36444	N	0.002595	T	0.34745	0.0908	L	0.42581	1.335	0.31365	N	0.68091	D	0.89917	1.0	D	0.77004	0.989	T	0.21484	-1.0244	10	0.87932	D	0	-21.2407	10.48	0.44687	0.0:0.3127:0.6873:0.0	.	728	Q8N393	ZN786_HUMAN	H	642;728;691	ENSP00000313516:P642H;ENSP00000417470:P728H;ENSP00000404984:P691H	ENSP00000313516:P642H	P	-	2	0	ZNF786	148398614	0.001000	0.12720	0.900000	0.35374	0.789000	0.44602	0.774000	0.26675	2.411000	0.81874	0.591000	0.81541	CCC	.	.	.	none		0.567	ZNF786-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352751.1	NM_152411		T	148767681	G	T	148767681	3	4	101	1	0	0	0	0	1	0	0	0	18170	1232	43	4	169	4	ZNF786	7	148767681	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08	49098416	148767681	10370982	42	6440											
GIMAP6	474344	hgsc.bcm.edu	37	chr7	150325338	150325338	+	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	ggccctggggcggataagacGatggcttggcagatagcgtc	8	7	17	9	3	0	2	0	0	0	2	1	4	0	3	1	6	1	2	1	6	2	3			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr7:150325338G>A	ENST00000328902.5	-	3	564	c.348C>T	c.(346-348)atC>atT	p.I116I	GIMAP6_ENST00000493969.1_Missense_Mutation_p.R42C	NM_001244072.1|NM_024711.5	NP_001231001.1|NP_078987.3	Q6P9H5	GIMA6_HUMAN	GTPase, IMAP family member 6	116	AIG1-type G.					cytosol (GO:0005829)	GTP binding (GO:0005525)			endometrium(4)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	29			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CGGATAAGACGATGGCTTGGC	0.632																																					p.R42C		Atlas-SNP	.											.	GIMAP6	60	.	0			c.C124T						PASS	.						57	59	58					7																	150325338		2203	4300	6503	SO:0001819	synonymous_variant	474344	exon3			TAAGACGATGGCT	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.348C>T	chr7.hg19:g.150325338G>A		137.0	0.0	.		155.0	36.0	.	NM_001244071	C9J7B6|D3DWZ4|Q5ZPR6|Q9H612	Missense_Mutation	SNP	ENST00000328902.5	hg19	CCDS34778.1	.	.	.	.	.	.	.	.	.	.	G	8.530	0.870870	0.17322	.	.	ENSG00000133561	ENST00000493969	.	.	.	4.07	-6.18	0.02085	.	.	.	.	.	T	0.30386	0.0763	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.44034	-0.9354	5	0.87932	D	0	.	2.4155	0.04435	0.2705:0.4128:0.199:0.1177	.	.	.	.	C	42	.	ENSP00000418304:R42C	R	-	1	0	GIMAP6	149956271	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.968000	0.03817	-1.017000	0.03367	-1.157000	0.01802	CGT	.	.	.	none		0.632	GIMAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353457.1	NM_024711		A	150325338	G	A	150325338	2	1	101	1	0	0	0	0	0	0	0	1	6390	1048	37	1		1	GIMAP6	7	150325338	Silent	SNP	G	TCGA-B9-5156-01A-01D-1589-08	1557657	150325338	8813325	43	6441											
PXDNL	137902	hgsc.bcm.edu	37	chr8	52336162	52336162	+	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	tgtaagaaacatgttggtcaCagcaaggccaaaagaattcc	16	8	9	8	0	1	2	1	0	0	2	2	2	2	2	2	2	2	3	2	2	6	3			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr8:52336162C>G	ENST00000356297.4	-	14	1868	c.1768G>C	c.(1768-1770)Gtg>Ctg	p.V590L	PXDNL_ENST00000543296.1_Missense_Mutation_p.V590L	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	590	Ig-like C2-type 4.				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)				ATGTTGGTCACAGCAAGGCCA	0.453																																					p.V590L		Atlas-SNP	.											.	PXDNL	414	.	0			c.G1768C						PASS	.						109	115	113					8																	52336162		2106	4234	6340	SO:0001583	missense	137902	exon14			TGGTCACAGCAAG		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.1768G>C	chr8.hg19:g.52336162C>G	ENSP00000348645:p.Val590Leu	40.0	0.0	.		36.0	17.0	.	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	hg19	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	C	9.782	1.175500	0.21704	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.66638	-0.22;-0.22	4.59	2.79	0.32731	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.50633	0.1627	N	0.25789	0.76	0.09310	N	1	B	0.14438	0.01	B	0.21151	0.033	T	0.36986	-0.9725	9	0.30854	T	0.27	.	7.6374	0.28274	0.0:0.7996:0.0:0.2004	.	590	A1KZ92	PXDNL_HUMAN	L	590	ENSP00000348645:V590L;ENSP00000444865:V590L	ENSP00000348645:V590L	V	-	1	0	PXDNL	52498715	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.388000	0.07352	0.476000	0.27440	-0.757000	0.03467	GTG	.	.	.	none		0.453	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		G	52336162	C	G	52336162	3	3	101	1	0	0	0	0	1	0	0	0	12861	478	17	4	2663	4	PXDNL	8	52336162	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08		52336162	94027860	44	6442											
TMEM67	91147	hgsc.bcm.edu	37	chr8	94797545	94797545	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatgaaaatcaacatcaataTattttggctgtgcctgtgtt	12	15	8	6	0	2	1	2	1	0	0	2	2	2	1	1	1	2	2	1	1	6	5			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr8:94797545T>C	ENST00000453321.3	+	12	1285	c.1227T>C	c.(1225-1227)taT>taC	p.Y409Y	TMEM67_ENST00000409623.3_Silent_p.Y328Y	NM_153704.5	NP_714915.3	Q5HYA8	MKS3_HUMAN	transmembrane protein 67	409					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of centrosome duplication (GO:0010826)	centrosome (GO:0005813)|ciliary membrane (GO:0060170)|cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)	filamin binding (GO:0031005)|unfolded protein binding (GO:0051082)			breast(3)|endometrium(8)|kidney(5)|large_intestine(4)|liver(2)|lung(15)|ovary(2)|skin(1)|urinary_tract(1)	41	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)			AACATCAATATATTTTGGCTG	0.338																																					p.Y409Y		Atlas-SNP	.											.	TMEM67	187	.	0			c.T1227C						PASS	.						141	148	146					8																	94797545		2202	4297	6499	SO:0001819	synonymous_variant	91147	exon12			TCAATATATTTTG	BX648768	CCDS6258.2, CCDS47893.1	8q22.1	2014-09-17			ENSG00000164953	ENSG00000164953			28396	protein-coding gene	gene with protein product	"Meckelin"	609884	"Meckel syndrome, type 3"	MKS3		12384791, 16415887, 19508969	Standard	NM_153704		Approved	MGC26979, JBTS6, NPHP11	uc011lgk.2	Q5HYA8	OTTHUMG00000153119	ENST00000453321.3:c.1227T>C	chr8.hg19:g.94797545T>C		269.0	0.0	.		228.0	68.0	.	NM_153704	B3KRU5|B3KT47|G5E9H2|Q3ZCX3|Q7Z5T8|Q8IZ06	Silent	SNP	ENST00000453321.3	hg19	CCDS6258.2	.	.	.	.	.	.	.	.	.	.	T	6.534	0.466810	0.12402	.	.	ENSG00000164953	ENST00000520680	D	0.96940	-4.18	4.53	1.01	0.19927	.	0.777204	0.11502	N	0.557622	D	0.93884	0.8043	.	.	.	0.45477	D	0.998442	.	.	.	.	.	.	D	0.86765	0.1969	7	0.19590	T	0.45	-2.1138	8.48	0.33036	0.0:0.401:0.0:0.599	.	.	.	.	H	17	ENSP00000428785:Y17H	ENSP00000428785:Y17H	Y	+	1	0	TMEM67	94866721	0.865000	0.29922	0.723000	0.30687	0.942000	0.58702	-0.048000	0.11944	0.356000	0.24157	0.482000	0.46254	TAT	.	.	.	none		0.338	TMEM67-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329641.2	NM_153704		C	94797545	T	C	94797545	2	2	101	1	0	0	0	0	0	0	0	1	16208	1413	49	3		3	TMEM67	8	94797545	Silent	SNP	T	TCGA-B9-5156-01A-01D-1589-08	42461383	94797545	51566477	45	6443											
LOC645961	645961	hgsc.bcm.edu	37	chr9	90744548	90744548	+	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	accggacacttttcaagggcTactgatctctgatttgtctg	8	14	9	10	1	3	2	1	2	2	0	4	3	3	3	1	2	1	1	1	2	2	4			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr9:90744548T>C								U6 (131298 upstream) : U3 (244635 downstream)																							TTTCAAGGGCTACTGATCTCT	0.527																																					p.X1135W		Atlas-SNP	.											.	.	.	.	0			c.A3404G						PASS	.						197	154	167					9																	90744548		692	1591	2283	SO:0001628	intergenic_variant	645961	exon4			AAGGGCTACTGAT																													chr9.hg19:g.90744548T>C		299.0	0.0	.		250.0	52.0	.	NM_001166137		Missense_Mutation	SNP		hg19																																																																																				.	.	.	none	0	0.527									C	90744548	T	C	90744548	1	2	101	0	1	0	0	0	0	0	0	0	8890	1535	53	3		3	LOC645961	9	90744548	IGR	SNP	T	TCGA-B9-5156-01A-01D-1589-08		90744548	50468883	46	6444											
TOR1A	1861	hgsc.bcm.edu	37	chr9	132576423	132576423	+	Missense_Mutation	SNP	T	T	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	ctcggatacacatttttaggTgtttgtattccagggggagg	8	14	13	6	1	0	0	0	0	0	0	2	2	1	2	1	5	1	2	1	5	3	7			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr9:132576423T>G	ENST00000351698.4	-	5	875	c.827A>C	c.(826-828)cAc>cCc	p.H276P		NM_000113.2	NP_000104.1	O14656	TOR1A_HUMAN	torsin family 1, member A (torsin A)	276	Interaction with KLC1.				ATP catabolic process (GO:0006200)|cell adhesion (GO:0007155)|chaperone mediated protein folding requiring cofactor (GO:0051085)|chaperone-mediated protein folding (GO:0061077)|chaperone-mediated protein transport (GO:0072321)|ER-associated misfolded protein catabolic process (GO:0071712)|intermediate filament cytoskeleton organization (GO:0045104)|neuron projection development (GO:0031175)|nuclear envelope organization (GO:0006998)|nuclear membrane organization (GO:0071763)|organelle organization (GO:0006996)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|protein deneddylation (GO:0000338)|protein homooligomerization (GO:0051260)|protein localization to nucleus (GO:0034504)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of protein localization to cell surface (GO:2000008)|response to oxidative stress (GO:0006979)|synaptic vesicle transport (GO:0048489)|wound healing, spreading of cells (GO:0044319)	cell junction (GO:0030054)|cytoplasmic vesicle membrane (GO:0030659)|cytoskeleton (GO:0005856)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cytoskeletal protein binding (GO:0008092)|kinesin binding (GO:0019894)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	20		Ovarian(14;0.00556)				CATTTTTAGGTGTTTGTATTC	0.453																																					p.H276P		Atlas-SNP	.											.	TOR1A	36	.	0			c.A827C						PASS	.						163	156	159					9																	132576423		2203	4300	6503	SO:0001583	missense	1861	exon5			TTTAGGTGTTTGT	AF007871	CCDS6930.1	9q32-q34	2008-07-21	2004-11-24	2004-11-26	ENSG00000136827	ENSG00000136827			3098	protein-coding gene	gene with protein product		605204	"dystonia 1, torsion (autosomal dominant; torsin A)"	DYT1		10644435	Standard	NM_000113		Approved	DQ2	uc004byl.3	O14656	OTTHUMG00000020794	ENST00000351698.4:c.827A>C	chr9.hg19:g.132576423T>G	ENSP00000345719:p.His276Pro	263.0	0.0	.		231.0	69.0	.	NM_000113	B2RB58|Q53Y64|Q96CA0	Missense_Mutation	SNP	ENST00000351698.4	hg19	CCDS6930.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.269693	0.80469	.	.	ENSG00000136827	ENST00000427355;ENST00000351698	T	0.71579	-0.58	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.87740	0.6253	M	0.94063	3.49	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90894	0.4763	10	0.87932	D	0	-9.1277	14.3493	0.66688	0.0:0.0:0.0:1.0	.	276	O14656	TOR1A_HUMAN	P	245;276	ENSP00000345719:H276P	ENSP00000345719:H276P	H	-	2	0	TOR1A	131616244	1.000000	0.71417	0.928000	0.36995	0.803000	0.45373	7.698000	0.84413	1.974000	0.57490	0.459000	0.35465	CAC	.	.	.	none		0.453	TOR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054611.1	NM_000113		G	132576423	T	G	132576423	3	3	101	1	0	0	0	0	1	0	0	0	16383	1696	59	5	175	5	TOR1A	9	132576423	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08	41831875	132576423	8637008	47	6445											
WNT8B	7479	hgsc.bcm.edu	37	chr10	102239758	102239758	+	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	gcagctgtccagccatggtgGgcttcgcagtggtaagaaaa	10	8	14	9	1	0	1	0	0	0	1	2	1	1	1	2	3	2	5	2	3	3	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr10:102239758G>A	ENST00000343737.5	+	3	358	c.230G>A	c.(229-231)gGg>gAg	p.G77E		NM_003393.3	NP_003384.2	Q93098	WNT8B_HUMAN	wingless-type MMTV integration site family, member 8B	77					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)		AGCCATGGTGGGCTTCGCAGT	0.582																																					p.G77E		Atlas-SNP	.											.	WNT8B	31	.	0			c.G230A						PASS	.						54	49	50					10																	102239758		2203	4300	6503	SO:0001583	missense	7479	exon3			ATGGTGGGCTTCG	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.230G>A	chr10.hg19:g.102239758G>A	ENSP00000340677:p.Gly77Glu	49.0	0.0	.		31.0	8.0	.	NM_003393	O00771|Q5VX55|Q8WYK9	Missense_Mutation	SNP	ENST00000343737.5	hg19	CCDS7494.1	.	.	.	.	.	.	.	.	.	.	G	13.88	2.368885	0.42003	.	.	ENSG00000075290	ENST00000343737	T	0.74947	-0.89	5.7	5.7	0.88788	.	1.622190	0.03427	N	0.207152	T	0.75606	0.3872	N	0.21373	0.66	0.54753	D	0.999988	P	0.38535	0.635	P	0.48982	0.597	T	0.60999	-0.7151	10	0.05351	T	0.99	.	19.8354	0.96655	0.0:0.0:1.0:0.0	.	77	Q93098	WNT8B_HUMAN	E	77	ENSP00000340677:G77E	ENSP00000340677:G77E	G	+	2	0	WNT8B	102229748	1.000000	0.71417	0.990000	0.47175	0.759000	0.43091	9.476000	0.97823	2.686000	0.91538	0.555000	0.69702	GGG	.	.	.	none		0.582	WNT8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049867.1	NM_003393		A	102239758	G	A	102239758	3	1	101	1	0	0	0	0	1	0	0	0	17409	1232	43	2	240	2	WNT8B	10	102239758	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08		102239758	33294989	48	6446											
PRKRIR	5612	hgsc.bcm.edu	37	chr11	76062971	76062971	+	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	tttctttactgttctgaaaaAgaacagaaattacgttgtca	14	15	6	6	1	3	3	1	1	2	2	3	3	3	3	0	0	3	2	0	0	6	6			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr11:76062971A>T	ENST00000260045.3	-	5	1328	c.1223T>A	c.(1222-1224)cTt>cAt	p.L408H	PRKRIR_ENST00000531878.1_5'Flank	NM_004705.2	NP_004696.2	O43422	P52K_HUMAN	protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor)	408					negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)|signal transduction (GO:0007165)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|large_intestine(4)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	25						GTTCTGAAAAAGAACAGAAAT	0.388																																					p.L408H		Atlas-SNP	.											.	PRKRIR	65	.	0			c.T1223A						PASS	.						19	19	19					11																	76062971		2163	4223	6386	SO:0001583	missense	5612	exon5			TGAAAAAGAACAG	AF007393	CCDS8243.1	11q13.5	2013-01-25			ENSG00000137492	ENSG00000137492		"THAP (C2CH-type zinc finger) domain containing"	9440	protein-coding gene	gene with protein product	"THAP domain containing 12"	607374				9447982	Standard	NM_004705		Approved	P52rIPK, DAP4, THAP12	uc001oxh.1	O43422	OTTHUMG00000165280	ENST00000260045.3:c.1223T>A	chr11.hg19:g.76062971A>T	ENSP00000260045:p.Leu408His	83.0	0.0	.		79.0	22.0	.	NM_004705	A8K728|Q17RY9|Q8WTW1|Q9Y3Z4	Missense_Mutation	SNP	ENST00000260045.3	hg19	CCDS8243.1	.	.	.	.	.	.	.	.	.	.	A	6.750	0.507246	0.12883	.	.	ENSG00000137492	ENST00000529901;ENST00000260045	.	.	.	4.78	4.78	0.61160	Ribonuclease H-like (1);	0.052433	0.85682	D	0.000000	T	0.50103	0.1596	L	0.45581	1.43	0.46131	D	0.998889	B	0.31318	0.319	B	0.26310	0.068	T	0.52764	-0.8532	9	0.46703	T	0.11	.	14.7428	0.69469	1.0:0.0:0.0:0.0	.	408	O43422	P52K_HUMAN	H	233;408	.	ENSP00000260045:L408H	L	-	2	0	PRKRIR	75740619	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	2.504000	0.45416	1.956000	0.56807	0.524000	0.50904	CTT	.	.	.	none		0.388	PRKRIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383188.1	NM_004705		T	76062971	A	T	76062971	3	4	101	1	0	0	0	0	1	0	0	0	12536	72	3	5	1066	5	PRKRIR	11	76062971	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08		76062971	58943545	49	6447											
SYTL2	54843	hgsc.bcm.edu	37	chr11	85445140	85445140	+	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	ttggaaaagaaccagaagtcAttggctgatgtgtttcactt	12	13	10	6	0	2	3	2	1	0	2	2	4	2	4	1	2	1	2	1	2	4	4			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr11:85445140A>T	ENST00000528231.1	-	6	1506	c.1229T>A	c.(1228-1230)aTg>aAg	p.M410K	SYTL2_ENST00000527523.1_Missense_Mutation_p.M362K|SYTL2_ENST00000524452.1_Missense_Mutation_p.M410K|SYTL2_ENST00000389960.4_Missense_Mutation_p.M410K|SYTL2_ENST00000316356.4_Missense_Mutation_p.M411K	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	410					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)		ACCAGAAGTCATTGGCTGATG	0.403																																					p.M411K		Atlas-SNP	.											.	SYTL2	231	.	0			c.T1232A						PASS	.						152	146	148					11																	85445140		2203	4299	6502	SO:0001583	missense	54843	exon6			GAAGTCATTGGCT	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.1229T>A	chr11.hg19:g.85445140A>T	ENSP00000431701:p.Met410Lys	182.0	0.0	.		156.0	43.0	.	NM_001162953	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	hg19	CCDS53688.1	.	.	.	.	.	.	.	.	.	.	A	7.911	0.736457	0.15574	.	.	ENSG00000137501	ENST00000389960;ENST00000316356;ENST00000528231;ENST00000527523;ENST00000524452	T;T;T;T;T	0.23348	2.0;2.01;2.01;1.91;2.0	5.81	-5.21	0.02815	.	.	.	.	.	T	0.10981	0.0268	N	0.22421	0.69	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.001;0.0;0.001;0.001	T	0.34104	-0.9842	8	.	.	.	.	1.191	0.01864	0.3579:0.26:0.0884:0.2937	.	362;410;410;411;268	Q9HCH5-14;Q9HCH5-6;Q9HCH5;Q9HCH5-13;Q9HCH5-15	.;.;SYTL2_HUMAN;.;.	K	410;411;410;362;410	ENSP00000374610:M410K;ENSP00000318803:M411K;ENSP00000431701:M410K;ENSP00000434010:M362K;ENSP00000435238:M410K	.	M	-	2	0	SYTL2	85122788	0.000000	0.05858	0.002000	0.10522	0.675000	0.39556	-2.151000	0.01289	-0.378000	0.07918	0.533000	0.62120	ATG	.	.	.	none		0.403	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927		T	85445140	A	T	85445140	3	4	101	1	0	0	0	0	1	0	0	0	15495	217	8	5	4108	5	SYTL2	11	85445140	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	9382169	85445140	49561376	50	6448											
ADAMTS8	11095	hgsc.bcm.edu	37	chr11	130284505	130284505	+	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	gcccgcacggcgtgccgtcaGcccagggcaggctgccattc	5	5	14	17	4	1	0	1	0	0	0	2	0	1	0	4	3	3	3	4	3	0	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr11:130284505G>T	ENST00000257359.6	-	5	2193	c.1487C>A	c.(1486-1488)gCt>gAt	p.A496D		NM_007037.4	NP_008968.4	Q9UP79	ATS8_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 8	496	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)		CGTGCCGTCAGCCCAGGGCAG	0.657																																					p.A496D		Atlas-SNP	.											.	ADAMTS8	172	.	0			c.C1487A						PASS	.						49	56	53					11																	130284505		2029	4184	6213	SO:0001583	missense	11095	exon5			CCGTCAGCCCAGG	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.1487C>A	chr11.hg19:g.130284505G>T	ENSP00000257359:p.Ala496Asp	170.0	0.0	.		124.0	39.0	.	NM_007037	Q9NZS0	Missense_Mutation	SNP	ENST00000257359.6	hg19	CCDS41732.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.252974	0.80135	.	.	ENSG00000134917	ENST00000257359;ENST00000414575	T	0.63255	-0.03	5.59	4.68	0.58851	.	0.000000	0.85682	D	0.000000	D	0.84234	0.5427	H	0.94964	3.605	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.88705	0.3218	10	0.87932	D	0	.	14.45	0.67379	0.0708:0.0:0.9292:0.0	.	496	Q9UP79	ATS8_HUMAN	D	496;525	ENSP00000257359:A496D	ENSP00000257359:A496D	A	-	2	0	ADAMTS8	129789715	1.000000	0.71417	0.873000	0.34254	0.657000	0.38888	3.871000	0.56077	1.355000	0.45865	0.655000	0.94253	GCT	.	.	.	none		0.657	ADAMTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385636.1	NM_007037		T	130284505	G	T	130284505	3	4	101	1	0	0	0	0	1	0	0	0	272	971	34	4	1202	4	ADAMTS8	11	130284505	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08	44839365	130284505	4722011	51	6449											
ITPR2	3709	hgsc.bcm.edu	37	chr12	26553127	26553127	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgaggccctggttcagcacGgtgacaatgcacataaggag	11	7	13	10	1	1	2	1	2	0	0	1	3	1	3	1	4	2	3	1	4	2	2	rs560385893		TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr12:26553127G>A	ENST00000381340.3	-	53	7880	c.7464C>T	c.(7462-7464)acC>acT	p.T2488T	RP11-513G19.1_ENST00000535324.1_RNA	NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	2488					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)	GGTTCAGCACGGTGACAATGC	0.413													g|||	1	0.000199681	0	0	5008	,	,		14883	0		0	False		,,,				2504	0.001				p.T2488T		Atlas-SNP	.											.	ITPR2	270	.	0			c.C7464T						PASS	.						122	119	120					12																	26553127		1920	4128	6048	SO:0001819	synonymous_variant	3709	exon53			CAGCACGGTGACA	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.7464C>T	chr12.hg19:g.26553127G>A		170.0	0.0	.		229.0	53.0	.	NM_002223	O94773	Silent	SNP	ENST00000381340.3	hg19	CCDS41764.1																																																																																			.	.	.	none		0.413	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		A	26553127	G	A	26553127	2	1	101	1	0	0	0	0	0	0	0	1	7928	1103	39	1		1	ITPR2	12	26553127	Silent	SNP	G	TCGA-B9-5156-01A-01D-1589-08		26553127	107298768	52	6450											
AMHR2	269	hgsc.bcm.edu	37	chr12	53824991	53824991	+	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	ggctgagggagctcctagaaGactgttgggatgcagaccca	10	7	15	9	0	0	4	0	1	0	3	1	6	1	6	2	3	2	4	2	3	2	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr12:53824991G>C	ENST00000257863.4	+	11	1536	c.1456G>C	c.(1456-1458)Gac>Cac	p.D486H	AMHR2_ENST00000550311.1_3'UTR|AMHR2_ENST00000379791.3_Missense_Mutation_p.D391H	NM_001164690.1|NM_020547.2	NP_001158162.1|NP_065434.1	Q16671	AMHR2_HUMAN	anti-Mullerian hormone receptor, type II	486	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				Mullerian duct regression (GO:0001880)|negative regulation of anti-Mullerian hormone signaling pathway (GO:1902613)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	integral component of plasma membrane (GO:0005887)	anti-Mullerian hormone receptor activity (GO:1990272)|ATP binding (GO:0005524)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor activity, type II (GO:0005026)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|skin(2)	34					Adenosine triphosphate(DB00171)	GCTCCTAGAAGACTGTTGGGA	0.592																																					p.D486H		Atlas-SNP	.											.	AMHR2	61	.	0			c.G1456C						PASS	.						77	78	78					12																	53824991		2203	4300	6503	SO:0001583	missense	269	exon11			CTAGAAGACTGTT	AF172932	CCDS8858.1, CCDS53798.1, CCDS55829.1	12q13	2013-03-14							465	protein-coding gene	gene with protein product	"Muellerian inhibiting substance type II receptor"	600956				7493017	Standard	NM_001164690		Approved	MISR2, MISRII	uc001scx.2	Q16671	OTTHUMG00000170048	ENST00000257863.4:c.1456G>C	chr12.hg19:g.53824991G>C	ENSP00000257863:p.Asp486His	193.0	0.0	.		166.0	83.0	.	NM_020547	A0AVE1|B9EGB7|E9PGD2|F8W1D2|Q13762|Q647K2	Missense_Mutation	SNP	ENST00000257863.4	hg19	CCDS8858.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.579839	0.86645	.	.	ENSG00000135409	ENST00000257863;ENST00000379791	T;D	0.93247	-0.21;-3.19	4.86	4.86	0.63082	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.39834	N	0.001257	D	0.95484	0.8533	L	0.56340	1.77	0.30411	N	0.779055	D	0.89917	1.0	D	0.97110	1.0	D	0.92996	0.6419	10	0.87932	D	0	.	15.3949	0.74784	0.0:0.0:1.0:0.0	.	486	Q16671	AMHR2_HUMAN	H	486;391	ENSP00000257863:D486H;ENSP00000369117:D391H	ENSP00000257863:D486H	D	+	1	0	AMHR2	52111258	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.206000	0.77891	2.691000	0.91804	0.563000	0.77884	GAC	.	.	.	none		0.592	AMHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407048.1	NM_020547		C	53824991	G	C	53824991	3	2	101	1	0	0	0	0	1	0	0	0	573	942	33	4	1498	4	AMHR2	12	53824991	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08	27271864	53824991	80026904	53	6451											
WSCD2	9671	hgsc.bcm.edu	37	chr12	108641980	108641980	+	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	agaaggatggcaacttcaagCgctcagggctccggaagctc	11	6	13	11	2	2	1	2	0	0	1	4	3	3	3	1	4	3	4	1	4	4	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr12:108641980C>T	ENST00000332082.4	+	10	2376	c.1558C>T	c.(1558-1560)Cgc>Tgc	p.R520C	WSCD2_ENST00000549903.1_Missense_Mutation_p.R540C|WSCD2_ENST00000547525.1_Missense_Mutation_p.R520C|WSCD2_ENST00000261400.3_Missense_Mutation_p.R540C			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	520						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						CAACTTCAAGCGCTCAGGGCT	0.602																																					p.R520C		Atlas-SNP	.											.	WSCD2	125	.	0			c.C1558T						PASS	.						59	66	64					12																	108641980		2036	4193	6229	SO:0001583	missense	9671	exon9			TTCAAGCGCTCAG		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.1558C>T	chr12.hg19:g.108641980C>T	ENSP00000331933:p.Arg520Cys	80.0	0.0	.		95.0	19.0	.	NM_014653	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Missense_Mutation	SNP	ENST00000332082.4	hg19	CCDS41828.1	.	.	.	.	.	.	.	.	.	.	C	19.35	3.809847	0.70797	.	.	ENSG00000075035	ENST00000547525;ENST00000261400;ENST00000332082;ENST00000549903	T;T;T;T	0.58060	0.36;3.98;0.36;3.98	4.46	4.46	0.54185	.	0.000000	0.85682	D	0.000000	T	0.73071	0.3540	M	0.78637	2.42	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.996	T	0.78285	-0.2263	10	0.87932	D	0	-44.2877	16.1113	0.81266	0.0:1.0:0.0:0.0	.	540;520	Q2TBF2-2;Q2TBF2	.;WSCD2_HUMAN	C	520;540;520;540	ENSP00000448047:R520C;ENSP00000261400:R540C;ENSP00000331933:R520C;ENSP00000447272:R540C	ENSP00000261400:R540C	R	+	1	0	WSCD2	107166110	1.000000	0.71417	1.000000	0.80357	0.795000	0.44927	5.717000	0.68446	2.029000	0.59856	0.655000	0.94253	CGC	.	.	.	none		0.602	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405554.1	NM_014653		T	108641980	C	T	108641980	3	4	101	1	0	0	0	0	1	0	0	0	17419	768	27	1	1588	1	WSCD2	12	108641980	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08	54816989	108641980	25209915	54	6452											
FREM2	341640	hgsc.bcm.edu	37	chr13	39452997	39452997	+	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	cagccagagacacaagcgacCagttttggaaatgtcctatt	13	9	9	10	1	0	1	0	0	0	1	1	4	1	2	3	1	2	1	3	1	3	4			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr13:39452997C>G	ENST00000280481.7	+	23	9105	c.8889C>G	c.(8887-8889)acC>acG	p.T2963T		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2963					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)		CACAAGCGACCAGTTTTGGAA	0.448																																					p.T2963T		Atlas-SNP	.											.	FREM2	385	.	0			c.C8889G						PASS	.						162	148	153					13																	39452997		2203	4300	6503	SO:0001819	synonymous_variant	341640	exon23			AGCGACCAGTTTT	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.8889C>G	chr13.hg19:g.39452997C>G		128.0	0.0	.		122.0	35.0	.	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	hg19	CCDS31960.1																																																																																			.	.	.	none		0.448	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		G	39452997	C	G	39452997	2	3	101	1	0	0	0	0	0	0	0	1	6052	581	21	4		4	FREM2	13	39452997	Silent	SNP	C	TCGA-B9-5156-01A-01D-1589-08		39452997	75716881	55	6453											
C13orf23	80209	hgsc.bcm.edu	37	chr13	39587574	39587574	+	Frame_Shift_Del	DEL	A	A	-																															gtgggctcagttttgatcatAacaggaagagttgttgcagc																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr13:39587574delA	ENST00000352251.3	-	11	2648	c.1815delT	c.(1813-1815)gttfs	p.V605fs	PROSER1_ENST00000484434.3_Intron|PROSER1_ENST00000350125.3_Frame_Shift_Del_p.V583fs	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	605	Ser-rich.																TTTTGATCATAACAGGAAGAG	0.517																																					p.M606X		Atlas-INDEL	.											.	.	.	.	0			c.1816delA						PASS	.						153	163	159					13																	39587574		2203	4300	6503	SO:0001589	frameshift_variant	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.1815delT	chr13.hg19:g.39587574delA	ENSP00000332034:p.Val605fs	247.0	0.0	0		191.0	72.0	0.376963	NM_025138	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Frame_Shift_Del	DEL	ENST00000352251.3	hg19	CCDS9368.2																																																																																			.	.	.	none		0.517	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138		-	39587574	A	-	39587574	7	5	101	1	0	1	0	1	0	0	0	0	1723	349	13	0	1031	0	C13orf23	13	39587574	Frame_Shift_Del	DEL	A	TCGA-B9-5156-01A-01D-1589-08	134577	39587574	75582304	56	6454											
MYH6	4624	hgsc.bcm.edu	37	chr14	23862897	23862897	+	Missense_Mutation	SNP	T	T	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	tgttctctgttgcatgcttcTccttctccaccttggccagt	3	17	7	14	0	3	0	0	0	3	0	6	0	3	0	4	1	2	4	4	1	0	5			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr14:23862897T>G	ENST00000356287.3	-	21	2935	c.2906A>C	c.(2905-2907)gAg>gCg	p.E969A	MYH6_ENST00000405093.3_Missense_Mutation_p.E969A			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	969					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)		TGCATGCTTCTCCTTCTCCAC	0.562																																					p.E969A		Atlas-SNP	.											.	MYH6	274	.	0			c.A2906C						PASS	.						206	174	185					14																	23862897		2203	4300	6503	SO:0001583	missense	4624	exon22			TGCTTCTCCTTCT	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.2906A>C	chr14.hg19:g.23862897T>G	ENSP00000348634:p.Glu969Ala	142.0	0.0	.		113.0	33.0	.	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	hg19	CCDS9600.1	.	.	.	.	.	.	.	.	.	.	t	18.08	3.544179	0.65198	.	.	ENSG00000197616	ENST00000405093;ENST00000356287	D;D	0.92911	-3.13;-3.13	4.95	4.95	0.65309	.	.	.	.	.	D	0.95143	0.8426	H	0.94964	3.605	0.58432	D	0.999999	P	0.35527	0.507	B	0.41764	0.366	D	0.95789	0.8823	9	0.62326	D	0.03	.	14.9359	0.70954	0.0:0.0:0.0:1.0	.	969	P13533	MYH6_HUMAN	A	969	ENSP00000386041:E969A;ENSP00000348634:E969A	ENSP00000348634:E969A	E	-	2	0	MYH6	22932737	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.776000	0.85560	1.992000	0.58205	0.528000	0.53228	GAG	.	.	.	none		0.562	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			G	23862897	T	G	23862897	3	3	101	1	0	0	0	0	1	0	0	0	10045	1551	54	5	2985	5	MYH6	14	23862897	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08		23862897	83486643	57	6455											
MYH7	4625	hgsc.bcm.edu	37	chr14	23897724	23897724	+	Missense_Mutation	SNP	A	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	ggcaccttctcgatgaggtcAatgcaggcctgcaggtccat	8	9	12	12	1	2	1	1	1	1	0	4	2	3	1	3	4	2	3	3	4	1	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr14:23897724A>C	ENST00000355349.3	-	15	1725	c.1563T>G	c.(1561-1563)atT>atG	p.I521M		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	521	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		CGATGAGGTCAATGCAGGCCT	0.517																																					p.I521M		Atlas-SNP	.											.	MYH7	349	.	0			c.T1563G						PASS	.						231	168	189					14																	23897724		2203	4300	6503	SO:0001583	missense	4625	exon15			GAGGTCAATGCAG	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.1563T>G	chr14.hg19:g.23897724A>C	ENSP00000347507:p.Ile521Met	123.0	0.0	.		82.0	6.0	.	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	hg19	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	A	16.30	3.084286	0.55861	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	D	0.96396	-4.0	4.63	-6.69	0.01772	Myosin head, motor domain (3);	.	.	.	.	D	0.98865	0.9616	H	0.98769	4.325	0.47476	D	0.999438	P	0.35551	0.509	D	0.63192	0.912	D	0.97432	1.0016	9	0.87932	D	0	.	16.9993	0.86377	0.8517:0.0:0.1483:0.0	.	521	P12883	MYH7_HUMAN	M	521	ENSP00000347507:I521M	ENSP00000347507:I521M	I	-	3	3	MYH7	22967564	0.716000	0.27956	0.769000	0.31535	0.940000	0.58332	-0.030000	0.12308	-1.432000	0.01979	-1.028000	0.02416	ATT	.	.	.	none		0.517	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		C	23897724	A	C	23897724	3	2	101	1	0	0	0	0	1	0	0	0	10046	126	5	5	4348	5	MYH7	14	23897724	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	34827	23897724	83451816	58	6456											
RIPK3	11035	hgsc.bcm.edu	37	chr14	24805465	24805465	+	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	tcttgcgaacctactggtggGgggtgctgcaagcccctccc	5	9	13	14	1	1	0	0	0	1	0	2	1	2	0	4	4	6	2	4	4	3	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr14:24805465G>T	ENST00000216274.5	-	10	1691	c.1473C>A	c.(1471-1473)ccC>ccA	p.P491P	ADCY4_ENST00000396747.3_5'Flank|ADCY4_ENST00000310677.4_5'Flank|RIPK3_ENST00000554338.1_5'Flank|ADCY4_ENST00000554068.2_5'Flank|RP11-934B9.3_ENST00000555591.1_Intron|ADCY4_ENST00000418030.2_5'Flank|ADCY4_ENST00000558563.1_5'Flank	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	491					activation of protein kinase activity (GO:0032147)|amyloid fibril formation (GO:1990000)|apoptotic signaling pathway (GO:0097190)|cellular protein modification process (GO:0006464)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of ligase activity (GO:0051351)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein deacetylation (GO:0090312)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of activated T cell proliferation (GO:0046006)|regulation of activation-induced cell death of T cells (GO:0070235)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000452)|regulation of interferon-gamma production (GO:0032649)|regulation of T cell mediated cytotoxicity (GO:0001914)|signal transduction (GO:0007165)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|NF-kappaB-inducing kinase activity (GO:0004704)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				GBM - Glioblastoma multiforme(265;0.0181)		CTACTGGTGGGGGGTGCTGCA	0.542																																					p.P491P	Pancreas(58;918 1191 4668 13304 15331)	Atlas-SNP	.											.	RIPK3	43	.	0			c.C1473A						PASS	.						75	78	77					14																	24805465		2203	4300	6503	SO:0001819	synonymous_variant	11035	exon10			TGGTGGGGGGTGC	AF156884	CCDS9628.1	14q12	2006-05-15			ENSG00000129465	ENSG00000129465			10021	protein-coding gene	gene with protein product		605817				10339433, 10358032	Standard	NM_006871		Approved	RIP3	uc001wpb.3	Q9Y572	OTTHUMG00000029349	ENST00000216274.5:c.1473C>A	chr14.hg19:g.24805465G>T		138.0	0.0	.		102.0	27.0	.	NM_006871	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Silent	SNP	ENST00000216274.5	hg19	CCDS9628.1																																																																																			.	.	.	none		0.542	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871		T	24805465	G	T	24805465	2	4	101	1	0	0	0	0	0	0	0	1	13395	1219	43	4		4	RIPK3	14	24805465	Silent	SNP	G	TCGA-B9-5156-01A-01D-1589-08	907741	24805465	82544075	59	6457											
NR2E3	10002	hgsc.bcm.edu	37	chr15	72104834	72104834	+	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	acctgcctgtgttctccagcCtgcccttccgggatcaggta	5	11	10	15	1	2	0	1	0	1	0	4	1	3	1	6	2	3	2	6	2	1	3			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr15:72104834C>T	ENST00000398840.2	+	0	920							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						GTTCTCCAGCCTGCCCTTCCG	0.647																																					p.L244L		Atlas-SNP	.											.	NR2E3	53	.	0			c.C730T						PASS	.						48	54	52					15																	72104834		2027	4165	6192			10002	exon5			TCCAGCCTGCCCT		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		chr15.hg19:g.72104834C>T		17.0	0.0	.		28.0	10.0	.	NM_016346	B6ZGU0|Q9UHM4	Silent	SNP	ENST00000398840.2	hg19																																																																																				.	.	.	none		0.647	NR2E3-202	KNOWN	basic	processed_transcript	processed_transcript		NM_014249		T	72104834	C	T	72104834	1	4	101	0	1	0	0	0	0	0	0	0	10633	680	24	2		2	NR2E3	15	72104834	RNA	SNP	C	TCGA-B9-5156-01A-01D-1589-08		72104834	30426558	60	6458											
PKD1	5310	hgsc.bcm.edu	37	chr16	2155892	2155892	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagcacggtgaccagggccaAcgagtactcgatgacgtgct	10	6	13	12	4	0	2	0	2	0	0	1	4	0	2	2	2	4	3	2	2	2	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr16:2155892A>G	ENST00000262304.4	-	20	8045	c.7837T>C	c.(7837-7839)Ttg>Ctg	p.L2613L	PKD1_ENST00000561991.1_5'UTR|PKD1_ENST00000423118.1_Silent_p.L2613L	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	2613	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.		Missing (in PKD1; unknown pathological significance). {ECO:0000269|PubMed:11571556}.		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)	p.L2613L(1)		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						ACCAGGGCCAACGAGTACTCG	0.657																																					p.L2613L		Atlas-SNP	.											PKD1,NS,carcinoma,0,1	PKD1	184	.	1	Substitution - coding silent(1)	lung(1)	c.T7837C						PASS	.						46	45	45					16																	2155892		1400	2465	3865	SO:0001819	synonymous_variant	5310	exon20			GGGCCAACGAGTA	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.7837T>C	chr16.hg19:g.2155892A>G		48.0	2.0	.		67.0	4.0	.	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	hg19	CCDS32369.1																																																																																			.	.	.	none		0.657	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			G	2155892	A	G	2155892	2	3	101	1	0	0	0	0	0	0	0	1	11970	40	2	3		3	PKD1	16	2155892	Silent	SNP	A	TCGA-B9-5156-01A-01D-1589-08		2155892	88198861	61	6459											
MYLK3	91807	hgsc.bcm.edu	37	chr16	46766187	46766187	+	Silent	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	gcttcagctctcaccggagcCctggctgcacagtcctgctc	5	9	10	17	1	2	0	2	0	1	0	5	1	3	1	3	2	4	5	3	2	0	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr16:46766187C>T	ENST00000394809.4	-	4	1510	c.1395G>A	c.(1393-1395)agG>agA	p.R465R	MYLK3_ENST00000536476.1_Silent_p.R124R	NM_182493.2	NP_872299.2	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3	465					cardiac myofibril assembly (GO:0055003)|cellular response to interleukin-1 (GO:0071347)|positive regulation of sarcomere organization (GO:0060298)|protein phosphorylation (GO:0006468)|regulation of vascular permeability involved in acute inflammatory response (GO:0002528)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(5)|stomach(3)	37		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				TCACCGGAGCCCTGGCTGCAC	0.657																																					p.R465R		Atlas-SNP	.											.	MYLK3	82	.	0			c.G1395A						PASS	.						35	39	37					16																	46766187		2203	4300	6503	SO:0001819	synonymous_variant	91807	exon4			CGGAGCCCTGGCT	AJ247087	CCDS10723.2	16q11.2	2008-10-23			ENSG00000140795	ENSG00000140795			29826	protein-coding gene	gene with protein product	"MLC kinase"	612147				17885681	Standard	NM_182493		Approved	caMLCK, MLCK	uc002eei.4	Q32MK0	OTTHUMG00000132543	ENST00000394809.4:c.1395G>A	chr16.hg19:g.46766187C>T		70.0	0.0	.		110.0	57.0	.	NM_182493	B5BUL9|B7Z5U8|Q32MK1|Q96DV1	Silent	SNP	ENST00000394809.4	hg19	CCDS10723.2																																																																																			.	.	.	none		0.657	MYLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255743.2	NM_182493		T	46766187	C	T	46766187	2	4	101	1	0	0	0	0	0	0	0	1	10065	622	22	2		2	MYLK3	16	46766187	Silent	SNP	C	TCGA-B9-5156-01A-01D-1589-08	44610295	46766187	43588566	62	6460											
AMFR	267	hgsc.bcm.edu	37	chr16	56435720	56435720	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agatggcacagtcgtcattgTtgacagccagctcctctgga	9	10	11	11	1	2	2	1	1	1	1	4	3	3	3	2	2	2	3	2	2	0	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr16:56435720T>C	ENST00000290649.5	-	8	1220	c.1010A>G	c.(1009-1011)aAc>aGc	p.N337S		NM_001144.5	NP_001135.3	Q9UKV5	AMFR_HUMAN	autocrine motility factor receptor, E3 ubiquitin protein ligase	337					aging (GO:0007568)|cellular component movement (GO:0006928)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|learning or memory (GO:0007611)|protein oligomerization (GO:0051259)|protein polyubiquitination (GO:0000209)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)	dendrite (GO:0030425)|endoplasmic reticulum membrane (GO:0005789)|growth cone (GO:0030426)|Hrd1p ubiquitin ligase complex (GO:0000836)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	ligase activity (GO:0016874)|receptor activity (GO:0004872)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17						GTCGTCATTGTTGACAGCCAG	0.522																																					p.N337S	Pancreas(2;144 323 39528)	Atlas-SNP	.											.	AMFR	40	.	0			c.A1010G						PASS	.						113	106	109					16																	56435720		2198	4300	6498	SO:0001583	missense	267	exon8			TCATTGTTGACAG	L35233	CCDS10758.1	16q21	2013-01-09	2012-02-23		ENSG00000159461	ENSG00000159461		"RING-type (C3HC4) zinc fingers"	463	protein-coding gene	gene with protein product		603243	"autocrine motility factor receptor"			1649192	Standard	NM_001144		Approved	RNF45, gp78	uc002eiy.4	Q9UKV5	OTTHUMG00000133239	ENST00000290649.5:c.1010A>G	chr16.hg19:g.56435720T>C	ENSP00000290649:p.Asn337Ser	143.0	0.0	.		174.0	85.0	.	NM_001144	P26442|Q8IZ70	Missense_Mutation	SNP	ENST00000290649.5	hg19	CCDS10758.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.281024	0.80692	.	.	ENSG00000159461	ENST00000290649	T	0.66280	-0.2	5.63	5.63	0.86233	Zinc finger, RING/FYVE/PHD-type (1);	0.083860	0.85682	D	0.000000	T	0.54515	0.1863	L	0.50333	1.59	0.80722	D	1	P	0.37061	0.58	B	0.34590	0.186	T	0.52823	-0.8524	10	0.13108	T	0.6	-19.7475	15.8526	0.78943	0.0:0.0:0.0:1.0	.	337	Q9UKV5	AMFR2_HUMAN	S	337	ENSP00000290649:N337S	ENSP00000290649:N337S	N	-	2	0	AMFR	54993221	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	7.862000	0.87013	2.141000	0.66446	0.528000	0.53228	AAC	.	.	.	none		0.522	AMFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256978.2			C	56435720	T	C	56435720	3	2	101	1	0	0	0	0	1	0	0	0	571	1725	60	3	949	3	AMFR	16	56435720	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08	9669533	56435720	33919033	63	6461											
EFCAB5	374786	hgsc.bcm.edu	37	chr17	28405254	28405255	+	Frame_Shift_Ins	INS	-	-	A																															aaactacacatccaatttccINSaaagccacaccctggtcacg																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr17:28405254_28405255insA	ENST00000394835.3	+	15	2951_2952	c.2759_2760insA	c.(2758-2763)ccaaagfs	p.PK920fs	EFCAB5_ENST00000394832.2_Intron|EFCAB5_ENST00000320856.5_Frame_Shift_Ins_p.PK796fs	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	920							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						ATCCAATTTCCAAAGCCACACC	0.411																																					p.P920fs		Atlas-INDEL	.											.	EFCAB5	122	.	0			c.2759_2760insA						PASS	.																																			SO:0001589	frameshift_variant	374786	exon15			.	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.2762dupA	chr17.hg19:g.28405257_28405257dupA	ENSP00000378312:p.Pro920fs	54.0	0.0	0		88.0	19.0	0.215909	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Frame_Shift_Ins	INS	ENST00000394835.3	hg19	CCDS11254.2																																																																																			.	.	.	none		0.411	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529		A	28405255	-	A	28405254	7	5	101	1	0	1	1	0	0	0	0	0	4940	594	21	0	2984	0	EFCAB5	17	28405254	Frame_Shift_Ins	INS	-	TCGA-B9-5156-01A-01D-1589-08		28405254	52789956	64	6462											
SMAD4	4089	hgsc.bcm.edu	37	chr18	48581177	48581177	+	Missense_Mutation	SNP	G	G	A																															caagtatgatggtgaaggatGaatatgtgcatgactttgag																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr18:48581177G>A	ENST00000342988.3	+	5	1019	c.481G>A	c.(481-483)Gaa>Aaa	p.E161K	SMAD4_ENST00000398417.2_Missense_Mutation_p.E161K|SMAD4_ENST00000588745.1_Missense_Mutation_p.E161K|RP11-729L2.2_ENST00000590722.2_3'UTR|SMAD4_ENST00000452201.2_3'UTR	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	161					atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(3)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		GGTGAAGGATGAATATGTGCA	0.358																																					p.E161K		Atlas-SNP	.											.	SMAD4	822	.	39	Whole gene deletion(36)|Unknown(3)	pancreas(26)|large_intestine(3)|stomach(3)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	c.G481A						PASS	.						127	92	104					18																	48581177		2203	4300	6503	SO:0001583	missense	4089	exon5			AAGGATGAATATG	U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.481G>A	chr18.hg19:g.48581177G>A	ENSP00000341551:p.Glu161Lys	107.0	0.0	.		86.0	19.0	.	NM_005359	A8K405	Missense_Mutation	SNP	ENST00000342988.3	hg19	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	G	35	5.555908	0.96514	.	.	ENSG00000141646	ENST00000342988;ENST00000544926;ENST00000398417	D;D	0.97688	-4.49;-4.49	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.96975	0.9012	M	0.67397	2.05	0.80722	D	1	P	0.44195	0.828	B	0.41666	0.363	D	0.97207	0.9868	10	0.59425	D	0.04	.	19.1262	0.93386	0.0:0.0:1.0:0.0	.	161	Q13485	SMAD4_HUMAN	K	161	ENSP00000341551:E161K;ENSP00000381452:E161K	ENSP00000341551:E161K	E	+	1	0	SMAD4	46835175	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.567000	0.98161	2.890000	0.99128	0.585000	0.79938	GAA	.	.	.	none		0.358	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		A	48581177	G	A	48581177	3	1	101	1	0	0	0	0	1	0	0	0	14773	1291	45	2	495	2	SMAD4	18	48581177	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08		48581177	29496071	65	6463	69	2									
SMAD4	4089	hgsc.bcm.edu	37	chr18	48581187	48581187	+	Missense_Mutation	SNP	A	A	G																															ggtgaaggatgaatatgtgcAtgactttgagggacagccat																										TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr18:48581187A>G	ENST00000342988.3	+	5	1029	c.491A>G	c.(490-492)cAt>cGt	p.H164R	SMAD4_ENST00000398417.2_Missense_Mutation_p.H164R|SMAD4_ENST00000588745.1_Missense_Mutation_p.H164R|RP11-729L2.2_ENST00000590722.2_3'UTR|SMAD4_ENST00000452201.2_3'UTR	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	164					atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(3)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		GAATATGTGCATGACTTTGAG	0.368																																					p.H164R		Atlas-SNP	.											.	SMAD4	822	.	39	Whole gene deletion(36)|Unknown(3)	pancreas(26)|large_intestine(3)|stomach(3)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	c.A491G						PASS	.						148	105	119					18																	48581187		2203	4300	6503	SO:0001583	missense	4089	exon5			ATGTGCATGACTT	U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.491A>G	chr18.hg19:g.48581187A>G	ENSP00000341551:p.His164Arg	117.0	0.0	.		102.0	26.0	.	NM_005359	A8K405	Missense_Mutation	SNP	ENST00000342988.3	hg19	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	A	13.16	2.154905	0.38021	.	.	ENSG00000141646	ENST00000342988;ENST00000544926;ENST00000398417	D;D	0.97378	-4.36;-4.36	5.86	4.64	0.57946	.	0.115658	0.64402	D	0.000020	D	0.92753	0.7696	L	0.29908	0.895	0.80722	D	1	B	0.25904	0.137	B	0.17979	0.02	D	0.90115	0.4195	10	0.20046	T	0.44	.	12.835	0.57767	0.8649:0.1351:0.0:0.0	.	164	Q13485	SMAD4_HUMAN	R	164	ENSP00000341551:H164R;ENSP00000381452:H164R	ENSP00000341551:H164R	H	+	2	0	SMAD4	46835185	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.912000	0.48782	2.367000	0.80283	0.528000	0.53228	CAT	.	.	.	none		0.368	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		G	48581187	A	G	48581187	3	3	101	1	0	0	0	0	1	0	0	0	14773	217	8	3	505	3	SMAD4	18	48581187	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	10	48581187	29496061	66	6464	69	2									
RNF152	220441	hgsc.bcm.edu	37	chr18	59483577	59483577	+	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	ttctggctggtcctcatctgCtgcaggcacactgaacagca	8	10	10	13	0	3	1	1	1	2	0	4	1	4	1	1	3	4	5	1	3	1	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr18:59483577C>A	ENST00000312828.3	-	2	1219	c.120G>T	c.(118-120)caG>caT	p.Q40H		NM_173557.2	NP_775828.1	Q8N8N0	RN152_HUMAN	ring finger protein 152	40					apoptotic process (GO:0006915)|protein K48-linked ubiquitination (GO:0070936)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(10)|skin(1)	17		Colorectal(73;0.186)				TCCTCATCTGCTGCAGGCACA	0.622																																					p.Q40H		Atlas-SNP	.											.	RNF152	37	.	0			c.G120T						PASS	.						48	50	49					18																	59483577		2203	4300	6503	SO:0001583	missense	220441	exon2			CATCTGCTGCAGG	AK096495	CCDS11978.1	18q21.33	2013-01-09			ENSG00000176641	ENSG00000176641		"RING-type (C3HC4) zinc fingers"	26811	protein-coding gene	gene with protein product							Standard	XM_005266650		Approved	FLJ39176	uc002lih.1	Q8N8N0	OTTHUMG00000132774	ENST00000312828.3:c.120G>T	chr18.hg19:g.59483577C>A	ENSP00000316628:p.Gln40His	74.0	0.0	.		70.0	29.0	.	NM_173557	B3KV99|Q52LA4	Missense_Mutation	SNP	ENST00000312828.3	hg19	CCDS11978.1	.	.	.	.	.	.	.	.	.	.	C	17.50	3.404965	0.62288	.	.	ENSG00000176641	ENST00000312828	D	0.92545	-3.06	4.97	4.97	0.65823	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.427187	0.24662	N	0.036625	D	0.91355	0.7273	L	0.37561	1.115	0.41272	D	0.986853	P	0.37781	0.608	P	0.45998	0.5	D	0.91326	0.5086	10	0.48119	T	0.1	-30.3756	18.4187	0.90579	0.0:1.0:0.0:0.0	.	40	Q8N8N0	RN152_HUMAN	H	40	ENSP00000316628:Q40H	ENSP00000316628:Q40H	Q	-	3	2	RNF152	57634557	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.177000	0.58276	2.600000	0.87896	0.655000	0.94253	CAG	.	.	.	none		0.622	RNF152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256180.1	NM_173557		A	59483577	C	A	59483577	3	1	101	1	0	0	0	0	1	0	0	0	13466	796	28	4	495	4	RNF152	18	59483577	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08	10902390	59483577	18593671	67	6465											
FZR1	51343	hgsc.bcm.edu	37	chr19	3527659	3527659	+	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	ctccggtccccccggaaaccCacccgcaagatctccaagat	10	5	7	19	3	1	2	0	0	1	2	4	3	3	3	7	2	1	1	7	2	3	0			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr19:3527659C>A	ENST00000395095.3	+	6	501	c.501C>A	c.(499-501)ccC>ccA	p.P167P	FZR1_ENST00000441788.2_Silent_p.P167P|FZR1_ENST00000313639.8_Intron	NM_001136198.1	NP_001129670.1	Q9UM11	FZR_HUMAN	fizzy/cell division cycle 20 related 1 (Drosophila)	167					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)		CCCGGAAACCCACCCGCAAGA	0.622																																					p.P167P		Atlas-SNP	.											.	FZR1	42	.	0			c.C501A						PASS	.						65	55	59					19																	3527659		2199	4296	6495	SO:0001819	synonymous_variant	51343	exon6			GAAACCCACCCGC	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.501C>A	chr19.hg19:g.3527659C>A		60.0	0.0	.		42.0	9.0	.	NM_001136198	O75869|Q86U66|Q96NW8|Q9UI96|Q9ULH8|Q9UM10|Q9UNQ1|Q9Y2T8	Silent	SNP	ENST00000395095.3	hg19	CCDS45916.1																																																																																			.	.	.	none		0.622	FZR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452869.2	NM_016263		A	3527659	C	A	3527659	2	1	101	1	0	0	0	0	0	0	0	1	6145	581	21	4		4	FZR1	19	3527659	Silent	SNP	C	TCGA-B9-5156-01A-01D-1589-08		3527659	55601324	68	6466											
MAP2K2	5605	hgsc.bcm.edu	37	chr19	4117623	4117623	+	Missense_Mutation	SNP	T	T	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	cttctgcaggtccaccaggtTtgccctgcagagacccccca	7	8	9	17	0	1	1	0	0	1	1	2	2	2	1	6	2	3	3	6	2	0	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr19:4117623T>G	ENST00000262948.5	-	2	350	c.97A>C	c.(97-99)Aac>Cac	p.N33H	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	33					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)	TCCACCAGGTTTGCCCTGCAG	0.607																																					p.N33H		Atlas-SNP	.											.	MAP2K2	72	.	0			c.A97C						PASS	.						61	63	62					19																	4117623		2203	4300	6503	SO:0001583	missense	5605	exon2			CCAGGTTTGCCCT	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.97A>C	chr19.hg19:g.4117623T>G	ENSP00000262948:p.Asn33His	103.0	0.0	.		64.0	23.0	.	NM_030662		Missense_Mutation	SNP	ENST00000262948.5	hg19	CCDS12120.1	.	.	.	.	.	.	.	.	.	.	t	10.40	1.339579	0.24339	.	.	ENSG00000126934	ENST00000262948	D	0.93189	-3.18	4.14	1.96	0.26148	.	0.114851	0.56097	N	0.000021	D	0.92057	0.7483	M	0.64997	1.995	0.80722	D	1	P	0.41597	0.756	P	0.45829	0.494	D	0.88376	0.2998	10	0.45353	T	0.12	-24.2755	10.059	0.42263	0.0:0.0:0.3226:0.6774	.	33	P36507	MP2K2_HUMAN	H	33	ENSP00000262948:N33H	ENSP00000262948:N33H	N	-	1	0	MAP2K2	4068623	1.000000	0.71417	0.448000	0.26945	0.147000	0.21601	4.829000	0.62737	0.137000	0.18759	0.454000	0.30748	AAC	.	.	.	none		0.607	MAP2K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258957.2			G	4117623	T	G	4117623	3	3	101	1	0	0	0	0	1	0	0	0	9244	1841	64	5	1145	5	MAP2K2	19	4117623	Missense_Mutation	SNP	T	TCGA-B9-5156-01A-01D-1589-08	589964	4117623	55011360	69	6467											
KDM4B	23030	hgsc.bcm.edu	37	chr19	5082513	5082513	+	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	actacggcaaagtggccactCaggtaaaagcttgcctgctg	11	8	11	11	1	1	0	1	0	0	0	1	0	1	0	2	3	4	4	2	3	4	3			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr19:5082513C>A	ENST00000159111.4	+	9	1134	c.916C>A	c.(916-918)Cag>Aag	p.Q306K	KDM4B_ENST00000536461.1_Missense_Mutation_p.Q306K|KDM4B_ENST00000381759.4_Missense_Mutation_p.Q306K	NM_015015.2	NP_055830	O94953	KDM4B_HUMAN	lysine (K)-specific demethylase 4B	306	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(1)|liver(1)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						AGTGGCCACTCAGGTAAAAGC	0.597																																					p.Q306K		Atlas-SNP	.											.	KDM4B	120	.	0			c.C916A						PASS	.						33	35	35					19																	5082513		2203	4300	6503	SO:0001583	missense	23030	exon9			GCCACTCAGGTAA	AB020683	CCDS12138.1	19p13.3	2013-01-23	2009-04-06	2009-04-06		ENSG00000127663		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	29136	protein-coding gene	gene with protein product	"tudor domain containing 14B"	609765	"jumonji domain containing 2B"	JMJD2B		10048485, 15138608	Standard	NM_015015		Approved	KIAA0876, TDRD14B	uc002mbq.4	O94953		ENST00000159111.4:c.916C>A	chr19.hg19:g.5082513C>A	ENSP00000159111:p.Gln306Lys	56.0	0.0	.		38.0	9.0	.	NM_015015	B9EGN8|D6W631|O75274|Q6P3R5|Q9P1V1|Q9UF40	Missense_Mutation	SNP	ENST00000159111.4	hg19	CCDS12138.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.174210	0.78452	.	.	ENSG00000127663	ENST00000159111;ENST00000381759;ENST00000536461	T;T;T	0.71222	-0.55;-0.55;-0.55	4.95	4.95	0.65309	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.064498	0.64402	D	0.000005	T	0.65450	0.2692	L	0.45285	1.41	0.52501	D	0.999957	B;B;P	0.38473	0.191;0.354;0.633	B;B;B	0.42738	0.268;0.283;0.396	T	0.62586	-0.6823	10	0.05436	T	0.98	-39.1865	18.1627	0.89714	0.0:1.0:0.0:0.0	.	306;306;306	F5GX28;O94953-2;O94953	.;.;KDM4B_HUMAN	K	306	ENSP00000159111:Q306K;ENSP00000371178:Q306K;ENSP00000440495:Q306K	ENSP00000159111:Q306K	Q	+	1	0	KDM4B	5033513	0.999000	0.42202	0.991000	0.47740	0.913000	0.54294	4.054000	0.57434	2.304000	0.77564	0.462000	0.41574	CAG	.	.	.	none		0.597	KDM4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450558.1	NM_015015		A	5082513	C	A	5082513	3	1	101	1	0	0	0	0	1	0	0	0	8136	827	29	4	942	4	KDM4B	19	5082513	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08	964890	5082513	54046470	70	6468											
KANK2	25959	hgsc.bcm.edu	37	chr19	11304538	11304538	+	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	aggagccagggccacggggcAgcgagctcaggcgggggcgg	7	1	22	11	4	1	0	1	0	0	0	1	2	1	1	2	8	3	2	2	8	0	0			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr19:11304538A>T	ENST00000586659.1	-	4	532	c.218T>A	c.(217-219)cTg>cAg	p.L73Q	KANK2_ENST00000589894.1_Missense_Mutation_p.L73Q|KANK2_ENST00000355150.5_Missense_Mutation_p.L73Q|KANK2_ENST00000589359.1_Missense_Mutation_p.L73Q|KANK2_ENST00000432929.2_Missense_Mutation_p.L73Q			Q63ZY3	KANK2_HUMAN	KN motif and ankyrin repeat domains 2	73					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						GCCACGGGGCAGCGAGCTCAG	0.672																																					p.L73Q		Atlas-SNP	.											.	KANK2	47	.	0			c.T218A						PASS	.						35	37	36					19																	11304538		2203	4297	6500	SO:0001583	missense	25959	exon2			CGGGGCAGCGAGC	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.218T>A	chr19.hg19:g.11304538A>T	ENSP00000465650:p.Leu73Gln	76.0	0.0	.		51.0	19.0	.	NM_015493	B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210	Missense_Mutation	SNP	ENST00000586659.1	hg19	CCDS12255.1	.	.	.	.	.	.	.	.	.	.	A	12.16	1.853681	0.32791	.	.	ENSG00000197256	ENST00000432929;ENST00000355150	T;T	0.48836	0.8;0.82	4.38	4.38	0.52667	.	0.000000	0.56097	D	0.000029	T	0.61800	0.2376	L	0.57536	1.79	0.35815	D	0.824149	D;D;D	0.89917	1.0;0.965;1.0	D;P;D	0.91635	0.999;0.862;0.999	T	0.67201	-0.5730	10	0.28530	T	0.3	-25.9043	12.5808	0.56390	1.0:0.0:0.0:0.0	.	73;73;73	Q63ZY3-3;Q63ZY3;Q63ZY3-2	.;KANK2_HUMAN;.	Q	73	ENSP00000395650:L73Q;ENSP00000347276:L73Q	ENSP00000347276:L73Q	L	-	2	0	KANK2	11165538	1.000000	0.71417	0.540000	0.28089	0.038000	0.13279	6.295000	0.72744	1.616000	0.50265	0.379000	0.24179	CTG	.	.	.	none		0.672	KANK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453066.2	NM_015493		T	11304538	A	T	11304538	3	4	101	1	0	0	0	0	1	0	0	0	7984	188	7	5	2401	5	KANK2	19	11304538	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08	6222025	11304538	47824445	71	6469											
ZNF791	163049	hgsc.bcm.edu	37	chr19	12739559	12739559	+	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	tgaaaatccacaagagaaatCacactggagaaaaaccctat	20	6	6	9	0	1	3	1	1	0	2	2	5	2	3	2	1	1	0	2	1	7	1			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr19:12739559C>A	ENST00000343325.4	+	4	1378	c.1216C>A	c.(1216-1218)Cac>Aac	p.H406N	AC010422.1_ENST00000408416.1_RNA|ZNF791_ENST00000540038.1_Missense_Mutation_p.H297N|ZNF490_ENST00000465656.1_Intron|ZNF791_ENST00000458122.3_Missense_Mutation_p.H374N|ZNF791_ENST00000446165.1_3'UTR	NM_153358.2	NP_699189.2	Q3KP31	ZN791_HUMAN	zinc finger protein 791	406					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(5)|lung(6)|ovary(2)|prostate(3)	19						CAAGAGAAATCACACTGGAGA	0.393																																					p.H406N		Atlas-SNP	.											.	ZNF791	53	.	0			c.C1216A						PASS	.						90	99	96					19																	12739559		2203	4300	6503	SO:0001583	missense	163049	exon4			AGAAATCACACTG	AK074877	CCDS12273.1	19p13.2-p13.13	2013-01-08			ENSG00000173875	ENSG00000173875		"Zinc fingers, C2H2-type", "-"	26895	protein-coding gene	gene with protein product							Standard	NM_153358		Approved	FLJ90396	uc002mua.2	Q3KP31	OTTHUMG00000156426	ENST00000343325.4:c.1216C>A	chr19.hg19:g.12739559C>A	ENSP00000342974:p.His406Asn	243.0	0.0	.		207.0	77.0	.	NM_153358	B7Z586|Q8NC99	Missense_Mutation	SNP	ENST00000343325.4	hg19	CCDS12273.1	.	.	.	.	.	.	.	.	.	.	C	15.42	2.828830	0.50845	.	.	ENSG00000173875	ENST00000343325;ENST00000393303;ENST00000458122;ENST00000540038	T;T;T	0.67345	-0.26;-0.26;-0.26	1.83	1.83	0.25207	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.81959	0.4933	M	0.88640	2.97	0.30637	N	0.756821	D	0.76494	0.999	D	0.91635	0.999	T	0.77763	-0.2466	9	0.87932	D	0	.	9.2247	0.37398	0.0:1.0:0.0:0.0	.	406	Q3KP31	ZN791_HUMAN	N	406;388;374;297	ENSP00000342974:H406N;ENSP00000441761:H374N;ENSP00000441038:H297N	ENSP00000342974:H406N	H	+	1	0	ZNF791	12600559	1.000000	0.71417	0.865000	0.33974	0.967000	0.64934	4.955000	0.63638	1.007000	0.39238	0.491000	0.48974	CAC	.	.	.	none		0.393	ZNF791-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344140.1	NM_153358		A	12739559	C	A	12739559	3	1	101	1	0	0	0	0	1	0	0	0	18175	826	29	4	1230	4	ZNF791	19	12739559	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08	1435021	12739559	46389424	72	6470											
ZNF260	339324	hgsc.bcm.edu	37	chr19	37005333	37005333	+	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	gtagggtttctctccaatatGaattttctcatgctctgtga	8	17	8	8	0	3	2	1	2	3	0	6	2	4	2	1	1	1	3	1	1	4	5			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr19:37005333G>A	ENST00000523638.1	-	3	1929	c.808C>T	c.(808-810)Cat>Tat	p.H270Y	ZNF260_ENST00000588993.1_Missense_Mutation_p.H270Y|ZNF260_ENST00000592282.1_Missense_Mutation_p.H270Y|ZNF260_ENST00000593142.1_Missense_Mutation_p.H270Y	NM_001166036.1|NM_001166037.1|NM_001166038.1	NP_001159508.1|NP_001159509.1|NP_001159510.1	Q3ZCT1	ZN260_HUMAN	zinc finger protein 260	270					multicellular organismal development (GO:0007275)|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)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)	15	Esophageal squamous(110;0.162)					TCTCCAATATGAATTTTCTCA	0.398																																					p.H270Y		Atlas-SNP	.											.	ZNF260	34	.	0			c.C808T						PASS	.						123	122	122					19																	37005333		2203	4300	6503	SO:0001583	missense	339324	exon3			CAATATGAATTTT	AK122854	CCDS33003.1	19q13.12	2013-01-08				ENSG00000254004		"Zinc fingers, C2H2-type"	13499	protein-coding gene	gene with protein product		613749					Standard	NM_001166036		Approved	ozrf1, Zfp260	uc002oed.2	Q3ZCT1		ENST00000523638.1:c.808C>T	chr19.hg19:g.37005333G>A	ENSP00000429803:p.His270Tyr	156.0	0.0	.		134.0	42.0	.	NM_001166038	Q0VF43	Missense_Mutation	SNP	ENST00000523638.1	hg19	CCDS33003.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.335259	0.81801	.	.	ENSG00000254004	ENST00000523638	T	0.67523	-0.27	4.54	4.54	0.55810	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.85720	0.5762	M	0.92412	3.305	0.50632	D	0.999883	D	0.89917	1.0	D	0.91635	0.999	D	0.89435	0.3719	9	0.87932	D	0	.	16.5613	0.84567	0.0:0.0:1.0:0.0	.	270	Q3ZCT1	ZN260_HUMAN	Y	270	ENSP00000429803:H270Y	ENSP00000429803:H270Y	H	-	1	0	ZNF260	41697173	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.645000	0.83430	2.496000	0.84212	0.561000	0.74099	CAT	.	.	.	none		0.398	ZNF260-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109564.2	NM_001012756		A	37005333	G	A	37005333	3	1	101	1	0	0	0	0	1	0	0	0	17814	1290	45	2	434	2	ZNF260	19	37005333	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08	24265774	37005333	22123650	73	6471											
FITM2	128486	hgsc.bcm.edu	37	chr20	42935425	42935425	+	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	acaagttgtggaaataaacaGctgtgcacagaaacatcaac	18	7	8	8	0	1	1	1	0	0	1	1	2	1	2	0	1	5	3	0	1	6	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr20:42935425G>T	ENST00000396825.3	-	2	649	c.629C>A	c.(628-630)gCt>gAt	p.A210D		NM_001080472.1	NP_001073941.1	Q8N6M3	FITM2_HUMAN	fat storage-inducing transmembrane protein 2	210					cellular triglyceride homeostasis (GO:0035356)|cytoskeleton organization (GO:0007010)|lipid particle organization (GO:0034389)|positive regulation of sequestering of triglyceride (GO:0010890)|regulation of cell morphogenesis (GO:0022604)|regulation of triglyceride biosynthetic process (GO:0010866)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|mitochondrion (GO:0005739)				endometrium(2)|lung(2)|skin(2)	6						GAAATAAACAGCTGTGCACAG	0.522																																					p.A210D		Atlas-SNP	.											.	FITM2	15	.	0			c.C629A						PASS	.						99	83	88					20																	42935425		2203	4300	6503	SO:0001583	missense	128486	exon2			TAAACAGCTGTGC	BC029662	CCDS33473.1	20q13.12	2009-04-29	2009-04-29	2009-04-29	ENSG00000197296	ENSG00000197296			16135	protein-coding gene	gene with protein product	"fat inducing transcript 2"	612029	"chromosome 20 open reading frame 142"	C20orf142		18160536	Standard	NM_001080472		Approved	dJ881L22.2, FIT2	uc002xlr.1	Q8N6M3	OTTHUMG00000032522	ENST00000396825.3:c.629C>A	chr20.hg19:g.42935425G>T	ENSP00000380037:p.Ala210Asp	64.0	0.0	.		55.0	18.0	.	NM_001080472	A1L492|B9EGQ4|Q5TE59|Q9H3Y1	Missense_Mutation	SNP	ENST00000396825.3	hg19	CCDS33473.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.600365	0.87055	.	.	ENSG00000197296	ENST00000396825	.	.	.	5.57	5.57	0.84162	.	0.217055	0.48286	D	0.000191	D	0.82747	0.5104	M	0.84082	2.675	0.80722	D	1	D	0.63880	0.993	D	0.63877	0.919	T	0.83306	-0.0025	9	0.48119	T	0.1	.	19.5462	0.95299	0.0:0.0:1.0:0.0	.	210	Q8N6M3	FITM2_HUMAN	D	210	.	ENSP00000380037:A210D	A	-	2	0	FITM2	42368839	1.000000	0.71417	0.620000	0.29132	0.912000	0.54170	9.397000	0.97276	2.609000	0.88269	0.563000	0.77884	GCT	.	.	.	none		0.522	FITM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079342.2	XM_371399		T	42935425	G	T	42935425	3	4	101	1	0	0	0	0	1	0	0	0	5906	971	34	4	163	4	FITM2	20	42935425	Missense_Mutation	SNP	G	TCGA-B9-5156-01A-01D-1589-08		42935425	20090095	74	6472											
MYH9	4627	hgsc.bcm.edu	37	chr22	36716872	36716872	+	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	gctctccagccccagacaggAgataatagaagatgtggaag	14	6	12	9	0	1	4	0	0	1	4	2	6	1	5	3	2	1	1	3	2	4	2			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chr22:36716872A>T	ENST00000216181.5	-	8	1069	c.839T>A	c.(838-840)cTc>cAc	p.L280H		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	280	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						CCCAGACAGGAGATAATAGAA	0.532			T	ALK	ALCL		"Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"		Hereditary Macrothrombocytopenia, MYH9-associated																												p.L280H		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"myosin, heavy polypeptide 9, non-muscle"	yes	L	.	MYH9	225	.	0			c.T839A						PASS	.						74	70	71					22																	36716872		2203	4300	6503	SO:0001583	missense	4627	exon8	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	GACAGGAGATAAT		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.839T>A	chr22.hg19:g.36716872A>T	ENSP00000216181:p.Leu280His	33.0	0.0	.		40.0	11.0	.	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Missense_Mutation	SNP	ENST00000216181.5	hg19	CCDS13927.1	.	.	.	.	.	.	.	.	.	.	A	28.6	4.937579	0.92458	.	.	ENSG00000100345	ENST00000337818;ENST00000216181	D	0.94092	-3.35	5.13	5.13	0.70059	Myosin head, motor domain (2);	0.073236	0.53938	D	0.000057	D	0.97405	0.9151	H	0.99357	4.53	0.80722	D	1	D	0.63880	0.993	P	0.51895	0.683	D	0.98753	1.0721	10	0.87932	D	0	.	14.9048	0.70709	1.0:0.0:0.0:0.0	.	280	P35579	MYH9_HUMAN	H	144;280	ENSP00000216181:L280H	ENSP00000216181:L280H	L	-	2	0	MYH9	35046818	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	9.287000	0.95975	2.053000	0.61076	0.482000	0.46254	CTC	.	.	.	none		0.532	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473		T	36716872	A	T	36716872	3	4	101	1	0	0	0	0	1	0	0	0	10049	304	11	5	5179	5	MYH9	22	36716872	Missense_Mutation	SNP	A	TCGA-B9-5156-01A-01D-1589-08		36716872	14587694	75	6473											
USP9X	8239	hgsc.bcm.edu	37	chrX	40999924	40999924	+	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	tacagggttggctagtggatCttctcaacaaatttggcact	10	13	10	8	0	2	0	1	0	2	0	3	1	2	1	0	4	2	3	0	4	4	5			TCGA-B9-5156-01A-01D-1589-08	TCGA-B9-5156-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8faa0a9e-10a4-41ed-8293-e403028434e8	8355a879-8264-4bba-88a4-f6db446dffa8	g.chrX:40999924C>A	ENST00000324545.8	+	7	1303	c.670C>A	c.(670-672)Ctt>Att	p.L224I	USP9X_ENST00000378308.2_Missense_Mutation_p.L224I	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	224					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						GCTAGTGGATCTTCTCAACAA	0.318																																					p.L224I	Ovarian(172;1807 2695 35459 49286)	Atlas-SNP	.											.	USP9X	385	.	0			c.C670A						PASS	.						111	99	103					X																	40999924		2203	4298	6501	SO:0001583	missense	8239	exon7			GTGGATCTTCTCA	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.670C>A	chrX.hg19:g.40999924C>A	ENSP00000316357:p.Leu224Ile	57.0	0.0	.		80.0	55.0	.	NM_001039591	O75550|Q8WWT3|Q8WX12	Missense_Mutation	SNP	ENST00000324545.8	hg19	CCDS43930.1	.	.	.	.	.	.	.	.	.	.	C	19.98	3.926912	0.73327	.	.	ENSG00000124486	ENST00000378308;ENST00000324545	T;T	0.03982	3.75;3.74	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.24044	0.0582	M	0.79475	2.455	0.58432	D	0.999998	D;D	0.89917	1.0;0.999	D;D	0.74348	0.983;0.963	T	0.00104	-1.2059	10	0.45353	T	0.12	.	19.5004	0.95091	0.0:1.0:0.0:0.0	.	224;224	Q93008-1;Q93008	.;USP9X_HUMAN	I	224	ENSP00000367558:L224I;ENSP00000316357:L224I	ENSP00000316357:L224I	L	+	1	0	USP9X	40884868	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.611000	0.61162	2.560000	0.86352	0.594000	0.82650	CTT	.	.	.	none		0.318	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		A	40999924	C	A	40999924	3	1	101	1	0	0	0	0	1	0	0	0	17102	913	32	4	692	4	USP9X	23	40999924	Missense_Mutation	SNP	C	TCGA-B9-5156-01A-01D-1589-08		40999924	114270636	76	6474											
PABPC4	8761	hgsc.bcm.edu	37	chr1	40029530	40029530	+	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	ccagactggcagctgtcagtCagcccttgctgggcggcacc	6	7	13	15	1	2	1	2	0	0	1	2	1	2	1	3	3	3	4	3	3	0	1			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr1:40029530C>T	ENST00000372857.3	-	11	2262	c.1470G>A	c.(1468-1470)ctG>ctA	p.L490L	PABPC4_ENST00000372858.3_Silent_p.L506L|RP11-69E11.8_ENST00000415255.1_RNA|PABPC4_ENST00000372862.3_Intron|PABPC4_ENST00000372856.3_Intron	NM_003819.3	NP_003810.1	Q13310	PABP4_HUMAN	poly(A) binding protein, cytoplasmic 4 (inducible form)	490					blood coagulation (GO:0007596)|RNA catabolic process (GO:0006401)|RNA processing (GO:0006396)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|prostate(1)|skin(3)	21	Lung NSC(20;1.55e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.89e-18)|Epithelial(16;6.17e-17)|all cancers(16;1.18e-15)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			AGCTGTCAGTCAGCCCTTGCT	0.557																																					p.L506L		Atlas-SNP	.											.	PABPC4	56	.	0			c.G1518A						PASS	.						60	61	61					1																	40029530		2203	4300	6503	SO:0001819	synonymous_variant	8761	exon11			GTCAGTCAGCCCT	U33818	CCDS438.1, CCDS44114.1, CCDS44115.1	1p34.2	2013-02-12	2001-11-28		ENSG00000090621	ENSG00000090621		"RNA binding motif (RRM) containing"	8557	protein-coding gene	gene with protein product		603407	"poly(A)-binding protein, cytoplasmic 4 (inducible form)"			10543404	Standard	NM_001135653		Approved	iPABP, APP-1	uc001cdl.2	Q13310	OTTHUMG00000009097	ENST00000372857.3:c.1470G>A	chr1.hg19:g.40029530C>T		97.0	0.0	.		116.0	51.0	.	NM_001135653	B1ANQ8|Q4VC03|Q6P0N3	Silent	SNP	ENST00000372857.3	hg19	CCDS438.1																																																																																			.	.	.	none		0.557	PABPC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025220.1	NM_001135653		T	40029530	C	T	40029530	2	4	102	1	0	0	0	0	0	0	0	1	11373	813	29	2		2	PABPC4	1	40029530	Silent	SNP	C	TCGA-B9-7268-01A-11D-2136-08		40029530	209221091	1	6475											
BEST4	266675	hgsc.bcm.edu	37	chr1	45250593	45250593	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcacctgcaagttgcggtctAtgagctgatttgtctcaaag	9	13	10	9	1	3	2	2	2	2	0	4	2	3	2	1	1	3	3	1	1	3	3	rs377207881		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr1:45250593A>G	ENST00000372207.3	-	7	976	c.977T>C	c.(976-978)aTa>aCa	p.I326T		NM_153274.2	NP_695006.1	Q8NFU0	BEST4_HUMAN	bestrophin 4	326						chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			large_intestine(1)|lung(4)|ovary(1)|skin(1)	7	Acute lymphoblastic leukemia(166;0.155)					GTTGCGGTCTATGAGCTGATT	0.562																																					p.I326T		Atlas-SNP	.											.	BEST4	20	.	0			c.T977C						PASS	.						76	81	79					1																	45250593		2203	4300	6503	SO:0001583	missense	266675	exon7			CGGTCTATGAGCT	AF440757	CCDS514.1	1p33-p32.3	2012-09-26	2006-10-18	2006-10-18	ENSG00000142959	ENSG00000142959		"Ion channels / Chloride channels : Calcium activated : Bestrophins"	17106	protein-coding gene	gene with protein product		607336	"vitelliform macular dystrophy 2-like 2"	VMD2L2		12032738, 16702355	Standard	NM_153274		Approved		uc001cmm.3	Q8NFU0	OTTHUMG00000008488	ENST00000372207.3:c.977T>C	chr1.hg19:g.45250593A>G	ENSP00000361281:p.Ile326Thr	117.0	0.0	.		135.0	11.0	.	NM_153274	Q5JR93	Missense_Mutation	SNP	ENST00000372207.3	hg19	CCDS514.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.072846	0.76415	.	.	ENSG00000142959	ENST00000372207	D	0.99270	-5.66	5.19	4.07	0.47477	.	0.051148	0.85682	D	0.000000	D	0.99518	0.9828	H	0.96269	3.795	0.51767	D	0.999939	D	0.71674	0.998	D	0.74348	0.983	D	0.98708	1.0703	10	0.87932	D	0	-16.684	9.7184	0.40289	0.9183:0.0:0.0816:0.0	.	326	Q8NFU0	BEST4_HUMAN	T	326	ENSP00000361281:I326T	ENSP00000361281:I326T	I	-	2	0	BEST4	45023180	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.946000	0.70234	0.998000	0.38996	0.533000	0.62120	ATA	.	.	.	none		0.562	BEST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023425.1	NM_153274		G	45250593	A	G	45250593	3	3	102	1	0	0	0	0	1	0	0	0	1407	449	16	3	456	3	BEST4	1	45250593	Missense_Mutation	SNP	A	TCGA-B9-7268-01A-11D-2136-08	5221063	45250593	204000028	2	6476											
STXBP3	6814	hgsc.bcm.edu	37	chr1	109302625	109302625	+	Missense_Mutation	SNP	T	T	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	agtttgccctgataatctctTtaacaaaattaaggcttctt	12	16	5	8	0	2	1	0	1	2	0	3	1	2	1	1	1	2	2	1	1	5	7			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr1:109302625T>G	ENST00000370008.3	+	6	406	c.356T>G	c.(355-357)tTt>tGt	p.F119C		NM_007269.2	NP_009200.2	O00186	STXB3_HUMAN	syntaxin binding protein 3	119	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)		GATAATCTCTTTAACAAAATT	0.289																																					p.F119C		Atlas-SNP	.											.	STXBP3	44	.	0			c.T356G						PASS	.						92	106	101					1																	109302625		2203	4288	6491	SO:0001583	missense	6814	exon6			ATCTCTTTAACAA	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.356T>G	chr1.hg19:g.109302625T>G	ENSP00000359025:p.Phe119Cys	172.0	0.0	.		216.0	94.0	.	NM_007269	A8K269|A8K5K7|Q53FW1|Q86YJ3|Q9UPD7	Missense_Mutation	SNP	ENST00000370008.3	hg19	CCDS790.1	.	.	.	.	.	.	.	.	.	.	T	19.62	3.861971	0.71949	.	.	ENSG00000116266	ENST00000370008	T	0.77098	-1.07	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.87083	0.6089	M	0.84846	2.72	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	D	0.89069	0.3468	10	0.62326	D	0.03	-18.7523	15.3518	0.74396	0.0:0.0:0.0:1.0	.	119	O00186	STXB3_HUMAN	C	119	ENSP00000359025:F119C	ENSP00000359025:F119C	F	+	2	0	STXBP3	109104148	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.164000	0.71885	2.110000	0.64415	0.477000	0.44152	TTT	.	.	.	none		0.289	STXBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030591.1	NM_007269		G	109302625	T	G	109302625	3	3	102	1	0	0	0	0	1	0	0	0	15366	1841	64	5	378	5	STXBP3	1	109302625	Missense_Mutation	SNP	T	TCGA-B9-7268-01A-11D-2136-08	64052032	109302625	139947996	3	6477											
C1orf54	79630	hgsc.bcm.edu	37	chr1	150248209	150248212	+	Splice_Site	DEL	GTGA	GTGA	-																															ttgagtcagaggacaggctgGtgagtgaactctacatctaa																										TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	GTGA	GTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr1:150248209_150248212delGTGA	ENST00000369102.1	+	5	959		c.e5+1		C1orf54_ENST00000369098.3_Splice_Site|C1orf54_ENST00000369099.3_Splice_Site			Q8WWF1	CA054_HUMAN	chromosome 1 open reading frame 54							extracellular region (GO:0005576)				breast(1)|endometrium(1)|large_intestine(2)|lung(2)|urinary_tract(1)	7	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)			GGACAGGCTGGTGAGTGAACTCTA	0.407																																					p.63_63del		Atlas-INDEL	.											.	C1orf54	20	.	0			c.189_189del						PASS	.																																			SO:0001630	splice_region_variant	79630	exon3			.	BC017761	CCDS948.1, CCDS72905.1	1q21.2	2012-06-25			ENSG00000118292	ENSG00000118292			26258	protein-coding gene	gene with protein product						12477932	Standard	NM_024579		Approved	FLJ23221	uc001eud.3	Q8WWF1	OTTHUMG00000012546	ENST00000369102.1:c.189+1GTGA>-	chr1.hg19:g.150248213_150248216delGTGA		48.0	0.0	0		75.0	17.0	0.226667	NM_024579	Q9H5P3	Frame_Shift_Del	DEL	ENST00000369102.1	hg19	CCDS948.1																																																																																			.	.	.	none		0.407	C1orf54-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035055.1	NM_024579	Intron	-	150248212	GTGA	-	150248209	8	5	102	1	0	1	0	1	0	0	1	0	2048	1275	44	0	200	0	C1orf54	1	150248209	Splice_Site	DEL	GTGA	TCGA-B9-7268-01A-11D-2136-08	40945584	150248209	99002412	4	6478											
ZNF687	57592	hgsc.bcm.edu	37	chr1	151259373	151259373	+	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	ccctcttcctttgagctggcCcaggagaatggcccaggcat	7	9	11	14	0	1	2	0	1	1	1	2	3	2	2	4	4	1	2	4	4	1	2			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr1:151259373C>G	ENST00000368879.2	+	2	704	c.606C>G	c.(604-606)gcC>gcG	p.A202A		NM_020832.1	NP_065883.1	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	202	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	32	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TTGAGCTGGCCCAGGAGAATG	0.652																																					p.A202A		Atlas-SNP	.											.	ZNF687	94	.	0			c.C606G						PASS	.						44	49	47					1																	151259373		2203	4300	6503	SO:0001819	synonymous_variant	57592	exon2			GCTGGCCCAGGAG		CCDS992.1	1q21.2	2008-05-02			ENSG00000143373	ENSG00000143373			29277	protein-coding gene	gene with protein product		610568				10718198	Standard	NM_020832		Approved	KIAA1441	uc001exq.3	Q8N1G0	OTTHUMG00000012347	ENST00000368879.2:c.606C>G	chr1.hg19:g.151259373C>G		115.0	0.0	.		122.0	59.0	.	NM_020832	D3DV17|Q68DQ8|Q9H937|Q9P2A7	Silent	SNP	ENST00000368879.2	hg19																																																																																				.	.	.	none		0.652	ZNF687-201	KNOWN	basic	protein_coding	protein_coding		NM_020832		G	151259373	C	G	151259373	2	3	102	1	0	0	0	0	0	0	0	1	18104	610	22	4		4	ZNF687	1	151259373	Silent	SNP	C	TCGA-B9-7268-01A-11D-2136-08	1011164	151259373	97991248	5	6479											
SPRR1B	6699	hgsc.bcm.edu	37	chr1	153004965	153004965	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caccccaaggtgcctgagccCtgccaccccaaagtgcccga	9	4	9	19	1	0	1	0	1	0	0	0	2	0	1	8	1	4	0	8	1	2	0			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr1:153004965C>T	ENST00000307098.4	+	2	209	c.144C>T	c.(142-144)ccC>ccT	p.P48P	SPRR1B_ENST00000392661.3_Silent_p.P48P	NM_003125.2	NP_003116.2	P22528	SPR1B_HUMAN	small proline-rich protein 1B	48	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)		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)			TGCCTGAGCCCTGCCACCCCA	0.627																																					p.P48P		Atlas-SNP	.											.	SPRR1B	18	.	1	Deletion - In frame(1)	ovary(1)	c.C144T						PASS	.						123	123	123					1																	153004965		2203	4300	6503	SO:0001819	synonymous_variant	6699	exon2			TGAGCCCTGCCAC	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.144C>T	chr1.hg19:g.153004965C>T		274.0	0.0	.		264.0	105.0	.	NM_003125	B2R5H7|P22529|P22530|Q5T524	Silent	SNP	ENST00000307098.4	hg19	CCDS30863.1																																																																																			.	.	.	none		0.627	SPRR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038906.1	NM_003125		T	153004965	C	T	153004965	2	4	102	1	0	0	0	0	0	0	0	1	15108	668	24	2		2	SPRR1B	1	153004965	Silent	SNP	C	TCGA-B9-7268-01A-11D-2136-08	1745592	153004965	96245656	6	6480											
LTBP1	4052	hgsc.bcm.edu	37	chr2	33412000	33412000	+	Frame_Shift_Del	DEL	G	G	-																															agtgccctccaaatttcacaGgaaaactttgtcagatccca																										TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr2:33412000delG	ENST00000404816.2	+	6	1632	c.1279delG	c.(1279-1281)ggafs	p.G427fs	LTBP1_ENST00000404525.1_Frame_Shift_Del_p.G101fs|LTBP1_ENST00000402934.1_Frame_Shift_Del_p.G101fs|LTBP1_ENST00000390003.4_Frame_Shift_Del_p.G101fs|LTBP1_ENST00000407925.1_Frame_Shift_Del_p.G101fs|LTBP1_ENST00000418533.2_Frame_Shift_Del_p.G101fs|LTBP1_ENST00000354476.3_Frame_Shift_Del_p.G427fs			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	427	EGF-like 2. {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)				AAATTTCACAGGAAAACTTTG	0.473																																					p.T426fs		Atlas-INDEL	.											.	LTBP1	317	.	0			c.1278delA						PASS	.						115	107	110					2																	33412000		2203	4300	6503	SO:0001589	frameshift_variant	4052	exon6			.		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.1279delG	chr2.hg19:g.33412000delG	ENSP00000386043:p.Gly427fs	64.0	0.0	0		57.0	20.0	0.350877	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Frame_Shift_Del	DEL	ENST00000404816.2	hg19	CCDS33177.2																																																																																			.	.	.	none		0.473	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		-	33412000	G	-	33412000	7	5	102	1	0	1	0	1	0	0	0	0	9080	1001	35	0	1356	0	LTBP1	2	33412000	Frame_Shift_Del	DEL	G	TCGA-B9-7268-01A-11D-2136-08		33412000	209787373	7	6481	70	2									
LTBP1	4052	hgsc.bcm.edu	37	chr2	33412006	33412006	+	Missense_Mutation	SNP	C	C	A																															ctccaaatttcacaggaaaaCtttgtcagatcccagtccat																										TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr2:33412006C>A	ENST00000404816.2	+	6	1638	c.1285C>A	c.(1285-1287)Ctt>Att	p.L429I	LTBP1_ENST00000404525.1_Missense_Mutation_p.L103I|LTBP1_ENST00000402934.1_Missense_Mutation_p.L103I|LTBP1_ENST00000390003.4_Missense_Mutation_p.L103I|LTBP1_ENST00000407925.1_Missense_Mutation_p.L103I|LTBP1_ENST00000418533.2_Missense_Mutation_p.L103I|LTBP1_ENST00000354476.3_Missense_Mutation_p.L429I			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	429	EGF-like 2. {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)				CACAGGAAAACTTTGTCAGAT	0.478																																					p.L429I		Atlas-SNP	.											.	LTBP1	317	.	0			c.C1285A						PASS	.						116	108	110					2																	33412006		2203	4300	6503	SO:0001583	missense	4052	exon6			GGAAAACTTTGTC		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.1285C>A	chr2.hg19:g.33412006C>A	ENSP00000386043:p.Leu429Ile	68.0	0.0	.		57.0	20.0	.	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	hg19	CCDS33177.2	.	.	.	.	.	.	.	.	.	.	C	15.88	2.962600	0.53400	.	.	ENSG00000049323	ENST00000404816;ENST00000354476;ENST00000432635;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925	D;D;D;D;D;D;D	0.91996	-2.95;-2.95;-2.95;-2.95;-2.95;-2.95;-2.95	5.3	5.3	0.74995	Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.87849	0.6281	L	0.32530	0.975	0.80722	D	1	B;B;B;B;B;B	0.25441	0.077;0.028;0.016;0.033;0.096;0.126	B;B;B;B;B;B	0.28709	0.043;0.016;0.017;0.027;0.05;0.093	D	0.85678	0.1299	9	0.66056	D	0.02	.	12.3249	0.55005	0.0:0.9228:0.0:0.0772	.	429;103;103;103;103;429	Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4	LTBP1_HUMAN;.;.;.;.;.	I	429;429;118;103;103;103;103;103	ENSP00000386043:L429I;ENSP00000346467:L429I;ENSP00000374653:L103I;ENSP00000393057:L103I;ENSP00000384373:L103I;ENSP00000385359:L103I;ENSP00000384091:L103I	ENSP00000346467:L429I	L	+	1	0	LTBP1	33265510	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	4.239000	0.58694	2.468000	0.83385	0.655000	0.94253	CTT	.	.	.	none		0.478	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		A	33412006	C	A	33412006	3	1	102	1	0	0	0	0	1	0	0	0	9080	565	20	4	1362	4	LTBP1	2	33412006	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08	6	33412006	209787367	8	6482	70	2									
GGCX	2677	hgsc.bcm.edu	37	chr2	85777685	85777685	+	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	gttgtgaacttacctgcggcGaaagacatagagctttcgca	11	10	11	9	3	0	3	0	1	0	2	1	4	0	3	1	1	4	3	1	1	4	4	rs372492949		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr2:85777685G>T	ENST00000233838.4	-	14	2157	c.2077C>A	c.(2077-2079)Cgc>Agc	p.R693S	GGCX_ENST00000473665.1_5'Flank|GGCX_ENST00000430215.3_Missense_Mutation_p.R636S	NM_000821.5	NP_000812.2	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase	693					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)	TACCTGCGGCGAAAGACATAG	0.468																																					p.R693S		Atlas-SNP	.											.	GGCX	44	.	0			c.C2077A						PASS	.						53	56	55					2																	85777685		2203	4300	6503	SO:0001583	missense	2677	exon14			TGCGGCGAAAGAC		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.2077C>A	chr2.hg19:g.85777685G>T	ENSP00000233838:p.Arg693Ser	85.0	0.0	.		92.0	42.0	.	NM_000821	B4DMC5|E9PEE1|Q14415|Q6GU45	Missense_Mutation	SNP	ENST00000233838.4	hg19	CCDS1978.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.395574	0.83011	.	.	ENSG00000115486	ENST00000233838;ENST00000430215	T;T	0.28895	1.59;1.59	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.56673	0.2001	M	0.72118	2.19	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.995;0.998	T	0.55302	-0.8162	10	0.54805	T	0.06	-15.286	17.5141	0.87768	0.0:0.0:1.0:0.0	.	636;509;693	E9PEE1;B4DQW4;P38435	.;.;VKGC_HUMAN	S	693;636	ENSP00000233838:R693S;ENSP00000408045:R636S	ENSP00000233838:R693S	R	-	1	0	GGCX	85631196	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.029000	0.57253	2.730000	0.93505	0.655000	0.94253	CGC	.	.	.	alt		0.468	GGCX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252490.3	NM_000821		T	85777685	G	T	85777685	3	4	102	1	0	0	0	0	1	0	0	0	6363	1058	37	4	207	4	GGCX	2	85777685	Missense_Mutation	SNP	G	TCGA-B9-7268-01A-11D-2136-08	52365679	85777685	157421688	9	6483											
NEB	4703	hgsc.bcm.edu	37	chr2	152507333	152507333	+	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	ggacaacacaagttttgggtCatcttgcagactccggaatc	11	10	10	10	1	2	1	1	0	1	1	4	3	3	3	1	3	2	2	1	3	3	3			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr2:152507333C>T	ENST00000172853.10	-	53	7129	c.6982G>A	c.(6982-6984)Gac>Aac	p.D2328N	NEB_ENST00000603639.1_Missense_Mutation_p.D2328N|NEB_ENST00000397345.3_Missense_Mutation_p.D2328N|NEB_ENST00000409198.1_Missense_Mutation_p.D2328N|NEB_ENST00000604864.1_Missense_Mutation_p.D2328N|NEB_ENST00000427231.2_Missense_Mutation_p.D2328N			P20929	NEBU_HUMAN	nebulin	2328					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)		AGTTTTGGGTCATCTTGCAGA	0.413																																					p.D2328N		Atlas-SNP	.											.	NEB	1697	.	0			c.G6982A						PASS	.						187	191	190					2																	152507333		1983	4164	6147	SO:0001583	missense	4703	exon53			TTGGGTCATCTTG	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.6982G>A	chr2.hg19:g.152507333C>T	ENSP00000172853:p.Asp2328Asn	231.0	0.0	.		287.0	142.0	.	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	hg19		.	.	.	.	.	.	.	.	.	.	C	34	5.297627	0.95574	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.50277	0.75;0.75;0.75;0.75	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.75903	0.3913	M	0.91249	3.19	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.77461	-0.2579	10	0.34782	T	0.22	.	19.3325	0.94297	0.0:1.0:0.0:0.0	.	2328	P20929	NEBU_HUMAN	N	2328	ENSP00000386259:D2328N;ENSP00000380505:D2328N;ENSP00000416578:D2328N;ENSP00000172853:D2328N	ENSP00000172853:D2328N	D	-	1	0	NEB	152215579	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.770000	0.85390	2.583000	0.87209	0.650000	0.86243	GAC	.	.	.	none		0.413	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152507333	C	T	152507333	3	4	102	1	0	0	0	0	1	0	0	0	10309	826	29	2	19224	2	NEB	2	152507333	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08	66729648	152507333	90692040	10	6484											
RAPGEF4	11069	hgsc.bcm.edu	37	chr2	173832042	173832042	+	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	tattctatcgatttctggatGatgagcacgaggatgcccct	9	13	10	9	2	2	2	0	2	2	0	3	6	2	4	2	2	2	1	2	2	2	4			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr2:173832042G>A	ENST00000397081.3	+	10	1017	c.874G>A	c.(874-876)Gat>Aat	p.D292N	RAPGEF4_ENST00000409036.1_Missense_Mutation_p.D292N|RAPGEF4_ENST00000535187.1_Missense_Mutation_p.D72N|RAPGEF4_ENST00000473043.1_3'UTR|RAPGEF4_ENST00000538974.1_Missense_Mutation_p.D121N|RAPGEF4_ENST00000397087.3_Missense_Mutation_p.D148N|RAPGEF4_ENST00000540783.1_Missense_Mutation_p.D139N|RAPGEF4_ENST00000264111.6_Missense_Mutation_p.D291N|RAPGEF4_ENST00000539331.1_Missense_Mutation_p.D139N	NM_007023.3	NP_008954.2	Q8WZA2	RPGF4_HUMAN	Rap guanine nucleotide exchange factor (GEF) 4	292					blood coagulation (GO:0007596)|calcium ion-dependent exocytosis (GO:0017156)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|insulin secretion (GO:0030073)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of exocytosis (GO:0017157)|regulation of insulin secretion (GO:0050796)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(14)|lung(13)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47			OV - Ovarian serous cystadenocarcinoma(117;0.194)			ATTTCTGGATGATGAGCACGA	0.527																																					p.D292N		Atlas-SNP	.											.	RAPGEF4	103	.	0			c.G874A						PASS	.						51	53	52					2																	173832042		2072	4228	6300	SO:0001583	missense	11069	exon10			CTGGATGATGAGC	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.874G>A	chr2.hg19:g.173832042G>A	ENSP00000380271:p.Asp292Asn	23.0	0.0	.		33.0	18.0	.	NM_007023	B2R7R3|B7Z283|B7Z3T6|B7Z912|O95636|Q8IXK6|Q8TAA4	Missense_Mutation	SNP	ENST00000397081.3	hg19	CCDS42775.1	.	.	.	.	.	.	.	.	.	.	G	35	5.453522	0.96223	.	.	ENSG00000091428	ENST00000264111;ENST00000397081;ENST00000409036;ENST00000397087;ENST00000538974;ENST00000540783;ENST00000539331;ENST00000539767;ENST00000535187	T;T;T;T;T;T;T;T	0.14516	2.5;2.5;2.5;2.5;2.5;2.5;2.5;2.5	5.31	5.31	0.75309	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.40862	0.1134	M	0.74258	2.255	0.80722	D	1	D;D;D;D;D	0.89917	0.993;1.0;0.996;0.992;1.0	P;D;D;P;D	0.87578	0.897;0.998;0.948;0.889;0.996	T	0.28681	-1.0036	10	0.72032	D	0.01	.	18.9765	0.92738	0.0:0.0:1.0:0.0	.	119;121;148;292;292	B7Z805;B7Z2R0;Q8WZA2-3;Q8WZA2;E9PB94	.;.;.;RPGF4_HUMAN;.	N	291;292;292;148;121;139;139;119;72	ENSP00000264111:D291N;ENSP00000380271:D292N;ENSP00000387104:D292N;ENSP00000380276:D148N;ENSP00000440135:D121N;ENSP00000440250:D139N;ENSP00000437384:D139N;ENSP00000438011:D72N	ENSP00000264111:D291N	D	+	1	0	RAPGEF4	173540288	1.000000	0.71417	0.999000	0.59377	0.885000	0.51271	9.822000	0.99363	2.478000	0.83669	0.561000	0.74099	GAT	.	.	.	none		0.527	RAPGEF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257864.2	NM_007023		A	173832042	G	A	173832042	3	1	102	1	0	0	0	0	1	0	0	0	13059	1290	45	2	928	2	RAPGEF4	2	173832042	Missense_Mutation	SNP	G	TCGA-B9-7268-01A-11D-2136-08	21324709	173832042	69367331	11	6485											
TNS1	7145	hgsc.bcm.edu	37	chr2	218712984	218712984	+	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	accggagctgggggcagctgGggttcagcttccgaaaagga	9	6	17	9	2	1	0	1	0	0	0	2	3	2	2	2	6	3	5	2	6	2	2			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr2:218712984G>C	ENST00000171887.4	-	17	2333	c.1881C>G	c.(1879-1881)ccC>ccG	p.P627P	TNS1_ENST00000430930.1_Silent_p.P627P|TNS1_ENST00000480665.1_5'Flank|TNS1_ENST00000419504.1_Silent_p.P627P	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	627					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)		GGGGCAGCTGGGGTTCAGCTT	0.652																																					p.P627P		Atlas-SNP	.											.	TNS1	251	.	0			c.C1881G						PASS	.						45	38	40					2																	218712984		2203	4299	6502	SO:0001819	synonymous_variant	7145	exon17			CAGCTGGGGTTCA	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.1881C>G	chr2.hg19:g.218712984G>C		59.0	0.0	.		79.0	37.0	.	NM_022648	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	hg19	CCDS2407.1																																																																																			.	.	.	none		0.652	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		C	218712984	G	C	218712984	2	2	102	1	0	0	0	0	0	0	0	1	16355	1219	43	4		4	TNS1	2	218712984	Silent	SNP	G	TCGA-B9-7268-01A-11D-2136-08	44880942	218712984	24486389	12	6486											
MYEOV2	150678	hgsc.bcm.edu	37	chr2	241073371	241073371	+	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	gttaaaaaagtctgcatgaaCggccttttcattggctgcca	11	12	9	9	1	2	1	1	1	1	0	2	1	2	1	2	2	3	3	2	2	4	4			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr2:241073371C>G	ENST00000607357.1	-	2	133	c.115G>C	c.(115-117)Gtt>Ctt	p.V39L	MYEOV2_ENST00000489698.1_5'UTR|MYEOV2_ENST00000307266.3_Missense_Mutation_p.V70L	NM_001163424.1	NP_001156896.1	Q8WXC6	MYOV2_HUMAN	myeloma overexpressed 2	39								p.V70F(1)		breast(1)|lung(5)|pancreas(1)	7		all_epithelial(40;1.56e-11)|Breast(86;0.0002)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;3.81e-30)|all cancers(36;1.1e-27)|OV - Ovarian serous cystadenocarcinoma(60;2.74e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;8.54e-06)|Lung(119;0.00361)|LUSC - Lung squamous cell carcinoma(224;0.0153)|Colorectal(34;0.0202)|COAD - Colon adenocarcinoma(134;0.143)		TCTGCATGAACGGCCTTTTCA	0.483																																					p.V70L		Atlas-SNP	.											MYEOV2,NS,carcinoma,0,1	MYEOV2	20	.	1	Substitution - Missense(1)	lung(1)	c.G208C						PASS	.						127	130	129					2																	241073371		2203	4300	6503	SO:0001583	missense	150678	exon2			CATGAACGGCCTT	AF453951	CCDS2532.1, CCDS63183.1	2q37.3	2008-02-05			ENSG00000172428	ENSG00000172428			21314	protein-coding gene	gene with protein product							Standard	NM_138336		Approved		uc002vyu.1	Q8WXC6	OTTHUMG00000133352	ENST00000607357.1:c.115G>C	chr2.hg19:g.241073371C>G	ENSP00000475979:p.Val39Leu	132.0	0.0	.		168.0	65.0	.	NM_138336	Q8N110	Missense_Mutation	SNP	ENST00000607357.1	hg19		.	.	.	.	.	.	.	.	.	.	C	21.1	4.096434	0.76870	.	.	ENSG00000172428	ENST00000307266;ENST00000403160	.	.	.	4.55	3.67	0.42095	.	0.000000	0.64402	U	0.000001	T	0.74137	0.3677	.	.	.	0.58432	D	0.999999	B;D	0.57899	0.04;0.981	B;P	0.62382	0.041;0.901	T	0.76203	-0.3045	8	0.72032	D	0.01	-4.0557	10.5952	0.45333	0.0:0.9036:0.0:0.0963	.	39;70	Q8WXC6;Q8WXC6-1	MYOV2_HUMAN;.	L	70;60	.	ENSP00000304147:V70L	V	-	1	0	MYEOV2	240722044	1.000000	0.71417	0.472000	0.27241	0.971000	0.66376	6.092000	0.71414	1.042000	0.40150	0.650000	0.86243	GTT	.	.	.	none		0.483	MYEOV2-005	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470698.1	NM_138336		G	241073371	C	G	241073371	3	3	102	1	0	0	0	0	1	0	0	0	10033	536	19	4	570	4	MYEOV2	2	241073371	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08	22360387	241073371	2126002	13	6487											
TTLL3	26140	hgsc.bcm.edu	37	chr3	9877081	9877081	+	Missense_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	caccaaataaaaagaaacaaGtgaagtatttggggcttgac	18	8	9	6	0	0	3	0	2	0	1	0	3	0	3	1	2	1	2	1	2	8	4			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr3:9877081G>A	ENST00000547186.1	+	13	2443	c.2227G>A	c.(2227-2229)Gtg>Atg	p.V743M	ARPC4-TTLL3_ENST00000397256.1_3'UTR|TTLL3_ENST00000426895.4_Missense_Mutation_p.V886M|TTLL3_ENST00000455274.1_Intron|TTLL3_ENST00000383827.1_3'UTR|TTLL3_ENST00000397241.1_3'UTR	NM_001025930.3	NP_001021100.3	Q9Y4R7	TTLL3_HUMAN	tubulin tyrosine ligase-like family, member 3	743					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)					AAAGAAACAAGTGAAGTATTT	0.567																																					p.V886M		Atlas-SNP	.											.	TTLL3	51	.	0			c.G2656A						PASS	.						122	128	126					3																	9877081		1906	4123	6029	SO:0001583	missense	26140	exon13			AAACAAGTGAAGT		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.2227G>A	chr3.hg19:g.9877081G>A	ENSP00000446659:p.Val743Met	160.0	0.0	.		311.0	108.0	.	NM_001025930	Q4KMS8|Q6AWA3|Q6ZU95|Q8NDN8|Q96GG8|Q9H876|Q9UI99	Missense_Mutation	SNP	ENST00000547186.1	hg19		.	.	.	.	.	.	.	.	.	.	G	9.673	1.147353	0.21288	.	.	ENSG00000214021	ENST00000426895;ENST00000547186	T;T	0.06294	3.32;3.44	3.94	-1.13	0.09775	.	.	.	.	.	T	0.02970	0.0088	N	0.08118	0	0.09310	N	1	B	0.19200	0.034	B	0.14023	0.01	T	0.42275	-0.9461	9	0.87932	D	0	.	3.4181	0.07382	0.437:0.0:0.3814:0.1815	.	743	Q9Y4R7	TTLL3_HUMAN	M	886;743	ENSP00000392549:V886M;ENSP00000446659:V743M	ENSP00000392549:V886M	V	+	1	0	TTLL3	9852081	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.357000	0.07651	-0.239000	0.09710	-0.314000	0.08810	GTG	.	.	.	none		0.567	TTLL3-203	KNOWN	basic	protein_coding	protein_coding		NM_001025930.2		A	9877081	G	A	9877081	3	1	102	1	0	0	0	0	1	0	0	0	16740	1029	36	2	2273	2	TTLL3	3	9877081	Missense_Mutation	SNP	G	TCGA-B9-7268-01A-11D-2136-08		9877081	188145349	14	6488											
NISCH	11188	hgsc.bcm.edu	37	chr3	52526307	52526307	+	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	atgacgtgcaaggtcatgacCtcatgggcagtgtcaccctg	9	9	12	11	1	3	2	3	2	0	0	3	2	3	2	2	2	1	2	2	2	1	0			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr3:52526307C>A	ENST00000479054.1	+	22	4396	c.4324C>A	c.(4324-4326)Ctc>Atc	p.L1442I	NISCH_ENST00000345716.4_Missense_Mutation_p.L1442I			Q9Y2I1	NISCH_HUMAN	nischarin	1442					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)	AGGTCATGACCTCATGGGCAG	0.657																																					p.L1442I		Atlas-SNP	.											.	NISCH	97	.	0			c.C4324A						PASS	.						154	153	153					3																	52526307		2203	4300	6503	SO:0001583	missense	11188	exon21			CATGACCTCATGG	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.4324C>A	chr3.hg19:g.52526307C>A	ENSP00000418232:p.Leu1442Ile	309.0	0.0	.		441.0	133.0	.	NM_007184	C9J245|Q6PGP3|Q6PIB4|Q7L8M3|Q7Z2X6|Q9UES6|Q9UEU4|Q9UFW3	Missense_Mutation	SNP	ENST00000479054.1	hg19	CCDS33767.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.107084	0.77096	.	.	ENSG00000010322	ENST00000479054;ENST00000345716;ENST00000433196;ENST00000414197	T;T	0.13089	2.62;2.62	5.37	4.3	0.51218	.	0.078630	0.51477	D	0.000098	T	0.18800	0.0451	L	0.27053	0.805	0.37589	D	0.920105	D	0.67145	0.996	P	0.58210	0.835	T	0.02307	-1.1179	10	0.72032	D	0.01	-30.3479	11.4769	0.50304	0.0:0.8448:0.0:0.1552	.	1442	Q9Y2I1	NISCH_HUMAN	I	1442;1442;366;786	ENSP00000418232:L1442I;ENSP00000339958:L1442I	ENSP00000339958:L1442I	L	+	1	0	NISCH	52501347	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	2.763000	0.47605	2.535000	0.85469	0.561000	0.74099	CTC	.	.	.	none		0.657	NISCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351357.1	NM_007184		A	52526307	C	A	52526307	3	1	102	1	0	0	0	0	1	0	0	0	10439	681	24	4	4406	4	NISCH	3	52526307	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08	42649226	52526307	145496123	15	6489											
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113376680	113376680	+	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	gatggtccaggaggttgactGccataggagctagatgaaac	12	8	14	7	0	0	3	0	2	0	1	1	6	1	5	2	4	3	2	2	4	3	3			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr3:113376680G>T	ENST00000478658.1	-	5	3866	c.3849C>A	c.(3847-3849)ggC>ggA	p.G1283G	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Silent_p.G1283G			Q68DE3	K2018_HUMAN	KIAA2018	1283						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						GAGGTTGACTGCCATAGGAGC	0.468																																					p.G1283G		Atlas-SNP	.											.	KIAA2018	180	.	0			c.C3849A						PASS	.						109	105	106					3																	113376680		1947	4151	6098	SO:0001819	synonymous_variant	205717	exon7			TTGACTGCCATAG	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.3849C>A	chr3.hg19:g.113376680G>T		165.0	0.0	.		222.0	140.0	.	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	hg19	CCDS43133.1																																																																																			.	.	.	none		0.468	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		T	113376680	G	T	113376680	2	4	102	1	0	0	0	0	0	0	0	1	8275	1306	46	4		4	KIAA2018	3	113376680	Silent	SNP	G	TCGA-B9-7268-01A-11D-2136-08	60850373	113376680	84645750	16	6490											
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123254840	123254840	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcaccttcaaaaaagaagaAgtttcaaactaattatgctt	17	13	4	7	0	3	2	3	0	0	2	3	2	3	2	1	0	2	2	1	0	8	6			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr4:123254840A>G	ENST00000264501.4	+	68	11895	c.11522A>G	c.(11521-11523)aAg>aGg	p.K3841R	KIAA1109_ENST00000388738.3_Missense_Mutation_p.K3841R			Q2LD37	K1109_HUMAN	KIAA1109	3841	Poly-Lys.				regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						AAAAAGAAGAAGTTTCAAACT	0.348																																					p.K3841R		Atlas-SNP	.											.	KIAA1109	424	.	0			c.A11522G						PASS	.						80	72	74					4																	123254840		1827	4081	5908	SO:0001583	missense	84162	exon66			AGAAGAAGTTTCA	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.11522A>G	chr4.hg19:g.123254840A>G	ENSP00000264501:p.Lys3841Arg	37.0	0.0	.		46.0	23.0	.	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.9|24.9	4.586223|4.586223	0.86851|0.86851	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000438707|ENST00000306802	T;T;T|.	0.35421|.	2.32;2.32;1.31|.	5.63|5.63	5.63|5.63	0.86233|0.86233	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72120|0.72120	0.3421|0.3421	M|M	0.63843|0.63843	1.955|1.955	0.80722|0.80722	D|D	1|1	D;D|.	0.69078|.	0.974;0.997|.	D;D|.	0.73380|.	0.969;0.98|.	T|T	0.70941|0.70941	-0.4735|-0.4735	10|5	0.45353|.	T|.	0.12|.	.|.	16.1413|16.1413	0.81528|0.81528	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	3840;3841|.	Q2LD37-4;Q2LD37|.	.;K1109_HUMAN|.	R|G	3841;3841;545|252	ENSP00000264501:K3841R;ENSP00000373390:K3841R;ENSP00000410874:K545R|.	ENSP00000264501:K3841R|.	K|S	+|+	2|1	0|0	KIAA1109|KIAA1109	123474290|123474290	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	8.910000|8.910000	0.92685|0.92685	2.270000|2.270000	0.75569|0.75569	0.482000|0.482000	0.46254|0.46254	AAG|AGT	.	.	.	none		0.348	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		G	123254840	A	G	123254840	3	3	102	1	0	0	0	0	1	0	0	0	8215	72	3	3	11784	3	KIAA1109	4	123254840	Missense_Mutation	SNP	A	TCGA-B9-7268-01A-11D-2136-08		123254840	67899436	17	6491											
CBR4	84869	hgsc.bcm.edu	37	chr4	169931208	169931208	+	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	acagctctgccaatgcctcgGgagcctccaaaaacagcaca	13	5	8	15	1	1	0	0	0	1	0	3	1	2	1	4	1	6	2	4	1	3	0			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr4:169931208G>T	ENST00000306193.3	-	1	201	c.33C>A	c.(31-33)tcC>tcA	p.S11S	CBR4_ENST00000504480.1_Silent_p.S11S|RP11-483A20.3_ENST00000506933.1_RNA	NM_032783.4	NP_116172.2	Q8N4T8	CBR4_HUMAN	carbonyl reductase 4	11					daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|fatty acid biosynthetic process (GO:0006633)|protein homotetramerization (GO:0051289)	mitochondrial matrix (GO:0005759)	NAD(P)H dehydrogenase (quinone) activity (GO:0003955)|NADPH binding (GO:0070402)|NADPH dehydrogenase (quinone) activity (GO:0008753)|quinone binding (GO:0048038)			kidney(1)|large_intestine(2)|lung(2)	5		Prostate(90;0.00263)|Renal(120;0.0183)|Melanoma(52;0.123)		GBM - Glioblastoma multiforme(119;0.0321)		CAATGCCTCGGGAGCCTCCAA	0.602											OREG0016397	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S11S		Atlas-SNP	.											.	CBR4	15	.	0			c.C33A						PASS	.						50	54	52					4																	169931208		2203	4300	6503	SO:0001819	synonymous_variant	84869	exon1			GCCTCGGGAGCCT	BC021973	CCDS3812.1	4q32.3	2013-10-11			ENSG00000145439	ENSG00000145439	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	25891	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 45C, member 1"					19027726	Standard	NM_032783		Approved	FLJ14431, SDR45C1	uc003iry.3	Q8N4T8	OTTHUMG00000161025	ENST00000306193.3:c.33C>A	chr4.hg19:g.169931208G>T		49.0	0.0	.	1881	44.0	22.0	.	NM_032783	Q8WTW8|Q96K93	Silent	SNP	ENST00000306193.3	hg19	CCDS3812.1																																																																																			.	.	.	none		0.602	CBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363441.2	NM_032783		T	169931208	G	T	169931208	2	4	102	1	0	0	0	0	0	0	0	1	2712	1219	43	4		4	CBR4	4	169931208	Silent	SNP	G	TCGA-B9-7268-01A-11D-2136-08	46676368	169931208	21223068	18	6492											
FAT1	2195	hgsc.bcm.edu	37	chr4	187540602	187540602	+	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	attatcattgaggtcggtaaCgtccaccgtgacaatcacat	12	11	8	10	3	2	2	2	2	0	0	4	2	3	2	2	2	1	1	2	2	3	3	rs201352448		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr4:187540602C>T	ENST00000441802.2	-	10	7347	c.7138G>A	c.(7138-7140)Gtt>Att	p.V2380I		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2380	Cadherin 21. {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						AGGTCGGTAACGTCCACCGTG	0.502										HNSCC(5;0.00058)																											p.V2380I	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.G7138A						PASS	.						67	68	67					4																	187540602		2106	4223	6329	SO:0001583	missense	2195	exon10			CGGTAACGTCCAC	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.7138G>A	chr4.hg19:g.187540602C>T	ENSP00000406229:p.Val2380Ile	52.0	0.0	.		67.0	35.0	.	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	hg19	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	12.95	2.092207	0.36952	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.61510	0.1	5.14	4.3	0.51218	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	0.121633	0.56097	N	0.000035	T	0.38799	0.1054	N	0.26130	0.795	0.58432	D	0.999996	B	0.30851	0.297	B	0.25614	0.062	T	0.20306	-1.0279	10	0.22109	T	0.4	.	9.4366	0.38643	0.0:0.8376:0.0:0.1624	.	2380	Q14517	FAT1_HUMAN	I	2380;2382	ENSP00000406229:V2380I	ENSP00000260147:V2382I	V	-	1	0	FAT1	187777596	0.992000	0.36948	0.999000	0.59377	0.398000	0.30690	1.481000	0.35476	1.527000	0.49086	0.650000	0.86243	GTT	.	C|0.999;T|0.001	0.001	weak		0.502	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		T	187540602	C	T	187540602	3	4	102	1	0	0	0	0	1	0	0	0	5696	536	19	1	6700	1	FAT1	4	187540602	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08	17609394	187540602	3613674	19	6493											
RGNEF	64283	hgsc.bcm.edu	37	chr5	73136427	73136427	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccttcctacagaaaccagTcccagtgtgtacccacttag	11	9	6	15	0	0	1	0	0	0	1	2	1	2	1	5	0	3	1	5	0	4	4			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr5:73136427T>C	ENST00000426542.2	+	10	1289	c.1269T>C	c.(1267-1269)agT>agC	p.S423S	ARHGEF28_ENST00000513042.2_Silent_p.S423S|ARHGEF28_ENST00000513841.1_3'UTR|ARHGEF28_ENST00000287898.5_Silent_p.S423S|ARHGEF28_ENST00000296799.4_Silent_p.S110S|ARHGEF28_ENST00000296794.6_Silent_p.S423S|ARHGEF28_ENST00000545377.1_Silent_p.S423S|ARHGEF28_ENST00000437974.1_Silent_p.S423S			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	423					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)										CAGAAACCAGTCCCAGTGTGT	0.493																																					p.S423S		Atlas-SNP	.											.	.	.	.	0			c.T1269C						PASS	.						69	68	68					5																	73136427		2002	4162	6164	SO:0001819	synonymous_variant	64283	exon11			AACCAGTCCCAGT		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.1269T>C	chr5.hg19:g.73136427T>C		54.0	0.0	.		57.0	27.0	.	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Silent	SNP	ENST00000426542.2	hg19	CCDS54870.1																																																																																			.	.	.	none		0.493	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			C	73136427	T	C	73136427	2	2	102	1	0	0	0	0	0	0	0	1	13296	1664	58	3		3	RGNEF	5	73136427	Silent	SNP	T	TCGA-B9-7268-01A-11D-2136-08		73136427	107778833	20	6494											
CDKL3	51265	hgsc.bcm.edu	37	chr5	133695635	133695635	+	Missense_Mutation	SNP	A	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	tcgaaggatctggaagaggtAttttctaagtcgcttactct	10	14	10	7	2	3	1	0	0	3	1	5	4	3	3	0	3	1	2	0	3	5	5			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr5:133695635A>C	ENST00000265334.4	-	3	431	c.313T>G	c.(313-315)Tac>Gac	p.Y105D	CDKL3_ENST00000435211.1_Missense_Mutation_p.Y105D|CDKL3_ENST00000536186.1_Intron|CDKL3_ENST00000521118.1_Missense_Mutation_p.Y105D|CDKL3_ENST00000523832.1_Missense_Mutation_p.Y105D|CTD-2410N18.4_ENST00000518409.1_RNA|CDKL3_ENST00000521755.1_Intron|CDKL3_ENST00000523054.1_5'UTR|CDKL3_ENST00000609654.1_Intron|CDKL3_ENST00000609383.1_Intron|CDKL3_ENST00000522501.1_Intron|CDKL3_ENST00000435240.2_Intron	NM_001113575.1	NP_001107047.1	Q8IVW4	CDKL3_HUMAN	cyclin-dependent kinase-like 3	105	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)			TGGAAGAGGTATTTTCTAAGT	0.328																																					p.Y105D		Atlas-SNP	.											.	CDKL3	76	.	0			c.T313G						PASS	.						99	90	93					5																	133695635		1826	4085	5911	SO:0001583	missense	51265	exon3			AGAGGTATTTTCT	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.313T>G	chr5.hg19:g.133695635A>C	ENSP00000265334:p.Tyr105Asp	6.0	0.0	.		17.0	8.0	.	NM_001113575	D3DQA0|D3DQA1|Q9P114	Missense_Mutation	SNP	ENST00000265334.4	hg19	CCDS47264.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.106870	0.77096	.	.	ENSG00000006837	ENST00000265334;ENST00000521118;ENST00000523832;ENST00000435211	T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27	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	0.56097	D	0.000039	T	0.82171	0.4979	M	0.81614	2.55	0.45733	D	0.998634	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.84940	0.0865	10	0.87932	D	0	-6.1958	14.5773	0.68258	1.0:0.0:0.0:0.0	.	105;105	E7ET86;Q8IVW4	.;CDKL3_HUMAN	D	105	ENSP00000265334:Y105D;ENSP00000428689:Y105D;ENSP00000430496:Y105D;ENSP00000395559:Y105D	ENSP00000265334:Y105D	Y	-	1	0	CDKL3	133723534	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.231000	0.72307	2.141000	0.66446	0.482000	0.46254	TAC	.	.	.	none		0.328	CDKL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377697.1	NM_001113575		C	133695635	A	C	133695635	3	2	102	1	0	0	0	0	1	0	0	0	3157	449	16	5	1513	5	CDKL3	5	133695635	Missense_Mutation	SNP	A	TCGA-B9-7268-01A-11D-2136-08	60559208	133695635	47219625	21	6495											
DNAH8	1769	hgsc.bcm.edu	37	chr6	38704982	38704982	+	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	gtccaagcagggagaatctgAaaaacatattttcactgaaa	17	9	8	7	0	2	3	1	2	1	1	3	4	3	3	1	1	2	1	1	1	6	3			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr6:38704982A>T	ENST00000359357.3	+	4	505	c.251A>T	c.(250-252)gAa>gTa	p.E84V	DNAH8_ENST00000441566.1_Missense_Mutation_p.E84V|DNAH8_ENST00000449981.2_Missense_Mutation_p.E301V			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	84					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						GGAGAATCTGAAAAACATATT	0.313																																					p.E301V		Atlas-SNP	.											.	DNAH8	1239	.	0			c.A902T						PASS	.						74	77	76					6																	38704982		2203	4300	6503	SO:0001583	missense	1769	exon6			AATCTGAAAAACA	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.251A>T	chr6.hg19:g.38704982A>T	ENSP00000352312:p.Glu84Val	70.0	0.0	.		108.0	50.0	.	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	A	6.965	0.548009	0.13312	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.23950	1.91;1.9;1.88	5.2	5.2	0.72013	.	0.348200	0.29980	N	0.010705	T	0.08268	0.0206	L	0.41236	1.265	0.32224	N	0.57484	B	0.02656	0.0	B	0.04013	0.001	T	0.17868	-1.0355	10	0.14252	T	0.57	.	11.237	0.48946	0.8476:0.1523:0.0:0.0	.	84	Q96JB1	DYH8_HUMAN	V	289;289;84;84	ENSP00000333363:E289V;ENSP00000352312:E84V;ENSP00000402294:E84V	ENSP00000333363:E289V	E	+	2	0	DNAH8	38812960	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.440000	0.44855	2.073000	0.62155	0.482000	0.46254	GAA	.	.	.	none		0.313	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		T	38704982	A	T	38704982	3	4	102	1	0	0	0	0	1	0	0	0	4609	246	9	5	257	5	DNAH8	6	38704982	Missense_Mutation	SNP	A	TCGA-B9-7268-01A-11D-2136-08		38704982	132410085	22	6496											
BCLAF1	9774	hgsc.bcm.edu	37	chr6	136582550	136582550	+	Frame_Shift_Del	DEL	T	T	-																															ttaaagcgccctctgccacgTtgaaaagtaccacgacctct																										TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr6:136582550delT	ENST00000531224.1	-	12	2862	c.2610delA	c.(2608-2610)caafs	p.Q870fs	BCLAF1_ENST00000031135.9_Frame_Shift_Del_p.Q88fs|BCLAF1_ENST00000353331.4_Frame_Shift_Del_p.Q819fs|BCLAF1_ENST00000530767.1_Frame_Shift_Del_p.Q697fs|BCLAF1_ENST00000392348.2_Frame_Shift_Del_p.Q819fs|BCLAF1_ENST00000529917.1_5'UTR|BCLAF1_ENST00000527536.1_Frame_Shift_Del_p.Q821fs|BCLAF1_ENST00000527759.1_Frame_Shift_Del_p.Q868fs	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	870					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)		CTCTGCCACGTTGAAAAGTAC	0.418																																					p.R871fs	Colon(142;1534 1789 5427 7063 28491)	Atlas-INDEL	.											.	BCLAF1	203	.	0			c.2611delC						PASS	.						218	218	218					6																	136582550		2203	4300	6503	SO:0001589	frameshift_variant	9774	exon12			.	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.2610delA	chr6.hg19:g.136582550delT	ENSP00000435210:p.Gln870fs	379.0	0.0	0		614.0	103.0	0.167752	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Frame_Shift_Del	DEL	ENST00000531224.1	hg19	CCDS5177.1																																																																																			.	.	.	none		0.418	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		-	136582550	T	-	136582550	7	5	102	1	0	1	0	1	0	0	0	0	1383	1722	60	0	160	0	BCLAF1	6	136582550	Frame_Shift_Del	DEL	T	TCGA-B9-7268-01A-11D-2136-08	97877568	136582550	34532517	23	6497											
DFNA5	1687	hgsc.bcm.edu	37	chr7	24745817	24745817	+	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	ccttacctgcgagggcactgAccaagaagtaggctgtcata	11	8	11	11	1	1	2	1	1	0	1	1	3	1	2	3	2	2	3	3	2	5	3			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr7:24745817A>T	ENST00000342947.3	-	8	1594	c.1169T>A	c.(1168-1170)gTc>gAc	p.V390D	DFNA5_ENST00000545231.1_Missense_Mutation_p.V226D|DFNA5_ENST00000409970.1_Missense_Mutation_p.V226D|DFNA5_ENST00000419307.1_Missense_Mutation_p.V226D|DFNA5_ENST00000409775.3_Missense_Mutation_p.V390D	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	390					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						GAGGGCACTGACCAAGAAGTA	0.537																																					p.V390D	GBM(78;184 1250 20134 20900 23600)	Atlas-SNP	.											.	DFNA5	51	.	0			c.T1169A						PASS	.						75	76	76					7																	24745817		2203	4300	6503	SO:0001583	missense	1687	exon8			GCACTGACCAAGA	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.1169T>A	chr7.hg19:g.24745817A>T	ENSP00000339587:p.Val390Asp	100.0	0.0	.		164.0	95.0	.	NM_001127453	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Missense_Mutation	SNP	ENST00000342947.3	hg19	CCDS5389.1	.	.	.	.	.	.	.	.	.	.	A	15.16	2.752032	0.49362	.	.	ENSG00000105928	ENST00000342947;ENST00000419307;ENST00000545231;ENST00000409970;ENST00000409775;ENST00000430096	T;T;T;T;T;T	0.26957	1.7;1.7;1.7;1.7;1.7;1.7	5.0	5.0	0.66597	.	0.415630	0.25613	N	0.029475	T	0.44074	0.1276	M	0.68317	2.08	0.80722	D	1	D	0.60575	0.988	P	0.59357	0.856	T	0.43048	-0.9415	10	0.87932	D	0	-18.5588	12.3301	0.55035	1.0:0.0:0.0:0.0	.	390	O60443	DFNA5_HUMAN	D	390;226;226;226;390;10	ENSP00000339587:V390D;ENSP00000401332:V226D;ENSP00000442661:V226D;ENSP00000387119:V226D;ENSP00000386670:V390D;ENSP00000395540:V10D	ENSP00000339587:V390D	V	-	2	0	DFNA5	24712342	1.000000	0.71417	1.000000	0.80357	0.119000	0.20118	5.025000	0.64097	2.091000	0.63221	0.460000	0.39030	GTC	.	.	.	none		0.537	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403		T	24745817	A	T	24745817	3	4	102	1	0	0	0	0	1	0	0	0	4456	275	10	5	333	5	DFNA5	7	24745817	Missense_Mutation	SNP	A	TCGA-B9-7268-01A-11D-2136-08		24745817	134392846	24	6498											
AEBP1	165	hgsc.bcm.edu	37	chr7	44146299	44146299	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagcccaaggagaagccaccTaaggccaccaagaagcccaa	17	1	9	14	0	0	2	0	0	0	2	0	3	0	2	6	2	3	0	6	2	7	1	rs539867334		TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr7:44146299T>C	ENST00000223357.3	+	2	713	c.408T>C	c.(406-408)ccT>ccC	p.P136P		NM_001129.3	NP_001120.3	Q8IUX7	AEBP1_HUMAN	AE binding protein 1	136	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						AGAAGCCACCTAAGGCCACCA	0.627													T|||	1	0.000199681	0	0	5008	,	,		12431	0		0.001	False		,,,				2504	0				p.P136P		Atlas-SNP	.											AEBP1,NS,carcinoma,0,2	AEBP1	102	.	0			c.T408C						PASS	.						102	108	106					7																	44146299		2199	4296	6495	SO:0001819	synonymous_variant	165	exon2			GCCACCTAAGGCC	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.408T>C	chr7.hg19:g.44146299T>C		31.0	0.0	.		41.0	3.0	.	NM_001129	Q14113|Q59ER7|Q6ZSC7|Q7KZ79	Silent	SNP	ENST00000223357.3	hg19	CCDS5476.1	.	.	.	.	.	.	.	.	.	.	T	9.564	1.119220	0.20877	.	.	ENSG00000106624	ENST00000455443	.	.	.	5.02	-4.0	0.04057	.	.	.	.	.	.	.	.	.	.	.	0.48901	D	0.999723	.	.	.	.	.	.	.	.	.	.	.	.	.	-13.6441	1.8939	0.03253	0.1952:0.3376:0.0967:0.3705	.	.	.	.	Q	94	.	.	X	+	1	0	AEBP1	44112824	0.000000	0.05858	0.758000	0.31321	0.945000	0.59286	-4.524000	0.00221	-0.739000	0.04809	-0.464000	0.05259	TAA	.	.	.	none		0.627	AEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250993.2	NM_001129		C	44146299	T	C	44146299	2	2	102	1	0	0	0	0	0	0	0	1	349	1509	53	3		3	AEBP1	7	44146299	Silent	SNP	T	TCGA-B9-7268-01A-11D-2136-08	19400482	44146299	114992364	25	6499											
TYW1	55253	hgsc.bcm.edu	37	chr7	66532281	66532281	+	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	acttgtcatagtccatgctcCgagggagaggaggttgttac	9	11	13	8	1	1	1	1	0	0	1	3	4	3	2	2	3	2	3	2	3	2	4			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr7:66532281C>A	ENST00000359626.5	+	10	1329	c.1165C>A	c.(1165-1167)Cga>Aga	p.R389R		NM_018264.2	NP_060734.2	Q9NV66	TYW1_HUMAN	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	389					tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(8)|kidney(10)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(3)|stomach(2)|urinary_tract(2)	46		Lung NSC(55;0.0846)|all_lung(88;0.183)				GTCCATGCTCCGAGGGAGAGG	0.413																																					p.R389R		Atlas-SNP	.											.	TYW1	71	.	0			c.C1165A						PASS	.						161	141	148					7																	66532281		2203	4300	6503	SO:0001819	synonymous_variant	55253	exon10			ATGCTCCGAGGGA	AK001762	CCDS5538.1	7q11.21	2007-11-29	2007-11-29	2007-11-29	ENSG00000198874	ENSG00000198874			25598	protein-coding gene	gene with protein product	"tRNA-yW synthesizing protein 1 homolog A (S. cerevisiae)"	611243	"radical S-adenosyl methionine and flavodoxin domains 1"	RSAFD1		16162496, 17150819	Standard	NM_018264		Approved	FLJ10900, MGC23001, MGC60291, YPL207W, TYW1A	uc003tvn.4	Q9NV66	OTTHUMG00000129723	ENST00000359626.5:c.1165C>A	chr7.hg19:g.66532281C>A		114.0	0.0	.		162.0	7.0	.	NM_018264	Q6PJG8|Q75MG8|Q75MN3|Q86V12|Q8IVS7|Q9H9C4	Silent	SNP	ENST00000359626.5	hg19	CCDS5538.1																																																																																			.	.	.	none		0.413	TYW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251932.2	NM_018264		A	66532281	C	A	66532281	2	1	102	1	0	0	0	0	0	0	0	1	16830	644	23	4		4	TYW1	7	66532281	Silent	SNP	C	TCGA-B9-7268-01A-11D-2136-08	22385982	66532281	92606382	26	6500											
REPIN1	29803	hgsc.bcm.edu	37	chr7	150068863	150068864	+	Frame_Shift_Ins	INS	-	-	A																															ccggaggcccggcccttcatINSatgcggcaactgtggccgga																										TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr7:150068863_150068864insA	ENST00000425389.2	+	1	611_612	c.533_534insA	c.(532-537)atatgcfs	p.C179fs	REPIN1_ENST00000479668.1_3'UTR|RP4-584D14.5_ENST00000488310.1_RNA|REPIN1_ENST00000397281.2_Frame_Shift_Ins_p.C179fs|REPIN1_ENST00000466559.1_3'UTR|REPIN1_ENST00000489432.2_Frame_Shift_Ins_p.C236fs|REPIN1_ENST00000540729.1_Frame_Shift_Ins_p.C179fs|REPIN1_ENST00000444957.1_Frame_Shift_Ins_p.C179fs|REPIN1_ENST00000482680.1_3'UTR	NM_014374.3	NP_055189.2	Q9BWE0	REPI1_HUMAN	replication initiator 1	179					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)			CGGCCCTTCATATGCGGCAACT	0.658																																					p.I235fs		Atlas-INDEL	.											.	REPIN1	74	.	0			c.704_705insA						PASS	.																																			SO:0001589	frameshift_variant	29803	exon3			.	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.534dupA	chr7.hg19:g.150068864_150068864dupA	ENSP00000388287:p.Cys179fs	38.0	0.0	0		41.0	10.0	0.243902	NM_001099695	C9J3L7|D3DWZ1|Q7LE03|Q9BUZ6|Q9NZH2|Q9UMP5	Frame_Shift_Ins	INS	ENST00000425389.2	hg19	CCDS43677.1																																																																																			.	.	.	none		0.658	REPIN1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376940.1	NM_014374		A	150068864	-	A	150068863	7	5	102	1	0	1	1	0	0	0	0	0	13240	1406	49	0	710	0	REPIN1	7	150068863	Frame_Shift_Ins	INS	-	TCGA-B9-7268-01A-11D-2136-08	83536582	150068863	9069800	27	6501											
SGK223	157285	hgsc.bcm.edu	37	chr8	8235103	8235103	+	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	tgcctgccccgggaacctgcAgtctgggaggcagccttggc	5	7	15	14	1	1	0	0	0	1	0	1	2	1	2	5	4	5	2	5	4	1	1			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr8:8235103A>T	ENST00000520004.1	-	3	1080	c.816T>A	c.(814-816)acT>acA	p.T272T	SGK223_ENST00000330777.4_Silent_p.T272T			Q86YV5	SG223_HUMAN		272							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GGGAACCTGCAGTCTGGGAGG	0.677																																					p.T272T	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.T816A						PASS	.						22	27	25					8																	8235103		1995	4154	6149	SO:0001819	synonymous_variant	0	exon2			ACCTGCAGTCTGG																												ENST00000520004.1:c.816T>A	chr8.hg19:g.8235103A>T		32.0	0.0	.		34.0	22.0	.	NM_001080826	Q8N3N5	Silent	SNP	ENST00000520004.1	hg19	CCDS43706.1																																																																																			.	.	.	none		0.677	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1			T	8235103	A	T	8235103	2	4	102	1	0	0	0	0	0	0	0	1	14223	175	7	5		5	SGK223	8	8235103	Silent	SNP	A	TCGA-B9-7268-01A-11D-2136-08		8235103	138128919	28	6502											
CSPP1	79848	hgsc.bcm.edu	37	chr8	68070755	68070755	+	Frame_Shift_Del	DEL	G	G	-																															agaagaaaaagaagaaagacGgcttgcagaacagagggcac																										TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr8:68070755delG	ENST00000262210.5	+	18	2331	c.2300delG	c.(2299-2301)cggfs	p.R767fs	CSPP1_ENST00000521168.1_3'UTR|CSPP1_ENST00000412460.1_Frame_Shift_Del_p.R422fs	NM_024790.6	NP_079066.5	Q1MSJ5	CSPP1_HUMAN	centrosome and spindle pole associated protein 1	802					positive regulation of cell division (GO:0051781)|positive regulation of cytokinesis (GO:0032467)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|spindle (GO:0005819)|spindle pole (GO:0000922)				NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|prostate(3)|skin(1)|urinary_tract(1)	49	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)			GAAGAAAGACGGCTTGCAGAA	0.388																																					p.R767fs		Atlas-INDEL	.											CSPP1,colon,carcinoma,0,1	CSPP1	129	.	0			c.2299delC						PASS	.						68	67	67					8																	68070755		1860	4092	5952	SO:0001589	frameshift_variant	79848	exon18			.	AJ583433	CCDS43744.1	8q13.2	2014-02-24			ENSG00000104218	ENSG00000104218			26193	protein-coding gene	gene with protein product		611654				15580290, 24360807	Standard	NM_024790		Approved	FLJ22490, CSPP, JBTS21	uc003xxj.3	Q1MSJ5	OTTHUMG00000164564	ENST00000262210.5:c.2300delG	chr8.hg19:g.68070755delG	ENSP00000262210:p.Arg767fs	49.0	0.0	0		47.0	13.0	0.276596	NM_024790	A6ND63|Q70F00|Q8TBC1	Frame_Shift_Del	DEL	ENST00000262210.5	hg19	CCDS43744.1																																																																																			.	.	.	none		0.388	CSPP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379254.1	NM_024790		-	68070755	G	-	68070755	7	5	102	1	0	1	0	1	0	0	0	0	3964	1116	39	0	2483	0	CSPP1	8	68070755	Frame_Shift_Del	DEL	G	TCGA-B9-7268-01A-11D-2136-08	59835652	68070755	78293267	29	6503											
ZBTB10	65986	hgsc.bcm.edu	37	chr8	81411997	81411997	+	Missense_Mutation	SNP	T	T	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	ccacttagatattgctgcagTtcaaggtttttcagtcatct	9	16	7	9	0	4	1	3	0	1	1	4	1	4	1	1	1	2	4	1	1	3	6			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr8:81411997T>G	ENST00000430430.1	+	3	2020	c.1241T>G	c.(1240-1242)gTt>gGt	p.V414G	ZBTB10_ENST00000426744.2_Missense_Mutation_p.V414G|ZBTB10_ENST00000455036.3_Missense_Mutation_p.V414G|ZBTB10_ENST00000379091.4_Missense_Mutation_p.V122G	NM_001277145.1	NP_001264074.1	Q96DT7	ZBT10_HUMAN	zinc finger and BTB domain containing 10	414	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(4)	20	all_cancers(3;1.68e-09)|all_epithelial(4;5.13e-11)|Lung NSC(7;1.75e-07)|all_lung(9;7.38e-07)|Breast(3;2.96e-06)		BRCA - Breast invasive adenocarcinoma(6;0.000434)|Epithelial(68;0.00486)|all cancers(69;0.0296)			ATTGCTGCAGTTCAAGGTTTT	0.408																																					p.V414G		Atlas-SNP	.											.	ZBTB10	51	.	0			c.T1241G						PASS	.						124	118	120					8																	81411997		1835	4102	5937	SO:0001583	missense	65986	exon2			CTGCAGTTCAAGG	AK022814	CCDS47880.1, CCDS64920.1	8q13-q21.1	2013-01-09			ENSG00000205189	ENSG00000205189		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	30953	protein-coding gene	gene with protein product						12477932	Standard	NM_001105539		Approved	RINZF, FLJ12752	uc003ybx.5	Q96DT7	OTTHUMG00000155016	ENST00000430430.1:c.1241T>G	chr8.hg19:g.81411997T>G	ENSP00000387462:p.Val414Gly	106.0	0.0	.		96.0	4.0	.	NM_023929	A4FVD0|Q86W96|Q8IXI9|Q96MH9	Missense_Mutation	SNP	ENST00000430430.1	hg19	CCDS47880.1	.	.	.	.	.	.	.	.	.	.	T	16.00	2.997599	0.54147	.	.	ENSG00000205189	ENST00000379091;ENST00000430430;ENST00000455036;ENST00000426744;ENST00000519370	T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31	5.54	5.54	0.83059	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.142348	0.44902	D	0.000418	T	0.79106	0.4390	L	0.58510	1.815	0.80722	D	1	B;D;D;D	0.89917	0.387;1.0;1.0;1.0	P;D;D;D	0.91635	0.512;0.998;0.998;0.999	T	0.79783	-0.1658	10	0.51188	T	0.08	.	15.6913	0.77457	0.0:0.0:0.0:1.0	.	270;414;414;122	A8E4L4;Q96DT7;Q96DT7-2;Q96DT7-4	.;ZBT10_HUMAN;.;.	G	122;414;414;414;242	ENSP00000368384:V122G;ENSP00000387462:V414G;ENSP00000412036:V414G;ENSP00000416134:V414G	ENSP00000368384:V122G	V	+	2	0	ZBTB10	81574552	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.698000	0.84413	2.113000	0.64589	0.528000	0.53228	GTT	.	.	.	none		0.408	ZBTB10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338055.2	NM_023929		G	81411997	T	G	81411997	3	3	102	1	0	0	0	0	1	0	0	0	17535	1725	60	5	1247	5	ZBTB10	8	81411997	Missense_Mutation	SNP	T	TCGA-B9-7268-01A-11D-2136-08	13341242	81411997	64952025	30	6504											
NIPAL2	79815	hgsc.bcm.edu	37	chr8	99215364	99215364	+	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	atggcactgattgtaaagaaAatatgattaactggcaccac	16	10	8	7	0	0	3	0	2	0	1	0	3	0	3	1	2	1	3	1	2	6	4			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr8:99215364A>T	ENST00000341166.3	-	8	1107	c.852T>A	c.(850-852)atT>atA	p.I284I	NIPAL2_ENST00000430223.2_Silent_p.I284I|NIPAL2_ENST00000520545.1_5'UTR	NM_024759.1	NP_079035.1	Q9H841	NPAL2_HUMAN	NIPA-like domain containing 2	284						integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			cervix(3)|kidney(1)|large_intestine(2)|lung(5)|stomach(1)	12						TTGTAAAGAAAATATGATTAA	0.408																																					p.I284I		Atlas-SNP	.											.	NIPAL2	23	.	0			c.T852A						PASS	.						185	162	170					8																	99215364		2203	4300	6503	SO:0001819	synonymous_variant	79815	exon8			AAAGAAAATATGA	AK024017	CCDS6278.1	8q22.2	2009-03-24		2009-03-24	ENSG00000104361	ENSG00000104361			25854	protein-coding gene	gene with protein product				NPAL2		14702039	Standard	NM_024759		Approved	FLJ13955	uc003yil.1	Q9H841	OTTHUMG00000164668	ENST00000341166.3:c.852T>A	chr8.hg19:g.99215364A>T		99.0	0.0	.		122.0	58.0	.	NM_024759	A2RTY8	Silent	SNP	ENST00000341166.3	hg19	CCDS6278.1																																																																																			.	.	.	none		0.408	NIPAL2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379677.1	NM_024759		T	99215364	A	T	99215364	2	4	102	1	0	0	0	0	0	0	0	1	10432	10	1	5		5	NIPAL2	8	99215364	Silent	SNP	A	TCGA-B9-7268-01A-11D-2136-08	17803367	99215364	47148658	31	6505											
C9orf91	203197	hgsc.bcm.edu	37	chr9	117400851	117400851	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgagaagcagattgagccagTtgtgtgttgtcatggagact	10	12	14	5	0	1	4	1	2	0	3	1	6	1	4	1	1	2	3	1	1	1	3			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr9:117400851T>C	ENST00000288502.4	+	8	1131	c.694T>C	c.(694-696)Ttg>Ctg	p.L232L	C9orf91_ENST00000374049.4_Silent_p.L233L			Q5VZI3	CI091_HUMAN	chromosome 9 open reading frame 91	232						integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(3)|lung(5)|pancreas(1)|skin(1)|urinary_tract(1)	13						ATTGAGCCAGTTGTGTGTTGT	0.562																																					p.L232L		Atlas-SNP	.											.	C9orf91	32	.	0			c.T694C						PASS	.						149	136	140					9																	117400851		2203	4300	6503	SO:0001819	synonymous_variant	203197	exon8			AGCCAGTTGTGTG	BX649023	CCDS6808.1	9q33.1	2008-02-05			ENSG00000157693	ENSG00000157693			24513	protein-coding gene	gene with protein product						14702039	Standard	NM_153045		Approved	DKFZp547P234, FLJ38045	uc004bjd.4	Q5VZI3	OTTHUMG00000020541	ENST00000288502.4:c.694T>C	chr9.hg19:g.117400851T>C		168.0	0.0	.		175.0	76.0	.	NM_153045	A0PJA3|Q3KNS4|Q5VZI2|Q6P5Z7|Q8N1P3|Q8ND43	Silent	SNP	ENST00000288502.4	hg19	CCDS6808.1																																																																																			.	.	.	none		0.562	C9orf91-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000053780.1	NM_153045		C	117400851	T	C	117400851	2	2	102	1	0	0	0	0	0	0	0	1	2507	1722	60	3		3	C9orf91	9	117400851	Silent	SNP	T	TCGA-B9-7268-01A-11D-2136-08		117400851	23812580	32	6506											
LIPA	3988	hgsc.bcm.edu	37	chr10	90974746	90974746	+	Frame_Shift_Del	DEL	G	G	-																															gacgtcgtagacatctgcaaGccagtcgtgacccccgctcc																										TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr10:90974746delG	ENST00000336233.5	-	10	1361	c.1039delC	c.(1039-1041)cttfs	p.L347fs	LIPA_ENST00000371837.1_Frame_Shift_Del_p.L291fs|LIPA_ENST00000456827.1_Frame_Shift_Del_p.L347fs			P38571	LICH_HUMAN	lipase A, lysosomal acid, cholesterol esterase	347					cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cytokine production (GO:0001816)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|lipid catabolic process (GO:0016042)|lung development (GO:0030324)|tissue remodeling (GO:0048771)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	lipase activity (GO:0016298)|sterol esterase activity (GO:0004771)			endometrium(1)|large_intestine(2)|lung(3)	6		Colorectal(252;0.0162)		GBM - Glioblastoma multiforme(2;0.00406)		ACATCTGCAAGCCAGTCGTGA	0.493																																					p.L347fs		Atlas-INDEL	.											.	LIPA	29	.	0			c.1040delT						PASS	.						93	84	87					10																	90974746		2203	4300	6503	SO:0001589	frameshift_variant	3988	exon10			.	M74775	CCDS7401.1, CCDS73160.1	10q23.2-q23.3	2012-07-13	2008-08-01		ENSG00000107798	ENSG00000107798	3.1.1.13		6617	protein-coding gene	gene with protein product	"Wolman disease"	613497				8432549	Standard	NM_000235		Approved	LAL, CESD	uc009xtq.3	P38571	OTTHUMG00000018716	ENST00000336233.5:c.1039delC	chr10.hg19:g.90974746delG	ENSP00000337354:p.Leu347fs	131.0	0.0	0		156.0	63.0	0.403846	NM_000235	B2RBH5|D3DR29|Q16529|Q53H21|Q5T074|Q5T771|Q96EJ0	Frame_Shift_Del	DEL	ENST00000336233.5	hg19	CCDS7401.1																																																																																			.	.	.	none		0.493	LIPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049308.1	NM_000235		-	90974746	G	-	90974746	7	5	102	1	0	1	0	1	0	0	0	0	8826	971	34	0	164	0	LIPA	10	90974746	Frame_Shift_Del	DEL	G	TCGA-B9-7268-01A-11D-2136-08		90974746	44560001	33	6507											
CUTC	51076	hgsc.bcm.edu	37	chr10	101507060	101507060	+	Missense_Mutation	SNP	A	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	gcagctctggagaccctcttAaccttgggatttgaacgcgt	8	11	11	11	2	2	2	0	1	2	1	2	4	2	3	2	2	3	2	2	2	2	3			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr10:101507060A>C	ENST00000370476.5	+	6	615	c.486A>C	c.(484-486)ttA>ttC	p.L162F		NM_015960.2	NP_057044.2	Q9NTM9	CUTC_HUMAN	cutC copper transporter	162					copper ion homeostasis (GO:0055070)|copper ion transport (GO:0006825)|protein tetramerization (GO:0051262)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	copper ion binding (GO:0005507)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Colorectal(252;0.234)		Epithelial(162;3e-10)|all cancers(201;2.37e-08)		AGACCCTCTTAACCTTGGGAT	0.438																																					p.L162F		Atlas-SNP	.											.	CUTC	32	.	0			c.A486C						PASS	.						178	165	170					10																	101507060		2203	4300	6503	SO:0001583	missense	51076	exon6			CCTCTTAACCTTG	AF132966	CCDS7483.1	10q24.31	2013-07-31	2013-07-31		ENSG00000119929	ENSG00000119929			24271	protein-coding gene	gene with protein product		610101	"cutC copper transporter homolog (E. coli)"			16182249	Standard	NM_015960		Approved	CGI-32	uc001kqd.4	Q9NTM9	OTTHUMG00000018889	ENST00000370476.5:c.486A>C	chr10.hg19:g.101507060A>C	ENSP00000359507:p.Leu162Phe	122.0	0.0	.		179.0	42.0	.	NM_015960	Q5TCZ8|Q9Y321	Missense_Mutation	SNP	ENST00000370476.5	hg19	CCDS7483.1	.	.	.	.	.	.	.	.	.	.	A	15.54	2.863855	0.51482	.	.	ENSG00000119929	ENST00000370476;ENST00000370472	.	.	.	5.75	1.83	0.25207	Copper homeostasis CutC domain (2);	0.362596	0.26478	N	0.024153	T	0.47097	0.1427	M	0.66439	2.03	0.40178	D	0.977255	P;B	0.35844	0.524;0.358	B;B	0.40940	0.241;0.344	T	0.52003	-0.8633	9	0.87932	D	0	-2.0266	1.2816	0.02042	0.5158:0.1141:0.1618:0.2083	.	162;162	B4DYM2;Q9NTM9	.;CUTC_HUMAN	F	162;99	.	ENSP00000359503:L99F	L	+	3	2	CUTC	101497050	0.287000	0.24315	0.936000	0.37596	0.989000	0.77384	-0.314000	0.08092	0.960000	0.38005	0.460000	0.39030	TTA	.	.	.	none		0.438	CUTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049811.1	NM_015960		C	101507060	A	C	101507060	3	2	102	1	0	0	0	0	1	0	0	0	4065	359	13	5	508	5	CUTC	10	101507060	Missense_Mutation	SNP	A	TCGA-B9-7268-01A-11D-2136-08	10532314	101507060	34027687	34	6508											
C10orf119	79892	hgsc.bcm.edu	37	chr10	121598084	121598084	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctgttccaggagagtctcAtcgattacaagggaagtatt	11	11	10	9	1	1	1	1	0	1	1	4	4	2	2	2	2	1	2	2	2	4	4			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr10:121598084A>G	ENST00000360003.3	-	12	1546	c.1377T>C	c.(1375-1377)gaT>gaC	p.D459D	MCMBP_ENST00000369077.3_Silent_p.D457D|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	459					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						GGAGAGTCTCATCGATTACAA	0.483																																					p.D459D		Atlas-SNP	.											.	MCMBP	49	.	0			c.T1377C						PASS	.						75	73	74					10																	121598084		2203	4300	6503	SO:0001819	synonymous_variant	79892	exon12			AGTCTCATCGATT	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.1377T>C	chr10.hg19:g.121598084A>G		60.0	0.0	.		80.0	29.0	.	NM_024834	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Silent	SNP	ENST00000360003.3	hg19	CCDS7617.1																																																																																			.	.	.	none		0.483	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834		G	121598084	A	G	121598084	2	3	102	1	0	0	0	0	0	0	0	1	1590	214	8	3		3	C10orf119	10	121598084	Silent	SNP	A	TCGA-B9-7268-01A-11D-2136-08	20091024	121598084	13936663	35	6509											
ENDOD1	23052	hgsc.bcm.edu	37	chr11	94862157	94862157	+	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	aaagagttctagtcccctttCtagcaccaggagcaagaggt	12	9	10	10	0	2	2	0	0	2	2	3	3	3	3	3	2	2	3	3	2	4	4	rs61734147	byFrequency	TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr11:94862157C>G	ENST00000278505.4	+	2	1035	c.917C>G	c.(916-918)tCt>tGt	p.S306C		NM_015036.2	NP_055851.1	O94919	ENDD1_HUMAN	endonuclease domain containing 1	306						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.S306C(1)		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)				AGTCCCCTTTCTAGCACCAGG	0.448																																					p.S306C		Atlas-SNP	.											ENDOD1,mouth,carcinoma,0,1	ENDOD1	26	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.C917G						PASS	.						85	82	83					11																	94862157		1855	4087	5942	SO:0001583	missense	23052	exon2			CCCTTTCTAGCAC	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.917C>G	chr11.hg19:g.94862157C>G	ENSP00000278505:p.Ser306Cys	121.0	0.0	.		116.0	47.0	.	NM_015036	A8K6K8|Q6GQY5|Q8TAQ8	Missense_Mutation	SNP	ENST00000278505.4	hg19	CCDS41699.1	.	.	.	.	.	.	.	.	.	.	C	14.15	2.450542	0.43531	.	.	ENSG00000149218	ENST00000278505	T	0.35973	1.28	5.79	5.79	0.91817	.	0.494397	0.18919	N	0.127530	T	0.44767	0.1309	M	0.62723	1.935	0.28948	N	0.890571	P	0.45283	0.855	B	0.44163	0.443	T	0.50171	-0.8859	10	0.87932	D	0	-0.6278	17.5334	0.87820	0.0:1.0:0.0:0.0	.	306	O94919	ENDD1_HUMAN	C	306	ENSP00000278505:S306C	ENSP00000278505:S306C	S	+	2	0	ENDOD1	94501805	0.020000	0.18652	0.551000	0.28230	0.151000	0.21798	2.730000	0.47335	2.742000	0.94016	0.455000	0.32223	TCT	.	C|0.998;T|0.002	.	alt		0.448	ENDOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396545.1	NM_015036		G	94862157	C	G	94862157	3	3	102	1	0	0	0	0	1	0	0	0	5116	913	32	4	923	4	ENDOD1	11	94862157	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08		94862157	40144359	36	6510											
UBE4A	9354	hgsc.bcm.edu	37	chr11	118243839	118243839	+	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	agtttctggaagaggtcattGaagccttgatattggatgag	11	13	13	4	0	2	4	1	3	1	1	2	6	2	6	1	3	1	1	1	3	3	5			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr11:118243839G>A	ENST00000431736.2	+	7	853	c.781G>A	c.(781-783)Gaa>Aaa	p.E261K	UBE4A_ENST00000252108.3_Missense_Mutation_p.E254K					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)		AGAGGTCATTGAAGCCTTGAT	0.368																																					p.E261K		Atlas-SNP	.											.	UBE4A	97	.	0			c.G781A						PASS	.						117	113	115					11																	118243839		2200	4296	6496	SO:0001583	missense	9354	exon7			GTCATTGAAGCCT	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.781G>A	chr11.hg19:g.118243839G>A	ENSP00000387362:p.Glu261Lys	94.0	0.0	.		89.0	42.0	.	NM_004788		Missense_Mutation	SNP	ENST00000431736.2	hg19	CCDS8396.1	.	.	.	.	.	.	.	.	.	.	g	14.87	2.663910	0.47572	.	.	ENSG00000110344	ENST00000252108;ENST00000431736	T;T	0.46063	0.88;0.88	6.04	1.95	0.26073	.	0.407974	0.28815	N	0.014059	T	0.23766	0.0575	N	0.24115	0.695	0.80722	D	1	B;B	0.19200	0.02;0.034	B;B	0.21708	0.016;0.036	T	0.05903	-1.0857	10	0.08837	T	0.75	-0.6425	8.9731	0.35919	0.1267:0.245:0.6283:0.0	.	254;261	Q14139;Q14139-2	UBE4A_HUMAN;.	K	254;261	ENSP00000252108:E254K;ENSP00000387362:E261K	ENSP00000252108:E254K	E	+	1	0	UBE4A	117749049	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.805000	0.55575	0.437000	0.26423	-0.213000	0.12676	GAA	.	.	.	none		0.368	UBE4A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398143.1	NM_004788		A	118243839	G	A	118243839	3	1	102	1	0	0	0	0	1	0	0	0	16894	1291	45	2	803	2	UBE4A	11	118243839	Missense_Mutation	SNP	G	TCGA-B9-7268-01A-11D-2136-08	23381682	118243839	16762677	37	6511											
MCAM	4162	hgsc.bcm.edu	37	chr11	119183001	119183001	+	Missense_Mutation	SNP	A	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	accagtagttcctgtggttcActcagcagcgatatcatggt	9	12	10	10	1	3	0	3	0	0	0	4	1	4	0	2	2	2	4	2	2	2	4			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr11:119183001A>C	ENST00000264036.4	-	8	1013	c.999T>G	c.(997-999)agT>agG	p.S333R	MCAM_ENST00000530144.2_5'Flank|MCAM_ENST00000392814.1_Missense_Mutation_p.S282R	NM_006500.2	NP_006491.2	P43121	MUC18_HUMAN	melanoma cell adhesion molecule	333					anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|glomerular filtration (GO:0003094)|vascular wound healing (GO:0061042)	external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|skin(1)	22		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.78e-05)		CCTGTGGTTCACTCAGCAGCG	0.622																																					p.S333R		Atlas-SNP	.											.	MCAM	57	.	0			c.T999G						PASS	.						96	92	94					11																	119183001		2199	4295	6494	SO:0001583	missense	4162	exon8			TGGTTCACTCAGC	X68264	CCDS31690.1	11q23.3	2013-01-29				ENSG00000076706		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6934	protein-coding gene	gene with protein product	"Gicerin"	155735				2602381, 10702685	Standard	XM_005271552		Approved	MUC18, CD146	uc001pwf.3	P43121		ENST00000264036.4:c.999T>G	chr11.hg19:g.119183001A>C	ENSP00000264036:p.Ser333Arg	110.0	0.0	.		107.0	38.0	.	NM_006500	O95812|Q59E86|Q6PHR3|Q6ZTR2	Missense_Mutation	SNP	ENST00000264036.4	hg19	CCDS31690.1	.	.	.	.	.	.	.	.	.	.	A	10.61	1.399560	0.25291	.	.	ENSG00000076706	ENST00000264036;ENST00000392814	T;T	0.06849	3.25;3.25	5.53	-3.57	0.04612	Immunoglobulin-like fold (1);	.	.	.	.	T	0.03739	0.0106	N	0.19112	0.55	0.09310	N	1	B	0.19331	0.035	B	0.15484	0.013	T	0.45614	-0.9249	9	0.18276	T	0.48	-16.5141	2.4635	0.04547	0.3729:0.2069:0.3187:0.1015	.	333	P43121	MUC18_HUMAN	R	333;282	ENSP00000264036:S333R;ENSP00000376561:S282R	ENSP00000264036:S333R	S	-	3	2	MCAM	118688211	0.000000	0.05858	0.024000	0.17045	0.080000	0.17528	-0.422000	0.07043	-0.700000	0.05070	-0.411000	0.06167	AGT	.	.	.	none		0.622	MCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388332.2			C	119183001	A	C	119183001	3	2	102	1	0	0	0	0	1	0	0	0	9375	156	6	5	977	5	MCAM	11	119183001	Missense_Mutation	SNP	A	TCGA-B9-7268-01A-11D-2136-08	939162	119183001	15823515	38	6512											
APOLD1	81575	hgsc.bcm.edu	37	chr12	12940182	12940182	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctgatcttctgcaactccCgggagctgcggagggtgcag	6	8	15	12	3	2	1	0	1	2	0	3	3	3	3	1	3	5	4	1	3	1	1			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr12:12940182C>T	ENST00000326765.6	+	2	506	c.436C>T	c.(436-438)Cgg>Tgg	p.R146W	APOLD1_ENST00000356591.4_Missense_Mutation_p.R115W	NM_001130415.1	NP_001123887.1	Q96LR9	APLD1_HUMAN	apolipoprotein L domain containing 1	146					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)		CTGCAACTCCCGGGAGCTGCG	0.682																																					p.R146W		Atlas-SNP	.											.	APOLD1	10	.	0			c.C436T						PASS	.						27	31	30					12																	12940182		2203	4300	6503	SO:0001583	missense	81575	exon2			AACTCCCGGGAGC	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.436C>T	chr12.hg19:g.12940182C>T	ENSP00000324277:p.Arg146Trp	65.0	0.0	.		93.0	23.0	.	NM_001130415	Q8IVR2|Q9H0I5	Missense_Mutation	SNP	ENST00000326765.6	hg19	CCDS44833.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.040822	0.75732	.	.	ENSG00000178878	ENST00000326765;ENST00000356591	T;T	0.03386	3.95;3.95	4.91	4.01	0.46588	.	0.395551	0.24623	U	0.036942	T	0.09730	0.0239	L	0.43152	1.355	0.31300	N	0.688457	D;D	0.76494	0.999;0.999	D;D	0.65987	0.94;0.94	T	0.02758	-1.1114	10	0.44086	T	0.13	-18.6983	9.3604	0.38192	0.2848:0.5756:0.1396:0.0	.	115;146	A0AVN6;Q96LR9	.;APLD1_HUMAN	W	146;115	ENSP00000324277:R146W;ENSP00000348998:R115W	ENSP00000324277:R146W	R	+	1	2	APOLD1	12831449	0.938000	0.31826	1.000000	0.80357	0.994000	0.84299	0.853000	0.27777	1.179000	0.42884	0.478000	0.44815	CGG	.	.	.	none		0.682	APOLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331627.1	NM_030817		T	12940182	C	T	12940182	3	4	102	1	0	0	0	0	1	0	0	0	811	643	23	1	449	1	APOLD1	12	12940182	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08		12940182	120911713	39	6513											
ANP32D	23519	hgsc.bcm.edu	37	chr12	48866497	48866497	+	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	gctgcggaacaggacgccctCcgatgtgaaagaacttttcc	10	8	11	12	3	0	2	0	1	0	1	2	5	2	4	3	2	3	1	3	2	3	2			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr12:48866497C>A	ENST00000266594.1	+	1	50	c.50C>A	c.(49-51)tCc>tAc	p.S17Y		NM_012404.2	NP_036536.2	O95626	AN32D_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32 family, member D	17						nuclear matrix (GO:0016363)				central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	9						AGGACGCCCTCCGATGTGAAA	0.448																																					p.S17Y		Atlas-SNP	.											.	ANP32D	15	.	0			c.C50A						PASS	.						115	117	117					12																	48866497		2203	4300	6503	SO:0001583	missense	23519	exon1			CGCCCTCCGATGT	U71084	CCDS31788.1	12q13.12	2008-08-04			ENSG00000139223	ENSG00000139223		"ANP32 acidic nuclear phosphoproteins"	16676	protein-coding gene	gene with protein product	"pp32 related 2"	606878				10086381, 10400610	Standard	NM_012404		Approved	PP32R2	uc010slt.2	O95626	OTTHUMG00000162681	ENST00000266594.1:c.50C>A	chr12.hg19:g.48866497C>A	ENSP00000266594:p.Ser17Tyr	167.0	0.0	.		258.0	135.0	.	NM_012404	Q6NTC4	Missense_Mutation	SNP	ENST00000266594.1	hg19	CCDS31788.1	.	.	.	.	.	.	.	.	.	.	C	14.73	2.624087	0.46840	.	.	ENSG00000139223	ENST00000266594	T	0.00468	7.22	1.48	0.203	0.15195	.	0.288521	0.34986	N	0.003527	T	0.00552	0.0018	M	0.86343	2.81	0.38870	D	0.95666	P	0.47106	0.89	B	0.41088	0.347	T	0.68458	-0.5403	10	0.72032	D	0.01	.	4.9765	0.14144	0.0:0.6111:0.3889:0.0	.	17	O95626	AN32D_HUMAN	Y	17	ENSP00000266594:S17Y	ENSP00000266594:S17Y	S	+	2	0	ANP32D	47152764	0.897000	0.30589	0.027000	0.17364	0.572000	0.35998	-0.183000	0.09712	0.856000	0.35383	0.289000	0.19496	TCC	.	.	.	none		0.448	ANP32D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370058.1	NM_012404		A	48866497	C	A	48866497	3	1	102	1	0	0	0	0	1	0	0	0	708	855	30	4	52	4	ANP32D	12	48866497	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08	35926315	48866497	84985398	40	6514											
KRT4	3851	hgsc.bcm.edu	37	chr12	53205646	53205646	+	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	ctagctgcttcctcaggacaCtgaggtaggtctcaaagagg	10	9	12	10	0	2	2	2	1	1	1	4	3	3	3	1	4	2	3	1	4	3	3			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr12:53205646C>G	ENST00000551956.1	-	2	1070	c.578G>C	c.(577-579)aGt>aCt	p.S193T	KRT4_ENST00000293774.4_Missense_Mutation_p.S267T|KRT4_ENST00000458244.2_Missense_Mutation_p.S173T			P19013	K2C4_HUMAN	keratin 4	207	Linker 1.|Rod.				cytoskeleton organization (GO:0007010)|epithelial cell differentiation (GO:0030855)|negative regulation of epithelial cell proliferation (GO:0050680)	cell surface (GO:0009986)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|prostate(2)|skin(2)	29						CCTCAGGACACTGAGGTAGGT	0.537																																					p.S193T	Pancreas(190;284 2995 41444 45903)	Atlas-SNP	.											.	KRT4	110	.	0			c.G578C						PASS	.						114	119	117					12																	53205646		2030	4201	6231	SO:0001583	missense	3851	exon2			AGGACACTGAGGT		CCDS41787.1, CCDS41787.2	12q13.13	2013-01-16			ENSG00000170477	ENSG00000170477		"-", "Intermediate filaments type II, keratins (basic)"	6441	protein-coding gene	gene with protein product	"cytokeratin 4", "keratin, type II cytoskeletal 4"	123940		CYK4		16831889	Standard	NM_002272		Approved	CK4, K4	uc031qhk.1	P19013		ENST00000551956.1:c.578G>C	chr12.hg19:g.53205646C>G	ENSP00000448220:p.Ser193Thr	71.0	0.0	.		124.0	44.0	.	NM_002272	F8VS64|Q6GTR8|Q96LA7|Q9BTL1	Missense_Mutation	SNP	ENST00000551956.1	hg19	CCDS41787.2	.	.	.	.	.	.	.	.	.	.	C	4.151	0.026479	0.08054	.	.	ENSG00000170477	ENST00000551956;ENST00000293774;ENST00000458244	T;T;T	0.76316	-1.01;-1.01;-1.01	4.54	-1.88	0.07713	Filament (1);	0.363501	0.23947	N	0.042986	T	0.65291	0.2677	L	0.61218	1.895	0.19945	N	0.999941	B	0.21452	0.056	B	0.25614	0.062	T	0.51818	-0.8657	10	0.34782	T	0.22	.	0.9077	0.01288	0.2253:0.3089:0.1121:0.3537	.	207	P19013	K2C4_HUMAN	T	193;267;173	ENSP00000448220:S193T;ENSP00000293774:S267T;ENSP00000387904:S173T	ENSP00000293774:S267T	S	-	2	0	KRT4	51491913	0.000000	0.05858	0.000000	0.03702	0.121000	0.20230	-1.038000	0.03553	-0.350000	0.08262	-0.137000	0.14449	AGT	.	.	.	none		0.537	KRT4-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405931.1	NM_002272		G	53205646	C	G	53205646	3	3	102	1	0	0	0	0	1	0	0	0	8484	565	20	4	1016	4	KRT4	12	53205646	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08	4339149	53205646	80646249	41	6515											
LRRIQ1	84125	hgsc.bcm.edu	37	chr12	85449852	85449852	+	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	gatatagccaaaaatctagtGgatgaaaattcaaagaagca	20	8	8	5	0	2	2	1	1	1	1	2	4	2	3	1	1	2	1	1	1	9	4			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr12:85449852G>T	ENST00000393217.2	+	8	1342	c.1281G>T	c.(1279-1281)gtG>gtT	p.V427V		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	427										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)		AAAATCTAGTGGATGAAAATT	0.294																																					p.V427V		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.G1281T						PASS	.						83	95	91					12																	85449852		2200	4297	6497	SO:0001819	synonymous_variant	84125	exon8			TCTAGTGGATGAA	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.1281G>T	chr12.hg19:g.85449852G>T		160.0	0.0	.		279.0	34.0	.	NM_001079910	Q567P4|Q9BS17|Q9HA36	Silent	SNP	ENST00000393217.2	hg19	CCDS41816.1																																																																																			.	.	.	none		0.294	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		T	85449852	G	T	85449852	2	4	102	1	0	0	0	0	0	0	0	1	9036	1335	47	4		4	LRRIQ1	12	85449852	Silent	SNP	G	TCGA-B9-7268-01A-11D-2136-08	32244206	85449852	48402043	42	6516											
SYCP3	50511	hgsc.bcm.edu	37	chr12	102125409	102125409	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggctctgaacaattctagaTtgttgaagaatcttttgttg	10	17	9	5	0	3	4	0	2	3	2	3	4	3	4	0	1	1	3	0	1	5	7			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr12:102125409T>C	ENST00000392927.3	-	7	620	c.489A>G	c.(487-489)caA>caG	p.Q163Q	SYCP3_ENST00000392924.1_Silent_p.Q163Q|SYCP3_ENST00000266743.2_Silent_p.Q163Q	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	163	Gln-rich.				male meiosis I (GO:0007141)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(1)	11						CAATTCTAGATTGTTGAAGAA	0.264																																					p.Q163Q		Atlas-SNP	.											.	SYCP3	19	.	0			c.A489G						PASS	.						61	59	60					12																	102125409		2202	4281	6483	SO:0001819	synonymous_variant	50511	exon7			TCTAGATTGTTGA	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.489A>G	chr12.hg19:g.102125409T>C		29.0	0.0	.		41.0	24.0	.	NM_001177949		Silent	SNP	ENST00000392927.3	hg19	CCDS9087.1																																																																																			.	.	.	none		0.264	SYCP3-001	KNOWN	alternative_5_UTR|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316478.2	NM_153694		C	102125409	T	C	102125409	2	2	102	1	0	0	0	0	0	0	0	1	15446	1490	52	3		3	SYCP3	12	102125409	Silent	SNP	T	TCGA-B9-7268-01A-11D-2136-08	16675557	102125409	31726486	43	6517											
GATC	51499	hgsc.bcm.edu	37	chr12	120884511	120884511	+	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	0	0	0	0	0	0	0	0	0	0	agcacctggagcgtctagcgCttgtggacttcggcagccgc	6	8	14	13	4	1	0	0	0	1	0	2	2	1	2	2	3	4	3	2	3	1	3			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr12:120884511C>T	ENST00000546954.1	-	0	0				GATC_ENST00000551765.1_Missense_Mutation_p.L45F|TRIAP1_ENST00000302432.3_5'Flank|AL021546.6_ENST00000551806.1_Missense_Mutation_p.A76V	NM_016399.2	NP_057483.1	O43715	TRIA1_HUMAN	TP53 regulated inhibitor of apoptosis 1						cellular response to UV (GO:0034644)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|phospholipid transport (GO:0015914)|positive regulation of phospholipid transport (GO:2001140)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of membrane lipid distribution (GO:0097035)	mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	p53 binding (GO:0002039)					all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GCGTCTAGCGCTTGTGGACTT	0.682																																					p.L45F		Atlas-SNP	.											.	GATC	12	.	0			c.C133T						PASS	.						29	33	32					12																	120884511		2202	4295	6497	SO:0001631	upstream_gene_variant	283459	exon2			CTAGCGCTTGTGG		CCDS9198.1	12q24.31	2012-10-15			ENSG00000170855	ENSG00000170855			26937	protein-coding gene	gene with protein product	"p53-inducible cell-survival factor", "mitochondrial distribution and morphology 35 homolog (S. cerevisiae)"	614943				11042152, 15735003	Standard	NM_016399		Approved	P53CSV, WF-1, HSPC132, p53CSV, MDM35	uc001tyg.3	O43715	OTTHUMG00000047787		chr12.hg19:g.120884511C>T	Exception_encountered	58.0	0.0	.		121.0	34.0	.	NM_176818	B2R4Z7|Q5RKS5|Q6LCA7	Missense_Mutation	SNP	ENST00000546954.1	hg19	CCDS9198.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.7|23.7	4.450683|4.450683	0.84101|0.84101	.|.	.|.	ENSG00000111780|ENSG00000257218	ENST00000551806|ENST00000551765	.|T	.|0.55413	.|0.52	5.08|5.08	5.08|5.08	0.68730|0.68730	.|.	.|0.000000	.|0.64402	.|D	.|0.000001	T|T	0.46483|0.46483	0.1395|0.1395	L|L	0.55213|0.55213	1.73|1.73	0.58432|0.58432	D|D	0.999996|0.999996	.|P	.|0.35456	.|0.502	.|B	.|0.31337	.|0.128	T|T	0.53272|0.53272	-0.8462|-0.8462	6|10	0.72032|0.87932	D|D	0.01|0	-15.3352|-15.3352	12.1028|12.1028	0.53794|0.53794	0.0:0.9221:0.0:0.0779|0.0:0.9221:0.0:0.0779	.|.	.|45	.|O43716	.|GATC_HUMAN	V|F	76|45	.|ENSP00000446872:L45F	ENSP00000450281:A76V|ENSP00000448397:L45F	A|L	+|+	2|1	0|0	GATC|AL021546.1	119368894|119368894	0.992000|0.992000	0.36948|0.36948	0.685000|0.685000	0.30070|0.30070	0.991000|0.991000	0.79684|0.79684	2.195000|2.195000	0.42677|0.42677	2.646000|2.646000	0.89796|0.89796	0.644000|0.644000	0.83932|0.83932	GCT|CTT	.	.	.	none		0.682	TRIAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108980.3	NM_016399		T	120884511	C	T	120884511	1	4	102	0	1	0	0	0	0	0	0	0	6269	797	28	2		2	GATC	12	120884511	5'Flank	SNP	C	TCGA-B9-7268-01A-11D-2136-08	18759102	120884511	12967384	44	6518											
PSME2	5721	hgsc.bcm.edu	37	chr14	24615760	24615760	+	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	tacctgtttgcgggcttcccCgctcaggcgcaccccacacg	5	8	10	18	4	1	0	1	0	0	0	2	0	2	0	5	2	2	4	5	2	1	3			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr14:24615760C>A	ENST00000216802.5	-	1	670	c.31G>T	c.(31-33)Ggg>Tgg	p.G11W	RNF31_ENST00000559275.1_5'Flank|PSME2_ENST00000471700.2_5'UTR|PSME2_ENST00000560410.1_Missense_Mutation_p.G11W|RNF31_ENST00000382687.3_5'Flank|RNF31_ENST00000324103.6_5'Flank	NM_002818.2	NP_002809.2	Q9UL46	PSME2_HUMAN	proteasome (prosome, macropain) activator subunit 2 (PA28 beta)	11					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome activator complex (GO:0008537)|proteasome complex (GO:0000502)				endometrium(1)|lung(3)|prostate(2)	6				GBM - Glioblastoma multiforme(265;0.00839)		CGGGCTTCCCCGCTCAGGCGC	0.632																																					p.G11W		Atlas-SNP	.											.	PSME2	21	.	0			c.G31T						PASS	.						67	66	66					14																	24615760		2203	4300	6503	SO:0001583	missense	5721	exon1			CTTCCCCGCTCAG		CCDS9614.1	14q11.2	2010-03-10			ENSG00000100911	ENSG00000100911		"Proteasome (prosome, macropain) subunits"	9569	protein-coding gene	gene with protein product		602161				7789512	Standard	NM_002818		Approved	PA28beta	uc001wmj.3	Q9UL46	OTTHUMG00000028797	ENST00000216802.5:c.31G>T	chr14.hg19:g.24615760C>A	ENSP00000216802:p.Gly11Trp	101.0	0.0	.		109.0	5.0	.	NM_002818	Q15129	Missense_Mutation	SNP	ENST00000216802.5	hg19	CCDS9614.1	.	.	.	.	.	.	.	.	.	.	C	14.23	2.473208	0.43942	.	.	ENSG00000100911	ENST00000216802	T	0.43294	0.95	5.22	4.32	0.51571	Proteasome activator pa28, REG alpha subunit (2);	0.926255	0.09349	N	0.814471	T	0.42404	0.1201	N	0.08118	0	0.30656	N	0.754954	D	0.58620	0.983	P	0.60609	0.877	T	0.47586	-0.9106	10	0.72032	D	0.01	0.1857	11.5808	0.50889	0.0:0.8208:0.1792:0.0	.	11	Q9UL46	PSME2_HUMAN	W	11	ENSP00000216802:G11W	ENSP00000216802:G11W	G	-	1	0	PSME2	23685600	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	2.201000	0.42734	1.391000	0.46566	0.561000	0.74099	GGG	.	.	.	none		0.632	PSME2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071918.3	NM_002818		A	24615760	C	A	24615760	3	1	102	1	0	0	0	0	1	0	0	0	12717	652	23	4	732	4	PSME2	14	24615760	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08		24615760	82733780	45	6519											
MNAT1	4331	hgsc.bcm.edu	37	chr14	61434959	61434959	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttttaggtatttaaaccaTgtcagagctgcctcaccaca	11	13	7	10	0	2	1	2	0	0	1	2	1	2	1	3	1	3	3	3	1	4	5			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr14:61434959T>C	ENST00000261245.4	+	8	923	c.822T>C	c.(820-822)caT>caC	p.H274H	MNAT1_ENST00000539616.2_Silent_p.H232H|RP11-193F5.1_ENST00000553946.1_RNA	NM_002431.3	NP_002422.1	P51948	MAT1_HUMAN	MNAT CDK-activating kinase assembly factor 1	274					7-methylguanosine mRNA capping (GO:0006370)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to calcium ion (GO:0051592)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|ventricular system development (GO:0021591)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein N-terminus binding (GO:0047485)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(2)	11				OV - Ovarian serous cystadenocarcinoma(108;0.0174)		ATTTAAACCATGTCAGAGCTG	0.388								Direct reversal of damage;Direct reversal of damage;Nucleotide excision repair (NER)																													p.H274H		Atlas-SNP	.											.	MNAT1	24	.	0			c.T822C						PASS	.						128	116	120					14																	61434959		2203	4300	6503	SO:0001819	synonymous_variant	4331	exon8			AAACCATGTCAGA	X87843	CCDS9750.1, CCDS53899.1	14q23	2013-07-31	2013-07-31		ENSG00000020426	ENSG00000020426		"RING-type (C3HC4) zinc fingers", "General transcription factor IIH complex subunits"	7181	protein-coding gene	gene with protein product	"CDK-activating kinase assembly factor"	602659	"menage a trois 1 (CAK assembly factor)", "menage a trois homolog 1, cyclin H assembly factor (Xenopus laevis)"			9465303	Standard	NM_002431		Approved	MAT1, RNF66	uc001xfd.3	P51948	OTTHUMG00000152340	ENST00000261245.4:c.822T>C	chr14.hg19:g.61434959T>C		110.0	0.0	.		102.0	33.0	.	NM_002431	G3V1U8|Q15817|Q6ICQ7	Silent	SNP	ENST00000261245.4	hg19	CCDS9750.1																																																																																			.	.	.	none		0.388	MNAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276956.1	NM_002431		C	61434959	T	C	61434959	2	2	102	1	0	0	0	0	0	0	0	1	9681	1461	51	3		3	MNAT1	14	61434959	Silent	SNP	T	TCGA-B9-7268-01A-11D-2136-08	36819199	61434959	45914581	46	6520											
MARK3	4140	hgsc.bcm.edu	37	chr14	103894758	103894758	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aattgacaaaactcagttgaAtccaacaagtctacaaaagg	19	8	6	8	0	2	2	1	2	1	0	3	2	3	2	1	1	3	1	1	1	9	3			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr14:103894758A>G	ENST00000429436.2	+	3	788	c.278A>G	c.(277-279)aAt>aGt	p.N93S	MARK3_ENST00000553942.1_Missense_Mutation_p.N93S|MARK3_ENST00000303622.9_Missense_Mutation_p.N93S|MARK3_ENST00000335102.5_Missense_Mutation_p.N93S|MARK3_ENST00000216288.7_Missense_Mutation_p.N93S|MARK3_ENST00000440884.3_Missense_Mutation_p.N93S|MARK3_ENST00000561071.1_3'UTR|MARK3_ENST00000416682.2_Missense_Mutation_p.N93S	NM_001128918.1|NM_001128919.1	NP_001122390.1|NP_001122391.1	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	93	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					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)			ACTCAGTTGAATCCAACAAGT	0.284																																					p.N93S		Atlas-SNP	.											.	MARK3	86	.	0			c.A278G						PASS	.						21	19	20					14																	103894758		1762	4021	5783	SO:0001583	missense	4140	exon3			AGTTGAATCCAAC	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.278A>G	chr14.hg19:g.103894758A>G	ENSP00000411397:p.Asn93Ser	3.0	0.0	.		12.0	8.0	.	NM_001128921	O60219|Q86TT8|Q8TB41|Q8WX83|Q96RG1|Q9UMY9|Q9UN34	Missense_Mutation	SNP	ENST00000429436.2	hg19	CCDS45165.1	.	.	.	.	.	.	.	.	.	.	A	8.139	0.784865	0.16189	.	.	ENSG00000075413	ENST00000335102;ENST00000440884;ENST00000416682;ENST00000429436;ENST00000303622;ENST00000216288;ENST00000553942	T;T;T;T;T;T;T	0.64618	-0.11;3.26;-0.11;-0.11;-0.11;-0.11;-0.11	5.27	4.12	0.48240	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.093621	0.64402	D	0.000001	T	0.40694	0.1127	N	0.10685	0.025	0.54753	D	0.99998	B;P;B;B;B;B	0.36183	0.164;0.542;0.026;0.04;0.366;0.021	B;B;B;B;B;B	0.34180	0.127;0.177;0.038;0.043;0.136;0.009	T	0.40683	-0.9550	10	0.54805	T	0.06	.	11.4976	0.50417	0.8493:0.1507:0.0:0.0	.	93;93;93;93;93;93	P27448-2;P27448-6;P27448;Q86TT8;P27448-4;P27448-3	.;.;MARK3_HUMAN;.;.;.	S	93	ENSP00000335347:N93S;ENSP00000402104:N93S;ENSP00000408092:N93S;ENSP00000411397:N93S;ENSP00000303698:N93S;ENSP00000216288:N93S;ENSP00000450772:N93S	ENSP00000216288:N93S	N	+	2	0	MARK3	102964511	1.000000	0.71417	1.000000	0.80357	0.001000	0.01503	6.709000	0.74665	0.836000	0.34901	-0.313000	0.08912	AAT	.	.	.	none		0.284	MARK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415144.1	NM_001128918		G	103894758	A	G	103894758	3	3	102	1	0	0	0	0	1	0	0	0	9321	101	4	3	288	3	MARK3	14	103894758	Missense_Mutation	SNP	A	TCGA-B9-7268-01A-11D-2136-08	42459799	103894758	3454782	47	6521											
SLTM	79811	hgsc.bcm.edu	37	chr15	59172211	59172211	+	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	ctcattttcagaatcgtcgcGgaggtccacccttaaatggc	9	11	9	12	3	2	1	2	0	0	1	5	2	3	2	2	3	0	0	2	3	3	3			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr15:59172211G>T	ENST00000380516.2	-	21	3179	c.3092C>A	c.(3091-3093)cCg>cAg	p.P1031Q	SLTM_ENST00000536328.1_Missense_Mutation_p.P600Q	NM_001013843.1|NM_024755.2	NP_001013865.1|NP_079031.2	Q9NWH9	SLTM_HUMAN	SAFB-like, transcription modulator	1031					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						GAATCGTCGCGGAGGTCCACC	0.408																																					p.P1031Q		Atlas-SNP	.											.	SLTM	90	.	0			c.C3092A						PASS	.						65	68	67					15																	59172211		2192	4292	6484	SO:0001583	missense	79811	exon21			CGTCGCGGAGGTC	BC046119	CCDS10168.2	15q21.3	2013-02-12			ENSG00000137776	ENSG00000137776		"RNA binding motif (RRM) containing"	20709	protein-coding gene	gene with protein product							Standard	XR_243128		Approved	Met, FLJ13213	uc002afp.3	Q9NWH9	OTTHUMG00000074033	ENST00000380516.2:c.3092C>A	chr15.hg19:g.59172211G>T	ENSP00000369887:p.Pro1031Gln	64.0	0.0	.		95.0	4.0	.	NM_024755	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000380516.2	hg19	CCDS10168.2	.	.	.	.	.	.	.	.	.	.	G	12.17	1.858179	0.32791	.	.	ENSG00000137776	ENST00000380516;ENST00000432750;ENST00000536328	T	0.13901	2.55	5.66	5.66	0.87406	.	0.000000	0.53938	D	0.000057	T	0.11495	0.0280	L	0.34521	1.04	0.45342	D	0.998331	P;P	0.41624	0.644;0.757	B;B	0.36378	0.159;0.223	T	0.05354	-1.0890	10	0.39692	T	0.17	.	14.5794	0.68274	0.0:0.0:0.854:0.146	.	1031;600	Q9NWH9;A8K5V8	SLTM_HUMAN;.	Q	1031;597;600	ENSP00000369887:P1031Q	ENSP00000369887:P1031Q	P	-	2	0	SLTM	56959503	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.125000	0.71627	2.665000	0.90641	0.563000	0.77884	CCG	.	.	.	none		0.408	SLTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157124.1	NM_024755		T	59172211	G	T	59172211	3	4	102	1	0	0	0	0	1	0	0	0	14767	1116	39	4	16	4	SLTM	15	59172211	Missense_Mutation	SNP	G	TCGA-B9-7268-01A-11D-2136-08		59172211	43359181	48	6522											
TERF2	7014	hgsc.bcm.edu	37	chr16	69402345	69402345	+	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	gtttatcttccttccctgtaCttgaggcagcggactcagat	7	14	9	11	1	2	2	1	1	1	1	4	3	4	3	2	2	2	3	2	2	2	6			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr16:69402345C>G	ENST00000254942.3	-	6	897	c.881G>C	c.(880-882)aGt>aCt	p.S294T	TERF2_ENST00000603068.1_Missense_Mutation_p.S252T|TERF2_ENST00000569611.2_5'Flank	NM_005652.3	NP_005643.2	Q15554	TERF2_HUMAN	telomeric repeat binding factor 2	294					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)				CTTCCCTGTACTTGAGGCAGC	0.478																																					p.S294T	Ovarian(13;63 524 30420 31710 34037)	Atlas-SNP	.											.	TERF2	24	.	0			c.G881C						PASS	.						133	121	125					16																	69402345		2198	4300	6498	SO:0001583	missense	7014	exon6			CCTGTACTTGAGG		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.881G>C	chr16.hg19:g.69402345C>G	ENSP00000254942:p.Ser294Thr	67.0	0.0	.		160.0	61.0	.	NM_005652		Missense_Mutation	SNP	ENST00000254942.3	hg19		.	.	.	.	.	.	.	.	.	.	C	4.457	0.084724	0.08583	.	.	ENSG00000132604	ENST00000254942	.	.	.	4.95	0.394	0.16299	.	0.964177	0.08668	N	0.911414	T	0.36826	0.0981	L	0.43152	1.355	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.31024	-0.9958	9	0.15066	T	0.55	0.7302	9.5105	0.39074	0.0:0.5756:0.3285:0.0959	.	252	Q15554	TERF2_HUMAN	T	252	.	ENSP00000254942:S252T	S	-	2	0	TERF2	67959846	.	.	0.002000	0.10522	0.255000	0.26057	.	.	0.218000	0.20820	0.555000	0.69702	AGT	.	.	.	none		0.478	TERF2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000268944.2			G	69402345	C	G	69402345	3	3	102	1	0	0	0	0	1	0	0	0	15774	565	20	4	767	4	TERF2	16	69402345	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08		69402345	20952408	49	6523											
GINS2	51659	hgsc.bcm.edu	37	chr16	85715212	85715212	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaacaggagcttcgtaagtTccatgtagtaagggctgggc	10	11	13	7	1	0	0	0	0	0	0	2	1	1	1	1	3	2	6	1	3	4	6			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr16:85715212T>C	ENST00000253462.3	-	3	381	c.281A>G	c.(280-282)gAa>gGa	p.E94G		NM_016095.2	NP_057179.1	Q9Y248	PSF2_HUMAN	GINS complex subunit 2 (Psf2 homolog)	94					DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)	nucleoplasm (GO:0005654)				endometrium(2)|large_intestine(2)|lung(2)	6						CTTCGTAAGTTCCATGTAGTA	0.448																																					p.E94G		Atlas-SNP	.											.,1	GINS2	15	.	0			c.A281G						PASS	.						183	164	170					16																	85715212		2198	4300	6498	SO:0001583	missense	51659	exon3			GTAAGTTCCATGT	BC003186	CCDS10953.1	16q24.1	2008-02-05			ENSG00000131153	ENSG00000131153			24575	protein-coding gene	gene with protein product		610609				11042152, 10810093	Standard	NM_016095		Approved	PSF2, Pfs2	uc002fja.3	Q9Y248	OTTHUMG00000137646	ENST00000253462.3:c.281A>G	chr16.hg19:g.85715212T>C	ENSP00000253462:p.Glu94Gly	50.0	0.0	.		130.0	66.0	.	NM_016095	D3DUM5|Q6IAG9	Missense_Mutation	SNP	ENST00000253462.3	hg19	CCDS10953.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.643560	0.87859	.	.	ENSG00000131153	ENST00000253462	.	.	.	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.81259	0.4785	M	0.86420	2.815	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.84916	0.0851	9	0.72032	D	0.01	-30.9692	14.3362	0.66592	0.0:0.0:0.0:1.0	.	94;94	Q53G08;Q9Y248	.;PSF2_HUMAN	G	94	.	ENSP00000253462:E94G	E	-	2	0	GINS2	84272713	1.000000	0.71417	0.970000	0.41538	0.939000	0.58152	7.531000	0.81973	1.874000	0.54306	0.459000	0.35465	GAA	.	.	.	none		0.448	GINS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269098.1	NM_016095		C	85715212	T	C	85715212	3	2	102	1	0	0	0	0	1	0	0	0	6395	1783	62	3	288	3	GINS2	16	85715212	Missense_Mutation	SNP	T	TCGA-B9-7268-01A-11D-2136-08	16312867	85715212	4639541	50	6524											
COX10	1352	hgsc.bcm.edu	37	chr17	14005508	14005508	+	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	gactggccctgtttcctgctTacttctgttgggacaggcct	4	14	11	12	0	1	0	0	0	1	0	2	2	2	1	3	3	2	3	3	3	1	4			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr17:14005508T>A	ENST00000261643.3	+	4	650	c.573T>A	c.(571-573)ctT>ctA	p.L191L	COX10_ENST00000536205.1_Intron|COX10_ENST00000537334.1_5'UTR	NM_001303.3	NP_001294.2	Q12887	COX10_HUMAN	cytochrome c oxidase assembly homolog 10 (yeast)	191					aerobic respiration (GO:0009060)|cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|heme O biosynthetic process (GO:0048034)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|mitochondrial fission (GO:0000266)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	farnesyltranstransferase activity (GO:0004311)|protoheme IX farnesyltransferase activity (GO:0008495)			cervix(1)|endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		GTTTCCTGCTTACTTCTGTTG	0.473																																					p.L191L		Atlas-SNP	.											.	COX10	36	.	0			c.T573A						PASS	.						174	152	160					17																	14005508		2203	4300	6503	SO:0001819	synonymous_variant	1352	exon4			CCTGCTTACTTCT	U09466	CCDS11166.1	17p12	2013-05-24	2012-10-15		ENSG00000006695	ENSG00000006695		"Mitochondrial respiratory chain complex assembly factors"	2260	protein-coding gene	gene with protein product	"heme A: farnesyltransferase", "protoheme IX farnesyltransferase, mitochondrial", "heme O synthase"	602125	"COX10 (yeast) homolog, cytochrome c oxidase assembly protein (heme A: farnesyltransferase)", "COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase (yeast)"			9177788, 12928484	Standard	NM_001303		Approved		uc002gof.4	Q12887	OTTHUMG00000058814	ENST00000261643.3:c.573T>A	chr17.hg19:g.14005508T>A		164.0	0.0	.		300.0	190.0	.	NM_001303	B2R6U5|B4DJ50|O15334|Q969F7	Silent	SNP	ENST00000261643.3	hg19	CCDS11166.1																																																																																			.	.	.	none		0.473	COX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130003.1	NM_001303		A	14005508	T	A	14005508	2	1	102	1	0	0	0	0	0	0	0	1	3764	1741	61	5		5	COX10	17	14005508	Silent	SNP	T	TCGA-B9-7268-01A-11D-2136-08		14005508	67189702	51	6525											
FAM187B	148109	hgsc.bcm.edu	37	chr19	35718874	35718874	+	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	tccatcacctgtacatggatCctaagggacagtcgagccac	11	8	9	13	1	1	0	1	0	0	0	4	3	3	2	4	2	2	1	4	2	2	2			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr19:35718874C>T	ENST00000324675.3	-	1	758	c.710G>A	c.(709-711)gGa>gAa	p.G237E		NM_152481.1	NP_689694.1	Q17R55	F187B_HUMAN	family with sequence similarity 187, member B	237						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	9						GTACATGGATCCTAAGGGACA	0.507																																					p.G237E		Atlas-SNP	.											.	FAM187B	28	.	0			c.G710A						PASS	.						67	57	60					19																	35718874		2203	4300	6503	SO:0001583	missense	148109	exon1			ATGGATCCTAAGG	AK098526	CCDS12448.1	19q13.12	2008-10-16	2008-10-16	2008-10-16	ENSG00000177558	ENSG00000177558			26366	protein-coding gene	gene with protein product			"transmembrane protein 162"	TMEM162			Standard	NM_152481		Approved	FLJ25660	uc002nyk.1	Q17R55	OTTHUMG00000164450	ENST00000324675.3:c.710G>A	chr19.hg19:g.35718874C>T	ENSP00000323355:p.Gly237Glu	26.0	0.0	.		37.0	13.0	.	NM_152481	Q8N7G6	Missense_Mutation	SNP	ENST00000324675.3	hg19	CCDS12448.1	.	.	.	.	.	.	.	.	.	.	C	11.60	1.687642	0.29962	.	.	ENSG00000177558	ENST00000324675	T	0.39592	1.07	4.91	1.25	0.21368	.	0.519698	0.15947	N	0.236896	T	0.50274	0.1606	L	0.57536	1.79	0.09310	N	1	D	0.57899	0.981	P	0.53401	0.725	T	0.49041	-0.8980	10	0.72032	D	0.01	-2.2526	13.4884	0.61379	0.0:0.4094:0.5906:0.0	.	237	Q17R55	F187B_HUMAN	E	237	ENSP00000323355:G237E	ENSP00000323355:G237E	G	-	2	0	FAM187B	40410714	0.319000	0.24607	0.289000	0.24876	0.145000	0.21501	0.869000	0.27996	0.564000	0.29238	-0.175000	0.13238	GGA	.	.	.	none		0.507	FAM187B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378854.1	NM_152481		T	35718874	C	T	35718874	3	4	102	1	0	0	0	0	1	0	0	0	5517	855	30	2	407	2	FAM187B	19	35718874	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08		35718874	23410109	52	6526											
ATP1A3	478	hgsc.bcm.edu	37	chr19	42492245	42492245	+	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	gcggtggcgtgagtgcgttaGgcccatcccgggccaggatc	5	7	17	12	4	0	1	0	1	0	0	2	2	1	2	3	5	1	1	3	5	1	1			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr19:42492245G>A	ENST00000302102.5	-	4	350	c.200C>T	c.(199-201)cCt>cTt	p.P67L	ATP1A3_ENST00000602133.1_Missense_Mutation_p.P37L|ATP1A3_ENST00000543770.1_Missense_Mutation_p.P78L|ATP1A3_ENST00000545399.1_Missense_Mutation_p.P80L|ATP1A3_ENST00000468774.2_5'UTR	NM_152296.4	NP_689509.1	P13637	AT1A3_HUMAN	ATPase, Na+/K+ transporting, alpha 3 polypeptide	67					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						GAGTGCGTTAGGCCCATCCCG	0.637																																					p.P80L		Atlas-SNP	.											.	ATP1A3	117	.	0			c.C239T						PASS	.						103	107	106					19																	42492245		2203	4300	6503	SO:0001583	missense	478	exon4			GCGTTAGGCCCAT		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.200C>T	chr19.hg19:g.42492245G>A	ENSP00000302397:p.Pro67Leu	118.0	0.0	.		133.0	16.0	.	NM_001256214	B7Z2T0|B7Z401|F5H6J6|Q16732|Q16735|Q969K5	Missense_Mutation	SNP	ENST00000302102.5	hg19	CCDS12594.1	.	.	.	.	.	.	.	.	.	.	G	16.34	3.095660	0.56075	.	.	ENSG00000105409	ENST00000302102;ENST00000441343;ENST00000545399;ENST00000368080;ENST00000543770;ENST00000448429	T;T;T;T	0.80909	-1.43;-1.43;-1.43;-1.43	4.09	4.09	0.47781	ATPase, P-type cation-transporter, N-terminal (2);	0.185108	0.46758	D	0.000274	D	0.89065	0.6609	M	0.80616	2.505	0.80722	D	1	B;D;D;D	0.76494	0.383;0.998;0.999;0.997	B;D;D;D	0.75484	0.126;0.965;0.986;0.979	D	0.90107	0.4189	10	0.54805	T	0.06	.	14.1703	0.65506	0.0:0.0:1.0:0.0	.	80;78;67;67	B7Z2T0;F5H6J6;E9PC51;P13637	.;.;.;AT1A3_HUMAN	L	67;67;80;37;78;80	ENSP00000302397:P67L;ENSP00000411503:P67L;ENSP00000444688:P80L;ENSP00000437577:P78L	ENSP00000302397:P67L	P	-	2	0	ATP1A3	47184085	1.000000	0.71417	0.945000	0.38365	0.021000	0.10359	9.808000	0.99193	2.010000	0.58986	0.491000	0.48974	CCT	.	.	.	none		0.637	ATP1A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268107.1	NM_152296		A	42492245	G	A	42492245	3	1	102	1	0	0	0	0	1	0	0	0	1130	1000	35	2	2921	2	ATP1A3	19	42492245	Missense_Mutation	SNP	G	TCGA-B9-7268-01A-11D-2136-08	6773371	42492245	16636738	53	6527											
ZNF836	162962	hgsc.bcm.edu	37	chr19	52660096	52660096	+	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	gaattttgtctgaagatcttGccacatacaccacattgata	13	13	6	9	0	2	3	0	2	2	1	2	4	2	3	2	0	2	0	2	0	4	6			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr19:52660096G>A	ENST00000322146.8	-	5	1361	c.840C>T	c.(838-840)ggC>ggT	p.G280G	ZNF836_ENST00000597252.1_Silent_p.G280G|CTC-471J1.8_ENST00000594362.1_RNA	NM_001102657.1	NP_001096127.1	Q6ZNA1	ZN836_HUMAN	zinc finger protein 836	280					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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						TGAAGATCTTGCCACATACAC	0.413																																					p.G280G		Atlas-SNP	.											.	ZNF836	158	.	0			c.C840T						PASS	.						85	90	88					19																	52660096		2176	4286	6462	SO:0001819	synonymous_variant	162962	exon5			GATCTTGCCACAT	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.840C>T	chr19.hg19:g.52660096G>A		69.0	0.0	.		114.0	46.0	.	NM_001102657		Silent	SNP	ENST00000322146.8	hg19	CCDS46162.1																																																																																			.	.	.	none		0.413	ZNF836-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462456.1	NM_001102657		A	52660096	G	A	52660096	2	1	102	1	0	0	0	0	0	0	0	1	18199	1306	46	2		2	ZNF836	19	52660096	Silent	SNP	G	TCGA-B9-7268-01A-11D-2136-08	10167851	52660096	6468887	54	6528											
ZNF264	9422	hgsc.bcm.edu	37	chr19	57724137	57724137	+	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	gctcgtccctcactcagcatCaaaggatgcatactgggaaa	12	8	9	12	1	3	0	3	0	0	0	5	2	4	2	1	2	3	3	1	2	3	1			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chr19:57724137C>G	ENST00000263095.6	+	4	2086	c.1672C>G	c.(1672-1674)Caa>Gaa	p.Q558E	ZNF264_ENST00000536056.1_Missense_Mutation_p.Q558E	NM_003417.4	NP_003408.1	O43296	ZN264_HUMAN	zinc finger protein 264	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)			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)		CACTCAGCATCAAAGGATGCA	0.453																																					p.Q558E		Atlas-SNP	.											.	ZNF264	65	.	0			c.C1672G						PASS	.						100	97	98					19																	57724137		2203	4300	6503	SO:0001583	missense	9422	exon4			CAGCATCAAAGGA	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.1672C>G	chr19.hg19:g.57724137C>G	ENSP00000263095:p.Gln558Glu	91.0	0.0	.		114.0	5.0	.	NM_003417	A8K8Y9|Q9P1V0	Missense_Mutation	SNP	ENST00000263095.6	hg19	CCDS33127.1	.	.	.	.	.	.	.	.	.	.	C	10.04	1.241123	0.22711	.	.	ENSG00000083844	ENST00000263095;ENST00000536056	T;T	0.07327	3.2;3.2	2.35	2.35	0.29111	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06234	0.0161	L	0.28014	0.82	0.21553	N	0.999646	B	0.27853	0.191	B	0.18263	0.021	T	0.27226	-1.0080	9	0.59425	D	0.04	.	8.9199	0.35605	0.0:0.7681:0.2319:0.0	.	558	O43296	ZN264_HUMAN	E	558	ENSP00000263095:Q558E;ENSP00000440376:Q558E	ENSP00000263095:Q558E	Q	+	1	0	ZNF264	62415949	0.000000	0.05858	0.624000	0.29186	0.955000	0.61496	0.743000	0.26231	1.644000	0.50603	0.491000	0.48974	CAA	.	.	.	none		0.453	ZNF264-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465080.1			G	57724137	C	G	57724137	3	3	102	1	0	0	0	0	1	0	0	0	17816	827	29	4	1686	4	ZNF264	19	57724137	Missense_Mutation	SNP	C	TCGA-B9-7268-01A-11D-2136-08	5064041	57724137	1404846	55	6529											
PHKA1	5255	hgsc.bcm.edu	37	chrX	71822085	71822085	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aacagcaccaatctcgtggaTagaaatagcaggactgacat	16	7	9	9	1	1	2	0	1	1	1	2	4	1	4	1	2	3	2	1	2	5	2			TCGA-B9-7268-01A-11D-2136-08	TCGA-B9-7268-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	23d1496c-de52-4d78-ba63-f8f751d546d5	d08b6d62-3120-49a5-9cd5-c671278e2eb8	g.chrX:71822085T>C	ENST00000373542.4	-	27	3115	c.2956A>G	c.(2956-2958)Atc>Gtc	p.I986V	PHKA1_ENST00000541944.1_Missense_Mutation_p.I927V|PHKA1_ENST00000373539.3_Missense_Mutation_p.I986V|PHKA1_ENST00000373545.3_Missense_Mutation_p.I927V|PHKA1_ENST00000339490.3_Missense_Mutation_p.I986V	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	986					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)					ATCTCGTGGATAGAAATAGCA	0.403																																					p.I986V		Atlas-SNP	.											.	PHKA1	129	.	0			c.A2956G						PASS	.						120	96	104					X																	71822085		2203	4300	6503	SO:0001583	missense	5255	exon27			CGTGGATAGAAAT		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.2956A>G	chrX.hg19:g.71822085T>C	ENSP00000362643:p.Ile986Val	21.0	0.0	.		39.0	4.0	.	NM_002637	B7ZL05|B7ZL07|Q2M3D7	Missense_Mutation	SNP	ENST00000373542.4	hg19	CCDS14421.1	.	.	.	.	.	.	.	.	.	.	T	15.77	2.931761	0.52866	.	.	ENSG00000067177	ENST00000373545;ENST00000373542;ENST00000541944;ENST00000339490;ENST00000373539	D;D;D;D;D	0.91295	-2.77;-2.79;-2.82;-2.78;-2.76	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	D	0.89884	0.6844	M	0.73372	2.23	0.52099	D	0.999948	B;B;B	0.19200	0.025;0.016;0.034	B;B;B	0.27608	0.038;0.073;0.081	D	0.86249	0.1648	10	0.34782	T	0.22	-12.1844	12.9234	0.58245	0.0:0.0:0.0:1.0	.	927;986;986	B7ZL07;P46020-2;P46020	.;.;KPB1_HUMAN	V	927;986;927;986;986	ENSP00000362646:I927V;ENSP00000362643:I986V;ENSP00000441251:I927V;ENSP00000342469:I986V;ENSP00000362640:I986V	ENSP00000342469:I986V	I	-	1	0	PHKA1	71738810	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	5.818000	0.69236	1.960000	0.56953	0.417000	0.27973	ATC	.	.	.	none		0.403	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1			C	71822085	T	C	71822085	3	2	102	1	0	0	0	0	1	0	0	0	11850	1406	49	3	739	3	PHKA1	23	71822085	Missense_Mutation	SNP	T	TCGA-B9-7268-01A-11D-2136-08		71822085	83448475	56	6530											
FAM132A	388581	hgsc.bcm.edu	37	chr1	1179848	1179848	+	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	agccatgtcatgtgggcgtcGgagaactcaggtcctgaggc	8	8	15	10	2	2	2	2	1	0	1	4	3	3	2	2	4	2	0	2	4	1	0	rs200735866		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:1179848G>C	ENST00000330388.2	-	2	238	c.207C>G	c.(205-207)tcC>tcG	p.S69S		NM_001014980.2	NP_001014980.1	Q5T7M4	ADIPL_HUMAN	family with sequence similarity 132, member A	69					negative regulation of gluconeogenesis (GO:0045721)|negative regulation of inflammatory response (GO:0050728)|positive regulation of glucose import (GO:0046326)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of glucose import (GO:0046324)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)			haematopoietic_and_lymphoid_tissue(1)|lung(1)	2	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.22e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		TGTGGGCGTCGGAGAACTCAG	0.682																																					p.S69S		Atlas-SNP	.											.	FAM132A	12	.	0			c.C207G						PASS	.						44	49	47					1																	1179848		2190	4289	6479	SO:0001819	synonymous_variant	388581	exon2			GGCGTCGGAGAAC	BC089443	CCDS30554.1	1p36.33	2012-03-26	2007-03-27	2007-03-27	ENSG00000184163	ENSG00000184163			32308	protein-coding gene	gene with protein product	"adipolin", "adipose-derived insulin-sensitizing factor"		"C1q domain containing 2"	C1QDC2		21849507	Standard	NM_001014980		Approved	MGC105127, C1QTNF12, CTRP12	uc001adl.2	Q5T7M4	OTTHUMG00000001412	ENST00000330388.2:c.207C>G	chr1.hg19:g.1179848G>C		104.0	0.0	.		90.0	18.0	.	NM_001014980	Q5EBL5	Silent	SNP	ENST00000330388.2	hg19	CCDS30554.1																																																																																			.	G|1.000;A|0.000	.	alt		0.682	FAM132A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004080.4	XM_371208		C	1179848	G	C	1179848	2	2	103	1	0	0	0	0	0	0	0	1	5446	1103	39	4		4	FAM132A	1	1179848	Silent	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10		1179848	248070773	1	6531											
KCNAB2	8514	hgsc.bcm.edu	37	chr1	6142274	6142274	+	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	gatggcagagcagctcatgaCcttggcctatgataatggca	11	9	12	9	0	1	3	1	2	0	1	1	4	1	3	2	3	2	4	2	3	2	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:6142274C>A	ENST00000164247.1	+	6	785	c.221C>A	c.(220-222)aCc>aAc	p.T74N	KCNAB2_ENST00000378087.3_Missense_Mutation_p.T74N|KCNAB2_ENST00000378092.1_Missense_Mutation_p.T60N|KCNAB2_ENST00000352527.1_Missense_Mutation_p.T60N|KCNAB2_ENST00000378111.1_Missense_Mutation_p.T74N|KCNAB2_ENST00000602612.1_Missense_Mutation_p.T74N|KCNAB2_ENST00000458166.2_Missense_Mutation_p.T7N|KCNAB2_ENST00000378097.1_Missense_Mutation_p.T74N|KCNAB2_ENST00000378083.3_Missense_Mutation_p.T107N|KCNAB2_ENST00000341524.1_Missense_Mutation_p.T74N	NM_001199860.1	NP_001186789.1	Q13303	KCAB2_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 2	74					hematopoietic progenitor cell differentiation (GO:0002244)|protein heterooligomerization (GO:0051291)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			large_intestine(1)|lung(4)|skin(3)	8	Ovarian(185;0.0634)	all_cancers(23;5.85e-39)|all_epithelial(116;4.88e-22)|all_lung(118;4.21e-08)|Lung NSC(185;9.77e-07)|all_hematologic(16;2.78e-06)|all_neural(13;3.18e-06)|Acute lymphoblastic leukemia(12;0.000272)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00106)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;6.9e-37)|GBM - Glioblastoma multiforme(13;8.8e-31)|OV - Ovarian serous cystadenocarcinoma(86;1.45e-19)|Colorectal(212;2.46e-07)|COAD - Colon adenocarcinoma(227;2.07e-05)|Kidney(185;7.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00131)|BRCA - Breast invasive adenocarcinoma(365;0.00133)|STAD - Stomach adenocarcinoma(132;0.00391)|READ - Rectum adenocarcinoma(331;0.0649)		CAGCTCATGACCTTGGCCTAT	0.562																																					p.T107N		Atlas-SNP	.											.	KCNAB2	23	.	0			c.C320A						PASS	.						138	123	129					1																	6142274		2203	4300	6503	SO:0001583	missense	8514	exon5			TCATGACCTTGGC	U33429	CCDS55.1, CCDS56.1, CCDS55570.1, CCDS55571.1	1p36.3	2008-02-05			ENSG00000069424	ENSG00000069424		"Potassium channels", "Aldo-keto reductases"	6229	protein-coding gene	gene with protein product		601142				8838324	Standard	NM_003636		Approved	AKR6A5, KCNA2B, HKvbeta2.1, HKvbeta2.2	uc001aly.2	Q13303	OTTHUMG00000000795	ENST00000164247.1:c.221C>A	chr1.hg19:g.6142274C>A	ENSP00000164247:p.Thr74Asn	97.0	0.0	.		80.0	29.0	.	NM_001199862	A0AVM9|A8K1A4|B0AZR7|O43659|Q5TG82|Q5TG83|Q6ZNE4|Q99411	Missense_Mutation	SNP	ENST00000164247.1	hg19	CCDS55.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.332367	0.81801	.	.	ENSG00000069424	ENST00000378111;ENST00000378097;ENST00000378092;ENST00000428161;ENST00000389632;ENST00000378087;ENST00000341524;ENST00000352527;ENST00000435937;ENST00000164247;ENST00000378083;ENST00000458166	T;T;T;T;T;T;T;T;T;T;T;T	0.21734	1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99	5.33	5.33	0.75918	NADP-dependent oxidoreductase domain (3);	0.095392	0.64402	D	0.000001	T	0.37019	0.0988	L	0.39467	1.215	0.58432	D	0.999997	D;D;D;D	0.65815	0.971;0.995;0.979;0.964	D;D;P;P	0.66979	0.948;0.936;0.88;0.766	T	0.02042	-1.1224	10	0.33940	T	0.23	-23.7432	17.5837	0.87974	0.0:1.0:0.0:0.0	.	107;60;74;74	Q13303-3;Q13303-2;Q13303;Q2YD85	.;.;KCAB2_HUMAN;.	N	74;74;60;60;74;74;74;60;60;74;107;7	ENSP00000367351:T74N;ENSP00000367337:T74N;ENSP00000367332:T60N;ENSP00000400285:T60N;ENSP00000374283:T74N;ENSP00000367327:T74N;ENSP00000340824:T74N;ENSP00000318772:T60N;ENSP00000389151:T60N;ENSP00000164247:T74N;ENSP00000367323:T107N;ENSP00000396167:T7N	ENSP00000164247:T74N	T	+	2	0	KCNAB2	6064861	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	6.706000	0.74649	2.482000	0.83794	0.563000	0.77884	ACC	.	.	.	none		0.562	KCNAB2-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000002114.3	NM_172130		A	6142274	C	A	6142274	3	1	103	1	0	0	0	0	1	0	0	0	8017	507	18	4	239	4	KCNAB2	1	6142274	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	4962426	6142274	243108347	2	6532											
SPEN	23013	hgsc.bcm.edu	37	chr1	16258337	16258337	+	Missense_Mutation	SNP	T	T	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	aagcacagaagcttttggaaTtgaagatggaggcagagaag	16	7	14	4	0	0	4	0	1	0	3	0	7	0	6	0	3	2	3	0	3	5	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:16258337T>G	ENST00000375759.3	+	11	5806	c.5602T>G	c.(5602-5604)Ttg>Gtg	p.L1868V		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1868					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)		GCTTTTGGAATTGAAGATGGA	0.498																																					p.L1868V		Atlas-SNP	.											.	SPEN	374	.	0			c.T5602G						PASS	.						67	73	71					1																	16258337		2203	4300	6503	SO:0001583	missense	23013	exon11			TTGGAATTGAAGA		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.5602T>G	chr1.hg19:g.16258337T>G	ENSP00000364912:p.Leu1868Val	81.0	0.0	.		67.0	48.0	.	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	hg19	CCDS164.1	.	.	.	.	.	.	.	.	.	.	T	8.066	0.769236	0.15983	.	.	ENSG00000065526	ENST00000375759	T	0.08807	3.05	5.27	-2.9	0.05648	.	.	.	.	.	T	0.06416	0.0165	L	0.36672	1.1	0.09310	N	1	B	0.22276	0.067	B	0.24155	0.051	T	0.40059	-0.9583	9	0.29301	T	0.29	-8.6361	7.649	0.28337	0.0:0.4283:0.1213:0.4504	.	1868	Q96T58	MINT_HUMAN	V	1868	ENSP00000364912:L1868V	ENSP00000364912:L1868V	L	+	1	2	SPEN	16130924	0.919000	0.31177	0.007000	0.13788	0.912000	0.54170	0.155000	0.16362	-0.878000	0.04007	0.383000	0.25322	TTG	.	.	.	none		0.498	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		G	16258337	T	G	16258337	3	3	103	1	0	0	0	0	1	0	0	0	15050	1490	52	5	5644	5	SPEN	1	16258337	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	10116063	16258337	232992284	3	6533											
RCAN3	11123	hgsc.bcm.edu	37	chr1	24840954	24840954	+	Frame_Shift_Del	DEL	A	A	-																															agaagagatgatttttggtgAaaatgaagatgatttggatg																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:24840954delA	ENST00000374395.4	+	2	405	c.92delA	c.(91-93)gaafs	p.E31fs	RCAN3_ENST00000436717.2_Frame_Shift_Del_p.E31fs|RCAN3_ENST00000412742.2_Frame_Shift_Del_p.E31fs|RCAN3_ENST00000538532.1_Frame_Shift_Del_p.E31fs|RCAN3_ENST00000374393.2_Frame_Shift_Del_p.E31fs	NM_001251978.1|NM_001251979.1|NM_001251984.1	NP_001238907.1|NP_001238908.1|NP_001238913.1	Q9UKA8	RCAN3_HUMAN	RCAN family member 3	31					anatomical structure morphogenesis (GO:0009653)|calcium-mediated signaling (GO:0019722)		RNA binding (GO:0003723)|troponin I binding (GO:0031013)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)	7		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00473)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0427)|OV - Ovarian serous cystadenocarcinoma(117;1.13e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;0.000923)|BRCA - Breast invasive adenocarcinoma(304;0.0018)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.00493)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.14)		ATTTTTGGTGAAAATGAAGAT	0.438																																					p.E31fs		Atlas-Indel,Pindel	.											.	RCAN3	22	.	0			c.91delG						PASS	.						199	184	189					1																	24840954		2203	4300	6503	SO:0001589	frameshift_variant	11123	exon1			.		CCDS254.1, CCDS57980.1, CCDS57981.1, CCDS57982.1, CCDS72730.1	1p35.3-p33	2008-02-05	2007-06-26	2007-06-26	ENSG00000117602	ENSG00000117602			3042	protein-coding gene	gene with protein product		605860	"Down syndrome critical region gene 1-like 2"	DSCR1L2		10756093	Standard	NM_001251984		Approved		uc001bjj.3	Q9UKA8	OTTHUMG00000003298	ENST00000374395.4:c.92delA	chr1.hg19:g.24840954delA	ENSP00000363516:p.Glu31fs	325.0	0.0	0		264.0	121.0	0.458333	NM_001251980	A4GU14|A4LA69|E3VWE2|E5L4P0|E5L4P7|E7ENV1|E7EWD8|G1FI66|G1FLF0|Q5ECL3|Q5TGC6|Q9NUC8|Q9UKA7	Frame_Shift_Del	DEL	ENST00000374395.4	hg19	CCDS254.1																																																																																			.	.	.	none		0.438	RCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009176.2			-	24840954	A	-	24840954	7	5	103	1	0	1	0	1	0	0	0	0	13183	246	9	0	94	0	RCAN3	1	24840954	Frame_Shift_Del	DEL	A	TCGA-B9-A44B-01A-11D-A25F-10	8582617	24840954	224409667	4	6534											
DNALI1	7802	hgsc.bcm.edu	37	chr1	38027791	38027793	+	In_Frame_Del	DEL	AGA	AGA	-																															cgagaggcggcaggtggaggAgaagaagcacaatgaggaga																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:38027791_38027793delAGA	ENST00000296218.7	+	5	762_764	c.752_754delAGA	c.(751-756)gagaag>gag	p.K253del	DNALI1_ENST00000541606.1_In_Frame_Del_p.K105del|DNALI1_ENST00000497858.1_3'UTR	NM_003462.3	NP_003453.2	O14645	IDLC_HUMAN	dynein, axonemal, light intermediate chain 1	231					cellular component movement (GO:0006928)|metabolic process (GO:0008152)|single fertilization (GO:0007338)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|filopodium (GO:0030175)	microtubule motor activity (GO:0003777)			breast(1)|kidney(1)|large_intestine(2)|ovary(1)	5		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CAGGTGGAGGAGAAGAAGCACAA	0.567																																					p.251_251del		Atlas-Indel,Pindel	.											.	DNALI1	25	.	0			c.751_753del						PASS	.			3,4263		0,3,2130						5.4	1			104	1,8253		0,1,4126	no	coding	DNALI1	NM_003462.3		0,4,6256	A1A1,A1R,RR		0.0121,0.0703,0.0319				4,12516				SO:0001651	inframe_deletion	7802	exon5			.	AF006386	CCDS420.1	1p35.1	2008-07-18	2006-09-04		ENSG00000163879	ENSG00000163879		"Axonemal dyneins"	14353	protein-coding gene	gene with protein product	"inner dynein arm, homolog of clamydomonas", "dJ423B22.5 (axonemal dynein light chain (hp28))"	602135	"dynein, axonemal, light intermediate polypeptide 1"			9284741	Standard	NM_003462		Approved	P28, hp28, dJ423B22.5	uc001cbj.3	O14645	OTTHUMG00000004222	ENST00000296218.7:c.752_754delAGA	chr1.hg19:g.38027794_38027796delAGA	ENSP00000296218:p.Lys253del	119.0	0.0	0		110.0	56.0	0.509091	NM_003462	A8K387|B4DHN6|Q05BL9|Q5HYE2|Q5TGH0|Q7L0I5	In_Frame_Del	DEL	ENST00000296218.7	hg19	CCDS420.1																																																																																			.	.	.	none		0.567	DNALI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012159.1	NM_003462		-	38027793	AGA	-	38027791	7	5	103	1	0	1	0	1	0	0	0	0	4661	304	11	0	770	0	DNALI1	1	38027791	In_Frame_Del	DEL	AGA	TCGA-B9-A44B-01A-11D-A25F-10	13186837	38027791	211222830	5	6535											
KIAA0494	9813	hgsc.bcm.edu	37	chr1	47144193	47144194	+	Frame_Shift_Del	DEL	AA	AA	-																															cttccatctccatcggaatcAaatgctctcaagctctctgg																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:47144193_47144194delAA	ENST00000371933.3	-	11	2403_2404	c.1427_1428delTT	c.(1426-1428)tttfs	p.F476fs	EFCAB14-AS1_ENST00000418985.1_RNA|EFCAB14-AS1_ENST00000442839.1_RNA|EFCAB14_ENST00000544071.1_Intron	NM_014774.2	NP_055589.1	O75071	EFC14_HUMAN	EF-hand calcium binding domain 14	476	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)										CATCGGAATCAAATGCTCTCAA	0.475																																					p.476_477del		Atlas-Indel,Pindel	.											.	.	.	.	0			c.1428_1429del						PASS	.																																			SO:0001589	frameshift_variant	9813	exon11			.	AB007963	CCDS30706.1	1p33	2013-01-10	2012-11-29	2012-11-29	ENSG00000159658	ENSG00000159658		"EF-hand domain containing"	29051	protein-coding gene	gene with protein product			"KIAA0494"	KIAA0494		9455484	Standard	NM_014774		Approved		uc001cqk.4	O75071	OTTHUMG00000007992	ENST00000371933.3:c.1427_1428delTT	chr1.hg19:g.47144193_47144194delAA	ENSP00000361001:p.Phe476fs	89.0	0.0	0		56.0	21.0	0.375	NM_014774	D3DQ23|Q5SXB8	Frame_Shift_Del	DEL	ENST00000371933.3	hg19	CCDS30706.1																																																																																			.	.	.	none		0.475	EFCAB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021931.1	NM_014774		-	47144194	AA	-	47144193	7	5	103	1	0	1	0	1	0	0	0	0	8186	127	5	0	63	0	KIAA0494	1	47144193	Frame_Shift_Del	DEL	AA	TCGA-B9-A44B-01A-11D-A25F-10	9116402	47144193	202106428	6	6536											
SLC44A3	126969	hgsc.bcm.edu	37	chr1	95360468	95360468	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggaacagaactccaggccaTtgtgagatagatacccattt	13	9	10	9	0	0	3	0	1	0	3	1	5	1	4	3	2	3	0	3	2	4	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:95360468T>C	ENST00000271227.6	+	15	2054	c.1952T>C	c.(1951-1953)aTt>aCt	p.I651T	SLC44A3_ENST00000532427.1_Missense_Mutation_p.I571T|SLC44A3_ENST00000529450.1_Missense_Mutation_p.I618T|SLC44A3_ENST00000527077.1_Missense_Mutation_p.I583T|SLC44A3_ENST00000446120.2_Missense_Mutation_p.I615T|SLC44A3_ENST00000467909.1_Missense_Mutation_p.I603T	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	651					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)	CTCCAGGCCATTGTGAGATAG	0.403																																					p.I651T		Atlas-SNP	.											.	SLC44A3	109	.	0			c.T1952C						PASS	.						93	83	87					1																	95360468		2203	4300	6503	SO:0001583	missense	126969	exon15			AGGCCATTGTGAG	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.1952T>C	chr1.hg19:g.95360468T>C	ENSP00000271227:p.Ile651Thr	295.0	0.0	.		294.0	58.0	.	NM_001114106	B4DVY4|B4E1M4|B7ZA08|E9PJH2|E9PJY8|Q6UWT1|Q7Z6C5|Q9BWY7	Missense_Mutation	SNP	ENST00000271227.6	hg19	CCDS44176.1	.	.	.	.	.	.	.	.	.	.	T	9.568	1.120299	0.20877	.	.	ENSG00000143036	ENST00000446120;ENST00000271227;ENST00000527077;ENST00000529450;ENST00000467909;ENST00000532427;ENST00000532670	T;T;T;T;T;T	0.20069	2.58;2.78;2.1;2.1;2.59;2.11	5.91	2.35	0.29111	.	1.131400	0.06831	N	0.793947	T	0.04861	0.0131	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	0.001;0.0;0.001;0.0;0.001	T	0.44574	-0.9319	10	0.72032	D	0.01	-0.1874	9.3576	0.38175	0.0:0.1722:0.0:0.8278	.	571;615;583;618;651	E9PIC5;Q8N4M1-3;E9PJY8;E9PJH2;Q8N4M1	.;.;.;.;CTL3_HUMAN	T	615;651;583;618;603;571;107	ENSP00000389143:I615T;ENSP00000271227:I651T;ENSP00000433641:I583T;ENSP00000431836:I618T;ENSP00000432789:I603T;ENSP00000436661:I571T	ENSP00000271227:I651T	I	+	2	0	SLC44A3	95133056	0.132000	0.22450	0.000000	0.03702	0.004000	0.04260	1.121000	0.31283	0.153000	0.19213	0.454000	0.30748	ATT	.	.	.	none		0.403	SLC44A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029544.3	NM_152369		C	95360468	T	C	95360468	3	2	103	1	0	0	0	0	1	0	0	0	14650	1493	52	3	2010	3	SLC44A3	1	95360468	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	48216275	95360468	153890153	7	6537											
ATXN7L2	127002	hgsc.bcm.edu	37	chr1	110029635	110029635	+	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	cctcctggtgacagaaagaaGacatgggcccctcagcaagc	12	5	11	13	0	1	4	1	1	0	3	2	4	2	4	4	2	2	1	4	2	3	0			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:110029635G>C	ENST00000369870.3	+	4	320	c.305G>C	c.(304-306)aGa>aCa	p.R102T		NM_153340.4	NP_699171.3	Q5T6C5	AT7L2_HUMAN	ataxin 7-like 2	102										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)	17		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0426)|Epithelial(280;0.0675)|READ - Rectum adenocarcinoma(129;0.0693)|all cancers(265;0.071)|LUSC - Lung squamous cell carcinoma(189;0.228)		ACAGAAAGAAGACATGGGCCC	0.547																																					p.R102T		Atlas-SNP	.											.	ATXN7L2	60	.	0			c.G305C						PASS	.						28	34	32					1																	110029635		2203	4299	6502	SO:0001583	missense	127002	exon4			AAAGAAGACATGG	BC037582	CCDS30794.1	1p13.2	2008-02-05			ENSG00000162650	ENSG00000162650			28713	protein-coding gene	gene with protein product						12477932	Standard	NM_153340		Approved	MGC46534, FLJ00381	uc001dxr.3	Q5T6C5	OTTHUMG00000011027	ENST00000369870.3:c.305G>C	chr1.hg19:g.110029635G>C	ENSP00000358886:p.Arg102Thr	124.0	0.0	.		130.0	17.0	.	NM_153340		Missense_Mutation	SNP	ENST00000369870.3	hg19	CCDS30794.1	.	.	.	.	.	.	.	.	.	.	G	18.52	3.640777	0.67244	.	.	ENSG00000162650	ENST00000369870;ENST00000541125	T	0.29397	1.57	4.57	4.57	0.56435	.	0.000000	0.52532	D	0.000067	T	0.38931	0.1059	L	0.56199	1.76	0.80722	D	1	D	0.54601	0.967	D	0.63597	0.916	T	0.31251	-0.9950	10	0.72032	D	0.01	-7.5006	14.2772	0.66187	0.0:0.0:1.0:0.0	.	102	Q5T6C5	AT7L2_HUMAN	T	102	ENSP00000358886:R102T	ENSP00000358886:R102T	R	+	2	0	ATXN7L2	109831158	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.555000	0.73928	2.090000	0.63153	0.591000	0.81541	AGA	.	.	.	none		0.547	ATXN7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030331.1	NM_153340		C	110029635	G	C	110029635	3	2	103	1	0	0	0	0	1	0	0	0	1217	942	33	4	319	4	ATXN7L2	1	110029635	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	14669167	110029635	139220986	8	6538											
CTTNBP2NL	55917	hgsc.bcm.edu	37	chr1	112999419	112999419	+	Frame_Shift_Del	DEL	G	G	-																															tcttcgccggtactcactaaGcgtttattggggtcatcagc																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:112999419delG	ENST00000271277.6	+	6	1530	c.1305delG	c.(1303-1305)aagfs	p.K435fs		NM_018704.2	NP_061174.1	Q9P2B4	CT2NL_HUMAN	CTTNBP2 N-terminal like	435					negative regulation of transmembrane transport (GO:0034763)|negative regulation of transporter activity (GO:0032410)|protein dephosphorylation (GO:0006470)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	protein phosphatase 2A binding (GO:0051721)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	29		all_cancers(81;0.00064)|all_epithelial(167;0.000415)|all_lung(203;0.00045)|Lung NSC(69;0.000705)		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)		TACTCACTAAGCGTTTATTGG	0.557																																					p.K435fs		Atlas-Indel,Pindel	.											.	CTTNBP2NL	65	.	0			c.1304delA						PASS	.						255	260	258					1																	112999419		2203	4300	6503	SO:0001589	frameshift_variant	55917	exon6			.	AB037854	CCDS845.1	1p13.2	2008-02-05			ENSG00000143079	ENSG00000143079			25330	protein-coding gene	gene with protein product		615100				10718198	Standard	NM_018704		Approved	DKFZp547A023	uc001ebx.3	Q9P2B4	OTTHUMG00000011154	ENST00000271277.6:c.1305delG	chr1.hg19:g.112999419delG	ENSP00000271277:p.Lys435fs	120.0	0.0	0		142.0	88.0	0.619718	NM_018704	B3KMS5|Q96B40	Frame_Shift_Del	DEL	ENST00000271277.6	hg19	CCDS845.1																																																																																			.	.	.	none		0.557	CTTNBP2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030686.1	NM_018704		-	112999419	G	-	112999419	7	5	103	1	0	1	0	1	0	0	0	0	4048	962	34	0	1319	0	CTTNBP2NL	1	112999419	Frame_Shift_Del	DEL	G	TCGA-B9-A44B-01A-11D-A25F-10	2969784	112999419	136251202	9	6539											
C1orf125	126859	hgsc.bcm.edu	37	chr1	179460842	179460842	+	Missense_Mutation	SNP	A	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	tgcgattgaactgacaaggaAgttgtaccaatactccagct	13	10	9	9	1	0	2	0	2	0	0	1	4	1	3	2	1	5	3	2	1	6	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:179460842A>C	ENST00000367618.3	+	19	2648	c.2261A>C	c.(2260-2262)aAg>aCg	p.K754T		NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	754										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						CTGACAAGGAAGTTGTACCAA	0.423																																					p.K754T		Atlas-SNP	.											.	AXDND1	142	.	0			c.A2261C						PASS	.						162	155	158					1																	179460842		2203	4300	6503	SO:0001583	missense	126859	exon19			CAAGGAAGTTGTA	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.2261A>C	chr1.hg19:g.179460842A>C	ENSP00000356590:p.Lys754Thr	309.0	0.0	.		309.0	52.0	.	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Missense_Mutation	SNP	ENST00000367618.3	hg19	CCDS30948.1	.	.	.	.	.	.	.	.	.	.	A	8.397	0.841178	0.16891	.	.	ENSG00000162779	ENST00000367618;ENST00000360322;ENST00000434088	T;T	0.27256	1.68;1.68	5.5	-3.94	0.04130	.	0.252664	0.37393	N	0.002104	T	0.15609	0.0376	L	0.60455	1.87	0.09310	N	1	B;B	0.22800	0.028;0.075	B;B	0.17098	0.01;0.017	T	0.11518	-1.0584	10	0.35671	T	0.21	-0.2597	1.2029	0.01889	0.2479:0.137:0.3481:0.2669	.	712;754	E9PCJ4;Q5T1B0	.;AXDN1_HUMAN	T	754;712;688	ENSP00000356590:K754T;ENSP00000391716:K688T	ENSP00000353471:K712T	K	+	2	0	AXDND1	177727465	0.109000	0.22037	0.000000	0.03702	0.156000	0.22039	-0.033000	0.12246	-0.147000	0.11254	-0.326000	0.08463	AAG	.	.	.	none		0.423	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696		C	179460842	A	C	179460842	3	2	103	1	0	0	0	0	1	0	0	0	1995	72	3	5	2331	5	C1orf125	1	179460842	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	66461423	179460842	69789779	10	6540											
ZNF648	127665	hgsc.bcm.edu	37	chr1	182026912	182026918	+	Frame_Shift_Del	DEL	TTCCTCT	TTCCTCT	-																															gaggagtcagagaatttctcTtcctctttgcccagtggatg																								rs145733361	byFrequency	TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	TTCCTCT	TTCCTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:182026912_182026918delTTCCTCT	ENST00000339948.3	-	2	435_441	c.228_234delAGAGGAA	c.(226-234)aaagaggaafs	p.KEE76fs		NM_001009992.1	NP_001009992.1	Q5T619	ZN648_HUMAN	zinc finger protein 648	76					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E77D(1)		breast(1)|endometrium(7)|large_intestine(10)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	40						AGAATTTCTCTTCCTCTTTGCCCAGTG	0.56																																					p.77_79del	NSCLC(71;908 1374 5429 20458 35642)	Atlas-Indel,Pindel	.											.	ZNF648	111	.	1	Substitution - Missense(1)	large_intestine(1)	c.229_235del						PASS	.																																			SO:0001589	frameshift_variant	127665	exon2			.	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.228_234delAGAGGAA	chr1.hg19:g.182026912_182026918delTTCCTCT	ENSP00000344129:p.Lys76fs	121.0	0.0	0		160.0	31.0	0.19375	NM_001009992	B2RP16	Frame_Shift_Del	DEL	ENST00000339948.3	hg19	CCDS30952.1																																																																																			.	.	.	none		0.56	ZNF648-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090794.1	XM_060597		-	182026918	TTCCTCT	-	182026912	7	5	103	1	0	1	0	1	0	0	0	0	18075	1606	56	0	1476	0	ZNF648	1	182026912	Frame_Shift_Del	DEL	TTCCTCT	TCGA-B9-A44B-01A-11D-A25F-10	2566070	182026912	67223709	11	6541											
ZNF281	23528	hgsc.bcm.edu	37	chr1	200376815	200376815	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtggatttttcaaaagcctgTtggaggtatttggagtattc	9	16	12	4	0	1	0	1	0	0	0	2	3	1	3	1	4	1	3	1	4	4	7			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr1:200376815T>C	ENST00000294740.3	-	2	2143	c.2019A>G	c.(2017-2019)caA>caG	p.Q673Q	ZNF281_ENST00000367353.1_Silent_p.Q673Q|ZNF281_ENST00000367352.3_Silent_p.Q637Q	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	673					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						CAAAAGCCTGTTGGAGGTATT	0.398																																					p.Q673Q		Atlas-SNP	.											.	ZNF281	74	.	0			c.A2019G						PASS	.						118	130	126					1																	200376815		2203	4300	6503	SO:0001819	synonymous_variant	23528	exon2			AGCCTGTTGGAGG	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.2019A>G	chr1.hg19:g.200376815T>C		53.0	0.0	.		66.0	13.0	.	NM_012482	A6NF48|B3KMX2|Q5RKW5|Q9NY92	Silent	SNP	ENST00000294740.3	hg19	CCDS1402.1																																																																																			.	.	.	none		0.398	ZNF281-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086879.2	NM_012482		C	200376815	T	C	200376815	2	2	103	1	0	0	0	0	0	0	0	1	17830	1722	60	3		3	ZNF281	1	200376815	Silent	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	18349903	200376815	48873806	12	6542											
HS1BP3	64342	hgsc.bcm.edu	37	chr2	20818857	20818857	+	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	ctgcggcttctgctgcccagCcacagcttcagccgggcccg	4	7	12	18	3	2	0	1	0	1	0	2	0	2	0	4	2	6	3	4	2	0	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr2:20818857C>G	ENST00000304031.3	-	7	1094	c.1069G>C	c.(1069-1071)Gct>Cct	p.A357P		NM_022460.3	NP_071905.3	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3	357							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)					TGCTGCCCAGCCACAGCTTCA	0.622																																					p.A357P		Atlas-SNP	.											.	HS1BP3	33	.	0			c.G1069C						PASS	.						86	96	93					2																	20818857		2203	4300	6503	SO:0001583	missense	64342	exon7			GCCCAGCCACAGC		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.1069G>C	chr2.hg19:g.20818857C>G	ENSP00000305193:p.Ala357Pro	153.0	0.0	.		210.0	93.0	.	NM_022460	B2RAW2|D6W529|Q86VC2|Q8N367	Missense_Mutation	SNP	ENST00000304031.3	hg19	CCDS1700.1	.	.	.	.	.	.	.	.	.	.	C	13.90	2.376332	0.42105	.	.	ENSG00000118960	ENST00000304031	T	0.19532	2.14	5.64	0.323	0.15893	.	1.521430	0.04126	N	0.317110	T	0.17280	0.0415	L	0.39898	1.24	0.09310	N	0.999997	B	0.10296	0.003	B	0.09377	0.004	T	0.29852	-0.9998	10	0.51188	T	0.08	-2.0508	3.1138	0.06367	0.2876:0.3492:0.2805:0.0827	.	357	Q53T59	H1BP3_HUMAN	P	357	ENSP00000305193:A357P	ENSP00000305193:A357P	A	-	1	0	HS1BP3	20682338	0.000000	0.05858	0.000000	0.03702	0.388000	0.30384	0.116000	0.15561	0.037000	0.15575	0.655000	0.94253	GCT	.	.	.	none		0.622	HS1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242863.1	NM_022460		G	20818857	C	G	20818857	3	3	103	1	0	0	0	0	1	0	0	0	7368	739	26	4	113	4	HS1BP3	2	20818857	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10		20818857	222380516	13	6543											
CCDC121	79635	hgsc.bcm.edu	37	chr2	27850548	27850548	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttgttagtcaggtattccAgaaagaatctgttttcagcc	10	16	8	7	0	3	2	2	0	1	2	4	2	4	2	2	1	1	3	2	1	4	7			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr2:27850548A>G	ENST00000324364.3	-	2	299	c.119T>C	c.(118-120)cTg>cCg	p.L40P	GPN1_ENST00000424214.1_5'Flank|CCDC121_ENST00000394775.3_Missense_Mutation_p.L202P|ZNF512_ENST00000556601.1_Intron|GPN1_ENST00000503738.1_5'Flank|GPN1_ENST00000407583.3_5'Flank|GPN1_ENST00000610189.1_5'Flank|GPN1_ENST00000458167.2_5'Flank|GPN1_ENST00000264718.3_5'Flank|GPN1_ENST00000515877.1_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA	NM_024584.4	NP_078860.2	Q6ZUS5	CC121_HUMAN	coiled-coil domain containing 121	40										breast(1)|endometrium(3)|large_intestine(2)|lung(6)|prostate(2)	14	Acute lymphoblastic leukemia(172;0.155)					CAGGTATTCCAGAAAGAATCT	0.418																																					p.L202P		Atlas-SNP	.											.	CCDC121	43	.	0			c.T605C						PASS	.						115	120	119					2																	27850548		2203	4300	6503	SO:0001583	missense	79635	exon2			TATTCCAGAAAGA	AK125354	CCDS1759.1, CCDS46247.1	2p23.2	2008-02-05			ENSG00000176714	ENSG00000176714			25833	protein-coding gene	gene with protein product							Standard	NM_024584		Approved	FLJ43364, FLJ13646	uc002rld.3	Q6ZUS5	OTTHUMG00000128427	ENST00000324364.3:c.119T>C	chr2.hg19:g.27850548A>G	ENSP00000339087:p.Leu40Pro	125.0	0.0	.		129.0	39.0	.	NM_001142683	B3KW66|J3KQZ8|Q9H8G6	Missense_Mutation	SNP	ENST00000324364.3	hg19	CCDS1759.1	.	.	.	.	.	.	.	.	.	.	A	16.62	3.174659	0.57692	.	.	ENSG00000176714	ENST00000324364;ENST00000394775	T;T	0.48201	0.82;0.82	5.09	1.14	0.20703	.	0.656444	0.13268	N	0.400745	T	0.62502	0.2433	M	0.70275	2.135	0.09310	N	0.999997	D	0.76494	0.999	D	0.70016	0.967	T	0.51663	-0.8677	10	0.72032	D	0.01	-22.9356	8.2278	0.31579	0.5274:0.0:0.0:0.4726	.	40	Q6ZUS5	CC121_HUMAN	P	40;202	ENSP00000339087:L40P;ENSP00000412150:L202P	ENSP00000339087:L40P	L	-	2	0	CCDC121	27704052	0.720000	0.27996	0.001000	0.08648	0.370000	0.29829	1.010000	0.29898	-0.057000	0.13199	0.482000	0.46254	CTG	.	.	.	none		0.418	CCDC121-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250215.1	NM_024584		G	27850548	A	G	27850548	3	3	103	1	0	0	0	0	1	0	0	0	2759	188	7	3	721	3	CCDC121	2	27850548	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	7031691	27850548	215348825	14	6544											
ALK	238	hgsc.bcm.edu	37	chr2	29420473	29420473	+	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	gtgacaaactccagaacttcCtggttgcttttgctggggta	8	13	11	9	0	0	2	0	1	0	1	2	2	2	2	2	3	4	4	2	3	3	5			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr2:29420473C>A	ENST00000389048.3	-	27	4914	c.4008G>T	c.(4006-4008)caG>caT	p.Q1336H	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1336	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)	CCAGAACTTCCTGGTTGCTTT	0.507			"T, Mis, A"	"NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"	"ALCL, NSCLC, Neuroblastoma"	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.Q1336H		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	.	ALK	533	.	0			c.G4008T						PASS	.						92	96	95					2																	29420473		2203	4300	6503	SO:0001583	missense	238	exon27	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	AACTTCCTGGTTG	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.4008G>T	chr2.hg19:g.29420473C>A	ENSP00000373700:p.Gln1336His	74.0	0.0	.		82.0	37.0	.	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	hg19	CCDS33172.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.093137	0.76756	.	.	ENSG00000171094	ENST00000389048	D	0.82984	-1.67	5.8	4.0	0.46444	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.44688	U	0.000424	D	0.84383	0.5460	L	0.31578	0.945	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.81876	-0.0731	9	.	.	.	.	12.0878	0.53708	0.0:0.8616:0.0:0.1384	.	1336	Q9UM73	ALK_HUMAN	H	1336	ENSP00000373700:Q1336H	.	Q	-	3	2	ALK	29273977	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.181000	0.42547	0.788000	0.33755	0.561000	0.74099	CAG	.	.	.	none		0.507	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		A	29420473	C	A	29420473	3	1	103	1	0	0	0	0	1	0	0	0	525	680	24	4	866	4	ALK	2	29420473	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	1569925	29420473	213778900	15	6545											
RGPD3	653489	hgsc.bcm.edu	37	chr2	107073432	107073432	+	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	gttttgtttgtttacctttaGtttataaattgcaggacttc	8	21	7	5	0	0	0	0	0	0	0	1	1	0	1	1	1	2	5	1	1	5	12			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr2:107073432G>A	ENST00000409886.3	-	4	487	c.400C>T	c.(400-402)Cta>Tta	p.L134L	RGPD3_ENST00000304514.7_Silent_p.L134L	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	134					protein targeting to Golgi (GO:0000042)					breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						TTTACCTTTAGTTTATAAATT	0.333																																					p.L134L		Atlas-SNP	.											.	RGPD3	316	.	0			c.C400T						PASS	.						9	21	17					2																	107073432		628	1473	2101	SO:0001819	synonymous_variant	653489	exon4			CCTTTAGTTTATA		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.400C>T	chr2.hg19:g.107073432G>A		342.0	0.0	.		384.0	132.0	.	NM_001144013	B8ZZM4	Silent	SNP	ENST00000409886.3	hg19	CCDS46379.1																																																																																			.	.	.	none		0.333	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931		A	107073432	G	A	107073432	2	1	103	1	0	0	0	0	0	0	0	1	13300	1020	36	2		2	RGPD3	2	107073432	Silent	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	77652959	107073432	136125941	16	6546											
SCN2A	6326	hgsc.bcm.edu	37	chr2	166153545	166153545	+	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	agacgtttatagtattgaatAaagggaaagcaatctctcga	16	11	9	5	2	1	2	0	1	1	1	3	4	1	3	0	1	1	3	0	1	8	6			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr2:166153545A>T	ENST00000375437.2	+	3	576	c.286A>T	c.(286-288)Aaa>Taa	p.K96*	SCN2A_ENST00000375427.2_Nonsense_Mutation_p.K96*|SCN2A_ENST00000357398.3_Nonsense_Mutation_p.K96*|SCN2A_ENST00000283256.6_Nonsense_Mutation_p.K96*	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	96					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)	AGTATTGAATAAAGGGAAAGC	0.289																																					p.K96X		Atlas-SNP	.											.	SCN2A	589	.	0			c.A286T						PASS	.						58	56	57					2																	166153545		2203	4298	6501	SO:0001587	stop_gained	6326	exon2			TTGAATAAAGGGA	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.286A>T	chr2.hg19:g.166153545A>T	ENSP00000364586:p.Lys96*	174.0	0.0	.		200.0	105.0	.	NM_001040143	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Nonsense_Mutation	SNP	ENST00000375437.2	hg19	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	A	38	6.708516	0.97780	.	.	ENSG00000136531	ENST00000424833;ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	.	.	.	5.32	5.32	0.75619	.	0.077674	0.56097	D	0.000038	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.5789	0.76418	1.0:0.0:0.0:0.0	.	.	.	.	X	96	.	ENSP00000283256:K96X	K	+	1	0	SCN2A	165861791	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.801000	0.55545	2.151000	0.67156	0.482000	0.46254	AAA	.	.	.	none		0.289	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		T	166153545	A	T	166153545	4	4	103	1	0	0	0	0	0	1	0	0	13929	363	13	5	292	5	SCN2A	2	166153545	Nonsense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	59080113	166153545	77045828	17	6547											
LRP2	4036	hgsc.bcm.edu	37	chr2	170055306	170055306	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcttactcactgcaataagtAgggttttcatcactgttatc	10	16	6	9	0	4	0	3	0	1	0	5	0	4	0	0	1	2	4	0	1	5	6			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr2:170055306A>G	ENST00000263816.3	-	45	8853	c.8568T>C	c.(8566-8568)ccT>ccC	p.P2856P		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2856	LDL-receptor class A 19. {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)"	TGCAATAAGTAGGGTTTTCAT	0.383																																					p.P2856P		Atlas-SNP	.											.	LRP2	751	.	0			c.T8568C						PASS	.						155	142	147					2																	170055306		2203	4300	6503	SO:0001819	synonymous_variant	4036	exon45			ATAAGTAGGGTTT		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.8568T>C	chr2.hg19:g.170055306A>G		119.0	0.0	.		149.0	49.0	.	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	hg19	CCDS2232.1																																																																																			.	.	.	none		0.383	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		G	170055306	A	G	170055306	2	3	103	1	0	0	0	0	0	0	0	1	8963	407	15	3		3	LRP2	2	170055306	Silent	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	3901761	170055306	73144067	18	6548											
PGAP1	80055	hgsc.bcm.edu	37	chr2	197784853	197784853	+	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	tgcgggatagcgttttgccaGtttctttggaagttctattt	6	18	11	6	2	2	0	0	0	2	0	2	2	2	2	1	2	3	3	1	2	3	8			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr2:197784853G>T	ENST00000354764.4	-	2	283	c.169C>A	c.(169-171)Ctg>Atg	p.L57M	PGAP1_ENST00000485830.1_5'UTR|PGAP1_ENST00000409188.1_Missense_Mutation_p.L15M|PGAP1_ENST00000409475.1_Missense_Mutation_p.L57M	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	57					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						CGTTTTGCCAGTTTCTTTGGA	0.343																																					p.L57M		Atlas-SNP	.											.	PGAP1	84	.	0			c.C169A						PASS	.						120	125	123					2																	197784853		2203	4300	6503	SO:0001583	missense	80055	exon2			TTGCCAGTTTCTT		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.169C>A	chr2.hg19:g.197784853G>T	ENSP00000346809:p.Leu57Met	43.0	0.0	.		56.0	28.0	.	NM_024989	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Missense_Mutation	SNP	ENST00000354764.4	hg19	CCDS2318.1	.	.	.	.	.	.	.	.	.	.	G	16.93	3.258007	0.59321	.	.	ENSG00000197121	ENST00000354764;ENST00000409475;ENST00000409188	.	.	.	5.11	3.32	0.38043	.	0.237063	0.36519	N	0.002555	T	0.33847	0.0877	L	0.29908	0.895	0.27991	N	0.935656	D;D	0.71674	0.958;0.998	P;P	0.59221	0.66;0.854	T	0.13202	-1.0518	9	0.35671	T	0.21	-5.081	2.3431	0.04264	0.1595:0.2325:0.4637:0.1442	.	57;57	Q75T13-3;Q75T13	.;PGAP1_HUMAN	M	57;57;15	.	ENSP00000346809:L57M	L	-	1	2	PGAP1	197493098	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.666000	0.37460	0.852000	0.35287	0.655000	0.94253	CTG	.	.	.	none		0.343	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989		T	197784853	G	T	197784853	3	4	103	1	0	0	0	0	1	0	0	0	11784	1020	36	4	2703	4	PGAP1	2	197784853	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	27729547	197784853	45414520	19	6549											
FARP2	9855	hgsc.bcm.edu	37	chr2	242407764	242407764	+	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	ctatgcggacattacagcccCgggcaccatgactacgctga	10	7	10	14	3	0	2	0	2	0	0	0	3	0	3	3	2	4	2	3	2	3	3	rs138469271		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr2:242407764C>G	ENST00000264042.3	+	18	2273	c.2103C>G	c.(2101-2103)ccC>ccG	p.P701P		NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	701	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)		ATTACAGCCCCGGGCACCATG	0.637																																					p.P701P		Atlas-SNP	.											.	FARP2	92	.	0			c.C2103G						PASS	.						42	36	38					2																	242407764		2203	4300	6503	SO:0001819	synonymous_variant	9855	exon18			CAGCCCCGGGCAC	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.2103C>G	chr2.hg19:g.242407764C>G		89.0	0.0	.		93.0	36.0	.	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Silent	SNP	ENST00000264042.3	hg19	CCDS33424.1																																																																																			.	C|1.000;T|0.000	.	alt		0.637	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1			G	242407764	C	G	242407764	2	3	103	1	0	0	0	0	0	0	0	1	5684	639	23	4		4	FARP2	2	242407764	Silent	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	44622911	242407764	791609	20	6550											
MKRN2	23609	hgsc.bcm.edu	37	chr3	12611673	12611673	+	Missense_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	gtcctcaccctccttccgagGtcactgcatccattgtgaaa	8	11	7	15	1	2	1	2	1	0	0	6	2	6	1	5	1	1	1	5	1	1	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr3:12611673G>A	ENST00000170447.7	+	3	396	c.259G>A	c.(259-261)Gtc>Atc	p.V87I	MKRN2_ENST00000411987.1_Missense_Mutation_p.V44I|MKRN2_ENST00000448482.1_Missense_Mutation_p.V85I	NM_001271707.1|NM_014160.3	NP_001258636.1|NP_054879.3	Q9H000	MKRN2_HUMAN	makorin ring finger protein 2	87					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						TCCTTCCGAGGTCACTGCATC	0.547																																					p.V87I		Atlas-SNP	.											.	MKRN2	32	.	0			c.G259A						PASS	.						97	82	87					3																	12611673		2203	4300	6503	SO:0001583	missense	23609	exon3			TCCGAGGTCACTG		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.259G>A	chr3.hg19:g.12611673G>A	ENSP00000170447:p.Val87Ile	76.0	0.0	.		83.0	77.0	.	NM_014160	A6NIA2|B3KRC5|B4DPR4|Q8N391|Q96BD4|Q9BUY2|Q9NRY1	Missense_Mutation	SNP	ENST00000170447.7	hg19	CCDS33702.1	.	.	.	.	.	.	.	.	.	.	G	2.117	-0.402351	0.04865	.	.	ENSG00000075975	ENST00000170447;ENST00000411987;ENST00000448482	T;T;T	0.22539	2.79;1.96;1.95	5.53	-1.17	0.09648	.	0.892392	0.09710	N	0.765804	T	0.05686	0.0149	N	0.00926	-1.1	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.35773	-0.9775	10	0.33141	T	0.24	.	4.2105	0.10509	0.361:0.332:0.2385:0.0685	.	44;85;87	B4DPR4;C9J494;Q9H000	.;.;MKRN2_HUMAN	I	87;44;85	ENSP00000170447:V87I;ENSP00000396340:V44I;ENSP00000397983:V85I	ENSP00000170447:V87I	V	+	1	0	MKRN2	12586673	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.048000	0.14078	0.001000	0.14605	-0.311000	0.09066	GTC	.	.	.	none		0.547	MKRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339679.1	NM_014160		A	12611673	G	A	12611673	3	1	103	1	0	0	0	0	1	0	0	0	9614	1261	44	2	269	2	MKRN2	3	12611673	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10		12611673	185410757	21	6551											
RPSA	3921	hgsc.bcm.edu	37	chr3	39453553	39453556	+	Splice_Site	DEL	GTAT	GTAT	-																															tattcagcaattccctactgGtatgtatcaggatagaggtg																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	GTAT	GTAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr3:39453553_39453556delGTAT	ENST00000301821.6	+	6	902		c.e6+1		SNORA62_ENST00000365493.1_RNA|RPSA_ENST00000443003.1_Splice_Site|RPSA_ENST00000478027.1_Splice_Site	NM_001012321.1|NM_002295.4	NP_001012321.1|NP_002286.2			ribosomal protein SA											endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.0509)|Kidney(284;0.064)		TTCCCTACTGGTATGTATCAGGAT	0.431																																					p.265_265del		Atlas-Indel,Pindel	.											.	RPSA	15	.	0			c.793_793del						PASS	.																																			SO:0001630	splice_region_variant	3921	exon5			.	S37431	CCDS2686.1	3p21.3	2014-09-17	2002-08-29	2005-02-11	ENSG00000168028	ENSG00000168028			6502	protein-coding gene	gene with protein product		150370	"laminin receptor 1 (67kD, ribosomal protein SA)"	LAMR1		1534510, 8760291	Standard	NM_001012321		Approved	LRP, 37LRP, p40, SA	uc003cjp.3	P08865	OTTHUMG00000131296	ENST00000301821.6:c.793+1GTAT>-	chr3.hg19:g.39453557_39453560delGTAT		39.0	0.0	0		23.0	17.0	0.73913	NM_001012321		Frame_Shift_Del	DEL	ENST00000301821.6	hg19	CCDS2686.1																																																																																			.	.	.	none		0.431	RPSA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254064.3	NM_002295	Intron	-	39453556	GTAT	-	39453553	8	5	103	1	0	1	0	1	0	0	1	0	13676	1275	44	0	812	0	RPSA	3	39453553	Splice_Site	DEL	GTAT	TCGA-B9-A44B-01A-11D-A25F-10	26841880	39453553	158568877	22	6552											
SETD2	29072	hgsc.bcm.edu	37	chr3	47163966	47163967	+	Frame_Shift_Ins	INS	-	-	C																															acctactaatattctgaaatINSccatttgatgaaagcatgca																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr3:47163966_47163967insC	ENST00000409792.3	-	3	2201_2202	c.2159_2160insG	c.(2158-2160)ggafs	p.G720fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	720					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TATTCTGAAATCCATTTGATGA	0.391			"N, F, S, Mis"		clear cell renal carcinoma																																p.G720fs		Atlas-Indel,Pindel	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.2160_2161insG						PASS	.																																			SO:0001589	frameshift_variant	29072	exon3			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.2160dupG	chr3.hg19:g.47163968_47163968dupC	ENSP00000386759:p.Gly720fs	71.0	0.0	0		49.0	37.0	0.755102	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Ins	INS	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.	.	none		0.391	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		C	47163967	-	C	47163966	7	5	103	1	0	1	1	0	0	0	0	0	14144	1422	50	0	5610	0	SETD2	3	47163966	Frame_Shift_Ins	INS	-	TCGA-B9-A44B-01A-11D-A25F-10	7710413	47163966	150858464	23	6553											
POC1A	25886	hgsc.bcm.edu	37	chr3	52181040	52181040	+	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	acgagtggacacattcccggCtgctcttgtcccacagctta	8	10	9	14	2	1	0	0	0	1	0	3	2	3	1	2	2	2	3	2	2	1	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr3:52181040C>A	ENST00000296484.2	-	5	566	c.527G>T	c.(526-528)aGc>aTc	p.S176I	POC1A_ENST00000394970.2_Missense_Mutation_p.S176I|POC1A_ENST00000474012.1_Missense_Mutation_p.S138I	NM_015426.4	NP_056241.3	Q8NBT0	POC1A_HUMAN	POC1 centriolar protein A	176					cell projection organization (GO:0030030)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|spindle pole (GO:0000922)				endometrium(1)|large_intestine(4)|liver(1)|lung(4)|prostate(3)|skin(1)	14						ACATTCCCGGCTGCTCTTGTC	0.592																																					p.S176I		Atlas-SNP	.											.	POC1A	32	.	0			c.G527T						PASS	.						107	98	101					3																	52181040		2203	4300	6503	SO:0001583	missense	25886	exon5			TCCCGGCTGCTCT	AL117629	CCDS2846.1, CCDS54591.1, CCDS54592.1	3p21.2	2014-05-02	2013-08-21	2010-03-26	ENSG00000164087	ENSG00000164087		"WD repeat domain containing"	24488	protein-coding gene	gene with protein product		614783	"WD repeat domain 51A", "POC1 centriolar protein homolog A (Chlamydomonas)"	WDR51A		19109428, 22840364	Standard	NM_015426		Approved	DKFZP434C245	uc003dcu.3	Q8NBT0	OTTHUMG00000157817	ENST00000296484.2:c.527G>T	chr3.hg19:g.52181040C>A	ENSP00000296484:p.Ser176Ile	150.0	0.0	.		127.0	32.0	.	NM_015426	A4FUW4|E9PFC6|Q0VDF8|Q2TAK6|Q96IK6|Q9UFJ8	Missense_Mutation	SNP	ENST00000296484.2	hg19	CCDS2846.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.831256	0.91036	.	.	ENSG00000164087	ENST00000296484;ENST00000394970;ENST00000474012	D;D;D	0.82803	-1.65;-1.65;-1.65	5.13	4.19	0.49359	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.041315	0.85682	D	0.000000	D	0.89160	0.6636	M	0.84082	2.675	0.80722	D	1	D;D	0.62365	0.974;0.991	P;P	0.56163	0.767;0.793	D	0.91017	0.4854	10	0.87932	D	0	.	15.0503	0.71862	0.0:0.8574:0.1426:0.0	.	176;176	Q8NBT0-2;Q8NBT0	.;POC1A_HUMAN	I	176;176;138	ENSP00000296484:S176I;ENSP00000378421:S176I;ENSP00000418968:S138I	ENSP00000296484:S176I	S	-	2	0	POC1A	52156080	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	3.074000	0.50065	2.555000	0.86185	0.563000	0.77884	AGC	.	.	.	none		0.592	POC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349685.1	NM_015426		A	52181040	C	A	52181040	3	1	103	1	0	0	0	0	1	0	0	0	12182	797	28	4	724	4	POC1A	3	52181040	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	5017074	52181040	145841390	24	6554											
STAB1	23166	hgsc.bcm.edu	37	chr3	52555670	52555671	+	Frame_Shift_Ins	INS	-	-	T																															ttgggggctctggctcctgcINSttctgtgatgaaggctggac																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr3:52555670_52555671insT	ENST00000321725.6	+	57	6193_6194	c.6117_6118insT	c.(6118-6120)ttcfs	p.F2040fs		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	2040					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)		CTGGCTCCTGCTTCTGTGATGA	0.604																																					p.C2039fs		Pindel	.											.	STAB1	178	.	0			c.6117_6118insT						PASS	.																																			SO:0001589	frameshift_variant	23166	exon57			.	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.6119dupT	chr3.hg19:g.52555672_52555672dupT	ENSP00000312946:p.Phe2040fs	108.0	0.0	.		92.0	14.0	0.152	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Frame_Shift_Ins	INS	ENST00000321725.6	hg19	CCDS33768.1																																																																																			.	.	.	none		0.604	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		T	52555671	-	T	52555670	7	5	103	1	0	1	1	0	0	0	0	0	15249	805	28	0	6343	0	STAB1	3	52555670	Frame_Shift_Ins	INS	-	TCGA-B9-A44B-01A-11D-A25F-10	374630	52555670	145466760	25	6555											
PBRM1	55193	hgsc.bcm.edu	37	chr3	52637647	52637647	+	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	gttttgtggtatagctgagtGccggtgaaagaagaatctct	10	13	13	5	1	1	4	0	2	1	2	2	4	1	4	1	2	2	3	1	2	5	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr3:52637647G>T	ENST00000296302.7	-	17	2670	c.2669C>A	c.(2668-2670)gCa>gAa	p.A890E	PBRM1_ENST00000409114.3_Missense_Mutation_p.A905E|PBRM1_ENST00000394830.3_Missense_Mutation_p.A890E|PBRM1_ENST00000337303.4_Missense_Mutation_p.A890E|PBRM1_ENST00000410007.1_Missense_Mutation_p.A890E|PBRM1_ENST00000356770.4_Missense_Mutation_p.A858E|PBRM1_ENST00000409057.1_Missense_Mutation_p.A890E|PBRM1_ENST00000409767.1_Missense_Mutation_p.A905E			Q86U86	PB1_HUMAN	polybromo 1	890					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)		ATAGCTGAGTGCCGGTGAAAG	0.338			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.A890E		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.C2669A						PASS	.						82	78	79					3																	52637647		2203	4299	6502	SO:0001583	missense	55193	exon18			CTGAGTGCCGGTG	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.2669C>A	chr3.hg19:g.52637647G>T	ENSP00000296302:p.Ala890Glu	23.0	0.0	.		32.0	28.0	.	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Missense_Mutation	SNP	ENST00000296302.7	hg19		.	.	.	.	.	.	.	.	.	.	G	33	5.240611	0.95240	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103	T;T;T;T;T;T;T;T;T;T	0.54675	0.67;0.59;0.71;0.66;0.68;0.56;1.14;0.67;0.69;0.97	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.76018	0.3929	M	0.80422	2.495	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D	0.97110	0.999;0.999;1.0;0.999;1.0;1.0;0.999;0.999;1.0	T	0.78237	-0.2282	10	0.87932	D	0	.	19.9278	0.97110	0.0:0.0:1.0:0.0	.	890;890;890;890;905;905;890;858;890	Q86U86-9;E7EVG2;Q86U86-4;Q86U86-2;Q86U86-8;Q86U86-7;Q86U86;Q86U86-3;Q86U86-5	.;.;.;.;.;.;PB1_HUMAN;.;.	E	858;890;890;890;890;890;905;905;890;849	ENSP00000349213:A858E;ENSP00000378307:A890E;ENSP00000296302:A890E;ENSP00000338302:A890E;ENSP00000386593:A890E;ENSP00000386529:A890E;ENSP00000386643:A905E;ENSP00000386601:A905E;ENSP00000387775:A890E;ENSP00000397662:A849E	ENSP00000296302:A890E	A	-	2	0	PBRM1	52612687	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.779000	0.99018	2.770000	0.95276	0.650000	0.86243	GCA	.	.	.	none		0.338	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		T	52637647	G	T	52637647	3	4	103	1	0	0	0	0	1	0	0	0	11498	1319	46	4	2287	4	PBRM1	3	52637647	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	81977	52637647	145384783	26	6556											
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-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr3:57743531A>G	ENST00000428312.1	+	1	247	c.153A>G	c.(151-153)ctA>ctG	p.L51L	SLMAP_ENST00000295951.3_Silent_p.L51L|SLMAP_ENST00000295952.3_Silent_p.L51L|SLMAP_ENST00000449503.2_Silent_p.L51L|SLMAP_ENST00000416870.1_5'UTR|SLMAP_ENST00000383718.3_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	chr3.hg19:g.57743531A>G		317.0	2.0	.		282.0	236.0	.	NM_007159	Q14C95|Q6AI54|Q6UXC9|Q6ZVQ8|Q8NCW9|Q9H297|Q9HCH1|Q9Y681	Silent	SNP	ENST00000428312.1	hg19																																																																																				.	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	103	1	0	0	0	0	0	0	0	1	14762	436	16	3		3	SLMAP	3	57743531	Silent	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	5105884	57743531	140278899	27	6557											
THPO	7066	hgsc.bcm.edu	37	chr3	184090635	184090635	+	Missense_Mutation	SNP	A	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	tcctgttcaggtatccggggAtttggtccagggacctggag	6	11	15	9	1	1	0	1	0	0	0	4	3	4	3	4	6	0	2	4	6	1	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr3:184090635A>C	ENST00000204615.7	-	6	942	c.728T>G	c.(727-729)aTc>aGc	p.I243S	THPO_ENST00000421442.2_Missense_Mutation_p.N204K|EIF2B5_ENST00000444495.1_Intron|THPO_ENST00000477594.1_5'Flank|THPO_ENST00000445696.2_Missense_Mutation_p.I239S	NM_000460.2|NM_001177597.1|NM_001177598.1	NP_000451.1|NP_001171068.1|NP_001171069.1	P40225	TPO_HUMAN	thrombopoietin	243					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|myeloid cell differentiation (GO:0030099)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|thrombopoietin-mediated signaling pathway (GO:0038163)	extracellular space (GO:0005615)	growth factor activity (GO:0008083)			NS(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)	16	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GTATCCGGGGATTTGGTCCAG	0.552																																					p.I243S		Atlas-SNP	.											.	THPO	37	.	0			c.T728G						PASS	.						88	86	87					3																	184090635		2203	4300	6503	SO:0001583	missense	7066	exon6			CCGGGGATTTGGT		CCDS3265.1, CCDS54693.1	3q27	2014-01-30	2008-07-31		ENSG00000090534	ENSG00000090534		"Endogenous ligands"	11795	protein-coding gene	gene with protein product	"prepro-thrombopoietin", "megakaryocyte stimulating factor", "myeloproliferative leukemia virus oncogene ligand", "megakaryocyte growth and development factor", "MPL ligand", "megakaryocyte colony-stimulating factor", "c-mpl ligand", "thrombopoietin nirs variant 1"	600044		MGDF		8202154	Standard	XM_006713738		Approved	TPO, MPLLG	uc003fol.1	P40225	OTTHUMG00000156745	ENST00000204615.7:c.728T>G	chr3.hg19:g.184090635A>C	ENSP00000204615:p.Ile243Ser	126.0	0.0	.		150.0	49.0	.	NM_000460	A1L3Y0|B7ZLR8|B9EGA8|Q13020|Q15790|Q15791|Q15792	Missense_Mutation	SNP	ENST00000204615.7	hg19	CCDS3265.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.184|0.184	-1.059924|-1.059924	0.01950|0.01950	.|.	.|.	ENSG00000090534|ENSG00000090534	ENST00000204615;ENST00000445696;ENST00000353488|ENST00000421442	T;T|T	0.34859|0.36157	1.34;1.35|1.27	4.34|4.34	-1.07|-1.07	0.09968|0.09968	Four-helical cytokine, core (1);|.	1.174950|.	0.06383|.	N|.	0.715527|.	T|T	0.21718|0.21718	0.0523|0.0523	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	1|1	B;B|B	0.24426|0.28291	0.103;0.063|0.206	B;B|B	0.25140|0.28139	0.058;0.026|0.086	T|T	0.23547|0.23547	-1.0185|-1.0185	10|9	0.66056|0.42905	D|T	0.02|0.14	-23.2862|-23.2862	3.8944|3.8944	0.09133|0.09133	0.3909:0.3883:0.2208:0.0|0.3909:0.3883:0.2208:0.0	.|.	239;243|204	P40225-2;P40225|F8W6L1	.;TPO_HUMAN|.	S|K	243;239;204|204	ENSP00000204615:I243S;ENSP00000410763:I239S|ENSP00000411704:N204K	ENSP00000204615:I243S|ENSP00000411704:N204K	I|N	-|-	2|3	0|2	THPO|THPO	185573329|185573329	0.002000|0.002000	0.14202|0.14202	0.093000|0.093000	0.20910|0.20910	0.720000|0.720000	0.41350|0.41350	-0.313000|-0.313000	0.08103|0.08103	0.205000|0.205000	0.20568|0.20568	0.378000|0.378000	0.23410|0.23410	ATC|AAT	.	.	.	none		0.552	THPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345554.1	NM_000460		C	184090635	A	C	184090635	3	2	103	1	0	0	0	0	1	0	0	0	15884	333	12	5	337	5	THPO	3	184090635	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	126347104	184090635	13931795	28	6558											
EIF4A2	1974	hgsc.bcm.edu	37	chr3	186503770	186503770	+	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	aatgaaatgcaaaaactgcaGgctgaagcaccacatattgt	17	8	8	8	0	0	2	0	2	0	0	0	2	0	2	1	1	4	4	1	1	6	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr3:186503770G>T	ENST00000323963.5	+	5	511	c.447G>T	c.(445-447)caG>caT	p.Q149H	SNORA81_ENST00000408493.2_RNA|SNORA63_ENST00000363548.1_RNA|SNORD2_ENST00000459163.1_RNA|EIF4A2_ENST00000440191.2_Missense_Mutation_p.Q150H|EIF4A2_ENST00000356531.5_Missense_Mutation_p.Q54H|RP11-573D15.9_ENST00000577781.1_RNA|SNORA63_ENST00000363450.1_RNA|SNORA4_ENST00000584302.1_RNA			Q14240	IF4A2_HUMAN	eukaryotic translation initiation factor 4A2	149	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|urinary_tract(1)	28	all_cancers(143;2.68e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.07e-20)	GBM - Glioblastoma multiforme(93;0.0704)		AAAAACTGCAGGCTGAAGCAC	0.393			T	BCL6	NHL																																p.Q149H		Atlas-SNP	.		Dom	yes		3	3q27.3	1974	"eukaryotic translation initiation factor 4A, isoform 2"		L	.	EIF4A2	55	.	0			c.G447T						PASS	.						94	87	90					3																	186503770		2203	4300	6503	SO:0001583	missense	1974	exon5			ACTGCAGGCTGAA	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.447G>T	chr3.hg19:g.186503770G>T	ENSP00000326381:p.Gln149His	121.0	0.0	.		149.0	34.0	.	NM_001967	D3DNU9|Q53XJ6|Q96B90|Q96EA8	Missense_Mutation	SNP	ENST00000323963.5	hg19	CCDS3282.1	.	.	.	.	.	.	.	.	.	.	G	19.10	3.761816	0.69763	.	.	ENSG00000156976	ENST00000323963;ENST00000440191;ENST00000356531	T;T;T	0.04917	3.53;3.53;3.53	4.51	4.51	0.55191	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.40818	U	0.001006	T	0.15089	0.0364	L	0.45051	1.395	0.80722	D	1	D;P;P;P	0.67145	0.996;0.913;0.836;0.865	P;P;B;P	0.59115	0.852;0.71;0.382;0.516	T	0.00389	-1.1770	10	0.87932	D	0	-9.8507	15.0932	0.72211	0.0:0.0:1.0:0.0	.	5;54;150;149	B4DJX6;Q9NZE6;Q14240-2;Q14240	.;.;.;IF4A2_HUMAN	H	149;150;54	ENSP00000326381:Q149H;ENSP00000398370:Q150H;ENSP00000348925:Q54H	ENSP00000326381:Q149H	Q	+	3	2	EIF4A2	187986464	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	5.890000	0.69774	2.497000	0.84241	0.650000	0.86243	CAG	.	.	.	none		0.393	EIF4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344609.1	NM_001967		T	186503770	G	T	186503770	3	4	103	1	0	0	0	0	1	0	0	0	5027	991	35	4	465	4	EIF4A2	3	186503770	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	2413135	186503770	11518660	29	6559											
TMPRSS11A	339967	hgsc.bcm.edu	37	chr4	68777111	68777111	+	Frame_Shift_Del	DEL	G	G	-																															cggtaataagtcacttgtgtGtagactccaggcttgtcctt																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr4:68777111delG	ENST00000334830.7	-	10	1961	c.1215delC	c.(1213-1215)tacfs	p.Y405fs	TMPRSS11A_ENST00000396188.2_Frame_Shift_Del_p.Y402fs|UBA6-AS1_ENST00000500538.2_RNA|TMPRSS11A_ENST00000508048.1_Frame_Shift_Del_p.Y401fs			Q6ZMR5	TM11A_HUMAN	transmembrane protease, serine 11A	405	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cell cycle (GO:0007049)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|cervix(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	29						TCACTTGTGTGTAGACTCCAG	0.408																																					p.T406fs	NSCLC(26;2 894 10941 14480 22546)	Atlas-INDEL	.											.	TMPRSS11A	74	.	0			c.1216delA						PASS	.						192	181	185					4																	68777111		2203	4300	6503	SO:0001589	frameshift_variant	339967	exon10			.	AF071882	CCDS3519.1	4q13.2	2010-04-13			ENSG00000187054	ENSG00000187054		"Serine peptidases / Transmembrane"	27954	protein-coding gene	gene with protein product		611704				15328353	Standard	NM_182606		Approved	ECRG1	uc003hdr.1	Q6ZMR5	OTTHUMG00000129303	ENST00000334830.7:c.1215delC	chr4.hg19:g.68777111delG	ENSP00000334611:p.Tyr405fs	206.0	0.0	0		163.0	70.0	0.429448	NM_182606	J3KNQ8|Q2NKI9|Q6JE90|Q7RTY4|Q86TK8	Frame_Shift_Del	DEL	ENST00000334830.7	hg19	CCDS3519.1																																																																																			.	.	.	none		0.408	TMPRSS11A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251433.3	NM_182606		-	68777111	G	-	68777111	7	5	103	1	0	1	0	1	0	0	0	0	16251	1372	48	0	54	0	TMPRSS11A	4	68777111	Frame_Shift_Del	DEL	G	TCGA-B9-A44B-01A-11D-A25F-10		68777111	122377165	30	6560											
ZNF622	90441	hgsc.bcm.edu	37	chr5	16465479	16465479	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttccgattcactgcctgcAcggccttcttctccagctca	5	13	6	17	2	4	0	2	0	2	0	6	1	5	0	4	1	3	2	4	1	0	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr5:16465479A>G	ENST00000308683.2	-	1	422	c.296T>C	c.(295-297)gTg>gCg	p.V99A		NM_033414.2	NP_219482.1	Q969S3	ZN622_HUMAN	zinc finger protein 622	99					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						CACTGCCTGCACGGCCTTCTT	0.537																																					p.V99A		Atlas-SNP	.											.	ZNF622	49	.	0			c.T296C						PASS	.						155	139	145					5																	16465479		2203	4300	6503	SO:0001583	missense	90441	exon1			GCCTGCACGGCCT	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.296T>C	chr5.hg19:g.16465479A>G	ENSP00000310042:p.Val99Ala	148.0	0.0	.		155.0	31.0	.	NM_033414		Missense_Mutation	SNP	ENST00000308683.2	hg19	CCDS3886.1	.	.	.	.	.	.	.	.	.	.	A	15.37	2.814522	0.50527	.	.	ENSG00000173545	ENST00000308683	.	.	.	4.81	3.65	0.41850	.	0.199006	0.45126	D	0.000388	T	0.46639	0.1403	M	0.65975	2.015	0.41784	D	0.989838	B	0.15141	0.012	B	0.09377	0.004	T	0.36432	-0.9748	9	0.02654	T	1	-37.7849	7.9359	0.29929	0.8407:0.0:0.1593:0.0	.	99	Q969S3	ZN622_HUMAN	A	99	.	ENSP00000310042:V99A	V	-	2	0	ZNF622	16518479	1.000000	0.71417	0.995000	0.50966	0.983000	0.72400	5.190000	0.65104	0.855000	0.35359	0.528000	0.53228	GTG	.	.	.	none		0.537	ZNF622-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207105.1	NM_033414		G	16465479	A	G	16465479	3	3	103	1	0	0	0	0	1	0	0	0	18058	159	6	3	1161	3	ZNF622	5	16465479	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10		16465479	164449781	31	6561											
MYO10	4651	hgsc.bcm.edu	37	chr5	16685914	16685914	+	Missense_Mutation	SNP	A	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	cctggtccgtggacgcgtggAcctgactcagcacgctgaac	7	7	13	14	4	1	2	1	2	0	0	2	4	2	4	3	3	2	2	3	3	1	0			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr5:16685914A>C	ENST00000513610.1	-	29	4377	c.3923T>G	c.(3922-3924)gTc>gGc	p.V1308G	MYO10_ENST00000427430.2_Missense_Mutation_p.V665G|MYO10_ENST00000274203.9_Missense_Mutation_p.V665G|MYO10_ENST00000505695.1_Missense_Mutation_p.V647G|MYO10_ENST00000515803.1_Missense_Mutation_p.V647G	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	1308	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						GGACGCGTGGACCTGACTCAG	0.592																																					p.V1308G		Atlas-SNP	.											.	MYO10	198	.	0			c.T3923G						PASS	.						61	61	61					5																	16685914		2160	4271	6431	SO:0001583	missense	4651	exon29			GCGTGGACCTGAC	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.3923T>G	chr5.hg19:g.16685914A>C	ENSP00000421280:p.Val1308Gly	60.0	0.0	.		56.0	24.0	.	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	hg19	CCDS54834.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.889699	0.91889	.	.	ENSG00000145555	ENST00000513610;ENST00000515803;ENST00000274203;ENST00000505695;ENST00000427430	T;T;T;T;T	0.14391	2.51;2.51;2.51;2.51;2.51	5.51	5.51	0.81932	Pleckstrin homology domain (3);	.	.	.	.	T	0.46151	0.1378	M	0.90542	3.125	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	T	0.57057	-0.7876	9	0.87932	D	0	.	15.6429	0.77020	1.0:0.0:0.0:0.0	.	187;949;1308	B4DIJ5;Q69YP8;Q9HD67	.;.;MYO10_HUMAN	G	1308;647;665;647;665	ENSP00000421280:V1308G;ENSP00000425051:V647G;ENSP00000274203:V665G;ENSP00000421170:V647G;ENSP00000391106:V665G	ENSP00000274203:V665G	V	-	2	0	MYO10	16738914	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.331000	0.96430	2.092000	0.63282	0.523000	0.50628	GTC	.	.	.	none		0.592	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		C	16685914	A	C	16685914	3	2	103	1	0	0	0	0	1	0	0	0	10069	275	10	5	2305	5	MYO10	5	16685914	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	220435	16685914	164229346	32	6562											
CDH9	1007	hgsc.bcm.edu	37	chr5	26915851	26915851	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgattccggttccacctgcCgcccagtttttctgtctata	5	14	7	15	3	2	0	0	0	2	0	4	1	4	0	6	1	1	2	6	1	2	6	rs150604531		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr5:26915851C>T	ENST00000231021.4	-	3	582	c.410G>A	c.(409-411)cGg>cAg	p.R137Q		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	137	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	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						TTCCACCTGCCGCCCAGTTTT	0.383																																					p.R137Q	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											CDH9,NS,carcinoma,-1,1	CDH9	305	.	0			c.G410A						PASS	.	C	GLN/ARG	0,4406		0,0,2203	136	136	136		410	4.6	0.5	5	dbSNP_134	136	3,8595	3.0+/-9.4	0,3,4296	no	missense	CDH9	NM_016279.3	43	0,3,6499	TT,TC,CC		0.0349,0.0,0.0231	benign	137/790	26915851	3,13001	2203	4299	6502	SO:0001583	missense	1007	exon3			ACCTGCCGCCCAG	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.410G>A	chr5.hg19:g.26915851C>T	ENSP00000231021:p.Arg137Gln	112.0	1.0	.		112.0	37.0	.	NM_016279	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	hg19	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	C	14.41	2.525965	0.44969	0.0	3.49E-4	ENSG00000113100	ENST00000231021	T	0.50548	0.74	4.62	4.62	0.57501	Cadherin (4);Cadherin-like (1);	0.353060	0.31031	N	0.008396	T	0.35595	0.0937	L	0.39514	1.22	0.09310	N	1	B	0.28512	0.214	B	0.25405	0.06	T	0.16424	-1.0403	9	.	.	.	.	10.1395	0.42728	0.0:0.9063:0.0:0.0937	.	137	Q9ULB4	CADH9_HUMAN	Q	137	ENSP00000231021:R137Q	.	R	-	2	0	CDH9	26951608	0.001000	0.12720	0.540000	0.28089	0.988000	0.76386	1.388000	0.34442	2.275000	0.75901	0.650000	0.86243	CGG	.	C|1.000;T|0.000	0.000	weak		0.383	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		T	26915851	C	T	26915851	3	4	103	1	0	0	0	0	1	0	0	0	3119	652	23	1	1999	1	CDH9	5	26915851	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	10229937	26915851	153999409	33	6563											
PRRC1	133619	hgsc.bcm.edu	37	chr5	126860514	126860514	+	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	ttcgggtcctcctatatcagGattttctgttggttcaactt	6	18	8	9	1	3	0	2	0	1	0	6	1	5	1	2	3	1	2	2	3	3	8			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr5:126860514G>C	ENST00000296666.8	+	3	583	c.395G>C	c.(394-396)gGa>gCa	p.G132A	PRRC1_ENST00000512635.2_Missense_Mutation_p.G132A|PRRC1_ENST00000442138.2_Missense_Mutation_p.G132A	NM_130809.3	NP_570721.1	Q96M27	PRRC1_HUMAN	proline-rich coiled-coil 1	132						Golgi apparatus (GO:0005794)				endometrium(1)|large_intestine(1)|lung(4)	6		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0851)|Epithelial(69;0.113)		CCTATATCAGGATTTTCTGTT	0.507																																					p.G132A		Atlas-SNP	.											.	PRRC1	22	.	0			c.G395C						PASS	.						145	149	148					5																	126860514		2203	4300	6503	SO:0001583	missense	133619	exon3			TATCAGGATTTTC	AJ515429	CCDS4143.1, CCDS68943.1	5q23.2	2008-02-05			ENSG00000164244	ENSG00000164244			28164	protein-coding gene	gene with protein product						15541471	Standard	NM_130809		Approved	FLJ32875	uc003kuk.3	Q96M27	OTTHUMG00000128982	ENST00000296666.8:c.395G>C	chr5.hg19:g.126860514G>C	ENSP00000296666:p.Gly132Ala	145.0	0.0	.		182.0	83.0	.	NM_130809	Q69YM8|Q7L2U7|Q86Y42|Q8IVJ4|Q8IVL4|Q8NEZ7|Q96AJ3	Missense_Mutation	SNP	ENST00000296666.8	hg19	CCDS4143.1	.	.	.	.	.	.	.	.	.	.	G	16.96	3.265327	0.59431	.	.	ENSG00000164244	ENST00000296666;ENST00000442138;ENST00000330542;ENST00000414018;ENST00000512635;ENST00000512535	.	.	.	5.06	5.06	0.68205	.	0.174179	0.49916	D	0.000122	T	0.41926	0.1180	L	0.31207	0.915	0.53005	D	0.999966	B;P	0.42375	0.214;0.778	B;B	0.37989	0.052;0.262	T	0.29971	-0.9994	9	0.30078	T	0.28	-20.0859	17.5874	0.87986	0.0:0.0:1.0:0.0	.	132;132	Q96M27;Q96M27-5	PRRC1_HUMAN;.	A	132	.	ENSP00000296666:G132A	G	+	2	0	PRRC1	126888413	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.592000	0.67543	2.632000	0.89209	0.655000	0.94253	GGA	.	.	.	none		0.507	PRRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250971.3	NM_130809		C	126860514	G	C	126860514	3	2	103	1	0	0	0	0	1	0	0	0	12614	1174	41	4	401	4	PRRC1	5	126860514	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	99944663	126860514	54054746	34	6564											
MATR3	9782	hgsc.bcm.edu	37	chr5	138643239	138643239	+	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	ccagcatctcttggaaggatGaaccagggtactgcacgcct	10	8	11	12	1	1	1	0	1	1	0	2	3	1	3	3	3	4	3	3	3	3	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr5:138643239G>A	ENST00000394805.3	+	2	470	c.135G>A	c.(133-135)atG>atA	p.M45I	MATR3_ENST00000361059.2_Missense_Mutation_p.M45I|MATR3_ENST00000503811.1_Intron|MATR3_ENST00000509990.1_Missense_Mutation_p.M45I|MATR3_ENST00000510056.1_Missense_Mutation_p.M45I|MATR3_ENST00000502929.1_Missense_Mutation_p.M45I|MATR3_ENST00000502499.1_Intron|MATR3_ENST00000504203.1_Intron|MATR3_ENST00000394800.2_Missense_Mutation_p.M45I	NM_001194955.1|NM_018834.5	NP_001181884.1|NP_061322.2	P43243	MATR3_HUMAN	matrin 3	45					cell death (GO:0008219)	membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|kidney(4)|large_intestine(6)|lung(9)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TTGGAAGGATGAACCAGGGTA	0.488																																					p.M45I		Atlas-SNP	.											.	MATR3	85	.	0			c.G135A						PASS	.						144	135	138					5																	138643239		2203	4300	6503	SO:0001583	missense	9782	exon2			AAGGATGAACCAG	M63483	CCDS4210.1, CCDS54908.1, CCDS75316.1	5q31.3	2010-08-12			ENSG00000015479	ENSG00000015479			6912	protein-coding gene	gene with protein product		164015	"myopathy, distal 2"	MPD2		2033075, 19344878	Standard	NM_018834		Approved	KIAA0723, MGC9105, VCPDM	uc003ldx.3	P43243	OTTHUMG00000129229	ENST00000394805.3:c.135G>A	chr5.hg19:g.138643239G>A	ENSP00000378284:p.Met45Ile	210.0	0.0	.		198.0	84.0	.	NM_018834	B7ZAV5|D3DQC3|Q9UHW0|Q9UQ27	Missense_Mutation	SNP	ENST00000394805.3	hg19	CCDS4210.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.461853	0.43736	.	.	ENSG00000015479	ENST00000509990;ENST00000361059;ENST00000514694;ENST00000502929;ENST00000394800;ENST00000505016;ENST00000502394;ENST00000394805;ENST00000504045;ENST00000510056;ENST00000508689;ENST00000514488;ENST00000503340;ENST00000504023	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.80480	-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.81044	0.4741	N	0.14661	0.345	0.51233	D	0.999917	P;B;P	0.45126	0.851;0.018;0.851	P;B;P	0.55391	0.775;0.131;0.775	T	0.83121	-0.0118	10	0.72032	D	0.01	-7.6365	20.4366	0.99092	0.0:0.0:1.0:0.0	.	45;45;45	D6REM6;A8MXP9;P43243	.;.;MATR3_HUMAN	I	45	ENSP00000423533:M45I;ENSP00000354346:M45I;ENSP00000422233:M45I;ENSP00000422319:M45I;ENSP00000378279:M45I;ENSP00000424431:M45I;ENSP00000427168:M45I;ENSP00000378284:M45I;ENSP00000423290:M45I;ENSP00000426743:M45I;ENSP00000422137:M45I;ENSP00000426801:M45I;ENSP00000422590:M45I;ENSP00000421145:M45I	ENSP00000354346:M45I	M	+	3	0	MATR3	138671138	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.685000	0.74543	2.843000	0.97960	0.585000	0.79938	ATG	.	.	.	none		0.488	MATR3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251324.2	NM_018834		A	138643239	G	A	138643239	3	1	103	1	0	0	0	0	1	0	0	0	9344	1290	45	2	137	2	MATR3	5	138643239	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	11782725	138643239	42272021	35	6565											
GRPEL2	134266	hgsc.bcm.edu	37	chr5	148730494	148730494	+	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	tctgcaggaatccagagtttCtgtaaggacttggtggaggt	9	12	14	6	0	2	1	0	0	2	1	3	4	3	4	1	5	1	3	1	5	2	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr5:148730494C>T	ENST00000329271.3	+	4	437	c.327C>T	c.(325-327)ttC>ttT	p.F109F	GRPEL2-AS1_ENST00000521295.1_RNA|GRPEL2_ENST00000416916.2_Missense_Mutation_p.S82F|GRPEL2_ENST00000507562.1_3'UTR	NM_152407.3	NP_689620.2	Q8TAA5	GRPE2_HUMAN	GrpE-like 2, mitochondrial (E. coli)	109					cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane (GO:0005743)	adenyl-nucleotide exchange factor activity (GO:0000774)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCAGAGTTTCTGTAAGGACT	0.478																																					p.F109F		Atlas-SNP	.											.	GRPEL2	18	.	0			c.C327T						PASS	.						90	99	96					5																	148730494		2203	4300	6503	SO:0001819	synonymous_variant	134266	exon4			GAGTTTCTGTAAG	AL832325	CCDS4295.1	5q33.1	2008-02-05			ENSG00000164284	ENSG00000164284			21060	protein-coding gene	gene with protein product							Standard	NM_152407		Approved	DKFZp451C205, Mt-GrpE#2, FLJ23713	uc003lqj.3	Q8TAA5	OTTHUMG00000130048	ENST00000329271.3:c.327C>T	chr5.hg19:g.148730494C>T		69.0	0.0	.		81.0	20.0	.	NM_152407	B4DFA6|Q49AJ6	Silent	SNP	ENST00000329271.3	hg19	CCDS4295.1	.	.	.	.	.	.	.	.	.	.	C	19.97	3.925419	0.73213	.	.	ENSG00000164284	ENST00000416916	.	.	.	6.06	4.27	0.50696	.	.	.	.	.	T	0.26882	0.0658	.	.	.	0.29129	N	0.879743	B	0.23249	0.082	B	0.22386	0.039	T	0.20739	-1.0266	6	.	.	.	-1.559	7.4128	0.27027	0.1374:0.7272:0.0:0.1354	.	82	B4DFA6	.	F	82	.	.	S	+	2	0	GRPEL2	148710687	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.587000	0.36622	0.866000	0.35629	0.655000	0.94253	TCT	.	.	.	none		0.478	GRPEL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252327.1	NM_152407		T	148730494	C	T	148730494	2	4	103	1	0	0	0	0	0	0	0	1	6814	912	32	2		2	GRPEL2	5	148730494	Silent	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	10087255	148730494	32184766	36	6566											
DSP	1832	hgsc.bcm.edu	37	chr6	7562996	7562996	+	Frame_Shift_Del	DEL	A	A	-																															actatcgctggcagctggacAaaatcaaagccgacctggta																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:7562996delA	ENST00000379802.3	+	5	1050	c.709delA	c.(709-711)aaafs	p.K237fs	DSP_ENST00000418664.2_Frame_Shift_Del_p.K237fs	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	237	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)		GCAGCTGGACAAAATCAAAGC	0.507																																					p.D236fs		Pindel	.											.	DSP	306	.	0			c.708delC						PASS	.						119	119	119					6																	7562996		2203	4300	6503	SO:0001589	frameshift_variant	1832	exon5			.	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.709delA	chr6.hg19:g.7562996delA	ENSP00000369129:p.Lys237fs	113.0	0.0	.		103.0	29.0	0.282	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Frame_Shift_Del	DEL	ENST00000379802.3	hg19	CCDS4501.1																																																																																			.	.	.	none		0.507	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		-	7562996	A	-	7562996	7	5	103	1	0	1	0	1	0	0	0	0	4783	131	5	0	727	0	DSP	6	7562996	Frame_Shift_Del	DEL	A	TCGA-B9-A44B-01A-11D-A25F-10		7562996	163552071	37	6567											
SLC17A3	10786	hgsc.bcm.edu	37	chr6	25850278	25850278	+	Frame_Shift_Del	DEL	A	A	-																															ctcaagctctgttcttacctAaaattgtggcaattttcctc																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:25850278delA	ENST00000360657.3	-	8	1172	c.887delT	c.(886-888)ttafs	p.L296fs	SLC17A3_ENST00000397060.4_Frame_Shift_Del_p.L374fs|SLC17A3_ENST00000361703.6_Frame_Shift_Del_p.L296fs			O00476	NPT4_HUMAN	solute carrier family 17 (organic anion transporter), member 3	296					drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|glucose-6-phosphate transport (GO:0015760)|ion transmembrane transport (GO:0034220)|organic acid transport (GO:0015849)|organic anion transport (GO:0015711)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|regulation of anion transport (GO:0044070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|efflux transmembrane transporter activity (GO:0015562)|organic anion transmembrane transporter activity (GO:0008514)|sodium:phosphate symporter activity (GO:0005436)|toxin transporter activity (GO:0019534)|urate transmembrane transporter activity (GO:0015143)|voltage-gated anion channel activity (GO:0008308)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)	20						GTTCTTACCTAAAATTGTGGC	0.408																																					p.L374fs		Atlas-Indel,Pindel	.											.	SLC17A3	95	.	0			c.1122delA						PASS	.						97	96	97					6																	25850278		2203	4300	6503	SO:0001589	frameshift_variant	10786	exon9			.	U90545	CCDS4566.2, CCDS47385.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124564	ENSG00000124564		"Solute carriers"	10931	protein-coding gene	gene with protein product		611034	"solute carrier family 17 (sodium phosphate), member 3"			9149941	Standard	NM_006632		Approved	NPT4	uc003nfk.4	O00476	OTTHUMG00000014412	ENST00000360657.3:c.887delT	chr6.hg19:g.25850278delA	ENSP00000353873:p.Leu296fs	95.0	0.0	0		99.0	41.0	0.414141	NM_001098486	B7WNJ5|B7Z511|Q8WWC7|Q9H533	Frame_Shift_Del	DEL	ENST00000360657.3	hg19	CCDS4566.2																																																																																			.	.	.	none		0.408	SLC17A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040070.2			-	25850278	A	-	25850278	7	5	103	1	0	1	0	1	0	0	0	0	14431	372	13	0	391	0	SLC17A3	6	25850278	Frame_Shift_Del	DEL	A	TCGA-B9-A44B-01A-11D-A25F-10	18287282	25850278	145264789	38	6568											
MDC1	9656	hgsc.bcm.edu	37	chr6	30681013	30681013	+	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	agtggcacctcttctggcagCtgaggaggcctcctctgtgg	5	10	14	12	0	3	1	0	1	3	0	4	2	4	2	3	5	1	3	3	5	0	1			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:30681013C>A	ENST00000376406.3	-	5	1353	c.706G>T	c.(706-708)Gct>Tct	p.A236S	MDC1-AS1_ENST00000442150.1_RNA|MDC1_ENST00000494654.1_5'Flank|MDC1_ENST00000376405.2_Missense_Mutation_p.A236S	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	236	Required for nuclear localization (NLS1).				DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						CTTCTGGCAGCTGAGGAGGCC	0.537								Other conserved DNA damage response genes																													p.A236S		Atlas-SNP	.											.	MDC1	218	.	0			c.G706T						PASS	.						90	99	96					6																	30681013		1509	2708	4217	SO:0001583	missense	9656	exon5			TGGCAGCTGAGGA	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.706G>T	chr6.hg19:g.30681013C>A	ENSP00000365588:p.Ala236Ser	126.0	0.0	.		126.0	7.0	.	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Missense_Mutation	SNP	ENST00000376406.3	hg19	CCDS34384.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.58|10.58	1.390558|1.390558	0.25118|0.25118	.|.	.|.	ENSG00000137337|ENSG00000137337	ENST00000376406;ENST00000376405;ENST00000429610;ENST00000422104;ENST00000435797|ENST00000452213	T;T|.	0.04119|.	3.79;3.7|.	5.31|5.31	-0.775|-0.775	0.10988|0.10988	.|.	0.429453|.	0.17269|.	N|.	0.180468|.	T|T	0.08802|0.08802	0.0218|0.0218	L|L	0.35723|0.35723	1.085|1.085	0.09310|0.09310	N|N	1|1	P;B;B|.	0.36392|.	0.551;0.129;0.261|.	B;B;B|.	0.31751|.	0.135;0.082;0.063|.	T|T	0.35624|0.35624	-0.9781|-0.9781	10|6	0.41790|0.30854	T|T	0.15|0.27	-1.711|-1.711	0.5485|0.5485	0.00658|0.00658	0.2846:0.3351:0.1383:0.242|0.2846:0.3351:0.1383:0.242	.|.	236;108;236|.	Q14676-2;B4DYH4;Q14676|.	.;.;MDC1_HUMAN|.	S|I	236;236;236;108;236|235	ENSP00000365588:A236S;ENSP00000365587:A236S|.	ENSP00000365587:A236S|ENSP00000404936:S235I	A|S	-|-	1|2	0|0	MDC1|MDC1	30788992|30788992	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	0.005000|0.005000	0.13129|0.13129	-0.368000|-0.368000	0.08040|0.08040	-0.844000|-0.844000	0.03045|0.03045	GCT|AGC	.	.	.	none		0.537	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641		A	30681013	C	A	30681013	3	1	103	1	0	0	0	0	1	0	0	0	9410	797	28	4	5607	4	MDC1	6	30681013	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	4830735	30681013	140434054	39	6569											
TCP11	6954	hgsc.bcm.edu	37	chr6	35086064	35086064	+	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	tatcaaacagactccactttTgtttccagtgcctgggctgg	8	13	9	11	0	1	1	1	0	0	1	3	1	3	1	3	2	2	2	3	2	2	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:35086064T>G	ENST00000512012.1	-	9	1650	c.1494A>C	c.(1492-1494)acA>acC	p.T498T	TCP11_ENST00000244645.3_Silent_p.T436T|TCP11_ENST00000373974.4_Silent_p.T465T|TCP11_ENST00000412155.2_Silent_p.T460T|TCP11_ENST00000418521.2_Silent_p.T435T|TCP11_ENST00000373979.2_Silent_p.T436T|TCP11_ENST00000444780.2_Silent_p.T506T|TCP11_ENST00000311875.5_Silent_p.T511T			Q8WWU5	TCP11_HUMAN	t-complex 11, testis-specific	498					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				breast(1)|kidney(5)|large_intestine(3)|lung(10)|ovary(3)|prostate(1)|skin(4)	27						ACTCCACTTTTGTTTCCAGTG	0.498																																					p.T511T		Atlas-SNP	.											.	TCP11	94	.	0			c.A1533C						PASS	.						133	135	134					6																	35086064		2203	4300	6503	SO:0001819	synonymous_variant	6954	exon10			CACTTTTGTTTCC		CCDS4799.1, CCDS47413.1, CCDS59015.1, CCDS59016.1, CCDS59017.1, CCDS59018.1	6p21.31	2012-09-20	2012-09-20		ENSG00000124678	ENSG00000124678			11658	protein-coding gene	gene with protein product	"fertilization-promoting peptide receptor"	186982	"t-complex 11 (a murine tcp homolog)", "t-complex 11 homolog (mouse)"	D6S230E		1427894, 11756566, 21597245	Standard	NM_001093728		Approved	KIAA0229, FPPR	uc003okd.2	Q8WWU5	OTTHUMG00000014560	ENST00000512012.1:c.1494A>C	chr6.hg19:g.35086064T>G		179.0	0.0	.		202.0	87.0	.	NM_001093728	B2RCE9|B3KQ27|B7Z7B5|B7Z7G1|B7Z7H4|B7Z7S8|E7EP29|J3KNG1|Q8NF85|Q9NQZ9|Q9NR39	Silent	SNP	ENST00000512012.1	hg19		.	.	.	.	.	.	.	.	.	.	T	11.91	1.779912	0.31502	.	.	ENSG00000124678	ENST00000502480	.	.	.	5.32	-1.75	0.08031	.	.	.	.	.	T	0.28200	0.0696	.	.	.	0.38093	D	0.937032	.	.	.	.	.	.	T	0.22765	-1.0207	4	.	.	.	-4.2485	6.0586	0.19824	0.0:0.1544:0.2928:0.5527	.	.	.	.	Q	240	.	.	K	-	1	0	TCP11	35194042	0.000000	0.05858	0.064000	0.19789	0.809000	0.45718	-1.209000	0.03002	-0.281000	0.09141	0.460000	0.39030	AAA	.	.	.	none		0.498	TCP11-014	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000370354.1	NM_001093728		G	35086064	T	G	35086064	2	3	103	1	0	0	0	0	0	0	0	1	15725	1799	63	5		5	TCP11	6	35086064	Silent	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	4405051	35086064	136029003	40	6570											
KLC4	89953	hgsc.bcm.edu	37	chr6	43041642	43041643	+	Frame_Shift_Ins	INS	-	-	CAACACGA																															tccgttttccattgtagcagINScaacatgaagcgagcagcct																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:43041642_43041643insCAACACGA	ENST00000394056.2	+	16	2243_2244	c.1748_1749insCAACACGA	c.(1747-1752)agcaacfs	p.-584fs	PTK7_ENST00000230419.4_5'Flank|KLC4_ENST00000453940.2_Frame_Shift_Ins_p.-507fs|KLC4_ENST00000479388.1_Frame_Shift_Ins_p.-584fs|PTK7_ENST00000349241.2_5'Flank|RP11-387M24.5_ENST00000606123.1_RNA|PTK7_ENST00000352931.2_5'Flank|KLC4_ENST00000347162.5_Frame_Shift_Ins_p.-584fs|PTK7_ENST00000481273.1_5'Flank|KLC4_ENST00000394058.1_Frame_Shift_Ins_p.-584fs|PTK7_ENST00000345201.2_5'Flank|PTK7_ENST00000471863.1_5'Flank|PTK7_ENST00000476760.1_5'Flank|KLC4_ENST00000259708.3_Frame_Shift_Ins_p.-602fs			Q9NSK0	KLC4_HUMAN	kinesin light chain 4							cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			endometrium(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(4)	23			all cancers(41;0.00169)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0376)|KIRC - Kidney renal clear cell carcinoma(2;0.0453)			CATTGTAGCAGCAACATGAAGC	0.54																																					p.S601fs		Atlas-Indel,Pindel	.											.	KLC4	89	.	0			c.1802_1803insCAACACGA						PASS	.																																			SO:0001589	frameshift_variant	89953	exon15			.	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	Exception_encountered	chr6.hg19:g.43041642_43041643insCAACACGA	ENSP00000377620:p.Asn584fs	147.0	0.0	0		123.0	21.0	0.170732	NM_201523	B3KNY4|B3KPI3|B3KSQ3|B4DME9|Q66K28|Q96EG6	Frame_Shift_Ins	INS	ENST00000394056.2	hg19	CCDS4883.1																																																																																			.	.	.	none		0.54	KLC4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040579.2	NM_138343		CAACACGA	43041643	-	CAACACGA	43041642	7	5	103	1	0	1	1	0	0	0	0	0	8343	971	34	0	1929	0	KLC4	6	43041642	Frame_Shift_Ins	INS	-	TCGA-B9-A44B-01A-11D-A25F-10	7955578	43041642	128073425	41	6571	71	2									
KLC4	89953	hgsc.bcm.edu	37	chr6	43041648	43041648	+	Missense_Mutation	SNP	T	T	C																															tttccattgtagcagcaacaTgaagcgagcagcctccttga																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:43041648T>C	ENST00000394056.2	+	16	2249	c.1754T>C	c.(1753-1755)aTg>aCg	p.M585T	PTK7_ENST00000230419.4_5'Flank|KLC4_ENST00000453940.2_Missense_Mutation_p.M508T|KLC4_ENST00000479388.1_Missense_Mutation_p.M585T|PTK7_ENST00000349241.2_5'Flank|RP11-387M24.5_ENST00000606123.1_RNA|PTK7_ENST00000352931.2_5'Flank|KLC4_ENST00000347162.5_Missense_Mutation_p.M585T|PTK7_ENST00000481273.1_5'Flank|KLC4_ENST00000394058.1_Missense_Mutation_p.M585T|PTK7_ENST00000345201.2_5'Flank|PTK7_ENST00000471863.1_5'Flank|PTK7_ENST00000476760.1_5'Flank|KLC4_ENST00000259708.3_Missense_Mutation_p.M603T			Q9NSK0	KLC4_HUMAN	kinesin light chain 4	585						cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			endometrium(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(4)	23			all cancers(41;0.00169)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0376)|KIRC - Kidney renal clear cell carcinoma(2;0.0453)			AGCAGCAACATGAAGCGAGCA	0.537																																					p.M603T		Atlas-SNP	.											.	KLC4	89	.	0			c.T1808C						PASS	.						138	119	125					6																	43041648		2203	4300	6503	SO:0001583	missense	89953	exon15			GCAACATGAAGCG	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.1754T>C	chr6.hg19:g.43041648T>C	ENSP00000377620:p.Met585Thr	149.0	0.0	.		128.0	40.0	.	NM_201523	B3KNY4|B3KPI3|B3KSQ3|B4DME9|Q66K28|Q96EG6	Missense_Mutation	SNP	ENST00000394056.2	hg19	CCDS4883.1	.	.	.	.	.	.	.	.	.	.	T	15.14	2.745697	0.49151	.	.	ENSG00000137171	ENST00000347162;ENST00000453940;ENST00000259708;ENST00000479388;ENST00000394056;ENST00000394058	D;D;D;D;D;D	0.85088	-1.86;-1.94;-1.87;-1.86;-1.86;-1.86	5.44	5.44	0.79542	.	0.000000	0.64402	D	0.000001	D	0.85141	0.5629	M	0.73217	2.22	0.53688	D	0.999979	P;D;P	0.53462	0.791;0.96;0.717	B;P;P	0.61397	0.212;0.888;0.599	D	0.83770	0.0219	10	0.11794	T	0.64	-11.1696	11.8821	0.52581	0.0:0.0:0.0:1.0	.	508;603;585	B4DME9;Q9NSK0-3;Q9NSK0	.;.;KLC4_HUMAN	T	585;508;603;585;585;585	ENSP00000340221:M585T;ENSP00000395806:M508T;ENSP00000259708:M603T;ENSP00000418031:M585T;ENSP00000377620:M585T;ENSP00000377622:M585T	ENSP00000259708:M603T	M	+	2	0	KLC4	43149626	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.911000	0.69939	2.054000	0.61138	0.459000	0.35465	ATG	.	.	.	none		0.537	KLC4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040579.2	NM_138343		C	43041648	T	C	43041648	3	2	103	1	0	0	0	0	1	0	0	0	8343	1464	51	3	1935	3	KLC4	6	43041648	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	6	43041648	128073419	42	6572	71	2									
YIPF3	25844	hgsc.bcm.edu	37	chr6	43480515	43480515	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaccatgcgcagtgtggacAgtccacccaccaacagccag	11	6	9	15	1	0	0	0	0	0	0	1	1	1	1	5	1	4	1	5	1	2	1			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:43480515A>G	ENST00000372422.2	-	7	946	c.764T>C	c.(763-765)cTg>cCg	p.L255P	YIPF3_ENST00000506469.1_Missense_Mutation_p.L261P|LRRC73_ENST00000372441.1_5'Flank	NM_015388.3	NP_056203.2	Q9GZM5	YIPF3_HUMAN	Yip1 domain family, member 3	255					cell differentiation (GO:0030154)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)				large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)	9	all_cancers(18;3.79e-05)|Lung NSC(15;0.00217)|all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00736)|OV - Ovarian serous cystadenocarcinoma(102;0.0711)			CAGTGTGGACAGTCCACCCAC	0.567																																					p.L255P		Atlas-SNP	.											.	YIPF3	20	.	0			c.T764C						PASS	.						89	76	81					6																	43480515		2203	4300	6503	SO:0001583	missense	25844	exon7			GTGGACAGTCCAC	AK000946	CCDS4899.1	6p21.1	2009-10-06	2005-07-04	2005-07-04	ENSG00000137207	ENSG00000137207		"Yip1 domain family"	21023	protein-coding gene	gene with protein product		609775	"chromosome 6 open reading frame 109"	C6orf109			Standard	NM_015388		Approved	DKFZp566C243, KLIP1, dJ337H4.3, FinGER3	uc003ovl.2	Q9GZM5	OTTHUMG00000014738	ENST00000372422.2:c.764T>C	chr6.hg19:g.43480515A>G	ENSP00000361499:p.Leu255Pro	165.0	0.0	.		189.0	75.0	.	NM_015388	Q5JTD2|Q6FI85|Q8NI57|Q9NWE3|Q9Y3U9	Missense_Mutation	SNP	ENST00000372422.2	hg19	CCDS4899.1	.	.	.	.	.	.	.	.	.	.	A	17.50	3.404720	0.62288	.	.	ENSG00000137207	ENST00000372422;ENST00000506469;ENST00000503972	T;T;T	0.53857	0.61;0.6;0.71	5.27	5.27	0.74061	.	0.000000	0.64402	D	0.000001	T	0.58680	0.2139	L	0.49126	1.545	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.87578	0.998;0.997;0.998	T	0.59653	-0.7414	10	0.41790	T	0.15	-11.2654	15.19	0.73035	1.0:0.0:0.0:0.0	.	261;220;255	E7EQR8;Q5JTD5;Q9GZM5	.;.;YIPF3_HUMAN	P	255;261;221	ENSP00000361499:L255P;ENSP00000425494:L261P;ENSP00000421461:L221P	ENSP00000361499:L255P	L	-	2	0	YIPF3	43588493	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	8.982000	0.93471	1.996000	0.58369	0.460000	0.39030	CTG	.	.	.	none		0.567	YIPF3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040639.2	NM_015388		G	43480515	A	G	43480515	3	3	103	1	0	0	0	0	1	0	0	0	17491	188	7	3	300	3	YIPF3	6	43480515	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	438867	43480515	127634552	43	6573											
SNAP91	9892	hgsc.bcm.edu	37	chr6	84371294	84371294	+	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	ttcattcaaatatctactatAgcgccttatgaaggtagaca	14	13	6	8	1	3	2	2	1	1	1	3	2	3	2	1	1	2	1	1	1	8	8			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:84371294A>T	ENST00000439399.2	-	5	695	c.379T>A	c.(379-381)Tat>Aat	p.Y127N	SNAP91_ENST00000195649.6_Missense_Mutation_p.Y127N|SNAP91_ENST00000520302.1_Missense_Mutation_p.Y127N|SNAP91_ENST00000369694.2_Missense_Mutation_p.Y127N|SNAP91_ENST00000521485.1_Missense_Mutation_p.Y127N|SNAP91_ENST00000428679.2_Missense_Mutation_p.Y127N|SNAP91_ENST00000437520.1_Missense_Mutation_p.Y127N|SNAP91_ENST00000521743.1_Missense_Mutation_p.Y127N|SNAP91_ENST00000520213.1_Missense_Mutation_p.Y127N	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	127	ENTH. {ECO:0000255|PROSITE- ProRule:PRU00243}.				clathrin coat assembly (GO:0048268)|protein transport (GO:0015031)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		TATCTACTATAGCGCCTTATG	0.328																																					p.Y127N		Atlas-SNP	.											.	SNAP91	199	.	0			c.T379A						PASS	.						56	54	54					6																	84371294		1805	4074	5879	SO:0001583	missense	9892	exon5			TACTATAGCGCCT	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.379T>A	chr6.hg19:g.84371294A>T	ENSP00000400459:p.Tyr127Asn	95.0	0.0	.		100.0	59.0	.	NM_001242794	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Missense_Mutation	SNP	ENST00000439399.2	hg19	CCDS47455.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.551977	0.86127	.	.	ENSG00000065609	ENST00000521485;ENST00000369694;ENST00000439399;ENST00000195649;ENST00000428679;ENST00000437520;ENST00000520302;ENST00000521743;ENST00000520213;ENST00000521931;ENST00000519779;ENST00000518309;ENST00000369690	T;T;T;T;T;T;T;T;T;T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68;-0.68	5.13	5.13	0.70059	ENTH/VHS (2);ANTH (1);Epsin-like, N-terminal (2);	0.000000	0.85682	D	0.000000	D	0.87358	0.6157	H	0.96547	3.84	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.999;0.996;0.999	D	0.91513	0.5228	10	0.87932	D	0	-8.3087	15.2297	0.73378	1.0:0.0:0.0:0.0	.	127;127;127;127	O60641-3;E5RI02;O60641;E1P549	.;.;AP180_HUMAN;.	N	127	ENSP00000429776:Y127N;ENSP00000358708:Y127N;ENSP00000400459:Y127N;ENSP00000195649:Y127N;ENSP00000412492:Y127N;ENSP00000413277:Y127N;ENSP00000428511:Y127N;ENSP00000428215:Y127N;ENSP00000428026:Y127N;ENSP00000430071:Y127N;ENSP00000429429:Y127N;ENSP00000430441:Y127N;ENSP00000358704:Y127N	ENSP00000195649:Y127N	Y	-	1	0	SNAP91	84428013	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.210000	0.95106	2.056000	0.61249	0.460000	0.39030	TAT	.	.	.	none		0.328	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1			T	84371294	A	T	84371294	3	4	103	1	0	0	0	0	1	0	0	0	14846	420	15	5	2440	5	SNAP91	6	84371294	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	40890779	84371294	86743773	44	6574											
SPACA1	81833	hgsc.bcm.edu	37	chr6	88775941	88775941	+	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	gggggcaaaagcctctacacCtgaggtacaatccgagcaga	13	5	12	11	1	1	2	0	1	1	1	2	3	2	2	3	3	4	3	3	3	5	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:88775941C>A	ENST00000237201.1	+	7	890	c.773C>A	c.(772-774)cCt>cAt	p.P258H	SPACA1_ENST00000462690.1_3'UTR	NM_030960.2	NP_112222.1	Q9HBV2	SACA1_HUMAN	sperm acrosome associated 1	258					acrosome assembly (GO:0001675)	acrosomal membrane (GO:0002080)|integral component of membrane (GO:0016021)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	20		all_cancers(76;8.24e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;4.11e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.00011)		BRCA - Breast invasive adenocarcinoma(108;0.11)		GCCTCTACACCTGAGGTACAA	0.413																																					p.P258H		Atlas-SNP	.											.	SPACA1	49	.	0			c.C773A						PASS	.						100	109	106					6																	88775941		2203	4300	6503	SO:0001583	missense	81833	exon7			CTACACCTGAGGT	AF203447	CCDS5014.1	6q15	2012-09-20			ENSG00000118434	ENSG00000118434			14967	protein-coding gene	gene with protein product		612739					Standard	NM_030960		Approved	SAMP32	uc003pmn.3	Q9HBV2	OTTHUMG00000015183	ENST00000237201.1:c.773C>A	chr6.hg19:g.88775941C>A	ENSP00000237201:p.Pro258His	67.0	0.0	.		39.0	14.0	.	NM_030960		Missense_Mutation	SNP	ENST00000237201.1	hg19	CCDS5014.1	.	.	.	.	.	.	.	.	.	.	C	11.76	1.734402	0.30774	.	.	ENSG00000118434	ENST00000237201	T	0.30448	1.53	4.81	4.81	0.61882	.	0.410909	0.23356	N	0.049061	T	0.16171	0.0389	N	0.22421	0.69	0.09310	N	0.999999	P	0.49447	0.924	P	0.47941	0.562	T	0.03545	-1.1026	10	0.66056	D	0.02	-5.1836	13.254	0.60068	0.0:1.0:0.0:0.0	.	258	Q9HBV2	SACA1_HUMAN	H	258	ENSP00000237201:P258H	ENSP00000237201:P258H	P	+	2	0	SPACA1	88832660	0.530000	0.26330	0.533000	0.28001	0.013000	0.08279	1.999000	0.40806	2.507000	0.84556	0.467000	0.42956	CCT	.	.	.	none		0.413	SPACA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041459.1			A	88775941	C	A	88775941	3	1	103	1	0	0	0	0	1	0	0	0	14985	681	24	4	799	4	SPACA1	6	88775941	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	4404647	88775941	82339126	45	6575											
HACE1	57531	hgsc.bcm.edu	37	chr6	105298839	105298839	+	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	cgaatgcataattgacatcaAattttgaatttgatagtagt	15	15	7	4	1	1	3	1	3	0	0	1	4	1	3	0	0	1	2	0	0	6	7			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:105298839A>T	ENST00000262903.4	-	3	440	c.164T>A	c.(163-165)tTt>tAt	p.F55Y	HACE1_ENST00000369125.2_Missense_Mutation_p.F55Y	NM_020771.3	NP_065822.2	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	55					cell cycle (GO:0007049)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|Rac protein signal transduction (GO:0016601)|regulation of cell migration (GO:0030334)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Rab GTPase binding (GO:0017137)|Rac GTPase binding (GO:0048365)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	44		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)		ATTGACATCAAATTTTGAATT	0.299																																					p.F55Y		Atlas-SNP	.											.	HACE1	96	.	0			c.T164A						PASS	.						152	157	156					6																	105298839		2203	4300	6503	SO:0001583	missense	57531	exon3			ACATCAAATTTTG	BC034982	CCDS5050.1	6q21	2013-01-10	2012-02-23		ENSG00000085382	ENSG00000085382		"Ankyrin repeat domain containing"	21033	protein-coding gene	gene with protein product		610876				10718198	Standard	NM_020771		Approved	KIAA1320	uc003pqu.1	Q8IYU2	OTTHUMG00000015287	ENST00000262903.4:c.164T>A	chr6.hg19:g.105298839A>T	ENSP00000262903:p.Phe55Tyr	128.0	0.0	.		105.0	61.0	.	NM_020771	A8K6U5|B3KY89|B4DFM6|B4DTQ4|B7Z9X6|E9PGP0|Q5VU99|Q5VUA0|Q8ND12|Q9P2M6	Missense_Mutation	SNP	ENST00000262903.4	hg19	CCDS5050.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.488630	0.84854	.	.	ENSG00000085382	ENST00000262903;ENST00000369125;ENST00000519645;ENST00000524020	T;T;T;T	0.72282	-0.64;-0.64;-0.09;1.51	5.97	5.97	0.96955	Ankyrin repeat-containing domain (2);	0.000000	0.85682	D	0.000000	T	0.68540	0.3012	N	0.21545	0.675	0.80722	D	1	D;D	0.53885	0.963;0.963	D;D	0.69824	0.966;0.966	T	0.73538	-0.3951	10	0.51188	T	0.08	.	15.4434	0.75208	1.0:0.0:0.0:0.0	.	55;55	E9PGP0;Q8IYU2	.;HACE1_HUMAN	Y	55;55;55;21	ENSP00000262903:F55Y;ENSP00000358121:F55Y;ENSP00000429765:F55Y;ENSP00000427901:F21Y	ENSP00000262903:F55Y	F	-	2	0	HACE1	105405532	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.328000	0.90014	2.288000	0.76882	0.533000	0.62120	TTT	.	.	.	none		0.299	HACE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041643.2	XM_045095		T	105298839	A	T	105298839	3	4	103	1	0	0	0	0	1	0	0	0	6947	14	1	5	2653	5	HACE1	6	105298839	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	16522898	105298839	65816228	46	6576											
SOBP	55084	hgsc.bcm.edu	37	chr6	107827527	107827527	+	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	cacaggctattcagggcttgCcactggaaatggactcagtg	10	9	12	10	0	2	0	2	0	0	0	2	2	2	2	1	4	1	2	1	4	2	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:107827527C>A	ENST00000317357.5	+	3	976	c.317C>A	c.(316-318)gCc>gAc	p.A106D		NM_018013.3	NP_060483.3			sine oculis binding protein homolog (Drosophila)											endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	26		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)		TCAGGGCTTGCCACTGGAAAT	0.413																																					p.A106D		Atlas-SNP	.											.	SOBP	53	.	0			c.C317A						PASS	.						193	185	188					6																	107827527		1908	4136	6044	SO:0001583	missense	55084	exon3			GGCTTGCCACTGG	AK001021	CCDS43488.1	6q21	2007-03-15			ENSG00000112320	ENSG00000112320			29256	protein-coding gene	gene with protein product		613667					Standard	NM_018013		Approved	FLJ10159	uc003prx.3	A7XYQ1	OTTHUMG00000015312	ENST00000317357.5:c.317C>A	chr6.hg19:g.107827527C>A	ENSP00000318900:p.Ala106Asp	96.0	0.0	.		89.0	16.0	.	NM_018013		Missense_Mutation	SNP	ENST00000317357.5	hg19	CCDS43488.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.145200	0.77888	.	.	ENSG00000112320	ENST00000317357	T	0.11277	2.79	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.07413	0.0187	N	0.08118	0	0.58432	D	0.999996	D	0.53312	0.959	P	0.52957	0.714	T	0.40720	-0.9548	10	0.66056	D	0.02	-11.9919	19.1981	0.93698	0.0:1.0:0.0:0.0	.	106	A7XYQ1	SOBP_HUMAN	D	106	ENSP00000318900:A106D	ENSP00000318900:A106D	A	+	2	0	SOBP	107934220	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.422000	0.66453	2.615000	0.88500	0.655000	0.94253	GCC	.	.	.	none		0.413	SOBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041693.2	NM_018013		A	107827527	C	A	107827527	3	1	103	1	0	0	0	0	1	0	0	0	14925	739	26	4	327	4	SOBP	6	107827527	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	2528688	107827527	63287540	47	6577											
NUS1	116150	hgsc.bcm.edu	37	chr6	118015319	118015319	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agagacccacagatttggatGtagatacgttagccagttta	13	11	10	7	1	0	3	0	0	0	3	0	5	0	4	2	1	2	3	2	1	4	6			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:118015319G>A	ENST00000368494.3	+	3	836	c.667G>A	c.(667-669)Gta>Ata	p.V223I		NM_138459.3	NP_612468.1	Q96E22	NGBR_HUMAN	nuclear undecaprenyl pyrophosphate synthase 1 homolog (S. cerevisiae)	223					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|intracellular cholesterol transport (GO:0032367)|protein glycosylation (GO:0006486)|sterol homeostasis (GO:0055092)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring alkyl or aryl (other than methyl) groups (GO:0016765)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(1)|prostate(2)	8		all_cancers(87;0.0395)|all_epithelial(87;0.0301)		GBM - Glioblastoma multiforme(226;0.02)|OV - Ovarian serous cystadenocarcinoma(136;0.115)|all cancers(137;0.146)		AGATTTGGATGTAGATACGTT	0.373																																					p.V223I		Atlas-SNP	.											.	NUS1	15	.	0			c.G667A						PASS	.						89	91	90					6																	118015319		2203	4300	6503	SO:0001583	missense	116150	exon3			TTGGATGTAGATA	BC013026	CCDS5118.1	6q22.1	2012-12-13	2006-11-24	2006-11-24	ENSG00000153989	ENSG00000153989			21042	protein-coding gene	gene with protein product	"Nogo-B receptor", "transport and golgi organization 14 homolog (Drosophila)"	610463	"chromosome 6 open reading frame 68"	C6orf68			Standard	NM_138459		Approved	MGC7199, NgBR, TANGO14	uc003pxw.3	Q96E22	OTTHUMG00000015458	ENST00000368494.3:c.667G>A	chr6.hg19:g.118015319G>A	ENSP00000357480:p.Val223Ile	125.0	0.0	.		87.0	50.0	.	NM_138459	B2RWQ4|O00251	Missense_Mutation	SNP	ENST00000368494.3	hg19	CCDS5118.1	.	.	.	.	.	.	.	.	.	.	G	14.49	2.550972	0.45383	.	.	ENSG00000153989	ENST00000368494	T	0.29397	1.57	5.1	5.1	0.69264	.	0.115570	0.64402	D	0.000015	T	0.16128	0.0388	L	0.47078	1.49	0.58432	D	0.999992	P	0.36086	0.536	B	0.34873	0.191	T	0.02713	-1.1120	10	0.37606	T	0.19	-0.3662	13.2505	0.60050	0.0769:0.0:0.9231:0.0	.	223	Q96E22	NGBR_HUMAN	I	223	ENSP00000357480:V223I	ENSP00000357480:V223I	V	+	1	0	NUS1	118122012	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.487000	0.60293	2.537000	0.85549	0.650000	0.86243	GTA	.	.	.	none		0.373	NUS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041989.1	NM_138459		A	118015319	G	A	118015319	3	1	103	1	0	0	0	0	1	0	0	0	10784	1377	48	2	677	2	NUS1	6	118015319	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	10187792	118015319	53099748	48	6578											
GPR126	57211	hgsc.bcm.edu	37	chr6	142691578	142691578	+	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	ttgaataatgcattacctgtCaaagaaaaagaagacatttt	18	12	6	5	0	1	4	1	1	0	3	1	4	1	4	1	0	2	1	1	0	7	5			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:142691578C>T	ENST00000230173.6	+	4	1193	c.717C>T	c.(715-717)gtC>gtT	p.V239V	GPR126_ENST00000367609.3_Silent_p.V239V|GPR126_ENST00000545477.1_Intron|GPR126_ENST00000367608.2_Silent_p.V239V|GPR126_ENST00000296932.8_Silent_p.V239V	NM_020455.5	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126	239	Pentaxin.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(12)|lung(10)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		CATTACCTGTCAAAGAAAAAG	0.353																																					p.V239V		Atlas-SNP	.											.	GPR126	192	.	0			c.C717T						PASS	.						64	63	63					6																	142691578		1828	4081	5909	SO:0001819	synonymous_variant	57211	exon4			ACCTGTCAAAGAA	AK027843	CCDS47489.1, CCDS47490.1, CCDS47491.1, CCDS55064.1	6q23.1-q24.3	2014-08-08			ENSG00000112414	ENSG00000112414		"-", "GPCR / Class B : Orphans"	13841	protein-coding gene	gene with protein product		612243				12565841	Standard	NM_001032395		Approved	FLJ14937	uc010khe.3	Q86SQ4	OTTHUMG00000015709	ENST00000230173.6:c.717C>T	chr6.hg19:g.142691578C>T		65.0	0.0	.		38.0	8.0	.	NM_198569	Q5TGN7|Q6DHZ4|Q6F3F5|Q6F3F6|Q6F3F7|Q6F3F8|Q6MZU7|Q8IXA4|Q8NC14|Q96JW0	Silent	SNP	ENST00000230173.6	hg19	CCDS47490.1																																																																																			.	.	.	none		0.353	GPR126-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042487.2			T	142691578	C	T	142691578	2	4	103	1	0	0	0	0	0	0	0	1	6647	813	29	2		2	GPR126	6	142691578	Silent	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	24676259	142691578	28423489	49	6579											
IGF2R	3482	hgsc.bcm.edu	37	chr6	160445676	160445676	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgatcaagcttagtggtgccTacttggtggatgactccgat	8	13	12	8	1	1	2	1	2	0	0	2	4	2	3	2	3	3	1	2	3	3	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr6:160445676T>C	ENST00000356956.1	+	5	734	c.586T>C	c.(586-588)Tac>Cac	p.Y196H		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	196					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)	TAGTGGTGCCTACTTGGTGGA	0.473																																					p.Y196H		Atlas-SNP	.											.	IGF2R	251	.	0			c.T586C						PASS	.						277	241	253					6																	160445676		2203	4300	6503	SO:0001583	missense	3482	exon5			GGTGCCTACTTGG	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.586T>C	chr6.hg19:g.160445676T>C	ENSP00000349437:p.Tyr196His	198.0	0.0	.		172.0	47.0	.	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	hg19	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	T	16.39	3.109386	0.56398	.	.	ENSG00000197081	ENST00000356956	T	0.02682	4.2	5.47	5.47	0.80525	Mannose-6-phosphate receptor, binding (1);	0.232876	0.45361	D	0.000378	T	0.08891	0.0220	M	0.77103	2.36	0.39897	D	0.97384	D	0.89917	1.0	D	0.91635	0.999	T	0.21109	-1.0255	10	0.30854	T	0.27	-3.4455	15.5981	0.76602	0.0:0.0:0.0:1.0	.	196	P11717	MPRI_HUMAN	H	196	ENSP00000349437:Y196H	ENSP00000349437:Y196H	Y	+	1	0	IGF2R	160365666	1.000000	0.71417	0.672000	0.29872	0.761000	0.43186	4.495000	0.60353	2.077000	0.62373	0.374000	0.22700	TAC	.	.	.	none		0.473	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		C	160445676	T	C	160445676	3	2	103	1	0	0	0	0	1	0	0	0	7583	1522	53	3	604	3	IGF2R	6	160445676	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	17754098	160445676	10669391	50	6580											
NEUROD6	63974	hgsc.bcm.edu	37	chr7	31378439	31378439	+	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	ctcttgccgattctcagaatTtcagaaagtgcccagatgta	11	12	8	10	1	3	3	2	0	2	3	4	4	3	3	2	0	2	1	2	0	3	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:31378439T>A	ENST00000297142.3	-	2	766	c.444A>T	c.(442-444)gaA>gaT	p.E148D		NM_022728.2	NP_073565.2	Q96NK8	NDF6_HUMAN	neuronal differentiation 6	148					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						TTCTCAGAATTTCAGAAAGTG	0.438																																					p.E148D		Atlas-SNP	.											.	NEUROD6	84	.	0			c.A444T						PASS	.						70	72	71					7																	31378439		2203	4300	6503	SO:0001583	missense	63974	exon2			CAGAATTTCAGAA	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.444A>T	chr7.hg19:g.31378439T>A	ENSP00000297142:p.Glu148Asp	81.0	0.0	.		96.0	36.0	.	NM_022728	Q548T9|Q9H3H6	Missense_Mutation	SNP	ENST00000297142.3	hg19	CCDS5434.1	.	.	.	.	.	.	.	.	.	.	T	14.63	2.594250	0.46214	.	.	ENSG00000164600	ENST00000297142	D	0.88509	-2.39	5.25	2.52	0.30459	Helix-loop-helix DNA-binding (3);	0.000000	0.85682	D	0.000000	D	0.85383	0.5684	N	0.05467	-0.045	0.53005	D	0.999961	D	0.58970	0.984	D	0.65443	0.935	D	0.83701	0.0182	10	0.39692	T	0.17	-17.2321	10.2375	0.43292	0.0:0.1596:0.0:0.8404	.	148	Q96NK8	NDF6_HUMAN	D	148	ENSP00000297142:E148D	ENSP00000297142:E148D	E	-	3	2	NEUROD6	31344964	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.915000	0.39976	0.841000	0.35020	0.528000	0.53228	GAA	.	.	.	none		0.438	NEUROD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215050.1	NM_022728		A	31378439	T	A	31378439	3	1	103	1	0	0	0	0	1	0	0	0	10358	1838	64	5	573	5	NEUROD6	7	31378439	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10		31378439	127760224	51	6581											
CCDC129	223075	hgsc.bcm.edu	37	chr7	31682718	31682718	+	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	cacgtcacagaaatgcaggaCagttttgtgaggcctgaggg	11	8	14	8	1	1	3	1	2	0	1	1	4	1	4	1	3	1	2	1	3	1	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:31682718C>A	ENST00000407970.3	+	11	1772	c.1734C>A	c.(1732-1734)gaC>gaA	p.D578E	CCDC129_ENST00000451887.2_Missense_Mutation_p.D604E|CCDC129_ENST00000319386.3_Missense_Mutation_p.D430E|CCDC129_ENST00000409210.1_Missense_Mutation_p.D486E	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	578										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						AAATGCAGGACAGTTTTGTGA	0.488																																					p.D604E		Atlas-SNP	.											.	CCDC129	127	.	0			c.C1812A						PASS	.						173	173	173					7																	31682718		2203	4300	6503	SO:0001583	missense	223075	exon11			GCAGGACAGTTTT	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.1734C>A	chr7.hg19:g.31682718C>A	ENSP00000384416:p.Asp578Glu	136.0	0.0	.		138.0	61.0	.	NM_001257968	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Missense_Mutation	SNP	ENST00000407970.3	hg19	CCDS5435.2	.	.	.	.	.	.	.	.	.	.	C	14.17	2.456804	0.43634	.	.	ENSG00000180347	ENST00000319386;ENST00000407970;ENST00000451887;ENST00000538406;ENST00000409210	T;T;T;T	0.25414	1.8;2.12;2.1;1.86	5.93	-11.6	0.00059	.	0.467692	0.20346	N	0.094142	T	0.15219	0.0367	M	0.69823	2.125	0.09310	N	1	P;P;P;P	0.41450	0.75;0.565;0.565;0.734	B;B;B;B	0.39503	0.168;0.107;0.107;0.301	T	0.00216	-1.1910	10	0.38643	T	0.18	-37.2348	1.7051	0.02880	0.2799:0.2778:0.079:0.3633	.	604;588;578;430	F5H3V5;F5H2J8;Q6ZRS4;Q6ZRS4-2	.;.;CC129_HUMAN;.	E	430;578;604;588;486	ENSP00000313062:D430E;ENSP00000384416:D578E;ENSP00000395835:D604E;ENSP00000387214:D486E	ENSP00000313062:D430E	D	+	3	2	CCDC129	31649243	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.334000	0.02665	-2.216000	0.00732	-1.094000	0.02160	GAC	.	.	.	none		0.488	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300		A	31682718	C	A	31682718	3	1	103	1	0	0	0	0	1	0	0	0	2766	477	17	4	1772	4	CCDC129	7	31682718	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	304279	31682718	127455945	52	6582											
HERPUD2	64224	hgsc.bcm.edu	37	chr7	35733937	35733937	+	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	aatctccatcccactttggtCcatggtgcccccaaagtcag	9	10	7	15	0	2	0	1	0	1	0	5	0	4	0	5	2	1	0	5	2	2	1			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:35733937C>T	ENST00000396081.1	-	1	808	c.4G>A	c.(4-6)Gac>Aac	p.D2N	HERPUD2_ENST00000311350.3_Missense_Mutation_p.D2N|RP11-379H18.1_ENST00000605778.1_RNA	NM_022373.4	NP_071768.3	Q9BSE4	HERP2_HUMAN	HERPUD family member 2	2					response to unfolded protein (GO:0006986)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				kidney(3)|large_intestine(5)|lung(6)|ovary(3)|prostate(1)	18						CCACTTTGGTCCATGGTGCCC	0.537																																					p.D2N		Atlas-SNP	.											.	HERPUD2	47	.	0			c.G4A						PASS	.						106	108	107					7																	35733937		2203	4300	6503	SO:0001583	missense	64224	exon2			TTTGGTCCATGGT	BC020264	CCDS5446.1	7p14.2	2006-03-20	2006-03-20		ENSG00000122557	ENSG00000122557			21915	protein-coding gene	gene with protein product	"homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 2"						Standard	NM_022373		Approved	FLJ22313	uc003tes.4	Q9BSE4	OTTHUMG00000128687	ENST00000396081.1:c.4G>A	chr7.hg19:g.35733937C>T	ENSP00000379390:p.Asp2Asn	156.0	0.0	.		166.0	62.0	.	NM_022373	A4D1Y8|Q9H6F9	Missense_Mutation	SNP	ENST00000396081.1	hg19	CCDS5446.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.779789	0.90195	.	.	ENSG00000122557	ENST00000396081;ENST00000311350;ENST00000438224;ENST00000413517;ENST00000427455	T;T;T;T;T	0.57436	1.52;1.52;1.21;1.55;0.4	3.53	3.53	0.40419	.	0.275735	0.39985	N	0.001216	T	0.57504	0.2058	L	0.50333	1.59	0.38724	D	0.953506	D	0.59767	0.986	P	0.55615	0.78	T	0.64275	-0.6446	10	0.72032	D	0.01	-3.5396	10.7536	0.46223	0.1906:0.8094:0.0:0.0	.	2	Q9BSE4	HERP2_HUMAN	N	2	ENSP00000379390:D2N;ENSP00000310729:D2N;ENSP00000415475:D2N;ENSP00000391015:D2N;ENSP00000412895:D2N	ENSP00000310729:D2N	D	-	1	0	HERPUD2	35700462	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	6.641000	0.74324	2.253000	0.74438	0.467000	0.42956	GAC	.	.	.	none		0.537	HERPUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250584.1	NM_022373		T	35733937	C	T	35733937	3	4	103	1	0	0	0	0	1	0	0	0	7071	855	30	2	1248	2	HERPUD2	7	35733937	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	4051219	35733937	123404726	53	6583											
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47853600	47853600	+	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	tattaggtagcattttcctcCaagagctccaggctgaaagg	11	11	10	9	0	0	2	0	1	0	1	3	2	3	2	3	3	2	4	3	3	5	5	rs147316882		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:47853600C>T	ENST00000289672.2	-	48	7152	c.7102G>A	c.(7102-7104)Gga>Aga	p.G2368R	C7orf69_ENST00000418326.2_Intron|C7orf69_ENST00000258776.4_Intron	NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2368					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						CATTTTCCTCCAAGAGCTCCA	0.458																																					p.G2368R		Atlas-SNP	.											.	PKD1L1	328	.	0			c.G7102A						PASS	.	C	,ARG/GLY	0,4406		0,0,2203	73	68	70		,7102	3.5	0.6	7	dbSNP_134	70	1,8599	1.2+/-3.3	0,1,4299	no	intron,missense	C7orf69,PKD1L1	NM_025031.2,NM_138295.3	,125	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,probably-damaging	,2368/2850	47853600	1,13005	2203	4300	6503	SO:0001583	missense	168507	exon48			TTCCTCCAAGAGC	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.7102G>A	chr7.hg19:g.47853600C>T	ENSP00000289672:p.Gly2368Arg	39.0	0.0	.		51.0	26.0	.	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	hg19	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	C	15.23	2.772575	0.49680	0.0	1.16E-4	ENSG00000158683	ENST00000289672	T	0.19250	2.16	5.3	3.48	0.39840	.	0.260784	0.26903	N	0.021910	T	0.35393	0.0930	L	0.60455	1.87	0.80722	D	1	D	0.65815	0.995	P	0.62435	0.902	T	0.02813	-1.1107	10	0.49607	T	0.09	-7.9894	9.0941	0.36629	0.0:0.7697:0.148:0.0823	.	2368	Q8TDX9	PK1L1_HUMAN	R	2368	ENSP00000289672:G2368R	ENSP00000289672:G2368R	G	-	1	0	PKD1L1	47820125	0.492000	0.26027	0.605000	0.28930	0.632000	0.37999	1.534000	0.36051	0.604000	0.29930	-0.172000	0.13284	GGA	.	C|1.000;T|0.000	0.000	weak		0.458	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		T	47853600	C	T	47853600	3	4	103	1	0	0	0	0	1	0	0	0	11971	603	21	2	1487	2	PKD1L1	7	47853600	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	12119663	47853600	111285063	54	6584											
VWC2	375567	hgsc.bcm.edu	37	chr7	49815193	49815193	+	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	cgtgagcacgcctctcgggaCggcccggggcgggtgaacga	6	4	18	13	7	1	2	0	2	1	0	2	4	1	3	2	5	2	1	2	5	1	0			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:49815193C>T	ENST00000340652.4	+	2	718	c.162C>T	c.(160-162)gaC>gaT	p.D54D		NM_198570.3	NP_940972.2	Q2TAL6	VWC2_HUMAN	von Willebrand factor C domain containing 2	54					negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of neuron differentiation (GO:0045666)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|basement membrane (GO:0005604)|cell junction (GO:0030054)|extracellular space (GO:0005615)|interstitial matrix (GO:0005614)|synapse (GO:0045202)				cervix(1)|endometrium(2)|large_intestine(1)|lung(3)|prostate(1)	8						CCTCTCGGGACGGCCCGGGGC	0.741																																					p.D54D		Atlas-SNP	.											.	VWC2	30	.	0			c.C162T						PASS	.						6	6	6					7																	49815193		2074	4046	6120	SO:0001819	synonymous_variant	375567	exon2			TCGGGACGGCCCG	AY358393	CCDS5508.1	7p12.3-p12.2	2007-07-19			ENSG00000188730	ENSG00000188730			30200	protein-coding gene	gene with protein product	"brorin", "brain-specific chordin-like"	611108				17400546	Standard	NM_198570		Approved	PSST739, UNQ739	uc003tot.1	Q2TAL6	OTTHUMG00000129265	ENST00000340652.4:c.162C>T	chr7.hg19:g.49815193C>T		5.0	0.0	.		8.0	7.0	.	NM_198570	Q6UXE2	Silent	SNP	ENST00000340652.4	hg19	CCDS5508.1																																																																																			.	.	.	none		0.741	VWC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251375.2	NM_198570		T	49815193	C	T	49815193	2	4	103	1	0	0	0	0	0	0	0	1	17255	535	19	1		1	VWC2	7	49815193	Silent	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	1961593	49815193	109323470	55	6585											
POMZP3	22932	hgsc.bcm.edu	37	chr7	76240801	76240801	+	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	gttacagggaagcagacgtgGaccactggctcacgacacga	12	5	13	11	3	1	1	1	0	0	1	1	5	1	3	1	3	2	3	1	3	2	1			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:76240801G>T	ENST00000310842.4	-	6	1229	c.545C>A	c.(544-546)tCc>tAc	p.S182Y	UPK3B_ENST00000419923.2_Intron|AC004980.7_ENST00000418663.1_RNA|POMZP3_ENST00000275569.4_Intron|UPK3B_ENST00000443097.2_Intron	NM_012230.3	NP_036362.3	Q6PJE2	POZP3_HUMAN	POM121 and ZP3 fusion	182										kidney(3)|lung(2)	5		Myeloproliferative disorder(862;0.204)				AGCAGACGTGGACCACTGGCT	0.537																																					p.S182Y		Atlas-SNP	.											.	POMZP3	19	.	0			c.C545A						PASS	.						72	71	72					7																	76240801		2200	4279	6479	SO:0001583	missense	22932	exon6			GACGTGGACCACT	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.545C>A	chr7.hg19:g.76240801G>T	ENSP00000309233:p.Ser182Tyr	373.0	1.0	.		382.0	118.0	.	NM_012230	F6STJ3|Q12903|Q9BWB4	Missense_Mutation	SNP	ENST00000310842.4	hg19	CCDS43606.1	.	.	.	.	.	.	.	.	.	.	N	8.381	0.837429	0.16891	.	.	ENSG00000146707	ENST00000310842	T	0.23950	1.88	0.786	-1.57	0.08506	.	3.392970	0.01303	U	0.010346	T	0.28134	0.0694	L	0.38175	1.15	0.09310	N	1	D	0.57257	0.979	P	0.50970	0.655	T	0.18241	-1.0343	10	0.87932	D	0	.	3.7228	0.08463	0.0:0.0:0.477:0.523	.	182	Q6PJE2	POZP3_HUMAN	Y	182	ENSP00000309233:S182Y	ENSP00000309233:S182Y	S	-	2	0	POMZP3	76078737	0.000000	0.05858	0.089000	0.20774	0.299000	0.27559	-0.671000	0.05250	-0.344000	0.08338	0.372000	0.22366	TCC	.	.	.	none		0.537	POMZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341775.1	NM_012230		T	76240801	G	T	76240801	3	4	103	1	0	0	0	0	1	0	0	0	12254	1174	41	4	29	4	POMZP3	7	76240801	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	26425608	76240801	82897862	56	6586											
PCLO	27445	hgsc.bcm.edu	37	chr7	82579041	82579041	+	Frame_Shift_Del	DEL	T	T	-																															gagatgggtgagtaaaggacTttgggggatttgggtgggga																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:82579041delT	ENST00000333891.9	-	6	11200	c.10863delA	c.(10861-10863)aaafs	p.K3621fs	PCLO_ENST00000437081.1_Frame_Shift_Del_p.K341fs|PCLO_ENST00000423517.2_Frame_Shift_Del_p.K3621fs	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						AGTAAAGGACTTTGGGGGATT	0.478																																					p.V3622fs		Atlas-Indel,Pindel	.											.	PCLO	1506	.	0			c.10864delG						PASS	.						106	107	106					7																	82579041		2005	4186	6191	SO:0001589	frameshift_variant	27445	exon6			.	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.10863delA	chr7.hg19:g.82579041delT	ENSP00000334319:p.Lys3621fs	87.0	0.0	0		111.0	46.0	0.414414	NM_014510		Frame_Shift_Del	DEL	ENST00000333891.9	hg19	CCDS47630.1																																																																																			.	.	.	none		0.478	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		-	82579041	T	-	82579041	7	5	103	1	0	1	0	1	0	0	0	0	11590	1606	56	0	4662	0	PCLO	7	82579041	Frame_Shift_Del	DEL	T	TCGA-B9-A44B-01A-11D-A25F-10	6338240	82579041	76559622	57	6587											
PCLO	27445	hgsc.bcm.edu	37	chr7	82585266	82585266	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tactgttgagctcaattgttTtaaatcggcgtagccctcct	8	15	8	10	2	1	1	1	1	0	0	3	1	2	1	2	1	3	4	2	1	5	6			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:82585266T>C	ENST00000333891.9	-	5	5340	c.5003A>G	c.(5002-5004)aAa>aGa	p.K1668R	PCLO_ENST00000423517.2_Missense_Mutation_p.K1668R	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						CTCAATTGTTTTAAATCGGCG	0.368																																					p.K1668R		Atlas-SNP	.											.	PCLO	1506	.	0			c.A5003G						PASS	.						107	99	102					7																	82585266		1859	4098	5957	SO:0001583	missense	27445	exon5			ATTGTTTTAAATC	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.5003A>G	chr7.hg19:g.82585266T>C	ENSP00000334319:p.Lys1668Arg	92.0	0.0	.		99.0	44.0	.	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	7.727	0.698443	0.15106	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.26810	1.71;1.73	5.31	5.31	0.75309	.	.	.	.	.	T	0.35068	0.0919	M	0.74881	2.28	0.80722	D	1	P;P	0.45715	0.865;0.865	B;B	0.42555	0.391;0.391	T	0.36359	-0.9751	9	0.87932	D	0	.	15.2616	0.73628	0.0:0.0:0.0:1.0	.	1668;1668	Q9Y6V0-5;Q9Y6V0-6	.;.	R	1599;1668;1668	ENSP00000334319:K1668R;ENSP00000388393:K1668R	ENSP00000334319:K1668R	K	-	2	0	PCLO	82423202	1.000000	0.71417	0.847000	0.33407	0.907000	0.53573	5.048000	0.64238	2.005000	0.58758	0.528000	0.53228	AAA	.	.	.	none		0.368	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		C	82585266	T	C	82585266	3	2	103	1	0	0	0	0	1	0	0	0	11590	1841	64	3	10526	3	PCLO	7	82585266	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	6225	82585266	76553397	58	6588											
PRKAR2B	5577	hgsc.bcm.edu	37	chr7	106799967	106799967	+	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	aaaaggaacatcgctacctaTgaagaacagttagttgccct	15	9	8	9	1	0	2	0	1	0	1	1	3	0	3	2	1	4	3	2	1	8	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:106799967T>A	ENST00000265717.4	+	11	1456	c.1197T>A	c.(1195-1197)taT>taA	p.Y399*		NM_002736.2	NP_002727.2	P31323	KAP3_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, beta	399					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						TCGCTACCTATGAAGAACAGT	0.388																																					p.Y399X		Atlas-SNP	.											.	PRKAR2B	34	.	0			c.T1197A						PASS	.						135	118	124					7																	106799967		2203	4300	6503	SO:0001587	stop_gained	5577	exon11			TACCTATGAAGAA		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.1197T>A	chr7.hg19:g.106799967T>A	ENSP00000265717:p.Tyr399*	111.0	0.0	.		114.0	42.0	.	NM_002736	A4D0R9	Nonsense_Mutation	SNP	ENST00000265717.4	hg19	CCDS5740.1	.	.	.	.	.	.	.	.	.	.	T	19.41	3.821472	0.71028	.	.	ENSG00000005249	ENST00000265717;ENST00000543645;ENST00000539794	.	.	.	5.68	2.05	0.26809	.	0.110083	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.3785	9.0728	0.36502	0.0:0.277:0.0:0.723	.	.	.	.	X	399;399;386	.	ENSP00000265717:Y399X	Y	+	3	2	PRKAR2B	106587203	0.950000	0.32346	1.000000	0.80357	0.997000	0.91878	0.030000	0.13688	0.113000	0.18004	0.528000	0.53228	TAT	.	.	.	none		0.388	PRKAR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268386.1			A	106799967	T	A	106799967	4	1	103	1	0	0	0	0	0	1	0	0	12516	1471	51	5	1239	5	PRKAR2B	7	106799967	Nonsense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	24214701	106799967	52338696	59	6589											
ADCK2	90956	hgsc.bcm.edu	37	chr7	140380887	140380887	+	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	agcaggcaggaattcccgtgGacttgaaaaggaagattgca	14	7	13	7	1	0	2	0	1	0	1	1	5	1	5	1	4	2	3	1	4	4	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:140380887G>T	ENST00000072869.4	+	4	1433	c.1255G>T	c.(1255-1257)Gac>Tac	p.D419Y	ADCK2_ENST00000476491.1_Missense_Mutation_p.D419Y	NM_052853.3	NP_443085.2	Q7Z695	ADCK2_HUMAN	aarF domain containing kinase 2	419	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)					AATTCCCGTGGACTTGAAAAG	0.562																																					p.D419Y		Atlas-SNP	.											.	ADCK2	37	.	0			c.G1255T						PASS	.						137	114	122					7																	140380887		2203	4300	6503	SO:0001583	missense	90956	exon4			CCCGTGGACTTGA	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.1255G>T	chr7.hg19:g.140380887G>T	ENSP00000072869:p.Asp419Tyr	278.0	0.0	.		287.0	122.0	.	NM_052853	Q96CN6|Q9Y6T5	Missense_Mutation	SNP	ENST00000072869.4	hg19	CCDS5861.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.78|14.78	2.638582|2.638582	0.47153|0.47153	.|.	.|.	ENSG00000133597|ENSG00000133597	ENST00000072869;ENST00000476491;ENST00000473512|ENST00000483369	T;T;T|.	0.12039|.	2.72;2.72;2.72|.	4.18|4.18	3.2|3.2	0.36748|0.36748	.|.	0.234009|.	0.34245|.	N|.	0.004140|.	T|T	0.55609|0.55609	0.1931|0.1931	M|M	0.70595|0.70595	2.14|2.14	0.19945|0.19945	N|N	0.999942|0.999942	D;D|.	0.54397|.	0.966;0.966|.	P;P|.	0.46718|.	0.525;0.525|.	T|T	0.46735|0.46735	-0.9170|-0.9170	10|5	0.66056|.	D|.	0.02|.	-50.6212|-50.6212	10.5732|10.5732	0.45212|0.45212	0.1074:0.0:0.8926:0.0|0.1074:0.0:0.8926:0.0	.|.	419;419|.	C9JE15;Q7Z695|.	.;ADCK2_HUMAN|.	Y|V	419;419;59|256	ENSP00000072869:D419Y;ENSP00000420512:D419Y;ENSP00000420288:D59Y|.	ENSP00000072869:D419Y|.	D|G	+|+	1|2	0|0	ADCK2|ADCK2	140027356|140027356	0.982000|0.982000	0.34865|0.34865	0.077000|0.077000	0.20336|0.20336	0.837000|0.837000	0.47467|0.47467	4.292000|4.292000	0.59031|0.59031	2.154000|2.154000	0.67381|0.67381	0.561000|0.561000	0.74099|0.74099	GAC|GGA	.	.	.	none		0.562	ADCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348734.1	NM_052853		T	140380887	G	T	140380887	3	4	103	1	0	0	0	0	1	0	0	0	289	1174	41	4	1269	4	ADCK2	7	140380887	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	33580920	140380887	18757776	60	6590											
RBM33	155435	hgsc.bcm.edu	37	chr7	155534581	155534582	+	Frame_Shift_Ins	INS	-	-	A																															ccactgcgccaaggaacagcINSaatttgcgtgaattacccat																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr7:155534581_155534582insA	ENST00000401878.3	+	13	2316_2317	c.2118_2119insA	c.(2119-2121)aatfs	p.N707fs		NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33	707							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)		CAAGGAACAGCAATTTGCGTGA	0.49																																					p.S706fs		Atlas-Indel,Pindel	.											.	RBM33	157	.	0			c.2118_2119insA						PASS	.																																			SO:0001589	frameshift_variant	155435	exon13			.	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.2120dupA	chr7.hg19:g.155534583_155534583dupA	ENSP00000384160:p.Asn707fs	190.0	0.0	0		165.0	69.0	0.418182	NM_053043	A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	Frame_Shift_Ins	INS	ENST00000401878.3	hg19	CCDS5941.2																																																																																			.	.	.	none		0.49	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317225.3	NM_001008408		A	155534582	-	A	155534581	7	5	103	1	0	1	1	0	0	0	0	0	13143	709	25	0	2168	0	RBM33	7	155534581	Frame_Shift_Ins	INS	-	TCGA-B9-A44B-01A-11D-A25F-10	15153694	155534581	3604082	61	6591											
FUT10	84750	hgsc.bcm.edu	37	chr8	33246682	33246683	+	Frame_Shift_Ins	INS	-	-	A																															catcagaatccagtcgtctgINSatgtaacttgccagttccct																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr8:33246682_33246683insA	ENST00000327671.5	-	4	1641_1642	c.1010_1011insT	c.(1009-1011)atcfs	p.I337fs	FUT10_ENST00000518076.1_5'UTR|FUT10_ENST00000524021.1_Frame_Shift_Ins_p.I309fs|FUT10_ENST00000335589.3_Frame_Shift_Ins_p.I275fs|FUT10_ENST00000518672.1_Frame_Shift_Ins_p.I309fs	NM_032664.3	NP_116053.3	Q6P4F1	FUT10_HUMAN	fucosyltransferase 10 (alpha (1,3) fucosyltransferase)	337					embryo development (GO:0009790)|fertilization (GO:0009566)|fucosylation (GO:0036065)|hemopoiesis (GO:0030097)|L-fucose catabolic process (GO:0042355)|nervous system development (GO:0007399)|protein folding (GO:0006457)|protein glycosylation (GO:0006486)|protein targeting (GO:0006605)|wound healing (GO:0042060)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)			cervix(1)|endometrium(1)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	29				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)		CCAGTCGTCTGATGTAACTTGC	0.46																																					p.I337fs		Atlas-Indel,Pindel	.											.	FUT10	62	.	0			c.1011_1012insT						PASS	.																																			SO:0001589	frameshift_variant	84750	exon4			.	AJ512465	CCDS6088.1	8p12	2013-02-26			ENSG00000172728	ENSG00000172728		"Fucosyltransferases"	19234	protein-coding gene	gene with protein product							Standard	NM_032664		Approved		uc003xje.3	Q6P4F1	OTTHUMG00000163954	ENST00000327671.5:c.1011dupT	chr8.hg19:g.33246683_33246683dupA	ENSP00000332757:p.Ile337fs	301.0	0.0	0		311.0	126.0	0.405145	NM_032664	A8KAC8|Q70GG3|Q8IVI6|Q8IVI7|Q8IVJ3|Q8TE43|Q9BSR3	Frame_Shift_Ins	INS	ENST00000327671.5	hg19	CCDS6088.1																																																																																			.	.	.	none		0.46	FUT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376540.1	NM_032664		A	33246683	-	A	33246682	7	5	103	1	0	1	1	0	0	0	0	0	6109	1280	45	0	436	0	FUT10	8	33246682	Frame_Shift_Ins	INS	-	TCGA-B9-A44B-01A-11D-A25F-10		33246682	113117340	62	6592											
RNF19A	25897	hgsc.bcm.edu	37	chr8	101276971	101276971	+	Missense_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	acctgctatggccaaattccGtttgtgctttgaaacatcct	9	14	7	11	1	0	1	0	1	0	0	2	1	2	1	4	1	3	3	4	1	3	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr8:101276971G>A	ENST00000519449.1	-	7	1550	c.1234C>T	c.(1234-1236)Cgg>Tgg	p.R412W	RNF19A_ENST00000341084.2_Missense_Mutation_p.R412W|RNF19A_ENST00000523255.1_5'UTR	NM_001280539.1|NM_015435.3	NP_001267468.1|NP_056250.3	Q9NV58	RN19A_HUMAN	ring finger protein 19A, RBR E3 ubiquitin protein ligase	412					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)	p.R412W(1)		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)			GCCAAATTCCGTTTGTGCTTT	0.373																																					p.R412W		Atlas-SNP	.											RNF19A,NS,carcinoma,0,1	RNF19A	67	.	1	Substitution - Missense(1)	endometrium(1)	c.C1234T						PASS	.						239	211	220					8																	101276971		2203	4300	6503	SO:0001583	missense	25897	exon7			AATTCCGTTTGTG	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.1234C>T	chr8.hg19:g.101276971G>A	ENSP00000428968:p.Arg412Trp	100.0	0.0	.		98.0	23.0	.	NM_015435	A3KCU9|Q52LG1|Q9H5H9|Q9H8M8|Q9UFG0|Q9UFX6|Q9Y4Y1	Missense_Mutation	SNP	ENST00000519449.1	hg19	CCDS6286.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.012643	0.75161	.	.	ENSG00000034677	ENST00000519449;ENST00000341084	D;D	0.86297	-2.1;-2.1	5.17	4.28	0.50868	.	0.053565	0.64402	D	0.000002	D	0.92704	0.7681	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93259	0.6641	10	0.87932	D	0	.	12.7055	0.57058	0.0:0.0:0.5807:0.4193	.	412	Q9NV58	RN19A_HUMAN	W	412	ENSP00000428968:R412W;ENSP00000342667:R412W	ENSP00000342667:R412W	R	-	1	2	RNF19A	101346147	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.083000	0.41615	1.305000	0.44909	0.650000	0.86243	CGG	.	.	.	none		0.373	RNF19A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380004.1	NM_015435		A	101276971	G	A	101276971	3	1	103	1	0	0	0	0	1	0	0	0	13483	1144	40	1	1302	1	RNF19A	8	101276971	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	68030289	101276971	45087051	63	6593											
RSPO2	340419	hgsc.bcm.edu	37	chr8	108970372	108970372	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaatggttggacacagtatTgtgtctttcactggcttttt	7	17	10	7	0	2	0	1	0	1	0	2	1	2	1	0	3	0	4	0	3	2	6			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr8:108970372T>C	ENST00000276659.5	-	5	1172	c.552A>G	c.(550-552)acA>acG	p.T184T	RSPO2_ENST00000517781.1_Silent_p.T120T|RSPO2_ENST00000517939.1_Silent_p.T117T|RSPO2_ENST00000378439.2_Silent_p.T120T	NM_178565.4	NP_848660.3	Q6UXX9	RSPO2_HUMAN	R-spondin 2	184	TSP type-1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				bone mineralization (GO:0030282)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|lung growth (GO:0060437)|osteoblast differentiation (GO:0001649)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|extracellular region (GO:0005576)	heparin binding (GO:0008201)|receptor binding (GO:0005102)		EIF3E/RSPO2(6)	haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	28			OV - Ovarian serous cystadenocarcinoma(57;1.55e-09)			GACACAGTATTGTGTCTTTCA	0.443																																					p.T184T		Atlas-SNP	.											.	RSPO2	65	.	0			c.A552G						PASS	.						328	281	297					8																	108970372		2203	4300	6503	SO:0001819	synonymous_variant	340419	exon5			CAGTATTGTGTCT	AK123023	CCDS6307.1, CCDS64953.1	8q23.1	2014-01-30	2011-06-29		ENSG00000147655	ENSG00000147655		"Endogenous ligands"	28583	protein-coding gene	gene with protein product		610575	"R-spondin 2 homolog (Xenopus laevis)"			15469841	Standard	NM_178565		Approved	MGC35555	uc003yms.3	Q6UXX9	OTTHUMG00000164893	ENST00000276659.5:c.552A>G	chr8.hg19:g.108970372T>C		217.0	0.0	.		239.0	112.0	.	NM_178565	B3KVP0|Q4G0U4|Q8N6X6	Silent	SNP	ENST00000276659.5	hg19	CCDS6307.1																																																																																			.	.	.	none		0.443	RSPO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380830.1	NM_178565		C	108970372	T	C	108970372	2	2	103	1	0	0	0	0	0	0	0	1	13723	1799	63	3		3	RSPO2	8	108970372	Silent	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	7693401	108970372	37393650	64	6594											
EEF1D	1936	hgsc.bcm.edu	37	chr8	144661995	144661995	+	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	aaagctgcgatatcgacactCtgcacctgaggagaggcgga	12	6	13	10	3	1	2	0	1	1	1	2	6	1	3	1	3	3	2	1	3	2	1	rs11548159		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr8:144661995C>G	ENST00000529272.1	-	8	1213	c.813G>C	c.(811-813)caG>caC	p.Q271H	NAPRT1_ENST00000435154.3_5'Flank|EEF1D_ENST00000442189.2_Missense_Mutation_p.Q637H|EEF1D_ENST00000395119.3_Missense_Mutation_p.Q271H|NAPRT1_ENST00000449291.2_5'Flank|EEF1D_ENST00000524624.1_Missense_Mutation_p.Q247H|EEF1D_ENST00000423316.2_Missense_Mutation_p.Q637H|EEF1D_ENST00000317198.6_Missense_Mutation_p.Q271H|NAPRT1_ENST00000276844.7_5'Flank|RP11-661A12.7_ENST00000529247.1_RNA|EEF1D_ENST00000532400.1_Missense_Mutation_p.R87T|EEF1D_ENST00000531621.1_Missense_Mutation_p.Q228H|EEF1D_ENST00000526838.1_Missense_Mutation_p.Q252H|NAPRT1_ENST00000426292.3_5'Flank|EEF1D_ENST00000532741.1_Missense_Mutation_p.Q687H|EEF1D_ENST00000419152.2_Missense_Mutation_p.Q271H|EEF1D_ENST00000528610.1_Missense_Mutation_p.Q247H|RP11-661A12.9_ENST00000531730.1_RNA			P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)	271	Catalytic (GEF).				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)			TATCGACACTCTGCACCTGAG	0.612																																					p.Q637H		Atlas-SNP	.											.	EEF1D	48	.	0			c.G1911C						PASS	.						116	108	111					8																	144661995		2203	4300	6503	SO:0001583	missense	1936	exon10			GACACTCTGCACC	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.813G>C	chr8.hg19:g.144661995C>G	ENSP00000434872:p.Gln271His	99.0	0.0	.		112.0	42.0	.	NM_001130053	B4DDU4|D3DWK3|E9PBQ9|Q4VBZ6|Q969J1|Q96I38	Missense_Mutation	SNP	ENST00000529272.1	hg19	CCDS6405.1	.|.|.|.	.|.|.|.	.|.|.|.	.|.|.|.	.|.|.|.	.|.|.|.	.|.|.|.	.|.|.|.	.|.|.|.	.|.|.|.	.|C|C|C	16.30|16.30|16.30|16.30	3.083562|3.083562|3.083562|3.083562	0.55861|0.55861|0.55861|0.55861	.|.|.|.	.|.|.|.	ENSG00000104529|ENSG00000104529|ENSG00000104529|ENSG00000104529	ENST00000529576|ENST00000530109|ENST00000419152;ENST00000532741;ENST00000526838;ENST00000442189;ENST00000528610;ENST00000395119;ENST00000529272;ENST00000423316;ENST00000356793;ENST00000317198;ENST00000531621;ENST00000524624|ENST00000532400	.|.|.|.	.|.|.|.	.|.|.|.	4.94|4.94|4.94|4.94	2.14|2.14|2.14|2.14	0.27477|0.27477|0.27477|0.27477	.|.|Translation elongation factor EF1B/ribosomal protein S6 (1);Translation elongation factor EF1B, beta/delta chains, conserved site (1);Translation elongation factor EF1B, beta/delta subunit, guanine nucleotide exchange (3);|.	.|.|0.121518|.	.|.|0.64402|.	.|.|D|.	.|.|0.000014|.	.|D|D|D	.|0.87525|0.87525|0.87525	.|0.6199|0.6199|0.6199	H|H|H|H	0.99182|0.99182|0.99182|0.99182	4.46|4.46|4.46|4.46	0.58432|0.58432|0.58432|0.58432	D|D|D|D	0.999996|0.999996|0.999996|0.999996	.|.|D;D;D;D;D;D|.	.|.|0.89917|.	.|.|1.0;0.999;1.0;0.999;1.0;1.0|.	.|.|D;D;D;D;D;D|.	.|.|0.97110|.	.|.|0.998;0.998;0.999;0.99;1.0;0.996|.	.|D|D|D	.|0.87780|0.87780|0.87780	.|0.2611|0.2611|0.2611	.|5|9|6	.|.|0.87932|0.87932	.|.|D|D	.|.|0|0	.|.|.|.	9.1243|9.1243|9.1243|9.1243	0.36805|0.36805|0.36805|0.36805	0.0:0.6883:0.0:0.3117|0.0:0.6883:0.0:0.3117|0.0:0.6883:0.0:0.3117|0.0:0.6883:0.0:0.3117	.|.|.|.	.|.|252;637;565;271;687;637|.	.|.|E9PBQ9;D3DWK1;F8W934;P29692;E9PRY8;P29692-2|.	.|.|.;.;.;EF1D_HUMAN;.;.|.	.|Q|H|T	-1|146|271;687;252;637;247;271;271;637;565;271;228;247|87	.|.|.|.	.|.|ENSP00000317399:Q271H|ENSP00000433784:R87T	.|E|Q|R	-|-|-|-	.|1|3|2	.|0|2|0	EEF1D|EEF1D|EEF1D|EEF1D	144733138|144733138|144733138|144733138	1.000000|1.000000|1.000000|1.000000	0.71417|0.71417|0.71417|0.71417	1.000000|1.000000|1.000000|1.000000	0.80357|0.80357|0.80357|0.80357	0.953000|0.953000|0.953000|0.953000	0.61014|0.61014|0.61014|0.61014	2.428000|2.428000|2.428000|2.428000	0.44749|0.44749|0.44749|0.44749	0.622000|0.622000|0.622000|0.622000	0.30249|0.30249|0.30249|0.30249	-0.136000|-0.136000|-0.136000|-0.136000	0.14681|0.14681|0.14681|0.14681	.|GAG|CAG|AGA	.	.	.	none		0.612	EEF1D-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382592.2	NM_032378		G	144661995	C	G	144661995	3	3	103	1	0	0	0	0	1	0	0	0	4928	912	32	4	36	4	EEF1D	8	144661995	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	35691623	144661995	1702027	65	6595											
MELK	9833	hgsc.bcm.edu	37	chr9	36583634	36583634	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctacttaggtggctttgcAaaggtcaaacttgcctgcca	9	12	9	11	0	1	0	1	0	0	0	2	0	2	0	3	3	5	2	3	3	4	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr9:36583634A>G	ENST00000298048.2	+	3	253	c.69A>G	c.(67-69)gcA>gcG	p.A23A	MELK_ENST00000545008.1_Silent_p.A23A|MELK_ENST00000536987.1_Intron|MELK_ENST00000543751.1_Intron|MELK_ENST00000536329.1_Intron|MELK_ENST00000487398.1_Intron|MELK_ENST00000536860.1_Silent_p.A23A|MELK_ENST00000541717.1_Silent_p.A23A|MELK_ENST00000538311.1_Intron	NM_014791.3	NP_055606.1	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase	23	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)			GTGGCTTTGCAAAGGTCAAAC	0.323																																					p.A23A	Ovarian(82;980 1317 7225 14391 18624)	Atlas-SNP	.											.	MELK	74	.	0			c.A69G						PASS	.						66	65	65					9																	36583634		2203	4300	6503	SO:0001819	synonymous_variant	9833	exon3			CTTTGCAAAGGTC	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.69A>G	chr9.hg19:g.36583634A>G		34.0	0.0	.		31.0	13.0	.	NM_001256688	A6P3A7|A6P3A8|B1AMQ6|B7Z1E6|B7Z5M5|B7Z6Q7|B7Z6R8|B7Z6Y0|B7Z7Q1|D3DRP8|F5H0Y0|F5H2R4|F5H689|Q7L3C3	Silent	SNP	ENST00000298048.2	hg19	CCDS6606.1																																																																																			.	.	.	none		0.323	MELK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052428.3	NM_014791		G	36583634	A	G	36583634	2	3	103	1	0	0	0	0	0	0	0	1	9477	117	5	3		3	MELK	9	36583634	Silent	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10		36583634	104629797	66	6596											
ZMYND17	118490	hgsc.bcm.edu	37	chr10	75187422	75187422	+	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	aaagcccactagggagtgctCtacagtgagcacagaatcga	14	6	11	10	1	1	2	0	1	1	1	2	4	1	3	1	1	4	2	1	1	4	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr10:75187422C>A	ENST00000372912.1	-	2	328	c.326G>T	c.(325-327)aGa>aTa	p.R109I	AL353731.1_ENST00000584907.1_RNA|MSS51_ENST00000299432.2_Missense_Mutation_p.R109I			Q4VC12	MSS51_HUMAN	MSS51 mitochondrial translational activator	109					social behavior (GO:0035176)		metal ion binding (GO:0046872)										AGGGAGTGCTCTACAGTGAGC	0.488																																					p.R109I		Atlas-SNP	.											.	.	.	.	0			c.G326T						PASS	.						150	152	151					10																	75187422		2203	4300	6503	SO:0001583	missense	118490	exon3			AGTGCTCTACAGT	AK096884	CCDS31221.1	10q22.3	2013-01-10	2013-01-10	2012-02-24	ENSG00000166343	ENSG00000166343		"Zinc fingers, MYND-type"	21000	protein-coding gene	gene with protein product		614773	"zinc finger, MYND-type containing 17", "MSS51 mitochondrial translational activator homolog (S. cerevisiae)"	ZMYND17		19710419	Standard	NM_001024593		Approved	FLJ39565	uc001jud.3	Q4VC12	OTTHUMG00000018464	ENST00000372912.1:c.326G>T	chr10.hg19:g.75187422C>A	ENSP00000362003:p.Arg109Ile	110.0	0.0	.		83.0	43.0	.	NM_001024593	A6NGH6|Q2VP95|Q5F2H5|Q7Z3M9|Q8N8G0	Missense_Mutation	SNP	ENST00000372912.1	hg19	CCDS31221.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.006937	0.74932	.	.	ENSG00000166343	ENST00000299432;ENST00000372912	T;T	0.47528	0.84;0.84	5.93	1.82	0.25136	Zinc finger, MYND-type (3);	0.272901	0.39985	N	0.001207	T	0.45915	0.1366	L	0.46157	1.445	0.28419	N	0.917817	P;P	0.42941	0.794;0.755	P;P	0.49192	0.602;0.466	T	0.37957	-0.9683	10	0.52906	T	0.07	-1.0575	7.4501	0.27234	0.0:0.5461:0.0:0.4539	.	109;109	Q4VC12;F6VAV3	ZMY17_HUMAN;.	I	109	ENSP00000299432:R109I;ENSP00000362003:R109I	ENSP00000299432:R109I	R	-	2	0	ZMYND17	74857428	0.998000	0.40836	0.944000	0.38274	0.974000	0.67602	0.901000	0.28445	0.332000	0.23536	0.591000	0.81541	AGA	.	.	.	none		0.488	MSS51-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048652.3	NM_178451		A	75187422	C	A	75187422	3	1	103	1	0	0	0	0	1	0	0	0	17721	913	32	4	1076	4	ZMYND17	10	75187422	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10		75187422	60347325	67	6597											
FUT11	170384	hgsc.bcm.edu	37	chr10	75533456	75533456	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatgccgagaaagcccacgCggcctctcccggggacagcc	8	3	14	16	4	1	1	0	0	1	1	2	4	1	3	5	4	3	0	5	4	1	0			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr10:75533456C>T	ENST00000372841.3	+	2	1260	c.1217C>T	c.(1216-1218)gCg>gTg	p.A406V	FUT11_ENST00000465695.1_3'UTR|AC022400.2_ENST00000595757.1_5'Flank|FUT11_ENST00000394790.1_Missense_Mutation_p.A406V|RMRPP1_ENST00000517236.1_RNA	NM_173540.2	NP_775811.2	Q495W5	FUT11_HUMAN	fucosyltransferase 11 (alpha (1,3) fucosyltransferase)	406					protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	7	Prostate(51;0.0112)					AAAGCCCACGCGGCCTCTCCC	0.597																																					p.A406V		Atlas-SNP	.											.	FUT11	30	.	0			c.C1217T						PASS	.						70	73	72					10																	75533456		2203	4300	6503	SO:0001583	missense	170384	exon2			CCCACGCGGCCTC	BC036037	CCDS7333.1, CCDS60558.1	10q22.3	2014-01-02			ENSG00000196968	ENSG00000196968		"Fucosyltransferases"	19233	protein-coding gene	gene with protein product						11698403, 24318988	Standard	NM_173540		Approved	MGC33202	uc001jva.3	Q495W5	OTTHUMG00000018483	ENST00000372841.3:c.1217C>T	chr10.hg19:g.75533456C>T	ENSP00000361932:p.Ala406Val	128.0	0.0	.		98.0	50.0	.	NM_173540	Q495W7|Q8IYE4	Missense_Mutation	SNP	ENST00000372841.3	hg19	CCDS7333.1	.	.	.	.	.	.	.	.	.	.	C	14.02	2.411217	0.42817	.	.	ENSG00000196968	ENST00000372841;ENST00000394790	T;T	0.35605	1.32;1.3	5.68	-3.31	0.04988	.	0.603818	0.19087	N	0.123083	T	0.12263	0.0298	N	0.14661	0.345	0.09310	N	1	B;B	0.34349	0.156;0.45	B;B	0.27500	0.061;0.08	T	0.33085	-0.9882	10	0.13853	T	0.58	-31.9131	4.6888	0.12771	0.5766:0.2067:0.0844:0.1324	.	406;406	Q495W5;Q495W5-2	FUT11_HUMAN;.	V	406	ENSP00000361932:A406V;ENSP00000378270:A406V	ENSP00000361932:A406V	A	+	2	0	FUT11	75203462	0.000000	0.05858	0.000000	0.03702	0.968000	0.65278	0.215000	0.17562	-0.197000	0.10350	0.563000	0.77884	GCG	.	.	.	none		0.597	FUT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048689.1	NM_173540		T	75533456	C	T	75533456	3	4	103	1	0	0	0	0	1	0	0	0	6110	768	27	1	1223	1	FUT11	10	75533456	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	346034	75533456	60001291	68	6598											
PDCD11	22984	hgsc.bcm.edu	37	chr10	105205187	105205189	+	In_Frame_Del	DEL	TTC	TTC	-																															tggcccccaagagaatgaagTtcttcttcaagcgctacctg																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr10:105205187_105205189delTTC	ENST00000369797.3	+	36	5591_5593	c.5497_5499delTTC	c.(5497-5499)ttcdel	p.F1835del		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	1835					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)		GAGAATGAAGTTCTTCTTCAAGC	0.542																																					p.1832_1833del		Atlas-Indel,Pindel	.											.	PDCD11	160	.	0			c.5496_5498del						PASS	.																																			SO:0001651	inframe_deletion	22984	exon36			.	D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.5497_5499delTTC	chr10.hg19:g.105205193_105205195delTTC	ENSP00000358812:p.Phe1835del	218.0	0.0	0		209.0	56.0	0.267943	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	In_Frame_Del	DEL	ENST00000369797.3	hg19	CCDS31276.1																																																																																			.	.	.	none		0.542	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1			-	105205189	TTC	-	105205187	7	5	103	1	0	1	0	1	0	0	0	0	11624	1725	60	0	5635	0	PDCD11	10	105205187	In_Frame_Del	DEL	TTC	TCGA-B9-A44B-01A-11D-A25F-10	29671731	105205187	30329560	69	6599											
FBXO3	26273	hgsc.bcm.edu	37	chr11	33770331	33770331	+	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	tgggttccataccaactactCcaggtccttgaacttcttcc	8	13	6	14	0	1	1	0	1	1	0	5	1	5	1	5	2	4	1	5	2	4	6			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr11:33770331C>T	ENST00000265651.3	-	9	1058	c.1040G>A	c.(1039-1041)gGa>gAa	p.G347E	FBXO3_ENST00000531080.1_Missense_Mutation_p.G34E|FBXO3_ENST00000532057.1_Missense_Mutation_p.G34E|FBXO3_ENST00000448981.2_Missense_Mutation_p.G347E|FBXO3_ENST00000526785.1_Missense_Mutation_p.G234E|FBXO3_ENST00000534136.1_Missense_Mutation_p.G347E|FBXO3_ENST00000530401.1_Missense_Mutation_p.G342E	NM_012175.3	NP_036307.2	Q9UK99	FBX3_HUMAN	F-box protein 3	347	ApaG. {ECO:0000255|PROSITE- ProRule:PRU00412}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|pancreas(1)|stomach(1)	13		Lung NSC(402;0.0804)		BRCA - Breast invasive adenocarcinoma(625;0.00315)|Lung(977;0.00488)|LUSC - Lung squamous cell carcinoma(625;0.008)		ACCAACTACTCCAGGTCCTTG	0.373																																					p.G347E		Atlas-SNP	.											.	FBXO3	37	.	0			c.G1040A						PASS	.						99	99	99					11																	33770331		2202	4298	6500	SO:0001583	missense	26273	exon9			ACTACTCCAGGTC	AK001943	CCDS7887.1, CCDS44566.1	11p13	2006-07-07	2004-06-15		ENSG00000110429	ENSG00000110429		"F-boxes /  "other""	13582	protein-coding gene	gene with protein product		609089	"F-box only protein 3"			10531037	Standard	NM_033406		Approved	FBX3, FBA	uc001muz.3	Q9UK99	OTTHUMG00000166244	ENST00000265651.3:c.1040G>A	chr11.hg19:g.33770331C>T	ENSP00000265651:p.Gly347Glu	50.0	0.0	.		51.0	14.0	.	NM_012175	B3KY16|D3DR05|Q86X90|Q9H0V2|Q9NUX2	Missense_Mutation	SNP	ENST00000265651.3	hg19	CCDS7887.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.567786	0.86439	.	.	ENSG00000110429	ENST00000526785;ENST00000265651;ENST00000530401;ENST00000531080;ENST00000532057;ENST00000534136;ENST00000448981	T;T;T;T;T	0.71934	-0.51;-0.61;-0.5;-0.54;-0.51	5.61	4.68	0.58851	ApaG domain (4);	0.000000	0.85682	D	0.000000	D	0.89518	0.6738	H	0.96633	3.855	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	0.93248	0.6632	10	0.87932	D	0	-21.1763	16.4024	0.83644	0.0:0.8681:0.1319:0.0	.	342;347;347	Q9UK99-3;Q9UK99-2;Q9UK99	.;.;FBX3_HUMAN	E	234;347;342;34;34;347;347	ENSP00000435680:G234E;ENSP00000265651:G347E;ENSP00000433781:G342E;ENSP00000431745:G347E;ENSP00000408836:G347E	ENSP00000265651:G347E	G	-	2	0	FBXO3	33726907	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.294000	0.78760	1.355000	0.45865	0.491000	0.48974	GGA	.	.	.	none		0.373	FBXO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388665.1	NM_012175		T	33770331	C	T	33770331	3	4	103	1	0	0	0	0	1	0	0	0	5746	855	30	2	396	2	FBXO3	11	33770331	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10		33770331	101236185	70	6600											
CD6	923	hgsc.bcm.edu	37	chr11	60778597	60778605	+	In_Frame_Del	DEL	AGTCACTAT	AGTCACTAT	-																															gtccctgcaagtgttcagacAgtcactataggtaagtgttg																								rs374328736		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	AGTCACTAT	AGTCACTAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr11:60778597_60778605delAGTCACTAT	ENST00000313421.7	+	6	1326_1334	c.1140_1148delAGTCACTAT	c.(1138-1149)acagtcactata>aca	p.VTI381del	CD6_ENST00000545105.1_3'UTR|CD6_ENST00000344028.5_In_Frame_Del_p.VTI381del|CD6_ENST00000352009.5_In_Frame_Del_p.VTI381del|CD6_ENST00000452451.2_In_Frame_Del_p.VTI381del|CD6_ENST00000346437.4_In_Frame_Del_p.VTI381del	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	381					cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						GTGTTCAGACAGTCACTATAGGTAAGTGT	0.526																																					p.380_383del	Pancreas(169;904 2017 4767 38890 42505)	Atlas-Indel,Pindel	.											.	CD6	122	.	0			c.1139_1147del						PASS	.																																			SO:0001651	inframe_deletion	923	exon6			.		CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"CD molecules"	1691	protein-coding gene	gene with protein product		186720	"CD6 antigen"			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.1140_1148delAGTCACTAT	chr11.hg19:g.60778597_60778605delAGTCACTAT	ENSP00000323280:p.Val381_Ile383del	230.0	0.0	0		171.0	38.0	0.222222	NM_006725	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	In_Frame_Del	DEL	ENST00000313421.7	hg19	CCDS7999.1																																																																																			.	.	.	none		0.526	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725		-	60778605	AGTCACTAT	-	60778597	7	5	103	1	0	1	0	1	0	0	0	0	3030	175	7	0	1162	0	CD6	11	60778597	In_Frame_Del	DEL	AGTCACTAT	TCGA-B9-A44B-01A-11D-A25F-10	27008266	60778597	74227919	71	6601											
HNRNPUL2	221092	hgsc.bcm.edu	37	chr11	62491416	62491416	+	Frame_Shift_Del	DEL	C	C	-																															gttcacaagagtttgatcctCctcctcatcttttgcctctt																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr11:62491416delC	ENST00000301785.5	-	3	913	c.721delG	c.(721-723)gagfs	p.E241fs	HNRNPUL2-BSCL2_ENST00000403734.2_Frame_Shift_Del_p.E241fs	NM_001079559.2	NP_001073027.1	Q1KMD3	HNRL2_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 2	241	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.|Glu-rich. {ECO:0000255}.					membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						GTTTGATCCTCCTCCTCATCT	0.383																																					p.E241fs		Atlas-Indel,Pindel	.											.	HNRNPUL2	41	.	0			c.722delA						PASS	.						196	187	190					11																	62491416		1958	4148	6106	SO:0001589	frameshift_variant	221092	exon3			.		CCDS41659.1	11q12	2013-07-16		2008-04-18	ENSG00000214753	ENSG00000214753			25451	protein-coding gene	gene with protein product				HNRPUL2			Standard	NM_001079559		Approved	DKFZp762N1910	uc001nuw.3	Q1KMD3	OTTHUMG00000167773	ENST00000301785.5:c.721delG	chr11.hg19:g.62491416delC	ENSP00000301785:p.Glu241fs	215.0	0.0	0		157.0	95.0	0.605096	NM_001079559	Q8N3B3	Frame_Shift_Del	DEL	ENST00000301785.5	hg19	CCDS41659.1																																																																																			.	.	.	none		0.383	HNRNPUL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396208.2	XM_495877		-	62491416	C	-	62491416	7	5	103	1	0	1	0	1	0	0	0	0	7282	864	30	0	1570	0	HNRNPUL2	11	62491416	Frame_Shift_Del	DEL	C	TCGA-B9-A44B-01A-11D-A25F-10	1712819	62491416	72515100	72	6602											
PPP2R5B	5526	hgsc.bcm.edu	37	chr11	64694184	64694184	+	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	ggatgccctctcctccccagAtgtgccggcttccgagctgc	4	9	11	17	2	1	1	0	0	1	1	4	3	3	2	6	2	4	2	6	2	0	1			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr11:64694184A>G	ENST00000164133.2	+	3	822	c.200A>G	c.(199-201)gAt>gGt	p.D67G		NM_006244.3	NP_006235.1	Q15173	2A5B_HUMAN	protein phosphatase 2, regulatory subunit B', beta	67					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						TCCTCCCCAGATGTGCCGGCT	0.662																																					p.D67G		Atlas-SNP	.											.	PPP2R5B	47	.	0			c.A200G						PASS	.						55	61	59					11																	64694184		2201	4297	6498	SO:0001630	splice_region_variant	5526	exon3			CCCCAGATGTGCC	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.200-1A>G	chr11.hg19:g.64694184A>G		44.0	0.0	.		35.0	6.0	.	NM_006244	Q13853	Missense_Mutation	SNP	ENST00000164133.2	hg19	CCDS8085.1	.	.	.	.	.	.	.	.	.	.	A	14.84	2.654294	0.47467	.	.	ENSG00000068971	ENST00000526559;ENST00000164133;ENST00000359279;ENST00000527441	.	.	.	4.6	4.6	0.57074	.	0.000000	0.85682	D	0.000000	T	0.68650	0.3024	M	0.82517	2.595	0.80722	D	1	B	0.14012	0.009	B	0.24974	0.057	T	0.66748	-0.5845	8	.	.	.	.	12.2855	0.54789	1.0:0.0:0.0:0.0	.	67	Q15173	2A5B_HUMAN	G	67;67;94;67	.	.	D	+	2	0	PPP2R5B	64450760	1.000000	0.71417	1.000000	0.80357	0.343000	0.28985	8.597000	0.90847	2.077000	0.62373	0.528000	0.53228	GAT	.	.	.	none		0.662	PPP2R5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385465.1	NM_006244	Missense_Mutation	G	64694184	A	G	64694184	5	3	103	1	0	0	0	0	0	0	1	0	12403	347	12	3	206	3	PPP2R5B	11	64694184	Splice_Site	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	2202768	64694184	70312332	73	6603											
MYO7A	4647	hgsc.bcm.edu	37	chr11	76925728	76925728	+	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	gagcaaacagcggggctccaGgagcggcaagtgaacagtca	13	3	15	10	2	1	1	1	1	0	0	2	3	2	2	1	4	5	3	1	4	3	0			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr11:76925728G>T	ENST00000409709.3	+	49	6907	c.6635G>T	c.(6634-6636)aGg>aTg	p.R2212M	MYO7A_ENST00000458637.2_Missense_Mutation_p.R2172M|MYO7A_ENST00000605744.1_3'UTR|MYO7A_ENST00000409619.2_Missense_Mutation_p.R2163M	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	2212					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						CGGGGCTCCAGGAGCGGCAAG	0.582																																					p.R2212M		Atlas-SNP	.											.	MYO7A	164	.	0			c.G6635T						PASS	.						28	31	30					11																	76925728		2034	4166	6200	SO:0001583	missense	4647	exon49			GCTCCAGGAGCGG	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.6635G>T	chr11.hg19:g.76925728G>T	ENSP00000386331:p.Arg2212Met	107.0	0.0	.		84.0	8.0	.	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	hg19	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	G	12.66	2.004181	0.35320	.	.	ENSG00000137474	ENST00000409709;ENST00000458637;ENST00000409619;ENST00000545136;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000458169	D;D;D;D	0.88664	-2.39;-2.39;-2.41;-2.2	5.47	4.55	0.56014	.	0.125567	0.64402	D	0.000013	D	0.91382	0.7281	M	0.73598	2.24	0.38514	D	0.948547	D;D	0.64830	0.991;0.994	P;P	0.60682	0.878;0.759	D	0.91720	0.5388	10	0.87932	D	0	.	5.1745	0.15127	0.2814:0.0:0.7186:0.0	.	2172;2212	F8VUN5;Q13402	.;MYO7A_HUMAN	M	2212;2172;2163;1385;2211;2181;2088;1354	ENSP00000386331:R2212M;ENSP00000392185:R2172M;ENSP00000386635:R2163M;ENSP00000417017:R1354M	ENSP00000345075:R2088M	R	+	2	0	MYO7A	76603376	1.000000	0.71417	0.998000	0.56505	0.371000	0.29859	4.530000	0.60595	2.558000	0.86282	0.467000	0.42956	AGG	.	.	.	none		0.582	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		T	76925728	G	T	76925728	3	4	103	1	0	0	0	0	1	0	0	0	10089	1000	35	4	6859	4	MYO7A	11	76925728	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	12231544	76925728	58080788	74	6604											
HEPHL1	341208	hgsc.bcm.edu	37	chr11	93797512	93797529	+	In_Frame_Del	DEL	ATTCAGGGACACGGAATG	ATTCAGGGACACGGAATG	-																															gacaggtatcctgaatagatAttcagggacacggaatgatg																								rs200031155|rs368679862|rs556983825		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	ATTCAGGGACACGGAATG	ATTCAGGGACACGGAATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr11:93797512_93797529delATTCAGGGACACGGAATG	ENST00000315765.9	+	4	652_669	c.644_661delATTCAGGGACACGGAATG	c.(643-663)tattcagggacacggaatgat>tat	p.SGTRND216del		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	216					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)				CTGAATAGATATTCAGGGACACGGAATGATGTGGATCG	0.394																																					p.215_220del		Atlas-Indel,Pindel	.											.	HEPHL1	144	.	0			c.643_660del						PASS	.																																			SO:0001651	inframe_deletion	341208	exon4			.	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.644_661delATTCAGGGACACGGAATG	chr11.hg19:g.93797512_93797529delATTCAGGGACACGGAATG	ENSP00000313699:p.Ser216_Asp221del	130.0	0.0	0		68.0	15.0	0.220588	NM_001098672	Q3C1W7	In_Frame_Del	DEL	ENST00000315765.9	hg19	CCDS44710.1																																																																																			.	.	.	none		0.394	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947		-	93797529	ATTCAGGGACACGGAATG	-	93797512	7	5	103	1	0	1	0	1	0	0	0	0	7062	449	16	0	658	0	HEPHL1	11	93797512	In_Frame_Del	DEL	ATTCAGGGACACGGAATG	TCGA-B9-A44B-01A-11D-A25F-10	16871784	93797512	41209004	75	6605											
PHLDB1	23187	hgsc.bcm.edu	37	chr11	118509935	118509935	+	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	ccactcactcacagggggcaGgcctttcccgaagaccacat	10	6	9	16	1	2	1	2	0	0	1	3	2	3	1	4	3	0	1	4	3	1	1			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr11:118509935G>A	ENST00000361417.2	+	13	3113	c.2702G>A	c.(2701-2703)aGg>aAg	p.R901K	PHLDB1_ENST00000527898.1_5'UTR|PHLDB1_ENST00000356063.5_Missense_Mutation_p.R901K|PHLDB1_ENST00000534672.1_3'UTR|PHLDB1_ENST00000524713.1_5'Flank|AP002954.3_ENST00000530198.1_RNA	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	901										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)		ACAGGGGGCAGGCCTTTCCCG	0.562																																					p.R901K		Atlas-SNP	.											.	PHLDB1	103	.	0			c.G2702A						PASS	.						97	84	88					11																	118509935		2200	4295	6495	SO:0001583	missense	23187	exon12			GGGGCAGGCCTTT		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.2702G>A	chr11.hg19:g.118509935G>A	ENSP00000354498:p.Arg901Lys	169.0	1.0	.		95.0	77.0	.	NM_001144758	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Missense_Mutation	SNP	ENST00000361417.2	hg19	CCDS8401.1	.	.	.	.	.	.	.	.	.	.	G	15.63	2.890173	0.52014	.	.	ENSG00000019144	ENST00000361417;ENST00000361465;ENST00000358191;ENST00000356063	T;T	0.41065	1.01;1.01	4.39	4.39	0.52855	.	0.120998	0.49916	D	0.000123	T	0.28067	0.0692	L	0.31065	0.9	0.80722	D	1	B;B;B;B	0.30482	0.002;0.281;0.062;0.003	B;B;B;B	0.34093	0.004;0.175;0.025;0.005	T	0.05954	-1.0854	10	0.02654	T	1	-25.2439	12.056	0.53536	0.0:0.1734:0.8266:0.0	.	645;901;901;901	Q5W9G0;Q86UU1-3;Q86UU1-2;Q86UU1	.;.;.;PHLB1_HUMAN	K	901;660;265;901	ENSP00000354498:R901K;ENSP00000348359:R901K	ENSP00000348359:R901K	R	+	2	0	PHLDB1	118015145	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	3.292000	0.51772	2.010000	0.58986	0.456000	0.33151	AGG	.	.	.	none		0.562	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157		A	118509935	G	A	118509935	3	1	103	1	0	0	0	0	1	0	0	0	11858	1000	35	2	2744	2	PHLDB1	11	118509935	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	24712423	118509935	16496581	76	6606											
KIAA0528	9847	hgsc.bcm.edu	37	chr12	22670928	22670928	+	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	gaagcgccttaccagttttgGgtgtcaaactcaaatctgtg	10	12	10	9	1	3	0	2	0	1	0	3	1	3	0	2	1	3	1	2	1	4	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr12:22670928G>T	ENST00000333957.4	-	8	1199	c.944C>A	c.(943-945)cCc>cAc	p.P315H	C2CD5_ENST00000544930.1_Intron|C2CD5_ENST00000446597.1_Missense_Mutation_p.P315H|C2CD5_ENST00000542676.1_Missense_Mutation_p.P315H|C2CD5_ENST00000536386.1_Intron|C2CD5_ENST00000396028.2_Intron|C2CD5_ENST00000545552.1_Intron|C2CD5_ENST00000540703.1_5'Flank	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	315					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)										ACCAGTTTTGGGTGTCAAACT	0.383																																					p.P315H		Atlas-SNP	.											.	.	.	.	0			c.C944A						PASS	.						177	174	175					12																	22670928		2203	4300	6503	SO:0001583	missense	9847	exon8			GTTTTGGGTGTCA	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.944C>A	chr12.hg19:g.22670928G>T	ENSP00000334229:p.Pro315His	70.0	0.0	.		85.0	36.0	.	NM_014802	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Missense_Mutation	SNP	ENST00000333957.4	hg19	CCDS31758.1	.	.	.	.	.	.	.	.	.	.	G	18.05	3.536609	0.65085	.	.	ENSG00000111731	ENST00000333957;ENST00000446597;ENST00000542676	T;T;T	0.50001	0.76;0.76;0.76	6.04	5.14	0.70334	.	.	.	.	.	T	0.66268	0.2772	M	0.75777	2.31	0.80722	D	1	D;D	0.65815	0.995;0.957	P;P	0.59288	0.855;0.58	T	0.71758	-0.4496	9	0.72032	D	0.01	-3.34	17.3582	0.87342	0.0:0.125:0.875:0.0	.	315;315	B4DRN7;Q86YS7	.;K0528_HUMAN	H	315	ENSP00000334229:P315H;ENSP00000388756:P315H;ENSP00000441951:P315H	ENSP00000334229:P315H	P	-	2	0	KIAA0528	22562195	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.606000	0.98325	1.538000	0.49270	0.561000	0.74099	CCC	.	.	.	none		0.383	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802		T	22670928	G	T	22670928	3	4	103	1	0	0	0	0	1	0	0	0	8189	1232	43	4	2130	4	KIAA0528	12	22670928	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10		22670928	111180967	77	6607											
ARID2	196528	hgsc.bcm.edu	37	chr12	46205220	46205221	+	Frame_Shift_Del	DEL	AA	AA	-																															gttacctagaaaagtacgagAaagttcatcattttggggag																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr12:46205220_46205221delAA	ENST00000334344.6	+	4	476_477	c.304_305delAA	c.(304-306)aaafs	p.K102fs	ARID2_ENST00000422737.1_5'UTR	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	102	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		AAAGTACGAGAAAGTTCATCAT	0.366			"N, S, F"		hepatocellular carcinoma																																p.101_102del		Atlas-Indel,Pindel	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.303_304del						PASS	.																																			SO:0001589	frameshift_variant	196528	exon4			.		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.304_305delAA	chr12.hg19:g.46205220_46205221delAA	ENSP00000335044:p.Lys102fs	85.0	0.0	0		82.0	33.0	0.402439	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Frame_Shift_Del	DEL	ENST00000334344.6	hg19	CCDS31783.1																																																																																			.	.	.	none		0.366	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		-	46205221	AA	-	46205220	7	5	103	1	0	1	0	1	0	0	0	0	915	247	9	0	318	0	ARID2	12	46205220	Frame_Shift_Del	DEL	AA	TCGA-B9-A44B-01A-11D-A25F-10	23534292	46205220	87646675	78	6608											
PRPH	5630	hgsc.bcm.edu	37	chr12	49690229	49690229	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgaaggacgtggacgatgcCactctgtcccgcctggaact	8	8	12	13	4	1	0	0	0	1	0	3	5	2	3	3	3	2	0	3	3	2	0			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr12:49690229C>T	ENST00000257860.4	+	3	2120	c.621C>T	c.(619-621)gcC>gcT	p.A207A	RP11-161H23.9_ENST00000553259.1_RNA	NM_006262.3	NP_006253.2	P23942	PRPH2_HUMAN	peripherin	0					cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(8)|skin(1)	12						TGGACGATGCCACTCTGTCCC	0.567																																					p.A207A		Atlas-SNP	.											.	PRPH	26	.	0			c.C621T						PASS	.						86	77	80					12																	49690229		2203	4300	6503	SO:0001819	synonymous_variant	5630	exon3			CGATGCCACTCTG		CCDS8783.1	12q12-q13	2013-01-16						"Intermediate filaments type III"	9461	protein-coding gene	gene with protein product		170710		NEF4		1378416	Standard	XM_005269025		Approved	PRPH1	uc001rtu.3	P41219		ENST00000257860.4:c.621C>T	chr12.hg19:g.49690229C>T		168.0	0.0	.		151.0	9.0	.	NM_006262	Q5TFH5|Q6DK65	Silent	SNP	ENST00000257860.4	hg19	CCDS8783.1																																																																																			.	.	.	none		0.567	PRPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393381.1	NM_006262		T	49690229	C	T	49690229	2	4	103	1	0	0	0	0	0	0	0	1	12586	581	21	2		2	PRPH	12	49690229	Silent	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	3485009	49690229	84161666	79	6609											
KCNH3	23416	hgsc.bcm.edu	37	chr12	49951017	49951018	+	Frame_Shift_Del	DEL	AC	AC	-																															cagcgaggcaaggaacacagAcacactggacaagcttcggc																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr12:49951017_49951018delAC	ENST00000257981.6	+	14	2887_2888	c.2627_2628delAC	c.(2626-2628)gacfs	p.D876fs	MCRS1_ENST00000547182.1_5'Flank	NM_012284.1	NP_036416.1	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 3	876					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36						AGGAACACAGACACACTGGACA	0.619																																					p.876_876del		Atlas-Indel,Pindel	.											.	KCNH3	88	.	0			c.2626_2627del						PASS	.																																			SO:0001589	frameshift_variant	23416	exon14			.	AB022696	CCDS8786.1	12q13	2012-07-05				ENSG00000135519		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6252	protein-coding gene	gene with protein product		604527				10455180, 16382104	Standard	NM_012284		Approved	Kv12.2, BEC1, elk2	uc001ruh.1	Q9ULD8	OTTHUMG00000169517	ENST00000257981.6:c.2627_2628delAC	chr12.hg19:g.49951021_49951022delAC	ENSP00000257981:p.Asp876fs	131.0	0.0	0		126.0	51.0	0.404762	NM_012284	Q9UQ06	Frame_Shift_Del	DEL	ENST00000257981.6	hg19	CCDS8786.1																																																																																			.	.	.	none		0.619	KCNH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404571.2	NM_012284		-	49951018	AC	-	49951017	7	5	103	1	0	1	0	1	0	0	0	0	8040	275	10	0	2681	0	KCNH3	12	49951017	Frame_Shift_Del	DEL	AC	TCGA-B9-A44B-01A-11D-A25F-10	260788	49951017	83900878	80	6610											
KRT85	3891	hgsc.bcm.edu	37	chr12	52754642	52754642	+	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	ggctccatgactctactaggCaaagcggaccgaccggctac	10	6	11	14	3	1	1	0	1	1	0	2	3	2	2	3	4	3	3	3	4	4	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr12:52754642C>T	ENST00000257901.3	-	9	1594	c.1519G>A	c.(1519-1521)Gcc>Acc	p.A507T	KRT85_ENST00000544265.1_Missense_Mutation_p.A295T	NM_002283.3	NP_002274.1	P78386	KRT85_HUMAN	keratin 85	507	Tail.				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)		CTCTACTAGGCAAAGCGGACC	0.607																																					p.A507T		Atlas-SNP	.											.	KRT85	78	.	0			c.G1519A						PASS	.						44	52	49					12																	52754642		2201	4300	6501	SO:0001583	missense	3891	exon9			ACTAGGCAAAGCG	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.1519G>A	chr12.hg19:g.52754642C>T	ENSP00000257901:p.Ala507Thr	77.0	0.0	.		68.0	29.0	.	NM_002283	Q9NSB1	Missense_Mutation	SNP	ENST00000257901.3	hg19	CCDS8824.1	.	.	.	.	.	.	.	.	.	.	C	11.80	1.746175	0.30955	.	.	ENSG00000135443	ENST00000257901;ENST00000544265	D;D	0.82255	-1.59;-1.5	5.22	3.31	0.37934	.	0.000000	0.44097	D	0.000485	T	0.72104	0.3419	N	0.22421	0.69	0.09310	N	1	B	0.27498	0.18	B	0.26517	0.07	T	0.67952	-0.5537	10	0.87932	D	0	.	12.1399	0.53993	0.0:0.6712:0.3288:0.0	.	507	P78386	KRT85_HUMAN	T	507;295	ENSP00000257901:A507T;ENSP00000440240:A295T	ENSP00000257901:A507T	A	-	1	0	KRT85	51040909	0.619000	0.27059	0.841000	0.33234	0.099000	0.18886	0.941000	0.29005	1.427000	0.47276	0.609000	0.83330	GCC	.	.	.	none		0.607	KRT85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405184.1	NM_002283		T	52754642	C	T	52754642	3	4	103	1	0	0	0	0	1	0	0	0	8506	710	25	2	8	2	KRT85	12	52754642	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	2803625	52754642	81097253	81	6611											
LRP1	4035	hgsc.bcm.edu	37	chr12	57587701	57587701	+	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	gagacagcctgtggtgtgggCgagttccgctgccgggacgg	5	7	19	10	4	0	1	0	0	0	1	1	4	1	2	3	4	2	2	3	4	0	1	rs367824154		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr12:57587701C>T	ENST00000243077.3	+	48	8290	c.7824C>T	c.(7822-7824)ggC>ggT	p.G2608G	MIR1228_ENST00000408438.1_RNA	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	2608	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)	GTGGTGTGGGCGAGTTCCGCT	0.612																																					p.G2608G		Atlas-SNP	.											.	LRP1	428	.	0			c.C7824T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	95	86	89		7824	-5.7	0.2	12		89	0,8600		0,0,4300	no	coding-synonymous	LRP1	NM_002332.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		2608/4545	57587701	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	4035	exon48			TGTGGGCGAGTTC	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.7824C>T	chr12.hg19:g.57587701C>T		127.0	0.0	.		140.0	6.0	.	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	hg19	CCDS8932.1																																																																																			.	.	.	weak		0.612	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		T	57587701	C	T	57587701	2	4	103	1	0	0	0	0	0	0	0	1	8958	755	27	1		1	LRP1	12	57587701	Silent	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	4833059	57587701	76264194	82	6612											
PTPRB	5787	hgsc.bcm.edu	37	chr12	70932007	70932007	+	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	gagagcttcactcgcgtggcAtcatctggaaggagagattt	10	10	13	8	2	3	2	2	0	1	2	4	6	3	4	0	3	1	2	0	3	1	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr12:70932007A>T	ENST00000261266.5	-	26	5249	c.5220T>A	c.(5218-5220)gaT>gaA	p.D1740E	PTPRB_ENST00000550358.1_Missense_Mutation_p.D1870E|RP11-588H23.3_ENST00000548687.1_RNA|RP11-588H23.3_ENST00000551438.1_RNA|PTPRB_ENST00000334414.6_Missense_Mutation_p.D1958E|PTPRB_ENST00000538708.1_Missense_Mutation_p.D1650E|RP11-588H23.3_ENST00000546836.1_RNA|RP11-588H23.3_ENST00000547656.1_RNA|RP11-588H23.3_ENST00000549460.1_RNA|PTPRB_ENST00000451516.2_Missense_Mutation_p.D1650E|PTPRB_ENST00000550857.1_Missense_Mutation_p.D1650E	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	1740	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			CTCGCGTGGCATCATCTGGAA	0.478																																					p.D1958E		Atlas-SNP	.											.	PTPRB	676	.	0			c.T5874A						PASS	.						162	159	160					12																	70932007		2102	4245	6347	SO:0001583	missense	5787	exon28			CGTGGCATCATCT	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.5220T>A	chr12.hg19:g.70932007A>T	ENSP00000261266:p.Asp1740Glu	145.0	0.0	.		184.0	74.0	.	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	hg19	CCDS44944.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.952571	0.73787	.	.	ENSG00000127329	ENST00000334414;ENST00000451516;ENST00000550358;ENST00000538708;ENST00000550857;ENST00000261266	D;D;D;D;D;D	0.87029	-2.2;-2.2;-2.2;-2.2;-2.2;-2.2	5.67	0.844	0.18943	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	D	0.91623	0.7353	M	0.78801	2.425	0.53688	D	0.999979	D;D;D;D;D	0.89917	0.999;0.999;1.0;1.0;0.999	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.999	D	0.89983	0.4102	10	0.87932	D	0	.	9.5604	0.39366	0.6532:0.0:0.3468:0.0	.	1650;1650;1958;1740;1870	P23467-2;F5H3G6;P23467-3;P23467;F8VU56	.;.;.;PTPRB_HUMAN;.	E	1958;1650;1870;1650;1650;1740	ENSP00000334928:D1958E;ENSP00000393028:D1650E;ENSP00000448058:D1870E;ENSP00000438927:D1650E;ENSP00000447302:D1650E;ENSP00000261266:D1740E	ENSP00000261266:D1740E	D	-	3	2	PTPRB	69218274	1.000000	0.71417	0.996000	0.52242	0.783000	0.44284	1.253000	0.32886	0.122000	0.18314	-0.371000	0.07208	GAT	.	.	.	none		0.478	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			T	70932007	A	T	70932007	3	4	103	1	0	0	0	0	1	0	0	0	12809	214	8	5	801	5	PTPRB	12	70932007	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	13344306	70932007	62919888	83	6613											
TMCC3	57458	hgsc.bcm.edu	37	chr12	94965249	94965249	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctttctatggcacacaggaTatggtcccagtttttacaaa	11	13	7	10	0	1	0	0	0	1	0	2	1	2	1	2	3	1	2	2	3	4	6			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr12:94965249T>C	ENST00000261226.4	-	4	1527	c.1396A>G	c.(1396-1398)Atc>Gtc	p.I466V	TMCC3_ENST00000551457.1_Missense_Mutation_p.I435V	NM_020698.2	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3	466						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	29						GCACACAGGATATGGTCCCAG	0.418																																					p.I466V		Atlas-SNP	.											.	TMCC3	63	.	0			c.A1396G						PASS	.						113	108	110					12																	94965249		2203	4300	6503	SO:0001583	missense	57458	exon4			ACAGGATATGGTC	AB032971	CCDS31877.1, CCDS73506.1	12q22	2005-01-21	2005-07-13			ENSG00000057704		"Transmembrane and coiled-coil domain containing"	29199	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 3"			10574461	Standard	XM_005269039		Approved	KIAA1145	uc001tdj.2	Q9ULS5	OTTHUMG00000170225	ENST00000261226.4:c.1396A>G	chr12.hg19:g.94965249T>C	ENSP00000261226:p.Ile466Val	176.0	0.0	.		139.0	66.0	.	NM_020698	Q8IWB2	Missense_Mutation	SNP	ENST00000261226.4	hg19	CCDS31877.1	.	.	.	.	.	.	.	.	.	.	T	10.54	1.378687	0.24944	.	.	ENSG00000057704	ENST00000261226;ENST00000551457	T;T	0.40756	1.02;1.02	5.33	5.33	0.75918	.	0.057274	0.64402	D	0.000001	T	0.49847	0.1581	L	0.32530	0.975	0.48185	D	0.999604	D	0.61697	0.99	D	0.68192	0.956	T	0.36212	-0.9757	10	0.13470	T	0.59	-18.6633	15.2998	0.73940	0.0:0.0:0.0:1.0	.	466	Q9ULS5	TMCC3_HUMAN	V	466;435	ENSP00000261226:I466V;ENSP00000449888:I435V	ENSP00000261226:I466V	I	-	1	0	TMCC3	93489380	1.000000	0.71417	0.950000	0.38849	0.986000	0.74619	2.358000	0.44134	2.019000	0.59389	0.459000	0.35465	ATC	.	.	.	none		0.418	TMCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408113.1	NM_020698		C	94965249	T	C	94965249	3	2	103	1	0	0	0	0	1	0	0	0	16006	1406	49	3	41	3	TMCC3	12	94965249	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	24033242	94965249	38886646	84	6614											
PXN	5829	hgsc.bcm.edu	37	chr12	120653013	120653013	+	Frame_Shift_Del	DEL	G	G	-																															ccccagcatgctgtccagctGgctcccgggcttcgggggcc																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr12:120653013delG	ENST00000228307.7	-	8	1138	c.997delC	c.(997-999)cagfs	p.Q333fs	PXN-AS1_ENST00000542265.1_RNA|PXN_ENST00000536957.1_Frame_Shift_Del_p.Q331fs|PXN_ENST00000424649.2_Frame_Shift_Del_p.Q299fs|PXN_ENST00000458477.2_Frame_Shift_Del_p.Q166fs|PXN_ENST00000538144.1_5'UTR|PXN_ENST00000267257.7_Frame_Shift_Del_p.Q347fs|PXN_ENST00000397506.3_Frame_Shift_Del_p.Q145fs|PXN-AS1_ENST00000535200.1_RNA	NM_001080855.2	NP_001074324.1	P49023	PAXI_HUMAN	paxillin	333					activation of MAPK activity (GO:0000187)|branching morphogenesis of an epithelial tube (GO:0048754)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cellular component movement (GO:0006928)|cellular response to reactive oxygen species (GO:0034614)|cytoskeleton organization (GO:0007010)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|growth hormone receptor signaling pathway (GO:0060396)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|muscle contraction (GO:0006936)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of cell shape (GO:0008360)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	beta-catenin binding (GO:0008013)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CTGTCCAGCTGGCTCCCGGGC	0.677																																					p.Q347fs		Atlas-Indel,Pindel	.											.	PXN	69	.	0			c.1040delA						PASS	.						11	13	12					12																	120653013		2038	4192	6230	SO:0001589	frameshift_variant	5829	exon7			.	U14588	CCDS44996.1, CCDS44997.1, CCDS44998.1, CCDS58281.1	12q24	2006-01-23			ENSG00000089159	ENSG00000089159			9718	protein-coding gene	gene with protein product		602505				7534286	Standard	NM_001080855		Approved		uc001txv.3	P49023	OTTHUMG00000169169	ENST00000228307.7:c.997delC	chr12.hg19:g.120653013delG	ENSP00000228307:p.Gln333fs	84.0	0.0	0		68.0	28.0	0.411765	NM_001243756	B2RAI3|B7ZMB4|O14970|O14971|O60360|Q5HYA4	Frame_Shift_Del	DEL	ENST00000228307.7	hg19	CCDS44997.1																																																																																			.	.	.	none		0.677	PXN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402679.4	NM_002859		-	120653013	G	-	120653013	7	5	103	1	0	1	0	1	0	0	0	0	12865	1357	47	0	798	0	PXN	12	120653013	Frame_Shift_Del	DEL	G	TCGA-B9-A44B-01A-11D-A25F-10	25687764	120653013	13198882	85	6615											
PABPC3	5042	hgsc.bcm.edu	37	chr13	25671122	25671122	+	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	ctcaatggaaaacaaatttaCgttggtcgagctcagaaaaa	17	9	8	7	2	2	1	2	0	0	1	3	3	2	2	0	2	3	2	0	2	7	3	rs79072440		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr13:25671122C>T	ENST00000281589.3	+	1	823	c.786C>T	c.(784-786)taC>taT	p.Y262Y		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	262	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				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)		AACAAATTTACGTTGGTCGAG	0.408																																					p.Y262Y		Atlas-SNP	.											.	PABPC3	129	.	0			c.C786T						PASS	.																																			SO:0001819	synonymous_variant	5042	exon1			AATTTACGTTGGT	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.786C>T	chr13.hg19:g.25671122C>T		159.0	0.0	.		153.0	13.0	.	NM_030979	Q8NHV0|Q9H086	Silent	SNP	ENST00000281589.3	hg19	CCDS9311.1																																																																																			.	C|0.500;T|0.500	0.500	weak		0.408	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979		T	25671122	C	T	25671122	2	4	103	1	0	0	0	0	0	0	0	1	11372	547	19	1		1	PABPC3	13	25671122	Silent	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10		25671122	89498756	86	6616											
ABCC4	10257	hgsc.bcm.edu	37	chr13	95840715	95840715	+	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	attctaactcaccttccctgCtcccacggggccgaccacag	8	8	7	18	2	2	0	1	0	1	0	4	1	4	0	5	2	2	1	5	2	1	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr13:95840715C>A	ENST00000376887.4	-	10	1459	c.1345G>T	c.(1345-1347)Gca>Tca	p.A449S	ABCC4_ENST00000536256.1_Missense_Mutation_p.A374S|ABCC4_ENST00000412704.1_Missense_Mutation_p.A449S|ABCC4_ENST00000431522.1_Missense_Mutation_p.A449S|ABCC4_ENST00000538287.1_3'UTR	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	449	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				blood coagulation (GO:0007596)|oxidation-reduction process (GO:0055114)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of smooth muscle cell proliferation (GO:0048661)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cefazolin(DB01327)|Celecoxib(DB00482)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Leucovorin(DB00650)|Meloxicam(DB00814)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Probenecid(DB01032)|Rosuvastatin(DB01098)|Sildenafil(DB00203)|Sorafenib(DB00398)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tenofovir(DB00300)|Tioguanine(DB00352)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Zidovudine(DB00495)	ACCTTCCCTGCTCCCACGGGG	0.468																																					p.A449S		Atlas-SNP	.											.	ABCC4	248	.	0			c.G1345T						PASS	.						120	109	113					13																	95840715		2203	4300	6503	SO:0001583	missense	10257	exon10			TCCCTGCTCCCAC	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.1345G>T	chr13.hg19:g.95840715C>A	ENSP00000366084:p.Ala449Ser	140.0	0.0	.		112.0	23.0	.	NM_005845	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Missense_Mutation	SNP	ENST00000376887.4	hg19	CCDS9474.1	.	.	.	.	.	.	.	.	.	.	C	14.90	2.673351	0.47781	.	.	ENSG00000125257	ENST00000412704;ENST00000376887;ENST00000536256;ENST00000431522	D;D;D;D	0.94687	-3.49;-3.49;-3.49;-3.49	5.22	4.29	0.51040	ABC transporter, transmembrane domain, type 1 (1);ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.050917	0.85682	D	0.000000	D	0.84316	0.5445	N	0.02751	-0.505	0.80722	D	1	B;B;B;B;B	0.27117	0.032;0.068;0.028;0.168;0.038	B;B;B;B;B	0.27262	0.039;0.05;0.076;0.078;0.034	T	0.81959	-0.0694	10	0.07175	T	0.84	.	16.4591	0.84031	0.1401:0.8598:0.0:0.0	.	374;449;449;449;449	B7Z3Q7;A8K2Q2;O15439-2;Q8IVZ4;O15439	.;.;.;.;MRP4_HUMAN	S	449;449;374;449	ENSP00000388657:A449S;ENSP00000366084:A449S;ENSP00000442024:A374S;ENSP00000398562:A449S	ENSP00000366084:A449S	A	-	1	0	ABCC4	94638716	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	3.665000	0.54532	2.447000	0.82792	0.637000	0.83480	GCA	.	.	.	none		0.468	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845		A	95840715	C	A	95840715	3	1	103	1	0	0	0	0	1	0	0	0	55	797	28	4	2769	4	ABCC4	13	95840715	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	70169593	95840715	19329163	87	6617											
ACIN1	22985	hgsc.bcm.edu	37	chr14	23549484	23549484	+	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	taaaggtggaggagtctcctCctcgctggcagtttgctctg	6	12	13	10	1	2	0	0	0	2	0	5	2	3	2	2	4	1	4	2	4	2	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr14:23549484C>G	ENST00000262710.1	-	6	1561	c.1234G>C	c.(1234-1236)Gag>Cag	p.E412Q	ACIN1_ENST00000605057.1_Missense_Mutation_p.E354Q|ACIN1_ENST00000457657.1_Missense_Mutation_p.E372Q|ACIN1_ENST00000555352.1_5'Flank|ACIN1_ENST00000555053.1_Missense_Mutation_p.E412Q	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	412	Glu-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		GGAGTCTCCTCCTCGCTGGCA	0.517																																					p.E412Q		Atlas-SNP	.											.	ACIN1	147	.	0			c.G1234C						PASS	.						59	61	61					14																	23549484		2203	4300	6503	SO:0001583	missense	22985	exon6			TCTCCTCCTCGCT	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.1234G>C	chr14.hg19:g.23549484C>G	ENSP00000262710:p.Glu412Gln	222.0	0.0	.		239.0	111.0	.	NM_001164814	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Missense_Mutation	SNP	ENST00000262710.1	hg19	CCDS9587.1	.	.	.	.	.	.	.	.	.	.	C	19.19	3.780380	0.70222	.	.	ENSG00000100813	ENST00000262710;ENST00000457657;ENST00000555053	T;T;T	0.30448	1.53;1.53;1.53	5.27	5.27	0.74061	.	0.000000	0.41605	D	0.000851	T	0.40886	0.1135	L	0.27053	0.805	0.34634	D	0.719933	D;D;D	0.67145	0.996;0.993;0.993	D;D;D	0.75484	0.986;0.968;0.968	T	0.43605	-0.9381	10	0.32370	T	0.25	-13.6658	14.2703	0.66147	0.0:1.0:0.0:0.0	.	412;412;372	G3V3M7;Q9UKV3;E7EQT4	.;ACINU_HUMAN;.	Q	412;372;412	ENSP00000262710:E412Q;ENSP00000405677:E372Q;ENSP00000451328:E412Q	ENSP00000262710:E412Q	E	-	1	0	ACIN1	22619324	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.347000	0.52200	2.752000	0.94435	0.650000	0.86243	GAG	.	.	.	none		0.517	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977		G	23549484	C	G	23549484	3	3	103	1	0	0	0	0	1	0	0	0	142	864	30	4	2994	4	ACIN1	14	23549484	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10		23549484	83800056	88	6618											
SAMD4A	23034	hgsc.bcm.edu	37	chr14	55203876	55203876	+	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	gagctagaggaccccagtgcCtcccatccgatcatgccccc	8	6	9	18	1	1	1	1	0	0	1	3	4	3	2	7	1	3	1	7	1	1	1	rs138744574	byFrequency	TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr14:55203876C>T	ENST00000554335.1	+	4	1513	c.850C>T	c.(850-852)Ctc>Ttc	p.L284F	SAMD4A_ENST00000357634.3_Missense_Mutation_p.L283F|SAMD4A_ENST00000251091.5_Intron|SAMD4A_ENST00000392067.3_Missense_Mutation_p.L284F			Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4A	284					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						ACCCCAGTGCCTCCCATCCGA	0.537																																					p.L284F		Atlas-SNP	.											.	SAMD4A	68	.	0			c.C850T						PASS	.						226	210	215					14																	55203876		2203	4300	6503	SO:0001583	missense	23034	exon3			CAGTGCCTCCCAT	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.850C>T	chr14.hg19:g.55203876C>T	ENSP00000452535:p.Leu284Phe	140.0	0.0	.		130.0	52.0	.	NM_015589	A8MPZ5|Q0VA96|Q6PEW4	Missense_Mutation	SNP	ENST00000554335.1	hg19	CCDS32084.2	.	.	.	.	.	.	.	.	.	.	C	13.83	2.354282	0.41700	.	.	ENSG00000020577	ENST00000554335;ENST00000392067;ENST00000357634	.	.	.	5.15	4.19	0.49359	.	0.203527	0.35615	N	0.003096	T	0.39410	0.1077	N	0.19112	0.55	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.33317	-0.9873	9	0.56958	D	0.05	-16.9697	8.4253	0.32725	0.1972:0.7168:0.0:0.086	.	284	Q9UPU9	SMAG1_HUMAN	F	284;284;283	.	ENSP00000350261:L283F	L	+	1	0	SAMD4A	54273626	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.201000	0.32259	2.673000	0.90976	0.655000	0.94253	CTC	.	C|0.999;A|0.001	.	alt		0.537	SAMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411186.1	NM_015589		T	55203876	C	T	55203876	3	4	103	1	0	0	0	0	1	0	0	0	13834	681	24	2	857	2	SAMD4A	14	55203876	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	31654392	55203876	52145664	89	6619											
SYNE2	23224	hgsc.bcm.edu	37	chr14	64610587	64610587	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgatgtagaaagcaagcgctAtgaaagaacggagtttgcag	15	8	13	5	2	0	4	0	2	0	2	0	5	0	5	0	1	4	5	0	1	6	3	rs556819169		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr14:64610587A>G	ENST00000344113.4	+	83	15616	c.15404A>G	c.(15403-15405)tAt>tGt	p.Y5135C	SYNE2_ENST00000555002.1_Missense_Mutation_p.Y1769C|SYNE2_ENST00000358025.3_Missense_Mutation_p.Y5135C|SYNE2_ENST00000357395.3_Missense_Mutation_p.Y1520C|SYNE2_ENST00000394768.2_Missense_Mutation_p.Y1520C|SYNE2_ENST00000554584.1_Missense_Mutation_p.Y5052C|ESR2_ENST00000542956.1_Intron	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5135					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)		AGCAAGCGCTATGAAAGAACG	0.458													A|||	1	0.000199681	8e-04	0	5008	,	,		19135	0		0	False		,,,				2504	0				p.Y5135C		Atlas-SNP	.											.	SYNE2	577	.	0			c.A15404G						PASS	.						276	278	277					14																	64610587		2203	4300	6503	SO:0001583	missense	23224	exon83			AGCGCTATGAAAG	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.15404A>G	chr14.hg19:g.64610587A>G	ENSP00000341781:p.Tyr5135Cys	216.0	1.0	.		169.0	88.0	.	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	A	16.34	3.096384	0.56075	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	T;T;T;T;T;T	0.52754	1.32;0.65;1.32;1.32;0.67;0.65	5.33	5.33	0.75918	.	0.000000	0.48286	D	0.000190	T	0.67979	0.2951	M	0.73598	2.24	0.80722	D	1	B;D;B;P	0.89917	0.081;1.0;0.382;0.644	B;D;B;B	0.73380	0.094;0.98;0.146;0.307	T	0.70633	-0.4818	10	0.51188	T	0.08	.	15.2733	0.73723	1.0:0.0:0.0:0.0	.	1520;5052;5135;5135	Q8WXH0-7;G3V5X4;Q8WXH0;Q8WXH0-2	.;.;SYNE2_HUMAN;.	C	5135;1520;5135;5052;5058;1769;1520	ENSP00000350719:Y5135C;ENSP00000349969:Y1520C;ENSP00000341781:Y5135C;ENSP00000452570:Y5052C;ENSP00000450831:Y1769C;ENSP00000378249:Y1520C	ENSP00000261678:Y5058C	Y	+	2	0	SYNE2	63680340	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.285000	0.65633	2.004000	0.58718	0.528000	0.53228	TAT	.	.	.	none		0.458	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		G	64610587	A	G	64610587	3	3	103	1	0	0	0	0	1	0	0	0	15458	449	16	3	15730	3	SYNE2	14	64610587	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	9406711	64610587	42738953	90	6620											
MTHFD1	4522	hgsc.bcm.edu	37	chr14	64924942	64924942	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacatcctagatgagcacaaTgcctggactccccacccggc	10	7	8	16	1	0	2	0	1	0	1	2	3	2	3	5	2	3	1	5	2	3	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr14:64924942T>C	ENST00000216605.8	+	27	2807	c.2729T>C	c.(2728-2730)aTg>aCg	p.M910T	MTHFD1_ENST00000545908.1_Intron|ZBTB25_ENST00000555220.1_Intron|ZBTB25_ENST00000555424.1_Intron|MTHFD1_ENST00000556284.1_3'UTR	NM_005956.3	NP_005947.3	P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	910	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)	ATGAGCACAATGCCTGGACTC	0.448																																					p.M910T	Colon(18;220 581 13419 18191 31512)|GBM(126;343 1658 28700 44425 52519)	Atlas-SNP	.											.	MTHFD1	61	.	0			c.T2729C						PASS	.						141	140	141					14																	64924942		2203	4300	6503	SO:0001583	missense	4522	exon27			GCACAATGCCTGG	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	ENST00000216605.8:c.2729T>C	chr14.hg19:g.64924942T>C	ENSP00000216605:p.Met910Thr	67.0	0.0	.		57.0	24.0	.	NM_005956	B2R5Y2|G3V2B8|Q86VC9|Q9BVP5	Missense_Mutation	SNP	ENST00000216605.8	hg19	CCDS9763.1	.	.	.	.	.	.	.	.	.	.	T	19.87	3.906782	0.72868	.	.	ENSG00000100714	ENST00000555709;ENST00000216605	T;T	0.29142	1.58;1.58	5.27	5.27	0.74061	.	0.179769	0.64402	D	0.000011	T	0.65831	0.2729	H	0.98199	4.17	0.80722	D	1	P	0.43909	0.821	P	0.54140	0.743	T	0.78607	-0.2138	10	0.87932	D	0	-32.6795	14.6571	0.68841	0.0:0.0:0.0:1.0	.	910	G3V2B8	.	T	910;966	ENSP00000450560:M910T;ENSP00000216605:M966T	ENSP00000216605:M910T	M	+	2	0	MTHFD1	63994695	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.503000	0.81632	2.117000	0.64856	0.482000	0.46254	ATG	.	.	.	none		0.448	MTHFD1-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471593.1			C	64924942	T	C	64924942	3	2	103	1	0	0	0	0	1	0	0	0	9934	1464	51	3	2835	3	MTHFD1	14	64924942	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	314355	64924942	42424598	91	6621											
RDH11	51109	hgsc.bcm.edu	37	chr14	68159767	68159767	+	Missense_Mutation	SNP	T	T	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	acaccccactggacagcattTtcctgcagacagagaaggag	13	6	10	12	0	0	2	0	0	0	2	1	5	1	4	3	2	2	2	3	2	1	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr14:68159767T>G	ENST00000381346.4	-	2	187	c.77A>C	c.(76-78)aAa>aCa	p.K26T	RDH11_ENST00000553384.1_Missense_Mutation_p.K26T|RP11-1012A1.4_ENST00000554493.1_5'Flank|RP11-1012A1.4_ENST00000553306.1_5'Flank|RDH11_ENST00000428130.2_Missense_Mutation_p.K26T	NM_001252650.1|NM_016026.3	NP_001239579.1|NP_057110.3	Q8TC12	RDH11_HUMAN	retinol dehydrogenase 11 (all-trans/9-cis/11-cis)	26					adaptation of rhodopsin mediated signaling (GO:0016062)|phototransduction, visible light (GO:0007603)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|photoreceptor inner segment (GO:0001917)	NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)			breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(3)|ovary(1)	12				all cancers(60;0.00047)|OV - Ovarian serous cystadenocarcinoma(108;0.00206)|BRCA - Breast invasive adenocarcinoma(234;0.00924)	Vitamin A(DB00162)	GGACAGCATTTTCCTGCAGAC	0.483																																					p.K26T		Atlas-SNP	.											.	RDH11	21	.	0			c.A77C						PASS	.						94	86	89					14																	68159767		2203	4300	6503	SO:0001583	missense	51109	exon2			AGCATTTTCCTGC	AF151840	CCDS32104.1, CCDS58326.1	14q24.1	2013-10-15	2006-05-09		ENSG00000072042	ENSG00000072042	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	17964	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 7C, member 1", "androgen-regulated short-chain dehydrogenase/reductase 1"	607849	"retinol dehydrogenase 11 (all-trans and 9-cis)"			12226107, 8018917, 19027726	Standard	NM_016026		Approved	MDT1, SDR7C1, ARSDR1	uc001xjv.4	Q8TC12	OTTHUMG00000171196	ENST00000381346.4:c.77A>C	chr14.hg19:g.68159767T>G	ENSP00000370750:p.Lys26Thr	96.0	0.0	.		93.0	35.0	.	NM_001252650	A6NDK3|A8K062|B2RB26|B4DDW0|Q0QD40|Q6IAH5|Q9NRW0|Q9Y391	Missense_Mutation	SNP	ENST00000381346.4	hg19	CCDS32104.1	.	.	.	.	.	.	.	.	.	.	T	14.89	2.669280	0.47677	.	.	ENSG00000072042	ENST00000381346;ENST00000553384;ENST00000428130;ENST00000557273;ENST00000557726	D;D;D;D;D	0.90133	-1.78;-1.5;-1.91;-2.34;-2.62	5.31	4.17	0.49024	.	0.298500	0.36234	N	0.002701	D	0.83459	0.5259	N	0.19112	0.55	0.38302	D	0.943	P;P;P	0.47910	0.902;0.716;0.594	P;P;B	0.45681	0.476;0.49;0.295	T	0.81688	-0.0819	10	0.34782	T	0.22	.	7.5042	0.27534	0.0:0.1787:0.0:0.8213	.	26;26;26	B4DDW0;Q8TC12-2;Q8TC12	.;.;RDH11_HUMAN	T	26	ENSP00000370750:K26T;ENSP00000452079:K26T;ENSP00000416395:K26T;ENSP00000450651:K26T;ENSP00000450435:K26T	ENSP00000370750:K26T	K	-	2	0	RDH11	67229520	0.987000	0.35691	0.999000	0.59377	0.943000	0.58893	1.910000	0.39927	1.044000	0.40200	0.533000	0.62120	AAA	.	.	.	none		0.483	RDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412257.3			G	68159767	T	G	68159767	3	3	103	1	0	0	0	0	1	0	0	0	13203	1841	64	5	903	5	RDH11	14	68159767	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	3234825	68159767	39189773	92	6622											
NUSAP1	51203	hgsc.bcm.edu	37	chr15	41657726	41657726	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtggccctgcaagtcagagtAccttgggtctgaaggggtca	8	9	15	9	0	3	2	2	1	1	1	3	2	3	2	2	4	2	2	2	4	3	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr15:41657726A>G	ENST00000559596.1	+	7	874	c.787A>G	c.(787-789)Acc>Gcc	p.T263A	NUSAP1_ENST00000558123.1_3'UTR|NUSAP1_ENST00000560747.1_Missense_Mutation_p.T261A|NUSAP1_ENST00000450318.1_Missense_Mutation_p.T263A|NUSAP1_ENST00000414849.2_Missense_Mutation_p.T262A|NUSAP1_ENST00000260359.6_Missense_Mutation_p.T248A|NUSAP1_ENST00000450592.2_Missense_Mutation_p.T239A|NUSAP1_ENST00000560177.1_Missense_Mutation_p.T262A			Q9BXS6	NUSAP_HUMAN	nucleolar and spindle associated protein 1	263	Interaction with microtubules. {ECO:0000250}.				establishment of mitotic spindle localization (GO:0040001)|mitotic chromosome condensation (GO:0007076)|mitotic cytokinesis (GO:0000281)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of mitosis (GO:0045840)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(3)|ovary(1)|prostate(2)|urinary_tract(2)	13		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;9.63e-17)|GBM - Glioblastoma multiforme(113;1.59e-06)|BRCA - Breast invasive adenocarcinoma(123;0.168)		AAGTCAGAGTACCTTGGGTCT	0.512																																					p.T263A		Atlas-SNP	.											.	NUSAP1	32	.	0			c.A787G						PASS	.						35	34	34					15																	41657726		1905	4133	6038	SO:0001583	missense	51203	exon7			CAGAGTACCTTGG	AF290612	CCDS45234.1, CCDS45236.1, CCDS58356.1, CCDS58357.1, CCDS58358.1, CCDS73708.1	15q14	2008-02-05				ENSG00000137804			18538	protein-coding gene	gene with protein product		612818				12963707	Standard	NM_016359		Approved	FLJ13421, LNP, ANKT, NuSAP1, SAPL, BM037, PRO0310p1, Q0310	uc001zns.4	Q9BXS6		ENST00000559596.1:c.787A>G	chr15.hg19:g.41657726A>G	ENSP00000453403:p.Thr263Ala	72.0	0.0	.		88.0	32.0	.	NM_016359	B4DDF1|E7ERR5|J3KN21|Q53GW2|Q8TBT4|Q96E58|Q96FJ1|Q9GZM9|Q9NZ85|Q9UI70	Missense_Mutation	SNP	ENST00000559596.1	hg19	CCDS45234.1	.	.	.	.	.	.	.	.	.	.	A	10.68	1.417901	0.25552	.	.	ENSG00000137804	ENST00000260359;ENST00000414849;ENST00000450318;ENST00000450592	T;T;T	0.33438	1.41;1.41;1.41	4.64	0.0292	0.14161	.	0.492803	0.22030	N	0.065603	T	0.18383	0.0441	L	0.45137	1.4	0.09310	N	1	B;B;B;B;B;B;B	0.20671	0.018;0.018;0.047;0.037;0.023;0.047;0.047	B;B;B;B;B;B;B	0.20767	0.007;0.016;0.031;0.022;0.007;0.031;0.031	T	0.22800	-1.0206	10	0.15499	T	0.54	.	3.8119	0.08801	0.5416:0.1864:0.272:0.0	.	239;263;261;262;263;263;262	E7ERR5;E9PB35;Q9BXS6-3;Q9BXS6-5;A8K4B4;Q9BXS6;Q9BXS6-2	.;.;.;.;.;NUSAP_HUMAN;.	A	263;262;263;239	ENSP00000400746:T262A;ENSP00000401351:T263A;ENSP00000401014:T239A	ENSP00000260359:T263A	T	+	1	0	NUSAP1	39445018	0.167000	0.22975	0.004000	0.12327	0.008000	0.06430	1.620000	0.36976	-0.153000	0.11137	-0.438000	0.05819	ACC	.	.	.	none		0.512	NUSAP1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000419427.1	NM_016359		G	41657726	A	G	41657726	3	3	103	1	0	0	0	0	1	0	0	0	10785	391	14	3	813	3	NUSAP1	15	41657726	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10		41657726	60873666	93	6623											
TP53BP1	7158	hgsc.bcm.edu	37	chr15	43771711	43771711	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atatcttcgttggactgttcTtcatgcttaattgctgagag	8	17	9	7	1	3	1	1	1	2	1	4	3	3	2	0	1	2	4	0	1	2	7			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr15:43771711T>C	ENST00000263801.3	-	7	909	c.657A>G	c.(655-657)gaA>gaG	p.E219E	TP53BP1_ENST00000450115.2_Silent_p.E224E|TP53BP1_ENST00000382039.3_Silent_p.E224E|TP53BP1_ENST00000382044.4_Silent_p.E224E	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	219					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)		TGGACTGTTCTTCATGCTTAA	0.378								Other conserved DNA damage response genes																													p.E224E		Atlas-SNP	.											.	TP53BP1	157	.	0			c.A672G						PASS	.						233	184	201					15																	43771711		2201	4298	6499	SO:0001819	synonymous_variant	7158	exon7			CTGTTCTTCATGC	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.657A>G	chr15.hg19:g.43771711T>C		270.0	0.0	.		287.0	103.0	.	NM_001141980	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Silent	SNP	ENST00000263801.3	hg19	CCDS10096.1																																																																																			.	.	.	none		0.378	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			C	43771711	T	C	43771711	2	2	103	1	0	0	0	0	0	0	0	1	16395	1606	56	3		3	TP53BP1	15	43771711	Silent	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	2113985	43771711	58759681	94	6624											
CATSPER2	117155	hgsc.bcm.edu	37	chr15	43940128	43940128	+	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	tgctgaccaagtaactccctGatagtgtgccgcggcacagc	9	8	11	13	2	0	2	0	2	0	0	1	2	1	2	3	1	4	3	3	1	3	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr15:43940128G>A	ENST00000321596.5	-	2	331	c.132C>T	c.(130-132)atC>atT	p.I44I	STRC_ENST00000541030.1_Intron|CATSPER2_ENST00000396879.1_Silent_p.I44I|CATSPER2_ENST00000464721.1_Intron|CATSPER2_ENST00000354127.4_Silent_p.I44I|CATSPER2_ENST00000381761.1_Silent_p.I50I|CATSPER2_ENST00000355438.2_Silent_p.I44I			Q96P56	CTSR2_HUMAN	cation channel, sperm associated 2	44					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)		GTAACTCCCTGATAGTGTGCC	0.453																																					p.I44I		Atlas-SNP	.											CATSPER2,right_upper_lobe,carcinoma,0,1	CATSPER2	49	.	0			c.C132T						PASS	.						118	123	122					15																	43940128		2199	4296	6495	SO:0001819	synonymous_variant	117155	exon2			CTCCCTGATAGTG	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.132C>T	chr15.hg19:g.43940128G>A		486.0	2.0	.		454.0	184.0	.	NM_172097	Q8NHT9|Q96P54|Q96P55	Silent	SNP	ENST00000321596.5	hg19	CCDS10099.1																																																																																			.	.	.	none		0.453	CATSPER2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133151.2	NM_054020		A	43940128	G	A	43940128	2	1	103	1	0	0	0	0	0	0	0	1	2690	1280	45	2		2	CATSPER2	15	43940128	Silent	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	168417	43940128	58591264	95	6625											
DAPK2	23604	hgsc.bcm.edu	37	chr15	64204316	64204316	+	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	cctggacacaccttccaccgCctgcggacatactgcttcct	7	9	7	18	2	0	0	0	0	0	0	2	2	2	2	6	2	3	1	6	2	1	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr15:64204316C>G	ENST00000457488.1	-	10	969	c.939G>C	c.(937-939)agG>agC	p.R313S	DAPK2_ENST00000261891.3_Missense_Mutation_p.R313S	NM_014326.3	NP_055141.2	Q9UIK4	DAPK2_HUMAN	death-associated protein kinase 2	313	Calmodulin-binding.				anoikis (GO:0043276)|apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	11				LUAD - Lung adenocarcinoma(2;0.215)		CCTTCCACCGCCTGCGGACAT	0.622																																					p.R313S		Atlas-SNP	.											.	DAPK2	31	.	0			c.G939C						PASS	.						59	48	52					15																	64204316		2203	4300	6503	SO:0001583	missense	23604	exon10			CCACCGCCTGCGG	AB018001	CCDS10188.1	15q22.1	2008-07-18			ENSG00000035664	ENSG00000035664			2675	protein-coding gene	gene with protein product						10376525	Standard	XM_005254265		Approved	DRP-1, MGC119312	uc002amr.3	Q9UIK4	OTTHUMG00000132947	ENST00000457488.1:c.939G>C	chr15.hg19:g.64204316C>G	ENSP00000408277:p.Arg313Ser	47.0	0.0	.		64.0	38.0	.	NM_014326	E9JGM7|O75892|Q24JS1	Missense_Mutation	SNP	ENST00000457488.1	hg19	CCDS10188.1	.	.	.	.	.	.	.	.	.	.	C	19.18	3.777111	0.70107	.	.	ENSG00000035664	ENST00000261891;ENST00000457488	T;T	0.68025	-0.3;-0.3	5.15	3.28	0.37604	Protein kinase-like domain (1);	0.000000	0.64402	D	0.000011	T	0.74191	0.3684	M	0.70275	2.135	0.43054	D	0.994667	D	0.67145	0.996	P	0.58454	0.839	T	0.74213	-0.3738	10	0.62326	D	0.03	.	8.8262	0.35057	0.0:0.8244:0.0:0.1756	.	313	Q9UIK4	DAPK2_HUMAN	S	313	ENSP00000261891:R313S;ENSP00000408277:R313S	ENSP00000261891:R313S	R	-	3	2	DAPK2	61991369	1.000000	0.71417	0.982000	0.44146	0.974000	0.67602	1.554000	0.36266	0.573000	0.29400	-0.192000	0.12808	AGG	.	.	.	none		0.622	DAPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256479.1	NM_014326		G	64204316	C	G	64204316	3	3	103	1	0	0	0	0	1	0	0	0	4238	738	26	4	185	4	DAPK2	15	64204316	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	20264188	64204316	38327076	96	6626											
SENP8	123228	hgsc.bcm.edu	37	chr15	72432461	72432461	+	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	cagctatgactgtgggatgtAcgtgatatgtaacactgagg	11	11	13	6	1	0	3	0	3	0	0	0	4	0	4	0	2	3	3	0	2	4	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr15:72432461A>T	ENST00000542035.2	+	2	830	c.497A>T	c.(496-498)tAc>tTc	p.Y166F	SENP8_ENST00000544171.1_Missense_Mutation_p.Y166F|SENP8_ENST00000544411.1_Missense_Mutation_p.Y166F|RP11-2I17.4_ENST00000568984.1_RNA|SENP8_ENST00000340912.4_Missense_Mutation_p.Y166F	NM_001166340.1	NP_001159812.1	Q96LD8	SENP8_HUMAN	SUMO/sentrin specific peptidase family member 8	166	Protease.						cysteine-type peptidase activity (GO:0008234)			breast(1)|kidney(2)|lung(1)|ovary(1)|skin(1)	6						TGTGGGATGTACGTGATATGT	0.478																																					p.Y166F		Atlas-SNP	.											.	SENP8	18	.	0			c.A497T						PASS	.						117	113	114					15																	72432461		2199	4297	6496	SO:0001583	missense	123228	exon2			GGATGTACGTGAT	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.497A>T	chr15.hg19:g.72432461A>T	ENSP00000446057:p.Tyr166Phe	33.0	0.0	.		33.0	10.0	.	NM_001166340	Q96QA4	Missense_Mutation	SNP	ENST00000542035.2	hg19	CCDS10240.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.150452	0.78001	.	.	ENSG00000166192	ENST00000542035;ENST00000544411;ENST00000340912;ENST00000544171	T;T;T;T	0.36699	1.24;1.24;1.24;1.24	5.86	4.72	0.59763	.	0.000000	0.85682	D	0.000000	T	0.46151	0.1378	L	0.51853	1.615	0.58432	D	0.999999	D	0.56521	0.976	P	0.56751	0.805	T	0.24657	-1.0154	10	0.25106	T	0.35	-15.1718	13.2186	0.59875	0.867:0.133:0.0:0.0	.	166	Q96LD8	SENP8_HUMAN	F	166	ENSP00000446057:Y166F;ENSP00000441753:Y166F;ENSP00000340505:Y166F;ENSP00000439415:Y166F	ENSP00000340505:Y166F	Y	+	2	0	SENP8	70219515	1.000000	0.71417	0.921000	0.36526	0.907000	0.53573	9.228000	0.95250	1.018000	0.39521	-0.323000	0.08544	TAC	.	.	.	none		0.478	SENP8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420036.1	NM_145204		T	72432461	A	T	72432461	3	4	103	1	0	0	0	0	1	0	0	0	14065	391	14	5	499	5	SENP8	15	72432461	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	8228145	72432461	30098931	97	6627											
PARP6	56965	hgsc.bcm.edu	37	chr15	72543559	72543559	+	Missense_Mutation	SNP	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	gtcacttaccctgctgagagGtagtttgacaatgtgtgacc	9	12	11	9	0	1	3	1	3	0	1	1	4	1	3	2	1	2	3	2	1	3	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr15:72543559G>A	ENST00000569795.1	-	17	1984	c.1297C>T	c.(1297-1299)Cct>Tct	p.P433S	PARP6_ENST00000260376.7_Missense_Mutation_p.P433S|PARP6_ENST00000413097.2_5'UTR|PARP6_ENST00000287196.9_Missense_Mutation_p.P433S			Q2NL67	PARP6_HUMAN	poly (ADP-ribose) polymerase family, member 6	433	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.						NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(8)|skin(1)|urinary_tract(1)	18						CTGCTGAGAGGTAGTTTGACA	0.413																																					p.P433S		Atlas-SNP	.											.	PARP6	44	.	0			c.C1297T						PASS	.						104	99	101					15																	72543559		1869	4113	5982	SO:0001583	missense	56965	exon16			TGAGAGGTAGTTT	AL390093	CCDS10241.2	15q22	2010-02-16			ENSG00000137817	ENSG00000137817		"Poly (ADP-ribose) polymerases"	26921	protein-coding gene	gene with protein product						15273990	Standard	XM_005254557		Approved	pART17	uc002auc.3	Q2NL67	OTTHUMG00000133443	ENST00000569795.1:c.1297C>T	chr15.hg19:g.72543559G>A	ENSP00000456348:p.Pro433Ser	90.0	0.0	.		100.0	48.0	.	NM_020214	Q9H7C5|Q9H9X6|Q9HAF3|Q9NPS6|Q9UFG4	Missense_Mutation	SNP	ENST00000569795.1	hg19	CCDS10241.2	.	.	.	.	.	.	.	.	.	.	G	23.1	4.378759	0.82682	.	.	ENSG00000137817	ENST00000419739;ENST00000287196;ENST00000260376;ENST00000413097	.	.	.	5.14	4.22	0.49857	Poly(ADP-ribose) polymerase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.66317	0.2777	L	0.41824	1.3	0.80722	D	1	B;D;D	0.89917	0.374;0.993;1.0	B;D;D	0.80764	0.117;0.979;0.994	T	0.66586	-0.5886	9	0.46703	T	0.11	-4.7079	12.9482	0.58384	0.0779:0.0:0.9221:0.0	.	433;433;365	Q0VDG0;Q2NL67;A0PJ50	.;PARP6_HUMAN;.	S	433;433;433;278	.	ENSP00000260376:P433S	P	-	1	0	PARP6	70330613	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.539000	0.98076	1.386000	0.46466	0.655000	0.94253	CCT	.	.	.	none		0.413	PARP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257315.2	NM_020214		A	72543559	G	A	72543559	3	1	103	1	0	0	0	0	1	0	0	0	11471	1261	44	2	627	2	PARP6	15	72543559	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	111098	72543559	29987833	98	6628											
FANCI	55215	hgsc.bcm.edu	37	chr15	89801970	89801970	+	Frame_Shift_Del	DEL	A	A	-																															cagaatcaagcagtgaaaggAaaagttgctggagcactcct																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr15:89801970delA	ENST00000310775.7	+	3	206	c.120delA	c.(118-120)ggafs	p.G40fs	FANCI_ENST00000451393.2_5'UTR|FANCI_ENST00000567996.1_Frame_Shift_Del_p.G40fs|FANCI_ENST00000300027.8_Frame_Shift_Del_p.G40fs	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	40					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)					CAGTGAAAGGAAAAGTTGCTG	0.388								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.G40fs		Atlas-Indel,Pindel	.											.	FANCI	129	.	0			c.119delG						PASS	.						181	178	179					15																	89801970		2200	4299	6499	SO:0001589	frameshift_variant	55215	exon3	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	.	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"Fanconi anemia, complementation groups"	25568	protein-coding gene	gene with protein product		611360	"KIAA1794"	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.120delA	chr15.hg19:g.89801970delA	ENSP00000310842:p.Gly40fs	82.0	0.0	0		102.0	46.0	0.45098	NM_001113378	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Frame_Shift_Del	DEL	ENST00000310775.7	hg19	CCDS45346.1																																																																																			.	.	.	none		0.388	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193		-	89801970	A	-	89801970	7	5	103	1	0	1	0	1	0	0	0	0	5676	233	9	0	126	0	FANCI	15	89801970	Frame_Shift_Del	DEL	A	TCGA-B9-A44B-01A-11D-A25F-10	17258411	89801970	12729422	99	6629											
OR4F6	390648	hgsc.bcm.edu	37	chr15	102346642	102346642	+	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	ttcaaggctttctctatgctGtcagctcatgtcattgtggt	6	17	9	9	0	5	0	4	0	1	0	6	0	5	0	0	2	2	3	0	2	2	4			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr15:102346642G>T	ENST00000328882.4	+	1	741	c.720G>T	c.(718-720)ctG>ctT	p.L240L		NM_001005326.1	NP_001005326.1	Q8NGB9	OR4F6_HUMAN	olfactory receptor, family 4, subfamily F, member 6	240						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|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)			TCTCTATGCTGTCAGCTCATG	0.353																																					p.L240L		Atlas-SNP	.											.	OR4F6	45	.	0			c.G720T						PASS	.						172	165	167					15																	102346642		2202	4300	6502	SO:0001819	synonymous_variant	390648	exon1			TATGCTGTCAGCT	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.720G>T	chr15.hg19:g.102346642G>T		180.0	0.0	.		124.0	42.0	.	NM_001005326	B9EH28|Q6IF95	Silent	SNP	ENST00000328882.4	hg19	CCDS32341.1																																																																																			.	.	.	none		0.353	OR4F6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417593.1			T	102346642	G	T	102346642	2	4	103	1	0	0	0	0	0	0	0	1	11073	1364	48	4		4	OR4F6	15	102346642	Silent	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	12544672	102346642	184750	100	6630											
PLK1	5347	hgsc.bcm.edu	37	chr16	23690422	23690422	+	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	ggcggcgctatgtgcggggcCgctttttgggcaagggcggc	3	8	20	10	5	0	0	0	0	0	0	0	0	0	0	1	7	1	3	1	7	2	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr16:23690422C>A	ENST00000300093.4	+	1	280	c.169C>A	c.(169-171)Cgc>Agc	p.R57S	PLK1_ENST00000564202.1_3'UTR	NM_005030.3	NP_005021.2	P53350	PLK1_HUMAN	polo-like kinase 1	57	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		TGTGCGGGGCCGCTTTTTGGG	0.657																																					p.R57S	Colon(12;240 564 27038 33155)	Atlas-SNP	.											.	PLK1	67	.	0			c.C169A						PASS	.						16	19	18					16																	23690422		2197	4300	6497	SO:0001583	missense	5347	exon1			CGGGGCCGCTTTT		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.169C>A	chr16.hg19:g.23690422C>A	ENSP00000300093:p.Arg57Ser	98.0	0.0	.		157.0	60.0	.	NM_005030	Q15153|Q99746	Missense_Mutation	SNP	ENST00000300093.4	hg19	CCDS10616.1	.	.	.	.	.	.	.	.	.	.	C	19.62	3.861173	0.71949	.	.	ENSG00000166851	ENST00000300093;ENST00000330792	T	0.25579	1.79	4.08	3.09	0.35607	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	0.24699	0.0599	L	0.37630	1.12	0.80722	D	1	P	0.49090	0.919	P	0.49752	0.621	T	0.01600	-1.1315	10	0.44086	T	0.13	-18.3883	7.0374	0.25000	0.198:0.6098:0.1921:0.0	.	57	P53350	PLK1_HUMAN	S	57	ENSP00000300093:R57S	ENSP00000300093:R57S	R	+	1	0	PLK1	23597923	0.986000	0.35501	0.991000	0.47740	0.995000	0.86356	2.740000	0.47418	1.026000	0.39733	0.561000	0.74099	CGC	.	.	.	none		0.657	PLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214057.2	NM_005030		A	23690422	C	A	23690422	3	1	103	1	0	0	0	0	1	0	0	0	12101	652	23	4	171	4	PLK1	16	23690422	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10		23690422	66664331	101	6631											
LONP2	83752	hgsc.bcm.edu	37	chr16	48311386	48311386	+	Missense_Mutation	SNP	T	T	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	tgatccagcagcagctctgcTtgaggtaagatttggaaaat	12	11	11	7	0	1	3	0	2	1	1	2	4	2	4	1	2	4	5	1	2	3	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr16:48311386T>G	ENST00000285737.4	+	8	1472	c.1379T>G	c.(1378-1380)cTt>cGt	p.L460R	LONP2_ENST00000535754.1_Missense_Mutation_p.L416R	NM_031490.2	NP_113678.2			lon peptidase 2, peroxisomal											breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						GCAGCTCTGCTTGAGGTAAGA	0.438																																					p.L460R		Atlas-SNP	.											.	LONP2	63	.	0			c.T1379G						PASS	.						81	73	76					16																	48311386		2200	4300	6500	SO:0001583	missense	83752	exon8			CTCTGCTTGAGGT	AJ548761	CCDS10734.1, CCDS73880.1	16q12.1	2010-04-21			ENSG00000102910	ENSG00000102910		"ATPases / AAA-type"	20598	protein-coding gene	gene with protein product						14561759	Standard	XM_005256191		Approved	MGC4840, LONP, LONPL	uc002efi.1	Q86WA8	OTTHUMG00000133144	ENST00000285737.4:c.1379T>G	chr16.hg19:g.48311386T>G	ENSP00000285737:p.Leu460Arg	123.0	0.0	.		188.0	63.0	.	NM_031490		Missense_Mutation	SNP	ENST00000285737.4	hg19	CCDS10734.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.426428	0.83667	.	.	ENSG00000102910	ENST00000285737;ENST00000544734;ENST00000535754;ENST00000416006	T;T;T	0.55760	0.5;0.5;0.5	5.96	5.96	0.96718	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.85592	0.5732	H	0.99705	4.715	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92181	0.5751	10	0.87932	D	0	-17.8825	16.4277	0.83824	0.0:0.0:0.0:1.0	.	416;460	B7ZKL7;Q86WA8	.;LONP2_HUMAN	R	460;189;416;416	ENSP00000285737:L460R;ENSP00000445426:L416R;ENSP00000415983:L416R	ENSP00000285737:L460R	L	+	2	0	LONP2	46868887	1.000000	0.71417	0.992000	0.48379	0.761000	0.43186	7.996000	0.88334	2.279000	0.76181	0.533000	0.62120	CTT	.	.	.	none		0.438	LONP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256839.2	NM_031490		G	48311386	T	G	48311386	3	3	103	1	0	0	0	0	1	0	0	0	8900	1609	56	5	1409	5	LONP2	16	48311386	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	24620964	48311386	42043367	102	6632											
GUCY2D	3000	hgsc.bcm.edu	37	chr17	7910749	7910749	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctctttctccaccaggcaccGgctacttcacatgcaaatgg	9	10	7	15	1	3	0	1	0	2	0	4	0	3	0	3	3	2	3	3	3	2	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr17:7910749G>A	ENST00000254854.4	+	6	1619	c.1469G>A	c.(1468-1470)cGg>cAg	p.R490Q		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	490					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)	p.R490Q(1)		skin(1)	1		Prostate(122;0.157)				ACCAGGCACCGGCTACTTCAC	0.592																																					p.R490Q		Atlas-SNP	.											GUCY2D_ENST00000254854,NS,carcinoma,0,1	GUCY2D	82	.	1	Substitution - Missense(1)	lung(1)	c.G1469A						PASS	.						105	102	103					17																	7910749		2203	4300	6503	SO:0001583	missense	3000	exon6			GGCACCGGCTACT	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.1469G>A	chr17.hg19:g.7910749G>A	ENSP00000254854:p.Arg490Gln	90.0	0.0	.		88.0	6.0	.	NM_000180	Q6LEA7	Missense_Mutation	SNP	ENST00000254854.4	hg19	CCDS11127.1	.	.	.	.	.	.	.	.	.	.	G	13.95	2.388655	0.42308	.	.	ENSG00000132518	ENST00000254854	D	0.83591	-1.74	5.52	0.753	0.18404	.	0.440036	0.19338	N	0.116724	T	0.74261	0.3693	L	0.41710	1.295	0.18873	N	0.999989	B	0.22146	0.065	B	0.11329	0.006	T	0.59768	-0.7392	10	0.28530	T	0.3	.	14.1923	0.65646	0.2084:0.0:0.7916:0.0	.	490	Q02846	GUC2D_HUMAN	Q	490	ENSP00000254854:R490Q	ENSP00000254854:R490Q	R	+	2	0	GUCY2D	7851474	0.946000	0.32159	0.998000	0.56505	0.972000	0.66771	2.884000	0.48562	0.309000	0.22966	-1.267000	0.01435	CGG	.	.	.	none		0.592	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2			A	7910749	G	A	7910749	3	1	103	1	0	0	0	0	1	0	0	0	6904	1116	39	1	1487	1	GUCY2D	17	7910749	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10		7910749	73284461	103	6633											
SGK494	9703	hgsc.bcm.edu	37	chr17	26938587	26938587	+	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	agctttaacctctctcacccAtgtactgaagagtgccacag	11	10	7	13	0	2	2	1	1	1	1	3	2	2	2	3	0	4	2	3	0	3	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr17:26938587A>G	ENST00000528896.2	-	0	7407				RP11-192H23.4_ENST00000534850.1_3'UTR|SGK494_ENST00000301037.5_Missense_Mutation_p.M270T|RP11-192H23.6_ENST00000579019.2_RNA|SPAG5-AS1_ENST00000414744.1_RNA|SPAG5-AS1_ENST00000554154.1_RNA|RP11-192H23.4_ENST00000577790.1_Intron|SGK494_ENST00000469832.3_5'Flank|SPAG5-AS1_ENST00000424210.1_RNA	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100							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)					TCTCTCACCCATGTACTGAAG	0.502																																					p.M270T		Atlas-SNP	.											.	.	.	.	0			c.T809C						PASS	.						184	156	165					17																	26938587		2203	4300	6503	SO:0001628	intergenic_variant	0	exon9			TCACCCATGTACT	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		chr17.hg19:g.26938587A>G		89.0	0.0	.		116.0	39.0	.	NM_001174103	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	hg19	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	A	16.88	3.245285	0.59103	.	.	ENSG00000167524	ENST00000301037	T	0.09817	2.94	5.45	5.45	0.79879	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	0.41766	0.1173	M	0.91972	3.26	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.53229	-0.8468	10	0.87932	D	0	-18.3153	14.6957	0.69121	1.0:0.0:0.0:0.0	.	270	Q96LW2	SG494_HUMAN	T	270	ENSP00000301037:M270T	ENSP00000301037:M270T	M	-	2	0	AC005726.6	23962714	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	6.546000	0.73887	2.074000	0.62210	0.383000	0.25322	ATG	.	.	.	none		0.502	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		G	26938587	A	G	26938587	1	3	103	0	1	0	0	0	0	0	0	0	14226	217	8	3		3	SGK494	17	26938587	IGR	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	19027838	26938587	54256623	104	6634											
EFCAB5	374786	hgsc.bcm.edu	37	chr17	28296149	28296149	+	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	actgcatatttgcttgacaaActtctacccaccttagttcc	10	14	4	13	0	1	1	0	1	1	0	2	1	2	1	3	0	4	3	3	0	4	7			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr17:28296149A>T	ENST00000394835.3	+	4	723	c.531A>T	c.(529-531)aaA>aaT	p.K177N	EFCAB5_ENST00000541045.1_Intron|EFCAB5_ENST00000536908.2_Missense_Mutation_p.K121N|EFCAB5_ENST00000320856.5_Missense_Mutation_p.K177N|EFCAB5_ENST00000534836.2_Intron|EFCAB5_ENST00000378738.3_Missense_Mutation_p.K177N|EFCAB5_ENST00000394832.2_Missense_Mutation_p.K177N	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	177							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						TGCTTGACAAACTTCTACCCA	0.373																																					p.K177N		Atlas-SNP	.											.	EFCAB5	122	.	0			c.A531T						PASS	.						45	43	44					17																	28296149		1839	4090	5929	SO:0001583	missense	374786	exon4			TGACAAACTTCTA	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.531A>T	chr17.hg19:g.28296149A>T	ENSP00000378312:p.Lys177Asn	162.0	0.0	.		118.0	52.0	.	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Missense_Mutation	SNP	ENST00000394835.3	hg19	CCDS11254.2	.	.	.	.	.	.	.	.	.	.	A	11.59	1.682704	0.29872	.	.	ENSG00000176927	ENST00000536908;ENST00000421238;ENST00000394835;ENST00000320856;ENST00000394832;ENST00000378738;ENST00000423598	T;T;T;T;T	0.32023	1.51;2.55;2.51;1.81;1.47	5.57	-0.614	0.11590	.	.	.	.	.	T	0.36771	0.0979	L	0.33485	1.01	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.995;0.995	D;D;D;D	0.91635	0.999;0.999;0.909;0.909	T	0.10177	-1.0641	8	.	.	.	-14.4895	8.1332	0.31039	0.4603:0.1168:0.4229:0.0	.	121;177;177;177	F5GYL2;B5MEA3;E7EVS9;A4FU69	.;.;.;EFCB5_HUMAN	N	121;121;177;177;177;177;121	ENSP00000440619:K121N;ENSP00000378312:K177N;ENSP00000322003:K177N;ENSP00000378309:K177N;ENSP00000368012:K177N	.	K	+	3	2	EFCAB5	25320275	1.000000	0.71417	0.998000	0.56505	0.492000	0.33523	0.654000	0.24918	-0.080000	0.12685	-0.290000	0.09829	AAA	.	.	.	none		0.373	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529		T	28296149	A	T	28296149	3	4	103	1	0	0	0	0	1	0	0	0	4940	40	2	5	545	5	EFCAB5	17	28296149	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	1357562	28296149	52899061	105	6635											
PTRF	284119	hgsc.bcm.edu	37	chr17	40557359	40557359	+	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	tctggcagcgcctccgactcTttcagcgatttgctgatgct	5	13	10	13	3	3	1	1	1	2	0	4	3	4	1	2	1	4	3	2	1	0	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr17:40557359T>A	ENST00000357037.5	-	2	938	c.519A>T	c.(517-519)aaA>aaT	p.K173N		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)		CCTCCGACTCTTTCAGCGATT	0.652																																					p.K173N		Atlas-SNP	.											.	PTRF	48	.	0			c.A519T						PASS	.						79	86	83					17																	40557359		2202	4300	6502	SO:0001583	missense	284119	exon2			CGACTCTTTCAGC	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.519A>T	chr17.hg19:g.40557359T>A	ENSP00000349541:p.Lys173Asn	16.0	0.0	.		20.0	4.0	.	NM_012232		Missense_Mutation	SNP	ENST00000357037.5	hg19	CCDS11425.1	.	.	.	.	.	.	.	.	.	.	T	16.67	3.186520	0.57909	.	.	ENSG00000177469	ENST00000357037;ENST00000357684	T	0.60171	0.21	5.35	-3.31	0.04988	.	0.183494	0.47455	D	0.000233	T	0.61924	0.2386	M	0.72353	2.195	0.50813	D	0.999894	D;D	0.56035	0.974;0.974	P;P	0.53146	0.719;0.719	T	0.65352	-0.6189	10	0.30078	T	0.28	-16.9364	14.7183	0.69286	0.0:0.6953:0.0:0.3047	.	155;173	B4DNU9;Q6NZI2	.;PTRF_HUMAN	N	173;128	ENSP00000349541:K173N	ENSP00000349541:K173N	K	-	3	2	PTRF	37810885	0.929000	0.31497	0.985000	0.45067	0.776000	0.43924	0.061000	0.14366	-0.544000	0.06232	-0.490000	0.04691	AAA	.	.	.	none		0.652	PTRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449938.1	NM_012232		A	40557359	T	A	40557359	3	1	103	1	0	0	0	0	1	0	0	0	12828	1606	56	5	657	5	PTRF	17	40557359	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	12261210	40557359	40637851	106	6636											
MBTD1	54799	hgsc.bcm.edu	37	chr17	49302371	49302371	+	Missense_Mutation	SNP	A	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	aaggttataaatactcacccAtgccagatttaccatctggg	13	11	7	10	0	2	1	1	0	1	1	2	1	2	1	3	2	3	1	3	2	6	5			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr17:49302371A>C	ENST00000586178.1	-	3	495	c.152T>G	c.(151-153)aTg>aGg	p.M51R	MBTD1_ENST00000415868.1_Missense_Mutation_p.M51R|MBTD1_ENST00000376381.2_Missense_Mutation_p.M51R|MBTD1_ENST00000593259.1_5'Flank	NM_017643.2	NP_060113.2	Q05BQ5	MBTD1_HUMAN	mbt domain containing 1	51					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)			ATACTCACCCATGCCAGATTT	0.393																																					p.M51R		Atlas-SNP	.											.	MBTD1	44	.	0			c.T152G						PASS	.						145	135	138					17																	49302371		692	1591	2283	SO:0001583	missense	54799	exon3			TCACCCATGCCAG	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.152T>G	chr17.hg19:g.49302371A>C	ENSP00000468304:p.Met51Arg	100.0	0.0	.		86.0	26.0	.	NM_017643	Q6ZVU7|Q9NXU1	Missense_Mutation	SNP	ENST00000586178.1	hg19	CCDS11581.2	.	.	.	.	.	.	.	.	.	.	A	23.1	4.377416	0.82682	.	.	ENSG00000011258	ENST00000405860;ENST00000415868;ENST00000376381	T;T	0.23950	1.9;1.88	5.21	5.21	0.72293	Zinc finger, FCS-type (1);	0.073350	0.85682	D	0.000000	T	0.39759	0.1090	L	0.40543	1.245	0.80722	D	1	D;D	0.60575	0.988;0.96	P;D	0.69142	0.701;0.962	T	0.06789	-1.0807	10	0.23891	T	0.37	.	15.3505	0.74380	1.0:0.0:0.0:0.0	.	51;51	Q05BQ5;Q05BQ5-2	MBTD1_HUMAN;.	R	51	ENSP00000403946:M51R;ENSP00000365561:M51R	ENSP00000365561:M51R	M	-	2	0	MBTD1	46657370	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.248000	0.95456	2.089000	0.63090	0.482000	0.46254	ATG	.	.	.	none		0.393	MBTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318124.1			C	49302371	A	C	49302371	3	2	103	1	0	0	0	0	1	0	0	0	9367	217	8	5	1794	5	MBTD1	17	49302371	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10	8745012	49302371	31892839	107	6637											
NAT9	26151	hgsc.bcm.edu	37	chr17	72768142	72768142	+	Missense_Mutation	SNP	T	T	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	acatccggatgcttggttcaTttccttgcccaattttagcc	7	15	7	12	1	1	0	1	0	0	0	3	1	3	1	4	2	3	2	4	2	2	6			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr17:72768142T>G	ENST00000357814.3	-	6	519	c.446A>C	c.(445-447)aAt>aCt	p.N149T	NAT9_ENST00000583476.1_Intron|NAT9_ENST00000581136.1_Missense_Mutation_p.N144T|NAT9_ENST00000578822.1_Missense_Mutation_p.N154T|NAT9_ENST00000580216.1_5'Flank|NAT9_ENST00000580301.1_Missense_Mutation_p.N148T|NAT9_ENST00000583757.1_Intron|NAT9_ENST00000582870.1_Missense_Mutation_p.N153T|NAT9_ENST00000580632.1_Missense_Mutation_p.N149T|NAT9_ENST00000582524.1_Intron	NM_015654.3	NP_056469.2	Q9BTE0	NAT9_HUMAN	N-acetyltransferase 9 (GCN5-related, putative)	149	N-acetyltransferase.					protein complex (GO:0043234)	N-acetyltransferase activity (GO:0008080)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)	8						GCTTGGTTCATTTCCTTGCCC	0.567																																					p.N149T		Atlas-SNP	.											.	NAT9	16	.	0			c.A446C						PASS	.						168	164	165					17																	72768142		2203	4300	6503	SO:0001583	missense	26151	exon6			GGTTCATTTCCTT	AK123115	CCDS11706.1	17q25.2	2011-11-25	2008-09-24		ENSG00000109065	ENSG00000109065			23133	protein-coding gene	gene with protein product			"N-acetyltransferase 9"			14608357	Standard	NM_015654		Approved	DKFZP564C103	uc002jlq.3	Q9BTE0		ENST00000357814.3:c.446A>C	chr17.hg19:g.72768142T>G	ENSP00000350467:p.Asn149Thr	108.0	0.0	.		126.0	54.0	.	NM_015654	B2R7F0|Q9BTD0|Q9Y3T3	Missense_Mutation	SNP	ENST00000357814.3	hg19	CCDS11706.1	.	.	.	.	.	.	.	.	.	.	T	14.32	2.499275	0.44455	.	.	ENSG00000109065	ENST00000357814	T	0.78364	-1.17	5.09	5.09	0.68999	GCN5-related N-acetyltransferase (GNAT) domain (1);Acyl-CoA N-acyltransferase (2);	0.000000	0.85682	D	0.000000	D	0.92704	0.7681	H	0.98295	4.195	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95440	0.8524	10	0.87932	D	0	-19.1654	15.1669	0.72837	0.0:0.0:0.0:1.0	.	148;149	Q9BTE0-2;Q9BTE0	.;NAT9_HUMAN	T	149	ENSP00000350467:N149T	ENSP00000350467:N149T	N	-	2	0	NAT9	70279737	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.519000	0.81809	2.055000	0.61198	0.459000	0.35465	AAT	.	.	.	none		0.567	NAT9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000443700.1	NM_015654		G	72768142	T	G	72768142	3	3	103	1	0	0	0	0	1	0	0	0	10189	1493	52	5	185	5	NAT9	17	72768142	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10	23465771	72768142	8427068	108	6638											
CARD14	79092	hgsc.bcm.edu	37	chr17	78166392	78166392	+	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	tctgccccagagacgacagcGactgcagcctcgtcagctcc	8	6	10	17	3	2	1	1	0	1	1	4	4	3	1	4	0	5	2	4	0	0	0			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr17:78166392G>A	ENST00000573882.1	+	11	1866	c.1330G>A	c.(1330-1332)Gac>Aac	p.D444N	CARD14_ENST00000344227.2_Missense_Mutation_p.D444N|CARD14_ENST00000392434.2_Missense_Mutation_p.D207N|CARD14_ENST00000573754.1_3'UTR|CARD14_ENST00000570421.1_Missense_Mutation_p.D444N			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	444					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)			AGACGACAGCGACTGCAGCCT	0.662																																					p.D444N		Atlas-SNP	.											.	CARD14	98	.	0			c.G1330A						PASS	.						50	51	51					17																	78166392		2203	4300	6503	SO:0001583	missense	79092	exon9			GACAGCGACTGCA	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.1330G>A	chr17.hg19:g.78166392G>A	ENSP00000458715:p.Asp444Asn	210.0	0.0	.		203.0	43.0	.	NM_024110	B8QQJ3|Q9BVB5	Missense_Mutation	SNP	ENST00000573882.1	hg19	CCDS11768.1	.	.	.	.	.	.	.	.	.	.	G	2.678	-0.275943	0.05679	.	.	ENSG00000141527	ENST00000344227;ENST00000392434;ENST00000309710	T;T	0.32515	1.45;1.45	3.64	0.451	0.16629	.	1.109330	0.06805	N	0.789318	T	0.16938	0.0407	L	0.27053	0.805	0.09310	N	1	B;B;B	0.14438	0.002;0.01;0.0	B;B;B	0.09377	0.001;0.004;0.001	T	0.29088	-1.0023	10	0.08599	T	0.76	-9.737	3.7718	0.08645	0.3225:0.1839:0.4936:0.0	.	444;207;444	B8QQJ3;E7ETJ2;Q9BXL6	.;.;CAR14_HUMAN	N	444;207;207	ENSP00000344549:D444N;ENSP00000376229:D207N	ENSP00000308507:D207N	D	+	1	0	CARD14	75780987	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.205000	0.09411	-0.044000	0.13491	-1.162000	0.01777	GAC	.	.	.	none		0.662	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1			A	78166392	G	A	78166392	3	1	103	1	0	0	0	0	1	0	0	0	2648	1058	37	1	1360	1	CARD14	17	78166392	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	5398250	78166392	3028818	109	6639											
NPTX1	4884	hgsc.bcm.edu	37	chr17	78449367	78449367	+	Frame_Shift_Del	DEL	A	A	-																															tcagggcggtctcgatcttgAccctctcctcggtgtcgttc																								rs375303530		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr17:78449367delA	ENST00000306773.4	-	2	753	c.596delT	c.(595-597)gtcfs	p.V199fs	NPTX1_ENST00000575212.1_5'UTR	NM_002522.3	NP_002513.2	Q15818	NPTX1_HUMAN	neuronal pentraxin I	199					axonogenesis involved in innervation (GO:0060385)|cellular response to glucose stimulus (GO:0071333)|cellular response to potassium ion (GO:0035865)|central nervous system development (GO:0007417)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial transport (GO:0006839)|synaptic transmission (GO:0007268)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			kidney(1)|large_intestine(2)|liver(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(1)	11	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487)			CTCGATCTTGACCCTCTCCTC	0.657																																					p.V199fs		Atlas-Indel,Pindel	.											.	NPTX1	28	.	0			c.597delC						PASS	.						55	41	46					17																	78449367		2202	4300	6502	SO:0001589	frameshift_variant	4884	exon2			.	U61849	CCDS32762.1	17q25.3	2008-05-14				ENSG00000171246			7952	protein-coding gene	gene with protein product		602367				8884281	Standard	NM_002522		Approved		uc002jyp.1	Q15818		ENST00000306773.4:c.596delT	chr17.hg19:g.78449367delA	ENSP00000307549:p.Val199fs	98.0	0.0	0		130.0	55.0	0.423077	NM_002522	B3KXH3|Q5FWE6	Frame_Shift_Del	DEL	ENST00000306773.4	hg19	CCDS32762.1																																																																																			.	.	.	none		0.657	NPTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438051.1			-	78449367	A	-	78449367	7	5	103	1	0	1	0	1	0	0	0	0	10609	275	10	0	718	0	NPTX1	17	78449367	Frame_Shift_Del	DEL	A	TCGA-B9-A44B-01A-11D-A25F-10	282975	78449367	2745843	110	6640											
DSG3	1830	hgsc.bcm.edu	37	chr18	29038453	29038453	+	Missense_Mutation	SNP	T	T	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	agaaaatcacctaccgaatcTctggagtgggaatcgatcag	14	8	10	9	2	3	1	2	0	1	1	5	5	3	3	2	2	1	0	2	2	5	1			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr18:29038453T>G	ENST00000257189.4	+	4	345	c.262T>G	c.(262-264)Tct>Gct	p.S88A		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	88	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			CTACCGAATCTCTGGAGTGGG	0.448																																					p.S88A		Atlas-SNP	.											.	DSG3	172	.	0			c.T262G						PASS	.						103	102	102					18																	29038453		2203	4300	6503	SO:0001583	missense	1830	exon4			CGAATCTCTGGAG	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.262T>G	chr18.hg19:g.29038453T>G	ENSP00000257189:p.Ser88Ala	102.0	0.0	.		108.0	56.0	.	NM_001944	A8K2V2	Missense_Mutation	SNP	ENST00000257189.4	hg19	CCDS11898.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.280611	0.80692	.	.	ENSG00000134757	ENST00000257189	T	0.52057	0.68	5.76	3.2	0.36748	Cadherin (4);Cadherin-like (1);	0.141448	0.32563	N	0.005937	T	0.69360	0.3102	M	0.91920	3.255	0.35383	D	0.790079	D	0.55385	0.971	P	0.60068	0.868	T	0.81453	-0.0926	10	0.87932	D	0	.	11.3024	0.49314	0.2412:0.0:0.0:0.7588	.	88	P32926	DSG3_HUMAN	A	88	ENSP00000257189:S88A	ENSP00000257189:S88A	S	+	1	0	DSG3	27292451	0.993000	0.37304	0.857000	0.33713	0.922000	0.55478	2.362000	0.44169	1.080000	0.41073	0.528000	0.53228	TCT	.	.	.	none		0.448	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944		G	29038453	T	G	29038453	3	3	103	1	0	0	0	0	1	0	0	0	4780	1551	54	5	276	5	DSG3	18	29038453	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10		29038453	49038795	111	6641											
ABCA7	10347	hgsc.bcm.edu	37	chr19	1059069	1059069	+	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	gttgaccgcttgtgcctgggGattccccctggtgaggtgag	4	11	16	10	1	0	3	0	3	0	0	1	4	1	4	4	4	1	2	4	4	0	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr19:1059069G>T	ENST00000263094.6	+	40	5679	c.5448G>T	c.(5446-5448)ggG>ggT	p.G1816G	ABCA7_ENST00000433129.1_Silent_p.G1816G|ABCA7_ENST00000435683.2_Silent_p.G1678G	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1816	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)		TGTGCCTGGGGATTCCCCCTG	0.617																																					p.G1816G		Atlas-SNP	.											.	ABCA7	174	.	0			c.G5448T						PASS	.						81	68	73					19																	1059069		2202	4300	6502	SO:0001819	synonymous_variant	10347	exon40			CCTGGGGATTCCC	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.5448G>T	chr19.hg19:g.1059069G>T		116.0	0.0	.		118.0	28.0	.	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	hg19	CCDS12055.1																																																																																			.	.	.	none		0.617	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		T	1059069	G	T	1059069	2	4	103	1	0	0	0	0	0	0	0	1	37	1161	41	4		4	ABCA7	19	1059069	Silent	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10		1059069	58069914	112	6642											
ZNF799	90576	hgsc.bcm.edu	37	chr19	12502558	12502558	+	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	tatggtttctctccagtgtgCgttctctcatgcatatgtaa	7	17	8	9	1	3	0	1	0	2	0	6	0	4	0	1	1	2	4	1	1	3	5			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr19:12502558C>T	ENST00000430385.3	-	4	854	c.654G>A	c.(652-654)acG>acA	p.T218T	CTD-3105H18.14_ENST00000435033.1_Intron|ZNF799_ENST00000419318.1_Silent_p.T186T	NM_001080821.2	NP_001074290.1	Q96GE5	ZN799_HUMAN	zinc finger protein 799	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)	p.T218T(2)|p.T5T(2)		breast(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(2)	19						CTCCAGTGTGCGTTCTCTCAT	0.403																																					p.T218T		Atlas-SNP	.											ZNF799_ENST00000430385,NS,carcinoma,0,2	ZNF799	111	.	4	Substitution - coding silent(4)	lung(4)	c.G654A						PASS	.						105	109	108					19																	12502558		2202	4298	6500	SO:0001819	synonymous_variant	90576	exon4			AGTGTGCGTTCTC	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.654G>A	chr19.hg19:g.12502558C>T		160.0	1.0	.		99.0	39.0	.	NM_001080821		Silent	SNP	ENST00000430385.3	hg19	CCDS45989.1																																																																																			.	.	.	none		0.403	ZNF799-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344099.2	NM_001080821		T	12502558	C	T	12502558	2	4	103	1	0	0	0	0	0	0	0	1	18178	755	27	1		1	ZNF799	19	12502558	Silent	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	11443489	12502558	46626425	113	6643											
CD97	976	hgsc.bcm.edu	37	chr19	14517156	14517156	+	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	cccgcaggtggggctgcgctGccgcctggtggccgggctgc	1	6	19	15	4	0	0	0	0	0	0	0	0	0	0	4	6	3	4	4	6	0	0			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr19:14517156G>T	ENST00000242786.5	+	15	1915	c.1835G>T	c.(1834-1836)tGc>tTc	p.C612F	CTC-548K16.5_ENST00000590626.1_RNA|CD97_ENST00000357355.3_Missense_Mutation_p.C563F|CD97_ENST00000358600.3_Missense_Mutation_p.C519F	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	612					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						GGGCTGCGCTGCCGCCTGGTG	0.706											OREG0025312	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C612F		Atlas-SNP	.											.	CD97	86	.	0			c.G1835T						PASS	.						30	24	26					19																	14517156		2190	4280	6470	SO:0001583	missense	976	exon15			TGCGCTGCCGCCT		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.1835G>T	chr19.hg19:g.14517156G>T	ENSP00000242786:p.Cys612Phe	18.0	0.0	.	695	28.0	15.0	.	NM_078481	A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	Missense_Mutation	SNP	ENST00000242786.5	hg19	CCDS32929.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.158116	0.78114	.	.	ENSG00000123146	ENST00000242786;ENST00000357355;ENST00000358600;ENST00000393059	D;D;D	0.82433	-1.61;-1.61;-1.61	4.42	3.33	0.38152	GPCR, family 2-like (1);	0.000000	0.36303	N	0.002674	D	0.93517	0.7931	H	0.97291	3.975	0.48236	D	0.999613	D;D;D	0.71674	0.959;0.976;0.998	D;D;D	0.87578	0.91;0.938;0.998	D	0.93810	0.7109	10	0.87932	D	0	.	11.004	0.47622	0.0:0.0:0.8118:0.1882	.	519;563;612	P48960-2;P48960-3;P48960	.;.;CD97_HUMAN	F	612;563;519;562	ENSP00000242786:C612F;ENSP00000349918:C563F;ENSP00000351413:C519F	ENSP00000242786:C612F	C	+	2	0	CD97	14378156	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.174000	0.89682	0.778000	0.33520	0.505000	0.49811	TGC	.	.	.	none		0.706	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459821.2	NM_078481		T	14517156	G	T	14517156	3	4	103	1	0	0	0	0	1	0	0	0	3051	1319	46	4	1893	4	CD97	19	14517156	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	2014598	14517156	44611827	114	6644											
EPS15L1	58513	hgsc.bcm.edu	37	chr19	16548668	16548669	+	Frame_Shift_Del	DEL	AT	AT	-																															gccaccagtctcagtgcaacAtagaaaccctgcaagtccaa																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr19:16548668_16548669delAT	ENST00000248070.6	-	5	360_361	c.221_222delAT	c.(220-222)tatfs	p.Y74fs	EPS15L1_ENST00000535753.2_Frame_Shift_Del_p.Y74fs|EPS15L1_ENST00000597937.1_Frame_Shift_Del_p.Y74fs|EPS15L1_ENST00000602009.1_5'Flank|EPS15L1_ENST00000455140.2_Frame_Shift_Del_p.Y74fs|EPS15L1_ENST00000594975.1_Frame_Shift_Del_p.Y74fs	NM_021235.2	NP_067058.1	Q9UBC2	EP15R_HUMAN	epidermal growth factor receptor pathway substrate 15-like 1	74	EH 1. {ECO:0000255|PROSITE- ProRule:PRU00077}.|Interaction with DAB2. {ECO:0000250}.				endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	clathrin coat of coated pit (GO:0030132)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(4)|skin(2)	30						TCAGTGCAACATAGAAACCCTG	0.5																																					p.74_75del		Atlas-Indel,Pindel	.											.	EPS15L1	81	.	0			c.222_223del						PASS	.																																			SO:0001589	frameshift_variant	58513	exon5			.	AF110265	CCDS32944.1, CCDS58653.1, CCDS58654.1, CCDS59363.1	19p13.12	2013-01-10				ENSG00000127527		"EF-hand domain containing"	24634	protein-coding gene	gene with protein product							Standard	NM_001258374		Approved	eps15R	uc002ndx.4	Q9UBC2		ENST00000248070.6:c.221_222delAT	chr19.hg19:g.16548668_16548669delAT	ENSP00000248070:p.Tyr74fs	103.0	0.0	0		113.0	34.0	0.300885	NM_021235	A2RRF3|A5PL29|B4DKA3	Frame_Shift_Del	DEL	ENST00000248070.6	hg19	CCDS32944.1																																																																																			.	.	.	none		0.5	EPS15L1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461040.1	NM_021235		-	16548669	AT	-	16548668	7	5	103	1	0	1	0	1	0	0	0	0	5195	224	8	0	2448	0	EPS15L1	19	16548668	Frame_Shift_Del	DEL	AT	TCGA-B9-A44B-01A-11D-A25F-10	2031512	16548668	42580315	115	6645											
IFI30	10437	hgsc.bcm.edu	37	chr19	18288015	18288015	+	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	gagtgtgcaatgggggaccgCggcatgcagctcatgcacgc	8	6	16	11	3	1	0	1	0	0	0	1	2	1	1	1	3	4	5	1	3	1	0			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr19:18288015C>T	ENST00000407280.3	+	5	724	c.549C>T	c.(547-549)cgC>cgT	p.R183R	PIK3R2_ENST00000593731.1_3'UTR	NM_006332.3	NP_006323.2	P13284	GILT_HUMAN	interferon, gamma-inducible protein 30	183					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						TGGGGGACCGCGGCATGCAGC	0.617																																					p.R183R		Atlas-SNP	.											.	IFI30	12	.	0			c.C549T						PASS	.						32	34	33					19																	18288015		2111	4231	6342	SO:0001819	synonymous_variant	10437	exon5			GGACCGCGGCATG	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.549C>T	chr19.hg19:g.18288015C>T		215.0	0.0	.		160.0	34.0	.	NM_006332	Q76MF9|Q8NEI4|Q8WU77|Q9UL08	Silent	SNP	ENST00000407280.3	hg19	CCDS46015.1																																																																																			.	.	.	none		0.617	IFI30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466396.3	NM_006332		T	18288015	C	T	18288015	2	4	103	1	0	0	0	0	0	0	0	1	7522	755	27	1		1	IFI30	19	18288015	Silent	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	1739347	18288015	40840968	116	6646											
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385790	58385790	+	Missense_Mutation	SNP	G	G	T																															cacattctccacattcataaGgtcttttcccagtgtgaact																								rs111727691		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr19:58385790G>T	ENST00000435989.2	-	3	1202	c.968C>A	c.(967-969)cCt>cAt	p.P323H	ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000596604.1_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	chr19.hg19:g.58385790G>T	ENSP00000410545:p.Pro323His	108.0	0.0	.		131.0	13.0	.	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	hg19	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	103	1	0	0	0	0	1	0	0	0	18188	1000	35	4	1603	4	ZNF814	19	58385790	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	40097775	58385790	743193	117	6647	72	2									
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385793	58385793	+	Missense_Mutation	SNP	C	C	T																															attctccacattcataaggtCttttcccagtgtgaactctc																								rs113623532		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr19:58385793C>T	ENST00000435989.2	-	3	1199	c.965G>A	c.(964-966)aGa>aAa	p.R322K	ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000596604.1_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	chr19.hg19:g.58385793C>T	ENSP00000410545:p.Arg322Lys	103.0	0.0	.		122.0	12.0	.	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	hg19	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	103	1	0	0	0	0	1	0	0	0	18188	913	32	2	1606	2	ZNF814	19	58385793	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	3	58385793	743190	118	6648	72	2									
CHD6	84181	hgsc.bcm.edu	37	chr20	40143495	40143495	+	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	ggactccgcagagatgggttCgtcaggccctgatccagctc	7	8	13	13	2	1	2	1	1	0	1	5	4	3	3	3	3	1	3	3	3	0	1			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr20:40143495C>A	ENST00000373233.3	-	4	828	c.651G>T	c.(649-651)acG>acT	p.T217T	CHD6_ENST00000309279.7_Silent_p.T217T|CHD6_ENST00000373222.3_Silent_p.T252T	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	217	Required for DNA-dependent ATPase activity.				ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				GAGATGGGTTCGTCAGGCCCT	0.537																																					p.T217T		Atlas-SNP	.											.	CHD6	312	.	0			c.G651T						PASS	.						131	122	125					20																	40143495		2203	4300	6503	SO:0001819	synonymous_variant	84181	exon4			TGGGTTCGTCAGG	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.651G>T	chr20.hg19:g.40143495C>A		92.0	0.0	.		99.0	38.0	.	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Silent	SNP	ENST00000373233.3	hg19	CCDS13317.1																																																																																			.	.	.	none		0.537	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			A	40143495	C	A	40143495	2	1	103	1	0	0	0	0	0	0	0	1	3331	871	31	4		4	CHD6	20	40143495	Silent	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10		40143495	22882025	119	6649											
MYBL2	4605	hgsc.bcm.edu	37	chr20	42328636	42328636	+	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	gaggcagctaacctcctcatCcctgctgtgggttctagcct	6	11	10	14	0	2	0	1	0	1	0	4	1	4	0	4	2	4	4	4	2	2	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr20:42328636C>T	ENST00000217026.4	+	7	1030	c.903C>T	c.(901-903)atC>atT	p.I301I	MYBL2_ENST00000396863.4_Silent_p.I277I	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	301					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)			ACCTCCTCATCCCTGCTGTGG	0.572																																					p.I301I		Atlas-SNP	.											.	MYBL2	82	.	0			c.C903T						PASS	.						78	56	63					20																	42328636		2203	4300	6503	SO:0001819	synonymous_variant	4605	exon7			CCTCATCCCTGCT		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.903C>T	chr20.hg19:g.42328636C>T		92.0	0.0	.		82.0	34.0	.	NM_002466	B2RBS5|B7Z8D9|F8W6N6|Q53F07	Silent	SNP	ENST00000217026.4	hg19	CCDS13322.1																																																																																			.	.	.	none		0.572	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080408.1	NM_002466		T	42328636	C	T	42328636	2	4	103	1	0	0	0	0	0	0	0	1	10017	845	30	2		2	MYBL2	20	42328636	Silent	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	2185141	42328636	20696884	120	6650											
WFDC8	90199	hgsc.bcm.edu	37	chr20	44181865	44181865	+	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	gtcactgtgacatgaaggtgGacactccttacgttcagtga	10	11	11	9	1	2	3	2	3	0	0	3	4	3	4	1	2	1	1	1	2	2	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr20:44181865G>T	ENST00000357199.4	-	5	574	c.496C>A	c.(496-498)Cca>Aca	p.P166T	WFDC8_ENST00000289953.2_Missense_Mutation_p.P166T	NM_181510.2	NP_852611.2	Q8IUA0	WFDC8_HUMAN	WAP four-disulfide core domain 8	166	WAP 2. {ECO:0000255|PROSITE- ProRule:PRU00722}.					extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(4)|stomach(1)|upper_aerodigestive_tract(1)	15		Myeloproliferative disorder(115;0.0122)				CATGAAGGTGGACACTCCTTA	0.488																																					p.P166T		Atlas-SNP	.											.	WFDC8	28	.	0			c.C496A						PASS	.						139	111	121					20																	44181865		2203	4300	6503	SO:0001583	missense	90199	exon5			AAGGTGGACACTC	AL031663	CCDS13361.1	20q13.11	2013-01-21	2003-02-21	2003-02-21	ENSG00000158901	ENSG00000158901		"WAP four-disulfide core domain containing"	16163	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 170"	C20orf170		12206714	Standard	NM_130896		Approved	dJ461P17.1, WAP8	uc002xow.3	Q8IUA0	OTTHUMG00000046342	ENST00000357199.4:c.496C>A	chr20.hg19:g.44181865G>T	ENSP00000361735:p.Pro166Thr	147.0	0.0	.		131.0	51.0	.	NM_181510	E1P623|Q5TDV2|Q96A34	Missense_Mutation	SNP	ENST00000357199.4	hg19	CCDS13361.1	.	.	.	.	.	.	.	.	.	.	G	13.37	2.218036	0.39201	.	.	ENSG00000158901	ENST00000357199;ENST00000289953	T;T	0.71934	-0.61;-0.61	4.91	0.245	0.15512	Whey acidic protein, 4-disulphide core (5);	0.596324	0.15342	N	0.267433	T	0.59074	0.2167	L	0.48986	1.54	0.26237	N	0.978939	P	0.36412	0.552	B	0.42462	0.388	T	0.49597	-0.8923	10	0.07175	T	0.84	.	4.7744	0.13171	0.2342:0.0:0.5927:0.1732	.	166	Q8IUA0	WFDC8_HUMAN	T	166	ENSP00000361735:P166T;ENSP00000289953:P166T	ENSP00000289953:P166T	P	-	1	0	WFDC8	43615279	0.501000	0.26099	0.751000	0.31187	0.050000	0.14768	-0.083000	0.11286	0.202000	0.20498	0.655000	0.94253	CCA	.	.	.	none		0.488	WFDC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106958.1			T	44181865	G	T	44181865	3	4	103	1	0	0	0	0	1	0	0	0	17368	1174	41	4	237	4	WFDC8	20	44181865	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	1853229	44181865	18843655	121	6651											
BCAS4	55653	hgsc.bcm.edu	37	chr20	49458324	49458324	+	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	ccttcgtcaagatggttggaCaccacgtcgccttcctggaa	8	10	10	13	3	1	1	1	0	0	1	4	3	2	3	4	3	0	1	4	3	2	3			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr20:49458324C>T	ENST00000358791.5	+	4	476	c.376C>T	c.(376-378)Cac>Tac	p.H126Y	BCAS4_ENST00000262591.5_Intron|BCAS4_ENST00000371608.2_Missense_Mutation_p.H126Y|BCAS4_ENST00000609336.1_Missense_Mutation_p.H96Y	NM_017843.3	NP_060313.3	Q8TDM0	BCAS4_HUMAN	breast carcinoma amplified sequence 4	126						cytoplasm (GO:0005737)				large_intestine(2)|lung(2)|pancreas(1)|upper_aerodigestive_tract(1)	6						GATGGTTGGACACCACGTCGC	0.657																																					p.H126Y		Atlas-SNP	.											.	BCAS4	41	.	0			c.C376T						PASS	.						76	59	65					20																	49458324		2203	4300	6503	SO:0001583	missense	55653	exon4			GTTGGACACCACG	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.376C>T	chr20.hg19:g.49458324C>T	ENSP00000351642:p.His126Tyr	333.0	0.0	.		250.0	109.0	.	NM_198799	Q5TD52|Q5TD53|Q5TD54|Q5U5K7|Q5XKE8|Q8IXI7|Q8NEZ6|Q8TDL9|Q9NX13|Q9Y511	Missense_Mutation	SNP	ENST00000358791.5	hg19	CCDS33487.1	.	.	.	.	.	.	.	.	.	.	C	1.847	-0.465944	0.04476	.	.	ENSG00000124243	ENST00000358791;ENST00000355583;ENST00000371608	T;T	0.45276	1.9;0.9	4.48	3.5	0.40072	.	0.340201	0.30593	N	0.009290	T	0.37919	0.1021	L	0.51422	1.61	0.50632	D	0.999888	P;P	0.50528	0.763;0.936	B;P	0.44359	0.181;0.447	T	0.11941	-1.0567	10	0.39692	T	0.17	-17.6017	9.5663	0.39400	0.2101:0.7899:0.0:0.0	.	126;126	Q8TDM0-3;Q8TDM0	.;BCAS4_HUMAN	Y	126	ENSP00000351642:H126Y;ENSP00000360669:H126Y	ENSP00000347789:H126Y	H	+	1	0	BCAS4	48891731	0.746000	0.28272	0.137000	0.22149	0.014000	0.08584	1.544000	0.36158	0.837000	0.34925	0.561000	0.74099	CAC	.	.	.	none		0.657	BCAS4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079700.1	NM_017843		T	49458324	C	T	49458324	3	4	103	1	0	0	0	0	1	0	0	0	1353	478	17	2	390	2	BCAS4	20	49458324	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	5276459	49458324	13567196	122	6652											
ZDHHC8	29801	hgsc.bcm.edu	37	chr22	20128194	20128194	+	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	tcacccgaggctgctgtgggAatgtggagcacgtgctgtgt	6	10	16	9	2	1	0	1	0	0	0	1	3	1	2	1	3	3	4	1	3	1	0			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr22:20128194A>T	ENST00000334554.7	+	6	856	c.715A>T	c.(715-717)Aat>Tat	p.N239Y	ZDHHC8_ENST00000320602.7_Missense_Mutation_p.N147Y|ZDHHC8_ENST00000405930.3_Missense_Mutation_p.N239Y|ZDHHC8_ENST00000468112.1_3'UTR	NM_013373.3	NP_037505.1	Q9ULC8	ZDHC8_HUMAN	zinc finger, DHHC-type containing 8	239					locomotory behavior (GO:0007626)|protein palmitoylation (GO:0018345)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	20	Colorectal(54;0.0993)					CTGCTGTGGGAATGTGGAGCA	0.697																																					p.N239Y		Atlas-SNP	.											.	ZDHHC8	77	.	0			c.A715T						PASS	.						39	35	36					22																	20128194		2198	4299	6497	SO:0001583	missense	29801	exon6			TGTGGGAATGTGG	AB033118	CCDS13776.1, CCDS54502.1	22q11.21	2009-10-06		2003-02-28	ENSG00000099904	ENSG00000099904		"Zinc fingers, DHHC-type"	18474	protein-coding gene	gene with protein product		608784				10574462, 15184899	Standard	NM_013373		Approved	ZNF378, KIAA1292	uc002zrr.2	Q9ULC8	OTTHUMG00000150499	ENST00000334554.7:c.715A>T	chr22.hg19:g.20128194A>T	ENSP00000334490:p.Asn239Tyr	40.0	0.0	.		32.0	16.0	.	NM_001185024	Q2TGE9|Q6ICL1|Q6ZNF5|Q7Z6L9	Missense_Mutation	SNP	ENST00000334554.7	hg19	CCDS13776.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.624495	0.87560	.	.	ENSG00000099904	ENST00000334554;ENST00000320602;ENST00000405930	T;T;T	0.79845	-0.2;-1.31;-0.32	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	D	0.88377	0.6420	M	0.67397	2.05	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	0.89618	0.3846	10	0.72032	D	0.01	.	15.1958	0.73088	1.0:0.0:0.0:0.0	.	147;239;239	Q9ULC8-2;Q9ULC8-3;Q9ULC8	.;.;ZDHC8_HUMAN	Y	239;147;239	ENSP00000334490:N239Y;ENSP00000317804:N147Y;ENSP00000384716:N239Y	ENSP00000317804:N147Y	N	+	1	0	ZDHHC8	18508194	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.875000	0.92372	2.035000	0.60131	0.533000	0.62120	AAT	.	.	.	none		0.697	ZDHHC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318564.1	NM_013373		T	20128194	A	T	20128194	3	4	103	1	0	0	0	0	1	0	0	0	17633	246	9	5	737	5	ZDHHC8	22	20128194	Missense_Mutation	SNP	A	TCGA-B9-A44B-01A-11D-A25F-10		20128194	31176372	123	6653											
C22orf42	150297	hgsc.bcm.edu	37	chr22	32555017	32555019	+	In_Frame_Del	DEL	CTG	CTG	-																															gtcttcgggaggctgaggtaCtgcatgagttgggccttctt																										TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chr22:32555017_32555019delCTG	ENST00000382097.3	-	1	256_258	c.184_186delCAG	c.(184-186)cagdel	p.Q62del	RP1-90G24.8_ENST00000426354.1_lincRNA	NM_001010859.1	NP_001010859.1	Q6IC83	CV042_HUMAN	chromosome 22 open reading frame 42	62										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(2)	24						GGCTGAGGTACTGCATGAGTTGG	0.537																																					p.62_63del		Atlas-Indel,Pindel	.											.	C22orf42	37	.	0			c.185_187del						PASS	.																																			SO:0001651	inframe_deletion	150297	exon1			.	BC040263	CCDS33639.1	22q12.3	2009-03-05			ENSG00000205856	ENSG00000205856			27160	protein-coding gene	gene with protein product						12477932	Standard	XM_005261369		Approved		uc003amd.3	Q6IC83	OTTHUMG00000030380	ENST00000382097.3:c.184_186delCAG	chr22.hg19:g.32555017_32555019delCTG	ENSP00000371529:p.Gln62del	290.0	0.0	0		274.0	49.0	0.178832	NM_001010859	A4QPH5	In_Frame_Del	DEL	ENST00000382097.3	hg19	CCDS33639.1																																																																																			.	.	.	none		0.537	C22orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075268.2	NM_001010859		-	32555019	CTG	-	32555017	7	5	103	1	0	1	0	1	0	0	0	0	2151	564	20	0	605	0	C22orf42	22	32555017	In_Frame_Del	DEL	CTG	TCGA-B9-A44B-01A-11D-A25F-10	12426823	32555017	18749549	124	6654											
POLA1	5422	hgsc.bcm.edu	37	chrX	24744126	24744126	+	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	aaagaactatgcttttgagaTacctgatgttccagaaaaat	16	12	7	6	0	0	4	0	2	0	3	1	5	1	4	2	0	3	2	2	0	6	5			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chrX:24744126T>A	ENST00000379059.3	+	13	1343	c.1328T>A	c.(1327-1329)aTa>aAa	p.I443K	POLA1_ENST00000379068.3_Missense_Mutation_p.I449K	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	443					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)	GCTTTTGAGATACCTGATGTT	0.328																																					p.I443K		Atlas-SNP	.											.	POLA1	117	.	0			c.T1328A						PASS	.						71	69	70					X																	24744126		2203	4300	6503	SO:0001583	missense	5422	exon13			TTGAGATACCTGA		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.1328T>A	chrX.hg19:g.24744126T>A	ENSP00000368349:p.Ile443Lys	99.0	0.0	.		34.0	26.0	.	NM_016937	Q86UQ7	Missense_Mutation	SNP	ENST00000379059.3	hg19	CCDS14214.1	.	.	.	.	.	.	.	.	.	.	t	11.79	1.743738	0.30865	.	.	ENSG00000101868	ENST00000379068;ENST00000379059	T;T	0.42900	0.96;0.96	5.36	4.2	0.49525	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.046811	0.85682	D	0.000000	T	0.30479	0.0766	L	0.42744	1.35	0.80722	D	1	B;B	0.14438	0.001;0.01	B;B	0.20384	0.016;0.029	T	0.08534	-1.0717	10	0.05959	T	0.93	-6.4004	10.4411	0.44466	0.0:0.0769:0.0:0.9231	.	449;443	A6NMQ1;P09884	.;DPOLA_HUMAN	K	449;443	ENSP00000368358:I449K;ENSP00000368349:I443K	ENSP00000368349:I443K	I	+	2	0	POLA1	24654047	1.000000	0.71417	1.000000	0.80357	0.765000	0.43378	7.333000	0.79214	0.832000	0.34804	-0.392000	0.06488	ATA	.	.	.	none		0.328	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937		A	24744126	T	A	24744126	3	1	103	1	0	0	0	0	1	0	0	0	12194	1406	49	5	1378	5	POLA1	23	24744126	Missense_Mutation	SNP	T	TCGA-B9-A44B-01A-11D-A25F-10		24744126	130526434	125	6655											
MCART6	401612	hgsc.bcm.edu	37	chrX	103349337	103349337	+	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	caggccttgctctgccaggcCatcctggatggggtccttga	5	10	13	13	0	1	1	0	1	1	0	3	2	3	2	5	5	2	1	5	5	0	2			TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chrX:103349337C>T	ENST00000357421.4	-	2	784	c.604G>A	c.(604-606)Ggc>Agc	p.G202S		NM_001012755.3	NP_001012773.2	Q5H9E4	S2553_HUMAN	solute carrier family 25, member 53	202					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)											TCTGCCAGGCCATCCTGGATG	0.552																																					p.G202S		Atlas-SNP	.											.	.	.	.	0			c.G604A						PASS	.						62	65	64					X																	103349337		2202	4300	6502	SO:0001583	missense	401612	exon2			CCAGGCCATCCTG		CCDS35363.1	Xq22.2	2013-05-22	2012-03-29	2012-03-29	ENSG00000176274	ENSG00000269743		"Solute carriers"	31894	protein-coding gene	gene with protein product			"mitochondrial carrier triple repeat 6"	MCART6			Standard	NM_001012755		Approved		uc004elu.3	Q5H9E4	OTTHUMG00000022124	ENST00000357421.4:c.604G>A	chrX.hg19:g.103349337C>T	ENSP00000361681:p.Gly202Ser	66.0	0.0	.		84.0	12.0	.	NM_001012755	B2RTT9	Missense_Mutation	SNP	ENST00000357421.4	hg19	CCDS35363.1	.	.	.	.	.	.	.	.	.	.	c	9.080	0.999007	0.19121	.	.	ENSG00000176274	ENST00000357421	T	0.77620	-1.11	4.18	2.25	0.28309	Mitochondrial carrier domain (2);	0.586966	0.16485	N	0.212372	T	0.48259	0.1490	N	0.01751	-0.74	0.29543	N	0.85193	B	0.02656	0.0	B	0.06405	0.002	T	0.39881	-0.9592	10	0.22109	T	0.4	-18.0741	7.4625	0.27304	0.0:0.7591:0.0:0.2409	.	202	Q5H9E4	MCAR6_HUMAN	S	202	ENSP00000361681:G202S	ENSP00000361681:G202S	G	-	1	0	MCART6	103235993	0.000000	0.05858	0.980000	0.43619	0.966000	0.64601	-0.866000	0.04245	0.295000	0.22570	0.594000	0.82650	GGC	.	.	.	none		0.552	SLC25A53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057761.1	NM_001012755		T	103349337	C	T	103349337	3	4	103	1	0	0	0	0	1	0	0	0	9378	594	21	2	323	2	MCART6	23	103349337	Missense_Mutation	SNP	C	TCGA-B9-A44B-01A-11D-A25F-10	78605211	103349337	51921223	126	6656											
COL4A5	1287	hgsc.bcm.edu	37	chrX	107938134	107938134	+	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	gatgggattctctgtggattGgttattccttcatgatggta	7	17	12	5	0	2	1	1	1	1	0	4	4	3	3	1	4	0	2	1	4	2	6	rs104886424		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	g.chrX:107938134G>A	ENST00000361603.2	+	49	5030	c.4786G>A	c.(4786-4788)Ggt>Agt	p.G1596S	COL4A5_ENST00000328300.6_Missense_Mutation_p.G1602S	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	1596	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.		G -> D (in APSX). {ECO:0000269|PubMed:9452056}.		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						TCTGTGGATTGGTTATTCCTT	0.453									Alport syndrome with Diffuse Leiomyomatosis																												p.G1596S		Atlas-SNP	.											.	COL4A5	262	.	0			c.G4786A						PASS	.						321	202	242					X																	107938134		2203	4300	6503	SO:0001583	missense	1287	exon49	Familial Cancer Database		TGGATTGGTTATT	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.4786G>A	chrX.hg19:g.107938134G>A	ENSP00000354505:p.Gly1596Ser	184.0	0.0	.		219.0	9.0	.	NM_000495	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Missense_Mutation	SNP	ENST00000361603.2	hg19	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	G	34	5.313598	0.95655	.	.	ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186;ENST00000504541	D;D;D	0.99557	-6.16;-6.16;-4.07	5.57	5.57	0.84162	C-type lectin fold (1);	0.000000	0.85682	D	0.000000	D	0.99813	0.9918	H	0.97265	3.97	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96778	0.9573	10	0.87932	D	0	.	18.5959	0.91229	0.0:0.0:1.0:0.0	.	1599;1596	E7EVY4;P29400	.;CO4A5_HUMAN	S	1602;1596;1602;68	ENSP00000331902:G1602S;ENSP00000354505:G1596S;ENSP00000424845:G68S	ENSP00000331902:G1602S	G	+	1	0	COL4A5	107824790	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.335000	0.79485	0.594000	0.82650	GGT	.	.	.	weak		0.453	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2			A	107938134	G	A	107938134	3	1	103	1	0	0	0	0	1	0	0	0	3696	1348	47	2	4991	2	COL4A5	23	107938134	Missense_Mutation	SNP	G	TCGA-B9-A44B-01A-11D-A25F-10	4588797	107938134	47332426	127	6657											
PIK3R4	30849	hgsc.bcm.edu	37	chr3	130425829	130425831	+	In_Frame_Del	DEL	GAG	GAG	-																															aagggacacaaatgccagcaGaggactcggaacgaggaggt																										TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr3:130425829_130425831delGAG	ENST00000356763.3	-	11	3239_3241	c.2682_2684delCTC	c.(2680-2685)tcctct>tct	p.894_895SS>S		NM_014602.2	NP_055417.1	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	894					innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(6)|large_intestine(16)|lung(28)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	77						AATGCCAGCAGAGGACTCGGAAC	0.502																																					p.895_895del		Atlas-Indel,Pindel	.											.	PIK3R4	145	.	0			c.2683_2685del						PASS	.																																			SO:0001651	inframe_deletion	30849	exon11			.	Y08991	CCDS3067.1	3q22.1	2013-01-10	2008-02-04		ENSG00000196455	ENSG00000196455		"WD repeat domain containing"	8982	protein-coding gene	gene with protein product		602610				8999962	Standard	NM_014602		Approved	VPS15, p150	uc003enj.3	Q99570	OTTHUMG00000159645	ENST00000356763.3:c.2682_2684delCTC	chr3.hg19:g.130425829_130425831delGAG	ENSP00000349205:p.Ser895del	150.0	0.0	0		112.0	12.0	0.107143	NM_014602	Q2TBF4	In_Frame_Del	DEL	ENST00000356763.3	hg19	CCDS3067.1																																																																																			.	.	.	none		0.502	PIK3R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356668.1	NM_014602		-	130425831	GAG	-	130425829	7	5	104	1	0	1	0	1	0	0	0	0	11928	942	33	0	1432	0	PIK3R4	3	130425829	In_Frame_Del	DEL	GAG	TCGA-B9-A5W7-01A-11D-A31X-10		130425829	67596601	1	6658											
COPS4	51138	hgsc.bcm.edu	37	chr4	83996480	83996480	+	Frame_Shift_Del	DEL	A	A	-																															cctgccaacgtgggataagcAgatccaatcactttgtttcc																										TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr4:83996480delA	ENST00000264389.2	+	10	1253	c.1118delA	c.(1117-1119)cagfs	p.Q373fs	COPS4_ENST00000509093.1_Frame_Shift_Del_p.R345fs|COPS4_ENST00000511653.1_3'UTR|COPS4_ENST00000503682.1_Frame_Shift_Del_p.Q405fs	NM_016129.2	NP_057213.2	Q9BT78	CSN4_HUMAN	COP9 signalosome subunit 4	373					cullin deneddylation (GO:0010388)|protein deneddylation (GO:0000338)	cell junction (GO:0030054)|COP9 signalosome (GO:0008180)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)				endometrium(2)|kidney(2)|large_intestine(3)|lung(4)|urinary_tract(2)	13		Hepatocellular(203;0.114)				TGGGATAAGCAGATCCAATCA	0.403																																					p.Q373fs		Atlas-Indel,Pindel	.											.	COPS4	31	.	0			c.1117delC						PASS	.						87	85	86					4																	83996480		2203	4300	6503	SO:0001589	frameshift_variant	51138	exon10			.	AF100757	CCDS3600.1, CCDS58909.1	4q21.22	2013-03-14	2013-03-14		ENSG00000138663	ENSG00000138663			16702	protein-coding gene	gene with protein product			"COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 4", "COP9 constitutive photomorphogenic homolog subunit 4 (Arabidopsis)"			9707402	Standard	NM_016129		Approved	CSN4	uc003hoa.3	Q9BT78	OTTHUMG00000130298	ENST00000264389.2:c.1118delA	chr4.hg19:g.83996480delA	ENSP00000264389:p.Gln373fs	79.0	0.0	0		71.0	15.0	0.211268	NM_016129	B3KN88|B3KST5|Q561W7|Q9NW31|Q9Y677	Frame_Shift_Del	DEL	ENST00000264389.2	hg19	CCDS3600.1																																																																																			.	.	.	none		0.403	COPS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252643.1			-	83996480	A	-	83996480	7	5	104	1	0	1	0	1	0	0	0	0	3737	188	7	0	1156	0	COPS4	4	83996480	Frame_Shift_Del	DEL	A	TCGA-B9-A5W7-01A-11D-A31X-10		83996480	107157796	2	6659											
MDGA1	266727	hgsc.bcm.edu	37	chr6	37606390	37606390	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgccactgagagaccaggCgtgcgtgtccagagcccctt	8	8	12	13	2	0	3	0	1	0	2	1	4	1	3	5	1	3	0	5	1	0	2	rs376783889		TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr6:37606390C>T	ENST00000434837.3	-	15	3768	c.2590G>A	c.(2590-2592)Gcc>Acc	p.A864T	MDGA1_ENST00000297153.7_Missense_Mutation_p.A868T|MDGA1_ENST00000505425.1_Missense_Mutation_p.A864T	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	864	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				brain development (GO:0007420)|cerebral cortex radially oriented cell migration (GO:0021799)|neuron migration (GO:0001764)|spinal cord association neuron differentiation (GO:0021527)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)				central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						AGAGACCAGGCGTGCGTGTCC	0.642													C|||	1	0.000199681	8e-04	0	5008	,	,		18090	0		0	False		,,,				2504	0				p.A864T		Atlas-SNP	.											MDGA1,NS,carcinoma,0,1	MDGA1	104	.	0			c.G2590A						PASS	.	C	THR/ALA	0,4120		0,0,2060	45	52	50		2590	4.2	0.9	6		50	1,8373		0,1,4186	no	missense	MDGA1	NM_153487.3	58	0,1,6246	TT,TC,CC		0.0119,0.0,0.0080	possibly-damaging	864/956	37606390	1,12493	2060	4187	6247	SO:0001583	missense	266727	exon15			ACCAGGCGTGCGT	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.2590G>A	chr6.hg19:g.37606390C>T	ENSP00000402584:p.Ala864Thr	92.0	0.0	.		69.0	3.0	.	NM_153487	A6NHG0|Q8NBE3	Missense_Mutation	SNP	ENST00000434837.3	hg19	CCDS47417.1	.	.	.	.	.	.	.	.	.	.	C	17.56	3.419072	0.62622	0.0	1.19E-4	ENSG00000112139	ENST00000434837;ENST00000297153;ENST00000505425	T;T;T	0.02158	4.42;4.42;4.42	5.04	4.17	0.49024	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.274741	0.25321	N	0.031518	T	0.01156	0.0038	N	0.20445	0.575	0.24994	N	0.991515	D;P	0.64830	0.994;0.898	P;B	0.51385	0.668;0.104	T	0.56565	-0.7958	10	0.26408	T	0.33	.	11.8151	0.52204	0.0:0.913:0.0:0.087	.	864;864	Q8NFP4-2;Q8NFP4	.;MDGA1_HUMAN	T	864;868;864	ENSP00000402584:A864T;ENSP00000297153:A868T;ENSP00000422042:A864T	ENSP00000297153:A868T	A	-	1	0	MDGA1	37714368	0.971000	0.33674	0.945000	0.38365	0.956000	0.61745	4.713000	0.61895	1.245000	0.43885	0.650000	0.86243	GCC	.	.	.	weak		0.642	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3			T	37606390	C	T	37606390	3	4	104	1	0	0	0	0	1	0	0	0	9413	768	27	1	289	1	MDGA1	6	37606390	Missense_Mutation	SNP	C	TCGA-B9-A5W7-01A-11D-A31X-10		37606390	133508677	3	6660											
TSPAN33	340348	hgsc.bcm.edu	37	chr7	128804350	128804350	+	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	agtgagatcatcaacaatgcCattgtgcactaccgagatga	14	9	9	9	1	2	3	2	2	0	2	2	5	2	3	2	0	4	1	2	0	3	2			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr7:128804350C>A	ENST00000289407.4	+	5	508	c.399C>A	c.(397-399)gcC>gcA	p.A133A	Y_RNA_ENST00000363759.1_RNA	NM_178562.3	NP_848657.1	Q86UF1	TSN33_HUMAN	tetraspanin 33	133					establishment of protein localization to plasma membrane (GO:0090002)|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)			NS(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	14						TCAACAATGCCATTGTGCACT	0.498											OREG0018304	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A133A		Atlas-SNP	.											.	TSPAN33	29	.	0			c.C399A						PASS	.						211	180	190					7																	128804350		2203	4300	6503	SO:0001819	synonymous_variant	340348	exon5			CAATGCCATTGTG		CCDS5810.1	7q32.3	2013-02-14			ENSG00000158457	ENSG00000158457		"Tetraspanins"	28743	protein-coding gene	gene with protein product		610120				16213355, 16242907	Standard	XM_006715960		Approved	MGC50844, Penumbra	uc003vop.2	Q86UF1	OTTHUMG00000158420	ENST00000289407.4:c.399C>A	chr7.hg19:g.128804350C>A		54.0	0.0	.	1567	76.0	48.0	.	NM_178562		Silent	SNP	ENST00000289407.4	hg19	CCDS5810.1																																																																																			.	.	.	none		0.498	TSPAN33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350983.1	NM_178562		A	128804350	C	A	128804350	2	1	104	1	0	0	0	0	0	0	0	1	16660	581	21	4		4	TSPAN33	7	128804350	Silent	SNP	C	TCGA-B9-A5W7-01A-11D-A31X-10		128804350	30334313	4	6661											
P2RY2	5029	hgsc.bcm.edu	37	chr11	72945937	72945937	+	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	gggccaagcgcaagtccgtgCgcaccatcgccgtggtgctg	6	6	15	14	5	0	0	0	0	0	0	2	0	1	0	4	2	3	3	4	2	2	0			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr11:72945937C>T	ENST00000311131.2	+	3	1200	c.733C>T	c.(733-735)Cgc>Tgc	p.R245C	P2RY2_ENST00000393597.2_Missense_Mutation_p.R245C|P2RY2_ENST00000393596.2_Missense_Mutation_p.R245C	NM_002564.2|NM_176072.1	NP_002555|NP_788086	P41231	P2RY2_HUMAN	purinergic receptor P2Y, G-protein coupled, 2	245					cellular ion homeostasis (GO:0006873)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of mucus secretion (GO:0070257)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25					Suramin(DB04786)	CAAGTCCGTGCGCACCATCGC	0.642																																					p.R245C		Atlas-SNP	.											.	P2RY2	54	.	0			c.C733T						PASS	.						101	92	95					11																	72945937		2200	4293	6493	SO:0001583	missense	5029	exon3			TCCGTGCGCACCA	U07225	CCDS8219.1	11q13.5-q14.1	2012-08-08				ENSG00000175591		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8541	protein-coding gene	gene with protein product		600041				8159738, 9286708	Standard	NM_002564		Approved	P2U	uc001otj.4	P41231		ENST00000311131.2:c.733C>T	chr11.hg19:g.72945937C>T	ENSP00000310305:p.Arg245Cys	51.0	0.0	.		33.0	13.0	.	NM_176071	B2R9W3|Q96EM8	Missense_Mutation	SNP	ENST00000311131.2	hg19	CCDS8219.1	.	.	.	.	.	.	.	.	.	.	C	16.27	3.076082	0.55646	.	.	ENSG00000175591	ENST00000393597;ENST00000311131;ENST00000393596	T;T;T	0.37411	1.2;1.2;1.2	4.42	3.34	0.38264	GPCR, rhodopsin-like superfamily (1);	0.057192	0.64402	D	0.000005	T	0.60830	0.2299	M	0.88450	2.955	0.52501	D	0.999954	D	0.89917	1.0	D	0.71414	0.973	T	0.66999	-0.5781	10	0.87932	D	0	.	9.3877	0.38354	0.4324:0.5676:0.0:0.0	.	245	P41231	P2RY2_HUMAN	C	245	ENSP00000377222:R245C;ENSP00000310305:R245C;ENSP00000377221:R245C	ENSP00000310305:R245C	R	+	1	0	P2RY2	72623585	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	3.622000	0.54217	2.170000	0.68504	0.561000	0.74099	CGC	.	.	.	none		0.642	P2RY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397336.1	NM_176072		T	72945937	C	T	72945937	3	4	104	1	0	0	0	0	1	0	0	0	11359	768	27	1	735	1	P2RY2	11	72945937	Missense_Mutation	SNP	C	TCGA-B9-A5W7-01A-11D-A31X-10		72945937	62060579	5	6662											
ATN1	1822	hgsc.bcm.edu	37	chr12	7045933	7045933	+	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	cagcagcagcagcagcagcaGcagcatcacggaaactctgg	13	3	12	13	1	2	0	1	0	1	0	2	1	2	1	0	2	9	8	0	2	1	0			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr12:7045933G>T	ENST00000356654.4	+	5	1740	c.1503G>T	c.(1501-1503)caG>caT	p.Q501H	ATN1_ENST00000396684.2_Missense_Mutation_p.Q501H	NM_001007026.1	NP_001007027.1	P54259	ATN1_HUMAN	atrophin 1	501	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						agcagcagcagcagcaTCACG	0.632																																					p.Q501H		Atlas-SNP	.											.	ATN1	95	.	0			c.G1503T						PASS	.						50	59	56					12																	7045933		2203	4300	6503	SO:0001583	missense	1822	exon5			GCAGCAGCAGCAT	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.1503G>T	chr12.hg19:g.7045933G>T	ENSP00000349076:p.Gln501His	78.0	0.0	.		109.0	10.0	.	NM_001007026	Q99495|Q99621|Q9UEK7	Missense_Mutation	SNP	ENST00000356654.4	hg19	CCDS31734.1	.	.	.	.	.	.	.	.	.	.	g	4.415	0.076769	0.08485	.	.	ENSG00000111676	ENST00000356654;ENST00000396684;ENST00000544325;ENST00000229279	T;T;T	0.56776	0.44;0.44;0.44	2.87	-4.98	0.03019	.	.	.	.	.	T	0.29158	0.0725	N	0.22421	0.69	0.09310	N	1	P	0.44521	0.837	B	0.36418	0.224	T	0.25537	-1.0129	9	0.12430	T	0.62	.	12.1608	0.54103	0.1812:0.0:0.8188:0.0	.	501	P54259	ATN1_HUMAN	H	501;501;501;86	ENSP00000349076:Q501H;ENSP00000379915:Q501H;ENSP00000441744:Q501H	ENSP00000229279:Q86H	Q	+	3	2	ATN1	6916194	0.370000	0.25047	0.054000	0.19295	0.338000	0.28826	0.810000	0.27183	-1.248000	0.02503	0.177000	0.17058	CAG	.	.	.	none		0.632	ATN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401948.2	NM_001940		T	7045933	G	T	7045933	3	4	104	1	0	0	0	0	1	0	0	0	1111	962	34	4	1517	4	ATN1	12	7045933	Missense_Mutation	SNP	G	TCGA-B9-A5W7-01A-11D-A31X-10		7045933	126805962	6	6663											
KIF26A	26153	hgsc.bcm.edu	37	chr14	104639376	104639376	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctgggcatcgtgccctgcGccatctcctggctcttcagg	3	10	12	16	2	3	0	1	0	2	0	5	0	3	0	4	3	2	2	4	3	0	1			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr14:104639376G>A	ENST00000423312.2	+	8	1483	c.1483G>A	c.(1483-1485)Gcc>Acc	p.A495T	KIF26A_ENST00000315264.7_Missense_Mutation_p.A356T	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	495	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)		CGTGCCCTGCGCCATCTCCTG	0.682																																					p.A495T		Atlas-SNP	.											.	KIF26A	84	.	0			c.G1483A						PASS	.						21	27	25					14																	104639376		2117	4214	6331	SO:0001583	missense	26153	exon8			CCCTGCGCCATCT	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.1483G>A	chr14.hg19:g.104639376G>A	ENSP00000388241:p.Ala495Thr	84.0	0.0	.		76.0	6.0	.	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Missense_Mutation	SNP	ENST00000423312.2	hg19	CCDS45171.1	.	.	.	.	.	.	.	.	.	.	G	35	5.536616	0.96460	.	.	ENSG00000066735	ENST00000423312;ENST00000315264	T;T	0.48522	0.81;0.81	4.84	4.84	0.62591	Kinesin, motor domain (4);	.	.	.	.	T	0.65616	0.2708	L	0.53617	1.68	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.68891	-0.5289	9	0.66056	D	0.02	.	17.9375	0.89017	0.0:0.0:1.0:0.0	.	495	Q9ULI4	KI26A_HUMAN	T	495;356	ENSP00000388241:A495T;ENSP00000325452:A356T	ENSP00000325452:A356T	A	+	1	0	KIF26A	103709129	1.000000	0.71417	1.000000	0.80357	0.739000	0.42172	7.702000	0.84576	2.223000	0.72356	0.462000	0.41574	GCC	.	.	.	none		0.682	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1			A	104639376	G	A	104639376	3	1	104	1	0	0	0	0	1	0	0	0	8301	1087	38	1	1513	1	KIF26A	14	104639376	Missense_Mutation	SNP	G	TCGA-B9-A5W7-01A-11D-A31X-10		104639376	2710164	7	6664											
ALKBH7	84266	hgsc.bcm.edu	37	chr19	6374248	6374248	+	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	ccgagagacagagaagtcgcGctggtcagaagccagccggg	11	3	16	11	4	1	3	1	0	0	3	2	6	1	3	3	2	2	1	3	2	2	0	rs377101608		TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr19:6374248G>T	ENST00000245812.3	+	2	627	c.239G>T	c.(238-240)cGc>cTc	p.R80L	ALKBH7_ENST00000596657.1_5'UTR|ALKBH7_ENST00000599849.1_Missense_Mutation_p.R19L	NM_032306.3	NP_115682.1	Q9BT30	ALKB7_HUMAN	alkB, alkylation repair homolog 7 (E. coli)	80					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						GAGAAGTCGCGCTGGTCAGAA	0.657																																					p.R80L		Atlas-SNP	.											.	ALKBH7	18	.	0			c.G239T						PASS	.						27	31	29					19																	6374248		2201	4299	6500	SO:0001583	missense	84266	exon2			AGTCGCGCTGGTC	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.239G>T	chr19.hg19:g.6374248G>T	ENSP00000245812:p.Arg80Leu	125.0	0.0	.		109.0	5.0	.	NM_032306	B2R4U9|Q53FF3	Missense_Mutation	SNP	ENST00000245812.3	hg19	CCDS12163.1	.	.	.	.	.	.	.	.	.	.	G	16.43	3.121815	0.56613	.	.	ENSG00000125652	ENST00000245812	T	0.13778	2.56	4.66	3.62	0.41486	.	0.393786	0.28062	N	0.016752	T	0.09291	0.0229	L	0.34521	1.04	0.28251	N	0.925264	P	0.40970	0.734	B	0.39904	0.313	T	0.10428	-1.0630	10	0.30078	T	0.28	-20.618	5.3379	0.15967	0.2546:0.0:0.7454:0.0	.	80	Q9BT30	ALKB7_HUMAN	L	80	ENSP00000245812:R80L	ENSP00000245812:R80L	R	+	2	0	ALKBH7	6325248	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	2.920000	0.48844	2.590000	0.87494	0.555000	0.69702	CGC	.	.	.	alt		0.657	ALKBH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453036.1	NM_032306		T	6374248	G	T	6374248	3	4	104	1	0	0	0	0	1	0	0	0	532	1087	38	4	245	4	ALKBH7	19	6374248	Missense_Mutation	SNP	G	TCGA-B9-A5W7-01A-11D-A31X-10		6374248	52754735	8	6665											
GRIK5	2901	hgsc.bcm.edu	37	chr19	42525580	42525580	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttctccaggatgtgggggcGtgcccgcaggcatgggtgtg	4	9	19	9	2	1	0	0	0	1	0	2	1	1	1	2	5	1	3	2	5	0	1			TCGA-B9-A5W7-01A-11D-A31X-10	TCGA-B9-A5W7-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	04439867-bb35-44ec-aedd-2cd6183e9b6c	9ef148bd-57c7-41bb-98f3-cb473f34b1ab	g.chr19:42525580G>A	ENST00000262895.3	-	14	1743	c.1744C>T	c.(1744-1746)Cgc>Tgc	p.R582C	GRIK5_ENST00000301218.4_Missense_Mutation_p.R582C|GRIK5_ENST00000593562.1_Missense_Mutation_p.R582C	NM_002088.4	NP_002079.3	Q16478	GRIK5_HUMAN	glutamate receptor, ionotropic, kainate 5	582					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)	p.R582C(2)		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)				ATGTGGGGGCGTGCCCGCAGG	0.652																																					p.R582C		Atlas-SNP	.											GRIK5_ENST00000301218,NS,carcinoma,0,2	GRIK5	220	.	2	Substitution - Missense(2)	prostate(2)	c.C1744T						PASS	.						35	29	31					19																	42525580		2203	4300	6503	SO:0001583	missense	2901	exon14			GGGGGCGTGCCCG		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.1744C>T	chr19.hg19:g.42525580G>A	ENSP00000262895:p.Arg582Cys	54.0	0.0	.		62.0	16.0	.	NM_002088	Q8WWG8	Missense_Mutation	SNP	ENST00000262895.3	hg19	CCDS12595.1	.	.	.	.	.	.	.	.	.	.	G	16.70	3.194809	0.58017	.	.	ENSG00000105737	ENST00000262895;ENST00000301218	T;T	0.14022	2.59;2.54	4.51	4.51	0.55191	Ionotropic glutamate receptor (2);	0.153806	0.42821	D	0.000644	T	0.24353	0.0590	L	0.32530	0.975	0.45621	D	0.99855	D	0.89917	1.0	D	0.70016	0.967	T	0.01114	-1.1447	10	0.62326	D	0.03	.	11.8849	0.52596	0.0:0.0:0.8248:0.1752	.	582	Q16478	GRIK5_HUMAN	C	582	ENSP00000262895:R582C;ENSP00000301218:R582C	ENSP00000262895:R582C	R	-	1	0	GRIK5	47217420	0.846000	0.29590	0.903000	0.35520	0.645000	0.38454	1.338000	0.33873	2.055000	0.61198	0.563000	0.77884	CGC	.	.	.	none		0.652	GRIK5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463453.1			A	42525580	G	A	42525580	3	1	104	1	0	0	0	0	1	0	0	0	6784	1145	40	1	1222	1	GRIK5	19	42525580	Missense_Mutation	SNP	G	TCGA-B9-A5W7-01A-11D-A31X-10	36151332	42525580	16603403	9	6666											
PBX1	5087	hgsc.bcm.edu	37	chr1	164761953	164761953	+	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	gatcagacaaatctaccataCggagctggagaaatacgagc	16	6	10	9	2	2	2	1	0	1	2	2	6	2	3	1	2	5	1	1	2	5	3			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr1:164761953C>T	ENST00000420696.2	+	3	676	c.488C>T	c.(487-489)aCg>aTg	p.T163M	PBX1_ENST00000540236.1_Missense_Mutation_p.T163M|PBX1_ENST00000559240.1_Missense_Mutation_p.T163M|PBX1_ENST00000540246.1_Missense_Mutation_p.T58M|PBX1_ENST00000367897.1_Missense_Mutation_p.T163M|PBX1_ENST00000560641.1_Missense_Mutation_p.T58M|PBX1_ENST00000401534.1_Missense_Mutation_p.T163M	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	163					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						ATCTACCATACGGAGCTGGAG	0.577			T	"TCF3, EWSR1"	"pre B-ALL, myoepithelioma"																																p.T163M		Atlas-SNP	.		Dom	yes		1	1q23	5087	pre-B-cell leukemia transcription factor 1		"L, M"	.	PBX1	60	.	0			c.C488T						PASS	.						27	31	30					1																	164761953		2202	4300	6502	SO:0001583	missense	5087	exon3			ACCATACGGAGCT	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.488C>T	chr1.hg19:g.164761953C>T	ENSP00000405890:p.Thr163Met	72.0	0.0	.		60.0	30.0	.	NM_001204963	B4DSC1|F5H4U9|Q5T488	Missense_Mutation	SNP	ENST00000420696.2	hg19	CCDS1246.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.709033	0.89018	.	.	ENSG00000185630	ENST00000340699;ENST00000420696;ENST00000367897;ENST00000540236;ENST00000401534;ENST00000540246	T;T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5;1.5	5.23	5.23	0.72850	PBX (1);	0.000000	0.85682	D	0.000000	T	0.43144	0.1234	L	0.54323	1.7	0.80722	D	1	D;D;D;D;D	0.65815	0.995;0.994;0.993;0.994;0.994	P;P;P;D;P	0.64877	0.738;0.806;0.852;0.93;0.82	T	0.39643	-0.9604	10	0.72032	D	0.01	-9.5716	18.3959	0.90497	0.0:1.0:0.0:0.0	.	58;163;163;163;163	B7Z774;A8K5V0;F5H4U9;P40424;Q53YC7	.;.;.;PBX1_HUMAN;.	M	163;163;163;163;163;58	ENSP00000341455:T163M;ENSP00000405890:T163M;ENSP00000356872:T163M;ENSP00000439943:T163M;ENSP00000384856:T163M;ENSP00000440869:T58M	ENSP00000341455:T163M	T	+	2	0	PBX1	163028577	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.376000	0.79658	2.405000	0.81733	0.563000	0.77884	ACG	.	.	.	none		0.577	PBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082864.4	NM_002585		T	164761953	C	T	164761953	3	4	105	1	0	0	0	0	1	0	0	0	11499	536	19	1	498	1	PBX1	1	164761953	Missense_Mutation	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10		164761953	84488668	1	6667											
SUSD4	55061	hgsc.bcm.edu	37	chr1	223438095	223438095	+	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	ggagatcacagtccccaccgGgaaggaggtctggagctcag	10	5	15	11	1	3	1	2	0	1	1	4	5	4	4	3	5	1	1	3	5	1	0			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr1:223438095G>A	ENST00000343846.3	-	4	1234	c.601C>T	c.(601-603)Ccg>Tcg	p.P201S	SUSD4_ENST00000478605.1_Intron|SUSD4_ENST00000454695.2_Missense_Mutation_p.P41S|SUSD4_ENST00000484758.2_Missense_Mutation_p.P130S|SUSD4_ENST00000344029.6_Missense_Mutation_p.P201S|SUSD4_ENST00000494793.2_Missense_Mutation_p.P201S|SUSD4_ENST00000366878.4_Missense_Mutation_p.P201S			Q5VX71	SUSD4_HUMAN	sushi domain containing 4	201	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|skin(1)	17				GBM - Glioblastoma multiforme(131;0.0611)		GTCCCCACCGGGAAGGAGGTC	0.498																																					p.P201S		Atlas-SNP	.											.	SUSD4	82	.	0			c.C601T						PASS	.						85	91	89					1																	223438095		2203	4300	6503	SO:0001583	missense	55061	exon5			CCACCGGGAAGGA	AK096265	CCDS31034.1, CCDS41471.1	1q41	2008-05-14			ENSG00000143502	ENSG00000143502			25470	protein-coding gene	gene with protein product		615827				12477932	Standard	NM_017982		Approved	FLJ10052	uc001hny.4	Q5VX71	OTTHUMG00000037936	ENST00000343846.3:c.601C>T	chr1.hg19:g.223438095G>A	ENSP00000344219:p.Pro201Ser	102.0	0.0	.		88.0	18.0	.	NM_017982	D3DTB9|Q6UX62|Q9BSR0|Q9NWG0	Missense_Mutation	SNP	ENST00000343846.3	hg19	CCDS41471.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.775431	0.49786	.	.	ENSG00000143502	ENST00000343846;ENST00000366878;ENST00000542750;ENST00000454695;ENST00000344029	T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01	5.32	4.38	0.52667	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.47093	D	0.000255	T	0.58764	0.2145	N	0.20685	0.6	0.80722	D	1	B;D;P	0.71674	0.426;0.998;0.626	B;D;B	0.80764	0.329;0.994;0.432	T	0.56890	-0.7904	10	0.05721	T	0.95	-16.3711	10.3108	0.43708	0.0756:0.1375:0.7869:0.0	.	130;201;201	B7Z369;Q5VX71-3;Q5VX71	.;.;SUSD4_HUMAN	S	201;201;130;41;201	ENSP00000344219:P201S;ENSP00000355843:P201S;ENSP00000399288:P41S;ENSP00000339926:P201S	ENSP00000344219:P201S	P	-	1	0	SUSD4	221504718	1.000000	0.71417	0.997000	0.53966	0.827000	0.46813	4.506000	0.60428	1.415000	0.47037	0.491000	0.48974	CCG	.	.	.	none		0.498	SUSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092592.2	NM_017982		A	223438095	G	A	223438095	3	1	105	1	0	0	0	0	1	0	0	0	15422	1232	43	2	1044	2	SUSD4	1	223438095	Missense_Mutation	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10	58676142	223438095	25812526	2	6668											
NEUROD1	4760	hgsc.bcm.edu	37	chr2	182543048	182543051	+	Frame_Shift_Del	DEL	GGTG	GGTG	-																															cagcccgcaaccaggttggtGgtgggttgggataagccctt																								rs565522208		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	GGTG	GGTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr2:182543048_182543051delGGTG	ENST00000295108.3	-	2	994_997	c.537_540delCACC	c.(535-540)cccaccfs	p.PT179fs	CERKL_ENST00000479558.1_Intron|NEUROD1_ENST00000496876.1_Intron	NM_002500.4	NP_002491.2	Q13562	NDF1_HUMAN	neuronal differentiation 1	179					amacrine cell differentiation (GO:0035881)|anterior/posterior pattern specification (GO:0009952)|cellular response to glucose stimulus (GO:0071333)|cerebellum development (GO:0021549)|dentate gyrus development (GO:0021542)|embryonic organ morphogenesis (GO:0048562)|endocrine pancreas development (GO:0031018)|enteroendocrine cell differentiation (GO:0035883)|glucose homeostasis (GO:0042593)|inner ear development (GO:0048839)|insulin secretion (GO:0030073)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurogenesis (GO:0022008)|nitric oxide mediated signal transduction (GO:0007263)|nucleocytoplasmic transport (GO:0006913)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle arrest (GO:0071156)|regulation of insulin secretion (GO:0050796)|regulation of intestinal epithelial structure maintenance (GO:0060730)|response to drug (GO:0042493)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|protein heterodimerization activity (GO:0046982)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			OV - Ovarian serous cystadenocarcinoma(117;0.088)			CCAGGTTGGTGGTGGGTTGGGATA	0.598																																					p.180_181del		Atlas-Indel,Pindel	.											.	NEUROD1	67	.	0			c.538_541del						PASS	.																																			SO:0001589	frameshift_variant	4760	exon2			.	U50823	CCDS2283.1	2q32	2013-05-21	2012-02-22		ENSG00000162992	ENSG00000162992		"Basic helix-loop-helix proteins"	7762	protein-coding gene	gene with protein product	"beta-cell E-box transactivator 2", "neurogenic helix-loop-helix protein NEUROD"	601724	"neurogenic differentiation 1"	NEUROD		7754368, 8786144	Standard	NM_002500		Approved	BETA2, BHF-1, NeuroD, bHLHa3, MODY6	uc002uof.4	Q13562	OTTHUMG00000132583	ENST00000295108.3:c.537_540delCACC	chr2.hg19:g.182543048_182543051delGGTG	ENSP00000295108:p.Pro179fs	75.0	0.0	0		80.0	22.0	0.275	NM_002500	B2R9I8|F1T0E1|O00343|Q13340|Q5U095|Q96TH0|Q99455|Q9UEC8	Frame_Shift_Del	DEL	ENST00000295108.3	hg19	CCDS2283.1																																																																																			.	.	.	none		0.598	NEUROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255792.2	NM_002500		-	182543051	GGTG	-	182543048	7	5	105	1	0	1	0	1	0	0	0	0	10355	1335	47	0	534	0	NEUROD1	2	182543048	Frame_Shift_Del	DEL	GGTG	TCGA-B9-A5W8-01A-11D-A28G-10		182543048	60656325	3	6669											
GIGYF2	26058	hgsc.bcm.edu	37	chr2	233651899	233651899	+	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	aggtggaccaacatcagtagGgagaaagcatgaatttatac	16	8	11	6	0	1	2	1	1	0	1	1	4	1	3	1	3	3	2	1	3	6	4			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr2:233651899G>C	ENST00000409547.1	+	11	883	c.572G>C	c.(571-573)gGg>gCg	p.G191A	GIGYF2_ENST00000409451.3_Missense_Mutation_p.G213A|GIGYF2_ENST00000373566.3_Missense_Mutation_p.G213A|GIGYF2_ENST00000452341.2_Missense_Mutation_p.G22A|GIGYF2_ENST00000409196.3_Missense_Mutation_p.G191A|GIGYF2_ENST00000409480.1_Missense_Mutation_p.G213A|GIGYF2_ENST00000373563.4_Missense_Mutation_p.G191A	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	191	Arg-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)		ACATCAGTAGGGAGAAAGCAT	0.403																																					p.G213A		Atlas-SNP	.											.	GIGYF2	288	.	0			c.G638C						PASS	.						104	106	106					2																	233651899		2203	4300	6503	SO:0001583	missense	26058	exon11			CAGTAGGGAGAAA	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.572G>C	chr2.hg19:g.233651899G>C	ENSP00000386537:p.Gly191Ala	78.0	0.0	.		92.0	16.0	.	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	hg19	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	G	17.89	3.498686	0.64298	.	.	ENSG00000204120	ENST00000373566;ENST00000414511;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000535418;ENST00000423659;ENST00000409196;ENST00000409451;ENST00000440945;ENST00000445650;ENST00000452341;ENST00000421778	T;T;T;T;T;T;T;T;T;T	0.78364	-0.69;-0.69;-0.69;-0.69;-1.02;-0.7;-0.69;-0.82;-1.17;-0.89	5.63	5.63	0.86233	.	0.192608	0.46442	D	0.000288	D	0.86247	0.5887	L	0.57536	1.79	0.36437	D	0.865276	D;D;P;D	0.76494	0.999;0.982;0.953;0.989	D;P;B;P	0.75484	0.986;0.898;0.371;0.874	D	0.84937	0.0863	10	0.29301	T	0.29	-24.5013	20.0345	0.97552	0.0:0.0:1.0:0.0	.	22;213;191;191	E9PC50;A6H8W4;Q6Y7W6;E9PBB0	.;.;PERQ2_HUMAN;.	A	213;140;191;213;191;191;140;191;213;191;22;22;18	ENSP00000362667:G213A;ENSP00000362664:G191A;ENSP00000386765:G213A;ENSP00000386537:G191A;ENSP00000404195:G140A;ENSP00000387070:G191A;ENSP00000387170:G213A;ENSP00000410297:G191A;ENSP00000392218:G22A;ENSP00000411505:G22A	ENSP00000362664:G191A	G	+	2	0	GIGYF2	233360143	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.552000	0.67281	2.797000	0.96272	0.655000	0.94253	GGG	.	.	.	none		0.403	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		C	233651899	G	C	233651899	3	2	105	1	0	0	0	0	1	0	0	0	6385	1232	43	4	668	4	GIGYF2	2	233651899	Missense_Mutation	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10	51108851	233651899	9547474	4	6670											
NUP210	23225	hgsc.bcm.edu	37	chr3	13438880	13438880	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cggagtccagggcctggatcTtcagctccaggggggagtcc	6	7	16	12	1	2	0	1	0	1	0	5	3	5	3	4	6	1	1	4	6	0	1			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr3:13438880T>C	ENST00000254508.5	-	3	495	c.413A>G	c.(412-414)aAg>aGg	p.K138R		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	138					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)					GGCCTGGATCTTCAGCTCCAG	0.602																																					p.K138R		Atlas-SNP	.											.	NUP210	182	.	0			c.A413G						PASS	.						67	63	64					3																	13438880		2203	4300	6503	SO:0001583	missense	23225	exon3			TGGATCTTCAGCT	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.413A>G	chr3.hg19:g.13438880T>C	ENSP00000254508:p.Lys138Arg	78.0	0.0	.		85.0	25.0	.	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	hg19	CCDS33704.1	.	.	.	.	.	.	.	.	.	.	T	5.986	0.365927	0.11352	.	.	ENSG00000132182	ENST00000254508	T	0.04758	3.56	3.96	2.77	0.32553	.	0.049223	0.85682	D	0.000000	T	0.03608	0.0103	L	0.33137	0.985	0.43203	D	0.995057	B	0.31817	0.341	B	0.31245	0.126	T	0.39099	-0.9630	10	0.07325	T	0.83	-12.7074	9.9009	0.41346	0.0:0.0:0.172:0.8279	.	138	Q8TEM1	PO210_HUMAN	R	138	ENSP00000254508:K138R	ENSP00000254508:K138R	K	-	2	0	NUP210	13413880	1.000000	0.71417	1.000000	0.80357	0.732000	0.41865	2.196000	0.42686	0.680000	0.31366	0.454000	0.30748	AAG	.	.	.	none		0.602	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923		C	13438880	T	C	13438880	3	2	105	1	0	0	0	0	1	0	0	0	10767	1609	56	3	5402	3	NUP210	3	13438880	Missense_Mutation	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10		13438880	184583550	5	6671											
RBM5	10181	hgsc.bcm.edu	37	chr3	50147868	50147868	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caggccccagccgcttccccTactggtgtagttcctggtac	5	10	10	16	1	0	0	0	0	0	0	2	0	2	0	6	3	3	4	6	3	3	5			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr3:50147868T>C	ENST00000347869.3	+	16	1510	c.1335T>C	c.(1333-1335)ccT>ccC	p.P445P	RBM5_ENST00000441812.2_Intron	NM_005778.3	NP_005769.1	P52756	RBM5_HUMAN	RNA binding motif protein 5	445	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)		CCGCTTCCCCTACTGGTGTAG	0.458																																					p.P445P		Atlas-SNP	.											.	RBM5	76	.	0			c.T1335C						PASS	.						54	58	56					3																	50147868		2203	4300	6503	SO:0001819	synonymous_variant	10181	exon16			TTCCCCTACTGGT	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.1335T>C	chr3.hg19:g.50147868T>C		180.0	0.0	.		149.0	36.0	.	NM_005778	B2RA45|B4DM16|B4DMF9|B4DZ63|Q93021|Q9BU14|Q9HDA6|Q9UKY8|Q9UL24	Silent	SNP	ENST00000347869.3	hg19	CCDS2810.1																																																																																			.	.	.	none		0.458	RBM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345797.3	NM_005778		C	50147868	T	C	50147868	2	2	105	1	0	0	0	0	0	0	0	1	13156	1509	53	3		3	RBM5	3	50147868	Silent	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10	36708988	50147868	147874562	6	6672											
GOLIM4	27333	hgsc.bcm.edu	37	chr3	167747034	167747034	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcctctccttggattcccTggtcctctgctccctgaacg	3	14	7	17	1	2	1	0	1	2	0	7	2	6	2	5	2	2	1	5	2	1	3			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr3:167747034T>C	ENST00000470487.1	-	11	2179	c.1490A>G	c.(1489-1491)cAg>cGg	p.Q497R	GOLIM4_ENST00000309027.4_Missense_Mutation_p.Q469R	NM_014498.3	NP_055313.1	O00461	GOLI4_HUMAN	golgi integral membrane protein 4	497	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						TTGGATTCCCTGGTCCTCTGC	0.383																																					p.Q497R		Atlas-SNP	.											.	GOLIM4	71	.	0			c.A1490G						PASS	.						133	116	122					3																	167747034		2203	4300	6503	SO:0001583	missense	27333	exon11			ATTCCCTGGTCCT	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.1490A>G	chr3.hg19:g.167747034T>C	ENSP00000417354:p.Gln497Arg	105.0	0.0	.		90.0	6.0	.	NM_014498		Missense_Mutation	SNP	ENST00000470487.1	hg19	CCDS3204.1	.	.	.	.	.	.	.	.	.	.	T	17.11	3.305022	0.60305	.	.	ENSG00000173905	ENST00000470487;ENST00000309027	.	.	.	4.97	4.97	0.65823	.	0.242984	0.44097	D	0.000487	T	0.69575	0.3126	M	0.74881	2.28	0.43029	D	0.994599	D;D	0.64830	0.994;0.989	D;P	0.67103	0.949;0.814	T	0.68405	-0.5417	9	0.09590	T	0.72	-18.1647	11.9183	0.52778	0.0:0.0:0.1451:0.8549	.	469;497	F8W785;O00461	.;GOLI4_HUMAN	R	497;469	.	ENSP00000309893:Q469R	Q	-	2	0	GOLIM4	169229728	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	4.279000	0.58953	1.884000	0.54569	0.449000	0.29647	CAG	.	.	.	none		0.383	GOLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351278.2			C	167747034	T	C	167747034	3	2	105	1	0	0	0	0	1	0	0	0	6573	1580	55	3	624	3	GOLIM4	3	167747034	Missense_Mutation	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10	117599166	167747034	30275396	7	6673											
APBB2	323	hgsc.bcm.edu	37	chr4	40818110	40818110	+	Nonstop_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	agtccttttgcatgtgcagcTatggcatttcggtgacaggg	7	13	13	8	1	0	1	0	1	0	0	2	1	1	1	1	3	3	4	1	3	1	4			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr4:40818110T>A	ENST00000295974.8	-	18	2905	c.2276A>T	c.(2275-2277)tAg>tTg	p.*759L	APBB2_ENST00000506352.1_Nonstop_Mutation_p.*738L|APBB2_ENST00000508593.1_Nonstop_Mutation_p.*760L|APBB2_ENST00000513140.1_Nonstop_Mutation_p.*737L|APBB2_ENST00000502841.1_Nonstop_Mutation_p.*211L|APBB2_ENST00000543538.1_Nonstop_Mutation_p.*211L|APBB2_ENST00000504305.1_Nonstop_Mutation_p.*211L|RP11-632F7.3_ENST00000513127.1_RNA	NM_001166050.1|NM_004307.1	NP_001159522.1|NP_004298.1	Q92870	APBB2_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 2	0					axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|extracellular matrix organization (GO:0030198)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|transcription factor binding (GO:0008134)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|skin(2)|urinary_tract(1)	34						CATGTGCAGCTATGGCATTTC	0.458																																					p.X760L	Ovarian(3;20 75 16686 49997)	Atlas-SNP	.											.	APBB2	61	.	0			c.A2279T						PASS	.						255	249	251					4																	40818110		1979	4157	6136	SO:0001578	stop_lost	323	exon18			TGCAGCTATGGCA	U62325	CCDS43224.1, CCDS54760.1, CCDS54761.1, CCDS54762.1	4p13	2011-10-10	2008-07-31		ENSG00000163697	ENSG00000163697			582	protein-coding gene	gene with protein product	"Fe65-like"	602710				8955346, 9585438	Standard	NM_173075		Approved	FE65L, FE65L1, MGC35575	uc003gvn.3	Q92870	OTTHUMG00000160416	ENST00000295974.8:c.2276A>T	chr4.hg19:g.40818110T>A		98.0	0.0	.		99.0	22.0	.	NM_004307	B4DSL4|E9PG87|Q8IUI6	Missense_Mutation	SNP	ENST00000295974.8	hg19	CCDS54761.1	.	.	.	.	.	.	.	.	.	.	T	14.70	2.614383	0.46631	.	.	ENSG00000163697	ENST00000295974;ENST00000316212;ENST00000543538;ENST00000513140;ENST00000508593;ENST00000502841;ENST00000506352;ENST00000504305	.	.	.	5.38	5.38	0.77491	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3812	0.74658	0.0:0.0:0.0:1.0	.	.	.	.	L	759;758;211;737;760;211;738;211	.	.	X	-	2	0	APBB2	40512867	1.000000	0.71417	0.936000	0.37596	0.073000	0.16967	8.000000	0.88501	2.040000	0.60383	0.477000	0.44152	TAG	.	.	.	none		0.458	APBB2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360523.3	NM_173075		A	40818110	T	A	40818110	4	1	105	1	0	0	0	0	0	0	0	0	761	1535	53	5	4	5	APBB2	4	40818110	Nonstop_Mutation	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10		40818110	150336166	8	6674											
FRYL	285527	hgsc.bcm.edu	37	chr4	48536646	48536646	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtcaatatgactcaatagActataaataatctgtagtaa	18	12	6	5	0	3	2	2	1	1	1	3	2	3	2	0	1	0	2	0	1	10	7			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr4:48536646A>G	ENST00000503238.1	-	46	6620	c.6621T>C	c.(6619-6621)agT>agC	p.S2207S	FRYL_ENST00000537810.1_Silent_p.S2207S|FRYL_ENST00000358350.4_Silent_p.S2207S|FRYL_ENST00000507873.2_5'UTR|FRYL_ENST00000264319.7_5'UTR			O94915	FRYL_HUMAN	FRY-like	2207					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						GACTCAATAGACTATAAATAA	0.333																																					p.S2207S		Atlas-SNP	.											.	FRYL	242	.	0			c.T6621C						PASS	.						76	72	73					4																	48536646		1829	4086	5915	SO:0001819	synonymous_variant	285527	exon49			CAATAGACTATAA	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.6621T>C	chr4.hg19:g.48536646A>G		66.0	0.0	.		67.0	10.0	.	NM_015030	O95640|Q8WTZ5|Q9NT40	Silent	SNP	ENST00000503238.1	hg19	CCDS43227.1	.	.	.	.	.	.	.	.	.	.	A	0.350	-0.945182	0.02304	.	.	ENSG00000075539	ENST00000514617	T	0.12879	2.64	5.57	-1.09	0.09904	.	0.000000	0.85682	D	0.000000	T	0.18882	0.0453	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.02844	-1.1103	7	0.35671	T	0.21	.	10.974	0.47454	0.529:0.0:0.471:0.0	.	.	.	.	P	1077	ENSP00000425344:S1077P	ENSP00000425344:S1077P	S	-	1	0	FRYL	48231403	1.000000	0.71417	0.766000	0.31476	0.006000	0.05464	1.028000	0.30128	0.032000	0.15435	-0.256000	0.11100	TCT	.	.	.	none		0.333	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			G	48536646	A	G	48536646	2	3	105	1	0	0	0	0	0	0	0	1	6071	272	10	3		3	FRYL	4	48536646	Silent	SNP	A	TCGA-B9-A5W8-01A-11D-A28G-10	7718536	48536646	142617630	9	6675											
PDLIM4	8572	hgsc.bcm.edu	37	chr5	131602211	131602211	+	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	gacagcaaggctcaggcacaCaggatccacatcgatcctga	13	5	10	13	1	1	1	1	1	0	0	4	4	3	2	2	3	1	3	2	3	1	0			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr5:131602211C>T	ENST00000253754.3	+	3	364	c.300C>T	c.(298-300)caC>caT	p.H100H	P4HA2_ENST00000471826.1_Intron|PDLIM4_ENST00000379018.3_Silent_p.H100H	NM_001131027.1|NM_003687.3	NP_001124499.1|NP_003678.2	P50479	PDLI4_HUMAN	PDZ and LIM domain 4	100							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)			CTCAGGCACACAGGATCCACA	0.592																																					p.H100H		Atlas-SNP	.											.	PDLIM4	22	.	0			c.C300T						PASS	.						93	69	77					5																	131602211		2203	4300	6503	SO:0001819	synonymous_variant	8572	exon3			GGCACACAGGATC	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.300C>T	chr5.hg19:g.131602211C>T		251.0	0.0	.		235.0	70.0	.	NM_003687	B2R8U1|Q53Y39|Q96AT8|Q9BTW8|Q9Y292	Silent	SNP	ENST00000253754.3	hg19	CCDS4152.1																																																																																			.	.	.	none		0.592	PDLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132644.2	NM_003687		T	131602211	C	T	131602211	2	4	105	1	0	0	0	0	0	0	0	1	11689	477	17	2		2	PDLIM4	5	131602211	Silent	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10		131602211	49313049	10	6676											
SLC22A4	6583	hgsc.bcm.edu	37	chr5	131647952	131647952	+	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	ttcgtgtccgggcagctgtcAgacaggtaagcacatgggag	9	8	15	9	2	1	1	1	0	0	1	3	2	2	2	1	3	2	4	1	3	1	2			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr5:131647952A>C	ENST00000200652.3	+	2	666	c.492A>C	c.(490-492)tcA>tcC	p.S164S	SLC22A4_ENST00000491257.1_3'UTR|AC034220.3_ENST00000417795.1_RNA	NM_003059.2	NP_003050.2	Q9H015	S22A4_HUMAN	solute carrier family 22 (organic cation/zwitterion transporter), member 4	164					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)	GGCAGCTGTCAGACAGGTAAG	0.572																																					p.S164S		Atlas-SNP	.											.	SLC22A4	45	.	0			c.A492C						PASS	.						132	107	116					5																	131647952		2203	4300	6503	SO:0001819	synonymous_variant	6583	exon2			GCTGTCAGACAGG	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.492A>C	chr5.hg19:g.131647952A>C		75.0	0.0	.		56.0	18.0	.	NM_003059	O14546	Silent	SNP	ENST00000200652.3	hg19	CCDS4153.1																																																																																			.	.	.	none		0.572	SLC22A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132661.1	NM_003059		C	131647952	A	C	131647952	2	2	105	1	0	0	0	0	0	0	0	1	14469	175	7	5		5	SLC22A4	5	131647952	Silent	SNP	A	TCGA-B9-A5W8-01A-11D-A28G-10	45741	131647952	49267308	11	6677											
TIFAB	140947	hgsc.bcm.edu	37	chr5	134785315	134785315	+	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	atctggatgcctgagaaggaGaccctgttgacggtgctcag	9	9	14	9	1	2	3	1	2	1	2	2	6	2	4	2	3	2	2	2	3	1	1			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr5:134785315G>C	ENST00000503143.2	-	0	0				TIFAB_ENST00000537858.1_Silent_p.V105V|CTB-138E5.1_ENST00000510230.1_RNA	NM_130848.2	NP_570900.1	Q8TF63	DCNP1_HUMAN								nucleus (GO:0005634)				endometrium(1)|lung(1)|prostate(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CTGAGAAGGAGACCCTGTTGA	0.577																																					p.V105V		Atlas-SNP	.											TIFAB,NS,carcinoma,0,1	TIFAB	23	.	0			c.C315G						PASS	.						101	104	103					5																	134785315		2082	4221	6303	SO:0001631	upstream_gene_variant	497189	exon2			GAAGGAGACCCTG																													chr5.hg19:g.134785315G>C	Exception_encountered	148.0	0.0	.		133.0	24.0	.	NM_001099221		Silent	SNP	ENST00000503143.2	hg19	CCDS4186.1																																																																																			.	.	.	none		0.577	C5orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372531.1			C	134785315	G	C	134785315	1	2	105	0	1	0	0	0	0	0	0	0	15907	929	33	4		4	TIFAB	5	134785315	5'Flank	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10	3137363	134785315	46129945	12	6678											
GABRA6	2559	hgsc.bcm.edu	37	chr5	161116041	161116041	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actgagattctgagtctgaaTaatttgatggtcagtaaaat	14	14	9	4	0	3	4	1	4	2	1	3	5	3	4	0	1	0	1	0	1	4	4			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr5:161116041T>C	ENST00000274545.5	+	4	745	c.312T>C	c.(310-312)aaT>aaC	p.N104N	RP11-348M17.2_ENST00000521984.1_RNA|GABRA6_ENST00000523217.1_Silent_p.N94N			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	104					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)	TGAGTCTGAATAATTTGATGG	0.403										TCGA Ovarian(5;0.080)																											p.N104N		Atlas-SNP	.											.	GABRA6	139	.	0			c.T312C						PASS	.						76	77	77					5																	161116041		2203	4299	6502	SO:0001819	synonymous_variant	2559	exon4			TCTGAATAATTTG		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.312T>C	chr5.hg19:g.161116041T>C		65.0	0.0	.		85.0	17.0	.	NM_000811	A8K096|Q4VAV2	Silent	SNP	ENST00000274545.5	hg19	CCDS4356.1	.	.	.	.	.	.	.	.	.	.	T	8.919	0.960604	0.18583	.	.	ENSG00000145863	ENST00000520000	.	.	.	5.65	2.01	0.26516	.	.	.	.	.	T	0.54581	0.1867	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45571	-0.9252	4	.	.	.	.	6.8819	0.24179	0.0:0.4395:0.0:0.5605	.	.	.	.	T	44	.	.	I	+	2	0	GABRA6	161048619	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.646000	0.46630	0.507000	0.28148	-0.274000	0.10170	ATA	.	.	.	none		0.403	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2			C	161116041	T	C	161116041	2	2	105	1	0	0	0	0	0	0	0	1	6172	1403	49	3		3	GABRA6	5	161116041	Silent	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10	26330726	161116041	19799219	13	6679											
DTNBP1	84062	hgsc.bcm.edu	37	chr6	15523339	15523339	+	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	ccccaccctcactgatgtccCgggtggccgagtcggtgcag	5	7	13	16	3	1	1	1	1	0	0	3	2	2	1	5	3	1	1	5	3	0	0	rs374085686		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr6:15523339C>G	ENST00000344537.5	-	10	1095	c.923G>C	c.(922-924)cGg>cCg	p.R308P	DTNBP1_ENST00000462989.2_Missense_Mutation_p.R152P|DTNBP1_ENST00000355917.3_Missense_Mutation_p.R309P	NM_032122.4	NP_115498.2	Q96EV8	DTBP1_HUMAN	dystrobrevin binding protein 1	308	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)			ACTGATGTCCCGGGTGGCCGA	0.567									Hermansky-Pudlak syndrome																												p.R308P		Atlas-SNP	.											.	DTNBP1	56	.	0			c.G923C						PASS	.						137	142	141					6																	15523339		2203	4300	6503	SO:0001583	missense	84062	exon10	Familial Cancer Database	HPS, HPS1-8	ATGTCCCGGGTGG	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.923G>C	chr6.hg19:g.15523339C>G	ENSP00000341680:p.Arg308Pro	163.0	0.0	.		197.0	32.0	.	NM_032122	A8K3V3|Q5THY3|Q5THY4|Q96NV2|Q9H0U2|Q9H3J5	Missense_Mutation	SNP	ENST00000344537.5	hg19	CCDS4534.1	.	.	.	.	.	.	.	.	.	.	T	11.68	1.710179	0.30322	.	.	ENSG00000047579	ENST00000344537;ENST00000462989;ENST00000355917;ENST00000397306;ENST00000509674	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	5.62	-7.93	0.01156	.	1.163890	0.06365	N	0.712440	T	0.01558	0.0050	N	0.01297	-0.9	0.19300	N	0.999978	B	0.02656	0.0	B	0.08055	0.003	T	0.27331	-1.0077	10	0.08179	T	0.78	-9.2314	4.2873	0.10862	0.0902:0.1668:0.4361:0.307	.	308	Q96EV8	DTBP1_HUMAN	P	308;152;309;227;125	ENSP00000341680:R308P;ENSP00000427239:R152P;ENSP00000348183:R309P;ENSP00000421797:R125P	ENSP00000341680:R308P	R	-	2	0	DTNBP1	15631318	0.501000	0.26099	0.000000	0.03702	0.022000	0.10575	0.142000	0.16096	-2.293000	0.00664	-0.254000	0.11334	CGG	.	.	.	alt		0.567	DTNBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000039933.2	NM_032122		G	15523339	C	G	15523339	3	3	105	1	0	0	0	0	1	0	0	0	4792	652	23	4	136	4	DTNBP1	6	15523339	Missense_Mutation	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10		15523339	155591728	14	6680											
HIST1H2AL	8332	hgsc.bcm.edu	37	chr6	27833355	27833357	+	In_Frame_Del	DEL	AAG	AAG	-																															gcaacgccgcccgcgacaacAagaagacccgcattatcccg																								rs376667817		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr6:27833355_27833357delAAG	ENST00000357320.2	+	1	322_324	c.223_225delAAG	c.(223-225)aagdel	p.K76del		NM_003511.2	NP_003502.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2al	76						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						CCGCGACAACAAGAAGACCCGCA	0.665																																					p.74_75del		Atlas-Indel,Pindel	.											HIST1H2AL,lower_third,carcinoma,0,1	HIST1H2AL	14	.	0			c.222_224del						PASS	.																																			SO:0001651	inframe_deletion	8332	exon1			.	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.223_225delAAG	chr6.hg19:g.27833358_27833360delAAG	ENSP00000349873:p.Lys76del	216.0	0.0	0		217.0	47.0	0.21659	NM_003511	P02261|Q2M1R2|Q76PA6	In_Frame_Del	DEL	ENST00000357320.2	hg19	CCDS4634.1																																																																																			.	.	.	none		0.665	HIST1H2AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040160.1	NM_003511		-	27833357	AAG	-	27833355	7	5	105	1	0	1	0	1	0	0	0	0	7145	131	5	0	225	0	HIST1H2AL	6	27833355	In_Frame_Del	DEL	AAG	TCGA-B9-A5W8-01A-11D-A28G-10	12310016	27833355	143281712	15	6681											
HIST1H3J	8356	hgsc.bcm.edu	37	chr6	27858516	27858516	+	Missense_Mutation	SNP	T	T	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	tgccttggtggccagctgctTccgcggtgccttgccgccgg	1	10	15	15	4	0	0	0	0	0	0	1	0	1	0	6	4	5	2	6	4	0	3			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr6:27858516T>G	ENST00000359303.2	-	1	54	c.55A>C	c.(55-57)Aag>Cag	p.K19Q	HIST1H3J_ENST00000479986.1_5'UTR|HIST1H2BO_ENST00000303806.4_5'Flank	NM_003535.2	NP_003526.1	P68431	H31_HUMAN	histone cluster 1, H3j	19					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						GCCAGCTGCTTCCGCGGTGCC	0.617																																					p.K19Q		Atlas-SNP	.											.	HIST1H3J	16	.	0			c.A55C						PASS	.						29	33	31					6																	27858516		2203	4299	6502	SO:0001583	missense	8356	exon1			GCTGCTTCCGCGG	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.55A>C	chr6.hg19:g.27858516T>G	ENSP00000352252:p.Lys19Gln	111.0	0.0	.		89.0	25.0	.	NM_003535	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Missense_Mutation	SNP	ENST00000359303.2	hg19	CCDS4638.1	.	.	.	.	.	.	.	.	.	.	T	14.56	2.572970	0.45798	.	.	ENSG00000197153	ENST00000359303	T	0.48522	0.81	4.06	4.06	0.47325	.	.	.	.	.	T	0.52224	0.1721	.	.	.	0.42070	D	0.991202	.	.	.	.	.	.	T	0.59316	-0.7477	6	0.87932	D	0	.	12.8321	0.57752	0.0:0.0:0.0:1.0	.	.	.	.	Q	19	ENSP00000352252:K19Q	ENSP00000352252:K19Q	K	-	1	0	HIST1H3J	27966495	1.000000	0.71417	0.997000	0.53966	0.747000	0.42532	7.496000	0.81526	2.071000	0.62044	0.533000	0.62120	AAG	.	.	.	none		0.617	HIST1H3J-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043453.2	NM_003535		G	27858516	T	G	27858516	3	3	105	1	0	0	0	0	1	0	0	0	7171	1792	62	5	359	5	HIST1H3J	6	27858516	Missense_Mutation	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10	25161	27858516	143256551	16	6682											
DNAJB9	4189	hgsc.bcm.edu	37	chr7	108212287	108212287	+	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	gtgccaaaatcggcatcagaGcgccaaatcaagaaggcctt	14	6	10	11	2	2	2	2	0	0	2	3	2	2	2	3	2	2	1	3	2	5	1			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr7:108212287G>A	ENST00000249356.3	+	2	663	c.117G>A	c.(115-117)gaG>gaA	p.E39E	THAP5_ENST00000493722.1_5'Flank|THAP5_ENST00000438865.1_5'Flank|THAP5_ENST00000415914.3_5'Flank|DNAJB9_ENST00000465725.1_3'UTR|THAP5_ENST00000313516.5_5'Flank	NM_012328.2	NP_036460.1	Q9UBS3	DNJB9_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 9	39	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				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						CGGCATCAGAGCGCCAAATCA	0.403																																					p.E39E		Atlas-SNP	.											.	DNAJB9	25	.	0			c.G117A						PASS	.						107	116	113					7																	108212287		2203	4300	6503	SO:0001819	synonymous_variant	4189	exon2			ATCAGAGCGCCAA	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.117G>A	chr7.hg19:g.108212287G>A		131.0	0.0	.		137.0	43.0	.	NM_012328		Silent	SNP	ENST00000249356.3	hg19	CCDS5752.1																																																																																			.	.	.	none		0.403	DNAJB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337414.1			A	108212287	G	A	108212287	2	1	105	1	0	0	0	0	0	0	0	1	4629	962	34	2		2	DNAJB9	7	108212287	Silent	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10		108212287	50926376	17	6683											
MLL3	58508	hgsc.bcm.edu	37	chr7	151859497	151859497	+	Frame_Shift_Del	DEL	T	T	-																															ggcaggactctgtctcagccTtttccagttttatctcttct																										TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr7:151859497delT	ENST00000262189.6	-	43	11383	c.11165delA	c.(11164-11166)aagfs	p.K3722fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.K3722fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	3722					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)										TGTCTCAGCCTTTTCCAGTTT	0.468																																					p.K3722fs		Atlas-Indel,Pindel	.											.	MLL3	1564	.	0			c.11166delG						PASS	.						178	182	181					7																	151859497		2203	4300	6503	SO:0001589	frameshift_variant	58508	exon43			.	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.11165delA	chr7.hg19:g.151859497delT	ENSP00000262189:p.Lys3722fs	75.0	0.0	0		80.0	23.0	0.2875	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	hg19	CCDS5931.1																																																																																			.	.	.	none		0.468	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			-	151859497	T	-	151859497	7	5	105	1	0	1	0	1	0	0	0	0	9629	1609	56	0	3638	0	MLL3	7	151859497	Frame_Shift_Del	DEL	T	TCGA-B9-A5W8-01A-11D-A28G-10	43647210	151859497	7279166	18	6684											
FAM83H	286077	hgsc.bcm.edu	37	chr8	144809730	144809730	+	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	ggaccttggtggggaaggctGctgggacgcggaaggccgag	7	5	21	8	3	0	0	0	0	0	0	0	5	0	4	2	8	1	2	2	8	2	1	rs367877690	byFrequency	TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr8:144809730G>C	ENST00000388913.3	-	5	2026	c.1901C>G	c.(1900-1902)gCa>gGa	p.A634G		NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	634					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)			GGGGAAGGCTGCTGGGACGCG	0.751													G|||	5	0.000998403	0.0038	0	5008	,	,		9374	0		0	False		,,,				2504	0				p.A634G		Atlas-SNP	.											.	FAM83H	68	.	0			c.C1901G						PASS	.	G	GLY/ALA	5,3093		0,5,1544	6	8	7		1901	0.6	0	8		7	0,7130		0,0,3565	no	missense	FAM83H	NM_198488.3	60	0,5,5109	CC,CG,GG		0.0,0.1614,0.0489	benign	634/1180	144809730	5,10223	1549	3565	5114	SO:0001583	missense	286077	exon5			AAGGCTGCTGGGA	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.1901C>G	chr8.hg19:g.144809730G>C	ENSP00000373565:p.Ala634Gly	3.0	0.0	.		12.0	6.0	.	NM_198488	A0JLS2|Q8N4W0	Missense_Mutation	SNP	ENST00000388913.3	hg19	CCDS6410.2	.	.	.	.	.	.	.	.	.	.	g	0.018	-1.474564	0.01044	0.001614	0.0	ENSG00000180921	ENST00000388913	T	0.14516	2.5	3.85	0.608	0.17569	.	16.316900	0.01476	U	0.016496	T	0.08980	0.0222	N	0.17474	0.49	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.27054	-1.0085	10	0.20519	T	0.43	.	5.3436	0.15996	0.2787:0.3057:0.4156:0.0	.	634	Q6ZRV2	FA83H_HUMAN	G	634	ENSP00000373565:A634G	ENSP00000373565:A634G	A	-	2	0	FAM83H	144881718	0.000000	0.05858	0.000000	0.03702	0.113000	0.19764	0.100000	0.15231	0.258000	0.21686	0.561000	0.74099	GCA	.	.	.	weak		0.751	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488		C	144809730	G	C	144809730	3	2	105	1	0	0	0	0	1	0	0	0	5647	1319	46	4	1642	4	FAM83H	8	144809730	Missense_Mutation	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10		144809730	1554292	19	6685											
PLEC	5339	hgsc.bcm.edu	37	chr8	145001217	145001217	+	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	gaggccaccggctcaagctgCgccttgtacgtcaccagctg	7	7	12	15	3	2	0	2	0	0	0	2	1	2	0	4	2	4	4	4	2	2	2	rs374669316		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr8:145001217C>T	ENST00000322810.4	-	29	4453	c.4284G>A	c.(4282-4284)gcG>gcA	p.A1428A	PLEC_ENST00000398774.2_Silent_p.A1259A|PLEC_ENST00000436759.2_Silent_p.A1318A|PLEC_ENST00000356346.3_Silent_p.A1277A|PLEC_ENST00000357649.2_Silent_p.A1295A|PLEC_ENST00000345136.3_Silent_p.A1291A|PLEC_ENST00000354958.2_Silent_p.A1269A|PLEC_ENST00000354589.3_Silent_p.A1291A|PLEC_ENST00000527096.1_Silent_p.A1314A	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	1428	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						GCTCAAGCTGCGCCTTGTACG	0.637																																					p.A1428A		Atlas-SNP	.											.	PLEC	1144	.	0			c.G4284A						PASS	.	C	,,,,,,,	1,4183		0,1,2091	58	63	62		3954,3831,3807,4284,3777,3873,3885,3873	-9.9	0.3	8		62	0,8434		0,0,4217	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	,,,,,,,	0,1,6308	TT,TC,CC		0.0,0.0239,0.0079	,,,,,,,	1318/4575,1277/4534,1269/4526,1428/4685,1259/4516,1291/4548,1295/4552,1291/4548	145001217	1,12617	2092	4217	6309	SO:0001819	synonymous_variant	5339	exon29			AAGCTGCGCCTTG	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.4284G>A	chr8.hg19:g.145001217C>T		64.0	0.0	.		69.0	4.0	.	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	hg19	CCDS43772.1																																																																																			.	.	.	weak		0.637	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		T	145001217	C	T	145001217	2	4	105	1	0	0	0	0	0	0	0	1	12059	755	27	1		1	PLEC	8	145001217	Silent	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10	191487	145001217	1362805	20	6686											
CDKN2A	1029	hgsc.bcm.edu	37	chr9	21971184	21971184	+	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	agcagcagcagctccgccacTcgggcgctgcccatcatcat	8	6	10	17	3	2	0	2	0	0	0	4	0	3	0	3	1	5	5	3	1	0	0	rs201208890	byFrequency	TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr9:21971184T>G	ENST00000304494.5	-	2	444	c.174A>C	c.(172-174)cgA>cgC	p.R58R	CDKN2A_ENST00000579122.1_Silent_p.R58R|CDKN2A_ENST00000579755.1_Missense_Mutation_p.S73R|CDKN2A_ENST00000479692.2_Silent_p.R7R|CDKN2A_ENST00000494262.1_Silent_p.R7R|CDKN2A_ENST00000530628.2_Missense_Mutation_p.S73R|CDKN2A_ENST00000578845.2_Silent_p.R7R|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000497750.1_Silent_p.R7R|CDKN2A_ENST00000361570.3_Missense_Mutation_p.S114R|CDKN2A_ENST00000498628.2_Silent_p.R7R|CDKN2A_ENST00000446177.1_Silent_p.R58R|CDKN2A_ENST00000498124.1_Silent_p.R58R	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	58			R -> Q (in dbSNP:rs36204273).		cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(45)|p.M53_R58del(3)|p.R58fs*59(2)|p.V59fs*82(2)|p.0(1)|p.V28_V51del(1)|p.V59fs*63(1)|p.V59fs*61(1)|p.V59fs*60(1)|p.G55fs*86(1)|p.A57fs*85(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)		GCTCCGCCACTCGGGCGCTGC	0.682		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)			G|||	15	0.00299521	0.0113	0	5008	,	,		11788	0		0	False		,,,				2504	0				p.S73R		Atlas-SNP	.											CDKN2A_ENST00000498124,mucosal,malignant_melanoma,-2,3	CDKN2A	4810	.	1374	Whole gene deletion(1316)|Unknown(45)|Deletion - Frameshift(7)|Deletion - In frame(4)|Insertion - Frameshift(2)	haematopoietic_and_lymphoid_tissue(285)|skin(176)|central_nervous_system(167)|lung(145)|urinary_tract(92)|bone(74)|soft_tissue(57)|upper_aerodigestive_tract(55)|oesophagus(52)|pleura(51)|ovary(37)|kidney(32)|breast(32)|pancreas(30)|thyroid(13)|NS(12)|biliary_tract(12)|stomach(12)|autonomic_ganglia(7)|meninges(7)|large_intestine(6)|liver(6)|salivary_gland(4)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	c.A217C						PASS	.	G	,,,ARG/SER	25,4025		0,25,2000	7	9	8		174,174,,217	-4.5	0	9		8	0,8162		0,0,4081	no	coding-synonymous,coding-synonymous,utr-3,missense	CDKN2A	NM_000077.4,NM_001195132.1,NM_058197.4,NM_058195.3	,,,110	0,25,6081	GG,GT,TT		0.0,0.6173,0.2047	,,,benign	58/157,58/168,,73/133	21971184	25,12187	2025	4081	6106	SO:0001819	synonymous_variant	1029	exon2			CGCCACTCGGGCG	L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.174A>C	chr9.hg19:g.21971184T>G		4.0	2.0	.		34.0	18.0	.	NM_058195	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Missense_Mutation	SNP	ENST00000304494.5	hg19	CCDS6510.1	.	.	.	.	.	.	.	.	.	.	G	6.483	0.457206	0.12342	0.006173	0.0	ENSG00000147889	ENST00000361570;ENST00000530628	T;T	0.76186	-1.0;-0.95	5.79	-4.48	0.03515	.	0.576553	0.14595	N	0.309984	T	0.41789	0.1174	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22941	-1.0202	8	.	.	.	-3.0019	5.0452	0.14480	0.1174:0.1641:0.1404:0.5781	.	114	Q8N726	CD2A2_HUMAN	R	114;73	ENSP00000355153:S114R;ENSP00000432664:S73R	.	S	-	1	0	CDKN2A	21961184	0.000000	0.05858	0.001000	0.08648	0.194000	0.23727	-2.443000	0.01013	-1.206000	0.02641	-2.190000	0.00312	AGT	.	.	.	weak		0.682	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077		G	21971184	T	G	21971184	2	3	105	1	0	0	0	0	0	0	0	1	3163	1551	54	5		5	CDKN2A	9	21971184	Silent	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10		21971184	119242247	21	6687											
GLYATL2	219970	hgsc.bcm.edu	37	chr11	58601915	58601915	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaatcaatcaacaatatttcTtgggggtgcatttccactga	12	13	8	8	0	3	1	2	1	1	0	4	2	4	1	1	2	2	1	1	2	5	4			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr11:58601915T>C	ENST00000287275.1	-	6	1262	c.872A>G	c.(871-873)aAg>aGg	p.K291R	GLYATL2_ENST00000532258.1_Missense_Mutation_p.K291R|GLYATL2_ENST00000533636.1_5'Flank	NM_145016.3	NP_659453.3	Q8WU03	GLYL2_HUMAN	glycine-N-acyltransferase-like 2	291						endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)			breast(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	23		Breast(21;0.0044)|all_epithelial(135;0.0216)			Glycine(DB00145)	ACAATATTTCTTGGGGGTGCA	0.363																																					p.K291R		Atlas-SNP	.											.	GLYATL2	40	.	0			c.A872G						PASS	.						53	49	50					11																	58601915		1831	4083	5914	SO:0001583	missense	219970	exon6			TATTTCTTGGGGG	AF426250	CCDS41649.1	11q12.1	2008-02-05				ENSG00000156689			24178	protein-coding gene	gene with protein product		614762				12477932	Standard	NM_145016		Approved	BXMAS2-10, MGC24009	uc001nnd.4	Q8WU03		ENST00000287275.1:c.872A>G	chr11.hg19:g.58601915T>C	ENSP00000287275:p.Lys291Arg	41.0	0.0	.		37.0	11.0	.	NM_145016	A5LGC7|Q86WC3|Q96AT2	Missense_Mutation	SNP	ENST00000287275.1	hg19	CCDS41649.1	.	.	.	.	.	.	.	.	.	.	T	7.457	0.643799	0.14451	.	.	ENSG00000156689	ENST00000287275;ENST00000532258	T;T	0.14640	2.49;2.49	2.81	-1.38	0.09027	.	0.816947	0.10184	U	0.705518	T	0.08133	0.0203	L	0.34521	1.04	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.39921	-0.9590	10	0.25106	T	0.35	.	3.0975	0.06314	0.0:0.2741:0.2254:0.5005	.	291	Q8WU03	GLYL2_HUMAN	R	291	ENSP00000287275:K291R;ENSP00000434277:K291R	ENSP00000287275:K291R	K	-	2	0	GLYATL2	58358491	0.008000	0.16893	0.022000	0.16811	0.453000	0.32348	0.974000	0.29436	-0.398000	0.07679	-1.222000	0.01597	AAG	.	.	.	none		0.363	GLYATL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394599.1	NM_145016		C	58601915	T	C	58601915	3	2	105	1	0	0	0	0	1	0	0	0	6488	1609	56	3	16	3	GLYATL2	11	58601915	Missense_Mutation	SNP	T	TCGA-B9-A5W8-01A-11D-A28G-10		58601915	76404601	22	6688											
MAML2	84441	hgsc.bcm.edu	37	chr11	95825395	95825395	+	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	tgctgctgctgctgctgctgCtgctgctgctgctgctgctg	0	14	14	13	0	0	0	0	0	0	0	0	0	0	0	0	0	13	13	0	0	0	0			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr11:95825395C>T	ENST00000524717.1	-	2	3084	c.1800G>A	c.(1798-1800)caG>caA	p.Q600Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	600					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)				gctgctgctgctgctgctgct	0.537			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.Q600Q		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2	94	.	0			c.G1800A						PASS	.						21	29	26					11																	95825395		1989	3928	5917	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.1800G>A	chr11.hg19:g.95825395C>T		159.0	0.0	.		137.0	16.0	.	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	hg19	CCDS44714.1																																																																																			.	.	.	none		0.537	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95825395	C	T	95825395	2	4	105	1	0	0	0	0	0	0	0	1	9213	796	28	2		2	MAML2	11	95825395	Silent	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10	37223480	95825395	39181121	23	6689											
CD163L1	283316	hgsc.bcm.edu	37	chr12	7526001	7526001	+	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	cactgccatatggagatatgCgttttaggacactgaatgtc	11	12	10	8	1	0	2	0	1	0	1	1	4	0	3	1	2	2	1	1	2	4	4	rs368002565		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr12:7526001C>T	ENST00000313599.3	-	14	3702	c.3645G>A	c.(3643-3645)acG>acA	p.T1215T	CD163L1_ENST00000544331.1_5'Flank|CD163L1_ENST00000396630.1_Silent_p.T1215T|CD163L1_ENST00000416109.2_Silent_p.T1225T			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	1215	SRCR 11. {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						TGGAGATATGCGTTTTAGGAC	0.527																																					p.T1215T		Atlas-SNP	.											.	CD163L1	238	.	0			c.G3645A						PASS	.	T		0,4406		0,0,2203	148	120	129		3645	-4.5	0	12		129	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CD163L1	NM_174941.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		1215/1454	7526001	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	283316	exon14			GATATGCGTTTTA	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.3645G>A	chr12.hg19:g.7526001C>T		332.0	0.0	.		280.0	46.0	.	NM_174941	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Silent	SNP	ENST00000313599.3	hg19	CCDS8577.1																																																																																			.	.	.	weak		0.527	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941		T	7526001	C	T	7526001	2	4	105	1	0	0	0	0	0	0	0	1	2970	755	27	1		1	CD163L1	12	7526001	Silent	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10		7526001	126325894	24	6690											
SLC38A4	55089	hgsc.bcm.edu	37	chr12	47170779	47170779	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acaccgtttgcatttttctcCgggaccgactggaaaaagaa	12	10	9	10	3	1	1	0	0	1	1	2	4	1	3	3	2	1	2	3	2	3	3			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr12:47170779C>T	ENST00000447411.1	-	12	1288	c.1082G>A	c.(1081-1083)cGg>cAg	p.R361Q	SLC38A4_ENST00000266579.4_Missense_Mutation_p.R361Q	NM_001143824.1	NP_001137296.1	Q969I6	S38A4_HUMAN	solute carrier family 38, member 4	361					amino acid transport (GO:0006865)|ion transport (GO:0006811)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|symporter activity (GO:0015293)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|skin(1)	21	Lung SC(27;0.192)|Renal(347;0.236)					CATTTTTCTCCGGGACCGACT	0.358																																					p.R361Q		Atlas-SNP	.											.	SLC38A4	58	.	0			c.G1082A						PASS	.						87	88	88					12																	47170779		2203	4299	6502	SO:0001583	missense	55089	exon12			TTTCTCCGGGACC	AF193836	CCDS8750.1	12q13	2013-05-22				ENSG00000139209		"Solute carriers"	14679	protein-coding gene	gene with protein product		608065				11414754	Standard	NM_018018		Approved	PAAT, NAT3, ATA3	uc001rpj.2	Q969I6		ENST00000447411.1:c.1082G>A	chr12.hg19:g.47170779C>T	ENSP00000389843:p.Arg361Gln	87.0	0.0	.		64.0	16.0	.	NM_001143824	A8K553	Missense_Mutation	SNP	ENST00000447411.1	hg19	CCDS8750.1	.	.	.	.	.	.	.	.	.	.	C	10.89	1.479698	0.26511	.	.	ENSG00000139209	ENST00000447411;ENST00000266579	T;T	0.02158	4.42;4.42	5.96	3.18	0.36537	.	0.116259	0.64402	N	0.000017	T	0.03871	0.0109	L	0.49640	1.575	0.45607	D	0.998544	B	0.24258	0.1	B	0.33890	0.172	T	0.41288	-0.9517	10	0.17369	T	0.5	-4.6085	15.3035	0.73972	0.0:0.872:0.0:0.128	.	361	Q969I6	S38A4_HUMAN	Q	361	ENSP00000389843:R361Q;ENSP00000266579:R361Q	ENSP00000266579:R361Q	R	-	2	0	SLC38A4	45457046	1.000000	0.71417	1.000000	0.80357	0.621000	0.37620	1.399000	0.34566	0.425000	0.26087	-0.940000	0.02684	CGG	.	.	.	none		0.358	SLC38A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404574.1			T	47170779	C	T	47170779	3	4	105	1	0	0	0	0	1	0	0	0	14619	652	23	1	581	1	SLC38A4	12	47170779	Missense_Mutation	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10	39644778	47170779	86681116	25	6691											
METTL7A	25840	hgsc.bcm.edu	37	chr12	51319010	51319030	+	In_Frame_Del	DEL	GGAGTTTGCGGGCCCCTCCGG	GGAGTTTGCGGGCCCCTCCGG	-																															gagctcttcagtaacctgcaGgagtttgcgggcccctccgg																								rs142438796		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	GGAGTTTGCGGGCCCCTCCGG	GGAGTTTGCGGGCCCCTCCGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr12:51319010_51319030delGGAGTTTGCGGGCCCCTCCGG	ENST00000548553.1	+	2	1170_1190	c.189_209delGGAGTTTGCGGGCCCCTCCGG	c.(187-210)caggagtttgcgggcccctccggg>cag	p.EFAGPSG64del	METTL7A_ENST00000332160.4_In_Frame_Del_p.EFAGPSG64del			Q9H8H3	MET7A_HUMAN	methyltransferase like 7A	64						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lipid particle (GO:0005811)|membrane (GO:0016020)	methyltransferase activity (GO:0008168)	p.A66V(1)		endometrium(1)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	10						GTAACCTGCAGGAGTTTGCGGGCCCCTCCGGGAAACTCTCC	0.543																																					p.63_70del		Pindel	.											.	METTL7A	19	.	1	Substitution - Missense(1)	lung(1)	c.188_208del						PASS	.																																			SO:0001651	inframe_deletion	25840	exon1			.		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.189_209delGGAGTTTGCGGGCCCCTCCGG	chr12.hg19:g.51319010_51319030delGGAGTTTGCGGGCCCCTCCGG	ENSP00000448785:p.Glu64_Gly70del	71.0	0.0	.		80.0	12.0	0.150	NM_014033	Q9H7R3|Q9UHZ7|Q9Y422	In_Frame_Del	DEL	ENST00000548553.1	hg19	CCDS8804.1																																																																																			.	.	.	none		0.543	METTL7A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404294.2	NM_014033		-	51319030	GGAGTTTGCGGGCCCCTCCGG	-	51319010	7	5	105	1	0	1	0	1	0	0	0	0	9512	991	35	0	191	0	METTL7A	12	51319010	In_Frame_Del	DEL	GGAGTTTGCGGGCCCCTCCGG	TCGA-B9-A5W8-01A-11D-A28G-10	4148231	51319010	82532885	26	6692											
XPOT	11260	hgsc.bcm.edu	37	chr12	64808728	64808728	+	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	ttaaaaatttccccagatgcCtggcaggtgtgtgcagaagc	11	10	11	9	0	0	2	0	0	0	2	1	2	1	2	3	2	3	2	3	2	4	2			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr12:64808728C>A	ENST00000332707.5	+	3	631	c.102C>A	c.(100-102)gcC>gcA	p.A34A		NM_007235.4	NP_009166.2	O43592	XPOT_HUMAN	exportin, tRNA	34	Necessary for interaction with Ran, nuclear localization and nuclear import.				intracellular protein transport (GO:0006886)|tRNA export from nucleus (GO:0006409)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(7)|lung(12)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				GBM - Glioblastoma multiforme(28;0.0404)		CCCCAGATGCCTGGCAGGTGT	0.388																																					p.A34A		Atlas-SNP	.											.	XPOT	105	.	0			c.C102A						PASS	.						91	97	95					12																	64808728		2203	4300	6503	SO:0001819	synonymous_variant	11260	exon3			AGATGCCTGGCAG	AF039022	CCDS31852.1	12q14.1	2012-10-17	2012-10-17		ENSG00000184575	ENSG00000184575		"Exportins"	12826	protein-coding gene	gene with protein product		603180	"exportin, tRNA (nuclear export receptor for tRNAs)"			9660920, 9512417	Standard	NM_007235		Approved	XPO3	uc001ssb.3	O43592	OTTHUMG00000168794	ENST00000332707.5:c.102C>A	chr12.hg19:g.64808728C>A		31.0	0.0	.		37.0	5.0	.	NM_007235	A6NLH1|O43784|Q8WUG2|Q9BVS7	Silent	SNP	ENST00000332707.5	hg19	CCDS31852.1																																																																																			.	.	.	none		0.388	XPOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401122.1	NM_007235		A	64808728	C	A	64808728	2	1	105	1	0	0	0	0	0	0	0	1	17462	668	24	4		4	XPOT	12	64808728	Silent	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10	13489718	64808728	69043167	27	6693											
TMCC3	57458	hgsc.bcm.edu	37	chr12	94975986	94975987	+	Frame_Shift_Ins	INS	-	-	A																															ctctctgagctttcgatgatINSactgctctaacttcttctgc																								rs530422400		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr12:94975986_94975987insA	ENST00000261226.4	-	2	537_538	c.406_407insT	c.(406-408)tatfs	p.Y136fs	TMCC3_ENST00000551457.1_Frame_Shift_Ins_p.Y105fs	NM_020698.2	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3	136						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	29						CTTTCGATGATACTGCTCTAAC	0.475																																					p.Y136fs		Atlas-INDEL	.											.	TMCC3	63	.	0			c.407_408insT						PASS	.																																			SO:0001589	frameshift_variant	57458	exon2			.	AB032971	CCDS31877.1, CCDS73506.1	12q22	2005-01-21	2005-07-13			ENSG00000057704		"Transmembrane and coiled-coil domain containing"	29199	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 3"			10574461	Standard	XM_005269039		Approved	KIAA1145	uc001tdj.2	Q9ULS5	OTTHUMG00000170225	ENST00000261226.4:c.407dupT	chr12.hg19:g.94975987_94975987dupA	ENSP00000261226:p.Tyr136fs	100.0	0.0	0		73.0	12.0	0.164384	NM_020698	Q8IWB2	Frame_Shift_Ins	INS	ENST00000261226.4	hg19	CCDS31877.1																																																																																			.	.	.	none		0.475	TMCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408113.1	NM_020698		A	94975987	-	A	94975986	7	5	105	1	0	1	1	0	0	0	0	0	16006	1406	49	0	1038	0	TMCC3	12	94975986	Frame_Shift_Ins	INS	-	TCGA-B9-A5W8-01A-11D-A28G-10	30167258	94975986	38875909	28	6694											
METAP2	84101	hgsc.bcm.edu	37	chr12	95907438	95907438	+	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	ctcctcttaggcttccaagaAcaaaacacttgttaaatgtc	13	12	5	11	0	1	1	0	0	1	1	4	1	3	1	2	1	2	2	2	1	7	4			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr12:95907438A>G	ENST00000258499.3	-	0	4022				METAP2_ENST00000261220.9_Missense_Mutation_p.T376A|METAP2_ENST00000546753.1_Missense_Mutation_p.T376A|METAP2_ENST00000323666.5_Missense_Mutation_p.T399A|METAP2_ENST00000551840.1_Missense_Mutation_p.T398A|METAP2_ENST00000550777.1_Missense_Mutation_p.T363A	NM_001278393.1|NM_032147.2	NP_001265322.1|NP_115523.2	Q9H0E7	UBP44_HUMAN	ubiquitin specific peptidase 44						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						GCTTCCAAGAACAAAACACTT	0.418																																					p.T399A		Atlas-SNP	.											.	METAP2	28	.	0			c.A1195G						PASS	.						84	82	83					12																	95907438		2203	4300	6503	SO:0001628	intergenic_variant	10988	exon11			CCAAGAACAAAAC	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			chr12.hg19:g.95907438A>G		69.0	0.0	.		88.0	21.0	.	NM_006838	B2RDW3	Missense_Mutation	SNP	ENST00000258499.3	hg19	CCDS9053.1	.	.	.	.	.	.	.	.	.	.	A	2.554	-0.303387	0.05495	.	.	ENSG00000111142	ENST00000323666;ENST00000546753;ENST00000261220;ENST00000550777;ENST00000551840	.	.	.	5.83	2.17	0.27698	Winged helix-turn-helix transcription repressor DNA-binding (1);Peptidase M24, structural domain (2);	0.135470	0.64402	N	0.000002	T	0.03220	0.0094	N	0.00003	-3.5	0.39326	D	0.96532	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.0;0.0;0.0;0.0	T	0.40194	-0.9576	9	0.02654	T	1	-9.0542	6.8846	0.24193	0.3929:0.0:0.6071:0.0	.	376;363;376;398;399	B4DUX5;F8VRR3;G3XA91;F8VQZ7;P50579	.;.;.;.;AMPM2_HUMAN	A	399;376;376;363;398	.	ENSP00000261220:T376A	T	+	1	0	METAP2	94431569	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	4.393000	0.59665	0.466000	0.27193	0.533000	0.62120	ACA	.	.	.	none		0.418	USP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408312.1	NM_032147		G	95907438	A	G	95907438	1	3	105	0	1	0	0	0	0	0	0	0	9494	43	2	3		3	METAP2	12	95907438	IGR	SNP	A	TCGA-B9-A5W8-01A-11D-A28G-10	931452	95907438	37944457	29	6695											
RFC5	5985	hgsc.bcm.edu	37	chr12	118462664	118462664	+	Frame_Shift_Del	DEL	A	A	-																															ttctcttactagtaattgagAaattcacagaaaataccaga																										TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr12:118462664delA	ENST00000454402.2	+	6	548	c.430delA	c.(430-432)aaafs	p.K144fs	RFC5_ENST00000229043.3_Frame_Shift_Del_p.K59fs|RFC5_ENST00000392542.2_Frame_Shift_Del_p.K123fs	NM_001206801.1|NM_007370.5	NP_001193730.1|NP_031396.1	P40937	RFC5_HUMAN	replication factor C (activator 1) 5, 36.5kDa	144					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)					AGTAATTGAGAAATTCACAGA	0.428																																					p.E143fs		Atlas-INDEL	.											RFC5,NS,carcinoma,0,1	RFC5	35	.	0			c.429delG						PASS	.						75	81	79					12																	118462664		2203	4300	6503	SO:0001589	frameshift_variant	5985	exon6			.		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.430delA	chr12.hg19:g.118462664delA	ENSP00000408295:p.Lys144fs	48.0	0.0	0		53.0	15.0	0.283019	NM_001206801	A8MZ62|B3KSX8	Frame_Shift_Del	DEL	ENST00000454402.2	hg19	CCDS9185.1																																																																																			.	.	.	none		0.428	RFC5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344196.2	NM_007370		-	118462664	A	-	118462664	7	5	105	1	0	1	0	1	0	0	0	0	13261	247	9	0	458	0	RFC5	12	118462664	Frame_Shift_Del	DEL	A	TCGA-B9-A5W8-01A-11D-A28G-10	22555226	118462664	15389231	30	6696											
LRRC16B	90668	hgsc.bcm.edu	37	chr14	24528535	24528547	+	Frame_Shift_Del	DEL	CATCAATGCCCTG	CATCAATGCCCTG	-																															aagcttcgcaccagcatcctCatcaatgccctgggcagcaa																										TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	CATCAATGCCCTG	CATCAATGCCCTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr14:24528535_24528547delCATCAATGCCCTG	ENST00000342740.5	+	21	1837_1849	c.1683_1695delCATCAATGCCCTG	c.(1681-1695)ctcatcaatgccctgfs	p.LINAL561fs	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	561						cytoplasm (GO:0005737)		p.N563D(1)		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)		CCAGCATCCTCATCAATGCCCTGGGCAGCAACA	0.62																																					p.561_565del		Atlas-Indel,Pindel	.											.	LRRC16B	120	.	1	Substitution - Missense(1)	large_intestine(1)	c.1682_1694del						PASS	.																																			SO:0001589	frameshift_variant	90668	exon21			.	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.1683_1695delCATCAATGCCCTG	chr14.hg19:g.24528535_24528547delCATCAATGCCCTG	ENSP00000340467:p.Leu561fs	288.0	0.0	0		154.0	40.0	0.25974	NM_138360	Q8TEF7|Q96HS9	Frame_Shift_Del	DEL	ENST00000342740.5	hg19	CCDS32054.1																																																																																			.	.	.	none		0.62	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360		-	24528547	CATCAATGCCCTG	-	24528535	7	5	105	1	0	1	0	1	0	0	0	0	8979	813	29	0	1765	0	LRRC16B	14	24528535	Frame_Shift_Del	DEL	CATCAATGCCCTG	TCGA-B9-A5W8-01A-11D-A28G-10		24528535	82821005	31	6697											
KBTBD13	390594	hgsc.bcm.edu	37	chr15	65369367	65369367	+	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	tgcgcggcgaccggccggcgCtggcggcggaggacgagctg	4	3	21	13	9	0	0	0	0	0	0	0	4	0	2	2	7	2	2	2	7	0	0	rs550537101	byFrequency	TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr15:65369367C>T	ENST00000432196.2	+	1	214	c.214C>T	c.(214-216)Ctg>Ttg	p.L72L	RASL12_ENST00000434605.2_5'Flank	NM_001101362.2	NP_001094832.1	C9JR72	KBTBD_HUMAN	kelch repeat and BTB (POZ) domain containing 13	72	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				lung(1)|prostate(1)|skin(1)	3						CCGGCCGGCGCTGGCGGCGGA	0.736													C|||	10	0.00199681	0.0068	0.0014	5008	,	,		9554	0		0	False		,,,				2504	0				p.L72L		Atlas-SNP	.											.	KBTBD13	9	.	0			c.C214T						PASS	.						2	2	2					15																	65369367		1202	2816	4018	SO:0001819	synonymous_variant	390594	exon1			CCGGCGCTGGCGG		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.214C>T	chr15.hg19:g.65369367C>T		0.0	0.0	.		7.0	5.0	.	NM_001101362		Silent	SNP	ENST00000432196.2	hg19	CCDS45281.1																																																																																			.	.	.	none		0.736	KBTBD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418468.2	NM_001101362		T	65369367	C	T	65369367	2	4	105	1	0	0	0	0	0	0	0	1	7999	796	28	2		2	KBTBD13	15	65369367	Silent	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10		65369367	37162025	32	6698											
CDR2	1039	hgsc.bcm.edu	37	chr16	22358803	22358803	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctctggctgggctctttgAaaggaacatacagagagtct	10	10	13	8	0	3	2	0	1	3	1	3	4	3	3	0	4	2	3	0	4	3	2			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr16:22358803A>G	ENST00000268383.2	-	5	1155	c.848T>C	c.(847-849)tTc>tCc	p.F283S		NM_001802.1	NP_001793.1	Q01850	CDR2_HUMAN	cerebellar degeneration-related protein 2, 62kDa	283						cytoplasm (GO:0005737)				endometrium(3)|large_intestine(3)|lung(3)|skin(1)|urinary_tract(1)	11				GBM - Glioblastoma multiforme(48;0.0188)		GGGCTCTTTGAAAGGAACATA	0.532																																					p.F283S		Atlas-SNP	.											.	CDR2	34	.	0			c.T848C						PASS	.						38	39	39					16																	22358803		2197	4300	6497	SO:0001583	missense	1039	exon5			TCTTTGAAAGGAA	M63256	CCDS32404.1	16p13.1-p12	2008-02-05	2002-08-29			ENSG00000140743			1799	protein-coding gene	gene with protein product	"Yo paraneoplastic antigen"	117340	"cerebellar degeneration-related protein (62kD)"			2014264	Standard	NM_001802		Approved	CDR62, Yo	uc002dkn.3	Q01850		ENST00000268383.2:c.848T>C	chr16.hg19:g.22358803A>G	ENSP00000268383:p.Phe283Ser	43.0	0.0	.		64.0	15.0	.	NM_001802	A8K8A8|Q13977	Missense_Mutation	SNP	ENST00000268383.2	hg19	CCDS32404.1	.	.	.	.	.	.	.	.	.	.	A	3.865	-0.029069	0.07589	.	.	ENSG00000140743	ENST00000268383	T	0.41065	1.01	5.79	4.68	0.58851	.	0.159588	0.56097	D	0.000023	T	0.29093	0.0723	L	0.27053	0.805	0.38438	D	0.946635	B	0.23185	0.081	B	0.20577	0.03	T	0.09100	-1.0690	10	0.15952	T	0.53	-9.0507	13.0653	0.59030	0.8657:0.1343:0.0:0.0	.	283	Q01850	CDR2_HUMAN	S	283	ENSP00000268383:F283S	ENSP00000268383:F283S	F	-	2	0	CDR2	22266304	0.890000	0.30428	0.599000	0.28851	0.617000	0.37484	3.322000	0.52007	0.991000	0.38814	0.533000	0.62120	TTC	.	.	.	none		0.532	CDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430081.1			G	22358803	A	G	22358803	3	3	105	1	0	0	0	0	1	0	0	0	3174	246	9	3	520	3	CDR2	16	22358803	Missense_Mutation	SNP	A	TCGA-B9-A5W8-01A-11D-A28G-10		22358803	67995950	33	6699											
ZNF629	23361	hgsc.bcm.edu	37	chr16	30794425	30794425	+	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	gagctgacgctgaagctcttGccgcactctgggcacttgta	7	10	12	12	2	2	2	0	2	2	0	2	3	2	2	1	1	3	6	1	1	2	3			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr16:30794425G>A	ENST00000262525.4	-	3	1431	c.1224C>T	c.(1222-1224)ggC>ggT	p.G408G	RP11-2C24.6_ENST00000575562.1_RNA	NM_001080417.1	NP_001073886.1	Q9UEG4	ZN629_HUMAN	zinc finger protein 629	408					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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)			TGAAGCTCTTGCCGCACTCTG	0.652																																					p.G408G		Atlas-SNP	.											.	ZNF629	44	.	0			c.C1224T						PASS	.						47	51	49					16																	30794425		2197	4300	6497	SO:0001819	synonymous_variant	23361	exon3			GCTCTTGCCGCAC	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.1224C>T	chr16.hg19:g.30794425G>A		184.0	0.0	.		179.0	51.0	.	NM_001080417	Q15938	Silent	SNP	ENST00000262525.4	hg19	CCDS45463.1																																																																																			.	.	.	none		0.652	ZNF629-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434291.1	NM_015309		A	30794425	G	A	30794425	2	1	105	1	0	0	0	0	0	0	0	1	18065	1306	46	2		2	ZNF629	16	30794425	Silent	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10	8435622	30794425	59560328	34	6700											
OSGIN1	29948	hgsc.bcm.edu	37	chr16	83994295	83994295	+	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	catgaagtcggtcctcacctGgaagcaccggaaggagcacg	11	5	13	12	3	1	1	1	1	0	0	3	4	2	4	3	4	2	2	3	4	3	0			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr16:83994295G>A	ENST00000343939.2	+	5	958	c.575G>A	c.(574-576)tGg>tAg	p.W192*	OSGIN1_ENST00000393306.1_Nonsense_Mutation_p.W109*|OSGIN1_ENST00000565123.1_Nonsense_Mutation_p.W109*|OSGIN1_ENST00000361711.3_Nonsense_Mutation_p.W109*			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	192					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						GTCCTCACCTGGAAGCACCGG	0.652																																					p.W109X		Atlas-SNP	.											.	OSGIN1	33	.	0			c.G326A						PASS	.						61	60	60					16																	83994295		2200	4300	6500	SO:0001587	stop_gained	29948	exon4			TCACCTGGAAGCA	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.575G>A	chr16.hg19:g.83994295G>A	ENSP00000343376:p.Trp192*	189.0	0.0	.		185.0	62.0	.	NM_182981	Q52M33|Q86UQ1|Q96S88|Q9BZ70	Nonsense_Mutation	SNP	ENST00000343939.2	hg19		.	.	.	.	.	.	.	.	.	.	G	38	7.081125	0.98051	.	.	ENSG00000140961	ENST00000343939;ENST00000361711;ENST00000393306	.	.	.	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.1195	16.9387	0.86210	0.0:0.0:1.0:0.0	.	.	.	.	X	192;109;109	.	ENSP00000343376:W192X	W	+	2	0	OSGIN1	82551796	1.000000	0.71417	0.998000	0.56505	0.495000	0.33615	5.463000	0.66712	2.228000	0.72767	0.491000	0.48974	TGG	.	.	.	none		0.652	OSGIN1-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000269081.1	NM_013370		A	83994295	G	A	83994295	4	1	105	1	0	0	0	0	0	1	0	0	11296	1357	47	2	593	2	OSGIN1	16	83994295	Nonsense_Mutation	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10	53199870	83994295	6360458	35	6701											
MTHFSD	64779	hgsc.bcm.edu	37	chr16	86565821	86565821	+	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	ttcaggtcactcacacgggcGtccccggggaggttcccaac	7	7	12	15	3	3	0	3	0	0	0	5	1	5	1	3	5	1	1	3	5	1	2			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr16:86565821G>A	ENST00000360900.6	-	8	973	c.948C>T	c.(946-948)gaC>gaT	p.D316D	MTHFSD_ENST00000381214.5_Silent_p.D316D|MTHFSD_ENST00000546093.1_Silent_p.D153D|MTHFSD_ENST00000543303.2_Silent_p.D315D|MTHFSD_ENST00000322911.6_Silent_p.D315D	NM_001159380.1	NP_001152852.1	Q2M296	MTHSD_HUMAN	methenyltetrahydrofolate synthetase domain containing	316	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(3)|lung(6)|skin(1)	11						TCACACGGGCGTCCCCGGGGA	0.682																																					p.D316D		Atlas-SNP	.											.	MTHFSD	52	.	0			c.C948T						PASS	.						11	14	13					16																	86565821		1876	4097	5973	SO:0001819	synonymous_variant	64779	exon8			ACGGGCGTCCCCG	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.948C>T	chr16.hg19:g.86565821G>A		131.0	0.0	.		143.0	25.0	.	NM_001159377	A8MQ77|B7ZLC0|B7ZLC2|D3DUM9|E9PAM1|Q9H878|Q9H954	Silent	SNP	ENST00000360900.6	hg19	CCDS54047.1																																																																																			.	.	.	none		0.682	MTHFSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432182.1	NM_022764		A	86565821	G	A	86565821	2	1	105	1	0	0	0	0	0	0	0	1	9940	1136	40	1		1	MTHFSD	16	86565821	Silent	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10	2571526	86565821	3788932	36	6702											
ACSF2	80221	hgsc.bcm.edu	37	chr17	48541577	48541577	+	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	gtcagccctctctctgattcAggtgtcattgctgggtcccc	4	13	10	14	0	5	1	3	1	2	0	7	1	6	1	3	2	2	1	3	2	0	2			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr17:48541577A>G	ENST00000300441.4	+	10	1242		c.e10-1		ACSF2_ENST00000502667.1_Splice_Site|ACSF2_ENST00000427954.2_Splice_Site|ACSF2_ENST00000541920.1_Splice_Site|ACSF2_ENST00000504392.1_Splice_Site	NM_025149.4	NP_079425.3	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2						fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ligase activity (GO:0016874)			endometrium(7)|kidney(3)|large_intestine(1)|lung(1)|stomach(1)	13	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			TCTCTGATTCAGGTGTCATTG	0.547																																					.		Atlas-SNP	.											.	ACSF2	46	.	0			c.1139-2A>G						PASS	.						130	117	121					17																	48541577		2203	4300	6503	SO:0001630	splice_region_variant	80221	exon10			TGATTCAGGTGTC	AK024573, BC012053	CCDS11567.1, CCDS74103.1, CCDS74104.1, CCDS74105.1	17q21.33	2007-10-17			ENSG00000167107	ENSG00000167107		"Acyl-CoA synthetase family"	26101	protein-coding gene	gene with protein product		610465				17762044	Standard	NM_001288968		Approved	FLJ20920, ACSMW	uc002iqu.2	Q96CM8	OTTHUMG00000162128	ENST00000300441.4:c.1139-1A>G	chr17.hg19:g.48541577A>G		150.0	0.0	.		129.0	44.0	.	NM_025149	B4DFQ6|B4DHT5|B4DUF5|Q9H7G2	Splice_Site	SNP	ENST00000300441.4	hg19	CCDS11567.1	.	.	.	.	.	.	.	.	.	.	A	18.16	3.562393	0.65538	.	.	ENSG00000167107	ENST00000300441;ENST00000541920;ENST00000504392;ENST00000427954;ENST00000502667	.	.	.	4.48	4.48	0.54585	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.256	0.66053	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ACSF2	45896576	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.372000	0.79612	2.016000	0.59253	0.533000	0.62120	.	.	.	.	none		0.547	ACSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367423.3	NM_025149	Intron	G	48541577	A	G	48541577	5	3	105	1	0	0	0	0	0	0	1	0	175	202	7	3	1175	3	ACSF2	17	48541577	Splice_Site	SNP	A	TCGA-B9-A5W8-01A-11D-A28G-10		48541577	32653633	37	6703											
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11134286	11134286	+	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	cgacgactcaagaaggaagtCgaggcccagttgcccgaaaa	14	4	12	11	4	1	1	1	0	0	1	2	6	1	2	2	2	1	1	2	2	5	1	rs371276213		TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr19:11134286C>G	ENST00000429416.3	+	21	3233	c.2952C>G	c.(2950-2952)gtC>gtG	p.V984V	SMARCA4_ENST00000344626.4_Silent_p.V984V|SMARCA4_ENST00000589677.1_Silent_p.V984V|SMARCA4_ENST00000413806.3_Silent_p.V984V|SMARCA4_ENST00000590574.1_Silent_p.V984V|SMARCA4_ENST00000444061.3_Silent_p.V984V|SMARCA4_ENST00000358026.2_Silent_p.V984V|SMARCA4_ENST00000541122.2_Silent_p.V984V|SMARCA4_ENST00000450717.3_Silent_p.V984V	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	984					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)				AGAAGGAAGTCGAGGCCCAGT	0.597			"F, N, Mis"		NSCLC																																p.V984V		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.C2952G						PASS	.						46	42	44					19																	11134286		2202	4300	6502	SO:0001819	synonymous_variant	6597	exon20			GGAAGTCGAGGCC	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.2952C>G	chr19.hg19:g.11134286C>G		141.0	0.0	.		142.0	26.0	.	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Silent	SNP	ENST00000429416.3	hg19	CCDS12253.1																																																																																			.	.	.	alt		0.597	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		G	11134286	C	G	11134286	2	3	105	1	0	0	0	0	0	0	0	1	14783	871	31	4		4	SMARCA4	19	11134286	Silent	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10		11134286	47994697	38	6704											
NCCRP1	342897	hgsc.bcm.edu	37	chr19	39687743	39687743	+	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	cgccgccgtcgccgccaccaCtgccctcgccgccgtcgctg	2	5	11	23	9	0	0	0	0	0	0	3	0	0	0	8	0	1	1	8	0	0	0			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr19:39687743C>T	ENST00000339852.4	+	1	143	c.121C>T	c.(121-123)Ctg>Ttg	p.L41L		NM_001001414.1	NP_001001414.1	Q6ZVX7	FBX50_HUMAN	non-specific cytotoxic cell receptor protein 1 homolog (zebrafish)	41	Pro-rich.				positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				kidney(1)|large_intestine(2)|liver(1)|lung(4)|ovary(1)|urinary_tract(1)	10						gccgccaccactgccctcgcc	0.776																																					p.L41L	Melanoma(107;1207 1556 14956 29427 52130)	Atlas-SNP	.											.	NCCRP1	25	.	0			c.C121T						PASS	.						2	3	3					19																	39687743		1158	2257	3415	SO:0001819	synonymous_variant	342897	exon1			CCACCACTGCCCT	AK123941, BC067874	CCDS12529.1	19q13.2	2013-07-31	2008-11-19		ENSG00000188505	ENSG00000188505			33739	protein-coding gene	gene with protein product		615901					Standard	NM_001001414		Approved	LOC342897, NCCRP-1, FBXO50	uc002okq.1	Q6ZVX7		ENST00000339852.4:c.121C>T	chr19.hg19:g.39687743C>T		0.0	0.0	.		9.0	5.0	.	NM_001001414	Q6NVV5	Silent	SNP	ENST00000339852.4	hg19	CCDS12529.1																																																																																			.	.	.	none		0.776	NCCRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463829.1	NM_001001414		T	39687743	C	T	39687743	2	4	105	1	0	0	0	0	0	0	0	1	10220	564	20	2		2	NCCRP1	19	39687743	Silent	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10	28553457	39687743	19441240	39	6705											
ZNF225	7768	hgsc.bcm.edu	37	chr19	44636876	44636889	+	Stop_Codon_Del	DEL	AAATGACACATAAC	AAATGACACATAAC	-																															acgcttttgtcattatttttAaatgacacataactgttgta																								rs143348426	byFrequency	TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	AAATGACACATAAC	AAATGACACATAAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr19:44636876_44636889delAAATGACACATAAC	ENST00000262894.6	+	0	2389_2402				ZNF225_ENST00000592780.1_3'UTR|ZNF225_ENST00000590612.1_Stop_Codon_Del	NM_013362.2	NP_037494.2	Q9UK10	ZN225_HUMAN	zinc finger protein 225						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	16		Prostate(69;0.0352)|all_neural(266;0.202)				CAttatttttaaatgacacataactgttgtactc	0.355																																					p.703_707del		Pindel	.											.	ZNF225	41	.	0			c.2108_2121del						PASS	.																																			SO:0001567	stop_retained_variant	7768	exon5			.	AF187991	CCDS46100.1	19q13.31	2013-01-08				ENSG00000256294		"Zinc fingers, C2H2-type", "-"	13018	protein-coding gene	gene with protein product							Standard	NM_013362		Approved		uc002oyj.1	Q9UK10		Exception_encountered	chr19.hg19:g.44636876_44636889delAAATGACACATAAC	ENSP00000262894:p.*707Pheext*8	117.0	0.0	.		91.0	16.0	0.176	NM_013362	A8K8S2|Q53F12|Q9NS46|Q9UID8	Frame_Shift_Del	DEL	ENST00000262894.6	hg19	CCDS46100.1																																																																																			.	.	.	none		0.355	ZNF225-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460581.1			-	44636889	AAATGACACATAAC	-	44636876	7	5	105	1	0	1	0	1	0	0	0	0	17791	359	13	0	2123	0	ZNF225	19	44636876	Stop_Codon_Del	DEL	AAATGACACATAAC	TCGA-B9-A5W8-01A-11D-A28G-10	4949133	44636876	14492107	40	6706											
LILRB1	10859	hgsc.bcm.edu	37	chr19	55143956	55143956	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctcagtgcagccaggtcctAtcgtggcccctgaggagacc	7	8	12	14	1	1	2	1	1	1	1	4	3	2	2	5	3	2	1	5	3	1	1			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr19:55143956A>G	ENST00000396331.1	+	7	1060	c.703A>G	c.(703-705)Atc>Gtc	p.I235V	LILRB1_ENST00000448689.1_Missense_Mutation_p.I235V|LILRB1_ENST00000434867.2_Missense_Mutation_p.I235V|LILRB1_ENST00000418536.2_Missense_Mutation_p.I235V|LILRB1_ENST00000396327.3_Missense_Mutation_p.I235V|LILRB1_ENST00000396321.2_Missense_Mutation_p.I235V|LILRB1_ENST00000324602.7_Missense_Mutation_p.I235V|LILRB1_ENST00000396315.1_Missense_Mutation_p.I235V|LILRB1_ENST00000396332.4_Missense_Mutation_p.I235V|LILRB1_ENST00000396317.1_Missense_Mutation_p.I235V|LILRB1_ENST00000427581.2_Missense_Mutation_p.I271V	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	235	Ig-like C2-type 3.				cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		GCCAGGTCCTATCGTGGCCCC	0.537										HNSCC(37;0.09)																											p.I235V		Atlas-SNP	.											.	LILRB1	140	.	0			c.A703G						PASS	.						98	102	101					19																	55143956		2203	4300	6503	SO:0001583	missense	10859	exon6			GGTCCTATCGTGG	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.703A>G	chr19.hg19:g.55143956A>G	ENSP00000379622:p.Ile235Val	333.0	0.0	.		264.0	83.0	.	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	hg19	CCDS42617.1	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.218786	0.00286	.	.	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T;T	0.10477	2.87;2.87;2.87;2.87;2.87;2.87;2.87;2.87;2.87;2.87;2.87	1.49	-1.31	0.09230	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.873016	0.09637	N	0.775542	T	0.01592	0.0051	N	0.00219	-1.825	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	0.11329	0.001;0.001;0.006;0.001;0.002	T	0.39014	-0.9634	10	0.02654	T	1	.	2.0446	0.03557	0.3776:0.0:0.3682:0.2542	.	235;235;235;235;235	A8MVE2;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;LIRB1_HUMAN	V	235;235;235;235;235;235;235;235;271;235;235	ENSP00000379614:I235V;ENSP00000391514:I235V;ENSP00000409968:I235V;ENSP00000379622:I235V;ENSP00000379618:I235V;ENSP00000315997:I235V;ENSP00000405243:I235V;ENSP00000379623:I235V;ENSP00000395004:I271V;ENSP00000379610:I235V;ENSP00000379608:I235V	ENSP00000315997:I235V	I	+	1	0	LILRB1	59835768	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.930000	0.03972	-0.750000	0.04740	-1.160000	0.01791	ATC	.	.	.	none		0.537	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4			G	55143956	A	G	55143956	3	3	105	1	0	0	0	0	1	0	0	0	8797	449	16	3	721	3	LILRB1	19	55143956	Missense_Mutation	SNP	A	TCGA-B9-A5W8-01A-11D-A28G-10	10507080	55143956	3985027	41	6707											
HNF4A	3172	hgsc.bcm.edu	37	chr20	42984469	42984469	+	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	tcagcgtgaacgcgcccctcGgggctccagtggagagttct	6	8	14	13	4	2	2	1	1	1	1	4	3	3	2	3	3	2	2	3	3	1	1			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr20:42984469G>T	ENST00000316673.4	+	1	130	c.25G>T	c.(25-27)Ggg>Tgg	p.G9W	HNF4A_ENST00000609795.1_Missense_Mutation_p.G9W|RP5-881L22.5_ENST00000438702.1_RNA|HNF4A_ENST00000457232.1_Missense_Mutation_p.G9W			P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4, alpha	157					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)	p.G9W(1)		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)			CGCGCCCCTCGGGGCTCCAGT	0.682																																					p.G9W	Colon(79;2 1269 8820 14841 52347)	Atlas-SNP	.											.	HNF4A	150	.	1	Substitution - Missense(1)	lung(1)	c.G25T						PASS	.						24	28	26					20																	42984469		2037	4184	6221	SO:0001583	missense	3172	exon1			CCCCTCGGGGCTC	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	ENST00000316673.4:c.25G>T	chr20.hg19:g.42984469G>T	ENSP00000315180:p.Gly9Trp	66.0	0.0	.		75.0	16.0	.	NM_001030003	A5JW41|B2RPP8|O00659|O00723|Q14540|Q5QPB8|Q6B4V5|Q6B4V6|Q6B4V7|Q92653|Q92654|Q92655|Q99864|Q9NQH0	Missense_Mutation	SNP	ENST00000316673.4	hg19	CCDS42876.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.213853	0.39102	.	.	ENSG00000101076	ENST00000316673;ENST00000457232	D;D	0.92595	-3.07;-3.06	4.98	3.04	0.35103	.	.	.	.	.	D	0.91099	0.7198	N	0.24115	0.695	0.80722	D	1	D;D;P	0.71674	0.998;0.998;0.948	D;D;P	0.70227	0.93;0.968;0.759	D	0.89491	0.3757	9	0.72032	D	0.01	.	7.9382	0.29941	0.1907:0.0:0.8093:0.0	.	9;9;9	F1D8T0;P41235-6;P41235-7	.;.;.	W	9	ENSP00000315180:G9W;ENSP00000396216:G9W	ENSP00000315180:G9W	G	+	1	0	HNF4A	42417883	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	2.571000	0.45990	0.635000	0.30488	-0.136000	0.14681	GGG	.	.	.	none		0.682	HNF4A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079362.2			T	42984469	G	T	42984469	3	4	105	1	0	0	0	0	1	0	0	0	7260	1116	39	4	27	4	HNF4A	20	42984469	Missense_Mutation	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10		42984469	20041051	42	6708											
GGT5	2687	hgsc.bcm.edu	37	chr22	24628898	24628898	+	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	agcagcgcgatggtgggctgGaacagctgcgcccagggcag	8	4	18	11	3	0	0	0	0	0	0	0	2	0	1	1	4	5	4	1	4	1	0			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr22:24628898G>C	ENST00000327365.4	-	4	905	c.489C>G	c.(487-489)ttC>ttG	p.F163L	GGT5_ENST00000398292.3_Missense_Mutation_p.F163L|GGT5_ENST00000418439.2_Missense_Mutation_p.P88A|GGT5_ENST00000263112.7_Missense_Mutation_p.F131L	NM_001099781.1|NM_004121.2	NP_001093251.1|NP_004112.2	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5	163					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						TGGTGGGCTGGAACAGCTGCG	0.701																																					p.F163L		Atlas-SNP	.											.	GGT5	61	.	0			c.C489G						PASS	.						23	25	24					22																	24628898		2184	4285	6469	SO:0001583	missense	2687	exon4			GGGCTGGAACAGC	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.489C>G	chr22.hg19:g.24628898G>C	ENSP00000330080:p.Phe163Leu	122.0	0.0	.		193.0	36.0	.	NM_001099781	Q53XM9|Q6GMP0|Q96FC1|Q9UFM5	Missense_Mutation	SNP	ENST00000327365.4	hg19	CCDS13825.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.5|24.5	4.533985|4.533985	0.85812|0.85812	.|.	.|.	ENSG00000099998|ENSG00000099998	ENST00000327365;ENST00000263112;ENST00000438024;ENST00000398292|ENST00000418439	T;T;T|T	0.03717|0.66638	3.83;3.83;3.83|-0.22	4.32|4.32	3.3|3.3	0.37823|0.37823	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.58264|0.58264	0.2110|0.2110	M|M	0.64997|0.64997	1.995|1.995	0.25198|0.25198	N|N	0.990074|0.990074	D;D;B;D|B	0.69078|0.25667	0.967;0.997;0.095;0.997|0.131	P;D;B;D|B	0.67900|0.25140	0.775;0.954;0.129;0.954|0.058	T|T	0.45469|0.45469	-0.9259|-0.9259	10|9	0.72032|0.17369	D|T	0.01|0.5	-37.4629|-37.4629	6.7667|6.7667	0.23571|0.23571	0.2119:0.0:0.7881:0.0|0.2119:0.0:0.7881:0.0	.|.	131;163;163;163|88	P36269-2;Q53XM9;Q6GMP0;P36269|E7EUG3	.;.;.;GGT5_HUMAN|.	L|A	163;131;78;163|88	ENSP00000330080:F163L;ENSP00000263112:F131L;ENSP00000381340:F163L|ENSP00000392146:P88A	ENSP00000263112:F131L|ENSP00000392146:P88A	F|P	-|-	3|1	2|0	GGT5|GGT5	22958898|22958898	0.997000|0.997000	0.39634|0.39634	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	1.180000|1.180000	0.32005|0.32005	1.170000|1.170000	0.42753|0.42753	0.585000|0.585000	0.79938|0.79938	TTC|CCA	.	.	.	none		0.701	GGT5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320119.1	NM_004121		C	24628898	G	C	24628898	3	2	105	1	0	0	0	0	1	0	0	0	6369	1165	41	4	1310	4	GGT5	22	24628898	Missense_Mutation	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10		24628898	26675668	43	6709											
NEFH	4744	hgsc.bcm.edu	37	chr22	29885571	29885572	+	In_Frame_Ins	INS	-	-	CCCCTGAGAAGGCCAAGT																															aacgaaggaggaagcaaagtINScccctgagaaggccaagtcc																										TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chr22:29885571_29885572insCCCCTGAGAAGGCCAAGT	ENST00000310624.6	+	4	1975_1976	c.1942_1943insCCCCTGAGAAGGCCAAGT	c.(1942-1944)tcc>tCCCCTGAGAAGGCCAAGTcc	p.648_648S>SPEKAKS		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	654	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.			Missing (in Ref. 1; CAA33366 and 5; AC000035). {ECO:0000305}.	axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						GGAAGCAAAGTCCCCTGAGAAG	0.569																																					p.S648delinsSPEKAKS		Atlas-INDEL	.											.	NEFH	178	.	0			c.1942_1943insCCCCTGAGAAGGCCAAGT						PASS	.																																			SO:0001652	inframe_insertion	4744	exon4			.		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1943_1960dupCCCCTGAGAAGGCCAAGT	chr22.hg19:g.29885571_29885572insCCCCTGAGAAGGCCAAGT	Exception_encountered	173.0	0.0	0		223.0	71.0	0.318386	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.	.	none		0.569	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		CCCCTGAGAAGGCCAAGT	29885572	-	CCCCTGAGAAGGCCAAGT	29885571	7	5	105	1	0	1	1	0	0	0	0	0	10321	1667	58	0	1956	0	NEFH	22	29885571	In_Frame_Ins	INS	-	TCGA-B9-A5W8-01A-11D-A28G-10	5256673	29885571	21418995	44	6710											
TCEANC	170082	hgsc.bcm.edu	37	chrX	13680806	13680808	+	In_Frame_Del	DEL	CCT	CCT	-																															cagagtcctcaaaaactgccCctctgtggctttgaaaaaga																										TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chrX:13680806_13680808delCCT	ENST00000380600.1	+	2	266_268	c.179_181delCCT	c.(178-183)ccctct>cct	p.S61del	TCEANC_ENST00000490617.1_3'UTR|TCEANC_ENST00000545566.1_In_Frame_Del_p.S61del|TCEANC_ENST00000314720.4_In_Frame_Del_p.S91del|TCEANC_ENST00000544987.1_In_Frame_Del_p.S61del			Q8N8B7	TEANC_HUMAN	transcription elongation factor A (SII) N-terminal and central domain containing	61	TFIIS N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00649}.				regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|large_intestine(5)|lung(2)|pancreas(1)	9						AAAAACTGCCCCTCTGTGGCTTT	0.443																																					p.90_90del		Atlas-Indel,Pindel	.											.	TCEANC	29	.	0			c.268_270del						PASS	.																																			SO:0001651	inframe_deletion	170082	exon4			.		CCDS48081.1, CCDS75954.1	Xp22.2	2009-01-30			ENSG00000176896	ENSG00000176896			28277	protein-coding gene	gene with protein product						12477932	Standard	XM_005274454		Approved	MGC17403	uc010neg.1	Q8N8B7	OTTHUMG00000021154	ENST00000380600.1:c.179_181delCCT	chrX.hg19:g.13680806_13680808delCCT	ENSP00000369974:p.Ser61del	64.0	0.0	0		58.0	33.0	0.568965	NM_152634	A6NI06|B2RDM3	In_Frame_Del	DEL	ENST00000380600.1	hg19																																																																																				.	.	.	none		0.443	TCEANC-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000055796.1	NM_152634		-	13680808	CCT	-	13680806	7	5	105	1	0	1	0	1	0	0	0	0	15690	623	22	0	275	0	TCEANC	23	13680806	In_Frame_Del	DEL	CCT	TCGA-B9-A5W8-01A-11D-A28G-10		13680806	141589754	45	6711											
SH3KBP1	30011	hgsc.bcm.edu	37	chrX	19560042	19560043	+	Splice_Site	INS	-	-	T																															aagagtccccaggcactcacINSttctgctggtccttcatggt																										TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chrX:19560042_19560043insT	ENST00000397821.3	-	16	2182_2183		c.e16+1		SH3KBP1_ENST00000541422.1_Splice_Site|SH3KBP1_ENST00000379698.4_Splice_Site|SH3KBP1_ENST00000379716.1_Splice_Site	NM_031892.2	NP_114098.1	Q96B97	SH3K1_HUMAN	SH3-domain kinase binding protein 1						apoptotic process (GO:0006915)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|regulation of cell shape (GO:0008360)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(4)	29						CAGGCACTCACTTCTGCTGGTC	0.634																																					.		Atlas-INDEL	.											.	SH3KBP1	96	.	0			c.1178+1->A						PASS	.																																			SO:0001630	splice_region_variant	30011	exon12			.	AF230904	CCDS14193.1, CCDS35213.1, CCDS55383.1	Xp22.1-p21.3	2008-02-05			ENSG00000147010	ENSG00000147010			13867	protein-coding gene	gene with protein product		300374				8889549, 7566098	Standard	NM_031892		Approved	CIN85	uc004czm.3	Q96B97	OTTHUMG00000021227	ENST00000397821.3:c.1892+1->A	chrX.hg19:g.19560044_19560044dupT		81.0	0.0	0		81.0	41.0	0.506173	NM_001184960	B7Z1D5|Q5JPT4|Q5JPT5|Q8IWX6|Q8IX98|Q96RN4|Q9NYR0	Splice_Site	INS	ENST00000397821.3	hg19	CCDS14193.1																																																																																			.	.	.	none		0.634	SH3KBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055992.1	NM_031892	Intron	T	19560043	-	T	19560042	8	5	105	1	0	1	1	0	0	0	1	0	14268	579	20	0	116	0	SH3KBP1	23	19560042	Splice_Site	INS	-	TCGA-B9-A5W8-01A-11D-A28G-10	5879236	19560042	135710518	46	6712	73	2									
SH3KBP1	30011	hgsc.bcm.edu	37	chrX	19560045	19560045	+	Missense_Mutation	SNP	C	C	A																															gagtccccaggcactcacttCtgctggtccttcatggtctc																										TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chrX:19560045C>A	ENST00000397821.3	-	16	2180	c.1890G>T	c.(1888-1890)caG>caT	p.Q630H	SH3KBP1_ENST00000541422.1_Missense_Mutation_p.Q369H|SH3KBP1_ENST00000379698.4_Missense_Mutation_p.Q593H|SH3KBP1_ENST00000379716.1_Missense_Mutation_p.Q392H	NM_031892.2	NP_114098.1	Q96B97	SH3K1_HUMAN	SH3-domain kinase binding protein 1	630					apoptotic process (GO:0006915)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|regulation of cell shape (GO:0008360)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(4)	29						GCACTCACTTCTGCTGGTCCT	0.627																																					p.Q630H		Atlas-SNP	.											.	SH3KBP1	96	.	0			c.G1890T						PASS	.						106	96	100					X																	19560045		2203	4300	6503	SO:0001583	missense	30011	exon16			TCACTTCTGCTGG	AF230904	CCDS14193.1, CCDS35213.1, CCDS55383.1	Xp22.1-p21.3	2008-02-05			ENSG00000147010	ENSG00000147010			13867	protein-coding gene	gene with protein product		300374				8889549, 7566098	Standard	NM_031892		Approved	CIN85	uc004czm.3	Q96B97	OTTHUMG00000021227	ENST00000397821.3:c.1890G>T	chrX.hg19:g.19560045C>A	ENSP00000380921:p.Gln630His	84.0	0.0	.		81.0	40.0	.	NM_031892	B7Z1D5|Q5JPT4|Q5JPT5|Q8IWX6|Q8IX98|Q96RN4|Q9NYR0	Missense_Mutation	SNP	ENST00000397821.3	hg19	CCDS14193.1	.	.	.	.	.	.	.	.	.	.	C	3.308	-0.141521	0.06669	.	.	ENSG00000147010	ENST00000379702;ENST00000397821;ENST00000379716;ENST00000379698;ENST00000541422;ENST00000379726	T;T;T;T;T	0.33654	1.4;1.4;1.4;1.4;1.4	5.39	4.41	0.53225	.	0.000000	0.64402	D	0.000010	T	0.30541	0.0768	N	0.12887	0.27	0.37413	D	0.9133	D;B;D	0.89917	1.0;0.156;0.997	D;B;D	0.85130	0.997;0.031;0.99	T	0.44050	-0.9353	10	0.02654	T	1	-14.024	6.2238	0.20695	0.0:0.7735:0.0:0.2265	.	392;630;593	Q5JPT4;Q96B97;Q5JPT5	.;SH3K1_HUMAN;.	H	615;630;392;593;369;610	ENSP00000380921:Q630H;ENSP00000369039:Q392H;ENSP00000369020:Q593H;ENSP00000442499:Q369H;ENSP00000369049:Q610H	ENSP00000369020:Q593H	Q	-	3	2	SH3KBP1	19469966	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	1.388000	0.34442	2.265000	0.75225	0.529000	0.55759	CAG	.	.	.	none		0.627	SH3KBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055992.1	NM_031892		A	19560045	C	A	19560045	3	1	105	1	0	0	0	0	1	0	0	0	14268	912	32	4	119	4	SH3KBP1	23	19560045	Missense_Mutation	SNP	C	TCGA-B9-A5W8-01A-11D-A28G-10	3	19560045	135710515	47	6713	73	2									
TAF1	6872	hgsc.bcm.edu	37	chrX	70618524	70618524	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttaagaggaaccaggaaaaGgagaagcttaagggtcctcc	15	6	12	8	0	0	2	0	0	0	2	2	5	2	4	3	4	2	1	3	4	6	2			TCGA-B9-A5W8-01A-11D-A28G-10	TCGA-B9-A5W8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	28255a70-00c1-45b8-ad54-33a2def9c843	7d548692-a558-4aaa-b70f-8b2861f275ff	g.chrX:70618524G>A	ENST00000373790.4	+	24	3771	c.3720G>A	c.(3718-3720)aaG>aaA	p.K1240K	TAF1_ENST00000449580.1_Silent_p.K1240K|TAF1_ENST00000276072.3_Silent_p.K1261K|TAF1_ENST00000423759.1_Silent_p.K1261K	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	1240					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)				ACCAGGAAAAGGAGAAGCTTA	0.458																																					p.K1261K		Atlas-SNP	.											.	TAF1	439	.	0			c.G3783A						PASS	.						93	79	84					X																	70618524		2203	4300	6503	SO:0001819	synonymous_variant	6872	exon24			GGAAAAGGAGAAG		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.3720G>A	chrX.hg19:g.70618524G>A		157.0	0.0	.		129.0	74.0	.	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Silent	SNP	ENST00000373790.4	hg19	CCDS35325.1	.	.	.	.	.	.	.	.	.	.	.	9.733	1.162842	0.21538	.	.	ENSG00000147133	ENST00000483985	.	.	.	5.54	3.77	0.43336	.	.	.	.	.	T	0.59074	0.2167	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53129	-0.8482	4	.	.	.	.	9.3163	0.37937	0.2564:0.0:0.7436:0.0	.	.	.	.	K	151	.	.	R	+	2	0	TAF1	70535249	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	0.737000	0.26144	0.520000	0.28426	0.468000	0.43344	AGG	.	.	.	none		0.458	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		A	70618524	G	A	70618524	2	1	105	1	0	0	0	0	0	0	0	1	15525	991	35	2		2	TAF1	23	70618524	Silent	SNP	G	TCGA-B9-A5W8-01A-11D-A28G-10	51058479	70618524	84652036	48	6714											
C1orf128	57095	hgsc.bcm.edu	37	chr1	24105128	24105128	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atcgacctggagcggctgcaAtgccttaacgagagccgcga	10	6	13	12	5	0	1	0	0	0	1	1	5	0	2	3	2	5	2	3	2	2	1	rs562148184		TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr1:24105128A>G	ENST00000246151.4	+	1	234	c.123A>G	c.(121-123)caA>caG	p.Q41Q	RP5-886K2.3_ENST00000427796.1_RNA	NM_020362.4	NP_065095.2	Q9GZP4	PITH1_HUMAN	PITH (C-terminal proteasome-interacting domain of thioredoxin-like) domain containing 1	41	PITH. {ECO:0000255|PROSITE- ProRule:PRU00864}.					nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	6						AGCGGCTGCAATGCCTTAACG	0.751													G|||	1	0.000199681	0	0.0014	5008	,	,		6646	0		0	False		,,,				2504	0				p.Q41Q		Atlas-SNP	.											.	PITHD1	20	.	0			c.A123G						PASS	.																																			SO:0001819	synonymous_variant	57095	exon1			GCTGCAATGCCTT		CCDS240.1	1p36.11	2011-02-21	2011-02-21	2011-02-21	ENSG00000057757	ENSG00000057757			25022	protein-coding gene	gene with protein product	"TXNL1 C-terminal like"		"chromosome 1 open reading frame 128"	C1orf128		12477932	Standard	NM_020362		Approved	HT014, TXNL1CL	uc001bhq.3	Q9GZP4	OTTHUMG00000002960	ENST00000246151.4:c.123A>G	chr1.hg19:g.24105128A>G		4.0	0.0	.		17.0	7.0	.	NM_020362	B2R7J4|Q5QPN6|Q5QPN7|Q9NRI8	Silent	SNP	ENST00000246151.4	hg19	CCDS240.1																																																																																			.	.	.	none		0.751	PITHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008243.1	NM_020362		G	24105128	A	G	24105128	2	3	106	1	0	0	0	0	0	0	0	1	1997	98	4	3		3	C1orf128	1	24105128	Silent	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10		24105128	225145493	1	6715											
HFM1	164045	hgsc.bcm.edu	37	chr1	91742587	91742587	+	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	tttacaaagatgattgcattCtcggttcccaggttttttgc	8	17	8	8	1	1	2	0	1	1	1	3	2	2	2	1	2	3	3	1	2	2	8			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr1:91742587C>G	ENST00000370425.3	-	31	3522	c.3424G>C	c.(3424-3426)Gaa>Caa	p.E1142Q	HFM1_ENST00000370424.3_Missense_Mutation_p.E821Q|HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000294696.5_Missense_Mutation_p.E374Q	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	1142					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)		TGATTGCATTCTCGGTTCCCA	0.289																																					p.E1142Q		Atlas-SNP	.											.	HFM1	188	.	0			c.G3424C						PASS	.						129	128	129					1																	91742587		2203	4299	6502	SO:0001583	missense	164045	exon31			TGCATTCTCGGTT	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.3424G>C	chr1.hg19:g.91742587C>G	ENSP00000359454:p.Glu1142Gln	109.0	0.0	.		88.0	30.0	.	NM_001017975	B1B0B6|Q8N9Q0	Missense_Mutation	SNP	ENST00000370425.3	hg19	CCDS30769.2	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	12.44|12.44|12.44	1.937796|1.937796|1.937796	0.34189|0.34189|0.34189	.|.|.	.|.|.	ENSG00000162669|ENSG00000162669|ENSG00000162669	ENST00000430465|ENST00000370425;ENST00000294696;ENST00000370424|ENST00000370421	.|T;T;T|.	.|0.64618|.	.|0.25;0.63;-0.11|.	5.71|5.71|5.71	5.71|5.71|5.71	0.89125|0.89125|0.89125	.|.|.	0.237508|0.237508|.	0.33005|0.33005|.	N|N|.	0.005389|0.005389|.	T|T|T	0.55481|0.55481|0.55481	0.1923|0.1923|0.1923	M|M|M	0.64997|0.64997|0.64997	1.995|1.995|1.995	0.36745|0.36745|0.36745	D|D|D	0.882419|0.882419|0.882419	.|B;B;B|.	.|0.28378|.	.|0.082;0.209;0.105|.	.|B;B;B|.	.|0.25614|.	.|0.045;0.062;0.034|.	T|T|T	0.59461|0.59461|0.59461	-0.7450|-0.7450|-0.7450	6|10|6	.|0.40728|0.42905	.|T|T	.|0.16|0.14	.|.|.	10.7947|10.7947|10.7947	0.46453|0.46453|0.46453	0.0:0.9137:0.0:0.0863|0.0:0.9137:0.0:0.0863|0.0:0.9137:0.0:0.0863	.|.|.	.|821;353;1142|.	.|A6NGI5;B1B0B5;A2PYH4|.	.|.;.;HFM1_HUMAN|.	D|Q|T	353|1142;374;821|825	.|ENSP00000359454:E1142Q;ENSP00000294696:E374Q;ENSP00000359453:E821Q|.	.|ENSP00000294696:E374Q|ENSP00000359450:R825T	E|E|R	-|-|-	3|1|2	2|0|0	HFM1|HFM1|HFM1	91515175|91515175|91515175	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.815000|0.815000|0.815000	0.46073|0.46073|0.46073	3.562000|3.562000|3.562000	0.53777|0.53777|0.53777	2.698000|2.698000|2.698000	0.92095|0.92095|0.92095	0.585000|0.585000|0.585000	0.79938|0.79938|0.79938	GAG|GAA|AGA	.	.	.	none		0.289	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		G	91742587	C	G	91742587	3	3	106	1	0	0	0	0	1	0	0	0	7090	922	32	4	919	4	HFM1	1	91742587	Missense_Mutation	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	67637459	91742587	157508034	2	6716											
SLC44A3	126969	hgsc.bcm.edu	37	chr1	95330398	95330398	+	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	aaagggtcatttttaatctcTgtggtgaggattccgagaat	11	14	11	5	1	2	2	1	1	1	1	4	4	3	3	1	3	0	0	1	3	3	4			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr1:95330398T>A	ENST00000271227.6	+	11	1440	c.1338T>A	c.(1336-1338)tcT>tcA	p.S446S	SLC44A3_ENST00000446120.2_Silent_p.S410S|SLC44A3_ENST00000529450.1_Silent_p.S414S|SLC44A3_ENST00000527077.1_Silent_p.S378S|SLC44A3_ENST00000467909.1_Silent_p.S398S|SLC44A3_ENST00000530397.1_3'UTR|SLC44A3_ENST00000532427.1_Silent_p.S366S	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	446					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)	TTTTAATCTCTGTGGTGAGGA	0.433																																					p.S446S		Atlas-SNP	.											.	SLC44A3	109	.	0			c.T1338A						PASS	.						217	202	207					1																	95330398		2203	4300	6503	SO:0001819	synonymous_variant	126969	exon11			AATCTCTGTGGTG	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.1338T>A	chr1.hg19:g.95330398T>A		87.0	0.0	.		68.0	22.0	.	NM_001114106	B4DVY4|B4E1M4|B7ZA08|E9PJH2|E9PJY8|Q6UWT1|Q7Z6C5|Q9BWY7	Silent	SNP	ENST00000271227.6	hg19	CCDS44176.1																																																																																			.	.	.	none		0.433	SLC44A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029544.3	NM_152369		A	95330398	T	A	95330398	2	1	106	1	0	0	0	0	0	0	0	1	14650	1567	55	5		5	SLC44A3	1	95330398	Silent	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10	3587811	95330398	153920223	3	6717											
DHX57	90957	hgsc.bcm.edu	37	chr2	39088916	39088916	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaaggagatgctctagtgaTgctcccacatctccatcaca	11	10	8	12	0	3	2	1	1	2	1	5	3	4	2	2	1	2	3	2	1	2	2			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr2:39088916T>C	ENST00000295373.6	-	5	762	c.636A>G	c.(634-636)gcA>gcG	p.A212A	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	212	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.						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)				GCTCTAGTGATGCTCCCACAT	0.448																																					p.A212A	Melanoma(191;1090 2095 4375 23729 47341)	Atlas-SNP	.											.	DHX57	127	.	0			c.A636G						PASS	.						84	79	81					2																	39088916		2203	4300	6503	SO:0001819	synonymous_variant	90957	exon5			TAGTGATGCTCCC	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.636A>G	chr2.hg19:g.39088916T>C		107.0	0.0	.		120.0	66.0	.	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Silent	SNP	ENST00000295373.6	hg19	CCDS1800.1																																																																																			.	.	.	none		0.448	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646		C	39088916	T	C	39088916	2	2	106	1	0	0	0	0	0	0	0	1	4515	1451	51	3		3	DHX57	2	39088916	Silent	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10		39088916	204110457	4	6718											
NBEAL1	65065	hgsc.bcm.edu	37	chr2	204009565	204009566	+	Frame_Shift_Ins	INS	-	-	T																															ttaccaatggtagctcctcaINSttttttgaagattttcaaga																										TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr2:204009565_204009566insT	ENST00000449802.1	+	31	5337_5338	c.5004_5005insT	c.(5005-5007)tttfs	p.F1669fs		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	1669										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						GTAGCTCCTCATTTTTTGAAGA	0.317																																					p.S1668fs		Atlas-Indel,Pindel	.											.	NBEAL1	266	.	0			c.5004_5005insT						PASS	.																																			SO:0001589	frameshift_variant	65065	exon31			.	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.5010dupT	chr2.hg19:g.204009571_204009571dupT	ENSP00000399903:p.Phe1669fs	52.0	0.0	0		45.0	16.0	0.355556	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Frame_Shift_Ins	INS	ENST00000449802.1	hg19	CCDS46495.1																																																																																			.	.	.	none		0.317	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4			T	204009566	-	T	204009565	7	5	106	1	0	1	1	0	0	0	0	0	10195	204	8	0	5122	0	NBEAL1	2	204009565	Frame_Shift_Ins	INS	-	TCGA-B9-A5W9-01A-11D-A28G-10	164920649	204009565	39189808	5	6719											
STK11IP	114790	hgsc.bcm.edu	37	chr2	220473931	220473931	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctgatgcccacgcagctgTccaggtgatggcgcccagag	7	6	14	14	2	0	3	0	2	0	1	1	3	1	3	4	2	2	2	4	2	0	0			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr2:220473931T>C	ENST00000456909.1	+	16	2012	c.1922T>C	c.(1921-1923)gTc>gCc	p.V641A	STK11IP_ENST00000295641.10_Missense_Mutation_p.V652A			Q8N1F8	S11IP_HUMAN	serine/threonine kinase 11 interacting protein	652					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)		CACGCAGCTGTCCAGGTGATG	0.662																																					p.V652A		Atlas-SNP	.											.	STK11IP	152	.	0			c.T1955C						PASS	.						23	22	23					2																	220473931		2018	4164	6182	SO:0001583	missense	114790	exon16			CAGCTGTCCAGGT	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.1922T>C	chr2.hg19:g.220473931T>C	ENSP00000389383:p.Val641Ala	82.0	0.0	.		89.0	35.0	.	NM_052902	Q8NAW9|Q8WXE4|Q96CN3|Q96PY9	Missense_Mutation	SNP	ENST00000456909.1	hg19		.	.	.	.	.	.	.	.	.	.	T	12.88	2.071525	0.36566	.	.	ENSG00000144589	ENST00000456909;ENST00000426736;ENST00000295641	T;T	0.05025	3.51;3.51	5.0	-0.564	0.11774	.	1.280970	0.05320	N	0.526447	T	0.07683	0.0193	L	0.43152	1.355	0.20821	N	0.999844	B;B;B	0.14012	0.009;0.004;0.002	B;B;B	0.15484	0.013;0.003;0.006	T	0.43956	-0.9359	10	0.72032	D	0.01	-0.0971	8.4014	0.32588	0.0:0.3626:0.0:0.6374	.	620;652;652	B4DUE4;Q8N1F8-2;Q8N1F8	.;.;S11IP_HUMAN	A	641;620;652	ENSP00000389383:V641A;ENSP00000295641:V652A	ENSP00000295641:V652A	V	+	2	0	STK11IP	220182175	0.431000	0.25546	0.117000	0.21633	0.652000	0.38707	0.654000	0.24918	-0.222000	0.09958	-0.250000	0.11733	GTC	.	.	.	none		0.662	STK11IP-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000131432.1	NM_052902		C	220473931	T	C	220473931	3	2	106	1	0	0	0	0	1	0	0	0	15300	1667	58	3	2017	3	STK11IP	2	220473931	Missense_Mutation	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10	16464366	220473931	22725442	6	6720											
DOCK3	1795	hgsc.bcm.edu	37	chr3	51393580	51393580	+	Frame_Shift_Del	DEL	G	G	-																															ggatgttctgcagatggataGggtaccagatcgagtcaaga																										TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr3:51393580delG	ENST00000266037.9	+	42	4333	c.4310delG	c.(4309-4311)aggfs	p.R1437fs		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	1437	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)		CAGATGGATAGGGTACCAGAT	0.493																																					p.R1437fs		Atlas-Indel,Pindel	.											.	DOCK3	397	.	0			c.4309delA						PASS	.						147	140	142					3																	51393580		1982	4180	6162	SO:0001589	frameshift_variant	1795	exon42			.	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.4310delG	chr3.hg19:g.51393580delG	ENSP00000266037:p.Arg1437fs	232.0	0.0	0		199.0	65.0	0.326633	NM_004947	O15017	Frame_Shift_Del	DEL	ENST00000266037.9	hg19	CCDS46835.1																																																																																			.	.	.	none		0.493	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		-	51393580	G	-	51393580	7	5	106	1	0	1	0	1	0	0	0	0	4690	1000	35	0	4476	0	DOCK3	3	51393580	Frame_Shift_Del	DEL	G	TCGA-B9-A5W9-01A-11D-A28G-10		51393580	146628850	7	6721											
ATXN7	6314	hgsc.bcm.edu	37	chr3	63983337	63983337	+	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	acgaacaggaatttcagcaaCatcaccccagagccctgact	14	6	7	14	1	2	2	2	1	0	1	2	4	2	3	3	1	4	1	3	1	3	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr3:63983337C>T	ENST00000295900.6	+	12	3211				ATXN7_ENST00000398590.3_Missense_Mutation_p.T901I|ATXN7_ENST00000484332.1_Intron|ATXN7_ENST00000487717.1_Intron|ATXN7_ENST00000538065.1_Missense_Mutation_p.T901I	NM_000333.3	NP_000324.1	O15265	ATX7_HUMAN	ataxin 7						cell death (GO:0008219)|chromatin organization (GO:0006325)|histone deubiquitination (GO:0016578)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|nucleus organization (GO:0006997)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|stomach(1)|urinary_tract(3)	35		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)		ATTTCAGCAACATCACCCCAG	0.428																																					p.T901I		Atlas-SNP	.											.	ATXN7	126	.	0			c.C2702T						PASS	.						296	237	255					3																	63983337		692	1591	2283	SO:0001627	intron_variant	6314	exon12			CAGCAACATCACC	AJ000517	CCDS43102.1, CCDS46861.1, CCDS46861.2, CCDS54603.1	3p21.1-p12	2014-09-17	2004-08-12	2004-08-12	ENSG00000163635	ENSG00000163635		"Ataxins"	10560	protein-coding gene	gene with protein product		607640	"spinocerebellar ataxia 7 (olivopontocerebellar atrophy with retinal degeneration)"	SCA7		7647798, 10598805	Standard	NM_000333		Approved	OPCA3, ADCAII	uc021wzy.1	O15265	OTTHUMG00000158763	ENST00000295900.6:c.2661+1178C>T	chr3.hg19:g.63983337C>T		64.0	0.0	.		66.0	27.0	.	NM_001177387	B4E207|E9PHP9|O75328|O75329|Q9Y6P8	Missense_Mutation	SNP	ENST00000295900.6	hg19	CCDS43102.1	.	.	.	.	.	.	.	.	.	.	C	12.80	2.045840	0.36085	.	.	ENSG00000163635	ENST00000398590;ENST00000538065;ENST00000522345	T;T;T	0.51071	2.49;2.49;0.72	4.03	3.14	0.36123	.	0.628911	0.14004	N	0.347922	T	0.26159	0.0638	N	0.08118	0	0.22521	N	0.99903	B	0.12013	0.005	B	0.11329	0.006	T	0.15321	-1.0441	10	0.56958	D	0.05	0.0408	7.1588	0.25652	0.0:0.8751:0.0:0.1249	.	901	O15265-2	.	I	901;901;72	ENSP00000381590:T901I;ENSP00000439585:T901I;ENSP00000428067:T72I	ENSP00000381590:T901I	T	+	2	0	ATXN7	63958377	0.005000	0.15991	0.963000	0.40424	0.987000	0.75469	0.983000	0.29552	1.254000	0.44035	0.644000	0.83932	ACA	.	.	.	none		0.428	ATXN7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352070.1	NM_000333		T	63983337	C	T	63983337	1	4	106	0	1	0	0	0	0	0	0	0	1215	478	17	2		2	ATXN7	3	63983337	Intron	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	12589757	63983337	134039093	8	6722											
TOPBP1	11073	hgsc.bcm.edu	37	chr3	133331389	133331389	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcactgcttttctatcacCaatccaccttaagcagagaa	14	10	5	12	0	2	1	1	0	1	1	3	2	3	1	3	0	3	3	3	0	5	4			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr3:133331389C>T	ENST00000260810.5	-	24	4010	c.3879G>A	c.(3877-3879)ttG>ttA	p.L1293L		NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	1293	BRCT 7. {ECO:0000255|PROSITE- ProRule:PRU00033}.				cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						TTTCTATCACCAATCCACCTT	0.383								Other conserved DNA damage response genes																													p.L1293L	Ovarian(21;193 658 4424 15423 17362)	Atlas-SNP	.											.	TOPBP1	218	.	0			c.G3879A						PASS	.						50	48	49					3																	133331389		1904	4132	6036	SO:0001819	synonymous_variant	11073	exon24			TATCACCAATCCA	AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.3879G>A	chr3.hg19:g.133331389C>T		69.0	0.0	.		52.0	20.0	.	NM_007027	B7Z7W8|Q7LGC1|Q9UEB9	Silent	SNP	ENST00000260810.5	hg19	CCDS46919.1																																																																																			.	.	.	none		0.383	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027		T	133331389	C	T	133331389	2	4	106	1	0	0	0	0	0	0	0	1	16381	593	21	2		2	TOPBP1	3	133331389	Silent	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	69348052	133331389	64691041	9	6723											
CLDN16	10686	hgsc.bcm.edu	37	chr3	190126252	190126252	+	Missense_Mutation	SNP	T	T	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	ctgggtctctgggttgctttTtggctggagctgttctcacc	2	16	13	10	0	2	0	1	0	2	0	4	1	2	1	1	4	2	5	1	4	0	4	rs143316426	byFrequency	TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr3:190126252T>G	ENST00000264734.2	+	4	990	c.742T>G	c.(742-744)Ttg>Gtg	p.L248V	CLDN16_ENST00000456423.1_Intron	NM_006580.3	NP_006571.1	Q9Y5I7	CLD16_HUMAN	claudin 16	248					calcium-independent cell-cell adhesion (GO:0016338)|cellular metal ion homeostasis (GO:0006875)|excretion (GO:0007588)|magnesium ion transport (GO:0015693)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|magnesium ion transmembrane transporter activity (GO:0015095)|structural molecule activity (GO:0005198)			breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|skin(1)	19	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.018)		GGGTTGCTTTTTGGCTGGAGC	0.393																																					p.L248V		Atlas-SNP	.											.	CLDN16	59	.	0			c.T742G						PASS	.						142	138	140					3																	190126252		2203	4300	6503	SO:0001583	missense	10686	exon4			TGCTTTTTGGCTG	AF152101	CCDS3296.1	3q28	2008-12-10			ENSG00000113946	ENSG00000113946		"Claudins"	2037	protein-coding gene	gene with protein product	"paracellin-1", "hypomagnesemia 3, with hypercalciuria and nephrocalcinosis"	603959				10390358	Standard	NM_006580		Approved	PCLN1, HOMG3	uc003fsi.3	Q9Y5I7	OTTHUMG00000156215	ENST00000264734.2:c.742T>G	chr3.hg19:g.190126252T>G	ENSP00000264734:p.Leu248Val	69.0	0.0	.		78.0	40.0	.	NM_006580		Missense_Mutation	SNP	ENST00000264734.2	hg19	CCDS3296.1	.	.	.	.	.	.	.	.	.	.	T	12.93	2.084809	0.36758	.	.	ENSG00000113946	ENST00000264734	D	0.89875	-2.58	5.6	3.12	0.35913	.	0.099830	0.43919	D	0.000514	D	0.82282	0.5003	L	0.39326	1.205	0.80722	D	1	P	0.42296	0.775	B	0.39660	0.306	T	0.78966	-0.1995	10	0.44086	T	0.13	-2.4464	8.0251	0.30431	0.0:0.0724:0.135:0.7926	.	248	Q9Y5I7	CLD16_HUMAN	V	248	ENSP00000264734:L248V	ENSP00000264734:L248V	L	+	1	2	CLDN16	191608946	1.000000	0.71417	1.000000	0.80357	0.594000	0.36715	1.133000	0.31430	0.909000	0.36697	0.455000	0.32223	TTG	.	T|0.999;C|0.001	.	alt		0.393	CLDN16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343519.1	NM_006580		G	190126252	T	G	190126252	3	3	106	1	0	0	0	0	1	0	0	0	3479	1838	64	5	756	5	CLDN16	3	190126252	Missense_Mutation	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10	56794863	190126252	7896178	10	6724											
PLK4	10733	hgsc.bcm.edu	37	chr4	128813596	128813596	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaatctcccaaaatcacttaTtttacaagatatgctaaatg	17	13	3	8	0	2	1	1	0	1	1	3	1	2	1	1	0	2	1	1	0	9	5			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr4:128813596T>C	ENST00000270861.5	+	10	2389	c.2115T>C	c.(2113-2115)taT>taC	p.Y705Y	PLK4_ENST00000507249.1_Silent_p.Y644Y|PLK4_ENST00000515069.1_Silent_p.Y627Y|PLK4_ENST00000514379.1_Silent_p.Y664Y|RNU6-583P_ENST00000516012.1_RNA|PLK4_ENST00000513090.1_Silent_p.Y673Y	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	705					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						AAATCACTTATTTTACAAGAT	0.313																																					p.Y705Y	Colon(135;508 1718 19061 31832 42879)	Atlas-SNP	.											.	PLK4	65	.	0			c.T2115C						PASS	.						121	116	118					4																	128813596		2202	4299	6501	SO:0001819	synonymous_variant	10733	exon10			CACTTATTTTACA	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.2115T>C	chr4.hg19:g.128813596T>C		72.0	0.0	.		115.0	31.0	.	NM_014264	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Silent	SNP	ENST00000270861.5	hg19	CCDS3735.1																																																																																			.	.	.	none		0.313	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3			C	128813596	T	C	128813596	2	2	106	1	0	0	0	0	0	0	0	1	12105	1500	52	3		3	PLK4	4	128813596	Silent	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10		128813596	62340680	11	6725											
CPE	1363	hgsc.bcm.edu	37	chr4	166300624	166300624	+	Missense_Mutation	SNP	A	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	cacggtggggcgcagcttcgAgggccgggagctcctggtca	5	6	18	12	4	1	0	1	0	0	0	3	2	2	1	2	6	2	3	2	6	0	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr4:166300624A>C	ENST00000402744.4	+	1	531	c.251A>C	c.(250-252)gAg>gCg	p.E84A		NM_001873.2	NP_001864.1	P16870	CBPE_HUMAN	carboxypeptidase E	84					cardiac left ventricle morphogenesis (GO:0003214)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|insulin processing (GO:0030070)|metabolic process (GO:0008152)|neuropeptide signaling pathway (GO:0007218)|protein localization to membrane (GO:0072657)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)	carboxypeptidase activity (GO:0004180)|cell adhesion molecule binding (GO:0050839)|metallocarboxypeptidase activity (GO:0004181)|neurexin family protein binding (GO:0042043)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	26	all_hematologic(180;0.221)	Prostate(90;0.0962)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.137)	"""Insulin(DB00071)|Insulin Regular(DB00030)"	CGCAGCTTCGAGGGCCGGGAG	0.682																																					p.E84A		Atlas-SNP	.											.	CPE	65	.	0			c.A251C						PASS	.						13	14	14					4																	166300624		2161	4236	6397	SO:0001583	missense	1363	exon1			GCTTCGAGGGCCG	X51405	CCDS3810.1	4q32.3	2012-02-10			ENSG00000109472	ENSG00000109472	3.4.17.10		2303	protein-coding gene	gene with protein product	"carboxypeptidase H", "enkephalin convertase", "insulin granule-associated carboxypeptidase", "cobalt-stimulated chromaffin granule carboxypeptidase"	114855				2334405	Standard	NM_001873		Approved		uc003irg.4	P16870	OTTHUMG00000150252	ENST00000402744.4:c.251A>C	chr4.hg19:g.166300624A>C	ENSP00000386104:p.Glu84Ala	111.0	0.0	.		156.0	91.0	.	NM_001873	A8K4N1|B3KR42|B4DFN4|D3DP33|Q9UIU9	Missense_Mutation	SNP	ENST00000402744.4	hg19	CCDS3810.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.301811	0.81136	.	.	ENSG00000109472	ENST00000402744;ENST00000261510	T	0.15372	2.43	4.1	4.1	0.47936	Peptidase M14, carboxypeptidase A (2);	0.098707	0.64402	D	0.000002	T	0.27697	0.0681	M	0.84082	2.675	0.58432	D	0.999999	B	0.24576	0.106	B	0.31245	0.126	T	0.14615	-1.0466	10	0.59425	D	0.04	-28.9098	12.8978	0.58109	1.0:0.0:0.0:0.0	.	84	P16870	CBPE_HUMAN	A	84;48	ENSP00000386104:E84A	ENSP00000261510:E48A	E	+	2	0	CPE	166520074	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.494000	0.73661	1.707000	0.51288	0.254000	0.18369	GAG	.	.	.	none		0.682	CPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317094.2	NM_001873		C	166300624	A	C	166300624	3	2	106	1	0	0	0	0	1	0	0	0	3801	304	11	5	253	5	CPE	4	166300624	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10	37487028	166300624	24853652	12	6726											
HIGD2A	192286	hgsc.bcm.edu	37	chr5	175816407	175816407	+	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	caacagccagcgctctcagcTcatgatgcgcacccggatcg	9	6	10	16	4	2	1	2	1	1	0	4	2	2	2	2	1	5	3	2	1	1	0			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr5:175816407T>A	ENST00000274787.2	+	2	303	c.230T>A	c.(229-231)cTc>cAc	p.L77H	NOP16_ENST00000510123.1_5'Flank|NOP16_ENST00000389158.5_5'Flank|NOP16_ENST00000509257.1_5'Flank|NOP16_ENST00000507413.1_5'Flank	NM_138820.2	NP_620175.1	Q9BW72	HIG2A_HUMAN	HIG1 hypoxia inducible domain family, member 2A	77	HIG1. {ECO:0000255|PROSITE- ProRule:PRU00836}.				negative regulation of apoptotic process (GO:0043066)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain (GO:0070469)				large_intestine(1)	1	all_cancers(89;0.00522)|Renal(175;0.000269)|Lung NSC(126;0.0105)|all_lung(126;0.0168)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Kidney(146;0.0965)		CGCTCTCAGCTCATGATGCGC	0.647																																					p.L77H		Atlas-SNP	.											.	HIGD2A	7	.	0			c.T230A						PASS	.						67	74	71					5																	175816407		2203	4300	6503	SO:0001583	missense	192286	exon2			CTCAGCTCATGAT	BC007502	CCDS4401.1	5q35.2	2009-03-17	2009-03-17		ENSG00000146066	ENSG00000146066			28311	protein-coding gene	gene with protein product			"HIG1 domain family, member 2A"			12477932	Standard	NM_138820		Approved	MGC2198	uc003meg.3	Q9BW72	OTTHUMG00000130657	ENST00000274787.2:c.230T>A	chr5.hg19:g.175816407T>A	ENSP00000274787:p.Leu77His	135.0	0.0	.		141.0	35.0	.	NM_138820		Missense_Mutation	SNP	ENST00000274787.2	hg19	CCDS4401.1	.	.	.	.	.	.	.	.	.	.	T	32	5.165072	0.94727	.	.	ENSG00000146066	ENST00000274787	.	.	.	5.89	5.89	0.94794	Hypoxia induced protein, domain (2);	0.244211	0.42548	D	0.000699	T	0.63965	0.2556	L	0.33710	1.025	0.80722	D	1	D	0.71674	0.998	D	0.68943	0.961	T	0.57911	-0.7729	9	0.13853	T	0.58	-17.0539	16.3158	0.82923	0.0:0.0:0.0:1.0	.	77	Q9BW72	HIG2A_HUMAN	H	77	.	ENSP00000274787:L77H	L	+	2	0	HIGD2A	175749013	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.646000	0.83445	2.254000	0.74563	0.533000	0.62120	CTC	.	.	.	none		0.647	HIGD2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253147.1	NM_138820		A	175816407	T	A	175816407	3	1	106	1	0	0	0	0	1	0	0	0	7116	1551	54	5	236	5	HIGD2A	5	175816407	Missense_Mutation	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10		175816407	5098853	13	6727											
UNC5A	90249	hgsc.bcm.edu	37	chr5	176300996	176300996	+	Missense_Mutation	SNP	T	T	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	tggccctgaggacgtggcccTctatgtgggcctcatcgccg	4	9	14	14	3	2	1	1	1	1	0	3	2	2	2	4	4	0	0	4	4	1	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr5:176300996T>G	ENST00000329542.4	+	7	1188	c.914T>G	c.(913-915)cTc>cGc	p.L305R	UNC5A_ENST00000261961.3_Missense_Mutation_p.L265R	NM_133369.2	NP_588610.2	Q6ZN44	UNC5A_HUMAN	unc-5 homolog A (C. elegans)	305					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)			GACGTGGCCCTCTATGTGGGC	0.627																																					p.L305R		Atlas-SNP	.											.	UNC5A	76	.	0			c.T914G						PASS	.						96	81	86					5																	176300996		2203	4300	6503	SO:0001583	missense	90249	exon7			TGGCCCTCTATGT	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.914T>G	chr5.hg19:g.176300996T>G	ENSP00000332737:p.Leu305Arg	102.0	0.0	.		113.0	68.0	.	NM_133369	B2RXE6|Q8TF26|Q96GP4	Missense_Mutation	SNP	ENST00000329542.4	hg19	CCDS34299.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.466120	0.84425	.	.	ENSG00000113763	ENST00000329542;ENST00000261961	T;T	0.58506	0.33;0.68	5.3	5.3	0.74995	.	0.000000	0.64402	D	0.000001	T	0.74261	0.3693	M	0.69248	2.105	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.77603	-0.2526	10	0.87932	D	0	-27.0982	15.222	0.73320	0.0:0.0:0.0:1.0	.	265;305	Q6ZN44-3;Q6ZN44	.;UNC5A_HUMAN	R	305;265	ENSP00000332737:L305R;ENSP00000261961:L265R	ENSP00000261961:L265R	L	+	2	0	UNC5A	176233602	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	7.627000	0.83176	2.010000	0.58986	0.402000	0.26972	CTC	.	.	.	none		0.627	UNC5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372166.1	XM_030300		G	176300996	T	G	176300996	3	3	106	1	0	0	0	0	1	0	0	0	17003	1551	54	5	940	5	UNC5A	5	176300996	Missense_Mutation	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10	484589	176300996	4614264	14	6728											
TNFRSF21	27242	hgsc.bcm.edu	37	chr6	47254097	47254097	+	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	cattggccatgggcatggctGactacagtcatggcatttct	8	12	11	10	0	2	1	1	1	1	0	2	1	2	1	1	4	1	3	1	4	1	3			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr6:47254097G>A	ENST00000296861.2	-	2	724	c.331C>T	c.(331-333)Cag>Tag	p.Q111*		NM_014452.3	NP_055267.1	O75509	TNR21_HUMAN	tumor necrosis factor receptor superfamily, member 21	111					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)			GGGCATGGCTGACTACAGTCA	0.522																																					p.Q111X		Atlas-SNP	.											.	TNFRSF21	61	.	0			c.C331T						PASS	.						162	141	149					6																	47254097		2203	4300	6503	SO:0001587	stop_gained	27242	exon2			ATGGCTGACTACA	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.331C>T	chr6.hg19:g.47254097G>A	ENSP00000296861:p.Gln111*	137.0	0.0	.		136.0	61.0	.	NM_014452	B2RDI9|Q0D2P5|Q96D86	Nonsense_Mutation	SNP	ENST00000296861.2	hg19	CCDS4921.1	.	.	.	.	.	.	.	.	.	.	G	39	7.562418	0.98361	.	.	ENSG00000146072	ENST00000296861	.	.	.	5.65	4.72	0.59763	.	0.399599	0.28612	N	0.014733	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	.	8.9938	0.36039	0.0:0.1192:0.6376:0.2432	.	.	.	.	X	111	.	ENSP00000296861:Q111X	Q	-	1	0	TNFRSF21	47362056	0.996000	0.38824	0.998000	0.56505	0.998000	0.95712	2.242000	0.43106	2.826000	0.97356	0.563000	0.77884	CAG	.	.	.	none		0.522	TNFRSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040814.1	NM_014452		A	47254097	G	A	47254097	4	1	106	1	0	0	0	0	0	1	0	0	16307	1299	45	2	1656	2	TNFRSF21	6	47254097	Nonsense_Mutation	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10		47254097	123860970	15	6729											
C6orf204	387119	hgsc.bcm.edu	37	chr6	118790282	118790282	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taggctccttgccctgagcaCgctgattaagaatactacac	11	10	8	12	1	0	3	0	2	0	1	1	3	1	3	2	1	4	3	2	1	5	5	rs371610026		TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr6:118790282C>T	ENST00000368491.3	-	12	2828	c.2207G>A	c.(2206-2208)cGt>cAt	p.R736H	CEP85L_ENST00000368488.5_Missense_Mutation_p.R739H	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like	736						centrosome (GO:0005813)|cytoplasm (GO:0005737)											GCCCTGAGCACGCTGATTAAG	0.378																																					p.R739H		Atlas-SNP	.											.	CEP85L	26	.	0			c.G2216A						PASS	.						93	91	92					6																	118790282		1996	4188	6184	SO:0001583	missense	387119	exon13			TGAGCACGCTGAT	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.2207G>A	chr6.hg19:g.118790282C>T	ENSP00000357477:p.Arg736His	121.0	0.0	.		105.0	22.0	.	NM_001178035	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	Missense_Mutation	SNP	ENST00000368491.3	hg19	CCDS43498.1	.	.	.	.	.	.	.	.	.	.	C	33	5.236142	0.95240	.	.	ENSG00000111860	ENST00000368491;ENST00000368488	T;T	0.12465	2.68;2.68	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.33411	0.0862	M	0.72118	2.19	0.52501	D	0.999954	D	0.89917	1.0	D	0.91635	0.999	T	0.01621	-1.1310	10	0.62326	D	0.03	-8.4553	20.6208	0.99490	0.0:1.0:0.0:0.0	.	736	Q5SZL2	CF204_HUMAN	H	736;739	ENSP00000357477:R736H;ENSP00000357474:R739H	ENSP00000357474:R739H	R	-	2	0	C6orf204	118896975	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.059000	0.64306	2.882000	0.98803	0.655000	0.94253	CGT	.	.	.	weak		0.378	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475		T	118790282	C	T	118790282	3	4	106	1	0	0	0	0	1	0	0	0	2355	536	19	1	218	1	C6orf204	6	118790282	Missense_Mutation	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	71536185	118790282	52324785	16	6730											
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138656258	138656258	+	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	gctgctgcgacaggacaagaGgccccgctcaggctccaccg	8	4	13	16	3	1	1	1	0	0	1	2	3	2	2	4	3	2	4	4	3	1	0			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr6:138656258G>A	ENST00000251691.4	+	33	6441	c.6275G>A	c.(6274-6276)aGg>aAg	p.R2092K		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)		CAGGACAAGAGGCCCCGCTCA	0.647																																					p.R2092K		Atlas-SNP	.											.	KIAA1244	236	.	0			c.G6275A						PASS	.						19	19	19					6																	138656258		2203	4297	6500	SO:0001583	missense	57221	exon33			ACAAGAGGCCCCG	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.6275G>A	chr6.hg19:g.138656258G>A	ENSP00000251691:p.Arg2092Lys	28.0	0.0	.		19.0	8.0	.	NM_020340		Missense_Mutation	SNP	ENST00000251691.4	hg19	CCDS5189.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.215145|5.215145	0.95104|0.95104	.|.	.|.	ENSG00000112379|ENSG00000112379	ENST00000367706|ENST00000251691	.|T	.|0.20598	.|2.06	5.76|5.76	5.76|5.76	0.90799|0.90799	.|.	.|0.156972	.|0.56097	.|D	.|0.000026	.|T	.|0.24812	.|0.0602	L|L	0.32530|0.32530	0.975|0.975	0.51012|0.51012	D|D	0.999903|0.999903	.|D	.|0.58268	.|0.982	.|D	.|0.67548	.|0.952	.|T	.|0.01301	.|-1.1391	.|10	.|0.18276	.|T	.|0.48	.|-24.3666	19.9626|19.9626	0.97256|0.97256	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|2092	.|Q5TH69	.|BIG3_HUMAN	.|K	-1|2092	.|ENSP00000251691:R2092K	.|ENSP00000251691:R2092K	.|R	+|+	.|2	.|0	KIAA1244|KIAA1244	138697951|138697951	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	9.198000|9.198000	0.94994|0.94994	2.723000|2.723000	0.93209|0.93209	0.511000|0.511000	0.50034|0.50034	.|AGG	.	.	.	none		0.647	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		A	138656258	G	A	138656258	3	1	106	1	0	0	0	0	1	0	0	0	8224	1000	35	2	6405	2	KIAA1244	6	138656258	Missense_Mutation	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10	19865976	138656258	32458809	17	6731											
ANLN	54443	hgsc.bcm.edu	37	chr7	36446013	36446013	+	Missense_Mutation	SNP	A	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	ggtaccgcttgtttatccaaAttttcctctgcaagtggagc	8	14	9	10	1	1	0	0	0	1	0	3	1	3	1	3	2	3	4	3	2	4	6			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr7:36446013A>C	ENST00000265748.2	+	4	932	c.711A>C	c.(709-711)aaA>aaC	p.K237N	ANLN_ENST00000396068.2_Missense_Mutation_p.K237N	NM_018685.2	NP_061155.2	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	237	Interaction with F-actin.				hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|regulation of exit from mitosis (GO:0007096)|septin ring assembly (GO:0000921)	actin cytoskeleton (GO:0015629)|actomyosin contractile ring (GO:0005826)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(2)|endometrium(5)|kidney(5)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(2)	45						GTTTATCCAAATTTTCCTCTG	0.428																																					p.K237N		Atlas-SNP	.											.	ANLN	101	.	0			c.A711C						PASS	.						125	118	120					7																	36446013		2203	4300	6503	SO:0001583	missense	54443	exon4			ATCCAAATTTTCC	AF273437	CCDS5447.1, CCDS64628.1	7p15-p14	2013-01-10	2006-08-22		ENSG00000011426	ENSG00000011426		"Pleckstrin homology (PH) domain containing"	14082	protein-coding gene	gene with protein product			"anillin (Drosophila Scraps homolog), actin binding protein", "anillin, actin binding protein (scraps homolog, Drosophila)"			10931866	Standard	NM_001284301		Approved	ANILLIN, Scraps, scra	uc003tff.3	Q9NQW6	OTTHUMG00000023143	ENST00000265748.2:c.711A>C	chr7.hg19:g.36446013A>C	ENSP00000265748:p.Lys237Asn	104.0	0.0	.		89.0	49.0	.	NM_018685	Q5CZ78|Q6NSK5|Q9H8Y4|Q9NVN9|Q9NVP0	Missense_Mutation	SNP	ENST00000265748.2	hg19	CCDS5447.1	.	.	.	.	.	.	.	.	.	.	A	16.86	3.239520	0.58995	.	.	ENSG00000011426	ENST00000265748;ENST00000396068	T;T	0.03004	4.08;4.08	5.51	4.35	0.52113	.	0.142348	0.64402	D	0.000007	T	0.16214	0.0390	M	0.71581	2.175	0.44067	D	0.99681	D;D;D;D	0.89917	1.0;0.998;0.999;0.998	D;D;D;D	0.87578	0.998;0.913;0.973;0.913	T	0.00176	-1.1953	10	0.72032	D	0.01	-27.164	12.9765	0.58540	0.8648:0.1352:0.0:0.0	.	114;237;237;237	B4DSL6;A8K5D9;Q9NQW6-2;Q9NQW6	.;.;.;ANLN_HUMAN	N	237	ENSP00000265748:K237N;ENSP00000379380:K237N	ENSP00000265748:K237N	K	+	3	2	ANLN	36412538	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.978000	0.63799	1.024000	0.39682	0.528000	0.53228	AAA	.	.	.	none		0.428	ANLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218582.3	NM_018685		C	36446013	A	C	36446013	3	2	106	1	0	0	0	0	1	0	0	0	694	98	4	5	725	5	ANLN	7	36446013	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10		36446013	122692650	18	6732											
MGC70857	414919	hgsc.bcm.edu	37	chr8	145753110	145753110	+	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	gagaggaaggggaaagcggcCtcgtagcgcccgctgcggtt	8	5	18	10	5	0	1	0	0	0	1	1	4	0	3	2	5	3	3	2	5	3	2			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr8:145753110C>A	ENST00000524821.1	-	3	482	c.267G>T	c.(265-267)gaG>gaT	p.E89D	C8orf82_ENST00000313465.5_3'UTR|LRRC24_ENST00000529415.2_5'Flank|LRRC24_ENST00000533758.1_5'Flank			Q6P1X6	CH082_HUMAN	chromosome 8 open reading frame 82	89										endometrium(1)|urinary_tract(1)	2						GGAAAGCGGCCTCGTAGCGCC	0.682																																					p.E89D		Atlas-SNP	.											.	C8orf82	7	.	0			c.G267T						PASS	.						38	48	45					8																	145753110		2179	4287	6466	SO:0001583	missense	414919	exon3			AGCGGCCTCGTAG		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.267G>T	chr8.hg19:g.145753110C>A	ENSP00000436621:p.Glu89Asp	8.0	0.0	.		30.0	16.0	.	NM_001001795	Q6GMR2|Q6P2Q7	Missense_Mutation	SNP	ENST00000524821.1	hg19	CCDS34970.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.5|20.5	3.998184|3.998184	0.74818|0.74818	.|.	.|.	ENSG00000213563|ENSG00000213563	ENST00000524821|ENST00000532827	.|.	.|.	.|.	3.97|3.97	2.88|2.88	0.33553|0.33553	.|.	0.238001|.	0.26891|.	U|.	0.021962|.	T|T	0.55752|0.55752	0.1940|0.1940	L|L	0.59436|0.59436	1.845|1.845	0.80722|0.80722	D|D	1|1	D;P|.	0.58268|.	0.982;0.939|.	P;P|.	0.58013|.	0.831;0.554|.	T|T	0.51872|0.51872	-0.8650|-0.8650	9|5	0.44086|.	T|.	0.13|.	-10.1373|-10.1373	3.8003|3.8003	0.08756|0.08756	0.0:0.6552:0.0:0.3448|0.0:0.6552:0.0:0.3448	.|.	81;89|.	Q6P1X6-2;Q6P1X6|.	.;CH082_HUMAN|.	D|C	89|134	.|.	ENSP00000436621:E89D|.	E|G	-|-	3|1	2|0	C8orf82|C8orf82	145723918|145723918	0.969000|0.969000	0.33509|0.33509	1.000000|1.000000	0.80357|0.80357	0.932000|0.932000	0.56968|0.56968	1.066000|1.066000	0.30604|0.30604	0.810000|0.810000	0.34279|0.34279	0.563000|0.563000	0.77884|0.77884	GAG|GGC	.	.	.	none		0.682	C8orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382503.1	NM_001001795		A	145753110	C	A	145753110	3	1	106	1	0	0	0	0	1	0	0	0	9560	680	24	4	387	4	MGC70857	8	145753110	Missense_Mutation	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10		145753110	610912	19	6733											
HK1	3098	hgsc.bcm.edu	37	chr10	71128300	71128300	+	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	tcttctttgcaggccatcctGatcacctggacaaagcgatt	9	12	8	12	1	3	1	1	1	2	0	4	3	4	2	3	2	2	1	3	2	1	3			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr10:71128300G>A	ENST00000359426.6	+	5	608	c.504G>A	c.(502-504)ctG>ctA	p.L168L	HK1_ENST00000404387.2_Silent_p.L172L|HK1_ENST00000360289.2_Silent_p.L156L|HK1_ENST00000494253.1_3'UTR|HK1_ENST00000298649.3_Silent_p.L167L|HK1_ENST00000448642.2_Silent_p.L203L	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	168	Hexokinase type-1 1.|Regulatory.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						AGGCCATCCTGATCACCTGGA	0.547																																					p.L172L		Atlas-SNP	.											.	HK1	170	.	0			c.G516A						PASS	.						97	85	89					10																	71128300		2203	4300	6503	SO:0001819	synonymous_variant	3098	exon8			CATCCTGATCACC	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.504G>A	chr10.hg19:g.71128300G>A		180.0	0.0	.		171.0	68.0	.	NM_033498	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Silent	SNP	ENST00000359426.6	hg19	CCDS7292.1																																																																																			.	.	.	none		0.547	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048429.2	NM_000188		A	71128300	G	A	71128300	2	1	106	1	0	0	0	0	0	0	0	1	7197	1277	45	2		2	HK1	10	71128300	Silent	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10		71128300	64406447	20	6734											
DHDPSL	112817	hgsc.bcm.edu	37	chr10	99358955	99358955	+	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	cgcatgagcagtgcggccctCattcaccactacaccaaggt	10	7	9	15	2	2	1	2	1	0	0	2	1	2	1	3	2	3	2	3	2	2	2			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr10:99358955C>T	ENST00000370646.4	+	3	811	c.450C>T	c.(448-450)ctC>ctT	p.L150L	HOGA1_ENST00000370647.4_Intron|PI4K2A_ENST00000555577.1_Intron|PI4K2A_ENST00000370649.3_Intron	NM_138413.3	NP_612422.2	Q86XE5	HOGA1_HUMAN	4-hydroxy-2-oxoglutarate aldolase 1	150					4-hydroxyproline catabolic process (GO:0019470)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|oxalate metabolic process (GO:0033609)|pyruvate biosynthetic process (GO:0042866)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	4-hydroxy-2-oxoglutarate aldolase activity (GO:0008700)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|prostate(2)|skin(1)|stomach(1)	14						GTGCGGCCCTCATTCACCACT	0.612																																					p.L150L		Atlas-SNP	.											.	HOGA1	25	.	0			c.C450T						PASS	.						52	47	49					10																	99358955		2203	4300	6503	SO:0001819	synonymous_variant	112817	exon3			GGCCCTCATTCAC	BC011916	CCDS7467.1, CCDS44469.1	10q24.1	2010-12-19	2010-12-19	2010-12-19	ENSG00000241935	ENSG00000241935			25155	protein-coding gene	gene with protein product	"dihydrodipicolinate synthetase homolog 2 (E. coli)", "N-acetylneuraminate pyruvate lyase 2 (putative)"	613597	"chromosome 10 open reading frame 65", "dihydrodipicolinate synthase-like, mitochondrial"	C10orf65, DHDPSL		20797690	Standard	NM_001134670		Approved	FLJ37472, DHDPS2, NPL2		Q86XE5	OTTHUMG00000018859	ENST00000370646.4:c.450C>T	chr10.hg19:g.99358955C>T		124.0	0.0	.		88.0	35.0	.	NM_138413	A8K075|Q5T680|Q5T684|Q711P0|Q8N9F2|Q96EV5	Silent	SNP	ENST00000370646.4	hg19	CCDS7467.1																																																																																			.	.	.	none		0.612	HOGA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049726.1	NM_138413		T	99358955	C	T	99358955	2	4	106	1	0	0	0	0	0	0	0	1	4482	813	29	2		2	DHDPSL	10	99358955	Silent	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	28230655	99358955	36175792	21	6735											
SLC18A2	6571	hgsc.bcm.edu	37	chr10	119003520	119003520	+	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	atctgtacagcattaagcatGagaagaatgctacagaaatc	17	9	8	7	0	1	3	0	1	1	3	2	4	1	3	0	0	5	4	0	0	6	3			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr10:119003520G>T	ENST00000298472.5	+	3	303	c.160G>T	c.(160-162)Gag>Tag	p.E54*	SLC18A2_ENST00000497497.1_3'UTR|RP11-501J20.5_ENST00000425264.1_RNA	NM_003054.4	NP_003045.2	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 2	54					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)	CATTAAGCATGAGAAGAATGC	0.478																																					p.E54X		Atlas-SNP	.											SLC18A2,right_lower_lobe,carcinoma,0,1	SLC18A2	58	.	0			c.G160T						PASS	.						70	61	64					10																	119003520		2203	4300	6503	SO:0001587	stop_gained	6571	exon3			AAGCATGAGAAGA	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.160G>T	chr10.hg19:g.119003520G>T	ENSP00000298472:p.Glu54*	88.0	0.0	.		64.0	29.0	.	NM_003054	B2RC96|D3DRC4|Q15876|Q4G147|Q5VW49|Q9H3P6	Nonsense_Mutation	SNP	ENST00000298472.5	hg19	CCDS7599.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.307301	0.81247	.	.	ENSG00000165646	ENST00000298472	.	.	.	5.82	5.82	0.92795	.	0.167513	0.52532	D	0.000078	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	-19.4478	14.7287	0.69365	0.0:0.144:0.856:0.0	.	.	.	.	X	54	.	ENSP00000298472:E54X	E	+	1	0	SLC18A2	118993510	0.976000	0.34144	0.990000	0.47175	0.418000	0.31294	1.665000	0.37449	2.756000	0.94617	0.563000	0.77884	GAG	.	.	.	none		0.478	SLC18A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050563.1	NM_003054		T	119003520	G	T	119003520	4	4	106	1	0	0	0	0	0	1	0	0	14439	1291	45	4	166	4	SLC18A2	10	119003520	Nonsense_Mutation	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10	19644565	119003520	16531227	22	6736											
C11orf46	120534	hgsc.bcm.edu	37	chr11	30352522	30352522	+	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	gatccatgttcagttggagtCcagcttcgtactacaaatga	11	12	9	9	1	1	1	1	1	0	0	4	3	3	2	2	1	3	4	2	1	3	5			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr11:30352522C>T	ENST00000282032.3	+	2	242	c.27C>T	c.(25-27)gtC>gtT	p.V9V		NM_152316.1	NP_689529.1	Q8N8R7	AL14E_HUMAN	ADP-ribosylation factor-like 14 effector protein	9						cytoplasm (GO:0005737)											CAGTTGGAGTCCAGCTTCGTA	0.378																																					p.V9V		Atlas-SNP	.											.	.	.	.	0			c.C27T						PASS	.						76	70	72					11																	30352522		2202	4299	6501	SO:0001819	synonymous_variant	120534	exon2			TGGAGTCCAGCTT	AK096287	CCDS7869.1	11p14.1	2014-09-17	2012-07-09	2012-07-09	ENSG00000152219	ENSG00000152219			26798	protein-coding gene	gene with protein product		612295	"chromosome 11 open reading frame 46"	C11orf46		21458045	Standard	XM_005252792		Approved	FLJ38968, ARF7EP	uc001mso.1	Q8N8R7	OTTHUMG00000166154	ENST00000282032.3:c.27C>T	chr11.hg19:g.30352522C>T		360.0	0.0	.		328.0	142.0	.	NM_152316	Q5HYH9	Silent	SNP	ENST00000282032.3	hg19	CCDS7869.1																																																																																			.	.	.	none		0.378	ARL14EP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388129.1	NM_152316		T	30352522	C	T	30352522	2	4	106	1	0	0	0	0	0	0	0	1	1645	842	30	2		2	C11orf46	11	30352522	Silent	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10		30352522	104653994	23	6737											
CCDC85B	11007	hgsc.bcm.edu	37	chr11	65658488	65658488	+	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	gcagagaaccgtgagctgcgCgacctctgctgcttcctgga	7	8	13	13	3	1	2	0	1	1	1	2	5	2	3	3	1	5	4	3	1	1	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr11:65658488C>T	ENST00000312579.2	+	1	614	c.234C>T	c.(232-234)cgC>cgT	p.R78R	FIBP_ENST00000426652.2_5'Flank|FIBP_ENST00000533045.1_5'Flank|FIBP_ENST00000357519.4_5'Flank|FIBP_ENST00000338369.2_5'Flank	NM_006848.2	NP_006839.2	Q15834	CC85B_HUMAN	coiled-coil domain containing 85B	78					cell differentiation (GO:0030154)|negative regulation of cell growth (GO:0030308)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)									READ - Rectum adenocarcinoma(159;0.166)		GTGAGCTGCGCGACCTCTGCT	0.701																																					p.R78R		Atlas-SNP	.											.	CCDC85B	1	.	0			c.C234T						PASS	.						5	6	5					11																	65658488		2076	4086	6162	SO:0001819	synonymous_variant	11007	exon1			GCTGCGCGACCTC	BC008796	CCDS8120.1	11q13.1	2010-12-24				ENSG00000175602			24926	protein-coding gene	gene with protein product	"hepatitis delta antigen interacting protein A"	605360				8810253, 15644333, 17873903	Standard	NM_006848		Approved	DIPA	uc001ogf.3	Q15834		ENST00000312579.2:c.234C>T	chr11.hg19:g.65658488C>T		0.0	0.0	.		19.0	9.0	.	NM_006848	B2R598|Q96HA0	Silent	SNP	ENST00000312579.2	hg19	CCDS8120.1																																																																																			.	.	.	none		0.701	CCDC85B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391196.1	NM_006848		T	65658488	C	T	65658488	2	4	106	1	0	0	0	0	0	0	0	1	2862	755	27	1		1	CCDC85B	11	65658488	Silent	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	35305966	65658488	69348028	24	6738											
SDHD	6392	hgsc.bcm.edu	37	chr11	111958619	111958619	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagtggtcagacctgctcatAtctcagcatttcttcaggac	9	12	8	12	0	5	1	4	0	2	1	6	2	5	2	1	2	2	2	1	2	1	3	rs397514034		TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr11:111958619A>G	ENST00000375549.3	+	2	226	c.91A>G	c.(91-93)Atc>Gtc	p.I31V	SDHD_ENST00000532699.1_Missense_Mutation_p.I31V|TIMM8B_ENST00000541231.1_5'Flank|SDHD_ENST00000528182.1_Missense_Mutation_p.I31V|TIMM8B_ENST00000507614.1_5'Flank|SDHD_ENST00000526592.1_Missense_Mutation_p.I31V|TIMM8B_ENST00000504148.2_5'Flank|SDHD_ENST00000528021.1_Missense_Mutation_p.I31V|SDHD_ENST00000528048.1_Missense_Mutation_p.I31V|SDHD_ENST00000525291.1_Intron	NM_003002.2	NP_002993.1	O14521	DHSD_HUMAN	succinate dehydrogenase complex, subunit D, integral membrane protein	31					cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|succinate dehydrogenase activity (GO:0000104)|ubiquinone binding (GO:0048039)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)|urinary_tract(1)	9		all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;6.13e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;1.05e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0515)	Hexachlorophene(DB00756)|Succinic acid(DB00139)	ACCTGCTCATATCTCAGCATT	0.473			"Mis, N, F, S"			"paraganglioma, pheochromocytoma"			Familial Paragangliomas;Cowden syndrome;Carney-Stratakis syndrome																												p.T31A		Atlas-SNP	.	yes	Rec		Familial paraganglioma	11	11q23	6392	"succinate dehydrogenase complex, subunit D, integral membrane protein"		O	.	SDHD	19	.	0			c.A91G						PASS	.						178	155	163					11																	111958619		2201	4297	6498	SO:0001583	missense	6392	exon2	Familial Cancer Database	Hereditary Glomus Tumors, Familial Paragangliomas, Hereditary Paragangliomas, type 1-3: PGL1, PGL2, PGL3, incl. Familial Carotid Body Paraganglioma and Sensorineural Hearing Loss;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;Carney-Stratakis dyad, Paraganglioma-Gastric Stromal Sarcoma dyad	GCTCATATCTCAG	AB006202	CCDS31678.1, CCDS60958.1, CCDS60959.1, CCDS60960.1	11q23	2014-09-17				ENSG00000204370		"Mitochondrial respiratory chain complex / Complex II"	10683	protein-coding gene	gene with protein product		602690		PGL, PGL1		9533030, 1301144	Standard	NM_003002		Approved		uc001pmz.4	O14521		ENST00000375549.3:c.91A>G	chr11.hg19:g.111958619A>G	ENSP00000364699:p.Ile31Val	67.0	0.0	.		60.0	26.0	.	NM_003002	A6ND90|B3KQQ8|E9PIC0|E9PIG3|E9PQI9|Q53XW5|Q6IRW2	Missense_Mutation	SNP	ENST00000375549.3	hg19	CCDS31678.1	.	.	.	.	.	.	.	.	.	.	A	0.223	-1.026824	0.02045	.	.	ENSG00000204370	ENST00000375549;ENST00000528182;ENST00000528048;ENST00000528021;ENST00000526592	D;D;T;D;D	0.94497	-3.44;-2.77;-1.48;-2.76;-2.9	4.81	2.78	0.32641	.	0.321128	0.32244	N	0.006373	T	0.77624	0.4158	N	0.01168	-0.975	0.19300	N	0.999977	B	0.02656	0.0	B	0.01281	0.0	T	0.68224	-0.5465	10	0.02654	T	1	-1.6835	6.2353	0.20760	0.2591:0.0:0.7409:0.0	.	31	O14521	DHSD_HUMAN	V	31	ENSP00000364699:I31V;ENSP00000435475:I31V;ENSP00000436217:I31V;ENSP00000432465:I31V;ENSP00000432005:I31V	ENSP00000436395:I31V	I	+	1	0	SDHD	111463829	0.331000	0.24713	0.060000	0.19600	0.783000	0.44284	0.435000	0.21510	0.511000	0.28236	-0.248000	0.11899	ATC	.	.	.	none		0.473	SDHD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392351.1	NM_003002		G	111958619	A	G	111958619	3	3	106	1	0	0	0	0	1	0	0	0	13980	449	16	3	97	3	SDHD	11	111958619	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10	46300131	111958619	23047897	25	6739											
GXYLT1	283464	hgsc.bcm.edu	37	chr12	42481671	42481671	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tattttgtaaatttttccacAgtatgtatgcactgtttttt	9	22	5	5	0	0	0	0	0	0	0	1	0	1	0	1	0	1	5	1	0	5	11	rs202200134		TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr12:42481671A>G	ENST00000398675.3	-	8	1472	c.1240T>C	c.(1240-1242)Tgt>Cgt	p.C414R	GXYLT1_ENST00000280876.6_Missense_Mutation_p.C383R	NM_001099650.1|NM_173601.1	NP_001093120.1|NP_775872.1	Q4G148	GXLT1_HUMAN	glucoside xylosyltransferase 1	414					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|O-glycan processing (GO:0016266)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	UDP-xylosyltransferase activity (GO:0035252)			kidney(2)|large_intestine(4)|liver(3)|lung(8)	17						ATTTTTCCACAGTATGTATGC	0.313																																					p.C414R		Atlas-SNP	.											Q8IXV1_HUMAN,NS,carcinoma,0,2	GXYLT1	47	.	0			c.T1240C						PASS	.						84	75	78					12																	42481671		1807	4070	5877	SO:0001583	missense	283464	exon8			TTCCACAGTATGT	BC015597	CCDS41771.1, CCDS41772.1	12q12	2013-10-11	2009-11-17	2009-11-17	ENSG00000151233	ENSG00000151233		"Glycosyltransferase family 8 domain containing"	27482	protein-coding gene	gene with protein product		613321	"glycosyltransferase 8 domain containing 3"	GLT8D3		19940119	Standard	NM_001099650		Approved	FLJ43151	uc001rms.4	Q4G148	OTTHUMG00000169379	ENST00000398675.3:c.1240T>C	chr12.hg19:g.42481671A>G	ENSP00000381666:p.Cys414Arg	50.0	0.0	.		67.0	5.0	.	NM_173601	B3KWJ2|Q8IXV1|Q96BH4	Missense_Mutation	SNP	ENST00000398675.3	hg19	CCDS41772.1	.	.	.	.	.	.	.	.	.	.	A	16.55	3.153536	0.57259	.	.	ENSG00000151233	ENST00000398675;ENST00000280876	.	.	.	4.9	3.75	0.43078	.	0.000000	0.85682	D	0.000000	T	0.79173	0.4401	M	0.85197	2.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.80804	-0.1219	9	0.87932	D	0	-22.3783	10.8349	0.46681	0.9248:0.0:0.0752:0.0	.	383;414	Q4G148-2;Q4G148	.;GXLT1_HUMAN	R	414;383	.	ENSP00000280876:C383R	C	-	1	0	GXYLT1	40767938	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.672000	0.83956	0.830000	0.34757	-0.254000	0.11334	TGT	.	.	.	weak		0.313	GXYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403778.1	XM_290597		G	42481671	A	G	42481671	3	3	106	1	0	0	0	0	1	0	0	0	6910	188	7	3	86	3	GXYLT1	12	42481671	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10		42481671	91370224	26	6740											
C12orf41	54934	hgsc.bcm.edu	37	chr12	49073468	49073468	+	Frame_Shift_Del	DEL	T	T	-																															gctggcttcactgcgactacTttctggagtctgagacccca																										TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr12:49073468delT	ENST00000420613.2	-	3	447	c.400delA	c.(400-402)agtfs	p.S135fs	KANSL2_ENST00000553086.1_Frame_Shift_Del_p.S135fs|KANSL2_ENST00000357861.3_5'UTR|KANSL2_ENST00000550347.1_Frame_Shift_Del_p.S318fs	NM_017822.3	NP_060292.3	Q9H9L4	KANL2_HUMAN	KAT8 regulatory NSL complex subunit 2	135					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)											CTGCGACTACTTTCTGGAGTC	0.493																																					p.S134fs		Atlas-INDEL	.											.	.	.	.	0			c.401delG						PASS	.						50	47	48					12																	49073468		1915	4135	6050	SO:0001589	frameshift_variant	54934	exon3			.	AK094528	CCDS44869.1	12q13.11	2011-10-31	2011-10-31	2011-10-31	ENSG00000139620	ENSG00000139620			26024	protein-coding gene	gene with protein product		615488	"chromosome 12 open reading frame 41"	C12orf41		12477932	Standard	NM_017822		Approved	FLJ20436, NSL2	uc001rrz.2	Q9H9L4	OTTHUMG00000170392	ENST00000420613.2:c.400delA	chr12.hg19:g.49073468delT	ENSP00000415436:p.Ser135fs	81.0	0.0	0		122.0	64.0	0.52459	NM_017822	Q8N3B5|Q96CV0|Q9NX51	Frame_Shift_Del	DEL	ENST00000420613.2	hg19	CCDS44869.1																																																																																			.	.	.	none		0.493	KANSL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408841.1	NM_017822		-	49073468	T	-	49073468	7	5	106	1	0	1	0	1	0	0	0	0	1689	1609	56	0	1110	0	C12orf41	12	49073468	Frame_Shift_Del	DEL	T	TCGA-B9-A5W9-01A-11D-A28G-10	6591797	49073468	84778427	27	6741											
MLL2	8085	hgsc.bcm.edu	37	chr12	49432161	49432161	+	Missense_Mutation	SNP	A	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	gggcatcaaaatcgtcatccAgctcgggatcctcacagggc	10	7	11	13	2	3	0	3	0	0	0	7	1	5	1	2	3	1	2	2	3	2	0			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr12:49432161A>C	ENST00000301067.7	-	34	8977	c.8978T>G	c.(8977-8979)cTg>cGg	p.L2993R	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2993					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)										ATCGTCATCCAGCTCGGGATC	0.597																																					p.L2993R		Atlas-SNP	.											.	MLL2	1173	.	0			c.T8978G						PASS	.						85	85	85					12																	49432161		2025	4193	6218	SO:0001583	missense	8085	exon34			TCATCCAGCTCGG	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.8978T>G	chr12.hg19:g.49432161A>C	ENSP00000301067:p.Leu2993Arg	153.0	0.0	.		173.0	49.0	.	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	A	10.65	1.408624	0.25378	.	.	ENSG00000167548	ENST00000301067	D	0.83335	-1.71	5.46	5.46	0.80206	.	0.000000	0.30428	N	0.009645	D	0.86053	0.5841	L	0.29908	0.895	0.38041	D	0.935458	D	0.89917	1.0	D	0.75484	0.986	D	0.88960	0.3393	10	0.87932	D	0	.	14.8421	0.70233	1.0:0.0:0.0:0.0	.	2993	O14686	MLL2_HUMAN	R	2993	ENSP00000301067:L2993R	ENSP00000301067:L2993R	L	-	2	0	MLL2	47718428	0.520000	0.26250	0.999000	0.59377	0.717000	0.41224	4.553000	0.60753	2.207000	0.71202	0.533000	0.62120	CTG	.	.	.	none		0.597	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			C	49432161	A	C	49432161	3	2	106	1	0	0	0	0	1	0	0	0	9628	188	7	5	7719	5	MLL2	12	49432161	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10	358693	49432161	84419734	28	6742											
RAB5B	5869	hgsc.bcm.edu	37	chr12	56384574	56384574	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgacctggccaacaaacgtAtggtggagtatgaagtaagg	13	8	13	7	1	0	2	0	2	0	0	0	3	0	3	2	4	2	3	2	4	6	3			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr12:56384574A>G	ENST00000360299.5	+	4	645	c.424A>G	c.(424-426)Atg>Gtg	p.M142V	RAB5B_ENST00000553116.1_Missense_Mutation_p.M142V|RAB5B_ENST00000448789.2_Intron	NM_002868.3	NP_002859.1	P61020	RAB5B_HUMAN	RAB5B, member RAS oncogene family	142					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)			CAACAAACGTATGGTGGAGTA	0.522																																					p.M142V		Atlas-SNP	.											.	RAB5B	22	.	0			c.A424G						PASS	.						126	120	122					12																	56384574		2203	4300	6503	SO:0001583	missense	5869	exon4			AAACGTATGGTGG		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.424A>G	chr12.hg19:g.56384574A>G	ENSP00000353444:p.Met142Val	102.0	0.0	.		151.0	87.0	.	NM_002868	A8K982|B4DKD7|P35239|P35277|Q6PIK9|Q86TH0|Q8IXL2	Missense_Mutation	SNP	ENST00000360299.5	hg19	CCDS8900.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.481|9.481	1.098275|1.098275	0.20552|0.20552	.|.	.|.	ENSG00000111540|ENSG00000111540	ENST00000553116;ENST00000360299|ENST00000549218	T;T|.	0.78364|.	-1.17;-1.17|.	4.81|4.81	3.66|3.66	0.41972|0.41972	Small GTP-binding protein domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.15782|0.15782	0.0380|0.0380	N|N	0.00633|0.00633	-1.31|-1.31	0.80722|0.80722	D|D	1|1	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.06991|0.06991	-1.0796|-1.0796	10|5	0.09843|.	T|.	0.71|.	-6.2164|-6.2164	9.8491|9.8491	0.41046|0.41046	0.9168:0.0:0.0832:0.0|0.9168:0.0:0.0832:0.0	.|.	142;142|.	Q6FI54;P61020|.	.;RAB5B_HUMAN|.	V|C	142|61	ENSP00000450168:M142V;ENSP00000353444:M142V|.	ENSP00000353444:M142V|.	M|Y	+|+	1|2	0|0	RAB5B|RAB5B	54670841|54670841	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	1.607000|1.607000	0.36836|0.36836	0.974000|0.974000	0.38366|0.38366	0.477000|0.477000	0.44152|0.44152	ATG|TAT	.	.	.	none		0.522	RAB5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405396.1			G	56384574	A	G	56384574	3	3	106	1	0	0	0	0	1	0	0	0	12962	449	16	3	434	3	RAB5B	12	56384574	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10	6952413	56384574	77467321	29	6743											
SLC17A8	246213	hgsc.bcm.edu	37	chr12	100811853	100811853	+	Missense_Mutation	SNP	T	T	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	gccccacgctatgccagcatTctcatggggatctcaaacgg	9	8	10	14	2	2	0	2	0	2	0	4	1	2	1	3	3	3	2	3	3	2	2			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr12:100811853T>G	ENST00000323346.5	+	11	1657	c.1344T>G	c.(1342-1344)atT>atG	p.I448M	SLC17A8_ENST00000552697.1_3'UTR|SLC17A8_ENST00000392989.3_Missense_Mutation_p.I398M	NM_001145288.1|NM_139319.2	NP_001138760.1|NP_647480.1	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 8	448					ion transport (GO:0006811)|neurotransmitter transport (GO:0006836)|sensory perception of sound (GO:0007605)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|synaptic vesicle membrane (GO:0030672)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	44						ATGCCAGCATTCTCATGGGGA	0.478																																					p.I448M		Atlas-SNP	.											.	SLC17A8	89	.	0			c.T1344G						PASS	.						177	163	167					12																	100811853		2203	4300	6503	SO:0001583	missense	246213	exon11			CAGCATTCTCATG	AJ459241	CCDS9077.1, CCDS44957.1	12q23.1	2013-07-18	2013-07-18		ENSG00000179520	ENSG00000179520		"Solute carriers"	20151	protein-coding gene	gene with protein product	"vesicular glutamate transporter 3"	607557	"deafness, autosomal dominant 25", "solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 8"	DFNA25		12151341	Standard	NM_139319		Approved	VGLUT3	uc010svi.2	Q8NDX2	OTTHUMG00000170358	ENST00000323346.5:c.1344T>G	chr12.hg19:g.100811853T>G	ENSP00000316909:p.Ile448Met	86.0	0.0	.		103.0	73.0	.	NM_139319	B3KXZ6|B7ZKV4|Q17RQ8	Missense_Mutation	SNP	ENST00000323346.5	hg19	CCDS9077.1	.	.	.	.	.	.	.	.	.	.	T	16.94	3.261452	0.59431	.	.	ENSG00000179520	ENST00000323346;ENST00000392989	T;T	0.55588	0.51;0.51	5.55	1.98	0.26296	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.73636	0.3612	M	0.90542	3.125	0.58432	D	0.999993	D;D	0.89917	0.999;1.0	D;D	0.87578	0.987;0.998	T	0.74121	-0.3767	10	0.66056	D	0.02	.	9.7886	0.40692	0.0:0.349:0.0:0.651	.	448;398	Q8NDX2;Q8NDX2-2	VGLU3_HUMAN;.	M	448;398	ENSP00000316909:I448M;ENSP00000376715:I398M	ENSP00000316909:I448M	I	+	3	3	SLC17A8	99335984	0.998000	0.40836	1.000000	0.80357	0.989000	0.77384	0.508000	0.22692	0.164000	0.19529	-0.250000	0.11733	ATT	.	.	.	none		0.478	SLC17A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408673.2	NM_139319		G	100811853	T	G	100811853	3	3	106	1	0	0	0	0	1	0	0	0	14436	1771	62	5	1386	5	SLC17A8	12	100811853	Missense_Mutation	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10	44427279	100811853	33040042	30	6744											
PEBP1	5037	hgsc.bcm.edu	37	chr12	118575948	118575948	+	Missense_Mutation	SNP	A	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	cccagcaggaaggatcccaaAtacaggtgagaggtgagaaa	16	4	13	8	0	0	2	0	2	0	2	1	6	1	4	2	4	2	1	2	4	4	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr12:118575948A>C	ENST00000261313.2	+	2	592	c.240A>C	c.(238-240)aaA>aaC	p.K80N		NM_002567.2	NP_002558.1	P30086	PEBP1_HUMAN	phosphatidylethanolamine binding protein 1	80						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|phosphatidylethanolamine binding (GO:0008429)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|serine-type endopeptidase inhibitor activity (GO:0004867)			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AGGATCCCAAATACAGGTGAG	0.517																																					p.K80N	NSCLC(44;94 1357 12187 49467)	Atlas-SNP	.											.	PEBP1	13	.	0			c.A240C						PASS	.						41	36	38					12																	118575948		2203	4300	6503	SO:0001583	missense	5037	exon2			TCCCAAATACAGG	X85033	CCDS9187.1	12q24	2009-06-16	2006-02-16	2006-02-16	ENSG00000089220	ENSG00000089220			8630	protein-coding gene	gene with protein product	"Raf kinase inhibitory protein", "hippocampal cholinergic neurostimulating peptide"	604591	"prostatic binding protein"	PBP		15782137	Standard	NM_002567		Approved	RKIP, HCNP, PEBP	uc001twu.1	P30086	OTTHUMG00000168860	ENST00000261313.2:c.240A>C	chr12.hg19:g.118575948A>C	ENSP00000261313:p.Lys80Asn	35.0	0.0	.		73.0	24.0	.	NM_002567	B2R4S1	Missense_Mutation	SNP	ENST00000261313.2	hg19	CCDS9187.1	.	.	.	.	.	.	.	.	.	.	A	14.07	2.425675	0.43020	.	.	ENSG00000089220	ENST00000261313;ENST00000418769	T	0.48522	0.81	4.42	0.684	0.18003	Phosphatidylethanolamine-binding, conserved site (1);	0.048518	0.85682	D	0.000000	T	0.37433	0.1003	L	0.60904	1.88	0.54753	D	0.999985	B;B	0.12013	0.005;0.001	B;B	0.23716	0.048;0.046	T	0.08554	-1.0716	10	0.30078	T	0.28	-8.474	4.709	0.12863	0.5104:0.0:0.3477:0.142	.	80;80	B4DRT4;P30086	.;PEBP1_HUMAN	N	80	ENSP00000261313:K80N	ENSP00000261313:K80N	K	+	3	2	PEBP1	117060331	0.829000	0.29322	0.997000	0.53966	0.937000	0.57800	0.050000	0.14120	-0.044000	0.13491	-0.274000	0.10170	AAA	.	.	.	none		0.517	PEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401405.1	NM_002567		C	118575948	A	C	118575948	3	2	106	1	0	0	0	0	1	0	0	0	11720	98	4	5	246	5	PEBP1	12	118575948	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10	17764095	118575948	15275947	31	6745											
KDM2B	84678	hgsc.bcm.edu	37	chr12	121881832	121881833	+	Missense_Mutation	DNP	GC	GC	AA																															tacccgcttgcgtccactcaGctcctggggcttctcgtatt																										TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr12:121881832_121881833GC>AA	ENST00000377071.4	-	16	2505_2506	c.2433_2434GC>TT	c.(2431-2436)gaGCtg>gaTTtg	p.E811D	KDM2B_ENST00000542973.1_Missense_Mutation_p.E179D|KDM2B_ENST00000377069.4_Missense_Mutation_p.E780D|KDM2B_ENST00000536437.1_Intron	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	811					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						CGTCCACTCAGCTCCTGGGGCT	0.649											OREG0022201	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L812L|p.E811D		Atlas-SNP	.											.	KDM2B	218	.	0			c.C2434T|c.G2433T						PASS	.																																			SO:0001583	missense	84678	exon16			CACTCAGCTCCTG|ACTCAGCTCCTGG	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.2433_2434delinsAA	chr12.hg19:g.121881832_121881833delinsAA	ENSP00000366271:p.Glu811Asp	54.0|55.0	0.0	.	1514	52.0|53.0	12.0	.	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Silent|Missense_Mutation	SNP	ENST00000377071.4	hg19	CCDS41850.1																																																																																			.	.	.	none		0.649	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590		AA	121881833	GC	AA	121881832	3	1	106	1	0	0	0	0	1	0	0	0	8132	962	34	2	1660	2	KDM2B	12	121881832	Missense_Mutation	DNP	GC	TCGA-B9-A5W9-01A-11D-A28G-10	3305884	121881832	11970063	32	6746											
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77714983	77714983	+	De_novo_Start_OutOfFrame	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aattcattctgccctaacctTattaggctgaggttcagact	10	14	7	10	0	3	2	2	1	1	1	3	2	3	2	2	2	2	2	2	2	4	6			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr13:77714983T>C	ENST00000360084.5	-	0	7377				MYCBP2_ENST00000407578.2_Missense_Mutation_p.K2467E|MYCBP2_ENST00000544440.2_Missense_Mutation_p.K2429E|MYCBP2_ENST00000357337.6_Missense_Mutation_p.K2429E					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)		GCCCTAACCTTATTAGGCTGA	0.403																																					p.K2467E		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.A7399G						PASS	.						220	222	222					13																	77714983		2203	4300	6503			23077	exon50			TAACCTTATTAGG	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.-327A>G	chr13.hg19:g.77714983T>C		124.0	0.0	.		107.0	6.0	.	NM_015057		Missense_Mutation	SNP	ENST00000360084.5	hg19		.	.	.	.	.	.	.	.	.	.	T	20.4	3.985587	0.74589	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	T;T;T	0.36520	1.26;1.25;1.26	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.56277	0.1974	M	0.61703	1.905	0.80722	D	1	P	0.52842	0.956	D	0.65010	0.931	T	0.59658	-0.7413	10	0.72032	D	0.01	.	15.2435	0.73488	0.0:0.0:0.0:1.0	.	2429	O75592	MYCB2_HUMAN	E	2429;2467;2429	ENSP00000349892:K2429E;ENSP00000384288:K2467E;ENSP00000444596:K2429E	ENSP00000349892:K2429E	K	-	1	0	MYCBP2	76612984	1.000000	0.71417	1.000000	0.80357	0.822000	0.46500	7.642000	0.83385	2.012000	0.59069	0.482000	0.46254	AAG	.	.	.	none		0.403	MYCBP2-202	KNOWN	basic	protein_coding	protein_coding		NM_015057		C	77714983	T	C	77714983	1	2	106	1	0	1	0	0	0	0	0	0	10025	1763	61	3		3	MYCBP2	13	77714983	De_novo_Start_OutOfFrame	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10		77714983	37454895	33	6747											
TM9SF1	10548	hgsc.bcm.edu	37	chr14	24661497	24661519	+	Frame_Shift_Del	DEL	CTGCTGAGTTAATGGCCCCATGA	CTGCTGAGTTAATGGCCCCATGA	-																															cagggcatacaacaagatggCtgctgagttaatggccccat																								rs150862560		TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	CTGCTGAGTTAATGGCCCCATGA	CTGCTGAGTTAATGGCCCCATGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr14:24661497_24661519delCTGCTGAGTTAATGGCCCCATGA	ENST00000261789.4	-	4	1369_1391	c.1011_1033delTCATGGGGCCATTAACTCAGCAG	c.(1009-1035)cgtcatggggccattaactcagcagccfs	p.HGAINSAA338fs	TM9SF1_ENST00000396854.4_Frame_Shift_Del_p.HGAINSAA338fs|TM9SF1_ENST00000530611.1_Frame_Shift_Del_p.HGAINSAA547fs|RP11-468E2.2_ENST00000561419.1_5'Flank|TM9SF1_ENST00000524835.1_Frame_Shift_Del_p.HGAINSAA251fs|TM9SF1_ENST00000556387.1_Frame_Shift_Del_p.HGAINSAA547fs|TM9SF1_ENST00000528669.1_Frame_Shift_Del_p.HGAINSAA338fs	NM_006405.5	NP_006396.2	O15321	TM9S1_HUMAN	transmembrane 9 superfamily member 1	338					autophagy (GO:0006914)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)		p.S343P(1)		NS(1)|breast(4)|endometrium(3)|large_intestine(11)|lung(4)|ovary(1)	24				GBM - Glioblastoma multiforme(265;0.0183)		AACAAGATGGCTGCTGAGTTAATGGCCCCATGACGGTGCACAT	0.538																																					p.338_345del		Atlas-Indel,Pindel	.											.	TM9SF1	58	.	1	Substitution - Missense(1)	large_intestine(1)	c.1012_1034del						PASS	.																																			SO:0001589	frameshift_variant	10548	exon4			.	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.1011_1033delTCATGGGGCCATTAACTCAGCAG	chr14.hg19:g.24661497_24661519delCTGCTGAGTTAATGGCCCCATGA	ENSP00000261789:p.His338fs	253.0	0.0	0		209.0	48.0	0.229665	NM_001014842	D3DS65|Q86SZ6|Q96FI8	Frame_Shift_Del	DEL	ENST00000261789.4	hg19	CCDS9617.1																																																																																			.	.	.	none		0.538	TM9SF1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073136.2	NM_006405		-	24661519	CTGCTGAGTTAATGGCCCCATGA	-	24661497	7	5	106	1	0	1	0	1	0	0	0	0	15989	797	28	0	842	0	TM9SF1	14	24661497	Frame_Shift_Del	DEL	CTGCTGAGTTAATGGCCCCATGA	TCGA-B9-A5W9-01A-11D-A28G-10		24661497	82688043	34	6748											
SPTB	6710	hgsc.bcm.edu	37	chr14	65253201	65253201	+	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	ggcactgagcgagggtgtggCtgcggctctcccacatcctg	5	8	15	13	2	1	1	0	1	1	0	3	2	2	1	2	4	2	3	2	4	0	0			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr14:65253201C>T	ENST00000389721.5	-	15	3514	c.3482G>A	c.(3481-3483)aGc>aAc	p.S1161N	SPTB_ENST00000556626.1_Missense_Mutation_p.S1161N|SPTB_ENST00000542895.1_Missense_Mutation_p.S1161N|SPTB_ENST00000389720.3_Missense_Mutation_p.S1161N|SPTB_ENST00000389722.3_Missense_Mutation_p.S1161N	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1161					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)		GAGGGTGTGGCTGCGGCTCTC	0.612																																					p.S1161N		Atlas-SNP	.											.	SPTB	378	.	0			c.G3482A						PASS	.						58	59	59					14																	65253201		2203	4300	6503	SO:0001583	missense	6710	exon15			GTGTGGCTGCGGC		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.3482G>A	chr14.hg19:g.65253201C>T	ENSP00000374371:p.Ser1161Asn	98.0	0.0	.		80.0	30.0	.	NM_001024858	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	hg19	CCDS32100.1	.	.	.	.	.	.	.	.	.	.	C	12.15	1.851576	0.32699	.	.	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T	0.50277	0.75;0.75;0.75;0.75;0.75	4.78	3.86	0.44501	.	0.412688	0.27549	N	0.018876	T	0.18551	0.0445	N	0.01352	-0.895	0.22096	N	0.999368	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.13176	-1.0519	10	0.59425	D	0.04	.	6.711	0.23276	0.0:0.7003:0.0:0.2997	.	1161;1165	P11277;Q59FP5	SPTB1_HUMAN;.	N	1165;1161;1161;1161;1161;1161	ENSP00000374372:S1161N;ENSP00000451752:S1161N;ENSP00000374371:S1161N;ENSP00000443882:S1161N;ENSP00000374370:S1161N	ENSP00000374370:S1161N	S	-	2	0	SPTB	64322954	0.429000	0.25530	0.066000	0.19879	0.879000	0.50718	3.324000	0.52022	1.079000	0.41038	0.549000	0.68633	AGC	.	.	.	none		0.612	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1			T	65253201	C	T	65253201	3	4	106	1	0	0	0	0	1	0	0	0	15130	797	28	2	3657	2	SPTB	14	65253201	Missense_Mutation	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	40591704	65253201	42096339	35	6749											
SPTBN5	51332	hgsc.bcm.edu	37	chr15	42166194	42166194	+	Missense_Mutation	SNP	A	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	ccaggctccgcccagaactcAgcacccgttgcacctgcccc	7	5	8	21	2	1	1	1	0	0	1	2	1	2	1	7	1	4	4	7	1	1	1	rs199969875		TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr15:42166194A>C	ENST00000320955.6	-	25	4966	c.4739T>G	c.(4738-4740)cTg>cGg	p.L1580R		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1580					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)		CCCAGAACTCAGCACCCGTTG	0.652																																					p.L1545R		Atlas-SNP	.											.	SPTBN5	171	.	0			c.T4634G						PASS	.						26	31	29					15																	42166194		2009	4188	6197	SO:0001583	missense	51332	exon25			GAACTCAGCACCC	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.4739T>G	chr15.hg19:g.42166194A>C	ENSP00000317790:p.Leu1580Arg	29.0	0.0	.		26.0	10.0	.	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	hg19		.	.	.	.	.	.	.	.	.	.	.	16.38	3.107363	0.56291	.	.	ENSG00000137877	ENST00000320955	T	0.51071	0.72	5.26	5.26	0.73747	.	0.111511	0.39909	N	0.001223	T	0.71484	0.3345	M	0.84683	2.71	0.34983	D	0.754273	D	0.89917	1.0	D	0.87578	0.998	T	0.83027	-0.0164	10	0.87932	D	0	.	14.1772	0.65549	1.0:0.0:0.0:0.0	.	1580	Q9NRC6	SPTN5_HUMAN	R	1580	ENSP00000317790:L1580R	ENSP00000317790:L1580R	L	-	2	0	SPTBN5	39953486	1.000000	0.71417	0.240000	0.24138	0.217000	0.24651	6.813000	0.75231	1.979000	0.57680	0.529000	0.55759	CTG	.	.	.	alt		0.652	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		C	42166194	A	C	42166194	3	2	106	1	0	0	0	0	1	0	0	0	15134	188	7	5	6461	5	SPTBN5	15	42166194	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10		42166194	60365198	36	6750											
GPR97	222487	hgsc.bcm.edu	37	chr16	57713092	57713092	+	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	gatctcccctttcacagggcCcccggctcggcctgggagat	5	8	12	16	2	2	1	1	0	1	1	4	3	2	1	5	4	0	1	5	4	0	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr16:57713092C>T	ENST00000333493.4	+	5	657	c.496C>T	c.(496-498)Ccc>Tcc	p.P166S	GPR97_ENST00000327655.6_5'UTR|GPR97_ENST00000450388.3_Missense_Mutation_p.P46S|RP11-405F3.4_ENST00000563062.1_RNA	NM_170776.4	NP_740746.4	Q86Y34	GPR97_HUMAN	G protein-coupled receptor 97	166					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TTCACAGGGCCCCCGGCTCGG	0.632																																					p.P166S		Atlas-SNP	.											.	GPR97	74	.	0			c.C496T						PASS	.						60	61	61					16																	57713092		2198	4300	6498	SO:0001583	missense	222487	exon5			CAGGGCCCCCGGC	AY140959	CCDS10786.1	16q13	2014-08-08			ENSG00000182885	ENSG00000182885		"-", "GPCR / Class B : Orphans"	13728	protein-coding gene	gene with protein product						12435584, 222487	Standard	NM_170776		Approved	Pb99, PGR26	uc002emh.3	Q86Y34	OTTHUMG00000133458	ENST00000333493.4:c.496C>T	chr16.hg19:g.57713092C>T	ENSP00000332900:p.Pro166Ser	68.0	0.0	.		90.0	25.0	.	NM_170776	Q6ZMF4|Q86SL9|Q8IZF1	Missense_Mutation	SNP	ENST00000333493.4	hg19	CCDS10786.1	.	.	.	.	.	.	.	.	.	.	C	6.016	0.371299	0.11409	.	.	ENSG00000182885	ENST00000333493;ENST00000450388	T;T	0.28454	1.61;1.7	4.3	-0.0636	0.13776	.	0.491076	0.17461	N	0.173450	T	0.19248	0.0462	L	0.38838	1.175	0.34925	D	0.748776	B	0.21071	0.051	B	0.18561	0.022	T	0.09015	-1.0694	10	0.52906	T	0.07	.	4.2438	0.10662	0.0:0.5249:0.1709:0.3042	.	166	Q86Y34	GPR97_HUMAN	S	166;46	ENSP00000332900:P166S;ENSP00000404803:P46S	ENSP00000332900:P166S	P	+	1	0	GPR97	56270593	0.001000	0.12720	0.670000	0.29842	0.078000	0.17371	-0.024000	0.12435	0.104000	0.17725	0.313000	0.20887	CCC	.	.	.	none		0.632	GPR97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257333.2	NM_170776		T	57713092	C	T	57713092	3	4	106	1	0	0	0	0	1	0	0	0	6727	623	22	2	514	2	GPR97	16	57713092	Missense_Mutation	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10		57713092	32641661	37	6751											
ZFHX3	463	hgsc.bcm.edu	37	chr16	72821093	72821093	+	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	aaggtgtccgttcctacactGgtcagaccactgtccttggg	7	11	11	12	1	1	1	1	0	0	1	4	1	4	1	4	3	1	1	4	3	2	3			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr16:72821093G>T	ENST00000268489.5	-	10	11754	c.11082C>A	c.(11080-11082)acC>acA	p.T3694T	AC004943.1_ENST00000584072.1_RNA|ZFHX3_ENST00000397992.5_Silent_p.T2780T|RP5-991G20.4_ENST00000569195.1_RNA|RP5-991G20.1_ENST00000563328.2_RNA	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	3694					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)				TTCCTACACTGGTCAGACCAC	0.463																																					p.T3694T		Atlas-SNP	.											.	ZFHX3	404	.	0			c.C11082A						PASS	.						161	173	169					16																	72821093		2198	4300	6498	SO:0001819	synonymous_variant	463	exon10			TACACTGGTCAGA	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.11082C>A	chr16.hg19:g.72821093G>T		112.0	0.0	.		127.0	37.0	.	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	hg19	CCDS10908.1																																																																																			.	.	.	none		0.463	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		T	72821093	G	T	72821093	2	4	106	1	0	0	0	0	0	0	0	1	17646	1335	47	4		4	ZFHX3	16	72821093	Silent	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10	15108001	72821093	17533660	38	6752											
GALNS	2588	hgsc.bcm.edu	37	chr16	88889080	88889080	+	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	tcttccagattgtgagttgtGacccctgaaacgttctgccc	7	13	9	12	1	2	4	0	3	2	1	3	4	3	4	4	0	2	2	4	0	1	4			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr16:88889080G>A	ENST00000268695.5	-	12	1369	c.1281C>T	c.(1279-1281)gtC>gtT	p.V427V	GALNS_ENST00000542788.1_Silent_p.V352V	NM_000512.4	NP_000503.1	P34059	GALNS_HUMAN	galactosamine (N-acetyl)-6-sulfatase	427					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)		TGTGAGTTGTGACCCCTGAAA	0.622																																					p.V427V	GBM(129;1929 2344 25209 33204)	Atlas-SNP	.											.	GALNS	37	.	0			c.C1281T						PASS	.						105	88	94					16																	88889080		2196	4299	6495	SO:0001819	synonymous_variant	2588	exon12			AGTTGTGACCCCT	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.1281C>T	chr16.hg19:g.88889080G>A		205.0	0.0	.		251.0	75.0	.	NM_000512	Q86VK3	Silent	SNP	ENST00000268695.5	hg19	CCDS10970.1																																																																																			.	.	.	none		0.622	GALNS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269543.1			A	88889080	G	A	88889080	2	1	106	1	0	0	0	0	0	0	0	1	6213	1277	45	2		2	GALNS	16	88889080	Silent	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10	16067987	88889080	1465673	39	6753											
MYO15A	51168	hgsc.bcm.edu	37	chr17	18058522	18058522	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgggaggtctacttctccCgcatcttccccgccacggtg	4	10	10	17	3	3	0	0	0	3	0	5	1	4	1	5	3	1	1	5	3	1	3			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr17:18058522C>T	ENST00000205890.5	+	46	8661	c.8323C>T	c.(8323-8325)Cgc>Tgc	p.R2775C	MYO15A_ENST00000585180.1_Missense_Mutation_p.R39C|MYO15A_ENST00000418233.3_Missense_Mutation_p.R39C	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2775	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)					CTACTTCTCCCGCATCTTCCC	0.607																																					p.R2775C		Atlas-SNP	.											.	MYO15A	268	.	0			c.C8323T						PASS	.						39	48	45					17																	18058522		2100	4218	6318	SO:0001583	missense	51168	exon45			TTCTCCCGCATCT	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.8323C>T	chr17.hg19:g.18058522C>T	ENSP00000205890:p.Arg2775Cys	65.0	0.0	.		108.0	12.0	.	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	hg19	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	C	15.66	2.898121	0.52227	.	.	ENSG00000091536	ENST00000205890	D	0.93488	-3.23	5.1	5.1	0.69264	.	.	.	.	.	D	0.97164	0.9073	M	0.87827	2.91	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.992;0.999	D	0.97931	1.0320	9	0.87932	D	0	.	18.5096	0.90911	0.0:1.0:0.0:0.0	.	39;2775	B4DFC7;Q9UKN7	.;MYO15_HUMAN	C	2775	ENSP00000205890:R2775C	ENSP00000205890:R2775C	R	+	1	0	MYO15A	17999247	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	7.086000	0.76885	2.363000	0.80096	0.561000	0.74099	CGC	.	.	.	none		0.607	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		T	18058522	C	T	18058522	3	4	106	1	0	0	0	0	1	0	0	0	10070	652	23	1	8497	1	MYO15A	17	18058522	Missense_Mutation	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10		18058522	63136688	40	6754											
AATF	26574	hgsc.bcm.edu	37	chr17	35345926	35345926	+	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	gaggactatcccagcttcatGgcaaagcgctttgccgactt	9	10	10	12	2	1	0	1	0	0	0	2	3	2	1	2	2	3	3	2	2	2	4			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr17:35345926G>A	ENST00000225402.5	+	6	1307	c.1056G>A	c.(1054-1056)atG>atA	p.M352I		NM_012138.3	NP_036270.1	Q9NY61	AATF_HUMAN	apoptosis antagonizing transcription factor	352	RB1 binding.				apoptotic signaling pathway (GO:0097190)|cell adhesion (GO:0007155)|cellular response to DNA damage stimulus (GO:0006974)|embryonic cleavage (GO:0040016)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of apoptotic process (GO:0043066)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of superoxide anion generation (GO:0032929)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mitotic cell cycle (GO:0007346)|ribosome biogenesis (GO:0042254)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	leucine zipper domain binding (GO:0043522)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(1)|large_intestine(4)|lung(7)|ovary(2)|skin(2)	18		Breast(25;0.00607)				CCAGCTTCATGGCAAAGCGCT	0.493																																					p.M352I	NSCLC(49;901 1159 19183 41572 46244)	Atlas-SNP	.											.	AATF	36	.	0			c.G1056A						PASS	.						97	90	93					17																	35345926		2203	4300	6503	SO:0001583	missense	26574	exon6			CTTCATGGCAAAG	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.1056G>A	chr17.hg19:g.35345926G>A	ENSP00000225402:p.Met352Ile	82.0	0.0	.		157.0	84.0	.	NM_012138	A6NCJ6|B3KQ26|Q9P0A4|Q9UNX5	Missense_Mutation	SNP	ENST00000225402.5	hg19	CCDS32632.1	.	.	.	.	.	.	.	.	.	.	G	11.78	1.740923	0.30865	.	.	ENSG00000108270	ENST00000225402	.	.	.	5.58	4.62	0.57501	.	0.033193	0.85682	D	0.000000	T	0.43722	0.1260	L	0.33339	1.005	0.52501	D	0.999955	B	0.12013	0.005	B	0.17098	0.017	T	0.26224	-1.0109	9	0.15066	T	0.55	-8.411	11.471	0.50268	0.1564:0.0:0.8436:0.0	.	352	Q9NY61	AATF_HUMAN	I	352	.	ENSP00000225402:M352I	M	+	3	0	AATF	32420039	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.264000	0.72527	1.370000	0.46153	0.561000	0.74099	ATG	.	.	.	none		0.493	AATF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451543.1	NM_012138		A	35345926	G	A	35345926	3	1	106	1	0	0	0	0	1	0	0	0	25	1348	47	2	1078	2	AATF	17	35345926	Missense_Mutation	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10	17287404	35345926	45849284	41	6755											
SCPEP1	59342	hgsc.bcm.edu	37	chr17	55058480	55058480	+	Missense_Mutation	SNP	A	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	cccacagaggagggcaaggaAgtatgggattatgtgacggt	12	7	16	6	1	0	2	0	1	0	1	0	5	0	5	1	5	0	2	1	5	4	2			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr17:55058480A>C	ENST00000262288.3	+	2	169	c.114A>C	c.(112-114)gaA>gaC	p.E38D	RP5-1107A17.4_ENST00000572877.1_RNA|SCPEP1_ENST00000571898.1_3'UTR	NM_021626.2	NP_067639.1	Q9HB40	RISC_HUMAN	serine carboxypeptidase 1	38					negative regulation of blood pressure (GO:0045776)|positive regulation of vasodilation (GO:0045909)|retinoic acid metabolic process (GO:0042573)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	serine-type carboxypeptidase activity (GO:0004185)			endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|skin(2)	14	Breast(9;2.86e-08)					AGGGCAAGGAAGTATGGGATT	0.493																																					p.E38D		Atlas-SNP	.											.	SCPEP1	35	.	0			c.A114C						PASS	.						128	105	113					17																	55058480		2203	4300	6503	SO:0001583	missense	59342	exon2			CAAGGAAGTATGG	AF282618	CCDS11593.1	17q22	2012-09-20			ENSG00000121064	ENSG00000121064			29507	protein-coding gene	gene with protein product	"retinoid inducible serine carboxypeptidase"					11447226, 12975309	Standard	NM_021626		Approved	RISC	uc002iuv.4	Q9HB40	OTTHUMG00000178129	ENST00000262288.3:c.114A>C	chr17.hg19:g.55058480A>C	ENSP00000262288:p.Glu38Asp	235.0	1.0	.		338.0	161.0	.	NM_021626	Q96A94|Q9H3F0	Missense_Mutation	SNP	ENST00000262288.3	hg19	CCDS11593.1	.	.	.	.	.	.	.	.	.	.	A	16.33	3.093414	0.56075	.	.	ENSG00000121064	ENST00000262288	D	0.85955	-2.05	5.84	3.64	0.41730	.	0.000000	0.85682	D	0.000000	D	0.91331	0.7266	M	0.89414	3.03	0.46954	D	0.99926	D	0.65815	0.995	D	0.70716	0.97	D	0.90110	0.4191	10	0.66056	D	0.02	-12.7064	5.5755	0.17220	0.71:0.0:0.29:0.0	.	38	Q9HB40	RISC_HUMAN	D	38	ENSP00000262288:E38D	ENSP00000262288:E38D	E	+	3	2	SCPEP1	52413479	0.816000	0.29132	0.975000	0.42487	0.312000	0.27988	0.445000	0.21677	1.036000	0.39998	0.533000	0.62120	GAA	.	.	.	none		0.493	SCPEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440622.1	NM_021626		C	55058480	A	C	55058480	3	2	106	1	0	0	0	0	1	0	0	0	13948	69	3	5	120	5	SCPEP1	17	55058480	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10	19712554	55058480	26136730	42	6756											
PODNL1	79883	hgsc.bcm.edu	37	chr19	14044012	14044012	+	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	ggctggaggcacgcggtccaGcccattgccatagaggtgca	8	6	15	12	2	0	1	0	0	0	1	1	2	1	2	3	5	3	3	3	5	1	2	rs79400921	byFrequency	TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr19:14044012G>A	ENST00000339560.5	-	8	1318	c.1045C>T	c.(1045-1047)Ctg>Ttg	p.L349L	PODNL1_ENST00000538371.2_Silent_p.L347L|PODNL1_ENST00000538517.2_Silent_p.L258L|PODNL1_ENST00000254320.3_Silent_p.L267L	NM_024825.3	NP_079101.3	Q6PEZ8	PONL1_HUMAN	podocan-like 1	349	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)			ACGCGGTCCAGCCCATTGCCA	0.726													G|||	17	0.00339457	0.0129	0	5008	,	,		12628	0		0	False		,,,				2504	0				p.L349L		Atlas-SNP	.											.	PODNL1	27	.	0			c.C1045T						PASS	.	G	,,	25,3857		0,25,1916	4	6	6		1039,772,1045	2.1	0.7	19	dbSNP_131	6	1,7563		0,1,3781	no	coding-synonymous,coding-synonymous,coding-synonymous	PODNL1	NM_001146254.1,NM_001146255.1,NM_024825.3	,,	0,26,5697	AA,AG,GG		0.0132,0.644,0.2272	,,	347/511,258/422,349/513	14044012	26,11420	1941	3782	5723	SO:0001819	synonymous_variant	79883	exon8			GGTCCAGCCCATT	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.1045C>T	chr19.hg19:g.14044012G>A		0.0	0.0	.		24.0	9.0	.	NM_024825	B7Z564|Q9H5G9	Silent	SNP	ENST00000339560.5	hg19	CCDS12300.1																																																																																			.	.	.	weak		0.726	PODNL1-003	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457967.1	NM_024825		A	14044012	G	A	14044012	2	1	106	1	0	0	0	0	0	0	0	1	12186	962	34	2		2	PODNL1	19	14044012	Silent	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10		14044012	45084971	43	6757											
CYP4F3	4051	hgsc.bcm.edu	37	chr19	15760902	15760902	+	Missense_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	cgtcatccaggagcggcgccGcaccctccctagccagggtg	6	5	13	17	4	1	0	1	0	0	0	3	1	3	1	5	3	2	1	5	3	1	1	rs113330239		TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr19:15760902G>A	ENST00000221307.8	+	7	874	c.827G>A	c.(826-828)cGc>cAc	p.R276H	CYP4F3_ENST00000585846.1_Missense_Mutation_p.R276H|CYP4F3_ENST00000591058.1_Missense_Mutation_p.R276H|CYP4F3_ENST00000586182.2_Missense_Mutation_p.R276H	NM_000896.2	NP_000887.2	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 3	276					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)	p.R276H(1)		endometrium(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|stomach(1)	34						GAGCGGCGCCGCACCCTCCCT	0.577													.|||	1	0.000199681	8e-04	0	5008	,	,		18604	0		0	False		,,,				2504	0				p.R276H		Atlas-SNP	.											CYP4F3,colon,NS,0,1	CYP4F3	69	.	1	Substitution - Missense(1)	large_intestine(1)	c.G827A						PASS	.						106	96	99					19																	15760902		2203	4300	6503	SO:0001583	missense	4051	exon7			GGCGCCGCACCCT	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.827G>A	chr19.hg19:g.15760902G>A	ENSP00000221307:p.Arg276His	254.0	2.0	.		202.0	91.0	.	NM_001199209	B7Z8Z3|O60634|Q5U740	Missense_Mutation	SNP	ENST00000221307.8	hg19	CCDS12332.1	.	.	.	.	.	.	.	.	.	.	.	14.12	2.441442	0.43326	.	.	ENSG00000186529	ENST00000538865;ENST00000221307	T	0.69561	-0.41	3.99	-0.166	0.13351	.	0.712480	0.12645	U	0.450940	T	0.63117	0.2484	M	0.77406	2.37	0.09310	N	1	B;B	0.13145	0.007;0.001	B;B	0.19148	0.015;0.024	T	0.58188	-0.7680	10	0.52906	T	0.07	.	7.3165	0.26503	0.4513:0.0:0.5487:0.0	.	276;276	B7Z8Z3;Q08477	.;CP4F3_HUMAN	H	203;276	ENSP00000221307:R276H	ENSP00000221307:R276H	R	+	2	0	CYP4F3	15621902	0.000000	0.05858	0.009000	0.14445	0.817000	0.46193	-1.012000	0.03649	0.173000	0.19788	0.313000	0.20887	CGC	.	G|0.500;A|0.500	0.500	weak		0.577	CYP4F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460819.3	NM_000896		A	15760902	G	A	15760902	3	1	106	1	0	0	0	0	1	0	0	0	4192	1087	38	1	849	1	CYP4F3	19	15760902	Missense_Mutation	SNP	G	TCGA-B9-A5W9-01A-11D-A28G-10	1716890	15760902	43368081	44	6758											
LRRC25	126364	hgsc.bcm.edu	37	chr19	18507658	18507658	+	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	tgaaattcaggcacgtggcaCtgaactccgcgttccagtcc	9	9	10	13	3	1	2	1	2	0	0	4	2	4	2	3	2	1	3	3	2	2	2			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr19:18507658C>G	ENST00000339007.3	-	1	769	c.116G>C	c.(115-117)aGt>aCt	p.S39T	LRRC25_ENST00000595840.1_Missense_Mutation_p.S39T	NM_145256.2	NP_660299.2	Q8N386	LRC25_HUMAN	leucine rich repeat containing 25	39						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(3)|skin(1)	8						GCACGTGGCACTGAACTCCGC	0.622																																					p.S39T		Atlas-SNP	.											.	LRRC25	16	.	0			c.G116C						PASS	.						76	57	64					19																	18507658		2203	4300	6503	SO:0001583	missense	126364	exon1			GTGGCACTGAACT	AK095435	CCDS12377.1	19p13.11	2013-09-20			ENSG00000175489	ENSG00000175489			29806	protein-coding gene	gene with protein product		607518				12384430	Standard	NM_145256		Approved	MAPA, FLJ38116	uc002niw.3	Q8N386	OTTHUMG00000183361	ENST00000339007.3:c.116G>C	chr19.hg19:g.18507658C>G	ENSP00000340983:p.Ser39Thr	256.0	1.0	.		195.0	85.0	.	NM_145256	Q6IQ00|Q8N9A5	Missense_Mutation	SNP	ENST00000339007.3	hg19	CCDS12377.1	.	.	.	.	.	.	.	.	.	.	C	0.518	-0.863567	0.02590	.	.	ENSG00000175489	ENST00000339007	T	0.31510	1.49	4.4	-4.55	0.03441	.	2.202890	0.02302	N	0.071289	T	0.10680	0.0261	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.20739	-1.0266	10	0.02654	T	1	2.5899	1.3392	0.02151	0.2155:0.2315:0.3888:0.1642	.	39	Q8N386	LRC25_HUMAN	T	39	ENSP00000340983:S39T	ENSP00000340983:S39T	S	-	2	0	LRRC25	18368658	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.684000	0.05173	-0.454000	0.07066	-0.367000	0.07326	AGT	.	.	.	none		0.622	LRRC25-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466342.1	NM_145256		G	18507658	C	G	18507658	3	3	106	1	0	0	0	0	1	0	0	0	8987	565	20	4	809	4	LRRC25	19	18507658	Missense_Mutation	SNP	C	TCGA-B9-A5W9-01A-11D-A28G-10	2746756	18507658	40621325	45	6759											
ZNF14	7561	hgsc.bcm.edu	37	chr19	19822257	19822257	+	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	ttgcattcataaggtttctcTccagtgtgagacctttcatg	8	16	8	9	0	3	1	2	1	1	1	5	2	4	1	2	1	1	2	2	1	1	5			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr19:19822257T>G	ENST00000344099.3	-	4	1971	c.1833A>C	c.(1831-1833)ggA>ggC	p.G611G		NM_021030.2	NP_066358.2	P17017	ZNF14_HUMAN	zinc finger protein 14	611					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(2)|endometrium(1)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32		Renal(1328;0.0474)				AAGGTTTCTCTCCAGTGTGAG	0.408																																					p.G611G		Atlas-SNP	.											.	ZNF14	89	.	0			c.A1833C						PASS	.						83	81	82					19																	19822257		2203	4300	6503	SO:0001819	synonymous_variant	7561	exon4			TTTCTCTCCAGTG	AA286756	CCDS12409.1	19p13.11	2013-01-08	2006-05-10					"Zinc fingers, C2H2-type", "-"	12924	protein-coding gene	gene with protein product		194556	"zinc finger protein 14 (KOX 6)"				Standard	NM_021030		Approved	KOX6, GIOT-4	uc002nnk.1	P17017		ENST00000344099.3:c.1833A>C	chr19.hg19:g.19822257T>G		64.0	0.0	.		84.0	38.0	.	NM_021030	B9EGA4|Q9ULZ5	Silent	SNP	ENST00000344099.3	hg19	CCDS12409.1																																																																																			.	.	.	none		0.408	ZNF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460775.1	NM_021030		G	19822257	T	G	19822257	2	3	106	1	0	0	0	0	0	0	0	1	17740	1538	54	5		5	ZNF14	19	19822257	Silent	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10	1314599	19822257	39306726	46	6760											
LIN37	126393	hgsc.bcm.edu	37	chr19	36243734	36243734	+	IGR	DEL	G	G	-																															catcgcagccactggcaaaaGgtaaggtggcagggtcccag																										TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr19:36243734delG	ENST00000592984.1	-	0	1634				AC002398.12_ENST00000587767.1_RNA|LIN37_ENST00000301159.9_Splice_Site_p.R64fs|AC002398.9_ENST00000591613.2_3'UTR|AC002398.11_ENST00000591091.1_RNA			O14558	HSPB6_HUMAN	heat shock protein, alpha-crystallin-related, B6						regulation of muscle contraction (GO:0006937)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)|structural constituent of eye lens (GO:0005212)			lung(1)	1	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			ACTGGCAAAAGGTAAGGTGGC	0.627																																					p.R64fs		Atlas-Indel,Pindel	.											.	LIN37	17	.	0			c.190delA						PASS	.						27	33	31					19																	36243734		2060	4204	6264	SO:0001628	intergenic_variant	55957	exon4			.	AJ278121	CCDS12475.1	19q13.13	2014-06-12			ENSG00000004776	ENSG00000004776		"Heat shock proteins / HSPB"	26511	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 91"	610695				12820654, 14717697	Standard	NM_144617		Approved	FLJ32389, Hsp20, PPP1R91	uc002obn.2	O14558	OTTHUMG00000048122		chr19.hg19:g.36243734delG		83.0	0.0	0		73.0	28.0	0.383562	NM_019104	O14551|Q6NVI3|Q96MG9	Frame_Shift_Del	DEL	ENST00000592984.1	hg19	CCDS12475.1																																																																																			.	.	.	none		0.627	HSPB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109498.3	NM_144617		-	36243734	G	-	36243734	6	5	106	0	1	1	0	1	0	0	0	0	8814	1014	35	0		0	LIN37	19	36243734	IGR	DEL	G	TCGA-B9-A5W9-01A-11D-A28G-10	16421477	36243734	22885249	47	6761											
ZNF835	90485	hgsc.bcm.edu	37	chr19	57175950	57175950	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgctgggtcaggtgcgtgAcgcgcgtgaaggccttgccg	4	8	19	10	5	1	2	1	2	0	0	1	2	1	2	2	4	3	1	2	4	1	1	rs369897881		TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr19:57175950A>G	ENST00000537055.2	-	2	848	c.617T>C	c.(616-618)gTc>gCc	p.V206A		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	206					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						CAGGTGCGTGACGCGCGTGAA	0.716																																					p.V206A		Atlas-SNP	.											.	ZNF835	106	.	0			c.T617C						PASS	.	A	ALA/VAL	3,4319		0,3,2158	15	16	16		617	-3.4	0	19		16	0,8402		0,0,4201	no	missense	ZNF835	NM_001005850.2	64	0,3,6359	GG,GA,AA		0.0,0.0694,0.0236	benign	206/538	57175950	3,12721	2161	4201	6362	SO:0001583	missense	90485	exon2			TGCGTGACGCGCG	AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"Zinc fingers, C2H2-type"	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.617T>C	chr19.hg19:g.57175950A>G	ENSP00000444747:p.Val206Ala	0.0	0.0	.		46.0	19.0	.	NM_001005850	B7Z5Y0|G3V1S0	Missense_Mutation	SNP	ENST00000537055.2	hg19	CCDS56105.1	.	.	.	.	.	.	.	.	.	.	A	7.598	0.672178	0.14776	6.94E-4	0.0	ENSG00000127903	ENST00000342088;ENST00000537055	T	0.07114	3.22	2.12	-3.43	0.04810	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02807	0.0084	N	0.04245	-0.25	0.09310	N	1	B	0.11235	0.004	B	0.14578	0.011	T	0.45920	-0.9228	9	0.16896	T	0.51	.	4.1371	0.10176	0.246:0.0:0.5433:0.2107	.	228	Q9Y2P0	ZN835_HUMAN	A	228;206	ENSP00000444747:V206A	ENSP00000341756:V228A	V	-	2	0	ZNF835	61867762	0.000000	0.05858	0.000000	0.03702	0.296000	0.27459	-1.731000	0.01853	-0.977000	0.03537	-0.411000	0.06167	GTC	.	.	.	weak		0.716	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850		G	57175950	A	G	57175950	3	3	106	1	0	0	0	0	1	0	0	0	18198	275	10	3	998	3	ZNF835	19	57175950	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10	20932216	57175950	1953033	48	6762											
C20orf186	149954	hgsc.bcm.edu	37	chr20	31685559	31685559	+	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	ggtcatggtctcccagcccaAagacctggagactaccatct	10	8	9	14	0	3	2	1	0	2	2	4	3	3	2	4	3	2	0	4	3	2	1			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chr20:31685559A>T	ENST00000375483.3	+	11	1535	c.1535A>T	c.(1534-1536)aAa>aTa	p.K512I		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	512						cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TCCCAGCCCAAAGACCTGGAG	0.577																																					p.K512I		Atlas-SNP	.											.	.	.	.	0			c.A1535T						PASS	.						100	72	81					20																	31685559		2203	4300	6503	SO:0001583	missense	149954	exon11			AGCCCAAAGACCT	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.1535A>T	chr20.hg19:g.31685559A>T	ENSP00000364632:p.Lys512Ile	137.0	0.0	.		169.0	79.0	.	NM_182519	Q5TDX6	Missense_Mutation	SNP	ENST00000375483.3	hg19	CCDS13213.2	.	.	.	.	.	.	.	.	.	.	A	14.60	2.582504	0.46006	.	.	ENSG00000186191	ENST00000375483	T	0.07327	3.2	5.26	5.26	0.73747	.	0.240028	0.35067	N	0.003468	T	0.07279	0.0184	N	0.24115	0.695	0.24134	N	0.995755	B	0.30937	0.301	B	0.31812	0.136	T	0.27773	-1.0064	10	0.62326	D	0.03	-11.2987	11.8323	0.52303	1.0:0.0:0.0:0.0	.	512	P59827	BPIB4_HUMAN	I	512	ENSP00000364632:K512I	ENSP00000364632:K512I	K	+	2	0	BPIFB4	31149220	0.981000	0.34729	0.940000	0.37924	0.577000	0.36160	2.261000	0.43276	2.108000	0.64289	0.379000	0.24179	AAA	.	.	.	none		0.577	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519		T	31685559	A	T	31685559	3	4	106	1	0	0	0	0	1	0	0	0	2100	14	1	5	1577	5	C20orf186	20	31685559	Missense_Mutation	SNP	A	TCGA-B9-A5W9-01A-11D-A28G-10		31685559	31339961	49	6763											
KIAA1210	57481	hgsc.bcm.edu	37	chrX	118219440	118219440	+	Missense_Mutation	SNP	T	T	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	gggccttgaaactcttctgcTtctgctttgccatagttatc	6	16	8	11	0	3	1	0	1	3	0	4	1	3	1	2	1	4	3	2	1	3	6			TCGA-B9-A5W9-01A-11D-A28G-10	TCGA-B9-A5W9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad4535df-a616-4440-8204-9a498d22beb5	869fc941-e464-4427-8385-d302bb618ea9	g.chrX:118219440T>G	ENST00000402510.2	-	12	4753	c.4754A>C	c.(4753-4755)aAg>aCg	p.K1585T		NM_020721.1	NP_065772.1	Q9ULL0	K1210_HUMAN	KIAA1210	1585										breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(31)|ovary(4)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	64						ACTCTTCTGCTTCTGCTTTGC	0.448																																					p.K1585T		Atlas-SNP	.											.	KIAA1210	171	.	0			c.A4754C						PASS	.						108	96	99					X																	118219440		1887	4103	5990	SO:0001583	missense	57481	exon12			TTCTGCTTCTGCT	AB033036	CCDS48156.1	Xq24	2012-10-04			ENSG00000250423	ENSG00000250423			29218	protein-coding gene	gene with protein product						10574462	Standard	NM_020721		Approved		uc004era.4	Q9ULL0	OTTHUMG00000162980	ENST00000402510.2:c.4754A>C	chrX.hg19:g.118219440T>G	ENSP00000384670:p.Lys1585Thr	29.0	0.0	.		46.0	6.0	.	NM_020721	B7ZCI8|Q5JPN4	Missense_Mutation	SNP	ENST00000402510.2	hg19	CCDS48156.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.05|11.05	1.525709|1.525709	0.27299|0.27299	.|.	.|.	ENSG00000248857|ENSG00000250423	ENST00000440399|ENST00000402510	.|T	.|0.22743	.|1.94	5.16|5.16	-4.73|-4.73	0.03259|0.03259	.|.	.|.	.|.	.|.	.|.	T|T	0.32912|0.32912	0.0845|0.0845	L|L	0.60455|0.60455	1.87|1.87	0.09310|0.09310	N|N	1|1	.|D	.|0.62365	.|0.991	.|P	.|0.61070	.|0.883	T|T	0.21930|0.21930	-1.0231|-1.0231	5|9	.|0.35671	.|T	.|0.21	.|.	12.3761|12.3761	0.55281|0.55281	0.0:0.2909:0.0:0.7091|0.0:0.2909:0.0:0.7091	.|.	.|1585	.|Q9ULL0	.|K1210_HUMAN	D|T	991|1585	.|ENSP00000384670:K1585T	.|ENSP00000384670:K1585T	E|K	-|-	3|2	2|0	KIAA1210|RP13-347D8.6	118103468|118103468	0.049000|0.049000	0.20398|0.20398	0.001000|0.001000	0.08648|0.08648	0.044000|0.044000	0.14063|0.14063	-0.389000|-0.389000	0.07342|0.07342	-1.098000|-1.098000	0.03038|0.03038	0.486000|0.486000	0.48141|0.48141	GAA|AAG	.	.	.	none		0.448	KIAA1210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371251.2	NM_020721		G	118219440	T	G	118219440	3	3	106	1	0	0	0	0	1	0	0	0	8221	1609	56	5	387	5	KIAA1210	23	118219440	Missense_Mutation	SNP	T	TCGA-B9-A5W9-01A-11D-A28G-10		118219440	37051120	50	6764											
ALPL	249	hgsc.bcm.edu	37	chr1	21889674	21889674	+	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	tacctgtgtggggtgaaggcCaatgagggcaccgtgggggt	7	8	19	7	1	0	2	0	2	0	0	0	2	0	2	3	6	1	1	3	6	3	1	rs201342272		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:21889674C>A	ENST00000374840.3	+	5	619	c.369C>A	c.(367-369)gcC>gcA	p.A123A	ALPL_ENST00000539907.1_Silent_p.A46A|ALPL_ENST00000468526.1_3'UTR|ALPL_ENST00000540617.1_Silent_p.A68A|ALPL_ENST00000425315.2_Silent_p.A123A|ALPL_ENST00000374832.1_Silent_p.A123A	NM_000478.4	NP_000469.3	P05186	PPBT_HUMAN	alkaline phosphatase, liver/bone/kidney	123					cellular response to organic cyclic compound (GO:0071407)|cementum mineralization (GO:0071529)|developmental process involved in reproduction (GO:0003006)|endochondral ossification (GO:0001958)|osteoblast differentiation (GO:0001649)|response to antibiotic (GO:0046677)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to vitamin D (GO:0033280)|skeletal system development (GO:0001501)	anchored component of membrane (GO:0031225)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	26		all_lung(284;2.19e-05)|Lung NSC(340;2.22e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;8.7e-28)|COAD - Colon adenocarcinoma(152;1.57e-05)|GBM - Glioblastoma multiforme(114;2.66e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000177)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00856)|READ - Rectum adenocarcinoma(331;0.0623)|Lung(427;0.146)	Amifostine(DB01143)|Fospropofol(DB06716)	GGGTGAAGGCCAATGAGGGCA	0.652													C|||	1	0.000199681	0	0	5008	,	,		17698	0		0	False		,,,				2504	0.001				p.A123A		Atlas-SNP	.											.	ALPL	50	.	0			c.C369A						PASS	.						84	75	78					1																	21889674		2203	4300	6503	SO:0001819	synonymous_variant	249	exon5			GAAGGCCAATGAG	BC021289	CCDS217.1, CCDS53274.1, CCDS53275.1	1p36.12	2008-02-05			ENSG00000162551	ENSG00000162551	3.1.3.1		438	protein-coding gene	gene with protein product		171760		HOPS		3532105, 3446011	Standard	NM_001127501		Approved	TNSALP	uc001bet.3	P05186	OTTHUMG00000002949	ENST00000374840.3:c.369C>A	chr1.hg19:g.21889674C>A		263.0	0.0	.		179.0	71.0	.	NM_000478	A1A4E7|B2RMP8|B7Z387|B7Z4Y6|O75090|Q2TAI7|Q59EJ7|Q5BKZ5|Q5VTG5|Q6NZI8|Q8WU32|Q9UBK0	Silent	SNP	ENST00000374840.3	hg19	CCDS217.1																																																																																			.	C|0.999;A|0.001	0.001	weak		0.652	ALPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000008202.1	NM_000478		A	21889674	C	A	21889674	2	1	107	1	0	0	0	0	0	0	0	1	547	581	21	4		4	ALPL	1	21889674	Silent	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10		21889674	227360947	1	6765											
FAM46B	115572	hgsc.bcm.edu	37	chr1	27333078	27333078	+	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	aggagtctatgctgaattcaAactggcgtctcaccgagtcc	10	10	10	11	2	3	1	2	1	2	0	5	3	4	2	2	2	2	1	2	2	3	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:27333078A>T	ENST00000289166.5	-	2	800	c.635T>A	c.(634-636)tTt>tAt	p.F212Y		NM_052943.3	NP_443175.2	Q96A09	FA46B_HUMAN	family with sequence similarity 46, member B	212										breast(1)|central_nervous_system(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;7.71e-51)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|STAD - Stomach adenocarcinoma(196;0.00114)|READ - Rectum adenocarcinoma(331;0.0419)		GCTGAATTCAAACTGGCGTCT	0.552																																					p.F212Y		Atlas-SNP	.											FAM46B,NS,carcinoma,0,1	FAM46B	44	.	0			c.T635A						PASS	.						108	110	110					1																	27333078		2203	4300	6503	SO:0001583	missense	115572	exon2			AATTCAAACTGGC	AK122816	CCDS294.2	1p35.3	2008-02-05			ENSG00000158246	ENSG00000158246			28273	protein-coding gene	gene with protein product						12477932	Standard	NM_052943		Approved	MGC16491	uc010ofj.2	Q96A09	OTTHUMG00000004278	ENST00000289166.5:c.635T>A	chr1.hg19:g.27333078A>T	ENSP00000289166:p.Phe212Tyr	96.0	0.0	.		53.0	16.0	.	NM_052943		Missense_Mutation	SNP	ENST00000289166.5	hg19	CCDS294.2	.	.	.	.	.	.	.	.	.	.	A	24.2	4.507004	0.85282	.	.	ENSG00000158246	ENST00000289166	T	0.28454	1.61	5.2	5.2	0.72013	Domain of unknown function DUF1693 (1);	0.045170	0.85682	D	0.000000	T	0.57066	0.2028	M	0.79614	2.46	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	T	0.61133	-0.7124	10	0.56958	D	0.05	-1.9476	15.2153	0.73261	1.0:0.0:0.0:0.0	.	212	Q96A09	FA46B_HUMAN	Y	212	ENSP00000289166:F212Y	ENSP00000289166:F212Y	F	-	2	0	FAM46B	27205665	1.000000	0.71417	0.999000	0.59377	0.970000	0.65996	9.135000	0.94478	2.178000	0.69098	0.459000	0.35465	TTT	.	.	.	none		0.552	FAM46B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012347.2	NM_052943		T	27333078	A	T	27333078	3	4	107	1	0	0	0	0	1	0	0	0	5573	14	1	5	646	5	FAM46B	1	27333078	Missense_Mutation	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10	5443404	27333078	221917543	2	6766											
C1orf94	84970	hgsc.bcm.edu	37	chr1	34643683	34643683	+	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	ccctgtggttggaactctaaGaggcaatgagctcagctttc	9	11	11	10	0	2	2	1	1	1	1	3	3	2	3	1	3	3	4	1	3	3	3			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:34643683G>C	ENST00000488417.1	+	1	413	c.293G>C	c.(292-294)aGa>aCa	p.R98T	AC115286.1_ENST00000408126.1_RNA|C1orf94_ENST00000373374.3_Intron	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	98										central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				GGAACTCTAAGAGGCAATGAG	0.537																																					p.R98T		Atlas-SNP	.											.	C1orf94	156	.	0			c.G293C						PASS	.						73	69	70					1																	34643683		692	1591	2283	SO:0001583	missense	84970	exon1			CTCTAAGAGGCAA	AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.293G>C	chr1.hg19:g.34643683G>C	ENSP00000435634:p.Arg98Thr	133.0	0.0	.		77.0	24.0	.	NM_001134734	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Missense_Mutation	SNP	ENST00000488417.1	hg19	CCDS44108.1	.	.	.	.	.	.	.	.	.	.	G	0.083	-1.180380	0.01633	.	.	ENSG00000142698	ENST00000488417	T	0.44881	0.91	4.99	2.08	0.27032	.	.	.	.	.	T	0.26666	0.0652	N	0.22421	0.69	0.09310	N	1	B	0.12013	0.005	B	0.10450	0.005	T	0.23261	-1.0193	9	0.66056	D	0.02	.	5.0027	0.14273	0.1877:0.173:0.6393:0.0	.	98	Q6P1W5	CA094_HUMAN	T	98	ENSP00000435634:R98T	ENSP00000435634:R98T	R	+	2	0	C1orf94	34416270	0.867000	0.29959	0.005000	0.12908	0.004000	0.04260	1.134000	0.31442	0.277000	0.22141	0.655000	0.94253	AGA	.	.	.	none		0.537	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2	NM_032884		C	34643683	G	C	34643683	3	2	107	1	0	0	0	0	1	0	0	0	2073	942	33	4	295	4	C1orf94	1	34643683	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	7310605	34643683	214606938	3	6767											
ZCCHC11	23318	hgsc.bcm.edu	37	chr1	52897102	52897102	+	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	agagttctgtggaaatggctGaggctgaggagaataagatg	13	9	16	3	0	1	5	0	2	1	3	1	7	1	6	0	4	0	3	0	4	3	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:52897102G>T	ENST00000371544.3	-	28	4553	c.4291C>A	c.(4291-4293)Cag>Aag	p.Q1431K	ZCCHC11_ENST00000257177.4_Missense_Mutation_p.Q1432K	NM_001009881.2|NM_015269.2	NP_001009881.1|NP_056084.1	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11	1431	Gln-rich.|Pro-rich.				cytokine production (GO:0001816)|miRNA catabolic process (GO:0010587)|miRNA metabolic process (GO:0010586)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|pre-miRNA processing (GO:0031054)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|RNA 3'-end processing (GO:0031123)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(17)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	58						GGAAATGGCTGAGGCTGAGGA	0.393																																					p.Q1432K		Atlas-SNP	.											.	ZCCHC11	151	.	0			c.C4294A						PASS	.						32	29	30					1																	52897102		2203	4298	6501	SO:0001583	missense	23318	exon28			ATGGCTGAGGCTG	D83776	CCDS30715.1, CCDS30716.1	1p32.3	2014-03-05			ENSG00000134744	ENSG00000134744		"Zinc fingers, CCHC domain containing"	28981	protein-coding gene	gene with protein product	"TUTase4"	613692				8724849, 12239557	Standard	NM_015269		Approved	KIAA0191, PAPD3, TUT4	uc001cty.2	Q5TAX3	OTTHUMG00000008200	ENST00000371544.3:c.4291C>A	chr1.hg19:g.52897102G>T	ENSP00000360599:p.Gln1431Lys	88.0	0.0	.		60.0	19.0	.	NM_001009881	A2RRP0|B7Z8J5|D3DQ35|Q12764|Q5TAX2|Q5TAX4|Q86XZ3	Missense_Mutation	SNP	ENST00000371544.3	hg19	CCDS30716.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.48|15.48	2.847224|2.847224	0.51164|0.51164	.|.	.|.	ENSG00000134744|ENSG00000134744	ENST00000257177;ENST00000371544;ENST00000531722|ENST00000474453	T;T|.	0.46451|.	0.87;0.88|.	5.27|5.27	5.27|5.27	0.74061|0.74061	.|.	0.248184|.	0.35466|.	N|.	0.003196|.	T|.	0.55433|.	0.1920|.	N|N	0.24115|0.24115	0.695|0.695	0.80722|0.80722	D|D	1|1	P|.	0.40144|.	0.704|.	B|.	0.32022|.	0.139|.	T|.	0.50668|.	-0.8801|.	10|.	0.40728|.	T|.	0.16|.	.|.	18.8838|18.8838	0.92367|0.92367	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1431|.	Q5TAX3|.	TUT4_HUMAN|.	K|X	1432;1431;269|276	ENSP00000257177:Q1432K;ENSP00000360599:Q1431K|.	ENSP00000257177:Q1432K|.	Q|S	-|-	1|2	0|0	ZCCHC11|ZCCHC11	52669690|52669690	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	5.423000|5.423000	0.66458|0.66458	2.459000|2.459000	0.83118|0.83118	0.557000|0.557000	0.71058|0.71058	CAG|TCA	.	.	.	none		0.393	ZCCHC11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022462.1	XM_038288		T	52897102	G	T	52897102	3	4	107	1	0	0	0	0	1	0	0	0	17592	1299	45	4	655	4	ZCCHC11	1	52897102	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	18253419	52897102	196353519	4	6768											
SPTA1	6708	hgsc.bcm.edu	37	chr1	158639217	158639217	+	Frame_Shift_Del	DEL	G	G	-																															ccttgtaatcttcatcatctGccaactttttcttcttgttg																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:158639217delG	ENST00000368147.4	-	14	1994	c.1814delC	c.(1813-1815)gcafs	p.A605fs		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	605					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)					TTCATCATCTGCCAACTTTTT	0.408																																					p.A605fs		Atlas-Indel,Pindel	.											.	SPTA1	720	.	0			c.1815delA						PASS	.						285	268	273					1																	158639217		1915	4136	6051	SO:0001589	frameshift_variant	6708	exon14			.	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.1814delC	chr1.hg19:g.158639217delG	ENSP00000357129:p.Ala605fs	65.0	0.0	0		73.0	19.0	0.260274	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Frame_Shift_Del	DEL	ENST00000368147.4	hg19	CCDS41423.1																																																																																			.	.	.	none		0.408	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		-	158639217	G	-	158639217	7	5	107	1	0	1	0	1	0	0	0	0	15128	1319	46	0	5601	0	SPTA1	1	158639217	Frame_Shift_Del	DEL	G	TCGA-B9-A69E-01A-11D-A31X-10	105742115	158639217	90611404	5	6769											
RABIF	5877	hgsc.bcm.edu	37	chr1	202850297	202850297	+	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	ttcctggaggagatcgccgtCaggattgctgccgtcagaca	8	9	13	11	3	2	2	2	0	0	2	4	5	3	4	3	3	2	1	3	3	0	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:202850297C>T	ENST00000367262.3	-	2	217	c.181G>A	c.(181-183)Gac>Aac	p.D61N		NM_002871.4	NP_002862.2	P47224	MSS4_HUMAN	RAB interacting factor	61					membrane fusion (GO:0061025)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(2)|ovary(1)	4			BRCA - Breast invasive adenocarcinoma(75;0.166)			AGATCGCCGTCAGGATTGCTG	0.507																																					p.D61N		Atlas-SNP	.											.	RABIF	11	.	0			c.G181A						PASS	.						68	64	65					1																	202850297		2203	4300	6503	SO:0001583	missense	5877	exon2			CGCCGTCAGGATT	S78873	CCDS1428.1	1q32.1	2008-05-14			ENSG00000183155	ENSG00000183155			9797	protein-coding gene	gene with protein product		603417		RASGRF3		9441742, 7619808	Standard	NM_002871		Approved	mss4	uc001gyl.3	P47224	OTTHUMG00000041400	ENST00000367262.3:c.181G>A	chr1.hg19:g.202850297C>T	ENSP00000356231:p.Asp61Asn	63.0	0.0	.		48.0	18.0	.	NM_002871	B2R4P4|Q92992	Missense_Mutation	SNP	ENST00000367262.3	hg19	CCDS1428.1	.	.	.	.	.	.	.	.	.	.	C	10.55	1.382058	0.24944	.	.	ENSG00000183155	ENST00000367262	.	.	.	5.75	4.84	0.62591	Mss4-like (1);Mss4/translationally controlled tumour-associated TCTP (1);	0.332353	0.37136	N	0.002226	T	0.55955	0.1953	L	0.40543	1.245	0.80722	D	1	B	0.25809	0.135	B	0.29176	0.099	T	0.55528	-0.8127	9	0.51188	T	0.08	-57.0511	14.6684	0.68926	0.0:0.9296:0.0:0.0704	.	61	P47224	MSS4_HUMAN	N	61	.	ENSP00000356231:D61N	D	-	1	0	RABIF	201116920	1.000000	0.71417	0.009000	0.14445	0.008000	0.06430	5.492000	0.66893	1.447000	0.47661	-0.254000	0.11334	GAC	.	.	.	none		0.507	RABIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099183.1			T	202850297	C	T	202850297	3	4	107	1	0	0	0	0	1	0	0	0	12982	826	29	2	194	2	RABIF	1	202850297	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	44211080	202850297	46400324	6	6770											
CENPF	1063	hgsc.bcm.edu	37	chr1	214826247	214826247	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagttcacagaagctggagaTagaccttttaaagtctagta	14	11	9	7	0	2	3	1	0	1	3	2	4	2	3	1	1	1	3	1	1	6	6			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:214826247T>C	ENST00000366955.3	+	16	8405	c.8237T>C	c.(8236-8238)aTa>aCa	p.I2746T	CENPF_ENST00000467765.1_3'UTR	NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2842	Sufficient for centromere localization.|Sufficient for self-association.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		AAGCTGGAGATAGACCTTTTA	0.328																																					p.I2746T	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.T8237C						PASS	.						91	94	93					1																	214826247		2203	4300	6503	SO:0001583	missense	1063	exon16			TGGAGATAGACCT	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.8237T>C	chr1.hg19:g.214826247T>C	ENSP00000355922:p.Ile2746Thr	101.0	0.0	.		120.0	25.0	.	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	hg19	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	T	11.84	1.757432	0.31137	.	.	ENSG00000117724	ENST00000366955;ENST00000391896	T	0.04234	3.67	3.93	3.93	0.45458	.	.	.	.	.	T	0.05410	0.0143	L	0.47716	1.5	0.20489	N	0.999898	B	0.33694	0.421	B	0.22152	0.038	T	0.28106	-1.0054	9	0.42905	T	0.14	.	11.9872	0.53155	0.0:0.0:0.0:1.0	.	2842	P49454	CENPF_HUMAN	T	2746;145	ENSP00000355922:I2746T	ENSP00000355922:I2746T	I	+	2	0	CENPF	212892870	0.990000	0.36364	0.042000	0.18584	0.923000	0.55619	3.757000	0.55212	1.429000	0.47314	0.418000	0.28097	ATA	.	.	.	none		0.328	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		C	214826247	T	C	214826247	3	2	107	1	0	0	0	0	1	0	0	0	3233	1406	49	3	8295	3	CENPF	1	214826247	Missense_Mutation	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10	11975950	214826247	34424374	7	6771											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228511117	228511117	+	Missense_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	gtggtgacaggtcagcccatGcccagtgtgcgctggttcaa	7	9	14	11	1	2	1	2	1	0	0	2	1	2	1	2	3	3	2	2	3	1	1			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:228511117G>A	ENST00000422127.1	+	56	15506	c.15462G>A	c.(15460-15462)atG>atA	p.M5154I	OBSCN_ENST00000366707.4_Missense_Mutation_p.M2788I|OBSCN_ENST00000284548.11_Missense_Mutation_p.M5154I|OBSCN_ENST00000570156.2_Missense_Mutation_p.M6111I|OBSCN_ENST00000366709.4_Missense_Mutation_p.M2273I	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5154	Ig-like 49.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GTCAGCCCATGCCCAGTGTGC	0.522																																					p.M6111I		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G18333A						PASS	.						92	94	93					1																	228511117		2155	4253	6408	SO:0001583	missense	84033	exon67			GCCCATGCCCAGT	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.15462G>A	chr1.hg19:g.228511117G>A	ENSP00000409493:p.Met5154Ile	112.0	0.0	.		102.0	23.0	.	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	10.73	1.431705	0.25813	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22	5.07	5.07	0.68467	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.660669	0.14435	N	0.319744	T	0.46034	0.1372	N	0.04959	-0.14	0.27969	N	0.936468	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.13629	-1.0502	10	0.16896	T	0.51	.	15.681	0.77367	0.0:0.2016:0.7984:0.0	.	5154;5154	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	I	5154;5154;2788;2273	ENSP00000284548:M5154I;ENSP00000409493:M5154I;ENSP00000355668:M2788I;ENSP00000355670:M2273I	ENSP00000284548:M5154I	M	+	3	0	OBSCN	226577740	1.000000	0.71417	0.991000	0.47740	0.034000	0.12701	1.113000	0.31184	2.629000	0.89072	0.655000	0.94253	ATG	.	.	.	none		0.522	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228511117	G	A	228511117	3	1	107	1	0	0	0	0	1	0	0	0	10819	1319	46	2	15680	2	OBSCN	1	228511117	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	13684870	228511117	20739504	8	6772											
OR2W3	343171	hgsc.bcm.edu	37	chr1	248059782	248059782	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcagaaacagagaggtgaaGggggcactgggaaggttgct	12	6	17	6	0	1	3	1	1	0	2	1	5	1	4	0	5	2	3	0	5	3	1			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:248059782G>A	ENST00000360358.3	+	1	894	c.894G>A	c.(892-894)aaG>aaA	p.K298K	OR2W3_ENST00000537741.1_Silent_p.K298K	NM_001001957.2	NP_001001957.2	Q7Z3T1	OR2W3_HUMAN	olfactory receptor, family 2, subfamily W, member 3	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)|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)			GAGAGGTGAAGGGGGCACTGG	0.537																																					p.K298K		Atlas-SNP	.											.	OR2W3	113	.	0			c.G894A						PASS	.						39	40	40					1																	248059782		2203	4300	6503	SO:0001819	synonymous_variant	343171	exon1			GGTGAAGGGGGCA	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.894G>A	chr1.hg19:g.248059782G>A		111.0	0.0	.		80.0	5.0	.	NM_001001957	Q6IF06|Q8NG86	Silent	SNP	ENST00000360358.3	hg19	CCDS31099.1																																																																																			.	.	.	none		0.537	OR2W3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096861.1	NM_001001957		A	248059782	G	A	248059782	2	1	107	1	0	0	0	0	0	0	0	1	11040	991	35	2		2	OR2W3	1	248059782	Silent	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	19548665	248059782	1190839	9	6773											
LRPPRC	10128	hgsc.bcm.edu	37	chr2	44116985	44116986	+	Missense_Mutation	DNP	GC	GC	AG																															cagtcaaatgttcatacagtGctttagcagatgtgacatct																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr2:44116985_44116986GC>AG	ENST00000260665.7	-	37	4072_4073	c.4015_4016GC>CT	c.(4015-4017)GCa>CTa	p.A1339L	RNU6-1048P_ENST00000364054.1_RNA	NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	1339	RNA-binding.				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)				TTCATACAGTGCTTTAGCAGAT	0.366																																					p.A1339V|p.A1339P		Atlas-SNP	.											.	LRPPRC	105	.	0			c.C4016T|c.G4015C						PASS	.																																			SO:0001583	missense	10128	exon37			TACAGTGCTTTAG|ACAGTGCTTTAGC	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.4015_4016delinsAG	chr2.hg19:g.44116985_44116986delinsAG	ENSP00000260665:p.Ala1339Leu	243.0|244.0	0.0	.		219.0|217.0	48.0	.	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Missense_Mutation	SNP	ENST00000260665.7	hg19	CCDS33189.1																																																																																			.	.	.	none		0.366	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259		AG	44116986	GC	AG	44116985	3	1	107	1	0	0	0	0	1	0	0	0	8972	1319	46	2	176	2	LRPPRC	2	44116985	Missense_Mutation	DNP	GC	TCGA-B9-A69E-01A-11D-A31X-10		44116985	199082388	10	6774											
ROBO2	6092	hgsc.bcm.edu	37	chr3	77671536	77671536	+	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	caggcccctgagagcactggAccagactcctggatccagca	10	5	11	15	0	0	2	0	1	0	2	2	5	2	4	5	3	2	2	5	3	0	0			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr3:77671536A>T	ENST00000461745.1	+	23	4613	c.3713A>T	c.(3712-3714)gAc>gTc	p.D1238V	ROBO2_ENST00000487694.3_Missense_Mutation_p.D1254V|ROBO2_ENST00000332191.8_Missense_Mutation_p.D1238V	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	1238					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)		AGAGCACTGGACCAGACTCCT	0.463																																					p.D1238V		Atlas-SNP	.											.	ROBO2	527	.	0			c.A3713T						PASS	.						74	77	76					3																	77671536		1902	4120	6022	SO:0001583	missense	6092	exon23			CACTGGACCAGAC	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.3713A>T	chr3.hg19:g.77671536A>T	ENSP00000417164:p.Asp1238Val	70.0	0.0	.		48.0	19.0	.	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	hg19	CCDS43109.1	.	.	.	.	.	.	.	.	.	.	A	15.72	2.917020	0.52546	.	.	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000461745;ENST00000332191	T;T;T	0.61510	0.1;0.14;0.12	5.56	5.56	0.83823	.	0.299670	0.23303	N	0.049659	T	0.43897	0.1268	N	0.08118	0	0.30052	N	0.811715	B;B;B	0.26512	0.151;0.096;0.151	B;B;B	0.34093	0.086;0.175;0.086	T	0.56667	-0.7941	9	0.56958	D	0.05	.	15.6959	0.77499	1.0:0.0:0.0:0.0	.	1254;1238;1238	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	V	1254;1254;1238;1238	ENSP00000417335:D1254V;ENSP00000417164:D1238V;ENSP00000327536:D1238V	ENSP00000327536:D1238V	D	+	2	0	ROBO2	77754226	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	8.962000	0.93254	2.110000	0.64415	0.528000	0.53228	GAC	.	.	.	none		0.463	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		T	77671536	A	T	77671536	3	4	107	1	0	0	0	0	1	0	0	0	13527	275	10	5	3805	5	ROBO2	3	77671536	Missense_Mutation	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10		77671536	120350894	11	6775											
ATP6V1A	523	hgsc.bcm.edu	37	chr3	113505224	113505224	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccagagagtccttgatgcccTttttccgtaagtttgagatg	8	14	10	9	1	0	3	0	2	0	2	2	5	2	3	4	0	1	2	4	0	1	5			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr3:113505224T>C	ENST00000273398.3	+	6	818	c.710T>C	c.(709-711)cTt>cCt	p.L237P	ATP6V1A_ENST00000538620.1_Missense_Mutation_p.L204P	NM_001690.3	NP_001681.2	P38606	VATA_HUMAN	ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A	237					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus (GO:0005902)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	ATP binding (GO:0005524)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Alendronate(DB00630)|Etidronic acid(DB01077)|Tiludronate(DB01133)	CTTGATGCCCTTTTTCCGTAA	0.423																																					p.L237P		Atlas-SNP	.											ATP6V1A,NS,malignant_melanoma,0,1	ATP6V1A	71	.	0			c.T710C						PASS	.						219	201	207					3																	113505224		2203	4300	6503	SO:0001583	missense	523	exon6			ATGCCCTTTTTCC	L09235	CCDS2976.1	3q13.31	2010-04-21	2002-08-29	2003-04-25	ENSG00000114573	ENSG00000114573	3.6.3.14	"ATPases / V-type"	851	protein-coding gene	gene with protein product		607027	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), alpha polypeptide, 70kD, isoform 1"	VPP2, ATP6A1, ATP6V1A1		8463241	Standard	NM_001690		Approved	Vma1, VA68	uc003eao.3	P38606	OTTHUMG00000159295	ENST00000273398.3:c.710T>C	chr3.hg19:g.113505224T>C	ENSP00000273398:p.Leu237Pro	102.0	0.0	.		88.0	4.0	.	NM_001690	B2RBR8|B7Z1R5|D3DN75|Q53YD9|Q96DY6|Q9UHY3	Missense_Mutation	SNP	ENST00000273398.3	hg19	CCDS2976.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.972517	0.74246	.	.	ENSG00000114573	ENST00000273398;ENST00000538620	D;D	0.84223	-1.82;-1.82	5.33	4.17	0.49024	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.94062	0.8097	H	0.96208	3.785	0.80722	D	1	D	0.71674	0.998	D	0.73708	0.981	D	0.94260	0.7501	10	0.87932	D	0	-16.1423	10.9912	0.47551	0.0:0.0737:0.0:0.9263	.	237	P38606	VATA_HUMAN	P	237;204	ENSP00000273398:L237P;ENSP00000439874:L204P	ENSP00000273398:L237P	L	+	2	0	ATP6V1A	114987914	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.484000	0.81180	0.873000	0.35799	-0.353000	0.07706	CTT	.	.	.	none		0.423	ATP6V1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354457.1	NM_001690		C	113505224	T	C	113505224	3	2	107	1	0	0	0	0	1	0	0	0	1177	1609	56	3	728	3	ATP6V1A	3	113505224	Missense_Mutation	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10	35833688	113505224	84517206	12	6776											
AMOTL2	51421	hgsc.bcm.edu	37	chr3	134078995	134078995	+	Missense_Mutation	SNP	A	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	ccaccagtgagcagaccctcAttgaagctgctgctgggtga	9	8	12	12	0	1	4	1	3	0	1	1	4	1	4	3	1	4	4	3	1	1	1			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr3:134078995A>C	ENST00000422605.2	-	7	2002	c.1836T>G	c.(1834-1836)aaT>aaG	p.N612K	AMOTL2_ENST00000513145.1_Missense_Mutation_p.N610K|AMOTL2_ENST00000514516.1_Missense_Mutation_p.N670K|AMOTL2_ENST00000249883.5_Missense_Mutation_p.N612K			Q9Y2J4	AMOL2_HUMAN	angiomotin like 2	612					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						GCAGACCCTCATTGAAGCTGC	0.622																																					p.N612K		Atlas-SNP	.											.	AMOTL2	52	.	0			c.T1836G						PASS	.						57	50	52					3																	134078995		2203	4300	6503	SO:0001583	missense	51421	exon7			ACCCTCATTGAAG	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.1836T>G	chr3.hg19:g.134078995A>C	ENSP00000409999:p.Asn612Lys	78.0	0.0	.		62.0	19.0	.	NM_016201	A8K6F1|B7Z5Q1|E9PHW3|Q53EP1|Q96F99|Q9UKB4	Missense_Mutation	SNP	ENST00000422605.2	hg19		.	.	.	.	.	.	.	.	.	.	A	16.66	3.183876	0.57800	.	.	ENSG00000114019	ENST00000249883;ENST00000422605;ENST00000514516;ENST00000513145	T;T;T;T	0.17370	2.29;2.29;2.28;2.29	5.23	-0.975	0.10289	.	0.000000	0.85682	D	0.000000	T	0.26810	0.0656	L	0.57536	1.79	0.58432	D	0.999996	D;D;D	0.64830	0.992;0.992;0.994	P;P;D	0.63793	0.866;0.866;0.918	T	0.14727	-1.0462	10	0.11794	T	0.64	-26.2587	11.2577	0.49063	0.5554:0.0:0.4446:0.0	.	610;612;670	Q9Y2J4-3;Q9Y2J4-2;E9PHW3	.;.;.	K	612;612;670;610	ENSP00000249883:N612K;ENSP00000409999:N612K;ENSP00000424765:N670K;ENSP00000425475:N610K	ENSP00000249883:N612K	N	-	3	2	AMOTL2	135561685	0.461000	0.25783	0.993000	0.49108	0.925000	0.55904	-0.316000	0.08071	-0.263000	0.09378	-0.441000	0.05720	AAT	.	.	.	none		0.622	AMOTL2-014	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000358149.1	NM_016201		C	134078995	A	C	134078995	3	2	107	1	0	0	0	0	1	0	0	0	584	214	8	5	522	5	AMOTL2	3	134078995	Missense_Mutation	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10	20573771	134078995	63943435	13	6777											
SLC25A36	55186	hgsc.bcm.edu	37	chr3	140675502	140675502	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctggagccagtgtcaaccgaGtagtgtctcccggacctctt	7	10	11	13	2	3	0	1	0	2	0	4	3	3	2	4	2	2	1	4	2	2	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr3:140675502G>A	ENST00000324194.6	+	2	343	c.175G>A	c.(175-177)Gta>Ata	p.V59I	SLC25A36_ENST00000453248.2_Missense_Mutation_p.V59I|SLC25A36_ENST00000446041.2_Missense_Mutation_p.V59I|SLC25A36_ENST00000393015.4_3'UTR|SLC25A36_ENST00000507429.1_Missense_Mutation_p.V59I			Q96CQ1	S2536_HUMAN	solute carrier family 25 (pyrimidine nucleotide carrier ), member 36	59					response to estradiol (GO:0032355)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	6						TGTCAACCGAGTAGTGTCTCC	0.433																																					p.V59I		Atlas-SNP	.											.	SLC25A36	24	.	0			c.G175A						PASS	.						140	135	137					3																	140675502		2203	4300	6503	SO:0001583	missense	55186	exon2			AACCGAGTAGTGT	AK001480	CCDS3114.1, CCDS46927.1	3q23	2013-05-22	2012-03-29		ENSG00000114120	ENSG00000114120		"Solute carriers"	25554	protein-coding gene	gene with protein product			"solute carrier family 25, member 36"				Standard	NM_001104647		Approved	FLJ10618, PNC2	uc003etr.2	Q96CQ1	OTTHUMG00000160260	ENST00000324194.6:c.175G>A	chr3.hg19:g.140675502G>A	ENSP00000320688:p.Val59Ile	85.0	0.0	.		73.0	24.0	.	NM_018155	A8MYF7|Q05CY1|Q9H0G8|Q9NVN5	Missense_Mutation	SNP	ENST00000324194.6	hg19	CCDS46927.1	.	.	.	.	.	.	.	.	.	.	G	11.53	1.666084	0.29604	.	.	ENSG00000114120	ENST00000446041;ENST00000507429;ENST00000324194;ENST00000453248;ENST00000513887	T;T;T;T	0.78924	-1.22;-1.22;-1.22;-1.17	5.29	-0.772	0.10998	Mitochondrial carrier domain (2);	0.517046	0.21808	N	0.068811	T	0.62551	0.2437	L	0.31578	0.945	0.09310	N	0.999996	B;B;B;B	0.13594	0.0;0.001;0.008;0.0	B;B;B;B	0.13407	0.005;0.003;0.009;0.005	T	0.43130	-0.9410	10	0.23302	T	0.38	-6.1006	11.8956	0.52654	0.3779:0.0:0.6221:0.0	.	59;59;59;59	B4DL01;Q96CQ1-3;Q96CQ1;F6SDC8	.;.;S2536_HUMAN;.	I	59;59;59;59;9	ENSP00000401938:V59I;ENSP00000421470:V59I;ENSP00000320688:V59I;ENSP00000391521:V59I	ENSP00000320688:V59I	V	+	1	0	SLC25A36	142158192	0.994000	0.37717	0.770000	0.31555	0.903000	0.53119	1.349000	0.33998	-0.689000	0.05149	-0.813000	0.03139	GTA	.	.	.	none		0.433	SLC25A36-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359929.1	NM_018155		A	140675502	G	A	140675502	3	1	107	1	0	0	0	0	1	0	0	0	14513	1029	36	2	181	2	SLC25A36	3	140675502	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	6596507	140675502	57346928	14	6778											
MED12L	116931	hgsc.bcm.edu	37	chr3	151107816	151107816	+	Missense_Mutation	SNP	T	T	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	gcctcctaattactcgcctaTctcctcccaaatgatgcacc	9	11	4	17	1	1	1	0	1	1	0	5	1	3	1	6	0	2	1	6	0	4	3			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr3:151107816T>G	ENST00000474524.1	+	36	5434	c.5396T>G	c.(5395-5397)aTc>aGc	p.I1799S	MED12L_ENST00000273432.4_Missense_Mutation_p.I1659S	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	1799						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)			TACTCGCCTATCTCCTCCCAA	0.468																																					p.I1799S		Atlas-SNP	.											.	MED12L	271	.	0			c.T5396G						PASS	.						175	171	172					3																	151107816		2203	4300	6503	SO:0001583	missense	116931	exon36			CGCCTATCTCCTC	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.5396T>G	chr3.hg19:g.151107816T>G	ENSP00000417235:p.Ile1799Ser	101.0	0.0	.		88.0	37.0	.	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	hg19	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	T	14.12	2.440148	0.43326	.	.	ENSG00000144893	ENST00000474524;ENST00000273432	T;T	0.60171	0.43;0.21	5.73	5.73	0.89815	.	0.222920	0.46442	D	0.000300	T	0.39682	0.1087	N	0.08118	0	0.32093	N	0.591569	B;B	0.23058	0.005;0.079	B;B	0.19666	0.002;0.026	T	0.52132	-0.8616	10	0.87932	D	0	-5.497	14.2508	0.66019	0.0:0.0:0.0:1.0	.	1659;1799	F8WAE6;Q86YW9	.;MD12L_HUMAN	S	1799;1659	ENSP00000417235:I1799S;ENSP00000273432:I1659S	ENSP00000273432:I1659S	I	+	2	0	MED12L	152590506	0.493000	0.26035	0.865000	0.33974	0.987000	0.75469	3.781000	0.55394	2.186000	0.69663	0.459000	0.35465	ATC	.	.	.	none		0.468	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		G	151107816	T	G	151107816	3	3	107	1	0	0	0	0	1	0	0	0	9436	1435	50	5	5538	5	MED12L	3	151107816	Missense_Mutation	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10	10432314	151107816	46914614	15	6779											
DOK7	285489	hgsc.bcm.edu	37	chr4	3478120	3478121	+	Frame_Shift_Ins	INS	-	-	GGCTA																															accaagttggagagcggcccINSggctaccctgcacctctgca																								rs376659660|rs539942267		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr4:3478120_3478121insGGCTA	ENST00000340083.5	+	4	448_449	c.383_384insGGCTA	c.(382-387)ccggctfs	p.-129fs	DOK7_ENST00000507039.1_Frame_Shift_Ins_p.-129fs|DOK7_ENST00000389653.2_Frame_Shift_Ins_p.-129fs	NM_173660.4	NP_775931.3	Q18PE1	DOK7_HUMAN	docking protein 7						neuromuscular junction development (GO:0007528)|positive regulation of protein tyrosine kinase activity (GO:0061098)|receptor clustering (GO:0043113)	cell junction (GO:0030054)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)			kidney(1)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		GAGAGCGGCCCGGCTACCCTGC	0.668																																					p.P128fs		Atlas-Indel,Pindel	.											.	DOK7	44	.	0			c.383_384insGGCTA						PASS	.																																			SO:0001589	frameshift_variant	285489	exon4			.	AK091037	CCDS3370.2, CCDS54717.1	4p16.2	2014-09-17	2006-08-24	2006-08-24	ENSG00000175920	ENSG00000175920			26594	protein-coding gene	gene with protein product		610285	"chromosome 4 open reading frame 25"	C4orf25		16794080	Standard	NM_173660		Approved	FLJ33718, FLJ39137, Dok-7	uc003ghd.3	Q18PE1	OTTHUMG00000122087	ENST00000340083.5:c.384_388dupGGCTA	chr4.hg19:g.3478121_3478125dupGGCTA	ENSP00000344432:p.Ala129fs	91.0	0.0	0		86.0	21.0	0.244186	NM_001164673	A2A499|A2RRD4|E9PB56|Q6P6A6|Q86XG5|Q8N2J3|Q8NBC1	Frame_Shift_Ins	INS	ENST00000340083.5	hg19	CCDS3370.2																																																																																			.	.	.	none		0.668	DOK7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313538.1	NM_173660		GGCTA	3478121	-	GGCTA	3478120	7	5	107	1	0	1	1	0	0	0	0	0	4704	652	23	0	397	0	DOK7	4	3478120	Frame_Shift_Ins	INS	-	TCGA-B9-A69E-01A-11D-A31X-10		3478120	187676156	16	6780											
TLR10	81793	hgsc.bcm.edu	37	chr4	38776735	38776735	+	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	tgcagatgagcaattttctgGaaatctgatttttgtatttt	10	19	8	4	0	2	3	0	2	2	1	2	4	2	4	0	1	2	3	0	1	3	7			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr4:38776735G>T	ENST00000308973.4	-	4	1082	c.477C>A	c.(475-477)ttC>ttA	p.F159L	TLR10_ENST00000506111.1_Missense_Mutation_p.F159L|TLR10_ENST00000361424.2_Missense_Mutation_p.F159L|TLR10_ENST00000507953.1_5'Flank|TLR10_ENST00000508334.1_Missense_Mutation_p.F159L	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	159					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						CAATTTTCTGGAAATCTGATT	0.398																																					p.F159L		Atlas-SNP	.											.	TLR10	87	.	0			c.C477A						PASS	.						57	61	59					4																	38776735		2202	4299	6501	SO:0001583	missense	81793	exon2			TTTCTGGAAATCT	AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"CD molecules"	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.477C>A	chr4.hg19:g.38776735G>T	ENSP00000308925:p.Phe159Leu	41.0	0.0	.		43.0	9.0	.	NM_001017388	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Missense_Mutation	SNP	ENST00000308973.4	hg19	CCDS3445.1	.	.	.	.	.	.	.	.	.	.	G	1.875	-0.459352	0.04508	.	.	ENSG00000174123	ENST00000308973;ENST00000506111;ENST00000361424;ENST00000508334	T;T;T;T	0.18338	2.22;2.22;2.22;2.22	5.23	2.42	0.29668	.	0.111310	0.38272	N	0.001753	T	0.07503	0.0189	N	0.17082	0.46	0.41978	D	0.990781	B	0.09022	0.002	B	0.10450	0.005	T	0.20107	-1.0285	10	0.10636	T	0.68	.	4.4622	0.11671	0.1433:0.1228:0.6077:0.1263	.	159	Q9BXR5	TLR10_HUMAN	L	159	ENSP00000308925:F159L;ENSP00000421483:F159L;ENSP00000354459:F159L;ENSP00000424923:F159L	ENSP00000308925:F159L	F	-	3	2	TLR10	38453130	0.010000	0.17322	1.000000	0.80357	0.982000	0.71751	-0.202000	0.09451	1.211000	0.43351	0.655000	0.94253	TTC	.	.	.	none		0.398	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1			T	38776735	G	T	38776735	3	4	107	1	0	0	0	0	1	0	0	0	15962	1165	41	4	1962	4	TLR10	4	38776735	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	35298615	38776735	152377541	17	6781											
SYNPO2	171024	hgsc.bcm.edu	37	chr4	119952865	119952865	+	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	tcaatgcatccttgtttactTtccaacctccagatgcaaag	11	13	5	12	0	1	1	1	0	0	1	4	1	4	1	4	0	4	3	4	0	4	4			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr4:119952865T>A	ENST00000429713.2	+	4	3117	c.2935T>A	c.(2935-2937)Ttc>Atc	p.F979I	SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000434046.2_Missense_Mutation_p.F979I|SYNPO2_ENST00000307142.4_Missense_Mutation_p.F979I	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	979						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						CTTGTTTACTTTCCAACCTCC	0.498																																					p.F979I		Atlas-SNP	.											.	SYNPO2	353	.	0			c.T2935A						PASS	.						96	78	84					4																	119952865		2203	4300	6503	SO:0001583	missense	171024	exon4			TTTACTTTCCAAC	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.2935T>A	chr4.hg19:g.119952865T>A	ENSP00000395143:p.Phe979Ile	129.0	0.0	.		140.0	28.0	.	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	hg19	CCDS47129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.5|23.5	4.425277|4.425277	0.83667|0.83667	.|.	.|.	ENSG00000172403|ENSG00000172403	ENST00000307142;ENST00000429713;ENST00000434046|ENST00000504178	T;T;T|.	0.16324|.	2.35;2.39;2.37|.	5.3|5.3	5.3|5.3	0.74995|0.74995	.|.	0.000000|0.000000	0.64402|0.64402	D|D	0.000004|0.000004	T|T	0.75398|0.75398	0.3844|0.3844	M|M	0.77103|0.77103	2.36|2.36	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	0.999;1.0;0.999;0.991|.	D;D;D;D|.	0.80764|.	0.994;0.992;0.991;0.955|.	T|T	0.76713|0.76713	-0.2858|-0.2858	9|6	.|.	.|.	.|.	-21.6986|-21.6986	15.246|15.246	0.73507|0.73507	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	979;979;979;979|.	B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6|.	.;.;.;SYNP2_HUMAN|.	I|Y	979|930	ENSP00000306015:F979I;ENSP00000395143:F979I;ENSP00000390965:F979I|.	.|.	F|F	+|+	1|2	0|0	SYNPO2|SYNPO2	120172313|120172313	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.992000|0.992000	0.81027|0.81027	7.841000|7.841000	0.86834|0.86834	2.013000|2.013000	0.59113|0.59113	0.533000|0.533000	0.62120|0.62120	TTC|TTT	.	.	.	none		0.498	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1			A	119952865	T	A	119952865	3	1	107	1	0	0	0	0	1	0	0	0	15469	1841	64	5	2949	5	SYNPO2	4	119952865	Missense_Mutation	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10	81176130	119952865	71201411	18	6782											
ODZ3	55714	hgsc.bcm.edu	37	chr4	183245385	183245385	+	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	ggatttggttcacagagaagCagacgagttcactagacaag	14	8	12	7	1	2	3	2	0	0	3	2	6	2	4	0	2	1	3	0	2	3	4			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr4:183245385C>A	ENST00000511685.1	+	2	335	c.212C>A	c.(211-213)gCa>gAa	p.A71E	TENM3_ENST00000406950.2_Missense_Mutation_p.A71E			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	71	Teneurin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00694}.				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)										CACAGAGAAGCAGACGAGTTC	0.458																																					p.A71E		Atlas-SNP	.											.	.	.	.	0			c.C212A						PASS	.						98	97	98					4																	183245385		1955	4146	6101	SO:0001583	missense	55714	exon1			GAGAAGCAGACGA	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.212C>A	chr4.hg19:g.183245385C>A	ENSP00000424226:p.Ala71Glu	58.0	0.0	.		66.0	9.0	.	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	hg19	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	C	16.66	3.184679	0.57909	.	.	ENSG00000218336	ENST00000512480;ENST00000511685;ENST00000406950	T;T;T	0.31769	1.48;1.48;1.48	5.65	5.65	0.86999	Teneurin intracellular, N-terminal (2);	.	.	.	.	T	0.52256	0.1723	L	0.60455	1.87	0.30938	N	0.726181	D;P	0.62365	0.991;0.77	P;B	0.61132	0.884;0.255	T	0.51934	-0.8642	9	0.72032	D	0.01	.	19.9142	0.97043	0.0:1.0:0.0:0.0	.	71;71	D6RGC5;Q9P273	.;TEN3_HUMAN	E	71	ENSP00000421320:A71E;ENSP00000424226:A71E;ENSP00000385276:A71E	ENSP00000385276:A71E	A	+	2	0	ODZ3	183482379	0.995000	0.38212	0.986000	0.45419	0.986000	0.74619	3.658000	0.54482	2.941000	0.99782	0.655000	0.94253	GCA	.	.	.	none		0.458	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			A	183245385	C	A	183245385	3	1	107	1	0	0	0	0	1	0	0	0	10843	710	25	4	214	4	ODZ3	4	183245385	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	63292520	183245385	7908891	19	6783											
FAT1	2195	hgsc.bcm.edu	37	chr4	187517964	187517964	+	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	aggcacctggggtggtatgtCtgagtaaatgttcttattta	9	15	12	5	0	2	1	0	1	2	0	2	1	2	1	1	4	0	4	1	4	5	6			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr4:187517964C>G	ENST00000441802.2	-	25	12939	c.12730G>C	c.(12730-12732)Gac>Cac	p.D4244H	FAT1_ENST00000512347.1_5'Flank	NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	4244					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						GGTGGTATGTCTGAGTAAATG	0.478										HNSCC(5;0.00058)																											p.D4244H	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.G12730C						PASS	.						70	69	69					4																	187517964		1861	4100	5961	SO:0001583	missense	2195	exon25			GTATGTCTGAGTA	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.12730G>C	chr4.hg19:g.187517964C>G	ENSP00000406229:p.Asp4244His	90.0	0.0	.		97.0	26.0	.	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	hg19	CCDS47177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.7|23.7	4.443680|4.443680	0.83993|0.83993	.|.	.|.	ENSG00000083857|ENSG00000083857	ENST00000441802;ENST00000260147|ENST00000512772	T|.	0.70869|.	-0.52|.	5.39|5.39	5.39|5.39	0.77823|0.77823	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72961|0.72961	0.3526|0.3526	L|L	0.60455|0.60455	1.87|1.87	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|T	0.69304|0.69304	-0.5180|-0.5180	10|5	0.66056|.	D|.	0.02|.	.|.	19.3359|19.3359	0.94319|0.94319	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	4244|.	Q14517|.	FAT1_HUMAN|.	H|T	4244;4246|11	ENSP00000406229:D4244H|.	ENSP00000260147:D4246H|.	D|R	-|-	1|2	0|0	FAT1|FAT1	187754958|187754958	1.000000|1.000000	0.71417|0.71417	0.831000|0.831000	0.32960|0.32960	0.737000|0.737000	0.42083|0.42083	7.651000|7.651000	0.83577|0.83577	2.809000|2.809000	0.96659|0.96659	0.555000|0.555000	0.69702|0.69702	GAC|AGA	.	.	.	none		0.478	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		G	187517964	C	G	187517964	3	3	107	1	0	0	0	0	1	0	0	0	5696	913	32	4	1048	4	FAT1	4	187517964	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	4272579	187517964	3636312	20	6784											
TRIP13	9319	hgsc.bcm.edu	37	chr5	908120	908120	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagtggcaagctggtaacCaagatgtttcagaagattca	14	9	11	7	0	2	4	2	0	0	4	2	4	2	4	1	2	2	4	1	2	4	3			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr5:908120C>T	ENST00000166345.3	+	8	1046	c.690C>T	c.(688-690)acC>acT	p.T230T		NM_004237.3	NP_004228.1	Q15645	PCH2_HUMAN	thyroid hormone receptor interactor 13	230					double-strand break repair (GO:0006302)|female meiosis I (GO:0007144)|male meiosis I (GO:0007141)|oocyte maturation (GO:0001556)|oogenesis (GO:0048477)|reciprocal meiotic recombination (GO:0007131)|regulation of RNA biosynthetic process (GO:2001141)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|transcription from RNA polymerase II promoter (GO:0006366)	male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)	ATP binding (GO:0005524)|transcription cofactor activity (GO:0003712)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	18			Epithelial(17;0.00147)|OV - Ovarian serous cystadenocarcinoma(19;0.00271)|all cancers(22;0.00622)|Lung(60;0.165)			AGCTGGTAACCAAGATGTTTC	0.498																																					p.T230T		Atlas-SNP	.											.	TRIP13	41	.	0			c.C690T						PASS	.						169	149	155					5																	908120		2203	4300	6503	SO:0001819	synonymous_variant	9319	exon8			GGTAACCAAGATG	L40384	CCDS3858.1	5p15	2010-04-21			ENSG00000071539	ENSG00000071539		"ATPases / AAA-type"	12307	protein-coding gene	gene with protein product	"thyroid receptor interacting protein 13"	604507				7776974	Standard	NM_004237		Approved	16E1BP	uc003jbr.3	Q15645	OTTHUMG00000090349	ENST00000166345.3:c.690C>T	chr5.hg19:g.908120C>T		96.0	0.0	.		123.0	38.0	.	NM_004237	C9K0T3|D3DTC0|O15324	Silent	SNP	ENST00000166345.3	hg19	CCDS3858.1	.	.	.	.	.	.	.	.	.	.	.	8.882	0.951814	0.18431	.	.	ENSG00000071539	ENST00000513435	.	.	.	5.62	-11.2	0.00127	.	.	.	.	.	T	0.41259	0.1151	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49214	-0.8963	4	.	.	.	-32.367	5.2498	0.15515	0.143:0.5019:0.2154:0.1397	.	.	.	.	L	226	.	.	P	+	2	0	TRIP13	961120	0.006000	0.16342	0.087000	0.20705	0.969000	0.65631	-1.282000	0.02799	-2.592000	0.00456	-0.345000	0.07892	CCA	.	.	.	none		0.498	TRIP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206721.2	NM_004237		T	908120	C	T	908120	2	4	107	1	0	0	0	0	0	0	0	1	16569	581	21	2		2	TRIP13	5	908120	Silent	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10		908120	180007140	21	6785											
SRD5A1	6715	hgsc.bcm.edu	37	chr5	6663046	6663047	+	Frame_Shift_Ins	INS	-	-	T																															tttgctttcttcacgttttgINSttttttatctggtagagcaa																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr5:6663046_6663047insT	ENST00000274192.5	+	4	914_915	c.680_681insT	c.(679-684)tgttttfs	p.CF227fs	SRD5A1_ENST00000538824.1_Frame_Shift_Ins_p.CF180fs|SRD5A1_ENST00000537411.1_3'UTR	NM_001047.2	NP_001038.1	P18405	S5A1_HUMAN	steroid-5-alpha-reductase, alpha polypeptide 1 (3-oxo-5 alpha-steroid delta 4-dehydrogenase alpha 1)	227					androgen biosynthetic process (GO:0006702)|cell differentiation (GO:0030154)|sex determination (GO:0007530)|sex differentiation (GO:0007548)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	3-oxo-5-alpha-steroid 4-dehydrogenase activity (GO:0003865)|cholestenone 5-alpha-reductase activity (GO:0047751)|electron carrier activity (GO:0009055)			endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19					Dutasteride(DB01126)|Finasteride(DB01216)|Levonorgestrel(DB00367)|Spironolactone(DB00421)	TTCACGTTTTGTTTTTTATCTG	0.396																																					p.C227fs		Atlas-Indel,Pindel	.											.	SRD5A1	31	.	0			c.680_681insT						PASS	.																																			SO:0001589	frameshift_variant	6715	exon4			.	M32313	CCDS3870.1	5p15.31	2008-02-05			ENSG00000145545	ENSG00000145545	1.3.99.5		11284	protein-coding gene	gene with protein product		184753				1686016	Standard	XR_427663		Approved		uc003jdw.3	P18405	OTTHUMG00000090456	ENST00000274192.5:c.686dupT	chr5.hg19:g.6663052_6663052dupT	ENSP00000274192:p.Cys227fs	92.0	0.0	0		91.0	23.0	0.252747	NM_001047	B2R7Q1|Q9UHY4|Q9UP36|Q9UP37	Frame_Shift_Ins	INS	ENST00000274192.5	hg19	CCDS3870.1																																																																																			.	.	.	none		0.396	SRD5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206903.1	NM_001047		T	6663047	-	T	6663046	7	5	107	1	0	1	1	0	0	0	0	0	15150	1377	48	0	694	0	SRD5A1	5	6663046	Frame_Shift_Ins	INS	-	TCGA-B9-A69E-01A-11D-A31X-10	5754926	6663046	174252214	22	6786											
CDH12	1010	hgsc.bcm.edu	37	chr5	21752166	21752166	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggttttatatccctgcgaaTtttgttctcctcaatcactt	7	19	5	10	1	3	0	2	0	1	0	5	1	4	0	2	1	1	2	2	1	4	7			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr5:21752166T>C	ENST00000382254.1	-	15	3151	c.2065A>G	c.(2065-2067)Att>Gtt	p.I689V	RP11-804N13.1_ENST00000522350.1_RNA|CDH12_ENST00000504376.2_Missense_Mutation_p.I689V|CDH12_ENST00000522262.1_Missense_Mutation_p.I649V|CDH12_ENST00000521384.1_5'UTR	NM_004061.3	NP_004052.2	P55289	CAD12_HUMAN	cadherin 12, type 2 (N-cadherin 2)	689					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)			NS(2)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(19)|lung(75)|ovary(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	120						TCCCTGCGAATTTTGTTCTCC	0.458										HNSCC(59;0.17)																											p.I689V		Atlas-SNP	.											.	CDH12	238	.	0			c.A2065G						PASS	.						188	161	171					5																	21752166		2203	4300	6503	SO:0001583	missense	1010	exon15			TGCGAATTTTGTT	L33477	CCDS3890.1	5p14.3	2010-01-26			ENSG00000154162	ENSG00000154162		"Cadherins / Major cadherins"	1751	protein-coding gene	gene with protein product		600562				7731968	Standard	NM_004061		Approved	Br-cadherin, CDHB	uc003jgk.2	P55289	OTTHUMG00000090591	ENST00000382254.1:c.2065A>G	chr5.hg19:g.21752166T>C	ENSP00000371689:p.Ile689Val	203.0	0.0	.		221.0	60.0	.	NM_004061	B2RBT1|B7Z2U6|Q86UD2	Missense_Mutation	SNP	ENST00000382254.1	hg19	CCDS3890.1	.	.	.	.	.	.	.	.	.	.	T	5.372	0.253855	0.10185	.	.	ENSG00000154162	ENST00000504376;ENST00000382254;ENST00000522262	T;T;T	0.76186	-1.0;-1.0;-1.0	5.12	3.92	0.45320	Cadherin, cytoplasmic domain (1);	0.479938	0.25538	N	0.029988	T	0.51958	0.1705	N	0.14661	0.345	0.31334	N	0.684456	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.46938	-0.9155	10	0.17369	T	0.5	.	6.6994	0.23217	0.0:0.0776:0.1551:0.7673	.	649;689	B7Z2U6;P55289	.;CAD12_HUMAN	V	689;689;649	ENSP00000423577:I689V;ENSP00000371689:I689V;ENSP00000428786:I649V	ENSP00000371689:I689V	I	-	1	0	CDH12	21787923	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	1.798000	0.38814	0.765000	0.33221	0.383000	0.25322	ATT	.	.	.	none		0.458	CDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207139.1	NM_004061		C	21752166	T	C	21752166	3	2	107	1	0	0	0	0	1	0	0	0	3100	1493	52	3	323	3	CDH12	5	21752166	Missense_Mutation	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10	15089120	21752166	159163094	23	6787											
DST	667	hgsc.bcm.edu	37	chr6	56504731	56504731	+	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	ttttaaattcacatacctcaCtgattttagcttctttgaga	11	18	4	8	0	3	2	2	2	1	1	3	3	3	2	1	0	2	1	1	0	4	8			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr6:56504731C>T	ENST00000361203.3	-	15	1989	c.1982G>A	c.(1981-1983)aGt>aAt	p.S661N	DST_ENST00000370769.4_Missense_Mutation_p.S661N|DST_ENST00000312431.6_Missense_Mutation_p.S661N|DST_ENST00000421834.2_Missense_Mutation_p.S661N|DST_ENST00000446842.2_Missense_Mutation_p.S335N|DST_ENST00000518935.1_Missense_Mutation_p.S335N|DST_ENST00000244364.6_Missense_Mutation_p.S335N|DST_ENST00000370788.2_Missense_Mutation_p.S661N|DST_ENST00000370754.5_Missense_Mutation_p.S839N|DST_ENST00000370765.6_Missense_Mutation_p.S335N			Q03001	DYST_HUMAN	dystonin	661					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)			ACATACCTCACTGATTTTAGC	0.284																																					p.S335N		Atlas-SNP	.											.	DST	1427	.	0			c.G1004A						PASS	.						47	51	50					6																	56504731		2203	4299	6502	SO:0001583	missense	667	exon5			ACCTCACTGATTT	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.1982G>A	chr6.hg19:g.56504731C>T	ENSP00000354508:p.Ser661Asn	98.0	0.0	.		81.0	30.0	.	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	hg19		.	.	.	.	.	.	.	.	.	.	C	17.97	3.519255	0.64634	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203;ENST00000439203;ENST00000520645;ENST00000370765;ENST00000518935	T;T;T;T;T;D;T;T;T;D;T;T	0.83992	1.18;0.02;0.02;0.17;0.96;-1.53;0.13;-0.0;-0.3;-1.79;-0.69;-0.14	5.45	4.58	0.56647	.	0.000000	0.64402	D	0.000017	T	0.80486	0.4632	L	0.44542	1.39	0.29528	N	0.852973	P;B;P;B;D;B;B;P;B;B	0.55385	0.899;0.235;0.944;0.354;0.971;0.016;0.115;0.917;0.235;0.277	B;B;D;B;P;B;B;P;B;B	0.63597	0.401;0.149;0.916;0.149;0.73;0.02;0.134;0.897;0.149;0.329	T	0.78265	-0.2271	9	0.17832	T	0.49	.	14.2099	0.65756	0.0:0.9287:0.0:0.0713	.	690;661;661;839;777;335;335;335;661;335	B4DGY0;Q5TBT1;E7ERU2;E9PEB9;Q03001-13;Q6P0N6;Q03001-3;Q03001-9;Q03001;Q03001-8	.;.;.;.;.;.;.;.;DYST_HUMAN;.	N	335;839;661;661;335;661;661;661;335;701;335;335	ENSP00000244364:S335N;ENSP00000359790:S839N;ENSP00000359805:S661N;ENSP00000400883:S661N;ENSP00000393645:S335N;ENSP00000307959:S661N;ENSP00000359824:S661N;ENSP00000354508:S661N;ENSP00000404924:S335N;ENSP00000431030:S701N;ENSP00000359801:S335N;ENSP00000431003:S335N	ENSP00000244364:S335N	S	-	2	0	DST	56612690	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	3.897000	0.56273	1.525000	0.49052	0.655000	0.94253	AGT	.	.	.	none		0.284	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		T	56504731	C	T	56504731	3	4	107	1	0	0	0	0	1	0	0	0	4785	565	20	2	19471	2	DST	6	56504731	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10		56504731	114610336	24	6788											
RIMS1	22999	hgsc.bcm.edu	37	chr6	72960096	72960096	+	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	atgttctgcaagcaacagatCtacctgctagagtagatgga	13	10	10	8	0	2	3	0	0	2	3	2	4	2	4	1	1	5	5	1	1	5	4			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr6:72960096C>G	ENST00000521978.1	+	13	2305	c.2305C>G	c.(2305-2307)Cta>Gta	p.L769V	RIMS1_ENST00000520567.1_Missense_Mutation_p.L769V|RIMS1_ENST00000522291.1_Missense_Mutation_p.L769V|RIMS1_ENST00000517827.1_Missense_Mutation_p.L228V|RIMS1_ENST00000264839.7_Missense_Mutation_p.L769V|RIMS1_ENST00000538414.1_5'Flank|RIMS1_ENST00000425662.2_Missense_Mutation_p.L162V|RIMS1_ENST00000348717.5_Missense_Mutation_p.L769V|RIMS1_ENST00000517960.1_Missense_Mutation_p.L769V|RIMS1_ENST00000401910.3_Missense_Mutation_p.L243V|RIMS1_ENST00000523963.1_Missense_Mutation_p.L243V|RIMS1_ENST00000518273.1_Missense_Mutation_p.L769V|RIMS1_ENST00000491071.2_Missense_Mutation_p.L769V	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	769	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				AGCAACAGATCTACCTGCTAG	0.348																																					p.L769V		Atlas-SNP	.											.	RIMS1	278	.	0			c.C2305G						PASS	.						89	83	84					6																	72960096		1846	4102	5948	SO:0001583	missense	22999	exon13			ACAGATCTACCTG	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.2305C>G	chr6.hg19:g.72960096C>G	ENSP00000428417:p.Leu769Val	71.0	0.0	.		90.0	14.0	.	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	hg19	CCDS47449.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.83|18.83	3.706633|3.706633	0.68615|0.68615	.|.	.|.	ENSG00000079841|ENSG00000079841	ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978;ENST00000401910;ENST00000523963;ENST00000425662;ENST00000453976;ENST00000517827|ENST00000517433	D;D;D;D;D;D;D;D;D;D;D;D;D|.	0.82344|.	-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6|.	5.28|5.28	4.38|4.38	0.52667|0.52667	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);|.	0.000000|.	0.52532|.	D|.	0.000072|.	T|T	0.69663|0.69663	0.3136|0.3136	M|M	0.87971|0.87971	2.92|2.92	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D|.	0.76494|.	0.999;0.962;0.99;0.99;0.998;0.994;0.99|.	D;D;D;D;D;D;D|.	0.97110|.	1.0;0.983;0.996;0.996;0.999;0.996;0.996|.	T|T	0.74475|0.74475	-0.3653|-0.3653	10|5	0.87932|.	D|.	0|.	-12.8523|-12.8523	10.4795|10.4795	0.44684|0.44684	0.0:0.8222:0.0:0.1778|0.0:0.8222:0.0:0.1778	.|.	228;243;769;228;243;769;769|.	B7Z3S3;E9PHF5;E9PHR1;B7Z9Z3;E9PF48;C9JNW6;Q86UR5|.	.;.;.;.;.;.;RIMS1_HUMAN|.	V|C	769;769;769;769;769;769;769;769;769;769;769;769;243;243;162;162;228|342	ENSP00000430101:L769V;ENSP00000275037:L769V;ENSP00000264839:L769V;ENSP00000429959:L769V;ENSP00000430408:L769V;ENSP00000430502:L769V;ENSP00000430932:L769V;ENSP00000428417:L769V;ENSP00000385649:L243V;ENSP00000428328:L243V;ENSP00000411235:L162V;ENSP00000389503:L162V;ENSP00000428367:L228V|.	ENSP00000264839:L769V|.	L|S	+|+	1|2	2|0	RIMS1|RIMS1	73016817|73016817	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.838000|0.838000	0.47535|0.47535	4.060000|4.060000	0.57477|0.57477	1.279000|1.279000	0.44446|0.44446	0.585000|0.585000	0.79938|0.79938	CTA|TCT	.	.	.	none		0.348	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			G	72960096	C	G	72960096	3	3	107	1	0	0	0	0	1	0	0	0	13380	912	32	4	2518	4	RIMS1	6	72960096	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	16455365	72960096	98154971	25	6789											
AKD1	221264	hgsc.bcm.edu	37	chr6	109977966	109977966	+	Frame_Shift_Del	DEL	G	G	-																															attttgttcttacttctaaaGtttggagaattgtttcctta																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr6:109977966delG	ENST00000424296.2	-	8	828	c.752delC	c.(751-753)actfs	p.T251fs	AK9_ENST00000368948.2_Frame_Shift_Del_p.T251fs|AK9_ENST00000341338.6_5'UTR|AK9_ENST00000285397.5_Frame_Shift_Del_p.T251fs	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	251	Adenylate kinase 1.|Glu-rich.				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)										TACTTCTAAAGTTTGGAGAAT	0.318																																					p.T251fs		Atlas-Indel,Pindel	.											.	AKD1	223	.	0			c.753delT						PASS	.						57	58	58					6																	109977966		2203	4294	6497	SO:0001589	frameshift_variant	221264	exon8			.	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.752delC	chr6.hg19:g.109977966delG	ENSP00000410186:p.Thr251fs	96.0	0.0	0		103.0	32.0	0.31068	NM_001145128	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Frame_Shift_Del	DEL	ENST00000424296.2	hg19	CCDS55048.1																																																																																			.	.	.	none		0.318	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128		-	109977966	G	-	109977966	7	5	107	1	0	1	0	1	0	0	0	0	460	1029	36	0	5131	0	AKD1	6	109977966	Frame_Shift_Del	DEL	G	TCGA-B9-A69E-01A-11D-A31X-10	37017870	109977966	61137101	26	6790											
VGLL2	245806	hgsc.bcm.edu	37	chr6	117591730	117591730	+	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	ctccttcccgatgagccagcGcagcttccccgcctccttct	4	10	7	20	3	1	1	0	1	1	0	5	2	5	1	7	0	3	2	7	0	0	3			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr6:117591730G>T	ENST00000326274.5	+	3	606	c.416G>T	c.(415-417)cGc>cTc	p.R139L	VGLL2_ENST00000352536.3_Intron	NM_182645.3	NP_872586.1	Q8N8G2	VGLL2_HUMAN	vestigial-like family member 2	139					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)		ATGAGCCAGCGCAGCTTCCCC	0.697																																					p.R139L		Atlas-SNP	.											.	VGLL2	18	.	0			c.G416T						PASS	.						13	15	14					6																	117591730		2195	4285	6480	SO:0001583	missense	245806	exon3			GCCAGCGCAGCTT	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.416G>T	chr6.hg19:g.117591730G>T	ENSP00000320957:p.Arg139Leu	72.0	0.0	.		53.0	4.0	.	NM_182645	Q8WWX1	Missense_Mutation	SNP	ENST00000326274.5	hg19	CCDS5115.1	.	.	.	.	.	.	.	.	.	.	G	34	5.331271	0.95733	.	.	ENSG00000170162	ENST00000326274	T	0.54866	0.55	4.86	4.86	0.63082	.	0.056880	0.64402	D	0.000003	T	0.68393	0.2996	M	0.73962	2.25	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.72360	-0.4317	10	0.72032	D	0.01	-24.0493	18.1693	0.89740	0.0:0.0:1.0:0.0	.	139	Q8N8G2	VGLL2_HUMAN	L	139	ENSP00000320957:R139L	ENSP00000320957:R139L	R	+	2	0	VGLL2	117698423	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.078000	0.94023	2.528000	0.85240	0.549000	0.68633	CGC	.	.	.	none		0.697	VGLL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041975.2	NM_153453		T	117591730	G	T	117591730	3	4	107	1	0	0	0	0	1	0	0	0	17171	1087	38	4	426	4	VGLL2	6	117591730	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	7613764	117591730	53523337	27	6791											
C6orf170	221322	hgsc.bcm.edu	37	chr6	121433801	121433801	+	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	ccagcataattcccttgcagGcagactgaaaaacacagtta	15	8	7	11	0	0	2	0	1	0	1	1	2	1	2	2	1	3	4	2	1	4	4			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr6:121433801G>T	ENST00000398212.2	-	29	3223	c.3174C>A	c.(3172-3174)tgC>tgA	p.C1058*	TBC1D32_ENST00000398197.2_5'UTR|TBC1D32_ENST00000275159.6_Nonsense_Mutation_p.C1099*	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	1058					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)										TCCCTTGCAGGCAGACTGAAA	0.274																																					p.C1058X		Atlas-SNP	.											.	C6orf170	146	.	0			c.C3174A						PASS	.						54	49	50					6																	121433801		1803	4070	5873	SO:0001587	stop_gained	221322	exon29			TTGCAGGCAGACT	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.3174C>A	chr6.hg19:g.121433801G>T	ENSP00000381270:p.Cys1058*	54.0	0.0	.		67.0	4.0	.	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Nonsense_Mutation	SNP	ENST00000398212.2	hg19	CCDS43501.1	.	.	.	.	.	.	.	.	.	.	G	33	5.220888	0.95139	.	.	ENSG00000146350	ENST00000275159;ENST00000398212	.	.	.	5.41	3.63	0.41609	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.3109	0.32071	0.3125:0.0:0.6875:0.0	.	.	.	.	X	1099;1058	.	ENSP00000275159:C1099X	C	-	3	2	C6orf170	121475500	1.000000	0.71417	0.998000	0.56505	0.007000	0.05969	2.668000	0.46816	0.674000	0.31244	0.585000	0.79938	TGC	.	.	.	none		0.274	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		T	121433801	G	T	121433801	4	4	107	1	0	0	0	0	0	1	0	0	2346	1195	42	4	615	4	C6orf170	6	121433801	Nonsense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	3842071	121433801	49681266	28	6792											
EGFR	1956	hgsc.bcm.edu	37	chr7	55272975	55272975	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taaaccagtccgttcccaaaAggcccgctggctctgtgcag	9	8	10	14	2	1	0	0	0	1	0	3	0	3	0	4	2	2	4	4	2	4	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr7:55272975A>G	ENST00000275493.2	+	28	3475	c.3298A>G	c.(3298-3300)Agg>Ggg	p.R1100G	EGFR_ENST00000442591.1_Intron|EGFR_ENST00000454757.2_Missense_Mutation_p.R1047G	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	1100					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)	CGTTCCCAAAAGGCCCGCTGG	0.532		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																											p.R1100G		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.A3298G						PASS	.						64	62	62					7																	55272975		2203	4300	6503	SO:0001583	missense	1956	exon28	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	CCCAAAAGGCCCG		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.3298A>G	chr7.hg19:g.55272975A>G	ENSP00000275493:p.Arg1100Gly	112.0	0.0	.		103.0	5.0	.	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	hg19	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	A	14.14	2.447696	0.43429	.	.	ENSG00000146648	ENST00000395504;ENST00000275493;ENST00000454757	T;T	0.77489	-1.1;-1.09	5.2	4.01	0.46588	.	0.344819	0.30519	N	0.009445	T	0.75324	0.3834	M	0.76328	2.33	0.23865	N	0.996623	B	0.20459	0.045	B	0.18263	0.021	T	0.66720	-0.5852	10	0.49607	T	0.09	.	10.3302	0.43818	0.6825:0.3175:0.0:0.0	.	1100	P00533	EGFR_HUMAN	G	970;1100;1047	ENSP00000275493:R1100G;ENSP00000395243:R1047G	ENSP00000275493:R1100G	R	+	1	2	EGFR	55240469	0.901000	0.30685	1.000000	0.80357	0.979000	0.70002	1.436000	0.34980	0.876000	0.35872	0.456000	0.33151	AGG	.	.	.	none		0.532	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		G	55272975	A	G	55272975	3	3	107	1	0	0	0	0	1	0	0	0	4969	63	3	3	3672	3	EGFR	7	55272975	Missense_Mutation	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10		55272975	103865688	29	6793											
GPR85	54329	hgsc.bcm.edu	37	chr7	112724144	112724146	+	In_Frame_Del	DEL	ATC	ATC	-																															actggcttcatttttcttcgAtcgtggacgaaaaatatcag																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	ATC	ATC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr7:112724144_112724146delATC	ENST00000297146.3	-	3	1234_1236	c.631_633delGAT	c.(631-633)gatdel	p.D211del	GPR85_ENST00000501255.2_In_Frame_Del_p.D211del|GPR85_ENST00000487573.1_5'Flank|GPR85_ENST00000424100.1_In_Frame_Del_p.D211del|GPR85_ENST00000449591.1_In_Frame_Del_p.D211del	NM_001146266.1	NP_001139738.1	P60893	GPR85_HUMAN	G protein-coupled receptor 85	211					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						TTTTTCTTCGATCGTGGACGAAA	0.493																																					p.211_212del		Atlas-INDEL	.											GPR85,NS,carcinoma,0,1	GPR85	49	.	0			c.632_634del						PASS	.																																			SO:0001651	inframe_deletion	54329	exon3			.	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.631_633delGAT	chr7.hg19:g.112724144_112724146delATC	ENSP00000297146:p.Asp211del	84.0	0.0	0		63.0	14.0	0.222222	NM_001146265	Q9JHI6|Q9NPD1	In_Frame_Del	DEL	ENST00000297146.3	hg19	CCDS5758.1																																																																																			.	.	.	none		0.493	GPR85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346650.2			-	112724146	ATC	-	112724144	7	5	107	1	0	1	0	1	0	0	0	0	6722	330	12	0	483	0	GPR85	7	112724144	In_Frame_Del	DEL	ATC	TCGA-B9-A69E-01A-11D-A31X-10	57451169	112724144	46414519	30	6794											
RBM28	55131	hgsc.bcm.edu	37	chr7	127958110	127958111	+	In_Frame_Ins	INS	-	-	GAC																															aaaggcgtagcccagggactINSgacccttcatgttcccatga																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr7:127958110_127958111insGAC	ENST00000223073.2	-	15	1726_1727	c.1612_1613insGTC	c.(1612-1614)cag>cGTCag	p.537_538insR	RBM28_ENST00000481788.1_Intron|RBM28_ENST00000415472.2_In_Frame_Ins_p.396_397insR	NM_018077.2	NP_060547.2	Q9NW13	RBM28_HUMAN	RNA binding motif protein 28	537	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|kidney(7)|large_intestine(3)|lung(8)|ovary(2)	21						GCCCAGGGACTGACCCTTCATG	0.485																																					p.Q538delinsRQ		Atlas-Indel,Pindel	.											.	RBM28	71	.	0			c.1613_1614insGTC						PASS	.																																			SO:0001652	inframe_insertion	55131	exon15			.	AK001239	CCDS5801.1, CCDS55159.1	7q32.2	2013-02-12			ENSG00000106344	ENSG00000106344		"RNA binding motif (RRM) containing"	21863	protein-coding gene	gene with protein product		612074					Standard	NM_018077		Approved	FLJ10377	uc003vmp.2	Q9NW13	OTTHUMG00000157711	ENST00000223073.2:c.1610_1612dupGTC	chr7.hg19:g.127958111_127958113dupGAC	ENSP00000223073:p.Gly537_Gln538insArg	101.0	0.0	0		88.0	19.0	0.215909	NM_018077	A4D100|B4DU52|E9PDD9|Q53H65|Q96CV3	In_Frame_Ins	INS	ENST00000223073.2	hg19	CCDS5801.1																																																																																			.	.	.	none		0.485	RBM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349442.2	NM_018077		GAC	127958111	-	GAC	127958110	7	5	107	1	0	1	1	0	0	0	0	0	13141	1580	55	0	686	0	RBM28	7	127958110	In_Frame_Ins	INS	-	TCGA-B9-A69E-01A-11D-A31X-10	15233966	127958110	31180553	31	6795											
LSM1	27257	hgsc.bcm.edu	37	chr8	38027436	38027436	+	Splice_Site	DEL	C	C	-																															ctgatgtagcactaagtttgCtgtaagtgtatagggaaaaa																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr8:38027436delC	ENST00000311351.4	-	3	511		c.e3-1		LSM1_ENST00000522515.1_Splice_Site|LSM1_ENST00000520755.1_Intron	NM_014462.2	NP_055277.1	O15116	LSM1_HUMAN	LSM1, U6 small nuclear RNA associated						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(3)|lung(2)	7	Colorectal(12;0.000442)					ACTAAGTTTGCTGTAAGTGTA	0.363																																					p.A39fs		Atlas-Indel,Pindel	.											.	LSM1	14	.	0			c.116delC						PASS	.						127	118	121					8																	38027436		2203	4300	6503	SO:0001630	splice_region_variant	27257	exon3			.	AF000177	CCDS6103.1	8p11.2	2014-02-14	2014-02-14		ENSG00000175324	ENSG00000175324			20472	protein-coding gene	gene with protein product		607281	"LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae)"			12515382, 11953827	Standard	NM_014462		Approved	CASM, YJL124C	uc003xkw.3	O15116	OTTHUMG00000164051	ENST00000311351.4:c.116-1G>-	chr8.hg19:g.38027436delC		122.0	0.0	0		129.0	33.0	0.255814	NM_014462	B2R5E6	Frame_Shift_Del	DEL	ENST00000311351.4	hg19	CCDS6103.1																																																																																			.	.	.	none		0.363	LSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376965.1	NM_014462	Intron	-	38027436	C	-	38027436	8	5	107	1	0	1	0	1	0	0	1	0	9057	811	28	0	294	0	LSM1	8	38027436	Splice_Site	DEL	C	TCGA-B9-A69E-01A-11D-A31X-10		38027436	108336586	32	6796											
TMEM67	91147	hgsc.bcm.edu	37	chr8	94805453	94805453	+	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	tgggtgtattgggtgggctaGctgttttagcatctcttttg	4	18	14	5	0	1	0	0	0	1	0	2	0	1	0	0	3	2	5	0	3	3	7			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr8:94805453G>C	ENST00000453321.3	+	16	1661	c.1603G>C	c.(1603-1605)Gct>Cct	p.A535P	TMEM67_ENST00000409623.3_Missense_Mutation_p.A454P	NM_153704.5	NP_714915.3	Q5HYA8	MKS3_HUMAN	transmembrane protein 67	535					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of centrosome duplication (GO:0010826)	centrosome (GO:0005813)|ciliary membrane (GO:0060170)|cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)	filamin binding (GO:0031005)|unfolded protein binding (GO:0051082)			breast(3)|endometrium(8)|kidney(5)|large_intestine(4)|liver(2)|lung(15)|ovary(2)|skin(1)|urinary_tract(1)	41	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)			GGGTGGGCTAGCTGTTTTAGC	0.368																																					p.A535P		Atlas-SNP	.											.	TMEM67	187	.	0			c.G1603C						PASS	.						157	153	154					8																	94805453		2203	4300	6503	SO:0001583	missense	91147	exon16			GGGCTAGCTGTTT	BX648768	CCDS6258.2, CCDS47893.1	8q22.1	2014-09-17			ENSG00000164953	ENSG00000164953			28396	protein-coding gene	gene with protein product	"Meckelin"	609884	"Meckel syndrome, type 3"	MKS3		12384791, 16415887, 19508969	Standard	NM_153704		Approved	MGC26979, JBTS6, NPHP11	uc011lgk.2	Q5HYA8	OTTHUMG00000153119	ENST00000453321.3:c.1603G>C	chr8.hg19:g.94805453G>C	ENSP00000389998:p.Ala535Pro	101.0	0.0	.		116.0	31.0	.	NM_153704	B3KRU5|B3KT47|G5E9H2|Q3ZCX3|Q7Z5T8|Q8IZ06	Missense_Mutation	SNP	ENST00000453321.3	hg19	CCDS6258.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.1|26.1	4.706160|4.706160	0.89018|0.89018	.|.	.|.	ENSG00000164953|ENSG00000164953	ENST00000453321;ENST00000409623|ENST00000520680	D;D|.	0.97256|.	-4.31;-4.31|.	5.6|5.6	5.6|5.6	0.85130|0.85130	.|.	0.111849|.	0.64402|.	D|.	0.000016|.	T|T	0.78317|0.78317	0.4264|0.4264	M|M	0.77103|0.77103	2.36|2.36	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.83275|.	0.993;0.996;0.992|.	T|T	0.77584|0.77584	-0.2533|-0.2533	10|5	0.66056|.	D|.	0.02|.	-17.8669|-17.8669	19.6017|19.6017	0.95566|0.95566	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	535;454;454|.	Q5HYA8;B3KRU5;G5E9H2|.	MKS3_HUMAN;.;.|.	P|T	535;454|183	ENSP00000389998:A535P;ENSP00000386966:A454P|.	ENSP00000314488:A525P|.	A|S	+|+	1|2	0|0	TMEM67|TMEM67	94874629|94874629	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.997000|0.997000	0.91878|0.91878	6.318000|6.318000	0.72866|0.72866	2.622000|2.622000	0.88805|0.88805	0.655000|0.655000	0.94253|0.94253	GCT|AGC	.	.	.	none		0.368	TMEM67-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329641.2	NM_153704		C	94805453	G	C	94805453	3	2	107	1	0	0	0	0	1	0	0	0	16208	971	34	4	1803	4	TMEM67	8	94805453	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	56778017	94805453	51558569	33	6797											
RECK	8434	hgsc.bcm.edu	37	chr9	36091304	36091304	+	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	ggaaccttgccagttgggctGtagaaaccttacttactgta	10	12	10	9	0	0	1	0	0	0	1	0	2	0	2	3	2	5	4	3	2	6	6			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr9:36091304G>T	ENST00000377966.3	+	10	1615	c.1049G>T	c.(1048-1050)tGt>tTt	p.C350F		NM_021111.2	NP_066934.1	O95980	RECK_HUMAN	reversion-inducing-cysteine-rich protein with kazal motifs	350					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)			CAGTTGGGCTGTAGAAACCTT	0.353																																					p.C350F		Atlas-SNP	.											.	RECK	73	.	0			c.G1049T						PASS	.						119	109	112					9																	36091304		2203	4300	6503	SO:0001583	missense	8434	exon10			TGGGCTGTAGAAA	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.1049G>T	chr9.hg19:g.36091304G>T	ENSP00000367202:p.Cys350Phe	137.0	0.0	.		100.0	4.0	.	NM_021111	B2RNS1|Q5W0K6|Q8WX37	Missense_Mutation	SNP	ENST00000377966.3	hg19	CCDS6597.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.556454	0.86231	.	.	ENSG00000122707	ENST00000377966	T	0.73575	-0.76	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	D	0.85999	0.5828	M	0.74467	2.265	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.86690	0.1922	10	0.87932	D	0	-10.6063	16.0667	0.80887	0.0:0.0:1.0:0.0	.	350;350	A8K9D8;O95980	.;RECK_HUMAN	F	350	ENSP00000367202:C350F	ENSP00000367202:C350F	C	+	2	0	RECK	36081304	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.854000	0.98071	0.655000	0.94253	TGT	.	.	.	none		0.353	RECK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052409.1			T	36091304	G	T	36091304	3	4	107	1	0	0	0	0	1	0	0	0	13213	1377	48	4	1087	4	RECK	9	36091304	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10		36091304	105122127	34	6798											
DNAJC25	548645	hgsc.bcm.edu	37	chr9	114412019	114412019	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccttttcacctatgctcatAtatagtttggtattgtcggt	7	19	7	8	1	2	0	2	0	0	0	4	0	3	0	2	2	1	3	2	2	5	9			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr9:114412019A>G	ENST00000313525.3	+	3	832	c.776A>G	c.(775-777)tAt>tGt	p.Y259C	DNAJC25_ENST00000556107.1_Intron|DNAJC25-GNG10_ENST00000374294.3_Intron	NM_001015882.2	NP_001015882.2	Q9H1X3	DJC25_HUMAN	DnaJ (Hsp40) homolog, subfamily C , member 25	259						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(1)|skin(4)	8						CTATGCTCATATATAGTTTGG	0.328																																					p.Y259C		Atlas-SNP	.											.	DNAJC25	20	.	0			c.A776G						PASS	.						48	50	49					9																	114412019		1817	4067	5884	SO:0001583	missense	548645	exon3			GCTCATATATAGT		CCDS43862.1	9q31.3	2011-09-02			ENSG00000059769	ENSG00000059769		"Heat shock proteins / DNAJ (HSP40)"	34187	protein-coding gene	gene with protein product							Standard	NM_001015882		Approved	bA16L21.2.1	uc004bfl.3	Q9H1X3	OTTHUMG00000020491	ENST00000313525.3:c.776A>G	chr9.hg19:g.114412019A>G	ENSP00000320650:p.Tyr259Cys	138.0	0.0	.		178.0	41.0	.	NM_001015882	Q5QTD8|Q96BN9	Missense_Mutation	SNP	ENST00000313525.3	hg19	CCDS43862.1	.	.	.	.	.	.	.	.	.	.	A	16.14	3.039309	0.55003	.	.	ENSG00000059769	ENST00000313525	T	0.52057	0.68	6.17	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.49729	0.1574	M	0.79475	2.455	0.80722	D	1	B	0.20887	0.049	B	0.19666	0.026	T	0.49244	-0.8960	10	0.56958	D	0.05	-6.1843	11.1739	0.48588	0.9308:0.0:0.0692:0.0	.	259	Q9H1X3	DJC25_HUMAN	C	259	ENSP00000320650:Y259C	ENSP00000320650:Y259C	Y	+	2	0	DNAJC25	113451840	1.000000	0.71417	0.055000	0.19348	0.793000	0.44817	6.943000	0.75934	1.144000	0.42321	0.533000	0.62120	TAT	.	.	.	none		0.328	DNAJC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156218.3	NM_001015882		G	114412019	A	G	114412019	3	3	107	1	0	0	0	0	1	0	0	0	4645	449	16	3	786	3	DNAJC25	9	114412019	Missense_Mutation	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10	78320715	114412019	26801412	35	6799											
MLLT10	8028	hgsc.bcm.edu	37	chr10	21970293	21970293	+	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	agtatcggcatgatggagctTgcccaacaactagtaagttg	12	10	11	8	1	0	1	0	1	0	0	1	2	0	2	1	2	4	5	1	2	5	5			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr10:21970293T>A	ENST00000307729.7	+	12	1832	c.1654T>A	c.(1654-1656)Tgc>Agc	p.C552S	MLLT10_ENST00000377072.3_Missense_Mutation_p.C552S|MLLT10_ENST00000446906.2_Missense_Mutation_p.C552S|MLLT10_ENST00000377059.3_Missense_Mutation_p.C552S			P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10	552	DNA-binding.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6						TGATGGAGcttgcccaacaac	0.428			T	"MLL, PICALM, CDK6"	AL																																p.C552S		Atlas-SNP	.		Dom	yes		10	10p12	8028	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10 (AF10)"		L	.	MLLT10	183	.	0			c.T1654A						PASS	.						118	114	115					10																	21970293		2203	4300	6503	SO:0001583	missense	8028	exon11			GGAGCTTGCCCAA	U13948	CCDS7135.1, CCDS55706.1, CCDS55707.1, CCDS55708.1	10p12	2013-01-28	2001-11-28		ENSG00000078403	ENSG00000078403		"Zinc fingers, PHD-type"	16063	protein-coding gene	gene with protein product		602409	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 10"			7888665	Standard	NM_004641		Approved	AF10	uc021pny.1	P55197	OTTHUMG00000017799	ENST00000307729.7:c.1654T>A	chr10.hg19:g.21970293T>A	ENSP00000307411:p.Cys552Ser	88.0	0.0	.		97.0	29.0	.	NM_001195626	B1ANA8|Q5JT37|Q5VX90|Q66K63	Missense_Mutation	SNP	ENST00000307729.7	hg19	CCDS55708.1	.	.	.	.	.	.	.	.	.	.	T	10.13	1.266891	0.23136	.	.	ENSG00000078403	ENST00000377072;ENST00000446906;ENST00000307729;ENST00000396529;ENST00000377059;ENST00000438473;ENST00000538639	T;T;T;T	0.14766	2.5;2.48;2.48;2.48	4.67	4.67	0.58626	.	0.392955	0.33309	N	0.005051	T	0.08670	0.0215	L	0.38175	1.15	0.48135	D	0.999596	B;B;B;B	0.33694	0.008;0.001;0.421;0.0	B;B;B;B	0.21360	0.004;0.0;0.034;0.001	T	0.22034	-1.0228	10	0.13470	T	0.59	.	10.6549	0.45669	0.0:0.0:0.0:1.0	.	247;552;552;552	Q5HYC6;E9PBP4;Q5VX90;P55197	.;.;.;AF10_HUMAN	S	552;552;552;398;552;195;194	ENSP00000366272:C552S;ENSP00000401406:C552S;ENSP00000307411:C552S;ENSP00000366258:C552S	ENSP00000307411:C552S	C	+	1	0	MLLT10	22010299	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.116000	0.41930	2.095000	0.63458	0.477000	0.44152	TGC	.	.	.	none		0.428	MLLT10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047136.1			A	21970293	T	A	21970293	3	1	107	1	0	0	0	0	1	0	0	0	9633	1812	63	5	1696	5	MLLT10	10	21970293	Missense_Mutation	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10		21970293	113564454	36	6800											
ENKUR	219670	hgsc.bcm.edu	37	chr10	25288439	25288439	+	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	gcagttttagctttttgcatGtcatcttttacagttgcctt	6	20	7	8	0	2	0	1	0	1	0	2	0	2	0	1	0	4	5	1	0	2	8			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr10:25288439G>T	ENST00000331161.4	-	2	333	c.114C>A	c.(112-114)gaC>gaA	p.D38E	ENKUR_ENST00000376363.1_Missense_Mutation_p.D38E	NM_145010.3	NP_659447.1	Q8TC29	ENKUR_HUMAN	enkurin, TRPC channel interacting protein	38						motile cilium (GO:0031514)				endometrium(2)|large_intestine(4)|lung(3)|skin(1)	10						CTTTTTGCATGTCATCTTTTA	0.299																																					p.D38E		Atlas-SNP	.											ENKUR,NS,carcinoma,-2,1	ENKUR	30	.	0			c.C114A						PASS	.						107	95	99					10																	25288439		2201	4297	6498	SO:0001583	missense	219670	exon2			TTGCATGTCATCT	AK095021	CCDS7146.1, CCDS73075.1	10p12.31	2014-08-13	2009-04-28	2009-04-28	ENSG00000151023	ENSG00000151023			28388	protein-coding gene	gene with protein product		611025	"chromosome 10 open reading frame 63"	C10orf63		17217053, 15385169	Standard	NM_145010		Approved	MGC26778, enkurin, CFAP106	uc001isg.2	Q8TC29	OTTHUMG00000017827	ENST00000331161.4:c.114C>A	chr10.hg19:g.25288439G>T	ENSP00000331044:p.Asp38Glu	72.0	0.0	.		86.0	19.0	.	NM_145010	A8K8Y0|D3DRV2	Missense_Mutation	SNP	ENST00000331161.4	hg19	CCDS7146.1	.	.	.	.	.	.	.	.	.	.	G	2.150	-0.394650	0.04899	.	.	ENSG00000151023	ENST00000331161;ENST00000376363	.	.	.	5.98	0.497	0.16902	.	0.090535	0.85682	D	0.000000	T	0.07413	0.0187	N	0.02539	-0.55	0.09310	N	0.999997	B	0.06786	0.001	B	0.01281	0.0	T	0.32079	-0.9920	9	0.02654	T	1	-22.9569	2.4844	0.04595	0.1405:0.2598:0.3993:0.2004	.	38	Q8TC29	ENKUR_HUMAN	E	38	.	ENSP00000331044:D38E	D	-	3	2	ENKUR	25328445	0.018000	0.18449	0.721000	0.30653	0.930000	0.56654	-0.003000	0.12901	0.428000	0.26173	0.591000	0.81541	GAC	.	.	.	none		0.299	ENKUR-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047239.2	NM_145010		T	25288439	G	T	25288439	3	4	107	1	0	0	0	0	1	0	0	0	5122	1368	48	4	676	4	ENKUR	10	25288439	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	3318146	25288439	110246308	37	6801											
HK1	3098	hgsc.bcm.edu	37	chr10	71136714	71136714	+	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	gagaagatggtcagtggcatGtacttgggagagctggttcg	9	10	17	5	1	1	3	1	0	0	3	2	5	1	3	0	4	2	4	0	4	2	3			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr10:71136714G>T	ENST00000359426.6	+	8	1004	c.900G>T	c.(898-900)atG>atT	p.M300I	HK1_ENST00000448642.2_Missense_Mutation_p.M335I|HK1_ENST00000360289.2_Missense_Mutation_p.M288I|HK1_ENST00000404387.2_Missense_Mutation_p.M304I|HK1_ENST00000298649.3_Missense_Mutation_p.M299I|HK1_ENST00000494253.1_3'UTR	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	300	Hexokinase type-2 1.|Regulatory.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						TCAGTGGCATGTACTTGGGAG	0.567																																					p.M304I		Atlas-SNP	.											.	HK1	170	.	0			c.G912T						PASS	.						163	143	150					10																	71136714		2203	4300	6503	SO:0001583	missense	3098	exon11			TGGCATGTACTTG	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.900G>T	chr10.hg19:g.71136714G>T	ENSP00000352398:p.Met300Ile	236.0	0.0	.		255.0	59.0	.	NM_033498	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Missense_Mutation	SNP	ENST00000359426.6	hg19	CCDS7292.1	.	.	.	.	.	.	.	.	.	.	G	17.53	3.413479	0.62511	.	.	ENSG00000156515	ENST00000360289;ENST00000448642;ENST00000404387;ENST00000298649;ENST00000359426;ENST00000405407	T;T;T;T;T	0.12255	2.7;2.7;2.7;2.7;2.7	4.94	4.94	0.65067	Hexokinase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.26011	0.0634	M	0.86573	2.825	0.80722	D	1	B;B;B;B;B;P	0.39717	0.191;0.191;0.004;0.013;0.05;0.684	B;B;B;B;B;B	0.37267	0.243;0.16;0.012;0.089;0.078;0.245	T	0.30880	-0.9963	10	0.72032	D	0.01	-26.1047	18.1516	0.89676	0.0:0.0:1.0:0.0	.	300;300;299;335;304;288	A8K7J7;P19367;P19367-2;E7ENR4;P19367-3;P19367-4	.;HXK1_HUMAN;.;.;.;.	I	288;335;304;299;300;300	ENSP00000353433:M288I;ENSP00000402103:M335I;ENSP00000384774:M304I;ENSP00000298649:M299I;ENSP00000352398:M300I	ENSP00000298649:M299I	M	+	3	0	HK1	70806720	1.000000	0.71417	1.000000	0.80357	0.561000	0.35649	7.941000	0.87700	2.293000	0.77203	0.585000	0.79938	ATG	.	.	.	none		0.567	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048429.2	NM_000188		T	71136714	G	T	71136714	3	4	107	1	0	0	0	0	1	0	0	0	7197	1377	48	4	1108	4	HK1	10	71136714	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	45848275	71136714	64398033	38	6802											
GBF1	8729	hgsc.bcm.edu	37	chr10	104103846	104103846	+	Missense_Mutation	SNP	T	T	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	ccaatgtattccttcgacctTttctggaagtgattcgctct	7	16	7	11	2	2	1	0	1	2	0	5	3	3	2	3	1	0	2	3	1	3	6			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr10:104103846T>G	ENST00000369983.3	+	4	462	c.202T>G	c.(202-204)Ttt>Gtt	p.F68V		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	68					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		CCTTCGACCTTTTCTGGAAGT	0.428																																					p.F68V		Atlas-SNP	.											.	GBF1	142	.	0			c.T202G						PASS	.						163	145	151					10																	104103846		2203	4300	6503	SO:0001583	missense	8729	exon4			CGACCTTTTCTGG	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.202T>G	chr10.hg19:g.104103846T>G	ENSP00000359000:p.Phe68Val	82.0	0.0	.		116.0	27.0	.	NM_001199378	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	hg19	CCDS7533.1	.	.	.	.	.	.	.	.	.	.	T	29.0	4.967181	0.92855	.	.	ENSG00000107862	ENST00000369983	T	0.68025	-0.3	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	D	0.85741	0.5767	M	0.91663	3.23	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.91635	0.998;0.999;0.994;0.999	D	0.88884	0.3341	10	0.87932	D	0	-13.687	16.3736	0.83374	0.0:0.0:0.0:1.0	.	68;68;68;68	Q149P1;Q149P0;Q92538;Q504U7	.;.;GBF1_HUMAN;.	V	68	ENSP00000359000:F68V	ENSP00000359000:F68V	F	+	1	0	GBF1	104093836	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	7.922000	0.87538	2.273000	0.75805	0.482000	0.46254	TTT	.	.	.	none		0.428	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			G	104103846	T	G	104103846	3	3	107	1	0	0	0	0	1	0	0	0	6278	1841	64	5	212	5	GBF1	10	104103846	Missense_Mutation	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10	32967132	104103846	31430901	39	6803											
MUC2	4583	hgsc.bcm.edu	37	chr11	1093271	1093271	+	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	caccggcacacagaccccaaCatcgacacccatcaccacca	14	2	4	21	2	1	1	1	0	0	1	2	2	1	1	6	1	1	1	6	1	1	0			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr11:1093271C>G	ENST00000441003.2	+	30	5117	c.5090C>G	c.(5089-5091)aCa>aGa	p.T1697R	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.T1664R	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.T1697R(2)|p.T1664R(2)		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)	cagaccccaacatcgacaccc	0.637																																					p.T1697R		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,-1,4	MUC2	614	.	4	Substitution - Missense(4)	kidney(2)|skin(2)	c.C5090G						PASS	.						126	165	151					11																	1093271		1844	3338	5182	SO:0001583	missense	4583	exon30			CCCCAACATCGAC	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.5090C>G	chr11.hg19:g.1093271C>G	ENSP00000415183:p.Thr1697Arg	82.0	0.0	.		94.0	8.0	.	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	C	5.778	0.327961	0.10956	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.13538	2.93;2.58	1.43	1.43	0.22495	.	27.718000	0.04275	U	0.342784	T	0.27027	0.0662	.	.	.	0.20307	N	0.999915	D	0.64830	0.994	D	0.67725	0.953	T	0.19647	-1.0299	9	0.30078	T	0.28	.	6.2291	0.20724	0.0:1.0:0.0:0.0	.	1697	E7EUV1	.	R	1697;1664	ENSP00000415183:T1697R;ENSP00000351956:T1664R	ENSP00000351956:T1664R	T	+	2	0	MUC2	1083271	0.001000	0.12720	0.002000	0.10522	0.003000	0.03518	0.752000	0.26362	0.796000	0.33947	0.184000	0.17185	ACA	.	.	.	none		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		G	1093271	C	G	1093271	3	3	107	1	0	0	0	0	1	0	0	0	9982	478	17	4	5208	4	MUC2	11	1093271	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10		1093271	133913245	40	6804											
OR52M1	119772	hgsc.bcm.edu	37	chr11	4567069	4567069	+	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	tgatcctggactcagtggctAttgctgcatcctatgtgatg	7	14	11	9	0	1	2	1	2	0	0	3	3	3	3	2	2	2	3	2	2	2	3			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr11:4567069A>T	ENST00000360213.1	+	1	649	c.649A>T	c.(649-651)Att>Ttt	p.I217F		NM_001004137.1	NP_001004137.1	Q8NGK5	O52M1_HUMAN	olfactory receptor, family 52, subfamily M, member 1	217						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			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)		CTCAGTGGCTATTGCTGCATC	0.532																																					p.I217F		Atlas-SNP	.											.	OR52M1	53	.	0			c.A649T						PASS	.						267	251	257					11																	4567069		2201	4298	6499	SO:0001583	missense	119772	exon1			GTGGCTATTGCTG	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.649A>T	chr11.hg19:g.4567069A>T	ENSP00000353343:p.Ile217Phe	155.0	0.0	.		144.0	32.0	.	NM_001004137		Missense_Mutation	SNP	ENST00000360213.1	hg19	CCDS31353.1	.	.	.	.	.	.	.	.	.	.	A	15.46	2.838966	0.51057	.	.	ENSG00000197790	ENST00000360213	T	0.00333	8.07	5.01	3.86	0.44501	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000207	T	0.01092	0.0036	H	0.96916	3.905	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.35450	-0.9788	10	0.87932	D	0	.	5.4232	0.16411	0.7442:0.0:0.0856:0.1702	.	217	Q8NGK5	O52M1_HUMAN	F	217	ENSP00000353343:I217F	ENSP00000353343:I217F	I	+	1	0	OR52M1	4523645	1.000000	0.71417	0.265000	0.24526	0.813000	0.45954	4.973000	0.63763	0.995000	0.38917	0.528000	0.53228	ATT	.	.	.	none		0.532	OR52M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385847.1	NM_001004137		T	4567069	A	T	4567069	3	4	107	1	0	0	0	0	1	0	0	0	11133	449	16	5	651	5	OR52M1	11	4567069	Missense_Mutation	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10	3473798	4567069	130439447	41	6805											
RIC3	79608	hgsc.bcm.edu	37	chr11	8132577	8132577	+	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	tcccattctttcagctatttCttcagcagaaagttcttttg	8	18	5	10	0	5	1	2	0	3	1	6	1	6	1	1	0	2	3	1	0	2	8			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr11:8132577C>T	ENST00000309737.6	-	6	777	c.778G>A	c.(778-780)Gaa>Aaa	p.E260K	RIC3_ENST00000335425.7_Missense_Mutation_p.E78K|RIC3_ENST00000343202.4_Missense_Mutation_p.E259K|RIC3_ENST00000530060.1_5'UTR|RIC3_ENST00000539720.1_Missense_Mutation_p.E211K|RIC3_ENST00000396677.2_Missense_Mutation_p.E98K|RIC3_ENST00000425599.2_Missense_Mutation_p.E179K			Q7Z5B4	RIC3_HUMAN	RIC3 acetylcholine receptor chaperone	260					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)		TCAGCTATTTCTTCAGCAGAA	0.428																																					p.E260K		Atlas-SNP	.											.	RIC3	42	.	0			c.G778A						PASS	.						112	111	112					11																	8132577		2201	4296	6497	SO:0001583	missense	79608	exon6			CTATTTCTTCAGC		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.778G>A	chr11.hg19:g.8132577C>T	ENSP00000308820:p.Glu260Lys	192.0	0.0	.		231.0	47.0	.	NM_001206671	B0B1U0|B2RD25|D3DQU5|Q6UX78|Q7Z5B3|Q86T94|Q8TBJ9|Q9HAH8	Missense_Mutation	SNP	ENST00000309737.6	hg19	CCDS55742.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.626069	0.87560	.	.	ENSG00000166405	ENST00000396677;ENST00000335425;ENST00000343202;ENST00000309737;ENST00000543346;ENST00000539720;ENST00000425599;ENST00000531450	T;T;T;T;T	0.37752	1.24;1.24;1.26;1.18;1.2	6.06	6.06	0.98353	.	0.154914	0.45606	D	0.000353	T	0.57651	0.2068	M	0.72118	2.19	0.51233	D	0.999912	D;D;D;D;D;D	0.67145	0.996;0.971;0.99;0.99;0.99;0.99	P;P;P;P;P;P	0.62560	0.904;0.651;0.817;0.857;0.857;0.766	T	0.58250	-0.7669	10	0.72032	D	0.01	.	16.0307	0.80574	0.0:0.8665:0.1335:0.0	.	288;179;78;260;259;98	B7Z1U4;B0B1U0;Q7Z5B4-3;Q7Z5B4;Q7Z5B4-5;D3DQU6	.;.;.;RIC3_HUMAN;.;.	K	98;78;259;260;288;211;179;288	ENSP00000344904:E259K;ENSP00000308820:E260K;ENSP00000443871:E211K;ENSP00000395320:E179K;ENSP00000431658:E288K	ENSP00000308820:E260K	E	-	1	0	RIC3	8089153	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.792000	0.62467	2.882000	0.98803	0.655000	0.94253	GAA	.	.	.	none		0.428	RIC3-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385900.1	NM_024557		T	8132577	C	T	8132577	3	4	107	1	0	0	0	0	1	0	0	0	13367	922	32	2	335	2	RIC3	11	8132577	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	3565508	8132577	126873939	42	6806											
LRP4	4038	hgsc.bcm.edu	37	chr11	46895104	46895104	+	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	agtggtcttcagccctcgccCgatcactgtctccatgttgc	5	12	9	15	2	4	0	2	0	2	0	6	1	4	0	3	1	2	1	3	1	0	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr11:46895104C>G	ENST00000378623.1	-	29	4512	c.4270G>C	c.(4270-4272)Ggg>Cgg	p.G1424R	LRP4-AS1_ENST00000502049.2_RNA|LRP4-AS1_ENST00000531719.1_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1424					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)		AGCCCTCGCCCGATCACTGTC	0.572																																					p.G1424R		Atlas-SNP	.											.	LRP4	160	.	0			c.G4270C						PASS	.						80	72	75					11																	46895104		2201	4299	6500	SO:0001583	missense	4038	exon29			CTCGCCCGATCAC	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.4270G>C	chr11.hg19:g.46895104C>G	ENSP00000367888:p.Gly1424Arg	78.0	0.0	.		84.0	25.0	.	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	hg19	CCDS31478.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.347774	0.82022	.	.	ENSG00000134569	ENST00000378623	D	0.95690	-3.78	5.91	5.91	0.95273	Six-bladed beta-propeller, TolB-like (1);	0.048798	0.85682	D	0.000000	D	0.91975	0.7458	N	0.12527	0.23	0.80722	D	1	P	0.35107	0.484	B	0.41088	0.347	D	0.89603	0.3836	10	0.22706	T	0.39	.	20.2985	0.98592	0.0:1.0:0.0:0.0	.	1424	O75096	LRP4_HUMAN	R	1424	ENSP00000367888:G1424R	ENSP00000367888:G1424R	G	-	1	0	LRP4	46851680	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	5.943000	0.70211	2.793000	0.96121	0.655000	0.94253	GGG	.	.	.	none		0.572	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334		G	46895104	C	G	46895104	3	3	107	1	0	0	0	0	1	0	0	0	8966	652	23	4	1487	4	LRP4	11	46895104	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	38762527	46895104	88111412	43	6807											
BRMS1	25855	hgsc.bcm.edu	37	chr11	66108763	66108763	+	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	ctctctcagcccccacttccTccagccgcaaccgcagctga	7	7	6	21	2	2	1	1	1	1	0	5	1	4	1	6	0	4	3	6	0	1	1	rs199933125	byFrequency	TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr11:66108763T>A	ENST00000359957.3	-	4	432	c.272A>T	c.(271-273)gAg>gTg	p.E91V	RP11-867G23.12_ENST00000526655.1_RNA|BRMS1_ENST00000425825.2_Missense_Mutation_p.E91V	NM_015399.3	NP_056214.1	Q9HCU9	BRMS1_HUMAN	breast cancer metastasis suppressor 1	91					apoptotic process (GO:0006915)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of anoikis (GO:2000210)|positive regulation of protein deacetylation (GO:0090312)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)			large_intestine(1)|liver(1)|lung(1)|prostate(1)|skin(1)	5						CCCCACTTCCTCCAGCCGCAA	0.602																																					p.E91V	GBM(7;55 307 2662 20856 28942)	Atlas-SNP	.											.	BRMS1	42	.	0			c.A272T						PASS	.						32	36	35					11																	66108763		2200	4295	6495	SO:0001583	missense	25855	exon4			ACTTCCTCCAGCC	AF147350	CCDS8135.1, CCDS44654.1	11q13-q13.2	2008-02-05				ENSG00000174744			17262	protein-coding gene	gene with protein product		606259				10850410	Standard	XM_005273883		Approved	DKFZP564A063	uc001oho.1	Q9HCU9		ENST00000359957.3:c.272A>T	chr11.hg19:g.66108763T>A	ENSP00000353042:p.Glu91Val	80.0	0.0	.		72.0	15.0	.	NM_015399	Q6IAI2	Missense_Mutation	SNP	ENST00000359957.3	hg19	CCDS8135.1	.	.	.	.	.	.	.	.	.	.	T	18.88	3.718118	0.68844	.	.	ENSG00000174744	ENST00000425825;ENST00000359957;ENST00000530756	.	.	.	4.17	4.17	0.49024	.	0.121890	0.53938	D	0.000052	T	0.54431	0.1858	L	0.45228	1.405	0.44175	D	0.99698	B;B	0.31790	0.256;0.34	B;B	0.41135	0.348;0.343	T	0.55075	-0.8197	9	0.38643	T	0.18	-29.1846	11.4756	0.50295	0.0:0.0:0.0:1.0	.	91;91	Q9HCU9;G5E9I4	BRMS1_HUMAN;.	V	91	.	ENSP00000353042:E91V	E	-	2	0	BRMS1	65865339	0.983000	0.35010	1.000000	0.80357	0.998000	0.95712	1.690000	0.37711	1.889000	0.54706	0.460000	0.39030	GAG	.	T|0.993;C|0.007	.	alt		0.602	BRMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392958.2	NM_015399		A	66108763	T	A	66108763	3	1	107	1	0	0	0	0	1	0	0	0	1518	1551	54	5	640	5	BRMS1	11	66108763	Missense_Mutation	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10	19213659	66108763	68897753	44	6808											
TAOK3	51347	hgsc.bcm.edu	37	chr12	118651868	118651868	+	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	gtcattctgggcaatgtgatAtaaggcactcattgcattca	11	13	9	8	0	4	1	3	1	1	0	4	1	4	1	0	2	1	3	0	2	3	5			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr12:118651868A>T	ENST00000392533.3	-	10	1181	c.691T>A	c.(691-693)Tat>Aat	p.Y231N	TAOK3_ENST00000419821.2_Missense_Mutation_p.Y231N	NM_016281.3	NP_057365.3	Q9H2K8	TAOK3_HUMAN	TAO kinase 3	231	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|MAPK cascade (GO:0000165)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of JNK cascade (GO:0046329)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)|transferase activity (GO:0016740)			central_nervous_system(1)|lung(5)|skin(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GCAATGTGATATAAGGCACTC	0.413																																					p.Y231N		Atlas-SNP	.											.	TAOK3	151	.	0			c.T691A						PASS	.						153	148	150					12																	118651868		2203	4300	6503	SO:0001583	missense	51347	exon10			TGTGATATAAGGC	AF135158	CCDS9188.1	12q	2007-08-03				ENSG00000135090			18133	protein-coding gene	gene with protein product						10559204, 10924369	Standard	NM_016281		Approved	JIK, DPK, MAP3K18	uc001twy.4	Q9H2K8		ENST00000392533.3:c.691T>A	chr12.hg19:g.118651868A>T	ENSP00000376317:p.Tyr231Asn	58.0	0.0	.		83.0	17.0	.	NM_016281	Q658N1|Q8IUM4|Q9HC79|Q9NZM9|Q9UHG7	Missense_Mutation	SNP	ENST00000392533.3	hg19	CCDS9188.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.731562	0.89390	.	.	ENSG00000135090	ENST00000419821;ENST00000392533;ENST00000538601	D;D;D	0.85484	-1.99;-1.99;-1.99	5.24	5.24	0.73138	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.072210	0.64402	D	0.000020	D	0.89245	0.6660	L	0.45228	1.405	0.80722	D	1	D	0.71674	0.998	D	0.74348	0.983	D	0.90431	0.4424	10	0.87932	D	0	.	15.3625	0.74492	1.0:0.0:0.0:0.0	.	231	Q9H2K8	TAOK3_HUMAN	N	231;231;129	ENSP00000416374:Y231N;ENSP00000376317:Y231N;ENSP00000437389:Y129N	ENSP00000376317:Y231N	Y	-	1	0	TAOK3	117136251	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.087000	0.94110	2.210000	0.71456	0.472000	0.43445	TAT	.	.	.	none		0.413	TAOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401456.2	NM_016281		T	118651868	A	T	118651868	3	4	107	1	0	0	0	0	1	0	0	0	15561	449	16	5	2053	5	TAOK3	12	118651868	Missense_Mutation	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10		118651868	15200027	45	6809											
G2E3	55632	hgsc.bcm.edu	37	chr14	31081505	31081505	+	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	ggatgtctcagacttataacGacattaagtgataaatatat	16	13	7	5	1	1	2	1	1	1	1	2	4	1	3	0	1	1	0	0	1	7	6			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr14:31081505G>A	ENST00000206595.6	+	13	1747	c.1593G>A	c.(1591-1593)acG>acA	p.T531T	G2E3_ENST00000438909.2_Silent_p.T485T|G2E3_ENST00000553504.1_Silent_p.T561T	NM_017769.3	NP_060239.2	Q7L622	G2E3_HUMAN	G2/M-phase specific E3 ubiquitin protein ligase	531	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				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						GACTTATAACGACATTAAGTG	0.313																																					p.T531T		Atlas-SNP	.											.	G2E3	82	.	0			c.G1593A						PASS	.						100	103	102					14																	31081505		2203	4295	6498	SO:0001819	synonymous_variant	55632	exon13			TATAACGACATTA	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.1593G>A	chr14.hg19:g.31081505G>A		183.0	0.0	.		175.0	40.0	.	NM_017769	Q9BVR2|Q9H9E9|Q9NXC0|Q9P2L3	Silent	SNP	ENST00000206595.6	hg19	CCDS9638.1																																																																																			.	.	.	none		0.313	G2E3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276613.2	NM_017769		A	31081505	G	A	31081505	2	1	107	1	0	0	0	0	0	0	0	1	6147	1045	37	1		1	G2E3	14	31081505	Silent	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10		31081505	76268035	46	6810											
FANCM	57697	hgsc.bcm.edu	37	chr14	45645152	45645152	+	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	tatccatctgaaaaaagttgCctttatgatatacctaatga	15	14	5	7	0	1	3	0	3	1	0	2	3	2	3	3	0	2	1	3	0	8	7			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr14:45645152C>G	ENST00000267430.5	+	14	3280	c.3195C>G	c.(3193-3195)tgC>tgG	p.C1065W	FANCM_ENST00000542564.2_Missense_Mutation_p.C1039W	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1065					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						AAAAAAGTTGCCTTTATGATA	0.299								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.C1065W		Atlas-SNP	.											.	FANCM	225	.	0			c.C3195G						PASS	.						25	26	25					14																	45645152		2203	4296	6499	SO:0001583	missense	57697	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AAGTTGCCTTTAT	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.3195C>G	chr14.hg19:g.45645152C>G	ENSP00000267430:p.Cys1065Trp	87.0	0.0	.		123.0	31.0	.	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	hg19	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	C	6.697	0.497283	0.12762	.	.	ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250	T;T;T	0.18657	2.79;2.79;2.2	5.23	-2.33	0.06724	.	1.440870	0.03493	N	0.216880	T	0.30885	0.0779	L	0.56769	1.78	0.09310	N	0.999999	D;D	0.58620	0.964;0.983	P;P	0.53006	0.624;0.715	T	0.38067	-0.9678	10	0.66056	D	0.02	.	5.9826	0.19415	0.0:0.3342:0.137:0.5287	.	1039;1065	B2RTQ9;Q8IYD8	.;FANCM_HUMAN	W	1065;1039;581	ENSP00000267430:C1065W;ENSP00000442493:C1039W;ENSP00000452033:C581W	ENSP00000267430:C1065W	C	+	3	2	FANCM	44714902	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.431000	0.06965	-0.270000	0.09285	-0.229000	0.12294	TGC	.	.	.	none		0.299	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		G	45645152	C	G	45645152	3	3	107	1	0	0	0	0	1	0	0	0	5678	747	26	4	3249	4	FANCM	14	45645152	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	14563647	45645152	61704388	47	6811											
DLGAP5	9787	hgsc.bcm.edu	37	chr14	55642723	55642723	+	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	tgccaaaatttcttttgttgCttgagactcatcactaaaaa	13	15	5	8	0	3	1	2	1	1	1	3	2	3	1	1	0	2	2	1	0	5	6			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr14:55642723C>A	ENST00000247191.2	-	9	1279	c.1063G>T	c.(1063-1065)Gca>Tca	p.A355S	DLGAP5_ENST00000395425.2_Missense_Mutation_p.A355S	NM_014750.4	NP_055565.3	Q15398	DLGP5_HUMAN	discs, large (Drosophila) homolog-associated protein 5	355					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|dephosphorylation (GO:0016311)|mitotic chromosome movement towards spindle pole (GO:0007079)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|spindle pole centrosome (GO:0031616)	phosphoprotein phosphatase activity (GO:0004721)			biliary_tract(1)|breast(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	44						TCTTTTGTTGCTTGAGACTCA	0.313																																					p.A355S		Atlas-SNP	.											.	DLGAP5	84	.	0			c.G1063T						PASS	.						131	125	127					14																	55642723		2203	4297	6500	SO:0001583	missense	9787	exon9			TTGTTGCTTGAGA	D13633	CCDS9723.1, CCDS53897.1	14q22.3	2008-05-30	2008-05-30	2008-05-30	ENSG00000126787	ENSG00000126787			16864	protein-coding gene	gene with protein product			"discs, large homolog 7 (Drosophila)"	DLG7		7584026, 7584028	Standard	NM_014750		Approved	KIAA0008, DLG1, HURP	uc001xbs.3	Q15398	OTTHUMG00000140310	ENST00000247191.2:c.1063G>T	chr14.hg19:g.55642723C>A	ENSP00000247191:p.Ala355Ser	71.0	0.0	.		73.0	10.0	.	NM_014750	A8MTM6|B4DRM8|Q86T11|Q8NG58	Missense_Mutation	SNP	ENST00000247191.2	hg19	CCDS9723.1	.	.	.	.	.	.	.	.	.	.	C	11.71	1.720936	0.30503	.	.	ENSG00000126787	ENST00000395425;ENST00000247191	T;T	0.15952	2.38;2.38	3.83	2.93	0.34026	.	1.470090	0.03875	N	0.276195	T	0.16342	0.0393	L	0.36672	1.1	0.24747	N	0.993003	B;B	0.26902	0.163;0.095	B;B	0.30105	0.111;0.078	T	0.32798	-0.9893	10	0.13108	T	0.6	.	9.5155	0.39102	0.0:0.7848:0.2152:0.0	.	355;355	A8MTM6;Q15398	.;DLGP5_HUMAN	S	355	ENSP00000378815:A355S;ENSP00000247191:A355S	ENSP00000247191:A355S	A	-	1	0	DLGAP5	54712476	0.784000	0.28713	0.566000	0.28421	0.957000	0.61999	1.018000	0.30002	1.213000	0.43380	0.650000	0.86243	GCA	.	.	.	none		0.313	DLGAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276908.2	NM_014750		A	55642723	C	A	55642723	3	1	107	1	0	0	0	0	1	0	0	0	4565	797	28	4	1616	4	DLGAP5	14	55642723	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	9997571	55642723	51706817	48	6812											
AP4E1	23431	hgsc.bcm.edu	37	chr15	51285700	51285700	+	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	agagtataatggagaatgtaGatcaagctataactaaaaag	20	9	9	3	0	1	3	1	0	0	3	1	4	1	3	0	1	2	3	0	1	10	6			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr15:51285700G>T	ENST00000261842.5	+	17	2330	c.2224G>T	c.(2224-2226)Gat>Tat	p.D742Y	AP4E1_ENST00000560508.1_Missense_Mutation_p.D667Y	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	742					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)		GGAGAATGTAGATCAAGCTAT	0.408																																					p.D742Y		Atlas-SNP	.											.	AP4E1	78	.	0			c.G2224T						PASS	.						105	92	97					15																	51285700		2196	4294	6490	SO:0001583	missense	23431	exon17			AATGTAGATCAAG	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.2224G>T	chr15.hg19:g.51285700G>T	ENSP00000261842:p.Asp742Tyr	59.0	0.0	.		56.0	8.0	.	NM_007347	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Missense_Mutation	SNP	ENST00000261842.5	hg19	CCDS32240.1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.969624	0.53614	.	.	ENSG00000081014	ENST00000261842	T	0.19250	2.16	5.29	5.29	0.74685	.	0.278842	0.38778	N	0.001568	T	0.22898	0.0553	N	0.24115	0.695	0.35318	D	0.784497	P	0.51653	0.947	P	0.47744	0.556	T	0.19844	-1.0293	10	0.72032	D	0.01	-17.9497	17.9229	0.88973	0.0:0.0:1.0:0.0	.	742	Q9UPM8	AP4E1_HUMAN	Y	742	ENSP00000261842:D742Y	ENSP00000261842:D742Y	D	+	1	0	AP4E1	49072992	0.989000	0.36119	0.774000	0.31636	0.968000	0.65278	3.111000	0.50360	2.455000	0.83008	0.563000	0.77884	GAT	.	.	.	none		0.408	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1			T	51285700	G	T	51285700	3	4	107	1	0	0	0	0	1	0	0	0	752	942	33	4	2290	4	AP4E1	15	51285700	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10		51285700	51245692	49	6813											
CHD2	1106	hgsc.bcm.edu	37	chr15	93541851	93541851	+	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	gctgtgacaggtggggaagaGgtgagtacgctgccagctgg	8	7	19	7	1	0	3	0	2	0	1	0	4	0	4	1	5	3	4	1	5	2	1			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr15:93541851G>T	ENST00000394196.4	+	31	5076	c.4008G>T	c.(4006-4008)gaG>gaT	p.E1336D	CHD2_ENST00000557381.1_Splice_Site_p.E1336D	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1336					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)			GTGGGGAAGAGGTGAGTACGC	0.552																																					p.E1336D		Atlas-SNP	.											.	CHD2	280	.	0			c.G4008T						PASS	.						92	92	92					15																	93541851		2197	4298	6495	SO:0001630	splice_region_variant	1106	exon31			GGAAGAGGTGAGT	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.4008+1G>T	chr15.hg19:g.93541851G>T		74.0	0.0	.		74.0	4.0	.	NM_001271	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	hg19	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	G	15.00	2.702923	0.48412	.	.	ENSG00000173575	ENST00000394196;ENST00000557381	D;D	0.89939	-2.59;-2.58	5.16	5.16	0.70880	.	0.000000	0.34484	U	0.003936	D	0.92410	0.7591	L	0.59436	1.845	0.80722	D	1	D;D	0.67145	0.984;0.996	D;P	0.68192	0.956;0.789	D	0.89962	0.4087	10	0.22109	T	0.4	-32.7161	17.2006	0.86904	0.0:0.0:1.0:0.0	.	1336;1336	O14647;O14647-2	CHD2_HUMAN;.	D	1336	ENSP00000377747:E1336D;ENSP00000451366:E1336D	ENSP00000377747:E1336D	E	+	3	2	CHD2	91342855	1.000000	0.71417	1.000000	0.80357	0.415000	0.31203	8.987000	0.93497	2.578000	0.87016	0.561000	0.74099	GAG	.	.	.	none		0.552	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271	Missense_Mutation	T	93541851	G	T	93541851	5	4	107	1	0	0	0	0	0	0	1	0	3327	1014	35	4	4130	4	CHD2	15	93541851	Splice_Site	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	42256151	93541851	8989541	50	6814											
CCDC64B	146439	hgsc.bcm.edu	37	chr16	3078701	3078701	+	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	gtcaatggcttgaggcttacTtgttcacggcctcgtcccgg	5	12	12	12	3	2	1	2	1	0	0	4	1	3	1	2	4	1	3	2	4	2	4			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr16:3078701T>A	ENST00000572449.1	-	8	1300	c.1238A>T	c.(1237-1239)aAg>aTg	p.K413M	CCDC64B_ENST00000389347.4_Splice_Site_p.K413M|CCDC64B_ENST00000573514.1_Splice_Site_p.K206M			A1A5D9	BICR2_HUMAN	coiled-coil domain containing 64B	413										breast(1)|endometrium(2)|large_intestine(1)	4						TGAGGCTTACTTGTTCACGGC	0.637																																					p.K413M		Atlas-SNP	.											.	CCDC64B	19	.	0			c.A1238T						PASS	.						35	49	44					16																	3078701		1994	4127	6121	SO:0001630	splice_region_variant	146439	exon7			GCTTACTTGTTCA	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.1238+1A>T	chr16.hg19:g.3078701T>A		72.0	0.0	.		70.0	16.0	.	NM_001103175	Q658L9	Missense_Mutation	SNP	ENST00000572449.1	hg19	CCDS45393.1	.	.	.	.	.	.	.	.	.	.	T	18.59	3.656736	0.67586	.	.	ENSG00000162069	ENST00000389347	T	0.39592	1.07	4.28	4.28	0.50868	.	0.067259	0.56097	D	0.000027	T	0.57989	0.2091	M	0.72118	2.19	0.58432	D	0.999993	D	0.76494	0.999	D	0.63192	0.912	T	0.59936	-0.7360	9	.	.	.	-53.638	11.4408	0.50096	0.0:0.0:0.0:1.0	.	413	A1A5D9	BICR2_HUMAN	M	413	ENSP00000373998:K413M	.	K	-	2	0	CCDC64B	3018702	1.000000	0.71417	1.000000	0.80357	0.619000	0.37552	2.792000	0.47837	1.814000	0.52955	0.459000	0.35465	AAG	.	.	.	none		0.637	CCDC64B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436991.1		Missense_Mutation	A	3078701	T	A	3078701	5	1	107	1	0	0	0	0	0	0	1	0	2838	1623	56	5	300	5	CCDC64B	16	3078701	Splice_Site	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10		3078701	87276052	51	6815											
GTF3C1	2975	hgsc.bcm.edu	37	chr16	27549611	27549611	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcttcaggtcgggatccccCtcctggcctatcaaggccct	6	9	10	16	1	2	0	2	0	0	0	5	1	4	1	5	4	1	1	5	4	2	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr16:27549611C>T	ENST00000356183.4	-	3	513	c.498G>A	c.(496-498)gaG>gaA	p.E166E	GTF3C1_ENST00000561623.1_Silent_p.E166E	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	166					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						CGGGATCCCCCTCCTGGCCTA	0.582																																					p.E166E		Atlas-SNP	.											.	GTF3C1	210	.	0			c.G498A						PASS	.						70	66	68					16																	27549611		2197	4300	6497	SO:0001819	synonymous_variant	2975	exon3			ATCCCCCTCCTGG	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.498G>A	chr16.hg19:g.27549611C>T		79.0	0.0	.		74.0	20.0	.	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Silent	SNP	ENST00000356183.4	hg19	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	C	8.560	0.877594	0.17395	.	.	ENSG00000077235	ENST00000388971	.	.	.	5.5	1.98	0.26296	.	.	.	.	.	T	0.61640	0.2363	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58036	-0.7707	5	0.38643	T	0.18	-3.8349	11.4639	0.50227	0.0:0.6864:0.0:0.3136	.	.	.	.	R	166	.	ENSP00000373623:G166R	G	-	1	0	GTF3C1	27457112	0.875000	0.30112	0.996000	0.52242	0.914000	0.54420	-0.027000	0.12371	0.389000	0.25086	-1.945000	0.00491	GGG	.	.	.	none		0.582	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520		T	27549611	C	T	27549611	2	4	107	1	0	0	0	0	0	0	0	1	6879	680	24	2		2	GTF3C1	16	27549611	Silent	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	24470910	27549611	62805142	52	6816											
CDH1	999	hgsc.bcm.edu	37	chr16	68853183	68853183	+	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	cagagcttgtccccgttcagAtatcggatttggagagacac	10	10	11	10	2	1	3	1	0	0	3	3	6	2	5	2	2	1	2	2	2	1	4			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr16:68853183A>C	ENST00000261769.5	+	11	1757	c.1566A>C	c.(1564-1566)acA>acC	p.T522T	RP11-354M1.2_ENST00000563916.1_RNA|CDH1_ENST00000562836.1_3'UTR|CDH1_ENST00000422392.2_Splice_Site_p.T461T	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	522	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.?(1)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		CCCCGTTCAGATATCGGATTT	0.493			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																												p.T522T		Atlas-SNP	.	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	.	CDH1	535	.	1	Unknown(1)	breast(1)	c.A1566C						PASS	.						89	78	82					16																	68853183		2198	4300	6498	SO:0001630	splice_region_variant	999	exon11	Familial Cancer Database	HDGC	GTTCAGATATCGG	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.1566-1A>C	chr16.hg19:g.68853183A>C		116.0	0.0	.		92.0	22.0	.	NM_004360	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Silent	SNP	ENST00000261769.5	hg19	CCDS10869.1																																																																																			.	.	.	none		0.493	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360	Silent	C	68853183	A	C	68853183	5	2	107	1	0	0	0	0	0	0	1	0	3097	347	12	5	1608	5	CDH1	16	68853183	Splice_Site	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10	41303572	68853183	21501570	53	6817											
CPNE7	27132	hgsc.bcm.edu	37	chr16	89650107	89650107	+	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	gacgcctctgacttacagatTgtggcccagaagaaggtgac	11	8	12	10	1	1	5	0	2	1	3	1	6	1	5	2	2	1	0	2	2	3	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr16:89650107T>A	ENST00000268720.5	+	5	715	c.585T>A	c.(583-585)atT>atA	p.I195I	CPNE7_ENST00000319518.8_Silent_p.I120I	NM_014427.4	NP_055242.1	Q9UBL6	CPNE7_HUMAN	copine VII	195					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)		ACTTACAGATTGTGGCCCAGA	0.672																																					p.I195I		Atlas-SNP	.											.	CPNE7	56	.	0			c.T585A						PASS	.						48	45	46					16																	89650107		2198	4300	6498	SO:0001819	synonymous_variant	27132	exon5			ACAGATTGTGGCC	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.585T>A	chr16.hg19:g.89650107T>A		120.0	0.0	.		107.0	29.0	.	NM_014427		Silent	SNP	ENST00000268720.5	hg19	CCDS10980.1																																																																																			.	.	.	none		0.672	CPNE7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269929.2			A	89650107	T	A	89650107	2	1	107	1	0	0	0	0	0	0	0	1	3819	1800	63	5		5	CPNE7	16	89650107	Silent	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10	20796924	89650107	704646	54	6818											
C17orf81	23587	hgsc.bcm.edu	37	chr17	7157996	7157996	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggagccttgagagccatgTgcaagaggacagatcctgtt	10	9	14	8	0	0	3	0	1	0	3	1	6	1	5	3	2	3	2	3	2	1	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr17:7157996T>C	ENST00000396628.2	+	4	548	c.331T>C	c.(331-333)Tgc>Cgc	p.C111R	CTDNEP1_ENST00000572043.1_5'Flank|ELP5_ENST00000356683.2_Missense_Mutation_p.C111R|ELP5_ENST00000574255.1_Missense_Mutation_p.C111R|ELP5_ENST00000574993.1_Missense_Mutation_p.C111R|ELP5_ENST00000396627.2_Missense_Mutation_p.C111R|RP1-4G17.5_ENST00000577138.1_Intron|ELP5_ENST00000573657.1_Missense_Mutation_p.C111R|CTDNEP1_ENST00000318988.6_5'Flank|CTDNEP1_ENST00000573600.1_5'Flank|ELP5_ENST00000354429.2_Missense_Mutation_p.C111R	NM_203414.1	NP_981959.1	Q8TE02	ELP5_HUMAN	elongator acetyltransferase complex subunit 5	111					chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Elongator holoenzyme complex (GO:0033588)|nucleus (GO:0005634)											GAGAGCCATGTGCAAGAGGAC	0.562																																					p.C111R		Atlas-SNP	.											.	.	.	.	0			c.T331C						PASS	.						126	93	104					17																	7157996		2203	4300	6503	SO:0001583	missense	23587	exon4			GCCATGTGCAAGA	BC002762	CCDS11094.1, CCDS11095.1	17p13.1	2012-08-14	2012-08-08	2012-08-08	ENSG00000170291	ENSG00000170291		"Elongator acetyltransferase complex subunits"	30617	protein-coding gene	gene with protein product	"dermal papilla derived protein 6", "S-phase 2 protein"	615019	"chromosome 17 open reading frame 81"	C17orf81		22854966	Standard	NM_203415		Approved	DERP6	uc002gfi.1	Q8TE02	OTTHUMG00000177974	ENST00000396628.2:c.331T>C	chr17.hg19:g.7157996T>C	ENSP00000379869:p.Cys111Arg	62.0	0.0	.		71.0	19.0	.	NM_203414	A8K1M5|D3DTN9|Q659B6|Q7Z2T4|Q8TDR9|Q9BUB2|Q9Y2Q4	Missense_Mutation	SNP	ENST00000396628.2	hg19	CCDS11094.1	.	.	.	.	.	.	.	.	.	.	T	12.68	2.009540	0.35415	.	.	ENSG00000170291	ENST00000354429;ENST00000396628;ENST00000396627;ENST00000356683	T;T;T;T	0.47869	1.54;1.54;1.54;0.83	5.51	0.78	0.18556	.	0.815021	0.11405	N	0.567376	T	0.41858	0.1177	L	0.56769	1.78	0.19575	N	0.999968	B;B;B;B	0.26002	0.029;0.114;0.139;0.021	B;B;B;B	0.31290	0.025;0.053;0.127;0.025	T	0.43925	-0.9361	10	0.56958	D	0.05	-0.1605	4.5046	0.11881	0.0:0.2406:0.3505:0.4089	.	111;111;111;111	Q8TE02-2;Q8TE02-3;A8K1M5;Q8TE02	.;.;.;DERP6_HUMAN	R	111	ENSP00000346412:C111R;ENSP00000379869:C111R;ENSP00000379868:C111R;ENSP00000349111:C111R	ENSP00000346412:C111R	C	+	1	0	C17orf81	7098720	0.003000	0.15002	0.001000	0.08648	0.794000	0.44872	0.167000	0.16602	0.127000	0.18452	0.482000	0.46254	TGC	.	.	.	none		0.562	ELP5-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440111.1	NM_015362		C	7157996	T	C	7157996	3	2	107	1	0	0	0	0	1	0	0	0	1888	1696	59	3	345	3	C17orf81	17	7157996	Missense_Mutation	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10		7157996	74037214	55	6819											
ATPAF2	91647	hgsc.bcm.edu	37	chr17	17925092	17925092	+	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	tgtgttgtaagatgccaggtGgctgacgagcacctcccgag	8	9	14	10	2	0	2	0	1	0	1	1	4	1	2	3	2	2	4	3	2	1	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr17:17925092G>A	ENST00000474627.3	-	6	737	c.583C>T	c.(583-585)Cac>Tac	p.H195Y	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	195					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)					GATGCCAGGTGGCTGACGAGC	0.547																																					p.H195Y		Atlas-SNP	.											.	ATPAF2	15	.	0			c.C583T						PASS	.						234	205	215					17																	17925092		2203	4300	6503	SO:0001583	missense	91647	exon6			CCAGGTGGCTGAC	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.583C>T	chr17.hg19:g.17925092G>A	ENSP00000417190:p.His195Tyr	126.0	0.0	.		125.0	34.0	.	NM_145691	A6NDE5|A8K2J2|Q6XYC7	Missense_Mutation	SNP	ENST00000474627.3	hg19	CCDS32585.1	.	.	.	.	.	.	.	.	.	.	G	16.89	3.247071	0.59103	.	.	ENSG00000171953	ENST00000474627;ENST00000444058	T;T	0.75821	-0.97;-0.97	5.41	5.41	0.78517	ATPase assembly, ATP12, domain (1);	0.000000	0.85682	D	0.000000	T	0.78767	0.4335	L	0.38175	1.15	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.70182	-0.4942	10	0.02654	T	1	4.9557	19.5423	0.95278	0.0:0.0:1.0:0.0	.	195	Q8N5M1	ATPF2_HUMAN	Y	195	ENSP00000417190:H195Y;ENSP00000397198:H195Y	ENSP00000434980:H195Y	H	-	1	0	ATPAF2	17865817	1.000000	0.71417	1.000000	0.80357	0.784000	0.44337	7.369000	0.79578	2.692000	0.91855	0.655000	0.94253	CAC	.	.	.	none		0.547	ATPAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131934.3	NM_145691		A	17925092	G	A	17925092	3	1	107	1	0	0	0	0	1	0	0	0	1201	1348	47	2	298	2	ATPAF2	17	17925092	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	10767096	17925092	63270118	56	6820											
C17orf57	124989	hgsc.bcm.edu	37	chr17	45468874	45468875	+	Frame_Shift_Ins	INS	-	-	G																															ttatgaggatctaaatacttINSgtcttcaaaattttggtatt																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr17:45468874_45468875insG	ENST00000331493.2	+	15	2065_2066	c.1654_1655insG	c.(1654-1656)tgtfs	p.C552fs	EFCAB13_ENST00000517484.1_Frame_Shift_Ins_p.C456fs	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	552	EF-hand 2.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										TCTAAATACTTGTCTTCAAAAT	0.327																																					p.C552fs		Pindel	.											.	.	.	.	0			c.1654_1655insG						PASS	.																																			SO:0001589	frameshift_variant	124989	exon15			.	BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"EF-hand domain containing"	26864	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 57"	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.1655dupG	chr17.hg19:g.45468875_45468875dupG	ENSP00000332111:p.Cys552fs	277.0	0.0	.		342.0	63.0	0.184	NM_152347	G3V128|Q49AG9	Frame_Shift_Ins	INS	ENST00000331493.2	hg19	CCDS11512.1																																																																																			.	.	.	none		0.327	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347		G	45468875	-	G	45468874	7	5	107	1	0	1	1	0	0	0	0	0	1867	1812	63	0	1700	0	C17orf57	17	45468874	Frame_Shift_Ins	INS	-	TCGA-B9-A69E-01A-11D-A31X-10	27543782	45468874	35726336	57	6821											
NDC80	10403	hgsc.bcm.edu	37	chr18	2610806	2610806	+	Frame_Shift_Del	DEL	A	A	-																															gaagaaagacgaaaagtgggAaataacttgcaacgtctgtt																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr18:2610806delA	ENST00000261597.4	+	16	1919	c.1737delA	c.(1735-1737)ggafs	p.G579fs		NM_006101.2	NP_006092.1	O14777	NDC80_HUMAN	NDC80 kinetochore complex component	579	Interaction with NEK2 and ZWINT.|Interaction with the C-terminus of CDCA1 and the SPBC24-SPBC25 subcomplex.				attachment of spindle microtubules to kinetochore (GO:0008608)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				NS(1)|biliary_tract(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)|urinary_tract(2)	22						GAAAAGTGGGAAATAACTTGC	0.368																																					p.G579fs		Atlas-Indel,Pindel	.											.	NDC80	62	.	0			c.1736delG						PASS	.						194	172	180					18																	2610806		2203	4300	6503	SO:0001589	frameshift_variant	10403	exon16			.	AF017790	CCDS11827.1	18p11.31	2013-01-17	2013-01-17	2007-03-02	ENSG00000080986	ENSG00000080986			16909	protein-coding gene	gene with protein product		607272	"highly expressed in cancer, rich in leucine heptad repeats (yeast)", "kinetochore associated 2", "NDC80 kinetochore complex component homolog (S. cerevisiae)"	KNTC2		9315664, 12351790	Standard	NM_006101		Approved	HEC, HEC1, hsNDC80, TID3	uc002kli.3	O14777	OTTHUMG00000131483	ENST00000261597.4:c.1737delA	chr18.hg19:g.2610806delA	ENSP00000261597:p.Gly579fs	151.0	0.0	0		157.0	36.0	0.229299	NM_006101	Q6PJX2	Frame_Shift_Del	DEL	ENST00000261597.4	hg19	CCDS11827.1																																																																																			.	.	.	none		0.368	NDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254327.1	NM_006101		-	2610806	A	-	2610806	7	5	107	1	0	1	0	1	0	0	0	0	10249	233	9	0	1795	0	NDC80	18	2610806	Frame_Shift_Del	DEL	A	TCGA-B9-A69E-01A-11D-A31X-10		2610806	75466442	58	6822											
DYM	54808	hgsc.bcm.edu	37	chr18	46798650	46798650	+	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	ttcctttcttcaacatgataCagaatctcaagaattggtaa	14	14	5	8	0	3	3	2	1	2	2	5	3	4	3	1	1	2	1	1	1	6	6			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr18:46798650C>G	ENST00000269445.6	-	11	1606	c.1149G>C	c.(1147-1149)ctG>ctC	p.L383L	DYM_ENST00000442713.2_Silent_p.L193L	NM_017653.3	NP_060123.3	Q7RTS9	DYM_HUMAN	dymeclin	383					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						CAACATGATACAGAATCTCAA	0.299																																					p.L383L		Atlas-SNP	.											DYM,NS,carcinoma,0,1	DYM	52	.	0			c.G1149C						PASS	.						77	72	74					18																	46798650		2203	4299	6502	SO:0001819	synonymous_variant	54808	exon11			ATGATACAGAATC	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.1149G>C	chr18.hg19:g.46798650C>G		151.0	1.0	.		123.0	35.0	.	NM_017653	A8K5I8|B2RCF9|B4DKI7|Q3ZTS8|Q6P2P5|Q8N2M0|Q9BVE9|Q9NPU7	Silent	SNP	ENST00000269445.6	hg19	CCDS11937.1																																																																																			.	.	.	none		0.299	DYM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255912.3	NM_017653		G	46798650	C	G	46798650	2	3	107	1	0	0	0	0	0	0	0	1	4842	465	17	4		4	DYM	18	46798650	Silent	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	44187844	46798650	31278598	59	6823											
HMHA1	23526	hgsc.bcm.edu	37	chr19	1082889	1082889	+	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	taccacgagctcgtagggctGgccaaggacagcctgaaggc	10	5	14	12	2	0	1	0	1	0	0	1	3	0	2	3	4	3	3	3	4	4	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:1082889G>T	ENST00000313093.2	+	20	2799	c.2568G>T	c.(2566-2568)ctG>ctT	p.L856L	HMHA1_ENST00000536472.1_Silent_p.L724L|HMHA1_ENST00000539243.2_Silent_p.L872L|HMHA1_ENST00000586866.1_Silent_p.L860L|HMHA1_ENST00000590577.1_Silent_p.L491L|HMHA1_ENST00000590214.1_Silent_p.L883L|HMHA1_ENST00000543365.1_Silent_p.L739L	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	856	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)		TCGTAGGGCTGGCCAAGGACA	0.711																																					p.L872L		Atlas-SNP	.											.	HMHA1	78	.	0			c.G2616T						PASS	.						13	12	12					19																	1082889		2193	4288	6481	SO:0001819	synonymous_variant	23526	exon20			AGGGCTGGCCAAG	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.2568G>T	chr19.hg19:g.1082889G>T		49.0	0.0	.		49.0	19.0	.	NM_001258328	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Silent	SNP	ENST00000313093.2	hg19	CCDS32863.1																																																																																			.	.	.	none		0.711	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1			T	1082889	G	T	1082889	2	4	107	1	0	0	0	0	0	0	0	1	7247	1335	47	4		4	HMHA1	19	1082889	Silent	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10		1082889	58046094	60	6824											
MRI1	28974	hgsc.bcm.edu	37	chr19	13883025	13883025	+	5'Flank	SNP	A	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	actgggggtctttgcccctgAggagctccggacagccctaa	7	8	13	13	1	1	1	0	1	1	0	2	3	2	3	4	4	3	1	4	4	1	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:13883025A>T	ENST00000588234.1	+	0	0				CTB-5E10.3_ENST00000586297.1_RNA|CTB-5E10.3_ENST00000591826.1_RNA|C19orf53_ENST00000593274.1_5'Flank|MRI1_ENST00000040663.6_Missense_Mutation_p.E347V|CTB-5E10.3_ENST00000586894.1_RNA|MRI1_ENST00000319545.8_Missense_Mutation_p.E300V	NM_014047.2	NP_054766.1	Q9UNZ5	L10K_HUMAN	chromosome 19 open reading frame 53											breast(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	6			OV - Ovarian serous cystadenocarcinoma(19;7.7e-24)|Epithelial(5;2.53e-19)			TTTGCCCCTGAGGAGCTCCGG	0.577																																					p.E347V		Atlas-SNP	.											.	MRI1	35	.	0			c.A1040T						PASS	.						95	88	91					19																	13883025		2203	4300	6503	SO:0001631	upstream_gene_variant	84245	exon6			CCCCTGAGGAGCT	AF078852	CCDS12298.1	19p13.2	2011-11-24			ENSG00000104979	ENSG00000104979			24991	protein-coding gene	gene with protein product	"leydig cell tumor 10 kDa protein homolog"					11042152	Standard	NM_014047		Approved	HSPC023, LYDG10	uc002mxg.3	Q9UNZ5			chr19.hg19:g.13883025A>T	Exception_encountered	217.0	0.0	.		208.0	48.0	.	NM_001031727	B2R4J9	Missense_Mutation	SNP	ENST00000588234.1	hg19	CCDS12298.1	.	.	.	.	.	.	.	.	.	.	A	11.35	1.611851	0.28712	.	.	ENSG00000037757	ENST00000040663;ENST00000319545	T;T	0.31247	1.5;1.5	4.88	3.84	0.44239	.	0.235842	0.36409	N	0.002620	T	0.27900	0.0687	L	0.48986	1.54	0.32290	N	0.566403	B;B	0.29085	0.232;0.011	B;B	0.30251	0.113;0.027	T	0.29518	-1.0009	10	0.42905	T	0.14	-48.5554	10.0893	0.42436	0.8314:0.1686:0.0:0.0	.	300;347	Q9BV20-2;Q9BV20	.;MTNA_HUMAN	V	347;300	ENSP00000040663:E347V;ENSP00000314871:E300V	ENSP00000040663:E347V	E	+	2	0	MRI1	13744025	0.000000	0.05858	0.400000	0.26346	0.621000	0.37620	0.854000	0.27791	0.685000	0.31468	0.397000	0.26171	GAG	.	.	.	none		0.577	C19orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453621.1	NM_014047		T	13883025	A	T	13883025	1	4	107	0	1	0	0	0	0	0	0	0	9777	304	11	5		5	MRI1	19	13883025	5'Flank	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10	12800136	13883025	45245958	61	6825											
USHBP1	83878	hgsc.bcm.edu	37	chr19	17366410	17366410	+	Silent	SNP	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	cgaagcatcaggtccgccagGgcctcctgtgggaccaagga	9	5	14	13	2	1	0	1	0	0	0	3	3	3	2	5	4	1	1	5	4	2	0			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:17366410G>A	ENST00000252597.3	-	10	1649	c.1476C>T	c.(1474-1476)gcC>gcT	p.A492A	AC010646.3_ENST00000594059.1_5'Flank|USHBP1_ENST00000431146.2_Silent_p.A428A	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						GGTCCGCCAGGGCCTCCTGTG	0.632																																					p.A492A		Atlas-SNP	.											.	USHBP1	85	.	0			c.C1476T						PASS	.						10	12	11					19																	17366410		2188	4264	6452	SO:0001819	synonymous_variant	83878	exon10			CGCCAGGGCCTCC	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.1476C>T	chr19.hg19:g.17366410G>A		79.0	0.0	.		79.0	14.0	.	NM_031941		Silent	SNP	ENST00000252597.3	hg19	CCDS12353.1																																																																																			.	.	.	none		0.632	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941		A	17366410	G	A	17366410	2	1	107	1	0	0	0	0	0	0	0	1	17049	1219	43	2		2	USHBP1	19	17366410	Silent	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	3483385	17366410	41762573	62	6826											
C19orf40	91442	hgsc.bcm.edu	37	chr19	33464971	33464972	+	Frame_Shift_Ins	INS	-	-	A																															tttttcctttcaagtccaatINSaatcttaaaggaattgtagt																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:33464971_33464972insA	ENST00000588258.1	+	4	359_360	c.249_250insA	c.(250-252)aatfs	p.N84fs	CEP89_ENST00000590597.2_5'Flank|CEP89_ENST00000591863.1_5'Flank|CEP89_ENST00000305768.5_5'Flank|C19orf40_ENST00000589646.1_5'UTR|C19orf40_ENST00000590281.1_Frame_Shift_Ins_p.N84fs|C19orf40_ENST00000590179.1_5'UTR	NM_152266.3	NP_689479.1	Q9BTP7	FAP24_HUMAN	chromosome 19 open reading frame 40	84					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)					TCAAGTCCAATAATCTTAAAGG	0.406								Direct reversal of damage																													p.N83fs		Atlas-Indel,Pindel	.											.	C19orf40	21	.	0			c.249_250insA						PASS	.																																			SO:0001589	frameshift_variant	91442	exon4			.	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.251dupA	chr19.hg19:g.33464973_33464973dupA	ENSP00000466121:p.Asn84fs	145.0	0.0	0		170.0	43.0	0.252941	NM_152266	B3KY46|Q8WUJ7|Q96FX6	Frame_Shift_Ins	INS	ENST00000588258.1	hg19	CCDS12426.1																																																																																			.	.	.	none		0.406	C19orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450823.2	NM_152266		A	33464972	-	A	33464971	7	5	107	1	0	1	1	0	0	0	0	0	1925	1403	49	0	259	0	C19orf40	19	33464971	Frame_Shift_Ins	INS	-	TCGA-B9-A69E-01A-11D-A31X-10	16098561	33464971	25664012	63	6827											
DMKN	93099	hgsc.bcm.edu	37	chr19	36002420	36002420	+	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	gctgctgccactgctgctgcCaccactgctgctgccattgt	4	11	10	16	0	0	0	0	0	0	0	0	0	0	0	4	0	8	6	4	0	0	1	rs72334573	byFrequency	TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:36002420C>T	ENST00000339686.3	-	5	987	c.811G>A	c.(811-813)Ggc>Agc	p.G271S	DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000424570.2_Missense_Mutation_p.G271S|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000451297.2_Missense_Mutation_p.G271S|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000447113.2_Missense_Mutation_p.G271S|DMKN_ENST00000440396.1_Missense_Mutation_p.G271S|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000418261.1_Missense_Mutation_p.G271S|DMKN_ENST00000480502.1_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	271	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)			ctgctgctgccaccactgctg	0.657																																					p.G271S		Atlas-SNP	.											DMKN,colon,carcinoma,0,1	DMKN	116	.	0			c.G811A						PASS	.						30	23	25					19																	36002420		2169	4246	6415	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.811G>A	chr19.hg19:g.36002420C>T	ENSP00000342012:p.Gly271Ser	22.0	2.0	.		26.0	3.0	.	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	hg19	CCDS12463.1	.	.	.	.	.	.	.	.	.	.	C	0.987	-0.695138	0.03303	.	.	ENSG00000161249	ENST00000339686;ENST00000392207;ENST00000447113;ENST00000440396;ENST00000418261;ENST00000424570;ENST00000451297	T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97	3.44	-2.87	0.05700	.	1.607200	0.03581	N	0.230096	T	0.18759	0.0450	N	0.12746	0.255	0.09310	N	1	B;B;B;B;B	0.31931	0.347;0.347;0.347;0.347;0.347	B;B;B;B;B	0.25140	0.058;0.058;0.058;0.058;0.058	T	0.16689	-1.0394	10	0.02654	T	1	.	7.7195	0.28723	0.0:0.3991:0.0:0.6009	.	271;271;271;271;271	E7EUS0;Q6E0U4-7;Q6E0U4-3;Q6E0U4-5;Q6E0U4	.;.;.;.;DMKN_HUMAN	S	271	ENSP00000342012:G271S;ENSP00000394908:G271S;ENSP00000415277:G271S;ENSP00000414743:G271S;ENSP00000388404:G271S;ENSP00000409513:G271S	ENSP00000342012:G271S	G	-	1	0	DMKN	40694260	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	0.439000	0.21575	-0.412000	0.07519	-0.418000	0.06021	GGC	.	.	.	none		0.657	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317		T	36002420	C	T	36002420	3	4	107	1	0	0	0	0	1	0	0	0	4584	594	21	2	984	2	DMKN	19	36002420	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	2537449	36002420	23126563	64	6828											
CBLC	23624	hgsc.bcm.edu	37	chr19	45281521	45281521	+	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	agtgccaacgacgagctcttCcgggcgggctccagactcag	8	6	13	14	4	2	1	1	0	1	1	4	3	4	1	3	2	3	2	3	2	1	1			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:45281521C>G	ENST00000270279.3	+	1	396	c.333C>G	c.(331-333)ttC>ttG	p.F111L	CBLC_ENST00000341505.4_Missense_Mutation_p.F111L	NM_012116.3	NP_036248.3	Q9ULV8	CBLC_HUMAN	Cbl proto-oncogene C, E3 ubiquitin protein ligase	111	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)				ACGAGCTCTTCCGGGCGGGCT	0.657			M		AML																																p.F111L		Atlas-SNP	.		Rec	yes		19	19q13.2	23624	Cas-Br-M (murine) ecotropic retroviral transforming sequence c		L	.	CBLC	41	.	0			c.C333G						PASS	.						4	5	5					19																	45281521		1948	3848	5796	SO:0001583	missense	23624	exon1			GCTCTTCCGGGCG	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.333C>G	chr19.hg19:g.45281521C>G	ENSP00000270279:p.Phe111Leu	18.0	0.0	.		19.0	5.0	.	NM_001130852	Q8N1E5|Q9Y5Z2|Q9Y5Z3	Missense_Mutation	SNP	ENST00000270279.3	hg19	CCDS12643.1	.	.	.	.	.	.	.	.	.	.	.	14.98	2.697608	0.48307	.	.	ENSG00000142273	ENST00000270279;ENST00000341505	T;T	0.78924	-1.22;-1.22	3.49	3.49	0.39957	Adaptor protein Cbl, N-terminal helical (3);Adaptor protein Cbl, PTB domain (1);	0.000000	0.64402	D	0.000016	T	0.78978	0.4369	M	0.81497	2.545	0.39134	D	0.961902	P;D	0.52996	0.939;0.957	P;P	0.45310	0.476;0.469	D	0.83554	0.0103	10	0.66056	D	0.02	-25.9304	10.6934	0.45884	0.0:1.0:0.0:0.0	.	111;111	Q9ULV8-2;Q9ULV8	.;CBLC_HUMAN	L	111	ENSP00000270279:F111L;ENSP00000340250:F111L	ENSP00000270279:F111L	F	+	3	2	CBLC	49973361	1.000000	0.71417	1.000000	0.80357	0.227000	0.25037	2.404000	0.44539	1.962000	0.57031	0.556000	0.70494	TTC	.	.	.	none		0.657	CBLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319732.2	NM_012116		G	45281521	C	G	45281521	3	3	107	1	0	0	0	0	1	0	0	0	2704	854	30	4	335	4	CBLC	19	45281521	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10	9279101	45281521	13847462	65	6829											
ZNF577	84765	hgsc.bcm.edu	37	chr19	52376955	52376955	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatcttctactctggattacAaaacctaaatgagatttcaa	15	14	4	8	0	4	1	1	1	3	1	4	3	4	2	1	1	3	0	1	1	8	6			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:52376955A>G	ENST00000301399.5	-	7	653	c.288T>C	c.(286-288)ttT>ttC	p.F96F	ZNF577_ENST00000412216.1_Intron|ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000420592.1_Intron|ZNF577_ENST00000451628.2_Intron	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	96					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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)		TCTGGATTACAAAACCTAAAT	0.358																																					p.F96F		Atlas-SNP	.											.	ZNF577	63	.	0			c.T288C						PASS	.						37	34	35					19																	52376955		2203	4299	6502	SO:0001819	synonymous_variant	84765	exon7			GATTACAAAACCT	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.288T>C	chr19.hg19:g.52376955A>G		41.0	0.0	.		59.0	13.0	.	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Silent	SNP	ENST00000301399.5	hg19	CCDS12842.2																																																																																			.	.	.	none		0.358	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679		G	52376955	A	G	52376955	2	3	107	1	0	0	0	0	0	0	0	1	18021	127	5	3		3	ZNF577	19	52376955	Silent	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10	7095434	52376955	6752028	66	6830											
ZNF606	80095	hgsc.bcm.edu	37	chr19	58489700	58489700	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcttcactgtgatttctcTggtgttgaagtagggctgag	6	16	12	7	0	3	3	1	3	2	0	5	3	3	3	0	2	0	3	0	2	2	4			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:58489700T>C	ENST00000341164.4	-	7	2968	c.2348A>G	c.(2347-2349)cAg>cGg	p.Q783R	ZNF606_ENST00000536132.1_Missense_Mutation_p.Q693R	NM_025027.3	NP_079303.2	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	783					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)		GTGATTTCTCTGGTGTTGAAG	0.368																																					p.Q783R		Atlas-SNP	.											.	ZNF606	155	.	0			c.A2348G						PASS	.						91	84	86					19																	58489700		2203	4300	6503	SO:0001583	missense	80095	exon7			TTTCTCTGGTGTT	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.2348A>G	chr19.hg19:g.58489700T>C	ENSP00000343617:p.Gln783Arg	134.0	0.0	.		152.0	39.0	.	NM_025027	A8KAN2|Q8NE04|Q96JH5	Missense_Mutation	SNP	ENST00000341164.4	hg19	CCDS12968.1	.	.	.	.	.	.	.	.	.	.	T	9.820	1.185460	0.21870	.	.	ENSG00000166704	ENST00000341164;ENST00000536132	T;T	0.25749	1.78;1.78	4.77	2.52	0.30459	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.40302	N	0.001121	T	0.18882	0.0453	L	0.39147	1.195	0.23988	N	0.996254	B	0.11235	0.004	B	0.10450	0.005	T	0.16217	-1.0410	10	0.49607	T	0.09	.	7.2862	0.26340	0.0:0.0828:0.145:0.7722	.	783	Q8WXB4	ZN606_HUMAN	R	783;693	ENSP00000343617:Q783R;ENSP00000445624:Q693R	ENSP00000343617:Q783R	Q	-	2	0	ZNF606	63181512	0.000000	0.05858	1.000000	0.80357	0.997000	0.91878	0.272000	0.18644	0.941000	0.37499	0.528000	0.53228	CAG	.	.	.	none		0.368	ZNF606-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405961.1	NM_025027		C	58489700	T	C	58489700	3	2	107	1	0	0	0	0	1	0	0	0	18044	1580	55	3	34	3	ZNF606	19	58489700	Missense_Mutation	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10	6112745	58489700	639283	67	6831											
BPIL3	128859	hgsc.bcm.edu	37	chr20	31627181	31627181	+	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	agcttatcccaagtcaaagcCcttgacgacccagatcaaga	14	7	7	13	1	2	3	2	1	0	2	3	4	3	3	3	0	2	1	3	0	4	2	rs370022331		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr20:31627181C>A	ENST00000349552.1	+	10	929	c.929C>A	c.(928-930)cCc>cAc	p.P310H		NM_174897.2	NP_777557.1	Q8NFQ5	BPIB6_HUMAN	BPI fold containing family B, member 6	310						extracellular region (GO:0005576)	lipid binding (GO:0008289)										AAGTCAAAGCCCTTGACGACC	0.522																																					p.P310H		Atlas-SNP	.											.	.	.	.	0			c.C929A						PASS	.						102	107	105					20																	31627181		2203	4300	6503	SO:0001583	missense	128859	exon10			CAAAGCCCTTGAC	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.929C>A	chr20.hg19:g.31627181C>A	ENSP00000344929:p.Pro310His	112.0	0.0	.		88.0	33.0	.	NM_174897		Missense_Mutation	SNP	ENST00000349552.1	hg19	CCDS13211.1	.	.	.	.	.	.	.	.	.	.	C	11.65	1.703220	0.30232	.	.	ENSG00000167104	ENST00000349552	T	0.08896	3.04	4.44	3.47	0.39725	.	0.000000	0.56097	D	0.000035	T	0.25606	0.0623	M	0.81497	2.545	0.29520	N	0.853577	D	0.71674	0.998	D	0.66716	0.946	T	0.05354	-1.0890	10	0.46703	T	0.11	.	10.1046	0.42526	0.0:0.7964:0.2036:0.0	.	310	Q8NFQ5	BPIB6_HUMAN	H	310	ENSP00000344929:P310H	ENSP00000344929:P310H	P	+	2	0	BPIFB6	31090842	1.000000	0.71417	0.986000	0.45419	0.039000	0.13416	1.937000	0.40193	1.047000	0.40274	0.561000	0.74099	CCC	.	.	.	alt		0.522	BPIFB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078658.2	NM_174897		A	31627181	C	A	31627181	3	1	107	1	0	0	0	0	1	0	0	0	1495	623	22	4	967	4	BPIL3	20	31627181	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10		31627181	31398339	68	6832											
TTPAL	79183	hgsc.bcm.edu	37	chr20	43108944	43108944	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctgcagctcctcgtcaactAccacagctgtagaagaagct	11	8	8	14	1	1	2	1	0	0	2	3	2	2	2	3	0	6	5	3	0	5	2			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr20:43108944A>G	ENST00000372904.3	+	3	448	c.305A>G	c.(304-306)tAc>tGc	p.Y102C	TTPAL_ENST00000372906.2_Missense_Mutation_p.Y102C|TTPAL_ENST00000262605.4_Missense_Mutation_p.Y102C	NM_024331.4	NP_077307.2	Q9BTX7	TTPAL_HUMAN	tocopherol (alpha) transfer protein-like	102						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						CTCGTCAACTACCACAGCTGT	0.567																																					p.Y102C		Atlas-SNP	.											.	TTPAL	31	.	0			c.A305G						PASS	.						51	44	46					20																	43108944		2203	4300	6503	SO:0001583	missense	79183	exon2			TCAACTACCACAG	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.305A>G	chr20.hg19:g.43108944A>G	ENSP00000361995:p.Tyr102Cys	167.0	0.0	.		153.0	49.0	.	NM_001039199	E1P5X3|Q5QPC1|Q9H1G2|Q9NQG8	Missense_Mutation	SNP	ENST00000372904.3	hg19	CCDS13332.2	.	.	.	.	.	.	.	.	.	.	A	22.6	4.306489	0.81247	.	.	ENSG00000124120	ENST00000262605;ENST00000372904;ENST00000372906;ENST00000456317	D;D;D;D	0.86432	-2.12;-2.12;-2.12;-2.12	5.1	5.1	0.69264	Phosphatidylinositol transfer protein-like, N-terminal (1);Cellular retinaldehyde-binding/triple function, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.92886	0.7737	M	0.76328	2.33	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93787	0.7089	10	0.87932	D	0	-22.794	14.903	0.70696	1.0:0.0:0.0:0.0	.	102	Q9BTX7	TTPAL_HUMAN	C	102	ENSP00000262605:Y102C;ENSP00000361995:Y102C;ENSP00000361997:Y102C;ENSP00000412720:Y102C	ENSP00000262605:Y102C	Y	+	2	0	TTPAL	42542358	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.317000	0.96327	1.909000	0.55274	0.533000	0.62120	TAC	.	.	.	none		0.567	TTPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106886.2	NM_024331		G	43108944	A	G	43108944	3	3	107	1	0	0	0	0	1	0	0	0	16749	391	14	3	307	3	TTPAL	20	43108944	Missense_Mutation	SNP	A	TCGA-B9-A69E-01A-11D-A31X-10	11481763	43108944	19916576	69	6833											
ADA	100	hgsc.bcm.edu	37	chr20	43251682	43251682	+	Missense_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	cggccgagcccacctccccgGcgtggacagtacggtgaatg	7	5	14	15	5	0	1	0	1	0	0	1	3	1	2	5	4	2	1	5	4	2	1			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr20:43251682G>A	ENST00000372874.4	-	7	778	c.644C>T	c.(643-645)gCc>gTc	p.A215V	ADA_ENST00000537820.1_Intron|PKIG_ENST00000372882.3_Intron|PKIG_ENST00000372887.1_Intron|ADA_ENST00000464097.1_5'UTR	NM_000022.2	NP_000013.2	P00813	ADA_HUMAN	adenosine deaminase	215			A -> T (in ADASCID; dbSNP:rs114025668). {ECO:0000269|PubMed:2166947}.		adenosine catabolic process (GO:0006154)|aging (GO:0007568)|cell adhesion (GO:0007155)|dATP catabolic process (GO:0046061)|deoxyadenosine catabolic process (GO:0006157)|embryonic digestive tract development (GO:0048566)|germinal center B cell differentiation (GO:0002314)|histamine secretion (GO:0001821)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|negative regulation of adenosine receptor signaling pathway (GO:0060169)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mature B cell apoptotic process (GO:0002906)|negative regulation of mucus secretion (GO:0070256)|negative regulation of penile erection (GO:0060407)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleobase-containing small molecule metabolic process (GO:0055086)|Peyer's patch development (GO:0048541)|placenta development (GO:0001890)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of germinal center formation (GO:0002636)|positive regulation of heart rate (GO:0010460)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide salvage (GO:0032261)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|purine-containing compound salvage (GO:0043101)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to morphine (GO:0043278)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|trophectodermal cell differentiation (GO:0001829)|xanthine biosynthetic process (GO:0046111)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|lysosome (GO:0005764)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenosine deaminase activity (GO:0004000)|purine nucleoside binding (GO:0001883)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|pancreas(2)|prostate(3)|skin(2)|urinary_tract(1)	18		all_lung(126;1.24e-07)|Lung NSC(126;1.94e-07)|Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)		Adenosine(DB00640)|Dipyridamole(DB00975)|Edetic Acid(DB00974)|Nelarabine(DB01280)|Pentostatin(DB00552)|Theophylline(DB00277)|Vidarabine(DB00194)	CACCTCCCCGGCGTGGACAGT	0.657									Adenosine Deaminase Deficiency																												p.A215V		Atlas-SNP	.											.	ADA	42	.	0			c.C644T						PASS	.						67	68	68					20																	43251682		2203	4300	6503	SO:0001583	missense	100	exon7	Familial Cancer Database	Severe Combined Immunodeficiency (SCID) due to ADA-deficiency	TCCCCGGCGTGGA	X02994	CCDS13335.1	20q13.12	2014-09-17			ENSG00000196839	ENSG00000196839	3.5.4.4		186	protein-coding gene	gene with protein product		608958				6198240, 6090454	Standard	NM_000022		Approved		uc002xmj.3	P00813	OTTHUMG00000033081	ENST00000372874.4:c.644C>T	chr20.hg19:g.43251682G>A	ENSP00000361965:p.Ala215Val	112.0	0.0	.		98.0	20.0	.	NM_000022	Q53F92|Q6LA59	Missense_Mutation	SNP	ENST00000372874.4	hg19	CCDS13335.1	.	.	.	.	.	.	.	.	.	.	G	17.39	3.377508	0.61735	.	.	ENSG00000196839	ENST00000372874	D	0.97114	-4.25	4.89	3.9	0.45041	Adenosine/AMP deaminase (1);	0.048514	0.85682	D	0.000000	D	0.98466	0.9489	M	0.91196	3.185	0.80722	D	1	D	0.89917	1.0	D	0.63113	0.911	D	0.98951	1.0794	10	0.87932	D	0	-9.5965	15.4157	0.74966	0.0:0.1385:0.8615:0.0	.	215	P00813	ADA_HUMAN	V	215	ENSP00000361965:A215V	ENSP00000361965:A215V	A	-	2	0	ADA	42685096	1.000000	0.71417	0.136000	0.22124	0.136000	0.21042	6.472000	0.73567	2.549000	0.85964	0.563000	0.77884	GCC	.	.	.	none		0.657	ADA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080509.2	NM_000022		A	43251682	G	A	43251682	3	1	107	1	0	0	0	0	1	0	0	0	230	1203	42	2	471	2	ADA	20	43251682	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	142738	43251682	19773838	70	6834											
PRIC285	85441	hgsc.bcm.edu	37	chr20	62201870	62201870	+	Missense_Mutation	SNP	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	cgctcacctcagagtggacgGcaaacgtccagctgtactgg	9	7	12	13	3	2	1	2	0	0	1	3	2	3	2	2	3	3	4	2	3	2	1			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr20:62201870G>A	ENST00000467148.1	-	3	626	c.557C>T	c.(556-558)gCc>gTc	p.A186V	HELZ2_ENST00000427522.2_5'Flank|HELZ2_ENST00000479540.1_5'UTR	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	186					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)										AGAGTGGACGGCAAACGTCCA	0.627																																					p.A186V		Atlas-SNP	.											.	.	.	.	0			c.C557T						PASS	.						82	71	75					20																	62201870		2202	4300	6502	SO:0001583	missense	85441	exon4			TGGACGGCAAACG	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.557C>T	chr20.hg19:g.62201870G>A	ENSP00000417401:p.Ala186Val	93.0	0.0	.		81.0	4.0	.	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	hg19	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	G	11.29	1.596213	0.28445	.	.	ENSG00000130589	ENST00000467148	T	0.02421	4.3	4.28	-7.27	0.01461	.	2.233770	0.02265	N	0.067890	T	0.01835	0.0058	N	0.19112	0.55	0.09310	N	1	B;B	0.18310	0.027;0.0	B;B	0.15052	0.012;0.0	T	0.43956	-0.9359	10	0.56958	D	0.05	-1.1836	0.4194	0.00453	0.206:0.2023:0.2358:0.3559	.	186;186	Q4VXQ0;Q9BYK8	.;PR285_HUMAN	V	186	ENSP00000417401:A186V	ENSP00000417401:A186V	A	-	2	0	RP4-697K14.7	61672314	0.000000	0.05858	0.000000	0.03702	0.041000	0.13682	-2.542000	0.00935	-1.101000	0.03027	0.558000	0.71614	GCC	.	.	.	none		0.627	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		A	62201870	G	A	62201870	3	1	107	1	0	0	0	0	1	0	0	0	12495	1203	42	2	7483	2	PRIC285	20	62201870	Missense_Mutation	SNP	G	TCGA-B9-A69E-01A-11D-A31X-10	18950188	62201870	823650	71	6835											
KCNE2	9992	hgsc.bcm.edu	37	chr21	35743124	35743124	+	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	catccatgagaacattggtgCggctgggttcaaaatgtccc	10	10	11	10	1	1	1	1	1	0	1	3	2	3	1	2	3	2	2	2	3	3	2	rs199473367		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr21:35743124C>T	ENST00000290310.3	+	2	487	c.347C>T	c.(346-348)gCg>gTg	p.A116V	AP000320.6_ENST00000440403.1_RNA	NM_172201.1	NP_751951.1	Q9Y6J6	KCNE2_HUMAN	potassium voltage-gated channel, Isk-related family, member 2	116					aging (GO:0007568)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cellular protein localization (GO:0034613)|cellular response to drug (GO:0035690)|membrane repolarization (GO:0086009)|membrane repolarization during action potential (GO:0086011)|positive regulation of proteasomal protein catabolic process (GO:1901800)|potassium ion export (GO:0071435)|potassium ion import (GO:0010107)|potassium ion transmembrane transport (GO:0071805)|regulation of cyclic nucleotide-gated ion channel activity (GO:1902159)|regulation of delayed rectifier potassium channel activity (GO:1902259)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of inward rectifier potassium channel activity (GO:1901979)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|tongue development (GO:0043586)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			endometrium(1)|large_intestine(1)	2						AACATTGGTGCGGCTGGGTTC	0.488																																					p.A116V		Atlas-SNP	.											KCNE2,colon,carcinoma,0,1	KCNE2	13	.	0			c.C347T	GRCh37	CM003450	KCNE2	M		PASS	.						44	40	42					21																	35743124		2203	4300	6503	SO:0001583	missense	9992	exon2			TTGGTGCGGCTGG	AF071002	CCDS13635.1	21q22.1	2014-09-17			ENSG00000159197	ENSG00000159197		"Potassium channels"	6242	protein-coding gene	gene with protein product		603796				10219239	Standard	NM_172201		Approved	MiRP1, LQT6	uc002ytt.1	Q9Y6J6	OTTHUMG00000086189	ENST00000290310.3:c.347C>T	chr21.hg19:g.35743124C>T	ENSP00000290310:p.Ala116Val	97.0	0.0	.		99.0	26.0	.	NM_172201	A5H1P3|D3DSF8|Q52LJ5	Missense_Mutation	SNP	ENST00000290310.3	hg19	CCDS13635.1	.	.	.	.	.	.	.	.	.	.	C	19.32	3.805758	0.70682	.	.	ENSG00000159197	ENST00000290310	D	0.93307	-3.2	5.66	5.66	0.87406	.	0.000000	0.64402	D	0.000007	D	0.94686	0.8286	L	0.32530	0.975	0.42882	D	0.994175	D	0.89917	1.0	D	0.78314	0.991	D	0.95265	0.8372	10	0.66056	D	0.02	-27.5208	17.5309	0.87814	0.0:1.0:0.0:0.0	.	116	Q9Y6J6	KCNE2_HUMAN	V	116	ENSP00000290310:A116V	ENSP00000290310:A116V	A	+	2	0	KCNE2	34664994	0.991000	0.36638	0.150000	0.22450	0.102000	0.19082	3.221000	0.51215	2.657000	0.90304	0.655000	0.94253	GCG	.	.	.	weak		0.488	KCNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194068.2			T	35743124	C	T	35743124	3	4	107	1	0	0	0	0	1	0	0	0	8030	768	27	1	349	1	KCNE2	21	35743124	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10		35743124	12386771	72	6836											
KCNJ15	3772	hgsc.bcm.edu	37	chr21	39671646	39671649	+	Frame_Shift_Del	DEL	TTGA	TTGA	-																															ctcagttggtcatcacgaccTtgattgagatcttcatcacc																										TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	TTGA	TTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr21:39671646_39671649delTTGA	ENST00000328656.4	+	4	766_769	c.463_466delTTGA	c.(463-468)ttgattfs	p.LI155fs	KCNJ15_ENST00000398938.2_Frame_Shift_Del_p.LI155fs|KCNJ15_ENST00000398932.1_Frame_Shift_Del_p.LI155fs|KCNJ15_ENST00000398934.1_Frame_Shift_Del_p.LI155fs|KCNJ15_ENST00000398930.1_Frame_Shift_Del_p.LI155fs	NM_001276437.1|NM_001276438.1|NM_001276439.1|NM_002243.3	NP_001263366.1|NP_001263367.1|NP_001263368.1|NP_002234.2	Q99712	KCJ15_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 15	155					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	24					Yohimbine(DB01392)	CATCACGACCTTGATTGAGATCTT	0.515																																					p.154_155del		Atlas-Indel,Pindel	.											.	KCNJ15	43	.	0			c.462_465del						PASS	.																																			SO:0001589	frameshift_variant	3772	exon3			.	Y10745	CCDS13656.1	21q22.2	2011-07-05			ENSG00000157551	ENSG00000157551		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6261	protein-coding gene	gene with protein product		602106				9299242, 8995301, 16382105	Standard	NM_170736		Approved	Kir4.2, Kir1.3, IRKK	uc002ywx.4	Q99712	OTTHUMG00000090609	ENST00000328656.4:c.463_466delTTGA	chr21.hg19:g.39671650_39671653delTTGA	ENSP00000331698:p.Leu155fs	115.0	0.0	0		105.0	28.0	0.266667	NM_170736	D3DSH5|O00564|Q96L28|Q99446	Frame_Shift_Del	DEL	ENST00000328656.4	hg19	CCDS13656.1																																																																																			.	.	.	none		0.515	KCNJ15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207181.2	NM_002243		-	39671649	TTGA	-	39671646	7	5	107	1	0	1	0	1	0	0	0	0	8056	1606	56	0	465	0	KCNJ15	21	39671646	Frame_Shift_Del	DEL	TTGA	TCGA-B9-A69E-01A-11D-A31X-10	3928522	39671646	8458249	73	6837											
USP9X	8239	hgsc.bcm.edu	37	chrX	41043810	41043810	+	Missense_Mutation	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	tatggaaactcgaaggggtgCctacctcaatgctcttaaaa	13	10	9	9	1	2	0	1	0	1	0	3	2	2	1	2	3	4	1	2	3	7	3			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chrX:41043810C>T	ENST00000324545.8	+	23	4073	c.3440C>T	c.(3439-3441)gCc>gTc	p.A1147V	USP9X_ENST00000378308.2_Missense_Mutation_p.A1147V	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	1147					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						CGAAGGGGTGCCTACCTCAAT	0.463																																					p.A1147V	Ovarian(172;1807 2695 35459 49286)	Atlas-SNP	.											.	USP9X	385	.	0			c.C3440T						PASS	.						107	99	101					X																	41043810		2177	4280	6457	SO:0001583	missense	8239	exon23			GGGGTGCCTACCT	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.3440C>T	chrX.hg19:g.41043810C>T	ENSP00000316357:p.Ala1147Val	154.0	0.0	.		143.0	72.0	.	NM_001039591	O75550|Q8WWT3|Q8WX12	Missense_Mutation	SNP	ENST00000324545.8	hg19	CCDS43930.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.984913	0.74474	.	.	ENSG00000124486	ENST00000378308;ENST00000324545	T;T	0.11712	2.75;2.75	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.10723	0.0262	L	0.35723	1.085	0.80722	D	1	B;B	0.16802	0.019;0.019	B;B	0.17098	0.017;0.017	T	0.15321	-1.0441	10	0.09843	T	0.71	.	18.7017	0.91623	0.0:1.0:0.0:0.0	.	1147;1147	Q93008-1;Q93008	.;USP9X_HUMAN	V	1147	ENSP00000367558:A1147V;ENSP00000316357:A1147V	ENSP00000316357:A1147V	A	+	2	0	USP9X	40928754	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.729000	0.84864	2.361000	0.80049	0.513000	0.50165	GCC	.	.	.	none		0.463	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		T	41043810	C	T	41043810	3	4	107	1	0	0	0	0	1	0	0	0	17102	739	26	2	3526	2	USP9X	23	41043810	Missense_Mutation	SNP	C	TCGA-B9-A69E-01A-11D-A31X-10		41043810	114226750	74	6838											
GPR174	84636	hgsc.bcm.edu	37	chrX	78426874	78426874	+	Frame_Shift_Del	DEL	T	T	-																															tttggtttctcatgtaccccTttcgcttccatgactgcaaa																								rs137871290		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chrX:78426874delT	ENST00000276077.1	+	1	406	c.370delT	c.(370-372)tttfs	p.F124fs		NM_032553.1	NP_115942.1	Q9BXC1	GP174_HUMAN	G protein-coupled receptor 174	124						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	38						CATGTACCCCTTTCGCTTCCA	0.458										HNSCC(63;0.18)																											p.P123fs		Pindel	.											.	GPR174	79	.	0			c.369delC						PASS	.						217	194	202					X																	78426874		2203	4300	6503	SO:0001589	frameshift_variant	84636	exon1			.	AF345567	CCDS14443.1	Xq13.3	2012-08-21			ENSG00000147138	ENSG00000147138		"GPCR / Class A : Orphans"	30245	protein-coding gene	gene with protein product		300903					Standard	NM_032553		Approved	FKSG79	uc004edg.1	Q9BXC1	OTTHUMG00000021898	ENST00000276077.1:c.370delT	chrX.hg19:g.78426874delT	ENSP00000276077:p.Phe124fs	128.0	0.0	.		144.0	59.0	0.410	NM_032553	Q2M3F7	Frame_Shift_Del	DEL	ENST00000276077.1	hg19	CCDS14443.1																																																																																			.	.	.	none		0.458	GPR174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057327.1	NM_032553		-	78426874	T	-	78426874	7	5	107	1	0	1	0	1	0	0	0	0	6679	1609	56	0	372	0	GPR174	23	78426874	Frame_Shift_Del	DEL	T	TCGA-B9-A69E-01A-11D-A31X-10	37383064	78426874	76843686	75	6839											
UPF3B	65109	hgsc.bcm.edu	37	chrX	118977251	118977251	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcataactttccaaaaacttTctatattctggatctaaata	15	15	3	8	0	3	0	0	0	3	0	4	1	4	1	1	1	2	1	1	1	8	8			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chrX:118977251T>C	ENST00000276201.2	-	5	552	c.483A>G	c.(481-483)agA>agG	p.R161R	UPF3B_ENST00000345865.2_Silent_p.R161R|UPF3B_ENST00000478840.1_5'UTR	NM_080632.2	NP_542199.1	Q9BZI7	REN3B_HUMAN	UPF3 regulator of nonsense transcripts homolog B (yeast)	161	Necessary for interaction with UPF2.|Sufficient for association with EJC core.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|prostate(1)	30						CCAAAAACTTTCTATATTCTG	0.279																																					p.R161R		Atlas-SNP	.											.	UPF3B	74	.	0			c.A483G						PASS	.						161	144	150					X																	118977251		2202	4300	6502	SO:0001819	synonymous_variant	65109	exon5			AAACTTTCTATAT	AF318576	CCDS14587.1, CCDS14588.1	Xq25-q26	2014-01-31			ENSG00000125351	ENSG00000125351			20439	protein-coding gene	gene with protein product		300298	"mental retardation, X-linked 62"	MRX62		11113196, 11163187, 19238151	Standard	NM_023010		Approved	RENT3B, UPF3X, HUPF3B	uc004erz.2	Q9BZI7	OTTHUMG00000022282	ENST00000276201.2:c.483A>G	chrX.hg19:g.118977251T>C		23.0	0.0	.		31.0	17.0	.	NM_023010	D3DWI3|D3DWI4|Q0VAK8|Q9H1J0	Silent	SNP	ENST00000276201.2	hg19	CCDS14588.1																																																																																			.	.	.	none		0.279	UPF3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058068.1			C	118977251	T	C	118977251	2	2	107	1	0	0	0	0	0	0	0	1	17018	1780	62	3		3	UPF3B	23	118977251	Silent	SNP	T	TCGA-B9-A69E-01A-11D-A31X-10	40550377	118977251	36293309	76	6840											
NPHP4	261734	hgsc.bcm.edu	37	chr1	5965397	5965397	+	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	ccatctcgttgctttgtagaCaatctgattcttccttctga	7	17	6	11	1	4	3	0	2	4	1	6	3	5	3	2	0	1	3	2	0	2	6			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr1:5965397C>G	ENST00000378156.4	-	15	2175	c.1910G>C	c.(1909-1911)tGt>tCt	p.C637S	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	637					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)		GCTTTGTAGACAATCTGATTC	0.458																																					p.C637S		Atlas-SNP	.											.	NPHP4	119	.	0			c.G1910C						PASS	.						162	162	162					1																	5965397		1983	4163	6146	SO:0001583	missense	261734	exon15			TGTAGACAATCTG	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.1910G>C	chr1.hg19:g.5965397C>G	ENSP00000367398:p.Cys637Ser	119.0	0.0	.		119.0	44.0	.	NM_015102	Q8IWC0	Missense_Mutation	SNP	ENST00000378156.4	hg19	CCDS44052.1	.	.	.	.	.	.	.	.	.	.	C	1.924	-0.447616	0.04572	.	.	ENSG00000131697	ENST00000378156;ENST00000378160	D	0.86097	-2.07	5.52	3.44	0.39384	.	0.958176	0.08697	N	0.907022	T	0.74329	0.3702	L	0.35414	1.06	0.09310	N	0.999991	B	0.14012	0.009	B	0.12837	0.008	T	0.58255	-0.7668	10	0.20046	T	0.44	.	3.0279	0.06097	0.2008:0.4175:0.2899:0.0917	.	637	O75161	NPHP4_HUMAN	S	637;40	ENSP00000367398:C637S	ENSP00000367398:C637S	C	-	2	0	NPHP4	5887984	0.225000	0.23685	0.034000	0.17996	0.361000	0.29550	0.868000	0.27982	1.283000	0.44513	0.561000	0.74099	TGT	.	.	.	none		0.458	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2			G	5965397	C	G	5965397	3	3	108	1	0	0	0	0	1	0	0	0	10588	478	17	4	2434	4	NPHP4	1	5965397	Missense_Mutation	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10		5965397	243285224	1	6841											
UBR4	23352	hgsc.bcm.edu	37	chr1	19526229	19526229	+	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	ttacaggctgctgccactgaCtgaagttggttccggggaac	8	10	13	10	1	0	2	0	2	0	0	1	3	1	3	2	4	4	4	2	4	3	3			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr1:19526229C>G	ENST00000375254.3	-	3	321	c.294G>C	c.(292-294)caG>caC	p.Q98H	UBR4_ENST00000375226.2_Missense_Mutation_p.Q98H|UBR4_ENST00000375217.2_Missense_Mutation_p.Q98H|UBR4_ENST00000375267.2_Missense_Mutation_p.Q98H	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	98					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)		CTGCCACTGACTGAAGTTGGT	0.448																																					p.Q98H		Atlas-SNP	.											.	UBR4	415	.	0			c.G294C						PASS	.						66	70	69					1																	19526229		2203	4300	6503	SO:0001583	missense	23352	exon3			CACTGACTGAAGT	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.294G>C	chr1.hg19:g.19526229C>G	ENSP00000364403:p.Gln98His	84.0	0.0	.		96.0	30.0	.	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	hg19	CCDS189.1	.	.	.	.	.	.	.	.	.	.	C	11.70	1.716487	0.30413	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226	T;T;T;T	0.22945	1.93;1.93;1.93;1.93	5.45	3.58	0.41010	.	0.070642	0.56097	D	0.000023	T	0.12220	0.0297	N	0.08118	0	0.80722	D	1	P	0.44090	0.826	B	0.38562	0.276	T	0.07712	-1.0758	10	0.48119	T	0.1	.	8.9721	0.35912	0.0:0.7689:0.0:0.2311	.	98	Q5T4S7	UBR4_HUMAN	H	98	ENSP00000364403:Q98H;ENSP00000364416:Q98H;ENSP00000364365:Q98H;ENSP00000364374:Q98H	ENSP00000364365:Q98H	Q	-	3	2	UBR4	19398816	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.114000	0.31196	0.780000	0.33566	-0.157000	0.13467	CAG	.	.	.	none		0.448	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		G	19526229	C	G	19526229	3	3	108	1	0	0	0	0	1	0	0	0	16916	564	20	4	15673	4	UBR4	1	19526229	Missense_Mutation	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10	13560832	19526229	229724392	2	6842											
GPBP1L1	60313	hgsc.bcm.edu	37	chr1	46120388	46120388	+	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	ttggctcatgccatcatgacCtcgggaagagctatgccaac	10	9	10	12	1	2	2	2	1	0	1	3	3	2	3	3	2	4	2	3	2	3	2			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr1:46120388C>T	ENST00000290795.3	-	5	1525	c.304G>A	c.(304-306)Ggt>Agt	p.G102S	GPBP1L1_ENST00000355105.3_Missense_Mutation_p.G102S			Q9HC44	GPBL1_HUMAN	GC-rich promoter binding protein 1-like 1	102					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)					CCATCATGACCTCGGGAAGAG	0.547																																					p.G102S		Atlas-SNP	.											.	GPBP1L1	43	.	0			c.G304A						PASS	.						89	79	83					1																	46120388		2203	4300	6503	SO:0001583	missense	60313	exon6			CATGACCTCGGGA		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.304G>A	chr1.hg19:g.46120388C>T	ENSP00000290795:p.Gly102Ser	134.0	0.0	.		113.0	42.0	.	NM_021639	D3DQ10|Q9H751	Missense_Mutation	SNP	ENST00000290795.3	hg19	CCDS528.1	.	.	.	.	.	.	.	.	.	.	C	34	5.363208	0.95877	.	.	ENSG00000159592	ENST00000290795;ENST00000355105	T;T	0.50277	0.75;0.75	5.95	5.05	0.67936	.	0.048934	0.85682	N	0.000000	T	0.67126	0.2860	M	0.66939	2.045	0.43207	D	0.995062	D	0.89917	1.0	D	0.91635	0.999	T	0.71279	-0.4640	10	0.87932	D	0	-17.3444	15.1228	0.72457	0.0:0.9326:0.0:0.0674	.	102	Q9HC44	GPBL1_HUMAN	S	102	ENSP00000290795:G102S;ENSP00000347224:G102S	ENSP00000290795:G102S	G	-	1	0	GPBP1L1	45892975	1.000000	0.71417	0.955000	0.39395	0.888000	0.51559	5.504000	0.66968	1.534000	0.49203	0.655000	0.94253	GGT	.	.	.	none		0.547	GPBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098375.1	NM_021639		T	46120388	C	T	46120388	3	4	108	1	0	0	0	0	1	0	0	0	6603	681	24	2	1152	2	GPBP1L1	1	46120388	Missense_Mutation	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10	26594159	46120388	203130233	3	6843											
PTGER3	5733	hgsc.bcm.edu	37	chr1	71513083	71513084	+	Missense_Mutation	DNP	GC	GC	TA																															gttgcccacgaaaccagtgaGcagcatggtgatcgggaagg																										TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr1:71513083_71513084GC>TA	ENST00000306666.5	-	1	387_388	c.177_178GC>TA	c.(175-180)ctGCtc>ctTAtc	p.L60I	ZRANB2-AS1_ENST00000450461.1_RNA|PTGER3_ENST00000370931.3_Missense_Mutation_p.L60I|PTGER3_ENST00000370932.2_Missense_Mutation_p.L60I|PTGER3_ENST00000460330.1_Missense_Mutation_p.L60I|PTGER3_ENST00000356595.4_Missense_Mutation_p.L60I|PTGER3_ENST00000370924.4_Missense_Mutation_p.L60I|PTGER3_ENST00000351052.5_Missense_Mutation_p.L60I|PTGER3_ENST00000354608.5_Missense_Mutation_p.L60I|PTGER3_ENST00000414819.1_Missense_Mutation_p.L60I	NM_198719.1	NP_942012.1	P43115	PE2R3_HUMAN	prostaglandin E receptor 3 (subtype EP3)	60					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)	AAACCAGTGAGCAGCATGGTGA	0.678																																					p.L60I|p.L59L		Atlas-SNP	.											.	PTGER3	246	.	0			c.C178A|c.G177T						PASS	.																																			SO:0001583	missense	5733	exon1			CAGTGAGCAGCAT|AGTGAGCAGCATG	X83863	CCDS652.1, CCDS655.1, CCDS656.1, CCDS657.1, CCDS658.1	1p31.2	2012-08-08			ENSG00000050628	ENSG00000050628		"GPCR / Class A : Prostanoid receptors"	9595	protein-coding gene	gene with protein product		176806				7759114, 9073510	Standard	NM_001126044		Approved	EP3	uc001dfo.3	P43115	OTTHUMG00000009399	ENST00000306666.5:c.177_178delinsTA	chr1.hg19:g.71513083_71513084delinsTA	ENSP00000302313:p.Leu60Ile	288.0|285.0	0.0	.		269.0|271.0	92.0	.	NM_001126044	B0AZN4|B1AK19|B5BUP5|O00326|Q12943|Q12944|Q12945|Q16546|Q5CZ59|Q5CZ61|Q5CZ62|Q5CZ63|Q5CZ64	Missense_Mutation|Silent	SNP	ENST00000306666.5	hg19	CCDS657.1																																																																																			.	.	.	none		0.678	PTGER3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026076.1	NM_000957		TA	71513084	GC	TA	71513083	3	4	108	1	0	0	0	0	1	0	0	0	12755	971	34	4	1313	4	PTGER3	1	71513083	Missense_Mutation	DNP	GC	TCGA-B9-A8YH-01A-11D-A36X-10	25392695	71513083	177737538	4	6844											
ADORA3	140	hgsc.bcm.edu	37	chr1	112029234	112029234	+	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	cggtcagccttgcggacaacTttgggagccttgcagcttct	6	11	12	12	2	2	0	1	0	1	0	2	2	2	2	2	3	6	2	2	3	1	4			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr1:112029234T>A	ENST00000369716.4	-	4	979	c.846A>T	c.(844-846)aaA>aaT	p.K282N	ADORA3_ENST00000369717.4_Missense_Mutation_p.K201N	NM_020683.6	NP_065734.5	P33765	AA3R_HUMAN	adenosine A3 receptor	0					activation of adenylate cyclase activity (GO:0007190)|histamine secretion by mast cell (GO:0002553)|inflammatory response (GO:0006954)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of mucus secretion (GO:0070257)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of heart contraction (GO:0008016)|response to wounding (GO:0009611)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	G-protein coupled adenosine receptor activity (GO:0001609)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|skin(1)	12		all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156)		all cancers(265;0.0185)|Colorectal(144;0.0186)|Lung(183;0.0238)|COAD - Colon adenocarcinoma(174;0.0644)|Epithelial(280;0.0872)|LUSC - Lung squamous cell carcinoma(189;0.134)	Adenosine(DB00640)|Aminophylline(DB01223)|Enprofylline(DB00824)	TGCGGACAACTTTGGGAGCCT	0.562																																					p.K282N		Atlas-SNP	.											.	ADORA3	104	.	0			c.A846T						PASS	.						102	92	96					1																	112029234		2203	4300	6503	SO:0001583	missense	140	exon4			GACAACTTTGGGA	BC029831	CCDS838.1, CCDS839.1, CCDS41369.1	1p13.2	2014-09-17			ENSG00000121933	ENSG00000121933		"GPCR / Class A : Adenosine receptors", "Immunoglobulin superfamily / V-set domain containing"	268	protein-coding gene	gene with protein product		600445				7607699	Standard	NM_020683		Approved	AD026	uc001ebf.3	P33765	OTTHUMG00000011957	ENST00000369716.4:c.846A>T	chr1.hg19:g.112029234T>A	ENSP00000358730:p.Lys282Asn	69.0	0.0	.		75.0	35.0	.	NM_020683	A2A3P4|Q6UWU0|Q9BYZ1	Missense_Mutation	SNP	ENST00000369716.4	hg19	CCDS838.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.82|11.82	1.752256|1.752256	0.31046|0.31046	.|.	.|.	ENSG00000121933|ENSG00000121933	ENST00000414219;ENST00000442484|ENST00000369717;ENST00000369716;ENST00000355437;ENST00000443498	T|T;T	0.20200|0.54279	2.09|2.4;0.58	4.5|4.5	-0.965|-0.965	0.10323|0.10323	.|.	0.649942|0.649942	0.14219|0.14219	N|N	0.333533|0.333533	T|T	0.18551|0.18551	0.0445|0.0445	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	1|1	.|B;B	.|0.30281	.|0.275;0.275	.|B;B	.|0.36418	.|0.224;0.104	T|T	0.25916|0.25916	-1.0118|-1.0118	8|10	0.45353|0.72032	T|D	0.12|0.01	-3.4141|-3.4141	3.1776|3.1776	0.06573|0.06573	0.1969:0.3231:0.0:0.48|0.1969:0.3231:0.0:0.48	.|.	.|201;282	.|Q5QNY7;P33765-2	.|.;.	M|N	142;95|201;282;113;107	ENSP00000415646:K142M|ENSP00000358731:K201N;ENSP00000358730:K282N	ENSP00000415646:K142M|ENSP00000347612:K113N	K|K	-|-	2|3	0|2	ADORA3|ADORA3	111830757|111830757	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	0.208000|0.208000	0.17415|0.17415	-0.015000|-0.015000	0.14150|0.14150	-0.441000|-0.441000	0.05720|0.05720	AAG|AAA	.	.	.	none		0.562	ADORA3-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157679.1	NM_000677, NM_020683		A	112029234	T	A	112029234	3	1	108	1	0	0	0	0	1	0	0	0	329	1606	56	5	209	5	ADORA3	1	112029234	Missense_Mutation	SNP	T	TCGA-B9-A8YH-01A-11D-A36X-10	40516151	112029234	137221387	5	6845											
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144882724	144882724	+	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	gagctttctgaactcagcctGaaggctactctcactcagac	10	10	8	13	0	4	3	3	2	2	1	5	4	4	3	1	1	4	2	1	1	3	2			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr1:144882724G>T	ENST00000369354.3	-	24	3484	c.3295C>A	c.(3295-3297)Cag>Aag	p.Q1099K	PDE4DIP_ENST00000369359.4_Missense_Mutation_p.Q1236K|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.Q1236K|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.Q1099K|PDE4DIP_ENST00000313382.9_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1099					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)		AACTCAGCCTGAAGGCTACTC	0.483			T	PDGFRB	MPD																																p.Q1099K		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	PDE4DIP_ENST00000369356,bladder,carcinoma,0,2	PDE4DIP	817	.	0			c.C3295A						PASS	.						273	257	262					1																	144882724		2203	4296	6499	SO:0001583	missense	9659	exon24			CAGCCTGAAGGCT	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.3295C>A	chr1.hg19:g.144882724G>T	ENSP00000358360:p.Gln1099Lys	164.0	0.0	.		140.0	29.0	.	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	hg19	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	G	8.520	0.868649	0.17322	.	.	ENSG00000178104	ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T	0.01464	4.86;4.86;4.87;4.87	5.84	4.75	0.60458	.	.	.	.	.	T	0.00784	0.0026	L	0.51422	1.61	0.80722	D	1	B	0.34015	0.435	B	0.24974	0.057	T	0.58418	-0.7640	9	0.14252	T	0.57	.	10.7121	0.45990	0.0993:0.0:0.9007:0.0	.	1099	Q5VU43	MYOME_HUMAN	K	1099;1099;1236;1236	ENSP00000358360:Q1099K;ENSP00000358363:Q1099K;ENSP00000435654:Q1236K;ENSP00000358366:Q1236K	ENSP00000358360:Q1099K	Q	-	1	0	PDE4DIP	143594081	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.424000	0.34848	2.778000	0.95560	0.655000	0.94253	CAG	.	.	.	none		0.483	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		T	144882724	G	T	144882724	3	4	108	1	0	0	0	0	1	0	0	0	11650	1299	45	4	3829	4	PDE4DIP	1	144882724	Missense_Mutation	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10	32853490	144882724	104367897	6	6846											
THEM4	117145	hgsc.bcm.edu	37	chr1	151867562	151867562	+	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	caaacgtttccaggagccgtCttcacatttcttcataaact	11	13	5	12	2	4	0	2	0	2	0	5	1	5	1	2	1	3	1	2	1	3	5			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr1:151867562C>G	ENST00000368814.3	-	2	557	c.208G>C	c.(208-210)Gac>Cac	p.D70H	THEM4_ENST00000489410.1_Missense_Mutation_p.D70H	NM_053055.4	NP_444283.2	Q5T1C6	THEM4_HUMAN	thioesterase superfamily member 4	70					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)			CAGGAGCCGTCTTCACATTTC	0.433																																					p.D70H		Atlas-SNP	.											.	THEM4	19	.	0			c.G208C						PASS	.						102	99	100					1																	151867562		2203	4298	6501	SO:0001583	missense	117145	exon2			AGCCGTCTTCACA	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.208G>C	chr1.hg19:g.151867562C>G	ENSP00000357804:p.Asp70His	146.0	0.0	.		108.0	39.0	.	NM_053055	B2RBX2|Q96KR2	Missense_Mutation	SNP	ENST00000368814.3	hg19	CCDS1006.1	.	.	.	.	.	.	.	.	.	.	C	17.45	3.392158	0.62066	.	.	ENSG00000159445	ENST00000368814;ENST00000489410	T;T	0.27256	1.78;1.68	4.16	4.16	0.48862	.	0.414693	0.26079	N	0.026465	T	0.28200	0.0696	M	0.74258	2.255	0.42205	D	0.991782	D	0.57571	0.98	P	0.50231	0.635	T	0.04752	-1.0929	10	0.54805	T	0.06	-16.359	12.2685	0.54691	0.0:1.0:0.0:0.0	.	70	Q5T1C6	THEM4_HUMAN	H	70	ENSP00000357804:D70H;ENSP00000433304:D70H	ENSP00000357804:D70H	D	-	1	0	THEM4	150134186	0.995000	0.38212	0.997000	0.53966	0.718000	0.41266	1.809000	0.38922	2.606000	0.88127	0.650000	0.86243	GAC	.	.	.	none		0.433	THEM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036615.1	NM_053055		G	151867562	C	G	151867562	3	3	108	1	0	0	0	0	1	0	0	0	15870	913	32	4	534	4	THEM4	1	151867562	Missense_Mutation	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10	6984838	151867562	97383059	7	6847											
ADAM15	8751	hgsc.bcm.edu	37	chr1	155034762	155034762	+	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	ccacccccaaggaagccactGcctgccgacccccagggccg	8	2	10	21	2	0	0	0	0	0	0	0	2	0	1	9	2	3	0	9	2	2	0			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr1:155034762G>A	ENST00000356955.2	+	22	2567	c.2466G>A	c.(2464-2466)ctG>ctA	p.L822L	EFNA3_ENST00000505139.1_5'Flank|ADAM15_ENST00000271836.6_Silent_p.L773L|ADAM15_ENST00000368410.2_Silent_p.L479L|ADAM15_ENST00000360674.4_Missense_Mutation_p.C750Y|ADAM15_ENST00000359280.4_Silent_p.L797L|ADAM15_ENST00000368413.1_Silent_p.L479L|ADAM15_ENST00000472434.1_3'UTR|ADAM15_ENST00000368412.3_Missense_Mutation_p.C774Y|ADAM15_ENST00000531455.1_Silent_p.L783L|ADAM15_ENST00000355956.2_Silent_p.L798L|ADAM15_ENST00000449910.2_Silent_p.L821L|EFNA3_ENST00000556931.1_5'Flank|EFNA4_ENST00000368409.3_5'Flank|EFNA4_ENST00000427683.2_5'Flank|EFNA4_ENST00000359751.4_5'Flank	NM_207197.2	NP_997080.1	Q13444	ADA15_HUMAN	ADAM metallopeptidase domain 15	822					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)			GGAAGCCACTGCCTGCCGACC	0.711											OREG0013848	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C774Y		Atlas-SNP	.											ADAM15,colon,carcinoma,0,1	ADAM15	92	.	0			c.G2321A						PASS	.						6	7	7					1																	155034762		2111	4155	6266	SO:0001819	synonymous_variant	8751	exon20			GCCACTGCCTGCC	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.2466G>A	chr1.hg19:g.155034762G>A		106.0	0.0	.	1767	82.0	36.0	.	NM_001261465	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	hg19	CCDS1087.1	.	.	.	.	.	.	.	.	.	.	G	10.29	1.308991	0.23821	.	.	ENSG00000143537	ENST00000360674;ENST00000368412	T;T	0.00932	5.76;5.53	4.37	2.39	0.29439	.	.	.	.	.	T	0.01156	0.0038	.	.	.	0.80722	D	1	D;D	0.54964	0.969;0.969	P;P	0.53809	0.735;0.735	T	0.63932	-0.6525	8	0.62326	D	0.03	.	10.3708	0.44053	0.0:0.3895:0.6105:0.0	.	750;774	Q13444-10;Q13444-9	.;.	Y	750;774	ENSP00000353892:C750Y;ENSP00000357397:C774Y	ENSP00000353892:C750Y	C	+	2	0	ADAM15	153301386	1.000000	0.71417	0.988000	0.46212	0.480000	0.33159	1.364000	0.34171	0.419000	0.25927	0.655000	0.94253	TGC	.	.	.	none		0.711	ADAM15-019	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387168.1	NM_003815		A	155034762	G	A	155034762	2	1	108	1	0	0	0	0	0	0	0	1	237	1319	46	2		2	ADAM15	1	155034762	Silent	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10	3167200	155034762	94215859	8	6848											
POU2F1	5451	hgsc.bcm.edu	37	chr1	167343431	167343431	+	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	gctgctgcagtgcagcagcaCtccgccagccagcagcacag	9	4	12	16	1	0	0	0	0	0	0	1	0	1	0	3	0	8	8	3	0	0	0			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr1:167343431C>G	ENST00000541643.3	+	7	582	c.420C>G	c.(418-420)caC>caG	p.H140Q	POU2F1_ENST00000452019.1_Missense_Mutation_p.H140Q|POU2F1_ENST00000367866.2_Missense_Mutation_p.H163Q|POU2F1_ENST00000420254.3_Missense_Mutation_p.H140Q|POU2F1_ENST00000429375.2_Intron|POU2F1_ENST00000367862.5_Missense_Mutation_p.H152Q|POU2F1_ENST00000367865.1_3'UTR			P14859	PO2F1_HUMAN	POU class 2 homeobox 1	140					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						TGCAGCAGCACTCCGCCAGCC	0.607																																					p.H163Q		Atlas-SNP	.											.	POU2F1	120	.	0			c.C489G						PASS	.						24	24	24					1																	167343431		2203	4300	6503	SO:0001583	missense	5451	exon6			GCAGCACTCCGCC	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.420C>G	chr1.hg19:g.167343431C>G	ENSP00000441285:p.His140Gln	188.0	0.0	.		198.0	81.0	.	NM_002697	B1AL91|B1AL93|B4E029|J3KP77|Q5TBT7|Q6PK46|Q8NEU9|Q9BPV1	Missense_Mutation	SNP	ENST00000541643.3	hg19		.	.	.	.	.	.	.	.	.	.	C	14.61	2.588083	0.46110	.	.	ENSG00000143190	ENST00000367866;ENST00000452019;ENST00000492850;ENST00000367865;ENST00000420254;ENST00000541643;ENST00000367862;ENST00000443275	T;T;T;T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07;-1.07;-1.07;-1.07	5.81	-5.64	0.02466	.	4.687520	0.00397	N	0.000049	T	0.75443	0.3850	L	0.32530	0.975	0.44985	D	0.998002	D;D;D;D	0.69078	0.96;0.997;0.997;0.995	D;D;D;D	0.78314	0.944;0.986;0.991;0.969	T	0.67413	-0.5677	10	0.41790	T	0.15	.	16.7965	0.85603	0.0:0.5772:0.0:0.4228	.	140;152;138;140	P14859-4;P14859-2;P14859-3;P14859	.;.;.;PO2F1_HUMAN	Q	163;140;17;138;140;140;152;48	ENSP00000356840:H163Q;ENSP00000391523:H140Q;ENSP00000356839:H138Q;ENSP00000414660:H140Q;ENSP00000441285:H140Q;ENSP00000356836:H152Q;ENSP00000415993:H48Q	ENSP00000356836:H152Q	H	+	3	2	POU2F1	165610055	0.003000	0.15002	0.669000	0.29828	0.687000	0.40016	-1.326000	0.02685	-1.120000	0.02953	-0.793000	0.03317	CAC	.	.	.	none		0.607	POU2F1-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_002697		G	167343431	C	G	167343431	3	3	108	1	0	0	0	0	1	0	0	0	12278	564	20	4	438	4	POU2F1	1	167343431	Missense_Mutation	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10	12308669	167343431	81907190	9	6849											
PRG4	10216	hgsc.bcm.edu	37	chr1	186277770	186277770	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gataccacaccattcaaaatTactactcttaaaacaactac	18	10	1	12	0	2	0	1	0	1	0	2	1	2	0	2	0	6	0	2	0	9	6			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr1:186277770T>C	ENST00000445192.2	+	7	2964	c.2919T>C	c.(2917-2919)atT>atC	p.I973I	PRG4_ENST00000367486.3_Silent_p.I930I|PRG4_ENST00000367485.4_Silent_p.I880I|PRG4_ENST00000367483.4_Silent_p.I932I|PRG4_ENST00000367484.3_Silent_p.I502I	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	973					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						CATTCAAAATTACTACTCTTA	0.353																																					p.I973I		Atlas-SNP	.											.	PRG4	259	.	0			c.T2919C						PASS	.						196	215	208					1																	186277770		2203	4300	6503	SO:0001819	synonymous_variant	10216	exon7			CAAAATTACTACT	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.2919T>C	chr1.hg19:g.186277770T>C		163.0	0.0	.		151.0	62.0	.	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Silent	SNP	ENST00000445192.2	hg19	CCDS1369.1																																																																																			.	.	.	none		0.353	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		C	186277770	T	C	186277770	2	2	108	1	0	0	0	0	0	0	0	1	12491	1742	61	3		3	PRG4	1	186277770	Silent	SNP	T	TCGA-B9-A8YH-01A-11D-A36X-10	18934339	186277770	62972851	10	6850											
F13B	2165	hgsc.bcm.edu	37	chr1	197026477	197026477	+	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	cgtatttctgctgacccatgGatctcaaaattaagttcaca	12	13	6	10	1	3	1	2	1	2	0	4	2	3	2	1	1	1	3	1	1	4	4	rs141627684		TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr1:197026477G>T	ENST00000367412.1	-	6	967	c.924C>A	c.(922-924)atC>atA	p.I308I		NM_001994.2	NP_001985.2	P05160	F13B_HUMAN	coagulation factor XIII, B polypeptide	308	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation (GO:0007596)	extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(40)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	66						CTGACCCATGGATCTCAAAAT	0.373																																					p.I308I		Atlas-SNP	.											F13B,NS,carcinoma,0,1	F13B	137	.	0			c.C924A						PASS	.						203	188	193					1																	197026477		2203	4300	6503	SO:0001819	synonymous_variant	2165	exon6			CCCATGGATCTCA	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.924C>A	chr1.hg19:g.197026477G>T		174.0	0.0	.		131.0	57.0	.	NM_001994	A8K3E5|Q5VYL5	Silent	SNP	ENST00000367412.1	hg19	CCDS1388.1																																																																																			.	G|1.000;A|0.000	.	alt		0.373	F13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088821.2	NM_001994		T	197026477	G	T	197026477	2	4	108	1	0	0	0	0	0	0	0	1	5343	1164	41	4		4	F13B	1	197026477	Silent	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10	10748707	197026477	52224144	11	6851											
PKP1	5317	hgsc.bcm.edu	37	chr1	201292313	201292313	+	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	gaacctgacagccagcaaggGgctggtgagtgggactgtac	10	6	16	9	0	0	2	0	2	0	0	0	4	0	3	2	4	4	3	2	4	3	1			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr1:201292313G>A	ENST00000352845.3	+	10	1739	c.1739G>A	c.(1738-1740)gGg>gAg	p.G580E	PKP1_ENST00000263946.3_Missense_Mutation_p.G580E|PKP1_ENST00000367324.3_Missense_Mutation_p.G559E			Q13835	PKP1_HUMAN	plakophilin 1	580					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						GCCAGCAAGGGGCTGGTGAGT	0.617																																					p.G580E		Atlas-SNP	.											.	PKP1	127	.	0			c.G1739A						PASS	.						95	89	91					1																	201292313		2203	4300	6503	SO:0001583	missense	5317	exon10			GCAAGGGGCTGGT	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.1739G>A	chr1.hg19:g.201292313G>A	ENSP00000295597:p.Gly580Glu	65.0	0.0	.		53.0	21.0	.	NM_000299	O00645|Q14CA0|Q15152	Missense_Mutation	SNP	ENST00000352845.3	hg19	CCDS30966.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.034838	0.75617	.	.	ENSG00000081277	ENST00000367324;ENST00000263946;ENST00000352845	T;T;T	0.46063	0.88;0.88;0.88	5.49	5.49	0.81192	Armadillo-like helical (1);Armadillo-type fold (1);	0.250213	0.45867	D	0.000326	T	0.65048	0.2654	M	0.73217	2.22	0.58432	D	0.999999	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.77557	0.99;0.975;0.974	T	0.61744	-0.7000	10	0.35671	T	0.21	-16.8875	19.3649	0.94458	0.0:0.0:1.0:0.0	.	167;559;580	Q14BN3;Q13835-2;Q13835	.;.;PKP1_HUMAN	E	559;580;580	ENSP00000356293:G559E;ENSP00000263946:G580E;ENSP00000295597:G580E	ENSP00000263946:G580E	G	+	2	0	PKP1	199558936	1.000000	0.71417	0.999000	0.59377	0.921000	0.55340	6.580000	0.74040	2.571000	0.86741	0.591000	0.81541	GGG	.	.	.	none		0.617	PKP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086897.1	NM_000299		A	201292313	G	A	201292313	3	1	108	1	0	0	0	0	1	0	0	0	11991	1232	43	2	1777	2	PKP1	1	201292313	Missense_Mutation	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10	4265836	201292313	47958308	12	6852											
NEK2	4751	hgsc.bcm.edu	37	chr1	211836794	211836794	+	Frame_Shift_Del	DEL	T	T	-																															catgcccaggatctgtctgcTtttcagttggtaatttttct																										TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr1:211836794delT	ENST00000366999.4	-	8	1450	c.1312delA	c.(1312-1314)agcfs	p.S438fs	NEK2_ENST00000462283.1_5'UTR|NEK2_ENST00000540251.1_Frame_Shift_Del_p.S395fs	NM_002497.3	NP_002488.1	P51955	NEK2_HUMAN	NIMA-related kinase 2	438	Interaction with PCNT.|Interaction with SAV1 and STK3/MST2.|Necessary for interaction with MAD1L1.				blastocyst development (GO:0001824)|centrosome separation (GO:0051299)|chromosome segregation (GO:0007059)|G2/M transition of mitotic cell cycle (GO:0000086)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of centriole-centriole cohesion (GO:1903126)|negative regulation of DNA binding (GO:0043392)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of mitosis (GO:0007088)|regulation of mitotic centrosome separation (GO:0046602)|spindle assembly (GO:0051225)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|microtubule (GO:0005874)|midbody (GO:0030496)|nucleus (GO:0005634)|protein complex (GO:0043234)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|stomach(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.00203)|all cancers(67;0.0339)|Epithelial(68;0.0546)		ATCTGTCTGCTTTTCAGTTGG	0.463																																					p.S438fs		Atlas-Indel,Pindel	.											.	NEK2	49	.	0			c.1313delG						PASS	.						43	40	41					1																	211836794		2203	4300	6503	SO:0001589	frameshift_variant	4751	exon8			.	U11050	CCDS1500.1, CCDS55682.1, CCDS73024.1	1q32.3	2014-06-12	2012-11-15		ENSG00000117650	ENSG00000117650			7745	protein-coding gene	gene with protein product	"HsPK 21", "protein phosphatase 1, regulatory subunit 111"	604043	"NIMA (never in mitosis gene a)-related kinase 2"			8274451, 24043777	Standard	NM_002497		Approved	NLK1, NEK2A, RP67, PPP1R111	uc001hir.2	P51955	OTTHUMG00000037121	ENST00000366999.4:c.1312delA	chr1.hg19:g.211836794delT	ENSP00000355966:p.Ser438fs	113.0	0.0	0		96.0	41.0	0.427083	NM_002497	Q53FD6|Q5I1Z9|Q5VXZ1|Q6NZX8|Q7Z634|Q86XH2|Q96QN9	Frame_Shift_Del	DEL	ENST00000366999.4	hg19	CCDS1500.1																																																																																			.	.	.	none		0.463	NEK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090154.1	NM_002497		-	211836794	T	-	211836794	7	5	108	1	0	1	0	1	0	0	0	0	10331	1609	56	0	29	0	NEK2	1	211836794	Frame_Shift_Del	DEL	T	TCGA-B9-A8YH-01A-11D-A36X-10	10544481	211836794	37413827	13	6853											
SMYD3	64754	hgsc.bcm.edu	37	chr1	246670463	246670463	+	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	gggcgcagcggggtcacggcGcgcagcccgtttcccctctt	3	7	15	16	6	2	0	1	0	1	0	3	0	3	0	3	4	2	3	3	4	0	2			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr1:246670463G>T	ENST00000388985.4	-	1	56	c.57C>A	c.(55-57)cgC>cgA	p.R19R	SMYD3_ENST00000490107.1_5'UTR|SMYD3_ENST00000403792.3_Silent_p.R19R			Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3	19	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				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)		GGGTCACGGCGCGCAGCCCGT	0.682																																					p.R19R		Atlas-SNP	.											.	SMYD3	77	.	0			c.C57A						PASS	.						31	42	39					1																	246670463		692	1591	2283	SO:0001819	synonymous_variant	64754	exon1			CACGGCGCGCAGC	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.57C>A	chr1.hg19:g.246670463G>T		174.0	0.0	.		153.0	65.0	.	NM_001167740	A8K0P0|B1AN38|Q86TL8|Q8N5Z6|Q96AI5	Silent	SNP	ENST00000388985.4	hg19	CCDS53486.1																																																																																			.	.	.	none		0.682	SMYD3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022743		T	246670463	G	T	246670463	2	4	108	1	0	0	0	0	0	0	0	1	14836	1074	38	4		4	SMYD3	1	246670463	Silent	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10	34833669	246670463	2580158	14	6854											
ALMS1	7840	hgsc.bcm.edu	37	chr2	73613065	73613065	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggaggaggaggaggaggaGgaggaagaggaggaggctgc	13	1	25	2	0	0	1	0	0	0	1	0	12	0	11	0	11	1	1	0	11	1	0			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr2:73613065G>A	ENST00000264448.6	+	1	180	c.69G>A	c.(67-69)gaG>gaA	p.E23E	ALMS1_ENST00000377715.1_Silent_p.E23E|ALMS1_ENST00000409009.1_Silent_p.E23E	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	23	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						aggaggaggaggaggaagagg	0.687																																					p.E23E		Atlas-SNP	.											.	ALMS1	384	.	0			c.G69A						PASS	.						6	9	8					2																	73613065		1849	3831	5680	SO:0001819	synonymous_variant	7840	exon1			GGAGGAGGAGGAA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.69G>A	chr2.hg19:g.73613065G>A		646.0	0.0	.		564.0	66.0	.	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.	.	none		0.687	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		A	73613065	G	A	73613065	2	1	108	1	0	0	0	0	0	0	0	1	535	991	35	2		2	ALMS1	2	73613065	Silent	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10		73613065	169586308	15	6855											
LRP2	4036	hgsc.bcm.edu	37	chr2	170097724	170097724	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtcacagtggaaatatgaTgaagggcaagtcttggggac	12	10	14	5	0	2	2	1	2	1	0	2	4	2	4	0	4	0	1	0	4	4	3			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr2:170097724T>C	ENST00000263816.3	-	25	4104	c.3819A>G	c.(3817-3819)tcA>tcG	p.S1273S	LRP2_ENST00000443831.1_Silent_p.S1136S	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1273	LDL-receptor class A 14. {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)"	GGAAATATGATGAAGGGCAAG	0.512																																					p.S1273S		Atlas-SNP	.											.	LRP2	751	.	0			c.A3819G						PASS	.						161	136	144					2																	170097724		2203	4300	6503	SO:0001819	synonymous_variant	4036	exon25			ATATGATGAAGGG		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.3819A>G	chr2.hg19:g.170097724T>C		133.0	0.0	.		133.0	42.0	.	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	hg19	CCDS2232.1																																																																																			.	.	.	none		0.512	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		C	170097724	T	C	170097724	2	2	108	1	0	0	0	0	0	0	0	1	8963	1451	51	3		3	LRP2	2	170097724	Silent	SNP	T	TCGA-B9-A8YH-01A-11D-A36X-10	96484659	170097724	73101649	16	6856											
TTN	7273	hgsc.bcm.edu	37	chr2	179424376	179424376	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcagcactcaaaacattcTgaattgttaatgtgtacttt	14	14	6	7	0	2	1	1	1	1	0	2	1	2	1	0	0	4	4	0	0	6	5			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr2:179424376T>C	ENST00000591111.1	-	276	81784	c.81560A>G	c.(81559-81561)cAg>cGg	p.Q27187R	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.Q28828R|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.Q26260R|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.Q19955R|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.Q19888R|TTN_ENST00000460472.2_Missense_Mutation_p.Q19763R|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	27187	Ig-like 129.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAAAACATTCTGAATTGTTAA	0.408																																					p.Q28828R		Atlas-SNP	.											.	TTN	18412	.	0			c.A86483G						PASS	.						178	166	170					2																	179424376		1953	4152	6105	SO:0001583	missense	7273	exon326			ACATTCTGAATTG	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.81560A>G	chr2.hg19:g.179424376T>C	ENSP00000465570:p.Gln27187Arg	91.0	0.0	.		104.0	35.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	13.02	2.113492	0.37339	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23	5.77	5.77	0.91146	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.53899	0.1825	N	0.17764	0.52	0.38198	D	0.940119	P;P;P;P	0.43231	0.801;0.801;0.801;0.684	B;B;B;B	0.38378	0.265;0.265;0.265;0.272	T	0.65179	-0.6231	9	0.87932	D	0	.	16.383	0.83481	0.0:0.0:0.0:1.0	.	19763;19888;19955;27187	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	R	26260;19763;19955;19888;19760	ENSP00000343764:Q26260R;ENSP00000434586:Q19763R;ENSP00000340554:Q19955R;ENSP00000352154:Q19888R	ENSP00000340554:Q19955R	Q	-	2	0	TTN	179132622	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.081000	0.64444	2.326000	0.78906	0.533000	0.62120	CAG	.	.	.	none		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179424376	T	C	179424376	3	2	108	1	0	0	0	0	1	0	0	0	16747	1580	55	3	21644	3	TTN	2	179424376	Missense_Mutation	SNP	T	TCGA-B9-A8YH-01A-11D-A36X-10	9326652	179424376	63774997	17	6857											
FASTKD2	22868	hgsc.bcm.edu	37	chr2	207655298	207655298	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtttatttttgttttcagagTagctgtgctatgtgtttcca	6	21	9	5	0	1	1	1	0	0	1	2	1	2	1	1	0	2	6	1	0	3	9			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr2:207655298T>C	ENST00000236980.6	+	11	2249	c.1901T>C	c.(1900-1902)gTa>gCa	p.V634A	FASTKD2_ENST00000402774.3_Missense_Mutation_p.V634A|FASTKD2_ENST00000403094.3_Missense_Mutation_p.V634A	NM_014929.3	NP_055744.2	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	634	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)|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)		GTTTTCAGAGTAGCTGTGCTA	0.383																																					p.V634A		Atlas-SNP	.											.	FASTKD2	49	.	0			c.T1901C						PASS	.						126	126	126					2																	207655298		2203	4300	6503	SO:0001583	missense	22868	exon11			TCAGAGTAGCTGT	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.1901T>C	chr2.hg19:g.207655298T>C	ENSP00000236980:p.Val634Ala	51.0	0.0	.		54.0	21.0	.	NM_001136193	Q9NVX6|Q9Y2H7	Missense_Mutation	SNP	ENST00000236980.6	hg19	CCDS2371.1	.	.	.	.	.	.	.	.	.	.	T	15.64	2.892723	0.52121	.	.	ENSG00000118246	ENST00000236980;ENST00000402774;ENST00000403094	T;T;T	0.21734	1.99;1.99;1.99	5.96	5.96	0.96718	RAP domain (1);	0.288889	0.34268	N	0.004111	T	0.24890	0.0604	M	0.68952	2.095	0.34651	D	0.721629	P	0.40431	0.717	B	0.35813	0.211	T	0.46373	-0.9196	10	0.87932	D	0	-20.0213	13.9717	0.64245	0.0:0.0:0.0:1.0	.	634	Q9NYY8	FAKD2_HUMAN	A	634	ENSP00000236980:V634A;ENSP00000385990:V634A;ENSP00000384929:V634A	ENSP00000236980:V634A	V	+	2	0	FASTKD2	207363543	1.000000	0.71417	1.000000	0.80357	0.610000	0.37248	2.909000	0.48758	2.285000	0.76669	0.533000	0.62120	GTA	.	.	.	none		0.383	FASTKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256428.2	NM_014929		C	207655298	T	C	207655298	3	2	108	1	0	0	0	0	1	0	0	0	5693	1638	57	3	1939	3	FASTKD2	2	207655298	Missense_Mutation	SNP	T	TCGA-B9-A8YH-01A-11D-A36X-10	28230922	207655298	35544075	18	6858											
AQP12B	653437	hgsc.bcm.edu	37	chr2	241621833	241621833	+	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	ccatgaggctctgcagcaggTgcaggtcactgagctcccag	8	7	13	13	0	2	2	1	2	1	0	3	2	3	2	2	3	4	5	2	3	0	0			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr2:241621833T>A	ENST00000407834.3	-	1	484	c.422A>T	c.(421-423)cAc>cTc	p.H141L		NM_001102467.1	NP_001095937.1	A6NM10	AQ12B_HUMAN	aquaporin 12B	129						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)		CTGCAGCAGGTGCAGGTCACT	0.697																																					p.H141L		Atlas-SNP	.											.	AQP12B	33	.	0			c.A422T						PASS	.						13	13	13					2																	241621833		2174	4214	6388	SO:0001583	missense	653437	exon1			AGCAGGTGCAGGT	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.422A>T	chr2.hg19:g.241621833T>A	ENSP00000384894:p.His141Leu	207.0	0.0	.		194.0	48.0	.	NM_001102467	A4QPB9	Missense_Mutation	SNP	ENST00000407834.3	hg19	CCDS46560.1	.	.	.	.	.	.	.	.	.	.	.	18.49	3.636002	0.67130	.	.	ENSG00000185176	ENST00000407834	T	0.38887	1.11	2.8	1.59	0.23543	.	0.103713	0.64402	D	0.000003	T	0.53578	0.1805	M	0.80982	2.52	0.42521	D	0.993008	D	0.58268	0.982	P	0.56042	0.79	T	0.55431	-0.8142	10	0.87932	D	0	1.3049	6.5696	0.22531	0.0:0.1293:0.0:0.8707	.	141	A6NM10-2	.	L	141	ENSP00000384894:H141L	ENSP00000384894:H141L	H	-	2	0	AQP12B	241270506	1.000000	0.71417	0.119000	0.21687	0.931000	0.56810	3.976000	0.56867	0.469000	0.27268	0.376000	0.23039	CAC	.	.	.	none		0.697	AQP12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325625.1			A	241621833	T	A	241621833	3	1	108	1	0	0	0	0	1	0	0	0	825	1696	59	5	513	5	AQP12B	2	241621833	Missense_Mutation	SNP	T	TCGA-B9-A8YH-01A-11D-A36X-10	33966535	241621833	1577540	19	6859											
D2HGDH	728294	hgsc.bcm.edu	37	chr2	242683053	242683053	+	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	gcaggaattctggtttgccaGgcgggctgcgtcctggagga	6	9	17	9	2	1	0	0	0	1	0	2	3	2	3	2	6	2	3	2	6	1	2			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr2:242683053G>T	ENST00000321264.4	+	5	716	c.507G>T	c.(505-507)caG>caT	p.Q169H	D2HGDH_ENST00000403782.1_Missense_Mutation_p.Q35H|D2HGDH_ENST00000537090.1_Missense_Mutation_p.Q169H|D2HGDH_ENST00000342518.6_Missense_Mutation_p.Q169H	NM_152783.3	NP_689996.4	Q8N465	D2HDH_HUMAN	D-2-hydroxyglutarate dehydrogenase	169	FAD-binding PCMH-type. {ECO:0000255|PROSITE-ProRule:PRU00718}.				2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular protein metabolic process (GO:0044267)|response to cobalt ion (GO:0032025)|response to manganese ion (GO:0010042)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	(R)-2-hydroxyglutarate dehydrogenase activity (GO:0051990)|flavin adenine dinucleotide binding (GO:0050660)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			breast(1)|endometrium(3)|lung(10)|skin(1)|urinary_tract(1)	16		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)		TGGTTTGCCAGGCGGGCTGCG	0.637																																					p.Q169H		Atlas-SNP	.											.	D2HGDH	39	.	0			c.G507T						PASS	.						35	35	35					2																	242683053		2203	4296	6499	SO:0001583	missense	728294	exon5			TTGCCAGGCGGGC	AK091725	CCDS33426.1, CCDS74684.1	2p25.3	2010-05-11			ENSG00000180902	ENSG00000180902	1.1.99.-		28358	protein-coding gene	gene with protein product		609186				15070399, 15609246	Standard	NM_152783		Approved	MGC25181, D2HGD, FLJ42195	uc002wce.1	Q8N465	OTTHUMG00000151474	ENST00000321264.4:c.507G>T	chr2.hg19:g.242683053G>T	ENSP00000315351:p.Gln169His	42.0	0.0	.		34.0	11.0	.	NM_152783	B4E3L6|E7ENP2|Q6IQ24|Q8N5Q8	Missense_Mutation	SNP	ENST00000321264.4	hg19	CCDS33426.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.75|12.75	2.032526|2.032526	0.35893|0.35893	.|.	.|.	ENSG00000180902|ENSG00000180902	ENST00000417686|ENST00000537090;ENST00000321264;ENST00000403782;ENST00000342518	.|D;D;D;D	.|0.96913	.|-4.17;-4.17;-4.17;-4.17	4.73|4.73	4.73|4.73	0.59995|0.59995	.|FAD-linked oxidase, FAD-binding, subdomain 2 (1);FAD-binding, type 2 (2);FAD linked oxidase, N-terminal (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.98369|0.98369	0.9458|0.9458	H|H	0.96269|0.96269	3.795|3.795	0.80722|0.80722	D|D	1|1	.|D	.|0.60160	.|0.987	.|P	.|0.61275	.|0.886	D|D	0.99063|0.99063	1.0831|1.0831	5|10	.|0.87932	.|D	.|0	.|.	11.7108|11.7108	0.51625|0.51625	0.0942:0.0:0.9058:0.0|0.0942:0.0:0.9058:0.0	.|.	.|169	.|Q8N465	.|D2HDH_HUMAN	C|H	11|169;169;35;169	.|ENSP00000442796:Q169H;ENSP00000315351:Q169H;ENSP00000384723:Q35H;ENSP00000339536:Q169H	.|ENSP00000315351:Q169H	G|Q	+|+	1|3	0|2	D2HGDH|D2HGDH	242331726|242331726	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.322000|0.322000	0.28314|0.28314	5.002000|5.002000	0.63952|0.63952	2.191000|2.191000	0.70037|0.70037	0.462000|0.462000	0.41574|0.41574	GGC|CAG	.	.	.	none		0.637	D2HGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322794.2	NM_152783		T	242683053	G	T	242683053	3	4	108	1	0	0	0	0	1	0	0	0	4215	991	35	4	521	4	D2HGDH	2	242683053	Missense_Mutation	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10	1061220	242683053	516320	20	6860											
SCN5A	6331	hgsc.bcm.edu	37	chr3	38592252	38592252	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcctccatctggatcttcaGggcgtccatctccccagact	6	11	7	17	1	4	1	1	0	3	1	8	2	7	2	5	2	0	0	5	2	0	1			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr3:38592252G>A	ENST00000333535.4	-	28	5760	c.5611C>T	c.(5611-5613)Ctg>Ttg	p.L1871L	SCN5A_ENST00000425664.1_Silent_p.L1853L|SCN5A_ENST00000414099.2_Silent_p.L1853L|SCN5A_ENST00000464652.1_5'Flank|SCN5A_ENST00000423572.2_Silent_p.L1870L|SCN5A_ENST00000455624.2_Silent_p.L1838L|SCN5A_ENST00000443581.1_Silent_p.L1870L|SCN5A_ENST00000451551.2_Silent_p.L1817L|SCN5A_ENST00000450102.2_Silent_p.L1817L|SCN5A_ENST00000449557.2_Silent_p.L1817L|SCN5A_ENST00000413689.1_Silent_p.L1871L			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	1871	Interaction with FGF13.				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)	TGGATCTTCAGGGCGTCCATC	0.577																																					p.L1871L		Atlas-SNP	.											.	SCN5A	634	.	0			c.C5611T						PASS	.						164	178	173					3																	38592252		2090	4210	6300	SO:0001819	synonymous_variant	6331	exon28			TCTTCAGGGCGTC	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.5611C>T	chr3.hg19:g.38592252G>A		81.0	0.0	.		130.0	43.0	.	NM_198056	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Silent	SNP	ENST00000333535.4	hg19	CCDS46796.1																																																																																			.	.	.	none		0.577	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056		A	38592252	G	A	38592252	2	1	108	1	0	0	0	0	0	0	0	1	13935	991	35	2		2	SCN5A	3	38592252	Silent	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10		38592252	159430178	21	6861											
CCDC66	285331	hgsc.bcm.edu	37	chr3	56649243	56649243	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gactaaaacaagaacaaagaAtccgagaattggcgcaaaag	21	4	9	7	2	0	3	0	0	0	3	1	5	1	3	1	1	2	1	1	1	9	2			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr3:56649243A>G	ENST00000394672.3	+	12	1724	c.1654A>G	c.(1654-1656)Atc>Gtc	p.I552V	CCDC66_ENST00000326595.7_Missense_Mutation_p.I518V|CCDC66_ENST00000436465.2_Missense_Mutation_p.I552V	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	552					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)		AGAACAAAGAATCCGAGAATT	0.383																																					p.I552V		Atlas-SNP	.											.	CCDC66	145	.	0			c.A1654G						PASS	.						112	112	112					3																	56649243		2203	4300	6503	SO:0001583	missense	285331	exon12			CAAAGAATCCGAG	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.1654A>G	chr3.hg19:g.56649243A>G	ENSP00000378167:p.Ile552Val	717.0	2.0	.		848.0	444.0	.	NM_001141947	B3KWL8|Q4VC34|Q8N949	Missense_Mutation	SNP	ENST00000394672.3	hg19	CCDS46852.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.241738	0.79912	.	.	ENSG00000180376	ENST00000422222;ENST00000394672;ENST00000326595;ENST00000436465	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	5.97	5.97	0.96955	.	0.181866	0.48286	D	0.000190	T	0.63570	0.2522	M	0.72118	2.19	0.80722	D	1	D	0.71674	0.998	D	0.72982	0.979	T	0.61652	-0.7019	10	0.35671	T	0.21	-10.0888	16.4562	0.84015	1.0:0.0:0.0:0.0	.	552	A2RUB6	CCD66_HUMAN	V	508;552;518;552	ENSP00000401451:I508V;ENSP00000378167:I552V;ENSP00000326050:I518V;ENSP00000404320:I552V	ENSP00000326050:I518V	I	+	1	0	CCDC66	56624283	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.384000	0.73177	2.289000	0.77006	0.459000	0.35465	ATC	.	.	.	none		0.383	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506		G	56649243	A	G	56649243	3	3	108	1	0	0	0	0	1	0	0	0	2840	101	4	3	1700	3	CCDC66	3	56649243	Missense_Mutation	SNP	A	TCGA-B9-A8YH-01A-11D-A36X-10	18056991	56649243	141373187	22	6862											
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121410064	121410064	+	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	tctgttccatctccaccaaaTctcttgctagctctgccact	7	14	4	16	0	4	0	0	0	4	0	7	0	5	0	4	0	3	3	4	0	2	3			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr3:121410064T>A	ENST00000340645.5	-	14	8257	c.8132A>T	c.(8131-8133)gAt>gTt	p.D2711V	GOLGB1_ENST00000393667.3_Missense_Mutation_p.D2716V	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	2711					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)		CTCCACCAAATCTCTTGCTAG	0.388																																					p.D2716V		Atlas-SNP	.											.	GOLGB1	319	.	0			c.A8147T						PASS	.						247	257	254					3																	121410064		2203	4300	6503	SO:0001583	missense	2804	exon14			ACCAAATCTCTTG	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.8132A>T	chr3.hg19:g.121410064T>A	ENSP00000341848:p.Asp2711Val	77.0	0.0	.		112.0	13.0	.	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	hg19	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	T	13.20	2.165936	0.38217	.	.	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.29142	1.58;1.59	5.46	5.46	0.80206	.	0.094413	0.45867	D	0.000327	T	0.54902	0.1887	M	0.73598	2.24	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.981;0.981;0.999	T	0.56625	-0.7948	10	0.48119	T	0.1	.	13.4815	0.61338	0.0:0.0:0.0:1.0	.	2716;2716;2711	E7EP74;B2ZZ91;Q14789	.;.;GOGB1_HUMAN	V	2711;2716	ENSP00000341848:D2711V;ENSP00000377275:D2716V	ENSP00000341848:D2711V	D	-	2	0	GOLGB1	122892754	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.548000	0.82154	2.062000	0.61559	0.533000	0.62120	GAT	.	.	.	none		0.388	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		A	121410064	T	A	121410064	3	1	108	1	0	0	0	0	1	0	0	0	6572	1435	50	5	1683	5	GOLGB1	3	121410064	Missense_Mutation	SNP	T	TCGA-B9-A8YH-01A-11D-A36X-10	64760821	121410064	76612366	23	6863											
CHST2	9435	hgsc.bcm.edu	37	chr3	142840256	142840256	+	Missense_Mutation	SNP	G	G	A																															tctacgagccagtgtggcatGtatggcaaaaactgtatccg																										TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr3:142840256G>A	ENST00000309575.3	+	2	1982	c.598G>A	c.(598-600)Gta>Ata	p.V200I		NM_004267.4	NP_004258.2	Q9Y4C5	CHST2_HUMAN	carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2	200					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						AGTGTGGCATGTATGGCAAAA	0.582																																					p.V200I		Atlas-SNP	.											.	CHST2	67	.	0			c.G598A						PASS	.						67	83	78					3																	142840256		2198	4297	6495	SO:0001583	missense	9435	exon2			TGGCATGTATGGC	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.598G>A	chr3.hg19:g.142840256G>A	ENSP00000307911:p.Val200Ile	133.0	0.0	.		166.0	109.0	.	NM_004267	D3DNG5|Q2M370|Q9GZN5|Q9UED5|Q9Y6F2	Missense_Mutation	SNP	ENST00000309575.3	hg19	CCDS3129.1	.	.	.	.	.	.	.	.	.	.	G	13.16	2.154982	0.38021	.	.	ENSG00000175040	ENST00000309575	D	0.96619	-4.07	4.45	4.45	0.53987	Sulfotransferase domain (1);	0.082297	0.48767	U	0.000162	D	0.91195	0.7226	N	0.10916	0.065	0.43084	D	0.994742	B	0.23591	0.088	B	0.27500	0.08	D	0.88039	0.2780	10	0.25106	T	0.35	-0.111	17.2545	0.87051	0.0:0.0:1.0:0.0	.	200	Q9Y4C5	CHST2_HUMAN	I	200	ENSP00000307911:V200I	ENSP00000307911:V200I	V	+	1	0	CHST2	144322946	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	3.671000	0.54576	2.295000	0.77249	0.407000	0.27541	GTA	.	.	.	none		0.582	CHST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354850.1	NM_004267		A	142840256	G	A	142840256	3	1	108	1	0	0	0	0	1	0	0	0	3406	1377	48	2	600	2	CHST2	3	142840256	Missense_Mutation	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10	21430192	142840256	55182174	24	6864	74	2									
CHST2	9435	hgsc.bcm.edu	37	chr3	142840258	142840258	+	Frame_Shift_Del	DEL	A	A	-																															tacgagccagtgtggcatgtAtggcaaaaactgtatccggg																										TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr3:142840258delA	ENST00000309575.3	+	2	1984	c.600delA	c.(598-600)gtafs	p.V200fs		NM_004267.4	NP_004258.2	Q9Y4C5	CHST2_HUMAN	carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2	200					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						TGTGGCATGTATGGCAAAAAC	0.577																																					p.V200fs		Atlas-INDEL	.											.	CHST2	67	.	0			c.599delT						PASS	.						67	83	78					3																	142840258		2198	4297	6495	SO:0001589	frameshift_variant	9435	exon2			.	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.600delA	chr3.hg19:g.142840258delA	ENSP00000307911:p.Val200fs	129.0	0.0	0		167.0	110.0	0.658683	NM_004267	D3DNG5|Q2M370|Q9GZN5|Q9UED5|Q9Y6F2	Frame_Shift_Del	DEL	ENST00000309575.3	hg19	CCDS3129.1																																																																																			.	.	.	none		0.577	CHST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354850.1	NM_004267		-	142840258	A	-	142840258	7	5	108	1	0	1	0	1	0	0	0	0	3406	436	16	0	602	0	CHST2	3	142840258	Frame_Shift_Del	DEL	A	TCGA-B9-A8YH-01A-11D-A36X-10	2	142840258	55182172	25	6865	74	2									
DSPP	1834	hgsc.bcm.edu	37	chr4	88536436	88536436	+	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	agcgatagcagtgacagcagCaacagcagtgacagcagtga	15	4	13	9	1	0	3	0	3	0	0	0	4	0	3	0	0	7	5	0	0	2	1			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr4:88536436C>T	ENST00000282478.7	+	4	2655	c.2622C>T	c.(2620-2622)agC>agT	p.S874S	DSPP_ENST00000399271.1_Silent_p.S874S|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	874	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gtgacagcagcaacagcagtg	0.502																																					p.S874S		Atlas-SNP	.											.	DSPP	174	.	0			c.C2622T						PASS	.						70	85	79					4																	88536436		1641	2936	4577	SO:0001819	synonymous_variant	1834	exon5			CAGCAGCAACAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2622C>T	chr4.hg19:g.88536436C>T		250.0	0.0	.		220.0	17.0	.	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	hg19	CCDS43248.1																																																																																			.	.	.	none		0.502	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		T	88536436	C	T	88536436	2	4	108	1	0	0	0	0	0	0	0	1	4784	709	25	2		2	DSPP	4	88536436	Silent	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10		88536436	102617840	26	6866											
RAP1GDS1	5910	hgsc.bcm.edu	37	chr4	99363256	99363257	+	Frame_Shift_Del	DEL	TG	TG	-																															ctcacagagcagagacttacTgtggaaagctgagaactgcc																										TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr4:99363256_99363257delTG	ENST00000408927.3	+	15	1925_1926	c.1812_1813delTG	c.(1810-1815)actgtgfs	p.V605fs	RAP1GDS1_ENST00000453712.2_Frame_Shift_Del_p.V605fs|RAP1GDS1_ENST00000380158.4_Frame_Shift_Del_p.V557fs|RAP1GDS1_ENST00000264572.7_Frame_Shift_Del_p.V514fs|RAP1GDS1_ENST00000339360.5_Frame_Shift_Del_p.V606fs|RAP1GDS1_ENST00000408900.3_Frame_Shift_Del_p.V556fs	NM_001100426.1|NM_001100427.1|NM_021159.4	NP_001093896.1|NP_001093897.1|NP_066982.3	P52306	GDS1_HUMAN	RAP1, GTP-GDP dissociation stimulator 1	605					myosin filament assembly (GO:0031034)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of Rho GTPase activity (GO:0032321)|vascular smooth muscle contraction (GO:0014829)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)	28				OV - Ovarian serous cystadenocarcinoma(123;2.9e-07)|LUSC - Lung squamous cell carcinoma(1;0.0253)|Lung(1;0.0576)		AGAGACTTACTGTGGAAAGCTG	0.49			T	NUP98	T-ALL																																p.605_605del		Atlas-INDEL	.		Dom	yes		4	4q21-q25	5910	"RAP1, GTP-GDP dissociation stimulator 1"		L	.	RAP1GDS1	61	.	0			c.1814_1815del						PASS	.																																			SO:0001589	frameshift_variant	5910	exon15			.		CCDS43253.1, CCDS43254.1, CCDS47105.1, CCDS47106.1, CCDS47107.1, CCDS47108.1	4q23-q25	2013-02-14			ENSG00000138698	ENSG00000138698		"Armadillo repeat containing"	9859	protein-coding gene	gene with protein product		179502				8262526, 17951244	Standard	NM_001100426		Approved	SmgGDS	uc003htw.4	P52306	OTTHUMG00000160987	ENST00000408927.3:c.1812_1813delTG	chr4.hg19:g.99363258_99363259delTG	ENSP00000386153:p.Val605fs	65.0	0.0	0		45.0	12.0	0.266667	NM_001100426	E9PH06|G5E9P9|Q499L7|Q4KMV2|Q4QQI8|Q9BUW9|Q9BUX6|Q9NYM2|Q9NZA8	Frame_Shift_Del	DEL	ENST00000408927.3	hg19	CCDS43253.1																																																																																			.	.	.	none		0.49	RAP1GDS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363273.2	NM_001100426		-	99363257	TG	-	99363256	7	5	108	1	0	1	0	1	0	0	0	0	13052	1567	55	0	1873	0	RAP1GDS1	4	99363256	Frame_Shift_Del	DEL	TG	TCGA-B9-A8YH-01A-11D-A36X-10	10826820	99363256	91791020	27	6867											
CCRN4L	25819	hgsc.bcm.edu	37	chr4	139965852	139965871	+	Frame_Shift_Del	DEL	GAAAGGAAATGTCTCATCCT	GAAAGGAAATGTCTCATCCT	-																															ttgaagcactcaaatgggaaGaaaggaaatgtctcatcctg																								rs527306073|rs150676868		TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	GAAAGGAAATGTCTCATCCT	GAAAGGAAATGTCTCATCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr4:139965852_139965871delGAAAGGAAATGTCTCATCCT	ENST00000280614.2	+	3	713_732	c.520_539delGAAAGGAAATGTCTCATCCT	c.(520-540)gaaaggaaatgtctcatcctgfs	p.ERKCLIL174fs	ELF2_ENST00000515489.1_Intron	NM_012118.2	NP_036250.2	Q9UK39	NOCT_HUMAN	CCR4 carbon catabolite repression 4-like (S. cerevisiae)	174					circadian regulation of gene expression (GO:0032922)|cytoplasmic mRNA processing body assembly (GO:0033962)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|negative regulation of gene expression (GO:0010629)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|regulation of circadian rhythm (GO:0042752)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|response to extracellular stimulus (GO:0009991)|response to lipopolysaccharide (GO:0032496)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A)-specific ribonuclease activity (GO:0004535)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(2)|large_intestine(3)|lung(3)|ovary(1)	9	all_hematologic(180;0.162)					CAAATGGGAAGAAAGGAAATGTCTCATCCTGGAAGAAATC	0.45																																					p.173_180del	Ovarian(144;566 1842 19130 21379 22209)	Atlas-Indel,Pindel	.											.	CCRN4L	22	.	0			c.519_538del						PASS	.																																			SO:0001589	frameshift_variant	25819	exon3			.	AF183961	CCDS3743.1	4q31.1	2014-06-18	2001-11-28		ENSG00000151014	ENSG00000151014			14254	protein-coding gene	gene with protein product		608468	"CCR4-like (carbon catabolite repression 4, S.cerevisiae)"			10521507	Standard	NM_012118		Approved	CCR4L, Ccr4c	uc003ihl.3	Q9UK39	OTTHUMG00000161271	ENST00000280614.2:c.520_539delGAAAGGAAATGTCTCATCCT	chr4.hg19:g.139965852_139965871delGAAAGGAAATGTCTCATCCT	ENSP00000280614:p.Glu174fs	159.0	0.0	0		113.0	30.0	0.265487	NM_012118	D3DNY5|Q14D51|Q9HD93|Q9HD94|Q9HD95	Frame_Shift_Del	DEL	ENST00000280614.2	hg19	CCDS3743.1																																																																																			.	.	.	none		0.45	CCRN4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257231.3	NM_012118		-	139965871	GAAAGGAAATGTCTCATCCT	-	139965852	7	5	108	1	0	1	0	1	0	0	0	0	2953	943	33	0	530	0	CCRN4L	4	139965852	Frame_Shift_Del	DEL	GAAAGGAAATGTCTCATCCT	TCGA-B9-A8YH-01A-11D-A36X-10	40602596	139965852	51188424	28	6868											
LRBA	987	hgsc.bcm.edu	37	chr4	151520233	151520233	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacgcacaaatcgtcgccggCgccgcaagtcatcttcccag	9	7	9	16	6	2	0	1	0	1	0	5	0	3	0	3	1	1	2	3	1	3	2			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr4:151520233C>T	ENST00000357115.3	-	38	6215	c.5972G>A	c.(5971-5973)cGc>cAc	p.R1991H	LRBA_ENST00000507224.1_Missense_Mutation_p.R1991H|LRBA_ENST00000535741.1_Missense_Mutation_p.R1991H|LRBA_ENST00000510413.1_Missense_Mutation_p.R1991H	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	1991	Poly-Arg.					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)					TCGTCGCCGGCGCCGCAAGTC	0.488																																					p.R1991H		Atlas-SNP	.											.	LRBA	253	.	0			c.G5972A						PASS	.						111	100	104					4																	151520233		2203	4300	6503	SO:0001583	missense	987	exon38			CGCCGGCGCCGCA	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.5972G>A	chr4.hg19:g.151520233C>T	ENSP00000349629:p.Arg1991His	67.0	0.0	.		95.0	41.0	.	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	hg19	CCDS3773.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.1|23.1	4.380224|4.380224	0.82682|0.82682	.|.	.|.	ENSG00000198589|ENSG00000198589	ENST00000509835|ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224	.|T;T;T;T	.|0.60672	.|0.17;0.17;0.17;0.17	5.55|5.55	5.55|5.55	0.83447|0.83447	.|Domain of unknown function DUF1088 (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.79627|0.79627	0.4478|0.4478	M|M	0.82823|0.82823	2.61|2.61	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;0.999	.|D;D	.|0.91635	.|0.999;0.989	T|T	0.81422|0.81422	-0.0940|-0.0940	5|10	.|0.72032	.|D	.|0.01	.|.	19.872|19.872	0.96854|0.96854	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1991;1991	.|P50851;P50851-2	.|LRBA_HUMAN;.	T|H	644|1991	.|ENSP00000446299:R1991H;ENSP00000421552:R1991H;ENSP00000349629:R1991H;ENSP00000422180:R1991H	.|ENSP00000349629:R1991H	A|R	-|-	1|2	0|0	LRBA|LRBA	151739683|151739683	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.776000|7.776000	0.85560|0.85560	2.779000|2.779000	0.95612|0.95612	0.585000|0.585000	0.79938|0.79938	GCC|CGC	.	.	.	none		0.488	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			T	151520233	C	T	151520233	3	4	108	1	0	0	0	0	1	0	0	0	8938	768	27	1	2703	1	LRBA	4	151520233	Missense_Mutation	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10	11554381	151520233	39634043	29	6869											
SLC12A7	10723	hgsc.bcm.edu	37	chr5	1087036	1087036	+	Frame_Shift_Del	DEL	C	C	-																															accagaaaaatctcgatggtCcccaaaatatacatggcccc																										TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr5:1087036delC	ENST00000264930.5	-	6	700	c.657delG	c.(655-657)gggfs	p.G219fs		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	219					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)	TCTCGATGGTCCCCAAAATAT	0.582																																					p.T220fs		Pindel	.											.	SLC12A7	97	.	0			c.658delA						PASS	.						74	73	73					5																	1087036		2203	4300	6503	SO:0001589	frameshift_variant	10723	exon6			.	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.657delG	chr5.hg19:g.1087036delC	ENSP00000264930:p.Gly219fs	312.0	0.0	.		223.0	59.0	0.265	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Frame_Shift_Del	DEL	ENST00000264930.5	hg19	CCDS34129.1																																																																																			.	.	.	none		0.582	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598		-	1087036	C	-	1087036	7	5	108	1	0	1	0	1	0	0	0	0	14401	842	30	0	2670	0	SLC12A7	5	1087036	Frame_Shift_Del	DEL	C	TCGA-B9-A8YH-01A-11D-A36X-10		1087036	179828224	30	6870	75	2									
SLC12A7	10723	hgsc.bcm.edu	37	chr5	1087045	1087045	+	Nonsense_Mutation	SNP	A	A	T																															atctcgatggtccccaaaatAtacatggcccctgcaaacgt																										TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr5:1087045A>T	ENST00000264930.5	-	6	691	c.648T>A	c.(646-648)taT>taA	p.Y216*		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	216					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)	TCCCCAAAATATACATGGCCC	0.587																																					p.Y216X		Atlas-SNP	.											.	SLC12A7	97	.	0			c.T648A						PASS	.						71	70	70					5																	1087045		2203	4300	6503	SO:0001587	stop_gained	10723	exon6			CAAAATATACATG	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.648T>A	chr5.hg19:g.1087045A>T	ENSP00000264930:p.Tyr216*	311.0	0.0	.		224.0	84.0	.	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Nonsense_Mutation	SNP	ENST00000264930.5	hg19	CCDS34129.1	.	.	.	.	.	.	.	.	.	.	A	18.59	3.656716	0.67586	.	.	ENSG00000113504	ENST00000264930;ENST00000343658	.	.	.	3.93	-0.467	0.12150	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.6725	0.34159	0.409:0.0:0.591:0.0	.	.	.	.	X	216	.	ENSP00000264930:Y216X	Y	-	3	2	SLC12A7	1140045	1.000000	0.71417	0.898000	0.35279	0.171000	0.22731	1.306000	0.33505	-0.071000	0.12886	-0.366000	0.07423	TAT	.	.	.	none		0.587	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598		T	1087045	A	T	1087045	4	4	108	1	0	0	0	0	0	1	0	0	14401	456	16	5	2679	5	SLC12A7	5	1087045	Nonsense_Mutation	SNP	A	TCGA-B9-A8YH-01A-11D-A36X-10	9	1087045	179828215	31	6871	75	2									
HEXB	3074	hgsc.bcm.edu	37	chr5	74009349	74009349	+	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	agggaagctattctttgtctCatgtttatacaccaaatgat	12	15	7	7	0	2	1	1	1	2	0	3	2	2	2	1	1	2	2	1	1	5	6			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr5:74009349C>A	ENST00000261416.7	+	7	907	c.790C>A	c.(790-792)Cat>Aat	p.H264N	HEXB_ENST00000511181.1_Missense_Mutation_p.H39N	NM_000521.3	NP_000512	P07686	HEXB_HUMAN	hexosaminidase B (beta polypeptide)	264					astrocyte cell migration (GO:0043615)|carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|ganglioside catabolic process (GO:0006689)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|lipid storage (GO:0019915)|locomotory behavior (GO:0007626)|lysosome organization (GO:0007040)|male courtship behavior (GO:0008049)|myelination (GO:0042552)|neuromuscular process controlling balance (GO:0050885)|oligosaccharide catabolic process (GO:0009313)|oogenesis (GO:0048477)|penetration of zona pellucida (GO:0007341)|phospholipid biosynthetic process (GO:0008654)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	acrosomal vesicle (GO:0001669)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-N-acetylhexosaminidase activity (GO:0004563)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(3)|large_intestine(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.72e-57)		TTCTTTGTCTCATGTTTATAC	0.373																																					p.H264N	Melanoma(66;841 1270 13391 18706 27225)	Atlas-SNP	.											.	HEXB	34	.	0			c.C790A						PASS	.						149	148	148					5																	74009349		2203	4300	6503	SO:0001583	missense	3074	exon7			TTGTCTCATGTTT	M13519	CCDS4022.1	5q13.3	2012-10-02			ENSG00000049860	ENSG00000049860	3.2.1.52		4879	protein-coding gene	gene with protein product		606873				2579389, 3013851	Standard	NM_000521		Approved		uc003kdf.4	P07686	OTTHUMG00000102057	ENST00000261416.7:c.790C>A	chr5.hg19:g.74009349C>A	ENSP00000261416:p.His264Asn	105.0	0.0	.		116.0	49.0	.	NM_000521		Missense_Mutation	SNP	ENST00000261416.7	hg19	CCDS4022.1	.	.	.	.	.	.	.	.	.	.	C	15.72	2.915689	0.52546	.	.	ENSG00000049860	ENST00000511181;ENST00000261416	D;D	0.95377	-3.69;-3.69	5.73	4.86	0.63082	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycoside hydrolase, family 20, catalytic core (1);	0.000000	0.85682	D	0.000000	D	0.97636	0.9225	M	0.83223	2.63	0.80722	D	1	D	0.58970	0.984	D	0.69142	0.962	D	0.97847	1.0272	10	0.52906	T	0.07	-19.5886	16.7955	0.85601	0.0:0.871:0.129:0.0	.	264	P07686	HEXB_HUMAN	N	39;264	ENSP00000426285:H39N;ENSP00000261416:H264N	ENSP00000261416:H264N	H	+	1	0	HEXB	74045105	1.000000	0.71417	0.982000	0.44146	0.733000	0.41908	4.019000	0.57181	1.406000	0.46857	0.650000	0.86243	CAT	.	.	.	none		0.373	HEXB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219859.6	NM_000521		A	74009349	C	A	74009349	3	1	108	1	0	0	0	0	1	0	0	0	7081	826	29	4	816	4	HEXB	5	74009349	Missense_Mutation	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10	72922304	74009349	106905911	32	6872											
LNPEP	4012	hgsc.bcm.edu	37	chr5	96329525	96329525	+	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	ttcctgttatgtccagatttGgtggctattcctgactttga	6	18	9	8	0	0	3	0	2	0	1	3	3	3	3	3	2	0	2	3	2	2	6			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr5:96329525G>T	ENST00000231368.5	+	6	1949	c.1257G>T	c.(1255-1257)ttG>ttT	p.L419F	LNPEP_ENST00000395770.3_Missense_Mutation_p.L405F	NM_005575.2	NP_005566.2	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase	419					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)		GTCCAGATTTGGTGGCTATTC	0.393																																					p.L419F		Atlas-SNP	.											.	LNPEP	80	.	0			c.G1257T						PASS	.						140	136	137					5																	96329525		2203	4300	6503	SO:0001583	missense	4012	exon6			AGATTTGGTGGCT	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.1257G>T	chr5.hg19:g.96329525G>T	ENSP00000231368:p.Leu419Phe	69.0	0.0	.		76.0	34.0	.	NM_005575	O00769|Q15145|Q59H76|Q9TNQ2|Q9TNQ3|Q9UIQ7	Missense_Mutation	SNP	ENST00000231368.5	hg19	CCDS4087.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.933413	0.73442	.	.	ENSG00000113441	ENST00000231368;ENST00000395770	T;T	0.05382	3.45;3.45	4.89	4.89	0.63831	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.64402	D	0.000003	T	0.24586	0.0596	M	0.75884	2.315	0.58432	D	0.999998	D	0.71674	0.998	D	0.81914	0.995	T	0.00465	-1.1723	10	0.66056	D	0.02	.	14.7976	0.69889	0.0:0.1448:0.8552:0.0	.	419	Q9UIQ6	LCAP_HUMAN	F	419;405	ENSP00000231368:L419F;ENSP00000379117:L405F	ENSP00000231368:L419F	L	+	3	2	LNPEP	96355281	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	3.863000	0.56016	2.409000	0.81822	0.655000	0.94253	TTG	.	.	.	none		0.393	LNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250624.1	NM_005575		T	96329525	G	T	96329525	3	4	108	1	0	0	0	0	1	0	0	0	8871	1339	47	4	1279	4	LNPEP	5	96329525	Missense_Mutation	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10	22320176	96329525	84585735	33	6873											
KIAA0141	9812	hgsc.bcm.edu	37	chr5	141313856	141313856	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agggccacagcctggctcagTaccgctatgccaggtgccta	8	7	12	14	1	1	0	1	0	0	0	1	0	1	0	5	3	4	3	5	3	3	3			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr5:141313856T>C	ENST00000432126.2	+	9	1083	c.949T>C	c.(949-951)Tac>Cac	p.Y317H	KIAA0141_ENST00000194118.4_Missense_Mutation_p.Y317H	NM_001142603.1|NM_014773.3	NP_001136075.1|NP_055588.3	Q14154	DELE_HUMAN	KIAA0141	317					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)			CCTGGCTCAGTACCGCTATGC	0.597																																					p.Y317H		Atlas-SNP	.											.	KIAA0141	44	.	0			c.T949C						PASS	.						44	42	43					5																	141313856		2203	4300	6503	SO:0001583	missense	9812	exon9			GCTCAGTACCGCT	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.949T>C	chr5.hg19:g.141313856T>C	ENSP00000396225:p.Tyr317His	119.0	0.0	.		130.0	56.0	.	NM_001142603	Q969R4|Q96EU9	Missense_Mutation	SNP	ENST00000432126.2	hg19	CCDS4268.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.451431	0.84209	.	.	ENSG00000081791	ENST00000432126;ENST00000194118;ENST00000508751	T;T;T	0.58060	0.55;0.55;0.36	5.82	5.82	0.92795	Tetratricopeptide-like helical (1);	0.124431	0.56097	D	0.000025	T	0.68723	0.3032	L	0.61218	1.895	0.40580	D	0.981385	D	0.89917	1.0	D	0.91635	0.999	T	0.71862	-0.4464	10	0.59425	D	0.04	-18.5976	12.5686	0.56323	0.0:0.0:0.0:1.0	.	317	Q14154	DELE_HUMAN	H	317;317;311	ENSP00000396225:Y317H;ENSP00000194118:Y317H;ENSP00000422686:Y311H	ENSP00000194118:Y317H	Y	+	1	0	KIAA0141	141294040	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.534000	0.67167	2.217000	0.71921	0.533000	0.62120	TAC	.	.	.	none		0.597	KIAA0141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251863.2	NM_014773		C	141313856	T	C	141313856	3	2	108	1	0	0	0	0	1	0	0	0	8163	1638	57	3	983	3	KIAA0141	5	141313856	Missense_Mutation	SNP	T	TCGA-B9-A8YH-01A-11D-A36X-10	44984331	141313856	39601404	34	6874											
DHX16	8449	hgsc.bcm.edu	37	chr6	30638231	30638231	+	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	catcttgaggcgcttctgagCctcttcataagcctagaaga	10	11	9	11	1	4	4	1	2	3	2	4	4	4	4	2	1	2	1	2	1	3	5			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr6:30638231C>G	ENST00000376442.3	-	4	817	c.622G>C	c.(622-624)Gct>Cct	p.A208P		NM_001164239.1|NM_003587.4	NP_001157711.1|NP_003578.2	O60231	DHX16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 16	208					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			kidney(2)|ovary(2)	4						CGCTTCTGAGCCTCTTCATAA	0.522																																					p.A208P		Atlas-SNP	.											.	DHX16	119	.	0			c.G622C						PASS	.						32	31	31					6																	30638231		1507	2708	4215	SO:0001583	missense	8449	exon4			TCTGAGCCTCTTC	AB001601	CCDS4685.1	6p21.3	2010-02-17	2003-06-13	2003-06-20	ENSG00000204560	ENSG00000204560		"DEAH-boxes"	2739	protein-coding gene	gene with protein product		603405	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 16"	DDX16		9547260	Standard	NM_003587		Approved	DBP2, Prp2, PRPF2	uc003nqz.3	O60231	OTTHUMG00000031060	ENST00000376442.3:c.622G>C	chr6.hg19:g.30638231C>G	ENSP00000365625:p.Ala208Pro	58.0	0.0	.		45.0	12.0	.	NM_003587	O60322|Q5JP45|Q969X7|Q96QC1	Missense_Mutation	SNP	ENST00000376442.3	hg19	CCDS4685.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.624830	0.87560	.	.	ENSG00000204560	ENST00000376442;ENST00000415603	T;T	0.52295	0.67;0.67	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.64811	0.2632	M	0.85197	2.74	0.80722	D	1	D;B	0.76494	0.999;0.029	D;B	0.67103	0.949;0.04	T	0.65882	-0.6060	10	0.38643	T	0.18	.	17.0904	0.86620	0.0:1.0:0.0:0.0	.	148;208	B4DZ28;O60231	.;DHX16_HUMAN	P	208;148	ENSP00000365625:A208P;ENSP00000399101:A148P	ENSP00000365625:A208P	A	-	1	0	DHX16	30746210	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	6.452000	0.73485	2.560000	0.86352	0.455000	0.32223	GCT	.	.	.	none		0.522	DHX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076076.2	NM_003587		G	30638231	C	G	30638231	3	3	108	1	0	0	0	0	1	0	0	0	4504	739	26	4	2571	4	DHX16	6	30638231	Missense_Mutation	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10		30638231	140476836	35	6875											
NFYA	4800	hgsc.bcm.edu	37	chr6	41046900	41046900	+	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	caggcaggacagattcagcaGcaggtatggaagcaaaactg	15	5	13	8	0	1	1	1	0	0	1	1	3	1	3	0	4	4	5	0	4	4	2			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr6:41046900G>T	ENST00000341376.6	+	2	273	c.72G>T	c.(70-72)caG>caT	p.Q24H	OARD1_ENST00000480585.1_Intron|NFYA_ENST00000353205.5_Missense_Mutation_p.Q24H	NM_002505.4	NP_002496.1	P23511	NFYA_HUMAN	nuclear transcription factor Y, alpha	24	Gln-rich.				cellular lipid metabolic process (GO:0044255)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)	CCAAT-binding factor complex (GO:0016602)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|large_intestine(4)|lung(2)|urinary_tract(1)	9	Ovarian(28;0.0418)|Colorectal(47;0.196)					AGATTCAGCAGCAGGTATGGA	0.443																																					p.Q24H		Atlas-SNP	.											.	NFYA	33	.	0			c.G72T						PASS	.						143	124	131					6																	41046900		2203	4300	6503	SO:0001583	missense	4800	exon2			TCAGCAGCAGGTA		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.72G>T	chr6.hg19:g.41046900G>T	ENSP00000345702:p.Gln24His	82.0	0.0	.		60.0	4.0	.	NM_002505	Q8IXU0	Missense_Mutation	SNP	ENST00000341376.6	hg19	CCDS4849.1	.	.	.	.	.	.	.	.	.	.	G	17.57	3.422564	0.62622	.	.	ENSG00000001167	ENST00000341376;ENST00000353205	.	.	.	6.17	4.38	0.52667	.	0.000000	0.85682	D	0.000000	T	0.56978	0.2022	L	0.44542	1.39	0.45883	D	0.998735	D;P	0.54397	0.966;0.943	P;D	0.66979	0.891;0.948	T	0.59952	-0.7357	9	0.46703	T	0.11	-3.2484	12.333	0.55049	0.1369:0.0:0.8631:0.0	.	24;24	P23511-2;P23511	.;NFYA_HUMAN	H	24	.	ENSP00000345702:Q24H	Q	+	3	2	NFYA	41154878	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.759000	0.38420	1.620000	0.50308	0.655000	0.94253	CAG	.	.	.	none		0.443	NFYA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040496.1			T	41046900	G	T	41046900	3	4	108	1	0	0	0	0	1	0	0	0	10396	962	34	4	74	4	NFYA	6	41046900	Missense_Mutation	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10	10408669	41046900	130068167	36	6876											
PHF3	23469	hgsc.bcm.edu	37	chr6	64395141	64395141	+	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	aacatgaccacagatgctccGaagaaaattgttgcagcaaa	17	7	8	9	1	0	3	0	1	0	2	1	4	1	3	2	0	4	4	2	0	5	2	rs149984169		TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr6:64395141G>A	ENST00000262043.3	+	4	1858	c.1518G>A	c.(1516-1518)ccG>ccA	p.P506P	PHF3_ENST00000393387.1_Silent_p.P506P|PHF3_ENST00000509330.1_Silent_p.P506P			Q92576	PHF3_HUMAN	PHD finger protein 3	506					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)			CAGATGCTCCGAAGAAAATTG	0.343																																					p.P506P	GBM(135;136 1820 29512 34071 46235)	Atlas-SNP	.											PHF3,NS,carcinoma,0,2	PHF3	191	.	0			c.G1518A						PASS	.						40	43	42					6																	64395141		2203	4297	6500	SO:0001819	synonymous_variant	23469	exon3			TGCTCCGAAGAAA	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.1518G>A	chr6.hg19:g.64395141G>A		336.0	0.0	.		298.0	114.0	.	NM_015153	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Silent	SNP	ENST00000262043.3	hg19	CCDS4966.1																																																																																			.	G|1.000;T|0.000	.	alt		0.343	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2			A	64395141	G	A	64395141	2	1	108	1	0	0	0	0	0	0	0	1	11843	1045	37	1		1	PHF3	6	64395141	Silent	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10	23348241	64395141	106719926	37	6877											
OGFRL1	79627	hgsc.bcm.edu	37	chr6	72011551	72011551	+	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	aggcccagcccagagcccagCaatgaagctgccaagccaag	13	2	11	15	0	0	2	0	1	0	1	0	2	0	2	5	1	6	2	5	1	4	0			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr6:72011551C>T	ENST00000370435.4	+	7	1289	c.1155C>T	c.(1153-1155)agC>agT	p.S385S	RP11-154D6.1_ENST00000423255.1_RNA|RP11-154D6.1_ENST00000587253.1_RNA|RP3-331H24.5_ENST00000602823.1_lincRNA|RP11-154D6.1_ENST00000412751.1_RNA|RP11-154D6.1_ENST00000591156.1_RNA|RP11-154D6.1_ENST00000585882.1_RNA|RP11-154D6.1_ENST00000587036.1_RNA|RP11-154D6.1_ENST00000587397.1_RNA|RP11-154D6.1_ENST00000588612.1_RNA|RP11-154D6.1_ENST00000586232.1_RNA|RP11-154D6.1_ENST00000432050.1_RNA|RP11-154D6.1_ENST00000450998.1_RNA|RP11-154D6.1_ENST00000586030.1_RNA	NM_024576.3	NP_078852.3	Q5TC84	OGRL1_HUMAN	opioid growth factor receptor-like 1	385						membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|upper_aerodigestive_tract(1)	13						CAGAGCCCAGCAATGAAGCTG	0.453																																					p.S385S		Atlas-SNP	.											.	OGFRL1	44	.	0			c.C1155T						PASS	.						51	58	56					6																	72011551		2203	4300	6503	SO:0001819	synonymous_variant	79627	exon7			GCCCAGCAATGAA		CCDS34482.1	6q13	2008-02-05			ENSG00000119900	ENSG00000119900			21378	protein-coding gene	gene with protein product							Standard	NM_024576		Approved	dJ331H24.1	uc003pfx.1	Q5TC84	OTTHUMG00000015000	ENST00000370435.4:c.1155C>T	chr6.hg19:g.72011551C>T		398.0	0.0	.		387.0	153.0	.	NM_024576	Q2TAC1|Q8NEQ4|Q9H7B5	Silent	SNP	ENST00000370435.4	hg19	CCDS34482.1																																																																																			.	.	.	none		0.453	OGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041153.2	NM_024576		T	72011551	C	T	72011551	2	4	108	1	0	0	0	0	0	0	0	1	10851	709	25	2		2	OGFRL1	6	72011551	Silent	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10	7616410	72011551	99103516	38	6878											
MYO6	4646	hgsc.bcm.edu	37	chr6	76621412	76621412	+	Missense_Mutation	SNP	T	T	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	ttgcaccatttttgaacaatTcacgtaagtcaatgggtggt	11	14	9	7	1	2	1	2	1	0	0	2	1	2	1	1	2	2	2	1	2	4	5			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr6:76621412T>G	ENST00000369977.3	+	33	3575	c.3436T>G	c.(3436-3438)Tca>Gca	p.S1146A	MYO6_ENST00000369985.4_Missense_Mutation_p.S1123A|MYO6_ENST00000369981.3_Intron|MYO6_ENST00000369975.1_Intron	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	1155					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)		TTTGAACAATTCACGTAAGTC	0.279																																					p.S1146A		Atlas-SNP	.											.	MYO6	124	.	0			c.T3436G						PASS	.						80	79	79					6																	76621412		2203	4298	6501	SO:0001583	missense	4646	exon33			AACAATTCACGTA	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.3436T>G	chr6.hg19:g.76621412T>G	ENSP00000358994:p.Ser1146Ala	446.0	0.0	.		325.0	137.0	.	NM_004999	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Missense_Mutation	SNP	ENST00000369977.3	hg19	CCDS34487.1	.	.	.	.	.	.	.	.	.	.	T	5.623	0.299601	0.10622	.	.	ENSG00000196586	ENST00000428345;ENST00000369985;ENST00000369977	D;T	0.88586	-2.4;-1.05	5.93	4.78	0.61160	.	0.536594	0.18535	N	0.138382	T	0.50171	0.1600	N	0.01352	-0.895	0.80722	D	1	B;B	0.24768	0.0;0.111	B;B	0.25405	0.0;0.06	T	0.57556	-0.7791	10	0.07644	T	0.81	.	8.5494	0.33442	0.0:0.0681:0.1314:0.8005	.	1123;1146	Q9UM54-2;Q9UM54-1	.;.	A	1156;1123;1146	ENSP00000359002:S1123A;ENSP00000358994:S1146A	ENSP00000358994:S1146A	S	+	1	0	MYO6	76678132	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.427000	0.44740	2.270000	0.75569	0.460000	0.39030	TCA	.	.	.	none		0.279	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999		G	76621412	T	G	76621412	3	3	108	1	0	0	0	0	1	0	0	0	10088	1783	62	5	3562	5	MYO6	6	76621412	Missense_Mutation	SNP	T	TCGA-B9-A8YH-01A-11D-A36X-10	4609861	76621412	94493655	39	6879											
SLC2A12	154091	hgsc.bcm.edu	37	chr6	134350058	134350058	+	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	caactgacttcaaaacagttGatgcatagaacaatatgttt	16	12	6	7	0	1	3	1	2	0	1	1	3	1	3	0	0	4	3	0	0	7	5			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr6:134350058G>A	ENST00000275230.5	-	2	1060	c.905C>T	c.(904-906)tCa>tTa	p.S302L		NM_145176.2	NP_660159.1	Q8TD20	GTR12_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 12	302					glucose transport (GO:0015758)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			NS(1)|breast(1)|large_intestine(6)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	17	Breast(56;0.214)|Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0101)|GBM - Glioblastoma multiforme(68;0.0123)		CAAAACAGTTGATGCATAGAA	0.438																																					p.S302L	Melanoma(122;1663 1672 14489 35294 41228)	Atlas-SNP	.											.	SLC2A12	43	.	0			c.C905T						PASS	.						78	71	73					6																	134350058		2203	4300	6503	SO:0001583	missense	154091	exon2			ACAGTTGATGCAT	AL035699	CCDS5169.1	6q23.2	2013-05-22			ENSG00000146411	ENSG00000146411		"Solute carriers"	18067	protein-coding gene	gene with protein product		610372				11780753, 11832379	Standard	XM_006715349		Approved	GLUT12, GLUT8	uc003qem.1	Q8TD20	OTTHUMG00000015611	ENST00000275230.5:c.905C>T	chr6.hg19:g.134350058G>A	ENSP00000275230:p.Ser302Leu	114.0	0.0	.		109.0	50.0	.	NM_145176	B3KV17|Q7Z6U3|Q96MR8	Missense_Mutation	SNP	ENST00000275230.5	hg19	CCDS5169.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.418468	0.83559	.	.	ENSG00000146411	ENST00000275230	T	0.81163	-1.46	5.16	5.16	0.70880	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.89164	0.6637	M	0.82923	2.615	0.80722	D	1	D	0.69078	0.997	D	0.70227	0.968	D	0.90629	0.4565	10	0.87932	D	0	-11.8076	18.6483	0.91419	0.0:0.0:1.0:0.0	.	302	Q8TD20	GTR12_HUMAN	L	302	ENSP00000275230:S302L	ENSP00000275230:S302L	S	-	2	0	SLC2A12	134391751	1.000000	0.71417	0.979000	0.43373	0.931000	0.56810	9.476000	0.97823	2.426000	0.82243	0.467000	0.42956	TCA	.	.	.	none		0.438	SLC2A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042302.1			A	134350058	G	A	134350058	3	1	108	1	0	0	0	0	1	0	0	0	14554	1294	45	2	964	2	SLC2A12	6	134350058	Missense_Mutation	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10	57728646	134350058	36765009	40	6880											
SGK1	6446	hgsc.bcm.edu	37	chr6	134495179	134495179	+	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	gcattcataagctcaggctcCtgaggttgggagatcttcaa	10	11	11	9	0	4	2	3	1	1	1	5	3	5	2	1	3	1	4	1	3	2	4			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr6:134495179C>A	ENST00000237305.7	-	3	280	c.192G>T	c.(190-192)caG>caT	p.Q64H	SGK1_ENST00000367858.5_Missense_Mutation_p.Q159H|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000475719.2_Missense_Mutation_p.Q64H|SGK1_ENST00000528577.1_Missense_Mutation_p.Q92H|SGK1_ENST00000367857.5_Missense_Mutation_p.Q54H|SGK1_ENST00000413996.3_Missense_Mutation_p.Q78H	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	64					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)		GCTCAGGCTCCTGAGGTTGGG	0.493																																					p.Q159H		Atlas-SNP	.											.	SGK1	387	.	0			c.G477T						PASS	.						146	139	141					6																	134495179		2203	4300	6503	SO:0001583	missense	6446	exon5			AGGCTCCTGAGGT	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.192G>T	chr6.hg19:g.134495179C>A	ENSP00000237305:p.Gln64His	138.0	0.0	.		107.0	41.0	.	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	hg19	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	C	15.59	2.879434	0.51801	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T	0.73258	-0.73;-0.71;-0.72;-0.72;-0.71;-0.73	5.99	2.79	0.32731	.	0.000000	0.85682	D	0.000000	T	0.55465	0.1922	L	0.59436	1.845	0.80722	D	1	B;D;B;B;B;B	0.54964	0.018;0.969;0.013;0.001;0.018;0.006	B;P;B;B;B;B	0.47981	0.021;0.563;0.009;0.008;0.037;0.006	T	0.59632	-0.7418	10	0.62326	D	0.03	.	5.6053	0.17377	0.0:0.383:0.0:0.617	.	92;78;64;54;159;64	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	H	159;78;64;54;92;64;128	ENSP00000356832:Q159H;ENSP00000396242:Q78H;ENSP00000237305:Q64H;ENSP00000356831:Q54H;ENSP00000434450:Q92H;ENSP00000434302:Q64H	ENSP00000237305:Q64H	Q	-	3	2	SGK1	134536872	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.913000	0.39956	0.797000	0.33971	0.655000	0.94253	CAG	.	.	.	none		0.493	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			A	134495179	C	A	134495179	3	1	108	1	0	0	0	0	1	0	0	0	14220	680	24	4	1143	4	SGK1	6	134495179	Missense_Mutation	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10	145121	134495179	36619888	41	6881											
AUTS2	26053	hgsc.bcm.edu	37	chr7	70239070	70239070	+	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	acagtcccacacactttactCcaaaaggacccgagggtacg	13	6	8	14	2	0	0	0	0	0	0	2	2	2	1	3	2	2	1	3	2	4	3	rs143201197		TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr7:70239070C>T	ENST00000342771.4	+	12	2208	c.1887C>T	c.(1885-1887)ctC>ctT	p.L629L	AUTS2_ENST00000406775.2_Intron	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	629										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)		ACACTTTACTCCAAAAGGACC	0.527																																					p.L629L		Atlas-SNP	.											.	AUTS2	173	.	0			c.C1887T						PASS	.						123	96	105					7																	70239070		2203	4300	6503	SO:0001819	synonymous_variant	26053	exon12			TTTACTCCAAAAG	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.1887C>T	chr7.hg19:g.70239070C>T		103.0	0.0	.		137.0	58.0	.	NM_015570	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Silent	SNP	ENST00000342771.4	hg19	CCDS5539.1	.	.	.	.	.	.	.	.	.	.	C	7.138	0.581166	0.13686	.	.	ENSG00000158321	ENST00000443672	.	.	.	6.06	-4.78	0.03209	.	.	.	.	.	T	0.35913	0.0948	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36114	-0.9761	4	.	.	.	-37.1785	1.0348	0.01546	0.1989:0.2867:0.2715:0.2428	.	.	.	.	F	156	.	.	S	+	2	0	AUTS2	69877006	0.606000	0.26949	0.424000	0.26647	0.944000	0.59088	-0.128000	0.10531	-0.883000	0.03982	-2.134000	0.00341	TCC	.	C|1.000;G|0.000	.	alt		0.527	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			T	70239070	C	T	70239070	2	4	108	1	0	0	0	0	0	0	0	1	1225	842	30	2		2	AUTS2	7	70239070	Silent	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10		70239070	88899593	42	6882											
TFR2	7036	hgsc.bcm.edu	37	chr7	100238449	100238449	+	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	accaccaacacagagtctccGcacgcctggcaggaccctcg	10	4	9	18	3	1	1	0	0	1	1	3	2	1	2	5	2	1	2	5	2	1	0			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr7:100238449G>A	ENST00000462107.1	-	4	620	c.333C>T	c.(331-333)tgC>tgT	p.C111C	TFR2_ENST00000431692.1_Silent_p.C111C|TFR2_ENST00000223051.3_Silent_p.C111C			Q9UP52	TFR2_HUMAN	transferrin receptor 2	111					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)	CAGAGTCTCCGCACGCCTGGC	0.592																																					p.C111C		Atlas-SNP	.											.	TFR2	53	.	0			c.C333T						PASS	.						68	63	64					7																	100238449		2203	4300	6503	SO:0001819	synonymous_variant	7036	exon3			GTCTCCGCACGCC	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.333C>T	chr7.hg19:g.100238449G>A		110.0	0.0	.		169.0	78.0	.	NM_003227	A6NGM7|O75422|Q1HE13|Q9HA99|Q9NX67	Silent	SNP	ENST00000462107.1	hg19	CCDS34707.1																																																																																			.	.	.	none		0.592	TFR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356392.3	NM_003227		A	100238449	G	A	100238449	2	1	108	1	0	0	0	0	0	0	0	1	15823	1079	38	1		1	TFR2	7	100238449	Silent	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10	29999379	100238449	58900214	43	6883											
AASS	10157	hgsc.bcm.edu	37	chr7	121755193	121755193	+	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	ttgcccggagccaggagactCtgagcatcttggcgggttag	7	9	15	10	2	2	2	0	1	2	1	2	4	2	3	2	4	3	2	2	4	1	3			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr7:121755193C>G	ENST00000393376.1	-	8	1073	c.978G>C	c.(976-978)caG>caC	p.Q326H	AASS_ENST00000473553.1_Intron|AASS_ENST00000417368.2_Missense_Mutation_p.Q326H			Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase	326	Lysine-ketoglutarate reductase.				cellular nitrogen compound metabolic process (GO:0034641)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity (GO:0047131)|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity (GO:0047130)			autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(6)|large_intestine(12)|lung(27)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	54						CCAGGAGACTCTGAGCATCTT	0.483																																					p.Q326H		Atlas-SNP	.											.	AASS	123	.	0			c.G978C						PASS	.						125	117	120					7																	121755193		2203	4300	6503	SO:0001583	missense	10157	exon9			GAGACTCTGAGCA	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.978G>C	chr7.hg19:g.121755193C>G	ENSP00000377040:p.Gln326His	139.0	0.0	.		208.0	87.0	.	NM_005763	O95462	Missense_Mutation	SNP	ENST00000393376.1	hg19	CCDS5783.1	.	.	.	.	.	.	.	.	.	.	C	18.81	3.702335	0.68501	.	.	ENSG00000008311	ENST00000393376;ENST00000417368	D;D	0.83755	-1.76;-1.76	5.68	1.33	0.21861	Alanine dehydrogenase/PNT, C-terminal (1);	0.051519	0.85682	D	0.000000	D	0.87549	0.6205	M	0.83483	2.645	0.54753	D	0.999989	P	0.45428	0.858	P	0.54312	0.748	D	0.85721	0.1325	10	0.72032	D	0.01	-9.2803	9.477	0.38878	0.0:0.6502:0.0:0.3498	.	326	Q9UDR5	AASS_HUMAN	H	326	ENSP00000377040:Q326H;ENSP00000403768:Q326H	ENSP00000351834:Q326H	Q	-	3	2	AASS	121542429	1.000000	0.71417	0.995000	0.50966	0.983000	0.72400	1.188000	0.32102	-0.038000	0.13624	-0.142000	0.14014	CAG	.	.	.	none		0.483	AASS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347300.1	NM_005763		G	121755193	C	G	121755193	3	3	108	1	0	0	0	0	1	0	0	0	24	912	32	4	1866	4	AASS	7	121755193	Missense_Mutation	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10	21516744	121755193	37383470	44	6884											
ZNF467	168544	hgsc.bcm.edu	37	chr7	149462502	149462502	+	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	aggttctttttccagccgaaGctcaagccgcagtcggagca	9	9	11	12	3	2	0	1	0	1	0	4	2	3	1	3	2	4	4	3	2	2	3			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr7:149462502G>A	ENST00000302017.3	-	5	1502	c.1089C>T	c.(1087-1089)agC>agT	p.S363S	ZNF467_ENST00000484747.1_Intron	NM_207336.1	NP_997219.1	Q7Z7K2	ZN467_HUMAN	zinc finger protein 467	363					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)			TCCAGCCGAAGCTCAAGCCGC	0.657																																					p.S363S		Atlas-SNP	.											.	ZNF467	50	.	0			c.C1089T						PASS	.						12	13	12					7																	149462502		2181	4279	6460	SO:0001819	synonymous_variant	168544	exon5			GCCGAAGCTCAAG	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.1089C>T	chr7.hg19:g.149462502G>A		163.0	0.0	.		287.0	136.0	.	NM_207336		Silent	SNP	ENST00000302017.3	hg19	CCDS5899.1																																																																																			.	.	.	none		0.657	ZNF467-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349833.1	NM_207336		A	149462502	G	A	149462502	2	1	108	1	0	0	0	0	0	0	0	1	17939	962	34	2		2	ZNF467	7	149462502	Silent	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10	27707309	149462502	9676161	45	6885											
CSMD1	64478	hgsc.bcm.edu	37	chr8	4494878	4494878	+	Frame_Shift_Del	DEL	C	C	-																															ccttacctcacttttaaattCccttgttgaggctgtccatc																										TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr8:4494878delC	ENST00000520002.1	-	2	843	c.288delG	c.(286-288)gggfs	p.G96fs	CSMD1_ENST00000602723.1_Frame_Shift_Del_p.G96fs|CSMD1_ENST00000400186.3_Frame_Shift_Del_p.G96fs|CSMD1_ENST00000542608.1_Frame_Shift_Del_p.G96fs|CSMD1_ENST00000602557.1_Frame_Shift_Del_p.G96fs|CSMD1_ENST00000539096.1_Frame_Shift_Del_p.G96fs|CSMD1_ENST00000537824.1_Frame_Shift_Del_p.G96fs			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	96	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)		CTTTTAAATTCCCTTGTTGAG	0.333																																					p.N97fs		Atlas-Indel,Pindel	.											.	CSMD1	1469	.	0			c.289delA						PASS	.						100	99	99					8																	4494878		1858	4100	5958	SO:0001589	frameshift_variant	64478	exon2			.			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.288delG	chr8.hg19:g.4494878delC	ENSP00000430733:p.Gly96fs	78.0	0.0	0		71.0	23.0	0.323944	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Frame_Shift_Del	DEL	ENST00000520002.1	hg19																																																																																				.	.	.	none		0.333	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		-	4494878	C	-	4494878	7	5	108	1	0	1	0	1	0	0	0	0	3946	842	30	0	10495	0	CSMD1	8	4494878	Frame_Shift_Del	DEL	C	TCGA-B9-A8YH-01A-11D-A36X-10		4494878	141869144	46	6886											
BLK	640	hgsc.bcm.edu	37	chr8	11412365	11412365	+	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	tctccccccggatcaccttcCcctcgctccaggccctggtg	3	9	8	21	2	2	0	1	0	1	0	6	1	4	1	8	3	0	1	8	3	0	1			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr8:11412365C>T	ENST00000259089.4	+	7	1178	c.586C>T	c.(586-588)Ccc>Tcc	p.P196S	RP11-148O21.4_ENST00000528629.1_RNA|RP11-148O21.3_ENST00000527922.1_RNA|BLK_ENST00000529894.1_Missense_Mutation_p.P125S|RP11-148O21.6_ENST00000602626.1_lincRNA	NM_001715.2	NP_001706.2	P51451	BLK_HUMAN	BLK proto-oncogene, Src family tyrosine kinase	196	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				B cell receptor signaling pathway (GO:0050853)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of insulin secretion (GO:0032024)	plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			endometrium(1)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(4)|stomach(1)	27			STAD - Stomach adenocarcinoma(15;0.00391)	COAD - Colon adenocarcinoma(149;0.207)		GATCACCTTCCCCTCGCTCCA	0.587																																					p.P196S		Atlas-SNP	.											.	BLK	78	.	0			c.C586T						PASS	.						45	42	43					8																	11412365		2203	4300	6503	SO:0001583	missense	640	exon7			ACCTTCCCCTCGC	BC004473	CCDS5982.1	8p23-p22	2014-06-25	2014-06-25		ENSG00000136573	ENSG00000136573		"SH2 domain containing"	1057	protein-coding gene	gene with protein product		191305	"B lymphoid tyrosine kinase"			7845672	Standard	NM_001715		Approved	MGC10442	uc003wty.3	P51451	OTTHUMG00000090729	ENST00000259089.4:c.586C>T	chr8.hg19:g.11412365C>T	ENSP00000259089:p.Pro196Ser	25.0	0.0	.		24.0	13.0	.	NM_001715	Q16291|Q96IN1	Missense_Mutation	SNP	ENST00000259089.4	hg19	CCDS5982.1	.	.	.	.	.	.	.	.	.	.	C	9.081	0.999208	0.19121	.	.	ENSG00000136573	ENST00000259089;ENST00000427279;ENST00000529894	T;T	0.25085	1.82;1.82	4.57	4.57	0.56435	SH2 motif (5);	0.171825	0.27807	N	0.017777	T	0.13543	0.0328	N	0.20986	0.625	0.80722	D	1	B	0.13594	0.008	B	0.25405	0.06	T	0.11941	-1.0567	10	0.07482	T	0.82	.	5.3329	0.15942	0.0:0.6497:0.1766:0.1737	.	196	P51451	BLK_HUMAN	S	196;196;125	ENSP00000259089:P196S;ENSP00000433663:P125S	ENSP00000259089:P196S	P	+	1	0	BLK	11449774	0.000000	0.05858	1.000000	0.80357	0.969000	0.65631	-0.136000	0.10405	2.249000	0.74217	0.462000	0.41574	CCC	.	.	.	none		0.587	BLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207460.1			T	11412365	C	T	11412365	3	4	108	1	0	0	0	0	1	0	0	0	1444	623	22	2	608	2	BLK	8	11412365	Missense_Mutation	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10	6917487	11412365	134951657	47	6887											
ASPH	444	hgsc.bcm.edu	37	chr8	62556523	62556523	+	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	cctggattttcctgctcagaCatcatctcttccatatcctg	7	15	5	14	0	3	1	2	0	1	1	7	2	6	2	4	1	1	1	4	1	1	4			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr8:62556523C>A	ENST00000379454.4	-	8	877	c.690G>T	c.(688-690)atG>atT	p.M230I	ASPH_ENST00000517847.2_Missense_Mutation_p.M216I|ASPH_ENST00000445642.3_Missense_Mutation_p.M216I|ASPH_ENST00000522919.1_Missense_Mutation_p.M43I|ASPH_ENST00000541428.1_Missense_Mutation_p.M201I|ASPH_ENST00000522835.1_Missense_Mutation_p.M173I|ASPH_ENST00000517903.1_Missense_Mutation_p.M216I|ASPH_ENST00000523897.1_5'Flank|ASPH_ENST00000356457.5_Missense_Mutation_p.M230I|ASPH_ENST00000518068.1_Missense_Mutation_p.M187I	NM_004318.3	NP_004309.2	Q12797	ASPH_HUMAN	aspartate beta-hydroxylase	230	Glu-rich.				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)	CCTGCTCAGACATCATCTCTT	0.328																																					p.M230I		Atlas-SNP	.											.	ASPH	87	.	0			c.G690T						PASS	.						80	77	78					8																	62556523		2202	4298	6500	SO:0001583	missense	444	exon8			CTCAGACATCATC	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.690G>T	chr8.hg19:g.62556523C>A	ENSP00000368767:p.Met230Ile	157.0	0.0	.		145.0	69.0	.	NM_032466	A6NDF4|A6NHI2|B4DIC9|B4E2K4|B7ZM95|E5RGP5|F5H667|Q6NXR7|Q8TB28|Q9H291|Q9H2C4|Q9NRI0|Q9NRI1|Q9Y4J0	Missense_Mutation	SNP	ENST00000379454.4	hg19	CCDS34898.1	.	.	.	.	.	.	.	.	.	.	C	0.036	-1.308824	0.01342	.	.	ENSG00000198363	ENST00000541428;ENST00000379454;ENST00000522919;ENST00000356457;ENST00000519234;ENST00000518068;ENST00000517903;ENST00000445642;ENST00000517847;ENST00000522835	T;T;T;T;T;T;T;T;T;T	0.55234	0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53	5.22	-3.83	0.04269	Aspartyl beta-hydroxylase/Triadin domain (1);	1.348970	0.04759	N	0.425950	T	0.40815	0.1132	L	0.40543	1.245	0.09310	N	1	B;B;B;B;B;B;B	0.13145	0.0;0.0;0.0;0.007;0.0;0.0;0.0	B;B;B;B;B;B;B	0.12837	0.003;0.002;0.002;0.008;0.001;0.002;0.003	T	0.30592	-0.9973	10	0.40728	T	0.16	0.7054	7.006	0.24836	0.1179:0.3434:0.0:0.5387	.	173;216;201;187;230;216;230	B4DIC9;B7ZM95;F5H667;Q8TB28;Q12797-2;Q9H291;Q12797	.;.;.;.;.;.;ASPH_HUMAN	I	201;230;43;230;245;187;216;216;216;173	ENSP00000437864:M201I;ENSP00000368767:M230I;ENSP00000430516:M43I;ENSP00000348841:M230I;ENSP00000427823:M245I;ENSP00000429286:M187I;ENSP00000430245:M216I;ENSP00000394013:M216I;ENSP00000429954:M216I;ENSP00000429160:M173I	ENSP00000348841:M230I	M	-	3	0	ASPH	62719077	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.322000	0.01118	-0.795000	0.04462	-0.895000	0.02911	ATG	.	.	.	none		0.328	ASPH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378510.3	NM_004318		A	62556523	C	A	62556523	3	1	108	1	0	0	0	0	1	0	0	0	1053	478	17	4	1670	4	ASPH	8	62556523	Missense_Mutation	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10	51144158	62556523	83807499	48	6888											
TAF2	6873	hgsc.bcm.edu	37	chr8	120831745	120831745	+	Splice_Site	DEL	C	C	-																															atatagtcagttccacaaatCcctgtaaagatagagaataa																										TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr8:120831745delC	ENST00000378164.2	-	3	438	c.140delG	c.(139-141)gga>ga	p.G47fs		NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	47					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)			TTCCACAAATCCCTGTAAAGA	0.308																																					p.G47fs		Atlas-Indel,Pindel	.											.	TAF2	204	.	0			c.141delA						PASS	.						84	84	84					8																	120831745		2203	4300	6503	SO:0001630	splice_region_variant	6873	exon3			.	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.139-1G>-	chr8.hg19:g.120831745delC		42.0	0.0	0		46.0	20.0	0.434783	NM_003184	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Frame_Shift_Del	DEL	ENST00000378164.2	hg19	CCDS34937.1																																																																																			.	.	.	none		0.308	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184	Frame_Shift_Del	-	120831745	C	-	120831745	8	5	108	1	0	1	0	1	0	0	1	0	15536	869	30	0	3555	0	TAF2	8	120831745	Splice_Site	DEL	C	TCGA-B9-A8YH-01A-11D-A36X-10	58275222	120831745	25532277	49	6889											
PYCRL	65263	hgsc.bcm.edu	37	chr8	144689268	144689268	+	Missense_Mutation	SNP	T	T	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	gcaggcagctctgcagcaccTcctggttggagtgcgtggtc	5	9	15	12	1	1	0	0	0	1	0	3	1	2	1	2	4	4	6	2	4	0	1			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr8:144689268T>G	ENST00000220966.6	-	3	256	c.227A>C	c.(226-228)gAg>gCg	p.E76A	PYCRL_ENST00000377579.3_5'UTR|PYCRL_ENST00000495276.1_5'UTR	NM_023078.3	NP_075566.2	Q53H96	P5CR3_HUMAN	pyrroline-5-carboxylate reductase-like	64					L-proline biosynthetic process (GO:0055129)		pyrroline-5-carboxylate reductase activity (GO:0004735)			central_nervous_system(1)|endometrium(1)|lung(2)|ovary(1)	5	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.17e-38)|Epithelial(56;7.17e-37)|all cancers(56;2.46e-32)|Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)		L-Proline(DB00172)	CTGCAGCACCTCCTGGTTGGA	0.632																																					p.E76A		Atlas-SNP	.											.	PYCRL	14	.	0			c.A227C						PASS	.						46	38	41					8																	144689268		2202	4294	6496	SO:0001583	missense	65263	exon3			AGCACCTCCTGGT	AF086378	CCDS6407.2	8q24.3	2011-09-30	2011-09-30	2011-09-30	ENSG00000104524	ENSG00000104524			25846	protein-coding gene	gene with protein product							Standard	NM_023078		Approved	FLJ13852	uc003yyy.3	Q53H96	OTTHUMG00000157010	ENST00000220966.6:c.227A>C	chr8.hg19:g.144689268T>G	ENSP00000220966:p.Glu76Ala	114.0	0.0	.		112.0	46.0	.	NM_023078	B3KMB5|B4DVT6|H0Y6C3|Q8N3N9|Q96HX4|Q9H896	Missense_Mutation	SNP	ENST00000220966.6	hg19	CCDS6407.2	.	.	.	.	.	.	.	.	.	.	T	17.02	3.280808	0.59758	.	.	ENSG00000104524	ENST00000220966;ENST00000433751	T;T	0.68181	-0.31;-0.31	4.67	4.67	0.58626	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.70395	0.3219	L	0.41124	1.26	0.80722	D	1	D;P	0.63046	0.992;0.934	D;P	0.63283	0.913;0.677	T	0.72001	-0.4422	10	0.59425	D	0.04	-26.6107	9.3378	0.38060	0.0:0.0:0.1806:0.8194	.	76;64	D3DWK4;Q53H96	.;P5CR3_HUMAN	A	76;71	ENSP00000220966:E76A;ENSP00000404493:E71A	ENSP00000220966:E76A	E	-	2	0	PYCRL	144760411	1.000000	0.71417	1.000000	0.80357	0.757000	0.42996	4.821000	0.62679	1.743000	0.51761	0.379000	0.24179	GAG	.	.	.	none		0.632	PYCRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347081.2	NM_023078		G	144689268	T	G	144689268	3	3	108	1	0	0	0	0	1	0	0	0	12870	1551	54	5	649	5	PYCRL	8	144689268	Missense_Mutation	SNP	T	TCGA-B9-A8YH-01A-11D-A36X-10	23857523	144689268	1674754	50	6890											
UNC13B	10497	hgsc.bcm.edu	37	chr9	35396502	35396502	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aagaccacctgtgtaaaagtGctgactacatgaacctgcac	14	8	8	11	0	0	3	0	2	0	1	0	3	0	3	3	0	4	3	3	0	5	2			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr9:35396502G>A	ENST00000378495.3	+	26	3313	c.3091G>A	c.(3091-3093)Gct>Act	p.A1031T	UNC13B_ENST00000378496.4_Missense_Mutation_p.A1031T|UNC13B_ENST00000396787.1_Missense_Mutation_p.A1043T	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	1031	MHD1. {ECO:0000255|PROSITE- ProRule:PRU00587}.				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)			GTGTAAAAGTGCTGACTACAT	0.552																																					p.A1031T		Atlas-SNP	.											.	UNC13B	153	.	0			c.G3091A						PASS	.						112	91	98					9																	35396502		2203	4300	6503	SO:0001583	missense	10497	exon26			AAAAGTGCTGACT	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.3091G>A	chr9.hg19:g.35396502G>A	ENSP00000367756:p.Ala1031Thr	78.0	0.0	.		65.0	31.0	.	NM_006377	Q5VYM8	Missense_Mutation	SNP	ENST00000378495.3	hg19	CCDS6579.1	.	.	.	.	.	.	.	.	.	.	G	14.33	2.503565	0.44558	.	.	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496;ENST00000535471	D;D;D	0.84146	-1.68;-1.62;-1.81	4.95	4.95	0.65309	Munc13 homology 1 (1);	0.095455	0.64402	D	0.000001	T	0.70020	0.3176	N	0.10972	0.075	0.51482	D	0.999927	B;B	0.32365	0.367;0.007	B;B	0.28232	0.087;0.014	T	0.70142	-0.4953	10	0.06625	T	0.88	-13.5866	18.3726	0.90412	0.0:0.0:1.0:0.0	.	1031;1031	F8W8M9;O14795	.;UN13B_HUMAN	T	1043;1031;1031;618	ENSP00000380006:A1043T;ENSP00000367756:A1031T;ENSP00000367757:A1031T	ENSP00000367756:A1031T	A	+	1	0	UNC13B	35386502	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	6.120000	0.71596	2.561000	0.86390	0.563000	0.77884	GCT	.	.	.	none		0.552	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377		A	35396502	G	A	35396502	3	1	108	1	0	0	0	0	1	0	0	0	16997	1319	46	2	3193	2	UNC13B	9	35396502	Missense_Mutation	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10		35396502	105816929	51	6891											
ECM2	1842	hgsc.bcm.edu	37	chr9	95272295	95272295	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attatttccatccatattcaAacgcattaacttcttcagaa	14	15	2	10	1	3	1	2	0	1	1	5	1	5	1	2	0	2	1	2	0	5	7			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr9:95272295A>G	ENST00000344604.5	-	6	1341	c.1192T>C	c.(1192-1194)Ttg>Ctg	p.L398L	ECM2_ENST00000444490.2_Silent_p.L376L|CENPP_ENST00000375587.3_Intron	NM_001197295.1|NM_001393.3	NP_001184224.1|NP_001384.1	O94769	ECM2_HUMAN	extracellular matrix protein 2, female organ and adipocyte specific	398					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						TCCATATTCAAACGCATTAAC	0.333																																					p.L398L		Atlas-SNP	.											.	ECM2	147	.	0			c.T1192C						PASS	.						81	80	80					9																	95272295		2201	4298	6499	SO:0001819	synonymous_variant	1842	exon6			TATTCAAACGCAT	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.1192T>C	chr9.hg19:g.95272295A>G		72.0	0.0	.		76.0	4.0	.	NM_001393	B2R730|E2PU11|Q5T9F2|Q7Z3D0	Silent	SNP	ENST00000344604.5	hg19	CCDS6698.1																																																																																			.	.	.	none		0.333	ECM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053091.1	NM_001393		G	95272295	A	G	95272295	2	3	108	1	0	0	0	0	0	0	0	1	4900	11	1	3		3	ECM2	9	95272295	Silent	SNP	A	TCGA-B9-A8YH-01A-11D-A36X-10	59875793	95272295	45941136	52	6892											
C9orf102	375748	hgsc.bcm.edu	37	chr9	98684631	98684631	+	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	aaaaccttgtatctcagttaCcttacagtccttcagaaggt	12	13	6	10	0	2	1	2	0	1	1	4	1	3	1	3	1	3	2	3	1	6	5			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr9:98684631C>T	ENST00000288985.7	+	8	1682	c.1377C>T	c.(1375-1377)taC>taT	p.Y459Y	ERCC6L2_ENST00000437817.1_Silent_p.Y270Y|ERCC6L2_ENST00000466840.1_3'UTR	NM_001010895.2	NP_001010895.1	Q5T890	ER6L2_HUMAN	excision repair cross-complementation group 6-like 2	459					DNA repair (GO:0006281)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)										ATCTCAGTTACCTTACAGTCC	0.393																																					p.Y459Y		Atlas-SNP	.											.	.	.	.	0			c.C1377T						PASS	.						101	89	93					9																	98684631		2203	4300	6503	SO:0001819	synonymous_variant	375748	exon8			CAGTTACCTTACA	BC022957	CCDS35072.1	9q22.32	2014-03-07	2014-03-07	2012-03-30	ENSG00000182150	ENSG00000182150			26922	protein-coding gene	gene with protein product		615667	"chromosome 9 open reading frame 102", "excision repair cross-complementing rodent repair deficiency, complementation group 6-like 2"	C9orf102			Standard	NM_001010895		Approved	FLJ37706, RAD26L	uc004avt.4	Q5T890	OTTHUMG00000020289	ENST00000288985.7:c.1377C>T	chr9.hg19:g.98684631C>T		71.0	0.0	.		52.0	18.0	.	NM_001010895	A4D997|B2RTP8|Q49AM9|Q5T892|Q8N663|Q8N9D0|Q9NPM7	Silent	SNP	ENST00000288985.7	hg19	CCDS35072.1																																																																																			.	.	.	none		0.393	ERCC6L2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053247.2	NM_001010895		T	98684631	C	T	98684631	2	4	108	1	0	0	0	0	0	0	0	1	2447	518	18	2		2	C9orf102	9	98684631	Silent	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10	3412336	98684631	42528800	53	6893											
DDX31	64794	hgsc.bcm.edu	37	chr9	135505682	135505682	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaagccaacgagttgacatAttctgcctccgaaggagcca	13	7	10	11	2	1	2	0	1	1	1	2	5	2	3	4	1	4	1	4	1	4	3			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr9:135505682A>G	ENST00000372159.3	-	16	2066	c.1915T>C	c.(1915-1917)Tat>Cat	p.Y639H	DDX31_ENST00000372153.1_Silent_p.N630N|DDX31_ENST00000438527.3_Missense_Mutation_p.Y510H	NM_022779.7	NP_073616.6	Q9H8H2	DDX31_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 31	639	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					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)		GAGTTGACATATTCTGCCTCC	0.493																																					p.Y639H		Atlas-SNP	.											.	DDX31	76	.	0			c.T1915C						PASS	.						118	125	122					9																	135505682		2203	4300	6503	SO:0001583	missense	64794	exon16			TGACATATTCTGC	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.1915T>C	chr9.hg19:g.135505682A>G	ENSP00000361232:p.Tyr639His	81.0	0.0	.		78.0	36.0	.	NM_022779	Q5K6N2|Q5K6N3|Q5K6N4|Q5VZJ4|Q5VZJ9|Q96E91|Q96NY2|Q96SX5|Q9H5K6	Missense_Mutation	SNP	ENST00000372159.3	hg19	CCDS6951.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.133832	0.77662	.	.	ENSG00000125485	ENST00000372159;ENST00000372155;ENST00000438527	T;T	0.04862	3.54;3.54	5.54	5.54	0.83059	Helicase, C-terminal (1);	0.109437	0.64402	D	0.000006	T	0.21550	0.0519	L	0.60067	1.865	0.80722	D	1	D	0.89917	1.0	D	0.72982	0.979	T	0.00184	-1.1944	10	0.87932	D	0	-14.67	14.9265	0.70881	1.0:0.0:0.0:0.0	.	639	Q9H8H2	DDX31_HUMAN	H	639;639;510	ENSP00000361232:Y639H;ENSP00000387730:Y510H	ENSP00000361228:Y639H	Y	-	1	0	DDX31	134495503	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.561000	0.82288	2.117000	0.64856	0.529000	0.55759	TAT	.	.	.	none		0.493	DDX31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054794.1	NM_138620		G	135505682	A	G	135505682	3	3	108	1	0	0	0	0	1	0	0	0	4358	449	16	3	660	3	DDX31	9	135505682	Missense_Mutation	SNP	A	TCGA-B9-A8YH-01A-11D-A36X-10	36821051	135505682	5707749	54	6894											
ARID5B	84159	hgsc.bcm.edu	37	chr10	63852419	63852419	+	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	tgggcattccgggggcggatCagaaggccacaagcttcccc	8	6	14	13	2	1	1	1	0	0	1	3	2	3	2	4	5	1	2	4	5	2	2			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr10:63852419C>T	ENST00000279873.7	+	10	3607	c.3197C>T	c.(3196-3198)tCa>tTa	p.S1066L	ARID5B_ENST00000309334.5_Missense_Mutation_p.S823L	NM_032199.2	NP_115575.1	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	1066					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)					GGGGGCGGATCAGAAGGCCAC	0.612																																					p.S1066L		Atlas-SNP	.											.	ARID5B	125	.	0			c.C3197T						PASS	.						72	70	71					10																	63852419		2203	4300	6503	SO:0001583	missense	84159	exon10			GCGGATCAGAAGG	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.3197C>T	chr10.hg19:g.63852419C>T	ENSP00000279873:p.Ser1066Leu	63.0	0.0	.		70.0	28.0	.	NM_032199	B4DLB3|Q05DG6|Q32Q59|Q5VST4|Q6NZ42|Q7Z3M4|Q8N421|Q9H786	Missense_Mutation	SNP	ENST00000279873.7	hg19	CCDS31208.1	.	.	.	.	.	.	.	.	.	.	C	0.017	-1.504483	0.00992	.	.	ENSG00000150347	ENST00000279873;ENST00000309334	T;T	0.42131	0.98;0.99	5.72	2.16	0.27623	.	0.521061	0.22867	N	0.054680	T	0.19446	0.0467	N	0.11560	0.145	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18713	-1.0328	10	0.17832	T	0.49	0.005	7.2708	0.26256	0.0:0.5022:0.0:0.4978	.	1066	Q14865	ARI5B_HUMAN	L	1066;823	ENSP00000279873:S1066L;ENSP00000308862:S823L	ENSP00000279873:S1066L	S	+	2	0	ARID5B	63522425	0.007000	0.16637	0.008000	0.14137	0.545000	0.35147	1.891000	0.39738	0.657000	0.30906	0.655000	0.94253	TCA	.	.	.	none		0.612	ARID5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048233.1	XM_084482		T	63852419	C	T	63852419	3	4	108	1	0	0	0	0	1	0	0	0	922	838	29	2	3235	2	ARID5B	10	63852419	Missense_Mutation	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10		63852419	71682328	55	6895											
WAPAL	23063	hgsc.bcm.edu	37	chr10	88197365	88197365	+	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	gccagttgttccaacagcacActgaaagcagggtgaagggg	12	6	14	9	0	0	2	0	2	0	0	1	2	1	2	2	3	3	4	2	3	3	2			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr10:88197365A>G	ENST00000298767.5	-	19	3980	c.3508T>C	c.(3508-3510)Tgt>Cgt	p.C1170R	WAPAL_ENST00000484070.1_5'UTR|WAPAL_ENST00000372075.1_Splice_Site_p.C382R|WAPAL_ENST00000263070.7_Splice_Site_p.C382R	NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	1170					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)				breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						CCAACAGCACACTGAAAGCAG	0.368																																					p.C1170R		Atlas-SNP	.											.	WAPAL	81	.	0			c.T3508C						PASS	.						73	66	68					10																	88197365		2203	4300	6503	SO:0001630	splice_region_variant	23063	exon19			CAGCACACTGAAA	AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"friend of EBNA2"	610754	"KIAA0261"	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.3508-1T>C	chr10.hg19:g.88197365A>G		81.0	0.0	.		74.0	32.0	.	NM_015045	A7E2B5|Q5VSK5|Q8IX10|Q92549	Missense_Mutation	SNP	ENST00000298767.5	hg19	CCDS7375.1	.	.	.	.	.	.	.	.	.	.	A	16.85	3.235515	0.58886	.	.	ENSG00000062650	ENST00000342368;ENST00000298767;ENST00000372076;ENST00000372075;ENST00000263070	T;T;T	0.36157	1.27;1.27;1.27	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.53094	0.1775	L	0.51422	1.61	0.80722	D	1	D;D;D;D	0.76494	0.99;0.99;0.99;0.999	P;P;P;D	0.68943	0.797;0.802;0.797;0.961	T	0.45687	-0.9244	10	0.32370	T	0.25	.	16.1534	0.81640	1.0:0.0:0.0:0.0	.	1164;1208;1170;1207	B2RTX8;E9PH12;Q7Z5K2;Q7Z5K2-2	.;.;WAPL_HUMAN;.	R	1255;1170;1255;382;382	ENSP00000298767:C1170R;ENSP00000361145:C382R;ENSP00000263070:C382R	ENSP00000263070:C382R	C	-	1	0	WAPAL	88187345	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	8.914000	0.92735	2.211000	0.71520	0.460000	0.39030	TGT	.	.	.	none		0.368	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045	Missense_Mutation	G	88197365	A	G	88197365	5	3	108	1	0	0	0	0	0	0	1	0	17260	173	6	3	68	3	WAPAL	10	88197365	Splice_Site	SNP	A	TCGA-B9-A8YH-01A-11D-A36X-10	24344946	88197365	47337382	56	6896											
PYROXD2	84795	hgsc.bcm.edu	37	chr10	100167377	100167377	+	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	gtaaatctgcggcctcagcaGgctgagcaggtaggacgcgc	9	6	15	11	3	2	1	1	1	1	0	2	2	2	2	1	4	3	5	1	4	3	2			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr10:100167377G>T	ENST00000370575.4	-	4	325	c.277C>A	c.(277-279)Ctg>Atg	p.L93M	PYROXD2_ENST00000483923.1_5'UTR	NM_032709.2	NP_116098.2	Q8N2H3	PYRD2_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 2	93							oxidoreductase activity (GO:0016491)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	12						GGCCTCAGCAGGCTGAGCAGG	0.612																																					p.L93M		Atlas-SNP	.											.	PYROXD2	43	.	0			c.C277A						PASS	.						43	49	47					10																	100167377		2203	4300	6503	SO:0001583	missense	84795	exon4			TCAGCAGGCTGAG	AK074429	CCDS7474.1	10q24.2	2009-04-22	2009-04-22	2009-04-22	ENSG00000119943	ENSG00000119943			23517	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 33"	C10orf33			Standard	NM_032709		Approved	FLJ23849	uc001kpc.3	Q8N2H3	OTTHUMG00000018877	ENST00000370575.4:c.277C>A	chr10.hg19:g.100167377G>T	ENSP00000359607:p.Leu93Met	28.0	0.0	.		47.0	16.0	.	NM_032709	D3DR61|Q5TAA9|Q9BRQ1	Missense_Mutation	SNP	ENST00000370575.4	hg19	CCDS7474.1	.	.	.	.	.	.	.	.	.	.	G	19.30	3.801114	0.70567	.	.	ENSG00000119943	ENST00000370575	T	0.61510	0.1	5.18	3.3	0.37823	.	0.077564	0.53938	D	0.000058	T	0.56804	0.2010	L	0.41236	1.265	0.58432	D	0.999998	P	0.46277	0.875	P	0.51016	0.656	T	0.57499	-0.7801	10	0.87932	D	0	-31.4788	10.2148	0.43162	0.1473:0.0:0.8527:0.0	.	93	Q8N2H3	PYRD2_HUMAN	M	93	ENSP00000359607:L93M	ENSP00000359607:L93M	L	-	1	2	PYROXD2	100157367	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	4.676000	0.61627	0.565000	0.29255	0.563000	0.77884	CTG	.	.	.	none		0.612	PYROXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049782.2	NM_032709		T	100167377	G	T	100167377	3	4	108	1	0	0	0	0	1	0	0	0	12880	991	35	4	1520	4	PYROXD2	10	100167377	Missense_Mutation	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10	11970012	100167377	35367370	57	6897											
ADRA2A	150	hgsc.bcm.edu	37	chr10	112837876	112837876	+	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	ggggggcggcgcccgggccaCcccttactccctgcaggtga	4	5	16	16	3	0	1	0	1	0	0	1	1	1	1	5	6	2	1	5	6	1	1			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr10:112837876C>A	ENST00000280155.2	+	1	1087	c.122C>A	c.(121-123)aCc>aAc	p.T41N		NM_000681.3	NP_000672.3	P08913	ADA2A_HUMAN	adrenoceptor alpha 2A	26					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)	gcccgggccACCCCTTACTCC	0.711																																					p.T41N	Esophageal Squamous(173;605 2658 7278 49362)	Atlas-SNP	.											.	ADRA2A	38	.	0			c.C122A						PASS	.						14	15	15					10																	112837876		2195	4289	6484	SO:0001583	missense	150	exon1			GGGCCACCCCTTA	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.122C>A	chr10.hg19:g.112837876C>A	ENSP00000280155:p.Thr41Asn	43.0	0.0	.		42.0	14.0	.	NM_000681	B0LPF6|Q2I8G2|Q2XN99|Q86TH8|Q9BZK1	Missense_Mutation	SNP	ENST00000280155.2	hg19	CCDS7569.2	.	.	.	.	.	.	.	.	.	.	C	11.59	1.683708	0.29872	.	.	ENSG00000150594	ENST00000280155	T	0.37584	1.19	4.91	3.02	0.34903	.	3.496670	0.01278	U	0.009655	T	0.21387	0.0515	N	0.08118	0	0.22171	N	0.999314	B	0.16802	0.019	B	0.17098	0.017	T	0.22977	-1.0201	10	0.15952	T	0.53	.	6.5228	0.22285	0.0:0.5318:0.3044:0.1638	.	26	P08913	ADA2A_HUMAN	N	41	ENSP00000280155:T41N	ENSP00000280155:T41N	T	+	2	0	ADRA2A	112827866	.	.	0.835000	0.33067	0.994000	0.84299	.	.	0.460000	0.27045	0.555000	0.69702	ACC	.	.	.	none		0.711	ADRA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050372.2	NM_000681		A	112837876	C	A	112837876	3	1	108	1	0	0	0	0	1	0	0	0	337	507	18	4	124	4	ADRA2A	10	112837876	Missense_Mutation	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10	12670499	112837876	22696871	58	6898											
ARHGAP1	392	hgsc.bcm.edu	37	chr11	46701795	46701795	+	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	acttcccggaccacttgggtGttggccgacctccggaagat	7	9	12	13	3	0	1	0	0	0	1	2	4	2	3	5	4	0	1	5	4	1	3			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr11:46701795G>A	ENST00000311956.4	-	10	955	c.858C>T	c.(856-858)aaC>aaT	p.N286N		NM_004308.3	NP_004299.1	Q07960	RHG01_HUMAN	Rho GTPase activating protein 1	286	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				positive regulation of signal transduction (GO:0009967)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	Rac GTPase activator activity (GO:0030675)|Rho GTPase activator activity (GO:0005100)|SH3/SH2 adaptor activity (GO:0005070)			endometrium(1)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	11		Lung NSC(402;1.76e-12)|all_lung(304;1.3e-11)		GBM - Glioblastoma multiforme(35;5.17e-06)|BRCA - Breast invasive adenocarcinoma(625;0.00112)|Lung(87;0.153)		CCACTTGGGTGTTGGCCGACC	0.627																																					p.N286N		Atlas-SNP	.											.	ARHGAP1	27	.	0			c.C858T						PASS	.						112	99	103					11																	46701795		2201	4299	6500	SO:0001819	synonymous_variant	392	exon10			TTGGGTGTTGGCC	BC018118	CCDS7922.1	11p11.2	2006-04-11			ENSG00000175220	ENSG00000175220		"Rho GTPase activating proteins"	673	protein-coding gene	gene with protein product		602732				8288572	Standard	NM_004308		Approved	RhoGAP, p50rhoGAP, CDC42GAP, Cdc42GAP	uc001ndd.4	Q07960	OTTHUMG00000166567	ENST00000311956.4:c.858C>T	chr11.hg19:g.46701795G>A		76.0	0.0	.		53.0	19.0	.	NM_004308	D3DQQ6	Silent	SNP	ENST00000311956.4	hg19	CCDS7922.1	.	.	.	.	.	.	.	.	.	.	G	1.017	-0.686082	0.03328	.	.	ENSG00000175220	ENST00000528837	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	T	0.60919	0.2306	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58940	-0.7547	4	.	.	.	.	9.5717	0.39431	0.0728:0.0:0.786:0.1411	.	.	.	.	Y	240	.	.	H	-	1	0	ARHGAP1	46658371	0.892000	0.30473	1.000000	0.80357	0.128000	0.20619	0.437000	0.21543	2.615000	0.88500	0.555000	0.69702	CAC	.	.	.	none		0.627	ARHGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390472.1	NM_004308		A	46701795	G	A	46701795	2	1	108	1	0	0	0	0	0	0	0	1	861	1368	48	2		2	ARHGAP1	11	46701795	Silent	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10		46701795	88304721	59	6899											
CKAP5	9793	hgsc.bcm.edu	37	chr11	46772905	46772905	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcttactcaccttgggcccTtttaatttgcataaggtgtg	7	17	8	9	0	2	0	1	0	1	0	2	0	2	0	2	2	2	1	2	2	3	7			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr11:46772905T>C	ENST00000529230.1	-	39	5359	c.5313A>G	c.(5311-5313)aaA>aaG	p.K1771K	CKAP5_ENST00000312055.5_Silent_p.K1711K|CKAP5_ENST00000354558.3_Silent_p.K1711K|CKAP5_ENST00000415402.1_Silent_p.K1771K|MIR5582_ENST00000579697.1_RNA			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	1771					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)		p.K1771K(1)		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						CCTTGGGCCCTTTTAATTTGC	0.443																																					p.K1771K	Ovarian(4;85 273 2202 4844 13323)	Atlas-SNP	.											CKAP5,NS,carcinoma,0,1	CKAP5	134	.	1	Substitution - coding silent(1)	lung(1)	c.A5313G						PASS	.						165	160	161					11																	46772905		2201	4299	6500	SO:0001819	synonymous_variant	9793	exon39			GGGCCCTTTTAAT		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.5313A>G	chr11.hg19:g.46772905T>C		82.0	0.0	.		89.0	4.0	.	NM_001008938	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	Silent	SNP	ENST00000529230.1	hg19	CCDS31477.1	.	.	.	.	.	.	.	.	.	.	T	8.631	0.893624	0.17613	.	.	ENSG00000175216	ENST00000525896	.	.	.	5.72	4.6	0.57074	.	.	.	.	.	T	0.57330	0.2046	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55604	-0.8115	4	.	.	.	-13.3618	7.7932	0.29133	0.0:0.1821:0.0:0.8179	.	.	.	.	G	10	.	.	R	-	1	2	CKAP5	46729481	0.978000	0.34361	1.000000	0.80357	0.988000	0.76386	0.096000	0.15147	2.183000	0.69458	0.533000	0.62120	AGG	.	.	.	none		0.443	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	NM_014756		C	46772905	T	C	46772905	2	2	108	1	0	0	0	0	0	0	0	1	3447	1606	56	3		3	CKAP5	11	46772905	Silent	SNP	T	TCGA-B9-A8YH-01A-11D-A36X-10	71110	46772905	88233611	60	6900											
MYBPC3	4607	hgsc.bcm.edu	37	chr11	47372130	47372130	+	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	gggctccagtggcctcagcaGgggcaggggcaggggccagc	6	3	20	12	0	1	0	1	0	0	0	2	0	2	0	3	8	2	4	3	8	0	0			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr11:47372130G>A	ENST00000545968.1	-	3	383	c.329C>T	c.(328-330)cCt>cTt	p.P110L	MYBPC3_ENST00000399249.2_Missense_Mutation_p.P110L|MYBPC3_ENST00000256993.4_Missense_Mutation_p.P110L	NM_000256.3	NP_000247.2	Q14896	MYPC3_HUMAN	myosin binding protein C, cardiac	110	Pro-rich.				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)		GGCCTCAGCAGGGGCAGGGGC	0.672																																					p.P110L		Atlas-SNP	.											.	MYBPC3	102	.	0			c.C329T						PASS	.						7	8	8					11																	47372130		1838	4050	5888	SO:0001583	missense	4607	exon3			TCAGCAGGGGCAG	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.329C>T	chr11.hg19:g.47372130G>A	ENSP00000442795:p.Pro110Leu	160.0	0.0	.		165.0	26.0	.	NM_000256	A5PL00|Q16410|Q6R2F7|Q9UE27|Q9UM53	Missense_Mutation	SNP	ENST00000545968.1	hg19	CCDS53621.1	.	.	.	.	.	.	.	.	.	.	G	15.13	2.742480	0.49151	.	.	ENSG00000134571	ENST00000545968;ENST00000399249;ENST00000256993	T;T;T	0.58940	0.3;0.3;0.36	2.16	2.16	0.27623	.	.	.	.	.	T	0.34890	0.0913	N	0.08118	0	0.24976	N	0.991637	B	0.13594	0.008	B	0.09377	0.004	T	0.27571	-1.0070	9	0.66056	D	0.02	.	7.7704	0.29004	0.0:0.0:1.0:0.0	.	110	Q14896	MYPC3_HUMAN	L	110	ENSP00000442795:P110L;ENSP00000382193:P110L;ENSP00000256993:P110L	ENSP00000256993:P110L	P	-	2	0	MYBPC3	47328706	0.590000	0.26815	0.347000	0.25668	0.645000	0.38454	1.834000	0.39171	1.229000	0.43630	0.462000	0.41574	CCT	.	.	.	none		0.672	MYBPC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392271.3			A	47372130	G	A	47372130	3	1	108	1	0	0	0	0	1	0	0	0	10020	1000	35	2	3616	2	MYBPC3	11	47372130	Missense_Mutation	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10	599225	47372130	87634386	61	6901											
CELF1	10658	hgsc.bcm.edu	37	chr11	47494737	47494737	+	Missense_Mutation	SNP	A	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	tgcagcaggtcctgatcaccAaactcctggggcaggtggta	9	8	13	11	0	1	1	1	1	0	0	3	1	3	1	3	5	3	4	3	5	2	1			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr11:47494737A>C	ENST00000358597.3	-	11	1235	c.1236T>G	c.(1234-1236)ttT>ttG	p.F412L	CELF1_ENST00000310513.5_Missense_Mutation_p.F408L|CELF1_ENST00000361904.3_Missense_Mutation_p.F409L|CELF1_ENST00000532048.1_Missense_Mutation_p.F438L|CELF1_ENST00000531165.1_Missense_Mutation_p.F440L|CELF1_ENST00000395292.2_Missense_Mutation_p.F409L|CELF1_ENST00000395290.2_Missense_Mutation_p.F411L|CELF1_ENST00000539455.1_5'UTR			Q92879	CELF1_HUMAN	CUGBP, Elav-like family member 1	412	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				embryo development (GO:0009790)|germ cell development (GO:0007281)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of translation (GO:0017148)|positive regulation of multicellular organism growth (GO:0040018)|regulation of RNA splicing (GO:0043484)|RNA interference (GO:0016246)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	BRE binding (GO:0042835)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation repressor activity, nucleic acid binding (GO:0000900)			central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|ovary(2)	18						CCTGATCACCAAACTCCTGGG	0.488																																					p.F438L	Pancreas(163;1949 1966 9906 43218 43785)	Atlas-SNP	.											.	CELF1	43	.	0			c.T1314G						PASS	.						108	95	100					11																	47494737		2201	4298	6499	SO:0001583	missense	10658	exon14			ATCACCAAACTCC	U63289	CCDS7938.1, CCDS7939.1, CCDS31482.1, CCDS53622.1, CCDS53623.1	11p11	2013-02-12	2010-02-19	2010-02-19				"RNA binding motif (RRM) containing"	2549	protein-coding gene	gene with protein product	"CUG RNA-binding protein", "nuclear polyadenylated RNA-binding protein, 50-kD", "bruno-like 2", "embryo deadenylation element binding protein"	601074	"CUG triplet repeat, RNA-binding protein 1", "CUG triplet repeat, RNA binding protein 1"	CUGBP1		8948631, 9371827	Standard	NM_006560		Approved	CUG-BP, hNab50, BRUNOL2, NAB50, CUGBP, NAPOR, EDEN-BP	uc001nfl.3	Q92879		ENST00000358597.3:c.1236T>G	chr11.hg19:g.47494737A>C	ENSP00000351409:p.Phe412Leu	80.0	0.0	.		76.0	37.0	.	NM_001172639	B4E2U5|D3DQS0|F8W940|Q4LE52|Q9NP83|Q9NR06	Missense_Mutation	SNP	ENST00000358597.3	hg19	CCDS31482.1	.	.	.	.	.	.	.	.	.	.	A	19.26	3.793578	0.70452	.	.	ENSG00000149187	ENST00000395290;ENST00000358597;ENST00000395292;ENST00000310513;ENST00000361904;ENST00000531165;ENST00000532048	T;T;T;T;T;T;T	0.14391	2.51;2.51;2.51;2.51;2.51;2.51;2.51	6.07	3.79	0.43588	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.096317	0.64402	D	0.000001	T	0.19248	0.0462	N	0.25957	0.775	0.80722	D	1	B;B;D;B;B;D	0.54601	0.004;0.004;0.967;0.082;0.004;0.964	B;B;P;B;B;P	0.61940	0.004;0.004;0.896;0.261;0.004;0.88	T	0.01242	-1.1408	10	0.49607	T	0.09	-11.2757	8.6583	0.34077	0.7964:0.0:0.2036:0.0	.	411;440;438;408;409;412	F8W940;G5EA30;Q92879-4;Q92879-2;Q92879-3;Q92879	.;.;.;.;.;CELF1_HUMAN	L	411;412;409;408;409;440;438	ENSP00000378705:F411L;ENSP00000351409:F412L;ENSP00000378706:F409L;ENSP00000308386:F408L;ENSP00000354639:F409L;ENSP00000436864:F440L;ENSP00000435926:F438L	ENSP00000308386:F408L	F	-	3	2	CELF1	47451313	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.627000	0.37050	0.550000	0.28991	0.533000	0.62120	TTT	.	.	.	none		0.488	CELF1-024	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398352.1	NM_006560		C	47494737	A	C	47494737	3	2	108	1	0	0	0	0	1	0	0	0	3217	127	5	5	232	5	CELF1	11	47494737	Missense_Mutation	SNP	A	TCGA-B9-A8YH-01A-11D-A36X-10	122607	47494737	87511779	62	6902											
OR10S1	219873	hgsc.bcm.edu	37	chr11	123847533	123847533	+	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	ttggagttacgattgtgtagAagacagcaggggccccagct	10	9	14	8	1	0	2	0	0	0	2	0	4	0	3	2	3	3	4	2	3	3	4			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr11:123847533A>T	ENST00000531945.1	-	1	955	c.866T>A	c.(865-867)tTc>tAc	p.F289Y		NM_001004474.1	NP_001004474.1	Q8NGN2	O10S1_HUMAN	olfactory receptor, family 10, subfamily S, member 1	289						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	36		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		GATTGTGTAGAAGACAGCAGG	0.547																																					p.F289Y		Atlas-SNP	.											.	OR10S1	78	.	0			c.T866A						PASS	.						89	93	91					11																	123847533		2202	4299	6501	SO:0001583	missense	219873	exon1			GTGTAGAAGACAG	BK004509	CCDS31701.1	11q24.1	2012-08-09			ENSG00000196248	ENSG00000196248		"GPCR / Class A : Olfactory receptors"	14807	protein-coding gene	gene with protein product							Standard	NM_001004474		Approved		uc001pzm.1	Q8NGN2	OTTHUMG00000165963	ENST00000531945.1:c.866T>A	chr11.hg19:g.123847533A>T	ENSP00000431914:p.Phe289Tyr	76.0	0.0	.		59.0	26.0	.	NM_001004474	B9EH43|Q6IEV3|Q96R78	Missense_Mutation	SNP	ENST00000531945.1	hg19	CCDS31701.1	.	.	.	.	.	.	.	.	.	.	A	16.80	3.222817	0.58668	.	.	ENSG00000196248	ENST00000531945	T	0.00224	8.51	4.85	4.85	0.62838	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36972	U	0.002306	T	0.00695	0.0023	H	0.95504	3.68	0.25935	N	0.98295	D	0.63880	0.993	P	0.60012	0.867	T	0.14309	-1.0477	10	0.87932	D	0	-26.4199	10.2325	0.43264	0.8516:0.0:0.0:0.1484	.	289	Q8NGN2	O10S1_HUMAN	Y	289	ENSP00000431914:F289Y	ENSP00000431914:F289Y	F	-	2	0	OR10S1	123352743	0.027000	0.19231	1.000000	0.80357	0.619000	0.37552	2.258000	0.43249	2.039000	0.60335	0.533000	0.62120	TTC	.	.	.	none		0.547	OR10S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387265.2	NM_001004474		T	123847533	A	T	123847533	3	4	108	1	0	0	0	0	1	0	0	0	10925	246	9	5	133	5	OR10S1	11	123847533	Missense_Mutation	SNP	A	TCGA-B9-A8YH-01A-11D-A36X-10	76352796	123847533	11158983	63	6903											
CLECL1	160365	hgsc.bcm.edu	37	chr12	9875396	9875396	+	Missense_Mutation	SNP	A	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	catgatttatggacagtagaAaagttgaaagaaactggaag	18	9	11	3	0	0	4	0	2	0	2	0	6	0	6	0	2	1	2	0	2	7	4			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr12:9875396A>C	ENST00000327839.3	-	2	364	c.330T>G	c.(328-330)ttT>ttG	p.F110L		NM_172004.3	NP_742001.1	Q8IZS7	CLCL1_HUMAN	C-type lectin-like 1	110						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|kidney(1)|large_intestine(4)|lung(3)	9						GGACAGTAGAAAAGTTGAAAG	0.328																																					p.F110L		Atlas-SNP	.											.	CLECL1	18	.	0			c.T330G						PASS	.						56	52	53					12																	9875396		2203	4299	6502	SO:0001583	missense	160365	exon2			AGTAGAAAAGTTG	AF518873	CCDS8603.1, CCDS73441.1	12p13.31	2007-06-21				ENSG00000184293			24462	protein-coding gene	gene with protein product	"dendritic cell associated lectin 1"	607467				12421943	Standard	NM_172004		Approved	DCAL1	uc001qwi.3	Q8IZS7		ENST00000327839.3:c.330T>G	chr12.hg19:g.9875396A>C	ENSP00000331766:p.Phe110Leu	116.0	0.0	.		124.0	76.0	.	NM_001267701		Missense_Mutation	SNP	ENST00000327839.3	hg19	CCDS8603.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	3.681|3.681	-0.065539|-0.065539	0.07273|0.07273	.|.	.|.	ENSG00000184293|ENSG00000184293	ENST00000542530|ENST00000327839	T|T	0.16597|0.15139	2.33|2.45	2.49|2.49	2.49|2.49	0.30216|0.30216	.|.	.|.	.|.	.|.	.|.	T|T	0.11153|0.11153	0.0272|0.0272	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	1|1	.|B	.|0.21452	.|0.056	.|B	.|0.17979	.|0.02	T|T	0.26155|0.26155	-1.0111|-1.0111	6|8	.|.	.|.	.|.	.|.	6.8863|6.8863	0.24202|0.24202	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|110	.|Q8IZS7	.|CLCL1_HUMAN	C|L	62|110	ENSP00000438981:F62C|ENSP00000331766:F110L	.|.	F|F	-|-	2|3	0|2	CLECL1|CLECL1	9766663|9766663	0.001000|0.001000	0.12720|0.12720	0.001000|0.001000	0.08648|0.08648	0.003000|0.003000	0.03518|0.03518	0.889000|0.889000	0.28282|0.28282	1.389000|1.389000	0.46526|0.46526	0.486000|0.486000	0.48141|0.48141	TTT|TTT	.	.	.	none		0.328	CLECL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399815.1	NM_172004		C	9875396	A	C	9875396	3	2	108	1	0	0	0	0	1	0	0	0	3525	11	1	5	177	5	CLECL1	12	9875396	Missense_Mutation	SNP	A	TCGA-B9-A8YH-01A-11D-A36X-10		9875396	123976499	64	6904											
OVCH1	341350	hgsc.bcm.edu	37	chr12	29639178	29639178	+	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	0	0	0	0	0	0	0	0	0	0	cttctctaattagaaccacaCataccctttcctctctggct	9	14	3	15	0	2	1	0	0	2	1	5	1	3	1	3	1	2	1	3	1	4	5			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr12:29639178C>A	ENST00000318184.5	-	8	995		c.e8+1		OVCH1-AS1_ENST00000551108.1_Intron|OVCH1-AS1_ENST00000549411.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1							extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.?(1)		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)					TAGAACCACACATACCCTTTC	0.428																																					.		Atlas-SNP	.											OVCH1,NS,carcinoma,0,1	OVCH1	195	.	1	Unknown(1)	lung(1)	c.995+1G>T						PASS	.						93	88	89					12																	29639178		1849	4098	5947	SO:0001630	splice_region_variant	341350	exon9			ACCACACATACCC	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.995+1G>T	chr12.hg19:g.29639178C>A		107.0	0.0	.		128.0	72.0	.	NM_183378		Splice_Site	SNP	ENST00000318184.5	hg19		.	.	.	.	.	.	.	.	.	.	C	3.919	-0.018587	0.07681	.	.	ENSG00000187950	ENST00000318184	.	.	.	1.94	1.02	0.19986	.	.	.	.	.	.	.	.	.	.	.	0.20196	N	0.999927	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.2497	0.10689	0.0:0.7911:0.0:0.2089	.	.	.	.	.	-1	.	.	.	-	.	.	OVCH1	29530445	0.000000	0.05858	0.001000	0.08648	0.024000	0.10985	0.230000	0.17852	0.359000	0.24239	0.563000	0.77884	.	.	.	.	none		0.428	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378	Intron	A	29639178	C	A	29639178	5	1	108	1	0	0	0	0	0	0	1	0	11330	492	17	4	2492	4	OVCH1	12	29639178	Splice_Site	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10	19763782	29639178	104212717	65	6905											
IPO8	10526	hgsc.bcm.edu	37	chr12	30834737	30834737	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttatgatggcacggagacacAttgttaattggactctacaa	13	12	9	7	1	1	2	0	1	1	1	1	4	1	3	0	3	1	2	0	3	4	5			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr12:30834737A>G	ENST00000256079.4	-	4	676	c.338T>C	c.(337-339)aTg>aCg	p.M113T		NM_006390.3	NP_006381.2	O15397	IPO8_HUMAN	importin 8	113					intracellular protein transport (GO:0006886)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	Ran GTPase binding (GO:0008536)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(16)|liver(1)|lung(22)|prostate(2)|skin(2)|urinary_tract(2)	52	all_lung(12;6.66e-10)|Lung NSC(12;4.84e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					ACGGAGACACATTGTTAATTG	0.373																																					p.M113T		Atlas-SNP	.											.	IPO8	105	.	0			c.T338C						PASS	.						68	65	66					12																	30834737		2201	4300	6501	SO:0001583	missense	10526	exon4			AGACACATTGTTA	U77494	CCDS8719.1, CCDS53773.1	12p11.21	2011-05-23	2003-03-11	2003-03-14	ENSG00000133704	ENSG00000133704		"Importins"	9853	protein-coding gene	gene with protein product		605600	"RAN binding protein 8"	RANBP8		9214382	Standard	NM_006390		Approved	IMP8	uc001rjd.3	O15397	OTTHUMG00000169172	ENST00000256079.4:c.338T>C	chr12.hg19:g.30834737A>G	ENSP00000256079:p.Met113Thr	133.0	0.0	.		149.0	50.0	.	NM_006390	B7Z7M3	Missense_Mutation	SNP	ENST00000256079.4	hg19	CCDS8719.1	.	.	.	.	.	.	.	.	.	.	A	5.572	0.290340	0.10567	.	.	ENSG00000133704	ENST00000256079;ENST00000535989	T;T	0.65732	-0.17;-0.17	5.13	5.13	0.70059	Armadillo-like helical (1);Armadillo-type fold (1);	0.161352	0.56097	D	0.000023	T	0.44414	0.1292	N	0.13043	0.29	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.33803	-0.9854	10	0.17832	T	0.49	-28.9758	15.0801	0.72108	1.0:0.0:0.0:0.0	.	113	O15397	IPO8_HUMAN	T	113;51	ENSP00000256079:M113T;ENSP00000440979:M51T	ENSP00000256079:M113T	M	-	2	0	IPO8	30726004	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.504000	0.53347	2.157000	0.67596	0.482000	0.46254	ATG	.	.	.	none		0.373	IPO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402700.2	NM_006390		G	30834737	A	G	30834737	3	3	108	1	0	0	0	0	1	0	0	0	7805	217	8	3	2863	3	IPO8	12	30834737	Missense_Mutation	SNP	A	TCGA-B9-A8YH-01A-11D-A36X-10	1195559	30834737	103017158	66	6906											
NXPH4	11247	hgsc.bcm.edu	37	chr12	57619121	57619121	+	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	ctggctgcccgggcctgtccCccaccctctgcagtctacgc	3	8	10	20	2	2	0	0	0	2	0	3	0	3	0	5	2	3	2	5	2	1	1			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr12:57619121C>A	ENST00000349394.5	+	2	693	c.518C>A	c.(517-519)cCc>cAc	p.P173H	NXPH4_ENST00000555154.1_3'UTR|Y_RNA_ENST00000365197.1_RNA	NM_007224.3	NP_009155.1	O95158	NXPH4_HUMAN	neurexophilin 4	173	IV (linker domain).				neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)	10						GGGCCTGTCCCCCACCCTCTG	0.716																																					p.P173H		Atlas-SNP	.											.	NXPH4	40	.	0			c.C518A						PASS	.						53	59	57					12																	57619121		2203	4300	6503	SO:0001583	missense	11247	exon2			CTGTCCCCCACCC	AF043469	CCDS8933.1	12q13.3	2014-09-04			ENSG00000182379	ENSG00000182379			8078	protein-coding gene	gene with protein product		604637				9570794	Standard	NM_007224		Approved	NPH4	uc009zpj.4	O95158	OTTHUMG00000171241	ENST00000349394.5:c.518C>A	chr12.hg19:g.57619121C>A	ENSP00000333593:p.Pro173His	36.0	0.0	.		73.0	40.0	.	NM_007224	A8K4I4|Q7Z6L3|Q8N462	Missense_Mutation	SNP	ENST00000349394.5	hg19	CCDS8933.1	.	.	.	.	.	.	.	.	.	.	C	12.17	1.857001	0.32791	.	.	ENSG00000182379	ENST00000349394	.	.	.	4.27	4.27	0.50696	.	0.218561	0.23194	N	0.050870	T	0.14657	0.0354	N	0.08118	0	0.23449	N	0.997656	P	0.40000	0.698	B	0.37091	0.241	T	0.07868	-1.0750	9	0.49607	T	0.09	-11.004	7.9642	0.30089	0.0:0.8893:0.0:0.1107	.	173	O95158	NXPH4_HUMAN	H	173	.	ENSP00000333593:P173H	P	+	2	0	NXPH4	55905388	0.851000	0.29673	0.999000	0.59377	0.608000	0.37181	1.983000	0.40648	2.211000	0.71520	0.462000	0.41574	CCC	.	.	.	none		0.716	NXPH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412474.1	NM_007224		A	57619121	C	A	57619121	3	1	108	1	0	0	0	0	1	0	0	0	10800	623	22	4	524	4	NXPH4	12	57619121	Missense_Mutation	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10	26784384	57619121	76232774	67	6907											
SLITRK1	114798	hgsc.bcm.edu	37	chr13	84453695	84453695	+	Missense_Mutation	SNP	T	T	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	ggagttggcatctcgtctctTggaccgctttcggttcctca	4	14	11	12	3	3	0	1	0	2	0	7	2	4	2	2	4	0	4	2	4	0	4			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr13:84453695T>G	ENST00000377084.2	-	1	2833	c.1948A>C	c.(1948-1950)Aag>Cag	p.K650Q		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	650					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)		TCTCGTCTCTTGGACCGCTTT	0.567																																					p.K650Q		Atlas-SNP	.											.	SLITRK1	196	.	0			c.A1948C						PASS	.						82	69	74					13																	84453695		2203	4300	6503	SO:0001583	missense	114798	exon1			GTCTCTTGGACCG	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.1948A>C	chr13.hg19:g.84453695T>G	ENSP00000366288:p.Lys650Gln	115.0	0.0	.		109.0	36.0	.	NM_052910	Q5U5I6|Q96SF9	Missense_Mutation	SNP	ENST00000377084.2	hg19	CCDS9464.1	.	.	.	.	.	.	.	.	.	.	T	13.86	2.363605	0.41902	.	.	ENSG00000178235	ENST00000377084	T	0.56776	0.44	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.31827	0.0809	N	0.08118	0	0.54753	D	0.99998	B	0.21520	0.057	B	0.27715	0.082	T	0.15235	-1.0444	10	0.09843	T	0.71	-15.9777	13.9372	0.64032	0.0:0.0:0.0:1.0	.	650	Q96PX8	SLIK1_HUMAN	Q	650	ENSP00000366288:K650Q	ENSP00000366288:K650Q	K	-	1	0	SLITRK1	83351696	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.085000	0.71343	2.225000	0.72522	0.533000	0.62120	AAG	.	.	.	none		0.567	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910		G	84453695	T	G	84453695	3	3	108	1	0	0	0	0	1	0	0	0	14755	1821	63	5	146	5	SLITRK1	13	84453695	Missense_Mutation	SNP	T	TCGA-B9-A8YH-01A-11D-A36X-10		84453695	30716183	68	6908											
EAPP	55837	hgsc.bcm.edu	37	chr14	35002688	35002688	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cggaatcagaatcaaaatatAtatcatcgtagtaccttgtc	15	12	6	8	2	3	1	3	0	0	1	5	2	3	2	1	1	1	2	1	1	9	6			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr14:35002688A>G	ENST00000250454.3	-	3	395	c.314T>C	c.(313-315)aTa>aCa	p.I105T		NM_018453.3	NP_060923.2	Q56P03	EAPP_HUMAN	E2F-associated phosphoprotein	105					negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|urinary_tract(2)	12	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00342)|Epithelial(34;0.18)	GBM - Glioblastoma multiforme(112;0.0196)		ATCAAAATATATATCATCGTA	0.338																																					p.I105T		Atlas-SNP	.											.	EAPP	28	.	0			c.T314C						PASS	.						139	129	132					14																	35002688		1853	4090	5943	SO:0001583	missense	55837	exon3			AAATATATATCAT	AF217512	CCDS41941.1	14q13	2007-03-26	2007-03-26	2007-03-26		ENSG00000129518			19312	protein-coding gene	gene with protein product		609486	"chromosome 14 open reading frame 11"	C14orf11		15716352	Standard	NM_018453		Approved	BM036, FLJ20578	uc001wsd.1	Q56P03		ENST00000250454.3:c.314T>C	chr14.hg19:g.35002688A>G	ENSP00000250454:p.Ile105Thr	99.0	0.0	.		106.0	49.0	.	NM_018453	Q9BVF4|Q9NWV5|Q9NZ86	Missense_Mutation	SNP	ENST00000250454.3	hg19	CCDS41941.1	.	.	.	.	.	.	.	.	.	.	A	16.06	3.015726	0.54468	.	.	ENSG00000129518	ENST00000250454;ENST00000554792	T;T	0.46063	0.89;0.88	5.54	5.54	0.83059	.	0.316524	0.38663	N	0.001606	T	0.44993	0.1320	M	0.70275	2.135	0.46203	D	0.998921	P	0.36753	0.568	B	0.34991	0.193	T	0.48422	-0.9037	10	0.49607	T	0.09	-4.4801	15.9956	0.80237	1.0:0.0:0.0:0.0	.	105	Q56P03	EAPP_HUMAN	T	105;84	ENSP00000250454:I105T;ENSP00000450908:I84T	ENSP00000250454:I105T	I	-	2	0	EAPP	34072439	1.000000	0.71417	0.998000	0.56505	0.937000	0.57800	5.183000	0.65065	2.248000	0.74166	0.533000	0.62120	ATA	.	.	.	none		0.338	EAPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409847.1	NM_018453		G	35002688	A	G	35002688	3	3	108	1	0	0	0	0	1	0	0	0	4879	449	16	3	559	3	EAPP	14	35002688	Missense_Mutation	SNP	A	TCGA-B9-A8YH-01A-11D-A36X-10		35002688	72346852	69	6909											
STYX	6815	hgsc.bcm.edu	37	chr14	53224474	53224474	+	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	0	0	0	0	0	0	0	0	0	ttttcaggaaaagttcttgtGcatggaaatgcagggatctc	11	13	11	6	0	3	0	1	0	2	0	4	3	3	3	0	3	2	3	0	3	3	4			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr14:53224474G>C	ENST00000354586.4	+	7	647	c.354G>C	c.(352-354)gtG>gtC	p.V118V	STYX_ENST00000442123.2_Silent_p.V118V|STYX_ENST00000556861.1_Intron	NM_145251.3	NP_660294.1	Q8WUJ0	STYX_HUMAN	serine/threonine/tyrosine interacting protein	118	Tyrosine-protein phosphatase.				MAPK export from nucleus (GO:0045204)|protein dephosphorylation (GO:0006470)|regulation of ERK1 and ERK2 cascade (GO:0070372)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5	Breast(41;0.176)					AAGTTCTTGTGCATGGAAATG	0.313																																					p.V118V		Atlas-SNP	.											.	STYX	14	.	0			c.G354C						PASS	.						70	75	73					14																	53224474		2203	4295	6498	SO:0001819	synonymous_variant	6815	exon8			TCTTGTGCATGGA		CCDS9711.1	14q22.1	2011-06-09	2001-11-29		ENSG00000198252	ENSG00000198252		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	11447	protein-coding gene	gene with protein product		615814	"serine/threonine/tyrosine-interacting protein"			7592916	Standard	NM_145251		Approved		uc010tqy.2	Q8WUJ0	OTTHUMG00000140306	ENST00000354586.4:c.354G>C	chr14.hg19:g.53224474G>C		75.0	0.0	.		72.0	22.0	.	NM_001130701	B9EJG0|Q99850	Silent	SNP	ENST00000354586.4	hg19	CCDS9711.1																																																																																			.	.	.	none		0.313	STYX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276902.1	NM_145251		C	53224474	G	C	53224474	2	2	108	1	0	0	0	0	0	0	0	1	15372	1306	46	4		4	STYX	14	53224474	Silent	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10	18221786	53224474	54125066	70	6910											
SERPINA12	145264	hgsc.bcm.edu	37	chr14	94956103	94956103	+	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	gggtacagacacgtctacgaCcctggggaattgacacgaca	12	6	12	11	3	1	2	0	1	1	1	1	5	1	3	1	3	2	1	1	3	3	3			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr14:94956103C>G	ENST00000341228.2	-	5	1702	c.907G>C	c.(907-909)Gtc>Ctc	p.V303L	SERPINA12_ENST00000556881.1_Splice_Site_p.V303L	NM_173850.2	NP_776249.1	Q8IW75	SPA12_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12	303					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	33				COAD - Colon adenocarcinoma(157;0.235)		ACGTCTACGACCCTGGGGAAT	0.522																																					p.V303L		Atlas-SNP	.											.	SERPINA12	93	.	0			c.G907C						PASS	.						115	91	99					14																	94956103		2203	4300	6503	SO:0001630	splice_region_variant	145264	exon5			CTACGACCCTGGG	AY177692	CCDS9926.1	14q32.13	2014-02-21	2005-08-18		ENSG00000165953	ENSG00000165953		"Serine (or cysteine) peptidase inhibitors"	18359	protein-coding gene	gene with protein product			"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 12"			24172014	Standard	NM_173850		Approved	OL-64, Vaspin	uc001ydj.3	Q8IW75	OTTHUMG00000171349	ENST00000341228.2:c.906-1G>C	chr14.hg19:g.94956103C>G		106.0	0.0	.		101.0	43.0	.	NM_173850		Missense_Mutation	SNP	ENST00000341228.2	hg19	CCDS9926.1	.	.	.	.	.	.	.	.	.	.	C	6.845	0.525180	0.13066	.	.	ENSG00000165953	ENST00000556881;ENST00000341228	D;D	0.84070	-1.8;-1.8	5.14	2.95	0.34219	Serpin domain (3);	0.253832	0.27759	N	0.017975	T	0.64724	0.2624	N	0.16066	0.365	0.09310	N	0.999995	B	0.11235	0.004	B	0.04013	0.001	T	0.49428	-0.8941	10	0.26408	T	0.33	.	5.9952	0.19489	0.4795:0.4268:0.0:0.0937	.	303	Q8IW75	SPA12_HUMAN	L	303	ENSP00000451738:V303L;ENSP00000342109:V303L	ENSP00000342109:V303L	V	-	1	0	SERPINA12	94025856	0.000000	0.05858	0.980000	0.43619	0.176000	0.22953	0.069000	0.14552	1.251000	0.43983	0.462000	0.41574	GTC	.	.	.	none		0.522	SERPINA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413097.1	NM_173850	Missense_Mutation	G	94956103	C	G	94956103	5	3	108	1	0	0	0	0	0	0	1	0	14102	521	18	4	345	4	SERPINA12	14	94956103	Splice_Site	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10	41731629	94956103	12393437	71	6911											
GCNT3	9245	hgsc.bcm.edu	37	chr15	59911624	59911624	+	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	tatctgcgtttatggggctgGggacttgaattggatgcttc	6	15	14	6	1	1	1	0	1	1	0	2	3	1	3	0	5	2	3	0	5	3	6			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr15:59911624G>A	ENST00000396065.1	+	3	1635	c.1187G>A	c.(1186-1188)gGg>gAg	p.G396E	GCNT3_ENST00000560585.1_Missense_Mutation_p.G396E	NM_004751.2	NP_004742.1	O95395	GCNT3_HUMAN	glucosaminyl (N-acetyl) transferase 3, mucin type	396					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|immunoglobulin production in mucosal tissue (GO:0002426)|intestinal absorption (GO:0050892)|kidney morphogenesis (GO:0060993)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|tissue morphogenesis (GO:0048729)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0047225)|beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TATGGGGCTGGGGACTTGAAT	0.498																																					p.G396E		Atlas-SNP	.											.	GCNT3	42	.	0			c.G1187A						PASS	.						143	138	139					15																	59911624		2190	4290	6480	SO:0001583	missense	9245	exon3			GGGCTGGGGACTT	AF102542	CCDS10172.1	15q22	2013-02-25			ENSG00000140297	ENSG00000140297	2.4.1.102, 2.4.1.150	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	4205	protein-coding gene	gene with protein product		606836				9915862, 9988682	Standard	NM_004751		Approved	C2GnT-M, C2/4GnT, C2GnT2	uc002age.3	O95395	OTTHUMG00000132726	ENST00000396065.1:c.1187G>A	chr15.hg19:g.59911624G>A	ENSP00000379377:p.Gly396Glu	103.0	0.0	.		75.0	28.0	.	NM_004751		Missense_Mutation	SNP	ENST00000396065.1	hg19	CCDS10172.1	.	.	.	.	.	.	.	.	.	.	G	15.55	2.866696	0.51588	.	.	ENSG00000140297	ENST00000396065	T	0.08370	3.1	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.35128	0.0921	M	0.89287	3.02	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.27502	-1.0072	10	0.21540	T	0.41	.	18.8129	0.92065	0.0:0.0:1.0:0.0	.	396	O95395	GCNT3_HUMAN	E	396	ENSP00000379377:G396E	ENSP00000379377:G396E	G	+	2	0	GCNT3	57698916	1.000000	0.71417	0.975000	0.42487	0.267000	0.26476	6.753000	0.74904	2.437000	0.82529	0.655000	0.94253	GGG	.	.	.	none		0.498	GCNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256068.1	NM_004751		A	59911624	G	A	59911624	3	1	108	1	0	0	0	0	1	0	0	0	6309	1232	43	2	1189	2	GCNT3	15	59911624	Missense_Mutation	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10		59911624	42619768	72	6912											
ALDH1A3	220	hgsc.bcm.edu	37	chr15	101438391	101438391	+	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	0	0	0	0	0	0	0	0	0	cgtgtgtgcggacgctgactGtgagtctctgccctcctggg	3	11	15	12	3	1	2	0	2	1	0	3	3	2	3	2	2	2	1	2	2	0	0			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr15:101438391G>C	ENST00000329841.5	+	8	1415		c.e8+1		RP11-66B24.4_ENST00000560351.1_RNA|ALDH1A3_ENST00000346623.6_Splice_Site	NM_000693.2	NP_000684.2	P47895	AL1A3_HUMAN	aldehyde dehydrogenase 1 family, member A3						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)	GACGCTGACTGTGAGTCTCTG	0.572																																					.		Atlas-SNP	.											.	ALDH1A3	61	.	0			c.883+1G>C						PASS	.						51	50	51					15																	101438391		2203	4300	6503	SO:0001630	splice_region_variant	220	exon8			CTGACTGTGAGTC	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.883+1G>C	chr15.hg19:g.101438391G>C		116.0	0.0	.		103.0	46.0	.	NM_000693	Q6NT64	Splice_Site	SNP	ENST00000329841.5	hg19	CCDS10389.1	.	.	.	.	.	.	.	.	.	.	G	12.98	2.101857	0.37048	.	.	ENSG00000184254	ENST00000329841;ENST00000346623	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4533	0.94876	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ALDH1A3	99255914	1.000000	0.71417	0.967000	0.41034	0.080000	0.17528	9.338000	0.96553	2.604000	0.88044	0.555000	0.69702	.	.	.	.	none		0.572	ALDH1A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313620.2		Intron	C	101438391	G	C	101438391	5	2	108	1	0	0	0	0	0	0	1	0	492	1391	48	4	914	4	ALDH1A3	15	101438391	Splice_Site	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10	41526767	101438391	1093001	73	6913											
CLN3	1201	hgsc.bcm.edu	37	chr16	28495396	28495396	+	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	gctctctgcttcttcttcccCtccagggtcctgggcctcag	2	13	9	17	0	4	0	1	0	3	0	8	0	7	0	5	2	1	2	5	2	0	3			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr16:28495396C>A	ENST00000569430.1	-	11	1540	c.721G>T	c.(721-723)Ggg>Tgg	p.G241W	CLN3_ENST00000568224.1_Missense_Mutation_p.G163W|CLN3_ENST00000333496.9_Missense_Mutation_p.G217W|CLN3_ENST00000395653.4_Missense_Mutation_p.G141W|CLN3_ENST00000354630.5_Missense_Mutation_p.G241W|CLN3_ENST00000565316.1_Missense_Mutation_p.G241W|CLN3_ENST00000535392.1_Missense_Mutation_p.G163W|CLN3_ENST00000359984.7_Missense_Mutation_p.G241W|CLN3_ENST00000357857.9_Missense_Mutation_p.G187W|CLN3_ENST00000357076.5_Intron|CLN3_ENST00000357806.7_Missense_Mutation_p.G142W|CLN3_ENST00000360019.2_Missense_Mutation_p.G241W|CLN3_ENST00000355477.5_Missense_Mutation_p.G193W|CLN3_ENST00000567963.1_Missense_Mutation_p.G241W			Q13286	CLN3_HUMAN	ceroid-lipofuscinosis, neuronal 3	241					action potential (GO:0001508)|amyloid precursor protein catabolic process (GO:0042987)|arginine transport (GO:0015809)|associative learning (GO:0008306)|autophagic vacuole fusion (GO:0000046)|cell death (GO:0008219)|cellular amino acid metabolic process (GO:0006520)|ceramide metabolic process (GO:0006672)|cytosolic calcium ion homeostasis (GO:0051480)|galactosylceramide metabolic process (GO:0006681)|globoside metabolic process (GO:0001575)|glucosylceramide metabolic process (GO:0006678)|ionotropic glutamate receptor signaling pathway (GO:0035235)|lysosomal lumen acidification (GO:0007042)|lysosomal lumen pH elevation (GO:0035752)|lysosome organization (GO:0007040)|macroautophagy (GO:0016236)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of macroautophagy (GO:0016242)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of proteolysis (GO:0045861)|neuromuscular process controlling balance (GO:0050885)|neurotransmitter metabolic process (GO:0042133)|protein catabolic process (GO:0030163)|protein processing (GO:0016485)|receptor-mediated endocytosis (GO:0006898)|sphingomyelin metabolic process (GO:0006684)|vacuolar transport (GO:0007034)|vesicle transport along microtubule (GO:0047496)	autophagic vacuole (GO:0005776)|caveola (GO:0005901)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|trans-Golgi network (GO:0005802)	unfolded protein binding (GO:0051082)			breast(1)|large_intestine(2)|lung(11)|upper_aerodigestive_tract(1)	15						TCTTCTTCCCCTCCAGGGTCC	0.592																																					p.G241W		Atlas-SNP	.											.	CLN3	33	.	0			c.G721T						PASS	.						44	42	42					16																	28495396		2197	4300	6497	SO:0001583	missense	1201	exon10			CTTCCCCTCCAGG	U32680	CCDS10632.1, CCDS73852.1, CCDS73853.1, CCDS73854.1, CCDS73855.1	16p12	2014-09-17	2008-07-29		ENSG00000188603	ENSG00000188603			2074	protein-coding gene	gene with protein product	"juvenile neuronal ceroid lipofuscinosis"	607042	"Batten, Spielmeyer-Vogt disease"	BTS		18317235	Standard	NM_001042432		Approved	JNCL	uc002dpp.3	Q13286	OTTHUMG00000097024	ENST00000569430.1:c.721G>T	chr16.hg19:g.28495396C>A	ENSP00000454229:p.Gly241Trp	58.0	0.0	.		63.0	33.0	.	NM_001042432	B2R7J1|O00668|O95089|Q549S9|Q9UP09|Q9UP11|Q9UP12|Q9UP13|Q9UP14	Missense_Mutation	SNP	ENST00000569430.1	hg19	CCDS10632.1	.	.	.	.	.	.	.	.	.	.	C	18.96	3.733284	0.69189	.	.	ENSG00000188603	ENST00000535392;ENST00000359984;ENST00000360019;ENST00000354630;ENST00000355477;ENST00000357857;ENST00000333496;ENST00000395653;ENST00000357806	D;D;D;D;D;D;D;D	0.96774	-4.12;-4.12;-4.12;-4.12;-4.12;-4.12;-4.12;-4.12	5.28	1.8	0.24995	Major facilitator superfamily domain, general substrate transporter (1);	0.386796	0.29212	N	0.012803	D	0.97222	0.9092	M	0.76838	2.35	0.58432	D	0.999991	D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.999;0.98;0.99;0.995;0.998;0.999;0.998;0.992;0.998;0.98;0.99;0.991;1.0	D;P;P;P;D;D;D;P;P;P;P;P;D	0.77557	0.975;0.796;0.708;0.839;0.954;0.98;0.964;0.792;0.907;0.796;0.694;0.855;0.99	D	0.96088	0.9059	10	0.87932	D	0	-3.7144	7.6992	0.28613	0.0:0.6916:0.0:0.3083	.	141;217;241;241;292;88;118;139;141;187;193;241;142	B4DFT5;B4DXL3;Q13286-3;Q13286-4;B4DIA8;O95093;O95090;O95086;B4DMY6;B4DFF3;Q13286-2;Q13286;O95089	.;.;.;.;.;.;.;.;.;.;.;CLN3_HUMAN;.	W	163;241;241;241;193;187;118;141;142	ENSP00000443221:G163W;ENSP00000353073:G241W;ENSP00000353116:G241W;ENSP00000346650:G241W;ENSP00000347660:G193W;ENSP00000350523:G187W;ENSP00000379014:G141W;ENSP00000350457:G142W	ENSP00000329171:G118W	G	-	1	0	CLN3	28402897	0.974000	0.33945	0.993000	0.49108	0.918000	0.54935	0.778000	0.26732	0.626000	0.30322	0.556000	0.70494	GGG	.	.	.	none		0.592	CLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214115.2			A	28495396	C	A	28495396	3	1	108	1	0	0	0	0	1	0	0	0	3545	681	24	4	623	4	CLN3	16	28495396	Missense_Mutation	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10		28495396	61859357	74	6914											
SHPK	23729	hgsc.bcm.edu	37	chr17	3539502	3539525	+	Start_Codon_Del	DEL	CCGCGCAGCCATTATCTCCCTGAC	CCGCGCAGCCATTATCTCCCTGAC	-																															tcaatgccgagggtgatcggCcgcgcagccattatctccct																								rs190457036|rs367944958|rs201343679	byFrequency	TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	CCGCGCAGCCATTATCTCCCTGAC	CCGCGCAGCCATTATCTCCCTGAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr17:3539502_3539525delCCGCGCAGCCATTATCTCCCTGAC	ENST00000225519.3	-	0	91_114				CTNS_ENST00000399306.2_5'Flank|CTNS_ENST00000046640.3_5'Flank|CTNS_ENST00000381870.3_5'Flank|CTNS_ENST00000414524.2_5'Flank|CTNS_ENST00000441220.2_5'Flank	NM_013276.2	NP_037408	Q9UHJ6	SHPK_HUMAN	sedoheptulokinase						carbohydrate metabolic process (GO:0005975)|cellular response to interleukin-13 (GO:0035963)|cellular response to interleukin-4 (GO:0071353)|cellular response to lipopolysaccharide (GO:0071222)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|phosphorylation (GO:0016310)|regulation of inflammatory response (GO:0050727)|regulation of macrophage activation (GO:0043030)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|sedoheptulokinase activity (GO:0050277)	p.A2V(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				COAD - Colon adenocarcinoma(5;0.0828)		GGGTGATCGGCCGCGCAGCCATTATCTCCCTGACCCGCGCAGCT	0.692																																					.		Atlas-Indel,Pindel	.											.	SHPK	34	.	1	Substitution - Missense(1)	lung(1)	.						PASS	.																																			SO:0001582	initiator_codon_variant	23729	wholegene			.	AF163573	CCDS11030.1	17p13	2008-02-08	2008-02-08	2008-02-08	ENSG00000197417	ENSG00000197417	2.7.1.14		1492	protein-coding gene	gene with protein product		605060	"carbohydrate kinase-like"	CARKL		10673275, 18186520	Standard	NM_013276		Approved	SHK	uc002fvz.1	Q9UHJ6	OTTHUMG00000090694		chr17.hg19:g.3539502_3539525delCCGCGCAGCCATTATCTCCCTGAC		139.0	0.0	0		184.0	14.0	0.076087	NM_013276	B2R640|Q8WUH3	Frame_Shift_Del	DEL	ENST00000225519.3	hg19	CCDS11030.1																																																																																			.	.	.	none		0.692	SHPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207378.2			-	3539525	CCGCGCAGCCATTATCTCCCTGAC	-	3539502	7	5	108	1	0	1	0	1	0	0	0	0	14303	726	26	0	1452	0	SHPK	17	3539502	Start_Codon_Del	DEL	CCGCGCAGCCATTATCTCCCTGAC	TCGA-B9-A8YH-01A-11D-A36X-10		3539502	77655708	75	6915											
DERL2	51009	hgsc.bcm.edu	37	chr17	5389469	5389469	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggtactccagccgcaagcTctggtacgccatcttcccca	8	8	8	17	2	2	0	0	0	2	0	4	0	4	0	5	2	4	4	5	2	3	3			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr17:5389469T>C	ENST00000158771.4	-	1	68	c.13A>G	c.(13-15)Agc>Ggc	p.S5G	MIS12_ENST00000381165.3_5'Flank|DERL2_ENST00000570848.1_Missense_Mutation_p.S5G|DERL2_ENST00000572834.1_Missense_Mutation_p.S5G|DERL2_ENST00000571968.1_Intron|MIS12_ENST00000573759.1_5'Flank	NM_016041.3	NP_057125.2	Q9GZP9	DERL2_HUMAN	derlin 2	5					endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|retrograde protein transport, ER to cytosol (GO:0030970)|suckling behavior (GO:0001967)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|late endosome (GO:0005770)|membrane (GO:0016020)				large_intestine(3)	3						AGCCGCAAGCTCTGGTACGCC	0.721																																					p.S5G		Atlas-SNP	.											.	DERL2	15	.	0			c.A13G						PASS	.						31	26	28					17																	5389469		2196	4291	6487	SO:0001583	missense	51009	exon1			GCAAGCTCTGGTA	BC010890	CCDS11073.1	17p13.2	2012-02-01	2012-02-01		ENSG00000072849	ENSG00000072849			17943	protein-coding gene	gene with protein product		610304	"Der1-like domain family, member 2"			10810093, 11500051	Standard	NM_016041		Approved	F-LAN-1, FLANa, F-LANa, CGI-101, derlin-2	uc002gcc.1	Q9GZP9	OTTHUMG00000102040	ENST00000158771.4:c.13A>G	chr17.hg19:g.5389469T>C	ENSP00000158771:p.Ser5Gly	228.0	0.0	.		295.0	71.0	.	NM_016041	Q9Y3A7	Missense_Mutation	SNP	ENST00000158771.4	hg19	CCDS11073.1	.	.	.	.	.	.	.	.	.	.	T	17.02	3.280895	0.59758	.	.	ENSG00000072849	ENST00000158771	T	0.23348	1.91	6.17	6.17	0.99709	.	0.047139	0.85682	D	0.000000	T	0.17066	0.0410	N	0.16708	0.43	0.48452	D	0.999658	B	0.02656	0.0	B	0.01281	0.0	T	0.11690	-1.0577	10	0.13853	T	0.58	-0.348	16.0034	0.80327	0.0:0.0:0.0:1.0	.	5	Q9GZP9	DERL2_HUMAN	G	5	ENSP00000158771:S5G	ENSP00000158771:S5G	S	-	1	0	DERL2	5330193	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.541000	0.60670	2.371000	0.80710	0.533000	0.62120	AGC	.	.	.	none		0.721	DERL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219825.1	NM_016041		C	5389469	T	C	5389469	3	2	108	1	0	0	0	0	1	0	0	0	4449	1551	54	3	734	3	DERL2	17	5389469	Missense_Mutation	SNP	T	TCGA-B9-A8YH-01A-11D-A36X-10	1849967	5389469	75805741	76	6916											
EVPLL	645027	hgsc.bcm.edu	37	chr17	18286356	18286356	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagggcggcgtcgtggcgCgggcagagcctgggcagcct	5	4	20	12	5	0	2	0	0	0	2	1	2	0	2	2	5	2	2	2	5	0	0			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr17:18286356C>T	ENST00000399134.4	+	7	887	c.529C>T	c.(529-531)Cgg>Tgg	p.R177W	RP1-37N7.1_ENST00000579352.1_RNA	NM_001145127.1	NP_001138599.1	A8MZ36	EVPLL_HUMAN	envoplakin-like	177										NS(1)|endometrium(1)|large_intestine(1)|lung(2)	5						CGTCGTGGCGCGGGCAGAGCC	0.706																																					p.R177W		Atlas-SNP	.											.	EVPLL	10	.	0			c.C529T						PASS	.						5	8	7					17																	18286356		666	1537	2203	SO:0001583	missense	645027	exon7			GTGGCGCGGGCAG		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.529C>T	chr17.hg19:g.18286356C>T	ENSP00000382086:p.Arg177Trp	39.0	0.0	.		60.0	15.0	.	NM_001145127	B4DPD4	Missense_Mutation	SNP	ENST00000399134.4	hg19	CCDS45626.1	.	.	.	.	.	.	.	.	.	.	.	14.63	2.591371	0.46214	.	.	ENSG00000214860	ENST00000399134	T	0.26373	1.74	0.505	0.505	0.16953	.	.	.	.	.	T	0.13200	0.0320	N	0.19112	0.55	0.24914	N	0.992025	D	0.67145	0.996	B	0.40982	0.345	T	0.17167	-1.0378	9	0.66056	D	0.02	.	3.564	0.07893	0.4389:0.561:1.0E-4:1.0E-4	.	177	A8MZ36	EVPLL_HUMAN	W	177	ENSP00000382086:R177W	ENSP00000382086:R177W	R	+	1	2	EVPLL	18227081	0.868000	0.29978	0.989000	0.46669	0.453000	0.32348	-0.765000	0.04730	0.554000	0.29061	0.089000	0.15464	CGG	.	.	.	none		0.706	EVPLL-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130836.2	NM_001145127		T	18286356	C	T	18286356	3	4	108	1	0	0	0	0	1	0	0	0	5295	759	27	1	551	1	EVPLL	17	18286356	Missense_Mutation	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10	12896887	18286356	62908854	77	6917											
CRYBA1	1411	hgsc.bcm.edu	37	chr17	27580671	27580672	+	Frame_Shift_Ins	INS	-	-	T																															ttacagaatcataaggagtcINStaagatgaccatctttgaga																										TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr17:27580671_27580672insT	ENST00000225387.3	+	5	372_373	c.371_372insT	c.(370-375)tctaagfs	p.K125fs		NM_005208.4	NP_005199.2	P05813	CRBA1_HUMAN	crystallin, beta A1	125	Beta/gamma crystallin 'Greek key' 3. {ECO:0000255|PROSITE-ProRule:PRU00028}.				lens development in camera-type eye (GO:0002088)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	structural constituent of eye lens (GO:0005212)			breast(1)|large_intestine(2)|lung(1)|prostate(1)	5			BRCA - Breast invasive adenocarcinoma(11;3.3e-05)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551)			CATAAGGAGTCTAAGATGACCA	0.386																																					p.S124fs		Atlas-Indel,Pindel	.											.	CRYBA1	15	.	0			c.371_372insT						PASS	.																																			SO:0001589	frameshift_variant	1411	exon5			.		CCDS11249.1	17q11.2-q12	2008-07-18			ENSG00000108255	ENSG00000108255			2394	protein-coding gene	gene with protein product	"eye lens structural protein"	123610		CRYB1		3745196, 3770741	Standard	NM_005208		Approved		uc002hdw.3	P05813	OTTHUMG00000132729	ENST00000225387.3:c.372dupT	chr17.hg19:g.27580672_27580672dupT	ENSP00000225387:p.Lys125fs	156.0	0.0	0		210.0	126.0	0.6	NM_005208	Q13633|Q14CM9	Frame_Shift_Ins	INS	ENST00000225387.3	hg19	CCDS11249.1																																																																																			.	.	.	none		0.386	CRYBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256071.2	NM_005208		T	27580672	-	T	27580671	7	5	108	1	0	1	1	0	0	0	0	0	3909	913	32	0	389	0	CRYBA1	17	27580671	Frame_Shift_Ins	INS	-	TCGA-B9-A8YH-01A-11D-A36X-10	9294315	27580671	53614539	78	6918											
SLFN11	91607	hgsc.bcm.edu	37	chr17	33679953	33679953	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agggaggccactgcaatccaAgtggctggtctgaaagtaat	12	8	13	8	0	1	1	0	1	1	0	2	2	2	2	2	4	1	3	2	4	4	1			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr17:33679953A>G	ENST00000394566.1	-	7	2400	c.2128T>C	c.(2128-2130)Ttg>Ctg	p.L710L	SLFN11_ENST00000308377.4_Silent_p.L710L	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	710					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)		CTGCAATCCAAGTGGCTGGTC	0.483																																					p.L710L		Atlas-SNP	.											SLFN11,right_upper_lobe,carcinoma,0,1	SLFN11	112	.	0			c.T2128C						PASS	.						115	120	118					17																	33679953		2203	4300	6503	SO:0001819	synonymous_variant	91607	exon5			AATCCAAGTGGCT	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.2128T>C	chr17.hg19:g.33679953A>G		94.0	0.0	.		136.0	46.0	.	NM_152270	E1P643|Q8N3S8|Q8N762|Q8TEE0	Silent	SNP	ENST00000394566.1	hg19	CCDS11294.1																																																																																			.	.	.	none		0.483	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270		G	33679953	A	G	33679953	2	3	108	1	0	0	0	0	0	0	0	1	14746	69	3	3		3	SLFN11	17	33679953	Silent	SNP	A	TCGA-B9-A8YH-01A-11D-A36X-10	6099282	33679953	47515257	79	6919											
TNS4	84951	hgsc.bcm.edu	37	chr17	38634839	38634839	+	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	gccttgaacttacttccgttGctcagggtccataccacaga	9	11	8	13	1	1	2	1	1	0	1	3	2	3	2	4	1	4	2	4	1	3	5			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr17:38634839G>A	ENST00000254051.6	-	11	2130	c.1972C>T	c.(1972-1974)Caa>Taa	p.Q658*		NM_032865.5	NP_116254.4	Q8IZW8	TENS4_HUMAN	tensin 4	658	Phosphatase tensin-type.				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)			TACTTCCGTTGCTCAGGGTCC	0.622																																					p.Q658X		Atlas-SNP	.											.	TNS4	72	.	0			c.C1972T						PASS	.						102	87	92					17																	38634839		2203	4300	6503	SO:0001587	stop_gained	84951	exon11			TCCGTTGCTCAGG	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.1972C>T	chr17.hg19:g.38634839G>A	ENSP00000254051:p.Gln658*	87.0	0.0	.		118.0	46.0	.	NM_032865	A6NMJ7|Q71RB7|Q8WV64|Q96JV4	Nonsense_Mutation	SNP	ENST00000254051.6	hg19	CCDS11368.1	.	.	.	.	.	.	.	.	.	.	G	39	7.830813	0.98513	.	.	ENSG00000131746	ENST00000377816;ENST00000394072;ENST00000254051	.	.	.	5.0	4.02	0.46733	.	0.000000	0.39475	N	0.001345	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-3.8218	7.5698	0.27900	0.0869:0.0:0.7019:0.2112	.	.	.	.	X	658;71;658	.	ENSP00000254051:Q658X	Q	-	1	0	TNS4	35888365	0.997000	0.39634	1.000000	0.80357	0.978000	0.69477	1.654000	0.37334	2.326000	0.78906	0.462000	0.41574	CAA	.	.	.	none		0.622	TNS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257154.3	NM_032865		A	38634839	G	A	38634839	4	1	108	1	0	0	0	0	0	1	0	0	16357	1328	46	2	187	2	TNS4	17	38634839	Nonsense_Mutation	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10	4954886	38634839	42560371	80	6920											
KRTAP4-5	85289	hgsc.bcm.edu	37	chr17	39305773	39305775	+	Missense_Mutation	TNP	TCT	TCT	GGC																															ggtggtcctgcagcaggtggTctggcagcagcaggggcggc																								rs137947981|rs141265645|rs201152898|rs535144703|rs58117746	byFrequency	TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	T|C|T	T|C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr17:39305773_39305775TCT>GGC	ENST00000343246.4	-	1	279_281	c.245_247AGA>GCC	c.(244-249)cAGAcc>cGCCcc	p.82_83QT>RP		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)			cagcaggtggtctggcagcagca	0.655																																					p.T83P|p.Q82H|p.Q82R		Atlas-SNP	.											.|KRTAP4-5,NS,carcinoma,0,1|KRTAP4-5,NS,carcinoma,+1,1	KRTAP4-5	34	.	1	Substitution - Missense(1)	lung(1)	c.A247C|c.G246C|c.A245G						PASS	.																																			SO:0001583	missense	85289	exon1			AGGTGGTCTGGCA|GGTGGTCTGGCAG|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.245_247AGA>GCC	chr17.hg19:g.39305773TCT>GGC	ENSP00000340546:p.Q82_T83delinsRP	56.0|55.0|52.0	0.0	.		84.0|83.0|81.0	32.0|32.0|33.0	.	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	hg19	CCDS32650.1																																																																																			.	.	.	weak		0.655	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1			GGC	39305775	TCT	GGC	39305773	3	3	108	1	0	0	0	0	1	0	0	0	8561	1667	58	5	302	5	KRTAP4-5	17	39305773	Missense_Mutation	TNP	TCT	TCGA-B9-A8YH-01A-11D-A36X-10	670934	39305773	41889437	81	6921											
CHAD	1101	hgsc.bcm.edu	37	chr17	48545565	48545565	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagctggacagctggttccTgtccacgtggaatttggcga	7	11	14	9	2	0	0	0	0	0	0	2	3	2	2	2	4	2	4	2	4	2	3			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr17:48545565T>C	ENST00000508540.1	-	1	762	c.610A>G	c.(610-612)Agg>Ggg	p.R204G	ACSF2_ENST00000502667.1_Intron|ACSF2_ENST00000504392.1_Intron|ACSF2_ENST00000300441.4_Intron|ACSF2_ENST00000541920.1_Intron|CHAD_ENST00000258969.4_Missense_Mutation_p.R204G|ACSF2_ENST00000427954.2_Intron	NM_001267.2	NP_001258.2	O15335	CHAD_HUMAN	chondroadherin	204					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)			AGCTGGTTCCTGTCCACGTGG	0.622																																					p.R204G		Atlas-SNP	.											.	CHAD	36	.	0			c.A610G						PASS	.						89	92	91					17																	48545565		2203	4300	6503	SO:0001583	missense	1101	exon1			GGTTCCTGTCCAC	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.610A>G	chr17.hg19:g.48545565T>C	ENSP00000423812:p.Arg204Gly	88.0	0.0	.		131.0	33.0	.	NM_001267	A8K812|Q6GTU0|Q96RJ5	Missense_Mutation	SNP	ENST00000508540.1	hg19	CCDS11568.1	.	.	.	.	.	.	.	.	.	.	T	9.910	1.209334	0.22205	.	.	ENSG00000136457	ENST00000508540;ENST00000258969	T;T	0.57107	0.42;0.42	4.59	2.26	0.28386	.	0.483431	0.24328	N	0.039484	T	0.22666	0.0547	N	0.03281	-0.365	0.27249	N	0.958952	B	0.02656	0.0	B	0.01281	0.0	T	0.18241	-1.0343	10	0.14252	T	0.57	.	6.2292	0.20726	0.0:0.0792:0.3141:0.6067	.	204	O15335	CHAD_HUMAN	G	204	ENSP00000423812:R204G;ENSP00000258969:R204G	ENSP00000258969:R204G	R	-	1	2	CHAD	45900564	0.939000	0.31865	0.994000	0.49952	0.979000	0.70002	0.446000	0.21694	0.242000	0.21303	0.460000	0.39030	AGG	.	.	.	none		0.622	CHAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367447.3	NM_001267		C	48545565	T	C	48545565	3	2	108	1	0	0	0	0	1	0	0	0	3312	1579	55	3	481	3	CHAD	17	48545565	Missense_Mutation	SNP	T	TCGA-B9-A8YH-01A-11D-A36X-10	9239792	48545565	32649645	82	6922											
CARD14	79092	hgsc.bcm.edu	37	chr17	78178935	78178935	+	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	cccggcctgtgctcctcgtgCccagggcggttgggaagatc	4	8	15	14	3	0	1	0	0	0	1	3	2	1	2	4	4	2	2	4	4	1	1			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr17:78178935C>A	ENST00000573882.1	+	20	3036	c.2500C>A	c.(2500-2502)Ccc>Acc	p.P834T	CARD14_ENST00000344227.2_Missense_Mutation_p.P834T|RP11-334C17.5_ENST00000576824.1_RNA|RP11-334C17.5_ENST00000573935.1_RNA|RP11-334C17.5_ENST00000573346.1_RNA|RP11-334C17.5_ENST00000572730.1_RNA|RP11-334C17.5_ENST00000570309.1_RNA			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	834	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)			NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(5)|prostate(1)|skin(1)	23	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			GCTCCTCGTGCCCAGGGCGGT	0.652																																					p.P834T		Atlas-SNP	.											.	CARD14	98	.	0			c.C2500A						PASS	.						75	72	73					17																	78178935		2203	4300	6503	SO:0001583	missense	79092	exon18			CTCGTGCCCAGGG	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.2500C>A	chr17.hg19:g.78178935C>A	ENSP00000458715:p.Pro834Thr	70.0	0.0	.		96.0	32.0	.	NM_024110	B8QQJ3|Q9BVB5	Missense_Mutation	SNP	ENST00000573882.1	hg19	CCDS11768.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.986821	0.74589	.	.	ENSG00000141527	ENST00000344227	T	0.06371	3.31	4.13	4.13	0.48395	Guanylate kinase/L-type calcium channel (1);	0.000000	0.85682	D	0.000000	T	0.25606	0.0623	M	0.80746	2.51	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.02345	-1.1173	10	0.54805	T	0.06	-27.3668	13.8635	0.63574	0.0:1.0:0.0:0.0	.	834	Q9BXL6	CAR14_HUMAN	T	834	ENSP00000344549:P834T	ENSP00000344549:P834T	P	+	1	0	CARD14	75793530	1.000000	0.71417	0.990000	0.47175	0.847000	0.48162	6.111000	0.71541	1.861000	0.53984	0.491000	0.48974	CCC	.	.	.	none		0.652	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1			A	78178935	C	A	78178935	3	1	108	1	0	0	0	0	1	0	0	0	2648	739	26	4	2731	4	CARD14	17	78178935	Missense_Mutation	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10	29633370	78178935	3016275	83	6923											
CEP192	55125	hgsc.bcm.edu	37	chr18	13105009	13105009	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatgaaagtggagatgttttTagagctacctatgcagcatt	12	13	11	5	0	0	3	0	1	0	2	0	5	0	3	1	1	4	4	1	1	4	6			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr18:13105009T>C	ENST00000325971.8	+	38	6783	c.5190T>C	c.(5188-5190)ttT>ttC	p.F1730F	CEP192_ENST00000540847.2_3'UTR|CEP192_ENST00000430049.2_Silent_p.F1851F|CEP192_ENST00000506447.1_Silent_p.F2326F			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	1730					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						GAGATGTTTTTAGAGCTACCT	0.373																																					p.F2326F		Atlas-SNP	.											.	CEP192	340	.	0			c.T6978C						PASS	.						232	218	223					18																	13105009		2203	4300	6503	SO:0001819	synonymous_variant	55125	exon40			TGTTTTTAGAGCT	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.5190T>C	chr18.hg19:g.13105009T>C		115.0	0.0	.		71.0	28.0	.	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Silent	SNP	ENST00000325971.8	hg19																																																																																				.	.	.	none		0.373	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142		C	13105009	T	C	13105009	2	2	108	1	0	0	0	0	0	0	0	1	3253	1751	61	3		3	CEP192	18	13105009	Silent	SNP	T	TCGA-B9-A8YH-01A-11D-A36X-10		13105009	64972239	84	6924											
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43481032	43481032	+	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	tccttctgactcaatagcacAgcagaggaaataactggcac	14	8	8	11	0	2	2	1	1	1	1	3	3	3	3	1	2	3	3	1	2	4	3			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr18:43481032A>C	ENST00000282041.5	-	26	4609	c.4575T>G	c.(4573-4575)gcT>gcG	p.A1525A	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1525					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						TCAATAGCACAGCAGAGGAAA	0.542																																					p.A1525A		Atlas-SNP	.											.	EPG5	199	.	0			c.T4575G						PASS	.						72	77	75					18																	43481032		2081	4216	6297	SO:0001819	synonymous_variant	57724	exon26			TAGCACAGCAGAG	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.4575T>G	chr18.hg19:g.43481032A>C		74.0	0.0	.		60.0	20.0	.	NM_020964	A2BDF3|Q9H8C8	Silent	SNP	ENST00000282041.5	hg19	CCDS11926.2																																																																																			.	.	.	none		0.542	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		C	43481032	A	C	43481032	2	2	108	1	0	0	0	0	0	0	0	1	8256	175	7	5		5	KIAA1632	18	43481032	Silent	SNP	A	TCGA-B9-A8YH-01A-11D-A36X-10	30376023	43481032	34596216	85	6925											
SLC44A2	57153	hgsc.bcm.edu	37	chr19	10742023	10742023	+	Missense_Mutation	SNP	T	T	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	gctcccgggactttgagtacTataagcagttctgtgttcct	7	14	10	10	1	1	1	0	1	1	0	3	2	3	2	2	1	2	5	2	1	3	6			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr19:10742023T>G	ENST00000335757.5	+	6	779	c.403T>G	c.(403-405)Tat>Gat	p.Y135D	SLC44A2_ENST00000407327.4_Missense_Mutation_p.Y133D|SLC44A2_ENST00000586078.1_Missense_Mutation_p.Y135D			Q8IWA5	CTL2_HUMAN	solute carrier family 44 (choline transporter), member 2	135					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)	CTTTGAGTACTATAAGCAGTT	0.522																																					p.Y135D		Atlas-SNP	.											.	SLC44A2	56	.	0			c.T403G						PASS	.						111	114	113					19																	10742023		2203	4300	6503	SO:0001583	missense	57153	exon6			GAGTACTATAAGC	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.403T>G	chr19.hg19:g.10742023T>G	ENSP00000336888:p.Tyr135Asp	50.0	0.0	.		60.0	23.0	.	NM_020428	B2RBB1|B3KNH3|B4DFJ0|F2Q9D7|Q658V1|Q658Z2|Q6PJV7|Q8N2F0|Q9NY68	Missense_Mutation	SNP	ENST00000335757.5	hg19	CCDS12245.1	.	.	.	.	.	.	.	.	.	.	T	16.07	3.019151	0.54576	.	.	ENSG00000129353	ENST00000407327;ENST00000335757;ENST00000380614	T;T	0.09538	2.97;2.98	4.86	4.86	0.63082	.	0.062114	0.64402	D	0.000003	T	0.19565	0.0470	M	0.87682	2.9	0.51482	D	0.999924	B;B	0.02656	0.0;0.0	B;B	0.12837	0.002;0.008	T	0.02560	-1.1141	10	0.36615	T	0.2	.	13.62	0.62132	0.0:0.0:0.0:1.0	.	135;133	Q8IWA5;Q8IWA5-3	CTL2_HUMAN;.	D	133;135;135	ENSP00000385135:Y133D;ENSP00000336888:Y135D	ENSP00000336888:Y135D	Y	+	1	0	SLC44A2	10603023	1.000000	0.71417	0.988000	0.46212	0.946000	0.59487	7.050000	0.76620	2.064000	0.61679	0.374000	0.22700	TAT	.	.	.	none		0.522	SLC44A2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452045.1			G	10742023	T	G	10742023	3	3	108	1	0	0	0	0	1	0	0	0	14649	1522	53	5	460	5	SLC44A2	19	10742023	Missense_Mutation	SNP	T	TCGA-B9-A8YH-01A-11D-A36X-10		10742023	48386960	86	6926											
SCGBL	284402	hgsc.bcm.edu	37	chr19	35085225	35085226	+	Frame_Shift_Del	DEL	AC	AC	-																															cttgggacacatcaaacacaAcattcgcaagcagtttatcg																										TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr19:35085225_35085226delAC	ENST00000601241.1	-	3	2200_2201	c.100_101delGT	c.(100-102)gttfs	p.V35fs	SCGB2B2_ENST00000595326.1_Intron|SCGB2B2_ENST00000379204.2_Frame_Shift_Del_p.V35fs			Q4G0G5	SC2B2_HUMAN	secretoglobin, family 2B, member 2	35						extracellular region (GO:0005576)											ATCAAACACAACATTCGCAAGC	0.505																																					p.34_34del		Atlas-Indel,Pindel	.											.	.	.	.	0			c.101_102del						PASS	.																																			SO:0001589	frameshift_variant	284402	exon2			.	AK093495	CCDS32989.1	19q13.12	2011-12-14	2011-12-14	2011-12-14	ENSG00000205209	ENSG00000205209		"Secretoglobins"	27616	protein-coding gene	gene with protein product		615063	"secretoglobin-like"	SCGBL		22155607	Standard	NM_001025591		Approved	SCGB4A2	uc002nvn.3	Q4G0G5		ENST00000601241.1:c.100_101delGT	chr19.hg19:g.35085225_35085226delAC	ENSP00000469876:p.Val35fs	97.0	0.0	0		87.0	34.0	0.390805	NM_001025591		Frame_Shift_Del	DEL	ENST00000601241.1	hg19	CCDS32989.1																																																																																			.	.	.	none		0.505	SCGB2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461457.2	NM_001025591		-	35085226	AC	-	35085225	7	5	108	1	0	1	0	1	0	0	0	0	13915	43	2	0	197	0	SCGBL	19	35085225	Frame_Shift_Del	DEL	AC	TCGA-B9-A8YH-01A-11D-A36X-10	24343202	35085225	24043758	87	6927											
FBL	2091	hgsc.bcm.edu	37	chr19	40330883	40330883	+	Missense_Mutation	SNP	A	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	cagttctcaccgaaatcgagActctcttctctccataaact	11	12	4	14	2	3	1	1	0	3	1	8	3	4	1	2	0	1	1	2	0	3	3			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr19:40330883A>C	ENST00000221801.3	-	4	481	c.368T>G	c.(367-369)gTc>gGc	p.V123G	FBL_ENST00000593503.1_5'Flank	NM_001436.3	NP_001427.2	P22087	FBRL_HUMAN	fibrillarin	123					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)		CGAAATCGAGACTCTCTTCTC	0.557																																					p.V123G		Atlas-SNP	.											.	FBL	37	.	0			c.T368G						PASS	.						97	84	88					19																	40330883		2203	4300	6503	SO:0001583	missense	2091	exon4			ATCGAGACTCTCT	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.368T>G	chr19.hg19:g.40330883A>C	ENSP00000221801:p.Val123Gly	103.0	0.0	.		112.0	13.0	.	NM_001436	B5BUE8|O75259|Q6IAT5|Q9UPI6	Missense_Mutation	SNP	ENST00000221801.3	hg19	CCDS12545.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.294597	0.81025	.	.	ENSG00000105202	ENST00000221801	.	.	.	5.08	5.08	0.68730	.	0.101737	0.64402	D	0.000005	T	0.74718	0.3753	M	0.72894	2.215	0.80722	D	1	D;P;D	0.62365	0.991;0.923;0.976	P;P;P	0.61722	0.864;0.64;0.893	T	0.78280	-0.2265	9	0.87932	D	0	-25.8191	12.8246	0.57712	1.0:0.0:0.0:0.0	.	123;62;123	B4DLD4;Q96BS4;P22087	.;.;FBRL_HUMAN	G	123	.	ENSP00000221801:V123G	V	-	2	0	FBL	45022723	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	8.304000	0.89958	1.909000	0.55274	0.418000	0.28097	GTC	.	.	.	none		0.557	FBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462509.4	NM_001436		C	40330883	A	C	40330883	3	2	108	1	0	0	0	0	1	0	0	0	5703	275	10	5	621	5	FBL	19	40330883	Missense_Mutation	SNP	A	TCGA-B9-A8YH-01A-11D-A36X-10	5245658	40330883	18798100	88	6928											
IRF2BP1	26145	hgsc.bcm.edu	37	chr19	46387877	46387878	+	Frame_Shift_Ins	INS	-	-	G																															gccgcctcgccctccggctcINSgggggatgccttgcgacggc																										TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr19:46387877_46387878insG	ENST00000302165.3	-	1	1498_1499	c.1155_1156insC	c.(1153-1158)cccgagfs	p.E386fs		NM_015649.1	NP_056464.1	Q8IU81	I2BP1_HUMAN	interferon regulatory factor 2 binding protein 1	386					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)			cervix(1)|kidney(1)|lung(2)	4		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00442)|GBM - Glioblastoma multiforme(486;0.0402)|Epithelial(262;0.231)		CCCTCCGGCTCGGGGGATGCCT	0.738																																					p.E386fs		Atlas-Indel,Pindel	.											.	IRF2BP1	23	.	0			c.1156_1157insC						PASS	.																																			SO:0001589	frameshift_variant	26145	exon1			.	AY278022	CCDS12678.1	19q13.32	2008-02-05							21728	protein-coding gene	gene with protein product		615331				12799427	Standard	NM_015649		Approved	DKFZP434M154, IRF-2BP1	uc002pds.1	Q8IU81		ENST00000302165.3:c.1156dupC	chr19.hg19:g.46387882_46387882dupG	ENSP00000307265:p.Glu386fs	43.0	0.0	0		46.0	16.0	0.347826	NM_015649	Q53EL7|Q6DC95|Q9BRZ9|Q9Y4P4	Frame_Shift_Ins	INS	ENST00000302165.3	hg19	CCDS12678.1																																																																																			.	.	.	none		0.738	IRF2BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461683.1	NM_015649		G	46387878	-	G	46387877	7	5	108	1	0	1	1	0	0	0	0	0	7836	893	31	0	602	0	IRF2BP1	19	46387877	Frame_Shift_Ins	INS	-	TCGA-B9-A8YH-01A-11D-A36X-10	6056994	46387877	12741106	89	6929											
XRN2	22803	hgsc.bcm.edu	37	chr20	21321426	21321426	+	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	cttgggttcaagaaattcacCaggttctcaagtagccagta	12	11	9	9	0	3	1	3	0	1	1	4	1	3	1	2	2	1	4	2	2	5	6			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr20:21321426C>G	ENST00000377191.3	+	15	1441	c.1346C>G	c.(1345-1347)cCa>cGa	p.P449R	XRN2_ENST00000430571.2_Missense_Mutation_p.P373R|XRN2_ENST00000539513.1_Missense_Mutation_p.P395R	NM_012255.3	NP_036387.2	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2	449					cell growth (GO:0016049)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA processing (GO:0006396)|spermatogenesis (GO:0007283)	aggresome (GO:0016235)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-3' exoribonuclease activity (GO:0004534)|nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(6)|large_intestine(10)|lung(12)|ovary(1)|skin(5)	39						AGAAATTCACCAGGTTCTCAA	0.383																																					p.P449R		Atlas-SNP	.											.	XRN2	90	.	0			c.C1346G						PASS	.						114	116	115					20																	21321426		2203	4300	6503	SO:0001583	missense	22803	exon15			ATTCACCAGGTTC	AF064257	CCDS13144.1	20p11.2-p11.1	2011-09-12			ENSG00000088930	ENSG00000088930	3.1.13.-		12836	protein-coding gene	gene with protein product		608851				10409438	Standard	NM_012255		Approved		uc002wsf.1	Q9H0D6	OTTHUMG00000032025	ENST00000377191.3:c.1346C>G	chr20.hg19:g.21321426C>G	ENSP00000366396:p.Pro449Arg	130.0	0.0	.		175.0	54.0	.	NM_012255	Q3L8N4|Q6KGZ9|Q9BQL1|Q9NTW0|Q9NXS6|Q9UL53	Missense_Mutation	SNP	ENST00000377191.3	hg19	CCDS13144.1	.	.	.	.	.	.	.	.	.	.	C	14.89	2.671790	0.47781	.	.	ENSG00000088930	ENST00000377191;ENST00000430571;ENST00000539513	T;T;T	0.72942	-0.7;-0.7;-0.7	4.72	3.71	0.42584	.	0.160480	0.56097	D	0.000025	T	0.71467	0.3343	M	0.74258	2.255	0.58432	D	0.999998	P	0.40578	0.722	B	0.41988	0.372	T	0.73052	-0.4104	10	0.32370	T	0.25	-6.9533	14.7454	0.69488	0.1445:0.8555:0.0:0.0	.	449	Q9H0D6	XRN2_HUMAN	R	449;373;395	ENSP00000366396:P449R;ENSP00000413548:P373R;ENSP00000441113:P395R	ENSP00000366396:P449R	P	+	2	0	XRN2	21269426	0.995000	0.38212	1.000000	0.80357	0.979000	0.70002	3.365000	0.52335	2.340000	0.79590	0.460000	0.39030	CCA	.	.	.	none		0.383	XRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078273.2	NM_012255		G	21321426	C	G	21321426	3	3	108	1	0	0	0	0	1	0	0	0	17472	594	21	4	1404	4	XRN2	20	21321426	Missense_Mutation	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10		21321426	41704094	90	6930											
SFRS6	6431	hgsc.bcm.edu	37	chr20	42088517	42088517	+	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	gaaaatctttctagtcggtgCagttggcaagatttaaaggt	12	13	11	5	1	2	1	0	0	2	1	3	2	2	1	0	3	1	3	0	3	6	5			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr20:42088517C>T	ENST00000244020.3	+	3	469	c.363C>T	c.(361-363)tgC>tgT	p.C121C		NM_006275.5	NP_006266.2	Q13247	SRSF6_HUMAN	serine/arginine-rich splicing factor 6	121	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell death (GO:0060548)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of keratinocyte proliferation (GO:0010837)|regulation of wound healing (GO:0061041)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|upper_aerodigestive_tract(2)	5						CTAGTCGGTGCAGTTGGCAAG	0.363																																					p.C121C		Atlas-SNP	.											.	SRSF6	37	.	0			c.C363T						PASS	.						129	121	124					20																	42088517		2203	4300	6503	SO:0001819	synonymous_variant	6431	exon3			TCGGTGCAGTTGG	U30883	CCDS13318.1	20q12-q13.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000124193	ENSG00000124193		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10788	protein-coding gene	gene with protein product	"pre-mRNA splicing factor SRP55", "SR splicing factor 6"	601944	"splicing factor, arginine/serine-rich 6"	SFRS6		7556075, 20516191	Standard	NM_006275		Approved	SRP55, B52	uc010zwg.2	Q13247	OTTHUMG00000032502	ENST00000244020.3:c.363C>T	chr20.hg19:g.42088517C>T		131.0	0.0	.		128.0	38.0	.	NM_006275	B7Z6J3|E1P5W6|Q13244|Q13245|Q96J06|Q9UJB8|Q9Y3N7	Silent	SNP	ENST00000244020.3	hg19	CCDS13318.1																																																																																			.	.	.	none		0.363	SRSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079292.1	NM_006275		T	42088517	C	T	42088517	2	4	108	1	0	0	0	0	0	0	0	1	14194	718	25	2		2	SFRS6	20	42088517	Silent	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10	20767091	42088517	20937003	91	6931											
CBLN4	140689	hgsc.bcm.edu	37	chr20	54579177	54579177	+	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	ggcagccccggcagcgtgagGaccagcagcacggccggcac	8	1	16	16	4	0	1	0	1	0	0	0	2	0	2	4	5	4	5	4	5	0	0			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr20:54579177G>A	ENST00000064571.2	-	1	1351	c.51C>T	c.(49-51)gtC>gtT	p.V17V		NM_080617.5	NP_542184.1	Q9NTU7	CBLN4_HUMAN	cerebellin 4 precursor	17					protein secretion (GO:0009306)	cell junction (GO:0030054)|extracellular space (GO:0005615)|synapse (GO:0045202)				endometrium(2)|large_intestine(1)|lung(10)|ovary(3)|pancreas(1)	17			Colorectal(105;0.202)			GCAGCGTGAGGACCAGCAGCA	0.746																																					p.V17V		Atlas-SNP	.											.	CBLN4	54	.	0			c.C51T						PASS	.						19	17	18					20																	54579177		2196	4292	6488	SO:0001819	synonymous_variant	140689	exon1			CGTGAGGACCAGC	AY358527	CCDS13448.1	20q13	2004-08-19	2004-08-19	2004-08-19	ENSG00000054803	ENSG00000054803			16231	protein-coding gene	gene with protein product		615029	"cerebellin precursor-like 1"	CBLNL1			Standard	NM_080617		Approved	dJ885A10.1	uc002xxa.4	Q9NTU7	OTTHUMG00000032782	ENST00000064571.2:c.51C>T	chr20.hg19:g.54579177G>A		27.0	0.0	.		40.0	11.0	.	NM_080617	A8K0S5	Silent	SNP	ENST00000064571.2	hg19	CCDS13448.1																																																																																			.	.	.	none		0.746	CBLN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079783.2	NM_080617		A	54579177	G	A	54579177	2	1	108	1	0	0	0	0	0	0	0	1	2709	1161	41	2		2	CBLN4	20	54579177	Silent	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10	12490660	54579177	8446343	92	6932											
CSTF1	1477	hgsc.bcm.edu	37	chr20	54972276	54972276	+	Missense_Mutation	SNP	T	T	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	ctttcaggaatggaaaacgaTgacaccgcagttcagtatgc	13	9	10	9	2	2	1	2	1	0	0	2	4	2	3	1	2	2	3	1	2	4	3			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr20:54972276T>G	ENST00000217109.4	+	3	535	c.183T>G	c.(181-183)gaT>gaG	p.D61E	CSTF1_ENST00000493039.1_3'UTR	NM_001033521.1|NM_001324.2	NP_001028693.1|NP_001315.1	Q05048	CSTF1_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 1, 50kDa	61					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	15			Colorectal(105;0.202)			TGGAAAACGATGACACCGCAG	0.408																																					p.D61E		Atlas-SNP	.											.	CSTF1	29	.	0			c.T183G						PASS	.						111	107	108					20																	54972276		2203	4300	6503	SO:0001583	missense	1477	exon3			AAACGATGACACC		CCDS13452.1	20q13.31	2013-01-10	2002-08-29		ENSG00000101138	ENSG00000101138		"WD repeat domain containing"	2483	protein-coding gene	gene with protein product		600369	"cleavage stimulation factor, 3' pre-RNA, subunit 1, 50kD"			1358884, 11257228	Standard	NM_001033521		Approved		uc002xxl.1	Q05048	OTTHUMG00000032791	ENST00000217109.4:c.183T>G	chr20.hg19:g.54972276T>G	ENSP00000217109:p.Asp61Glu	124.0	0.0	.		107.0	53.0	.	NM_001033522	Q5QPD8	Missense_Mutation	SNP	ENST00000217109.4	hg19	CCDS13452.1	.	.	.	.	.	.	.	.	.	.	T	5.796	0.331191	0.10956	.	.	ENSG00000101138	ENST00000415828;ENST00000217109;ENST00000428552;ENST00000425890;ENST00000452950	T;T;T	0.55760	0.5;0.52;0.5	6.06	2.6	0.31112	.	0.127094	0.64402	D	0.000001	T	0.22475	0.0542	N	0.03608	-0.345	0.48040	D	0.999574	B	0.12630	0.006	B	0.06405	0.002	T	0.24048	-1.0171	10	0.02654	T	1	5.922	9.8264	0.40914	0.0:0.3244:0.0:0.6756	.	61	Q05048	CSTF1_HUMAN	E	61;61;61;48;61	ENSP00000387968:D61E;ENSP00000217109:D61E;ENSP00000409035:D61E	ENSP00000217109:D61E	D	+	3	2	CSTF1	54405683	0.978000	0.34361	0.433000	0.26760	0.981000	0.71138	0.092000	0.15066	0.182000	0.20032	-0.256000	0.11100	GAT	.	.	.	none		0.408	CSTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079794.2	NM_001033521		G	54972276	T	G	54972276	3	3	108	1	0	0	0	0	1	0	0	0	3985	1461	51	5	189	5	CSTF1	20	54972276	Missense_Mutation	SNP	T	TCGA-B9-A8YH-01A-11D-A36X-10	393099	54972276	8053244	93	6933											
RTEL1	51750	hgsc.bcm.edu	37	chr20	62322275	62322275	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctggagcacagcgaacagcGggcggggagccctggcgagg	8	2	19	12	4	0	0	0	0	0	0	0	4	0	2	2	6	5	1	2	6	1	0			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr20:62322275G>A	ENST00000360203.5	+	27	2856	c.2531G>A	c.(2530-2532)cGg>cAg	p.R844Q	RTEL1-TNFRSF6B_ENST00000482936.1_Missense_Mutation_p.R844Q|RTEL1_ENST00000370018.3_Missense_Mutation_p.R844Q|RTEL1_ENST00000370003.1_Missense_Mutation_p.R89Q|RTEL1_ENST00000508582.2_Missense_Mutation_p.R868Q|RTEL1_ENST00000318100.4_Missense_Mutation_p.R844Q					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)			AGCGAACAGCGGGCGGGGAGC	0.682																																					p.R868Q		Atlas-SNP	.											.	RTEL1	114	.	0			c.G2603A						PASS	.						15	17	16					20																	62322275		2121	4219	6340	SO:0001583	missense	51750	exon27			AACAGCGGGCGGG	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.2531G>A	chr20.hg19:g.62322275G>A	ENSP00000353332:p.Arg844Gln	81.0	0.0	.		104.0	39.0	.	NM_032957		Missense_Mutation	SNP	ENST00000360203.5	hg19		.	.	.	.	.	.	.	.	.	.	G	9.354	1.066199	0.20067	.	.	ENSG00000258366	ENST00000370018;ENST00000318100;ENST00000508582;ENST00000360203;ENST00000370003	T;T;T;T;T	0.08896	3.04;3.04;3.04;3.04;3.04	4.77	-9.54	0.00572	.	2.650120	0.01147	N	0.006331	T	0.02848	0.0085	N	0.03608	-0.345	0.09310	N	1	B;B;B;B	0.14012	0.009;0.003;0.0;0.001	B;B;B;B	0.06405	0.002;0.001;0.0;0.001	T	0.33137	-0.9880	10	0.14252	T	0.57	-0.0689	6.1268	0.20184	0.4743:0.0:0.3168:0.2089	.	868;89;844;844	Q9NZ71-7;Q9NZ71-5;Q9NZ71;Q9NZ71-6	.;.;RTEL1_HUMAN;.	Q	844;844;868;844;89	ENSP00000359035:R844Q;ENSP00000322287:R844Q;ENSP00000424307:R868Q;ENSP00000353332:R844Q;ENSP00000359020:R89Q	ENSP00000353332:R844Q	R	+	2	0	AL353715.1	61792719	0.000000	0.05858	0.004000	0.12327	0.003000	0.03518	-1.477000	0.02331	-2.313000	0.00648	-1.008000	0.02478	CGG	.	.	.	none		0.682	RTEL1-011	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000289781.1	NM_032957		A	62322275	G	A	62322275	3	1	108	1	0	0	0	0	1	0	0	0	13733	1116	39	1	2633	1	RTEL1	20	62322275	Missense_Mutation	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10	7349999	62322275	703245	94	6934											
PTTG1IP	754	hgsc.bcm.edu	37	chr21	46285323	46285323	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacttacggagacgttcttcAggcactcttcacaggttttg	8	14	9	10	2	4	1	2	0	2	1	4	2	4	1	0	3	2	3	0	3	2	7			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr21:46285323A>G	ENST00000330938.3	-	2	375	c.155T>C	c.(154-156)cTg>cCg	p.L52P	PTTG1IP_ENST00000445724.2_Missense_Mutation_p.L52P|PTTG1IP_ENST00000494690.1_5'UTR|PTTG1IP_ENST00000397887.3_Missense_Mutation_p.L52P	NM_004339.3	NP_004330.1	P53801	PTTG_HUMAN	pituitary tumor-transforming 1 interacting protein	52	PSI.				multicellular organismal development (GO:0007275)|protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	receptor activity (GO:0004872)			ovary(1)|prostate(1)	2				Colorectal(79;0.0659)		GACGTTCTTCAGGCACTCTTC	0.507																																					p.L52P		Atlas-SNP	.											.	PTTG1IP	22	.	0			c.T155C						PASS	.						198	145	163					21																	46285323		2203	4300	6503	SO:0001583	missense	754	exon2			TTCTTCAGGCACT	AF149785	CCDS13715.1, CCDS68221.1	21q22.3	2008-07-04			ENSG00000183255	ENSG00000183255			13524	protein-coding gene	gene with protein product		603784		C21orf3, C21orf1		9570958, 10830953	Standard	NM_004339		Approved	PBF	uc002zgb.2	P53801	OTTHUMG00000090254	ENST00000330938.3:c.155T>C	chr21.hg19:g.46285323A>G	ENSP00000328325:p.Leu52Pro	65.0	0.0	.		45.0	17.0	.	NM_004339	B2RDP7|D3DSL9|Q9NS09	Missense_Mutation	SNP	ENST00000330938.3	hg19	CCDS13715.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.965227	0.74131	.	.	ENSG00000183255	ENST00000397887;ENST00000330938;ENST00000445724	T;T;T	0.69806	-0.43;-0.43;0.8	4.66	4.66	0.58398	.	0.000000	0.64402	D	0.000001	T	0.80507	0.4636	M	0.76170	2.325	0.80722	D	1	D;D	0.89917	1.0;0.996	D;D	0.87578	0.998;0.958	T	0.83101	-0.0128	10	0.87932	D	0	-45.6165	13.1312	0.59382	1.0:0.0:0.0:0.0	.	52;52	B4DPZ0;P53801	.;PTTG_HUMAN	P	52	ENSP00000380984:L52P;ENSP00000328325:L52P;ENSP00000395374:L52P	ENSP00000328325:L52P	L	-	2	0	PTTG1IP	45109751	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.973000	0.70456	1.735000	0.51646	0.451000	0.29950	CTG	.	.	.	none		0.507	PTTG1IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206553.1			G	46285323	A	G	46285323	3	3	108	1	0	0	0	0	1	0	0	0	12833	188	7	3	407	3	PTTG1IP	21	46285323	Missense_Mutation	SNP	A	TCGA-B9-A8YH-01A-11D-A36X-10		46285323	1844572	95	6935											
MICAL3	57553	hgsc.bcm.edu	37	chr22	18369959	18369959	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctgattgactggtctttcTcctcttcccagcaccatcca	6	14	5	16	0	4	2	0	2	4	0	7	2	6	2	4	1	1	1	4	1	0	3			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr22:18369959T>C	ENST00000441493.2	-	15	2396	c.2044A>G	c.(2044-2046)Aga>Gga	p.R682G	MICAL3_ENST00000207726.7_Missense_Mutation_p.R682G|MICAL3_ENST00000383094.3_Missense_Mutation_p.R682G|MICAL3_ENST00000414725.2_Missense_Mutation_p.R682G|MICAL3_ENST00000429452.1_Missense_Mutation_p.R682G|MICAL3_ENST00000400561.2_Missense_Mutation_p.R682G|MICAL3_ENST00000444520.1_Missense_Mutation_p.R682G|MICAL3_ENST00000585038.1_Missense_Mutation_p.R682G	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	682					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)		CTGGTCTTTCTCCTCTTCCCA	0.428																																					p.R682G		Atlas-SNP	.											.	MICAL3	53	.	0			c.A2044G						PASS	.						143	122	129					22																	18369959		1568	3582	5150	SO:0001583	missense	57553	exon15			TCTTTCTCCTCTT	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.2044A>G	chr22.hg19:g.18369959T>C	ENSP00000416015:p.Arg682Gly	137.0	0.0	.		128.0	47.0	.	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Missense_Mutation	SNP	ENST00000441493.2	hg19	CCDS46659.1	.	.	.	.	.	.	.	.	.	.	T	18.79	3.699631	0.68501	.	.	ENSG00000093100;ENSG00000093100;ENSG00000243156;ENSG00000243156;ENSG00000243156;ENSG00000243156;ENSG00000243156	ENST00000441493;ENST00000429452;ENST00000400561;ENST00000444520;ENST00000414725;ENST00000383094;ENST00000207726	T;T;T;T;T;T;T	0.69806	-0.19;-0.43;-0.27;-0.27;-0.26;-0.26;-0.26	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.73666	0.3616	M	0.77820	2.39	0.58432	D	0.999998	P;B;B;P;P	0.43633	0.546;0.438;0.38;0.554;0.813	B;B;P;B;B	0.46049	0.156;0.343;0.502;0.322;0.202	T	0.75193	-0.3404	10	0.42905	T	0.14	.	16.3721	0.83368	0.0:0.0:0.0:1.0	.	682;682;682;682;682	B2RXJ5;Q7RTP6-3;Q7RTP6-2;Q7RTP6-4;Q7RTP6	.;.;.;.;MICA3_HUMAN	G	682	ENSP00000416015:R682G;ENSP00000414846:R682G;ENSP00000383406:R682G;ENSP00000410315:R682G;ENSP00000391827:R682G;ENSP00000372574:R682G;ENSP00000207726:R682G	ENSP00000207726:R682G	R	-	1	2	XXbac-B461K10.4;MICAL3	16749959	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.495000	0.66912	2.257000	0.74773	0.533000	0.62120	AGA	.	.	.	none		0.428	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			C	18369959	T	C	18369959	3	2	108	1	0	0	0	0	1	0	0	0	9578	1559	54	3	4773	3	MICAL3	22	18369959	Missense_Mutation	SNP	T	TCGA-B9-A8YH-01A-11D-A36X-10		18369959	32934607	96	6936											
RGL4	266747	hgsc.bcm.edu	37	chr22	24036113	24036113	+	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	ctcggggaccacagcatgagGgcccgggacagggccagggt	8	3	18	12	2	0	1	0	1	0	0	1	3	0	3	3	6	1	1	3	6	0	0			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr22:24036113G>C	ENST00000290691.5	+	4	2034	c.864G>C	c.(862-864)agG>agC	p.R288S	RGL4_ENST00000401461.1_Missense_Mutation_p.R152S|KB-1572G7.2_ENST00000421064.1_RNA|AP000347.2_ENST00000417194.1_RNA|GUSBP11_ENST00000455485.1_RNA	NM_153615.1	NP_705843.1	Q8IZJ4	RGDSR_HUMAN	ral guanine nucleotide dissociation stimulator-like 4	288	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)	guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(3)	15						ACAGCATGAGGGCCCGGGACA	0.592																																					p.R288S		Atlas-SNP	.											.	RGL4	29	.	0			c.G864C						PASS	.						83	62	69					22																	24036113		2203	4300	6503	SO:0001583	missense	266747	exon4			CATGAGGGCCCGG		CCDS13811.1	22q11.23	2008-02-22			ENSG00000159496	ENSG00000159496			31911	protein-coding gene	gene with protein product	"RalGDS related oncogene"	612214				9178890, 10851075	Standard	NM_153615		Approved	Rgr	uc002zxn.3	Q8IZJ4	OTTHUMG00000150711	ENST00000290691.5:c.864G>C	chr22.hg19:g.24036113G>C	ENSP00000290691:p.Arg288Ser	146.0	0.0	.		117.0	33.0	.	NM_153615	Q495L8	Missense_Mutation	SNP	ENST00000290691.5	hg19	CCDS13811.1	.	.	.	.	.	.	.	.	.	.	g	10.17	1.277356	0.23307	.	.	ENSG00000159496	ENST00000401461;ENST00000290691;ENST00000382833;ENST00000423392	T;T;T	0.27104	1.69;1.69;1.69	2.6	-3.45	0.04781	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.412983	0.19855	N	0.104560	T	0.22360	0.0539	L	0.33668	1.02	0.09310	N	1	P;P;B;P	0.45986	0.87;0.87;0.043;0.87	P;P;B;P	0.54815	0.61;0.61;0.079;0.761	T	0.13019	-1.0525	10	0.36615	T	0.2	.	3.8098	0.08792	0.45:0.0:0.382:0.168	.	152;152;288;288	E7EW79;Q495L8;E9PH87;Q8IZJ4	.;.;.;RGDSR_HUMAN	S	152;288;288;288	ENSP00000383951:R152S;ENSP00000290691:R288S;ENSP00000402142:R288S	ENSP00000290691:R288S	R	+	3	2	RGL4	22366113	1.000000	0.71417	0.000000	0.03702	0.025000	0.11179	2.771000	0.47670	-0.757000	0.04697	-0.399000	0.06403	AGG	.	.	.	none		0.592	RGL4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319711.1	NM_153615		C	24036113	G	C	24036113	3	2	108	1	0	0	0	0	1	0	0	0	13292	1223	43	4	878	4	RGL4	22	24036113	Missense_Mutation	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10	5666154	24036113	27268453	97	6937											
CCDC117	150275	hgsc.bcm.edu	37	chr22	29182126	29182126	+	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	ggaaacccctccctgaactcCtttctgataagccaaagcca	12	8	6	15	0	1	2	0	2	1	0	3	3	3	3	6	1	4	0	6	1	4	2			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr22:29182126C>G	ENST00000249064.4	+	5	828	c.652C>G	c.(652-654)Ctt>Gtt	p.L218V	CCDC117_ENST00000448492.2_Missense_Mutation_p.L200V|CCDC117_ENST00000421503.2_Missense_Mutation_p.L143V|CCDC117_ENST00000443309.2_Missense_Mutation_p.L86V	NM_001284263.1|NM_001284265.1|NM_173510.2	NP_001271192.1|NP_001271194.1|NP_775781.1	Q8IWD4	CC117_HUMAN	coiled-coil domain containing 117	218										breast(1)|kidney(1)|large_intestine(4)|upper_aerodigestive_tract(1)	7						CCCTGAACTCCTTTCTGATAA	0.433																																					p.L218V		Atlas-SNP	.											.	CCDC117	26	.	0			c.C652G						PASS	.						76	75	75					22																	29182126		2203	4300	6503	SO:0001583	missense	150275	exon5			GAACTCCTTTCTG	AK091133	CCDS13846.1, CCDS63435.1, CCDS63436.1	22q12.1	2006-06-27			ENSG00000159873	ENSG00000159873			26599	protein-coding gene	gene with protein product						12477932	Standard	NM_001284263		Approved	FLJ33814	uc003aeb.3	Q8IWD4	OTTHUMG00000151091	ENST00000249064.4:c.652C>G	chr22.hg19:g.29182126C>G	ENSP00000249064:p.Leu218Val	165.0	0.0	.		156.0	68.0	.	NM_173510	A8K0F1|B7Z2V1|B7Z860|Q6ICA7|Q8N278	Missense_Mutation	SNP	ENST00000249064.4	hg19	CCDS13846.1	.	.	.	.	.	.	.	.	.	.	C	19.85	3.904080	0.72754	.	.	ENSG00000159873	ENST00000249064;ENST00000448492;ENST00000421503;ENST00000443309	T;T;T;T	0.18502	2.21;2.21;2.21;2.21	5.94	5.94	0.96194	.	0.072659	0.56097	D	0.000021	T	0.30324	0.0761	L	0.36672	1.1	0.43564	D	0.995887	D;D;D	0.65815	0.995;0.995;0.995	P;P;P	0.61800	0.894;0.857;0.857	T	0.00455	-1.1729	10	0.72032	D	0.01	.	15.7233	0.77732	0.1369:0.863:0.0:0.0	.	143;200;218	B7Z2V1;B7Z860;Q8IWD4	.;.;CC117_HUMAN	V	218;200;143;86	ENSP00000249064:L218V;ENSP00000389478:L200V;ENSP00000387827:L143V;ENSP00000399363:L86V	ENSP00000249064:L218V	L	+	1	0	CCDC117	27512126	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.531000	0.45650	2.816000	0.96949	0.561000	0.74099	CTT	.	.	.	none		0.433	CCDC117-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321258.1	NM_173510		G	29182126	C	G	29182126	3	3	108	1	0	0	0	0	1	0	0	0	2756	681	24	4	670	4	CCDC117	22	29182126	Missense_Mutation	SNP	C	TCGA-B9-A8YH-01A-11D-A36X-10	5146013	29182126	22122440	98	6938											
TMPRSS6	164656	hgsc.bcm.edu	37	chr22	37471189	37471189	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actcacggtccgactggttgTacaagccatagtgcacccgc	9	8	10	14	3	1	0	1	0	0	0	2	1	2	0	3	2	3	3	3	2	3	3			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr22:37471189T>C	ENST00000346753.3	-	11	1471	c.1355A>G	c.(1354-1356)tAc>tGc	p.Y452C	TMPRSS6_ENST00000381792.2_Missense_Mutation_p.Y443C|TMPRSS6_ENST00000406725.1_Missense_Mutation_p.Y443C|TMPRSS6_ENST00000406856.1_Missense_Mutation_p.Y443C	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	452	CUB 2. {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						CGACTGGTTGTACAAGCCATA	0.662																																					p.Y452C		Atlas-SNP	.											.	TMPRSS6	99	.	0			c.A1355G						PASS	.						56	61	60					22																	37471189		2203	4300	6503	SO:0001583	missense	164656	exon11			TGGTTGTACAAGC	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.1355A>G	chr22.hg19:g.37471189T>C	ENSP00000334962:p.Tyr452Cys	113.0	0.0	.		96.0	42.0	.	NM_153609	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Missense_Mutation	SNP	ENST00000346753.3	hg19	CCDS13941.1	.	.	.	.	.	.	.	.	.	.	T	19.34	3.809609	0.70797	.	.	ENSG00000187045	ENST00000381792;ENST00000346753;ENST00000406725;ENST00000406856	D;D;D;D	0.92805	-3.11;-3.1;-3.09;-3.11	5.27	5.27	0.74061	CUB (3);	0.067665	0.64402	D	0.000008	D	0.94262	0.8157	M	0.62723	1.935	0.48762	D	0.9997	D;D	0.69078	0.997;0.994	P;P	0.58873	0.847;0.707	D	0.94866	0.8026	10	0.87932	D	0	.	15.1744	0.72899	0.0:0.0:0.0:1.0	.	443;452	Q8IU80-5;Q8IU80	.;TMPS6_HUMAN	C	443;452;443;443	ENSP00000371211:Y443C;ENSP00000334962:Y452C;ENSP00000385453:Y443C;ENSP00000384964:Y443C	ENSP00000334962:Y452C	Y	-	2	0	TMPRSS6	35801135	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	5.548000	0.67255	1.986000	0.57962	0.459000	0.35465	TAC	.	.	.	none		0.662	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609		C	37471189	T	C	37471189	3	2	108	1	0	0	0	0	1	0	0	0	16263	1638	57	3	1112	3	TMPRSS6	22	37471189	Missense_Mutation	SNP	T	TCGA-B9-A8YH-01A-11D-A36X-10	8289063	37471189	13833377	99	6939											
EP300	2033	hgsc.bcm.edu	37	chr22	41572322	41572322	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccattgttgatcctgatccTctcatcccctgcgatctgat	6	14	6	15	1	2	3	1	3	2	0	6	4	5	3	5	0	1	1	5	0	0	2			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chr22:41572322T>C	ENST00000263253.7	+	30	6070	c.4851T>C	c.(4849-4851)ccT>ccC	p.P1617P	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	1617	Binding region for E1A adenovirus.|CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.				apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						ATCCTGATCCTCTCATCCCCT	0.532			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.P1617P		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300	367	.	0			c.T4851C						PASS	.						129	118	122					22																	41572322		2203	4300	6503	SO:0001819	synonymous_variant	2033	exon30	Familial Cancer Database	Broad Thumb-Hallux syndrome	TGATCCTCTCATC	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.4851T>C	chr22.hg19:g.41572322T>C		84.0	0.0	.		90.0	34.0	.	NM_001429	B1AKC2	Silent	SNP	ENST00000263253.7	hg19	CCDS14010.1																																																																																			.	.	.	none		0.532	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		C	41572322	T	C	41572322	2	2	108	1	0	0	0	0	0	0	0	1	5150	1538	54	3		3	EP300	22	41572322	Silent	SNP	T	TCGA-B9-A8YH-01A-11D-A36X-10	4101133	41572322	9732244	100	6940											
ARSE	415	hgsc.bcm.edu	37	chrX	2867593	2867593	+	Frame_Shift_Del	DEL	T	T	-																															agggcaaccaaggccaggacTtggaagaggaagttgagttt																										TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chrX:2867593delT	ENST00000381134.3	-	6	672	c.606delA	c.(604-606)caafs	p.Q202fs	ARSE_ENST00000540563.1_Frame_Shift_Del_p.Q157fs|ARSE_ENST00000545496.1_Frame_Shift_Del_p.Q227fs	NM_000047.2	NP_000038.2	P51690	ARSE_HUMAN	arylsulfatase E (chondrodysplasia punctata 1)	202					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)				AGGCCAGGACTTGGAAGAGGA	0.552																																					p.V203fs		Atlas-Indel,Pindel	.											.	ARSE	43	.	0			c.607delG						PASS	.						132	109	116					X																	2867593		2203	4300	6503	SO:0001589	frameshift_variant	415	exon6			.	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.606delA	chrX.hg19:g.2867593delT	ENSP00000370526:p.Gln202fs	151.0	0.0	0		139.0	105.0	0.755396	NM_000047	Q53FT2|Q53FU8	Frame_Shift_Del	DEL	ENST00000381134.3	hg19	CCDS14122.1																																																																																			.	.	.	none		0.552	ARSE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055643.1	NM_000047		-	2867593	T	-	2867593	7	5	108	1	0	1	0	1	0	0	0	0	990	1606	56	0	1187	0	ARSE	23	2867593	Frame_Shift_Del	DEL	T	TCGA-B9-A8YH-01A-11D-A36X-10		2867593	152402967	101	6941											
RBM10	8241	hgsc.bcm.edu	37	chrX	47030585	47030585	+	Missense_Mutation	SNP	T	T	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	gaggaggaggaggaggaggaTgaggaggaggaggagaaggc	14	1	25	1	0	0	2	0	1	0	1	0	13	0	11	0	11	0	0	0	11	1	0	rs377667483		TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chrX:47030585T>G	ENST00000377604.3	+	4	1102	c.360T>G	c.(358-360)gaT>gaG	p.D120E	RBM10_ENST00000329236.7_Intron|RBM10_ENST00000345781.6_Intron	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	120	Poly-Glu.				3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						aggaggaggatgaggaggagg	0.667													T|||	2	0.000529801	0	0	3775	,	,		8316	0.002		0	False		,,,				2504	0				p.D185E	Melanoma(171;120 2705 19495 39241)	Atlas-SNP	.											.	RBM10	117	.	0			c.T555G						PASS	.						20	19	20					X																	47030585		2202	4297	6499	SO:0001583	missense	8241	exon4			GGAGGATGAGGAG	U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"Zinc fingers, RAN-binding domain containing", "G patch domain containing", "RNA binding motif (RRM) containing"	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.360T>G	chrX.hg19:g.47030585T>G	ENSP00000366829:p.Asp120Glu	54.0	0.0	.		68.0	4.0	.	NM_001204468	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Missense_Mutation	SNP	ENST00000377604.3	hg19	CCDS14274.1	.	.	.	.	.	.	.	.	.	.	T	1.034	-0.680868	0.03353	.	.	ENSG00000182872	ENST00000377604	T	0.10960	2.82	2.89	-2.28	0.06826	Nucleotide-binding, alpha-beta plait (1);	0.397395	0.18197	N	0.148658	T	0.03783	0.0107	N	0.08118	0	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.49153	-0.8969	10	0.02654	T	1	-3.1034	10.6013	0.45369	0.0:0.0:0.7699:0.2301	.	185;120;120	Q7Z3D7;P98175-2;P98175	.;.;RBM10_HUMAN	E	120	ENSP00000366829:D120E	ENSP00000366829:D120E	D	+	3	2	RBM10	46915529	0.996000	0.38824	0.881000	0.34555	0.930000	0.56654	-0.096000	0.11059	-0.655000	0.05387	-0.549000	0.04216	GAT	.	.	.	weak		0.667	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676		G	47030585	T	G	47030585	3	3	108	1	0	0	0	0	1	0	0	0	13124	1461	51	5	370	5	RBM10	23	47030585	Missense_Mutation	SNP	T	TCGA-B9-A8YH-01A-11D-A36X-10	44162992	47030585	108239975	102	6942											
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50378467	50378467	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctggcctgagggaaagggcAcagtcagaagcatttgagct	11	8	14	8	0	2	3	1	2	1	1	2	4	2	4	1	3	2	3	1	3	2	1			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chrX:50378467A>G	ENST00000289292.7	-	4	889	c.606T>C	c.(604-606)tgT>tgC	p.C202C	SHROOM4_ENST00000376020.2_Silent_p.C202C|SHROOM4_ENST00000460112.3_Silent_p.C86C			Q9ULL8	SHRM4_HUMAN	shroom family member 4	202					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)					GGGAAAGGGCACAGTCAGAAG	0.572																																					p.C202C		Atlas-SNP	.											.	SHROOM4	171	.	0			c.T606C						PASS	.						49	34	39					X																	50378467		2203	4299	6502	SO:0001819	synonymous_variant	57477	exon4			AAGGGCACAGTCA	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.606T>C	chrX.hg19:g.50378467A>G		109.0	0.0	.		84.0	70.0	.	NM_020717	A7E2X9|D6RFW0|Q96LA0	Silent	SNP	ENST00000289292.7	hg19	CCDS35277.1																																																																																			.	.	.	none		0.572	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		G	50378467	A	G	50378467	2	3	108	1	0	0	0	0	0	0	0	1	14309	157	6	3		3	SHROOM4	23	50378467	Silent	SNP	A	TCGA-B9-A8YH-01A-11D-A36X-10	3347882	50378467	104892093	103	6943											
CENPI	2491	hgsc.bcm.edu	37	chrX	100375404	100375404	+	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	ttaacagtgcccttatgtttGccatttgttatatttactta	9	20	5	7	0	0	0	0	0	0	0	0	0	0	0	2	0	4	2	2	0	6	9			TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chrX:100375404G>C	ENST00000372927.1	+	6	882	c.605G>C	c.(604-606)tGc>tCc	p.C202S	CENPI_ENST00000218507.5_Missense_Mutation_p.C202S|CENPI_ENST00000423383.1_Missense_Mutation_p.C202S|CENPI_ENST00000372926.1_Missense_Mutation_p.C202S	NM_006733.2	NP_006724.2	Q92674	CENPI_HUMAN	centromere protein I	202					CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)|sex differentiation (GO:0007548)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)				breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(19)|prostate(1)|skin(2)	30						CCTTATGTTTGCCATTTGTTA	0.289																																					p.C202S		Atlas-SNP	.											.	CENPI	70	.	0			c.G605C						PASS	.						76	66	70					X																	100375404		2197	4291	6488	SO:0001583	missense	2491	exon6			ATGTTTGCCATTT	X97249	CCDS14479.1	Xq22.1	2013-11-05	2006-06-15	2006-06-15	ENSG00000102384	ENSG00000102384			3968	protein-coding gene	gene with protein product		300065	"FSH primary response (LRPR1, rat) homolog 1", "FSH primary response (LRPR1 homolog, rat) 1"	FSHPRH1		16622420	Standard	NM_006733		Approved	LRPR1, CENP-I, Mis6	uc004egx.3	Q92674	OTTHUMG00000022018	ENST00000372927.1:c.605G>C	chrX.hg19:g.100375404G>C	ENSP00000362018:p.Cys202Ser	198.0	1.0	.		189.0	139.0	.	NM_006733	Q5JWZ9|Q96ED0	Missense_Mutation	SNP	ENST00000372927.1	hg19	CCDS14479.1	.	.	.	.	.	.	.	.	.	.	G	19.76	3.887294	0.72410	.	.	ENSG00000102384	ENST00000423383;ENST00000218507;ENST00000372926;ENST00000372927	.	.	.	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.77857	0.4193	M	0.78801	2.425	0.58432	D	0.999999	D;D	0.60575	0.988;0.988	P;P	0.61940	0.896;0.896	T	0.77859	-0.2431	9	0.37606	T	0.19	-7.424	18.0793	0.89438	0.0:0.0:1.0:0.0	.	202;202	B4DZL4;Q92674	.;CENPI_HUMAN	S	202	.	ENSP00000218507:C202S	C	+	2	0	CENPI	100262060	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.845000	0.75394	2.293000	0.77203	0.590000	0.80494	TGC	.	.	.	none		0.289	CENPI-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057519.1	NM_006733		C	100375404	G	C	100375404	3	2	108	1	0	0	0	0	1	0	0	0	3235	1319	46	4	623	4	CENPI	23	100375404	Missense_Mutation	SNP	G	TCGA-B9-A8YH-01A-11D-A36X-10	49996937	100375404	54895156	104	6944											
PLXNA3	55558	hgsc.bcm.edu	37	chrX	153695615	153695615	+	Frame_Shift_Del	DEL	C	C	-																															cactgccatgctgtgtaaggCccccggcatctttcttgggc																										TCGA-B9-A8YH-01A-11D-A36X-10	TCGA-B9-A8YH-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e6bab9a-ad14-4f30-93d9-00dede084e9c	60ce4360-70f6-4ad0-9057-9fe7428603f7	g.chrX:153695615delC	ENST00000369682.3	+	19	3417	c.3242delC	c.(3241-3243)gccfs	p.A1081fs		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	1081	IPT/TIG 3.				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)					CTGTGTAAGGCCCCCGGCATC	0.642																																					p.A1081fs		Atlas-Indel,Pindel	.											.	PLXNA3	156	.	0			c.3241delG						PASS	.						50	48	49					X																	153695615		2202	4299	6501	SO:0001589	frameshift_variant	55558	exon19			.	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.3242delC	chrX.hg19:g.153695615delC	ENSP00000358696:p.Ala1081fs	42.0	0.0	0		44.0	31.0	0.704545	NM_017514	Q5HY36	Frame_Shift_Del	DEL	ENST00000369682.3	hg19	CCDS14752.1																																																																																			.	.	.	none		0.642	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514		-	153695615	C	-	153695615	7	5	108	1	0	1	0	1	0	0	0	0	12128	739	26	0	3312	0	PLXNA3	23	153695615	Frame_Shift_Del	DEL	C	TCGA-B9-A8YH-01A-11D-A36X-10	53320211	153695615	1574945	105	6945											
CHD5	26038	hgsc.bcm.edu	37	chr1	6214783	6214783	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcacctgcggggggctgaCggctagcggaggggagatgg	6	4	23	8	3	0	2	0	1	0	1	0	4	0	3	1	9	2	3	1	9	1	1			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr1:6214783C>T	ENST00000262450.3	-	5	781	c.682G>A	c.(682-684)Gtc>Atc	p.V228I	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)		GGGGGGCTGACGGCTAGCGGA	0.687																																					p.V228I		Atlas-SNP	.											.	CHD5	267	.	0			c.G682A						PASS	.						23	21	22					1																	6214783		2180	4275	6455	SO:0001583	missense	26038	exon5			GGCTGACGGCTAG	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.682G>A	chr1.hg19:g.6214783C>T	ENSP00000262450:p.Val228Ile	95.0	0.0	.		129.0	55.0	.	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Missense_Mutation	SNP	ENST00000262450.3	hg19	CCDS57.1	.	.	.	.	.	.	.	.	.	.	C	2.102	-0.405865	0.04832	.	.	ENSG00000116254	ENST00000262450	D	0.90563	-2.69	3.84	-2.17	0.07059	.	0.808768	0.10850	N	0.627297	T	0.79650	0.4482	N	0.12746	0.255	0.21473	N	0.999679	B	0.02656	0.0	B	0.01281	0.0	T	0.64287	-0.6443	10	0.36615	T	0.2	-17.4027	10.8414	0.46718	0.0:0.6614:0.0:0.3386	.	228	Q8TDI0	CHD5_HUMAN	I	228	ENSP00000262450:V228I	ENSP00000262450:V228I	V	-	1	0	CHD5	6137370	0.004000	0.15560	0.842000	0.33263	0.036000	0.12997	-0.171000	0.09883	-0.238000	0.09724	-0.657000	0.03884	GTC	.	.	.	none		0.687	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557		T	6214783	C	T	6214783	3	4	109	1	0	0	0	0	1	0	0	0	3330	536	19	1	5330	1	CHD5	1	6214783	Missense_Mutation	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10		6214783	243035838	1	6946											
ENO1	2023	hgsc.bcm.edu	37	chr1	8926559	8926559	+	Splice_Site	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	cgccattgatgacattgaacGcctggggagagcagagcaga	12	6	14	9	2	0	6	0	3	0	3	0	7	0	6	2	2	3	2	2	2	1	2			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr1:8926559G>T	ENST00000234590.4	-	7	565	c.446C>A	c.(445-447)gCg>gAg	p.A149E		NM_001428.3	NP_001419.1	P06733	ENOA_HUMAN	enolase 1, (alpha)	149	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)		GACATTGAACGCCTGGGGAGA	0.567																																					p.A149E	Esophageal Squamous(21;302 608 19946 22210 33560)	Atlas-SNP	.											.	ENO1	38	.	0			c.C446A						PASS	.						77	75	76					1																	8926559		2203	4300	6503	SO:0001630	splice_region_variant	2023	exon7			TTGAACGCCTGGG	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.445-1C>A	chr1.hg19:g.8926559G>T		42.0	0.0	.		52.0	20.0	.	NM_001428	B2RD59|P22712|Q16704|Q4TUS4|Q53FT9|Q53HR3|Q658M5|Q6GMP2|Q71V37|Q7Z3V6|Q8WU71|Q96GV1|Q9BT62|Q9UCH6|Q9UM55	Missense_Mutation	SNP	ENST00000234590.4	hg19	CCDS97.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.804238	0.90623	.	.	ENSG00000074800	ENST00000234590	T	0.18016	2.24	5.33	5.33	0.75918	Enolase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.48732	0.1516	M	0.85462	2.755	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;0.997;0.996;0.998	T	0.55515	-0.8129	10	0.87932	D	0	-16.4671	18.013	0.89230	0.0:0.0:1.0:0.0	.	53;116;56;149	E2DRY6;A4UCS8;P06733-2;P06733	.;.;.;ENOA_HUMAN	E	149	ENSP00000234590:A149E	ENSP00000234590:A149E	A	-	2	0	ENO1	8849146	1.000000	0.71417	0.982000	0.44146	0.696000	0.40369	9.824000	0.99380	2.492000	0.84095	0.563000	0.77884	GCG	.	.	.	none		0.567	ENO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004945.1	NM_001428	Missense_Mutation	T	8926559	G	T	8926559	5	4	109	1	0	0	0	0	0	0	1	0	5123	1101	38	4	882	4	ENO1	1	8926559	Splice_Site	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10	2711776	8926559	240324062	2	6947											
TMEM57	55219	hgsc.bcm.edu	37	chr1	25784936	25784936	+	Missense_Mutation	SNP	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	ccttatacaccacaatggagGtatcccagccaacaaaaaac	17	6	5	13	0	0	0	0	0	0	0	1	1	1	1	4	2	4	1	4	2	8	3			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr1:25784936G>A	ENST00000374343.4	+	6	886	c.707G>A	c.(706-708)gGt>gAt	p.G236D	TMEM57_ENST00000470035.1_3'UTR|TMEM57_ENST00000399766.3_Intron|TMEM57_ENST00000399763.3_Intron	NM_018202.4	NP_060672.2	Q8N5G2	MACOI_HUMAN	transmembrane protein 57	236					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)		CACAATGGAGGTATCCCAGCC	0.418																																					p.G236D		Atlas-SNP	.											.	TMEM57	72	.	0			c.G707A						PASS	.						114	123	120					1																	25784936		2203	4300	6503	SO:0001583	missense	55219	exon6			ATGGAGGTATCCC	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.707G>A	chr1.hg19:g.25784936G>A	ENSP00000363463:p.Gly236Asp	297.0	0.0	.		302.0	111.0	.	NM_018202	B1AK00|Q2TLX5|Q2TLX6|Q9NVG6	Missense_Mutation	SNP	ENST00000374343.4	hg19	CCDS30638.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.448157	0.84101	.	.	ENSG00000204178	ENST00000374343	.	.	.	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.78375	0.4273	M	0.77820	2.39	0.80722	D	1	D	0.89917	1.0	D	0.70487	0.969	T	0.72865	-0.4163	9	0.15499	T	0.54	-9.6004	19.0021	0.92838	0.0:0.0:1.0:0.0	.	236	Q8N5G2	MACOI_HUMAN	D	236	.	ENSP00000363463:G236D	G	+	2	0	TMEM57	25657523	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.476000	0.97823	2.724000	0.93272	0.563000	0.77884	GGT	.	.	.	none		0.418	TMEM57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009659.2	NM_018202		A	25784936	G	A	25784936	3	1	109	1	0	0	0	0	1	0	0	0	16196	1261	44	2	729	2	TMEM57	1	25784936	Missense_Mutation	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10	16858377	25784936	223465685	3	6948											
STMN1	3925	hgsc.bcm.edu	37	chr1	26230144	26230144	+	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	tcgtttaccttgcgtctttcTtctgcagcttctaatttctt	4	21	5	11	2	5	0	0	0	5	0	6	0	5	0	1	0	4	3	1	0	2	9			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr1:26230144T>A	ENST00000399728.1	-	3	537	c.174A>T	c.(172-174)gaA>gaT	p.E58D	STMN1_ENST00000465604.1_5'UTR|STMN1_ENST00000374291.1_Missense_Mutation_p.E58D|MIR3917_ENST00000580971.1_RNA|STMN1_ENST00000426559.2_Missense_Mutation_p.E58D|STMN1_ENST00000357865.2_Missense_Mutation_p.E58D|STMN1_ENST00000455785.2_Missense_Mutation_p.E58D	NM_203401.1	NP_981946.1	P16949	STMN1_HUMAN	stathmin 1	58	SLD. {ECO:0000255|PROSITE- ProRule:PRU00998}.				axonogenesis (GO:0007409)|intracellular signal transduction (GO:0035556)|microtubule depolymerization (GO:0007019)|mitotic spindle organization (GO:0007052)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of cellular component movement (GO:0051272)|response to virus (GO:0009615)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|microtubule (GO:0005874)	signal transducer activity (GO:0004871)|tubulin binding (GO:0015631)			breast(2)|large_intestine(2)|skin(2)	6		Colorectal(325;3.46e-05)|Lung NSC(340;0.000163)|all_lung(284;0.000234)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0505)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.85e-25)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.013)|READ - Rectum adenocarcinoma(331;0.0649)		TGCGTCTTTCTTCTGCAGCTT	0.388																																					p.E58D		Atlas-SNP	.											.	STMN1	22	.	0			c.A174T						PASS	.						166	179	175					1																	26230144		2203	4300	6503	SO:0001583	missense	3925	exon3			TCTTTCTTCTGCA	J04991	CCDS269.1, CCDS44090.1	1p36.11	2011-02-09	2009-04-28	2001-07-13	ENSG00000117632	ENSG00000117632			6510	protein-coding gene	gene with protein product	"oncoprotein 18"	151442	"chromosome 1 open reading frame 215", "stathmin 1/oncoprotein 18"	LAP18, C1orf215		2917975	Standard	NM_005563		Approved	SMN, OP18, PR22, PP19, PP17, Lag, FLJ32206	uc010oev.2	P16949	OTTHUMG00000007389	ENST00000399728.1:c.174A>T	chr1.hg19:g.26230144T>A	ENSP00000382633:p.Glu58Asp	65.0	0.0	.		61.0	15.0	.	NM_005563	A2A2D1|B2R4E7|B7Z8N4|D3DPJ5	Missense_Mutation	SNP	ENST00000399728.1	hg19	CCDS269.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.140629	0.77775	.	.	ENSG00000117632	ENST00000426559;ENST00000455785;ENST00000399728;ENST00000357865;ENST00000374291;ENST00000446334	.	.	.	5.54	1.94	0.25998	.	0.000000	0.85682	D	0.000000	T	0.74884	0.3775	M	0.93507	3.425	0.26297	N	0.978036	D;D;D	0.62365	0.991;0.972;0.972	D;D;D	0.68943	0.961;0.958;0.958	T	0.67921	-0.5545	9	0.87932	D	0	.	9.3358	0.38049	0.0:0.2825:0.0:0.7175	.	58;58;58	P16949-2;B5BU83;P16949	.;.;STMN1_HUMAN	D	58	.	ENSP00000350531:E58D	E	-	3	2	STMN1	26102731	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.000000	0.29770	0.080000	0.16959	0.533000	0.62120	GAA	.	.	.	none		0.388	STMN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019359.1	NM_005563		A	26230144	T	A	26230144	3	1	109	1	0	0	0	0	1	0	0	0	15320	1606	56	5	438	5	STMN1	1	26230144	Missense_Mutation	SNP	T	TCGA-B9-A8YI-01A-21D-A36X-10	445208	26230144	223020477	4	6949											
UBXN11	91544	hgsc.bcm.edu	37	chr1	26608865	26608865	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggactggggccgggaccgggAccgggactggggccgggacc	5	2	22	12	4	0	0	0	0	0	0	0	5	0	5	5	9	0	0	5	9	0	0			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr1:26608865A>G	ENST00000374222.1	-	16	1952	c.1488T>C	c.(1486-1488)ggT>ggC	p.G496G	UBXN11_ENST00000374221.3_Silent_p.G496G|UBXN11_ENST00000374217.2_Silent_p.G463G|UBXN11_ENST00000314675.7_Silent_p.G376G|UBXN11_ENST00000357089.4_Silent_p.G463G|UBXN11_ENST00000374223.1_Silent_p.G253G			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						cgggaccgggaccgggactgg	0.721																																					p.G496G		Atlas-SNP	.											.	UBXN11	54	.	1	Deletion - In frame(1)	ovary(1)	c.T1488C						PASS	.						25	29	28					1																	26608865		1768	4016	5784	SO:0001819	synonymous_variant	91544	exon16			ACCGGGACCGGGA	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.1488T>C	chr1.hg19:g.26608865A>G		31.0	0.0	.		33.0	24.0	.	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Silent	SNP	ENST00000374222.1	hg19	CCDS41288.1																																																																																			.	.	.	none		0.721	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345		G	26608865	A	G	26608865	2	3	109	1	0	0	0	0	0	0	0	1	16925	262	10	3		3	UBXN11	1	26608865	Silent	SNP	A	TCGA-B9-A8YI-01A-21D-A36X-10	378721	26608865	222641756	5	6950											
WASF2	10163	hgsc.bcm.edu	37	chr1	27742557	27742557	+	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	caaagatcaaagaagtatgaAgggtctgtgtagaatttgag	16	10	12	3	0	2	5	1	2	1	3	2	5	2	5	0	1	0	2	0	1	7	3			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr1:27742557A>C	ENST00000430629.2	-	5	674	c.459T>G	c.(457-459)ccT>ccG	p.P153P	WASF2_ENST00000536657.1_Silent_p.P153P	NM_001201404.1|NM_006990.3	NP_001188333.1|NP_008921.1	Q9Y6W5	WASF2_HUMAN	WAS protein family, member 2	153					actin cytoskeleton organization (GO:0030036)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of lamellipodium assembly (GO:0010592)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|SCAR complex (GO:0031209)	actin binding (GO:0003779)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	18		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0446)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.7e-08)|COAD - Colon adenocarcinoma(152;2e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00139)|KIRC - Kidney renal clear cell carcinoma(1967;0.00204)|STAD - Stomach adenocarcinoma(196;0.00325)|READ - Rectum adenocarcinoma(331;0.0481)		AGAAGTATGAAGGGTCTGTGT	0.458																																					p.P153P		Atlas-SNP	.											.	WASF2	41	.	0			c.T459G						PASS	.						202	177	186					1																	27742557		2203	4300	6503	SO:0001819	synonymous_variant	10163	exon5			GTATGAAGGGTCT	AB026542	CCDS304.1, CCDS55582.1	1p36.11	2011-05-10			ENSG00000158195	ENSG00000158195			12733	protein-coding gene	gene with protein product		605875				10381382	Standard	NM_006990		Approved	WAVE2, SCAR2	uc001bof.2	Q9Y6W5	OTTHUMG00000003393	ENST00000430629.2:c.459T>G	chr1.hg19:g.27742557A>C		88.0	0.0	.		103.0	31.0	.	NM_006990	B4DZN0|O60794|Q9UDY7	Silent	SNP	ENST00000430629.2	hg19	CCDS304.1																																																																																			.	.	.	none		0.458	WASF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009516.1	NM_006990		C	27742557	A	C	27742557	2	2	109	1	0	0	0	0	0	0	0	1	17265	59	3	5		5	WASF2	1	27742557	Silent	SNP	A	TCGA-B9-A8YI-01A-21D-A36X-10	1133692	27742557	221508064	6	6951											
PTPRU	10076	hgsc.bcm.edu	37	chr1	29585188	29585188	+	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	ctacgtgcgcgttaatggggGccccctgggcagtgctgtgt	4	10	16	11	3	0	0	0	0	0	0	0	0	0	0	2	3	3	3	2	3	2	2			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr1:29585188G>C	ENST00000345512.3	+	3	506	c.377G>C	c.(376-378)gGc>gCc	p.G126A	PTPRU_ENST00000323874.8_Missense_Mutation_p.G126A|PTPRU_ENST00000428026.2_Missense_Mutation_p.G126A|PTPRU_ENST00000356870.3_Missense_Mutation_p.G126A|PTPRU_ENST00000460170.2_Missense_Mutation_p.G126A|PTPRU_ENST00000373779.3_Missense_Mutation_p.G126A	NM_005704.4	NP_005695.3	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	126	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				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)		GTTAATGGGGGCCCCCTGGGC	0.607																																					p.G126A		Atlas-SNP	.											.	PTPRU	374	.	0			c.G377C						PASS	.						78	86	83					1																	29585188		2203	4300	6503	SO:0001583	missense	10076	exon3			ATGGGGGCCCCCT	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.377G>C	chr1.hg19:g.29585188G>C	ENSP00000334941:p.Gly126Ala	121.0	0.0	.		132.0	50.0	.	NM_001195001	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	Missense_Mutation	SNP	ENST00000345512.3	hg19	CCDS334.1	.	.	.	.	.	.	.	.	.	.	G	34	5.382138	0.95967	.	.	ENSG00000060656	ENST00000345512;ENST00000373779;ENST00000356870;ENST00000323874;ENST00000428026;ENST00000460170	T;T;T;T;T;T	0.02631	4.22;4.22;4.22;4.22;4.22;4.22	5.72	5.72	0.89469	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.000000	0.85682	D	0.000000	T	0.13543	0.0328	L	0.58583	1.82	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	T	0.00498	-1.1704	9	.	.	.	.	18.8634	0.92281	0.0:0.0:1.0:0.0	.	126;126;126;126;126	Q92729-3;Q92729-4;Q92729-2;E9PH42;Q92729	.;.;.;.;PTPRU_HUMAN	A	126	ENSP00000334941:G126A;ENSP00000362884:G126A;ENSP00000349333:G126A;ENSP00000314987:G126A;ENSP00000392332:G126A;ENSP00000432906:G126A	.	G	+	2	0	PTPRU	29457775	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.960000	0.87893	2.699000	0.92147	0.591000	0.81541	GGC	.	.	.	none		0.607	PTPRU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010447.1			C	29585188	G	C	29585188	3	2	109	1	0	0	0	0	1	0	0	0	12826	1203	42	4	387	4	PTPRU	1	29585188	Missense_Mutation	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10	1842631	29585188	219665433	7	6952											
DLGAP3	58512	hgsc.bcm.edu	37	chr1	35370206	35370206	+	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	agttgtcatcggaactccacCagcctgtggacttggcctgg	7	10	12	12	1	1	0	1	0	0	0	3	2	2	2	4	4	2	1	4	4	1	2			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr1:35370206C>T	ENST00000373347.1	-	3	1047	c.779G>A	c.(778-780)tGg>tAg	p.W260*	DLGAP3_ENST00000235180.4_Nonsense_Mutation_p.W260*|DLGAP3_ENST00000495979.1_5'Flank			O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated protein 3	260					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)				GGAACTCCACCAGCCTGTGGA	0.652																																					p.W260X		Atlas-SNP	.											.	DLGAP3	107	.	0			c.G779A						PASS	.						124	114	117					1																	35370206		2203	4300	6503	SO:0001587	stop_gained	58512	exon1			CTCCACCAGCCTG	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.779G>A	chr1.hg19:g.35370206C>T	ENSP00000362444:p.Trp260*	99.0	0.0	.		93.0	33.0	.	NM_001080418	Q5TDD5|Q9H3X7	Nonsense_Mutation	SNP	ENST00000373347.1	hg19	CCDS30670.1	.	.	.	.	.	.	.	.	.	.	C	38	7.264207	0.98171	.	.	ENSG00000116544	ENST00000373347;ENST00000235180	.	.	.	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.5694	18.7023	0.91625	0.0:1.0:0.0:0.0	.	.	.	.	X	260	.	ENSP00000235180:W260X	W	-	2	0	DLGAP3	35142793	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	7.378000	0.79679	2.492000	0.84095	0.655000	0.94253	TGG	.	.	.	none		0.652	DLGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011554.1	NM_021234		T	35370206	C	T	35370206	4	4	109	1	0	0	0	0	0	1	0	0	4563	595	21	2	2200	2	DLGAP3	1	35370206	Nonsense_Mutation	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10	5785018	35370206	213880415	8	6953											
KLHL20	27252	hgsc.bcm.edu	37	chr1	173754361	173754361	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaggagttattaaaatgacAcattgtgaatcccatatttg	14	14	8	5	0	0	2	0	2	0	0	1	3	1	3	1	1	0	2	1	1	6	6			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr1:173754361A>G	ENST00000209884.4	+	12	1942	c.1806A>G	c.(1804-1806)acA>acG	p.T602T	KLHL20_ENST00000546011.1_Silent_p.T413T	NM_014458.3	NP_055273.2	Q9Y2M5	KLH20_HUMAN	kelch-like family member 20	602					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						TTAAAATGACACATTGTGAAT	0.408																																					p.T602T	GBM(159;862 2695 6559 23041)	Atlas-SNP	.											.	KLHL20	54	.	0			c.A1806G						PASS	.						110	110	110					1																	173754361		2203	4300	6503	SO:0001819	synonymous_variant	27252	exon12			AATGACACATTGT	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.1806A>G	chr1.hg19:g.173754361A>G		51.0	0.0	.		44.0	20.0	.	NM_014458	B3KMA0|B4DUR0|Q5TZF2|Q5ZF45|Q9H457	Silent	SNP	ENST00000209884.4	hg19	CCDS1310.1																																																																																			.	.	.	none		0.408	KLHL20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097582.1	NM_014458		G	173754361	A	G	173754361	2	3	109	1	0	0	0	0	0	0	0	1	8382	146	6	3		3	KLHL20	1	173754361	Silent	SNP	A	TCGA-B9-A8YI-01A-21D-A36X-10	138384155	173754361	75496260	9	6954											
RFWD2	64326	hgsc.bcm.edu	37	chr1	176105635	176105635	+	Missense_Mutation	SNP	T	T	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	attccttacttccactctctTaatatcctcttccaaaacac	11	15	0	15	0	2	0	0	0	2	0	7	0	6	0	4	0	2	0	4	0	5	6			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr1:176105635T>G	ENST00000367669.3	-	7	1394	c.880A>C	c.(880-882)Aag>Cag	p.K294Q	RFWD2_ENST00000308769.8_Intron	NM_022457.5	NP_071902.2	Q8NHY2	RFWD2_HUMAN	ring finger and WD repeat domain 2, E3 ubiquitin protein ligase	294					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin protein ligase activity (GO:0061630)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						TCCACTCTCTTAATATCCTCT	0.343																																					p.K294Q	Ovarian(134;1413 1765 5706 35534 51541)	Atlas-SNP	.											.	RFWD2	67	.	0			c.A880C						PASS	.						119	113	115					1																	176105635		2202	4300	6502	SO:0001583	missense	64326	exon7			CTCTCTTAATATC	AK001278	CCDS30944.1, CCDS44279.1	1q25.1-q25.2	2013-01-09	2012-02-23		ENSG00000143207	ENSG00000143207		"WD repeat domain containing", "RING-type (C3HC4) zinc fingers"	17440	protein-coding gene	gene with protein product		608067	"ring finger and WD repeat domain 2"			10395541	Standard	XM_005245447		Approved	FLJ10416, COP1, RNF200	uc001gku.1	Q8NHY2	OTTHUMG00000034986	ENST00000367669.3:c.880A>C	chr1.hg19:g.176105635T>G	ENSP00000356641:p.Lys294Gln	168.0	0.0	.		191.0	60.0	.	NM_022457	E9PKI0|Q504W6|Q6H103|Q9H6L7|X5D9B4	Missense_Mutation	SNP	ENST00000367669.3	hg19	CCDS30944.1	.	.	.	.	.	.	.	.	.	.	T	13.08	2.128960	0.37533	.	.	ENSG00000143207	ENST00000367665;ENST00000367669	T	0.12147	2.71	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.21718	0.0523	N	0.21448	0.665	0.80722	D	1	B;P;D	0.57899	0.2;0.659;0.981	B;P;D	0.67231	0.175;0.775;0.95	T	0.06881	-1.0802	10	0.21014	T	0.42	-14.9048	15.0966	0.72238	0.0:0.0:0.0:1.0	.	30;54;294	Q8NHY2-3;B1AMD2;Q8NHY2	.;.;RFWD2_HUMAN	Q	30;294	ENSP00000356641:K294Q	ENSP00000356637:K30Q	K	-	1	0	RFWD2	174372258	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.068000	0.71201	2.060000	0.61445	0.528000	0.53228	AAG	.	.	.	none		0.343	RFWD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084672.2	NM_022457		G	176105635	T	G	176105635	3	3	109	1	0	0	0	0	1	0	0	0	13273	1763	61	5	1371	5	RFWD2	1	176105635	Missense_Mutation	SNP	T	TCGA-B9-A8YI-01A-21D-A36X-10	2351274	176105635	73144986	10	6955											
PTPN14	5784	hgsc.bcm.edu	37	chr1	214568286	214568292	+	Frame_Shift_Del	DEL	GAATGGT	GAATGGT	-																															tttgttgatgagctccactaGaatggtcgacttgttatgag																										TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	GAATGGT	GAATGGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr1:214568286_214568292delGAATGGT	ENST00000366956.5	-	9	990_996	c.796_802delACCATTC	c.(796-804)accattctafs	p.TIL266fs	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	266	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)	p.L268L(1)		NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		AGCTCCACTAGAATGGTCGACTTGTTA	0.43																																					p.266_268del	Colon(92;557 1424 24372 34121 40073)	Atlas-INDEL	.											.	PTPN14	168	.	1	Substitution - coding silent(1)	lung(1)	c.797_803del						PASS	.																																			SO:0001589	frameshift_variant	5784	exon9			.	X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.796_802delACCATTC	chr1.hg19:g.214568286_214568292delGAATGGT	ENSP00000355923:p.Thr266fs	66.0	0.0	0		62.0	15.0	0.241935	NM_005401	Q5VSI0	Frame_Shift_Del	DEL	ENST00000366956.5	hg19	CCDS1514.1																																																																																			.	.	.	none		0.43	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401		-	214568292	GAATGGT	-	214568286	7	5	109	1	0	1	0	1	0	0	0	0	12794	933	33	0	2805	0	PTPN14	1	214568286	Frame_Shift_Del	DEL	GAATGGT	TCGA-B9-A8YI-01A-21D-A36X-10	38462651	214568286	34682335	11	6956											
IARS2	55699	hgsc.bcm.edu	37	chr1	220316411	220316411	+	Frame_Shift_Del	DEL	A	A	-																															ttcttggaagcatccctggcAaaaatgcagctgagtacaag																										TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr1:220316411delA	ENST00000302637.5	+	21	2790	c.2686delA	c.(2686-2688)aaafs	p.K896fs	IARS2_ENST00000366922.1_Frame_Shift_Del_p.K824fs|IARS2_ENST00000467924.1_3'UTR	NM_018060.3	NP_060530.3	Q9NSE4	SYIM_HUMAN	isoleucyl-tRNA synthetase 2, mitochondrial	896					gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)			NS(1)|breast(1)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(7)|lung(17)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)	CATCCCTGGCAAAAATGCAGC	0.433																																					p.G895fs		Atlas-Indel,Pindel	.											.	IARS2	106	.	0			c.2685delC						PASS	.						144	136	139					1																	220316411		2203	4300	6503	SO:0001589	frameshift_variant	55699	exon21			.	AK022665	CCDS1523.1	1q41	2011-07-01	2007-02-26		ENSG00000067704	ENSG00000067704	6.1.1.5	"Aminoacyl tRNA synthetases / Class I"	29685	protein-coding gene	gene with protein product	"isoleucine tRNA ligase 2, mitochondrial"	612801					Standard	NM_018060		Approved	FLJ10326	uc001hmc.3	Q9NSE4	OTTHUMG00000037287	ENST00000302637.5:c.2686delA	chr1.hg19:g.220316411delA	ENSP00000303279:p.Lys896fs	106.0	0.0	0		146.0	40.0	0.273973	NM_018060	B2RPG8|Q1M2P9|Q6PI85|Q7L439|Q86WU9|Q96D91|Q9H9Q8|Q9NW42	Frame_Shift_Del	DEL	ENST00000302637.5	hg19	CCDS1523.1																																																																																			.	.	.	none		0.433	IARS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018060		-	220316411	A	-	220316411	7	5	109	1	0	1	0	1	0	0	0	0	7481	131	5	0	2768	0	IARS2	1	220316411	Frame_Shift_Del	DEL	A	TCGA-B9-A8YI-01A-21D-A36X-10	5748125	220316411	28934210	12	6957											
WDR64	128025	hgsc.bcm.edu	37	chr1	241823862	241823862	+	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	ttatgacaagttttatgcatCggtacagaagctctttggtc	10	15	9	7	1	1	2	0	1	1	1	3	2	1	2	0	2	3	4	0	2	5	5	rs150170869	byFrequency	TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr1:241823862C>A	ENST00000366552.2	+	2	383	c.176C>A	c.(175-177)tCg>tAg	p.S59*	WDR64_ENST00000461971.1_3'UTR|WDR64_ENST00000437684.2_Nonsense_Mutation_p.S59*	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	59										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)			TTTTATGCATCGGTACAGAAG	0.393																																					p.S59X		Atlas-SNP	.											.	WDR64	234	.	0			c.C176A						PASS	.						262	219	232					1																	241823862		692	1591	2283	SO:0001587	stop_gained	128025	exon2			ATGCATCGGTACA	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.176C>A	chr1.hg19:g.241823862C>A	ENSP00000355510:p.Ser59*	243.0	0.0	.		241.0	76.0	.	NM_144625	B1ANT0|Q7Z573|Q96LY9	Nonsense_Mutation	SNP	ENST00000366552.2	hg19		.	.	.	.	.	.	.	.	.	.	C	37	6.339487	0.97489	.	.	ENSG00000162843	ENST00000366552;ENST00000437684	.	.	.	5.36	2.28	0.28536	.	1.244700	0.05867	N	0.623941	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	0.5859	4.3923	0.11346	0.3709:0.4575:0.0:0.1716	.	.	.	.	X	59	.	ENSP00000355510:S59X	S	+	2	0	WDR64	239890485	0.000000	0.05858	0.000000	0.03702	0.721000	0.41392	0.083000	0.14871	0.148000	0.19059	0.655000	0.94253	TCG	.	C|0.997;T|0.003	.	alt		0.393	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625		A	241823862	C	A	241823862	4	1	109	1	0	0	0	0	0	1	0	0	17327	893	31	4	182	4	WDR64	1	241823862	Nonsense_Mutation	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10	21507451	241823862	7426759	13	6958											
OR11L1	391189	hgsc.bcm.edu	37	chr1	248004550	248004550	+	Missense_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	ggacacaatgaaaacataggGccccagtgtcagaaaaaaac	19	4	9	9	0	1	2	1	1	0	1	1	3	1	3	2	2	2	0	2	2	7	1	rs563634223		TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr1:248004550G>A	ENST00000355784.2	-	1	704	c.649C>T	c.(649-651)Ccc>Tcc	p.P217S		NM_001001959.1	NP_001001959.1	Q8NGX0	O11L1_HUMAN	olfactory receptor, family 11, subfamily L, member 1	217						extracellular vesicular exosome (GO:0070062)|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(5)|large_intestine(5)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57	all_cancers(71;8.78e-05)|all_epithelial(71;9.15e-06)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			AAAACATAGGGCCCCAGTGTC	0.488													G|||	1	0.000199681	0	0	5008	,	,		20737	0		0	False		,,,				2504	0.001				p.P217S		Atlas-SNP	.											.	OR11L1	108	.	0			c.C649T						PASS	.						83	87	86					1																	248004550		2203	4300	6503	SO:0001583	missense	391189	exon1			CATAGGGCCCCAG	AB065646	CCDS31098.1	1q44	2013-09-24			ENSG00000197591	ENSG00000197591		"GPCR / Class A : Olfactory receptors"	14998	protein-coding gene	gene with protein product							Standard	NM_001001959		Approved		uc001idn.1	Q8NGX0	OTTHUMG00000040193	ENST00000355784.2:c.649C>T	chr1.hg19:g.248004550G>A	ENSP00000348033:p.Pro217Ser	304.0	0.0	.		302.0	96.0	.	NM_001001959		Missense_Mutation	SNP	ENST00000355784.2	hg19	CCDS31098.1	.	.	.	.	.	.	.	.	.	.	G	0.004	-2.365610	0.00212	.	.	ENSG00000197591	ENST00000355784	T	0.28895	1.59	4.27	3.13	0.36017	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34245	N	0.004124	T	0.02649	0.0080	N	0.00004	-3.355	0.21553	N	0.999641	B	0.02656	0.0	B	0.01281	0.0	T	0.40869	-0.9540	10	0.02654	T	1	.	5.3774	0.16172	0.7611:0.0:0.0856:0.1533	.	217	Q8NGX0	O11L1_HUMAN	S	217	ENSP00000348033:P217S	ENSP00000348033:P217S	P	-	1	0	OR11L1	246071173	0.973000	0.33851	0.617000	0.29091	0.139000	0.21198	3.184000	0.50926	0.774000	0.33427	-0.474000	0.04947	CCC	.	.	.	none		0.488	OR11L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096850.1	NM_001001959		A	248004550	G	A	248004550	3	1	109	1	0	0	0	0	1	0	0	0	10937	1203	42	2	323	2	OR11L1	1	248004550	Missense_Mutation	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10	6180688	248004550	1246071	14	6959											
PNPT1	87178	hgsc.bcm.edu	37	chr2	55900032	55900032	+	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	gcacagatgttcttacttatGagtatatttcacaatctctg	11	16	6	8	0	3	2	1	1	2	1	4	2	3	2	0	0	1	3	0	0	5	6	rs141543222	byFrequency	TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr2:55900032G>C	ENST00000447944.2	-	9	948	c.862C>G	c.(862-864)Cat>Gat	p.H288D		NM_033109.3	NP_149100.2	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	288					cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA polyadenylation (GO:0097222)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA 5'-end processing (GO:0000964)|mitochondrial RNA catabolic process (GO:0000957)|mitochondrion morphogenesis (GO:0070584)|mitotic cell cycle arrest (GO:0071850)|mRNA catabolic process (GO:0006402)|negative regulation of growth (GO:0045926)|nuclear polyadenylation-dependent mRNA catabolic process (GO:0071042)|positive regulation of miRNA catabolic process (GO:2000627)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|positive regulation of mRNA catabolic process (GO:0061014)|protein homooligomerization (GO:0051260)|protein homotrimerization (GO:0070207)|regulation of cellular respiration (GO:0043457)|regulation of cellular senescence (GO:2000772)|RNA catabolic process (GO:0006401)|RNA import into mitochondrion (GO:0035927)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA polyadenylation (GO:0043631)|rRNA import into mitochondrion (GO:0035928)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrial degradosome (GO:0045025)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	3'-5'-exoribonuclease activity (GO:0000175)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|polyribonucleotide nucleotidyltransferase activity (GO:0004654)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			TCTTACTTATGAGTATATTTC	0.388																																					p.H288D		Atlas-SNP	.											.	PNPT1	68	.	0			c.C862G						PASS	.						120	122	122					2																	55900032		2203	4300	6503	SO:0001583	missense	87178	exon9			ACTTATGAGTATA	BC053660	CCDS1856.1	2p15	2013-01-08			ENSG00000138035	ENSG00000138035			23166	protein-coding gene	gene with protein product	"polynucleotide phosphorylase", "3'-5' RNA exonuclease"	610316	"deafness, autosomal recessive 70"	DFNB70		12419256	Standard	NM_033109		Approved	PNPase, OLD35, old-35	uc002rzf.3	Q8TCS8	OTTHUMG00000129335	ENST00000447944.2:c.862C>G	chr2.hg19:g.55900032G>C	ENSP00000400646:p.His288Asp	92.0	0.0	.		97.0	39.0	.	NM_033109	Q53SU0|Q68CN1|Q7Z7D1|Q8IWX1|Q96T05|Q9BRU3|Q9BVX0	Missense_Mutation	SNP	ENST00000447944.2	hg19	CCDS1856.1	.	.	.	.	.	.	.	.	.	.	G	9.531	1.110961	0.20714	.	.	ENSG00000138035	ENST00000447944	T	0.56444	0.46	5.77	1.71	0.24356	Polynucleotide phosphorylase, phosphorolytic RNA-binding, bacterial/organelle-type (3);	0.736854	0.13396	N	0.390997	T	0.30696	0.0773	N	0.08118	0	0.21416	N	0.999699	B	0.02656	0.0	B	0.06405	0.002	T	0.20773	-1.0265	10	0.44086	T	0.13	.	9.8321	0.40948	0.071:0.0:0.4272:0.5018	.	288	Q8TCS8	PNPT1_HUMAN	D	288	ENSP00000400646:H288D	ENSP00000386075:H288D	H	-	1	0	PNPT1	55753536	0.997000	0.39634	0.469000	0.27204	0.706000	0.40770	2.348000	0.44045	0.435000	0.26365	-0.169000	0.13324	CAT	.	G|0.998;A|0.002	.	alt		0.388	PNPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251481.2	NM_033109		C	55900032	G	C	55900032	3	2	109	1	0	0	0	0	1	0	0	0	12180	1290	45	4	1569	4	PNPT1	2	55900032	Missense_Mutation	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10		55900032	187299341	15	6960											
CNNM4	26504	hgsc.bcm.edu	37	chr2	97427711	97427711	+	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	cccattagcaagctcctggaCttttttctgggccaggagat	8	12	10	11	0	1	1	0	0	1	1	2	3	2	2	3	3	2	2	3	3	2	4			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr2:97427711C>G	ENST00000377075.2	+	1	1073	c.975C>G	c.(973-975)gaC>gaG	p.D325E		NM_020184.3	NP_064569.3	Q6P4Q7	CNNM4_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 4	325	DUF21.				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						AGCTCCTGGACTTTTTTCTGG	0.517																																					p.D325E		Atlas-SNP	.											.	CNNM4	48	.	0			c.C975G						PASS	.						94	98	97					2																	97427711		2203	4300	6503	SO:0001583	missense	26504	exon1			CCTGGACTTTTTT	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.975C>G	chr2.hg19:g.97427711C>G	ENSP00000366275:p.Asp325Glu	154.0	0.0	.		174.0	65.0	.	NM_020184	B7Z1U0|C7SQM3|C7SQM4|C7SQM5|Q53RE5|Q9H9G3|Q9HCI0|Q9NRN1	Missense_Mutation	SNP	ENST00000377075.2	hg19	CCDS2024.2	.	.	.	.	.	.	.	.	.	.	C	15.01	2.706539	0.48412	.	.	ENSG00000158158	ENST00000377075	D	0.88509	-2.39	5.03	0.441	0.16577	Domain of unknown function DUF21 (1);	0.000000	0.85682	D	0.000000	D	0.90964	0.7159	M	0.81239	2.535	0.80722	D	1	P	0.47191	0.891	P	0.53809	0.735	D	0.88147	0.2848	10	0.38643	T	0.18	-3.7681	10.429	0.44395	0.0:0.6505:0.0:0.3495	.	325	Q6P4Q7	CNNM4_HUMAN	E	325	ENSP00000366275:D325E	ENSP00000366275:D325E	D	+	3	2	CNNM4	96791438	0.977000	0.34250	0.961000	0.40146	0.995000	0.86356	0.470000	0.22084	0.136000	0.18733	0.655000	0.94253	GAC	.	.	.	none		0.517	CNNM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252954.1	NM_020184		G	97427711	C	G	97427711	3	3	109	1	0	0	0	0	1	0	0	0	3617	564	20	4	977	4	CNNM4	2	97427711	Missense_Mutation	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10	41527679	97427711	145771662	16	6961											
MCM6	4175	hgsc.bcm.edu	37	chr2	136614438	136614438	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgctgccaaaatggacgtccGggcgttcagagtagcctgac	9	8	13	11	3	1	2	1	1	0	1	2	3	2	3	3	2	3	3	3	2	3	2	rs202222981		TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr2:136614438G>A	ENST00000264156.2	-	11	1546	c.1486C>T	c.(1486-1488)Cgg>Tgg	p.R496W	MCM6_ENST00000492091.1_Intron	NM_005915.5	NP_005906.2	Q14566	MCM6_HUMAN	minichromosome maintenance complex component 6	496	MCM.				DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|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)		ATGGACGTCCGGGCGTTCAGA	0.388																																					p.R496W	Ovarian(196;141 2104 8848 24991 25939)	Atlas-SNP	.											.	MCM6	64	.	0			c.C1486T						PASS	.						79	77	78					2																	136614438		2203	4300	6503	SO:0001583	missense	4175	exon11			ACGTCCGGGCGTT		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.1486C>T	chr2.hg19:g.136614438G>A	ENSP00000264156:p.Arg496Trp	106.0	0.0	.		112.0	32.0	.	NM_005915	B2R6H2|Q13504|Q99859	Missense_Mutation	SNP	ENST00000264156.2	hg19	CCDS2179.1	.	.	.	.	.	.	.	.	.	.	G	17.19	3.325884	0.60743	.	.	ENSG00000076003	ENST00000264156	T	0.12672	2.66	5.87	3.46	0.39613	.	0.000000	0.85682	D	0.000000	T	0.57359	0.2048	H	0.99626	4.665	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74140	-0.3761	10	0.87932	D	0	-14.5676	12.8383	0.57786	0.0:0.0:0.4151:0.5849	.	496	Q14566	MCM6_HUMAN	W	496	ENSP00000264156:R496W	ENSP00000264156:R496W	R	-	1	2	MCM6	136330908	1.000000	0.71417	1.000000	0.80357	0.690000	0.40134	3.514000	0.53422	0.460000	0.27045	-0.467000	0.05162	CGG	.	G|1.000;T|0.000	.	alt		0.388	MCM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254658.1	NM_005915		A	136614438	G	A	136614438	3	1	109	1	0	0	0	0	1	0	0	0	9398	1115	39	1	1007	1	MCM6	2	136614438	Missense_Mutation	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10	39186727	136614438	106584935	17	6962											
TTN	7273	hgsc.bcm.edu	37	chr2	179604477	179604477	+	Missense_Mutation	SNP	T	T	A																															tgttttggctccttgctgaaTtctaggaccctcagctgtta																										TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr2:179604477T>A	ENST00000591111.1	-	46	12756	c.12532A>T	c.(12532-12534)Att>Ttt	p.I4178F	TTN_ENST00000359218.5_Missense_Mutation_p.I4257F|TTN_ENST00000460472.2_Missense_Mutation_p.I4132F|TTN_ENST00000342175.6_Missense_Mutation_p.I4324F|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.I4495F|TTN-AS1_ENST00000582847.1_RNA|TTN-AS1_ENST00000590773.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCTTGCTGAATTCTAGGACCC	0.383																																					p.I4495F		Atlas-SNP	.											.	TTN	18412	.	0			c.A13483T						PASS	.						189	188	188					2																	179604477		1861	4101	5962	SO:0001583	missense	7273	exon48			GCTGAATTCTAGG	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.12532A>T	chr2.hg19:g.179604477T>A	ENSP00000465570:p.Ile4178Phe	155.0	0.0	.		153.0	56.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	4.968	0.179779	0.09443	.	.	ENSG00000155657	ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T	0.63580	0.01;-0.04;-0.05	5.44	1.48	0.22813	.	.	.	.	.	T	0.47322	0.1439	L	0.42245	1.32	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	0.47355	-0.9124	9	0.87932	D	0	.	0.8604	0.01192	0.1519:0.2518:0.1568:0.4394	.	4132;4257;4324	D3DPF9;E7EQE6;E7ET18	.;.;.	F	4132;4324;4257;4132	ENSP00000434586:I4132F;ENSP00000340554:I4324F;ENSP00000352154:I4257F	ENSP00000340554:I4324F	I	-	1	0	TTN	179312722	0.000000	0.05858	0.195000	0.23364	0.349000	0.29174	-0.311000	0.08124	0.354000	0.24105	0.533000	0.62120	ATT	.	.	.	none		0.383	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179604477	T	A	179604477	3	1	109	1	0	0	0	0	1	0	0	0	16747	1493	52	5	91306	5	TTN	2	179604477	Missense_Mutation	SNP	T	TCGA-B9-A8YI-01A-21D-A36X-10	42990039	179604477	63594896	18	6963	76	2									
TTN	7273	hgsc.bcm.edu	37	chr2	179604480	179604480	+	Silent	SNP	T	T	G																															tttggctccttgctgaattcTaggaccctcagctgttagga																										TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr2:179604480T>G	ENST00000591111.1	-	46	12753	c.12529A>C	c.(12529-12531)Aga>Cga	p.R4177R	TTN_ENST00000359218.5_Silent_p.R4256R|TTN_ENST00000460472.2_Silent_p.R4131R|TTN_ENST00000342175.6_Silent_p.R4323R|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Silent_p.R4494R|TTN-AS1_ENST00000582847.1_RNA|TTN-AS1_ENST00000590773.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGCTGAATTCTAGGACCCTCA	0.388																																					p.R4494R		Atlas-SNP	.											.	TTN	18412	.	0			c.A13480C						PASS	.						189	187	188					2																	179604480		1855	4102	5957	SO:0001819	synonymous_variant	7273	exon48			GAATTCTAGGACC	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.12529A>C	chr2.hg19:g.179604480T>G		153.0	0.0	.		153.0	57.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.	.	none		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179604480	T	G	179604480	2	3	109	1	0	0	0	0	0	0	0	1	16747	1530	53	5		5	TTN	2	179604480	Silent	SNP	T	TCGA-B9-A8YI-01A-21D-A36X-10	3	179604480	63594893	19	6964	76	2									
CUL3	8452	hgsc.bcm.edu	37	chr2	225360561	225360561	+	Frame_Shift_Del	DEL	T	T	-																															atccatacctcaaatgtgtaTttttctctattattaaagag																										TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr2:225360561delT	ENST00000264414.4	-	13	2168	c.1830delA	c.(1828-1830)aaafs	p.K610fs	CUL3_ENST00000409777.1_Frame_Shift_Del_p.K586fs|CUL3_ENST00000409096.1_Frame_Shift_Del_p.K586fs|CUL3_ENST00000344951.4_Frame_Shift_Del_p.K544fs	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	610					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)		CAAATGTGTATTTTTCTCTAT	0.333																																					p.Y617fs		Atlas-Indel,Pindel	.											.	CUL3	96	.	0			c.1849delT						PASS	.						103	101	101					2																	225360561		2202	4300	6502	SO:0001589	frameshift_variant	8452	exon13			.	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.1830delA	chr2.hg19:g.225360561delT	ENSP00000264414:p.Lys610fs	118.0	0.0	0		109.0	43.0	0.394495	NM_001257198	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Frame_Shift_Del	DEL	ENST00000264414.4	hg19	CCDS2462.1																																																																																			.	.	.	none		0.333	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2			-	225360561	T	-	225360561	7	5	109	1	0	1	0	1	0	0	0	0	4058	1490	52	0	492	0	CUL3	2	225360561	Frame_Shift_Del	DEL	T	TCGA-B9-A8YI-01A-21D-A36X-10	45756081	225360561	17838812	20	6965											
DIS3L2	129563	hgsc.bcm.edu	37	chr2	233001388	233001388	+	Missense_Mutation	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	gccaacacactgttcatctgCcgcattgtggactggaagga	10	9	11	11	1	2	0	1	0	1	0	2	3	2	3	2	3	2	2	2	3	2	2			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr2:233001388C>T	ENST00000360410.4	+	9	1244	c.968C>T	c.(967-969)gCc>gTc	p.A323V	DIS3L2_ENST00000273009.6_Silent_p.C303C|DIS3L2_ENST00000409307.1_Silent_p.C303C|DIS3L2_ENST00000325385.7_Silent_p.C303C					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)		TGTTCATCTGCCGCATTGTGG	0.517																																					p.C303C		Atlas-SNP	.											.	DIS3L2	77	.	0			c.C909T						PASS	.						115	110	112					2																	233001388		1948	4147	6095	SO:0001583	missense	129563	exon8			CATCTGCCGCATT	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.968C>T	chr2.hg19:g.233001388C>T	ENSP00000353584:p.Ala323Val	138.0	0.0	.		148.0	49.0	.	NM_152383		Silent	SNP	ENST00000360410.4	hg19		.	.	.	.	.	.	.	.	.	.	C	24.4	4.524345	0.85600	.	.	ENSG00000144535	ENST00000360410	T	0.38560	1.13	6.08	5.21	0.72293	.	.	.	.	.	T	0.49270	0.1547	.	.	.	0.25328	N	0.989053	.	.	.	.	.	.	T	0.47560	-0.9108	6	0.87932	D	0	-20.4148	11.8835	0.52589	0.0:0.8511:0.0:0.1489	.	.	.	.	V	323	ENSP00000353584:A323V	ENSP00000353584:A323V	A	+	2	0	DIS3L2	232709632	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.662000	0.37418	1.592000	0.50018	0.591000	0.81541	GCC	.	.	.	none		0.517	DIS3L2-202	KNOWN	basic	protein_coding	protein_coding		NM_152383		T	233001388	C	T	233001388	3	4	109	1	0	0	0	0	1	0	0	0	4539	747	26	2	935	2	DIS3L2	2	233001388	Missense_Mutation	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10	7640827	233001388	10197985	21	6966											
NUP210	23225	hgsc.bcm.edu	37	chr3	13383246	13383246	+	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	gtgtgggaagaactcgtcttActtcaatctgttgtggggct	7	14	13	7	1	3	1	1	0	2	1	4	2	3	2	0	3	2	2	0	3	4	3			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr3:13383246A>G	ENST00000254508.5	-	23	3311		c.e23+1		NUP210_ENST00000485755.1_5'Flank	NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa						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)					AACTCGTCTTACTTCAATCTG	0.507																																					.		Atlas-SNP	.											.	NUP210	182	.	0			c.3228+2T>C						PASS	.						158	130	140					3																	13383246		2203	4300	6503	SO:0001630	splice_region_variant	23225	exon24			CGTCTTACTTCAA	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.3228+1T>C	chr3.hg19:g.13383246A>G		46.0	0.0	.		47.0	17.0	.	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Splice_Site	SNP	ENST00000254508.5	hg19	CCDS33704.1	.	.	.	.	.	.	.	.	.	.	A	15.91	2.972046	0.53614	.	.	ENSG00000132182	ENST00000254508	.	.	.	5.64	5.64	0.86602	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8389	0.70209	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NUP210	13358246	1.000000	0.71417	0.859000	0.33776	0.496000	0.33645	8.214000	0.89760	2.147000	0.66899	0.455000	0.32223	.	.	.	.	none		0.507	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923	Intron	G	13383246	A	G	13383246	5	3	109	1	0	0	0	0	0	0	1	0	10767	405	14	3	2505	3	NUP210	3	13383246	Splice_Site	SNP	A	TCGA-B9-A8YI-01A-21D-A36X-10		13383246	184639184	22	6967											
COLQ	8292	hgsc.bcm.edu	37	chr3	15531095	15531095	+	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	ggtggaggaggcgtcagcagGcagcatgctttgtggccacc	7	7	17	10	1	1	0	1	0	0	0	1	2	1	2	2	6	3	4	2	6	0	1			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr3:15531095G>T	ENST00000383788.5	-	2	281	c.156C>A	c.(154-156)tgC>tgA	p.C52*	COLQ_ENST00000383786.5_Nonsense_Mutation_p.C52*|COLQ_ENST00000603808.1_Nonsense_Mutation_p.C52*|COLQ_ENST00000435459.2_Nonsense_Mutation_p.C42*|COLQ_ENST00000383781.4_Nonsense_Mutation_p.C42*|COLQ_ENST00000383785.2_Nonsense_Mutation_p.C52*|COLQ_ENST00000383787.2_Nonsense_Mutation_p.C52*	NM_005677.3	NP_005668.2	Q9Y215	COLQ_HUMAN	collagen-like tail subunit (single strand of homotrimer) of asymmetric acetylcholinesterase	52	PRAD.				acetylcholine catabolic process in synaptic cleft (GO:0001507)|asymmetric protein localization (GO:0008105)	basal lamina (GO:0005605)|cell junction (GO:0030054)|collagen trimer (GO:0005581)|extracellular space (GO:0005615)|synapse (GO:0045202)				endometrium(2)|large_intestine(4)|lung(10)|skin(3)	19						GCGTCAGCAGGCAGCATGCTT	0.552																																					p.C52X		Atlas-SNP	.											.	COLQ	82	.	0			c.C156A						PASS	.						97	79	85					3																	15531095		2203	4300	6503	SO:0001587	stop_gained	8292	exon2			CAGCAGGCAGCAT	AF057036	CCDS33709.1, CCDS43057.1, CCDS46768.1	3p	2008-07-18			ENSG00000206561	ENSG00000206561			2226	protein-coding gene	gene with protein product	"single strand of homotrimeric collagen-like tail subunit of asymmetric acetylcholinesterase", "collagenic tail of endplate acetylcholinesterase", "AChE Q subunit", "acetylcholinesterase-associated collagen"	603033				9689136	Standard	NM_005677		Approved	EAD	uc003bzx.3	Q9Y215	OTTHUMG00000156233	ENST00000383788.5:c.156C>A	chr3.hg19:g.15531095G>T	ENSP00000373298:p.Cys52*	48.0	0.0	.		66.0	22.0	.	NM_080539	B3KY09|Q6DK18|Q6YH18|Q6YH19|Q6YH20|Q6YH21|Q9NP18|Q9NP19|Q9NP20|Q9NP21|Q9NP22|Q9NP23|Q9NP24|Q9UP88	Nonsense_Mutation	SNP	ENST00000383788.5	hg19	CCDS33709.1	.	.	.	.	.	.	.	.	.	.	G	34	5.335466	0.95758	.	.	ENSG00000206561	ENST00000383787;ENST00000383781;ENST00000435459;ENST00000383785;ENST00000383788;ENST00000420589;ENST00000454772;ENST00000383786;ENST00000430319	.	.	.	5.31	2.52	0.30459	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.6715	6.8574	0.24048	0.2721:0.0:0.7279:0.0	.	.	.	.	X	52;42;42;52;52;42;52;52;29	.	ENSP00000373291:C42X	C	-	3	2	COLQ	15506099	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	1.188000	0.32102	1.249000	0.43950	0.561000	0.74099	TGC	.	.	.	none		0.552	COLQ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000343575.1	NM_005677		T	15531095	G	T	15531095	4	4	109	1	0	0	0	0	0	1	0	0	3715	1195	42	4	1275	4	COLQ	3	15531095	Nonsense_Mutation	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10	2147849	15531095	182491335	23	6968											
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41275683	41275683	+	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	tgtcccgcaaatcatgcaccTttgcgtgagcagggtgccat	8	10	11	12	2	1	1	1	1	0	0	2	1	2	1	3	1	4	3	3	1	1	1			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr3:41275683T>G	ENST00000349496.5	+	10	1858	c.1578T>G	c.(1576-1578)ccT>ccG	p.P526P	CTNNB1_ENST00000396185.3_Silent_p.P526P|CTNNB1_ENST00000405570.1_Silent_p.P526P|CTNNB1_ENST00000396183.3_Silent_p.P526P|CTNNB1_ENST00000453024.1_Silent_p.P519P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	526					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		ATCATGCACCTTTGCGTGAGC	0.483		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.P526P	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	.	CTNNB1	4904	.	0			c.T1578G						PASS	.						157	134	142					3																	41275683		2203	4300	6503	SO:0001819	synonymous_variant	1499	exon10	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TGCACCTTTGCGT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.1578T>G	chr3.hg19:g.41275683T>G		123.0	0.0	.		157.0	61.0	.	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Silent	SNP	ENST00000349496.5	hg19	CCDS2694.1																																																																																			.	.	.	none		0.483	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		G	41275683	T	G	41275683	2	3	109	1	0	0	0	0	0	0	0	1	4018	1596	56	5		5	CTNNB1	3	41275683	Silent	SNP	T	TCGA-B9-A8YI-01A-21D-A36X-10	25744588	41275683	156746747	24	6969											
GPR87	53836	hgsc.bcm.edu	37	chr3	151012726	151012726	+	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	tgaagtaccaaggtccaaatCctgcatcatggactattcga	13	10	8	10	1	1	1	1	1	0	0	4	3	3	2	3	2	2	2	3	2	5	3			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr3:151012726C>G	ENST00000260843.4	-	3	772	c.308G>C	c.(307-309)gGa>gCa	p.G103A	MED12L_ENST00000491549.1_Intron|MED12L_ENST00000273432.4_Intron|MED12L_ENST00000474524.1_Intron	NM_023915.3	NP_076404.3	Q9BY21	GPR87_HUMAN	G protein-coupled receptor 87	103					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)			AGGTCCAAATCCTGCATCATG	0.378																																					p.G103A		Atlas-SNP	.											.	GPR87	52	.	0			c.G308C						PASS	.						130	129	129					3																	151012726		2203	4300	6503	SO:0001583	missense	53836	exon3			CCAAATCCTGCAT	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.308G>C	chr3.hg19:g.151012726C>G	ENSP00000260843:p.Gly103Ala	84.0	0.0	.		94.0	27.0	.	NM_023915	Q5KU35|Q96JZ8|Q9BXC2	Missense_Mutation	SNP	ENST00000260843.4	hg19	CCDS3157.1	.	.	.	.	.	.	.	.	.	.	C	15.73	2.920883	0.52653	.	.	ENSG00000138271	ENST00000260843	T	0.70631	-0.5	5.4	5.4	0.78164	GPCR, rhodopsin-like superfamily (1);	0.138010	0.47852	D	0.000213	T	0.71929	0.3398	L	0.46741	1.465	0.44771	D	0.99777	D	0.56746	0.977	P	0.57204	0.815	T	0.65825	-0.6074	10	0.07644	T	0.81	-8.5498	13.8439	0.63455	0.0:0.9243:0.0:0.0757	.	103	Q9BY21	GPR87_HUMAN	A	103	ENSP00000260843:G103A	ENSP00000260843:G103A	G	-	2	0	GPR87	152495416	0.975000	0.34042	0.899000	0.35326	0.921000	0.55340	3.443000	0.52907	2.688000	0.91661	0.655000	0.94253	GGA	.	.	.	none		0.378	GPR87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357788.1			G	151012726	C	G	151012726	3	3	109	1	0	0	0	0	1	0	0	0	6723	855	30	4	772	4	GPR87	3	151012726	Missense_Mutation	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10	109737043	151012726	47009704	25	6970											
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-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr3:178936082G>A	ENST00000263967.3	+	10	1781	c.1624G>A	c.(1624-1626)Gaa>Aaa	p.E542K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	542	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> K (in CLOVE, KERSEB, CRC and BC; also found in glioblastoma multiforme and endometrial carcinoma; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N- terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|E -> Q (found in an endometrial carcinoma sample; unknown pathological significance). {ECO:0000269|PubMed:16322209}.|E -> V (in BC; unknown pathological significance). {ECO:0000269|PubMed:16353168}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E542K(545)|p.E542Q(10)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TCCTCTCTCTGAAATCACTGA	0.333	E542K(BT483_BREAST)|E542K(CAL51_BREAST)|E542K(HGC27_STOMACH)|E542K(IM95_STOMACH)|E542K(JHUEM1_ENDOMETRIUM)|E542K(NCIH1341_LUNG)|E542K(SW948_LARGE_INTESTINE)|E542K(T84_LARGE_INTESTINE)|E542K(VMCUB1_URINARY_TRACT)	57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.E542K	Colon(199;1504 1750 3362 26421 31210 32040)	Atlas-SNP	.		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	PIK3CA_ENST00000263967,NS,carcinoma,0,2	PIK3CA	8460	.	555	Substitution - Missense(555)	breast(176)|large_intestine(166)|urinary_tract(45)|endometrium(37)|skin(19)|lung(18)|stomach(16)|ovary(16)|thyroid(14)|upper_aerodigestive_tract(9)|central_nervous_system(7)|cervix(6)|liver(6)|oesophagus(5)|penis(4)|kidney(3)|soft_tissue(2)|haematopoietic_and_lymphoid_tissue(2)|prostate(2)|biliary_tract(1)|pituitary(1)	c.G1624A						PASS	.						56	56	56					3																	178936082		1809	4069	5878	SO:0001583	missense	5290	exon10			CTCTCTGAAATCA		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1624G>A	chr3.hg19:g.178936082G>A	ENSP00000263967:p.Glu542Lys	468.0	0.0	.		502.0	193.0	.	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	hg19	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	34	5.360420	0.95877	.	.	ENSG00000121879	ENST00000263967	T	0.62105	0.05	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69287	0.3094	L	0.41356	1.27	0.80722	D	1	D	0.65815	0.995	D	0.63192	0.912	T	0.60296	-0.7291	10	0.09843	T	0.71	-23.9623	20.0024	0.97423	0.0:0.0:1.0:0.0	.	542	P42336	PK3CA_HUMAN	K	542	ENSP00000263967:E542K	ENSP00000263967:E542K	E	+	1	0	PIK3CA	180418776	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAA	.	.	.	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	109	1	0	0	0	0	1	0	0	0	11920	1291	45	2	1658	2	PIK3CA	3	178936082	Missense_Mutation	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10	27923356	178936082	19086348	26	6971											
PIGG	54872	hgsc.bcm.edu	37	chr4	514958	514958	+	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	acctgggctccaaggttctcAggcagtacctggatgctctg	7	10	12	12	0	2	0	1	0	2	0	4	1	3	1	3	4	2	5	3	4	2	2			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr4:514958A>C	ENST00000453061.2	+	7	1334	c.1228A>C	c.(1228-1230)Agg>Cgg	p.R410R	PIGG_ENST00000310340.5_Silent_p.R410R|PIGG_ENST00000383028.4_Silent_p.R277R|PIGG_ENST00000504346.1_Silent_p.R321R|PIGG_ENST00000536264.1_Silent_p.R288R|PIGG_ENST00000503111.1_Intron|PIGG_ENST00000296306.7_Intron|PIGG_ENST00000509768.1_Silent_p.R321R	NM_001127178.1	NP_001120650.1	Q5H8A4	PIGG_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class G	410					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						CAAGGTTCTCAGGCAGTACCT	0.488																																					p.R410R		Atlas-SNP	.											.	PIGG	86	.	0			c.A1228C						PASS	.						137	113	121					4																	514958		2203	4300	6503	SO:0001819	synonymous_variant	54872	exon7			GTTCTCAGGCAGT		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.1228A>C	chr4.hg19:g.514958A>C		117.0	0.0	.		141.0	54.0	.	NM_017733	B4DKC7|Q2TAK5|Q6UX31|Q7L5Y4|Q8N866|Q8NCC9|Q96SY9|Q9BVT7|Q9NXG5	Silent	SNP	ENST00000453061.2	hg19	CCDS46992.1																																																																																			.	.	.	none		0.488	PIGG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357494.1	NM_017733		C	514958	A	C	514958	2	2	109	1	0	0	0	0	0	0	0	1	11895	179	7	5		5	PIGG	4	514958	Silent	SNP	A	TCGA-B9-A8YI-01A-21D-A36X-10		514958	190639318	27	6972											
D4S234E	27065	hgsc.bcm.edu	37	chr4	4389387	4389387	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggaacaatttcgcagagAagggcaccaagcagccgctg	12	5	14	10	2	0	1	0	0	0	1	1	3	0	2	2	3	3	4	2	3	4	1			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr4:4389387A>G	ENST00000421177.2	+	6	2022	c.31A>G	c.(31-33)Aag>Gag	p.K11E	NSG1_ENST00000433139.2_Missense_Mutation_p.K11E|NSG1_ENST00000505246.1_Missense_Mutation_p.K11E|NSG1_ENST00000504171.1_Missense_Mutation_p.K11E|NSG1_ENST00000513555.1_Missense_Mutation_p.K11E|NSG1_ENST00000506380.1_Missense_Mutation_p.K11E|NSG1_ENST00000397958.1_Missense_Mutation_p.K11E			P42857	NSG1_HUMAN		11					clathrin coat assembly (GO:0048268)|dopamine receptor signaling pathway (GO:0007212)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)											TTTCGCAGAGAAGGGCACCAA	0.637																																					p.K11E		Atlas-SNP	.											.	.	.	.	0			c.A31G						PASS	.						75	70	72					4																	4389387		2203	4300	6503	SO:0001583	missense	0	exon2			GCAGAGAAGGGCA																												ENST00000421177.2:c.31A>G	chr4.hg19:g.4389387A>G	ENSP00000388823:p.Lys11Glu	243.0	0.0	.		347.0	120.0	.	NM_014392	B4DXC5|Q49AQ1	Missense_Mutation	SNP	ENST00000421177.2	hg19	CCDS3376.1	.	.	.	.	.	.	.	.	.	.	A	17.52	3.410458	0.62399	.	.	ENSG00000168824	ENST00000421177;ENST00000513555;ENST00000505246;ENST00000506380;ENST00000397958;ENST00000433139;ENST00000504171	.	.	.	3.41	3.41	0.39046	.	0.184924	0.35013	N	0.003502	T	0.68540	0.3012	M	0.73217	2.22	0.48511	D	0.999661	B;B	0.31054	0.043;0.306	B;B	0.43360	0.073;0.417	T	0.72836	-0.4172	9	0.87932	D	0	-11.9118	12.1775	0.54194	1.0:0.0:0.0:0.0	.	11;11	B4DXC5;P42857	.;NSG1_HUMAN	E	11	.	ENSP00000381049:K11E	K	+	1	0	AC110814.1	4440288	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.816000	0.86201	1.334000	0.45468	0.260000	0.18958	AAG	.	.	.	none		0.637	NSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246799.1			G	4389387	A	G	4389387	3	3	109	1	0	0	0	0	1	0	0	0	4216	247	9	3	33	3	D4S234E	4	4389387	Missense_Mutation	SNP	A	TCGA-B9-A8YI-01A-21D-A36X-10	3874429	4389387	186764889	28	6973											
KLF3	51274	hgsc.bcm.edu	37	chr4	38690438	38690438	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcctcgcctgggttgagcaTgccttcttccagcccaccga	6	9	10	16	2	1	1	0	1	1	0	3	2	2	1	6	1	4	2	6	1	0	3			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr4:38690438T>C	ENST00000261438.5	+	3	595	c.290T>C	c.(289-291)aTg>aCg	p.M97T	KLF3_ENST00000514033.1_Missense_Mutation_p.M97T	NM_016531.5	NP_057615.3	P57682	KLF3_HUMAN	Kruppel-like factor 3 (basic)	97	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						GGGTTGAGCATGCCTTCTTCC	0.612																																					p.M97T		Atlas-SNP	.											.	KLF3	40	.	0			c.T290C						PASS	.						77	75	76					4																	38690438		2203	4300	6503	SO:0001583	missense	51274	exon3			TGAGCATGCCTTC	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.290T>C	chr4.hg19:g.38690438T>C	ENSP00000261438:p.Met97Thr	108.0	0.0	.		129.0	46.0	.	NM_016531	Q6PIR1|Q86TN0|Q9P2X6	Missense_Mutation	SNP	ENST00000261438.5	hg19	CCDS3444.1	.	.	.	.	.	.	.	.	.	.	T	10.08	1.252657	0.22965	.	.	ENSG00000109787	ENST00000261438;ENST00000514033	T;T	0.48522	0.81;0.81	6.06	6.06	0.98353	.	0.400686	0.28077	N	0.016682	T	0.33000	0.0848	N	0.14661	0.345	0.30663	N	0.754158	B	0.11235	0.004	B	0.09377	0.004	T	0.18398	-1.0338	10	0.22706	T	0.39	.	16.6093	0.84858	0.0:0.0:0.0:1.0	.	97	P57682	KLF3_HUMAN	T	97	ENSP00000261438:M97T;ENSP00000421252:M97T	ENSP00000261438:M97T	M	+	2	0	KLF3	38366833	1.000000	0.71417	1.000000	0.80357	0.114000	0.19823	3.153000	0.50685	2.324000	0.78689	0.533000	0.62120	ATG	.	.	.	none		0.612	KLF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215093.2			C	38690438	T	C	38690438	3	2	109	1	0	0	0	0	1	0	0	0	8354	1464	51	3	296	3	KLF3	4	38690438	Missense_Mutation	SNP	T	TCGA-B9-A8YI-01A-21D-A36X-10	34301051	38690438	152463838	29	6974											
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-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	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	chr4.hg19:g.71468348G>T	ENSP00000313809:p.Gly180Val	247.0	0.0	.		309.0	16.0	.	NM_016519	Q3B862|Q9H2X1|Q9H4L1	Missense_Mutation	SNP	ENST00000322937.6	hg19	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	109	1	0	0	0	0	1	0	0	0	563	1174	41	4	565	4	AMBN	4	71468348	Missense_Mutation	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10	32777910	71468348	119685928	30	6975											
TMEM150C	441027	hgsc.bcm.edu	37	chr4	83424056	83424056	+	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	ttgctgggttaccttatataTggtgcatgcttcacaccagg	8	14	10	9	0	1	0	1	0	0	0	1	0	1	0	2	3	4	4	2	3	4	6			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr4:83424056T>G	ENST00000515780.2	-	4	363	c.159A>C	c.(157-159)ccA>ccC	p.P53P	TMEM150C_ENST00000449862.2_Silent_p.P53P|TMEM150C_ENST00000508701.1_Silent_p.P53P			B9EJG8	T150C_HUMAN	transmembrane protein 150C	53						integral component of membrane (GO:0016021)				ovary(1)	1						ACCTTATATATGGTGCATGCT	0.378																																					p.P53P		Atlas-SNP	.											.	TMEM150C	16	.	0			c.A159C						PASS	.						54	50	51					4																	83424056		1818	4082	5900	SO:0001819	synonymous_variant	441027	exon4			TATATATGGTGCA	BC147027	CCDS47087.1	4q21.22	2010-06-25			ENSG00000249242	ENSG00000249242			37263	protein-coding gene	gene with protein product							Standard	NM_001080506		Approved	FLJ12993	uc003hmy.1	B9EJG8	OTTHUMG00000161083	ENST00000515780.2:c.159A>C	chr4.hg19:g.83424056T>G		181.0	0.0	.		182.0	65.0	.	NM_001080506	B7Z4J5|B7Z4L3|B7Z692|B7Z6X6	Silent	SNP	ENST00000515780.2	hg19	CCDS47087.1																																																																																			.	.	.	none		0.378	TMEM150C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363685.2	NM_001080506		G	83424056	T	G	83424056	2	3	109	1	0	0	0	0	0	0	0	1	16081	1451	51	5		5	TMEM150C	4	83424056	Silent	SNP	T	TCGA-B9-A8YI-01A-21D-A36X-10	11955708	83424056	107730220	31	6976											
WDFY3	23001	hgsc.bcm.edu	37	chr4	85748064	85748064	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcactgacaccatatgttgTtagggaagttatcagattaa	13	14	8	6	0	2	2	2	1	0	1	2	3	2	3	1	1	0	3	1	1	5	6			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr4:85748064T>C	ENST00000295888.4	-	10	1434	c.1027A>G	c.(1027-1029)Aca>Gca	p.T343A	WDFY3_ENST00000322366.6_Missense_Mutation_p.T343A	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	343					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)		CCATATGTTGTTAGGGAAGTT	0.403																																					p.T343A		Atlas-SNP	.											.	WDFY3	314	.	0			c.A1027G						PASS	.						131	120	124					4																	85748064		2203	4300	6503	SO:0001583	missense	23001	exon10			ATGTTGTTAGGGA	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.1027A>G	chr4.hg19:g.85748064T>C	ENSP00000295888:p.Thr343Ala	92.0	0.0	.		117.0	41.0	.	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	hg19	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	T	14.31	2.497563	0.44455	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.15372	2.43;2.43	5.54	5.54	0.83059	.	0.102926	0.64402	D	0.000003	T	0.12092	0.0294	L	0.36672	1.1	0.54753	D	0.999988	B;B	0.28378	0.209;0.129	B;B	0.25140	0.058;0.058	T	0.07693	-1.0759	10	0.08837	T	0.75	.	10.8264	0.46635	0.0:0.0736:0.0:0.9264	.	343;343	E2QRK8;Q8IZQ1	.;WDFY3_HUMAN	A	343	ENSP00000318466:T343A;ENSP00000295888:T343A	ENSP00000295888:T343A	T	-	1	0	WDFY3	85967088	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	3.679000	0.54634	2.102000	0.63906	0.533000	0.62120	ACA	.	.	.	none		0.403	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		C	85748064	T	C	85748064	3	2	109	1	0	0	0	0	1	0	0	0	17282	1725	60	3	9832	3	WDFY3	4	85748064	Missense_Mutation	SNP	T	TCGA-B9-A8YI-01A-21D-A36X-10	2324008	85748064	105406212	32	6977											
SPRY1	10252	hgsc.bcm.edu	37	chr4	124323105	124323105	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atcaaccagcactggaagtgCagccagctctgggagcaaca	13	5	11	12	0	2	0	1	0	1	0	2	2	2	2	2	2	7	4	2	2	3	0			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr4:124323105C>T	ENST00000394339.2	+	2	699	c.359C>T	c.(358-360)gCa>gTa	p.A120V	SPRY1_ENST00000339241.1_Missense_Mutation_p.A120V	NM_001258039.1|NM_005841.2	NP_001244968.1|NP_005832.1	O43609	SPY1_HUMAN	sprouty homolog 1, antagonist of FGF signaling (Drosophila)	120					epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	cytosol (GO:0005829)|plasma membrane (GO:0005886)				NS(1)|large_intestine(4)|lung(2)|ovary(1)|skin(3)	11						ACTGGAAGTGCAGCCAGCTCT	0.542																																					p.A120V		Atlas-SNP	.											.	SPRY1	28	.	0			c.C359T						PASS	.						55	59	58					4																	124323105		2203	4300	6503	SO:0001583	missense	10252	exon2			GAAGTGCAGCCAG	AF041037	CCDS3731.1	4q	2009-04-17	2001-11-28		ENSG00000164056	ENSG00000164056			11269	protein-coding gene	gene with protein product		602465	"sprouty (Drosophila) homolog 1 (antagonist of FGF signaling)"			9458049, 15962011	Standard	NM_001258038		Approved	hSPRY1	uc003ifa.4	O43609	OTTHUMG00000133071	ENST00000394339.2:c.359C>T	chr4.hg19:g.124323105C>T	ENSP00000377871:p.Ala120Val	195.0	0.0	.		227.0	91.0	.	NM_001258039	D3DNX6|Q6PNE0	Missense_Mutation	SNP	ENST00000394339.2	hg19	CCDS3731.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.022104	0.75275	.	.	ENSG00000164056	ENST00000339241;ENST00000507703;ENST00000394339	T;T;T	0.55760	0.5;1.48;0.5	5.06	5.06	0.68205	.	0.066264	0.64402	D	0.000017	T	0.66336	0.2779	M	0.63428	1.95	0.58432	D	0.999997	D	0.61080	0.989	P	0.57846	0.828	T	0.65500	-0.6153	9	.	.	.	-14.3112	18.2393	0.89961	0.0:1.0:0.0:0.0	.	120	O43609	SPY1_HUMAN	V	120	ENSP00000343785:A120V;ENSP00000421036:A120V;ENSP00000377871:A120V	.	A	+	2	0	SPRY1	124542555	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.292000	0.65673	2.622000	0.88805	0.561000	0.74099	GCA	.	.	.	none		0.542	SPRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256711.1			T	124323105	C	T	124323105	3	4	109	1	0	0	0	0	1	0	0	0	15117	710	25	2	361	2	SPRY1	4	124323105	Missense_Mutation	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10	38575041	124323105	66831171	33	6978											
NAA15	80155	hgsc.bcm.edu	37	chr4	140291525	140291525	+	Frame_Shift_Del	DEL	A	A	-																															gatgaggagataggaggtccAaaagaagaacttattccaga																										TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr4:140291525delA	ENST00000296543.5	+	15	2237	c.1914delA	c.(1912-1914)ccafs	p.P638fs	NAA15_ENST00000398947.1_Frame_Shift_Del_p.P638fs	NM_057175.3	NP_476516.1	Q9BXJ9	NAA15_HUMAN	N(alpha)-acetyltransferase 15, NatA auxiliary subunit	638	Interaction with HYPK.				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						taggaggtccaaaagaagaaC	0.353																																					p.P638fs		Pindel	.											.	NAA15	88	.	0			c.1913delC						PASS	.						81	81	81					4																	140291525		1855	4102	5957	SO:0001589	frameshift_variant	80155	exon15			.	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.1914delA	chr4.hg19:g.140291525delA	ENSP00000296543:p.Pro638fs	577.0	0.0	.		673.0	113.0	0.168	NM_057175	D3DNY6|Q52LG9|Q8IWH4|Q8NEV2|Q9H8P6	Frame_Shift_Del	DEL	ENST00000296543.5	hg19	CCDS43270.1																																																																																			.	.	.	none		0.353	NAA15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000267839.2	NM_057175		-	140291525	A	-	140291525	7	5	109	1	0	1	0	1	0	0	0	0	10125	117	5	0	1972	0	NAA15	4	140291525	Frame_Shift_Del	DEL	A	TCGA-B9-A8YI-01A-21D-A36X-10	15968420	140291525	50862751	34	6979											
TLR2	7097	hgsc.bcm.edu	37	chr4	154625017	154625017	+	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	caatccggaggctgcatattCcaaggttttacttattttat	10	16	7	8	1	0	0	0	0	0	0	2	1	2	1	2	3	2	3	2	3	6	7			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr4:154625017C>T	ENST00000260010.6	+	1	2366	c.958C>T	c.(958-960)Cca>Tca	p.P320S		NM_003264.3	NP_003255.2	O60603	TLR2_HUMAN	toll-like receptor 2	320					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)	GCTGCATATTCCAAGGTTTTA	0.348																																					p.P320S		Atlas-SNP	.											.	TLR2	84	.	0			c.C958T						PASS	.						64	68	66					4																	154625017		2203	4298	6501	SO:0001583	missense	7097	exon3			CATATTCCAAGGT	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.958C>T	chr4.hg19:g.154625017C>T	ENSP00000260010:p.Pro320Ser	99.0	0.0	.		116.0	42.0	.	NM_003264	B3Y612|D1CS45|D1CS48|D1CS49|O15454|Q8NI00	Missense_Mutation	SNP	ENST00000260010.6	hg19	CCDS3784.1	.	.	.	.	.	.	.	.	.	.	C	9.250	1.040467	0.19669	.	.	ENSG00000137462	ENST00000260010	T	0.45668	0.89	6.06	3.3	0.37823	.	0.968721	0.08531	N	0.932044	T	0.38134	0.1029	L	0.55481	1.735	0.09310	N	1	B	0.13145	0.007	B	0.11329	0.006	T	0.22487	-1.0215	10	0.31617	T	0.26	.	8.4038	0.32603	0.0969:0.6591:0.1723:0.0718	.	320	O60603	TLR2_HUMAN	S	320	ENSP00000260010:P320S	ENSP00000260010:P320S	P	+	1	0	TLR2	154844467	0.000000	0.05858	0.033000	0.17914	0.002000	0.02628	0.533000	0.23082	1.581000	0.49865	-0.140000	0.14226	CCA	.	.	.	none		0.348	TLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365205.1			T	154625017	C	T	154625017	3	4	109	1	0	0	0	0	1	0	0	0	15963	855	30	2	960	2	TLR2	4	154625017	Missense_Mutation	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10	14333492	154625017	36529259	35	6980											
FNIP2	57600	hgsc.bcm.edu	37	chr4	159816926	159816926	+	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	tcatgcatcttgaagatagaCtacaggagatgtaccttaaa	15	11	8	7	0	2	4	1	1	1	3	2	5	2	4	1	1	3	2	1	1	6	5			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr4:159816926C>G	ENST00000264433.6	+	16	3250	c.3175C>G	c.(3175-3177)Cta>Gta	p.L1059V	C4orf45_ENST00000508011.1_Intron|C4orf45_ENST00000434826.2_Intron|FNIP2_ENST00000379346.3_Missense_Mutation_p.L1082V	NM_020840.1	NP_065891.1	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	1059					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)		TGAAGATAGACTACAGGAGAT	0.403																																					p.L1059V		Atlas-SNP	.											.	FNIP2	90	.	0			c.C3175G						PASS	.						118	117	117					4																	159816926		1907	4124	6031	SO:0001583	missense	57600	exon16			GATAGACTACAGG	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.3175C>G	chr4.hg19:g.159816926C>G	ENSP00000264433:p.Leu1059Val	73.0	0.0	.		80.0	22.0	.	NM_020840	Q05DC3|Q96I31|Q9H994	Missense_Mutation	SNP	ENST00000264433.6	hg19	CCDS47155.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.094483	0.76870	.	.	ENSG00000052795	ENST00000264433;ENST00000379346	T;T	0.60797	0.16;0.16	5.49	3.74	0.42951	.	0.074626	0.56097	D	0.000035	T	0.77089	0.4079	M	0.87900	2.915	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80446	-0.1379	9	.	.	.	.	12.08	0.53665	0.0:0.8584:0.0:0.1416	.	1059	Q9P278	FNIP2_HUMAN	V	1059;1082	ENSP00000264433:L1059V;ENSP00000368651:L1082V	.	L	+	1	2	FNIP2	160036376	1.000000	0.71417	0.946000	0.38457	0.996000	0.88848	4.894000	0.63206	1.333000	0.45449	0.591000	0.81541	CTA	.	.	.	none		0.403	FNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366602.1	NM_020840		G	159816926	C	G	159816926	3	3	109	1	0	0	0	0	1	0	0	0	5983	564	20	4	3237	4	FNIP2	4	159816926	Missense_Mutation	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10	5191909	159816926	31337350	36	6981											
UGT3A2	167127	hgsc.bcm.edu	37	chr5	36049438	36049439	+	Frame_Shift_Del	DEL	AT	AT	-																															aagttctcattctttaaggaAtccatgatatcctttctatt																										TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr5:36049438_36049439delAT	ENST00000282507.3	-	4	496_497	c.395_396delAT	c.(394-396)gatfs	p.D132fs	UGT3A2_ENST00000504954.1_Intron|UGT3A2_ENST00000513300.1_Frame_Shift_Del_p.D98fs|UGT3A2_ENST00000545528.1_Intron	NM_174914.3	NP_777574.2	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2	132					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)			TCTTTAAGGAATCCATGATATC	0.351																																					p.132_133del		Pindel	.											.	UGT3A2	117	.	0			c.396_397del						PASS	.																																			SO:0001589	frameshift_variant	167127	exon4			.		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.395_396delAT	chr5.hg19:g.36049438_36049439delAT	ENSP00000282507:p.Asp132fs	134.0	0.0	.		159.0	44.0	0.277	NM_174914	B4DUQ7|E9PFK7|Q6UXC4|Q8NBP2	Frame_Shift_Del	DEL	ENST00000282507.3	hg19	CCDS3914.1																																																																																			.	.	.	none		0.351	UGT3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253771.2	NM_174914		-	36049439	AT	-	36049438	7	5	109	1	0	1	0	1	0	0	0	0	16976	98	4	0	1191	0	UGT3A2	5	36049438	Frame_Shift_Del	DEL	AT	TCGA-B9-A8YI-01A-21D-A36X-10		36049438	144865822	37	6982											
C5orf36	285600	hgsc.bcm.edu	37	chr5	93722048	93722048	+	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	tcaaggtcgtctttaaaggtCggatgggtaatggcttttcc	8	14	12	7	2	2	0	1	0	1	0	5	1	3	1	1	5	0	2	1	5	4	5			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr5:93722048C>T	ENST00000513200.3	-	18	3590	c.3518G>A	c.(3517-3519)cGa>cAa	p.R1173Q	KIAA0825_ENST00000427991.2_Missense_Mutation_p.R1173Q	NM_001145678.1	NP_001139150.1	Q8IV33	K0825_HUMAN	KIAA0825	1173										breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(1)	13						CTTTAAAGGTCGGATGGGTAA	0.383																																					p.R1173Q		Atlas-SNP	.											.	KIAA0825	172	.	0			c.G3518A						PASS	.						160	139	145					5																	93722048		692	1591	2283	SO:0001583	missense	285600	exon19			AAAGGTCGGATGG	BX648338	CCDS4070.1	5q15	2011-02-23	2011-02-23	2011-02-23	ENSG00000185261	ENSG00000185261			28532	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 36"	C5orf36		12477932	Standard	NM_173665		Approved	DKFZp686F0372, MGC34713	uc011cuk.2	Q8IV33	OTTHUMG00000131331	ENST00000513200.3:c.3518G>A	chr5.hg19:g.93722048C>T	ENSP00000424618:p.Arg1173Gln	132.0	0.0	.		167.0	56.0	.	NM_001145678	O94914|Q6ZNN2	Missense_Mutation	SNP	ENST00000513200.3	hg19		.	.	.	.	.	.	.	.	.	.	C	12.03	1.814698	0.32053	.	.	ENSG00000185261	ENST00000513200;ENST00000427991	T;T	0.42900	0.96;0.96	5.97	-1.74	0.08056	.	.	.	.	.	T	0.25269	0.0614	L	0.28740	0.885	0.26413	N	0.976228	B;B	0.22346	0.03;0.068	B;B	0.15052	0.012;0.007	T	0.17471	-1.0368	9	0.27082	T	0.32	2.5431	6.6098	0.22745	0.0:0.3608:0.2184:0.4208	.	1173;1173	Q8IV33;C9J0Q2	K0825_HUMAN;.	Q	1173	ENSP00000424618:R1173Q;ENSP00000400288:R1173Q	ENSP00000400288:R1173Q	R	-	2	0	KIAA0825	93747804	0.011000	0.17503	0.425000	0.26659	0.952000	0.60782	-0.055000	0.11807	-0.732000	0.04856	-0.142000	0.14014	CGA	.	.	.	none		0.383	KIAA0825-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000254102.5	NM_173665		T	93722048	C	T	93722048	3	4	109	1	0	0	0	0	1	0	0	0	2297	884	31	1	321	1	C5orf36	5	93722048	Missense_Mutation	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10	57672610	93722048	87193212	38	6983											
CSF1R	1436	hgsc.bcm.edu	37	chr5	149449790	149449790	+	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	gccatgtcacgttgggctggGggtacccagaggcagcacac	8	6	15	12	1	1	1	1	0	0	1	1	1	1	1	2	4	2	5	2	4	1	2			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr5:149449790G>A	ENST00000286301.3	-	9	1565	c.1274C>T	c.(1273-1275)cCc>cTc	p.P425L		NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	425	Ig-like C2-type 5.				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)	GTTGGGCTGGGGGTACCCAGA	0.607																																					p.P425L		Atlas-SNP	.											.	CSF1R	250	.	0			c.C1274T						PASS	.						76	72	73					5																	149449790		2203	4300	6503	SO:0001583	missense	1436	exon9			GGCTGGGGGTACC	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.1274C>T	chr5.hg19:g.149449790G>A	ENSP00000286301:p.Pro425Leu	53.0	0.0	.		80.0	33.0	.	NM_005211	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Missense_Mutation	SNP	ENST00000286301.3	hg19	CCDS4302.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.658484	0.88154	.	.	ENSG00000182578	ENST00000286301;ENST00000394307	T	0.61392	0.11	5.89	5.89	0.94794	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.56097	D	0.000032	T	0.78201	0.4246	M	0.83774	2.66	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.80585	-0.1317	10	0.87932	D	0	.	15.7567	0.78037	0.0:0.0:1.0:0.0	.	277;425	B4E2Y8;P07333	.;CSF1R_HUMAN	L	425;277	ENSP00000286301:P425L	ENSP00000286301:P425L	P	-	2	0	CSF1R	149429983	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	5.043000	0.64208	2.793000	0.96121	0.561000	0.74099	CCC	.	.	.	none		0.607	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211		A	149449790	G	A	149449790	3	1	109	1	0	0	0	0	1	0	0	0	3934	1232	43	2	1700	2	CSF1R	5	149449790	Missense_Mutation	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10	55727742	149449790	31465470	39	6984											
GABRB2	2561	hgsc.bcm.edu	37	chr5	160763641	160763641	+	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	cttttccatgatacaaacctGtggaaaaaacaaccttcttg	14	12	5	10	0	1	1	0	1	1	0	2	2	2	2	3	1	4	0	3	1	6	5			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr5:160763641G>T	ENST00000393959.1	-	6	676	c.677C>A	c.(676-678)aCa>aAa	p.T226K	GABRB2_ENST00000520240.1_Missense_Mutation_p.T226K|GABRB2_ENST00000274547.2_Missense_Mutation_p.T226K|GABRB2_ENST00000353437.6_Missense_Mutation_p.T226K|GABRB2_ENST00000517901.1_Missense_Mutation_p.T163K|GABRB2_ENST00000517547.1_Missense_Mutation_p.T66K			P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 2	226					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|GABA-A receptor activity (GO:0004890)|inhibitory extracellular ligand-gated ion channel activity (GO:0005237)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(9)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	26	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	ATACAAACCTGTGGAAAAAAC	0.368																																					p.T226K		Atlas-SNP	.											.	GABRB2	161	.	0			c.C677A						PASS	.						86	87	87					5																	160763641		2202	4300	6502	SO:0001583	missense	2561	exon7			AAACCTGTGGAAA		CCDS4354.1, CCDS4355.1	5q34	2012-06-22			ENSG00000145864	ENSG00000145864		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4082	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 2"	600232				7851879	Standard	NM_000813		Approved		uc003lys.1	P47870	OTTHUMG00000130349	ENST00000393959.1:c.677C>A	chr5.hg19:g.160763641G>T	ENSP00000377531:p.Thr226Lys	84.0	0.0	.		105.0	39.0	.	NM_021911	A8K115|A8K1A0|D1LYT0|D1LYT1|Q16323|Q4FZB2	Missense_Mutation	SNP	ENST00000393959.1	hg19	CCDS4355.1	.	.	.	.	.	.	.	.	.	.	G	32	5.128847	0.94473	.	.	ENSG00000145864	ENST00000393959;ENST00000274547;ENST00000353437;ENST00000520240;ENST00000517901;ENST00000517547	T;T;T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24;-1.24;-1.24	5.47	5.47	0.80525	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.90421	0.7001	M	0.88105	2.93	0.80722	D	1	D;P;D;D	0.89917	1.0;0.952;0.984;0.989	D;D;D;D	0.87578	0.998;0.969;0.969;0.962	D	0.91866	0.5503	10	0.87932	D	0	.	19.3443	0.94357	0.0:0.0:1.0:0.0	.	66;163;226;226	B7Z279;E7EV50;P47870;P47870-1	.;.;GBRB2_HUMAN;.	K	226;226;226;226;163;66	ENSP00000377531:T226K;ENSP00000274547:T226K;ENSP00000274546:T226K;ENSP00000429320:T226K;ENSP00000430532:T163K;ENSP00000429750:T66K	ENSP00000274547:T226K	T	-	2	0	GABRB2	160696219	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.638000	0.98445	2.561000	0.86390	0.655000	0.94253	ACA	.	.	.	none		0.368	GABRB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252704.1			T	160763641	G	T	160763641	3	4	109	1	0	0	0	0	1	0	0	0	6174	1377	48	4	881	4	GABRB2	5	160763641	Missense_Mutation	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10	11313851	160763641	20151619	40	6985											
RGS14	10636	hgsc.bcm.edu	37	chr5	176799074	176799074	+	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	ccaccaccgactcagccctcTgacagctacccaacagtcca	11	5	5	20	1	2	1	1	1	1	0	3	2	3	1	6	0	4	1	6	0	2	1			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr5:176799074T>C	ENST00000408923.3	+	15	1887	c.1699T>C	c.(1699-1701)Tga>Cga	p.*567R	RGS14_ENST00000506944.1_3'UTR	NM_006480.4	NP_006471.2	O43566	RGS14_HUMAN	regulator of G-protein signaling 14	0					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)			CTCAGCCCTCTGACAGCTACC	0.657																																					p.X567R	NSCLC(47;353 1896 28036)	Atlas-SNP	.											.	RGS14	34	.	0			c.T1699C						PASS	.						74	88	83					5																	176799074		2092	4193	6285	SO:0001578	stop_lost	10636	exon15			GCCCTCTGACAGC	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.1699T>C	chr5.hg19:g.176799074T>C	ENSP00000386229:p.*567Argext*163	63.0	0.0	.		58.0	12.0	.	NM_006480	O43565|Q506M1|Q6ZWA4|Q8TD62	Missense_Mutation	SNP	ENST00000408923.3	hg19	CCDS43405.1	.	.	.	.	.	.	.	.	.	.	T	9.365	1.069109	0.20147	.	.	ENSG00000169220	ENST00000408923;ENST00000336477	.	.	.	4.75	4.75	0.60458	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.2366	0.37470	0.0:0.0:0.2464:0.7536	.	.	.	.	R	567;348	.	.	X	+	1	0	RGS14	176731680	0.997000	0.39634	1.000000	0.80357	0.194000	0.23727	0.357000	0.20199	1.999000	0.58509	0.454000	0.30748	TGA	.	.	.	none		0.657	RGS14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372676.1	NM_006480		C	176799074	T	C	176799074	4	2	109	1	0	0	0	0	0	0	0	0	13310	1593	55	3	1757	3	RGS14	5	176799074	Nonstop_Mutation	SNP	T	TCGA-B9-A8YI-01A-21D-A36X-10	16035433	176799074	4116186	41	6986											
DPCR1	135656	hgsc.bcm.edu	37	chr6	30917945	30917945	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aatggagacaggactcctttGgccaatgagaagaccacgcc	13	6	11	11	1	0	3	0	1	0	3	1	6	1	4	4	3	0	0	4	3	3	1			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr6:30917945G>A	ENST00000462446.1	+	2	1732	c.1704G>A	c.(1702-1704)ttG>ttA	p.L568L	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_5'UTR			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	120						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						GGACTCCTTTGGCCAATGAGA	0.502																																					p.L568L		Atlas-SNP	.											.	DPCR1	99	.	0			c.G1704A						PASS	.						65	64	64					6																	30917945		692	1591	2283	SO:0001819	synonymous_variant	135656	exon2			TCCTTTGGCCAAT	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.1704G>A	chr6.hg19:g.30917945G>A		123.0	0.0	.		113.0	45.0	.	NM_080870	C9IZC0|Q658M7|Q8WYN2	Silent	SNP	ENST00000462446.1	hg19	CCDS4692.2																																																																																			.	.	.	none		0.502	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870		A	30917945	G	A	30917945	2	1	109	1	0	0	0	0	0	0	0	1	4714	1339	47	2		2	DPCR1	6	30917945	Silent	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10		30917945	140197122	42	6987											
FKBP5	2289	hgsc.bcm.edu	37	chr6	35604801	35604826	+	Frame_Shift_Del	DEL	ACTAAAGACAAATGGTTCATTTCTAT	ACTAAAGACAAATGGTTCATTTCTAT	-																															accctcttacctttgccaagActaaagacaaatggttcatt																										TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	ACTAAAGACAAATGGTTCATTTCTAT	ACTAAAGACAAATGGTTCATTTCTAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr6:35604801_35604826delACTAAAGACAAATGGTTCATTTCTAT	ENST00000539068.1	-	3	417_442	c.215_240delATAGAAATGAACCATTTGTCTTTAGT	c.(214-240)gatagaaatgaaccatttgtctttagtfs	p.DRNEPFVFS72fs	FKBP5_ENST00000357266.4_Frame_Shift_Del_p.DRNEPFVFS72fs|FKBP5_ENST00000542713.1_Frame_Shift_Del_p.DRNEPFVFS72fs|FKBP5_ENST00000536438.1_Frame_Shift_Del_p.DRNEPFVFS72fs|FKBP5_ENST00000540787.1_Intron	NM_001145776.1	NP_001139248.1	Q13451	FKBP5_HUMAN	FK506 binding protein 5	72	PPIase FKBP-type 1. {ECO:0000255|PROSITE- ProRule:PRU00277}.				chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	FK506 binding (GO:0005528)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(3)|urinary_tract(2)	17						CTTTGCCAAGACTAAAGACAAATGGTTCATTTCTATCATGACTGGA	0.345																																					p.72_81del		Atlas-Indel,Pindel	.											.	FKBP5	64	.	0			c.216_241del						PASS	.																																			SO:0001589	frameshift_variant	2289	exon4			.	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.215_240delATAGAAATGAACCATTTGTCTTTAGT	chr6.hg19:g.35604801_35604826delACTAAAGACAAATGGTTCATTTCTAT	ENSP00000441205:p.Asp72fs	77.0	0.0	0		59.0	10.0	0.169492	NM_001145775	F5H7R1|Q59EB8|Q5TGM6	Frame_Shift_Del	DEL	ENST00000539068.1	hg19	CCDS4808.1																																																																																			.	.	.	none		0.345	FKBP5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040309.2			-	35604826	ACTAAAGACAAATGGTTCATTTCTAT	-	35604801	7	5	109	1	0	1	0	1	0	0	0	0	5918	272	10	0	1227	0	FKBP5	6	35604801	Frame_Shift_Del	DEL	ACTAAAGACAAATGGTTCATTTCTAT	TCGA-B9-A8YI-01A-21D-A36X-10	4686856	35604801	135510266	43	6988											
CRISP2	7180	hgsc.bcm.edu	37	chr6	49668403	49668403	+	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	tctttagcatgttactggcaGgtggagagactgctttcctt	7	15	11	8	0	1	1	0	0	1	1	2	3	2	2	1	3	3	4	1	3	2	5			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr6:49668403G>A	ENST00000339139.4	-	5	397	c.161C>T	c.(160-162)cCt>cTt	p.P54L		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	54	SCP.				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)			GTTACTGGCAGGTGGAGAGAC	0.468																																					p.P54L		Atlas-SNP	.											.	CRISP2	53	.	0			c.C161T						PASS	.						108	91	97					6																	49668403		2203	4299	6502	SO:0001583	missense	7180	exon5			CTGGCAGGTGGAG	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.161C>T	chr6.hg19:g.49668403G>A	ENSP00000339155:p.Pro54Leu	100.0	0.0	.		112.0	43.0	.	NM_001142408	A8K8M0|Q53FF2|Q5U8Z9|Q7Z7B2	Missense_Mutation	SNP	ENST00000339139.4	hg19	CCDS4928.1	.	.	.	.	.	.	.	.	.	.	G	13.70	2.315527	0.40996	.	.	ENSG00000124490	ENST00000339139;ENST00000211238	T	0.13196	2.61	5.23	4.36	0.52297	CAP domain (3);	0.666605	0.15704	N	0.248777	T	0.14141	0.0342	M	0.85299	2.745	0.38730	D	0.953655	B;B	0.23650	0.089;0.049	B;B	0.33254	0.109;0.16	T	0.02132	-1.1208	10	0.66056	D	0.02	.	11.5043	0.50456	0.0864:0.0:0.9136:0.0	.	54;54	Q7Z7B2;P16562	.;CRIS2_HUMAN	L	54	ENSP00000339155:P54L	ENSP00000211238:P54L	P	-	2	0	CRISP2	49776362	0.998000	0.40836	0.969000	0.41365	0.801000	0.45260	2.993000	0.49425	1.441000	0.47550	-0.225000	0.12378	CCT	.	.	.	none		0.468	CRISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040870.2	NM_003296		A	49668403	G	A	49668403	3	1	109	1	0	0	0	0	1	0	0	0	3882	1000	35	2	594	2	CRISP2	6	49668403	Missense_Mutation	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10	14063602	49668403	121446664	44	6989											
C6orf150	115004	hgsc.bcm.edu	37	chr6	74149944	74149944	+	Missense_Mutation	SNP	T	T	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	taaaataccttggaaaccatTtccttcctttgcatgcttgg	10	15	6	10	0	0	0	0	0	0	0	2	1	2	1	4	2	4	2	4	2	4	7			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr6:74149944T>G	ENST00000370315.3	-	3	1196	c.1102A>C	c.(1102-1104)Aat>Cat	p.N368H	MB21D1_ENST00000370318.1_Missense_Mutation_p.N368H	NM_138441.2	NP_612450.2	Q8N884	CGAS_HUMAN	Mab-21 domain containing 1	368					activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|cyclic nucleotide biosynthetic process (GO:0009190)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of type I interferon production (GO:0032481)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cyclic-GMP-AMP synthase activity (GO:0061501)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|lung(1)	6						TGGAAACCATTTCCTTCCTTT	0.363																																					p.N368H		Atlas-SNP	.											.	MB21D1	33	.	0			c.A1102C						PASS	.						64	62	62					6																	74149944		2203	4300	6503	SO:0001583	missense	115004	exon3			AACCATTTCCTTC	BC012928	CCDS4978.1	6q13	2011-02-23	2011-02-23	2011-02-23	ENSG00000164430	ENSG00000164430			21367	protein-coding gene	gene with protein product		613973	"chromosome 6 open reading frame 150"	C6orf150			Standard	NM_138441		Approved		uc003pgx.1	Q8N884	OTTHUMG00000015034	ENST00000370315.3:c.1102A>C	chr6.hg19:g.74149944T>G	ENSP00000359339:p.Asn368His	108.0	0.0	.		108.0	29.0	.	NM_138441	L0L2J9|Q14CV6|Q32NC9|Q5SWL0|Q5SWL1|Q96E45	Missense_Mutation	SNP	ENST00000370315.3	hg19	CCDS4978.1	.	.	.	.	.	.	.	.	.	.	T	14.56	2.572058	0.45798	.	.	ENSG00000164430	ENST00000370318;ENST00000370315;ENST00000296913	T;T	0.08370	3.1;3.1	5.35	-0.905	0.10527	.	0.884083	0.09786	N	0.755980	T	0.07773	0.0195	L	0.48362	1.52	0.25017	N	0.991369	D	0.67145	0.996	D	0.66847	0.947	T	0.21449	-1.0245	10	0.62326	D	0.03	-6.9955	6.3604	0.21425	0.0:0.1059:0.4453:0.4488	.	368	Q8N884	M21D1_HUMAN	H	368	ENSP00000359342:N368H;ENSP00000359339:N368H	ENSP00000296913:N368H	N	-	1	0	MB21D1	74206665	0.590000	0.26815	0.251000	0.24312	0.771000	0.43674	0.625000	0.24477	-0.053000	0.13289	0.374000	0.22700	AAT	.	.	.	none		0.363	MB21D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041221.5	NM_138441		G	74149944	T	G	74149944	3	3	109	1	0	0	0	0	1	0	0	0	2339	1841	64	5	478	5	C6orf150	6	74149944	Missense_Mutation	SNP	T	TCGA-B9-A8YI-01A-21D-A36X-10	24481541	74149944	96965123	45	6990											
SHPRH	257218	hgsc.bcm.edu	37	chr6	146215295	146215296	+	Frame_Shift_Ins	INS	-	-	T																															cttaacatacctgaaatgtcINSttaacacgactgatttgtgc																										TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr6:146215295_146215296insT	ENST00000367505.2	-	27	4949_4950	c.4685_4686insA	c.(4684-4686)aagfs	p.K1562fs	SHPRH_ENST00000438092.2_Frame_Shift_Ins_p.K1566fs|SHPRH_ENST00000275233.7_Frame_Shift_Ins_p.K1562fs|SHPRH_ENST00000367503.3_Frame_Shift_Ins_p.K1566fs			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	1562	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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)		CCTGAAATGTCTTAACACGACT	0.317																																					p.K1566fs		Atlas-Indel,Pindel	.											.	SHPRH	169	.	0			c.4698_4699insA						PASS	.																																			SO:0001589	frameshift_variant	257218	exon27			.	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.4686dupA	chr6.hg19:g.146215297_146215297dupT	ENSP00000356475:p.Lys1562fs	81.0	0.0	0		86.0	33.0	0.383721	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Frame_Shift_Ins	INS	ENST00000367505.2	hg19	CCDS43513.2																																																																																			.	.	.	none		0.317	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082		T	146215296	-	T	146215295	7	5	109	1	0	1	1	0	0	0	0	0	14304	912	32	0	398	0	SHPRH	6	146215295	Frame_Shift_Ins	INS	-	TCGA-B9-A8YI-01A-21D-A36X-10	72065351	146215295	24899772	46	6991											
SASH1	23328	hgsc.bcm.edu	37	chr6	148855991	148855991	+	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	aatatcagggacccggaacaCagagctgttctcttgacagc	12	8	10	11	1	2	2	1	1	1	1	3	4	2	4	1	2	3	2	1	2	3	3			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr6:148855991C>T	ENST00000367467.3	+	16	2524	c.2049C>T	c.(2047-2049)caC>caT	p.H683H		NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	683	SAM 1. {ECO:0000255|PROSITE- ProRule:PRU00184}.				positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044)	membrane (GO:0016020)|protein complex (GO:0043234)	mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901)			breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		ACCCGGAACACAGAGCTGTTC	0.493																																					p.H683H		Atlas-SNP	.											.	SASH1	123	.	0			c.C2049T						PASS	.						109	105	106					6																	148855991		2203	4300	6503	SO:0001819	synonymous_variant	23328	exon16			GGAACACAGAGCT	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.2049C>T	chr6.hg19:g.148855991C>T		91.0	0.0	.		103.0	44.0	.	NM_015278	Q5TGN5|Q8TAI0|Q9H7R7	Silent	SNP	ENST00000367467.3	hg19	CCDS5212.1																																																																																			.	.	.	none		0.493	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278		T	148855991	C	T	148855991	2	4	109	1	0	0	0	0	0	0	0	1	13861	477	17	2		2	SASH1	6	148855991	Silent	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10	2640696	148855991	22259076	47	6992											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152473219	152473219	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctccctggccaggcggcggtActgcttgttgatcagttcca	5	11	12	13	2	1	1	1	1	0	0	3	1	3	1	3	4	2	4	3	4	1	4			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr6:152473219A>G	ENST00000367255.5	-	134	24788	c.24187T>C	c.(24187-24189)Tac>Cac	p.Y8063H	SYNE1_ENST00000448038.1_Missense_Mutation_p.Y7992H|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000356820.4_Missense_Mutation_p.Y2587H|SYNE1_ENST00000354674.4_Missense_Mutation_p.Y218H|SYNE1_ENST00000265368.4_Missense_Mutation_p.Y8063H|SYNE1_ENST00000539504.1_Missense_Mutation_p.Y218H|SYNE1_ENST00000341594.5_Missense_Mutation_p.Y7675H|SYNE1_ENST00000423061.1_Missense_Mutation_p.Y7992H	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8063					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)		AGGCGGCGGTACTGCTTGTTG	0.542										HNSCC(10;0.0054)																											p.Y8063H		Atlas-SNP	.											.	SYNE1	3227	.	0			c.T24187C						PASS	.						109	86	94					6																	152473219		2203	4300	6503	SO:0001583	missense	23345	exon134			GGCGGTACTGCTT	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.24187T>C	chr6.hg19:g.152473219A>G	ENSP00000356224:p.Tyr8063His	71.0	0.0	.		71.0	24.0	.	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	A	33	5.209411	0.95069	.	.	ENSG00000131018	ENST00000367255;ENST00000539504;ENST00000367257;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000313630;ENST00000367247;ENST00000367251;ENST00000354674	T;T;T;T;T;T;T;T;T;T	0.34667	1.37;1.35;1.37;1.37;1.37;1.37;1.37;1.37;1.37;1.35	5.96	5.96	0.96718	.	0.000000	0.50627	D	0.000110	T	0.56630	0.1998	M	0.80982	2.52	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.999;1.0;0.999;0.996	T	0.62798	-0.6778	10	0.66056	D	0.02	.	16.4447	0.83919	1.0:0.0:0.0:0.0	.	8063;8063;7992;7992;265	Q8NF91;E7EQI5;Q8NF91-4;E9PEL9;B7Z9Y6	SYNE1_HUMAN;.;.;.;.	H	8063;218;709;7992;8063;7992;7675;2587;225;220;985;218	ENSP00000356224:Y8063H;ENSP00000441052:Y218H;ENSP00000356226:Y709H;ENSP00000396024:Y7992H;ENSP00000265368:Y8063H;ENSP00000390975:Y7992H;ENSP00000341887:Y7675H;ENSP00000349276:Y2587H;ENSP00000356220:Y985H;ENSP00000346701:Y218H	ENSP00000265368:Y8063H	Y	-	1	0	SYNE1	152514912	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.108000	0.94275	2.284000	0.76573	0.528000	0.53228	TAC	.	.	.	none		0.542	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		G	152473219	A	G	152473219	3	3	109	1	0	0	0	0	1	0	0	0	15457	391	14	3	2331	3	SYNE1	6	152473219	Missense_Mutation	SNP	A	TCGA-B9-A8YI-01A-21D-A36X-10	3617228	152473219	18641848	48	6993											
ARID1B	57492	hgsc.bcm.edu	37	chr6	157099429	157099429	+	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	cagcagcagcagcagcaacaGcagcagcagcagcagcagca	15	0	12	14	0	0	0	0	0	0	0	0	0	0	0	0	0	13	12	0	0	1	0			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr6:157099429G>A	ENST00000350026.5	+	1	367	c.366G>A	c.(364-366)caG>caA	p.Q122Q	ARID1B_ENST00000275248.4_Silent_p.Q64Q|ARID1B_ENST00000346085.5_Silent_p.Q122Q|ARID1B_ENST00000367148.1_Silent_p.Q122Q|RP11-230C9.3_ENST00000604792.1_RNA|RP11-230C9.2_ENST00000603191.1_lincRNA|MIR4466_ENST00000606121.1_RNA	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	122	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)		agcagcaacagcagcagcagc	0.647																																					p.Q122Q		Atlas-SNP	.											.	ARID1B	320	.	0			c.G366A						PASS	.						4	7	6					6																	157099429		1651	3290	4941	SO:0001819	synonymous_variant	57492	exon1			GCAACAGCAGCAG	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.366G>A	chr6.hg19:g.157099429G>A		29.0	0.0	.		43.0	8.0	.	NM_017519	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Silent	SNP	ENST00000350026.5	hg19	CCDS5251.2																																																																																			.	.	.	none		0.647	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		A	157099429	G	A	157099429	2	1	109	1	0	0	0	0	0	0	0	1	914	962	34	2		2	ARID1B	6	157099429	Silent	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10	4626210	157099429	14015638	49	6994											
IGF2R	3482	hgsc.bcm.edu	37	chr6	160466824	160466824	+	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	gaacttctggggaaggcggtTgcttttatgagtttgagtgg	7	14	16	4	1	1	2	0	2	1	0	1	4	1	3	0	5	2	3	0	5	3	5			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr6:160466824T>A	ENST00000356956.1	+	14	1961	c.1813T>A	c.(1813-1815)Tgc>Agc	p.C605S		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	605					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)	GGAAGGCGGTTGCTTTTATGA	0.502																																					p.C605S		Atlas-SNP	.											.	IGF2R	251	.	0			c.T1813A						PASS	.						173	183	180					6																	160466824		2203	4300	6503	SO:0001583	missense	3482	exon14			GGCGGTTGCTTTT	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.1813T>A	chr6.hg19:g.160466824T>A	ENSP00000349437:p.Cys605Ser	79.0	0.0	.		90.0	24.0	.	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	hg19	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.688195	0.88639	.	.	ENSG00000197081	ENST00000356956	T	0.15834	2.39	5.67	5.67	0.87782	Mannose-6-phosphate receptor, binding (1);	0.000000	0.85682	D	0.000000	T	0.44932	0.1317	M	0.92268	3.29	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.58853	-0.7563	10	0.62326	D	0.03	-13.6324	15.9212	0.79575	0.0:0.0:0.0:1.0	.	605	P11717	MPRI_HUMAN	S	605	ENSP00000349437:C605S	ENSP00000349437:C605S	C	+	1	0	IGF2R	160386814	1.000000	0.71417	0.996000	0.52242	0.789000	0.44602	7.637000	0.83313	2.155000	0.67459	0.460000	0.39030	TGC	.	.	.	none		0.502	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		A	160466824	T	A	160466824	3	1	109	1	0	0	0	0	1	0	0	0	7583	1812	63	5	1867	5	IGF2R	6	160466824	Missense_Mutation	SNP	T	TCGA-B9-A8YI-01A-21D-A36X-10	3367395	160466824	10648243	50	6995											
ITGB8	3696	hgsc.bcm.edu	37	chr7	20418715	20418715	+	Missense_Mutation	SNP	A	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	tgaaagttcatcctctgaagAaatatcctgtggatctttat	12	15	7	7	0	3	3	1	2	2	1	5	4	5	4	2	1	0	1	2	1	5	4			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr7:20418715A>C	ENST00000222573.4	+	4	1114	c.430A>C	c.(430-432)Aaa>Caa	p.K144Q	ITGB8_ENST00000537992.1_Missense_Mutation_p.K9Q|SNORD56_ENST00000363883.1_RNA	NM_002214.2	NP_002205.1	P26012	ITB8_HUMAN	integrin, beta 8	144					cartilage development (GO:0051216)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|ganglioside metabolic process (GO:0001573)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of gene expression (GO:0010629)|placenta blood vessel development (GO:0060674)|positive regulation of gene expression (GO:0010628)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	extracellular matrix protein binding (GO:1990430)|receptor activity (GO:0004872)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(4)|stomach(2)|urinary_tract(1)	37						TCCTCTGAAGAAATATCCTGT	0.308																																					p.K144Q		Atlas-SNP	.											.	ITGB8	159	.	0			c.A430C						PASS	.						70	81	77					7																	20418715		2193	4298	6491	SO:0001583	missense	3696	exon4			CTGAAGAAATATC		CCDS5370.1	7p15.3	2010-03-23			ENSG00000105855	ENSG00000105855		"Integrins"	6163	protein-coding gene	gene with protein product		604160					Standard	XM_005249751		Approved		uc003suu.3	P26012	OTTHUMG00000023594	ENST00000222573.4:c.430A>C	chr7.hg19:g.20418715A>C	ENSP00000222573:p.Lys144Gln	95.0	0.0	.		109.0	34.0	.	NM_002214	A4D133|B4DHD4	Missense_Mutation	SNP	ENST00000222573.4	hg19	CCDS5370.1	.	.	.	.	.	.	.	.	.	.	A	14.02	2.410153	0.42715	.	.	ENSG00000105855	ENST00000537992;ENST00000222573	D;D	0.92495	-3.05;-3.05	5.42	4.25	0.50352	Integrin beta subunit, N-terminal (2);	0.067674	0.64402	N	0.000011	D	0.89097	0.6618	L	0.47716	1.5	0.35175	D	0.771931	B;B	0.10296	0.001;0.003	B;B	0.19666	0.014;0.026	D	0.88226	0.2900	10	0.66056	D	0.02	-20.749	12.8016	0.57588	0.863:0.137:0.0:0.0	.	144;144	P26012;Q9BUG9	ITB8_HUMAN;.	Q	9;144	ENSP00000441561:K9Q;ENSP00000222573:K144Q	ENSP00000222573:K144Q	K	+	1	0	ITGB8	20385240	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.942000	0.49018	0.972000	0.38314	0.528000	0.53228	AAA	.	.	.	none		0.308	ITGB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059915.3	NM_002214		C	20418715	A	C	20418715	3	2	109	1	0	0	0	0	1	0	0	0	7908	247	9	5	444	5	ITGB8	7	20418715	Missense_Mutation	SNP	A	TCGA-B9-A8YI-01A-21D-A36X-10		20418715	138719948	51	6996											
HOXA10	3206	hgsc.bcm.edu	37	chr7	27211696	27211696	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tattgaacagaaactccttcTccagctccagtgtctggtgc	9	12	8	12	0	2	2	0	1	2	1	5	2	4	2	3	1	4	1	3	1	3	3			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr7:27211696T>C	ENST00000283921.4	-	2	1054	c.1055A>G	c.(1054-1056)gAg>gGg	p.E352G	HOXA10_ENST00000396344.4_Missense_Mutation_p.E36G|HOXA-AS4_ENST00000519694.1_RNA|RP1-170O19.20_ENST00000470747.4_Intron|MIR196B_ENST00000384852.1_RNA|HOXA-AS4_ENST00000523790.1_RNA|HOXA10_ENST00000521421.1_5'UTR|HOXA-AS4_ENST00000519935.1_RNA|RP1-170O19.20_ENST00000465941.1_Intron|HOXA9_ENST00000497089.1_5'Flank	NM_018951.3	NP_061824.3	P31260	HXA10_HUMAN	homeobox A10	352					anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|male gonad development (GO:0008584)|multicellular organismal development (GO:0007275)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase binding (GO:0042826)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	9						AAACTCCTTCTCCAGCTCCAG	0.537																																					p.E352G		Atlas-SNP	.											.	HOXA10	55	.	0			c.A1055G						PASS	.						110	105	107					7																	27211696		2203	4300	6503	SO:0001583	missense	3206	exon2			TCCTTCTCCAGCT		CCDS5410.2	7p15.2	2011-06-20	2005-12-22		ENSG00000253293	ENSG00000253293		"Homeoboxes / ANTP class : HOXL subclass"	5100	protein-coding gene	gene with protein product		142957	"homeo box A10"	HOX1H, HOX1		1973146, 1358459	Standard	NR_037939		Approved		uc011jzm.2	P31260	OTTHUMG00000023436	ENST00000283921.4:c.1055A>G	chr7.hg19:g.27211696T>C	ENSP00000283921:p.Glu352Gly	131.0	0.0	.		154.0	42.0	.	NM_018951	O43370|O43605|Q15949|Q504T1	Missense_Mutation	SNP	ENST00000283921.4	hg19	CCDS5410.2	.	.	.	.	.	.	.	.	.	.	T	21.7	4.191945	0.78902	.	.	ENSG00000253293	ENST00000283921;ENST00000396344	D;D	0.97831	-4.56;-4.56	5.7	5.7	0.88788	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99236	0.9734	H	0.97587	4.035	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	D	0.98858	1.0761	10	0.87932	D	0	.	15.9644	0.79956	0.0:0.0:0.0:1.0	.	352;36	P31260;Q504T1	HXA10_HUMAN;.	G	352;36	ENSP00000283921:E352G;ENSP00000379633:E36G	ENSP00000283921:E352G	E	-	2	0	HOXA10	27178221	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.040000	0.89188	2.172000	0.68678	0.460000	0.39030	GAG	.	.	.	none		0.537	HOXA10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358724.2			C	27211696	T	C	27211696	3	2	109	1	0	0	0	0	1	0	0	0	7296	1551	54	3	181	3	HOXA10	7	27211696	Missense_Mutation	SNP	T	TCGA-B9-A8YI-01A-21D-A36X-10	6792981	27211696	131926967	52	6997											
ABCA13	154664	hgsc.bcm.edu	37	chr7	48317949	48317949	+	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	gaaaataatatagactttttCacagtggtgagtcagttgtt	13	15	9	4	0	2	2	2	1	0	1	2	3	2	2	0	1	0	2	0	1	5	7			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr7:48317949C>A	ENST00000435803.1	+	18	7182	c.7158C>A	c.(7156-7158)ttC>ttA	p.F2386L		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2386					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						TAGACTTTTTCACAGTGGTGA	0.358																																					p.F2386L		Atlas-SNP	.											.	ABCA13	1192	.	0			c.C7158A						PASS	.						35	34	35					7																	48317949		1817	4072	5889	SO:0001583	missense	154664	exon18			CTTTTTCACAGTG	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.7158C>A	chr7.hg19:g.48317949C>A	ENSP00000411096:p.Phe2386Leu	141.0	0.0	.		155.0	52.0	.	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	C	1.034	-0.680960	0.03353	.	.	ENSG00000179869	ENST00000435803	T	0.49720	0.77	4.99	-2.02	0.07388	.	0.495153	0.16799	N	0.199073	T	0.21631	0.0521	N	0.12746	0.255	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29088	-1.0023	10	0.08179	T	0.78	.	9.2681	0.37654	0.0:0.4592:0.0:0.5408	.	2386	Q86UQ4	ABCAD_HUMAN	L	2386	ENSP00000411096:F2386L	ENSP00000411096:F2386L	F	+	3	2	ABCA13	48288495	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.668000	0.05268	-0.566000	0.06054	-0.140000	0.14226	TTC	.	.	.	none		0.358	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48317949	C	A	48317949	3	1	109	1	0	0	0	0	1	0	0	0	31	825	29	4	7057	4	ABCA13	7	48317949	Missense_Mutation	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10	21106253	48317949	110820714	53	6998											
CLDN3	1365	hgsc.bcm.edu	37	chr7	73184246	73184246	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatccacaggccctcccagAtgttctgcgacgtgatgatg	8	10	10	13	2	2	3	1	2	1	1	4	4	4	3	3	1	1	1	3	1	0	1			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr7:73184246A>G	ENST00000395145.2	-	1	354	c.134T>C	c.(133-135)aTc>aCc	p.I45T		NM_001306.3	NP_001297.1	O15551	CLD3_HUMAN	claudin 3	45					calcium-independent cell-cell adhesion (GO:0016338)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)|transmembrane signaling receptor activity (GO:0004888)			kidney(1)|lung(1)	2		Lung NSC(55;0.159)				GCCCTCCCAGATGTTCTGCGA	0.642																																					p.I45T		Atlas-SNP	.											.	CLDN3	6	.	0			c.T134C						PASS	.						76	65	69					7																	73184246		2203	4300	6503	SO:0001583	missense	1365	exon1			TCCCAGATGTTCT	AF007189	CCDS5559.1	7q11	2008-07-18			ENSG00000165215	ENSG00000165215		"Claudins"	2045	protein-coding gene	gene with protein product	"Clostridium perfringens enterotoxin receptor 2", "ventral prostate.1-like protein", "claudin-3", "CPE-receptor 2"	602910		C7orf1, CPETR2		9441748, 9892664	Standard	NM_001306		Approved	RVP1, CPE-R2, HRVP1	uc003tzg.4	O15551	OTTHUMG00000023424	ENST00000395145.2:c.134T>C	chr7.hg19:g.73184246A>G	ENSP00000378577:p.Ile45Thr	112.0	0.0	.		138.0	46.0	.	NM_001306		Missense_Mutation	SNP	ENST00000395145.2	hg19	CCDS5559.1	.	.	.	.	.	.	.	.	.	.	A	7.850	0.723712	0.15439	.	.	ENSG00000165215	ENST00000395145	D	0.88354	-2.37	4.83	-3.28	0.05033	.	0.255462	0.36740	N	0.002431	T	0.81678	0.4873	L	0.52573	1.65	0.26410	N	0.976288	B	0.06786	0.001	B	0.15052	0.012	T	0.65459	-0.6163	10	0.20046	T	0.44	.	11.5454	0.50690	0.8061:0.0:0.1939:0.0	.	45	O15551	CLD3_HUMAN	T	45	ENSP00000378577:I45T	ENSP00000378577:I45T	I	-	2	0	CLDN3	72822182	0.005000	0.15991	0.951000	0.38953	0.520000	0.34377	-0.052000	0.11865	-0.606000	0.05746	-0.375000	0.07067	ATC	.	.	.	none		0.642	CLDN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252310.1	NM_001306		G	73184246	A	G	73184246	3	3	109	1	0	0	0	0	1	0	0	0	3488	333	12	3	532	3	CLDN3	7	73184246	Missense_Mutation	SNP	A	TCGA-B9-A8YI-01A-21D-A36X-10	24866297	73184246	85954417	54	6999											
ZNF804B	219578	hgsc.bcm.edu	37	chr7	88964261	88964261	+	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	gaagatgaaagacaattcaaCtgcaagtccagtccttgtac	15	9	8	9	0	1	3	1	1	0	2	3	4	3	3	2	0	3	2	2	0	6	3			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr7:88964261C>G	ENST00000333190.4	+	4	2574	c.1965C>G	c.(1963-1965)aaC>aaG	p.N655K		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	655							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)			GACAATTCAACTGCAAGTCCA	0.408										HNSCC(36;0.09)																											p.N655K		Atlas-SNP	.											.	ZNF804B	322	.	0			c.C1965G						PASS	.						102	95	97					7																	88964261		2203	4300	6503	SO:0001583	missense	219578	exon4			ATTCAACTGCAAG	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.1965C>G	chr7.hg19:g.88964261C>G	ENSP00000329638:p.Asn655Lys	205.0	0.0	.		233.0	83.0	.	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	hg19	CCDS5613.1	.	.	.	.	.	.	.	.	.	.	C	2.059	-0.415957	0.04766	.	.	ENSG00000182348	ENST00000333190	T	0.04603	3.59	5.48	-2.51	0.06365	.	0.797440	0.11763	N	0.531868	T	0.01661	0.0053	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46034	-0.9220	10	0.05525	T	0.97	-1.7321	3.2285	0.06740	0.1081:0.35:0.1062:0.4357	.	655	A4D1E1	Z804B_HUMAN	K	655	ENSP00000329638:N655K	ENSP00000329638:N655K	N	+	3	2	ZNF804B	88802197	0.000000	0.05858	0.021000	0.16686	0.022000	0.10575	-1.055000	0.03493	-0.334000	0.08463	0.650000	0.86243	AAC	.	.	.	none		0.408	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		G	88964261	C	G	88964261	3	3	109	1	0	0	0	0	1	0	0	0	18183	564	20	4	1979	4	ZNF804B	7	88964261	Missense_Mutation	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10	15780015	88964261	70174402	55	7000											
ZNF3	7551	hgsc.bcm.edu	37	chr7	99674930	99674930	+	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	agtccttattcctcaccactGtcaagcagggcctgaggttc	8	11	9	13	0	2	1	2	1	0	0	5	1	4	1	4	2	1	2	4	2	2	3			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr7:99674930G>A	ENST00000424697.1	-	3	357	c.51C>T	c.(49-51)gaC>gaT	p.D17D	ZNF3_ENST00000303915.6_Silent_p.D17D|ZNF3_ENST00000413658.2_Silent_p.D17D|ZNF3_ENST00000299667.4_Silent_p.D17D	NM_001278284.1|NM_001278287.1|NM_001278290.1|NM_001278291.1|NM_001278292.1|NM_032924.3	NP_001265213.1|NP_001265216.1|NP_001265219.1|NP_001265220.1|NP_001265221.1|NP_116313.3	P17036	ZNF3_HUMAN	zinc finger protein 3	17					cell differentiation (GO:0030154)|leukocyte activation (GO:0045321)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	25	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)	Ovarian(593;2.06e-05)|Myeloproliferative disorder(862;0.0122)|Breast(660;0.029)	STAD - Stomach adenocarcinoma(171;0.129)			CCTCACCACTGTCAAGCAGGG	0.488																																					p.D17D		Atlas-SNP	.											.	ZNF3	54	.	0			c.C51T						PASS	.						143	147	146					7																	99674930		1992	4179	6171	SO:0001819	synonymous_variant	7551	exon3			ACCACTGTCAAGC	AF027136	CCDS43618.1, CCDS43619.1	7q22.1	2013-01-08	2006-05-05					"Zinc fingers, C2H2-type", "-"	13089	protein-coding gene	gene with protein product		194510	"zinc finger protein 3 (A8-51)"				Standard	NM_032924		Approved	A8-51, KOX25, PP838, FLJ20216, HF.12, Zfp113	uc003usr.4	P17036		ENST00000424697.1:c.51C>T	chr7.hg19:g.99674930G>A		91.0	0.0	.		130.0	6.0	.	NM_032924	D6W5U0|P13683|Q9HBR4|Q9NNX8|Q9NXJ1|Q9UC15|Q9UC16	Silent	SNP	ENST00000424697.1	hg19	CCDS43619.1																																																																																			.	.	.	none		0.488	ZNF3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336247.3	NM_017715		A	99674930	G	A	99674930	2	1	109	1	0	0	0	0	0	0	0	1	17841	1368	48	2		2	ZNF3	7	99674930	Silent	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10	10710669	99674930	59463733	56	7001											
ATXN7L1	222255	hgsc.bcm.edu	37	chr7	105516974	105516974	+	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	ttcggcagcagcagccgagaGacacgggattcgagaacgct	11	5	14	11	5	0	2	0	0	0	2	2	6	0	3	1	2	4	4	1	2	1	2			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr7:105516974G>C	ENST00000419735.3	-	1	76	c.31C>G	c.(31-33)Ctc>Gtc	p.L11V	ATXN7L1_ENST00000478915.1_5'Flank|ATXN7L1_ENST00000318724.4_Missense_Mutation_p.L11V	NM_020725.1	NP_065776.1	Q9ULK2	AT7L1_HUMAN	ataxin 7-like 1	11										endometrium(1)|large_intestine(4)|lung(5)	10						GCAGCCGAGAGACACGGGATT	0.587																																					p.L11V		Atlas-SNP	.											.	ATXN7L1	56	.	0			c.C31G						PASS	.						73	64	67					7																	105516974		2203	4300	6503	SO:0001583	missense	222255	exon1			CCGAGAGACACGG	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.31C>G	chr7.hg19:g.105516974G>C	ENSP00000410759:p.Leu11Val	88.0	0.0	.		87.0	25.0	.	NM_020725	A4D0Q2|B4DTS1|Q8N2T0	Missense_Mutation	SNP	ENST00000419735.3	hg19	CCDS47682.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.475744	0.44044	.	.	ENSG00000146776	ENST00000419735;ENST00000318724	T	0.16597	2.33	4.77	4.77	0.60923	.	.	.	.	.	T	0.17492	0.0420	L	0.36672	1.1	0.80722	D	1	P;P	0.41673	0.728;0.759	B;B	0.38500	0.275;0.259	T	0.03443	-1.1036	9	0.72032	D	0.01	.	18.1766	0.89764	0.0:0.0:1.0:0.0	.	11;11	A4D0Q2;Q9ULK2	.;AT7L1_HUMAN	V	11	ENSP00000410759:L11V	ENSP00000326344:L11V	L	-	1	0	ATXN7L1	105304210	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.485000	0.60279	2.342000	0.79632	0.555000	0.69702	CTC	.	.	.	none		0.587	ATXN7L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349037.2			C	105516974	G	C	105516974	3	2	109	1	0	0	0	0	1	0	0	0	1216	942	33	4	2695	4	ATXN7L1	7	105516974	Missense_Mutation	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10	5842044	105516974	53621689	57	7002											
ARHGEF5	7984	hgsc.bcm.edu	37	chr7	144062673	144062673	+	Frame_Shift_Del	DEL	A	A	-																															cgagagaacctttgagaaggAcaacccctcagcaaggagcc																										TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr7:144062673delA	ENST00000056217.5	+	2	3085	c.2911delA	c.(2911-2913)acafs	p.T972fs	ARHGEF5_ENST00000471847.2_5'Flank	NM_005435.3	NP_005426.2	Q12774	ARHG5_HUMAN	Rho guanine nucleotide exchange factor (GEF) 5	972					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)					TTTGAGAAGGACAACCCCTCA	0.612																																					p.R970fs		Atlas-Indel,Pindel	.											.	ARHGEF5	73	.	0			c.2910delG						PASS	.						1	1	1					7																	144062673		462	1119	1581	SO:0001589	frameshift_variant	7984	exon2			.	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.2911delA	chr7.hg19:g.144062673delA	ENSP00000056217:p.Thr972fs	180.0	0.0	0		195.0	26.0	0.133333	NM_005435	A6NNJ2|Q6ZML7	Frame_Shift_Del	DEL	ENST00000056217.5	hg19	CCDS34771.1																																																																																			.	.	.	none		0.612	ARHGEF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349981.1	NM_005435		-	144062673	A	-	144062673	7	5	109	1	0	1	0	1	0	0	0	0	909	275	10	0	2913	0	ARHGEF5	7	144062673	Frame_Shift_Del	DEL	A	TCGA-B9-A8YI-01A-21D-A36X-10	38545699	144062673	15075990	58	7003											
MLL3	58508	hgsc.bcm.edu	37	chr7	151874116	151874116	+	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	tttctgtggtgaatgtttatCagagagaaccagagttttgt	10	16	11	4	0	2	4	1	1	1	3	2	5	2	4	1	1	1	2	1	1	3	5			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr7:151874116C>T	ENST00000262189.6	-	38	8640	c.8422G>A	c.(8422-8424)Gat>Aat	p.D2808N	KMT2C_ENST00000355193.2_Missense_Mutation_p.D2808N	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2808					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)										GAATGTTTATCAGAGAGAACC	0.348																																					p.D2808N		Atlas-SNP	.											.	MLL3	1564	.	0			c.G8422A						PASS	.						149	143	145					7																	151874116		2203	4300	6503	SO:0001583	missense	58508	exon38			GTTTATCAGAGAG	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.8422G>A	chr7.hg19:g.151874116C>T	ENSP00000262189:p.Asp2808Asn	65.0	0.0	.		80.0	23.0	.	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	11.33	1.605994	0.28623	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.85339	-1.97;-1.96	5.58	3.75	0.43078	.	0.136399	0.32578	N	0.005917	T	0.81187	0.4770	L	0.29908	0.895	0.20196	N	0.999929	P;D;B	0.56521	0.682;0.976;0.302	B;P;B	0.51701	0.326;0.677;0.08	T	0.72717	-0.4209	10	0.72032	D	0.01	.	7.3772	0.26835	0.0:0.7163:0.1392:0.1445	.	2808;1869;2808	Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3	MLL3_HUMAN;.;.	N	2808	ENSP00000262189:D2808N;ENSP00000347325:D2808N	ENSP00000262189:D2808N	D	-	1	0	MLL3	151505049	0.517000	0.26226	0.044000	0.18714	0.763000	0.43281	2.280000	0.43443	0.692000	0.31613	0.650000	0.86243	GAT	.	.	.	none		0.348	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			T	151874116	C	T	151874116	3	4	109	1	0	0	0	0	1	0	0	0	9629	826	29	2	6401	2	MLL3	7	151874116	Missense_Mutation	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10	7811443	151874116	7264547	59	7004											
TNKS	8658	hgsc.bcm.edu	37	chr8	9564428	9564428	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgttacttagccatggcgcTgatcctacattagtcaactg	9	14	8	10	1	1	1	1	1	0	0	2	1	2	1	2	1	4	2	2	1	5	5			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr8:9564428T>C	ENST00000310430.6	+	8	1403	c.1377T>C	c.(1375-1377)gcT>gcC	p.A459A	TNKS_ENST00000518027.1_3'UTR|TNKS_ENST00000520408.1_Silent_p.A459A|TNKS_ENST00000518281.1_Silent_p.A222A	NM_003747.2	NP_003738.2	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	459					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)		GCCATGGCGCTGATCCTACAT	0.473																																					p.A459A		Atlas-SNP	.											.	TNKS	198	.	0			c.T1377C						PASS	.						104	88	94					8																	9564428		2203	4300	6503	SO:0001819	synonymous_variant	8658	exon8			TGGCGCTGATCCT	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.1377T>C	chr8.hg19:g.9564428T>C		89.0	0.0	.		105.0	41.0	.	NM_003747	O95272|Q4G0F2	Silent	SNP	ENST00000310430.6	hg19	CCDS5974.1																																																																																			.	.	.	none		0.473	TNKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206935.1	NM_003747		C	9564428	T	C	9564428	2	2	109	1	0	0	0	0	0	0	0	1	16331	1567	55	3		3	TNKS	8	9564428	Silent	SNP	T	TCGA-B9-A8YI-01A-21D-A36X-10		9564428	136799594	60	7005											
B4GALT1	2683	hgsc.bcm.edu	37	chr9	33167143	33167148	+	In_Frame_Del	DEL	TCAGGA	TCAGGA	-																															tggcatcgcggcgctgccgcTcaggagcggctcccgaagcc																										TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	TCAGGA	TCAGGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr9:33167143_33167148delTCAGGA	ENST00000379731.4	-	1	206_211	c.20_25delTCCTGA	c.(19-27)ctcctgagc>cgc	p.7_9LLS>R	B4GALT1_ENST00000535206.1_In_Frame_Del_p.7_9LLS>R|RP11-326F20.5_ENST00000426270.1_RNA|RP11-326F20.5_ENST00000442432.1_RNA	NM_001497.3	NP_001488.2	P15291	B4GT1_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1	7					acute inflammatory response (GO:0002526)|angiogenesis involved in wound healing (GO:0060055)|binding of sperm to zona pellucida (GO:0007339)|branching morphogenesis of an epithelial tube (GO:0048754)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|development of secondary sexual characteristics (GO:0045136)|epithelial cell development (GO:0002064)|extracellular matrix organization (GO:0030198)|galactose metabolic process (GO:0006012)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|lactose biosynthetic process (GO:0005989)|leukocyte migration (GO:0050900)|mammary gland development (GO:0030879)|multicellular organism reproduction (GO:0032504)|negative regulation of cell proliferation (GO:0008285)|Notch signaling pathway (GO:0007219)|oligosaccharide biosynthetic process (GO:0009312)|penetration of zona pellucida (GO:0007341)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of acrosome reaction (GO:0060046)|regulation of cellular component movement (GO:0051270)|single fertilization (GO:0007338)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|desmosome (GO:0030057)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|glycocalyx (GO:0030112)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi trans cisterna (GO:0000138)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alpha-tubulin binding (GO:0043014)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|beta-tubulin binding (GO:0048487)|galactosyltransferase activity (GO:0008378)|lactose synthase activity (GO:0004461)|manganese ion binding (GO:0030145)|N-acetyllactosamine synthase activity (GO:0003945)|protein homodimerization activity (GO:0042803)|UDP-galactosyltransferase activity (GO:0035250)			endometrium(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)	14			LUSC - Lung squamous cell carcinoma(29;0.0084)	GBM - Glioblastoma multiforme(74;0.121)	N-Acetyl-D-glucosamine(DB00141)	GCGCTGCCGCTCAGGAGCGGCTCCCG	0.723																																					p.7_9del		Atlas-INDEL	.											.	B4GALT1	28	.	0			c.21_26del						PASS	.																																			SO:0001651	inframe_deletion	2683	exon1			.	X14085	CCDS6535.1	9p13	2013-02-19			ENSG00000086062	ENSG00000086062	2.4.1.22	"Beta 4-glycosyltransferases"	924	protein-coding gene	gene with protein product		137060		GGTB2		9597550	Standard	NM_001497		Approved	beta4Gal-T1	uc003zsg.2	P15291	OTTHUMG00000019764	ENST00000379731.4:c.20_25delTCCTGA	chr9.hg19:g.33167143_33167148delTCAGGA	ENSP00000369055:p.Leu7_Ser9delinsArg	66.0	0.0	0		76.0	20.0	0.263158	NM_001497	B2R710|D3DRL2|Q12909|Q12910|Q12911|Q14456|Q14509|Q14523	In_Frame_Del	DEL	ENST00000379731.4	hg19	CCDS6535.1																																																																																			.	.	.	none		0.723	B4GALT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052039.1	NM_001497		-	33167148	TCAGGA	-	33167143	7	5	109	1	0	1	0	1	0	0	0	0	1270	1551	54	0	1195	0	B4GALT1	9	33167143	In_Frame_Del	DEL	TCAGGA	TCGA-B9-A8YI-01A-21D-A36X-10		33167143	108046288	61	7006	77	2									
B4GALT1	2683	hgsc.bcm.edu	37	chr9	33167151	33167151	+	Frame_Shift_Del	DEL	G	G	-																															cggcgctgccgctcaggagcGgctcccgaagcctcatcttc																										TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr9:33167151delG	ENST00000379731.4	-	1	203	c.17delC	c.(16-18)ccgfs	p.P6fs	B4GALT1_ENST00000535206.1_Frame_Shift_Del_p.P6fs|RP11-326F20.5_ENST00000426270.1_RNA|RP11-326F20.5_ENST00000442432.1_RNA	NM_001497.3	NP_001488.2	P15291	B4GT1_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1	6					acute inflammatory response (GO:0002526)|angiogenesis involved in wound healing (GO:0060055)|binding of sperm to zona pellucida (GO:0007339)|branching morphogenesis of an epithelial tube (GO:0048754)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|development of secondary sexual characteristics (GO:0045136)|epithelial cell development (GO:0002064)|extracellular matrix organization (GO:0030198)|galactose metabolic process (GO:0006012)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|lactose biosynthetic process (GO:0005989)|leukocyte migration (GO:0050900)|mammary gland development (GO:0030879)|multicellular organism reproduction (GO:0032504)|negative regulation of cell proliferation (GO:0008285)|Notch signaling pathway (GO:0007219)|oligosaccharide biosynthetic process (GO:0009312)|penetration of zona pellucida (GO:0007341)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of acrosome reaction (GO:0060046)|regulation of cellular component movement (GO:0051270)|single fertilization (GO:0007338)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|desmosome (GO:0030057)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|glycocalyx (GO:0030112)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi trans cisterna (GO:0000138)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alpha-tubulin binding (GO:0043014)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|beta-tubulin binding (GO:0048487)|galactosyltransferase activity (GO:0008378)|lactose synthase activity (GO:0004461)|manganese ion binding (GO:0030145)|N-acetyllactosamine synthase activity (GO:0003945)|protein homodimerization activity (GO:0042803)|UDP-galactosyltransferase activity (GO:0035250)			endometrium(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)	14			LUSC - Lung squamous cell carcinoma(29;0.0084)	GBM - Glioblastoma multiforme(74;0.121)	N-Acetyl-D-glucosamine(DB00141)	GCTCAGGAGCGGCTCCCGAAG	0.736																																					p.P6fs		Atlas-INDEL	.											.	B4GALT1	28	.	0			c.18delG						PASS	.						6	10	9					9																	33167151		1694	3514	5208	SO:0001589	frameshift_variant	2683	exon1			.	X14085	CCDS6535.1	9p13	2013-02-19			ENSG00000086062	ENSG00000086062	2.4.1.22	"Beta 4-glycosyltransferases"	924	protein-coding gene	gene with protein product		137060		GGTB2		9597550	Standard	NM_001497		Approved	beta4Gal-T1	uc003zsg.2	P15291	OTTHUMG00000019764	ENST00000379731.4:c.17delC	chr9.hg19:g.33167151delG	ENSP00000369055:p.Pro6fs	71.0	0.0	0		77.0	20.0	0.25974	NM_001497	B2R710|D3DRL2|Q12909|Q12910|Q12911|Q14456|Q14509|Q14523	Frame_Shift_Del	DEL	ENST00000379731.4	hg19	CCDS6535.1																																																																																			.	.	.	none		0.736	B4GALT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052039.1	NM_001497		-	33167151	G	-	33167151	7	5	109	1	0	1	0	1	0	0	0	0	1270	1116	39	0	1203	0	B4GALT1	9	33167151	Frame_Shift_Del	DEL	G	TCGA-B9-A8YI-01A-21D-A36X-10	8	33167151	108046280	62	7007	77	2									
DPP7	29952	hgsc.bcm.edu	37	chr9	140009153	140009153	+	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	cagcaggaccggggcccaggGagcggagcccatgtcgcctt	7	4	16	14	3	0	0	0	0	0	0	1	3	0	3	4	5	3	1	4	5	0	1			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr9:140009153G>C	ENST00000371579.2	-	1	17	c.13C>G	c.(13-15)Ccc>Gcc	p.P5A		NM_013379.2	NP_037511.2	Q9UHL4	DPP2_HUMAN	dipeptidyl-peptidase 7	5						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)		GGGGCCCAGGGAGCGGAGCCC	0.811																																					p.P5A		Atlas-SNP	.											.	DPP7	22	.	0			c.C13G						PASS	.						1	1	1					9																	140009153		699	1539	2238	SO:0001583	missense	29952	exon1			CCCAGGGAGCGGA	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.13C>G	chr9.hg19:g.140009153G>C	ENSP00000360635:p.Pro5Ala	34.0	0.0	.		34.0	11.0	.	NM_013379	A8K7U7|Q5VSF1|Q969X4	Missense_Mutation	SNP	ENST00000371579.2	hg19	CCDS7030.1	.	.	.	.	.	.	.	.	.	.	G	10.11	1.260209	0.23051	.	.	ENSG00000176978	ENST00000371579;ENST00000443858	T	0.12465	2.68	2.39	0.47	0.16747	.	1.637370	0.03575	N	0.229169	T	0.07007	0.0178	N	0.08118	0	0.09310	N	1	B;B	0.19331	0.002;0.035	B;B	0.08055	0.002;0.003	T	0.33624	-0.9861	10	0.16896	T	0.51	.	5.9139	0.19043	0.1339:0.1986:0.6675:0.0	.	5;5	E7EQS4;Q9UHL4	.;DPP2_HUMAN	A	5	ENSP00000360635:P5A	ENSP00000360635:P5A	P	-	1	0	DPP7	139128974	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.158000	0.03153	-0.164000	0.10927	-1.961000	0.00478	CCC	.	.	.	none		0.811	DPP7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055279.1	NM_013379		C	140009153	G	C	140009153	3	2	109	1	0	0	0	0	1	0	0	0	4733	1174	41	4	1517	4	DPP7	9	140009153	Missense_Mutation	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10	106842002	140009153	1204278	63	7008											
PNPLA7	375775	hgsc.bcm.edu	37	chr9	140354898	140354898	+	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	ttttgggaaagccagactggGgtgtcgatgccgcagtgagg	8	9	17	7	2	0	2	0	1	0	1	1	4	0	3	2	4	2	1	2	4	1	2			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr9:140354898G>T	ENST00000277531.4	-	34	4087	c.3901C>A	c.(3901-3903)Ccc>Acc	p.P1301T	PNPLA7_ENST00000492278.1_5'UTR|NSMF_ENST00000339554.3_5'Flank|NSMF_ENST00000371472.2_5'Flank|NSMF_ENST00000371473.3_5'Flank|NSMF_ENST00000371474.3_5'Flank|NSMF_ENST00000392812.4_5'Flank|NSMF_ENST00000437259.1_5'Flank|NSMF_ENST00000265663.7_5'Flank|PNPLA7_ENST00000406427.1_Missense_Mutation_p.P1326T|NSMF_ENST00000371475.3_5'Flank|PNPLA7_ENST00000371457.1_Missense_Mutation_p.P907T	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	1301					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)		GCCAGACTGGGGTGTCGATGC	0.627																																					p.P1326T		Atlas-SNP	.											.	PNPLA7	124	.	0			c.C3976A						PASS	.						53	48	50					9																	140354898		2203	4300	6503	SO:0001583	missense	375775	exon35			GACTGGGGTGTCG	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.3901C>A	chr9.hg19:g.140354898G>T	ENSP00000277531:p.Pro1301Thr	51.0	0.0	.		61.0	22.0	.	NM_001098537	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Missense_Mutation	SNP	ENST00000277531.4	hg19	CCDS7045.1	.	.	.	.	.	.	.	.	.	.	G	9.846	1.192362	0.21954	.	.	ENSG00000130653	ENST00000371457;ENST00000371446;ENST00000277531;ENST00000406427;ENST00000371451	T;T;T;T	0.70045	-0.45;3.47;0.36;0.36	3.27	1.01	0.19927	.	2.580500	0.01842	U	0.035387	T	0.46229	0.1382	N	0.19112	0.55	0.09310	N	1	B;P;P;B	0.45348	0.294;0.59;0.856;0.078	B;B;B;B	0.38803	0.084;0.168;0.282;0.035	T	0.44697	-0.9311	10	0.22109	T	0.4	-1.2333	1.2022	0.01887	0.1471:0.215:0.4191:0.2189	.	709;1326;1301;548	E2QRF8;Q6ZV29-5;Q6ZV29;B3KXH5	.;.;PLPL7_HUMAN;.	T	907;709;1301;1326;1238	ENSP00000360512:P907T;ENSP00000360501:P709T;ENSP00000277531:P1301T;ENSP00000384610:P1326T	ENSP00000277531:P1301T	P	-	1	0	PNPLA7	139474719	0.000000	0.05858	0.001000	0.08648	0.019000	0.09904	-0.123000	0.10611	0.620000	0.30215	0.457000	0.33378	CCC	.	.	.	none		0.627	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286		T	140354898	G	T	140354898	3	4	109	1	0	0	0	0	1	0	0	0	12177	1232	43	4	56	4	PNPLA7	9	140354898	Missense_Mutation	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10	345745	140354898	858533	64	7009											
GAD2	2572	hgsc.bcm.edu	37	chr10	26505778	26505778	+	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	gcttttggtctttcgggtcgGaagatggctctggggattcc	4	14	15	8	2	2	1	0	0	2	1	5	3	3	3	1	6	0	2	1	6	1	4			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr10:26505778G>T	ENST00000376261.3	+	1	543	c.40G>T	c.(40-42)Gaa>Taa	p.E14*	GAD2_ENST00000259271.3_Nonsense_Mutation_p.E14*|GAD2_ENST00000376248.1_5'Flank	NM_001134366.1	NP_001127838.1	Q05329	DCE2_HUMAN	glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa)	14					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						TTTCGGGTCGGAAGATGGCTC	0.647																																					p.E14X		Atlas-SNP	.											.	GAD2	116	.	0			c.G40T						PASS	.						64	70	68					10																	26505778		2203	4300	6503	SO:0001587	stop_gained	2572	exon1			GGGTCGGAAGATG	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.40G>T	chr10.hg19:g.26505778G>T	ENSP00000365437:p.Glu14*	80.0	0.0	.		107.0	41.0	.	NM_000818	Q9UD87	Nonsense_Mutation	SNP	ENST00000376261.3	hg19	CCDS7149.1	.	.	.	.	.	.	.	.	.	.	G	35	5.435317	0.96150	.	.	ENSG00000136750	ENST00000376261;ENST00000259271;ENST00000428517	.	.	.	4.92	4.92	0.64577	.	0.070572	0.56097	D	0.000033	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-22.9908	16.9203	0.86162	0.0:0.0:1.0:0.0	.	.	.	.	X	14	.	ENSP00000259271:E14X	E	+	1	0	GAD2	26545784	1.000000	0.71417	1.000000	0.80357	0.380000	0.30137	5.787000	0.69013	2.282000	0.76494	0.455000	0.32223	GAA	.	.	.	none		0.647	GAD2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047255.1	NM_000818		T	26505778	G	T	26505778	4	4	109	1	0	0	0	0	0	1	0	0	6187	1175	41	4	42	4	GAD2	10	26505778	Nonsense_Mutation	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10		26505778	109028969	65	7010											
WAC	51322	hgsc.bcm.edu	37	chr10	28908467	28908468	+	Splice_Site	INS	-	-	TACT																															tctgcttttttttttcaggaINStactatttttgagacaacaa																										TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr10:28908467_28908468insTACT	ENST00000354911.4	+	14	2037_2038	c.1876_1877insTACT	c.(1876-1878)ata>aTACTta	p.-627fs	WAC_ENST00000347934.4_Splice_Site_p.-524fs|WAC_ENST00000375646.1_Splice_Site_p.-475fs|WAC_ENST00000375664.4_Splice_Site_p.-582fs	NM_016628.4	NP_057712.2	Q9BTA9	WAC_HUMAN	WW domain containing adaptor with coiled-coil						cellular response to DNA damage stimulus (GO:0006974)|G1 DNA damage checkpoint (GO:0044783)|histone H2B conserved C-terminal lysine ubiquitination (GO:0071894)|histone monoubiquitination (GO:0010390)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	chromatin binding (GO:0003682)|RNA polymerase II core binding (GO:0000993)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|urinary_tract(1)	32						TTTTTTCAGGATACTATTTTTG	0.277																																					p.I626fs		Atlas-Indel,Pindel	.											.	WAC	77	.	0			c.1876_1877insTACT						PASS	.																																			SO:0001630	splice_region_variant	51322	exon14			.	AK055852	CCDS7159.1, CCDS7160.1, CCDS7161.1	10p12.1	2007-05-17	2003-03-19		ENSG00000095787	ENSG00000095787			17327	protein-coding gene	gene with protein product		615049	"WW domain-containing adaptor with coiled coil"			11827461	Standard	NR_024557		Approved	Wwp4, FLJ31290, PRO1741, BM-016, MGC10753	uc001iuf.3	Q9BTA9	OTTHUMG00000017872	ENST00000354911.4:c.1875-1->TACT	chr10.hg19:g.28908468_28908471dupTACT		232.0	0.0	0		244.0	62.0	0.254098	NM_016628	A8K2A9|C9JBT9|D3DRW5|D3DRW6|D3DRW7|Q53EN9|Q5JU75|Q5JU77|Q5VXK0|Q5VXK2|Q8TCK1|Q96DP3|Q96FW6|Q96JI3	Frame_Shift_Ins	INS	ENST00000354911.4	hg19	CCDS7159.1																																																																																			.	.	.	none		0.277	WAC-017	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000047371.1	NM_100264	Frame_Shift_Ins	TACT	28908468	-	TACT	28908467	8	5	109	1	0	1	1	0	0	0	1	0	17259	347	12	0	1930	0	WAC	10	28908467	Splice_Site	INS	-	TCGA-B9-A8YI-01A-21D-A36X-10	2402689	28908467	106626280	66	7011											
NRP1	8829	hgsc.bcm.edu	37	chr10	33496597	33496597	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatcgcgtggagagagctggAaaagtccgcagctcaggtgt	11	7	15	8	3	1	1	1	0	0	1	3	4	2	3	1	3	2	3	1	3	3	0			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr10:33496597A>G	ENST00000265371.4	-	11	2187	c.1662T>C	c.(1660-1662)ttT>ttC	p.F554F	NRP1_ENST00000395995.1_Silent_p.F554F|NRP1_ENST00000374867.2_Silent_p.F554F|NRP1_ENST00000374816.3_Silent_p.F554F|NRP1_ENST00000374822.4_Silent_p.F554F|NRP1_ENST00000374821.5_Silent_p.F554F|NRP1_ENST00000374823.5_Silent_p.F554F|NRP1_ENST00000374875.1_Silent_p.F373F			O14786	NRP1_HUMAN	neuropilin 1	554	F5/8 type C 2. {ECO:0000255|PROSITE- ProRule:PRU00081}.				angiogenesis (GO:0001525)|angiogenesis involved in coronary vascular morphogenesis (GO:0060978)|artery morphogenesis (GO:0048844)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|commissural neuron axon guidance (GO:0071679)|coronary artery morphogenesis (GO:0060982)|dendrite development (GO:0016358)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell chemotaxis (GO:0035767)|endothelial tip cell fate specification (GO:0097102)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|patterning of blood vessels (GO:0001569)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of cytokine activity (GO:0060301)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of retinal ganglion cell axon guidance (GO:1902336)|positive regulation of smooth muscle cell migration (GO:0014911)|protein localization to early endosome (GO:1902946)|regulation of retinal ganglion cell axon guidance (GO:0090259)|regulation of vesicle-mediated transport (GO:0060627)|renal artery morphogenesis (GO:0061441)|response to wounding (GO:0009611)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal ganglion cell axon guidance (GO:0031290)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|VEGF-activated neuropilin signaling pathway (GO:0038190)|VEGF-activated neuropilin signaling pathway involved in axon guidance (GO:1902378)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neurofilament (GO:0005883)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|semaphorin receptor complex (GO:0002116)|sorting endosome (GO:0097443)	coreceptor activity (GO:0015026)|cytokine binding (GO:0019955)|growth factor binding (GO:0019838)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|semaphorin receptor activity (GO:0017154)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	48					Palifermin(DB00039)|Pegaptanib(DB04895)	AGAGAGCTGGAAAAGTCCGCA	0.507																																					p.F554F	Melanoma(104;886 1489 44640 45944 51153)	Atlas-SNP	.											.	NRP1	126	.	0			c.T1662C						PASS	.						168	158	161					10																	33496597		2203	4300	6503	SO:0001819	synonymous_variant	8829	exon10			AGCTGGAAAAGTC	AF016050	CCDS7177.1, CCDS31179.1, CCDS31180.1	10p12	2006-02-23			ENSG00000099250	ENSG00000099250		"CD molecules"	8004	protein-coding gene	gene with protein product		602069				9529250, 9331348	Standard	NM_003873		Approved	NRP, VEGF165R, CD304	uc001iwx.4	O14786	OTTHUMG00000019343	ENST00000265371.4:c.1662T>C	chr10.hg19:g.33496597A>G		62.0	0.0	.		103.0	8.0	.	NM_001244973	B0LPG9|O60461|Q5T7F1|Q5T7F2|Q5T7F3|Q86T59|Q96I90|Q96IH5	Silent	SNP	ENST00000265371.4	hg19	CCDS7177.1																																																																																			.	.	.	none		0.507	NRP1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051203.2			G	33496597	A	G	33496597	2	3	109	1	0	0	0	0	0	0	0	1	10667	243	9	3		3	NRP1	10	33496597	Silent	SNP	A	TCGA-B9-A8YI-01A-21D-A36X-10	4588130	33496597	102038150	67	7012											
BICC1	80114	hgsc.bcm.edu	37	chr10	60549020	60549020	+	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	gattctcatcatttcattttAggagctgcttcctttggtgc	6	18	8	9	0	3	0	3	0	1	0	5	2	4	1	1	2	3	2	1	2	1	6			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr10:60549020A>G	ENST00000373886.3	+	7	604		c.e7-1			NM_001080512.1	NP_001073981.1	Q9H694	BICC1_HUMAN	BicC family RNA binding protein 1						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						ATTTCATTTTAGGAGCTGCTT	0.378																																					.		Atlas-SNP	.											.	BICC1	121	.	0			c.601-2A>G						PASS	.						94	89	91					10																	60549020		2203	4300	6503	SO:0001630	splice_region_variant	80114	exon7			CATTTTAGGAGCT	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.601-1A>G	chr10.hg19:g.60549020A>G		80.0	0.0	.		91.0	40.0	.	NM_001080512		Splice_Site	SNP	ENST00000373886.3	hg19	CCDS31206.1	.	.	.	.	.	.	.	.	.	.	A	19.84	3.902221	0.72754	.	.	ENSG00000122870	ENST00000373886	.	.	.	5.66	5.66	0.87406	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9023	0.79387	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BICC1	60219026	1.000000	0.71417	0.988000	0.46212	0.717000	0.41224	9.064000	0.93933	2.153000	0.67306	0.533000	0.62120	.	.	.	.	none		0.378	BICC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048150.2	NM_025044	Intron	G	60549020	A	G	60549020	5	3	109	1	0	0	0	0	0	0	1	0	1427	434	15	3	625	3	BICC1	10	60549020	Splice_Site	SNP	A	TCGA-B9-A8YI-01A-21D-A36X-10	27052423	60549020	74985727	68	7013											
UBTD1	80019	hgsc.bcm.edu	37	chr10	99330070	99330070	+	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	aaggtgcgcctgtccacgggCaaggacgtgaggctcagcgc	8	5	16	12	4	1	1	1	1	0	0	2	2	2	2	2	4	2	2	2	4	2	0			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr10:99330070C>A	ENST00000370664.3	+	3	810	c.474C>A	c.(472-474)ggC>ggA	p.G158G	ANKRD2_ENST00000455090.1_5'Flank|ANKRD2_ENST00000298808.5_5'Flank|ANKRD2_ENST00000370655.1_5'Flank|ANKRD2_ENST00000307518.5_5'Flank	NM_024954.3	NP_079230.1	Q9HAC8	UBTD1_HUMAN	ubiquitin domain containing 1	158	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.									central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(1)|skin(1)	7		Colorectal(252;0.162)		Epithelial(162;3.04e-10)|all cancers(201;2.86e-08)		TGTCCACGGGCAAGGACGTGA	0.697																																					p.G158G	Pancreas(100;169 2668 32720)	Atlas-SNP	.											.	UBTD1	19	.	0			c.C474A						PASS	.						43	43	43					10																	99330070		2203	4299	6502	SO:0001819	synonymous_variant	80019	exon3			CACGGGCAAGGAC	BC007331	CCDS7465.1	10q24.2	2005-09-22			ENSG00000165886	ENSG00000165886			25683	protein-coding gene	gene with protein product						12477932	Standard	NM_024954		Approved	FLJ11807	uc001knv.1	Q9HAC8	OTTHUMG00000018856	ENST00000370664.3:c.474C>A	chr10.hg19:g.99330070C>A		81.0	0.0	.		76.0	25.0	.	NM_024954	D3DR57|Q53HI3	Silent	SNP	ENST00000370664.3	hg19	CCDS7465.1																																																																																			.	.	.	none		0.697	UBTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049701.1	NM_024954		A	99330070	C	A	99330070	2	1	109	1	0	0	0	0	0	0	0	1	16919	697	25	4		4	UBTD1	10	99330070	Silent	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10	38781050	99330070	36204677	69	7014											
MKI67	4288	hgsc.bcm.edu	37	chr10	129909928	129909929	+	Missense_Mutation	DNP	GT	GT	AA																															cctgaaagatcttccttaaaGtccattttttggttggaaat																										TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G|T	G|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr10:129909928_129909929GT>AA	ENST00000368654.3	-	11	2615_2616	c.2240_2241AC>TT	c.(2239-2241)gAC>gTT	p.D747V	MKI67_ENST00000484853.1_5'UTR|MKI67_ENST00000368653.3_Missense_Mutation_p.D387V	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)				CTTCCTTAAAGTCCATTTTTTG	0.347																																					p.D747D|p.D747V		Atlas-SNP	.											.	MKI67	363	.	0			c.C2241T|c.A2240T						PASS	.																																			SO:0001583	missense	4288	exon11			CTTAAAGTCCATT|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.2240_2241delinsAA	chr10.hg19:g.129909928_129909929delinsAA	ENSP00000357643:p.Asp747Val	64.0|65.0	0.0	.		90.0|94.0	27.0	.	NM_002417	Q5VWH2	Silent|Missense_Mutation	SNP	ENST00000368654.3	hg19	CCDS7659.1																																																																																			.	.	.	none		0.347	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		AA	129909929	GT	AA	129909928	3	1	109	1	0	0	0	0	1	0	0	0	9605	1020	36	2	7549	2	MKI67	10	129909928	Missense_Mutation	DNP	GT	TCGA-B9-A8YI-01A-21D-A36X-10	30579858	129909928	5624819	70	7015											
MUC6	4588	hgsc.bcm.edu	37	chr11	1020248	1020248	+	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	tcatgggccagacttgcgtgGgccgtgagcctgggtgggcg	4	8	19	10	3	1	2	1	1	0	1	1	2	1	2	3	4	2	0	3	4	0	1			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr11:1020248G>T	ENST00000421673.2	-	29	3700	c.3650C>A	c.(3649-3651)cCc>cAc	p.P1217H		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1217					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)		GACTTGCGTGGGCCGTGAGCC	0.672																																					p.P1217H		Atlas-SNP	.											.	MUC6	408	.	0			c.C3650A						PASS	.						71	83	79					11																	1020248		2115	4209	6324	SO:0001583	missense	4588	exon29			TGCGTGGGCCGTG	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.3650C>A	chr11.hg19:g.1020248G>T	ENSP00000406861:p.Pro1217His	67.0	0.0	.		94.0	32.0	.	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	hg19	CCDS44513.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	3.420|3.420	-0.118416|-0.118416	0.06838|0.06838	.|.	.|.	ENSG00000184956|ENSG00000184956	ENST00000421673|ENST00000527242	T|.	0.20463|.	2.07|.	1.31|1.31	1.31|1.31	0.21738|0.21738	.|.	.|.	.|.	.|.	.|.	T|T	0.35799|0.35799	0.0944|0.0944	L|L	0.36672|0.36672	1.1|1.1	0.09310|0.09310	N|N	1|1	D|.	0.63046|.	0.992|.	B|.	0.41332|.	0.354|.	T|T	0.33752|0.33752	-0.9856|-0.9856	9|6	0.62326|0.87932	D|D	0.03|0	.|.	6.0061|6.0061	0.19547|0.19547	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1217|.	Q6W4X9|.	MUC6_HUMAN|.	H|T	1217|22	ENSP00000406861:P1217H|.	ENSP00000406861:P1217H|ENSP00000436903:P22T	P|P	-|-	2|1	0|0	MUC6|MUC6	1010248|1010248	0.006000|0.006000	0.16342|0.16342	0.004000|0.004000	0.12327|0.12327	0.105000|0.105000	0.19272|0.19272	1.607000|1.607000	0.36836|0.36836	1.027000|1.027000	0.39758|0.39758	0.313000|0.313000	0.20887|0.20887	CCC|CCA	.	.	.	none		0.672	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		T	1020248	G	T	1020248	3	4	109	1	0	0	0	0	1	0	0	0	9987	1232	43	4	3689	4	MUC6	11	1020248	Missense_Mutation	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10		1020248	133986268	71	7016											
OR56A3	390083	hgsc.bcm.edu	37	chr11	5969097	5969097	+	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	agcacaactccgttattgtgGaagaaatgtcattgagaact	14	11	9	7	1	1	2	1	1	0	2	2	4	2	3	1	1	3	2	1	1	5	3			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr11:5969097G>T	ENST00000329564.6	+	1	528	c.521G>T	c.(520-522)gGa>gTa	p.G174V	AC025016.1_ENST00000528915.1_lincRNA	NM_001003443.2	NP_001003443.2	Q8NH54	O56A3_HUMAN	olfactory receptor, family 56, subfamily A, member 3	174						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)		CGTTATTGTGGAAGAAATGTC	0.443																																					p.G174V		Atlas-SNP	.											.	OR56A3	81	.	0			c.G521T						PASS	.						102	103	103					11																	5969097		2165	4289	6454	SO:0001583	missense	390083	exon1			ATTGTGGAAGAAA		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.521G>T	chr11.hg19:g.5969097G>T	ENSP00000331572:p.Gly174Val	81.0	0.0	.		81.0	25.0	.	NM_001003443	A6NN77|Q6IFF7	Missense_Mutation	SNP	ENST00000329564.6	hg19	CCDS41614.1	.	.	.	.	.	.	.	.	.	.	G	1.952	-0.440878	0.04636	.	.	ENSG00000184478	ENST00000329564	T	0.00123	8.7	5.13	-1.72	0.08107	GPCR, rhodopsin-like superfamily (1);	0.742131	0.12370	N	0.474882	T	0.00210	0.0006	M	0.78344	2.41	0.18873	N	0.999982	B	0.15473	0.013	B	0.29176	0.099	T	0.23048	-1.0199	10	0.54805	T	0.06	-1.8477	6.3867	0.21563	0.3047:0.23:0.4653:0.0	.	174	Q8NH54	O56A3_HUMAN	V	174	ENSP00000331572:G174V	ENSP00000331572:G174V	G	+	2	0	OR56A3	5925673	0.000000	0.05858	0.002000	0.10522	0.020000	0.10135	0.057000	0.14279	-0.148000	0.11234	0.650000	0.86243	GGA	.	.	.	none		0.443	OR56A3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383753.1	NM_001003443		T	5969097	G	T	5969097	3	4	109	1	0	0	0	0	1	0	0	0	11141	1174	41	4	523	4	OR56A3	11	5969097	Missense_Mutation	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10	4948849	5969097	129037419	72	7017											
RRP8	23378	hgsc.bcm.edu	37	chr11	6622765	6622765	+	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	cttaatgtatgagggggtttAggggaagtggacccagggct	9	10	17	5	0	0	1	0	1	0	0	0	3	0	3	1	6	0	3	1	6	4	4			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr11:6622765A>C	ENST00000254605.6	-	3	648	c.531T>G	c.(529-531)ccT>ccG	p.P177P	ILK_ENST00000537806.1_5'Flank|RRP8_ENST00000534343.1_Intron|RP11-732A19.8_ENST00000527191.1_RNA|ILK_ENST00000528995.1_5'Flank|ILK_ENST00000299421.4_5'Flank|ILK_ENST00000420936.2_5'Flank|ILK_ENST00000396751.2_5'Flank	NM_015324.3	NP_056139.1	O43159	RRP8_HUMAN	ribosomal RNA processing 8, methyltransferase, homolog (yeast)	177					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						GAGGGGGTTTAGGGGAAGTGG	0.527																																					p.P177P		Atlas-SNP	.											.	RRP8	40	.	0			c.T531G						PASS	.						107	104	105					11																	6622765		2201	4296	6497	SO:0001819	synonymous_variant	23378	exon3			GGGTTTAGGGGAA	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.531T>G	chr11.hg19:g.6622765A>C		19.0	0.0	.		23.0	4.0	.	NM_015324	Q7KZ78|Q9BVM6	Silent	SNP	ENST00000254605.6	hg19	CCDS31411.1																																																																																			.	.	.	none		0.527	RRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384505.1	NM_015324		C	6622765	A	C	6622765	2	2	109	1	0	0	0	0	0	0	0	1	13703	407	15	5		5	RRP8	11	6622765	Silent	SNP	A	TCGA-B9-A8YI-01A-21D-A36X-10	653668	6622765	128383751	73	7018											
PRDM11	56981	hgsc.bcm.edu	37	chr11	45203876	45203876	+	Missense_Mutation	SNP	A	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	gcgacctcatcgtgcccaaaAgcttccagcaagtggacttc	10	8	9	14	2	1	0	1	0	0	0	4	2	2	1	3	1	3	2	3	1	3	2			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr11:45203876A>C	ENST00000530656.1	+	3	301	c.301A>C	c.(301-303)Agc>Cgc	p.S101R	PRDM11_ENST00000424263.2_Missense_Mutation_p.S67R|PRDM11_ENST00000263765.4_Missense_Mutation_p.S101R			Q9NQV5	PRD11_HUMAN	PR domain containing 11	101							methyltransferase activity (GO:0008168)			endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	26						CGTGCCCAAAAGCTTCCAGCA	0.607																																					p.S67R	NSCLC(118;1511 1736 6472 36603 43224)	Atlas-SNP	.											.	PRDM11	53	.	0			c.A199C						PASS	.						76	70	72					11																	45203876		2203	4299	6502	SO:0001583	missense	56981	exon3			CCCAAAAGCTTCC	AF275818	CCDS58130.1, CCDS73277.1	11p11	2008-07-21			ENSG00000019485	ENSG00000019485			13996	protein-coding gene	gene with protein product	"PR-domain containing protein 11"						Standard	NM_001256695		Approved	PFM8	uc031qab.1	Q9NQV5	OTTHUMG00000166478	ENST00000530656.1:c.301A>C	chr11.hg19:g.45203876A>C	ENSP00000435976:p.Ser101Arg	106.0	0.0	.		101.0	35.0	.	NM_001256695	Q8N9F1	Missense_Mutation	SNP	ENST00000530656.1	hg19		.	.	.	.	.	.	.	.	.	.	A	20.4	3.983774	0.74474	.	.	ENSG00000019485	ENST00000263765;ENST00000530656;ENST00000526442;ENST00000424263	T;T;T;T	0.51817	0.69;0.69;0.69;0.69	5.18	4.05	0.47172	.	0.159392	0.45126	D	0.000396	T	0.53818	0.1820	L	0.29908	0.895	0.32518	N	0.536669	D	0.76494	0.999	D	0.78314	0.991	T	0.63024	-0.6729	10	0.54805	T	0.06	-23.6209	10.7232	0.46052	0.9247:0.0:0.0753:0.0	.	101	Q9NQV5	PRD11_HUMAN	R	101;101;67;67	ENSP00000263765:S101R;ENSP00000435976:S101R;ENSP00000431898:S67R;ENSP00000394314:S67R	ENSP00000263765:S101R	S	+	1	0	PRDM11	45160452	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	4.780000	0.62382	0.821000	0.34540	0.402000	0.26972	AGC	.	.	.	none		0.607	PRDM11-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000389928.1	NM_020229		C	45203876	A	C	45203876	3	2	109	1	0	0	0	0	1	0	0	0	12462	72	3	5	311	5	PRDM11	11	45203876	Missense_Mutation	SNP	A	TCGA-B9-A8YI-01A-21D-A36X-10	38581111	45203876	89802640	74	7019											
SYTL2	54843	hgsc.bcm.edu	37	chr11	85416053	85416053	+	Frame_Shift_Del	DEL	T	T	-																															caatttctgtgtctttaagaTttgtttttcaattttatact																										TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr11:85416053delT	ENST00000528231.1	-	14	2399	c.2122delA	c.(2122-2124)atcfs	p.I708fs	SYTL2_ENST00000525423.1_Frame_Shift_Del_p.I1030fs|SYTL2_ENST00000527523.1_Frame_Shift_Del_p.I676fs|SYTL2_ENST00000525702.1_Frame_Shift_Del_p.I150fs|SYTL2_ENST00000389958.3_Frame_Shift_Del_p.I139fs|SYTL2_ENST00000524452.1_Frame_Shift_Del_p.I684fs|SYTL2_ENST00000389960.4_Frame_Shift_Del_p.I684fs|SYTL2_ENST00000533892.1_Frame_Shift_Del_p.I110fs|SYTL2_ENST00000529581.1_Frame_Shift_Del_p.I150fs|SYTL2_ENST00000316356.4_Frame_Shift_Del_p.I709fs|SYTL2_ENST00000359152.5_Frame_Shift_Del_p.I1554fs|SYTL2_ENST00000354566.3_Frame_Shift_Del_p.I1046fs	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	708	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		GTCTTTAAGATTTGTTTTTCA	0.333																																					p.I1046fs		Atlas-Indel,Pindel	.											SYTL2_ENST00000316356,colon,carcinoma,0,2	SYTL2	231	.	0			c.3137delT						PASS	.						102	97	99					11																	85416053		2203	4299	6502	SO:0001589	frameshift_variant	54843	exon9			.	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.2122delA	chr11.hg19:g.85416053delT	ENSP00000431701:p.Ile708fs	96.0	0.0	0		103.0	36.0	0.349515	NM_206927	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Frame_Shift_Del	DEL	ENST00000528231.1	hg19	CCDS53688.1																																																																																			.	.	.	none		0.333	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927		-	85416053	T	-	85416053	7	5	109	1	0	1	0	1	0	0	0	0	15495	1493	52	0	702	0	SYTL2	11	85416053	Frame_Shift_Del	DEL	T	TCGA-B9-A8YI-01A-21D-A36X-10	40212177	85416053	49590463	75	7020											
USP28	57646	hgsc.bcm.edu	37	chr11	113683009	113683009	+	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	tacttttacctgcattgaagTagggtagtttgtcattaatg	10	17	9	5	0	1	1	1	1	0	0	1	1	1	1	1	1	3	4	1	1	6	8			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr11:113683009T>A	ENST00000003302.4	-	16	2029	c.1961A>T	c.(1960-1962)tAc>tTc	p.Y654F	USP28_ENST00000544967.1_Missense_Mutation_p.Y362F|USP28_ENST00000260188.5_Missense_Mutation_p.Y654F|USP28_ENST00000545540.1_Missense_Mutation_p.Y529F	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN	ubiquitin specific peptidase 28	654					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		TGCATTGAAGTAGGGTAGTTT	0.378																																					p.Y654F	Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)	Atlas-SNP	.											.	USP28	135	.	0			c.A1961T						PASS	.						84	78	80					11																	113683009		2201	4296	6497	SO:0001583	missense	57646	exon16			TTGAAGTAGGGTA	AB040948	CCDS31680.1, CCDS73394.1	11q23	2008-04-11	2005-08-08		ENSG00000048028	ENSG00000048028		"Ubiquitin-specific peptidases"	12625	protein-coding gene	gene with protein product		610748	"ubiquitin specific protease 28"			12838346, 11597335	Standard	XM_005271630		Approved	KIAA1515	uc001poh.3	Q96RU2	OTTHUMG00000168205	ENST00000003302.4:c.1961A>T	chr11.hg19:g.113683009T>A	ENSP00000003302:p.Tyr654Phe	91.0	0.0	.		118.0	39.0	.	NM_020886	B0YJC0|B0YJC1|Q9P213	Missense_Mutation	SNP	ENST00000003302.4	hg19	CCDS31680.1	.	.	.	.	.	.	.	.	.	.	T	4.187	0.033316	0.08101	.	.	ENSG00000048028	ENST00000003302;ENST00000260188;ENST00000544967;ENST00000545540;ENST00000538475	T;T;T;T;T	0.44083	1.51;1.52;0.93;1.52;0.93	5.0	3.83	0.44106	.	0.355351	0.34879	N	0.003616	T	0.22898	0.0553	N	0.14661	0.345	0.33755	D	0.62112	B;B;B	0.28605	0.042;0.001;0.217	B;B;B	0.27608	0.037;0.001;0.081	T	0.24941	-1.0146	10	0.09338	T	0.73	-8.4386	11.7095	0.51616	0.0:0.0:0.2787:0.7212	.	529;654;362	B4E3L3;Q96RU2;G3V1N5	.;UBP28_HUMAN;.	F	654;654;362;529;358	ENSP00000003302:Y654F;ENSP00000260188:Y654F;ENSP00000442431:Y362F;ENSP00000444991:Y529F;ENSP00000442257:Y358F	ENSP00000003302:Y654F	Y	-	2	0	USP28	113188219	0.982000	0.34865	0.509000	0.27700	0.927000	0.56198	2.490000	0.45294	0.883000	0.36040	0.533000	0.62120	TAC	.	.	.	none		0.378	USP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398789.1			A	113683009	T	A	113683009	3	1	109	1	0	0	0	0	1	0	0	0	17070	1638	57	5	1312	5	USP28	11	113683009	Missense_Mutation	SNP	T	TCGA-B9-A8YI-01A-21D-A36X-10	28266956	113683009	21323507	76	7021											
ETS1	2113	hgsc.bcm.edu	37	chr11	128354849	128354849	+	Missense_Mutation	SNP	T	T	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	aggggtagtcattctcatacTtgagggagaggagctcttcc	9	11	13	8	0	3	2	2	1	2	1	5	4	4	3	1	4	2	2	1	4	2	5			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr11:128354849T>G	ENST00000319397.6	-	5	908	c.599A>C	c.(598-600)aAg>aCg	p.K200T	ETS1_ENST00000345075.4_Missense_Mutation_p.K200T|ETS1_ENST00000531611.1_Missense_Mutation_p.K200T|ETS1_ENST00000392668.4_Missense_Mutation_p.K244T|ETS1_ENST00000526145.2_Missense_Mutation_p.K200T|ETS1_ENST00000535549.1_Intron	NM_005238.3	NP_005229.1	P14921	ETS1_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 1	200	Activation domain; required for transcription activation.				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)		ATTCTCATACTTGAGGGAGAG	0.527																																					p.K244T		Atlas-SNP	.											.	ETS1	123	.	0			c.A731C						PASS	.						152	135	141					11																	128354849		2201	4297	6498	SO:0001583	missense	2113	exon7			TCATACTTGAGGG		CCDS8475.1, CCDS44767.1, CCDS53724.1	11q23.3	2013-07-09	2013-07-09		ENSG00000134954	ENSG00000134954			3488	protein-coding gene	gene with protein product	"Avian erythroblastosis virus E26 (v-ets) oncogene homolog-1", "ets protein"	164720		EWSR2		1522903	Standard	NM_005238		Approved	FLJ10768, ETS-1	uc001qej.2	P14921	OTTHUMG00000165799	ENST00000319397.6:c.599A>C	chr11.hg19:g.128354849T>G	ENSP00000324578:p.Lys200Thr	95.0	0.0	.		130.0	62.0	.	NM_001143820	A9UL17|F5GYX9|Q14278|Q16080|Q6N087|Q96AC5	Missense_Mutation	SNP	ENST00000319397.6	hg19	CCDS8475.1	.	.	.	.	.	.	.	.	.	.	T	19.35	3.809866	0.70797	.	.	ENSG00000134954	ENST00000345075;ENST00000392668;ENST00000531611;ENST00000319397;ENST00000526145	T;T;T;T;T	0.55413	2.96;2.62;0.52;2.62;2.96	5.67	5.67	0.87782	.	0.197284	0.52532	D	0.000076	T	0.68128	0.2967	L	0.55481	1.735	0.80722	D	1	D;P;P	0.71674	0.998;0.651;0.791	D;B;B	0.76071	0.987;0.214;0.273	T	0.68150	-0.5485	10	0.46703	T	0.11	.	15.9141	0.79496	0.0:0.0:0.0:1.0	.	200;200;244	P14921;Q96AC5;Q6N087	ETS1_HUMAN;.;.	T	200;244;200;200;200	ENSP00000340485:K200T;ENSP00000376436:K244T;ENSP00000435666:K200T;ENSP00000324578:K200T;ENSP00000433500:K200T	ENSP00000324578:K200T	K	-	2	0	ETS1	127860059	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.004000	0.88535	2.159000	0.67721	0.459000	0.35465	AAG	.	.	.	none		0.527	ETS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386269.2	NM_005238		G	128354849	T	G	128354849	3	3	109	1	0	0	0	0	1	0	0	0	5277	1609	56	5	742	5	ETS1	11	128354849	Missense_Mutation	SNP	T	TCGA-B9-A8YI-01A-21D-A36X-10	14671840	128354849	6651667	77	7022											
SFRS2IP	9169	hgsc.bcm.edu	37	chr12	46322508	46322509	+	Frame_Shift_Ins	INS	-	-	A																															gctgtttcagctcttgtgttINSacgtgtagacctccttgtag																										TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr12:46322508_46322509insA	ENST00000369367.3	-	11	1208_1209	c.975_976insT	c.(973-978)cgtaacfs	p.N326fs	SCAF11_ENST00000419565.2_Frame_Shift_Ins_p.N326fs|SCAF11_ENST00000549162.1_Frame_Shift_Ins_p.N134fs|SCAF11_ENST00000465950.1_Frame_Shift_Ins_p.N11fs	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	326					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						GCTCTTGTGTTACGTGTAGACC	0.446																																					p.N326_T327delinsX		Atlas-Indel,Pindel	.											.	SCAF11	145	.	0			c.976_977insT						PASS	.																																			SO:0001589	frameshift_variant	9169	exon11			.	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.976dupT	chr12.hg19:g.46322509_46322509dupA	ENSP00000358374:p.Asn326fs	56.0	0.0	0		80.0	28.0	0.35	NM_004719	A6NEU9|A6NLW5|Q8IW59	Frame_Shift_Ins	INS	ENST00000369367.3	hg19	CCDS8748.2																																																																																			.	.	.	none		0.446	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719		A	46322509	-	A	46322508	7	5	109	1	0	1	1	0	0	0	0	0	14190	1754	61	0	3435	0	SFRS2IP	12	46322508	Frame_Shift_Ins	INS	-	TCGA-B9-A8YI-01A-21D-A36X-10		46322508	87529387	78	7023											
ANP32D	23519	hgsc.bcm.edu	37	chr12	48866715	48866715	+	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	tggcagaaaagtgtccaaacCtcatacatctaaatttaagt	16	11	6	8	0	2	1	1	0	1	1	3	1	3	1	2	1	2	1	2	1	7	4	rs147147368		TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr12:48866715C>G	ENST00000266594.1	+	1	268	c.268C>G	c.(268-270)Ctc>Gtc	p.L90V		NM_012404.2	NP_036536.2	O95626	AN32D_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32 family, member D	90						nuclear matrix (GO:0016363)				central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	9						GTGTCCAAACCTCATACATCT	0.388																																					p.L90V		Atlas-SNP	.											ANP32D,NS,malignant_melanoma,0,1	ANP32D	15	.	0			c.C268G						PASS	.						90	89	90					12																	48866715		2203	4300	6503	SO:0001583	missense	23519	exon1			CCAAACCTCATAC	U71084	CCDS31788.1	12q13.12	2008-08-04			ENSG00000139223	ENSG00000139223		"ANP32 acidic nuclear phosphoproteins"	16676	protein-coding gene	gene with protein product	"pp32 related 2"	606878				10086381, 10400610	Standard	NM_012404		Approved	PP32R2	uc010slt.2	O95626	OTTHUMG00000162681	ENST00000266594.1:c.268C>G	chr12.hg19:g.48866715C>G	ENSP00000266594:p.Leu90Val	107.0	1.0	.		122.0	40.0	.	NM_012404	Q6NTC4	Missense_Mutation	SNP	ENST00000266594.1	hg19	CCDS31788.1	.	.	.	.	.	.	.	.	.	.	c	11.53	1.665208	0.29604	.	.	ENSG00000139223	ENST00000266594	T	0.62105	0.05	1.55	0.553	0.17235	.	0.000000	0.85682	D	0.000000	T	0.80116	0.4564	H	0.95645	3.7	0.52099	D	0.999941	D	0.58970	0.984	D	0.67382	0.951	T	0.77351	-0.2620	10	0.87932	D	0	.	6.048	0.19770	0.0:0.8125:0.0:0.1875	.	90	O95626	AN32D_HUMAN	V	90	ENSP00000266594:L90V	ENSP00000266594:L90V	L	+	1	0	ANP32D	47152982	1.000000	0.71417	0.001000	0.08648	0.039000	0.13416	1.769000	0.38522	0.039000	0.15632	-1.057000	0.02308	CTC	.	C|1.000;T|0.000	.	alt		0.388	ANP32D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370058.1	NM_012404		G	48866715	C	G	48866715	3	3	109	1	0	0	0	0	1	0	0	0	708	681	24	4	270	4	ANP32D	12	48866715	Missense_Mutation	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10	2544207	48866715	84985180	79	7024											
SCN8A	6334	hgsc.bcm.edu	37	chr12	52201156	52201161	+	In_Frame_Del	DEL	GGAAGG	GGAAGG	-																															gagaaacagcagcgggcagaGgaaggaagaagggaaagagc																										TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	GGAAGG	GGAAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr12:52201156_52201161delGGAAGG	ENST00000354534.6	+	27	6064_6069	c.5886_5891delGGAAGG	c.(5884-5892)gaggaagga>gaa	p.EG1963del	SCN8A_ENST00000545061.1_In_Frame_Del_p.EG1922del|AC068987.1_ENST00000599343.1_5'Flank|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	1963					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)	AGCGGGCAGAGGAAGGAAGAAGGGAA	0.451																																					p.1962_1964del		Atlas-Indel,Pindel	.											.	SCN8A	331	.	0			c.5885_5890del						PASS	.																																			SO:0001651	inframe_deletion	6334	exon27			.	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.5886_5891delGGAAGG	chr12.hg19:g.52201156_52201161delGGAAGG	ENSP00000346534:p.Glu1963_Gly1964del	343.0	0.0	0		349.0	104.0	0.297994	NM_014191	B9VWG8|O95788|Q9NYX2|Q9UPB2	In_Frame_Del	DEL	ENST00000354534.6	hg19	CCDS44891.1																																																																																			.	.	.	none		0.451	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404372.3	NM_014191		-	52201161	GGAAGG	-	52201156	7	5	109	1	0	1	0	1	0	0	0	0	13937	991	35	0	5988	0	SCN8A	12	52201156	In_Frame_Del	DEL	GGAAGG	TCGA-B9-A8YI-01A-21D-A36X-10	3334441	52201156	81650739	80	7025											
NCKAP1L	3071	hgsc.bcm.edu	37	chr12	54930731	54930733	+	In_Frame_Del	DEL	ACA	ACA	-																															tatcaataataacctaggttAcaacaacaatattcattgct																										TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	ACA	ACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr12:54930731_54930733delACA	ENST00000293373.6	+	29	3156_3158	c.3077_3079delACA	c.(3076-3081)tacaac>tac	p.N1029del	NCKAP1L_ENST00000545638.2_In_Frame_Del_p.N979del	NM_005337.4	NP_005328.2	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	1029					actin polymerization-dependent cell motility (GO:0070358)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|chemotaxis (GO:0006935)|cortical actin cytoskeleton organization (GO:0030866)|erythrocyte development (GO:0048821)|maintenance of cell polarity (GO:0030011)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of myosin-light-chain-phosphatase activity (GO:0035509)|neutrophil chemotaxis (GO:0030593)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of CD8-positive, alpha-beta T cell differentiation (GO:0043378)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of lymphocyte differentiation (GO:0045621)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of T cell proliferation (GO:0042102)|protein complex assembly (GO:0006461)|response to drug (GO:0042493)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)|protein kinase activator activity (GO:0030295)|Rac GTPase activator activity (GO:0030675)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(37)|ovary(3)|prostate(3)|skin(3)|stomach(2)	80						AACCTAGGTTACAACAACAATAT	0.394																																					p.1026_1026del		Atlas-Indel,Pindel	.											.	NCKAP1L	180	.	0			c.3076_3078del						PASS	.																																			SO:0001651	inframe_deletion	3071	exon29			.	AI924363	CCDS31813.1, CCDS53799.1	12q13.1	2005-10-11	2005-10-11	2005-10-11		ENSG00000123338			4862	protein-coding gene	gene with protein product		141180	"hematopoietic protein 1"	HEM1		1932118	Standard	NM_005337		Approved		uc001sgc.4	P55160	OTTHUMG00000169843	ENST00000293373.6:c.3077_3079delACA	chr12.hg19:g.54930737_54930739delACA	ENSP00000293373:p.Asn1029del	66.0	0.0	0		47.0	17.0	0.361702	NM_005337	B4DUT5|Q52LW0	In_Frame_Del	DEL	ENST00000293373.6	hg19	CCDS31813.1																																																																																			.	.	.	none		0.394	NCKAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406195.1	NM_005337		-	54930733	ACA	-	54930731	7	5	109	1	0	1	0	1	0	0	0	0	10229	391	14	0	3191	0	NCKAP1L	12	54930731	In_Frame_Del	DEL	ACA	TCGA-B9-A8YI-01A-21D-A36X-10	2729575	54930731	78921164	81	7026	78	2									
NCKAP1L	3071	hgsc.bcm.edu	37	chr12	54930739	54930739	+	Missense_Mutation	SNP	A	A	T																															ataacctaggttacaacaacAatattcattgcttgaccaaa																										TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr12:54930739A>T	ENST00000293373.6	+	29	3164	c.3085A>T	c.(3085-3087)Aat>Tat	p.N1029Y	NCKAP1L_ENST00000545638.2_Missense_Mutation_p.N979Y	NM_005337.4	NP_005328.2	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	1029					actin polymerization-dependent cell motility (GO:0070358)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|chemotaxis (GO:0006935)|cortical actin cytoskeleton organization (GO:0030866)|erythrocyte development (GO:0048821)|maintenance of cell polarity (GO:0030011)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of myosin-light-chain-phosphatase activity (GO:0035509)|neutrophil chemotaxis (GO:0030593)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of CD8-positive, alpha-beta T cell differentiation (GO:0043378)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of lymphocyte differentiation (GO:0045621)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of T cell proliferation (GO:0042102)|protein complex assembly (GO:0006461)|response to drug (GO:0042493)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)|protein kinase activator activity (GO:0030295)|Rac GTPase activator activity (GO:0030675)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(37)|ovary(3)|prostate(3)|skin(3)|stomach(2)	80						TTACAACAACAATATTCATTG	0.403																																					p.N1029Y		Atlas-SNP	.											.	NCKAP1L	180	.	0			c.A3085T						PASS	.						109	104	106					12																	54930739		2203	4300	6503	SO:0001583	missense	3071	exon29			AACAACAATATTC	AI924363	CCDS31813.1, CCDS53799.1	12q13.1	2005-10-11	2005-10-11	2005-10-11		ENSG00000123338			4862	protein-coding gene	gene with protein product		141180	"hematopoietic protein 1"	HEM1		1932118	Standard	NM_005337		Approved		uc001sgc.4	P55160	OTTHUMG00000169843	ENST00000293373.6:c.3085A>T	chr12.hg19:g.54930739A>T	ENSP00000293373:p.Asn1029Tyr	78.0	0.0	.		57.0	19.0	.	NM_005337	B4DUT5|Q52LW0	Missense_Mutation	SNP	ENST00000293373.6	hg19	CCDS31813.1	.	.	.	.	.	.	.	.	.	.	A	18.20	3.571514	0.65765	.	.	ENSG00000123338	ENST00000293373;ENST00000545638	T;T	0.54479	0.57;0.57	3.99	2.83	0.33086	.	0.118609	0.56097	D	0.000030	T	0.66366	0.2782	M	0.75615	2.305	0.52501	D	0.999952	D	0.69078	0.997	D	0.67900	0.954	T	0.67401	-0.5680	10	0.87932	D	0	-18.7262	8.0508	0.30577	0.9:0.0:0.1:0.0	.	1029	P55160	NCKPL_HUMAN	Y	1029;979	ENSP00000293373:N1029Y;ENSP00000445596:N979Y	ENSP00000293373:N1029Y	N	+	1	0	NCKAP1L	53217006	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	8.733000	0.91539	0.880000	0.35969	0.533000	0.62120	AAT	.	.	.	none		0.403	NCKAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406195.1	NM_005337		T	54930739	A	T	54930739	3	4	109	1	0	0	0	0	1	0	0	0	10229	130	5	5	3199	5	NCKAP1L	12	54930739	Missense_Mutation	SNP	A	TCGA-B9-A8YI-01A-21D-A36X-10	8	54930739	78921156	82	7027	78	2									
RAB21	23011	hgsc.bcm.edu	37	chr12	72179447	72179448	+	Missense_Mutation	DNP	TG	TG	CA																															ggtggagggtgctgttcttcTggataactgttcacgcctaa																										TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr12:72179447_72179448TG>CA	ENST00000261263.3	+	7	928_929	c.672_673TG>CA	c.(670-675)tcTGga>tcCAga	p.G225R		NM_014999.2	NP_055814.1	Q9UL25	RAB21_HUMAN	RAB21, member RAS oncogene family	225					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						GCTGTTCTTCTGGATAACTGTT	0.45																																					p.S224S|p.G225R		Atlas-SNP	.											.	RAB21	17	.	0			c.T672C|c.G673A						PASS	.																																			SO:0001583	missense	23011	exon7			TTCTTCTGGATAA|TCTTCTGGATAAC	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	Exception_encountered	chr12.hg19:g.72179447_72179448delinsCA	ENSP00000261263:p.Gly225Arg	169.0|166.0	0.0	.		159.0|158.0	50.0|49.0	.	NM_014999	Q14466|Q569H3	Silent|Missense_Mutation	SNP	ENST00000261263.3	hg19	CCDS9003.1																																																																																			.	.	.	none		0.45	RAB21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404855.1			CA	72179448	TG	CA	72179447	3	2	109	1	0	0	0	0	1	0	0	0	12921	1567	55	3	698	3	RAB21	12	72179447	Missense_Mutation	DNP	TG	TCGA-B9-A8YI-01A-21D-A36X-10	17248708	72179447	61672448	83	7028											
PAH	5053	hgsc.bcm.edu	37	chr12	103248991	103248991	+	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	agtacttttcaagaagtggaAaaatgtgattgtactcatag	15	13	9	4	0	2	2	2	1	0	1	2	3	2	3	0	1	2	2	0	1	7	6			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr12:103248991A>T	ENST00000553106.1	-	6	1101	c.629T>A	c.(628-630)tTt>tAt	p.F210Y	PAH_ENST00000307000.2_Missense_Mutation_p.F205Y|PAH_ENST00000551988.1_5'Flank	NM_000277.1	NP_000268.1	P00439	PH4H_HUMAN	phenylalanine hydroxylase	210					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)	AAGAAGTGGAAAAATGTGATT	0.428																																					p.F210Y		Atlas-SNP	.											.	PAH	77	.	0			c.T629A						PASS	.						138	129	132					12																	103248991		2203	4300	6503	SO:0001583	missense	5053	exon6			AGTGGAAAAATGT	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.629T>A	chr12.hg19:g.103248991A>T	ENSP00000448059:p.Phe210Tyr	108.0	0.0	.		107.0	46.0	.	NM_000277	Q16717|Q8TC14	Missense_Mutation	SNP	ENST00000553106.1	hg19	CCDS9092.1	.	.	.	.	.	.	.	.	.	.	A	33	5.265919	0.95399	.	.	ENSG00000171759	ENST00000553106;ENST00000307000	D;D	0.99674	-6.36;-6.36	5.63	5.63	0.86233	Aromatic amino acid hydroxylase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.99729	0.9894	M	0.88031	2.925	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.993	D	0.97321	0.9944	10	0.87932	D	0	-26.0147	15.8352	0.78793	1.0:0.0:0.0:0.0	.	210;210	B4DPN2;P00439	.;PH4H_HUMAN	Y	210;205	ENSP00000448059:F210Y;ENSP00000303500:F205Y	ENSP00000303500:F205Y	F	-	2	0	PAH	101773121	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.339000	0.96797	2.149000	0.67028	0.528000	0.53228	TTT	.	.	.	none		0.428	PAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406692.1			T	103248991	A	T	103248991	3	4	109	1	0	0	0	0	1	0	0	0	11401	14	1	5	761	5	PAH	12	103248991	Missense_Mutation	SNP	A	TCGA-B9-A8YI-01A-21D-A36X-10	31069544	103248991	30602904	84	7029											
SSH1	54434	hgsc.bcm.edu	37	chr12	109212091	109212091	+	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	agatgttgaggcagatcaccTgttggaccaataaagaaagc	15	8	11	7	0	1	4	1	1	0	3	1	5	1	5	2	2	1	3	2	2	4	3			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr12:109212091T>A	ENST00000326495.5	-	4	308		c.e4-2		SSH1_ENST00000326470.5_Splice_Site|SSH1_ENST00000551165.1_Splice_Site|SSH1_ENST00000546812.1_Intron|SSH1_ENST00000360239.3_Splice_Site	NM_018984.3	NP_061857.3	Q8WYL5	SSH1_HUMAN	slingshot protein phosphatase 1						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						GCAGATCACCTGTTGGACCAA	0.398																																					.		Atlas-SNP	.											.	SSH1	144	.	0			c.215-2A>T						PASS	.						99	98	98					12																	109212091		2203	4300	6503	SO:0001630	splice_region_variant	54434	exon5			ATCACCTGTTGGA	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.215-2A>T	chr12.hg19:g.109212091T>A		205.0	0.0	.		188.0	84.0	.	NM_018984	Q6P6C0|Q8N9A7|Q8WYL3|Q8WYL4|Q9P2P8	Splice_Site	SNP	ENST00000326495.5	hg19	CCDS9121.1	.	.	.	.	.	.	.	.	.	.	T	16.19	3.052953	0.55218	.	.	ENSG00000084112	ENST00000326495;ENST00000551165;ENST00000326470;ENST00000546697	.	.	.	5.79	5.79	0.91817	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2992	0.73933	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SSH1	107736220	1.000000	0.71417	0.992000	0.48379	0.533000	0.34776	7.845000	0.86875	2.205000	0.71048	0.528000	0.53228	.	.	.	.	none		0.398	SSH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403724.1	NM_018984	Intron	A	109212091	T	A	109212091	5	1	109	1	0	0	0	0	0	0	1	0	15196	1594	55	5	3170	5	SSH1	12	109212091	Splice_Site	SNP	T	TCGA-B9-A8YI-01A-21D-A36X-10	5963100	109212091	24639804	85	7030											
ERP29	10961	hgsc.bcm.edu	37	chr12	112457648	112457648	+	Missense_Mutation	SNP	A	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	tgagttcaagcgtcttgctgAaaactcggcttccagcgatg	9	11	11	10	3	2	2	1	2	1	0	4	3	3	2	1	1	4	3	1	1	3	3			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr12:112457648A>C	ENST00000261735.3	+	2	383	c.233A>C	c.(232-234)gAa>gCa	p.E78A	ERP29_ENST00000455836.1_Intron|ERP29_ENST00000546477.1_5'UTR	NM_006817.3	NP_006808.1	P30040	ERP29_HUMAN	endoplasmic reticulum protein 29	78					intracellular protein transport (GO:0006886)|protein folding (GO:0006457)|protein secretion (GO:0009306)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein disulfide isomerase activity (GO:0003756)			cervix(1)|endometrium(1)|large_intestine(1)|lung(1)|prostate(1)	5						CGTCTTGCTGAAAACTCGGCT	0.552																																					p.E78A		Atlas-SNP	.											.	ERP29	17	.	0			c.A233C						PASS	.						101	89	93					12																	112457648		2203	4300	6503	SO:0001583	missense	10961	exon2			TTGCTGAAAACTC	X94910	CCDS9158.1, CCDS44977.1	12q24.13	2011-10-19	2005-10-05	2005-10-05		ENSG00000089248		"Protein disulfide isomerases"	13799	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 9"	602287	"chromosome 12 open reading frame 8"	C12orf8		9738895, 9037184	Standard	NM_006817		Approved	ERp28, ERp31, ERp29, PDI-DB, PDIA9	uc001ttk.1	P30040	OTTHUMG00000169637	ENST00000261735.3:c.233A>C	chr12.hg19:g.112457648A>C	ENSP00000261735:p.Glu78Ala	74.0	0.0	.		114.0	38.0	.	NM_006817	C9J183|Q3MJC3|Q6FHT4	Missense_Mutation	SNP	ENST00000261735.3	hg19	CCDS9158.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.449258	0.84101	.	.	ENSG00000089248	ENST00000261735	.	.	.	5.59	5.59	0.84812	ERp29, N-terminal (1);Thioredoxin-like fold (2);	0.000000	0.64402	D	0.000001	T	0.53238	0.1784	L	0.52126	1.63	0.80722	D	1	P	0.48640	0.913	B	0.42995	0.404	T	0.50906	-0.8772	9	0.18276	T	0.48	-1.0617	15.7616	0.78087	1.0:0.0:0.0:0.0	.	78	P30040	ERP29_HUMAN	A	78	.	ENSP00000261735:E78A	E	+	2	0	ERP29	110942031	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.414000	0.73318	2.118000	0.64928	0.533000	0.62120	GAA	.	.	.	none		0.552	ERP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405200.1			C	112457648	A	C	112457648	3	2	109	1	0	0	0	0	1	0	0	0	5244	246	9	5	239	5	ERP29	12	112457648	Missense_Mutation	SNP	A	TCGA-B9-A8YI-01A-21D-A36X-10	3245557	112457648	21394247	86	7031											
SUDS3	64426	hgsc.bcm.edu	37	chr12	118852238	118852238	+	Nonstop_Mutation	SNP	A	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	cgccggcgctcagctgcttgActttctacagtgctcttctc	4	13	9	15	3	4	1	1	1	3	0	5	1	4	1	1	1	4	4	1	1	1	4			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr12:118852238A>C	ENST00000543473.1	+	12	1299	c.987A>C	c.(985-987)tgA>tgC	p.*329C	SUDS3_ENST00000397564.2_Nonstop_Mutation_p.*330C	NM_022491.2	NP_071936.2	Q9H7L9	SDS3_HUMAN	suppressor of defective silencing 3 homolog (S. cerevisiae)	0					apoptotic process (GO:0006915)|histone deacetylation (GO:0016575)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|substantia nigra development (GO:0021762)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Sin3 complex (GO:0016580)	enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)			breast(1)|lung(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CAGCTGCTTGACTTTCTACAG	0.468																																					p.X329C		Atlas-SNP	.											.	SUDS3	26	.	0			c.A987C						PASS	.						24	23	23					12																	118852238		1860	4095	5955	SO:0001578	stop_lost	64426	exon12			TGCTTGACTTTCT	AK023801	CCDS44993.1	12q24.23	2006-02-13	2006-02-13		ENSG00000111707	ENSG00000111707			29545	protein-coding gene	gene with protein product	"sin3A-associated protein, 45kDa"	608250	"suppressor of defective silencing 3 homolog (SDS3, S. cerevisiae)"			11909966	Standard	NM_022491		Approved	SDS3, FLJ00052, SAP45	uc001twz.3	Q9H7L9	OTTHUMG00000168884	ENST00000543473.1:c.987A>C	chr12.hg19:g.118852238A>C	ENSP00000443988:p.*329Cysext*8	35.0	0.0	.		35.0	13.0	.	NM_022491	Q4KMQ5|Q8N6H0|Q9H8D2	Missense_Mutation	SNP	ENST00000543473.1	hg19	CCDS44993.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.242032	0.79912	.	.	ENSG00000111707	ENST00000543473;ENST00000397564	.	.	.	5.7	5.7	0.88788	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.638	0.76970	1.0:0.0:0.0:0.0	.	.	.	.	C	329;330	.	.	X	+	3	0	SUDS3	117336621	1.000000	0.71417	0.974000	0.42286	0.918000	0.54935	6.310000	0.72830	2.172000	0.68678	0.533000	0.62120	TGA	.	.	.	none		0.468	SUDS3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401504.1	NM_022491		C	118852238	A	C	118852238	4	2	109	1	0	0	0	0	0	0	0	0	15379	288	10	5	1033	5	SUDS3	12	118852238	Nonstop_Mutation	SNP	A	TCGA-B9-A8YI-01A-21D-A36X-10	6394590	118852238	14999657	87	7032											
KLHL1	57626	hgsc.bcm.edu	37	chr13	70371015	70371015	+	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	tcaataacagccacaccaaaCtgcagccttctgccattcat	13	9	4	15	0	3	0	2	0	1	0	3	0	3	0	4	0	6	1	4	0	3	3			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr13:70371015C>G	ENST00000377844.4	-	7	2253	c.1494G>C	c.(1492-1494)caG>caC	p.Q498H	KLHL1_ENST00000545028.1_Missense_Mutation_p.Q305H	NM_020866.2	NP_065917.1	Q9NR64	KLHL1_HUMAN	kelch-like family member 1	498					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)		CCACACCAAACTGCAGCCTTC	0.388																																					p.Q498H		Atlas-SNP	.											.	KLHL1	164	.	0			c.G1494C						PASS	.						202	179	186					13																	70371015		2203	4300	6503	SO:0001583	missense	57626	exon7			ACCAAACTGCAGC	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.1494G>C	chr13.hg19:g.70371015C>G	ENSP00000367075:p.Gln498His	103.0	0.0	.		146.0	58.0	.	NM_020866	A8K5X0|Q5VZ64|Q9H4X4|Q9NR65|Q9P238	Missense_Mutation	SNP	ENST00000377844.4	hg19	CCDS9445.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.616437	0.87359	.	.	ENSG00000150361	ENST00000377844;ENST00000545028	T;T	0.76448	-1.02;-1.02	5.45	5.45	0.79879	Galactose oxidase, beta-propeller (1);	0.000000	0.64402	D	0.000009	T	0.78253	0.4254	N	0.05031	-0.125	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.82989	-0.0183	10	0.54805	T	0.06	.	19.6558	0.95837	0.0:1.0:0.0:0.0	.	498;498	Q8TBJ7;Q9NR64	.;KLHL1_HUMAN	H	498;305	ENSP00000367075:Q498H;ENSP00000439602:Q305H	ENSP00000367075:Q498H	Q	-	3	2	KLHL1	69269016	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.939000	0.63526	2.719000	0.93026	0.655000	0.94253	CAG	.	.	.	none		0.388	KLHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045231.3	NM_020866		G	70371015	C	G	70371015	3	3	109	1	0	0	0	0	1	0	0	0	8372	564	20	4	772	4	KLHL1	13	70371015	Missense_Mutation	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10		70371015	44798863	88	7033											
PCCA	5095	hgsc.bcm.edu	37	chr13	101077890	101077890	+	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	atttggtgtcacaacaggtgGaagttgatgggtcgaaacta	12	11	13	5	1	1	1	1	1	0	0	2	3	1	2	0	4	2	1	0	4	4	3			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr13:101077890G>C	ENST00000376285.1	+	20	1788	c.1750G>C	c.(1750-1752)Gaa>Caa	p.E584Q	PCCA_ENST00000376279.3_Missense_Mutation_p.E584Q|PCCA_ENST00000376286.4_Missense_Mutation_p.E558Q	NM_000282.3	NP_000273.2	P05165	PCCA_HUMAN	propionyl CoA carboxylase, alpha polypeptide	584					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)	ACAACAGGTGGAAGTTGATGG	0.458																																					p.E584Q		Atlas-SNP	.											.	PCCA	59	.	0			c.G1750C						PASS	.						160	133	142					13																	101077890		2203	4300	6503	SO:0001583	missense	5095	exon20			CAGGTGGAAGTTG	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.1750G>C	chr13.hg19:g.101077890G>C	ENSP00000365462:p.Glu584Gln	141.0	0.0	.		142.0	52.0	.	NM_001178004	B4DKY8|B4DPF9|C9JPQ8|Q15979|Q8WXQ7	Missense_Mutation	SNP	ENST00000376285.1	hg19	CCDS9496.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.1|27.1	4.798318|4.798318	0.90538|0.90538	.|.	.|.	ENSG00000175198|ENSG00000175198	ENST00000376286;ENST00000376279;ENST00000376285;ENST00000424527;ENST00000536640|ENST00000458283;ENST00000413170	T;T;T;T|.	0.78246|.	-1.16;-1.16;-1.16;-1.16|.	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.69984|0.69984	0.3172|0.3172	L|L	0.47716|0.47716	1.5|1.5	0.80722|0.80722	D|D	1|1	B;B;B|.	0.28933|.	0.017;0.013;0.228|.	B;B;B|.	0.40228|.	0.04;0.037;0.323|.	T|T	0.64905|0.64905	-0.6297|-0.6297	10|5	0.22109|.	T|.	0.4|.	.|.	19.8351|19.8351	0.96655|0.96655	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	584;558;584|.	C9JPQ8;P05165-2;P05165|.	.;.;PCCA_HUMAN|.	Q|A	558;584;584;118;80|36;27	ENSP00000365463:E558Q;ENSP00000365456:E584Q;ENSP00000365462:E584Q;ENSP00000396050:E118Q|.	ENSP00000365456:E584Q|.	E|G	+|+	1|2	0|0	PCCA|PCCA	99875891|99875891	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	8.621000|8.621000	0.90949|0.90949	2.693000|2.693000	0.91896|0.91896	0.650000|0.650000	0.86243|0.86243	GAA|GGA	.	.	.	none		0.458	PCCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045627.2			C	101077890	G	C	101077890	3	2	109	1	0	0	0	0	1	0	0	0	11511	1175	41	4	1828	4	PCCA	13	101077890	Missense_Mutation	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10	30706875	101077890	14091988	89	7034											
ABHD13	84945	hgsc.bcm.edu	37	chr13	108882094	108882094	+	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	gaagctgtgttagactacgtGatgactagacctgaccttga	11	11	11	8	1	0	6	0	4	0	2	0	7	0	6	2	0	2	2	2	0	4	4			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr13:108882094G>A	ENST00000375898.3	+	2	829	c.528G>A	c.(526-528)gtG>gtA	p.V176V		NM_032859.2	NP_116248.2	Q7L211	ABHDD_HUMAN	abhydrolase domain containing 13	176						integral component of membrane (GO:0016021)|membrane (GO:0016020)	hydrolase activity (GO:0016787)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	17	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					TAGACTACGTGATGACTAGAC	0.393																																					p.V176V	Pancreas(22;506 789 38166 45896 51596)	Atlas-SNP	.											.	ABHD13	39	.	0			c.G528A						PASS	.						108	95	100					13																	108882094		2203	4300	6503	SO:0001819	synonymous_variant	84945	exon2			CTACGTGATGACT	AK027812	CCDS32007.1	13q33.2	2007-04-03	2006-03-10	2006-03-10	ENSG00000139826	ENSG00000139826		"Abhydrolase domain containing"	20293	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 6"	C13orf6			Standard	NM_032859		Approved	bA153I24.2, FLJ14906, BEM46L1	uc001vqq.3	Q7L211	OTTHUMG00000017330	ENST00000375898.3:c.528G>A	chr13.hg19:g.108882094G>A		75.0	0.0	.		81.0	27.0	.	NM_032859	B3KWE7|Q8NBW1|Q96JX9	Silent	SNP	ENST00000375898.3	hg19	CCDS32007.1																																																																																			.	.	.	none		0.393	ABHD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045743.1	NM_032859		A	108882094	G	A	108882094	2	1	109	1	0	0	0	0	0	0	0	1	78	1277	45	2		2	ABHD13	13	108882094	Silent	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10	7804204	108882094	6287784	90	7035											
BTBD6	90135	hgsc.bcm.edu	37	chr14	105716843	105716843	+	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	tgaacaagacaccttctacaCggccagtgccgtcctggacg	10	7	10	14	3	1	2	0	1	1	1	2	3	2	3	4	2	3	0	4	2	3	2			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr14:105716843C>A	ENST00000392554.3	+	4	1589	c.1292C>A	c.(1291-1293)aCg>aAg	p.T431K	BRF1_ENST00000446501.2_5'Flank|BRF1_ENST00000440513.3_Intron|BTBD6_ENST00000463376.2_Missense_Mutation_p.T356K|BTBD6_ENST00000536364.1_Missense_Mutation_p.T431K|BRF1_ENST00000327359.3_Intron|BRF1_ENST00000379937.2_Intron|BRF1_ENST00000392557.4_5'Flank|BRF1_ENST00000546474.1_Intron|BTBD6_ENST00000327471.3_Missense_Mutation_p.T356K			Q96KE9	BTBD6_HUMAN	BTB (POZ) domain containing 6	431						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)		ACCTTCTACACGGCCAGTGCC	0.567																																					p.T431K		Atlas-SNP	.											.	BTBD6	24	.	0			c.C1292A						PASS	.						93	79	84					14																	105716843		2203	4300	6503	SO:0001583	missense	90135	exon5			TCTACACGGCCAG	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.1292C>A	chr14.hg19:g.105716843C>A	ENSP00000376337:p.Thr431Lys	57.0	0.0	.		78.0	12.0	.	NM_033271	Q8IVQ7|Q9BR94	Missense_Mutation	SNP	ENST00000392554.3	hg19	CCDS10002.2	.	.	.	.	.	.	.	.	.	.	C	18.65	3.670003	0.67814	.	.	ENSG00000184887	ENST00000536364;ENST00000392554;ENST00000327471	T;T;T	0.76186	-1.0;-1.0;-0.86	5.16	4.19	0.49359	PHR (1);	0.117488	0.56097	D	0.000021	D	0.86188	0.5873	M	0.88450	2.955	0.58432	D	0.999994	D	0.69078	0.997	D	0.67231	0.95	D	0.87972	0.2737	9	.	.	.	-21.705	11.8691	0.52511	0.2103:0.7897:0.0:0.0	.	431	Q96KE9	BTBD6_HUMAN	K	431;431;356	ENSP00000443091:T431K;ENSP00000376337:T431K;ENSP00000329361:T356K	.	T	+	2	0	BTBD6	104787888	0.998000	0.40836	0.953000	0.39169	0.765000	0.43378	3.980000	0.56895	2.392000	0.81423	0.655000	0.94253	ACG	.	.	.	none		0.567	BTBD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074556.4			A	105716843	C	A	105716843	3	1	109	1	0	0	0	0	1	0	0	0	1547	536	19	4	1306	4	BTBD6	14	105716843	Missense_Mutation	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10		105716843	1632697	91	7036											
VPS18	57617	hgsc.bcm.edu	37	chr15	41191884	41191884	+	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	ccttcgcctggatgatggggGatggtgtgttgtatggggca	5	12	18	6	1	0	1	0	1	0	0	1	3	0	3	2	6	0	3	2	6	1	3			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr15:41191884G>A	ENST00000220509.5	+	4	1207	c.868G>A	c.(868-870)Gat>Aat	p.D290N	VPS18_ENST00000558474.1_Intron	NM_020857.2	NP_065908.1	Q9P253	VPS18_HUMAN	vacuolar protein sorting 18 homolog (S. cerevisiae)	290					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)		GATGATGGGGGATGGTGTGTT	0.642																																					p.D290N		Atlas-SNP	.											.	VPS18	67	.	0			c.G868A						PASS	.						68	67	67					15																	41191884		2203	4300	6503	SO:0001583	missense	57617	exon4			ATGGGGGATGGTG	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.868G>A	chr15.hg19:g.41191884G>A	ENSP00000220509:p.Asp290Asn	48.0	0.0	.		26.0	17.0	.	NM_020857	Q8TCG0|Q96DI3|Q9H268	Missense_Mutation	SNP	ENST00000220509.5	hg19	CCDS10069.1	.	.	.	.	.	.	.	.	.	.	G	4.362	0.066694	0.08388	.	.	ENSG00000104142	ENST00000220509	T	0.41400	1.0	4.81	4.81	0.61882	.	0.045890	0.85682	D	0.000000	T	0.11410	0.0278	N	0.00677	-1.265	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.28586	-1.0039	10	0.10902	T	0.67	-29.5425	5.9914	0.19465	0.2254:0.0:0.7746:0.0	.	290	Q9P253	VPS18_HUMAN	N	290	ENSP00000220509:D290N	ENSP00000220509:D290N	D	+	1	0	VPS18	38979176	1.000000	0.71417	0.941000	0.38009	0.986000	0.74619	6.007000	0.70731	2.646000	0.89796	0.655000	0.94253	GAT	.	.	.	none		0.642	VPS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252443.2			A	41191884	G	A	41191884	3	1	109	1	0	0	0	0	1	0	0	0	17206	1174	41	2	882	2	VPS18	15	41191884	Missense_Mutation	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10		41191884	61339508	92	7037											
CEP152	22995	hgsc.bcm.edu	37	chr15	49089695	49089695	+	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	aggatggtacacaggatgtcGgtcttcagttttacttctat	9	15	10	7	1	3	0	1	0	2	0	4	2	3	2	0	4	2	2	0	4	3	6			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr15:49089695G>T	ENST00000380950.2	-	5	530	c.343C>A	c.(343-345)Cga>Aga	p.R115R	CEP152_ENST00000325747.5_Intron|CEP152_ENST00000399334.3_Silent_p.R115R	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	115					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		ACAGGATGTCGGTCTTCAGTT	0.378																																					p.R115R		Atlas-SNP	.											.	CEP152	145	.	0			c.C343A						PASS	.						108	97	100					15																	49089695		1868	4103	5971	SO:0001819	synonymous_variant	22995	exon5			GATGTCGGTCTTC	AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"asterless"	613529	"microcephaly, primary autosomal recessive 4"	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.343C>A	chr15.hg19:g.49089695G>T		139.0	0.0	.		125.0	50.0	.	NM_014985	E7ER66|Q17RV1|Q6NTA0	Silent	SNP	ENST00000380950.2	hg19	CCDS58361.1																																																																																			.	.	.	none		0.378	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985		T	49089695	G	T	49089695	2	4	109	1	0	0	0	0	0	0	0	1	3250	1124	39	4		4	CEP152	15	49089695	Silent	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10	7897811	49089695	53441697	93	7038											
HERC1	8925	hgsc.bcm.edu	37	chr15	63991178	63991178	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agagtcactcagggattccaAttgactgtgcataggaccta	12	10	10	9	0	2	2	2	1	0	1	3	4	3	4	2	2	1	1	2	2	3	4			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr15:63991178A>G	ENST00000443617.2	-	26	4741	c.4654T>C	c.(4654-4656)Ttg>Ctg	p.L1552L	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	1552					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						AGGGATTCCAATTGACTGTGC	0.408																																					p.L1552L		Atlas-SNP	.											.	HERC1	624	.	0			c.T4654C						PASS	.						168	164	165					15																	63991178		1907	4120	6027	SO:0001819	synonymous_variant	8925	exon26			ATTCCAATTGACT	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.4654T>C	chr15.hg19:g.63991178A>G		141.0	0.0	.		133.0	57.0	.	NM_003922	Q8IW65	Silent	SNP	ENST00000443617.2	hg19	CCDS45277.1																																																																																			.	.	.	none		0.408	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		G	63991178	A	G	63991178	2	3	109	1	0	0	0	0	0	0	0	1	7064	98	4	3		3	HERC1	15	63991178	Silent	SNP	A	TCGA-B9-A8YI-01A-21D-A36X-10	14901483	63991178	38540214	94	7039											
CIB1	10519	hgsc.bcm.edu	37	chr15	90774633	90774633	+	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	acttgatgtctggcgtggctGtgtcactgaacacactgagg	8	11	13	9	1	2	3	1	3	1	0	2	3	2	3	0	3	1	1	0	3	1	1			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr15:90774633G>T	ENST00000328649.6	-	4	463	c.302C>A	c.(301-303)aCa>aAa	p.T101K	GDPGP1_ENST00000558017.1_5'Flank	NM_006384.3	NP_006375.2	Q99828	CIB1_HUMAN	calcium and integrin binding 1 (calmyrin)	101					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)			TGGCGTGGCTGTGTCACTGAA	0.567																																					p.T101K		Atlas-SNP	.											.	CIB1	8	.	0			c.C302A						PASS	.						113	92	99					15																	90774633		2199	4298	6497	SO:0001583	missense	10519	exon4			GTGGCTGTGTCAC	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	ENST00000328649.6:c.302C>A	chr15.hg19:g.90774633G>T	ENSP00000333873:p.Thr101Lys	103.0	0.0	.		111.0	41.0	.	NM_006384	B5BU40|H6WJF3|O00693|O00735|Q6IB49|Q96J54|Q99971	Missense_Mutation	SNP	ENST00000328649.6	hg19	CCDS10360.1	.	.	.	.	.	.	.	.	.	.	G	13.82	2.352680	0.41700	.	.	ENSG00000185043	ENST00000328649	T	0.08807	3.05	4.35	4.35	0.52113	EF-hand-like domain (1);	0.119263	0.64402	D	0.000017	T	0.04679	0.0127	N	0.04746	-0.17	0.43803	D	0.996356	B	0.20459	0.045	B	0.20384	0.029	T	0.42464	-0.9450	10	0.11794	T	0.64	-0.1605	16.0477	0.80731	0.0:0.0:1.0:0.0	.	101	Q99828	CIB1_HUMAN	K	101	ENSP00000333873:T101K	ENSP00000333873:T101K	T	-	2	0	CIB1	88575637	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	7.143000	0.77348	2.254000	0.74563	0.563000	0.77884	ACA	.	.	.	none		0.567	CIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313419.1			T	90774633	G	T	90774633	3	4	109	1	0	0	0	0	1	0	0	0	3422	1377	48	4	289	4	CIB1	15	90774633	Missense_Mutation	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10	26783455	90774633	11756759	95	7040											
ABCC6	368	hgsc.bcm.edu	37	chr16	16244452	16244452	+	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	taccgggcacagtccatcacGgagcgcaggcggtgggcaat	9	5	15	12	4	1	0	1	0	0	0	2	1	2	1	2	5	2	3	2	5	2	1			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr16:16244452G>C	ENST00000205557.7	-	30	4415	c.4386C>G	c.(4384-4386)tcC>tcG	p.S1462S		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1462	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)	AGTCCATCACGGAGCGCAGGC	0.687																																					p.S1462S		Atlas-SNP	.											.	ABCC6	110	.	0			c.C4386G						PASS	.						38	31	33					16																	16244452		2197	4298	6495	SO:0001819	synonymous_variant	368	exon30			CATCACGGAGCGC	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.4386C>G	chr16.hg19:g.16244452G>C		104.0	0.0	.		164.0	62.0	.	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Silent	SNP	ENST00000205557.7	hg19	CCDS10568.1																																																																																			.	.	.	none		0.687	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2			C	16244452	G	C	16244452	2	2	109	1	0	0	0	0	0	0	0	1	57	1103	39	4		4	ABCC6	16	16244452	Silent	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10		16244452	74110301	96	7041											
FHOD1	29109	hgsc.bcm.edu	37	chr16	67264360	67264360	+	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	gaactgcatgatgcgcacttCacgggccgcctgcggggtgt	6	8	15	12	4	1	1	1	1	0	0	1	2	1	1	2	3	4	2	2	3	1	1			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr16:67264360C>T	ENST00000258201.4	-	19	3155	c.2908G>A	c.(2908-2910)Gaa>Aaa	p.E970K		NM_013241.2	NP_037373.2	Q9Y613	FHOD1_HUMAN	formin homology 2 domain containing 1	970	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			breast(4)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	34		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)		ATGCGCACTTCACGGGCCGCC	0.592																																					p.E970K		Atlas-SNP	.											.	FHOD1	86	.	0			c.G2908A						PASS	.						85	84	84					16																	67264360		2198	4300	6498	SO:0001583	missense	29109	exon19			GCACTTCACGGGC	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.2908G>A	chr16.hg19:g.67264360C>T	ENSP00000258201:p.Glu970Lys	91.0	0.0	.		217.0	32.0	.	NM_013241	Q59F76|Q6Y1F2|Q76MS8|Q8N521	Missense_Mutation	SNP	ENST00000258201.4	hg19	CCDS10834.1	.	.	.	.	.	.	.	.	.	.	C	15.81	2.943253	0.53079	.	.	ENSG00000135723	ENST00000258201	T	0.17854	2.25	5.76	5.76	0.90799	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.097634	0.64402	D	0.000002	T	0.22475	0.0542	L	0.35644	1.08	0.58432	D	0.999997	B	0.24963	0.115	B	0.37989	0.262	T	0.03922	-1.0992	10	0.35671	T	0.21	.	18.5254	0.90969	0.0:1.0:0.0:0.0	.	970	Q9Y613	FHOD1_HUMAN	K	970	ENSP00000258201:E970K	ENSP00000258201:E970K	E	-	1	0	FHOD1	65821861	1.000000	0.71417	0.305000	0.25099	0.164000	0.22412	7.609000	0.82925	2.724000	0.93272	0.561000	0.74099	GAA	.	.	.	none		0.592	FHOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268844.2			T	67264360	C	T	67264360	3	4	109	1	0	0	0	0	1	0	0	0	5889	835	29	2	602	2	FHOD1	16	67264360	Missense_Mutation	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10	51019908	67264360	23090393	97	7042											
CENPT	80152	hgsc.bcm.edu	37	chr16	67862427	67862427	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcacagtcttgcggccagcAtgagcagcaaatacctccag	11	8	9	13	1	2	1	1	1	1	0	3	1	3	1	3	1	5	3	3	1	2	3			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr16:67862427A>G	ENST00000562787.1	-	15	2060	c.1512T>C	c.(1510-1512)caT>caC	p.H504H	CENPT_ENST00000562947.1_5'Flank|CENPT_ENST00000564817.1_Silent_p.H449H|CENPT_ENST00000440851.2_Silent_p.H504H|CENPT_ENST00000219172.3_Silent_p.H504H	NM_025082.3	NP_079358.3	Q96BT3	CENPT_HUMAN	centromere protein T	504					chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|lung(6)|urinary_tract(1)	10		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00429)|Epithelial(162;0.019)|all cancers(182;0.124)		TGCGGCCAGCATGAGCAGCAA	0.542																																					p.H504H		Atlas-SNP	.											.	CENPT	26	.	0			c.T1512C						PASS	.						121	130	127					16																	67862427		2055	4208	6263	SO:0001819	synonymous_variant	80152	exon15			GCCAGCATGAGCA	AK056097	CCDS42182.1	16q22.1	2013-11-05	2006-06-15	2006-06-15		ENSG00000102901			25787	protein-coding gene	gene with protein product		611510	"chromosome 16 open reading frame 56"	C16orf56		16622420, 16622419	Standard	NM_025082		Approved	FLJ13111, CENP-T	uc002eun.4	Q96BT3		ENST00000562787.1:c.1512T>C	chr16.hg19:g.67862427A>G		76.0	0.0	.		200.0	36.0	.	NM_025082	Q96I29|Q96IC6|Q96NK9|Q9H901	Silent	SNP	ENST00000562787.1	hg19	CCDS42182.1	.	.	.	.	.	.	.	.	.	.	A	7.927	0.739794	0.15642	.	.	ENSG00000102901	ENST00000436104	.	.	.	5.67	1.04	0.20106	.	.	.	.	.	T	0.46210	0.1381	.	.	.	0.80722	D	1	B	0.19583	0.037	B	0.18561	0.022	T	0.38178	-0.9673	7	0.87932	D	0	-4.3691	8.2039	0.31441	0.7038:0.0:0.2962:0.0	.	256	F5H5A6	.	T	256	.	ENSP00000404857:M256T	M	-	2	0	CENPT	66419928	0.999000	0.42202	1.000000	0.80357	0.864000	0.49448	0.466000	0.22019	0.113000	0.18004	0.459000	0.35465	ATG	.	.	.	none		0.542	CENPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422020.1	NM_025082		G	67862427	A	G	67862427	2	3	109	1	0	0	0	0	0	0	0	1	3244	214	8	3		3	CENPT	16	67862427	Silent	SNP	A	TCGA-B9-A8YI-01A-21D-A36X-10	598067	67862427	22492326	98	7043											
CDH1	999	hgsc.bcm.edu	37	chr16	68867229	68867229	+	Frame_Shift_Del	DEL	C	C	-																															atactgaccccacagccccgCcttatgattctctgctcgtg																										TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr16:68867229delC	ENST00000261769.5	+	16	2667	c.2476delC	c.(2476-2478)cctfs	p.P826fs	CDH1_ENST00000562836.1_3'UTR|CDH1_ENST00000422392.2_Frame_Shift_Del_p.P765fs	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	826	Required for binding alpha, beta and gamma catenins.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)			NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		CACAGCCCCGCCTTATGATTC	0.498			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer																												p.P825fs		Atlas-Indel,Pindel	.	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	.	CDH1	535	.	0			c.2475delG						PASS	.						83	84	84					16																	68867229		2198	4300	6498	SO:0001589	frameshift_variant	999	exon16	Familial Cancer Database	HDGC	.	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"CD molecules", "Cadherins / Major cadherins"	1748	protein-coding gene	gene with protein product	"E-Cadherin"	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.2476delC	chr16.hg19:g.68867229delC	ENSP00000261769:p.Pro826fs	59.0	0.0	0		161.0	44.0	0.273292	NM_004360	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Frame_Shift_Del	DEL	ENST00000261769.5	hg19	CCDS10869.1																																																																																			.	.	.	none		0.498	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360		-	68867229	C	-	68867229	7	5	109	1	0	1	0	1	0	0	0	0	3097	739	26	0	2538	0	CDH1	16	68867229	Frame_Shift_Del	DEL	C	TCGA-B9-A8YI-01A-21D-A36X-10	1004802	68867229	21487524	99	7044											
GEMIN4	50628	hgsc.bcm.edu	37	chr17	649755	649755	+	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	cagcaacttttcagagaggcCctttcgcccccaggaacgca	10	7	9	15	2	1	1	1	0	0	1	2	3	1	2	3	2	3	2	3	2	2	3			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr17:649755C>T	ENST00000319004.5	-	2	1646	c.1528G>A	c.(1528-1530)Ggc>Agc	p.G510S	GEMIN4_ENST00000576778.1_Missense_Mutation_p.G499S	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	510					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)		TCAGAGAGGCCCTTTCGCCCC	0.527																																					p.G510S		Atlas-SNP	.											.	GEMIN4	116	.	0			c.G1528A						PASS	.						41	43	42					17																	649755		1929	4135	6064	SO:0001583	missense	50628	exon2			AGAGGCCCTTTCG	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.1528G>A	chr17.hg19:g.649755C>T	ENSP00000321706:p.Gly510Ser	119.0	0.0	.		122.0	34.0	.	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Missense_Mutation	SNP	ENST00000319004.5	hg19	CCDS45559.1	.	.	.	.	.	.	.	.	.	.	C	17.03	3.284219	0.59867	.	.	ENSG00000179409	ENST00000319004	T	0.14893	2.47	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.43389	0.1245	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.22173	-1.0224	10	0.87932	D	0	-19.9739	18.8377	0.92169	0.0:1.0:0.0:0.0	.	510	P57678	GEMI4_HUMAN	S	510	ENSP00000321706:G510S	ENSP00000321706:G510S	G	-	1	0	GEMIN4	596505	1.000000	0.71417	0.999000	0.59377	0.093000	0.18481	7.423000	0.80229	2.779000	0.95612	0.591000	0.81541	GGC	.	.	.	none		0.527	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721		T	649755	C	T	649755	3	4	109	1	0	0	0	0	1	0	0	0	6337	623	22	2	1652	2	GEMIN4	17	649755	Missense_Mutation	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10		649755	80545455	100	7045											
SCO1	6341	hgsc.bcm.edu	37	chr17	10596136	10596136	+	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	tcttctggacagacatcaggGcaatgagtgaagccaaaata	15	8	10	8	0	3	3	1	2	2	1	3	4	3	4	1	2	1	1	1	2	5	2			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr17:10596136G>C	ENST00000255390.5	-	3	567	c.507C>G	c.(505-507)tgC>tgG	p.C169W	SCO1_ENST00000582053.1_5'Flank|SCO1_ENST00000577427.1_Intron	NM_004589.2	NP_004580.1	O75880	SCO1_HUMAN	SCO1 cytochrome c oxidase assembly protein	169					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						AGACATCAGGGCAATGAGTGA	0.403																																					p.C169W	Melanoma(128;591 1731 19711 31891 44645)	Atlas-SNP	.											.	SCO1	24	.	0			c.C507G						PASS	.						131	116	121					17																	10596136		2203	4300	6503	SO:0001583	missense	6341	exon3			ATCAGGGCAATGA	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.507C>G	chr17.hg19:g.10596136G>C	ENSP00000255390:p.Cys169Trp	62.0	0.0	.		82.0	30.0	.	NM_004589	B2RDM0	Missense_Mutation	SNP	ENST00000255390.5	hg19	CCDS11158.1	.	.	.	.	.	.	.	.	.	.	G	17.69	3.451580	0.63290	.	.	ENSG00000133028	ENST00000255390	D	0.94497	-3.44	6.08	1.4	0.22301	Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	D	0.98121	0.9380	H	0.98802	4.335	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97288	0.9922	10	0.87932	D	0	-14.6714	10.5038	0.44821	0.4036:0.0:0.5964:0.0	.	169	O75880	SCO1_HUMAN	W	169	ENSP00000255390:C169W	ENSP00000255390:C169W	C	-	3	2	SCO1	10536861	0.995000	0.38212	1.000000	0.80357	0.997000	0.91878	0.367000	0.20382	0.466000	0.27193	0.591000	0.81541	TGC	.	.	.	none		0.403	SCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252729.2	NM_004589		C	10596136	G	C	10596136	3	2	109	1	0	0	0	0	1	0	0	0	13944	1195	42	4	414	4	SCO1	17	10596136	Missense_Mutation	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10	9946381	10596136	70599074	101	7046											
KRTAP4-5	85289	hgsc.bcm.edu	37	chr17	39305774	39305775	+	Missense_Mutation	DNP	CT	CT	GC																															gtggtcctgcagcaggtggtCtggcagcagcaggggcggca																								rs137947981|rs535144703|rs141265645|rs58117746	byFrequency	TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr17:39305774_39305775CT>GC	ENST00000343246.4	-	1	279_280	c.245_246AG>GC	c.(244-246)cAG>cGC	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)		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.Q82H|p.Q82R		Atlas-SNP	.											KRTAP4-5,NS,carcinoma,0,1|KRTAP4-5,NS,carcinoma,+1,1	KRTAP4-5	34	.	1	Substitution - Missense(1)	lung(1)	c.G246C|c.A245G						PASS	.																																			SO:0001583	missense	85289	exon1			GGTGGTCTGGCAG|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.245_246delinsGC	chr17.hg19:g.39305774_39305775delinsGC	ENSP00000340546:p.Gln82Arg	34.0	2.0	.		57.0|56.0	36.0	.	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	hg19	CCDS32650.1																																																																																			.	.	.	weak		0.653	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1			GC	39305775	CT	GC	39305774	3	3	109	1	0	0	0	0	1	0	0	0	8561	912	32	4	303	4	KRTAP4-5	17	39305774	Missense_Mutation	DNP	CT	TCGA-B9-A8YI-01A-21D-A36X-10	28709638	39305774	41889436	102	7047											
KRT9	3857	hgsc.bcm.edu	37	chr17	39723874	39723874	+	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	ctcccctggacccacttcctCcaccatagccacctccactt	7	9	3	22	0	0	0	0	0	0	0	4	1	4	1	9	1	1	0	9	1	1	3			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr17:39723874C>G	ENST00000246662.4	-	7	1588	c.1523G>C	c.(1522-1524)gGa>gCa	p.G508A	KRT9_ENST00000588431.1_Missense_Mutation_p.G275A	NM_000226.3	NP_000217.2	P35527	K1C9_HUMAN	keratin 9	508	Tail.				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)				cccacttcctccaccatagcc	0.597																																					p.G508A		Atlas-SNP	.											.	KRT9	78	.	0			c.G1523C						PASS	.						195	129	151					17																	39723874		2200	4294	6494	SO:0001583	missense	3857	exon7			CTTCCTCCACCAT		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.1523G>C	chr17.hg19:g.39723874C>G	ENSP00000246662:p.Gly508Ala	93.0	0.0	.		116.0	49.0	.	NM_000226	O00109|Q0IJ47|Q14665	Missense_Mutation	SNP	ENST00000246662.4	hg19	CCDS32654.1	.	.	.	.	.	.	.	.	.	.	C	8.973	0.973413	0.18736	.	.	ENSG00000171403	ENST00000246662	D	0.96554	-4.05	3.1	2.11	0.27256	.	0.270585	0.19745	N	0.107025	D	0.91229	0.7236	N	0.24115	0.695	0.26842	N	0.96836	D	0.56035	0.974	P	0.49252	0.604	D	0.85008	0.0904	10	0.07482	T	0.82	.	6.2431	0.20801	0.0:0.8527:0.0:0.1473	.	508	P35527	K1C9_HUMAN	A	508	ENSP00000246662:G508A	ENSP00000246662:G508A	G	-	2	0	KRT9	36977400	0.090000	0.21635	0.757000	0.31301	0.407000	0.30961	1.505000	0.35736	0.531000	0.28639	0.458000	0.33432	GGA	.	.	.	none		0.597	KRT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257707.1	NM_000226		G	39723874	C	G	39723874	3	3	109	1	0	0	0	0	1	0	0	0	8508	855	30	4	352	4	KRT9	17	39723874	Missense_Mutation	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10	418100	39723874	41471336	103	7048											
NT5C3L	115024	hgsc.bcm.edu	37	chr17	39981892	39981892	+	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	tcataggagtccatgtagcgCtcccgccgctcctccacctg	6	9	9	17	3	1	0	1	0	0	0	5	1	5	1	6	1	1	3	6	1	2	2			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr17:39981892C>T	ENST00000435506.2	-	9	855	c.786G>A	c.(784-786)gaG>gaA	p.E262E	NT5C3B_ENST00000269534.8_Silent_p.E254E|NT5C3B_ENST00000521789.1_Silent_p.E162E			Q969T7	5NT3B_HUMAN	5'-nucleotidase, cytosolic IIIB	262					nucleotide metabolic process (GO:0009117)	cytoplasm (GO:0005737)	5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)										CCATGTAGCGCTCCCGCCGCT	0.632																																					p.E262E		Atlas-SNP	.											.	.	.	.	0			c.G786A						PASS	.						88	89	88					17																	39981892		2203	4300	6503	SO:0001819	synonymous_variant	115024	exon9			GTAGCGCTCCCGC		CCDS11410.1, CCDS11410.2	17q21.2	2013-01-31	2013-01-31	2013-01-31	ENSG00000141698	ENSG00000141698	3.1.3.5		28300	protein-coding gene	gene with protein product			"5'-nucleotidase, cytosolic III-like"	NT5C3L		23223233	Standard	NM_052935		Approved	MGC20781	uc021txo.1	Q969T7	OTTHUMG00000133499	ENST00000435506.2:c.786G>A	chr17.hg19:g.39981892C>T		67.0	0.0	.		94.0	43.0	.	NM_052935	A8MWB9|C9JKC4|Q7L3B7	Silent	SNP	ENST00000435506.2	hg19	CCDS11410.2																																																																																			.	.	.	none		0.632	NT5C3B-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257430.2	NM_052935		T	39981892	C	T	39981892	2	4	109	1	0	0	0	0	0	0	0	1	10696	796	28	2		2	NT5C3L	17	39981892	Silent	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10	258018	39981892	41213318	104	7049											
ITGA2B	3674	hgsc.bcm.edu	37	chr17	42457409	42457409	+	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	gtgtggcagatggggctgtgCtttccgcccagatccaggtt	5	11	15	10	1	0	2	0	0	0	2	2	2	2	2	3	4	1	4	3	4	0	2			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr17:42457409C>A	ENST00000262407.5	-	17	1744	c.1713G>T	c.(1711-1713)aaG>aaT	p.K571N	ITGA2B_ENST00000353281.4_Missense_Mutation_p.K571N	NM_000419.3	NP_000410.2	P08514	ITA2B_HUMAN	integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)	571					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)	TGGGGCTGTGCTTTCCGCCCA	0.647																																					p.K571N		Atlas-SNP	.											.	ITGA2B	88	.	0			c.G1713T						PASS	.						46	47	47					17																	42457409		2201	4296	6497	SO:0001583	missense	3674	exon17			GCTGTGCTTTCCG		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.1713G>T	chr17.hg19:g.42457409C>A	ENSP00000262407:p.Lys571Asn	67.0	0.0	.		90.0	37.0	.	NM_000419	B2RCY8|O95366|Q14443|Q17R67	Missense_Mutation	SNP	ENST00000262407.5	hg19	CCDS32665.1	.	.	.	.	.	.	.	.	.	.	C	7.724	0.697783	0.15106	.	.	ENSG00000005961	ENST00000262407;ENST00000353281	T;T	0.48522	0.81;0.81	4.69	0.243	0.15503	Integrin alpha-2 (1);	0.641780	0.12817	N	0.436713	T	0.18130	0.0435	N	0.02539	-0.55	0.09310	N	1	B;B	0.18863	0.031;0.015	B;B	0.18561	0.008;0.022	T	0.17899	-1.0354	10	0.30078	T	0.28	.	4.1669	0.10310	0.1606:0.5581:0.0:0.2812	.	169;571	Q59FA8;P08514	.;ITA2B_HUMAN	N	571	ENSP00000262407:K571N;ENSP00000340536:K571N	ENSP00000262407:K571N	K	-	3	2	ITGA2B	39812935	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	0.024000	0.13555	0.180000	0.19960	0.561000	0.74099	AAG	.	.	.	none		0.647	ITGA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439823.1			A	42457409	C	A	42457409	3	1	109	1	0	0	0	0	1	0	0	0	7883	796	28	4	1462	4	ITGA2B	17	42457409	Missense_Mutation	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10	2475517	42457409	38737801	105	7050											
SCRN2	90507	hgsc.bcm.edu	37	chr17	45916949	45916949	+	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	cccccctgcccatagtgctcCagtaaccctgtgatcacatg	8	9	7	17	0	1	1	1	1	0	0	2	1	2	1	6	0	3	2	6	0	2	2			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr17:45916949C>A	ENST00000290216.9	-	4	542	c.417G>T	c.(415-417)ctG>ctT	p.L139L	SCRN2_ENST00000584123.1_Silent_p.L147L|SCRN2_ENST00000407215.3_Silent_p.L139L	NM_001145023.1|NM_138355.3	NP_001138495.1|NP_612364.2	Q96FV2	SCRN2_HUMAN	secernin 2	139						extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)			cervix(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	14						CATAGTGCTCCAGTAACCCTG	0.612																																					p.L139L		Atlas-SNP	.											.	SCRN2	35	.	0			c.G417T						PASS	.						135	130	132					17																	45916949		2203	4300	6503	SO:0001819	synonymous_variant	90507	exon4			GTGCTCCAGTAAC	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.417G>T	chr17.hg19:g.45916949C>A		101.0	0.0	.		117.0	33.0	.	NM_138355	A8K3N1|B7Z8S7|E9PBV5|Q96AC3|Q9BU04	Silent	SNP	ENST00000290216.9	hg19	CCDS11519.1																																																																																			.	.	.	none		0.612	SCRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441383.1	NM_138355		A	45916949	C	A	45916949	2	1	109	1	0	0	0	0	0	0	0	1	13952	581	21	4		4	SCRN2	17	45916949	Silent	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10	3459540	45916949	35278261	106	7051											
B4GALNT2	124872	hgsc.bcm.edu	37	chr17	47219412	47219413	+	Frame_Shift_Del	DEL	TC	TC	-																															ttcaggctgttcccgaaaaaTcagtgcaaatgtgaagccaa																										TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr17:47219412_47219413delTC	ENST00000300404.2	+	3	470_471	c.411_412delTC	c.(409-414)aatcagfs	p.NQ137fs	B4GALNT2_ENST00000393354.2_Frame_Shift_Del_p.NQ77fs|B4GALNT2_ENST00000504681.1_Frame_Shift_Del_p.NQ51fs	NM_153446.2	NP_703147.2	Q8NHY0	B4GN2_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 2	137					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)			TCCCGAAAAATCAGTGCAAATG	0.52																																					p.137_137del	GBM(124;244 1635 8663 18097 33175)	Atlas-Indel,Pindel	.											.	B4GALNT2	67	.	0			c.410_411del						PASS	.																																			SO:0001589	frameshift_variant	124872	exon3			.	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.411_412delTC	chr17.hg19:g.47219412_47219413delTC	ENSP00000300404:p.Asn137fs	104.0	0.0	0		96.0	31.0	0.322917	NM_153446	B4DZE4|Q14CP1|Q86Y40	Frame_Shift_Del	DEL	ENST00000300404.2	hg19	CCDS11544.1																																																																																			.	.	.	none		0.52	B4GALNT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364477.1	NM_153446		-	47219413	TC	-	47219412	7	5	109	1	0	1	0	1	0	0	0	0	1267	1432	50	0	439	0	B4GALNT2	17	47219412	Frame_Shift_Del	DEL	TC	TCGA-B9-A8YI-01A-21D-A36X-10	1302463	47219412	33975798	107	7052											
MYST2	11143	hgsc.bcm.edu	37	chr17	47888871	47888871	+	Missense_Mutation	SNP	A	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	gacagcttcgatataaggaaAaagtggctgaactcaggaag	16	7	12	6	1	1	1	1	1	0	0	2	5	1	3	0	3	2	2	0	3	6	3			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr17:47888871A>C	ENST00000259021.4	+	7	1067	c.787A>C	c.(787-789)Aaa>Caa	p.K263Q	KAT7_ENST00000503935.2_Missense_Mutation_p.K107Q|KAT7_ENST00000424009.2_Missense_Mutation_p.K233Q|KAT7_ENST00000509773.1_Missense_Mutation_p.K153Q|KAT7_ENST00000510819.1_Missense_Mutation_p.K94Q|KAT7_ENST00000454930.2_Missense_Mutation_p.K124Q|KAT7_ENST00000435742.2_Missense_Mutation_p.K77Q	NM_007067.4	NP_008998.1	O95251	KAT7_HUMAN	K(lysine) acetyltransferase 7	263					chromatin organization (GO:0006325)|DNA replication (GO:0006260)|histone H3 acetylation (GO:0043966)|histone H4-K12 acetylation (GO:0043983)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										ATATAAGGAAAAAGTGGCTGA	0.368																																					p.K263Q		Atlas-SNP	.											.	.	.	.	0			c.A787C						PASS	.						53	56	55					17																	47888871		2203	4300	6503	SO:0001583	missense	11143	exon7			AAGGAAAAAGTGG	AF074606	CCDS11554.1, CCDS56035.1, CCDS56036.1, CCDS56037.1, CCDS56038.1	17q21.32	2013-01-10	2011-07-21	2011-07-21	ENSG00000136504	ENSG00000136504	2.3.1.48	"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing"	17016	protein-coding gene	gene with protein product	"histone acetyltransferase binding to ORC1"	609880	"MYST histone acetyltransferase 2"	MYST2		10438470, 10930412	Standard	NM_001199155		Approved	HBOA, HBO1, ZC2HC7	uc002ipm.3	O95251	OTTHUMG00000161770	ENST00000259021.4:c.787A>C	chr17.hg19:g.47888871A>C	ENSP00000259021:p.Lys263Gln	480.0	0.0	.		515.0	225.0	.	NM_007067	B3KN74|B4DF85|B4DFB4|B4DFE0|B4DGY4|E7ER15|G5E9K7	Missense_Mutation	SNP	ENST00000259021.4	hg19	CCDS11554.1	.	.	.	.	.	.	.	.	.	.	A	13.35	2.210633	0.39102	.	.	ENSG00000136504	ENST00000259021;ENST00000454930;ENST00000509773;ENST00000510819;ENST00000424009;ENST00000503935;ENST00000435742	.	.	.	5.65	5.65	0.86999	.	0.097322	0.64402	D	0.000002	T	0.57475	0.2056	L	0.47716	1.5	0.58432	D	0.999991	B;B;B;B;B;B	0.20052	0.024;0.006;0.024;0.007;0.031;0.041	B;B;B;B;B;B	0.17433	0.005;0.002;0.003;0.007;0.007;0.018	T	0.54583	-0.8272	9	0.48119	T	0.1	-20.7432	15.6986	0.77521	1.0:0.0:0.0:0.0	.	226;94;153;124;263;233	B4DGY4;B4DFE0;B4DFB4;E7ER15;O95251;G5E9K7	.;.;.;.;KAT7_HUMAN;.	Q	263;124;153;94;233;107;77	.	ENSP00000259021:K263Q	K	+	1	0	KAT7	45243870	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	5.394000	0.66285	2.371000	0.80710	0.533000	0.62120	AAA	.	.	.	none		0.368	KAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366032.1	NM_007067		C	47888871	A	C	47888871	3	2	109	1	0	0	0	0	1	0	0	0	10110	15	1	5	813	5	MYST2	17	47888871	Missense_Mutation	SNP	A	TCGA-B9-A8YI-01A-21D-A36X-10	669459	47888871	33306339	108	7053											
ST8SIA5	29906	hgsc.bcm.edu	37	chr18	44260388	44260388	+	Missense_Mutation	SNP	A	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	gtcggtgttgcgcgtgttgtAgaaggcaggcagcagcaccg	7	8	17	9	4	0	1	0	0	0	1	1	1	0	1	1	3	3	7	1	3	2	3			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr18:44260388A>C	ENST00000315087.7	-	7	1408	c.748T>G	c.(748-750)Tac>Gac	p.Y250D	ST8SIA5_ENST00000590497.1_5'UTR|ST8SIA5_ENST00000538168.1_Missense_Mutation_p.Y286D|ST8SIA5_ENST00000536490.1_Missense_Mutation_p.Y219D	NM_013305.4	NP_037437.2	O15466	SIA8E_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	250					carbohydrate metabolic process (GO:0005975)|glycosphingolipid biosynthetic process (GO:0006688)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialyltransferase activity (GO:0008373)			kidney(1)|large_intestine(10)|lung(7)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	22						CGCGTGTTGTAGAAGGCAGGC	0.602																																					p.Y250D		Atlas-SNP	.											.	ST8SIA5	57	.	0			c.T748G						PASS	.						89	51	64					18																	44260388		2203	4300	6503	SO:0001583	missense	29906	exon7			TGTTGTAGAAGGC	U91641	CCDS11930.1	18q12.3	2013-03-01	2003-01-14	2005-02-07	ENSG00000101638	ENSG00000101638		"Sialyltransferases"	17827	protein-coding gene	gene with protein product	"ST8Sia V"	607162	"sialyltransferase 8E (alpha-2, 8-polysialytransferase)"	SIAT8E		9199191	Standard	XM_005258250		Approved		uc002lcj.1	O15466	OTTHUMG00000132643	ENST00000315087.7:c.748T>G	chr18.hg19:g.44260388A>C	ENSP00000321343:p.Tyr250Asp	65.0	0.0	.		96.0	51.0	.	NM_013305	B7Z1K9|Q6IAW7	Missense_Mutation	SNP	ENST00000315087.7	hg19	CCDS11930.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.508290	0.85282	.	.	ENSG00000101638	ENST00000315087;ENST00000538168;ENST00000536490	T;T;T	0.32023	1.47;1.47;1.47	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.46795	0.1411	L	0.41415	1.275	0.80722	D	1	D;B;D	0.89917	1.0;0.15;1.0	D;B;D	0.87578	0.998;0.246;0.995	T	0.31392	-0.9945	10	0.36615	T	0.2	-9.7928	15.6254	0.76851	1.0:0.0:0.0:0.0	.	219;286;250	F5H8D1;B7Z1K9;O15466	.;.;SIA8E_HUMAN	D	250;286;219	ENSP00000321343:Y250D;ENSP00000445492:Y286D;ENSP00000443683:Y219D	ENSP00000321343:Y250D	Y	-	1	0	ST8SIA5	42514386	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.339000	0.96797	2.090000	0.63153	0.459000	0.35465	TAC	.	.	.	none		0.602	ST8SIA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255892.1	NM_013305		C	44260388	A	C	44260388	3	2	109	1	0	0	0	0	1	0	0	0	15247	420	15	5	386	5	ST8SIA5	18	44260388	Missense_Mutation	SNP	A	TCGA-B9-A8YI-01A-21D-A36X-10		44260388	33816860	109	7054											
ZNF844	284391	hgsc.bcm.edu	37	chr19	12187708	12187708	+	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	cctatgaatgtaaagagtgtGacaaagcattcatatctgcc	14	11	8	8	0	2	3	1	2	1	1	2	3	2	3	2	0	2	2	2	0	6	4			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr19:12187708G>C	ENST00000439326.3	+	4	1948	c.1773G>C	c.(1771-1773)gtG>gtC	p.V591V	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	591					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						TAAAGAGTGTGACAAAGCATT	0.393																																					p.V591V		Atlas-SNP	.											.	ZNF844	69	.	0			c.G1773C						PASS	.						122	108	112					19																	12187708		692	1591	2283	SO:0001819	synonymous_variant	284391	exon4			GAGTGTGACAAAG	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.1773G>C	chr19.hg19:g.12187708G>C		137.0	0.0	.		155.0	55.0	.	NM_001136501	Q5JPI8	Silent	SNP	ENST00000439326.3	hg19	CCDS45985.1																																																																																			.	.	.	none		0.393	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2			C	12187708	G	C	12187708	2	2	109	1	0	0	0	0	0	0	0	1	18202	1277	45	4		4	ZNF844	19	12187708	Silent	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10		12187708	46941275	110	7055											
ILVBL	10994	hgsc.bcm.edu	37	chr19	15230250	15230250	+	Frame_Shift_Del	DEL	G	G	-																															gaagcttgtcggcagacgttGgggtgagcagggcctgactc																										TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr19:15230250delG	ENST00000263383.3	-	8	1032	c.893delC	c.(892-894)ccafs	p.P298fs	ILVBL_ENST00000531635.1_5'UTR|ILVBL_ENST00000534378.1_Frame_Shift_Del_p.P191fs	NM_006844.3	NP_006835.2	A1L0T0	ILVBL_HUMAN	ilvB (bacterial acetolactate synthase)-like	298						integral component of membrane (GO:0016021)|membrane (GO:0016020)	magnesium ion binding (GO:0000287)|thiamine pyrophosphate binding (GO:0030976)|transferase activity (GO:0016740)			NS(3)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)	26						GGCAGACGTTGGGGTGAGCAG	0.647																																					p.P298fs		Atlas-Indel,Pindel	.											.	ILVBL	54	.	0			c.894delA						PASS	.						53	48	50					19																	15230250		2203	4300	6503	SO:0001589	frameshift_variant	10994	exon8			.	U61263	CCDS12325.1	19p13.1	2008-07-16			ENSG00000105135	ENSG00000105135			6041	protein-coding gene	gene with protein product	"acetolactate synthase homolog"	605770				8954801	Standard	NM_006844		Approved	209L8, AHAS, ILV2H, MGC1269, FLJ39061, MGC19535	uc002nam.3	A1L0T0	OTTHUMG00000165630	ENST00000263383.3:c.893delC	chr19.hg19:g.15230250delG	ENSP00000263383:p.Pro298fs	201.0	0.0	0		228.0	79.0	0.346491	NM_006844	O43341|Q96F08|Q99651|Q9BWN5|Q9UEB2	Frame_Shift_Del	DEL	ENST00000263383.3	hg19	CCDS12325.1																																																																																			.	.	.	none		0.647	ILVBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385439.1	NM_006844		-	15230250	G	-	15230250	7	5	109	1	0	1	0	1	0	0	0	0	7722	1348	47	0	1041	0	ILVBL	19	15230250	Frame_Shift_Del	DEL	G	TCGA-B9-A8YI-01A-21D-A36X-10	3042542	15230250	43898733	111	7056											
PARD6B	84612	hgsc.bcm.edu	37	chr20	49354467	49354467	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgaggagttttatggattacTacaacatgttcataagatcc	13	14	8	6	0	1	2	1	1	0	1	2	4	2	4	1	2	3	2	1	2	5	6			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr20:49354467T>C	ENST00000371610.2	+	2	383	c.140T>C	c.(139-141)cTa>cCa	p.L47P	PARD6B_ENST00000396039.1_Missense_Mutation_p.L47P	NM_032521.2	NP_115910.1	Q9BYG5	PAR6B_HUMAN	par-6 family cell polarity regulator beta	47	OPR.				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						TATGGATTACTACAACATGTT	0.343																																					p.L47P		Atlas-SNP	.											.	PARD6B	31	.	0			c.T140C						PASS	.						84	83	84					20																	49354467		2203	4300	6503	SO:0001583	missense	84612	exon2			GATTACTACAACA	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.140T>C	chr20.hg19:g.49354467T>C	ENSP00000360672:p.Leu47Pro	165.0	0.0	.		173.0	52.0	.	NM_032521	A2A2A7|Q9Y510	Missense_Mutation	SNP	ENST00000371610.2	hg19	CCDS33485.1	.	.	.	.	.	.	.	.	.	.	T	19.79	3.892162	0.72524	.	.	ENSG00000124171	ENST00000371610;ENST00000396039	T;T	0.27890	1.64;1.64	5.92	5.92	0.95590	Phox/Bem1p (2);	0.000000	0.64402	D	0.000001	T	0.56804	0.2010	M	0.75615	2.305	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	T	0.60732	-0.7205	10	0.87932	D	0	-21.6554	15.5593	0.76229	0.0:0.0:0.0:1.0	.	47	Q9BYG5	PAR6B_HUMAN	P	47	ENSP00000360672:L47P;ENSP00000379354:L47P	ENSP00000360672:L47P	L	+	2	0	PARD6B	48787874	1.000000	0.71417	0.749000	0.31150	0.589000	0.36550	7.662000	0.83803	2.277000	0.76020	0.528000	0.53228	CTA	.	.	.	none		0.343	PARD6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079697.2	NM_032521		C	49354467	T	C	49354467	3	2	109	1	0	0	0	0	1	0	0	0	11453	1522	53	3	146	3	PARD6B	20	49354467	Missense_Mutation	SNP	T	TCGA-B9-A8YI-01A-21D-A36X-10		49354467	13671053	112	7057											
CHRNA4	1137	hgsc.bcm.edu	37	chr20	61981808	61981808	+	Frame_Shift_Del	DEL	G	G	-																															gaccgtgatgacgatggacaGggtgacgaagatcatggtga																										TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr20:61981808delG	ENST00000370263.4	-	5	1176	c.955delC	c.(955-957)ctgfs	p.L319fs	CHRNA4_ENST00000463705.1_5'UTR	NM_000744.6|NM_001256573.1	NP_000735.1|NP_001243502.1	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 (neuronal)	319					action potential (GO:0001508)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cognition (GO:0050890)|DNA repair (GO:0006281)|exploration behavior (GO:0035640)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|neurological system process (GO:0050877)|regulation of dopamine secretion (GO:0014059)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(19)|prostate(3)|skin(3)|soft_tissue(1)	33	all_cancers(38;1.71e-10)				Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	ACGATGGACAGGGTGACGAAG	0.597																																					p.L319fs		Atlas-Indel,Pindel	.											.	CHRNA4	98	.	0			c.956delT						PASS	.						233	160	185					20																	61981808		2203	4300	6503	SO:0001589	frameshift_variant	1137	exon5			.		CCDS13517.1	20q13.33	2013-09-20	2012-02-07		ENSG00000101204	ENSG00000101204		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1958	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 4 (neuronal)"	118504	"cholinergic receptor, nicotinic, alpha polypeptide 4"	EBN, EBN1		1505988	Standard	NM_000744		Approved	BFNC	uc002yes.3	P43681	OTTHUMG00000033080	ENST00000370263.4:c.955delC	chr20.hg19:g.61981808delG	ENSP00000359285:p.Leu319fs	117.0	0.0	0		136.0	49.0	0.360294	NM_000744	Q4JGR7|Q4VAQ5|Q4VAQ6	Frame_Shift_Del	DEL	ENST00000370263.4	hg19	CCDS13517.1																																																																																			.	.	.	none		0.597	CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3			-	61981808	G	-	61981808	7	5	109	1	0	1	0	1	0	0	0	0	3387	991	35	0	936	0	CHRNA4	20	61981808	Frame_Shift_Del	DEL	G	TCGA-B9-A8YI-01A-21D-A36X-10	12627341	61981808	1043712	113	7058											
DIP2A	23181	hgsc.bcm.edu	37	chr21	47986481	47986481	+	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	cactgttcacagggcggcacGatgcactgtatgtggttggg	7	10	15	9	2	1	0	1	0	0	0	1	1	1	0	0	4	1	5	0	4	1	3	rs537914823		TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr21:47986481G>T	ENST00000417564.2	+	37	4369	c.4348G>T	c.(4348-4350)Gat>Tat	p.D1450Y	DIP2A_ENST00000479654.1_3'UTR|DIP2A_ENST00000400274.1_Missense_Mutation_p.D1446Y|DIP2A_ENST00000318711.7_Missense_Mutation_p.D1451Y			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	1450					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)		AGGGCGGCACGATGCACTGTA	0.557																																					p.D1450Y		Atlas-SNP	.											.	DIP2A	332	.	0			c.G4348T						PASS	.						112	118	116					21																	47986481		2195	4299	6494	SO:0001583	missense	23181	exon37			CGGCACGATGCAC	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.4348G>T	chr21.hg19:g.47986481G>T	ENSP00000392066:p.Asp1450Tyr	68.0	0.0	.		93.0	4.0	.	NM_015151	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Missense_Mutation	SNP	ENST00000417564.2	hg19	CCDS46655.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.444922	0.83993	.	.	ENSG00000160305	ENST00000400274;ENST00000318711;ENST00000417564	T;T;T	0.26957	1.7;1.7;1.7	5.52	5.52	0.82312	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.56992	0.2023	M	0.83012	2.62	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.62210	-0.6902	10	0.87932	D	0	-18.8768	18.425	0.90606	0.0:0.0:1.0:0.0	.	1451;1450	E9PER1;Q14689	.;DIP2A_HUMAN	Y	1446;1451;1450	ENSP00000383133:D1446Y;ENSP00000323633:D1451Y;ENSP00000392066:D1450Y	ENSP00000323633:D1451Y	D	+	1	0	DIP2A	46810909	1.000000	0.71417	0.728000	0.30774	0.707000	0.40811	9.627000	0.98412	2.599000	0.87857	0.655000	0.94253	GAT	.	.	.	none		0.557	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151		T	47986481	G	T	47986481	3	4	109	1	0	0	0	0	1	0	0	0	4529	1058	37	4	4607	4	DIP2A	21	47986481	Missense_Mutation	SNP	G	TCGA-B9-A8YI-01A-21D-A36X-10		47986481	143414	114	7059											
POTEH	23784	hgsc.bcm.edu	37	chr22	16258291	16258294	+	Frame_Shift_Del	DEL	ATTT	ATTT	-																															gaaagttgcttctgagtatcAttttgttcatcactagaaaa																								rs200891952|rs565828046	byFrequency	TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	ATTT	ATTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr22:16258291_16258294delATTT	ENST00000343518.6	-	10	1581_1584	c.1530_1533delAAAT	c.(1528-1533)caaaatfs	p.QN510fs		NM_001136213.1	NP_001129685.1	Q6S545	POTEH_HUMAN	POTE ankyrin domain family, member H	510										NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(20)|ovary(1)|skin(7)|urinary_tract(2)	37						TCTGAGTATCATTTTGTTCATCAC	0.358																																					p.511_512del		Pindel	.											.	POTEH	114	.	0			c.1531_1534del						PASS	.																																			SO:0001589	frameshift_variant	23784	exon10			.	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.1530_1533delAAAT	chr22.hg19:g.16258291_16258294delATTT	ENSP00000340610:p.Gln510fs	783.0	0.0	.		886.0	61.0	0.069	NM_001136213	A2CEK4|A6NCI1|A9Z1W0	Frame_Shift_Del	DEL	ENST00000343518.6	hg19	CCDS46658.1																																																																																			.	.	.	none		0.358	POTEH-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276918.4	NM_001136213		-	16258294	ATTT	-	16258291	7	5	109	1	0	1	0	1	0	0	0	0	12274	214	8	0	108	0	POTEH	22	16258291	Frame_Shift_Del	DEL	ATTT	TCGA-B9-A8YI-01A-21D-A36X-10		16258291	35046275	115	7060											
TBC1D22A	25771	hgsc.bcm.edu	37	chr22	47433038	47433038	+	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	ccttccgctggatgaacaacCtgctgatgagggaggtgccc	8	8	13	12	1	0	3	0	3	0	0	1	5	1	5	4	3	4	2	4	3	2	1			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chr22:47433038C>A	ENST00000337137.4	+	11	1439	c.1273C>A	c.(1273-1275)Ctg>Atg	p.L425M	TBC1D22A_ENST00000406733.1_Missense_Mutation_p.L378M|TBC1D22A_ENST00000355704.3_Missense_Mutation_p.L347M|TBC1D22A_ENST00000407381.3_Missense_Mutation_p.L366M	NM_001284304.1|NM_001284305.1|NM_014346.2	NP_001271233.1|NP_001271234.1|NP_055161.1	Q8WUA7	TB22A_HUMAN	TBC1 domain family, member 22A	425	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						protein homodimerization activity (GO:0042803)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(3)|large_intestine(10)|lung(5)|ovary(2)|prostate(1)	22		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)		GATGAACAACCTGCTGATGAG	0.607																																					p.L425M		Atlas-SNP	.											.	TBC1D22A	54	.	0			c.C1273A						PASS	.						122	99	107					22																	47433038		2203	4300	6503	SO:0001583	missense	25771	exon11			AACAACCTGCTGA	AK125705	CCDS14078.1, CCDS63511.1, CCDS63512.1, CCDS74877.1	22q13	2008-01-22	2005-01-05	2005-01-05	ENSG00000054611	ENSG00000054611			1309	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 4"	C22orf4			Standard	XM_005261496		Approved		uc003bib.3	Q8WUA7	OTTHUMG00000150332	ENST00000337137.4:c.1273C>A	chr22.hg19:g.47433038C>A	ENSP00000336724:p.Leu425Met	64.0	0.0	.		88.0	26.0	.	NM_014346	B0QYI2|B0QYI3|B9A6M3|Q5TE47|Q6ZUH2|Q92680|Q9BVD6|Q9UGG0|Q9UGT2|Q9UGU6|Q9UH25|Q9Y4W5	Missense_Mutation	SNP	ENST00000337137.4	hg19	CCDS14078.1	.	.	.	.	.	.	.	.	.	.	C	17.81	3.481640	0.63849	.	.	ENSG00000054611	ENST00000337137;ENST00000407381;ENST00000355704;ENST00000406733	T;T;T;T	0.18657	2.2;2.2;2.2;2.2	4.59	2.39	0.29439	Rab-GAP/TBC domain (4);	0.000000	0.64402	D	0.000001	T	0.43122	0.1233	M	0.82923	2.615	0.80722	D	1	D;D;D;D	0.89917	0.995;0.999;1.0;0.995	D;D;D;D	0.76071	0.969;0.977;0.987;0.969	T	0.35599	-0.9782	10	0.59425	D	0.04	.	7.0227	0.24922	0.0:0.7199:0.0:0.2801	.	425;347;366;425	B9A6M3;Q8WUA7-2;B0QYI1;Q8WUA7	.;.;.;TB22A_HUMAN	M	425;366;347;378	ENSP00000336724:L425M;ENSP00000384036:L366M;ENSP00000347932:L347M;ENSP00000385634:L378M	ENSP00000336724:L425M	L	+	1	2	TBC1D22A	45811702	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.985000	0.40668	1.137000	0.42214	0.462000	0.41574	CTG	.	.	.	none		0.607	TBC1D22A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317600.3	NM_014346		A	47433038	C	A	47433038	3	1	109	1	0	0	0	0	1	0	0	0	15623	680	24	4	1315	4	TBC1D22A	22	47433038	Missense_Mutation	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10	31174747	47433038	3871528	116	7061											
PHF16	9767	hgsc.bcm.edu	37	chrX	46898381	46898381	+	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	cttgtcctgagaggatggaaCcgatcacgaagatctcccac	11	8	10	12	2	2	2	1	1	1	2	4	7	3	4	3	2	1	0	3	2	2	1			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chrX:46898381C>G	ENST00000218343.4	+	8	1184	c.886C>G	c.(886-888)Ccg>Gcg	p.P296A	PHF16_ENST00000397189.1_Missense_Mutation_p.P296A	NM_014735.3	NP_055550.1														NS(2)|endometrium(8)|kidney(4)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(2)	33						GAGGATGGAACCGATCACGAA	0.483																																					p.P296A		Atlas-SNP	.											.	PHF16	72	.	0			c.C886G						PASS	.						174	152	160					X																	46898381		2203	4300	6503	SO:0001583	missense	9767	exon8			ATGGAACCGATCA																												ENST00000218343.4:c.886C>G	chrX.hg19:g.46898381C>G	ENSP00000218343:p.Pro296Ala	66.0	0.0	.		68.0	46.0	.	NM_001077445		Missense_Mutation	SNP	ENST00000218343.4	hg19	CCDS14271.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.680539	0.88542	.	.	ENSG00000102221	ENST00000397189;ENST00000218343	T;T	0.15139	2.45;2.45	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.51092	0.1654	M	0.89478	3.035	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.61073	-0.7136	10	0.87932	D	0	.	18.4146	0.90565	0.0:1.0:0.0:0.0	.	296	Q92613	JADE3_HUMAN	A	296	ENSP00000380373:P296A;ENSP00000218343:P296A	ENSP00000218343:P296A	P	+	1	0	PHF16	46783325	1.000000	0.71417	0.994000	0.49952	0.881000	0.50899	7.367000	0.79558	2.289000	0.77006	0.513000	0.50165	CCG	.	.	.	none		0.483	PHF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056376.1			G	46898381	C	G	46898381	3	3	109	1	0	0	0	0	1	0	0	0	11834	507	18	4	912	4	PHF16	23	46898381	Missense_Mutation	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10		46898381	108372179	117	7062											
UBL4A	8266	hgsc.bcm.edu	37	chrX	153713966	153713966	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgatgtcgtccagcgtcaggCgactcagggacctctcgtaa	8	8	12	13	5	3	0	2	0	1	0	6	3	4	1	2	2	1	1	2	2	1	1			TCGA-B9-A8YI-01A-21D-A36X-10	TCGA-B9-A8YI-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b4b55b-1ee7-4b50-838e-95aa7d2fcd51	7aa75db8-fcf8-49cb-b097-27dc79933907	g.chrX:153713966C>T	ENST00000369660.4	-	4	471	c.386G>A	c.(385-387)cGc>cAc	p.R129H	UBL4A_ENST00000477777.1_5'UTR|UBL4A_ENST00000369653.4_Missense_Mutation_p.R129H	NM_014235.3	NP_055050.1	P11441	UBL4A_HUMAN	ubiquitin-like 4A	129					cellular protein modification process (GO:0006464)|tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)	small conjugating protein ligase activity (GO:0019787)			endometrium(5)|lung(1)|urinary_tract(1)	7	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CAGCGTCAGGCGACTCAGGGA	0.597																																					p.R129H	Esophageal Squamous(74;88 1215 11149 34177 46777)	Atlas-SNP	.											.	UBL4A	12	.	0			c.G386A						PASS	.						89	83	85					X																	153713966		2203	4300	6503	SO:0001583	missense	8266	exon4			GTCAGGCGACTCA	J03589	CCDS14754.1	Xq28	2010-08-05	2005-09-27	2005-09-27	ENSG00000102178	ENSG00000102178			12505	protein-coding gene	gene with protein product		312070	"ubiquitin-like 4"	UBL4		2829204, 16872915	Standard	NM_014235		Approved	GDX, DXS254E, GET5, MDY2, TMA24	uc004flo.3	P11441	OTTHUMG00000013370	ENST00000369660.4:c.386G>A	chrX.hg19:g.153713966C>T	ENSP00000358674:p.Arg129His	45.0	0.0	.		65.0	43.0	.	NM_014235	Q5HY80	Missense_Mutation	SNP	ENST00000369660.4	hg19	CCDS14754.1	.	.	.	.	.	.	.	.	.	.	C	16.81	3.227136	0.58668	.	.	ENSG00000102178	ENST00000369660;ENST00000369653	T;T	0.47528	0.88;0.84	5.35	3.31	0.37934	.	0.203112	0.42821	D	0.000656	T	0.53981	0.1830	M	0.74258	2.255	0.32176	N	0.580979	D	0.67145	0.996	P	0.53689	0.732	T	0.64723	-0.6340	10	0.66056	D	0.02	-0.0623	5.1063	0.14785	0.3116:0.5794:0.0:0.109	.	129	P11441	UBL4A_HUMAN	H	129	ENSP00000358674:R129H;ENSP00000358667:R129H	ENSP00000358667:R129H	R	-	2	0	UBL4A	153367160	1.000000	0.71417	1.000000	0.80357	0.085000	0.17905	1.164000	0.31810	1.161000	0.42604	0.529000	0.55759	CGC	.	.	.	none		0.597	UBL4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037238.2	NM_014235		T	153713966	C	T	153713966	3	4	109	1	0	0	0	0	1	0	0	0	16899	768	27	1	91	1	UBL4A	23	153713966	Missense_Mutation	SNP	C	TCGA-B9-A8YI-01A-21D-A36X-10	106815585	153713966	1556594	118	7063											
DNAJC16	23341	hgsc.bcm.edu	37	chr1	15894410	15894410	+	Missense_Mutation	SNP	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	catggagcgtgactacactgGttatgtactggctctgaatg	9	12	12	8	1	1	2	0	2	1	0	1	3	1	3	0	3	3	3	0	3	4	3			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr1:15894410G>A	ENST00000375847.3	+	15	2251	c.2087G>A	c.(2086-2088)gGt>gAt	p.G696D	RP4-680D5.8_ENST00000606186.1_RNA|DNAJC16_ENST00000375849.1_Intron|DNAJC16_ENST00000483270.1_3'UTR	NM_015291.2	NP_056106.1	Q9Y2G8	DJC16_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 16	696					cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(7)|urinary_tract(1)	18		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		GACTACACTGGTTATGTACTG	0.443																																					p.G696D		Atlas-SNP	.											.	DNAJC16	59	.	0			c.G2087A						PASS	.						148	134	139					1																	15894410		2203	4300	6503	SO:0001583	missense	23341	exon15			ACACTGGTTATGT	AB023179	CCDS30606.1, CCDS72710.1	1p36.1	2011-09-02			ENSG00000116138	ENSG00000116138		"Heat shock proteins / DNAJ (HSP40)"	29157	protein-coding gene	gene with protein product							Standard	NM_015291		Approved	KIAA0962	uc001aws.3	Q9Y2G8	OTTHUMG00000002358	ENST00000375847.3:c.2087G>A	chr1.hg19:g.15894410G>A	ENSP00000365007:p.Gly696Asp	162.0	0.0	.		123.0	26.0	.	NM_015291	Q68D57|Q86X32|Q8N5P4	Missense_Mutation	SNP	ENST00000375847.3	hg19	CCDS30606.1	.	.	.	.	.	.	.	.	.	.	G	31	5.059726	0.93846	.	.	ENSG00000116138	ENST00000375847	D	0.94417	-3.42	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	D	0.97173	0.9076	M	0.76170	2.325	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97352	0.9964	10	0.87932	D	0	-20.3895	18.8118	0.92061	0.0:0.0:1.0:0.0	.	696	Q9Y2G8	DJC16_HUMAN	D	696	ENSP00000365007:G696D	ENSP00000365007:G696D	G	+	2	0	DNAJC16	15766997	1.000000	0.71417	0.501000	0.27601	0.987000	0.75469	9.238000	0.95380	2.790000	0.95986	0.655000	0.94253	GGT	.	.	.	none		0.443	DNAJC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006764.1	NM_015291		A	15894410	G	A	15894410	3	1	110	1	0	0	0	0	1	0	0	0	4637	1261	44	2	2141	2	DNAJC16	1	15894410	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08		15894410	233356211	1	7064											
DNAJC16	23341	hgsc.bcm.edu	37	chr1	15894493	15894493	+	Frame_Shift_Del	DEL	G	G	-																															tcgaagaggaggaagccataGggtcgtgcagtgatgttgac																										TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr1:15894493delG	ENST00000375847.3	+	15	2334	c.2170delG	c.(2170-2172)gggfs	p.G724fs	RP4-680D5.8_ENST00000606186.1_RNA|DNAJC16_ENST00000375849.1_Intron|DNAJC16_ENST00000483270.1_3'UTR	NM_015291.2	NP_056106.1	Q9Y2G8	DJC16_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 16	724					cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(7)|urinary_tract(1)	18		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		GGAAGCCATAGGGTCGTGCAG	0.512																																					p.I723fs		Atlas-INDEL	.											.	DNAJC16	59	.	0			c.2169delA						PASS	.						124	103	110					1																	15894493		2203	4300	6503	SO:0001589	frameshift_variant	23341	exon15			.	AB023179	CCDS30606.1, CCDS72710.1	1p36.1	2011-09-02			ENSG00000116138	ENSG00000116138		"Heat shock proteins / DNAJ (HSP40)"	29157	protein-coding gene	gene with protein product							Standard	NM_015291		Approved	KIAA0962	uc001aws.3	Q9Y2G8	OTTHUMG00000002358	ENST00000375847.3:c.2170delG	chr1.hg19:g.15894493delG	ENSP00000365007:p.Gly724fs	110.0	0.0	0		75.0	17.0	0.226667	NM_015291	Q68D57|Q86X32|Q8N5P4	Frame_Shift_Del	DEL	ENST00000375847.3	hg19	CCDS30606.1																																																																																			.	.	.	none		0.512	DNAJC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006764.1	NM_015291		-	15894493	G	-	15894493	7	5	110	1	0	1	0	1	0	0	0	0	4637	1000	35	0	2224	0	DNAJC16	1	15894493	Frame_Shift_Del	DEL	G	TCGA-BQ-5875-01A-11D-1589-08	83	15894493	233356128	2	7065											
BAI2	576	hgsc.bcm.edu	37	chr1	32203282	32203282	+	Silent	SNP	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	gcggcatagatggcgagcagGgtgagcagcgccatgcacga	10	4	17	10	4	0	2	0	1	0	1	0	4	0	2	1	3	4	4	1	3	1	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr1:32203282G>A	ENST00000373658.3	-	19	3188	c.2847C>T	c.(2845-2847)acC>acT	p.T949T	BAI2_ENST00000440175.2_Silent_p.T591T|BAI2_ENST00000398542.1_Silent_p.T882T|BAI2_ENST00000373655.2_Silent_p.T949T|BAI2_ENST00000257070.4_Silent_p.T949T|BAI2_ENST00000398547.1_Silent_p.T882T|BAI2_ENST00000398538.1_Silent_p.T937T|BAI2_ENST00000527361.1_Silent_p.T949T|BAI2_ENST00000398556.3_Silent_p.T897T|BAI2_ENST00000465256.1_5'Flank	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	949					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)		TGGCGAGCAGGGTGAGCAGCG	0.667																																					p.T949T		Atlas-SNP	.											.	BAI2	128	.	0			c.C2847T						PASS	.						40	39	39					1																	32203282		2202	4299	6501	SO:0001819	synonymous_variant	576	exon19			GAGCAGGGTGAGC	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.2847C>T	chr1.hg19:g.32203282G>A		59.0	0.0	.		56.0	22.0	.	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Silent	SNP	ENST00000373658.3	hg19	CCDS346.2																																																																																			.	.	.	none		0.667	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703		A	32203282	G	A	32203282	2	1	110	1	0	0	0	0	0	0	0	1	1299	1219	43	2		2	BAI2	1	32203282	Silent	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	16308789	32203282	217047339	3	7066											
ABCA4	24	hgsc.bcm.edu	37	chr1	94502837	94502837	+	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	gaaggaagataagttcttgaCcaatgcactccaccagcttt	13	10	8	10	0	1	2	0	1	1	1	2	4	2	3	3	1	2	3	3	1	4	4			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr1:94502837C>A	ENST00000370225.3	-	25	3763	c.3677G>T	c.(3676-3678)gGt>gTt	p.G1226V		NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1226					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)		AAGTTCTTGACCAATGCACTC	0.478																																					p.G1226V		Atlas-SNP	.											.	ABCA4	275	.	0			c.G3677T						PASS	.						120	117	118					1																	94502837		2203	4300	6503	SO:0001583	missense	24	exon25			TCTTGACCAATGC	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.3677G>T	chr1.hg19:g.94502837C>A	ENSP00000359245:p.Gly1226Val	161.0	0.0	.		80.0	14.0	.	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	hg19	CCDS747.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.522436	0.85600	.	.	ENSG00000198691	ENST00000546054;ENST00000370225	T	0.80123	-1.34	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	D	0.90954	0.7156	H	0.96080	3.765	0.80722	D	1	D	0.56746	0.977	P	0.55011	0.766	D	0.93070	0.6482	10	0.87932	D	0	.	19.5916	0.95514	0.0:1.0:0.0:0.0	.	1226	P78363	ABCA4_HUMAN	V	18;1226	ENSP00000359245:G1226V	ENSP00000359245:G1226V	G	-	2	0	ABCA4	94275425	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	7.320000	0.79064	2.861000	0.98227	0.655000	0.94253	GGT	.	.	.	none		0.478	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		A	94502837	C	A	94502837	3	1	110	1	0	0	0	0	1	0	0	0	34	507	18	4	3248	4	ABCA4	1	94502837	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	62299555	94502837	154747784	4	7067											
KCNA2	3737	hgsc.bcm.edu	37	chr1	111146524	111146524	+	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	ctcttaccaaccggatgacaCggaggatggccagtgacatg	11	7	12	11	2	1	2	0	2	1	0	1	5	1	5	3	4	2	0	3	4	2	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr1:111146524C>A	ENST00000485317.1	-	3	1554	c.881G>T	c.(880-882)cGt>cTt	p.R294L	KCNA2_ENST00000316361.4_Missense_Mutation_p.R294L|KCNA2_ENST00000440270.1_Missense_Mutation_p.R294L|KCNA2_ENST00000369770.3_Missense_Mutation_p.R294L|KCNA2_ENST00000525120.1_5'Flank			P16389	KCNA2_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 2	294					optic nerve structural organization (GO:0021633)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	juxtaparanode region of axon (GO:0044224)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		all_cancers(81;5.55e-06)|all_epithelial(167;1.87e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Colorectal(144;0.00878)|Lung(183;0.0234)|all cancers(265;0.0492)|Epithelial(280;0.0529)|COAD - Colon adenocarcinoma(174;0.131)|LUSC - Lung squamous cell carcinoma(189;0.133)|READ - Rectum adenocarcinoma(129;0.191)	Dalfampridine(DB06637)	CCGGATGACACGGAGGATGGC	0.537																																					p.R294L	Pancreas(18;568 735 10587 23710 36357)	Atlas-SNP	.											.	KCNA2	61	.	0			c.G881T						PASS	.						102	103	103					1																	111146524		2203	4300	6503	SO:0001583	missense	3737	exon3			ATGACACGGAGGA	L02752	CCDS827.1, CCDS55625.1	1p13	2012-07-05			ENSG00000177301	ENSG00000177301		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6220	protein-coding gene	gene with protein product		176262				16382104	Standard	NM_004974		Approved	Kv1.2, HK4	uc009wfw.3	P16389	OTTHUMG00000011567	ENST00000485317.1:c.881G>T	chr1.hg19:g.111146524C>A	ENSP00000433109:p.Arg294Leu	170.0	0.0	.		92.0	33.0	.	NM_001204269	Q86XG6	Missense_Mutation	SNP	ENST00000485317.1	hg19	CCDS827.1	.	.	.	.	.	.	.	.	.	.	C	16.76	3.212566	0.58452	.	.	ENSG00000177301	ENST00000369770;ENST00000485317;ENST00000440270;ENST00000316361	D;D;D;D	0.99005	-4.93;-5.32;-5.32;-5.32	5.87	5.87	0.94306	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99704	0.9887	H	0.98818	4.34	0.80722	D	1	D;D	0.71674	0.998;0.962	D;P	0.71414	0.973;0.748	D	0.97484	1.0049	10	0.87932	D	0	.	20.2182	0.98305	0.0:1.0:0.0:0.0	.	294;294	Q86XG6;P16389	.;KCNA2_HUMAN	L	294	ENSP00000358785:R294L;ENSP00000433109:R294L;ENSP00000415257:R294L;ENSP00000314520:R294L	ENSP00000314520:R294L	R	-	2	0	KCNA2	110948047	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	7.770000	0.85390	2.785000	0.95823	0.655000	0.94253	CGT	.	.	.	none		0.537	KCNA2-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128001.2	NM_004974		A	111146524	C	A	111146524	3	1	110	1	0	0	0	0	1	0	0	0	8010	536	19	4	622	4	KCNA2	1	111146524	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	16643687	111146524	138104097	5	7068											
SPAG17	200162	hgsc.bcm.edu	37	chr1	118535132	118535132	+	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	gtttcacctcattctttatgAcctcatgctgaatgaattgg	9	16	7	9	0	4	3	3	3	1	0	4	3	4	3	2	1	1	2	2	1	3	5			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr1:118535132A>T	ENST00000336338.5	-	36	5383	c.5318T>A	c.(5317-5319)gTc>gAc	p.V1773D		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1773						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)		ATTCTTTATGACCTCATGCTG	0.473																																					p.V1773D		Atlas-SNP	.											.	SPAG17	263	.	0			c.T5318A						PASS	.						116	112	113					1																	118535132		2203	4300	6503	SO:0001583	missense	200162	exon36			TTTATGACCTCAT		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.5318T>A	chr1.hg19:g.118535132A>T	ENSP00000337804:p.Val1773Asp	174.0	0.0	.		100.0	25.0	.	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	hg19	CCDS899.1	.	.	.	.	.	.	.	.	.	.	A	18.16	3.562988	0.65538	.	.	ENSG00000155761	ENST00000336338;ENST00000437255	T	0.19105	2.17	5.38	3.1	0.35709	.	0.311094	0.33854	N	0.004486	T	0.13329	0.0323	L	0.54323	1.7	0.41943	D	0.990622	P	0.47677	0.899	P	0.48227	0.571	T	0.02301	-1.1180	10	0.66056	D	0.02	.	5.9646	0.19318	0.6602:0.0:0.3398:0.0	.	1773	Q6Q759	SPG17_HUMAN	D	1773;253	ENSP00000337804:V1773D	ENSP00000337804:V1773D	V	-	2	0	SPAG17	118336655	1.000000	0.71417	0.993000	0.49108	0.946000	0.59487	3.048000	0.49862	0.886000	0.36113	-0.250000	0.11733	GTC	.	.	.	none		0.473	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		T	118535132	A	T	118535132	3	4	110	1	0	0	0	0	1	0	0	0	14992	275	10	5	1405	5	SPAG17	1	118535132	Missense_Mutation	SNP	A	TCGA-BQ-5875-01A-11D-1589-08	7388608	118535132	130715489	6	7069											
FMO4	2329	hgsc.bcm.edu	37	chr1	171303684	171303684	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgggacagtggaagaaaacaTtgatgttgtgatcttcacta	13	12	11	5	0	2	3	1	2	1	1	2	5	2	5	0	2	1	1	0	2	4	4			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr1:171303684T>C	ENST00000367749.3	+	8	1292	c.962T>C	c.(961-963)aTt>aCt	p.I321T		NM_002022.1	NP_002013.1	P31512	FMO4_HUMAN	flavin containing monooxygenase 4	321					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)					GAAGAAAACATTGATGTTGTG	0.368																																					p.I321T	Pancreas(24;816 862 7754 7993 32832)	Atlas-SNP	.											.	FMO4	64	.	0			c.T962C						PASS	.						92	95	94					1																	171303684		2203	4300	6503	SO:0001583	missense	2329	exon8			AAAACATTGATGT	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.962T>C	chr1.hg19:g.171303684T>C	ENSP00000356723:p.Ile321Thr	124.0	0.0	.		79.0	31.0	.	NM_002022	Q53XR0	Missense_Mutation	SNP	ENST00000367749.3	hg19	CCDS1295.1	.	.	.	.	.	.	.	.	.	.	T	18.64	3.668252	0.67814	.	.	ENSG00000076258	ENST00000367749	T	0.56941	0.43	5.63	4.47	0.54385	.	0.249916	0.40144	N	0.001171	T	0.72170	0.3427	M	0.93978	3.48	0.41142	D	0.985967	D	0.69078	0.997	D	0.77557	0.99	T	0.80176	-0.1491	10	0.87932	D	0	-9.0886	12.3662	0.55230	0.0:0.0:0.1412:0.8588	.	321	P31512	FMO4_HUMAN	T	321	ENSP00000356723:I321T	ENSP00000356723:I321T	I	+	2	0	FMO4	169570308	1.000000	0.71417	0.246000	0.24233	0.910000	0.53928	6.102000	0.71486	0.918000	0.36919	0.528000	0.53228	ATT	.	.	.	none		0.368	FMO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086223.1	NM_002022		C	171303684	T	C	171303684	3	2	110	1	0	0	0	0	1	0	0	0	5964	1493	52	3	984	3	FMO4	1	171303684	Missense_Mutation	SNP	T	TCGA-BQ-5875-01A-11D-1589-08	52768552	171303684	77946937	7	7070											
CEP350	9857	hgsc.bcm.edu	37	chr1	180063597	180063597	+	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	gaaaatccagcttagcaatcAggagcttcttggtgatgacc	12	10	10	9	0	2	2	1	2	1	0	3	4	3	3	2	2	3	3	2	2	4	3	rs573430116		TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr1:180063597A>T	ENST00000367607.3	+	34	8775	c.8357A>T	c.(8356-8358)cAg>cTg	p.Q2786L	CEP350_ENST00000490141.1_3'UTR	NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	2786					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						CTTAGCAATCAGGAGCTTCTT	0.388																																					p.Q2786L		Atlas-SNP	.											.	CEP350	418	.	0			c.A8357T						PASS	.						59	59	59					1																	180063597		2203	4300	6503	SO:0001583	missense	9857	exon34			GCAATCAGGAGCT	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.8357A>T	chr1.hg19:g.180063597A>T	ENSP00000356579:p.Gln2786Leu	37.0	0.0	.		47.0	16.0	.	NM_014810	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	hg19	CCDS1336.1	.	.	.	.	.	.	.	.	.	.	A	17.39	3.377132	0.61735	.	.	ENSG00000135837	ENST00000367607;ENST00000417046	T	0.61859	0.07	5.31	5.31	0.75309	.	0.000000	0.44902	D	0.000414	T	0.70657	0.3249	M	0.72118	2.19	0.45662	D	0.998587	D;P	0.60160	0.987;0.935	D;P	0.67725	0.953;0.614	T	0.72007	-0.4420	9	.	.	.	.	9.4328	0.38620	0.9192:0.0:0.0808:0.0	.	2786;2786	E7EU22;Q5VT06	.;CE350_HUMAN	L	2786;250	ENSP00000356579:Q2786L	.	Q	+	2	0	CEP350	178330220	1.000000	0.71417	0.993000	0.49108	0.935000	0.57460	2.342000	0.43992	2.126000	0.65437	0.482000	0.46254	CAG	.	.	.	none		0.388	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		T	180063597	A	T	180063597	3	4	110	1	0	0	0	0	1	0	0	0	3256	188	7	5	8487	5	CEP350	1	180063597	Missense_Mutation	SNP	A	TCGA-BQ-5875-01A-11D-1589-08	8759913	180063597	69187024	8	7071											
ADAM17	6868	hgsc.bcm.edu	37	chr2	9630624	9630624	+	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	atgcgaaccgatgcagaatcCatgctgctcagcatttcgac	11	9	9	12	3	1	1	1	0	0	1	3	4	2	1	2	0	6	4	2	0	2	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr2:9630624C>T	ENST00000310823.3	-	19	2339	c.2157G>A	c.(2155-2157)atG>atA	p.M719I	IAH1_ENST00000545602.1_Intron	NM_003183.4	NP_003174.3	P78536	ADA17_HUMAN	ADAM metallopeptidase domain 17	719					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell motility (GO:0048870)|collagen catabolic process (GO:0030574)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|germinal center formation (GO:0002467)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil mediated immunity (GO:0002446)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of chemokine production (GO:0032722)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|proteolysis (GO:0006508)|regulation of mast cell apoptotic process (GO:0033025)|response to drug (GO:0042493)|response to high density lipoprotein particle (GO:0055099)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|wound healing, spreading of epidermal cells (GO:0035313)	actin cytoskeleton (GO:0015629)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|interleukin-6 receptor binding (GO:0005138)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|Notch binding (GO:0005112)|PDZ domain binding (GO:0030165)|zinc ion binding (GO:0008270)			breast(1)|cervix(4)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	28	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.225)		ATGCAGAATCCATGCTGCTCA	0.537																																					p.M719I		Atlas-SNP	.											.	ADAM17	61	.	0			c.G2157A						PASS	.						54	51	52					2																	9630624		2203	4300	6503	SO:0001583	missense	6868	exon19			AGAATCCATGCTG	U69611	CCDS1665.1	2p25	2010-08-05	2008-07-31		ENSG00000151694	ENSG00000151694		"ADAM metallopeptidase domain containing", "CD molecules"	195	protein-coding gene	gene with protein product		603639	"tumor necrosis factor, alpha, converting enzyme"	TACE		9034190, 9574564	Standard	NM_003183		Approved	cSVP, CD156B	uc002qzu.3	P78536	OTTHUMG00000090425	ENST00000310823.3:c.2157G>A	chr2.hg19:g.9630624C>T	ENSP00000309968:p.Met719Ile	50.0	0.0	.		55.0	11.0	.	NM_003183	O60226	Missense_Mutation	SNP	ENST00000310823.3	hg19	CCDS1665.1	.	.	.	.	.	.	.	.	.	.	C	9.835	1.189343	0.21954	.	.	ENSG00000151694	ENST00000310823	T	0.19806	2.12	5.46	5.46	0.80206	.	0.145332	0.64402	N	0.000007	T	0.14399	0.0348	N	0.12182	0.205	0.80722	D	1	B;B;B	0.13145	0.0;0.007;0.007	B;B;B	0.12156	0.0;0.007;0.007	T	0.11792	-1.0573	10	0.19590	T	0.45	.	19.3715	0.94490	0.0:1.0:0.0:0.0	.	438;719;719	Q53RS1;B2RNB2;P78536	.;.;ADA17_HUMAN	I	719	ENSP00000309968:M719I	ENSP00000309968:M719I	M	-	3	0	ADAM17	9548075	1.000000	0.71417	1.000000	0.80357	0.113000	0.19764	2.684000	0.46951	2.570000	0.86706	0.456000	0.33151	ATG	.	.	.	none		0.537	ADAM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206857.1			T	9630624	C	T	9630624	3	4	110	1	0	0	0	0	1	0	0	0	238	594	21	2	321	2	ADAM17	2	9630624	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08		9630624	233568749	9	7072											
TTC7A	57217	hgsc.bcm.edu	37	chr2	47300864	47300864	+	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	ctgatgctgagtcggctgggCcacaagagcttggcccagaa	9	7	14	11	1	0	4	0	2	0	2	1	4	0	4	2	3	2	3	2	3	2	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr2:47300864C>T	ENST00000319190.5	+	20	2747	c.2379C>T	c.(2377-2379)ggC>ggT	p.G793G	TTC7A_ENST00000263737.6_Silent_p.G439G|RP11-761B3.1_ENST00000422269.1_Intron|AC073283.7_ENST00000421759.1_RNA|TTC7A_ENST00000394850.2_Silent_p.G817G|C2orf61_ENST00000464527.2_Intron|TTC7A_ENST00000409245.1_Silent_p.G759G	NM_020458.2	NP_065191.2	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A	793					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)			GTCGGCTGGGCCACAAGAGCT	0.652																																					p.G793G		Atlas-SNP	.											.	TTC7A	80	.	0			c.C2379T						PASS	.						66	61	63					2																	47300864		2203	4300	6503	SO:0001819	synonymous_variant	57217	exon20			GCTGGGCCACAAG	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.2379C>T	chr2.hg19:g.47300864C>T		111.0	0.0	.		62.0	24.0	.	NM_020458	Q6PIX4|Q8ND67|Q9BUS3	Silent	SNP	ENST00000319190.5	hg19	CCDS33193.1																																																																																			.	.	.	none		0.652	TTC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329667.2	XM_372927		T	47300864	C	T	47300864	2	4	110	1	0	0	0	0	0	0	0	1	16724	726	26	2		2	TTC7A	2	47300864	Silent	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	37670240	47300864	195898509	10	7073											
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54876308	54876308	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggtcccatgaactgggacAggactatgagcatgtcacgg	11	7	14	9	1	1	2	1	2	0	0	2	4	2	4	1	4	2	1	1	4	2	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr2:54876308A>G	ENST00000356805.4	+	25	5464	c.5183A>G	c.(5182-5184)cAg>cGg	p.Q1728R	SPTBN1_ENST00000333896.5_Missense_Mutation_p.Q1715R	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1728	Interaction with ANK2.				actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			GAACTGGGACAGGACTATGAG	0.552																																					p.Q1728R		Atlas-SNP	.											.	SPTBN1	378	.	0			c.A5183G						PASS	.						82	70	74					2																	54876308		2203	4300	6503	SO:0001583	missense	6711	exon25			TGGGACAGGACTA		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.5183A>G	chr2.hg19:g.54876308A>G	ENSP00000349259:p.Gln1728Arg	75.0	0.0	.		74.0	4.0	.	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	hg19	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	A	28.6	4.936737	0.92458	.	.	ENSG00000115306	ENST00000356805;ENST00000333896	T;T	0.48201	0.82;0.82	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.73385	0.3580	M	0.86343	2.81	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.985;0.996	T	0.77840	-0.2438	10	0.59425	D	0.04	.	16.2826	0.82703	1.0:0.0:0.0:0.0	.	1715;1728	Q01082-3;Q01082	.;SPTB2_HUMAN	R	1728;1715	ENSP00000349259:Q1728R;ENSP00000334156:Q1715R	ENSP00000334156:Q1715R	Q	+	2	0	SPTBN1	54729812	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.281000	0.95811	2.253000	0.74438	0.454000	0.30748	CAG	.	.	.	none		0.552	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			G	54876308	A	G	54876308	3	3	110	1	0	0	0	0	1	0	0	0	15131	188	7	3	5390	3	SPTBN1	2	54876308	Missense_Mutation	SNP	A	TCGA-BQ-5875-01A-11D-1589-08	7575444	54876308	188323065	11	7074											
IL1R2	7850	hgsc.bcm.edu	37	chr2	102626224	102626224	+	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	agacacggatgtgggcccagGacggtgctctgtggcttctg	6	9	16	10	2	2	1	0	0	2	1	2	3	2	3	1	5	1	2	1	5	0	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr2:102626224G>T	ENST00000332549.3	+	3	497	c.268G>T	c.(268-270)Gac>Tac	p.D90Y	IL1R2_ENST00000393414.2_Missense_Mutation_p.D90Y|IL1R2_ENST00000441002.1_Missense_Mutation_p.D90Y	NM_004633.3	NP_004624.1	P27930	IL1R2_HUMAN	interleukin 1 receptor, type II	90	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						GTGGGCCCAGGACGGTGCTCT	0.597																																					p.D90Y	Pancreas(106;189 1628 2302 5133 12295)	Atlas-SNP	.											.	IL1R2	58	.	0			c.G268T						PASS	.						139	147	145					2																	102626224		2203	4300	6503	SO:0001583	missense	7850	exon3			GCCCAGGACGGTG	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.268G>T	chr2.hg19:g.102626224G>T	ENSP00000330959:p.Asp90Tyr	359.0	1.0	.		270.0	85.0	.	NM_001261419	D3DVJ5|Q6LCE6|Q9UE68	Missense_Mutation	SNP	ENST00000332549.3	hg19	CCDS2054.1	.	.	.	.	.	.	.	.	.	.	G	11.68	1.711212	0.30322	.	.	ENSG00000115590	ENST00000332549;ENST00000393414;ENST00000457817;ENST00000441002	T;T;T;T	0.62788	0.0;0.0;0.0;0.0	5.8	4.92	0.64577	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.512100	0.21363	N	0.075776	T	0.59770	0.2218	M	0.76002	2.32	0.09310	N	1	B	0.16396	0.017	B	0.14023	0.01	T	0.57039	-0.7879	10	0.56958	D	0.05	.	7.7685	0.28993	0.0807:0.0:0.756:0.1633	.	90	P27930	IL1R2_HUMAN	Y	90	ENSP00000330959:D90Y;ENSP00000377066:D90Y;ENSP00000408415:D90Y;ENSP00000414611:D90Y	ENSP00000330959:D90Y	D	+	1	0	IL1R2	101992656	0.347000	0.24853	0.015000	0.15790	0.125000	0.20455	1.279000	0.33191	1.466000	0.48025	-0.268000	0.10319	GAC	.	.	.	none		0.597	IL1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253191.1	NM_004633		T	102626224	G	T	102626224	3	4	110	1	0	0	0	0	1	0	0	0	7666	1174	41	4	274	4	IL1R2	2	102626224	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	47749916	102626224	140573149	12	7075											
SLC4A10	57282	hgsc.bcm.edu	37	chr2	162711596	162711597	+	Missense_Mutation	DNP	CT	CT	AG																															aagttgtattctgaatggaaCtgtgttgctggacatgcatg																										TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr2:162711596_162711597CT>AG	ENST00000446997.1	+	5	626_627	c.533_534CT>AG	c.(532-534)aCT>aAG	p.T178K	SLC4A10_ENST00000535165.1_Missense_Mutation_p.T178K|SLC4A10_ENST00000272716.5_Missense_Mutation_p.T178K|SLC4A10_ENST00000375514.5_Missense_Mutation_p.T189K|SLC4A10_ENST00000421911.1_Missense_Mutation_p.T178K|SLC4A10_ENST00000493021.1_3'UTR|SLC4A10_ENST00000415876.2_Missense_Mutation_p.T178K	NM_001178015.1	NP_001171486.1	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate transporter, member 10	178					bicarbonate transport (GO:0015701)|chloride transport (GO:0006821)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|symporter activity (GO:0015293)			endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(35)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60					Sodium bicarbonate(DB01390)	CTGAATGGAACTGTGTTGCTGG	0.396																																					p.T189N|p.T189T		Atlas-SNP	.											.	SLC4A10	309	.	0			c.C566A|c.T567G						PASS	.																																			SO:0001583	missense	57282	exon6			ATGGAACTGTGTT|TGGAACTGTGTTG		CCDS46438.1, CCDS54411.1, CCDS54412.1	2q24.2	2013-05-22	2008-09-15		ENSG00000144290	ENSG00000144290		"Solute carriers"	13811	protein-coding gene	gene with protein product		605556	"solute carrier family 4, sodium bicarbonate transporter-like, member 10"			10964153, 18319254	Standard	NM_022058		Approved	NBCn2, NCBE	uc002ubx.4	Q6U841	OTTHUMG00000153938	Exception_encountered	chr2.hg19:g.162711596_162711597delinsAG	ENSP00000393066:p.Thr178Lys	82.0|83.0	0.0	.		77.0|76.0	33.0	.	NM_001178016	B7Z1R0|B7Z2J0|B7ZLC5|B9EG69|F8W675|Q4ZFX6|Q8TCP2|Q9HCQ6	Missense_Mutation|Silent	SNP	ENST00000446997.1	hg19	CCDS54411.1																																																																																			.	.	.	none		0.396	SLC4A10-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333090.1	NM_022058		AG	162711597	CT	AG	162711596	3	1	110	1	0	0	0	0	1	0	0	0	14664	565	20	4	636	4	SLC4A10	2	162711596	Missense_Mutation	DNP	CT	TCGA-BQ-5875-01A-11D-1589-08	60085372	162711596	80487777	13	7076											
UGT1A9	54600	hgsc.bcm.edu	37	chr2	234580748	234580748	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcagggggcatgaggtggtTgtagtcatgccagaggtgag	8	9	18	6	0	2	3	2	2	0	1	2	3	2	3	1	5	1	3	1	5	1	2			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr2:234580748T>C	ENST00000354728.4	+	1	250	c.168T>C	c.(166-168)gtT>gtC	p.V56V	UGT1A1_ENST00000609637.1_Silent_p.V56V|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A10_ENST00000373445.1_Intron			O60656	UD19_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A9	56					cellular glucuronidation (GO:0052695)|cellular lipid metabolic process (GO:0044255)|drug metabolic process (GO:0017144)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|metabolic process (GO:0008152)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|small molecule metabolic process (GO:0044281)|xenobiotic glucuronidation (GO:0052697)|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)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)	p.V56V(1)		breast(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	37		Breast(86;0.000766)|all_lung(227;0.00269)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0331)|Lung NSC(271;0.0459)|Lung SC(224;0.128)		Epithelial(121;1.26e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000436)|Lung(119;0.00347)|LUSC - Lung squamous cell carcinoma(224;0.00757)	Acetaminophen(DB00316)|Buprenorphine(DB00921)|Canagliflozin(DB08907)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Entacapone(DB00494)|Etodolac(DB00749)|Ezogabine(DB04953)|Flurbiprofen(DB00712)|Haloperidol(DB00502)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ketobemidone(DB06738)|Lumiracoxib(DB01283)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Nateglinide(DB00731)|Niflumic Acid(DB04552)|Oxazepam(DB00842)|Propofol(DB00818)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sulfamethoxazole(DB01015)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zileuton(DB00744)	ATGAGGTGGTTGTAGTCATGC	0.532																																					p.V56V		Atlas-SNP	.											UGT1A9,NS,carcinoma,0,1	UGT1A9	79	.	1	Substitution - coding silent(1)	kidney(1)	c.T168C						PASS	.						100	85	90					2																	234580748		2203	4300	6503	SO:0001819	synonymous_variant	54600	exon1			GGTGGTTGTAGTC	AF056188	CCDS2505.1	2q37	2010-03-05	2005-07-20		ENSG00000241119	ENSG00000241119		"UDP glucuronosyltransferases"	12541	other	complex locus constituent		606434	"UDP glycosyltransferase 1 family, polypeptide A9"			9295054, 1910331	Standard	NM_021027		Approved	HLUGP4, LUGP4, UGT1AI		O60656	OTTHUMG00000059124	ENST00000354728.4:c.168T>C	chr2.hg19:g.234580748T>C		107.0	1.0	.		96.0	4.0	.	NM_021027	B8K285|P36509|Q9HAX0	Silent	SNP	ENST00000354728.4	hg19	CCDS2505.1																																																																																			.	.	.	none		0.532	UGT1A9-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130995.1	NM_021027		C	234580748	T	C	234580748	2	2	110	1	0	0	0	0	0	0	0	1	16964	1799	63	3		3	UGT1A9	2	234580748	Silent	SNP	T	TCGA-BQ-5875-01A-11D-1589-08	71869152	234580748	8618625	14	7077											
STAC	6769	hgsc.bcm.edu	37	chr3	36587768	36587768	+	Missense_Mutation	SNP	T	T	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	cctcatcccccttgatgtacTagaaaacatctgattgctgg	10	12	7	12	0	2	3	1	2	1	1	3	3	3	3	3	1	3	2	3	1	4	4			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr3:36587768T>G	ENST00000273183.3	+	11	1496	c.1196T>G	c.(1195-1197)cTa>cGa	p.L399R	STAC_ENST00000457375.2_Missense_Mutation_p.L338R	NM_003149.1	NP_003140.1	Q99469	STAC_HUMAN	SH3 and cysteine rich domain	399					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						CTTGATGTACTAGAAAACATC	0.493																																					p.L399R		Atlas-SNP	.											.	STAC	78	.	0			c.T1196G						PASS	.						151	131	138					3																	36587768		2203	4300	6503	SO:0001583	missense	6769	exon11			ATGTACTAGAAAA	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.1196T>G	chr3.hg19:g.36587768T>G	ENSP00000273183:p.Leu399Arg	86.0	0.0	.		80.0	62.0	.	NM_003149	B2R8S8	Missense_Mutation	SNP	ENST00000273183.3	hg19	CCDS2662.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.126023	0.77436	.	.	ENSG00000144681	ENST00000273183;ENST00000457375;ENST00000544687	T;T	0.09445	2.98;2.98	5.17	5.17	0.71159	Src homology-3 domain (1);Variant SH3 (1);	0.074155	0.56097	D	0.000036	T	0.33904	0.0879	M	0.78801	2.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.10200	-1.0640	10	0.87932	D	0	.	13.5546	0.61751	0.0:0.0:0.0:1.0	.	338;399	E9PEA7;Q99469	.;STAC_HUMAN	R	399;338;331	ENSP00000273183:L399R;ENSP00000393713:L338R	ENSP00000273183:L399R	L	+	2	0	STAC	36562772	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	5.936000	0.70153	2.074000	0.62210	0.533000	0.62120	CTA	.	.	.	none		0.493	STAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253338.2	NM_003149		G	36587768	T	G	36587768	3	3	110	1	0	0	0	0	1	0	0	0	15251	1522	53	5	1238	5	STAC	3	36587768	Missense_Mutation	SNP	T	TCGA-BQ-5875-01A-11D-1589-08		36587768	161434662	15	7078											
SETD2	29072	hgsc.bcm.edu	37	chr3	47061276	47061276	+	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	tctgaatacttctttgctttTctttgctagttcactggagg	6	19	8	8	0	4	1	1	1	3	0	4	2	4	2	0	2	3	3	0	2	3	8			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr3:47061276T>A	ENST00000409792.3	-	19	7447	c.7405A>T	c.(7405-7407)Aaa>Taa	p.K2469*		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2469	Interaction with POLR2A.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TCTTTGCTTTTCTTTGCTAGT	0.428			"N, F, S, Mis"		clear cell renal carcinoma																																p.K2469X		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.A7405T						PASS	.						286	251	263					3																	47061276		2203	4300	6503	SO:0001587	stop_gained	29072	exon19			TGCTTTTCTTTGC	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.7405A>T	chr3.hg19:g.47061276T>A	ENSP00000386759:p.Lys2469*	151.0	1.0	.		85.0	72.0	.	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Nonsense_Mutation	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	T	48	14.332947	0.99790	.	.	ENSG00000181555	ENST00000451092;ENST00000409792	.	.	.	5.64	5.64	0.86602	.	0.000000	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.6824	0.77381	0.0:0.0:0.0:1.0	.	.	.	.	X	2469	.	ENSP00000386759:K2469X	K	-	1	0	SETD2	47036280	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.701000	0.84566	2.367000	0.80283	0.528000	0.53228	AAA	.	.	.	none		0.428	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		A	47061276	T	A	47061276	4	1	110	1	0	0	0	0	0	1	0	0	14144	1792	62	5	301	5	SETD2	3	47061276	Nonsense_Mutation	SNP	T	TCGA-BQ-5875-01A-11D-1589-08	10473508	47061276	150961154	16	7079											
NPRL2	10641	hgsc.bcm.edu	37	chr3	50386372	50386372	+	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	ctttggtaaagacaggtacaTcatactcctgggccaccgga	11	9	10	11	1	1	1	1	0	0	1	2	2	2	2	3	4	2	2	3	4	4	4			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr3:50386372T>A	ENST00000232501.3	-	5	956	c.518A>T	c.(517-519)gAt>gTt	p.D173V	CYB561D2_ENST00000418577.1_5'Flank|NPRL2_ENST00000493465.1_5'Flank|ZMYND10_ENST00000231749.3_5'Flank|CYB561D2_ENST00000232508.5_5'Flank|XXcos-LUCA11.5_ENST00000606589.1_5'Flank|CYB561D2_ENST00000424512.1_5'Flank|CYB561D2_ENST00000425346.1_5'Flank	NM_006545.4	NP_006536.3	Q8WTW4	NPRL2_HUMAN	nitrogen permease regulator-like 2 (S. cerevisiae)	173					negative regulation of kinase activity (GO:0033673)|protein phosphorylation (GO:0006468)		GTPase activator activity (GO:0005096)|protein kinase activity (GO:0004672)			breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|urinary_tract(1)	11						GACAGGTACATCATACTCCTG	0.537																																					p.D173V		Atlas-SNP	.											NPRL2,NS,carcinoma,0,1	NPRL2	27	.	0			c.A518T						PASS	.						133	126	128					3																	50386372		2203	4300	6503	SO:0001583	missense	10641	exon5			GGTACATCATACT	AF040708	CCDS2826.1	3p21.3	2010-03-30	2010-03-30	2010-03-30	ENSG00000114388	ENSG00000114388			24969	protein-coding gene	gene with protein product		607072	"tumor suppressor candidate 4"	TUSC4		11085536	Standard	NM_006545		Approved	NPR2L, NPR2	uc003daj.1	Q8WTW4	OTTHUMG00000156864	ENST00000232501.3:c.518A>T	chr3.hg19:g.50386372T>A	ENSP00000232501:p.Asp173Val	165.0	1.0	.		149.0	107.0	.	NM_006545	A8K831|Q6FGS2|Q9Y249|Q9Y497	Missense_Mutation	SNP	ENST00000232501.3	hg19	CCDS2826.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.945242	0.73672	.	.	ENSG00000114388	ENST00000232501	.	.	.	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.72534	0.3472	M	0.80422	2.495	0.80722	D	1	P	0.51057	0.941	P	0.51016	0.656	T	0.73113	-0.4085	9	0.30854	T	0.27	-20.1441	15.7486	0.77967	0.0:0.0:0.0:1.0	.	173	Q8WTW4	NPRL2_HUMAN	V	173	.	ENSP00000232501:D173V	D	-	2	0	NPRL2	50361376	1.000000	0.71417	0.990000	0.47175	0.940000	0.58332	7.968000	0.87980	2.122000	0.65172	0.533000	0.62120	GAT	.	.	.	none		0.537	NPRL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346299.1	NM_006545		A	50386372	T	A	50386372	3	1	110	1	0	0	0	0	1	0	0	0	10604	1435	50	5	652	5	NPRL2	3	50386372	Missense_Mutation	SNP	T	TCGA-BQ-5875-01A-11D-1589-08	3325096	50386372	147636058	17	7080											
BAP1	8314	hgsc.bcm.edu	37	chr3	52441190	52441190	+	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	ctccagctcatggtgcctacCatggtcaatggggtagacct	8	10	11	12	0	2	1	2	0	0	1	3	1	3	1	4	4	3	2	4	4	3	2			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr3:52441190C>T	ENST00000460680.1	-	7	1051	c.580G>A	c.(580-582)Ggg>Agg	p.G194R	BAP1_ENST00000296288.5_Splice_Site_p.G194R	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.?(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		TGGTGCCTACCATGGTCAATG	0.597			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.G194R	GBM(101;493 1458 7992 21037 25532)	Atlas-SNP	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	1	Unknown(1)	eye(1)	c.G580A						PASS	.						59	57	58					3																	52441190		2203	4300	6503	SO:0001630	splice_region_variant	8314	exon7			GCCTACCATGGTC	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.580+1G>A	chr3.hg19:g.52441190C>T		66.0	0.0	.		52.0	34.0	.	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Missense_Mutation	SNP	ENST00000460680.1	hg19	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	C	35	5.425433	0.96131	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	T;T	0.66995	-0.24;-0.24	6.05	6.05	0.98169	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (3);	0.000000	0.85682	D	0.000000	D	0.86756	0.6009	M	0.91038	3.17	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87932	0.2711	10	0.66056	D	0.02	-7.544	20.6086	0.99469	0.0:1.0:0.0:0.0	.	194	Q92560	BAP1_HUMAN	R	194	ENSP00000417132:G194R;ENSP00000296288:G194R	ENSP00000296288:G194R	G	-	1	0	BAP1	52416230	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.783000	0.85696	2.880000	0.98712	0.655000	0.94253	GGG	.	.	.	none		0.597	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1		Missense_Mutation	T	52441190	C	T	52441190	5	4	110	1	0	0	0	0	0	0	1	0	1311	608	21	2	1653	2	BAP1	3	52441190	Splice_Site	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	2054818	52441190	145581240	18	7081											
ZBTB11	27107	hgsc.bcm.edu	37	chr3	101378652	101378652	+	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	atgcatgtggctttacacctGtgtgctttaacatatgtatt	9	17	8	7	0	0	0	0	0	0	0	0	0	0	0	1	1	4	4	1	1	4	7			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr3:101378652G>C	ENST00000312938.4	-	6	2601	c.2021C>G	c.(2020-2022)aCa>aGa	p.T674R	Y_RNA_ENST00000364251.1_RNA	NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	674					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						CTTTACACCTGTGTGCTTTAA	0.373																																					p.T674R		Atlas-SNP	.											.	ZBTB11	77	.	0			c.C2021G						PASS	.						118	117	117					3																	101378652		2203	4300	6503	SO:0001583	missense	27107	exon6			ACACCTGTGTGCT	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.2021C>G	chr3.hg19:g.101378652G>C	ENSP00000326200:p.Thr674Arg	125.0	0.0	.		99.0	36.0	.	NM_014415	Q2NKP9	Missense_Mutation	SNP	ENST00000312938.4	hg19	CCDS2943.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.560004	0.86335	.	.	ENSG00000066422	ENST00000312938	T	0.25749	1.78	5.09	5.09	0.68999	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.054542	0.64402	D	0.000001	T	0.47838	0.1467	L	0.52206	1.635	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.48103	-0.9064	10	0.87932	D	0	-12.7873	18.48	0.90808	0.0:0.0:1.0:0.0	.	674	O95625	ZBT11_HUMAN	R	674	ENSP00000326200:T674R	ENSP00000326200:T674R	T	-	2	0	ZBTB11	102861342	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.181000	0.94874	2.387000	0.81309	0.491000	0.48974	ACA	.	.	.	none		0.373	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415		C	101378652	G	C	101378652	3	2	110	1	0	0	0	0	1	0	0	0	17536	1377	48	4	1164	4	ZBTB11	3	101378652	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	48937462	101378652	96643778	19	7082											
KCTD8	386617	hgsc.bcm.edu	37	chr4	44450342	44450342	+	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	catgctggccaaagtactgtCcgggacgctgagcagcgtcg	8	7	14	12	4	0	1	0	1	0	0	2	2	1	2	2	2	4	4	2	2	2	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr4:44450342C>T	ENST00000360029.3	-	1	482	c.199G>A	c.(199-201)Gac>Aac	p.D67N	AC131951.1_ENST00000584757.1_RNA	NM_198353.2	NP_938167.1	Q6ZWB6	KCTD8_HUMAN	potassium channel tetramerization domain containing 8	67	BTB.				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						AAAGTACTGTCCGGGACGCTG	0.682										HNSCC(17;0.042)																											p.D67N		Atlas-SNP	.											.	KCTD8	96	.	0			c.G199A						PASS	.						25	21	22					4																	44450342		2190	4277	6467	SO:0001583	missense	386617	exon1			TACTGTCCGGGAC	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.199G>A	chr4.hg19:g.44450342C>T	ENSP00000353129:p.Asp67Asn	23.0	0.0	.		36.0	14.0	.	NM_198353	A2RU39	Missense_Mutation	SNP	ENST00000360029.3	hg19	CCDS3467.1	.	.	.	.	.	.	.	.	.	.	C	16.67	3.187972	0.57909	.	.	ENSG00000183783	ENST00000360029	T	0.46451	0.87	3.59	3.59	0.41128	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.64402	D	0.000001	T	0.34337	0.0894	L	0.28014	0.82	0.58432	D	0.999992	B	0.31640	0.333	B	0.37091	0.241	T	0.28902	-1.0029	10	0.42905	T	0.14	.	14.3619	0.66779	0.0:1.0:0.0:0.0	.	67	Q6ZWB6	KCTD8_HUMAN	N	67	ENSP00000353129:D67N	ENSP00000353129:D67N	D	-	1	0	KCTD8	44145099	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.682000	0.68182	1.810000	0.52873	0.467000	0.42956	GAC	.	.	.	none		0.682	KCTD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216868.1			T	44450342	C	T	44450342	3	4	110	1	0	0	0	0	1	0	0	0	8122	855	30	2	1230	2	KCTD8	4	44450342	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08		44450342	146703934	20	7083											
TMEM144	55314	hgsc.bcm.edu	37	chr4	159138552	159138552	+	Frame_Shift_Del	DEL	A	A	-																															tggggatcatttaatgccttAactggctgggcaagctcaag																										TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr4:159138552delA	ENST00000296529.6	+	5	832	c.312delA	c.(310-312)ttafs	p.L104fs	TMEM144_ENST00000514558.1_Frame_Shift_Del_p.L104fs	NM_018342.4	NP_060812.2	Q7Z5S9	TM144_HUMAN	transmembrane protein 144	104						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)		TTAATGCCTTAACTGGCTGGG	0.378																																					p.L104X		Atlas-INDEL	.											.	TMEM144	34	.	0			c.311delT						PASS	.						110	105	107					4																	159138552		2203	4300	6503	SO:0001589	frameshift_variant	55314	exon5			.	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.312delA	chr4.hg19:g.159138552delA	ENSP00000296529:p.Leu104fs	92.0	0.0	0		62.0	26.0	0.419355	NM_018342	D3DP24|Q49A05|Q9NUT3	Frame_Shift_Del	DEL	ENST00000296529.6	hg19	CCDS3799.1																																																																																			.	.	.	none		0.378	TMEM144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365597.1	NM_018342		-	159138552	A	-	159138552	7	5	110	1	0	1	0	1	0	0	0	0	16070	359	13	0	322	0	TMEM144	4	159138552	Frame_Shift_Del	DEL	A	TCGA-BQ-5875-01A-11D-1589-08	114688210	159138552	32015724	21	7084											
CDC20B	166979	hgsc.bcm.edu	37	chr5	54429246	54429246	+	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	aaatgataacttacagtagtCatttcgaagaccagtaatat	17	12	6	6	1	1	2	1	1	0	1	2	3	1	2	1	0	2	2	1	0	7	6			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr5:54429246C>A	ENST00000381375.2	-	6	836	c.691G>T	c.(691-693)Gac>Tac	p.D231Y	CDC20B_ENST00000296733.1_Missense_Mutation_p.D231Y|CDC20B_ENST00000334206.5_Missense_Mutation_p.D231Y|CDC20B_ENST00000322374.6_Missense_Mutation_p.D231Y			Q86Y33	CD20B_HUMAN	cell division cycle 20B	231										kidney(1)|large_intestine(5)|lung(7)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	19		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			TTACAGTAGTCATTTCGAAGA	0.353																																					p.D231Y		Atlas-SNP	.											.	CDC20B	61	.	0			c.G691T						PASS	.						99	100	100					5																	54429246		2203	4300	6503	SO:0001583	missense	166979	exon6			AGTAGTCATTTCG	AB086378	CCDS3966.1, CCDS47207.1, CCDS54852.1	5q11.2	2013-01-17	2013-01-17		ENSG00000164287	ENSG00000164287		"WD repeat domain containing"	24222	protein-coding gene	gene with protein product			"CDC20 cell division cycle 20 homolog B (S. cerevisiae)", "cell division cycle 20 homolog B (S. cerevisiae)"				Standard	NM_152623		Approved	FLJ37927	uc003jpo.2	Q86Y33	OTTHUMG00000131185	ENST00000381375.2:c.691G>T	chr5.hg19:g.54429246C>A	ENSP00000370781:p.Asp231Tyr	139.0	0.0	.		99.0	37.0	.	NM_001170402	B7WNV8|B9EGL8|C9J6X8|C9JHE9|C9JKL5|Q86Y31|Q86Y32|Q8IUZ8|Q8N1S1|Q8NG56	Missense_Mutation	SNP	ENST00000381375.2	hg19	CCDS54852.1	.	.	.	.	.	.	.	.	.	.	C	18.52	3.642068	0.67244	.	.	ENSG00000164287	ENST00000334206;ENST00000296733;ENST00000381375;ENST00000322374	T;T;T;T	0.10099	2.91;2.91;2.91;2.91	4.97	4.1	0.47936	WD40 repeat-like-containing domain (1);	0.000000	0.49305	D	0.000156	T	0.41789	0.1174	M	0.93328	3.405	0.80722	D	1	D;D;P;D	0.89917	0.999;0.97;0.949;1.0	D;P;P;D	0.74348	0.976;0.808;0.648;0.983	T	0.56607	-0.7951	10	0.87932	D	0	-6.0811	13.2244	0.59907	0.0:0.9223:0.0:0.0777	.	231;231;231;231	Q86Y33-4;Q86Y33-3;Q86Y33;Q86Y33-2	.;.;CD20B_HUMAN;.	Y	231	ENSP00000335664:D231Y;ENSP00000296733:D231Y;ENSP00000370781:D231Y;ENSP00000315720:D231Y	ENSP00000296733:D231Y	D	-	1	0	CDC20B	54465003	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.180000	0.65048	1.303000	0.44873	0.650000	0.86243	GAC	.	.	.	none		0.353	CDC20B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369715.1	NM_152623		A	54429246	C	A	54429246	3	1	110	1	0	0	0	0	1	0	0	0	3062	826	29	4	896	4	CDC20B	5	54429246	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08		54429246	126486014	22	7085											
OTP	23440	hgsc.bcm.edu	37	chr5	76932809	76932809	+	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	gttggccctgctgctggccgGcttggctggggttcgggccg	0	10	19	12	3	0	0	0	0	0	0	1	0	0	0	3	7	2	6	3	7	0	3	rs148662448	byFrequency	TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr5:76932809G>C	ENST00000306422.3	-	2	1422	c.284C>G	c.(283-285)gCc>gGc	p.A95G	OTP_ENST00000515716.1_5'UTR	NM_032109.2	NP_115485.1	Q5XKR4	OTP_HUMAN	orthopedia homeobox	95					forebrain neuron differentiation (GO:0021879)|hypothalamus cell differentiation (GO:0021979)|neurohypophysis development (GO:0021985)|positive regulation of neuroblast proliferation (GO:0002052)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|pancreas(1)	13		all_lung(232;0.00051)|Lung NSC(167;0.000601)|Ovarian(174;0.0105)|Prostate(461;0.214)		OV - Ovarian serous cystadenocarcinoma(54;9.04e-51)|Epithelial(54;1.62e-45)|all cancers(79;4.4e-41)		CTGCTGGCCGGCTTGGCTGGG	0.677																																					p.A95G		Atlas-SNP	.											.	OTP	29	.	0			c.C284G						PASS	.						56	64	61					5																	76932809		2203	4300	6503	SO:0001583	missense	23440	exon2			TGGCCGGCTTGGC		CCDS4039.1	5q14.1	2011-06-20	2007-02-15		ENSG00000171540	ENSG00000171540		"Homeoboxes / PRD class"	8518	protein-coding gene	gene with protein product		604529	"orthopedia homolog (Drosophila)"			10458915	Standard	NM_032109		Approved		uc003kfg.3	Q5XKR4	OTTHUMG00000102171	ENST00000306422.3:c.284C>G	chr5.hg19:g.76932809G>C	ENSP00000302814:p.Ala95Gly	141.0	0.0	.		152.0	49.0	.	NM_032109		Missense_Mutation	SNP	ENST00000306422.3	hg19	CCDS4039.1	.	.	.	.	.	.	.	.	.	.	G	17.92	3.506573	0.64410	.	.	ENSG00000171540	ENST00000306422	D	0.95588	-3.75	5.42	4.53	0.55603	Homeodomain-related (1);Homeodomain-like (1);	1.125700	0.06735	N	0.777347	D	0.90143	0.6920	N	0.08118	0	0.36166	D	0.848472	B	0.06786	0.001	B	0.04013	0.001	T	0.76332	-0.2998	10	0.21014	T	0.42	.	15.0725	0.72049	0.0:0.1428:0.8572:0.0	.	95	Q5XKR4	OTP_HUMAN	G	95	ENSP00000302814:A95G	ENSP00000302814:A95G	A	-	2	0	OTP	76968565	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	4.154000	0.58125	1.376000	0.46267	0.655000	0.94253	GCC	.	G|0.995;A|0.005	.	alt		0.677	OTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220016.2			C	76932809	G	C	76932809	3	2	110	1	0	0	0	0	1	0	0	0	11317	1203	42	4	701	4	OTP	5	76932809	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	22503563	76932809	103982451	23	7086											
AFF4	27125	hgsc.bcm.edu	37	chr5	132270292	132270292	+	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	ctgctcccactattgttataTgactcacggtcgtgcctctg	6	14	8	13	2	2	1	1	1	1	0	4	1	3	1	2	1	2	2	2	1	3	4			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr5:132270292T>G	ENST00000265343.5	-	3	844	c.465A>C	c.(463-465)tcA>tcC	p.S155S	AFF4_ENST00000491831.1_5'UTR|AFF4_ENST00000378595.3_Silent_p.S155S	NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	155	Ser-rich.				spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)		SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TATTGTTATATGACTCACGGT	0.522																																					p.S155S	Ovarian(126;889 1733 2942 10745 11605)	Atlas-SNP	.											.	AFF4	120	.	0			c.A465C						PASS	.						146	141	143					5																	132270292		2203	4300	6503	SO:0001819	synonymous_variant	27125	exon3			GTTATATGACTCA	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.465A>C	chr5.hg19:g.132270292T>G		183.0	0.0	.		147.0	65.0	.	NM_014423	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Silent	SNP	ENST00000265343.5	hg19	CCDS4164.1																																																																																			.	.	.	none		0.522	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133049.1	NM_014423		G	132270292	T	G	132270292	2	3	110	1	0	0	0	0	0	0	0	1	359	1451	51	5		5	AFF4	5	132270292	Silent	SNP	T	TCGA-BQ-5875-01A-11D-1589-08	55337483	132270292	48644968	24	7087											
CDHR2	54825	hgsc.bcm.edu	37	chr5	175995765	175995765	+	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	gccccaatgcctacttcttcGctgtcactccgaaaactggg	8	10	8	15	2	2	0	1	0	1	0	4	1	3	0	4	1	3	1	4	1	4	3			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr5:175995765G>T	ENST00000510636.1	+	4	485	c.211G>T	c.(211-213)Gct>Tct	p.A71S	CDHR2_ENST00000506348.1_Missense_Mutation_p.A71S|CDHR2_ENST00000261944.5_Missense_Mutation_p.A71S	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	71	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						CTACTTCTTCGCTGTCACTCC	0.612																																					p.A71S		Atlas-SNP	.											CDHR2,colon,carcinoma,0,1	CDHR2	152	.	0			c.G211T						PASS	.						93	92	92					5																	175995765		2203	4300	6503	SO:0001583	missense	54825	exon4			TTCTTCGCTGTCA	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.211G>T	chr5.hg19:g.175995765G>T	ENSP00000424565:p.Ala71Ser	125.0	1.0	.		123.0	7.0	.	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	hg19	CCDS34297.1	.	.	.	.	.	.	.	.	.	.	G	2.961	-0.214546	0.06101	.	.	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.60171	0.21;0.21;0.21	4.8	-8.08	0.01094	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.17492	0.0420	N	0.01284	-0.91	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.25847	-1.0120	9	0.07990	T	0.79	0.5066	4.5371	0.12038	0.2851:0.0:0.3045:0.4103	.	71	Q9BYE9	CDHR2_HUMAN	S	71	ENSP00000424565:A71S;ENSP00000261944:A71S;ENSP00000421078:A71S	ENSP00000261944:A71S	A	+	1	0	CDHR2	175928371	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-2.753000	0.00791	-0.928000	0.03761	-1.233000	0.01565	GCT	.	.	.	none		0.612	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675		T	175995765	G	T	175995765	3	4	110	1	0	0	0	0	1	0	0	0	3121	1087	38	4	221	4	CDHR2	5	175995765	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	43725473	175995765	4919495	25	7088											
DST	667	hgsc.bcm.edu	37	chr6	56480769	56480769	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tatgcaaagcttcggccaccCggtactttttgccagtaaga	10	11	9	11	2	0	1	0	0	0	1	1	1	0	1	3	2	4	4	3	2	4	6	rs148062292		TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr6:56480769C>T	ENST00000370765.6	-	24	7603	c.7496G>A	c.(7495-7497)cGg>cAg	p.R2499Q	DST_ENST00000312431.6_Intron|DST_ENST00000244364.6_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000370769.4_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000361203.3_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	1795					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)			TTCGGCCACCCGGTACTTTTT	0.512																																					p.R2499Q		Atlas-SNP	.											.	DST	1427	.	0			c.G7496A						PASS	.	C	GLN/ARG,	0,4406		0,0,2203	71	77	75		7496,	5.9	1	6	dbSNP_134	75	1,8599	1.2+/-3.3	0,1,4299	no	missense,intron	DST	NM_001723.5,NM_015548.4	43,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	2499/2650,	56480769	1,13005	2203	4300	6503	SO:0001583	missense	667	exon24			GCCACCCGGTACT	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.7496G>A	chr6.hg19:g.56480769C>T	ENSP00000359801:p.Arg2499Gln	141.0	0.0	.		114.0	44.0	.	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000370765.6	hg19	CCDS4959.1	.	.	.	.	.	.	.	.	.	.	C	9.658	1.143434	0.21205	0.0	1.16E-4	ENSG00000151914	ENST00000370765	T	0.72725	-0.68	5.94	5.94	0.96194	.	.	.	.	.	T	0.55033	0.1895	.	.	.	0.09310	N	0.999998	B	0.29253	0.239	B	0.15870	0.014	T	0.58730	-0.7585	7	0.66056	D	0.02	.	20.3593	0.98849	0.0:1.0:0.0:0.0	.	2499	Q03001-3	.	Q	2499	ENSP00000359801:R2499Q	ENSP00000359801:R2499Q	R	-	2	0	DST	56588728	0.989000	0.36119	0.993000	0.49108	0.251000	0.25915	3.295000	0.51794	2.822000	0.97130	0.557000	0.71058	CGG	.	C|1.000;T|0.000	0.000	weak		0.512	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723		T	56480769	C	T	56480769	3	4	110	1	0	0	0	0	1	0	0	0	4785	652	23	1	12903	1	DST	6	56480769	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08		56480769	114634298	26	7089											
SEPT7	989	hgsc.bcm.edu	37	chr7	35930341	35930341	+	Frame_Shift_Del	DEL	A	A	-																															tatgagaactacagaagcagAaaacttgcagctgtgactta																										TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr7:35930341delA	ENST00000435235.1	+	10	1209	c.777delA	c.(775-777)agafs	p.R259fs	SEPT7_ENST00000494488.2_Frame_Shift_Del_p.R298fs|SEPT7_ENST00000399035.3_Frame_Shift_Del_p.R311fs|SEPT7_ENST00000432293.2_Intron|SEPT7_ENST00000399034.2_Frame_Shift_Del_p.R313fs|SEPT7_ENST00000350320.6_Frame_Shift_Del_p.R311fs			Q16181	SEPT7_HUMAN	septin 7	312	Septin-type G.				cilium morphogenesis (GO:0060271)|cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein heterooligomerization (GO:0051291)|regulation of embryonic cell shape (GO:0016476)	actin cytoskeleton (GO:0015629)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|septin complex (GO:0031105)|stress fiber (GO:0001725)	GTP binding (GO:0005525)|identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)	14						ACAGAAGCAGAAAACTTGCAG	0.333																																					p.R311fs		Atlas-INDEL	.											.	SEPT7	24	.	0			c.932delG						PASS	.						51	46	48					7																	35930341		1835	4089	5924	SO:0001589	frameshift_variant	989	exon10			.	S72008	CCDS75582.1	7p14.2	2013-01-21	2005-01-11	2005-01-12	ENSG00000122545	ENSG00000122545		"Septins"	1717	protein-coding gene	gene with protein product		603151	"CDC10 cell division cycle 10 homolog (S. cerevisiae)"	CDC10		8037772	Standard	NM_001788		Approved	CDC3, SEPT7A	uc011kau.2	Q16181	OTTHUMG00000155063	ENST00000435235.1:c.777delA	chr7.hg19:g.35930341delA	ENSP00000413507:p.Arg259fs	30.0	0.0	0		31.0	15.0	0.483871	NM_001011553	Q52M76|Q6NX50	Frame_Shift_Del	DEL	ENST00000435235.1	hg19																																																																																				.	.	.	none		0.333	SEPT7-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000338285.1	NM_001788		-	35930341	A	-	35930341	7	5	110	1	0	1	0	1	0	0	0	0	14082	243	9	0	972	0	SEPT7	7	35930341	Frame_Shift_Del	DEL	A	TCGA-BQ-5875-01A-11D-1589-08		35930341	123208322	27	7090	79	2									
SEPT7	989	hgsc.bcm.edu	37	chr7	35930344	35930344	+	Missense_Mutation	SNP	A	A	T																															gagaactacagaagcagaaaActtgcagctgtgacttataa																										TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr7:35930344A>T	ENST00000435235.1	+	10	1212	c.780A>T	c.(778-780)aaA>aaT	p.K260N	SEPT7_ENST00000494488.2_Missense_Mutation_p.K299N|SEPT7_ENST00000399035.3_Missense_Mutation_p.K312N|SEPT7_ENST00000432293.2_Intron|SEPT7_ENST00000399034.2_Missense_Mutation_p.K314N|SEPT7_ENST00000350320.6_Missense_Mutation_p.K312N			Q16181	SEPT7_HUMAN	septin 7	313	Septin-type G.				cilium morphogenesis (GO:0060271)|cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein heterooligomerization (GO:0051291)|regulation of embryonic cell shape (GO:0016476)	actin cytoskeleton (GO:0015629)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|septin complex (GO:0031105)|stress fiber (GO:0001725)	GTP binding (GO:0005525)|identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)	14						GAAGCAGAAAACTTGCAGCTG	0.338																																					p.K312N		Atlas-SNP	.											.	SEPT7	24	.	0			c.A936T						PASS	.						51	46	48					7																	35930344		1836	4089	5925	SO:0001583	missense	989	exon10			CAGAAAACTTGCA	S72008	CCDS75582.1	7p14.2	2013-01-21	2005-01-11	2005-01-12	ENSG00000122545	ENSG00000122545		"Septins"	1717	protein-coding gene	gene with protein product		603151	"CDC10 cell division cycle 10 homolog (S. cerevisiae)"	CDC10		8037772	Standard	NM_001788		Approved	CDC3, SEPT7A	uc011kau.2	Q16181	OTTHUMG00000155063	ENST00000435235.1:c.780A>T	chr7.hg19:g.35930344A>T	ENSP00000413507:p.Lys260Asn	30.0	0.0	.		27.0	15.0	.	NM_001011553	Q52M76|Q6NX50	Missense_Mutation	SNP	ENST00000435235.1	hg19		.	.	.	.	.	.	.	.	.	.	A	15.31	2.797066	0.50208	.	.	ENSG00000122545	ENST00000435235;ENST00000399034;ENST00000350320;ENST00000399035;ENST00000537785;ENST00000493670;ENST00000494488	T;T;T;T;T	0.54479	0.57;0.57;0.57;0.57;0.57	4.94	0.725	0.18242	.	0.000000	0.85682	U	0.000000	T	0.52338	0.1728	M	0.71920	2.185	0.80722	D	1	P;P;P	0.38420	0.63;0.63;0.63	B;B;B	0.42625	0.393;0.393;0.393	T	0.54364	-0.8305	10	0.62326	D	0.03	.	9.3111	0.37905	0.7223:0.0:0.2777:0.0	.	258;312;313	B4DNE4;E7EPK1;Q16181	.;.;SEPT7_HUMAN	N	260;314;312;312;258;260;299	ENSP00000413507:K260N;ENSP00000381992:K314N;ENSP00000344868:K312N;ENSP00000381993:K312N;ENSP00000438395:K299N	ENSP00000344868:K312N	K	+	3	2	SEPT7	35896869	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.373000	0.34272	0.300000	0.22699	0.460000	0.39030	AAA	.	.	.	none		0.338	SEPT7-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000338285.1	NM_001788		T	35930344	A	T	35930344	3	4	110	1	0	0	0	0	1	0	0	0	14082	40	2	5	975	5	SEPT7	7	35930344	Missense_Mutation	SNP	A	TCGA-BQ-5875-01A-11D-1589-08	3	35930344	123208319	28	7091	79	2									
FOXP2	93986	hgsc.bcm.edu	37	chr7	114299729	114299729	+	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	gtaatgcagcaacttggaagGtaactacttttccagcagtt	12	12	9	8	0	0	0	0	0	0	0	1	1	1	1	1	2	6	6	1	2	5	7			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr7:114299729G>A	ENST00000393494.2	+	13	1926		c.e13+1		FOXP2_ENST00000403559.4_Splice_Site|FOXP2_ENST00000350908.4_Splice_Site|FOXP2_ENST00000393491.3_Splice_Site|FOXP2_ENST00000393500.3_Splice_Site|FOXP2_ENST00000408937.3_Splice_Site|FOXP2_ENST00000393498.2_Splice_Site|FOXP2_ENST00000393489.3_Splice_Site			O15409	FOXP2_HUMAN	forkhead box P2						camera-type eye development (GO:0043010)|caudate nucleus development (GO:0021757)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|growth (GO:0040007)|lung alveolus development (GO:0048286)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of mesenchymal cell proliferation (GO:0002053)|post-embryonic development (GO:0009791)|putamen development (GO:0021758)|righting reflex (GO:0060013)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|vocal learning (GO:0042297)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						AACTTGGAAGGTAACTACTTT	0.388																																					.		Atlas-SNP	.											.	FOXP2	133	.	0			c.1647+1G>A						PASS	.						109	103	105					7																	114299729		2203	4300	6503	SO:0001630	splice_region_variant	93986	exon13			TGGAAGGTAACTA	U80741	CCDS5760.1, CCDS5761.1, CCDS43635.1, CCDS5761.2, CCDS55154.1	7q31	2008-07-18			ENSG00000128573	ENSG00000128573		"Forkhead boxes"	13875	protein-coding gene	gene with protein product	"trinucleotide repeat containing 10", "forkhead/winged-helix transcription factor", "speech and language disorder 1", "CAG repeat protein 44"	605317		TNRC10, SPCH1		11586359, 9225980	Standard	NM_014491		Approved	CAGH44	uc003vgz.3	O15409	OTTHUMG00000023131	ENST00000393494.2:c.1647+1G>A	chr7.hg19:g.114299729G>A		96.0	0.0	.		58.0	25.0	.	NM_014491	A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	Splice_Site	SNP	ENST00000393494.2	hg19	CCDS5760.1	.	.	.	.	.	.	.	.	.	.	G	16.68	3.189262	0.57909	.	.	ENSG00000128573	ENST00000393494;ENST00000408937;ENST00000403559;ENST00000350908;ENST00000393498;ENST00000393489;ENST00000393491	.	.	.	6.06	6.06	0.98353	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.6243	0.99512	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FOXP2	114086965	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.879000	0.98667	0.650000	0.86243	.	.	.	.	none		0.388	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1	NM_014491	Intron	A	114299729	G	A	114299729	5	1	110	1	0	0	0	0	0	0	1	0	6034	1275	44	2	1861	2	FOXP2	7	114299729	Splice_Site	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	78369385	114299729	44838934	29	7092											
SGK223	157285	hgsc.bcm.edu	37	chr8	8234118	8234118	+	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	tgggtcactgatagcgacacCgttggtccggcaggaaggag	9	7	16	9	3	1	1	1	1	0	0	2	4	2	3	2	5	1	2	2	5	2	2			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr8:8234118C>A	ENST00000520004.1	-	3	2065	c.1801G>T	c.(1801-1803)Ggt>Tgt	p.G601C	SGK223_ENST00000330777.4_Missense_Mutation_p.G601C			Q86YV5	SG223_HUMAN		603							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										ATAGCGACACCGTTGGTCCGG	0.662																																					p.G601C	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.G1801T						PASS	.						33	37	36					8																	8234118		1991	4172	6163	SO:0001583	missense	0	exon2			CGACACCGTTGGT																												ENST00000520004.1:c.1801G>T	chr8.hg19:g.8234118C>A	ENSP00000428054:p.Gly601Cys	76.0	0.0	.		88.0	23.0	.	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	hg19	CCDS43706.1	.	.	.	.	.	.	.	.	.	.	C	15.89	2.965915	0.53507	.	.	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.60299	0.2;0.2	4.16	3.28	0.37604	.	0.672928	0.13029	N	0.419511	T	0.62588	0.2440	L	0.29908	0.895	0.25653	N	0.986074	D	0.76494	0.999	D	0.65010	0.931	T	0.54077	-0.8347	10	0.72032	D	0.01	.	11.5527	0.50729	0.0:0.9104:0.0:0.0896	.	601	Q86YV5	SG223_HUMAN	C	601	ENSP00000330930:G601C;ENSP00000428054:G601C	ENSP00000330930:G601C	G	-	1	0	AC068353.1	8271528	0.017000	0.18338	0.019000	0.16419	0.011000	0.07611	0.576000	0.23744	1.057000	0.40506	0.467000	0.42956	GGT	.	.	.	none		0.662	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1			A	8234118	C	A	8234118	3	1	110	1	0	0	0	0	1	0	0	0	14223	652	23	4	2423	4	SGK223	8	8234118	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08		8234118	138129904	30	7093											
ZNF395	55893	hgsc.bcm.edu	37	chr8	28209093	28209093	+	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	cctgagggcagggaggactcCgggccaggatgttctgggcc	6	6	18	11	1	1	1	0	1	1	0	2	4	2	4	4	6	0	2	4	6	0	1	rs145491469	byFrequency	TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr8:28209093C>A	ENST00000344423.5	-	7	1283	c.1152G>T	c.(1150-1152)ccG>ccT	p.P384P	ZNF395_ENST00000523202.1_Silent_p.P384P|ZNF395_ENST00000523095.1_Silent_p.P384P	NM_018660.2	NP_061130.1	Q9H8N7	ZN395_HUMAN	zinc finger protein 395	384					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(5)|large_intestine(6)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.102)|Kidney(114;0.123)|Colorectal(74;0.142)		GGGAGGACTCCGGGCCAGGAT	0.642																																					p.P384P		Atlas-SNP	.											ZNF395,NS,carcinoma,0,1	ZNF395	54	.	0			c.G1152T						PASS	.						62	73	69					8																	28209093		2203	4299	6502	SO:0001819	synonymous_variant	55893	exon7			GGACTCCGGGCCA	AB044750	CCDS6067.1	8p21	2008-05-02			ENSG00000186918	ENSG00000186918		"Zinc fingers, C2H2-type"	18737	protein-coding gene	gene with protein product		609494				14625278	Standard	NM_018660		Approved	PRF-1, HDBP2, PBF, DKFZp434K1210	uc003xgr.3	Q9H8N7	OTTHUMG00000102137	ENST00000344423.5:c.1152G>T	chr8.hg19:g.28209093C>A		160.0	1.0	.		178.0	62.0	.	NM_018660	B3KUY7|D3DST4|Q6F6H2|Q9BY72|Q9NPB2|Q9NS57|Q9NS58|Q9NS59	Silent	SNP	ENST00000344423.5	hg19	CCDS6067.1																																																																																			.	C|1.000;T|0.000	.	alt		0.642	ZNF395-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219976.1			A	28209093	C	A	28209093	2	1	110	1	0	0	0	0	0	0	0	1	17893	639	23	4		4	ZNF395	8	28209093	Silent	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	19974975	28209093	118154929	31	7094											
PLEC	5339	hgsc.bcm.edu	37	chr8	144998457	144998457	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttgcgcggcctgctcctcCagccgccgccgctggaaggc	3	7	14	17	5	0	0	0	0	0	0	2	1	2	1	6	3	3	3	6	3	1	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr8:144998457C>T	ENST00000322810.4	-	31	6220	c.6051G>A	c.(6049-6051)ctG>ctA	p.L2017L	PLEC_ENST00000354958.2_Silent_p.L1858L|PLEC_ENST00000357649.2_Silent_p.L1884L|PLEC_ENST00000356346.3_Silent_p.L1866L|PLEC_ENST00000345136.3_Silent_p.L1880L|PLEC_ENST00000436759.2_Silent_p.L1907L|PLEC_ENST00000527096.1_Silent_p.L1903L|PLEC_ENST00000398774.2_Silent_p.L1848L|PLEC_ENST00000354589.3_Silent_p.L1880L	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2017	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						CCTGCTCCTCCAGCCGCCGCC	0.706																																					p.L2017L		Atlas-SNP	.											.	PLEC	1144	.	0			c.G6051A						PASS	.						7	9	8					8																	144998457		1983	4065	6048	SO:0001819	synonymous_variant	5339	exon31			CTCCTCCAGCCGC	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.6051G>A	chr8.hg19:g.144998457C>T		23.0	0.0	.		18.0	8.0	.	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	hg19	CCDS43772.1																																																																																			.	.	.	none		0.706	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		T	144998457	C	T	144998457	2	4	110	1	0	0	0	0	0	0	0	1	12059	581	21	2		2	PLEC	8	144998457	Silent	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	116789364	144998457	1365565	32	7095											
VPS13A	23230	hgsc.bcm.edu	37	chr9	79955424	79955424	+	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	aaataccatatatcagtggcTgaagaaggaaatgataaatg	19	9	9	4	0	1	3	1	2	0	1	1	4	1	4	1	2	1	1	1	2	9	4	rs144477984	byFrequency	TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr9:79955424T>A	ENST00000360280.3	+	50	7244	c.6984T>A	c.(6982-6984)gcT>gcA	p.A2328A	VPS13A_ENST00000376636.3_Silent_p.A2289A|VPS13A_ENST00000376634.4_Silent_p.A2328A|VPS13A_ENST00000357409.5_Silent_p.A2328A	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	2328					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						TATCAGTGGCTGAAGAAGGAA	0.333																																					p.A2328A		Atlas-SNP	.											.	VPS13A	735	.	0			c.T6984A						PASS	.						88	91	90					9																	79955424		2203	4295	6498	SO:0001819	synonymous_variant	23230	exon50			AGTGGCTGAAGAA	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.6984T>A	chr9.hg19:g.79955424T>A		122.0	0.0	.		91.0	42.0	.	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Silent	SNP	ENST00000360280.3	hg19	CCDS6655.1																																																																																			.	T|1.000;C|0.000	.	alt		0.333	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		A	79955424	T	A	79955424	2	1	110	1	0	0	0	0	0	0	0	1	17201	1567	55	5		5	VPS13A	9	79955424	Silent	SNP	T	TCGA-BQ-5875-01A-11D-1589-08		79955424	61258007	33	7096											
TLL2	7093	hgsc.bcm.edu	37	chr10	98136535	98136535	+	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	gtcaggccagttggggctcgCcagggtcccctccacactgc	5	7	13	16	1	1	0	1	0	0	0	4	0	3	0	5	4	1	2	5	4	0	1	rs150738442		TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr10:98136535C>A	ENST00000357947.3	-	18	2587	c.2362G>T	c.(2362-2364)Gcg>Tcg	p.A788S		NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	788	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(15)|lung(22)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	58		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		TTGGGGCTCGCCAGGGTCCCC	0.567																																					p.A788S		Atlas-SNP	.											.	TLL2	122	.	0			c.G2362T						PASS	.						66	66	66					10																	98136535		2203	4300	6503	SO:0001583	missense	7093	exon18			GGCTCGCCAGGGT	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.2362G>T	chr10.hg19:g.98136535C>A	ENSP00000350630:p.Ala788Ser	86.0	0.0	.		104.0	33.0	.	NM_012465	A6NDK0|Q2M1H1|Q6PJN5|Q9UQ00	Missense_Mutation	SNP	ENST00000357947.3	hg19	CCDS7449.1	.	.	.	.	.	.	.	.	.	.	C	11.34	1.609563	0.28623	.	.	ENSG00000095587	ENST00000357947	T	0.16897	2.31	4.98	4.07	0.47477	CUB (5);	1.170570	0.06454	N	0.728224	T	0.05044	0.0135	N	0.00666	-1.275	0.22842	N	0.998661	B	0.10296	0.003	B	0.11329	0.006	T	0.36648	-0.9739	10	0.17832	T	0.49	.	3.874	0.09048	0.193:0.6039:0.0:0.2031	.	788	Q9Y6L7	TLL2_HUMAN	S	788	ENSP00000350630:A788S	ENSP00000350630:A788S	A	-	1	0	TLL2	98126525	0.000000	0.05858	0.988000	0.46212	0.744000	0.42396	0.481000	0.22260	1.431000	0.47355	0.655000	0.94253	GCG	.	C|1.000;T|0.000	.	alt		0.567	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049608.1			A	98136535	C	A	98136535	3	1	110	1	0	0	0	0	1	0	0	0	15958	739	26	4	701	4	TLL2	10	98136535	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08		98136535	37398212	34	7097											
GBF1	8729	hgsc.bcm.edu	37	chr10	104130546	104130546	+	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	cacaagatttctgcttccttGtggagcgggcagtggtgggg	6	11	16	8	1	1	1	0	0	1	1	2	2	2	2	1	5	2	2	1	5	1	3	rs7894865	byFrequency	TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr10:104130546G>T	ENST00000369983.3	+	29	3846	c.3586G>T	c.(3586-3588)Gtg>Ttg	p.V1196L		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	1196					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		CTGCTTCCTTGTGGAGCGGGC	0.542																																					p.V1197L		Atlas-SNP	.											.	GBF1	142	.	0			c.G3589T						PASS	.						182	147	159					10																	104130546		2203	4300	6503	SO:0001583	missense	8729	exon29			TTCCTTGTGGAGC	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.3586G>T	chr10.hg19:g.104130546G>T	ENSP00000359000:p.Val1196Leu	133.0	0.0	.		101.0	40.0	.	NM_001199378	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	hg19	CCDS7533.1	.	.	.	.	.	.	.	.	.	.	G	10.48	1.360689	0.24598	.	.	ENSG00000107862	ENST00000369983	T	0.12569	2.67	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.22936	0.0554	N	0.17872	0.535	0.80722	D	1	B;B;D	0.58970	0.107;0.025;0.984	B;B;D	0.68192	0.037;0.016;0.956	T	0.05289	-1.0894	10	0.19590	T	0.45	-16.6116	19.277	0.94036	0.0:0.0:1.0:0.0	.	1196;1196;1196	Q149P1;Q149P0;Q92538	.;.;GBF1_HUMAN	L	1196	ENSP00000359000:V1196L	ENSP00000359000:V1196L	V	+	1	0	GBF1	104120536	1.000000	0.71417	1.000000	0.80357	0.625000	0.37756	7.674000	0.83992	2.782000	0.95742	0.655000	0.94253	GTG	.	G|0.996;A|0.004	.	alt		0.542	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			T	104130546	G	T	104130546	3	4	110	1	0	0	0	0	1	0	0	0	6278	1377	48	4	3696	4	GBF1	10	104130546	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	5994011	104130546	31404201	35	7098											
SUFU	51684	hgsc.bcm.edu	37	chr10	104353417	104353417	+	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	ttggtgtctgcactgaagagCtacactcagcccagcagtgg	9	9	12	11	0	2	2	1	1	1	1	2	2	2	2	1	2	5	3	1	2	2	2			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr10:104353417C>A	ENST00000369902.3	+	5	788	c.622C>A	c.(622-624)Cta>Ata	p.L208I	RNU6-43P_ENST00000384302.1_RNA|SUFU_ENST00000423559.2_Missense_Mutation_p.L208I|SUFU_ENST00000369899.2_Missense_Mutation_p.L208I|SUFU_ENST00000471000.1_3'UTR	NM_016169.3	NP_057253.2	Q9UMX1	SUFU_HUMAN	suppressor of fused homolog (Drosophila)	208					cytoplasmic sequestering of transcription factor (GO:0042994)|heart looping (GO:0001947)|multicellular organismal development (GO:0007275)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of transcription factor import into nucleus (GO:0042992)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|skin development (GO:0043588)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|primary cilium (GO:0072372)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(7)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(2)	24		Colorectal(252;0.207)		Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242)		CACTGAAGAGCTACACTCAGC	0.607			"D, F, S"		medulloblastoma	medulloblastoma			Medulloblastoma, associated with Germline SUFU Mutation																												p.L208I		Atlas-SNP	.	yes	Rec	yes	Medulloblastoma predisposition	10	10q24.32	51684	suppressor of fused homolog (Drosophila)		O	.	SUFU	44	.	0			c.C622A						PASS	.						99	83	89					10																	104353417		2203	4300	6503	SO:0001583	missense	51684	exon5	Familial Cancer Database		GAAGAGCTACACT	AF175770	CCDS7537.1, CCDS53571.1	10q24.32	2014-09-17			ENSG00000107882	ENSG00000107882			16466	protein-coding gene	gene with protein product		607035				15367681	Standard	NM_016169		Approved	SUFUH, SUFUXL, PRO1280	uc001kvy.2	Q9UMX1	OTTHUMG00000018966	ENST00000369902.3:c.622C>A	chr10.hg19:g.104353417C>A	ENSP00000358918:p.Leu208Ile	89.0	0.0	.		73.0	39.0	.	NM_001178133	Q7LCP7|Q9NT90|Q9NZ07|Q9UHK2|Q9UHM8|Q9UMY0	Missense_Mutation	SNP	ENST00000369902.3	hg19	CCDS7537.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.614385	0.87359	.	.	ENSG00000107882	ENST00000369902;ENST00000369899;ENST00000423559	D;D;D	0.83755	-1.76;-1.76;-1.76	6.08	4.21	0.49690	Suppressor of fused domain (1);	0.062987	0.64402	D	0.000004	D	0.91088	0.7195	M	0.93763	3.455	0.53005	D	0.999963	P;P;D	0.61697	0.816;0.78;0.99	P;P;P	0.61132	0.789;0.683;0.884	D	0.91841	0.5483	10	0.72032	D	0.01	-14.0459	8.8655	0.35282	0.0:0.7723:0.0:0.2277	.	208;208;208	Q9UMX1;Q9UMX1-2;Q9UMX1-3	SUFU_HUMAN;.;.	I	208	ENSP00000358918:L208I;ENSP00000358915:L208I;ENSP00000411597:L208I	ENSP00000358915:L208I	L	+	1	2	SUFU	104343407	1.000000	0.71417	0.997000	0.53966	0.958000	0.62258	2.022000	0.41030	1.557000	0.49525	0.655000	0.94253	CTA	.	.	.	none		0.607	SUFU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050089.1	NM_016169		A	104353417	C	A	104353417	3	1	110	1	0	0	0	0	1	0	0	0	15380	796	28	4	640	4	SUFU	10	104353417	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	222871	104353417	31181330	36	7099											
POLR2L	5441	hgsc.bcm.edu	37	chr11	840428	840428	+	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	gatcaggtccacgtgggccaGcagcatccggcggcagcagt	8	5	15	13	3	1	0	1	0	0	0	3	1	3	0	3	4	3	4	3	4	0	0			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr11:840428G>A	ENST00000322028.4	-	2	184	c.148C>T	c.(148-150)Ctg>Ttg	p.L50L	TSPAN4_ENST00000397397.2_5'Flank|TSPAN4_ENST00000397408.1_5'Flank|TSPAN4_ENST00000397396.1_5'Flank|TSPAN4_ENST00000397411.2_5'Flank	NM_021128.4	NP_066951.1	P62875	RPAB5_HUMAN	polymerase (RNA) II (DNA directed) polypeptide L, 7.6kDa	50					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)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|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)|zinc ion binding (GO:0008270)			lung(1)	1		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;4.1e-25)|Epithelial(43;3.15e-24)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		ACGTGGGCCAGCAGCATCCGG	0.637																																					p.L50L		Atlas-SNP	.											.	POLR2L	2	.	0			c.C148T						PASS	.						159	125	137					11																	840428		2203	4298	6501	SO:0001819	synonymous_variant	5441	exon2			GGGCCAGCAGCAT	U37690	CCDS7720.1	11p15	2013-01-21	2002-08-29		ENSG00000177700	ENSG00000177700		"RNA polymerase subunits"	9199	protein-coding gene	gene with protein product		601189	"polymerase (RNA) II (DNA directed) polypeptide L (7.6kD)"			8786124	Standard	NM_021128		Approved	RPB10beta, RBP10, RPABC5, RPB7.6, hRPB7.6, hsRPB10b	uc001lsc.3	P62875	OTTHUMG00000133316	ENST00000322028.4:c.148C>T	chr11.hg19:g.840428G>A		193.0	0.0	.		173.0	48.0	.	NM_021128	P52436|Q6FHX3	Silent	SNP	ENST00000322028.4	hg19	CCDS7720.1																																																																																			.	.	.	none		0.637	POLR2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257114.1	NM_021128		A	840428	G	A	840428	2	1	110	1	0	0	0	0	0	0	0	1	12234	962	34	2		2	POLR2L	11	840428	Silent	SNP	G	TCGA-BQ-5875-01A-11D-1589-08		840428	134166088	37	7100											
OR51A2	401667	hgsc.bcm.edu	37	chr11	4976463	4976469	+	Frame_Shift_Del	DEL	AGGGAAG	AGGGAAG	-																															gcttcttaaagtgaaagggaAgggaagaaccaggagcatgc																										TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	AGGGAAG	AGGGAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr11:4976463_4976469delAGGGAAG	ENST00000380371.1	-	1	474_480	c.475_481delCTTCCCT	c.(475-483)cttcccttcfs	p.LPF159fs	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004748.1	NP_001004748.1	Q8NGJ7	O51A2_HUMAN	olfactory receptor, family 51, subfamily A, member 2	159						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		GTGAAAGGGAAGGGAAGAACCAGGAGC	0.44																																					p.159_161del		Atlas-INDEL	.											.	OR51A2	40	.	0			c.476_482del						PASS	.																																			SO:0001589	frameshift_variant	401667	exon1			.	AB065797	CCDS31368.1	11p15.4	2012-08-09			ENSG00000205496	ENSG00000205496		"GPCR / Class A : Olfactory receptors"	14764	protein-coding gene	gene with protein product							Standard	NM_001004748		Approved		uc010qyt.2	Q8NGJ7	OTTHUMG00000066602	ENST00000380371.1:c.475_481delCTTCCCT	chr11.hg19:g.4976463_4976469delAGGGAAG	ENSP00000369729:p.Leu159fs	244.0	0.0	0		164.0	27.0	0.164634	NM_001004748		Frame_Shift_Del	DEL	ENST00000380371.1	hg19	CCDS31368.1																																																																																			.	.	.	none		0.44	OR51A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142809.1	NM_001004748		-	4976469	AGGGAAG	-	4976463	7	5	110	1	0	1	0	1	0	0	0	0	11093	72	3	0	462	0	OR51A2	11	4976463	Frame_Shift_Del	DEL	AGGGAAG	TCGA-BQ-5875-01A-11D-1589-08	4136035	4976463	130030053	38	7101											
SAAL1	113174	hgsc.bcm.edu	37	chr11	18101957	18101957	+	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	attcaggttttaagtctgaaCcttcaaacttgggaagtttt	11	16	8	6	0	3	1	2	1	1	0	3	2	3	2	1	2	2	2	1	2	4	7			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr11:18101957C>G	ENST00000524803.1	-	12	1463	c.1414G>C	c.(1414-1416)Gtt>Ctt	p.V472L	SAAL1_ENST00000300013.4_Missense_Mutation_p.V471L|SAAL1_ENST00000529318.1_Missense_Mutation_p.V474L			Q96ER3	SAAL1_HUMAN	serum amyloid A-like 1	472										breast(2)|large_intestine(5)|lung(8)	15						TAAGTCTGAACCTTCAAACTT	0.318																																					p.V472L		Atlas-SNP	.											.	SAAL1	34	.	0			c.G1414C						PASS	.						59	62	61					11																	18101957		2200	4293	6493	SO:0001583	missense	113174	exon12			TCTGAACCTTCAA	AK123457	CCDS31439.1	11p15.1	2005-10-28			ENSG00000166788	ENSG00000166788			25158	protein-coding gene	gene with protein product							Standard	NM_138421		Approved	FLJ41463	uc001mnq.3	Q96ER3	OTTHUMG00000166428	ENST00000524803.1:c.1414G>C	chr11.hg19:g.18101957C>G	ENSP00000432487:p.Val472Leu	102.0	0.0	.		68.0	16.0	.	NM_138421	A6NH05	Missense_Mutation	SNP	ENST00000524803.1	hg19	CCDS31439.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.29|11.29	1.595377|1.595377	0.28445|0.28445	.|.	.|.	ENSG00000166788|ENSG00000166788	ENST00000532452|ENST00000524803;ENST00000300013;ENST00000529318	.|T;T;T	.|0.32023	.|1.47;1.47;1.47	5.56|5.56	4.65|4.65	0.58169|0.58169	.|.	.|0.883413	.|0.10083	.|N	.|0.718158	T|T	0.25568|0.25568	0.0622|0.0622	L|L	0.40543|0.40543	1.245|1.245	0.25551|0.25551	N|N	0.987081|0.987081	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.08055	.|0.003;0.003;0.003	T|T	0.20207|0.20207	-1.0282|-1.0282	5|10	.|0.22109	.|T	.|0.4	-0.1106|-0.1106	9.5663|9.5663	0.39400|0.39400	0.0:0.783:0.1416:0.0753|0.0:0.783:0.1416:0.0753	.|.	.|474;472;472	.|E9PRZ1;G1UCX3;Q96ER3	.|.;.;SAAL1_HUMAN	S|L	130|472;471;474	.|ENSP00000432487:V472L;ENSP00000300013:V471L;ENSP00000432216:V474L	.|ENSP00000300013:V471L	R|V	-|-	3|1	2|0	SAAL1|SAAL1	18058533|18058533	0.998000|0.998000	0.40836|0.40836	0.998000|0.998000	0.56505|0.56505	0.389000|0.389000	0.30415|0.30415	1.161000|1.161000	0.31773|0.31773	1.485000|1.485000	0.48380|0.48380	0.549000|0.549000	0.68633|0.68633	AGG|GTT	.	.	.	none		0.318	SAAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389728.1	NM_138421		G	18101957	C	G	18101957	3	3	110	1	0	0	0	0	1	0	0	0	13814	507	18	4	14	4	SAAL1	11	18101957	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	13125494	18101957	116904559	39	7102											
GAB2	9846	hgsc.bcm.edu	37	chr11	77934564	77934564	+	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	gttgatgggtagccaagtgaGtcaaagtgatgggcccctgg	9	9	16	7	0	1	3	1	3	0	0	1	3	1	3	3	3	1	2	3	3	3	2			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr11:77934564G>A	ENST00000361507.4	-	6	1546	c.1461C>T	c.(1459-1461)gaC>gaT	p.D487D	GAB2_ENST00000340149.2_Silent_p.D449D	NM_080491.2	NP_536739.1	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2	487					cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mast cell degranulation (GO:0043306)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)		INTS4/GAB2(2)	NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)			AGCCAAGTGAGTCAAAGTGAT	0.557																																					p.D487D		Atlas-SNP	.											.	GAB2	63	.	0			c.C1461T						PASS	.						218	207	211					11																	77934564		2200	4292	6492	SO:0001819	synonymous_variant	9846	exon6			AAGTGAGTCAAAG	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.1461C>T	chr11.hg19:g.77934564G>A		270.0	0.0	.		229.0	70.0	.	NM_080491	A2RRM2|A6NEW9|A7MD36|O60317	Silent	SNP	ENST00000361507.4	hg19	CCDS8259.1																																																																																			.	.	.	none		0.557	GAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391085.1	NM_080491		A	77934564	G	A	77934564	2	1	110	1	0	0	0	0	0	0	0	1	6156	1020	36	2		2	GAB2	11	77934564	Silent	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	59832607	77934564	57071952	40	7103											
CASP5	838	hgsc.bcm.edu	37	chr11	104879534	104879534	+	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	tgtaaaatatccagtcttacTttttacactggtcgactttt	10	18	5	8	1	1	0	0	0	1	0	3	1	2	0	1	1	2	1	1	1	5	8			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr11:104879534T>G	ENST00000260315.3	-	2	180	c.181A>C	c.(181-183)Aaa>Caa	p.K61Q	CASP5_ENST00000393139.2_Splice_Site_p.K28Q|CASP5_ENST00000418434.1_Intron|CASP5_ENST00000444749.2_Intron|CASP5_ENST00000393141.2_Splice_Site_p.K74Q|CASP5_ENST00000526056.1_Splice_Site_p.K74Q|CASP5_ENST00000531367.1_Intron			P51878	CASP5_HUMAN	caspase 5, apoptosis-related cysteine peptidase	61	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				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)		CCAGTCTTACTTTTTACACTG	0.388																																					p.K74Q		Atlas-SNP	.											.	CASP5	213	.	0			c.A220C						PASS	.						101	95	97					11																	104879534		2202	4299	6501	SO:0001630	splice_region_variant	838	exon2			TCTTACTTTTTAC		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.181+1A>C	chr11.hg19:g.104879534T>G		83.0	0.0	.		58.0	23.0	.	NM_001136112	B4DKP5|Q0QVY7|Q0QVY8|Q0QVZ0|Q0QVZ1|Q0QVZ2|Q14DD6|Q1HBJ3|Q6DJV7	Missense_Mutation	SNP	ENST00000260315.3	hg19	CCDS8328.2	.	.	.	.	.	.	.	.	.	.	.	8.417	0.845448	0.16963	.	.	ENSG00000137757	ENST00000393141;ENST00000393139;ENST00000260315;ENST00000526056;ENST00000456094	T;T;T;T;T	0.26810	4.66;1.71;4.68;4.66;2.75	1.45	0.338	0.15974	DEATH-like (1);Caspase Recruitment (2);	0.671852	0.11352	U	0.572858	T	0.09642	0.0237	N	0.08118	0	0.09310	N	1	B;B	0.28636	0.218;0.183	B;B	0.21546	0.035;0.021	T	0.31916	-0.9926	9	.	.	.	.	3.7847	0.08695	0.0:0.7446:0.0:0.2554	.	61;74	P51878;P51878-5	CASP5_HUMAN;.	Q	74;28;61;74;45	ENSP00000376849:K74Q;ENSP00000376847:K28Q;ENSP00000260315:K61Q;ENSP00000436877:K74Q;ENSP00000415241:K45Q	.	K	-	1	0	CASP5	104384744	0.989000	0.36119	0.124000	0.21820	0.011000	0.07611	0.266000	0.18534	0.155000	0.19261	-0.182000	0.12963	AAA	.	.	.	none		0.388	CASP5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109397.2	NM_004347	Missense_Mutation	G	104879534	T	G	104879534	5	3	110	1	0	0	0	0	0	0	1	0	2676	1623	56	5	1155	5	CASP5	11	104879534	Splice_Site	SNP	T	TCGA-BQ-5875-01A-11D-1589-08	26944970	104879534	30126982	41	7104											
KDM5A	5927	hgsc.bcm.edu	37	chr12	404935	404935	+	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	gcaccaaagggctcttccgaGgttgtttccttggggtgcta	6	12	13	10	1	1	0	0	0	1	0	3	1	3	0	3	4	1	5	3	4	2	5			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr12:404935G>C	ENST00000399788.2	-	26	4621	c.4259C>G	c.(4258-4260)cCt>cGt	p.P1420R	KDM5A_ENST00000382815.4_Missense_Mutation_p.P1420R|KDM5A_ENST00000540838.1_5'Flank	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	1420					chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|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 coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						GCTCTTCCGAGGTTGTTTCCT	0.408			T	NUP98	AML																																p.P1420R		Atlas-SNP	.		Dom	yes		12	12p11	5927	"lysine (K)-specific demethylase 5A, JARID1A"		L	.	KDM5A	307	.	0			c.C4259G						PASS	.						97	94	95					12																	404935		1825	4074	5899	SO:0001583	missense	5927	exon26			TTCCGAGGTTGTT		CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	9886	protein-coding gene	gene with protein product		180202	"retinoblastoma-binding protein 2", "Jumonji, AT rich interactive domain 1A (RBBP2-like)", "jumonji, AT rich interactive domain 1A"	RBBP2, JARID1A		1857421	Standard	NM_001042603		Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.4259C>G	chr12.hg19:g.404935G>C	ENSP00000382688:p.Pro1420Arg	199.0	0.0	.		143.0	54.0	.	NM_001042603	A8MV76|Q4LE72|Q86XZ1	Missense_Mutation	SNP	ENST00000399788.2	hg19	CCDS41736.1	.	.	.	.	.	.	.	.	.	.	G	18.11	3.551819	0.65311	.	.	ENSG00000073614	ENST00000399788;ENST00000382815	D;D	0.85171	-1.95;-1.77	5.42	5.42	0.78866	.	0.118506	0.64402	D	0.000015	D	0.88254	0.6387	L	0.29908	0.895	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.85541	0.1215	10	0.25751	T	0.34	-15.9882	19.5762	0.95446	0.0:0.0:1.0:0.0	.	1420;1420	P29375;P29375-2	KDM5A_HUMAN;.	R	1420	ENSP00000382688:P1420R;ENSP00000372265:P1420R	ENSP00000372265:P1420R	P	-	2	0	KDM5A	275196	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.505000	0.97989	2.699000	0.92147	0.561000	0.74099	CCT	.	.	.	none		0.408	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397812.1	NM_005056		C	404935	G	C	404935	3	2	110	1	0	0	0	0	1	0	0	0	8140	1000	35	4	825	4	KDM5A	12	404935	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08		404935	133446960	42	7105											
AEBP2	121536	hgsc.bcm.edu	37	chr12	19615463	19615463	+	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	gcataagcagtactataatgGatgtagacagcacaatttcc	15	10	8	8	0	0	1	0	0	0	1	1	2	1	2	1	1	3	5	1	1	6	6			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr12:19615463G>C	ENST00000398864.3	+	2	717	c.691G>C	c.(691-693)Gat>Cat	p.D231H	AEBP2_ENST00000541908.1_Missense_Mutation_p.D2H|AEBP2_ENST00000266508.9_Missense_Mutation_p.D231H|AEBP2_ENST00000360995.4_Missense_Mutation_p.D15H	NM_001114176.1	NP_001107648.1	Q6ZN18	AEBP2_HUMAN	AE binding protein 2	231	Interaction with RBBP4.|Ser-rich.				chromatin modification (GO:0016568)	ESC/E(Z) complex (GO:0035098)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription corepressor activity (GO:0003714)			ovary(1)	1	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)|Esophageal squamous(101;0.143)					TACTATAATGGATGTAGACAG	0.328																																					p.D231H		Atlas-SNP	.											.	AEBP2	21	.	0			c.G691C						PASS	.						57	51	53					12																	19615463		1877	4113	5990	SO:0001583	missense	121536	exon2			ATAATGGATGTAG		CCDS44841.1, CCDS44842.1, CCDS58215.1	12p12.3	2012-10-02			ENSG00000139154	ENSG00000139154			24051	protein-coding gene	gene with protein product						10329662	Standard	NM_153207		Approved	MGC17922	uc001ref.2	Q6ZN18	OTTHUMG00000168906	ENST00000398864.3:c.691G>C	chr12.hg19:g.19615463G>C	ENSP00000381840:p.Asp231His	25.0	0.0	.		32.0	13.0	.	NM_001114176	Q59FS5|Q6ZN62|Q96BG3	Missense_Mutation	SNP	ENST00000398864.3	hg19	CCDS44841.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.961310	0.74016	.	.	ENSG00000139154	ENST00000538425;ENST00000541908;ENST00000398864;ENST00000435841;ENST00000266508;ENST00000360995	D;T;D;D;T	0.91631	-2.52;-0.65;-2.88;-2.88;-0.45	5.55	4.66	0.58398	.	.	.	.	.	D	0.91938	0.7447	N	0.24115	0.695	0.80722	D	1	D	0.71674	0.998	P	0.62885	0.908	D	0.93102	0.6509	9	0.66056	D	0.02	4.244	14.732	0.69388	0.0692:0.0:0.9308:0.0	.	231	Q6ZN18	AEBP2_HUMAN	H	2;2;231;165;231;15	ENSP00000444255:D2H;ENSP00000437983:D2H;ENSP00000381840:D231H;ENSP00000266508:D231H;ENSP00000354267:D15H	ENSP00000266508:D231H	D	+	1	0	AEBP2	19506730	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.263000	0.95617	1.578000	0.49821	0.655000	0.94253	GAT	.	.	.	none		0.328	AEBP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401575.1	NM_153207		C	19615463	G	C	19615463	3	2	110	1	0	0	0	0	1	0	0	0	350	1174	41	4	697	4	AEBP2	12	19615463	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	19210528	19615463	114236432	43	7106											
PFKM	5213	hgsc.bcm.edu	37	chr12	48538849	48538849	+	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	ccatttgataggaattttgcCactaagatgggcgccaaggc	11	10	11	9	1	0	2	0	1	0	1	0	3	0	3	3	3	1	0	3	3	4	5			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr12:48538849C>A	ENST00000312352.7	+	21	2067	c.2028C>A	c.(2026-2028)gcC>gcA	p.A676A	PFKM_ENST00000551804.1_Silent_p.A645A|PFKM_ENST00000340802.6_Silent_p.A747A|PFKM_ENST00000395233.2_Silent_p.A645A|PFKM_ENST00000359794.5_Silent_p.A676A|PFKM_ENST00000547587.1_Silent_p.A676A	NM_001166687.1	NP_001160159.1	P08237	PFKAM_HUMAN	phosphofructokinase, muscle	676	C-terminal regulatory PFK domain 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|muscle cell cellular homeostasis (GO:0046716)|positive regulation of insulin secretion (GO:0032024)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	6-phosphofructokinase complex (GO:0005945)|apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|sperm principal piece (GO:0097228)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|fructose binding (GO:0070061)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			NS(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						GGAATTTTGCCACTAAGATGG	0.473																																					p.A747A		Atlas-SNP	.											.	PFKM	117	.	0			c.C2241A						PASS	.						99	96	97					12																	48538849		2203	4300	6503	SO:0001819	synonymous_variant	5213	exon23			TTTTGCCACTAAG	M26066	CCDS8760.1, CCDS53786.1	12q13.11	2014-06-13					2.7.1.11		8877	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 122"	610681	"phosphofructokinase, polypeptide X"	PFKX			Standard	NM_001166686		Approved	PFK-1, PPP1R122	uc001rrb.2	P08237		ENST00000312352.7:c.2028C>A	chr12.hg19:g.48538849C>A		71.0	0.0	.		119.0	42.0	.	NM_001166686	J3KNX3|Q16814|Q16815|Q6ZTT1	Silent	SNP	ENST00000312352.7	hg19	CCDS8760.1																																																																																			.	.	.	none		0.473	PFKM-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406490.1	NM_000289		A	48538849	C	A	48538849	2	1	110	1	0	0	0	0	0	0	0	1	11772	581	21	4		4	PFKM	12	48538849	Silent	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	28923386	48538849	85313046	44	7107											
NCKAP1L	3071	hgsc.bcm.edu	37	chr12	54903761	54903761	+	Missense_Mutation	SNP	T	T	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	ccatgattaaccctgctaatTcagatacagtgagtgccctt	11	12	7	11	0	1	3	1	2	0	1	1	3	1	3	3	0	4	1	3	0	3	5			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr12:54903761T>G	ENST00000293373.6	+	7	806	c.727T>G	c.(727-729)Tca>Gca	p.S243A	NCKAP1L_ENST00000552211.1_3'UTR|NCKAP1L_ENST00000545638.2_Missense_Mutation_p.S193A	NM_005337.4	NP_005328.2	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	243					actin polymerization-dependent cell motility (GO:0070358)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|chemotaxis (GO:0006935)|cortical actin cytoskeleton organization (GO:0030866)|erythrocyte development (GO:0048821)|maintenance of cell polarity (GO:0030011)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of myosin-light-chain-phosphatase activity (GO:0035509)|neutrophil chemotaxis (GO:0030593)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of CD8-positive, alpha-beta T cell differentiation (GO:0043378)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of lymphocyte differentiation (GO:0045621)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of T cell proliferation (GO:0042102)|protein complex assembly (GO:0006461)|response to drug (GO:0042493)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)|protein kinase activator activity (GO:0030295)|Rac GTPase activator activity (GO:0030675)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(37)|ovary(3)|prostate(3)|skin(3)|stomach(2)	80						CCCTGCTAATTCAGATACAGT	0.488																																					p.S243A		Atlas-SNP	.											.	NCKAP1L	180	.	0			c.T727G						PASS	.						146	139	141					12																	54903761		2203	4300	6503	SO:0001583	missense	3071	exon7			GCTAATTCAGATA	AI924363	CCDS31813.1, CCDS53799.1	12q13.1	2005-10-11	2005-10-11	2005-10-11		ENSG00000123338			4862	protein-coding gene	gene with protein product		141180	"hematopoietic protein 1"	HEM1		1932118	Standard	NM_005337		Approved		uc001sgc.4	P55160	OTTHUMG00000169843	ENST00000293373.6:c.727T>G	chr12.hg19:g.54903761T>G	ENSP00000293373:p.Ser243Ala	142.0	0.0	.		150.0	56.0	.	NM_005337	B4DUT5|Q52LW0	Missense_Mutation	SNP	ENST00000293373.6	hg19	CCDS31813.1	.	.	.	.	.	.	.	.	.	.	T	15.83	2.948714	0.53186	.	.	ENSG00000123338	ENST00000293373;ENST00000545638	T;T	0.32515	1.45;1.45	5.83	5.83	0.93111	.	0.066512	0.64402	D	0.000007	T	0.25791	0.0628	L	0.38838	1.175	0.40526	D	0.980889	P	0.38473	0.633	B	0.38194	0.267	T	0.06058	-1.0848	10	0.18276	T	0.48	-7.392	14.1522	0.65392	0.0:0.0:0.0:1.0	.	243	P55160	NCKPL_HUMAN	A	243;193	ENSP00000293373:S243A;ENSP00000445596:S193A	ENSP00000293373:S243A	S	+	1	0	NCKAP1L	53190028	1.000000	0.71417	0.930000	0.37139	0.606000	0.37113	7.701000	0.84566	2.216000	0.71823	0.460000	0.39030	TCA	.	.	.	none		0.488	NCKAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406195.1	NM_005337		G	54903761	T	G	54903761	3	3	110	1	0	0	0	0	1	0	0	0	10229	1783	62	5	753	5	NCKAP1L	12	54903761	Missense_Mutation	SNP	T	TCGA-BQ-5875-01A-11D-1589-08	6364912	54903761	78948134	45	7108											
GDE1	51573	hgsc.bcm.edu	37	chr16	19516303	19516303	+	Missense_Mutation	SNP	A	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	caaaatgtccatcataacaaAtataaaatgtttccagaaag	20	10	4	7	0	1	1	1	0	0	1	3	1	3	1	2	0	1	1	2	0	8	4			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr16:19516303A>C	ENST00000353258.3	-	5	928	c.748T>G	c.(748-750)Ttt>Gtt	p.F250V	CTA-363E6.7_ENST00000569345.1_RNA	NM_016641.3	NP_057725.1	Q9NZC3	GDE1_HUMAN	glycerophosphodiester phosphodiesterase 1	250	GP-PDE.				glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|glycerophosphoinositol glycerophosphodiesterase activity (GO:0047395)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)	13						ATCATAACAAATATAAAATGT	0.403																																					p.F250V		Atlas-SNP	.											.	GDE1	31	.	0			c.T748G						PASS	.						161	151	154					16																	19516303		2197	4300	6497	SO:0001583	missense	51573	exon5			TAACAAATATAAA		CCDS10578.1	16p12-p11.2	2011-01-25			ENSG00000006007	ENSG00000006007	3.1.4.46		29644	protein-coding gene	gene with protein product	"membrane interacting protein of RGS16"	605943				12576545, 16472945	Standard	NM_016641		Approved	MIR16	uc002dgh.3	Q9NZC3	OTTHUMG00000131454	ENST00000353258.3:c.748T>G	chr16.hg19:g.19516303A>C	ENSP00000261386:p.Phe250Val	145.0	0.0	.		164.0	51.0	.	NM_016641	O43334|Q6PKF7|Q7KYR4	Missense_Mutation	SNP	ENST00000353258.3	hg19	CCDS10578.1	.	.	.	.	.	.	.	.	.	.	A	5.389	0.256908	0.10185	.	.	ENSG00000006007	ENST00000353258	T	0.27557	1.66	5.66	3.41	0.39046	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	0.193879	0.56097	D	0.000040	T	0.13884	0.0336	N	0.08118	0	0.23533	N	0.997474	B	0.24368	0.102	B	0.24701	0.055	T	0.20840	-1.0263	10	0.28530	T	0.3	-7.2402	5.9584	0.19286	0.7453:0.0:0.1327:0.122	.	250	Q9NZC3	GDE1_HUMAN	V	250	ENSP00000261386:F250V	ENSP00000261386:F250V	F	-	1	0	GDE1	19423804	0.998000	0.40836	0.125000	0.21846	0.104000	0.19210	3.728000	0.54991	0.417000	0.25871	0.533000	0.62120	TTT	.	.	.	none		0.403	GDE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254274.2	NM_016641		C	19516303	A	C	19516303	3	2	110	1	0	0	0	0	1	0	0	0	6317	101	4	5	255	5	GDE1	16	19516303	Missense_Mutation	SNP	A	TCGA-BQ-5875-01A-11D-1589-08		19516303	70838450	46	7109											
EEF2K	29904	hgsc.bcm.edu	37	chr16	22237117	22237117	+	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	gccagtccccccgagctggcCatgatggtgattctgatggg	6	9	14	12	1	1	3	0	3	1	0	2	4	2	3	5	3	1	1	5	3	0	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr16:22237117C>T	ENST00000263026.5	+	2	541	c.67C>T	c.(67-69)Cat>Tat	p.H23Y		NM_013302.3	NP_037434	O00418	EF2K_HUMAN	eukaryotic elongation factor-2 kinase	23			H -> R (in dbSNP:rs9935059). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		insulin receptor signaling pathway (GO:0008286)|protein autophosphorylation (GO:0046777)|regulation of protein autophosphorylation (GO:0031952)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|elongation factor-2 kinase activity (GO:0004686)|protein kinase activity (GO:0004672)|translation factor activity, nucleic acid binding (GO:0008135)			breast(1)|central_nervous_system(1)|endometrium(8)|large_intestine(2)|lung(13)|ovary(1)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(48;0.0223)		CCGAGCTGGCCATGATGGTGA	0.557																																					p.H23Y	NSCLC(195;1411 2157 20319 27471 51856)	Atlas-SNP	.											.	EEF2K	142	.	0			c.C67T						PASS	.						56	55	55					16																	22237117		2197	4300	6497	SO:0001583	missense	29904	exon2			GCTGGCCATGATG	U93850	CCDS10604.1	16p12	2008-02-05			ENSG00000103319	ENSG00000103319			24615	protein-coding gene	gene with protein product		606968				9144159, 12051769	Standard	NM_013302		Approved	eEF-2K	uc002dki.3	O00418	OTTHUMG00000094771	ENST00000263026.5:c.67C>T	chr16.hg19:g.22237117C>T	ENSP00000263026:p.His23Tyr	82.0	0.0	.		92.0	20.0	.	NM_013302	Q8N588	Missense_Mutation	SNP	ENST00000263026.5	hg19	CCDS10604.1	.	.	.	.	.	.	.	.	.	.	C	1.297	-0.605948	0.03717	.	.	ENSG00000103319	ENST00000263026	T	0.08102	3.13	5.82	5.82	0.92795	.	0.750933	0.13237	N	0.403188	T	0.06142	0.0159	L	0.34521	1.04	0.09310	N	1	B	0.18863	0.031	B	0.19148	0.024	T	0.45891	-0.9230	10	0.02654	T	1	-9.8593	8.7204	0.34436	0.1519:0.7677:0.0:0.0804	.	23	O00418	EF2K_HUMAN	Y	23	ENSP00000263026:H23Y	ENSP00000263026:H23Y	H	+	1	0	EEF2K	22144618	0.005000	0.15991	0.338000	0.25549	0.158000	0.22134	0.566000	0.23593	2.757000	0.94681	0.655000	0.94253	CAT	.	.	.	none		0.557	EEF2K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211580.2	NM_013302		T	22237117	C	T	22237117	3	4	110	1	0	0	0	0	1	0	0	0	4932	594	21	2	69	2	EEF2K	16	22237117	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	2720814	22237117	68117636	47	7110											
CX3CL1	6376	hgsc.bcm.edu	37	chr16	57413588	57413588	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgcaacatcacgtgcagcaAgatgacatcaaagatacctg	16	7	8	10	1	2	3	2	1	0	2	2	3	2	3	1	0	5	3	1	0	4	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr16:57413588A>G	ENST00000006053.6	+	2	224	c.113A>G	c.(112-114)aAg>aGg	p.K38R	CX3CL1_ENST00000565912.1_5'UTR|CX3CL1_ENST00000563383.1_Missense_Mutation_p.K44R|CX3CL1_ENST00000564948.1_Intron	NM_002996.3	NP_002987.1	P78423	X3CL1_HUMAN	chemokine (C-X3-C motif) ligand 1	38	Chemokine.				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						ACGTGCAGCAAGATGACATCA	0.522																																					p.K38R		Atlas-SNP	.											.	CX3CL1	27	.	0			c.A113G						PASS	.						181	129	146					16																	57413588		2198	4300	6498	SO:0001583	missense	6376	exon2			GCAGCAAGATGAC	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.113A>G	chr16.hg19:g.57413588A>G	ENSP00000006053:p.Lys38Arg	71.0	0.0	.		85.0	19.0	.	NM_002996	O00672	Missense_Mutation	SNP	ENST00000006053.6	hg19	CCDS10779.1	.	.	.	.	.	.	.	.	.	.	A	10.55	1.382853	0.25031	.	.	ENSG00000006210	ENST00000006053	T	0.05199	3.48	2.87	0.504	0.16946	Chemokine interleukin-8-like domain (3);	0.903877	0.09116	N	0.846367	T	0.05777	0.0151	L	0.41710	1.295	0.23421	N	0.997716	B	0.17268	0.021	B	0.18871	0.023	T	0.42481	-0.9449	10	0.87932	D	0	-13.2272	3.0514	0.06171	0.602:0.2553:0.1427:0.0	.	38	P78423	X3CL1_HUMAN	R	38	ENSP00000006053:K38R	ENSP00000006053:K38R	K	+	2	0	CX3CL1	55971089	0.037000	0.19845	0.149000	0.22428	0.245000	0.25701	-0.164000	0.09983	0.081000	0.16988	0.254000	0.18369	AAG	.	.	.	none		0.522	CX3CL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257345.3	NM_002996		G	57413588	A	G	57413588	3	3	110	1	0	0	0	0	1	0	0	0	4076	72	3	3	119	3	CX3CL1	16	57413588	Missense_Mutation	SNP	A	TCGA-BQ-5875-01A-11D-1589-08	35176471	57413588	32941165	48	7111											
SLC12A4	6560	hgsc.bcm.edu	37	chr16	67981315	67981315	+	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	tcagggacaggcctcggatcCcgtcaccccactccttctca	7	8	8	18	2	3	0	3	0	1	0	7	2	5	2	5	3	0	0	5	3	0	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr16:67981315C>G	ENST00000316341.3	-	16	2131	c.1991G>C	c.(1990-1992)gGg>gCg	p.G664A	SLC12A4_ENST00000572037.1_Missense_Mutation_p.G616A|SLC12A4_ENST00000576616.1_Missense_Mutation_p.G664A|SLC12A4_ENST00000541864.2_Missense_Mutation_p.G633A|SLC12A4_ENST00000338335.3_Missense_Mutation_p.G664A|SLC12A4_ENST00000537830.2_Missense_Mutation_p.G658A|SLC12A4_ENST00000422611.2_Missense_Mutation_p.G666A|CTC-479C5.17_ENST00000590594.1_lincRNA	NM_001145961.1|NM_005072.4	NP_001139433.1|NP_005063.1	Q9UP95	S12A4_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 4	664					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|prostate(4)|skin(2)|urinary_tract(3)	29		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	GCCTCGGATCCCGTCACCCCA	0.672																																					p.G666A		Atlas-SNP	.											.	SLC12A4	81	.	0			c.G1997C						PASS	.						46	56	53					16																	67981315		2195	4299	6494	SO:0001583	missense	6560	exon15			CGGATCCCGTCAC		CCDS10855.1, CCDS54030.1, CCDS54031.1, CCDS54032.1	16q22.1	2013-07-18	2013-07-18		ENSG00000124067	ENSG00000124067		"Solute carriers"	10913	protein-coding gene	gene with protein product		604119				8663127	Standard	NM_005072		Approved	KCC1	uc010ceu.2	Q9UP95	OTTHUMG00000137535	ENST00000316341.3:c.1991G>C	chr16.hg19:g.67981315C>G	ENSP00000318557:p.Gly664Ala	37.0	0.0	.		34.0	8.0	.	NM_001145962	B4DF69|B4DR04|B4DZ82|B7ZAV0|F5H066|F5H0S9|F5H3C0|O60632|O75893|Q13953|Q96LD5	Missense_Mutation	SNP	ENST00000316341.3	hg19	CCDS10855.1	.	.	.	.	.	.	.	.	.	.	C	35	5.435871	0.96168	.	.	ENSG00000124067	ENST00000422611;ENST00000541864;ENST00000537830;ENST00000338335;ENST00000316341	D;D;D;D;D	0.98550	-4.99;-4.99;-4.99;-4.99;-4.99	5.76	5.76	0.90799	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.98748	0.9579	M	0.61703	1.905	0.80722	D	1	D;D;D;D;D;D	0.89917	0.994;0.999;1.0;0.982;0.982;0.986	D;D;D;P;P;D	0.97110	0.95;0.992;1.0;0.854;0.854;0.91	D	0.99872	1.1098	10	0.72032	D	0.01	.	19.9738	0.97296	0.0:1.0:0.0:0.0	.	666;664;633;658;664;664	F5H3C0;B4DF30;F5H066;F5H0S9;Q9UP95-2;Q9UP95	.;.;.;.;.;S12A4_HUMAN	A	666;633;658;664;664	ENSP00000395983:G666A;ENSP00000438334:G633A;ENSP00000445962:G658A;ENSP00000343374:G664A;ENSP00000318557:G664A	ENSP00000318557:G664A	G	-	2	0	SLC12A4	66538816	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	7.760000	0.85248	2.732000	0.93576	0.655000	0.94253	GGG	.	.	.	none		0.672	SLC12A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268864.4	NM_005072		G	67981315	C	G	67981315	3	3	110	1	0	0	0	0	1	0	0	0	14398	623	22	4	1302	4	SLC12A4	16	67981315	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	10567727	67981315	22373438	49	7112											
NFATC3	4775	hgsc.bcm.edu	37	chr16	68224719	68224719	+	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	gattgatttgtcttcagttcCatctttgcctgtgcctcatc	5	18	7	11	0	4	1	2	1	2	0	6	2	5	1	3	0	2	1	3	0	0	5			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr16:68224719C>A	ENST00000346183.3	+	9	2171	c.2147C>A	c.(2146-2148)cCa>cAa	p.P716Q	NFATC3_ENST00000329524.4_Missense_Mutation_p.P716Q|NFATC3_ENST00000349223.5_Missense_Mutation_p.P716Q|NFATC3_ENST00000575270.1_Missense_Mutation_p.P716Q|SNORA48_ENST00000391143.1_RNA|NFATC3_ENST00000535127.2_3'UTR	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	716					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)		TCTTCAGTTCCATCTTTGCCT	0.383																																					p.P716Q		Atlas-SNP	.											.	NFATC3	190	.	0			c.C2147A						PASS	.						107	99	101					16																	68224719		2198	4300	6498	SO:0001583	missense	4775	exon9			CAGTTCCATCTTT	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.2147C>A	chr16.hg19:g.68224719C>A	ENSP00000300659:p.Pro716Gln	206.0	0.0	.		171.0	95.0	.	NM_173163	O75211|Q14516|Q99840|Q99841|Q99842	Missense_Mutation	SNP	ENST00000346183.3	hg19	CCDS10860.1	.	.	.	.	.	.	.	.	.	.	C	19.34	3.808656	0.70797	.	.	ENSG00000072736	ENST00000349223;ENST00000346183;ENST00000329524;ENST00000535127	T;T;T	0.14516	2.5;2.5;2.5	5.55	4.59	0.56863	.	0.059669	0.64402	D	0.000002	T	0.33206	0.0855	M	0.72894	2.215	0.44079	D	0.996834	P;D;P;P	0.57257	0.747;0.979;0.747;0.747	P;P;P;P	0.58970	0.499;0.849;0.499;0.499	T	0.14144	-1.0483	10	0.72032	D	0.01	-2.556	15.7347	0.77834	0.1378:0.8622:0.0:0.0	.	716;716;716;716	Q12968;Q12968-3;B5B2S0;B5B2S2	NFAC3_HUMAN;.;.;.	Q	716;716;716;237	ENSP00000264008:P716Q;ENSP00000300659:P716Q;ENSP00000331324:P716Q	ENSP00000331324:P716Q	P	+	2	0	NFATC3	66782220	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	7.294000	0.78760	1.330000	0.45394	-0.321000	0.08615	CCA	.	.	.	none		0.383	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555		A	68224719	C	A	68224719	3	1	110	1	0	0	0	0	1	0	0	0	10371	594	21	4	2181	4	NFATC3	16	68224719	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	243404	68224719	22130034	50	7113											
CHMP1A	5119	hgsc.bcm.edu	37	chr16	89715819	89715819	+	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	gcgtctacgcgggacgccatCcgaagccagttcacaccttc	8	7	10	16	5	2	0	1	0	1	0	4	2	3	1	4	1	2	1	4	1	2	3			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr16:89715819C>T	ENST00000397901.3	-	4	448	c.192G>A	c.(190-192)cgG>cgA	p.R64R	CHMP1A_ENST00000535997.2_5'UTR|CHMP1A_ENST00000253475.5_Missense_Mutation_p.D58N|CHMP1A_ENST00000547614.1_5'UTR|CHMP1A_ENST00000550102.1_Silent_p.R64R	NM_002768.3	NP_002759.2	Q9HD42	CHM1A_HUMAN	charged multivesicular body protein 1A	64					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)		GGGACGCCATCCGAAGCCAGT	0.602																																					p.D58N		Atlas-SNP	.											.	CHMP1A	15	.	0			c.G172A						PASS	.						90	104	99					16																	89715819		2154	4245	6399	SO:0001819	synonymous_variant	5119	exon3			CGCCATCCGAAGC	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.192G>A	chr16.hg19:g.89715819C>T		150.0	0.0	.		210.0	63.0	.	NM_001083314	A2RU09|Q14468|Q15779|Q96G31	Missense_Mutation	SNP	ENST00000397901.3	hg19	CCDS45552.1	.	.	.	.	.	.	.	.	.	.	C	11.56	1.674550	0.29693	.	.	ENSG00000131165	ENST00000253475	.	.	.	5.38	-6.01	0.02199	.	0.480369	0.15538	N	0.257085	T	0.22244	0.0536	.	.	.	0.09310	N	0.999992	B	0.12013	0.005	B	0.09377	0.004	T	0.15009	-1.0452	8	0.87932	D	0	0.0142	3.6277	0.08119	0.1185:0.3755:0.2125:0.2936	.	58	A6NG32	.	N	58	.	ENSP00000253475:D58N	D	-	1	0	CHMP1A	88243320	0.002000	0.14202	0.974000	0.42286	0.700000	0.40528	-1.471000	0.02344	-0.529000	0.06358	-1.157000	0.01802	GAT	.	.	.	none		0.602	CHMP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404581.1	NM_002768		T	89715819	C	T	89715819	2	4	110	1	0	0	0	0	0	0	0	1	3354	855	30	2		2	CHMP1A	16	89715819	Silent	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	21491100	89715819	638934	51	7114											
CDK10	8558	hgsc.bcm.edu	37	chr16	89756963	89756963	+	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	aatgtgtttccattccagatCgggcccgggacacccagaca	10	8	10	13	2	0	2	0	0	0	2	3	3	2	3	4	2	0	1	4	2	1	2			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr16:89756963C>T	ENST00000353379.7	+	3	206	c.163C>T	c.(163-165)Cgg>Tgg	p.R55W	CDK10_ENST00000505473.1_5'UTR|CDK10_ENST00000514965.1_3'UTR|CDK10_ENST00000331006.8_Missense_Mutation_p.R8W	NM_001098533.2|NM_001160367.1|NM_052988.4	NP_001092003.2|NP_001153839.1|NP_443714.3	Q15131	CDK10_HUMAN	cyclin-dependent kinase 10	55	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of cell proliferation (GO:0008285)|traversing start control point of mitotic cell cycle (GO:0007089)		ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			ovary(1)	1		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0276)		CATTCCAGATCGGGCCCGGGA	0.592																																					p.R55W		Atlas-SNP	.											.	CDK10	26	.	0			c.C163T						PASS	.						195	162	173					16																	89756963		2198	4300	6498	SO:0001583	missense	8558	exon3			CCAGATCGGGCCC	L33264	CCDS10984.2, CCDS32514.1, CCDS32514.2	16q24.3	2011-11-08	2007-11-21		ENSG00000185324	ENSG00000185324		"Cyclin-dependent kinases"	1770	protein-coding gene	gene with protein product		603464	"cyclin-dependent kinase (CDC2-like) 10"			8208557, 8084611	Standard	NM_052988		Approved	PISSLRE	uc010cio.3	Q15131	OTTHUMG00000138049	ENST00000353379.7:c.163C>T	chr16.hg19:g.89756963C>T	ENSP00000338673:p.Arg55Trp	111.0	0.0	.		144.0	28.0	.	NM_052988	A8K370|A8K8I6|A8MXU6|B3KQJ3|B7Z420|D3DX82|D3DX83|Q0VGZ7|Q15130|Q6PJC0	Missense_Mutation	SNP	ENST00000353379.7	hg19	CCDS10984.2	.	.	.	.	.	.	.	.	.	.	C	25.2	4.617358	0.87359	.	.	ENSG00000185324	ENST00000331006;ENST00000393082;ENST00000353379	T;T	0.66995	0.87;-0.24	5.1	3.11	0.35812	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	0.84906	0.5576	M	0.92268	3.29	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.996;0.999	D	0.87752	0.2592	10	0.87932	D	0	-35.2961	14.2251	0.65853	0.2716:0.7284:0.0:0.0	.	49;55;49	B7Z319;Q15131;B3KQJ3	.;CDK10_HUMAN;.	W	8;26;55	ENSP00000329957:R8W;ENSP00000338673:R55W	ENSP00000329957:R8W	R	+	1	2	CDK10	88284464	1.000000	0.71417	0.996000	0.52242	0.815000	0.46073	3.632000	0.54287	0.517000	0.28361	0.561000	0.74099	CGG	.	.	.	none		0.592	CDK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269925.2			T	89756963	C	T	89756963	3	4	110	1	0	0	0	0	1	0	0	0	3127	875	31	1	173	1	CDK10	16	89756963	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	41144	89756963	597790	52	7115											
ACAP1	9744	hgsc.bcm.edu	37	chr17	7250507	7250507	+	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	ccgggagccagccccggagtGggccagcatcaaccttggtg	7	5	15	14	2	1	0	1	0	0	0	1	2	1	2	6	4	4	1	6	4	1	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr17:7250507G>A	ENST00000158762.3	+	14	1495	c.1289G>A	c.(1288-1290)tGg>tAg	p.W430*		NM_014716.3	NP_055531.1	Q15027	ACAP1_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	430	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.|Required for interaction with GULP1.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)	endosome (GO:0005768)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(3)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(3)|skin(1)|urinary_tract(1)	33						GCCCCGGAGTGGGCCAGCATC	0.657																																					p.W430X		Atlas-SNP	.											.	ACAP1	66	.	0			c.G1289A						PASS	.						75	86	82					17																	7250507		2203	4300	6503	SO:0001587	stop_gained	9744	exon14			CGGAGTGGGCCAG	D30758	CCDS11101.1	17p13.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000072818	ENSG00000072818		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16467	protein-coding gene	gene with protein product		607763	"centaurin, beta 1"	CENTB1		11050434, 11062263	Standard	NM_014716		Approved	KIAA0050	uc002ggd.2	Q15027	OTTHUMG00000102199	ENST00000158762.3:c.1289G>A	chr17.hg19:g.7250507G>A	ENSP00000158762:p.Trp430*	105.0	0.0	.		121.0	38.0	.	NM_014716	Q53XN9	Nonsense_Mutation	SNP	ENST00000158762.3	hg19	CCDS11101.1	.	.	.	.	.	.	.	.	.	.	G	40	8.222149	0.98712	.	.	ENSG00000072818	ENST00000158762	.	.	.	4.77	4.77	0.60923	.	0.120594	0.64402	D	0.000011	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.3166	0.74085	0.0:0.0:1.0:0.0	.	.	.	.	X	430	.	ENSP00000158762:W430X	W	+	2	0	ACAP1	7191231	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.244000	0.95423	2.480000	0.83734	0.462000	0.41574	TGG	.	.	.	none		0.657	ACAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220049.4	NM_014716		A	7250507	G	A	7250507	4	1	110	1	0	0	0	0	0	1	0	0	118	1357	47	2	1343	2	ACAP1	17	7250507	Nonsense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08		7250507	73944703	53	7116											
ATAD5	79915	hgsc.bcm.edu	37	chr17	29162059	29162059	+	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	tcccagcaggtacgctttaaGacagttactgttcttgcaca	10	12	8	11	1	1	1	0	0	1	1	2	1	2	1	1	1	4	6	1	1	3	6			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr17:29162059G>C	ENST00000321990.4	+	2	1338	c.960G>C	c.(958-960)aaG>aaC	p.K320N	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	320					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)				TACGCTTTAAGACAGTTACTG	0.378																																					p.K320N		Atlas-SNP	.											.	ATAD5	150	.	0			c.G960C						PASS	.						51	54	53					17																	29162059		2173	4287	6460	SO:0001583	missense	79915	exon2			CTTTAAGACAGTT		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.960G>C	chr17.hg19:g.29162059G>C	ENSP00000313171:p.Lys320Asn	108.0	0.0	.		61.0	22.0	.	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	hg19	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	G	9.891	1.204236	0.22205	.	.	ENSG00000176208	ENST00000321990	T	0.11930	2.73	5.91	2.57	0.30868	.	0.221364	0.38778	N	0.001570	T	0.29061	0.0722	M	0.66939	2.045	0.29942	N	0.821002	D;D	0.76494	0.999;0.997	D;P	0.71656	0.974;0.879	T	0.06789	-1.0807	10	0.87932	D	0	.	7.1115	0.25392	0.4358:0.0:0.5642:0.0	.	320;320	Q96QE3-2;Q96QE3	.;ATAD5_HUMAN	N	320	ENSP00000313171:K320N	ENSP00000313171:K320N	K	+	3	2	ATAD5	26186185	1.000000	0.71417	0.993000	0.49108	0.993000	0.82548	1.162000	0.31786	0.850000	0.35239	-0.136000	0.14681	AAG	.	.	.	none		0.378	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		C	29162059	G	C	29162059	3	2	110	1	0	0	0	0	1	0	0	0	1076	933	33	4	966	4	ATAD5	17	29162059	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	21911552	29162059	52033151	54	7117											
LRRC37B	114659	hgsc.bcm.edu	37	chr17	30348539	30348539	+	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	tcaggacttaaatgacaagcGgactccagaagaaaggctcc	15	6	10	10	1	1	3	1	1	0	2	3	5	3	5	2	3	1	1	2	3	5	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr17:30348539G>T	ENST00000341671.7	+	1	379	c.374G>T	c.(373-375)cGg>cTg	p.R125L	LRRC37B_ENST00000394713.3_Missense_Mutation_p.R125L|LRRC37B_ENST00000543378.2_Missense_Mutation_p.R43L|LRRC37B_ENST00000327564.7_Missense_Mutation_p.R152L|LRRC37B_ENST00000584368.1_Missense_Mutation_p.R137L	NM_052888.2	NP_443120.2	Q96QE4	LR37B_HUMAN	leucine rich repeat containing 37B	125						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	29		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.111)|Ovarian(249;0.182)|Breast(31;0.244)				AATGACAAGCGGACTCCAGAA	0.537																																					p.R125L		Atlas-SNP	.											.	LRRC37B	67	.	0			c.G374T						PASS	.						67	72	70					17																	30348539		2203	4299	6502	SO:0001583	missense	114659	exon1			ACAAGCGGACTCC	AJ314647	CCDS32609.1	17q11.2	2006-11-29		2005-08-09	ENSG00000185158	ENSG00000185158			29070	protein-coding gene	gene with protein product	"KIAA0563-related"					11468690, 10843809	Standard	NM_052888		Approved		uc002hgu.3	Q96QE4	OTTHUMG00000132785	ENST00000341671.7:c.374G>T	chr17.hg19:g.30348539G>T	ENSP00000340519:p.Arg125Leu	167.0	0.0	.		153.0	49.0	.	NM_052888	Q17RC9|Q5YKG6	Missense_Mutation	SNP	ENST00000341671.7	hg19	CCDS32609.1	.	.	.	.	.	.	.	.	.	.	N	0	-2.679426	0.00102	.	.	ENSG00000185158	ENST00000543378;ENST00000327564;ENST00000394713;ENST00000341671	T;T;T;T	0.48836	1.03;0.8;1.92;0.83	1.88	-3.76	0.04359	.	.	.	.	.	T	0.08846	0.0219	N	0.00210	-1.845	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.08027	-1.0742	9	0.09338	T	0.73	.	1.1007	0.01683	0.17:0.2722:0.3459:0.2118	.	125;125	Q17RC9;Q96QE4	.;LR37B_HUMAN	L	43;152;125;125	ENSP00000443345:R43L;ENSP00000332536:R152L;ENSP00000378202:R125L;ENSP00000340519:R125L	ENSP00000332536:R152L	R	+	2	0	LRRC37B	27372652	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.498000	0.06420	-2.354000	0.00614	-1.626000	0.00786	CGG	.	.	.	none		0.537	LRRC37B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446508.1	NM_052888		T	30348539	G	T	30348539	3	4	110	1	0	0	0	0	1	0	0	0	9001	1116	39	4	376	4	LRRC37B	17	30348539	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	1186480	30348539	50846671	55	7118											
MFSD11	79157	hgsc.bcm.edu	37	chr17	74772621	74772621	+	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	ttgccatcttcaagtttgttCaggtaacctcttcagattgt	8	17	7	9	0	5	1	3	0	2	1	5	1	5	1	2	1	2	3	2	1	2	7			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr17:74772621C>T	ENST00000588460.1	+	12	3225	c.1183C>T	c.(1183-1185)Cag>Tag	p.Q395*	MFSD11_ENST00000590514.1_Nonsense_Mutation_p.Q395*|MFSD11_ENST00000590070.1_3'UTR|MFSD11_ENST00000586622.1_Nonsense_Mutation_p.Q395*|MFSD11_ENST00000336509.4_Nonsense_Mutation_p.Q395*|MFSD11_ENST00000593181.1_Nonsense_Mutation_p.Q343*|MFSD11_ENST00000355954.3_Nonsense_Mutation_p.Q343*	NM_001242534.1	NP_001229463.1	O43934	MFS11_HUMAN	major facilitator superfamily domain containing 11	395						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)	17						CAAGTTTGTTCAGGTAACCTC	0.423																																					p.Q395X		Atlas-SNP	.											.	MFSD11	47	.	0			c.C1183T						PASS	.						165	158	160					17																	74772621		2203	4300	6503	SO:0001587	stop_gained	79157	exon12			TTTGTTCAGGTAA	BC002753	CCDS11750.1, CCDS56045.1	17q25.1	2012-03-09			ENSG00000092931	ENSG00000092931			25458	protein-coding gene	gene with protein product						9358160	Standard	NM_001242532		Approved	FLJ22196, FLJ20226	uc002jte.3	O43934		ENST00000588460.1:c.1183C>T	chr17.hg19:g.74772621C>T	ENSP00000464932:p.Gln395*	236.0	0.0	.		220.0	108.0	.	NM_001242532	O43442|Q9NXI5	Nonsense_Mutation	SNP	ENST00000588460.1	hg19	CCDS11750.1	.	.	.	.	.	.	.	.	.	.	C	39	7.628628	0.98399	.	.	ENSG00000092931	ENST00000336509;ENST00000355954	.	.	.	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-9.9106	19.2358	0.93858	0.0:1.0:0.0:0.0	.	.	.	.	X	395;343	.	ENSP00000337240:Q395X	Q	+	1	0	MFSD11	72284216	1.000000	0.71417	0.995000	0.50966	0.966000	0.64601	7.624000	0.83124	2.529000	0.85273	0.563000	0.77884	CAG	.	.	.	none		0.423	MFSD11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451516.1	NM_024311		T	74772621	C	T	74772621	4	4	110	1	0	0	0	0	0	1	0	0	9536	827	29	2	1229	2	MFSD11	17	74772621	Nonsense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08	44424082	74772621	6422589	56	7119											
SYT4	6860	hgsc.bcm.edu	37	chr18	40853823	40853823	+	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	cgtcattttgatatatgggtCagaggtcatcgactgctcat	9	14	10	8	2	4	2	4	1	0	1	5	3	4	2	0	2	1	1	0	2	2	4			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr18:40853823C>T	ENST00000255224.3	-	2	939	c.571G>A	c.(571-573)Gac>Aac	p.D191N	SYT4_ENST00000590752.1_Missense_Mutation_p.D173N|SYT4_ENST00000586678.1_Intron	NM_020783.3	NP_065834.1	Q9H2B2	SYT4_HUMAN	synaptotagmin IV	191	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Phospholipid binding. {ECO:0000305}.				exocytosis (GO:0006887)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of vesicle fusion (GO:0031339)|neurotransmitter secretion (GO:0007269)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44						ATATATGGGTCAGAGGTCATC	0.438																																					p.D191N	NSCLC(85;81 1419 2855 22820 35912)	Atlas-SNP	.											.	SYT4	162	.	0			c.G571A						PASS	.						78	77	78					18																	40853823		2203	4300	6503	SO:0001583	missense	6860	exon2			ATGGGTCAGAGGT	BC036538	CCDS11922.1	18q12.3	2013-01-21			ENSG00000132872	ENSG00000132872		"Synaptotagmins"	11512	protein-coding gene	gene with protein product		600103				8058779	Standard	NM_020783		Approved	KIAA1342, HsT1192	uc002law.3	Q9H2B2	OTTHUMG00000132610	ENST00000255224.3:c.571G>A	chr18.hg19:g.40853823C>T	ENSP00000255224:p.Asp191Asn	109.0	0.0	.		112.0	46.0	.	NM_020783	B4DEU3|Q9P2K4	Missense_Mutation	SNP	ENST00000255224.3	hg19	CCDS11922.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.979225	0.92982	.	.	ENSG00000132872	ENST00000255224	T	0.14516	2.5	5.87	5.87	0.94306	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	0.43188	0.1236	M	0.78637	2.42	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.19192	-1.0313	10	0.87932	D	0	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	173;191	B4DEU3;Q9H2B2	.;SYT4_HUMAN	N	191	ENSP00000255224:D191N	ENSP00000255224:D191N	D	-	1	0	SYT4	39107821	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.729000	0.84864	2.941000	0.99782	0.655000	0.94253	GAC	.	.	.	none		0.438	SYT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255851.2	NM_020783		T	40853823	C	T	40853823	3	4	110	1	0	0	0	0	1	0	0	0	15488	826	29	2	718	2	SYT4	18	40853823	Missense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08		40853823	37223425	57	7120											
MRPL54	116541	hgsc.bcm.edu	37	chr19	3765208	3765208	+	Missense_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	aaggtgcagtgaccagcgagGccctcaaggaccccgacgta	11	4	13	13	3	1	1	1	1	0	0	1	4	1	2	4	3	2	2	4	3	3	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr19:3765208G>A	ENST00000330133.4	+	2	200	c.163G>A	c.(163-165)Gcc>Acc	p.A55T		NM_172251.2	NP_758455.1	Q6P161	RM54_HUMAN	mitochondrial ribosomal protein L54	55						mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|lung(1)|ovary(1)	5		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)		GACCAGCGAGGCCCTCAAGGA	0.572																																					p.A55T		Atlas-SNP	.											MRPL54,colon,carcinoma,0,1	MRPL54	9	.	0			c.G163A						PASS	.						109	90	96					19																	3765208		2202	4300	6502	SO:0001583	missense	116541	exon2			AGCGAGGCCCTCA		CCDS12111.1	19p13.3	2012-11-14			ENSG00000183617	ENSG00000183617		"Mitochondrial ribosomal proteins / large subunits"	16685	protein-coding gene	gene with protein product		611858				11551941	Standard	NM_172251		Approved		uc002lyq.4	Q6P161	OTTHUMG00000180873	ENST00000330133.4:c.163G>A	chr19.hg19:g.3765208G>A	ENSP00000331849:p.Ala55Thr	90.0	0.0	.		50.0	24.0	.	NM_172251		Missense_Mutation	SNP	ENST00000330133.4	hg19	CCDS12111.1	.	.	.	.	.	.	.	.	.	.	G	5.440	0.266338	0.10294	.	.	ENSG00000183617	ENST00000330133	.	.	.	4.9	1.59	0.23543	.	0.387651	0.25753	N	0.028522	T	0.22704	0.0548	N	0.19112	0.55	0.09310	N	0.999999	B	0.14438	0.01	B	0.12837	0.008	T	0.18840	-1.0324	9	0.16420	T	0.52	-5.8698	8.109	0.30903	0.2723:0.0:0.7277:0.0	.	55	Q6P161	RM54_HUMAN	T	55	.	ENSP00000331849:A55T	A	+	1	0	MRPL54	3716208	0.988000	0.35896	0.368000	0.25939	0.019000	0.09904	2.395000	0.44459	0.485000	0.27652	0.462000	0.41574	GCC	.	.	.	none		0.572	MRPL54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453443.1	NM_172251		A	3765208	G	A	3765208	3	1	110	1	0	0	0	0	1	0	0	0	9825	1203	42	2	169	2	MRPL54	19	3765208	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08		3765208	55363775	58	7121											
ZNF225	7768	hgsc.bcm.edu	37	chr19	44635911	44635911	+	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	aagaatgtggaaagagcttcAgatgggcctcaggtctttca	12	10	12	7	0	4	3	3	0	1	3	4	4	4	4	1	3	1	1	1	3	3	2			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr19:44635911A>C	ENST00000262894.6	+	5	1424	c.1144A>C	c.(1144-1146)Aga>Cga	p.R382R	ZNF225_ENST00000592780.1_3'UTR|ZNF225_ENST00000590612.1_Silent_p.R382R	NM_013362.2	NP_037494.2	Q9UK10	ZN225_HUMAN	zinc finger protein 225	382					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	16		Prostate(69;0.0352)|all_neural(266;0.202)				AAAGAGCTTCAGATGGGCCTC	0.408																																					p.R382R		Atlas-SNP	.											.	ZNF225	41	.	0			c.A1144C						PASS	.						74	80	78					19																	44635911		2182	4282	6464	SO:0001819	synonymous_variant	7768	exon5			AGCTTCAGATGGG	AF187991	CCDS46100.1	19q13.31	2013-01-08				ENSG00000256294		"Zinc fingers, C2H2-type", "-"	13018	protein-coding gene	gene with protein product							Standard	NM_013362		Approved		uc002oyj.1	Q9UK10		ENST00000262894.6:c.1144A>C	chr19.hg19:g.44635911A>C		113.0	0.0	.		101.0	47.0	.	NM_013362	A8K8S2|Q53F12|Q9NS46|Q9UID8	Silent	SNP	ENST00000262894.6	hg19	CCDS46100.1																																																																																			.	.	.	none		0.408	ZNF225-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460581.1			C	44635911	A	C	44635911	2	2	110	1	0	0	0	0	0	0	0	1	17791	180	7	5		5	ZNF225	19	44635911	Silent	SNP	A	TCGA-BQ-5875-01A-11D-1589-08	40870703	44635911	14493072	59	7122											
ZNF547	284306	hgsc.bcm.edu	37	chr19	57888699	57888699	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agggactgtacacgtgtccaGcacatcttcaccagcaccaa	12	7	8	14	1	2	0	1	0	1	0	3	1	3	1	3	1	3	3	3	1	2	2			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr19:57888699G>A	ENST00000282282.3	+	4	505	c.355G>A	c.(355-357)Gca>Aca	p.A119T	AC003002.4_ENST00000597658.1_Intron	NM_173631.2	NP_775902.2	Q8IVP9	ZN547_HUMAN	zinc finger protein 547	119					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			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)		CACGTGTCCAGCACATCTTCA	0.517																																					p.A119T		Atlas-SNP	.											.	ZNF547	45	.	0			c.G355A						PASS	.						100	88	92					19																	57888699		2203	4300	6503	SO:0001583	missense	284306	exon4			TGTCCAGCACATC	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.355G>A	chr19.hg19:g.57888699G>A	ENSP00000282282:p.Ala119Thr	97.0	0.0	.		91.0	27.0	.	NM_173631	A8K5Z9|Q96NC4	Missense_Mutation	SNP	ENST00000282282.3	hg19	CCDS33131.1	.	.	.	.	.	.	.	.	.	.	G	11.74	1.727951	0.30593	.	.	ENSG00000152433	ENST00000391704;ENST00000282282	T	0.05855	3.38	2.09	-1.39	0.08997	.	.	.	.	.	T	0.05823	0.0152	L	0.37800	1.135	0.09310	N	1	P;B;P	0.51057	0.728;0.141;0.941	B;B;B	0.43889	0.358;0.031;0.435	T	0.36311	-0.9753	9	0.42905	T	0.14	.	6.7967	0.23729	0.4946:0.0:0.5054:0.0	.	119;119;119	Q8IVP9-2;C9JTQ3;Q8IVP9	.;.;ZN547_HUMAN	T	119	ENSP00000282282:A119T	ENSP00000282282:A119T	A	+	1	0	ZNF547	62580511	0.000000	0.05858	0.004000	0.12327	0.227000	0.25037	-0.074000	0.11450	-0.246000	0.09611	0.491000	0.48974	GCA	.	.	.	none		0.517	ZNF547-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465787.1	NM_173631		A	57888699	G	A	57888699	3	1	110	1	0	0	0	0	1	0	0	0	17991	971	34	2	365	2	ZNF547	19	57888699	Missense_Mutation	SNP	G	TCGA-BQ-5875-01A-11D-1589-08	13252788	57888699	1240284	60	7123											
ITGB2	3689	hgsc.bcm.edu	37	chr21	46306670	46306670	+	Missense_Mutation	SNP	A	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	cattgttccactgggacttgAgcttctccttctcaaagcgc	7	13	8	13	1	2	1	1	1	2	0	5	2	3	2	2	1	2	2	2	1	1	5			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr21:46306670A>C	ENST00000397850.2	-	16	2680	c.2228T>G	c.(2227-2229)cTc>cGc	p.L743R	ITGB2_ENST00000397857.1_Missense_Mutation_p.L743R|ITGB2_ENST00000302347.5_Missense_Mutation_p.L743R|ITGB2_ENST00000397854.3_Missense_Mutation_p.L686R|ITGB2_ENST00000397852.1_Missense_Mutation_p.L743R|ITGB2_ENST00000355153.4_Missense_Mutation_p.L743R			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	743					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)	CTGGGACTTGAGCTTCTCCTT	0.617																																					p.L743R		Atlas-SNP	.											.	ITGB2	107	.	0			c.T2228G						PASS	.						110	88	96					21																	46306670		2203	4300	6503	SO:0001583	missense	3689	exon15			GACTTGAGCTTCT	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.2228T>G	chr21.hg19:g.46306670A>C	ENSP00000380948:p.Leu743Arg	73.0	0.0	.		43.0	6.0	.	NM_000211	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Missense_Mutation	SNP	ENST00000397850.2	hg19	CCDS13716.1	.	.	.	.	.	.	.	.	.	.	A	2.100	-0.406333	0.04832	.	.	ENSG00000160255	ENST00000397852;ENST00000397857;ENST00000397854;ENST00000355153;ENST00000397850;ENST00000302347	D;D;D;D;D;D	0.87966	-2.32;-2.32;-2.32;-2.32;-2.32;-2.32	4.62	2.16	0.27623	Integrin beta subunit, cytoplasmic (2);	.	.	.	.	T	0.78483	0.4290	L	0.34521	1.04	0.30302	N	0.789334	P;P	0.37276	0.589;0.589	B;B	0.43018	0.405;0.315	T	0.67795	-0.5578	9	0.15066	T	0.55	.	1.6167	0.02705	0.5553:0.1773:0.0964:0.171	.	686;743	A8MYE6;P05107	.;ITB2_HUMAN	R	743;743;686;743;743;743	ENSP00000380950:L743R;ENSP00000380955:L743R;ENSP00000380952:L686R;ENSP00000347279:L743R;ENSP00000380948:L743R;ENSP00000303242:L743R	ENSP00000303242:L743R	L	-	2	0	ITGB2	45131098	1.000000	0.71417	0.996000	0.52242	0.100000	0.18952	1.319000	0.33655	0.157000	0.19338	-0.250000	0.11733	CTC	.	.	.	none		0.617	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211		C	46306670	A	C	46306670	3	2	110	1	0	0	0	0	1	0	0	0	7901	304	11	5	89	5	ITGB2	21	46306670	Missense_Mutation	SNP	A	TCGA-BQ-5875-01A-11D-1589-08		46306670	1823225	61	7124											
NF2	4771	hgsc.bcm.edu	37	chr22	30038223	30038223	+	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	attttagatgaaaagatctaCtgccctcctgaggcttctgt	10	14	8	9	0	2	4	0	2	2	2	3	4	3	4	2	1	2	1	2	1	4	4			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chr22:30038223C>A	ENST00000338641.4	+	4	837	c.396C>A	c.(394-396)taC>taA	p.Y132*	NF2_ENST00000397789.3_Nonsense_Mutation_p.Y132*|NF2_ENST00000361166.4_Nonsense_Mutation_p.Y132*|NF2_ENST00000361452.4_Nonsense_Mutation_p.Y91*|NF2_ENST00000413209.2_Nonsense_Mutation_p.Y132*|NF2_ENST00000361676.4_Nonsense_Mutation_p.Y90*|NF2_ENST00000403435.1_Nonsense_Mutation_p.Y132*|NF2_ENST00000403999.3_Nonsense_Mutation_p.Y132*|NF2_ENST00000347330.5_Nonsense_Mutation_p.Y49*|NF2_ENST00000353887.4_Nonsense_Mutation_p.Y49*|NF2_ENST00000334961.7_Nonsense_Mutation_p.Y49*	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	132	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.V122_K149del(5)|p.?(3)|p.L127_P134del(1)|p.K123fs*2(1)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						AAAAGATCTACTGCCCTCCTG	0.468			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																												p.Y132X		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	.	NF2	1312	.	10	Deletion - In frame(6)|Unknown(3)|Deletion - Frameshift(1)	soft_tissue(8)|large_intestine(1)|stomach(1)	c.C396A						PASS	.						95	90	92					22																	30038223		2203	4300	6503	SO:0001587	stop_gained	4771	exon4	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	GATCTACTGCCCT	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"A-kinase anchor proteins"	7773	protein-coding gene	gene with protein product	"moesin-ezrin-radixin like", "schwannomin"	607379	"neurofibromin 2 (bilateral acoustic neuroma)"			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.396C>A	chr22.hg19:g.30038223C>A	ENSP00000344666:p.Tyr132*	66.0	0.0	.		55.0	37.0	.	NM_000268	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Nonsense_Mutation	SNP	ENST00000338641.4	hg19	CCDS13861.1	.	.	.	.	.	.	.	.	.	.	C	39	7.545417	0.98348	.	.	ENSG00000186575	ENST00000413209;ENST00000347330;ENST00000338641;ENST00000403435;ENST00000361452;ENST00000397822;ENST00000403999;ENST00000334961;ENST00000353887;ENST00000397789;ENST00000361676;ENST00000361166	.	.	.	5.45	2.11	0.27256	.	0.116668	0.64402	D	0.000011	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.5018	0.50441	0.0:0.7981:0.0:0.2019	.	.	.	.	X	132;49;132;132;91;132;132;49;49;132;90;132	.	.	Y	+	3	2	NF2	28368223	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.702000	0.37836	0.657000	0.30906	0.655000	0.94253	TAC	.	.	.	none		0.468	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268		A	30038223	C	A	30038223	4	1	110	1	0	0	0	0	0	1	0	0	10364	576	20	4	410	4	NF2	22	30038223	Nonsense_Mutation	SNP	C	TCGA-BQ-5875-01A-11D-1589-08		30038223	21266343	62	7125											
SLC9A7	84679	hgsc.bcm.edu	37	chrX	46491075	46491075	+	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	ggtgggtcttgatcggggtcAacaccaactctgaaagtcac	10	9	12	10	1	4	2	2	2	2	0	5	2	4	2	1	4	2	0	1	4	3	1			TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chrX:46491075A>T	ENST00000328306.4	-	14	1708	c.1683T>A	c.(1681-1683)gtT>gtA	p.V561V	SLC9A7_ENST00000464933.1_5'UTR	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	561					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						GATCGGGGTCAACACCAACTC	0.498																																					p.V562V	Pancreas(118;454 1696 1930 13865 39976)	Atlas-SNP	.											.	SLC9A7	73	.	0			c.T1686A						PASS	.						110	90	97					X																	46491075		2203	4300	6503	SO:0001819	synonymous_variant	84679	exon14			GGGGTCAACACCA	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.1683T>A	chrX.hg19:g.46491075A>T		26.0	0.0	.		48.0	17.0	.	NM_001257291	O75827|Q5JXP9	Silent	SNP	ENST00000328306.4	hg19	CCDS14269.1																																																																																			.	.	.	none		0.498	SLC9A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056370.1	NM_032591		T	46491075	A	T	46491075	2	4	110	1	0	0	0	0	0	0	0	1	14732	117	5	5		5	SLC9A7	23	46491075	Silent	SNP	A	TCGA-BQ-5875-01A-11D-1589-08		46491075	108779485	63	7126											
MCTS1	28985	hgsc.bcm.edu	37	chrX	119739292	119739293	+	Frame_Shift_Ins	INS	-	-	AT																															aagaaaatgtgtccaactgcINSatccagttgaaaacttcagt																										TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chrX:119739292_119739293insAT	ENST00000371317.5	+	2	299_300	c.42_43insAT	c.(43-45)atcfs	p.I15fs	MCTS1_ENST00000487133.1_3'UTR|MCTS1_ENST00000371315.3_Frame_Shift_Ins_p.I16fs	NM_014060.2	NP_054779.1	Q9ULC4	MCTS1_HUMAN	malignant T cell amplified sequence 1	15					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|formation of translation preinitiation complex (GO:0001731)|IRES-dependent translational initiation (GO:0002192)|positive regulation of cell proliferation (GO:0008284)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|ribosome disassembly (GO:0032790)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	translation initiation factor activity (GO:0003743)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|stomach(1)|urinary_tract(1)	10						TGTCCAACTGCATCCAGTTGAA	0.332																																					p.C15fs		Atlas-INDEL	.											.	MCTS1	40	.	0			c.45_46insAT						PASS	.																																			SO:0001589	frameshift_variant	28985	exon2			.	AB034206	CCDS14601.1, CCDS48160.1	Xq24	2008-05-14			ENSG00000232119	ENSG00000232119			23357	protein-coding gene	gene with protein product		300587				9766643	Standard	NM_014060		Approved	MCT-1	uc011mub.2	Q9ULC4	OTTHUMG00000022303	ENST00000371317.5:c.43_44dupAT	chrX.hg19:g.119739293_119739294dupAT	ENSP00000360367:p.Ile15fs	159.0	0.0	0		131.0	28.0	0.21374	NM_001137554	B4DGY2|Q502X6	Frame_Shift_Ins	INS	ENST00000371317.5	hg19	CCDS14601.1																																																																																			.	.	.	none		0.332	MCTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058110.1	NM_014060		AT	119739293	-	AT	119739292	7	5	110	1	0	1	1	0	0	0	0	0	9409	718	25	0	66	0	MCTS1	23	119739292	Frame_Shift_Ins	INS	-	TCGA-BQ-5875-01A-11D-1589-08	73248217	119739292	35531268	64	7127	80	2									
MCTS1	28985	hgsc.bcm.edu	37	chrX	119739295	119739296	+	Nonsense_Mutation	DNP	CC	CC	AT																															gaaaatgtgtccaactgcatCcagttgaaaacttcagttat																										TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chrX:119739295_119739296CC>AT	ENST00000371317.5	+	2	302_303	c.45_46CC>AT	c.(43-48)atCCag>atATag	p.Q16*	MCTS1_ENST00000487133.1_3'UTR|MCTS1_ENST00000371315.3_Nonsense_Mutation_p.Q17*	NM_014060.2	NP_054779.1	Q9ULC4	MCTS1_HUMAN	malignant T cell amplified sequence 1	16					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|formation of translation preinitiation complex (GO:0001731)|IRES-dependent translational initiation (GO:0002192)|positive regulation of cell proliferation (GO:0008284)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|ribosome disassembly (GO:0032790)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	translation initiation factor activity (GO:0003743)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|stomach(1)|urinary_tract(1)	10						CCAACTGCATCCAGTTGAAAAC	0.337																																					p.I16I|p.Q17X		Atlas-SNP	.											.	MCTS1	40	.	0			c.C48A|c.C49T						PASS	.																																			SO:0001587	stop_gained	28985	exon2			CTGCATCCAGTTG|TGCATCCAGTTGA	AB034206	CCDS14601.1, CCDS48160.1	Xq24	2008-05-14			ENSG00000232119	ENSG00000232119			23357	protein-coding gene	gene with protein product		300587				9766643	Standard	NM_014060		Approved	MCT-1	uc011mub.2	Q9ULC4	OTTHUMG00000022303	Exception_encountered	chrX.hg19:g.119739295_119739296delinsAT	ENSP00000360367:p.Gln16*	163.0|165.0	0.0	.		126.0|123.0	30.0	.	NM_001137554	B4DGY2|Q502X6	Silent|Nonsense_Mutation	SNP	ENST00000371317.5	hg19	CCDS14601.1																																																																																			.	.	.	none		0.337	MCTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058110.1	NM_014060		AT	119739296	CC	AT	119739295	4	1	110	1	0	0	0	0	0	1	0	0	9409	845	30	4	69	4	MCTS1	23	119739295	Nonsense_Mutation	DNP	CC	TCGA-BQ-5875-01A-11D-1589-08	3	119739295	35531265	65	7128	80	2									
STAG2	10735	hgsc.bcm.edu	37	chrX	123184115	123184118	+	Frame_Shift_Del	DEL	AATG	AATG	-																															tgtatagtgatgcctttcttAatgacagttatttaaaatat																										TCGA-BQ-5875-01A-11D-1589-08	TCGA-BQ-5875-11A-01D-1589-08	AATG	AATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1f52ff0c-1578-4669-ad59-9130f5d4d0e6	f76f9283-5634-45e1-a751-f3275a7a0d7e	g.chrX:123184115_123184118delAATG	ENST00000371160.1	+	11	1263_1266	c.973_976delAATG	c.(973-978)aatgacfs	p.ND325fs	STAG2_ENST00000371145.3_Frame_Shift_Del_p.ND325fs|STAG2_ENST00000354548.5_Frame_Shift_Del_p.ND256fs|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Frame_Shift_Del_p.ND325fs|STAG2_ENST00000371144.3_Frame_Shift_Del_p.ND325fs|STAG2_ENST00000371157.3_Frame_Shift_Del_p.ND325fs	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	325	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						TGCCTTTCTTAATGACAGTTATTT	0.412																																					p.324_325del		Atlas-INDEL	.											.	STAG2	309	.	0			c.972_975del						PASS	.																																			SO:0001589	frameshift_variant	10735	exon11			.	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.973_976delAATG	chrX.hg19:g.123184115_123184118delAATG	ENSP00000360202:p.Asn325fs	252.0	0.0	0		179.0	61.0	0.340782	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Frame_Shift_Del	DEL	ENST00000371160.1	hg19	CCDS14607.1																																																																																			.	.	.	none		0.412	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		-	123184118	AATG	-	123184115	7	5	110	1	0	1	0	1	0	0	0	0	15255	362	13	0	1007	0	STAG2	23	123184115	Frame_Shift_Del	DEL	AATG	TCGA-BQ-5875-01A-11D-1589-08	3444820	123184115	32086445	66	7129											
VPS13D	55187	hgsc.bcm.edu	37	chr1	12327038	12327038	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gacctggctacagaaggaacTatgtttcctcttctagtctt	9	14	8	10	0	3	1	0	0	3	1	4	3	4	2	2	2	2	2	2	2	5	6			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr1:12327038T>C	ENST00000358136.3	+	14	1825	c.1695T>C	c.(1693-1695)acT>acC	p.T565T	VPS13D_ENST00000356315.4_Silent_p.T565T	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)		CAGAAGGAACTATGTTTCCTC	0.408																																					p.T565T		Atlas-SNP	.											.	VPS13D	316	.	0			c.T1695C						PASS	.						124	114	117					1																	12327038		2203	4300	6503	SO:0001819	synonymous_variant	55187	exon14			AGGAACTATGTTT	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.1695T>C	chr1.hg19:g.12327038T>C		141.0	0.0	.		168.0	30.0	.	NM_015378		Silent	SNP	ENST00000358136.3	hg19	CCDS30588.1																																																																																			.	.	.	none		0.408	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		C	12327038	T	C	12327038	2	2	111	1	0	0	0	0	0	0	0	1	17204	1509	53	3		3	VPS13D	1	12327038	Silent	SNP	T	TCGA-BQ-5876-01A-11D-1589-08		12327038	236923583	1	7130											
FAM73A	374986	hgsc.bcm.edu	37	chr1	78325733	78325733	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atattttttcaggtaattctTtcagaatcagctaacaggat	13	16	6	6	0	4	1	3	0	1	1	4	2	4	2	0	2	2	2	0	2	4	8			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr1:78325733T>C	ENST00000370791.3	+	11	1229	c.1197T>C	c.(1195-1197)ctT>ctC	p.L399L	FAM73A_ENST00000443751.2_Silent_p.L361L	NM_001270384.1|NM_198549.3	NP_001257313.1|NP_940951.1	Q8NAN2	FA73A_HUMAN	family with sequence similarity 73, member A	399						integral component of membrane (GO:0016021)				breast(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	19				Colorectal(170;0.226)		AGGTAATTCTTTCAGAATCAG	0.343																																					p.L399L		Atlas-SNP	.											.	FAM73A	56	.	0			c.T1197C						PASS	.						43	44	44					1																	78325733		2203	4300	6503	SO:0001819	synonymous_variant	374986	exon11			AATTCTTTCAGAA		CCDS681.1, CCDS72809.1	1p31.1	2008-02-05			ENSG00000180488	ENSG00000180488			24741	protein-coding gene	gene with protein product							Standard	NM_001270384		Approved	FLJ35093	uc010ork.3	Q8NAN2	OTTHUMG00000009766	ENST00000370791.3:c.1197T>C	chr1.hg19:g.78325733T>C		51.0	0.0	.		86.0	4.0	.	NM_001270384	Q6MZG0	Silent	SNP	ENST00000370791.3	hg19	CCDS681.1																																																																																			.	.	.	none		0.343	FAM73A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026931.1	NM_198549		C	78325733	T	C	78325733	2	2	111	1	0	0	0	0	0	0	0	1	5624	1828	64	3		3	FAM73A	1	78325733	Silent	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	65998695	78325733	170924888	2	7131											
LRRC8D	55144	hgsc.bcm.edu	37	chr1	90399406	90399406	+	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	gatcaataaaactggctttaAattttcagctgagaagcctg	14	12	8	7	0	2	1	2	1	0	1	2	3	2	1	1	1	3	2	1	1	6	5			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr1:90399406A>T	ENST00000337338.5	+	3	1186	c.779A>T	c.(778-780)aAa>aTa	p.K260I	LRRC8D_ENST00000394593.3_Missense_Mutation_p.K260I	NM_001134479.1	NP_001127951.1	Q7L1W4	LRC8D_HUMAN	leucine rich repeat containing 8 family, member D	260					ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(2)|skin(1)	29		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)		ACTGGCTTTAAATTTTCAGCT	0.458																																					p.K260I		Atlas-SNP	.											.	LRRC8D	78	.	0			c.A779T						PASS	.						44	42	43					1																	90399406		2203	4300	6503	SO:0001583	missense	55144	exon3			GCTTTAAATTTTC	AK001332	CCDS726.1	1p22.2	2008-02-05	2005-06-29	2005-06-29	ENSG00000171492	ENSG00000171492			16992	protein-coding gene	gene with protein product		612890	"leucine rich repeat containing 5"	LRRC5			Standard	NM_018103		Approved	FLJ10470	uc001dnn.3	Q7L1W4	OTTHUMG00000010583	ENST00000337338.5:c.779A>T	chr1.hg19:g.90399406A>T	ENSP00000338887:p.Lys260Ile	33.0	0.0	.		44.0	16.0	.	NM_018103	D3DT29|Q6UWB2|Q9NVW3	Missense_Mutation	SNP	ENST00000337338.5	hg19	CCDS726.1	.	.	.	.	.	.	.	.	.	.	A	14.20	2.464588	0.43736	.	.	ENSG00000171492	ENST00000337338;ENST00000394593;ENST00000441269	T;T;T	0.49432	1.35;1.35;0.78	5.88	5.88	0.94601	.	0.111169	0.64402	D	0.000017	T	0.30070	0.0753	L	0.36672	1.1	0.48696	D	0.99969	P	0.40376	0.715	B	0.42062	0.374	T	0.07121	-1.0789	9	.	.	.	.	16.3009	0.82811	1.0:0.0:0.0:0.0	.	260	Q7L1W4	LRC8D_HUMAN	I	260	ENSP00000338887:K260I;ENSP00000378093:K260I;ENSP00000405784:K260I	.	K	+	2	0	LRRC8D	90171994	1.000000	0.71417	0.980000	0.43619	0.959000	0.62525	4.701000	0.61810	2.246000	0.74042	0.533000	0.62120	AAA	.	.	.	none		0.458	LRRC8D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029203.2	NM_018103		T	90399406	A	T	90399406	3	4	111	1	0	0	0	0	1	0	0	0	9031	14	1	5	781	5	LRRC8D	1	90399406	Missense_Mutation	SNP	A	TCGA-BQ-5876-01A-11D-1589-08	12073673	90399406	158851215	3	7132											
DNTTIP2	30836	hgsc.bcm.edu	37	chr1	94342829	94342829	+	Missense_Mutation	SNP	A	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	gtttctcatttcctggtacaAtcttactatctttcttttca	7	21	3	10	0	5	0	2	0	4	0	7	0	6	0	1	1	2	2	1	1	4	8			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr1:94342829A>C	ENST00000436063.2	-	2	719	c.662T>G	c.(661-663)aTt>aGt	p.I221S	DNTTIP2_ENST00000460191.1_5'UTR	NM_014597.4	NP_055412.2	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 2	221					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	38		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		TCCTGGTACAATCTTACTATC	0.393																																					p.I221S		Atlas-SNP	.											.	DNTTIP2	59	.	0			c.T662G						PASS	.						157	156	157					1																	94342829		1874	4097	5971	SO:0001583	missense	30836	exon2			GGTACAATCTTAC	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.662T>G	chr1.hg19:g.94342829A>C	ENSP00000411010:p.Ile221Ser	264.0	0.0	.		295.0	109.0	.	NM_014597	Q12987|Q53H59|Q5TFJ4|Q6TLI0|Q76MJ8|Q86WX9	Missense_Mutation	SNP	ENST00000436063.2	hg19	CCDS44174.1	.	.	.	.	.	.	.	.	.	.	A	7.865	0.726984	0.15439	.	.	ENSG00000067334	ENST00000436063	T	0.16743	2.32	4.97	-4.84	0.03151	.	1.525530	0.03836	N	0.269774	T	0.04998	0.0134	L	0.56769	1.78	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.45308	-0.9270	10	0.72032	D	0.01	.	0.8184	0.01107	0.315:0.2126:0.2868:0.1855	.	221	Q5QJE6	TDIF2_HUMAN	S	221	ENSP00000411010:I221S	ENSP00000352137:I221S	I	-	2	0	DNTTIP2	94115417	0.000000	0.05858	0.000000	0.03702	0.318000	0.28184	0.416000	0.21198	-0.444000	0.07170	0.533000	0.62120	ATT	.	.	.	none		0.393	DNTTIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028317.2	NM_014597		C	94342829	A	C	94342829	3	2	111	1	0	0	0	0	1	0	0	0	4684	101	4	5	1632	5	DNTTIP2	1	94342829	Missense_Mutation	SNP	A	TCGA-BQ-5876-01A-11D-1589-08	3943423	94342829	154907792	4	7133											
SASS6	163786	hgsc.bcm.edu	37	chr1	100572514	100572514	+	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	ttgctttcttcaagttttttAactgtagcttctaattgttc	7	22	5	7	0	3	0	1	0	2	0	4	0	3	0	0	0	3	5	0	0	4	11			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr1:100572514A>C	ENST00000287482.5	-	12	1502	c.1362T>G	c.(1360-1362)gtT>gtG	p.V454V	SASS6_ENST00000535161.1_Silent_p.V287V|SASS6_ENST00000462159.1_5'UTR	NM_194292.1	NP_919268.1	Q6UVJ0	SAS6_HUMAN	spindle assembly 6 homolog (C. elegans)	454					centriole replication (GO:0007099)|centrosome duplication (GO:0051298)	centriole (GO:0005814)|centrosome (GO:0005813)|deuterosome (GO:0098536)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	19		all_epithelial(167;4.58e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.085)|all cancers(265;0.139)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.197)		CAAGTTTTTTAACTGTAGCTT	0.249																																					p.V454V		Atlas-SNP	.											.	SASS6	61	.	0			c.T1362G						PASS	.						68	68	68					1																	100572514		2189	4293	6482	SO:0001819	synonymous_variant	163786	exon12			TTTTTTAACTGTA	AL834265	CCDS764.1	1p21.3	2008-02-05			ENSG00000156876	ENSG00000156876			25403	protein-coding gene	gene with protein product		609321				15665853, 14654843	Standard	NM_194292		Approved	DKFZp761A078, SAS-6, FLJ22097, SAS6	uc001dsu.3	Q6UVJ0	OTTHUMG00000010754	ENST00000287482.5:c.1362T>G	chr1.hg19:g.100572514A>C		37.0	0.0	.		38.0	11.0	.	NM_194292	D3DT55|Q8N3K0	Silent	SNP	ENST00000287482.5	hg19	CCDS764.1																																																																																			.	.	.	none		0.249	SASS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029656.2	NM_194292		C	100572514	A	C	100572514	2	2	111	1	0	0	0	0	0	0	0	1	13863	349	13	5		5	SASS6	1	100572514	Silent	SNP	A	TCGA-BQ-5876-01A-11D-1589-08	6229685	100572514	148678107	5	7134											
HORMAD1	84072	hgsc.bcm.edu	37	chr1	150679129	150679129	+	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	atagtatagttgagtcaataTtttccattcgttctctctca	10	18	5	8	1	3	1	2	1	2	0	7	1	4	1	1	0	0	3	1	0	5	9			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr1:150679129T>A	ENST00000361824.2	-	10	809	c.704A>T	c.(703-705)aAt>aTt	p.N235I	HORMAD1_ENST00000368993.2_Missense_Mutation_p.N235I|HORMAD1_ENST00000368995.4_Missense_Mutation_p.N155I|HORMAD1_ENST00000322343.7_Missense_Mutation_p.N228I	NM_032132.4	NP_115508.2	Q86X24	HORM1_HUMAN	HORMA domain containing 1	235					blastocyst development (GO:0001824)|meiotic DNA double-strand break formation (GO:0042138)|meiotic nuclear division (GO:0007126)|meiotic recombination checkpoint (GO:0051598)|meiotic sister chromatid cohesion (GO:0051177)|oogenesis (GO:0048477)|regulation of homologous chromosome segregation (GO:0060629)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(3)	16	all_cancers(9;3.23e-52)|all_epithelial(9;4.68e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.0009)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;2.32e-23)|all cancers(9;5.21e-23)|OV - Ovarian serous cystadenocarcinoma(6;6.72e-15)|BRCA - Breast invasive adenocarcinoma(12;0.000479)|LUSC - Lung squamous cell carcinoma(543;0.171)			TGAGTCAATATTTTCCATTCG	0.343																																					p.N235I		Atlas-SNP	.											.,1	HORMAD1	59	.	0			c.A704T						PASS	.						202	191	195					1																	150679129		2203	4300	6503	SO:0001583	missense	84072	exon10			TCAATATTTTCCA	AL136755	CCDS967.1, CCDS55633.1	1q21.2	2009-03-09			ENSG00000143452	ENSG00000143452			25245	protein-coding gene	gene with protein product	"cancer/testis antigen 46"	609824				11230166, 15999985	Standard	NM_032132		Approved	DKFZP434A1315, CT46	uc001evk.2	Q86X24	OTTHUMG00000035005	ENST00000361824.2:c.704A>T	chr1.hg19:g.150679129T>A	ENSP00000355167:p.Asn235Ile	209.0	0.0	.		226.0	86.0	.	NM_032132	A6NMK2|B3KUK1|Q4G114|Q5T5I3|Q5T5I4|Q5T5I5|Q6FIC1|Q9H0K8	Missense_Mutation	SNP	ENST00000361824.2	hg19	CCDS967.1	.	.	.	.	.	.	.	.	.	.	T	18.41	3.617697	0.66787	.	.	ENSG00000143452	ENST00000368995;ENST00000368993;ENST00000368992;ENST00000540570;ENST00000322343;ENST00000361824;ENST00000368987;ENST00000442853	T;T;T;T	0.47177	0.85;1.42;1.43;1.42	5.48	4.34	0.51931	.	0.219611	0.53938	D	0.000043	T	0.38188	0.1031	L	0.32530	0.975	0.28943	N	0.890864	D;D;D	0.71674	0.998;0.988;0.964	D;P;P	0.65010	0.931;0.878;0.65	T	0.28004	-1.0057	10	0.72032	D	0.01	-12.6203	7.2033	0.25893	0.0:0.2218:0.0:0.7781	.	155;228;235	Q86X24-4;Q86X24-2;Q86X24	.;.;HORM1_HUMAN	I	155;235;164;155;228;235;164;157	ENSP00000357991:N155I;ENSP00000357989:N235I;ENSP00000326489:N228I;ENSP00000355167:N235I	ENSP00000326489:N228I	N	-	2	0	HORMAD1	148945753	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	1.692000	0.37731	2.092000	0.63282	0.383000	0.25322	AAT	.	.	.	none		0.343	HORMAD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084722.1	NM_032132		A	150679129	T	A	150679129	3	1	111	1	0	0	0	0	1	0	0	0	7293	1493	52	5	504	5	HORMAD1	1	150679129	Missense_Mutation	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	50106615	150679129	98571492	6	7135											
CREG1	8804	hgsc.bcm.edu	37	chr1	167515357	167515357	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgaactgtgacattataatAttcttctggtgtcacgattt	10	17	7	7	1	3	2	1	2	2	0	3	3	3	2	0	1	1	0	0	1	4	6			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr1:167515357A>G	ENST00000370509.4	-	3	665	c.640T>C	c.(640-642)Tat>Cat	p.Y214H	CREG1_ENST00000466652.1_5'UTR	NM_003851.2	NP_003842.1	O75629	CREG1_HUMAN	cellular repressor of E1A-stimulated genes 1	214					cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	extracellular vesicular exosome (GO:0070062)|transcription factor complex (GO:0005667)	FMN binding (GO:0010181)|oxidoreductase activity (GO:0016491)|transcription corepressor activity (GO:0003714)										ACATTATAATATTCTTCTGGT	0.438																																					p.Y214H		Atlas-SNP	.											.	CREG1	6	.	0			c.T640C						PASS	.						70	73	72					1																	167515357		2203	4300	6503	SO:0001583	missense	8804	exon3			TATAATATTCTTC	AF084523	CCDS1262.1	1q24	2008-02-05	2004-09-22	2004-09-22	ENSG00000143162	ENSG00000143162			2351	protein-coding gene	gene with protein product			"cellular repressor of E1A-stimulated genes"	CREG		9710587	Standard	NM_003851		Approved		uc001gel.3	O75629	OTTHUMG00000034682	ENST00000370509.4:c.640T>C	chr1.hg19:g.167515357A>G	ENSP00000359540:p.Tyr214His	66.0	0.0	.		67.0	29.0	.	NM_003851	B2RDD4|Q8N9A3	Missense_Mutation	SNP	ENST00000370509.4	hg19	CCDS1262.1	.	.	.	.	.	.	.	.	.	.	A	19.78	3.891151	0.72524	.	.	ENSG00000143162	ENST00000370509	.	.	.	5.86	5.86	0.93980	FMN-binding split barrel-related (1);FMN-binding split barrel (1);	0.000000	0.85682	D	0.000000	D	0.83326	0.5230	M	0.91818	3.245	0.53005	D	0.999968	D	0.89917	1.0	D	0.97110	1.0	D	0.87426	0.2385	8	0.87932	D	0	-7.3711	16.2453	0.82441	1.0:0.0:0.0:0.0	.	214	O75629	CREG1_HUMAN	H	214	.	ENSP00000359540:Y214H	Y	-	1	0	CREG1	165781981	1.000000	0.71417	0.810000	0.32431	0.581000	0.36288	8.428000	0.90278	2.241000	0.73720	0.533000	0.62120	TAT	.	.	.	none		0.438	CREG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083911.1	NM_003851		G	167515357	A	G	167515357	3	3	111	1	0	0	0	0	1	0	0	0	3866	449	16	3	30	3	CREG1	1	167515357	Missense_Mutation	SNP	A	TCGA-BQ-5876-01A-11D-1589-08	16836228	167515357	81735264	7	7136											
HMCN1	83872	hgsc.bcm.edu	37	chr1	185984290	185984290	+	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	ttgttctgaaatcctttgtaGttccacctagtattaaagga	11	16	7	7	0	1	1	0	1	1	0	3	2	3	2	3	1	0	4	3	1	6	8	rs568290303	byFrequency	TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr1:185984290G>A	ENST00000271588.4	+	31	4859		c.e31-1		HMCN1_ENST00000367492.2_Splice_Site	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1						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						ATCCTTTGTAGTTCCACCTAG	0.338																																					.		Atlas-SNP	.											HMCN1,NS,carcinoma,0,1	HMCN1	797	.	0			c.4631-1G>A						PASS	.						72	71	71					1																	185984290		2203	4299	6502	SO:0001630	splice_region_variant	83872	exon31			TTTGTAGTTCCAC	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.4631-1G>A	chr1.hg19:g.185984290G>A		129.0	1.0	.		93.0	37.0	.	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Splice_Site	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.501313	0.85176	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	.	.	.	5.22	5.22	0.72569	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.1551	0.93507	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	HMCN1	184250913	1.000000	0.71417	0.999000	0.59377	0.957000	0.61999	8.911000	0.92721	2.583000	0.87209	0.557000	0.71058	.	.	.	.	none		0.338	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	Intron	A	185984290	G	A	185984290	5	1	111	1	0	0	0	0	0	0	1	0	7227	1043	36	2	4752	2	HMCN1	1	185984290	Splice_Site	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	18468933	185984290	63266331	8	7137											
ASAP2	8853	hgsc.bcm.edu	37	chr2	9533671	9533671	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccagcgtaatggaagcctTgagccagccgagcaagcctg	10	5	13	13	2	0	1	0	1	0	0	0	3	0	2	5	1	6	2	5	1	3	2			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr2:9533671T>C	ENST00000281419.3	+	24	2919	c.2579T>C	c.(2578-2580)tTg>tCg	p.L860S	ASAP2_ENST00000315273.4_Missense_Mutation_p.L815S|ASAP2_ENST00000491413.1_3'UTR	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	860	Pro-rich.				positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						ATGGAAGCCTTGAGCCAGCCG	0.701																																					p.L860S		Atlas-SNP	.											.	ASAP2	91	.	0			c.T2579C						PASS	.						13	15	14					2																	9533671		2199	4294	6493	SO:0001583	missense	8853	exon24			AAGCCTTGAGCCA	AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2721	protein-coding gene	gene with protein product	"centaurin, beta 3"	603817	"development and differentiation enhancing factor 2"	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.2579T>C	chr2.hg19:g.9533671T>C	ENSP00000281419:p.Leu860Ser	27.0	0.0	.		19.0	6.0	.	NM_003887	D6W4Y8	Missense_Mutation	SNP	ENST00000281419.3	hg19	CCDS1661.1	.	.	.	.	.	.	.	.	.	.	T	10.11	1.260257	0.23051	.	.	ENSG00000151693	ENST00000281419;ENST00000315273	T;T	0.58506	0.42;0.33	5.36	5.36	0.76844	Src homology-3 domain (1);	4.673060	0.00166	N	0.000005	T	0.67702	0.2921	N	0.19112	0.55	0.35637	D	0.81066	D;B	0.69078	0.997;0.011	D;B	0.75484	0.986;0.01	T	0.56956	-0.7893	10	0.18710	T	0.47	.	15.3426	0.74309	0.0:0.0:0.0:1.0	.	815;860	O43150-2;O43150	.;ASAP2_HUMAN	S	860;815	ENSP00000281419:L860S;ENSP00000316404:L815S	ENSP00000281419:L860S	L	+	2	0	ASAP2	9451122	1.000000	0.71417	0.799000	0.32177	0.419000	0.31324	4.442000	0.59988	2.034000	0.60081	0.379000	0.24179	TTG	.	.	.	none		0.701	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887		C	9533671	T	C	9533671	3	2	111	1	0	0	0	0	1	0	0	0	1011	1821	63	3	2673	3	ASAP2	2	9533671	Missense_Mutation	SNP	T	TCGA-BQ-5876-01A-11D-1589-08		9533671	233665702	9	7138											
NRBP1	29959	hgsc.bcm.edu	37	chr2	27664588	27664588	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccccaggctgaccagagccGgttgacttctctgctagaag	8	8	11	14	1	1	4	0	2	1	2	2	4	1	4	4	2	2	3	4	2	2	3	rs141700147	byFrequency	TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr2:27664588G>A	ENST00000233557.3	+	19	2349	c.1517G>A	c.(1516-1518)cGg>cAg	p.R506Q	KRTCAP3_ENST00000407293.1_5'Flank|NRBP1_ENST00000379852.3_Missense_Mutation_p.R506Q|KRTCAP3_ENST00000543753.1_5'Flank|KRTCAP3_ENST00000288873.3_5'Flank|NRBP1_ENST00000379863.3_Missense_Mutation_p.R514Q			Q9UHY1	NRBP_HUMAN	nuclear receptor binding protein 1	506					ER to Golgi vesicle-mediated transport (GO:0006888)|gene expression (GO:0010467)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell projection (GO:0042995)|endomembrane system (GO:0012505)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)	p.R506Q(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19	Acute lymphoblastic leukemia(172;0.155)					GACCAGAGCCGGTTGACTTCT	0.547													G|||	6	0.00119808	0.0045	0	5008	,	,		18142	0		0	False		,,,				2504	0				p.R506Q		Atlas-SNP	.											NRBP1,colon,carcinoma,0,1	NRBP1	40	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1517A						PASS	.	G	GLN/ARG	4,4402	9.9+/-24.2	0,4,2199	179	183	182		1517	5.7	1	2	dbSNP_134	182	1,8599	1.2+/-3.3	0,1,4299	yes	missense	NRBP1	NM_013392.2	43	0,5,6498	AA,AG,GG		0.0116,0.0908,0.0384	possibly-damaging	506/536	27664588	5,13001	2203	4300	6503	SO:0001583	missense	29959	exon18			AGAGCCGGTTGAC	AF113249	CCDS1753.1	2p23	2008-02-05	2005-12-22	2005-12-22	ENSG00000115216	ENSG00000115216			7993	protein-coding gene	gene with protein product		606010	"nuclear receptor binding protein"	NRBP		10843813, 11956649	Standard	NM_013392		Approved	BCON3, MUDPNP, MADM	uc002rkp.3	Q9UHY1	OTTHUMG00000097789	ENST00000233557.3:c.1517G>A	chr2.hg19:g.27664588G>A	ENSP00000233557:p.Arg506Gln	314.0	1.0	.		334.0	127.0	.	NM_013392	B3KV40|D6W558|Q53FZ5|Q96SU3	Missense_Mutation	SNP	ENST00000233557.3	hg19	CCDS1753.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.944186	0.73672	9.08E-4	1.16E-4	ENSG00000115216	ENST00000233557;ENST00000421823;ENST00000379852;ENST00000379863	T;T;T	0.14022	2.84;2.84;2.54	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.14399	0.0348	L	0.43152	1.355	0.58432	D	0.999999	B;B;B	0.32302	0.363;0.239;0.154	B;B;B	0.24701	0.022;0.055;0.025	T	0.02093	-1.1215	10	0.45353	T	0.12	-8.6676	18.2912	0.90131	0.0:0.0:1.0:0.0	.	486;514;506	B4DW31;F8W6G1;Q9UHY1	.;.;NRBP_HUMAN	Q	506;486;506;514	ENSP00000233557:R506Q;ENSP00000369181:R506Q;ENSP00000369192:R514Q	ENSP00000233557:R506Q	R	+	2	0	NRBP1	27518092	1.000000	0.71417	0.999000	0.59377	0.972000	0.66771	6.787000	0.75099	2.662000	0.90505	0.561000	0.74099	CGG	.	G|1.000;A|0.000	0.000	weak		0.547	NRBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215033.1	NM_013392		A	27664588	G	A	27664588	3	1	111	1	0	0	0	0	1	0	0	0	10649	1116	39	1	1583	1	NRBP1	2	27664588	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	18130917	27664588	215534785	10	7139											
SLC8A1	6546	hgsc.bcm.edu	37	chr2	40656328	40656328	+	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	gaggcgagtagcttgaatgcGataaaatgctctactttttt	11	14	10	6	2	1	1	0	1	1	0	1	4	1	1	0	1	4	3	0	1	5	7	rs370199920		TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr2:40656328G>T	ENST00000403092.1	-	2	1126	c.1093C>A	c.(1093-1095)Cgc>Agc	p.R365S	SLC8A1_ENST00000402441.1_Missense_Mutation_p.R365S|SLC8A1_ENST00000405901.3_Missense_Mutation_p.R365S|SLC8A1_ENST00000332839.4_Missense_Mutation_p.R365S|SLC8A1_ENST00000406391.2_Missense_Mutation_p.R365S|SLC8A1_ENST00000406785.2_Missense_Mutation_p.R365S|SLC8A1_ENST00000408028.2_Missense_Mutation_p.R365S|SLC8A1_ENST00000405269.1_Missense_Mutation_p.R365S|SLC8A1_ENST00000542024.1_Missense_Mutation_p.R365S|SLC8A1_ENST00000542756.1_Missense_Mutation_p.R365S			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1	365					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)	GCTTGAATGCGATAAAATGCT	0.433																																					p.R365S		Atlas-SNP	.											SLC8A1,colon,carcinoma,+1,1	SLC8A1	221	.	0			c.C1093A						PASS	.						165	157	160					2																	40656328		2203	4300	6503	SO:0001583	missense	6546	exon1			GAATGCGATAAAA		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.1093C>A	chr2.hg19:g.40656328G>T	ENSP00000384763:p.Arg365Ser	236.0	0.0	.		267.0	14.0	.	NM_001252624	A8K6N1|D6W595|O95849|Q4QQG6|Q587I6|Q59GN4|Q9UBL8|Q9UD55|Q9UDN1|Q9UDN2|Q9UKX6	Missense_Mutation	SNP	ENST00000403092.1	hg19	CCDS1806.1	.	.	.	.	.	.	.	.	.	.	G	17.93	3.509948	0.64522	.	.	ENSG00000183023	ENST00000406785;ENST00000378715;ENST00000542756;ENST00000403092;ENST00000405901;ENST00000402441;ENST00000405269;ENST00000332839;ENST00000408028;ENST00000535962;ENST00000406391;ENST00000542024	T;T;T;T;T;T;T;T;T;T	0.53857	0.65;0.68;0.67;0.68;0.65;0.65;0.67;0.6;0.65;0.64	6.17	5.29	0.74685	Heat shock protein DnaJ, N-terminal (1);	0.049164	0.85682	D	0.000000	T	0.78233	0.4251	M	0.91663	3.23	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.996;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.995;1.0;0.996;1.0	D	0.83814	0.0243	10	0.87932	D	0	.	14.9877	0.71362	0.0:0.0:0.857:0.143	.	365;365;365;365;365	P32418-4;P32418-2;P32418-3;F6VPY9;P32418	.;.;.;.;NAC1_HUMAN	S	365	ENSP00000383886:R365S;ENSP00000440727:R365S;ENSP00000384763:R365S;ENSP00000385678:R365S;ENSP00000385188:R365S;ENSP00000385535:R365S;ENSP00000332931:R365S;ENSP00000384908:R365S;ENSP00000385811:R365S;ENSP00000443515:R365S	ENSP00000332931:R365S	R	-	1	0	SLC8A1	40509832	1.000000	0.71417	0.992000	0.48379	0.990000	0.78478	7.812000	0.86109	1.600000	0.50102	0.655000	0.94253	CGC	.	.	.	alt		0.433	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	NM_021097		T	40656328	G	T	40656328	3	4	111	1	0	0	0	0	1	0	0	0	14719	1058	37	4	1976	4	SLC8A1	2	40656328	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	12991740	40656328	202543045	11	7140											
MSH6	2956	hgsc.bcm.edu	37	chr2	48027125	48027125	+	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	tatgacttcagagtctgattCcattgggttgacaccaggag	10	12	11	8	0	2	4	1	3	1	1	3	5	3	5	2	2	0	1	2	2	1	5			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr2:48027125C>G	ENST00000234420.5	+	4	2155	c.2003C>G	c.(2002-2004)tCc>tGc	p.S668C	FBXO11_ENST00000405808.1_Intron|MSH6_ENST00000540021.1_Missense_Mutation_p.S538C|MSH6_ENST00000538136.1_Missense_Mutation_p.S366C	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	668					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)			GAGTCTGATTCCATTGGGTTG	0.433			"Mis, N, F, S"		colorectal	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.S668C		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.C2003G						PASS	.						152	146	148					2																	48027125		2203	4300	6503	SO:0001583	missense	2956	exon4	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	CTGATTCCATTGG	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.2003C>G	chr2.hg19:g.48027125C>G	ENSP00000234420:p.Ser668Cys	274.0	0.0	.		282.0	107.0	.	NM_000179	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Missense_Mutation	SNP	ENST00000234420.5	hg19	CCDS1836.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.735857	0.49045	.	.	ENSG00000116062	ENST00000234420;ENST00000544857;ENST00000540021;ENST00000538136	D;D;D	0.88664	-2.04;-2.12;-2.41	4.8	3.92	0.45320	DNA mismatch repair protein MutS, connector (1);	0.361706	0.32518	N	0.005990	D	0.93112	0.7807	M	0.76574	2.34	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.976	D;D;P	0.67231	0.95;0.95;0.738	D	0.93502	0.6845	10	0.72032	D	0.01	-2.7325	12.8528	0.57867	0.0:0.9212:0.0:0.0788	.	538;668;668	B4DF41;P52701;P52701-2	.;MSH6_HUMAN;.	C	668;666;538;366	ENSP00000234420:S668C;ENSP00000446475:S538C;ENSP00000438580:S366C	ENSP00000234420:S668C	S	+	2	0	MSH6	47880629	1.000000	0.71417	0.996000	0.52242	0.942000	0.58702	5.875000	0.69660	1.243000	0.43853	0.460000	0.39030	TCC	.	.	.	none		0.433	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179		G	48027125	C	G	48027125	3	3	111	1	0	0	0	0	1	0	0	0	9881	855	30	4	2017	4	MSH6	2	48027125	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	7370797	48027125	195172248	12	7141											
TCF7L1	83439	hgsc.bcm.edu	37	chr2	85536242	85536242	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcctcctcccacgggagcaTgctggactccccggccactc	5	7	10	19	2	0	0	0	0	0	0	4	2	3	2	6	3	3	2	6	3	0	0			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr2:85536242T>C	ENST00000282111.3	+	12	1699	c.1424T>C	c.(1423-1425)aTg>aCg	p.M475T		NM_031283.2	NP_112573.1	Q9HCS4	TF7L1_HUMAN	transcription factor 7-like 1 (T-cell specific, HMG-box)	475					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						CACGGGAGCATGCTGGACTCC	0.652																																					p.M475T		Atlas-SNP	.											.	TCF7L1	44	.	0			c.T1424C						PASS	.						93	102	99					2																	85536242		2203	4300	6503	SO:0001583	missense	83439	exon12			GGAGCATGCTGGA	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.1424T>C	chr2.hg19:g.85536242T>C	ENSP00000282111:p.Met475Thr	307.0	1.0	.		264.0	89.0	.	NM_031283	Q53R97|Q6PD70|Q9NP00	Missense_Mutation	SNP	ENST00000282111.3	hg19	CCDS1971.1	.	.	.	.	.	.	.	.	.	.	T	16.35	3.097296	0.56075	.	.	ENSG00000152284	ENST00000282111	T	0.34072	1.38	5.11	0.36	0.16097	.	0.117117	0.85682	N	0.000000	T	0.37972	0.1023	L	0.54323	1.7	0.29754	N	0.836071	P	0.50156	0.932	P	0.58391	0.838	T	0.35301	-0.9794	10	0.13108	T	0.6	.	3.6615	0.08240	0.1572:0.2705:0.0:0.5722	.	475	Q9HCS4	TF7L1_HUMAN	T	475	ENSP00000282111:M475T	ENSP00000282111:M475T	M	+	2	0	TCF7L1	85389753	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	2.286000	0.43496	-0.075000	0.12798	0.448000	0.29417	ATG	.	.	.	none		0.652	TCF7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252301.2	NM_031283		C	85536242	T	C	85536242	3	2	111	1	0	0	0	0	1	0	0	0	15709	1464	51	3	1470	3	TCF7L1	2	85536242	Missense_Mutation	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	37509117	85536242	157663131	13	7142											
EIF5B	9669	hgsc.bcm.edu	37	chr2	100015354	100015354	+	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	ggaagacattttgaagctacAgatattcttgttagtaaggt	13	14	10	4	0	1	3	0	1	1	2	1	4	1	4	0	2	2	3	0	2	6	8			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr2:100015354A>C	ENST00000289371.6	+	23	3739	c.3537A>C	c.(3535-3537)acA>acC	p.T1179T		NM_015904.3	NP_056988.3	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B	1179					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|regulation of translational initiation (GO:0006446)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						TTGAAGCTACAGATATTCTTG	0.398																																					p.T1179T	Colon(162;2388 2567 2705 3444)	Atlas-SNP	.											.	EIF5B	95	.	0			c.A3537C						PASS	.						70	64	66					2																	100015354		1859	4090	5949	SO:0001819	synonymous_variant	9669	exon23			AGCTACAGATATT	AF078035	CCDS42721.1	2q11.2	2012-09-20			ENSG00000158417	ENSG00000158417			30793	protein-coding gene	gene with protein product	"translation initiation factor IF2"	606086				10200264, 10432305	Standard	XM_005264075		Approved	IF2, KIAA0741, DKFZp434I036, FLJ10524	uc002tab.3	O60841	OTTHUMG00000153242	ENST00000289371.6:c.3537A>C	chr2.hg19:g.100015354A>C		81.0	0.0	.		86.0	33.0	.	NM_015904	O95805|Q53RV7|Q53SI8|Q9UF81|Q9UMN7	Silent	SNP	ENST00000289371.6	hg19	CCDS42721.1																																																																																			.	.	.	none		0.398	EIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330364.2	NM_015904		C	100015354	A	C	100015354	2	2	111	1	0	0	0	0	0	0	0	1	5046	175	7	5		5	EIF5B	2	100015354	Silent	SNP	A	TCGA-BQ-5876-01A-11D-1589-08	14479112	100015354	143184019	14	7143											
WDR33	55339	hgsc.bcm.edu	37	chr2	128484249	128484249	+	Frame_Shift_Del	DEL	T	T	-																															ttgcaagactctgcccagtcTtgggatcccagaacttgatt																										TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr2:128484249delT	ENST00000322313.4	-	8	985	c.827delA	c.(826-828)aagfs	p.K276fs		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	276					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)		CTGCCCAGTCTTGGGATCCCA	0.468																																					p.K276fs		Atlas-INDEL	.											.	WDR33	136	.	0			c.828delG						PASS	.						154	153	153					2																	128484249		2203	4300	6503	SO:0001589	frameshift_variant	55339	exon8			.		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.827delA	chr2.hg19:g.128484249delT	ENSP00000325377:p.Lys276fs	130.0	0.0	0		136.0	38.0	0.279412	NM_018383	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Frame_Shift_Del	DEL	ENST00000322313.4	hg19	CCDS2150.1																																																																																			.	.	.	none		0.468	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383		-	128484249	T	-	128484249	7	5	111	1	0	1	0	1	0	0	0	0	17299	1609	56	0	3243	0	WDR33	2	128484249	Frame_Shift_Del	DEL	T	TCGA-BQ-5876-01A-11D-1589-08	28468895	128484249	114715124	15	7144											
CXCR4	7852	hgsc.bcm.edu	37	chr2	136873381	136873381	+	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	gagtagatggtgggcaggaaGattttattgaaattagcatt	13	13	13	2	0	0	3	0	1	0	2	0	5	0	4	0	3	1	3	0	3	5	6			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr2:136873381G>T	ENST00000241393.3	-	2	221	c.117C>A	c.(115-117)atC>atA	p.I39I	CXCR4_ENST00000466288.1_5'UTR|CXCR4_ENST00000409817.1_Silent_p.I43I	NM_003467.2	NP_003458.1	P61073	CXCR4_HUMAN	chemokine (C-X-C motif) receptor 4	39					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)	TGGGCAGGAAGATTTTATTGA	0.438																																					p.I43I		Atlas-SNP	.											CXCR4,NS,carcinoma,0,1	CXCR4	51	.	0			c.C129A						PASS	.						128	129	128					2																	136873381		2203	4300	6503	SO:0001819	synonymous_variant	7852	exon1			CAGGAAGATTTTA	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.117C>A	chr2.hg19:g.136873381G>T		145.0	1.0	.		163.0	61.0	.	NM_001008540	B2R5N0|O60835|P30991|P56438|Q53S69|Q9BXA0|Q9UKN2	Silent	SNP	ENST00000241393.3	hg19	CCDS46420.1																																																																																			.	.	.	none		0.438	CXCR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331732.1			T	136873381	G	T	136873381	2	4	111	1	0	0	0	0	0	0	0	1	4095	932	33	4		4	CXCR4	2	136873381	Silent	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	8389132	136873381	106325992	16	7145											
DNAH7	56171	hgsc.bcm.edu	37	chr2	196749321	196749321	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actcttacctcagtgacaaaTtgataatcataaattgttcc	14	14	4	9	0	3	2	2	2	1	0	4	2	4	2	2	0	1	1	2	0	5	6			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr2:196749321T>C	ENST00000312428.6	-	35	5851	c.5751A>G	c.(5749-5751)caA>caG	p.Q1917Q		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1917					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						CAGTGACAAATTGATAATCAT	0.433																																					p.Q1917Q		Atlas-SNP	.											.	DNAH7	512	.	0			c.A5751G						PASS	.						77	75	76					2																	196749321		1911	4123	6034	SO:0001819	synonymous_variant	56171	exon35			GACAAATTGATAA	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.5751A>G	chr2.hg19:g.196749321T>C		83.0	0.0	.		106.0	33.0	.	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	hg19	CCDS42794.1																																																																																			.	.	.	none		0.433	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		C	196749321	T	C	196749321	2	2	111	1	0	0	0	0	0	0	0	1	4608	1490	52	3		3	DNAH7	2	196749321	Silent	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	59875940	196749321	46450052	17	7146											
ERBB4	2066	hgsc.bcm.edu	37	chr2	212426810	212426810	+	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	catacttgccatgatcagagCttcctgtaagaaaaaaatgc	15	10	7	9	0	1	3	1	1	0	2	2	3	2	3	2	0	4	2	2	0	5	4			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr2:212426810C>A	ENST00000342788.4	-	20	2615	c.2305G>T	c.(2305-2307)Gct>Tct	p.A769S	ERBB4_ENST00000436443.1_Missense_Mutation_p.A769S|ERBB4_ENST00000402597.1_Missense_Mutation_p.A759S	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	769	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	ATGATCAGAGCTTCCTGTAAG	0.403										TSP Lung(8;0.080)																											p.A769S		Atlas-SNP	.											.	ERBB4	480	.	0			c.G2305T						PASS	.						81	75	77					2																	212426810		2203	4300	6503	SO:0001583	missense	2066	exon20			TCAGAGCTTCCTG	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.2305G>T	chr2.hg19:g.212426810C>A	ENSP00000342235:p.Ala769Ser	80.0	0.0	.		107.0	42.0	.	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	hg19	CCDS2394.1	.	.	.	.	.	.	.	.	.	.	C	32	5.153661	0.94645	.	.	ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597	T;T;T	0.64085	-0.08;-0.08;-0.08	5.36	5.36	0.76844	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	0.81847	0.4909	M	0.82517	2.595	0.80722	D	1	D;P;D;D	0.76494	0.999;0.738;0.999;0.999	D;D;D;D	0.91635	0.999;0.911;0.998;0.999	D	0.83933	0.0307	10	0.72032	D	0.01	.	19.4633	0.94927	0.0:1.0:0.0:0.0	.	759;759;769;769	Q15303-4;Q15303-2;Q15303-3;Q15303	.;.;.;ERBB4_HUMAN	S	769;769;759	ENSP00000342235:A769S;ENSP00000403204:A769S;ENSP00000385565:A759S	ENSP00000342235:A769S	A	-	1	0	ERBB4	212135055	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.776000	0.85560	2.666000	0.90696	0.655000	0.94253	GCT	.	.	.	none		0.403	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		A	212426810	C	A	212426810	3	1	111	1	0	0	0	0	1	0	0	0	5211	797	28	4	1657	4	ERBB4	2	212426810	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	15677489	212426810	30772563	18	7147											
FBXO45	200933	hgsc.bcm.edu	37	chr3	196304554	196304554	+	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	cgggcccccatgcagtgccaAggttatgtggcattgctggg	6	9	15	11	1	0	0	0	0	0	0	0	0	0	0	3	4	3	4	3	4	2	2			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr3:196304554A>T	ENST00000311630.6	+	2	846	c.549A>T	c.(547-549)caA>caT	p.Q183H	FBXO45_ENST00000440469.1_Missense_Mutation_p.Q4H	NM_001105573.1	NP_001099043.1	P0C2W1	FBSP1_HUMAN	F-box protein 45	183	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				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)		TGCAGTGCCAAGGTTATGTGG	0.547																																					p.Q183H		Atlas-SNP	.											.	FBXO45	18	.	0			c.A549T						PASS	.						48	49	49					3																	196304554		1953	4148	6101	SO:0001583	missense	200933	exon2			GTGCCAAGGTTAT	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.549A>T	chr3.hg19:g.196304554A>T	ENSP00000310332:p.Gln183His	31.0	0.0	.		27.0	23.0	.	NM_001105573	A6NF90|D3DXB5	Missense_Mutation	SNP	ENST00000311630.6	hg19	CCDS46985.1	.	.	.	.	.	.	.	.	.	.	A	9.264	1.043862	0.19748	.	.	ENSG00000174013	ENST00000440469;ENST00000311630	T;T	0.60171	0.21;0.21	4.95	2.42	0.29668	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.052694	0.85682	N	0.000000	T	0.25754	0.0627	N	0.01789	-0.72	0.54753	D	0.999983	B	0.11235	0.004	B	0.12156	0.007	T	0.02450	-1.1157	10	0.25106	T	0.35	-22.4406	6.7957	0.23725	0.6401:0.0:0.3599:0.0	.	183	P0C2W1	FBSP1_HUMAN	H	4;183	ENSP00000389868:Q4H;ENSP00000310332:Q183H	ENSP00000310332:Q183H	Q	+	3	2	FBXO45	197788951	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.363000	0.52321	0.403000	0.25479	0.374000	0.22700	CAA	.	.	.	none		0.547	FBXO45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340687.2			T	196304554	A	T	196304554	3	4	111	1	0	0	0	0	1	0	0	0	5761	69	3	5	555	5	FBXO45	3	196304554	Missense_Mutation	SNP	A	TCGA-BQ-5876-01A-11D-1589-08		196304554	1717876	19	7148											
MYO10	4651	hgsc.bcm.edu	37	chr5	16764479	16764479	+	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	cagcacgcatacagagccatGgccagggagtccctgctgtc	9	6	12	14	1	0	1	0	0	0	1	2	2	1	2	3	2	4	3	3	2	1	1			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr5:16764479G>T	ENST00000513610.1	-	12	1660	c.1206C>A	c.(1204-1206)gcC>gcA	p.A402A		NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	402	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						ACAGAGCCATGGCCAGGGAGT	0.547																																					p.A402A		Atlas-SNP	.											.	MYO10	198	.	0			c.C1206A						PASS	.						107	103	105					5																	16764479		2098	4241	6339	SO:0001819	synonymous_variant	4651	exon12			AGCCATGGCCAGG	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.1206C>A	chr5.hg19:g.16764479G>T		111.0	0.0	.		103.0	44.0	.	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	hg19	CCDS54834.1																																																																																			.	.	.	none		0.547	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		T	16764479	G	T	16764479	2	4	111	1	0	0	0	0	0	0	0	1	10069	1335	47	4		4	MYO10	5	16764479	Silent	SNP	G	TCGA-BQ-5876-01A-11D-1589-08		16764479	164150781	20	7149											
SPEF2	79925	hgsc.bcm.edu	37	chr5	35771741	35771743	+	In_Frame_Del	DEL	GAA	GAA	-																															aaattcatcagaggcttatgGaagaagaaaaagaaaaccag																										TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr5:35771741_35771743delGAA	ENST00000356031.3	+	27	3986_3988	c.3832_3834delGAA	c.(3832-3834)gaadel	p.E1280del	CTD-2113L7.1_ENST00000510433.1_RNA|SPEF2_ENST00000440995.2_In_Frame_Del_p.E1275del	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	1280					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)			GAGGCTTATGGAAGAAGAAAAAG	0.399																																					p.1277_1278del		Atlas-INDEL	.											.	SPEF2	324	.	0			c.3831_3833del						PASS	.																																			SO:0001651	inframe_deletion	79925	exon27			.	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.3832_3834delGAA	chr5.hg19:g.35771747_35771749delGAA	ENSP00000348314:p.Glu1280del	54.0	0.0	0		58.0	12.0	0.206897	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	In_Frame_Del	DEL	ENST00000356031.3	hg19	CCDS43309.1																																																																																			.	.	.	none		0.399	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722		-	35771743	GAA	-	35771741	7	5	111	1	0	1	0	1	0	0	0	0	15047	1175	41	0	3959	0	SPEF2	5	35771741	In_Frame_Del	DEL	GAA	TCGA-BQ-5876-01A-11D-1589-08	19007262	35771741	145143519	21	7150											
PARP8	79668	hgsc.bcm.edu	37	chr5	50137860	50137860	+	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	caagaaggaggcattcacaaAgagatcctccgagtaattgg	15	7	11	8	1	1	2	1	0	0	2	3	5	3	3	2	3	0	2	2	3	4	3			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr5:50137860A>T	ENST00000281631.5	+	26	2681	c.2523A>T	c.(2521-2523)aaA>aaT	p.K841N	PARP8_ENST00000505554.1_Missense_Mutation_p.K820N|PARP8_ENST00000511363.2_3'UTR|PARP8_ENST00000505697.2_Missense_Mutation_p.K841N|PARP8_ENST00000514067.2_Missense_Mutation_p.K799N|PARP8_ENST00000503750.2_Missense_Mutation_p.K799N	NM_001178056.1|NM_024615.3	NP_001171527.1|NP_078891.2	Q8N3A8	PARP8_HUMAN	poly (ADP-ribose) polymerase family, member 8	841	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.					intracellular (GO:0005622)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Lung NSC(810;0.0305)|Breast(144;0.222)				GCATTCACAAAGAGATCCTCC	0.358																																					p.K841N		Atlas-SNP	.											.	PARP8	93	.	0			c.A2523T						PASS	.						86	82	83					5																	50137860		2203	4300	6503	SO:0001583	missense	79668	exon27			TCACAAAGAGATC	AL834477	CCDS3954.1, CCDS54849.1	5q11.2	2010-02-16			ENSG00000151883	ENSG00000151883		"Poly (ADP-ribose) polymerases"	26124	protein-coding gene	gene with protein product						15273990	Standard	NM_001178055		Approved	FLJ21308, pART16	uc003joo.3	Q8N3A8	OTTHUMG00000096969	ENST00000281631.5:c.2523A>T	chr5.hg19:g.50137860A>T	ENSP00000281631:p.Lys841Asn	112.0	0.0	.		101.0	43.0	.	NM_001178055	Q3KRB7|Q6DHZ1|Q9H754	Missense_Mutation	SNP	ENST00000281631.5	hg19	CCDS3954.1	.	.	.	.	.	.	.	.	.	.	A	15.51	2.855481	0.51376	.	.	ENSG00000151883	ENST00000505697;ENST00000503750;ENST00000281631;ENST00000514067;ENST00000505554	.	.	.	6.08	3.7	0.42460	Poly(ADP-ribose) polymerase, catalytic domain (1);	0.058378	0.64402	D	0.000002	T	0.41465	0.1160	L	0.44542	1.39	0.80722	D	1	P;B;B	0.37781	0.608;0.447;0.319	B;B;B	0.35114	0.193;0.196;0.096	T	0.12941	-1.0528	8	.	.	.	-15.5759	10.485	0.44717	0.8695:0.0:0.1305:0.0	.	733;799;841	B4DQ81;Q8N3A8-2;Q8N3A8	.;.;PARP8_HUMAN	N	841;799;841;799;820	.	.	K	+	3	2	PARP8	50173617	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.471000	0.45127	0.545000	0.28902	-0.256000	0.11100	AAA	.	.	.	none		0.358	PARP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214035.3	NM_024615		T	50137860	A	T	50137860	3	4	111	1	0	0	0	0	1	0	0	0	11472	69	3	5	2625	5	PARP8	5	50137860	Missense_Mutation	SNP	A	TCGA-BQ-5876-01A-11D-1589-08	14366119	50137860	130777400	22	7151											
GPR98	84059	hgsc.bcm.edu	37	chr5	89989974	89989974	+	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	ccccagtgtttctggatgacAtcatggatcagcccagctgt	8	11	10	12	0	3	1	2	1	1	0	3	3	3	3	3	2	2	2	3	2	0	1			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr5:89989974A>T	ENST00000405460.2	+	33	7497	c.7401A>T	c.(7399-7401)acA>acT	p.T2467T		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	2467	Calx-beta 17. {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)		TCTGGATGACATCATGGATCA	0.488																																					p.T2467T		Atlas-SNP	.											.	GPR98	605	.	0			c.A7401T						PASS	.						67	66	66					5																	89989974		1926	4127	6053	SO:0001819	synonymous_variant	84059	exon33			GATGACATCATGG	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.7401A>T	chr5.hg19:g.89989974A>T		52.0	0.0	.		51.0	23.0	.	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	9.244	1.039019	0.19669	.	.	ENSG00000164199	ENST00000509621	.	.	.	5.92	-3.15	0.05233	.	.	.	.	.	T	0.36908	0.0984	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35968	-0.9767	4	.	.	.	.	1.1269	0.01736	0.4642:0.1847:0.1714:0.1797	.	.	.	.	L	33	.	.	H	+	2	0	GPR98	90025730	0.645000	0.27286	0.979000	0.43373	0.943000	0.58893	-0.090000	0.11163	-0.108000	0.12066	0.533000	0.62120	CAT	.	.	.	none		0.488	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		T	89989974	A	T	89989974	2	4	111	1	0	0	0	0	0	0	0	1	6728	204	8	5		5	GPR98	5	89989974	Silent	SNP	A	TCGA-BQ-5876-01A-11D-1589-08	39852114	89989974	90925286	23	7152											
TRIM41	90933	hgsc.bcm.edu	37	chr5	180661231	180661232	+	Frame_Shift_Ins	INS	-	-	C																															ctgatgctgtcccctgaccgINSccggggggtccgcctggcag																								rs138245799		TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr5:180661231_180661232insC	ENST00000315073.5	+	6	2059_2060	c.1349_1350insC	c.(1348-1353)cgccggfs	p.R451fs	TRIM41_ENST00000351937.5_Frame_Shift_Ins_p.R451fs|TRIM41_ENST00000510072.1_3'UTR	NM_033549.4	NP_291027.3	Q8WV44	TRI41_HUMAN	tripartite motif containing 41	451	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)			TCCCCTGACCGCCGGGGGGTCC	0.698																																					p.R450fs		Atlas-INDEL	.											.	TRIM41	96	.	0			c.1349_1350insC						PASS	.																																			SO:0001589	frameshift_variant	90933	exon6			.	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.1351dupC	chr5.hg19:g.180661233_180661233dupC	ENSP00000320869:p.Arg451fs	121.0	0.0	0		104.0	38.0	0.365385	NM_033549	B3KNJ6|D3DWR9|Q5BKT0|Q7L484|Q96Q10|Q9BSL8	Frame_Shift_Ins	INS	ENST00000315073.5	hg19	CCDS4466.1																																																																																			.	.	.	none		0.698	TRIM41-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253574.3	NM_201627		C	180661232	-	C	180661231	7	5	111	1	0	1	1	0	0	0	0	0	16528	1087	38	0	1371	0	TRIM41	5	180661231	Frame_Shift_Ins	INS	-	TCGA-BQ-5876-01A-11D-1589-08	90671257	180661231	254029	24	7153											
CRIP3	401262	hgsc.bcm.edu	37	chr6	43275360	43275360	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccagccttacttttcttgccTtgggggaggccagtccttgg	4	13	12	12	0	1	0	0	0	1	0	2	1	2	1	5	4	3	0	5	4	1	6	rs568254475		TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr6:43275360T>C	ENST00000274990.4	-	4	322	c.318A>G	c.(316-318)caA>caG	p.Q106Q	CRIP3_ENST00000372569.3_Silent_p.Q106Q|ZNF318_ENST00000607252.1_5'UTR			Q6Q6R5	CRIP3_HUMAN	cysteine-rich protein 3	106					T cell proliferation (GO:0042098)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)			TTTTCTTGCCTTGGGGGAGGC	0.642													T|||	1	0.000199681	0	0	5008	,	,		16423	0		0	False		,,,				2504	0.001				p.Q106Q		Atlas-SNP	.											.	CRIP3	30	.	0			c.A318G						PASS	.						44	50	48					6																	43275360		2203	4300	6503	SO:0001819	synonymous_variant	401262	exon4			CTTGCCTTGGGGG	AY555741	CCDS4894.2	6p21	2008-02-05			ENSG00000146215	ENSG00000146215			17751	protein-coding gene	gene with protein product						15380775	Standard	NM_206922		Approved	TLP-A, bA480N24.2, TLP	uc003ouu.1	Q6Q6R5	OTTHUMG00000014727	ENST00000274990.4:c.318A>G	chr6.hg19:g.43275360T>C		99.0	0.0	.		121.0	46.0	.	NM_206922	A2A436|Q5T043|Q6Q6R4|Q6Q6R6|Q6Q6R7	Silent	SNP	ENST00000274990.4	hg19		.	.	.	.	.	.	.	.	.	.	T	3.522	-0.097611	0.07010	.	.	ENSG00000146215	ENST00000416431	.	.	.	5.28	-4.75	0.03239	.	.	.	.	.	T	0.06735	0.0172	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.34054	-0.9844	4	.	.	.	0.0414	3.3614	0.07188	0.1112:0.4248:0.1114:0.3527	.	.	.	.	G	54	.	.	R	-	1	2	CRIP3	43383338	0.138000	0.22547	0.008000	0.14137	0.650000	0.38633	-0.340000	0.07821	-0.788000	0.04504	0.533000	0.62120	AGG	.	.	.	none		0.642	CRIP3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000313968.1			C	43275360	T	C	43275360	2	2	111	1	0	0	0	0	0	0	0	1	3878	1606	56	3		3	CRIP3	6	43275360	Silent	SNP	T	TCGA-BQ-5876-01A-11D-1589-08		43275360	127839707	25	7154											
OGFRL1	79627	hgsc.bcm.edu	37	chr6	72011098	72011098	+	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	ctctcttccaggtcccagcaCaactatttaagaatcactcg	11	11	5	14	1	2	1	1	0	1	1	6	1	4	1	2	1	2	1	2	1	4	4			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr6:72011098C>A	ENST00000370435.4	+	7	836	c.702C>A	c.(700-702)caC>caA	p.H234Q	RP11-154D6.1_ENST00000586232.1_RNA|RP11-154D6.1_ENST00000587397.1_RNA|RP11-154D6.1_ENST00000586030.1_RNA|RP11-154D6.1_ENST00000423255.1_RNA|RP11-154D6.1_ENST00000591156.1_RNA|RP11-154D6.1_ENST00000412751.1_RNA|RP11-154D6.1_ENST00000587253.1_RNA|RP11-154D6.1_ENST00000588612.1_RNA|RP11-154D6.1_ENST00000432050.1_RNA|RP11-154D6.1_ENST00000585882.1_RNA|RP11-154D6.1_ENST00000587036.1_RNA|RP11-154D6.1_ENST00000450998.1_RNA|RP3-331H24.5_ENST00000602823.1_lincRNA	NM_024576.3	NP_078852.3	Q5TC84	OGRL1_HUMAN	opioid growth factor receptor-like 1	234						membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|upper_aerodigestive_tract(1)	13						GGTCCCAGCACAACTATTTAA	0.358																																					p.H234Q		Atlas-SNP	.											.	OGFRL1	44	.	0			c.C702A						PASS	.						224	259	247					6																	72011098		2203	4299	6502	SO:0001583	missense	79627	exon7			CCAGCACAACTAT		CCDS34482.1	6q13	2008-02-05			ENSG00000119900	ENSG00000119900			21378	protein-coding gene	gene with protein product							Standard	NM_024576		Approved	dJ331H24.1	uc003pfx.1	Q5TC84	OTTHUMG00000015000	ENST00000370435.4:c.702C>A	chr6.hg19:g.72011098C>A	ENSP00000359464:p.His234Gln	782.0	1.0	.		745.0	267.0	.	NM_024576	Q2TAC1|Q8NEQ4|Q9H7B5	Missense_Mutation	SNP	ENST00000370435.4	hg19	CCDS34482.1	.	.	.	.	.	.	.	.	.	.	C	18.16	3.561728	0.65538	.	.	ENSG00000119900	ENST00000370435	T	0.67345	-0.26	5.94	4.16	0.48862	Opioid growth factor receptor (OGFr) conserved domain (1);	0.094242	0.85682	D	0.000000	T	0.74535	0.3729	M	0.83012	2.62	0.46749	D	0.999187	D	0.76494	0.999	D	0.68039	0.955	T	0.78663	-0.2116	10	0.87932	D	0	-12.2653	10.4706	0.44635	0.0:0.741:0.0:0.259	.	234	Q5TC84	OGRL1_HUMAN	Q	234	ENSP00000359464:H234Q	ENSP00000359464:H234Q	H	+	3	2	OGFRL1	72067819	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.730000	0.47335	0.846000	0.35142	0.563000	0.77884	CAC	.	.	.	none		0.358	OGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041153.2	NM_024576		A	72011098	C	A	72011098	3	1	111	1	0	0	0	0	1	0	0	0	10851	477	17	4	728	4	OGFRL1	6	72011098	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	28735738	72011098	99103969	26	7155											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152658075	152658075	+	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	tcagcatcttgcaggtaaatCcagagctcagacttcaggtg	11	10	10	10	0	4	2	3	0	1	2	5	2	5	2	1	2	3	4	1	2	2	3			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr6:152658075C>G	ENST00000367255.5	-	76	13030	c.12429G>C	c.(12427-12429)tgG>tgC	p.W4143C	SYNE1_ENST00000341594.5_Missense_Mutation_p.W4008C|SYNE1_ENST00000265368.4_Missense_Mutation_p.W4143C|SYNE1_ENST00000423061.1_Missense_Mutation_p.W4072C|SYNE1_ENST00000448038.1_Missense_Mutation_p.W4072C	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4143					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)		GCAGGTAAATCCAGAGCTCAG	0.458										HNSCC(10;0.0054)																											p.W4143C		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G12429C						PASS	.						109	99	102					6																	152658075		2203	4300	6503	SO:0001583	missense	23345	exon76			GTAAATCCAGAGC	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.12429G>C	chr6.hg19:g.152658075C>G	ENSP00000356224:p.Trp4143Cys	106.0	0.0	.		73.0	22.0	.	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	13.68	2.309305	0.40895	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.52754	0.74;0.7;0.65;0.7;0.73	5.47	5.47	0.80525	.	0.000000	0.56097	D	0.000036	T	0.50154	0.1599	L	0.57536	1.79	0.80722	D	1	D;D;D;D	0.71674	0.996;0.996;0.996;0.998	P;P;P;P	0.59703	0.608;0.608;0.608;0.862	T	0.49513	-0.8932	10	0.44086	T	0.13	.	12.6398	0.56702	0.0:0.9245:0.0:0.0755	.	4143;4143;4143;4072	B7ZBC3;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	C	4143;4072;4143;4072;4008	ENSP00000356224:W4143C;ENSP00000396024:W4072C;ENSP00000265368:W4143C;ENSP00000390975:W4072C;ENSP00000341887:W4008C	ENSP00000265368:W4143C	W	-	3	0	SYNE1	152699768	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	1.774000	0.38573	2.572000	0.86782	0.655000	0.94253	TGG	.	.	.	none		0.458	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		G	152658075	C	G	152658075	3	3	111	1	0	0	0	0	1	0	0	0	15457	856	30	4	14321	4	SYNE1	6	152658075	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	80646977	152658075	18456992	27	7156											
RNF216	54476	hgsc.bcm.edu	37	chr7	5781025	5781025	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actctcctagatttgataacAgctctgtctctgagtcttcg	8	15	7	11	1	4	3	0	2	4	1	7	3	4	3	1	0	2	1	1	0	2	4			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr7:5781025A>G	ENST00000425013.2	-	4	676	c.452T>C	c.(451-453)cTg>cCg	p.L151P	RNF216_ENST00000389902.3_Missense_Mutation_p.L208P	NM_207111.3|NM_207116.2	NP_996994.1|NP_996999.1	Q9NWF9	RN216_HUMAN	ring finger protein 216	151					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)		ATTTGATAACAGCTCTGTCTC	0.458																																					p.L208P		Atlas-SNP	.											.	RNF216	71	.	0			c.T623C						PASS	.						172	174	174					7																	5781025		2203	4300	6503	SO:0001583	missense	54476	exon4			GATAACAGCTCTG	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.452T>C	chr7.hg19:g.5781025A>G	ENSP00000404602:p.Leu151Pro	328.0	1.0	.		350.0	117.0	.	NM_207111	Q6Y691|Q75ML7|Q7Z2H7|Q7Z7C1|Q8NHW7|Q9NYT1	Missense_Mutation	SNP	ENST00000425013.2	hg19	CCDS34595.1	.	.	.	.	.	.	.	.	.	.	A	17.96	3.515649	0.64634	.	.	ENSG00000011275	ENST00000425013;ENST00000389902	T;T	0.64803	-0.12;0.2	5.97	5.97	0.96955	.	0.000000	0.64402	D	0.000002	T	0.73737	0.3625	L	0.54323	1.7	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.67548	0.952;0.916	T	0.75593	-0.3264	10	0.62326	D	0.03	-11.2668	13.8294	0.63370	1.0:0.0:0.0:0.0	.	151;208	Q9NWF9;Q9NWF9-1	RN216_HUMAN;.	P	151;208	ENSP00000404602:L151P;ENSP00000374552:L208P	ENSP00000374550:L151P	L	-	2	0	RNF216	5747551	1.000000	0.71417	0.836000	0.33094	0.819000	0.46315	3.643000	0.54374	2.289000	0.77006	0.459000	0.35465	CTG	.	.	.	none		0.458	RNF216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340374.1	NM_207111		G	5781025	A	G	5781025	3	3	111	1	0	0	0	0	1	0	0	0	13493	188	7	3	2204	3	RNF216	7	5781025	Missense_Mutation	SNP	A	TCGA-BQ-5876-01A-11D-1589-08		5781025	153357638	28	7157											
OR2A14	135941	hgsc.bcm.edu	37	chr7	143826220	143826220	+	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	aagagcatggaaggcaacaaGacatggatcacagacatcac	18	4	10	9	0	2	3	2	0	0	3	2	5	2	5	0	3	2	2	0	3	4	0			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr7:143826220G>T	ENST00000408899.2	+	1	70	c.15G>T	c.(13-15)aaG>aaT	p.K5N		NM_001001659.1	NP_001001659.1	Q96R47	O2A14_HUMAN	olfactory receptor, family 2, subfamily A, member 14	5						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(4)|lung(17)|skin(1)	22	Melanoma(164;0.0783)					AAGGCAACAAGACATGGATCA	0.498																																					p.K5N		Atlas-SNP	.											.	OR2A14	66	.	0			c.G15T						PASS	.						80	77	78					7																	143826220		2034	4193	6227	SO:0001583	missense	135941	exon1			CAACAAGACATGG		CCDS43672.1	7q35	2013-09-20		2004-03-08	ENSG00000221938	ENSG00000221938		"GPCR / Class A : Olfactory receptors"	15084	protein-coding gene	gene with protein product				OR2A14P, OR2A6			Standard	NM_001001659		Approved	OST182	uc011kua.2	Q96R47	OTTHUMG00000158003	ENST00000408899.2:c.15G>T	chr7.hg19:g.143826220G>T	ENSP00000386137:p.Lys5Asn	57.0	0.0	.		53.0	23.0	.	NM_001001659	Q6IF41|Q8NGT8	Missense_Mutation	SNP	ENST00000408899.2	hg19	CCDS43672.1	.	.	.	.	.	.	.	.	.	.	G	8.070	0.770134	0.15983	.	.	ENSG00000221938	ENST00000408899	T	0.00348	8.0	4.18	4.18	0.49190	.	.	.	.	.	T	0.00144	0.0004	N	0.04320	-0.23	0.09310	N	1	B	0.23591	0.088	B	0.20184	0.028	T	0.50372	-0.8836	9	0.48119	T	0.1	-2.9556	12.1908	0.54270	0.0:0.0:1.0:0.0	.	5	Q96R47	O2A14_HUMAN	N	5	ENSP00000386137:K5N	ENSP00000386137:K5N	K	+	3	2	OR2A14	143457153	0.000000	0.05858	0.341000	0.25589	0.476000	0.33039	-0.561000	0.05957	2.303000	0.77524	0.561000	0.74099	AAG	.	.	.	none		0.498	OR2A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349980.1			T	143826220	G	T	143826220	3	4	111	1	0	0	0	0	1	0	0	0	10983	933	33	4	17	4	OR2A14	7	143826220	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	138045195	143826220	15312443	29	7158											
IFNA2	3440	hgsc.bcm.edu	37	chr9	21385064	21385067	+	Frame_Shift_Del	DEL	GATT	GATT	-																															tgagtcctttgtgctgaagaGattgaagatctgctggatca																										TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	GATT	GATT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr9:21385064_21385067delGATT	ENST00000380206.2	-	1	329_332	c.262_265delAATC	c.(262-267)aatctcfs	p.NL88fs		NM_000605.3	NP_000596.2	P01563	IFNA2_HUMAN	interferon, alpha 2	88					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of gene expression (GO:0010629)|negative regulation of interleukin-13 secretion (GO:2000666)|negative regulation of interleukin-5 secretion (GO:2000663)|negative regulation of T cell differentiation (GO:0045581)|negative regulation of T-helper 2 cell cytokine production (GO:2000552)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral entry into host cell (GO:0046597)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	type I interferon receptor binding (GO:0005132)			breast(2)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)	13				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0173)		GTGCTGAAGAGATTGAAGATCTGC	0.49																																					p.88_89del		Atlas-INDEL	.											.	IFNA2	32	.	0			c.263_266del						PASS	.																																			SO:0001589	frameshift_variant	3440	exon1			.		CCDS6506.1	9p22	2010-08-24			ENSG00000188379	ENSG00000188379		"Interferons"	5423	protein-coding gene	gene with protein product	"alpha-2a interferon", "interferon alpha 2b", "interferon alpha A"	147562				1385305	Standard	NM_000605		Approved	IFNA, IFN-alphaA	uc003zpb.3	P01563	OTTHUMG00000019674	ENST00000380206.2:c.262_265delAATC	chr9.hg19:g.21385064_21385067delGATT	ENSP00000369554:p.Asn88fs	216.0	0.0	0		215.0	87.0	0.404651	NM_000605	H2DF54|H2DF55|P01564|Q14606|Q6DJX8|Q96KI6	Frame_Shift_Del	DEL	ENST00000380206.2	hg19	CCDS6506.1																																																																																			.	.	.	none		0.49	IFNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051903.1	NM_000605		-	21385067	GATT	-	21385064	7	5	111	1	0	1	0	1	0	0	0	0	7544	942	33	0	305	0	IFNA2	9	21385064	Frame_Shift_Del	DEL	GATT	TCGA-BQ-5876-01A-11D-1589-08		21385064	119828367	30	7159											
ENTPD7	57089	hgsc.bcm.edu	37	chr10	101460770	101460770	+	Missense_Mutation	SNP	T	T	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	gtcggtactaactcagagatTcaagaatggcctcttttcat	11	13	8	9	1	4	2	3	0	1	2	5	3	4	2	1	2	2	1	1	2	4	5			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr10:101460770T>G	ENST00000370489.4	+	11	1554	c.1376T>G	c.(1375-1377)tTc>tGc	p.F459C		NM_020354.3	NP_065087.1	Q9NQZ7	ENTP7_HUMAN	ectonucleoside triphosphate diphosphohydrolase 7	459						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)		ACTCAGAGATTCAAGAATGGC	0.433																																					p.F459C		Atlas-SNP	.											.	ENTPD7	44	.	0			c.T1376G						PASS	.						361	321	334					10																	101460770		2203	4300	6503	SO:0001583	missense	57089	exon11			AGAGATTCAAGAA	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.1376T>G	chr10.hg19:g.101460770T>G	ENSP00000359520:p.Phe459Cys	407.0	0.0	.		272.0	93.0	.	NM_020354	B2RB83|B3KP21|D3DR64	Missense_Mutation	SNP	ENST00000370489.4	hg19	CCDS7480.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.321910	0.81580	.	.	ENSG00000198018	ENST00000370489	T	0.12255	2.7	5.21	5.21	0.72293	.	0.056019	0.64402	D	0.000001	T	0.41282	0.1152	M	0.85197	2.74	0.53688	D	0.999977	D	0.76494	0.999	D	0.70935	0.971	T	0.42949	-0.9421	10	0.59425	D	0.04	-26.5929	14.9011	0.70681	0.0:0.0:0.0:1.0	.	459	Q9NQZ7	ENTP7_HUMAN	C	459	ENSP00000359520:F459C	ENSP00000359520:F459C	F	+	2	0	ENTPD7	101450760	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	7.860000	0.86993	2.192000	0.70111	0.523000	0.50628	TTC	.	.	.	none		0.433	ENTPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049809.2	NM_020354		G	101460770	T	G	101460770	3	3	111	1	0	0	0	0	1	0	0	0	5146	1783	62	5	1414	5	ENTPD7	10	101460770	Missense_Mutation	SNP	T	TCGA-BQ-5876-01A-11D-1589-08		101460770	34073977	31	7160											
DPF2	5977	hgsc.bcm.edu	37	chr11	65113198	65113198	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cactatgcccactcccacttGgctgaggaggagggcgagga	9	6	14	12	1	0	1	0	1	0	0	1	5	1	4	2	5	1	1	2	5	1	2			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr11:65113198G>A	ENST00000528416.1	+	7	832	c.699G>A	c.(697-699)ttG>ttA	p.L233L	DPF2_ENST00000415073.2_Intron|DPF2_ENST00000532264.1_3'UTR|DPF2_ENST00000252268.4_Silent_p.L247L	NM_006268.4	NP_006259.1	Q92785	REQU_HUMAN	D4, zinc and double PHD fingers family 2	233					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						ACTCCCACTTGGCTGAGGAGG	0.512																																					p.L233L		Atlas-SNP	.											.	DPF2	54	.	0			c.G699A						PASS	.						78	71	73					11																	65113198		2201	4297	6498	SO:0001819	synonymous_variant	5977	exon7			CCACTTGGCTGAG	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.699G>A	chr11.hg19:g.65113198G>A		81.0	0.0	.		66.0	27.0	.	NM_006268	A8K7C9|B4DT58	Silent	SNP	ENST00000528416.1	hg19	CCDS8100.1																																																																																			.	.	.	none		0.512	DPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387293.3	NM_006268		A	65113198	G	A	65113198	2	1	111	1	0	0	0	0	0	0	0	1	4719	1339	47	2		2	DPF2	11	65113198	Silent	SNP	G	TCGA-BQ-5876-01A-11D-1589-08		65113198	69893318	32	7161											
SPTBN2	6712	hgsc.bcm.edu	37	chr11	66468283	66468283	+	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	gggcctctgcctcaggcaggGtggccggcccttcttcagag	4	8	15	14	1	4	1	2	0	2	1	4	1	4	1	4	5	1	1	4	5	0	2			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr11:66468283G>T	ENST00000533211.1	-	17	3618	c.3287C>A	c.(3286-3288)aCc>aAc	p.T1096N	SPTBN2_ENST00000309996.2_Missense_Mutation_p.T1096N|SPTBN2_ENST00000529997.1_Missense_Mutation_p.T1096N			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	1096					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						CTCAGGCAGGGTGGCCGGCCC	0.692																																					p.T1096N		Atlas-SNP	.											.	SPTBN2	188	.	0			c.C3287A						PASS	.						16	18	17					11																	66468283		2193	4285	6478	SO:0001583	missense	6712	exon16			GGCAGGGTGGCCG	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.3287C>A	chr11.hg19:g.66468283G>T	ENSP00000432568:p.Thr1096Asn	51.0	0.0	.		27.0	15.0	.	NM_006946	O14872|O14873	Missense_Mutation	SNP	ENST00000533211.1	hg19	CCDS8150.1	.	.	.	.	.	.	.	.	.	.	G	17.54	3.414677	0.62511	.	.	ENSG00000173898	ENST00000533211;ENST00000309996;ENST00000529997	T;T;T	0.34275	1.37;1.37;1.37	4.7	4.7	0.59300	.	0.059484	0.64402	D	0.000001	T	0.20981	0.0505	N	0.12182	0.205	0.36280	D	0.855746	B	0.28026	0.198	B	0.28305	0.088	T	0.20075	-1.0286	10	0.27785	T	0.31	.	11.7357	0.51763	0.0:0.0:0.8233:0.1767	.	1096	O15020	SPTN2_HUMAN	N	1096	ENSP00000432568:T1096N;ENSP00000311489:T1096N;ENSP00000433593:T1096N	ENSP00000311489:T1096N	T	-	2	0	SPTBN2	66224859	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	6.377000	0.73145	2.446000	0.82766	0.491000	0.48974	ACC	.	.	.	none		0.692	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946		T	66468283	G	T	66468283	3	4	111	1	0	0	0	0	1	0	0	0	15132	1261	44	4	3973	4	SPTBN2	11	66468283	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	1355085	66468283	68538233	33	7162											
PCF11	51585	hgsc.bcm.edu	37	chr11	82877600	82877600	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tactaaacaggatattcgggAtccaaggcgaatgaaaaaga	18	7	10	6	2	0	2	0	1	0	1	2	5	1	4	1	3	2	0	1	3	8	4			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr11:82877600A>G	ENST00000298281.4	+	5	2113	c.1661A>G	c.(1660-1662)gAt>gGt	p.D554G		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	554					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						GATATTCGGGATCCAAGGCGA	0.423																																					p.D554G		Atlas-SNP	.											.	PCF11	220	.	0			c.A1661G						PASS	.						80	76	77					11																	82877600		1873	4113	5986	SO:0001583	missense	51585	exon5			TTCGGGATCCAAG	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.1661A>G	chr11.hg19:g.82877600A>G	ENSP00000298281:p.Asp554Gly	81.0	0.0	.		73.0	19.0	.	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	hg19	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.007795	0.75046	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.56611	1.4;0.45;0.46	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000008	T	0.63189	0.2490	L	0.32530	0.975	0.58432	D	0.999996	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.94	T	0.60409	-0.7269	9	.	.	.	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	554;554	E9PQ01;O94913	.;PCF11_HUMAN	G	554	ENSP00000298281:D554G;ENSP00000434540:D554G;ENSP00000431567:D554G	.	D	+	2	0	PCF11	82555248	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.615000	0.90920	2.326000	0.78906	0.533000	0.62120	GAT	.	.	.	none		0.423	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		G	82877600	A	G	82877600	3	3	111	1	0	0	0	0	1	0	0	0	11580	333	12	3	1679	3	PCF11	11	82877600	Missense_Mutation	SNP	A	TCGA-BQ-5876-01A-11D-1589-08	16409317	82877600	52128916	34	7163											
SNX19	399979	hgsc.bcm.edu	37	chr11	130785820	130785820	+	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	gtttcctggaacggtggcacTgtttctgtcttcatggctga	5	15	12	9	1	3	1	1	1	2	0	4	2	4	2	1	4	1	4	1	4	1	3			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr11:130785820T>A	ENST00000265909.4	-	1	584	c.15A>T	c.(13-15)acA>acT	p.T5T	SNX19_ENST00000530356.1_Intron|SNX19_ENST00000528555.1_Intron|SNX19_ENST00000533214.1_Silent_p.T5T|SNX19_ENST00000539184.1_Intron|SNX19_ENST00000533318.1_Intron	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	5					protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		ACGGTGGCACTGTTTCTGTCT	0.542																																					p.T5T		Atlas-SNP	.											.	SNX19	84	.	0			c.A15T						PASS	.						50	44	46					11																	130785820		2201	4297	6498	SO:0001819	synonymous_variant	399979	exon1			TGGCACTGTTTCT	D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"Sorting nexins"	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.15A>T	chr11.hg19:g.130785820T>A		56.0	0.0	.		29.0	13.0	.	NM_014758	E9PKB9|Q8IV55	Silent	SNP	ENST00000265909.4	hg19	CCDS31721.1																																																																																			.	.	.	none		0.542	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758		A	130785820	T	A	130785820	2	1	111	1	0	0	0	0	0	0	0	1	14903	1567	55	5		5	SNX19	11	130785820	Silent	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	47908220	130785820	4220696	35	7164											
ATN1	1822	hgsc.bcm.edu	37	chr12	7045767	7045767	+	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	ccagggtcccccaccacctcCtccctatggccgcctcttag	5	8	7	21	1	1	0	0	0	1	0	4	0	4	0	9	2	0	0	9	2	2	2			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr12:7045767C>A	ENST00000356654.4	+	5	1574	c.1337C>A	c.(1336-1338)cCt>cAt	p.P446H	ATN1_ENST00000396684.2_Missense_Mutation_p.P446H	NM_001007026.1	NP_001007027.1	P54259	ATN1_HUMAN	atrophin 1	446	Poly-Pro.				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						CCACCACCTCCTCCCTATGGC	0.627																																					p.P446H		Atlas-SNP	.											.	ATN1	95	.	0			c.C1337A						PASS	.						149	144	146					12																	7045767		2203	4300	6503	SO:0001583	missense	1822	exon5			CACCTCCTCCCTA	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.1337C>A	chr12.hg19:g.7045767C>A	ENSP00000349076:p.Pro446His	377.0	0.0	.		366.0	144.0	.	NM_001007026	Q99495|Q99621|Q9UEK7	Missense_Mutation	SNP	ENST00000356654.4	hg19	CCDS31734.1	.	.	.	.	.	.	.	.	.	.	c	12.53	1.964846	0.34659	.	.	ENSG00000111676	ENST00000356654;ENST00000396684;ENST00000544325;ENST00000229279	T;T;T	0.55413	0.52;0.52;0.52	3.88	3.88	0.44766	.	.	.	.	.	T	0.63390	0.2507	L	0.40543	1.245	0.46416	D	0.999032	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.988	T	0.63721	-0.6573	9	0.38643	T	0.18	.	16.2396	0.82401	0.0:1.0:0.0:0.0	.	446;446	Q86V38;P54259	.;ATN1_HUMAN	H	446;446;446;31	ENSP00000349076:P446H;ENSP00000379915:P446H;ENSP00000441744:P446H	ENSP00000229279:P31H	P	+	2	0	ATN1	6916028	0.028000	0.19301	0.947000	0.38551	0.354000	0.29330	0.722000	0.25925	1.883000	0.54544	0.586000	0.80456	CCT	.	.	.	none		0.627	ATN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401948.2	NM_001940		A	7045767	C	A	7045767	3	1	111	1	0	0	0	0	1	0	0	0	1111	681	24	4	1351	4	ATN1	12	7045767	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08		7045767	126806128	36	7165											
PITPNM2	57605	hgsc.bcm.edu	37	chr12	123479959	123479959	+	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	gacaggaaggcctggtgctgCtggatggtatccagctcgta	8	9	15	9	1	0	0	0	0	0	0	2	3	1	2	2	5	3	5	2	5	3	2			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr12:123479959C>T	ENST00000542749.1	-	12	2094	c.2031G>A	c.(2029-2031)caG>caA	p.Q677Q	PITPNM2_ENST00000392428.1_Silent_p.Q398Q|PITPNM2_ENST00000280562.5_Silent_p.Q677Q|PITPNM2_ENST00000320201.4_Silent_p.Q677Q			Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein, membrane-associated 2	677					metabolic process (GO:0008152)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)			NS(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	39	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		CCTGGTGCTGCTGGATGGTAT	0.637																																					p.Q677Q		Atlas-SNP	.											.	PITPNM2	105	.	0			c.G2031A						PASS	.						58	67	64					12																	123479959		2203	4299	6502	SO:0001819	synonymous_variant	57605	exon13			GTGCTGCTGGATG	AF334585	CCDS9242.1, CCDS73543.1	12q24.31	2008-02-05				ENSG00000090975			21044	protein-coding gene	gene with protein product		608920				10022914	Standard	XM_005253582		Approved	RDGBA2, RDGB2, NIR3	uc001uej.1	Q9BZ72		ENST00000542749.1:c.2031G>A	chr12.hg19:g.123479959C>T		104.0	0.0	.		150.0	43.0	.	NM_020845	Q9P271	Silent	SNP	ENST00000542749.1	hg19	CCDS9242.1																																																																																			.	.	.	none		0.637	PITPNM2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401342.1	NM_020845		T	123479959	C	T	123479959	2	4	111	1	0	0	0	0	0	0	0	1	11958	796	28	2		2	PITPNM2	12	123479959	Silent	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	116434192	123479959	10371936	37	7166											
ERCC5	2073	hgsc.bcm.edu	37	chr13	103510748	103510748	+	Frame_Shift_Del	DEL	T	T	-																															tcaccaagcgcagaagaacaTtatttgaagcaatgccagag																										TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr13:103510748delT	ENST00000355739.4	+	6	2075	c.652delT	c.(652-654)ttafs	p.L218fs	BIVM-ERCC5_ENST00000602836.1_Frame_Shift_Del_p.I644fs|ERCC5_ENST00000535557.1_Frame_Shift_Del_p.L218fs	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	218					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)					CAGAAGAACATTATTTGAAGC	0.373			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.T671fs		Atlas-INDEL	.	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.2013delA						PASS	.						96	99	98					13																	103510748		2203	4300	6503	SO:0001589	frameshift_variant	0	exon14	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	.	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.652delT	chr13.hg19:g.103510748delT	ENSP00000347978:p.Leu218fs	132.0	0.0	0		144.0	51.0	0.354167	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Frame_Shift_Del	DEL	ENST00000355739.4	hg19	CCDS32004.1																																																																																			.	.	.	none		0.373	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1			-	103510748	T	-	103510748	7	5	111	1	0	1	0	1	0	0	0	0	5218	1490	52	0	674	0	ERCC5	13	103510748	Frame_Shift_Del	DEL	T	TCGA-BQ-5876-01A-11D-1589-08		103510748	11659130	38	7167											
TTC7B	145567	hgsc.bcm.edu	37	chr14	91161893	91161893	+	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	caactgctctgagaagctctCtaaatcttccgactcctctt	9	13	5	14	1	4	1	0	1	4	1	7	3	6	1	2	0	3	2	2	0	4	3			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr14:91161893C>G	ENST00000328459.6	-	6	849	c.728G>C	c.(727-729)aGa>aCa	p.R243T	RP11-661G16.2_ENST00000553712.1_RNA|TTC7B_ENST00000357056.2_Missense_Mutation_p.R243T	NM_001010854.1	NP_001010854.1	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B	243										NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	36		Melanoma(154;0.222)				GAGAAGCTCTCTAAATCTTCC	0.413																																					p.R243T		Atlas-SNP	.											.	TTC7B	93	.	0			c.G728C						PASS	.						138	111	120					14																	91161893		2203	4300	6503	SO:0001583	missense	145567	exon6			AGCTCTCTAAATC	BC035865	CCDS32140.1	14q32.12	2013-01-11	2004-06-02	2004-06-04		ENSG00000165914		"Tetratricopeptide (TTC) repeat domain containing"	19858	protein-coding gene	gene with protein product			"tetratricopeptide repeat domain 7 like 1"	TTC7L1			Standard	XM_005267367		Approved		uc001xyp.3	Q86TV6		ENST00000328459.6:c.728G>C	chr14.hg19:g.91161893C>G	ENSP00000336127:p.Arg243Thr	64.0	0.0	.		42.0	23.0	.	NM_001010854	Q86U24|Q86VT3	Missense_Mutation	SNP	ENST00000328459.6	hg19	CCDS32140.1	.	.	.	.	.	.	.	.	.	.	C	14.89	2.671065	0.47781	.	.	ENSG00000165914	ENST00000555768;ENST00000357056;ENST00000328459;ENST00000557766	T;T	0.66638	0.45;-0.22	5.72	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.69278	0.3093	M	0.82517	2.595	0.80722	D	1	B	0.30482	0.281	B	0.27796	0.083	T	0.72279	-0.4340	10	0.87932	D	0	-14.3324	14.3423	0.66636	0.0:0.9283:0.0:0.0717	.	243	Q86TV6	TTC7B_HUMAN	T	141;243;243;163	ENSP00000349564:R243T;ENSP00000336127:R243T	ENSP00000336127:R243T	R	-	2	0	TTC7B	90231646	1.000000	0.71417	0.781000	0.31783	0.002000	0.02628	7.184000	0.77705	1.420000	0.47138	-0.229000	0.12294	AGA	.	.	.	none		0.413	TTC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411364.2			G	91161893	C	G	91161893	3	3	111	1	0	0	0	0	1	0	0	0	16725	913	32	4	1863	4	TTC7B	14	91161893	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08		91161893	16187647	39	7168											
TYRO3	7301	hgsc.bcm.edu	37	chr15	41854918	41854918	+	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	tctgttttaaatgtaacaggTgagcagcctcagaagggggc	11	10	13	7	0	2	2	1	1	1	1	2	2	2	2	1	3	3	3	1	3	4	3			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr15:41854918T>G	ENST00000263798.3	+	4	804		c.e4+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)		ATGTAACAGGTGAGCAGCCTC	0.582																																					.		Atlas-SNP	.											.	TYRO3	169	.	0			c.580+2T>G						PASS	.						22	20	21					15																	41854918		2203	4300	6503	SO:0001630	splice_region_variant	7301	exon4			AACAGGTGAGCAG	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.580+2T>G	chr15.hg19:g.41854918T>G		23.0	0.0	.		31.0	8.0	.	NM_006293	O14953|Q86VR3	Splice_Site	SNP	ENST00000263798.3	hg19	CCDS10080.1	.	.	.	.	.	.	.	.	.	.	t	21.2	4.113398	0.77210	.	.	ENSG00000092445	ENST00000540218;ENST00000263798	.	.	.	4.8	4.8	0.61643	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5013	0.67724	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	TYRO3	39642210	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.037000	0.70956	2.007000	0.58848	0.387000	0.25754	.	.	.	.	none		0.582	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		Intron	G	41854918	T	G	41854918	5	3	111	1	0	0	0	0	0	0	1	0	16826	1710	59	5	596	5	TYRO3	15	41854918	Splice_Site	SNP	T	TCGA-BQ-5876-01A-11D-1589-08		41854918	60676474	40	7169											
MAPKBP1	23005	hgsc.bcm.edu	37	chr15	42105966	42105966	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggacagacattgctagcGtcaccgaggccaggtgagct	9	7	15	10	2	1	2	1	1	0	1	1	4	1	3	2	4	3	2	2	4	1	2	rs374717785		TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr15:42105966G>A	ENST00000456763.2	+	10	1181	c.985G>A	c.(985-987)Gtc>Atc	p.V329I	MAPKBP1_ENST00000457542.2_Missense_Mutation_p.V323I|MAPKBP1_ENST00000221214.6_Intron|MAPKBP1_ENST00000260357.7_Missense_Mutation_p.V211I|MAPKBP1_ENST00000514566.1_Missense_Mutation_p.V323I	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	329								p.V323I(1)		breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		CATTGCTAGCGTCACCGAGGC	0.592																																					p.V329I		Atlas-SNP	.											MAPKBP1,colon,carcinoma,0,1	MAPKBP1	120	.	1	Substitution - Missense(1)	large_intestine(1)	c.G985A						PASS	.	A	ILE/VAL,ILE/VAL	3,4403	6.2+/-15.9	0,3,2200	115	106	109		985,967	-6.3	0.1	15		109	0,8600		0,0,4300	no	missense,missense	MAPKBP1	NM_001128608.1,NM_014994.2	29,29	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	benign,benign	329/1515,323/1509	42105966	3,13003	2203	4300	6503	SO:0001583	missense	23005	exon10			GCTAGCGTCACCG	AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"WD repeat domain containing"	29536	protein-coding gene	gene with protein product			"mitogen activated protein kinase binding protein 1"			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.985G>A	chr15.hg19:g.42105966G>A	ENSP00000393099:p.Val329Ile	180.0	0.0	.		153.0	42.0	.	NM_001128608	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Missense_Mutation	SNP	ENST00000456763.2	hg19	CCDS45239.1	.	.	.	.	.	.	.	.	.	.	g	0.324	-0.960053	0.02267	6.81E-4	0.0	ENSG00000137802	ENST00000457542;ENST00000260357;ENST00000456763;ENST00000514566	T;T;T;T	0.42131	1.08;0.98;1.15;1.24	5.64	-6.33	0.01988	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.593302	0.19314	N	0.117308	T	0.28962	0.0719	L	0.38531	1.155	0.09310	N	0.999993	B;B;B;B	0.12013	0.001;0.005;0.001;0.001	B;B;B;B	0.13407	0.001;0.009;0.001;0.002	T	0.05053	-1.0909	10	0.21014	T	0.42	-1.6987	18.1757	0.89760	0.2499:0.0:0.7501:0.0	.	211;323;329;323	F8WC21;O60336-2;O60336;O60336-6	.;.;MABP1_HUMAN;.	I	323;211;329;323	ENSP00000397570:V323I;ENSP00000260357:V211I;ENSP00000393099:V329I;ENSP00000426154:V323I	ENSP00000260357:V211I	V	+	1	0	MAPKBP1	39893258	0.000000	0.05858	0.055000	0.19348	0.822000	0.46500	-0.443000	0.06862	-1.516000	0.01782	-1.913000	0.00520	GTC	.	.	.	weak		0.592	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359745.1	NM_014994		A	42105966	G	A	42105966	3	1	111	1	0	0	0	0	1	0	0	0	9299	1145	40	1	1019	1	MAPKBP1	15	42105966	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	251048	42105966	60425426	41	7170											
AP4E1	23431	hgsc.bcm.edu	37	chr15	51289917	51289917	+	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	ggaagaaactactgaatacaTacactcaaatgctatggaag	18	8	8	7	0	1	2	1	1	0	1	1	4	1	4	0	2	5	1	0	2	9	4			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr15:51289917T>A	ENST00000261842.5	+	18	2847	c.2741T>A	c.(2740-2742)aTa>aAa	p.I914K	AP4E1_ENST00000560508.1_Missense_Mutation_p.I839K	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	914					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)		ACTGAATACATACACTCAAAT	0.353																																					p.I914K		Atlas-SNP	.											.	AP4E1	78	.	0			c.T2741A						PASS	.						66	68	67					15																	51289917		2196	4294	6490	SO:0001583	missense	23431	exon18			AATACATACACTC	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.2741T>A	chr15.hg19:g.51289917T>A	ENSP00000261842:p.Ile914Lys	117.0	0.0	.		146.0	65.0	.	NM_007347	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Missense_Mutation	SNP	ENST00000261842.5	hg19	CCDS32240.1	.	.	.	.	.	.	.	.	.	.	T	4.902	0.167570	0.09339	.	.	ENSG00000081014	ENST00000261842	T	0.16457	2.34	5.2	4.06	0.47325	Coatomer, beta subunit, C-terminal (1);	0.708362	0.14326	N	0.326718	T	0.08179	0.0204	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.13407	0.009	T	0.26430	-1.0103	10	0.52906	T	0.07	-0.4045	3.9914	0.09538	0.0:0.1738:0.2024:0.6238	.	914	Q9UPM8	AP4E1_HUMAN	K	914	ENSP00000261842:I914K	ENSP00000261842:I914K	I	+	2	0	AP4E1	49077209	0.972000	0.33761	0.226000	0.23910	0.357000	0.29423	2.092000	0.41700	0.804000	0.34136	0.383000	0.25322	ATA	.	.	.	none		0.353	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1			A	51289917	T	A	51289917	3	1	111	1	0	0	0	0	1	0	0	0	752	1406	49	5	2811	5	AP4E1	15	51289917	Missense_Mutation	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	9183951	51289917	51241475	42	7171											
PIAS1	8554	hgsc.bcm.edu	37	chr15	68479999	68479999	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtttcttgatcagttaagTgcaggaggcagtacttctct	9	15	10	7	0	3	1	1	1	2	0	4	2	3	2	0	2	2	5	0	2	2	5			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr15:68479999T>C	ENST00000249636.6	+	14	1930	c.1782T>C	c.(1780-1782)agT>agC	p.S594S	PIAS1_ENST00000545237.1_Silent_p.S596S	NM_016166.1	NP_057250.1	O75925	PIAS1_HUMAN	protein inhibitor of activated STAT, 1	594	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						ATCAGTTAAGTGCAGGAGGCA	0.502																																					p.S594S		Atlas-SNP	.											.	PIAS1	42	.	0			c.T1782C						PASS	.						85	83	83					15																	68479999		2018	4191	6209	SO:0001819	synonymous_variant	8554	exon14			GTTAAGTGCAGGA	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.1782T>C	chr15.hg19:g.68479999T>C		66.0	0.0	.		77.0	34.0	.	NM_016166	B2RB67|B3KSY9|C5J4B4|Q147X4|Q99751|Q9UN02	Silent	SNP	ENST00000249636.6	hg19	CCDS45290.1																																																																																			.	.	.	none		0.502	PIAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419642.2			C	68479999	T	C	68479999	2	2	111	1	0	0	0	0	0	0	0	1	11882	1693	59	3		3	PIAS1	15	68479999	Silent	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	17190082	68479999	34051393	43	7172											
ZNF688	146542	hgsc.bcm.edu	37	chr16	30581595	30581595	+	Missense_Mutation	SNP	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	ctcctgtggtcgggtcccagGcagcatttttgggtggctgt	3	13	15	10	1	0	0	0	0	0	0	3	0	2	0	2	5	1	3	2	5	0	2			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr16:30581595G>A	ENST00000223459.6	-	3	1577	c.473C>T	c.(472-474)gCc>gTc	p.A158V	AC002310.7_ENST00000492040.1_RNA|AC002310.7_ENST00000486926.1_RNA|ZNF688_ENST00000395219.1_Missense_Mutation_p.A144V	NM_145271.3	NP_660314.1	P0C7X2	ZN688_HUMAN	zinc finger protein 688	158					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(2)|lung(2)|ovary(1)	8						CGGGTCCCAGGCAGCATTTTT	0.672																																					p.A158V		Atlas-SNP	.											.	ZNF688	37	.	0			c.C473T						PASS	.						29	32	31					16																	30581595		2197	4299	6496	SO:0001583	missense	146542	exon3			TCCCAGGCAGCAT	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.473C>T	chr16.hg19:g.30581595G>A	ENSP00000223459:p.Ala158Val	38.0	0.0	.		46.0	19.0	.	NM_145271	A8MV39|B3KV51|O75701|Q8IW91|Q8WV14|Q96MN0	Missense_Mutation	SNP	ENST00000223459.6	hg19	CCDS10684.1	.	.	.	.	.	.	.	.	.	.	G	12.04	1.817925	0.32145	.	.	ENSG00000229809	ENST00000395219;ENST00000223459	T;T	0.04194	3.68;3.91	4.26	0.961	0.19638	.	.	.	.	.	T	0.04003	0.0112	L	0.41236	1.265	0.09310	N	1	B;B	0.14438	0.002;0.01	B;B	0.11329	0.003;0.006	T	0.43523	-0.9386	9	0.28530	T	0.3	.	3.1826	0.06589	0.2262:0.0:0.5648:0.209	.	158;144	P0C7X2;A8MV39	ZN688_HUMAN;.	V	144;158	ENSP00000378645:A144V;ENSP00000223459:A158V	ENSP00000223459:A158V	A	-	2	0	ZNF688	30489096	0.018000	0.18449	0.721000	0.30653	0.192000	0.23643	1.655000	0.37345	0.546000	0.28920	0.460000	0.39030	GCC	.	.	.	none		0.672	ZNF688-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255544.2	NM_145271		A	30581595	G	A	30581595	3	1	111	1	0	0	0	0	1	0	0	0	18105	1203	42	2	361	2	ZNF688	16	30581595	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08		30581595	59773158	44	7173											
RPGRIP1L	23322	hgsc.bcm.edu	37	chr16	53708941	53708941	+	Missense_Mutation	SNP	A	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	cactgtacctcttgaagctgAataaattttccttccattgc	10	15	5	11	0	1	2	0	2	1	0	3	2	3	2	3	0	3	2	3	0	5	7			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr16:53708941A>C	ENST00000379925.3	-	7	920	c.870T>G	c.(868-870)atT>atG	p.I290M	RPGRIP1L_ENST00000563746.1_Missense_Mutation_p.I290M|RPGRIP1L_ENST00000262135.4_Missense_Mutation_p.I290M|RPGRIP1L_ENST00000564374.1_Missense_Mutation_p.I290M	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	290					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)				CTTGAAGCTGAATAAATTTTC	0.308																																					p.I290M		Atlas-SNP	.											.	RPGRIP1L	118	.	0			c.T870G						PASS	.						131	117	122					16																	53708941		2197	4297	6494	SO:0001583	missense	23322	exon7			AAGCTGAATAAAT		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.870T>G	chr16.hg19:g.53708941A>C	ENSP00000369257:p.Ile290Met	68.0	0.0	.		71.0	31.0	.	NM_001127897	A0PJ88|Q9Y2K8	Missense_Mutation	SNP	ENST00000379925.3	hg19	CCDS32447.1	.	.	.	.	.	.	.	.	.	.	A	11.30	1.597979	0.28445	.	.	ENSG00000103494	ENST00000379925;ENST00000262135	D;D	0.89875	-2.58;-2.58	5.98	4.87	0.63330	.	0.287071	0.33834	N	0.004504	T	0.77638	0.4160	L	0.36672	1.1	0.80722	D	1	B;B;B;P	0.38250	0.351;0.241;0.241;0.624	B;B;B;B	0.32342	0.071;0.071;0.071;0.144	T	0.76244	-0.3030	10	0.48119	T	0.1	-8.1579	0.3735	0.00383	0.3487:0.18:0.1302:0.3411	.	290;290;290;290	B4E3M8;B7ZKJ9;Q68CZ1;Q68CZ1-2	.;.;FTM_HUMAN;.	M	290	ENSP00000369257:I290M;ENSP00000262135:I290M	ENSP00000262135:I290M	I	-	3	3	RPGRIP1L	52266442	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.557000	0.36299	2.293000	0.77203	0.477000	0.44152	ATT	.	.	.	none		0.308	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272		C	53708941	A	C	53708941	3	2	111	1	0	0	0	0	1	0	0	0	13563	242	9	5	3161	5	RPGRIP1L	16	53708941	Missense_Mutation	SNP	A	TCGA-BQ-5876-01A-11D-1589-08	23127346	53708941	36645812	45	7174											
CHRNB1	1140	hgsc.bcm.edu	37	chr17	7357711	7357711	+	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	ctgagacctcactatcagtaCccattattatcaagtacctc	12	12	4	13	0	3	1	3	1	0	1	4	2	3	1	3	0	2	2	3	0	6	5			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr17:7357711C>G	ENST00000306071.2	+	8	983	c.916C>G	c.(916-918)Ccc>Gcc	p.P306A	CHRNB1_ENST00000536404.2_Missense_Mutation_p.P234A|CHRNB1_ENST00000576360.1_Intron|CHRNB1_ENST00000575379.1_5'Flank	NM_000747.2	NP_000738.2	P11230	ACHB_HUMAN	cholinergic receptor, nicotinic, beta 1 (muscle)	306					behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|neurological system process (GO:0050877)|neuromuscular synaptic transmission (GO:0007274)|postsynaptic membrane organization (GO:0001941)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|ligand-gated ion channel activity (GO:0015276)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|ovary(3)	23		Prostate(122;0.157)			Galantamine(DB00674)	ACTATCAGTACCCATTATTAT	0.512																																					p.P306A		Atlas-SNP	.											.	CHRNB1	46	.	0			c.C916G						PASS	.						307	238	262					17																	7357711		2203	4300	6503	SO:0001583	missense	1140	exon8			TCAGTACCCATTA	X14830	CCDS11106.1	17p13.1	2012-02-11	2006-02-01		ENSG00000170175	ENSG00000170175		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1961	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 1 (muscle)"	100710	"cholinergic receptor, nicotinic, beta polypeptide 1 (muscle)"	CHRNB			Standard	NM_000747		Approved		uc002ghb.3	P11230	OTTHUMG00000108139	ENST00000306071.2:c.916C>G	chr17.hg19:g.7357711C>G	ENSP00000304290:p.Pro306Ala	183.0	0.0	.		214.0	60.0	.	NM_000747	B7Z5H1|Q8IZ46|Q96FB8	Missense_Mutation	SNP	ENST00000306071.2	hg19	CCDS11106.1	.	.	.	.	.	.	.	.	.	.	C	16.76	3.212473	0.58452	.	.	ENSG00000170175	ENST00000306071;ENST00000536404	D;D	0.85339	-1.97;-1.97	4.92	4.92	0.64577	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.95245	0.8458	H	0.99074	4.42	0.80722	D	1	D	0.63880	0.993	P	0.61132	0.884	D	0.97341	0.9957	10	0.87932	D	0	.	15.675	0.77311	0.0:1.0:0.0:0.0	.	306	P11230	ACHB_HUMAN	A	306;234	ENSP00000304290:P306A;ENSP00000439209:P234A	ENSP00000304290:P306A	P	+	1	0	CHRNB1	7298435	1.000000	0.71417	0.998000	0.56505	0.270000	0.26580	7.818000	0.86416	2.300000	0.77407	0.298000	0.19748	CCC	.	.	.	none		0.512	CHRNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226942.3			G	7357711	C	G	7357711	3	3	111	1	0	0	0	0	1	0	0	0	3392	507	18	4	946	4	CHRNB1	17	7357711	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08		7357711	73837499	46	7175											
MYL4	4635	hgsc.bcm.edu	37	chr17	45286883	45286883	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcccctgccccagctcctgAggctcccaaggaacctgcct	7	6	9	19	0	0	1	0	1	0	0	2	2	2	2	8	2	5	2	8	2	2	0			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr17:45286883A>G	ENST00000354968.1	+	2	223	c.95A>G	c.(94-96)gAg>gGg	p.E32G	MYL4_ENST00000572316.1_Missense_Mutation_p.E32G|MYL4_ENST00000393450.1_Missense_Mutation_p.E32G	NM_001002841.1	NP_001002841.1	P12829	MYL4_HUMAN	myosin, light chain 4, alkali; atrial, embryonic	32					cardiac muscle contraction (GO:0060048)|muscle filament sliding (GO:0030049)|positive regulation of ATPase activity (GO:0032781)|regulation of the force of heart contraction (GO:0002026)	A band (GO:0031672)|cytosol (GO:0005829)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|calcium ion binding (GO:0005509)|myosin II heavy chain binding (GO:0032038)			endometrium(2)|large_intestine(1)|lung(4)|ovary(3)|prostate(1)	11						ccagctcctgAGGCTCCCAAG	0.582																																					p.E32G		Atlas-SNP	.											.	MYL4	27	.	0			c.A95G						PASS	.						65	64	64					17																	45286883		2203	4300	6503	SO:0001583	missense	4635	exon2			CTCCTGAGGCTCC		CCDS11510.1	17q21.32	2013-09-19	2006-09-29		ENSG00000198336	ENSG00000198336		"Myosins / Light chain", "EF-hand domain containing"	7585	protein-coding gene	gene with protein product	"myosin, atrial/fetal muscle, light chain"	160770	"myosin, light polypeptide 4, alkali; atrial, embryonic"			3417683	Standard	NM_002476		Approved	ALC1, AMLC, GT1, PRO1957	uc002ilg.3	P12829	OTTHUMG00000178232	ENST00000354968.1:c.95A>G	chr17.hg19:g.45286883A>G	ENSP00000347055:p.Glu32Gly	115.0	0.0	.		104.0	5.0	.	NM_001002841	D3DXJ7|P11783	Missense_Mutation	SNP	ENST00000354968.1	hg19	CCDS11510.1	.	.	.	.	.	.	.	.	.	.	A	13.90	2.376256	0.42105	.	.	ENSG00000198336	ENST00000354968;ENST00000393450;ENST00000536623	D;D	0.88124	-2.34;-2.34	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	D	0.91965	0.7455	M	0.81942	2.565	0.42862	D	0.994118	D	0.57899	0.981	D	0.65140	0.932	D	0.90935	0.4793	10	0.29301	T	0.29	-32.6232	11.5071	0.50472	1.0:0.0:0.0:0.0	.	32	P12829	MYL4_HUMAN	G	32;32;2	ENSP00000347055:E32G;ENSP00000377096:E32G	ENSP00000347055:E32G	E	+	2	0	MYL4	42641882	0.998000	0.40836	0.994000	0.49952	0.561000	0.35649	2.795000	0.47861	1.991000	0.58162	0.459000	0.35465	GAG	.	.	.	none		0.582	MYL4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441059.1	NM_001002841		G	45286883	A	G	45286883	3	3	111	1	0	0	0	0	1	0	0	0	10056	304	11	3	97	3	MYL4	17	45286883	Missense_Mutation	SNP	A	TCGA-BQ-5876-01A-11D-1589-08	37929172	45286883	35908327	47	7176											
HDHD2	84064	hgsc.bcm.edu	37	chr18	44639349	44639349	+	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	ttatacagaagatacataccAgtctttactaagatgcccag	15	11	6	9	0	1	3	0	0	1	3	1	3	1	3	2	0	5	0	2	0	7	7			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr18:44639349A>T	ENST00000300605.6	-	6	827	c.675T>A	c.(673-675)acT>acA	p.T225T	HDHD2_ENST00000587841.1_5'UTR	NM_032124.4	NP_115500.1	Q9H0R4	HDHD2_HUMAN	haloacid dehalogenase-like hydrolase domain containing 2	225						extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)			kidney(2)|large_intestine(2)|lung(1)|skin(1)	6						GATACATACCAGTCTTTACTA	0.408																																					p.T225T		Atlas-SNP	.											.	HDHD2	12	.	0			c.T675A						PASS	.						115	100	105					18																	44639349		2203	4300	6503	SO:0001630	splice_region_variant	84064	exon6			CATACCAGTCTTT	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.676+1T>A	chr18.hg19:g.44639349A>T		72.0	0.0	.		86.0	28.0	.	NM_032124	A8K7T3|Q96NV4	Silent	SNP	ENST00000300605.6	hg19	CCDS32829.1																																																																																			.	.	.	none		0.408	HDHD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450668.2	NM_032124	Silent	T	44639349	A	T	44639349	5	4	111	1	0	0	0	0	0	0	1	0	7030	202	7	5	112	5	HDHD2	18	44639349	Splice_Site	SNP	A	TCGA-BQ-5876-01A-11D-1589-08		44639349	33437899	48	7177											
MUC16	94025	hgsc.bcm.edu	37	chr19	9083127	9083127	+	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	ttagtatccaaacttgggacCtcagaaaactcaaatgtcaa	16	10	6	9	0	3	1	3	0	0	1	4	2	4	2	2	1	2	1	2	1	7	3			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr19:9083127C>A	ENST00000397910.4	-	1	8891	c.8688G>T	c.(8686-8688)gaG>gaT	p.E2896D		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2897	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						AACTTGGGACCTCAGAAAACT	0.507																																					p.E2896D		Atlas-SNP	.											.	MUC16	4315	.	0			c.G8688T						PASS	.						75	69	71					19																	9083127		1897	4124	6021	SO:0001583	missense	94025	exon1			TGGGACCTCAGAA	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.8688G>T	chr19.hg19:g.9083127C>A	ENSP00000381008:p.Glu2896Asp	46.0	0.0	.		29.0	6.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	2.382	-0.341788	0.05243	.	.	ENSG00000181143	ENST00000397910	T	0.02606	4.23	0.773	-1.55	0.08558	.	.	.	.	.	T	0.01489	0.0048	N	0.08118	0	.	.	.	B	0.19817	0.039	B	0.15484	0.013	T	0.45906	-0.9229	8	0.87932	D	0	.	2.2074	0.03939	0.0:0.3584:0.3406:0.301	.	2896	B5ME49	.	D	2896	ENSP00000381008:E2896D	ENSP00000381008:E2896D	E	-	3	2	MUC16	8944127	0.000000	0.05858	0.000000	0.03702	0.154000	0.21943	-0.875000	0.04205	-0.903000	0.03881	0.313000	0.20887	GAG	.	.	.	none		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9083127	C	A	9083127	3	1	111	1	0	0	0	0	1	0	0	0	9980	680	24	4	35171	4	MUC16	19	9083127	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08		9083127	50045856	49	7178											
IRF2BP1	26145	hgsc.bcm.edu	37	chr19	46387423	46387423	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctccccggccgggccctgcGccttgatgaactcccgggag	4	6	13	18	4	0	2	0	2	0	0	2	3	2	3	7	3	2	0	7	3	1	1			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr19:46387423G>A	ENST00000302165.3	-	1	1953	c.1610C>T	c.(1609-1611)gCg>gTg	p.A537V		NM_015649.1	NP_056464.1	Q8IU81	I2BP1_HUMAN	interferon regulatory factor 2 binding protein 1	537	Cys-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)			cervix(1)|kidney(1)|lung(2)	4		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00442)|GBM - Glioblastoma multiforme(486;0.0402)|Epithelial(262;0.231)		CGGGCCCTGCGCCTTGATGAA	0.677																																					p.A537V		Atlas-SNP	.											.	IRF2BP1	23	.	0			c.C1610T						PASS	.						30	30	30					19																	46387423		2203	4299	6502	SO:0001583	missense	26145	exon1			CCCTGCGCCTTGA	AY278022	CCDS12678.1	19q13.32	2008-02-05							21728	protein-coding gene	gene with protein product		615331				12799427	Standard	NM_015649		Approved	DKFZP434M154, IRF-2BP1	uc002pds.1	Q8IU81		ENST00000302165.3:c.1610C>T	chr19.hg19:g.46387423G>A	ENSP00000307265:p.Ala537Val	73.0	0.0	.		67.0	7.0	.	NM_015649	Q53EL7|Q6DC95|Q9BRZ9|Q9Y4P4	Missense_Mutation	SNP	ENST00000302165.3	hg19	CCDS12678.1	.	.	.	.	.	.	.	.	.	.	G	18.22	3.574987	0.65878	.	.	ENSG00000170604	ENST00000302165	D	0.86230	-2.09	4.58	4.58	0.56647	Zinc finger, C3HC4 RING-type (1);	0.382217	0.24182	N	0.040786	T	0.75961	0.3921	N	0.22421	0.69	0.30785	N	0.741587	P	0.43750	0.816	B	0.32533	0.147	T	0.77253	-0.2656	10	0.33940	T	0.23	.	14.914	0.70781	0.0:0.0:1.0:0.0	.	537	Q8IU81	I2BP1_HUMAN	V	537	ENSP00000307265:A537V	ENSP00000307265:A537V	A	-	2	0	IRF2BP1	51079263	0.964000	0.33143	0.999000	0.59377	0.968000	0.65278	2.896000	0.48656	2.362000	0.80069	0.563000	0.77884	GCG	.	.	.	none		0.677	IRF2BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461683.1	NM_015649		A	46387423	G	A	46387423	3	1	111	1	0	0	0	0	1	0	0	0	7836	1087	38	1	148	1	IRF2BP1	19	46387423	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	37304296	46387423	12741560	50	7179											
FAM71E1	112703	hgsc.bcm.edu	37	chr19	50970929	50970929	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcagagaggaagcgcaggcGgtagagcagccgcacccact	12	2	15	12	3	0	2	0	0	0	2	0	4	0	3	2	3	4	5	2	3	2	1			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr19:50970929G>A	ENST00000600100.1	-	4	1061	c.697C>T	c.(697-699)Cgc>Tgc	p.R233C	FAM71E1_ENST00000595790.1_Missense_Mutation_p.R217C			Q6IPT2	F71E1_HUMAN	family with sequence similarity 71, member E1	233										breast(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.0077)|GBM - Glioblastoma multiforme(134;0.026)		AAGCGCAGGCGGTAGAGCAGC	0.612																																					p.R217C		Atlas-SNP	.											.	FAM71E1	21	.	0			c.C649T						PASS	.						26	27	26					19																	50970929		2195	4290	6485	SO:0001583	missense	112703	exon4			GCAGGCGGTAGAG		CCDS33081.1	19q13.33	2007-11-20				ENSG00000142530			25107	protein-coding gene	gene with protein product							Standard	XM_005258472		Approved		uc002psg.3	Q6IPT2		ENST00000600100.1:c.697C>T	chr19.hg19:g.50970929G>A	ENSP00000472421:p.Arg233Cys	14.0	0.0	.		11.0	4.0	.	NM_138411	Q96EJ5|Q9BSM9	Missense_Mutation	SNP	ENST00000600100.1	hg19		.	.	.	.	.	.	.	.	.	.	g	15.85	2.955383	0.53293	.	.	ENSG00000142530	ENST00000391816;ENST00000270620	T;T	0.17854	2.25;2.25	4.0	0.356	0.16074	.	0.791977	0.10938	N	0.617646	T	0.29914	0.0748	L	0.51422	1.61	0.42510	D	0.992969	D;D	0.89917	1.0;1.0	D;D	0.73380	0.98;0.95	T	0.19877	-1.0292	10	0.66056	D	0.02	-6.3609	5.8158	0.18492	0.096:0.0:0.5658:0.3382	.	233;217	Q6IPT2;Q6IPT2-2	F71E1_HUMAN;.	C	233;217	ENSP00000375692:R233C;ENSP00000270620:R217C	ENSP00000270620:R217C	R	-	1	0	FAM71E1	55662741	1.000000	0.71417	0.998000	0.56505	0.724000	0.41520	2.576000	0.46033	0.057000	0.16193	0.462000	0.41574	CGC	.	.	.	none		0.612	FAM71E1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464754.2			A	50970929	G	A	50970929	3	1	111	1	0	0	0	0	1	0	0	0	5618	1116	39	1	50	1	FAM71E1	19	50970929	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	4583506	50970929	8158054	51	7180											
ZFP28	140612	hgsc.bcm.edu	37	chr19	57066282	57066282	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtatggaatgtgggaaggccTttggtgataactcatcctgt	9	13	13	6	0	1	1	1	1	0	0	2	3	2	3	2	4	1	1	2	4	4	3			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr19:57066282T>C	ENST00000301318.3	+	8	2199	c.2128T>C	c.(2128-2130)Ttt>Ctt	p.F710L	AC007228.11_ENST00000596587.1_RNA	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	710					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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)		TGGGAAGGCCTTTGGTGATAA	0.443																																					p.F710L	Ovarian(124;554 1662 19430 21141 52494)	Atlas-SNP	.											.	ZFP28	99	.	0			c.T2128C						PASS	.						105	105	105					19																	57066282		2203	4300	6503	SO:0001583	missense	140612	exon8			AAGGCCTTTGGTG		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.2128T>C	chr19.hg19:g.57066282T>C	ENSP00000301318:p.Phe710Leu	124.0	0.0	.		128.0	45.0	.	NM_020828	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Missense_Mutation	SNP	ENST00000301318.3	hg19	CCDS12946.1	.	.	.	.	.	.	.	.	.	.	T	18.87	3.714627	0.68730	.	.	ENSG00000196867	ENST00000301318	T	0.46063	0.88	4.0	2.98	0.34508	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.47093	D	0.000249	T	0.64659	0.2618	M	0.87097	2.86	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.66488	-0.5911	10	0.87932	D	0	.	8.4668	0.32960	0.0:0.0964:0.0:0.9036	.	710	Q8NHY6	ZFP28_HUMAN	L	710	ENSP00000301318:F710L	ENSP00000301318:F710L	F	+	1	0	ZFP28	61758094	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.655000	0.67981	0.710000	0.31997	0.454000	0.30748	TTT	.	.	.	none		0.443	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828		C	57066282	T	C	57066282	3	2	111	1	0	0	0	0	1	0	0	0	17654	1609	56	3	2158	3	ZFP28	19	57066282	Missense_Mutation	SNP	T	TCGA-BQ-5876-01A-11D-1589-08	6095353	57066282	2062701	52	7181			1	16		2	2	17	N	T_C	3.101053e-05
ZFP28	140612	hgsc.bcm.edu	37	chr19	57066298	57066298	+	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	ggcctttggtgataactcatCctgtactcaacatcaaagac	12	11	7	11	0	3	2	3	1	0	1	4	2	4	2	2	2	3	1	2	2	4	3			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr19:57066298C>A	ENST00000301318.3	+	8	2215	c.2144C>A	c.(2143-2145)tCc>tAc	p.S715Y	AC007228.11_ENST00000596587.1_RNA	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	715					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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)		GATAACTCATCCTGTACTCAA	0.433																																					p.S715Y	Ovarian(124;554 1662 19430 21141 52494)	Atlas-SNP	.											.	ZFP28	99	.	0			c.C2144A						PASS	.						108	108	108					19																	57066298		2203	4300	6503	SO:0001583	missense	140612	exon8			ACTCATCCTGTAC		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.2144C>A	chr19.hg19:g.57066298C>A	ENSP00000301318:p.Ser715Tyr	129.0	0.0	.		130.0	45.0	.	NM_020828	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Missense_Mutation	SNP	ENST00000301318.3	hg19	CCDS12946.1	.	.	.	.	.	.	.	.	.	.	C	0.336	-0.953021	0.02285	.	.	ENSG00000196867	ENST00000301318	T	0.36878	1.23	4.0	2.86	0.33363	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.44902	D	0.000413	T	0.22742	0.0549	L	0.35723	1.085	0.20074	N	0.999935	P	0.39181	0.663	B	0.37346	0.247	T	0.07481	-1.0770	10	0.17832	T	0.49	.	7.0155	0.24885	0.0:0.7197:0.1785:0.1018	.	715	Q8NHY6	ZFP28_HUMAN	Y	715	ENSP00000301318:S715Y	ENSP00000301318:S715Y	S	+	2	0	ZFP28	61758110	0.001000	0.12720	0.992000	0.48379	0.984000	0.73092	1.178000	0.31981	2.228000	0.72767	0.555000	0.69702	TCC	.	.	.	none		0.433	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828		A	57066298	C	A	57066298	3	1	111	1	0	0	0	0	1	0	0	0	17654	855	30	4	2174	4	ZFP28	19	57066298	Missense_Mutation	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	16	57066298	2062685	53	7182			1	16		2	2	17	N	T_C	3.101053e-05
NCOA6	23054	hgsc.bcm.edu	37	chr20	33329544	33329544	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atctgtaagcccagggggttTaattgtcacattgggagctc	9	12	12	8	0	2	0	1	0	1	0	3	1	2	1	1	3	2	3	1	3	2	5			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr20:33329544T>C	ENST00000374796.2	-	12	7086	c.4516A>G	c.(4516-4518)Aaa>Gaa	p.K1506E	NCOA6_ENST00000359003.2_Missense_Mutation_p.K1506E			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1506					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						CCAGGGGGTTTAATTGTCACA	0.463																																					p.K1506E		Atlas-SNP	.											.	NCOA6	219	.	0			c.A4516G						PASS	.						78	70	73					20																	33329544		2203	4300	6503	SO:0001583	missense	23054	exon11			GGGGTTTAATTGT	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.4516A>G	chr20.hg19:g.33329544T>C	ENSP00000363929:p.Lys1506Glu	132.0	0.0	.		107.0	43.0	.	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	hg19	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	T	16.73	3.203458	0.58234	.	.	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.34859	1.34;1.34	5.37	5.37	0.77165	.	0.000000	0.64402	D	0.000002	T	0.38852	0.1056	L	0.27053	0.805	0.39212	D	0.963341	D	0.60575	0.988	P	0.54759	0.76	T	0.16482	-1.0401	10	0.25106	T	0.35	-8.9946	15.5409	0.76048	0.0:0.0:0.0:1.0	.	1506	Q14686	NCOA6_HUMAN	E	1506	ENSP00000363929:K1506E;ENSP00000351894:K1506E	ENSP00000351894:K1506E	K	-	1	0	NCOA6	32793205	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.330000	0.65899	2.254000	0.74563	0.482000	0.46254	AAA	.	.	.	none		0.463	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		C	33329544	T	C	33329544	3	2	111	1	0	0	0	0	1	0	0	0	10240	1763	61	3	1695	3	NCOA6	20	33329544	Missense_Mutation	SNP	T	TCGA-BQ-5876-01A-11D-1589-08		33329544	29695976	54	7183											
SLC5A3	6526	hgsc.bcm.edu	37	chr21	35468362	35468362	+	Missense_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	tcgtgcagagggtccttgcaGccaaaaacattgctcatgcc	10	9	10	12	1	1	1	1	0	0	1	3	1	2	1	3	1	6	3	3	1	2	2			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr21:35468362G>A	ENST00000381151.3	+	2	1377	c.865G>A	c.(865-867)Gcc>Acc	p.A289T	AP000320.7_ENST00000362077.4_RNA|MRPS6_ENST00000399312.2_Intron|SLC5A3_ENST00000608209.1_Missense_Mutation_p.A289T			P53794	SC5A3_HUMAN	solute carrier family 5 (sodium/myo-inositol cotransporter), member 3	289					inositol metabolic process (GO:0006020)|peripheral nervous system development (GO:0007422)|regulation of respiratory gaseous exchange (GO:0043576)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	myo-inositol:sodium symporter activity (GO:0005367)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	20						GGTCCTTGCAGCCAAAAACAT	0.478																																					p.A289T		Atlas-SNP	.											.	SLC5A3	52	.	0			c.G865A						PASS	.						102	98	100					21																	35468362		2203	4300	6503	SO:0001583	missense	6526	exon2			CTTGCAGCCAAAA		CCDS33549.1	21q22.11	2013-05-22	2008-09-02		ENSG00000198743	ENSG00000198743		"Solute carriers"	11038	protein-coding gene	gene with protein product		600444	"solute carrier family 5 (inositol transporter), member 3"			7789985	Standard	NM_006933		Approved	SMIT, SMIT1	uc002yto.3	P53794	OTTHUMG00000065821	ENST00000381151.3:c.865G>A	chr21.hg19:g.35468362G>A	ENSP00000370543:p.Ala289Thr	217.0	0.0	.		190.0	80.0	.	NM_006933	O43489	Missense_Mutation	SNP	ENST00000381151.3	hg19	CCDS33549.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.936080	0.73442	.	.	ENSG00000198743	ENST00000381151	D	0.88975	-2.45	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.96482	0.8852	H	0.96365	3.81	0.58432	D	0.999999	D	0.89917	1.0	D	0.79108	0.992	D	0.97583	1.0112	10	0.87932	D	0	.	18.2056	0.89853	0.0:0.0:1.0:0.0	.	289	P53794	SC5A3_HUMAN	T	289	ENSP00000370543:A289T	ENSP00000370543:A289T	A	+	1	0	SLC5A3	34390232	1.000000	0.71417	0.922000	0.36590	0.963000	0.63663	9.869000	0.99810	2.589000	0.87451	0.609000	0.83330	GCC	.	.	.	none		0.478	SLC5A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000141037.1			A	35468362	G	A	35468362	3	1	111	1	0	0	0	0	1	0	0	0	14679	971	34	2	867	2	SLC5A3	21	35468362	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08		35468362	12661533	55	7184											
POTEH	23784	hgsc.bcm.edu	37	chr22	16287580	16287580	+	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	cagcaggggaagcagtggcaGcaccacttgcccatcttgct	9	7	12	13	0	1	0	0	0	1	0	1	1	1	1	2	3	5	5	2	3	1	2			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr22:16287580G>T	ENST00000343518.6	-	1	357	c.306C>A	c.(304-306)tgC>tgA	p.C102*		NM_001136213.1	NP_001129685.1	Q6S545	POTEH_HUMAN	POTE ankyrin domain family, member H	102										NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(20)|ovary(1)|skin(7)|urinary_tract(2)	37						AGCAGTGGCAGCACCACTTGC	0.597																																					p.C102X		Atlas-SNP	.											POTEH,caecum,carcinoma,0,1	POTEH	114	.	0			c.C306A						PASS	.						67	81	76					22																	16287580		1945	3669	5614	SO:0001587	stop_gained	23784	exon1			GTGGCAGCACCAC	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.306C>A	chr22.hg19:g.16287580G>T	ENSP00000340610:p.Cys102*	1092.0	2.0	.		417.0	167.0	.	NM_001136213	A2CEK4|A6NCI1|A9Z1W0	Nonsense_Mutation	SNP	ENST00000343518.6	hg19	CCDS46658.1	.	.	.	.	.	.	.	.	.	.	.	13.12	2.143668	0.37825	.	.	ENSG00000198062	ENST00000343518;ENST00000355872	.	.	.	0.168	0.168	0.15012	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	.	.	.	.	.	.	.	X	102	.	ENSP00000340610:C102X	C	-	3	2	POTEH	14667580	0.005000	0.15991	0.025000	0.17156	0.026000	0.11368	0.263000	0.18478	0.278000	0.22164	0.283000	0.19423	TGC	.	.	.	none		0.597	POTEH-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276918.4	NM_001136213		T	16287580	G	T	16287580	4	4	111	1	0	0	0	0	0	1	0	0	12274	963	34	4	1371	4	POTEH	22	16287580	Nonsense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08		16287580	35016986	56	7185											
SMARCB1	6598	hgsc.bcm.edu	37	chr22	24167461	24167461	+	Frame_Shift_Del	DEL	A	A	-																															ggtggaccagtttgagtgggAcatgtcagagaaggagaact																										TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr22:24167461delA	ENST00000263121.7	+	7	1041	c.845delA	c.(844-846)gacfs	p.D282fs	SMARCB1_ENST00000407422.3_Frame_Shift_Del_p.D273fs|SMARCB1_ENST00000407082.3_Frame_Shift_Del_p.D236fs|SMARCB1_ENST00000477836.1_3'UTR|SMARCB1_ENST00000344921.6_Frame_Shift_Del_p.D291fs	NM_003073.3	NP_003064.2	Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	282	2 X approximate tandem repeats.				ATP-dependent chromatin remodeling (GO:0043044)|blastocyst hatching (GO:0001835)|cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|DNA integration (GO:0015074)|DNA repair (GO:0006281)|mitotic cell cycle phase transition (GO:0044772)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	p53 binding (GO:0002039)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)	p.?(6)|p.L266_*386del(1)		bone(4)|central_nervous_system(198)|endometrium(4)|haematopoietic_and_lymphoid_tissue(25)|kidney(3)|large_intestine(5)|liver(2)|lung(5)|meninges(5)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|soft_tissue(194)	458		Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05)				TTTGAGTGGGACATGTCAGAG	0.537			"D, N, F, S"		malignant rhabdoid	malignant rhabdoid																															p.D282fs		Atlas-INDEL	.	yes	Rec	yes	Rhabdoid predisposition syndrome	22	22q11	6598	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1"		M	.	SMARCB1	586	.	7	Unknown(6)|Deletion - In frame(1)	central_nervous_system(6)|soft_tissue(1)	c.844delG						PASS	.						126	101	110					22																	24167461		2203	4300	6503	SO:0001589	frameshift_variant	6598	exon7			.	U04847	CCDS13817.1, CCDS46671.1	22q11.23	2014-09-17			ENSG00000099956	ENSG00000099956			11103	protein-coding gene	gene with protein product	"sucrose nonfermenting, yeast, homolog-like 1", "integrase interactor 1", "malignant rhabdoid tumor suppressor", "protein phosphatase 1, regulatory subunit 144"	601607		SNF5L1		7801128, 10319872, 10365963	Standard	NM_003073		Approved	BAF47, Ini1, Snr1, hSNFS, Sfh1p, RDT, PPP1R144	uc002zyb.3	Q12824	OTTHUMG00000150737	ENST00000263121.7:c.845delA	chr22.hg19:g.24167461delA	ENSP00000263121:p.Asp282fs	92.0	0.0	0		75.0	57.0	0.76	NM_003073	O75784|O95474|Q17S11|Q38GA1|Q76N08|Q9UBH2	Frame_Shift_Del	DEL	ENST00000263121.7	hg19	CCDS13817.1																																																																																			.	.	.	none		0.537	SMARCB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319872.1	NM_003073		-	24167461	A	-	24167461	7	5	111	1	0	1	0	1	0	0	0	0	14787	275	10	0	871	0	SMARCB1	22	24167461	Frame_Shift_Del	DEL	A	TCGA-BQ-5876-01A-11D-1589-08	7879881	24167461	27137105	57	7186											
CENPM	79019	hgsc.bcm.edu	37	chr22	42342456	42342456	+	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	gcgcagtcctctttgagcatCgagtccgccagctgctgcag	6	9	12	14	3	1	1	0	1	1	0	4	2	3	1	3	0	4	5	3	0	0	1	rs372178394		TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chr22:42342456C>G	ENST00000215980.5	-	2	189	c.102G>C	c.(100-102)tcG>tcC	p.S34S	CENPM_ENST00000402420.1_5'UTR|CENPM_ENST00000402338.1_5'UTR|CENPM_ENST00000407253.3_Silent_p.S34S|CENPM_ENST00000404067.1_5'UTR	NM_024053.3	NP_076958.1	Q9NSP4	CENPM_HUMAN	centromere protein M	34					mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)				kidney(1)|large_intestine(1)|prostate(1)	3						CTTTGAGCATCGAGTCCGCCA	0.647											OREG0026600	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S34S		Atlas-SNP	.											.	CENPM	8	.	0			c.G102C						PASS	.						36	31	33					22																	42342456		2203	4299	6502	SO:0001819	synonymous_variant	79019	exon2			GAGCATCGAGTCC	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.102G>C	chr22.hg19:g.42342456C>G		39.0	0.0	.	908	32.0	4.0	.	NM_024053	A7LM22|B1AHQ9|Q6I9W3	Silent	SNP	ENST00000215980.5	hg19	CCDS14025.1																																																																																			.	.	.	alt		0.647	CENPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322058.1	NM_024053		G	42342456	C	G	42342456	2	3	111	1	0	0	0	0	0	0	0	1	3239	871	31	4		4	CENPM	22	42342456	Silent	SNP	C	TCGA-BQ-5876-01A-11D-1589-08	18174995	42342456	8962110	58	7187											
TAF1	6872	hgsc.bcm.edu	37	chrX	70643918	70643918	+	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	tttagagaccatacgtaaggTgagtgagtgatttgatctaa	13	13	11	4	1	1	5	0	4	1	1	1	6	1	5	1	1	1	1	1	1	4	6			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chrX:70643918T>C	ENST00000373790.4	+	31	4716		c.e31+2		TAF1_ENST00000423759.1_Splice_Site|TAF1_ENST00000461764.1_Splice_Site|TAF1_ENST00000449580.1_Splice_Site|TAF1_ENST00000276072.3_Splice_Site	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						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)				ATACGTAAGGTGAGTGAGTGA	0.373																																					.		Atlas-SNP	.											.	TAF1	439	.	0			c.4728+2T>C						PASS	.						133	107	116					X																	70643918		2203	4300	6503	SO:0001630	splice_region_variant	6872	exon31			GTAAGGTGAGTGA		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.4665+2T>C	chrX.hg19:g.70643918T>C		73.0	0.0	.		65.0	49.0	.	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Splice_Site	SNP	ENST00000373790.4	hg19	CCDS35325.1	.	.	.	.	.	.	.	.	.	.	T	16.92	3.255554	0.59321	.	.	ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000395779;ENST00000538124;ENST00000276072;ENST00000437147	.	.	.	4.85	4.85	0.62838	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8076	0.63243	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	TAF1	70560643	1.000000	0.71417	0.992000	0.48379	0.831000	0.47069	7.412000	0.80091	1.704000	0.51252	0.486000	0.48141	.	.	.	.	none		0.373	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606	Intron	C	70643918	T	C	70643918	5	2	111	1	0	0	0	0	0	0	1	0	15525	1710	59	3	4852	3	TAF1	23	70643918	Splice_Site	SNP	T	TCGA-BQ-5876-01A-11D-1589-08		70643918	84626642	59	7188											
ODZ1	10178	hgsc.bcm.edu	37	chrX	123518587	123518587	+	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	aaagatctataggcaaagggGtttcattgattacagcttgc	13	12	10	6	0	2	2	1	1	1	1	2	2	2	2	0	3	3	3	0	3	5	6			TCGA-BQ-5876-01A-11D-1589-08	TCGA-BQ-5876-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ffc588e2-0513-4495-b578-d028131a1dc3	a1a3e47d-ca70-49d5-8599-c60c433343f0	g.chrX:123518587G>C	ENST00000371130.3	-	29	6236	c.6173C>G	c.(6172-6174)aCc>aGc	p.T2058S	STAG2_ENST00000469481.1_Intron|TENM1_ENST00000422452.2_Missense_Mutation_p.T2065S	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	2058					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)										AGGCAAAGGGGTTTCATTGAT	0.393																																					p.T2065S		Atlas-SNP	.											.	.	.	.	0			c.C6194G						PASS	.						125	106	112					X																	123518587		2203	4300	6503	SO:0001583	missense	10178	exon30			AAAGGGGTTTCAT	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.6173C>G	chrX.hg19:g.123518587G>C	ENSP00000360171:p.Thr2058Ser	117.0	0.0	.		97.0	81.0	.	NM_001163278	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	hg19	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.184284	0.78677	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.86097	-2.07;-2.03	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	D	0.90992	0.7167	M	0.62723	1.935	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.999	D;D;D	0.70716	0.97;0.918;0.937	D	0.90198	0.4255	10	0.39692	T	0.17	.	18.3227	0.90244	0.0:0.0:1.0:0.0	.	2064;2065;2058	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	S	2058;2065	ENSP00000360171:T2058S;ENSP00000403954:T2065S	ENSP00000360171:T2058S	T	-	2	0	ODZ1	123346268	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.964000	0.87933	2.265000	0.75225	0.600000	0.82982	ACC	.	.	.	none		0.393	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		C	123518587	G	C	123518587	3	2	111	1	0	0	0	0	1	0	0	0	10841	1261	44	4	2016	4	ODZ1	23	123518587	Missense_Mutation	SNP	G	TCGA-BQ-5876-01A-11D-1589-08	52874669	123518587	31751973	60	7189											
CTRC	11330	hgsc.bcm.edu	37	chr1	15766798	15766798	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcctcctgtctccccagccTccagctgtggggtgcccagc	3	8	12	18	0	1	0	0	0	1	0	4	0	3	0	7	3	4	1	7	3	0	0			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr1:15766798T>C	ENST00000375949.4	+	2	69	c.43T>C	c.(43-45)Tcc>Ccc	p.S15P	CTRC_ENST00000375943.2_Intron	NM_007272.2	NP_009203.2	Q99895	CTRC_HUMAN	chymotrypsin C (caldecrin)	15					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)		CTCCCCAGCCTCCAGCTGTGG	0.662																																					p.S15P		Atlas-SNP	.											.	CTRC	28	.	0			c.T43C						PASS	.						13	15	14					1																	15766798		2195	4289	6484	SO:0001583	missense	11330	exon2			CCAGCCTCCAGCT	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.43T>C	chr1.hg19:g.15766798T>C	ENSP00000365116:p.Ser15Pro	15.0	0.0	.		26.0	4.0	.	NM_007272	A8K082|O00765|Q9NUH5	Missense_Mutation	SNP	ENST00000375949.4	hg19	CCDS156.1	.	.	.	.	.	.	.	.	.	.	.	12.00	1.806468	0.31961	.	.	ENSG00000162438	ENST00000375949	D	0.92699	-3.09	4.94	3.78	0.43462	.	0.380815	0.30293	N	0.009943	D	0.82522	0.5055	N	0.12961	0.28	0.80722	D	1	P;B	0.34837	0.472;0.198	B;B	0.30943	0.122;0.122	T	0.78914	-0.2016	10	0.35671	T	0.21	-29.5492	10.7713	0.46325	0.0:0.0:0.1596:0.8404	.	15;15	A8MTQ9;Q99895	.;CTRC_HUMAN	P	15	ENSP00000365116:S15P	ENSP00000365116:S15P	S	+	1	0	CTRC	15639385	1.000000	0.71417	1.000000	0.80357	0.574000	0.36063	1.777000	0.38604	0.881000	0.35993	0.533000	0.62120	TCC	.	.	.	none		0.662	CTRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006435.1	NM_007272		C	15766798	T	C	15766798	3	2	112	1	0	0	0	0	1	0	0	0	4029	1551	54	3	49	3	CTRC	1	15766798	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08		15766798	233483823	1	7190											
BCAN	63827	hgsc.bcm.edu	37	chr1	156628454	156628454	+	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	aaggactggcccagcgcaatCtgccgctgatccgatgccaa	10	6	11	14	3	1	1	0	1	1	0	2	3	2	2	4	2	3	2	4	2	3	0			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr1:156628454C>A	ENST00000329117.5	+	13	2893	c.2557C>A	c.(2557-2559)Ctg>Atg	p.L853M	RP11-284F21.7_ENST00000448869.1_RNA	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	853	Sushi. {ECO:0000255|PROSITE- ProRule:PRU00302}.				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)					CCAGCGCAATCTGCCGCTGAT	0.647																																					p.L853M		Atlas-SNP	.											.	BCAN	174	.	0			c.C2557A						PASS	.						76	82	80					1																	156628454		2203	4300	6503	SO:0001583	missense	63827	exon13			CGCAATCTGCCGC	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.2557C>A	chr1.hg19:g.156628454C>A	ENSP00000331210:p.Leu853Met	138.0	0.0	.		203.0	83.0	.	NM_021948	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Missense_Mutation	SNP	ENST00000329117.5	hg19	CCDS1149.1	.	.	.	.	.	.	.	.	.	.	C	14.28	2.488032	0.44249	.	.	ENSG00000132692	ENST00000329117	T	0.63744	-0.06	4.96	2.91	0.33838	Complement control module (2);Sushi/SCR/CCP (3);	0.749157	0.11026	N	0.607755	T	0.48352	0.1495	L	0.45051	1.395	0.30868	N	0.73272	D	0.56287	0.975	P	0.55011	0.766	T	0.36456	-0.9747	10	0.44086	T	0.13	-3.4908	5.7222	0.17992	0.0:0.6921:0.0:0.3079	.	853	Q96GW7	PGCB_HUMAN	M	853	ENSP00000331210:L853M	ENSP00000331210:L853M	L	+	1	2	BCAN	154895078	0.002000	0.14202	0.999000	0.59377	0.591000	0.36615	0.020000	0.13466	1.299000	0.44798	0.555000	0.69702	CTG	.	.	.	none		0.647	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948		A	156628454	C	A	156628454	3	1	112	1	0	0	0	0	1	0	0	0	1345	912	32	4	2677	4	BCAN	1	156628454	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	140861656	156628454	92622167	2	7191											
HMCN1	83872	hgsc.bcm.edu	37	chr1	186072770	186072770	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagtgcaaactctaggaggAggagaggttcttcgaatttc	12	10	12	7	1	2	1	0	0	2	1	4	5	2	3	0	4	2	2	0	4	4	4			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr1:186072770A>G	ENST00000271588.4	+	69	10969	c.10740A>G	c.(10738-10740)ggA>ggG	p.G3580G	HMCN1_ENST00000367492.2_Silent_p.G3580G	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3580	Ig-like C2-type 34.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CTCTAGGAGGAGGAGAGGTTC	0.433																																					p.G3580G		Atlas-SNP	.											.	HMCN1	797	.	0			c.A10740G						PASS	.						58	60	59					1																	186072770		2203	4299	6502	SO:0001819	synonymous_variant	83872	exon69			AGGAGGAGGAGAG	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.10740A>G	chr1.hg19:g.186072770A>G		61.0	0.0	.		74.0	18.0	.	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.	.	none		0.433	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		G	186072770	A	G	186072770	2	3	112	1	0	0	0	0	0	0	0	1	7227	291	11	3		3	HMCN1	1	186072770	Silent	SNP	A	TCGA-BQ-5877-01A-11D-1589-08	29444316	186072770	63177851	3	7192											
KIF21B	23046	hgsc.bcm.edu	37	chr1	200974516	200974517	+	Frame_Shift_Del	DEL	TC	TC	-																															gcgtgagctctgcacgttcaTctgggtgctggctgtggtgc																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	TC	TC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr1:200974516_200974517delTC	ENST00000422435.2	-	5	967_968	c.651_652delGA	c.(649-654)cagatgfs	p.QM217fs	KIF21B_ENST00000360529.5_Frame_Shift_Del_p.QM217fs|KIF21B_ENST00000332129.2_Frame_Shift_Del_p.QM217fs|KIF21B_ENST00000461742.2_Frame_Shift_Del_p.QM217fs	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	217	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						TGCACGTTCATCTGGGTGCTGG	0.639																																					p.218_218del		Atlas-INDEL	.											.	KIF21B	208	.	0			c.652_653del						PASS	.																																			SO:0001589	frameshift_variant	23046	exon5			.	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.651_652delGA	chr1.hg19:g.200974516_200974517delTC	ENSP00000411831:p.Gln217fs	96.0	0.0	0		142.0	48.0	0.338028	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Frame_Shift_Del	DEL	ENST00000422435.2	hg19	CCDS58056.1																																																																																			.	.	.	none		0.639	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332		-	200974517	TC	-	200974516	7	5	112	1	0	1	0	1	0	0	0	0	8296	1435	50	0	4342	0	KIF21B	1	200974516	Frame_Shift_Del	DEL	TC	TCGA-BQ-5877-01A-11D-1589-08	14901746	200974516	48276105	4	7193											
EXOC8	149371	hgsc.bcm.edu	37	chr1	231472695	231472695	+	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	actctcgtttgattttagcaTtttcggcctggaaaatacgg	9	15	9	8	3	1	1	0	1	1	0	3	2	1	2	1	3	2	2	1	3	4	6			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr1:231472695T>A	ENST00000360394.2	-	1	883	c.797A>T	c.(796-798)aAt>aTt	p.N266I	SPRTN_ENST00000391858.4_5'Flank|EXOC8_ENST00000366645.1_Missense_Mutation_p.N262I|SPRTN_ENST00000295050.7_5'Flank|SPRTN_ENST00000008440.9_5'Flank	NM_175876.3	NP_787072.2	Q8IYI6	EXOC8_HUMAN	exocyst complex component 8	266	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)				GATTTTAGCATTTTCGGCCTG	0.547																																					p.N266I		Atlas-SNP	.											.	EXOC8	42	.	0			c.A797T						PASS	.						69	70	69					1																	231472695		2203	4300	6503	SO:0001583	missense	149371	exon1			TTAGCATTTTCGG	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.797A>T	chr1.hg19:g.231472695T>A	ENSP00000353564:p.Asn266Ile	123.0	0.0	.		172.0	67.0	.	NM_175876	B3KU33|Q5TE82	Missense_Mutation	SNP	ENST00000360394.2	hg19	CCDS1593.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.175994	0.78564	.	.	ENSG00000116903	ENST00000360394;ENST00000366645	T;T	0.79653	-1.29;-1.29	5.69	5.69	0.88448	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	D	0.88130	0.6354	M	0.64997	1.995	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	D	0.88677	0.3199	10	0.56958	D	0.05	-22.853	15.9478	0.79806	0.0:0.0:0.0:1.0	.	266	Q8IYI6	EXOC8_HUMAN	I	266;262	ENSP00000353564:N266I;ENSP00000355605:N262I	ENSP00000353564:N266I	N	-	2	0	EXOC8	229539318	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.040000	0.89188	2.165000	0.68154	0.459000	0.35465	AAT	.	.	.	none		0.547	EXOC8-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_175876		A	231472695	T	A	231472695	3	1	112	1	0	0	0	0	1	0	0	0	5313	1493	52	5	1384	5	EXOC8	1	231472695	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	30498179	231472695	17777926	5	7194											
NBAS	51594	hgsc.bcm.edu	37	chr2	15542368	15542368	+	Missense_Mutation	SNP	T	T	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	atttcgttcacaggtatagaTgcactctagtgctattgcca	10	14	8	9	1	2	1	1	0	1	1	3	1	2	1	1	1	3	4	1	1	4	7			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr2:15542368T>G	ENST00000281513.5	-	26	3020	c.2995A>C	c.(2995-2997)Atc>Ctc	p.I999L	NBAS_ENST00000441750.1_Missense_Mutation_p.I879L	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	999					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						CAGGTATAGATGCACTCTAGT	0.383																																					p.I999L		Atlas-SNP	.											.	NBAS	246	.	0			c.A2995C						PASS	.						156	148	151					2																	15542368		2203	4300	6503	SO:0001583	missense	51594	exon26			TATAGATGCACTC	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.2995A>C	chr2.hg19:g.15542368T>G	ENSP00000281513:p.Ile999Leu	145.0	0.0	.		137.0	43.0	.	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	hg19	CCDS1685.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.90|16.90	3.250228|3.250228	0.59212|0.59212	.|.	.|.	ENSG00000151779|ENSG00000151779	ENST00000429842|ENST00000441750;ENST00000281513;ENST00000441755	.|T;T;T	.|0.18016	.|2.24;2.24;2.24	5.65|5.65	4.5|4.5	0.54988|0.54988	.|Secretory pathway Sec39 (1);	.|0.044348	.|0.85682	.|D	.|0.000000	T|T	0.24890|0.24890	0.0604|0.0604	M|M	0.67953|0.67953	2.075|2.075	0.58432|0.58432	D|D	0.999998|0.999998	.|P;P	.|0.43024	.|0.798;0.771	.|B;P	.|0.45428	.|0.39;0.48	T|T	0.01613|0.01613	-1.1312|-1.1312	5|10	.|0.87932	.|D	.|0	.|.	10.3793|10.3793	0.44101|0.44101	0.0:0.0774:0.0:0.9226|0.0:0.0774:0.0:0.9226	.|.	.|879;999	.|A2RRP1-2;A2RRP1	.|.;NBAS_HUMAN	P|L	96|879;999;46	.|ENSP00000413201:I879L;ENSP00000281513:I999L;ENSP00000396501:I46L	.|ENSP00000281513:I999L	H|I	-|-	2|1	0|0	NBAS|NBAS	15459819|15459819	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.939000|0.939000	0.58152|0.58152	4.514000|4.514000	0.60482|0.60482	0.976000|0.976000	0.38417|0.38417	0.533000|0.533000	0.62120|0.62120	CAT|ATC	.	.	.	none		0.383	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		G	15542368	T	G	15542368	3	3	112	1	0	0	0	0	1	0	0	0	10193	1464	51	5	4228	5	NBAS	2	15542368	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08		15542368	227657005	6	7195											
CENPA	1058	hgsc.bcm.edu	37	chr2	27016052	27016052	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcatctctttgaggacgccTatctcctcaccttacatgca	8	14	5	14	1	4	1	2	1	2	0	6	2	4	2	3	1	2	1	3	1	2	4			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr2:27016052T>C	ENST00000335756.4	+	4	528	c.328T>C	c.(328-330)Tat>Cat	p.Y110H	CENPA_ENST00000233505.8_Missense_Mutation_p.Y84H|CENPA_ENST00000475662.1_3'UTR	NM_001809.3	NP_001800.1	P49450	CENPA_HUMAN	centromere protein A	110	CATD.|H3-like.				CENP-A containing nucleosome assembly (GO:0034080)|establishment of mitotic spindle orientation (GO:0000132)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)|protein localization to chromosome, centromeric region (GO:0071459)|viral process (GO:0016032)	chromosome, centromeric region (GO:0000775)|condensed chromosome inner kinetochore (GO:0000939)|condensed nuclear chromosome kinetochore (GO:0000778)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|large_intestine(3)|lung(3)|urinary_tract(1)	8	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGAGGACGCCTATCTCCTCAC	0.542																																					p.Y110H	Pancreas(28;769 878 30250 30578 41330)	Atlas-SNP	.											.	CENPA	13	.	0			c.T328C						PASS	.						185	191	189					2																	27016052		2203	4300	6503	SO:0001583	missense	1058	exon4			GACGCCTATCTCC	U14518	CCDS1729.1, CCDS42662.1	2p23.3	2013-11-05	2006-06-16		ENSG00000115163	ENSG00000115163			1851	protein-coding gene	gene with protein product	"centromere-specific histone", "histone H3-like centromeric protein A"	117139	"centromere protein A (17kD)", "centromere protein A, 17kDa"				Standard	NM_001042426		Approved	CENP-A, CenH3	uc002rhr.3	P49450	OTTHUMG00000097073	ENST00000335756.4:c.328T>C	chr2.hg19:g.27016052T>C	ENSP00000336868:p.Tyr110His	336.0	1.0	.		433.0	159.0	.	NM_001809	D6W544|Q53T74|Q9BVW2	Missense_Mutation	SNP	ENST00000335756.4	hg19	CCDS1729.1	.	.	.	.	.	.	.	.	.	.	T	16.66	3.184197	0.57800	.	.	ENSG00000115163	ENST00000335756;ENST00000233505	T;T	0.68331	-0.32;-0.32	5.96	5.96	0.96718	Histone-fold (2);Histone core (1);	0.408748	0.26258	N	0.025404	T	0.79137	0.4395	L	0.61387	1.9	0.41321	D	0.987178	D;D	0.76494	0.999;0.999	D;D	0.71184	0.968;0.972	T	0.81182	-0.1049	10	0.72032	D	0.01	-24.0282	14.3967	0.67015	0.0:0.0:0.0:1.0	.	84;110	P49450-2;P49450	.;CENPA_HUMAN	H	110;84	ENSP00000336868:Y110H;ENSP00000233505:Y84H	ENSP00000233505:Y84H	Y	+	1	0	CENPA	26869556	1.000000	0.71417	0.741000	0.31004	0.367000	0.29736	4.210000	0.58500	2.284000	0.76573	0.528000	0.53228	TAT	.	.	.	none		0.542	CENPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214190.2	NM_001809		C	27016052	T	C	27016052	3	2	112	1	0	0	0	0	1	0	0	0	3228	1522	53	3	342	3	CENPA	2	27016052	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	11473684	27016052	216183321	7	7196											
SLC5A6	8884	hgsc.bcm.edu	37	chr2	27427450	27427450	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctggaaggggaacactgcaTaacaggagctgcaaaagagg	15	4	15	7	0	0	1	0	0	0	1	0	4	0	4	0	5	5	4	0	5	5	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr2:27427450T>C	ENST00000310574.3	-	9	1357	c.884A>G	c.(883-885)tAt>tGt	p.Y295C	SLC5A6_ENST00000461319.1_5'Flank|SLC5A6_ENST00000408041.1_Missense_Mutation_p.Y295C	NM_021095.2	NP_066918.2	Q9Y289	SC5A6_HUMAN	solute carrier family 5 (sodium/multivitamin and iodide cotransporter), member 6	295					biotin metabolic process (GO:0006768)|biotin transport (GO:0015878)|pantothenate metabolic process (GO:0015939)|pantothenate transmembrane transport (GO:0015887)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)			endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|ovary(3)|prostate(1)|skin(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Biotin(DB00121)|gabapentin enacarbil(DB08872)|Lipoic Acid(DB00166)	GAACACTGCATAACAGGAGCT	0.572																																					p.Y295C		Atlas-SNP	.											.	SLC5A6	63	.	0			c.A884G						PASS	.						80	74	76					2																	27427450		2203	4300	6503	SO:0001583	missense	8884	exon9			ACTGCATAACAGG	AF069307	CCDS1740.1	2p23	2013-07-19	2013-07-19		ENSG00000138074	ENSG00000138074		"Solute carriers"	11041	protein-coding gene	gene with protein product		604024	"solute carrier family 5 (sodium-dependent vitamin transporter), member 6"			9516450, 10329687	Standard	NM_021095		Approved	SMVT	uc002rjd.3	Q9Y289	OTTHUMG00000097075	ENST00000310574.3:c.884A>G	chr2.hg19:g.27427450T>C	ENSP00000310208:p.Tyr295Cys	55.0	0.0	.		104.0	35.0	.	NM_021095	B2RB85|D6W549|Q969Y5	Missense_Mutation	SNP	ENST00000310574.3	hg19	CCDS1740.1	.	.	.	.	.	.	.	.	.	.	T	17.44	3.389077	0.61956	.	.	ENSG00000138074	ENST00000310574;ENST00000408041	D;D	0.87809	-2.3;-2.3	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	D	0.92714	0.7684	M	0.81802	2.56	0.80722	D	1	D	0.76494	0.999	D	0.70935	0.971	D	0.93087	0.6496	10	0.54805	T	0.06	.	12.8283	0.57733	0.0:0.0:0.0:1.0	.	295	Q9Y289	SC5A6_HUMAN	C	295	ENSP00000310208:Y295C;ENSP00000384853:Y295C	ENSP00000310208:Y295C	Y	-	2	0	SLC5A6	27280954	1.000000	0.71417	0.958000	0.39756	0.397000	0.30659	5.786000	0.69006	1.986000	0.57962	0.533000	0.62120	TAT	.	.	.	none		0.572	SLC5A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214194.1	NM_021095		C	27427450	T	C	27427450	3	2	112	1	0	0	0	0	1	0	0	0	14682	1406	49	3	1059	3	SLC5A6	2	27427450	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	411398	27427450	215771923	8	7197											
TTC27	55622	hgsc.bcm.edu	37	chr2	33036148	33036148	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgactgatcgaagtggagatGttgcaactggcctcaaagga	12	9	13	7	1	1	3	1	2	0	1	2	6	1	4	1	3	2	2	1	3	3	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr2:33036148G>A	ENST00000317907.4	+	17	2287	c.2056G>A	c.(2056-2058)Gtt>Att	p.V686I		NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	686										breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38						AAGTGGAGATGTTGCAACTGG	0.428																																					p.V686I		Atlas-SNP	.											.	TTC27	71	.	0			c.G2056A						PASS	.						129	122	125					2																	33036148		2203	4300	6503	SO:0001583	missense	55622	exon17			GGAGATGTTGCAA	BC063791, AK000279	CCDS33176.1	2p22.3	2013-01-10			ENSG00000018699	ENSG00000018699		"Tetratricopeptide (TTC) repeat domain containing"	25986	protein-coding gene	gene with protein product							Standard	NM_001193509		Approved	FLJ20272	uc002rom.3	Q6P3X3	OTTHUMG00000152134	ENST00000317907.4:c.2056G>A	chr2.hg19:g.33036148G>A	ENSP00000313953:p.Val686Ile	111.0	0.0	.		130.0	51.0	.	NM_017735	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	Missense_Mutation	SNP	ENST00000317907.4	hg19	CCDS33176.1	.	.	.	.	.	.	.	.	.	.	G	1.700	-0.501793	0.04261	.	.	ENSG00000018699	ENST00000317907	T	0.37584	1.19	5.22	2.23	0.28157	.	0.494754	0.21950	N	0.066749	T	0.11153	0.0272	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19031	-1.0318	10	0.32370	T	0.25	-11.2027	5.2727	0.15634	0.2963:0.0:0.5626:0.1412	.	686	Q6P3X3	TTC27_HUMAN	I	686	ENSP00000313953:V686I	ENSP00000313953:V686I	V	+	1	0	TTC27	32889652	0.000000	0.05858	0.868000	0.34077	0.084000	0.17831	0.052000	0.14163	0.765000	0.33221	0.650000	0.86243	GTT	.	.	.	none		0.428	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325395.1	NM_017735		A	33036148	G	A	33036148	3	1	112	1	0	0	0	0	1	0	0	0	16707	1377	48	2	2122	2	TTC27	2	33036148	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	5608698	33036148	210163225	9	7198											
THUMPD2	80745	hgsc.bcm.edu	37	chr2	39983057	39983058	+	Frame_Shift_Ins	INS	-	-	T																															tttagcagcttccaaaagtaINSttgttccaagtccacacatt																								rs202183716		TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr2:39983057_39983058insT	ENST00000505747.1	-	7	961_962	c.934_935insA	c.(934-936)atafs	p.I312fs	THUMPD2_ENST00000260619.6_Frame_Shift_Ins_p.I282fs	NM_025264.4	NP_079540.2	Q9BTF0	THUM2_HUMAN	THUMP domain containing 2	312							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|skin(1)	17		all_hematologic(82;0.248)				TTCCAAAAGTATTGTTCCAAGT	0.322																																					p.I312fs		Atlas-INDEL	.											.	THUMPD2	35	.	0			c.935_936insA						PASS	.																																			SO:0001589	frameshift_variant	80745	exon7			.	AF380576	CCDS1805.1, CCDS1805.2	2p22.2	2004-06-04	2004-06-04	2004-06-04	ENSG00000138050	ENSG00000138050			14890	protein-coding gene	gene with protein product		611751	"chromosome 2 open reading frame 8"	C2orf8		12063391	Standard	NM_025264		Approved	MGC2454	uc002rru.2	Q9BTF0	OTTHUMG00000102149	ENST00000505747.1:c.935dupA	chr2.hg19:g.39983059_39983059dupT	ENSP00000423933:p.Ile312fs	101.0	0.0	0		98.0	32.0	0.326531	NM_025264	A8K7I7|Q53TT8|Q53TV0	Frame_Shift_Ins	INS	ENST00000505747.1	hg19	CCDS1805.2																																																																																			.	.	.	none		0.322	THUMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219991.2	NM_025264		T	39983058	-	T	39983057	7	5	112	1	0	1	1	0	0	0	0	0	15895	449	16	0	592	0	THUMPD2	2	39983057	Frame_Shift_Ins	INS	-	TCGA-BQ-5877-01A-11D-1589-08	6946909	39983057	203216316	10	7199											
PSME4	23198	hgsc.bcm.edu	37	chr2	54125075	54125075	+	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	tatggcacgaagaggcaacaCtcggtcatctctcagcagta	12	8	10	11	2	3	1	2	0	1	1	5	2	3	1	0	3	2	4	0	3	4	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr2:54125075C>G	ENST00000404125.1	-	31	3593	c.3538G>C	c.(3538-3540)Gtg>Ctg	p.V1180L	PSME4_ENST00000421748.2_Missense_Mutation_p.V324L	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	1180					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)			AGAGGCAACACTCGGTCATCT	0.408																																					p.V1180L		Atlas-SNP	.											.	PSME4	247	.	0			c.G3538C						PASS	.						155	149	151					2																	54125075		2203	4300	6503	SO:0001583	missense	23198	exon31			GCAACACTCGGTC	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.3538G>C	chr2.hg19:g.54125075C>G	ENSP00000384211:p.Val1180Leu	132.0	0.0	.		162.0	44.0	.	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	hg19	CCDS33197.2	.	.	.	.	.	.	.	.	.	.	C	13.13	2.143792	0.37825	.	.	ENSG00000068878	ENST00000421748;ENST00000404125	T;T	0.63417	-0.04;-0.04	5.64	5.64	0.86602	Armadillo-like helical (1);Armadillo-type fold (1);	0.196755	0.45361	D	0.000375	T	0.47525	0.1450	N	0.22421	0.69	0.37075	D	0.898738	B;B;B	0.15473	0.009;0.013;0.013	B;B;B	0.15484	0.007;0.013;0.008	T	0.47686	-0.9098	10	0.25106	T	0.35	.	13.4018	0.60887	0.0:0.9192:0.0:0.0808	.	555;324;1180	Q14997-2;Q14997-3;Q14997	.;.;PSME4_HUMAN	L	324;1180	ENSP00000410830:V324L;ENSP00000384211:V1180L	ENSP00000384211:V1180L	V	-	1	0	PSME4	53978579	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.276000	0.58933	2.667000	0.90743	0.655000	0.94253	GTG	.	.	.	none		0.408	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		G	54125075	C	G	54125075	3	3	112	1	0	0	0	0	1	0	0	0	12719	565	20	4	2057	4	PSME4	2	54125075	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	14142018	54125075	189074298	11	7200											
RGPD1	729857	hgsc.bcm.edu	37	chr2	88081658	88081659	+	Frame_Shift_Ins	INS	-	-	A																															ctacccttttctggtgttttINSaaatgtgtagttgattgaag																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr2:88081658_88081659insA	ENST00000398146.3	-	20	5106_5107	c.4884_4885insT	c.(4882-4887)tttaaafs	p.K1629fs	RGPD2_ENST00000420840.2_Frame_Shift_Ins_p.K1621fs|RGPD2_ENST00000327544.6_Frame_Shift_Ins_p.K886fs|RGPD2_ENST00000494592.1_5'UTR			P0DJD1	RGPD2_HUMAN	RANBP2-like and GRIP domain containing 2	1629					protein targeting to Golgi (GO:0000042)					breast(1)|pancreas(1)	2						TCTGGTGTTTTAAATGTGTAGT	0.342																																					p.K1629_T1630delinsX		Atlas-INDEL	.											.	RGPD2	14	.	0			c.4885_4886insT						PASS	.																																			SO:0001589	frameshift_variant	729857	exon20			.		CCDS42710.1, CCDS42710.2	2p11.2	2013-01-10			ENSG00000185304	ENSG00000185304		"Tetratricopeptide (TTC) repeat domain containing"	32415	protein-coding gene	gene with protein product		612705				15710750, 15815621	Standard	NM_001078170		Approved	RGP2, RANBP2L2		P0DJD1	OTTHUMG00000153276	ENST00000398146.3:c.4885dupT	chr2.hg19:g.88081661_88081661dupA	ENSP00000381214:p.Lys1629fs	417.0	0.0	0		532.0	88.0	0.165414	NM_001078170	P0C839|Q68DN6|Q6V1X0	Frame_Shift_Ins	INS	ENST00000398146.3	hg19	CCDS42710.2																																																																																			.	.	.	none		0.342	RGPD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330534.2	NM_001078170		A	88081659	-	A	88081658	7	5	112	1	0	1	1	0	0	0	0	0	13298	1763	61	0	5740	0	RGPD1	2	88081658	Frame_Shift_Ins	INS	-	TCGA-BQ-5877-01A-11D-1589-08	33956583	88081658	155117715	12	7201											
RGPD4	285190	hgsc.bcm.edu	37	chr2	108489365	108489366	+	Frame_Shift_Ins	INS	-	-	T																															aatcttcaatcaactacacaINStttaaaacaccagaaaaggg																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr2:108489365_108489366insT	ENST00000408999.3	+	20	4982_4983	c.4905_4906insT	c.(4906-4908)tttfs	p.F1636fs	RGPD4_ENST00000354986.4_Frame_Shift_Ins_p.F1636fs	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	1636					protein targeting to Golgi (GO:0000042)					breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						TCAACTACACATTTAAAACACC	0.347																																					p.T1635fs		Atlas-INDEL	.											.	RGPD4	112	.	0			c.4905_4906insT						PASS	.																																			SO:0001589	frameshift_variant	285190	exon20			.	BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"Tetratricopeptide (TTC) repeat domain containing"	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.4908dupT	chr2.hg19:g.108489368_108489368dupT	ENSP00000386810:p.Phe1636fs	406.0	0.0	0		478.0	43.0	0.0899582	NM_182588	B9A029	Frame_Shift_Ins	INS	ENST00000408999.3	hg19	CCDS46381.1																																																																																			.	.	.	none		0.347	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581		T	108489366	-	T	108489365	7	5	112	1	0	1	1	0	0	0	0	0	13301	204	8	0	4983	0	RGPD4	2	108489365	Frame_Shift_Ins	INS	-	TCGA-BQ-5877-01A-11D-1589-08	20407707	108489365	134710008	13	7202											
RANBP2	5903	hgsc.bcm.edu	37	chr2	109392304	109392304	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gattctattaccaaatccatTagttcaccatctgtttcctc	10	16	3	12	0	3	0	1	0	2	0	6	1	5	0	4	0	1	2	4	0	4	6			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr2:109392304T>C	ENST00000283195.6	+	24	8535	c.8409T>C	c.(8407-8409)atT>atC	p.I2803I		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	2803					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						CCAAATCCATTAGTTCACCAT	0.363																																					p.I2803I		Atlas-SNP	.											.	RANBP2	488	.	0			c.T8409C						PASS	.						130	130	130					2																	109392304		2203	4300	6503	SO:0001819	synonymous_variant	5903	exon24			ATCCATTAGTTCA	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.8409T>C	chr2.hg19:g.109392304T>C		113.0	0.0	.		113.0	46.0	.	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Silent	SNP	ENST00000283195.6	hg19	CCDS2079.1																																																																																			.	.	.	none		0.363	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		C	109392304	T	C	109392304	2	2	112	1	0	0	0	0	0	0	0	1	13041	1742	61	3		3	RANBP2	2	109392304	Silent	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	902939	109392304	133807069	14	7203											
ORC2L	4999	hgsc.bcm.edu	37	chr2	201790562	201790562	+	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	catctacttcatgttaccttCtttaaatttgtttactatcc	9	20	2	10	0	3	0	1	0	2	0	4	0	4	0	2	0	3	2	2	0	6	10			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr2:201790562C>A	ENST00000234296.2	-	13	1393	c.1144G>T	c.(1144-1146)Gaa>Taa	p.E382*	RN7SL694P_ENST00000584245.1_RNA	NM_006190.4	NP_006181.1	Q13416	ORC2_HUMAN	origin recognition complex, subunit 2	382					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	condensed chromosome inner kinetochore (GO:0000939)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)|plasma membrane (GO:0005886)	DNA replication origin binding (GO:0003688)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	20						ATGTTACCTTCTTTAAATTTG	0.308																																					p.E382X		Atlas-SNP	.											.	ORC2	48	.	0			c.G1144T						PASS	.						139	133	135					2																	201790562		2203	4300	6503	SO:0001587	stop_gained	4999	exon13			TACCTTCTTTAAA		CCDS2334.1	2q33	2010-10-12	2010-10-12	2010-10-12	ENSG00000115942	ENSG00000115942			8488	protein-coding gene	gene with protein product		601182	"origin recognition complex, subunit 2 (yeast homolog)-like", "origin recognition complex, subunit 2-like (yeast)", "origin recognition complex, subunit 2 homolog (yeast)"	ORC2L		8808289	Standard	NM_006190		Approved		uc002uwr.3	Q13416	OTTHUMG00000132783	ENST00000234296.2:c.1144G>T	chr2.hg19:g.201790562C>A	ENSP00000234296:p.Glu382*	130.0	0.0	.		168.0	49.0	.	NM_006190	Q13204|Q53TX5	Nonsense_Mutation	SNP	ENST00000234296.2	hg19	CCDS2334.1	.	.	.	.	.	.	.	.	.	.	C	39	7.716939	0.98450	.	.	ENSG00000115942	ENST00000234296	.	.	.	5.34	5.34	0.76211	.	0.148032	0.64402	D	0.000011	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	.	19.3943	0.94601	0.0:1.0:0.0:0.0	.	.	.	.	X	382	.	ENSP00000234296:E382X	E	-	1	0	ORC2	201498807	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	3.237000	0.51344	2.671000	0.90904	0.585000	0.79938	GAA	.	.	.	none		0.308	ORC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256191.2	NM_006190		A	201790562	C	A	201790562	4	1	112	1	0	0	0	0	0	1	0	0	11269	922	32	4	613	4	ORC2L	2	201790562	Nonsense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	92398258	201790562	41408811	15	7204											
KAT2B	8850	hgsc.bcm.edu	37	chr3	20187858	20187858	+	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	gcacaaattcgaaaagtttaCcctggactttcatgttttaa	13	14	6	8	1	1	0	1	0	0	0	2	2	1	1	1	1	1	3	1	1	5	6			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr3:20187858C>T	ENST00000263754.4	+	14	2510	c.2055C>T	c.(2053-2055)taC>taT	p.Y685Y		NM_003884.4	NP_003875.3	Q92831	KAT2B_HUMAN	K(lysine) acetyltransferase 2B	685					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						GAAAAGTTTACCCTGGACTTT	0.333																																					p.Y685Y		Atlas-SNP	.											.	KAT2B	73	.	0			c.C2055T						PASS	.						127	135	132					3																	20187858		2203	4300	6503	SO:0001819	synonymous_variant	8850	exon14			AGTTTACCCTGGA	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.2055C>T	chr3.hg19:g.20187858C>T		209.0	0.0	.		146.0	70.0	.	NM_003884	Q6NSK1	Silent	SNP	ENST00000263754.4	hg19	CCDS2634.1																																																																																			.	.	.	none		0.333	KAT2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252880.1	NM_003884		T	20187858	C	T	20187858	2	4	112	1	0	0	0	0	0	0	0	1	7989	518	18	2		2	KAT2B	3	20187858	Silent	SNP	C	TCGA-BQ-5877-01A-11D-1589-08		20187858	177834572	16	7205											
SETD2	29072	hgsc.bcm.edu	37	chr3	47161751	47161757	+	Frame_Shift_Del	DEL	GCTGTGG	GCTGTGG	-																															cttggcacattccttccatcGctgtgggtccctgaagtcat																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	GCTGTGG	GCTGTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr3:47161751_47161757delGCTGTGG	ENST00000409792.3	-	3	4411_4417	c.4369_4375delCCACAGC	c.(4369-4377)ccacagcgafs	p.PQR1457fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1457					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TCCTTCCATCGCTGTGGGTCCCTGAAG	0.444			"N, F, S, Mis"		clear cell renal carcinoma																																p.1457_1459del		Atlas-INDEL	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.4370_4376del						PASS	.																																			SO:0001589	frameshift_variant	29072	exon3			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4369_4375delCCACAGC	chr3.hg19:g.47161751_47161757delGCTGTGG	ENSP00000386759:p.Pro1457fs	180.0	0.0	0		92.0	40.0	0.434783	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Del	DEL	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.	.	none		0.444	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		-	47161757	GCTGTGG	-	47161751	7	5	112	1	0	1	0	1	0	0	0	0	14144	1095	38	0	3395	0	SETD2	3	47161751	Frame_Shift_Del	DEL	GCTGTGG	TCGA-BQ-5877-01A-11D-1589-08	26973893	47161751	150860679	17	7206											
BAP1	8314	hgsc.bcm.edu	37	chr3	52439900	52439900	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttgagacttgtgggtctgaAtcagctctggctgtgttact	6	15	12	8	0	3	2	1	2	2	1	3	3	3	2	0	2	2	3	0	2	2	3			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr3:52439900A>G	ENST00000460680.1	-	10	1283	c.812T>C	c.(811-813)aTt>aCt	p.I271T	BAP1_ENST00000296288.5_Missense_Mutation_p.I253T	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.I271fs*61(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		GTGGGTCTGAATCAGCTCTGG	0.542			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.I271T	GBM(101;493 1458 7992 21037 25532)	Atlas-SNP	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	1	Deletion - Frameshift(1)	eye(1)	c.T812C						PASS	.						67	68	68					3																	52439900		2203	4300	6503	SO:0001583	missense	8314	exon10			GTCTGAATCAGCT	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.812T>C	chr3.hg19:g.52439900A>G	ENSP00000417132:p.Ile271Thr	66.0	0.0	.		37.0	14.0	.	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Missense_Mutation	SNP	ENST00000460680.1	hg19	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	A	15.54	2.864400	0.51482	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	T;T	0.56275	0.47;0.49	5.35	5.35	0.76521	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (1);	0.102540	0.64402	D	0.000002	T	0.46249	0.1383	L	0.54323	1.7	0.50813	D	0.999895	B	0.27068	0.167	B	0.16722	0.016	T	0.39722	-0.9600	10	0.15066	T	0.55	-9.2188	15.6343	0.76937	1.0:0.0:0.0:0.0	.	271	Q92560	BAP1_HUMAN	T	271;253	ENSP00000417132:I271T;ENSP00000296288:I253T	ENSP00000296288:I253T	I	-	2	0	BAP1	52414940	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.318000	0.72866	2.152000	0.67230	0.459000	0.35465	ATT	.	.	.	none		0.542	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			G	52439900	A	G	52439900	3	3	112	1	0	0	0	0	1	0	0	0	1311	101	4	3	1409	3	BAP1	3	52439900	Missense_Mutation	SNP	A	TCGA-BQ-5877-01A-11D-1589-08	5278149	52439900	145582530	18	7207											
CADM2	253559	hgsc.bcm.edu	37	chr3	86114798	86114799	+	Frame_Shift_Ins	INS	-	-	T																															atggccctgaccatgctctcINSataggaggaatagtggctgt																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr3:86114798_86114799insT	ENST00000407528.2	+	9	1169_1170	c.1107_1108insT	c.(1108-1110)atafs	p.I370fs	CADM2_ENST00000405615.2_Frame_Shift_Ins_p.I372fs|CADM2_ENST00000383699.3_Frame_Shift_Ins_p.I339fs	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	370					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)		ACCATGCTCTCATAGGAGGAAT	0.406																																					p.L371fs		Atlas-INDEL	.											.	CADM2	195	.	0			c.1113_1114insT						PASS	.																																			SO:0001589	frameshift_variant	253559	exon9			.	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	Exception_encountered	chr3.hg19:g.86114798_86114799insT	ENSP00000384575:p.Ile370fs	82.0	0.0	0		62.0	28.0	0.451613	NM_153184	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Frame_Shift_Ins	INS	ENST00000407528.2	hg19	CCDS54614.1																																																																																			.	.	.	none		0.406	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184		T	86114799	-	T	86114798	7	5	112	1	0	1	1	0	0	0	0	0	2569	813	29	0	1212	0	CADM2	3	86114798	Frame_Shift_Ins	INS	-	TCGA-BQ-5877-01A-11D-1589-08	33674898	86114798	111907632	19	7208											
CCDC80	151887	hgsc.bcm.edu	37	chr3	112324460	112324460	+	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	ttaaatcgtacacaatcaccAtggaccacattggggaagga	15	8	9	9	1	1	0	1	0	0	0	2	3	1	3	2	4	1	1	2	4	5	3			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr3:112324460A>T	ENST00000206423.3	-	8	3610	c.2657T>A	c.(2656-2658)aTg>aAg	p.M886K	CCDC80_ENST00000439685.2_Missense_Mutation_p.M886K	NM_199511.1|NM_199512.1	NP_955805.1|NP_955806.1	Q76M96	CCD80_HUMAN	coiled-coil domain containing 80	886					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						CACAATCACCATGGACCACAT	0.463																																					p.M886K		Atlas-SNP	.											.	CCDC80	100	.	0			c.T2657A						PASS	.						122	101	108					3																	112324460		2203	4300	6503	SO:0001583	missense	151887	exon8			ATCACCATGGACC	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.2657T>A	chr3.hg19:g.112324460A>T	ENSP00000206423:p.Met886Lys	76.0	0.0	.		51.0	20.0	.	NM_199511	D3DN67|Q5PR20|Q6GPG9|Q8IVT6|Q8NBV1|Q8NHY8	Missense_Mutation	SNP	ENST00000206423.3	hg19	CCDS2968.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.1|24.1	4.497724|4.497724	0.85069|0.85069	.|.	.|.	ENSG00000091986|ENSG00000091986	ENST00000461431|ENST00000206423;ENST00000439685;ENST00000444594;ENST00000479368	.|T;T;T	.|0.43688	.|0.94;0.94;0.94	5.83|5.83	5.83|5.83	0.93111|0.93111	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.64918|0.64918	0.2642|0.2642	M|M	0.71581|0.71581	2.175|2.175	0.80722|0.80722	D|D	1|1	.|D;D	.|0.58268	.|0.978;0.982	.|D;D	.|0.77004	.|0.98;0.989	T|T	0.67856|0.67856	-0.5562|-0.5562	5|10	.|0.72032	.|D	.|0.01	-33.8731|-33.8731	16.1894|16.1894	0.81975|0.81975	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|897;886	.|Q76M96-2;Q76M96	.|.;CCD80_HUMAN	Q|K	256|886;886;487;164	.|ENSP00000206423:M886K;ENSP00000411814:M886K;ENSP00000418188:M164K	.|ENSP00000206423:M886K	H|M	-|-	3|2	2|0	CCDC80|CCDC80	113807150|113807150	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.287000|9.287000	0.95975|0.95975	2.222000|2.222000	0.72286|0.72286	0.477000|0.477000	0.44152|0.44152	CAT|ATG	.	.	.	none		0.463	CCDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354219.1	NM_199511		T	112324460	A	T	112324460	3	4	112	1	0	0	0	0	1	0	0	0	2856	217	8	5	199	5	CCDC80	3	112324460	Missense_Mutation	SNP	A	TCGA-BQ-5877-01A-11D-1589-08	26209662	112324460	85697970	20	7209											
MCF2L2	23101	hgsc.bcm.edu	37	chr3	183013205	183013205	+	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	cagtttcatcagactcacttGcctcttgtgaaatatttcct	9	16	5	11	0	4	2	3	1	1	1	5	2	5	2	2	0	1	1	2	0	2	5			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr3:183013205G>A	ENST00000328913.3	-	13	1855	c.1558C>T	c.(1558-1560)Caa>Taa	p.Q520*	MCF2L2_ENST00000447025.2_Nonsense_Mutation_p.Q520*|B3GNT5_ENST00000462559.1_Intron|MCF2L2_ENST00000414362.2_Nonsense_Mutation_p.Q520*|MCF2L2_ENST00000473233.1_Nonsense_Mutation_p.Q520*	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	520							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)			AGACTCACTTGCCTCTTGTGA	0.468																																					p.Q520X		Atlas-SNP	.											.	MCF2L2	164	.	0			c.C1558T						PASS	.						173	146	156					3																	183013205		2203	4300	6503	SO:0001587	stop_gained	23101	exon13			TCACTTGCCTCTT	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.1558C>T	chr3.hg19:g.183013205G>A	ENSP00000328118:p.Gln520*	87.0	0.0	.		118.0	39.0	.	NM_015078	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Nonsense_Mutation	SNP	ENST00000328913.3	hg19	CCDS3243.1	.	.	.	.	.	.	.	.	.	.	G	39	7.604425	0.98384	.	.	ENSG00000053524	ENST00000328913;ENST00000473233;ENST00000447025;ENST00000437431;ENST00000414362	.	.	.	4.82	4.82	0.62117	.	0.064498	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	18.1577	0.89699	0.0:0.0:1.0:0.0	.	.	.	.	X	520;520;520;56;520	.	ENSP00000328118:Q520X	Q	-	1	0	MCF2L2	184495899	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.725000	0.68507	2.535000	0.85469	0.650000	0.86243	CAA	.	.	.	none		0.468	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078		A	183013205	G	A	183013205	4	1	112	1	0	0	0	0	0	1	0	0	9387	1328	46	2	1858	2	MCF2L2	3	183013205	Nonsense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	70688745	183013205	15009225	21	7210											
TRIM2	23321	hgsc.bcm.edu	37	chr4	154249812	154249812	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtggccgactggggaaacaGcaggatccaggtagatcaat	12	7	14	8	1	1	1	1	0	0	1	2	4	2	3	2	5	2	2	2	5	3	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr4:154249812G>A	ENST00000437508.2	+	11	2273	c.2072G>A	c.(2071-2073)aGc>aAc	p.S691N	TRIM2_ENST00000338700.5_Missense_Mutation_p.S718N	NM_001130067.1	NP_001123539.1	Q9C040	TRIM2_HUMAN	tripartite motif containing 2	691					cell death (GO:0008219)|regulation of neuron apoptotic process (GO:0043523)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)	19	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)		TGGGGAAACAGCAGGATCCAG	0.418																																					p.S718N		Atlas-SNP	.											.	TRIM2	105	.	0			c.G2153A						PASS	.						150	142	144					4																	154249812		2203	4300	6503	SO:0001583	missense	23321	exon11			GAAACAGCAGGAT	AF220018	CCDS3781.2, CCDS47147.1	4q31.3	2013-01-09	2011-01-25		ENSG00000109654	ENSG00000109654		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	15974	protein-coding gene	gene with protein product		614141	"tripartite motif-containing 2"			9628581, 11331580	Standard	NM_015271		Approved	KIAA0517, RNF86	uc003inh.2	Q9C040	OTTHUMG00000155991	ENST00000437508.2:c.2072G>A	chr4.hg19:g.154249812G>A	ENSP00000415812:p.Ser691Asn	88.0	0.0	.		121.0	44.0	.	NM_015271	D3DP09|O60272|Q9BSI9|Q9UFZ1	Missense_Mutation	SNP	ENST00000437508.2	hg19	CCDS47147.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.058382	0.76074	.	.	ENSG00000109654	ENST00000437508;ENST00000338700	T;T	0.71222	-0.55;-0.55	5.42	5.42	0.78866	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.69052	0.3068	N	0.10664	0.02	0.80722	D	1	D;D	0.62365	0.991;0.991	D;D	0.74023	0.982;0.982	T	0.65709	-0.6102	10	0.11485	T	0.65	-19.2289	19.2133	0.93766	0.0:0.0:1.0:0.0	.	718;691	D3DP09;Q9C040	.;TRIM2_HUMAN	N	691;718	ENSP00000415812:S691N;ENSP00000339659:S718N	ENSP00000339659:S718N	S	+	2	0	TRIM2	154469262	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.865000	0.99609	2.534000	0.85438	0.650000	0.86243	AGC	.	.	.	none		0.418	TRIM2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342652.1			A	154249812	G	A	154249812	3	1	112	1	0	0	0	0	1	0	0	0	16506	971	34	2	2195	2	TRIM2	4	154249812	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08		154249812	36904464	22	7211											
FAT1	2195	hgsc.bcm.edu	37	chr4	187541245	187541245	+	Frame_Shift_Del	DEL	T	T	-																															atcggaacgataacttccgcTgaaaaggccgggttccctcc																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr4:187541245delT	ENST00000441802.2	-	10	6704	c.6495delA	c.(6493-6495)tcafs	p.S2165fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2165	Cadherin 19. {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						TAACTTCCGCTGAAAAGGCCG	0.423										HNSCC(5;0.00058)																											p.A2166fs	Colon(197;1040 2055 4143 4984 49344)	Atlas-INDEL	.											.	FAT1	500	.	0			c.6496delG						PASS	.						59	58	59					4																	187541245		1894	4111	6005	SO:0001589	frameshift_variant	2195	exon10			.	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.6495delA	chr4.hg19:g.187541245delT	ENSP00000406229:p.Ser2165fs	55.0	0.0	0		79.0	26.0	0.329114	NM_005245		Frame_Shift_Del	DEL	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.	.	none		0.423	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		-	187541245	T	-	187541245	7	5	112	1	0	1	0	1	0	0	0	0	5696	1567	55	0	7343	0	FAT1	4	187541245	Frame_Shift_Del	DEL	T	TCGA-BQ-5877-01A-11D-1589-08	33291433	187541245	3613031	23	7212	81	2									
FAT1	2195	hgsc.bcm.edu	37	chr4	187541246	187541246	+	Missense_Mutation	SNP	G	G	A																															tcggaacgataacttccgctGaaaaggccgggttccctcca																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr4:187541246G>A	ENST00000441802.2	-	10	6703	c.6494C>T	c.(6493-6495)tCa>tTa	p.S2165L		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2165	Cadherin 19. {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						AACTTCCGCTGAAAAGGCCGG	0.423										HNSCC(5;0.00058)																											p.S2165L	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C6494T						PASS	.						59	58	59					4																	187541246		1893	4111	6004	SO:0001583	missense	2195	exon10			TCCGCTGAAAAGG	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.6494C>T	chr4.hg19:g.187541246G>A	ENSP00000406229:p.Ser2165Leu	58.0	0.0	.		55.0	5.0	.	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	hg19	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	G	14.60	2.585000	0.46110	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.03553	3.89	5.05	5.05	0.67936	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.19927	0.0479	M	0.85099	2.735	0.80722	D	1	D	0.59767	0.986	D	0.63033	0.91	T	0.00679	-1.1613	10	0.44086	T	0.13	.	18.5902	0.91208	0.0:0.0:1.0:0.0	.	2165	Q14517	FAT1_HUMAN	L	2165;2167	ENSP00000406229:S2165L	ENSP00000260147:S2167L	S	-	2	0	FAT1	187778240	1.000000	0.71417	0.148000	0.22405	0.036000	0.12997	9.615000	0.98356	2.619000	0.88677	0.655000	0.94253	TCA	.	.	.	none		0.423	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		A	187541246	G	A	187541246	3	1	112	1	0	0	0	0	1	0	0	0	5696	1294	45	2	7344	2	FAT1	4	187541246	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	1	187541246	3613030	24	7213	81	2									
MAP1B	4131	hgsc.bcm.edu	37	chr5	71479648	71479648	+	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	ttctgatgaagcagtcagcaCcgaggtaagcattcagctct	11	10	10	10	1	4	2	2	2	2	0	4	3	4	2	1	1	4	5	1	1	2	3			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr5:71479648C>A	ENST00000296755.7	+	3	663	c.365C>A	c.(364-366)aCc>aAc	p.T122N		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	122					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)		GCAGTCAGCACCGAGGTAAGC	0.527																																					p.T122N	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.C365A						PASS	.						129	124	126					5																	71479648		2203	4300	6503	SO:0001583	missense	4131	exon3			TCAGCACCGAGGT	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.365C>A	chr5.hg19:g.71479648C>A	ENSP00000296755:p.Thr122Asn	109.0	0.0	.		143.0	44.0	.	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	hg19	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	C	19.54	3.846103	0.71603	.	.	ENSG00000131711	ENST00000512974;ENST00000296755;ENST00000511641	T;T;T	0.19806	3.77;2.12;2.12	5.14	5.14	0.70334	.	0.000000	0.64402	D	0.000004	T	0.44435	0.1293	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.28996	-1.0026	10	0.56958	D	0.05	-15.6336	18.9656	0.92695	0.0:1.0:0.0:0.0	.	122	P46821	MAP1B_HUMAN	N	122	ENSP00000426312:T122N;ENSP00000296755:T122N;ENSP00000423444:T122N	ENSP00000296755:T122N	T	+	2	0	MAP1B	71515404	1.000000	0.71417	0.983000	0.44433	0.241000	0.25554	7.301000	0.78850	2.543000	0.85770	0.637000	0.83480	ACC	.	.	.	none		0.527	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		A	71479648	C	A	71479648	3	1	112	1	0	0	0	0	1	0	0	0	9235	507	18	4	375	4	MAP1B	5	71479648	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08		71479648	109435612	25	7214											
RGNEF	64283	hgsc.bcm.edu	37	chr5	73165934	73165934	+	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	tggagtgacctcagcagtgaTgcccaggagtttgaagcaga	11	8	14	8	0	1	4	1	3	0	1	1	6	1	6	2	2	3	3	2	2	1	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr5:73165934T>A	ENST00000426542.2	+	20	2486	c.2466T>A	c.(2464-2466)gaT>gaA	p.D822E	ARHGEF28_ENST00000296794.6_Missense_Mutation_p.D822E|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.D822E|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.D822E|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.D822E|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.D509E|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.D822E			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	822					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)										TCAGCAGTGATGCCCAGGAGT	0.413																																					p.D822E		Atlas-SNP	.											.	.	.	.	0			c.T2466A						PASS	.						196	184	188					5																	73165934		1924	4131	6055	SO:0001583	missense	64283	exon21			CAGTGATGCCCAG		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.2466T>A	chr5.hg19:g.73165934T>A	ENSP00000412175:p.Asp822Glu	168.0	0.0	.		185.0	67.0	.	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	hg19	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	T	13.25	2.182575	0.38511	.	.	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799	T;T;T;T;T;T;T	0.11821	2.92;2.91;2.91;2.8;2.91;2.91;2.74	5.95	-3.02	0.05446	.	.	.	.	.	T	0.10294	0.0252	L	0.55834	1.745	0.26232	N	0.979	B;B;B;B	0.26318	0.146;0.09;0.017;0.029	B;B;B;B	0.23852	0.036;0.047;0.049;0.045	T	0.35226	-0.9797	9	0.25106	T	0.35	.	4.0067	0.09605	0.1088:0.3977:0.1124:0.3811	.	509;822;822;822	B5MDA3;Q8N1W1;E9PC75;Q8N1W1-4	.;RGNEF_HUMAN;.;.	E	822;822;822;822;822;822;509	ENSP00000296794:D822E;ENSP00000441913:D822E;ENSP00000441436:D822E;ENSP00000287898:D822E;ENSP00000411459:D822E;ENSP00000412175:D822E;ENSP00000296799:D509E	ENSP00000287898:D822E	D	+	3	2	RP11-428C6.1	73201690	0.517000	0.26226	0.967000	0.41034	0.996000	0.88848	-0.287000	0.08388	-0.749000	0.04747	-0.250000	0.11733	GAT	.	.	.	none		0.413	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			A	73165934	T	A	73165934	3	1	112	1	0	0	0	0	1	0	0	0	13296	1461	51	5	2544	5	RGNEF	5	73165934	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	1686286	73165934	107749326	26	7215											
SNCAIP	9627	hgsc.bcm.edu	37	chr5	121787084	121787084	+	Missense_Mutation	SNP	T	T	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	gcaggactctccagcggaccTccacaagtaacgaatcgggg	11	5	12	13	3	1	0	0	0	1	0	4	3	2	2	3	4	2	2	3	4	3	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr5:121787084T>G	ENST00000261368.8	+	10	2804	c.2542T>G	c.(2542-2544)Tcc>Gcc	p.S848A	CTC-210G5.1_ENST00000510972.1_RNA|CTC-210G5.1_ENST00000505546.1_RNA|SNCAIP_ENST00000261367.7_Missense_Mutation_p.S895A|SNCAIP_ENST00000379538.3_Missense_Mutation_p.S482A|SNCAIP_ENST00000504884.2_3'UTR|SNCAIP_ENST00000414317.2_Missense_Mutation_p.S450A|CTC-210G5.1_ENST00000509993.1_RNA|CTC-210G5.1_ENST00000506053.1_RNA|SNCAIP_ENST00000542191.1_Missense_Mutation_p.S406A|SNCAIP_ENST00000503116.2_3'UTR|CTC-210G5.1_ENST00000503529.1_RNA|SNCAIP_ENST00000379536.2_Missense_Mutation_p.S788A|SNCAIP_ENST00000379533.2_Missense_Mutation_p.S895A	NM_005460.2	NP_005451.2	Q9Y6H5	SNCAP_HUMAN	synuclein, alpha interacting protein	848					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)		CCAGCGGACCTCCACAAGTAA	0.463																																					p.S848A		Atlas-SNP	.											.	SNCAIP	308	.	0			c.T2542G						PASS	.						88	92	91					5																	121787084		2203	4300	6503	SO:0001583	missense	9627	exon10			CGGACCTCCACAA	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.2542T>G	chr5.hg19:g.121787084T>G	ENSP00000261368:p.Ser848Ala	104.0	0.0	.		96.0	31.0	.	NM_005460	D3DSZ1|Q05BS1|Q1PSC2|Q49AC6|Q504U9|Q6L984|Q6L985|Q6L986|Q9HC59	Missense_Mutation	SNP	ENST00000261368.8	hg19	CCDS4131.1	.	.	.	.	.	.	.	.	.	.	T	10.08	1.252348	0.22880	.	.	ENSG00000064692	ENST00000542191;ENST00000509154;ENST00000261368;ENST00000379533;ENST00000379536;ENST00000379538;ENST00000261367;ENST00000414317	T;T;T;T;T;T;T;T	0.14266	4.35;4.88;2.57;2.52;4.88;4.81;2.52;4.56	5.69	2.03	0.26663	.	0.412591	0.28730	N	0.014337	T	0.08935	0.0221	L	0.36672	1.1	0.22737	N	0.998792	B;B;B;B;B;B;B;B	0.33777	0.3;0.048;0.252;0.264;0.425;0.264;0.264;0.104	B;B;B;B;B;B;B;B	0.31101	0.049;0.024;0.035;0.124;0.105;0.124;0.124;0.058	T	0.25257	-1.0137	10	0.31617	T	0.26	-3.6974	6.4307	0.21794	0.0:0.5607:0.0:0.4393	.	788;476;450;788;482;482;895;848	D6R9G8;Q9NVG1;B7Z995;Q9Y6H5-4;Q9Y6H5-5;Q9Y6H5-2;Q9Y6H5-3;Q9Y6H5	.;.;.;.;.;.;.;SNCAP_HUMAN	A	406;788;848;895;788;482;895;450	ENSP00000441681:S406A;ENSP00000422106:S788A;ENSP00000261368:S848A;ENSP00000368848:S895A;ENSP00000368851:S788A;ENSP00000368854:S482A;ENSP00000261367:S895A;ENSP00000394392:S450A	ENSP00000261367:S895A	S	+	1	0	SNCAIP	121814983	0.997000	0.39634	0.066000	0.19879	0.144000	0.21451	1.753000	0.38359	0.438000	0.26450	0.533000	0.62120	TCC	.	.	.	none		0.463	SNCAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250888.1			G	121787084	T	G	121787084	3	3	112	1	0	0	0	0	1	0	0	0	14854	1551	54	5	2576	5	SNCAIP	5	121787084	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	48621150	121787084	59128176	27	7216											
FAT2	2196	hgsc.bcm.edu	37	chr5	150946163	150946163	+	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	tggtggcttcatagtccaagGgagcagctacagtgagcagc	10	8	14	9	0	1	1	1	1	0	0	2	2	2	2	1	3	5	4	1	3	3	3			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr5:150946163G>C	ENST00000261800.5	-	1	2342	c.2330C>G	c.(2329-2331)cCc>cGc	p.P777R		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	777	Cadherin 6. {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)			ATAGTCCAAGGGAGCAGCTAC	0.498																																					p.P777R		Atlas-SNP	.											.	FAT2	465	.	0			c.C2330G						PASS	.						60	60	60					5																	150946163		2203	4300	6503	SO:0001583	missense	2196	exon1			TCCAAGGGAGCAG	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.2330C>G	chr5.hg19:g.150946163G>C	ENSP00000261800:p.Pro777Arg	68.0	0.0	.		69.0	25.0	.	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	hg19	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	15.69	2.907163	0.52333	.	.	ENSG00000086570	ENST00000261800	T	0.54071	0.59	5.78	4.91	0.64330	Cadherin (4);Cadherin-like (1);	0.317848	0.27336	N	0.019825	T	0.64227	0.2579	M	0.76002	2.32	0.35862	D	0.827587	D	0.55172	0.97	P	0.57101	0.813	T	0.69771	-0.5055	10	0.21540	T	0.41	.	12.0874	0.53706	0.1385:0.0:0.8615:0.0	.	777	Q9NYQ8	FAT2_HUMAN	R	777	ENSP00000261800:P777R	ENSP00000261800:P777R	P	-	2	0	FAT2	150926356	1.000000	0.71417	0.369000	0.25952	0.700000	0.40528	6.639000	0.74314	1.580000	0.49851	0.655000	0.94253	CCC	.	.	.	none		0.498	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		C	150946163	G	C	150946163	3	2	112	1	0	0	0	0	1	0	0	0	5697	1232	43	4	10811	4	FAT2	5	150946163	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	29159079	150946163	29969097	28	7217											
ATP6V0E1	8992	hgsc.bcm.edu	37	chr5	172410944	172410944	+	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	ggcttcttggtgccttggttCatccctaagggtcctaaccg	5	13	11	12	1	2	0	1	0	1	0	4	0	4	0	4	4	2	2	4	4	2	6			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr5:172410944C>T	ENST00000519374.1	+	1	185	c.81C>T	c.(79-81)ttC>ttT	p.F27F	ATP6V0E1_ENST00000517669.1_Silent_p.F27F|ATP6V0E1_ENST00000519911.1_Silent_p.F27F|ATP6V0E1_ENST00000265093.4_Silent_p.F27F	NM_003945.3	NP_003936.1	O15342	VA0E1_HUMAN	ATPase, H+ transporting, lysosomal 9kDa, V0 subunit e1	27					ATP hydrolysis coupled proton transport (GO:0015991)|cell growth (GO:0016049)|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)|response to amino acid (GO:0043200)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|vacuolar acidification (GO:0007035)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)	ATPase activity, coupled to transmembrane movement of ions (GO:0042625)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transporter activity (GO:0005215)			lung(2)	2	Renal(175;0.000159)|Lung NSC(126;0.00223)|all_lung(126;0.00391)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TGCCTTGGTTCATCCCTAAGG	0.647																																					p.F27F		Atlas-SNP	.											.	ATP6V0E1	3	.	0			c.C81T						PASS	.						188	172	177					5																	172410944		2203	4300	6503	SO:0001819	synonymous_variant	8992	exon1			TTGGTTCATCCCT	Y15286	CCDS4383.1	5q35.2	2010-04-21	2006-10-12	2006-10-12	ENSG00000113732	ENSG00000113732		"ATPases / V-type"	863	protein-coding gene	gene with protein product		603931	"ATPase, H+ transporting, lysosomal (vacuolar proton pump) 9kD", "ATPase, H+ transporting, lysosomal 9kDa, V0 subunit e"	ATP6H, ATP6V0E		9556572, 14970230	Standard	NM_003945		Approved	M9.2	uc003mcd.1	O15342	OTTHUMG00000130518	ENST00000519374.1:c.81C>T	chr5.hg19:g.172410944C>T		228.0	0.0	.		261.0	93.0	.	NM_003945	B2R557|D3DQM1|Q6IBE8	Silent	SNP	ENST00000519374.1	hg19	CCDS4383.1																																																																																			.	.	.	none		0.647	ATP6V0E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252935.2	NM_003945		T	172410944	C	T	172410944	2	4	112	1	0	0	0	0	0	0	0	1	1175	825	29	2		2	ATP6V0E1	5	172410944	Silent	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	21464781	172410944	8504316	29	7218											
DSP	1832	hgsc.bcm.edu	37	chr6	7562980	7562980	+	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	cacaactccatcggcgactaTcgctggcagctggacaaaat	12	7	9	13	3	0	0	0	0	0	0	3	2	1	1	1	3	2	3	1	3	4	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr6:7562980T>A	ENST00000379802.3	+	5	1034	c.693T>A	c.(691-693)taT>taA	p.Y231*	DSP_ENST00000418664.2_Nonsense_Mutation_p.Y231*	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	231	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)		TCGGCGACTATCGCTGGCAGC	0.522																																					p.Y231X		Atlas-SNP	.											.	DSP	306	.	0			c.T693A						PASS	.						119	121	120					6																	7562980		2203	4300	6503	SO:0001587	stop_gained	1832	exon5			CGACTATCGCTGG	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.693T>A	chr6.hg19:g.7562980T>A	ENSP00000369129:p.Tyr231*	97.0	0.0	.		117.0	82.0	.	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Nonsense_Mutation	SNP	ENST00000379802.3	hg19	CCDS4501.1	.	.	.	.	.	.	.	.	.	.	T	39	7.901730	0.98551	.	.	ENSG00000096696	ENST00000379802;ENST00000418664;ENST00000397483	.	.	.	5.76	-1.12	0.09808	.	0.000000	0.53938	D	0.000046	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	11.7621	0.51910	0.0:0.2532:0.0:0.7468	.	.	.	.	X	231;231;36	.	ENSP00000369129:Y231X	Y	+	3	2	DSP	7507979	0.948000	0.32251	0.998000	0.56505	0.948000	0.59901	0.032000	0.13732	-0.099000	0.12263	0.533000	0.62120	TAT	.	.	.	none		0.522	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		A	7562980	T	A	7562980	4	1	112	1	0	0	0	0	0	1	0	0	4783	1442	50	5	711	5	DSP	6	7562980	Nonsense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08		7562980	163552087	30	7219											
HCRTR2	3062	hgsc.bcm.edu	37	chr6	55142265	55142265	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccaggacagccaacgaagTcccggatgagcgctgtggcg	9	4	16	12	4	0	1	0	1	0	0	1	4	1	3	3	4	3	1	3	4	2	0			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr6:55142265T>C	ENST00000370862.3	+	5	1186	c.850T>C	c.(850-852)Tcc>Ccc	p.S284P		NM_001526.3	NP_001517.2	O43614	OX2R_HUMAN	hypocretin (orexin) receptor 2	284					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)			GCCAACGAAGTCCCGGATGAG	0.507																																					p.S284P		Atlas-SNP	.											.	HCRTR2	112	.	0			c.T850C						PASS	.						70	74	73					6																	55142265		2203	4300	6503	SO:0001583	missense	3062	exon5			ACGAAGTCCCGGA	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.850T>C	chr6.hg19:g.55142265T>C	ENSP00000359899:p.Ser284Pro	57.0	0.0	.		75.0	28.0	.	NM_001526	Q5VTM0	Missense_Mutation	SNP	ENST00000370862.3	hg19	CCDS4956.1	.	.	.	.	.	.	.	.	.	.	T	9.734	1.163040	0.21538	.	.	ENSG00000137252	ENST00000370862	T	0.63580	-0.05	5.84	2.09	0.27110	GPCR, rhodopsin-like superfamily (1);	0.177378	0.51477	D	0.000100	T	0.28896	0.0717	L	0.44542	1.39	0.33540	D	0.594739	B	0.02656	0.0	B	0.08055	0.003	T	0.04607	-1.0939	10	0.25751	T	0.34	.	8.2143	0.31503	0.0:0.0661:0.262:0.6719	.	284	O43614	OX2R_HUMAN	P	284	ENSP00000359899:S284P	ENSP00000359899:S284P	S	+	1	0	HCRTR2	55250224	1.000000	0.71417	0.999000	0.59377	0.622000	0.37654	2.200000	0.42724	0.123000	0.18342	0.528000	0.53228	TCC	.	.	.	none		0.507	HCRTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043392.1			C	55142265	T	C	55142265	3	2	112	1	0	0	0	0	1	0	0	0	7009	1667	58	3	868	3	HCRTR2	6	55142265	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	47579285	55142265	115972802	31	7220											
AMD1	262	hgsc.bcm.edu	37	chr6	111213388	111213388	+	Missense_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	agcagcatattgtatgggacGtatgaattctgactgttggt	10	14	12	5	1	1	2	0	2	1	0	1	3	1	3	0	2	2	5	0	2	4	6			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr6:111213388G>A	ENST00000368885.3	+	5	788	c.452G>A	c.(451-453)cGt>cAt	p.R151H	AMD1_ENST00000368876.1_Missense_Mutation_p.R82H|AMD1_ENST00000368882.3_Missense_Mutation_p.R3H|AMD1_ENST00000451850.2_Intron|AMD1_ENST00000368877.5_Missense_Mutation_p.R122H	NM_001634.4	NP_001625.2	P17707	DCAM_HUMAN	adenosylmethionine decarboxylase 1	151					cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|S-adenosylmethioninamine biosynthetic process (GO:0006557)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)|spermine biosynthetic process (GO:0006597)	cytosol (GO:0005829)	adenosylmethionine decarboxylase activity (GO:0004014)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(2)	8		all_cancers(87;3.83e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0209)		OV - Ovarian serous cystadenocarcinoma(136;0.0522)|Epithelial(106;0.111)|all cancers(137;0.143)	S-Adenosylmethionine(DB00118)	TGTATGGGACGTATGAATTCT	0.333																																					p.R151H		Atlas-SNP	.											.	AMD1	23	.	0			c.G452A						PASS	.						316	293	301					6																	111213388		2203	4300	6503	SO:0001583	missense	262	exon5			TGGGACGTATGAA	M88006	CCDS5086.1, CCDS75504.1, CCDS75505.1	6q21	2014-05-13			ENSG00000123505	ENSG00000123505	4.1.1.50		457	protein-coding gene	gene with protein product		180980	"S-adenosylmethionine decarboxylase 1"				Standard	NM_001634		Approved	SAMDC	uc003puk.1	P17707	OTTHUMG00000015369	ENST00000368885.3:c.452G>A	chr6.hg19:g.111213388G>A	ENSP00000357880:p.Arg151His	358.0	0.0	.		392.0	130.0	.	NM_001634	E1P5F7|Q5VXN4|Q5VXN6|Q9BWK4	Missense_Mutation	SNP	ENST00000368885.3	hg19	CCDS5086.1	.	.	.	.	.	.	.	.	.	.	G	15.38	2.816905	0.50633	.	.	ENSG00000123505	ENST00000368885;ENST00000368882;ENST00000368877;ENST00000368876	.	.	.	5.3	4.43	0.53597	S-adenosylmethionine decarboxylase, core (2);	0.108147	0.64402	D	0.000006	T	0.26011	0.0634	N	0.20304	0.555	0.58432	D	0.999999	B;B	0.24721	0.038;0.11	B;B	0.21546	0.007;0.035	T	0.13019	-1.0525	9	0.46703	T	0.11	.	12.2225	0.54441	0.0796:0.0:0.9204:0.0	.	122;151	A6NNH3;P17707	.;DCAM_HUMAN	H	151;3;122;82	.	ENSP00000357870:R82H	R	+	2	0	AMD1	111320081	1.000000	0.71417	0.985000	0.45067	0.991000	0.79684	7.503000	0.81632	1.237000	0.43756	0.491000	0.48974	CGT	.	.	.	none		0.333	AMD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041816.1			A	111213388	G	A	111213388	3	1	112	1	0	0	0	0	1	0	0	0	566	1145	40	1	470	1	AMD1	6	111213388	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	56071123	111213388	59901679	32	7221											
FAM54A	113115	hgsc.bcm.edu	37	chr6	136562761	136562761	+	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	acagtggatcccgaactagtCgcaaaggatgaaaaatttcc	15	8	9	9	2	0	1	0	1	0	0	3	4	2	3	2	2	1	1	2	2	5	2	rs150447506		TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr6:136562761C>T	ENST00000420702.1	-	5	724	c.335G>A	c.(334-336)cGa>cAa	p.R112Q	MTFR2_ENST00000451457.2_Missense_Mutation_p.R112Q	NM_001099286.1	NP_001092756.1	Q6P444	MTFR2_HUMAN	mitochondrial fission regulator 2	112					aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	mitochondrion (GO:0005739)											CCGAACTAGTCGCAAAGGATG	0.368																																					p.R112Q		Atlas-SNP	.											.	.	.	.	0			c.G335A						PASS	.	C	GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	103	98	100		335,335	0.4	0	6	dbSNP_134	100	0,8600		0,0,4300	no	missense,missense	FAM54A	NM_001099286.1,NM_138419.3	43,43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	112/386,112/386	136562761	1,13005	2203	4300	6503	SO:0001583	missense	113115	exon5			ACTAGTCGCAAAG	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.335G>A	chr6.hg19:g.136562761C>T	ENSP00000395232:p.Arg112Gln	110.0	0.0	.		108.0	26.0	.	NM_138419	A8K8D8|E1P585|Q5JWR7|Q6ZUE8|Q7L3U6|Q9BZ39	Missense_Mutation	SNP	ENST00000420702.1	hg19	CCDS5176.1	.	.	.	.	.	.	.	.	.	.	C	7.761	0.705340	0.15172	2.27E-4	0.0	ENSG00000146410	ENST00000451457;ENST00000420702;ENST00000418509	T;T;T	0.40225	1.04;1.04;1.04	5.59	0.386	0.16254	.	1.138940	0.06310	N	0.702535	T	0.04543	0.0124	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34875	-0.9811	10	0.12103	T	0.63	-2.0017	7.6241	0.28202	0.0:0.1662:0.5365:0.2973	.	112	Q6P444	FA54A_HUMAN	Q	112;112;69	ENSP00000407010:R112Q;ENSP00000395232:R112Q;ENSP00000410861:R69Q	ENSP00000410861:R69Q	R	-	2	0	FAM54A	136604454	0.001000	0.12720	0.029000	0.17559	0.165000	0.22458	0.681000	0.25320	0.072000	0.16694	-1.673000	0.00743	CGA	.	C|1.000;T|0.000	0.000	weak		0.368	MTFR2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042378.2	NM_138419		T	136562761	C	T	136562761	3	4	112	1	0	0	0	0	1	0	0	0	5589	884	31	1	838	1	FAM54A	6	136562761	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	25349373	136562761	34552306	33	7222											
ABCA13	154664	hgsc.bcm.edu	37	chr7	48284203	48284203	+	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	ctgtggaaattgcaaagcttGctgcaaaacctgccccagtg	11	9	10	11	0	0	0	0	0	0	0	0	1	0	1	3	1	6	4	3	1	4	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr7:48284203G>A	ENST00000435803.1	+	11	1317	c.1293G>A	c.(1291-1293)ttG>ttA	p.L431L		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	431					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						TGCAAAGCTTGCTGCAAAACC	0.388																																					p.L431L		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G1293A						PASS	.						58	57	57					7																	48284203		1824	4082	5906	SO:0001819	synonymous_variant	154664	exon11			AAGCTTGCTGCAA	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.1293G>A	chr7.hg19:g.48284203G>A		47.0	0.0	.		54.0	21.0	.	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	hg19	CCDS47584.1																																																																																			.	.	.	none		0.388	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48284203	G	A	48284203	2	1	112	1	0	0	0	0	0	0	0	1	31	1310	46	2		2	ABCA13	7	48284203	Silent	SNP	G	TCGA-BQ-5877-01A-11D-1589-08		48284203	110854460	34	7223											
XKR4	114786	hgsc.bcm.edu	37	chr8	56015502	56015504	+	In_Frame_Del	DEL	GTG	GTG	-																															tcgggctcacgctcttcttcGtggtgctcggctctctgtcg																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	GTG	GTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr8:56015502_56015504delGTG	ENST00000327381.6	+	1	554_556	c.454_456delGTG	c.(454-456)gtgdel	p.V153del		NM_052898.1	NP_443130.1	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related family, member 4	153						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)			GCTCTTCTTCGTGGTGCTCGGCT	0.655																																					p.151_152del		Atlas-INDEL	.											XKR4,NS,carcinoma,0,1	XKR4	104	.	0			c.453_455del						PASS	.																																			SO:0001651	inframe_deletion	114786	exon1			.	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.454_456delGTG	chr8.hg19:g.56015505_56015507delGTG	ENSP00000328326:p.Val153del	57.0	0.0	0		80.0	22.0	0.275	NM_052898	Q96PZ8	In_Frame_Del	DEL	ENST00000327381.6	hg19	CCDS34893.1																																																																																			.	.	.	none		0.655	XKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378129.2	NM_052898		-	56015504	GTG	-	56015502	7	5	112	1	0	1	0	1	0	0	0	0	17445	1145	40	0	456	0	XKR4	8	56015502	In_Frame_Del	DEL	GTG	TCGA-BQ-5877-01A-11D-1589-08		56015502	90348520	35	7224											
TG	7038	hgsc.bcm.edu	37	chr8	133898849	133898849	+	Frame_Shift_Del	DEL	C	C	-																															tgccacatcctgcccacccaCgatcaaggagctctttgtgg																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr8:133898849delC	ENST00000220616.4	+	9	1272	c.1232delC	c.(1231-1233)acgfs	p.T411fs	TG_ENST00000377869.1_Frame_Shift_Del_p.T411fs	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	411					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)		TGCCCACCCACGATCAAGGAG	0.537																																					p.T411fs		Atlas-INDEL	.											.	TG	416	.	0			c.1231delA						PASS	.						144	152	150					8																	133898849		2203	4300	6503	SO:0001589	frameshift_variant	7038	exon9			.	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.1232delC	chr8.hg19:g.133898849delC	ENSP00000220616:p.Thr411fs	258.0	0.0	0		368.0	113.0	0.307065	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Frame_Shift_Del	DEL	ENST00000220616.4	hg19	CCDS34944.1																																																																																			.	.	.	none		0.537	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		-	133898849	C	-	133898849	7	5	112	1	0	1	0	1	0	0	0	0	15825	536	19	0	1266	0	TG	8	133898849	Frame_Shift_Del	DEL	C	TCGA-BQ-5877-01A-11D-1589-08	77883347	133898849	12465173	36	7225											
SPINK4	27290	hgsc.bcm.edu	37	chr9	33246702	33246702	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggctcacatatacgaatgAatgccagctctgcttggccc	9	10	10	12	1	2	1	1	1	1	0	2	2	2	1	2	2	4	3	2	2	4	3			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr9:33246702A>G	ENST00000379721.3	+	3	236	c.191A>G	c.(190-192)gAa>gGa	p.E64G	SPINK4_ENST00000379725.1_Missense_Mutation_p.E87G|SPINK4_ENST00000379723.1_Missense_Mutation_p.E87G	NM_014471.1	NP_055286.1	O60575	ISK4_HUMAN	serine peptidase inhibitor, Kazal type 4	64	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				response to drug (GO:0042493)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			lung(1)	1			LUSC - Lung squamous cell carcinoma(29;0.00506)			TATACGAATGAATGCCAGCTC	0.552																																					p.E64G		Atlas-SNP	.											.	SPINK4	7	.	0			c.A191G						PASS	.						173	145	154					9																	33246702		2203	4300	6503	SO:0001583	missense	27290	exon3			CGAATGAATGCCA	AF048700	CCDS6536.1	9p13.3	2011-08-31	2005-08-17		ENSG00000122711	ENSG00000122711		"Serine peptidase inhibitors, Kazal type"	16646	protein-coding gene	gene with protein product		613929	"serine protease inhibitor, Kazal type 4"			1400298, 17333166	Standard	NM_014471		Approved	PEC-60, MGC133107	uc003zsh.3	O60575	OTTHUMG00000019762	ENST00000379721.3:c.191A>G	chr9.hg19:g.33246702A>G	ENSP00000369045:p.Glu64Gly	86.0	0.0	.		128.0	39.0	.	NM_014471	Q2YDT7	Missense_Mutation	SNP	ENST00000379721.3	hg19	CCDS6536.1	.	.	.	.	.	.	.	.	.	.	A	15.12	2.738172	0.49045	.	.	ENSG00000122711	ENST00000379725;ENST00000379723;ENST00000379721	T;T;T	0.79554	-1.28;-1.28;-1.28	4.81	4.81	0.61882	Proteinase inhibitor I1, Kazal (3);	0.000000	0.64402	D	0.000001	D	0.86698	0.5995	.	.	.	0.46564	D	0.999105	D	0.58620	0.983	P	0.60473	0.875	D	0.88001	0.2756	9	0.87932	D	0	-33.3681	10.9375	0.47253	1.0:0.0:0.0:0.0	.	64	O60575	ISK4_HUMAN	G	87;87;64	ENSP00000369048:E87G;ENSP00000369046:E87G;ENSP00000369045:E64G	ENSP00000369045:E64G	E	+	2	0	SPINK4	33236702	1.000000	0.71417	0.995000	0.50966	0.167000	0.22549	4.175000	0.58263	2.165000	0.68154	0.379000	0.24179	GAA	.	.	.	none		0.552	SPINK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052035.1	NM_014471		G	33246702	A	G	33246702	3	3	112	1	0	0	0	0	1	0	0	0	15073	246	9	3	201	3	SPINK4	9	33246702	Missense_Mutation	SNP	A	TCGA-BQ-5877-01A-11D-1589-08		33246702	107966729	37	7226											
PCDH15	65217	hgsc.bcm.edu	37	chr10	55626411	55626411	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tatctacttacgagtacatcGgctttgccgctcagtccctt	7	14	7	13	3	2	0	1	0	1	0	4	1	3	0	2	1	4	3	2	1	4	6	rs374185988		TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr10:55626411G>A	ENST00000320301.6	-	27	4102	c.3708C>T	c.(3706-3708)gcC>gcT	p.A1236A	PCDH15_ENST00000361849.3_Silent_p.A1236A|PCDH15_ENST00000395433.1_Silent_p.A1214A|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000437009.1_Silent_p.A1165A|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000414778.1_Silent_p.A1241A|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395445.1_Silent_p.A1243A|PCDH15_ENST00000395430.1_Silent_p.A1236A|PCDH15_ENST00000409834.1_Silent_p.A847A|PCDH15_ENST00000395432.2_Silent_p.A1199A|PCDH15_ENST00000373965.2_Silent_p.A1243A|PCDH15_ENST00000395438.1_Silent_p.A1236A	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1236	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)				CGAGTACATCGGCTTTGCCGC	0.383										HNSCC(58;0.16)																											p.A1241A		Atlas-SNP	.											.	PCDH15	1715	.	0			c.C3723T						PASS	.	G	,,,,,,,,,,,	0,4406		0,0,2203	94	81	86		3723,3708,3495,3708,3597,3642,3744,3708,3723,3708,3642,3708	-2.8	1	10		86	2,8598	2.2+/-6.3	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,coding-synonymous	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	,,,,,,,,,,,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,,,,,,,,,,,	1241/1963,1236/1958,1165/1887,1236/1953,1199/1916,1214/1936,1248/1791,1236/1540,1241/1683,1236/1678,1214/1933,1236/1956	55626411	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	65217	exon28			TACATCGGCTTTG	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.3708C>T	chr10.hg19:g.55626411G>A		71.0	0.0	.		118.0	31.0	.	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	hg19	CCDS7248.1																																																																																			.	.	.	none		0.383	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		A	55626411	G	A	55626411	2	1	112	1	0	0	0	0	0	0	0	1	11518	1103	39	1		1	PCDH15	10	55626411	Silent	SNP	G	TCGA-BQ-5877-01A-11D-1589-08		55626411	79908336	38	7227											
TTC18	118491	hgsc.bcm.edu	37	chr10	75037057	75037057	+	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	catgaagatggtggtagtttGagaaacaccataatgaaggc	15	9	12	5	0	0	4	0	3	0	2	0	5	0	4	1	3	1	2	1	3	5	3			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr10:75037057G>A	ENST00000310715.3	-	22	2791	c.2671C>T	c.(2671-2673)Caa>Taa	p.Q891*	TTC18_ENST00000401621.2_Nonsense_Mutation_p.Q891*|TTC18_ENST00000493787.1_Intron|TTC18_ENST00000355577.3_Nonsense_Mutation_p.Q360*|RNU6-833P_ENST00000363486.1_RNA|TTC18_ENST00000394865.1_Nonsense_Mutation_p.Q891*|DNAJC9-AS1_ENST00000440197.2_RNA|TTC18_ENST00000340329.3_Intron	NM_145170.3	NP_660153.3	Q5T0N1	TTC18_HUMAN		891						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)					GTGGTAGTTTGAGAAACACCA	0.378																																					p.Q891X		Atlas-SNP	.											.	TTC18	106	.	0			c.C2671T						PASS	.						127	123	124					10																	75037057		2203	4300	6503	SO:0001587	stop_gained	118491	exon22			TAGTTTGAGAAAC																												ENST00000310715.3:c.2671C>T	chr10.hg19:g.75037057G>A	ENSP00000310829:p.Gln891*	161.0	0.0	.		195.0	64.0	.	NM_145170	C9JIZ9|Q5T0M4|Q5T0M9|Q5T0N0|Q69YH9|Q8IYZ8|Q8N7D5|Q8NI30|Q8NI31	Nonsense_Mutation	SNP	ENST00000310715.3	hg19	CCDS7324.3	.	.	.	.	.	.	.	.	.	.	G	39	7.846379	0.98522	.	.	ENSG00000156042	ENST00000310715;ENST00000401621;ENST00000355577;ENST00000433268;ENST00000394865	.	.	.	5.62	4.66	0.58398	.	0.570630	0.17764	N	0.162782	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	1.6662	11.0106	0.47661	0.0:0.0:0.8145:0.1855	.	.	.	.	X	891;891;891;298;891	.	ENSP00000310829:Q891X	Q	-	1	0	TTC18	74707063	0.996000	0.38824	0.998000	0.56505	0.827000	0.46813	3.669000	0.54561	2.642000	0.89623	0.655000	0.94253	CAA	.	.	.	none		0.378	TTC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	75037057	G	A	75037057	4	1	112	1	0	0	0	0	0	1	0	0	16697	1299	45	2	722	2	TTC18	10	75037057	Nonsense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	19410646	75037057	60497690	39	7228											
C10orf79	80217	hgsc.bcm.edu	37	chr10	105944865	105944865	+	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	tctcattgactgaatcccatGaccctggtgagaatgactcc	10	11	8	12	0	1	5	1	5	1	1	4	6	3	5	3	1	0	0	3	1	2	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr10:105944865G>T	ENST00000278064.2	-	16	2168	c.1843C>A	c.(1843-1845)Cat>Aat	p.H615N	WDR96_ENST00000357060.3_Missense_Mutation_p.H684N|WDR96_ENST00000428666.1_Missense_Mutation_p.H685N														p.H684Y(1)		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						TGAATCCCATGACCCTGGTGA	0.403																																					p.H684N		Atlas-SNP	.											WDR96,NS,carcinoma,0,1	WDR96	183	.	1	Substitution - Missense(1)	lung(1)	c.C2050A						PASS	.						174	152	160					10																	105944865		2203	4300	6503	SO:0001583	missense	80217	exon16			TCCCATGACCCTG																												ENST00000278064.2:c.1843C>A	chr10.hg19:g.105944865G>T	ENSP00000278064:p.His615Asn	127.0	1.0	.		150.0	52.0	.	NM_025145		Missense_Mutation	SNP	ENST00000278064.2	hg19		.	.	.	.	.	.	.	.	.	.	G	0.191	-1.053696	0.01965	.	.	ENSG00000197748	ENST00000357060;ENST00000428666;ENST00000278064	T;T;T	0.12879	2.65;2.64;2.66	5.24	3.28	0.37604	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	1.001350	0.08054	N	0.997084	T	0.16300	0.0392	L	0.57536	1.79	0.09310	N	1	B;B	0.12013	0.005;0.001	B;B	0.09377	0.004;0.003	T	0.06881	-1.0802	10	0.51188	T	0.08	.	9.3605	0.38192	0.0:0.2545:0.6054:0.1402	.	685;684	B4DHB6;Q8NDM7	.;WDR96_HUMAN	N	684;685;615	ENSP00000349568:H684N;ENSP00000400289:H685N;ENSP00000278064:H615N	ENSP00000278064:H615N	H	-	1	0	WDR96	105934855	0.000000	0.05858	0.014000	0.15608	0.983000	0.72400	0.646000	0.24797	2.439000	0.82584	0.655000	0.94253	CAT	.	.	.	none		0.403	WDR96-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050200.1			T	105944865	G	T	105944865	3	4	112	1	0	0	0	0	1	0	0	0	1620	1290	45	4	3039	4	C10orf79	10	105944865	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	30907808	105944865	29589882	40	7229											
EBF3	253738	hgsc.bcm.edu	37	chr10	131755589	131755589	+	Splice_Site	DEL	G	G	-																															acttttcttgtcacagcaccGgctgtggagcaattgtaaac																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr10:131755589delG	ENST00000355311.5	-	6	559	c.487delC	c.(487-489)cgg>gg	p.R163fs	EBF3_ENST00000368648.3_Splice_Site_p.R163fs			Q9H4W6	COE3_HUMAN	early B-cell factor 3	163		Interaction with DNA. {ECO:0000250}.			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)		TCACAGCACCGGCTGTGGAGC	0.388																																					p.R163fs		Atlas-INDEL	.											.	EBF3	193	.	0			c.488delG						PASS	.						127	119	121					10																	131755589		2203	4300	6503	SO:0001630	splice_region_variant	253738	exon6			.		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.486-1C>-	chr10.hg19:g.131755589delG		142.0	0.0	0		181.0	50.0	0.276243	NM_001005463	A0AUY1|Q5T6H9|Q9H4W5	Frame_Shift_Del	DEL	ENST00000355311.5	hg19																																																																																				.	.	.	none		0.388	EBF3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051015.2	NM_001005463	Frame_Shift_Del	-	131755589	G	-	131755589	8	5	112	1	0	1	0	1	0	0	1	0	4884	1130	39	0	1212	0	EBF3	10	131755589	Splice_Site	DEL	G	TCGA-BQ-5877-01A-11D-1589-08	25810724	131755589	3779158	41	7230											
LSP1	4046	hgsc.bcm.edu	37	chr11	1907965	1907965	+	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	cttttcctcctctgcagaccGctggccggacccccaagcta	6	9	8	18	2	1	1	0	0	1	1	3	2	3	2	6	2	2	3	6	2	2	3	rs370626038		TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr11:1907965G>T	ENST00000311604.3	+	8	896	c.721G>T	c.(721-723)Gct>Tct	p.A241S	LSP1_ENST00000485341.1_3'UTR|LSP1_ENST00000405957.2_Missense_Mutation_p.A179S|LSP1_ENST00000381775.1_Missense_Mutation_p.A369S|LSP1_ENST00000406638.2_Missense_Mutation_p.A179S	NM_002339.2	NP_002330.1	P33241	LSP1_HUMAN	lymphocyte-specific protein 1	241					cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemotaxis (GO:0006935)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|signal transducer activity (GO:0004871)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)		TCTGCAGACCGCTGGCCGGAC	0.602																																					p.A369S		Atlas-SNP	.											.	LSP1	59	.	0			c.G1105T						PASS	.						76	81	79					11																	1907965		2202	4299	6501	SO:0001583	missense	4046	exon9			CAGACCGCTGGCC	M33552	CCDS31334.1, CCDS31335.1, CCDS58110.1	11p15.5	2008-02-05			ENSG00000130592	ENSG00000130592			6707	protein-coding gene	gene with protein product		153432				2174784	Standard	NM_001242932		Approved	WP34	uc001luj.3	P33241	OTTHUMG00000012252	ENST00000311604.3:c.721G>T	chr11.hg19:g.1907965G>T	ENSP00000308383:p.Ala241Ser	147.0	0.0	.		106.0	44.0	.	NM_001242932	B3KPP1|B3KRR6|E9PBV6|E9PFP3|Q16096|Q53H48|Q6FHM3|Q9BUY8	Missense_Mutation	SNP	ENST00000311604.3	hg19	CCDS31334.1	.	.	.	.	.	.	.	.	.	.	.	0.003	-2.516709	0.00151	.	.	ENSG00000130592	ENST00000311604;ENST00000381775;ENST00000405957;ENST00000457279;ENST00000406638;ENST00000417766;ENST00000432093	T;T;T;T;T;T;T	0.37584	1.19;1.19;1.19;1.19;1.19;1.19;1.19	3.3	1.31	0.21738	.	0.438819	0.16421	N	0.215179	T	0.19565	0.0470	N	0.16307	0.4	0.09310	N	0.99999	B;B	0.33299	0.407;0.039	B;B	0.37387	0.248;0.056	T	0.25813	-1.0121	10	0.02654	T	1	-10.7455	10.0636	0.42290	0.0:0.0:0.3863:0.6137	.	369;241	E9PFP3;P33241	.;LSP1_HUMAN	S	241;369;179;232;179;179;179	ENSP00000308383:A241S;ENSP00000371194:A369S;ENSP00000383932:A179S;ENSP00000400346:A232S;ENSP00000384022:A179S;ENSP00000416363:A179S;ENSP00000412405:A179S	ENSP00000308383:A241S	A	+	1	0	LSP1	1864541	0.342000	0.24809	0.255000	0.24374	0.071000	0.16799	1.196000	0.32198	0.203000	0.20529	-0.493000	0.04662	GCT	.	.	.	alt		0.602	LSP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034045.3	NM_002339		T	1907965	G	T	1907965	3	4	112	1	0	0	0	0	1	0	0	0	9070	1087	38	4	751	4	LSP1	11	1907965	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08		1907965	133098551	42	7231											
TNKS1BP1	85456	hgsc.bcm.edu	37	chr11	57080232	57080232	+	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	ggcctcctcctcaacaggcaGtgcctgtccaggctcagggg	6	7	13	15	0	2	0	2	0	0	0	5	0	5	0	5	5	2	2	5	5	1	0			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr11:57080232G>T	ENST00000532437.1	-	4	2241	c.1930C>A	c.(1930-1932)Ctg>Atg	p.L644M	TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.L644M|TNKS1BP1_ENST00000530920.1_5'Flank			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	644	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)				TCAACAGGCAGTGCCTGTCCA	0.652																																					p.L644M		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.C1930A						PASS	.						40	43	42					11																	57080232		2201	4296	6497	SO:0001583	missense	85456	exon5			CAGGCAGTGCCTG	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.1930C>A	chr11.hg19:g.57080232G>T	ENSP00000437271:p.Leu644Met	72.0	0.0	.		62.0	17.0	.	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	hg19	CCDS7951.1	.	.	.	.	.	.	.	.	.	.	G	3.119	-0.180918	0.06380	.	.	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.33865	1.39;1.39	3.52	-7.04	0.01578	.	0.599176	0.12691	N	0.447197	T	0.14743	0.0356	L	0.27053	0.805	0.09310	N	1	B	0.32101	0.356	B	0.28305	0.088	T	0.11991	-1.0565	10	0.32370	T	0.25	-3.6489	2.1814	0.03876	0.1527:0.1225:0.4815:0.2434	.	644	Q9C0C2	TB182_HUMAN	M	644	ENSP00000350990:L644M;ENSP00000437271:L644M	ENSP00000350990:L644M	L	-	1	2	TNKS1BP1	56836808	0.000000	0.05858	0.005000	0.12908	0.035000	0.12851	-1.072000	0.03434	-0.816000	0.04340	0.455000	0.32223	CTG	.	.	.	none		0.652	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396		T	57080232	G	T	57080232	3	4	112	1	0	0	0	0	1	0	0	0	16332	1020	36	4	3287	4	TNKS1BP1	11	57080232	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	55172267	57080232	77926284	43	7232											
CACNA1C	775	hgsc.bcm.edu	37	chr12	2760913	2760913	+	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	ggcatccggacgctgctgtgGaccttcatcaagtccttcca	7	10	10	14	2	2	0	2	0	0	0	5	2	5	2	4	3	1	3	4	3	1	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr12:2760913G>T	ENST00000347598.4	+	34	4197	c.4197G>T	c.(4195-4197)tgG>tgT	p.W1399C	CACNA1C_ENST00000399629.1_Missense_Mutation_p.W1368C|CACNA1C_ENST00000344100.3_Missense_Mutation_p.W1373C|CACNA1C_ENST00000399591.1_Missense_Mutation_p.W1340C|CACNA1C_ENST00000399603.1_Missense_Mutation_p.W1351C|CACNA1C_ENST00000327702.7_Missense_Mutation_p.W1351C|CACNA1C_ENST00000335762.5_Missense_Mutation_p.W1376C|CACNA1C_ENST00000399638.1_Missense_Mutation_p.W1379C|CACNA1C_ENST00000406454.3_Missense_Mutation_p.W1351C|CACNA1C_ENST00000399641.1_Missense_Mutation_p.W1351C|CACNA1C_ENST00000399621.1_Missense_Mutation_p.W1351C|CACNA1C_ENST00000399634.1_Missense_Mutation_p.W1351C|CACNA1C_ENST00000399655.1_Missense_Mutation_p.W1351C|CACNA1C_ENST00000399649.1_Missense_Mutation_p.W1338C|CACNA1C_ENST00000399601.1_Missense_Mutation_p.W1351C|CACNA1C_ENST00000399637.1_Missense_Mutation_p.W1351C|CACNA1C_ENST00000399606.1_Missense_Mutation_p.W1371C|CACNA1C_ENST00000402845.3_Missense_Mutation_p.W1351C|CACNA1C_ENST00000399597.1_Missense_Mutation_p.W1351C|CACNA1C_ENST00000399595.1_Missense_Mutation_p.W1340C|CACNA1C_ENST00000399617.1_Missense_Mutation_p.W1351C|CACNA1C_ENST00000399644.1_Missense_Mutation_p.W1351C	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1399					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)	CGCTGCTGTGGACCTTCATCA	0.632																																					p.W1399C		Atlas-SNP	.											.	CACNA1C	1023	.	0			c.G4197T						PASS	.						44	53	50					12																	2760913		2195	4295	6490	SO:0001583	missense	775	exon34			GCTGTGGACCTTC	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.4197G>T	chr12.hg19:g.2760913G>T	ENSP00000266376:p.Trp1399Cys	30.0	0.0	.		50.0	14.0	.	NM_199460	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	hg19	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.274714	0.80580	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.98512	-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97	5.17	4.27	0.50696	Ion transport (1);	0.125129	0.64402	D	0.000017	D	0.99275	0.9747	H	0.97186	3.955	0.80722	D	1	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	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.998;0.998;0.995;0.999;0.998;0.995;0.995;0.996;0.999;0.999;0.995;0.995;0.999;0.999;0.999;0.998;0.995;1.0;0.999;0.997;0.995;0.999;0.999;0.995;0.995	D	0.98781	1.0732	10	0.87932	D	0	.	13.5755	0.61873	0.0758:0.0:0.9242:0.0	.	42;1373;1348;1399;1351;1351;1351;1368;1379;1351;1371;1351;1311;1399;1351;1351;1351;1340;1338;1340;1340;1351;1351;1351;1351	B7Z7Z5;Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	C	1376;1351;1351;1379;1351;1351;1351;1340;1351;1399;1371;1351;1373;1368;1351;1338;1351;1351;1351;1351;1351;1340;1181	ENSP00000336982:W1376C;ENSP00000382563:W1351C;ENSP00000382552:W1351C;ENSP00000382547:W1379C;ENSP00000382506:W1351C;ENSP00000382530:W1351C;ENSP00000382546:W1351C;ENSP00000382500:W1340C;ENSP00000382549:W1351C;ENSP00000266376:W1399C;ENSP00000382515:W1371C;ENSP00000382510:W1351C;ENSP00000341092:W1373C;ENSP00000382537:W1368C;ENSP00000329877:W1351C;ENSP00000382557:W1338C;ENSP00000385724:W1351C;ENSP00000382512:W1351C;ENSP00000382542:W1351C;ENSP00000382526:W1351C;ENSP00000385896:W1351C;ENSP00000382504:W1340C	ENSP00000323129:W1181C	W	+	3	0	CACNA1C	2631174	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.805000	0.99149	1.171000	0.42768	0.491000	0.48974	TGG	.	.	.	none		0.632	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		T	2760913	G	T	2760913	3	4	112	1	0	0	0	0	1	0	0	0	2542	1183	41	4	4505	4	CACNA1C	12	2760913	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08		2760913	131090982	44	7233											
GPR133	283383	hgsc.bcm.edu	37	chr12	131439188	131439188	+	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	ggtgcgtggcgtctactccaGatcgcaggaccatccaggta	8	8	13	12	3	1	1	0	0	1	1	4	2	3	2	3	4	2	2	3	4	2	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr12:131439188G>C	ENST00000261654.5	+	2	645	c.86G>C	c.(85-87)aGa>aCa	p.R29T	GPR133_ENST00000535015.1_Missense_Mutation_p.R29T	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	29					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)		GTCTACTCCAGATCGCAGGAC	0.562																																					p.R29T		Atlas-SNP	.											.	GPR133	136	.	0			c.G86C						PASS	.						114	98	103					12																	131439188		2203	4300	6503	SO:0001583	missense	283383	exon2			ACTCCAGATCGCA	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.86G>C	chr12.hg19:g.131439188G>C	ENSP00000261654:p.Arg29Thr	119.0	0.0	.		163.0	37.0	.	NM_198827	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Missense_Mutation	SNP	ENST00000261654.5	hg19	CCDS9272.1	.	.	.	.	.	.	.	.	.	.	G	11.63	1.695276	0.30052	.	.	ENSG00000111452	ENST00000261654;ENST00000543826;ENST00000542091;ENST00000535015	T;T	0.41400	1.0;1.03	4.42	1.96	0.26148	.	0.754074	0.11519	N	0.555971	T	0.33673	0.0871	L	0.56769	1.78	0.09310	N	1	B;B	0.29432	0.244;0.118	B;B	0.26770	0.073;0.023	T	0.37798	-0.9690	10	0.72032	D	0.01	.	2.9661	0.05908	0.2203:0.2806:0.4991:0.0	.	29;29	B7ZLF7;Q6QNK2	.;GP133_HUMAN	T	29	ENSP00000261654:R29T;ENSP00000444425:R29T	ENSP00000261654:R29T	R	+	2	0	GPR133	130005141	0.001000	0.12720	0.007000	0.13788	0.055000	0.15305	0.979000	0.29500	2.023000	0.59567	0.561000	0.74099	AGA	.	.	.	none		0.562	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827		C	131439188	G	C	131439188	3	2	112	1	0	0	0	0	1	0	0	0	6650	942	33	4	92	4	GPR133	12	131439188	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	128678275	131439188	2412707	45	7234											
JPH4	84502	hgsc.bcm.edu	37	chr14	24040204	24040204	+	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	tcaggcacccagcatcaggaCccctcgaggacgagcccctc	9	4	10	18	2	2	0	2	0	0	0	4	4	2	2	5	3	2	2	5	3	0	0			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr14:24040204C>G	ENST00000397118.3	-	6	2638	c.1736G>C	c.(1735-1737)gGt>gCt	p.G579A	JPH4_ENST00000356300.4_Missense_Mutation_p.G579A|AP1G2_ENST00000308724.5_5'Flank|RP11-66N24.3_ENST00000555968.1_RNA|JPH4_ENST00000544177.1_Missense_Mutation_p.G244A	NM_032452.2	NP_115828.2	Q96JJ6	JPH4_HUMAN	junctophilin 4	579					calcium ion transport into cytosol (GO:0060402)|learning (GO:0007612)|neuromuscular process controlling balance (GO:0050885)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of synaptic plasticity (GO:0048167)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)				endometrium(1)|large_intestine(2)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00654)		AGCATCAGGACCCCTCGAGGA	0.687																																					p.G579A		Atlas-SNP	.											.	JPH4	64	.	0			c.G1736C						PASS	.						31	33	32					14																	24040204		2203	4299	6502	SO:0001583	missense	84502	exon5			TCAGGACCCCTCG	AB058734	CCDS9603.1	14q11	2004-05-28	2004-05-28	2004-05-28	ENSG00000092051	ENSG00000092051			20156	protein-coding gene	gene with protein product			"junctophilin like 1"	JPHL1		11347906	Standard	NM_032452		Approved	KIAA1831	uc001wkr.2	Q96JJ6	OTTHUMG00000028769	ENST00000397118.3:c.1736G>C	chr14.hg19:g.24040204C>G	ENSP00000380307:p.Gly579Ala	55.0	0.0	.		46.0	15.0	.	NM_001146028	D3DS53|Q8ND44|Q96DQ0	Missense_Mutation	SNP	ENST00000397118.3	hg19	CCDS9603.1	.	.	.	.	.	.	.	.	.	.	C	11.95	1.792770	0.31685	.	.	ENSG00000092051	ENST00000356300;ENST00000397118;ENST00000543864;ENST00000267407;ENST00000544177	T;T;T	0.54866	0.55;0.55;0.93	4.93	0.601	0.17529	.	0.326972	0.16970	U	0.192130	T	0.27419	0.0673	N	0.12182	0.205	0.26864	N	0.967898	B;B	0.11235	0.004;0.001	B;B	0.11329	0.006;0.002	T	0.17410	-1.0370	10	0.16420	T	0.52	.	6.9268	0.24419	0.3209:0.3658:0.3132:0.0	.	244;579	F5H1L9;Q96JJ6	.;JPH4_HUMAN	A	579;579;579;580;244	ENSP00000348648:G579A;ENSP00000380307:G579A;ENSP00000439562:G244A	ENSP00000267407:G580A	G	-	2	0	JPH4	23110044	0.797000	0.28877	0.998000	0.56505	0.975000	0.68041	0.344000	0.19962	0.546000	0.28920	-0.152000	0.13540	GGT	.	.	.	none		0.687	JPH4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413853.1	NM_032452		G	24040204	C	G	24040204	3	3	112	1	0	0	0	0	1	0	0	0	7970	507	18	4	158	4	JPH4	14	24040204	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08		24040204	83309336	46	7235											
NYNRIN	57523	hgsc.bcm.edu	37	chr14	24885007	24885007	+	Frame_Shift_Del	DEL	C	C	-																															ctgctccccttacacgccaaCctatgcccacctggcagccg																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr14:24885007delC	ENST00000382554.3	+	9	4370	c.4052delC	c.(4051-4053)accfs	p.T1351fs		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	1351					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						TACACGCCAACCTATGCCCAC	0.602																																					p.T1351fs		Atlas-INDEL	.											.	NYNRIN	120	.	0			c.4051delA						PASS	.						95	101	99					14																	24885007		2016	4157	6173	SO:0001589	frameshift_variant	57523	exon9			.	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.4052delC	chr14.hg19:g.24885007delC	ENSP00000371994:p.Thr1351fs	120.0	0.0	0		152.0	48.0	0.315789	NM_025081	Q6P153|Q86TR3|Q9HAC4	Frame_Shift_Del	DEL	ENST00000382554.3	hg19	CCDS45090.1																																																																																			.	.	.	none		0.602	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1			-	24885007	C	-	24885007	7	5	112	1	0	1	0	1	0	0	0	0	10803	507	18	0	4082	0	NYNRIN	14	24885007	Frame_Shift_Del	DEL	C	TCGA-BQ-5877-01A-11D-1589-08	844803	24885007	82464533	47	7236											
FBXO33	254170	hgsc.bcm.edu	37	chr14	39868808	39868808	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgattcgatgtccatgactGcatgccaaggttgacccagg	9	10	12	10	1	0	3	0	3	0	0	2	4	1	3	3	2	2	2	3	2	1	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr14:39868808G>A	ENST00000298097.7	-	4	1917	c.1580C>T	c.(1579-1581)gCa>gTa	p.A527V	FBXO33_ENST00000554190.1_3'UTR	NM_203301.3	NP_976046.1	Q7Z6M2	FBX33_HUMAN	F-box protein 33	527					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)		GTCCATGACTGCATGCCAAGG	0.438																																					p.A527V		Atlas-SNP	.											.	FBXO33	21	.	0			c.C1580T						PASS	.						127	98	108					14																	39868808		2203	4300	6503	SO:0001583	missense	254170	exon4			ATGACTGCATGCC	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.1580C>T	chr14.hg19:g.39868808G>A	ENSP00000298097:p.Ala527Val	60.0	0.0	.		52.0	18.0	.	NM_203301	Q6PIR2|Q86TR2|Q86YE0	Missense_Mutation	SNP	ENST00000298097.7	hg19	CCDS9677.1	.	.	.	.	.	.	.	.	.	.	G	17.27	3.347997	0.61183	.	.	ENSG00000165355	ENST00000298097	T	0.34072	1.38	5.85	5.85	0.93711	.	0.051431	0.85682	D	0.000000	T	0.38108	0.1028	N	0.14661	0.345	0.80722	D	1	D	0.60575	0.988	P	0.54759	0.76	T	0.09885	-1.0654	9	.	.	.	-19.5419	20.1542	0.98100	0.0:0.0:1.0:0.0	.	527	Q7Z6M2	FBX33_HUMAN	V	527	ENSP00000298097:A527V	.	A	-	2	0	FBXO33	38938559	1.000000	0.71417	0.508000	0.27688	0.970000	0.65996	9.124000	0.94394	2.767000	0.95098	0.563000	0.77884	GCA	.	.	.	none		0.438	FBXO33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276769.2			A	39868808	G	A	39868808	3	1	112	1	0	0	0	0	1	0	0	0	5750	1319	46	2	91	2	FBXO33	14	39868808	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	14983801	39868808	67480732	48	7237											
NUMB	8650	hgsc.bcm.edu	37	chr14	73750966	73750966	+	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	ccggcgtgggatggcatgagGattgttcatctccagagagg	8	9	16	8	2	2	2	1	1	1	1	3	5	2	4	2	5	0	2	2	5	0	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr14:73750966G>A	ENST00000355058.3	-	10	1050	c.772C>T	c.(772-774)Cct>Tct	p.P258S	NUMB_ENST00000555394.1_Missense_Mutation_p.P258S|NUMB_ENST00000554546.1_Missense_Mutation_p.P247S|NUMB_ENST00000560335.1_Intron|NUMB_ENST00000554521.2_Intron|NUMB_ENST00000559312.1_Intron|NUMB_ENST00000359560.3_Missense_Mutation_p.P247S|NUMB_ENST00000535282.1_Missense_Mutation_p.P247S|NUMB_ENST00000544991.3_Intron|NUMB_ENST00000557597.1_Missense_Mutation_p.P247S|NUMB_ENST00000555738.2_Intron|NUMB_ENST00000454166.4_Intron|NUMB_ENST00000555238.1_Missense_Mutation_p.P258S|NUMB_ENST00000556772.1_Missense_Mutation_p.P114S|NUMB_ENST00000356296.4_Missense_Mutation_p.P258S			P49757	NUMB_HUMAN	numb homolog (Drosophila)	258					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|lateral ventricle development (GO:0021670)|lung epithelial cell differentiation (GO:0060487)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of protein localization to plasma membrane (GO:1903077)|neuroblast division in subventricular zone (GO:0021849)|Notch signaling pathway (GO:0007219)|positive regulation of cell migration (GO:0030335)|positive regulation of neurogenesis (GO:0050769)|positive regulation of polarized epithelial cell differentiation (GO:0030862)	apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00471)|OV - Ovarian serous cystadenocarcinoma(108;0.161)		ATGGCATGAGGATTGTTCATC	0.542																																					p.P258S		Atlas-SNP	.											.	NUMB	56	.	0			c.C772T						PASS	.						177	165	169					14																	73750966		2203	4300	6503	SO:0001583	missense	8650	exon10			CATGAGGATTGTT	L40393	CCDS9814.1, CCDS32115.1, CCDS32116.1, CCDS55927.1	14q24.3	2011-11-25	2001-11-28			ENSG00000133961			8060	protein-coding gene	gene with protein product		603728	"numb (Drosophila) homolog", "chromosome 14 open reading frame 41"	C14orf41			Standard	NM_003744		Approved		uc001xny.1	P49757		ENST00000355058.3:c.772C>T	chr14.hg19:g.73750966G>A	ENSP00000347169:p.Pro258Ser	186.0	0.0	.		210.0	62.0	.	NM_001005744	B1P2N5|B1P2N6|B1P2N7|B1P2N8|B1P2N9|B4E2B1|Q6NUQ7|Q86SY1|Q8WW73|Q9UBG1|Q9UEQ4|Q9UKE8|Q9UKE9|Q9UKF0|Q9UQJ4	Missense_Mutation	SNP	ENST00000355058.3	hg19	CCDS32116.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.596077	0.86953	.	.	ENSG00000133961	ENST00000554546;ENST00000356296;ENST00000557597;ENST00000555238;ENST00000556772;ENST00000355058;ENST00000359560;ENST00000555394;ENST00000535282;ENST00000326018;ENST00000555859;ENST00000555307;ENST00000554394	T;T;T;T;T;T;T;T;T;T;T	0.66815	0.28;0.24;0.66;0.66;1.27;0.66;0.66;0.24;0.66;-0.23;-0.23	5.39	5.39	0.77823	NUMB domain (1);	0.000000	0.85682	D	0.000000	T	0.76564	0.4005	L	0.38175	1.15	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.999	D;D;D;D;D;D	0.97110	1.0;0.998;0.999;0.992;0.992;0.98	T	0.77616	-0.2521	10	0.66056	D	0.02	-12.4282	19.34	0.94337	0.0:0.0:1.0:0.0	.	4;247;247;258;247;258	B1P2N9;B2RCI6;P49757-4;P49757-2;P49757-3;P49757	.;.;.;.;.;NUMB_HUMAN	S	247;258;247;258;114;258;247;258;247;222;222;258;258	ENSP00000452416:P247S;ENSP00000348644:P258S;ENSP00000451117:P247S;ENSP00000451300:P258S;ENSP00000451513:P114S;ENSP00000347169:P258S;ENSP00000352563:P247S;ENSP00000451625:P258S;ENSP00000441258:P247S;ENSP00000452357:P258S;ENSP00000451374:P258S	ENSP00000315193:P222S	P	-	1	0	NUMB	72820719	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.343000	0.72986	2.808000	0.96608	0.655000	0.94253	CCT	.	.	.	none		0.542	NUMB-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414416.1			A	73750966	G	A	73750966	3	1	112	1	0	0	0	0	1	0	0	0	10758	1174	41	2	1199	2	NUMB	14	73750966	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	33882158	73750966	33598574	49	7238											
CLMN	79789	hgsc.bcm.edu	37	chr14	95660233	95660233	+	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	tccagatctgctgcgttcctCaactgaacatagctaaaatg	12	11	7	11	1	2	2	1	1	1	1	4	2	4	2	2	0	5	3	2	0	5	3			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr14:95660233C>G	ENST00000298912.4	-	12	2906	c.2793G>C	c.(2791-2793)ttG>ttC	p.L931F	CLMN_ENST00000557215.1_5'UTR|CLMN_ENST00000556441.1_5'UTR	NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	931					negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		CTGCGTTCCTCAACTGAACAT	0.373																																					p.L931F		Atlas-SNP	.											.	CLMN	103	.	0			c.G2793C						PASS	.						116	111	112					14																	95660233		2203	4300	6503	SO:0001583	missense	79789	exon12			GTTCCTCAACTGA	AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.2793G>C	chr14.hg19:g.95660233C>G	ENSP00000298912:p.Leu931Phe	88.0	0.0	.		100.0	19.0	.	NM_024734	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Missense_Mutation	SNP	ENST00000298912.4	hg19	CCDS9933.1	.	.	.	.	.	.	.	.	.	.	C	16.76	3.211197	0.58343	.	.	ENSG00000165959	ENST00000298912	D	0.93426	-3.22	4.77	3.87	0.44632	.	0.800724	0.10248	N	0.697563	D	0.94571	0.8251	M	0.64997	1.995	0.80722	D	1	D	0.59767	0.986	P	0.56916	0.809	D	0.91007	0.4847	10	0.46703	T	0.11	.	10.1749	0.42933	0.1987:0.8012:0.0:0.0	.	931	Q96JQ2	CLMN_HUMAN	F	931	ENSP00000298912:L931F	ENSP00000298912:L931F	L	-	3	2	CLMN	94729986	0.998000	0.40836	0.922000	0.36590	0.861000	0.49209	3.347000	0.52200	1.223000	0.43536	-0.314000	0.08810	TTG	.	.	.	none		0.373	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2			G	95660233	C	G	95660233	3	3	112	1	0	0	0	0	1	0	0	0	3544	825	29	4	223	4	CLMN	14	95660233	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	21909267	95660233	11689307	50	7239											
AK7	122481	hgsc.bcm.edu	37	chr14	96924426	96924426	+	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	cctgtggtatgcaggaggcgAttgttgcccctaacgatgta	8	11	13	9	2	0	0	0	0	0	0	0	3	0	1	3	3	3	4	3	3	3	5			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr14:96924426A>T	ENST00000267584.4	+	12	1278	c.1234A>T	c.(1234-1236)Att>Ttt	p.I412F		NM_152327.3	NP_689540.2	Q96M32	KAD7_HUMAN	adenylate kinase 7	412	Adenylate kinase.|NMPbind. {ECO:0000250}.				axoneme assembly (GO:0035082)|brain development (GO:0007420)|epithelial cilium movement (GO:0003351)|inflammatory response to antigenic stimulus (GO:0002437)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			breast(2)|cervix(2)|endometrium(3)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		GCAGGAGGCGATTGTTGCCCC	0.493																																					p.I412F		Atlas-SNP	.											.	AK7	69	.	0			c.A1234T						PASS	.						98	86	90					14																	96924426		2203	4300	6503	SO:0001583	missense	122481	exon12			GAGGCGATTGTTG	AK057426	CCDS9945.1	14q32.31	2012-08-15			ENSG00000140057	ENSG00000140057		"Adenylate kinases"	20091	protein-coding gene	gene with protein product		615364					Standard	NM_152327		Approved	FLJ32864	uc001yfn.3	Q96M32	OTTHUMG00000171421	ENST00000267584.4:c.1234A>T	chr14.hg19:g.96924426A>T	ENSP00000267584:p.Ile412Phe	43.0	0.0	.		70.0	20.0	.	NM_152327	Q8IYP6	Missense_Mutation	SNP	ENST00000267584.4	hg19	CCDS9945.1	.	.	.	.	.	.	.	.	.	.	A	3.590	-0.083768	0.07141	.	.	ENSG00000140057	ENST00000267584	D	0.92858	-3.12	4.89	2.31	0.28768	.	0.577652	0.18744	N	0.132380	D	0.85418	0.5692	L	0.29908	0.895	0.09310	N	0.999999	B	0.13594	0.008	B	0.24394	0.053	T	0.76263	-0.3023	10	0.52906	T	0.07	-2.9231	7.0702	0.25173	0.7494:0.1595:0.0911:0.0	.	412	Q96M32	KAD7_HUMAN	F	412	ENSP00000267584:I412F	ENSP00000267584:I412F	I	+	1	0	AK7	95994179	0.939000	0.31865	0.041000	0.18516	0.049000	0.14656	2.486000	0.45259	0.720000	0.32209	0.260000	0.18958	ATT	.	.	.	none		0.493	AK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413340.1			T	96924426	A	T	96924426	3	4	112	1	0	0	0	0	1	0	0	0	444	333	12	5	1280	5	AK7	14	96924426	Missense_Mutation	SNP	A	TCGA-BQ-5877-01A-11D-1589-08	1264193	96924426	10425114	51	7240											
DUOX1	53905	hgsc.bcm.edu	37	chr15	45445603	45445603	+	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	cacagtgtgggccatgtggtGaatgtgtacctgttctccat	7	13	12	9	0	1	1	0	1	1	0	2	1	1	1	3	2	1	2	3	2	2	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr15:45445603G>C	ENST00000321429.4	+	27	3857	c.3450G>C	c.(3448-3450)gtG>gtC	p.V1150V	CTD-2651B20.1_ENST00000558039.1_lincRNA|DUOX1_ENST00000559221.1_3'UTR|DUOX1_ENST00000561166.1_Silent_p.V796V|DUOX1_ENST00000389037.3_Silent_p.V1150V	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	1150	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)		GCCATGTGGTGAATGTGTACC	0.547																																					p.V1150V		Atlas-SNP	.											.	DUOX1	125	.	0			c.G3450C						PASS	.						311	237	262					15																	45445603		2198	4298	6496	SO:0001819	synonymous_variant	53905	exon27			TGTGGTGAATGTG	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.3450G>C	chr15.hg19:g.45445603G>C		167.0	0.0	.		194.0	69.0	.	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Silent	SNP	ENST00000321429.4	hg19	CCDS32221.1																																																																																			.	.	.	none		0.547	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434		C	45445603	G	C	45445603	2	2	112	1	0	0	0	0	0	0	0	1	4802	1277	45	4		4	DUOX1	15	45445603	Silent	SNP	G	TCGA-BQ-5877-01A-11D-1589-08		45445603	57085789	52	7241											
CILP	8483	hgsc.bcm.edu	37	chr15	65490142	65490142	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttgcagttcctccccagccaGgcttgccaagacataggcag	9	8	10	14	0	0	1	0	0	0	1	2	1	2	1	5	2	3	4	5	2	2	4			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr15:65490142G>A	ENST00000261883.4	-	9	2648	c.2482C>T	c.(2482-2484)Ctg>Ttg	p.L828L		NM_003613.3	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	828					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						TCCCCAGCCAGGCTTGCCAAG	0.557																																					p.L828L		Atlas-SNP	.											.	CILP	124	.	0			c.C2482T						PASS	.						63	57	59					15																	65490142		2200	4295	6495	SO:0001819	synonymous_variant	8483	exon9			CAGCCAGGCTTGC	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.2482C>T	chr15.hg19:g.65490142G>A		118.0	0.0	.		98.0	31.0	.	NM_003613	B2R8F7|Q6UW99|Q8IYI5	Silent	SNP	ENST00000261883.4	hg19	CCDS10203.1																																																																																			.	.	.	none		0.557	CILP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256829.1	NM_003613		A	65490142	G	A	65490142	2	1	112	1	0	0	0	0	0	0	0	1	3431	991	35	2		2	CILP	15	65490142	Silent	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	20044539	65490142	37041250	53	7242											
SRRM2	23524	hgsc.bcm.edu	37	chr16	2817459	2817459	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgccttggcagctctgagTctcacaggctctggcacacc	6	9	11	15	0	3	1	1	1	3	0	4	1	3	1	2	3	2	5	2	3	0	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr16:2817459T>C	ENST00000301740.8	+	11	7479	c.6930T>C	c.(6928-6930)agT>agC	p.S2310S	AC092117.2_ENST00000581119.1_RNA	NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	2310	Ala-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						CAGCTCTGAGTCTCACAGGCT	0.622																																					p.S2310S		Atlas-SNP	.											.	SRRM2	263	.	0			c.T6930C						PASS	.						162	169	166					16																	2817459		2198	4300	6498	SO:0001819	synonymous_variant	23524	exon11			TCTGAGTCTCACA	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.6930T>C	chr16.hg19:g.2817459T>C		409.0	1.0	.		501.0	143.0	.	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Silent	SNP	ENST00000301740.8	hg19	CCDS32373.1																																																																																			.	.	.	none		0.622	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			C	2817459	T	C	2817459	2	2	112	1	0	0	0	0	0	0	0	1	15181	1664	58	3		3	SRRM2	16	2817459	Silent	SNP	T	TCGA-BQ-5877-01A-11D-1589-08		2817459	87537294	54	7243											
MEFV	4210	hgsc.bcm.edu	37	chr16	3297239	3297240	+	Frame_Shift_Ins	INS	-	-	T																															ccgctgcttcagcgcttcagINStttgtttctggggagcagag																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr16:3297239_3297240insT	ENST00000219596.1	-	5	1402_1403	c.1363_1364insA	c.(1363-1365)actfs	p.T455fs	MEFV_ENST00000339854.4_Frame_Shift_Ins_p.T275fs|MEFV_ENST00000536379.1_Frame_Shift_Ins_p.T244fs|MEFV_ENST00000541159.1_Frame_Shift_Ins_p.T244fs	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	455	Required for homotrimerization and induction of pyroptosomes.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						CAGCGCTTCAGTTTGTTTCTGG	0.594																																					p.T455fs		Atlas-INDEL	.											.	MEFV	170	.	0			c.1364_1365insA						PASS	.																																			SO:0001589	frameshift_variant	4210	exon5			.	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"Tripartite motif containing / Tripartite motif containing"	6998	protein-coding gene	gene with protein product	"pyrin"	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.1364dupA	chr16.hg19:g.3297242_3297242dupT	ENSP00000219596:p.Thr455fs	96.0	0.0	0		146.0	45.0	0.308219	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Frame_Shift_Ins	INS	ENST00000219596.1	hg19	CCDS10498.1																																																																																			.	.	.	none		0.594	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243		T	3297240	-	T	3297239	7	5	112	1	0	1	1	0	0	0	0	0	9466	1029	36	0	1005	0	MEFV	16	3297239	Frame_Shift_Ins	INS	-	TCGA-BQ-5877-01A-11D-1589-08	479780	3297239	87057514	55	7244											
ANKS4B	257629	hgsc.bcm.edu	37	chr16	21261659	21261659	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agttgtcagcagaggaggacGgcagtgtgcaccatgaatcc	11	7	14	9	1	1	2	1	1	0	1	2	4	2	4	2	3	2	4	2	3	1	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr16:21261659G>A	ENST00000311620.5	+	2	845	c.772G>A	c.(772-774)Ggc>Agc	p.G258S		NM_145865.2	NP_665872.2	Q8N8V4	ANS4B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 4B	258					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)		AGAGGAGGACGGCAGTGTGCA	0.478																																					p.G258S		Atlas-SNP	.											.	ANKS4B	43	.	0			c.G772A						PASS	.						105	113	111					16																	21261659		2087	4214	6301	SO:0001583	missense	257629	exon2			GAGGACGGCAGTG	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.772G>A	chr16.hg19:g.21261659G>A	ENSP00000308772:p.Gly258Ser	96.0	0.0	.		90.0	17.0	.	NM_145865		Missense_Mutation	SNP	ENST00000311620.5	hg19	CCDS42130.1	.	.	.	.	.	.	.	.	.	.	A	3.131	-0.178370	0.06380	.	.	ENSG00000175311	ENST00000311620	T	0.39997	1.05	5.77	-1.61	0.08399	.	1.096410	0.06713	N	0.773573	T	0.22513	0.0543	N	0.04880	-0.145	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.29549	-1.0008	10	0.08179	T	0.78	0.0056	16.0383	0.80645	0.3534:0.0:0.6466:0.0	.	258	Q8N8V4	ANS4B_HUMAN	S	258	ENSP00000308772:G258S	ENSP00000308772:G258S	G	+	1	0	ANKS4B	21169160	0.000000	0.05858	0.000000	0.03702	0.834000	0.47266	0.038000	0.13862	-0.644000	0.05465	-0.332000	0.08345	GGC	.	.	.	none		0.478	ANKS4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436535.1	NM_145865		A	21261659	G	A	21261659	3	1	112	1	0	0	0	0	1	0	0	0	691	1116	39	1	778	1	ANKS4B	16	21261659	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	17964420	21261659	69093094	56	7245											
SALL1	6299	hgsc.bcm.edu	37	chr16	51174769	51174769	+	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	tgtcactcccaaagaccttcGcgcagaacctgcacttgtgt	9	10	8	14	2	1	2	1	0	0	2	3	2	2	2	3	0	2	2	3	0	2	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr16:51174769G>C	ENST00000251020.4	-	2	1397	c.1364C>G	c.(1363-1365)gCg>gGg	p.A455G	SALL1_ENST00000541611.1_Intron|SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Missense_Mutation_p.A358G|SALL1_ENST00000562674.1_5'Flank	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	455					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)			AAAGACCTTCGCGCAGAACCT	0.512																																					p.A455G	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.C1364G						PASS	.						104	96	99					16																	51174769		2198	4300	6498	SO:0001583	missense	6299	exon2			ACCTTCGCGCAGA	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.1364C>G	chr16.hg19:g.51174769G>C	ENSP00000251020:p.Ala455Gly	132.0	0.0	.		188.0	57.0	.	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	hg19	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	G	11.14	1.550286	0.27739	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.07800	3.16;3.16	5.18	5.18	0.71444	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.048774	0.85682	D	0.000000	T	0.05090	0.0136	N	0.11560	0.145	0.58432	D	0.999992	B	0.17667	0.023	B	0.13407	0.009	T	0.17899	-1.0354	10	0.02654	T	1	.	18.685	0.91560	0.0:0.0:1.0:0.0	.	455	Q9NSC2	SALL1_HUMAN	G	455;358;419	ENSP00000251020:A455G;ENSP00000407914:A358G	ENSP00000251020:A455G	A	-	2	0	SALL1	49732270	1.000000	0.71417	0.817000	0.32601	0.990000	0.78478	6.217000	0.72218	2.386000	0.81285	0.563000	0.77884	GCG	.	.	.	none		0.512	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		C	51174769	G	C	51174769	3	2	112	1	0	0	0	0	1	0	0	0	13823	1087	38	4	2618	4	SALL1	16	51174769	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	29913110	51174769	39179984	57	7246											
IRX5	10265	hgsc.bcm.edu	37	chr16	54966812	54966813	+	Frame_Shift_Del	DEL	GC	GC	-																															gcgaccccgagggccccgaaGcaggttggtggacatgggaa																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr16:54966812_54966813delGC	ENST00000394636.4	+	2	989_990	c.652_653delGC	c.(652-654)gcafs	p.A218fs	IRX5_ENST00000320990.5_Frame_Shift_Del_p.A218fs|CTD-3032H12.2_ENST00000560487.1_lincRNA|IRX5_ENST00000560154.1_Intron|IRX5_ENST00000558597.1_Frame_Shift_Del_p.A152fs			P78411	IRX5_HUMAN	iroquois homeobox 5	218					embryonic cranial skeleton morphogenesis (GO:0048701)|gonad development (GO:0008406)|neuron maturation (GO:0042551)|regulation of heart rate (GO:0002027)|regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|vitamin D binding (GO:0005499)			kidney(3)|large_intestine(6)|lung(4)|prostate(1)	14						GGGCCCCGAAGCAGGTTGGTGG	0.649																																					p.217_218del		Atlas-INDEL	.											.	IRX5	41	.	0			c.651_652del						PASS	.																																			SO:0001589	frameshift_variant	10265	exon2			.	U90309	CCDS10751.1, CCDS58462.1	16q12.2	2011-06-20	2007-07-13		ENSG00000176842	ENSG00000176842		"Homeoboxes / TALE class"	14361	protein-coding gene	gene with protein product		606195					Standard	NM_005853		Approved	IRX-2a	uc002ehv.3	P78411	OTTHUMG00000133201	ENST00000394636.4:c.652_653delGC	chr16.hg19:g.54966812_54966813delGC	ENSP00000378132:p.Ala218fs	172.0	0.0	0		225.0	71.0	0.315556	NM_001252197	H0YMS7|P78416|Q7Z2E1	Frame_Shift_Del	DEL	ENST00000394636.4	hg19	CCDS10751.1																																																																																			.	.	.	none		0.649	IRX5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256911.2			-	54966813	GC	-	54966812	7	5	112	1	0	1	0	1	0	0	0	0	7854	971	34	0	658	0	IRX5	16	54966812	Frame_Shift_Del	DEL	GC	TCGA-BQ-5877-01A-11D-1589-08	3792043	54966812	35387941	58	7247											
SLC6A2	6530	hgsc.bcm.edu	37	chr16	55705980	55705980	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggaccgactgtggccacacCtggaacagccccaactgtac	10	6	10	15	1	0	0	0	0	0	0	0	3	0	2	5	3	4	1	5	3	3	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr16:55705980C>T	ENST00000379906.2	+	3	792	c.537C>T	c.(535-537)acC>acT	p.T179T	SLC6A2_ENST00000414754.3_Silent_p.T179T|SLC6A2_ENST00000567238.1_Silent_p.T74T|SLC6A2_ENST00000566163.1_Silent_p.T179T|SLC6A2_ENST00000561820.1_Silent_p.T179T|SLC6A2_ENST00000219833.8_Silent_p.T179T|SLC6A2_ENST00000568943.1_Silent_p.T179T	NM_001043.3	NP_001034.1	P23975	SC6A2_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 2	179					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)	GTGGCCACACCTGGAACAGCC	0.567																																					p.T179T		Atlas-SNP	.											.	SLC6A2	189	.	0			c.C537T						PASS	.						164	114	131					16																	55705980		2198	4300	6498	SO:0001819	synonymous_variant	6530	exon4			CCACACCTGGAAC		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.537C>T	chr16.hg19:g.55705980C>T		61.0	0.0	.		66.0	15.0	.	NM_001172501	B2R707|B4DX48|Q96KH8	Silent	SNP	ENST00000379906.2	hg19	CCDS10754.1																																																																																			.	.	.	none		0.567	SLC6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256922.2			T	55705980	C	T	55705980	2	4	112	1	0	0	0	0	0	0	0	1	14696	668	24	2		2	SLC6A2	16	55705980	Silent	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	739168	55705980	34648773	59	7248											
MYH4	4622	hgsc.bcm.edu	37	chr17	10366488	10366488	+	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	ctttagctgaaaagtaactcGggacttctctagcagatctg	11	12	9	9	1	2	2	0	1	2	1	4	3	2	3	0	1	3	3	0	1	5	5			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr17:10366488G>A	ENST00000255381.2	-	10	933	c.823C>T	c.(823-825)Cga>Tga	p.R275*	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	275	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						AAAGTAACTCGGGACTTCTCT	0.353																																					p.R275X		Atlas-SNP	.											.	MYH4	349	.	0			c.C823T						PASS	.						76	78	77					17																	10366488		2203	4300	6503	SO:0001587	stop_gained	4622	exon10			TAACTCGGGACTT		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.823C>T	chr17.hg19:g.10366488G>A	ENSP00000255381:p.Arg275*	69.0	0.0	.		103.0	20.0	.	NM_017533		Nonsense_Mutation	SNP	ENST00000255381.2	hg19	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	G	34	5.353656	0.95830	.	.	ENSG00000141048	ENST00000255381	.	.	.	5.37	-0.0246	0.13938	.	0.000000	0.35320	U	0.003296	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.5683	0.76313	0.0:0.0:0.2102:0.7898	.	.	.	.	X	275	.	ENSP00000255381:R275X	R	-	1	2	MYH4	10307213	0.139000	0.22563	0.530000	0.27963	0.997000	0.91878	0.358000	0.20216	0.248000	0.21435	0.650000	0.86243	CGA	.	.	.	none		0.353	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		A	10366488	G	A	10366488	4	1	112	1	0	0	0	0	0	1	0	0	10044	1124	39	1	5120	1	MYH4	17	10366488	Nonsense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08		10366488	70828722	60	7249											
PLD6	201164	hgsc.bcm.edu	37	chr17	17106274	17106274	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacgtactcgtcgtcctccGtgatgagaacattctccctg	7	11	9	14	4	1	2	0	2	1	1	6	3	3	2	3	0	2	2	3	0	2	2	rs139543758		TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr17:17106274G>A	ENST00000321560.3	-	2	594	c.566C>T	c.(565-567)aCg>aTg	p.T189M	RP11-45M22.4_ENST00000427497.3_3'UTR	NM_178836.3	NP_849158.2	Q8N2A8	PLD6_HUMAN	phospholipase D family, member 6	189					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						GTCGTCCTCCGTGATGAGAAC	0.488																																					p.T189M		Atlas-SNP	.											.	PLD6	9	.	0			c.C566T						PASS	.						158	143	148					17																	17106274		2203	4300	6503	SO:0001583	missense	201164	exon2			TCCTCCGTGATGA	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.566C>T	chr17.hg19:g.17106274G>A	ENSP00000317177:p.Thr189Met	82.0	0.0	.		109.0	29.0	.	NM_178836	Q8N5Y1	Missense_Mutation	SNP	ENST00000321560.3	hg19	CCDS11182.1	.	.	.	.	.	.	.	.	.	.	A	10.27	1.302941	0.23736	.	.	ENSG00000179598	ENST00000321560	T	0.24350	1.86	5.6	5.6	0.85130	.	0.181068	0.49916	N	0.000129	T	0.27629	0.0679	M	0.74258	2.255	0.24632	N	0.993617	B	0.29136	0.234	B	0.28784	0.094	T	0.27434	-1.0074	10	0.26408	T	0.33	-6.0E-4	8.0312	0.30465	0.782:0.0:0.218:0.0	.	189	Q8N2A8	PLD6_HUMAN	M	189	ENSP00000317177:T189M	ENSP00000317177:T189M	T	-	2	0	PLD6	17046999	0.974000	0.33945	0.967000	0.41034	0.665000	0.39181	2.538000	0.45710	0.963000	0.38082	-0.254000	0.11334	ACG	.	G|1.000;T|0.000	.	alt		0.488	PLD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131600.2	NM_178836		A	17106274	G	A	17106274	3	1	112	1	0	0	0	0	1	0	0	0	12057	1145	40	1	196	1	PLD6	17	17106274	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	6739786	17106274	64088936	61	7250											
MYO15A	51168	hgsc.bcm.edu	37	chr17	18039921	18039921	+	Missense_Mutation	SNP	T	T	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	tgcactgctgttcagctggcTcatcaccagggtcaacgcgc	7	9	11	14	2	4	0	4	0	0	0	4	0	4	0	1	2	4	5	1	2	1	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr17:18039921T>G	ENST00000205890.5	+	15	5038	c.4700T>G	c.(4699-4701)cTc>cGc	p.L1567R		NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	1567	Myosin motor.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					TTCAGCTGGCTCATCACCAGG	0.622																																					p.L1567R		Atlas-SNP	.											.	MYO15A	268	.	0			c.T4700G						PASS	.						68	73	71					17																	18039921		2194	4278	6472	SO:0001583	missense	51168	exon14			GCTGGCTCATCAC	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.4700T>G	chr17.hg19:g.18039921T>G	ENSP00000205890:p.Leu1567Arg	61.0	0.0	.		71.0	19.0	.	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	hg19	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	T	18.05	3.536870	0.65085	.	.	ENSG00000091536	ENST00000205890	D	0.89939	-2.59	5.7	5.7	0.88788	Myosin head, motor domain (2);	.	.	.	.	D	0.96599	0.8890	H	0.97564	4.03	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.98055	1.0390	9	0.87932	D	0	.	15.97	0.80008	0.0:0.0:0.0:1.0	.	1567	Q9UKN7	MYO15_HUMAN	R	1567	ENSP00000205890:L1567R	ENSP00000205890:L1567R	L	+	2	0	MYO15A	17980646	1.000000	0.71417	0.982000	0.44146	0.669000	0.39330	7.902000	0.87389	2.189000	0.69895	0.459000	0.35465	CTC	.	.	.	none		0.622	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		G	18039921	T	G	18039921	3	3	112	1	0	0	0	0	1	0	0	0	10070	1551	54	5	4750	5	MYO15A	17	18039921	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	933647	18039921	63155289	62	7251											
NSF	4905	hgsc.bcm.edu	37	chr17	44806264	44806264	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttttcaaatcttgtattacaGgctcttctcgttttactgaa	9	19	5	8	1	4	1	1	1	3	0	5	1	4	1	0	1	2	3	0	1	5	8			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr17:44806264G>A	ENST00000398238.4	+	17	1979	c.1872G>A	c.(1870-1872)caG>caA	p.Q624Q	NSF_ENST00000225282.8_Silent_p.Q530Q|NSF_ENST00000575068.1_Silent_p.Q619Q	NM_006178.3	NP_006169.2	P46459	NSF_HUMAN	N-ethylmaleimide-sensitive factor	624					exocytosis (GO:0006887)|plasma membrane fusion (GO:0045026)|positive regulation of receptor recycling (GO:0001921)|potassium ion transport (GO:0006813)|protein transport (GO:0015031)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|syntaxin-1 binding (GO:0017075)			kidney(2)|large_intestine(1)|liver(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	14		Melanoma(429;0.203)	BRCA - Breast invasive adenocarcinoma(9;0.0257)	BRCA - Breast invasive adenocarcinoma(366;0.241)		TTGTATTACAGGCTCTTCTCG	0.323																																					p.Q624Q	Ovarian(25;472 742 1472 36813 50223)	Atlas-SNP	.											.	NSF	27	.	0			c.G1872A						PASS	.						141	120	126					17																	44806264		1805	4065	5870	SO:0001819	synonymous_variant	4905	exon17			ATTACAGGCTCTT		CCDS42354.1	17q21	2010-04-21			ENSG00000073969	ENSG00000073969		"ATPases / AAA-type"	8016	protein-coding gene	gene with protein product	"N-ethylmaleimide-sensitive factor-like protein"	601633				1315316, 8875895	Standard	NM_006178		Approved	SKD2	uc002iku.3	P46459	OTTHUMG00000134315	ENST00000398238.4:c.1872G>A	chr17.hg19:g.44806264G>A		148.0	0.0	.		118.0	40.0	.	NM_006178	A8K2D9|B4DFA2|Q8N6D7|Q9UKZ2	Silent	SNP	ENST00000398238.4	hg19	CCDS42354.1																																																																																			.	.	.	none		0.323	NSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259348.2	NM_006178		A	44806264	G	A	44806264	2	1	112	1	0	0	0	0	0	0	0	1	10678	991	35	2		2	NSF	17	44806264	Silent	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	26766343	44806264	36388946	63	7252											
USP32	84669	hgsc.bcm.edu	37	chr17	58348812	58348812	+	Missense_Mutation	SNP	T	T	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	ccttcaataaccaatagcgtTtctcaagatcaatgatgtct	13	13	5	10	1	4	2	3	1	2	1	5	2	4	2	2	0	2	1	2	0	6	4			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr17:58348812T>G	ENST00000300896.4	-	6	796	c.602A>C	c.(601-603)aAa>aCa	p.K201T	USP32_ENST00000393003.3_Missense_Mutation_p.K201T	NM_032582.3	NP_115971.2	Q8NFA0	UBP32_HUMAN	ubiquitin specific peptidase 32	201					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			NS(3)|breast(5)|endometrium(5)|kidney(4)|large_intestine(12)|liver(1)|lung(24)|pancreas(1)|prostate(3)|skin(3)|urinary_tract(1)	62	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			CCAATAGCGTTTCTCAAGATC	0.398																																					p.K201T		Atlas-SNP	.											.	USP32	128	.	0			c.A602C						PASS	.						137	119	125					17																	58348812		2203	4300	6503	SO:0001583	missense	84669	exon6			TAGCGTTTCTCAA	AF533230	CCDS32697.1	17q23.3	2013-01-10	2005-08-08		ENSG00000170832	ENSG00000170832		"Ubiquitin-specific peptidases", "EF-hand domain containing"	19143	protein-coding gene	gene with protein product		607740	"ubiquitin specific protease 32"			12838346	Standard	NM_032582		Approved	NY-REN-60, USP10	uc002iyo.1	Q8NFA0		ENST00000300896.4:c.602A>C	chr17.hg19:g.58348812T>G	ENSP00000300896:p.Lys201Thr	81.0	0.0	.		138.0	42.0	.	NM_032582	Q7Z5T3|Q9BX85|Q9Y591	Missense_Mutation	SNP	ENST00000300896.4	hg19	CCDS32697.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.820035	0.90873	.	.	ENSG00000170832	ENST00000300896;ENST00000393003	T;T	0.68765	-0.35;-0.35	5.35	5.35	0.76521	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.79811	0.4510	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	0.993;1.0	D;D	0.85130	0.968;0.997	T	0.82137	-0.0606	10	0.87932	D	0	.	15.332	0.74219	0.0:0.0:0.0:1.0	.	201;201	Q7Z5T3;Q8NFA0	.;UBP32_HUMAN	T	201	ENSP00000300896:K201T;ENSP00000376727:K201T	ENSP00000300896:K201T	K	-	2	0	USP32	55703594	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.983000	0.88140	2.014000	0.59158	0.460000	0.39030	AAA	.	.	.	none		0.398	USP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449235.2	NM_032582		G	58348812	T	G	58348812	3	3	112	1	0	0	0	0	1	0	0	0	17075	1841	64	5	4328	5	USP32	17	58348812	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	13542548	58348812	22846398	64	7253											
SPHK1	8877	hgsc.bcm.edu	37	chr17	74383269	74383269	+	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	cctctcactggacagtggtgCccgacgaggactttgtgcta	7	10	12	12	2	1	0	1	0	1	0	2	4	1	2	2	3	2	1	2	3	1	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr17:74383269C>G	ENST00000545180.1	+	8	1566	c.757C>G	c.(757-759)Ccc>Gcc	p.P253A	SPHK1_ENST00000590959.1_Missense_Mutation_p.P267A|SPHK1_ENST00000323374.4_Missense_Mutation_p.P339A|SPHK1_ENST00000392496.3_Missense_Mutation_p.P253A|SPHK1_ENST00000592299.1_Missense_Mutation_p.P253A			Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1	253					'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)	GACAGTGGTGCCCGACGAGGA	0.627																																					p.P339A	GBM(90;966 1307 27369 33775 44498)	Atlas-SNP	.											.	SPHK1	24	.	0			c.C1015G						PASS	.						57	43	48					17																	74383269		2203	4300	6503	SO:0001583	missense	8877	exon6			GTGGTGCCCGACG	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.757C>G	chr17.hg19:g.74383269C>G	ENSP00000440970:p.Pro253Ala	24.0	0.0	.		37.0	8.0	.	NM_182965	Q8N632|Q96GK1|Q9HD92|Q9NY70|Q9NYL3	Missense_Mutation	SNP	ENST00000545180.1	hg19	CCDS45785.1	.	.	.	.	.	.	.	.	.	.	C	17.37	3.373733	0.61624	.	.	ENSG00000176170	ENST00000545180;ENST00000323374;ENST00000392496;ENST00000543830	T;T;T	0.13778	2.56;2.56;2.56	5.08	5.08	0.68730	.	0.252689	0.40144	N	0.001161	T	0.17746	0.0426	M	0.70595	2.14	0.37430	D	0.914003	B;P;P	0.51351	0.175;0.756;0.944	B;B;P	0.45343	0.088;0.374;0.477	T	0.10497	-1.0627	10	0.06236	T	0.91	-5.9695	13.4531	0.61182	0.1567:0.8433:0.0:0.0	.	339;267;253	Q9NYA1-2;Q96GK1;Q9NYA1	.;.;SPHK1_HUMAN	A	253;339;253;252	ENSP00000440970:P253A;ENSP00000313681:P339A;ENSP00000376285:P253A	ENSP00000313681:P339A	P	+	1	0	SPHK1	71894864	0.949000	0.32298	0.993000	0.49108	0.818000	0.46254	2.111000	0.41883	2.346000	0.79739	0.563000	0.77884	CCC	.	.	.	none		0.627	SPHK1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450113.1	NM_182965, NM_021972		G	74383269	C	G	74383269	3	3	112	1	0	0	0	0	1	0	0	0	15058	739	26	4	1079	4	SPHK1	17	74383269	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	16034457	74383269	6811941	65	7254											
DCC	1630	hgsc.bcm.edu	37	chr18	51025752	51025752	+	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	tagcagcgaggaggcaccaaGcagaaccatccccacagctt	13	4	10	14	1	0	1	0	0	0	1	1	3	1	2	4	2	5	4	4	2	3	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr18:51025752G>T	ENST00000442544.2	+	27	4599	c.3983G>T	c.(3982-3984)aGc>aTc	p.S1328I	DCC_ENST00000581580.1_Missense_Mutation_p.S961I|RP11-671P2.1_ENST00000582064.1_RNA	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	1328					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)		GAGGCACCAAGCAGAACCATC	0.537																																					p.S1328I		Atlas-SNP	.											.	DCC	360	.	0			c.G3983T						PASS	.						232	178	196					18																	51025752		2203	4300	6503	SO:0001583	missense	1630	exon27			CACCAAGCAGAAC	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.3983G>T	chr18.hg19:g.51025752G>T	ENSP00000389140:p.Ser1328Ile	142.0	0.0	.		96.0	53.0	.	NM_005215		Missense_Mutation	SNP	ENST00000442544.2	hg19	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	G	14.17	2.454949	0.43634	.	.	ENSG00000187323	ENST00000442544	T	0.46819	0.86	6.17	6.17	0.99709	Neogenin, C-terminal (1);	0.168925	0.51477	D	0.000094	T	0.53802	0.1819	L	0.47716	1.5	0.54753	D	0.999981	P	0.49696	0.927	P	0.48952	0.596	T	0.46133	-0.9213	10	0.44086	T	0.13	-9.5941	19.6509	0.95805	0.0:0.0:1.0:0.0	.	1328	P43146	DCC_HUMAN	I	1328	ENSP00000389140:S1328I	ENSP00000389140:S1328I	S	+	2	0	DCC	49279750	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	7.871000	0.87180	2.941000	0.99782	0.655000	0.94253	AGC	.	.	.	none		0.537	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		T	51025752	G	T	51025752	3	4	112	1	0	0	0	0	1	0	0	0	4284	971	34	4	4089	4	DCC	18	51025752	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08		51025752	27051496	66	7255											
BTBD2	55643	hgsc.bcm.edu	37	chr19	1986877	1986877	+	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	acgttgggcagcacctccacCggctccttgaacatgacgcg	8	7	11	15	4	0	2	0	2	0	0	2	2	2	2	4	2	2	4	4	2	1	2			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr19:1986877C>G	ENST00000255608.4	-	8	1384	c.1368G>C	c.(1366-1368)ccG>ccC	p.P456P	AC005306.3_ENST00000587498.1_RNA	NM_017797.3	NP_060267.2	Q9BX70	BTBD2_HUMAN	BTB (POZ) domain containing 2	456						cytoplasmic mRNA processing body (GO:0000932)				endometrium(5)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)	12		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)		GCACCTCCACCGGCTCCTTGA	0.632																																					p.P456P		Atlas-SNP	.											.	BTBD2	31	.	0			c.G1368C						PASS	.						52	54	53					19																	1986877		2203	4300	6503	SO:0001819	synonymous_variant	55643	exon8			CTCCACCGGCTCC	AF355797	CCDS12078.1	19p13.3	2013-10-02			ENSG00000133243	ENSG00000133243		"BTB/POZ domain containing"	15504	protein-coding gene	gene with protein product		608531				11179693	Standard	XM_005259593		Approved		uc002lup.1	Q9BX70	OTTHUMG00000180017	ENST00000255608.4:c.1368G>C	chr19.hg19:g.1986877C>G		59.0	0.0	.		62.0	12.0	.	NM_017797	O60418|O75248|Q4VBZ1|Q6IAC5|Q7Z5W0|Q96SX8|Q9NPS1|Q9NX81	Silent	SNP	ENST00000255608.4	hg19	CCDS12078.1																																																																																			.	.	.	none		0.632	BTBD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449300.2			G	1986877	C	G	1986877	2	3	112	1	0	0	0	0	0	0	0	1	1545	639	23	4		4	BTBD2	19	1986877	Silent	SNP	C	TCGA-BQ-5877-01A-11D-1589-08		1986877	57142106	67	7256											
SLC44A2	57153	hgsc.bcm.edu	37	chr19	10745556	10745556	+	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	cacttacggcagacctggttGgcctttagtgagtcacagtc	8	11	11	11	1	1	2	1	1	0	1	2	2	1	2	2	3	1	2	2	3	2	4			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr19:10745556G>C	ENST00000335757.5	+	11	1324	c.948G>C	c.(946-948)ttG>ttC	p.L316F	SLC44A2_ENST00000407327.4_Missense_Mutation_p.L314F|SLC44A2_ENST00000586078.1_Missense_Mutation_p.L316F			Q8IWA5	CTL2_HUMAN	solute carrier family 44 (choline transporter), member 2	316					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)	AGACCTGGTTGGCCTTTAGTG	0.597																																					p.L316F		Atlas-SNP	.											.	SLC44A2	56	.	0			c.G948C						PASS	.						151	140	144					19																	10745556		2203	4300	6503	SO:0001583	missense	57153	exon11			CTGGTTGGCCTTT	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.948G>C	chr19.hg19:g.10745556G>C	ENSP00000336888:p.Leu316Phe	166.0	0.0	.		206.0	58.0	.	NM_020428	B2RBB1|B3KNH3|B4DFJ0|F2Q9D7|Q658V1|Q658Z2|Q6PJV7|Q8N2F0|Q9NY68	Missense_Mutation	SNP	ENST00000335757.5	hg19	CCDS12245.1	.	.	.	.	.	.	.	.	.	.	G	13.24	2.177297	0.38413	.	.	ENSG00000129353	ENST00000407327;ENST00000335757;ENST00000380614	T;T	0.14266	2.52;2.53	5.46	3.27	0.37495	.	0.532611	0.23295	N	0.049756	T	0.17534	0.0421	L	0.58101	1.795	0.45161	D	0.998171	B;B;B	0.20887	0.049;0.013;0.014	B;B;B	0.35727	0.209;0.04;0.16	T	0.03175	-1.1064	10	0.30854	T	0.27	-23.7844	9.2861	0.37758	0.0773:0.0:0.7775:0.1453	.	316;316;314	Q8IWA5-2;Q8IWA5;Q8IWA5-3	.;CTL2_HUMAN;.	F	314;316;316	ENSP00000385135:L314F;ENSP00000336888:L316F	ENSP00000336888:L316F	L	+	3	2	SLC44A2	10606556	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.740000	0.62087	0.641000	0.30601	0.557000	0.71058	TTG	.	.	.	none		0.597	SLC44A2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452045.1			C	10745556	G	C	10745556	3	2	112	1	0	0	0	0	1	0	0	0	14649	1339	47	4	1025	4	SLC44A2	19	10745556	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	8758679	10745556	48383427	68	7257											
ZNF823	55552	hgsc.bcm.edu	37	chr19	11833231	11833231	+	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	tcatgtgacttcgaaagctcGagctatgagataacactttc	12	12	8	9	2	1	2	1	2	0	1	4	5	1	2	0	0	3	2	0	0	3	4			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr19:11833231G>C	ENST00000341191.6	-	4	1271	c.1118C>G	c.(1117-1119)tCg>tGg	p.S373W	ZNF823_ENST00000545749.1_Missense_Mutation_p.S191W	NM_001080493.2	NP_001073962.1	P16415	ZN823_HUMAN	zinc finger protein 823	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(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)	26						TCGAAAGCTCGAGCTATGAGA	0.423										HNSCC(68;0.2)																											p.S373W		Atlas-SNP	.											.	ZNF823	104	.	0			c.C1118G						PASS	.						109	114	112					19																	11833231		2203	4300	6503	SO:0001583	missense	55552	exon4			AAGCTCGAGCTAT	X51760	CCDS45981.1	19p13.2	2013-01-08			ENSG00000197933	ENSG00000197933		"Zinc fingers, C2H2-type", "-"	30936	protein-coding gene	gene with protein product	"ZFP 36 for a zinc finger protein"						Standard	XM_006722789		Approved	HSZFP36	uc002msm.2	P16415	OTTHUMG00000156528	ENST00000341191.6:c.1118C>G	chr19.hg19:g.11833231G>C	ENSP00000340683:p.Ser373Trp	126.0	0.0	.		154.0	47.0	.	NM_001080493	A0PJL4|B7Z8D4|Q6P4A9	Missense_Mutation	SNP	ENST00000341191.6	hg19	CCDS45981.1	.	.	.	.	.	.	.	.	.	.	N	11.84	1.757736	0.31137	.	.	ENSG00000197933	ENST00000545749;ENST00000341191;ENST00000431998	T;T;T	0.08282	3.11;3.11;3.11	0.632	0.632	0.17705	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.30293	0.0760	M	0.90425	3.115	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.03384	-1.1042	9	0.87932	D	0	.	7.1241	0.25461	1.0E-4:0.0:0.9999:0.0	.	373	P16415	ZN823_HUMAN	W	191;373;329	ENSP00000440162:S191W;ENSP00000340683:S373W;ENSP00000410654:S329W	ENSP00000340683:S373W	S	-	2	0	ZNF823	11694231	0.000000	0.05858	0.001000	0.08648	0.423000	0.31445	-0.236000	0.09003	0.618000	0.30179	0.298000	0.19748	TCG	.	.	.	none		0.423	ZNF823-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344516.2	NM_001080493		C	11833231	G	C	11833231	3	2	112	1	0	0	0	0	1	0	0	0	18191	1059	37	4	718	4	ZNF823	19	11833231	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	1087675	11833231	47295752	69	7258											
GRAMD1A	57655	hgsc.bcm.edu	37	chr19	35500801	35500802	+	Frame_Shift_Ins	INS	-	-	CA																															acttcctcagatgctgagccINSccacttataagcagcgtaat																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr19:35500801_35500802insCA	ENST00000317991.5	+	4	442_443	c.250_251insCA	c.(250-252)cccfs	p.P84fs	GRAMD1A_ENST00000598073.1_3'UTR|GRAMD1A_ENST00000424536.2_Frame_Shift_Ins_p.P84fs|GRAMD1A_ENST00000504615.2_5'UTR|GRAMD1A_ENST00000599564.1_Frame_Shift_Ins_p.P171fs|GRAMD1A_ENST00000411896.2_Frame_Shift_Ins_p.P77fs	NM_020895.3	NP_065946.2	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A	84						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)			GATGCTGAGCCCCACTTATAAG	0.559																																					p.P84fs		Atlas-INDEL	.											.	GRAMD1A	39	.	0			c.250_251insCA						PASS	.																																			SO:0001589	frameshift_variant	57655	exon4			.	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		Exception_encountered	chr19.hg19:g.35500801_35500802insCA	ENSP00000441032:p.Pro84fs	142.0	0.0	0		147.0	50.0	0.340136	NM_020895	A6NKY7|Q8NC77|Q9P1Z5	Frame_Shift_Ins	INS	ENST00000317991.5	hg19	CCDS42546.1																																																																																			.	.	.	none		0.559	GRAMD1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461557.1	NM_020895		CA	35500802	-	CA	35500801	7	5	112	1	0	1	1	0	0	0	0	0	6754	623	22	0	264	0	GRAMD1A	19	35500801	Frame_Shift_Ins	INS	-	TCGA-BQ-5877-01A-11D-1589-08	23667570	35500801	23628182	70	7259											
ZFP82	284406	hgsc.bcm.edu	37	chr19	36883897	36883897	+	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	acattccttacatttataagGtttctcaccaatatgaatac	14	15	3	9	0	1	1	1	1	1	0	3	1	2	1	2	1	2	1	2	1	7	8	rs143115887		TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr19:36883897G>T	ENST00000392161.3	-	5	1587	c.1345C>A	c.(1345-1347)Cct>Act	p.P449T	ZFP82_ENST00000392171.1_Missense_Mutation_p.P449T	NM_133466.2	NP_597723.1	Q8N141	ZFP82_HUMAN	ZFP82 zinc finger protein	449					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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.P449S(1)		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						CATTTATAAGGTTTCTCACCA	0.413																																					p.P449T		Atlas-SNP	.											ZFP82,upper_arm,malignant_melanoma,0,1	ZFP82	71	.	1	Substitution - Missense(1)	skin(1)	c.C1345A						PASS	.						92	90	91					19																	36883897		2203	4300	6503	SO:0001583	missense	284406	exon5			TATAAGGTTTCTC	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.1345C>A	chr19.hg19:g.36883897G>T	ENSP00000431265:p.Pro449Thr	164.0	0.0	.		170.0	54.0	.	NM_133466	Q8NC63|Q8TF53	Missense_Mutation	SNP	ENST00000392161.3	hg19	CCDS12493.1	.	.	.	.	.	.	.	.	.	.	G	18.05	3.536339	0.65085	.	.	ENSG00000181007	ENST00000392161;ENST00000392171	T;T	0.16897	2.31;2.31	4.2	4.2	0.49525	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.41294	D	0.000902	T	0.42698	0.1214	M	0.79343	2.45	0.49915	D	0.999832	D	0.89917	1.0	D	0.97110	1.0	T	0.44003	-0.9356	10	0.72032	D	0.01	.	14.447	0.67359	0.0:0.0:1.0:0.0	.	449	Q8N141	ZFP82_HUMAN	T	449	ENSP00000431265:P449T;ENSP00000446080:P449T	ENSP00000431265:P449T	P	-	1	0	ZFP82	41575737	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.542000	0.82095	2.352000	0.79861	0.591000	0.81541	CCT	.	.	.	alt		0.413	ZFP82-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109552.2	NM_133466		T	36883897	G	T	36883897	3	4	112	1	0	0	0	0	1	0	0	0	17665	1261	44	4	257	4	ZFP82	19	36883897	Missense_Mutation	SNP	G	TCGA-BQ-5877-01A-11D-1589-08	1383096	36883897	22245086	71	7260											
CPT1C	126129	hgsc.bcm.edu	37	chr19	50200612	50200612	+	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	ctcaccggtgtgtttcctgcCagccccctcagttggctttt	3	14	9	15	1	2	0	2	0	0	0	3	0	3	0	5	2	2	3	5	2	0	4			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr19:50200612C>A	ENST00000392518.4	+	4	543	c.171C>A	c.(169-171)gcC>gcA	p.A57A	CPT1C_ENST00000354199.5_Silent_p.A57A|CPT1C_ENST00000405931.2_Silent_p.A57A|CPT1C_ENST00000323446.5_Silent_p.A57A|CPT1C_ENST00000598293.1_Silent_p.A57A	NM_001199752.1	NP_001186681.1	Q8TCG5	CPT1C_HUMAN	carnitine palmitoyltransferase 1C	57					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)		TGTTTCCTGCCAGCCCCCTCA	0.542																																					p.A57A		Atlas-SNP	.											.	CPT1C	93	.	0			c.C171A						PASS	.						194	139	158					19																	50200612		2203	4300	6503	SO:0001819	synonymous_variant	126129	exon4			TCCTGCCAGCCCC	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.171C>A	chr19.hg19:g.50200612C>A		87.0	0.0	.		101.0	27.0	.	NM_001199752	A8K0Z8|Q5K6N5|Q8N6Q9|Q8NDS6|Q8TE84	Silent	SNP	ENST00000392518.4	hg19	CCDS12779.1																																																																																			.	.	.	none		0.542	CPT1C-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465873.1	NM_152359		A	50200612	C	A	50200612	2	1	112	1	0	0	0	0	0	0	0	1	3835	581	21	4		4	CPT1C	19	50200612	Silent	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	13316715	50200612	8928371	72	7261											
ZNF613	79898	hgsc.bcm.edu	37	chr19	52447643	52447643	+	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	tccttccttcatgccaagcaTgaacaatttcataatgaaat	14	13	4	10	0	2	2	2	2	0	0	4	2	4	2	3	0	3	1	3	0	5	4			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr19:52447643T>A	ENST00000293471.6	+	6	1186	c.507T>A	c.(505-507)caT>caA	p.H169Q	ZNF613_ENST00000391794.4_Missense_Mutation_p.H133Q	NM_001031721.3	NP_001026891.2	Q6PF04	ZN613_HUMAN	zinc finger protein 613	169					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	19		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.0183)		ATGCCAAGCATGAACAATTTC	0.348																																					p.H169Q		Atlas-SNP	.											.	ZNF613	62	.	0			c.T507A						PASS	.						94	102	99					19																	52447643		2203	4300	6503	SO:0001583	missense	79898	exon6			CAAGCATGAACAA	AK027565	CCDS12844.1, CCDS33089.1	19q13.41	2013-01-08						"Zinc fingers, C2H2-type", "-"	25827	protein-coding gene	gene with protein product						12477932	Standard	NM_001031721		Approved	FLJ13590	uc002pxz.2	Q6PF04		ENST00000293471.6:c.507T>A	chr19.hg19:g.52447643T>A	ENSP00000293471:p.His169Gln	203.0	0.0	.		196.0	77.0	.	NM_001031721	Q96SS9	Missense_Mutation	SNP	ENST00000293471.6	hg19	CCDS33089.1	.	.	.	.	.	.	.	.	.	.	T	10.57	1.386951	0.25031	.	.	ENSG00000176024	ENST00000293471;ENST00000391794	T;T	0.28454	1.61;1.61	2.9	1.88	0.25563	.	0.429945	0.17365	N	0.176876	T	0.18882	0.0453	N	0.24115	0.695	0.25401	N	0.988446	P	0.51791	0.948	B	0.42555	0.391	T	0.08973	-1.0696	10	0.62326	D	0.03	.	6.0884	0.19980	0.0:0.1332:0.0:0.8668	.	169	Q6PF04	ZN613_HUMAN	Q	169;133	ENSP00000293471:H169Q;ENSP00000375671:H133Q	ENSP00000293471:H169Q	H	+	3	2	ZNF613	57139455	0.003000	0.15002	0.186000	0.23195	0.107000	0.19398	0.002000	0.13061	0.531000	0.28639	0.528000	0.53228	CAT	.	.	.	none		0.348	ZNF613-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461104.2	NM_024840		A	52447643	T	A	52447643	3	1	112	1	0	0	0	0	1	0	0	0	18050	1461	51	5	521	5	ZNF613	19	52447643	Missense_Mutation	SNP	T	TCGA-BQ-5877-01A-11D-1589-08	2247031	52447643	6681340	73	7262											
CPXM1	56265	hgsc.bcm.edu	37	chr20	2775062	2775063	+	Frame_Shift_Ins	INS	-	-	A																															tggggtcagcagacgccaatINSaatccccgccccacgctgag																										TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr20:2775062_2775063insA	ENST00000380605.2	-	14	2042_2043	c.1978_1979insT	c.(1978-1980)tatfs	p.Y660fs		NM_001184699.1|NM_019609.4	NP_001171628.1|NP_062555.1	Q96SM3	CPXM1_HUMAN	carboxypeptidase X (M14 family), member 1	660					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						CAGACGCCAATAATCCCCGCCC	0.599																																					p.Y660fs		Atlas-INDEL	.											.	CPXM1	107	.	0			c.1979_1980insT						PASS	.																																			SO:0001589	frameshift_variant	56265	exon14			.	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.1979dupT	chr20.hg19:g.2775064_2775064dupA	ENSP00000369979:p.Tyr660fs	66.0	0.0	0		73.0	28.0	0.383562	NM_019609	Q6P4G8|Q6UW65|Q9NUB5	Frame_Shift_Ins	INS	ENST00000380605.2	hg19	CCDS13033.1																																																																																			.	.	.	none		0.599	CPXM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077643.2	NM_019609		A	2775063	-	A	2775062	7	5	112	1	0	1	1	0	0	0	0	0	3839	1406	49	0	229	0	CPXM1	20	2775062	Frame_Shift_Ins	INS	-	TCGA-BQ-5877-01A-11D-1589-08		2775062	60250458	74	7263											
ZNF341	84905	hgsc.bcm.edu	37	chr20	32357951	32357951	+	Missense_Mutation	SNP	A	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	aaagctcgacacatttctggAgcacatcaagagccaccagg	14	6	9	12	1	2	1	1	0	1	1	3	3	2	2	2	2	3	2	2	2	2	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr20:32357951A>C	ENST00000375200.1	+	10	1840	c.1475A>C	c.(1474-1476)gAg>gCg	p.E492A	ZNF341_ENST00000342427.2_Missense_Mutation_p.E485A	NM_001282933.1	NP_001269862.1	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	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)			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						ACATTTCTGGAGCACATCAAG	0.597																																					p.E485A		Atlas-SNP	.											.	ZNF341	73	.	0			c.A1454C						PASS	.						69	58	61					20																	32357951		2203	4300	6503	SO:0001583	missense	84905	exon10			TTCTGGAGCACAT	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.1475A>C	chr20.hg19:g.32357951A>C	ENSP00000364346:p.Glu492Ala	40.0	0.0	.		43.0	15.0	.	NM_032819	A2RUF4|B2RXE5|B7ZM09|Q5JXM8|Q96ST5	Missense_Mutation	SNP	ENST00000375200.1	hg19		.	.	.	.	.	.	.	.	.	.	A	25.6	4.651504	0.88056	.	.	ENSG00000131061	ENST00000342427;ENST00000375200	T;T	0.31247	1.5;1.5	5.35	5.35	0.76521	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.051359	0.85682	D	0.000000	T	0.30696	0.0773	N	0.17872	0.535	0.53005	D	0.999962	P;P;P	0.50819	0.792;0.939;0.925	B;P;P	0.53809	0.257;0.735;0.616	T	0.03608	-1.1020	10	0.13470	T	0.59	-36.6794	15.6282	0.76878	1.0:0.0:0.0:0.0	.	433;492;485	Q504V9;Q9BYN7;Q9BYN7-2	.;ZN341_HUMAN;.	A	485;492	ENSP00000344308:E485A;ENSP00000364346:E492A	ENSP00000344308:E485A	E	+	2	0	ZNF341	31821612	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.898000	0.92538	2.152000	0.67230	0.443000	0.29094	GAG	.	.	.	none		0.597	ZNF341-201	KNOWN	basic	protein_coding	protein_coding				C	32357951	A	C	32357951	3	2	112	1	0	0	0	0	1	0	0	0	17869	304	11	5	1492	5	ZNF341	20	32357951	Missense_Mutation	SNP	A	TCGA-BQ-5877-01A-11D-1589-08	29582889	32357951	30667569	75	7264											
CECR6	27439	hgsc.bcm.edu	37	chr22	17600589	17600589	+	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	cgccagcaagggcacgtccaCcaggcagccgcccagcaggc	9	1	13	18	3	0	0	0	0	0	0	1	0	1	0	5	3	3	4	5	3	1	0			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr22:17600589C>G	ENST00000331437.3	-	1	1554	c.1429G>C	c.(1429-1431)Gtg>Ctg	p.V477L	CECR6_ENST00000399875.1_Missense_Mutation_p.V122L|AC006946.15_ENST00000441544.1_5'Flank	NM_031890.3	NP_114096.1	Q9BXQ6	CECR6_HUMAN	cat eye syndrome chromosome region, candidate 6	477										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)		GGCACGTCCACCAGGCAGCCG	0.697																																					p.V477L		Atlas-SNP	.											CECR6,colon,carcinoma,0,1	CECR6	11	.	0			c.G1429C						PASS	.						4	4	4					22																	17600589		2023	4042	6065	SO:0001583	missense	27439	exon1			CGTCCACCAGGCA	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.1429G>C	chr22.hg19:g.17600589C>G	ENSP00000329318:p.Val477Leu	1.0	0.0	.		5.0	2.0	.	NM_031890	A8MYY1	Missense_Mutation	SNP	ENST00000331437.3	hg19	CCDS13740.1	.	.	.	.	.	.	.	.	.	.	C	13.11	2.137885	0.37728	.	.	ENSG00000183307	ENST00000399875;ENST00000331437	.	.	.	4.32	4.32	0.51571	.	0.000000	0.53938	U	0.000050	T	0.47820	0.1466	N	0.20986	0.625	0.40994	D	0.984875	P	0.35745	0.518	B	0.39531	0.302	T	0.56571	-0.7957	9	0.59425	D	0.04	.	14.668	0.68924	0.0:1.0:0.0:0.0	.	477	Q9BXQ6	CECR6_HUMAN	L	122;477	.	ENSP00000329318:V477L	V	-	1	0	CECR6	15980589	1.000000	0.71417	1.000000	0.80357	0.501000	0.33797	4.385000	0.59613	2.116000	0.64780	0.462000	0.41574	GTG	.	.	.	none		0.697	CECR6-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000075359.4	NM_031890		G	17600589	C	G	17600589	3	3	112	1	0	0	0	0	1	0	0	0	3210	507	18	4	311	4	CECR6	22	17600589	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08		17600589	33703977	76	7265											
PPM1F	9647	hgsc.bcm.edu	37	chr22	22285579	22285579	+	Frame_Shift_Del	DEL	T	T	-																															ctgtccctgctgtaccaaaaTgacctgggaatccccgagcc																								rs376795506		TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr22:22285579delT	ENST00000263212.5	-	6	937	c.832delA	c.(832-834)attfs	p.I278fs	PPM1F_ENST00000407142.1_Frame_Shift_Del_p.I110fs|PPM1F_ENST00000397495.4_Frame_Shift_Del_p.I278fs|PPM1F_ENST00000538191.1_Frame_Shift_Del_p.I174fs	NM_014634.3	NP_055449.1	P49593	PPM1F_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1F	278					cellular response to drug (GO:0035690)|histone dephosphorylation (GO:0016576)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of growth (GO:0045927)|positive regulation of stress fiber assembly (GO:0051496)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	calmodulin-dependent protein phosphatase activity (GO:0033192)|metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	12	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.155)		TGTACCAAAATGACCTGGGAA	0.637																																					p.I278fs		Atlas-INDEL	.											.	PPM1F	34	.	0			c.833delT						PASS	.						124	98	107					22																	22285579		2203	4300	6503	SO:0001589	frameshift_variant	9647	exon6			.	D13640	CCDS13796.1	22q11.22	2012-04-17	2010-03-05		ENSG00000100034	ENSG00000100034	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	19388	protein-coding gene	gene with protein product	"partner of PIX 2", "Ca(2+)/calmodulin-dependent protein kinase phosphatase"		"protein phosphatase 1F (PP2C domain containing)"			11864573, 11559703	Standard	NM_014634		Approved	FEM-2, KIAA0015, POPX2, CaMKPase, CAMKP	uc002zvp.2	P49593	OTTHUMG00000150835	ENST00000263212.5:c.832delA	chr22.hg19:g.22285579delT	ENSP00000263212:p.Ile278fs	109.0	0.0	0		90.0	41.0	0.455556	NM_014634	A8K6G3|B7Z2C3|Q96PM2	Frame_Shift_Del	DEL	ENST00000263212.5	hg19	CCDS13796.1																																																																																			.	.	.	none		0.637	PPM1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320267.2	NM_014634		-	22285579	T	-	22285579	7	5	112	1	0	1	0	1	0	0	0	0	12349	1464	51	0	544	0	PPM1F	22	22285579	Frame_Shift_Del	DEL	T	TCGA-BQ-5877-01A-11D-1589-08	4684990	22285579	29018987	77	7266											
CABIN1	23523	hgsc.bcm.edu	37	chr22	24447376	24447376	+	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	gctgcgaaaaaagaggcaagCgctgattgtgcgggagaagg	13	5	17	6	3	0	3	0	1	0	2	0	5	0	3	0	3	3	3	0	3	5	1			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr22:24447376C>T	ENST00000398319.2	+	8	1131	c.746C>T	c.(745-747)gCg>gTg	p.A249V	CABIN1_ENST00000263119.5_Missense_Mutation_p.A249V|CABIN1_ENST00000405822.2_Intron	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	249					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						AAGAGGCAAGCGCTGATTGTG	0.542																																					p.A249V		Atlas-SNP	.											.	CABIN1	153	.	0			c.C746T						PASS	.						117	102	107					22																	24447376		2203	4300	6503	SO:0001583	missense	23523	exon8			GGCAAGCGCTGAT	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.746C>T	chr22.hg19:g.24447376C>T	ENSP00000381364:p.Ala249Val	68.0	0.0	.		58.0	25.0	.	NM_001199281	G5E9F3|Q6PHY0|Q9Y460	Missense_Mutation	SNP	ENST00000398319.2	hg19	CCDS13823.1	.	.	.	.	.	.	.	.	.	.	C	18.70	3.679191	0.68042	.	.	ENSG00000099991	ENST00000454754;ENST00000263119;ENST00000445422;ENST00000398319;ENST00000536026	T;T;T;T	0.63096	0.33;-0.02;0.33;-0.02	5.32	5.32	0.75619	.	0.105434	0.64402	D	0.000006	T	0.73969	0.3655	L	0.56769	1.78	0.80722	D	1	D;D;D	0.71674	0.986;0.963;0.998	P;B;P	0.61132	0.457;0.373;0.884	T	0.72418	-0.4300	10	0.40728	T	0.16	.	18.4214	0.90591	0.0:1.0:0.0:0.0	.	204;249;249	C9J068;F5H5W5;Q9Y6J0	.;.;CABIN_HUMAN	V	204;249;204;249;249	ENSP00000394209:A204V;ENSP00000263119:A249V;ENSP00000412389:A204V;ENSP00000381364:A249V	ENSP00000263119:A249V	A	+	2	0	CABIN1	22777376	1.000000	0.71417	0.979000	0.43373	0.279000	0.26890	6.486000	0.73629	2.666000	0.90696	0.551000	0.68910	GCG	.	.	.	none		0.542	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295		T	24447376	C	T	24447376	3	4	112	1	0	0	0	0	1	0	0	0	2530	768	27	1	772	1	CABIN1	22	24447376	Missense_Mutation	SNP	C	TCGA-BQ-5877-01A-11D-1589-08	2161797	24447376	26857190	78	7267											
NF2	4771	hgsc.bcm.edu	37	chr22	30050709	30050709	+	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	cccaagaggaattgcttccaAaaagggtaagagattaaatt	17	9	9	6	0	0	2	0	0	0	2	1	4	1	3	2	2	1	2	2	2	7	5			TCGA-BQ-5877-01A-11D-1589-08	TCGA-BQ-5877-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7377aeb8-7349-4771-96c7-26f8e493de59	0a320a35-d24f-4c14-9e58-8ac73b6a4c03	g.chr22:30050709A>T	ENST00000338641.4	+	5	952	c.511A>T	c.(511-513)Aaa>Taa	p.K171*	NF2_ENST00000347330.5_Intron|NF2_ENST00000361452.4_Nonsense_Mutation_p.K130*|NF2_ENST00000413209.2_Intron|NF2_ENST00000334961.7_Nonsense_Mutation_p.K88*|NF2_ENST00000397789.3_Nonsense_Mutation_p.K171*|NF2_ENST00000403435.1_Nonsense_Mutation_p.K171*|NF2_ENST00000403999.3_Nonsense_Mutation_p.K171*|NF2_ENST00000361676.4_Nonsense_Mutation_p.K129*|NF2_ENST00000353887.4_Nonsense_Mutation_p.K88*|NF2_ENST00000361166.4_Nonsense_Mutation_p.K171*	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	171	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(3)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						ATTGCTTCCAAAAAGGGTAAG	0.423			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																												p.K171X		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	.	NF2	1312	.	3	Unknown(3)	large_intestine(1)|stomach(1)|central_nervous_system(1)	c.A511T						PASS	.						113	114	114					22																	30050709		2203	4300	6503	SO:0001587	stop_gained	4771	exon5	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	CTTCCAAAAAGGG	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"A-kinase anchor proteins"	7773	protein-coding gene	gene with protein product	"moesin-ezrin-radixin like", "schwannomin"	607379	"neurofibromin 2 (bilateral acoustic neuroma)"			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.511A>T	chr22.hg19:g.30050709A>T	ENSP00000344666:p.Lys171*	209.0	0.0	.		145.0	73.0	.	NM_000268	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Nonsense_Mutation	SNP	ENST00000338641.4	hg19	CCDS13861.1	.	.	.	.	.	.	.	.	.	.	A	41	8.773705	0.98948	.	.	ENSG00000186575	ENST00000338641;ENST00000403435;ENST00000361452;ENST00000397822;ENST00000403999;ENST00000334961;ENST00000353887;ENST00000397789;ENST00000361676;ENST00000361166	.	.	.	5.99	5.99	0.97316	.	0.049049	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4943	0.84223	1.0:0.0:0.0:0.0	.	.	.	.	X	171;171;130;171;171;88;88;171;129;171	.	.	K	+	1	0	NF2	28380709	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.185000	0.94900	2.291000	0.77112	0.533000	0.62120	AAA	.	.	.	none		0.423	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268		T	30050709	A	T	30050709	4	4	112	1	0	0	0	0	0	1	0	0	10364	15	1	5	529	5	NF2	22	30050709	Nonsense_Mutation	SNP	A	TCGA-BQ-5877-01A-11D-1589-08	5603333	30050709	21253857	79	7268											
CHD5	26038	hgsc.bcm.edu	37	chr1	6204188	6204188	+	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	aggtctttccacttgatcagGtagtgcacatcccccttctt	7	14	7	13	0	3	1	1	1	2	0	5	1	5	1	3	2	1	2	3	2	1	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr1:6204188G>A	ENST00000262450.3	-	12	1929	c.1830C>T	c.(1828-1830)taC>taT	p.Y610Y	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)		ACTTGATCAGGTAGTGCACAT	0.567																																					p.Y610Y		Atlas-SNP	.											.	CHD5	267	.	0			c.C1830T						PASS	.						245	196	213					1																	6204188		2203	4300	6503	SO:0001819	synonymous_variant	26038	exon12			GATCAGGTAGTGC	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.1830C>T	chr1.hg19:g.6204188G>A		187.0	0.0	.		169.0	82.0	.	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Silent	SNP	ENST00000262450.3	hg19	CCDS57.1																																																																																			.	.	.	none		0.567	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557		A	6204188	G	A	6204188	2	1	113	1	0	0	0	0	0	0	0	1	3330	1256	44	2		2	CHD5	1	6204188	Silent	SNP	G	TCGA-BQ-5878-01A-11D-1589-08		6204188	243046433	1	7269											
ARID1A	8289	hgsc.bcm.edu	37	chr1	27057775	27057775	+	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	aaccaccgtcccagacccctCatgcccaaccttcgtatcag	10	7	5	19	2	2	1	2	0	0	1	4	1	3	1	7	0	3	1	7	0	3	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr1:27057775C>T	ENST00000324856.7	+	3	1854	c.1483C>T	c.(1483-1485)Cat>Tat	p.H495Y	ARID1A_ENST00000374152.2_Missense_Mutation_p.H112Y|ARID1A_ENST00000457599.2_Missense_Mutation_p.H495Y	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	495					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)		CCAGACCCCTCATGCCCAACC	0.582			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.H495Y		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.C1483T						PASS	.						347	315	326					1																	27057775		2203	4300	6503	SO:0001583	missense	8289	exon3			ACCCCTCATGCCC	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.1483C>T	chr1.hg19:g.27057775C>T	ENSP00000320485:p.His495Tyr	443.0	0.0	.		446.0	61.0	.	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	hg19	CCDS285.1	.	.	.	.	.	.	.	.	.	.	C	12.43	1.935864	0.34189	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000524572;ENST00000374152	T;T;T;T	0.43688	4.5;4.28;0.94;4.29	5.33	5.33	0.75918	.	0.344170	0.34046	N	0.004318	T	0.22437	0.0541	N	0.08118	0	0.80722	D	1	B;B;B	0.29988	0.068;0.264;0.068	B;B;B	0.24701	0.014;0.055;0.014	T	0.12993	-1.0526	10	0.02654	T	1	-11.5851	19.2116	0.93757	0.0:1.0:0.0:0.0	.	495;495;149	O14497;O14497-2;Q4LE49	ARI1A_HUMAN;.;.	Y	495;495;112;112	ENSP00000320485:H495Y;ENSP00000387636:H495Y;ENSP00000432473:H112Y;ENSP00000363267:H112Y	ENSP00000320485:H495Y	H	+	1	0	ARID1A	26930362	1.000000	0.71417	1.000000	0.80357	0.678000	0.39670	3.260000	0.51523	2.766000	0.95052	0.655000	0.94253	CAT	.	.	.	none		0.582	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		T	27057775	C	T	27057775	3	4	113	1	0	0	0	0	1	0	0	0	913	826	29	2	1493	2	ARID1A	1	27057775	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	20853587	27057775	222192846	2	7270											
POMGNT1	55624	hgsc.bcm.edu	37	chr1	46662703	46662704	+	Frame_Shift_Del	DEL	GA	GA	-																															atggctcgccgagtgtccagGatcaacttgatattgacaat																										TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	GA	GA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr1:46662703_46662704delGA	ENST00000371984.3	-	3	330_331	c.173_174delTC	c.(172-174)atcfs	p.I58fs	POMGNT1_ENST00000371986.3_Frame_Shift_Del_p.I58fs|POMGNT1_ENST00000535522.1_Frame_Shift_Del_p.I36fs|POMGNT1_ENST00000396420.3_Frame_Shift_Del_p.I58fs|POMGNT1_ENST00000371992.1_Frame_Shift_Del_p.I58fs	NM_017739.3	NP_060209	Q8WZA1	PMGT1_HUMAN	protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-)	58					protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity (GO:0047223)			breast(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20	Acute lymphoblastic leukemia(166;0.155)					GAGTGTCCAGGATCAACTTGAT	0.55																																					p.58_59del		Atlas-INDEL	.											.	POMGNT1	96	.	0			c.174_175del						PASS	.																																			SO:0001589	frameshift_variant	55624	exon3			.		CCDS531.1, CCDS57995.1	1p34.1	2014-09-17	2013-07-31		ENSG00000085998	ENSG00000085998	2.4.1.-	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	19139	protein-coding gene	gene with protein product	"protein O-mannose beta-1,2-N-acetylglucosaminyltransferase"	606822	"muscle-eye-brain disease", "protein O-linked mannose beta1,2-N-acetylglucosaminyltransferase"	MEB		11742540, 12788071	Standard	NM_017739		Approved	FLJ20277, MGAT1.2, LGMD2O	uc001cpg.3	Q8WZA1	OTTHUMG00000007604	ENST00000371984.3:c.173_174delTC	chr1.hg19:g.46662703_46662704delGA	ENSP00000361052:p.Ile58fs	312.0	0.0	0		257.0	97.0	0.377432	NM_017739	D3DQ16|Q5VST2|Q5VST3|Q9BV55|Q9H9L8|Q9NXF9|Q9NYF7	Frame_Shift_Del	DEL	ENST00000371984.3	hg19	CCDS531.1																																																																																			.	.	.	none		0.55	POMGNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020146.1	NM_017739		-	46662704	GA	-	46662703	7	5	113	1	0	1	0	1	0	0	0	0	12250	1164	41	0	1888	0	POMGNT1	1	46662703	Frame_Shift_Del	DEL	GA	TCGA-BQ-5878-01A-11D-1589-08	19604928	46662703	202587918	3	7271											
C1orf177	163747	hgsc.bcm.edu	37	chr1	55272686	55272686	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taggtttgacatctctgctgTttatcccaactggaagaagt	10	14	9	8	0	1	2	0	1	1	1	3	3	2	3	1	2	2	3	1	2	5	4			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr1:55272686T>C	ENST00000371273.3	+	2	137	c.122T>C	c.(121-123)gTt>gCt	p.V41A	C1orf177_ENST00000358193.3_Missense_Mutation_p.V41A	NM_001110533.1	NP_001104003	Q3ZCV2	CA177_HUMAN	chromosome 1 open reading frame 177	41										breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(6)|prostate(2)	17						ATCTCTGCTGTTTATCCCAAC	0.582																																					p.V41A		Atlas-SNP	.											.	C1orf177	36	.	0			c.T122C						PASS	.						230	214	219					1																	55272686		2203	4300	6503	SO:0001583	missense	163747	exon2			CTGCTGTTTATCC	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.122T>C	chr1.hg19:g.55272686T>C	ENSP00000360320:p.Val41Ala	304.0	0.0	.		240.0	97.0	.	NM_001110533	B7WPL2|Q8N7Y9	Missense_Mutation	SNP	ENST00000371273.3	hg19	CCDS44153.1	.	.	.	.	.	.	.	.	.	.	T	13.45	2.241605	0.39598	.	.	ENSG00000162398	ENST00000358193;ENST00000371273	T;T	0.26518	1.73;1.73	3.72	3.72	0.42706	.	0.129282	0.31821	N	0.007008	T	0.36138	0.0956	L	0.59436	1.845	0.36448	D	0.865922	D;D	0.56035	0.974;0.974	P;P	0.54499	0.754;0.754	T	0.43589	-0.9382	10	0.48119	T	0.1	-2.4596	10.7545	0.46228	0.0:0.0:0.0:1.0	.	41;41	Q3ZCV2;Q3ZCV2-2	CA177_HUMAN;.	A	41	ENSP00000350924:V41A;ENSP00000360320:V41A	ENSP00000350924:V41A	V	+	2	0	C1orf177	55045274	0.977000	0.34250	0.832000	0.32986	0.687000	0.40016	2.492000	0.45311	1.929000	0.55896	0.379000	0.24179	GTT	.	.	.	none		0.582	C1orf177-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027674.1	NM_152607		C	55272686	T	C	55272686	3	2	113	1	0	0	0	0	1	0	0	0	2019	1725	60	3	128	3	C1orf177	1	55272686	Missense_Mutation	SNP	T	TCGA-BQ-5878-01A-11D-1589-08	8609983	55272686	193977935	4	7272											
L1TD1	54596	hgsc.bcm.edu	37	chr1	62672679	62672679	+	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	aaggagaaaactctaaaataGgtgatgataatgaaaattta	21	10	8	2	0	1	4	0	3	1	1	1	5	1	4	0	2	1	0	0	2	10	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr1:62672679G>C	ENST00000498273.1	+	3	674	c.379G>C	c.(379-381)Ggt>Cgt	p.G127R		NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	127										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						ctctaaaataggtgatgataa	0.308																																					p.G127R		Atlas-SNP	.											.	L1TD1	114	.	0			c.G379C						PASS	.						59	70	66					1																	62672679		2194	4294	6488	SO:0001583	missense	54596	exon4			AAAATAGGTGATG	BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.379G>C	chr1.hg19:g.62672679G>C	ENSP00000419901:p.Gly127Arg	118.0	0.0	.		96.0	46.0	.	NM_001164835	Q8NDA1|Q9NUV8|Q9NV78	Missense_Mutation	SNP	ENST00000498273.1	hg19	CCDS619.1	.	.	.	.	.	.	.	.	.	.	G	6.882	0.532168	0.13127	.	.	ENSG00000240563	ENST00000498273	T	0.11277	2.79	2.07	1.1	0.20463	.	.	.	.	.	T	0.06142	0.0159	N	0.14661	0.345	0.09310	N	1	B	0.27594	0.182	B	0.25291	0.059	T	0.36504	-0.9745	9	0.54805	T	0.06	.	6.423	0.21754	0.0:0.3091:0.6909:0.0	.	127	Q5T7N2	LITD1_HUMAN	R	127	ENSP00000419901:G127R	ENSP00000419901:G127R	G	+	1	0	L1TD1	62445267	0.034000	0.19679	0.001000	0.08648	0.024000	0.10985	1.838000	0.39211	0.419000	0.25927	0.313000	0.20887	GGT	.	.	.	none		0.308	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079		C	62672679	G	C	62672679	3	2	113	1	0	0	0	0	1	0	0	0	8596	1000	35	4	381	4	L1TD1	1	62672679	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	7399993	62672679	186577942	5	7273											
VANGL1	81839	hgsc.bcm.edu	37	chr1	116202267	116202267	+	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	attgttgtttttcagggaaaGaactagagagagacacaagt	15	11	11	4	0	1	3	1	0	0	3	1	6	1	4	0	1	1	2	0	1	4	5	rs143990097		TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr1:116202267G>C	ENST00000355485.2	+	3	348	c.77G>C	c.(76-78)aGa>aCa	p.R26T	VANGL1_ENST00000369510.4_Missense_Mutation_p.R26T|VANGL1_ENST00000310260.3_Missense_Mutation_p.R26T|VANGL1_ENST00000369509.1_Missense_Mutation_p.R26T	NM_001172411.1|NM_138959.2	NP_001165882.1|NP_620409.1	Q8TAA9	VANG1_HUMAN	VANGL planar cell polarity protein 1	26					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)		TTCAGGGAAAGAACTAGAGAG	0.413																																					p.R26T		Atlas-SNP	.											.	VANGL1	65	.	0			c.G77C						PASS	.						127	138	134					1																	116202267		2203	4300	6503	SO:0001583	missense	81839	exon3			GGGAAAGAACTAG	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.77G>C	chr1.hg19:g.116202267G>C	ENSP00000347672:p.Arg26Thr	199.0	0.0	.		207.0	9.0	.	NM_001172411	Q5T1D3|Q5T1D4|Q86WG8|Q8N559	Missense_Mutation	SNP	ENST00000355485.2	hg19	CCDS883.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.572304	0.86542	.	.	ENSG00000173218	ENST00000355485;ENST00000369510;ENST00000310260;ENST00000369509	D;D;D;D	0.86297	-2.1;-2.1;-2.1;-2.1	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	D	0.88381	0.6421	M	0.70595	2.14	0.58432	D	0.999999	P;P	0.48998	0.9;0.918	P;P	0.50378	0.506;0.639	D	0.89451	0.3730	10	0.62326	D	0.03	-9.9475	17.453	0.87597	0.0:0.0:1.0:0.0	.	26;26	Q8TAA9-2;Q8TAA9	.;VANG1_HUMAN	T	26	ENSP00000347672:R26T;ENSP00000358523:R26T;ENSP00000310800:R26T;ENSP00000358522:R26T	ENSP00000310800:R26T	R	+	2	0	VANGL1	116003790	1.000000	0.71417	0.995000	0.50966	0.934000	0.57294	7.940000	0.87693	2.561000	0.86390	0.563000	0.77884	AGA	.	G|1.000;A|0.000	.	alt		0.413	VANGL1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033096.1			C	116202267	G	C	116202267	3	2	113	1	0	0	0	0	1	0	0	0	17131	942	33	4	83	4	VANGL1	1	116202267	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	53529588	116202267	133048354	6	7274											
NTRK1	4914	hgsc.bcm.edu	37	chr1	156849153	156849153	+	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	ctacagcaccgactattaccGtgtaagggtcctttgtcccc	8	11	8	14	2	0	0	0	0	0	0	2	1	2	0	5	1	3	2	5	1	4	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr1:156849153G>A	ENST00000524377.1	+	15	2086	c.2045G>A	c.(2044-2046)cGt>cAt	p.R682H	NTRK1_ENST00000358660.3_Splice_Site_p.R679H|NTRK1_ENST00000368196.3_Splice_Site_p.R676H|NTRK1_ENST00000392302.2_Splice_Site_p.R646H	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	682	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|axon guidance (GO:0007411)|axonogenesis involved in innervation (GO:0060385)|B cell differentiation (GO:0030183)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to nicotine (GO:0071316)|circadian rhythm (GO:0007623)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|developmental programmed cell death (GO:0010623)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory nerve development (GO:0021553)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to hydrostatic pressure (GO:0051599)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|Sertoli cell development (GO:0060009)|small GTPase mediated signal transduction (GO:0007264)|sympathetic nervous system development (GO:0048485)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	74	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Amitriptyline(DB00321)|Imatinib(DB00619)|Regorafenib(DB08896)	GACTATTACCGTGTAAGGGTC	0.562			T	"TPM3, TPR, TFG"	papillary thyroid					TSP Lung(10;0.080)																											p.R682H		Atlas-SNP	.		Dom	yes		1	1q21-q22	4914	"neurotrophic tyrosine kinase, receptor, type 1"		E	.	NTRK1	287	.	0			c.G2045A						PASS	.						84	75	78					1																	156849153		2203	4300	6503	SO:0001630	splice_region_variant	4914	exon15			ATTACCGTGTAAG	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.2046+1G>A	chr1.hg19:g.156849153G>A		74.0	0.0	.		79.0	42.0	.	NM_002529	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Missense_Mutation	SNP	ENST00000524377.1	hg19	CCDS1161.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.953656	0.73902	.	.	ENSG00000198400	ENST00000392302;ENST00000368196;ENST00000524377;ENST00000358660	D;D;D;D	0.83163	-1.69;-1.69;-1.69;-1.69	4.13	4.13	0.48395	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Tyrosine-protein kinase, receptor class II, conserved site (1);Protein kinase, catalytic domain (1);	0.000000	0.45126	D	0.000390	D	0.86764	0.6011	L	0.56280	1.765	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.997;0.987;0.938;0.99	D	0.88394	0.3010	10	0.87932	D	0	.	15.4596	0.75342	0.0:0.0:1.0:0.0	.	679;676;682;646	A8K3Z4;P04629-2;P04629;A6NF12	.;.;NTRK1_HUMAN;.	H	646;676;682;679	ENSP00000376120:R646H;ENSP00000357179:R676H;ENSP00000431418:R682H;ENSP00000351486:R679H	ENSP00000351486:R679H	R	+	2	0	NTRK1	155115777	1.000000	0.71417	0.930000	0.37139	0.719000	0.41307	7.703000	0.84585	2.315000	0.78130	0.561000	0.74099	CGT	.	.	.	none		0.562	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1	NM_002529	Missense_Mutation	A	156849153	G	A	156849153	5	1	113	1	0	0	0	0	0	0	1	0	10713	1159	40	1	2233	1	NTRK1	1	156849153	Splice_Site	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	40646886	156849153	92401468	7	7275											
GLRX2	51022	hgsc.bcm.edu	37	chr1	193074704	193074704	+	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	agcgctggattccagcgagtGccacccacgtgtaaacatcc	10	7	10	14	3	0	0	0	0	0	0	2	2	2	1	4	1	4	2	4	1	2	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr1:193074704G>A	ENST00000367439.3	-	0	0				GLRX2_ENST00000367440.3_Missense_Mutation_p.A22V|GLRX2_ENST00000472197.1_Intron	NM_197962.2	NP_932066.1	Q9NS18	GLRX2_HUMAN	glutaredoxin 2						apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|DNA protection (GO:0042262)|glutathione metabolic process (GO:0006749)|protein folding (GO:0006457)|regulation of signal transduction (GO:0009966)|regulation of transcription, DNA-templated (GO:0006355)|response to hydrogen peroxide (GO:0042542)|response to organic substance (GO:0010033)|response to redox state (GO:0051775)|response to temperature stimulus (GO:0009266)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	2 iron, 2 sulfur cluster binding (GO:0051537)|arsenate reductase (glutaredoxin) activity (GO:0008794)|electron carrier activity (GO:0009055)|glutathione disulfide oxidoreductase activity (GO:0015038)|metal ion binding (GO:0046872)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)			breast(1)|large_intestine(1)|lung(3)	5					Glutathione(DB00143)	TCCAGCGAGTGCCACCCACGT	0.652																																					p.A22V		Atlas-SNP	.											.	GLRX2	9	.	0			c.C65T						PASS	.						41	44	43					1																	193074704		2203	4300	6503	SO:0001631	upstream_gene_variant	51022	exon1			GCGAGTGCCACCC	AF132495	CCDS1380.1, CCDS1381.1	1q31.2	2012-09-20			ENSG00000023572	ENSG00000023572			16065	protein-coding gene	gene with protein product	"bA101E13.1 (GRX2 glutaredoxin (thioltransferase) 2)"	606820				11297543	Standard	NM_016066		Approved	GRX2, bA101E13.1	uc001gsz.2	Q9NS18	OTTHUMG00000035677		chr1.hg19:g.193074704G>A	Exception_encountered	33.0	0.0	.		31.0	14.0	.	NM_016066	Q3LR69|Q7L1N7|Q96JC0|Q9Y3D4	Missense_Mutation	SNP	ENST00000367439.3	hg19	CCDS1381.1	.	.	.	.	.	.	.	.	.	.	G	9.608	1.130447	0.21041	.	.	ENSG00000023572	ENST00000367440	T	0.35236	1.32	2.13	-4.26	0.03755	.	595.624000	0.00166	N	0.000000	T	0.23171	0.0560	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.11421	-1.0588	9	0.33940	T	0.23	2.0784	2.9471	0.05849	0.1273:0.3676:0.3584:0.1468	.	22	Q9NS18-2	.	V	22	ENSP00000356410:A22V	ENSP00000356410:A22V	A	-	2	0	GLRX2	191341327	0.000000	0.05858	0.000000	0.03702	0.082000	0.17680	-1.156000	0.03160	-3.466000	0.00158	-0.687000	0.03738	GCA	.	.	.	none		0.652	GLRX2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000086699.1	NM_016066		A	193074704	G	A	193074704	1	1	113	0	1	0	0	0	0	0	0	0	6467	1319	46	2		2	GLRX2	1	193074704	5'Flank	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	36225551	193074704	56175917	8	7276											
NEK7	140609	hgsc.bcm.edu	37	chr1	198266319	198266319	+	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	ttatactcactgtgtaagaaGatagaacagtgtgactaccc	14	11	8	8	0	1	4	1	1	0	3	1	4	1	4	1	0	3	1	1	0	7	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr1:198266319G>C	ENST00000367385.4	+	9	1089	c.747G>C	c.(745-747)aaG>aaC	p.K249N	NEK7_ENST00000538004.1_Missense_Mutation_p.K249N	NM_133494.2	NP_598001.1	Q8TDX7	NEK7_HUMAN	NIMA-related kinase 7	249	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)			endometrium(3)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21						TGTGTAAGAAGATAGAACAGT	0.378																																					p.K249N		Atlas-SNP	.											.	NEK7	42	.	0			c.G747C						PASS	.						150	150	150					1																	198266319		2203	4300	6503	SO:0001583	missense	140609	exon9			TAAGAAGATAGAA	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.747G>C	chr1.hg19:g.198266319G>C	ENSP00000356355:p.Lys249Asn	206.0	0.0	.		188.0	84.0	.	NM_133494	A6NGT8	Missense_Mutation	SNP	ENST00000367385.4	hg19	CCDS1394.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.279186	0.80692	.	.	ENSG00000151414	ENST00000367385;ENST00000538004	T;T	0.66460	-0.21;-0.21	5.98	5.06	0.68205	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	0.69700	0.3140	L	0.42744	1.35	0.80722	D	1	P	0.39737	0.685	P	0.50049	0.629	T	0.70777	-0.4780	10	0.59425	D	0.04	.	14.6335	0.68673	0.0693:0.0:0.9307:0.0	.	249	Q8TDX7	NEK7_HUMAN	N	249	ENSP00000356355:K249N;ENSP00000444621:K249N	ENSP00000356355:K249N	K	+	3	2	NEK7	196532942	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.580000	0.60942	2.838000	0.97847	0.655000	0.94253	AAG	.	.	.	none		0.378	NEK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086550.2	NM_133494		C	198266319	G	C	198266319	3	2	113	1	0	0	0	0	1	0	0	0	10336	933	33	4	777	4	NEK7	1	198266319	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	5191615	198266319	50984302	9	7277											
GDF7	151449	hgsc.bcm.edu	37	chr2	20871056	20871056	+	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	ctcaactccatggcaccagaCgcggcgccggcctcctgctg	6	6	11	18	4	1	1	1	0	0	1	3	1	3	1	5	3	2	2	5	3	1	0	rs376857749		TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr2:20871056C>T	ENST00000272224.3	+	2	1800	c.1224C>T	c.(1222-1224)gaC>gaT	p.D408D		NM_182828.2	NP_878248.2	Q7Z4P5	GDF7_HUMAN	growth differentiation factor 7	408					activin receptor signaling pathway (GO:0032924)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|branching morphogenesis of an epithelial tube (GO:0048754)|cell fate commitment (GO:0045165)|epithelial cell differentiation (GO:0030855)|forebrain morphogenesis (GO:0048853)|gland morphogenesis (GO:0022612)|growth (GO:0040007)|midbrain development (GO:0030901)|morphogenesis of an epithelial fold (GO:0060571)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of tendon cell differentiation (GO:2001051)|positive regulation of transcription, DNA-templated (GO:0045893)|reproductive structure development (GO:0048608)|roof plate formation (GO:0021509)|spinal cord association neuron differentiation (GO:0021527)	extracellular space (GO:0005615)				breast(1)|cervix(1)|endometrium(2)|lung(1)|prostate(1)|skin(1)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGGCACCAGACGCGGCGCCGG	0.612																																					p.D408D		Atlas-SNP	.											.	GDF7	21	.	0			c.C1224T						PASS	.						69	60	63					2																	20871056		2203	4300	6503	SO:0001819	synonymous_variant	151449	exon2			ACCAGACGCGGCG	AF522369	CCDS1701.1	2p24.1	2008-05-22			ENSG00000143869	ENSG00000143869			4222	protein-coding gene	gene with protein product		604651				10022976, 9808626	Standard	NM_182828		Approved	BMP12	uc002rdz.1	Q7Z4P5	OTTHUMG00000090781	ENST00000272224.3:c.1224C>T	chr2.hg19:g.20871056C>T		39.0	0.0	.		15.0	11.0	.	NM_182828		Silent	SNP	ENST00000272224.3	hg19	CCDS1701.1																																																																																			.	.	.	alt		0.612	GDF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207563.2	NM_182828		T	20871056	C	T	20871056	2	4	113	1	0	0	0	0	0	0	0	1	6325	535	19	1		1	GDF7	2	20871056	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08		20871056	222328317	10	7278											
AUP1	27429	hgsc.bcm.edu	37	chr2	74756587	74756587	+	5'UTR	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	cagaacccgactggcgcgtaGagcagcagcacgagcagtag	12	3	14	12	4	0	2	0	0	0	2	0	4	0	2	1	1	5	6	1	1	3	2	rs376231592		TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr2:74756587G>C	ENST00000258080.3	+	0	84				AUP1_ENST00000377526.3_Silent_p.L30L|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						CTGGCGCGTAGAGCAGCAGCA	0.667													G|||	1	0.000199681	0	0	5008	,	,		17159	0		0.001	False		,,,				2504	0				p.L30L		Atlas-SNP	.											.	AUP1	29	.	0			c.C90G						PASS	.	G	,,	0,4280		0,0,2140	25	38	33		,,90	4.7	1	2		33	1,8483		0,1,4241	no	utr-5,utr-5,coding-synonymous	AUP1,HTRA2	NM_013247.4,NM_145074.2,NM_181575.3	,,	0,1,6381	CC,CG,GG		0.0118,0.0,0.0078	,,	,,30/411	74756587	1,12763	2140	4242	6382	SO:0001623	5_prime_UTR_variant	550	exon2			CGCGTAGAGCAGC		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.-547G>C	chr2.hg19:g.74756587G>C		5.0	0.0	.		10.0	6.0	.	NM_181575	Q9HBZ4|Q9P0Y3|Q9P0Y4	Silent	SNP	ENST00000258080.3	hg19	CCDS1951.1																																																																																			.	.	.	weak		0.667	HTRA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252219.2	NM_013247		C	74756587	G	C	74756587	1	2	113	0	1	0	0	0	0	0	0	0	1220	929	33	4		4	AUP1	2	74756587	5'UTR	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	53885531	74756587	168442786	11	7279											
TTN	7273	hgsc.bcm.edu	37	chr2	179401833	179401833	+	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	caattgccattcagccccctCcttggcctcacatttttcca	7	13	4	17	0	2	0	2	0	0	0	4	0	4	0	6	1	2	0	6	1	1	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr2:179401833C>T	ENST00000591111.1	-	306	95304	c.95080G>A	c.(95080-95082)Gag>Aag	p.E31694K	TTN_ENST00000359218.5_Missense_Mutation_p.E24395K|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.E24270K|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.E33335K|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.E24462K|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E30767K|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586707.1_RNA			Q8WZ42	TITIN_HUMAN	titin	31694	Fibronectin type-III 130. {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)			TCAGCCCCCTCCTTGGCCTCA	0.502																																					p.E33335K		Atlas-SNP	.											.	TTN	18412	.	0			c.G100003A						PASS	.						67	66	66					2																	179401833		1941	4126	6067	SO:0001583	missense	7273	exon356			CCCCCTCCTTGGC	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.95080G>A	chr2.hg19:g.179401833C>T	ENSP00000465570:p.Glu31694Lys	27.0	0.0	.		79.0	15.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	22.5	4.293637	0.80914	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57273	0.41;0.41;0.41;0.41	5.41	5.41	0.78517	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.56731	0.2005	N	0.05554	-0.025	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.83275	0.996;0.996;0.996;0.996	T	0.67806	-0.5575	9	0.87932	D	0	.	19.1973	0.93695	0.0:1.0:0.0:0.0	.	24270;24395;24462;31694	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	30767;24270;24462;24395;24267	ENSP00000343764:E30767K;ENSP00000434586:E24270K;ENSP00000340554:E24462K;ENSP00000352154:E24395K	ENSP00000340554:E24462K	E	-	1	0	TTN	179110079	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.818000	0.86416	2.544000	0.85801	0.462000	0.41574	GAG	.	.	.	none		0.502	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179401833	C	T	179401833	3	4	113	1	0	0	0	0	1	0	0	0	16747	864	30	2	8004	2	TTN	2	179401833	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	104645246	179401833	63797540	12	7280											
TTN	7273	hgsc.bcm.edu	37	chr2	179452053	179452053	+	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	atataatgtgtcacttggctCccaccgtcgttttcaggagg	8	13	10	10	2	2	0	2	0	0	0	4	1	3	1	2	3	0	2	2	3	2	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr2:179452053C>T	ENST00000591111.1	-	257	59186	c.58962G>A	c.(58960-58962)ggG>ggA	p.G19654G	TTN_ENST00000359218.5_Silent_p.G12355G|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Silent_p.G12230G|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000589042.1_Silent_p.G21295G|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000342175.6_Silent_p.G12422G|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000342992.6_Silent_p.G18727G|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA			Q8WZ42	TITIN_HUMAN	titin	19654	Fibronectin type-III 42. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCACTTGGCTCCCACCGTCGT	0.468																																					p.G21295G		Atlas-SNP	.											.	TTN	18412	.	0			c.G63885A						PASS	.						69	65	66					2																	179452053		1909	4130	6039	SO:0001819	synonymous_variant	7273	exon307			TTGGCTCCCACCG	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.58962G>A	chr2.hg19:g.179452053C>T		29.0	0.0	.		92.0	6.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.	.	none		0.468	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179452053	C	T	179452053	2	4	113	1	0	0	0	0	0	0	0	1	16747	842	30	2		2	TTN	2	179452053	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	50220	179452053	63747320	13	7281											
CPO	130749	hgsc.bcm.edu	37	chr2	207833968	207833968	+	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	ttctcatatacgtttgagctGagggacagtggaacatatgg	11	12	12	6	1	1	2	1	2	1	0	2	4	1	4	0	3	3	2	0	3	4	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr2:207833968G>C	ENST00000272852.3	+	9	979	c.933G>C	c.(931-933)ctG>ctC	p.L311L		NM_173077.2	NP_775100.1	Q8IVL8	CBPO_HUMAN	carboxypeptidase O	311						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)		CGTTTGAGCTGAGGGACAGTG	0.512																																					p.L311L		Atlas-SNP	.											.	CPO	42	.	0			c.G933C						PASS	.						147	133	138					2																	207833968		2203	4300	6503	SO:0001819	synonymous_variant	130749	exon9			TGAGCTGAGGGAC		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.933G>C	chr2.hg19:g.207833968G>C		89.0	0.0	.		81.0	36.0	.	NM_173077	Q2M277|Q7RTW7	Silent	SNP	ENST00000272852.3	hg19	CCDS2372.1																																																																																			.	.	.	none		0.512	CPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202040.2	NM_173077		C	207833968	G	C	207833968	2	2	113	1	0	0	0	0	0	0	0	1	3822	1277	45	4		4	CPO	2	207833968	Silent	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	28381915	207833968	35365405	14	7282											
ABCA12	26154	hgsc.bcm.edu	37	chr2	215840568	215840568	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggagatctgaatctctggAtaactgttgctggaatttct	9	14	12	6	0	3	2	0	1	3	1	4	5	3	4	0	4	2	2	0	4	3	3			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr2:215840568A>G	ENST00000272895.7	-	34	5541	c.5322T>C	c.(5320-5322)taT>taC	p.Y1774Y	ABCA12_ENST00000389661.4_Silent_p.Y1456Y	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1774					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)		GAATCTCTGGATAACTGTTGC	0.453																																					p.Y1774Y	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.T5322C						PASS	.						147	142	144					2																	215840568		2203	4300	6503	SO:0001819	synonymous_variant	26154	exon34			CTCTGGATAACTG	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.5322T>C	chr2.hg19:g.215840568A>G		130.0	0.0	.		87.0	31.0	.	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Silent	SNP	ENST00000272895.7	hg19	CCDS33372.1																																																																																			.	.	.	none		0.453	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		G	215840568	A	G	215840568	2	3	113	1	0	0	0	0	0	0	0	1	30	340	12	3		3	ABCA12	2	215840568	Silent	SNP	A	TCGA-BQ-5878-01A-11D-1589-08	8006600	215840568	27358805	15	7283											
TMPPE	643853	hgsc.bcm.edu	37	chr3	33135655	33135655	+	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	acagcagccagggtggccttCgcgcctagggacagctgcct	7	6	14	14	2	0	0	0	0	0	0	1	1	0	1	4	3	4	2	4	3	1	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr3:33135655C>T	ENST00000342462.4	-	2	223	c.33G>A	c.(31-33)gcG>gcA	p.A11A	GLB1_ENST00000399402.3_Intron|GLB1_ENST00000307377.8_Intron|GLB1_ENST00000445488.2_Intron|GLB1_ENST00000307363.5_Intron|TMPPE_ENST00000416695.2_Intron	NM_001039770.2	NP_001034859.2	Q6ZT21	TMPPE_HUMAN	transmembrane protein with metallophosphoesterase domain	11						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.A11A(1)		breast(1)|large_intestine(5)|lung(6)|prostate(1)	13						GGGTGGCCTTCGCGCCTAGGG	0.587																																					p.A11A		Atlas-SNP	.											TMPPE,colon,carcinoma,-2,1	TMPPE	24	.	1	Substitution - coding silent(1)	lung(1)	c.G33A						PASS	.																																			SO:0001819	synonymous_variant	643853	exon2			GGCCTTCGCGCCT	AK126979	CCDS33732.1, CCDS46786.1	3p22.3	2014-02-12	2009-02-24		ENSG00000188167	ENSG00000188167			33865	protein-coding gene	gene with protein product							Standard	NM_001039770		Approved	FLJ45032	uc003cfk.2	Q6ZT21	OTTHUMG00000155779	ENST00000342462.4:c.33G>A	chr3.hg19:g.33135655C>T		91.0	0.0	.		82.0	8.0	.	NM_001039770	B2RNG5|Q6ZRG1	Silent	SNP	ENST00000342462.4	hg19	CCDS33732.1																																																																																			.	.	.	none		0.587	TMPPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341566.1	NM_001039770		T	33135655	C	T	33135655	2	4	113	1	0	0	0	0	0	0	0	1	16250	871	31	1		1	TMPPE	3	33135655	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08		33135655	164886775	16	7284											
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41274905	41274905	+	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	cagaactgtctttggactctCaggaatctttcagatgctgc	9	13	9	10	0	4	2	2	0	3	2	5	4	4	4	0	2	3	1	0	2	2	2	rs74692094	byFrequency	TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr3:41274905C>T	ENST00000349496.5	+	8	1435	c.1155C>T	c.(1153-1155)ctC>ctT	p.L385L	CTNNB1_ENST00000405570.1_Silent_p.L385L|CTNNB1_ENST00000453024.1_Silent_p.L378L|CTNNB1_ENST00000396185.3_Silent_p.L385L|CTNNB1_ENST00000396183.3_Silent_p.L385L	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	385					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TTTGGACTCTCAGGAATCTTT	0.413		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.L385L	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	.	CTNNB1	4904	.	0			c.C1155T						PASS	.						102	93	96					3																	41274905		2203	4300	6503	SO:0001819	synonymous_variant	1499	exon8	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	GACTCTCAGGAAT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.1155C>T	chr3.hg19:g.41274905C>T		103.0	0.0	.		126.0	47.0	.	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Silent	SNP	ENST00000349496.5	hg19	CCDS2694.1																																																																																			.	C|0.999;A|0.001	.	alt		0.413	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		T	41274905	C	T	41274905	2	4	113	1	0	0	0	0	0	0	0	1	4018	813	29	2		2	CTNNB1	3	41274905	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	8139250	41274905	156747525	17	7285											
TMF1	7110	hgsc.bcm.edu	37	chr3	69101211	69101211	+	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	gcctgcttagcgaagctggaGagctgggaggcgttgaacca	9	7	16	9	2	0	2	0	1	0	1	0	5	0	3	2	3	5	4	2	3	3	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr3:69101211G>A	ENST00000398559.2	-	1	243	c.27C>T	c.(25-27)ctC>ctT	p.L9L	CTD-2013N24.2_ENST00000595925.1_RNA|TMF1_ENST00000543976.1_Silent_p.L9L			P82094	TMF1_HUMAN	TATA element modulatory factor 1	9					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)		CGAAGCTGGAGAGCTGGGAGG	0.642																																					p.L9L		Atlas-SNP	.											.	TMF1	77	.	0			c.C27T						PASS	.						62	65	64					3																	69101211		1931	4151	6082	SO:0001819	synonymous_variant	7110	exon1			GCTGGAGAGCTGG		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.27C>T	chr3.hg19:g.69101211G>A		129.0	0.0	.		133.0	57.0	.	NM_007114	B7ZLJ2|Q17R87|Q59GK0	Silent	SNP	ENST00000398559.2	hg19	CCDS43105.1																																																																																			.	.	.	none		0.642	TMF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352106.1	NM_007114		A	69101211	G	A	69101211	2	1	113	1	0	0	0	0	0	0	0	1	16240	929	33	2		2	TMF1	3	69101211	Silent	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	27826306	69101211	128921219	18	7286											
MAPK10	5602	hgsc.bcm.edu	37	chr4	86950416	86950416	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctgaattcattacttcctTgtagataagttctgtaagaa	12	17	6	6	0	3	3	1	1	2	2	4	3	4	3	1	0	1	3	1	0	6	9			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr4:86950416T>C	ENST00000359221.3	-	13	1712	c.1186A>G	c.(1186-1188)Aag>Gag	p.K396E	MAPK10_ENST00000395157.3_Missense_Mutation_p.K251E|MAPK10_ENST00000395160.3_Missense_Mutation_p.K251E|MAPK10_ENST00000395161.2_Missense_Mutation_p.K396E|MAPK10_ENST00000361569.2_Missense_Mutation_p.K396E|MAPK10_ENST00000395169.3_Missense_Mutation_p.K358E|MAPK10_ENST00000395166.1_Missense_Mutation_p.K358E|MAPK10_ENST00000449047.2_Missense_Mutation_p.K251E			P53779	MK10_HUMAN	mitogen-activated protein kinase 10	396					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)		ATTACTTCCTTGTAGATAAGT	0.328																																					p.K396E		Atlas-SNP	.											.	MAPK10	106	.	0			c.A1186G						PASS	.						172	162	166					4																	86950416		2203	4300	6503	SO:0001583	missense	5602	exon13			CTTCCTTGTAGAT	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.1186A>G	chr4.hg19:g.86950416T>C	ENSP00000352157:p.Lys396Glu	110.0	0.0	.		79.0	41.0	.	NM_002753	A6NFS3|A6NG28|B3KQ94|Q15707|Q49AP1	Missense_Mutation	SNP	ENST00000359221.3	hg19	CCDS34026.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.80|15.80	2.940106|2.940106	0.52972|0.52972	.|.	.|.	ENSG00000109339|ENSG00000109339	ENST00000395169;ENST00000359221;ENST00000395157;ENST00000361569;ENST00000395166;ENST00000395160;ENST00000449047;ENST00000395161|ENST00000515400	T;T;T;T;T;T;T;T|.	0.59083|.	0.29;0.29;0.29;0.29;0.29;0.29;0.29;0.29|.	5.96|5.96	5.96|5.96	0.96718|0.96718	Protein kinase-like domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.68696|0.68696	0.3029|0.3029	L|L	0.52206|0.52206	1.635|1.635	0.80722|0.80722	D|D	1|1	B;B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0;0.0|.	B;B;B;B;B|.	0.08055|.	0.0;0.002;0.003;0.002;0.001|.	T|T	0.66023|0.66023	-0.6026|-0.6026	10|5	0.33141|.	T|.	0.24|.	-19.5226|-19.5226	16.0984|16.0984	0.81148|0.81148	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	282;251;358;396;396|.	B7Z1Z1;Q499Y8;P53779-3;P53779-2;P53779|.	.;.;.;.;MK10_HUMAN|.	E|R	358;396;251;396;358;251;251;396|308	ENSP00000378598:K358E;ENSP00000352157:K396E;ENSP00000378586:K251E;ENSP00000355297:K396E;ENSP00000378595:K358E;ENSP00000378589:K251E;ENSP00000414469:K251E;ENSP00000378590:K396E|.	ENSP00000352157:K396E|.	K|Q	-|-	1|2	0|0	MAPK10|MAPK10	87169440|87169440	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	6.935000|6.935000	0.75886|0.75886	2.278000|2.278000	0.76064|0.76064	0.533000|0.533000	0.62120|0.62120	AAG|CAA	.	.	.	none		0.328	MAPK10-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000361363.2			C	86950416	T	C	86950416	3	2	113	1	0	0	0	0	1	0	0	0	9279	1821	63	3	221	3	MAPK10	4	86950416	Missense_Mutation	SNP	T	TCGA-BQ-5878-01A-11D-1589-08		86950416	104203860	19	7287											
LRBA	987	hgsc.bcm.edu	37	chr4	151827110	151827110	+	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	gaaaatgcaaggcaaagttcAagtactgctctgctaacatg	15	9	9	8	0	2	0	1	0	1	0	2	1	2	0	0	1	5	6	0	1	7	3			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr4:151827110A>T	ENST00000357115.3	-	13	1878	c.1635T>A	c.(1633-1635)ctT>ctA	p.L545L	LRBA_ENST00000510413.1_Silent_p.L545L|LRBA_ENST00000535741.1_Silent_p.L545L|LRBA_ENST00000507224.1_Silent_p.L545L	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	545						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)					GGCAAAGTTCAAGTACTGCTC	0.388																																					p.L545L		Atlas-SNP	.											.	LRBA	253	.	0			c.T1635A						PASS	.						83	81	82					4																	151827110		2203	4300	6503	SO:0001819	synonymous_variant	987	exon13			AAGTTCAAGTACT	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.1635T>A	chr4.hg19:g.151827110A>T		76.0	0.0	.		82.0	37.0	.	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Silent	SNP	ENST00000357115.3	hg19	CCDS3773.1																																																																																			.	.	.	none		0.388	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			T	151827110	A	T	151827110	2	4	113	1	0	0	0	0	0	0	0	1	8938	117	5	5		5	LRBA	4	151827110	Silent	SNP	A	TCGA-BQ-5878-01A-11D-1589-08	64876694	151827110	39327166	20	7288											
ACCN5	51802	hgsc.bcm.edu	37	chr4	156763435	156763436	+	Missense_Mutation	DNP	GC	GC	AT																															tccttcaagcaaccagaagtGctgtagctgctaaaattctg																										TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr4:156763435_156763436GC>AT	ENST00000537611.2	-	6	978_979	c.932_933GC>AT	c.(931-933)aGC>aAT	p.S311N		NM_017419.2	NP_059115.1	Q9NY37	ASIC5_HUMAN	acid-sensing (proton-gated) ion channel family member 5	311					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)										AACCAGAAGTGCTGTAGCTGCT	0.416																																					p.S311S|p.S311N		Atlas-SNP	.											.	.	.	.	0			c.C933T|c.G932A						PASS	.																																			SO:0001583	missense	51802	exon6			AGAAGTGCTGTAG|GAAGTGCTGTAGC	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.932_933delinsAT	chr4.hg19:g.156763435_156763436delinsAT	ENSP00000442477:p.Ser311Asn	106.0|104.0	0.0	.		117.0|112.0	64.0	.	NM_017419		Silent|Missense_Mutation	SNP	ENST00000537611.2	hg19	CCDS3793.1																																																																																			.	.	.	none		0.416	ASIC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366464.1			AT	156763436	GC	AT	156763435	3	1	113	1	0	0	0	0	1	0	0	0	132	1310	46	2	604	2	ACCN5	4	156763435	Missense_Mutation	DNP	GC	TCGA-BQ-5878-01A-11D-1589-08	4936325	156763435	34390841	21	7289											
HMGB2	3148	hgsc.bcm.edu	37	chr4	174254775	174254775	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acgaggacattttgccccgcGgcttgttggggtctccttta	5	13	12	11	3	1	0	0	0	1	0	2	2	1	1	3	4	1	2	3	4	1	6			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr4:174254775G>A	ENST00000296503.5	-	2	899	c.26C>T	c.(25-27)cCg>cTg	p.P9L	HMGB2_ENST00000446922.2_Missense_Mutation_p.P9L|HMGB2_ENST00000438704.2_Missense_Mutation_p.P9L			P26583	HMGB2_HUMAN	high mobility group box 2	9					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)		TTTGCCCCGCGGCTTGTTGGG	0.627																																					p.P9L		Atlas-SNP	.											.	HMGB2	24	.	0			c.C26T						PASS	.						68	71	70					4																	174254775		2203	4300	6503	SO:0001583	missense	3148	exon1			CCCCGCGGCTTGT		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.26C>T	chr4.hg19:g.174254775G>A	ENSP00000296503:p.Pro9Leu	99.0	0.0	.		87.0	43.0	.	NM_001130689	B2R4K8|D3DP37|Q5U072	Missense_Mutation	SNP	ENST00000296503.5	hg19	CCDS3816.1	.	.	.	.	.	.	.	.	.	.	G	18.67	3.673983	0.67928	.	.	ENSG00000164104	ENST00000296503;ENST00000446922;ENST00000438704;ENST00000506267	T;T;T;T	0.26067	1.76;1.76;1.76;1.76	5.45	4.61	0.57282	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (3);	0.088329	0.48767	D	0.000173	T	0.35128	0.0921	M	0.86097	2.795	0.80722	D	1	B	0.29481	0.245	B	0.28709	0.093	T	0.21621	-1.0240	10	0.42905	T	0.14	.	13.8749	0.63647	0.0744:0.0:0.9256:0.0	.	9	P26583	HMGB2_HUMAN	L	9	ENSP00000296503:P9L;ENSP00000393448:P9L;ENSP00000404912:P9L;ENSP00000423001:P9L	ENSP00000296503:P9L	P	-	2	0	HMGB2	174491350	1.000000	0.71417	0.938000	0.37757	0.038000	0.13279	9.505000	0.97989	1.313000	0.45069	0.563000	0.77884	CCG	.	.	.	none		0.627	HMGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362362.1	NM_001130688		A	174254775	G	A	174254775	3	1	113	1	0	0	0	0	1	0	0	0	7233	1116	39	1	619	1	HMGB2	4	174254775	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	17491340	174254775	16899501	22	7290											
ODZ3	55714	hgsc.bcm.edu	37	chr4	183664509	183664515	+	Frame_Shift_Del	DEL	GCGATTT	GCGATTT	-																															cgatggcagtctgtacgtagGcgatttcaactatgtgcggc																								rs189480567		TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	GCGATTT	GCGATTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr4:183664509_183664515delGCGATTT	ENST00000511685.1	+	19	3689_3695	c.3566_3572delGCGATTT	c.(3565-3573)ggcgatttcfs	p.GDF1189fs	TENM3_ENST00000502950.1_3'UTR|TENM3_ENST00000406950.2_Frame_Shift_Del_p.GDF1189fs			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1189					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.G1189G(1)									CTGTACGTAGGCGATTTCAACTATGTG	0.473																																					p.1189_1191del		Atlas-INDEL	.											.	.	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.3565_3571del						PASS	.																																			SO:0001589	frameshift_variant	55714	exon18			.	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.3566_3572delGCGATTT	chr4.hg19:g.183664509_183664515delGCGATTT	ENSP00000424226:p.Gly1189fs	112.0	0.0	0		70.0	19.0	0.271429	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Frame_Shift_Del	DEL	ENST00000511685.1	hg19	CCDS47165.1																																																																																			.	.	.	none		0.473	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			-	183664515	GCGATTT	-	183664509	7	5	113	1	0	1	0	1	0	0	0	0	10843	1203	42	0	3636	0	ODZ3	4	183664509	Frame_Shift_Del	DEL	GCGATTT	TCGA-BQ-5878-01A-11D-1589-08	9409734	183664509	7489767	23	7291											
PRLR	5618	hgsc.bcm.edu	37	chr5	35070231	35070231	+	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	agccaagacgctcaccactaGgtatctgaatgaaggtcgct	12	8	10	11	2	2	3	1	2	1	1	3	3	2	3	2	2	1	3	2	2	5	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr5:35070231G>C	ENST00000382002.5	-	7	1106	c.680C>G	c.(679-681)cCt>cGt	p.P227R	PRLR_ENST00000342362.5_Missense_Mutation_p.P126R|PRLR_ENST00000509934.1_5'UTR|PRLR_ENST00000511486.1_Missense_Mutation_p.P126R|PRLR_ENST00000231423.3_Missense_Mutation_p.P227R|PRLR_ENST00000348262.3_Missense_Mutation_p.P227R|PRLR_ENST00000542609.1_Missense_Mutation_p.P227R|PRLR_ENST00000397391.3_Missense_Mutation_p.P156R|PRLR_ENST00000310101.5_Missense_Mutation_p.P227R|PRLR_ENST00000513753.1_Missense_Mutation_p.P227R	NM_000949.5	NP_000940.1	P16471	PRLR_HUMAN	prolactin receptor	227	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of JAK2 kinase activity (GO:0042977)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cell surface receptor signaling pathway (GO:0007166)|embryo implantation (GO:0007566)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|prolactin signaling pathway (GO:0038161)|steroid biosynthetic process (GO:0006694)|T cell activation (GO:0042110)	cell surface (GO:0009986)|endosome lumen (GO:0031904)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|ornithine decarboxylase activator activity (GO:0042978)|peptide hormone binding (GO:0017046)|prolactin receptor activity (GO:0004925)|protein homodimerization activity (GO:0042803)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	48	all_lung(31;3.83e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)		Fluoxymesterone(DB01185)|Somatropin recombinant(DB00052)	CTCACCACTAGGTATCTGAAT	0.418																																					p.P227R		Atlas-SNP	.											.	PRLR	90	.	0			c.C680G						PASS	.						105	89	94					5																	35070231		2203	4300	6503	SO:0001583	missense	5618	exon7			CCACTAGGTATCT		CCDS3909.1, CCDS56358.1, CCDS56359.1, CCDS56360.1, CCDS56361.1, CCDS56362.1	5p14-p13	2013-02-27			ENSG00000113494	ENSG00000113494			9446	protein-coding gene	gene with protein product		176761					Standard	NM_001204315		Approved		uc003jjm.3	P16471	OTTHUMG00000090789	ENST00000382002.5:c.680C>G	chr5.hg19:g.35070231G>C	ENSP00000371432:p.Pro227Arg	66.0	0.0	.		49.0	19.0	.	NM_000949	B2R882|D1MDP1|Q16354|Q8TD75|Q8TD78|Q96P35|Q96P36|Q9BX87|Q9UHJ5	Missense_Mutation	SNP	ENST00000382002.5	hg19	CCDS3909.1	.	.	.	.	.	.	.	.	.	.	G	14.72	2.620133	0.46736	.	.	ENSG00000113494	ENST00000231423;ENST00000513753;ENST00000348262;ENST00000397391;ENST00000542609;ENST00000342362;ENST00000382002;ENST00000511486;ENST00000310101	T;T;T;T;T;T;T;T;T	0.49432	0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78	5.65	5.65	0.86999	Fibronectin, type III (2);	0.000000	0.85682	D	0.000000	T	0.74382	0.3709	M	0.90542	3.125	0.58432	D	0.999993	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.998;0.999;1.0;0.998;0.997;0.996;0.994	T	0.79629	-0.1724	10	0.87932	D	0	-15.5927	15.3486	0.74363	0.0:0.0:0.8598:0.1401	.	227;227;126;156;227;227;227	P16471-3;P16471;P16471-2;Q8TD76;P16471-7;P16471-6;P16471-4	.;PRLR_HUMAN;.;.;.;.;.	R	227;227;227;156;227;126;227;126;227	ENSP00000231423:P227R;ENSP00000424841:P227R;ENSP00000311613:P227R;ENSP00000380546:P156R;ENSP00000441813:P227R;ENSP00000339213:P126R;ENSP00000371432:P227R;ENSP00000422556:P126R;ENSP00000309008:P227R	ENSP00000231423:P227R	P	-	2	0	PRLR	35105988	1.000000	0.71417	0.986000	0.45419	0.092000	0.18411	6.868000	0.75516	2.668000	0.90789	0.655000	0.94253	CCT	.	.	.	none		0.418	PRLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207575.2			C	35070231	G	C	35070231	3	2	113	1	0	0	0	0	1	0	0	0	12541	1000	35	4	1204	4	PRLR	5	35070231	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08		35070231	145845029	24	7292											
SPOCK1	6695	hgsc.bcm.edu	37	chr5	136328174	136328174	+	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	atatttaaaatggtcttactGccttgggctgtgttggagct	8	16	11	6	0	1	0	0	0	1	0	1	1	1	1	1	3	3	3	1	3	4	6			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr5:136328174G>A	ENST00000394945.1	-	7	874	c.705C>T	c.(703-705)ggC>ggT	p.G235G	SPOCK1_ENST00000282223.7_Splice_Site_p.G235G	NM_004598.3	NP_004589.1	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1	235					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)			TGGTCTTACTGCCTTGGGCTG	0.438																																					p.G235G		Atlas-SNP	.											.	SPOCK1	58	.	0			c.C705T						PASS	.						161	152	155					5																	136328174		2203	4300	6503	SO:0001630	splice_region_variant	6695	exon7			CTTACTGCCTTGG	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.706+1C>T	chr5.hg19:g.136328174G>A		163.0	0.0	.		122.0	48.0	.	NM_004598	B3KSW3|Q59EW0|Q8N630|Q9UCL8	Silent	SNP	ENST00000394945.1	hg19	CCDS4191.1																																																																																			.	.	.	none		0.438	SPOCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251222.1	NM_004598	Silent	A	136328174	G	A	136328174	5	1	113	1	0	0	0	0	0	0	1	0	15091	1333	46	2	634	2	SPOCK1	5	136328174	Splice_Site	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	101257943	136328174	44587086	25	7293											
KDM3B	51780	hgsc.bcm.edu	37	chr5	137715373	137715373	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcaggactccatcactcgTcttatggaggtgtctgtaac	9	12	9	11	1	4	0	2	0	2	0	6	2	5	2	1	3	1	1	1	3	2	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr5:137715373T>C	ENST00000314358.5	+	5	881	c.681T>C	c.(679-681)cgT>cgC	p.R227R		NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	227					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						CCATCACTCGTCTTATGGAGG	0.483																																					p.R227R		Atlas-SNP	.											.	KDM3B	177	.	0			c.T681C						PASS	.						174	148	157					5																	137715373		2203	4300	6503	SO:0001819	synonymous_variant	51780	exon5			CACTCGTCTTATG	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.681T>C	chr5.hg19:g.137715373T>C		105.0	0.0	.		103.0	37.0	.	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Silent	SNP	ENST00000314358.5	hg19	CCDS34242.1																																																																																			.	.	.	none		0.483	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604		C	137715373	T	C	137715373	2	2	113	1	0	0	0	0	0	0	0	1	8134	1654	58	3		3	KDM3B	5	137715373	Silent	SNP	T	TCGA-BQ-5878-01A-11D-1589-08	1387199	137715373	43199887	26	7294											
PSD2	84249	hgsc.bcm.edu	37	chr5	139197069	139197069	+	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	ccatactctcctggcagcaaCgagtttagcaggctggtggc	8	9	12	12	1	1	0	0	0	1	0	2	1	1	0	2	4	4	5	2	4	3	3	rs142589356		TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr5:139197069C>T	ENST00000274710.3	+	5	1225	c.1020C>T	c.(1018-1020)aaC>aaT	p.N340N		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	340	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGCAGCAACGAGTTTAGCA	0.592																																					p.N340N		Atlas-SNP	.											.	PSD2	88	.	0			c.C1020T						PASS	.	C		0,4406		0,0,2203	81	76	78		1020	-0.2	1	5	dbSNP_134	78	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	PSD2	NM_032289.2		0,4,6499	TT,TC,CC		0.0465,0.0,0.0308		340/772	139197069	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	84249	exon5			CAGCAACGAGTTT	AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"Pleckstrin homology (PH) domain containing"	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.1020C>T	chr5.hg19:g.139197069C>T		68.0	0.0	.		62.0	21.0	.	NM_032289	D3DQD3|Q8N3J8	Silent	SNP	ENST00000274710.3	hg19	CCDS4216.1																																																																																			.	C|1.000;T|0.000	0.000	weak		0.592	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289		T	139197069	C	T	139197069	2	4	113	1	0	0	0	0	0	0	0	1	12657	535	19	1		1	PSD2	5	139197069	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	1481696	139197069	41718191	27	7295											
PCDHB15	56121	hgsc.bcm.edu	37	chr5	140625417	140625417	+	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	tgatattaaatgagaagctgGaccgggagaagctgtgtggc	12	9	15	5	1	0	3	0	2	0	2	0	6	0	4	1	3	2	2	1	3	5	2	rs564192004		TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr5:140625417G>C	ENST00000231173.3	+	1	271	c.271G>C	c.(271-273)Gac>Cac	p.D91H		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	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)|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)			TGAGAAGCTGGACCGGGAGAA	0.498													G|||	1	0.000199681	8e-04	0	5008	,	,		17009	0		0	False		,,,				2504	0				p.D91H		Atlas-SNP	.											.	PCDHB15	138	.	0			c.G271C						PASS	.						54	61	59					5																	140625417		2203	4300	6503	SO:0001583	missense	56121	exon1			AAGCTGGACCGGG	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.271G>C	chr5.hg19:g.140625417G>C	ENSP00000231173:p.Asp91His	127.0	0.0	.		99.0	8.0	.	NM_018935	Q8IUX5	Missense_Mutation	SNP	ENST00000231173.3	hg19	CCDS4257.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.964851	0.74131	.	.	ENSG00000113248	ENST00000231173	T	0.53640	0.61	4.92	4.92	0.64577	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.82121	0.4968	H	0.98849	4.35	0.58432	D	0.999994	D	0.89917	1.0	D	0.97110	1.0	D	0.89982	0.4101	9	0.87932	D	0	.	18.0878	0.89463	0.0:0.0:1.0:0.0	.	91	Q9Y5E8	PCDBF_HUMAN	H	91	ENSP00000231173:D91H	ENSP00000231173:D91H	D	+	1	0	PCDHB15	140605601	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	9.804000	0.99143	2.442000	0.82660	0.491000	0.48974	GAC	.	.	.	none		0.498	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935		C	140625417	G	C	140625417	3	2	113	1	0	0	0	0	1	0	0	0	11547	1174	41	4	273	4	PCDHB15	5	140625417	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	1428348	140625417	40289843	28	7296											
F13A1	2162	hgsc.bcm.edu	37	chr6	6196094	6196094	+	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	cgtgcttgatggcttgaaccGaggcggggccacaccgatac	8	7	14	12	4	0	2	0	2	0	0	0	4	0	2	3	4	3	2	3	4	2	3			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr6:6196094G>A	ENST00000264870.3	-	10	1506	c.1241C>T	c.(1240-1242)tCg>tTg	p.S414L		NM_000129.3	NP_000120.2	P00488	F13A_HUMAN	coagulation factor XIII, A1 polypeptide	414					blood coagulation (GO:0007596)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	62	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	GGCTTGAACCGAGGCGGGGCC	0.502																																					p.S414L		Atlas-SNP	.											.	F13A1	135	.	0			c.C1241T	GRCh37	CM023371|CM993150	F13A1	M		PASS	.						96	77	84					6																	6196094		2203	4300	6503	SO:0001583	missense	2162	exon10			TGAACCGAGGCGG	M14539	CCDS4496.1	6p24.2-p23	2014-01-24			ENSG00000124491	ENSG00000124491		"Transglutaminases"	3531	protein-coding gene	gene with protein product		134570		F13A			Standard	NM_000129		Approved		uc003mwv.3	P00488	OTTHUMG00000014186	ENST00000264870.3:c.1241C>T	chr6.hg19:g.6196094G>A	ENSP00000264870:p.Ser414Leu	37.0	0.0	.		37.0	10.0	.	NM_000129	Q59HA7|Q8N6X2|Q96P24|Q9BX29	Missense_Mutation	SNP	ENST00000264870.3	hg19	CCDS4496.1	.	.	.	.	.	.	.	.	.	.	G	19.46	3.831865	0.71258	.	.	ENSG00000124491	ENST00000264870;ENST00000441301	T	0.55234	0.53	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.71400	0.3335	M	0.81802	2.56	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.989;0.999	T	0.74621	-0.3604	10	0.87932	D	0	.	18.7232	0.91703	0.0:0.0:1.0:0.0	.	351;414	F5H080;P00488	.;F13A_HUMAN	L	414;351	ENSP00000264870:S414L	ENSP00000264870:S414L	S	-	2	0	F13A1	6141093	1.000000	0.71417	0.928000	0.36995	0.036000	0.12997	9.131000	0.94446	2.728000	0.93425	0.655000	0.94253	TCG	.	.	.	none		0.502	F13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039756.3	NM_000129		A	6196094	G	A	6196094	3	1	113	1	0	0	0	0	1	0	0	0	5342	1059	37	1	981	1	F13A1	6	6196094	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08		6196094	164918973	29	7297											
ZNF318	24149	hgsc.bcm.edu	37	chr6	43320114	43320114	+	Splice_Site	DEL	C	C	-																															gtcatgcaaagcagctgataCcttgttgtttatgaagccgc																										TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr6:43320114delC	ENST00000361428.2	-	5	2848		c.e5+1		ZNF318_ENST00000318149.3_Splice_Site	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318						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)			GCAGCTGATACCTTGTTGTTT	0.418																																					.		Atlas-INDEL	.											.	ZNF318	175	.	0			c.2770+2G>-						PASS	.						110	97	102					6																	43320114		2203	4300	6503	SO:0001630	splice_region_variant	24149	exon6			.	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.2770+1G>-	chr6.hg19:g.43320114delC		66.0	0.0	0		68.0	30.0	0.441176	NM_014345	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Splice_Site	DEL	ENST00000361428.2	hg19	CCDS4895.2																																																																																			.	.	.	none		0.418	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345	Intron	-	43320114	C	-	43320114	8	5	113	1	0	1	0	1	0	0	1	0	17848	521	18	0	4092	0	ZNF318	6	43320114	Splice_Site	DEL	C	TCGA-BQ-5878-01A-11D-1589-08	37124020	43320114	127794953	30	7298											
GFRAL	389400	hgsc.bcm.edu	37	chr6	55223928	55223928	+	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	gcacatgcttcatagaaaatCatgtttcagtaagttcccca	13	12	6	10	0	3	1	3	0	0	1	4	1	4	1	2	0	1	5	2	0	4	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr6:55223928C>T	ENST00000340465.2	+	6	1030	c.944C>T	c.(943-945)tCa>tTa	p.S315L		NM_207410.2	NP_997293.2	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like	315					negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|stress-activated protein kinase signaling cascade (GO:0031098)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.S315L(1)		NS(1)|breast(1)|endometrium(2)|kidney(5)|large_intestine(2)|liver(1)|lung(31)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	48	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			CATAGAAAATCATGTTTCAGT	0.343																																					p.S315L		Atlas-SNP	.											GFRAL,NS,carcinoma,0,1	GFRAL	91	.	1	Substitution - Missense(1)	lung(1)	c.C944T						PASS	.						62	61	61					6																	55223928		2203	4299	6502	SO:0001583	missense	389400	exon6			GAAAATCATGTTT	AY358198	CCDS4957.1	6p12.1	2007-06-22			ENSG00000187871	ENSG00000187871			32789	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 144"	C6orf144		16086688	Standard	NM_207410		Approved	GRAL, UNQ9356, bA360D14.1	uc003pcm.1	Q6UXV0	OTTHUMG00000014900	ENST00000340465.2:c.944C>T	chr6.hg19:g.55223928C>T	ENSP00000343636:p.Ser315Leu	88.0	0.0	.		85.0	9.0	.	NM_207410	Q5VTF6	Missense_Mutation	SNP	ENST00000340465.2	hg19	CCDS4957.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.941217	0.73557	.	.	ENSG00000187871	ENST00000340465	T	0.63417	-0.04	5.52	4.66	0.58398	GDNF/GAS1 (2);	0.157695	0.42682	D	0.000663	T	0.70193	0.3196	M	0.65498	2.005	0.39285	D	0.964639	D	0.89917	1.0	D	0.97110	1.0	T	0.74589	-0.3615	10	0.54805	T	0.06	-7.1541	14.1925	0.65646	0.0:0.9283:0.0:0.0717	.	315	Q6UXV0	GFRAL_HUMAN	L	315	ENSP00000343636:S315L	ENSP00000343636:S315L	S	+	2	0	GFRAL	55331887	1.000000	0.71417	0.682000	0.30024	0.971000	0.66376	5.350000	0.66016	1.327000	0.45338	0.557000	0.71058	TCA	.	.	.	none		0.343	GFRAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040995.2	NM_207410		T	55223928	C	T	55223928	3	4	113	1	0	0	0	0	1	0	0	0	6358	838	29	2	966	2	GFRAL	6	55223928	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	11903814	55223928	115891139	31	7299											
AIM1	202	hgsc.bcm.edu	37	chr6	106968949	106968949	+	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	agtgtcacagcccacgactgAgggtgccccgccctgtggtt	6	8	13	14	2	1	1	1	1	0	0	1	2	1	1	4	2	2	1	4	2	0	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr6:106968949A>T	ENST00000369066.3	+	2	3129	c.2642A>T	c.(2641-2643)gAg>gTg	p.E881V		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)		CCCACGACTGAGGGTGCCCCG	0.478																																					p.E881V		Atlas-SNP	.											.	AIM1	161	.	0			c.A2642T						PASS	.						70	75	73					6																	106968949		2203	4300	6503	SO:0001583	missense	202	exon2			CGACTGAGGGTGC	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.2642A>T	chr6.hg19:g.106968949A>T	ENSP00000358062:p.Glu881Val	127.0	0.0	.		142.0	62.0	.	NM_001624	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	hg19	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	A	13.00	2.105028	0.37145	.	.	ENSG00000112297	ENST00000285105;ENST00000369066	T	0.73047	-0.71	5.99	4.82	0.62117	.	1.203230	0.05682	N	0.590607	T	0.57770	0.2076	M	0.68317	2.08	0.48830	D	0.999719	B	0.26672	0.156	B	0.21917	0.037	T	0.57277	-0.7839	10	0.72032	D	0.01	.	10.8946	0.47015	0.9291:0.0:0.0709:0.0	.	881	Q9Y4K1	AIM1_HUMAN	V	1289;881	ENSP00000358062:E881V	ENSP00000285105:E1289V	E	+	2	0	AIM1	107075642	1.000000	0.71417	0.609000	0.28983	0.728000	0.41692	4.089000	0.57685	1.079000	0.41038	0.533000	0.62120	GAG	.	.	.	none		0.478	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			T	106968949	A	T	106968949	3	4	113	1	0	0	0	0	1	0	0	0	430	304	11	5	2648	5	AIM1	6	106968949	Missense_Mutation	SNP	A	TCGA-BQ-5878-01A-11D-1589-08	51745021	106968949	64146118	32	7300											
CTGF	1490	hgsc.bcm.edu	37	chr6	132271489	132271489	+	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	ctcgtcacacacccactcctCgcagcatttcccgggcagct	7	8	7	19	3	1	0	1	0	0	0	5	0	3	0	3	1	2	4	3	1	0	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr6:132271489C>T	ENST00000367976.3	-	3	684	c.484G>A	c.(484-486)Gag>Aag	p.E162K	RP11-69I8.3_ENST00000435287.1_RNA	NM_001901.2	NP_001892	P29279	CTGF_HUMAN	connective tissue growth factor	162	VWFC. {ECO:0000255|PROSITE- ProRule:PRU00220}.				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)		ACCCACTCCTCGCAGCATTTC	0.652											OREG0017666	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E162K	Esophageal Squamous(127;510 1660 12817 24400 38449)	Atlas-SNP	.											.	CTGF	36	.	0			c.G484A						PASS	.						90	91	91					6																	132271489		2203	4300	6503	SO:0001583	missense	1490	exon3			ACTCCTCGCAGCA	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.484G>A	chr6.hg19:g.132271489C>T	ENSP00000356954:p.Glu162Lys	170.0	0.0	.	1594	185.0	79.0	.	NM_001901	E1P578|Q6LCY0|Q96A79|Q96QX2|Q9UDL6	Missense_Mutation	SNP	ENST00000367976.3	hg19	CCDS5151.1	.	.	.	.	.	.	.	.	.	.	C	37	5.984351	0.97173	.	.	ENSG00000118523	ENST00000367976	T	0.71579	-0.58	5.57	5.57	0.84162	von Willebrand factor, type C (4);	0.049682	0.85682	D	0.000000	T	0.80732	0.4679	M	0.63208	1.945	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80946	-0.1155	10	0.59425	D	0.04	.	19.5503	0.95314	0.0:1.0:0.0:0.0	.	162	P29279	CTGF_HUMAN	K	162	ENSP00000356954:E162K	ENSP00000356954:E162K	E	-	1	0	CTGF	132313182	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	7.818000	0.86416	2.619000	0.88677	0.561000	0.74099	GAG	.	.	.	none		0.652	CTGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042239.2	NM_001901		T	132271489	C	T	132271489	3	4	113	1	0	0	0	0	1	0	0	0	4010	893	31	1	577	1	CTGF	6	132271489	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	25302540	132271489	38843578	33	7301											
BCLAF1	9774	hgsc.bcm.edu	37	chr6	136596669	136596669	+	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	tactaaacatactaagcataCctttaacatgatgaaccaag	18	10	4	9	0	0	2	0	2	0	0	0	2	0	2	2	0	7	1	2	0	9	7			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr6:136596669C>T	ENST00000531224.1	-	6	2105		c.e6+1		BCLAF1_ENST00000530767.1_Splice_Site|BCLAF1_ENST00000353331.4_Splice_Site|BCLAF1_ENST00000527536.1_Splice_Site|BCLAF1_ENST00000527759.1_Splice_Site|BCLAF1_ENST00000392348.2_Splice_Site	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1						apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		ACTAAGCATACCTTTAACATG	0.358																																					.	Colon(142;1534 1789 5427 7063 28491)	Atlas-SNP	.											.	BCLAF1	203	.	0			c.1852+1G>A						PASS	.						146	131	136					6																	136596669		2203	4300	6503	SO:0001630	splice_region_variant	9774	exon7			AGCATACCTTTAA	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.1852+1G>A	chr6.hg19:g.136596669C>T		143.0	0.0	.		175.0	8.0	.	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Splice_Site	SNP	ENST00000531224.1	hg19	CCDS5177.1	.	.	.	.	.	.	.	.	.	.	C	16.19	3.053045	0.55218	.	.	ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000530767;ENST00000527759;ENST00000392348;ENST00000529826	.	.	.	5.14	5.14	0.70334	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.9665	0.86287	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	BCLAF1	136638362	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	6.683000	0.74533	2.661000	0.90470	0.460000	0.39030	.	.	.	.	none		0.358	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739	Intron	T	136596669	C	T	136596669	5	4	113	1	0	0	0	0	0	0	1	0	1383	521	18	2	941	2	BCLAF1	6	136596669	Splice_Site	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	4325180	136596669	34518398	34	7302											
SASH1	23328	hgsc.bcm.edu	37	chr6	148808752	148808752	+	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	catttcttcttgttacagctCaaggaatacgaggcccagca	11	11	8	11	1	3	0	1	0	2	0	3	2	3	1	1	2	4	3	1	2	4	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr6:148808752C>G	ENST00000367467.3	+	8	1105	c.630C>G	c.(628-630)ctC>ctG	p.L210L		NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	210					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)		TGTTACAGCTCAAGGAATACG	0.488																																					p.L210L		Atlas-SNP	.											.	SASH1	123	.	0			c.C630G						PASS	.						93	99	97					6																	148808752		2203	4300	6503	SO:0001819	synonymous_variant	23328	exon8			ACAGCTCAAGGAA	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.630C>G	chr6.hg19:g.148808752C>G		221.0	0.0	.		194.0	68.0	.	NM_015278	Q5TGN5|Q8TAI0|Q9H7R7	Silent	SNP	ENST00000367467.3	hg19	CCDS5212.1																																																																																			.	.	.	none		0.488	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278		G	148808752	C	G	148808752	2	3	113	1	0	0	0	0	0	0	0	1	13861	813	29	4		4	SASH1	6	148808752	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	12212083	148808752	22306315	35	7303											
TNRC18	84629	hgsc.bcm.edu	37	chr7	5352384	5352384	+	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	tcttgcctggggagtgggccGagggccgcgccttgccggcc	2	7	18	14	4	1	0	0	0	1	0	1	2	1	1	6	5	2	0	6	5	0	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr7:5352384G>A	ENST00000430969.1	-	27	8486	c.8138C>T	c.(8137-8139)tCg>tTg	p.S2713L	TNRC18_ENST00000399537.4_Missense_Mutation_p.S2713L	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2713							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)		GGAGTGGGCCGAGGGCCGCGC	0.761																																					p.S2713L		Atlas-SNP	.											TNRC18_ENST00000430969,colon,carcinoma,0,3	TNRC18	311	.	0			c.C8138T						PASS	.						4	6	6					7																	5352384		1215	2847	4062	SO:0001583	missense	84629	exon27			TGGGCCGAGGGCC	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.8138C>T	chr7.hg19:g.5352384G>A	ENSP00000395538:p.Ser2713Leu	39.0	0.0	.		38.0	7.0	.	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	hg19	CCDS47534.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	6.791|6.791	0.514848|0.514848	0.12944|0.12944	.|.	.|.	ENSG00000182095|ENSG00000182095	ENST00000399544|ENST00000399537;ENST00000430969	.|T;T	.|0.05258	.|3.47;3.47	4.31|4.31	2.46|2.46	0.29980|0.29980	.|.	.|.	.|.	.|.	.|.	T|T	0.06280|0.06280	0.0162|0.0162	L|L	0.46157|0.46157	1.445|1.445	0.09310|0.09310	N|N	1|1	.|B	.|0.12013	.|0.005	.|B	.|0.06405	.|0.002	T|T	0.45026|0.45026	-0.9289|-0.9289	6|9	0.87932|0.09590	D|T	0|0.72	.|.	10.6731|10.6731	0.45770|0.45770	0.1532:0.0:0.8468:0.0|0.1532:0.0:0.8468:0.0	.|.	.|2713	.|O15417	.|TNC18_HUMAN	W|L	1226|2713	.|ENSP00000382452:S2713L;ENSP00000395538:S2713L	ENSP00000382459:R1226W|ENSP00000382452:S2713L	R|S	-|-	1|2	2|0	TNRC18|TNRC18	5318910|5318910	0.746000|0.746000	0.28272|0.28272	0.001000|0.001000	0.08648|0.08648	0.012000|0.012000	0.07955|0.07955	2.496000|2.496000	0.45346|0.45346	0.246000|0.246000	0.21394|0.21394	0.484000|0.484000	0.47621|0.47621	CGG|TCG	.	.	.	none		0.761	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	5352384	G	A	5352384	3	1	113	1	0	0	0	0	1	0	0	0	16351	1059	37	1	784	1	TNRC18	7	5352384	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08		5352384	153786279	36	7304											
TNS3	64759	hgsc.bcm.edu	37	chr7	47440438	47440438	+	Missense_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	ccagcccgtagccctgcacaGccccagtgtgaaactgcagg	9	5	11	16	1	0	1	0	1	0	0	0	1	0	1	5	1	6	3	5	1	2	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr7:47440438G>A	ENST00000398879.1	-	14	1163	c.797C>T	c.(796-798)gCt>gTt	p.A266V	TNS3_ENST00000311160.9_Missense_Mutation_p.A266V|TNS3_ENST00000355730.3_Intron			Q68CZ2	TENS3_HUMAN	tensin 3	266	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				cell migration (GO:0016477)|lung alveolus development (GO:0048286)|positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(17)|endometrium(5)|kidney(4)|large_intestine(7)|liver(1)|lung(16)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	64						GCCCTGCACAGCCCCAGTGTG	0.577																																					p.A266V		Atlas-SNP	.											.	TNS3	140	.	0			c.C797T						PASS	.						78	98	91					7																	47440438		2047	4182	6229	SO:0001583	missense	64759	exon14			TGCACAGCCCCAG	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.797C>T	chr7.hg19:g.47440438G>A	ENSP00000381854:p.Ala266Val	95.0	0.0	.		92.0	38.0	.	NM_022748	B2RNV1|Q6IPQ2|Q8IZW7|Q8NAD0|Q96PE0|Q96S48	Missense_Mutation	SNP	ENST00000398879.1	hg19	CCDS5506.2	.	.	.	.	.	.	.	.	.	.	G	25.5	4.643525	0.87859	.	.	ENSG00000136205	ENST00000311160;ENST00000538633;ENST00000398879;ENST00000457718;ENST00000450444	D;D;D;D	0.84800	-1.9;-1.9;-1.9;-1.9	4.99	4.99	0.66335	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.86793	0.6018	M	0.74546	2.27	0.80722	D	1	P	0.46859	0.885	P	0.45753	0.492	D	0.87020	0.2128	10	0.39692	T	0.17	-16.8831	15.8183	0.78621	0.0:0.0:1.0:0.0	.	266	Q68CZ2	TENS3_HUMAN	V	266;376;266;369;355	ENSP00000312143:A266V;ENSP00000381854:A266V;ENSP00000414358:A369V;ENSP00000396914:A355V	ENSP00000312143:A266V	A	-	2	0	TNS3	47406963	1.000000	0.71417	0.436000	0.26797	0.965000	0.64279	7.322000	0.79097	2.337000	0.79520	0.456000	0.33151	GCT	.	.	.	none		0.577	TNS3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157253.1	NM_022748		A	47440438	G	A	47440438	3	1	113	1	0	0	0	0	1	0	0	0	16356	971	34	2	3612	2	TNS3	7	47440438	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	42088054	47440438	111698225	37	7305											
PPP1R9A	55607	hgsc.bcm.edu	37	chr7	94915545	94915545	+	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	ccttcaatgatgacttcagtCccagcagtaccagttcagca	11	10	7	13	0	3	2	3	2	0	0	4	2	4	2	3	0	3	4	3	0	2	4			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr7:94915545C>A	ENST00000433881.1	+	13	3317	c.2785C>A	c.(2785-2787)Ccc>Acc	p.P929T	PPP1R9A_ENST00000340694.4_Missense_Mutation_p.P929T|PPP1R9A_ENST00000289495.5_Missense_Mutation_p.P1135T|PPP1R9A_ENST00000433360.1_Missense_Mutation_p.P1213T|PPP1R9A_ENST00000424654.1_Missense_Mutation_p.P1153T|PPP1R9A_ENST00000456331.2_Missense_Mutation_p.P1153T			Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory subunit 9A	929	Interacts with TGN38. {ECO:0000250}.				actin filament organization (GO:0007015)|calcium-mediated signaling (GO:0019722)|neuron projection development (GO:0031175)	cell junction (GO:0030054)|cortical actin cytoskeleton (GO:0030864)|dendritic spine (GO:0043197)|filopodium (GO:0030175)|growth cone (GO:0030426)|synapse (GO:0045202)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(11)|liver(2)|lung(22)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(8)|urinary_tract(5)	71	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)			TGACTTCAGTCCCAGCAGTAC	0.453										HNSCC(28;0.073)																											p.P1213T		Atlas-SNP	.											.	PPP1R9A	264	.	0			c.C3637A						PASS	.						94	84	87					7																	94915545		2203	4300	6503	SO:0001583	missense	55607	exon18			TTCAGTCCCAGCA	AB033048	CCDS34683.1, CCDS55127.1, CCDS55128.1	7q21.3	2013-01-10	2011-10-04		ENSG00000158528	ENSG00000158528		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Sterile alpha motif (SAM) domain containing"	14946	protein-coding gene	gene with protein product		602468	"protein phosphatase 1, regulatory (inhibitor) subunit 9A"			10574462	Standard	NM_001166160		Approved	Neurabin-I, KIAA1222, FLJ20068	uc010lfj.3	Q9ULJ8	OTTHUMG00000155566	ENST00000433881.1:c.2785C>A	chr7.hg19:g.94915545C>A	ENSP00000398870:p.Pro929Thr	55.0	0.0	.		64.0	23.0	.	NM_001166160	A1L494|B2RWQ1|E9PCA0|E9PCK6|E9PDX1|F8W7J9|O76059|Q9NXT2	Missense_Mutation	SNP	ENST00000433881.1	hg19	CCDS34683.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.022533	0.75275	.	.	ENSG00000158528	ENST00000433360;ENST00000340694;ENST00000424654;ENST00000433881;ENST00000289495;ENST00000456331	T;T;T;T;T;T	0.19669	2.14;2.32;2.18;2.32;2.13;2.18	4.99	4.99	0.66335	.	0.219511	0.40728	N	0.001031	T	0.37183	0.0994	L	0.34521	1.04	0.35638	D	0.810778	D;D;D;D;D;P	0.89917	0.979;1.0;0.999;1.0;0.999;0.682	P;D;D;D;D;B	0.79108	0.525;0.992;0.973;0.972;0.941;0.096	T	0.31888	-0.9927	10	0.45353	T	0.12	.	18.8526	0.92238	0.0:1.0:0.0:0.0	.	929;1135;1213;1153;1153;929	B7ZLX4;F8W7J9;E9PDX1;D6W5R0;E9PCK6;Q9ULJ8	.;.;.;.;.;NEB1_HUMAN	T	1213;929;1153;929;1135;1153	ENSP00000405514:P1213T;ENSP00000344524:P929T;ENSP00000411342:P1153T;ENSP00000398870:P929T;ENSP00000289495:P1135T;ENSP00000402893:P1153T	ENSP00000289495:P1135T	P	+	1	0	PPP1R9A	94753481	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	2.886000	0.48578	2.758000	0.94735	0.655000	0.94253	CCC	.	.	.	none		0.453	PPP1R9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340662.1	NM_001166160		A	94915545	C	A	94915545	3	1	113	1	0	0	0	0	1	0	0	0	12388	855	30	4	3703	4	PPP1R9A	7	94915545	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	47475107	94915545	64223118	38	7306											
AMAC1L2	83650	hgsc.bcm.edu	37	chr8	11188670	11188670	+	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	actccacacacccatcgccgCcctccgctccacccagcctc	7	5	4	25	3	0	0	0	0	0	0	5	0	3	0	8	0	1	1	8	0	0	0			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr8:11188670C>T	ENST00000382435.4	+	1	274	c.55C>T	c.(55-57)Ccc>Tcc	p.P19S		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	19						integral component of membrane (GO:0016021)											CCCATCGCCGCCCTCCGCTCC	0.677																																					p.P19S		Atlas-SNP	.											.	.	.	.	0			c.C55T						PASS	.						54	56	55					8																	11188670		2203	4300	6503	SO:0001583	missense	83650	exon1			TCGCCGCCCTCCG	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"Solute carriers"	15546	protein-coding gene	gene with protein product		615199	"acyl-malonyl condensing enzyme 1-like 2"	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.55C>T	chr8.hg19:g.11188670C>T	ENSP00000371872:p.Pro19Ser	82.0	0.0	.		72.0	28.0	.	NM_054028	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	hg19	CCDS5980.1	.	.	.	.	.	.	.	.	.	.	C	10.07	1.250440	0.22880	.	.	ENSG00000177710	ENST00000382435	T	0.27256	1.68	0.34	0.34	0.15985	.	0.159640	0.29321	N	0.012484	T	0.28797	0.0714	N	0.24115	0.695	0.09310	N	0.999993	D	0.89917	1.0	D	0.80764	0.994	T	0.08310	-1.0728	9	0.35671	T	0.21	-11.4858	.	.	.	.	19	Q96KT7	S35G5_HUMAN	S	19	ENSP00000371872:P19S	ENSP00000371872:P19S	P	+	1	0	SLC35G5	11226080	0.007000	0.16637	0.221000	0.23827	0.172000	0.22775	0.166000	0.16583	0.426000	0.26116	0.089000	0.15464	CCC	.	.	.	none		0.677	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028		T	11188670	C	T	11188670	3	4	113	1	0	0	0	0	1	0	0	0	560	739	26	2	57	2	AMAC1L2	8	11188670	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08		11188670	135175352	39	7307											
ANK1	286	hgsc.bcm.edu	37	chr8	41577342	41577342	+	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	ggacacagtcgaggtggtctCcctgagccgccatgtgaatt	8	9	13	11	2	1	2	0	2	1	0	3	4	1	3	3	3	1	0	3	3	1	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr8:41577342C>T	ENST00000347528.4	-	10	1027	c.944G>A	c.(943-945)gGa>gAa	p.G315E	ANK1_ENST00000265709.8_Missense_Mutation_p.G348E|ANK1_ENST00000396942.1_Missense_Mutation_p.G315E|ANK1_ENST00000379758.2_Missense_Mutation_p.G315E|ANK1_ENST00000352337.4_Missense_Mutation_p.G315E|ANK1_ENST00000289734.7_Missense_Mutation_p.G315E|ANK1_ENST00000396945.1_Missense_Mutation_p.G315E	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	315	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)			GAGGTGGTCTCCCTGAGCCGC	0.567																																					p.G348E		Atlas-SNP	.											.	ANK1	497	.	0			c.G1043A						PASS	.						178	151	160					8																	41577342		2203	4300	6503	SO:0001583	missense	286	exon10			TGGTCTCCCTGAG	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.944G>A	chr8.hg19:g.41577342C>T	ENSP00000339620:p.Gly315Glu	157.0	0.0	.		142.0	57.0	.	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Missense_Mutation	SNP	ENST00000347528.4	hg19	CCDS6119.1	.	.	.	.	.	.	.	.	.	.	C	32	5.138021	0.94517	.	.	ENSG00000029534	ENST00000347528;ENST00000289734;ENST00000379758;ENST00000396945;ENST00000396942;ENST00000352337;ENST00000265709;ENST00000358820	T;T;T;T;T;T;T	0.62232	0.04;0.04;0.04;0.04;0.04;0.04;0.04	5.91	5.91	0.95273	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.69106	0.3074	N	0.17345	0.48	0.80722	D	1	D;D;P;D;D	0.89917	1.0;1.0;0.744;1.0;1.0	D;D;B;D;D	0.97110	1.0;1.0;0.414;0.988;1.0	T	0.71728	-0.4505	10	0.54805	T	0.06	.	20.2963	0.98556	0.0:1.0:0.0:0.0	.	348;315;315;315;315	P16157-21;P16157-4;P16157;P16157-5;P16157-3	.;.;ANK1_HUMAN;.;.	E	315;315;315;315;315;315;348;315	ENSP00000339620:G315E;ENSP00000289734:G315E;ENSP00000369082:G315E;ENSP00000380149:G315E;ENSP00000380147:G315E;ENSP00000309131:G315E;ENSP00000265709:G348E	ENSP00000265709:G348E	G	-	2	0	ANK1	41696499	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.757000	0.85209	2.813000	0.96785	0.655000	0.94253	GGA	.	.	.	none		0.567	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		T	41577342	C	T	41577342	3	4	113	1	0	0	0	0	1	0	0	0	620	855	30	2	5187	2	ANK1	8	41577342	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	30388672	41577342	104786680	40	7308											
SPIN1	10927	hgsc.bcm.edu	37	chr9	91083448	91083448	+	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	tttacattacctatgagaaaGaccctgtcttgtacatgtac	12	14	6	9	0	1	2	0	1	1	2	1	3	1	2	2	0	4	2	2	0	6	7			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr9:91083448G>C	ENST00000375859.3	+	5	795	c.517G>C	c.(517-519)Gac>Cac	p.D173H	SPIN1_ENST00000541629.1_Missense_Mutation_p.D173H|SPIN1_ENST00000469017.2_3'UTR	NM_006717.2	NP_006708.2	Q9Y657	SPIN1_HUMAN	spindlin 1	173	Tudor-like domain 2.				chromatin modification (GO:0016568)|gamete generation (GO:0007276)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|positive regulation of Wnt signaling pathway (GO:0030177)|rRNA transcription (GO:0009303)|Wnt signaling pathway (GO:0016055)	nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle (GO:0005819)	methylated histone binding (GO:0035064)			endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	4						CTATGAGAAAGACCCTGTCTT	0.403																																					p.D173H		Atlas-SNP	.											.	SPIN1	22	.	0			c.G517C						PASS	.						188	182	184					9																	91083448		2158	4287	6445	SO:0001583	missense	10927	exon5			GAGAAAGACCCTG	AF317228	CCDS43843.1	9q22.1	2008-02-05	2007-01-03	2007-01-03	ENSG00000106723	ENSG00000106723			11243	protein-coding gene	gene with protein product		609936	"spindlin"	SPIN		16098913	Standard	NM_006717		Approved		uc004apy.3	Q9Y657	OTTHUMG00000020168	ENST00000375859.3:c.517G>C	chr9.hg19:g.91083448G>C	ENSP00000365019:p.Asp173His	173.0	0.0	.		132.0	11.0	.	NM_006717	A8K0X6|B3KRQ4|Q7KZJ8|Q9GZT2|Q9H0N7	Missense_Mutation	SNP	ENST00000375859.3	hg19	CCDS43843.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.466930	0.84425	.	.	ENSG00000106723	ENST00000375859;ENST00000541629	T;T	0.55588	0.51;0.51	5.12	4.2	0.49525	.	0.000000	0.85682	D	0.000000	T	0.69088	0.3072	M	0.63843	1.955	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.73353	-0.4009	10	0.87932	D	0	-20.5419	14.8406	0.70220	0.0:0.0:0.8552:0.1448	.	173	Q9Y657	SPIN1_HUMAN	H	173	ENSP00000365019:D173H;ENSP00000441864:D173H	ENSP00000365019:D173H	D	+	1	0	SPIN1	90273268	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	9.155000	0.94700	1.327000	0.45338	0.655000	0.94253	GAC	.	.	.	none		0.403	SPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052967.1	NM_006717		C	91083448	G	C	91083448	3	2	113	1	0	0	0	0	1	0	0	0	15064	942	33	4	531	4	SPIN1	9	91083448	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08		91083448	50129983	41	7309											
SPAG6	9576	hgsc.bcm.edu	37	chr10	22676767	22676767	+	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	cacagcatcagatcctttcaGctctcagtcaggtttcaaaa	12	11	6	12	0	5	1	5	0	1	1	7	1	6	1	1	1	2	3	1	1	2	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr10:22676767G>T	ENST00000376624.3	+	6	836	c.694G>T	c.(694-696)Gct>Tct	p.A232S	SPAG6_ENST00000376603.2_Missense_Mutation_p.A308S|SPAG6_ENST00000313311.6_Missense_Mutation_p.A232S|RP11-301N24.3_ENST00000422675.1_RNA|SPAG6_ENST00000538630.1_Missense_Mutation_p.A207S|SPAG6_ENST00000376601.1_Intron	NM_001253855.1|NM_012443.3	NP_001240784.1|NP_036575.1	O75602	SPAG6_HUMAN	sperm associated antigen 6	232					cell projection organization (GO:0030030)|spermatid development (GO:0007286)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|prostate(1)|skin(2)	27						GATCCTTTCAGCTCTCAGTCA	0.373																																					p.A232S		Atlas-SNP	.											.	SPAG6	90	.	0			c.G694T						PASS	.						78	77	77					10																	22676767		2203	4300	6503	SO:0001583	missense	9576	exon6			CTTTCAGCTCTCA	AF079363	CCDS7139.1, CCDS7140.1, CCDS58071.1, CCDS73072.1	10p12.31	2014-01-21			ENSG00000077327	ENSG00000077327		"Armadillo repeat containing"	11215	protein-coding gene	gene with protein product	"axoneme central apparatus protein"	605730				10493827	Standard	NM_012443		Approved	Repro-SA-1, pf16, CT141	uc001iri.3	O75602	OTTHUMG00000017808	ENST00000376624.3:c.694G>T	chr10.hg19:g.22676767G>T	ENSP00000365811:p.Ala232Ser	129.0	0.0	.		80.0	27.0	.	NM_172242	A8K1I8|B4DXZ4|Q5VUX5|Q5VUX6|Q5VUX7|Q6FI74|Q8NHQ6	Missense_Mutation	SNP	ENST00000376624.3	hg19	CCDS7139.1	.	.	.	.	.	.	.	.	.	.	G	14.72	2.620704	0.46736	.	.	ENSG00000077327	ENST00000376624;ENST00000376603;ENST00000538630;ENST00000313311	T;T;T;T	0.80738	-1.41;-1.41;-1.41;-1.41	5.64	3.8	0.43715	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.86936	0.6053	M	0.83953	2.67	0.58432	D	0.999999	P;P;P;P	0.49783	0.795;0.928;0.866;0.74	P;P;P;P	0.55222	0.714;0.771;0.508;0.588	D	0.87333	0.2326	10	0.66056	D	0.02	-21.9001	12.0263	0.53373	0.1391:0.0:0.8609:0.0	.	207;308;232;232	B4DXZ4;O75602-3;O75602-2;O75602	.;.;.;SPAG6_HUMAN	S	232;308;207;232	ENSP00000365811:A232S;ENSP00000365788:A308S;ENSP00000441325:A207S;ENSP00000323599:A232S	ENSP00000323599:A232S	A	+	1	0	SPAG6	22716773	1.000000	0.71417	0.582000	0.28627	0.580000	0.36256	6.587000	0.74071	0.744000	0.32741	0.655000	0.94253	GCT	.	.	.	none		0.373	SPAG6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047187.1			T	22676767	G	T	22676767	3	4	113	1	0	0	0	0	1	0	0	0	14995	971	34	4	716	4	SPAG6	10	22676767	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08		22676767	112857980	42	7310											
PIP4K2A	5305	hgsc.bcm.edu	37	chr10	23003187	23003187	+	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	agcttcactttctgcgctacGaagtgcttcttcttggtctt	5	17	8	11	2	5	0	1	0	4	0	5	1	5	0	0	1	4	3	0	1	2	7			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr10:23003187G>A	ENST00000376573.4	-	1	297	c.69C>T	c.(67-69)ttC>ttT	p.F23F	PIP4K2A_ENST00000545335.1_5'Flank	NM_005028.4	NP_005019.2	P48426	PI42A_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	23					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						TCTGCGCTACGAAGTGCTTCT	0.647																																					p.F23F		Atlas-SNP	.											.	PIP4K2A	59	.	0			c.C69T						PASS	.						94	85	88					10																	23003187		2203	4300	6503	SO:0001819	synonymous_variant	5305	exon1			CGCTACGAAGTGC	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.69C>T	chr10.hg19:g.23003187G>A		63.0	0.0	.		48.0	23.0	.	NM_005028	B0YJ66|B4DGX2|D3DRV1|P53807|Q5VUX3	Silent	SNP	ENST00000376573.4	hg19	CCDS7141.1																																																																																			.	.	.	none		0.647	PIP4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047193.1	NM_005028		A	23003187	G	A	23003187	2	1	113	1	0	0	0	0	0	0	0	1	11943	1049	37	1		1	PIP4K2A	10	23003187	Silent	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	326420	23003187	112531560	43	7311											
ZNF485	220992	hgsc.bcm.edu	37	chr10	44112496	44112496	+	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	agtaaatgtggaaaatctttCaggtatagctcatcctttgc	12	14	8	7	0	3	0	2	0	1	0	4	1	4	1	1	2	2	3	1	2	6	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr10:44112496C>T	ENST00000361807.3	+	5	1199	c.1005C>T	c.(1003-1005)ttC>ttT	p.F335F	ZNF485_ENST00000374437.2_Silent_p.F244F|ZNF485_ENST00000374435.3_Silent_p.F335F	NM_145312.3	NP_660355.2	Q8NCK3	ZN485_HUMAN	zinc finger protein 485	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)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16						GAAAATCTTTCAGGTATAGCT	0.428																																					p.F335F		Atlas-SNP	.											.	ZNF485	102	.	0			c.C1005T						PASS	.						117	117	117					10																	44112496		2203	4300	6503	SO:0001819	synonymous_variant	220992	exon5			ATCTTTCAGGTAT	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.1005C>T	chr10.hg19:g.44112496C>T		145.0	0.0	.		119.0	46.0	.	NM_145312	B4DSE6|Q96CL0	Silent	SNP	ENST00000361807.3	hg19	CCDS7205.2																																																																																			.	.	.	none		0.428	ZNF485-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047719.2	NM_145312		T	44112496	C	T	44112496	2	4	113	1	0	0	0	0	0	0	0	1	17950	825	29	2		2	ZNF485	10	44112496	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	21109309	44112496	91422251	44	7312											
PCDH15	65217	hgsc.bcm.edu	37	chr10	55583106	55583106	+	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	ctgctttgttgaaaatggtaGagaaggaaaagacttgaaag	16	10	12	3	0	0	4	0	2	0	2	0	6	0	5	0	2	1	3	0	2	7	4			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr10:55583106G>C	ENST00000320301.6	-	33	4774	c.4380C>G	c.(4378-4380)ctC>ctG	p.L1460L	PCDH15_ENST00000395432.2_Silent_p.L1420L|PCDH15_ENST00000395430.1_Silent_p.L1457L|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000414778.1_Intron|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395438.1_Intron|PCDH15_ENST00000395433.1_Silent_p.L1437L|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000361849.3_Silent_p.L1462L|PCDH15_ENST00000437009.1_Silent_p.L1391L|PCDH15_ENST00000395445.1_Intron|PCDH15_ENST00000373965.2_Intron|PCDH15_ENST00000395446.1_Intron	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1460					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)				GAAAATGGTAGAGAAGGAAAA	0.363										HNSCC(58;0.16)																											p.L1467L		Atlas-SNP	.											.	PCDH15	1715	.	0			c.C4401G						PASS	.						94	97	96					10																	55583106		2203	4300	6503	SO:0001819	synonymous_variant	65217	exon35			ATGGTAGAGAAGG	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.4380C>G	chr10.hg19:g.55583106G>C		104.0	0.0	.		79.0	12.0	.	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	hg19	CCDS7248.1																																																																																			.	.	.	none		0.363	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		C	55583106	G	C	55583106	2	2	113	1	0	0	0	0	0	0	0	1	11518	929	33	4		4	PCDH15	10	55583106	Silent	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	11470610	55583106	79951641	45	7313											
FAM178A	55719	hgsc.bcm.edu	37	chr10	102683799	102683799	+	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	gtggactcagatctgaaaagCacaagagaatctatgatacc	16	8	9	8	0	3	4	1	2	2	2	3	6	3	5	1	1	2	1	1	1	6	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr10:102683799C>T	ENST00000238961.4	+	5	1583	c.1041C>T	c.(1039-1041)agC>agT	p.S347S	FAM178A_ENST00000370271.3_Silent_p.S347S|FAM178A_ENST00000370269.3_Silent_p.S347S	NM_018121.3	NP_060591.3	Q8IX21	F178A_HUMAN	family with sequence similarity 178, member A	347						chromatin (GO:0000785)|extracellular space (GO:0005615)|nucleus (GO:0005634)											ATCTGAAAAGCACAAGAGAAT	0.343																																					p.S347S		Atlas-SNP	.											.	FAM178A	9	.	0			c.C1041T						PASS	.						44	43	43					10																	102683799		2203	4300	6503	SO:0001819	synonymous_variant	55719	exon5			GAAAAGCACAAGA	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.1041C>T	chr10.hg19:g.102683799C>T		76.0	0.0	.		50.0	22.0	.	NM_001136123	A8K950|B1AL17|Q5W0L8|Q6GMU6|Q9NPE8	Silent	SNP	ENST00000238961.4	hg19	CCDS7500.1																																																																																			.	.	.	none		0.343	FAM178A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049897.3			T	102683799	C	T	102683799	2	4	113	1	0	0	0	0	0	0	0	1	5507	709	25	2		2	FAM178A	10	102683799	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	47100693	102683799	32850948	46	7314											
NFKB2	4791	hgsc.bcm.edu	37	chr10	104161522	104161522	+	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	ggccgggactgtcacttggtGatacagctctgcagaacctg	8	9	13	11	1	2	2	1	1	1	1	2	3	2	3	2	3	4	2	2	3	2	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr10:104161522G>C	ENST00000369966.3	+	21	2564	c.2314G>C	c.(2314-2316)Gat>Cat	p.D772H	NFKB2_ENST00000189444.6_Missense_Mutation_p.D772H|NFKB2_ENST00000428099.1_Missense_Mutation_p.D772H	NM_001077494.2	NP_001070962.1	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)	772	Death.		Missing (in truncated form EB308).|Missing (in truncated form LB40).|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)	GTCACTTGGTGATACAGCTCT	0.597			T	IGH@	B-NHL																																p.D772H		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.G2314C						PASS	.						47	47	47					10																	104161522		1987	4164	6151	SO:0001583	missense	4791	exon21			CTTGGTGATACAG	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.2314G>C	chr10.hg19:g.104161522G>C	ENSP00000358983:p.Asp772His	37.0	0.0	.		43.0	9.0	.	NM_001077494	A8K9D9|D3DR83|Q04860|Q9BU75|Q9H471|Q9H472	Missense_Mutation	SNP	ENST00000369966.3	hg19	CCDS41564.1	.	.	.	.	.	.	.	.	.	.	g	15.85	2.954405	0.53293	.	.	ENSG00000077150	ENST00000428099;ENST00000369966;ENST00000336486;ENST00000189444	T;T;T	0.21543	2.0;2.0;2.0	3.79	3.79	0.43588	Death (1);DEATH-like (2);	0.428788	0.25052	N	0.033513	T	0.17109	0.0411	L	0.36672	1.1	0.20403	N	0.999908	P;P	0.50943	0.94;0.94	P;P	0.44732	0.459;0.459	T	0.11397	-1.0589	10	0.59425	D	0.04	.	6.0921	0.20001	0.1804:0.0:0.8196:0.0	.	772;772	Q00653;A8K9D9	NFKB2_HUMAN;.	H	772	ENSP00000410256:D772H;ENSP00000358983:D772H;ENSP00000189444:D772H	ENSP00000189444:D772H	D	+	1	0	NFKB2	104151512	1.000000	0.71417	0.127000	0.21898	0.959000	0.62525	4.901000	0.63259	2.105000	0.64084	0.556000	0.70494	GAT	.	.	.	none		0.597	NFKB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050080.2			C	104161522	G	C	104161522	3	2	113	1	0	0	0	0	1	0	0	0	10383	1290	45	4	2392	4	NFKB2	10	104161522	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	1477723	104161522	31373225	47	7315											
OR51B6	390058	hgsc.bcm.edu	37	chr11	5373545	5373545	+	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	gaaagcatgttcctcatgtcGttcacatcacaatgagctac	12	11	7	11	1	3	1	3	1	0	0	5	2	4	1	1	0	3	4	1	0	3	3	rs138981931		TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr11:5373545G>T	ENST00000380219.1	+	1	808	c.808G>T	c.(808-810)Gtt>Ttt	p.V270F	HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	270					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			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)		TCCTCATGTCGTTCACATCAC	0.398																																					p.V270F		Atlas-SNP	.											.	OR51B6	53	.	0			c.G808T						PASS	.						215	193	200					11																	5373545		2201	4297	6498	SO:0001583	missense	390058	exon1			CATGTCGTTCACA		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.808G>T	chr11.hg19:g.5373545G>T	ENSP00000369568:p.Val270Phe	220.0	0.0	.		195.0	83.0	.	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	hg19	CCDS31379.1	.	.	.	.	.	.	.	.	.	.	G	14.71	2.618023	0.46736	.	.	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.00130	8.69	5.13	4.22	0.49857	GPCR, rhodopsin-like superfamily (1);	0.136091	0.33127	N	0.005251	T	0.00412	0.0013	M	0.76838	2.35	0.09310	N	1	D	0.71674	0.998	D	0.74674	0.984	T	0.38222	-0.9671	10	0.87932	D	0	.	8.1363	0.31056	0.0849:0.1595:0.7556:0.0	.	270	Q9H340	O51B6_HUMAN	F	269;270	ENSP00000369568:V270F	ENSP00000369568:V270F	V	+	1	0	OR51B6	5330121	0.114000	0.22134	0.847000	0.33407	0.957000	0.61999	0.805000	0.27112	1.379000	0.46325	0.650000	0.86243	GTT	.	G|1.000;A|0.000	.	alt		0.398	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750		T	5373545	G	T	5373545	3	4	113	1	0	0	0	0	1	0	0	0	11099	1145	40	4	810	4	OR51B6	11	5373545	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08		5373545	129632971	48	7316											
TUB	7275	hgsc.bcm.edu	37	chr11	8120419	8120419	+	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	caggagctggcagctgtgtgCtacgtgagtcctaggttcgg	6	10	16	9	2	0	1	0	1	0	0	2	2	1	2	1	4	4	5	1	4	2	3			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr11:8120419C>G	ENST00000299506.2	+	9	1262	c.1113C>G	c.(1111-1113)tgC>tgG	p.C371W	TUB_ENST00000305253.4_Missense_Mutation_p.C426W|TUB_ENST00000534099.1_Missense_Mutation_p.C377W	NM_177972.2	NP_813977.1	P50607	TUB_HUMAN	tubby bipartite transcription factor	371					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)		CAGCTGTGTGCTACGTGAGTC	0.502											OREG0020732	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C426W		Atlas-SNP	.											.	TUB	71	.	0			c.C1278G						PASS	.						114	108	110					11																	8120419		2201	4296	6497	SO:0001583	missense	7275	exon10			TGTGTGCTACGTG	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.1113C>G	chr11.hg19:g.8120419C>G	ENSP00000299506:p.Cys371Trp	99.0	0.0	.	646	101.0	37.0	.	NM_003320	D3DQU4|O00293|Q6B007	Missense_Mutation	SNP	ENST00000299506.2	hg19	CCDS7787.1	.	.	.	.	.	.	.	.	.	.	C	16.44	3.122978	0.56613	.	.	ENSG00000166402	ENST00000534099;ENST00000305253;ENST00000299506	D;D;D	0.96300	-3.97;-3.97;-3.97	5.27	3.41	0.39046	Tubby, C-terminal (4);	0.000000	0.85682	D	0.000000	D	0.97473	0.9173	M	0.78456	2.415	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.992;0.995;0.987	D	0.96862	0.9633	10	0.62326	D	0.03	0.2328	10.0609	0.42275	0.0:0.7635:0.0:0.2365	.	377;371;426	E9PQR4;P50607;P50607-2	.;TUB_HUMAN;.	W	377;426;371	ENSP00000434400:C377W;ENSP00000305426:C426W;ENSP00000299506:C371W	ENSP00000299506:C371W	C	+	3	2	TUB	8076995	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	2.369000	0.44231	0.723000	0.32274	0.555000	0.69702	TGC	.	.	.	none		0.502	TUB-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385823.1	NM_003320		G	8120419	C	G	8120419	3	3	113	1	0	0	0	0	1	0	0	0	16754	805	28	4	1358	4	TUB	11	8120419	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	2746874	8120419	126886097	49	7317											
ELP4	26610	hgsc.bcm.edu	37	chr11	31561263	31561263	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcaagtatttcctggcagAaggaattgtcaatgggcata	12	12	10	7	0	2	1	2	0	0	1	3	2	3	2	1	3	0	3	1	3	6	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr11:31561263A>G	ENST00000350638.5	+	3	349	c.314A>G	c.(313-315)gAa>gGa	p.E105G	ELP4_ENST00000379163.5_Missense_Mutation_p.E105G|ELP4_ENST00000395934.2_Missense_Mutation_p.E105G	NM_019040.3	NP_061913.3	Q96EB1	ELP4_HUMAN	elongator acetyltransferase complex subunit 4	105					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)			breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(3)	20	Lung SC(675;0.225)					TTCCTGGCAGAAGGAATTGTC	0.338																																					p.E105G		Atlas-SNP	.											.	ELP4	78	.	0			c.A314G						PASS	.						192	161	170					11																	31561263		1821	4080	5901	SO:0001583	missense	26610	exon3			TGGCAGAAGGAAT	AJ276005	CCDS7875.2, CCDS73271.1, CCDS73272.1	11p13	2012-08-14	2012-08-08	2002-05-24	ENSG00000109911	ENSG00000109911		"Elongator acetyltransferase complex subunits"	1171	protein-coding gene	gene with protein product		606985	"chromosome 11 open reading frame 19", "elongation protein 4 homolog (S. cerevisiae)"	C11orf19		11889558, 11435442	Standard	XM_005252865		Approved	PAXNEB	uc001mtb.3	Q96EB1	OTTHUMG00000142919	ENST00000350638.5:c.314A>G	chr11.hg19:g.31561263A>G	ENSP00000298937:p.Glu105Gly	271.0	1.0	.		211.0	85.0	.	NM_019040	B4E3W0|E7EPZ6|Q9H4E8|Q9NX11	Missense_Mutation	SNP	ENST00000350638.5	hg19	CCDS7875.2	.	.	.	.	.	.	.	.	.	.	A	22.2	4.257149	0.80246	.	.	ENSG00000109911	ENST00000350638;ENST00000379163;ENST00000395934	T;T;T	0.57595	0.39;0.39;0.39	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.77491	0.4138	M	0.90309	3.105	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	0.82748	-0.0304	10	0.72032	D	0.01	-12.448	15.207	0.73186	1.0:0.0:0.0:0.0	.	105;105;105	B4E3W0;G5E9D4;Q96EB1	.;.;ELP4_HUMAN	G	105	ENSP00000298937:E105G;ENSP00000368461:E105G;ENSP00000379267:E105G	ENSP00000298937:E105G	E	+	2	0	ELP4	31517839	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	7.890000	0.87313	2.124000	0.65301	0.383000	0.25322	GAA	.	.	.	none		0.338	ELP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286640.1	NM_019040		G	31561263	A	G	31561263	3	3	113	1	0	0	0	0	1	0	0	0	5084	246	9	3	324	3	ELP4	11	31561263	Missense_Mutation	SNP	A	TCGA-BQ-5878-01A-11D-1589-08	23440844	31561263	103445253	50	7318											
OR4A16	81327	hgsc.bcm.edu	37	chr11	55111508	55111508	+	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	tgttttattcaattatcacaCtcatgttgaatcctttaata	12	19	3	7	0	3	1	3	1	0	0	4	1	4	1	1	0	0	2	1	0	6	8			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr11:55111508C>A	ENST00000314721.2	+	1	882	c.832C>A	c.(832-834)Ctc>Atc	p.L278I		NM_001005274.1	NP_001005274.1	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A, member 16	278						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						AATTATCACACTCATGTTGAA	0.323																																					p.L278I		Atlas-SNP	.											.	OR4A16	120	.	0			c.C832A						PASS	.						89	85	86					11																	55111508		2201	4296	6497	SO:0001583	missense	81327	exon1			ATCACACTCATGT	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.832C>A	chr11.hg19:g.55111508C>A	ENSP00000325128:p.Leu278Ile	87.0	0.0	.		93.0	28.0	.	NM_001005274	Q6IFL3	Missense_Mutation	SNP	ENST00000314721.2	hg19	CCDS31499.1	.	.	.	.	.	.	.	.	.	.	c	10.38	1.333574	0.24167	.	.	ENSG00000181961	ENST00000314721	T	0.37058	1.22	2.86	2.86	0.33363	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.26304	0.0642	N	0.08118	0	0.21802	N	0.999535	B	0.31599	0.33	B	0.40602	0.334	T	0.37126	-0.9719	9	0.87932	D	0	.	11.4549	0.50176	0.0:1.0:0.0:0.0	.	278	Q8NH70	O4A16_HUMAN	I	278	ENSP00000325128:L278I	ENSP00000325128:L278I	L	+	1	0	OR4A16	54868084	0.438000	0.25602	0.986000	0.45419	0.221000	0.24807	6.035000	0.70940	1.606000	0.50161	0.423000	0.28283	CTC	.	.	.	none		0.323	OR4A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391160.1	NM_001005274		A	55111508	C	A	55111508	3	1	113	1	0	0	0	0	1	0	0	0	11048	565	20	4	834	4	OR4A16	11	55111508	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	23550245	55111508	79895008	51	7319											
RAB6A	5870	hgsc.bcm.edu	37	chr11	73418504	73418504	+	Frame_Shift_Del	DEL	A	A	-																															gcttttgcactagtttcaatAaacataacattcagctcttt																										TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr11:73418504delA	ENST00000336083.3	-	6	911	c.456delT	c.(454-456)tttfs	p.F152fs	RAB6A_ENST00000541588.1_Intron|RAB6A_ENST00000536566.1_Frame_Shift_Del_p.F119fs|RAB6A_ENST00000310653.6_Frame_Shift_Del_p.F152fs	NM_198896.1	NP_942599.1	P20340	RAB6A_HUMAN	RAB6A, member RAS oncogene family	152					antigen processing and presentation (GO:0019882)|early endosome to Golgi transport (GO:0034498)|GTP catabolic process (GO:0006184)|minus-end-directed organelle transport along microtubule (GO:0072385)|peptidyl-cysteine methylation (GO:0018125)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)|protein domain specific binding (GO:0019904)			large_intestine(2)|lung(2)	4						TAGTTTCAATAAACATAACAT	0.348																																					p.I153fs		Atlas-INDEL	.											.	RAB6A	17	.	0			c.457delA						PASS	.						189	175	180					11																	73418504		2200	4293	6493	SO:0001589	frameshift_variant	5870	exon6			.	AF130986	CCDS8223.1, CCDS8224.1, CCDS58155.1, CCDS58156.1	11q13.3	2008-08-08			ENSG00000175582	ENSG00000175582		"RAB, member RAS oncogene"	9786	protein-coding gene	gene with protein product		179513		RAB6			Standard	NM_001243718		Approved		uc001ouf.3	P20340	OTTHUMG00000134308	ENST00000336083.3:c.456delT	chr11.hg19:g.73418504delA	ENSP00000336850:p.Phe152fs	184.0	0.0	0		121.0	51.0	0.421488	NM_002869	A8K133|B7Z772|F5H668|Q1W5D8|Q5U0A8|Q9UBE4	Frame_Shift_Del	DEL	ENST00000336083.3	hg19	CCDS8224.1																																																																																			.	.	.	none		0.348	RAB6A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259241.2			-	73418504	A	-	73418504	7	5	113	1	0	1	0	1	0	0	0	0	12964	359	13	0	182	0	RAB6A	11	73418504	Frame_Shift_Del	DEL	A	TCGA-BQ-5878-01A-11D-1589-08	18306996	73418504	61588012	52	7320											
USP28	57646	hgsc.bcm.edu	37	chr11	113679118	113679119	+	Frame_Shift_Ins	INS	-	-	TG																															acaatcacagcatgctcagaINScgacaagcagcgaaccccat																								rs2465647	byFrequency	TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr11:113679118_113679119insTG	ENST00000003302.4	-	18	2273_2274	c.2205_2206insCA	c.(2203-2208)tcgtctfs	p.S736fs	USP28_ENST00000545540.1_Frame_Shift_Ins_p.S611fs|USP28_ENST00000260188.5_Frame_Shift_Ins_p.S736fs|USP28_ENST00000544967.1_Frame_Shift_Ins_p.S444fs	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN	ubiquitin specific peptidase 28	736					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		GCATGCTCAGACGACAAGCAGC	0.47																																					p.S736fs	Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)	Atlas-INDEL	.											.	USP28	135	.	0			c.2206_2207insCA						PASS	.																																			SO:0001589	frameshift_variant	57646	exon18			.	AB040948	CCDS31680.1, CCDS73394.1	11q23	2008-04-11	2005-08-08		ENSG00000048028	ENSG00000048028		"Ubiquitin-specific peptidases"	12625	protein-coding gene	gene with protein product		610748	"ubiquitin specific protease 28"			12838346, 11597335	Standard	XM_005271630		Approved	KIAA1515	uc001poh.3	Q96RU2	OTTHUMG00000168205	ENST00000003302.4:c.2205_2206insCA	chr11.hg19:g.113679118_113679119insTG	ENSP00000003302:p.Ser736fs	122.0	0.0	0		142.0	54.0	0.380282	NM_020886	B0YJC0|B0YJC1|Q9P213	Frame_Shift_Ins	INS	ENST00000003302.4	hg19	CCDS31680.1																																																																																			.	.	.	none		0.47	USP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398789.1			TG	113679119	-	TG	113679118	7	5	113	1	0	1	1	0	0	0	0	0	17070	275	10	0	1059	0	USP28	11	113679118	Frame_Shift_Ins	INS	-	TCGA-BQ-5878-01A-11D-1589-08	40260614	113679118	21327398	53	7321											
MAGOHB	55110	hgsc.bcm.edu	37	chr12	10766047	10766047	+	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	cctcttctcaccgtccggccGaaattcgaactccagaaact	10	9	6	16	4	2	1	1	0	2	1	6	3	4	1	5	1	2	0	5	1	3	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr12:10766047G>T	ENST00000320756.2	-	1	175	c.85C>A	c.(85-87)Cgg>Agg	p.R29R	MAGOHB_ENST00000539554.1_Intron|MAGOHB_ENST00000381881.2_Silent_p.R29R	NM_018048.3	NP_060518.1	Q96A72	MGN2_HUMAN	mago-nashi homolog B (Drosophila)	29					mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|large_intestine(2)	4						CCGTCCGGCCGAAATTCGAAC	0.617																																					p.R29R		Atlas-SNP	.											.	MAGOHB	17	.	0			c.C85A						PASS	.						97	98	97					12																	10766047		2203	4300	6503	SO:0001819	synonymous_variant	55110	exon1			CCGGCCGAAATTC		CCDS8628.1	12p13.2	2014-02-12	2008-01-24		ENSG00000111196	ENSG00000111196			25504	protein-coding gene	gene with protein product							Standard	NM_018048		Approved	FLJ10292, MGN2	uc001qyq.2	Q96A72	OTTHUMG00000168407	ENST00000320756.2:c.85C>A	chr12.hg19:g.10766047G>T		96.0	0.0	.		110.0	9.0	.	NM_018048		Silent	SNP	ENST00000320756.2	hg19	CCDS8628.1																																																																																			.	.	.	none		0.617	MAGOHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399616.1	NM_018048		T	10766047	G	T	10766047	2	4	113	1	0	0	0	0	0	0	0	1	9202	1057	37	4		4	MAGOHB	12	10766047	Silent	SNP	G	TCGA-BQ-5878-01A-11D-1589-08		10766047	123085848	54	7322											
MLL2	8085	hgsc.bcm.edu	37	chr12	49434210	49434210	+	Frame_Shift_Del	DEL	T	T	-																															agggtgggcgagaataagggTcaggggactggaagcgaggg																										TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr12:49434210delT	ENST00000301067.7	-	31	7342	c.7343delA	c.(7342-7344)gacfs	p.D2448fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2448	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)										AGAATAAGGGTCAGGGGACTG	0.612																																					p.D2448fs		Atlas-INDEL	.											.	MLL2	1173	.	0			c.7344delC						PASS	.						43	49	47					12																	49434210		2063	4194	6257	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.7343delA	chr12.hg19:g.49434210delT	ENSP00000301067:p.Asp2448fs	76.0	0.0	0		76.0	31.0	0.407895	NM_003482	O14687	Frame_Shift_Del	DEL	ENST00000301067.7	hg19	CCDS44873.1																																																																																			.	.	.	none		0.612	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			-	49434210	T	-	49434210	7	5	113	1	0	1	0	1	0	0	0	0	9628	1667	58	0	9366	0	MLL2	12	49434210	Frame_Shift_Del	DEL	T	TCGA-BQ-5878-01A-11D-1589-08	38668163	49434210	84417685	55	7323											
CIT	11113	hgsc.bcm.edu	37	chr12	120173153	120173153	+	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	gtttagctgctcctccaggtCtgtgattacctaaaagagga	10	12	10	9	0	1	2	0	1	1	1	3	3	3	3	3	2	3	3	3	2	4	4			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr12:120173153C>T	ENST00000261833.7	-	24	2894	c.2842G>A	c.(2842-2844)Gac>Aac	p.D948N	CIT_ENST00000392521.2_Missense_Mutation_p.D990N|CIT_ENST00000537607.1_5'UTR	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	948					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)		TCCTCCAGGTCTGTGATTACC	0.458																																					p.D990N		Atlas-SNP	.											.	CIT	535	.	0			c.G2968A						PASS	.						190	170	177					12																	120173153		2203	4300	6503	SO:0001583	missense	11113	exon25			CCAGGTCTGTGAT	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.2842G>A	chr12.hg19:g.120173153C>T	ENSP00000261833:p.Asp948Asn	108.0	0.0	.		110.0	43.0	.	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	hg19	CCDS9192.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.553919	0.86231	.	.	ENSG00000122966	ENST00000392521;ENST00000261833	T;T	0.65178	-0.08;-0.14	5.06	5.06	0.68205	.	0.054479	0.64402	D	0.000001	T	0.58104	0.2099	N	0.24115	0.695	0.80722	D	1	D;P;B	0.56035	0.974;0.805;0.447	P;B;B	0.47981	0.563;0.346;0.223	T	0.65059	-0.6260	10	0.72032	D	0.01	.	18.797	0.91999	0.0:1.0:0.0:0.0	.	990;948;481	Q2M5E1;O14578;O14578-3	.;CTRO_HUMAN;.	N	990;948	ENSP00000376306:D990N;ENSP00000261833:D948N	ENSP00000261833:D948N	D	-	1	0	CIT	118657536	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.776000	0.85560	2.505000	0.84491	0.655000	0.94253	GAC	.	.	.	none		0.458	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174		T	120173153	C	T	120173153	3	4	113	1	0	0	0	0	1	0	0	0	3440	913	32	2	3337	2	CIT	12	120173153	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	70738943	120173153	13678742	56	7324											
OASL	8638	hgsc.bcm.edu	37	chr12	121465530	121465530	+	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	caacatgaaattctcgtcttCttcagtacccatttcccagg	10	13	5	13	1	4	1	1	1	3	0	6	1	5	1	2	1	2	1	2	1	3	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr12:121465530C>A	ENST00000257570.5	-	4	1018	c.748G>T	c.(748-750)Gaa>Taa	p.E250*	OASL_ENST00000339275.5_Intron	NM_003733.3	NP_003724.1	Q15646	OASL_HUMAN	2'-5'-oligoadenylate synthetase-like	250					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)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|transferase activity (GO:0016740)			NS(1)|endometrium(3)|large_intestine(4)|lung(4)|skin(2)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TTCTCGTCTTCTTCAGTACCC	0.478																																					p.E250X	Colon(192;517 2041 31392 31913 39966)	Atlas-SNP	.											.	OASL	49	.	0			c.G748T						PASS	.						142	116	125					12																	121465530		2203	4300	6503	SO:0001587	stop_gained	8638	exon4			CGTCTTCTTCAGT	AF063611	CCDS9211.1, CCDS9212.1, CCDS73536.1	12q24.2	2008-08-05			ENSG00000135114	ENSG00000135114			8090	protein-coding gene	gene with protein product		603281				10087211	Standard	NM_003733		Approved	TRIP14, p59OASL	uc001tzj.2	Q15646	OTTHUMG00000154981	ENST00000257570.5:c.748G>T	chr12.hg19:g.121465530C>A	ENSP00000257570:p.Glu250*	84.0	0.0	.		73.0	26.0	.	NM_003733	B2RAZ2|I1YDD2|O75686|Q17R95|Q9Y6K6|Q9Y6K7	Nonsense_Mutation	SNP	ENST00000257570.5	hg19	CCDS9211.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.434616	0.83885	.	.	ENSG00000135114	ENST00000257570	.	.	.	5.58	-2.54	0.06307	.	3.081050	0.00951	N	0.002969	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	-20.7634	0.3898	0.00408	0.2468:0.2802:0.242:0.231	.	.	.	.	X	250	.	ENSP00000257570:E250X	E	-	1	0	OASL	119949913	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.430000	0.02434	-0.099000	0.12263	-0.302000	0.09304	GAA	.	.	.	none		0.478	OASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337875.2	NM_003733		A	121465530	C	A	121465530	4	1	113	1	0	0	0	0	0	1	0	0	10809	922	32	4	808	4	OASL	12	121465530	Nonsense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	1292377	121465530	12386365	57	7325											
C14orf93	60686	hgsc.bcm.edu	37	chr14	23467861	23467861	+	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	ggactttccttgagaggcccAggctcctcaggtggggaact	7	9	14	11	0	1	1	1	1	0	1	3	4	3	3	3	6	1	1	3	6	1	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr14:23467861A>C	ENST00000299088.6	-	2	801	c.372T>G	c.(370-372)ccT>ccG	p.P124P	RP11-298I3.4_ENST00000555294.1_RNA|RP11-298I3.4_ENST00000556503.1_RNA|C14orf93_ENST00000397379.3_Silent_p.P124P|C14orf93_ENST00000341470.4_Silent_p.P124P|C14orf93_ENST00000397382.4_Silent_p.P124P|C14orf93_ENST00000406429.2_Silent_p.P124P|C14orf93_ENST00000397377.1_5'UTR|C14orf93_ENST00000557513.1_5'Flank	NM_001130708.1|NM_021944.2	NP_001124180.1|NP_068763.2	Q9H972	CN093_HUMAN	chromosome 14 open reading frame 93	124						extracellular region (GO:0005576)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	17	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0127)		TGAGAGGCCCAGGCTCCTCAG	0.597																																					p.P124P		Atlas-SNP	.											.	C14orf93	33	.	0			c.T372G						PASS	.						58	60	59					14																	23467861		2203	4300	6503	SO:0001819	synonymous_variant	60686	exon2			AGGCCCAGGCTCC	AK023026	CCDS9583.1, CCDS61399.1, CCDS61400.1	14q11.1	2012-09-25			ENSG00000100802	ENSG00000100802			20162	protein-coding gene	gene with protein product							Standard	XM_005267971		Approved	FLJ12154	uc001wih.3	Q9H972	OTTHUMG00000028712	ENST00000299088.6:c.372T>G	chr14.hg19:g.23467861A>C		98.0	0.0	.		53.0	23.0	.	NM_021944	B7WP03|D3DS38|D3DS39|Q86SE6|Q96CF7|Q9HA68	Silent	SNP	ENST00000299088.6	hg19	CCDS9583.1																																																																																			.	.	.	none		0.597	C14orf93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071688.5	NM_021944		C	23467861	A	C	23467861	2	2	113	1	0	0	0	0	0	0	0	1	1784	175	7	5		5	C14orf93	14	23467861	Silent	SNP	A	TCGA-BQ-5878-01A-11D-1589-08		23467861	83881679	58	7326											
SOS2	6655	hgsc.bcm.edu	37	chr14	50605361	50605361	+	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	gttctatccgtaaacagtaaGgctgattctgatactgctga	11	13	9	8	1	2	3	0	3	2	0	3	3	3	3	1	1	3	5	1	1	5	6			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr14:50605361G>A	ENST00000216373.5	-	18	3201	c.2927C>T	c.(2926-2928)cCt>cTt	p.P976L	SOS2_ENST00000543680.1_Missense_Mutation_p.P943L	NM_006939.2	NP_008870.2	Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	976	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				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)					TAAACAGTAAGGCTGATTCTG	0.308																																					p.P976L		Atlas-SNP	.											.	SOS2	195	.	0			c.C2927T						PASS	.						92	92	92					14																	50605361		2201	4299	6500	SO:0001583	missense	6655	exon18			CAGTAAGGCTGAT	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.2927C>T	chr14.hg19:g.50605361G>A	ENSP00000216373:p.Pro976Leu	161.0	0.0	.		110.0	46.0	.	NM_006939	B7ZKT6|D3DSB4|Q15503|Q17RN1	Missense_Mutation	SNP	ENST00000216373.5	hg19	CCDS9697.1	.	.	.	.	.	.	.	.	.	.	G	33	5.254361	0.95336	.	.	ENSG00000100485	ENST00000216373;ENST00000543680	T;T	0.35048	1.33;1.33	5.6	5.6	0.85130	Guanine-nucleotide dissociation stimulator CDC25 (3);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.61862	0.2381	M	0.87381	2.88	0.80722	D	1	D;D	0.58620	0.983;0.965	P;P	0.55087	0.768;0.708	T	0.69198	-0.5208	10	0.87932	D	0	.	19.6046	0.95575	0.0:0.0:1.0:0.0	.	943;976	B7ZKT6;Q07890	.;SOS2_HUMAN	L	976;943	ENSP00000216373:P976L;ENSP00000445328:P943L	ENSP00000216373:P976L	P	-	2	0	SOS2	49675111	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.405000	0.97313	2.640000	0.89533	0.655000	0.94253	CCT	.	.	.	none		0.308	SOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276878.2			A	50605361	G	A	50605361	3	1	113	1	0	0	0	0	1	0	0	0	14950	1000	35	2	1095	2	SOS2	14	50605361	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	27137500	50605361	56744179	59	7327											
AK7	122481	hgsc.bcm.edu	37	chr14	96917831	96917831	+	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	gaaggagaattttaatattcGatgggctgcccaaacaggat	14	10	11	6	1	0	1	0	0	0	1	1	5	0	2	1	3	2	1	1	3	5	4			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr14:96917831G>A	ENST00000267584.4	+	10	1066	c.1022G>A	c.(1021-1023)cGa>cAa	p.R341Q		NM_152327.3	NP_689540.2	Q96M32	KAD7_HUMAN	adenylate kinase 7	341					axoneme assembly (GO:0035082)|brain development (GO:0007420)|epithelial cilium movement (GO:0003351)|inflammatory response to antigenic stimulus (GO:0002437)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			breast(2)|cervix(2)|endometrium(3)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		TTTAATATTCGATGGGCTGCC	0.393																																					p.R341Q		Atlas-SNP	.											.	AK7	69	.	0			c.G1022A						PASS	.						94	90	91					14																	96917831		2203	4300	6503	SO:0001583	missense	122481	exon10			ATATTCGATGGGC	AK057426	CCDS9945.1	14q32.31	2012-08-15			ENSG00000140057	ENSG00000140057		"Adenylate kinases"	20091	protein-coding gene	gene with protein product		615364					Standard	NM_152327		Approved	FLJ32864	uc001yfn.3	Q96M32	OTTHUMG00000171421	ENST00000267584.4:c.1022G>A	chr14.hg19:g.96917831G>A	ENSP00000267584:p.Arg341Gln	78.0	0.0	.		78.0	29.0	.	NM_152327	Q8IYP6	Missense_Mutation	SNP	ENST00000267584.4	hg19	CCDS9945.1	.	.	.	.	.	.	.	.	.	.	G	9.591	1.126082	0.20959	.	.	ENSG00000140057	ENST00000267584	T	0.61040	0.14	5.72	5.72	0.89469	.	0.354917	0.31772	N	0.007090	T	0.47948	0.1473	L	0.60455	1.87	0.54753	D	0.999986	P	0.35527	0.507	B	0.19666	0.026	T	0.46830	-0.9163	10	0.30078	T	0.28	-17.9477	12.7326	0.57206	0.0789:0.0:0.9211:0.0	.	341	Q96M32	KAD7_HUMAN	Q	341	ENSP00000267584:R341Q	ENSP00000267584:R341Q	R	+	2	0	AK7	95987584	0.290000	0.24343	0.621000	0.29145	0.004000	0.04260	2.176000	0.42500	2.711000	0.92665	0.655000	0.94253	CGA	.	.	.	none		0.393	AK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413340.1			A	96917831	G	A	96917831	3	1	113	1	0	0	0	0	1	0	0	0	444	1058	37	1	1060	1	AK7	14	96917831	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	46312470	96917831	10431709	60	7328											
ARHGAP11A	9824	hgsc.bcm.edu	37	chr15	32929514	32929514	+	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	gtccgtcagaagaattaattCtttgttggagtatagcagac	12	13	10	6	1	2	3	1	0	1	3	3	4	3	4	1	1	1	3	1	1	5	6			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr15:32929514C>T	ENST00000361627.3	+	12	3262	c.2540C>T	c.(2539-2541)tCt>tTt	p.S847F	ARHGAP11A_ENST00000543522.1_Missense_Mutation_p.S658F|ARHGAP11A_ENST00000565905.1_Missense_Mutation_p.S658F	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	847					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)		AGAATTAATTCTTTGTTGGAG	0.408																																					p.S847F	Colon(45;757 1134 30003 36652)	Atlas-SNP	.											.	ARHGAP11A	84	.	0			c.C2540T						PASS	.						121	128	125					15																	32929514		2201	4300	6501	SO:0001583	missense	9824	exon12			TTAATTCTTTGTT	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.2540C>T	chr15.hg19:g.32929514C>T	ENSP00000355090:p.Ser847Phe	160.0	0.0	.		148.0	6.0	.	NM_014783	B4DZN9|Q6PI96|Q9Y3S6	Missense_Mutation	SNP	ENST00000361627.3	hg19	CCDS10028.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.331080	0.81690	.	.	ENSG00000198826	ENST00000361627;ENST00000543522	T	0.34667	1.35	5.67	5.67	0.87782	.	0.000000	0.56097	D	0.000025	T	0.65450	0.2692	M	0.80847	2.515	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.68655	-0.5351	10	0.87932	D	0	.	19.7686	0.96352	0.0:1.0:0.0:0.0	.	847	Q6P4F7	RHGBA_HUMAN	F	847;658	ENSP00000355090:S847F	ENSP00000355090:S847F	S	+	2	0	ARHGAP11A	30716806	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	6.951000	0.75983	2.665000	0.90641	0.591000	0.81541	TCT	.	.	.	none		0.408	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783		T	32929514	C	T	32929514	3	4	113	1	0	0	0	0	1	0	0	0	863	913	32	2	2609	2	ARHGAP11A	15	32929514	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08		32929514	69601878	61	7329											
MAP2K5	5607	hgsc.bcm.edu	37	chr15	67956981	67956981	+	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	gagtttaaagattttacataGaggtatgtgctgggcttata	12	15	11	3	0	0	2	0	0	0	2	0	3	0	2	0	2	2	4	0	2	7	8			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr15:67956981G>C	ENST00000178640.5	+	13	1472	c.845G>C	c.(844-846)aGa>aCa	p.R282T	MAP2K5_ENST00000354498.5_Missense_Mutation_p.R246T|MAP2K5_ENST00000340972.4_Missense_Mutation_p.R92T|MAP2K5_ENST00000395476.2_Missense_Mutation_p.R282T	NM_145160.2	NP_660143.1	Q13163	MP2K5_HUMAN	mitogen-activated protein kinase kinase 5	282	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cellular response to growth factor stimulus (GO:0071363)|cellular response to laminar fluid shear stress (GO:0071499)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|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 extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of response to cytokine stimulus (GO:0060761)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleus (GO:0005634)|spindle (GO:0005819)	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.R282T(2)		breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|skin(1)	16						ATTTTACATAGAGGTATGTGC	0.333																																					p.R282T		Atlas-SNP	.											MAP2K5_ENST00000178640,NS,carcinoma,0,2	MAP2K5	70	.	2	Substitution - Missense(2)	endometrium(2)	c.G845C						PASS	.						112	114	113					15																	67956981		2199	4297	6496	SO:0001583	missense	5607	exon13			TACATAGAGGTAT	U25265	CCDS10224.1, CCDS42051.1, CCDS55970.1	15q22.31	2011-06-09			ENSG00000137764	ENSG00000137764		"Mitogen-activated protein kinase cascade / Kinase kinases"	6845	protein-coding gene	gene with protein product		602520		PRKMK5		7759517	Standard	NM_002757		Approved	MEK5, MAPKK5, HsT17454	uc002aqu.3	Q13163	OTTHUMG00000133264	ENST00000178640.5:c.845G>C	chr15.hg19:g.67956981G>C	ENSP00000178640:p.Arg282Thr	105.0	0.0	.		93.0	8.0	.	NM_145160	B4DE43|Q92961|Q92962	Missense_Mutation	SNP	ENST00000178640.5	hg19	CCDS10224.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.501730	0.85176	.	.	ENSG00000137764	ENST00000541298;ENST00000395476;ENST00000178640;ENST00000354498;ENST00000340972	T;T;T;T	0.19105	2.17;2.17;2.17;2.17	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	0.65616	0.2708	H	0.98048	4.135	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	0.78226	-0.2286	10	0.87932	D	0	-21.9076	18.7754	0.91910	0.0:0.0:1.0:0.0	.	92;282;282	A6NK28;Q13163-2;Q13163	.;.;MP2K5_HUMAN	T	282;282;282;246;92	ENSP00000378859:R282T;ENSP00000178640:R282T;ENSP00000346493:R246T;ENSP00000342101:R92T	ENSP00000178640:R282T	R	+	2	0	MAP2K5	65744035	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.843000	0.86859	2.873000	0.98535	0.563000	0.77884	AGA	.	.	.	none		0.333	MAP2K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257041.1	NM_145162		C	67956981	G	C	67956981	3	2	113	1	0	0	0	0	1	0	0	0	9247	942	33	4	895	4	MAP2K5	15	67956981	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	35027467	67956981	34574411	62	7330											
AGBL1	123624	hgsc.bcm.edu	37	chr15	87217502	87217502	+	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	taatgctttgtttaactggcAgggtctacagtttggtacca	9	15	10	7	0	1	0	0	0	1	0	1	0	1	0	1	3	4	5	1	3	4	7			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr15:87217502A>G	ENST00000441037.2	+	22	3014		c.e22-1		AGBL1_ENST00000389298.3_Splice_Site|AGBL1_ENST00000421325.2_Splice_Site	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1						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)	p.?(1)		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						TTTAACTGGCAGGGTCTACAG	0.478																																					.		Atlas-SNP	.											AGBL1,NS,carcinoma,0,1	AGBL1	151	.	1	Unknown(1)	lung(1)	c.2920-2A>G						PASS	.						52	49	50					15																	87217502		1970	4174	6144	SO:0001630	splice_region_variant	123624	exon22			ACTGGCAGGGTCT	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.2920-1A>G	chr15.hg19:g.87217502A>G		16.0	0.0	.		18.0	8.0	.	NM_152336	A1A4X5|A6NJH6|C9JHL5	Splice_Site	SNP	ENST00000441037.2	hg19	CCDS58398.1	.	.	.	.	.	.	.	.	.	.	A	19.01	3.744859	0.69418	.	.	ENSG00000166748	ENST00000421325;ENST00000389298	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.967	0.58490	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AGBL1	85018506	1.000000	0.71417	0.987000	0.45799	0.840000	0.47671	5.346000	0.65992	2.068000	0.61886	0.460000	0.39030	.	.	.	.	none		0.478	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	Intron	G	87217502	A	G	87217502	5	3	113	1	0	0	0	0	0	0	1	0	375	202	7	3	3000	3	AGBL1	15	87217502	Splice_Site	SNP	A	TCGA-BQ-5878-01A-11D-1589-08	19260521	87217502	15313890	63	7331											
SRRM2	23524	hgsc.bcm.edu	37	chr16	2816146	2816146	+	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	ctcgagcctctccagccactCaccggcgatccaggtccaga	8	6	9	18	3	2	1	1	0	1	1	6	3	4	1	6	2	2	0	6	2	0	0			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr16:2816146C>G	ENST00000301740.8	+	11	6166	c.5617C>G	c.(5617-5619)Cac>Gac	p.H1873D		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	1873	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						TCCAGCCACTCACCGGCGATC	0.612																																					p.H1873D		Atlas-SNP	.											.	SRRM2	263	.	0			c.C5617G						PASS	.						80	77	78					16																	2816146		2198	4300	6498	SO:0001583	missense	23524	exon11			GCCACTCACCGGC	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.5617C>G	chr16.hg19:g.2816146C>G	ENSP00000301740:p.His1873Asp	88.0	0.0	.		73.0	22.0	.	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	hg19	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	C	2.782	-0.253191	0.05829	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	T	0.24538	1.85	5.34	5.34	0.76211	.	0.000000	0.64402	D	0.000006	T	0.27489	0.0675	N	0.08118	0	0.35745	D	0.819014	D	0.65815	0.995	P	0.57911	0.829	T	0.42189	-0.9466	10	0.52906	T	0.07	-12.2072	16.5384	0.84377	0.0:1.0:0.0:0.0	.	1873	Q9UQ35	SRRM2_HUMAN	D	1873;1873;1125	ENSP00000301740:H1873D	ENSP00000301740:H1873D	H	+	1	0	SRRM2	2756147	0.881000	0.30235	1.000000	0.80357	0.997000	0.91878	1.956000	0.40382	2.492000	0.84095	0.650000	0.86243	CAC	.	.	.	none		0.612	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			G	2816146	C	G	2816146	3	3	113	1	0	0	0	0	1	0	0	0	15181	826	29	4	5655	4	SRRM2	16	2816146	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08		2816146	87538607	64	7332											
SRRM2	23524	hgsc.bcm.edu	37	chr16	2818196	2818196	+	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	gtcgtcgtcctcctcctcctCtggctccagttctagtgact	3	14	8	16	2	2	1	0	1	2	0	9	1	7	1	5	1	0	2	5	1	1	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr16:2818196C>G	ENST00000301740.8	+	11	8216	c.7667C>G	c.(7666-7668)tCt>tGt	p.S2556C	AC092117.2_ENST00000581119.1_RNA|SRRM2_ENST00000574593.1_3'UTR	NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	2556	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						tcctcctcctcTGGCTCCAGT	0.572																																					p.S2556C		Atlas-SNP	.											.	SRRM2	263	.	0			c.C7667G						PASS	.						56	51	53					16																	2818196		2198	4300	6498	SO:0001583	missense	23524	exon11			CCTCCTCTGGCTC	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.7667C>G	chr16.hg19:g.2818196C>G	ENSP00000301740:p.Ser2556Cys	44.0	0.0	.		42.0	15.0	.	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	hg19	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.951695	0.73787	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	T	0.77877	-1.13	5.91	5.91	0.95273	.	0.000000	0.51477	D	0.000098	D	0.82586	0.5069	L	0.32530	0.975	0.36253	D	0.854052	D	0.76494	0.999	D	0.77557	0.99	D	0.85933	0.1453	10	0.62326	D	0.03	-5.5072	15.8054	0.78501	0.0:1.0:0.0:0.0	.	2556	Q9UQ35	SRRM2_HUMAN	C	2556;2138;1808	ENSP00000301740:S2556C	ENSP00000301740:S2556C	S	+	2	0	SRRM2	2758197	0.998000	0.40836	1.000000	0.80357	0.886000	0.51366	4.236000	0.58675	2.808000	0.96608	0.655000	0.94253	TCT	.	.	.	none		0.572	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			G	2818196	C	G	2818196	3	3	113	1	0	0	0	0	1	0	0	0	15181	913	32	4	7705	4	SRRM2	16	2818196	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	2050	2818196	87536557	65	7333											
LONP2	83752	hgsc.bcm.edu	37	chr16	48385617	48385617	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtacgacaggatttaagtttTgtcacagcaagctgcctgga	11	11	11	8	1	1	0	1	0	0	0	1	3	1	2	1	2	4	4	1	2	3	5			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr16:48385617T>C	ENST00000285737.4	+	15	2556	c.2463T>C	c.(2461-2463)ttT>ttC	p.F821F	LONP2_ENST00000564259.1_3'UTR|LONP2_ENST00000535754.1_Silent_p.F777F	NM_031490.2	NP_113678.2			lon peptidase 2, peroxisomal											breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						ATTTAAGTTTTGTCACAGCAA	0.473																																					p.F821F		Atlas-SNP	.											.	LONP2	63	.	0			c.T2463C						PASS	.						89	85	86					16																	48385617		2200	4300	6500	SO:0001819	synonymous_variant	83752	exon15			AAGTTTTGTCACA	AJ548761	CCDS10734.1, CCDS73880.1	16q12.1	2010-04-21			ENSG00000102910	ENSG00000102910		"ATPases / AAA-type"	20598	protein-coding gene	gene with protein product						14561759	Standard	XM_005256191		Approved	MGC4840, LONP, LONPL	uc002efi.1	Q86WA8	OTTHUMG00000133144	ENST00000285737.4:c.2463T>C	chr16.hg19:g.48385617T>C		100.0	0.0	.		89.0	34.0	.	NM_031490		Silent	SNP	ENST00000285737.4	hg19	CCDS10734.1																																																																																			.	.	.	none		0.473	LONP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256839.2	NM_031490		C	48385617	T	C	48385617	2	2	113	1	0	0	0	0	0	0	0	1	8900	1809	63	3		3	LONP2	16	48385617	Silent	SNP	T	TCGA-BQ-5878-01A-11D-1589-08	45567421	48385617	41969136	66	7334											
ZFHX3	463	hgsc.bcm.edu	37	chr16	72828734	72828734	+	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	tggccttttcctccagcttcCtcttgagagtgttcattgtg	4	17	9	11	0	2	1	1	1	1	1	5	2	5	1	4	1	1	2	4	1	0	6			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr16:72828734C>T	ENST00000268489.5	-	9	8519	c.7847G>A	c.(7846-7848)aGg>aAg	p.R2616K	ZFHX3_ENST00000397992.5_Missense_Mutation_p.R1702K	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	2616					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)				CTCCAGCTTCCTCTTGAGAGT	0.547																																					p.R2616K		Atlas-SNP	.											.	ZFHX3	404	.	0			c.G7847A						PASS	.						207	212	210					16																	72828734		2198	4300	6498	SO:0001583	missense	463	exon9			AGCTTCCTCTTGA	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.7847G>A	chr16.hg19:g.72828734C>T	ENSP00000268489:p.Arg2616Lys	533.0	1.0	.		461.0	188.0	.	NM_006885	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	hg19	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	C	13.86	2.362208	0.41902	.	.	ENSG00000140836	ENST00000268489;ENST00000397992	T;T	0.74737	-0.87;-0.86	5.64	5.64	0.86602	.	0.000000	0.56097	D	0.000033	D	0.84014	0.5379	L	0.56199	1.76	0.80722	D	1	D	0.58970	0.984	D	0.68192	0.956	D	0.83807	0.0239	10	0.54805	T	0.06	.	19.683	0.95971	0.0:1.0:0.0:0.0	.	2616	Q15911	ZFHX3_HUMAN	K	2616;1702	ENSP00000268489:R2616K;ENSP00000438926:R1702K	ENSP00000268489:R2616K	R	-	2	0	ZFHX3	71386235	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.818000	0.86416	2.653000	0.90120	0.561000	0.74099	AGG	.	.	.	none		0.547	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		T	72828734	C	T	72828734	3	4	113	1	0	0	0	0	1	0	0	0	17646	681	24	2	3272	2	ZFHX3	16	72828734	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	24443117	72828734	17526019	67	7335											
GEMIN4	50628	hgsc.bcm.edu	37	chr17	649344	649344	+	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	cttcagcacctcgtctggctCaagaagagcagccactggaa	11	7	10	13	1	3	2	2	0	1	2	4	3	3	3	2	2	3	3	2	2	3	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr17:649344C>G	ENST00000319004.5	-	2	2057	c.1939G>C	c.(1939-1941)Gag>Cag	p.E647Q	GEMIN4_ENST00000576778.1_Missense_Mutation_p.E636Q	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	647					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)		TCGTCTGGCTCAAGAAGAGCA	0.488																																					p.E647Q		Atlas-SNP	.											.	GEMIN4	116	.	0			c.G1939C						PASS	.						64	67	66					17																	649344		1893	4118	6011	SO:0001583	missense	50628	exon2			CTGGCTCAAGAAG	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.1939G>C	chr17.hg19:g.649344C>G	ENSP00000321706:p.Glu647Gln	82.0	0.0	.		84.0	10.0	.	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Missense_Mutation	SNP	ENST00000319004.5	hg19	CCDS45559.1	.	.	.	.	.	.	.	.	.	.	C	4.186	0.033188	0.08101	.	.	ENSG00000179409	ENST00000319004	T	0.05786	3.39	5.57	4.6	0.57074	.	0.448686	0.24490	N	0.038075	T	0.05456	0.0144	L	0.41236	1.265	0.22378	N	0.999157	B	0.21225	0.053	B	0.17722	0.019	T	0.35076	-0.9803	10	0.30078	T	0.28	-12.805	5.0874	0.14691	0.1555:0.6319:0.1337:0.0789	.	647	P57678	GEMI4_HUMAN	Q	647	ENSP00000321706:E647Q	ENSP00000321706:E647Q	E	-	1	0	GEMIN4	596094	0.185000	0.23213	0.959000	0.39883	0.826000	0.46750	0.956000	0.29202	1.358000	0.45922	0.655000	0.94253	GAG	.	.	.	none		0.488	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721		G	649344	C	G	649344	3	3	113	1	0	0	0	0	1	0	0	0	6337	835	29	4	1241	4	GEMIN4	17	649344	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08		649344	80545866	68	7336											
C17orf48	56985	hgsc.bcm.edu	37	chr17	10608559	10608559	+	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	ggcttaaagttccagttcatCatacatggggaaaccatgaa	14	10	9	8	0	2	1	2	1	0	0	3	2	3	2	2	3	2	3	2	3	5	4			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr17:10608559C>T	ENST00000379774.4	+	2	407	c.316C>T	c.(316-318)Cat>Tat	p.H106Y	ADPRM_ENST00000609540.1_Missense_Mutation_p.H106Y	NM_020233.4	NP_064618.3	Q3LIE5	ADPRM_HUMAN	ADP-ribose/CDP-alcohol diphosphatase, manganese-dependent	106							ADP-ribose diphosphatase activity (GO:0047631)|CDP-glycerol diphosphatase activity (GO:0047734)|metal ion binding (GO:0046872)										TCCAGTTCATCATACATGGGG	0.353																																					p.H106Y		Atlas-SNP	.											.	.	.	.	0			c.C316T						PASS	.						88	82	84					17																	10608559		2203	4300	6503	SO:0001583	missense	56985	exon2			GTTCATCATACAT	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.316C>T	chr17.hg19:g.10608559C>T	ENSP00000369099:p.His106Tyr	106.0	0.0	.		115.0	18.0	.	NM_020233	A8K9B4|D3DTS4|Q9BVD4|Q9NRU8	Missense_Mutation	SNP	ENST00000379774.4	hg19	CCDS11159.2	.	.	.	.	.	.	.	.	.	.	C	24.7	4.565615	0.86439	.	.	ENSG00000170222	ENST00000379774	D	0.84660	-1.88	5.64	5.64	0.86602	Metallophosphoesterase domain (1);	0.000000	0.85682	D	0.000000	D	0.89949	0.6863	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83803	0.0237	10	0.02654	T	1	-8.9416	19.5025	0.95103	0.0:1.0:0.0:0.0	.	106	Q3LIE5	ADPRM_HUMAN	Y	106	ENSP00000369099:H106Y	ENSP00000369099:H106Y	H	+	1	0	C17orf48	10549284	1.000000	0.71417	0.964000	0.40570	0.988000	0.76386	6.987000	0.76206	2.937000	0.99478	0.650000	0.86243	CAT	.	.	.	none		0.353	ADPRM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252732.2	NM_020233		T	10608559	C	T	10608559	3	4	113	1	0	0	0	0	1	0	0	0	1861	826	29	2	318	2	C17orf48	17	10608559	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	9959215	10608559	70586651	69	7337											
MYO18A	399687	hgsc.bcm.edu	37	chr17	27430634	27430634	+	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	cacccggctcaggcccatgcAgcagctgctcttctccagat	7	8	9	17	1	3	1	1	0	2	1	4	1	3	1	3	2	4	5	3	2	0	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr17:27430634A>T	ENST00000527372.1	-	21	3670	c.3490T>A	c.(3490-3492)Tgc>Agc	p.C1164S	MYO18A_ENST00000533112.1_Missense_Mutation_p.C1164S|MYO18A_ENST00000531253.1_Missense_Mutation_p.C1164S|MYO18A_ENST00000354329.4_Missense_Mutation_p.C1164S	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	1164	Myosin motor.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			AGGCCCATGCAGCAGCTGCTC	0.657																																					p.C1164S	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.T3490A						PASS	.						47	54	52					17																	27430634		2074	4207	6281	SO:0001583	missense	399687	exon21			CCATGCAGCAGCT	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.3490T>A	chr17.hg19:g.27430634A>T	ENSP00000437073:p.Cys1164Ser	61.0	0.0	.		32.0	16.0	.	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	hg19	CCDS45642.1	.	.	.	.	.	.	.	.	.	.	A	12.27	1.887500	0.33348	.	.	ENSG00000196535	ENST00000354329;ENST00000359450;ENST00000533112;ENST00000531253;ENST00000527372;ENST00000529799;ENST00000540575;ENST00000458428	D;D;D;D	0.86366	-2.11;-2.11;-2.11;-2.11	5.44	3.22	0.36961	Myosin head, motor domain (2);	0.313479	0.39544	N	0.001332	T	0.74680	0.3748	N	0.25890	0.77	0.37666	D	0.922943	B;B;B;B;B	0.22346	0.006;0.009;0.009;0.009;0.068	B;B;B;B;B	0.21708	0.003;0.015;0.009;0.009;0.036	T	0.66392	-0.5935	10	0.32370	T	0.25	.	3.1069	0.06345	0.6565:0.0:0.1571:0.1864	.	833;776;1164;1164;1164	Q92614-2;F8W6Y3;Q92614-3;Q92614-4;Q92614	.;.;.;.;MY18A_HUMAN	S	1164;1164;1164;1164;1164;60;60;776	ENSP00000346291:C1164S;ENSP00000435932:C1164S;ENSP00000434228:C1164S;ENSP00000437073:C1164S	ENSP00000346291:C1164S	C	-	1	0	MYO18A	24454760	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.734000	0.47368	0.878000	0.35920	0.459000	0.35465	TGC	.	.	.	none		0.657	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		T	27430634	A	T	27430634	3	4	113	1	0	0	0	0	1	0	0	0	10072	188	7	5	2762	5	MYO18A	17	27430634	Missense_Mutation	SNP	A	TCGA-BQ-5878-01A-11D-1589-08	16822075	27430634	53764576	70	7338											
KCNJ16	3773	hgsc.bcm.edu	37	chr17	68129360	68129360	+	Missense_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	gaaggtcatttagtgcagttGccattgtcagcagctgtgaa	10	12	12	7	0	2	1	2	1	0	0	2	2	2	1	1	1	4	4	1	1	3	4			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr17:68129360G>A	ENST00000589377.1	+	2	1295	c.1132G>A	c.(1132-1134)Gcc>Acc	p.A378T	KCNJ16_ENST00000586462.1_Missense_Mutation_p.A417T|KCNJ16_ENST00000283936.1_Missense_Mutation_p.A378T|KCNJ16_ENST00000585558.1_Missense_Mutation_p.A413T|KCNJ16_ENST00000392670.1_Missense_Mutation_p.A378T|KCNJ16_ENST00000392671.1_Missense_Mutation_p.A378T	NM_001270422.1	NP_001257351.1	Q9NPI9	KCJ16_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 16	378					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)					TAGTGCAGTTGCCATTGTCAG	0.498																																					p.A378T		Atlas-SNP	.											.	KCNJ16	72	.	0			c.G1132A						PASS	.						109	92	98					17																	68129360		2203	4300	6503	SO:0001583	missense	3773	exon6			GCAGTTGCCATTG	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.1132G>A	chr17.hg19:g.68129360G>A	ENSP00000465967:p.Ala378Thr	80.0	0.0	.		84.0	43.0	.	NM_001270422		Missense_Mutation	SNP	ENST00000589377.1	hg19	CCDS11687.1	.	.	.	.	.	.	.	.	.	.	G	12.84	2.058214	0.36277	.	.	ENSG00000153822	ENST00000283936;ENST00000392671;ENST00000392670	D;D;D	0.89270	-2.49;-2.49;-2.49	5.8	5.8	0.92144	.	1.758860	0.02733	N	0.115373	D	0.84584	0.5504	L	0.27053	0.805	0.36349	D	0.859948	B;B	0.29909	0.261;0.01	B;B	0.21546	0.035;0.007	T	0.60910	-0.7169	9	.	.	.	.	13.9035	0.63819	0.0735:0.0:0.9265:0.0	.	378;378	A8K434;Q9NPI9	.;IRK16_HUMAN	T	378	ENSP00000283936:A378T;ENSP00000376439:A378T;ENSP00000376438:A378T	.	A	+	1	0	KCNJ16	65640955	0.999000	0.42202	0.952000	0.39060	0.454000	0.32378	6.073000	0.71245	2.736000	0.93811	0.591000	0.81541	GCC	.	.	.	none		0.498	KCNJ16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450880.1	NM_018658		A	68129360	G	A	68129360	3	1	113	1	0	0	0	0	1	0	0	0	8057	1319	46	2	1134	2	KCNJ16	17	68129360	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	40698726	68129360	13065850	71	7339											
YES1	7525	hgsc.bcm.edu	37	chr18	756694	756694	+	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	ctgctgttccctttgctgaaGatgacggacatggtgacact	8	12	11	10	1	0	4	0	3	0	1	1	5	1	5	1	2	2	3	1	2	1	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr18:756694G>A	ENST00000584307.1	-	2	304	c.134C>T	c.(133-135)tCt>tTt	p.S45F	YES1_ENST00000577961.1_Missense_Mutation_p.S50F|YES1_ENST00000577611.1_5'UTR|YES1_ENST00000314574.4_Missense_Mutation_p.S45F			P07947	YES_HUMAN	YES proto-oncogene 1, Src family tyrosine kinase	45					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)	CTTTGCTGAAGATGACGGACA	0.468																																					p.S45F		Atlas-SNP	.											.	YES1	50	.	0			c.C134T						PASS	.						248	208	222					18																	756694		2203	4300	6503	SO:0001583	missense	7525	exon2			GCTGAAGATGACG	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.134C>T	chr18.hg19:g.756694G>A	ENSP00000462468:p.Ser45Phe	289.0	0.0	.		235.0	33.0	.	NM_005433	A6NLB3|D3DUH1	Missense_Mutation	SNP	ENST00000584307.1	hg19	CCDS11824.1	.	.	.	.	.	.	.	.	.	.	G	6.428	0.447146	0.12223	.	.	ENSG00000176105	ENST00000359834;ENST00000314574	T	0.75050	-0.9	4.66	4.66	0.58398	.	0.822602	0.09557	U	0.786109	T	0.66297	0.2775	L	0.29908	0.895	0.45366	D	0.998353	B	0.02656	0.0	B	0.08055	0.003	T	0.53851	-0.8380	10	0.16420	T	0.52	.	17.9046	0.88914	0.0:0.0:1.0:0.0	.	45	P07947	YES_HUMAN	F	45	ENSP00000324740:S45F	ENSP00000324740:S45F	S	-	2	0	YES1	746694	1.000000	0.71417	0.017000	0.16124	0.934000	0.57294	6.760000	0.74939	2.299000	0.77371	0.313000	0.20887	TCT	.	.	.	none		0.468	YES1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440827.2	NM_005433		A	756694	G	A	756694	3	1	113	1	0	0	0	0	1	0	0	0	17486	942	33	2	1541	2	YES1	18	756694	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08		756694	77320554	72	7340											
DSC3	1825	hgsc.bcm.edu	37	chr18	28576918	28576918	+	Frame_Shift_Del	DEL	T	T	-																															tcctttcatcatttcaatggTttcctgccctccatttttca																										TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr18:28576918delT	ENST00000360428.4	-	15	2412	c.2332delA	c.(2332-2334)accfs	p.T778fs	DSC3_ENST00000434452.1_Frame_Shift_Del_p.T778fs	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3	778					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)			ATTTCAATGGTTTCCTGCCCT	0.502																																					p.T778fs		Atlas-INDEL	.											.	DSC3	225	.	0			c.2333delC						PASS	.						119	96	104					18																	28576918		2203	4300	6503	SO:0001589	frameshift_variant	1825	exon15			.	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.2332delA	chr18.hg19:g.28576918delT	ENSP00000353608:p.Thr778fs	62.0	0.0	0		60.0	22.0	0.366667	NM_024423	A6NN35|Q14200|Q9HAZ9	Frame_Shift_Del	DEL	ENST00000360428.4	hg19	CCDS32810.1																																																																																			.	.	.	none		0.502	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	NM_001941, NM_024423		-	28576918	T	-	28576918	7	5	113	1	0	1	0	1	0	0	0	0	4769	1725	60	0	397	0	DSC3	18	28576918	Frame_Shift_Del	DEL	T	TCGA-BQ-5878-01A-11D-1589-08	27820224	28576918	49500330	73	7341											
NEDD4L	23327	hgsc.bcm.edu	37	chr18	55996285	55996285	+	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	tcaaccaggaggcagcacacCggcgcttccgctcccgcagg	8	4	12	17	4	1	0	1	0	0	0	3	1	3	1	4	4	2	5	4	4	1	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr18:55996285C>A	ENST00000400345.3	+	10	1022	c.739C>A	c.(739-741)Cgg>Agg	p.R247R	NEDD4L_ENST00000357895.5_Silent_p.R239R|NEDD4L_ENST00000256830.9_Silent_p.R247R|NEDD4L_ENST00000435432.2_Silent_p.R126R|NEDD4L_ENST00000586263.1_Silent_p.R239R|NEDD4L_ENST00000456986.1_Silent_p.R126R|NEDD4L_ENST00000431212.2_Silent_p.R126R|NEDD4L_ENST00000356462.6_Silent_p.R247R|NEDD4L_ENST00000456173.2_Silent_p.R126R|NEDD4L_ENST00000382850.4_Silent_p.R247R|NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000256832.7_Silent_p.R126R	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	247					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						GGCAGCACACCGGCGCTTCCG	0.597																																					p.R247R		Atlas-SNP	.											.	NEDD4L	126	.	0			c.C739A						PASS	.						38	45	43					18																	55996285		2100	4227	6327	SO:0001819	synonymous_variant	23327	exon10			GCACACCGGCGCT	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.739C>A	chr18.hg19:g.55996285C>A		41.0	0.0	.		44.0	4.0	.	NM_015277	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Silent	SNP	ENST00000400345.3	hg19	CCDS45872.1																																																																																			.	.	.	none		0.597	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1			A	55996285	C	A	55996285	2	1	113	1	0	0	0	0	0	0	0	1	10318	643	23	4		4	NEDD4L	18	55996285	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	27419367	55996285	22080963	74	7342											
MUC16	94025	hgsc.bcm.edu	37	chr19	9087506	9087506	+	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	caggggttcccctgggacatCagaagttagttccaatgtgc	9	10	12	10	0	1	1	1	0	0	1	3	2	3	2	3	3	1	3	3	3	3	3			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:9087506C>T	ENST00000397910.4	-	1	4512	c.4309G>A	c.(4309-4311)Gat>Aat	p.D1437N		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1437	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						CCTGGGACATCAGAAGTTAGT	0.512																																					p.D1437N		Atlas-SNP	.											.	MUC16	4315	.	0			c.G4309A						PASS	.						118	114	116					19																	9087506		1966	4148	6114	SO:0001583	missense	94025	exon1			GGACATCAGAAGT	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.4309G>A	chr19.hg19:g.9087506C>T	ENSP00000381008:p.Asp1437Asn	130.0	0.0	.		149.0	12.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	3.824	-0.037221	0.07497	.	.	ENSG00000181143	ENST00000397910	T	0.02944	4.1	1.0	-0.286	0.12862	.	.	.	.	.	T	0.01489	0.0048	N	0.08118	0	.	.	.	B	0.26845	0.161	B	0.18263	0.021	T	0.44190	-0.9344	8	0.87932	D	0	.	3.1617	0.06522	0.0:0.617:0.0:0.383	.	1437	B5ME49	.	N	1437	ENSP00000381008:D1437N	ENSP00000381008:D1437N	D	-	1	0	MUC16	8948506	0.001000	0.12720	0.002000	0.10522	0.042000	0.13812	-0.052000	0.11865	-0.065000	0.13021	0.305000	0.20034	GAT	.	.	.	none		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9087506	C	T	9087506	3	4	113	1	0	0	0	0	1	0	0	0	9980	826	29	2	39550	2	MUC16	19	9087506	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08		9087506	50041477	75	7343											
ECSIT	51295	hgsc.bcm.edu	37	chr19	11618829	11618829	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgatgtggggctgggggggaTctgctgcacctgttgagtct	4	11	18	8	1	2	1	0	1	2	0	2	3	2	2	1	5	2	4	1	5	0	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:11618829T>C	ENST00000270517.7	-	5	908	c.773A>G	c.(772-774)gAt>gGt	p.D258G	ECSIT_ENST00000591352.1_5'UTR|ECSIT_ENST00000592312.1_Missense_Mutation_p.D142G|ECSIT_ENST00000252440.7_Missense_Mutation_p.D258G|ZNF653_ENST00000593191.1_5'Flank|ECSIT_ENST00000588998.1_Missense_Mutation_p.D44G|ECSIT_ENST00000591104.1_Missense_Mutation_p.D258G|ZNF653_ENST00000293771.5_5'Flank|CTC-398G3.6_ENST00000585656.1_5'Flank|ECSIT_ENST00000417981.2_Missense_Mutation_p.D44G	NM_016581.4	NP_057665.2	Q9BQ95	ECSIT_HUMAN	ECSIT signalling integrator	258					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						CTGGGGGGGATCTGCTGCACC	0.577																																					p.D258G		Atlas-SNP	.											.	ECSIT	32	.	0			c.A773G						PASS	.						99	108	105					19																	11618829		2203	4300	6503	SO:0001583	missense	51295	exon5			GGGGGATCTGCTG	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.773A>G	chr19.hg19:g.11618829T>C	ENSP00000270517:p.Asp258Gly	105.0	0.0	.		117.0	39.0	.	NM_001142464	E9PAN9|K7EMM0|Q96HQ7|Q9NYI1	Missense_Mutation	SNP	ENST00000270517.7	hg19	CCDS12262.1	.	.	.	.	.	.	.	.	.	.	T	15.67	2.901102	0.52227	.	.	ENSG00000130159	ENST00000270517;ENST00000417981;ENST00000252440	T;T;T	0.80480	-1.38;1.22;-1.38	3.81	2.67	0.31697	.	0.528567	0.19970	N	0.102018	T	0.77343	0.4116	M	0.73598	2.24	0.09310	N	1	P;P;P	0.44139	0.827;0.557;0.485	B;B;B	0.41510	0.359;0.178;0.248	T	0.71646	-0.4530	10	0.66056	D	0.02	-5.0804	6.5677	0.22521	0.0:0.0:0.2477:0.7523	.	44;258;258	E9PAN9;Q9BQ95-2;Q9BQ95	.;.;ECSIT_HUMAN	G	258;44;258	ENSP00000270517:D258G;ENSP00000412712:D44G;ENSP00000252440:D258G	ENSP00000252440:D258G	D	-	2	0	ECSIT	11479829	0.181000	0.23161	0.007000	0.13788	0.266000	0.26442	2.000000	0.40816	1.671000	0.50874	0.459000	0.35465	GAT	.	.	.	none		0.577	ECSIT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442603.2	NM_016581		C	11618829	T	C	11618829	3	2	113	1	0	0	0	0	1	0	0	0	4902	1435	50	3	538	3	ECSIT	19	11618829	Missense_Mutation	SNP	T	TCGA-BQ-5878-01A-11D-1589-08	2531323	11618829	47510154	76	7344											
HOOK2	29911	hgsc.bcm.edu	37	chr19	12875721	12875721	+	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	ttatgctgcagctcctcgatCcgccgggctgctggcggaag	5	9	14	13	4	0	0	0	0	0	0	3	2	2	1	3	3	4	5	3	3	2	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:12875721C>T	ENST00000397668.3	-	20	1807	c.1734G>A	c.(1732-1734)cgG>cgA	p.R578R	HOOK2_ENST00000264827.5_Silent_p.R576R|HOOK2_ENST00000589965.1_5'Flank	NM_013312.2	NP_037444.2	Q96ED9	HOOK2_HUMAN	hook microtubule-tethering protein 2	578	Required for localization to the centrosome and induction of aggresome formation.				early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	centrosome (GO:0005813)|FHF complex (GO:0070695)|microtubule (GO:0005874)	identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(5)|skin(1)	20						GCTCCTCGATCCGCCGGGCTG	0.632											OREG0025273	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R578R		Atlas-SNP	.											.	HOOK2	73	.	0			c.G1734A						PASS	.						67	73	71					19																	12875721		2018	4169	6187	SO:0001819	synonymous_variant	29911	exon20			CTCGATCCGCCGG	AF044924	CCDS42507.1, CCDS42508.1	19p13.2	2013-08-21	2013-08-21						19885	protein-coding gene	gene with protein product		607824	"hook homolog 2 (Drosophila)"			9927460	Standard	NM_013312		Approved	HK2	uc002muy.2	Q96ED9		ENST00000397668.3:c.1734G>A	chr19.hg19:g.12875721C>T		108.0	0.0	.	683	145.0	9.0	.	NM_013312	O60562	Silent	SNP	ENST00000397668.3	hg19	CCDS42508.1																																																																																			.	.	.	none		0.632	HOOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451008.1	NM_013312		T	12875721	C	T	12875721	2	4	113	1	0	0	0	0	0	0	0	1	7290	842	30	2		2	HOOK2	19	12875721	Silent	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	1256892	12875721	46253262	77	7345											
NOTCH3	4854	hgsc.bcm.edu	37	chr19	15288375	15288375	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caccggcgtggcagtcgaagTtgtcgtagaggcaggcgggc	7	6	18	10	5	0	1	0	0	0	1	2	2	0	1	1	5	0	4	1	5	2	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:15288375T>C	ENST00000263388.2	-	24	4439	c.4364A>G	c.(4363-4365)aAc>aGc	p.N1455S		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	1455					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)			GCAGTCGAAGTTGTCGTAGAG	0.657																																					p.N1455S		Atlas-SNP	.											.	NOTCH3	340	.	0			c.A4364G						PASS	.						14	13	13					19																	15288375		2111	4180	6291	SO:0001583	missense	4854	exon24			TCGAAGTTGTCGT	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.4364A>G	chr19.hg19:g.15288375T>C	ENSP00000263388:p.Asn1455Ser	28.0	0.0	.		15.0	4.0	.	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	hg19	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	T	19.38	3.816967	0.70912	.	.	ENSG00000074181	ENST00000263388	T	0.63913	-0.07	4.66	4.66	0.58398	Notch domain (5);	.	.	.	.	T	0.56746	0.2006	L	0.47016	1.485	0.45883	D	0.998736	B	0.31968	0.349	B	0.33799	0.17	T	0.60255	-0.7299	9	0.56958	D	0.05	.	13.0613	0.59008	0.0:0.0:0.0:1.0	.	1455	Q9UM47	NOTC3_HUMAN	S	1455	ENSP00000263388:N1455S	ENSP00000263388:N1455S	N	-	2	0	NOTCH3	15149375	1.000000	0.71417	1.000000	0.80357	0.817000	0.46193	1.398000	0.34554	1.728000	0.51552	0.260000	0.18958	AAC	.	.	.	none		0.657	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		C	15288375	T	C	15288375	3	2	113	1	0	0	0	0	1	0	0	0	10557	1725	60	3	2641	3	NOTCH3	19	15288375	Missense_Mutation	SNP	T	TCGA-BQ-5878-01A-11D-1589-08	2412654	15288375	43840608	78	7346											
UNC13A	23025	hgsc.bcm.edu	37	chr19	17750273	17750273	+	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	gaaagaaggtgatgctggtgAgaaggtccacagtggatttg	12	9	16	4	0	0	3	0	2	0	2	1	6	1	4	1	4	1	1	1	4	3	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:17750273A>T	ENST00000519716.2	-	24	2917	c.2918T>A	c.(2917-2919)cTc>cAc	p.L973H	UNC13A_ENST00000552293.1_Missense_Mutation_p.L973H|UNC13A_ENST00000550896.1_Missense_Mutation_p.L971H|UNC13A_ENST00000428389.2_Missense_Mutation_p.L1061H|UNC13A_ENST00000551649.1_Missense_Mutation_p.L973H|UNC13A_ENST00000252773.7_Missense_Mutation_p.L973H	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	973					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						GATGCTGGTGAGAAGGTCCAC	0.532																																					p.L973H		Atlas-SNP	.											.	UNC13A	299	.	0			c.T2918A						PASS	.						79	78	79					19																	17750273		1967	4144	6111	SO:0001583	missense	23025	exon23			CTGGTGAGAAGGT	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.2918T>A	chr19.hg19:g.17750273A>T	ENSP00000429562:p.Leu973His	40.0	0.0	.		32.0	8.0	.	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	hg19	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	A	20.4	3.975812	0.74360	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	D;D;D;D;D;D	0.87729	-2.28;-2.29;-2.27;-2.12;-2.16;-2.29	3.95	3.95	0.45737	.	0.179999	0.36303	U	0.002675	D	0.92619	0.7655	M	0.80183	2.485	0.52501	D	0.999952	D	0.89917	1.0	D	0.83275	0.996	D	0.93099	0.6507	10	0.87932	D	0	-16.3271	11.1266	0.48322	1.0:0.0:0.0:0.0	.	973	Q9UPW8	UN13A_HUMAN	H	973;1061;973;973;973;971	ENSP00000429562:L973H;ENSP00000400409:L1061H;ENSP00000252773:L973H;ENSP00000447236:L973H;ENSP00000447572:L973H;ENSP00000446831:L971H	ENSP00000252773:L973H	L	-	2	0	UNC13A	17611273	1.000000	0.71417	0.892000	0.35008	0.984000	0.73092	9.105000	0.94246	1.568000	0.49683	0.248000	0.18094	CTC	.	.	.	none		0.532	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		T	17750273	A	T	17750273	3	4	113	1	0	0	0	0	1	0	0	0	16996	304	11	5	2273	5	UNC13A	19	17750273	Missense_Mutation	SNP	A	TCGA-BQ-5878-01A-11D-1589-08	2461898	17750273	41378710	79	7347											
CYP2A13	1553	hgsc.bcm.edu	37	chr19	41596079	41596079	+	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	gaggaggcgggcttcctcatCgacgccctccggggcacgca	6	5	15	15	5	1	0	1	0	0	0	4	3	3	1	3	5	0	3	3	5	0	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:41596079C>G	ENST00000330436.3	+	3	471	c.471C>G	c.(469-471)atC>atG	p.I157M		NM_000766.4	NP_000757.2	Q16696	CP2AD_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 13	157					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)	GCTTCCTCATCGACGCCCTCC	0.687																																					p.I157M		Atlas-SNP	.											.	CYP2A13	90	.	0			c.C471G						PASS	.						31	32	31					19																	41596079		2202	4300	6502	SO:0001583	missense	1553	exon3			CCTCATCGACGCC	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.471C>G	chr19.hg19:g.41596079C>G	ENSP00000332679:p.Ile157Met	76.0	0.0	.		75.0	46.0	.	NM_000766	Q53YR8|Q6R569|Q6R570|Q9H2X2	Missense_Mutation	SNP	ENST00000330436.3	hg19	CCDS12571.1	.	.	.	.	.	.	.	.	.	.	.	11.11	1.542221	0.27563	.	.	ENSG00000197838	ENST00000330436	T	0.01379	4.96	3.43	-3.64	0.04515	.	0.840898	0.10215	U	0.701698	T	0.01353	0.0044	L	0.45285	1.41	0.09310	N	1	B	0.25667	0.131	B	0.30029	0.11	T	0.47623	-0.9103	10	0.49607	T	0.09	.	1.1459	0.01775	0.1312:0.246:0.2879:0.3349	.	157	Q16696	CP2AD_HUMAN	M	157	ENSP00000332679:I157M	ENSP00000332679:I157M	I	+	3	3	CYP2A13	46287919	0.000000	0.05858	0.053000	0.19242	0.011000	0.07611	-2.752000	0.00791	-0.321000	0.08627	0.305000	0.20034	ATC	.	.	.	none		0.687	CYP2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463505.1	NM_000766		G	41596079	C	G	41596079	3	3	113	1	0	0	0	0	1	0	0	0	4163	874	31	4	481	4	CYP2A13	19	41596079	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	23845806	41596079	17532904	80	7348											
DMWD	1762	hgsc.bcm.edu	37	chr19	46289265	46289265	+	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	gcccccgccagctgggtgcgGgagactgttggagcgggaca	6	5	18	12	3	0	1	0	0	0	1	0	4	0	3	3	4	3	2	3	4	0	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:46289265G>A	ENST00000270223.6	-	3	1534	c.1489C>T	c.(1489-1491)Ccg>Tcg	p.P497S	DMWD_ENST00000377735.3_Missense_Mutation_p.P497S|DMWD_ENST00000601370.1_5'Flank|AC011530.4_ENST00000593999.1_5'Flank	NM_004943.1	NP_004934.1	Q09019	DMWD_HUMAN	dystrophia myotonica, WD repeat containing	497										central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00604)|GBM - Glioblastoma multiforme(486;0.0807)|Epithelial(262;0.236)		GCTGGGTGCGGGAGACTGTTG	0.731																																					p.P497S		Atlas-SNP	.											.	DMWD	46	.	0			c.C1489T						PASS	.						6	7	7					19																	46289265		1846	3685	5531	SO:0001583	missense	1762	exon3			GGTGCGGGAGACT	L19267	CCDS33054.1	19q13.32	2013-01-09	2007-02-20		ENSG00000185800	ENSG00000185800		"WD repeat domain containing"	2936	protein-coding gene	gene with protein product		609857	"dystrophia myotonica-containing WD repeat motif"			1302022	Standard	NM_004943		Approved	DMR-N9, gene59, D19S593E	uc021uwc.1	Q09019	OTTHUMG00000169044	ENST00000270223.6:c.1489C>T	chr19.hg19:g.46289265G>A	ENSP00000270223:p.Pro497Ser	25.0	0.0	.		19.0	7.0	.	NM_004943		Missense_Mutation	SNP	ENST00000270223.6	hg19	CCDS33054.1	.	.	.	.	.	.	.	.	.	.	G	18.03	3.533457	0.64972	.	.	ENSG00000185800	ENST00000377735;ENST00000270223	T;T	0.59906	0.25;0.23	4.21	4.21	0.49690	.	0.000000	0.85682	D	0.000000	T	0.64516	0.2605	L	0.49126	1.545	0.58432	D	0.99999	D;D;D	0.71674	0.997;0.998;0.997	P;D;P	0.64776	0.888;0.929;0.888	T	0.58549	-0.7617	10	0.09084	T	0.74	-15.5092	14.4428	0.67330	0.0:0.0:1.0:0.0	.	182;497;497	Q8WUW6;G5E9A7;Q09019	.;.;DMWD_HUMAN	S	497	ENSP00000366964:P497S;ENSP00000270223:P497S	ENSP00000270223:P497S	P	-	1	0	DMWD	50981105	1.000000	0.71417	0.939000	0.37840	0.356000	0.29392	9.141000	0.94612	2.365000	0.80145	0.462000	0.41574	CCG	.	.	.	none		0.731	DMWD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402063.1	NM_004943		A	46289265	G	A	46289265	3	1	113	1	0	0	0	0	1	0	0	0	4595	1232	43	2	547	2	DMWD	19	46289265	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	4693186	46289265	12839718	81	7349											
HRC	3270	hgsc.bcm.edu	37	chr19	49658341	49658341	+	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	gcgaagctctgctgatgcctCctcggagagcccggcgactc	6	7	13	15	4	1	2	0	1	1	1	4	5	2	2	3	2	4	2	3	2	1	0			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:49658341C>T	ENST00000252825.4	-	1	340	c.154G>A	c.(154-156)Gag>Aag	p.E52K	TRPM4_ENST00000355712.5_5'Flank|TRPM4_ENST00000427978.2_5'Flank|HRC_ENST00000595625.1_Missense_Mutation_p.E52K|TRPM4_ENST00000252826.5_5'Flank	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	52					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)		GCTGATGCCTCCTCGGAGAGC	0.597																																					p.E52K	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.G154A						PASS	.						168	147	154					19																	49658341		2203	4300	6503	SO:0001583	missense	3270	exon1			ATGCCTCCTCGGA		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.154G>A	chr19.hg19:g.49658341C>T	ENSP00000252825:p.Glu52Lys	187.0	0.0	.		173.0	24.0	.	NM_002152	Q504Y6	Missense_Mutation	SNP	ENST00000252825.4	hg19	CCDS12759.1	.	.	.	.	.	.	.	.	.	.	C	19.95	3.921389	0.73213	.	.	ENSG00000130528	ENST00000252825	T	0.06687	3.27	3.26	3.26	0.37387	.	.	.	.	.	T	0.08802	0.0218	L	0.47716	1.5	0.09310	N	0.999997	B	0.33694	0.421	B	0.24701	0.055	T	0.16188	-1.0411	9	0.66056	D	0.02	-4.7962	12.7671	0.57399	0.0:1.0:0.0:0.0	.	52	P23327	SRCH_HUMAN	K	52	ENSP00000252825:E52K	ENSP00000252825:E52K	E	-	1	0	HRC	54350153	0.554000	0.26522	0.204000	0.23530	0.009000	0.06853	1.738000	0.38207	2.104000	0.64026	0.561000	0.74099	GAG	.	.	.	none		0.597	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		T	49658341	C	T	49658341	3	4	113	1	0	0	0	0	1	0	0	0	7359	864	30	2	1969	2	HRC	19	49658341	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	3369076	49658341	9470642	82	7350											
NAPSA	9476	hgsc.bcm.edu	37	chr19	50862007	50862007	+	Frame_Shift_Del	DEL	A	A	-																															atccagggcctggaaaccggAcaagcagaggcggacgccat																										TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:50862007delA	ENST00000253719.2	-	9	1274	c.1066delT	c.(1066-1068)tccfs	p.S356fs	NR1H2_ENST00000600978.1_Intron|NR1H2_ENST00000542413.1_Intron	NM_004851.1	NP_004842.1	O96009	NAPSA_HUMAN	napsin A aspartic peptidase	356					membrane protein proteolysis (GO:0033619)|proteolysis (GO:0006508)|surfactant homeostasis (GO:0043129)	alveolar lamellar body (GO:0097208)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	aspartic-type endopeptidase activity (GO:0004190)|endopeptidase activity (GO:0004175)|peptidase activity (GO:0008233)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(3)	12		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00743)|GBM - Glioblastoma multiforme(134;0.0183)		TGGAAACCGGACAAGCAGAGG	0.632																																					p.S356fs		Atlas-INDEL	.											.	NAPSA	38	.	0			c.1067delC						PASS	.						24	26	25					19																	50862007		2200	4299	6499	SO:0001589	frameshift_variant	9476	exon9			.	AF090386	CCDS12794.1	19q13.33	2011-08-25				ENSG00000131400			13395	protein-coding gene	gene with protein product	"kidney-derived aspartic protease-like protein"	605631					Standard	NM_004851		Approved	NAP1, NAPA, Kdap, KAP	uc002prx.3	O96009		ENST00000253719.2:c.1066delT	chr19.hg19:g.50862007delA	ENSP00000253719:p.Ser356fs	31.0	0.0	0		22.0	11.0	0.5	NM_004851	Q8WWD9	Frame_Shift_Del	DEL	ENST00000253719.2	hg19	CCDS12794.1																																																																																			.	.	.	none		0.632	NAPSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464714.1	NM_004851		-	50862007	A	-	50862007	7	5	113	1	0	1	0	1	0	0	0	0	10173	275	10	0	200	0	NAPSA	19	50862007	Frame_Shift_Del	DEL	A	TCGA-BQ-5878-01A-11D-1589-08	1203666	50862007	8266976	83	7351											
FPR2	2358	hgsc.bcm.edu	37	chr19	52272650	52272650	+	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	tacgggtcctcactgctgtgGtggcttctttcttcatctgt	3	17	10	11	1	5	0	2	0	3	0	6	0	6	0	1	3	2	2	1	3	1	4			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:52272650G>C	ENST00000598776.1	+	2	1511	c.739G>C	c.(739-741)Gtg>Ctg	p.V247L	FPR2_ENST00000340023.6_Missense_Mutation_p.V247L|FPR2_ENST00000598953.1_Missense_Mutation_p.V247L	NM_001462.3	NP_001453.1	P25090	FPR2_HUMAN	formyl peptide receptor 2	247					cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|N-formyl peptide receptor activity (GO:0004982)			endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	33						CACTGCTGTGGTGGCTTCTTT	0.483																																					p.V247L		Atlas-SNP	.											.	FPR2	66	.	0			c.G739C						PASS	.						162	129	140					19																	52272650		2203	4300	6503	SO:0001583	missense	2358	exon2			GCTGTGGTGGCTT	M88107	CCDS12840.1	19q13.3-q13.4	2012-08-10	2008-04-17	2008-04-17		ENSG00000171049		"GPCR / Class A : Formyl peptide receptors", "GPCR / Class A : Leukotriene receptors"	3827	protein-coding gene	gene with protein product		136538	"formyl peptide receptor-like 1"	FPRL1		9054386	Standard	NM_001462		Approved	LXA4R, HM63, FPRH2, FMLPX, FPR2A, FMLP-R-II, ALXR	uc002pxr.3	P25090		ENST00000598776.1:c.739G>C	chr19.hg19:g.52272650G>C	ENSP00000468897:p.Val247Leu	81.0	0.0	.		63.0	28.0	.	NM_001005738	A8K3E2	Missense_Mutation	SNP	ENST00000598776.1	hg19	CCDS12840.1	.	.	.	.	.	.	.	.	.	.	.	17.61	3.432553	0.62844	.	.	ENSG00000171049	ENST00000340023	T	0.72051	-0.62	3.79	2.69	0.31865	GPCR, rhodopsin-like superfamily (1);	0.083720	0.47455	U	0.000226	T	0.81659	0.4869	M	0.85777	2.775	0.31492	N	0.66581	D	0.55800	0.973	D	0.64506	0.926	T	0.81373	-0.0962	10	0.54805	T	0.06	.	8.5694	0.33561	0.1273:0.0:0.8727:0.0	.	247	P25090	FPR2_HUMAN	L	247	ENSP00000340191:V247L	ENSP00000340191:V247L	V	+	1	0	FPR2	56964462	0.210000	0.23517	0.680000	0.29994	0.976000	0.68499	1.340000	0.33896	0.909000	0.36697	0.484000	0.47621	GTG	.	.	.	none		0.483	FPR2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466912.2	NM_001005738		C	52272650	G	C	52272650	3	2	113	1	0	0	0	0	1	0	0	0	6046	1261	44	4	741	4	FPR2	19	52272650	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	1410643	52272650	6856333	84	7352											
LAIR2	3904	hgsc.bcm.edu	37	chr19	55019129	55019129	+	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	cccttcccagaccctccatcTcggctgagccaggcactgtg	6	8	9	18	1	1	2	0	1	1	1	4	2	3	2	5	2	1	2	5	2	0	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr19:55019129T>A	ENST00000301202.2	+	3	216	c.94T>A	c.(94-96)Tcg>Acg	p.S32T	LAIR2_ENST00000351841.2_Missense_Mutation_p.S32T	NM_002288.4	NP_002279.2	Q6ISS4	LAIR2_HUMAN	leukocyte-associated immunoglobulin-like receptor 2	32	Ig-like C2-type.					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)		ACCCTCCATCTCGGCTGAGCC	0.577																																					p.S32T		Atlas-SNP	.											.	LAIR2	30	.	0			c.T94A						PASS	.						116	129	124					19																	55019129		2203	4300	6503	SO:0001583	missense	3904	exon3			TCCATCTCGGCTG	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.94T>A	chr19.hg19:g.55019129T>A	ENSP00000301202:p.Ser32Thr	259.0	0.0	.		222.0	79.0	.	NM_002288	Q6PEZ4	Missense_Mutation	SNP	ENST00000301202.2	hg19	CCDS12897.1	.	.	.	.	.	.	.	.	.	.	T	11.56	1.675150	0.29783	.	.	ENSG00000167618	ENST00000412608;ENST00000452094;ENST00000301202;ENST00000351841	T;T;T	0.23147	1.92;2.69;2.69	3.39	0.919	0.19392	Immunoglobulin-like fold (1);	2.380980	0.01840	N	0.035242	T	0.39064	0.1064	M	0.69358	2.11	0.09310	N	1	P;P;P	0.48589	0.911;0.873;0.912	P;B;P	0.50708	0.648;0.275;0.597	T	0.16512	-1.0400	10	0.72032	D	0.01	.	5.5099	0.16874	0.4585:0.0:0.0:0.5414	.	26;32;32	C9JFQ0;Q6ISS4-2;Q6ISS4	.;.;LAIR2_HUMAN	T	26;14;32;32	ENSP00000390729:S26T;ENSP00000301202:S32T;ENSP00000301203:S32T	ENSP00000301202:S32T	S	+	1	0	LAIR2	59710941	0.002000	0.14202	0.041000	0.18516	0.736000	0.42039	-0.423000	0.07034	0.452000	0.26830	0.260000	0.18958	TCG	.	.	.	none		0.577	LAIR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140801.1			A	55019129	T	A	55019129	3	1	113	1	0	0	0	0	1	0	0	0	8610	1551	54	5	104	5	LAIR2	19	55019129	Missense_Mutation	SNP	T	TCGA-BQ-5878-01A-11D-1589-08	2746479	55019129	4109854	85	7353											
PROCR	10544	hgsc.bcm.edu	37	chr20	33762617	33762617	+	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	acgcacgtgctggaaggcccAgacaccaacaccacgatcat	13	4	9	15	3	1	1	1	0	0	1	1	3	1	2	3	2	2	2	3	2	2	0			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr20:33762617A>T	ENST00000216968.4	+	2	265	c.183A>T	c.(181-183)ccA>ccT	p.P61P	EDEM2_ENST00000540582.1_Intron	NM_006404.3	NP_006395.2	Q9UNN8	EPCR_HUMAN	protein C receptor, endothelial	61					antigen processing and presentation (GO:0019882)|blood coagulation (GO:0007596)|immune response (GO:0006955)|negative regulation of coagulation (GO:0050819)	cell surface (GO:0009986)|centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			breast(1)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	10			BRCA - Breast invasive adenocarcinoma(18;0.0152)		Drotrecogin alfa(DB00055)	TGGAAGGCCCAGACACCAACA	0.622																																					p.P61P		Atlas-SNP	.											.	PROCR	26	.	0			c.A183T						PASS	.						93	70	78					20																	33762617		2203	4300	6503	SO:0001819	synonymous_variant	10544	exon2			AGGCCCAGACACC	L35545	CCDS13248.1	20q11.2	2010-05-04	2010-05-04		ENSG00000101000	ENSG00000101000		"CD molecules"	9452	protein-coding gene	gene with protein product		600646				7929370, 10518938	Standard	NM_006404		Approved	EPCR, CCD41, CD201	uc002xbt.3	Q9UNN8	OTTHUMG00000032323	ENST00000216968.4:c.183A>T	chr20.hg19:g.33762617A>T		63.0	0.0	.		75.0	30.0	.	NM_006404	B2RC04|Q14218|Q6IB56|Q96CB3|Q9ULX1	Silent	SNP	ENST00000216968.4	hg19	CCDS13248.1																																																																																			.	.	.	none		0.622	PROCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078843.3			T	33762617	A	T	33762617	2	4	113	1	0	0	0	0	0	0	0	1	12557	175	7	5		5	PROCR	20	33762617	Silent	SNP	A	TCGA-BQ-5878-01A-11D-1589-08		33762617	29262903	86	7354											
SLC13A3	64849	hgsc.bcm.edu	37	chr20	45204227	45204227	+	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	cttacctcacagcctttggcCatggcgaagccccctcccag	7	8	8	18	1	1	0	1	0	0	0	2	1	2	0	6	2	3	0	6	2	2	2			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr20:45204227C>A	ENST00000279027.4	-	10	1335	c.1317G>T	c.(1315-1317)atG>atT	p.M439I	SLC13A3_ENST00000413164.2_Missense_Mutation_p.M389I|SLC13A3_ENST00000495082.1_Missense_Mutation_p.M392I|SLC13A3_ENST00000472148.1_Missense_Mutation_p.M357I|SLC13A3_ENST00000290317.5_Missense_Mutation_p.M392I|SLC13A3_ENST00000435032.1_Intron|SLC13A3_ENST00000396360.1_Missense_Mutation_p.M357I	NM_001193342.1|NM_022829.5	NP_001180271.1|NP_073740.2	Q8WWT9	S13A3_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	439					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-affinity sodium:dicarboxylate symporter activity (GO:0015362)			breast(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	AGCCTTTGGCCATGGCGAAGC	0.632																																					p.M439I		Atlas-SNP	.											.	SLC13A3	88	.	0			c.G1317T						PASS	.						63	49	54					20																	45204227		2203	4300	6503	SO:0001583	missense	64849	exon10			TTTGGCCATGGCG	AF154121	CCDS13400.1, CCDS42886.1, CCDS54469.1, CCDS54470.1	20q13.12	2013-05-22			ENSG00000158296	ENSG00000158296		"Solute carriers"	14430	protein-coding gene	gene with protein product		606411				10794676, 10992006	Standard	NM_001011554		Approved	NADC3, SDCT2	uc002xsf.2	Q8WWT9	OTTHUMG00000033042	ENST00000279027.4:c.1317G>T	chr20.hg19:g.45204227C>A	ENSP00000279027:p.Met439Ile	25.0	0.0	.		17.0	7.0	.	NM_022829	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Missense_Mutation	SNP	ENST00000279027.4	hg19	CCDS13400.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.386648	0.82902	.	.	ENSG00000158296	ENST00000290317;ENST00000396360;ENST00000279027;ENST00000472148;ENST00000413164;ENST00000495082;ENST00000468915	T;T;T;T;T;T;T	0.03386	3.95;3.95;3.95;3.95;3.95;3.95;3.95	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.06690	0.0171	N	0.25031	0.7	0.80722	D	1	P;P;P;P	0.46020	0.775;0.843;0.746;0.871	P;P;P;P	0.49799	0.507;0.544;0.487;0.622	T	0.36866	-0.9730	10	0.72032	D	0.01	-34.8403	17.6296	0.88103	0.0:1.0:0.0:0.0	.	389;357;392;439	B4DIR8;Q8WWT9-3;F6WI18;Q8WWT9	.;.;.;S13A3_HUMAN	I	392;357;439;357;389;392;392	ENSP00000290317:M392I;ENSP00000379648:M357I;ENSP00000279027:M439I;ENSP00000420177:M357I;ENSP00000415852:M389I;ENSP00000419621:M392I;ENSP00000417784:M392I	ENSP00000279027:M439I	M	-	3	0	SLC13A3	44637634	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.897000	0.69831	2.399000	0.81585	0.655000	0.94253	ATG	.	.	.	none		0.632	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2			A	45204227	C	A	45204227	3	1	113	1	0	0	0	0	1	0	0	0	14406	594	21	4	507	4	SLC13A3	20	45204227	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	11441610	45204227	17821293	87	7355											
ZNF831	128611	hgsc.bcm.edu	37	chr20	57766279	57766279	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtaccacacggtgcctcccGggggcctccagccccgcgcc	4	5	12	20	4	0	0	0	0	0	0	2	0	2	0	8	3	3	1	8	3	1	1	rs375833789		TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr20:57766279G>A	ENST00000371030.2	+	1	205	c.205G>A	c.(205-207)Ggg>Agg	p.G69R		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	69	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)					GGTGCCTCCCGGGGGCCTCCA	0.706																																					p.G69R		Atlas-SNP	.											.	ZNF831	287	.	0			c.G205A						PASS	.	G	ARG/GLY	1,3705		0,1,1852	9	11	10		205	5.6	0.9	20		10	0,8092		0,0,4046	no	missense	ZNF831	NM_178457.1	125	0,1,5898	AA,AG,GG		0.0,0.027,0.0085	probably-damaging	69/1678	57766279	1,11797	1853	4046	5899	SO:0001583	missense	128611	exon1			CCTCCCGGGGGCC	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.205G>A	chr20.hg19:g.57766279G>A	ENSP00000360069:p.Gly69Arg	29.0	0.0	.		25.0	11.0	.	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	hg19	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.011024	0.75046	2.7E-4	0.0	ENSG00000124203	ENST00000371030	T	0.05081	3.5	5.55	5.55	0.83447	.	.	.	.	.	T	0.16854	0.0405	L	0.27053	0.805	0.33846	D	0.632	D	0.89917	1.0	D	0.91635	0.999	T	0.05146	-1.0903	9	0.87932	D	0	-18.5525	18.4859	0.90828	0.0:0.0:1.0:0.0	.	69	Q5JPB2	ZN831_HUMAN	R	69	ENSP00000360069:G69R	ENSP00000360069:G69R	G	+	1	0	ZNF831	57199674	0.950000	0.32346	0.917000	0.36280	0.949000	0.60115	2.282000	0.43461	2.608000	0.88229	0.462000	0.41574	GGG	.	.	.	weak		0.706	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		A	57766279	G	A	57766279	3	1	113	1	0	0	0	0	1	0	0	0	18197	1116	39	1	207	1	ZNF831	20	57766279	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08	12562052	57766279	5259241	88	7356											
LIPI	149998	hgsc.bcm.edu	37	chr21	15554081	15554081	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taaatcctgatttgttaccaTtggagtcagaatggatgaca	13	13	9	6	0	1	3	1	2	0	1	2	5	2	5	2	2	1	1	2	2	4	4			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr21:15554081T>C	ENST00000536861.1	-	4	640	c.641A>G	c.(640-642)aAt>aGt	p.N214S	LIPI_ENST00000344577.2_Missense_Mutation_p.N235S			Q6XZB0	LIPI_HUMAN	lipase, member I	214					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		TTTGTTACCATTGGAGTCAGA	0.398																																					p.N235S		Atlas-SNP	.											.	LIPI	95	.	0			c.A704G						PASS	.						76	71	73					21																	15554081		2203	4300	6503	SO:0001583	missense	149998	exon4			TTACCATTGGAGT	BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"membrane-associated phospholipase A1 beta", "cancer/testis antigen 17"	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.641A>G	chr21.hg19:g.15554081T>C	ENSP00000440381:p.Asn214Ser	42.0	0.0	.		45.0	22.0	.	NM_198996	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Missense_Mutation	SNP	ENST00000536861.1	hg19		.	.	.	.	.	.	.	.	.	.	T	9.157	1.017856	0.19355	.	.	ENSG00000188992	ENST00000344577;ENST00000536861;ENST00000382981	D;D	0.90069	-2.61;-2.61	5.46	4.31	0.51392	.	0.306919	0.38548	N	0.001658	T	0.77177	0.4092	N	0.13235	0.315	0.28263	N	0.924755	B;B	0.18741	0.03;0.03	B;B	0.21151	0.033;0.02	T	0.60172	-0.7315	10	0.08381	T	0.77	.	11.4777	0.50308	0.0:0.0716:0.0:0.9284	.	214;235	G1JSG6;Q6XZB0-2	.;.	S	235;214;109	ENSP00000343331:N235S;ENSP00000440381:N214S	ENSP00000343331:N235S	N	-	2	0	LIPI	14475952	1.000000	0.71417	0.643000	0.29450	0.055000	0.15305	5.357000	0.66058	1.007000	0.39238	0.533000	0.62120	AAT	.	.	.	none		0.398	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996		C	15554081	T	C	15554081	3	2	113	1	0	0	0	0	1	0	0	0	8832	1493	52	3	769	3	LIPI	21	15554081	Missense_Mutation	SNP	T	TCGA-BQ-5878-01A-11D-1589-08		15554081	32575814	89	7357											
DEPDC5	9681	hgsc.bcm.edu	37	chr22	32301997	32301997	+	Missense_Mutation	SNP	T	T	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	tttgtacaagataaatattcTgcctctgcttttaacttccc	10	17	4	10	0	2	1	0	0	2	1	3	1	3	1	2	0	4	2	2	0	6	8			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr22:32301997T>G	ENST00000382111.2	+	40	4463	c.4403T>G	c.(4402-4404)cTg>cGg	p.L1468R	DEPDC5_ENST00000266091.3_Silent_p.S1466S|DEPDC5_ENST00000400246.1_Missense_Mutation_p.L1468R|DEPDC5_ENST00000539165.1_Silent_p.S305S|DEPDC5_ENST00000535622.1_Silent_p.S1388S|DEPDC5_ENST00000382105.2_3'UTR|DEPDC5_ENST00000400248.2_Silent_p.S1457S|DEPDC5_ENST00000400249.2_Silent_p.S1457S|DEPDC5_ENST00000382112.3_Silent_p.S1479S			O75140	DEPD5_HUMAN	DEP domain containing 5	0					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						ATAAATATTCTGCCTCTGCTT	0.488																																					p.S1488S		Atlas-SNP	.											.	DEPDC5	266	.	0			c.T4464G						PASS	.						89	85	86					22																	32301997		1943	4137	6080	SO:0001583	missense	9681	exon42			ATATTCTGCCTCT	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	ENST00000382111.2:c.4403T>G	chr22.hg19:g.32301997T>G	ENSP00000371545:p.Leu1468Arg	61.0	0.0	.		39.0	20.0	.	NM_001242896	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Silent	SNP	ENST00000382111.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.81|11.81	1.751165|1.751165	0.31046|0.31046	.|.	.|.	ENSG00000100150|ENSG00000100150	ENST00000433147|ENST00000400246;ENST00000382111	.|T;T	.|0.29655	.|1.56;1.56	5.01|5.01	-1.17|-1.17	0.09648|0.09648	.|.	.|.	.|.	.|.	.|.	T|T	0.29389|0.29389	0.0732|0.0732	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.29761|0.29761	-1.0001|-1.0001	4|6	.|0.72032	.|D	.|0.01	.|.	0.9017|0.9017	0.01275|0.01275	0.3175:0.289:0.1114:0.2822|0.3175:0.289:0.1114:0.2822	.|.	.|.	.|.	.|.	G|R	864|1468	.|ENSP00000383105:L1468R;ENSP00000371545:L1468R	.|ENSP00000371545:L1468R	C|L	+|+	1|2	0|0	DEPDC5|DEPDC5	30631997|30631997	0.011000|0.011000	0.17503|0.17503	0.969000|0.969000	0.41365|0.41365	0.990000|0.990000	0.78478|0.78478	-1.295000|-1.295000	0.02764|0.02764	-0.538000|-0.538000	0.06281|0.06281	0.459000|0.459000	0.35465|0.35465	TGC|CTG	.	.	.	none		0.488	DEPDC5-004	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000129085.1	NM_014662		G	32301997	T	G	32301997	3	3	113	1	0	0	0	0	1	0	0	0	4444	1567	55	5	4617	5	DEPDC5	22	32301997	Missense_Mutation	SNP	T	TCGA-BQ-5878-01A-11D-1589-08		32301997	19002569	90	7358											
PLXNB2	23654	hgsc.bcm.edu	37	chr22	50719301	50719302	+	Frame_Shift_Ins	INS	-	-	T																															tccttgtcgccgtccttggaINSgggcaggaagaagacgcggt																										TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chr22:50719301_50719302insT	ENST00000449103.1	-	24	4004_4005	c.3864_3865insA	c.(3862-3867)ccctccfs	p.S1289fs	PLXNB2_ENST00000359337.4_Frame_Shift_Ins_p.S1289fs|PLXNB2_ENST00000496720.1_5'Flank			O15031	PLXB2_HUMAN	plexin B2	1289					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)		CCGTCCTTGGAGGGCAGGAAGA	0.629																																					p.S1289fs		Atlas-INDEL	.											.	PLXNB2	172	.	0			c.3865_3866insA						PASS	.																																			SO:0001589	frameshift_variant	23654	exon24			.		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.3864_3865insA	chr22.hg19:g.50719301_50719302insT	ENSP00000409171:p.Ser1289fs	52.0	0.0	0		42.0	13.0	0.309524	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Frame_Shift_Ins	INS	ENST00000449103.1	hg19	CCDS43035.1																																																																																			.	.	.	none		0.629	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401		T	50719302	-	T	50719301	7	5	113	1	0	1	1	0	0	0	0	0	12131	304	11	0	1707	0	PLXNB2	22	50719301	Frame_Shift_Ins	INS	-	TCGA-BQ-5878-01A-11D-1589-08	18417304	50719301	585265	91	7359											
GPKOW	27238	hgsc.bcm.edu	37	chrX	48979068	48979068	+	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	ccgggctggtggctgcctgcGatggccattctggatcaaag	6	9	15	11	2	2	0	1	0	1	0	2	2	2	1	3	5	2	2	3	5	1	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chrX:48979068G>A	ENST00000156109.5	-	2	313	c.235C>T	c.(235-237)Cgc>Tgc	p.R79C		NM_015698.4	NP_056513.2	Q92917	GPKOW_HUMAN	G patch domain and KOW motifs	79						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(2)	21						GGCTGCCTGCGATGGCCATTC	0.637																																					p.R79C		Atlas-SNP	.											.	GPKOW	38	.	0			c.C235T						PASS	.						37	39	38					X																	48979068		2203	4300	6503	SO:0001583	missense	27238	exon2			GCCTGCGATGGCC	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.235C>T	chrX.hg19:g.48979068G>A	ENSP00000156109:p.Arg79Cys	24.0	0.0	.		35.0	17.0	.	NM_015698	Q59EK5|Q9BQA8	Missense_Mutation	SNP	ENST00000156109.5	hg19	CCDS35251.1	.	.	.	.	.	.	.	.	.	.	G	11.21	1.571866	0.28003	.	.	ENSG00000068394	ENST00000156109	.	.	.	4.73	0.739	0.18324	.	0.440958	0.26038	N	0.026709	T	0.28366	0.0701	L	0.51422	1.61	0.09310	N	0.999999	D	0.65815	0.995	B	0.44315	0.446	T	0.18209	-1.0344	9	0.59425	D	0.04	-3.2051	3.9276	0.09270	0.4817:0.1829:0.3353:0.0	.	79	Q92917	GPKOW_HUMAN	C	79	.	ENSP00000156109:R79C	R	-	1	0	GPKOW	48866012	0.070000	0.21116	0.006000	0.13384	0.580000	0.36256	2.429000	0.44758	0.398000	0.25338	-0.300000	0.09419	CGC	.	.	.	none		0.637	GPKOW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056535.2	NM_015698		A	48979068	G	A	48979068	3	1	113	1	0	0	0	0	1	0	0	0	6620	1058	37	1	1235	1	GPKOW	23	48979068	Missense_Mutation	SNP	G	TCGA-BQ-5878-01A-11D-1589-08		48979068	106291492	92	7360											
ESX1	80712	hgsc.bcm.edu	37	chrX	103499100	103499100	+	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	ctcctgctgttgctccggctCgtggccgccgccaccctcac	2	9	10	20	4	1	0	1	0	0	0	4	0	3	0	6	2	2	4	6	2	0	1			TCGA-BQ-5878-01A-11D-1589-08	TCGA-BQ-5878-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01600b4b-cddc-41a5-b541-326677217bc2	0d002eab-1f4e-4846-b2cc-25aae886715d	g.chrX:103499100C>T	ENST00000372588.4	-	2	324	c.241G>A	c.(241-243)Gag>Aag	p.E81K		NM_153448.3	NP_703149.1	Q8N693	ESX1_HUMAN	ESX homeobox 1	81					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						TGCTCCGGCTCGTGGCCGCCG	0.662																																					p.E81K	Pancreas(200;1705 2227 25194 28471 45274)	Atlas-SNP	.											.	ESX1	57	.	0			c.G241A						PASS	.						62	70	67					X																	103499100		2200	4276	6476	SO:0001583	missense	80712	exon2			CCGGCTCGTGGCC	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.241G>A	chrX.hg19:g.103499100C>T	ENSP00000361669:p.Glu81Lys	283.0	0.0	.		274.0	33.0	.	NM_153448	B0QYU3|Q7Z6K7	Missense_Mutation	SNP	ENST00000372588.4	hg19	CCDS14516.1	.	.	.	.	.	.	.	.	.	.	c	9.690	1.151579	0.21371	.	.	ENSG00000123576	ENST00000372588	D	0.91521	-2.86	3.13	-6.25	0.02039	.	.	.	.	.	T	0.77011	0.4068	N	0.24115	0.695	0.09310	N	1	P	0.35011	0.48	B	0.18561	0.022	T	0.63902	-0.6532	9	0.13853	T	0.58	-2.0978	12.3476	0.55130	0.0:0.1335:0.6842:0.1822	.	81	Q8N693	ESX1_HUMAN	K	81	ENSP00000361669:E81K	ENSP00000361669:E81K	E	-	1	0	ESX1	103385756	0.000000	0.05858	0.000000	0.03702	0.080000	0.17528	-0.657000	0.05335	-2.111000	0.00836	-0.560000	0.04181	GAG	.	.	.	none		0.662	ESX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057763.2	NM_153448		T	103499100	C	T	103499100	3	4	113	1	0	0	0	0	1	0	0	0	5265	893	31	1	991	1	ESX1	23	103499100	Missense_Mutation	SNP	C	TCGA-BQ-5878-01A-11D-1589-08	54520032	103499100	51771460	93	7361											
ELTD1	64123	hgsc.bcm.edu	37	chr1	79386001	79386001	+	Missense_Mutation	SNP	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	agaaggtaaaaatgcatatgGcaagacaaatcagtgaaata	21	7	9	4	0	1	3	1	1	0	2	1	3	1	3	0	2	1	3	0	2	9	3			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr1:79386001G>A	ENST00000370742.3	-	10	1391	c.1328C>T	c.(1327-1329)gCc>gTc	p.A443V		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	443					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		AATGCATATGGCAAGACAAAT	0.313																																					p.A443V		Atlas-SNP	.											.	ELTD1	143	.	0			c.C1328T						PASS	.						103	97	99					1																	79386001		1812	4078	5890	SO:0001583	missense	64123	exon10			CATATGGCAAGAC	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"-", "GPCR / Class B : Orphans"	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.1328C>T	chr1.hg19:g.79386001G>A	ENSP00000359778:p.Ala443Val	161.0	0.0	.		135.0	37.0	.	NM_022159	B1AR71|Q5KU34	Missense_Mutation	SNP	ENST00000370742.3	hg19	CCDS41352.1	.	.	.	.	.	.	.	.	.	.	G	15.22	2.768298	0.49680	.	.	ENSG00000162618	ENST00000370742	T	0.41065	1.01	5.0	5.0	0.66597	GPCR, family 2-like (1);	0.175937	0.50627	D	0.000111	T	0.21921	0.0528	L	0.45422	1.42	0.40567	D	0.981269	B	0.10296	0.003	B	0.23018	0.043	T	0.04537	-1.0944	9	.	.	.	.	14.2963	0.66316	0.0:0.1486:0.8513:0.0	.	443	Q9HBW9	ELTD1_HUMAN	V	443	ENSP00000359778:A443V	.	A	-	2	0	ELTD1	79158589	1.000000	0.71417	0.996000	0.52242	0.995000	0.86356	5.598000	0.67585	2.469000	0.83416	0.650000	0.86243	GCC	.	.	.	none		0.313	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159		A	79386001	G	A	79386001	3	1	114	1	0	0	0	0	1	0	0	0	5086	1203	42	2	768	2	ELTD1	1	79386001	Missense_Mutation	SNP	G	TCGA-BQ-5879-01A-11D-1589-08		79386001	169864620	1	7362											
LMNA	4000	hgsc.bcm.edu	37	chr1	156105085	156105085	+	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	gacagcctctctgcccagctCagccagctccagaagcaggt	9	6	10	16	0	2	1	1	0	1	1	4	2	3	1	4	1	6	3	4	1	1	0			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr1:156105085C>T	ENST00000368300.4	+	5	1130	c.918C>T	c.(916-918)ctC>ctT	p.L306L	LMNA_ENST00000368301.2_Silent_p.L306L|LMNA_ENST00000392353.3_Silent_p.L225L|LMNA_ENST00000361308.4_Silent_p.L306L|LMNA_ENST00000368299.3_Silent_p.L306L|LMNA_ENST00000496738.1_3'UTR|LMNA_ENST00000473598.2_Silent_p.L207L|LMNA_ENST00000448611.2_Silent_p.L194L|LMNA_ENST00000368297.1_Silent_p.L225L|LMNA_ENST00000347559.2_Silent_p.L306L	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C	306	Coil 2.|Rod.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|endoplasmic reticulum unfolded protein response (GO:0030968)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle organ development (GO:0007517)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|positive regulation of cell aging (GO:0090343)|protein localization to nucleus (GO:0034504)|regulation of cell migration (GO:0030334)|regulation of protein localization to nucleus (GO:1900180)|sterol regulatory element binding protein import into nucleus (GO:0035105)|ventricular cardiac muscle cell development (GO:0055015)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|lamin filament (GO:0005638)|nuclear envelope (GO:0005635)|nuclear lamina (GO:0005652)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4)	10	Hepatocellular(266;0.158)					CTGCCCAGCTCAGCCAGCTCC	0.662									Werner syndrome;Hutchinson-Gilford Progeria Syndrome																												p.L306L		Atlas-SNP	.											.	LMNA	31	.	0			c.C918T						PASS	.						25	28	27					1																	156105085		2202	4299	6501	SO:0001819	synonymous_variant	4000	exon5	Familial Cancer Database	WS, Adult Progeria;HGPS, Progeria	CCAGCTCAGCCAG	BC014507	CCDS1129.1, CCDS1131.1, CCDS58038.1, CCDS72941.1, CCDS72942.1	1q22	2014-09-17			ENSG00000160789	ENSG00000160789		"Intermediate filaments type V, lamins"	6636	protein-coding gene	gene with protein product		150330	"cardiomyopathy, dilated 1A (autosomal dominant)", "limb girdle muscular dystrophy 1B (autosomal dominant)", "progeria 1 (Hutchinson-Gilford type)", "lamin A/C-like 1"	LMN1, CMD1A, LGMD1B, PRO1, LMNL1		8511676, 8838815, 12702809	Standard	NM_005572		Approved	HGPS	uc001fni.3	P02545	OTTHUMG00000013961	ENST00000368300.4:c.918C>T	chr1.hg19:g.156105085C>T		37.0	0.0	.		35.0	10.0	.	NM_170707	B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2	Silent	SNP	ENST00000368300.4	hg19	CCDS1129.1																																																																																			.	.	.	none		0.662	LMNA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039200.2	NM_170707		T	156105085	C	T	156105085	2	4	114	1	0	0	0	0	0	0	0	1	8855	813	29	2		2	LMNA	1	156105085	Silent	SNP	C	TCGA-BQ-5879-01A-11D-1589-08	76719084	156105085	93145536	2	7363											
SLC5A6	8884	hgsc.bcm.edu	37	chr2	27427384	27427384	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggatactcctggtaatacGcgaacatgaccaggccaatg	12	8	11	10	2	0	1	0	1	0	0	1	3	1	2	3	3	3	1	3	3	5	3	rs199587675		TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr2:27427384G>A	ENST00000310574.3	-	9	1423	c.950C>T	c.(949-951)gCg>gTg	p.A317V	SLC5A6_ENST00000461319.1_5'Flank|SLC5A6_ENST00000408041.1_Missense_Mutation_p.A317V	NM_021095.2	NP_066918.2	Q9Y289	SC5A6_HUMAN	solute carrier family 5 (sodium/multivitamin and iodide cotransporter), member 6	317					biotin metabolic process (GO:0006768)|biotin transport (GO:0015878)|pantothenate metabolic process (GO:0015939)|pantothenate transmembrane transport (GO:0015887)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)	p.A317V(1)		endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|ovary(3)|prostate(1)|skin(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Biotin(DB00121)|gabapentin enacarbil(DB08872)|Lipoic Acid(DB00166)	CTGGTAATACGCGAACATGAC	0.597																																					p.A317V		Atlas-SNP	.											SLC5A6,colon,carcinoma,0,1	SLC5A6	63	.	1	Substitution - Missense(1)	large_intestine(1)	c.C950T						PASS	.						99	95	96					2																	27427384		2203	4300	6503	SO:0001583	missense	8884	exon9			TAATACGCGAACA	AF069307	CCDS1740.1	2p23	2013-07-19	2013-07-19		ENSG00000138074	ENSG00000138074		"Solute carriers"	11041	protein-coding gene	gene with protein product		604024	"solute carrier family 5 (sodium-dependent vitamin transporter), member 6"			9516450, 10329687	Standard	NM_021095		Approved	SMVT	uc002rjd.3	Q9Y289	OTTHUMG00000097075	ENST00000310574.3:c.950C>T	chr2.hg19:g.27427384G>A	ENSP00000310208:p.Ala317Val	109.0	0.0	.		107.0	33.0	.	NM_021095	B2RB85|D6W549|Q969Y5	Missense_Mutation	SNP	ENST00000310574.3	hg19	CCDS1740.1	.	.	.	.	.	.	.	.	.	.	G	11.01	1.513536	0.27123	.	.	ENSG00000138074	ENST00000310574;ENST00000408041	D;D	0.88586	-2.4;-2.4	4.93	2.04	0.26737	.	0.604283	0.16756	N	0.200821	D	0.85733	0.5765	M	0.67569	2.06	0.39947	D	0.974481	B	0.33345	0.409	B	0.34242	0.178	T	0.82370	-0.0491	10	0.52906	T	0.07	.	7.2906	0.26364	0.1706:0.1441:0.6852:0.0	.	317	Q9Y289	SC5A6_HUMAN	V	317	ENSP00000310208:A317V;ENSP00000384853:A317V	ENSP00000310208:A317V	A	-	2	0	SLC5A6	27280888	0.999000	0.42202	0.226000	0.23910	0.215000	0.24574	3.539000	0.53604	0.585000	0.29608	0.655000	0.94253	GCG	.	.	.	weak		0.597	SLC5A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214194.1	NM_021095		A	27427384	G	A	27427384	3	1	114	1	0	0	0	0	1	0	0	0	14682	1087	38	1	993	1	SLC5A6	2	27427384	Missense_Mutation	SNP	G	TCGA-BQ-5879-01A-11D-1589-08		27427384	215771989	3	7364											
ACTR1B	10120	hgsc.bcm.edu	37	chr2	98275011	98275014	+	Frame_Shift_Del	DEL	GAGT	GAGT	-																															caatgtccacccgcatgatgGagtgaggcatggcaaagccc																								rs200965492		TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	GAGT	GAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr2:98275011_98275014delGAGT	ENST00000289228.5	-	6	749_752	c.533_536delACTC	c.(532-537)cactccfs	p.HS178fs		NM_005735.3	NP_005726.1	P42025	ACTY_HUMAN	ARP1 actin-related protein 1 homolog B, centractin beta (yeast)	178					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)			endometrium(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	15						CCGCATGATGGAGTGAGGCATGGC	0.603																																					p.178_179del		Atlas-INDEL	.											.	ACTR1B	34	.	0			c.534_537del						PASS	.																																			SO:0001589	frameshift_variant	10120	exon6			.	X82207	CCDS2033.1	2q11.1-q11.2	2008-05-20	2001-11-28		ENSG00000115073	ENSG00000115073			168	protein-coding gene	gene with protein product		605144	"ARP1 (actin-related protein 1, yeast) homolog B (centractin beta)"	CTRN2		7696711, 10343100	Standard	NM_005735		Approved		uc002syb.2	P42025	OTTHUMG00000130549	ENST00000289228.5:c.533_536delACTC	chr2.hg19:g.98275011_98275014delGAGT	ENSP00000289228:p.His178fs	105.0	0.0	0		73.0	10.0	0.136986	NM_005735	D3DVH2|Q53SK5|Q9BRB7	Frame_Shift_Del	DEL	ENST00000289228.5	hg19	CCDS2033.1																																																																																			.	.	.	none		0.603	ACTR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252973.1	NM_005735		-	98275014	GAGT	-	98275011	7	5	114	1	0	1	0	1	0	0	0	0	210	1174	41	0	618	0	ACTR1B	2	98275011	Frame_Shift_Del	DEL	GAGT	TCGA-BQ-5879-01A-11D-1589-08	70847627	98275011	144924362	4	7365											
RAB3GAP1	22930	hgsc.bcm.edu	37	chr2	135815628	135815628	+	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	gaatgactggaaactgattgGaaactctttgggaaagccac	14	9	11	7	0	1	2	0	2	1	0	1	6	1	5	1	3	3	0	1	3	4	2			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr2:135815628G>A	ENST00000264158.8	+	3	165	c.122G>A	c.(121-123)gGa>gAa	p.G41E	RAB3GAP1_ENST00000442034.1_Missense_Mutation_p.G41E|RAB3GAP1_ENST00000539493.1_5'UTR|RAB3GAP1_ENST00000425393.1_Missense_Mutation_p.G41E	NM_012233.2	NP_036365.1	Q15042	RB3GP_HUMAN	RAB3 GTPase activating protein subunit 1 (catalytic)	41					brain development (GO:0007420)|camera-type eye development (GO:0043010)|establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|face morphogenesis (GO:0060325)|hypothalamus development (GO:0021854)|lipid particle organization (GO:0034389)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of calcium ion-dependent exocytosis of neurotransmitter (GO:1903233)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of GTPase activity (GO:0043087)|regulation of short-term neuronal synaptic plasticity (GO:0048172)	cytoplasm (GO:0005737)|endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(10)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32				BRCA - Breast invasive adenocarcinoma(221;0.117)		AAACTGATTGGAAACTCTTTG	0.383																																					p.G41E		Atlas-SNP	.											.	RAB3GAP1	87	.	0			c.G122A						PASS	.						91	86	88					2																	135815628		2203	4300	6503	SO:0001583	missense	22930	exon3			TGATTGGAAACTC	D31886	CCDS33294.1, CCDS54402.1	2q21.3	2013-07-09			ENSG00000115839	ENSG00000115839			17063	protein-coding gene	gene with protein product		602536				9030515, 15696165	Standard	NM_012233		Approved	RAB3GAP, KIAA0066, RAB3GAP130, WARBM1	uc010fnf.3	Q15042	OTTHUMG00000154889	ENST00000264158.8:c.122G>A	chr2.hg19:g.135815628G>A	ENSP00000264158:p.Gly41Glu	66.0	0.0	.		76.0	27.0	.	NM_001172435	A6H8Z3|C9J837|Q659F5|Q8TBB4	Missense_Mutation	SNP	ENST00000264158.8	hg19	CCDS33294.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.554169	0.86231	.	.	ENSG00000115839	ENST00000264158;ENST00000442034;ENST00000425393	T;T	0.48201	0.84;0.82	5.62	5.62	0.85841	.	0.174050	0.52532	D	0.000076	T	0.66268	0.2772	M	0.69823	2.125	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.70227	0.927;0.968	T	0.61466	-0.7057	10	0.25751	T	0.34	-20.0075	16.5774	0.84705	0.0:0.0:1.0:0.0	.	41;41	C9J837;Q15042	.;RB3GP_HUMAN	E	41	ENSP00000264158:G41E;ENSP00000411418:G41E	ENSP00000264158:G41E	G	+	2	0	RAB3GAP1	135532098	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.478000	0.81082	2.642000	0.89623	0.655000	0.94253	GGA	.	.	.	none		0.383	RAB3GAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337514.2	NM_012233		A	135815628	G	A	135815628	3	1	114	1	0	0	0	0	1	0	0	0	12948	1174	41	2	132	2	RAB3GAP1	2	135815628	Missense_Mutation	SNP	G	TCGA-BQ-5879-01A-11D-1589-08	37540617	135815628	107383745	5	7366											
TTN	7273	hgsc.bcm.edu	37	chr2	179429062	179429062	+	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	gtgcatcaatttcatctcttGcagtaatggcaccactacta	11	13	6	11	0	3	0	2	0	1	0	4	0	3	0	1	1	3	4	1	1	4	5			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr2:179429062G>T	ENST00000591111.1	-	276	77098	c.76874C>A	c.(76873-76875)gCa>gAa	p.A25625E	TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.A27266E|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.A18326E|TTN_ENST00000460472.2_Missense_Mutation_p.A18201E|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A24698E|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.A18393E|TTN-AS1_ENST00000592600.1_RNA			Q8WZ42	TITIN_HUMAN	titin	25625	Fibronectin type-III 86. {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)			TTCATCTCTTGCAGTAATGGC	0.393																																					p.A27266E		Atlas-SNP	.											.	TTN	18412	.	0			c.C81797A						PASS	.						106	104	105					2																	179429062		1912	4119	6031	SO:0001583	missense	7273	exon326			TCTCTTGCAGTAA	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.76874C>A	chr2.hg19:g.179429062G>T	ENSP00000465570:p.Ala25625Glu	138.0	0.0	.		135.0	31.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	15.43	2.830143	0.50845	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.54279	0.58;0.58;0.58;0.58	6.07	6.07	0.98685	Fibronectin, type III (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.79287	0.4420	M	0.89478	3.035	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	0.81406	-0.0947	9	0.87932	D	0	.	20.6452	0.99591	0.0:0.0:1.0:0.0	.	18201;18326;18393;25625	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	E	24698;18201;18393;18326;18199	ENSP00000343764:A24698E;ENSP00000434586:A18201E;ENSP00000340554:A18393E;ENSP00000352154:A18326E	ENSP00000340554:A18393E	A	-	2	0	TTN	179137308	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.030000	0.88816	2.885000	0.99019	0.650000	0.86243	GCA	.	.	.	none		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179429062	G	T	179429062	3	4	114	1	0	0	0	0	1	0	0	0	16747	1319	46	4	26330	4	TTN	2	179429062	Missense_Mutation	SNP	G	TCGA-BQ-5879-01A-11D-1589-08	43613434	179429062	63770311	6	7367											
FYTTD1	84248	hgsc.bcm.edu	37	chr3	197501076	197501076	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgtagtagcaaagagaacTcgtcagtaagtttccatttg	13	12	10	6	1	1	1	1	0	0	1	3	3	2	1	1	0	2	5	1	0	5	5			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr3:197501076T>C	ENST00000241502.4	+	6	873	c.651T>C	c.(649-651)acT>acC	p.T217T	FYTTD1_ENST00000415708.2_Silent_p.T191T|FYTTD1_ENST00000428395.2_Silent_p.T126T|FYTTD1_ENST00000424384.2_Silent_p.T150T	NM_032288.6	NP_115664.2	Q96QD9	UIF_HUMAN	forty-two-three domain containing 1	217					mRNA export from nucleus (GO:0006406)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	13	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	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;0.175)		CAAAGAGAACTCGTCAGTAAG	0.378																																					p.T217T		Atlas-SNP	.											.	FYTTD1	34	.	0			c.T651C						PASS	.						171	168	169					3																	197501076		2203	4300	6503	SO:0001819	synonymous_variant	84248	exon6			GAGAACTCGTCAG	AJ344094	CCDS3329.1, CCDS43196.1, CCDS43196.2	3q29	2011-03-03			ENSG00000122068	ENSG00000122068			25407	protein-coding gene	gene with protein product	"UAP56-interacting factor"					19836239	Standard	NM_001011537		Approved	DKFZp761B1514, UIF	uc003fyi.2	Q96QD9	OTTHUMG00000155453	ENST00000241502.4:c.651T>C	chr3.hg19:g.197501076T>C		150.0	0.0	.		139.0	6.0	.	NM_032288	A8MY74|B2RCB2|B7Z3R4|B7Z7V1|B7Z8I0|B7ZAJ3|C9J7P6|C9JNG6|C9JTH3|C9JY50|Q96SL9|Q9BQI8	Silent	SNP	ENST00000241502.4	hg19	CCDS3329.1																																																																																			.	.	.	none		0.378	FYTTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340185.3	NM_032288		C	197501076	T	C	197501076	2	2	114	1	0	0	0	0	0	0	0	1	6134	1538	54	3		3	FYTTD1	3	197501076	Silent	SNP	T	TCGA-BQ-5879-01A-11D-1589-08		197501076	521354	7	7368											
PRSS12	8492	hgsc.bcm.edu	37	chr4	119273492	119273492	+	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	tggcgctgtcctcgcagctgAgcccagctcgctgggggcga	4	7	16	14	4	0	1	0	1	0	0	3	2	1	1	2	3	3	5	2	3	0	0			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr4:119273492A>T	ENST00000296498.3	-	1	666	c.384T>A	c.(382-384)gcT>gcA	p.A128A		NM_003619.3	NP_003610.2	P56730	NETR_HUMAN	protease, serine, 12 (neurotrypsin, motopsin)	128	Kringle. {ECO:0000255|PROSITE- ProRule:PRU00121}.				exocytosis (GO:0006887)|zymogen activation (GO:0031638)	axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)|terminal bouton (GO:0043195)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(3)|kidney(1)|large_intestine(9)|lung(11)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	29						CTCGCAGCTGAGCCCAGCTCG	0.706																																					p.A128A		Atlas-SNP	.											.	PRSS12	71	.	0			c.T384A						PASS	.						9	10	10					4																	119273492		2194	4283	6477	SO:0001819	synonymous_variant	8492	exon1			CAGCTGAGCCCAG	AJ001531	CCDS3709.1	4q25-q26	2010-05-07			ENSG00000164099	ENSG00000164099		"Serine peptidases / Serine peptidases"	9477	protein-coding gene	gene with protein product		606709				9540828, 9245503	Standard	NM_003619		Approved	BSSP-3, MRT1	uc003ica.2	P56730	OTTHUMG00000161166	ENST00000296498.3:c.384T>A	chr4.hg19:g.119273492A>T		3.0	0.0	.		8.0	4.0	.	NM_003619	Q9UP16	Silent	SNP	ENST00000296498.3	hg19	CCDS3709.1																																																																																			.	.	.	none		0.706	PRSS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256516.2			T	119273492	A	T	119273492	2	4	114	1	0	0	0	0	0	0	0	1	12625	291	11	5		5	PRSS12	4	119273492	Silent	SNP	A	TCGA-BQ-5879-01A-11D-1589-08		119273492	71880784	8	7369											
SLC12A7	10723	hgsc.bcm.edu	37	chr5	1094290	1094290	+	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	tcgaaaagtgccatgttcttCccttcaaagaagctctcttg	10	13	7	11	1	3	1	1	0	2	1	6	2	4	1	2	0	2	2	2	0	4	4			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr5:1094290C>T	ENST00000264930.5	-	2	241	c.198G>A	c.(196-198)ggG>ggA	p.G66G		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	66					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)	CCATGTTCTTCCCTTCAAAGA	0.468																																					p.G66G		Atlas-SNP	.											.	SLC12A7	97	.	0			c.G198A						PASS	.						128	120	123					5																	1094290		2203	4300	6503	SO:0001819	synonymous_variant	10723	exon2			GTTCTTCCCTTCA	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.198G>A	chr5.hg19:g.1094290C>T		171.0	0.0	.		87.0	49.0	.	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Silent	SNP	ENST00000264930.5	hg19	CCDS34129.1																																																																																			.	.	.	none		0.468	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598		T	1094290	C	T	1094290	2	4	114	1	0	0	0	0	0	0	0	1	14401	842	30	2		2	SLC12A7	5	1094290	Silent	SNP	C	TCGA-BQ-5879-01A-11D-1589-08		1094290	179820970	9	7370											
POP1	10940	hgsc.bcm.edu	37	chr8	99142345	99142345	+	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	agaaactcacatctggcacgCcaagcggtttcatatggtca	12	9	9	11	2	4	1	3	0	1	1	4	1	4	1	1	3	2	2	1	3	3	2			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr8:99142345C>T	ENST00000401707.2	+	5	707	c.626C>T	c.(625-627)gCc>gTc	p.A209V	POP1_ENST00000349693.3_Missense_Mutation_p.A209V	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)	209					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)	p.A209V(1)		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)			ATCTGGCACGCCAAGCGGTTT	0.488																																					p.A209V		Atlas-SNP	.											POP1,NS,carcinoma,0,1	POP1	85	.	1	Substitution - Missense(1)	lung(1)	c.C626T						PASS	.						75	72	73					8																	99142345		2203	4300	6503	SO:0001583	missense	10940	exon5			GGCACGCCAAGCG	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.626C>T	chr8.hg19:g.99142345C>T	ENSP00000385787:p.Ala209Val	128.0	0.0	.		115.0	45.0	.	NM_001145860	A8K5W9|Q15037	Missense_Mutation	SNP	ENST00000401707.2	hg19	CCDS6277.1	.	.	.	.	.	.	.	.	.	.	C	36	5.647996	0.96714	.	.	ENSG00000104356	ENST00000401707;ENST00000349693	T;T	0.61980	0.06;0.06	5.81	5.81	0.92471	Ribonuclease P/MRP, subunit POP1 (1);	0.139825	0.47093	D	0.000247	T	0.76905	0.4053	M	0.66378	2.025	0.80722	D	1	D	0.56287	0.975	D	0.65323	0.934	T	0.75004	-0.3470	9	.	.	.	-3.0517	17.8794	0.88835	0.0:1.0:0.0:0.0	.	209	Q99575	POP1_HUMAN	V	209	ENSP00000385787:A209V;ENSP00000339529:A209V	.	A	+	2	0	POP1	99211521	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.731000	0.84895	2.746000	0.94184	0.591000	0.81541	GCC	.	.	.	none		0.488	POP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379470.1	NM_015029		T	99142345	C	T	99142345	3	4	114	1	0	0	0	0	1	0	0	0	12258	739	26	2	640	2	POP1	8	99142345	Missense_Mutation	SNP	C	TCGA-BQ-5879-01A-11D-1589-08		99142345	47221677	10	7371											
RDX	5962	hgsc.bcm.edu	37	chr11	110124813	110124813	+	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	ccgcttattgattctcagacGaggtgcataaaacacaaaat	15	10	7	9	2	1	2	1	1	1	1	2	3	1	2	1	1	2	2	1	1	5	4	rs370869036		TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr11:110124813G>T	ENST00000343115.4	-	9	1136	c.817C>A	c.(817-819)Cgt>Agt	p.R273S	RDX_ENST00000528900.1_Intron|RDX_ENST00000405097.1_Missense_Mutation_p.R273S|RDX_ENST00000528498.1_Missense_Mutation_p.R273S|RDX_ENST00000544551.1_Missense_Mutation_p.R137S|RDX_ENST00000530301.1_Intron	NM_001260494.1|NM_002906.3	NP_001247423.1|NP_002897.1	P35241	RADI_HUMAN	radixin	273	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				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)		ATTCTCAGACGAGGTGCATAA	0.338																																					p.R273S	Esophageal Squamous(55;25 1062 11040 28755 44273)	Atlas-SNP	.											.	RDX	59	.	0			c.C817A						PASS	.						81	72	75					11																	110124813		2201	4298	6499	SO:0001583	missense	5962	exon9			TCAGACGAGGTGC	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.817C>A	chr11.hg19:g.110124813G>T	ENSP00000342830:p.Arg273Ser	80.0	0.0	.		77.0	4.0	.	NM_001260493	A7YIJ8|A7YIK0|A7YIK3|B7Z9U6|F5H1A7|Q86Y61	Missense_Mutation	SNP	ENST00000343115.4	hg19	CCDS8343.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.599569	0.87055	.	.	ENSG00000137710	ENST00000528498;ENST00000429481;ENST00000405097;ENST00000343115;ENST00000544551	T;T;T;T	0.79554	-1.28;-1.28;-1.28;-1.28	5.72	5.72	0.89469	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	D	0.86969	0.6061	L	0.54908	1.71	0.80722	D	1	P;D;B	0.64830	0.501;0.994;0.026	B;P;B	0.62298	0.206;0.9;0.089	D	0.85377	0.1117	10	0.41790	T	0.15	.	19.8831	0.96905	0.0:0.0:1.0:0.0	.	137;273;273	F5H1A7;A7YIJ8;P35241	.;.;RADI_HUMAN	S	273;273;273;273;137	ENSP00000432112:R273S;ENSP00000384136:R273S;ENSP00000342830:R273S;ENSP00000445826:R137S	ENSP00000342830:R273S	R	-	1	0	RDX	109630023	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.799000	0.99117	2.705000	0.92388	0.655000	0.94253	CGT	.	.	.	alt		0.338	RDX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390535.2	NM_002906		T	110124813	G	T	110124813	3	4	114	1	0	0	0	0	1	0	0	0	13211	1058	37	4	958	4	RDX	11	110124813	Missense_Mutation	SNP	G	TCGA-BQ-5879-01A-11D-1589-08		110124813	24881703	11	7372											
NELL2	4753	hgsc.bcm.edu	37	chr12	45097517	45097517	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tacaaggattaccttcacagTaggcattatcctctcgaaga	13	11	7	10	1	2	1	1	0	1	1	4	3	3	2	2	2	2	2	2	2	6	5			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr12:45097517T>C	ENST00000429094.2	-	12	1814	c.1310A>G	c.(1309-1311)tAc>tGc	p.Y437C	NELL2_ENST00000437801.2_Missense_Mutation_p.Y487C|NELL2_ENST00000395487.2_Missense_Mutation_p.Y436C|NELL2_ENST00000452445.2_Missense_Mutation_p.Y437C|NELL2_ENST00000551601.1_Missense_Mutation_p.Y436C|NELL2_ENST00000549027.1_Missense_Mutation_p.Y436C|NELL2_ENST00000333837.4_Missense_Mutation_p.Y460C	NM_001145108.1	NP_001138580.1	Q99435	NELL2_HUMAN	NEL-like 2 (chicken)	437	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(16)|lung(30)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	65	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		ACCTTCACAGTAGGCATTATC	0.403																																					p.Y487C		Atlas-SNP	.											.	NELL2	286	.	0			c.A1460G						PASS	.						97	89	92					12																	45097517		2203	4300	6503	SO:0001583	missense	4753	exon13			TCACAGTAGGCAT	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.1310A>G	chr12.hg19:g.45097517T>C	ENSP00000390680:p.Tyr437Cys	136.0	0.0	.		104.0	32.0	.	NM_001145107	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Missense_Mutation	SNP	ENST00000429094.2	hg19	CCDS8746.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.07|19.07	3.756435|3.756435	0.69648|0.69648	.|.	.|.	ENSG00000184613|ENSG00000184613	ENST00000550313|ENST00000395487;ENST00000429094;ENST00000551601;ENST00000452445;ENST00000549027;ENST00000333837;ENST00000437801;ENST00000543684	.|D;D;T;D;D;D;D	.|0.95622	.|-1.56;-1.56;-0.63;-1.56;-1.56;-2.26;-3.76	5.6|5.6	5.6|5.6	0.85130|0.85130	.|Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.97396|0.97396	0.9148|0.9148	M|M	0.77616|0.77616	2.38|2.38	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;0.999;1.0;1.0	.|D;D;D;D;D;D	.|0.80764	.|0.956;0.984;0.986;0.994;0.968;0.993	D|D	0.97098|0.97098	0.9795|0.9795	5|10	.|0.36615	.|T	.|0.2	-30.8204|-30.8204	15.7975|15.7975	0.78423|0.78423	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|460;487;436;437;437;436	.|B7Z2U7;B7Z9U3;F8VVB6;B3KTI3;Q99435;Q96JS2	.|.;.;.;.;NELL2_HUMAN;.	A|C	181|436;437;436;437;436;460;487;436	.|ENSP00000378866:Y436C;ENSP00000390680:Y437C;ENSP00000449332:Y436C;ENSP00000394612:Y437C;ENSP00000447927:Y436C;ENSP00000327988:Y460C;ENSP00000416341:Y487C	.|ENSP00000327988:Y460C	T|Y	-|-	1|2	0|0	NELL2|NELL2	43383784|43383784	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.089000|7.089000	0.76909|0.76909	2.135000|2.135000	0.66039|0.66039	0.528000|0.528000	0.53228|0.53228	ACT|TAC	.	.	.	none		0.403	NELL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404180.1	NM_006159		C	45097517	T	C	45097517	3	2	114	1	0	0	0	0	1	0	0	0	10341	1638	57	3	1176	3	NELL2	12	45097517	Missense_Mutation	SNP	T	TCGA-BQ-5879-01A-11D-1589-08		45097517	88754378	12	7373											
C14orf43	91748	hgsc.bcm.edu	37	chr14	74196477	74196477	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgaggatggggggcggcgtgTagggaggtagctcaaagctc	8	7	20	6	2	1	1	1	1	0	0	2	3	1	3	0	7	2	4	0	7	3	2			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr14:74196477T>C	ENST00000286523.5	-	4	2743	c.1961A>G	c.(1960-1962)tAc>tGc	p.Y654C	ELMSAN1_ENST00000394071.2_Missense_Mutation_p.Y654C	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	654					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										GGGCGGCGTGTAGGGAGGTAG	0.627																																					p.Y654C		Atlas-SNP	.											.	.	.	.	0			c.A1961G						PASS	.						69	63	65					14																	74196477		2203	4300	6503	SO:0001583	missense	91748	exon4			GGCGTGTAGGGAG	BF971739	CCDS9819.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000156030	ENSG00000156030			19853	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 117", "chromosome 14 open reading frame 43"	C14orf117, C14orf43			Standard	NM_194278		Approved	LSR68	uc001xou.3	Q6PJG2	OTTHUMG00000150359	ENST00000286523.5:c.1961A>G	chr14.hg19:g.74196477T>C	ENSP00000286523:p.Tyr654Cys	95.0	0.0	.		78.0	23.0	.	NM_194278	Q6PK13|Q6PK59|Q6ZS23	Missense_Mutation	SNP	ENST00000286523.5	hg19	CCDS9819.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.429427	0.83776	.	.	ENSG00000156030	ENST00000394071;ENST00000286523;ENST00000423556;ENST00000435371	T;T;T;T	0.51071	0.72;0.72;0.72;0.74	5.27	5.27	0.74061	.	0.000000	0.64402	D	0.000018	T	0.70404	0.3220	M	0.81497	2.545	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.75608	-0.3259	10	0.87932	D	0	-12.2873	15.1835	0.72978	0.0:0.0:0.0:1.0	.	654;654	A0PJD3;Q6PJG2	.;CN043_HUMAN	C	654	ENSP00000377634:Y654C;ENSP00000286523:Y654C;ENSP00000407767:Y654C;ENSP00000402380:Y654C	ENSP00000286523:Y654C	Y	-	2	0	C14orf43	73266230	1.000000	0.71417	0.999000	0.59377	0.972000	0.66771	8.032000	0.88838	1.977000	0.57605	0.391000	0.25812	TAC	.	.	.	none		0.627	ELMSAN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317793.1	NM_194278		C	74196477	T	C	74196477	3	2	114	1	0	0	0	0	1	0	0	0	1776	1638	57	3	1212	3	C14orf43	14	74196477	Missense_Mutation	SNP	T	TCGA-BQ-5879-01A-11D-1589-08		74196477	33153063	13	7374											
RYR3	6263	hgsc.bcm.edu	37	chr15	33905537	33905537	+	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	tgagaacttcaacacagacgGgctcttcttccctgtgatga	10	11	9	11	1	3	4	1	3	2	2	4	5	4	4	1	1	2	1	1	1	2	3			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr15:33905537G>T	ENST00000389232.4	+	19	2388	c.2318G>T	c.(2317-2319)gGg>gTg	p.G773V	RYR3_ENST00000415757.3_Missense_Mutation_p.G773V	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	773	B30.2/SPRY 1. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		AACACAGACGGGCTCTTCTTC	0.552																																					p.G773V		Atlas-SNP	.											.	RYR3	760	.	0			c.G2318T						PASS	.						50	54	53					15																	33905537		2107	4260	6367	SO:0001583	missense	6263	exon19			CAGACGGGCTCTT		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.2318G>T	chr15.hg19:g.33905537G>T	ENSP00000373884:p.Gly773Val	52.0	0.0	.		32.0	18.0	.	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.821891	0.90873	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	T;T	0.70869	-0.52;-0.52	5.4	5.4	0.78164	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.85682	D	0.000000	T	0.80944	0.4721	L	0.47190	1.495	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.96	T	0.79305	-0.1858	10	0.45353	T	0.12	.	19.4159	0.94700	0.0:0.0:1.0:0.0	.	773;773	Q15413-2;Q15413	.;RYR3_HUMAN	V	773	ENSP00000373884:G773V;ENSP00000399610:G773V	ENSP00000354735:G773V	G	+	2	0	RYR3	31692829	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.715000	0.84713	2.821000	0.97095	0.650000	0.86243	GGG	.	.	.	none		0.552	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	33905537	G	T	33905537	3	4	114	1	0	0	0	0	1	0	0	0	13783	1232	43	4	2392	4	RYR3	15	33905537	Missense_Mutation	SNP	G	TCGA-BQ-5879-01A-11D-1589-08		33905537	68625855	14	7375											
NUP88	4927	hgsc.bcm.edu	37	chr17	5314095	5314095	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagtgggtgtctgcggctcaCgtagtgagtaaattctagca	9	12	13	7	2	3	1	1	1	2	0	3	1	3	1	0	2	2	4	0	2	5	5			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr17:5314095C>T	ENST00000573584.1	-	4	1117	c.608G>A	c.(607-609)cGt>cAt	p.R203H		NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	203					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						CTGCGGCTCACGTAGTGAGTA	0.388																																					p.R203H		Atlas-SNP	.											.	NUP88	47	.	0			c.G608A						PASS	.						107	114	112					17																	5314095		2203	4300	6503	SO:0001583	missense	4927	exon4			GGCTCACGTAGTG	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.608G>A	chr17.hg19:g.5314095C>T	ENSP00000458954:p.Arg203His	254.0	0.0	.		240.0	84.0	.	NM_002532	D3DTM2|Q9BWE5	Missense_Mutation	SNP	ENST00000573584.1	hg19	CCDS11070.1	.	.	.	.	.	.	.	.	.	.	C	11.84	1.757883	0.31137	.	.	ENSG00000108559	ENST00000225696;ENST00000543132	.	.	.	5.47	3.46	0.39613	.	0.364516	0.30126	N	0.010346	T	0.36936	0.0985	L	0.44542	1.39	0.28618	N	0.908315	B;B;B	0.09022	0.002;0.002;0.001	B;B;B	0.08055	0.002;0.002;0.003	T	0.28776	-1.0033	9	0.45353	T	0.12	-6.739	8.1438	0.31100	0.0:0.6984:0.0:0.3016	.	203;72;203	B7Z5I6;B4DP20;Q99567	.;.;NUP88_HUMAN	H	203;72	.	ENSP00000225696:R203H	R	-	2	0	NUP88	5254819	0.997000	0.39634	0.947000	0.38551	0.620000	0.37586	1.229000	0.32600	0.794000	0.33899	0.561000	0.74099	CGT	.	.	.	none		0.388	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532		T	5314095	C	T	5314095	3	4	114	1	0	0	0	0	1	0	0	0	10778	536	19	1	1673	1	NUP88	17	5314095	Missense_Mutation	SNP	C	TCGA-BQ-5879-01A-11D-1589-08		5314095	75881115	15	7376											
MYH3	4621	hgsc.bcm.edu	37	chr17	10554908	10554908	+	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	tggcgctttttgcctcggtaGccttccaccacctcggggtt	3	13	11	14	3	0	0	0	0	0	0	3	0	1	0	5	4	2	3	5	4	1	5	rs577513442		TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr17:10554908G>A	ENST00000583535.1	-	5	513	c.426C>T	c.(424-426)ggC>ggT	p.G142G	MYH3_ENST00000226209.7_Silent_p.G142G	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	142	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						TGCCTCGGTAGCCTTCCACCA	0.557													G|||	1	0.000199681	0	0	5008	,	,		14358	0.001		0	False		,,,				2504	0				p.G142G		Atlas-SNP	.											.	MYH3	227	.	0			c.C426T						PASS	.						137	137	137					17																	10554908		2203	4300	6503	SO:0001819	synonymous_variant	4621	exon5			TCGGTAGCCTTCC		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"Myosins / Myosin superfamily : Class II"	7573	protein-coding gene	gene with protein product	"myosin, skeletal, heavy chain, embryonic 1", "muscle embryonic myosin heavy chain 3"	160720	"myosin, heavy polypeptide 3, skeletal muscle, embryonic"			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.426C>T	chr17.hg19:g.10554908G>A		243.0	0.0	.		232.0	68.0	.	NM_002470	Q15492	Silent	SNP	ENST00000583535.1	hg19	CCDS11157.1																																																																																			.	.	.	none		0.557	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470		A	10554908	G	A	10554908	2	1	114	1	0	0	0	0	0	0	0	1	10043	958	34	2		2	MYH3	17	10554908	Silent	SNP	G	TCGA-BQ-5879-01A-11D-1589-08	5240813	10554908	70640302	16	7377											
GH1	2688	hgsc.bcm.edu	37	chr17	61995168	61995168	+	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	aggtcctttaggaggtcataGacgttgctgtcagaggcgcc	8	10	14	9	2	2	2	2	0	0	2	3	3	3	3	2	4	1	2	2	4	2	4			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr17:61995168G>T	ENST00000323322.5	-	4	450	c.408C>A	c.(406-408)gtC>gtA	p.V136V	GH1_ENST00000458650.2_Silent_p.V121V|GH1_ENST00000342364.4_Intron|CSHL1_ENST00000392824.4_Intron|GH1_ENST00000351388.4_Silent_p.V96V	NM_000515.3	NP_000506.2	P01241	SOMA_HUMAN	growth hormone 1	136			V -> I (in dbSNP:rs5388). {ECO:0000269|PubMed:12655557, ECO:0000269|PubMed:15001589}.		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						GGAGGTCATAGACGTTGCTGT	0.607																																					p.V136V		Atlas-SNP	.											.	GH1	39	.	0			c.C408A						PASS	.						68	68	68					17																	61995168		2203	4300	6503	SO:0001819	synonymous_variant	2688	exon4			GTCATAGACGTTG	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.408C>A	chr17.hg19:g.61995168G>T		128.0	0.0	.		131.0	57.0	.	NM_000515	A6NEF6|Q14405|Q16631|Q5EB53|Q9HBZ1|Q9UMJ7|Q9UNL5	Silent	SNP	ENST00000323322.5	hg19	CCDS11653.1																																																																																			.	.	.	none		0.607	GH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417708.1	NM_000515		T	61995168	G	T	61995168	2	4	114	1	0	0	0	0	0	0	0	1	6374	929	33	4		4	GH1	17	61995168	Silent	SNP	G	TCGA-BQ-5879-01A-11D-1589-08	51440260	61995168	19200042	17	7378											
LSM14A	26065	hgsc.bcm.edu	37	chr19	34710448	34710449	+	Frame_Shift_Del	DEL	AG	AG	-																															tcaacaaggaagagattgacAgagagtttcataataaactt																								rs372366966		TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr19:34710448_34710449delAG	ENST00000433627.5	+	7	1009_1010	c.934_935delAG	c.(934-936)agafs	p.R312fs	LSM14A_ENST00000540746.2_Frame_Shift_Del_p.R271fs|LSM14A_ENST00000544216.3_Frame_Shift_Del_p.R312fs	NM_001114093.1	NP_001107565.1	Q8ND56	LS14A_HUMAN	LSM14A, SCD6 homolog A (S. cerevisiae)	312	DFDF. {ECO:0000255|PROSITE- ProRule:PRU00845}.				cytoplasmic mRNA processing body assembly (GO:0033962)|multicellular organismal development (GO:0007275)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of translation (GO:0006417)|RIG-I signaling pathway (GO:0039529)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|intracellular membrane-bounded organelle (GO:0043231)	double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)	p.R312K(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(7)|skin(1)	22	Esophageal squamous(110;0.162)					AGAGATTGACAGAGAGTTTCAT	0.327																																					p.311_312del		Atlas-INDEL	.											.	LSM14A	44	.	1	Substitution - Missense(1)	large_intestine(1)	c.933_934del						PASS	.																																			SO:0001589	frameshift_variant	26065	exon7			.	AL834398	CCDS12435.1, CCDS46040.1	19q13.12	2010-01-27	2006-12-21	2006-01-24		ENSG00000257103			24489	protein-coding gene	gene with protein product		610677	"chromosome 19 open reading frame 13", "family with sequence similarity 61, member A", "LSM14 homolog A (SCD6, S. cerevisiae)"	C19orf13, FAM61A		12477932	Standard	NM_015578		Approved	DKFZP434D1335, RAP55A, RAP55	uc002nva.4	Q8ND56		ENST00000433627.5:c.934_935delAG	chr19.hg19:g.34710452_34710453delAG	ENSP00000413964:p.Arg312fs	144.0	0.0	0		142.0	59.0	0.415493	NM_001114093	B4DTG6|Q76LX7|Q96AR3|Q96K73|Q96SN5|Q9UFR3	Frame_Shift_Del	DEL	ENST00000433627.5	hg19	CCDS46040.1																																																																																			.	.	.	none		0.327	LSM14A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451576.3	NM_015578		-	34710449	AG	-	34710448	7	5	114	1	0	1	0	1	0	0	0	0	9061	180	7	0	960	0	LSM14A	19	34710448	Frame_Shift_Del	DEL	AG	TCGA-BQ-5879-01A-11D-1589-08		34710448	24418535	18	7379											
RYR1	6261	hgsc.bcm.edu	37	chr19	38948197	38948197	+	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	tggctgtacgctccaaccaaGatcttattactgagaacttg	11	12	8	10	1	1	2	0	1	1	2	2	3	2	2	2	1	4	3	2	1	6	4			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr19:38948197G>T	ENST00000359596.3	+	17	1852	c.1852G>T	c.(1852-1854)Gat>Tat	p.D618Y	RYR1_ENST00000360985.3_Missense_Mutation_p.D618Y|RYR1_ENST00000355481.4_Missense_Mutation_p.D618Y			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	618	B30.2/SPRY 1. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CTCCAACCAAGATCTTATTAC	0.522																																					p.D618Y		Atlas-SNP	.											RYR1,caecum,carcinoma,0,1	RYR1	708	.	0			c.G1852T						PASS	.						341	275	297					19																	38948197		2203	4300	6503	SO:0001583	missense	6261	exon17			AACCAAGATCTTA	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.1852G>T	chr19.hg19:g.38948197G>T	ENSP00000352608:p.Asp618Tyr	293.0	0.0	.		311.0	14.0	.	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	14.39	2.521791	0.44866	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.97089	-4.24;-4.24;-4.24	3.76	3.76	0.43208	Intracellular calcium-release channel (1);B30.2/SPRY domain (1);	0.075267	0.49916	U	0.000125	D	0.95912	0.8669	L	0.36672	1.1	0.42899	D	0.99422	D;D	0.64830	0.994;0.98	P;P	0.61722	0.862;0.893	D	0.94764	0.7939	10	0.87932	D	0	.	5.1222	0.14865	0.2768:0.0:0.7232:0.0	.	618;618	P21817-2;P21817	.;RYR1_HUMAN	Y	618	ENSP00000352608:D618Y;ENSP00000347667:D618Y;ENSP00000354254:D618Y	ENSP00000347667:D618Y	D	+	1	0	RYR1	43640037	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.680000	0.54641	2.113000	0.64589	0.555000	0.69702	GAT	.	.	.	none		0.522	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	38948197	G	T	38948197	3	4	114	1	0	0	0	0	1	0	0	0	13781	942	33	4	1918	4	RYR1	19	38948197	Missense_Mutation	SNP	G	TCGA-BQ-5879-01A-11D-1589-08	4237749	38948197	20180786	19	7380											
ZNF175	7728	hgsc.bcm.edu	37	chr19	52091521	52091521	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agagaaaccctatgaatgccTtgactgtgggaaatcgttca	13	10	10	8	1	1	3	1	2	0	1	2	5	1	4	2	1	2	1	2	1	4	3			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr19:52091521T>C	ENST00000262259.2	+	5	2295	c.1937T>C	c.(1936-1938)cTt>cCt	p.L646P	ZNF175_ENST00000436511.2_Intron	NM_007147.2	NP_009078.1	Q9Y473	ZN175_HUMAN	zinc finger protein 175	646					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)		TATGAATGCCTTGACTGTGGG	0.443																																					p.L646P		Atlas-SNP	.											.	ZNF175	65	.	0			c.T1937C						PASS	.						86	84	85					19																	52091521		2203	4300	6503	SO:0001583	missense	7728	exon5			AATGCCTTGACTG	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.1937T>C	chr19.hg19:g.52091521T>C	ENSP00000262259:p.Leu646Pro	154.0	0.0	.		156.0	50.0	.	NM_007147	A8K9H2	Missense_Mutation	SNP	ENST00000262259.2	hg19	CCDS12837.1	.	.	.	.	.	.	.	.	.	.	T	1.034	-0.680825	0.03353	.	.	ENSG00000105497	ENST00000262259	T	0.10763	2.84	2.14	-2.05	0.07321	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02418	0.0074	N	0.00707	-1.245	0.09310	N	1	B	0.28324	0.207	B	0.29663	0.105	T	0.37009	-0.9724	9	0.48119	T	0.1	.	0.6964	0.00900	0.1625:0.18:0.2558:0.4017	.	646	Q9Y473	ZN175_HUMAN	P	646	ENSP00000262259:L646P	ENSP00000262259:L646P	L	+	2	0	ZNF175	56783333	0.000000	0.05858	0.066000	0.19879	0.247000	0.25773	-3.014000	0.00646	-0.395000	0.07715	-1.142000	0.01873	CTT	.	.	.	none		0.443	ZNF175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396205.1	NM_007147		C	52091521	T	C	52091521	3	2	114	1	0	0	0	0	1	0	0	0	17757	1609	56	3	1951	3	ZNF175	19	52091521	Missense_Mutation	SNP	T	TCGA-BQ-5879-01A-11D-1589-08	13143324	52091521	7037462	20	7381											
PTPRA	5786	hgsc.bcm.edu	37	chr20	2998529	2998529	+	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	caaaacacagccaccatcgtCatggttaccaacctgaagga	15	6	7	13	1	1	1	1	1	0	0	2	2	1	2	4	2	4	1	4	2	5	1			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chr20:2998529C>T	ENST00000216877.6	+	12	1384	c.984C>T	c.(982-984)gtC>gtT	p.V328V	PTPRA_ENST00000425918.2_Silent_p.V348V|PTPRA_ENST00000358719.4_Silent_p.V193V|PTPRA_ENST00000399903.2_Silent_p.V337V|PTPRA_ENST00000318266.5_Silent_p.V328V|PTPRA_ENST00000356147.3_Silent_p.V328V|PTPRA_ENST00000380393.3_Silent_p.V337V	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	337	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|insulin receptor signaling pathway (GO:0008286)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein phosphorylation (GO:0006468)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						CCACCATCGTCATGGTTACCA	0.433																																					p.V337V		Atlas-SNP	.											.	PTPRA	75	.	0			c.C1011T						PASS	.						114	105	108					20																	2998529		2203	4300	6503	SO:0001819	synonymous_variant	5786	exon17			CATCGTCATGGTT		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.984C>T	chr20.hg19:g.2998529C>T		69.0	0.0	.		57.0	27.0	.	NM_002836	A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	Silent	SNP	ENST00000216877.6	hg19	CCDS13039.1																																																																																			.	.	.	none		0.433	PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077682.3			T	2998529	C	T	2998529	2	4	114	1	0	0	0	0	0	0	0	1	12808	813	29	2		2	PTPRA	20	2998529	Silent	SNP	C	TCGA-BQ-5879-01A-11D-1589-08		2998529	60026991	21	7382											
SSX1	6756	hgsc.bcm.edu	37	chrX	48123289	48123289	+	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	aagcatctggcccacaaaacGatgggaaacaactgcacccc	15	4	8	14	1	1	0	0	0	1	0	1	2	1	1	3	2	5	2	3	2	5	0			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chrX:48123289G>A	ENST00000376919.3	+	6	539	c.403G>A	c.(403-405)Gat>Aat	p.D135N		NM_001278691.1|NM_005635.2	NP_001265620.1|NP_005626.1	Q16384	SSX1_HUMAN	synovial sarcoma, X breakpoint 1	135					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|transcription corepressor activity (GO:0003714)		SS18/SSX1(1169)|SS18L1/SSX1(2)	endometrium(2)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	9						CCCACAAAACGATGGGAAACA	0.423			T	SS18	synovial sarcoma																																p.D135N	Esophageal Squamous(175;994 1982 2214 6527 18857)	Atlas-SNP	.		Dom	yes		X	Xp11.23-p11.22	6756	"synovial sarcoma, X breakpoint 1"		M	.	SSX1	27	.	0			c.G403A						PASS	.						153	141	145					X																	48123289		2203	4299	6502	SO:0001583	missense	6756	exon6			CAAAACGATGGGA	BC001003	CCDS14290.1	Xp11.23	2009-03-12			ENSG00000126752	ENSG00000126752			11335	protein-coding gene	gene with protein product	"cancer/testis antigen family 5, member 1"	312820				7655467	Standard	NM_005635		Approved	CT5.1	uc004djb.1	Q16384	OTTHUMG00000021488	ENST00000376919.3:c.403G>A	chrX.hg19:g.48123289G>A	ENSP00000366118:p.Asp135Asn	334.0	0.0	.		345.0	19.0	.	NM_005635	A3KN76|Q08AJ2|Q5JQ64	Missense_Mutation	SNP	ENST00000376919.3	hg19	CCDS14290.1	.	.	.	.	.	.	.	.	.	.	N	0.021	-1.430282	0.01117	.	.	ENSG00000126752	ENST00000376919	T	0.07327	3.2	2.1	1.21	0.21127	.	1.694760	0.03640	N	0.239416	T	0.04318	0.0119	L	0.38175	1.15	0.09310	N	1	P	0.47545	0.897	B	0.29524	0.103	T	0.32903	-0.9889	10	0.02654	T	1	.	4.011	0.09623	0.2273:0.0:0.7727:0.0	.	135	Q16384	SSX1_HUMAN	N	135	ENSP00000366118:D135N	ENSP00000366118:D135N	D	+	1	0	SSX1	48008233	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.159000	0.10056	0.336000	0.23639	0.380000	0.24917	GAT	.	.	.	none		0.423	SSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056485.1	NM_005635		A	48123289	G	A	48123289	3	1	114	1	0	0	0	0	1	0	0	0	15215	1058	37	1	421	1	SSX1	23	48123289	Missense_Mutation	SNP	G	TCGA-BQ-5879-01A-11D-1589-08		48123289	107147271	22	7383											
USP26	83844	hgsc.bcm.edu	37	chrX	132160221	132160221	+	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	ggtgtgcctgggctgctggcAggtttacctccagctttgtg	3	13	15	10	0	0	0	0	0	0	0	1	0	1	0	3	4	4	5	3	4	1	3			TCGA-BQ-5879-01A-11D-1589-08	TCGA-BQ-5879-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c4bbd9ac-1407-4318-a83b-19f1b5b92604	23e170f1-858d-4c25-95c7-ef04b3ffa05a	g.chrX:132160221A>C	ENST00000511190.1	-	6	2497	c.2028T>G	c.(2026-2028)ccT>ccG	p.P676P	USP26_ENST00000370832.1_Silent_p.P676P|USP26_ENST00000406273.1_Silent_p.P676P	NM_031907.1	NP_114113.1	Q9BXU7	UBP26_HUMAN	ubiquitin specific peptidase 26	676	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	60	Acute lymphoblastic leukemia(192;0.000127)					GGCTGCTGGCAGGTTTACCTC	0.428																																					p.P676P	NSCLC(104;342 1621 36940 47097 52632)	Atlas-SNP	.											.	USP26	135	.	0			c.T2028G						PASS	.						83	79	81					X																	132160221		2203	4299	6502	SO:0001819	synonymous_variant	83844	exon1			GCTGGCAGGTTTA	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.2028T>G	chrX.hg19:g.132160221A>C		215.0	0.0	.		196.0	41.0	.	NM_031907	B9WRT6|Q5H9H4	Silent	SNP	ENST00000511190.1	hg19	CCDS14635.1																																																																																			.	.	.	none		0.428	USP26-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359441.1	NM_031907		C	132160221	A	C	132160221	2	2	114	1	0	0	0	0	0	0	0	1	17069	175	7	5		5	USP26	23	132160221	Silent	SNP	A	TCGA-BQ-5879-01A-11D-1589-08	84036932	132160221	23110339	23	7384											
MACF1	23499	hgsc.bcm.edu	37	chr1	39775962	39775962	+	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	gccatcagattatgaagaacCttcaggcccactatgaagac	14	8	8	11	0	2	5	2	2	0	3	2	5	2	5	3	1	1	0	3	1	5	3			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr1:39775962C>A	ENST00000372915.3	+	24	3064	c.2977C>A	c.(2977-2979)Ctt>Att	p.L993I	MACF1_ENST00000564288.1_Missense_Mutation_p.L988I|MACF1_ENST00000539005.1_Missense_Mutation_p.L993I|MACF1_ENST00000317713.7_Missense_Mutation_p.L993I|MACF1_ENST00000545844.1_Missense_Mutation_p.L993I|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000361689.2_Missense_Mutation_p.L993I|MACF1_ENST00000567887.1_Missense_Mutation_p.L1025I			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	993					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)			TATGAAGAACCTTCAGGCCCA	0.463																																					p.L993I		Atlas-SNP	.											.	MACF1	909	.	0			c.C2977A						PASS	.						114	94	101					1																	39775962		2203	4300	6503	SO:0001583	missense	23499	exon26			AAGAACCTTCAGG	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.2977C>A	chr1.hg19:g.39775962C>A	ENSP00000362006:p.Leu993Ile	52.0	0.0	.		53.0	12.0	.	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.6|20.6	4.013512|4.013512	0.75161|0.75161	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000524432;ENST00000530262|ENST00000372925	D;D;D;D;D;D;D|.	0.95035|.	-1.71;-1.73;-1.71;-1.74;-1.62;-3.08;-3.59|.	5.21|5.21	5.21|5.21	0.72293|0.72293	.|.	.|.	.|.	.|.	.|.	T|T	0.77987|0.77987	0.4213|0.4213	M|M	0.87456|0.87456	2.885|2.885	0.80722|0.80722	D|D	1|1	P;D;D|.	0.89917|.	0.524;0.997;1.0|.	B;P;D|.	0.78314|.	0.3;0.839;0.991|.	T|T	0.80953|0.80953	-0.1152|-0.1152	9|5	0.72032|.	D|.	0.01|.	.|.	12.1581|12.1581	0.54089|0.54089	0.0:0.9218:0.0:0.0782|0.0:0.9218:0.0:0.0782	.|.	993;993;958|.	F8W8Q1;Q9UPN3-2;Q9UPN3-3|.	.;.;.|.	I|H	993;993;993;993;993;951;1142|126	ENSP00000439537:L993I;ENSP00000362006:L993I;ENSP00000354573:L993I;ENSP00000313438:L993I;ENSP00000444364:L993I;ENSP00000435070:L951I;ENSP00000437059:L1142I|.	ENSP00000313438:L993I|.	L|P	+|+	1|2	0|0	MACF1|MACF1	39548549|39548549	1.000000|1.000000	0.71417|0.71417	0.989000|0.989000	0.46669|0.46669	0.721000|0.721000	0.41392|0.41392	3.237000|3.237000	0.51344|0.51344	2.430000|2.430000	0.82344|0.82344	0.655000|0.655000	0.94253|0.94253	CTT|CCT	.	.	.	none		0.463	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		A	39775962	C	A	39775962	3	1	115	1	0	0	0	0	1	0	0	0	9151	681	24	4	3071	4	MACF1	1	39775962	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08		39775962	209474659	1	7385											
HIVEP3	59269	hgsc.bcm.edu	37	chr1	41976755	41976755	+	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	accatctggatcccaccgatGggaatcaagggacatggggc	11	6	13	11	1	2	0	1	0	1	0	3	4	3	3	3	5	0	0	3	5	2	0			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr1:41976755G>C	ENST00000372583.1	-	9	7473	c.6588C>G	c.(6586-6588)ccC>ccG	p.P2196P	HIVEP3_ENST00000372584.1_Silent_p.P2195P|HIVEP3_ENST00000460604.1_5'UTR|HIVEP3_ENST00000247584.5_Silent_p.P2196P|HIVEP3_ENST00000429157.2_Silent_p.P2195P	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	2196					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)				TCCCACCGATGGGAATCAAGG	0.667																																					p.P2196P		Atlas-SNP	.											.	HIVEP3	235	.	0			c.C6588G						PASS	.						101	103	102					1																	41976755		2203	4300	6503	SO:0001819	synonymous_variant	59269	exon9			ACCGATGGGAATC	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.6588C>G	chr1.hg19:g.41976755G>C		149.0	0.0	.		122.0	22.0	.	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Silent	SNP	ENST00000372583.1	hg19	CCDS463.1																																																																																			.	.	.	none		0.667	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		C	41976755	G	C	41976755	2	2	115	1	0	0	0	0	0	0	0	1	7195	1335	47	4		4	HIVEP3	1	41976755	Silent	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	2200793	41976755	207273866	2	7386											
NTNG1	22854	hgsc.bcm.edu	37	chr1	107937850	107937850	+	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	atgcgaatgtgagcacaacaCtacaggtccagactgtggga	13	7	12	9	1	0	2	0	1	0	1	1	4	1	3	1	2	4	1	1	2	3	1			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr1:107937850C>A	ENST00000370068.1	+	4	1808	c.962C>A	c.(961-963)aCt>aAt	p.T321N	NTNG1_ENST00000370070.2_Missense_Mutation_p.T321N|NTNG1_ENST00000542803.1_Missense_Mutation_p.T321N|NTNG1_ENST00000370066.1_Missense_Mutation_p.T321N|NTNG1_ENST00000370061.3_Missense_Mutation_p.T321N|NTNG1_ENST00000370072.3_Missense_Mutation_p.T321N|NTNG1_ENST00000370071.2_Missense_Mutation_p.T321N|NTNG1_ENST00000370065.1_Missense_Mutation_p.T321N|NTNG1_ENST00000370074.4_Missense_Mutation_p.T321N|NTNG1_ENST00000370067.1_Missense_Mutation_p.T321N|NTNG1_ENST00000370073.2_Missense_Mutation_p.T321N			Q9Y2I2	NTNG1_HUMAN	netrin G1	321	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axonogenesis (GO:0007409)	anchored component of plasma membrane (GO:0046658)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(3)|soft_tissue(1)|urinary_tract(1)	37		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)		GAGCACAACACTACAGGTCCA	0.493																																					p.T321N		Atlas-SNP	.											.	NTNG1	274	.	0			c.C962A						PASS	.						203	192	196					1																	107937850		2203	4300	6503	SO:0001583	missense	22854	exon4			ACAACACTACAGG	AB023193	CCDS30785.1, CCDS44179.1, CCDS44180.1	1p13.2-p13.1	2013-03-01			ENSG00000162631	ENSG00000162631		"Netrins"	23319	protein-coding gene	gene with protein product	"netrin G1f", "Netrin-G1"	608818				10964959	Standard	NM_001113226		Approved	KIAA0976, Lmnt1	uc001dvh.4	Q9Y2I2	OTTHUMG00000010965	ENST00000370068.1:c.962C>A	chr1.hg19:g.107937850C>A	ENSP00000359085:p.Thr321Asn	203.0	0.0	.		199.0	35.0	.	NM_014917	Q5VU86|Q5VU87|Q5VU89|Q5VU90|Q5VU91|Q7Z2Y3|Q8N633	Missense_Mutation	SNP	ENST00000370068.1	hg19	CCDS44180.1	.	.	.	.	.	.	.	.	.	.	C	32	5.127060	0.94429	.	.	ENSG00000162631	ENST00000370076;ENST00000370073;ENST00000370071;ENST00000542803;ENST00000370061;ENST00000370072;ENST00000370070;ENST00000535584;ENST00000370064;ENST00000370062;ENST00000370074;ENST00000370068;ENST00000294649;ENST00000370067;ENST00000370066;ENST00000370065	T;T;T;T;T;T;T;T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12;-0.12;-0.12;-0.12;-0.12;-0.12;-0.12;-0.12	5.8	5.8	0.92144	EGF-like, laminin (3);EGF-like region, conserved site (1);	0.000000	0.64402	D	0.000006	D	0.87366	0.6159	H	0.98487	4.245	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.998;1.0;0.98;1.0	D;D;D;D;D	0.91635	0.997;0.994;0.999;0.912;0.998	D	0.91580	0.5278	10	0.87932	D	0	.	20.0637	0.97700	0.0:1.0:0.0:0.0	.	321;321;321;321;321	B4DKF0;Q9Y2I2;Q9Y2I2-4;Q9Y2I2-2;Q9Y2I2-1	.;NTNG1_HUMAN;.;.;.	N	321;321;321;321;321;321;321;321;82;82;321;321;321;321;321;321	ENSP00000359090:T321N;ENSP00000359088:T321N;ENSP00000440561:T321N;ENSP00000359078:T321N;ENSP00000359089:T321N;ENSP00000359087:T321N;ENSP00000359091:T321N;ENSP00000359085:T321N;ENSP00000359084:T321N;ENSP00000359083:T321N;ENSP00000359082:T321N	ENSP00000294649:T321N	T	+	2	0	NTNG1	107739373	1.000000	0.71417	0.999000	0.59377	0.965000	0.64279	7.818000	0.86416	2.751000	0.94390	0.650000	0.86243	ACT	.	.	.	none		0.493	NTNG1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000030340.1	NM_014917		A	107937850	C	A	107937850	3	1	115	1	0	0	0	0	1	0	0	0	10711	565	20	4	972	4	NTNG1	1	107937850	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	65961095	107937850	141312771	3	7387											
IGSF3	3321	hgsc.bcm.edu	37	chr1	117131439	117131439	+	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	gctgccgctgtcgctgacctCggctctctggacggtgaggc	3	9	15	14	4	1	2	0	2	1	0	4	3	1	3	2	4	1	4	2	4	0	0			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr1:117131439C>T	ENST00000369486.3	-	8	3082	c.2317G>A	c.(2317-2319)Gag>Aag	p.E773K	IGSF3_ENST00000369483.1_Missense_Mutation_p.E793K|IGSF3_ENST00000318837.6_Missense_Mutation_p.E793K	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	773	Ig-like C2-type 6.				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)		TCGCTGACCTCGGCTCTCTGG	0.627																																					p.E793K		Atlas-SNP	.											.	IGSF3	294	.	0			c.G2377A						PASS	.						29	29	29					1																	117131439		2201	4295	6496	SO:0001583	missense	3321	exon9			TGACCTCGGCTCT	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.2317G>A	chr1.hg19:g.117131439C>T	ENSP00000358498:p.Glu773Lys	35.0	0.0	.		56.0	12.0	.	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	hg19	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.152472	0.57259	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.64438	-0.1;-0.1;-0.1	3.98	3.01	0.34805	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.410465	0.24846	N	0.035140	T	0.43634	0.1256	M	0.66939	2.045	0.49483	D	0.999798	P;P;P	0.45212	0.604;0.853;0.656	B;B;B	0.38106	0.073;0.265;0.12	T	0.50285	-0.8846	10	0.41790	T	0.15	-28.9037	10.5216	0.44922	0.0:0.6523:0.3476:0.0	.	793;773;793	O75054-2;O75054;A6NJZ6	.;IGSF3_HUMAN;.	K	773;793;793	ENSP00000358498:E773K;ENSP00000358495:E793K;ENSP00000321184:E793K	ENSP00000321184:E793K	E	-	1	0	IGSF3	116932962	0.956000	0.32656	0.994000	0.49952	0.981000	0.71138	2.102000	0.41796	2.050000	0.60909	0.462000	0.41574	GAG	.	.	.	none		0.627	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		T	117131439	C	T	117131439	3	4	115	1	0	0	0	0	1	0	0	0	7608	893	31	1	1283	1	IGSF3	1	117131439	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	9193589	117131439	132119182	4	7388											
SELL	6402	hgsc.bcm.edu	37	chr1	169677647	169677647	+	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	tcttgatatagatctccacgCagtcctccttgttcttcttg	6	17	6	12	1	4	2	0	1	4	1	7	2	6	2	3	0	0	2	3	0	2	7			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr1:169677647C>T	ENST00000236147.4	-	3	582	c.422G>A	c.(421-423)tGc>tAc	p.C141Y	SELL_ENST00000463108.1_5'UTR|C1orf112_ENST00000498289.1_Intron	NM_000655.4	NP_000646.2	P14151	LYAM1_HUMAN	selectin L	128	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				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)					GATCTCCACGCAGTCCTCCTT	0.488																																					p.C141Y		Atlas-SNP	.											.	SELL	43	.	0			c.G422A						PASS	.						99	98	98					1																	169677647		2057	4216	6273	SO:0001583	missense	6402	exon3			TCCACGCAGTCCT	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.422G>A	chr1.hg19:g.169677647C>T	ENSP00000236147:p.Cys141Tyr	76.0	0.0	.		86.0	23.0	.	NM_000655	B2R6Q8|P15023|Q9UJ43	Missense_Mutation	SNP	ENST00000236147.4	hg19	CCDS53427.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.592012	0.86953	.	.	ENSG00000188404	ENST00000236147	T	0.61980	0.06	5.71	5.71	0.89125	C-type lectin fold (1);C-type lectin, conserved site (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.56097	D	0.000024	D	0.84279	0.5437	H	0.95539	3.685	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.88376	0.2998	10	0.87932	D	0	-22.4594	18.4088	0.90543	0.0:1.0:0.0:0.0	.	141;128	Q8WW79;P14151	.;LYAM1_HUMAN	Y	141	ENSP00000236147:C141Y	ENSP00000236147:C141Y	C	-	2	0	SELL	167944271	1.000000	0.71417	0.997000	0.53966	0.938000	0.57974	7.487000	0.81328	2.698000	0.92095	0.650000	0.86243	TGC	.	.	.	none		0.488	SELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084233.1	NM_000655		T	169677647	C	T	169677647	3	4	115	1	0	0	0	0	1	0	0	0	14029	710	25	2	763	2	SELL	1	169677647	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	52546208	169677647	79572974	5	7389											
CAD	790	hgsc.bcm.edu	37	chr2	27459639	27459639	+	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	cctaggccagatcgggccagCccctcctttgaaggtgcatg	7	8	12	14	1	0	2	0	1	0	1	2	2	1	2	6	3	2	1	6	3	2	2			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr2:27459639C>A	ENST00000403525.1	+	26	4292	c.4148C>A	c.(4147-4149)gCc>gAc	p.A1383D	CAD_ENST00000264705.4_Missense_Mutation_p.A1446D			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)					ATCGGGCCAGCCCCTCCTTTG	0.537																																					p.A1446D		Atlas-SNP	.											.	CAD	199	.	0			c.C4337A						PASS	.						121	117	118					2																	27459639		2203	4300	6503	SO:0001583	missense	790	exon27			GGCCAGCCCCTCC	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.4148C>A	chr2.hg19:g.27459639C>A	ENSP00000384510:p.Ala1383Asp	183.0	0.0	.		189.0	42.0	.	NM_004341	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Missense_Mutation	SNP	ENST00000403525.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.3|20.3	3.962670|3.962670	0.74016|0.74016	.|.	.|.	ENSG00000084774|ENSG00000084774	ENST00000264705;ENST00000403525|ENST00000458503	D;D|.	0.86694|.	-2.16;-2.16|.	5.58|5.58	5.58|5.58	0.84498|0.84498	Methylglyoxal synthase-like domain (1);|.	0.092996|.	0.85682|.	D|.	0.000000|.	T|T	0.69931|0.69931	0.3166|0.3166	L|L	0.50333|0.50333	1.59|1.59	0.80722|0.80722	D|D	1|1	P;D|.	0.71674|.	0.919;0.998|.	P;D|.	0.80764|.	0.587;0.994|.	T|T	0.66064|0.66064	-0.6016|-0.6016	10|5	0.12103|.	T|.	0.63|.	-6.9253|-6.9253	18.128|18.128	0.89592|0.89592	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1383;1446|.	F8VPD4;P27708|.	.;PYR1_HUMAN|.	D|T	1446;1383|98	ENSP00000264705:A1446D;ENSP00000384510:A1383D|.	ENSP00000264705:A1446D|.	A|P	+|+	2|1	0|0	CAD|CAD	27313143|27313143	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.966000|0.966000	0.64601|0.64601	4.299000|4.299000	0.59073|0.59073	2.622000|2.622000	0.88805|0.88805	0.561000|0.561000	0.74099|0.74099	GCC|CCC	.	.	.	none		0.537	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1			A	27459639	C	A	27459639	3	1	115	1	0	0	0	0	1	0	0	0	2567	739	26	4	4443	4	CAD	2	27459639	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08		27459639	215739734	6	7390											
VWA3B	200403	hgsc.bcm.edu	37	chr2	98744846	98744846	+	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	gcactatagcttttctaaagGatctgagtgccaagacccac	12	10	8	11	0	2	2	0	1	2	1	2	3	2	3	2	1	2	2	2	1	5	5			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr2:98744846G>T	ENST00000477737.1	+	6	1051	c.847G>T	c.(847-849)Gat>Tat	p.D283Y	VWA3B_ENST00000435344.1_Missense_Mutation_p.D283Y|VWA3B_ENST00000451075.2_Missense_Mutation_p.D133Y	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	283										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						TTTTCTAAAGGATCTGAGTGC	0.527																																					p.D283Y		Atlas-SNP	.											VWA3B,NS,carcinoma,0,1	VWA3B	138	.	0			c.G847T						PASS	.						96	96	96					2																	98744846		2002	4172	6174	SO:0001583	missense	200403	exon6			CTAAAGGATCTGA	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.847G>T	chr2.hg19:g.98744846G>T	ENSP00000417955:p.Asp283Tyr	78.0	1.0	.		74.0	15.0	.	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	hg19	CCDS42718.1	.	.	.	.	.	.	.	.	.	.	G	18.32	3.598190	0.66332	.	.	ENSG00000168658	ENST00000435344;ENST00000477737;ENST00000451075	T;T;T	0.15718	7.36;7.36;2.4	5.24	3.39	0.38822	.	0.502898	0.19634	N	0.109604	T	0.36413	0.0966	M	0.65975	2.015	0.26308	N	0.977864	D;D;D	0.76494	0.991;0.999;0.998	P;D;D	0.71656	0.844;0.974;0.946	T	0.07083	-1.0791	10	0.87932	D	0	.	10.7231	0.46052	0.0773:0.1356:0.7872:0.0	.	133;283;283	B7Z7Q7;Q502W6;Q502W6-8	.;VWA3B_HUMAN;.	Y	283;283;133	ENSP00000401959:D283Y;ENSP00000417955:D283Y;ENSP00000389463:D133Y	ENSP00000411168:D283Y	D	+	1	0	VWA3B	98111278	1.000000	0.71417	0.950000	0.38849	0.861000	0.49209	2.541000	0.45735	1.324000	0.45282	-0.175000	0.13238	GAT	.	.	.	none		0.527	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992		T	98744846	G	T	98744846	3	4	115	1	0	0	0	0	1	0	0	0	17253	1174	41	4	865	4	VWA3B	2	98744846	Missense_Mutation	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	71285207	98744846	144454527	7	7391											
ACAA1	30	hgsc.bcm.edu	37	chr3	38167081	38167092	+	In_Frame_Del	DEL	TGAGCAGCGTGA	TGAGCAGCGTGA	-																															cccacggcgcttcagctcatTgagcagcgtgatgacctgtc																								rs138308587		TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	TGAGCAGCGTGA	TGAGCAGCGTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr3:38167081_38167092delTGAGCAGCGTGA	ENST00000333167.8	-	11	1335_1346	c.1163_1174delTCACGCTGCTCA	c.(1162-1176)atcacgctgctcaat>aat	p.ITLL388del	ACAA1_ENST00000301810.7_In_Frame_Del_p.ITLL295del|Y_RNA_ENST00000365095.1_RNA|ACAA1_ENST00000480865.1_5'UTR|ACAA1_ENST00000450296.1_In_Frame_Del_p.ITLL347del	NM_001607.3	NP_001598.1	P09110	THIK_HUMAN	acetyl-CoA acyltransferase 1	388					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)		TTCAGCTCATTGAGCAGCGTGATGACCTGTCG	0.618																																					p.388_392del		Atlas-INDEL	.											ACAA1,NS,carcinoma,0,1	ACAA1	32	.	0			c.1164_1175del						PASS	.																																			SO:0001651	inframe_deletion	30	exon11			.	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.1163_1174delTCACGCTGCTCA	chr3.hg19:g.38167081_38167092delTGAGCAGCGTGA	ENSP00000333664:p.Ile388_Leu391del	96.0	0.0	0		94.0	13.0	0.138298	NM_001607	G5E935|Q96CA6	In_Frame_Del	DEL	ENST00000333167.8	hg19	CCDS2673.1																																																																																			.	.	.	none		0.618	ACAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342980.1	NM_001607		-	38167092	TGAGCAGCGTGA	-	38167081	7	5	115	1	0	1	0	1	0	0	0	0	104	1812	63	0	108	0	ACAA1	3	38167081	In_Frame_Del	DEL	TGAGCAGCGTGA	TCGA-BQ-5880-01A-11D-1589-08		38167081	159855349	8	7392											
DNAH1	25981	hgsc.bcm.edu	37	chr3	52398951	52398951	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtccgacctgtttcccaccAtcaaggaggaggacacggac	10	7	11	13	2	1	0	1	0	0	0	3	5	3	4	4	4	0	1	4	4	1	1			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr3:52398951A>G	ENST00000420323.2	+	34	5695	c.5434A>G	c.(5434-5436)Atc>Gtc	p.I1812V		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1812					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)		GTTTCCCACCATCAAGGAGGA	0.612																																					p.I1812V		Atlas-SNP	.											.	DNAH1	534	.	0			c.A5434G						PASS	.						86	89	88					3																	52398951		2137	4249	6386	SO:0001583	missense	25981	exon34			CCCACCATCAAGG	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.5434A>G	chr3.hg19:g.52398951A>G	ENSP00000401514:p.Ile1812Val	93.0	0.0	.		100.0	30.0	.	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	hg19	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	A	4.931	0.172935	0.09391	.	.	ENSG00000114841	ENST00000420323	T	0.37411	1.2	4.49	4.49	0.54785	.	0.143268	0.31358	N	0.007794	T	0.17704	0.0425	N	0.10945	0.07	0.46774	D	0.999194	B	0.12013	0.005	B	0.09377	0.004	T	0.08597	-1.0714	10	0.02654	T	1	.	13.8185	0.63306	1.0:0.0:0.0:0.0	.	1812	C9JXH6	.	V	1812	ENSP00000401514:I1812V	ENSP00000401514:I1812V	I	+	1	0	DNAH1	52373991	1.000000	0.71417	1.000000	0.80357	0.786000	0.44442	5.138000	0.64795	1.682000	0.51000	0.383000	0.25322	ATC	.	.	.	none		0.612	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		G	52398951	A	G	52398951	3	3	115	1	0	0	0	0	1	0	0	0	4599	217	8	3	5564	3	DNAH1	3	52398951	Missense_Mutation	SNP	A	TCGA-BQ-5880-01A-11D-1589-08	14231870	52398951	145623479	9	7393											
GBE1	2632	hgsc.bcm.edu	37	chr3	81698998	81698998	+	Frame_Shift_Del	DEL	A	A	-																															caatcataattcacattatcAccttcacgaaccacatactt																										TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr3:81698998delA	ENST00000429644.2	-	4	1147	c.504delT	c.(502-504)ggtfs	p.G168fs	GBE1_ENST00000489715.1_Frame_Shift_Del_p.G127fs	NM_000158.3	NP_000149	Q04446	GLGB_HUMAN	glucan (1,4-alpha-), branching enzyme 1	168					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)		TCACATTATCACCTTCACGAA	0.348									Glycogen Storage Disease, type IV																												p.D169fs		Atlas-INDEL	.											.	GBE1	111	.	0			c.505delG						PASS	.						102	101	101					3																	81698998		1874	4119	5993	SO:0001589	frameshift_variant	2632	exon4	Familial Cancer Database	Andersen Disease, Brancher deficiency	.		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.504delT	chr3.hg19:g.81698998delA	ENSP00000410833:p.Gly168fs	63.0	0.0	0		60.0	11.0	0.183333	NM_000158	B3KWV3|Q96EN0	Frame_Shift_Del	DEL	ENST00000429644.2	hg19	CCDS54612.1																																																																																			.	.	.	none		0.348	GBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352760.2			-	81698998	A	-	81698998	7	5	115	1	0	1	0	1	0	0	0	0	6277	146	6	0	1656	0	GBE1	3	81698998	Frame_Shift_Del	DEL	A	TCGA-BQ-5880-01A-11D-1589-08	29300047	81698998	116323432	10	7394											
NFXL1	152518	hgsc.bcm.edu	37	chr4	47901107	47901107	+	Missense_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	tcttacagtaacaagtagttGtgaccatctttggacaagga	13	12	9	7	0	2	1	0	1	2	0	2	3	2	3	1	2	2	3	1	2	5	5			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr4:47901107G>A	ENST00000507489.1	-	7	1033	c.857C>T	c.(856-858)aCa>aTa	p.T286I	NFXL1_ENST00000329043.3_Missense_Mutation_p.T286I|NFXL1_ENST00000381538.3_Missense_Mutation_p.T286I	NM_001278624.1	NP_001265553.1	Q6ZNB6	NFXL1_HUMAN	nuclear transcription factor, X-box binding-like 1	286						integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(4)	27						ACAAGTAGTTGTGACCATCTT	0.388																																					p.T286I		Atlas-SNP	.											.	NFXL1	79	.	0			c.C857T						PASS	.						85	79	81					4																	47901107		2203	4300	6503	SO:0001583	missense	152518	exon7			GTAGTTGTGACCA	AY134856	CCDS3478.2	4p12	2008-02-05			ENSG00000170448	ENSG00000170448			18726	protein-coding gene	gene with protein product	"ovarian zinc finger protein"						Standard	NM_152995		Approved	HOZFP	uc003gxp.3	Q6ZNB6	OTTHUMG00000128621	ENST00000507489.1:c.857C>T	chr4.hg19:g.47901107G>A	ENSP00000422037:p.Thr286Ile	55.0	0.0	.		54.0	10.0	.	NM_152995	B1Q2K1|Q86VG1|Q8WVH1	Missense_Mutation	SNP	ENST00000507489.1	hg19	CCDS3478.2	.	.	.	.	.	.	.	.	.	.	G	11.50	1.656404	0.29425	.	.	ENSG00000170448	ENST00000381538;ENST00000507489;ENST00000329043	T;T;T	0.42131	0.98;0.98;0.98	4.85	4.85	0.62838	.	0.275863	0.32918	N	0.005484	T	0.46151	0.1378	M	0.62723	1.935	0.43126	D	0.994855	P	0.36683	0.565	B	0.37888	0.26	T	0.53201	-0.8472	10	0.56958	D	0.05	-8.3899	17.9625	0.89090	0.0:0.0:1.0:0.0	.	286	Q6ZNB6	NFXL1_HUMAN	I	286	ENSP00000370949:T286I;ENSP00000422037:T286I;ENSP00000333113:T286I	ENSP00000333113:T286I	T	-	2	0	NFXL1	47595864	1.000000	0.71417	1.000000	0.80357	0.283000	0.27025	5.916000	0.69981	2.215000	0.71742	0.655000	0.94253	ACA	.	.	.	none		0.388	NFXL1-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361636.1	NM_152995		A	47901107	G	A	47901107	3	1	115	1	0	0	0	0	1	0	0	0	10395	1377	48	2	1946	2	NFXL1	4	47901107	Missense_Mutation	SNP	G	TCGA-BQ-5880-01A-11D-1589-08		47901107	143253169	11	7395											
SLC4A4	8671	hgsc.bcm.edu	37	chr4	72429512	72429512	+	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	tgtacatttttttcacagtcTgactgcccatactcagaaaa	12	14	5	10	0	3	2	2	1	1	1	3	2	3	2	1	0	3	1	1	0	4	5			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr4:72429512T>A	ENST00000264485.5	+	24	3219	c.3102T>A	c.(3100-3102)tcT>tcA	p.S1034S	SLC4A4_ENST00000425175.1_Intron|SLC4A4_ENST00000351898.6_Silent_p.S950S|SLC4A4_ENST00000340595.3_Silent_p.S990S	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	1034					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)	TTTCACAGTCTGACTGCCCAT	0.363																																					p.S1034S		Atlas-SNP	.											SLC4A4,NS,carcinoma,+2,1	SLC4A4	269	.	0			c.T3102A						PASS	.						124	135	131					4																	72429512		2203	4300	6503	SO:0001819	synonymous_variant	8671	exon24			ACAGTCTGACTGC	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.3102T>A	chr4.hg19:g.72429512T>A		199.0	0.0	.		195.0	35.0	.	NM_001098484	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Silent	SNP	ENST00000264485.5	hg19	CCDS43236.1																																																																																			.	.	.	none		0.363	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		A	72429512	T	A	72429512	2	1	115	1	0	0	0	0	0	0	0	1	14669	1567	55	5		5	SLC4A4	4	72429512	Silent	SNP	T	TCGA-BQ-5880-01A-11D-1589-08	24528405	72429512	118724764	12	7396											
PSD2	84249	hgsc.bcm.edu	37	chr5	139193812	139193812	+	Frame_Shift_Del	DEL	G	G	-																															tctgagctcagcagctcggaGgggttggagcctggtagtgc																										TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr5:139193812delG	ENST00000274710.3	+	4	1084	c.879delG	c.(877-879)gagfs	p.E293fs		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	293	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAGCTCGGAGGGGTTGGAGC	0.632																																					p.E293fs		Atlas-INDEL	.											.	PSD2	88	.	0			c.878delA						PASS	.						89	81	84					5																	139193812		2203	4300	6503	SO:0001589	frameshift_variant	84249	exon4			.	AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"Pleckstrin homology (PH) domain containing"	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.879delG	chr5.hg19:g.139193812delG	ENSP00000274710:p.Glu293fs	122.0	0.0	0		170.0	27.0	0.158824	NM_032289	D3DQD3|Q8N3J8	Frame_Shift_Del	DEL	ENST00000274710.3	hg19	CCDS4216.1																																																																																			.	.	.	none		0.632	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289		-	139193812	G	-	139193812	7	5	115	1	0	1	0	1	0	0	0	0	12657	991	35	0	889	0	PSD2	5	139193812	Frame_Shift_Del	DEL	G	TCGA-BQ-5880-01A-11D-1589-08		139193812	41721448	13	7397											
SLC26A8	116369	hgsc.bcm.edu	37	chr6	35949921	35949921	+	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	taaggaatcatgtcaataagCgtctggctggtttctgtggc	9	13	12	7	1	4	0	2	0	2	0	4	1	4	1	0	4	1	2	0	4	4	3	rs547194034		TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr6:35949921C>T	ENST00000490799.1	-	8	1355	c.1002G>A	c.(1000-1002)acG>acA	p.T334T	SLC26A8_ENST00000355574.2_Silent_p.T334T|SLC26A8_ENST00000394602.2_Silent_p.T229T	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						TGTCAATAAGCGTCTGGCTGG	0.423													C|||	1	0.000199681	0	0.0014	5008	,	,		20134	0		0	False		,,,				2504	0				p.T334T		Atlas-SNP	.											.	SLC26A8	95	.	0			c.G1002A						PASS	.						123	113	116					6																	35949921		2203	4300	6503	SO:0001819	synonymous_variant	116369	exon8			AATAAGCGTCTGG	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.1002G>A	chr6.hg19:g.35949921C>T		146.0	0.0	.		125.0	19.0	.	NM_052961		Silent	SNP	ENST00000490799.1	hg19	CCDS4813.1																																																																																			.	.	.	none		0.423	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2			T	35949921	C	T	35949921	2	4	115	1	0	0	0	0	0	0	0	1	14536	755	27	1		1	SLC26A8	6	35949921	Silent	SNP	C	TCGA-BQ-5880-01A-11D-1589-08		35949921	135165146	14	7398											
RBAK	57786	hgsc.bcm.edu	37	chr7	5104736	5104736	+	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	atgtggaaagttattcaatgAgttgtcatactatactgaac	14	14	8	5	0	2	2	2	2	0	0	2	3	2	3	0	1	3	2	0	1	7	6			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr7:5104736A>T	ENST00000353796.3	+	6	1973	c.1649A>T	c.(1648-1650)gAg>gTg	p.E550V	RBAK-RBAKDN_ENST00000396904.2_Intron|RBAK-RBAKDN_ENST00000407184.1_Intron|RBAK_ENST00000396912.1_Missense_Mutation_p.E550V	NM_001204456.1	NP_001191385.1	Q9NYW8	RBAK_HUMAN	RB-associated KRAB zinc finger	550	Interaction with AR.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(2)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	10		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0916)|OV - Ovarian serous cystadenocarcinoma(56;2.44e-14)		TTATTCAATGAGTTGTCATAC	0.393																																					p.E550V		Atlas-SNP	.											.	RBAK	82	.	0			c.A1649T						PASS	.						63	63	63					7																	5104736		2203	4299	6502	SO:0001583	missense	57786	exon6			TCAATGAGTTGTC	AF226869	CCDS5337.1	7p22.1	2013-01-08			ENSG00000146587	ENSG00000146587		"Zinc fingers, C2H2-type", "-"	17680	protein-coding gene	gene with protein product		608191					Standard	NM_021163		Approved	ZNF769	uc003sns.1	Q9NYW8	OTTHUMG00000121155	ENST00000353796.3:c.1649A>T	chr7.hg19:g.5104736A>T	ENSP00000275423:p.Glu550Val	94.0	0.0	.		107.0	35.0	.	NM_001204456	A6NDF2|A8KAK4|B2RN44|B9EGS1|F8W6M7	Missense_Mutation	SNP	ENST00000353796.3	hg19	CCDS5337.1	.	.	.	.	.	.	.	.	.	.	A	13.27	2.187436	0.38609	.	.	ENSG00000146587	ENST00000353796;ENST00000396912	T;T	0.14516	2.5;2.5	3.76	3.76	0.43208	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.572849	0.15837	N	0.242235	T	0.15003	0.0362	L	0.33753	1.03	0.26673	N	0.971686	P	0.42123	0.771	P	0.46885	0.53	T	0.13872	-1.0493	8	.	.	.	.	11.0559	0.47918	1.0:0.0:0.0:0.0	.	550	Q9NYW8	RBAK_HUMAN	V	550	ENSP00000275423:E550V;ENSP00000380120:E550V	.	E	+	2	0	RBAK	5071262	0.000000	0.05858	0.706000	0.30403	0.897000	0.52465	0.042000	0.13949	1.931000	0.55961	0.454000	0.30748	GAG	.	.	.	none		0.393	RBAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241640.2	NM_021163		T	5104736	A	T	5104736	3	4	115	1	0	0	0	0	1	0	0	0	13113	304	11	5	1663	5	RBAK	7	5104736	Missense_Mutation	SNP	A	TCGA-BQ-5880-01A-11D-1589-08		5104736	154033927	15	7399											
SP4	6671	hgsc.bcm.edu	37	chr7	21468915	21468915	+	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	cattttgggtaggactctcaGccctctcctctggctttact	5	15	8	13	0	3	0	1	0	3	0	5	1	3	1	2	3	2	2	2	3	2	5			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr7:21468915G>A	ENST00000222584.3	+	3	350	c.132G>A	c.(130-132)caG>caA	p.Q44Q		NM_003112.3	NP_003103.2	Q02446	SP4_HUMAN	Sp4 transcription factor	44					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						AGGACTCTCAGCCCTCTCCTC	0.483																																					p.Q44Q		Atlas-SNP	.											.	SP4	91	.	0			c.G132A						PASS	.						34	37	36					7																	21468915		2201	4300	6501	SO:0001819	synonymous_variant	6671	exon3			CTCTCAGCCCTCT		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.132G>A	chr7.hg19:g.21468915G>A		60.0	0.0	.		71.0	9.0	.	NM_003112	O60402|Q32M52	Silent	SNP	ENST00000222584.3	hg19	CCDS5373.1																																																																																			.	.	.	none		0.483	SP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211617.2	NM_003112		A	21468915	G	A	21468915	2	1	115	1	0	0	0	0	0	0	0	1	14979	962	34	2		2	SP4	7	21468915	Silent	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	16364179	21468915	137669748	16	7400											
CCDC132	55610	hgsc.bcm.edu	37	chr7	92932848	92932848	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgttaagtcaaatttcagcAtcttgcaacttcatgtaagt	12	15	6	8	0	4	0	3	0	1	0	4	0	4	0	0	0	3	4	0	0	4	5			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr7:92932848A>G	ENST00000305866.5	+	17	1566	c.1438A>G	c.(1438-1440)Atc>Gtc	p.I480V	CCDC132_ENST00000541136.1_Missense_Mutation_p.I291V|CCDC132_ENST00000317751.6_Missense_Mutation_p.I211V|CCDC132_ENST00000535481.1_Missense_Mutation_p.I200V|CCDC132_ENST00000544910.1_Missense_Mutation_p.I450V	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	480						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)			AAATTTCAGCATCTTGCAACT	0.308																																					p.I480V		Atlas-SNP	.											.	CCDC132	136	.	0			c.A1438G						PASS	.						138	134	135					7																	92932848		1818	4077	5895	SO:0001583	missense	55610	exon17			TTCAGCATCTTGC	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.1438A>G	chr7.hg19:g.92932848A>G	ENSP00000307666:p.Ile480Val	210.0	0.0	.		254.0	48.0	.	NM_017667	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	hg19	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	A	11.98	1.801621	0.31869	.	.	ENSG00000004766	ENST00000305866;ENST00000544910;ENST00000541136;ENST00000535481;ENST00000317751	T	0.39229	1.09	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	T	0.44829	0.1312	L	0.27053	0.805	0.80722	D	1	P;P;P	0.38863	0.518;0.65;0.518	P;P;P	0.54140	0.558;0.743;0.558	T	0.19257	-1.0311	10	0.14252	T	0.57	-8.589	15.0541	0.71897	1.0:0.0:0.0:0.0	.	200;450;480	B4DS55;F5H5U7;Q96JG6	.;.;CC132_HUMAN	V	480;450;291;200;211	ENSP00000325582:I211V	ENSP00000307666:I480V	I	+	1	0	CCDC132	92770784	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.051000	0.93849	2.200000	0.70718	0.460000	0.39030	ATC	.	.	.	none		0.308	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667		G	92932848	A	G	92932848	3	3	115	1	0	0	0	0	1	0	0	0	2769	217	8	3	1546	3	CCDC132	7	92932848	Missense_Mutation	SNP	A	TCGA-BQ-5880-01A-11D-1589-08	71463933	92932848	66205815	17	7401											
STAG3	10734	hgsc.bcm.edu	37	chr7	99779767	99779767	+	Frame_Shift_Del	DEL	T	T	-																															gactttgaagacagcttgaaTcgcaatgtgaagaagagagc																										TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr7:99779767delT	ENST00000426455.1	+	3	578	c.171delT	c.(169-171)aatfs	p.N57fs	STAG3_ENST00000394018.2_Frame_Shift_Del_p.N57fs|STAG3_ENST00000317296.5_Frame_Shift_Del_p.N57fs	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	57					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ACAGCTTGAATCGCAATGTGA	0.438																																					p.N57fs		Atlas-INDEL	.											.	STAG3	121	.	0			c.170delA						PASS	.						122	112	115					7																	99779767		2203	4300	6503	SO:0001589	frameshift_variant	10734	exon3			.	AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.171delT	chr7.hg19:g.99779767delT	ENSP00000400359:p.Asn57fs	76.0	0.0	0		71.0	10.0	0.140845	NM_012447	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Frame_Shift_Del	DEL	ENST00000426455.1	hg19	CCDS34703.1																																																																																			.	.	.	none		0.438	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447		-	99779767	T	-	99779767	7	5	115	1	0	1	0	1	0	0	0	0	15256	1432	50	0	177	0	STAG3	7	99779767	Frame_Shift_Del	DEL	T	TCGA-BQ-5880-01A-11D-1589-08	6846919	99779767	59358896	18	7402											
RGP1	57704	hgsc.bcm.edu	37	chr9	35751270	35751270	+	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	attctttctctaggccttcaGgatgtccggtttccccagga	6	14	9	12	1	3	0	1	0	2	0	6	2	5	2	4	4	0	1	4	4	1	5			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr9:35751270G>A	ENST00000378103.3	-	0	0				RGP1_ENST00000378078.4_Silent_p.Q165Q|RGP1_ENST00000456972.2_Silent_p.Q205Q|GBA2_ENST00000378094.4_5'Flank|GBA2_ENST00000545786.1_5'Flank|MSMP_ENST00000414286.1_5'Flank	NM_020944.2	NP_065995.1	Q9HCG7	GBA2_HUMAN	glucosidase, beta (bile acid) 2						bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|central nervous system neuron development (GO:0021954)|glucosylceramide catabolic process (GO:0006680)|glycoside catabolic process (GO:0016139)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)	beta-glucosidase activity (GO:0008422)|glucosylceramidase activity (GO:0004348)			NS(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(4)|skin(3)	21	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TAGGCCTTCAGGATGTCCGGT	0.498																																					p.Q165Q		Atlas-SNP	.											.	RGP1	60	.	0			c.G495A						PASS	.						226	221	222					9																	35751270		1947	4138	6085	SO:0001631	upstream_gene_variant	9827	exon6			CCTTCAGGATGTC	AJ309567	CCDS6589.1	9p13.2	2013-09-11			ENSG00000070610	ENSG00000070610			18986	protein-coding gene	gene with protein product	"bile acid beta-glucosidase", "non-lysosomal glucosylceramidase"	609471	"spastic paraplegia 46 (autosomal recessive)"	SPG46		11489889, 23332916, 23332917	Standard	NM_020944		Approved	KIAA1605, AD035, DKFZp762K054	uc003zxw.3	Q9HCG7	OTTHUMG00000021024		chr9.hg19:g.35751270G>A	Exception_encountered	404.0	0.0	.		410.0	87.0	.	NM_001080496	D3DRP2|Q5TCV6|Q96A51|Q96LY1|Q96SJ2|Q9H2L8	Silent	SNP	ENST00000378103.3	hg19	CCDS6589.1																																																																																			.	.	.	none		0.498	GBA2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055456.1	NM_020944		A	35751270	G	A	35751270	1	1	115	0	1	0	0	0	0	0	0	0	13297	991	35	2		2	RGP1	9	35751270	5'Flank	SNP	G	TCGA-BQ-5880-01A-11D-1589-08		35751270	105462161	19	7403											
NUP214	8021	hgsc.bcm.edu	37	chr9	134020018	134020018	+	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	agctgcttcattctcctttgGatcatctggttttaagccta	7	17	7	10	0	4	0	2	0	2	0	5	1	4	1	2	2	3	3	2	2	2	6			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr9:134020018G>T	ENST00000359428.5	+	12	1790	c.1646G>T	c.(1645-1647)gGa>gTa	p.G549V	RP11-544A12.4_ENST00000590461.1_RNA|RP11-544A12.4_ENST00000589667.1_RNA|RP11-544A12.4_ENST00000586290.1_RNA|NUP214_ENST00000451030.1_Missense_Mutation_p.G549V|RP11-544A12.4_ENST00000415391.2_RNA|RP11-544A12.4_ENST00000587408.1_RNA|RP11-544A12.4_ENST00000589540.1_RNA|NUP214_ENST00000411637.2_Missense_Mutation_p.G549V|RP11-544A12.4_ENST00000587264.1_RNA|RP11-544A12.4_ENST00000588378.1_RNA			P35658	NU214_HUMAN	nucleoporin 214kDa	549	11 X 5 AA approximate repeats.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		TTCTCCTTTGGATCATCTGGT	0.537			T	"DEK, SET, ABL1"	"AML, T-ALL"																																p.G549V	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.G1646T						PASS	.						82	78	79					9																	134020018		2203	4300	6503	SO:0001583	missense	8021	exon12			CCTTTGGATCATC	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.1646G>T	chr9.hg19:g.134020018G>T	ENSP00000352400:p.Gly549Val	125.0	0.0	.		107.0	24.0	.	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	hg19	CCDS6940.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.7|21.7	4.184253|4.184253	0.78677|0.78677	.|.	.|.	ENSG00000126883|ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899|ENST00000530863	T;T;T|.	0.40756|.	1.24;1.02;1.25|.	5.89|5.89	5.89|5.89	0.94794|0.94794	.|.	0.000000|.	0.42172|.	D|.	0.000758|.	T|T	0.45935|0.45935	0.1367|0.1367	N|N	0.08118|0.08118	0|0	0.58432|0.58432	D|D	0.999998|0.999998	D;D|.	0.63046|.	0.992;0.992|.	P;P|.	0.59357|.	0.856;0.856|.	T|T	0.41034|0.41034	-0.9531|-0.9531	10|5	0.51188|.	T|.	0.08|.	-8.3011|-8.3011	17.3793|17.3793	0.87400|0.87400	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	549;549|.	P35658-4;P35658|.	.;NU214_HUMAN|.	V|C	549;549;549;549;142|124	ENSP00000352400:G549V;ENSP00000396576:G549V;ENSP00000405014:G549V|.	ENSP00000352400:G549V|.	G|W	+|+	2|3	0|0	NUP214|NUP214	133009839|133009839	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.875000|0.875000	0.50365|0.50365	5.666000|5.666000	0.68059|0.68059	2.778000|2.778000	0.95560|0.95560	0.655000|0.655000	0.94253|0.94253	GGA|TGG	.	.	.	none		0.537	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		T	134020018	G	T	134020018	3	4	115	1	0	0	0	0	1	0	0	0	10769	1174	41	4	1692	4	NUP214	9	134020018	Missense_Mutation	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	98268748	134020018	7193413	20	7404											
CUBN	8029	hgsc.bcm.edu	37	chr10	16918967	16918967	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agtagaagttaagcagaaccGgcccagcgatggtgagggga	13	5	16	7	2	0	3	0	1	0	2	0	5	0	4	2	4	3	3	2	4	4	2	rs143741363		TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr10:16918967G>A	ENST00000377833.4	-	57	9100	c.9035C>T	c.(9034-9036)cCg>cTg	p.P3012L		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	3012	CUB 22. {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)	AAGCAGAACCGGCCCAGCGAT	0.483													G|||	1	0.000199681	0	0	5008	,	,		17695	0.001		0	False		,,,				2504	0				p.P3012L		Atlas-SNP	.											.	CUBN	515	.	0			c.C9035T						PASS	.	G	LEU/PRO	2,4404	4.2+/-10.8	0,2,2201	124	108	114		9035	5.8	0.3	10	dbSNP_134	114	1,8599	1.2+/-3.3	0,1,4299	no	missense	CUBN	NM_001081.3	98	0,3,6500	AA,AG,GG		0.0116,0.0454,0.0231	probably-damaging	3012/3624	16918967	3,13003	2203	4300	6503	SO:0001583	missense	8029	exon57			AGAACCGGCCCAG	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.9035C>T	chr10.hg19:g.16918967G>A	ENSP00000367064:p.Pro3012Leu	113.0	0.0	.		119.0	18.0	.	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.015130	0.75161	4.54E-4	1.16E-4	ENSG00000107611	ENST00000377833	T	0.16897	2.31	5.8	5.8	0.92144	CUB (5);	0.000000	0.46758	D	0.000275	T	0.22781	0.0550	L	0.48362	1.52	0.80722	D	1	D	0.55800	0.973	P	0.44897	0.463	T	0.00402	-1.1762	10	0.54805	T	0.06	.	18.8345	0.92155	0.0:0.0:1.0:0.0	.	3012	O60494	CUBN_HUMAN	L	3012	ENSP00000367064:P3012L	ENSP00000367064:P3012L	P	-	2	0	CUBN	16958973	1.000000	0.71417	0.339000	0.25562	0.006000	0.05464	7.336000	0.79245	2.735000	0.93741	0.655000	0.94253	CCG	.	G|1.000;A|0.000	0.000	weak		0.483	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		A	16918967	G	A	16918967	3	1	115	1	0	0	0	0	1	0	0	0	4053	1116	39	1	1880	1	CUBN	10	16918967	Missense_Mutation	SNP	G	TCGA-BQ-5880-01A-11D-1589-08		16918967	118615780	21	7405											
ACADSB	36	hgsc.bcm.edu	37	chr10	124793900	124793900	+	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	aaatttcctgacttgtttgtCttcttggaagattcctcctc	7	18	6	10	0	2	2	0	1	2	1	6	3	5	3	3	1	0	1	3	1	2	6			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr10:124793900C>T	ENST00000358776.4	+	2	85	c.71C>T	c.(70-72)tCt>tTt	p.S24F	ACADSB_ENST00000496730.2_3'UTR|ACADSB_ENST00000368869.4_5'UTR	NM_001609.3	NP_001600.1	P45954	ACDSB_HUMAN	acyl-CoA dehydrogenase, short/branched chain	24					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)	ACTTGTTTGTCTTCTTGGAAG	0.363																																					p.S24F		Atlas-SNP	.											.	ACADSB	45	.	0			c.C71T						PASS	.						143	141	142					10																	124793900		2203	4300	6503	SO:0001583	missense	36	exon2			GTTTGTCTTCTTG	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.71C>T	chr10.hg19:g.124793900C>T	ENSP00000357873:p.Ser24Phe	118.0	0.0	.		168.0	37.0	.	NM_001609	B4DQ51|Q5SQN6|Q96CX7	Missense_Mutation	SNP	ENST00000358776.4	hg19	CCDS7634.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.85|16.85	3.235388|3.235388	0.58886|0.58886	.|.	.|.	ENSG00000196177|ENSG00000196177	ENST00000411816|ENST00000358776	.|D	.|0.97430	.|-4.38	4.95|4.95	4.02|4.02	0.46733|0.46733	.|.	.|0.689788	.|0.14097	.|N	.|0.341677	D|D	0.93792|0.93792	0.8015|0.8015	L|L	0.27053|0.27053	0.805|0.805	0.26364|0.26364	N|N	0.976999|0.976999	.|P	.|0.45283	.|0.855	.|B	.|0.41510	.|0.359	D|D	0.87882|0.87882	0.2678|0.2678	5|10	.|0.49607	.|T	.|0.09	.|.	12.9162|12.9162	0.58207|0.58207	0.0:0.6883:0.3117:0.0|0.0:0.6883:0.3117:0.0	.|.	.|24	.|P45954	.|ACDSB_HUMAN	F|F	30|24	.|ENSP00000357873:S24F	.|ENSP00000357873:S24F	L|S	+|+	1|2	0|0	ACADSB|ACADSB	124783890|124783890	0.776000|0.776000	0.28616|0.28616	0.955000|0.955000	0.39395|0.39395	0.812000|0.812000	0.45895|0.45895	1.477000|1.477000	0.35431|0.35431	1.167000|1.167000	0.42706|0.42706	0.591000|0.591000	0.81541|0.81541	CTT|TCT	.	.	.	none		0.363	ACADSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050843.1	NM_001609		T	124793900	C	T	124793900	3	4	115	1	0	0	0	0	1	0	0	0	115	913	32	2	77	2	ACADSB	10	124793900	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	107874933	124793900	10740847	22	7406											
LGR4	55366	hgsc.bcm.edu	37	chr11	27390335	27390336	+	Frame_Shift_Ins	INS	-	-	A																															tcattatatcttttgcagatINSaagcttctttcgacagttgc																										TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr11:27390335_27390336insA	ENST00000379214.4	-	18	2377_2378	c.1934_1935insT	c.(1933-1935)ttafs	p.L645fs	LGR4_ENST00000389858.4_Frame_Shift_Ins_p.L621fs	NM_018490.2	NP_060960.2	Q9BXB1	LGR4_HUMAN	leucine-rich repeat containing G protein-coupled receptor 4	645					bone mineralization (GO:0030282)|bone remodeling (GO:0046849)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cell differentiation involved in metanephros development (GO:0072202)|epithelial cell proliferation (GO:0050673)|innate immune response (GO:0045087)|male genitalia development (GO:0030539)|metanephric glomerulus development (GO:0072224)|metanephric nephron tubule morphogenesis (GO:0072282)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(10)|ovary(1)	32						CTTTTGCAGATAAGCTTCTTTC	0.431																																					p.L645fs		Atlas-INDEL	.											.	LGR4	87	.	0			c.1935_1936insT						PASS	.																																			SO:0001589	frameshift_variant	55366	exon18			.	AF257182	CCDS31449.1	11p14-p13	2012-08-21	2011-01-25	2004-11-12	ENSG00000205213	ENSG00000205213		"GPCR / Class A : Orphans"	13299	protein-coding gene	gene with protein product		606666	"G protein-coupled receptor 48", "leucine-rich repeat-containing G protein-coupled receptor 4"	GPR48		10894923	Standard	NM_018490		Approved		uc001mrj.4	Q9BXB1	OTTHUMG00000133508	ENST00000379214.4:c.1935dupT	chr11.hg19:g.27390337_27390337dupA	ENSP00000368516:p.Leu645fs	102.0	0.0	0		112.0	21.0	0.1875	NM_018490	A6NCH3|G5E9B3|Q8N537|Q9NYD1	Frame_Shift_Ins	INS	ENST00000379214.4	hg19	CCDS31449.1																																																																																			.	.	.	none		0.431	LGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257467.1	NM_018490		A	27390336	-	A	27390335	7	5	115	1	0	1	1	0	0	0	0	0	8763	1403	49	0	924	0	LGR4	11	27390335	Frame_Shift_Ins	INS	-	TCGA-BQ-5880-01A-11D-1589-08		27390335	107616181	23	7407											
OR8J3	81168	hgsc.bcm.edu	37	chr11	55904466	55904466	+	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	accgtgactgctatcatatgCgaagcgcaggtggaaaaggc	12	7	13	9	3	1	1	1	1	0	0	1	3	1	2	1	3	3	2	1	3	5	2			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr11:55904466C>T	ENST00000301529.1	-	1	728	c.729G>A	c.(727-729)tcG>tcA	p.S243S		NM_001004064.1	NP_001004064.1	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J, member 3	243						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S243S(1)		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)					CTATCATATGCGAAGCGCAGG	0.403																																					p.S243S		Atlas-SNP	.											OR8J3,NS,carcinoma,0,3	OR8J3	112	.	1	Substitution - coding silent(1)	endometrium(1)	c.G729A						PASS	.						122	113	116					11																	55904466		2201	4296	6497	SO:0001819	synonymous_variant	81168	exon1			CATATGCGAAGCG		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.729G>A	chr11.hg19:g.55904466C>T		119.0	1.0	.		117.0	25.0	.	NM_001004064	Q6IFB6|Q96RC2	Silent	SNP	ENST00000301529.1	hg19	CCDS31520.1																																																																																			.	.	.	none		0.403	OR8J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391542.1	NM_001004064		T	55904466	C	T	55904466	2	4	115	1	0	0	0	0	0	0	0	1	11249	755	27	1		1	OR8J3	11	55904466	Silent	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	28514131	55904466	79102050	24	7408											
DPAGT1	1798	hgsc.bcm.edu	37	chr11	118971040	118971040	+	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	gtgactggccagcctctaggCcgttaattcctgctaggata	8	11	11	11	1	1	1	0	1	1	0	2	2	2	2	4	3	2	2	4	3	4	5			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr11:118971040C>T	ENST00000409993.2	-	6	2126	c.575G>A	c.(574-576)gGc>gAc	p.G192D	DPAGT1_ENST00000445653.1_5'Flank|DPAGT1_ENST00000354202.4_Missense_Mutation_p.G192D|DPAGT1_ENST00000432443.2_Missense_Mutation_p.G85D			Q9H3H5	GPT_HUMAN	dolichyl-phosphate (UDP-N-acetylglucosamine) N-acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	192			G -> S (in CMSTA2). {ECO:0000269|PubMed:22742743}.		cellular protein metabolic process (GO:0044267)|dolichol biosynthetic process (GO:0019408)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|protein oligomerization (GO:0051259)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	phospho-N-acetylmuramoyl-pentapeptide-transferase activity (GO:0008963)|transferase activity, transferring glycosyl groups (GO:0016757)|UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity (GO:0003975)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2)	17	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.55e-05)		AGCCTCTAGGCCGTTAATTCC	0.507											OREG0021396	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G192D		Atlas-SNP	.											.	DPAGT1	43	.	0			c.G575A						PASS	.						107	104	105					11																	118971040		2200	4295	6495	SO:0001583	missense	1798	exon4			TCTAGGCCGTTAA	Z82022	CCDS8411.1	11q23.3	2007-12-14			ENSG00000172269	ENSG00000172269	2.7.8.15		2995	protein-coding gene	gene with protein product		191350		DPAGT2, DPAGT		8244387	Standard	NM_001382		Approved	GPT, D11S366, DGPT, ALG7, CDG-Ij	uc001pvi.3	Q9H3H5	OTTHUMG00000153533	ENST00000409993.2:c.575G>A	chr11.hg19:g.118971040C>T	ENSP00000386597:p.Gly192Asp	153.0	0.0	.	1492	166.0	28.0	.	NM_001382	O15216|Q86WV9|Q9BWE6	Missense_Mutation	SNP	ENST00000409993.2	hg19	CCDS8411.1	.	.	.	.	.	.	.	.	.	.	C	34	5.350440	0.95830	.	.	ENSG00000172269	ENST00000409993;ENST00000354202;ENST00000432443	D;D;D	0.98914	-5.23;-5.23;-5.23	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.99554	0.9840	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	0.97880	1.0291	10	0.87932	D	0	-21.1374	18.6978	0.91607	0.0:1.0:0.0:0.0	.	85;192	E7EW40;Q9H3H5	.;GPT_HUMAN	D	192;192;85	ENSP00000386597:G192D;ENSP00000346142:G192D;ENSP00000404036:G85D	ENSP00000346142:G192D	G	-	2	0	DPAGT1	118476250	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.652000	0.90054	0.655000	0.94253	GGC	.	.	.	none		0.507	DPAGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331527.2	NM_001382		T	118971040	C	T	118971040	3	4	115	1	0	0	0	0	1	0	0	0	4712	739	26	2	675	2	DPAGT1	11	118971040	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	63066574	118971040	16035476	25	7409											
PRB4	5545	hgsc.bcm.edu	37	chr12	11461597	11461597	+	Frame_Shift_Del	DEL	C	C	-																															gggtaccttgggactggtttCctccttgtgggggtggtctt																										TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr12:11461597delC	ENST00000535904.1	-	3	353	c.320delG	c.(319-321)ggafs	p.G107fs	PRB4_ENST00000279575.1_Frame_Shift_Del_p.G107fs|PRB4_ENST00000445719.2_Frame_Shift_Del_p.G107fs			P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4	128	9.5 X 21 AA tandem repeats of K-P-[EQ]- [GR]-[PR]-[PR]-P-Q-G-G-N-Q-[PS]-[QH]- [RG]-[PT]-P-P-[PH]-P-G.					extracellular region (GO:0005576)				breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|skin(4)|upper_aerodigestive_tract(3)	30						GGACTGGTTTCCTCCTTGTGG	0.612										HNSCC(22;0.051)																											p.G107fs		Atlas-INDEL	.											.	PRB4	59	.	0			c.321delA						PASS	.						190	200	197					12																	11461597		2203	4299	6502	SO:0001589	frameshift_variant	5545	exon3			.		CCDS8641.1, CCDS58208.1	12p13.2	2012-10-02			ENSG00000230657	ENSG00000230657			9340	protein-coding gene	gene with protein product		180990					Standard	NM_002723		Approved		uc001qzt.4	P10163	OTTHUMG00000169116	ENST00000535904.1:c.320delG	chr12.hg19:g.11461597delC	ENSP00000442834:p.Gly107fs	633.0	0.0	0		789.0	116.0	0.147022	NM_002723	A1L439|O00600|P02813|P10161|P10162|P81489	Frame_Shift_Del	DEL	ENST00000535904.1	hg19	CCDS8641.1																																																																																			.	.	.	none		0.612	PRB4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402308.1	NM_002723		-	11461597	C	-	11461597	7	5	115	1	0	1	0	1	0	0	0	0	12455	855	30	0	427	0	PRB4	12	11461597	Frame_Shift_Del	DEL	C	TCGA-BQ-5880-01A-11D-1589-08		11461597	122390298	26	7410											
MLL2	8085	hgsc.bcm.edu	37	chr12	49443557	49443558	+	Frame_Shift_Del	DEL	AT	AT	-																															agctgtcccagcatcgcacaAtagtgagtcatcagtctctg																								rs201794205		TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr12:49443557_49443558delAT	ENST00000301067.7	-	11	3812_3813	c.3813_3814delAT	c.(3811-3816)ctattgfs	p.LL1271fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1271					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)										GCATCGCACAATAGTGAGTCAT	0.609																																					p.1272_1272del		Atlas-INDEL	.											.	MLL2	1173	.	0			c.3814_3815del						PASS	.																																			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.3813_3814delAT	chr12.hg19:g.49443557_49443558delAT	ENSP00000301067:p.Leu1271fs	116.0	0.0	0		158.0	24.0	0.151899	NM_003482	O14687	Frame_Shift_Del	DEL	ENST00000301067.7	hg19	CCDS44873.1																																																																																			.	.	.	none		0.609	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			-	49443558	AT	-	49443557	7	5	115	1	0	1	0	1	0	0	0	0	9628	98	4	0	12975	0	MLL2	12	49443557	Frame_Shift_Del	DEL	AT	TCGA-BQ-5880-01A-11D-1589-08	37981960	49443557	84408338	27	7411											
DGKA	1606	hgsc.bcm.edu	37	chr12	56346149	56346149	+	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	aagaacaagctatggtacttCgaatttgccacatctgaatc	14	11	7	9	1	1	2	0	1	1	1	3	3	1	2	1	1	4	2	1	1	7	4	rs546159503		TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr12:56346149C>G	ENST00000331886.5	+	20	2131	c.1677C>G	c.(1675-1677)ttC>ttG	p.F559L	DGKA_ENST00000551156.1_Missense_Mutation_p.F559L|DGKA_ENST00000549079.2_3'UTR|DGKA_ENST00000394147.1_Missense_Mutation_p.F559L	NM_001345.4	NP_001336.2	P23743	DGKA_HUMAN	diacylglycerol kinase, alpha 80kDa	559					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)	TATGGTACTTCGAATTTGCCA	0.478																																					p.F559L		Atlas-SNP	.											.	DGKA	70	.	0			c.C1677G						PASS	.						163	139	147					12																	56346149		2203	4300	6503	SO:0001583	missense	1606	exon20			GTACTTCGAATTT	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.1677C>G	chr12.hg19:g.56346149C>G	ENSP00000328405:p.Phe559Leu	133.0	0.0	.		172.0	57.0	.	NM_201554	O75481|O75482|O75483|O95217|Q3ZE25|Q8IZ56|Q8N5Q2	Missense_Mutation	SNP	ENST00000331886.5	hg19	CCDS8896.1	.	.	.	.	.	.	.	.	.	.	C	14.00	2.404771	0.42613	.	.	ENSG00000065357	ENST00000331886;ENST00000555218;ENST00000394147;ENST00000551156;ENST00000552903	T;T;T;T;T	0.39229	1.09;1.67;1.09;1.09;1.67	5.02	-9.21	0.00678	Diacylglycerol kinase, accessory domain (2);	0.053094	0.85682	N	0.000000	T	0.34600	0.0903	L	0.43923	1.385	0.45914	D	0.998757	B;B	0.29378	0.01;0.243	B;B	0.42214	0.054;0.38	T	0.43294	-0.9400	10	0.49607	T	0.09	.	11.684	0.51474	0.0:0.1096:0.2082:0.6822	.	478;559	G3V4E1;P23743	.;DGKA_HUMAN	L	559;478;559;559;169	ENSP00000328405:F559L;ENSP00000451743:F478L;ENSP00000377703:F559L;ENSP00000450359:F559L;ENSP00000451518:F169L	ENSP00000328405:F559L	F	+	3	2	DGKA	54632416	0.169000	0.23002	0.857000	0.33713	0.979000	0.70002	-0.687000	0.05156	-1.471000	0.01886	-0.339000	0.08088	TTC	.	.	.	none		0.478	DGKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407291.1			G	56346149	C	G	56346149	3	3	115	1	0	0	0	0	1	0	0	0	4467	883	31	4	1751	4	DGKA	12	56346149	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	6902592	56346149	77505746	28	7412											
RDH11	51109	hgsc.bcm.edu	37	chr14	68157017	68157017	+	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	cctgcattgtagaatttctcGccctgcaggttatggaagtg	8	13	11	9	1	1	1	0	0	1	1	2	2	1	2	2	2	2	4	2	2	4	4			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr14:68157017G>A	ENST00000381346.4	-	5	686	c.576C>T	c.(574-576)ggC>ggT	p.G192G	RP11-1012A1.4_ENST00000553306.1_Missense_Mutation_p.A23V|RDH11_ENST00000428130.2_Intron|RDH11_ENST00000553384.1_Silent_p.G179G|RP11-1012A1.4_ENST00000554493.1_5'Flank	NM_001252650.1|NM_016026.3	NP_001239579.1|NP_057110.3	Q8TC12	RDH11_HUMAN	retinol dehydrogenase 11 (all-trans/9-cis/11-cis)	192					adaptation of rhodopsin mediated signaling (GO:0016062)|phototransduction, visible light (GO:0007603)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|photoreceptor inner segment (GO:0001917)	NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)			breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(3)|ovary(1)	12				all cancers(60;0.00047)|OV - Ovarian serous cystadenocarcinoma(108;0.00206)|BRCA - Breast invasive adenocarcinoma(234;0.00924)	Vitamin A(DB00162)	AGAATTTCTCGCCCTGCAGGT	0.517																																					p.G192G		Atlas-SNP	.											.	RDH11	21	.	0			c.C576T						PASS	.						186	159	168					14																	68157017		2203	4300	6503	SO:0001819	synonymous_variant	51109	exon5			TTTCTCGCCCTGC	AF151840	CCDS32104.1, CCDS58326.1	14q24.1	2013-10-15	2006-05-09		ENSG00000072042	ENSG00000072042	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	17964	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 7C, member 1", "androgen-regulated short-chain dehydrogenase/reductase 1"	607849	"retinol dehydrogenase 11 (all-trans and 9-cis)"			12226107, 8018917, 19027726	Standard	NM_016026		Approved	MDT1, SDR7C1, ARSDR1	uc001xjv.4	Q8TC12	OTTHUMG00000171196	ENST00000381346.4:c.576C>T	chr14.hg19:g.68157017G>A		110.0	0.0	.		90.0	26.0	.	NM_016026	A6NDK3|A8K062|B2RB26|B4DDW0|Q0QD40|Q6IAH5|Q9NRW0|Q9Y391	Silent	SNP	ENST00000381346.4	hg19	CCDS32104.1	.	.	.	.	.	.	.	.	.	.	G	9.466	1.094486	0.20471	.	.	ENSG00000258466	ENST00000557564	.	.	.	5.67	-11.3	0.00108	.	.	.	.	.	T	0.33440	0.0863	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41124	-0.9526	4	.	.	.	.	3.1001	0.06323	0.2592:0.1913:0.4203:0.1292	.	.	.	.	V	23	.	.	A	-	2	0	RP11-1012A1.4	67226770	0.000000	0.05858	0.230000	0.23976	0.971000	0.66376	-1.633000	0.02022	-2.268000	0.00685	-0.150000	0.13652	GCG	.	.	.	none		0.517	RDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412257.3			A	68157017	G	A	68157017	2	1	115	1	0	0	0	0	0	0	0	1	13203	1074	38	1		1	RDH11	14	68157017	Silent	SNP	G	TCGA-BQ-5880-01A-11D-1589-08		68157017	39192523	29	7413											
RFX7	64864	hgsc.bcm.edu	37	chr15	56387238	56387238	+	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	gaattgttcattgacatttgCtgctccataagcaccagctc	10	13	7	11	0	1	1	1	1	0	0	3	2	2	1	2	0	4	5	2	0	2	5			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr15:56387238C>G	ENST00000559447.2	-	9	2668	c.2397G>C	c.(2395-2397)caG>caC	p.Q799H	RFX7_ENST00000423270.1_Missense_Mutation_p.Q896H|RFX7_ENST00000422057.1_Missense_Mutation_p.Q799H|RFX7_ENST00000317318.6_Missense_Mutation_p.Q896H			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	799					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						TTGACATTTGCTGCTCCATAA	0.418																																					p.Q896H		Atlas-SNP	.											.	RFX7	170	.	0			c.G2688C						PASS	.						105	103	103					15																	56387238		1983	4164	6147	SO:0001583	missense	64864	exon9			CATTTGCTGCTCC			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.2397G>C	chr15.hg19:g.56387238C>G	ENSP00000453281:p.Gln799His	57.0	0.0	.		81.0	15.0	.	NM_022841	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Missense_Mutation	SNP	ENST00000559447.2	hg19		.	.	.	.	.	.	.	.	.	.	C	12.40	1.925982	0.34002	.	.	ENSG00000181827	ENST00000422057;ENST00000317318;ENST00000423270	T;T;T	0.53423	0.62;0.62;0.62	5.57	4.46	0.54185	.	0.069338	0.51477	D	0.000090	T	0.33614	0.0869	N	0.14661	0.345	0.38957	D	0.95847	P;P	0.49961	0.855;0.93	B;P	0.44732	0.359;0.459	T	0.34304	-0.9834	10	0.87932	D	0	-7.1862	10.8605	0.46823	0.0:0.8402:0.0:0.1598	.	799;799	Q2KHR2;C9JU50	RFX7_HUMAN;.	H	799;896;896	ENSP00000387504:Q799H;ENSP00000313299:Q896H;ENSP00000397644:Q896H	ENSP00000313299:Q896H	Q	-	3	2	RFX7	54174530	0.998000	0.40836	1.000000	0.80357	0.994000	0.84299	0.596000	0.24044	2.602000	0.87976	0.514000	0.50259	CAG	.	.	.	none		0.418	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841		G	56387238	C	G	56387238	3	3	115	1	0	0	0	0	1	0	0	0	13281	796	28	4	1698	4	RFX7	15	56387238	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08		56387238	46144154	30	7414											
FASN	2194	hgsc.bcm.edu	37	chr17	80041413	80041413	+	Missense_Mutation	SNP	A	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	cgagcgggtggttctgagaaAggtcgaatttgccaatttcc	9	11	13	8	3	1	1	0	1	1	1	3	4	2	1	2	3	2	1	2	3	3	3			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr17:80041413A>C	ENST00000306749.2	-	31	5539	c.5321T>G	c.(5320-5322)cTt>cGt	p.L1774R	FASN_ENST00000579758.1_5'Flank	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	1774	Enoyl reductase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	GTTCTGAGAAAGGTCGAATTT	0.637																																					p.L1774R	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.T5321G						PASS	.						54	53	54					17																	80041413		2199	4298	6497	SO:0001583	missense	2194	exon31			TGAGAAAGGTCGA	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.5321T>G	chr17.hg19:g.80041413A>C	ENSP00000304592:p.Leu1774Arg	60.0	0.0	.		100.0	11.0	.	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	A	15.48	2.846071	0.51164	.	.	ENSG00000169710	ENST00000306749;ENST00000545909	T	0.04083	3.71	4.77	3.69	0.42338	Alcohol dehydrogenase, C-terminal (1);Polyketide synthase, enoylreductase (1);NAD(P)-binding domain (1);	0.076785	0.56097	D	0.000039	T	0.24236	0.0587	M	0.90252	3.1	0.58432	D	0.999998	D	0.89917	1.0	D	0.83275	0.996	T	0.01127	-1.1443	10	0.87932	D	0	-12.1836	9.8571	0.41092	0.9181:0.0:0.0819:0.0	.	1774	P49327	FAS_HUMAN	R	1774;739	ENSP00000304592:L1774R	ENSP00000304592:L1774R	L	-	2	0	FASN	77634702	1.000000	0.71417	0.518000	0.27811	0.128000	0.20619	8.901000	0.92560	0.675000	0.31264	0.459000	0.35465	CTT	.	.	.	none		0.637	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		C	80041413	A	C	80041413	3	2	115	1	0	0	0	0	1	0	0	0	5690	72	3	5	2266	5	FASN	17	80041413	Missense_Mutation	SNP	A	TCGA-BQ-5880-01A-11D-1589-08		80041413	1153797	31	7415											
LAMA1	284217	hgsc.bcm.edu	37	chr18	7025998	7025998	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgttggaggctatggtgagAgggcaggcgcagggctggca	7	8	20	6	1	0	1	0	1	0	1	0	3	0	2	0	7	0	6	0	7	1	3			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr18:7025998A>G	ENST00000389658.3	-	17	2475	c.2382T>C	c.(2380-2382)ccT>ccC	p.P794P		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	794	Laminin EGF-like 7. {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)				CTATGGTGAGAGGGCAGGCGC	0.622																																					p.P794P		Atlas-SNP	.											.	LAMA1	458	.	0			c.T2382C						PASS	.						51	42	45					18																	7025998		2203	4300	6503	SO:0001819	synonymous_variant	284217	exon17			GGTGAGAGGGCAG	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.2382T>C	chr18.hg19:g.7025998A>G		23.0	0.0	.		21.0	4.0	.	NM_005559		Silent	SNP	ENST00000389658.3	hg19	CCDS32787.1																																																																																			.	.	.	none		0.622	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		G	7025998	A	G	7025998	2	3	115	1	0	0	0	0	0	0	0	1	8612	291	11	3		3	LAMA1	18	7025998	Silent	SNP	A	TCGA-BQ-5880-01A-11D-1589-08		7025998	71051250	32	7416											
ZNF236	7776	hgsc.bcm.edu	37	chr18	74622686	74622686	+	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	caacagctacaggattccagCacacttgagtctcaggccct	11	8	8	14	0	1	1	1	1	1	0	3	2	2	2	2	2	4	2	2	2	2	3			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr18:74622686C>T	ENST00000253159.8	+	16	2916	c.2718C>T	c.(2716-2718)agC>agT	p.S906S	ZNF236_ENST00000320610.9_Silent_p.S908S	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	906					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)		AGGATTCCAGCACACTTGAGT	0.493																																					p.S906S		Atlas-SNP	.											.	ZNF236	325	.	0			c.C2718T						PASS	.						73	72	72					18																	74622686		2000	4185	6185	SO:0001819	synonymous_variant	7776	exon16			TTCCAGCACACTT	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.2718C>T	chr18.hg19:g.74622686C>T		97.0	0.0	.		132.0	29.0	.	NM_007345	B2RTX9|Q9UL37	Silent	SNP	ENST00000253159.8	hg19	CCDS42447.1																																																																																			.	.	.	none		0.493	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1			T	74622686	C	T	74622686	2	4	115	1	0	0	0	0	0	0	0	1	17801	709	25	2		2	ZNF236	18	74622686	Silent	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	67596688	74622686	3454562	33	7417											
ZNF266	10781	hgsc.bcm.edu	37	chr19	9524367	9524367	+	Missense_Mutation	SNP	T	T	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	agcaaaggctttcccacattTgacacattcaaaaggcttct	13	11	6	11	0	2	1	1	1	1	0	3	1	3	1	1	2	1	3	1	2	3	4			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr19:9524367T>G	ENST00000592904.1	-	5	3310	c.1234A>C	c.(1234-1236)Aaa>Caa	p.K412Q	ZNF266_ENST00000592292.1_Missense_Mutation_p.K412Q|ZNF266_ENST00000361151.1_Missense_Mutation_p.K412Q|ZNF266_ENST00000588221.1_Missense_Mutation_p.K412Q|ZNF266_ENST00000590306.1_Missense_Mutation_p.K412Q|ZNF266_ENST00000588933.1_Missense_Mutation_p.K412Q|ZNF266_ENST00000361451.2_Missense_Mutation_p.K412Q			Q14584	ZN266_HUMAN	zinc finger protein 266	412					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(2)|large_intestine(11)|lung(8)|ovary(1)|skin(2)|stomach(1)	28						TTCCCACATTTGACACATTCA	0.433																																					p.K412Q		Atlas-SNP	.											.	ZNF266	65	.	0			c.A1234C						PASS	.						72	72	72					19																	9524367		2203	4300	6503	SO:0001583	missense	10781	exon11			CACATTTGACACA	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.1234A>C	chr19.hg19:g.9524367T>G	ENSP00000466714:p.Lys412Gln	73.0	0.0	.		75.0	22.0	.	NM_001271314	A0AV90|A4FU85|Q6IQ07|Q6U8A5|Q8IVG3|Q8WVX1|Q96SX9	Missense_Mutation	SNP	ENST00000592904.1	hg19	CCDS12213.1	.	.	.	.	.	.	.	.	.	.	T	13.51	2.259791	0.39995	.	.	ENSG00000174652	ENST00000361451;ENST00000361151	T;T	0.07444	3.19;3.19	2.76	-5.41	0.02648	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02533	0.0077	N	0.03029	-0.43	0.09310	N	1	B	0.22604	0.072	B	0.17098	0.017	T	0.45848	-0.9233	9	0.21014	T	0.42	.	5.5147	0.16900	0.0:0.411:0.2893:0.2997	.	412	Q14584	ZN266_HUMAN	Q	412	ENSP00000354680:K412Q;ENSP00000355047:K412Q	ENSP00000355047:K412Q	K	-	1	0	ZNF266	9385367	0.000000	0.05858	0.000000	0.03702	0.998000	0.95712	-1.671000	0.01954	-1.372000	0.02137	0.454000	0.30748	AAA	.	.	.	none		0.433	ZNF266-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449033.1			G	9524367	T	G	9524367	3	3	115	1	0	0	0	0	1	0	0	0	17817	1821	63	5	419	5	ZNF266	19	9524367	Missense_Mutation	SNP	T	TCGA-BQ-5880-01A-11D-1589-08		9524367	49604616	34	7418											
ZNF561	93134	hgsc.bcm.edu	37	chr19	9721627	9721627	+	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	cacactgctttaggtgtgaaGaagctgtgacagctctccca	10	10	10	11	0	1	3	0	2	1	1	2	3	1	3	1	1	3	3	1	1	3	2			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr19:9721627G>A	ENST00000302851.3	-	6	1073	c.710C>T	c.(709-711)tCt>tTt	p.S237F	ZNF561_ENST00000354661.4_Missense_Mutation_p.S101F|ZNF561_ENST00000495503.1_5'UTR|ZNF561_ENST00000326044.5_3'UTR|ZNF561_ENST00000424629.1_Missense_Mutation_p.S168F	NM_152289.2	NP_689502.2	Q8N587	ZN561_HUMAN	zinc finger protein 561	237					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)	14						TAGGTGTGAAGAAGCTGTGAC	0.373																																					p.S237F		Atlas-SNP	.											.	ZNF561	64	.	0			c.C710T						PASS	.						65	63	63					19																	9721627		2203	4300	6503	SO:0001583	missense	93134	exon6			TGTGAAGAAGCTG	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.710C>T	chr19.hg19:g.9721627G>A	ENSP00000303915:p.Ser237Phe	117.0	0.0	.		113.0	24.0	.	NM_152289	B4E2Q8|Q6PJS0	Missense_Mutation	SNP	ENST00000302851.3	hg19	CCDS12216.2	.	.	.	.	.	.	.	.	.	.	G	11.49	1.655669	0.29425	.	.	ENSG00000171469	ENST00000424629;ENST00000302851;ENST00000354661;ENST00000444611	T;T;T;T	0.29917	1.55;1.55;1.55;2.36	1.1	1.1	0.20463	.	.	.	.	.	T	0.48223	0.1488	M	0.77486	2.375	0.09310	N	1	D	0.61697	0.99	D	0.71656	0.974	T	0.22312	-1.0220	9	0.37606	T	0.19	.	5.1359	0.14934	0.0:0.3792:0.6208:0.0	.	237	Q8N587	ZN561_HUMAN	F	168;237;101;243	ENSP00000393074:S168F;ENSP00000303915:S237F;ENSP00000346687:S101F;ENSP00000392013:S243F	ENSP00000303915:S237F	S	-	2	0	ZNF561	9582627	0.019000	0.18553	0.002000	0.10522	0.033000	0.12548	2.273000	0.43381	0.905000	0.36596	0.298000	0.19748	TCT	.	.	.	none		0.373	ZNF561-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347272.2	NM_152289		A	9721627	G	A	9721627	3	1	115	1	0	0	0	0	1	0	0	0	18004	942	33	2	754	2	ZNF561	19	9721627	Missense_Mutation	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	197260	9721627	49407356	35	7419											
MYO9B	4650	hgsc.bcm.edu	37	chr19	17311587	17311587	+	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	cgggaatcggtgttccgccaGatcaccaacgccaatgagct	10	7	11	13	4	1	2	1	1	0	1	3	3	2	3	4	2	2	2	4	2	3	1			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr19:17311587G>T	ENST00000594824.1	+	26	4659	c.4512G>T	c.(4510-4512)caG>caT	p.Q1504H	MYO9B_ENST00000397274.2_Missense_Mutation_p.Q1504H|MYO9B_ENST00000595618.1_Missense_Mutation_p.Q1504H			Q13459	MYO9B_HUMAN	myosin IXB	1504	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						TGTTCCGCCAGATCACCAACG	0.577																																					p.Q1504H		Atlas-SNP	.											.	MYO9B	264	.	0			c.G4512T						PASS	.						127	138	135					19																	17311587		2113	4228	6341	SO:0001583	missense	4650	exon26			CCGCCAGATCACC		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.4512G>T	chr19.hg19:g.17311587G>T	ENSP00000471367:p.Gln1504His	86.0	0.0	.		96.0	25.0	.	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Missense_Mutation	SNP	ENST00000594824.1	hg19		.	.	.	.	.	.	.	.	.	.	G	12.57	1.977073	0.34848	.	.	ENSG00000099331	ENST00000397274	D	0.84223	-1.82	4.75	2.43	0.29744	.	0.446964	0.20636	N	0.088489	T	0.68137	0.2968	N	0.08118	0	0.29597	N	0.848014	P;P;P;P	0.37708	0.472;0.606;0.472;0.472	B;B;B;B	0.37422	0.116;0.249;0.116;0.126	T	0.65508	-0.6151	10	0.44086	T	0.13	.	7.4385	0.27169	0.2708:0.0:0.7292:0.0	.	1504;1504;1504;1510	Q13459;Q13459-2;B0I1T6;Q4LE74	MYO9B_HUMAN;.;.;.	H	1504	ENSP00000380444:Q1504H	ENSP00000380444:Q1504H	Q	+	3	2	MYO9B	17172587	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	1.332000	0.33805	1.006000	0.39211	0.491000	0.48974	CAG	.	.	.	none		0.577	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1			T	17311587	G	T	17311587	3	4	115	1	0	0	0	0	1	0	0	0	10092	933	33	4	4610	4	MYO9B	19	17311587	Missense_Mutation	SNP	G	TCGA-BQ-5880-01A-11D-1589-08	7589960	17311587	41817396	36	7420											
UMODL1	89766	hgsc.bcm.edu	37	chr21	43505425	43505425	+	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	agagagggaccctgtgggctCctggtacaacgtcaccatac	10	7	12	12	1	1	1	1	0	0	1	2	3	2	2	3	3	3	2	3	3	3	2			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr21:43505425C>T	ENST00000408910.2	+	4	506	c.506C>T	c.(505-507)tCc>tTc	p.S169F	UMODL1_ENST00000408989.2_Missense_Mutation_p.S169F|UMODL1_ENST00000400427.1_Missense_Mutation_p.S97F|UMODL1_ENST00000400424.2_Missense_Mutation_p.S97F	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	169					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						CCTGTGGGCTCCTGGTACAAC	0.537																																					p.S169F	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.C506T						PASS	.						113	117	116					21																	43505425		1912	4141	6053	SO:0001583	missense	89766	exon4			TGGGCTCCTGGTA		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.506C>T	chr21.hg19:g.43505425C>T	ENSP00000386147:p.Ser169Phe	147.0	0.0	.		181.0	34.0	.	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	hg19	CCDS42936.1	.	.	.	.	.	.	.	.	.	.	C	8.956	0.969471	0.18659	.	.	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910;ENST00000380462;ENST00000400417;ENST00000423139	T;T;T;T	0.72394	-0.65;-0.63;-0.65;-0.63	3.02	-6.05	0.02172	.	0.899723	0.09081	N	0.851345	T	0.29423	0.0733	N	0.00823	-1.155	0.20703	N	0.999862	B;B	0.20261	0.043;0.0	B;B	0.15052	0.012;0.0	T	0.18178	-1.0345	10	0.32370	T	0.25	-0.4883	1.9738	0.03412	0.1682:0.5079:0.1126:0.2114	.	169;169	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	F	97;97;169;169;15;15;4	ENSP00000383279:S97F;ENSP00000383276:S97F;ENSP00000386126:S169F;ENSP00000386147:S169F	ENSP00000369829:S15F	S	+	2	0	UMODL1	42378494	0.020000	0.18652	0.030000	0.17652	0.492000	0.33523	-1.121000	0.03270	-1.577000	0.01650	-0.253000	0.11424	TCC	.	.	.	none		0.537	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2			T	43505425	C	T	43505425	3	4	115	1	0	0	0	0	1	0	0	0	16992	855	30	2	520	2	UMODL1	21	43505425	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08		43505425	4624470	37	7421											
MYO18B	84700	hgsc.bcm.edu	37	chr22	26400727	26400727	+	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	cccagccagagggcagcctgCagtcctggttgagctgtact	7	8	13	13	0	0	2	0	1	0	1	1	2	1	2	4	2	5	5	4	2	1	2			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr22:26400727C>T	ENST00000407587.2	+	42	6548	c.6379C>T	c.(6379-6381)Cag>Tag	p.Q2127*	MYO18B_ENST00000335473.7_Nonsense_Mutation_p.Q2126*|MYO18B_ENST00000536101.1_Nonsense_Mutation_p.Q2126*			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2126						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						GGGCAGCCTGCAGTCCTGGTT	0.532																																					p.Q2126X		Atlas-SNP	.											.	MYO18B	322	.	0			c.C6376T						PASS	.						79	83	81					22																	26400727		2115	4248	6363	SO:0001587	stop_gained	84700	exon42			AGCCTGCAGTCCT	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.6379C>T	chr22.hg19:g.26400727C>T	ENSP00000386096:p.Gln2127*	87.0	0.0	.		102.0	13.0	.	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Nonsense_Mutation	SNP	ENST00000407587.2	hg19		.	.	.	.	.	.	.	.	.	.	C	48	14.649130	0.99804	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	.	.	.	4.33	3.25	0.37280	.	1.244550	0.05893	N	0.628605	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	.	8.5131	0.33229	0.2492:0.7508:0.0:0.0	.	.	.	.	X	2126;2126;2127	.	ENSP00000334563:Q2126X	Q	+	1	0	MYO18B	24730727	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.482000	0.45224	2.246000	0.74042	0.650000	0.86243	CAG	.	.	.	none		0.532	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		T	26400727	C	T	26400727	4	4	115	1	0	0	0	0	0	1	0	0	10073	711	25	2	6538	2	MYO18B	22	26400727	Nonsense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08		26400727	24903839	38	7422											
MKL1	57591	hgsc.bcm.edu	37	chr22	40814880	40814880	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcatctggtccttgtcgCgcccctctagctccgcccgc	3	9	10	19	4	2	0	0	0	2	0	5	0	4	0	5	1	2	3	5	1	1	2			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chr22:40814880C>T	ENST00000355630.3	-	12	2152	c.1562G>A	c.(1561-1563)cGc>cAc	p.R521H	MKL1_ENST00000402042.1_Missense_Mutation_p.R471H|MKL1_ENST00000407029.1_Missense_Mutation_p.R521H|MKL1_ENST00000396617.3_Missense_Mutation_p.R521H	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	521					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						GTCCTTGTCGCGCCCCTCTAG	0.682			T	RBM15	acute megakaryocytic leukemia																																p.R521H		Atlas-SNP	.		Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	.	MKL1	69	.	0			c.G1562A						PASS	.						28	33	31					22																	40814880		2203	4297	6500	SO:0001583	missense	57591	exon12			TTGTCGCGCCCCT	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.1562G>A	chr22.hg19:g.40814880C>T	ENSP00000347847:p.Arg521His	100.0	0.0	.		98.0	21.0	.	NM_020831	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Missense_Mutation	SNP	ENST00000355630.3	hg19	CCDS14003.1	.	.	.	.	.	.	.	.	.	.	C	12.77	2.039005	0.35989	.	.	ENSG00000196588	ENST00000355630;ENST00000396617;ENST00000402042;ENST00000407029	T;T;T;T	0.44482	0.93;0.92;0.93;0.93	4.89	3.86	0.44501	.	0.428770	0.23016	N	0.052902	T	0.30230	0.0758	N	0.04959	-0.14	0.09310	N	0.999999	D;D;D	0.67145	0.968;0.996;0.993	B;P;P	0.53185	0.374;0.72;0.609	T	0.05852	-1.0860	10	0.45353	T	0.12	-4.7852	8.2012	0.31426	0.1863:0.7301:0.0:0.0835	.	471;521;521	B0QY83;E7ER32;Q969V6	.;.;MKL1_HUMAN	H	521;521;471;521	ENSP00000347847:R521H;ENSP00000379861:R521H;ENSP00000385584:R471H;ENSP00000385835:R521H	ENSP00000347847:R521H	R	-	2	0	MKL1	39144826	0.227000	0.23707	0.758000	0.31321	0.866000	0.49608	0.691000	0.25467	1.165000	0.42670	0.591000	0.81541	CGC	.	.	.	none		0.682	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831		T	40814880	C	T	40814880	3	4	115	1	0	0	0	0	1	0	0	0	9608	768	27	1	1249	1	MKL1	22	40814880	Missense_Mutation	SNP	C	TCGA-BQ-5880-01A-11D-1589-08	14414153	40814880	10489686	39	7423											
MAOB	4129	hgsc.bcm.edu	37	chrX	43702915	43702915	+	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	tccggattcttaatgccttaCcctaagagtgtaagtcctgc	9	13	8	11	1	1	1	0	0	1	1	3	2	3	2	4	1	3	1	4	1	4	5			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chrX:43702915C>G	ENST00000378069.4	-	2	289		c.e2+1		MAOB_ENST00000536181.1_Splice_Site|MAOB_ENST00000487544.1_Splice_Site|MAOB_ENST00000538942.1_Splice_Site	NM_000898.4	NP_000889.3	P27338	AOFB_HUMAN	monoamine oxidase B						negative regulation of serotonin secretion (GO:0014063)|positive regulation of dopamine metabolic process (GO:0045964)|response to aluminum ion (GO:0010044)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|primary amine oxidase activity (GO:0008131)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(2)|skin(5)	21					Amantadine(DB00915)|Amphetamine(DB00182)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Procaine(DB00721)|Rasagiline(DB01367)|Selegiline(DB01037)|Sertraline(DB01104)|Tranylcypromine(DB00752)|Zonisamide(DB00909)	TAATGCCTTACCCTAAGAGTG	0.478																																					.		Atlas-SNP	.											.	MAOB	52	.	0			c.141+1G>C						PASS	.						83	67	73					X																	43702915		2203	4300	6503	SO:0001630	splice_region_variant	4129	exon3			GCCTTACCCTAAG		CCDS14261.1	Xp11.4-p11.3	2008-02-05			ENSG00000069535	ENSG00000069535	1.4.3.4		6834	protein-coding gene	gene with protein product		309860					Standard	NM_000898		Approved		uc004dfz.4	P27338	OTTHUMG00000021388	ENST00000378069.4:c.141+1G>C	chrX.hg19:g.43702915C>G		30.0	0.0	.		30.0	14.0	.	NM_000898	B2R6R3|B7Z5H3|D3DWC3|Q7Z6S2	Splice_Site	SNP	ENST00000378069.4	hg19	CCDS14261.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.440115	0.83993	.	.	ENSG00000069535	ENST00000378069;ENST00000536181;ENST00000538942	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.5321	0.90996	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MAOB	43587859	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	5.391000	0.66266	2.318000	0.78349	0.600000	0.82982	.	.	.	.	none		0.478	MAOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056303.1	NM_000898	Intron	G	43702915	C	G	43702915	5	3	115	1	0	0	0	0	0	0	1	0	9233	521	18	4	1476	4	MAOB	23	43702915	Splice_Site	SNP	C	TCGA-BQ-5880-01A-11D-1589-08		43702915	111567645	40	7424											
SMC1A	8243	hgsc.bcm.edu	37	chrX	53407985	53407985	+	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	cagcatcaatctcatccaggAcgaagaagggggctggcttg	11	7	13	10	1	2	1	2	0	1	1	4	3	3	2	1	4	1	3	1	4	3	1			TCGA-BQ-5880-01A-11D-1589-08	TCGA-BQ-5880-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fc77da41-c3ab-470a-9835-cd90efad8943	0e3be903-bd00-42d6-8510-f71f823a5f29	g.chrX:53407985A>T	ENST00000322213.4	-	23	3588	c.3461T>A	c.(3460-3462)gTc>gAc	p.V1154D	SMC1A_ENST00000469129.1_5'Flank	NM_006306.2	NP_006297.2	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	1154	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						CTCATCCAGGACGAAGAAGGG	0.632																																					p.V1154D		Atlas-SNP	.											.	SMC1A	112	.	0			c.T3461A						PASS	.						69	60	63					X																	53407985		2203	4300	6503	SO:0001583	missense	8243	exon23			TCCAGGACGAAGA	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.3461T>A	chrX.hg19:g.53407985A>T	ENSP00000323421:p.Val1154Asp	78.0	0.0	.		67.0	27.0	.	NM_006306	O14995|Q16351|Q2M228	Missense_Mutation	SNP	ENST00000322213.4	hg19	CCDS14352.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.943345	0.73672	.	.	ENSG00000072501	ENST00000322213	D	0.92099	-2.97	5.29	5.29	0.74685	RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	D	0.96901	0.8988	M	0.93150	3.385	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97755	1.0217	10	0.87932	D	0	.	13.4304	0.61051	1.0:0.0:0.0:0.0	.	1154	Q14683	SMC1A_HUMAN	D	1154	ENSP00000323421:V1154D	ENSP00000323421:V1154D	V	-	2	0	SMC1A	53424710	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.113000	0.94321	1.882000	0.54519	0.481000	0.45027	GTC	.	.	.	none		0.632	SMC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056756.2	NM_006306		T	53407985	A	T	53407985	3	4	115	1	0	0	0	0	1	0	0	0	14794	275	10	5	252	5	SMC1A	23	53407985	Missense_Mutation	SNP	A	TCGA-BQ-5880-01A-11D-1589-08	9705070	53407985	101862575	41	7425											
LPPR5	163404	hgsc.bcm.edu	37	chr1	99418655	99418655	+	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	catagctgcatagacactgaGagctgcttctttggatggaa	11	11	11	8	0	1	2	0	1	1	2	1	5	1	4	0	2	4	4	0	2	3	4			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr1:99418655G>T	ENST00000263177.4	-	3	813	c.592C>A	c.(592-594)Ctc>Atc	p.L198I	LPPR5_ENST00000370188.3_Missense_Mutation_p.L198I	NM_001037317.1	NP_001032394.1	Q32ZL2	LPPR5_HUMAN		198						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)										TAGACACTGAGAGCTGCTTCT	0.388																																					p.L198I		Atlas-SNP	.											.	.	.	.	0			c.C592A						PASS	.						122	111	115					1																	99418655		2203	4300	6503	SO:0001583	missense	0	exon3			CACTGAGAGCTGC																												ENST00000263177.4:c.592C>A	chr1.hg19:g.99418655G>T	ENSP00000263177:p.Leu198Ile	96.0	0.0	.		97.0	4.0	.	NM_001010861	A8MPX4|B7UCH3|Q32ZD0|Q3ZCU7	Missense_Mutation	SNP	ENST00000263177.4	hg19	CCDS30778.1	.	.	.	.	.	.	.	.	.	.	G	19.34	3.807957	0.70797	.	.	ENSG00000117598	ENST00000370188;ENST00000263177	T;T	0.56776	0.44;0.44	5.16	4.25	0.50352	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.49389	0.1554	L	0.45285	1.41	0.45390	D	0.998374	D;D	0.64830	0.992;0.994	P;P	0.59012	0.652;0.85	T	0.55270	-0.8167	10	0.62326	D	0.03	.	12.987	0.58598	0.0783:0.0:0.9217:0.0	.	198;198	Q32ZL2-2;Q32ZL2	.;LPPR5_HUMAN	I	198	ENSP00000359207:L198I;ENSP00000263177:L198I	ENSP00000263177:L198I	L	-	1	0	AL161744.1	99191243	1.000000	0.71417	0.959000	0.39883	0.950000	0.60333	7.449000	0.80643	1.311000	0.45024	0.655000	0.94253	CTC	.	.	.	none		0.388	LPPR5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393221.1			T	99418655	G	T	99418655	3	4	116	1	0	0	0	0	1	0	0	0	8935	942	33	4	389	4	LPPR5	1	99418655	Missense_Mutation	SNP	G	TCGA-BQ-5881-01A-11D-1589-08		99418655	149831966	1	7426											
SMG5	23381	hgsc.bcm.edu	37	chr1	156236156	156236156	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctctttctccacaggttccTtggactctggttcatctgcg	4	15	8	14	1	5	0	1	0	4	0	7	1	6	1	3	3	1	2	3	3	0	4			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr1:156236156T>C	ENST00000361813.5	-	12	1415	c.1271A>G	c.(1270-1272)aAg>aGg	p.K424R	SMG5_ENST00000368267.5_Intron|SMG5_ENST00000489907.2_5'UTR	NM_015327.2	NP_056142.2	Q9UPR3	SMG5_HUMAN	SMG5 nonsense mediated mRNA decay factor	424					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)					CACAGGTTCCTTGGACTCTGG	0.582																																					p.K424R		Atlas-SNP	.											.	SMG5	98	.	0			c.A1271G						PASS	.						40	42	41					1																	156236156		2203	4300	6503	SO:0001583	missense	23381	exon12			GGTTCCTTGGACT	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.1271A>G	chr1.hg19:g.156236156T>C	ENSP00000355261:p.Lys424Arg	85.0	0.0	.		89.0	31.0	.	NM_015327	D3DVB7|Q5QJE7|Q659C7|Q8IXC0|Q8IY09|Q96IJ7	Missense_Mutation	SNP	ENST00000361813.5	hg19	CCDS1137.1	.	.	.	.	.	.	.	.	.	.	T	9.820	1.185549	0.21870	.	.	ENSG00000198952	ENST00000361813	T	0.29142	1.58	5.28	1.67	0.24075	.	0.436632	0.25777	N	0.028378	T	0.04048	0.0113	N	0.12182	0.205	0.80722	D	1	B	0.06786	0.001	B	0.09377	0.004	T	0.33266	-0.9875	10	0.09843	T	0.71	-8.5258	5.1542	0.15027	0.0:0.2355:0.1441:0.6204	.	424	Q9UPR3	SMG5_HUMAN	R	424	ENSP00000355261:K424R	ENSP00000355261:K424R	K	-	2	0	SMG5	154502780	1.000000	0.71417	0.364000	0.25888	0.638000	0.38207	0.547000	0.23299	0.030000	0.15379	0.460000	0.39030	AAG	.	.	.	none		0.582	SMG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046308.1	NM_015327		C	156236156	T	C	156236156	3	2	116	1	0	0	0	0	1	0	0	0	14809	1609	56	3	1823	3	SMG5	1	156236156	Missense_Mutation	SNP	T	TCGA-BQ-5881-01A-11D-1589-08	56817501	156236156	93014465	2	7427											
POMC	5443	hgsc.bcm.edu	37	chr2	25387619	25387619	+	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	ccagcaacagggcccccgagCggctgcagcacgatctcggc	8	3	13	17	4	1	0	0	0	1	0	2	2	1	0	3	3	5	4	3	3	1	0	rs146551109		TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr2:25387619C>T	ENST00000405623.1	-	2	478	c.23G>A	c.(22-24)cGc>cAc	p.R8H	POMC_ENST00000264708.3_Missense_Mutation_p.R8H|POMC_ENST00000395826.2_Missense_Mutation_p.R8H|POMC_ENST00000380794.1_Missense_Mutation_p.R8H			P01189	COLI_HUMAN	proopiomelanocortin	8					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)	p.R8H(1)		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)	GGCCCCCGAGCGGCTGCAGCA	0.612																																					p.R8H	Colon(110;1515 1566 8452 10082 43216)	Atlas-SNP	.											POMC,NS,lymphoid_neoplasm,0,1	POMC	33	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G23A						PASS	.	C	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	41	44	43		23,23	3.8	0	2	dbSNP_134	43	0,8598		0,0,4299	no	missense,missense	POMC	NM_000939.2,NM_001035256.1	29,29	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	8/268,8/268	25387619	1,13003	2203	4299	6502	SO:0001583	missense	5443	exon3			CCCGAGCGGCTGC		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.23G>A	chr2.hg19:g.25387619C>T	ENSP00000384092:p.Arg8His	63.0	0.0	.		98.0	27.0	.	NM_001035256	P78442|Q53T23|Q9UD39|Q9UD40	Missense_Mutation	SNP	ENST00000405623.1	hg19	CCDS1717.1	.	.	.	.	.	.	.	.	.	.	C	10.91	1.485311	0.26598	2.27E-4	0.0	ENSG00000115138	ENST00000380794;ENST00000405623;ENST00000264708;ENST00000395826;ENST00000449220	T;T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24;-1.24	5.64	3.82	0.43975	.	0.809526	0.10655	N	0.649411	T	0.64800	0.2631	L	0.33485	1.01	0.09310	N	1	D	0.60575	0.988	B	0.43916	0.436	T	0.52011	-0.8632	10	0.15952	T	0.53	-24.4143	4.8248	0.13410	0.1512:0.6107:0.0:0.2382	.	8	P01189	COLI_HUMAN	H	8	ENSP00000370171:R8H;ENSP00000384092:R8H;ENSP00000264708:R8H;ENSP00000379170:R8H;ENSP00000387993:R8H	ENSP00000264708:R8H	R	-	2	0	POMC	25241123	0.278000	0.24230	0.019000	0.16419	0.096000	0.18686	0.717000	0.25851	1.381000	0.46364	0.462000	0.41574	CGC	.	C|1.000;T|0.000	0.000	weak		0.612	POMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211573.3	NM_001035256		T	25387619	C	T	25387619	3	4	116	1	0	0	0	0	1	0	0	0	12249	768	27	1	788	1	POMC	2	25387619	Missense_Mutation	SNP	C	TCGA-BQ-5881-01A-11D-1589-08		25387619	217811754	3	7428											
BIRC6	57448	hgsc.bcm.edu	37	chr2	32656054	32656054	+	Missense_Mutation	SNP	A	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	gttcctccatgctgggtagaAgttcaacaagaacagcagca	13	8	10	10	0	1	2	1	0	0	2	3	2	3	2	2	1	5	6	2	1	5	3			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr2:32656054A>C	ENST00000421745.2	+	12	3278	c.3144A>C	c.(3142-3144)gaA>gaC	p.E1048D		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1048					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)					GCTGGGTAGAAGTTCAACAAG	0.483																																					p.E1048D	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.A3144C						PASS	.						92	80	84					2																	32656054		2203	4300	6503	SO:0001583	missense	57448	exon12			GGTAGAAGTTCAA	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.3144A>C	chr2.hg19:g.32656054A>C	ENSP00000393596:p.Glu1048Asp	76.0	0.0	.		63.0	20.0	.	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	A	17.67	3.447198	0.63178	.	.	ENSG00000115760	ENST00000421745	D	0.84070	-1.8	5.62	0.657	0.17850	.	0.000000	0.85682	D	0.000000	D	0.83894	0.5353	L	0.36672	1.1	0.45541	D	0.998494	D	0.58970	0.984	D	0.68192	0.956	T	0.81510	-0.0900	10	0.87932	D	0	.	9.7011	0.40187	0.6633:0.0:0.3367:0.0	.	1048	Q9NR09	BIRC6_HUMAN	D	1048	ENSP00000393596:E1048D	ENSP00000393596:E1048D	E	+	3	2	BIRC6	32509558	1.000000	0.71417	0.985000	0.45067	0.974000	0.67602	1.623000	0.37008	-0.105000	0.12132	0.533000	0.62120	GAA	.	.	.	none		0.483	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		C	32656054	A	C	32656054	3	2	116	1	0	0	0	0	1	0	0	0	1438	69	3	5	3190	5	BIRC6	2	32656054	Missense_Mutation	SNP	A	TCGA-BQ-5881-01A-11D-1589-08	7268435	32656054	210543319	4	7429											
NFE2L2	4780	hgsc.bcm.edu	37	chr2	178098956	178098956	+	Missense_Mutation	SNP	A	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	atacttctcgacttactccaAgatctatatcttgcctccaa	11	14	3	13	1	3	1	0	0	3	1	6	2	5	1	3	0	3	0	3	0	6	6			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr2:178098956A>C	ENST00000397062.3	-	2	643	c.89T>G	c.(88-90)cTt>cGt	p.L30R	NFE2L2_ENST00000446151.2_Missense_Mutation_p.L14R|NFE2L2_ENST00000464747.1_Missense_Mutation_p.L14R|NFE2L2_ENST00000397063.4_Missense_Mutation_p.L14R|NFE2L2_ENST00000423513.1_Missense_Mutation_p.L14R	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	30					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L30R(2)|p.L30H(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			ACTTACTCCAAGATCTATATC	0.363			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.L30R		Atlas-SNP	.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	NFE2L2,NS,carcinoma,0,5	NFE2L2	225	.	3	Substitution - Missense(3)	endometrium(2)|kidney(1)	c.T89G						PASS	.						68	61	63					2																	178098956		1839	4101	5940	SO:0001583	missense	4780	exon2			ACTCCAAGATCTA		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.89T>G	chr2.hg19:g.178098956A>C	ENSP00000380252:p.Leu30Arg	62.0	0.0	.		66.0	7.0	.	NM_006164	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	hg19	CCDS42782.1	.	.	.	.	.	.	.	.	.	.	A	19.55	3.849301	0.71603	.	.	ENSG00000116044	ENST00000397063;ENST00000397062;ENST00000446151;ENST00000449627;ENST00000448782;ENST00000421929;ENST00000423513	T;T;T;T;T;T;T	0.39056	1.1;1.1;1.1;1.1;1.1;1.1;1.1	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.69931	0.3166	M	0.86953	2.85	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.91635	0.998;0.998;0.999;0.998	T	0.76061	-0.3097	10	0.87932	D	0	.	16.098	0.81144	1.0:0.0:0.0:0.0	.	14;14;14;30	E9PGJ7;B4DNB0;C9JFL6;Q16236	.;.;.;NF2L2_HUMAN	R	14;30;14;14;14;14;14	ENSP00000380253:L14R;ENSP00000380252:L30R;ENSP00000411575:L14R;ENSP00000391590:L14R;ENSP00000400073:L14R;ENSP00000412191:L14R;ENSP00000410015:L14R	ENSP00000380252:L30R	L	-	2	0	NFE2L2	177807202	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.962000	0.93254	2.210000	0.71456	0.460000	0.39030	CTT	.	.	.	none		0.363	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		C	178098956	A	C	178098956	3	2	116	1	0	0	0	0	1	0	0	0	10375	72	3	5	1744	5	NFE2L2	2	178098956	Missense_Mutation	SNP	A	TCGA-BQ-5881-01A-11D-1589-08	145442902	178098956	65100417	5	7430											
SSFA2	6744	hgsc.bcm.edu	37	chr2	182786760	182786760	+	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	gggatttgaaattcctcctgGagaaagctcagaatctgttt	11	13	10	7	0	2	3	1	1	1	2	4	5	4	4	2	2	1	2	2	2	3	3			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr2:182786760G>C	ENST00000431877.2	+	16	3475	c.3296G>C	c.(3295-3297)gGa>gCa	p.G1099A	SSFA2_ENST00000428267.2_Missense_Mutation_p.G924A|SSFA2_ENST00000409001.1_Missense_Mutation_p.G1077A|SSFA2_ENST00000409136.1_Missense_Mutation_p.G608A|SSFA2_ENST00000320370.7_Missense_Mutation_p.G1099A|SSFA2_ENST00000467172.2_3'UTR	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	1099						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)			ATTCCTCCTGGAGAAAGCTCA	0.438																																					p.G1099A		Atlas-SNP	.											.	SSFA2	130	.	0			c.G3296C						PASS	.						86	89	88					2																	182786760		2203	4300	6503	SO:0001583	missense	6744	exon16			CTCCTGGAGAAAG	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.3296G>C	chr2.hg19:g.182786760G>C	ENSP00000388731:p.Gly1099Ala	114.0	0.0	.		134.0	30.0	.	NM_001130445	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Missense_Mutation	SNP	ENST00000431877.2	hg19	CCDS46467.1	.	.	.	.	.	.	.	.	.	.	G	11.09	1.536228	0.27475	.	.	ENSG00000138434	ENST00000431877;ENST00000320370;ENST00000409001;ENST00000428267;ENST00000409136;ENST00000451836	T;T;T;T;T	0.13420	2.84;2.59;2.81;2.81;2.6	5.81	3.98	0.46160	.	0.255590	0.34156	N	0.004205	T	0.09512	0.0234	L	0.31120	0.905	0.33216	D	0.554017	B;B;B;B;B	0.20261	0.043;0.043;0.043;0.043;0.043	B;B;B;B;B	0.19148	0.024;0.024;0.024;0.024;0.024	T	0.10847	-1.0612	10	0.29301	T	0.29	-16.5272	8.2067	0.31458	0.1663:0.1882:0.6455:0.0	.	924;608;1077;1099;1099	E7END2;E7EUL7;E9PHV5;P28290;P28290-3	.;.;.;SSFA2_HUMAN;.	A	1099;1099;1077;924;608;44	ENSP00000388731:G1099A;ENSP00000314669:G1099A;ENSP00000387319:G1077A;ENSP00000409867:G924A;ENSP00000386916:G608A	ENSP00000314669:G1099A	G	+	2	0	SSFA2	182495005	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.480000	0.45206	1.461000	0.47929	0.563000	0.77884	GGA	.	.	.	none		0.438	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2	NM_006751		C	182786760	G	C	182786760	3	2	116	1	0	0	0	0	1	0	0	0	15195	1174	41	4	3358	4	SSFA2	2	182786760	Missense_Mutation	SNP	G	TCGA-BQ-5881-01A-11D-1589-08	4687804	182786760	60412613	6	7431											
ZFAND2B	130617	hgsc.bcm.edu	37	chr2	220072989	220072989	+	Missense_Mutation	SNP	T	T	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	tccctacagacttgctgccaTctccagagcacaagctgtgg	9	9	9	14	0	1	2	0	0	1	2	3	2	2	2	3	1	5	3	3	1	2	2			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr2:220072989T>G	ENST00000289528.5	+	5	641	c.446T>G	c.(445-447)aTc>aGc	p.I149S	ZFAND2B_ENST00000444522.2_Missense_Mutation_p.I149S|ZFAND2B_ENST00000409097.1_Missense_Mutation_p.I149S|ZFAND2B_ENST00000409336.1_Missense_Mutation_p.I149S|ZFAND2B_ENST00000409206.1_Missense_Mutation_p.I149S|ZFAND2B_ENST00000409217.1_Missense_Mutation_p.I149S|ZFAND2B_ENST00000409594.1_Missense_Mutation_p.I149S	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	149						endoplasmic reticulum (GO:0005783)	zinc ion binding (GO:0008270)	p.I149T(1)		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)		CTTGCTGCCATCTCCAGAGCA	0.532																																					p.I149S		Atlas-SNP	.											ZFAND2B,NS,carcinoma,-1,1	ZFAND2B	28	.	1	Substitution - Missense(1)	kidney(1)	c.T446G						PASS	.						75	62	66					2																	220072989		2203	4300	6503	SO:0001583	missense	130617	exon5			CTGCCATCTCCAG	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.446T>G	chr2.hg19:g.220072989T>G	ENSP00000289528:p.Ile149Ser	40.0	0.0	.		54.0	18.0	.	NM_138802	Q8NB98	Missense_Mutation	SNP	ENST00000289528.5	hg19	CCDS2435.1	.	.	.	.	.	.	.	.	.	.	T	16.31	3.088523	0.55968	.	.	ENSG00000158552	ENST00000409206;ENST00000409594;ENST00000289528;ENST00000422255;ENST00000409097;ENST00000409336;ENST00000409217;ENST00000444522	T;T;T;T;T;T;T;T	0.44881	0.96;0.96;0.92;0.92;0.91;0.92;0.92;0.91	5.32	5.32	0.75619	Zinc finger, AN1-type (1);	0.400654	0.26646	N	0.023223	T	0.48241	0.1489	L	0.54323	1.7	0.40724	D	0.982682	D;B;B	0.57571	0.98;0.329;0.069	P;B;B	0.51550	0.673;0.116;0.053	T	0.52230	-0.8603	10	0.59425	D	0.04	-15.7601	11.5973	0.50981	0.0:0.0:0.0:1.0	.	40;149;149	B3KQB0;Q8WV99;B4DEN4	.;ZFN2B_HUMAN;.	S	149	ENSP00000386824:I149S;ENSP00000386399:I149S;ENSP00000289528:I149S;ENSP00000409931:I149S;ENSP00000387179:I149S;ENSP00000386898:I149S;ENSP00000386370:I149S;ENSP00000411334:I149S	ENSP00000289528:I149S	I	+	2	0	ZFAND2B	219781233	0.998000	0.40836	1.000000	0.80357	0.961000	0.63080	3.720000	0.54933	2.233000	0.73108	0.533000	0.62120	ATC	.	.	.	none		0.532	ZFAND2B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256824.2	NM_138802		G	220072989	T	G	220072989	3	3	116	1	0	0	0	0	1	0	0	0	17640	1435	50	5	464	5	ZFAND2B	2	220072989	Missense_Mutation	SNP	T	TCGA-BQ-5881-01A-11D-1589-08	37286229	220072989	23126384	7	7432											
UGT1A3	54659	hgsc.bcm.edu	37	chr2	234637943	234637943	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctccatgccagaggccaccaGgcagtggtcctcaccccaga	9	5	10	17	0	1	2	1	0	0	2	3	2	3	2	7	3	1	1	7	3	0	0	rs374045195		TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr2:234637943G>A	ENST00000482026.1	+	1	190	c.171G>A	c.(169-171)caG>caA	p.Q57Q	UGT1A1_ENST00000609637.1_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A1_ENST00000609767.1_Silent_p.Q57Q|UGT1A5_ENST00000373414.3_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A6_ENST00000305139.6_Intron			P35503	UD13_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A3	57					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)	GAGGCCACCAGGCAGTGGTCC	0.552																																					p.Q57Q		Atlas-SNP	.											.	UGT1A3	91	.	0			c.G171A						PASS	.	G	,,,,,,,,	1,4405	2.1+/-5.4	0,1,2202	78	79	78		,,,,,,171,,	-2.3	0	2		78	0,8600		0,0,4300	no	intron,intron,intron,intron,intron,intron,coding-synonymous,intron,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A6,UGT1A5,UGT1A9,UGT1A4,UGT1A3	NM_001072.3,NM_007120.2,NM_019075.2,NM_019076.4,NM_019077.2,NM_019078.1,NM_019093.2,NM_021027.2,NM_205862.1	,,,,,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,,,,,	,,,,,,57/535,,	234637943	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	54659	exon1			CCACCAGGCAGTG	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.171G>A	chr2.hg19:g.234637943G>A		70.0	0.0	.		76.0	21.0	.	NM_019093	B8K287	Silent	SNP	ENST00000482026.1	hg19	CCDS2509.1																																																																																			.	.	.	weak		0.552	UGT1A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130983.1	NM_019093		A	234637943	G	A	234637943	2	1	116	1	0	0	0	0	0	0	0	1	16958	991	35	2		2	UGT1A3	2	234637943	Silent	SNP	G	TCGA-BQ-5881-01A-11D-1589-08	14564954	234637943	8561430	8	7433											
C3orf23	285343	hgsc.bcm.edu	37	chr3	44438258	44438258	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtacaatcatatttacagacCgttctggcatgagtgcagtg	11	12	10	8	1	2	2	1	1	1	1	2	2	2	2	1	1	3	4	1	1	4	5			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr3:44438258C>T	ENST00000342649.4	+	8	1244	c.817C>T	c.(817-819)Cgt>Tgt	p.R273C	TCAIM_ENST00000417237.1_Missense_Mutation_p.R273C	NM_001282913.1|NM_173826.3	NP_001269842.1|NP_776187.2	Q8N3R3	TCAIM_HUMAN	T cell activation inhibitor, mitochondrial	273						mitochondrion (GO:0005739)		p.R273G(1)									ATTTACAGACCGTTCTGGCAT	0.408																																					p.R273C		Atlas-SNP	.											C3orf23,NS,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	lung(1)	c.C817T						PASS	.						135	124	128					3																	44438258		2203	4300	6503	SO:0001583	missense	285343	exon8			ACAGACCGTTCTG		CCDS2712.1, CCDS43076.1	3p21.33-p21.32	2012-08-22	2012-08-22	2012-08-22	ENSG00000179152	ENSG00000179152			25241	protein-coding gene	gene with protein product	"tolerance associated gene-1"		"chromosome 3 open reading frame 23"	C3orf23		12477932	Standard	NM_001029840		Approved	DKFZp313N0621, TOAG-1	uc003cnd.4	Q8N3R3	OTTHUMG00000133049	ENST00000342649.4:c.817C>T	chr3.hg19:g.44438258C>T	ENSP00000341539:p.Arg273Cys	91.0	0.0	.		128.0	55.0	.	NM_173826	A8K9P1|Q0P5T9|Q495R1|Q495R3|Q4G0M4|Q6GMU8	Missense_Mutation	SNP	ENST00000342649.4	hg19	CCDS2712.1	.	.	.	.	.	.	.	.	.	.	C	17.47	3.396479	0.62177	.	.	ENSG00000179152	ENST00000417237;ENST00000342649	T;T	0.48201	0.82;0.82	5.6	3.8	0.43715	.	0.255107	0.43747	N	0.000534	T	0.56046	0.1959	L	0.51422	1.61	0.46396	D	0.999026	D	0.89917	1.0	P	0.60682	0.878	T	0.56007	-0.8050	10	0.66056	D	0.02	.	9.6854	0.40096	0.0:0.6626:0.267:0.0703	.	273	Q8N3R3	CC023_HUMAN	C	273	ENSP00000402581:R273C;ENSP00000341539:R273C	ENSP00000341539:R273C	R	+	1	0	C3orf23	44413262	1.000000	0.71417	0.930000	0.37139	0.684000	0.39900	2.565000	0.45939	0.718000	0.32166	0.655000	0.94253	CGT	.	.	.	none		0.408	TCAIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256655.2	NM_173826		T	44438258	C	T	44438258	3	4	116	1	0	0	0	0	1	0	0	0	2218	652	23	1	895	1	C3orf23	3	44438258	Missense_Mutation	SNP	C	TCGA-BQ-5881-01A-11D-1589-08		44438258	153584172	9	7434											
CCDC58	131076	hgsc.bcm.edu	37	chr3	122102042	122102042	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggaactcggcgaactcctcAcagttcacaccgccactggg	9	7	10	15	3	2	0	2	0	0	0	4	2	3	1	3	3	2	1	3	3	2	1			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr3:122102042A>G	ENST00000291458.5	-	1	36	c.30T>C	c.(28-30)tgT>tgC	p.C10C	CCDC58_ENST00000497726.1_Silent_p.C10C|FAM162A_ENST00000469967.1_5'Flank|FAM162A_ENST00000477892.1_5'Flank|FAM162A_ENST00000232125.5_5'Flank|CCDC58_ENST00000479899.1_5'UTR	NM_001017928.2	NP_001017928.1	Q4VC31	CCD58_HUMAN	coiled-coil domain containing 58	10						mitochondrion (GO:0005739)				large_intestine(1)|lung(1)	2				GBM - Glioblastoma multiforme(114;0.148)		CGAACTCCTCACAGTTCACAC	0.602																																					p.C10C		Atlas-SNP	.											.	CCDC58	14	.	0			c.T30C						PASS	.						83	73	76					3																	122102042		2203	4300	6503	SO:0001819	synonymous_variant	131076	exon1			CTCCTCACAGTTC	AK090592	CCDS33838.1	3q21.1	2006-01-17			ENSG00000160124	ENSG00000160124			31136	protein-coding gene	gene with protein product							Standard	XM_005247108		Approved	FLJ33273	uc003eey.3	Q4VC31	OTTHUMG00000159490	ENST00000291458.5:c.30T>C	chr3.hg19:g.122102042A>G		96.0	0.0	.		125.0	14.0	.	NM_001017928	Q32LY6	Silent	SNP	ENST00000291458.5	hg19	CCDS33838.1																																																																																			.	.	.	none		0.602	CCDC58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355754.1	NM_001017928		G	122102042	A	G	122102042	2	3	116	1	0	0	0	0	0	0	0	1	2830	157	6	3		3	CCDC58	3	122102042	Silent	SNP	A	TCGA-BQ-5881-01A-11D-1589-08	77663784	122102042	75920388	10	7435											
PIK3CB	5291	hgsc.bcm.edu	37	chr3	138409857	138409857	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttacctaagatgccaaaatAgaaactgccctatcctccga	14	9	5	13	1	0	2	0	0	0	2	2	3	2	2	5	0	4	0	5	0	7	4			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr3:138409857A>G	ENST00000477593.1	-	14	2094	c.2021T>C	c.(2020-2022)cTa>cCa	p.L674P	PIK3CB_ENST00000289153.2_Missense_Mutation_p.L674P|PIK3CB_ENST00000544716.1_Missense_Mutation_p.L120P			P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	674	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	ATGCCAAAATAGAAACTGCCC	0.353																																					p.L674P		Atlas-SNP	.											.	PIK3CB	103	.	0			c.T2021C						PASS	.						135	140	138					3																	138409857		2203	4300	6503	SO:0001583	missense	5291	exon13			CAAAATAGAAACT		CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	"phosphoinositide-3-kinase, catalytic, beta polypeptide"	PIK3C1		8246984	Standard	NM_006219		Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.2021T>C	chr3.hg19:g.138409857A>G	ENSP00000418143:p.Leu674Pro	188.0	0.0	.		269.0	63.0	.	NM_006219	D3DNF0|Q24JU2	Missense_Mutation	SNP	ENST00000477593.1	hg19	CCDS3104.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.8|21.8	4.204435|4.204435	0.79127|0.79127	.|.	.|.	ENSG00000051382|ENSG00000051382	ENST00000477593;ENST00000544716;ENST00000289153|ENST00000493568	T;T;T|.	0.77358|.	-1.09;-1.09;-1.09|.	5.66|5.66	5.66|5.66	0.87406|0.87406	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.86142|0.86142	0.5862|0.5862	M|M	0.93420|0.93420	3.415|3.415	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	0.998;0.997;1.0|.	D|D	0.89873|0.89873	0.4024|0.4024	10|5	0.87932|.	D|.	0|.	-9.4984|-9.4984	15.8807|15.8807	0.79201|0.79201	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	674;261;120|.	P42338;B4DZI3;Q68DL0|.	PK3CB_HUMAN;.;.|.	P|H	674;120;674|306	ENSP00000418143:L674P;ENSP00000438259:L120P;ENSP00000289153:L674P|.	ENSP00000289153:L674P|.	L|Y	-|-	2|1	0|0	PIK3CB|PIK3CB	139892547|139892547	1.000000|1.000000	0.71417|0.71417	0.989000|0.989000	0.46669|0.46669	0.983000|0.983000	0.72400|0.72400	9.339000|9.339000	0.96797|0.96797	2.151000|2.151000	0.67156|0.67156	0.533000|0.533000	0.62120|0.62120	CTA|TAT	.	.	.	none		0.353	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358019.1			G	138409857	A	G	138409857	3	3	116	1	0	0	0	0	1	0	0	0	11921	420	15	3	1229	3	PIK3CB	3	138409857	Missense_Mutation	SNP	A	TCGA-BQ-5881-01A-11D-1589-08	16307815	138409857	59612573	11	7436											
PDE6B	5158	hgsc.bcm.edu	37	chr4	619837	619837	+	Missense_Mutation	SNP	A	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	ggacatcggggtcgtgggccAcgtggctcagaccaaaaaga	11	5	15	10	3	1	2	1	0	0	2	3	3	1	3	2	5	0	1	2	5	2	0			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr4:619837A>C	ENST00000496514.1	+	1	443	c.422A>C	c.(421-423)cAc>cCc	p.H141P	PDE6B_ENST00000255622.6_Missense_Mutation_p.H141P			P35913	PDE6B_HUMAN	phosphodiesterase 6B, cGMP-specific, rod, beta	141	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)			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)	GTCGTGGGCCACGTGGCTCAG	0.642																																					p.H141P	GBM(71;463 1194 9848 25922 46834)	Atlas-SNP	.											.	PDE6B	80	.	0			c.A422C						PASS	.						22	16	18					4																	619837		2193	4298	6491	SO:0001583	missense	5158	exon1			TGGGCCACGTGGC	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.422A>C	chr4.hg19:g.619837A>C	ENSP00000420295:p.His141Pro	12.0	0.0	.		9.0	5.0	.	NM_001145291	B7Z9T9|E7ETT3|Q53XN5|Q9BWH5|Q9UD49	Missense_Mutation	SNP	ENST00000496514.1	hg19	CCDS33932.1	.	.	.	.	.	.	.	.	.	.	A	19.70	3.877195	0.72294	.	.	ENSG00000133256	ENST00000255622;ENST00000496514	T;T	0.67523	-0.27;-0.27	4.88	4.88	0.63580	GAF (2);	0.103854	0.64402	D	0.000005	T	0.81418	0.4818	M	0.91406	3.205	0.80722	D	1	D;D	0.55385	0.971;0.964	P;P	0.56865	0.808;0.709	D	0.84544	0.0640	10	0.49607	T	0.09	.	12.4206	0.55518	1.0:0.0:0.0:0.0	.	141;141	P35913;P35913-2	PDE6B_HUMAN;.	P	141	ENSP00000255622:H141P;ENSP00000420295:H141P	ENSP00000255622:H141P	H	+	2	0	PDE6B	609837	0.663000	0.27448	1.000000	0.80357	0.862000	0.49288	5.590000	0.67530	1.845000	0.53610	0.459000	0.35465	CAC	.	.	.	none		0.642	PDE6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358109.1	NM_000283		C	619837	A	C	619837	3	2	116	1	0	0	0	0	1	0	0	0	11653	159	6	5	424	5	PDE6B	4	619837	Missense_Mutation	SNP	A	TCGA-BQ-5881-01A-11D-1589-08		619837	190534439	12	7437											
CMYA5	202333	hgsc.bcm.edu	37	chr5	79032748	79032748	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaagttttggtggagaaaacTaagactttcctgccagtggt	12	12	11	6	0	0	2	0	0	0	2	1	3	1	2	2	3	2	1	2	3	4	4			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr5:79032748T>C	ENST00000446378.2	+	2	8191	c.8160T>C	c.(8158-8160)acT>acC	p.T2720T		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2720					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)		TGGAGAAAACTAAGACTTTCC	0.378																																					p.T2720T		Atlas-SNP	.											CMYA5_ENST00000446378,colon,carcinoma,0,2	CMYA5	643	.	0			c.T8160C						PASS	.						41	41	41					5																	79032748		1825	4074	5899	SO:0001819	synonymous_variant	202333	exon2			GAAAACTAAGACT	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.8160T>C	chr5.hg19:g.79032748T>C		38.0	0.0	.		26.0	3.0	.	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Silent	SNP	ENST00000446378.2	hg19	CCDS47238.1																																																																																			.	.	.	none		0.378	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		C	79032748	T	C	79032748	2	2	116	1	0	0	0	0	0	0	0	1	3592	1509	53	3		3	CMYA5	5	79032748	Silent	SNP	T	TCGA-BQ-5881-01A-11D-1589-08		79032748	101882512	13	7438											
SCAND3	114821	hgsc.bcm.edu	37	chr6	28543371	28543371	+	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	tacttggcatcttgaactaaCttccttaattgattttgatg	10	18	6	7	0	1	3	0	3	1	0	2	3	2	3	1	1	3	1	1	1	4	9			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr6:28543371C>A	ENST00000452236.2	-	3	1728	c.1111G>T	c.(1111-1113)Gtt>Ttt	p.V371F	SCAND3_ENST00000530247.1_5'Flank	NM_052923.1	NP_443155.1														NS(3)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(14)|liver(1)|lung(29)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)	71						CTTGAACTAACTTCCTTAATT	0.343																																					p.V371F		Atlas-SNP	.											.	SCAND3	156	.	0			c.G1111T						PASS	.						122	124	124					6																	28543371		2203	4300	6503	SO:0001583	missense	114821	exon3			AACTAACTTCCTT																												ENST00000452236.2:c.1111G>T	chr6.hg19:g.28543371C>A	ENSP00000395259:p.Val371Phe	195.0	0.0	.		199.0	63.0	.	NM_052923		Missense_Mutation	SNP	ENST00000452236.2	hg19	CCDS34355.1	.	.	.	.	.	.	.	.	.	.	C	16.74	3.208100	0.58343	.	.	ENSG00000232040	ENST00000452236	T	0.01474	4.85	3.45	2.58	0.30949	Integrase, catalytic core (1);Ribonuclease H-like (1);	.	.	.	.	T	0.01320	0.0043	L	0.29908	0.895	0.27530	N	0.951136	D	0.69078	0.997	D	0.63488	0.915	T	0.54337	-0.8309	9	0.23891	T	0.37	.	6.9505	0.24542	0.0:0.8705:0.0:0.1295	.	371	Q6R2W3	SCND3_HUMAN	F	371	ENSP00000395259:V371F	ENSP00000395259:V371F	V	-	1	0	SCAND3	28651350	0.993000	0.37304	0.998000	0.56505	0.998000	0.95712	0.080000	0.14802	0.789000	0.33779	0.655000	0.94253	GTT	.	.	.	none		0.343	SCAND3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000043551.3			A	28543371	C	A	28543371	3	1	116	1	0	0	0	0	1	0	0	0	13889	565	20	4	2874	4	SCAND3	6	28543371	Missense_Mutation	SNP	C	TCGA-BQ-5881-01A-11D-1589-08		28543371	142571696	14	7439											
BAT5	7920	hgsc.bcm.edu	37	chr6	31655645	31655646	+	Frame_Shift_Ins	INS	-	-	G																															caaccactgcctcaccactcINSgaagaccctcctctgccatc																										TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr6:31655645_31655646insG	ENST00000395952.3	-	17	1564_1565	c.1402_1403insC	c.(1402-1404)cgafs	p.R468fs	XXbac-BPG32J3.20_ENST00000461287.1_3'UTR|ABHD16A_ENST00000471644.1_5'UTR|ABHD16A_ENST00000440843.2_Frame_Shift_Ins_p.R435fs|ABHD16A_ENST00000375842.4_Frame_Shift_Ins_p.R249fs	NM_021160.2	NP_066983.1	O95870	ABHGA_HUMAN	abhydrolase domain containing 16A	468						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	10						CCTCACCACTCGAAGACCCTCC	0.594																																					p.R468fs		Atlas-INDEL	.											.	ABHD16A	34	.	0			c.1403_1404insC						PASS	.																																			SO:0001589	frameshift_variant	7920	exon17			.	AF129756	CCDS4713.1, CCDS54988.1	6p21.3	2013-01-17	2010-12-09	2010-12-09	ENSG00000204427	ENSG00000204427		"Abhydrolase domain containing"	13921	protein-coding gene	gene with protein product		142620	"HLA-B associated transcript 5"	BAT5		2911734, 2813433	Standard	NM_021160		Approved	NG26, D6S82E	uc003nvy.2	O95870	OTTHUMG00000031177	ENST00000395952.3:c.1403dupC	chr6.hg19:g.31655646_31655646dupG	ENSP00000379282:p.Arg468fs	135.0	0.0	0		118.0	21.0	0.177966	NM_021160	A2BEY3|B7Z4R6|Q5SRR1|Q5SRR2|Q8WYH0|Q9NW33	Frame_Shift_Ins	INS	ENST00000395952.3	hg19	CCDS4713.1																																																																																			.	.	.	none		0.594	ABHD16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076342.4			G	31655646	-	G	31655645	7	5	116	1	0	1	1	0	0	0	0	0	1324	884	31	0	289	0	BAT5	6	31655645	Frame_Shift_Ins	INS	-	TCGA-BQ-5881-01A-11D-1589-08	3112274	31655645	139459422	15	7440											
INTS1	26173	hgsc.bcm.edu	37	chr7	1535858	1535858	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctgtgatgcccagcatcaTggacacggccaggacgtcgg	8	6	14	13	4	1	1	1	1	0	0	2	3	1	3	2	4	2	2	2	4	0	0			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr7:1535858T>C	ENST00000404767.3	-	12	1730	c.1645A>G	c.(1645-1647)Atg>Gtg	p.M549V	INTS1_ENST00000389470.4_Missense_Mutation_p.M677V	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	549					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)		CCCAGCATCATGGACACGGCC	0.632																																					p.M549V		Atlas-SNP	.											.	INTS1	145	.	0			c.A1645G						PASS	.						84	95	91					7																	1535858		2106	4225	6331	SO:0001583	missense	26173	exon12			GCATCATGGACAC	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.1645A>G	chr7.hg19:g.1535858T>C	ENSP00000385722:p.Met549Val	93.0	0.0	.		136.0	35.0	.	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Missense_Mutation	SNP	ENST00000404767.3	hg19	CCDS47526.1	.	.	.	.	.	.	.	.	.	.	T	18.94	3.730230	0.69074	.	.	ENSG00000164880	ENST00000404767;ENST00000389470	T;T	0.47528	0.84;0.85	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.48021	0.1477	L	0.52011	1.625	0.80722	D	1	P	0.39044	0.656	B	0.42361	0.385	T	0.47509	-0.9112	10	0.41790	T	0.15	.	14.7485	0.69508	0.0:0.0:0.0:1.0	.	549	Q8N201	INT1_HUMAN	V	549;677	ENSP00000385722:M549V;ENSP00000374121:M677V	ENSP00000374121:M677V	M	-	1	0	INTS1	1502384	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	7.866000	0.87056	1.897000	0.54924	0.533000	0.62120	ATG	.	.	.	none		0.632	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1			C	1535858	T	C	1535858	3	2	116	1	0	0	0	0	1	0	0	0	7782	1464	51	3	5075	3	INTS1	7	1535858	Missense_Mutation	SNP	T	TCGA-BQ-5881-01A-11D-1589-08		1535858	157602805	16	7441											
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121668665	121668665	+	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	tacatcccctagagttatatCcacacctccaacacctatct	12	11	2	16	0	1	1	0	0	1	1	4	1	4	1	6	0	2	1	6	0	6	5	rs368834797		TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr7:121668665C>A	ENST00000393386.2	+	14	5459	c.5048C>A	c.(5047-5049)tCc>tAc	p.S1683Y	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.S823Y	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1683					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						AGAGTTATATCCACACCTCCA	0.383																																					p.S1683Y		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.C5048A						PASS	.						184	155	165					7																	121668665		2203	4300	6503	SO:0001583	missense	5803	exon14			TTATATCCACACC	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.5048C>A	chr7.hg19:g.121668665C>A	ENSP00000377047:p.Ser1683Tyr	132.0	0.0	.		173.0	11.0	.	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	hg19	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.480370	0.84747	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	T;T	0.79141	0.76;-1.24	5.8	5.8	0.92144	.	0.000000	0.64402	D	0.000002	D	0.84880	0.5570	L	0.46157	1.445	0.53688	D	0.999977	D;D;P	0.67145	0.996;0.97;0.95	D;P;P	0.65874	0.939;0.682;0.736	D	0.84173	0.0435	10	0.51188	T	0.08	.	20.0637	0.97700	0.0:1.0:0.0:0.0	.	822;823;1683	P23471-2;C9JFM0;P23471	.;.;PTPRZ_HUMAN	Y	1683;823	ENSP00000377047:S1683Y;ENSP00000410000:S823Y	ENSP00000377047:S1683Y	S	+	2	0	PTPRZ1	121455901	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.356000	0.79445	2.751000	0.94390	0.650000	0.86243	TCC	.	.	.	alt		0.383	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		A	121668665	C	A	121668665	3	1	116	1	0	0	0	0	1	0	0	0	12827	855	30	4	5102	4	PTPRZ1	7	121668665	Missense_Mutation	SNP	C	TCGA-BQ-5881-01A-11D-1589-08	120132807	121668665	37469998	17	7442											
SVEP1	79987	hgsc.bcm.edu	37	chr9	113259109	113259109	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttaccttttcaccagagtTgtctttagctgttggaatct	7	17	7	10	0	3	1	1	0	2	1	3	2	3	2	3	1	2	3	3	1	3	7			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr9:113259109T>C	ENST00000401783.2	-	8	2122	c.1786A>G	c.(1786-1788)Aac>Gac	p.N596D	SVEP1_ENST00000302728.8_Missense_Mutation_p.N596D|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374469.1_Missense_Mutation_p.N573D|SVEP1_ENST00000374461.1_Missense_Mutation_p.N573D	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	596	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)			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						TCACCAGAGTTGTCTTTAGCT	0.398																																					p.N596D		Atlas-SNP	.											.	SVEP1	326	.	0			c.A1786G						PASS	.						115	107	109					9																	113259109		1881	4083	5964	SO:0001583	missense	79987	exon8			CAGAGTTGTCTTT	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.1786A>G	chr9.hg19:g.113259109T>C	ENSP00000384917:p.Asn596Asp	4.0	0.0	.		12.0	4.0	.	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.505631	0.85282	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728;ENST00000374461	T;T;T;T	0.25579	1.79;1.79;1.79;1.79	5.71	5.71	0.89125	Hyalin (2);	0.000000	0.85682	D	0.000000	T	0.59088	0.2168	M	0.90759	3.145	0.38327	D	0.943687	D;D;D	0.89917	0.999;1.0;0.996	D;D;D	0.87578	0.995;0.998;0.99	T	0.71155	-0.4675	10	0.72032	D	0.01	.	14.9529	0.71088	0.0:0.0:0.0:1.0	.	596;596;596	E9PBN8;Q4LDE5;Q4LDE5-2	.;SVEP1_HUMAN;.	D	596;573;596;573	ENSP00000384917:N596D;ENSP00000363593:N573D;ENSP00000304118:N596D;ENSP00000363585:N573D	ENSP00000304118:N596D	N	-	1	0	SVEP1	112298930	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.259000	0.72494	2.181000	0.69327	0.477000	0.44152	AAC	.	.	.	none		0.398	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	113259109	T	C	113259109	3	2	116	1	0	0	0	0	1	0	0	0	15432	1812	63	3	9093	3	SVEP1	9	113259109	Missense_Mutation	SNP	T	TCGA-BQ-5881-01A-11D-1589-08		113259109	27954322	18	7443											
INTS5	80789	hgsc.bcm.edu	37	chr11	62417117	62417117	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgaggtcaatggaccatgcActaatcacaggtgcccaggc	12	7	11	11	0	2	1	2	1	0	0	2	2	2	2	2	4	2	1	2	4	2	1			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr11:62417117A>G	ENST00000330574.2	-	2	487	c.435T>C	c.(433-435)agT>agC	p.S145S		NM_030628.1	NP_085131.1	Q6P9B9	INT5_HUMAN	integrator complex subunit 5	145					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						TGGACCATGCACTAATCACAG	0.572																																					p.S145S		Atlas-SNP	.											.	INTS5	81	.	0			c.T435C						PASS	.						108	107	107					11																	62417117		2202	4299	6501	SO:0001819	synonymous_variant	80789	exon2			CCATGCACTAATC	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.435T>C	chr11.hg19:g.62417117A>G		126.0	0.0	.		111.0	44.0	.	NM_030628	Q8N6W5|Q9C0G5	Silent	SNP	ENST00000330574.2	hg19	CCDS8027.1																																																																																			.	.	.	none		0.572	INTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395327.1	NM_030628		G	62417117	A	G	62417117	2	3	116	1	0	0	0	0	0	0	0	1	7788	156	6	3		3	INTS5	11	62417117	Silent	SNP	A	TCGA-BQ-5881-01A-11D-1589-08		62417117	72589399	19	7444											
ARAP1	116985	hgsc.bcm.edu	37	chr11	72423355	72423355	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctattgtgctgggcaaggacAagctcaggctgctggtatgc	8	10	14	9	0	1	0	1	0	0	0	1	1	1	1	0	4	4	6	0	4	4	3			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr11:72423355A>G	ENST00000393609.3	-	7	1110	c.908T>C	c.(907-909)tTg>tCg	p.L303S	ARAP1_ENST00000426523.1_Missense_Mutation_p.L58S|ARAP1_ENST00000455638.2_Missense_Mutation_p.L303S|ARAP1_ENST00000429686.1_Missense_Mutation_p.L58S|ARAP1_ENST00000359373.5_Missense_Mutation_p.L303S|ARAP1_ENST00000334211.8_Missense_Mutation_p.L58S|ARAP1_ENST00000393605.3_Missense_Mutation_p.L63S	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	303					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						GGGCAAGGACAAGCTCAGGCT	0.672																																					p.L303S	Ovarian(102;1198 1520 13195 17913 37529)	Atlas-SNP	.											.	ARAP1	168	.	0			c.T908C						PASS	.						28	28	28					11																	72423355		2200	4293	6493	SO:0001583	missense	116985	exon7			AAGGACAAGCTCA	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.908T>C	chr11.hg19:g.72423355A>G	ENSP00000377233:p.Leu303Ser	20.0	0.0	.		23.0	6.0	.	NM_001040118	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Missense_Mutation	SNP	ENST00000393609.3	hg19	CCDS41687.1	.	.	.	.	.	.	.	.	.	.	A	0.304	-0.971901	0.02215	.	.	ENSG00000186635	ENST00000359373;ENST00000455638;ENST00000393605;ENST00000334211;ENST00000393609;ENST00000426523;ENST00000429686;ENST00000340247	T;T;T;T;T;T;T	0.13538	2.58;2.58;2.58;2.58;2.58;2.58;2.58	4.44	2.14	0.27477	.	0.724250	0.11919	N	0.516857	T	0.05135	0.0137	N	0.03608	-0.345	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.43621	-0.9380	10	0.07990	T	0.79	.	8.6422	0.33983	0.16:0.0:0.84:0.0	.	58;58;303;303;63	E7EU13;B2RTS2;Q96P48-3;Q96P48;Q96P48-1	.;.;.;ARAP1_HUMAN;.	S	303;303;63;58;303;58;58;92	ENSP00000352332:L303S;ENSP00000390461:L303S;ENSP00000377230:L63S;ENSP00000335506:L58S;ENSP00000377233:L303S;ENSP00000392264:L58S;ENSP00000403127:L58S	ENSP00000335506:L58S	L	-	2	0	ARAP1	72101003	0.145000	0.22656	0.008000	0.14137	0.081000	0.17604	0.839000	0.27586	0.330000	0.23485	0.459000	0.35465	TTG	.	.	.	none		0.672	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118		G	72423355	A	G	72423355	3	3	116	1	0	0	0	0	1	0	0	0	838	131	5	3	3560	3	ARAP1	11	72423355	Missense_Mutation	SNP	A	TCGA-BQ-5881-01A-11D-1589-08	10006238	72423355	62583161	20	7445											
ZW10	9183	hgsc.bcm.edu	37	chr11	113628545	113628545	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggatgggcaagatgccagcGgcctaaggatatacttcagc	11	7	14	9	1	1	1	1	0	0	1	1	3	1	3	2	4	4	1	2	4	4	4	rs377079908		TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr11:113628545G>A	ENST00000200135.3	-	7	908	c.764C>T	c.(763-765)cCg>cTg	p.P255L		NM_004724.3	NP_004715.1	O43264	ZW10_HUMAN	zw10 kinetochore protein	255	Interaction with RINT1.				ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic metaphase plate congression (GO:0007080)|mitotic sister chromatid segregation (GO:0000070)|protein complex assembly (GO:0006461)|protein localization to kinetochore (GO:0034501)|protein transport (GO:0015031)|regulation of exit from mitosis (GO:0007096)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|nucleus (GO:0005634)|spindle pole (GO:0000922)	centromeric DNA binding (GO:0019237)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)	18		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)		AGATGCCAGCGGCCTAAGGAT	0.403													G|||	1	0.000199681	8e-04	0	5008	,	,		18410	0		0	False		,,,				2504	0				p.P255L		Atlas-SNP	.											.	ZW10	49	.	0			c.C764T						PASS	.	G	LEU/PRO	0,4402		0,0,2201	66	69	68		764	5.5	1	11		68	1,8591	1.2+/-3.3	0,1,4295	no	missense	ZW10	NM_004724.3	98	0,1,6496	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	255/780	113628545	1,12993	2201	4296	6497	SO:0001583	missense	9183	exon7			GCCAGCGGCCTAA	U54996	CCDS8363.1	11q23	2013-01-17	2012-12-13		ENSG00000086827	ENSG00000086827			13194	protein-coding gene	gene with protein product		603954	"ZW10 (Drosophila) homolog, centromere/kinetochore protein", "ZW10, kinetochore associated, homolog (Drosophila)"			9298984	Standard	NM_004724		Approved	KNTC1AP	uc001poe.3	O43264	OTTHUMG00000168190	ENST00000200135.3:c.764C>T	chr11.hg19:g.113628545G>A	ENSP00000200135:p.Pro255Leu	73.0	0.0	.		65.0	19.0	.	NM_004724	A1A528	Missense_Mutation	SNP	ENST00000200135.3	hg19	CCDS8363.1	.	.	.	.	.	.	.	.	.	.	G	19.95	3.921357	0.73213	0.0	1.16E-4	ENSG00000086827	ENST00000200135	T	0.64438	-0.1	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.62392	0.2424	L	0.53249	1.67	0.80722	D	1	P	0.43857	0.819	B	0.41374	0.355	T	0.68330	-0.5437	10	0.87932	D	0	-10.4182	18.3058	0.90180	0.0:0.0:1.0:0.0	.	255	O43264	ZW10_HUMAN	L	255	ENSP00000200135:P255L	ENSP00000200135:P255L	P	-	2	0	ZW10	113133755	1.000000	0.71417	0.999000	0.59377	0.869000	0.49853	8.079000	0.89508	2.571000	0.86741	0.650000	0.86243	CCG	.	.	.	weak		0.403	ZW10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398700.1	NM_004724		A	113628545	G	A	113628545	3	1	116	1	0	0	0	0	1	0	0	0	18259	1116	39	1	1615	1	ZW10	11	113628545	Missense_Mutation	SNP	G	TCGA-BQ-5881-01A-11D-1589-08	41205190	113628545	21377971	21	7446											
AKAP6	9472	hgsc.bcm.edu	37	chr14	33204952	33204952	+	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	ctctcctgaaagtggaagccTggtaaggcagctggaggtca	10	8	14	9	0	2	1	1	1	1	0	3	3	2	3	2	5	2	3	2	5	3	1	rs201928179		TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr14:33204952T>A	ENST00000280979.4	+	11	3406	c.3236T>A	c.(3235-3237)cTg>cAg	p.L1079Q	AKAP6_ENST00000557272.1_Missense_Mutation_p.L1079Q	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	1079					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)		AGTGGAAGCCTGGTAAGGCAG	0.488																																					p.L1079Q	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.T3236A						PASS	.						70	72	71					14																	33204952		2203	4300	6503	SO:0001583	missense	9472	exon11			GAAGCCTGGTAAG	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.3236T>A	chr14.hg19:g.33204952T>A	ENSP00000280979:p.Leu1079Gln	92.0	0.0	.		77.0	26.0	.	NM_004274	A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	hg19	CCDS9644.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.981383	0.74474	.	.	ENSG00000151320	ENST00000280979;ENST00000557272	T;T	0.22539	3.18;1.95	5.7	4.54	0.55810	.	0.118007	0.37809	N	0.001926	T	0.26629	0.0651	N	0.14661	0.345	0.44000	D	0.996707	D	0.71674	0.998	D	0.63488	0.915	T	0.07385	-1.0775	10	0.62326	D	0.03	-5.2892	12.8687	0.57953	0.0:0.0:0.1363:0.8637	.	1079	Q13023	AKAP6_HUMAN	Q	1079	ENSP00000280979:L1079Q;ENSP00000451247:L1079Q	ENSP00000280979:L1079Q	L	+	2	0	AKAP6	32274703	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.041000	0.76558	0.961000	0.38030	0.477000	0.44152	CTG	.	T|1.000;C|0.000	.	alt		0.488	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274		A	33204952	T	A	33204952	3	1	116	1	0	0	0	0	1	0	0	0	455	1580	55	5	3274	5	AKAP6	14	33204952	Missense_Mutation	SNP	T	TCGA-BQ-5881-01A-11D-1589-08		33204952	74144588	22	7447											
DAAM1	23002	hgsc.bcm.edu	37	chr14	59791109	59791109	+	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	tcatcttcgctatgaatttcTgatgttaggaattcaacctg	10	16	7	8	1	4	2	2	2	2	0	5	3	4	3	1	1	1	2	1	1	5	5			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr14:59791109T>A	ENST00000395125.1	+	7	949	c.926T>A	c.(925-927)cTg>cAg	p.L309Q	DAAM1_ENST00000360909.3_Missense_Mutation_p.L309Q|DAAM1_ENST00000351081.1_Missense_Mutation_p.L309Q	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	309	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)		TATGAATTTCTGATGTTAGGA	0.308																																					p.L309Q		Atlas-SNP	.											.	DAAM1	95	.	0			c.T926A						PASS	.						87	91	90					14																	59791109		2203	4300	6503	SO:0001583	missense	23002	exon8			AATTTCTGATGTT	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.926T>A	chr14.hg19:g.59791109T>A	ENSP00000378557:p.Leu309Gln	134.0	0.0	.		117.0	35.0	.	NM_001270520	Q86U34|Q8N1Z8|Q8TB39	Missense_Mutation	SNP	ENST00000395125.1	hg19	CCDS9737.1	.	.	.	.	.	.	.	.	.	.	T	17.20	3.330005	0.60743	.	.	ENSG00000100592	ENST00000360909;ENST00000351081;ENST00000358498;ENST00000395125	D;D;D	0.84516	-1.86;-1.86;-1.86	5.17	4.01	0.46588	GTPase-binding/formin homology 3 (1);Diaphanous FH3 (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.88377	0.6420	M	0.80508	2.5	0.80722	D	1	P;P	0.45634	0.835;0.863	P;P	0.49140	0.466;0.601	D	0.88524	0.3098	10	0.62326	D	0.03	.	12.2246	0.54453	0.0:0.0:0.1426:0.8574	.	309;309	Q9Y4D1-2;Q9Y4D1	.;DAAM1_HUMAN	Q	309	ENSP00000354162:L309Q;ENSP00000247170:L309Q;ENSP00000378557:L309Q	ENSP00000247170:L309Q	L	+	2	0	DAAM1	58860862	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.841000	0.86834	0.965000	0.38133	0.533000	0.62120	CTG	.	.	.	none		0.308	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992		A	59791109	T	A	59791109	3	1	116	1	0	0	0	0	1	0	0	0	4217	1580	55	5	952	5	DAAM1	14	59791109	Missense_Mutation	SNP	T	TCGA-BQ-5881-01A-11D-1589-08	26586157	59791109	47558431	23	7448											
MGA	23269	hgsc.bcm.edu	37	chr15	42005411	42005411	+	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	cgagcccctccctgcaacaaTgacttctgtcgactgggttg	7	10	10	14	2	1	1	0	1	1	0	3	3	2	1	3	1	3	2	3	1	2	2			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr15:42005411T>A	ENST00000570161.1	+	8	3147	c.3147T>A	c.(3145-3147)aaT>aaA	p.N1049K	MGA_ENST00000389936.4_Missense_Mutation_p.N1049K|MGA_ENST00000545763.1_Missense_Mutation_p.N1049K|MGA_ENST00000219905.7_Missense_Mutation_p.N1049K|MGA_ENST00000566586.1_Missense_Mutation_p.N1049K			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	CCTGCAACAATGACTTCTGTC	0.463																																					p.N1049K		Atlas-SNP	.											.	MGA	264	.	0			c.T3147A						PASS	.						156	153	154					15																	42005411		1992	4139	6131	SO:0001583	missense	23269	exon9			CAACAATGACTTC	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.3147T>A	chr15.hg19:g.42005411T>A	ENSP00000457035:p.Asn1049Lys	132.0	0.0	.		117.0	32.0	.	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	hg19	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	T	15.20	2.762234	0.49468	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	T;T;T	0.16457	2.34;2.34;2.34	5.75	3.24	0.37175	.	0.270326	0.40144	N	0.001172	T	0.15739	0.0379	N	0.14661	0.345	0.36995	D	0.894984	P;P	0.50272	0.933;0.533	P;B	0.56865	0.808;0.305	T	0.15983	-1.0418	10	0.44086	T	0.13	.	4.9526	0.14023	0.1341:0.1556:0.0:0.7103	.	1049;1049	F5H7K2;E7ENI0	.;.	K	1049	ENSP00000219905:N1049K;ENSP00000374586:N1049K;ENSP00000442467:N1049K	ENSP00000219905:N1049K	N	+	3	2	MGA	39792703	0.996000	0.38824	1.000000	0.80357	0.997000	0.91878	0.237000	0.17985	0.882000	0.36016	0.533000	0.62120	AAT	.	.	.	none		0.463	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		A	42005411	T	A	42005411	3	1	116	1	0	0	0	0	1	0	0	0	9547	1461	51	5	3177	5	MGA	15	42005411	Missense_Mutation	SNP	T	TCGA-BQ-5881-01A-11D-1589-08		42005411	60525981	24	7449											
VPS13C	54832	hgsc.bcm.edu	37	chr15	62167108	62167108	+	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	aaagaggcttctcactccaaTcactaacccctctgcaaatt	13	10	4	14	0	3	1	2	0	2	1	5	1	4	1	3	1	2	2	3	1	4	3			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr15:62167108T>A	ENST00000261517.5	-	77	10454	c.10381A>T	c.(10381-10383)Att>Ttt	p.I3461F	VPS13C_ENST00000558919.1_5'Flank|VPS13C_ENST00000395898.3_Missense_Mutation_p.I3418F|VPS13C_ENST00000249837.3_Missense_Mutation_p.I3418F|VPS13C_ENST00000395896.4_Missense_Mutation_p.I3461F	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						CTCACTCCAATCACTAACCCC	0.303																																					p.I3461F		Atlas-SNP	.											.	VPS13C	506	.	0			c.A10381T						PASS	.						104	104	104					15																	62167108		2203	4300	6503	SO:0001583	missense	54832	exon77			CTCCAATCACTAA	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.10381A>T	chr15.hg19:g.62167108T>A	ENSP00000261517:p.Ile3461Phe	141.0	0.0	.		173.0	60.0	.	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	hg19	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.404605	0.83230	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.43294	0.95;0.95;1.12	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.56108	0.1963	L	0.40543	1.245	0.80722	D	1	D;D;D;D	0.69078	0.978;0.995;0.997;0.997	D;D;D;D	0.71656	0.923;0.962;0.974;0.92	T	0.56511	-0.7967	10	0.54805	T	0.06	.	16.1946	0.82018	0.0:0.0:0.0:1.0	.	3418;3461;3418;3461	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	F	3418;3461;3461;3461	ENSP00000249837:I3418F;ENSP00000261517:I3461F;ENSP00000379233:I3461F	ENSP00000249837:I3418F	I	-	1	0	VPS13C	59954400	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	4.402000	0.59722	2.228000	0.72767	0.528000	0.53228	ATT	.	.	.	none		0.303	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		A	62167108	T	A	62167108	3	1	116	1	0	0	0	0	1	0	0	0	17203	1435	50	5	944	5	VPS13C	15	62167108	Missense_Mutation	SNP	T	TCGA-BQ-5881-01A-11D-1589-08	20161697	62167108	40364284	25	7450											
TP53	7157	hgsc.bcm.edu	37	chr17	7578190	7578190	+	Missense_Mutation	SNP	T	T	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	accagacctcaggcggctcaTagggcaccaccacactatgt	11	6	9	15	1	2	1	2	0	0	1	2	1	2	1	4	3	0	2	4	3	2	2	rs121912666		TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr17:7578190T>G	ENST00000269305.4	-	6	848	c.659A>C	c.(658-660)tAt>tCt	p.Y220S	TP53_ENST00000413465.2_Missense_Mutation_p.Y220S|TP53_ENST00000420246.2_Missense_Mutation_p.Y220S|TP53_ENST00000455263.2_Missense_Mutation_p.Y220S|TP53_ENST00000574684.1_Intron|TP53_ENST00000359597.4_Missense_Mutation_p.Y220S|TP53_ENST00000445888.2_Missense_Mutation_p.Y220S	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	220	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Y -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:9450901}.|Y -> D (in sporadic cancers; somatic mutation).|Y -> F (in a sporadic cancer; somatic mutation).|Y -> H (in sporadic cancers; somatic mutation).|Y -> N (in sporadic cancers; somatic mutation).|Y -> S (in a brain tumor with no family history; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Y220C(278)|p.Y127C(24)|p.Y220S(12)|p.?(11)|p.0?(8)|p.D208fs*1(1)|p.Y220_P223delYEPP(1)|p.V218_E224delVPYEPPE(1)|p.V218_E221delVPYE(1)|p.Y127S(1)|p.V218_Y220delVPY(1)|p.Y220fs*25(1)|p.V216_Y220delVVVPY(1)|p.Y220fs*2(1)|p.V218fs*26(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	AGGCGGCTCATAGGGCACCAC	0.557		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.Y220S	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,NS,carcinoma,0,1	TP53	33396	.	343	Substitution - Missense(315)|Unknown(11)|Whole gene deletion(8)|Deletion - In frame(5)|Deletion - Frameshift(3)|Insertion - Frameshift(1)	ovary(55)|breast(54)|lung(37)|upper_aerodigestive_tract(35)|urinary_tract(19)|oesophagus(19)|large_intestine(17)|liver(17)|central_nervous_system(16)|stomach(15)|haematopoietic_and_lymphoid_tissue(15)|endometrium(14)|soft_tissue(8)|biliary_tract(6)|bone(5)|pancreas(4)|prostate(4)|peritoneum(2)|small_intestine(1)	c.A659C	GRCh37	CM015378|CM951227	TP53	M	rs121912666	PASS	.						102	94	97					17																	7578190		2203	4300	6503	SO:0001583	missense	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GGCTCATAGGGCA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"Li-Fraumeni syndrome"	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.659A>C	chr17.hg19:g.7578190T>G	ENSP00000269305:p.Tyr220Ser	44.0	0.0	.		61.0	9.0	.	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.447753	0.84101	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99833	-7.03;-7.03;-7.03;-7.03;-7.03;-7.03;-7.03;-7.03	5.28	5.28	0.74379	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99822	0.9921	M	0.89287	3.02	0.80722	A	1	D;D;D;D;D;D;D	0.89917	1.0;0.994;0.997;1.0;0.995;0.968;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.921;0.963;1.0;0.977;0.926;1.0	D	0.96735	0.9542	9	0.87932	D	0	-1.87	13.4753	0.61306	0.0:0.0:0.0:1.0	.	181;220;220;127;220;220;220	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	S	220;220;220;220;220;220;209;127;88;127	ENSP00000410739:Y220S;ENSP00000352610:Y220S;ENSP00000269305:Y220S;ENSP00000398846:Y220S;ENSP00000391127:Y220S;ENSP00000391478:Y220S;ENSP00000425104:Y88S;ENSP00000423862:Y127S	ENSP00000269305:Y220S	Y	-	2	0	TP53	7518915	1.000000	0.71417	0.585000	0.28666	0.993000	0.82548	6.232000	0.72313	2.128000	0.65567	0.460000	0.39030	TAT	.	.	.	weak		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		G	7578190	T	G	7578190	3	3	116	1	0	0	0	0	1	0	0	0	16393	1406	49	5	635	5	TP53	17	7578190	Missense_Mutation	SNP	T	TCGA-BQ-5881-01A-11D-1589-08		7578190	73617020	26	7451											
CHAD	1101	hgsc.bcm.edu	37	chr17	48546019	48546019	+	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	tgtaggttgagcagcttggtCttctctgacaccttggggat	6	14	13	8	0	2	2	0	2	2	0	3	3	2	3	1	4	2	4	1	4	1	5			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr17:48546019C>A	ENST00000508540.1	-	1	308	c.156G>T	c.(154-156)aaG>aaT	p.K52N	ACSF2_ENST00000502667.1_Intron|ACSF2_ENST00000504392.1_Intron|ACSF2_ENST00000300441.4_Intron|CHAD_ENST00000258969.4_Missense_Mutation_p.K52N|ACSF2_ENST00000506085.1_Intron|ACSF2_ENST00000541920.1_Intron|ACSF2_ENST00000427954.2_Intron	NM_001267.2	NP_001258.2	O15335	CHAD_HUMAN	chondroadherin	52	LRRNT.				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)			GCAGCTTGGTCTTCTCTGACA	0.622																																					p.K52N		Atlas-SNP	.											.	CHAD	36	.	0			c.G156T						PASS	.						92	77	82					17																	48546019		2203	4300	6503	SO:0001583	missense	1101	exon1			CTTGGTCTTCTCT	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.156G>T	chr17.hg19:g.48546019C>A	ENSP00000423812:p.Lys52Asn	70.0	0.0	.		86.0	17.0	.	NM_001267	A8K812|Q6GTU0|Q96RJ5	Missense_Mutation	SNP	ENST00000508540.1	hg19	CCDS11568.1	.	.	.	.	.	.	.	.	.	.	C	9.129	1.010904	0.19277	.	.	ENSG00000136457	ENST00000508540;ENST00000258969	T;T	0.04015	3.73;3.73	4.31	2.29	0.28610	Leucine-rich repeat-containing N-terminal (1);	0.490348	0.23123	N	0.051679	T	0.01835	0.0058	N	0.04018	-0.295	0.28724	N	0.902844	B	0.17465	0.022	B	0.14578	0.011	T	0.45086	-0.9285	10	0.09084	T	0.74	.	4.7213	0.12920	0.1537:0.601:0.0:0.2453	.	52	O15335	CHAD_HUMAN	N	52	ENSP00000423812:K52N;ENSP00000258969:K52N	ENSP00000258969:K52N	K	-	3	2	CHAD	45901018	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	1.268000	0.33062	0.442000	0.26555	0.462000	0.41574	AAG	.	.	.	none		0.622	CHAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367447.3	NM_001267		A	48546019	C	A	48546019	3	1	116	1	0	0	0	0	1	0	0	0	3312	912	32	4	935	4	CHAD	17	48546019	Missense_Mutation	SNP	C	TCGA-BQ-5881-01A-11D-1589-08	40967829	48546019	32649191	27	7452											
ZNF559	84527	hgsc.bcm.edu	37	chr19	9452840	9452840	+	Frame_Shift_Del	DEL	A	A	-																															catgcaaactcaagatggagAaaaattctatgaatgtaaag																										TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr19:9452840delA	ENST00000393883.2	+	6	1361	c.713delA	c.(712-714)gaafs	p.E238fs	ZNF559_ENST00000592896.1_3'UTR|ZNF177_ENST00000602738.1_Intron|ZNF559_ENST00000538743.1_Frame_Shift_Del_p.E158fs|ZNF559_ENST00000603380.1_Frame_Shift_Del_p.E238fs|ZNF177_ENST00000541595.2_Intron|CTC-325H20.2_ENST00000592371.1_lincRNA|ZNF559_ENST00000586255.1_Intron|ZNF559_ENST00000317221.7_3'UTR|ZNF177_ENST00000605471.1_Intron|ZNF177_ENST00000446085.4_Intron|ZNF559_ENST00000587557.1_Frame_Shift_Del_p.E302fs|ZNF177_ENST00000602856.1_Intron	NM_001202412.1	NP_001189341.1	Q9BR84	ZN559_HUMAN	zinc finger protein 559	238					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						CAAGATGGAGAAAAATTCTAT	0.363																																					p.E302fs		Atlas-INDEL	.											.	ZNF559	77	.	0			c.904delG						PASS	.						77	79	79					19																	9452840		2201	4300	6501	SO:0001589	frameshift_variant	84527	exon6			.	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.713delA	chr19.hg19:g.9452840delA	ENSP00000377461:p.Glu238fs	106.0	0.0	0		110.0	38.0	0.345455	NM_001202406	K7EMG6	Frame_Shift_Del	DEL	ENST00000393883.2	hg19	CCDS12211.1																																																																																			.	.	.	none		0.363	ZNF559-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449021.1	NM_032497		-	9452840	A	-	9452840	7	5	116	1	0	1	0	1	0	0	0	0	18002	246	9	0	727	0	ZNF559	19	9452840	Frame_Shift_Del	DEL	A	TCGA-BQ-5881-01A-11D-1589-08		9452840	49676143	28	7453											
RBPJL	11317	hgsc.bcm.edu	37	chr20	43940944	43940944	+	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	gtgctgcggctggtgctgcgCgggggccgggagctgggtac	2	7	22	10	4	0	0	0	0	0	0	0	1	0	1	1	6	6	5	1	6	1	1			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr20:43940944C>T	ENST00000343694.3	+	6	600	c.528C>T	c.(526-528)cgC>cgT	p.R176R	RBPJL_ENST00000372741.3_Silent_p.R176R|RBPJL_ENST00000372743.1_Silent_p.R176R	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	176					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)				tggtgctgcgCGGGGGCCGGG	0.602																																					p.R176R		Atlas-SNP	.											RBPJL,NS,chondrosarcoma,0,1	RBPJL	67	.	0			c.C528T						PASS	.						28	31	30					20																	43940944		2203	4300	6503	SO:0001819	synonymous_variant	11317	exon6			GCTGCGCGGGGGC	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.528C>T	chr20.hg19:g.43940944C>T		39.0	1.0	.		44.0	14.0	.	NM_014276	O95723|Q5QPU9|Q5QPV0|Q9ULV9	Silent	SNP	ENST00000343694.3	hg19	CCDS13349.1																																																																																			.	.	.	none		0.602	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276		T	43940944	C	T	43940944	2	4	116	1	0	0	0	0	0	0	0	1	13175	755	27	1		1	RBPJL	20	43940944	Silent	SNP	C	TCGA-BQ-5881-01A-11D-1589-08		43940944	19084576	29	7454											
TOP3B	8940	hgsc.bcm.edu	37	chr22	22327036	22327036	+	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	tagcttctttcttctccgtgGgagcttggctgaacagttct	5	16	10	10	1	4	1	0	1	4	0	5	2	4	2	1	2	3	4	1	2	2	6			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr22:22327036G>T	ENST00000398793.2	-	4	691	c.257C>A	c.(256-258)cCc>cAc	p.P86H	TOP3B_ENST00000357179.5_Missense_Mutation_p.P86H|TOP3B_ENST00000413067.2_5'UTR	NM_003935.3	NP_003926.1	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	86	Toprim. {ECO:0000255|PROSITE- ProRule:PRU00995}.				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)		CTTCTCCGTGGGAGCTTGGCT	0.562											OREG0026347	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P86H		Atlas-SNP	.											.	TOP3B	107	.	0			c.C257A						PASS	.						155	123	134					22																	22327036		2203	4300	6503	SO:0001583	missense	8940	exon4			TCCGTGGGAGCTT	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.257C>A	chr22.hg19:g.22327036G>T	ENSP00000381773:p.Pro86His	65.0	0.0	.	755	69.0	29.0	.	NM_003935	A0M8Q3|Q9BUP5	Missense_Mutation	SNP	ENST00000398793.2	hg19	CCDS13797.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.372315	0.82573	.	.	ENSG00000100038	ENST00000357179;ENST00000398793;ENST00000449517;ENST00000424393;ENST00000437929;ENST00000430142	T;T;T;T;T	0.21543	2.0;2.0;2.0;2.0;2.0	5.0	3.97	0.46021	DNA topoisomerase, type IA, core domain (1);Toprim domain (2);	0.052237	0.85682	D	0.000000	T	0.47563	0.1452	H	0.94620	3.56	0.80722	D	1	P	0.41848	0.763	P	0.48030	0.564	T	0.65166	-0.6234	10	0.87932	D	0	-8.5874	15.6079	0.76689	0.0:0.1378:0.8622:0.0	.	86	O95985	TOP3B_HUMAN	H	86	ENSP00000349705:P86H;ENSP00000381773:P86H;ENSP00000390977:P86H;ENSP00000402622:P86H;ENSP00000414538:P86H	ENSP00000349705:P86H	P	-	2	0	TOP3B	20657036	1.000000	0.71417	0.432000	0.26747	0.906000	0.53458	9.361000	0.97122	1.317000	0.45149	0.563000	0.77884	CCC	.	.	.	none		0.562	TOP3B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320251.1	NM_003935		T	22327036	G	T	22327036	3	4	116	1	0	0	0	0	1	0	0	0	16380	1232	43	4	2391	4	TOP3B	22	22327036	Missense_Mutation	SNP	G	TCGA-BQ-5881-01A-11D-1589-08		22327036	28977530	30	7455											
CABIN1	23523	hgsc.bcm.edu	37	chr22	24483456	24483456	+	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	cgggccagccgcattcaggaCaagctgaactccaatgagct	11	6	11	13	2	1	2	1	2	0	0	2	3	2	3	3	2	4	3	3	2	3	1			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chr22:24483456C>A	ENST00000398319.2	+	23	3700	c.3315C>A	c.(3313-3315)gaC>gaA	p.D1105E	CABIN1_ENST00000263119.5_Missense_Mutation_p.D1105E|CABIN1_ENST00000405822.2_Missense_Mutation_p.D1055E	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	1105					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						GCATTCAGGACAAGCTGAACT	0.547																																					p.D1105E		Atlas-SNP	.											.	CABIN1	153	.	0			c.C3315A						PASS	.						70	64	66					22																	24483456		2203	4300	6503	SO:0001583	missense	23523	exon23			TCAGGACAAGCTG	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.3315C>A	chr22.hg19:g.24483456C>A	ENSP00000381364:p.Asp1105Glu	85.0	0.0	.		61.0	15.0	.	NM_001199281	G5E9F3|Q6PHY0|Q9Y460	Missense_Mutation	SNP	ENST00000398319.2	hg19	CCDS13823.1	.	.	.	.	.	.	.	.	.	.	C	16.53	3.149010	0.57151	.	.	ENSG00000099991	ENST00000263119;ENST00000405822;ENST00000398319	T;T;T	0.75477	-0.94;-0.94;-0.94	5.1	1.91	0.25777	Tetratricopeptide-like helical (1);	0.055118	0.64402	D	0.000001	T	0.54111	0.1838	L	0.27053	0.805	0.80722	D	1	P;P	0.40619	0.724;0.603	B;B	0.34452	0.183;0.089	T	0.42899	-0.9424	10	0.23302	T	0.38	.	9.3964	0.38406	0.0:0.7705:0.0:0.2295	.	1055;1105	G5E9F3;Q9Y6J0	.;CABIN_HUMAN	E	1105;1055;1105	ENSP00000263119:D1105E;ENSP00000384694:D1055E;ENSP00000381364:D1105E	ENSP00000263119:D1105E	D	+	3	2	CABIN1	22813456	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.242000	0.32755	0.299000	0.22661	0.650000	0.86243	GAC	.	.	.	none		0.547	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295		A	24483456	C	A	24483456	3	1	116	1	0	0	0	0	1	0	0	0	2530	477	17	4	3401	4	CABIN1	22	24483456	Missense_Mutation	SNP	C	TCGA-BQ-5881-01A-11D-1589-08	2156420	24483456	26821110	31	7456											
DDX53	168400	hgsc.bcm.edu	37	chrX	23019108	23019108	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctagagagttggctcttcacGtggaagctgaatgttcaaag	11	11	12	7	1	3	2	2	1	1	1	3	4	3	3	0	2	1	4	0	2	4	4			TCGA-BQ-5881-01A-11D-1589-08	TCGA-BQ-5881-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	759af132-b471-4ceb-b72a-3c665d2fd20c	6cd411c9-9521-4a49-9caf-2b2652a4c0e4	g.chrX:23019108G>A	ENST00000327968.5	+	1	1022	c.934G>A	c.(934-936)Gtg>Atg	p.V312M	RP11-40F8.2_ENST00000455399.1_lincRNA	NM_182699.3	NP_874358.2	Q86TM3	DDX53_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 53	312	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|RNA binding (GO:0003723)			breast(2)|endometrium(5)|kidney(4)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	35						GGCTCTTCACGTGGAAGCTGA	0.408													G|||	1	0.000264901	8e-04	0	3775	,	,		16112	0		0	False		,,,				2504	0				p.V312M		Atlas-SNP	.											.	DDX53	76	.	0			c.G934A						PASS	.						74	73	73					X																	23019108		2203	4300	6503	SO:0001583	missense	168400	exon1			CTTCACGTGGAAG	AY039237	CCDS35214.1	Xp22.13	2009-03-25			ENSG00000184735	ENSG00000184735		"DEAD-boxes"	20083	protein-coding gene	gene with protein product	"cancer associated gene", "cancer/testis antigen 26"						Standard	NM_182699		Approved	CAGE, CT26	uc004daj.3	Q86TM3	OTTHUMG00000021248	ENST00000327968.5:c.934G>A	chrX.hg19:g.23019108G>A	ENSP00000368667:p.Val312Met	68.0	0.0	.		64.0	36.0	.	NM_182699	Q0D2N2|Q6NVV4	Missense_Mutation	SNP	ENST00000327968.5	hg19	CCDS35214.1	.	.	.	.	.	.	.	.	.	.	G	9.356	1.066739	0.20067	.	.	ENSG00000184735	ENST00000327968	T	0.05139	3.49	4.3	1.28	0.21552	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.300009	0.31370	N	0.007767	T	0.24586	0.0596	M	0.91920	3.255	0.09310	N	1	D	0.89917	1.0	D	0.85130	0.997	T	0.02877	-1.1099	10	0.87932	D	0	-6.7638	4.8973	0.13757	0.2269:0.1801:0.593:0.0	.	312	Q86TM3	DDX53_HUMAN	M	312	ENSP00000368667:V312M	ENSP00000368667:V312M	V	+	1	0	DDX53	22929029	1.000000	0.71417	0.029000	0.17559	0.023000	0.10783	2.224000	0.42945	0.759000	0.33084	0.600000	0.82982	GTG	.	.	.	none		0.408	DDX53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056043.1	NM_182699		A	23019108	G	A	23019108	3	1	116	1	0	0	0	0	1	0	0	0	4373	1145	40	1	936	1	DDX53	23	23019108	Missense_Mutation	SNP	G	TCGA-BQ-5881-01A-11D-1589-08		23019108	132251452	32	7457											
ZBTB8OS	339487	hgsc.bcm.edu	37	chr1	33099257	33099257	+	Missense_Mutation	SNP	A	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	tttgcttacccggggtatgaAgaattcatcagcactgaact	11	12	9	9	1	2	3	2	2	0	1	2	3	2	3	1	2	4	3	1	2	5	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr1:33099257A>C	ENST00000468695.1	-	4	370	c.352T>G	c.(352-354)Ttc>Gtc	p.F118V	ZBTB8OS_ENST00000373501.2_Missense_Mutation_p.F106V|ZBTB8OS_ENST00000492007.1_Intron|ZBTB8OS_ENST00000341885.5_Intron	NM_178547.2	NP_848642.1	Q8IWT0	ARCH_HUMAN	zinc finger and BTB domain containing 8 opposite strand	106					tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	extracellular vesicular exosome (GO:0070062)|tRNA-splicing ligase complex (GO:0072669)	metal ion binding (GO:0046872)			endometrium(1)|lung(4)|upper_aerodigestive_tract(1)	6		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				CGGGGTATGAAGAATTCATCA	0.313																																					p.F118V		Atlas-SNP	.											.	ZBTB8OS	9	.	0			c.T352G						PASS	.						52	56	55					1																	33099257		2203	4296	6499	SO:0001583	missense	339487	exon4			GTATGAAGAATTC	AY151084	CCDS365.1	1p35.1	2010-09-30			ENSG00000176261	ENSG00000176261			24094	protein-coding gene	gene with protein product	"archease"	615891				12477932	Standard	NM_178547		Approved	ARCH	uc001bvp.3	Q8IWT0	OTTHUMG00000007856	ENST00000468695.1:c.352T>G	chr1.hg19:g.33099257A>C	ENSP00000417677:p.Phe118Val	104.0	0.0	.		70.0	40.0	.	NM_178547	Q5TGK5|Q6PDA1|Q8IWS9|Q8NEV6|Q8NEV7	Missense_Mutation	SNP	ENST00000468695.1	hg19	CCDS365.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.0|22.0	4.225490|4.225490	0.79576|0.79576	.|.	.|.	ENSG00000176261|ENSG00000176261	ENST00000468695;ENST00000373501|ENST00000436661	.|.	.|.	.|.	5.4|5.4	5.4|5.4	0.78164|0.78164	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72431|0.72431	0.3459|0.3459	M|M	0.77820|0.77820	2.39|2.39	0.80722|0.80722	D|D	1|1	P;D|.	0.89917|.	0.712;1.0|.	P;D|.	0.87578|.	0.525;0.998|.	T|T	0.73855|0.73855	-0.3851|-0.3851	9|5	0.07990|.	T|.	0.79|.	-14.6218|-14.6218	10.1989|10.1989	0.43071|0.43071	0.8518:0.0:0.0:0.1482|0.8518:0.0:0.0:0.1482	.|.	106;118|.	Q8IWT0-2;A8K0B5|.	.;.|.	V|R	118;106|116	.|.	ENSP00000362600:F106V|.	F|L	-|-	1|2	0|0	ZBTB8OS|ZBTB8OS	32871844|32871844	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.227000|7.227000	0.78070|0.78070	2.180000|2.180000	0.69256|0.69256	0.533000|0.533000	0.62120|0.62120	TTC|CTT	.	.	.	none		0.313	ZBTB8OS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021669.3	NM_178547		C	33099257	A	C	33099257	3	2	117	1	0	0	0	0	1	0	0	0	17569	72	3	5	203	5	ZBTB8OS	1	33099257	Missense_Mutation	SNP	A	TCGA-BQ-5882-01A-11D-1589-08		33099257	216151364	1	7458											
RLF	6018	hgsc.bcm.edu	37	chr1	40701983	40701983	+	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	atcagcataaggagaaaagaGacaaaaaacctattggctct	19	7	8	7	0	2	2	1	0	1	2	2	4	2	2	1	2	2	2	1	2	7	3			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr1:40701983G>A	ENST00000372771.4	+	8	1636	c.1609G>A	c.(1609-1611)Gac>Aac	p.D537N		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	537					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)			GGAGAAAAGAGACAAAAAACC	0.358																																					p.D537N		Atlas-SNP	.											.	RLF	152	.	0			c.G1609A						PASS	.						65	70	68					1																	40701983		2199	4298	6497	SO:0001583	missense	6018	exon8			AAAAGAGACAAAA		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.1609G>A	chr1.hg19:g.40701983G>A	ENSP00000361857:p.Asp537Asn	147.0	0.0	.		101.0	34.0	.	NM_012421	Q14CQ1|Q9NU60	Missense_Mutation	SNP	ENST00000372771.4	hg19	CCDS448.1	.	.	.	.	.	.	.	.	.	.	G	15.03	2.710822	0.48517	.	.	ENSG00000117000	ENST00000372771;ENST00000535839	T	0.36699	1.24	6.07	6.07	0.98685	.	0.378317	0.33144	N	0.005225	T	0.42877	0.1222	L	0.40543	1.245	0.37876	D	0.930215	B;D	0.67145	0.23;0.996	B;P	0.56216	0.064;0.794	T	0.15983	-1.0418	10	0.18710	T	0.47	-14.4249	14.7663	0.69642	0.0684:0.0:0.9316:0.0	.	230;537	F5H2M5;Q13129	.;RLF_HUMAN	N	537;230	ENSP00000361857:D537N	ENSP00000361857:D537N	D	+	1	0	RLF	40474570	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.802000	0.47916	2.885000	0.99019	0.655000	0.94253	GAC	.	.	.	none		0.358	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421		A	40701983	G	A	40701983	3	1	117	1	0	0	0	0	1	0	0	0	13402	942	33	2	1639	2	RLF	1	40701983	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	7602726	40701983	208548638	2	7459											
TMEM53	79639	hgsc.bcm.edu	37	chr1	45120714	45120714	+	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	agcacgtagcggtacagcatGacgccaccgttgctgaagac	11	6	12	12	4	0	3	0	2	0	1	0	3	0	3	2	1	5	6	2	1	3	3			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr1:45120714G>T	ENST00000372237.3	-	3	514	c.351C>A	c.(349-351)gtC>gtA	p.V117V	TMEM53_ENST00000476724.1_5'UTR|TMEM53_ENST00000372243.3_Intron|TMEM53_ENST00000372242.3_Silent_p.V117V|TMEM53_ENST00000372235.3_Silent_p.V87V|TMEM53_ENST00000372244.3_Intron	NM_024587.2	NP_078863.2	Q6P2H8	TMM53_HUMAN	transmembrane protein 53	117						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(3)|ovary(2)|urinary_tract(1)	10	Acute lymphoblastic leukemia(166;0.155)					GGTACAGCATGACGCCACCGT	0.577											OREG0013446	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V117V		Atlas-SNP	.											.	TMEM53	40	.	0			c.C351A						PASS	.						60	62	62					1																	45120714		2203	4300	6503	SO:0001819	synonymous_variant	79639	exon3			CAGCATGACGCCA		CCDS511.1, CCDS72773.1	1p34.1	2008-02-26			ENSG00000126106	ENSG00000126106			26186	protein-coding gene	gene with protein product						12958361	Standard	XR_425151		Approved	FLJ22353, NET4	uc001cmc.3	Q6P2H8	OTTHUMG00000007833	ENST00000372237.3:c.351C>A	chr1.hg19:g.45120714G>T		82.0	0.0	.	929	46.0	26.0	.	NM_024587	B4DKG0|Q5JPH2|Q6IA07|Q9H6E2	Silent	SNP	ENST00000372237.3	hg19	CCDS511.1																																																																																			.	.	.	none		0.577	TMEM53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021599.1	NM_024587		T	45120714	G	T	45120714	2	4	117	1	0	0	0	0	0	0	0	1	16191	1277	45	4		4	TMEM53	1	45120714	Silent	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	4418731	45120714	204129907	3	7460											
DAP3	7818	hgsc.bcm.edu	37	chr1	155695184	155695185	+	Frame_Shift_Ins	INS	-	-	A																															tttatcaggtgaagacattcINSagtgaagcttgcctgatggt																										TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr1:155695184_155695185insA	ENST00000368336.5	+	5	406_407	c.282_283insA	c.(283-285)agtfs	p.S95fs	DAP3_ENST00000535183.1_Frame_Shift_Ins_p.S54fs|DAP3_ENST00000496863.1_3'UTR|DAP3_ENST00000471642.2_Frame_Shift_Ins_p.S54fs|DAP3_ENST00000421487.2_Frame_Shift_Ins_p.S61fs|MSTO1_ENST00000538143.1_Intron|MSTO1_ENST00000452804.2_Intron|DAP3_ENST00000343043.3_Frame_Shift_Ins_p.S95fs	NM_001199849.1|NM_004632.3	NP_001186778.1|NP_004623.1	P51398	RT29_HUMAN	death associated protein 3	95					apoptotic mitochondrial changes (GO:0008637)|apoptotic signaling pathway (GO:0097190)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	24	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					TGAAGACATTCAGTGAAGCTTG	0.45																																					p.F94fs		Atlas-INDEL	.											.	DAP3	46	.	0			c.282_283insA						PASS	.																																			SO:0001589	frameshift_variant	7818	exon5			.	X83544	CCDS1120.1, CCDS55646.1, CCDS55647.1	1q22	2012-11-14			ENSG00000132676	ENSG00000132676		"Mitochondrial ribosomal proteins / small subunits"	2673	protein-coding gene	gene with protein product	"mitochondrial 28S ribosomal protein S29"	602074				7499268, 9284927	Standard	NM_004632		Approved	MRPS29, DAP-3, MRP-S29, bMRP-10, MGC126058, MGC126059, DKFZp686G12159	uc001flr.3	P51398	OTTHUMG00000035439	ENST00000368336.5:c.283dupA	chr1.hg19:g.155695185_155695185dupA	ENSP00000357320:p.Ser95fs	163.0	0.0	0		178.0	63.0	0.353933	NM_033657	B4DP59|B4DY62|E7EM60|Q13044|Q68CT7|Q96Q20	Frame_Shift_Ins	INS	ENST00000368336.5	hg19	CCDS1120.1																																																																																			.	.	.	none		0.45	DAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086042.1	NM_004632		A	155695185	-	A	155695184	7	5	117	1	0	1	1	0	0	0	0	0	4236	825	29	0	296	0	DAP3	1	155695184	Frame_Shift_Ins	INS	-	TCGA-BQ-5882-01A-11D-1589-08	110574470	155695184	93555437	4	7461	82	2									
DAP3	7818	hgsc.bcm.edu	37	chr1	155695186	155695186	+	Missense_Mutation	SNP	G	G	A																															ttatcaggtgaagacattcaGtgaagcttgcctgatggtaa																										TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr1:155695186G>A	ENST00000368336.5	+	5	408	c.284G>A	c.(283-285)aGt>aAt	p.S95N	DAP3_ENST00000535183.1_Missense_Mutation_p.S54N|DAP3_ENST00000496863.1_3'UTR|DAP3_ENST00000471642.2_Missense_Mutation_p.S54N|DAP3_ENST00000421487.2_Missense_Mutation_p.S61N|MSTO1_ENST00000538143.1_Intron|MSTO1_ENST00000452804.2_Intron|DAP3_ENST00000343043.3_Missense_Mutation_p.S95N	NM_001199849.1|NM_004632.3	NP_001186778.1|NP_004623.1	P51398	RT29_HUMAN	death associated protein 3	95					apoptotic mitochondrial changes (GO:0008637)|apoptotic signaling pathway (GO:0097190)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	24	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					AAGACATTCAGTGAAGCTTGC	0.453																																					p.S95N		Atlas-SNP	.											.	DAP3	46	.	0			c.G284A						PASS	.						187	174	178					1																	155695186		2203	4300	6503	SO:0001583	missense	7818	exon5			CATTCAGTGAAGC	X83544	CCDS1120.1, CCDS55646.1, CCDS55647.1	1q22	2012-11-14			ENSG00000132676	ENSG00000132676		"Mitochondrial ribosomal proteins / small subunits"	2673	protein-coding gene	gene with protein product	"mitochondrial 28S ribosomal protein S29"	602074				7499268, 9284927	Standard	NM_004632		Approved	MRPS29, DAP-3, MRP-S29, bMRP-10, MGC126058, MGC126059, DKFZp686G12159	uc001flr.3	P51398	OTTHUMG00000035439	ENST00000368336.5:c.284G>A	chr1.hg19:g.155695186G>A	ENSP00000357320:p.Ser95Asn	165.0	0.0	.		182.0	66.0	.	NM_033657	B4DP59|B4DY62|E7EM60|Q13044|Q68CT7|Q96Q20	Missense_Mutation	SNP	ENST00000368336.5	hg19	CCDS1120.1	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.629646	0.00813	.	.	ENSG00000132676	ENST00000368336;ENST00000343043;ENST00000421487;ENST00000535183	T;T;T;T	0.40756	1.03;1.03;1.06;1.02	5.65	-2.53	0.06326	.	0.680865	0.15179	N	0.276217	T	0.01835	0.0058	N	0.00114	-2.085	0.09310	N	0.999999	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	0.46665	-0.9175	10	0.02654	T	1	0.0	11.3623	0.49651	0.6267:0.0:0.3733:0.0	.	54;61;61;95	B4DP59;B4DY62;E7EM60;P51398	.;.;.;RT29_HUMAN	N	95;95;61;54	ENSP00000357320:S95N;ENSP00000341692:S95N;ENSP00000412605:S61N;ENSP00000445003:S54N	ENSP00000341692:S95N	S	+	2	0	DAP3	153961810	0.928000	0.31464	0.005000	0.12908	0.078000	0.17371	1.904000	0.39868	-0.315000	0.08703	-0.136000	0.14681	AGT	.	.	.	none		0.453	DAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086042.1	NM_004632		A	155695186	G	A	155695186	3	1	117	1	0	0	0	0	1	0	0	0	4236	1029	36	2	298	2	DAP3	1	155695186	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	2	155695186	93555435	5	7462	82	2									
TIPRL	261726	hgsc.bcm.edu	37	chr1	168168189	168168189	+	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	tacatgttacgagaatatacGtcacgagaaagcaaaatttc	17	10	7	7	3	1	2	1	0	0	2	2	4	1	2	0	0	4	2	0	0	8	5			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr1:168168189G>A	ENST00000367833.2	+	6	790	c.645G>A	c.(643-645)acG>acA	p.T215T		NM_152902.3	NP_690866.1	O75663	TIPRL_HUMAN	TOR signaling pathway regulator	215	Interaction with PPP2CA.				DNA damage checkpoint (GO:0000077)|negative regulation of protein phosphatase type 2A activity (GO:0034048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				breast(1)|kidney(1)|large_intestine(1)|ovary(2)|skin(1)	6	all_hematologic(923;0.215)					GAGAATATACGTCACGAGAAA	0.259																																					p.T215T		Atlas-SNP	.											.	TIPRL	16	.	0			c.G645A						PASS	.						56	60	59					1																	168168189		2200	4299	6499	SO:0001819	synonymous_variant	261726	exon6			ATATACGTCACGA	AB097034	CCDS1270.1, CCDS30935.1	1q23.2	2014-03-07	2014-03-07		ENSG00000143155	ENSG00000143155			30231	protein-coding gene	gene with protein product		611807	"TIP41, TOR signaling pathway regulator-like (S. cerevisiae)"			12761501	Standard	NM_001031800		Approved	MGC3794, dJ69E11.3, TIP41	uc001gfg.3	O75663	OTTHUMG00000034646	ENST00000367833.2:c.645G>A	chr1.hg19:g.168168189G>A		40.0	0.0	.		51.0	11.0	.	NM_152902	B2R8V3|Q5HYB2|Q8IZ86	Silent	SNP	ENST00000367833.2	hg19	CCDS1270.1																																																																																			.	.	.	none		0.259	TIPRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083822.1	NM_152902		A	168168189	G	A	168168189	2	1	117	1	0	0	0	0	0	0	0	1	15938	1132	40	1		1	TIPRL	1	168168189	Silent	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	12473003	168168189	81082432	6	7463											
RFWD2	64326	hgsc.bcm.edu	37	chr1	175914297	175914297	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgagttaacccttcataccaAttctagcacctaattggggg	11	12	8	10	0	2	1	1	1	1	0	2	1	2	1	3	2	3	2	3	2	5	7			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr1:175914297A>G	ENST00000367669.3	-	20	2702	c.2188T>C	c.(2188-2190)Ttg>Ctg	p.L730L	RFWD2_ENST00000308769.8_Silent_p.L706L	NM_022457.5	NP_071902.2	Q8NHY2	RFWD2_HUMAN	ring finger and WD repeat domain 2, E3 ubiquitin protein ligase	730					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin protein ligase activity (GO:0061630)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						CTTCATACCAATTCTAGCACC	0.318																																					p.L730L	Ovarian(134;1413 1765 5706 35534 51541)	Atlas-SNP	.											.	RFWD2	67	.	0			c.T2188C						PASS	.						49	44	46					1																	175914297		2203	4300	6503	SO:0001819	synonymous_variant	64326	exon20			ATACCAATTCTAG	AK001278	CCDS30944.1, CCDS44279.1	1q25.1-q25.2	2013-01-09	2012-02-23		ENSG00000143207	ENSG00000143207		"WD repeat domain containing", "RING-type (C3HC4) zinc fingers"	17440	protein-coding gene	gene with protein product		608067	"ring finger and WD repeat domain 2"			10395541	Standard	XM_005245447		Approved	FLJ10416, COP1, RNF200	uc001gku.1	Q8NHY2	OTTHUMG00000034986	ENST00000367669.3:c.2188T>C	chr1.hg19:g.175914297A>G		52.0	0.0	.		77.0	4.0	.	NM_022457	E9PKI0|Q504W6|Q6H103|Q9H6L7|X5D9B4	Silent	SNP	ENST00000367669.3	hg19	CCDS30944.1																																																																																			.	.	.	none		0.318	RFWD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084672.2	NM_022457		G	175914297	A	G	175914297	2	3	117	1	0	0	0	0	0	0	0	1	13273	98	4	3		3	RFWD2	1	175914297	Silent	SNP	A	TCGA-BQ-5882-01A-11D-1589-08	7746108	175914297	73336324	7	7464											
KLHDC8A	55220	hgsc.bcm.edu	37	chr1	205312513	205312513	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcttccccagggcggtgaCggccacccccgcccgggctg	3	4	14	20	5	0	1	0	1	0	0	1	1	1	1	7	4	0	2	7	4	0	1			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr1:205312513C>T	ENST00000367156.3	-	5	1036	c.220G>A	c.(220-222)Gtc>Atc	p.V74I	KLHDC8A_ENST00000367155.3_Missense_Mutation_p.V74I|KLHDC8A_ENST00000539253.1_Missense_Mutation_p.V74I|KLHDC8A_ENST00000460687.1_Intron|KLHDC8A_ENST00000537168.1_Intron|KLHDC8A_ENST00000606529.1_5'Flank	NM_001271863.1	NP_001258792.1	Q8IYD2	KLD8A_HUMAN	kelch domain containing 8A	74										breast(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(84;0.23)		BRCA - Breast invasive adenocarcinoma(75;0.117)			AGGGCGGTGACGGCCACCCCC	0.672																																					p.V74I		Atlas-SNP	.											.	KLHDC8A	31	.	0			c.G220A						PASS	.						61	64	63					1																	205312513		2203	4300	6503	SO:0001583	missense	55220	exon2			CGGTGACGGCCAC		CCDS30985.1	1q32.1	2008-02-05			ENSG00000162873	ENSG00000162873			25573	protein-coding gene	gene with protein product		614503					Standard	NM_018203		Approved	FLJ10748	uc031prx.1	Q8IYD2	OTTHUMG00000037199	ENST00000367156.3:c.220G>A	chr1.hg19:g.205312513C>T	ENSP00000356124:p.Val74Ile	172.0	0.0	.		174.0	52.0	.	NM_018203	B3KU70|Q9NVG5	Missense_Mutation	SNP	ENST00000367156.3	hg19	CCDS30985.1	.	.	.	.	.	.	.	.	.	.	C	16.14	3.040035	0.55003	.	.	ENSG00000162873	ENST00000367155;ENST00000367156;ENST00000539253	T;T;T	0.80304	-1.36;-1.36;-1.36	5.65	4.73	0.59995	Kelch-type beta propeller (1);	0.190308	0.45361	N	0.000376	T	0.78065	0.4225	M	0.72576	2.205	0.31222	N	0.697307	B	0.13594	0.008	B	0.08055	0.003	T	0.76753	-0.2843	10	0.51188	T	0.08	-18.7937	10.6433	0.45604	0.0:0.8425:0.0:0.1575	.	74	Q8IYD2	KLD8A_HUMAN	I	74	ENSP00000356123:V74I;ENSP00000356124:V74I;ENSP00000442229:V74I	ENSP00000356123:V74I	V	-	1	0	KLHDC8A	203579136	0.981000	0.34729	0.230000	0.23976	0.980000	0.70556	2.591000	0.46163	1.346000	0.45694	0.655000	0.94253	GTC	.	.	.	none		0.672	KLHDC8A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090397.1	NM_018203		T	205312513	C	T	205312513	3	4	117	1	0	0	0	0	1	0	0	0	8369	536	19	1	852	1	KLHDC8A	1	205312513	Missense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	29398216	205312513	43938108	8	7465											
HEATR5B	54497	hgsc.bcm.edu	37	chr2	37267620	37267620	+	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	tagccacgatacatcggaccActagaatccactatcaaagc	15	7	6	13	2	1	1	1	0	0	1	3	3	2	2	3	1	3	0	3	1	6	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:37267620A>T	ENST00000233099.5	-	20	2993	c.2898T>A	c.(2896-2898)agT>agA	p.S966R	HEATR5B_ENST00000354531.2_Missense_Mutation_p.S966R	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	966						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)				ACATCGGACCACTAGAATCCA	0.373																																					p.S966R		Atlas-SNP	.											.	HEATR5B	185	.	0			c.T2898A						PASS	.						107	92	97					2																	37267620		2203	4300	6503	SO:0001583	missense	54497	exon20			CGGACCACTAGAA	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.2898T>A	chr2.hg19:g.37267620A>T	ENSP00000233099:p.Ser966Arg	120.0	0.0	.		125.0	38.0	.	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Missense_Mutation	SNP	ENST00000233099.5	hg19	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	A	14.94	2.686846	0.48097	.	.	ENSG00000008869	ENST00000233099;ENST00000354531	T;T	0.06528	3.29;3.29	5.5	1.75	0.24633	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.06096	0.0158	L	0.38175	1.15	0.51767	D	0.999939	B	0.32425	0.371	B	0.32149	0.141	T	0.35599	-0.9782	10	0.52906	T	0.07	-15.7822	11.2928	0.49261	0.805:0.0:0.195:0.0	.	966	Q9P2D3	HTR5B_HUMAN	R	966	ENSP00000233099:S966R;ENSP00000346531:S966R	ENSP00000233099:S966R	S	-	3	2	HEATR5B	37121124	1.000000	0.71417	0.999000	0.59377	0.938000	0.57974	1.659000	0.37387	0.035000	0.15519	-1.139000	0.01908	AGT	.	.	.	none		0.373	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		T	37267620	A	T	37267620	3	4	117	1	0	0	0	0	1	0	0	0	7039	156	6	5	3385	5	HEATR5B	2	37267620	Missense_Mutation	SNP	A	TCGA-BQ-5882-01A-11D-1589-08		37267620	205931753	9	7466											
UGGT1	56886	hgsc.bcm.edu	37	chr2	128918714	128918714	+	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	ctcttctctccttcacagatCattgggccactggaggatag	8	12	9	12	0	4	1	2	0	2	1	6	3	5	3	2	3	0	0	2	3	1	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:128918714C>A	ENST00000259253.6	+	25	2744	c.2697C>A	c.(2695-2697)atC>atA	p.I899I	UGGT1_ENST00000375990.3_Silent_p.I875I	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	899					'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						CTTCACAGATCATTGGGCCAC	0.478																																					p.I899I		Atlas-SNP	.											.	UGGT1	126	.	0			c.C2697A						PASS	.						96	95	95					2																	128918714		2203	4300	6503	SO:0001819	synonymous_variant	56886	exon25			ACAGATCATTGGG	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.2697C>A	chr2.hg19:g.128918714C>A		135.0	0.0	.		139.0	45.0	.	NM_020120	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Silent	SNP	ENST00000259253.6	hg19	CCDS2154.1																																																																																			.	.	.	none		0.478	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120		A	128918714	C	A	128918714	2	1	117	1	0	0	0	0	0	0	0	1	16953	816	29	4		4	UGGT1	2	128918714	Silent	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	91651094	128918714	114280659	10	7467											
MGAT5	4249	hgsc.bcm.edu	37	chr2	135206357	135206357	+	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	cgcccaccccaggcaccagaGggtctgcccctgccgggact	6	4	12	19	2	1	1	0	0	1	1	1	2	1	2	7	3	2	1	7	3	0	0			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:135206357G>A	ENST00000409645.1	+	17	2417	c.2165G>A	c.(2164-2166)aGg>aAg	p.R722K	MGAT5_ENST00000281923.2_Missense_Mutation_p.R722K			Q09328	MGT5A_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase	722					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)		AGGCACCAGAGGGTCTGCCCC	0.597																																					p.R722K		Atlas-SNP	.											.	MGAT5	84	.	0			c.G2165A						PASS	.						66	66	66					2																	135206357		2203	4300	6503	SO:0001583	missense	4249	exon16			ACCAGAGGGTCTG	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.2165G>A	chr2.hg19:g.135206357G>A	ENSP00000386377:p.Arg722Lys	100.0	0.0	.		113.0	36.0	.	NM_002410	D3DP70	Missense_Mutation	SNP	ENST00000409645.1	hg19	CCDS2171.1	.	.	.	.	.	.	.	.	.	.	G	34	5.389249	0.95988	.	.	ENSG00000152127	ENST00000409645;ENST00000281923	.	.	.	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	D	0.82958	0.5150	M	0.81341	2.54	0.80722	D	1	D	0.56035	0.974	D	0.70487	0.969	D	0.85213	0.1022	9	0.72032	D	0.01	-17.0654	18.7668	0.91876	0.0:0.0:1.0:0.0	.	722	Q09328	MGT5A_HUMAN	K	722	.	ENSP00000281923:R722K	R	+	2	0	MGAT5	134922827	1.000000	0.71417	0.998000	0.56505	0.896000	0.52359	9.702000	0.98712	2.523000	0.85059	0.655000	0.94253	AGG	.	.	.	none		0.597	MGAT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254584.3	NM_002410		A	135206357	G	A	135206357	3	1	117	1	0	0	0	0	1	0	0	0	9555	1000	35	2	2227	2	MGAT5	2	135206357	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	6287643	135206357	107993016	11	7468											
FMNL2	114793	hgsc.bcm.edu	37	chr2	153471511	153471511	+	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	gaactggaagaaaacatttcTcatgtaactatatctcagaa	17	11	6	7	0	2	2	2	0	2	2	4	4	2	3	0	1	3	1	0	1	8	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:153471511T>A	ENST00000288670.9	+	12	1576	c.1209T>A	c.(1207-1209)tcT>tcA	p.S403S		NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	403	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						AAAACATTTCTCATGTAACTA	0.378																																					p.S403S		Atlas-SNP	.											.	FMNL2	75	.	0			c.T1209A						PASS	.						84	84	84					2																	153471511		1882	4124	6006	SO:0001819	synonymous_variant	114793	exon12			CATTTCTCATGTA	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.1209T>A	chr2.hg19:g.153471511T>A		61.0	0.0	.		106.0	38.0	.	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Silent	SNP	ENST00000288670.9	hg19	CCDS46429.1																																																																																			.	.	.	none		0.378	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905		A	153471511	T	A	153471511	2	1	117	1	0	0	0	0	0	0	0	1	5959	1538	54	5		5	FMNL2	2	153471511	Silent	SNP	T	TCGA-BQ-5882-01A-11D-1589-08	18265154	153471511	89727862	12	7469											
GPD2	2820	hgsc.bcm.edu	37	chr2	157367411	157367411	+	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	agatatctgcagaaggccatCatgaagttggatattgagca	14	10	11	6	0	2	4	1	2	1	2	2	5	2	5	1	2	2	3	1	2	4	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:157367411C>T	ENST00000310454.6	+	4	750	c.378C>T	c.(376-378)atC>atT	p.I126I	GPD2_ENST00000540309.1_Silent_p.I126I|GPD2_ENST00000409674.1_Silent_p.I126I|GPD2_ENST00000438166.2_Silent_p.I126I|GPD2_ENST00000409125.4_Intron	NM_001083112.2	NP_001076581.2	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2 (mitochondrial)	126					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						AGAAGGCCATCATGAAGTTGG	0.378																																					p.I126I		Atlas-SNP	.											.	GPD2	59	.	0			c.C378T						PASS	.						178	177	178					2																	157367411		2203	4300	6503	SO:0001819	synonymous_variant	2820	exon4			GGCCATCATGAAG		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.378C>T	chr2.hg19:g.157367411C>T		256.0	0.0	.		277.0	76.0	.	NM_001083112	A8K4V0|B3KSA9|Q59FR1|Q9HAP9	Silent	SNP	ENST00000310454.6	hg19	CCDS2202.1																																																																																			.	.	.	none		0.378	GPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254910.3			T	157367411	C	T	157367411	2	4	117	1	0	0	0	0	0	0	0	1	6613	816	29	2		2	GPD2	2	157367411	Silent	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	3895900	157367411	85831962	13	7470											
TTN	7273	hgsc.bcm.edu	37	chr2	179575504	179575504	+	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	taactaatctggtactttccGccacttcgtatttctctgct	7	17	5	12	2	2	0	0	0	2	0	5	0	3	0	2	1	3	3	2	1	4	7	rs375083775		TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:179575504G>A	ENST00000591111.1	-	96	27593	c.27369C>T	c.(27367-27369)ggC>ggT	p.G9123G	TTN_ENST00000342992.6_Silent_p.G8196G|TTN_ENST00000460472.2_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000589042.1_Silent_p.G9440G|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000431752.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13254	Ig-like 74.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.G8196G(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGTACTTTCCGCCACTTCGTA	0.488																																					p.G9440G		Atlas-SNP	.											TTN_ENST00000356127,rectum,carcinoma,0,1	TTN	18412	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C28320T						PASS	.	G	,,,	1,3979		0,1,1989	148	143	144		,24588,,	-12.3	0.4	2		144	0,8340		0,0,4170	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	0,1,6159	AA,AG,GG		0.0,0.0251,0.0081	,,,	,8196/33424,,	179575504	1,12319	1990	4170	6160	SO:0001819	synonymous_variant	7273	exon98			CTTTCCGCCACTT	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.27369C>T	chr2.hg19:g.179575504G>A		144.0	2.0	.		182.0	52.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.	.	weak		0.488	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179575504	G	A	179575504	2	1	117	1	0	0	0	0	0	0	0	1	16747	1074	38	1		1	TTN	2	179575504	Silent	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	22208093	179575504	63623869	14	7471											
ACADL	33	hgsc.bcm.edu	37	chr2	211081192	211081192	+	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	aatataggacatgacaatacCtgaatgaatactaaaacctg	19	9	6	7	0	0	3	0	3	0	0	0	4	0	4	2	1	3	0	2	1	10	5			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:211081192C>T	ENST00000233710.3	-	4	642	c.415G>A	c.(415-417)Ggt>Agt	p.G139S	AC006994.2_ENST00000412065.1_RNA	NM_001608.3	NP_001599.1	P28330	ACADL_HUMAN	acyl-CoA dehydrogenase, long chain	139					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)		ATGACAATACCTGAATGAATA	0.338																																					p.G139S		Atlas-SNP	.											.	ACADL	38	.	0			c.G415A						PASS	.						107	101	103					2																	211081192		2202	4300	6502	SO:0001583	missense	33	exon4			CAATACCTGAATG	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.415G>A	chr2.hg19:g.211081192C>T	ENSP00000233710:p.Gly139Ser	105.0	0.0	.		112.0	44.0	.	NM_001608	B2R8T3|Q8IUN8	Missense_Mutation	SNP	ENST00000233710.3	hg19	CCDS2389.1	.	.	.	.	.	.	.	.	.	.	C	18.70	3.679212	0.68042	.	.	ENSG00000115361	ENST00000233710	D	0.99683	-6.39	5.77	4.9	0.64082	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, N-terminal (1);Acyl-CoA dehydrogenase/oxidase, N-terminal (1);	0.179938	0.64402	D	0.000017	D	0.98469	0.9490	N	0.16266	0.395	0.30365	N	0.783448	B	0.26445	0.149	B	0.34038	0.174	D	0.99899	1.1157	10	0.66056	D	0.02	.	15.4418	0.75190	0.0:0.933:0.0:0.067	.	139	P28330	ACADL_HUMAN	S	139	ENSP00000233710:G139S	ENSP00000233710:G139S	G	-	1	0	ACADL	210789437	1.000000	0.71417	0.998000	0.56505	0.919000	0.55068	5.531000	0.67148	1.578000	0.49821	0.655000	0.94253	GGT	.	.	.	none		0.338	ACADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256561.2	NM_001608		T	211081192	C	T	211081192	3	4	117	1	0	0	0	0	1	0	0	0	112	681	24	2	909	2	ACADL	2	211081192	Missense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	31505688	211081192	32118181	15	7472											
DGKD	8527	hgsc.bcm.edu	37	chr2	234363455	234363455	+	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	tgaacaactattttggcattGgcctggatgcgaagatatcc	11	12	10	8	1	0	2	0	1	0	1	1	4	1	3	2	3	3	1	2	3	5	5			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:234363455G>T	ENST00000264057.2	+	19	2323	c.2311G>T	c.(2311-2313)Ggc>Tgc	p.G771C	DGKD_ENST00000409813.3_Missense_Mutation_p.G727C	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	771					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)	TTTTGGCATTGGCCTGGATGC	0.453																																					p.G771C		Atlas-SNP	.											.	DGKD	106	.	0			c.G2311T						PASS	.						168	145	153					2																	234363455		2203	4300	6503	SO:0001583	missense	8527	exon19			GGCATTGGCCTGG	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.2311G>T	chr2.hg19:g.234363455G>T	ENSP00000264057:p.Gly771Cys	124.0	0.0	.		148.0	41.0	.	NM_152879	Q14158|Q6PK55|Q8NG53	Missense_Mutation	SNP	ENST00000264057.2	hg19	CCDS2504.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.405390	0.83230	.	.	ENSG00000077044	ENST00000264057;ENST00000409813	D;D	0.89270	-2.49;-2.49	3.57	3.57	0.40892	Diacylglycerol kinase, accessory domain (2);	0.000000	0.64402	D	0.000004	D	0.96324	0.8801	H	0.97077	3.935	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	0.97837	1.0266	10	0.87932	D	0	.	16.4941	0.84223	0.0:0.0:1.0:0.0	.	655;727;771	Q53SE4;Q16760-2;Q16760	.;.;DGKD_HUMAN	C	771;727	ENSP00000264057:G771C;ENSP00000386455:G727C	ENSP00000264057:G771C	G	+	1	0	DGKD	234028194	1.000000	0.71417	0.973000	0.42090	0.987000	0.75469	9.627000	0.98412	2.305000	0.77605	0.643000	0.83706	GGC	.	.	.	none		0.453	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648		T	234363455	G	T	234363455	3	4	117	1	0	0	0	0	1	0	0	0	4469	1348	47	4	2409	4	DGKD	2	234363455	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	23282263	234363455	8835918	16	7473											
CCDC13	152206	hgsc.bcm.edu	37	chr3	42793437	42793438	+	Frame_Shift_Ins	INS	-	-	TC																															gaattcataccaatgctctgINStctcccatctgggccctcgg																										TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr3:42793437_42793438insTC	ENST00000310232.6	-	5	676_677	c.593_594insGA	c.(592-594)gacfs	p.D198fs	CCDC13_ENST00000435327.2_5'UTR	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	198										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						CCAATGCTCTGTCTCCCATCTG	0.609																																					p.D198fs		Atlas-INDEL	.											.	CCDC13	71	.	0			c.594_595insGA						PASS	.																																			SO:0001589	frameshift_variant	152206	exon5			.	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.592_593dupGA	chr3.hg19:g.42793440_42793441dupTC	ENSP00000309836:p.Asp198fs	124.0	0.0	0		83.0	25.0	0.301205	NM_144719		Frame_Shift_Ins	INS	ENST00000310232.6	hg19	CCDS2705.1																																																																																			.	.	.	none		0.609	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719		TC	42793438	-	TC	42793437	7	5	117	1	0	1	1	0	0	0	0	0	2767	1368	48	0	1601	0	CCDC13	3	42793437	Frame_Shift_Ins	INS	-	TCGA-BQ-5882-01A-11D-1589-08		42793437	155228993	17	7474	83	2									
CCDC13	152206	hgsc.bcm.edu	37	chr3	42793447	42793447	+	Missense_Mutation	SNP	T	T	G																															ccaatgctctgtctcccatcTgggccctcggtggcttggct																										TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr3:42793447T>G	ENST00000310232.6	-	5	667	c.584A>C	c.(583-585)cAg>cCg	p.Q195P	CCDC13_ENST00000435327.2_5'UTR	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	195										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						GTCTCCCATCTGGGCCCTCGG	0.592																																					p.Q195P		Atlas-SNP	.											.	CCDC13	71	.	0			c.A584C						PASS	.						84	77	79					3																	42793447		2203	4300	6503	SO:0001583	missense	152206	exon5			CCCATCTGGGCCC	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.584A>C	chr3.hg19:g.42793447T>G	ENSP00000309836:p.Gln195Pro	135.0	0.0	.		94.0	33.0	.	NM_144719		Missense_Mutation	SNP	ENST00000310232.6	hg19	CCDS2705.1	.	.	.	.	.	.	.	.	.	.	T	4.532	0.098801	0.08681	.	.	ENSG00000244607	ENST00000310232	T	0.24723	1.84	4.01	1.44	0.22558	.	0.735360	0.13594	N	0.376366	T	0.23451	0.0567	L	0.55103	1.725	0.20403	N	0.999901	B;B;B	0.09022	0.001;0.002;0.001	B;B;B	0.06405	0.002;0.002;0.001	T	0.21586	-1.0241	10	0.56958	D	0.05	.	8.5317	0.33337	0.0:0.0:0.4318:0.5682	.	195;195;195	B4DZD2;Q96LI1;Q8IYE1	.;.;CCD13_HUMAN	P	195	ENSP00000309836:Q195P	ENSP00000309836:Q195P	Q	-	2	0	CCDC13	42768451	0.092000	0.21681	0.182000	0.23118	0.423000	0.31445	-0.078000	0.11375	0.286000	0.22352	0.533000	0.62120	CAG	.	.	.	none		0.592	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719		G	42793447	T	G	42793447	3	3	117	1	0	0	0	0	1	0	0	0	2767	1580	55	5	1611	5	CCDC13	3	42793447	Missense_Mutation	SNP	T	TCGA-BQ-5882-01A-11D-1589-08	10	42793447	155228983	18	7475	83	2									
STAB1	23166	hgsc.bcm.edu	37	chr3	52544437	52544437	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctggagtggggatggccgcGtctgtgtggctattgacgag	5	10	19	7	3	1	1	0	1	1	0	1	4	1	3	1	5	0	2	1	5	1	2	rs569908210		TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr3:52544437G>A	ENST00000321725.6	+	25	2777	c.2701G>A	c.(2701-2703)Gtc>Atc	p.V901I		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	901	EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00076, ECO:0000305}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		GGATGGCCGCGTCTGTGTGGC	0.612													G|||	1	0.000199681	8e-04	0	5008	,	,		18485	0		0	False		,,,				2504	0				p.V901I		Atlas-SNP	.											STAB1,colon,carcinoma,0,1	STAB1	178	.	0			c.G2701A						PASS	.						95	86	89					3																	52544437		2203	4300	6503	SO:0001583	missense	23166	exon25			GGCCGCGTCTGTG	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.2701G>A	chr3.hg19:g.52544437G>A	ENSP00000312946:p.Val901Ile	119.0	0.0	.		70.0	37.0	.	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	hg19	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	G	11.43	1.637778	0.29157	.	.	ENSG00000010327	ENST00000321725	T	0.42131	0.98	5.86	1.84	0.25277	Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1);	0.431461	0.22025	N	0.065676	T	0.29850	0.0746	L	0.37697	1.125	0.19575	N	0.999963	B	0.20988	0.05	B	0.12837	0.008	T	0.16719	-1.0393	10	0.36615	T	0.2	.	9.6284	0.39765	0.3064:0.0:0.6936:0.0	.	901	Q9NY15	STAB1_HUMAN	I	901	ENSP00000312946:V901I	ENSP00000312946:V901I	V	+	1	0	STAB1	52519477	0.886000	0.30341	0.825000	0.32803	0.923000	0.55619	1.548000	0.36201	0.322000	0.23283	-0.345000	0.07892	GTC	.	.	.	none		0.612	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		A	52544437	G	A	52544437	3	1	117	1	0	0	0	0	1	0	0	0	15249	1145	40	1	2799	1	STAB1	3	52544437	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	9750990	52544437	145477993	19	7476											
EPHB1	2047	hgsc.bcm.edu	37	chr3	134670526	134670526	+	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	cattgctgcagatgagagctTctcccaggtggactttgggg	7	11	14	9	0	1	2	0	1	1	2	2	4	1	3	1	4	3	3	1	4	0	3			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr3:134670526T>A	ENST00000398015.3	+	3	807	c.437T>A	c.(436-438)tTc>tAc	p.F146Y	EPHB1_ENST00000488154.1_3'UTR	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	146	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						GATGAGAGCTTCTCCCAGGTG	0.493																																					p.F146Y		Atlas-SNP	.											.	EPHB1	519	.	0			c.T437A						PASS	.						154	151	152					3																	134670526		1972	4204	6176	SO:0001583	missense	2047	exon3			AGAGCTTCTCCCA	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.437T>A	chr3.hg19:g.134670526T>A	ENSP00000381097:p.Phe146Tyr	273.0	0.0	.		222.0	112.0	.	NM_004441	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Missense_Mutation	SNP	ENST00000398015.3	hg19	CCDS46921.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.644684	0.87859	.	.	ENSG00000154928	ENST00000398015;ENST00000474732	T;T	0.04234	3.67;3.67	5.49	5.49	0.81192	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	T	0.25232	0.0613	M	0.86097	2.795	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.91635	0.999;0.991	T	0.01725	-1.1287	9	.	.	.	.	15.6027	0.76636	0.0:0.0:0.0:1.0	.	146;146	B5A969;P54762	.;EPHB1_HUMAN	Y	146;124	ENSP00000381097:F146Y;ENSP00000418352:F124Y	.	F	+	2	0	EPHB1	136153216	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.085000	0.62840	0.533000	0.62120	TTC	.	.	.	none		0.493	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441		A	134670526	T	A	134670526	3	1	117	1	0	0	0	0	1	0	0	0	5176	1783	62	5	447	5	EPHB1	3	134670526	Missense_Mutation	SNP	T	TCGA-BQ-5882-01A-11D-1589-08	82126089	134670526	63351904	20	7477											
MED12L	116931	hgsc.bcm.edu	37	chr3	151078359	151078359	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgatctctatgtgtcatgtAgccacctcagaagtaaattt	12	14	7	8	0	3	2	2	1	1	1	4	2	3	2	2	0	1	2	2	0	5	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr3:151078359A>G	ENST00000474524.1	+	19	2856	c.2818A>G	c.(2818-2820)Agc>Ggc	p.S940G	MED12L_ENST00000273432.4_Missense_Mutation_p.S800G|P2RY12_ENST00000302632.3_Intron	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	940						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)			TGTGTCATGTAGCCACCTCAG	0.438																																					p.S940G		Atlas-SNP	.											.	MED12L	271	.	0			c.A2818G						PASS	.						211	195	201					3																	151078359		2203	4300	6503	SO:0001583	missense	116931	exon19			TCATGTAGCCACC	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.2818A>G	chr3.hg19:g.151078359A>G	ENSP00000417235:p.Ser940Gly	280.0	0.0	.		239.0	125.0	.	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	hg19	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.133418	0.77662	.	.	ENSG00000144893	ENST00000474524;ENST00000273432	T;T	0.79653	-1.29;-1.29	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	D	0.85660	0.5748	L	0.45228	1.405	0.80722	D	1	P;D;P	0.56035	0.48;0.974;0.956	B;D;D	0.67725	0.412;0.953;0.931	D	0.87163	0.2216	10	0.87932	D	0	-22.6472	15.5111	0.75782	1.0:0.0:0.0:0.0	.	800;940;940	F8WAE6;Q86YW9-4;Q86YW9	.;.;MD12L_HUMAN	G	940;800	ENSP00000417235:S940G;ENSP00000273432:S800G	ENSP00000273432:S800G	S	+	1	0	MED12L	152561049	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.649000	0.91067	2.199000	0.70637	0.533000	0.62120	AGC	.	.	.	none		0.438	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		G	151078359	A	G	151078359	3	3	117	1	0	0	0	0	1	0	0	0	9436	420	15	3	2892	3	MED12L	3	151078359	Missense_Mutation	SNP	A	TCGA-BQ-5882-01A-11D-1589-08	16407833	151078359	46944071	21	7478											
NAF1	92345	hgsc.bcm.edu	37	chr4	164050121	164050121	+	Silent	SNP	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	ggcagtggtggagggggaggGggtgggggtagggagtatgg	6	6	28	1	0	0	0	0	0	0	0	0	3	0	3	0	11	0	3	0	11	2	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr4:164050121G>A	ENST00000274054.2	-	8	1606	c.1413C>T	c.(1411-1413)ccC>ccT	p.P471P	NAF1_ENST00000509434.1_Intron|NAF1_ENST00000422287.2_Intron	NM_138386.2	NP_612395.2	Q96HR8	NAF1_HUMAN	nuclear assembly factor 1 ribonucleoprotein	471	Pro-rich.				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)				gagggggagggggtgggggta	0.517																																					p.P471P		Atlas-SNP	.											.	NAF1	69	.	0			c.C1413T						PASS	.						10	11	10					4																	164050121		2191	4274	6465	SO:0001819	synonymous_variant	92345	exon8			GGGAGGGGGTGGG		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.1413C>T	chr4.hg19:g.164050121G>A		26.0	0.0	.		22.0	16.0	.	NM_138386	D3DP28|E9PAZ2	Silent	SNP	ENST00000274054.2	hg19	CCDS3803.1																																																																																			.	.	.	none		0.517	NAF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364684.2	NM_138386		A	164050121	G	A	164050121	2	1	117	1	0	0	0	0	0	0	0	1	10147	1219	43	2		2	NAF1	4	164050121	Silent	SNP	G	TCGA-BQ-5882-01A-11D-1589-08		164050121	27104155	22	7479											
TERT	7015	hgsc.bcm.edu	37	chr5	1255515	1255515	+	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	gaaatgggagctgcagcacaCatgcgtgaaacctgagagga	14	5	14	8	1	0	2	0	2	0	1	0	6	0	4	1	2	5	3	1	2	2	0			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr5:1255515C>A	ENST00000310581.5	-	14	3101	c.3044G>T	c.(3043-3045)tGt>tTt	p.C1015F	TERT_ENST00000296820.5_3'UTR|TERT_ENST00000334602.6_Missense_Mutation_p.C952F	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	telomerase reverse transcriptase	1015	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)	CTGCAGCACACATGCGTGAAA	0.572									TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis																												p.C1015F		Atlas-SNP	.											.	TERT	2594	.	0			c.G3044T						PASS	.						76	82	80					5																	1255515		2161	4266	6427	SO:0001583	missense	7015	exon14	Familial Cancer Database	;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	AGCACACATGCGT	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.3044G>T	chr5.hg19:g.1255515C>A	ENSP00000309572:p.Cys1015Phe	49.0	0.0	.		51.0	14.0	.	NM_198253	O14783|Q2XS35|Q8N6C3|Q8NG38|Q8NG46	Missense_Mutation	SNP	ENST00000310581.5	hg19	CCDS3861.2	.	.	.	.	.	.	.	.	.	.	c	14.17	2.454152	0.43634	.	.	ENSG00000164362	ENST00000310581;ENST00000334602	T;T	0.66815	-0.23;-0.23	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	D	0.83622	0.5294	M	0.88704	2.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.83650	0.0155	10	0.27082	T	0.32	-0.9462	16.718	0.85402	0.0:1.0:0.0:0.0	.	952;1015	O14746-3;O14746	.;TERT_HUMAN	F	1015;952	ENSP00000309572:C1015F;ENSP00000334346:C952F	ENSP00000309572:C1015F	C	-	2	0	TERT	1308515	1.000000	0.71417	0.180000	0.23079	0.008000	0.06430	6.534000	0.73833	2.237000	0.73441	0.655000	0.94253	TGT	.	.	.	none		0.572	TERT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206729.2			A	1255515	C	A	1255515	3	1	117	1	0	0	0	0	1	0	0	0	15776	478	17	4	366	4	TERT	5	1255515	Missense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08		1255515	179659745	23	7480											
CCNI2	645121	hgsc.bcm.edu	37	chr5	132084160	132084160	+	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	ctttggccgcctcctgatttCagtgaaggtagggaggcctc	6	11	13	11	1	1	2	1	2	0	0	3	3	2	3	4	4	0	1	4	4	2	3			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr5:132084160C>A	ENST00000378731.1	+	2	602	c.551C>A	c.(550-552)tCa>tAa	p.S184*	SEPT8_ENST00000481030.1_5'Flank	NM_001039780.2	NP_001034869.1	Q6ZMN8	CCNI2_HUMAN	cyclin I family, member 2	184					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)					haematopoietic_and_lymphoid_tissue(1)|prostate(1)|urinary_tract(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTCCTGATTTCAGTGAAGGTA	0.542																																					p.S184X		Atlas-SNP	.											.	CCNI2	11	.	0			c.C551A						PASS	.						78	76	77					5																	132084160		2203	4300	6503	SO:0001587	stop_gained	645121	exon2			TGATTTCAGTGAA	BC132837	CCDS34236.1, CCDS75297.1	5q31.1	2014-07-03			ENSG00000205089	ENSG00000205089			33869	protein-coding gene	gene with protein product						23707792	Standard	NM_001287252		Approved	FLJ16793	uc003kxq.1	Q6ZMN8	OTTHUMG00000059737	ENST00000378731.1:c.551C>A	chr5.hg19:g.132084160C>A	ENSP00000368005:p.Ser184*	122.0	0.0	.		163.0	47.0	.	NM_001039780	B2RNE2|B7ZMB7|B7ZMB8	Nonsense_Mutation	SNP	ENST00000378731.1	hg19	CCDS34236.1	.	.	.	.	.	.	.	.	.	.	C	17.38	3.374680	0.61735	.	.	ENSG00000205089	ENST00000378731	.	.	.	4.74	2.95	0.34219	.	0.352786	0.29699	N	0.011430	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	.	10.896	0.47023	0.0:0.8799:0.0:0.1201	.	.	.	.	X	184	.	ENSP00000368005:S184X	S	+	2	0	CCNI2	132112059	0.186000	0.23225	0.002000	0.10522	0.016000	0.09150	2.489000	0.45285	0.667000	0.31107	0.651000	0.88453	TCA	.	.	.	none		0.542	CCNI2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132833.1	NM_001039780		A	132084160	C	A	132084160	4	1	117	1	0	0	0	0	0	1	0	0	2929	838	29	4	557	4	CCNI2	5	132084160	Nonsense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	130828645	132084160	48831100	24	7481											
OR5V1	81696	hgsc.bcm.edu	37	chr6	29323498	29323498	+	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	gcagaatgtcaacactgtatGcaccactgagttaaggaaac	15	8	9	9	0	1	2	1	1	0	1	1	3	1	3	1	1	3	4	1	1	5	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr6:29323498G>C	ENST00000377154.1	-	4	774	c.475C>G	c.(475-477)Cat>Gat	p.H159D	OR5V1_ENST00000543825.1_Missense_Mutation_p.H159D			Q9UGF6	OR5V1_HUMAN	olfactory receptor, family 5, subfamily V, member 1	159						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(3)|large_intestine(3)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						AACACTGTATGCACCACTGAG	0.438																																					p.H159D	Ovarian(32;43 883 21137 32120 42650)	Atlas-SNP	.											.	OR5V1	63	.	0			c.C475G						PASS	.						88	85	86					6																	29323498		2203	4299	6502	SO:0001583	missense	81696	exon1			CTGTATGCACCAC		CCDS4657.1	6p22.1	2013-09-23				ENSG00000243729		"GPCR / Class A : Olfactory receptors"	13972	protein-coding gene	gene with protein product							Standard	NM_030876		Approved	hs6M1-21	uc011dlo.2	Q9UGF6		ENST00000377154.1:c.475C>G	chr6.hg19:g.29323498G>C	ENSP00000366359:p.His159Asp	104.0	0.0	.		67.0	37.0	.	NM_030876	A2BDZ0|B0S860|Q5SQI9|Q6NTB5|Q8IVL3	Missense_Mutation	SNP	ENST00000377154.1	hg19	CCDS4657.1	.	.	.	.	.	.	.	.	.	.	G	10.69	1.420539	0.25639	.	.	ENSG00000243729	ENST00000377154;ENST00000377151;ENST00000543825	T;T	0.00262	8.4;8.4	4.28	4.28	0.50868	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34484	N	0.003929	T	0.00328	0.0010	M	0.88512	2.96	0.26396	N	0.976491	D	0.89917	1.0	D	0.91635	0.999	T	0.37291	-0.9712	10	0.51188	T	0.08	-51.5055	12.8107	0.57637	0.0:0.0:0.8357:0.1643	.	159	Q9UGF6	OR5V1_HUMAN	D	159	ENSP00000366359:H159D;ENSP00000443309:H159D	ENSP00000366356:H159D	H	-	1	0	OR5V1	29431477	0.000000	0.05858	0.876000	0.34364	0.772000	0.43724	-0.032000	0.12266	2.374000	0.81015	0.543000	0.68304	CAT	.	.	.	none		0.438	OR5V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076398.3			C	29323498	G	C	29323498	3	2	117	1	0	0	0	0	1	0	0	0	11191	1319	46	4	493	4	OR5V1	6	29323498	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08		29323498	141791569	25	7482											
RIMS1	22999	hgsc.bcm.edu	37	chr6	73108662	73108662	+	Missense_Mutation	SNP	T	T	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	tatacctttgtttagctccaTatgtcaaagtatatcttttg	10	19	5	7	0	2	0	1	0	1	0	3	0	3	0	2	0	2	3	2	0	7	10			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr6:73108662T>G	ENST00000521978.1	+	33	4726	c.4726T>G	c.(4726-4728)Tat>Gat	p.Y1576D	RIMS1_ENST00000517960.1_Missense_Mutation_p.Y1359D|RIMS1_ENST00000538414.1_Missense_Mutation_p.Y382D|RIMS1_ENST00000520567.1_Missense_Mutation_p.Y1226D|RIMS1_ENST00000518273.1_Missense_Mutation_p.Y1255D|RIMS1_ENST00000517827.1_Missense_Mutation_p.Y710D|RIMS1_ENST00000491071.2_Missense_Mutation_p.Y1365D|RIMS1_ENST00000401910.3_Missense_Mutation_p.Y896D|RIMS1_ENST00000522291.1_Missense_Mutation_p.Y1175D|RIMS1_ENST00000431478.2_3'UTR|RIMS1_ENST00000348717.5_Missense_Mutation_p.Y1359D|RIMS1_ENST00000523963.1_Missense_Mutation_p.Y701D|RIMS1_ENST00000414192.2_Missense_Mutation_p.Y103D|RIMS1_ENST00000425662.2_Missense_Mutation_p.Y644D|RIMS1_ENST00000264839.7_Missense_Mutation_p.Y1425D	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	1576	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				TTTAGCTCCATATGTCAAAGT	0.318																																					p.Y1576D		Atlas-SNP	.											.	RIMS1	278	.	0			c.T4726G						PASS	.						66	62	63					6																	73108662		1796	4064	5860	SO:0001583	missense	22999	exon33			GCTCCATATGTCA	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.4726T>G	chr6.hg19:g.73108662T>G	ENSP00000428417:p.Tyr1576Asp	57.0	0.0	.		39.0	15.0	.	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	hg19	CCDS47449.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	23.1|23.1|23.1	4.374106|4.374106|4.374106	0.82573|0.82573|0.82573	.|.|.	.|.|.	ENSG00000079841|ENSG00000079841|ENSG00000079841	ENST00000522211|ENST00000517433|ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978;ENST00000401910;ENST00000523963;ENST00000425662;ENST00000453976;ENST00000517827;ENST00000370420;ENST00000538414;ENST00000414192	.|.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|.|0.80033	.|.|-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;0.34;-1.33;-1.33;-1.33;-1.33	5.37|5.37|5.37	5.37|5.37|5.37	0.77165|0.77165|0.77165	.|.|C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.|.|0.000000	.|.|0.56097	.|.|D	.|.|0.000022	D|D|D	0.93953|0.93953|0.93953	0.8064|0.8064|0.8064	H|H|H	0.99516|0.99516|0.99516	4.605|4.605|4.605	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|D;D;D;D;D;D;D;D;D;D;D;D;D	.|.|0.89917	.|.|1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0	.|.|D;D;D;D;D;D;D;D;D;D;D;D;D	.|.|0.97110	.|.|1.0;1.0;1.0;1.0;0.999;1.0;0.999;1.0;0.999;0.999;0.999;0.994;0.999	D|D|D	0.96600|0.96600|0.96600	0.9444|0.9444|0.9444	5|5|10	.|.|0.87932	.|.|D	.|.|0	-24.6441|-24.6441|-24.6441	15.6587|15.6587|15.6587	0.77165|0.77165|0.77165	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.|.	.|.|200;382;710;701;1425;896;1175;479;1255;1359;652;1365;1576	.|.|B7Z6K9;B7Z7W2;B7Z3S3;E9PHF5;E9PHR1;E9PF48;E7EX08;Q5JY22;E7ERQ1;E7ENC2;Q5JY21;C9JNW6;Q86UR5	.|.|.;.;.;.;.;.;.;.;.;.;.;.;RIMS1_HUMAN	Q|R|D	493|921|1365;1425;1365;1359;1255;1175;1425;1359;1255;1226;1175;1576;896;701;644;741;710;624;382;103	.|.|ENSP00000430101:Y1365D;ENSP00000275037:Y1359D;ENSP00000264839:Y1425D;ENSP00000429959:Y1359D;ENSP00000430408:Y1255D;ENSP00000430502:Y1226D;ENSP00000430932:Y1175D;ENSP00000428417:Y1576D;ENSP00000385649:Y896D;ENSP00000428328:Y701D;ENSP00000411235:Y644D;ENSP00000389503:Y741D;ENSP00000428367:Y710D;ENSP00000359448:Y624D;ENSP00000439730:Y382D;ENSP00000402273:Y103D	.|.|ENSP00000264839:Y1425D	H|I|Y	+|+|+	3|2|1	2|0|0	RIMS1|RIMS1|RIMS1	73165383|73165383|73165383	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.987000|0.987000|0.987000	0.45799|0.45799|0.45799	0.938000|0.938000|0.938000	0.57974|0.57974|0.57974	7.934000|7.934000|7.934000	0.87649|0.87649|0.87649	2.157000|2.157000|2.157000	0.67596|0.67596|0.67596	0.482000|0.482000|0.482000	0.46254|0.46254|0.46254	CAT|ATA|TAT	.	.	.	none		0.318	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			G	73108662	T	G	73108662	3	3	117	1	0	0	0	0	1	0	0	0	13380	1406	49	5	5019	5	RIMS1	6	73108662	Missense_Mutation	SNP	T	TCGA-BQ-5882-01A-11D-1589-08	43785164	73108662	98006405	26	7483											
ANLN	54443	hgsc.bcm.edu	37	chr7	36445953	36445953	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctgggaagatgatgtaaaTcactcatttgcaaaacaaaa	17	10	7	7	0	2	2	2	1	0	1	3	3	3	3	1	1	2	2	1	1	7	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr7:36445953T>C	ENST00000265748.2	+	4	872	c.651T>C	c.(649-651)aaT>aaC	p.N217N	ANLN_ENST00000396068.2_Silent_p.N217N	NM_018685.2	NP_061155.2	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	217	Nuclear localization.				hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|regulation of exit from mitosis (GO:0007096)|septin ring assembly (GO:0000921)	actin cytoskeleton (GO:0015629)|actomyosin contractile ring (GO:0005826)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(2)|endometrium(5)|kidney(5)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(2)	45						ATGATGTAAATCACTCATTTG	0.468																																					p.N217N		Atlas-SNP	.											.	ANLN	101	.	0			c.T651C						PASS	.						108	105	106					7																	36445953		2203	4300	6503	SO:0001819	synonymous_variant	54443	exon4			TGTAAATCACTCA	AF273437	CCDS5447.1, CCDS64628.1	7p15-p14	2013-01-10	2006-08-22		ENSG00000011426	ENSG00000011426		"Pleckstrin homology (PH) domain containing"	14082	protein-coding gene	gene with protein product			"anillin (Drosophila Scraps homolog), actin binding protein", "anillin, actin binding protein (scraps homolog, Drosophila)"			10931866	Standard	NM_001284301		Approved	ANILLIN, Scraps, scra	uc003tff.3	Q9NQW6	OTTHUMG00000023143	ENST00000265748.2:c.651T>C	chr7.hg19:g.36445953T>C		138.0	0.0	.		143.0	48.0	.	NM_018685	Q5CZ78|Q6NSK5|Q9H8Y4|Q9NVN9|Q9NVP0	Silent	SNP	ENST00000265748.2	hg19	CCDS5447.1																																																																																			.	.	.	none		0.468	ANLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218582.3	NM_018685		C	36445953	T	C	36445953	2	2	117	1	0	0	0	0	0	0	0	1	694	1432	50	3		3	ANLN	7	36445953	Silent	SNP	T	TCGA-BQ-5882-01A-11D-1589-08		36445953	122692710	27	7484											
MUC17	140453	hgsc.bcm.edu	37	chr7	100681165	100681165	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcatgcaaacctcaacttaTagtgacagaagaactccttt	15	10	6	10	0	1	3	1	1	0	2	2	3	2	3	2	0	5	2	2	0	6	3			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr7:100681165T>C	ENST00000306151.4	+	3	6532	c.6468T>C	c.(6466-6468)taT>taC	p.Y2156Y		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2156	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)					CCTCAACTTATAGTGACAGAA	0.463																																					p.Y2156Y		Atlas-SNP	.											.	MUC17	804	.	0			c.T6468C						PASS	.						221	219	220					7																	100681165		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			AACTTATAGTGAC	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.6468T>C	chr7.hg19:g.100681165T>C		335.0	0.0	.		383.0	130.0	.	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	hg19	CCDS34711.1																																																																																			.	.	.	none		0.463	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		C	100681165	T	C	100681165	2	2	117	1	0	0	0	0	0	0	0	1	9981	1413	49	3		3	MUC17	7	100681165	Silent	SNP	T	TCGA-BQ-5882-01A-11D-1589-08	64235212	100681165	58457498	28	7485											
MET	4233	hgsc.bcm.edu	37	chr7	116340025	116340025	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcctacatggaaatgcctcTggagtgtattctcacagaaa	12	12	8	9	0	2	1	1	0	2	1	4	3	3	3	2	2	2	1	2	2	4	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr7:116340025T>C	ENST00000318493.6	+	2	1074	c.887T>C	c.(886-888)cTg>cCg	p.L296P	MET_ENST00000436117.2_Missense_Mutation_p.L296P|MET_ENST00000397752.3_Missense_Mutation_p.L296P			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)			GAAATGCCTCTGGAGTGTATT	0.428			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.L296P		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.T887C						PASS	.						81	77	78					7																	116340025		1839	4092	5931	SO:0001583	missense	4233	exon2	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	TGCCTCTGGAGTG	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.887T>C	chr7.hg19:g.116340025T>C	ENSP00000317272:p.Leu296Pro	191.0	0.0	.		199.0	57.0	.	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	T	12.57	1.978979	0.34942	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000436117	T;T;T	0.17691	2.26;2.26;2.26	6.17	6.17	0.99709	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.068376	0.64402	D	0.000011	T	0.51601	0.1684	M	0.90595	3.13	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.998;0.999;1.0;0.999;0.999;0.999;0.999;0.999;1.0;0.996;0.999;1.0;1.0	T	0.60895	-0.7172	10	0.87932	D	0	-8.4229	16.8222	0.85835	0.0:0.0:0.0:1.0	.	296;296;296;296;296;296;296;296;296;296;296;296;296	B5A929;E7EQ94;B5A930;B5A934;B5A936;B5A937;B5A939;B5A941;B5A940;P08581-2;B5A942;P08581;A1L467	.;.;.;.;.;.;.;.;.;.;.;MET_HUMAN;.	P	296	ENSP00000380860:L296P;ENSP00000317272:L296P;ENSP00000410980:L296P	ENSP00000317272:L296P	L	+	2	0	MET	116127261	1.000000	0.71417	1.000000	0.80357	0.010000	0.07245	7.636000	0.83301	2.371000	0.80710	0.533000	0.62120	CTG	.	.	.	none		0.428	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			C	116340025	T	C	116340025	3	2	117	1	0	0	0	0	1	0	0	0	9492	1580	55	3	889	3	MET	7	116340025	Missense_Mutation	SNP	T	TCGA-BQ-5882-01A-11D-1589-08	15658860	116340025	42798638	29	7486											
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121651531	121651531	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtgtcatttgaatccatcCtgtcttcctatgatggtgca	8	16	8	9	0	2	2	1	2	1	0	5	2	5	2	3	1	1	1	3	1	2	3	rs143422308		TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr7:121651531C>T	ENST00000393386.2	+	12	2842	c.2431C>T	c.(2431-2433)Ctg>Ttg	p.L811L	PTPRZ1_ENST00000483028.1_Intron|PTPRZ1_ENST00000449182.1_Intron	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	811					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						TGAATCCATCCTGTCTTCCTA	0.458																																					p.L811L		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.C2431T						PASS	.						281	232	249					7																	121651531		2203	4300	6503	SO:0001819	synonymous_variant	5803	exon12			TCCATCCTGTCTT	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.2431C>T	chr7.hg19:g.121651531C>T		344.0	0.0	.		398.0	114.0	.	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Silent	SNP	ENST00000393386.2	hg19	CCDS34740.1																																																																																			.	C|1.000;G|0.000	.	alt		0.458	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		T	121651531	C	T	121651531	2	4	117	1	0	0	0	0	0	0	0	1	12827	680	24	2		2	PTPRZ1	7	121651531	Silent	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	5311506	121651531	37487132	30	7487											
WRN	7486	hgsc.bcm.edu	37	chr8	30938567	30938567	+	Missense_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	aacatgaagttttaattcacGttgaagatgaaacatgggac	16	11	9	5	1	1	4	1	3	0	1	1	5	1	5	0	1	2	2	0	1	5	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr8:30938567G>A	ENST00000298139.5	+	9	1273	c.1024G>A	c.(1024-1026)Gtt>Att	p.V342I		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	342					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)		TTTAATTCACGTTGAAGATGA	0.353			"Mis, N, F, S"			"osteosarcoma, meningioma, others"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome																												p.V342I	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.G1024A						PASS	.						105	101	103					8																	30938567		2203	4300	6503	SO:0001583	missense	7486	exon9	Familial Cancer Database	WS, Adult Progeria	ATTCACGTTGAAG		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.1024G>A	chr8.hg19:g.30938567G>A	ENSP00000298139:p.Val342Ile	114.0	0.0	.		142.0	31.0	.	NM_000553	A1KYY9	Missense_Mutation	SNP	ENST00000298139.5	hg19	CCDS6082.1	.	.	.	.	.	.	.	.	.	.	G	4.269	0.049074	0.08243	.	.	ENSG00000165392	ENST00000298139	T	0.41758	0.99	5.27	-3.21	0.05140	.	0.909998	0.09395	N	0.807993	T	0.17534	0.0421	N	0.20401	0.57	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.28427	-1.0044	10	0.10111	T	0.7	-0.4055	0.2738	0.00235	0.3113:0.1387:0.2652:0.2848	.	342	Q14191	WRN_HUMAN	I	342	ENSP00000298139:V342I	ENSP00000298139:V342I	V	+	1	0	WRN	31058109	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.336000	0.07863	-0.260000	0.09418	-0.143000	0.13931	GTT	.	.	.	none		0.353	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1			A	30938567	G	A	30938567	3	1	117	1	0	0	0	0	1	0	0	0	17414	1145	40	1	1054	1	WRN	8	30938567	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08		30938567	115425455	31	7488											
TTC35	9694	hgsc.bcm.edu	37	chr8	109489022	109489022	+	Silent	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	ttttaacaggttaagtatacCcaaggtggacttgaaaacct	14	12	8	7	0	0	1	0	1	0	0	0	2	0	2	2	3	3	2	2	3	7	6			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr8:109489022C>T	ENST00000220853.3	+	9	638	c.603C>T	c.(601-603)acC>acT	p.T201T	EMC2_ENST00000520294.1_3'UTR	NM_014673.3	NP_055488.1	Q15006	EMC2_HUMAN	ER membrane protein complex subunit 2	201						cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|ER membrane protein complex (GO:0072546)|mitochondrion (GO:0005739)|nucleus (GO:0005634)											TTAAGTATACCCAAGGTGGAC	0.338																																					p.T201T		Atlas-SNP	.											.	.	.	.	0			c.C603T						PASS	.						100	100	100					8																	109489022		2203	4300	6503	SO:0001819	synonymous_variant	9694	exon9			GTATACCCAAGGT	BC021667	CCDS6309.1	8q23.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000104412	ENSG00000104412			28963	protein-coding gene	gene with protein product		607722	"tetratricopeptide repeat domain 35"	KIAA0103, TTC35		7788527, 22119785	Standard	NM_014673		Approved		uc003ymw.1	Q15006	OTTHUMG00000164873	ENST00000220853.3:c.603C>T	chr8.hg19:g.109489022C>T		67.0	0.0	.		85.0	27.0	.	NM_014673	Q8WUE1	Silent	SNP	ENST00000220853.3	hg19	CCDS6309.1																																																																																			.	.	.	none		0.338	EMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380717.1	NM_014673		T	109489022	C	T	109489022	2	4	117	1	0	0	0	0	0	0	0	1	16715	610	22	2		2	TTC35	8	109489022	Silent	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	78550455	109489022	36875000	32	7489											
FAM49B	51571	hgsc.bcm.edu	37	chr8	130883632	130883632	+	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	gcgctttacctctcgtatttCgtggccagctcctctgtatg	4	15	9	13	3	2	0	0	0	2	0	5	0	3	0	3	1	2	4	3	1	3	5			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr8:130883632C>A	ENST00000519824.2	-	4	457	c.184G>T	c.(184-186)Gaa>Taa	p.E62*	FAM49B_ENST00000401979.2_Nonsense_Mutation_p.E62*|FAM49B_ENST00000523509.1_Nonsense_Mutation_p.E62*|FAM49B_ENST00000522250.1_5'UTR|FAM49B_ENST00000517654.1_Nonsense_Mutation_p.E62*|FAM49B_ENST00000519540.1_Nonsense_Mutation_p.E62*|FAM49B_ENST00000522941.1_5'UTR|FAM49B_ENST00000519110.1_Nonsense_Mutation_p.E62*|FAM49B_ENST00000522746.1_Nonsense_Mutation_p.E62*|FAM49B_ENST00000518879.1_Intron|SNORA25_ENST00000363205.1_RNA	NM_016623.4	NP_057707.3	Q9NUQ9	FA49B_HUMAN	family with sequence similarity 49, member B	62						cilium (GO:0005929)|extracellular vesicular exosome (GO:0070062)		p.E62K(1)		kidney(1)|large_intestine(6)|lung(4)|prostate(1)	12	Ovarian(5;0.000567)|Esophageal squamous(12;0.00693)|Acute lymphoblastic leukemia(118;0.155)		LUAD - Lung adenocarcinoma(14;0.0989)			TCTCGTATTTCGTGGCCAGCT	0.378																																					p.E62X		Atlas-SNP	.											FAM49B,colon,carcinoma,0,1	FAM49B	36	.	1	Substitution - Missense(1)	large_intestine(1)	c.G184T						PASS	.						110	106	108					8																	130883632		2203	4300	6503	SO:0001587	stop_gained	51571	exon4			GTATTTCGTGGCC	AF208851	CCDS6361.1	8q24	2004-08-20				ENSG00000153310			25216	protein-coding gene	gene with protein product							Standard	NM_001256763		Approved	BM-009	uc003ysu.4	Q9NUQ9		ENST00000519824.2:c.184G>T	chr8.hg19:g.130883632C>A	ENSP00000429150:p.Glu62*	122.0	0.0	.		153.0	56.0	.	NM_016623	Q96AZ5|Q9NW21|Q9NZE7	Nonsense_Mutation	SNP	ENST00000519824.2	hg19	CCDS6361.1	.	.	.	.	.	.	.	.	.	.	C	37	6.228266	0.97394	.	.	ENSG00000153310	ENST00000522746;ENST00000523509;ENST00000401979;ENST00000519110;ENST00000519824;ENST00000517654;ENST00000519540;ENST00000519142;ENST00000520204;ENST00000518283;ENST00000523993;ENST00000520254;ENST00000519020;ENST00000518167;ENST00000517672	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	-18.5272	19.0946	0.93244	0.0:1.0:0.0:0.0	.	.	.	.	X	62	.	ENSP00000384880:E62X	E	-	1	0	FAM49B	130952814	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.487000	0.81328	2.745000	0.94114	0.650000	0.86243	GAA	.	.	.	none		0.378	FAM49B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380390.2	NM_016623		A	130883632	C	A	130883632	4	1	117	1	0	0	0	0	0	1	0	0	5583	893	31	4	826	4	FAM49B	8	130883632	Nonsense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	21394610	130883632	15480390	33	7490											
PHF20L1	51105	hgsc.bcm.edu	37	chr8	133816926	133816926	+	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	gagcacattatcaaacaagaGgaaaaataatcaaggcaact	21	6	7	7	0	2	1	2	0	0	1	2	3	2	2	0	2	3	2	0	2	8	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr8:133816926G>C	ENST00000395386.2	+	8	1087	c.788G>C	c.(787-789)aGg>aCg	p.R263T	PHF20L1_ENST00000395376.1_Missense_Mutation_p.R268T|PHF20L1_ENST00000220847.7_5'UTR|PHF20L1_ENST00000395379.1_Missense_Mutation_p.R263T|PHF20L1_ENST00000337920.4_Missense_Mutation_p.R237T|PHF20L1_ENST00000395390.2_Missense_Mutation_p.R238T	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	263							zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			TCAAACAAGAGGAAAAATAAT	0.378																																					p.R263T		Atlas-SNP	.											.	PHF20L1	129	.	0			c.G788C						PASS	.						106	100	102					8																	133816926		2203	4300	6503	SO:0001583	missense	51105	exon8			ACAAGAGGAAAAA	AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"Tudor domain containing", "Zinc fingers, PHD-type"	24280	protein-coding gene	gene with protein product	"tudor domain containing 20B"					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.788G>C	chr8.hg19:g.133816926G>C	ENSP00000378784:p.Arg263Thr	128.0	0.0	.		164.0	48.0	.	NM_016018	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Missense_Mutation	SNP	ENST00000395386.2	hg19	CCDS6367.2	.	.	.	.	.	.	.	.	.	.	G	23.0	4.365266	0.82463	.	.	ENSG00000129292	ENST00000395383;ENST00000395379;ENST00000361997;ENST00000395386;ENST00000315808;ENST00000337920;ENST00000395376;ENST00000395382;ENST00000395390;ENST00000395374	T;T;T;T;T;T;T;T	0.69685	-0.35;-0.18;0.1;0.49;-0.42;0.23;-0.16;0.92	5.5	5.5	0.81552	.	0.189440	0.56097	D	0.000032	T	0.75213	0.3819	L	0.32530	0.975	0.80722	D	1	D;D;D;D;D	0.89917	0.996;0.997;0.999;1.0;0.996	D;D;D;D;D	0.87578	0.99;0.993;0.997;0.998;0.99	T	0.75590	-0.3265	10	0.49607	T	0.09	-16.2918	18.372	0.90409	0.0:0.0:1.0:0.0	.	238;102;263;263;237	F8W9L8;G5E9D0;A8MW92;A8MW92-4;A8MW92-2	.;.;P20L1_HUMAN;.;.	T	267;263;238;263;263;237;268;133;238;102	ENSP00000378781:R267T;ENSP00000378777:R263T;ENSP00000355301:R238T;ENSP00000378784:R263T;ENSP00000324519:R263T;ENSP00000338269:R237T;ENSP00000378775:R268T;ENSP00000378788:R238T	ENSP00000324519:R263T	R	+	2	0	PHF20L1	133886108	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.969000	0.70422	2.596000	0.87737	0.585000	0.79938	AGG	.	.	.	none		0.378	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018		C	133816926	G	C	133816926	3	2	117	1	0	0	0	0	1	0	0	0	11839	1000	35	4	814	4	PHF20L1	8	133816926	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	2933294	133816926	12547096	34	7491											
FBXO10	26267	hgsc.bcm.edu	37	chr9	37537307	37537307	+	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	ctcctgctgcagtgagttcaGcactaggcagctgggcagct	7	9	13	12	0	1	1	1	1	0	0	2	1	2	1	1	2	5	8	1	2	1	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr9:37537307G>T	ENST00000432825.2	-	3	1267	c.1219C>A	c.(1219-1221)Ctg>Atg	p.L407M	RP11-613M10.8_ENST00000544475.1_5'UTR|FBXO10_ENST00000543968.1_5'Flank|FBXO10_ENST00000541829.1_Intron	NM_012166.2	NP_036298.2	Q9UK96	FBX10_HUMAN	F-box protein 10	407					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)		AGTGAGTTCAGCACTAGGCAG	0.612																																					p.L407M		Atlas-SNP	.											.	FBXO10	75	.	0			c.C1219A						PASS	.						22	24	23					9																	37537307		2000	4176	6176	SO:0001583	missense	26267	exon3			AGTTCAGCACTAG	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.1219C>A	chr9.hg19:g.37537307G>T	ENSP00000403802:p.Leu407Met	24.0	0.0	.		32.0	11.0	.	NM_012166	Q08AL3|Q08AL4|Q5JRT8|Q9UKC3	Missense_Mutation	SNP	ENST00000432825.2	hg19	CCDS47966.1	.	.	.	.	.	.	.	.	.	.	G	16.16	3.044290	0.55110	.	.	ENSG00000147912	ENST00000432825	T	0.51071	0.72	5.46	3.59	0.41128	Carbohydrate-binding/sugar hydrolysis domain (1);	0.084546	0.50627	D	0.000114	T	0.45657	0.1353	L	0.29908	0.895	0.80722	D	1	D	0.64830	0.994	P	0.56343	0.796	T	0.42413	-0.9453	10	0.72032	D	0.01	-14.4477	7.4587	0.27283	0.1335:0.1507:0.7157:0.0	.	407	Q9UK96	FBX10_HUMAN	M	407	ENSP00000403802:L407M	ENSP00000276960:L407M	L	-	1	2	FBXO10	37527307	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.365000	0.59486	2.543000	0.85770	0.655000	0.94253	CTG	.	.	.	none		0.612	FBXO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052472.3			T	37537307	G	T	37537307	3	4	117	1	0	0	0	0	1	0	0	0	5733	962	34	4	1687	4	FBXO10	9	37537307	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08		37537307	103676124	35	7492											
KIAA1217	56243	hgsc.bcm.edu	37	chr10	24508666	24508666	+	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	ttcagtttccaagtcttcccGcaatatcccaaggagacaca	12	10	6	13	1	2	1	1	0	1	1	5	2	5	1	3	1	0	2	3	1	4	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr10:24508666G>T	ENST00000376454.3	+	2	212	c.182G>T	c.(181-183)cGc>cTc	p.R61L	KIAA1217_ENST00000376452.3_Missense_Mutation_p.R61L|KIAA1217_ENST00000376462.1_5'UTR|KIAA1217_ENST00000458595.1_Missense_Mutation_p.R61L	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	61					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						AAGTCTTCCCGCAATATCCCA	0.498																																					p.R61L		Atlas-SNP	.											.	KIAA1217	235	.	0			c.G182T						PASS	.						71	69	70					10																	24508666		2203	4300	6503	SO:0001583	missense	56243	exon2			CTTCCCGCAATAT	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.182G>T	chr10.hg19:g.24508666G>T	ENSP00000365637:p.Arg61Leu	81.0	0.0	.		106.0	25.0	.	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Missense_Mutation	SNP	ENST00000376454.3	hg19	CCDS31165.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.029194	0.93518	.	.	ENSG00000120549	ENST00000376456;ENST00000458595;ENST00000376454;ENST00000376452	T;T;T;T	0.62788	0.0;0.0;0.0;0.0	5.77	5.77	0.91146	.	0.093558	0.39985	N	0.001204	T	0.74981	0.3788	L	0.43923	1.385	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.997;0.999;0.998	T	0.73588	-0.3935	10	0.49607	T	0.09	.	19.9927	0.97374	0.0:0.0:1.0:0.0	.	61;61;61;61	Q5T5P2-7;A6NLF3;Q5T5P2;Q5T5P2-2	.;.;SKT_HUMAN;.	L	61	ENSP00000365639:R61L;ENSP00000392625:R61L;ENSP00000365637:R61L;ENSP00000365635:R61L	ENSP00000365635:R61L	R	+	2	0	KIAA1217	24548672	1.000000	0.71417	0.997000	0.53966	0.873000	0.50193	6.115000	0.71566	2.745000	0.94114	0.655000	0.94253	CGC	.	.	.	none		0.498	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		T	24508666	G	T	24508666	3	4	117	1	0	0	0	0	1	0	0	0	8223	1087	38	4	188	4	KIAA1217	10	24508666	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08		24508666	111026081	36	7493											
EPC1	80314	hgsc.bcm.edu	37	chr10	32580239	32580239	+	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	tgatctctccattgtagtcgCccaaattatacctaaaatta	13	14	4	10	1	1	1	0	1	1	0	4	1	2	1	3	0	1	1	3	0	7	6			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr10:32580239C>G	ENST00000263062.8	-	6	1096	c.827G>C	c.(826-828)gGc>gCc	p.G276A	EPC1_ENST00000375110.2_Missense_Mutation_p.G226A|EPC1_ENST00000319778.6_Missense_Mutation_p.G276A	NM_025209.2	NP_079485.1	Q9H2F5	EPC1_HUMAN	enhancer of polycomb homolog 1 (Drosophila)	276					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(5)|urinary_tract(1)	24		Prostate(175;0.0199)				ATTGTAGTCGCCCAAATTATA	0.313																																					p.G276A		Atlas-SNP	.											.	EPC1	74	.	0			c.G827C						PASS	.						75	73	74					10																	32580239		2203	4300	6503	SO:0001583	missense	80314	exon6			TAGTCGCCCAAAT	AF277374	CCDS7172.1, CCDS60511.1, CCDS73083.1	10p11	2005-12-12			ENSG00000120616	ENSG00000120616			19876	protein-coding gene	gene with protein product		610999				10976108	Standard	NM_025209		Approved	Epl1	uc001iwg.2	Q9H2F5	OTTHUMG00000017925	ENST00000263062.8:c.827G>C	chr10.hg19:g.32580239C>G	ENSP00000263062:p.Gly276Ala	102.0	0.0	.		176.0	31.0	.	NM_025209	B4DSC3|D3DRX7|Q5VW54|Q5VW56|Q5VW58|Q8NAQ4|Q8NE21|Q96LF4|Q96RR6|Q9H7T7	Missense_Mutation	SNP	ENST00000263062.8	hg19	CCDS7172.1	.	.	.	.	.	.	.	.	.	.	C	13.21	2.170633	0.38315	.	.	ENSG00000120616	ENST00000375110;ENST00000319778;ENST00000263062	T;T;T	0.66099	-0.19;-0.19;-0.19	4.89	4.89	0.63831	.	0.214139	0.49305	D	0.000142	T	0.55497	0.1924	L	0.39245	1.2	0.45594	D	0.99853	B;B;B;B	0.25667	0.048;0.131;0.097;0.059	B;B;B;B	0.27380	0.015;0.019;0.079;0.008	T	0.51124	-0.8745	10	0.22109	T	0.4	-15.0295	18.3946	0.90494	0.0:1.0:0.0:0.0	.	276;226;276;276	B8XCX7;Q9H2F5-3;Q9H2F5-2;Q9H2F5	.;.;.;EPC1_HUMAN	A	226;276;276	ENSP00000364251:G226A;ENSP00000318559:G276A;ENSP00000263062:G276A	ENSP00000263062:G276A	G	-	2	0	EPC1	32620245	1.000000	0.71417	1.000000	0.80357	0.755000	0.42902	3.929000	0.56514	2.419000	0.82065	0.467000	0.42956	GGC	.	.	.	none		0.313	EPC1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047484.1			G	32580239	C	G	32580239	3	3	117	1	0	0	0	0	1	0	0	0	5162	739	26	4	1723	4	EPC1	10	32580239	Missense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	8071573	32580239	102954508	37	7494											
OSBPL5	114879	hgsc.bcm.edu	37	chr11	3141834	3141834	+	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	acgcaccacagcttggtccaGctcttcagggtgccgcggat	7	8	12	14	3	2	0	1	0	1	0	3	1	3	1	3	3	3	3	3	3	0	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr11:3141834G>C	ENST00000263650.7	-	6	582	c.423C>G	c.(421-423)agC>agG	p.S141R	OSBPL5_ENST00000348039.5_Intron|OSBPL5_ENST00000389989.3_Intron|OSBPL5_ENST00000525498.1_Missense_Mutation_p.S93R|OSBPL5_ENST00000542243.1_Intron	NM_020896.3	NP_065947.1	Q9H0X9	OSBL5_HUMAN	oxysterol binding protein-like 5	141	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|Golgi to plasma membrane transport (GO:0006893)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|oxysterol binding (GO:0008142)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	25		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		GCTTGGTCCAGCTCTTCAGGG	0.677																																					p.S141R		Atlas-SNP	.											.	OSBPL5	78	.	0			c.C423G						PASS	.						53	49	51					11																	3141834		2202	4298	6500	SO:0001583	missense	114879	exon6			GGTCCAGCTCTTC	AF392453	CCDS31343.1, CCDS31344.1	11p15.4	2013-01-10			ENSG00000021762	ENSG00000021762		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16392	protein-coding gene	gene with protein product		606733					Standard	NM_145638		Approved	KIAA1534, ORP5	uc001lxk.2	Q9H0X9	OTTHUMG00000011702	ENST00000263650.7:c.423C>G	chr11.hg19:g.3141834G>C	ENSP00000263650:p.Ser141Arg	94.0	0.0	.		64.0	36.0	.	NM_020896	A6NDP0|A6NJS8|Q54A90|Q8N596|Q9BZB0|Q9P1Z4	Missense_Mutation	SNP	ENST00000263650.7	hg19	CCDS31344.1	.	.	.	.	.	.	.	.	.	.	G	15.20	2.763077	0.49574	.	.	ENSG00000021762	ENST00000263650;ENST00000525498	T;T	0.76186	-1.0;2.64	4.38	4.38	0.52667	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.115051	0.64402	D	0.000020	T	0.74786	0.3762	L	0.54323	1.7	0.80722	D	1	P;B;B	0.36753	0.568;0.056;0.425	B;B;B	0.44278	0.175;0.149;0.445	T	0.78091	-0.2339	10	0.72032	D	0.01	-34.5207	12.7278	0.57180	0.0829:0.0:0.9171:0.0	.	93;102;141	B4DVB0;E7EP03;Q9H0X9	.;.;OSBL5_HUMAN	R	141;93	ENSP00000263650:S141R;ENSP00000433342:S93R	ENSP00000263650:S141R	S	-	3	2	OSBPL5	3098410	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	0.883000	0.28200	2.285000	0.76669	0.555000	0.69702	AGC	.	.	.	none		0.677	OSBPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032332.2			C	3141834	G	C	3141834	3	2	117	1	0	0	0	0	1	0	0	0	11287	962	34	4	2284	4	OSBPL5	11	3141834	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08		3141834	131864682	38	7495											
OR8H3	390152	hgsc.bcm.edu	37	chr11	55890629	55890629	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctatgatttttacttacttaAagccaagaaagtcttattcc	13	16	4	8	0	1	2	0	1	1	1	2	2	2	2	2	0	3	0	2	0	8	8			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr11:55890629A>G	ENST00000313472.3	+	1	781	c.781A>G	c.(781-783)Aag>Gag	p.K261E		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	261						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)					TACTTACTTAAAGCCAAGAAA	0.373																																					p.K261E		Atlas-SNP	.											.	OR8H3	92	.	0			c.A781G						PASS	.						102	101	101					11																	55890629		2201	4296	6497	SO:0001583	missense	390152	exon1			TACTTAAAGCCAA	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.781A>G	chr11.hg19:g.55890629A>G	ENSP00000323928:p.Lys261Glu	168.0	0.0	.		121.0	58.0	.	NM_001005201	Q6IFB7	Missense_Mutation	SNP	ENST00000313472.3	hg19	CCDS31519.1	.	.	.	.	.	.	.	.	.	.	A	10.17	1.276100	0.23307	.	.	ENSG00000181761	ENST00000313472	T	0.37411	1.2	3.62	2.35	0.29111	GPCR, rhodopsin-like superfamily (1);	0.222186	0.32134	N	0.006528	T	0.54822	0.1882	M	0.83774	2.66	0.09310	N	1	D	0.76494	0.999	D	0.71414	0.973	T	0.40194	-0.9576	10	0.87932	D	0	.	5.4761	0.16695	0.5957:0.3026:0.1016:0.0	.	261	Q8N146	OR8H3_HUMAN	E	261	ENSP00000323928:K261E	ENSP00000323928:K261E	K	+	1	0	OR8H3	55647205	0.000000	0.05858	0.804000	0.32291	0.121000	0.20230	-0.491000	0.06474	1.415000	0.47037	0.145000	0.16022	AAG	.	.	.	none		0.373	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201		G	55890629	A	G	55890629	3	3	117	1	0	0	0	0	1	0	0	0	11246	15	1	3	783	3	OR8H3	11	55890629	Missense_Mutation	SNP	A	TCGA-BQ-5882-01A-11D-1589-08	52748795	55890629	79115887	39	7496											
IFLTD1	160492	hgsc.bcm.edu	37	chr12	25702289	25702289	+	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	tttccactctggaacagctaCctacagtagctttagaagtc	11	12	7	11	0	1	1	0	0	1	1	3	2	2	2	2	1	5	3	2	1	6	6			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr12:25702289C>A	ENST00000282881.6	-	2	367	c.218G>T	c.(217-219)gGt>gTt	p.G73V	IFLTD1_ENST00000413632.2_Missense_Mutation_p.G94V|IFLTD1_ENST00000445693.1_Intron|IFLTD1_ENST00000539744.1_5'UTR|IFLTD1_ENST00000458174.2_Missense_Mutation_p.G94V	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		73					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)					GGAACAGCTACCTACAGTAGC	0.353																																					p.G94V		Atlas-SNP	.											.	IFLTD1	121	.	0			c.G281T						PASS	.						55	50	52					12																	25702289		2203	4300	6503	SO:0001583	missense	160492	exon3			CAGCTACCTACAG																												ENST00000282881.6:c.218G>T	chr12.hg19:g.25702289C>A	ENSP00000282881:p.Gly73Val	78.0	0.0	.		70.0	19.0	.	NM_001145728	B4DL27|B4DY70|Q8IY38	Missense_Mutation	SNP	ENST00000282881.6	hg19	CCDS8704.1	.	.	.	.	.	.	.	.	.	.	C	4.838	0.155802	0.09236	.	.	ENSG00000152936	ENST00000282881;ENST00000458174;ENST00000413632;ENST00000538178;ENST00000540106;ENST00000542224	T;T;T	0.13538	2.74;2.77;2.58	3.4	-6.81	0.01704	.	.	.	.	.	T	0.03305	0.0096	N	0.04508	-0.205	0.09310	N	1	B;B;B	0.10296	0.003;0.002;0.001	B;B;B	0.09377	0.004;0.002;0.001	T	0.36915	-0.9728	9	0.06625	T	0.88	-7.9674	1.5985	0.02669	0.1745:0.4041:0.1887:0.2328	.	94;94;73	Q8N9Z9-5;Q8N9Z9-4;Q8N9Z9	.;.;ILFT1_HUMAN	V	73;94;94;48;48;48	ENSP00000282881:G73V;ENSP00000407353:G94V;ENSP00000393150:G94V	ENSP00000282881:G73V	G	-	2	0	IFLTD1	25593556	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.175000	0.01263	-1.982000	0.00988	0.460000	0.39030	GGT	.	.	.	none		0.353	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1			A	25702289	C	A	25702289	3	1	117	1	0	0	0	0	1	0	0	0	7537	507	18	4	976	4	IFLTD1	12	25702289	Missense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08		25702289	108149606	40	7497											
ALG10B	144245	hgsc.bcm.edu	37	chr12	38714192	38714192	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcttctgtgcagggaatgTcattgcacaaaagttaactg	11	13	10	7	0	3	0	1	0	2	0	3	1	3	1	0	1	3	3	0	1	4	3			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr12:38714192T>C	ENST00000308742.4	+	3	915	c.599T>C	c.(598-600)gTc>gCc	p.V200A	ALG10B_ENST00000551464.1_Intron|AC117372.1_ENST00000401168.2_RNA	NM_001013620.3	NP_001013642.1	Q5I7T1	AG10B_HUMAN	ALG10B, alpha-1,2-glucosyltransferase	200					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transferase activity, transferring hexosyl groups (GO:0016758)			breast(2)|kidney(3)|large_intestine(7)|lung(8)|ovary(4)|skin(1)	25	Esophageal squamous(101;0.187)	Lung NSC(34;0.204)|all_lung(34;0.235)				GCAGGGAATGTCATTGCACAA	0.388																																					p.V200A		Atlas-SNP	.											.	ALG10B	58	.	0			c.T599C						PASS	.						167	169	168					12																	38714192		2203	4300	6503	SO:0001583	missense	144245	exon3			GGAATGTCATTGC	AY845858	CCDS31772.1	12q12	2013-03-04	2013-03-04		ENSG00000175548	ENSG00000175548	2.4.1.256		31088	protein-coding gene	gene with protein product	"potassium channel regulator 1", "dolichyl-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-dolichol alpha-1,2- glucosyltransferase"		"asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog B (yeast)"				Standard	NM_001013620		Approved	KCR1	uc001rln.4	Q5I7T1	OTTHUMG00000169298	ENST00000308742.4:c.599T>C	chr12.hg19:g.38714192T>C	ENSP00000310120:p.Val200Ala	418.0	0.0	.		442.0	140.0	.	NM_001013620	B2RPF4	Missense_Mutation	SNP	ENST00000308742.4	hg19	CCDS31772.1	.	.	.	.	.	.	.	.	.	.	N	7.218	0.596709	0.13875	.	.	ENSG00000175548	ENST00000308742	T	0.55760	0.5	3.24	3.24	0.37175	.	0.332405	0.30771	N	0.008920	T	0.35219	0.0924	L	0.31420	0.93	0.80722	D	1	B	0.15719	0.014	B	0.10450	0.005	T	0.10941	-1.0608	10	0.12103	T	0.63	.	10.1623	0.42860	0.0:0.0:0.0:1.0	.	200	Q5I7T1	AG10B_HUMAN	A	200	ENSP00000310120:V200A	ENSP00000310120:V200A	V	+	2	0	ALG10B	37000459	0.999000	0.42202	0.009000	0.14445	0.383000	0.30230	5.798000	0.69095	1.719000	0.51432	0.448000	0.29417	GTC	.	.	.	none		0.388	ALG10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403349.1	NM_001013620		C	38714192	T	C	38714192	3	2	117	1	0	0	0	0	1	0	0	0	512	1667	58	3	609	3	ALG10B	12	38714192	Missense_Mutation	SNP	T	TCGA-BQ-5882-01A-11D-1589-08	13011903	38714192	95137703	41	7498											
MLL2	8085	hgsc.bcm.edu	37	chr12	49427714	49427714	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgttccgatattctgccaTgagattagtgtgctccttct	6	17	8	10	1	2	1	0	1	2	1	4	3	4	1	3	0	2	2	3	0	2	6	rs372758101		TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr12:49427714T>C	ENST00000301067.7	-	39	10773	c.10774A>G	c.(10774-10776)Atg>Gtg	p.M3592V	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3592	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)										TATTCTGCCATGAGATTAGTG	0.582																																					p.M3592V		Atlas-SNP	.											.	MLL2	1173	.	0			c.A10774G						PASS	.	T	VAL/MET	1,4325		0,1,2162	14	13	14		10774	5.4	1	12		14	0,8464		0,0,4232	no	missense	MLL2	NM_003482.3	21	0,1,6394	CC,CT,TT		0.0,0.0231,0.0078	benign	3592/5538	49427714	1,12789	2163	4232	6395	SO:0001583	missense	8085	exon39			CTGCCATGAGATT	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.10774A>G	chr12.hg19:g.49427714T>C	ENSP00000301067:p.Met3592Val	0.0	0.0	.		9.0	5.0	.	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	T	9.346	1.064224	0.20067	2.31E-4	0.0	ENSG00000167548	ENST00000301067	T	0.39056	1.1	5.38	5.38	0.77491	.	0.000000	0.44688	D	0.000428	T	0.25791	0.0628	N	0.08118	0	0.31092	N	0.71073	B	0.26483	0.15	B	0.19946	0.027	T	0.30563	-0.9974	10	0.87932	D	0	.	14.6888	0.69068	0.0:0.0:0.0:1.0	.	3592	O14686	MLL2_HUMAN	V	3592	ENSP00000301067:M3592V	ENSP00000301067:M3592V	M	-	1	0	MLL2	47713981	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.118000	0.71583	2.189000	0.69895	0.460000	0.39030	ATG	.	.	.	weak		0.582	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			C	49427714	T	C	49427714	3	2	117	1	0	0	0	0	1	0	0	0	9628	1464	51	3	5903	3	MLL2	12	49427714	Missense_Mutation	SNP	T	TCGA-BQ-5882-01A-11D-1589-08	10713522	49427714	84424181	42	7499											
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120582190	120582190	+	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	gctgtctcagcgtacatggaGataacccgctggcccgcgcg	7	7	13	14	5	1	1	1	0	1	1	2	2	1	1	2	2	3	3	2	2	2	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr12:120582190G>T	ENST00000300648.6	-	42	5427	c.5415C>A	c.(5413-5415)atC>atA	p.I1805I		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1805					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)					CGTACATGGAGATAACCCGCT	0.597																																					p.I1805I		Atlas-SNP	.											.	GCN1L1	207	.	0			c.C5415A						PASS	.						58	63	61					12																	120582190		2058	4197	6255	SO:0001819	synonymous_variant	10985	exon42			CATGGAGATAACC	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.5415C>A	chr12.hg19:g.120582190G>T		75.0	0.0	.		93.0	29.0	.	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Silent	SNP	ENST00000300648.6	hg19	CCDS41847.1																																																																																			.	.	.	none		0.597	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			T	120582190	G	T	120582190	2	4	117	1	0	0	0	0	0	0	0	1	6306	932	33	4		4	GCN1L1	12	120582190	Silent	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	71154476	120582190	13269705	43	7500											
C13orf23	80209	hgsc.bcm.edu	37	chr13	39596542	39596542	+	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	ggtaccagacctgcattgttAtaagcacctaaaataaaaac	17	9	6	9	0	0	1	0	0	0	1	0	1	0	1	3	1	4	4	3	1	8	6			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr13:39596542A>T	ENST00000352251.3	-	9	1484	c.651T>A	c.(649-651)taT>taA	p.Y217*	PROSER1_ENST00000484434.3_Intron|PROSER1_ENST00000350125.3_Nonsense_Mutation_p.Y195*	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	217	Pro-rich.																CTGCATTGTTATAAGCACCTA	0.378																																					p.Y217X		Atlas-SNP	.											.	.	.	.	0			c.T651A						PASS	.						132	130	131					13																	39596542		2203	4300	6503	SO:0001587	stop_gained	80209	exon9			ATTGTTATAAGCA	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.651T>A	chr13.hg19:g.39596542A>T	ENSP00000332034:p.Tyr217*	139.0	0.0	.		145.0	72.0	.	NM_025138	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Nonsense_Mutation	SNP	ENST00000352251.3	hg19	CCDS9368.2	.	.	.	.	.	.	.	.	.	.	A	44	11.133907	0.99521	.	.	ENSG00000120685	ENST00000352251;ENST00000350125	.	.	.	5.69	-5.32	0.02722	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-7.1752	17.3861	0.87416	0.267:0.0:0.733:0.0	.	.	.	.	X	217;195	.	.	Y	-	3	2	PROSER1	38494542	0.996000	0.38824	0.817000	0.32601	0.961000	0.63080	0.263000	0.18478	-1.201000	0.02659	-0.250000	0.11733	TAT	.	.	.	none		0.378	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138		T	39596542	A	T	39596542	4	4	117	1	0	0	0	0	0	1	0	0	1723	456	16	5	2203	5	C13orf23	13	39596542	Nonsense_Mutation	SNP	A	TCGA-BQ-5882-01A-11D-1589-08		39596542	75573336	44	7501											
TRIM9	114088	hgsc.bcm.edu	37	chr14	51475908	51475908	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagtgtgcctttaccccacTgatcctcagtcaggtgcact	7	12	9	13	0	2	2	2	2	0	0	3	2	3	2	4	1	3	1	4	1	1	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr14:51475908T>C	ENST00000298355.3	-	5	2317	c.1196A>G	c.(1195-1197)cAg>cGg	p.Q399R	TRIM9_ENST00000360392.4_Missense_Mutation_p.Q399R|TRIM9_ENST00000338969.5_Missense_Mutation_p.Q399R	NM_015163.5	NP_055978.4	Q9C026	TRIM9_HUMAN	tripartite motif containing 9	399	COS. {ECO:0000255|PROSITE- ProRule:PRU00586}.				negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of SNARE complex assembly (GO:0035544)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|synaptic vesicle (GO:0008021)	ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_epithelial(31;0.00418)|Breast(41;0.148)					TTTACCCCACTGATCCTCAGT	0.488																																					p.Q399R		Atlas-SNP	.											.	TRIM9	188	.	0			c.A1196G						PASS	.						179	132	148					14																	51475908		2203	4300	6503	SO:0001583	missense	114088	exon5			CCCCACTGATCCT	AF220036	CCDS9703.1, CCDS45105.1	14q21.3	2013-02-11	2011-01-25		ENSG00000100505	ENSG00000100505		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	16288	protein-coding gene	gene with protein product		606555	"tripartite motif-containing 9"			11331580, 11524423	Standard	NM_015163		Approved	SPRING, RNF91	uc001wyx.4	Q9C026	OTTHUMG00000140291	ENST00000298355.3:c.1196A>G	chr14.hg19:g.51475908T>C	ENSP00000298355:p.Gln399Arg	105.0	0.0	.		149.0	49.0	.	NM_052978	D3DSB7|D3DSB8|Q92557|Q96D24|Q96NI4|Q9C025|Q9C027	Missense_Mutation	SNP	ENST00000298355.3	hg19	CCDS9703.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.412686	0.83340	.	.	ENSG00000100505	ENST00000298355;ENST00000338969;ENST00000360392	T;T;T	0.70986	-0.37;-0.53;0.54	5.94	5.94	0.96194	B-box, C-terminal (1);COS domain (1);	0.000000	0.85682	D	0.000000	T	0.80722	0.4677	M	0.62723	1.935	0.54753	D	0.99998	D;D;P	0.61697	0.986;0.99;0.901	D;D;P	0.67382	0.951;0.941;0.482	T	0.77872	-0.2426	10	0.26408	T	0.33	.	15.5887	0.76506	0.0:0.0:0.0:1.0	.	399;399;399	Q9C026-5;Q9C026-4;Q9C026	.;.;TRIM9_HUMAN	R	399	ENSP00000298355:Q399R;ENSP00000342970:Q399R;ENSP00000353561:Q399R	ENSP00000298355:Q399R	Q	-	2	0	TRIM9	50545658	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.997000	0.88414	2.275000	0.75901	0.528000	0.53228	CAG	.	.	.	none		0.488	TRIM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276874.1	NM_015163		C	51475908	T	C	51475908	3	2	117	1	0	0	0	0	1	0	0	0	16561	1580	55	3	1010	3	TRIM9	14	51475908	Missense_Mutation	SNP	T	TCGA-BQ-5882-01A-11D-1589-08		51475908	55873632	45	7502											
RTL1	388015	hgsc.bcm.edu	37	chr14	101348358	101348358	+	Frame_Shift_Del	DEL	T	T	-																															cagcccgtattggaagaatcTtcatctccgcttgagagtac																										TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr14:101348358delT	ENST00000534062.1	-	1	2826	c.2768delA	c.(2767-2769)aagfs	p.K923fs	MIR127_ENST00000384876.1_RNA|MIR431_ENST00000385266.1_RNA|MIR433_ENST00000384837.1_RNA|MIR136_ENST00000385207.1_RNA|MIR432_ENST00000606207.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	923					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						TGGAAGAATCTTCATCTCCGC	0.537																																					p.K923fs		Atlas-INDEL	.											.	RTL1	120	.	0			c.2769delG						PASS	.						38	37	37					14																	101348358		1568	3582	5150	SO:0001589	frameshift_variant	388015	exon1			.		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.2768delA	chr14.hg19:g.101348358delT	ENSP00000435342:p.Lys923fs	42.0	0.0	0		53.0	17.0	0.320755	NM_001134888	E9PKS8	Frame_Shift_Del	DEL	ENST00000534062.1	hg19	CCDS53910.1																																																																																			.	.	.	none		0.537	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888		-	101348358	T	-	101348358	7	5	117	1	0	1	0	1	0	0	0	0	13737	1609	56	0	1312	0	RTL1	14	101348358	Frame_Shift_Del	DEL	T	TCGA-BQ-5882-01A-11D-1589-08	49872450	101348358	6001182	46	7503											
EARS2	124454	hgsc.bcm.edu	37	chr16	23540828	23540828	+	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	cctgcgggtactcaccccagCacacgcttggcaatcacatc	9	7	8	17	2	2	0	2	0	0	0	3	0	2	0	3	2	3	4	3	2	2	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr16:23540828C>T	ENST00000563459.1	-	7	1353	c.1347G>A	c.(1345-1347)gtG>gtA	p.V449V	EARS2_ENST00000564501.1_Silent_p.V449V|EARS2_ENST00000563232.1_Silent_p.V449V|EARS2_ENST00000449606.1_Silent_p.V449V|EARS2_ENST00000564987.1_5'UTR			Q5JPH6	SYEM_HUMAN	glutamyl-tRNA synthetase 2, mitochondrial	449					gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|tRNA aminoacylation for mitochondrial protein translation (GO:0070127)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|glutamate-tRNA(Gln) ligase activity (GO:0050561)|tRNA binding (GO:0000049)			central_nervous_system(1)|endometrium(1)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	8				GBM - Glioblastoma multiforme(48;0.0353)		CTCACCCCAGCACACGCTTGG	0.607																																					p.V449V		Atlas-SNP	.											.	EARS2	26	.	0			c.G1347A						PASS	.						38	42	41					16																	23540828		2124	4249	6373	SO:0001819	synonymous_variant	124454	exon7			CCCCAGCACACGC	AB075850	CCDS42132.1	16p12.2	2014-05-06	2012-10-26		ENSG00000103356	ENSG00000103356	6.1.1.17	"Aminoacyl tRNA synthetases / Class I"	29419	protein-coding gene	gene with protein product	"glutamate tRNA ligase 2, mitochondrial"	612799	"glutamyl-tRNA synthetase 2, mitochondrial (putative)"			15779907, 19805282, 22492562	Standard	NM_001083614		Approved	KIAA1970, MSE1	uc002dlt.4	Q5JPH6	OTTHUMG00000177018	ENST00000563459.1:c.1347G>A	chr16.hg19:g.23540828C>T		47.0	0.0	.		46.0	13.0	.	NM_001083614	B3KTT2|D3DWF1|Q86YH3|Q8TF31	Silent	SNP	ENST00000563459.1	hg19	CCDS42132.1																																																																																			.	.	.	none		0.607	EARS2-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434844.1	NM_133451		T	23540828	C	T	23540828	2	4	117	1	0	0	0	0	0	0	0	1	4880	697	25	2		2	EARS2	16	23540828	Silent	SNP	C	TCGA-BQ-5882-01A-11D-1589-08		23540828	66813925	47	7504											
RNF166	115992	hgsc.bcm.edu	37	chr16	88765421	88765421	+	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	tggctttccacacagtgcttCaccagctcctgctggtccag	6	11	9	15	0	1	0	1	0	0	0	4	0	4	0	4	2	3	4	4	2	0	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr16:88765421C>A	ENST00000312838.4	-	4	593	c.498G>T	c.(496-498)gtG>gtT	p.V166V	RNF166_ENST00000537718.2_Silent_p.V57V|RNF166_ENST00000568683.1_Silent_p.V57V|RNF166_ENST00000541206.2_Silent_p.V57V|RNF166_ENST00000567844.1_Silent_p.V85V|RP5-1142A6.5_ENST00000561699.1_RNA|RNF166_ENST00000562499.1_5'Flank	NM_178841.3	NP_849163.1	Q96A37	RN166_HUMAN	ring finger protein 166	166							zinc ion binding (GO:0008270)			endometrium(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0476)		CACAGTGCTTCACCAGCTCCT	0.677																																					p.V166V		Atlas-SNP	.											.	RNF166	3	.	0			c.G498T						PASS	.						52	49	50					16																	88765421		2191	4293	6484	SO:0001819	synonymous_variant	115992	exon4			GTGCTTCACCAGC	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.498G>T	chr16.hg19:g.88765421C>A		14.0	0.0	.		14.0	8.0	.	NM_178841	B3KQ03|D3DX75|H3BTU8|Q96DM0	Silent	SNP	ENST00000312838.4	hg19	CCDS10969.1																																																																																			.	.	.	none		0.677	RNF166-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269544.1	NM_178841		A	88765421	C	A	88765421	2	1	117	1	0	0	0	0	0	0	0	1	13470	813	29	4		4	RNF166	16	88765421	Silent	SNP	C	TCGA-BQ-5882-01A-11D-1589-08	65224593	88765421	1589332	48	7505											
UNC13D	201294	hgsc.bcm.edu	37	chr17	73837041	73837041	+	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	caggccaggtcactcaccacAtgtccagatgaaagctcgca	12	6	9	14	1	2	2	2	1	0	1	4	2	3	2	3	2	1	2	3	2	1	0			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr17:73837041A>T	ENST00000207549.4	-	7	990	c.611T>A	c.(610-612)aTg>aAg	p.M204K	UNC13D_ENST00000587504.1_5'UTR|UNC13D_ENST00000412096.2_Missense_Mutation_p.M204K	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	204	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)			CACTCACCACATGTCCAGATG	0.592									Familial Hemophagocytic Lymphohistiocytosis																												p.M204K		Atlas-SNP	.											.	UNC13D	68	.	0			c.T611A						PASS	.						250	240	243					17																	73837041		2203	4300	6503	SO:0001583	missense	201294	exon7	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	CACCACATGTCCA	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.611T>A	chr17.hg19:g.73837041A>T	ENSP00000207549:p.Met204Lys	451.0	0.0	.		474.0	146.0	.	NM_199242	B4DWG9|Q9H7K5	Missense_Mutation	SNP	ENST00000207549.4	hg19	CCDS11730.1	.	.	.	.	.	.	.	.	.	.	A	19.45	3.830248	0.71258	.	.	ENSG00000092929	ENST00000207549;ENST00000412096;ENST00000448606	T;T	0.39406	1.08;1.08	4.44	4.44	0.53790	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.059897	0.64402	D	0.000004	T	0.61887	0.2383	M	0.82323	2.585	0.80722	D	1	D;B	0.53312	0.959;0.132	P;B	0.57244	0.816;0.207	T	0.69544	-0.5117	10	0.87932	D	0	.	13.7049	0.62631	1.0:0.0:0.0:0.0	.	204;204	B4DTQ6;Q70J99	.;UN13D_HUMAN	K	204	ENSP00000207549:M204K;ENSP00000388093:M204K	ENSP00000207549:M204K	M	-	2	0	UNC13D	71348636	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	8.339000	0.90041	1.650000	0.50662	0.460000	0.39030	ATG	.	.	.	none		0.592	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950		T	73837041	A	T	73837041	3	4	117	1	0	0	0	0	1	0	0	0	16999	217	8	5	2765	5	UNC13D	17	73837041	Missense_Mutation	SNP	A	TCGA-BQ-5882-01A-11D-1589-08		73837041	7358169	49	7506											
QRICH2	84074	hgsc.bcm.edu	37	chr17	74288035	74288035	+	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	caggccatgtggatctgcctGaggttgcaccataccttgct	7	11	11	12	0	1	1	0	1	1	0	1	2	1	2	4	3	4	3	4	3	1	3			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr17:74288035G>A	ENST00000262765.5	-	4	2454	c.2275C>T	c.(2275-2277)Cag>Tag	p.Q759*		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	759	Gln-rich.									breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						GGATCTGCCTGAGGTTGCACC	0.522																																					p.Q759X		Atlas-SNP	.											.	QRICH2	143	.	0			c.C2275T						PASS	.						181	166	171					17																	74288035		2203	4300	6503	SO:0001587	stop_gained	84074	exon4			CTGCCTGAGGTTG	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.2275C>T	chr17.hg19:g.74288035G>A	ENSP00000262765:p.Gln759*	223.0	0.0	.		219.0	74.0	.	NM_032134	A2RRE1|Q96LM3	Nonsense_Mutation	SNP	ENST00000262765.5	hg19	CCDS32741.1	.	.	.	.	.	.	.	.	.	.	g	38	6.650945	0.97734	.	.	ENSG00000129646	ENST00000262765;ENST00000301613	.	.	.	4.21	0.735	0.18300	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	-0.4735	11.7828	0.52023	0.0:0.4377:0.5623:0.0	.	.	.	.	X	759	.	ENSP00000262765:Q759X	Q	-	1	0	QRICH2	71799630	0.000000	0.05858	0.003000	0.11579	0.066000	0.16364	-1.577000	0.02127	0.500000	0.27991	-0.537000	0.04273	CAG	.	.	.	none		0.522	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134		A	74288035	G	A	74288035	4	1	117	1	0	0	0	0	0	1	0	0	12893	1299	45	2	2780	2	QRICH2	17	74288035	Nonsense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	450994	74288035	6907175	50	7507											
TAF4B	6875	hgsc.bcm.edu	37	chr18	23865865	23865865	+	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	gaaaagcgtggttgccttacGacaacttctgcctaactccc	10	10	8	13	2	1	0	0	0	1	0	2	2	2	0	3	1	6	1	3	1	5	4			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr18:23865865G>A	ENST00000269142.5	+	7	1990	c.992G>A	c.(991-993)cGa>cAa	p.R331Q	TAF4B_ENST00000578121.1_Missense_Mutation_p.R331Q|TAF4B_ENST00000400466.2_Missense_Mutation_p.R331Q	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	331	TAFH. {ECO:0000255|PROSITE- ProRule:PRU00440}.				gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			GTTGCCTTACGACAACTTCTG	0.408																																					p.R331Q		Atlas-SNP	.											.	TAF4B	71	.	0			c.G992A						PASS	.						117	105	108					18																	23865865		1933	4147	6080	SO:0001583	missense	6875	exon7			CCTTACGACAACT	Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"TATA box binding protein (TBP)-associated factor 4B"	601689	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.992G>A	chr18.hg19:g.23865865G>A	ENSP00000269142:p.Arg331Gln	234.0	0.0	.		197.0	104.0	.	NM_005640	Q29YA4|Q29YA5	Missense_Mutation	SNP	ENST00000269142.5	hg19	CCDS42421.1	.	.	.	.	.	.	.	.	.	.	g	15.30	2.793145	0.50102	.	.	ENSG00000141384	ENST00000418698;ENST00000269142;ENST00000400466	T;T;T	0.49720	0.77;0.77;0.77	5.72	4.83	0.62350	TAFH/NHR1 (3);	0.124363	0.56097	D	0.000033	T	0.62768	0.2455	L	0.58428	1.81	0.54753	D	0.999986	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.961	T	0.58907	-0.7553	10	0.16420	T	0.52	-9.2264	15.6095	0.76704	0.0:0.0:0.861:0.139	.	331;331	Q92750;A4PBF7	TAF4B_HUMAN;.	Q	331	ENSP00000389365:R331Q;ENSP00000269142:R331Q;ENSP00000383314:R331Q	ENSP00000269142:R331Q	R	+	2	0	TAF4B	22119863	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.418000	0.80167	1.388000	0.46506	0.558000	0.71614	CGA	.	.	.	none		0.408	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640		A	23865865	G	A	23865865	3	1	117	1	0	0	0	0	1	0	0	0	15539	1058	37	1	1018	1	TAF4B	18	23865865	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08		23865865	54211383	51	7508											
LPPR3	79948	hgsc.bcm.edu	37	chr19	814747	814747	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgtgctgggacgggaaggtcTtcctgtaagaggcgtccagc	7	8	16	10	3	1	1	0	0	1	1	3	3	3	3	2	4	2	2	2	4	2	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr19:814747T>C	ENST00000520876.3	-	6	680	c.602A>G	c.(601-603)aAg>aGg	p.K201R	MIR3187_ENST00000583431.1_RNA|LPPR3_ENST00000359894.2_Missense_Mutation_p.K201R	NM_001270366.1	NP_001257295.1	Q6T4P5	LPPR3_HUMAN		201						integral component of membrane (GO:0016021)	phosphatidate phosphatase activity (GO:0008195)										CGGGAAGGTCTTCCTGTAAGA	0.667																																					p.K201R		Atlas-SNP	.											.	.	.	.	0			c.A602G						PASS	.						40	33	35					19																	814747		2187	4296	6483	SO:0001583	missense	0	exon6			AAGGTCTTCCTGT																												ENST00000520876.3:c.602A>G	chr19.hg19:g.814747T>C	ENSP00000430297:p.Lys201Arg	34.0	0.0	.		36.0	11.0	.	NM_001270366	Q86XQ4|Q96EH1|Q9BQF9|Q9HAJ4	Missense_Mutation	SNP	ENST00000520876.3	hg19	CCDS58636.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.010930	0.75046	.	.	ENSG00000129951	ENST00000300947;ENST00000359894;ENST00000520876	T;T	0.48201	0.82;0.82	4.77	4.77	0.60923	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.53110	0.1776	L	0.46567	1.45	0.39303	D	0.964943	P;P;D	0.56746	0.918;0.933;0.977	P;P;P	0.55871	0.596;0.718;0.786	T	0.54370	-0.8304	10	0.35671	T	0.21	-24.8006	12.0107	0.53286	0.0:0.0:0.0:1.0	.	202;201;201	Q6T4P5-2;Q6T4P5;Q6T4P5-3	.;LPPR3_HUMAN;.	R	202;201;201	ENSP00000352962:K201R;ENSP00000430297:K201R	ENSP00000300947:K202R	K	-	2	0	AC006273.1	765747	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	4.722000	0.61958	1.780000	0.52325	0.454000	0.30748	AAG	.	.	.	none		0.667	LPPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379096.3			C	814747	T	C	814747	3	2	117	1	0	0	0	0	1	0	0	0	8933	1609	56	3	1646	3	LPPR3	19	814747	Missense_Mutation	SNP	T	TCGA-BQ-5882-01A-11D-1589-08		814747	58314236	52	7509											
ZNF607	84775	hgsc.bcm.edu	37	chr19	38190209	38190209	+	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	atgtggcttctctccagtatGaatactctgatgtactttaa	10	16	7	8	0	2	2	0	2	2	0	4	2	3	2	1	1	2	3	1	1	5	6			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr19:38190209G>T	ENST00000355202.4	-	5	1418	c.823C>A	c.(823-825)Cat>Aat	p.H275N	CTD-2528L19.4_ENST00000586606.2_Intron|ZNF607_ENST00000395835.3_Missense_Mutation_p.H274N	NM_032689.4	NP_116078.4	Q96SK3	ZN607_HUMAN	zinc finger protein 607	275					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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)			TCTCCAGTATGAATACTCTGA	0.423																																					p.H275N		Atlas-SNP	.											.	ZNF607	82	.	0			c.C823A						PASS	.						48	48	48					19																	38190209		2203	4300	6503	SO:0001583	missense	84775	exon5			CAGTATGAATACT	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.823C>A	chr19.hg19:g.38190209G>T	ENSP00000347338:p.His275Asn	103.0	0.0	.		119.0	49.0	.	NM_032689	F5H141|Q6ZMN2|Q6ZMN4|Q96C40	Missense_Mutation	SNP	ENST00000355202.4	hg19	CCDS33006.1	.	.	.	.	.	.	.	.	.	.	G	15.02	2.708084	0.48412	.	.	ENSG00000198182	ENST00000355202;ENST00000395835	T;T	0.67345	-0.26;-0.26	2.27	2.27	0.28462	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.84005	0.5377	M	0.92923	3.36	0.33659	D	0.609455	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.88981	0.3408	9	0.87932	D	0	.	11.6009	0.51001	0.0:0.0:1.0:0.0	.	275;274	Q96SK3;F5H141	ZN607_HUMAN;.	N	275;274	ENSP00000347338:H275N;ENSP00000438015:H274N	ENSP00000347338:H275N	H	-	1	0	ZNF607	42882049	1.000000	0.71417	0.991000	0.47740	0.731000	0.41821	7.908000	0.87438	1.255000	0.44051	0.561000	0.74099	CAT	.	.	.	none		0.423	ZNF607-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459502.2	NM_032689		T	38190209	G	T	38190209	3	4	117	1	0	0	0	0	1	0	0	0	18045	1290	45	4	1271	4	ZNF607	19	38190209	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	37375462	38190209	20938774	53	7510											
SIPA1L3	23094	hgsc.bcm.edu	37	chr19	38621370	38621370	+	Missense_Mutation	SNP	A	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	gcgcacctctgtcactgtgaAggtggtcatcatcccgcctt	6	11	10	14	2	4	1	3	1	1	0	5	1	5	1	3	2	0	1	3	2	1	1			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr19:38621370A>C	ENST00000222345.6	+	10	3610	c.3101A>C	c.(3100-3102)aAg>aCg	p.K1034T		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	1034	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)			GTCACTGTGAAGGTGGTCATC	0.627																																					p.K1034T		Atlas-SNP	.											.	SIPA1L3	150	.	0			c.A3101C						PASS	.						67	60	62					19																	38621370		2203	4300	6503	SO:0001583	missense	23094	exon10			CTGTGAAGGTGGT	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.3101A>C	chr19.hg19:g.38621370A>C	ENSP00000222345:p.Lys1034Thr	87.0	0.0	.		92.0	28.0	.	NM_015073	Q2TV87	Missense_Mutation	SNP	ENST00000222345.6	hg19	CCDS33007.1	.	.	.	.	.	.	.	.	.	.	A	17.63	3.437903	0.62955	.	.	ENSG00000105738	ENST00000222345	T	0.62788	0.0	5.33	5.33	0.75918	PDZ/DHR/GLGF (2);	0.108901	0.64402	D	0.000008	T	0.33673	0.0871	N	0.00972	-1.085	0.58432	D	0.999992	B	0.33212	0.402	B	0.33846	0.171	T	0.42999	-0.9418	10	0.28530	T	0.3	-40.8953	14.5799	0.68282	1.0:0.0:0.0:0.0	.	1034	O60292	SI1L3_HUMAN	T	1034	ENSP00000222345:K1034T	ENSP00000222345:K1034T	K	+	2	0	SIPA1L3	43313210	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.751000	0.55165	2.148000	0.66965	0.533000	0.62120	AAG	.	.	.	none		0.627	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278		C	38621370	A	C	38621370	3	2	117	1	0	0	0	0	1	0	0	0	14344	72	3	5	3131	5	SIPA1L3	19	38621370	Missense_Mutation	SNP	A	TCGA-BQ-5882-01A-11D-1589-08	431161	38621370	20507613	54	7511											
ZNF780B	163131	hgsc.bcm.edu	37	chr19	40540344	40540344	+	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	cacatttcttacattcaaagGgtttctcacctgtacaagtt	11	15	5	10	0	3	0	2	0	2	0	4	0	3	0	1	1	2	3	1	1	4	6			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr19:40540344G>A	ENST00000434248.1	-	5	2487	c.2422C>T	c.(2422-2424)Cct>Tct	p.P808S	ZNF780B_ENST00000221355.6_Missense_Mutation_p.P660S	NM_001005851.2	NP_001005851.1	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	808					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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)					ACATTCAAAGGGTTTCTCACC	0.393																																					p.P808S		Atlas-SNP	.											.	ZNF780B	143	.	0			c.C2422T						PASS	.						59	64	62					19																	40540344		2188	4297	6485	SO:0001583	missense	163131	exon5			TCAAAGGGTTTCT	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.2422C>T	chr19.hg19:g.40540344G>A	ENSP00000391641:p.Pro808Ser	63.0	0.0	.		100.0	38.0	.	NM_001005851	B9EH00	Missense_Mutation	SNP	ENST00000434248.1	hg19	CCDS46077.1	.	.	.	.	.	.	.	.	.	.	G	10.62	1.400412	0.25291	.	.	ENSG00000128000	ENST00000434248;ENST00000221355	T;T	0.06142	3.55;3.34	2.24	1.16	0.20824	Zinc finger, C2H2 (1);	.	.	.	.	T	0.06050	0.0157	L	0.41906	1.305	0.20926	N	0.999822	B	0.02656	0.0	B	0.04013	0.001	T	0.34153	-0.9840	9	0.59425	D	0.04	.	6.6373	0.22889	0.1624:0.0:0.8376:0.0	.	808	Q9Y6R6	Z780B_HUMAN	S	808;660	ENSP00000391641:P808S;ENSP00000221355:P660S	ENSP00000221355:P660S	P	-	1	0	ZNF780B	45232184	0.008000	0.16893	0.148000	0.22405	0.135000	0.20990	0.773000	0.26661	0.135000	0.18707	-0.448000	0.05591	CCT	.	.	.	none		0.393	ZNF780B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338466.1	NM_001005851		A	40540344	G	A	40540344	3	1	117	1	0	0	0	0	1	0	0	0	18165	1232	43	2	83	2	ZNF780B	19	40540344	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	1918974	40540344	18588639	55	7512											
CLPTM1	1209	hgsc.bcm.edu	37	chr19	45495628	45495628	+	Missense_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	cctttgtcatcaagatgcccGttatgtaccggatcggctgc	7	12	10	12	3	2	1	2	0	0	1	3	2	2	2	3	2	3	3	3	2	3	3	rs369873479		TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr19:45495628G>A	ENST00000337392.5	+	13	1843	c.1693G>A	c.(1693-1695)Gtt>Att	p.V565I	CLPTM1_ENST00000541297.2_Missense_Mutation_p.V551I|CLPTM1_ENST00000546079.1_Missense_Mutation_p.V463I	NM_001282175.1|NM_001282176.1|NM_001294.2	NP_001269104.1|NP_001269105.1|NP_001285.1	O96005	CLPT1_HUMAN	cleft lip and palate associated transmembrane protein 1	565					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of T cell differentiation in thymus (GO:0033081)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)		CAAGATGCCCGTTATGTACCG	0.627																																					p.V565I		Atlas-SNP	.											.	CLPTM1	109	.	0			c.G1693A						PASS	.	G	ILE/VAL	0,4406		0,0,2203	203	182	190		1693	4.2	0.4	19		190	1,8599	1.2+/-3.3	0,1,4299	no	missense	CLPTM1	NM_001294.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	565/670	45495628	1,13005	2203	4300	6503	SO:0001583	missense	1209	exon13			ATGCCCGTTATGT	AF037339	CCDS12651.1, CCDS74394.1, CCDS74395.1	19q13.3	2008-02-05				ENSG00000104853			2087	protein-coding gene	gene with protein product		604783				9828125	Standard	NM_001294		Approved		uc002pai.3	O96005		ENST00000337392.5:c.1693G>A	chr19.hg19:g.45495628G>A	ENSP00000336994:p.Val565Ile	282.0	0.0	.		261.0	100.0	.	NM_001294	B3KQH2|B4DDS3|B4E2X9|B7Z9X9|F5H8J3|Q53ET6|Q9BSS5	Missense_Mutation	SNP	ENST00000337392.5	hg19	CCDS12651.1	.	.	.	.	.	.	.	.	.	.	G	13.28	2.191286	0.38707	0.0	1.16E-4	ENSG00000104853	ENST00000546079;ENST00000541297;ENST00000337392;ENST00000347493	.	.	.	5.21	4.17	0.49024	.	0.186290	0.46758	D	0.000276	T	0.11836	0.0288	N	0.02916	-0.46	0.31931	N	0.612128	P;P	0.40602	0.723;0.602	B;B	0.30316	0.114;0.053	T	0.10636	-1.0621	9	0.17369	T	0.5	-31.7339	9.7828	0.40658	0.0929:0.0:0.9071:0.0	.	551;565	F5H8J3;O96005	.;CLPT1_HUMAN	I	463;551;565;565	.	ENSP00000336994:V565I	V	+	1	0	CLPTM1	50187468	1.000000	0.71417	0.352000	0.25734	0.978000	0.69477	6.750000	0.74888	1.443000	0.47586	0.650000	0.86243	GTT	.	.	.	weak		0.627	CLPTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453267.1	NM_001294		A	45495628	G	A	45495628	3	1	117	1	0	0	0	0	1	0	0	0	3556	1145	40	1	1743	1	CLPTM1	19	45495628	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08	4955284	45495628	13633355	56	7513											
NLRP2	55655	hgsc.bcm.edu	37	chr19	55493701	55493701	+	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	ctcatacacggtggtgctgtAtggtcctgcaggccttggga	6	11	14	10	1	1	0	1	0	0	0	2	1	2	1	2	5	3	3	2	5	2	3			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr19:55493701A>T	ENST00000543010.1	+	6	778	c.635A>T	c.(634-636)tAt>tTt	p.Y212F	NLRP2_ENST00000339757.7_Missense_Mutation_p.Y190F|NLRP2_ENST00000448584.2_Missense_Mutation_p.Y212F|NLRP2_ENST00000427260.2_Missense_Mutation_p.Y189F|NLRP2_ENST00000263437.6_Missense_Mutation_p.Y209F|NLRP2_ENST00000391721.4_Missense_Mutation_p.Y188F|NLRP2_ENST00000538819.1_Missense_Mutation_p.Y188F|NLRP2_ENST00000537859.1_Missense_Mutation_p.Y190F	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	212	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		GTGGTGCTGTATGGTCCTGCA	0.527																																					p.Y212F		Atlas-SNP	.											.	NLRP2	161	.	0			c.A635T						PASS	.						78	79	79					19																	55493701		2203	4300	6503	SO:0001583	missense	55655	exon6			TGCTGTATGGTCC	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"Nucleotide-binding domain and leucine rich repeat containing"	22948	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"	609364	"NACHT, leucine rich repeat and PYD containing 2"	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.635A>T	chr19.hg19:g.55493701A>T	ENSP00000445135:p.Tyr212Phe	113.0	0.0	.		135.0	53.0	.	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Missense_Mutation	SNP	ENST00000543010.1	hg19	CCDS12913.1	.	.	.	.	.	.	.	.	.	.	A	9.855	1.194818	0.22037	.	.	ENSG00000022556	ENST00000543010;ENST00000391721;ENST00000339757;ENST00000448584;ENST00000537859;ENST00000427260;ENST00000538819;ENST00000263437	D;D;D;D;D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66;-1.66;-1.66;-1.66;-1.66	1.62	0.524	0.17066	NACHT nucleoside triphosphatase (1);	1.825070	0.03631	N	0.237909	T	0.71913	0.3396	N	0.10972	0.075	0.09310	N	1	B;B;B;B;P	0.35433	0.213;0.284;0.332;0.284;0.501	B;B;B;B;B	0.41412	0.356;0.128;0.295;0.195;0.295	T	0.63193	-0.6692	10	0.48119	T	0.1	.	4.2437	0.10662	0.6116:0.0:0.3884:0.0	.	189;190;209;188;212	B4DZL7;Q9NX02-2;A8K9G6;Q9NX02-4;Q9NX02	.;.;.;.;NALP2_HUMAN	F	212;188;190;212;190;189;188;209	ENSP00000445135:Y212F;ENSP00000375601:Y188F;ENSP00000344074:Y190F;ENSP00000409370:Y212F;ENSP00000440601:Y190F;ENSP00000402474:Y189F;ENSP00000441133:Y188F;ENSP00000263437:Y209F	ENSP00000263437:Y209F	Y	+	2	0	NLRP2	60185513	0.000000	0.05858	0.009000	0.14445	0.001000	0.01503	0.117000	0.15583	0.085000	0.17107	0.402000	0.26972	TAT	.	.	.	none		0.527	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852		T	55493701	A	T	55493701	3	4	117	1	0	0	0	0	1	0	0	0	10484	449	16	5	653	5	NLRP2	19	55493701	Missense_Mutation	SNP	A	TCGA-BQ-5882-01A-11D-1589-08	9998073	55493701	3635282	57	7514											
RPL3	6122	hgsc.bcm.edu	37	chr22	39714484	39714484	+	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	aaggctgtgaggtggaccggCttggacgggtcatccttagg	7	9	17	8	2	1	1	1	1	0	0	2	3	2	3	2	7	0	2	2	7	2	2			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr22:39714484C>A	ENST00000216146.4	-	2	290	c.117G>T	c.(115-117)aaG>aaT	p.K39N	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	39					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)	GGTGGACCGGCTTGGACGGGT	0.592																																					p.K39N		Atlas-SNP	.											.	RPL3	29	.	0			c.G117T						PASS	.						58	54	55					22																	39714484		2203	4298	6501	SO:0001583	missense	6122	exon2			GACCGGCTTGGAC	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.117G>T	chr22.hg19:g.39714484C>A	ENSP00000346001:p.Lys39Asn	68.0	0.0	.		55.0	13.0	.	NM_001033853	B2RDV9|Q15548|Q5I0G0	Missense_Mutation	SNP	ENST00000216146.4	hg19	CCDS13988.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.63|16.63	3.175374|3.175374	0.57692|0.57692	.|.	.|.	ENSG00000100316|ENSG00000100316	ENST00000427905|ENST00000216146;ENST00000453303	.|T;T	.|0.49720	.|1.38;0.77	4.5|4.5	3.48|3.48	0.39840|0.39840	.|Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.61123|0.61123	0.2322|0.2322	M|M	0.88842|0.88842	2.985|2.985	0.80722|0.80722	D|D	1|1	.|D;P	.|0.57899	.|0.981;0.715	.|P;P	.|0.48982	.|0.597;0.477	T|T	0.69982|0.69982	-0.4997|-0.4997	5|10	.|0.72032	.|D	.|0.01	.|.	12.3136|12.3136	0.54942|0.54942	0.0:0.9173:0.0:0.0827|0.0:0.9173:0.0:0.0827	.|.	.|39;39	.|P39023;B3KS36	.|RL3_HUMAN;.	S|N	71|39;66	.|ENSP00000346001:K39N;ENSP00000415198:K66N	.|ENSP00000346001:K39N	A|K	-|-	1|3	0|2	RPL3|RPL3	38044430|38044430	1.000000|1.000000	0.71417|0.71417	0.787000|0.787000	0.31911|0.31911	0.431000|0.431000	0.31685|0.31685	2.393000|2.393000	0.44442|0.44442	0.884000|0.884000	0.36064|0.36064	0.455000|0.455000	0.32223|0.32223	GCC|AAG	.	.	.	none		0.592	RPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321196.1	NM_000967		A	39714484	C	A	39714484	3	1	117	1	0	0	0	0	1	0	0	0	13592	796	28	4	1130	4	RPL3	22	39714484	Missense_Mutation	SNP	C	TCGA-BQ-5882-01A-11D-1589-08		39714484	11590082	58	7515											
EFCAB6	64800	hgsc.bcm.edu	37	chr22	44107398	44107399	+	Frame_Shift_Ins	INS	-	-	A																															cttcttggtatttggtatacINSaaaagtgtcgaggacaatct																										TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr22:44107398_44107399insA	ENST00000262726.7	-	10	1240_1241	c.987_988insT	c.(985-990)tttgtafs	p.V330fs	EFCAB6_ENST00000358439.4_Frame_Shift_Ins_p.V224fs|EFCAB6_ENST00000396231.2_Frame_Shift_Ins_p.V178fs	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	330	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				ATTTGGTATACAAAAGTGTCGA	0.381																																					p.V330fs		Atlas-INDEL	.											.	EFCAB6	177	.	0			c.988_989insT						PASS	.																																			SO:0001589	frameshift_variant	64800	exon10			.	Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"EF-hand domain containing"	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.988dupT	chr22.hg19:g.44107402_44107402dupA	ENSP00000262726:p.Val330fs	74.0	0.0	0		88.0	25.0	0.284091	NM_022785	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Frame_Shift_Ins	INS	ENST00000262726.7	hg19	CCDS14049.1																																																																																			.	.	.	none		0.381	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785		A	44107399	-	A	44107398	7	5	117	1	0	1	1	0	0	0	0	0	4941	478	17	0	3609	0	EFCAB6	22	44107398	Frame_Shift_Ins	INS	-	TCGA-BQ-5882-01A-11D-1589-08	4392914	44107398	7197168	59	7516											
YY2	404281	hgsc.bcm.edu	37	chrX	21875588	21875588	+	Missense_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	ttcccttgatttcaatttgcGcacacacttgcgcatccaca	9	13	5	14	2	1	1	1	1	0	0	3	1	3	1	2	0	2	2	2	0	1	5			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chrX:21875588G>A	ENST00000429584.2	+	1	1484	c.986G>A	c.(985-987)cGc>cAc	p.R329H	MBTPS2_ENST00000365779.2_Intron|MBTPS2_ENST00000379484.5_Intron|MBTPS2_ENST00000465888.1_3'UTR	NM_206923.3	NP_996806.2	O15391	TYY2_HUMAN	YY2 transcription factor	329	Mediates transcriptional repression.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(2)	19						TTCAATTTGCGCACACACTTG	0.532																																					p.R329H		Atlas-SNP	.											.	YY2	43	.	0			c.G986A						PASS	.						182	181	181					X																	21875588		2203	4300	6503	SO:0001583	missense	404281	exon1			ATTTGCGCACACA	AK091850	CCDS14202.1	Xp22.2-p22.1	2011-02-11			ENSG00000230797	ENSG00000230797		"Zinc fingers, C2H2-type"	31684	protein-coding gene	gene with protein product	"transcription factor yin yang 2"	300570				14702039	Standard	NM_206923		Approved	ZNF631	uc011mjp.2	O15391	OTTHUMG00000021236	ENST00000429584.2:c.986G>A	chrX.hg19:g.21875588G>A	ENSP00000389381:p.Arg329His	253.0	0.0	.		289.0	203.0	.	NM_206923	B2RP10|Q6Q1S4	Missense_Mutation	SNP	ENST00000429584.2	hg19	CCDS14202.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.787837	0.90367	.	.	ENSG00000230797	ENST00000429584	T	0.41400	1.0	4.6	4.6	0.57074	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	U	0.000000	T	0.52273	0.1724	L	0.35288	1.05	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.53222	-0.8469	10	0.52906	T	0.07	.	14.034	0.64634	0.0:0.0:1.0:0.0	.	329	O15391	TYY2_HUMAN	H	329	ENSP00000389381:R329H	ENSP00000389381:R329H	R	+	2	0	YY2	21785509	1.000000	0.71417	0.992000	0.48379	0.757000	0.42996	7.776000	0.85560	2.276000	0.75962	0.544000	0.68410	CGC	.	.	.	none		0.532	YY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056025.1	NM_206923		A	21875588	G	A	21875588	3	1	117	1	0	0	0	0	1	0	0	0	17521	1087	38	1	988	1	YY2	23	21875588	Missense_Mutation	SNP	G	TCGA-BQ-5882-01A-11D-1589-08		21875588	133394972	60	7517											
KIAA0090	23065	hgsc.bcm.edu	37	chr1	19545821	19545821	+	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	cgccaggcccgattcaggagCttcacctgtgccagtctctt	6	10	10	15	2	3	0	2	0	1	0	4	2	3	1	4	2	2	1	4	2	0	3			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr1:19545821C>T	ENST00000477853.1	-	23	3000	c.2958G>A	c.(2956-2958)aaG>aaA	p.K986K	RP1-43E13.2_ENST00000437898.1_RNA|EMC1_ENST00000480380.1_5'UTR|EMC1_ENST00000375208.3_Silent_p.K964K|EMC1_ENST00000375199.3_Silent_p.K985K	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	986						ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)											GATTCAGGAGCTTCACCTGTG	0.502																																					p.K986K		Atlas-SNP	.											.	.	.	.	0			c.G2958A						PASS	.						76	71	72					1																	19545821		2203	4300	6503	SO:0001819	synonymous_variant	23065	exon23			CAGGAGCTTCACC		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.2958G>A	chr1.hg19:g.19545821C>T		75.0	0.0	.		75.0	4.0	.	NM_015047	A8K6F3|Q14700|Q5TG62|Q63HL0|Q63HL3|Q8NBH8	Silent	SNP	ENST00000477853.1	hg19	CCDS190.1	.	.	.	.	.	.	.	.	.	.	C	9.326	1.059255	0.19987	.	.	ENSG00000127463	ENST00000375197	.	.	.	6.06	-0.986	0.10252	.	.	.	.	.	T	0.58977	0.2160	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56153	-0.8026	4	.	.	.	.	12.1403	0.53994	0.0:0.5935:0.0:0.4065	.	.	.	.	T	611	.	.	A	-	1	0	KIAA0090	19418408	0.934000	0.31675	0.995000	0.50966	0.993000	0.82548	0.012000	0.13287	-0.119000	0.11830	-0.312000	0.09012	GCT	.	.	.	none		0.502	EMC1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007076.2	NM_015047		T	19545821	C	T	19545821	2	4	118	1	0	0	0	0	0	0	0	1	8160	796	28	2		2	KIAA0090	1	19545821	Silent	SNP	C	TCGA-BQ-5883-01A-11D-1589-08		19545821	229704800	1	7518											
KIF3C	3797	hgsc.bcm.edu	37	chr2	26203576	26203576	+	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	tgcggctgctcttcctccggGgccgcttccccagcatcccc	2	9	10	20	3	1	0	0	0	1	0	5	0	5	0	7	3	3	4	7	3	0	2			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr2:26203576G>A	ENST00000264712.3	-	1	1790	c.1211C>T	c.(1210-1212)cCc>cTc	p.P404L	KIF3C_ENST00000405914.1_Missense_Mutation_p.P404L	NM_002254.6	NP_002245	O14782	KIF3C_HUMAN	kinesin family member 3C	404					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)					CTTCCTCCGGGGCCGCTTCCC	0.652																																					p.P404L		Atlas-SNP	.											.	KIF3C	79	.	0			c.C1211T						PASS	.						46	48	47					2																	26203576		2203	4300	6503	SO:0001583	missense	3797	exon1			CTCCGGGGCCGCT		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.1211C>T	chr2.hg19:g.26203576G>A	ENSP00000264712:p.Pro404Leu	124.0	0.0	.		119.0	5.0	.	NM_002254	O43544|Q4ZG18|Q53SX5|Q562F7	Missense_Mutation	SNP	ENST00000264712.3	hg19	CCDS1719.1	.	.	.	.	.	.	.	.	.	.	G	8.691	0.907521	0.17833	.	.	ENSG00000084731	ENST00000264712;ENST00000542511;ENST00000405914	T;T	0.73258	-0.73;-0.73	5.0	4.04	0.47022	Kinesin, motor domain (1);	0.465840	0.23937	N	0.043100	T	0.46580	0.1400	N	0.12182	0.205	0.40162	D	0.977078	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34453	-0.9828	10	0.27082	T	0.32	.	4.7743	0.13171	0.2331:0.0:0.7669:0.0	.	404;404	B7ZM25;O14782	.;KIF3C_HUMAN	L	404;210;404	ENSP00000264712:P404L;ENSP00000385030:P404L	ENSP00000264712:P404L	P	-	2	0	KIF3C	26057080	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	2.612000	0.46343	1.249000	0.43950	0.655000	0.94253	CCC	.	.	.	none		0.652	KIF3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211611.1			A	26203576	G	A	26203576	3	1	118	1	0	0	0	0	1	0	0	0	8309	1232	43	2	1202	2	KIF3C	2	26203576	Missense_Mutation	SNP	G	TCGA-BQ-5883-01A-11D-1589-08		26203576	216995797	2	7519											
SMPD4	55627	hgsc.bcm.edu	37	chr2	130931124	130931124	+	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	catcacgatgctgtactccaCaggattcacgcgcccctgta	9	9	8	15	3	2	0	2	0	0	0	3	2	3	1	3	1	2	3	3	1	2	3			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr2:130931124C>T	ENST00000409031.1	-	4	1497	c.349G>A	c.(349-351)Gtg>Atg	p.V117M	SMPD4_ENST00000339679.7_Missense_Mutation_p.C29Y|SMPD4_ENST00000452225.2_Intron|SMPD4_ENST00000431183.2_Intron|SMPD4_ENST00000426662.2_Intron|SMPD4_ENST00000473720.1_Intron|SMPD4_ENST00000351288.6_Missense_Mutation_p.V117M|SMPD4_ENST00000453750.1_Intron|SMPD4_ENST00000443958.2_Intron	NM_017951.4	NP_060421.2	Q9NXE4	NSMA3_HUMAN	sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)	78					cellular response to tumor necrosis factor (GO:0071356)|ceramide biosynthetic process (GO:0046513)|glycerophospholipid catabolic process (GO:0046475)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)|sphingomyelin phosphodiesterase D activity (GO:0050290)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(17)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29	Colorectal(110;0.1)				Phosphatidylserine(DB00144)	CTGTACTCCACAGGATTCACG	0.542																																					p.V117M		Atlas-SNP	.											.	SMPD4	67	.	0			c.G349A						PASS	.						59	54	56					2																	130931124		2203	4300	6503	SO:0001583	missense	55627	exon4			ACTCCACAGGATT	AF052134	CCDS2156.2, CCDS42751.1, CCDS54398.1	2q21.1	2009-11-06			ENSG00000136699	ENSG00000136699			32949	protein-coding gene	gene with protein product		610457				16517606	Standard	NM_001171083		Approved	FLJ20297, FLJ20756, nSMase-3, KIAA1418, NSMASE3, NET13	uc002tqr.2	Q9NXE4	OTTHUMG00000131624	ENST00000409031.1:c.349G>A	chr2.hg19:g.130931124C>T	ENSP00000386531:p.Val117Met	39.0	0.0	.		50.0	7.0	.	NM_017751	B4DM23|B4DQ31|B4DRB8|B4DWK7|B4E0L6|E7ESA2|E9PCE6|Q6FI76|Q6P1P7|Q6ZT43|Q9H0M2|Q9NW20|Q9NWL2|Q9P2C9	Missense_Mutation	SNP	ENST00000409031.1	hg19	CCDS42751.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	0.864|0.864	-0.734336|-0.734336	0.03111|0.03111	.|.	.|.	ENSG00000136699|ENSG00000136699	ENST00000339679|ENST00000351288;ENST00000409031;ENST00000441135	.|.	.|.	.|.	3.74|3.74	0.579|0.579	0.17397|0.17397	.|.	.|0.842482	.|0.10004	.|N	.|0.728107	T|T	0.30230|0.30230	0.0758|0.0758	L|L	0.43152|0.43152	1.355|1.355	0.09310|0.09310	N|N	1|1	B|B;B	0.02656|0.15719	0.0|0.014;0.007	B|B;B	0.01281|0.17098	0.0|0.017;0.008	T|T	0.27640|0.27640	-1.0068|-1.0068	8|9	0.22109|0.36615	T|T	0.4|0.2	.|.	3.3119|3.3119	0.07020|0.07020	0.0:0.4028:0.2084:0.3888|0.0:0.4028:0.2084:0.3888	.|.	29|78;117	B4E0T5|Q9NXE4;B1PBA3	.|NSMA3_HUMAN;.	Y|M	29|117;117;78	.|.	ENSP00000339721:C29Y|ENSP00000259217:V117M	C|V	-|-	2|1	0|0	SMPD4|SMPD4	130647594|130647594	0.367000|0.367000	0.25023|0.25023	0.045000|0.045000	0.18777|0.18777	0.188000|0.188000	0.23474|0.23474	1.298000|1.298000	0.33412|0.33412	0.248000|0.248000	0.21435|0.21435	0.455000|0.455000	0.32223|0.32223	TGT|GTG	.	.	.	none		0.542	SMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254516.3	NM_017751		T	130931124	C	T	130931124	3	4	118	1	0	0	0	0	1	0	0	0	14820	478	17	2	2319	2	SMPD4	2	130931124	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08	104727548	130931124	112268249	3	7520											
TRIM71	131405	hgsc.bcm.edu	37	chr3	32927537	32927537	+	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	ataagaaagccctggaggaaCgcgagtgtgagctgctgtgg	11	7	16	7	2	0	2	0	1	0	1	0	5	0	4	1	3	4	2	1	3	3	1			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr3:32927537C>A	ENST00000383763.5	+	3	1195	c.1132C>A	c.(1132-1134)Cgc>Agc	p.R378S		NM_001039111.1	NP_001034200.1	Q2Q1W2	LIN41_HUMAN	tripartite motif containing 71, E3 ubiquitin protein ligase	378					fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|miRNA metabolic process (GO:0010586)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|positive regulation of gene silencing by miRNA (GO:2000637)|protein autoubiquitination (GO:0051865)|regulation of gene silencing by miRNA (GO:0060964)|regulation of neural precursor cell proliferation (GO:2000177)|stem cell proliferation (GO:0072089)	cytoplasmic mRNA processing body (GO:0000932)	ligase activity (GO:0016874)|miRNA binding (GO:0035198)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CCTGGAGGAACGCGAGTGTGA	0.612																																					p.R378S		Atlas-SNP	.											TRIM71,NS,carcinoma,0,1	TRIM71	73	.	0			c.C1132A						PASS	.						74	85	81					3																	32927537		2153	4244	6397	SO:0001583	missense	131405	exon3			GAGGAACGCGAGT		CCDS43060.1	3p22.3	2014-02-17	2012-02-29		ENSG00000206557	ENSG00000206557		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	32669	protein-coding gene	gene with protein product			"tripartite motif-containing 71", "tripartite motif containing 71"				Standard	NM_001039111		Approved	LIN41, LIN-41	uc003cff.3	Q2Q1W2	OTTHUMG00000155778	ENST00000383763.5:c.1132C>A	chr3.hg19:g.32927537C>A	ENSP00000373272:p.Arg378Ser	50.0	0.0	.		65.0	3.0	.	NM_001039111		Missense_Mutation	SNP	ENST00000383763.5	hg19	CCDS43060.1	.	.	.	.	.	.	.	.	.	.	C	18.39	3.613528	0.66672	.	.	ENSG00000206557	ENST00000383763	D	0.85171	-1.95	5.0	2.98	0.34508	.	0.000000	0.85682	D	0.000000	T	0.82162	0.4977	N	0.24115	0.695	0.80722	D	1	D	0.69078	0.997	P	0.54815	0.761	D	0.84124	0.0408	10	0.72032	D	0.01	-29.8714	12.0485	0.53493	0.3404:0.6596:0.0:0.0	.	378	Q2Q1W2	LIN41_HUMAN	S	378	ENSP00000373272:R378S	ENSP00000373272:R378S	R	+	1	0	TRIM71	32902541	0.999000	0.42202	0.998000	0.56505	0.688000	0.40055	0.771000	0.26633	2.318000	0.78349	0.462000	0.41574	CGC	.	.	.	none		0.612	TRIM71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341565.3	NM_001039111		A	32927537	C	A	32927537	3	1	118	1	0	0	0	0	1	0	0	0	16556	536	19	4	1142	4	TRIM71	3	32927537	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08		32927537	165094893	4	7521											
ENTPD3	956	hgsc.bcm.edu	37	chr3	40465427	40465427	+	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	tacaaattcacagaggagacTtggccccaaatacactttga	15	9	7	10	0	1	3	1	1	0	2	1	4	1	3	2	2	2	0	2	2	4	5			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr3:40465427T>A	ENST00000301825.3	+	10	1444	c.1326T>A	c.(1324-1326)acT>acA	p.T442T	ENTPD3-AS1_ENST00000452768.1_RNA|ENTPD3-AS1_ENST00000439293.1_RNA|ENTPD3-AS1_ENST00000425156.1_RNA|ENTPD3_ENST00000456402.1_Silent_p.T442T|ENTPD3_ENST00000445129.1_Silent_p.T442T	NM_001248.2	NP_001239.2	O75355	ENTP3_HUMAN	ectonucleoside triphosphate diphosphohydrolase 3	442					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)		CAGAGGAGACTTGGCCCCAAA	0.408																																					p.T442T		Atlas-SNP	.											.	ENTPD3	48	.	0			c.T1326A						PASS	.						118	109	112					3																	40465427		2203	4300	6503	SO:0001819	synonymous_variant	956	exon10			GGAGACTTGGCCC	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.1326T>A	chr3.hg19:g.40465427T>A		141.0	0.0	.		179.0	9.0	.	NM_001248	B2R8D0|G5E9N0|O60495|Q8N6K2	Silent	SNP	ENST00000301825.3	hg19	CCDS2691.1																																																																																			.	.	.	none		0.408	ENTPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254179.2	NM_001248		A	40465427	T	A	40465427	2	1	118	1	0	0	0	0	0	0	0	1	5142	1596	56	5		5	ENTPD3	3	40465427	Silent	SNP	T	TCGA-BQ-5883-01A-11D-1589-08	7537890	40465427	157557003	5	7522											
CENPC1	1060	hgsc.bcm.edu	37	chr4	68338326	68338326	+	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	taaggttggttgatctttcaTctttttatctgagtaaaaag	11	18	8	4	0	4	2	1	2	3	0	4	2	4	2	0	2	0	3	0	2	5	8			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr4:68338326T>A	ENST00000273853.6	-	19	3079	c.2829A>T	c.(2827-2829)agA>agT	p.R943S		NM_001812.2	NP_001803.2	Q03188	CENPC_HUMAN	centromere protein C	943	MIF2 homology domain III.				chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	centromeric DNA binding (GO:0019237)|DNA binding (GO:0003677)										TGATCTTTCATCTTTTTATCT	0.249																																					p.R943S		Atlas-SNP	.											.	CENPC1	66	.	0			c.A2829T						PASS	.						25	23	24					4																	68338326		1675	3879	5554	SO:0001583	missense	1060	exon19			CTTTCATCTTTTT	M95724	CCDS47063.1	4q13.2	2013-11-05	2013-07-03	2013-07-03	ENSG00000145241	ENSG00000145241			1854	protein-coding gene	gene with protein product		117141	"centromere protein C 1"	CENPC1		7959789	Standard	XR_245245		Approved	CENP-C, hcp-4, MIF2	uc003hdd.1	Q03188	OTTHUMG00000160735	ENST00000273853.6:c.2829A>T	chr4.hg19:g.68338326T>A	ENSP00000273853:p.Arg943Ser	2.0	0.0	.		9.0	8.0	.	NM_001812	Q8IW27|Q9P0M5	Missense_Mutation	SNP	ENST00000273853.6	hg19	CCDS47063.1	.	.	.	.	.	.	.	.	.	.	T	16.45	3.126153	0.56721	.	.	ENSG00000145241	ENST00000273853	.	.	.	3.59	-2.03	0.07365	.	0.474882	0.18938	N	0.127023	T	0.15478	0.0373	N	0.12182	0.205	0.27738	N	0.944564	B	0.19445	0.036	B	0.12837	0.008	T	0.07693	-1.0759	9	0.72032	D	0.01	.	3.7757	0.08659	0.5677:0.1197:0.0:0.3126	.	943	Q03188	CENPC_HUMAN	S	943	.	ENSP00000273853:R943S	R	-	3	2	CENPC1	68020921	0.998000	0.40836	0.995000	0.50966	0.790000	0.44656	0.133000	0.15912	-0.350000	0.08262	0.402000	0.26972	AGA	.	.	.	none		0.249	CENPC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362001.2			A	68338326	T	A	68338326	3	1	118	1	0	0	0	0	1	0	0	0	3231	1432	50	5	6	5	CENPC1	4	68338326	Missense_Mutation	SNP	T	TCGA-BQ-5883-01A-11D-1589-08		68338326	122815950	6	7523											
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123264653	123264653	+	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	tccagcagtagttcatctggCttgagcttcactgcatgcat	8	13	9	11	0	3	1	2	1	1	0	4	1	4	1	1	1	4	7	1	1	1	4			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr4:123264653C>G	ENST00000264501.4	+	73	12814	c.12441C>G	c.(12439-12441)ggC>ggG	p.G4147G	KIAA1109_ENST00000388738.3_Silent_p.G4147G			Q2LD37	K1109_HUMAN	KIAA1109	4147	Ser-rich.				regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						GTTCATCTGGCTTGAGCTTCA	0.478																																					p.G4147G		Atlas-SNP	.											.	KIAA1109	424	.	0			c.C12441G						PASS	.						121	111	114					4																	123264653		1972	4163	6135	SO:0001819	synonymous_variant	84162	exon71			ATCTGGCTTGAGC	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.12441C>G	chr4.hg19:g.123264653C>G		111.0	0.0	.		91.0	7.0	.	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Silent	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.957|8.957	0.969706|0.969706	0.18659|0.18659	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000306802|ENST00000442707	.|.	.|.	.|.	5.78|5.78	-3.62|-3.62	0.04543|0.04543	.|.	.|.	.|.	.|.	.|.	T|T	0.40767|0.40767	0.1130|0.1130	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.37337|0.37337	-0.9710|-0.9710	4|4	.|.	.|.	.|.	.|.	4.0748|4.0748	0.09899|0.09899	0.0995:0.2869:0.4148:0.1987|0.0995:0.2869:0.4148:0.1987	.|.	.|.	.|.	.|.	G|V	523|93	.|.	.|.	A|L	+|+	2|1	0|0	KIAA1109|KIAA1109	123484103|123484103	0.019000|0.019000	0.18553|0.18553	0.092000|0.092000	0.20876|0.20876	0.981000|0.981000	0.71138|0.71138	-0.715000|-0.715000	0.04997|0.04997	-0.295000|-0.295000	0.08960|0.08960	0.591000|0.591000	0.81541|0.81541	GCT|CTT	.	.	.	none		0.478	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		G	123264653	C	G	123264653	2	3	118	1	0	0	0	0	0	0	0	1	8215	784	28	4		4	KIAA1109	4	123264653	Silent	SNP	C	TCGA-BQ-5883-01A-11D-1589-08	54926327	123264653	67889623	7	7524											
PCDHA9	9752	hgsc.bcm.edu	37	chr5	140229899	140229899	+	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	actcgggctacaacgcgtggCtttcatacgagctgcagcca	9	8	11	13	4	1	0	1	0	0	0	2	1	1	0	1	2	6	4	1	2	3	3			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr5:140229899C>T	ENST00000532602.1	+	1	2852	c.1819C>T	c.(1819-1821)Ctt>Ttt	p.L607F	PCDHA9_ENST00000378122.3_Missense_Mutation_p.L607F|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	607	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)			CAACGCGTGGCTTTCATACGA	0.672																																					p.L607F	Melanoma(55;1800 1972 14909)	Atlas-SNP	.											.	PCDHA9	373	.	0			c.C1819T						PASS	.						64	70	68					5																	140229899		2196	4268	6464	SO:0001583	missense	9752	exon1			GCGTGGCTTTCAT	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.1819C>T	chr5.hg19:g.140229899C>T	ENSP00000436042:p.Leu607Phe	82.0	0.0	.		110.0	9.0	.	NM_031857	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	hg19	CCDS54920.1	.	.	.	.	.	.	.	.	.	.	C	14.38	2.518012	0.44763	.	.	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.53640	0.61;0.61	3.36	3.36	0.38483	Cadherin (4);Cadherin-like (1);	0.000000	0.26156	U	0.026019	T	0.70544	0.3236	M	0.89478	3.035	0.28601	N	0.909177	D;D	0.89917	1.0;1.0	D;D	0.91635	0.993;0.999	T	0.66756	-0.5843	10	0.87932	D	0	.	11.3375	0.49513	0.0:0.8154:0.1846:0.0	.	607;607	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	F	607	ENSP00000436042:L607F;ENSP00000367362:L607F	ENSP00000367362:L607F	L	+	1	0	PCDHA9	140210083	0.962000	0.33011	1.000000	0.80357	0.276000	0.26787	0.080000	0.14802	1.839000	0.53478	0.313000	0.20887	CTT	.	.	.	none		0.672	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		T	140229899	C	T	140229899	3	4	118	1	0	0	0	0	1	0	0	0	11538	797	28	2	1821	2	PCDHA9	5	140229899	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08		140229899	40685361	8	7525											
KCNB2	9312	hgsc.bcm.edu	37	chr8	73850210	73850210	+	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	tttaccatgctgtgagtgaaGtcaaaaaggacagtagtcaa	15	10	10	6	0	2	2	2	2	0	0	2	3	2	3	1	1	2	2	1	1	6	3			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr8:73850210G>T	ENST00000523207.1	+	3	3208	c.2620G>T	c.(2620-2622)Gtc>Ttc	p.V874F		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	874					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)	TGTGAGTGAAGTCAAAAAGGA	0.493																																					p.V874F		Atlas-SNP	.											.	KCNB2	228	.	0			c.G2620T						PASS	.						94	91	92					8																	73850210		2203	4300	6503	SO:0001583	missense	9312	exon3			AGTGAAGTCAAAA	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.2620G>T	chr8.hg19:g.73850210G>T	ENSP00000430846:p.Val874Phe	98.0	0.0	.		112.0	5.0	.	NM_004770	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	hg19	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	G	8.944	0.966598	0.18659	.	.	ENSG00000182674	ENST00000523207	D	0.97303	-4.33	5.46	3.64	0.41730	.	1.710450	0.04454	U	0.373160	D	0.93805	0.8019	L	0.29908	0.895	0.23994	N	0.996234	B	0.19445	0.036	B	0.15052	0.012	D	0.85473	0.1174	10	0.45353	T	0.12	.	6.0774	0.19923	0.0712:0.1353:0.6532:0.1403	.	874	Q92953	KCNB2_HUMAN	F	874	ENSP00000430846:V874F	ENSP00000430846:V874F	V	+	1	0	KCNB2	74012764	0.805000	0.28982	0.063000	0.19743	0.690000	0.40134	1.546000	0.36179	0.841000	0.35020	0.591000	0.81541	GTC	.	.	.	none		0.493	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		T	73850210	G	T	73850210	3	4	118	1	0	0	0	0	1	0	0	0	8020	1029	36	4	2626	4	KCNB2	8	73850210	Missense_Mutation	SNP	G	TCGA-BQ-5883-01A-11D-1589-08		73850210	72513812	9	7526											
ADCY8	114	hgsc.bcm.edu	37	chr8	131916171	131916174	+	Frame_Shift_Del	DEL	TAAG	TAAG	-																															ctgtcctcaggctgcttaatTaagtaagtttcgatattatg																										TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	TAAG	TAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr8:131916171_131916174delTAAG	ENST00000286355.5	-	7	3847_3850	c.1755_1758delCTTA	c.(1753-1758)tacttafs	p.YL585fs	ADCY8_ENST00000377928.3_Frame_Shift_Del_p.YL585fs	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	585					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			GCTGCTTAATTAAGTAAGTTTCGA	0.49										HNSCC(32;0.087)																											p.586_587del		Atlas-INDEL	.											ADCY8,NS,carcinoma,0,1	ADCY8	291	.	0			c.1756_1759del						PASS	.																																			SO:0001589	frameshift_variant	114	exon7			.	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.1755_1758delCTTA	chr8.hg19:g.131916175_131916178delTAAG	ENSP00000286355:p.Tyr585fs	216.0	0.0	0		214.0	22.0	0.102804	NM_001115		Frame_Shift_Del	DEL	ENST00000286355.5	hg19	CCDS6363.1																																																																																			.	.	.	none		0.49	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			-	131916174	TAAG	-	131916171	7	5	118	1	0	1	0	1	0	0	0	0	300	1751	61	0	2045	0	ADCY8	8	131916171	Frame_Shift_Del	DEL	TAAG	TCGA-BQ-5883-01A-11D-1589-08	58065961	131916171	14447851	10	7527											
TMEM2	23670	hgsc.bcm.edu	37	chr9	74300679	74300679	+	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	ctttgtcataaagatgagctGgtttggctaatcccagaggt	10	13	11	7	0	1	3	1	1	0	2	2	3	2	3	1	3	1	3	1	3	3	4			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr9:74300679G>C	ENST00000377044.4	-	23	4474	c.3935C>G	c.(3934-3936)cCa>cGa	p.P1312R	TMEM2_ENST00000377066.5_Missense_Mutation_p.P1249R|TMEM2_ENST00000396272.3_Missense_Mutation_p.P305R	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	1312					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)		AAGATGAGCTGGTTTGGCTAA	0.373																																					p.P1312R		Atlas-SNP	.											.	TMEM2	112	.	0			c.C3935G						PASS	.						115	107	110					9																	74300679		2203	4300	6503	SO:0001583	missense	23670	exon23			TGAGCTGGTTTGG		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.3935C>G	chr9.hg19:g.74300679G>C	ENSP00000366243:p.Pro1312Arg	107.0	0.0	.		106.0	8.0	.	NM_013390	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Missense_Mutation	SNP	ENST00000377044.4	hg19	CCDS6638.1	.	.	.	.	.	.	.	.	.	.	G	18.12	3.553987	0.65425	.	.	ENSG00000135048	ENST00000377044;ENST00000377066;ENST00000396272	T;T;T	0.73469	-0.75;-0.68;2.49	5.78	5.78	0.91487	.	0.109175	0.64402	D	0.000005	T	0.78842	0.4347	M	0.61703	1.905	0.48087	D	0.999587	P;P	0.47604	0.836;0.898	B;P	0.47299	0.342;0.543	T	0.79548	-0.1758	10	0.52906	T	0.07	.	19.6126	0.95616	0.0:0.0:1.0:0.0	.	1312;1249	Q9UHN6;Q9UHN6-2	TMEM2_HUMAN;.	R	1312;1249;305	ENSP00000366243:P1312R;ENSP00000366266:P1249R;ENSP00000379569:P305R	ENSP00000366243:P1312R	P	-	2	0	TMEM2	73490499	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.685000	0.74543	2.730000	0.93505	0.650000	0.86243	CCA	.	.	.	none		0.373	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390		C	74300679	G	C	74300679	3	2	118	1	0	0	0	0	1	0	0	0	16133	1348	47	4	224	4	TMEM2	9	74300679	Missense_Mutation	SNP	G	TCGA-BQ-5883-01A-11D-1589-08		74300679	66912752	11	7528											
TDRD1	56165	hgsc.bcm.edu	37	chr10	115978231	115978231	+	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	ttaccaaatggacatgttaaAgtacattttgtggattatgg	13	15	9	4	0	0	0	0	0	0	0	0	2	0	2	1	3	2	2	1	3	6	6			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr10:115978231A>T	ENST00000369280.1	+	18	2842	c.2382A>T	c.(2380-2382)aaA>aaT	p.K794N	TDRD1_ENST00000422662.1_Missense_Mutation_p.K398N|TDRD1_ENST00000369281.2_Intron|TDRD1_ENST00000369282.1_Missense_Mutation_p.K794N|TDRD1_ENST00000251864.2_Missense_Mutation_p.K794N			Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	794	Tudor 3. {ECO:0000255|PROSITE- ProRule:PRU00211}.				DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ cell development (GO:0007281)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)	metal ion binding (GO:0046872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(5)	48		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		GACATGTTAAAGTACATTTTG	0.373																																					p.K794N		Atlas-SNP	.											.	TDRD1	126	.	0			c.A2382T						PASS	.						202	183	190					10																	115978231		2203	4300	6503	SO:0001583	missense	56165	exon18			TGTTAAAGTACAT	AF285606	CCDS7588.1	10q26.11	2013-01-23			ENSG00000095627	ENSG00000095627		"Tudor domain containing"	11712	protein-coding gene	gene with protein product	"cancer/testis antigen 41.1"	605796				11279525	Standard	NM_198795		Approved	CT41.1	uc001lbg.1	Q9BXT4	OTTHUMG00000019083	ENST00000369280.1:c.2382A>T	chr10.hg19:g.115978231A>T	ENSP00000358286:p.Lys794Asn	196.0	0.0	.		195.0	13.0	.	NM_198795	A6NEN3|A6NMN2|B3KVI4|B4E2L5|D3DRC2|Q4G0Y8|Q6P518|Q9H7B3	Missense_Mutation	SNP	ENST00000369280.1	hg19		.	.	.	.	.	.	.	.	.	.	A	16.91	3.252942	0.59212	.	.	ENSG00000095627	ENST00000369282;ENST00000251864;ENST00000422662;ENST00000369280	T;T;T;T	0.10192	2.9;2.9;2.9;2.9	5.93	4.8	0.61643	Tudor subgroup (1);Maternal tudor protein (1);Tudor domain (1);	0.542996	0.21329	N	0.076323	T	0.28466	0.0704	M	0.63843	1.955	0.38193	D	0.939969	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.91635	0.95;0.998;0.999	T	0.03981	-1.0987	10	0.62326	D	0.03	-24.3657	10.4344	0.44426	0.9269:0.0:0.0731:0.0	.	398;794;794	Q9BXT4-4;Q9BXT4;Q9BXT4-3	.;TDRD1_HUMAN;.	N	794;794;398;794	ENSP00000358288:K794N;ENSP00000251864:K794N;ENSP00000402794:K398N;ENSP00000358286:K794N	ENSP00000251864:K794N	K	+	3	2	TDRD1	115968221	0.923000	0.31300	0.942000	0.38095	0.647000	0.38526	1.723000	0.38053	1.082000	0.41137	0.533000	0.62120	AAA	.	.	.	none		0.373	TDRD1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050457.2			T	115978231	A	T	115978231	3	4	118	1	0	0	0	0	1	0	0	0	15742	69	3	5	2448	5	TDRD1	10	115978231	Missense_Mutation	SNP	A	TCGA-BQ-5883-01A-11D-1589-08		115978231	19556516	12	7529											
MMP21	118856	hgsc.bcm.edu	37	chr10	127459092	127459092	+	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	tgtgctaaatctcaccatcaCctctccatattggtttctct	8	16	4	13	0	4	0	2	0	3	0	7	0	4	0	3	1	1	2	3	1	3	4			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr10:127459092C>T	ENST00000368808.3	-	5	1047	c.1048G>A	c.(1048-1050)Gtg>Atg	p.V350M		NM_147191.1	NP_671724.1	Q8N119	MMP21_HUMAN	matrix metallopeptidase 21	350					hematopoietic progenitor cell differentiation (GO:0002244)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	16		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)			Marimastat(DB00786)	CTCACCATCACCTCTCCATAT	0.413																																					p.V350M		Atlas-SNP	.											.	MMP21	46	.	0			c.G1048A						PASS	.						191	172	178					10																	127459092		2203	4300	6503	SO:0001583	missense	118856	exon5			CCATCACCTCTCC	AF331526	CCDS7647.1	10q26.3	2008-07-28	2005-08-08		ENSG00000154485	ENSG00000154485			14357	protein-coding gene	gene with protein product		608416	"matrix metalloproteinase 21"			11255011	Standard	NM_147191		Approved		uc001liu.3	Q8N119	OTTHUMG00000019235	ENST00000368808.3:c.1048G>A	chr10.hg19:g.127459092C>T	ENSP00000357798:p.Val350Met	108.0	0.0	.		148.0	8.0	.	NM_147191	Q5VZP9|Q8NG02	Missense_Mutation	SNP	ENST00000368808.3	hg19	CCDS7647.1	.	.	.	.	.	.	.	.	.	.	C	13.20	2.165493	0.38217	.	.	ENSG00000154485	ENST00000368808	T	0.20332	2.08	5.62	-0.228	0.13098	Hemopexin/matrixin (2);	0.651830	0.14795	N	0.297980	T	0.12987	0.0315	N	0.22421	0.69	0.09310	N	1	B	0.19935	0.04	B	0.15484	0.013	T	0.21793	-1.0235	10	0.59425	D	0.04	-28.7392	9.267	0.37647	0.0:0.2518:0.5805:0.1677	.	350	Q8N119	MMP21_HUMAN	M	350	ENSP00000357798:V350M	ENSP00000357798:V350M	V	-	1	0	MMP21	127449082	0.001000	0.12720	0.000000	0.03702	0.638000	0.38207	-0.056000	0.11787	-0.027000	0.13873	-0.150000	0.13652	GTG	.	.	.	none		0.413	MMP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050928.1			T	127459092	C	T	127459092	3	4	118	1	0	0	0	0	1	0	0	0	9667	507	18	2	673	2	MMP21	10	127459092	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08	11480861	127459092	8075655	13	7530											
DCPS	28960	hgsc.bcm.edu	37	chr11	126201299	126201299	+	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	ggctgtgctgtatcattgcaGatgtaaagacgaccgtggtt	9	12	13	7	2	1	2	1	0	0	2	1	3	1	2	1	2	2	6	1	2	3	4			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr11:126201299G>T	ENST00000263579.4	+	3	705		c.e3-1		DCPS_ENST00000530860.1_3'UTR	NM_014026.3	NP_054745.1	Q96C86	DCPS_HUMAN	decapping enzyme, scavenger						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)		TATCATTGCAGATGTAAAGAC	0.567																																					.		Atlas-SNP	.											.	DCPS	33	.	0			c.377-1G>T						PASS	.						137	131	133					11																	126201299		2201	4298	6499	SO:0001630	splice_region_variant	28960	exon3			ATTGCAGATGTAA	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.377-1G>T	chr11.hg19:g.126201299G>T		191.0	0.0	.		200.0	12.0	.	NM_014026	Q8NHL8|Q9Y2S5	Splice_Site	SNP	ENST00000263579.4	hg19	CCDS8473.1	.	.	.	.	.	.	.	.	.	.	G	14.60	2.584618	0.46110	.	.	ENSG00000110063	ENST00000263579	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.9226	0.92530	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DCPS	125706509	1.000000	0.71417	0.996000	0.52242	0.450000	0.32258	8.744000	0.91596	2.778000	0.95560	0.655000	0.94253	.	.	.	.	none		0.567	DCPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386455.1	NM_014026	Intron	T	126201299	G	T	126201299	5	4	118	1	0	0	0	0	0	0	1	0	4303	956	33	4	386	4	DCPS	11	126201299	Splice_Site	SNP	G	TCGA-BQ-5883-01A-11D-1589-08		126201299	8805217	14	7531											
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	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	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-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000556131.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.G12D	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	Atlas-SNP	.		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	KRAS_ENST00000256078,NS,adenocarcinoma,0,66	KRAS	30930	.	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	c.G35A						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>A	chr12.hg19:g.25398284C>T	ENSP00000256078:p.Gly12Asp	36.0	0.0	.		40.0	13.0	.	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT	.	.	.	weak		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398284	C	T	25398284	3	4	118	1	0	0	0	0	1	0	0	0	8445	507	18	2	671	2	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08		25398284	108453611	15	7532											
OR10AD1	121275	hgsc.bcm.edu	37	chr12	48596939	48596939	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtccaggaggtgataaagAtgatgaggccattcatggcc	11	9	13	8	0	1	4	1	3	0	1	2	5	2	5	3	4	0	0	3	4	2	2			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr12:48596939A>G	ENST00000310248.2	-	1	231	c.137T>C	c.(136-138)aTc>aCc	p.I46T		NM_001004134.1	NP_001004134.1	Q8NGE0	O10AD_HUMAN	olfactory receptor, family 10, subfamily AD, member 1	46						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(2)|lung(3)|ovary(1)|stomach(1)|urinary_tract(1)	9						GGTGATAAAGATGATGAGGCC	0.542																																					p.I46T		Atlas-SNP	.											.	OR10AD1	24	.	0			c.T137C						PASS	.						96	81	86					12																	48596939		2203	4300	6503	SO:0001583	missense	121275	exon1			ATAAAGATGATGA		CCDS31787.1	12q13.11	2013-09-24	2002-11-13	2002-11-15	ENSG00000172640	ENSG00000172640		"GPCR / Class A : Olfactory receptors"	14819	protein-coding gene	gene with protein product			"olfactory receptor, family 10, subfamily AD, member 1 pseudogene"	OR10AD1P			Standard	NM_001004134		Approved		uc001rrl.1	Q8NGE0	OTTHUMG00000168027	ENST00000310248.2:c.137T>C	chr12.hg19:g.48596939A>G	ENSP00000308689:p.Ile46Thr	45.0	0.0	.		53.0	5.0	.	NM_001004134	B9EGT9|Q6IFA8	Missense_Mutation	SNP	ENST00000310248.2	hg19	CCDS31787.1	.	.	.	.	.	.	.	.	.	.	A	15.20	2.762337	0.49468	.	.	ENSG00000172640	ENST00000310248	T	0.00531	6.76	4.97	4.97	0.65823	GPCR, rhodopsin-like superfamily (1);	0.189939	0.25929	N	0.027383	T	0.01061	0.0035	M	0.79475	2.455	0.33098	D	0.53878	D	0.59357	0.985	P	0.50537	0.643	T	0.47586	-0.9106	10	0.72032	D	0.01	-30.4283	12.9182	0.58216	1.0:0.0:0.0:0.0	.	46	Q8NGE0	O10AD_HUMAN	T	46	ENSP00000308689:I46T	ENSP00000308689:I46T	I	-	2	0	OR10AD1	46883206	0.910000	0.30920	1.000000	0.80357	0.519000	0.34347	6.493000	0.73658	2.213000	0.71641	0.533000	0.62120	ATC	.	.	.	none		0.542	OR10AD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397577.1			G	48596939	A	G	48596939	3	3	118	1	0	0	0	0	1	0	0	0	10903	333	12	3	820	3	OR10AD1	12	48596939	Missense_Mutation	SNP	A	TCGA-BQ-5883-01A-11D-1589-08	23198655	48596939	85254956	16	7533											
STON2	85439	hgsc.bcm.edu	37	chr14	81862455	81862455	+	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	cctccatccaccacatggttCtccccggaggagctctcgga	7	8	9	17	2	2	0	0	0	2	0	6	3	4	3	6	4	1	2	6	4	0	1			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr14:81862455C>G	ENST00000267540.2	-	2	356	c.156G>C	c.(154-156)gaG>gaC	p.E52D	STON2_ENST00000555447.1_Missense_Mutation_p.E52D	NM_033104.3	NP_149095.2	Q8WXE9	STON2_HUMAN	stonin 2	52					hematopoietic progenitor cell differentiation (GO:0002244)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleolus (GO:0005730)|synaptic vesicle (GO:0008021)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|pancreas(2)|prostate(1)|skin(5)	34				BRCA - Breast invasive adenocarcinoma(234;0.0348)		CCACATGGTTCTCCCCGGAGG	0.577																																					p.E52D		Atlas-SNP	.											.	STON2	94	.	0			c.G156C						PASS	.						71	64	66					14																	81862455		2203	4300	6503	SO:0001583	missense	85439	exon4			ATGGTTCTCCCCG	AB208948	CCDS9875.1, CCDS58332.1	14q31.1	2007-08-01				ENSG00000140022			30652	protein-coding gene	gene with protein product	"stoned B homolog 2 (Drosophila)"	608467				11381094, 11454741	Standard	NM_033104		Approved	STNB2, STN2	uc001xvk.2	Q8WXE9		ENST00000267540.2:c.156G>C	chr14.hg19:g.81862455C>G	ENSP00000267540:p.Glu52Asp	90.0	0.0	.		82.0	7.0	.	NM_001256430	G3V2T7|Q17R24|Q59H11|Q6NT47|Q96RI7|Q96RU6	Missense_Mutation	SNP	ENST00000267540.2	hg19	CCDS9875.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.938177	0.52972	.	.	ENSG00000140022	ENST00000555447;ENST00000546306;ENST00000267540	T;T	0.54866	0.55;0.55	5.8	1.95	0.26073	Stonin-2, N-terminal (1);	0.362161	0.29040	N	0.013335	T	0.44456	0.1294	L	0.59436	1.845	0.23309	N	0.997936	P;B;P	0.35714	0.517;0.334;0.461	B;B;B	0.36504	0.226;0.122;0.145	T	0.43702	-0.9375	10	0.87932	D	0	-12.0903	5.4312	0.16454	0.0:0.4999:0.2873:0.2127	.	52;52;52	Q8WXE9;Q17R23;G3V2T7	STON2_HUMAN;.;.	D	52;64;52	ENSP00000450857:E52D;ENSP00000267540:E52D	ENSP00000267540:E52D	E	-	3	2	STON2	80932208	0.910000	0.30920	0.991000	0.47740	0.836000	0.47400	-0.309000	0.08145	0.801000	0.34066	-0.179000	0.13096	GAG	.	.	.	none		0.577	STON2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413317.1	NM_033104		G	81862455	C	G	81862455	3	3	118	1	0	0	0	0	1	0	0	0	15330	912	32	4	2575	4	STON2	14	81862455	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08		81862455	25487085	17	7534											
MFAP1	4236	hgsc.bcm.edu	37	chr15	44109600	44109600	+	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	ggggcatagtctggccttttTccggacacataacgctttac	8	12	10	11	2	1	0	0	0	1	0	2	1	2	1	2	4	2	2	2	4	3	6			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr15:44109600T>G	ENST00000267812.3	-	2	358	c.126A>C	c.(124-126)ggA>ggC	p.G42G		NM_005926.2	NP_005917.2	P55081	MFAP1_HUMAN	microfibrillar-associated protein 1	42					extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|microfibril (GO:0001527)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|lung(6)|skin(2)|upper_aerodigestive_tract(3)	15		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.33e-07)		CTGGCCTTTTTCCGGACACAT	0.433																																					p.G42G		Atlas-SNP	.											.	MFAP1	36	.	0			c.A126C						PASS	.						128	118	121					15																	44109600		2198	4298	6496	SO:0001819	synonymous_variant	4236	exon2			CCTTTTTCCGGAC		CCDS10105.1	15q15-q21	2014-05-20			ENSG00000140259	ENSG00000140259			7032	protein-coding gene	gene with protein product		600215				7835894	Standard	NM_005926		Approved		uc001zth.1	P55081	OTTHUMG00000060145	ENST00000267812.3:c.126A>C	chr15.hg19:g.44109600T>G		184.0	0.0	.		214.0	12.0	.	NM_005926	Q86TG6	Silent	SNP	ENST00000267812.3	hg19	CCDS10105.1																																																																																			.	.	.	none		0.433	MFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133491.2	NM_005926		G	44109600	T	G	44109600	2	3	118	1	0	0	0	0	0	0	0	1	9520	1770	62	5		5	MFAP1	15	44109600	Silent	SNP	T	TCGA-BQ-5883-01A-11D-1589-08		44109600	58421792	18	7535											
LASS3	204219	hgsc.bcm.edu	37	chr15	101013174	101013174	+	Frame_Shift_Del	DEL	C	C	-																															tgtacaatcatcacgagggtCccactgcgaatataattagc																										TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr15:101013174delC	ENST00000394113.1	-	11	1383	c.693delG	c.(691-693)gggfs	p.G231fs	CERS3_ENST00000284382.4_Frame_Shift_Del_p.G231fs|CERS3_ENST00000538112.2_Frame_Shift_Del_p.G231fs|CERS3_ENST00000560944.1_Intron			Q8IU89	CERS3_HUMAN	ceramide synthase 3	231	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|keratinocyte differentiation (GO:0030216)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										TCACGAGGGTCCCACTGCGAA	0.433																																					p.T232fs		Atlas-INDEL	.											.	.	.	.	0			c.694delA						PASS	.						118	101	107					15																	101013174		2203	4300	6503	SO:0001589	frameshift_variant	204219	exon10			.		CCDS10384.1	15q26.3	2012-11-19	2011-07-08	2011-07-08	ENSG00000154227	ENSG00000154227		"Homeoboxes / CERS class"	23752	protein-coding gene	gene with protein product		615276	"LAG1 longevity assurance homolog 3 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 3"	LASS3			Standard	NM_178842		Approved	MGC27091	uc002bwb.3	Q8IU89	OTTHUMG00000172568	ENST00000394113.1:c.693delG	chr15.hg19:g.101013174delC	ENSP00000377672:p.Gly231fs	147.0	0.0	0		140.0	17.0	0.121429	NM_178842	Q8NE64|Q8NEN6	Frame_Shift_Del	DEL	ENST00000394113.1	hg19	CCDS10384.1																																																																																			.	.	.	none		0.433	CERS3-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313594.4	NM_178842		-	101013174	C	-	101013174	7	5	118	1	0	1	0	1	0	0	0	0	8647	842	30	0	474	0	LASS3	15	101013174	Frame_Shift_Del	DEL	C	TCGA-BQ-5883-01A-11D-1589-08	56903574	101013174	1518218	19	7536											
RBBP8	5932	hgsc.bcm.edu	37	chr18	20573491	20573491	+	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	cttcagcccttgaataaatgCtctccagacaataaaccatc	14	10	4	13	0	2	2	1	1	1	1	4	2	2	2	3	0	3	1	3	0	6	4			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr18:20573491C>G	ENST00000399722.2	+	11	2052	c.1701C>G	c.(1699-1701)tgC>tgG	p.C567W	RBBP8_ENST00000327155.5_Missense_Mutation_p.C567W|RBBP8_ENST00000399725.2_Missense_Mutation_p.C567W|RBBP8_ENST00000360790.5_Missense_Mutation_p.C567W	NM_203291.1	NP_976036.1	Q99708	COM1_HUMAN	retinoblastoma binding protein 8	567					blastocyst hatching (GO:0001835)|cell cycle checkpoint (GO:0000075)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|G2 DNA damage checkpoint (GO:0031572)|meiotic nuclear division (GO:0007126)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	damaged DNA binding (GO:0003684)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			central_nervous_system(1)|cervix(2)|endometrium(5)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	24	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)		OV - Ovarian serous cystadenocarcinoma(1;0.00196)			TGAATAAATGCTCTCCAGACA	0.438								Homologous recombination																													p.C567W		Atlas-SNP	.											.	RBBP8	138	.	0			c.C1701G						PASS	.						42	43	43					18																	20573491		2203	4300	6503	SO:0001583	missense	5932	exon11			TAAATGCTCTCCA	AF043431	CCDS11874.1, CCDS11875.1	18q11.2	2012-11-05	2001-11-28		ENSG00000101773	ENSG00000101773			9891	protein-coding gene	gene with protein product	"CTBP-interacting protein"	604124	"retinoblastoma-binding protein 8", "Seckel syndrome 2"	SCKL2		9721205, 17965729, 21998596	Standard	NM_002894		Approved	CtIP, RIM, COM1	uc002ktw.3	Q99708	OTTHUMG00000131769	ENST00000399722.2:c.1701C>G	chr18.hg19:g.20573491C>G	ENSP00000382628:p.Cys567Trp	105.0	0.0	.		87.0	5.0	.	NM_203292	A6NKN2|A8K8W6|E7ETY1|O75371|Q8NHQ3	Missense_Mutation	SNP	ENST00000399722.2	hg19	CCDS11875.1	.	.	.	.	.	.	.	.	.	.	C	8.135	0.783853	0.16189	.	.	ENSG00000101773	ENST00000327155;ENST00000399725;ENST00000399722;ENST00000399721;ENST00000360790	T;T;T;T;T	0.30182	1.56;1.54;1.56;1.56;1.56	5.47	-1.84	0.07809	.	0.955160	0.08781	N	0.894641	T	0.13713	0.0332	N	0.08118	0	0.80722	D	1	B;B;B	0.26845	0.161;0.161;0.05	B;B;B	0.27262	0.078;0.078;0.078	T	0.11348	-1.0591	10	0.42905	T	0.14	2.5577	4.5073	0.11894	0.398:0.2625:0.0:0.3395	.	567;567;567	E7ETY1;A6NKN2;Q99708	.;.;COM1_HUMAN	W	567	ENSP00000323050:C567W;ENSP00000382630:C567W;ENSP00000382628:C567W;ENSP00000382627:C567W;ENSP00000354024:C567W	ENSP00000323050:C567W	C	+	3	2	RBBP8	18827489	0.237000	0.23815	0.580000	0.28601	0.726000	0.41606	-0.151000	0.10175	-0.215000	0.10063	-0.150000	0.13652	TGC	.	.	.	none		0.438	RBBP8-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446387.1	NM_203291		G	20573491	C	G	20573491	3	3	118	1	0	0	0	0	1	0	0	0	13118	805	28	4	1739	4	RBBP8	18	20573491	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08		20573491	57503757	20	7537											
ZFP30	22835	hgsc.bcm.edu	37	chr19	38126264	38126264	+	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	gtgaaataagttctgagtaaCgacgaaagaacttctgacat	16	10	9	6	2	2	4	0	3	2	1	2	6	2	4	0	0	2	2	0	0	5	4			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr19:38126264C>T	ENST00000351218.2	-	6	1735	c.1178G>A	c.(1177-1179)cGt>cAt	p.R393H	ZFP30_ENST00000514101.2_Missense_Mutation_p.R393H|ZFP30_ENST00000392144.1_Missense_Mutation_p.R393H|ZFP30_ENST00000589018.1_Intron	NM_014898.2	NP_055713.1	Q9Y2G7	ZFP30_HUMAN	ZFP30 zinc finger protein	393					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	21			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TTCTGAGTAACGACGAAAGAA	0.408																																					p.R393H		Atlas-SNP	.											.	ZFP30	68	.	0			c.G1178A						PASS	.						69	72	71					19																	38126264		2203	4300	6503	SO:0001583	missense	22835	exon6			GAGTAACGACGAA	AB023178	CCDS33005.1	19q13.13	2013-01-08	2012-11-27		ENSG00000120784	ENSG00000120784		"Zinc fingers, C2H2-type", "-"	29555	protein-coding gene	gene with protein product			"zinc finger protein 30 homolog (mouse)"			10231032	Standard	NM_014898		Approved	ZNF745, KIAA0961	uc002ogx.1	Q9Y2G7	OTTHUMG00000048177	ENST00000351218.2:c.1178G>A	chr19.hg19:g.38126264C>T	ENSP00000343581:p.Arg393His	97.0	0.0	.		114.0	5.0	.	NM_014898	Q58EY8	Missense_Mutation	SNP	ENST00000351218.2	hg19	CCDS33005.1	.	.	.	.	.	.	.	.	.	.	C	8.628	0.893085	0.17613	.	.	ENSG00000120784	ENST00000351218;ENST00000514101;ENST00000392144;ENST00000440715	T;T;T	0.36340	1.26;1.26;1.26	3.9	2.86	0.33363	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35262	N	0.003340	T	0.34716	0.0907	L	0.27975	0.815	0.23851	N	0.996661	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.33059	-0.9883	10	0.11485	T	0.65	.	3.6934	0.08354	0.0:0.5686:0.2232:0.2082	.	393;393	D3Y2A0;Q9Y2G7	.;ZFP30_HUMAN	H	393;393;393;308	ENSP00000343581:R393H;ENSP00000422930:R393H;ENSP00000375988:R393H	ENSP00000343581:R393H	R	-	2	0	ZFP30	42818104	0.000000	0.05858	1.000000	0.80357	0.996000	0.88848	-0.122000	0.10627	2.175000	0.68902	0.591000	0.81541	CGT	.	.	.	none		0.408	ZFP30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109601.2	NM_014898		T	38126264	C	T	38126264	3	4	118	1	0	0	0	0	1	0	0	0	17656	536	19	1	385	1	ZFP30	19	38126264	Missense_Mutation	SNP	C	TCGA-BQ-5883-01A-11D-1589-08		38126264	21002719	21	7538											
ARFGEF2	10564	hgsc.bcm.edu	37	chr20	47632919	47632919	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgaagttcttctttctgatGtatttgcacaattgcagtgg	9	17	9	6	0	3	2	0	2	3	0	3	2	3	2	0	1	2	4	0	1	3	6			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr20:47632919G>A	ENST00000371917.4	+	31	4282	c.4282G>A	c.(4282-4284)Gta>Ata	p.V1428I		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	1428					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)			TCTTTCTGATGTATTTGCACA	0.353																																					p.V1428I	Esophageal Squamous(176;1738 1974 26285 33069 35354)	Atlas-SNP	.											.	ARFGEF2	160	.	0			c.G4282A						PASS	.						208	185	193					20																	47632919		2203	4300	6503	SO:0001583	missense	10564	exon31			TCTGATGTATTTG	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.4282G>A	chr20.hg19:g.47632919G>A	ENSP00000360985:p.Val1428Ile	132.0	0.0	.		147.0	43.0	.	NM_006420	Q5TFT9|Q9NTS1	Missense_Mutation	SNP	ENST00000371917.4	hg19	CCDS13411.1	.	.	.	.	.	.	.	.	.	.	G	7.760	0.705132	0.15172	.	.	ENSG00000124198	ENST00000371917	T	0.38722	1.12	5.52	5.52	0.82312	Armadillo-like helical (1);Armadillo-type fold (1);	0.054023	0.64402	D	0.000002	T	0.11580	0.0282	N	0.00841	-1.15	0.43069	D	0.994705	B	0.02656	0.0	B	0.01281	0.0	T	0.33189	-0.9878	10	0.02654	T	1	.	7.2277	0.26024	0.206:0.0:0.794:0.0	.	1428	Q9Y6D5	BIG2_HUMAN	I	1428	ENSP00000360985:V1428I	ENSP00000360985:V1428I	V	+	1	0	ARFGEF2	47066326	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	5.353000	0.66034	2.587000	0.87381	0.591000	0.81541	GTA	.	.	.	none		0.353	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420		A	47632919	G	A	47632919	3	1	118	1	0	0	0	0	1	0	0	0	853	1377	48	2	4404	2	ARFGEF2	20	47632919	Missense_Mutation	SNP	G	TCGA-BQ-5883-01A-11D-1589-08		47632919	15392601	22	7539											
MMP11	4320	hgsc.bcm.edu	37	chr22	24123480	24123480	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggctttgtgtggcgcctccGtgggggccagctgcagcccg	2	8	18	13	3	0	0	0	0	0	0	1	0	1	0	4	4	3	3	4	4	0	1			TCGA-BQ-5883-01A-11D-1589-08	TCGA-BQ-5883-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6c69acfc-a1cb-443f-b402-13ee50da93b7	517cb40d-9cef-49ff-a7ce-5b9c539c2b09	g.chr22:24123480G>A	ENST00000215743.3	+	6	1011	c.959G>A	c.(958-960)cGt>cAt	p.R320H		NM_005940.3	NP_005931.2	P24347	MMP11_HUMAN	matrix metallopeptidase 11 (stromelysin 3)	320					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)	TGGCGCCTCCGTGGGGGCCAG	0.672																																					p.R320H		Atlas-SNP	.											.	MMP11	53	.	0			c.G959A						PASS	.						41	43	43					22																	24123480		2203	4300	6503	SO:0001583	missense	4320	exon6			GCCTCCGTGGGGG		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.959G>A	chr22.hg19:g.24123480G>A	ENSP00000215743:p.Arg320His	75.0	0.0	.		77.0	21.0	.	NM_005940	Q5FX24|Q6PEZ6|Q9UC26	Missense_Mutation	SNP	ENST00000215743.3	hg19	CCDS13816.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.546617	0.86022	.	.	ENSG00000099953	ENST00000215743	T	0.02421	4.3	4.73	4.73	0.59995	Hemopexin/matrixin (2);	0.000000	0.85682	D	0.000000	T	0.08891	0.0220	L	0.41124	1.26	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.18840	-1.0324	10	0.38643	T	0.18	.	12.7499	0.57302	0.0822:0.0:0.9178:0.0	.	320	P24347	MMP11_HUMAN	H	320	ENSP00000215743:R320H	ENSP00000215743:R320H	R	+	2	0	MMP11	22453480	0.998000	0.40836	0.968000	0.41197	0.986000	0.74619	8.987000	0.93497	2.649000	0.89929	0.650000	0.86243	CGT	.	.	.	none		0.672	MMP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319891.2	NM_005940		A	24123480	G	A	24123480	3	1	118	1	0	0	0	0	1	0	0	0	9657	1145	40	1	981	1	MMP11	22	24123480	Missense_Mutation	SNP	G	TCGA-BQ-5883-01A-11D-1589-08		24123480	27181086	23	7540											
SRRM1	10250	hgsc.bcm.edu	37	chr1	24979017	24979017	+	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	aaaagaaaaggagaaggagaAgacccgaccacgatctcggt	18	3	12	8	3	1	4	0	0	1	4	2	8	1	4	2	3	0	0	2	3	6	0			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr1:24979017A>T	ENST00000323848.9	+	7	1133	c.818A>T	c.(817-819)aAg>aTg	p.K273M	SRRM1_ENST00000374389.4_Missense_Mutation_p.K273M|SRRM1_ENST00000447431.2_Missense_Mutation_p.K273M|SRRM1_ENST00000479034.1_3'UTR|SRRM1_ENST00000537199.1_Missense_Mutation_p.K142M	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	273	Arg-rich.|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)		GAGAAGGAGAAGACCCGACCA	0.502																																					p.K273M	Ovarian(68;897 1494 3282 17478)	Atlas-SNP	.											.	SRRM1	81	.	0			c.A818T						PASS	.						34	36	36					1																	24979017		2203	4300	6503	SO:0001583	missense	10250	exon7			AGGAGAAGACCCG	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.818A>T	chr1.hg19:g.24979017A>T	ENSP00000326261:p.Lys273Met	44.0	0.0	.		25.0	7.0	.	NM_005839	O60585|Q5VVN4	Missense_Mutation	SNP	ENST00000323848.9	hg19	CCDS255.1	.	.	.	.	.	.	.	.	.	.	A	16.33	3.093181	0.56075	.	.	ENSG00000133226	ENST00000323848;ENST00000447431;ENST00000374389;ENST00000537199	T;T;T;T	0.52754	0.76;0.76;0.76;0.65	6.05	6.05	0.98169	.	0.000000	0.64402	D	0.000003	T	0.46347	0.1388	N	0.19112	0.55	0.45791	D	0.998673	D;D	0.58620	0.983;0.971	P;P	0.55824	0.785;0.615	T	0.50233	-0.8852	10	0.66056	D	0.02	-2.6317	10.596	0.45338	0.9281:0.0:0.0719:0.0	.	273;273	E9PCT1;Q8IYB3	.;SRRM1_HUMAN	M	273;273;273;142	ENSP00000326261:K273M;ENSP00000391430:K273M;ENSP00000363510:K273M;ENSP00000441776:K142M	ENSP00000326261:K273M	K	+	2	0	SRRM1	24851604	1.000000	0.71417	1.000000	0.80357	0.736000	0.42039	3.872000	0.56085	2.320000	0.78422	0.528000	0.53228	AAG	.	.	.	none		0.502	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839		T	24979017	A	T	24979017	3	4	119	1	0	0	0	0	1	0	0	0	15180	72	3	5	844	5	SRRM1	1	24979017	Missense_Mutation	SNP	A	TCGA-BQ-5884-01A-11D-1589-08		24979017	224271604	1	7541											
PEF1	553115	hgsc.bcm.edu	37	chr1	32100869	32100869	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaccgtaggaacttggaggTggctgaccataggggccccc	8	6	15	12	1	0	1	0	1	0	0	0	3	0	3	4	6	1	3	4	6	3	3			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr1:32100869T>C	ENST00000373703.4	-	2	301	c.279A>G	c.(277-279)ccA>ccG	p.P93P	PEF1_ENST00000440872.2_Silent_p.P93P|PEF1_ENST00000492061.1_5'UTR	NM_012392.3	NP_036524.1	Q9UBV8	PEF1_HUMAN	penta-EF-hand domain containing 1	93	9 X 9 AA approximate tandem repeat of [AP]-P-G-G-P-Y-G-G-P-P.				proteolysis (GO:0006508)|response to calcium ion (GO:0051592)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|poly(A) RNA binding (GO:0044822)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(2)|upper_aerodigestive_tract(1)	7		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)|all_neural(195;0.186)		STAD - Stomach adenocarcinoma(196;0.0546)		AACTTGGAGGTGGCTGACCAT	0.587																																					p.P93P		Atlas-SNP	.											.	PEF1	20	.	0			c.A279G						PASS	.						49	51	50					1																	32100869		2203	4300	6503	SO:0001819	synonymous_variant	553115	exon2			TGGAGGTGGCTGA		CCDS345.1	1p34	2013-01-10			ENSG00000162517	ENSG00000162517		"EF-hand domain containing"	30009	protein-coding gene	gene with protein product	"peflin"	610033				10486255, 11883899	Standard	NM_012392		Approved	PEF1A	uc001bth.2	Q9UBV8	OTTHUMG00000003877	ENST00000373703.4:c.279A>G	chr1.hg19:g.32100869T>C		126.0	0.0	.		93.0	21.0	.	NM_012392		Silent	SNP	ENST00000373703.4	hg19	CCDS345.1																																																																																			.	.	.	none		0.587	PEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011046.1	NM_012392		C	32100869	T	C	32100869	2	2	119	1	0	0	0	0	0	0	0	1	11725	1683	59	3		3	PEF1	1	32100869	Silent	SNP	T	TCGA-BQ-5884-01A-11D-1589-08	7121852	32100869	217149752	2	7542											
SIPA1L2	57568	hgsc.bcm.edu	37	chr1	232650793	232650793	+	Missense_Mutation	SNP	A	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	tctgagaccggctttcccacAgtgccttgcatgttagctcc	6	12	9	14	1	1	1	0	1	1	1	3	2	3	1	4	1	3	4	4	1	1	3			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr1:232650793A>C	ENST00000366630.1	-	2	651	c.293T>G	c.(292-294)cTg>cGg	p.L98R	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.L98R			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	98					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)				GCTTTCCCACAGTGCCTTGCA	0.517																																					p.L98R		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.T293G						PASS	.						156	154	155					1																	232650793		2020	4187	6207	SO:0001583	missense	57568	exon1			TCCCACAGTGCCT	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.293T>G	chr1.hg19:g.232650793A>C	ENSP00000355589:p.Leu98Arg	224.0	0.0	.		177.0	39.0	.	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	hg19	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	A	0.689	-0.795281	0.02862	.	.	ENSG00000116991	ENST00000366630;ENST00000262861	T;T	0.78816	-1.21;-1.21	5.19	4.02	0.46733	.	0.630597	0.14001	N	0.348152	T	0.50171	0.1600	N	0.08118	0	0.09310	N	1	P	0.39216	0.664	B	0.32289	0.143	T	0.35325	-0.9793	10	0.14252	T	0.57	-9.9849	5.5611	0.17144	0.6384:0.0:0.3616:0.0	.	98	Q9P2F8	SI1L2_HUMAN	R	98	ENSP00000355589:L98R;ENSP00000262861:L98R	ENSP00000262861:L98R	L	-	2	0	SIPA1L2	230717416	0.005000	0.15991	0.062000	0.19696	0.262000	0.26303	1.251000	0.32862	0.942000	0.37525	0.528000	0.53228	CTG	.	.	.	none		0.517	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		C	232650793	A	C	232650793	3	2	119	1	0	0	0	0	1	0	0	0	14343	188	7	5	4959	5	SIPA1L2	1	232650793	Missense_Mutation	SNP	A	TCGA-BQ-5884-01A-11D-1589-08	200549924	232650793	16599828	3	7543											
SOS1	6654	hgsc.bcm.edu	37	chr2	39285904	39285904	+	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	gattgggcatcagctattgcCcatttatcaattggatgagg	10	13	11	7	0	2	1	2	1	0	0	2	3	2	2	1	3	2	2	1	3	3	6			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr2:39285904C>T	ENST00000426016.1	-	4	341	c.255G>A	c.(253-255)tgG>tgA	p.W85*	SOS1_ENST00000395038.2_Nonsense_Mutation_p.W85*|SOS1_ENST00000428721.2_Nonsense_Mutation_p.W28*|SOS1_ENST00000402219.2_Nonsense_Mutation_p.W85*			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	85					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				CAGCTATTGCCCATTTATCAA	0.338									Noonan syndrome																												p.W85X		Atlas-SNP	.											.	SOS1	134	.	0			c.G255A						PASS	.						75	76	76					2																	39285904		2202	4300	6502	SO:0001587	stop_gained	6654	exon3	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	TATTGCCCATTTA	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11187	protein-coding gene	gene with protein product		182530	"gingival fibromatosis, hereditary, 1"	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.255G>A	chr2.hg19:g.39285904C>T	ENSP00000387784:p.Trp85*	156.0	0.0	.		109.0	33.0	.	NM_005633	A8K2G3|B4DXG2	Nonsense_Mutation	SNP	ENST00000426016.1	hg19	CCDS1802.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.005675	0.93287	.	.	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000395038;ENST00000263879;ENST00000428721;ENST00000451331	.	.	.	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.9598	0.97242	0.0:1.0:0.0:0.0	.	.	.	.	X	85;85;85;85;28;28	.	ENSP00000263879:W85X	W	-	3	0	SOS1	39139408	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.711000	0.84669	2.716000	0.92895	0.655000	0.94253	TGG	.	.	.	none		0.338	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633		T	39285904	C	T	39285904	4	4	119	1	0	0	0	0	0	1	0	0	14949	624	22	2	3830	2	SOS1	2	39285904	Nonsense_Mutation	SNP	C	TCGA-BQ-5884-01A-11D-1589-08		39285904	203913469	4	7544											
TANC1	85461	hgsc.bcm.edu	37	chr2	160086335	160086335	+	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	gaagaggaagaaacttctccCcaggaagaatctgtttcccc	13	8	9	11	0	2	3	0	0	2	3	4	6	3	5	4	2	1	1	4	2	5	2			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr2:160086335C>A	ENST00000263635.6	+	27	4635	c.4398C>A	c.(4396-4398)ccC>ccA	p.P1466P	TANC1_ENST00000454300.1_Silent_p.P1360P	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	1466					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						AAACTTCTCCCCAGGAAGAAT	0.517																																					p.P1466P		Atlas-SNP	.											TANC1,NS,neuroblastoma,0,1	TANC1	157	.	0			c.C4398A						PASS	.						94	104	101					2																	160086335		1964	4133	6097	SO:0001819	synonymous_variant	85461	exon27			TTCTCCCCAGGAA	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.4398C>A	chr2.hg19:g.160086335C>A		146.0	1.0	.		144.0	36.0	.	NM_033394	C9JD88|Q49AI8	Silent	SNP	ENST00000263635.6	hg19	CCDS42766.1																																																																																			.	.	.	none		0.517	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1			A	160086335	C	A	160086335	2	1	119	1	0	0	0	0	0	0	0	1	15556	610	22	4		4	TANC1	2	160086335	Silent	SNP	C	TCGA-BQ-5884-01A-11D-1589-08	120800431	160086335	83113038	5	7545											
IRS1	3667	hgsc.bcm.edu	37	chr2	227662872	227662872	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcctccgagttcagcttcaCgaagctgatggtcttgctgg	6	12	12	11	2	3	1	2	1	1	0	4	3	4	1	2	2	4	4	2	2	1	3			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr2:227662872C>T	ENST00000305123.5	-	1	1603	c.583G>A	c.(583-585)Gtg>Atg	p.V195M	IRS1_ENST00000498335.1_5'Flank|RP11-395N3.2_ENST00000607970.1_lincRNA	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN	insulin receptor substrate 1	195	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.				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)		TTCAGCTTCACGAAGCTGATG	0.567											OREG0015248	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V195M		Atlas-SNP	.											.	IRS1	141	.	0			c.G583A						PASS	.						57	55	56					2																	227662872		2203	4300	6503	SO:0001583	missense	3667	exon1			GCTTCACGAAGCT		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.583G>A	chr2.hg19:g.227662872C>T	ENSP00000304895:p.Val195Met	86.0	0.0	.	2321	93.0	23.0	.	NM_005544		Missense_Mutation	SNP	ENST00000305123.5	hg19	CCDS2463.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.366266	0.82463	.	.	ENSG00000169047	ENST00000305123	T	0.74526	-0.85	5.79	5.79	0.91817	Pleckstrin homology-type (1);Insulin receptor substrate-1, PTB (4);	0.000000	0.64402	D	0.000017	D	0.87661	0.6233	M	0.81497	2.545	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87579	0.2483	10	0.56958	D	0.05	-29.8384	20.0212	0.97504	0.0:1.0:0.0:0.0	.	195	P35568	IRS1_HUMAN	M	195	ENSP00000304895:V195M	ENSP00000304895:V195M	V	-	1	0	IRS1	227371116	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.735000	0.93741	0.561000	0.74099	GTG	.	.	.	none		0.567	IRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256886.3	NM_005544		T	227662872	C	T	227662872	3	4	119	1	0	0	0	0	1	0	0	0	7847	536	19	1	3149	1	IRS1	2	227662872	Missense_Mutation	SNP	C	TCGA-BQ-5884-01A-11D-1589-08	67576537	227662872	15536501	6	7546											
SFMBT1	51460	hgsc.bcm.edu	37	chr3	52939193	52939193	+	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	aaaagcaaacttgatcctctCtatgtgatggcaaagtttga	14	12	8	7	0	1	3	0	3	1	0	3	3	2	3	1	1	2	3	1	1	5	3			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr3:52939193C>A	ENST00000394752.3	-	21	2942	c.2560G>T	c.(2560-2562)Gag>Tag	p.E854*	SFMBT1_ENST00000358080.2_Nonsense_Mutation_p.E854*|SFMBT1_ENST00000394750.1_Nonsense_Mutation_p.E854*|SFMBT1_ENST00000296295.6_Nonsense_Mutation_p.E811*	NM_016329.3	NP_057413.2	Q9UHJ3	SMBT1_HUMAN	Scm-like with four mbt domains 1	854	SAM.				cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|negative regulation of muscle organ development (GO:0048635)|negative regulation of transcription, DNA-templated (GO:0045892)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)			breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	24				BRCA - Breast invasive adenocarcinoma(193;9.91e-05)|Kidney(197;0.000644)|KIRC - Kidney renal clear cell carcinoma(197;0.000792)|OV - Ovarian serous cystadenocarcinoma(275;0.113)		TTGATCCTCTCTATGTGATGG	0.458																																					p.E854X		Atlas-SNP	.											.	SFMBT1	53	.	0			c.G2560T						PASS	.						122	110	114					3																	52939193		2203	4300	6503	SO:0001587	stop_gained	51460	exon21			TCCTCTCTATGTG	AF168132	CCDS2867.1	3p21.31	2013-01-10			ENSG00000163935	ENSG00000163935		"Sterile alpha motif (SAM) domain containing"	20255	protein-coding gene	gene with protein product		607319				10661410	Standard	NM_016329		Approved	RU1, DKFZp434L243, SFMBT	uc003dgh.3	Q9UHJ3	OTTHUMG00000159052	ENST00000394752.3:c.2560G>T	chr3.hg19:g.52939193C>A	ENSP00000378235:p.Glu854*	153.0	0.0	.		118.0	5.0	.	NM_016329	Q402F7|Q96C73|Q9Y4Q9	Nonsense_Mutation	SNP	ENST00000394752.3	hg19	CCDS2867.1	.	.	.	.	.	.	.	.	.	.	C	44	10.576888	0.99431	.	.	ENSG00000163935	ENST00000394752;ENST00000358080;ENST00000296295;ENST00000394750	.	.	.	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	.	.	.	X	854;854;811;854	.	ENSP00000296295:E811X	E	-	1	0	SFMBT1	52914233	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.818000	0.86416	2.937000	0.99478	0.650000	0.86243	GAG	.	.	.	none		0.458	SFMBT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353040.3	NM_016329		A	52939193	C	A	52939193	4	1	119	1	0	0	0	0	0	1	0	0	14170	922	32	4	44	4	SFMBT1	3	52939193	Nonsense_Mutation	SNP	C	TCGA-BQ-5884-01A-11D-1589-08		52939193	145083237	7	7547											
CPNE4	131034	hgsc.bcm.edu	37	chr3	131254172	131254172	+	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	ttgccagggcagctggagatGcctgcagggaagaagaaatc	12	6	15	8	0	0	3	0	0	0	3	1	5	0	4	2	3	4	3	2	3	3	1			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr3:131254172G>A	ENST00000512055.1	-	20	3667	c.1541C>T	c.(1540-1542)gCa>gTa	p.A514V	CPNE4_ENST00000502818.1_Splice_Site_p.A532V|CPNE4_ENST00000511604.1_Splice_Site_p.A514V|CPNE4_ENST00000429747.1_Splice_Site_p.A514V|CPNE4_ENST00000503204.1_5'UTR|CPNE4_ENST00000512332.1_Splice_Site_p.A532V			Q96A23	CPNE4_HUMAN	copine IV	514						extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|liver(1)|lung(16)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	39						AGCTGGAGATGCCTGCAGGGA	0.453																																					p.A514V		Atlas-SNP	.											.	CPNE4	112	.	0			c.C1541T						PASS	.						97	91	93					3																	131254172		2203	4300	6503	SO:0001630	splice_region_variant	131034	exon16			GGAGATGCCTGCA	H29499	CCDS3072.1, CCDS75010.1	3q22.1	2014-09-04			ENSG00000196353	ENSG00000196353			2317	protein-coding gene	gene with protein product	"copine 8"	604208				9430674, 12670487	Standard	XM_005247107		Approved	COPN4, CPN4	uc003eok.3	Q96A23	OTTHUMG00000159631	ENST00000512055.1:c.1540-1C>T	chr3.hg19:g.131254172G>A		124.0	0.0	.		114.0	25.0	.	NM_130808	D3DNC5|Q8TEX1	Missense_Mutation	SNP	ENST00000512055.1	hg19	CCDS3072.1	.	.	.	.	.	.	.	.	.	.	G	19.12	3.766296	0.69878	.	.	ENSG00000196353	ENST00000512055;ENST00000429747;ENST00000512332;ENST00000511604;ENST00000502818	T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;0.55	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.70996	0.3288	M	0.76838	2.35	0.80722	D	1	P;B	0.44627	0.839;0.361	P;B	0.56563	0.801;0.134	T	0.72050	-0.4407	10	0.48119	T	0.1	-15.9346	18.8677	0.92300	0.0:0.0:1.0:0.0	.	532;514	Q96A23-2;Q96A23	.;CPNE4_HUMAN	V	514;514;532;514;532	ENSP00000421705:A514V;ENSP00000411904:A514V;ENSP00000424853:A532V;ENSP00000423811:A514V;ENSP00000421646:A532V	ENSP00000411904:A514V	A	-	2	0	CPNE4	132736862	1.000000	0.71417	0.998000	0.56505	0.601000	0.36947	9.476000	0.97823	2.460000	0.83146	0.557000	0.71058	GCA	.	.	.	none		0.453	CPNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356583.4	NM_130808	Missense_Mutation	A	131254172	G	A	131254172	5	1	119	1	0	0	0	0	0	0	1	0	3816	1333	46	2	136	2	CPNE4	3	131254172	Splice_Site	SNP	G	TCGA-BQ-5884-01A-11D-1589-08	78314979	131254172	66768258	8	7548											
TIFA	92610	hgsc.bcm.edu	37	chr4	113199250	113199250	+	Missense_Mutation	SNP	T	T	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	acctgtatggcaggtccattTtatttaggtagcccagctct	8	14	9	10	0	1	0	0	0	1	0	2	0	2	0	3	3	2	4	3	3	4	6			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr4:113199250T>G	ENST00000361717.3	-	2	604	c.323A>C	c.(322-324)aAa>aCa	p.K108T	TIFA_ENST00000500655.2_Missense_Mutation_p.K108T	NM_052864.2	NP_443096.1	Q96CG3	TIFA_HUMAN	TRAF-interacting protein with forkhead-associated domain	108					I-kappaB kinase/NF-kappaB signaling (GO:0007249)					breast(2)|endometrium(1)|large_intestine(1)|lung(1)|skin(1)	6		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00172)		CAGGTCCATTTTATTTAGGTA	0.388																																					p.K108T		Atlas-SNP	.											.	TIFA	15	.	0			c.A323C						PASS	.						45	42	43					4																	113199250		2203	4300	6503	SO:0001583	missense	92610	exon2			TCCATTTTATTTA	BC008294	CCDS34051.1	4q25	2008-03-17				ENSG00000145365			19075	protein-coding gene	gene with protein product	"TRAF2 binding protein", "TRAF6 binding protein"	609028				1179819	Standard	NM_052864		Approved	MGC20791, T2BP, T6BP, TIFAA	uc003ial.3	Q96CG3		ENST00000361717.3:c.323A>C	chr4.hg19:g.113199250T>G	ENSP00000354911:p.Lys108Thr	86.0	0.0	.		56.0	16.0	.	NM_052864		Missense_Mutation	SNP	ENST00000361717.3	hg19	CCDS34051.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.382639	0.82792	.	.	ENSG00000145365	ENST00000361717;ENST00000500655	D;D	0.86694	-2.16;-2.16	5.79	5.79	0.91817	Forkhead-associated (FHA) domain (2);	0.092657	0.64402	D	0.000001	D	0.92916	0.7746	M	0.71581	2.175	0.50813	D	0.999896	D	0.89917	1.0	D	0.91635	0.999	D	0.93532	0.6870	10	0.72032	D	0.01	-34.6044	16.1303	0.81428	0.0:0.0:0.0:1.0	.	108	Q96CG3	TIFA_HUMAN	T	108	ENSP00000354911:K108T;ENSP00000424231:K108T	ENSP00000354911:K108T	K	-	2	0	TIFA	113418699	1.000000	0.71417	0.077000	0.20336	0.992000	0.81027	3.462000	0.53042	2.218000	0.71995	0.533000	0.62120	AAA	.	.	.	none		0.388	TIFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363647.2	NM_052864		G	113199250	T	G	113199250	3	3	119	1	0	0	0	0	1	0	0	0	15906	1841	64	5	235	5	TIFA	4	113199250	Missense_Mutation	SNP	T	TCGA-BQ-5884-01A-11D-1589-08		113199250	77955026	9	7549											
METTL14	57721	hgsc.bcm.edu	37	chr4	119631350	119631350	+	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	gtggaggaagaggtggaactTctgctggccgtggacgagaa	10	7	18	6	2	1	2	0	0	1	2	1	7	1	6	1	6	2	1	1	6	3	1			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr4:119631350T>A	ENST00000388822.5	+	11	1431	c.1264T>A	c.(1264-1266)Tct>Act	p.S422T	METTL14_ENST00000506780.1_Missense_Mutation_p.S384T			Q9HCE5	MET14_HUMAN	methyltransferase like 14	422	Gly-rich.				mRNA destabilization (GO:0061157)|mRNA methylation (GO:0080009)|stem cell maintenance (GO:0019827)	MIS complex (GO:0036396)|nucleus (GO:0005634)	mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity (GO:0016422)|RNA binding (GO:0003723)			endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|stomach(1)	16						AGGTGGAACTTCTGCTGGCCG	0.527																																					p.S422T		Atlas-SNP	.											.	METTL14	41	.	0			c.T1264A						PASS	.						56	58	58					4																	119631350		2203	4300	6503	SO:0001583	missense	57721	exon11			GGAACTTCTGCTG	AB046847	CCDS34053.1	4q26	2009-02-24			ENSG00000145388	ENSG00000145388			29330	protein-coding gene	gene with protein product						10997877	Standard	NM_020961		Approved	KIAA1627	uc003icf.3	Q9HCE5	OTTHUMG00000161167	ENST00000388822.5:c.1264T>A	chr4.hg19:g.119631350T>A	ENSP00000373474:p.Ser422Thr	88.0	0.0	.		93.0	16.0	.	NM_020961	A6NIG1|Q969V2	Missense_Mutation	SNP	ENST00000388822.5	hg19	CCDS34053.1	.	.	.	.	.	.	.	.	.	.	T	14.22	2.469312	0.43839	.	.	ENSG00000145388	ENST00000388822;ENST00000506780	.	.	.	5.62	4.42	0.53409	.	0.215770	0.49305	D	0.000149	T	0.30448	0.0765	N	0.14661	0.345	0.38962	D	0.958572	B;B	0.29037	0.231;0.139	B;B	0.19946	0.027;0.027	T	0.11916	-1.0568	9	0.08381	T	0.77	-2.7465	12.8488	0.57846	0.0:0.0:0.1363:0.8637	.	384;422	D6RBL4;Q9HCE5	.;MTL14_HUMAN	T	422;384	.	ENSP00000373474:S422T	S	+	1	0	METTL14	119850798	1.000000	0.71417	0.961000	0.40146	0.958000	0.62258	4.909000	0.63314	0.937000	0.37394	0.528000	0.53228	TCT	.	.	.	none		0.527	METTL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364034.3	NM_020961		A	119631350	T	A	119631350	3	1	119	1	0	0	0	0	1	0	0	0	9505	1783	62	5	1306	5	METTL14	4	119631350	Missense_Mutation	SNP	T	TCGA-BQ-5884-01A-11D-1589-08	6432100	119631350	71522926	10	7550											
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123161284	123161284	+	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	tagaacatctatatattgtaGaaggtgagaaaacagtggag	17	10	11	3	0	1	3	0	1	1	3	1	5	1	4	0	2	2	1	0	2	9	6			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr4:123161284G>C	ENST00000264501.4	+	29	4820	c.4447G>C	c.(4447-4449)Gaa>Caa	p.E1483Q	KIAA1109_ENST00000455637.1_Missense_Mutation_p.E1483Q|KIAA1109_ENST00000388738.3_Missense_Mutation_p.E1483Q			Q2LD37	K1109_HUMAN	KIAA1109	1483					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						ATATATTGTAGAAGGTGAGAA	0.398																																					p.E1483Q		Atlas-SNP	.											.	KIAA1109	424	.	0			c.G4447C						PASS	.						118	113	114					4																	123161284		1871	4109	5980	SO:0001583	missense	84162	exon27			ATTGTAGAAGGTG	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.4447G>C	chr4.hg19:g.123161284G>C	ENSP00000264501:p.Glu1483Gln	117.0	0.0	.		103.0	23.0	.	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.16|17.16	3.318796|3.318796	0.60524|0.60524	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637|ENST00000446180	T;T;T|.	0.24908|.	2.42;2.42;1.83|.	5.91|5.91	5.91|5.91	0.95273|0.95273	.|.	0.000000|.	0.44285|.	U|.	0.000466|.	T|.	0.57125|.	0.2032|.	N|N	0.24115|0.24115	0.695|0.695	0.49798|0.49798	D|D	0.999822|0.999822	B;B|.	0.32245|.	0.361;0.247|.	B;B|.	0.42343|.	0.384;0.214|.	T|.	0.49184|.	-0.8966|.	10|.	0.66056|.	D|.	0.02|.	.|.	20.2885|20.2885	0.98538|0.98538	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1482;1483|.	Q2LD37-2;Q2LD37|.	.;K1109_HUMAN|.	Q|Y	1483|55	ENSP00000264501:E1483Q;ENSP00000373390:E1483Q;ENSP00000389925:E1483Q|.	ENSP00000264501:E1483Q|.	E|X	+|+	1|3	0|2	KIAA1109|KIAA1109	123380734|123380734	1.000000|1.000000	0.71417|0.71417	0.874000|0.874000	0.34290|0.34290	0.951000|0.951000	0.60555|0.60555	8.632000|8.632000	0.90995|0.90995	2.791000|2.791000	0.96007|0.96007	0.650000|0.650000	0.86243|0.86243	GAA|TAG	.	.	.	none		0.398	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		C	123161284	G	C	123161284	3	2	119	1	0	0	0	0	1	0	0	0	8215	943	33	4	4553	4	KIAA1109	4	123161284	Missense_Mutation	SNP	G	TCGA-BQ-5884-01A-11D-1589-08	3529934	123161284	67992992	11	7551											
ARHGAP26	23092	hgsc.bcm.edu	37	chr5	142283206	142283206	+	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	accatcagtccctacaccatGgagggatacctctacgtgca	11	8	8	14	1	2	0	1	0	1	0	3	2	3	2	4	2	4	1	4	2	3	3			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr5:142283206G>C	ENST00000274498.4	+	8	1182	c.804G>C	c.(802-804)atG>atC	p.M268I	ARHGAP26_ENST00000378004.3_Missense_Mutation_p.M268I	NM_015071.4	NP_055886.1	Q9UNA1	RHG26_HUMAN	Rho GTPase activating protein 26	268	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|filopodium assembly (GO:0046847)|nervous system development (GO:0007399)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(7)|ovary(1)	25		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCTACACCATGGAGGGATACC	0.473																																					p.M268I		Atlas-SNP	.											.	ARHGAP26	57	.	0			c.G804C						PASS	.						97	84	88					5																	142283206		2203	4300	6503	SO:0001583	missense	23092	exon8			CACCATGGAGGGA	AB014521	CCDS4277.1, CCDS47297.1	5q31	2011-06-29			ENSG00000145819	ENSG00000145819		"Rho GTPase activating proteins"	17073	protein-coding gene	gene with protein product	"GTPase regulator associated with the focal adhesion kinase pp125"	605370				9858476, 8649427	Standard	NM_001135608		Approved	GRAF, KIAA0621, OPHN1L, OPHN1L1	uc011dbj.2	Q9UNA1	OTTHUMG00000059705	ENST00000274498.4:c.804G>C	chr5.hg19:g.142283206G>C	ENSP00000274498:p.Met268Ile	60.0	0.0	.		54.0	11.0	.	NM_015071	O75117|Q5D035|Q9BYS6|Q9BYS7|Q9UJ00	Missense_Mutation	SNP	ENST00000274498.4	hg19	CCDS4277.1	.	.	.	.	.	.	.	.	.	.	G	12.71	2.018359	0.35606	.	.	ENSG00000145819	ENST00000274498;ENST00000378004	T;T	0.04317	3.65;3.65	5.49	5.49	0.81192	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	T	0.09379	0.0231	L	0.38953	1.18	0.80722	D	1	P;P	0.37548	0.481;0.599	B;P	0.46076	0.186;0.503	T	0.39231	-0.9624	10	0.25751	T	0.34	.	19.3843	0.94550	0.0:0.0:1.0:0.0	.	268;268	Q9UNA1;Q9UNA1-2	RHG26_HUMAN;.	I	268	ENSP00000274498:M268I;ENSP00000367243:M268I	ENSP00000274498:M268I	M	+	3	0	ARHGAP26	142263390	1.000000	0.71417	1.000000	0.80357	0.801000	0.45260	6.162000	0.71874	2.574000	0.86865	0.563000	0.77884	ATG	.	.	.	none		0.473	ARHGAP26-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132744.3	NM_015071		C	142283206	G	C	142283206	3	2	119	1	0	0	0	0	1	0	0	0	875	1348	47	4	834	4	ARHGAP26	5	142283206	Missense_Mutation	SNP	G	TCGA-BQ-5884-01A-11D-1589-08		142283206	38632054	12	7552											
GABRB2	2561	hgsc.bcm.edu	37	chr5	160753381	160753381	+	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	actggctatctaaccgtataCagagagaaatcgtaattggt	14	11	9	7	2	1	2	0	0	1	2	2	3	1	2	1	2	2	3	1	2	6	6			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr5:160753381C>G	ENST00000393959.1	-	9	1184	c.1185G>C	c.(1183-1185)ctG>ctC	p.L395L	GABRB2_ENST00000517547.1_Intron|GABRB2_ENST00000274547.2_Silent_p.L395L|GABRB2_ENST00000517901.1_Intron|GABRB2_ENST00000353437.6_Intron|GABRB2_ENST00000520240.1_Intron			P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 2	395					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|GABA-A receptor activity (GO:0004890)|inhibitory extracellular ligand-gated ion channel activity (GO:0005237)	p.L395L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(9)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	26	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TAACCGTATACAGAGAGAAAT	0.388																																					p.L395L		Atlas-SNP	.											GABRB2_ENST00000274547,NS,carcinoma,0,1	GABRB2	161	.	1	Substitution - coding silent(1)	endometrium(1)	c.G1185C						PASS	.						110	107	108					5																	160753381		2203	4299	6502	SO:0001819	synonymous_variant	2561	exon10			CGTATACAGAGAG		CCDS4354.1, CCDS4355.1	5q34	2012-06-22			ENSG00000145864	ENSG00000145864		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4082	protein-coding gene	gene with protein product	"GABA(A) receptor, beta 2"	600232				7851879	Standard	NM_000813		Approved		uc003lys.1	P47870	OTTHUMG00000130349	ENST00000393959.1:c.1185G>C	chr5.hg19:g.160753381C>G		143.0	0.0	.		122.0	5.0	.	NM_021911	A8K115|A8K1A0|D1LYT0|D1LYT1|Q16323|Q4FZB2	Silent	SNP	ENST00000393959.1	hg19	CCDS4355.1																																																																																			.	.	.	none		0.388	GABRB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252704.1			G	160753381	C	G	160753381	2	3	119	1	0	0	0	0	0	0	0	1	6174	465	17	4		4	GABRB2	5	160753381	Silent	SNP	C	TCGA-BQ-5884-01A-11D-1589-08	18470175	160753381	20161879	13	7553											
DOCK2	1794	hgsc.bcm.edu	37	chr5	169477372	169477372	+	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	gaacaccacctctgccccggGagatgatgtgaagaatgccc	11	6	11	13	1	1	4	0	2	1	2	1	6	1	4	5	1	3	0	5	1	3	0			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr5:169477372G>C	ENST00000256935.8	+	41	4264	c.4184G>C	c.(4183-4185)gGa>gCa	p.G1395A	DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000540750.1_Missense_Mutation_p.G456A|DOCK2_ENST00000520908.1_Missense_Mutation_p.G887A	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1395	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)			TCTGCCCCGGGAGATGATGTG	0.562																																					p.G1395A		Atlas-SNP	.											.	DOCK2	389	.	0			c.G4184C						PASS	.						119	111	114					5																	169477372		2203	4300	6503	SO:0001583	missense	1794	exon41			CCCCGGGAGATGA	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.4184G>C	chr5.hg19:g.169477372G>C	ENSP00000256935:p.Gly1395Ala	148.0	0.0	.		137.0	32.0	.	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	G	14.85	2.658712	0.47467	.	.	ENSG00000134516	ENST00000256935;ENST00000520908;ENST00000540750	T;T;T	0.08896	3.7;3.33;3.04	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.27313	0.0670	M	0.63428	1.95	0.58432	D	0.999999	D;D	0.71674	0.998;0.994	D;P	0.72075	0.976;0.839	T	0.00320	-1.1820	10	0.30854	T	0.27	.	19.427	0.94746	0.0:0.0:1.0:0.0	.	887;1395	E7ERW7;Q92608	.;DOCK2_HUMAN	A	1395;887;456	ENSP00000256935:G1395A;ENSP00000429283:G887A;ENSP00000438827:G456A	ENSP00000256935:G1395A	G	+	2	0	DOCK2	169409950	1.000000	0.71417	0.332000	0.25469	0.198000	0.23893	7.884000	0.87274	2.603000	0.88011	0.655000	0.94253	GGA	.	.	.	none		0.562	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		C	169477372	G	C	169477372	3	2	119	1	0	0	0	0	1	0	0	0	4689	1174	41	4	4346	4	DOCK2	5	169477372	Missense_Mutation	SNP	G	TCGA-BQ-5884-01A-11D-1589-08	8723991	169477372	11437888	14	7554											
F12	2161	hgsc.bcm.edu	37	chr5	176831305	176831305	+	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	cctaggggacaccggggtcgGaggcgccgcctgggttgggg	4	5	21	11	4	0	0	0	0	0	0	1	2	0	2	4	9	0	1	4	9	1	2			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr5:176831305G>A	ENST00000253496.3	-	9	958	c.910C>T	c.(910-912)Ccg>Tcg	p.P304S	F12_ENST00000514943.1_5'Flank	NM_000505.3	NP_000496.2	P00748	FA12_HUMAN	coagulation factor XII (Hageman factor)	304	Pro-rich.				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)	ACCGGGGTCGGAGGCGCCGCC	0.701									Hereditary Angioedema		OREG0017088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P304S		Atlas-SNP	.											.	F12	35	.	0			c.C910T						PASS	.						16	21	19					5																	176831305		2200	4295	6495	SO:0001583	missense	2161	exon9	Familial Cancer Database	HAE, type I-III, Hereditary Angioneurotic Edema, HANE,	GGGTCGGAGGCGC	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.910C>T	chr5.hg19:g.176831305G>A	ENSP00000253496:p.Pro304Ser	38.0	0.0	.	1934	30.0	7.0	.	NM_000505	P78339	Missense_Mutation	SNP	ENST00000253496.3	hg19	CCDS34302.1	.	.	.	.	.	.	.	.	.	.	G	12.87	2.068656	0.36470	.	.	ENSG00000131187	ENST00000253496	T	0.62364	0.03	3.94	1.0	0.19881	Kringle-like fold (1);	0.463200	0.16155	N	0.227071	T	0.32912	0.0845	N	0.14661	0.345	0.19300	N	0.999975	B	0.34103	0.437	B	0.27500	0.08	T	0.22103	-1.0226	10	0.09084	T	0.74	.	6.3798	0.21527	0.0:0.1784:0.4636:0.358	.	304	P00748	FA12_HUMAN	S	304	ENSP00000253496:P304S	ENSP00000253496:P304S	P	-	1	0	F12	176763911	0.000000	0.05858	0.000000	0.03702	0.121000	0.20230	-0.786000	0.04623	0.206000	0.20587	0.561000	0.74099	CCG	.	.	.	none		0.701	F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373217.1			A	176831305	G	A	176831305	3	1	119	1	0	0	0	0	1	0	0	0	5341	1174	41	2	961	2	F12	5	176831305	Missense_Mutation	SNP	G	TCGA-BQ-5884-01A-11D-1589-08	7353933	176831305	4083955	15	7555											
BRD2	6046	hgsc.bcm.edu	37	chr6	32945545	32945545	+	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	tctttgtaggatgtatttgaGttccgttatgccaagatgcc	8	16	10	7	1	1	2	0	1	1	1	2	3	2	3	3	1	2	4	3	1	4	6	rs55650066		TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr6:32945545G>T	ENST00000374825.4	+	9	3042	c.1341G>T	c.(1339-1341)gaG>gaT	p.E447D	BRD2_ENST00000395287.1_Missense_Mutation_p.E447D|BRD2_ENST00000374831.4_Missense_Mutation_p.E447D|BRD2_ENST00000443797.2_Missense_Mutation_p.E327D|BRD2_ENST00000395289.2_Missense_Mutation_p.E447D|BRD2_ENST00000449085.2_Missense_Mutation_p.E400D	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	447					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						ATGTATTTGAGTTCCGTTATG	0.468																																					p.E447D		Atlas-SNP	.											.	BRD2	70	.	0			c.G1341T						PASS	.						124	138	133					6																	32945545		1510	2709	4219	SO:0001583	missense	6046	exon9			ATTTGAGTTCCGT	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.1341G>T	chr6.hg19:g.32945545G>T	ENSP00000363958:p.Glu447Asp	143.0	0.0	.		108.0	5.0	.	NM_005104	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Missense_Mutation	SNP	ENST00000374825.4	hg19	CCDS4762.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.69|19.69	3.874670|3.874670	0.72180|0.72180	.|.	.|.	ENSG00000204256|ENSG00000204256	ENST00000374825;ENST00000374831;ENST00000395289;ENST00000443797;ENST00000395287;ENST00000449085|ENST00000449025	T;T;T;T;T;T|.	0.20332|.	2.08;2.08;2.08;2.08;2.08;2.08|.	5.63|5.63	4.76|4.76	0.60689|0.60689	Bromodomain (3);|.	0.000000|.	0.51477|.	D|.	0.000096|.	T|T	0.74176|0.74176	0.3682|0.3682	M|M	0.89968|0.89968	3.075|3.075	0.58432|0.58432	D|D	0.999999|0.999999	D;D|.	0.71674|.	0.998;0.985|.	P;P|.	0.62382|.	0.901;0.842|.	T|T	0.79883|0.79883	-0.1615|-0.1615	10|5	0.44086|.	T|.	0.13|.	-29.6263|-29.6263	12.3553|12.3553	0.55171|0.55171	0.0804:0.0:0.9196:0.0|0.0804:0.0:0.9196:0.0	.|.	447;447|.	A2AAU0;P25440|.	.;BRD2_HUMAN|.	D|I	447;447;447;327;447;400|453	ENSP00000363958:E447D;ENSP00000363964:E447D;ENSP00000378704:E447D;ENSP00000413495:E327D;ENSP00000378702:E447D;ENSP00000409145:E400D|.	ENSP00000363958:E447D|.	E|S	+|+	3|2	2|0	BRD2|BRD2	33053523|33053523	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.362000|3.362000	0.52314|0.52314	1.619000|1.619000	0.50296|0.50296	0.643000|0.643000	0.83706|0.83706	GAG|AGT	.	.	.	alt		0.468	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2			T	32945545	G	T	32945545	3	4	119	1	0	0	0	0	1	0	0	0	1504	1020	36	4	1371	4	BRD2	6	32945545	Missense_Mutation	SNP	G	TCGA-BQ-5884-01A-11D-1589-08		32945545	138169522	16	7556											
ZNF318	24149	hgsc.bcm.edu	37	chr6	43333130	43333130	+	Frame_Shift_Del	DEL	T	T	-																															gtggtcattgccaacagtgaTccttaagctcttttccaaag																										TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr6:43333130delT	ENST00000361428.2	-	2	525	c.448delA	c.(448-450)atcfs	p.I150fs	ZNF318_ENST00000318149.3_Frame_Shift_Del_p.I150fs	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	150					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)			CCAACAGTGATCCTTAAGCTC	0.473																																					p.I150fs		Atlas-INDEL	.											.	ZNF318	175	.	0			c.449delT						PASS	.						104	99	101					6																	43333130		2203	4300	6503	SO:0001589	frameshift_variant	24149	exon2			.	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.448delA	chr6.hg19:g.43333130delT	ENSP00000354964:p.Ile150fs	85.0	0.0	0		73.0	25.0	0.342466	NM_014345	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Frame_Shift_Del	DEL	ENST00000361428.2	hg19	CCDS4895.2																																																																																			.	.	.	none		0.473	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345		-	43333130	T	-	43333130	7	5	119	1	0	1	0	1	0	0	0	0	17848	1435	50	0	6427	0	ZNF318	6	43333130	Frame_Shift_Del	DEL	T	TCGA-BQ-5884-01A-11D-1589-08	10387585	43333130	127781937	17	7557											
EEF1A1	1915	hgsc.bcm.edu	37	chr6	74229620	74229620	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatacctcagcagcctcctTctcaaatttttcaatggttc	10	14	4	13	0	3	0	3	0	1	0	6	0	4	0	3	1	3	2	3	1	3	5			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr6:74229620T>C	ENST00000316292.9	-	1	1121	c.130A>G	c.(130-132)Aag>Gag	p.K44E	EEF1A1_ENST00000491404.1_5'Flank|EEF1A1_ENST00000309268.6_Missense_Mutation_p.K44E|EEF1A1_ENST00000331523.2_Missense_Mutation_p.K44E	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1	44	tr-type G.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation elongation factor activity (GO:0003746)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						GCAGCCTCCTTCTCAAATTTT	0.423																																					p.K44E		Atlas-SNP	.											.	EEF1A1	56	.	0			c.A130G						PASS	.						127	129	128					6																	74229620		2203	4300	6503	SO:0001583	missense	1915	exon2			CCTCCTTCTCAAA	BC019669	CCDS4980.1	6q14.1	2010-06-30	2004-11-19		ENSG00000156508	ENSG00000156508			3189	protein-coding gene	gene with protein product		130590	"leukocyte receptor cluster (LRC) member 7"	EF1A, EEF1A, LENG7		8812466, 10941842	Standard	NM_001402		Approved	EE1A1	uc003phj.3	P68104	OTTHUMG00000015031	ENST00000316292.9:c.130A>G	chr6.hg19:g.74229620T>C	ENSP00000339063:p.Lys44Glu	185.0	0.0	.		162.0	13.0	.	NM_001402	P04719|P04720|Q6IQ15	Missense_Mutation	SNP	ENST00000316292.9	hg19	CCDS4980.1	.	.	.	.	.	.	.	.	.	.	T	13.92	2.380554	0.42207	.	.	ENSG00000156508	ENST00000316292;ENST00000358190;ENST00000309268;ENST00000331523;ENST00000391977;ENST00000456206;ENST00000356303;ENST00000455918	T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91	4.15	4.15	0.48705	Protein synthesis factor, GTP-binding (2);	0.000000	0.85682	U	0.000000	T	0.23965	0.0580	L	0.39326	1.205	0.80722	D	1	B;B;B;B;B	0.14012	0.002;0.009;0.009;0.009;0.009	B;B;B;B;B	0.26416	0.013;0.069;0.069;0.069;0.069	T	0.21999	-1.0229	10	0.87932	D	0	.	13.6597	0.62359	0.0:0.0:0.0:1.0	.	44;44;44;44;44	A6PW80;P68104;Q53HR5;Q6IPS9;Q5VTE0	.;EF1A1_HUMAN;.;.;EF1A3_HUMAN	E	44	ENSP00000339063:K44E;ENSP00000339053:K44E;ENSP00000330054:K44E;ENSP00000348651:K44E;ENSP00000392366:K44E	ENSP00000339053:K44E	K	-	1	0	EEF1A1	74286341	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	7.669000	0.83911	1.874000	0.54306	0.454000	0.30748	AAG	.	.	.	weak		0.423	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041210.2	NM_001402		C	74229620	T	C	74229620	3	2	119	1	0	0	0	0	1	0	0	0	4925	1792	62	3	1286	3	EEF1A1	6	74229620	Missense_Mutation	SNP	T	TCGA-BQ-5884-01A-11D-1589-08	30896490	74229620	96885447	18	7558											
ZNF292	23036	hgsc.bcm.edu	37	chr6	87964665	87964665	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacttgtattgaaaactcaaTggccctttgatccagaattc	12	14	6	9	0	1	3	1	2	0	1	3	3	2	3	2	1	2	1	2	1	6	6			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr6:87964665T>C	ENST00000369577.3	+	8	1361	c.1318T>C	c.(1318-1320)Tgg>Cgg	p.W440R	ZNF292_ENST00000339907.4_Missense_Mutation_p.W435R	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	440						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		GAAAACTCAATGGCCCTTTGA	0.378																																					p.W440R		Atlas-SNP	.											.	ZNF292	479	.	0			c.T1318C						PASS	.						75	69	71					6																	87964665		1844	4086	5930	SO:0001583	missense	23036	exon8			ACTCAATGGCCCT	AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.1318T>C	chr6.hg19:g.87964665T>C	ENSP00000358590:p.Trp440Arg	53.0	0.0	.		38.0	5.0	.	NM_015021	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	hg19	CCDS47457.1	.	.	.	.	.	.	.	.	.	.	T	16.87	3.241783	0.58995	.	.	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.39787	1.06;1.06	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.58424	0.2121	M	0.72894	2.215	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	T	0.63435	-0.6638	10	0.87932	D	0	.	16.6245	0.84952	0.0:0.0:0.0:1.0	.	440	O60281	ZN292_HUMAN	R	440;435	ENSP00000358590:W440R;ENSP00000342847:W435R	ENSP00000342847:W435R	W	+	1	0	ZNF292	88021384	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	8.040000	0.89188	2.323000	0.78572	0.528000	0.53228	TGG	.	.	.	none		0.378	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		C	87964665	T	C	87964665	3	2	119	1	0	0	0	0	1	0	0	0	17838	1464	51	3	1348	3	ZNF292	6	87964665	Missense_Mutation	SNP	T	TCGA-BQ-5884-01A-11D-1589-08	13735045	87964665	83150402	19	7559											
ANKIB1	54467	hgsc.bcm.edu	37	chr7	92019370	92019370	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcattctcaagtgttcttaTccatatggatttttcttgga	8	18	7	8	1	3	0	1	0	3	0	5	2	4	2	1	2	0	2	1	2	3	7			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr7:92019370T>C	ENST00000265742.3	+	15	2368	c.1992T>C	c.(1990-1992)taT>taC	p.Y664Y		NM_019004.1	NP_061877.1	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	664							zinc ion binding (GO:0008270)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(19)|skin(1)	41	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			AGTGTTCTTATCCATATGGAT	0.333																																					p.Y664Y		Atlas-SNP	.											.	ANKIB1	92	.	0			c.T1992C						PASS	.						107	102	103					7																	92019370		1828	4082	5910	SO:0001819	synonymous_variant	54467	exon15			TTCTTATCCATAT	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.1992T>C	chr7.hg19:g.92019370T>C		109.0	0.0	.		120.0	29.0	.	NM_019004	Q6GMS4|Q6P3S9|Q9NTD7|Q9NW49	Silent	SNP	ENST00000265742.3	hg19	CCDS47639.1																																																																																			.	.	.	none		0.333	ANKIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342018.1			C	92019370	T	C	92019370	2	2	119	1	0	0	0	0	0	0	0	1	630	1442	50	3		3	ANKIB1	7	92019370	Silent	SNP	T	TCGA-BQ-5884-01A-11D-1589-08		92019370	67119293	20	7560											
SLC26A5	375611	hgsc.bcm.edu	37	chr7	103019735	103019735	+	Missense_Mutation	SNP	A	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	aagtcgctatttgcatagtaAattggtgcatttatttgaaa	13	16	8	4	1	0	1	0	1	0	0	1	1	0	1	0	1	2	4	0	1	7	8			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr7:103019735A>C	ENST00000306312.3	-	16	1893	c.1632T>G	c.(1630-1632)atT>atG	p.I544M	SLC26A5_ENST00000393723.1_Missense_Mutation_p.I512M|SLC26A5_ENST00000356767.4_Intron|SLC26A5_ENST00000393735.2_Intron|SLC26A5_ENST00000393727.1_Missense_Mutation_p.I544M|SLC26A5_ENST00000354356.4_De_novo_Start_InFrame|SLC26A5_ENST00000393730.1_Missense_Mutation_p.I512M|SLC26A5_ENST00000393729.1_Missense_Mutation_p.I507M|SLC26A5_ENST00000432958.2_Missense_Mutation_p.I512M|SLC26A5_ENST00000339444.6_Missense_Mutation_p.I544M	NM_198999.2	NP_945350.1	P58743	S26A5_HUMAN	solute carrier family 26 (anion exchanger), member 5	544	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				regulation of cell shape (GO:0008360)|regulation of membrane potential (GO:0042391)|sensory perception of sound (GO:0007605)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)	secondary active sulfate transmembrane transporter activity (GO:0008271)			endometrium(5)|kidney(2)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)	43						TTGCATAGTAAATTGGTGCAT	0.318																																					p.I544M		Atlas-SNP	.											.	SLC26A5	231	.	0			c.T1632G						PASS	.						112	107	109					7																	103019735		2203	4299	6502	SO:0001583	missense	375611	exon16			ATAGTAAATTGGT	AC005064	CCDS5733.1, CCDS43630.1, CCDS55150.1, CCDS5732.1, CCDS43629.1	7q22	2013-07-18	2013-07-18	2005-09-13	ENSG00000170615	ENSG00000170615		"Solute carriers"	9359	protein-coding gene	gene with protein product	"deafness, neurosensory, autosomal recessive, 61"	604943	"prestin (motor protein)"	PRES		10821263	Standard	NM_206883		Approved	DFNB61	uc003vbz.3	P58743	OTTHUMG00000149911	ENST00000306312.3:c.1632T>G	chr7.hg19:g.103019735A>C	ENSP00000304783:p.Ile544Met	113.0	0.0	.		100.0	34.0	.	NM_206883	Q496J2|Q7Z7F3|Q86UF8|Q86UF9|Q86UG0	Missense_Mutation	SNP	ENST00000306312.3	hg19	CCDS5733.1	.	.	.	.	.	.	.	.	.	.	A	16.19	3.052577	0.55218	.	.	ENSG00000170615	ENST00000339444;ENST00000306312;ENST00000393730;ENST00000432958;ENST00000393729;ENST00000393727;ENST00000393723	D;D;D;D;D;D;D	0.94862	-3.54;-3.54;-3.54;-3.54;-3.54;-3.54;-3.54	6.13	4.99	0.66335	Sulphate transporter/antisigma-factor antagonist STAS (4);	0.151455	0.56097	D	0.000021	D	0.96288	0.8789	M	0.82056	2.57	0.80722	D	1	P;D;D	0.67145	0.645;0.996;0.995	P;D;D	0.67382	0.643;0.951;0.918	D	0.95580	0.8645	10	0.49607	T	0.09	.	8.2331	0.31610	0.8582:0.0:0.1418:0.0	.	544;512;544	P58743;Q496J2;P58743-2	S26A5_HUMAN;.;.	M	544;544;512;512;507;544;512	ENSP00000342396:I544M;ENSP00000304783:I544M;ENSP00000377331:I512M;ENSP00000389733:I512M;ENSP00000377330:I507M;ENSP00000377328:I544M;ENSP00000377324:I512M	ENSP00000304783:I544M	I	-	3	3	SLC26A5	102806971	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.023000	0.30065	2.364000	0.80123	0.524000	0.50904	ATT	.	.	.	none		0.318	SLC26A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313860.1	NM_198999		C	103019735	A	C	103019735	3	2	119	1	0	0	0	0	1	0	0	0	14533	10	1	5	663	5	SLC26A5	7	103019735	Missense_Mutation	SNP	A	TCGA-BQ-5884-01A-11D-1589-08	11000365	103019735	56118928	21	7561											
UBE3C	9690	hgsc.bcm.edu	37	chr7	157046775	157046775	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcactgcctggctttccgccAgggccttgccaatgtcgtca	5	10	11	15	2	1	0	1	0	0	0	3	0	2	0	5	2	2	2	5	2	1	2			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr7:157046775A>G	ENST00000348165.5	+	20	3182	c.2822A>G	c.(2821-2823)cAg>cGg	p.Q941R		NM_014671.2	NP_055486.2	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	941	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(2)|endometrium(3)|kidney(16)|large_intestine(13)|lung(25)|ovary(2)|prostate(1)|urinary_tract(1)	63		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		GCTTTCCGCCAGGGCCTTGCC	0.567																																					p.Q941R		Atlas-SNP	.											.	UBE3C	124	.	0			c.A2822G						PASS	.						56	53	54					7																	157046775		2203	4300	6503	SO:0001583	missense	9690	exon20			TCCGCCAGGGCCT	AK127280	CCDS34789.1	7q36.3	2004-05-04			ENSG00000009335	ENSG00000009335			16803	protein-coding gene	gene with protein product		614454				7584026, 11278995	Standard	NM_014671		Approved	KIAA0010, KIAA10	uc010lqs.3	Q15386	OTTHUMG00000157239	ENST00000348165.5:c.2822A>G	chr7.hg19:g.157046775A>G	ENSP00000309198:p.Gln941Arg	59.0	0.0	.		60.0	21.0	.	NM_014671	A4D235|A6NCP3|Q8TC15|Q96CR4|Q9UDU3	Missense_Mutation	SNP	ENST00000348165.5	hg19	CCDS34789.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.268398	0.80469	.	.	ENSG00000009335	ENST00000348165	T	0.56103	0.48	5.31	5.31	0.75309	HECT (4);	0.000000	0.85682	D	0.000000	T	0.45115	0.1326	N	0.20610	0.595	0.80722	D	1	B;P	0.38677	0.437;0.642	P;P	0.48334	0.475;0.574	T	0.30357	-0.9981	10	0.05833	T	0.94	.	15.5565	0.76200	1.0:0.0:0.0:0.0	.	941;794	Q15386;B4DHJ9	UBE3C_HUMAN;.	R	941	ENSP00000309198:Q941R	ENSP00000309198:Q941R	Q	+	2	0	UBE3C	156739536	1.000000	0.71417	0.996000	0.52242	0.769000	0.43574	8.946000	0.92992	2.143000	0.66587	0.533000	0.62120	CAG	.	.	.	none		0.567	UBE3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348108.1	NM_014671		G	157046775	A	G	157046775	3	3	119	1	0	0	0	0	1	0	0	0	16893	188	7	3	2900	3	UBE3C	7	157046775	Missense_Mutation	SNP	A	TCGA-BQ-5884-01A-11D-1589-08	54027040	157046775	2091888	22	7562											
PDLIM2	64236	hgsc.bcm.edu	37	chr8	22452077	22452077	+	IGR	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	tatggagggaatgagattgtCactggaagctttggagggga	11	10	17	3	0	1	1	1	1	0	1	1	7	1	6	0	6	1	1	0	6	3	3			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr8:22452077C>T	ENST00000397760.4	+	0	1837				AC037459.4_ENST00000430850.2_Intron|PDLIM2_ENST00000265810.4_Missense_Mutation_p.S339L			Q96JY6	PDLI2_HUMAN	PDZ and LIM domain 2 (mystique)							actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00579)|Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0626)		ATGAGATTGTCACTGGAAGCT	0.527																																					p.S339L		Atlas-SNP	.											.	PDLIM2	42	.	0			c.C1016T						PASS	.						167	167	167					8																	22452077		2203	4300	6503	SO:0001628	intergenic_variant	64236	exon10			GATTGTCACTGGA	AY007729	CCDS34860.1, CCDS6032.1, CCDS34861.1, CCDS6032.2	8p21.3	2012-06-27			ENSG00000120913	ENSG00000120913			13992	protein-coding gene	gene with protein product		609722					Standard	NM_021630		Approved		uc003xby.4	Q96JY6	OTTHUMG00000164270		chr8.hg19:g.22452077C>T		193.0	0.0	.		167.0	11.0	.	NM_176871	D3DSR5|J3KNH4|Q7Z584|Q86WM8|Q8WZ29|Q9H4L9|Q9H7I2	Missense_Mutation	SNP	ENST00000397760.4	hg19		.	.	.	.	.	.	.	.	.	.	C	13.63	2.293984	0.40594	.	.	ENSG00000120913	ENST00000265810	T	0.13538	2.58	1.84	0.907	0.19321	.	.	.	.	.	T	0.08582	0.0213	.	.	.	0.09310	N	0.999999	B	0.23185	0.081	B	0.15052	0.012	T	0.31971	-0.9924	8	0.49607	T	0.09	.	3.5437	0.07820	0.0:0.7384:0.0:0.2616	.	339	Q96JY6-3	.	L	339	ENSP00000265810:S339L	ENSP00000265810:S339L	S	+	2	0	PDLIM2	22508022	0.004000	0.15560	0.006000	0.13384	0.019000	0.09904	0.023000	0.13533	0.318000	0.23185	0.491000	0.48974	TCA	.	.	.	none		0.527	PDLIM2-202	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000334167.1			T	22452077	C	T	22452077	1	4	119	0	1	0	0	0	0	0	0	0	11687	838	29	2		2	PDLIM2	8	22452077	IGR	SNP	C	TCGA-BQ-5884-01A-11D-1589-08		22452077	123911945	23	7563											
SLC7A13	157724	hgsc.bcm.edu	37	chr8	87226722	87226722	+	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	cttctcaaaccaagccaatcTtattttaaaatgtattaaag	16	14	3	8	0	2	0	1	0	2	0	3	0	2	0	2	0	2	1	2	0	9	6			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr8:87226722T>A	ENST00000297524.3	-	4	1436	c.1333A>T	c.(1333-1335)Aga>Tga	p.R445*	SLC7A13_ENST00000419776.2_3'UTR|CTD-3118D11.3_ENST00000523112.1_RNA	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	445						integral component of membrane (GO:0016021)	amino acid transmembrane transporter activity (GO:0015171)	p.R445*(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	45						CAAGCCAATCTTATTTTAAAA	0.348																																					p.R445X		Atlas-SNP	.											SLC7A13,colon,carcinoma,0,1	SLC7A13	97	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.A1333T						PASS	.						56	61	60					8																	87226722		2203	4300	6503	SO:0001587	stop_gained	157724	exon4			CCAATCTTATTTT	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.1333A>T	chr8.hg19:g.87226722T>A	ENSP00000297524:p.Arg445*	72.0	0.0	.		53.0	17.0	.	NM_138817	Q05C37|Q08AH9|Q96N84	Nonsense_Mutation	SNP	ENST00000297524.3	hg19	CCDS34917.1	.	.	.	.	.	.	.	.	.	.	T	12.75	2.030925	0.35797	.	.	ENSG00000164893	ENST00000297524	.	.	.	4.13	-0.155	0.13395	.	0.844613	0.10208	N	0.702444	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.19590	T	0.45	.	5.8345	0.18599	0.0:0.1058:0.4904:0.4039	.	.	.	.	X	445	.	ENSP00000297524:R445X	R	-	1	2	SLC7A13	87295838	0.001000	0.12720	0.000000	0.03702	0.068000	0.16541	1.079000	0.30766	0.195000	0.20347	0.533000	0.62120	AGA	.	.	.	none		0.348	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817		A	87226722	T	A	87226722	4	1	119	1	0	0	0	0	0	1	0	0	14708	1617	56	5	83	5	SLC7A13	8	87226722	Nonsense_Mutation	SNP	T	TCGA-BQ-5884-01A-11D-1589-08	64774645	87226722	59137300	24	7564											
ZHX2	22882	hgsc.bcm.edu	37	chr8	123965936	123965936	+	Missense_Mutation	SNP	A	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	cgggggtgatgtggttccacAatattacaaggaccccaaaa	13	8	11	9	1	0	1	0	1	0	0	1	2	1	2	3	4	1	1	3	4	6	3			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr8:123965936A>C	ENST00000314393.4	+	3	3021	c.2186A>C	c.(2185-2187)cAa>cCa	p.Q729P		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	729					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)			GTGGTTCCACAATATTACAAG	0.527																																					p.Q729P	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											.	ZHX2	106	.	0			c.A2186C						PASS	.						96	101	100					8																	123965936		2203	4300	6503	SO:0001583	missense	22882	exon3			TTCCACAATATTA	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.2186A>C	chr8.hg19:g.123965936A>C	ENSP00000314709:p.Gln729Pro	128.0	0.0	.		107.0	27.0	.	NM_014943		Missense_Mutation	SNP	ENST00000314393.4	hg19	CCDS6336.1	.	.	.	.	.	.	.	.	.	.	A	4.171	0.030196	0.08101	.	.	ENSG00000178764	ENST00000314393	T	0.18502	2.21	5.94	0.233	0.15386	.	0.814635	0.11109	N	0.598853	T	0.09202	0.0227	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.33085	-0.9882	10	0.36615	T	0.2	-0.5406	4.2111	0.10512	0.4285:0.383:0.0659:0.1227	.	729	Q9Y6X8	ZHX2_HUMAN	P	729	ENSP00000314709:Q729P	ENSP00000314709:Q729P	Q	+	2	0	ZHX2	124035117	0.000000	0.05858	0.002000	0.10522	0.014000	0.08584	0.379000	0.20585	0.099000	0.17552	-0.466000	0.05196	CAA	.	.	.	none		0.527	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943		C	123965936	A	C	123965936	3	2	119	1	0	0	0	0	1	0	0	0	17688	130	5	5	2188	5	ZHX2	8	123965936	Missense_Mutation	SNP	A	TCGA-BQ-5884-01A-11D-1589-08	36739214	123965936	22398086	25	7565											
EPC1	80314	hgsc.bcm.edu	37	chr10	32582651	32582651	+	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	atcataatcaggctgttcagCatccaaactaaaagctgaca	16	9	6	10	0	3	1	3	1	0	0	4	1	4	1	1	1	3	4	1	1	4	3			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr10:32582651C>A	ENST00000263062.8	-	3	597	c.328G>T	c.(328-330)Gct>Tct	p.A110S	EPC1_ENST00000375110.2_Missense_Mutation_p.A60S|EPC1_ENST00000319778.6_Missense_Mutation_p.A110S	NM_025209.2	NP_079485.1	Q9H2F5	EPC1_HUMAN	enhancer of polycomb homolog 1 (Drosophila)	110					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(5)|urinary_tract(1)	24		Prostate(175;0.0199)				GGCTGTTCAGCATCCAAACTA	0.368																																					p.A110S		Atlas-SNP	.											.	EPC1	74	.	0			c.G328T						PASS	.						51	46	48					10																	32582651		2203	4300	6503	SO:0001583	missense	80314	exon3			GTTCAGCATCCAA	AF277374	CCDS7172.1, CCDS60511.1, CCDS73083.1	10p11	2005-12-12			ENSG00000120616	ENSG00000120616			19876	protein-coding gene	gene with protein product		610999				10976108	Standard	NM_025209		Approved	Epl1	uc001iwg.2	Q9H2F5	OTTHUMG00000017925	ENST00000263062.8:c.328G>T	chr10.hg19:g.32582651C>A	ENSP00000263062:p.Ala110Ser	54.0	0.0	.		37.0	11.0	.	NM_025209	B4DSC3|D3DRX7|Q5VW54|Q5VW56|Q5VW58|Q8NAQ4|Q8NE21|Q96LF4|Q96RR6|Q9H7T7	Missense_Mutation	SNP	ENST00000263062.8	hg19	CCDS7172.1	.	.	.	.	.	.	.	.	.	.	C	10.97	1.501195	0.26861	.	.	ENSG00000120616	ENST00000375110;ENST00000319778;ENST00000263062	T;T;T	0.40476	1.03;1.03;1.03	5.67	4.76	0.60689	Enhancer of polycomb-like, N-terminal (1);	0.091656	0.85682	D	0.000000	T	0.17959	0.0431	N	0.04508	-0.205	0.42849	D	0.994075	B;P;B;B	0.39022	0.073;0.655;0.02;0.073	B;B;B;B	0.30855	0.105;0.121;0.037;0.105	T	0.09509	-1.0671	10	0.10902	T	0.67	-6.3339	14.4806	0.67579	0.0:0.9292:0.0:0.0708	.	110;60;110;110	B8XCX7;Q9H2F5-3;Q9H2F5-2;Q9H2F5	.;.;.;EPC1_HUMAN	S	60;110;110	ENSP00000364251:A60S;ENSP00000318559:A110S;ENSP00000263062:A110S	ENSP00000263062:A110S	A	-	1	0	EPC1	32622657	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.957000	0.56730	1.389000	0.46526	0.467000	0.42956	GCT	.	.	.	none		0.368	EPC1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047484.1			A	32582651	C	A	32582651	3	1	119	1	0	0	0	0	1	0	0	0	5162	710	25	4	2234	4	EPC1	10	32582651	Missense_Mutation	SNP	C	TCGA-BQ-5884-01A-11D-1589-08		32582651	102952096	26	7566											
ZNF33B	7582	hgsc.bcm.edu	37	chr10	43088537	43088537	+	Missense_Mutation	SNP	T	T	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	atgctgagtgagttgtgactTctggcagaaggtttttccac	8	14	12	7	0	1	4	0	3	1	1	2	4	2	4	1	2	1	4	1	2	1	4			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr10:43088537T>G	ENST00000359467.3	-	5	1975	c.1861A>C	c.(1861-1863)Aag>Cag	p.K621Q	ZNF33B_ENST00000486187.1_RNA	NM_006955.1	NP_008886.1	Q06732	ZN33B_HUMAN	zinc finger protein 33B	621					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(15)|skin(1)|stomach(1)	29						AGTTGTGACTTCTGGCAGAAG	0.363																																					p.K621Q	Melanoma(137;1247 1767 16772 25727 43810)	Atlas-SNP	.											.	ZNF33B	78	.	0			c.A1861C						PASS	.						96	96	96					10																	43088537		2203	4300	6503	SO:0001583	missense	7582	exon5			GTGACTTCTGGCA	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.1861A>C	chr10.hg19:g.43088537T>G	ENSP00000352444:p.Lys621Gln	205.0	0.0	.		183.0	42.0	.	NM_006955	Q06731|Q32MA2|Q86XY8|Q8NDW3	Missense_Mutation	SNP	ENST00000359467.3	hg19	CCDS7198.1	.	.	.	.	.	.	.	.	.	.	T	9.434	1.086178	0.20390	.	.	ENSG00000196693	ENST00000359467;ENST00000395836	T	0.01015	5.44	2.58	2.58	0.30949	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35646	N	0.003071	T	0.02807	0.0084	L	0.56124	1.755	0.09310	N	1	D	0.71674	0.998	D	0.68621	0.959	T	0.40021	-0.9585	10	0.38643	T	0.18	.	9.025	0.36224	0.0:0.0:0.0:1.0	.	621	Q06732	ZN33B_HUMAN	Q	621;587	ENSP00000352444:K621Q	ENSP00000352444:K621Q	K	-	1	0	ZNF33B	42408543	0.000000	0.05858	1.000000	0.80357	0.991000	0.79684	0.848000	0.27710	1.446000	0.47643	0.336000	0.21669	AAG	.	.	.	none		0.363	ZNF33B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_006955		G	43088537	T	G	43088537	3	3	119	1	0	0	0	0	1	0	0	0	17867	1792	62	5	479	5	ZNF33B	10	43088537	Missense_Mutation	SNP	T	TCGA-BQ-5884-01A-11D-1589-08	10505886	43088537	92446210	27	7567											
IFIT5	24138	hgsc.bcm.edu	37	chr10	91178386	91178387	+	Frame_Shift_Ins	INS	-	-	GCTC																															ttcctgactgctctctgtgaINSgctccgactttccatttaaa																										TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr10:91178386_91178387insGCTC	ENST00000371795.4	+	2	1643_1644	c.1430_1431insGCTC	c.(1429-1434)gagctcfs	p.-478fs	IFIT5_ENST00000416601.1_Frame_Shift_Ins_p.-430fs	NM_012420.2	NP_036552.1	Q13325	IFIT5_HUMAN	interferon-induced protein with tetratricopeptide repeats 5						defense response to virus (GO:0051607)|innate immune response (GO:0045087)	actin cytoskeleton (GO:0015629)|apical part of cell (GO:0045177)|ruffle membrane (GO:0032587)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)|tRNA binding (GO:0000049)			endometrium(1)|large_intestine(4)|lung(4)	9						GCTCTCTGTGAGCTCCGACTTT	0.371																																					p.E477fs		Atlas-INDEL	.											.	IFIT5	32	.	0			c.1430_1431insGCTC						PASS	.																																			SO:0001589	frameshift_variant	24138	exon2			.	U34605	CCDS7403.1	10q23.31	2013-01-10			ENSG00000152778	ENSG00000152778		"Tetratricopeptide (TTC) repeat domain containing"	13328	protein-coding gene	gene with protein product	"retinoic acid- and interferon-inducible protein (58kD)"					9398535	Standard	NM_012420		Approved	RI58	uc010qnh.2	Q13325	OTTHUMG00000018713	ENST00000371795.4:c.1431_1434dupGCTC	chr10.hg19:g.91178387_91178390dupGCTC	ENSP00000360860:p.Leu478fs	127.0	0.0	0		113.0	11.0	0.0973451	NM_012420	B2R5X9|B4DDV1|Q5T7I9|Q6IAX3	Frame_Shift_Ins	INS	ENST00000371795.4	hg19	CCDS7403.1																																																																																			.	.	.	none		0.371	IFIT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049303.1	NM_012420		GCTC	91178387	-	GCTC	91178386	7	5	119	1	0	1	1	0	0	0	0	0	7532	304	11	0	1436	0	IFIT5	10	91178386	Frame_Shift_Ins	INS	-	TCGA-BQ-5884-01A-11D-1589-08	48089849	91178386	44356361	28	7568											
SLC39A5	283375	hgsc.bcm.edu	37	chr12	56630209	56630209	+	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	aggcgaaaacgaaggaatctCgaaacacgcaacttggatcc	16	5	10	10	4	1	0	0	0	1	0	3	5	2	2	1	3	3	1	1	3	6	1	rs139155884	byFrequency	TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr12:56630209C>G	ENST00000266980.4	+	7	1268	c.975C>G	c.(973-975)ctC>ctG	p.L325L	ANKRD52_ENST00000548241.1_5'Flank|SLC39A5_ENST00000454355.2_Silent_p.L325L	NM_001135195.1	NP_001128667.1	Q6ZMH5	S39A5_HUMAN	solute carrier family 39 (zinc transporter), member 5	325					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						GAAGGAATCTCGAAACACGCA	0.557																																					p.L325L		Atlas-SNP	.											.	SLC39A5	52	.	0			c.C975G						PASS	.						134	129	131					12																	56630209		2203	4300	6503	SO:0001819	synonymous_variant	283375	exon9			GAATCTCGAAACA		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.975C>G	chr12.hg19:g.56630209C>G		86.0	0.0	.		100.0	27.0	.	NM_173596	B2R808|Q8N6Y3	Silent	SNP	ENST00000266980.4	hg19	CCDS8912.2																																																																																			.	C|0.999;T|0.001	.	alt		0.557	SLC39A5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346834.1	NM_173596		G	56630209	C	G	56630209	2	3	119	1	0	0	0	0	0	0	0	1	14634	871	31	4		4	SLC39A5	12	56630209	Silent	SNP	C	TCGA-BQ-5884-01A-11D-1589-08		56630209	77221686	29	7569											
STAT2	6773	hgsc.bcm.edu	37	chr12	56742947	56742947	+	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	tgtcggccccactcccctacCtgaaggtttgggctgagcaa	7	9	11	14	1	0	2	0	2	0	0	2	2	1	2	5	3	2	3	5	3	3	2			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr12:56742947C>T	ENST00000314128.4	-	16	1463	c.1440G>A	c.(1438-1440)caG>caA	p.Q480Q	STAT2_ENST00000557235.1_Splice_Site_p.Q476Q|STAT2_ENST00000556539.1_5'UTR|STAT2_ENST00000418572.2_Intron			P52630	STAT2_HUMAN	signal transducer and activator of transcription 2, 113kDa	480					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						ACTCCCCTACCTGAAGGTTTG	0.562																																					p.Q480Q		Atlas-SNP	.											.	STAT2	70	.	0			c.G1440A						PASS	.						93	93	93					12																	56742947		2203	4300	6503	SO:0001630	splice_region_variant	6773	exon16			CCCTACCTGAAGG	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.1440+1G>A	chr12.hg19:g.56742947C>T		165.0	0.0	.		160.0	41.0	.	NM_005419	B4DLC7|G3V2M6|Q16430|Q16431|Q9UDL4	Silent	SNP	ENST00000314128.4	hg19	CCDS8917.1																																																																																			.	.	.	none		0.562	STAT2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410277.1	NM_005419	Silent	T	56742947	C	T	56742947	5	4	119	1	0	0	0	0	0	0	1	0	15277	695	24	2	1151	2	STAT2	12	56742947	Splice_Site	SNP	C	TCGA-BQ-5884-01A-11D-1589-08	112738	56742947	77108948	30	7570											
DENR	8562	hgsc.bcm.edu	37	chr12	123253468	123253468	+	Splice_Site	DEL	G	G	-																															attcaggaaaaatggccagaGgtgagtgcatggaacacata																										TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr12:123253468delG	ENST00000280557.6	+	7	738	c.552delG	c.(550-552)gag>ga	p.E184fs	DENR_ENST00000455982.2_Intron|Y_RNA_ENST00000384187.1_RNA	NM_003677.3	NP_003668.2	O43583	DENR_HUMAN	density-regulated protein	184					formation of translation preinitiation complex (GO:0001731)|IRES-dependent translational initiation (GO:0002192)|ribosome disassembly (GO:0032790)		translation initiation factor activity (GO:0003743)			kidney(1)|large_intestine(1)|urinary_tract(1)	3	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.28e-05)|Epithelial(86;6.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.199)		AATGGCCAGAGGTGAGTGCAT	0.363																																					p.E184fs		Atlas-INDEL	.											.	DENR	8	.	0			c.551delA						PASS	.						70	67	68					12																	123253468		1874	4097	5971	SO:0001630	splice_region_variant	8562	exon7			.	AF038554	CCDS45003.1	12q24.31	1999-06-17			ENSG00000139726	ENSG00000139726			2769	protein-coding gene	gene with protein product		604550				9628587	Standard	NM_003677		Approved	DRP, DRP1, SMAP-3	uc001uda.3	O43583	OTTHUMG00000168844	ENST00000280557.6:c.552+1G>-	chr12.hg19:g.123253468delG		60.0	0.0	0		54.0	16.0	0.296296	NM_003677	Q9H3U6|Q9UKZ0	Frame_Shift_Del	DEL	ENST00000280557.6	hg19	CCDS45003.1																																																																																			.	.	.	none		0.363	DENR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401336.1	NM_003677	Frame_Shift_Del	-	123253468	G	-	123253468	8	5	119	1	0	1	0	1	0	0	1	0	4440	1014	35	0	574	0	DENR	12	123253468	Splice_Site	DEL	G	TCGA-BQ-5884-01A-11D-1589-08	66510521	123253468	10598427	31	7571											
FREM2	341640	hgsc.bcm.edu	37	chr13	39265553	39265553	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tattacagagacgaaaacctActggtgcctttgaaaatatc	15	11	7	8	1	0	2	0	1	0	1	1	4	0	2	2	1	4	0	2	1	8	5			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr13:39265553A>G	ENST00000280481.7	+	1	4288	c.4072A>G	c.(4072-4074)Act>Gct	p.T1358A		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1358					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)		ACGAAAACCTACTGGTGCCTT	0.383																																					p.T1358A		Atlas-SNP	.											.	FREM2	385	.	0			c.A4072G						PASS	.						64	65	64					13																	39265553		2203	4300	6503	SO:0001583	missense	341640	exon1			AAACCTACTGGTG	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.4072A>G	chr13.hg19:g.39265553A>G	ENSP00000280481:p.Thr1358Ala	97.0	0.0	.		98.0	23.0	.	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	hg19	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	A	0.011	-1.720360	0.00700	.	.	ENSG00000150893	ENST00000280481	T	0.40756	1.02	5.81	-0.554	0.11811	.	1.289890	0.04720	N	0.419174	T	0.13927	0.0337	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.19063	-1.0317	10	0.08837	T	0.75	.	1.7548	0.02980	0.3096:0.2411:0.3249:0.1243	.	1358	Q5SZK8	FREM2_HUMAN	A	1358	ENSP00000280481:T1358A	ENSP00000280481:T1358A	T	+	1	0	FREM2	38163553	0.000000	0.05858	0.001000	0.08648	0.731000	0.41821	0.004000	0.13106	0.122000	0.18314	0.533000	0.62120	ACT	.	.	.	none		0.383	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		G	39265553	A	G	39265553	3	3	119	1	0	0	0	0	1	0	0	0	6052	391	14	3	4074	3	FREM2	13	39265553	Missense_Mutation	SNP	A	TCGA-BQ-5884-01A-11D-1589-08		39265553	75904325	32	7572											
MLNR	2862	hgsc.bcm.edu	37	chr13	49796387	49796387	+	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	gcggcctttaaactgctgctCgcaaggaagtccaggccgag	9	7	13	12	3	0	0	0	0	0	0	2	2	1	1	3	3	3	3	3	3	4	2			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr13:49796387C>G	ENST00000218721.1	+	2	1113	c.1113C>G	c.(1111-1113)ctC>ctG	p.L371L	MLNR_ENST00000398307.1_3'UTR	NM_001507.1	NP_001498.1	O43193	MTLR_HUMAN	motilin receptor	371					digestion (GO:0007586)|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)|growth hormone-releasing hormone receptor activity (GO:0016520)			endometrium(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)	14		all_lung(13;8.31e-06)|Lung NSC(96;0.000251)|Breast(56;0.0008)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;6.1e-09)		AACTGCTGCTCGCAAGGAAGT	0.547																																					p.L371L		Atlas-SNP	.											MLNR,NS,carcinoma,0,1	MLNR	26	.	0			c.C1113G						PASS	.						81	81	81					13																	49796387		2203	4300	6503	SO:0001819	synonymous_variant	2862	exon2			GCTGCTCGCAAGG	AF034632	CCDS9414.1	13q14-q21	2012-08-08	2004-05-27	2004-05-28	ENSG00000102539	ENSG00000102539		"GPCR / Class A : Motilin receptors"	4495	protein-coding gene	gene with protein product		602885	"G protein-coupled receptor 38"	GPR38		9441746	Standard	NM_001507		Approved		uc010tgj.2	O43193	OTTHUMG00000016909	ENST00000218721.1:c.1113C>G	chr13.hg19:g.49796387C>G		119.0	1.0	.		85.0	24.0	.	NM_001507		Silent	SNP	ENST00000218721.1	hg19	CCDS9414.1																																																																																			.	.	.	none		0.547	MLNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044897.1	NM_001507		G	49796387	C	G	49796387	2	3	119	1	0	0	0	0	0	0	0	1	9639	871	31	4		4	MLNR	13	49796387	Silent	SNP	C	TCGA-BQ-5884-01A-11D-1589-08	10530834	49796387	65373491	33	7573											
TSC2	7249	hgsc.bcm.edu	37	chr16	2122849	2122849	+	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	atgcctggatttggtcatcaGctttcaggcccaaagacact	10	11	9	11	0	3	1	3	0	0	1	3	2	3	2	2	3	2	1	2	3	1	2	rs45517218		TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr16:2122849G>A	ENST00000219476.3	+	21	2850		c.e21-1		TSC2_ENST00000353929.4_Splice_Site|TSC2_ENST00000568454.1_Splice_Site|TSC2_ENST00000439673.2_Splice_Site|TSC2_ENST00000350773.4_Splice_Site|TSC2_ENST00000382538.6_Splice_Site|TSC2_ENST00000401874.2_Splice_Site	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)				TTGGTCATCAGCTTTCAGGCC	0.627			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												.		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	TSC2_ENST00000219476,colon,carcinoma,0,2	TSC2	364	.	0			c.2221-1G>A						PASS	.						53	58	56					16																	2122849		2198	4300	6498	SO:0001630	splice_region_variant	7249	exon21	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	TCATCAGCTTTCA	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.2221-1G>A	chr16.hg19:g.2122849G>A		102.0	0.0	.		60.0	29.0	.	NM_000548	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Splice_Site	SNP	ENST00000219476.3	hg19	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	G	13.55	2.269512	0.40095	.	.	ENSG00000103197	ENST00000219476;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000382538;ENST00000350773	.	.	.	5.46	5.46	0.80206	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.3044	0.94155	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TSC2	2062850	1.000000	0.71417	0.996000	0.52242	0.714000	0.41099	7.284000	0.78650	2.551000	0.86045	0.655000	0.94253	.	.	.	.	alt		0.627	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548	Intron	A	2122849	G	A	2122849	5	1	119	1	0	0	0	0	0	0	1	0	16618	985	34	2	2298	2	TSC2	16	2122849	Splice_Site	SNP	G	TCGA-BQ-5884-01A-11D-1589-08		2122849	88231904	34	7574											
NLRC3	197358	hgsc.bcm.edu	37	chr16	3598164	3598164	+	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	gtgaggctcctgttgagctgTagtgcttgtcccagggcctg	4	12	15	10	0	0	2	0	2	0	0	2	2	2	2	3	2	2	5	3	2	1	3			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr16:3598164T>C	ENST00000301749.7	-	0	3147				NLRC3_ENST00000603507.1_RNA|LA16c-390H2.4_ENST00000573820.1_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000359128.5_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						TGTTGAGCTGTAGTGCTTGTC	0.587																																					p.L914L		Atlas-SNP	.											.	NLRC3	103	.	0			c.A2742G						PASS	.						33	35	34					16																	3598164		1962	4132	6094			197358	exon16			GAGCTGTAGTGCT	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		chr16.hg19:g.3598164T>C		10.0	0.0	.		9.0	8.0	.	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Silent	SNP	ENST00000301749.7	hg19																																																																																				.	.	.	none		0.587	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844		C	3598164	T	C	3598164	1	2	119	0	1	0	0	0	0	0	0	0	10475	1625	57	3		3	NLRC3	16	3598164	RNA	SNP	T	TCGA-BQ-5884-01A-11D-1589-08	1475315	3598164	86756589	35	7575											
NOS2	4843	hgsc.bcm.edu	37	chr17	26107895	26107895	+	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	ccagggggaccacatcgaagCggccgtacttgggcttccag	8	6	14	13	3	0	0	0	0	0	0	2	2	1	1	4	4	2	2	4	4	2	3	rs200678947		TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr17:26107895C>A	ENST00000313735.6	-	9	1135	c.902G>T	c.(901-903)cGc>cTc	p.R301L		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	301					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)	CACATCGAAGCGGCCGTACTT	0.627																																					p.R301L		Atlas-SNP	.											NOS2,NS,carcinoma,0,1	NOS2	113	.	0			c.G902T						PASS	.						58	54	56					17																	26107895		2203	4300	6503	SO:0001583	missense	4843	exon9			TCGAAGCGGCCGT	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.902G>T	chr17.hg19:g.26107895C>A	ENSP00000327251:p.Arg301Leu	65.0	0.0	.		66.0	3.0	.	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Missense_Mutation	SNP	ENST00000313735.6	hg19	CCDS11223.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.545019	0.86022	.	.	ENSG00000007171	ENST00000313735;ENST00000302153	T	0.23147	1.92	5.33	5.33	0.75918	Nitric oxide synthase, oxygenase domain (2);	0.000000	0.85682	D	0.000000	T	0.30947	0.0781	M	0.70903	2.155	0.80722	D	1	P;B	0.35628	0.513;0.012	B;B	0.30251	0.113;0.015	T	0.17745	-1.0359	10	0.56958	D	0.05	.	18.0142	0.89233	0.0:1.0:0.0:0.0	.	301;301	F8WEM3;P35228	.;NOS2_HUMAN	L	301	ENSP00000327251:R301L	ENSP00000305638:R301L	R	-	2	0	NOS2	23132022	1.000000	0.71417	1.000000	0.80357	0.373000	0.29922	4.831000	0.62752	2.465000	0.83290	0.655000	0.94253	CGC	.	.	.	alt		0.627	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625		A	26107895	C	A	26107895	3	1	119	1	0	0	0	0	1	0	0	0	10550	768	27	4	2635	4	NOS2	17	26107895	Missense_Mutation	SNP	C	TCGA-BQ-5884-01A-11D-1589-08		26107895	55087315	36	7576											
SLC38A10	124565	hgsc.bcm.edu	37	chr17	79220316	79220316	+	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	tcagagtgctccagggagcgCtggttaaggtcctgggatgg	7	9	17	8	1	1	1	1	0	0	1	3	3	3	3	2	5	2	3	2	5	1	1			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr17:79220316C>T	ENST00000374759.3	-	16	2783	c.2400G>A	c.(2398-2400)caG>caA	p.Q800Q		NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	800					amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			CCAGGGAGCGCTGGTTAAGGT	0.682																																					p.Q800Q		Atlas-SNP	.											.	SLC38A10	133	.	0			c.G2400A						PASS	.						18	20	19					17																	79220316		1869	4067	5936	SO:0001819	synonymous_variant	124565	exon16			GGAGCGCTGGTTA	BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637		"Solute carriers"	28237	protein-coding gene	gene with protein product							Standard	XM_005257019		Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.2400G>A	chr17.hg19:g.79220316C>T		53.0	0.0	.		45.0	13.0	.	NM_001037984	Q6ZRC5|Q8NA99|Q96C66	Silent	SNP	ENST00000374759.3	hg19	CCDS42397.1																																																																																			.	.	.	none		0.682	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	NM_138570		T	79220316	C	T	79220316	2	4	119	1	0	0	0	0	0	0	0	1	14615	796	28	2		2	SLC38A10	17	79220316	Silent	SNP	C	TCGA-BQ-5884-01A-11D-1589-08	53112421	79220316	1974894	37	7577											
ZNF532	55205	hgsc.bcm.edu	37	chr18	56587630	56587630	+	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	tacttccacttcaacttccaCtcttcagagccctgtgggag	8	12	7	14	0	3	1	2	0	1	1	5	2	5	2	3	1	3	0	3	1	2	5			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr18:56587630C>T	ENST00000336078.4	+	4	2887	c.2111C>T	c.(2110-2112)aCt>aTt	p.T704I	ZNF532_ENST00000591230.1_Missense_Mutation_p.T704I|ZNF532_ENST00000589288.1_Missense_Mutation_p.T704I|ZNF532_ENST00000591083.1_Missense_Mutation_p.T704I|ZNF532_ENST00000591808.1_Missense_Mutation_p.T704I	NM_018181.4	NP_060651.2	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	704					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						TCAACTTCCACTCTTCAGAGC	0.473																																					p.T704I		Atlas-SNP	.											.	ZNF532	108	.	0			c.C2111T						PASS	.						63	67	65					18																	56587630		2203	4300	6503	SO:0001583	missense	55205	exon4			CTTCCACTCTTCA	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.2111C>T	chr18.hg19:g.56587630C>T	ENSP00000338217:p.Thr704Ile	74.0	0.0	.		80.0	18.0	.	NM_018181	Q4G0V6|Q7L7Z7|Q96QR7|Q9NVJ6	Missense_Mutation	SNP	ENST00000336078.4	hg19	CCDS11969.1	.	.	.	.	.	.	.	.	.	.	c	2.772	-0.255447	0.05829	.	.	ENSG00000074657	ENST00000336078	T	0.32515	1.45	5.43	4.55	0.56014	.	0.394325	0.27526	N	0.018974	T	0.17023	0.0409	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.13845	-1.0494	10	0.35671	T	0.21	-5.4027	8.1333	0.31039	0.0:0.7358:0.1536:0.1107	.	704	Q9HCE3	ZN532_HUMAN	I	704	ENSP00000338217:T704I	ENSP00000338217:T704I	T	+	2	0	ZNF532	54738610	0.026000	0.19158	0.014000	0.15608	0.567000	0.35839	2.740000	0.47418	1.298000	0.44778	0.544000	0.68410	ACT	.	.	.	none		0.473	ZNF532-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256130.1	NM_018181		T	56587630	C	T	56587630	3	4	119	1	0	0	0	0	1	0	0	0	17984	565	20	2	2113	2	ZNF532	18	56587630	Missense_Mutation	SNP	C	TCGA-BQ-5884-01A-11D-1589-08		56587630	21489618	38	7578											
ZNF57	126295	hgsc.bcm.edu	37	chr19	2916127	2916127	+	Missense_Mutation	SNP	A	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	agtttctctgcaggatatgtAcgggcaagaaaaatctaagg	14	10	11	6	1	2	1	0	0	2	1	3	2	2	2	0	3	2	4	0	3	6	4			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr19:2916127A>C	ENST00000306908.5	+	3	330	c.182A>C	c.(181-183)tAc>tCc	p.Y61S	ZNF57_ENST00000523428.1_Missense_Mutation_p.Y29S|AC006277.2_ENST00000520090.2_RNA	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	61	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)|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)		CAGGATATGTACGGGCAAGAA	0.363																																					p.Y61S	NSCLC(150;910 1964 4303 10464 26498)	Atlas-SNP	.											.	ZNF57	57	.	0			c.A182C						PASS	.						125	111	116					19																	2916127		2203	4300	6503	SO:0001583	missense	126295	exon3			ATATGTACGGGCA	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.182A>C	chr19.hg19:g.2916127A>C	ENSP00000303696:p.Tyr61Ser	113.0	0.0	.		96.0	4.0	.	NM_173480	Q8N6R9	Missense_Mutation	SNP	ENST00000306908.5	hg19	CCDS12098.1	.	.	.	.	.	.	.	.	.	.	A	6.519	0.463953	0.12402	.	.	ENSG00000171970	ENST00000306908;ENST00000395204;ENST00000522294;ENST00000523428	T;T;T	0.05258	3.58;6.04;3.47	1.38	1.38	0.22167	Krueppel-associated box (2);	.	.	.	.	T	0.02610	0.0079	N	0.12569	0.235	0.09310	N	1	B	0.33494	0.414	B	0.18263	0.021	T	0.45041	-0.9288	9	0.20519	T	0.43	.	4.9023	0.13781	1.0:0.0:0.0:0.0	.	61	Q68EA5	ZNF57_HUMAN	S	61;61;29;29	ENSP00000303696:Y61S;ENSP00000430905:Y29S;ENSP00000430223:Y29S	ENSP00000303696:Y61S	Y	+	2	0	ZNF57	2867127	0.000000	0.05858	0.001000	0.08648	0.026000	0.11368	-1.333000	0.02667	0.877000	0.35895	0.486000	0.48141	TAC	.	.	.	none		0.363	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480		C	2916127	A	C	2916127	3	2	119	1	0	0	0	0	1	0	0	0	18013	391	14	5	192	5	ZNF57	19	2916127	Missense_Mutation	SNP	A	TCGA-BQ-5884-01A-11D-1589-08		2916127	56212856	39	7579											
HNRNPUL1	11100	hgsc.bcm.edu	37	chr19	41800265	41800265	+	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	tctgatgatggtgggcctgcCtgctgctggcaagaccacat	7	10	13	11	0	1	3	0	2	1	1	1	3	1	3	3	3	3	3	3	3	1	0			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr19:41800265C>G	ENST00000392006.3	+	9	1462	c.1289C>G	c.(1288-1290)cCt>cGt	p.P430R	HNRNPUL1_ENST00000593587.1_Missense_Mutation_p.P330R|HNRNPUL1_ENST00000602130.1_Missense_Mutation_p.P430R|HNRNPUL1_ENST00000595018.1_Missense_Mutation_p.P330R|HNRNPUL1_ENST00000378215.4_Missense_Mutation_p.P316R|HNRNPUL1_ENST00000352456.3_Missense_Mutation_p.P330R|HNRNPUL1_ENST00000263367.3_Missense_Mutation_p.P341R	NM_007040.3	NP_008971.2	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1	430	Necessary for interaction with TP53.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	29						GTGGGCCTGCCTGCTGCTGGC	0.537																																					p.P430R		Atlas-SNP	.											.	HNRNPUL1	73	.	0			c.C1289G						PASS	.						166	120	135					19																	41800265		2203	4300	6503	SO:0001583	missense	11100	exon9			GCCTGCCTGCTGC	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.1289C>G	chr19.hg19:g.41800265C>G	ENSP00000375863:p.Pro430Arg	89.0	0.0	.		69.0	15.0	.	NM_007040	B3KMW7|O76022|Q6ZSZ0|Q7L8P4|Q8N6Z4|Q96G37|Q9HAL3|Q9UG75	Missense_Mutation	SNP	ENST00000392006.3	hg19	CCDS12576.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.717475	0.89205	.	.	ENSG00000105323	ENST00000352456;ENST00000392006;ENST00000378215;ENST00000263367	T;T;T;T	0.54479	0.57;0.57;0.57;0.57	5.46	5.46	0.80206	.	0.105015	0.64402	D	0.000003	T	0.78685	0.4322	M	0.90425	3.115	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.973;1.0;1.0	D;D;D;P;D;D	0.97110	0.999;0.999;0.999;0.816;1.0;0.999	T	0.82489	-0.0432	10	0.87932	D	0	-7.8178	18.2528	0.90009	0.0:1.0:0.0:0.0	.	341;330;430;316;430;330	B7Z4B8;A8K3W4;Q9BUJ2-2;Q9BUJ2-3;Q9BUJ2;Q9BUJ2-4	.;.;.;.;HNRL1_HUMAN;.	R	330;430;316;341	ENSP00000340857:P330R;ENSP00000375863:P430R;ENSP00000367460:P316R;ENSP00000263367:P341R	ENSP00000263367:P341R	P	+	2	0	HNRNPUL1	46492105	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.557000	0.82243	2.840000	0.97914	0.655000	0.94253	CCT	.	.	.	none		0.537	HNRNPUL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463406.1	NM_144732, NM_007040		G	41800265	C	G	41800265	3	3	119	1	0	0	0	0	1	0	0	0	7281	681	24	4	1323	4	HNRNPUL1	19	41800265	Missense_Mutation	SNP	C	TCGA-BQ-5884-01A-11D-1589-08	38884138	41800265	17328718	40	7580											
ZFP64	55734	hgsc.bcm.edu	37	chr20	50769885	50769885	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacttgaaaggcttctccccCgagtgcacccgcatgtgcct	7	9	9	16	2	1	1	0	1	1	0	2	2	1	1	4	1	2	3	4	1	1	2			TCGA-BQ-5884-01A-11D-1589-08	TCGA-BQ-5884-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f2fe918-229b-4e08-a866-96bb1c6fc7d9	9f67477d-e1e3-4aa5-9789-db50e9359ddd	g.chr20:50769885C>T	ENST00000216923.4	-	6	1195	c.846G>A	c.(844-846)tcG>tcA	p.S282S	ZFP64_ENST00000477786.1_Intron|ZFP64_ENST00000361387.2_Intron|ZFP64_ENST00000371518.2_Intron|ZFP64_ENST00000371515.4_Silent_p.S280S|ZFP64_ENST00000346617.4_Silent_p.S228S	NM_018197.2|NM_199426.1	NP_060667.2|NP_955458.1	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	282					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						GCTTCTCCCCCGAGTGCACCC	0.552																																					p.S282S		Atlas-SNP	.											.	ZFP64	240	.	0			c.G846A						PASS	.						80	72	75					20																	50769885		2203	4300	6503	SO:0001819	synonymous_variant	55734	exon6			CTCCCCCGAGTGC	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"Zinc fingers, C2H2-type"	15940	protein-coding gene	gene with protein product			"zinc finger protein 338", "zinc finger protein 64 homolog (mouse)", "zinc finger protein 64"	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000216923.4:c.846G>A	chr20.hg19:g.50769885C>T		75.0	0.0	.		46.0	16.0	.	NM_018197	Q9NTS7|Q9NVH4	Silent	SNP	ENST00000216923.4	hg19	CCDS13440.1																																																																																			.	.	.	none		0.552	ZFP64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079744.1	NM_018197		T	50769885	C	T	50769885	2	4	119	1	0	0	0	0	0	0	0	1	17664	639	23	1		1	ZFP64	20	50769885	Silent	SNP	C	TCGA-BQ-5884-01A-11D-1589-08		50769885	12255635	41	7581											
FMO4	2329	hgsc.bcm.edu	37	chr1	171303821	171303822	+	Missense_Mutation	DNP	AT	AT	GC																															tagagagagcgacattagccAtcatcggccttatcggcctt																										TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A|T	A|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr1:171303821_171303822AT>GC	ENST00000367749.3	+	8	1429_1430	c.1099_1100AT>GC	c.(1099-1101)ATc>GCc	p.I367A		NM_002022.1	NP_002013.1	P31512	FMO4_HUMAN	flavin containing monooxygenase 4	367					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)					GACATTAGCCATCATCGGCCTT	0.411																																					p.I367V|p.I367T	Pancreas(24;816 862 7754 7993 32832)	Atlas-SNP	.											.	FMO4	64	.	0			c.A1099G|c.T1100C						PASS	.																																			SO:0001583	missense	2329	exon8			TTAGCCATCATCG|TAGCCATCATCGG	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	Exception_encountered	chr1.hg19:g.171303821_171303822delinsGC	ENSP00000356723:p.Ile367Ala	176.0|171.0	0.0	.		138.0|136.0	43.0	.	NM_002022	Q53XR0	Missense_Mutation	SNP	ENST00000367749.3	hg19	CCDS1295.1																																																																																			.	.	.	none		0.411	FMO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086223.1	NM_002022		GC	171303822	AT	GC	171303821	3	3	120	1	0	0	0	0	1	0	0	0	5964	217	8	3	1121	3	FMO4	1	171303821	Missense_Mutation	DNP	AT	TCGA-BQ-5885-01A-11D-1589-08		171303821	77946800	1	7582											
HEATR1	55127	hgsc.bcm.edu	37	chr1	236738095	236738095	+	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	tgaaaattcattatactttcCcagagtgagatgcagaacca	15	11	7	8	0	1	4	1	2	0	3	2	5	2	4	2	0	3	1	2	0	5	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr1:236738095C>T	ENST00000366582.3	-	23	3307	c.3193G>A	c.(3193-3195)Gga>Aga	p.G1065R	HEATR1_ENST00000366581.2_Intron	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	1065					rRNA processing (GO:0006364)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(18)|lung(28)|ovary(3)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	87	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			TTATACTTTCCCAGAGTGAGA	0.423																																					p.G1065R		Atlas-SNP	.											.	HEATR1	197	.	0			c.G3193A						PASS	.						72	72	72					1																	236738095		2203	4300	6503	SO:0001583	missense	55127	exon23			ACTTTCCCAGAGT	BC065205	CCDS31066.1	1q43	2011-08-12			ENSG00000119285	ENSG00000119285			25517	protein-coding gene	gene with protein product	"UTP10, small subunit (SSU) processome component, homolog (yeast)"					17699751	Standard	NM_018072		Approved	FLJ10359, BAP28, UTP10	uc001hyd.2	Q9H583	OTTHUMG00000040061	ENST00000366582.3:c.3193G>A	chr1.hg19:g.236738095C>T	ENSP00000355541:p.Gly1065Arg	117.0	0.0	.		108.0	43.0	.	NM_018072	Q5T3Q8|Q6P197|Q9NW23	Missense_Mutation	SNP	ENST00000366582.3	hg19	CCDS31066.1	.	.	.	.	.	.	.	.	.	.	C	18.60	3.659073	0.67586	.	.	ENSG00000119285	ENST00000366582	T	0.66099	-0.19	5.73	5.73	0.89815	Armadillo-type fold (2);	0.167388	0.52532	D	0.000065	T	0.65059	0.2655	M	0.62723	1.935	0.80722	D	1	P	0.42735	0.788	B	0.42495	0.389	T	0.62334	-0.6876	10	0.28530	T	0.3	.	19.904	0.97001	0.0:1.0:0.0:0.0	.	1065	Q9H583	HEAT1_HUMAN	R	1065	ENSP00000355541:G1065R	ENSP00000355541:G1065R	G	-	1	0	HEATR1	234804718	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	2.615000	0.46368	2.689000	0.91719	0.655000	0.94253	GGA	.	.	.	none		0.423	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853		T	236738095	C	T	236738095	3	4	120	1	0	0	0	0	1	0	0	0	7034	632	22	2	3333	2	HEATR1	1	236738095	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	65434274	236738095	12512526	2	7583											
HEATR1	55127	hgsc.bcm.edu	37	chr1	236749736	236749736	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aattaatatgtcagcggctaTcttaagtacctcgtacctaa	13	13	6	9	2	2	0	1	0	1	0	3	0	2	0	2	1	3	3	2	1	8	7			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr1:236749736T>C	ENST00000366582.3	-	15	1846	c.1732A>G	c.(1732-1734)Ata>Gta	p.I578V	HEATR1_ENST00000366581.2_Missense_Mutation_p.I578V	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	578					rRNA processing (GO:0006364)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(18)|lung(28)|ovary(3)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	87	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			TCAGCGGCTATCTTAAGTACC	0.368																																					p.I578V		Atlas-SNP	.											.	HEATR1	197	.	0			c.A1732G						PASS	.																																			SO:0001583	missense	55127	exon15			CGGCTATCTTAAG	BC065205	CCDS31066.1	1q43	2011-08-12			ENSG00000119285	ENSG00000119285			25517	protein-coding gene	gene with protein product	"UTP10, small subunit (SSU) processome component, homolog (yeast)"					17699751	Standard	NM_018072		Approved	FLJ10359, BAP28, UTP10	uc001hyd.2	Q9H583	OTTHUMG00000040061	ENST00000366582.3:c.1732A>G	chr1.hg19:g.236749736T>C	ENSP00000355541:p.Ile578Val	170.0	0.0	.		156.0	50.0	.	NM_018072	Q5T3Q8|Q6P197|Q9NW23	Missense_Mutation	SNP	ENST00000366582.3	hg19	CCDS31066.1	.	.	.	.	.	.	.	.	.	.	T	0.008	-1.926731	0.00493	.	.	ENSG00000119285	ENST00000366582;ENST00000366581	T;T	0.42900	0.96;0.96	5.28	-2.98	0.05513	Armadillo-like helical (1);Armadillo-type fold (1);	0.667620	0.15450	N	0.261734	T	0.13157	0.0319	N	0.03115	-0.41	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.13019	-1.0525	10	0.26408	T	0.33	.	1.7301	0.02930	0.1285:0.3195:0.2162:0.3358	.	578	Q9H583	HEAT1_HUMAN	V	578	ENSP00000355541:I578V;ENSP00000355540:I578V	ENSP00000355540:I578V	I	-	1	0	HEATR1	234816359	0.001000	0.12720	0.931000	0.37212	0.129000	0.20672	-0.294000	0.08309	-0.174000	0.10743	0.460000	0.39030	ATA	.	.	.	none		0.368	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853		C	236749736	T	C	236749736	3	2	120	1	0	0	0	0	1	0	0	0	7034	1435	50	3	4826	3	HEATR1	1	236749736	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	11641	236749736	12500885	3	7584											
CAD	51374	hgsc.bcm.edu	37	chr2	27440797	27440797	+	IGR	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	gccctcaccgatccctcctaCaaggcacagatcttagtgct	9	9	7	16	1	2	1	1	0	1	1	4	2	4	1	4	1	2	2	4	1	3	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:27440797C>A	ENST00000606999.1	+	0	956				CAD_ENST00000264705.4_Nonsense_Mutation_p.Y45*|CAD_ENST00000403525.1_Nonsense_Mutation_p.Y45*	NM_001170795.1	NP_001164266.1	Q6UW56	ARAID_HUMAN	all-trans retinoic acid-induced differentiation factor						cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)											ATCCCTCCTACAAGGCACAGA	0.572																																					p.Y45X		Atlas-SNP	.											.	CAD	199	.	0			c.C135A						PASS	.						124	115	118					2																	27440797		2203	4300	6503	SO:0001628	intergenic_variant	790	exon2			CTCCTACAAGGCA	BC021237	CCDS1741.1, CCDS46243.1, CCDS62877.1	2p23.3	2012-08-01	2012-07-30	2012-07-30	ENSG00000138085	ENSG00000138085			24090	protein-coding gene	gene with protein product	"apoptosis-related protein 3"		"chromosome 2 open reading frame 28"	C2orf28		17524364, 21723284	Standard	NM_016085		Approved	HSPC013, p18, APR3	uc002rjf.3	Q6UW56	OTTHUMG00000128405		chr2.hg19:g.27440797C>A		189.0	0.0	.		143.0	54.0	.	NM_004341	A8C1S2|A8K779|Q96FF6|Q96RT2|Q9Y2R7|Q9Y5L7	Nonsense_Mutation	SNP	ENST00000606999.1	hg19		.	.	.	.	.	.	.	.	.	.	C	31	5.075282	0.94000	.	.	ENSG00000084774	ENST00000264705;ENST00000403525	.	.	.	5.05	4.17	0.49024	.	0.070247	0.64402	D	0.000015	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.0623	12.2333	0.54500	0.0:0.917:0.0:0.083	.	.	.	.	X	45	.	ENSP00000264705:Y45X	Y	+	3	2	CAD	27294301	1.000000	0.71417	1.000000	0.80357	0.725000	0.41563	2.602000	0.46257	1.351000	0.45789	0.484000	0.47621	TAC	.	.	.	none		0.572	ATRAID-007	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470709.1	NM_016085		A	27440797	C	A	27440797	1	1	120	0	1	0	0	0	0	0	0	0	2567	489	17	4		4	CAD	2	27440797	IGR	SNP	C	TCGA-BQ-5885-01A-11D-1589-08		27440797	215758576	4	7585											
RTN4	57142	hgsc.bcm.edu	37	chr2	55253513	55253514	+	Missense_Mutation	DNP	TT	TT	AG																															tgaaccaagtccatttttgtTtcataagcaatctttgtacc																										TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:55253513_55253514TT>AG	ENST00000337526.6	-	3	1964_1965	c.1721_1722AA>CT	c.(1720-1722)gAA>gCT	p.E574A	RTN4_ENST00000357732.4_Intron|RTN4_ENST00000405240.1_Missense_Mutation_p.E368A|RTN4_ENST00000404909.1_Missense_Mutation_p.E368A|RTN4_ENST00000394611.2_Missense_Mutation_p.E368A|RTN4_ENST00000354474.6_Missense_Mutation_p.E342A|RTN4_ENST00000317610.7_Intron|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000357376.3_Missense_Mutation_p.E368A	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN	reticulon 4	574					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						CCATTTTTGTTTCATAAGCAAT	0.416																																					p.E574D|p.E574A		Atlas-SNP	.											.	RTN4	189	.	0			c.A1722T|c.A1721C						PASS	.																																			SO:0001583	missense	57142	exon3			TTTTGTTTCATAA|TTTGTTTCATAAG	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.1721_1722delinsAG	chr2.hg19:g.55253513_55253514delinsAG	ENSP00000337838:p.Glu574Ala	165.0	0.0	.		130.0|132.0	32.0|33.0	.	NM_020532	O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6	Missense_Mutation	SNP	ENST00000337526.6	hg19	CCDS42684.1																																																																																			.	.	.	none		0.416	RTN4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251484.1			AG	55253514	TT	AG	55253513	3	1	120	1	0	0	0	0	1	0	0	0	13741	1838	64	5	1922	5	RTN4	2	55253513	Missense_Mutation	DNP	TT	TCGA-BQ-5885-01A-11D-1589-08	27812716	55253513	187945860	5	7586											
USP34	9736	hgsc.bcm.edu	37	chr2	61505306	61505306	+	Frame_Shift_Del	DEL	T	T	-																															atcttaacacttacctgtccTtcccttgaaaatttaaaggg																										TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:61505306delT	ENST00000398571.2	-	41	5503	c.5427delA	c.(5425-5427)gaafs	p.E1809fs		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	1809					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)			TTACCTGTCCTTCCCTTGAAA	0.343																																					p.G1810fs		Atlas-INDEL	.											.	USP34	334	.	0			c.5428delG						PASS	.						92	79	84					2																	61505306		1864	4092	5956	SO:0001589	frameshift_variant	9736	exon41			.	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.5427delA	chr2.hg19:g.61505306delT	ENSP00000381577:p.Glu1809fs	69.0	0.0	0		38.0	12.0	0.315789	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Frame_Shift_Del	DEL	ENST00000398571.2	hg19	CCDS42686.1																																																																																			.	.	.	none		0.343	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			-	61505306	T	-	61505306	7	5	120	1	0	1	0	1	0	0	0	0	17077	1606	56	0	5373	0	USP34	2	61505306	Frame_Shift_Del	DEL	T	TCGA-BQ-5885-01A-11D-1589-08	6251793	61505306	181694067	6	7587											
ALMS1	7840	hgsc.bcm.edu	37	chr2	73680677	73680677	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatattggcacacagacgaaTttgaaatgccggagaggcat	14	8	12	7	2	0	3	0	1	0	2	0	6	0	3	1	3	1	2	1	3	3	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:73680677T>C	ENST00000264448.6	+	8	7131	c.7020T>C	c.(7018-7020)aaT>aaC	p.N2340N	ALMS1_ENST00000377715.1_Silent_p.N2340N|ALMS1_ENST00000409009.1_Silent_p.N2298N	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2340					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						CACAGACGAATTTGAAATGCC	0.448																																					p.N2340N		Atlas-SNP	.											.	ALMS1	384	.	0			c.T7020C						PASS	.						56	53	54					2																	73680677		1872	4112	5984	SO:0001819	synonymous_variant	7840	exon8			GACGAATTTGAAA	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.7020T>C	chr2.hg19:g.73680677T>C		80.0	0.0	.		71.0	14.0	.	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.	.	none		0.448	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		C	73680677	T	C	73680677	2	2	120	1	0	0	0	0	0	0	0	1	535	1490	52	3		3	ALMS1	2	73680677	Silent	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	12175371	73680677	169518696	7	7588											
SEMA4F	10505	hgsc.bcm.edu	37	chr2	74902749	74902749	+	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	ccacagccagttgagaacatGaaattgtaccacgtgagttg	13	9	10	9	1	0	3	0	3	0	1	0	4	0	3	3	0	3	3	3	0	3	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:74902749G>A	ENST00000357877.2	+	11	1619	c.1470G>A	c.(1468-1470)atG>atA	p.M490I	SEMA4F_ENST00000339773.5_Missense_Mutation_p.M335I|SEMA4F_ENST00000473350.1_3'UTR	NM_004263.3	NP_004254.2	O95754	SEM4F_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F	490	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)	p.M490I(1)		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						TTGAGAACATGAAATTGTACC	0.512																																					p.M490I		Atlas-SNP	.											SEMA4F,rectum,carcinoma,0,1	SEMA4F	89	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1470A						PASS	.						102	91	95					2																	74902749		2203	4300	6503	SO:0001583	missense	10505	exon11			GAACATGAAATTG	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.1470G>A	chr2.hg19:g.74902749G>A	ENSP00000350547:p.Met490Ile	123.0	0.0	.		134.0	40.0	.	NM_004263	Q542Y7|Q9NS35	Missense_Mutation	SNP	ENST00000357877.2	hg19	CCDS1955.1	.	.	.	.	.	.	.	.	.	.	G	12.04	1.818592	0.32145	.	.	ENSG00000135622	ENST00000357877;ENST00000339773	T;T	0.32023	1.47;1.47	4.5	3.58	0.41010	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.129054	0.51477	D	0.000093	T	0.17916	0.0430	N	0.12887	0.27	0.34285	D	0.682588	B;B	0.14012	0.003;0.009	B;B	0.15052	0.007;0.012	T	0.15983	-1.0418	10	0.46703	T	0.11	.	12.2822	0.54771	0.0:0.1859:0.814:0.0	.	335;490	O95754-2;O95754	.;SEM4F_HUMAN	I	490;335	ENSP00000350547:M490I;ENSP00000342675:M335I	ENSP00000342675:M335I	M	+	3	0	SEMA4F	74756257	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	1.936000	0.40183	2.333000	0.79357	0.467000	0.42956	ATG	.	.	.	none		0.512	SEMA4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252214.2	NM_004263		A	74902749	G	A	74902749	3	1	120	1	0	0	0	0	1	0	0	0	14048	1290	45	2	1512	2	SEMA4F	2	74902749	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	1222072	74902749	168296624	8	7589											
TBC1D8	11138	hgsc.bcm.edu	37	chr2	101670697	101670697	+	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	accagcttctccgcctcgggGaagttgaacctggcctcgaa	8	8	11	14	3	1	1	0	1	1	0	4	3	1	2	5	3	2	2	5	3	3	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:101670697G>A	ENST00000376840.4	-	4	458	c.459C>T	c.(457-459)ttC>ttT	p.F153F	TBC1D8_ENST00000409318.1_Silent_p.F168F			O95759	TBCD8_HUMAN	TBC1 domain family, member 8 (with GRAM domain)	153	GRAM 1.				blood circulation (GO:0008015)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	32						CCGCCTCGGGGAAGTTGAACC	0.617																																					p.F153F		Atlas-SNP	.											.	TBC1D8	169	.	0			c.C459T						PASS	.						35	41	39					2																	101670697		2066	4231	6297	SO:0001819	synonymous_variant	11138	exon4			CTCGGGGAAGTTG	AB024057	CCDS46375.1	2q12.1	2011-11-30			ENSG00000204634	ENSG00000204634			17791	protein-coding gene	gene with protein product	"BUB2-like protein 1", "vascular Rab-GAP/TBC-containing protein"					10373574	Standard	NM_001102426		Approved	HBLP1, VRP, AD3	uc010fiv.3	O95759	OTTHUMG00000153040	ENST00000376840.4:c.459C>T	chr2.hg19:g.101670697G>A		20.0	0.0	.		18.0	12.0	.	NM_001102426	A6NDL4|A8K9W1|B9A6K4|Q53SQ4|Q9UQ32	Silent	SNP	ENST00000376840.4	hg19	CCDS46375.1																																																																																			.	.	.	none		0.617	TBC1D8-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376092.1	NM_007063		A	101670697	G	A	101670697	2	1	120	1	0	0	0	0	0	0	0	1	15637	1165	41	2		2	TBC1D8	2	101670697	Silent	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	26767948	101670697	141528676	9	7590											
TMEM177	80775	hgsc.bcm.edu	37	chr2	120439354	120439354	+	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	ggagggggatgctcaatccgGgccgctcctgatgggctcat	6	8	16	11	2	2	1	2	1	0	0	4	3	4	3	3	5	1	3	3	5	1	0			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:120439354G>A	ENST00000424086.1	+	2	1398	c.925G>A	c.(925-927)Ggc>Agc	p.G309S	TMEM177_ENST00000272521.6_Missense_Mutation_p.G309S|TMEM177_ENST00000496203.1_Intron|TMEM177_ENST00000409951.1_Intron|TMEM177_ENST00000401466.1_Missense_Mutation_p.G309S	NM_001105198.1	NP_001098668.1	Q53S58	TM177_HUMAN	transmembrane protein 177	309						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)					GCTCAATCCGGGCCGCTCCTG	0.577																																					p.G309S		Atlas-SNP	.											.	TMEM177	26	.	0			c.G925A						PASS	.						43	47	46					2																	120439354		2201	4299	6500	SO:0001583	missense	80775	exon2			AATCCGGGCCGCT	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.925G>A	chr2.hg19:g.120439354G>A	ENSP00000402661:p.Gly309Ser	139.0	0.0	.		129.0	44.0	.	NM_030577	Q9BT20	Missense_Mutation	SNP	ENST00000424086.1	hg19	CCDS2128.1	.	.	.	.	.	.	.	.	.	.	G	12.41	1.928205	0.34002	.	.	ENSG00000144120	ENST00000401466;ENST00000424086;ENST00000272521;ENST00000415646	T;T;T	0.31510	1.49;1.49;1.49	4.44	2.51	0.30379	.	0.000000	0.53938	D	0.000044	T	0.16041	0.0386	N	0.17674	0.51	0.09310	N	1	B	0.14012	0.009	B	0.15052	0.012	T	0.18085	-1.0348	10	0.25751	T	0.34	-4.387	5.7699	0.18247	0.1213:0.1952:0.6835:0.0	.	309	Q53S58	TM177_HUMAN	S	309;309;309;248	ENSP00000385966:G309S;ENSP00000402661:G309S;ENSP00000272521:G309S	ENSP00000272521:G309S	G	+	1	0	TMEM177	120155824	0.003000	0.15002	0.010000	0.14722	0.097000	0.18754	0.068000	0.14531	0.514000	0.28300	0.549000	0.68633	GGC	.	.	.	none		0.577	TMEM177-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330673.1	NM_030577		A	120439354	G	A	120439354	3	1	120	1	0	0	0	0	1	0	0	0	16106	1232	43	2	927	2	TMEM177	2	120439354	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	18768657	120439354	122760019	10	7591											
LRP1B	53353	hgsc.bcm.edu	37	chr2	141819633	141819633	+	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	tacttacttgtctgccttgaAtgacagtgtgtctatttttt	7	20	7	7	0	2	2	0	2	2	0	2	2	2	2	1	0	3	0	1	0	4	8			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:141819633A>T	ENST00000389484.3	-	8	2194	c.1223T>A	c.(1222-1224)aTt>aAt	p.I408N		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	408					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)		TCTGCCTTGAATGACAGTGTG	0.358										TSP Lung(27;0.18)																											p.I408N	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.T1223A						PASS	.						217	197	204					2																	141819633		2203	4300	6503	SO:0001583	missense	53353	exon8			CCTTGAATGACAG	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.1223T>A	chr2.hg19:g.141819633A>T	ENSP00000374135:p.Ile408Asn	201.0	0.0	.		212.0	76.0	.	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	A	14.29	2.491685	0.44249	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.91686	-2.89	5.63	4.48	0.54585	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.371653	0.26734	N	0.022764	D	0.92047	0.7480	M	0.85630	2.765	0.23260	N	0.99803	B	0.27192	0.171	B	0.28849	0.095	D	0.86417	0.1752	10	0.72032	D	0.01	.	10.4218	0.44354	0.8641:0.0:0.1359:0.0	.	408	Q9NZR2	LRP1B_HUMAN	N	408;346	ENSP00000374135:I408N	ENSP00000374135:I408N	I	-	2	0	LRP1B	141536103	1.000000	0.71417	0.763000	0.31416	0.516000	0.34256	5.279000	0.65597	1.070000	0.40811	0.533000	0.62120	ATT	.	.	.	none		0.358	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141819633	A	T	141819633	3	4	120	1	0	0	0	0	1	0	0	0	8962	101	4	5	12912	5	LRP1B	2	141819633	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	21380279	141819633	101379740	11	7592											
LRP2	4036	hgsc.bcm.edu	37	chr2	170083080	170083080	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttatatgttgccttacagttAttaagaaaggttgatcatct	12	17	7	5	0	2	2	1	1	1	1	2	2	2	2	1	1	2	3	1	1	6	7			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:170083080A>G	ENST00000263816.3	-	32	5531	c.5246T>C	c.(5245-5247)aTa>aCa	p.I1749T		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1749					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)"	CCTTACAGTTATTAAGAAAGG	0.368																																					p.I1749T		Atlas-SNP	.											.	LRP2	751	.	0			c.T5246C						PASS	.						79	76	77					2																	170083080		2203	4300	6503	SO:0001583	missense	4036	exon32			ACAGTTATTAAGA		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.5246T>C	chr2.hg19:g.170083080A>G	ENSP00000263816:p.Ile1749Thr	105.0	0.0	.		119.0	26.0	.	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	hg19	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	A	18.57	3.652915	0.67472	.	.	ENSG00000081479	ENST00000263816	D	0.90900	-2.75	5.83	5.83	0.93111	Six-bladed beta-propeller, TolB-like (1);	0.111411	0.64402	D	0.000005	D	0.90943	0.7153	M	0.83223	2.63	0.80722	D	1	P	0.40144	0.704	B	0.35971	0.215	D	0.92052	0.5649	10	0.87932	D	0	.	16.2041	0.82108	1.0:0.0:0.0:0.0	.	1749	P98164	LRP2_HUMAN	T	1749	ENSP00000263816:I1749T	ENSP00000263816:I1749T	I	-	2	0	LRP2	169791326	1.000000	0.71417	0.916000	0.36221	0.996000	0.88848	9.310000	0.96267	2.219000	0.72066	0.533000	0.62120	ATA	.	.	.	none		0.368	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		G	170083080	A	G	170083080	3	3	120	1	0	0	0	0	1	0	0	0	8963	449	16	3	8913	3	LRP2	2	170083080	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	28263447	170083080	73116293	12	7593											
EPHA4	2043	hgsc.bcm.edu	37	chr2	222365873	222365873	+	Frame_Shift_Del	DEL	G	G	-																															gcatccgtggagagagccttGtaatatccaattttgcaagc																										TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:222365873delG	ENST00000281821.2	-	4	884	c.843delC	c.(841-843)tacfs	p.Y281fs	EPHA4_ENST00000409854.1_Frame_Shift_Del_p.Y281fs|EPHA4_ENST00000409938.1_Frame_Shift_Del_p.Y281fs|EPHA4_ENST00000392071.4_Frame_Shift_Del_p.Y230fs	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	281	Cys-rich.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		AGAGAGCCTTGTAATATCCAA	0.483																																					p.K282fs		Atlas-INDEL	.											.	EPHA4	263	.	0			c.844delA						PASS	.						59	57	57					2																	222365873		2203	4300	6503	SO:0001589	frameshift_variant	2043	exon4			.	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.843delC	chr2.hg19:g.222365873delG	ENSP00000281821:p.Tyr281fs	65.0	0.0	0		92.0	57.0	0.619565	NM_004438	A8K2P1|B2R601|B7Z6Q8|Q2M380	Frame_Shift_Del	DEL	ENST00000281821.2	hg19	CCDS2447.1																																																																																			.	.	.	none		0.483	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			-	222365873	G	-	222365873	7	5	120	1	0	1	0	1	0	0	0	0	5171	1372	48	0	2173	0	EPHA4	2	222365873	Frame_Shift_Del	DEL	G	TCGA-BQ-5885-01A-11D-1589-08	52282793	222365873	20833500	13	7594											
CUL3	8452	hgsc.bcm.edu	37	chr2	225422516	225422516	+	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	attcttacgctggatttcttGaattgcatttttcagaaggt	9	18	8	6	1	3	2	1	1	2	1	3	3	3	3	0	2	2	2	0	2	3	7			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:225422516G>A	ENST00000264414.4	-	2	462	c.124C>T	c.(124-126)Caa>Taa	p.Q42*	CUL3_ENST00000409777.1_Nonsense_Mutation_p.Q18*|CUL3_ENST00000344951.4_Intron|CUL3_ENST00000409096.1_Nonsense_Mutation_p.Q18*|CUL3_ENST00000432260.2_5'UTR	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	42					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)		TGGATTTCTTGAATTGCATTT	0.333																																					p.Q48X		Atlas-SNP	.											.	CUL3	96	.	0			c.C142T						PASS	.						88	85	86					2																	225422516		2201	4298	6499	SO:0001587	stop_gained	8452	exon2			TTTCTTGAATTGC	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.124C>T	chr2.hg19:g.225422516G>A	ENSP00000264414:p.Gln42*	81.0	0.0	.		99.0	53.0	.	NM_001257198	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Nonsense_Mutation	SNP	ENST00000264414.4	hg19	CCDS2462.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	41|41	8.780125|8.780125	0.98952|0.98952	.|.	.|.	ENSG00000036257|ENSG00000036257	ENST00000264414;ENST00000409096;ENST00000409777|ENST00000436172	.|.	.|.	.|.	5.85|5.85	5.85|5.85	0.93711|0.93711	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.76941	.|0.4058	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.74262	.|-0.3722	.|4	0.07030|.	T|.	0.85|.	.|.	20.1731|20.1731	0.98165|0.98165	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|L	42;18;18|62	.|.	ENSP00000264414:Q42X|.	Q|S	-|-	1|2	0|0	CUL3|CUL3	225130760|225130760	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.714000|9.714000	0.98744|0.98744	2.768000|2.768000	0.95171|0.95171	0.655000|0.655000	0.94253|0.94253	CAA|TCA	.	.	.	none		0.333	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2			A	225422516	G	A	225422516	4	1	120	1	0	0	0	0	0	1	0	0	4058	1299	45	2	2242	2	CUL3	2	225422516	Nonsense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	3056643	225422516	17776857	14	7595											
USP40	55230	hgsc.bcm.edu	37	chr2	234449396	234449396	+	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	tctggcccagctgatcaacaGgaattagattattctcctcc	10	12	7	12	0	3	2	1	1	2	1	5	3	4	3	3	2	2	1	3	2	4	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:234449396G>T	ENST00000427112.2	-	9	1114	c.1079C>A	c.(1078-1080)cCt>cAt	p.P360H	USP40_ENST00000251722.6_Missense_Mutation_p.P360H|USP40_ENST00000450966.1_Missense_Mutation_p.P372H			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	360	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)	p.P372R(2)		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)		CTGATCAACAGGAATTAGATT	0.378																																					p.P372H		Atlas-SNP	.											USP40_ENST00000450966,NS,carcinoma,0,4	USP40	174	.	2	Substitution - Missense(2)	lung(2)	c.C1115A						PASS	.						169	157	160					2																	234449396		1838	4092	5930	SO:0001583	missense	55230	exon9			TCAACAGGAATTA	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.1079C>A	chr2.hg19:g.234449396G>T	ENSP00000387898:p.Pro360His	254.0	2.0	.		248.0	111.0	.	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	hg19	CCDS46547.1	.	.	.	.	.	.	.	.	.	.	G	18.08	3.544257	0.65198	.	.	ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112	T;T;T	0.05258	3.47;3.48;3.48	5.31	3.39	0.38822	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	1.336030	0.05934	U	0.635709	T	0.18718	0.0449	L	0.55481	1.735	0.30283	N	0.791122	D;D	0.57899	0.981;0.976	P;P	0.60068	0.868;0.792	T	0.07214	-1.0784	10	0.72032	D	0.01	.	9.7296	0.40352	0.0745:0.0:0.7855:0.1401	.	360;372	Q9NVE5;Q9NVE5-3	UBP40_HUMAN;.	H	372;360;360	ENSP00000415434:P372H;ENSP00000251722:P360H;ENSP00000387898:P360H	ENSP00000251722:P360H	P	-	2	0	USP40	234114135	1.000000	0.71417	0.952000	0.39060	0.980000	0.70556	2.988000	0.49386	1.373000	0.46208	0.561000	0.74099	CCT	.	.	.	none		0.378	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294		T	234449396	G	T	234449396	3	4	120	1	0	0	0	0	1	0	0	0	17084	1000	35	4	2720	4	USP40	2	234449396	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	9026880	234449396	8749977	15	7596											
TRPM8	79054	hgsc.bcm.edu	37	chr2	234847784	234847784	+	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	gaagccgcgcatgcgcaagaTcttcagccggctcatctaca	10	7	10	14	4	4	1	2	0	2	1	4	2	4	1	2	1	4	3	2	1	3	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr2:234847784T>A	ENST00000324695.4	+	5	531	c.491T>A	c.(490-492)aTc>aAc	p.I164N	TRPM8_ENST00000355722.4_Missense_Mutation_p.I114N|TRPM8_ENST00000409625.1_Missense_Mutation_p.I87N|TRPM8_ENST00000433712.2_5'UTR	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	164					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	ATGCGCAAGATCTTCAGCCGG	0.607																																					p.I164N		Atlas-SNP	.											.	TRPM8	146	.	0			c.T491A						PASS	.						36	38	37					2																	234847784		2203	4300	6503	SO:0001583	missense	79054	exon5			GCAAGATCTTCAG	AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"Voltage-gated ion channels / Transient receptor potential cation channels"	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.491T>A	chr2.hg19:g.234847784T>A	ENSP00000323926:p.Ile164Asn	64.0	0.0	.		82.0	32.0	.	NM_024080	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	hg19	CCDS33407.1	.	.	.	.	.	.	.	.	.	.	t	21.2	4.109476	0.77096	.	.	ENSG00000144481	ENST00000324695;ENST00000355722;ENST00000409625	T;T;T	0.81163	-1.46;-1.46;-1.46	5.62	5.62	0.85841	.	0.000000	0.64402	D	0.000001	D	0.90181	0.6931	M	0.84585	2.705	0.80722	D	1	P;D	0.71674	0.567;0.998	B;D	0.74023	0.343;0.982	D	0.91731	0.5396	10	0.87932	D	0	-40.7179	14.6612	0.68873	0.0:0.0:0.0:1.0	.	114;164	Q7Z2W7-2;Q7Z2W7	.;TRPM8_HUMAN	N	164;114;87	ENSP00000323926:I164N;ENSP00000347956:I114N;ENSP00000386771:I87N	ENSP00000323926:I164N	I	+	2	0	TRPM8	234512523	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.795000	0.62489	2.154000	0.67381	0.478000	0.44815	ATC	.	.	.	none		0.607	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080		A	234847784	T	A	234847784	3	1	120	1	0	0	0	0	1	0	0	0	16604	1435	50	5	505	5	TRPM8	2	234847784	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	398388	234847784	8351589	16	7597											
ATP2B2	491	hgsc.bcm.edu	37	chr3	10387742	10387742	+	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	aagcccacgtcggccttcttGagtgcaggcccgtcgttggt	5	10	13	13	4	1	1	0	1	1	0	3	1	1	1	3	3	2	2	3	3	1	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr3:10387742G>A	ENST00000352432.4	-	16	2553	c.2484C>T	c.(2482-2484)ctC>ctT	p.L828L	ATP2B2_ENST00000360273.2_Silent_p.L828L|ATP2B2_ENST00000383800.4_Silent_p.L783L|ATP2B2_ENST00000397077.1_Silent_p.L783L|ATP2B2_ENST00000343816.4_Silent_p.L814L			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	828					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						CGGCCTTCTTGAGTGCAGGCC	0.652																																					p.L828L	Ovarian(125;1619 1709 15675 19819 38835)	Atlas-SNP	.											.	ATP2B2	304	.	0			c.C2484T						PASS	.						62	56	58					3																	10387742		2203	4300	6503	SO:0001819	synonymous_variant	491	exon17			CTTCTTGAGTGCA	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"ATPases / P-type"	815	protein-coding gene	gene with protein product	"plasma membrane Ca2+ pump 2", "plasma membrane calcium-transporting ATPase 2"	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.2484C>T	chr3.hg19:g.10387742G>A		72.0	0.0	.		67.0	17.0	.	NM_001001331	O00766|Q12994|Q16818	Silent	SNP	ENST00000352432.4	hg19	CCDS33701.1																																																																																			.	.	.	none		0.652	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683		A	10387742	G	A	10387742	2	1	120	1	0	0	0	0	0	0	0	1	1140	1277	45	2		2	ATP2B2	3	10387742	Silent	SNP	G	TCGA-BQ-5885-01A-11D-1589-08		10387742	187634688	17	7598											
ZNF502	91392	hgsc.bcm.edu	37	chr3	44762384	44762384	+	Frame_Shift_Del	DEL	G	G	-																															ggctgggtaaacaagaacaaGcctgctctggagcaggatgt																										TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr3:44762384delG	ENST00000296091.4	+	4	331	c.75delG	c.(73-75)aagfs	p.K25fs	ZNF502_ENST00000436624.2_Frame_Shift_Del_p.K25fs|ZNF502_ENST00000449836.1_Frame_Shift_Del_p.K25fs	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	25					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)		ACAAGAACAAGCCTGCTCTGG	0.418																																					p.K25fs		Atlas-INDEL	.											.	ZNF502	58	.	0			c.74delA						PASS	.						59	63	61					3																	44762384		2203	4300	6503	SO:0001589	frameshift_variant	91392	exon4			.	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.75delG	chr3.hg19:g.44762384delG	ENSP00000296091:p.Lys25fs	142.0	0.0	0		115.0	33.0	0.286957	NM_033210		Frame_Shift_Del	DEL	ENST00000296091.4	hg19	CCDS2719.1																																																																																			.	.	.	none		0.418	ZNF502-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256744.4	NM_033210		-	44762384	G	-	44762384	7	5	120	1	0	1	0	1	0	0	0	0	17962	962	34	0	81	0	ZNF502	3	44762384	Frame_Shift_Del	DEL	G	TCGA-BQ-5885-01A-11D-1589-08	34374642	44762384	153260046	18	7599											
FYCO1	79443	hgsc.bcm.edu	37	chr3	46009968	46009968	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caagtgaggcgaacgttgtcCtccgctgcagtgcgccccct	6	8	12	15	4	0	1	0	1	0	0	2	2	2	1	4	1	3	3	4	1	2	1			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr3:46009968C>T	ENST00000296137.2	-	8	1063	c.858G>A	c.(856-858)gaG>gaA	p.E286E	FYCO1_ENST00000535325.1_Silent_p.E286E	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	286					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)		GAACGTTGTCCTCCGCTGCAG	0.617																																					p.E286E		Atlas-SNP	.											.	FYCO1	115	.	0			c.G858A						PASS	.						102	85	91					3																	46009968		2203	4300	6503	SO:0001819	synonymous_variant	79443	exon8			GTTGTCCTCCGCT	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.858G>A	chr3.hg19:g.46009968C>T		115.0	0.0	.		91.0	20.0	.	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Silent	SNP	ENST00000296137.2	hg19	CCDS2734.1																																																																																			.	.	.	none		0.617	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513		T	46009968	C	T	46009968	2	4	120	1	0	0	0	0	0	0	0	1	6132	680	24	2		2	FYCO1	3	46009968	Silent	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	1247584	46009968	152012462	19	7600											
CCR5	1234	hgsc.bcm.edu	37	chr3	46415150	46415150	+	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	tcttctgggctccctacaacAttgtccttctcctgaacacc	7	13	5	16	0	3	1	0	1	3	0	6	1	5	1	4	1	3	1	4	1	3	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr3:46415150A>T	ENST00000292303.4	+	2	903	c.757A>T	c.(757-759)Att>Ttt	p.I253F	CCR5_ENST00000445772.1_Missense_Mutation_p.I253F|CCR5_ENST00000343801.4_Missense_Mutation_p.I253F|RP11-24F11.2_ENST00000451485.1_RNA	NM_001100168.1	NP_001093638.1	P51681	CCR5_HUMAN	chemokine (C-C motif) receptor 5 (gene/pseudogene)	253					calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|entry into host cell (GO:0030260)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to cholesterol (GO:0070723)|signaling (GO:0023052)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|C-C chemokine binding (GO:0019957)|C-C chemokine receptor activity (GO:0016493)|chemokine (C-C motif) ligand 5 binding (GO:0071791)|chemokine receptor activity (GO:0004950)|coreceptor activity (GO:0015026)|phosphatidylinositol phospholipase C activity (GO:0004435)			central_nervous_system(1)|large_intestine(2)|lung(13)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02)	Maraviroc(DB04835)	TCCCTACAACATTGTCCTTCT	0.463																																					p.I253F		Atlas-SNP	.											.	CCR5	128	.	0			c.A757T						PASS	.						227	243	237					3																	46415150		2203	4296	6499	SO:0001583	missense	1234	exon3			TACAACATTGTCC		CCDS2739.1	3p21	2012-08-08	2012-01-23		ENSG00000160791	ENSG00000160791		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1606	protein-coding gene	gene with protein product		601373	"chemokine (C-C motif) receptor 5"	CMKBR5		8639485	Standard	NM_001100168		Approved	CKR-5, CC-CKR-5, CKR5, CD195, IDDM22	uc003cpo.4	P51681	OTTHUMG00000133481	ENST00000292303.4:c.757A>T	chr3.hg19:g.46415150A>T	ENSP00000292303:p.Ile253Phe	688.0	0.0	.		556.0	164.0	.	NM_000579	O14692|O14693|O14695|O14696|O14697|O14698|O14699|O14700|O14701|O14702|O14703|O14704|O14705|O14706|O14707|O14708|O15538|Q9UPA4	Missense_Mutation	SNP	ENST00000292303.4	hg19	CCDS2739.1	.	.	.	.	.	.	.	.	.	.	A	19.96	3.923708	0.73213	.	.	ENSG00000160791	ENST00000343801;ENST00000400886;ENST00000292303;ENST00000445772	T;T;T	0.76060	-0.99;-0.99;-0.99	5.69	-3.74	0.04385	GPCR, rhodopsin-like superfamily (1);	0.268702	0.24301	U	0.039739	D	0.85128	0.5626	H	0.96691	3.865	0.49687	D	0.999818	D	0.53885	0.963	P	0.59889	0.865	D	0.83665	0.0163	10	0.87932	D	0	.	6.5629	0.22495	0.4959:0.3178:0.1864:0.0	.	253	P51681	CCR5_HUMAN	F	253;233;253;253	ENSP00000343985:I253F;ENSP00000292303:I253F;ENSP00000404881:I253F	ENSP00000292303:I253F	I	+	1	0	CCR5	46390154	0.942000	0.31987	0.996000	0.52242	0.849000	0.48306	0.234000	0.17930	-0.152000	0.11156	0.459000	0.35465	ATT	.	.	.	none		0.463	CCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257377.2	NM_000579		T	46415150	A	T	46415150	3	4	120	1	0	0	0	0	1	0	0	0	2946	217	8	5	759	5	CCR5	3	46415150	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	405182	46415150	151607280	20	7601											
QTRTD1	79691	hgsc.bcm.edu	37	chr3	113798773	113798773	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctcatatctggtgttagtcGgccagatgaggtgctcgagt	7	12	14	8	2	2	2	1	1	1	1	4	3	2	2	1	3	1	3	1	3	2	2	rs199551955		TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr3:113798773G>A	ENST00000493014.1	+	4	517	c.449G>A	c.(448-450)cGg>cAg	p.R150Q	QTRTD1_ENST00000479882.1_Missense_Mutation_p.R133Q|QTRTD1_ENST00000485050.1_Missense_Mutation_p.R268Q|QTRTD1_ENST00000281273.4_Missense_Mutation_p.R256Q	NM_001256836.1	NP_001243765.1			queuine tRNA-ribosyltransferase domain containing 1											central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|skin(2)	10						GGTGTTAGTCGGCCAGATGAG	0.423													G|||	1	0.000199681	0	0.0014	5008	,	,		19554	0		0	False		,,,				2504	0				p.R268Q		Atlas-SNP	.											.	QTRTD1	29	.	0			c.G803A						PASS	.						180	174	176					3																	113798773		2203	4300	6503	SO:0001583	missense	79691	exon7			TTAGTCGGCCAGA	AK023022	CCDS33828.1, CCDS58846.1, CCDS58845.1, CCDS58844.1	3q13.31	2010-11-16			ENSG00000151576	ENSG00000151576			25771	protein-coding gene	gene with protein product						12477932	Standard	NM_024638		Approved	FLJ12960	uc003eaz.4	Q9H974	OTTHUMG00000159336	ENST00000493014.1:c.449G>A	chr3.hg19:g.113798773G>A	ENSP00000419169:p.Arg150Gln	320.0	0.0	.		280.0	111.0	.	NM_001256835		Missense_Mutation	SNP	ENST00000493014.1	hg19	CCDS58845.1	.	.	.	.	.	.	.	.	.	.	G	10.98	1.505730	0.26949	.	.	ENSG00000151576	ENST00000485050;ENST00000281273;ENST00000479882;ENST00000493014	.	.	.	5.58	-1.43	0.08884	.	0.364818	0.28760	N	0.014230	T	0.33702	0.0872	L	0.40543	1.245	0.34875	D	0.744043	B;B	0.29590	0.25;0.015	B;B	0.20384	0.029;0.006	T	0.13098	-1.0522	9	0.44086	T	0.13	-0.6577	6.1058	0.20073	0.3234:0.0:0.4693:0.2072	.	150;256	B7Z472;Q9H974	.;QTRD1_HUMAN	Q	268;256;133;150	.	ENSP00000281273:R256Q	R	+	2	0	QTRTD1	115281463	0.996000	0.38824	0.856000	0.33681	0.200000	0.23975	1.800000	0.38833	-0.186000	0.10533	0.555000	0.69702	CGG	.	.	.	weak		0.423	QTRTD1-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000354711.1	NM_024638		A	113798773	G	A	113798773	3	1	120	1	0	0	0	0	1	0	0	0	12899	1116	39	1	789	1	QTRTD1	3	113798773	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	67383623	113798773	84223657	21	7602											
ZBBX	79740	hgsc.bcm.edu	37	chr3	167083714	167083714	+	Missense_Mutation	SNP	T	T	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	tttgtgacatcatatatgatTgattgaccaatttgcccact	11	16	6	8	0	1	4	1	4	0	0	1	4	1	4	2	0	1	0	2	0	3	6			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr3:167083714T>G	ENST00000392766.2	-	6	573	c.233A>C	c.(232-234)cAa>cCa	p.Q78P	ZBBX_ENST00000455345.2_Missense_Mutation_p.Q78P|ZBBX_ENST00000307529.5_Missense_Mutation_p.Q78P|ZBBX_ENST00000392767.2_Missense_Mutation_p.Q78P|ZBBX_ENST00000392764.1_Missense_Mutation_p.Q49P|ZBBX_ENST00000469220.1_Intron	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	78						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						CATATATGATTGATTGACCAA	0.289																																					p.Q78P		Atlas-SNP	.											.	ZBBX	299	.	0			c.A233C						PASS	.						116	108	111					3																	167083714		1824	4071	5895	SO:0001583	missense	79740	exon6			TATGATTGATTGA	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.233A>C	chr3.hg19:g.167083714T>G	ENSP00000376519:p.Gln78Pro	134.0	0.0	.		108.0	39.0	.	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	hg19	CCDS3199.2	.	.	.	.	.	.	.	.	.	.	T	5.789	0.329827	0.10956	.	.	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764;ENST00000474464	T;T;T;T;T;T	0.32988	2.92;2.92;2.92;2.92;2.74;1.43	5.26	-1.63	0.08345	.	.	.	.	.	T	0.20047	0.0482	L	0.44542	1.39	0.09310	N	0.999994	B;B	0.12630	0.006;0.003	B;B	0.16289	0.015;0.004	T	0.31530	-0.9940	9	0.52906	T	0.07	-2.1505	1.0522	0.01582	0.1499:0.2902:0.1547:0.4052	.	78;78	A8MT70-2;A8MT70	.;ZBBX_HUMAN	P	78;78;78;78;49;78	ENSP00000376519:Q78P;ENSP00000376520:Q78P;ENSP00000390232:Q78P;ENSP00000305065:Q78P;ENSP00000376517:Q49P;ENSP00000419307:Q78P	ENSP00000305065:Q78P	Q	-	2	0	ZBBX	168566408	0.486000	0.25980	0.013000	0.15412	0.018000	0.09664	0.353000	0.20130	-0.448000	0.07128	-0.386000	0.06593	CAA	.	.	.	none		0.289	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687		G	167083714	T	G	167083714	3	3	120	1	0	0	0	0	1	0	0	0	17528	1812	63	5	2233	5	ZBBX	3	167083714	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	53284941	167083714	30938716	22	7603											
TNFSF10	8743	hgsc.bcm.edu	37	chr3	172224404	172224404	+	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	aaatattcccccttgatagaTggaatagagtccatattctg	13	13	7	8	0	1	3	0	1	1	2	3	4	3	4	3	1	0	0	3	1	6	7			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr3:172224404T>A	ENST00000241261.2	-	5	846	c.724A>T	c.(724-726)Atc>Ttc	p.I242F	TNFSF10_ENST00000420541.2_3'UTR	NM_003810.3	NP_003801.1	P50591	TNF10_HUMAN	tumor necrosis factor (ligand) superfamily, member 10	242					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|immune response (GO:0006955)|male gonad development (GO:0008584)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to insulin (GO:0032868)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)			breast(2)|cervix(1)|large_intestine(1)|lung(6)|ovary(1)|skin(4)	15	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.67e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)			CCTTGATAGATGGAATAGAGT	0.333																																					p.I242F		Atlas-SNP	.											.	TNFSF10	30	.	0			c.A724T						PASS	.						168	163	165					3																	172224404		2203	4300	6503	SO:0001583	missense	8743	exon5			GATAGATGGAATA	U37518	CCDS3219.1, CCDS54680.1	3q26	2006-09-20			ENSG00000121858	ENSG00000121858		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11925	protein-coding gene	gene with protein product		603598				8777713, 8663110	Standard	NM_003810		Approved	TRAIL, Apo-2L, TL2, CD253	uc003fid.3	P50591	OTTHUMG00000156917	ENST00000241261.2:c.724A>T	chr3.hg19:g.172224404T>A	ENSP00000241261:p.Ile242Phe	171.0	0.0	.		176.0	60.0	.	NM_003810	A1Y9B3	Missense_Mutation	SNP	ENST00000241261.2	hg19	CCDS3219.1	.	.	.	.	.	.	.	.	.	.	T	14.66	2.600378	0.46423	.	.	ENSG00000121858	ENST00000241261	D	0.95412	-3.7	5.68	4.5	0.54988	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	0.323500	0.37530	N	0.002051	D	0.97604	0.9215	M	0.85373	2.75	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	D	0.97812	1.0251	10	0.72032	D	0.01	-18.1925	13.2187	0.59875	0.0:0.0:0.1329:0.8671	.	242	P50591	TNF10_HUMAN	F	242	ENSP00000241261:I242F	ENSP00000241261:I242F	I	-	1	0	TNFSF10	173707098	1.000000	0.71417	1.000000	0.80357	0.057000	0.15508	3.882000	0.56160	1.065000	0.40693	0.482000	0.46254	ATC	.	.	.	none		0.333	TNFSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346601.1			A	172224404	T	A	172224404	3	1	120	1	0	0	0	0	1	0	0	0	16313	1464	51	5	125	5	TNFSF10	3	172224404	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	5140690	172224404	25798026	23	7604											
OTOP1	133060	hgsc.bcm.edu	37	chr4	4199006	4199007	+	Missense_Mutation	DNP	TC	TC	CT																															tgggctccctccccagctgcTctcctcctgcttctcctcct																										TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr4:4199006_4199007TC>CT	ENST00000296358.4	-	5	1578_1579	c.1554_1555GA>AG	c.(1552-1557)gaGAgc>gaAGgc	p.S519G		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	519					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)		CCCCAGCTGCTCTCCTCCTGCT	0.564																																					p.S519G|p.E518E		Atlas-SNP	.											.	OTOP1	118	.	0			c.A1555G|c.G1554A						PASS	.																																			SO:0001583	missense	133060	exon5			AGCTGCTCTCCTC|GCTGCTCTCCTCC	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.1554_1555delinsCT	chr4.hg19:g.4199006_4199007delinsCT	ENSP00000296358:p.Ser519Gly	119.0|117.0	0.0	.		94.0|96.0	25.0|27.0	.	NM_177998	A1L476	Missense_Mutation|Silent	SNP	ENST00000296358.4	hg19	CCDS3372.1																																																																																			.	.	.	none		0.564	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998		CT	4199007	TC	CT	4199006	3	2	120	1	0	0	0	0	1	0	0	0	11312	1551	54	3	291	3	OTOP1	4	4199006	Missense_Mutation	DNP	TC	TCGA-BQ-5885-01A-11D-1589-08		4199006	186955270	24	7605											
SDAD1	55153	hgsc.bcm.edu	37	chr4	76877179	76877179	+	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	gaccggacattctggctataCcgcatcatcataaagttctt	11	12	7	11	2	4	0	2	0	2	0	4	2	4	1	2	2	1	3	2	2	4	6			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr4:76877179C>T	ENST00000356260.5	-	21	2083	c.1965G>A	c.(1963-1965)cgG>cgA	p.R655R	AC110615.1_ENST00000599764.1_Silent_p.Y41Y|SDAD1_ENST00000395711.4_Silent_p.R618R	NM_018115.2	NP_060585.2	Q9NVU7	SDA1_HUMAN	SDA1 domain containing 1	655					actin cytoskeleton organization (GO:0030036)|protein transport (GO:0015031)|ribosomal large subunit biogenesis (GO:0042273)|ribosomal large subunit export from nucleus (GO:0000055)	nucleolus (GO:0005730)				breast(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	19			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			TCTGGCTATACCGCATCATCA	0.393																																					p.R655R		Atlas-SNP	.											.	SDAD1	47	.	0			c.G1965A						PASS	.						242	227	232					4																	76877179		2203	4300	6503	SO:0001819	synonymous_variant	55153	exon21			GCTATACCGCATC	AF132198	CCDS3573.2, CCDS75147.1	4q21.21	2010-11-24			ENSG00000198301	ENSG00000198301			25537	protein-coding gene	gene with protein product						11483580	Standard	NM_001288984		Approved	FLJ10498	uc003hje.4	Q9NVU7	OTTHUMG00000130111	ENST00000356260.5:c.1965G>A	chr4.hg19:g.76877179C>T		392.0	0.0	.		311.0	101.0	.	NM_018115	Q32Q11|Q68D52|Q7Z5U4|Q9H831|Q9H9P6	Silent	SNP	ENST00000356260.5	hg19	CCDS3573.2																																																																																			.	.	.	none		0.393	SDAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252418.3	NM_018115		T	76877179	C	T	76877179	2	4	120	1	0	0	0	0	0	0	0	1	13963	494	18	2		2	SDAD1	4	76877179	Silent	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	72678173	76877179	114277097	25	7606											
ADAD1	132612	hgsc.bcm.edu	37	chr4	123336554	123336554	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtgatgggaattgcagtgatAccagaggcttagaaatcgct	12	10	13	6	1	0	4	0	2	0	2	1	5	0	5	1	2	2	3	1	2	4	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr4:123336554A>G	ENST00000296513.2	+	11	1455	c.1270A>G	c.(1270-1272)Acc>Gcc	p.T424A	ADAD1_ENST00000388725.2_Missense_Mutation_p.T406A|ADAD1_ENST00000388724.2_Missense_Mutation_p.T413A	NM_139243.3	NP_640336.1	Q96M93	ADAD1_HUMAN	adenosine deaminase domain containing 1 (testis-specific)	424	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				multicellular organismal development (GO:0007275)|RNA processing (GO:0006396)|spermatid development (GO:0007286)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	35						TTGCAGTGATACCAGAGGCTT	0.333																																					p.T424A		Atlas-SNP	.											ADAD1,colon,carcinoma,0,1	ADAD1	94	.	0			c.A1270G						PASS	.						103	100	101					4																	123336554		2203	4300	6503	SO:0001583	missense	132612	exon11			AGTGATACCAGAG	AK057303	CCDS34058.1, CCDS54800.1, CCDS54801.1	4q27	2007-05-31			ENSG00000164113	ENSG00000164113			30713	protein-coding gene	gene with protein product		614130				7543294, 9541871	Standard	NM_139243		Approved	Tenr	uc003iep.3	Q96M93	OTTHUMG00000150128	ENST00000296513.2:c.1270A>G	chr4.hg19:g.123336554A>G	ENSP00000296513:p.Thr424Ala	171.0	1.0	.		125.0	10.0	.	NM_139243	A6NKN4|B7WPB0|D3DNX2|Q8IWG6|Q8NA06	Missense_Mutation	SNP	ENST00000296513.2	hg19	CCDS34058.1	.	.	.	.	.	.	.	.	.	.	A	13.21	2.169474	0.38315	.	.	ENSG00000164113	ENST00000296513;ENST00000388724;ENST00000388725	D;D;D	0.93133	-3.17;-3.17;-3.17	5.12	3.94	0.45596	Adenosine deaminase/editase (3);	0.310779	0.32987	N	0.005405	D	0.91375	0.7279	L	0.39020	1.185	0.31646	N	0.64739	P;D	0.58620	0.745;0.983	B;P	0.60286	0.382;0.872	D	0.86329	0.1697	10	0.08599	T	0.76	-14.2059	7.0801	0.25227	0.7952:0.0:0.0737:0.1312	.	413;424	Q96M93-2;Q96M93	.;ADAD1_HUMAN	A	424;413;406	ENSP00000296513:T424A;ENSP00000373376:T413A;ENSP00000373377:T406A	ENSP00000296513:T424A	T	+	1	0	ADAD1	123556004	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.208000	0.58486	0.800000	0.34041	0.528000	0.53228	ACC	.	.	.	none		0.333	ADAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316452.1	NM_139243		G	123336554	A	G	123336554	3	3	120	1	0	0	0	0	1	0	0	0	231	391	14	3	1304	3	ADAD1	4	123336554	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	46459375	123336554	67817722	26	7607											
PLK4	10733	hgsc.bcm.edu	37	chr4	128804442	128804442	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	taagaaagccatgtacaaagCaggaatggtacagagagtcc	17	6	11	7	0	0	2	0	0	0	2	1	4	1	3	2	2	4	3	2	2	6	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr4:128804442C>T	ENST00000270861.5	+	3	426	c.152C>T	c.(151-153)gCa>gTa	p.A51V	PLK4_ENST00000507249.1_Missense_Mutation_p.A51V|PLK4_ENST00000515069.1_Missense_Mutation_p.A51V|PLK4_ENST00000513090.1_Intron|PLK4_ENST00000514379.1_Missense_Mutation_p.A10V|PLK4_ENST00000511942.1_3'UTR	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	51	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						ATGTACAAAGCAGGAATGGTA	0.308																																					p.A51V	Colon(135;508 1718 19061 31832 42879)	Atlas-SNP	.											.	PLK4	65	.	0			c.C152T						PASS	.						71	71	71					4																	128804442		2203	4299	6502	SO:0001583	missense	10733	exon3			ACAAAGCAGGAAT	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.152C>T	chr4.hg19:g.128804442C>T	ENSP00000270861:p.Ala51Val	53.0	0.0	.		48.0	13.0	.	NM_014264	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Missense_Mutation	SNP	ENST00000270861.5	hg19	CCDS3735.1	.	.	.	.	.	.	.	.	.	.	C	15.38	2.815330	0.50527	.	.	ENSG00000142731	ENST00000270861;ENST00000515069;ENST00000507249;ENST00000514379	T;T;T;T	0.65732	-0.17;-0.17;-0.17;1.83	5.39	5.39	0.77823	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.110302	0.64402	D	0.000009	T	0.49218	0.1544	L	0.36672	1.1	0.48901	D	0.999727	B	0.23128	0.08	B	0.27608	0.081	T	0.46105	-0.9215	10	0.31617	T	0.26	-8.6513	7.0116	0.24865	0.0:0.79:0.0:0.21	.	51	O00444	PLK4_HUMAN	V	51;51;51;10	ENSP00000270861:A51V;ENSP00000421774:A51V;ENSP00000423412:A51V;ENSP00000423582:A10V	ENSP00000270861:A51V	A	+	2	0	PLK4	129023892	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.422000	0.52749	2.520000	0.84964	0.655000	0.94253	GCA	.	.	.	none		0.308	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3			T	128804442	C	T	128804442	3	4	120	1	0	0	0	0	1	0	0	0	12105	710	25	2	162	2	PLK4	4	128804442	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	5467888	128804442	62349834	27	7608											
LRBA	987	hgsc.bcm.edu	37	chr4	151829520	151829520	+	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	aatctcatcagacaaatattGcctgtaatccaactgtgcaa	15	11	5	10	0	2	1	2	0	1	1	4	1	3	1	2	0	3	2	2	0	6	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr4:151829520G>A	ENST00000357115.3	-	11	1702	c.1459C>T	c.(1459-1461)Caa>Taa	p.Q487*	LRBA_ENST00000507224.1_Nonsense_Mutation_p.Q487*|LRBA_ENST00000535741.1_Nonsense_Mutation_p.Q487*|LRBA_ENST00000510413.1_Nonsense_Mutation_p.Q487*	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	487						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)					GACAAATATTGCCTGTAATCC	0.363																																					p.Q487X		Atlas-SNP	.											.	LRBA	253	.	0			c.C1459T						PASS	.						126	121	122					4																	151829520		2203	4300	6503	SO:0001587	stop_gained	987	exon11			AATATTGCCTGTA	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.1459C>T	chr4.hg19:g.151829520G>A	ENSP00000349629:p.Gln487*	115.0	0.0	.		93.0	31.0	.	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Nonsense_Mutation	SNP	ENST00000357115.3	hg19	CCDS3773.1	.	.	.	.	.	.	.	.	.	.	G	43	9.887563	0.99288	.	.	ENSG00000198589	ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224	.	.	.	5.63	5.63	0.86233	.	0.000000	0.48286	U	0.000186	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	.	20.047	0.97613	0.0:0.0:1.0:0.0	.	.	.	.	X	487	.	ENSP00000349629:Q487X	Q	-	1	0	LRBA	152048970	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	9.120000	0.94369	2.802000	0.96397	0.563000	0.77884	CAA	.	.	.	none		0.363	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			A	151829520	G	A	151829520	4	1	120	1	0	0	0	0	0	1	0	0	8938	1328	46	2	7324	2	LRBA	4	151829520	Nonsense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	23025078	151829520	39324756	28	7609											
FAT1	2195	hgsc.bcm.edu	37	chr4	187540288	187540291	+	Frame_Shift_Del	DEL	TCCA	TCCA	-																															gcaggactgtgcaaattgccTccaattacagttacatgaac																										TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	TCCA	TCCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr4:187540288_187540291delTCCA	ENST00000441802.2	-	10	7658_7661	c.7449_7452delTGGA	c.(7447-7452)attggafs	p.IG2483fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2483	Cadherin 22. {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						GCAAATTGCCTCCAATTACAGTTA	0.471										HNSCC(5;0.00058)																											p.2484_2485del	Colon(197;1040 2055 4143 4984 49344)	Atlas-INDEL	.											.	FAT1	500	.	0			c.7450_7453del						PASS	.																																			SO:0001589	frameshift_variant	2195	exon10			.	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.7449_7452delTGGA	chr4.hg19:g.187540288_187540291delTCCA	ENSP00000406229:p.Ile2483fs	443.0	0.0	0		385.0	90.0	0.233766	NM_005245		Frame_Shift_Del	DEL	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.	.	none		0.471	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		-	187540291	TCCA	-	187540288	7	5	120	1	0	1	0	1	0	0	0	0	5696	1538	54	0	6386	0	FAT1	4	187540288	Frame_Shift_Del	DEL	TCCA	TCGA-BQ-5885-01A-11D-1589-08	35710768	187540288	3613988	29	7610											
GOLPH3	64083	hgsc.bcm.edu	37	chr5	32126417	32126417	+	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	tcgagaagctgccgcactctCttggtagccaaatcatactg	10	10	9	12	2	2	1	1	0	1	1	4	2	2	1	2	1	4	3	2	1	4	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr5:32126417C>A	ENST00000265070.6	-	4	1113	c.798G>T	c.(796-798)aaG>aaT	p.K266N	GOLPH3_ENST00000512668.1_5'Flank	NM_022130.3	NP_071413.1	Q9H4A6	GOLP3_HUMAN	golgi phosphoprotein 3 (coat-protein)	266					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						GCCGCACTCTCTTGGTAGCCA	0.552																																					p.K266N		Atlas-SNP	.											.	GOLPH3	25	.	0			c.G798T						PASS	.						94	80	85					5																	32126417		2203	4300	6503	SO:0001583	missense	64083	exon4			CACTCTCTTGGTA	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.798G>T	chr5.hg19:g.32126417C>A	ENSP00000265070:p.Lys266Asn	155.0	0.0	.		142.0	33.0	.	NM_022130	Q9UIW5	Missense_Mutation	SNP	ENST00000265070.6	hg19	CCDS3896.1	.	.	.	.	.	.	.	.	.	.	C	8.954	0.968949	0.18659	.	.	ENSG00000113384	ENST00000265070;ENST00000542582	.	.	.	6.17	4.38	0.52667	.	0.000000	0.85682	D	0.000000	T	0.63745	0.2537	L	0.60845	1.875	0.80722	D	1	D	0.63046	0.992	P	0.61328	0.887	T	0.60944	-0.7162	9	0.23302	T	0.38	.	7.4739	0.27365	0.1395:0.7289:0.0:0.1316	.	266	Q9H4A6	GOLP3_HUMAN	N	266;249	.	ENSP00000265070:K266N	K	-	3	2	GOLPH3	32162174	1.000000	0.71417	1.000000	0.80357	0.002000	0.02628	2.589000	0.46145	1.606000	0.50161	-0.182000	0.12963	AAG	.	.	.	none		0.552	GOLPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207363.2	NM_022130		A	32126417	C	A	32126417	3	1	120	1	0	0	0	0	1	0	0	0	6575	912	32	4	102	4	GOLPH3	5	32126417	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08		32126417	148788843	30	7611											
GPBP1	65056	hgsc.bcm.edu	37	chr5	56545332	56545332	+	Missense_Mutation	SNP	T	T	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	gcactgataagaagagtgaaTttttgaaagcattgaaaaga	18	10	10	3	0	0	7	0	4	0	3	0	7	0	7	0	0	1	2	0	0	6	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr5:56545332T>G	ENST00000506184.2	+	9	2006	c.901T>G	c.(901-903)Ttt>Gtt	p.F301V	GPBP1_ENST00000454432.2_Missense_Mutation_p.F321V|GPBP1_ENST00000514387.2_Missense_Mutation_p.F130V|GPBP1_ENST00000538707.1_Missense_Mutation_p.F308V|GPBP1_ENST00000424459.3_Missense_Mutation_p.F321V|GPBP1_ENST00000264779.6_Missense_Mutation_p.F308V|GPBP1_ENST00000511209.1_Missense_Mutation_p.F293V			Q86WP2	GPBP1_HUMAN	GC-rich promoter binding protein 1	301					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	19		Lung NSC(810;0.000861)|Prostate(74;0.0305)|Breast(144;0.222)		OV - Ovarian serous cystadenocarcinoma(10;7.64e-39)		GAAGAGTGAATTTTTGAAAGC	0.388																																					p.F308V		Atlas-SNP	.											.	GPBP1	51	.	0			c.T922G						PASS	.						107	104	105					5																	56545332		2203	4299	6502	SO:0001583	missense	65056	exon8			AGTGAATTTTTGA		CCDS34162.1, CCDS47211.1, CCDS47212.1, CCDS47212.2, CCDS56368.1	5q11.2	2008-02-05				ENSG00000062194			29520	protein-coding gene	gene with protein product		608412				12842993	Standard	NM_022913		Approved	DKFZp761C169, vasculin	uc003jrk.4	Q86WP2		ENST00000506184.2:c.901T>G	chr5.hg19:g.56545332T>G	ENSP00000421202:p.Phe301Val	95.0	0.0	.		107.0	32.0	.	NM_001127236	A6NKW3|Q6NSH6|Q9H0D4|Q9H785|Q9NSN4	Missense_Mutation	SNP	ENST00000506184.2	hg19	CCDS34162.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.987062	0.74589	.	.	ENSG00000062194	ENST00000424459;ENST00000514387;ENST00000506184;ENST00000454432;ENST00000511209;ENST00000264779;ENST00000538707	T;T;T;T;T;T;T	0.59364	1.24;0.27;1.3;1.24;1.24;1.3;1.3	6.16	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.55970	0.1954	M	0.62723	1.935	0.46701	D	0.999164	P;P;P;P	0.47545	0.897;0.728;0.728;0.728	B;B;B;B	0.42214	0.38;0.294;0.23;0.294	T	0.60632	-0.7225	10	0.87932	D	0	-10.4	11.4966	0.50413	0.1338:0.0:0.0:0.8662	.	321;308;293;301	D4PHA4;Q86WP2-2;Q86WP2-3;Q86WP2	.;.;.;GPBP1_HUMAN	V	321;130;301;321;293;308;308	ENSP00000401596:F321V;ENSP00000421709:F130V;ENSP00000421202:F301V;ENSP00000403522:F321V;ENSP00000422337:F293V;ENSP00000264779:F308V;ENSP00000440090:F308V	ENSP00000264779:F308V	F	+	1	0	GPBP1	56581089	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	5.480000	0.66820	1.110000	0.41699	0.528000	0.53228	TTT	.	.	.	none		0.388	GPBP1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000374496.1	NM_022913		G	56545332	T	G	56545332	3	3	120	1	0	0	0	0	1	0	0	0	6602	1493	52	5	952	5	GPBP1	5	56545332	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	24418915	56545332	124369928	31	7612											
CD180	4064	hgsc.bcm.edu	37	chr5	66478708	66478708	+	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	aatgtgttggtatttccaccTgagaaggtatttaactgcaa	12	14	9	6	0	0	1	0	1	0	1	1	2	1	1	2	2	2	4	2	2	6	6			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr5:66478708T>G	ENST00000256447.4	-	3	2120	c.1963A>C	c.(1963-1965)Agg>Cgg	p.R655R	CTD-2306M10.1_ENST00000602471.1_lincRNA	NM_005582.2	NP_005573.2	Q99467	CD180_HUMAN	CD180 molecule	655					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)		TATTTCCACCTGAGAAGGTAT	0.373																																					p.R655R		Atlas-SNP	.											.	CD180	78	.	0			c.A1963C						PASS	.						36	39	38					5																	66478708		2203	4300	6503	SO:0001819	synonymous_variant	4064	exon3			TCCACCTGAGAAG	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.1963A>C	chr5.hg19:g.66478708T>G		84.0	0.0	.		51.0	18.0	.	NM_005582	B2R7Z7|Q32MM5	Silent	SNP	ENST00000256447.4	hg19	CCDS3992.1																																																																																			.	.	.	none		0.373	CD180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253973.2	NM_005582		G	66478708	T	G	66478708	2	3	120	1	0	0	0	0	0	0	0	1	2974	1579	55	5		5	CD180	5	66478708	Silent	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	9933376	66478708	114436552	32	7613											
LNPEP	4012	hgsc.bcm.edu	37	chr5	96328816	96328816	+	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	ttttcaaaactactttgaaaTtcagtacccacttaagaaat	16	14	3	8	0	2	2	2	1	0	1	2	2	2	2	1	0	3	1	1	0	7	7			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr5:96328816T>A	ENST00000231368.5	+	5	1921	c.1229T>A	c.(1228-1230)aTt>aAt	p.I410N	LNPEP_ENST00000395770.3_Missense_Mutation_p.I396N	NM_005575.2	NP_005566.2	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase	410					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-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)		TACTTTGAAATTCAGTACCCA	0.303																																					p.I410N		Atlas-SNP	.											.	LNPEP	80	.	0			c.T1229A						PASS	.						66	67	67					5																	96328816		2202	4299	6501	SO:0001583	missense	4012	exon5			TTGAAATTCAGTA	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.1229T>A	chr5.hg19:g.96328816T>A	ENSP00000231368:p.Ile410Asn	130.0	0.0	.		112.0	46.0	.	NM_005575	O00769|Q15145|Q59H76|Q9TNQ2|Q9TNQ3|Q9UIQ7	Missense_Mutation	SNP	ENST00000231368.5	hg19	CCDS4087.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.278587	0.80692	.	.	ENSG00000113441	ENST00000231368;ENST00000395770	T;T	0.03035	4.07;4.07	4.94	4.94	0.65067	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.25082	0.0609	M	0.92880	3.355	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.16100	-1.0414	10	0.87932	D	0	.	14.5573	0.68109	0.0:0.0:0.0:1.0	.	410	Q9UIQ6	LCAP_HUMAN	N	410;396	ENSP00000231368:I410N;ENSP00000379117:I396N	ENSP00000231368:I410N	I	+	2	0	LNPEP	96354572	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.757000	0.68766	1.964000	0.57103	0.455000	0.32223	ATT	.	.	.	none		0.303	LNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250624.1	NM_005575		A	96328816	T	A	96328816	3	1	120	1	0	0	0	0	1	0	0	0	8871	1493	52	5	1247	5	LNPEP	5	96328816	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	29850108	96328816	84586444	33	7614											
PCDHA9	9752	hgsc.bcm.edu	37	chr5	140228538	140228538	+	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	gccgcttgactctcggtttcCactagagggcgcgtccgatg	5	10	13	13	5	1	2	0	1	1	1	4	3	3	2	3	2	0	2	3	2	1	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr5:140228538C>A	ENST00000532602.1	+	1	1491	c.458C>A	c.(457-459)cCa>cAa	p.P153Q	PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000378122.3_Missense_Mutation_p.P153Q|PCDHA4_ENST00000530339.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000529310.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	153	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(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)			TCTCGGTTTCCACTAGAGGGC	0.547																																					p.P153Q	Melanoma(55;1800 1972 14909)	Atlas-SNP	.											.	PCDHA9	373	.	0			c.C458A						PASS	.						54	51	52					5																	140228538		2202	4292	6494	SO:0001583	missense	9752	exon1			GGTTTCCACTAGA	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.458C>A	chr5.hg19:g.140228538C>A	ENSP00000436042:p.Pro153Gln	189.0	0.0	.		194.0	45.0	.	NM_031857	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	hg19	CCDS54920.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.352609	0.82132	.	.	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.48201	0.82;0.82	4.13	4.13	0.48395	Cadherin (3);Cadherin-like (1);	0.000000	0.31697	U	0.007216	T	0.67552	0.2905	M	0.83384	2.64	0.28140	N	0.929845	D;D	0.62365	0.986;0.991	D;P	0.64877	0.93;0.894	T	0.64719	-0.6341	10	0.87932	D	0	.	12.8791	0.58008	0.1634:0.8366:0.0:0.0	.	153;153	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	Q	153	ENSP00000436042:P153Q;ENSP00000367362:P153Q	ENSP00000367362:P153Q	P	+	2	0	PCDHA9	140208722	0.000000	0.05858	0.994000	0.49952	0.994000	0.84299	1.041000	0.30291	2.263000	0.75096	0.591000	0.81541	CCA	.	.	.	none		0.547	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		A	140228538	C	A	140228538	3	1	120	1	0	0	0	0	1	0	0	0	11538	594	21	4	460	4	PCDHA9	5	140228538	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	43899722	140228538	40686722	34	7615											
BAT1	7919	hgsc.bcm.edu	37	chr6	31507042	31507042	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatggcctgagggatgcacTcatgctggactaaaagttgg	11	9	14	7	0	1	1	1	1	0	0	1	4	1	3	1	4	2	3	1	4	3	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr6:31507042T>C	ENST00000396172.1	-	3	851	c.221A>G	c.(220-222)gAg>gGg	p.E74G	ATP6V1G2-DDX39B_ENST00000376185.1_3'UTR|DDX39B_ENST00000458640.1_Missense_Mutation_p.E74G|DDX39B_ENST00000376177.2_Missense_Mutation_p.E74G|DDX39B_ENST00000453105.2_Intron|DDX39B_ENST00000417556.2_Missense_Mutation_p.E74G|DDX39B_ENST00000449074.2_Missense_Mutation_p.E74G|SNORD117_ENST00000364915.1_RNA|SNORD84_ENST00000584275.1_RNA|DDX39B_ENST00000415382.2_Intron|ATP6V1G2-DDX39B_ENST00000475917.1_5'Flank	NM_004640.6	NP_004631.1	Q13838	DX39B_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	74					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						AGGGATGCACTCATGCTGGAC	0.507																																					p.E74G		Atlas-SNP	.											.	DDX39B	38	.	0			c.A221G						PASS	.						100	108	105					6																	31507042		1511	2709	4220	SO:0001583	missense	7919	exon3			ATGCACTCATGCT	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.221A>G	chr6.hg19:g.31507042T>C	ENSP00000379475:p.Glu74Gly	146.0	0.0	.		114.0	48.0	.	NM_004640	B0S8C0|O43496|Q0EFA1|Q2L6F9|Q53GL9|Q5RJ64|Q5RJ66|Q5ST94|Q5STB4|Q5STB5|Q5STB7|Q5STB8|Q5STU4|Q5STU5|Q5STU6|Q5STU8|Q71V76	Missense_Mutation	SNP	ENST00000396172.1	hg19	CCDS4697.1	.	.	.	.	.	.	.	.	.	.	T	19.66	3.869256	0.72065	.	.	ENSG00000198563	ENST00000376177;ENST00000458640;ENST00000396172;ENST00000417556;ENST00000427214;ENST00000428098;ENST00000419338;ENST00000456662;ENST00000449074;ENST00000428450;ENST00000449757;ENST00000456976;ENST00000418897;ENST00000419020;ENST00000458215	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68	5.53	5.53	0.82687	DEAD-like helicase (1);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.48295	0.1492	L	0.50993	1.605	0.80722	D	1	D;D;P	0.58970	0.984;0.972;0.897	P;P;P	0.57371	0.735;0.819;0.635	T	0.54221	-0.8326	10	0.72032	D	0.01	-22.5551	13.6077	0.62056	0.0:0.0:0.0:1.0	.	94;74;74	Q59G92;Q13838;Q5STU3	.;DX39B_HUMAN;.	G	74;74;74;74;74;74;74;74;74;74;97;74;89;74;74	ENSP00000365347:E74G;ENSP00000416269:E74G;ENSP00000379475:E74G;ENSP00000412582:E74G;ENSP00000399371:E74G;ENSP00000392672:E74G;ENSP00000410313:E74G;ENSP00000416350:E74G;ENSP00000391946:E74G;ENSP00000405707:E74G;ENSP00000409426:E97G;ENSP00000393984:E74G;ENSP00000399841:E89G;ENSP00000405245:E74G	ENSP00000365347:E74G	E	-	2	0	DDX39B	31615021	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	7.568000	0.82369	2.095000	0.63458	0.460000	0.39030	GAG	.	.	.	none		0.507	DDX39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259083.1	NM_004640		C	31507042	T	C	31507042	3	2	120	1	0	0	0	0	1	0	0	0	1318	1551	54	3	1101	3	BAT1	6	31507042	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08		31507042	139608025	35	7616											
DST	667	hgsc.bcm.edu	37	chr6	56347659	56347659	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgctggtcctcttccccAactctttttggaaggcctaa	7	13	7	14	0	2	0	0	0	2	0	4	1	4	1	4	3	2	1	4	3	3	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr6:56347659A>G	ENST00000361203.3	-	84	20271	c.20264T>C	c.(20263-20265)tTg>tCg	p.L6755S	DST_ENST00000244364.6_Missense_Mutation_p.L4452S|DST_ENST00000446842.2_Missense_Mutation_p.L6540S|DST_ENST00000312431.6_3'UTR|DST_ENST00000370788.2_Missense_Mutation_p.L4669S|DST_ENST00000421834.2_Missense_Mutation_p.L4778S|DST_ENST00000370769.4_Missense_Mutation_p.L6866S|DST_ENST00000370754.5_Missense_Mutation_p.L7044S			Q03001	DYST_HUMAN	dystonin	6754					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)			CCTCTTCCCCAACTCTTTTTG	0.448																																					p.L4452S		Atlas-SNP	.											.	DST	1427	.	0			c.T13355C						PASS	.						53	52	52					6																	56347659		1871	4102	5973	SO:0001583	missense	667	exon70			TTCCCCAACTCTT	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.20264T>C	chr6.hg19:g.56347659A>G	ENSP00000354508:p.Leu6755Ser	79.0	0.0	.		63.0	22.0	.	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	hg19		.	.	.	.	.	.	.	.	.	.	A	18.68	3.676124	0.67928	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.59772	0.24;0.24;0.24;0.24;0.24;0.24;0.24	5.65	5.65	0.86999	.	0.000000	0.41396	D	0.000891	T	0.75671	0.3881	M	0.87682	2.9	0.32532	N	0.534844	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.998;0.999;0.999	T	0.81079	-0.1095	9	0.87932	D	0	.	16.1657	0.81754	1.0:0.0:0.0:0.0	.	4778;6866;7044;6864;4452	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	S	4452;7044;6866;4778;6540;4669;6755	ENSP00000244364:L4452S;ENSP00000359790:L7044S;ENSP00000359805:L6866S;ENSP00000400883:L4778S;ENSP00000393645:L6540S;ENSP00000359824:L4669S;ENSP00000354508:L6755S	ENSP00000244364:L4452S	L	-	2	0	DST	56455618	1.000000	0.71417	0.987000	0.45799	0.992000	0.81027	9.307000	0.96226	2.276000	0.75962	0.528000	0.53228	TTG	.	.	.	none		0.448	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		G	56347659	A	G	56347659	3	3	120	1	0	0	0	0	1	0	0	0	4785	131	5	3	2220	3	DST	6	56347659	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	24840617	56347659	114767408	36	7617											
SLC35D3	340146	hgsc.bcm.edu	37	chr6	137243696	137243696	+	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	agttctccttcctgaccctgGtgcagtgcctgaccagctcc	5	11	9	16	0	1	2	0	2	1	0	4	2	3	2	6	1	3	3	6	1	0	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr6:137243696G>C	ENST00000331858.4	+	1	295	c.130G>C	c.(130-132)Gtg>Ctg	p.V44L		NM_001008783.1	NP_001008783.1	Q5M8T2	S35D3_HUMAN	solute carrier family 35, member D3	44					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)		CCTGACCCTGGTGCAGTGCCT	0.677																																					p.V44L		Atlas-SNP	.											.	SLC35D3	33	.	0			c.G130C						PASS	.						41	37	38					6																	137243696		2202	4298	6500	SO:0001583	missense	340146	exon1			ACCCTGGTGCAGT		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.130G>C	chr6.hg19:g.137243696G>C	ENSP00000333591:p.Val44Leu	61.0	0.0	.		50.0	17.0	.	NM_001008783	B4DI58|Q5QNZ6|Q6NX71	Missense_Mutation	SNP	ENST00000331858.4	hg19	CCDS34544.1	.	.	.	.	.	.	.	.	.	.	G	6.901	0.535701	0.13188	.	.	ENSG00000182747	ENST00000331858	T	0.50277	0.75	4.53	4.53	0.55603	.	0.154256	0.43110	D	0.000610	T	0.09642	0.0237	N	0.04880	-0.145	0.43608	D	0.995972	B	0.09022	0.002	B	0.06405	0.002	T	0.16928	-1.0386	10	0.02654	T	1	-17.4101	13.2101	0.59819	0.0:0.213:0.787:0.0	.	44	Q5M8T2	S35D3_HUMAN	L	44	ENSP00000333591:V44L	ENSP00000333591:V44L	V	+	1	0	SLC35D3	137285389	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.017000	0.57167	2.074000	0.62210	0.491000	0.48974	GTG	.	.	.	none		0.677	SLC35D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042389.2	XM_294017		C	137243696	G	C	137243696	3	2	120	1	0	0	0	0	1	0	0	0	14596	1261	44	4	132	4	SLC35D3	6	137243696	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	80896037	137243696	33871371	37	7618											
TAX1BP1	8887	hgsc.bcm.edu	37	chr7	27856087	27856087	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatgttctcacattgtcaaaTgcacaaccagttctgcaata	13	13	5	10	0	3	0	2	0	2	0	4	0	3	0	1	0	3	4	1	0	5	5			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr7:27856087T>C	ENST00000396319.2	+	14	1972	c.1884T>C	c.(1882-1884)aaT>aaC	p.N628N	TAX1BP1_ENST00000265393.6_Intron|TAX1BP1_ENST00000543117.1_Intron|TAX1BP1_ENST00000433216.2_Intron|TAX1BP1_ENST00000409980.1_Silent_p.N652N	NM_006024.6	NP_006015.4	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I) binding protein 1	628					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	kinase binding (GO:0019900)			breast(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(8)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31			GBM - Glioblastoma multiforme(3;0.0823)			CATTGTCAAATGCACAACCAG	0.378																																					p.N628N		Atlas-SNP	.											.	TAX1BP1	71	.	0			c.T1884C						PASS	.						160	156	157					7																	27856087		2203	4300	6503	SO:0001819	synonymous_variant	8887	exon14			GTCAAATGCACAA	U33821	CCDS5415.1, CCDS43561.1, CCDS56471.1	7p15	2010-08-05			ENSG00000106052	ENSG00000106052			11575	protein-coding gene	gene with protein product		605326				10435631	Standard	NM_006024		Approved	TXBP151, CALCOCO3	uc003szl.3	Q86VP1	OTTHUMG00000023377	ENST00000396319.2:c.1884T>C	chr7.hg19:g.27856087T>C		347.0	0.0	.		298.0	100.0	.	NM_006024	B4DKU7|E7ENV2|O60398|O95770|Q13311|Q9BQG5|Q9UI88	Silent	SNP	ENST00000396319.2	hg19	CCDS5415.1																																																																																			.	.	.	none		0.378	TAX1BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214142.1	NM_006024		C	27856087	T	C	27856087	2	2	120	1	0	0	0	0	0	0	0	1	15606	1461	51	3		3	TAX1BP1	7	27856087	Silent	SNP	T	TCGA-BQ-5885-01A-11D-1589-08		27856087	131282576	38	7619											
ZNF679	168417	hgsc.bcm.edu	37	chr7	63721262	63721262	+	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	cctgtctggagcaaaataaaGagccttggaatataaagaga	17	8	10	6	0	1	2	0	0	1	2	1	5	1	4	2	2	2	1	2	2	8	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr7:63721262G>A	ENST00000421025.1	+	4	486	c.217G>A	c.(217-219)Gag>Aag	p.E73K	ZNF679_ENST00000255746.4_Missense_Mutation_p.E73K	NM_001159524.1|NM_153363.2	NP_001152996.1|NP_699194.2	Q8IYX0	ZN679_HUMAN	zinc finger protein 679	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)			endometrium(2)|kidney(3)|lung(11)|skin(1)|stomach(1)	18						GCAAAATAAAGAGCCTTGGAA	0.378																																					p.E73K		Atlas-SNP	.											.	ZNF679	80	.	0			c.G217A						PASS	.						121	109	113					7																	63721262		692	1591	2283	SO:0001583	missense	168417	exon4			AATAAAGAGCCTT	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.217G>A	chr7.hg19:g.63721262G>A	ENSP00000416809:p.Glu73Lys	73.0	0.0	.		60.0	24.0	.	NM_153363		Missense_Mutation	SNP	ENST00000421025.1	hg19	CCDS47592.1	.	.	.	.	.	.	.	.	.	.	G	5.786	0.329447	0.10956	.	.	ENSG00000197123	ENST00000421025;ENST00000255746	T;T	0.07800	3.16;3.16	0.235	0.235	0.15431	Krueppel-associated box (2);	.	.	.	.	T	0.07818	0.0196	L	0.47716	1.5	0.09310	N	1	B	0.14012	0.009	B	0.15052	0.012	T	0.32241	-0.9914	8	0.46703	T	0.11	.	.	.	.	.	73	Q8IYX0	ZN679_HUMAN	K	73	ENSP00000416809:E73K;ENSP00000255746:E73K	ENSP00000255746:E73K	E	+	1	0	ZNF679	63358697	0.303000	0.24463	0.027000	0.17364	0.031000	0.12232	1.500000	0.35682	0.308000	0.22923	0.313000	0.20887	GAG	.	.	.	none		0.378	ZNF679-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344317.2	NM_153363		A	63721262	G	A	63721262	3	1	120	1	0	0	0	0	1	0	0	0	18098	943	33	2	227	2	ZNF679	7	63721262	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	35865175	63721262	95417401	39	7620											
DMTF1	9988	hgsc.bcm.edu	37	chr7	86802963	86802966	+	Splice_Site	DEL	AAGG	AAGG	-																															taaggattctctgactaataAaggtaagataacactgtgaa																								rs138809401		TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	AAGG	AAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr7:86802963_86802966delAAGG	ENST00000394703.5	+	8	1003_1005	c.440_442delAAGG	c.(439-444)aaaggg>agg	p.KG147fs	DMTF1_ENST00000411766.2_Splice_Site_p.KG106fs|DMTF1_ENST00000331242.7_Splice_Site_p.KG147fs|DMTF1_ENST00000413276.2_Splice_Site_p.KG147fs|DMTF1_ENST00000414194.2_5'UTR|DMTF1_ENST00000394702.3_Splice_Site_p.KG147fs|DMTF1_ENST00000432937.2_Splice_Site_p.KG59fs	NM_021145.3	NP_066968.3	Q9Y222	DMTF1_HUMAN	cyclin D binding myb-like transcription factor 1	147	Interaction with CCND2. {ECO:0000250}.|Required for DNA-binding. {ECO:0000250}.|Required for transcriptional activation. {ECO:0000250}.				cell cycle (GO:0007049)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)	16	Esophageal squamous(14;0.0058)					CTGACTAATAAAGGTAAGATAACA	0.382																																					p.147_148del		Atlas-INDEL	.											.	DMTF1	48	.	0			c.439_442del						PASS	.																																			SO:0001630	splice_region_variant	9988	exon6			.	AF084530	CCDS5601.1, CCDS47633.1	7q21	2014-06-25			ENSG00000135164	ENSG00000135164			14603	protein-coding gene	gene with protein product	"cyclin D-binding Myb-like protein"	608491				10095122, 24958102	Standard	NR_024549		Approved	DMP1, DMTF, hDMP1, MRUL	uc003uih.3	Q9Y222	OTTHUMG00000154135	ENST00000394703.5:c.442+1AAGG>-	chr7.hg19:g.86802963_86802966delAAGG		74.0	0.0	0		53.0	12.0	0.226415	NM_001142327	B2RBE1|B4DJS5|Q05C48|Q59G79|Q6IS13|Q969T2|Q9H2Z2|Q9H2Z3	Frame_Shift_Del	DEL	ENST00000394703.5	hg19	CCDS5601.1																																																																																			.	.	.	none		0.382	DMTF1-002	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334025.5	NM_021145	Frame_Shift_Del	-	86802966	AAGG	-	86802963	8	5	120	1	0	1	0	1	0	0	1	0	4594	14	1	0	454	0	DMTF1	7	86802963	Splice_Site	DEL	AAGG	TCGA-BQ-5885-01A-11D-1589-08	23081701	86802963	72335700	40	7621											
AKAP9	10142	hgsc.bcm.edu	37	chr7	91631868	91631868	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaagtaaaagatgatttagaAgacagtaaaaataaacagga	24	7	8	2	0	0	4	0	1	0	3	0	5	0	5	0	1	1	2	0	1	10	5			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr7:91631868A>G	ENST00000359028.2	+	9	2898	c.2673A>G	c.(2671-2673)gaA>gaG	p.E891E	AKAP9_ENST00000356239.3_Silent_p.E879E|AKAP9_ENST00000358100.2_Silent_p.E891E			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	891	Glu-rich.				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)			ATGATTTAGAAGACAGTAAAA	0.294			T	BRAF	papillary thyroid																																p.E879E		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.A2637G						PASS	.						45	50	48					7																	91631868		2199	4289	6488	SO:0001819	synonymous_variant	10142	exon8			TTTAGAAGACAGT	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.2673A>G	chr7.hg19:g.91631868A>G		98.0	0.0	.		75.0	21.0	.	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Silent	SNP	ENST00000359028.2	hg19																																																																																				.	.	.	none		0.294	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		G	91631868	A	G	91631868	2	3	120	1	0	0	0	0	0	0	0	1	459	69	3	3		3	AKAP9	7	91631868	Silent	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	4828905	91631868	67506795	41	7622											
PEX1	5189	hgsc.bcm.edu	37	chr7	92119227	92119227	+	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	cagagagacattgtgagctcTgcatggtaaattgtagtaat	13	12	11	5	0	1	3	0	1	1	2	1	4	1	3	0	1	2	5	0	1	4	5			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr7:92119227T>C	ENST00000248633.4	-	22	3534		c.e22-2		PEX1_ENST00000438045.1_Splice_Site|AC007566.10_ENST00000427458.1_RNA|AC007566.10_ENST00000441539.1_RNA|PEX1_ENST00000428214.1_Splice_Site	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1						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)			TTGTGAGCTCTGCATGGTAAA	0.393																																					.		Atlas-SNP	.											.	PEX1	102	.	0			c.3439-2A>G						PASS	.						48	44	45					7																	92119227		2203	4300	6503	SO:0001630	splice_region_variant	5189	exon23			GAGCTCTGCATGG	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.3439-2A>G	chr7.hg19:g.92119227T>C		63.0	0.0	.		48.0	21.0	.	NM_000466	A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Splice_Site	SNP	ENST00000248633.4	hg19	CCDS5627.1	.	.	.	.	.	.	.	.	.	.	T	16.09	3.023778	0.54683	.	.	ENSG00000127980	ENST00000438045;ENST00000248633;ENST00000428214	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2209	0.65826	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PEX1	91957163	1.000000	0.71417	0.995000	0.50966	0.747000	0.42532	6.048000	0.71046	2.230000	0.72887	0.528000	0.53228	.	.	.	.	none		0.393	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466	Intron	C	92119227	T	C	92119227	5	2	120	1	0	0	0	0	0	0	1	0	11742	1594	55	3	426	3	PEX1	7	92119227	Splice_Site	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	487359	92119227	67019436	42	7623											
SLC7A2	6542	hgsc.bcm.edu	37	chr8	17401959	17401959	+	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	tctctgttctgttttgggaaGgtacatcaagtgttgcaaga	9	15	11	6	0	3	1	1	0	2	1	4	2	3	2	0	2	2	5	0	2	4	5			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr8:17401959G>T	ENST00000494857.1	+	4	594		c.e4-1		SLC7A2_ENST00000004531.10_Splice_Site|SLC7A2_ENST00000398090.3_Splice_Site|SLC7A2_ENST00000522656.1_Splice_Site|SLC7A2_ENST00000470360.1_Splice_Site	NM_001008539.3	NP_001008539.3	P52569	CTR2_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2						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)	GTTTTGGGAAGGTACATCAAG	0.388																																					.		Atlas-SNP	.											.	SLC7A2	157	.	0			c.377-1G>T						PASS	.						120	121	121					8																	17401959		2203	4300	6503	SO:0001630	splice_region_variant	6542	exon3			TGGGAAGGTACAT	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.377-1G>T	chr8.hg19:g.17401959G>T		142.0	0.0	.		127.0	41.0	.	NM_001008539	B7ZL54|O15291|O15292|Q14CQ6|Q6NSZ7|Q86TC6	Splice_Site	SNP	ENST00000494857.1	hg19	CCDS34852.1	.	.	.	.	.	.	.	.	.	.	G	17.63	3.437083	0.62955	.	.	ENSG00000003989	ENST00000494857;ENST00000522656;ENST00000470360;ENST00000004531;ENST00000398090	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8219	0.96602	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC7A2	17446335	1.000000	0.71417	1.000000	0.80357	0.574000	0.36063	9.823000	0.99369	2.767000	0.95098	0.563000	0.77884	.	.	.	.	none		0.388	SLC7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253367.3	NM_003046	Intron	T	17401959	G	T	17401959	5	4	120	1	0	0	0	0	0	0	1	0	14710	1014	35	4	506	4	SLC7A2	8	17401959	Splice_Site	SNP	G	TCGA-BQ-5885-01A-11D-1589-08		17401959	128962063	43	7624											
ADAMDEC1	27299	hgsc.bcm.edu	37	chr8	24256052	24256052	+	Frame_Shift_Del	DEL	C	C	-																															tttgtgtttgatgtgatgaaCctactcaatgtggtaagaca																								rs2291576	byFrequency	TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr8:24256052delC	ENST00000256412.4	+	8	970	c.750delC	c.(748-750)aacfs	p.N250fs	RP11-624C23.1_ENST00000523578.1_RNA|ADAMDEC1_ENST00000538205.1_Frame_Shift_Del_p.N171fs|RP11-624C23.1_ENST00000519689.1_RNA|ADAMDEC1_ENST00000522298.1_Frame_Shift_Del_p.N171fs	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	250	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)		ATGTGATGAACCTACTCAATG	0.338																																					p.N250fs	Ovarian(147;687 1849 3699 25981 31337)	Atlas-INDEL	.											ADAMDEC1_ENST00000256412,NS,malignant_melanoma,0,1	ADAMDEC1	69	.	0			c.749delA						PASS	.						190	182	185					8																	24256052		2203	4300	6503	SO:0001589	frameshift_variant	27299	exon8			.	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.750delC	chr8.hg19:g.24256052delC	ENSP00000256412:p.Asn250fs	186.0	0.0	0		165.0	55.0	0.333333	NM_014479	B7ZAK5	Frame_Shift_Del	DEL	ENST00000256412.4	hg19	CCDS6044.1																																																																																			.	.	.	none		0.338	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479		-	24256052	C	-	24256052	7	5	120	1	0	1	0	1	0	0	0	0	254	506	18	0	780	0	ADAMDEC1	8	24256052	Frame_Shift_Del	DEL	C	TCGA-BQ-5885-01A-11D-1589-08	6854093	24256052	122107970	44	7625											
EBF2	64641	hgsc.bcm.edu	37	chr8	25715868	25715868	+	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	gccggtgggtgagccatttaGaaatcctggtgaacctggaa	10	9	14	8	1	0	3	0	2	0	1	1	4	1	4	4	4	2	0	4	4	4	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr8:25715868G>A	ENST00000520164.1	-	14	2032	c.1495C>T	c.(1495-1497)Cta>Tta	p.L499L	EBF2_ENST00000535548.1_Silent_p.L230L|EBF2_ENST00000408929.3_Silent_p.L351L	NM_022659.3	NP_073150.2	Q9HAK2	COE2_HUMAN	early B-cell factor 2	499	Pro/Ser/Thr-rich.				adipose tissue development (GO:0060612)|brown fat cell differentiation (GO:0050873)|cell fate determination (GO:0001709)|positive regulation of chromatin binding (GO:0035563)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(3)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)		GAGCCATTTAGAAATCCTGGT	0.483																																					p.L499L	Esophageal Squamous(166;1018 1046 3854 8328 13429 13634 14071 26624 32918)	Atlas-SNP	.											.	EBF2	138	.	0			c.C1495T						PASS	.						125	125	125					8																	25715868		1950	4140	6090	SO:0001819	synonymous_variant	64641	exon14			CATTTAGAAATCC	AK021562, AK001144	CCDS43726.1	8p21.1	2007-07-26			ENSG00000221818	ENSG00000221818			19090	protein-coding gene	gene with protein product		609934				9151732	Standard	NM_022659		Approved	FLJ11500, COE2	uc003xes.2	Q9HAK2	OTTHUMG00000163838	ENST00000520164.1:c.1495C>T	chr8.hg19:g.25715868G>A		120.0	0.0	.		74.0	24.0	.	NM_022659	A0PJM4|A6NMF7|F5H645|Q66VZ3|Q6DK36|Q6IS86|Q6ISA4	Silent	SNP	ENST00000520164.1	hg19	CCDS43726.1																																																																																			.	.	.	none		0.483	EBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375886.2	NM_022659		A	25715868	G	A	25715868	2	1	120	1	0	0	0	0	0	0	0	1	4883	933	33	2		2	EBF2	8	25715868	Silent	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	1459816	25715868	120648154	45	7626											
SYBU	55638	hgsc.bcm.edu	37	chr8	110587763	110587763	+	Frame_Shift_Del	DEL	T	T	-																															tggaatgcacaagctccaggTcaccagattctgtggtggtg																										TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr8:110587763delT	ENST00000422135.1	-	8	1879	c.1364delA	c.(1363-1365)gacfs	p.D455fs	SYBU_ENST00000399066.3_Frame_Shift_Del_p.D452fs|SYBU_ENST00000440310.1_Frame_Shift_Del_p.D455fs|SYBU_ENST00000528647.1_Frame_Shift_Del_p.D454fs|SYBU_ENST00000528331.1_Frame_Shift_Del_p.D336fs|SYBU_ENST00000533895.1_Frame_Shift_Del_p.D454fs|SYBU_ENST00000276646.9_Frame_Shift_Del_p.D455fs|SYBU_ENST00000529175.1_Frame_Shift_Del_p.D249fs|SYBU_ENST00000419099.1_Frame_Shift_Del_p.D454fs|SYBU_ENST00000529690.1_Frame_Shift_Del_p.D325fs|SYBU_ENST00000533065.1_Frame_Shift_Del_p.D336fs|SYBU_ENST00000533171.1_Frame_Shift_Del_p.D455fs|SYBU_ENST00000433638.1_Frame_Shift_Del_p.D455fs|SYBU_ENST00000424158.2_Frame_Shift_Del_p.D460fs|SYBU_ENST00000527707.1_5'Flank|SYBU_ENST00000532779.1_Frame_Shift_Del_p.D387fs|SYBU_ENST00000408889.3_Frame_Shift_Del_p.D336fs|SYBU_ENST00000408908.2_Frame_Shift_Del_p.D455fs|SYBU_ENST00000446070.2_Frame_Shift_Del_p.D454fs	NM_001099744.1	NP_001093214.1	Q9NX95	SYBU_HUMAN	syntabulin (syntaxin-interacting)	455					regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|dense body (GO:0097433)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	30						AAGCTCCAGGTCACCAGATTC	0.577																																					p.D455fs		Atlas-INDEL	.											SYBU,NS,carcinoma,0,1	SYBU	71	.	0			c.1365delC						PASS	.						133	137	136					8																	110587763		2102	4215	6317	SO:0001589	frameshift_variant	55638	exon8			.	AB040905	CCDS43763.1, CCDS43764.1, CCDS47912.1, CCDS55271.1	8q23.2	2010-08-27				ENSG00000147642			26011	protein-coding gene	gene with protein product	"syntaphilin-like"	611568				17611281, 16750881, 16157705, 15656992, 15459722	Standard	NM_001099743		Approved	FLJ20366, GOLSYN, KIAA1472, OCSYN, SNPHL	uc003ynj.4	Q9NX95		ENST00000422135.1:c.1364delA	chr8.hg19:g.110587763delT	ENSP00000407118:p.Asp455fs	109.0	0.0	0		122.0	40.0	0.327869	NM_001099752	A8K354|B3KQX3|B3KU61|Q5R1T1|Q5R1T2|Q5R1T3|Q5Y2M6|Q8ND49|Q8TCR6|Q96D80|Q9P256	Frame_Shift_Del	DEL	ENST00000422135.1	hg19	CCDS47912.1																																																																																			.	.	.	none		0.577	SYBU-204	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385501.1	NM_017786		-	110587763	T	-	110587763	7	5	120	1	0	1	0	1	0	0	0	0	15439	1667	58	0	631	0	SYBU	8	110587763	Frame_Shift_Del	DEL	T	TCGA-BQ-5885-01A-11D-1589-08	84871895	110587763	35776259	46	7627											
PHF20L1	51105	hgsc.bcm.edu	37	chr8	133854952	133854952	+	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	ggaacttatataacaagtgaGcatagctatcaaaagccaca	18	8	7	8	0	1	1	1	1	0	0	1	2	1	2	1	1	5	2	1	1	9	5			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr8:133854952G>C	ENST00000395386.2	+	19	2879	c.2580G>C	c.(2578-2580)gaG>gaC	p.E860D	AF230666.2_ENST00000429151.1_RNA|PHF20L1_ENST00000395390.2_Missense_Mutation_p.E835D|PHF20L1_ENST00000220847.7_Missense_Mutation_p.E247D|AF230666.2_ENST00000608375.1_RNA	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	860							zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			TAACAAGTGAGCATAGCTATC	0.398																																					p.E860D		Atlas-SNP	.											.	PHF20L1	129	.	0			c.G2580C						PASS	.						74	70	71					8																	133854952		1849	4099	5948	SO:0001583	missense	51105	exon19			AAGTGAGCATAGC	AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"Tudor domain containing", "Zinc fingers, PHD-type"	24280	protein-coding gene	gene with protein product	"tudor domain containing 20B"					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.2580G>C	chr8.hg19:g.133854952G>C	ENSP00000378784:p.Glu860Asp	86.0	0.0	.		104.0	49.0	.	NM_016018	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Missense_Mutation	SNP	ENST00000395386.2	hg19	CCDS6367.2	.	.	.	.	.	.	.	.	.	.	G	19.31	3.803425	0.70682	.	.	ENSG00000129292	ENST00000395386;ENST00000220847;ENST00000395390	T;T	0.54479	0.61;0.57	5.11	1.23	0.21249	.	0.365573	0.21339	U	0.076161	T	0.66655	0.2811	M	0.76574	2.34	0.33710	D	0.6156	D;D	0.67145	0.996;0.993	D;D	0.75484	0.986;0.967	T	0.71424	-0.4597	10	0.39692	T	0.17	-4.2073	9.4695	0.38833	0.2956:0.0:0.7044:0.0	.	835;860	F8W9L8;A8MW92	.;P20L1_HUMAN	D	860;247;835	ENSP00000378784:E860D;ENSP00000378788:E835D	ENSP00000220847:E247D	E	+	3	2	PHF20L1	133924134	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.184000	0.32053	0.261000	0.21753	0.650000	0.86243	GAG	.	.	.	none		0.398	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018		C	133854952	G	C	133854952	3	2	120	1	0	0	0	0	1	0	0	0	11839	962	34	4	2746	4	PHF20L1	8	133854952	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	23267189	133854952	12509070	47	7628											
EPPK1	83481	hgsc.bcm.edu	37	chr8	144944250	144944250	+	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	aatggccactggcatggggaGgtggtggtggctggtggggt	5	9	22	5	0	0	0	0	0	0	0	0	1	0	1	1	11	0	2	1	11	1	0			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr8:144944250G>T	ENST00000525985.1	-	2	3243	c.3172C>A	c.(3172-3174)Ctc>Atc	p.L1058I				P58107	EPIPL_HUMAN	epiplakin 1	1058						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)			GGCATGGGGAGGTGGTGGTGG	0.622																																					p.L1058I		Atlas-SNP	.											.	EPPK1	199	.	0			c.C3172A						PASS	.						33	38	36					8																	144944250		2118	4239	6357	SO:0001583	missense	83481	exon1			TGGGGAGGTGGTG	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.3172C>A	chr8.hg19:g.144944250G>T	ENSP00000436337:p.Leu1058Ile	20.0	0.0	.		22.0	6.0	.	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	hg19		.	.	.	.	.	.	.	.	.	.	G	12.43	1.936941	0.34189	.	.	ENSG00000227184	ENST00000525985	T	0.79247	-1.25	4.4	2.49	0.30216	.	.	.	.	.	T	0.61813	0.2377	L	0.31207	0.915	0.25590	N	0.98671	B	0.27700	0.186	B	0.24701	0.055	T	0.46034	-0.9220	9	0.19590	T	0.45	.	7.0089	0.24851	0.0:0.32:0.5041:0.1759	.	1058	E9PPU0	.	I	1058	ENSP00000436337:L1058I	ENSP00000436337:L1058I	L	-	1	0	EPPK1	145016238	0.002000	0.14202	0.982000	0.44146	0.140000	0.21249	-0.269000	0.08596	2.242000	0.73789	0.563000	0.77884	CTC	.	.	.	none		0.622	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		T	144944250	G	T	144944250	3	4	120	1	0	0	0	0	1	0	0	0	5192	1000	35	4	4094	4	EPPK1	8	144944250	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	11089298	144944250	1419772	48	7629											
ARHGAP39	80728	hgsc.bcm.edu	37	chr8	145806407	145806407	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggcgcgcggggactccgtgTtctgcttcagcgtctgcagc	4	9	15	13	5	3	0	1	0	2	0	4	1	4	1	1	3	4	3	1	3	0	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr8:145806407T>C	ENST00000276826.5	-	2	536	c.335A>G	c.(334-336)aAc>aGc	p.N112S	ARHGAP39_ENST00000540274.1_Missense_Mutation_p.N112S|ARHGAP39_ENST00000377307.2_Missense_Mutation_p.N112S			Q9C0H5	RHG39_HUMAN	Rho GTPase activating protein 39	112					axon guidance (GO:0007411)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22						GGACTCCGTGTTCTGCTTCAG	0.706																																					p.N112S		Atlas-SNP	.											.	ARHGAP39	80	.	0			c.A335G						PASS	.						14	15	15					8																	145806407		2190	4288	6478	SO:0001583	missense	80728	exon4			TCCGTGTTCTGCT		CCDS34971.1	8q24.3	2011-06-29			ENSG00000147799	ENSG00000147799		"Rho GTPase activating proteins"	29351	protein-coding gene	gene with protein product	"RhoGAP93B homolog (Drosophila)", "crossGAP homolog (Drosophila)"	615880				15755809	Standard	XM_005272344		Approved	KIAA1688, Vilse, CrGAP	uc003zds.1	Q9C0H5	OTTHUMG00000165182	ENST00000276826.5:c.335A>G	chr8.hg19:g.145806407T>C	ENSP00000276826:p.Asn112Ser	9.0	0.0	.		16.0	7.0	.	NM_025251	B4E1I1	Missense_Mutation	SNP	ENST00000276826.5	hg19		.	.	.	.	.	.	.	.	.	.	T	14.91	2.676795	0.47886	.	.	ENSG00000147799	ENST00000276826;ENST00000377307;ENST00000540274	T;T;T	0.14022	2.54;2.54;2.54	5.4	4.25	0.50352	.	0.385486	0.28865	N	0.013896	T	0.10680	0.0261	N	0.20574	0.59	0.33264	D	0.560137	B;B	0.28512	0.111;0.214	B;B	0.37239	0.074;0.244	T	0.17930	-1.0353	10	0.37606	T	0.19	-3.2953	7.9013	0.29736	0.0:0.0945:0.0:0.9055	.	112;112	Q9C0H5;Q9C0H5-2	RHG39_HUMAN;.	S	112	ENSP00000276826:N112S;ENSP00000366522:N112S;ENSP00000445075:N112S	ENSP00000276826:N112S	N	-	2	0	ARHGAP39	145777215	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	0.946000	0.29069	0.882000	0.36016	0.445000	0.29226	AAC	.	.	.	none		0.706	ARHGAP39-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382509.1			C	145806407	T	C	145806407	3	2	120	1	0	0	0	0	1	0	0	0	884	1725	60	3	3049	3	ARHGAP39	8	145806407	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	862157	145806407	557615	49	7630											
SMC5	23137	hgsc.bcm.edu	37	chr9	72901129	72901129	+	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	tttacaggcaacagatattaAggaggcatctcaaaaatgca	17	9	8	7	0	1	1	1	0	1	1	2	2	1	2	0	3	3	3	0	3	6	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr9:72901129A>T	ENST00000361138.5	+	8	1053	c.995A>T	c.(994-996)aAg>aTg	p.K332M		NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	332					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						ACAGATATTAAGGAGGCATCT	0.353																																					p.K332M		Atlas-SNP	.											.	SMC5	96	.	0			c.A995T						PASS	.						65	74	71					9																	72901129		2203	4300	6503	SO:0001583	missense	23137	exon8			ATATTAAGGAGGC	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.995A>T	chr9.hg19:g.72901129A>T	ENSP00000354957:p.Lys332Met	167.0	0.0	.		104.0	37.0	.	NM_015110	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Missense_Mutation	SNP	ENST00000361138.5	hg19	CCDS6632.1	.	.	.	.	.	.	.	.	.	.	A	17.68	3.450498	0.63290	.	.	ENSG00000198887	ENST00000361138	T	0.20598	2.06	5.34	2.93	0.34026	RecF/RecN/SMC (1);	0.052632	0.64402	D	0.000001	T	0.37999	0.1024	M	0.66939	2.045	0.54753	D	0.999983	D	0.89917	1.0	D	0.81914	0.995	T	0.10382	-1.0632	10	0.54805	T	0.06	-18.9526	6.4737	0.22024	0.7458:0.0:0.1261:0.1282	.	332	Q8IY18	SMC5_HUMAN	M	332	ENSP00000354957:K332M	ENSP00000354957:K332M	K	+	2	0	SMC5	72090949	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	1.657000	0.37366	0.949000	0.37715	0.402000	0.26972	AAG	.	.	.	none		0.353	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110		T	72901129	A	T	72901129	3	4	120	1	0	0	0	0	1	0	0	0	14799	72	3	5	1025	5	SMC5	9	72901129	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08		72901129	68312302	50	7631											
PAPPA	5069	hgsc.bcm.edu	37	chr9	118997553	118997553	+	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	cgagctggagttcctctaccCcttggtccctgagtctctga	5	12	10	14	1	2	2	0	2	2	0	5	4	4	3	4	2	2	2	4	2	1	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr9:118997553C>G	ENST00000328252.3	+	7	2738	c.2369C>G	c.(2368-2370)cCc>cGc	p.P790R	PAPPA_ENST00000534838.1_Intron	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	790					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						TTCCTCTACCCCTTGGTCCCT	0.567																																					p.P790R		Atlas-SNP	.											.	PAPPA	243	.	0			c.C2369G						PASS	.						116	93	101					9																	118997553		2203	4300	6503	SO:0001583	missense	5069	exon7			TCTACCCCTTGGT		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.2369C>G	chr9.hg19:g.118997553C>G	ENSP00000330658:p.Pro790Arg	110.0	0.0	.		85.0	31.0	.	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Missense_Mutation	SNP	ENST00000328252.3	hg19	CCDS6813.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.446744	0.63178	.	.	ENSG00000182752	ENST00000328252;ENST00000443904	T	0.01947	4.54	6.04	6.04	0.98038	.	0.148253	0.64402	D	0.000007	T	0.14184	0.0343	M	0.74881	2.28	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74023	0.982;0.921	T	0.00005	-1.2530	10	0.87932	D	0	-8.2519	20.5948	0.99439	0.0:1.0:0.0:0.0	.	234;790	E7EMD3;Q13219	.;PAPP1_HUMAN	R	790;234	ENSP00000330658:P790R	ENSP00000330658:P790R	P	+	2	0	PAPPA	118037374	1.000000	0.71417	0.819000	0.32651	0.753000	0.42808	7.779000	0.85648	2.873000	0.98535	0.563000	0.77884	CCC	.	.	.	none		0.567	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		G	118997553	C	G	118997553	3	3	120	1	0	0	0	0	1	0	0	0	11439	623	22	4	2395	4	PAPPA	9	118997553	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	46096424	118997553	22215878	51	7632											
JMJD1C	221037	hgsc.bcm.edu	37	chr10	64960365	64960365	+	Frame_Shift_Del	DEL	A	A	-																															cacagcaggagtcatcctgtAaaaaggattccccagtttgc																										TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr10:64960365delA	ENST00000399262.2	-	11	5365	c.5147delT	c.(5146-5148)ttafs	p.L1716fs	JMJD1C_ENST00000399251.1_Intron|JMJD1C_ENST00000542921.1_Frame_Shift_Del_p.L1534fs|JMJD1C_ENST00000402544.1_Frame_Shift_Del_p.L1497fs	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	1716					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)					GTCATCCTGTAAAAAGGATTC	0.413																																					p.L1716fs		Atlas-INDEL	.											.	JMJD1C	347	.	0			c.5148delA						PASS	.						83	76	78					10																	64960365		1855	4105	5960	SO:0001589	frameshift_variant	221037	exon11			.	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.5147delT	chr10.hg19:g.64960365delA	ENSP00000382204:p.Leu1716fs	91.0	0.0	0		89.0	32.0	0.359551	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Frame_Shift_Del	DEL	ENST00000399262.2	hg19	CCDS41532.1																																																																																			.	.	.	none		0.413	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		-	64960365	A	-	64960365	7	5	120	1	0	1	0	1	0	0	0	0	7957	372	13	0	2539	0	JMJD1C	10	64960365	Frame_Shift_Del	DEL	A	TCGA-BQ-5885-01A-11D-1589-08		64960365	70574382	52	7633											
USP54	159195	hgsc.bcm.edu	37	chr10	75294429	75294429	+	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	ctgtcccctgagaatcagaaGagaagtgactgaccacagac	14	6	10	11	0	1	6	1	3	0	4	2	8	2	6	3	0	0	0	3	0	3	0			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr10:75294429G>A	ENST00000339859.4	-	11	1344	c.1244C>T	c.(1243-1245)tCt>tTt	p.S415F	USP54_ENST00000408019.1_Missense_Mutation_p.S415F|USP54_ENST00000428547.1_Missense_Mutation_p.S265F|USP54_ENST00000319786.7_Missense_Mutation_p.S415F|USP54_ENST00000394811.2_5'UTR|USP54_ENST00000497106.1_Intron			Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54	415					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)					AGAATCAGAAGAGAAGTGACT	0.498																																					p.S415F	Colon(195;880 2046 8854 25025 38456)	Atlas-SNP	.											.	USP54	178	.	0			c.C1244T						PASS	.						134	130	131					10																	75294429		1925	4124	6049	SO:0001583	missense	159195	exon10			TCAGAAGAGAAGT	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.1244C>T	chr10.hg19:g.75294429G>A	ENSP00000345216:p.Ser415Phe	100.0	0.0	.		89.0	31.0	.	NM_152586	A1L4Q4|A3KFK3|A3KFK5|A3KFK6|A3KFK7|A6PVS4|A6PVS5|A6PVS6|A6PVS7|B3KVY1|B9ZVM1|Q5F2F4|Q6P1N6|Q6ZSP1|Q6ZSR1|Q6ZTM0|Q8N1X2	Missense_Mutation	SNP	ENST00000339859.4	hg19	CCDS7329.2	.	.	.	.	.	.	.	.	.	.	G	28.4	4.915589	0.92178	.	.	ENSG00000166348	ENST00000339859;ENST00000408019;ENST00000428547;ENST00000319786	T;T;T	0.38240	1.25;1.25;1.15	5.54	5.54	0.83059	.	0.801566	0.09945	U	0.735488	T	0.56411	0.1983	L	0.38175	1.15	0.46774	D	0.999197	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.85130	0.996;0.996;0.997	T	0.54029	-0.8354	10	0.72032	D	0.01	-5.8858	19.5024	0.95100	0.0:0.0:1.0:0.0	.	415;415;415	B7Z7X1;Q70EL1-6;Q70EL1	.;.;UBP54_HUMAN	F	415;415;265;415	ENSP00000345216:S415F;ENSP00000386080:S415F;ENSP00000408714:S265F	ENSP00000326547:S415F	S	-	2	0	USP54	74964435	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.017000	0.93651	2.607000	0.88179	0.655000	0.94253	TCT	.	.	.	none		0.498	USP54-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316563.2	NM_152586		A	75294429	G	A	75294429	3	1	120	1	0	0	0	0	1	0	0	0	17097	942	33	2	3862	2	USP54	10	75294429	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	10334064	75294429	60240318	53	7634											
GBF1	8729	hgsc.bcm.edu	37	chr10	104130513	104130513	+	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	ttcgagaccatctataccacCtctgtgttcaggcacaagat	11	11	7	12	1	3	2	1	0	2	2	4	3	3	2	3	1	1	2	3	1	3	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr10:104130513C>A	ENST00000369983.3	+	29	3813	c.3553C>A	c.(3553-3555)Ctc>Atc	p.L1185I		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	1185					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		TCTATACCACCTCTGTGTTCA	0.552																																					p.L1186I		Atlas-SNP	.											.	GBF1	142	.	0			c.C3556A						PASS	.						225	181	196					10																	104130513		2203	4300	6503	SO:0001583	missense	8729	exon29			TACCACCTCTGTG	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.3553C>A	chr10.hg19:g.104130513C>A	ENSP00000359000:p.Leu1185Ile	239.0	0.0	.		179.0	62.0	.	NM_001199378	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	hg19	CCDS7533.1	.	.	.	.	.	.	.	.	.	.	C	18.07	3.541954	0.65198	.	.	ENSG00000107862	ENST00000369983	T	0.10573	2.86	5.36	2.53	0.30540	.	0.000000	0.85682	D	0.000000	T	0.15609	0.0376	L	0.29908	0.895	0.53005	D	0.999965	D;D;D	0.63880	0.985;0.968;0.993	P;P;D	0.70016	0.614;0.53;0.967	T	0.09862	-1.0655	10	0.12766	T	0.61	-10.2271	9.4682	0.38826	0.0:0.7169:0.0:0.2831	.	1185;1185;1185	Q149P1;Q149P0;Q92538	.;.;GBF1_HUMAN	I	1185	ENSP00000359000:L1185I	ENSP00000359000:L1185I	L	+	1	0	GBF1	104120503	0.999000	0.42202	0.991000	0.47740	0.997000	0.91878	2.530000	0.45641	0.402000	0.25451	0.655000	0.94253	CTC	.	.	.	none		0.552	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			A	104130513	C	A	104130513	3	1	120	1	0	0	0	0	1	0	0	0	6278	681	24	4	3663	4	GBF1	10	104130513	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	28836084	104130513	31404234	54	7635											
CNNM2	54805	hgsc.bcm.edu	37	chr10	104679308	104679308	+	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	ggtatcgtcatcttcggagaGatcgtgccccaggccatctg	7	10	12	12	3	3	1	1	0	2	1	6	3	3	2	3	3	1	1	3	3	1	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr10:104679308G>T	ENST00000369878.4	+	1	1259	c.1071G>T	c.(1069-1071)gaG>gaT	p.E357D	CNNM2_ENST00000433628.2_Missense_Mutation_p.E357D|CNNM2_ENST00000369875.3_Missense_Mutation_p.E357D	NM_017649.4	NP_060119.3	Q9H8M5	CNNM2_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 2	357	DUF21.				magnesium ion homeostasis (GO:0010960)|magnesium ion transport (GO:0015693)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	adenyl nucleotide binding (GO:0030554)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		TCTTCGGAGAGATCGTGCCCC	0.607																																					p.E357D		Atlas-SNP	.											.	CNNM2	119	.	0			c.G1071T						PASS	.						76	75	75					10																	104679308		2203	4300	6503	SO:0001583	missense	54805	exon1			CGGAGAGATCGTG	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.1071G>T	chr10.hg19:g.104679308G>T	ENSP00000358894:p.Glu357Asp	129.0	0.0	.		125.0	42.0	.	NM_199076	Q5T569|Q5T570|Q8WU59|Q9H952|Q9NRK5|Q9NXT4	Missense_Mutation	SNP	ENST00000369878.4	hg19	CCDS44474.1	.	.	.	.	.	.	.	.	.	.	G	14.63	2.594054	0.46214	.	.	ENSG00000148842	ENST00000457502;ENST00000433628;ENST00000369875;ENST00000369878;ENST00000345419;ENST00000541201	D;D;D	0.94576	-3.46;-3.46;-3.46	4.32	2.42	0.29668	Domain of unknown function DUF21 (1);	0.112531	0.64402	D	0.000007	D	0.97642	0.9227	H	0.95950	3.745	0.80722	D	1	D;D;D	0.89917	0.985;0.988;1.0	D;D;D	0.91635	0.972;0.984;0.999	D	0.96198	0.9143	10	0.87932	D	0	.	8.1171	0.30950	0.2718:0.0:0.7282:0.0	.	357;357;357	Q9H8M5-2;Q9H8M5;F5H1I3	.;CNNM2_HUMAN;.	D	357	ENSP00000392875:E357D;ENSP00000358891:E357D;ENSP00000358894:E357D	ENSP00000286899:E357D	E	+	3	2	CNNM2	104669298	1.000000	0.71417	0.998000	0.56505	0.690000	0.40134	2.046000	0.41260	0.262000	0.21774	0.561000	0.74099	GAG	.	.	.	none		0.607	CNNM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050113.3	NM_017649		T	104679308	G	T	104679308	3	4	120	1	0	0	0	0	1	0	0	0	3615	933	33	4	1073	4	CNNM2	10	104679308	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	548795	104679308	30855439	55	7636											
SORCS1	114815	hgsc.bcm.edu	37	chr10	108412294	108412294	+	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	cgccatcagtgcaattattgGaaaccaccttcctgtaccta	11	11	6	13	1	1	0	1	0	0	0	2	1	2	1	5	1	3	2	5	1	5	5			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr10:108412294G>A	ENST00000263054.6	-	18	2328	c.2321C>T	c.(2320-2322)tCc>tTc	p.S774F	SORCS1_ENST00000344440.6_Missense_Mutation_p.S774F|SORCS1_ENST00000369698.1_Missense_Mutation_p.S309F	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	774					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)		GCAATTATTGGAAACCACCTT	0.468																																					p.S774F		Atlas-SNP	.											.	SORCS1	534	.	0			c.C2321T						PASS	.						112	106	108					10																	108412294		2203	4300	6503	SO:0001583	missense	114815	exon18			TTATTGGAAACCA	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.2321C>T	chr10.hg19:g.108412294G>A	ENSP00000263054:p.Ser774Phe	137.0	0.0	.		116.0	37.0	.	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	hg19	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.482881	0.84747	.	.	ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440	T;T;T	0.67523	-0.27;-0.27;-0.27	5.74	5.74	0.90152	VPS10 (1);PKD domain (1);	0.000000	0.85682	D	0.000000	T	0.81735	0.4885	M	0.75777	2.31	0.45979	D	0.998792	D;D;D;D;D	0.58620	0.972;0.983;0.983;0.972;0.983	P;D;D;P;D	0.65684	0.825;0.937;0.915;0.866;0.937	T	0.80571	-0.1323	9	.	.	.	-16.8758	19.9145	0.97053	0.0:0.0:1.0:0.0	.	774;774;774;774;774	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	F	309;774;774	ENSP00000358712:S309F;ENSP00000263054:S774F;ENSP00000345964:S774F	.	S	-	2	0	SORCS1	108402284	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.448000	0.80631	2.709000	0.92574	0.655000	0.94253	TCC	.	.	.	none		0.468	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		A	108412294	G	A	108412294	3	1	120	1	0	0	0	0	1	0	0	0	14943	1174	41	2	1455	2	SORCS1	10	108412294	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	3732986	108412294	27122453	56	7637											
MMP21	118856	hgsc.bcm.edu	37	chr10	127455494	127455494	+	Missense_Mutation	SNP	T	T	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	aatcctctttggataagaatTaagtactcgatttctgttga	12	16	7	6	1	2	2	0	1	2	1	4	4	3	3	1	1	1	2	1	1	5	6			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr10:127455494T>G	ENST00000368808.3	-	7	1446	c.1447A>C	c.(1447-1449)Aat>Cat	p.N483H		NM_147191.1	NP_671724.1	Q8N119	MMP21_HUMAN	matrix metallopeptidase 21	483					hematopoietic progenitor cell differentiation (GO:0002244)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	16		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)			Marimastat(DB00786)	GGATAAGAATTAAGTACTCGA	0.303																																					p.N483H		Atlas-SNP	.											.	MMP21	46	.	0			c.A1447C						PASS	.						67	70	69					10																	127455494		2203	4300	6503	SO:0001583	missense	118856	exon7			AAGAATTAAGTAC	AF331526	CCDS7647.1	10q26.3	2008-07-28	2005-08-08		ENSG00000154485	ENSG00000154485			14357	protein-coding gene	gene with protein product		608416	"matrix metalloproteinase 21"			11255011	Standard	NM_147191		Approved		uc001liu.3	Q8N119	OTTHUMG00000019235	ENST00000368808.3:c.1447A>C	chr10.hg19:g.127455494T>G	ENSP00000357798:p.Asn483His	120.0	0.0	.		98.0	27.0	.	NM_147191	Q5VZP9|Q8NG02	Missense_Mutation	SNP	ENST00000368808.3	hg19	CCDS7647.1	.	.	.	.	.	.	.	.	.	.	T	16.98	3.271658	0.59649	.	.	ENSG00000154485	ENST00000368808	T	0.02446	4.29	5.95	-4.11	0.03928	Hemopexin/matrixin (2);	0.904543	0.09772	N	0.757825	T	0.02688	0.0081	N	0.19112	0.55	0.09310	N	1	P	0.40282	0.711	P	0.47528	0.549	T	0.38607	-0.9653	10	0.56958	D	0.05	-10.6851	3.1826	0.06589	0.1141:0.3438:0.3474:0.1948	.	483	Q8N119	MMP21_HUMAN	H	483	ENSP00000357798:N483H	ENSP00000357798:N483H	N	-	1	0	MMP21	127445484	0.000000	0.05858	0.000000	0.03702	0.422000	0.31414	-0.140000	0.10342	-0.647000	0.05444	-0.274000	0.10170	AAT	.	.	.	none		0.303	MMP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050928.1			G	127455494	T	G	127455494	3	3	120	1	0	0	0	0	1	0	0	0	9667	1754	61	5	266	5	MMP21	10	127455494	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	19043200	127455494	8079253	57	7638											
PHRF1	57661	hgsc.bcm.edu	37	chr11	601639	601639	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catccgcaaaaagtaagagcTcagcgacaagatctaagaaa	19	5	8	9	2	2	3	1	0	1	3	3	4	3	3	1	0	2	3	1	0	6	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr11:601639T>C	ENST00000264555.5	+	10	1218	c.1090T>C	c.(1090-1092)Tca>Cca	p.S364P	PHRF1_ENST00000416188.2_Missense_Mutation_p.S364P|PHRF1_ENST00000533464.1_Missense_Mutation_p.S360P|PHRF1_ENST00000413872.2_Missense_Mutation_p.S363P	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	364	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						AAGTAAGAGCTCAGCGACAAG	0.507																																					p.S364P		Atlas-SNP	.											.	PHRF1	188	.	0			c.T1090C						PASS	.						85	94	91					11																	601639		1969	4145	6114	SO:0001583	missense	57661	exon10			AAGAGCTCAGCGA	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.1090T>C	chr11.hg19:g.601639T>C	ENSP00000264555:p.Ser364Pro	70.0	0.0	.		59.0	29.0	.	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Missense_Mutation	SNP	ENST00000264555.5	hg19		.	.	.	.	.	.	.	.	.	.	T	13.18	2.160816	0.38119	.	.	ENSG00000070047	ENST00000264555;ENST00000413872;ENST00000416188;ENST00000533464	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	4.37	0.796	0.18648	.	0.956972	0.08463	N	0.942121	T	0.29652	0.0740	L	0.35414	1.06	0.09310	N	1	B;B;B;B	0.11235	0.002;0.004;0.004;0.002	B;B;B;B	0.14578	0.005;0.011;0.011;0.005	T	0.26155	-1.0111	10	0.33940	T	0.23	-5.4809	5.8681	0.18789	0.0:0.1006:0.4218:0.4776	.	360;363;364;364	E9PJ24;F8WEF5;Q9P1Y6-3;Q9P1Y6	.;.;.;PHRF1_HUMAN	P	364;363;364;360	ENSP00000264555:S364P;ENSP00000388589:S363P;ENSP00000410626:S364P;ENSP00000431870:S360P	ENSP00000264555:S364P	S	+	1	0	PHRF1	591639	0.001000	0.12720	0.002000	0.10522	0.005000	0.04900	0.583000	0.23849	-0.016000	0.14127	-1.252000	0.01501	TCA	.	.	.	none		0.507	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901		C	601639	T	C	601639	3	2	120	1	0	0	0	0	1	0	0	0	11868	1551	54	3	1124	3	PHRF1	11	601639	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08		601639	134404877	58	7639											
FAU	740	hgsc.bcm.edu	37	chr11	64888258	64888258	+	5'Flank	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	gcccgacctgtcttcttcttCttcttctcctgtttggccac	2	17	6	16	1	6	0	0	0	6	0	7	1	6	0	4	1	0	1	4	1	0	6	rs3202210		TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr11:64888258C>A	ENST00000279242.2	+	0	0				MRPL49_ENST00000531705.1_5'Flank|FAU_ENST00000279259.3_Nonsense_Mutation_p.E81*|FAU_ENST00000529639.1_Missense_Mutation_p.K99N|MRPL49_ENST00000534078.1_5'Flank|MRPL49_ENST00000526171.1_5'Flank|FAU_ENST00000531743.1_Missense_Mutation_p.K99N|FAU_ENST00000529259.1_3'UTR|FAU_ENST00000527548.1_Missense_Mutation_p.K99N|FAU_ENST00000525297.1_Missense_Mutation_p.K64N	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						TCTTCTTCTTCTTCTTCTCCT	0.557																																					p.K99N		Atlas-SNP	.											.	FAU	17	.	0			c.G297T						PASS	.						82	88	86					11																	64888258		2201	4297	6498	SO:0001631	upstream_gene_variant	2197	exon5			CTTCTTCTTCTTC		CCDS8096.1	11q13.1	2012-11-14	2001-10-16	2001-10-19	ENSG00000149792	ENSG00000149792		"Mitochondrial ribosomal proteins / large subunits"	1176	protein-coding gene	gene with protein product	"neighbor of FAU", "next to FAU"	606866	"chromosome 11 open reading frame 4"	C11orf4		8786148	Standard	NM_004927		Approved	NOF, NOF1, L49mt	uc001oda.2	Q13405	OTTHUMG00000165608		chr11.hg19:g.64888258C>A	Exception_encountered	254.0	0.0	.		220.0	80.0	.	NM_001997	B2R4G6	Missense_Mutation	SNP	ENST00000279242.2	hg19	CCDS8096.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.0|21.0	4.082357|4.082357	0.76528|0.76528	.|.	.|.	ENSG00000149806|ENSG00000149806	ENST00000279259|ENST00000529639;ENST00000531743;ENST00000525297;ENST00000527548;ENST00000526555	.|T;T;T;T;T	.|0.50277	.|0.75;0.75;0.75;0.75;0.75	5.7|5.7	4.79|4.79	0.61399|0.61399	.|.	.|0.045214	.|0.85682	.|D	.|0.000000	.|T	.|0.72503	.|0.3468	M|M	0.93016|0.93016	3.37|3.37	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.79541	.|-0.1761	.|8	0.25106|0.72032	T|D	0.35|0.01	.|.	12.7196|12.7196	0.57134|0.57134	0.0:0.9196:0.0:0.0804|0.0:0.9196:0.0:0.0804	.|.	.|.	.|.	.|.	X|N	81|99;99;64;99;99	.|ENSP00000435370:K99N;ENSP00000431822:K99N;ENSP00000436110:K64N;ENSP00000434440:K99N;ENSP00000433139:K99N	ENSP00000279259:E81X|ENSP00000436110:K64N	E|K	-|-	1|3	0|2	FAU|FAU	64644834|64644834	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	2.548000|2.548000	0.45794|0.45794	1.411000|1.411000	0.46957|0.46957	0.655000|0.655000	0.94253|0.94253	GAA|AAG	.	.	.	alt		0.557	MRPL49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385293.1	NM_004927		A	64888258	C	A	64888258	1	1	120	0	1	0	0	0	0	0	0	0	5701	912	32	4		4	FAU	11	64888258	5'Flank	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	64286619	64888258	70118258	59	7640											
DPP3	10072	hgsc.bcm.edu	37	chr11	66260242	66260242	+	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	aagtttgagcggctggtggcGagcgcagagcagctgctgaa	9	7	17	8	3	0	3	0	2	0	1	0	4	0	3	0	3	5	6	0	3	2	1	rs200674271		TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr11:66260242G>A	ENST00000360510.2	+	10	1109	c.1044G>A	c.(1042-1044)gcG>gcA	p.A348A	DPP3_ENST00000531863.1_Silent_p.A368A|DPP3_ENST00000530165.1_Silent_p.A318A|DPP3_ENST00000541961.1_Silent_p.A348A|DPP3_ENST00000532677.1_Silent_p.A367A|DPP3_ENST00000533799.1_3'UTR|DPP3_ENST00000453114.1_Silent_p.A348A			Q9NY33	DPP3_HUMAN	dipeptidyl-peptidase 3	348					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)	23						GGCTGGTGGCGAGCGCAGAGC	0.602																																					p.A348A		Atlas-SNP	.											.	DPP3	61	.	0			c.G1044A						PASS	.						95	89	91					11																	66260242		2200	4295	6495	SO:0001819	synonymous_variant	10072	exon10			GGTGGCGAGCGCA	AB017970	CCDS8141.1, CCDS58147.1	11q12-q13.1	2008-02-05	2006-01-12		ENSG00000254986	ENSG00000254986	3.4.14.4		3008	protein-coding gene	gene with protein product		606818	"dipeptidylpeptidase III", "dipeptidylpeptidase 3"			10773679	Standard	NM_005700		Approved		uc001oif.2	Q9NY33	OTTHUMG00000167143	ENST00000360510.2:c.1044G>A	chr11.hg19:g.66260242G>A		145.0	0.0	.		149.0	64.0	.	NM_130443	B2RDB5|B4DLX4|F5H8L6|O95748|Q969H2|Q9BV67|Q9HAL6	Silent	SNP	ENST00000360510.2	hg19	CCDS8141.1																																																																																			.	.	.	weak		0.602	DPP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393424.2			A	66260242	G	A	66260242	2	1	120	1	0	0	0	0	0	0	0	1	4730	1045	37	1		1	DPP3	11	66260242	Silent	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	1371984	66260242	68746274	60	7641											
DGAT2	84649	hgsc.bcm.edu	37	chr11	75509461	75509461	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggtgccctactccaagccCatcaccactgttggtaagcc	8	9	8	16	0	1	0	1	0	0	0	2	0	2	0	5	2	4	2	5	2	3	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr11:75509461C>T	ENST00000228027.7	+	7	1259	c.999C>T	c.(997-999)ccC>ccT	p.P333P	RP11-535A19.1_ENST00000534354.1_RNA|DGAT2_ENST00000376262.3_Silent_p.P290P	NM_032564.4	NP_115953.2	Q96PD7	DGAT2_HUMAN	diacylglycerol O-acyltransferase 2	333					acylglycerol acyl-chain remodeling (GO:0036155)|cellular lipid metabolic process (GO:0044255)|cellular response to oleic acid (GO:0071400)|cellular triglyceride homeostasis (GO:0035356)|cholesterol homeostasis (GO:0042632)|diacylglycerol metabolic process (GO:0046339)|fat pad development (GO:0060613)|fatty acid homeostasis (GO:0055089)|glycerol metabolic process (GO:0006071)|glycerophospholipid biosynthetic process (GO:0046474)|lipid storage (GO:0019915)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid metabolic process (GO:0006644)|regulation of plasma lipoprotein particle levels (GO:0097006)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)	2-acylglycerol O-acyltransferase activity (GO:0003846)|diacylglycerol O-acyltransferase activity (GO:0004144)|protein homodimerization activity (GO:0042803)|retinol O-fatty-acyltransferase activity (GO:0050252)			endometrium(3)|large_intestine(5)|lung(5)|prostate(2)|skin(2)	17	Ovarian(111;0.103)					ACTCCAAGCCCATCACCACTG	0.552																																					p.P333P	Melanoma(35;811 1096 8354 24009 39363)	Atlas-SNP	.											.	DGAT2	37	.	0			c.C999T						PASS	.						48	43	45					11																	75509461		2200	4293	6493	SO:0001819	synonymous_variant	84649	exon7			CAAGCCCATCACC		CCDS31642.1, CCDS58162.1	11q13.3	2010-06-24	2010-06-24		ENSG00000062282	ENSG00000062282			16940	protein-coding gene	gene with protein product		606983	"diacylglycerol O-acyltransferase homolog 2 (mouse)"			11481335, 14970677	Standard	NM_032564		Approved		uc001oxa.3	Q96PD7	OTTHUMG00000165338	ENST00000228027.7:c.999C>T	chr11.hg19:g.75509461C>T		58.0	0.0	.		51.0	17.0	.	NM_032564	A6ND76|Q5U810|Q68CL3|Q68DJ0|Q8NDB7|Q96BS0|Q9BYE5	Silent	SNP	ENST00000228027.7	hg19	CCDS31642.1																																																																																			.	.	.	none		0.552	DGAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383506.1	NM_032564		T	75509461	C	T	75509461	2	4	120	1	0	0	0	0	0	0	0	1	4460	581	21	2		2	DGAT2	11	75509461	Silent	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	9249219	75509461	59497055	61	7642											
CNTN5	53942	hgsc.bcm.edu	37	chr11	99690367	99690367	+	Missense_Mutation	SNP	A	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	catctctctttggttccaaaAccagaccacgatacagcagc	12	9	6	14	1	2	1	0	0	2	1	4	2	3	1	3	1	4	2	3	1	3	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr11:99690367A>C	ENST00000524871.1	+	4	438	c.148A>C	c.(148-150)Acc>Ccc	p.T50P	CNTN5_ENST00000527185.1_Missense_Mutation_p.T50P|CNTN5_ENST00000528682.1_Missense_Mutation_p.T50P|CNTN5_ENST00000279463.3_Missense_Mutation_p.T50P|CNTN5_ENST00000418526.2_Intron	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	50					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)		TGGTTCCAAAACCAGACCACG	0.423																																					p.T50P		Atlas-SNP	.											.	CNTN5	324	.	0			c.A148C						PASS	.						115	117	116					11																	99690367		1906	4138	6044	SO:0001583	missense	53942	exon3			TCCAAAACCAGAC	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.148A>C	chr11.hg19:g.99690367A>C	ENSP00000435637:p.Thr50Pro	164.0	0.0	.		107.0	13.0	.	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	hg19	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	A	11.45	1.642177	0.29157	.	.	ENSG00000149972	ENST00000527185;ENST00000528682;ENST00000524871;ENST00000279463	T;T;T;T	0.56941	0.43;0.5;0.5;0.5	5.06	-2.19	0.07015	.	1.005590	0.08006	N	0.989611	T	0.28699	0.0711	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	0.23583	-1.0184	10	0.62326	D	0.03	.	1.2696	0.02018	0.5048:0.1176:0.1378:0.2399	.	50;50	E9PKE8;O94779	.;CNTN5_HUMAN	P	50	ENSP00000433575:T50P;ENSP00000436185:T50P;ENSP00000435637:T50P;ENSP00000279463:T50P	ENSP00000279463:T50P	T	+	1	0	CNTN5	99195577	0.217000	0.23597	0.017000	0.16124	0.764000	0.43329	0.669000	0.25142	-0.145000	0.11294	0.528000	0.53228	ACC	.	.	.	none		0.423	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361		C	99690367	A	C	99690367	3	2	120	1	0	0	0	0	1	0	0	0	3646	43	2	5	154	5	CNTN5	11	99690367	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	24180906	99690367	35316149	62	7643											
BCL9L	283149	hgsc.bcm.edu	37	chr11	118771686	118771686	+	Missense_Mutation	SNP	A	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	atgcccggtgagcccatctgAttaatactgatggtgaggtc	9	11	12	9	1	1	4	0	4	1	0	2	4	1	4	2	3	3	0	2	3	2	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr11:118771686A>C	ENST00000334801.3	-	6	3730	c.2766T>G	c.(2764-2766)aaT>aaG	p.N922K	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	922	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)		AGCCCATCTGATTAATACTGA	0.632																																					p.N922K		Atlas-SNP	.											.	BCL9L	254	.	0			c.T2766G						PASS	.						62	60	61					11																	118771686		2200	4295	6495	SO:0001583	missense	283149	exon6			CATCTGATTAATA	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.2766T>G	chr11.hg19:g.118771686A>C	ENSP00000335320:p.Asn922Lys	92.0	0.0	.		70.0	19.0	.	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Missense_Mutation	SNP	ENST00000334801.3	hg19	CCDS8403.1	.	.	.	.	.	.	.	.	.	.	A	12.59	1.982733	0.34942	.	.	ENSG00000186174	ENST00000334801;ENST00000526143;ENST00000525300;ENST00000392849;ENST00000431085	T	0.66280	-0.2	4.48	-0.626	0.11544	.	0.114359	0.38663	N	0.001612	T	0.39009	0.1062	N	0.19112	0.55	0.45129	D	0.998148	P;P	0.44734	0.728;0.842	B;B	0.39217	0.294;0.236	T	0.14090	-1.0485	10	0.54805	T	0.06	-7.3556	6.4799	0.22057	0.2778:0.1784:0.5439:0.0	.	917;922	Q86UU0-2;Q86UU0	.;BCL9L_HUMAN	K	922;885;215;922;922	ENSP00000335320:N922K	ENSP00000335320:N922K	N	-	3	2	BCL9L	118276896	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	1.052000	0.30429	-0.032000	0.13758	0.533000	0.62120	AAT	.	.	.	none		0.632	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557		C	118771686	A	C	118771686	3	2	120	1	0	0	0	0	1	0	0	0	1382	330	12	5	1745	5	BCL9L	11	118771686	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	19081319	118771686	16234830	63	7644											
OR8B8	26493	hgsc.bcm.edu	37	chr11	124310919	124310919	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagagggggatctggactccCggttggtcagttaagcctgc	8	9	15	9	1	2	1	1	0	1	1	3	3	3	3	2	5	2	2	2	5	2	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr11:124310919C>T	ENST00000328064.2	-	1	135	c.63G>A	c.(61-63)ccG>ccA	p.P21P		NM_012378.1	NP_036510.1	Q15620	OR8B8_HUMAN	olfactory receptor, family 8, subfamily B, member 8	21					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		TCTGGACTCCCGGTTGGTCAG	0.502																																					p.P21P		Atlas-SNP	.											.	OR8B8	76	.	0			c.G63A						PASS	.						62	61	61					11																	124310919		2201	4299	6500	SO:0001819	synonymous_variant	26493	exon1			GACTCCCGGTTGG	AF238488	CCDS8446.1	11q24.2	2012-08-09			ENSG00000197125	ENSG00000197125		"GPCR / Class A : Olfactory receptors"	8477	protein-coding gene	gene with protein product						9119360	Standard	NM_012378		Approved	TPCR85	uc010sal.2	Q15620	OTTHUMG00000165917	ENST00000328064.2:c.63G>A	chr11.hg19:g.124310919C>T		113.0	0.0	.		76.0	28.0	.	NM_012378	A1L446|Q96RC8	Silent	SNP	ENST00000328064.2	hg19	CCDS8446.1																																																																																			.	.	.	none		0.502	OR8B8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387056.1	NM_012378		T	124310919	C	T	124310919	2	4	120	1	0	0	0	0	0	0	0	1	11237	639	23	1		1	OR8B8	11	124310919	Silent	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	5539233	124310919	10695597	64	7645											
C3AR1	719	hgsc.bcm.edu	37	chr12	8212439	8212439	+	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	acagcgatccaggctaatggCagtaagcaggaagacactgg	14	5	13	9	1	0	1	0	0	0	1	1	3	1	2	1	4	2	4	1	4	3	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr12:8212439C>T	ENST00000307637.4	-	2	546	c.343G>A	c.(343-345)Gcc>Acc	p.A115T		NM_004054.2	NP_004045.1	Q16581	C3AR_HUMAN	complement component 3a receptor 1	115					blood circulation (GO:0008015)|chemotaxis (GO:0006935)|complement receptor mediated signaling pathway (GO:0002430)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation vascular endothelial growth factor production (GO:0010575)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C3a anaphylatoxin receptor activity (GO:0004943)|complement component C3a receptor activity (GO:0004876)|G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)	20				Kidney(36;0.0893)		AGGCTAATGGCAGTAAGCAGG	0.517																																					p.A115T		Atlas-SNP	.											.	C3AR1	61	.	0			c.G343A						PASS	.						186	151	163					12																	8212439		2203	4300	6503	SO:0001583	missense	719	exon2			TAATGGCAGTAAG	U28488	CCDS8588.1	12p13.31	2012-08-10				ENSG00000171860		"Complement system", "GPCR / Class A : Complement component receptors"	1319	protein-coding gene	gene with protein product		605246				8605247	Standard	NM_004054		Approved	C3AR, AZ3B	uc001qtv.1	Q16581		ENST00000307637.4:c.343G>A	chr12.hg19:g.8212439C>T	ENSP00000302079:p.Ala115Thr	73.0	0.0	.		80.0	22.0	.	NM_004054	O43771|Q92868	Missense_Mutation	SNP	ENST00000307637.4	hg19	CCDS8588.1	.	.	.	.	.	.	.	.	.	.	C	16.21	3.059489	0.55325	.	.	ENSG00000171860	ENST00000307637;ENST00000546241	T;T	0.44482	0.92;0.92	5.64	4.76	0.60689	GPCR, rhodopsin-like superfamily (1);	0.379197	0.23680	N	0.045625	T	0.39835	0.1093	L	0.54965	1.715	0.40028	D	0.975498	P	0.41475	0.751	B	0.40375	0.327	T	0.26643	-1.0097	10	0.33141	T	0.24	.	12.4036	0.55426	0.0:0.9187:0.0:0.0813	.	115	Q16581	C3AR_HUMAN	T	115	ENSP00000302079:A115T;ENSP00000444500:A115T	ENSP00000302079:A115T	A	-	1	0	C3AR1	8103706	0.993000	0.37304	0.990000	0.47175	0.984000	0.73092	3.119000	0.50422	1.388000	0.46506	0.655000	0.94253	GCC	.	.	.	none		0.517	C3AR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400254.1			T	8212439	C	T	8212439	3	4	120	1	0	0	0	0	1	0	0	0	2207	710	25	2	1109	2	C3AR1	12	8212439	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08		8212439	125639456	65	7646											
DENND5B	160518	hgsc.bcm.edu	37	chr12	31586129	31586130	+	In_Frame_Ins	INS	-	-	GGCGAA																															cccaacatgctcagaatgctINSggcgaaggcgttctttcctg																										TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr12:31586129_31586130insGGCGAA	ENST00000389082.5	-	8	2329_2330	c.2065_2066insTTCGCC	c.(2065-2067)cag>cTTCGCCag	p.688_689insLR	DENND5B_ENST00000536562.1_In_Frame_Ins_p.723_724insLR|DENND5B_ENST00000306833.6_In_Frame_Ins_p.723_724insLR|DENND5B_ENST00000354285.4_In_Frame_Ins_p.710_711insLR	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	688					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						CTCAGAATGCTGGCGAAGGCGT	0.48																																					p.Q689delinsLRQ		Atlas-INDEL	.											.	DENND5B	114	.	0			c.2066_2067insTTCGCC						PASS	.																																			SO:0001652	inframe_insertion	160518	exon8			.	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.2060_2065dupTTCGCC	chr12.hg19:g.31586130_31586135dupGGCGAA	ENSP00000373734:p.Leu687_Arg688dup	254.0	0.0	0		188.0	25.0	0.132979	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	In_Frame_Ins	INS	ENST00000389082.5	hg19	CCDS44857.1																																																																																			.	.	.	none		0.48	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973		GGCGAA	31586130	-	GGCGAA	31586129	7	5	120	1	0	1	1	0	0	0	0	0	4439	1580	55	0	1814	0	DENND5B	12	31586129	In_Frame_Ins	INS	-	TCGA-BQ-5885-01A-11D-1589-08	23373690	31586129	102265766	66	7647											
ATF7	11016	hgsc.bcm.edu	37	chr12	53931334	53931334	+	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	atgtcaaggggcccagcagcAgcctgttgtgaaagaaaaat	14	7	12	8	0	1	2	1	1	0	1	1	2	1	2	2	2	3	3	2	2	4	1			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr12:53931334A>T	ENST00000548446.2	-	5	412	c.300T>A	c.(298-300)gcT>gcA	p.A100A	ATF7_ENST00000456903.4_Silent_p.A89A|ATF7_ENST00000420353.2_Silent_p.A89A|RP11-793H13.10_ENST00000591834.1_Silent_p.A89A|ATF7_ENST00000415113.1_Silent_p.A89A|ATF7_ENST00000328463.7_Silent_p.A100A			P17544	ATF7_HUMAN	activating transcription factor 7	100	Transactivation domain.				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)	GCCCAGCAGCAGCCTGTTGTG	0.443																																					p.A89A		Atlas-SNP	.											.	ATF7	51	.	0			c.T267A						PASS	.						68	70	69					12																	53931334		1903	4133	6036	SO:0001819	synonymous_variant	11016	exon5			AGCAGCAGCCTGT	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.300T>A	chr12.hg19:g.53931334A>T		59.0	0.0	.		49.0	16.0	.	NM_001130060	A5D6Y4|B2RMP1|B4DQL4|Q13814|Q8IVR8|Q9UD83	Silent	SNP	ENST00000548446.2	hg19																																																																																				.	.	.	none		0.443	ATF7-007	KNOWN	NMD_exception|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000406302.2	NM_001130059		T	53931334	A	T	53931334	2	4	120	1	0	0	0	0	0	0	0	1	1086	175	7	5		5	ATF7	12	53931334	Silent	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	22345205	53931334	79920561	67	7648											
SRGAP1	57522	hgsc.bcm.edu	37	chr12	64521913	64521913	+	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	cagccctcccattagaaggtCcacgtcatcagggcaataca	12	7	8	14	1	2	1	2	0	0	1	4	1	4	1	3	2	2	1	3	2	4	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr12:64521913C>A	ENST00000355086.3	+	21	3337	c.2813C>A	c.(2812-2814)tCc>tAc	p.S938Y	SRGAP1_ENST00000543397.1_Missense_Mutation_p.S875Y|SRGAP1_ENST00000357825.3_Missense_Mutation_p.S915Y	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	938					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)	p.S938C(1)		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)		ATTAGAAGGTCCACGTCATCA	0.532																																					p.S938Y		Atlas-SNP	.											SRGAP1,NS,carcinoma,0,1	SRGAP1	146	.	1	Substitution - Missense(1)	ovary(1)	c.C2813A						PASS	.						53	49	50					12																	64521913		2203	4300	6503	SO:0001583	missense	57522	exon21			GAAGGTCCACGTC	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.2813C>A	chr12.hg19:g.64521913C>A	ENSP00000347198:p.Ser938Tyr	46.0	0.0	.		43.0	12.0	.	NM_020762	Q9H8A3|Q9P2P2	Missense_Mutation	SNP	ENST00000355086.3	hg19	CCDS8967.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.781515	0.90282	.	.	ENSG00000196935	ENST00000355086;ENST00000357825;ENST00000543397	T;T;T	0.21191	3.02;2.6;2.02	5.65	5.65	0.86999	.	0.000000	0.34986	U	0.003527	T	0.42449	0.1203	L	0.58101	1.795	0.80722	D	1	D;D	0.60160	0.987;0.98	P;P	0.61592	0.851;0.891	T	0.02553	-1.1142	9	.	.	.	.	20.1057	0.97893	0.0:1.0:0.0:0.0	.	938;875	Q7Z6B7;G5EA48	SRGP1_HUMAN;.	Y	938;915;875	ENSP00000347198:S938Y;ENSP00000350480:S915Y;ENSP00000437948:S875Y	.	S	+	2	0	SRGAP1	62808180	1.000000	0.71417	1.000000	0.80357	0.723000	0.41478	7.695000	0.84257	2.827000	0.97445	0.650000	0.86243	TCC	.	.	.	none		0.532	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1			A	64521913	C	A	64521913	3	1	120	1	0	0	0	0	1	0	0	0	15157	855	30	4	2895	4	SRGAP1	12	64521913	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	10590579	64521913	69329982	68	7649											
EID3	493861	hgsc.bcm.edu	37	chr12	104698219	104698219	+	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	gtaaaagctgagacattccaTtttgtttttggttcattcaa	11	17	7	6	0	2	1	2	1	0	1	3	2	3	1	1	1	1	4	1	1	3	8			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr12:104698219T>A	ENST00000527879.1	+	1	703	c.507T>A	c.(505-507)caT>caA	p.H169Q	TXNRD1_ENST00000526691.1_Intron|TXNRD1_ENST00000397736.2_Intron|TXNRD1_ENST00000526390.1_Intron|TXNRD1_ENST00000529546.1_Intron|TXNRD1_ENST00000525566.1_Intron|TXNRD1_ENST00000524698.1_Intron|TXNRD1_ENST00000378070.4_Intron|TXNRD1_ENST00000388854.3_Intron|TXNRD1_ENST00000542918.1_Intron|TXNRD1_ENST00000540716.1_Intron|TXNRD1_ENST00000503506.2_Intron|TXNRD1_ENST00000429002.2_Intron|TXNRD1_ENST00000354940.6_Intron	NM_001008394.2	NP_001008395.1			EP300 interacting inhibitor of differentiation 3											large_intestine(5)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						AGACATTCCATTTTGTTTTTG	0.418																																					p.H169Q		Atlas-SNP	.											.	EID3	28	.	0			c.T507A						PASS	.						188	184	185					12																	104698219		1919	4136	6055	SO:0001583	missense	493861	exon1			ATTCCATTTTGTT	BC027612	CCDS53822.1	12q23.3	2006-11-24				ENSG00000255150			32961	protein-coding gene	gene with protein product		612986				15987788, 15752197	Standard	NM_001008394		Approved	FLJ25832, NSMCE4B, NSE4B	uc001tkw.3	Q8N140		ENST00000527879.1:c.507T>A	chr12.hg19:g.104698219T>A	ENSP00000435619:p.His169Gln	355.0	0.0	.		282.0	113.0	.	NM_001008394		Missense_Mutation	SNP	ENST00000527879.1	hg19	CCDS53822.1	.	.	.	.	.	.	.	.	.	.	T	13.41	2.228683	0.39399	.	.	ENSG00000255150	ENST00000527879	T	0.43688	0.94	4.94	0.971	0.19698	.	.	.	.	.	T	0.53546	0.1803	M	0.72118	2.19	0.30872	N	0.732351	D	0.76494	0.999	D	0.77557	0.99	T	0.54139	-0.8338	9	0.10636	T	0.68	.	7.1994	0.25873	0.0:0.6158:0.0:0.3842	.	169	Q8N140	EID3_HUMAN	Q	169	ENSP00000435619:H169Q	ENSP00000435619:H169Q	H	+	3	2	EID3	103222349	0.586000	0.26782	0.839000	0.33178	0.046000	0.14306	-0.290000	0.08354	0.077000	0.16863	-0.375000	0.07067	CAT	.	.	.	none		0.418	EID3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387034.1	NM_001008394		A	104698219	T	A	104698219	3	1	120	1	0	0	0	0	1	0	0	0	4991	1490	52	5	509	5	EID3	12	104698219	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08	40176306	104698219	29153676	69	7650											
ARHGEF7	8874	hgsc.bcm.edu	37	chr13	111885553	111885553	+	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	tgttacattttcatttcagaGaagcctgtgtctcccaaatc	10	15	6	10	0	3	1	2	0	1	1	5	2	3	1	2	0	2	1	2	0	3	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr13:111885553G>A	ENST00000375741.2	+	7	985	c.735G>A	c.(733-735)gaG>gaA	p.E245E	ARHGEF7_ENST00000375736.4_Splice_Site_p.E67E|ARHGEF7_ENST00000370623.3_Splice_Site_p.E152E|ARHGEF7_ENST00000375723.1_Splice_Site_p.E67E|ARHGEF7_ENST00000218789.5_Splice_Site_p.E67E|ARHGEF7_ENST00000375739.2_Splice_Site_p.E195E|ARHGEF7_ENST00000375737.5_Splice_Site_p.E142E|ARHGEF7_ENST00000544132.1_5'UTR|ARHGEF7_ENST00000317133.5_Splice_Site_p.E224E|ARHGEF7_ENST00000426073.2_Splice_Site_p.E67E	NM_001113511.1|NM_145735.2	NP_001106983.1|NP_663788.1	Q14155	ARHG7_HUMAN	Rho guanine nucleotide exchange factor (GEF) 7	245					apoptotic signaling pathway (GO:0097190)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|hematopoietic progenitor cell differentiation (GO:0002244)|lamellipodium assembly (GO:0030032)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of GTPase activity (GO:0043547)|positive regulation of lamellipodium morphogenesis (GO:2000394)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase binding (GO:0019901)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	41	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			TCATTTCAGAGAAGCCTGTGT	0.428																																					p.E245E		Atlas-SNP	.											.	ARHGEF7	157	.	0			c.G735A						PASS	.						102	103	103					13																	111885553		2203	4300	6503	SO:0001630	splice_region_variant	8874	exon7			TTCAGAGAAGCCT	D63476	CCDS9521.1, CCDS32009.1, CCDS45068.1, CCDS45069.1	13q33.3	2013-01-10			ENSG00000102606	ENSG00000102606		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	15607	protein-coding gene	gene with protein product	"SH3 domain-containing proline-rich protein", "PAK-interacting exchange factor beta", "rho", "guanine nucleotide exchange factor 7"	605477				9207241, 9726964	Standard	NM_003899		Approved	KIAA0142, PIXB, DKFZp761K1021, Nbla10314, DKFZp686C12170, BETA-PIX, COOL1, P85SPR, P85, P85COOL1, P50BP, PAK3, P50	uc001vrs.2	Q14155	OTTHUMG00000017357	ENST00000375741.2:c.734-1G>A	chr13.hg19:g.111885553G>A		192.0	1.0	.		132.0	76.0	.	NM_001113511	B1ALK6|B1ALK8|Q3LIA4|Q5W9H0|Q6P9G3|Q6PII2|Q86W63|Q8N3M1	Silent	SNP	ENST00000375741.2	hg19	CCDS45068.1																																																																																			.	.	.	none		0.428	ARHGEF7-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113511	Silent	A	111885553	G	A	111885553	5	1	120	1	0	0	0	0	0	0	1	0	911	956	33	2	761	2	ARHGEF7	13	111885553	Splice_Site	SNP	G	TCGA-BQ-5885-01A-11D-1589-08		111885553	3284325	70	7651											
SMG1	23049	hgsc.bcm.edu	37	chr16	18841597	18841597	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcaaacatgccatcgaatgCtaccaaaagcatctggccag	15	6	8	12	1	1	0	0	0	1	0	2	1	1	0	3	1	6	3	3	1	5	1	rs371226711		TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr16:18841597C>T	ENST00000446231.2	-	52	9299	c.8887G>A	c.(8887-8889)Gca>Aca	p.A2963T	SMG1_ENST00000389467.3_Missense_Mutation_p.A2963T			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2963					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						CCATCGAATGCTACCAAAAGC	0.393																																					p.A2963T		Atlas-SNP	.											.	SMG1	401	.	0			c.G8887A						PASS	.						78	73	74					16																	18841597		1886	4116	6002	SO:0001583	missense	23049	exon52			CGAATGCTACCAA	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.8887G>A	chr16.hg19:g.18841597C>T	ENSP00000402515:p.Ala2963Thr	49.0	0.0	.		47.0	21.0	.	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	hg19	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.524254	0.85600	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.01165	5.24;5.24	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000002	T	0.03783	0.0107	N	0.19112	0.55	0.54753	D	0.999988	D	0.63880	0.993	D	0.74674	0.984	T	0.61382	-0.7074	10	0.72032	D	0.01	.	20.6593	0.99626	0.0:1.0:0.0:0.0	.	2963	Q96Q15	SMG1_HUMAN	T	2963	ENSP00000402515:A2963T;ENSP00000374118:A2963T	ENSP00000374118:A2963T	A	-	1	0	SMG1	18749098	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.594000	0.82698	2.885000	0.99019	0.655000	0.94253	GCA	.	.	.	alt		0.393	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		T	18841597	C	T	18841597	3	4	120	1	0	0	0	0	1	0	0	0	14808	797	28	2	2146	2	SMG1	16	18841597	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08		18841597	71513156	71	7652											
NKD1	85407	hgsc.bcm.edu	37	chr16	50667463	50667463	+	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	ggccctcctcccctccctagCccccctcgggcacaagaagc	6	5	8	22	1	0	1	0	0	0	1	4	1	3	1	8	2	2	1	8	2	3	1			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr16:50667463C>G	ENST00000268459.3	+	10	1408	c.1184C>G	c.(1183-1185)gCc>gGc	p.A395G		NM_033119.4	NP_149110.1	Q969G9	NKD1_HUMAN	naked cuticle homolog 1 (Drosophila)	395					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)		CCCTCCCTAGCCCCCCTCGGG	0.721																																					p.A395G		Atlas-SNP	.											.	NKD1	43	.	0			c.C1184G						PASS	.						9	12	11					16																	50667463		2160	4247	6407	SO:0001583	missense	85407	exon10			CCCTAGCCCCCCT	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.1184C>G	chr16.hg19:g.50667463C>G	ENSP00000268459:p.Ala395Gly	34.0	0.0	.		32.0	11.0	.	NM_033119	B2RC39|Q8WZ08	Missense_Mutation	SNP	ENST00000268459.3	hg19	CCDS10743.1	.	.	.	.	.	.	.	.	.	.	C	9.960	1.222465	0.22457	.	.	ENSG00000140807	ENST00000268459	T	0.65364	-0.15	4.05	4.05	0.47172	.	0.262951	0.37178	N	0.002203	T	0.57681	0.2070	L	0.51422	1.61	0.09310	N	0.999994	P	0.37330	0.59	B	0.40410	0.328	T	0.50792	-0.8786	10	0.21014	T	0.42	-8.4212	14.5612	0.68136	0.0:1.0:0.0:0.0	.	395	Q969G9	NKD1_HUMAN	G	395	ENSP00000268459:A395G	ENSP00000268459:A395G	A	+	2	0	NKD1	49224964	0.004000	0.15560	0.909000	0.35828	0.607000	0.37147	1.081000	0.30791	2.092000	0.63282	0.305000	0.20034	GCC	.	.	.	none		0.721	NKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256873.1			G	50667463	C	G	50667463	3	3	120	1	0	0	0	0	1	0	0	0	10448	739	26	4	1222	4	NKD1	16	50667463	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	31825866	50667463	39687290	72	7653											
TRPV3	162514	hgsc.bcm.edu	37	chr17	3458126	3458126	+	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	gcccatgagaggcaccatctCcttggggtgggctttcatgg	6	10	14	11	0	2	1	1	1	1	1	3	2	2	1	3	5	0	2	3	5	0	2			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr17:3458126C>T	ENST00000576742.1	-	2	340	c.19G>A	c.(19-21)Gag>Aag	p.E7K	TRPV3_ENST00000301365.4_Missense_Mutation_p.E7K|TRPV3_ENST00000572519.1_Missense_Mutation_p.E7K	NM_001258205.1|NM_145068.3	NP_001245134.1|NP_659505.1	Q8NET8	TRPV3_HUMAN	transient receptor potential cation channel, subfamily V, member 3	7					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|negative regulation of hair cycle (GO:0042636)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium channel activity (GO:0005262)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(12)|ovary(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	35					Menthol(DB00825)	GGCACCATCTCCTTGGGGTGG	0.622																																					p.E7K		Atlas-SNP	.											.	TRPV3	85	.	0			c.G19A						PASS	.						39	40	39					17																	3458126		2203	4300	6503	SO:0001583	missense	162514	exon2			CCATCTCCTTGGG	AF514998	CCDS11029.1, CCDS58500.1	17p13.3	2013-01-10			ENSG00000167723	ENSG00000167723		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	18084	protein-coding gene	gene with protein product		607066				12016205, 12077606, 16382100	Standard	NM_001258205		Approved	VRL3	uc002fvr.3	Q8NET8	OTTHUMG00000090695	ENST00000576742.1:c.19G>A	chr17.hg19:g.3458126C>T	ENSP00000461518:p.Glu7Lys	73.0	0.0	.		80.0	25.0	.	NM_001258205	Q8NDW7|Q8NET9|Q8NFH2	Missense_Mutation	SNP	ENST00000576742.1	hg19	CCDS11029.1	.	.	.	.	.	.	.	.	.	.	C	19.36	3.812560	0.70912	.	.	ENSG00000167723	ENST00000381913;ENST00000301365	T	0.42131	0.98	4.79	4.79	0.61399	.	0.098779	0.43747	D	0.000525	T	0.33323	0.0859	N	0.24115	0.695	0.35360	D	0.788099	P;P;P	0.40534	0.59;0.598;0.72	B;B;B	0.41202	0.111;0.19;0.35	T	0.51988	-0.8635	10	0.87932	D	0	-16.4794	13.7071	0.62646	0.0:1.0:0.0:0.0	.	7;7;7	Q8NET8-3;Q8NET8;Q8NET8-2	.;TRPV3_HUMAN;.	K	7	ENSP00000301365:E7K	ENSP00000301365:E7K	E	-	1	0	TRPV3	3404876	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	4.073000	0.57570	2.399000	0.81585	0.462000	0.41574	GAG	.	.	.	none		0.622	TRPV3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207379.2	NM_145068		T	3458126	C	T	3458126	3	4	120	1	0	0	0	0	1	0	0	0	16609	864	30	2	2421	2	TRPV3	17	3458126	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08		3458126	77737084	73	7654											
COX10	1352	hgsc.bcm.edu	37	chr17	13977738	13977738	+	Missense_Mutation	SNP	A	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	ggaatgtcaataagcagtggAttacatttcagcactttagc	13	12	9	7	0	2	0	2	0	0	0	2	2	2	2	0	2	4	2	0	2	5	5			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr17:13977738A>C	ENST00000261643.3	+	2	219	c.142A>C	c.(142-144)Att>Ctt	p.I48L	COX10_ENST00000537334.1_5'UTR|COX10_ENST00000536205.1_5'UTR|COX10_ENST00000429152.2_Missense_Mutation_p.I48L	NM_001303.3	NP_001294.2	Q12887	COX10_HUMAN	cytochrome c oxidase assembly homolog 10 (yeast)	48					aerobic respiration (GO:0009060)|cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|heme O biosynthetic process (GO:0048034)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|mitochondrial fission (GO:0000266)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	farnesyltranstransferase activity (GO:0004311)|protoheme IX farnesyltransferase activity (GO:0008495)			cervix(1)|endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		TAAGCAGTGGATTACATTTCA	0.408																																					p.I48L		Atlas-SNP	.											.	COX10	36	.	0			c.A142C						PASS	.						187	183	185					17																	13977738		2203	4300	6503	SO:0001583	missense	1352	exon2			CAGTGGATTACAT	U09466	CCDS11166.1	17p12	2013-05-24	2012-10-15		ENSG00000006695	ENSG00000006695		"Mitochondrial respiratory chain complex assembly factors"	2260	protein-coding gene	gene with protein product	"heme A: farnesyltransferase", "protoheme IX farnesyltransferase, mitochondrial", "heme O synthase"	602125	"COX10 (yeast) homolog, cytochrome c oxidase assembly protein (heme A: farnesyltransferase)", "COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase (yeast)"			9177788, 12928484	Standard	NM_001303		Approved		uc002gof.4	Q12887	OTTHUMG00000058814	ENST00000261643.3:c.142A>C	chr17.hg19:g.13977738A>C	ENSP00000261643:p.Ile48Leu	383.0	1.0	.		324.0	115.0	.	NM_001303	B2R6U5|B4DJ50|O15334|Q969F7	Missense_Mutation	SNP	ENST00000261643.3	hg19	CCDS11166.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.45|12.45	1.940770|1.940770	0.34283|0.34283	.|.	.|.	ENSG00000006695|ENSG00000006695	ENST00000429152|ENST00000261643	.|T	.|0.37915	.|1.17	5.03|5.03	-3.34|-3.34	0.04943|0.04943	.|.	.|0.618238	.|0.17063	.|N	.|0.188488	T|T	0.24699|0.24699	0.0599|0.0599	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	.|B	.|0.06786	.|0.001	.|B	.|0.08055	.|0.003	T|T	0.02037|0.02037	-1.1225|-1.1225	5|10	.|0.45353	.|T	.|0.12	-18.4175|-18.4175	8.3088|8.3088	0.32058|0.32058	0.3998:0.1258:0.4744:0.0|0.3998:0.1258:0.4744:0.0	.|.	.|48	.|Q12887	.|COX10_HUMAN	A|L	8|48	.|ENSP00000261643:I48L	.|ENSP00000261643:I48L	D|I	+|+	2|1	0|0	COX10|COX10	13918463|13918463	0.992000|0.992000	0.36948|0.36948	0.409000|0.409000	0.26459|0.26459	0.912000|0.912000	0.54170|0.54170	0.470000|0.470000	0.22084|0.22084	-0.785000|-0.785000	0.04522|0.04522	0.528000|0.528000	0.53228|0.53228	GAT|ATT	.	.	.	none		0.408	COX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130003.1	NM_001303		C	13977738	A	C	13977738	3	2	120	1	0	0	0	0	1	0	0	0	3764	333	12	5	148	5	COX10	17	13977738	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	10519612	13977738	67217472	74	7655											
TEX19	400629	hgsc.bcm.edu	37	chr17	80320426	80320426	+	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	aggaggctgtgcccctgggcCtgggccttgaggatgctgac	5	8	17	11	0	0	2	0	2	0	0	0	4	0	4	4	5	2	2	4	5	0	1			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr17:80320426C>A	ENST00000333437.4	+	2	710	c.400C>A	c.(400-402)Ctg>Atg	p.L134M		NM_207459.3	NP_997342.1	Q8NA77	TEX19_HUMAN	testis expressed 19	134					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						GCCCCTGGGCCTGGGCCTTGA	0.597																																					p.L134M		Atlas-SNP	.											.	TEX19	17	.	0			c.C400A						PASS	.						68	68	68					17																	80320426		2203	4300	6503	SO:0001583	missense	400629	exon2			CTGGGCCTGGGCC	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.400C>A	chr17.hg19:g.80320426C>A	ENSP00000331500:p.Leu134Met	178.0	0.0	.		202.0	78.0	.	NM_207459		Missense_Mutation	SNP	ENST00000333437.4	hg19	CCDS11809.1	.	.	.	.	.	.	.	.	.	.	C	8.539	0.872893	0.17322	.	.	ENSG00000182459	ENST00000333437	.	.	.	3.79	-0.753	0.11068	.	.	.	.	.	T	0.40297	0.1111	L	0.34521	1.04	0.09310	N	0.999999	D	0.76494	0.999	D	0.68943	0.961	T	0.23583	-1.0184	8	0.87932	D	0	-8.5728	4.373	0.11256	0.0:0.4173:0.3653:0.2174	.	134	Q8NA77	TEX19_HUMAN	M	134	.	ENSP00000331500:L134M	L	+	1	2	TEX19	77913715	0.093000	0.21703	0.021000	0.16686	0.007000	0.05969	0.763000	0.26517	-0.070000	0.12908	-0.251000	0.11542	CTG	.	.	.	none		0.597	TEX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256331.1	NM_207459		A	80320426	C	A	80320426	3	1	120	1	0	0	0	0	1	0	0	0	15792	680	24	4	402	4	TEX19	17	80320426	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	66342688	80320426	874784	75	7656											
PSMA8	143471	hgsc.bcm.edu	37	chr18	23731852	23731852	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgatgctagagtagtaataaAcagagcccgtgtggagtgcc	12	9	13	7	1	0	3	0	1	0	2	0	4	0	4	2	1	4	3	2	1	5	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr18:23731852A>G	ENST00000308268.6	+	3	367	c.278A>G	c.(277-279)aAc>aGc	p.N93S	PSMA8_ENST00000415576.2_Missense_Mutation_p.N87S|PSMA8_ENST00000343848.6_Missense_Mutation_p.N49S	NM_001025096.1|NM_144662.2	NP_001020267.1|NP_653263.2	Q8TAA3	PSA7L_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 8	93					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|proteasome core complex, alpha-subunit complex (GO:0019773)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|skin(2)	16	all_cancers(21;0.000585)|Lung NSC(5;0.00148)|all_lung(6;0.0038)|Ovarian(20;0.124)		OV - Ovarian serous cystadenocarcinoma(3;0.000324)|all cancers(3;0.000954)|LUSC - Lung squamous cell carcinoma(2;0.181)			GTAGTAATAAACAGAGCCCGT	0.378																																					p.N93S		Atlas-SNP	.											.	PSMA8	36	.	0			c.A278G						PASS	.						104	103	104					18																	23731852		2203	4300	6503	SO:0001583	missense	143471	exon3			TAATAAACAGAGC	BC047355	CCDS32808.1, CCDS45842.1, CCDS45843.1	18q11.2	2006-12-18				ENSG00000154611		"Proteasome (prosome, macropain) subunits"	22985	protein-coding gene	gene with protein product							Standard	XM_005258199		Approved	MGC26605, PSMA7L	uc002kvq.3	Q8TAA3		ENST00000308268.6:c.278A>G	chr18.hg19:g.23731852A>G	ENSP00000311121:p.Asn93Ser	130.0	0.0	.		116.0	39.0	.	NM_144662	B0YJ75|Q8IVP4|Q8TA98|Q8TAA2	Missense_Mutation	SNP	ENST00000308268.6	hg19	CCDS32808.1	.	.	.	.	.	.	.	.	.	.	A	14.38	2.518879	0.44763	.	.	ENSG00000154611	ENST00000308268;ENST00000415576;ENST00000343848;ENST00000538664;ENST00000536423	T;T;T	0.21361	2.01;2.01;2.01	5.34	2.96	0.34315	.	0.096815	0.64402	N	0.000002	T	0.20251	0.0487	L	0.60012	1.86	0.44579	D	0.997548	B;B;B;B	0.30193	0.052;0.041;0.214;0.272	B;B;B;B	0.33750	0.019;0.083;0.079;0.169	T	0.03306	-1.1050	10	0.42905	T	0.14	-9.0093	6.0378	0.19718	0.7464:0.1656:0.088:0.0	.	61;93;87;49	F5GY34;Q8TAA3;Q8TAA3-5;Q8TAA3-2	.;PSA7L_HUMAN;.;.	S	93;87;49;61;49	ENSP00000311121:N93S;ENSP00000409284:N87S;ENSP00000345584:N49S	ENSP00000311121:N93S	N	+	2	0	PSMA8	21985850	1.000000	0.71417	0.988000	0.46212	0.969000	0.65631	5.075000	0.64407	0.479000	0.27511	0.533000	0.62120	AAC	.	.	.	none		0.378	PSMA8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000446255.1	NM_144662		G	23731852	A	G	23731852	3	3	120	1	0	0	0	0	1	0	0	0	12683	43	2	3	288	3	PSMA8	18	23731852	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08		23731852	54345396	76	7657											
ZNF57	126295	hgsc.bcm.edu	37	chr19	2917763	2917763	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggtcctcaacgtttagagaaCatgtgagaattcacacgcaa	14	9	9	9	2	2	2	2	1	0	2	3	4	3	2	1	1	2	2	1	1	5	3	rs549800352	byFrequency	TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr19:2917763C>T	ENST00000306908.5	+	4	1292	c.1144C>T	c.(1144-1146)Cat>Tat	p.H382Y	ZNF57_ENST00000523428.1_Missense_Mutation_p.H350Y|AC006277.2_ENST00000520090.2_RNA	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	382					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)		GTTTAGAGAACATGTGAGAAT	0.448																																					p.H382Y	NSCLC(150;910 1964 4303 10464 26498)	Atlas-SNP	.											.	ZNF57	57	.	0			c.C1144T						PASS	.						90	82	84					19																	2917763		2203	4300	6503	SO:0001583	missense	126295	exon4			AGAGAACATGTGA	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.1144C>T	chr19.hg19:g.2917763C>T	ENSP00000303696:p.His382Tyr	156.0	0.0	.		134.0	52.0	.	NM_173480	Q8N6R9	Missense_Mutation	SNP	ENST00000306908.5	hg19	CCDS12098.1	.	.	.	.	.	.	.	.	.	.	C	12.93	2.084453	0.36758	.	.	ENSG00000171970	ENST00000306908;ENST00000395204;ENST00000523428	D;D	0.86769	-2.17;-2.17	2.25	2.25	0.28309	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94693	0.8288	H	0.96175	3.78	0.09310	N	0.999999	D	0.89917	1.0	D	0.69479	0.964	D	0.86081	0.1544	9	0.87932	D	0	.	10.1544	0.42814	0.0:1.0:0.0:0.0	.	382	Q68EA5	ZNF57_HUMAN	Y	382;384;350	ENSP00000303696:H382Y;ENSP00000430223:H350Y	ENSP00000303696:H382Y	H	+	1	0	ZNF57	2868763	0.980000	0.34600	0.002000	0.10522	0.002000	0.02628	2.918000	0.48829	1.259000	0.44117	0.511000	0.50034	CAT	.	.	.	none		0.448	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480		T	2917763	C	T	2917763	3	4	120	1	0	0	0	0	1	0	0	0	18013	478	17	2	1158	2	ZNF57	19	2917763	Missense_Mutation	SNP	C	TCGA-BQ-5885-01A-11D-1589-08		2917763	56211220	77	7658											
ZNF846	162993	hgsc.bcm.edu	37	chr19	9868191	9868191	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tagttcttagatgtttagcaAgtgctgaagattgagtgaag	12	14	12	3	0	1	5	0	3	1	2	1	5	1	5	0	0	2	4	0	0	6	6			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr19:9868191A>G	ENST00000397902.2	-	6	1975	c.1562T>C	c.(1561-1563)cTt>cCt	p.L521P	ZNF846_ENST00000588267.1_Intron|ZNF846_ENST00000586293.1_3'UTR|ZNF846_ENST00000592859.1_Intron	NM_001077624.1	NP_001071092.1	Q147U1	ZN846_HUMAN	zinc finger protein 846	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)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22						ATGTTTAGCAAGTGCTGAAGA	0.368																																					p.L521P		Atlas-SNP	.											.	ZNF846	61	.	0			c.T1562C						PASS	.						150	158	155					19																	9868191		2050	4222	6272	SO:0001583	missense	162993	exon6			TTAGCAAGTGCTG	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.1562T>C	chr19.hg19:g.9868191A>G	ENSP00000380999:p.Leu521Pro	317.0	0.0	.		279.0	100.0	.	NM_001077624	A8K0H1|B3KUP1	Missense_Mutation	SNP	ENST00000397902.2	hg19	CCDS42496.1	.	.	.	.	.	.	.	.	.	.	.	18.50	3.637264	0.67130	.	.	ENSG00000196605	ENST00000397902	T	0.14266	2.52	1.74	1.74	0.24563	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41119	0.1145	M	0.91717	3.235	0.21579	N	0.999631	D	0.89917	1.0	D	0.91635	0.999	T	0.09465	-1.0673	9	0.87932	D	0	.	7.5297	0.27677	1.0:0.0:0.0:0.0	.	521	Q147U1	ZN846_HUMAN	P	521	ENSP00000380999:L521P	ENSP00000380999:L521P	L	-	2	0	ZNF846	9729191	0.712000	0.27916	0.008000	0.14137	0.897000	0.52465	5.067000	0.64357	1.067000	0.40740	0.374000	0.22700	CTT	.	.	.	none		0.368	ZNF846-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450253.1	NM_001077624		G	9868191	A	G	9868191	3	3	120	1	0	0	0	0	1	0	0	0	18204	72	3	3	43	3	ZNF846	19	9868191	Missense_Mutation	SNP	A	TCGA-BQ-5885-01A-11D-1589-08	6950428	9868191	49260792	78	7659											
GATAD2A	54815	hgsc.bcm.edu	37	chr19	19603133	19603133	+	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	agtgacatgaagtccgagagGagacccccctcacctgacgt	11	6	11	13	2	1	5	1	3	0	2	2	7	2	5	5	1	0	0	5	1	1	0			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr19:19603133G>T	ENST00000360315.3	+	3	600	c.288G>T	c.(286-288)agG>agT	p.R96S	GATAD2A_ENST00000429563.2_Intron|GATAD2A_ENST00000537887.1_Intron|GATAD2A_ENST00000473184.1_3'UTR|GATAD2A_ENST00000358713.3_Missense_Mutation_p.R96S|GATAD2A_ENST00000404158.1_Missense_Mutation_p.R96S|GATAD2A_ENST00000252577.5_Missense_Mutation_p.R96S	NM_017660.3	NP_060130.3	Q86YP4	P66A_HUMAN	GATA zinc finger domain containing 2A	96					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						AGTCCGAGAGGAGACCCCCCT	0.617																																					p.R96S		Atlas-SNP	.											.	GATAD2A	81	.	0			c.G288T						PASS	.						48	48	48					19																	19603133		1568	3582	5150	SO:0001583	missense	54815	exon3			CGAGAGGAGACCC	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.288G>T	chr19.hg19:g.19603133G>T	ENSP00000353463:p.Arg96Ser	15.0	0.0	.		17.0	9.0	.	NM_017660	B5MC40|Q7L3J2|Q96F28|Q9NPU2|Q9NXS1	Missense_Mutation	SNP	ENST00000360315.3	hg19	CCDS12402.2	.	.	.	.	.	.	.	.	.	.	G	14.79	2.640385	0.47153	.	.	ENSG00000167491	ENST00000417582;ENST00000360315;ENST00000252577;ENST00000457895;ENST00000432704;ENST00000404158;ENST00000429242;ENST00000358713	T;T;T;T;T;T;T	0.56444	0.49;0.98;1.01;0.46;0.53;0.55;0.98	5.61	5.61	0.85477	.	0.219648	0.47093	D	0.000252	T	0.48519	0.1504	L	0.38175	1.15	0.80722	D	1	B;B	0.25351	0.124;0.124	B;B	0.27500	0.08;0.074	T	0.47446	-0.9117	10	0.87932	D	0	-15.9509	18.201	0.89838	0.0:0.0:1.0:0.0	.	115;96	B5MC40;Q86YP4	.;P66A_HUMAN	S	96;96;96;96;96;115;96;96	ENSP00000403703:R96S;ENSP00000353463:R96S;ENSP00000252577:R96S;ENSP00000404212:R96S;ENSP00000390495:R96S;ENSP00000414252:R96S;ENSP00000351552:R96S	ENSP00000252577:R96S	R	+	3	2	GATAD2A	19464133	1.000000	0.71417	0.997000	0.53966	0.494000	0.33585	1.747000	0.38298	2.642000	0.89623	0.561000	0.74099	AGG	.	.	.	none		0.617	GATAD2A-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326671.4	NM_017660		T	19603133	G	T	19603133	3	4	120	1	0	0	0	0	1	0	0	0	6267	1165	41	4	294	4	GATAD2A	19	19603133	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	9734942	19603133	39525850	79	7660											
PAK4	10298	hgsc.bcm.edu	37	chr19	39667267	39667267	+	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	tgggttctgcgcccaggtgaGcaaggaagtgccccgaagga	9	6	16	10	2	1	1	0	1	1	0	1	4	1	3	3	4	3	2	3	4	3	1			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr19:39667267G>T	ENST00000593690.1	+	9	1824	c.1397G>T	c.(1396-1398)aGc>aTc	p.S466I	PAK4_ENST00000599386.1_Missense_Mutation_p.S313I|PAK4_ENST00000358301.3_Missense_Mutation_p.S466I|PAK4_ENST00000599470.1_Missense_Mutation_p.S313I|PAK4_ENST00000435673.2_Missense_Mutation_p.S466I|PAK4_ENST00000360442.3_Missense_Mutation_p.S466I|PAK4_ENST00000321944.4_Missense_Mutation_p.S376I	NM_001014831.2	NP_001014831.1	O96013	PAK4_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 4	466	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)			GCCCAGGTGAGCAAGGAAGTG	0.672																																					p.S466I		Atlas-SNP	.											.	PAK4	40	.	0			c.G1397T						PASS	.						134	138	136					19																	39667267		2203	4300	6503	SO:0001583	missense	10298	exon7			AGGTGAGCAAGGA	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.1397G>T	chr19.hg19:g.39667267G>T	ENSP00000469413:p.Ser466Ile	367.0	0.0	.		225.0	94.0	.	NM_001014832	B4DGG6|Q8N4E1|Q8NCH5|Q8NDE3|Q9BU33|Q9ULS8	Missense_Mutation	SNP	ENST00000593690.1	hg19	CCDS12528.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.310361	0.81358	.	.	ENSG00000130669	ENST00000358301;ENST00000321944;ENST00000358801;ENST00000542377;ENST00000435673;ENST00000360442	T;T;T	0.65549	-0.16;-0.16;-0.16	4.87	3.79	0.43588	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.174438	0.51477	D	0.000092	T	0.62816	0.2459	L	0.35249	1.045	0.49213	D	0.999762	P;P;D	0.54964	0.927;0.946;0.969	P;P;D	0.63703	0.479;0.807;0.917	T	0.64462	-0.6402	10	0.87932	D	0	.	5.7648	0.18221	0.2083:0.0:0.7917:0.0	.	376;313;466	O96013-4;O96013-3;O96013	.;.;PAK4_HUMAN	I	466;313;270;222;466;466	ENSP00000351049:S466I;ENSP00000392753:S466I;ENSP00000353625:S466I	ENSP00000326864:S313I	S	+	2	0	PAK4	44359107	0.904000	0.30761	1.000000	0.80357	0.989000	0.77384	1.132000	0.31418	2.525000	0.85131	0.655000	0.94253	AGC	.	.	.	none		0.672	PAK4-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463823.1			T	39667267	G	T	39667267	3	4	120	1	0	0	0	0	1	0	0	0	11410	971	34	4	1419	4	PAK4	19	39667267	Missense_Mutation	SNP	G	TCGA-BQ-5885-01A-11D-1589-08	20064134	39667267	19461716	80	7661											
SIRPB1	10326	hgsc.bcm.edu	37	chr20	1551504	1551504	+	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	gcgctgagatctccagggcaTagcttttgctgactgcttgc	6	12	12	11	1	1	2	0	2	1	1	2	3	1	2	1	1	4	5	1	1	1	4			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr20:1551504T>A	ENST00000381605.4	-	4	1095	c.1031A>T	c.(1030-1032)tAt>tTt	p.Y344F	SIRPB1_ENST00000381603.3_Intron|SIRPB1_ENST00000262929.5_Intron|RP4-576H24.4_ENST00000564763.1_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	344	Ig-like C1-type 2.				cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						CTCCAGGGCATAGCTTTTGCT	0.507																																					p.Y344F		Atlas-SNP	.											.	SIRPB1	83	.	0			c.A1031T						PASS	.						191	178	183					20																	1551504		2203	4300	6503	SO:0001583	missense	10326	exon4			AGGGCATAGCTTT	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.1031A>T	chr20.hg19:g.1551504T>A	ENSP00000371018:p.Tyr344Phe	274.0	0.0	.		201.0	78.0	.	NM_006065	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	hg19	CCDS13019.1	.	.	.	.	.	.	.	.	.	.	.	0.112	-1.137007	0.01742	.	.	ENSG00000101307	ENST00000381605	T	0.02015	4.5	1.96	-3.91	0.04168	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.801060	0.02558	N	0.096430	T	0.01156	0.0038	N	0.04959	-0.14	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.44907	-0.9297	10	0.10636	T	0.68	.	3.3438	0.07128	0.5823:0.1453:0.0:0.2723	.	344	O00241	SIRB1_HUMAN	F	344	ENSP00000371018:Y344F	ENSP00000371018:Y344F	Y	-	2	0	SIRPB1	1499504	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.905000	0.04075	-1.342000	0.02222	-0.728000	0.03583	TAT	.	.	.	none		0.507	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065		A	1551504	T	A	1551504	3	1	120	1	0	0	0	0	1	0	0	0	14346	1406	49	5	173	5	SIRPB1	20	1551504	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08		1551504	61474016	81	7662											
SF3A1	10291	hgsc.bcm.edu	37	chr22	30737847	30737847	+	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	ggattcgggcccccagctccTctggcgtggtggggggaggg	3	7	20	11	2	1	0	0	0	1	0	3	2	2	2	3	8	1	1	3	8	0	1			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr22:30737847T>A	ENST00000215793.8	-	7	1059	c.905A>T	c.(904-906)gAg>gTg	p.E302V	SF3A1_ENST00000439242.1_Missense_Mutation_p.E237V	NM_005877.4	NP_005868.1	Q15459	SF3A1_HUMAN	splicing factor 3a, subunit 1, 120kDa	302					gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U2-type spliceosomal complex (GO:0005684)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|urinary_tract(1)	29						CCCCAGCTCCTCTGGCGTGGT	0.547																																					p.E302V		Atlas-SNP	.											.	SF3A1	61	.	0			c.A905T						PASS	.						60	57	58					22																	30737847		2203	4300	6503	SO:0001583	missense	10291	exon7			AGCTCCTCTGGCG	X85237	CCDS13875.1	22q12.2	2014-09-17	2002-08-29		ENSG00000099995	ENSG00000099995			10765	protein-coding gene	gene with protein product		605595	"splicing factor 3a, subunit 1, 120kD"			7489498	Standard	NM_005877		Approved	SF3a120, SAP114, PRPF21, Prp21	uc003ahl.3	Q15459	OTTHUMG00000151005	ENST00000215793.8:c.905A>T	chr22.hg19:g.30737847T>A	ENSP00000215793:p.Glu302Val	113.0	0.0	.		104.0	31.0	.	NM_005877	E9PAW1	Missense_Mutation	SNP	ENST00000215793.8	hg19	CCDS13875.1	.	.	.	.	.	.	.	.	.	.	T	16.21	3.058118	0.55325	.	.	ENSG00000099995	ENST00000439242;ENST00000215793;ENST00000536049	T;T	0.34667	1.37;1.35	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.61311	0.2337	M	0.73598	2.24	0.80722	D	1	D	0.62365	0.991	D	0.76071	0.987	T	0.61987	-0.6949	10	0.48119	T	0.1	-28.8415	16.4504	0.83984	0.0:0.0:0.0:1.0	.	302	Q15459	SF3A1_HUMAN	V	237;302;199	ENSP00000390336:E237V;ENSP00000215793:E302V	ENSP00000215793:E302V	E	-	2	0	SF3A1	29067847	1.000000	0.71417	0.996000	0.52242	0.359000	0.29487	7.958000	0.87877	2.288000	0.76882	0.533000	0.62120	GAG	.	.	.	none		0.547	SF3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320916.2	NM_005877		A	30737847	T	A	30737847	3	1	120	1	0	0	0	0	1	0	0	0	14159	1551	54	5	1516	5	SF3A1	22	30737847	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08		30737847	20566719	82	7663											
APOBEC3G	60489	hgsc.bcm.edu	37	chr22	39482535	39482535	+	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	gaggggctgcgcaccctggcCgaggctggggccaaaatttc	7	6	16	12	2	0	0	0	0	0	0	1	2	0	0	3	6	1	3	3	6	2	1	rs138907659		TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chr22:39482535C>G	ENST00000407997.3	+	6	1344	c.987C>G	c.(985-987)gcC>gcG	p.A329A	APOBEC3G_ENST00000452957.2_Silent_p.A329A	NM_021822.3	NP_068594.1	Q9HC16	ABC3G_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3G	329	Necessary for homooligomerization.				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)					GCACCCTGGCCGAGGCTGGGG	0.522																																					p.A329A		Atlas-SNP	.											.	APOBEC3G	69	.	0			c.C987G						PASS	.						101	112	108					22																	39482535		2203	4300	6503	SO:0001819	synonymous_variant	60489	exon6			CCTGGCCGAGGCT	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.987C>G	chr22.hg19:g.39482535C>G		319.0	0.0	.		206.0	59.0	.	NM_021822	B2RDR9|Q45F02|Q5TF77|Q7Z2N1|Q7Z2N4|Q9H9H8	Silent	SNP	ENST00000407997.3	hg19	CCDS13984.1																																																																																			.	C|1.000;T|0.000	.	alt		0.522	APOBEC3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321219.1	NM_021822		G	39482535	C	G	39482535	2	3	120	1	0	0	0	0	0	0	0	1	794	639	23	4		4	APOBEC3G	22	39482535	Silent	SNP	C	TCGA-BQ-5885-01A-11D-1589-08	8744688	39482535	11822031	83	7664											
AGTR2	186	hgsc.bcm.edu	37	chrX	115303624	115303624	+	Missense_Mutation	SNP	T	T	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	acatctctggcaacaatgagTctaccttgaactgttcacag	12	11	7	11	0	3	2	1	2	2	0	4	2	3	2	1	1	3	2	1	1	4	3			TCGA-BQ-5885-01A-11D-1589-08	TCGA-BQ-5885-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fefc32ae-2b8e-46c8-8a7b-d536f9c71568	762ffc49-9149-4ea9-9dce-33e726dee43d	g.chrX:115303624T>G	ENST00000371906.4	+	3	281	c.91T>G	c.(91-93)Tct>Gct	p.S31A		NM_000686.4	NP_000677.2	P50052	AGTR2_HUMAN	angiotensin II receptor, type 2	31					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)	CAACAATGAGTCTACCTTGAA	0.383																																					p.S31A		Atlas-SNP	.											.	AGTR2	62	.	0			c.T91G						PASS	.						125	107	113					X																	115303624		2203	4300	6503	SO:0001583	missense	186	exon3			AATGAGTCTACCT	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.91T>G	chrX.hg19:g.115303624T>G	ENSP00000360973:p.Ser31Ala	104.0	0.0	.		98.0	63.0	.	NM_000686	B2R9V1|Q13016|Q6FGY7	Missense_Mutation	SNP	ENST00000371906.4	hg19	CCDS14569.1	.	.	.	.	.	.	.	.	.	.	T	7.505	0.653477	0.14580	.	.	ENSG00000180772	ENST00000371906	T	0.37752	1.18	4.14	4.14	0.48551	.	0.844018	0.10647	N	0.650365	T	0.24353	0.0590	N	0.19112	0.55	0.09310	N	1	B	0.16396	0.017	B	0.14023	0.01	T	0.13019	-1.0525	10	0.39692	T	0.17	-5.3221	8.5784	0.33612	0.0:0.0:0.0:1.0	.	31	P50052	AGTR2_HUMAN	A	31	ENSP00000360973:S31A	ENSP00000360973:S31A	S	+	1	0	AGTR2	115217652	0.012000	0.17670	0.098000	0.21074	0.802000	0.45316	1.925000	0.40074	1.537000	0.49254	0.412000	0.27726	TCT	.	.	.	none		0.383	AGTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057984.1	NM_000686		G	115303624	T	G	115303624	3	3	120	1	0	0	0	0	1	0	0	0	402	1667	58	5	93	5	AGTR2	23	115303624	Missense_Mutation	SNP	T	TCGA-BQ-5885-01A-11D-1589-08		115303624	39966936	84	7665											
SLC6A17	388662	hgsc.bcm.edu	37	chr1	110709565	110709565	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcatcaatgccgaagaacaGcaaagtgacccagcgtgagc	14	4	12	11	2	1	3	1	2	0	1	1	4	1	3	2	1	5	2	2	1	4	0			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr1:110709565G>A	ENST00000331565.4	+	2	499	c.14G>A	c.(13-15)aGc>aAc	p.S5N	RP5-1028L10.1_ENST00000430098.1_RNA|RP5-1028L10.1_ENST00000418579.1_RNA|RP5-1028L10.1_ENST00000443008.1_RNA	NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	5					alanine transport (GO:0032328)|glycine transport (GO:0015816)|leucine transport (GO:0015820)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		CCGAAGAACAGCAAAGTGACC	0.577																																					p.S5N		Atlas-SNP	.											.	SLC6A17	86	.	0			c.G14A						PASS	.						54	49	51					1																	110709565		2203	4300	6503	SO:0001583	missense	388662	exon2			AGAACAGCAAAGT		CCDS30799.1	1p13.2	2013-07-19	2013-07-19		ENSG00000197106	ENSG00000197106		"Solute carriers"	31399	protein-coding gene	gene with protein product		610299	"solute carrier family 6 (neurotransmitter transporter), member 17", "solute carrier family 6, member 17"				Standard	NM_001010898		Approved		uc009wfq.3	Q9H1V8	OTTHUMG00000011761	ENST00000331565.4:c.14G>A	chr1.hg19:g.110709565G>A	ENSP00000330199:p.Ser5Asn	45.0	0.0	.		45.0	11.0	.	NM_001010898	A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Missense_Mutation	SNP	ENST00000331565.4	hg19	CCDS30799.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.201454	0.79015	.	.	ENSG00000197106	ENST00000331565;ENST00000450985	T	0.75938	-0.98	4.31	4.31	0.51392	.	0.091130	0.64402	D	0.000001	T	0.71921	0.3397	M	0.67397	2.05	0.44834	D	0.997843	P	0.42203	0.773	P	0.46208	0.507	T	0.76203	-0.3045	10	0.51188	T	0.08	.	16.9598	0.86269	0.0:0.0:1.0:0.0	.	5	Q9H1V8	S6A17_HUMAN	N	5	ENSP00000330199:S5N	ENSP00000330199:S5N	S	+	2	0	SLC6A17	110511088	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.350000	0.59392	2.221000	0.72209	0.563000	0.77884	AGC	.	.	.	none		0.577	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2	XM_371280		A	110709565	G	A	110709565	3	1	121	1	0	0	0	0	1	0	0	0	14693	971	34	2	16	2	SLC6A17	1	110709565	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08		110709565	138541056	1	7666											
ELF3	1999	hgsc.bcm.edu	37	chr1	201984378	201984378	+	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	cctggaacgggtggatggccGgcgactcgtctacaagtttg	7	9	15	10	4	1	0	0	0	1	0	2	3	1	2	2	5	2	1	2	5	3	2			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr1:201984378G>C	ENST00000359651.3	+	8	4235	c.1043G>C	c.(1042-1044)cGg>cCg	p.R348P	RP11-510N19.5_ENST00000504773.1_RNA|ELF3_ENST00000367283.3_Missense_Mutation_p.R348P|ELF3_ENST00000367284.5_Missense_Mutation_p.R348P					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						GTGGATGGCCGGCGACTCGTC	0.557																																					p.R348P		Atlas-SNP	.											.	ELF3	92	.	0			c.G1043C						PASS	.						84	86	85					1																	201984378		2203	4300	6503	SO:0001583	missense	1999	exon9			ATGGCCGGCGACT	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.1043G>C	chr1.hg19:g.201984378G>C	ENSP00000352673:p.Arg348Pro	100.0	0.0	.		69.0	15.0	.	NM_001114309		Missense_Mutation	SNP	ENST00000359651.3	hg19	CCDS1419.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.878405	0.91740	.	.	ENSG00000163435	ENST00000359651;ENST00000367284;ENST00000367283;ENST00000310044	T;T;T	0.15372	2.43;2.43;2.43	4.61	4.61	0.57282	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (4);	0.000000	0.64402	D	0.000001	T	0.48241	0.1489	M	0.86502	2.82	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.57877	-0.7735	10	0.87932	D	0	.	16.4352	0.83873	0.0:0.0:1.0:0.0	.	348	P78545	ELF3_HUMAN	P	348;348;348;325	ENSP00000352673:R348P;ENSP00000356253:R348P;ENSP00000356252:R348P	ENSP00000311348:R325P	R	+	2	0	ELF3	200251001	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.616000	0.98359	2.421000	0.82119	0.555000	0.69702	CGG	.	.	.	none		0.557	ELF3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087360.1	NM_004433		C	201984378	G	C	201984378	3	2	121	1	0	0	0	0	1	0	0	0	5057	1116	39	4	1073	4	ELF3	1	201984378	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	91274813	201984378	47266243	2	7667											
NID1	4811	hgsc.bcm.edu	37	chr1	236208870	236208870	+	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	gcaaccacggcaggaacttgGttgttttccttctttgagaa	9	13	10	9	1	1	1	0	1	1	1	2	3	2	2	2	3	2	4	2	3	3	6			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr1:236208870G>C	ENST00000264187.6	-	3	721	c.639C>G	c.(637-639)aaC>aaG	p.N213K	NID1_ENST00000366595.3_Missense_Mutation_p.N213K	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	213	NIDO. {ECO:0000255|PROSITE- ProRule:PRU00570}.				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)	CAGGAACTTGGTTGTTTTCCT	0.448																																					p.N213K		Atlas-SNP	.											.	NID1	196	.	0			c.C639G						PASS	.						111	104	106					1																	236208870		2203	4300	6503	SO:0001583	missense	4811	exon3			AACTTGGTTGTTT	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.639C>G	chr1.hg19:g.236208870G>C	ENSP00000264187:p.Asn213Lys	100.0	0.0	.		99.0	4.0	.	NM_002508	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Missense_Mutation	SNP	ENST00000264187.6	hg19	CCDS1608.1	.	.	.	.	.	.	.	.	.	.	G	3.031	-0.199616	0.06219	.	.	ENSG00000116962	ENST00000264187;ENST00000366595	T;T	0.71461	-0.57;-0.57	5.81	0.342	0.15996	Nidogen, extracellular domain (3);	1.058890	0.07141	N	0.847269	T	0.57344	0.2047	L	0.29908	0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.46205	-0.9208	10	0.54805	T	0.06	.	6.9876	0.24737	0.0648:0.096:0.2443:0.5949	.	213;213	P14543-2;P14543	.;NID1_HUMAN	K	213	ENSP00000264187:N213K;ENSP00000355554:N213K	ENSP00000264187:N213K	N	-	3	2	NID1	234275493	0.001000	0.12720	0.035000	0.18076	0.061000	0.15899	-0.029000	0.12329	-0.172000	0.10779	0.561000	0.74099	AAC	.	.	.	none		0.448	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508		C	236208870	G	C	236208870	3	2	121	1	0	0	0	0	1	0	0	0	10421	1252	44	4	3176	4	NID1	1	236208870	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	34224492	236208870	13041751	3	7668											
FAM161A	84140	hgsc.bcm.edu	37	chr2	62066806	62066806	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	taagagttttggagacttgtGttctgagaggtgtttctggt	7	17	14	3	0	2	3	0	1	2	3	2	5	2	3	0	3	0	3	0	3	1	6			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr2:62066806G>A	ENST00000405894.3	-	3	1434	c.1333C>T	c.(1333-1335)Cac>Tac	p.H445Y	FAM161A_ENST00000404929.1_Missense_Mutation_p.H445Y	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	445					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						GGAGACTTGTGTTCTGAGAGG	0.408																																					p.H445Y		Atlas-SNP	.											.	FAM161A	200	.	0			c.C1333T						PASS	.						122	110	114					2																	62066806		1874	4103	5977	SO:0001583	missense	84140	exon3			ACTTGTGTTCTGA		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.1333C>T	chr2.hg19:g.62066806G>A	ENSP00000385893:p.His445Tyr	179.0	0.0	.		170.0	52.0	.	NM_032180	B4DJV7|Q9H8R2	Missense_Mutation	SNP	ENST00000405894.3	hg19	CCDS42687.2	.	.	.	.	.	.	.	.	.	.	G	7.735	0.700095	0.15106	.	.	ENSG00000170264	ENST00000404929;ENST00000405894	T;T	0.21734	1.99;1.99	5.19	-0.0571	0.13803	.	0.977729	0.08450	N	0.943967	T	0.08980	0.0222	N	0.08118	0	0.09310	N	1	B;B	0.17268	0.003;0.021	B;B	0.17098	0.013;0.017	T	0.36841	-0.9731	10	0.28530	T	0.3	-13.5655	2.5423	0.04729	0.1324:0.2247:0.4122:0.2308	.	445;445	Q3B820;Q3B820-3	F161A_HUMAN;.	Y	445	ENSP00000385158:H445Y;ENSP00000385893:H445Y	ENSP00000385158:H445Y	H	-	1	0	FAM161A	61920310	0.001000	0.12720	0.001000	0.08648	0.044000	0.14063	0.602000	0.24134	-0.235000	0.09767	-0.185000	0.12909	CAC	.	.	.	none		0.408	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180		A	62066806	G	A	62066806	3	1	121	1	0	0	0	0	1	0	0	0	5476	1377	48	2	665	2	FAM161A	2	62066806	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08		62066806	181132567	4	7669											
LMAN2L	81562	hgsc.bcm.edu	37	chr2	97373520	97373520	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagcttttcctcttctggggTtctctccactgtcagttcaa	5	16	8	12	0	5	0	2	0	3	0	8	1	7	0	2	2	1	3	2	2	1	5			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr2:97373520T>C	ENST00000264963.4	-	7	857	c.835A>G	c.(835-837)Acc>Gcc	p.T279A	LMAN2L_ENST00000534882.1_Missense_Mutation_p.T134A|FER1L5_ENST00000457909.1_RNA|LMAN2L_ENST00000377079.4_Missense_Mutation_p.T290A|LMAN2L_ENST00000426463.2_Missense_Mutation_p.T145A|LMAN2L_ENST00000537039.1_Missense_Mutation_p.T141A	NM_030805.3	NP_110432.1	Q9H0V9	LMA2L_HUMAN	lectin, mannose-binding 2-like	279					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						TCTTCTGGGGTTCTCTCCACT	0.468																																					p.T290A		Atlas-SNP	.											.	LMAN2L	27	.	0			c.A868G						PASS	.						111	111	111					2																	97373520		2203	4300	6503	SO:0001583	missense	81562	exon8			CTGGGGTTCTCTC	AL136617	CCDS2023.1, CCDS46365.1	2q11.1	2008-02-05			ENSG00000114988	ENSG00000114988			19263	protein-coding gene	gene with protein product		609552				12609988	Standard	NM_001142292		Approved	DKFZp564L2423, VIPL	uc002swv.3	Q9H0V9	OTTHUMG00000130453	ENST00000264963.4:c.835A>G	chr2.hg19:g.97373520T>C	ENSP00000264963:p.Thr279Ala	167.0	0.0	.		154.0	37.0	.	NM_001142292	B4DSH3|D3DXH6|Q53GV3|Q53S67|Q63HN6|Q8NBQ6|Q9BQ14	Missense_Mutation	SNP	ENST00000264963.4	hg19	CCDS2023.1	.	.	.	.	.	.	.	.	.	.	T	18.08	3.544490	0.65198	.	.	ENSG00000114988	ENST00000264963;ENST00000377079;ENST00000426463;ENST00000537039;ENST00000534882	T;T;T;T;T	0.77358	0.91;0.9;-1.09;-1.04;-1.08	5.62	5.62	0.85841	Concanavalin A-like lectin/glucanase, subgroup (1);	0.095537	0.64402	D	0.000001	T	0.69106	0.3074	L	0.46157	1.445	0.51482	D	0.999927	B;B;B;B;B	0.26081	0.141;0.031;0.141;0.004;0.065	B;B;B;B;B	0.20955	0.021;0.023;0.021;0.002;0.032	T	0.64846	-0.6311	10	0.09590	T	0.72	.	14.8095	0.69982	0.0:0.0:0.0:1.0	.	134;152;145;290;279	B4DVH1;B4DI83;B4DSH3;Q9H0V9-2;Q9H0V9	.;.;.;.;LMA2L_HUMAN	A	279;290;145;141;134	ENSP00000264963:T279A;ENSP00000366280:T290A;ENSP00000396391:T145A;ENSP00000441701:T141A;ENSP00000438501:T134A	ENSP00000264963:T279A	T	-	1	0	LMAN2L	96737247	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	5.930000	0.70104	2.129000	0.65627	0.533000	0.62120	ACC	.	.	.	none		0.468	LMAN2L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252844.1	NM_030805		C	97373520	T	C	97373520	3	2	121	1	0	0	0	0	1	0	0	0	8846	1725	60	3	219	3	LMAN2L	2	97373520	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	35306714	97373520	145825853	5	7670											
LRP2	4036	hgsc.bcm.edu	37	chr2	170072853	170072853	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgaggttcccagtaaagagAgttttcacagatgtgccatc	11	11	10	9	1	1	2	1	0	0	2	4	4	2	2	2	1	1	3	2	1	2	4			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr2:170072853A>G	ENST00000263816.3	-	35	6021	c.5736T>C	c.(5734-5736)acT>acC	p.T1912T		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1912					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)"	CAGTAAAGAGAGTTTTCACAG	0.502																																					p.T1912T		Atlas-SNP	.											.	LRP2	751	.	0			c.T5736C						PASS	.						150	136	141					2																	170072853		2203	4300	6503	SO:0001819	synonymous_variant	4036	exon35			AAAGAGAGTTTTC		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.5736T>C	chr2.hg19:g.170072853A>G		102.0	0.0	.		105.0	41.0	.	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	hg19	CCDS2232.1																																																																																			.	.	.	none		0.502	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		G	170072853	A	G	170072853	2	3	121	1	0	0	0	0	0	0	0	1	8963	291	11	3		3	LRP2	2	170072853	Silent	SNP	A	TCGA-BQ-5886-01A-11D-1589-08	72699333	170072853	73126520	6	7671											
GOLGA4	2803	hgsc.bcm.edu	37	chr3	37340849	37340849	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaagaacttaattgaacagcTtgaacaagataaggtaaaac	21	8	7	5	0	0	4	0	2	0	2	0	4	0	4	0	1	5	2	0	1	9	5			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr3:37340849T>C	ENST00000361924.2	+	9	1447	c.1073T>C	c.(1072-1074)cTt>cCt	p.L358P	GOLGA4_ENST00000444882.1_Intron|GOLGA4_ENST00000435830.2_3'UTR|GOLGA4_ENST00000356847.4_Missense_Mutation_p.L380P	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	358	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						ATTGAACAGCTTGAACAAGAT	0.333																																					p.L380P		Atlas-SNP	.											.	GOLGA4	173	.	0			c.T1139C						PASS	.						44	44	44					3																	37340849		2203	4297	6500	SO:0001583	missense	2803	exon10			AACAGCTTGAACA	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.1073T>C	chr3.hg19:g.37340849T>C	ENSP00000354486:p.Leu358Pro	72.0	0.0	.		78.0	41.0	.	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	hg19	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.388371	0.82902	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000450863;ENST00000437131	T;T;T;T	0.34072	1.38;1.38;1.38;1.38	5.45	5.45	0.79879	.	0.000000	0.29830	N	0.011099	T	0.61825	0.2378	M	0.78637	2.42	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.998	T	0.64939	-0.6289	10	0.52906	T	0.07	.	15.519	0.75851	0.0:0.0:0.0:1.0	.	358;380;358	Q13439-4;F8W8Q7;Q13439	.;.;GOGA4_HUMAN	P	358;380;363;229	ENSP00000354486:L358P;ENSP00000349305:L380P;ENSP00000387633:L363P;ENSP00000405842:L229P	ENSP00000349305:L380P	L	+	2	0	GOLGA4	37315853	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.923000	0.87546	2.077000	0.62373	0.372000	0.22366	CTT	.	.	.	none		0.333	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		C	37340849	T	C	37340849	3	2	121	1	0	0	0	0	1	0	0	0	6562	1609	56	3	1177	3	GOLGA4	3	37340849	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08		37340849	160681581	7	7672											
MORC1	27136	hgsc.bcm.edu	37	chr3	108788509	108788509	+	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	agaggcaatagcaaagatgtTtagttttaactctcttggct	12	14	9	6	0	1	2	0	0	1	2	2	2	1	2	0	2	2	5	0	2	5	6			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr3:108788509T>A	ENST00000483760.1	-	9	828	c.785A>T	c.(784-786)aAa>aTa	p.K262I	MORC1_ENST00000232603.5_Missense_Mutation_p.K262I					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						GCAAAGATGTTTAGTTTTAAC	0.373																																					p.K262I		Atlas-SNP	.											.	MORC1	211	.	0			c.A785T						PASS	.						113	113	113					3																	108788509		2203	4300	6503	SO:0001583	missense	27136	exon9			AGATGTTTAGTTT	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.785A>T	chr3.hg19:g.108788509T>A	ENSP00000417282:p.Lys262Ile	119.0	0.0	.		156.0	42.0	.	NM_014429		Missense_Mutation	SNP	ENST00000483760.1	hg19		.	.	.	.	.	.	.	.	.	.	T	20.8	4.054789	0.75960	.	.	ENSG00000114487	ENST00000232603;ENST00000483760	T;T	0.74106	-0.81;-0.81	4.84	3.68	0.42216	ATPase-like, ATP-binding domain (1);	0.128321	0.35708	N	0.003033	D	0.82365	0.5021	M	0.69185	2.1	0.46298	D	0.998976	D;P	0.89917	1.0;0.892	D;P	0.87578	0.998;0.54	T	0.81984	-0.0682	10	0.62326	D	0.03	-23.3217	8.914	0.35570	0.0:0.0897:0.0:0.9103	.	262;262	E7ERX1;Q86VD1	.;MORC1_HUMAN	I	262	ENSP00000232603:K262I;ENSP00000417282:K262I	ENSP00000232603:K262I	K	-	2	0	MORC1	110271199	1.000000	0.71417	0.933000	0.37362	0.947000	0.59692	3.950000	0.56676	0.972000	0.38314	0.482000	0.46254	AAA	.	.	.	none		0.373	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1			A	108788509	T	A	108788509	3	1	121	1	0	0	0	0	1	0	0	0	9708	1841	64	5	2249	5	MORC1	3	108788509	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	71447660	108788509	89233921	8	7673											
SLC30A5	64924	hgsc.bcm.edu	37	chr5	68399835	68399835	+	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	tagaaaagaatttaaagacaAaaagttaaatgatcctagga	22	9	7	3	0	0	4	0	1	0	3	1	5	1	5	1	1	0	1	1	1	11	5			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr5:68399835A>G	ENST00000396591.3	+	4	883				SLC30A5_ENST00000502979.1_Missense_Mutation_p.K66R|SLC30A5_ENST00000380860.4_Missense_Mutation_p.K107R	NM_022902.4	NP_075053.2	Q8TAD4	ZNT5_HUMAN	solute carrier family 30 (zinc transporter), member 5						cellular protein metabolic process (GO:0044267)|cellular zinc ion homeostasis (GO:0006882)|cobalt ion transport (GO:0006824)|regulation of proton transport (GO:0010155)|response to zinc ion (GO:0010043)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	apical plasma membrane (GO:0016324)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Lung NSC(167;0.000986)|Prostate(74;0.00809)|Colorectal(97;0.0508)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		TTTAAAGACAAAAAGTTAAAT	0.284																																					p.K107R		Atlas-SNP	.											.	SLC30A5	54	.	0			c.A320G						PASS	.						22	23	23					5																	68399835		2178	4287	6465	SO:0001627	intron_variant	64924	exon4			AAGACAAAAAGTT	AF212235	CCDS3996.1, CCDS34173.1, CCDS58955.1	5q13.1	2013-05-22			ENSG00000145740	ENSG00000145740		"Solute carriers"	19089	protein-coding gene	gene with protein product		607819				11937503, 11904301	Standard	NM_022902		Approved	ZTL1, ZnT-5, FLJ12496, FLJ12756, ZNT5, MGC5499, ZNTL1	uc003jvh.3	Q8TAD4	OTTHUMG00000131253	ENST00000396591.3:c.274-623A>G	chr5.hg19:g.68399835A>G		31.0	0.0	.		30.0	10.0	.	NM_024055	B7ZM89|Q6UX54|Q7L4M4|Q8TDG3|Q9BVY8|Q9H9H1	Missense_Mutation	SNP	ENST00000396591.3	hg19	CCDS3996.1	.	.	.	.	.	.	.	.	.	.	A	12.48	1.950224	0.34377	.	.	ENSG00000145740	ENST00000380860;ENST00000502979	.	.	.	2.74	2.74	0.32292	.	.	.	.	.	T	0.42832	0.1220	.	.	.	0.19300	N	0.99998	P	0.37398	0.593	P	0.45577	0.486	T	0.36696	-0.9737	7	0.87932	D	0	.	7.3651	0.26768	1.0:0.0:0.0:0.0	.	107	Q9BVY8	.	R	107;66	.	ENSP00000370241:K107R	K	+	2	0	SLC30A5	68435591	0.144000	0.22641	0.636000	0.29352	0.015000	0.08874	1.174000	0.31932	1.510000	0.48803	0.459000	0.35465	AAA	.	.	.	none		0.284	SLC30A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254017.2			G	68399835	A	G	68399835	1	3	121	0	1	0	0	0	0	0	0	0	14571	14	1	3		3	SLC30A5	5	68399835	Intron	SNP	A	TCGA-BQ-5886-01A-11D-1589-08		68399835	112515425	9	7674											
F2RL2	2151	hgsc.bcm.edu	37	chr5	75913735	75913735	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaagaatccaaagaatgccAaggagatgaagtaatagagt	19	8	10	4	0	0	5	0	1	0	4	1	6	1	5	2	1	1	1	2	1	8	3			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr5:75913735A>G	ENST00000296641.4	-	2	1000	c.797T>C	c.(796-798)tTg>tCg	p.L266S	IQGAP2_ENST00000274364.6_Intron|IQGAP2_ENST00000396234.3_Intron|F2RL2_ENST00000504899.1_Missense_Mutation_p.L244S|IQGAP2_ENST00000502745.1_Intron|IQGAP2_ENST00000379730.3_Intron	NM_004101.3	NP_004092.1	O00254	PAR3_HUMAN	coagulation factor II (thrombin) receptor-like 2	266					blood coagulation (GO:0007596)|metabolic process (GO:0008152)|platelet activation (GO:0030168)|response to wounding (GO:0009611)	apical plasma membrane (GO:0016324)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|thrombin receptor activity (GO:0015057)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(3)	32		all_lung(232;0.000462)|Lung NSC(167;0.00124)|Prostate(461;0.00955)|Ovarian(174;0.0129)		all cancers(79;4.43e-43)		AAAGAATGCCAAGGAGATGAA	0.423																																					p.L266S		Atlas-SNP	.											.	F2RL2	57	.	0			c.T797C						PASS	.						76	72	73					5																	75913735		2203	4300	6503	SO:0001583	missense	2151	exon2			AATGCCAAGGAGA	U92971	CCDS4031.1, CCDS58959.1	5q13	2012-08-08			ENSG00000164220	ENSG00000164220		"GPCR / Class A : Protease activated receptors"	3539	protein-coding gene	gene with protein product	"proteinase-activated receptor-3"	601919				9087410, 9722561	Standard	NM_004101		Approved	PAR3	uc003kem.4	O00254	OTTHUMG00000102119	ENST00000296641.4:c.797T>C	chr5.hg19:g.75913735A>G	ENSP00000296641:p.Leu266Ser	45.0	0.0	.		59.0	14.0	.	NM_004101	B2R754|B4DQ13|Q52M68|Q7Z3W3	Missense_Mutation	SNP	ENST00000296641.4	hg19	CCDS4031.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.155954	0.78114	.	.	ENSG00000164220	ENST00000296641;ENST00000504899	T;T	0.70045	-0.45;-0.45	5.3	5.3	0.74995	GPCR, rhodopsin-like superfamily (1);	0.152354	0.43579	D	0.000549	T	0.76695	0.4023	L	0.56340	1.77	0.46678	D	0.999155	D	0.89917	1.0	D	0.80764	0.994	T	0.73272	-0.4035	10	0.22706	T	0.39	-8.0196	15.2748	0.73734	1.0:0.0:0.0:0.0	.	266	O00254	PAR3_HUMAN	S	266;244	ENSP00000296641:L266S;ENSP00000426703:L244S	ENSP00000296641:L266S	L	-	2	0	F2RL2	75949491	1.000000	0.71417	0.860000	0.33809	0.967000	0.64934	8.850000	0.92190	2.006000	0.58801	0.460000	0.39030	TTG	.	.	.	none		0.423	F2RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219958.3			G	75913735	A	G	75913735	3	3	121	1	0	0	0	0	1	0	0	0	5347	131	5	3	331	3	F2RL2	5	75913735	Missense_Mutation	SNP	A	TCGA-BQ-5886-01A-11D-1589-08	7513900	75913735	105001525	10	7675											
BHMT	635	hgsc.bcm.edu	37	chr5	78415082	78415082	+	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	ttcctcattcactctcccagTtcgccagcttcatcgagagt	7	13	6	15	2	4	1	3	0	1	1	8	2	5	1	3	0	1	2	3	0	0	4			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr5:78415082T>C	ENST00000274353.5	+	3	274	c.167T>C	c.(166-168)gTt>gCt	p.V56A	BHMT_ENST00000524080.1_Intron|DMGDH_ENST00000520388.1_Intron	NM_001713.2	NP_001704.2	Q93088	BHMT1_HUMAN	betaine--homocysteine S-methyltransferase	56	Hcy-binding. {ECO:0000255|PROSITE- ProRule:PRU00333}.				amino-acid betaine catabolic process (GO:0006579)|amino-acid betaine metabolic process (GO:0006577)|cellular nitrogen compound metabolic process (GO:0034641)|L-methionine salvage (GO:0071267)|protein methylation (GO:0006479)|regulation of homocysteine metabolic process (GO:0050666)|response to organonitrogen compound (GO:0010243)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	betaine-homocysteine S-methyltransferase activity (GO:0047150)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)	29		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.88e-45)|Epithelial(54;8.07e-41)|all cancers(79;3.51e-36)	L-Methionine(DB00134)	ACTCTCCCAGTTCGCCAGCTT	0.433																																					p.V56A		Atlas-SNP	.											.	BHMT	53	.	0			c.T167C						PASS	.						92	87	89					5																	78415082		2203	4300	6503	SO:0001630	splice_region_variant	635	exon3			TCCCAGTTCGCCA	BC012616	CCDS4046.1	5q14.1	2012-09-20	2010-04-28		ENSG00000145692	ENSG00000145692	2.1.1.5		1047	protein-coding gene	gene with protein product	"betaine homocysteine methyltransferase"	602888				8798461, 9281325	Standard	NM_001713		Approved	BHMT1	uc003kfu.4	Q93088	OTTHUMG00000108157	ENST00000274353.5:c.167-1T>C	chr5.hg19:g.78415082T>C		151.0	0.0	.		125.0	41.0	.	NM_001713	Q9UNI9	Missense_Mutation	SNP	ENST00000274353.5	hg19	CCDS4046.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.388243	0.82902	.	.	ENSG00000145692	ENST00000274353	T	0.45276	0.9	5.6	5.6	0.85130	Homocysteine S-methyltransferase (4);	0.000000	0.85682	D	0.000000	T	0.73249	0.3563	M	0.93678	3.445	0.80722	D	1	D	0.89917	1.0	D	0.73708	0.981	T	0.81360	-0.0968	9	.	.	.	.	16.0786	0.80985	0.0:0.0:0.0:1.0	.	56	Q93088	BHMT1_HUMAN	A	56	ENSP00000274353:V56A	.	V	+	2	0	BHMT	78450838	1.000000	0.71417	1.000000	0.80357	0.616000	0.37450	7.669000	0.83911	2.254000	0.74563	0.460000	0.39030	GTT	.	.	.	none		0.433	BHMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226961.1	NM_001713	Missense_Mutation	C	78415082	T	C	78415082	5	2	121	1	0	0	0	0	0	0	1	0	1425	1739	60	3	177	3	BHMT	5	78415082	Splice_Site	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	2501347	78415082	102500178	11	7676											
PCDHB3	56132	hgsc.bcm.edu	37	chr5	140481178	140481178	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgaagcgattaatagttaTgaagtcgacatcgaggccaa	14	11	10	6	3	0	2	0	2	0	0	2	5	0	2	1	1	1	1	1	1	6	4			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr5:140481178T>C	ENST00000231130.2	+	1	945	c.945T>C	c.(943-945)taT>taC	p.Y315Y	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	315	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)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TTAATAGTTATGAAGTCGACA	0.428																																					p.Y315Y		Atlas-SNP	.											.	PCDHB3	208	.	0			c.T945C						PASS	.						54	58	56					5																	140481178		2203	4300	6503	SO:0001819	synonymous_variant	56132	exon1			TAGTTATGAAGTC	AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"Cadherins / Protocadherins : Clustered"	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.945T>C	chr5.hg19:g.140481178T>C		98.0	0.0	.		86.0	32.0	.	NM_018937	B2R8P2	Silent	SNP	ENST00000231130.2	hg19	CCDS4245.1																																																																																			.	.	.	none		0.428	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937		C	140481178	T	C	140481178	2	2	121	1	0	0	0	0	0	0	0	1	11550	1471	51	3		3	PCDHB3	5	140481178	Silent	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	62066096	140481178	40434082	12	7677											
ODZ2	57451	hgsc.bcm.edu	37	chr5	167674296	167674296	+	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	ccctccccgttgacctctacCgctatgatgagatttctggc	6	12	8	15	2	2	3	0	3	2	1	3	4	3	3	5	1	1	2	5	1	2	4			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr5:167674296C>A	ENST00000518659.1	+	27	6391	c.6352C>A	c.(6352-6354)Cgc>Agc	p.R2118S	TENM2_ENST00000545108.1_Missense_Mutation_p.R2117S|TENM2_ENST00000403607.2_Missense_Mutation_p.R1942S|TENM2_ENST00000520394.1_Missense_Mutation_p.R1879S|TENM2_ENST00000519204.1_Missense_Mutation_p.R1997S	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2118					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)										TGACCTCTACCGCTATGATGA	0.493																																					p.R2109S		Atlas-SNP	.											.	.	.	.	0			c.C6325A						PASS	.						167	167	167					5																	167674296		2016	4172	6188	SO:0001583	missense	57451	exon27			CTCTACCGCTATG	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.6352C>A	chr5.hg19:g.167674296C>A	ENSP00000429430:p.Arg2118Ser	182.0	0.0	.		185.0	57.0	.	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	hg19		.	.	.	.	.	.	.	.	.	.	C	18.69	3.678710	0.68042	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.89123	-1.99;-1.98;-2.09;-2.44;-2.47	5.44	5.44	0.79542	.	0.103671	0.64402	D	0.000001	D	0.93861	0.8036	M	0.71581	2.175	0.54753	D	0.999989	D;P;D	0.69078	0.974;0.899;0.997	P;B;D	0.75484	0.807;0.44;0.986	D	0.92184	0.5754	10	0.30854	T	0.27	.	19.2461	0.93902	0.0:1.0:0.0:0.0	.	2117;2118;1879	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	S	2118;2117;1997;1879;1942	ENSP00000429430:R2118S;ENSP00000438635:R2117S;ENSP00000428964:R1997S;ENSP00000427874:R1879S;ENSP00000384905:R1942S	ENSP00000384905:R1942S	R	+	1	0	ODZ2	167606874	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	3.906000	0.56340	2.560000	0.86352	0.561000	0.74099	CGC	.	.	.	none		0.493	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		A	167674296	C	A	167674296	3	1	121	1	0	0	0	0	1	0	0	0	10842	652	23	4	6431	4	ODZ2	5	167674296	Missense_Mutation	SNP	C	TCGA-BQ-5886-01A-11D-1589-08	27193118	167674296	13240964	13	7678											
PFN3	345456	hgsc.bcm.edu	37	chr5	176827191	176827191	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccctgcatgcgcagcccgcgTatgagttcgtgcaccgtctt	5	10	11	15	5	1	1	0	1	1	0	2	1	1	1	3	0	4	5	3	0	1	3			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr5:176827191T>C	ENST00000358571.2	-	1	446	c.387A>G	c.(385-387)atA>atG	p.I129M	F12_ENST00000514943.1_5'Flank	NM_001029886.2	NP_001025057.1	P60673	PROF3_HUMAN	profilin 3	129					actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	lipid binding (GO:0008289)			lung(1)	1	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCAGCCCGCGTATGAGTTCGT	0.706																																					p.I129M		Atlas-SNP	.											.	PFN3	4	.	0			c.A387G						PASS	.						18	19	19					5																	176827191		2099	4229	6328	SO:0001583	missense	345456	exon1			CCCGCGTATGAGT	AC090063	CCDS34301.1	5q35.2	2008-08-26			ENSG00000196570	ENSG00000196570			18627	protein-coding gene	gene with protein product		612812				11867228	Standard	NM_001029886		Approved		uc003mgl.2	P60673	OTTHUMG00000163408	ENST00000358571.2:c.387A>G	chr5.hg19:g.176827191T>C	ENSP00000351379:p.Ile129Met	39.0	0.0	.		52.0	14.0	.	NM_001029886	A2RUL3	Missense_Mutation	SNP	ENST00000358571.2	hg19	CCDS34301.1	.	.	.	.	.	.	.	.	.	.	T	11.75	1.732218	0.30684	.	.	ENSG00000196570	ENST00000358571	D	0.85861	-2.04	4.76	2.91	0.33838	.	0.294068	0.29459	N	0.012099	D	0.86167	0.5868	L	0.44542	1.39	0.21652	N	0.999609	D	0.71674	0.998	D	0.79108	0.992	T	0.74847	-0.3525	10	0.39692	T	0.17	.	5.3821	0.16197	0.1086:0.0:0.6881:0.2033	.	129	P60673	PROF3_HUMAN	M	129	ENSP00000351379:I129M	ENSP00000351379:I129M	I	-	3	3	PFN3	176759797	0.015000	0.18098	0.596000	0.28811	0.168000	0.22595	-0.004000	0.12878	0.415000	0.25817	-0.724000	0.03597	ATA	.	.	.	none		0.706	PFN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373234.1	NM_001029886		C	176827191	T	C	176827191	3	2	121	1	0	0	0	0	1	0	0	0	11776	1628	57	3	30	3	PFN3	5	176827191	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	9152895	176827191	4088069	14	7679											
VARS2	57176	hgsc.bcm.edu	37	chr6	30893383	30893383	+	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	aggccttcttggagcccctgGgcaccctgggctactgtggg	4	9	15	13	0	1	0	0	0	1	0	1	1	1	1	4	5	2	2	4	5	1	3			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr6:30893383G>C	ENST00000321897.5	+	27	3480	c.2848G>C	c.(2848-2850)Ggc>Cgc	p.G950R	VARS2_ENST00000542001.1_Missense_Mutation_p.G810R|VARS2_ENST00000416670.2_Missense_Mutation_p.G950R|VARS2_ENST00000541562.1_Missense_Mutation_p.G980R|VARS2_ENST00000476162.1_3'UTR			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	950					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						GGAGCCCCTGGGCACCCTGGG	0.647																																					p.G980R		Atlas-SNP	.											.	VARS2	60	.	0			c.G2938C						PASS	.						19	22	21					6																	30893383		1493	2701	4194	SO:0001583	missense	57176	exon28			CCCCTGGGCACCC	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.2848G>C	chr6.hg19:g.30893383G>C	ENSP00000316092:p.Gly950Arg	58.0	0.0	.		41.0	9.0	.	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Missense_Mutation	SNP	ENST00000321897.5	hg19	CCDS34387.1	.	.	.	.	.	.	.	.	.	.	G	5.589	0.293519	0.10567	.	.	ENSG00000137411	ENST00000321897;ENST00000416670;ENST00000542001;ENST00000541562	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	5.62	3.84	0.44239	Aminoacyl-tRNA synthetase, class 1a, anticodon-binding (1);	0.708730	0.14077	N	0.342996	T	0.13628	0.0330	L	0.44542	1.39	0.30330	N	0.78675	B;B;B;B	0.29988	0.264;0.001;0.002;0.0	B;B;B;B	0.26094	0.066;0.001;0.001;0.0	T	0.15378	-1.0439	10	0.15952	T	0.53	-9.346	8.9906	0.36022	0.1719:0.0:0.8281:0.0	.	388;948;980;950	Q5ST30-2;B7ZL25;F5GXJ0;Q5ST30	.;.;.;SYVM_HUMAN	R	950;950;810;980	ENSP00000316092:G950R;ENSP00000394802:G950R;ENSP00000438200:G810R;ENSP00000441000:G980R	ENSP00000316092:G950R	G	+	1	0	VARS2	31001362	0.997000	0.39634	1.000000	0.80357	0.153000	0.21895	0.990000	0.29642	0.737000	0.32582	-0.140000	0.14226	GGC	.	.	.	none		0.647	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442		C	30893383	G	C	30893383	3	2	121	1	0	0	0	0	1	0	0	0	17136	1232	43	4	3048	4	VARS2	6	30893383	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08		30893383	140221684	15	7680											
TTBK1	84630	hgsc.bcm.edu	37	chr6	43226956	43226956	+	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	gggggtcctgaggctgaagtCtgggaggagacagatgtcaa	10	7	18	6	0	2	4	1	2	1	2	3	6	3	5	1	5	0	1	1	5	2	0			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr6:43226956C>G	ENST00000259750.4	+	11	1280	c.1197C>G	c.(1195-1197)gtC>gtG	p.V399V	TTBK1_ENST00000304139.5_Silent_p.V348V	NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	399					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)			AGGCTGAAGTCTGGGAGGAGA	0.642																																					p.V399V		Atlas-SNP	.											.	TTBK1	124	.	0			c.C1197G						PASS	.						51	58	56					6																	43226956		2203	4300	6503	SO:0001819	synonymous_variant	84630	exon11			TGAAGTCTGGGAG	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.1197C>G	chr6.hg19:g.43226956C>G		100.0	0.0	.		104.0	26.0	.	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Silent	SNP	ENST00000259750.4	hg19	CCDS34455.1																																																																																			.	.	.	none		0.642	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3			G	43226956	C	G	43226956	2	3	121	1	0	0	0	0	0	0	0	1	16688	900	32	4		4	TTBK1	6	43226956	Silent	SNP	C	TCGA-BQ-5886-01A-11D-1589-08	12333573	43226956	127888111	16	7681											
GPR110	266977	hgsc.bcm.edu	37	chr6	46977043	46977043	+	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	aatgacagatataatgagagGgcacccataacccaggcaaa	18	5	9	9	0	0	3	0	2	0	2	0	4	0	3	2	2	1	2	2	2	5	3			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr6:46977043G>A	ENST00000371253.2	-	11	2343	c.2128C>T	c.(2128-2130)Cct>Tct	p.P710S	GPR110_ENST00000283297.5_Missense_Mutation_p.P513S|GPR110_ENST00000449332.2_5'UTR	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	710					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						ATAATGAGAGGGCACCCATAA	0.478																																					p.P710S		Atlas-SNP	.											.	GPR110	102	.	0			c.C2128T						PASS	.						88	80	83					6																	46977043		2203	4300	6503	SO:0001583	missense	266977	exon11			TGAGAGGGCACCC	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.2128C>T	chr6.hg19:g.46977043G>A	ENSP00000360299:p.Pro710Ser	54.0	0.0	.		56.0	16.0	.	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Missense_Mutation	SNP	ENST00000371253.2	hg19	CCDS34471.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.576276	0.86645	.	.	ENSG00000153292	ENST00000371253;ENST00000283297	D;D	0.84516	-1.86;-1.86	5.9	5.9	0.94986	GPCR, family 2-like (1);	0.000000	0.64402	D	0.000013	D	0.93572	0.7948	M	0.88377	2.95	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93726	0.7037	10	0.87932	D	0	-22.4263	20.2789	0.98501	0.0:0.0:1.0:0.0	.	710	Q5T601	GP110_HUMAN	S	710;513	ENSP00000360299:P710S;ENSP00000283297:P513S	ENSP00000283297:P513S	P	-	1	0	GPR110	47085002	1.000000	0.71417	0.995000	0.50966	0.855000	0.48748	9.861000	0.99562	2.788000	0.95919	0.650000	0.86243	CCT	.	.	.	none		0.478	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840		A	46977043	G	A	46977043	3	1	121	1	0	0	0	0	1	0	0	0	6634	1232	43	2	624	2	GPR110	6	46977043	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	3750087	46977043	124138024	17	7682											
C6orf170	221322	hgsc.bcm.edu	37	chr6	121576521	121576521	+	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	gaaacagaatcagaaccctcTactggagtaggaattctttc	14	10	8	9	0	3	2	1	0	2	2	4	5	3	4	1	2	3	1	1	2	6	4			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr6:121576521T>A	ENST00000398212.2	-	17	2020	c.1971A>T	c.(1969-1971)gtA>gtT	p.V657V	TBC1D32_ENST00000275159.6_Silent_p.V657V	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	657					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)										CAGAACCCTCTACTGGAGTAG	0.289																																					p.V657V		Atlas-SNP	.											.	C6orf170	146	.	0			c.A1971T						PASS	.						55	55	55					6																	121576521		1794	4047	5841	SO:0001819	synonymous_variant	221322	exon17			ACCCTCTACTGGA	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.1971A>T	chr6.hg19:g.121576521T>A		118.0	0.0	.		116.0	43.0	.	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Silent	SNP	ENST00000398212.2	hg19	CCDS43501.1																																																																																			.	.	.	none		0.289	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		A	121576521	T	A	121576521	2	1	121	1	0	0	0	0	0	0	0	1	2346	1509	53	5		5	C6orf170	6	121576521	Silent	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	74599478	121576521	49538546	18	7683											
HIVEP2	3097	hgsc.bcm.edu	37	chr6	143091819	143091819	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcccaagtatctgagaaaTgcttgtgtacatgacacttc	11	12	8	10	0	1	2	0	2	1	1	2	3	1	2	1	0	3	3	1	0	4	4			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr6:143091819T>C	ENST00000367604.1	-	4	4696	c.4057A>G	c.(4057-4059)Att>Gtt	p.I1353V	HIVEP2_ENST00000367603.2_Missense_Mutation_p.I1353V|HIVEP2_ENST00000012134.2_Missense_Mutation_p.I1353V			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	1353					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		ATCTGAGAAATGCTTGTGTAC	0.507																																					p.I1353V	Esophageal Squamous(107;843 1510 13293 16805 42198)	Atlas-SNP	.											.	HIVEP2	225	.	0			c.A4057G						PASS	.						81	80	80					6																	143091819		2007	4178	6185	SO:0001583	missense	3097	exon5			GAGAAATGCTTGT	M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"Zinc fingers, C2H2-type"	4921	protein-coding gene	gene with protein product	"c-myc intron binding protein 1"	143054	"human immunodeficiency virus type I enhancer-binding protein 2"			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.4057A>G	chr6.hg19:g.143091819T>C	ENSP00000356576:p.Ile1353Val	90.0	0.0	.		96.0	29.0	.	NM_006734	Q02646|Q5THT5|Q9NS05	Missense_Mutation	SNP	ENST00000367604.1	hg19	CCDS43510.1	.	.	.	.	.	.	.	.	.	.	T	9.819	1.185356	0.21870	.	.	ENSG00000010818	ENST00000367604;ENST00000367603;ENST00000012134	T;T;T	0.02121	4.44;4.44;4.44	6.08	6.08	0.98989	.	0.046170	0.85682	D	0.000000	T	0.01092	0.0036	L	0.38953	1.18	0.46927	D	0.999254	B	0.30236	0.274	B	0.19666	0.026	T	0.62296	-0.6884	10	0.23891	T	0.37	-16.7632	16.6438	0.85155	0.0:0.0:0.0:1.0	.	1353	P31629	ZEP2_HUMAN	V	1353	ENSP00000356576:I1353V;ENSP00000356575:I1353V;ENSP00000012134:I1353V	ENSP00000012134:I1353V	I	-	1	0	HIVEP2	143133512	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.593000	0.61034	2.333000	0.79357	0.533000	0.62120	ATT	.	.	.	none		0.507	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1			C	143091819	T	C	143091819	3	2	121	1	0	0	0	0	1	0	0	0	7194	1464	51	3	3307	3	HIVEP2	6	143091819	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	21515298	143091819	28023248	19	7684											
CADPS2	93664	hgsc.bcm.edu	37	chr7	122269335	122269335	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgccaattgcagccggccAtcaagttcccttctgatctg	7	12	8	14	1	4	1	1	1	3	0	5	1	5	1	4	1	3	2	4	1	2	3			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr7:122269335A>G	ENST00000449022.2	-	4	853	c.834T>C	c.(832-834)gaT>gaC	p.D278D	CADPS2_ENST00000412584.2_Silent_p.D278D|CADPS2_ENST00000313070.7_Silent_p.D278D|CADPS2_ENST00000334010.7_Silent_p.D278D	NM_017954.10	NP_060424.9	Q86UW7	CAPS2_HUMAN	Ca++-dependent secretion activator 2	278					cellular response to starvation (GO:0009267)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasmic membrane-bounded vesicle (GO:0016023)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(2)	43						GCAGCCGGCCATCAAGTTCCC	0.358																																					p.D278D		Atlas-SNP	.											.	CADPS2	116	.	0			c.T834C						PASS	.						67	64	65					7																	122269335		1866	4095	5961	SO:0001819	synonymous_variant	93664	exon4			CCGGCCATCAAGT		CCDS47691.1, CCDS55158.1	7q31.32	2013-01-10	2008-08-28		ENSG00000081803	ENSG00000081803		"Pleckstrin homology (PH) domain containing"	16018	protein-coding gene	gene with protein product		609978	"Ca++-dependent activator protein for secretion 2"				Standard	NM_017954		Approved		uc010lkq.3	Q86UW7	OTTHUMG00000157093	ENST00000449022.2:c.834T>C	chr7.hg19:g.122269335A>G		35.0	0.0	.		33.0	6.0	.	NM_001167940	A4D0X3|B7ZM56|Q658Q2|Q7Z5T7|Q8IZW9|Q8N7M4|Q9H6P4|Q9HCI1|Q9NWK8	Silent	SNP	ENST00000449022.2	hg19	CCDS55158.1																																																																																			.	.	.	none		0.358	CADPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347414.2	NM_017954		G	122269335	A	G	122269335	2	3	121	1	0	0	0	0	0	0	0	1	2573	214	8	3		3	CADPS2	7	122269335	Silent	SNP	A	TCGA-BQ-5886-01A-11D-1589-08		122269335	36869328	20	7685											
NUP205	23165	hgsc.bcm.edu	37	chr7	135276257	135276257	+	Missense_Mutation	SNP	T	T	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	ttgcctccaactatttatatTccttatttgaagatgctcca	10	17	4	10	0	0	2	0	1	0	1	3	2	3	2	4	0	3	1	4	0	6	8			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr7:135276257T>G	ENST00000285968.6	+	11	1559	c.1533T>G	c.(1531-1533)atT>atG	p.I511M	NUP205_ENST00000440390.2_Intron	NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	511					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						CTATTTATATTCCTTATTTGA	0.403																																					p.I511M		Atlas-SNP	.											.	NUP205	198	.	0			c.T1533G						PASS	.						122	115	117					7																	135276257		2203	4300	6503	SO:0001583	missense	23165	exon11			TTATATTCCTTAT	D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"chromosome 7 open reading frame 14"	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.1533T>G	chr7.hg19:g.135276257T>G	ENSP00000285968:p.Ile511Met	150.0	0.0	.		130.0	46.0	.	NM_015135	A6H8X3|Q86YC1	Missense_Mutation	SNP	ENST00000285968.6	hg19	CCDS34759.1	.	.	.	.	.	.	.	.	.	.	T	19.33	3.806891	0.70797	.	.	ENSG00000155561	ENST00000285968	T	0.32023	1.47	5.96	3.3	0.37823	.	0.043164	0.85682	D	0.000000	T	0.32615	0.0835	L	0.55481	1.735	0.80722	D	1	P	0.51653	0.947	P	0.50231	0.635	T	0.06427	-1.0827	10	0.46703	T	0.11	-10.0959	4.1716	0.10332	0.1437:0.2942:0.0:0.5621	.	511	Q92621	NU205_HUMAN	M	511	ENSP00000285968:I511M	ENSP00000285968:I511M	I	+	3	3	NUP205	134926797	0.999000	0.42202	1.000000	0.80357	0.999000	0.98932	0.569000	0.23638	0.394000	0.25230	0.533000	0.62120	ATT	.	.	.	none		0.403	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1			G	135276257	T	G	135276257	3	3	121	1	0	0	0	0	1	0	0	0	10766	1771	62	5	1575	5	NUP205	7	135276257	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	13006922	135276257	23862406	21	7686											
RGS20	8601	hgsc.bcm.edu	37	chr8	54764571	54764572	+	Frame_Shift_Del	DEL	AT	AT	-																															ctcagagatataatacagacAttcaccaaatcacagaaaat																										TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr8:54764571_54764572delAT	ENST00000297313.3	+	1	204_205	c.112_113delAT	c.(112-114)attfs	p.I38fs	RGS20_ENST00000344277.6_Frame_Shift_Del_p.I38fs	NM_170587.2	NP_733466.1	O76081	RGS20_HUMAN	regulator of G-protein signaling 20	38					positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(7;1.37e-06)|Epithelial(17;0.000126)|all cancers(17;0.0009)			TAATACAGACATTCACCAAATC	0.455																																					p.37_38del		Atlas-INDEL	.											.	RGS20	51	.	0			c.111_112del						PASS	.																																			SO:0001589	frameshift_variant	8601	exon1			.	AF074979	CCDS6155.1, CCDS6156.1, CCDS69482.1	8q11.23	2008-07-25	2007-08-14		ENSG00000147509	ENSG00000147509		"Regulators of G-protein signaling"	14600	protein-coding gene	gene with protein product		607193	"regulator of G-protein signalling 20"			9748279, 9748280	Standard	NM_003702		Approved	RGSZ1, ZGAP1	uc003xrp.3	O76081	OTTHUMG00000164750	ENST00000297313.3:c.112_113delAT	chr8.hg19:g.54764571_54764572delAT	ENSP00000297313:p.Ile38fs	126.0	0.0	0		119.0	38.0	0.319328	NM_170587	Q96BG9	Frame_Shift_Del	DEL	ENST00000297313.3	hg19	CCDS6155.1																																																																																			.	.	.	none		0.455	RGS20-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000380058.1			-	54764572	AT	-	54764571	7	5	121	1	0	1	0	1	0	0	0	0	13316	217	8	0	114	0	RGS20	8	54764571	Frame_Shift_Del	DEL	AT	TCGA-BQ-5886-01A-11D-1589-08		54764571	91599451	22	7687											
SMC2	10592	hgsc.bcm.edu	37	chr9	106862707	106862707	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tactccaaccattcaaaaatTaaaagaggtatattctgtat	17	13	4	7	0	2	1	1	0	1	1	3	1	3	1	2	1	2	2	2	1	9	7			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr9:106862707T>C	ENST00000286398.7	+	7	917	c.629T>C	c.(628-630)tTa>tCa	p.L210S	SMC2_ENST00000374793.3_Missense_Mutation_p.L210S|SMC2_ENST00000374787.3_Missense_Mutation_p.L210S|SMC2_ENST00000303219.8_Missense_Mutation_p.L210S	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	210					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						ATTCAAAAATTAAAAGAGGTA	0.274																																					p.L210S		Atlas-SNP	.											.	SMC2	127	.	0			c.T629C						PASS	.						37	45	42					9																	106862707		2179	4270	6449	SO:0001583	missense	10592	exon7			AAAAATTAAAAGA	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.629T>C	chr9.hg19:g.106862707T>C	ENSP00000286398:p.Leu210Ser	142.0	0.0	.		118.0	35.0	.	NM_006444	Q6IEE0|Q9P1P2	Missense_Mutation	SNP	ENST00000286398.7	hg19	CCDS35086.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.465044	0.84425	.	.	ENSG00000136824	ENST00000286398;ENST00000440179;ENST00000374793;ENST00000303219;ENST00000536893;ENST00000374787	T;T;T;T;T	0.11385	2.78;2.78;2.78;2.78;2.78	5.57	5.57	0.84162	RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	T	0.44095	0.1277	M	0.93898	3.47	0.52501	D	0.999959	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.57940	-0.7724	10	0.87932	D	0	-5.7921	14.5587	0.68120	0.0:0.0:0.0:1.0	.	210;210;210	A8K984;O95347;Q2KQ72	.;SMC2_HUMAN;.	S	210;65;210;210;210;210	ENSP00000286398:L210S;ENSP00000414999:L65S;ENSP00000363925:L210S;ENSP00000306152:L210S;ENSP00000363919:L210S	ENSP00000286398:L210S	L	+	2	0	SMC2	105902528	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.677000	0.84024	2.109000	0.64355	0.528000	0.53228	TTA	.	.	.	none		0.274	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1			C	106862707	T	C	106862707	3	2	121	1	0	0	0	0	1	0	0	0	14796	1764	61	3	651	3	SMC2	9	106862707	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08		106862707	34350724	23	7688											
PTGR1	22949	hgsc.bcm.edu	37	chr9	114359672	114359672	+	Missense_Mutation	SNP	T	T	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	aggatagccaacaaagtgctTcttcagggtccatgtcttag	11	11	10	9	0	3	0	1	0	2	0	4	1	4	1	2	2	3	1	2	2	4	4			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr9:114359672T>G	ENST00000407693.2	-	2	293	c.31A>C	c.(31-33)Aag>Cag	p.K11Q	PTGR1_ENST00000538962.1_Missense_Mutation_p.K11Q|PTGR1_ENST00000238248.3_5'UTR|PTGR1_ENST00000309195.5_Missense_Mutation_p.K11Q	NM_001146108.1	NP_001139580.1	Q14914	PTGR1_HUMAN	prostaglandin reductase 1	11					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|leukotriene metabolic process (GO:0006691)|lipoxin metabolic process (GO:2001300)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	13-prostaglandin reductase activity (GO:0036132)|15-oxoprostaglandin 13-oxidase activity (GO:0047522)|2-alkenal reductase [NAD(P)] activity (GO:0032440)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)	11						ACAAAGTGCTTCTTCAGGGTC	0.403																																					p.K11Q	Ovarian(200;132 2151 7551 19220 46064)	Atlas-SNP	.											.	PTGR1	23	.	0			c.A31C						PASS	.						109	95	100					9																	114359672		2203	4300	6503	SO:0001583	missense	22949	exon2			AGTGCTTCTTCAG	D49387	CCDS6779.1, CCDS55331.1	9q32	2008-06-04	2008-06-02	2008-06-02	ENSG00000106853	ENSG00000106853	1.3.1.74, 1.3.1.48		18429	protein-coding gene	gene with protein product	"zinc binding alcohol dehydrogenase domain containing 3"	601274	"leukotriene B4 12-hydroxydehydrogenase"	LTB4DH		8576264, 17449869	Standard	NM_001146109		Approved	ZADH3	uc004bfh.2	Q14914	OTTHUMG00000020493	ENST00000407693.2:c.31A>C	chr9.hg19:g.114359672T>G	ENSP00000385763:p.Lys11Gln	46.0	0.0	.		35.0	15.0	.	NM_001146108	A8K0N2|B4DPK3|F5GY50|Q8IYQ0|Q9H1X6	Missense_Mutation	SNP	ENST00000407693.2	hg19	CCDS6779.1	.	.	.	.	.	.	.	.	.	.	T	10.91	1.483746	0.26598	.	.	ENSG00000106853	ENST00000538962;ENST00000309195;ENST00000407693;ENST00000333580;ENST00000422125;ENST00000374313;ENST00000374308	T;T;T;T	0.51817	0.69;0.69;0.69;0.69	4.62	4.62	0.57501	GroES-like (1);	0.092047	0.85682	D	0.000000	T	0.43656	0.1257	M	0.62154	1.92	0.80722	D	1	B;B;B	0.33171	0.4;0.278;0.077	B;B;B	0.29440	0.102;0.061;0.015	T	0.46665	-0.9175	10	0.48119	T	0.1	2.0981	12.2191	0.54423	0.0:0.0:0.0:1.0	.	11;11;11	F5GY50;B4DPK3;Q14914	.;.;PTGR1_HUMAN	Q	11	ENSP00000440281:K11Q;ENSP00000311572:K11Q;ENSP00000385763:K11Q;ENSP00000395965:K11Q	ENSP00000311572:K11Q	K	-	1	0	PTGR1	113399493	1.000000	0.71417	1.000000	0.80357	0.589000	0.36550	2.756000	0.47549	2.020000	0.59435	0.374000	0.22700	AAG	.	.	.	none		0.403	PTGR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053647.2			G	114359672	T	G	114359672	3	3	121	1	0	0	0	0	1	0	0	0	12764	1792	62	5	1025	5	PTGR1	9	114359672	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	7496965	114359672	26853759	24	7689											
C10orf62	414157	hgsc.bcm.edu	37	chr10	99349694	99349694	+	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	agaggagaagaaaggaaaccTctgagtgtccatcagacaag	17	5	12	7	0	2	5	1	1	1	4	3	7	3	6	2	2	1	0	2	2	4	0			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr10:99349694T>A	ENST00000370640.3	+	1	245	c.40T>A	c.(40-42)Tct>Act	p.S14T	PI4K2A_ENST00000555577.1_Intron|HOGA1_ENST00000370647.4_Intron|HOGA1_ENST00000370646.4_Intron|PI4K2A_ENST00000370649.3_Intron	NM_001009997.2	NP_001009997.2	Q5T681	CJ062_HUMAN	chromosome 10 open reading frame 62	14										endometrium(2)|kidney(1)|lung(1)	4		Colorectal(252;0.162)		Epithelial(162;9.58e-11)|all cancers(201;8.62e-09)		AAAGGAAACCTCTGAGTGTCC	0.502																																					p.S14T		Atlas-SNP	.											.	C10orf62	14	.	0			c.T40A						PASS	.						100	100	100					10																	99349694		2203	4300	6503	SO:0001583	missense	414157	exon1			GAAACCTCTGAGT		CCDS31261.1	10q24.2	2012-05-31			ENSG00000203942	ENSG00000203942			23294	protein-coding gene	gene with protein product							Standard	NM_001009997		Approved	bA548K23.1	uc001koa.3	Q5T681	OTTHUMG00000018858	ENST00000370640.3:c.40T>A	chr10.hg19:g.99349694T>A	ENSP00000359674:p.Ser14Thr	117.0	0.0	.		97.0	7.0	.	NM_001009997	Q49A70|Q8N3Y6	Missense_Mutation	SNP	ENST00000370640.3	hg19	CCDS31261.1	.	.	.	.	.	.	.	.	.	.	T	4.766	0.142421	0.09083	.	.	ENSG00000203942	ENST00000370640	T	0.42513	0.97	5.27	-10.5	0.00291	.	3.688920	0.00929	N	0.002686	T	0.15522	0.0374	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.18777	-1.0326	10	0.14656	T	0.56	.	1.8333	0.03134	0.3493:0.094:0.1283:0.4284	.	14	Q5T681	CJ062_HUMAN	T	14	ENSP00000359674:S14T	ENSP00000359674:S14T	S	+	1	0	C10orf62	99339684	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.585000	0.00903	-2.847000	0.00332	-1.294000	0.01345	TCT	.	.	.	none		0.502	C10orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049723.1	NM_001009997		A	99349694	T	A	99349694	3	1	121	1	0	0	0	0	1	0	0	0	1613	1551	54	5	42	5	C10orf62	10	99349694	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08		99349694	36185053	25	7690											
NPS	594857	hgsc.bcm.edu	37	chr10	129350829	129350829	+	Frame_Shift_Del	DEL	T	T	-																															agccaattttggagaagatgTttgtgaaaaggtcctttcgc																										TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr10:129350829delT	ENST00000398023.1	+	3	216	c.196delT	c.(196-198)tttfs	p.F66fs		NM_001030013.1	NP_001025184.1	P0C0P6	NPS_HUMAN	neuropeptide S	66					neuropeptide signaling pathway (GO:0007218)|positive regulation of action potential (GO:0045760)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|visual learning (GO:0008542)	extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|lung(4)	5						GGAGAAGATGTTTGTGAAAAG	0.413																																					p.M65fs		Atlas-INDEL	.											.	NPS	14	.	0			c.195delG						PASS	.						204	199	201					10																	129350829		1843	4101	5944	SO:0001589	frameshift_variant	594857	exon3			.	BC148465	CCDS41577.1	10q26.2	2013-02-26			ENSG00000214285	ENSG00000214285		"Endogenous ligands"	33940	protein-coding gene	gene with protein product	"prepro-neuropeptide S"	609513				18181564, 15312648	Standard	NM_001030013		Approved		uc001ljx.1	P0C0P6		ENST00000398023.1:c.196delT	chr10.hg19:g.129350829delT	ENSP00000381105:p.Phe66fs	430.0	0.0	0		357.0	50.0	0.140056	NM_001030013		Frame_Shift_Del	DEL	ENST00000398023.1	hg19	CCDS41577.1																																																																																			.	.	.	none		0.413	NPS-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001030013		-	129350829	T	-	129350829	7	5	121	1	0	1	0	1	0	0	0	0	10606	1725	60	0	206	0	NPS	10	129350829	Frame_Shift_Del	DEL	T	TCGA-BQ-5886-01A-11D-1589-08	30001135	129350829	6183918	26	7691											
ST5	6764	hgsc.bcm.edu	37	chr11	8751785	8751785	+	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	cactgccttccctctctgggGgtgggcccgcctcccccgca	2	8	11	20	2	1	0	0	0	1	0	4	0	3	0	6	3	1	1	6	3	0	1			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr11:8751785G>A	ENST00000534127.1	-	6	1437	c.1052C>T	c.(1051-1053)cCc>cTc	p.P351L	ST5_ENST00000313726.6_Missense_Mutation_p.P351L|ST5_ENST00000357665.1_Missense_Mutation_p.P351L|ST5_ENST00000530438.1_Intron|ST5_ENST00000526757.1_Intron	NM_005418.3	NP_005409.3	P78524	ST5_HUMAN	suppression of tumorigenicity 5	351	Pro-rich.				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)		CCTCTCTGGGGGTGGGCCCGC	0.687																																					p.P351L		Atlas-SNP	.											.	ST5	85	.	0			c.C1052T						PASS	.						41	47	45					11																	8751785		2201	4296	6497	SO:0001583	missense	6764	exon6			TCTGGGGGTGGGC	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.1052C>T	chr11.hg19:g.8751785G>A	ENSP00000433528:p.Pro351Leu	125.0	0.0	.		109.0	25.0	.	NM_005418	B2R6X7|B3KXQ6|P78523|Q16492|Q7KYY2|Q7KZ12|Q8NE12|Q9BQQ6	Missense_Mutation	SNP	ENST00000534127.1	hg19	CCDS7791.1	.	.	.	.	.	.	.	.	.	.	G	14.28	2.487492	0.44249	.	.	ENSG00000166444	ENST00000534127;ENST00000313726;ENST00000357665	T;T;T	0.04809	3.55;3.55;3.55	6.17	5.27	0.74061	.	0.340768	0.28409	N	0.015455	T	0.06325	0.0163	L	0.41236	1.265	0.46798	D	0.999205	B	0.06786	0.001	B	0.06405	0.002	T	0.28808	-1.0032	10	0.33940	T	0.23	-18.7575	15.9068	0.79436	0.0643:0.0:0.9357:0.0	.	351	P78524	ST5_HUMAN	L	351	ENSP00000433528:P351L;ENSP00000319678:P351L;ENSP00000350294:P351L	ENSP00000319678:P351L	P	-	2	0	ST5	8708361	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	4.667000	0.61561	1.642000	0.50584	-0.123000	0.14984	CCC	.	.	.	none		0.687	ST5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386518.1	NM_005418		A	8751785	G	A	8751785	3	1	121	1	0	0	0	0	1	0	0	0	15232	1232	43	2	2433	2	ST5	11	8751785	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08		8751785	126254731	27	7692											
AHNAK	79026	hgsc.bcm.edu	37	chr11	62290316	62290316	+	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	caggcatcttgaatttgggaCctttcaactttccctctggg	7	14	9	11	0	3	1	1	1	2	0	4	2	4	2	2	3	1	1	2	3	2	4			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr11:62290316C>T	ENST00000378024.4	-	5	11847	c.11573G>A	c.(11572-11574)gGt>gAt	p.G3858D	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	3858					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)				GAATTTGGGACCTTTCAACTT	0.478																																					p.G3858D		Atlas-SNP	.											.	AHNAK	532	.	0			c.G11573A						PASS	.						196	202	200					11																	62290316		2202	4299	6501	SO:0001583	missense	79026	exon5			TTGGGACCTTTCA	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.11573G>A	chr11.hg19:g.62290316C>T	ENSP00000367263:p.Gly3858Asp	422.0	0.0	.		412.0	35.0	.	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	hg19	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	-	12.21	1.869769	0.33069	.	.	ENSG00000124942	ENST00000378024	T	0.03496	3.91	4.51	4.51	0.55191	.	0.000000	0.42053	D	0.000767	T	0.21227	0.0511	M	0.93594	3.435	0.46678	D	0.999153	D	0.65815	0.995	P	0.61201	0.885	T	0.41106	-0.9527	10	0.15499	T	0.54	.	17.021	0.86433	0.0:1.0:0.0:0.0	.	3858	Q09666	AHNK_HUMAN	D	3858	ENSP00000367263:G3858D	ENSP00000367263:G3858D	G	-	2	0	AHNAK	62046892	0.954000	0.32549	0.066000	0.19879	0.046000	0.14306	4.583000	0.60964	2.350000	0.79820	0.543000	0.68304	GGT	.	.	.	none		0.478	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		T	62290316	C	T	62290316	3	4	121	1	0	0	0	0	1	0	0	0	414	507	18	2	6219	2	AHNAK	11	62290316	Missense_Mutation	SNP	C	TCGA-BQ-5886-01A-11D-1589-08	53538531	62290316	72716200	28	7693											
TUT1	64852	hgsc.bcm.edu	37	chr11	62346405	62346405	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagaagcaggaggttgtgaaTctggaggggaagctggggtg	10	7	21	3	0	1	2	0	1	1	1	1	6	1	5	0	7	2	3	0	7	3	1			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr11:62346405T>C	ENST00000476907.1	-	5	1479	c.788A>G	c.(787-789)gAt>gGt	p.D263G	MIR3654_ENST00000496634.2_Missense_Mutation_p.D263G|TUT1_ENST00000308436.7_Missense_Mutation_p.D301G			Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6 snRNA-specific	263	Pro-rich.				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						AGGTTGTGAATCTGGAGGGGA	0.627																																					p.D301G		Atlas-SNP	.											.	TUT1	122	.	0			c.A902G						PASS	.						38	45	43					11																	62346405		2202	4299	6501	SO:0001583	missense	64852	exon5			TGTGAATCTGGAG	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.788A>G	chr11.hg19:g.62346405T>C	ENSP00000419607:p.Asp263Gly	76.0	0.0	.		70.0	19.0	.	NM_022830	A1A527|A8K995|Q2NL65|Q7L583|Q9H6H7	Missense_Mutation	SNP	ENST00000476907.1	hg19		.	.	.	.	.	.	.	.	.	.	T	10.15	1.271130	0.23221	.	.	ENSG00000149016	ENST00000308436;ENST00000476907;ENST00000278279	T;T	0.40476	1.03;1.05	4.91	2.58	0.30949	.	0.311232	0.25590	N	0.029624	T	0.29256	0.0728	L	0.36672	1.1	0.24619	N	0.993685	B	0.12013	0.005	B	0.12156	0.007	T	0.20940	-1.0260	10	0.54805	T	0.06	1.3697	5.9223	0.19088	0.0:0.2193:0.0:0.7807	.	301	F5H0R1	.	G	301;263;124	ENSP00000308000:D301G;ENSP00000419607:D263G	ENSP00000441670:D263G	D	-	2	0	TUT1	62102981	1.000000	0.71417	0.932000	0.37286	0.144000	0.21451	1.147000	0.31602	0.370000	0.24538	0.460000	0.39030	GAT	.	.	.	none		0.627	TUT1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000351319.2	NM_022830		C	62346405	T	C	62346405	3	2	121	1	0	0	0	0	1	0	0	0	16792	1435	50	3	1856	3	TUT1	11	62346405	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	56089	62346405	72660111	29	7694											
ARHGEF12	23365	hgsc.bcm.edu	37	chr11	120336044	120336044	+	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	atcaaatctcgtcagaaaaaGgattctcgatttcagacttt	14	13	6	8	2	5	2	3	0	2	2	7	4	5	3	0	1	0	0	0	1	3	3			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr11:120336044G>T	ENST00000397843.2	+	28	2878	c.2712G>T	c.(2710-2712)aaG>aaT	p.K904N	ARHGEF12_ENST00000532993.1_Missense_Mutation_p.K801N|ARHGEF12_ENST00000356641.3_Missense_Mutation_p.K885N	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	904	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				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)		GTCAGAAAAAGGATTCTCGAT	0.393			T	MLL	AML																																p.K904N		Atlas-SNP	.		Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	.	ARHGEF12	133	.	0			c.G2712T						PASS	.						94	89	91					11																	120336044		1863	4111	5974	SO:0001583	missense	23365	exon28			GAAAAAGGATTCT	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.2712G>T	chr11.hg19:g.120336044G>T	ENSP00000380942:p.Lys904Asn	118.0	0.0	.		101.0	30.0	.	NM_015313	O15086|Q6P526	Missense_Mutation	SNP	ENST00000397843.2	hg19	CCDS41727.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.000713	0.74818	.	.	ENSG00000196914	ENST00000397843;ENST00000356641;ENST00000532993	T;T;T	0.70282	-0.47;-0.47;-0.47	5.69	4.78	0.61160	Dbl homology (DH) domain (5);	0.000000	0.51477	D	0.000085	D	0.82577	0.5067	M	0.79123	2.44	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.998;0.999	D	0.83981	0.0332	10	0.66056	D	0.02	-17.5309	10.7839	0.46395	0.1444:0.0:0.8556:0.0	.	801;885;904	B4DGW2;Q9NZN5-2;Q9NZN5	.;.;ARHGC_HUMAN	N	904;885;801	ENSP00000380942:K904N;ENSP00000349056:K885N;ENSP00000432984:K801N	ENSP00000349056:K885N	K	+	3	2	ARHGEF12	119841254	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.679000	0.46909	1.424000	0.47217	0.650000	0.86243	AAG	.	.	.	none		0.393	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313		T	120336044	G	T	120336044	3	4	121	1	0	0	0	0	1	0	0	0	897	991	35	4	2822	4	ARHGEF12	11	120336044	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	57989639	120336044	14670472	30	7695											
MCRS1	10445	hgsc.bcm.edu	37	chr12	49956786	49956786	+	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	cagctcctggggcgttacctGtctggtcctccagcaggtaa	6	10	12	13	1	1	0	0	0	1	0	4	0	4	0	4	4	3	4	4	4	2	2			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr12:49956786G>C	ENST00000550165.1	-	9	1069	c.803C>G	c.(802-804)aCa>aGa	p.T268R	MCRS1_ENST00000547182.1_5'UTR|MCRS1_ENST00000546244.1_Missense_Mutation_p.T77R|MCRS1_ENST00000357123.4_Missense_Mutation_p.T281R|MCRS1_ENST00000343810.4_Missense_Mutation_p.T268R			Q96EZ8	MCRS1_HUMAN	microspherule protein 1	268					cellular protein modification process (GO:0006464)|chromatin organization (GO:0006325)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|Ino80 complex (GO:0031011)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(11)	23						GGCGTTACCTGTCTGGTCCTC	0.587																																					p.T281R		Atlas-SNP	.											MCRS1,NS,carcinoma,0,1	MCRS1	40	.	0			c.C842G						PASS	.						45	36	39					12																	49956786		2203	4298	6501	SO:0001583	missense	10445	exon7			TTACCTGTCTGGT	BC011794	CCDS8787.1, CCDS31795.1, CCDS61118.1	12q13.12	2011-07-06				ENSG00000187778		"INO80 complex subunits"	6960	protein-coding gene	gene with protein product	"INO80 complex subunit Q"	609504				9765390, 9654073	Standard	NM_006337		Approved	ICP22BP, MSP58, P78, MCRS2, INO80Q	uc001rui.1	Q96EZ8		ENST00000550165.1:c.803C>G	chr12.hg19:g.49956786G>C	ENSP00000448056:p.Thr268Arg	19.0	0.0	.		28.0	2.0	.	NM_001012300	O14742|O75497|Q6VN53|Q7Z372	Missense_Mutation	SNP	ENST00000550165.1	hg19	CCDS8787.1	.	.	.	.	.	.	.	.	.	.	G	19.55	3.848843	0.71603	.	.	ENSG00000187778	ENST00000546244;ENST00000343810;ENST00000550165;ENST00000357123;ENST00000553173	.	.	.	5.64	5.64	0.86602	.	0.086145	0.85682	D	0.000000	T	0.66723	0.2818	L	0.47716	1.5	0.53005	D	0.999967	P;P;P	0.51351	0.944;0.642;0.887	P;B;P	0.56042	0.79;0.305;0.668	T	0.68372	-0.5426	9	0.72032	D	0.01	-8.7582	17.2003	0.86904	0.0:0.0:1.0:0.0	.	255;268;281	F8W126;Q96EZ8;Q96EZ8-2	.;MCRS1_HUMAN;.	R	77;268;268;281;255	.	ENSP00000345358:T268R	T	-	2	0	MCRS1	48243053	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.847000	0.69451	2.662000	0.90505	0.555000	0.69702	ACA	.	.	.	none		0.587	MCRS1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405102.1	NM_006337		C	49956786	G	C	49956786	3	2	121	1	0	0	0	0	1	0	0	0	9406	1377	48	4	617	4	MCRS1	12	49956786	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08		49956786	83895109	31	7696											
MON2	23041	hgsc.bcm.edu	37	chr12	62972277	62972277	+	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	ttcaaagaaatgaaaatattGatgtcgaggtaaggaggcta	17	10	11	3	1	1	3	1	2	0	1	2	5	1	4	0	3	0	2	0	3	7	5			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr12:62972277G>A	ENST00000393632.2	+	31	4958	c.4567G>A	c.(4567-4569)Gat>Aat	p.D1523N	MON2_ENST00000552738.1_Missense_Mutation_p.D1494N|MON2_ENST00000393630.3_Missense_Mutation_p.D1524N|MON2_ENST00000546600.1_Missense_Mutation_p.D1523N|MON2_ENST00000393629.2_Missense_Mutation_p.D1517N|MON2_ENST00000280379.6_Missense_Mutation_p.D1524N	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	1523					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)		TGAAAATATTGATGTCGAGGT	0.284																																					p.D1523N		Atlas-SNP	.											.	MON2	160	.	0			c.G4567A						PASS	.						30	30	30					12																	62972277		2200	4284	6484	SO:0001583	missense	23041	exon31			AATATTGATGTCG		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.4567G>A	chr12.hg19:g.62972277G>A	ENSP00000377252:p.Asp1523Asn	46.0	0.0	.		47.0	9.0	.	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	ENST00000393632.2	hg19	CCDS31849.1	.	.	.	.	.	.	.	.	.	.	G	32	5.188128	0.94923	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000552738;ENST00000393629	T;T;T;T;T;T	0.61627	0.09;0.09;0.09;0.09;0.09;0.09	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.76506	0.3997	M	0.69823	2.125	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0	D;D;D;D;D	0.97110	0.993;0.997;0.982;0.992;1.0	T	0.74993	-0.3474	9	.	.	.	-19.6244	19.7297	0.96177	0.0:0.0:1.0:0.0	.	1517;1494;1523;392;1523	B9EGP5;F8VWA6;F8W1Z6;Q7Z3U7-3;Q7Z3U7-4	.;.;.;.;.	N	1523;1524;1524;1523;1494;1517	ENSP00000377252:D1523N;ENSP00000377250:D1524N;ENSP00000280379:D1524N;ENSP00000447407:D1523N;ENSP00000449215:D1494N;ENSP00000377249:D1517N	.	D	+	1	0	MON2	61258544	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	9.471000	0.97696	2.658000	0.90341	0.650000	0.86243	GAT	.	.	.	none		0.284	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		A	62972277	G	A	62972277	3	1	121	1	0	0	0	0	1	0	0	0	9707	1290	45	2	4689	2	MON2	12	62972277	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	13015491	62972277	70879618	32	7697											
NAP1L1	4673	hgsc.bcm.edu	37	chr12	76444427	76444427	+	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	agcaaggatagcttcagcatCatcatcctatttttaaagga	14	12	7	8	0	3	0	3	0	0	0	4	2	4	2	1	2	3	3	1	2	5	6			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr12:76444427C>T	ENST00000261182.8	-	12	1429	c.943G>A	c.(943-945)Gat>Aat	p.D315N	NAP1L1_ENST00000544816.1_Missense_Mutation_p.D132N|NAP1L1_ENST00000393263.3_Missense_Mutation_p.D315N|NAP1L1_ENST00000547993.1_Missense_Mutation_p.D132N|NAP1L1_ENST00000542344.1_Missense_Mutation_p.D273N|NAP1L1_ENST00000549596.1_Missense_Mutation_p.D315N|NAP1L1_ENST00000535020.2_Missense_Mutation_p.D315N|NAP1L1_ENST00000548044.1_Missense_Mutation_p.D274N|NAP1L1_ENST00000431879.3_Missense_Mutation_p.D247N|NAP1L1_ENST00000552342.1_Missense_Mutation_p.D326N|NAP1L1_ENST00000547773.1_Missense_Mutation_p.D252N	NM_004537.4|NM_139207.2	NP_004528.1|NP_631946.1	P55209	NP1L1_HUMAN	nucleosome assembly protein 1-like 1	315					DNA replication (GO:0006260)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	9		Colorectal(145;0.09)				GCTTCAGCATCATCATCCTAT	0.373																																					p.D315N		Atlas-SNP	.											.	NAP1L1	33	.	0			c.G943A						PASS	.						63	60	61					12																	76444427		2203	4300	6503	SO:0001583	missense	4673	exon12			CAGCATCATCATC		CCDS9013.1	12q21.1	2010-03-17			ENSG00000187109	ENSG00000187109			7637	protein-coding gene	gene with protein product		164060				8297347	Standard	NM_004537		Approved	NRP, NAP1, NAP1L, MGC8688, MGC23410	uc001sxx.2	P55209		ENST00000261182.8:c.943G>A	chr12.hg19:g.76444427C>T	ENSP00000261182:p.Asp315Asn	85.0	0.0	.		82.0	27.0	.	NM_004537	B3KNT8	Missense_Mutation	SNP	ENST00000261182.8	hg19	CCDS9013.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.682803	0.88542	.	.	ENSG00000187109	ENST00000261182;ENST00000552056;ENST00000393263;ENST00000431879;ENST00000547773;ENST00000544816;ENST00000542344;ENST00000535020;ENST00000549596;ENST00000547993;ENST00000552342;ENST00000548044	T;T;T;T;T;T;T;T;T;T;T;T	0.27720	1.65;1.65;1.65;1.65;1.65;1.65;1.65;1.65;1.65;1.65;1.65;1.65	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.45034	0.1322	M	0.68952	2.095	0.80722	D	1	B;B;B;B;B;B;B	0.34226	0.389;0.18;0.389;0.443;0.18;0.162;0.202	B;B;B;B;B;B;B	0.42163	0.274;0.378;0.274;0.196;0.285;0.135;0.196	T	0.40701	-0.9549	10	0.66056	D	0.02	.	19.7712	0.96366	0.0:1.0:0.0:0.0	.	315;273;326;315;247;252;315	F5H4R6;B7Z9C2;F8W0J6;B3KNT8;B3KV44;F8W543;P55209	.;.;.;.;.;.;NP1L1_HUMAN	N	315;309;315;247;252;132;273;315;315;132;326;274	ENSP00000261182:D315N;ENSP00000450236:D309N;ENSP00000376947:D315N;ENSP00000409795:D247N;ENSP00000448167:D252N;ENSP00000437507:D132N;ENSP00000444759:D273N;ENSP00000445008:D315N;ENSP00000447793:D315N;ENSP00000448007:D132N;ENSP00000447196:D326N;ENSP00000449649:D274N	ENSP00000261182:D315N	D	-	1	0	NAP1L1	74730694	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.818000	0.86416	2.677000	0.91161	0.585000	0.79938	GAT	.	.	.	none		0.373	NAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405850.3	NM_139207		T	76444427	C	T	76444427	3	4	121	1	0	0	0	0	1	0	0	0	10163	826	29	2	248	2	NAP1L1	12	76444427	Missense_Mutation	SNP	C	TCGA-BQ-5886-01A-11D-1589-08	13472150	76444427	57407468	33	7698											
HMGB1	3146	hgsc.bcm.edu	37	chr13	31036826	31036826	+	Missense_Mutation	SNP	G	G	A																															tgatttttgggcgatactcaGagcagaagaggaagaaggcc																										TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr13:31036826G>A	ENST00000405805.1	-	4	1260	c.320C>T	c.(319-321)tCt>tTt	p.S107F	HMGB1_ENST00000399494.1_Missense_Mutation_p.S107F|HMGB1_ENST00000341423.5_Missense_Mutation_p.S107F|HMGB1_ENST00000468384.1_5'Flank|HMGB1_ENST00000399489.1_Missense_Mutation_p.S107F|HMGB1_ENST00000326004.4_Missense_Mutation_p.S107F|HMGB1_ENST00000339872.4_Missense_Mutation_p.S107F			P09429	HMGB1_HUMAN	high mobility group box 1	107					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)		GCGATACTCAGAGCAGAAGAG	0.393																																					p.S107F		Atlas-SNP	.											.	HMGB1	21	.	0			c.C320T						PASS	.						45	46	46					13																	31036826		2187	4290	6477	SO:0001583	missense	3146	exon4			TACTCAGAGCAGA	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.320C>T	chr13.hg19:g.31036826G>A	ENSP00000384678:p.Ser107Phe	108.0	0.0	.		99.0	23.0	.	NM_002128	A5D8W9|Q14321|Q5T7C3|Q6IBE1	Missense_Mutation	SNP	ENST00000405805.1	hg19	CCDS9335.1	.	.	.	.	.	.	.	.	.	.	G	19.66	3.868452	0.72065	.	.	ENSG00000189403	ENST00000405805;ENST00000339872;ENST00000341423;ENST00000399489;ENST00000399494;ENST00000426225;ENST00000326004	D;D;D;D;D;D	0.98150	-4.75;-4.75;-4.75;-4.75;-4.75;-4.75	5.5	3.76	0.43208	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.000000	0.53938	D	0.000050	D	0.97977	0.9334	M	0.85373	2.75	0.80722	D	1	B;P;B;B	0.37176	0.099;0.586;0.314;0.204	B;P;P;B	0.49047	0.2;0.599;0.498;0.264	D	0.97456	1.0031	10	0.87932	D	0	.	10.4698	0.44629	0.0694:0.0:0.7963:0.1343	.	107;68;107;107	B7Z965;B3KQ05;P09429;Q5T7C4	.;.;HMGB1_HUMAN;.	F	107	ENSP00000384678:S107F;ENSP00000343040:S107F;ENSP00000345347:S107F;ENSP00000382412:S107F;ENSP00000382417:S107F;ENSP00000369904:S107F	ENSP00000369904:S107F	S	-	2	0	HMGB1	29934826	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	7.536000	0.82023	0.683000	0.31428	-0.148000	0.13756	TCT	.	.	.	none		0.393	HMGB1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303998.2	NM_002128		A	31036826	G	A	31036826	3	1	121	1	0	0	0	0	1	0	0	0	7232	942	33	2	335	2	HMGB1	13	31036826	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08		31036826	84133052	34	7699	84	2									
HMGB1	3146	hgsc.bcm.edu	37	chr13	31036836	31036836	+	Frame_Shift_Del	DEL	G	G	-																															gcgatactcagagcagaagaGgaagaaggccgaactaaaaa																										TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr13:31036836delG	ENST00000405805.1	-	4	1250	c.310delC	c.(310-312)ctcfs	p.L104fs	HMGB1_ENST00000399494.1_Frame_Shift_Del_p.L104fs|HMGB1_ENST00000341423.5_Frame_Shift_Del_p.L104fs|HMGB1_ENST00000468384.1_5'Flank|HMGB1_ENST00000399489.1_Frame_Shift_Del_p.L104fs|HMGB1_ENST00000326004.4_Frame_Shift_Del_p.L104fs|HMGB1_ENST00000339872.4_Frame_Shift_Del_p.L104fs			P09429	HMGB1_HUMAN	high mobility group box 1	104					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)		GAGCAGAAGAGGAAGAAGGCC	0.378																																					p.L104fs		Atlas-INDEL	.											.	HMGB1	21	.	0			c.311delT						PASS	.						42	43	43					13																	31036836		2183	4287	6470	SO:0001589	frameshift_variant	3146	exon4			.	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.310delC	chr13.hg19:g.31036836delG	ENSP00000384678:p.Leu104fs	102.0	0.0	0		82.0	19.0	0.231707	NM_002128	A5D8W9|Q14321|Q5T7C3|Q6IBE1	Frame_Shift_Del	DEL	ENST00000405805.1	hg19	CCDS9335.1																																																																																			.	.	.	none		0.378	HMGB1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303998.2	NM_002128		-	31036836	G	-	31036836	7	5	121	1	0	1	0	1	0	0	0	0	7232	1000	35	0	345	0	HMGB1	13	31036836	Frame_Shift_Del	DEL	G	TCGA-BQ-5886-01A-11D-1589-08	10	31036836	84133042	35	7700	84	2									
ELF1	1997	hgsc.bcm.edu	37	chr13	41515309	41515309	+	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	tggctcctccttttacccctGgacttgaagatactctcgac	7	13	7	14	1	1	2	0	1	1	1	4	4	3	3	4	2	2	1	4	2	3	4			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr13:41515309G>A	ENST00000239882.3	-	8	1318	c.1004C>T	c.(1003-1005)cCa>cTa	p.P335L	ELF1_ENST00000498824.1_5'UTR|ELF1_ENST00000442101.1_Missense_Mutation_p.P311L	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)	335					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)		TTTTACCCCTGGACTTGAAGA	0.453																																					p.P335L		Atlas-SNP	.											.	ELF1	65	.	0			c.C1004T						PASS	.						131	134	133					13																	41515309		2203	4300	6503	SO:0001583	missense	1997	exon8			ACCCCTGGACTTG	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.1004C>T	chr13.hg19:g.41515309G>A	ENSP00000239882:p.Pro335Leu	235.0	0.0	.		211.0	46.0	.	NM_172373	B4E2I5|E9PDQ9|Q8N6F6|Q9UDE1	Missense_Mutation	SNP	ENST00000239882.3	hg19	CCDS9374.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.460748	0.43736	.	.	ENSG00000120690	ENST00000442101;ENST00000379498;ENST00000239882	T;T	0.55413	0.52;0.52	5.47	5.47	0.80525	.	0.503265	0.21383	N	0.075437	T	0.43612	0.1255	L	0.29908	0.895	0.38663	D	0.952122	B;B	0.25235	0.059;0.121	B;B	0.18263	0.015;0.021	T	0.41752	-0.9491	10	0.54805	T	0.06	.	16.6683	0.85259	0.0:0.1294:0.8706:0.0	.	311;335	E9PDQ9;P32519	.;ELF1_HUMAN	L	311;77;335	ENSP00000405580:P311L;ENSP00000239882:P335L	ENSP00000239882:P335L	P	-	2	0	ELF1	40413309	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	4.056000	0.57448	2.729000	0.93468	0.655000	0.94253	CCA	.	.	.	none		0.453	ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	NM_172373		A	41515309	G	A	41515309	3	1	121	1	0	0	0	0	1	0	0	0	5055	1348	47	2	863	2	ELF1	13	41515309	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	10478473	41515309	73654569	36	7701											
GPHN	10243	hgsc.bcm.edu	37	chr14	67389425	67389425	+	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	cagctctacctcatgccattGaccttttacgtgatgccatt	8	14	6	13	1	2	2	1	2	1	0	2	2	2	2	4	0	5	1	4	0	2	5			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr14:67389425G>C	ENST00000315266.5	+	7	1620	c.499G>C	c.(499-501)Gac>Cac	p.D167H	GPHN_ENST00000544752.2_3'UTR|GPHN_ENST00000459628.1_Missense_Mutation_p.D149H|GPHN_ENST00000543237.1_Missense_Mutation_p.D180H|GPHN_ENST00000478722.1_Missense_Mutation_p.D167H|GPHN_ENST00000305960.9_Missense_Mutation_p.D136H	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	167	Interaction with GABARAP. {ECO:0000250}.				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)		TCATGCCATTGACCTTTTACG	0.403			T	MLL	AL																																p.D167H		Atlas-SNP	.		Dom	yes		14	14q24	10243	gephyrin (GPH)		L	.	GPHN	79	.	0			c.G499C						PASS	.						187	164	172					14																	67389425		2203	4300	6503	SO:0001583	missense	10243	exon7			GCCATTGACCTTT	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.499G>C	chr14.hg19:g.67389425G>C	ENSP00000312771:p.Asp167His	255.0	0.0	.		221.0	63.0	.	NM_001024218	Q9H4E9|Q9P2G2	Missense_Mutation	SNP	ENST00000315266.5	hg19	CCDS32103.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.999756	0.74818	.	.	ENSG00000171723	ENST00000315266;ENST00000478722;ENST00000459628;ENST00000543237;ENST00000305960;ENST00000555456	.	.	.	5.02	4.12	0.48240	Molybdopterin binding (2);	0.000000	0.85682	D	0.000000	T	0.52386	0.1731	N	0.08118	0	0.58432	D	0.999994	B;D;B;D;D	0.89917	0.343;1.0;0.047;0.999;0.999	B;D;B;D;D	0.91635	0.281;0.999;0.052;0.993;0.989	T	0.62946	-0.6746	9	0.87932	D	0	-6.4813	13.7767	0.63057	0.0761:0.0:0.9239:0.0	.	136;180;167;167;149	F8W7D6;F5H039;Q9NQX3;Q9NQX3-2;G3V582	.;.;GEPH_HUMAN;.;.	H	167;167;149;180;136;100	.	ENSP00000303019:D136H	D	+	1	0	GPHN	66459178	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.550000	0.98110	2.321000	0.78463	0.655000	0.94253	GAC	.	.	.	none		0.403	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806		C	67389425	G	C	67389425	3	2	121	1	0	0	0	0	1	0	0	0	6617	1290	45	4	525	4	GPHN	14	67389425	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08		67389425	39960115	37	7702											
ATG2B	55102	hgsc.bcm.edu	37	chr14	96761860	96761860	+	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	gaagctctacttctgcagaaAgacttgtgaagaaatccttc	13	11	8	9	0	2	4	0	1	2	3	4	5	3	4	1	0	3	2	1	0	5	4			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr14:96761860A>T	ENST00000359933.4	-	35	6070	c.5177T>A	c.(5176-5178)cTt>cAt	p.L1726H	ATG2B_ENST00000261834.5_5'UTR	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	1726					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)		TTCTGCAGAAAGACTTGTGAA	0.308																																					p.L1726H		Atlas-SNP	.											.	ATG2B	169	.	0			c.T5177A						PASS	.						55	54	55					14																	96761860		2203	4290	6493	SO:0001583	missense	55102	exon35			GCAGAAAGACTTG	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.5177T>A	chr14.hg19:g.96761860A>T	ENSP00000353010:p.Leu1726His	134.0	0.0	.		112.0	36.0	.	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	hg19	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	A	26.0	4.697600	0.88830	.	.	ENSG00000066739	ENST00000359933	T	0.13657	2.57	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.40886	0.1135	M	0.80332	2.49	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.31613	-0.9937	10	0.54805	T	0.06	.	15.8864	0.79251	1.0:0.0:0.0:0.0	.	1726	Q96BY7	ATG2B_HUMAN	H	1726	ENSP00000353010:L1726H	ENSP00000261834:L370H	L	-	2	0	ATG2B	95831613	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.539000	0.90637	2.223000	0.72356	0.454000	0.30748	CTT	.	.	.	none		0.308	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		T	96761860	A	T	96761860	3	4	121	1	0	0	0	0	1	0	0	0	1094	72	3	5	1091	5	ATG2B	14	96761860	Missense_Mutation	SNP	A	TCGA-BQ-5886-01A-11D-1589-08	29372435	96761860	10587680	38	7703											
ITGAX	3687	hgsc.bcm.edu	37	chr16	31371300	31371300	+	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	ttcactttcgaggaattcagGcgcagctcaaaccccctcag	10	9	8	14	2	4	0	4	0	0	0	5	2	4	1	2	2	2	2	2	2	2	3			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr16:31371300G>A	ENST00000268296.4	+	7	742	c.621G>A	c.(619-621)agG>agA	p.R207R	ITGAX_ENST00000562522.1_Silent_p.R207R	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	207	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						AGGAATTCAGGCGCAGCTCAA	0.522																																					p.R207R		Atlas-SNP	.											.	ITGAX	198	.	0			c.G621A						PASS	.						103	105	104					16																	31371300		2197	4300	6497	SO:0001819	synonymous_variant	3687	exon7			ATTCAGGCGCAGC	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.621G>A	chr16.hg19:g.31371300G>A		136.0	0.0	.		223.0	108.0	.	NM_000887	Q8IVA6	Silent	SNP	ENST00000268296.4	hg19	CCDS10711.1																																																																																			.	.	.	none		0.522	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887		A	31371300	G	A	31371300	2	1	121	1	0	0	0	0	0	0	0	1	7896	1194	42	2		2	ITGAX	16	31371300	Silent	SNP	G	TCGA-BQ-5886-01A-11D-1589-08		31371300	58983453	39	7704											
SLC13A5	284111	hgsc.bcm.edu	37	chr17	6606332	6606332	+	Missense_Mutation	SNP	T	T	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	cacgttgggtcccgtcccggTcagggtggcggtgcccccga	3	7	16	15	5	1	0	1	0	0	0	3	1	3	0	4	5	1	1	4	5	0	1			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr17:6606332T>G	ENST00000433363.2	-	5	906	c.673A>C	c.(673-675)Acc>Ccc	p.T225P	SLC13A5_ENST00000381074.4_Missense_Mutation_p.T182P|SLC13A5_ENST00000293800.6_Missense_Mutation_p.T208P|SLC13A5_ENST00000573648.1_Missense_Mutation_p.T225P	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	225					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						CCCGTCCCGGTCAGGGTGGCG	0.642																																					p.T225P		Atlas-SNP	.											.	SLC13A5	57	.	0			c.A673C						PASS	.						117	98	105					17																	6606332		2203	4300	6503	SO:0001583	missense	284111	exon5			TCCCGGTCAGGGT	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.673A>C	chr17.hg19:g.6606332T>G	ENSP00000406220:p.Thr225Pro	123.0	0.0	.		141.0	39.0	.	NM_001143838	B3KXR0|B7Z4P2|B7ZLB4|F8W7N2|Q6ZMG1	Missense_Mutation	SNP	ENST00000433363.2	hg19	CCDS11079.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.384652	0.82792	.	.	ENSG00000141485	ENST00000293800;ENST00000433363;ENST00000381074	T;T	0.11169	2.8;2.8	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.40473	0.1118	M	0.89715	3.055	0.80722	D	1	D;D;D;D;D	0.89917	0.998;0.996;0.994;0.994;1.0	D;D;D;D;D	0.97110	0.967;0.945;0.967;0.967;1.0	T	0.48364	-0.9042	10	0.87932	D	0	.	13.806	0.63233	0.0:0.0:0.0:1.0	.	225;182;182;208;225	B7ZLB4;F8W7N2;B7Z4P2;B3KXR0;Q86YT5	.;.;.;.;S13A5_HUMAN	P	225;225;182	ENSP00000406220:T225P;ENSP00000370464:T182P	ENSP00000293800:T225P	T	-	1	0	SLC13A5	6547056	1.000000	0.71417	0.991000	0.47740	0.674000	0.39518	5.844000	0.69430	2.216000	0.71823	0.459000	0.35465	ACC	.	.	.	none		0.642	SLC13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219853.2	NM_177550		G	6606332	T	G	6606332	3	3	121	1	0	0	0	0	1	0	0	0	14408	1667	58	5	1065	5	SLC13A5	17	6606332	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08		6606332	74588878	40	7705											
PIK3R5	23533	hgsc.bcm.edu	37	chr17	8812455	8812455	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcccgggtccctgctgaccAgctcctgcaggctccagcag	5	6	13	17	1	0	1	0	1	0	0	3	1	3	1	5	3	4	5	5	3	0	0			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr17:8812455A>G	ENST00000447110.1	-	3	264	c.140T>C	c.(139-141)cTg>cCg	p.L47P	PIK3R5_ENST00000581552.1_Missense_Mutation_p.L47P|PIK3R5_ENST00000584803.1_Missense_Mutation_p.L47P	NM_001142633.2|NM_001251851.1|NM_001251852.1|NM_001251853.1|NM_001251855.1	NP_001136105.1|NP_001238780.1|NP_001238781.1|NP_001238782.1|NP_001238784.1	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5	47	Heterodimerization. {ECO:0000250}.			L -> Q (in Ref. 6; AAW63122). {ECO:0000305}.	blood coagulation (GO:0007596)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|small molecule metabolic process (GO:0044281)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|G-protein beta/gamma-subunit complex binding (GO:0031683)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(14)|prostate(3)|skin(4)|urinary_tract(1)	34						CCTGCTGACCAGCTCCTGCAG	0.597																																					p.L47P	NSCLC(18;589 615 7696 20311 50332)	Atlas-SNP	.											.	PIK3R5	79	.	0			c.T140C						PASS	.						29	25	27					17																	8812455		2203	4300	6503	SO:0001583	missense	23533	exon3			CTGACCAGCTCCT	AF128881	CCDS11147.1, CCDS73986.1	17p13.1	2011-10-13	2008-02-04		ENSG00000141506	ENSG00000141506			30035	protein-coding gene	gene with protein product		611317				12507995	Standard	NM_014308		Approved	P101-PI3K, p101	uc002glt.3	Q8WYR1	OTTHUMG00000108197	ENST00000447110.1:c.140T>C	chr17.hg19:g.8812455A>G	ENSP00000392812:p.Leu47Pro	36.0	0.0	.		26.0	4.0	.	NM_001142633	B0LPH4|D3DTS3|Q5G936|Q5G938|Q5G939|Q8IZ23|Q9Y2Y2	Missense_Mutation	SNP	ENST00000447110.1	hg19	CCDS11147.1	.	.	.	.	.	.	.	.	.	.	A	14.09	2.433132	0.43224	.	.	ENSG00000141506	ENST00000269300;ENST00000447110	T;T	0.80123	-1.34;-1.34	5.22	5.22	0.72569	.	0.076071	0.53938	D	0.000052	D	0.83459	0.5259	L	0.29908	0.895	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	D	0.85017	0.0909	10	0.59425	D	0.04	-7.8781	13.6276	0.62176	1.0:0.0:0.0:0.0	.	47	Q8WYR1	PI3R5_HUMAN	P	47	ENSP00000269300:L47P;ENSP00000392812:L47P	ENSP00000269300:L47P	L	-	2	0	PIK3R5	8753180	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.181000	0.77682	2.100000	0.63781	0.528000	0.53228	CTG	.	.	.	none		0.597	PIK3R5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000227003.2	NM_014308		G	8812455	A	G	8812455	3	3	121	1	0	0	0	0	1	0	0	0	11929	188	7	3	2570	3	PIK3R5	17	8812455	Missense_Mutation	SNP	A	TCGA-BQ-5886-01A-11D-1589-08	2206123	8812455	72382755	41	7706											
KIAA0100	9703	hgsc.bcm.edu	37	chr17	26948415	26948415	+	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	gcagaggagggggagggctgAcctgtggttgtggtaaccat	8	8	19	6	0	0	2	0	1	0	1	0	4	0	4	2	6	1	4	2	6	1	2			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr17:26948415A>G	ENST00000528896.2	-	27	5134		c.e27+1		KIAA0100_ENST00000579924.2_5'Flank|KIAA0100_ENST00000389003.3_Splice_Site|KIAA0100_ENST00000544884.1_Splice_Site	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100							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)					GGGAGGGCTGACCTGTGGTTG	0.542																																					.		Atlas-SNP	.											.	KIAA0100	175	.	0			c.5059+2T>C						PASS	.						113	103	106					17																	26948415		2203	4300	6503	SO:0001630	splice_region_variant	9703	exon28			GGGCTGACCTGTG	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.5059+1T>C	chr17.hg19:g.26948415A>G		252.0	0.0	.		283.0	62.0	.	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Splice_Site	SNP	ENST00000528896.2	hg19	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	A	19.19	3.779355	0.70107	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4732	0.67531	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KIAA0100	23972542	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	8.702000	0.91338	2.211000	0.71520	0.402000	0.26972	.	.	.	.	none		0.542	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680	Intron	G	26948415	A	G	26948415	5	3	121	1	0	0	0	0	0	0	1	0	8161	289	10	3	1698	3	KIAA0100	17	26948415	Splice_Site	SNP	A	TCGA-BQ-5886-01A-11D-1589-08	18135960	26948415	54246795	42	7707											
C17orf28	283987	hgsc.bcm.edu	37	chr17	72954436	72954436	+	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	cctcaccacaatgagcaggtCggcgtgggtccctgtgaaga	9	7	13	12	2	1	3	1	2	0	1	3	3	2	3	3	3	1	1	3	3	2	0			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr17:72954436C>G	ENST00000425042.2	-	11	1455	c.1378G>C	c.(1378-1380)Gac>Cac	p.D460H		NM_030630.2	NP_085133.1	Q8IV36	HID1_HUMAN	HID1 domain containing	460					intracellular protein transport (GO:0006886)|response to brefeldin A (GO:0031001)	cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi medial cisterna (GO:0005797)|Golgi trans cisterna (GO:0000138)											ATGAGCAGGTCGGCGTGGGTC	0.667											OREG0024721	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D460H		Atlas-SNP	.											.	.	.	.	0			c.G1378C						PASS	.						55	43	47					17																	72954436		2203	4300	6503	SO:0001583	missense	283987	exon11			GCAGGTCGGCGTG		CCDS32726.1	17q25.1	2012-10-10	2012-10-10	2012-10-10	ENSG00000167861	ENSG00000167861			15736	protein-coding gene	gene with protein product	"downregulated in multiple cancer 1"	605752	"chromosome 17 open reading frame 28"	C17orf28		11281419, 21337012	Standard	NM_030630		Approved	DMC1, HID-1	uc002jmj.4	Q8IV36	OTTHUMG00000166490	ENST00000425042.2:c.1378G>C	chr17.hg19:g.72954436C>G	ENSP00000413520:p.Asp460His	28.0	0.0	.	1141	48.0	5.0	.	NM_030630	Q8N5L6|Q8TE83|Q9NT34	Missense_Mutation	SNP	ENST00000425042.2	hg19	CCDS32726.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.918325	0.92249	.	.	ENSG00000167861	ENST00000525426;ENST00000425042;ENST00000318565	.	.	.	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	D	0.86732	0.6003	M	0.93978	3.48	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90618	0.4557	9	0.87932	D	0	-29.5566	18.1326	0.89606	0.0:1.0:0.0:0.0	.	460	Q8IV36	CQ028_HUMAN	H	232;460;232	.	ENSP00000317795:D232H	D	-	1	0	C17orf28	70466031	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	7.550000	0.82173	2.284000	0.76573	0.561000	0.74099	GAC	.	.	.	none		0.667	HID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390011.2	NM_030630		G	72954436	C	G	72954436	3	3	121	1	0	0	0	0	1	0	0	0	1855	884	31	4	1024	4	C17orf28	17	72954436	Missense_Mutation	SNP	C	TCGA-BQ-5886-01A-11D-1589-08	46006021	72954436	8240774	43	7708											
ITGB4	3691	hgsc.bcm.edu	37	chr17	73752809	73752809	+	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	cgccttcactttgagcactcCcagtgccccaggcccgctgg	5	8	10	18	2	1	1	1	1	0	0	2	1	2	1	5	2	2	2	5	2	0	2			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr17:73752809C>T	ENST00000200181.3	+	37	5109	c.4922C>T	c.(4921-4923)cCc>cTc	p.P1641L	ITGB4_ENST00000449880.2_Missense_Mutation_p.P1624L|ITGB4_ENST00000579662.1_Missense_Mutation_p.P1571L|ITGB4_ENST00000339591.3_Missense_Mutation_p.P1624L|GALK1_ENST00000225614.2_Intron|ITGB4_ENST00000450894.3_Missense_Mutation_p.P1571L	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	1641					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)			TTGAGCACTCCCAGTGCCCCA	0.667																																					p.P1641L		Atlas-SNP	.											.	ITGB4	165	.	0			c.C4922T						PASS	.						53	55	54					17																	73752809		2203	4299	6502	SO:0001583	missense	3691	exon37			GCACTCCCAGTGC		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.4922C>T	chr17.hg19:g.73752809C>T	ENSP00000200181:p.Pro1641Leu	112.0	0.0	.		124.0	29.0	.	NM_000213	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	ENST00000200181.3	hg19	CCDS11727.1	.	.	.	.	.	.	.	.	.	.	C	14.80	2.644502	0.47258	.	.	ENSG00000132470	ENST00000200181;ENST00000339591;ENST00000449880	T;T;T	0.61627	0.09;0.09;0.09	5.04	5.04	0.67666	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.82802	0.5116	M	0.93978	3.48	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	0.87598	0.2495	10	0.87932	D	0	.	18.7536	0.91823	0.0:1.0:0.0:0.0	.	1624;1571;1641	P16144-3;A0AVL6;P16144	.;.;ITB4_HUMAN	L	1641;1624;1624	ENSP00000200181:P1641L;ENSP00000344079:P1624L;ENSP00000400217:P1624L	ENSP00000200181:P1641L	P	+	2	0	ITGB4	71264404	1.000000	0.71417	1.000000	0.80357	0.543000	0.35085	7.776000	0.85560	2.518000	0.84900	0.462000	0.41574	CCC	.	.	.	none		0.667	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			T	73752809	C	T	73752809	3	4	121	1	0	0	0	0	1	0	0	0	7904	623	22	2	5227	2	ITGB4	17	73752809	Missense_Mutation	SNP	C	TCGA-BQ-5886-01A-11D-1589-08	798373	73752809	7442401	44	7709											
GADD45B	4616	hgsc.bcm.edu	37	chr19	2477582	2477582	+	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	accagtgggtcccctacatcTctcttcaggaacgctgaggc	8	9	10	14	1	3	1	1	1	2	0	5	2	4	2	3	3	2	1	3	3	2	2			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr19:2477582T>A	ENST00000215631.4	+	4	698	c.466T>A	c.(466-468)Tct>Act	p.S156T		NM_015675.3	NP_056490.2	O75293	GA45B_HUMAN	growth arrest and DNA-damage-inducible, beta	156					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)		CCCCTACATCTCTCTTCAGGA	0.552																																					p.S156T		Atlas-SNP	.											.	GADD45B	6	.	0			c.T466A						PASS	.						39	40	40					19																	2477582		2203	4300	6503	SO:0001583	missense	4616	exon4			TACATCTCTCTTC	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.466T>A	chr19.hg19:g.2477582T>A	ENSP00000215631:p.Ser156Thr	27.0	0.0	.		39.0	13.0	.	NM_015675	A8KAM2|O75960|Q17R46	Missense_Mutation	SNP	ENST00000215631.4	hg19	CCDS32868.1	.	.	.	.	.	.	.	.	.	.	T	2.003	-0.428988	0.04701	.	.	ENSG00000099860	ENST00000215631	T	0.40756	1.02	4.66	-0.362	0.12560	.	0.260085	0.37012	N	0.002300	T	0.15522	0.0374	N	0.24115	0.695	0.58432	D	0.999999	B	0.29716	0.255	B	0.21917	0.037	T	0.29971	-0.9994	10	0.02654	T	1	.	1.0667	0.01612	0.1464:0.2718:0.1505:0.4313	.	156	O75293	GA45B_HUMAN	T	156	ENSP00000215631:S156T	ENSP00000215631:S156T	S	+	1	0	GADD45B	2428582	0.000000	0.05858	0.307000	0.25127	0.709000	0.40893	-1.720000	0.01871	-0.128000	0.11641	0.443000	0.29094	TCT	.	.	.	none		0.552	GADD45B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451337.1	NM_015675		A	2477582	T	A	2477582	3	1	121	1	0	0	0	0	1	0	0	0	6189	1551	54	5	480	5	GADD45B	19	2477582	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08		2477582	56651401	45	7710											
S1PR4	8698	hgsc.bcm.edu	37	chr19	3179456	3179456	+	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	ctggccaccatcatgggcctCtatggggccatcttccgcct	5	10	10	16	1	3	0	1	0	2	0	4	0	4	0	6	4	0	0	6	4	1	2			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr19:3179456C>T	ENST00000246115.3	+	1	721	c.666C>T	c.(664-666)ctC>ctT	p.L222L	S1PR4_ENST00000591346.1_3'UTR	NM_003775.3	NP_003766.1	O95977	S1PR4_HUMAN	sphingosine-1-phosphate receptor 4	222					activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)			breast(1)|kidney(2)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	13						TCATGGGCCTCTATGGGGCCA	0.672																																					p.L222L	GBM(82;318 1638 33279 49708)	Atlas-SNP	.											.	S1PR4	31	.	0			c.C666T						PASS	.						86	93	91					19																	3179456		2203	4300	6503	SO:0001819	synonymous_variant	8698	exon1			GGGCCTCTATGGG	AJ000479	CCDS12105.1	19p13.3	2012-08-08	2008-04-30	2008-04-30		ENSG00000125910		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"	3170	protein-coding gene	gene with protein product		603751	"endothelial differentiation, G-protein-coupled receptor 6", "endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 6"	EDG6		9790765	Standard	NM_003775		Approved		uc002lxg.3	O95977		ENST00000246115.3:c.666C>T	chr19.hg19:g.3179456C>T		245.0	0.0	.		263.0	85.0	.	NM_003775	D6W612	Silent	SNP	ENST00000246115.3	hg19	CCDS12105.1																																																																																			.	.	.	none		0.672	S1PR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452517.1	NM_003775		T	3179456	C	T	3179456	2	4	121	1	0	0	0	0	0	0	0	1	13809	900	32	2		2	S1PR4	19	3179456	Silent	SNP	C	TCGA-BQ-5886-01A-11D-1589-08	701874	3179456	55949527	46	7711											
ZFP14	57677	hgsc.bcm.edu	37	chr19	36831480	36831481	+	Missense_Mutation	DNP	GC	GC	AT																															ggtctctcaccaatatgaatGctctggtgtgaaataagctg																										TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr19:36831480_36831481GC>AT	ENST00000270001.7	-	5	1362_1363	c.1247_1248GC>AT	c.(1246-1248)aGC>aAT	p.S416N		NM_020917.2	NP_065968.1	Q9HCL3	ZFP14_HUMAN	ZFP14 zinc finger protein	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)|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)					CAATATGAATGCTCTGGTGTGA	0.416																																					p.S416S|p.S416N		Atlas-SNP	.											.	ZFP14	68	.	0			c.C1248T|c.G1247A						PASS	.																																			SO:0001583	missense	57677	exon5			ATGAATGCTCTGG|TGAATGCTCTGGT	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.1247_1248delinsAT	chr19.hg19:g.36831480_36831481delinsAT	ENSP00000270001:p.Ser416Asn	142.0	0.0	.		163.0|164.0	53.0	.	NM_020917	A7MD23	Silent|Missense_Mutation	SNP	ENST00000270001.7	hg19	CCDS33002.1																																																																																			.	.	.	none		0.416	ZFP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452528.1	NM_020917		AT	36831481	GC	AT	36831480	3	1	121	1	0	0	0	0	1	0	0	0	17651	1310	46	2	357	2	ZFP14	19	36831480	Missense_Mutation	DNP	GC	TCGA-BQ-5886-01A-11D-1589-08	33652024	36831480	22297503	47	7712											
BCAM	4059	hgsc.bcm.edu	37	chr19	45322968	45322968	+	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	cccctgctgccgccagcggcGggagaagggggctccgtgag	5	4	18	14	4	0	2	0	1	0	1	1	3	1	2	5	4	3	2	5	4	1	0			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr19:45322968G>T	ENST00000270233.6	+	13	1770	c.1748G>T	c.(1747-1749)cGg>cTg	p.R583L	BCAM_ENST00000589651.1_Missense_Mutation_p.R583L	NM_001013257.2|NM_005581.4	NP_001013275.1|NP_005572.2	P50895	BCAM_HUMAN	basal cell adhesion molecule (Lutheran blood group)	583					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	laminin binding (GO:0043236)|laminin receptor activity (GO:0005055)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				CGCCAGCGGCGGGAGAAGGGG	0.637																																					p.R583L		Atlas-SNP	.											BCAM,middle_lobe,carcinoma,0,1	BCAM	53	.	0			c.G1748T						PASS	.						14	17	16					19																	45322968		2183	4244	6427	SO:0001583	missense	4059	exon13			AGCGGCGGGAGAA	X83425	CCDS12644.1, CCDS42575.1	19q12-q13	2014-07-18	2006-02-23	2006-01-12		ENSG00000187244		"CD molecules", "Blood group antigens", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6722	protein-coding gene	gene with protein product		612773	"Lutheran blood group (Auberger b antigen included)", "basal cell adhesion molecule (Lu and Au blood groups)"	LU			Standard	NM_005581		Approved	CD239	uc002ozu.4	P50895		ENST00000270233.6:c.1748G>T	chr19.hg19:g.45322968G>T	ENSP00000270233:p.Arg583Leu	42.0	0.0	.		39.0	18.0	.	NM_001013257	A8MYF9|A9YWT5|A9YWT6|Q86VC7	Missense_Mutation	SNP	ENST00000270233.6	hg19	CCDS12644.1	.	.	.	.	.	.	.	.	.	.	.	4.697	0.129623	0.08981	.	.	ENSG00000187244	ENST00000270233;ENST00000391955	T;T	0.59772	0.24;0.34	4.08	1.68	0.24146	.	.	.	.	.	T	0.33904	0.0879	N	0.08118	0	0.09310	N	1	B	0.24092	0.097	B	0.15870	0.014	T	0.15521	-1.0434	9	0.30078	T	0.28	-5.8905	10.1318	0.42682	0.0:0.4182:0.5817:0.0	.	583	P50895	BCAM_HUMAN	L	583	ENSP00000270233:R583L;ENSP00000375817:R583L	ENSP00000270233:R583L	R	+	2	0	BCAM	50014808	0.003000	0.15002	0.037000	0.18230	0.042000	0.13812	1.344000	0.33941	0.242000	0.21303	0.531000	0.56144	CGG	.	.	.	none		0.637	BCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453220.1	NM_005581		T	45322968	G	T	45322968	3	4	121	1	0	0	0	0	1	0	0	0	1344	1116	39	4	1798	4	BCAM	19	45322968	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	8491488	45322968	13806015	48	7713											
HRC	3270	hgsc.bcm.edu	37	chr19	49657763	49657763	+	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	tcatcatcatcgtcatcttcTtcatggccttggtgcctgtg	5	16	8	12	1	7	0	5	0	2	0	8	0	7	0	2	2	1	0	2	2	0	3			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr19:49657763T>A	ENST00000252825.4	-	1	918	c.732A>T	c.(730-732)gaA>gaT	p.E244D	HRC_ENST00000595625.1_Missense_Mutation_p.E244D	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	244	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)	p.E244E(1)		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)		cgtcatcttcttcatGGCCTT	0.522																																					p.E244D	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											HRC,NS,carcinoma,0,1	HRC	85	.	1	Substitution - coding silent(1)	lung(1)	c.A732T						PASS	.						118	85	96					19																	49657763		2203	4300	6503	SO:0001583	missense	3270	exon1			ATCTTCTTCATGG		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.732A>T	chr19.hg19:g.49657763T>A	ENSP00000252825:p.Glu244Asp	30.0	1.0	.		33.0	2.0	.	NM_002152	Q504Y6	Missense_Mutation	SNP	ENST00000252825.4	hg19	CCDS12759.1	.	.	.	.	.	.	.	.	.	.	t	8.405	0.842850	0.16963	.	.	ENSG00000130528	ENST00000252825;ENST00000434964	T	0.06294	3.32	3.24	2.17	0.27698	.	.	.	.	.	T	0.07593	0.0191	L	0.57536	1.79	0.09310	N	0.999998	B	0.28820	0.224	B	0.33846	0.171	T	0.37641	-0.9697	9	0.13853	T	0.58	0.3786	7.0233	0.24926	0.0:0.1288:0.0:0.8712	.	244	P23327	SRCH_HUMAN	D	244;214	ENSP00000252825:E244D	ENSP00000252825:E244D	E	-	3	2	HRC	54349575	0.001000	0.12720	0.040000	0.18447	0.049000	0.14656	0.298000	0.19120	1.251000	0.43983	0.375000	0.23000	GAA	.	.	.	none		0.522	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		A	49657763	T	A	49657763	3	1	121	1	0	0	0	0	1	0	0	0	7359	1606	56	5	1391	5	HRC	19	49657763	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	4334795	49657763	9471220	49	7714											
ZNF543	125919	hgsc.bcm.edu	37	chr19	57839185	57839185	+	Frame_Shift_Del	DEL	G	G	-																															cctcaaagaactcccaattaGggcaatccaaggatcaggat																										TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr19:57839185delG	ENST00000321545.4	+	4	700	c.355delG	c.(355-357)gggfs	p.G119fs		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	119					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			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)		CTCCCAATTAGGGCAATCCAA	0.512																																					p.L118fs		Atlas-INDEL	.											.	ZNF543	61	.	0			c.354delA						PASS	.						64	67	66					19																	57839185		2203	4300	6503	SO:0001589	frameshift_variant	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		ENST00000321545.4:c.355delG	chr19.hg19:g.57839185delG	ENSP00000322545:p.Gly119fs	69.0	0.0	0		69.0	15.0	0.217391	NM_213598	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	Frame_Shift_Del	DEL	ENST00000321545.4	hg19	CCDS33130.1																																																																																			.	.	.	none		0.512	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865		-	57839185	G	-	57839185	7	5	121	1	0	1	0	1	0	0	0	0	17988	1000	35	0	369	0	ZNF543	19	57839185	Frame_Shift_Del	DEL	G	TCGA-BQ-5886-01A-11D-1589-08	8181422	57839185	1289798	50	7715											
PTPRA	5786	hgsc.bcm.edu	37	chr20	3016279	3016279	+	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	atggactggtgtcctatggaGatattacagtggaactgaag	12	11	13	5	0	0	2	0	1	0	1	1	5	1	4	1	4	2	0	1	4	5	3			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr20:3016279G>T	ENST00000216877.6	+	20	2342	c.1942G>T	c.(1942-1944)Gat>Tat	p.D648Y	PTPRA_ENST00000399903.2_Missense_Mutation_p.D657Y|PTPRA_ENST00000318266.5_Missense_Mutation_p.D648Y|PTPRA_ENST00000356147.3_Missense_Mutation_p.D648Y|PTPRA_ENST00000380393.3_Missense_Mutation_p.D657Y|PTPRA_ENST00000425918.2_Missense_Mutation_p.D668Y|PTPRA_ENST00000358719.4_Missense_Mutation_p.D513Y	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	657	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|insulin receptor signaling pathway (GO:0008286)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein phosphorylation (GO:0006468)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						GTCCTATGGAGATATTACAGT	0.532																																					p.D657Y		Atlas-SNP	.											.	PTPRA	75	.	0			c.G1969T						PASS	.						106	94	98					20																	3016279		2203	4300	6503	SO:0001583	missense	5786	exon25			TATGGAGATATTA		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.1942G>T	chr20.hg19:g.3016279G>T	ENSP00000216877:p.Asp648Tyr	40.0	0.0	.		26.0	12.0	.	NM_002836	A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	Missense_Mutation	SNP	ENST00000216877.6	hg19	CCDS13039.1	.	.	.	.	.	.	.	.	.	.	G	12.18	1.860550	0.32884	.	.	ENSG00000132670	ENST00000380393;ENST00000216877;ENST00000399903;ENST00000358719;ENST00000542217;ENST00000425918;ENST00000318266;ENST00000356147	D;D;D;D;D;D;D	0.84516	-1.86;-1.86;-1.86;-1.86;-1.86;-1.86;-1.86	5.57	5.57	0.84162	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	U	0.000000	D	0.90597	0.7052	M	0.72353	2.195	0.80722	D	1	P;D;D	0.89917	0.49;1.0;1.0	B;D;D	0.91635	0.143;0.999;0.963	D	0.85912	0.1441	10	0.02654	T	1	.	19.5578	0.95358	0.0:0.0:1.0:0.0	.	668;657;648	B7Z2A4;P18433;P18433-4	.;PTPRA_HUMAN;.	Y	657;648;657;513;267;668;648;648	ENSP00000369756:D657Y;ENSP00000216877:D648Y;ENSP00000382787:D657Y;ENSP00000351559:D513Y;ENSP00000393553:D668Y;ENSP00000314568:D648Y;ENSP00000348468:D648Y	ENSP00000216877:D648Y	D	+	1	0	PTPRA	2964279	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	9.869000	0.99810	2.604000	0.88044	0.563000	0.77884	GAT	.	.	.	none		0.532	PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077682.3			T	3016279	G	T	3016279	3	4	121	1	0	0	0	0	1	0	0	0	12808	942	33	4	2039	4	PTPRA	20	3016279	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08		3016279	60009241	51	7716											
PARD6B	84612	hgsc.bcm.edu	37	chr20	49366607	49366607	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttgatcaagtaacagacaTgatgattgcaaatagccgta	15	10	8	8	1	1	4	1	3	0	1	1	4	1	4	2	0	3	3	2	0	5	5			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr20:49366607T>C	ENST00000371610.2	+	3	944	c.701T>C	c.(700-702)aTg>aCg	p.M234T	PARD6B_ENST00000396039.1_Intron	NM_032521.2	NP_115910.1	Q9BYG5	PAR6B_HUMAN	par-6 family cell polarity regulator beta	234	Interaction with PARD3 and CDC42. {ECO:0000250}.|PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell junction assembly (GO:0034329)|cell-cell junction assembly (GO:0007043)|cell-cell junction organization (GO:0045216)|establishment or maintenance of cell polarity (GO:0007163)|protein complex assembly (GO:0006461)|regulation of cell migration (GO:0030334)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				NS(1)|breast(1)|endometrium(1)|kidney(4)|lung(3)|urinary_tract(1)	11						GTAACAGACATGATGATTGCA	0.433																																					p.M234T		Atlas-SNP	.											.	PARD6B	31	.	0			c.T701C						PASS	.						124	117	120					20																	49366607		2203	4300	6503	SO:0001583	missense	84612	exon3			CAGACATGATGAT	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.701T>C	chr20.hg19:g.49366607T>C	ENSP00000360672:p.Met234Thr	153.0	0.0	.		156.0	52.0	.	NM_032521	A2A2A7|Q9Y510	Missense_Mutation	SNP	ENST00000371610.2	hg19	CCDS33485.1	.	.	.	.	.	.	.	.	.	.	T	18.60	3.659758	0.67586	.	.	ENSG00000124171	ENST00000371610	T	0.27402	1.67	6.02	6.02	0.97574	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.54727	0.1876	M	0.63169	1.94	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.56456	-0.7976	10	0.87932	D	0	-60.5095	16.5446	0.84426	0.0:0.0:0.0:1.0	.	234	Q9BYG5	PAR6B_HUMAN	T	234	ENSP00000360672:M234T	ENSP00000360672:M234T	M	+	2	0	PARD6B	48800014	1.000000	0.71417	1.000000	0.80357	0.638000	0.38207	5.917000	0.69989	2.311000	0.77944	0.533000	0.62120	ATG	.	.	.	none		0.433	PARD6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079697.2	NM_032521		C	49366607	T	C	49366607	3	2	121	1	0	0	0	0	1	0	0	0	11453	1464	51	3	711	3	PARD6B	20	49366607	Missense_Mutation	SNP	T	TCGA-BQ-5886-01A-11D-1589-08	46350328	49366607	13658913	52	7717											
EMID1	129080	hgsc.bcm.edu	37	chr22	29627008	29627008	+	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	cgtccctgtcttcctcttcaGatgaccatgctgactgtcat	6	14	7	14	1	4	3	2	2	2	1	6	3	6	3	3	0	1	1	3	0	0	2			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr22:29627008G>T	ENST00000404820.3	+	6	592		c.e6-1		EMID1_ENST00000404755.3_Splice_Site|EMID1_ENST00000334018.6_Splice_Site|EMID1_ENST00000484039.1_Splice_Site			Q96A84	EMID1_HUMAN	EMI domain containing 1							collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(2)|skin(3)	12						TTCCTCTTCAGATGACCATGC	0.587																																					.		Atlas-SNP	.											.	EMID1	33	.	0			c.466-1G>T						PASS	.						68	65	66					22																	29627008		2203	4300	6503	SO:0001630	splice_region_variant	129080	exon6			TCTTCAGATGACC	AJ416090	CCDS33630.1	22q12.2	2009-08-04			ENSG00000186998	ENSG00000186998		"EMI domain containing"	18036	protein-coding gene	gene with protein product	"emilin and multimerin-domain containing protein 1", "putative emu1"	608926				12221002	Standard	NM_001267895		Approved	EMU1, hEmu1, EMI5	uc003aem.4	Q96A84	OTTHUMG00000151013	ENST00000404820.3:c.466-1G>T	chr22.hg19:g.29627008G>T		85.0	0.0	.		103.0	27.0	.	NM_133455	B0QYK6|Q6ICG1|Q86SS7	Splice_Site	SNP	ENST00000404820.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.15|10.15	1.270790|1.270790	0.23221|0.23221	.|.	.|.	ENSG00000186998|ENSG00000186998	ENST00000334018;ENST00000429226;ENST00000404755;ENST00000404820;ENST00000430127|ENST00000433143	.|.	.|.	.|.	4.64|4.64	4.64|4.64	0.57946|0.57946	.|.	.|.	.|.	.|.	.|.	.|T	.|0.64735	.|0.2625	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.63537	.|-0.6615	.|4	.|.	.|.	.|.	.|.	13.3293|13.3293	0.60477|0.60477	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	.|I	-1|1	.|.	.|.	.|R	+|+	.|2	.|0	EMID1|EMID1	27957008|27957008	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.024000|0.024000	0.10985|0.10985	4.969000|4.969000	0.63735|0.63735	2.293000|2.293000	0.77203|0.77203	0.591000|0.591000	0.81541|0.81541	.|AGA	.	.	.	none		0.587	EMID1-002	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321075.1	NM_133455	Intron	T	29627008	G	T	29627008	5	4	121	1	0	0	0	0	0	0	1	0	5093	956	33	4	487	4	EMID1	22	29627008	Splice_Site	SNP	G	TCGA-BQ-5886-01A-11D-1589-08		29627008	21677558	53	7718											
SBF1	6305	hgsc.bcm.edu	37	chr22	50885659	50885659	+	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	agaagttgtaaacgcgacgcGttgtcttcacctggggaagg	10	9	14	8	4	2	1	1	0	1	1	2	3	2	2	1	3	1	3	1	3	4	4	rs375012426	byFrequency	TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chr22:50885659G>C	ENST00000390679.3	-	40	5700	c.5516C>G	c.(5515-5517)aCg>aGg	p.T1839R	SBF1_ENST00000380817.3_Missense_Mutation_p.T1865R|SBF1_ENST00000348911.6_Missense_Mutation_p.T1840R			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)		AACGCGACGCGTTGTCTTCAC	0.667																																					p.T1865R		Atlas-SNP	.											.	SBF1	211	.	0			c.C5594G						PASS	.						48	59	55					22																	50885659		2096	4202	6298	SO:0001583	missense	6305	exon41			CGACGCGTTGTCT	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.5516C>G	chr22.hg19:g.50885659G>C	ENSP00000375097:p.Thr1839Arg	53.0	0.0	.		56.0	13.0	.	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Missense_Mutation	SNP	ENST00000390679.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.51|17.51	3.408090|3.408090	0.62399|0.62399	.|.	.|.	ENSG00000100241|ENSG00000100241	ENST00000418590|ENST00000380817;ENST00000348911;ENST00000337034;ENST00000390679	.|T;T;T	.|0.12255	.|2.7;2.7;2.7	3.51|3.51	3.51|3.51	0.40186|0.40186	.|Pleckstrin homology-type (1);Pleckstrin homology domain (3);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.26448|0.26448	0.0646|0.0646	L|L	0.31845|0.31845	0.965|0.965	0.58432|0.58432	D|D	0.999997|0.999997	.|D;D;D	.|0.89917	.|0.959;1.0;0.979	.|P;D;D	.|0.91635	.|0.85;0.999;0.913	T|T	0.06058|0.06058	-1.0848|-1.0848	5|10	.|0.66056	.|D	.|0.02	.|.	15.1872|15.1872	0.73012|0.73012	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1839;1865;386	.|O95248;O95248-4;A6PVG7	.|MTMR5_HUMAN;.;.	K|R	386|1865;1840;1875;1839	.|ENSP00000370196:T1865R;ENSP00000252027:T1840R;ENSP00000375097:T1839R	.|ENSP00000336522:T1875R	N|T	-|-	3|2	2|0	SBF1|SBF1	49232525|49232525	0.998000|0.998000	0.40836|0.40836	0.998000|0.998000	0.56505|0.56505	0.777000|0.777000	0.43975|0.43975	2.406000|2.406000	0.44557|0.44557	1.989000|1.989000	0.58080|0.58080	0.462000|0.462000	0.41574|0.41574	AAC|ACG	.	.	.	alt		0.667	SBF1-201	KNOWN	basic	protein_coding	protein_coding				C	50885659	G	C	50885659	3	2	121	1	0	0	0	0	1	0	0	0	13871	1145	40	4	91	4	SBF1	22	50885659	Missense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	21258651	50885659	418907	54	7719											
EIF2S3	1968	hgsc.bcm.edu	37	chrX	24089815	24089815	+	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	ttagacggcttctaggtgtaCgcactgaaggagacaagaaa	14	8	12	7	2	1	4	0	1	1	3	1	5	1	4	0	3	1	3	0	3	6	4			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chrX:24089815C>T	ENST00000253039.4	+	10	1406	c.1153C>T	c.(1153-1155)Cgc>Tgc	p.R385C		NM_001415.3	NP_001406.1	P41091	IF2G_HUMAN	eukaryotic translation initiation factor 2, subunit 3 gamma, 52kDa	385					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						TCTAGGTGTACGCACTGAAGG	0.403																																					p.R385C		Atlas-SNP	.											.	EIF2S3	31	.	0			c.C1153T						PASS	.						37	37	37					X																	24089815		2203	4298	6501	SO:0001583	missense	1968	exon10			GGTGTACGCACTG	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.1153C>T	chrX.hg19:g.24089815C>T	ENSP00000253039:p.Arg385Cys	68.0	0.0	.		46.0	30.0	.	NM_001415	B5BTZ4	Missense_Mutation	SNP	ENST00000253039.4	hg19	CCDS14210.1	.	.	.	.	.	.	.	.	.	.	c	27.8	4.868409	0.91587	.	.	ENSG00000130741	ENST00000253039	T	0.65549	-0.16	4.95	4.95	0.65309	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal (1);Translation initiation factor 2, gamma subunit, C-terminal (1);	0.052313	0.85682	D	0.000000	T	0.78830	0.4345	M	0.91972	3.26	0.80722	D	1	D	0.56746	0.977	P	0.52109	0.69	D	0.85370	0.1113	10	0.87932	D	0	.	17.6111	0.88053	0.0:1.0:0.0:0.0	.	385	P41091	IF2G_HUMAN	C	385	ENSP00000253039:R385C	ENSP00000253039:R385C	R	+	1	0	EIF2S3	23999736	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	7.363000	0.79516	2.175000	0.68902	0.597000	0.82753	CGC	.	.	.	none		0.403	EIF2S3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056079.1	NM_001415		T	24089815	C	T	24089815	3	4	121	1	0	0	0	0	1	0	0	0	5013	536	19	1	1191	1	EIF2S3	23	24089815	Missense_Mutation	SNP	C	TCGA-BQ-5886-01A-11D-1589-08		24089815	131180745	55	7720											
KDM6A	7403	hgsc.bcm.edu	37	chrX	44949021	44949021	+	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	1	0	0	0	0	0	0	0	0	ttcctaatgggttcttggtgGcccaatcttgaagatcttta	8	16	9	8	0	3	2	0	1	3	1	4	2	4	2	2	3	0	1	2	3	4	7			TCGA-BQ-5886-01A-11D-1589-08	TCGA-BQ-5886-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	74be0abf-970a-477d-aa8c-7982e32b739f	9d0a86f4-1735-4a01-8c16-37b05d7bc326	g.chrX:44949021G>A	ENST00000377967.4	+	25	3623	c.3582G>A	c.(3580-3582)tgG>tgA	p.W1194*	KDM6A_ENST00000543216.1_Nonsense_Mutation_p.W1115*|KDM6A_ENST00000382899.4_Nonsense_Mutation_p.W1201*|KDM6A_ENST00000536777.1_Nonsense_Mutation_p.W1149*	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	1194	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)|p.W1194*(1)		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						GTTCTTGGTGGCCCAATCTTG	0.368			"D, N, F, S"		"renal, oesophageal SCC, MM"																																p.W1194X	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	.	7	Whole gene deletion(6)|Substitution - Nonsense(1)	oesophagus(2)|breast(2)|pancreas(2)|urinary_tract(1)	c.G3582A						PASS	.						115	98	103					X																	44949021		2203	4300	6503	SO:0001587	stop_gained	7403	exon25			TTGGTGGCCCAAT	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.3582G>A	chrX.hg19:g.44949021G>A	ENSP00000367203:p.Trp1194*	47.0	0.0	.		37.0	29.0	.	NM_021140	Q52LL9|Q5JVQ7	Nonsense_Mutation	SNP	ENST00000377967.4	hg19	CCDS14265.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	39|39	7.566749|7.566749	0.98361|0.98361	.|.	.|.	ENSG00000147050|ENSG00000147050	ENST00000414389;ENST00000433797|ENST00000334516;ENST00000377967;ENST00000536777;ENST00000382899;ENST00000543216	.|.	.|.	.|.	5.16|5.16	5.16|5.16	0.70880|0.70880	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.45538|.	0.1347|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.42258|.	-0.9462|.	3|.	.|0.02654	.|T	.|1	-5.5328|-5.5328	17.8727|17.8727	0.88815|0.88815	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	T|X	792;837|891;1194;1149;1201;1115	.|.	.|ENSP00000334340:W891X	A|W	+|+	1|3	0|0	KDM6A|KDM6A	44833965|44833965	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	9.358000|9.358000	0.97109|0.97109	2.153000|2.153000	0.67306|0.67306	0.468000|0.468000	0.43344|0.43344	GCC|TGG	.	.	.	none		0.368	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140		A	44949021	G	A	44949021	4	1	121	1	0	0	0	0	0	1	0	0	8144	1212	42	2	3680	2	KDM6A	23	44949021	Nonsense_Mutation	SNP	G	TCGA-BQ-5886-01A-11D-1589-08	20859206	44949021	110321539	56	7721											
OR2G2	81470	hgsc.bcm.edu	37	chr1	247751788	247751788	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttctgtatttactaactattTtggggaataccaccatcatt	11	17	5	8	0	2	0	1	0	1	0	2	1	2	1	2	2	3	1	2	2	6	10			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr1:247751788T>C	ENST00000320065.1	+	1	127	c.127T>C	c.(127-129)Ttg>Ctg	p.L43L	RP11-978I15.10_ENST00000435333.1_RNA|RP11-978I15.10_ENST00000446347.1_RNA	NM_001001915.1	NP_001001915.1	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G, member 2	43						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)			ACTAACTATTTTGGGGAATAC	0.408																																					p.L43L		Atlas-SNP	.											.	OR2G2	88	.	0			c.T127C						PASS	.						227	217	220					1																	247751788		2203	4300	6503	SO:0001819	synonymous_variant	81470	exon1			ACTATTTTGGGGA	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.127T>C	chr1.hg19:g.247751788T>C		178.0	0.0	.		319.0	87.0	.	NM_001001915	Q5JQT2|Q6IEZ0	Silent	SNP	ENST00000320065.1	hg19	CCDS31092.1																																																																																			.	.	.	none		0.408	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1			C	247751788	T	C	247751788	2	2	122	1	0	0	0	0	0	0	0	1	11005	1838	64	3		3	OR2G2	1	247751788	Silent	SNP	T	TCGA-BQ-5887-01A-11D-1961-08		247751788	1498833	1	7722											
CCT4	10575	hgsc.bcm.edu	37	chr2	62115531	62115531	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatacctttggcggcggaaaTgttgctgaagcggatctggg	8	10	16	7	3	1	1	0	1	1	0	1	4	1	3	1	5	3	2	1	5	3	3	rs199542002		TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr2:62115531T>C	ENST00000394440.3	-	1	408	c.112A>G	c.(112-114)Att>Gtt	p.I38V	CCT4_ENST00000544185.1_5'UTR|CCT4_ENST00000538252.1_5'UTR|CCT4_ENST00000544079.1_Missense_Mutation_p.I38V|AC107081.5_ENST00000425779.1_RNA	NM_006430.3	NP_006421.2	P50991	TCPD_HUMAN	chaperonin containing TCP1, subunit 4 (delta)	38					'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)			GCGGCGGAAATGTTGCTGAAG	0.677																																					p.I38V		Atlas-SNP	.											.	CCT4	38	.	0			c.A112G						PASS	.	T	VAL/ILE	0,4404		0,0,2202	47	43	45		112	3.3	0.8	2		45	1,8599	1.2+/-3.3	0,1,4299	no	missense	CCT4	NM_006430.2	29	0,1,6501	CC,CT,TT		0.0116,0.0,0.0077	probably-damaging	38/540	62115531	1,13003	2202	4300	6502	SO:0001583	missense	10575	exon1			CGGAAATGTTGCT		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.112A>G	chr2.hg19:g.62115531T>C	ENSP00000377958:p.Ile38Val	40.0	0.0	.		50.0	23.0	.	NM_001256721	B2R6I3|B7Z8B1|F5H5W3|O14870|Q53QP9|Q96C51	Missense_Mutation	SNP	ENST00000394440.3	hg19	CCDS33206.1	.	.	.	.	.	.	.	.	.	.	T	17.95	3.513788	0.64522	0.0	1.16E-4	ENSG00000115484	ENST00000394440;ENST00000544079	T;T	0.12984	2.63;2.63	4.44	3.27	0.37495	.	0.053328	0.64402	D	0.000001	T	0.14570	0.0352	L	0.36672	1.1	0.80722	D	1	P;P	0.48834	0.916;0.847	P;B	0.47134	0.539;0.399	T	0.01520	-1.1334	10	0.87932	D	0	-12.7568	9.5232	0.39149	0.1581:0.0:0.0:0.8419	.	38;38	F5H5W3;P50991	.;TCPD_HUMAN	V	38	ENSP00000377958:I38V;ENSP00000443061:I38V	ENSP00000377958:I38V	I	-	1	0	CCT4	61969035	1.000000	0.71417	0.823000	0.32752	0.746000	0.42486	5.484000	0.66844	0.722000	0.32252	0.529000	0.55759	ATT	.	T|0.998;C|0.002	0.002	weak		0.677	CCT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325548.2			C	62115531	T	C	62115531	3	2	122	1	0	0	0	0	1	0	0	0	2957	1464	51	3	1563	3	CCT4	2	62115531	Missense_Mutation	SNP	T	TCGA-BQ-5887-01A-11D-1961-08		62115531	181083842	2	7723											
ZSWIM2	151112	hgsc.bcm.edu	37	chr2	187693177	187693177	+	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	cataggttaatttttttgaaTttgaattatctaatttgata	13	21	5	2	0	1	3	0	3	1	0	1	3	1	3	0	1	0	1	0	1	7	10			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr2:187693177T>A	ENST00000295131.2	-	9	1475	c.1436A>T	c.(1435-1437)aAt>aTt	p.N479I		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	479					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			TTTTTTTGAATTTGAATTATC	0.299																																					p.N479I		Atlas-SNP	.											.	ZSWIM2	119	.	0			c.A1436T						PASS	.						36	42	40					2																	187693177		2202	4298	6500	SO:0001583	missense	151112	exon9			TTTGAATTTGAAT	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"Zinc fingers, SWIM-type", "Zinc fingers, ZZ-type"	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.1436A>T	chr2.hg19:g.187693177T>A	ENSP00000295131:p.Asn479Ile	43.0	0.0	.		43.0	7.0	.	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Missense_Mutation	SNP	ENST00000295131.2	hg19	CCDS33348.1	.	.	.	.	.	.	.	.	.	.	T	6.741	0.505511	0.12822	.	.	ENSG00000163012	ENST00000295131	T	0.28895	1.59	5.6	1.83	0.25207	.	1.004620	0.08011	N	0.990290	T	0.21186	0.0510	L	0.32530	0.975	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.36890	-0.9729	10	0.87932	D	0	0.0079	1.3043	0.02085	0.1451:0.1617:0.1507:0.5425	.	479	Q8NEG5	ZSWM2_HUMAN	I	479	ENSP00000295131:N479I	ENSP00000295131:N479I	N	-	2	0	ZSWIM2	187401422	0.045000	0.20229	0.035000	0.18076	0.220000	0.24768	0.733000	0.26087	0.070000	0.16634	-0.376000	0.06991	AAT	.	.	.	none		0.299	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521		A	187693177	T	A	187693177	3	1	122	1	0	0	0	0	1	0	0	0	18253	1493	52	5	469	5	ZSWIM2	2	187693177	Missense_Mutation	SNP	T	TCGA-BQ-5887-01A-11D-1961-08	125577646	187693177	55506196	3	7724											
RCHY1	25898	hgsc.bcm.edu	37	chr4	76439476	76439476	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttgaccgctggcgccatcTtcccgggccgtcgccgccat	3	9	11	18	6	2	1	0	1	2	0	4	1	3	1	6	2	0	1	6	2	0	2			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr4:76439476T>C	ENST00000324439.5	-	1	419	c.21A>G	c.(19-21)gaA>gaG	p.E7E	RCHY1_ENST00000451788.1_Silent_p.E7E|THAP6_ENST00000514480.1_5'Flank|RCHY1_ENST00000512706.1_5'UTR|THAP6_ENST00000508105.1_5'Flank|THAP6_ENST00000504190.1_5'Flank|THAP6_ENST00000502620.1_5'Flank|RCHY1_ENST00000514021.1_Intron|THAP6_ENST00000507885.1_5'Flank|THAP6_ENST00000311638.3_5'Flank|RCHY1_ENST00000380840.2_Silent_p.E7E|THAP6_ENST00000507557.1_5'Flank|THAP6_ENST00000507556.1_5'Flank|THAP6_ENST00000380837.3_5'Flank|RCHY1_ENST00000513257.1_Silent_p.E7E	NM_001278536.1|NM_001278538.1|NM_001278539.1	NP_001265465.1|NP_001265467.1|NP_001265468.1	Q96PM5	ZN363_HUMAN	ring finger and CHY zinc finger domain containing 1, E3 ubiquitin protein ligase	7					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(2)|pancreas(1)	3			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			TGGCGCCATCTTCCCGGGCCG	0.602																																					p.E7E		Atlas-SNP	.											.	RCHY1	17	.	0			c.A21G						PASS	.						78	69	72					4																	76439476		2203	4300	6503	SO:0001819	synonymous_variant	25898	exon1			GCCATCTTCCCGG	AF255666	CCDS3567.1, CCDS34012.1, CCDS63990.1, CCDS63991.1, CCDS63992.1	4q21.1-q21.3	2014-02-17	2012-02-23	2004-03-30	ENSG00000163743	ENSG00000163743		"RING-type (C3HC4) zinc fingers"	17479	protein-coding gene	gene with protein product	"androgen-receptor N-terminal-interacting protein", "p53-induced protein with a RING-H2 domain", "zinc finger, CHY-type"	607680	"zinc finger protein 363", "ring finger and CHY zinc finger domain containing 1"	ZNF363		12654245	Standard	NM_015436		Approved	CHIMP, DKFZp586C1620, PRO1996, RNF199, ARNIP, PIRH2, ZCHY	uc003hik.3	Q96PM5	OTTHUMG00000130105	ENST00000324439.5:c.21A>G	chr4.hg19:g.76439476T>C		67.0	0.0	.		74.0	12.0	.	NM_001008925	B3KRG3|C7E541|C7E542|C7E543|D3YRV2|E7EMC8|E7ETW5|J3KPI0|Q2KN33|Q59GN7|Q86X26|Q96PR5	Silent	SNP	ENST00000324439.5	hg19	CCDS3567.1																																																																																			.	.	.	none		0.602	RCHY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252411.2	NM_015436		C	76439476	T	C	76439476	2	2	122	1	0	0	0	0	0	0	0	1	13190	1606	56	3		3	RCHY1	4	76439476	Silent	SNP	T	TCGA-BQ-5887-01A-11D-1961-08		76439476	114714800	4	7725											
GPR98	84059	hgsc.bcm.edu	37	chr5	90052799	90052799	+	Missense_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	atattctttacttaaagggcGctggggaagttattactgcc	10	14	10	7	1	1	0	0	0	1	0	1	1	1	1	1	3	3	2	1	3	7	7	rs200576500	byFrequency	TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr5:90052799G>A	ENST00000405460.2	+	57	11857	c.11761G>A	c.(11761-11763)Gct>Act	p.A3921T		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	3921	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)		CTTAAAGGGCGCTGGGGAAGT	0.388													G|||	2	0.000399361	0.0015	0	5008	,	,		16046	0		0	False		,,,				2504	0				p.A3921T		Atlas-SNP	.											.	GPR98	605	.	0			c.G11761A						PASS	.	G	THR/ALA	5,3673		0,5,1834	77	75	76		11761	2.3	0.1	5		76	0,8158		0,0,4079	yes	missense	GPR98	NM_032119.3	58	0,5,5913	AA,AG,GG		0.0,0.1359,0.0422	benign	3921/6307	90052799	5,11831	1839	4079	5918	SO:0001583	missense	84059	exon57			AAGGGCGCTGGGG	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.11761G>A	chr5.hg19:g.90052799G>A	ENSP00000384582:p.Ala3921Thr	110.0	0.0	.		109.0	26.0	.	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	G	0.526	-0.860029	0.02610	0.001359	0.0	ENSG00000164199	ENST00000405460;ENST00000296619	T	0.27256	1.68	5.3	2.27	0.28462	Na-Ca exchanger/integrin-beta4 (1);	0.732108	0.13525	N	0.381387	T	0.11879	0.0289	N	0.14661	0.345	0.22050	N	0.999396	B;B	0.23058	0.079;0.013	B;B	0.10450	0.005;0.002	T	0.25012	-1.0144	10	0.25751	T	0.34	.	4.1082	0.10047	0.2731:0.3558:0.3711:0.0	.	3921;3921	E7ETI5;Q8WXG9	.;GPR98_HUMAN	T	3921	ENSP00000384582:A3921T	ENSP00000296619:A3921T	A	+	1	0	GPR98	90088555	0.001000	0.12720	0.090000	0.20809	0.015000	0.08874	-0.111000	0.10807	0.694000	0.31654	0.467000	0.42956	GCT	.	.	.	weak		0.388	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		A	90052799	G	A	90052799	3	1	122	1	0	0	0	0	1	0	0	0	6728	1087	38	1	11987	1	GPR98	5	90052799	Missense_Mutation	SNP	G	TCGA-BQ-5887-01A-11D-1961-08		90052799	90862461	5	7726											
KDM3B	51780	hgsc.bcm.edu	37	chr5	137766032	137766032	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaccctccgtaagcgactctAtgaggagtatggcgtgcaag	10	8	13	10	3	1	1	0	1	1	0	2	4	2	2	2	2	2	3	2	2	4	3			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr5:137766032A>G	ENST00000314358.5	+	22	5188	c.4988A>G	c.(4987-4989)tAt>tGt	p.Y1663C	KDM3B_ENST00000394866.1_Missense_Mutation_p.Y1319C|KDM3B_ENST00000542866.1_Missense_Mutation_p.Y695C	NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	1663	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						AAGCGACTCTATGAGGAGTAT	0.542																																					p.Y1663C		Atlas-SNP	.											.	KDM3B	177	.	0			c.A4988G						PASS	.						146	136	140					5																	137766032		2203	4300	6503	SO:0001583	missense	51780	exon22			GACTCTATGAGGA	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.4988A>G	chr5.hg19:g.137766032A>G	ENSP00000326563:p.Tyr1663Cys	142.0	0.0	.		191.0	27.0	.	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Missense_Mutation	SNP	ENST00000314358.5	hg19	CCDS34242.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.178274	0.78564	.	.	ENSG00000120733	ENST00000314358;ENST00000545151;ENST00000394866;ENST00000542866	T;T;T	0.70631	-0.5;-0.5;-0.5	5.71	4.51	0.55191	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.056809	0.64402	D	0.000001	T	0.72550	0.3474	L	0.41824	1.3	0.58432	D	0.999997	P;P	0.46457	0.878;0.786	P;P	0.54544	0.575;0.755	T	0.72181	-0.4368	10	0.51188	T	0.08	-12.6174	11.8878	0.52613	0.8691:0.0:0.0:0.1309	.	1319;1663	Q7LBC6-2;Q7LBC6	.;KDM3B_HUMAN	C	1663;1453;1319;695	ENSP00000326563:Y1663C;ENSP00000378335:Y1319C;ENSP00000439462:Y695C	ENSP00000326563:Y1663C	Y	+	2	0	KDM3B	137793931	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	4.941000	0.63540	0.939000	0.37446	0.533000	0.62120	TAT	.	.	.	none		0.542	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604		G	137766032	A	G	137766032	3	3	122	1	0	0	0	0	1	0	0	0	8134	449	16	3	5074	3	KDM3B	5	137766032	Missense_Mutation	SNP	A	TCGA-BQ-5887-01A-11D-1961-08	47713233	137766032	43149228	6	7727											
C6orf211	79624	hgsc.bcm.edu	37	chr6	151789725	151789725	+	Missense_Mutation	SNP	T	T	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	tttaatattagccgacttctTgttgtcctctgaactggcta	8	17	7	9	1	2	1	0	1	2	0	3	2	3	1	2	1	2	2	2	1	5	8			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr6:151789725T>G	ENST00000367294.3	+	5	1065	c.806T>G	c.(805-807)tTg>tGg	p.L269W	C6orf211_ENST00000545879.1_Missense_Mutation_p.L150W	NM_024573.1	NP_078849.1	Q9H993	CF211_HUMAN	chromosome 6 open reading frame 211	269										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)		GCCGACTTCTTGTTGTCCTCT	0.328																																					p.L269W		Atlas-SNP	.											.	C6orf211	30	.	0			c.T806G						PASS	.						132	138	136					6																	151789725		2203	4300	6503	SO:0001583	missense	79624	exon5			ACTTCTTGTTGTC	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.806T>G	chr6.hg19:g.151789725T>G	ENSP00000356263:p.Leu269Trp	169.0	0.0	.		141.0	12.0	.	NM_024573	Q96FC6|Q9UFY5	Missense_Mutation	SNP	ENST00000367294.3	hg19	CCDS5233.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.593869	0.86953	.	.	ENSG00000146476	ENST00000367294;ENST00000545879	T;T	0.23552	1.9;1.9	6.02	6.02	0.97574	Domain of unknown function DUF89 (2);	0.141422	0.45126	D	0.000394	T	0.59959	0.2232	H	0.95884	3.735	0.58432	D	0.999993	D	0.89917	1.0	D	0.85130	0.997	T	0.74682	-0.3583	10	0.87932	D	0	.	16.5494	0.84464	0.0:0.0:0.0:1.0	.	269	Q9H993	CF211_HUMAN	W	269;150	ENSP00000356263:L269W;ENSP00000444121:L150W	ENSP00000356263:L269W	L	+	2	0	C6orf211	151831418	1.000000	0.71417	0.087000	0.20705	0.990000	0.78478	7.963000	0.87922	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		G	151789725	T	G	151789725	3	3	122	1	0	0	0	0	1	0	0	0	2356	1821	63	5	824	5	C6orf211	6	151789725	Missense_Mutation	SNP	T	TCGA-BQ-5887-01A-11D-1961-08		151789725	19325342	7	7728											
COL28A1	340267	hgsc.bcm.edu	37	chr7	7412962	7412963	+	Missense_Mutation	DNP	CC	CC	AT																															cacagccaacttgaagtcatCcttgctggagaactgcttca																										TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr7:7412962_7412963CC>AT	ENST00000399429.3	-	32	2714_2715	c.2574_2575GG>AT	c.(2572-2577)aaGGat>aaATat	p.D859Y		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	859	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		TTGAAGTCATCCTTGCTGGAGA	0.515																																					p.D859Y|p.K858K		Atlas-SNP	.											.	COL28A1	113	.	0			c.G2575T|c.G2574A						PASS	.																																			SO:0001583	missense	340267	exon32			AGTCATCCTTGCT|GTCATCCTTGCTG	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.2574_2575delinsAT	chr7.hg19:g.7412962_7412963delinsAT	ENSP00000382356:p.Asp859Tyr	90.0|92.0	0.0	.		114.0|116.0	23.0|25.0	.	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Missense_Mutation|Silent	SNP	ENST00000399429.3	hg19	CCDS43553.1																																																																																			.	.	.	none		0.515	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763		AT	7412963	CC	AT	7412962	3	1	122	1	0	0	0	0	1	0	0	0	3688	855	30	4	818	4	COL28A1	7	7412962	Missense_Mutation	DNP	CC	TCGA-BQ-5887-01A-11D-1961-08		7412962	151725701	8	7729											
SVIL	6840	hgsc.bcm.edu	37	chr10	29788191	29788191	+	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	tctctcgactttctgtgaccCgctgttcataaatgtacaga	9	14	7	11	2	3	2	1	1	2	1	5	3	3	2	1	0	1	3	1	0	3	4	rs372472784		TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr10:29788191C>A	ENST00000355867.4	-	18	4270	c.3518G>T	c.(3517-3519)cGg>cTg	p.R1173L	SVIL_ENST00000535393.1_Splice_Site_p.R87L|SVIL_ENST00000375398.2_Splice_Site_p.R1173L|SVIL_ENST00000375400.3_Splice_Site_p.R747L|SVIL_ENST00000538146.1_5'Flank	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1173					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)				TTCTGTGACCCGCTGTTCATA	0.507																																					p.R1173L		Atlas-SNP	.											.	SVIL	226	.	0			c.G3518T						PASS	.						79	68	72					10																	29788191		2203	4300	6503	SO:0001630	splice_region_variant	6840	exon18			GTGACCCGCTGTT	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.3517-1G>T	chr10.hg19:g.29788191C>A		91.0	0.0	.		97.0	4.0	.	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	hg19	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	C	13.17	2.156495	0.38119	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867;ENST00000535393;ENST00000535994	T;T;T;T	0.14266	2.63;2.66;2.66;2.52	4.13	2.28	0.28536	.	0.324362	0.34853	N	0.003624	T	0.17195	0.0413	M	0.68952	2.095	0.80722	D	1	B;P;B	0.41159	0.403;0.74;0.38	B;B;B	0.41374	0.119;0.355;0.274	T	0.02042	-1.1224	10	0.59425	D	0.04	-10.9371	10.3423	0.43887	0.0:0.8378:0.0:0.1622	.	87;747;1173	F5H2Q5;O95425-2;O95425	.;.;SVIL_HUMAN	L	747;1173;1173;87;127	ENSP00000364549:R747L;ENSP00000364547:R1173L;ENSP00000348128:R1173L;ENSP00000445472:R87L	ENSP00000348128:R1173L	R	-	2	0	SVIL	29828197	0.999000	0.42202	0.998000	0.56505	0.608000	0.37181	2.104000	0.41815	0.417000	0.25871	-1.100000	0.02121	CGG	.	.	.	none		0.507	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		Missense_Mutation	A	29788191	C	A	29788191	5	1	122	1	0	0	0	0	0	0	1	0	15433	666	23	4	3210	4	SVIL	10	29788191	Splice_Site	SNP	C	TCGA-BQ-5887-01A-11D-1961-08		29788191	105746556	9	7730											
AKAP3	10566	hgsc.bcm.edu	37	chr12	4736579	4736579	+	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	gaggttgccaatatcttcagGgtactcaaaggaaatgtctg	12	11	11	7	0	4	0	2	0	2	0	4	2	4	1	1	3	2	2	1	3	5	4			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr12:4736579G>C	ENST00000545990.2	-	5	2013	c.1489C>G	c.(1489-1491)Cct>Gct	p.P497A	AKAP3_ENST00000228850.1_Missense_Mutation_p.P497A|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	497					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						ATATCTTCAGGGTACTCAAAG	0.463																																					p.P497A		Atlas-SNP	.											.	AKAP3	212	.	0			c.C1489G						PASS	.						67	64	65					12																	4736579		2203	4300	6503	SO:0001583	missense	10566	exon4			CTTCAGGGTACTC	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.1489C>G	chr12.hg19:g.4736579G>C	ENSP00000440994:p.Pro497Ala	48.0	0.0	.		47.0	10.0	.	NM_006422	O75945|Q86X01|Q9UM61	Missense_Mutation	SNP	ENST00000545990.2	hg19	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	G	0.811	-0.752022	0.03041	.	.	ENSG00000111254	ENST00000228850;ENST00000545990	T;T	0.11821	2.74;2.74	4.5	-1.34	0.09143	A-kinase anchor 110kDa, C-terminal (1);	0.887861	0.09758	N	0.759675	T	0.13457	0.0326	M	0.68317	2.08	0.09310	N	1	B	0.29481	0.245	B	0.32090	0.14	T	0.40194	-0.9576	10	0.72032	D	0.01	0.0048	1.207	0.01896	0.1864:0.1329:0.362:0.3187	.	497	O75969	AKAP3_HUMAN	A	497	ENSP00000228850:P497A;ENSP00000440994:P497A	ENSP00000228850:P497A	P	-	1	0	AKAP3	4606840	0.215000	0.23574	0.000000	0.03702	0.001000	0.01503	1.832000	0.39151	-0.187000	0.10516	-0.136000	0.14681	CCT	.	.	.	none		0.463	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422		C	4736579	G	C	4736579	3	2	122	1	0	0	0	0	1	0	0	0	452	1232	43	4	1080	4	AKAP3	12	4736579	Missense_Mutation	SNP	G	TCGA-BQ-5887-01A-11D-1961-08		4736579	129115316	10	7731											
ATXN2	6311	hgsc.bcm.edu	37	chr12	111923516	111923516	+	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	acatcaaattctatgacttaCttgcacgcctgggctcactg	10	12	7	12	1	3	1	2	1	1	0	3	1	3	1	1	1	2	2	1	1	3	4			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr12:111923516C>A	ENST00000377617.3	-	17	3099		c.e17+1		AC002395.1_ENST00000581907.1_RNA|ATXN2_ENST00000542287.2_Splice_Site|ATXN2_ENST00000389153.4_Splice_Site|ATXN2_ENST00000550104.1_Splice_Site|ATXN2_ENST00000535949.1_Splice_Site|ATXN2_ENST00000608853.1_Splice_Site	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2						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						CTATGACTTACTTGCACGCCT	0.438																																					.		Atlas-SNP	.											.	ATXN2	99	.	0			c.2937+1G>T						PASS	.						165	142	150					12																	111923516		2203	4300	6503	SO:0001630	splice_region_variant	6311	exon18			GACTTACTTGCAC	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.2937+1G>T	chr12.hg19:g.111923516C>A		67.0	0.0	.		88.0	6.0	.	NM_002973	A6NLD4|Q6ZQZ7|Q99493	Splice_Site	SNP	ENST00000377617.3	hg19	CCDS31902.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.146986	0.77888	.	.	ENSG00000204842	ENST00000389154;ENST00000389153;ENST00000377617;ENST00000550104;ENST00000542287;ENST00000535949	.	.	.	5.71	5.71	0.89125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8673	0.96808	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ATXN2	110407899	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.076000	0.71267	2.709000	0.92574	0.655000	0.94253	.	.	.	.	none		0.438	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973	Intron	A	111923516	C	A	111923516	5	1	122	1	0	0	0	0	0	0	1	0	1211	579	20	4	1039	4	ATXN2	12	111923516	Splice_Site	SNP	C	TCGA-BQ-5887-01A-11D-1961-08	107186937	111923516	21928379	11	7732											
FLII	2314	hgsc.bcm.edu	37	chr17	18149935	18149935	+	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	ttcccagggaagaggctctcGaacttcttttgcaggctgaa	9	11	11	10	1	2	2	0	1	2	1	4	4	3	3	1	3	2	3	1	3	3	4			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr17:18149935G>A	ENST00000327031.4	-	23	3249	c.3024C>T	c.(3022-3024)ttC>ttT	p.F1008F	FLII_ENST00000545457.2_Silent_p.F953F|FLII_ENST00000579294.1_Silent_p.F997F|FLII_ENST00000578558.1_Intron|FLII_ENST00000379450.4_Silent_p.F922F	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	1008					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)					AGAGGCTCTCGAACTTCTTTT	0.627																																					p.F1008F		Atlas-SNP	.											.	FLII	79	.	0			c.C3024T						PASS	.						60	53	56					17																	18149935		2203	4300	6503	SO:0001819	synonymous_variant	2314	exon23			GCTCTCGAACTTC	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.3024C>T	chr17.hg19:g.18149935G>A		19.0	0.0	.		52.0	13.0	.	NM_002018	B4DIL0|F5H407|J3QLG3	Silent	SNP	ENST00000327031.4	hg19	CCDS11192.1																																																																																			.	.	.	none		0.627	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018		A	18149935	G	A	18149935	2	1	122	1	0	0	0	0	0	0	0	1	5932	1049	37	1		1	FLII	17	18149935	Silent	SNP	G	TCGA-BQ-5887-01A-11D-1961-08		18149935	63045275	12	7733											
FDXR	2232	hgsc.bcm.edu	37	chr17	72860612	72860612	+	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	ggcccctcacccttgatcttGtcctggagacccaagaaatc	9	9	8	15	0	2	3	1	1	1	2	4	4	3	3	5	2	0	0	5	2	2	2			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr17:72860612G>C	ENST00000293195.5	-	8	870	c.792C>G	c.(790-792)gaC>gaG	p.D264E	FDXR_ENST00000420580.2_Missense_Mutation_p.D224E|FDXR_ENST00000583917.1_Intron|FDXR_ENST00000442102.2_Missense_Mutation_p.D307E|FDXR_ENST00000455107.2_Missense_Mutation_p.D220E|GRIN2C_ENST00000578159.1_5'Flank|FDXR_ENST00000581969.1_5'Flank|FDXR_ENST00000544854.1_Missense_Mutation_p.D212E|FDXR_ENST00000413947.2_Missense_Mutation_p.D295E|FDXR_ENST00000581530.1_Missense_Mutation_p.D270E|FDXR_ENST00000582944.1_Missense_Mutation_p.D256E	NM_001258014.1|NM_004110.3|NM_024417.2	NP_001244943.1|NP_004101.2|NP_077728.2	P22570	ADRO_HUMAN	ferredoxin reductase	264					cholesterol metabolic process (GO:0008203)|generation of precursor metabolites and energy (GO:0006091)|NADPH oxidation (GO:0070995)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ferredoxin-NADP+ reductase activity (GO:0004324)|NADPH binding (GO:0070402)|NADPH-adrenodoxin reductase activity (GO:0015039)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16	all_lung(278;0.172)|Lung NSC(278;0.207)				Flavin adenine dinucleotide(DB03147)	CCTTGATCTTGTCCTGGAGAC	0.612											OREG0024720	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D307E		Atlas-SNP	.											.	FDXR	68	.	0			c.C921G						PASS	.						42	47	45					17																	72860612		2203	4300	6503	SO:0001583	missense	2232	exon8			GATCTTGTCCTGG	J03826	CCDS11707.1, CCDS58591.1, CCDS58592.1, CCDS58593.1, CCDS58594.1, CCDS58595.1, CCDS58596.1	17q25.1	2013-06-18			ENSG00000161513	ENSG00000161513	1.18.1.6		3642	protein-coding gene	gene with protein product	"adrenodoxin-NADP(+) reductase", "adrenodoxin reductase"	103270		ADXR		2969697	Standard	NM_001258014		Approved		uc010wrl.2	P22570	OTTHUMG00000179026	ENST00000293195.5:c.792C>G	chr17.hg19:g.72860612G>C	ENSP00000293195:p.Asp264Glu	50.0	0.0	.	1140	88.0	7.0	.	NM_001258012	B4DDI7|B4DHX5|B4DQQ4|B4DX24|B7Z7G2|E7EQC1|Q13716|Q4PJI0|Q9BU12	Missense_Mutation	SNP	ENST00000293195.5	hg19	CCDS58593.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.556819	0.00910	.	.	ENSG00000161513	ENST00000420580;ENST00000544854;ENST00000293195;ENST00000455107;ENST00000442102;ENST00000413947	T;T;T;T;T	0.16324	2.35;2.35;2.35;2.35;2.35	4.65	2.43	0.29744	.	0.279368	0.40554	N	0.001071	T	0.04724	0.0128	N	0.04162	-0.26	0.33484	D	0.587776	B;B;B;B;B;B;B;B;B	0.06786	0.001;0.001;0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B;B	0.09377	0.004;0.003;0.0;0.0;0.0;0.0;0.0;0.0;0.0	T	0.31613	-0.9937	10	0.05351	T	0.99	-16.3668	2.2561	0.04055	0.1249:0.3442:0.3522:0.1788	.	224;307;295;262;212;264;256;264;270	B4DQQ4;B4DHX5;E7EQC1;B4DDI9;B7Z7G2;Q6GSK2;B4DX24;P22570;P22570-2	.;.;.;.;.;.;.;ADRO_HUMAN;.	E	224;212;270;220;307;295	ENSP00000414172:D224E;ENSP00000445432:D212E;ENSP00000390875:D220E;ENSP00000416515:D307E;ENSP00000408595:D295E	ENSP00000293195:D270E	D	-	3	2	FDXR	70372207	0.964000	0.33143	1.000000	0.80357	0.295000	0.27426	0.151000	0.16283	0.910000	0.36722	0.561000	0.74099	GAC	.	.	.	none		0.612	FDXR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000444449.1	NM_004110		C	72860612	G	C	72860612	3	2	122	1	0	0	0	0	1	0	0	0	5814	1368	48	4	703	4	FDXR	17	72860612	Missense_Mutation	SNP	G	TCGA-BQ-5887-01A-11D-1961-08	54710677	72860612	8334598	13	7734											
RNMT	8731	hgsc.bcm.edu	37	chr18	13731629	13731630	+	Frame_Shift_Ins	INS	-	-	T																															attaatgaaaacacaacagcINSttctgggactgggctttctg																										TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr18:13731629_13731630insT	ENST00000383314.2	+	3	353_354	c.113_114insT	c.(112-117)gcttctfs	p.S39fs	RNMT_ENST00000592764.1_Frame_Shift_Ins_p.S39fs|RNMT_ENST00000262173.3_Frame_Shift_Ins_p.S39fs|RNMT_ENST00000589866.1_Frame_Shift_Ins_p.S39fs|RNMT_ENST00000535051.1_Intron|RNMT_ENST00000543302.2_Frame_Shift_Ins_p.S39fs			O43148	MCES_HUMAN	RNA (guanine-7-) methyltransferase	39					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|RNA (guanine-N7)-methylation (GO:0036265)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|receptor complex (GO:0043235)	mRNA (guanine-N7-)-methyltransferase activity (GO:0004482)|RNA binding (GO:0003723)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|skin(2)	18						AACACAACAGCTTCTGGGACTG	0.371																																					p.A38fs	GBM(29;474 594 19092 36647 41529)	Atlas-INDEL	.											.	RNMT	42	.	0			c.113_114insT						PASS	.																																			SO:0001589	frameshift_variant	8731	exon3			.	AF067791	CCDS11867.1	18p11.21	2008-05-14			ENSG00000101654	ENSG00000101654	2.1.1.56		10075	protein-coding gene	gene with protein product		603514				9828141, 9705270	Standard	NM_003799		Approved	RG7MT1	uc002ksl.1	O43148	OTTHUMG00000131718	ENST00000383314.2:c.115dupT	chr18.hg19:g.13731631_13731631dupT	ENSP00000372804:p.Ser39fs	222.0	0.0	0		140.0	31.0	0.221429	NM_003799	B0YJ90|D3DUJ5|O94996|Q9UIJ9	Frame_Shift_Ins	INS	ENST00000383314.2	hg19	CCDS11867.1																																																																																			.	.	.	none		0.371	RNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254636.1	NM_003799		T	13731630	-	T	13731629	7	5	122	1	0	1	1	0	0	0	0	0	13519	797	28	0	115	0	RNMT	18	13731629	Frame_Shift_Ins	INS	-	TCGA-BQ-5887-01A-11D-1961-08		13731629	64345619	14	7735											
NLRP7	199713	hgsc.bcm.edu	37	chr19	55452315	55452315	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacctggctttgctaactcCgagtcttcttctgcatctcc	5	14	6	16	1	4	0	0	0	4	0	6	1	5	0	4	1	3	3	4	1	1	4			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr19:55452315C>T	ENST00000590030.1	-	2	376	c.336G>A	c.(334-336)tcG>tcA	p.S112S	NLRP7_ENST00000446217.1_Silent_p.S140S|NLRP7_ENST00000592784.1_Silent_p.S112S|NLRP7_ENST00000448121.2_Silent_p.S112S|NLRP7_ENST00000588756.1_Silent_p.S112S|NLRP7_ENST00000340844.2_Silent_p.S112S|NLRP7_ENST00000328092.5_Silent_p.S112S			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	112							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)		TTGCTAACTCCGAGTCTTCTT	0.433																																					p.S112S		Atlas-SNP	.											.	NLRP7	411	.	0			c.G336A						PASS	.						239	189	206					19																	55452315		2203	4300	6503	SO:0001819	synonymous_variant	199713	exon3			TAACTCCGAGTCT	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.336G>A	chr19.hg19:g.55452315C>T		215.0	0.0	.		255.0	60.0	.	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Silent	SNP	ENST00000590030.1	hg19	CCDS33109.1																																																																																			.	.	.	none		0.433	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		T	55452315	C	T	55452315	2	4	122	1	0	0	0	0	0	0	0	1	10489	639	23	1		1	NLRP7	19	55452315	Silent	SNP	C	TCGA-BQ-5887-01A-11D-1961-08		55452315	3676668	15	7736											
PRIC285	85441	hgsc.bcm.edu	37	chr20	62198513	62198513	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaagaccaggcggctctgcCgcgccacctcgtgagtctcc	6	6	13	16	4	2	2	0	1	2	1	4	3	2	3	5	3	1	1	5	3	1	0			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr20:62198513C>T	ENST00000467148.1	-	6	2267	c.2198G>A	c.(2197-2199)cGg>cAg	p.R733Q	HELZ2_ENST00000427522.2_Missense_Mutation_p.R164Q|HELZ2_ENST00000479540.1_5'Flank	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	733	Interaction with THRAP3.				cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										GCGGCTCTGCCGCGCCACCTC	0.662																																					p.R733Q		Atlas-SNP	.											.	.	.	.	0			c.G2198A						PASS	.						42	45	44					20																	62198513		2201	4296	6497	SO:0001583	missense	85441	exon7			CTCTGCCGCGCCA	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.2198G>A	chr20.hg19:g.62198513C>T	ENSP00000417401:p.Arg733Gln	91.0	0.0	.		156.0	9.0	.	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	hg19	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	C	0.028	-1.354760	0.01256	.	.	ENSG00000130589	ENST00000427522;ENST00000467148	D;D	0.92199	-2.99;-2.99	5.06	-10.1	0.00402	.	1.876900	0.02583	N	0.099118	T	0.75027	0.3794	N	0.04880	-0.145	0.09310	N	1	B;B	0.16603	0.018;0.014	B;B	0.06405	0.002;0.001	T	0.70296	-0.4911	10	0.05959	T	0.93	-12.0678	6.0815	0.19944	0.1162:0.2139:0.0711:0.5987	.	733;164	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	Q	164;733	ENSP00000393257:R164Q;ENSP00000417401:R733Q	ENSP00000393257:R164Q	R	-	2	0	RP4-697K14.7	61668957	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.789000	0.04609	-1.726000	0.01370	-1.028000	0.02416	CGG	.	.	.	none		0.662	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		T	62198513	C	T	62198513	3	4	122	1	0	0	0	0	1	0	0	0	12495	652	23	1	5807	1	PRIC285	20	62198513	Missense_Mutation	SNP	C	TCGA-BQ-5887-01A-11D-1961-08		62198513	827007	16	7737											
KHDRBS1	10657	hgsc.bcm.edu	37	chr1	32508212	32508212	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcatacagagagcacccatAtggacgttattaaaaacaaa	19	7	7	8	1	0	1	0	0	0	1	0	3	0	2	1	1	4	3	1	1	7	4			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr1:32508212A>G	ENST00000327300.7	+	9	1486	c.1319A>G	c.(1318-1320)tAt>tGt	p.Y440C	KHDRBS1_ENST00000492989.1_Missense_Mutation_p.Y401C|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)				GAGCACCCATATGGACGTTAT	0.483																																					p.Y440C	Ovarian(173;401 1982 12359 31110 42403)	Atlas-SNP	.											.	KHDRBS1	34	.	0			c.A1319G						PASS	.						59	57	58					1																	32508212		2203	4300	6503	SO:0001583	missense	10657	exon9			ACCCATATGGACG	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.1319A>G	chr1.hg19:g.32508212A>G	ENSP00000313829:p.Tyr440Cys	66.0	0.0	.		58.0	13.0	.	NM_006559		Missense_Mutation	SNP	ENST00000327300.7	hg19	CCDS350.1	.	.	.	.	.	.	.	.	.	.	A	13.93	2.382684	0.42207	.	.	ENSG00000121774	ENST00000327300;ENST00000492989;ENST00000355201	T;T	0.71103	-0.54;-0.51	5.85	4.72	0.59763	.	0.057453	0.64402	D	0.000001	T	0.81735	0.4885	M	0.78456	2.415	0.80722	D	1	D;D	0.69078	0.996;0.997	P;D	0.63192	0.819;0.912	D	0.83637	0.0148	10	0.87932	D	0	.	12.1125	0.53848	0.9331:0.0:0.0668:0.0	.	440;401	Q07666;Q07666-3	KHDR1_HUMAN;.	C	440;401;416	ENSP00000313829:Y440C;ENSP00000417731:Y401C	ENSP00000313829:Y440C	Y	+	2	0	KHDRBS1	32280799	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	8.716000	0.91420	1.156000	0.42514	-0.256000	0.11100	TAT	.	.	.	none		0.483	KHDRBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011199.4	NM_006559		G	32508212	A	G	32508212	3	3	123	1	0	0	0	0	1	0	0	0	8153	449	16	3	1353	3	KHDRBS1	1	32508212	Missense_Mutation	SNP	A	TCGA-BQ-5888-01A-11D-1589-08		32508212	216742409	1	7738											
TTLL7	79739	hgsc.bcm.edu	37	chr1	84348653	84348653	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtgaacaagtacctggaatTaccccagtcaggaccaatgc	13	8	9	11	0	1	1	1	1	0	0	1	3	1	3	4	2	4	1	4	2	6	2			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr1:84348653T>C	ENST00000260505.8	-	20	2913	c.2536A>G	c.(2536-2538)Aat>Gat	p.N846D	TTLL7_ENST00000477524.1_5'UTR	NM_024686.4	NP_078962.4	Q6ZT98	TTLL7_HUMAN	tubulin tyrosine ligase-like family, member 7	846					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)			kidney(1)|large_intestine(8)|lung(15)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29				all cancers(265;0.0126)|Epithelial(280;0.0372)|OV - Ovarian serous cystadenocarcinoma(397;0.16)		TACCTGGAATTACCCCAGTCA	0.398																																					p.N846D		Atlas-SNP	.											.	TTLL7	93	.	0			c.A2536G						PASS	.						156	150	152					1																	84348653		2203	4300	6503	SO:0001583	missense	79739	exon20			TGGAATTACCCCA	AY170843	CCDS690.2	1p31.1	2013-02-14			ENSG00000137941	ENSG00000137941		"Tubulin tyrosine ligase-like family"	26242	protein-coding gene	gene with protein product						15890843	Standard	XM_005271208		Approved	FLJ23033	uc001djc.3	Q6ZT98	OTTHUMG00000009932	ENST00000260505.8:c.2536A>G	chr1.hg19:g.84348653T>C	ENSP00000260505:p.Asn846Asp	209.0	0.0	.		162.0	21.0	.	NM_024686	Q5TAX8|Q5TAX9|Q6P990|Q86YS1|Q9H5U4	Missense_Mutation	SNP	ENST00000260505.8	hg19	CCDS690.2	.	.	.	.	.	.	.	.	.	.	T	11.08	1.532905	0.27387	.	.	ENSG00000137941	ENST00000260505	T	0.03004	4.08	5.5	1.79	0.24919	.	0.504331	0.23351	N	0.049127	T	0.00468	0.0015	N	0.04880	-0.145	0.28908	N	0.892872	B	0.06786	0.001	B	0.04013	0.001	T	0.44711	-0.9310	10	0.12766	T	0.61	.	3.8611	0.08996	0.0:0.188:0.414:0.398	.	846	Q6ZT98	TTLL7_HUMAN	D	846	ENSP00000260505:N846D	ENSP00000260505:N846D	N	-	1	0	TTLL7	84121241	1.000000	0.71417	0.971000	0.41717	0.928000	0.56348	3.636000	0.54317	0.417000	0.25871	-0.321000	0.08615	AAT	.	.	.	none		0.398	TTLL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027498.1	NM_024686		C	84348653	T	C	84348653	3	2	123	1	0	0	0	0	1	0	0	0	16744	1754	61	3	135	3	TTLL7	1	84348653	Missense_Mutation	SNP	T	TCGA-BQ-5888-01A-11D-1589-08	51840441	84348653	164901968	2	7739											
CFH	3075	hgsc.bcm.edu	37	chr1	196706023	196706023	+	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	caatatgacaaccacactgaAttatcgggatggagaaaaag	18	7	9	7	1	0	3	0	2	0	1	1	5	0	4	1	2	1	0	1	2	7	2			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr1:196706023A>T	ENST00000367429.4	+	16	2723	c.2483A>T	c.(2482-2484)aAt>aTt	p.N828I		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	828	Sushi 14. {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						ACCACACTGAATTATCGGGAT	0.333																																					p.N828I		Atlas-SNP	.											.	CFH	251	.	0			c.A2483T						PASS	.						65	62	63					1																	196706023		2203	4300	6503	SO:0001583	missense	3075	exon16			CACTGAATTATCG	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.2483A>T	chr1.hg19:g.196706023A>T	ENSP00000356399:p.Asn828Ile	84.0	0.0	.		61.0	6.0	.	NM_000186	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Missense_Mutation	SNP	ENST00000367429.4	hg19	CCDS1385.1	.	.	.	.	.	.	.	.	.	.	.	12.36	1.913921	0.33815	.	.	ENSG00000000971	ENST00000367429	T	0.65732	-0.17	5.91	3.6	0.41247	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.69735	0.3144	M	0.73372	2.23	0.80722	D	1	D	0.60160	0.987	P	0.59357	0.856	T	0.68217	-0.5467	9	0.42905	T	0.14	.	6.5067	0.22198	0.7623:0.1583:0.0794:0.0	.	828	P08603	CFAH_HUMAN	I	828	ENSP00000356399:N828I	ENSP00000356399:N828I	N	+	2	0	CFH	194972646	0.999000	0.42202	0.929000	0.37066	0.092000	0.18411	1.560000	0.36331	1.049000	0.40321	0.454000	0.30748	AAT	.	.	.	none		0.333	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186		T	196706023	A	T	196706023	3	4	123	1	0	0	0	0	1	0	0	0	3285	101	4	5	2563	5	CFH	1	196706023	Missense_Mutation	SNP	A	TCGA-BQ-5888-01A-11D-1589-08	112357370	196706023	52544598	3	7740											
DIS3L2	129563	hgsc.bcm.edu	37	chr2	233075106	233075106	+	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	atgccctctcctgcaagccaCtcgctgacggtaggatggaa	9	8	11	13	2	1	1	0	1	1	0	3	3	1	3	3	3	3	3	3	3	3	1			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr2:233075106C>G	ENST00000409307.1	+	9	1195	c.1195C>G	c.(1195-1197)Ctc>Gtc	p.L399V	DIS3L2_ENST00000273009.6_Missense_Mutation_p.L399V|DIS3L2_ENST00000325385.7_Missense_Mutation_p.L399V					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)		CTGCAAGCCACTCGCTGACGG	0.512																																					p.L399V		Atlas-SNP	.											.	DIS3L2	77	.	0			c.C1195G						PASS	.						97	98	98					2																	233075106		2074	4234	6308	SO:0001583	missense	129563	exon10			AAGCCACTCGCTG	BC026166	CCDS42834.1, CCDS58752.1, CCDS58753.1	2q37.1	2014-09-17	2014-03-05		ENSG00000144535	ENSG00000144535			28648	protein-coding gene	gene with protein product		614184	"family with sequence similarity 6, member A", "DIS3 mitotic control homolog (S. cerevisiae)-like 2"	FAM6A		22306653, 23503588	Standard	NM_152383		Approved	FLJ36974, MGC42174	uc010fxz.3	Q8IYB7	OTTHUMG00000153385	ENST00000409307.1:c.1195C>G	chr2.hg19:g.233075106C>G	ENSP00000386799:p.Leu399Val	77.0	0.0	.		79.0	9.0	.	NM_152383		Missense_Mutation	SNP	ENST00000409307.1	hg19	CCDS42834.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.954379	0.73902	.	.	ENSG00000144535	ENST00000273009;ENST00000542873;ENST00000325385;ENST00000431466;ENST00000409307;ENST00000424049	T;T;T;T	0.37915	1.17;1.17;1.17;1.17	5.16	5.16	0.70880	Ribonuclease II/R (2);	0.000000	0.85682	D	0.000000	T	0.62159	0.2405	M	0.79693	2.465	0.80722	D	1	D	0.71674	0.998	D	0.73380	0.98	T	0.67409	-0.5678	10	0.72032	D	0.01	-16.4035	15.5539	0.76177	0.0:1.0:0.0:0.0	.	399	Q8IYB7	DI3L2_HUMAN	V	399;399;399;399;399;34	ENSP00000273009:L399V;ENSP00000315569:L399V;ENSP00000386799:L399V;ENSP00000415419:L34V	ENSP00000273009:L399V	L	+	1	0	DIS3L2	232783350	0.994000	0.37717	0.445000	0.26908	0.945000	0.59286	3.829000	0.55760	2.381000	0.81170	0.455000	0.32223	CTC	.	.	.	none		0.512	DIS3L2-015	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330988.1	NM_152383		G	233075106	C	G	233075106	3	3	123	1	0	0	0	0	1	0	0	0	4539	565	20	4	1229	4	DIS3L2	2	233075106	Missense_Mutation	SNP	C	TCGA-BQ-5888-01A-11D-1589-08		233075106	10124267	4	7741											
OTOL1	131149	hgsc.bcm.edu	37	chr3	161221062	161221062	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaggggaggaaaaggacagAaaggtgaggggggtatgaaa	17	3	20	1	0	0	4	0	2	0	2	0	7	0	7	0	8	0	1	0	8	5	1			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr3:161221062A>G	ENST00000327928.4	+	4	766	c.766A>G	c.(766-768)Aaa>Gaa	p.K256E		NM_001080440.1	NP_001073909.1	A6NHN0	OTOL1_HUMAN	otolin 1	256	Collagen-like 2.					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						AAAAGGACAGAAAGGTGAGGG	0.582																																					p.K256E		Atlas-SNP	.											.	OTOL1	63	.	0			c.A766G						PASS	.						6	6	6					3																	161221062		1882	4058	5940	SO:0001583	missense	131149	exon4			GGACAGAAAGGTG		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.766A>G	chr3.hg19:g.161221062A>G	ENSP00000330808:p.Lys256Glu	4.0	0.0	.		4.0	4.0	.	NM_001080440		Missense_Mutation	SNP	ENST00000327928.4	hg19	CCDS46948.1	.	.	.	.	.	.	.	.	.	.	A	14.65	2.600002	0.46318	.	.	ENSG00000182447	ENST00000327928	D	0.93247	-3.19	4.79	3.6	0.41247	.	0.260709	0.36519	N	0.002555	D	0.93713	0.7991	M	0.74546	2.27	0.09310	N	1	D	0.53619	0.961	P	0.52957	0.714	D	0.86251	0.1649	10	0.22109	T	0.4	.	10.4489	0.44509	0.836:0.164:0.0:0.0	.	256	A6NHN0	OTOL1_HUMAN	E	256	ENSP00000330808:K256E	ENSP00000330808:K256E	K	+	1	0	OTOL1	162703756	0.044000	0.20184	0.039000	0.18376	0.750000	0.42670	2.908000	0.48750	0.649000	0.30751	0.455000	0.32223	AAA	.	.	.	none		0.582	OTOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353184.1	NM_001080440		G	161221062	A	G	161221062	3	3	123	1	0	0	0	0	1	0	0	0	11311	247	9	3	780	3	OTOL1	3	161221062	Missense_Mutation	SNP	A	TCGA-BQ-5888-01A-11D-1589-08		161221062	36801368	5	7742											
WASF1	8936	hgsc.bcm.edu	37	chr6	110424747	110424747	+	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	agatccatccatatgatccaCgtatgtctgaggtctaaaag	13	11	8	9	1	2	3	0	2	2	1	5	3	5	3	3	1	0	1	3	1	4	3			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr6:110424747C>A	ENST00000392589.1	-	9	1563	c.727G>T	c.(727-729)Gtg>Ttg	p.V243L	WASF1_ENST00000392588.1_Missense_Mutation_p.V243L|WASF1_ENST00000359451.2_Missense_Mutation_p.V243L|WASF1_ENST00000392586.1_Missense_Mutation_p.V243L|WASF1_ENST00000392587.2_Missense_Mutation_p.V243L	NM_003931.2	NP_003922.1	Q92558	WASF1_HUMAN	WAS protein family, member 1	243					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)		ATATGATCCACGTATGTCTGA	0.358																																					p.V243L		Atlas-SNP	.											.	WASF1	35	.	0			c.G727T						PASS	.						100	92	95					6																	110424747		2203	4300	6503	SO:0001583	missense	8936	exon8			GATCCACGTATGT	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.727G>T	chr6.hg19:g.110424747C>A	ENSP00000376368:p.Val243Leu	99.0	0.0	.		70.0	4.0	.	NM_001024935	E1P5F2|Q5SZK7	Missense_Mutation	SNP	ENST00000392589.1	hg19	CCDS5080.1	.	.	.	.	.	.	.	.	.	.	C	14.70	2.612405	0.46631	.	.	ENSG00000112290	ENST00000392586;ENST00000392587;ENST00000392589;ENST00000392588;ENST00000359451	T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97	5.51	5.51	0.81932	.	0.213000	0.48286	D	0.000185	T	0.12263	0.0298	N	0.08118	0	0.34639	D	0.720416	B	0.14012	0.009	B	0.09377	0.004	T	0.07366	-1.0776	10	0.10902	T	0.67	.	19.7791	0.96410	0.0:1.0:0.0:0.0	.	243	Q92558	WASF1_HUMAN	L	243	ENSP00000376365:V243L;ENSP00000376366:V243L;ENSP00000376368:V243L;ENSP00000376367:V243L;ENSP00000352425:V243L	ENSP00000352425:V243L	V	-	1	0	WASF1	110531440	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.456000	0.60081	2.763000	0.94921	0.650000	0.86243	GTG	.	.	.	none		0.358	WASF1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041784.3	NM_003931		A	110424747	C	A	110424747	3	1	123	1	0	0	0	0	1	0	0	0	17264	536	19	4	964	4	WASF1	6	110424747	Missense_Mutation	SNP	C	TCGA-BQ-5888-01A-11D-1589-08		110424747	60690320	6	7743											
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121681010	121681010	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tatgccaagcgccatgcagtGgggcctgttgtcgtccactg	6	10	13	12	2	0	0	0	0	0	0	2	0	1	0	4	2	3	2	4	2	2	2			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr7:121681010G>A	ENST00000393386.2	+	21	6189	c.5778G>A	c.(5776-5778)gtG>gtA	p.V1926V	PTPRZ1_ENST00000449182.1_Silent_p.V1059V	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1926	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						GCCATGCAGTGGGGCCTGTTG	0.498																																					p.V1926V		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.G5778A						PASS	.						74	66	69					7																	121681010		2203	4300	6503	SO:0001819	synonymous_variant	5803	exon21			TGCAGTGGGGCCT	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.5778G>A	chr7.hg19:g.121681010G>A		118.0	0.0	.		108.0	18.0	.	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Silent	SNP	ENST00000393386.2	hg19	CCDS34740.1																																																																																			.	.	.	none		0.498	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		A	121681010	G	A	121681010	2	1	123	1	0	0	0	0	0	0	0	1	12827	1335	47	2		2	PTPRZ1	7	121681010	Silent	SNP	G	TCGA-BQ-5888-01A-11D-1589-08		121681010	37457653	7	7744											
MTBP	27085	hgsc.bcm.edu	37	chr8	121518998	121518998	+	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	tgctgggccacaaagagggtCctcgggactcaatcacattg	10	8	12	11	1	2	1	2	0	0	1	4	2	3	2	2	3	1	1	2	3	2	1			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr8:121518998C>T	ENST00000305949.1	+	16	1825	c.1780C>T	c.(1780-1782)Cct>Tct	p.P594S		NM_022045.4	NP_071328.2	Q96DY7	MTBP_HUMAN	MDM2 binding protein	594	Interaction with MDM2. {ECO:0000250}.				cell cycle arrest (GO:0007050)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cell proliferation (GO:0008285)|protein localization to kinetochore (GO:0034501)|traversing start control point of mitotic cell cycle (GO:0007089)	chromatin (GO:0000785)|kinetochore (GO:0000776)				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			CAAAGAGGGTCCTCGGGACTC	0.398																																					p.P594S		Atlas-SNP	.											.	MTBP	77	.	0			c.C1780T						PASS	.						83	79	80					8																	121518998		2203	4300	6503	SO:0001583	missense	27085	exon16			GAGGGTCCTCGGG		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.1780C>T	chr8.hg19:g.121518998C>T	ENSP00000303398:p.Pro594Ser	87.0	0.0	.		84.0	6.0	.	NM_022045	B4DUR5|Q9HA89	Missense_Mutation	SNP	ENST00000305949.1	hg19	CCDS6333.1	.	.	.	.	.	.	.	.	.	.	C	11.26	1.586138	0.28268	.	.	ENSG00000172167	ENST00000305949	.	.	.	5.44	4.55	0.56014	.	0.197586	0.44902	D	0.000417	T	0.49047	0.1534	L	0.60455	1.87	0.32183	N	0.58014	P	0.38078	0.617	B	0.33960	0.173	T	0.61978	-0.6951	9	0.46703	T	0.11	-8.4215	15.931	0.79659	0.0:0.8506:0.1494:0.0	.	594	Q96DY7	MTBP_HUMAN	S	594	.	ENSP00000303398:P594S	P	+	1	0	MTBP	121588179	1.000000	0.71417	0.997000	0.53966	0.864000	0.49448	2.735000	0.47377	1.267000	0.44247	0.563000	0.77884	CCT	.	.	.	none		0.398	MTBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381530.1	NM_022045		T	121518998	C	T	121518998	3	4	123	1	0	0	0	0	1	0	0	0	9919	855	30	2	1842	2	MTBP	8	121518998	Missense_Mutation	SNP	C	TCGA-BQ-5888-01A-11D-1589-08		121518998	24845024	8	7745											
CAMK1D	57118	hgsc.bcm.edu	37	chr10	12811756	12811756	+	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	tgtcaaaaatggagggcaaaGgagatgtgatgtccactgcc	13	8	13	7	0	1	2	1	1	0	1	2	4	2	3	2	3	1	1	2	3	3	0			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr10:12811756G>A	ENST00000378847.3	+	5	860	c.523G>A	c.(523-525)Gga>Aga	p.G175R	CAMK1D_ENST00000378845.1_Missense_Mutation_p.G175R	NM_153498.2	NP_705718.1	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID	175	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				inflammatory response (GO:0006954)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis (GO:0050766)|positive regulation of respiratory burst (GO:0060267)|regulation of dendrite development (GO:0050773)|regulation of granulocyte chemotaxis (GO:0071622)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)	16				GBM - Glioblastoma multiforme(1;3.16e-05)		GGAGGGCAAAGGAGATGTGAT	0.458																																					p.G175R		Atlas-SNP	.											CAMK1D_ENST00000378847,NS,carcinoma,0,2	CAMK1D	99	.	0			c.G523A						PASS	.						177	140	153					10																	12811756		2203	4300	6503	SO:0001583	missense	57118	exon5			GGCAAAGGAGATG	AF286366	CCDS7091.1, CCDS7092.1	10p13	2003-11-05			ENSG00000183049	ENSG00000183049			19341	protein-coding gene	gene with protein product		607957				11050006	Standard	XM_006717481		Approved	CKLiK	uc001ilo.3	Q8IU85	OTTHUMG00000017683	ENST00000378847.3:c.523G>A	chr10.hg19:g.12811756G>A	ENSP00000368124:p.Gly175Arg	123.0	0.0	.		92.0	17.0	.	NM_153498	B0YIY0|Q9HD31	Missense_Mutation	SNP	ENST00000378847.3	hg19	CCDS7091.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.892484	0.91889	.	.	ENSG00000183049	ENST00000378847;ENST00000378845	T;T	0.65364	-0.15;-0.15	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);	0.115496	0.64402	D	0.000017	T	0.68796	0.3040	N	0.25060	0.705	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.79784	0.993;0.987	T	0.71912	-0.4449	10	0.52906	T	0.07	-14.2799	17.7041	0.88303	0.0:0.0:1.0:0.0	.	175;175	Q8IU85;Q5SQQ7	KCC1D_HUMAN;.	R	175	ENSP00000368124:G175R;ENSP00000368122:G175R	ENSP00000368122:G175R	G	+	1	0	CAMK1D	12851762	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.950000	0.87804	2.403000	0.81681	0.561000	0.74099	GGA	.	.	.	none		0.458	CAMK1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046820.1	NM_020397		A	12811756	G	A	12811756	3	1	123	1	0	0	0	0	1	0	0	0	2599	1001	35	2	541	2	CAMK1D	10	12811756	Missense_Mutation	SNP	G	TCGA-BQ-5888-01A-11D-1589-08		12811756	122722991	9	7746											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1253260	1253260	+	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	ttcaaccagaaccaggctgaCgacttcacggccctcagcgg	10	6	10	15	3	3	2	3	1	0	1	3	3	3	2	3	3	3	1	3	3	2	2			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr11:1253260C>A	ENST00000529681.1	+	15	1771	c.1713C>A	c.(1711-1713)gaC>gaA	p.D571E	MUC5B_ENST00000447027.1_Missense_Mutation_p.D574E	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	571	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)		ACCAGGCTGACGACTTCACGG	0.672																																					p.D571E		Atlas-SNP	.											.	MUC5B	473	.	0			c.C1713A						PASS	.						42	50	48					11																	1253260		2049	4192	6241	SO:0001583	missense	727897	exon15			GGCTGACGACTTC	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.1713C>A	chr11.hg19:g.1253260C>A	ENSP00000436812:p.Asp571Glu	59.0	0.0	.		43.0	4.0	.	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	hg19	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	C	10.09	1.254981	0.22965	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.65364	-0.15;-0.15	3.77	-5.54	0.02544	von Willebrand factor, type D domain (3);	.	.	.	.	D	0.83982	0.5372	H	0.98314	4.2	0.36992	D	0.894823	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.984;0.996;0.996	D	0.86512	0.1810	9	0.87932	D	0	.	12.6531	0.56772	0.0:0.2249:0.0:0.7751	.	571;1230;574	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	E	571;574;572;607	ENSP00000436812:D571E;ENSP00000415793:D574E	ENSP00000343037:D572E	D	+	3	2	MUC5B	1209836	0.027000	0.19231	0.934000	0.37439	0.455000	0.32408	-1.078000	0.03413	-1.179000	0.02737	-0.369000	0.07265	GAC	.	.	.	none		0.672	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1253260	C	A	1253260	3	1	123	1	0	0	0	0	1	0	0	0	9986	535	19	4	1780	4	MUC5B	11	1253260	Missense_Mutation	SNP	C	TCGA-BQ-5888-01A-11D-1589-08		1253260	133753256	10	7747											
KCNK7	10089	hgsc.bcm.edu	37	chr11	65360850	65360850	+	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	gtgccctggagtgaggtcccTccacctgcaaggcccagccc	6	6	12	17	0	0	1	0	1	0	0	2	2	2	2	6	3	3	1	6	3	1	0			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr11:65360850T>C	ENST00000340313.4	-	2	942				AP001362.1_ENST00000597463.1_5'Flank|KCNK7_ENST00000394216.2_3'UTR|KCNK7_ENST00000342202.4_Silent_p.G241G|KCNK7_ENST00000394217.2_Silent_p.G241G	NM_033347.1	NP_203133.1	Q9Y2U2	KCNK7_HUMAN	potassium channel, subfamily K, member 7						potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			endometrium(1)|liver(1)|lung(1)	3						GTGAGGTCCCTCCACCTGCAA	0.627																																					p.G241G		Atlas-SNP	.											.	KCNK7	22	.	0			c.A723G						PASS	.						82	83	82					11																	65360850		2201	4297	6498	SO:0001627	intron_variant	10089	exon3			GGTCCCTCCACCT	AF110522	CCDS8106.1, CCDS31608.1, CCDS41673.1	11q13	2012-03-07			ENSG00000173338	ENSG00000173338		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6282	protein-coding gene	gene with protein product		603940				10206991, 11256078, 16382106	Standard	NM_033347		Approved	K2p7.1	uc001oes.3	Q9Y2U2	OTTHUMG00000166528	ENST00000340313.4:c.718+96A>G	chr11.hg19:g.65360850T>C		107.0	0.0	.		98.0	4.0	.	NM_033348	Q3SYI2|Q9Y2U3|Q9Y2U4	Silent	SNP	ENST00000340313.4	hg19	CCDS31608.1	.	.	.	.	.	.	.	.	.	.	T	6.803	0.517237	0.13005	.	.	ENSG00000173338	ENST00000525254	.	.	.	4.14	-4.28	0.03732	.	.	.	.	.	T	0.20170	0.0485	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.29397	-1.0013	4	.	.	.	.	4.0939	0.09982	0.3119:0.4105:0.0:0.2776	.	.	.	.	G	17	.	.	R	-	1	2	KCNK7	65117426	0.000000	0.05858	0.000000	0.03702	0.048000	0.14542	-1.096000	0.03353	-0.723000	0.04915	0.459000	0.35465	AGG	.	.	.	none		0.627	KCNK7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390206.1	NM_005714		C	65360850	T	C	65360850	1	2	123	0	1	0	0	0	0	0	0	0	8078	1538	54	3		3	KCNK7	11	65360850	Intron	SNP	T	TCGA-BQ-5888-01A-11D-1589-08	64107590	65360850	69645666	11	7748											
CELA1	1990	hgsc.bcm.edu	37	chr12	51740415	51740415	+	Missense_Mutation	SNP	A	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	atatccacttaccataaaggAccagcatgttgccgatggag	13	9	9	10	1	0	0	0	0	0	0	1	3	1	2	4	2	3	2	4	2	4	4	rs370927847|rs386762976|rs55827519	byFrequency	TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr12:51740415A>C	ENST00000293636.1	-	1	48	c.8T>G	c.(7-9)gTc>gGc	p.V3G		NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1	3					exocrine pancreas development (GO:0031017)|inflammatory response (GO:0006954)|multicellular organism growth (GO:0035264)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas morphogenesis (GO:0061113)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.V3fs*21(1)		NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15						ACCATAAAGGACCAGCATGTT	0.512																																					p.V3G		Atlas-SNP	.											.,3	CELA1	39	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.T8G						PASS	.						198	125	149					12																	51740415		2199	4290	6489	SO:0001583	missense	1990	exon1			TAAAGGACCAGCA		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.8T>G	chr12.hg19:g.51740415A>C	ENSP00000293636:p.Val3Gly	81.0	1.0	.		80.0	4.0	.	NM_001971	Q5MLF0|Q6DJT0|Q6ISM6	Missense_Mutation	SNP	ENST00000293636.1	hg19	CCDS8812.1	.	.	.	.	.	.	.	.	.	.	-	10.50	1.368338	0.24771	.	.	ENSG00000139610	ENST00000293636	D	0.89552	-2.53	3.61	0.701	0.18104	.	0.180867	0.43747	D	0.000529	T	0.82121	0.4968	L	0.55990	1.75	0.28932	N	0.891491	B	0.27823	0.19	B	0.26517	0.07	T	0.73855	-0.3851	10	0.87932	D	0	-1.5222	3.134	0.06433	0.3198:0.0:0.4933:0.1868	.	3	Q9UNI1	CELA1_HUMAN	G	3	ENSP00000293636:V3G	ENSP00000293636:V3G	V	-	2	0	CELA1	50026682	0.009000	0.17119	0.433000	0.26760	0.045000	0.14185	0.204000	0.17335	-0.043000	0.13513	-0.633000	0.03987	GTC	.	.	.	alt		0.512	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1	NM_001971		C	51740415	A	C	51740415	3	2	123	1	0	0	0	0	1	0	0	0	3212	275	10	5	800	5	CELA1	12	51740415	Missense_Mutation	SNP	A	TCGA-BQ-5888-01A-11D-1589-08		51740415	82111480	12	7749											
ANKRD11	29123	hgsc.bcm.edu	37	chr16	89345492	89345492	+	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	gcactcaccacggggatgtgGagcttgctgagcggcttgcc	6	8	15	12	2	1	1	1	1	0	0	1	3	1	3	2	4	4	4	2	4	0	2	rs569755271		TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr16:89345492G>A	ENST00000301030.4	-	9	7918	c.7458C>T	c.(7456-7458)ctC>ctT	p.L2486L	ANKRD11_ENST00000378330.2_Silent_p.L2486L	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	2486					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)		CGGGGATGTGGAGCTTGCTGA	0.657																																					p.L2486L		Atlas-SNP	.											.	ANKRD11	195	.	0			c.C7458T						PASS	.						25	22	23					16																	89345492		2197	4298	6495	SO:0001819	synonymous_variant	29123	exon9			GATGTGGAGCTTG	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.7458C>T	chr16.hg19:g.89345492G>A		28.0	0.0	.		50.0	11.0	.	NM_001256183	Q6NTG1|Q6QMF8	Silent	SNP	ENST00000301030.4	hg19	CCDS32513.1																																																																																			.	.	.	none		0.657	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		A	89345492	G	A	89345492	2	1	123	1	0	0	0	0	0	0	0	1	639	1161	41	2		2	ANKRD11	16	89345492	Silent	SNP	G	TCGA-BQ-5888-01A-11D-1589-08		89345492	1009261	13	7750											
SLFN11	91607	hgsc.bcm.edu	37	chr17	33679780	33679780	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgaacaccctgggaccattcGgcttcaggaaatacctcgag	11	8	10	12	2	1	1	1	1	0	0	3	4	1	3	3	3	2	1	3	3	3	3	rs377363363		TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr17:33679780G>A	ENST00000394566.1	-	7	2573	c.2301C>T	c.(2299-2301)gcC>gcT	p.A767A	SLFN11_ENST00000308377.4_Silent_p.A767A	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	767					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)		GGGACCATTCGGCTTCAGGAA	0.443																																					p.A767A		Atlas-SNP	.											.	SLFN11	112	.	0			c.C2301T						PASS	.	G	,,,,	0,4406		0,0,2203	65	61	62		2301,2301,2301,2301,2301	1.7	0	17		62	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLFN11	NM_001104587.1,NM_001104588.1,NM_001104589.1,NM_001104590.1,NM_152270.3	,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,	767/902,767/902,767/902,767/902,767/902	33679780	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	91607	exon5			CCATTCGGCTTCA	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.2301C>T	chr17.hg19:g.33679780G>A		117.0	0.0	.		94.0	21.0	.	NM_152270	E1P643|Q8N3S8|Q8N762|Q8TEE0	Silent	SNP	ENST00000394566.1	hg19	CCDS11294.1																																																																																			.	.	.	weak		0.443	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270		A	33679780	G	A	33679780	2	1	123	1	0	0	0	0	0	0	0	1	14746	1103	39	1		1	SLFN11	17	33679780	Silent	SNP	G	TCGA-BQ-5888-01A-11D-1589-08		33679780	47515430	14	7751											
PTPRM	5797	hgsc.bcm.edu	37	chr18	8379245	8379245	+	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	cggaaccatgagaaaaaccgGtgcatggacatcctgccccc	12	5	10	14	2	0	1	0	1	0	1	1	4	1	3	5	3	4	1	5	3	3	0			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr18:8379245G>A	ENST00000332175.8	+	26	4691	c.3654G>A	c.(3652-3654)cgG>cgA	p.R1218R	PTPRM_ENST00000400060.4_Silent_p.R1232R|PTPRM_ENST00000580170.1_Silent_p.R1231R|PTPRM_ENST00000400053.4_Silent_p.R1156R|PTPRM_ENST00000444013.1_Silent_p.R1005R	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	1218	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				AGAAAAACCGGTGCATGGACA	0.562																																					p.R1231R		Atlas-SNP	.											.	PTPRM	185	.	0			c.G3693A						PASS	.						138	108	118					18																	8379245		2203	4300	6503	SO:0001819	synonymous_variant	5797	exon28			AAACCGGTGCATG	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.3654G>A	chr18.hg19:g.8379245G>A		73.0	0.0	.		107.0	22.0	.	NM_001105244	A7MBN1|D3DUH8|J3QL11	Silent	SNP	ENST00000332175.8	hg19	CCDS11840.1																																																																																			.	.	.	none		0.562	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			A	8379245	G	A	8379245	2	1	123	1	0	0	0	0	0	0	0	1	12819	1248	44	2		2	PTPRM	18	8379245	Silent	SNP	G	TCGA-BQ-5888-01A-11D-1589-08		8379245	69698003	15	7752											
PRTN3	5657	hgsc.bcm.edu	37	chr19	841048	841048	+	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	gccctgccctggcgtccgtgCtgctggccttgctgctgagc	1	10	14	16	2	0	1	0	1	0	0	1	1	1	1	4	2	6	4	4	2	0	1			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr19:841048C>T	ENST00000234347.5	+	1	86	c.40C>T	c.(40-42)Ctg>Ttg	p.L14L	PRTN3_ENST00000544537.2_5'Flank	NM_002777.3	NP_002768.3	P24158	PRTN3_HUMAN	proteinase 3	14					collagen catabolic process (GO:0030574)|mature dendritic cell differentiation (GO:0097029)|negative regulation of phagocytosis (GO:0050765)|positive regulation of cell proliferation (GO:0008284)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			lung(1)|ovary(2)|urinary_tract(1)	4		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)		GGCGTCCGTGCTGCTGGCCTT	0.657																																					p.L14L		Atlas-SNP	.											.	PRTN3	9	.	0			c.C40T						PASS	.						32	30	31					19																	841048		2202	4300	6502	SO:0001819	synonymous_variant	5657	exon1			TCCGTGCTGCTGG		CCDS32860.1	19p13.3	2008-07-31	2008-07-31			ENSG00000196415			9495	protein-coding gene	gene with protein product	"myeloblastin", "serine proteinase, neutrophil", "Wegener granulomatosis autoantigen"	177020				2258701	Standard	NM_002777		Approved	PR-3, ACPA, C-ANCA, AGP7, MBT, P29	uc002lqa.1	P24158		ENST00000234347.5:c.40C>T	chr19.hg19:g.841048C>T		32.0	0.0	.		49.0	12.0	.	NM_002777	P15637|P18078|Q4VB08|Q4VB09|Q6LBM7|Q6LBN2|Q9UD25|Q9UQD8	Silent	SNP	ENST00000234347.5	hg19	CCDS32860.1																																																																																			.	.	.	none		0.657	PRTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457888.2	NM_002777		T	841048	C	T	841048	2	4	123	1	0	0	0	0	0	0	0	1	12649	796	28	2		2	PRTN3	19	841048	Silent	SNP	C	TCGA-BQ-5888-01A-11D-1589-08		841048	58287935	16	7753											
HNRNPL	3191	hgsc.bcm.edu	37	chr19	39336576	39336576	+	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	gtcatccgagtccccagggcGggagatcttctggctggtag	6	9	15	11	2	3	1	1	0	2	1	5	3	5	1	3	4	0	2	3	4	1	2			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr19:39336576G>C	ENST00000221419.5	-	3	907	c.541C>G	c.(541-543)Cgc>Ggc	p.R181G	HNRNPL_ENST00000600873.1_Missense_Mutation_p.R48G|AC008982.2_ENST00000600473.1_RNA	NM_001533.2	NP_001524.2	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	181					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)			TCCCCAGGGCGGGAGATCTTC	0.542																																					p.R181G		Atlas-SNP	.											.	HNRNPL	67	.	0			c.C541G						PASS	.						117	115	115					19																	39336576		2203	4300	6503	SO:0001583	missense	3191	exon3			CAGGGCGGGAGAT	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.541C>G	chr19.hg19:g.39336576G>C	ENSP00000221419:p.Arg181Gly	188.0	0.0	.		227.0	31.0	.	NM_001533	A6ND69|A6NIT8|Q9H3P3	Missense_Mutation	SNP	ENST00000221419.5	hg19	CCDS33015.1	.	.	.	.	.	.	.	.	.	.	G	16.02	3.004874	0.54254	.	.	ENSG00000104824	ENST00000221419;ENST00000388749;ENST00000388750;ENST00000423415;ENST00000536292	.	.	.	5.39	5.39	0.77823	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	T	0.69655	0.3135	M	0.74258	2.255	0.58432	D	0.999995	B	0.18461	0.028	B	0.20767	0.031	T	0.68812	-0.5310	9	0.66056	D	0.02	.	17.9088	0.88928	0.0:0.0:1.0:0.0	.	181	P14866	HNRPL_HUMAN	G	181;48;48;48;109	.	ENSP00000221419:R181G	R	-	1	0	HNRNPL	44028416	1.000000	0.71417	0.994000	0.49952	0.984000	0.73092	5.035000	0.64158	2.541000	0.85698	0.462000	0.41574	CGC	.	.	.	none		0.542	HNRNPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462670.1			C	39336576	G	C	39336576	3	2	123	1	0	0	0	0	1	0	0	0	7277	1116	39	4	1272	4	HNRNPL	19	39336576	Missense_Mutation	SNP	G	TCGA-BQ-5888-01A-11D-1589-08	38495528	39336576	19792407	17	7754											
LILRA6	79168	hgsc.bcm.edu	37	chr19	54745734	54745734	+	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	agggctgggcagggctgagaGggtgggtttgttgtagaatc	7	10	20	4	0	0	2	0	1	0	2	1	3	0	2	0	5	0	6	0	5	2	3			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr19:54745734G>T	ENST00000396365.2	-	4	415	c.376C>A	c.(376-378)Ctc>Atc	p.L126I	LILRA6_ENST00000245621.5_Missense_Mutation_p.L126I|LILRA6_ENST00000440558.2_Missense_Mutation_p.L126I|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000419410.2_Missense_Mutation_p.L126I|LILRA6_ENST00000270464.5_Missense_Mutation_p.L126I|LILRA6_ENST00000391735.3_Missense_Mutation_p.L126I	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	126					immune system process (GO:0002376)	integral component of membrane (GO:0016021)		p.L126F(2)		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)		AGGGCTGAGAGGGTGGGTTTG	0.567																																					p.L126I		Atlas-SNP	.											A2RRG4_HUMAN,NS,carcinoma,0,1	LILRA6	75	.	2	Substitution - Missense(2)	lung(2)	c.C376A						PASS	.						62	102	89					19																	54745734		2108	4294	6402	SO:0001583	missense	79168	exon4			CTGAGAGGGTGGG	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.376C>A	chr19.hg19:g.54745734G>T	ENSP00000379651:p.Leu126Ile	90.0	0.0	.		64.0	23.0	.	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	hg19	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	G	16.76	3.212570	0.58452	.	.	ENSG00000244482	ENST00000440558;ENST00000270464;ENST00000419410;ENST00000391735;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T;T;T	0.01981	5.38;5.38;5.38;4.52;5.38;5.38	3.4	3.4	0.38934	Immunoglobulin-like fold (1);	0.278862	0.25747	N	0.028562	T	0.11153	0.0272	M	0.81942	2.565	0.23546	N	0.997443	D;P;D;D;D;D	0.76494	0.995;0.947;0.982;0.997;0.997;0.999	D;D;D;D;D;D	0.81914	0.986;0.959;0.949;0.987;0.995;0.995	T	0.00984	-1.1491	10	0.87932	D	0	.	10.5189	0.44907	0.0:0.0:1.0:0.0	.	126;126;126;126;126;126	C9JFH3;Q6PI73-2;Q6PI73;F8WCY4;D3YTC4;F8W6G6	.;.;LIRA6_HUMAN;.;.;.	I	126	ENSP00000390120:L126I;ENSP00000270464:L126I;ENSP00000411227:L126I;ENSP00000375615:L126I;ENSP00000379651:L126I;ENSP00000245621:L126I	ENSP00000245621:L126I	L	-	1	0	LILRA6	59437546	0.011000	0.17503	0.553000	0.28255	0.078000	0.17371	1.276000	0.33156	1.936000	0.56123	0.184000	0.17185	CTC	.	.	.	none		0.567	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318		T	54745734	G	T	54745734	3	4	123	1	0	0	0	0	1	0	0	0	8796	1000	35	4	1089	4	LILRA6	19	54745734	Missense_Mutation	SNP	G	TCGA-BQ-5888-01A-11D-1589-08	15409158	54745734	4383249	18	7755											
KRTAP10-3	386682	hgsc.bcm.edu	37	chr21	45978127	45978127	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggcggcagaggagggacaCggaggaggagggtctgcagc	9	2	23	7	2	1	1	0	0	1	1	1	6	1	6	0	9	2	2	0	9	0	0	rs369545090		TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr21:45978127C>T	ENST00000391620.1	-	1	516	c.472G>A	c.(472-474)Gtg>Atg	p.V158M	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198696.2	NP_941969.2	P60369	KR103_HUMAN	keratin associated protein 10-3	158	18 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				kidney(1)|lung(4)|prostate(1)|skin(1)	7						AGGAGGGACACGGAGGAGGAG	0.692																																					p.V158M		Atlas-SNP	.											.	KRTAP10-3	17	.	0			c.G472A						PASS	.	C	MET/VAL,	1,4405	2.1+/-5.4	0,1,2202	89	96	93		472,	2.6	0.6	21		93	1,8599	1.2+/-3.3	0,1,4299	no	missense,intron	TSPEAR,KRTAP10-3	NM_198696.2,NM_144991.2	21,	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging,	158/222,	45978127	2,13004	2203	4300	6503	SO:0001583	missense	386682	exon1			GGGACACGGAGGA	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.472G>A	chr21.hg19:g.45978127C>T	ENSP00000375478:p.Val158Met	162.0	0.0	.		152.0	31.0	.	NM_198696	A3KN67|Q70LJ4	Missense_Mutation	SNP	ENST00000391620.1	hg19	CCDS42956.1	.	.	.	.	.	.	.	.	.	.	c	3.276	-0.148013	0.06627	2.27E-4	1.16E-4	ENSG00000212935	ENST00000391620	T	0.01438	4.89	3.53	2.61	0.31194	.	.	.	.	.	T	0.05823	0.0152	M	0.84948	2.725	0.09310	N	1	D	0.59357	0.985	P	0.53593	0.73	T	0.14144	-1.0483	9	0.59425	D	0.04	.	9.6661	0.39986	0.0:0.5593:0.4407:0.0	.	158	P60369	KR103_HUMAN	M	158	ENSP00000375478:V158M	ENSP00000375478:V158M	V	-	1	0	KRTAP10-3	44802555	0.060000	0.20803	0.577000	0.28562	0.005000	0.04900	0.116000	0.15561	0.772000	0.33382	0.561000	0.74099	GTG	.	.	.	weak		0.692	KRTAP10-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128031.1			T	45978127	C	T	45978127	3	4	123	1	0	0	0	0	1	0	0	0	8517	536	19	1	197	1	KRTAP10-3	21	45978127	Missense_Mutation	SNP	C	TCGA-BQ-5888-01A-11D-1589-08		45978127	2151768	19	7756											
GTSE1	51512	hgsc.bcm.edu	37	chr22	46724721	46724721	+	Missense_Mutation	SNP	A	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	aaagcgattctactttctccAaaagtactgccacagaagta	15	10	6	10	1	2	1	0	0	2	1	3	2	2	1	2	0	4	2	2	0	7	5			TCGA-BQ-5888-01A-11D-1589-08	TCGA-BQ-5888-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	31e068e4-adc9-4148-b785-8deb4ef1637a	2d3ada40-7a55-492a-9f70-0cfe97cc66ea	g.chr22:46724721A>C	ENST00000454366.1	+	10	2073	c.1861A>C	c.(1861-1863)Aaa>Caa	p.K621Q		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	602					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		TACTTTCTCCAAAAGTACTGC	0.567																																					p.K621Q	GBM(153;542 1915 12487 29016 50495)	Atlas-SNP	.											.	GTSE1	100	.	0			c.A1861C						PASS	.						88	95	93					22																	46724721		2203	4300	6503	SO:0001583	missense	51512	exon10			TTCTCCAAAAGTA	AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.1861A>C	chr22.hg19:g.46724721A>C	ENSP00000415430:p.Lys621Gln	226.0	0.0	.		255.0	43.0	.	NM_016426	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Missense_Mutation	SNP	ENST00000454366.1	hg19	CCDS14074.2	.	.	.	.	.	.	.	.	.	.	A	7.057	0.565524	0.13560	.	.	ENSG00000075218	ENST00000454366;ENST00000361934	T	0.07021	3.23	4.41	-0.765	0.11023	.	0.925293	0.09363	N	0.812463	T	0.03871	0.0109	N	0.12471	0.22	0.09310	N	1	B;B	0.25312	0.123;0.123	B;B	0.21360	0.023;0.034	T	0.45687	-0.9244	10	0.25751	T	0.34	-5.7757	4.1358	0.10170	0.3102:0.4118:0.278:0.0	.	602;581	Q9NYZ3;B4DZT6	GTSE1_HUMAN;.	Q	621;581	ENSP00000415430:K621Q	ENSP00000354634:K581Q	K	+	1	0	GTSE1	45103385	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.240000	0.08952	-0.032000	0.13758	0.533000	0.62120	AAA	.	.	.	none		0.567	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426		C	46724721	A	C	46724721	3	2	123	1	0	0	0	0	1	0	0	0	6892	131	5	5	1895	5	GTSE1	22	46724721	Missense_Mutation	SNP	A	TCGA-BQ-5888-01A-11D-1589-08		46724721	4579845	20	7757											
PHACTR4	65979	hgsc.bcm.edu	37	chr1	28800653	28800653	+	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	ctcttcccatcactattgaaAtgctaaaagtgtaagtgcct	12	13	6	10	0	2	1	1	1	1	0	3	1	3	1	2	0	2	2	2	0	5	5			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr1:28800653A>T	ENST00000373839.3	+	7	1672	c.1411A>T	c.(1411-1413)Atg>Ttg	p.M471L	PHACTR4_ENST00000493669.1_3'UTR|PHACTR4_ENST00000373836.3_Missense_Mutation_p.M481L	NM_001048183.1	NP_001041648.1	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	471					actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		CACTATTGAAATGCTAAAAGT	0.413																																					p.M481L		Atlas-SNP	.											.	PHACTR4	64	.	0			c.A1441T						PASS	.						102	103	103					1																	28800653		1898	4120	6018	SO:0001583	missense	65979	exon6			ATTGAAATGCTAA	AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138		"Phosphatase and actin regulators"	25793	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 124"	608726				11483580, 15107502	Standard	NM_023923		Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373839.3:c.1411A>T	chr1.hg19:g.28800653A>T	ENSP00000362945:p.Met471Leu	211.0	0.0	.		214.0	19.0	.	NM_023923	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	Missense_Mutation	SNP	ENST00000373839.3	hg19	CCDS41293.1	.	.	.	.	.	.	.	.	.	.	A	4.322	0.059030	0.08339	.	.	ENSG00000204138	ENST00000373839;ENST00000373836;ENST00000373838	T;T	0.21191	2.02;2.02	5.75	4.55	0.56014	.	0.347042	0.36134	N	0.002762	T	0.13286	0.0322	N	0.20401	0.57	0.30856	N	0.734034	B;B	0.19073	0.033;0.009	B;B	0.18871	0.023;0.004	T	0.06972	-1.0797	10	0.27785	T	0.31	-6.0179	10.959	0.47374	0.7173:0.2827:0.0:0.0	.	481;471	Q8IZ21-2;Q8IZ21	.;PHAR4_HUMAN	L	471;481;470	ENSP00000362945:M471L;ENSP00000362942:M481L	ENSP00000362942:M481L	M	+	1	0	PHACTR4	28673240	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.932000	0.56537	2.190000	0.69967	0.533000	0.62120	ATG	.	.	.	none		0.413	PHACTR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009868.4	NM_023923		T	28800653	A	T	28800653	3	4	124	1	0	0	0	0	1	0	0	0	11819	101	4	5	1483	5	PHACTR4	1	28800653	Missense_Mutation	SNP	A	TCGA-BQ-5889-01A-11D-1589-08		28800653	220449968	1	7758											
FAM151A	338094	hgsc.bcm.edu	37	chr1	55077293	55077293	+	Missense_Mutation	SNP	A	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	ccttacaggccagctgcttgAactgtgacaggagaggctca	10	8	12	11	0	1	3	1	2	0	1	1	4	1	3	2	3	4	3	2	3	2	2			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr1:55077293A>C	ENST00000302250.2	-	6	1086	c.926T>G	c.(925-927)tTc>tGc	p.F309C	FAM151A_ENST00000371304.2_Intron|ACOT11_ENST00000371316.3_Intron	NM_176782.2	NP_788954.2	Q8WW52	F151A_HUMAN	family with sequence similarity 151, member A	309						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						CAGCTGCTTGAACTGTGACAG	0.567																																					p.F309C		Atlas-SNP	.											.	FAM151A	58	.	0			c.T926G						PASS	.						127	111	116					1																	55077293		2203	4300	6503	SO:0001583	missense	338094	exon6			TGCTTGAACTGTG	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.926T>G	chr1.hg19:g.55077293A>C	ENSP00000306888:p.Phe309Cys	137.0	0.0	.		157.0	9.0	.	NM_176782	Q5VUG5|Q6DKH5|Q6UWV0|Q8NAX9|Q96KY5	Missense_Mutation	SNP	ENST00000302250.2	hg19	CCDS594.1	.	.	.	.	.	.	.	.	.	.	A	18.15	3.560447	0.65538	.	.	ENSG00000162391	ENST00000302250	T	0.15017	2.46	4.59	4.59	0.56863	.	0.064498	0.64402	D	0.000009	T	0.30198	0.0757	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.68192	0.956	T	0.03413	-1.1039	10	0.87932	D	0	-31.1715	13.3708	0.60711	1.0:0.0:0.0:0.0	.	309	Q8WW52	F151A_HUMAN	C	309	ENSP00000306888:F309C	ENSP00000306888:F309C	F	-	2	0	FAM151A	54849881	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	6.952000	0.75989	2.039000	0.60335	0.533000	0.62120	TTC	.	.	.	none		0.567	FAM151A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027342.1	NM_176782		C	55077293	A	C	55077293	3	2	124	1	0	0	0	0	1	0	0	0	5462	246	9	5	843	5	FAM151A	1	55077293	Missense_Mutation	SNP	A	TCGA-BQ-5889-01A-11D-1589-08	26276640	55077293	194173328	2	7759											
SSX2IP	117178	hgsc.bcm.edu	37	chr1	85121610	85121610	+	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	aagggaccattcttctttgaGacgttccttttcttccaaca	9	15	6	11	1	3	1	0	1	3	1	5	3	5	2	3	1	1	1	3	1	2	7			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr1:85121610G>A	ENST00000342203.3	-	11	1557	c.1294C>T	c.(1294-1296)Ctc>Ttc	p.L432F	SSX2IP_ENST00000437941.2_Missense_Mutation_p.L405F|SSX2IP_ENST00000605755.1_Missense_Mutation_p.L405F|SSX2IP_ENST00000370612.4_Missense_Mutation_p.L432F|SSX2IP_ENST00000603677.1_Intron	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	432					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)		TCTTCTTTGAGACGTTCCTTT	0.388																																					p.L432F		Atlas-SNP	.											.	SSX2IP	53	.	0			c.C1294T						PASS	.						86	85	86					1																	85121610		2203	4300	6503	SO:0001583	missense	117178	exon11			CTTTGAGACGTTC		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.1294C>T	chr1.hg19:g.85121610G>A	ENSP00000340279:p.Leu432Phe	81.0	0.0	.		82.0	6.0	.	NM_001166293	A8K8W0|B4DFE3|D3DT13|J3KR02|Q6P2P8|Q6ULS1|Q7L168|Q9UIX0	Missense_Mutation	SNP	ENST00000342203.3	hg19	CCDS699.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.495910	0.85069	.	.	ENSG00000117155	ENST00000342203;ENST00000437941;ENST00000544699;ENST00000370612	T;T	0.67345	-0.21;-0.26	5.07	5.07	0.68467	.	0.116998	0.64402	D	0.000014	T	0.71392	0.3334	M	0.62723	1.935	0.49798	D	0.999822	D;D;D	0.67145	0.996;0.987;0.987	P;P;P	0.56474	0.799;0.635;0.635	T	0.72064	-0.4403	10	0.49607	T	0.09	-20.4465	18.6376	0.91384	0.0:0.0:1.0:0.0	.	428;432;405	F5H549;Q9Y2D8;B4DFE3	.;ADIP_HUMAN;.	F	432;405;428;432	ENSP00000340279:L432F;ENSP00000412781:L405F	ENSP00000340279:L432F	L	-	1	0	SSX2IP	84894198	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.237000	0.65360	2.648000	0.89879	0.591000	0.81541	CTC	.	.	.	none		0.388	SSX2IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027469.1	NM_014021		A	85121610	G	A	85121610	3	1	124	1	0	0	0	0	1	0	0	0	15216	942	33	2	566	2	SSX2IP	1	85121610	Missense_Mutation	SNP	G	TCGA-BQ-5889-01A-11D-1589-08	30044317	85121610	164129011	3	7760											
TXNIP	10628	hgsc.bcm.edu	37	chr1	145439917	145439917	+	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	tggtggatgtcaatacccctGatttaatggtgagatccatt	10	14	10	7	0	1	2	1	2	0	1	2	4	2	3	3	3	1	0	3	3	3	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr1:145439917G>A	ENST00000369317.4	+	3	797	c.463G>A	c.(463-465)Gat>Aat	p.D155N	TXNIP_ENST00000475171.1_Intron	NM_006472.3	NP_006463.3	Q9H3M7	TXNIP_HUMAN	thioredoxin interacting protein	155					cell cycle (GO:0007049)|cellular response to tumor cell (GO:0071228)|innate immune response (GO:0045087)|keratinocyte differentiation (GO:0030216)|negative regulation of cell division (GO:0051782)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|protein import into nucleus (GO:0006606)|regulation of cell proliferation (GO:0042127)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucose (GO:0009749)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)	enzyme inhibitor activity (GO:0004857)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(1)|lung(5)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	21	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CAATACCCCTGATTTAATGGT	0.428																																					p.D155N		Atlas-SNP	.											.	TXNIP	51	.	0			c.G463A						PASS	.						86	92	90					1																	145439917		2202	4299	6501	SO:0001583	missense	10628	exon3			ACCCCTGATTTAA	S73591	CCDS72876.1	1q11	2008-07-18			ENSG00000117289	ENSG00000265972			16952	protein-coding gene	gene with protein product	"upregulated by 1,25-dihydroxyvitamin D-3", "thioredoxin binding protein 2"	606599				8086474	Standard	NM_006472		Approved	VDUP1, EST01027, HHCPA78, THIF	uc001enn.4	Q9H3M7	OTTHUMG00000013755	ENST00000369317.4:c.463G>A	chr1.hg19:g.145439917G>A	ENSP00000358323:p.Asp155Asn	206.0	0.0	.		171.0	19.0	.	NM_006472	B4E3D3|Q16226|Q6PML0|Q9BXG9	Missense_Mutation	SNP	ENST00000369317.4	hg19	CCDS913.1	.	.	.	.	.	.	.	.	.	.	G	18.02	3.529556	0.64860	.	.	ENSG00000117289	ENST00000369317;ENST00000425134	T;T	0.11169	3.17;2.8	5.27	5.27	0.74061	Immunoglobulin E-set (1);	0.048081	0.85682	D	0.000000	T	0.06371	0.0164	N	0.25485	0.75	0.80722	D	1	P;P	0.51791	0.938;0.948	P;P	0.49528	0.532;0.614	T	0.46034	-0.9220	10	0.15499	T	0.54	-0.5065	16.4254	0.83813	0.0:0.0:1.0:0.0	.	100;155	B4E3D3;Q9H3M7	.;TXNIP_HUMAN	N	155;100	ENSP00000358323:D155N;ENSP00000396322:D100N	ENSP00000358323:D155N	D	+	1	0	TXNIP	144151274	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.243000	0.78219	2.753000	0.94483	0.651000	0.88453	GAT	.	.	.	none		0.428	TXNIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038547.1	NM_006472		A	145439917	G	A	145439917	3	1	124	1	0	0	0	0	1	0	0	0	16815	1290	45	2	473	2	TXNIP	1	145439917	Missense_Mutation	SNP	G	TCGA-BQ-5889-01A-11D-1589-08	60318307	145439917	103810704	4	7761											
PYHIN1	149628	hgsc.bcm.edu	37	chr1	158912063	158912063	+	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	gcctcttctgtatctgaagcTggtcctgaccaaacgtttga	8	13	9	11	1	3	3	0	3	3	0	4	3	4	3	3	1	2	3	3	1	3	3			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr1:158912063T>G	ENST00000368140.1	+	5	1121	c.876T>G	c.(874-876)gcT>gcG	p.A292A	PYHIN1_ENST00000485134.1_3'UTR|PYHIN1_ENST00000368138.3_Silent_p.A283A|PYHIN1_ENST00000392252.3_Silent_p.A283A|PYHIN1_ENST00000392254.2_Silent_p.A292A	NM_152501.4|NM_198928.4|NM_198929.4	NP_689714.2|NP_945146.1|NP_945147.1	Q6K0P9	IFIX_HUMAN	pyrin and HIN domain family, member 1	292	HIN-200. {ECO:0000255|PROSITE- ProRule:PRU00106}.				cell cycle (GO:0007049)	nucleus (GO:0005634)				breast(2)|endometrium(3)|large_intestine(10)|lung(32)|ovary(3)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_hematologic(112;0.0378)					TATCTGAAGCTGGTCCTGACC	0.353																																					p.A292A		Atlas-SNP	.											.	PYHIN1	208	.	0			c.T876G						PASS	.						49	50	50					1																	158912063		2203	4298	6501	SO:0001819	synonymous_variant	149628	exon5			TGAAGCTGGTCCT	AY185344	CCDS1178.1, CCDS1179.1, CCDS30907.1, CCDS30908.1	1q23.1	2008-02-05			ENSG00000163564	ENSG00000163564			28894	protein-coding gene	gene with protein product		612677				15122330	Standard	NM_152501		Approved	IFIX, MGC23885	uc001ftb.3	Q6K0P9	OTTHUMG00000037109	ENST00000368140.1:c.876T>G	chr1.hg19:g.158912063T>G		78.0	0.0	.		72.0	8.0	.	NM_152501	Q5T3W6|Q6K0P6|Q6K0P7|Q6K0P8|Q8WW65	Silent	SNP	ENST00000368140.1	hg19	CCDS1178.1																																																																																			.	.	.	none		0.353	PYHIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090110.1	NM_152501		G	158912063	T	G	158912063	2	3	124	1	0	0	0	0	0	0	0	1	12878	1567	55	5		5	PYHIN1	1	158912063	Silent	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	13472146	158912063	90338558	5	7762											
ZP4	57829	hgsc.bcm.edu	37	chr1	238053765	238053765	+	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	aagtcatcaaacttaccccaAgctattagtacaggaggaga	16	8	8	9	0	2	1	2	0	0	1	2	3	2	2	2	2	4	2	2	2	7	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr1:238053765A>T	ENST00000366570.4	-	1	329	c.171T>A	c.(169-171)gcT>gcA	p.A57A	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	57					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)			ACTTACCCCAAGCTATTAGTA	0.478																																					p.A57A	NSCLC(166;160 2029 11600 18754 19936)	Atlas-SNP	.											.	ZP4	161	.	0			c.T171A						PASS	.						68	67	67					1																	238053765		2203	4300	6503	SO:0001819	synonymous_variant	57829	exon1			ACCCCAAGCTATT	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.171T>A	chr1.hg19:g.238053765A>T		61.0	0.0	.		89.0	9.0	.	NM_021186	B2RAE1	Silent	SNP	ENST00000366570.4	hg19	CCDS1615.1																																																																																			.	.	.	none		0.478	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1			T	238053765	A	T	238053765	2	4	124	1	0	0	0	0	0	0	0	1	18230	59	3	5		5	ZP4	1	238053765	Silent	SNP	A	TCGA-BQ-5889-01A-11D-1589-08	79141702	238053765	11196856	6	7763											
CRIM1	51232	hgsc.bcm.edu	37	chr2	36583678	36583678	+	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	ggcggcaccttcgggatttaCggaacctgcgaccgggggct	6	7	16	12	5	0	0	0	0	0	0	1	3	0	2	3	6	3	2	3	6	2	3	rs369487866		TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr2:36583678C>G	ENST00000280527.2	+	1	610	c.243C>G	c.(241-243)taC>taG	p.Y81*	RP11-490M8.1_ENST00000565283.1_lincRNA	NM_016441.2	NP_057525.1	Q9NZV1	CRIM1_HUMAN	cysteine rich transmembrane BMP regulator 1 (chordin-like)	81	IGFBP N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00653}.				insulin-like growth factor receptor signaling pathway (GO:0048009)|nervous system development (GO:0007399)|regulation of cell growth (GO:0001558)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	insulin-like growth factor-activated receptor activity (GO:0005010)|PDZ domain binding (GO:0030165)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(15)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	45		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				TCGGGATTTACGGAACCTGCG	0.682																																					p.Y81X		Atlas-SNP	.											.	CRIM1	88	.	0			c.C243G						PASS	.						40	42	41					2																	36583678		2202	4298	6500	SO:0001587	stop_gained	51232	exon1			GATTTACGGAACC	AF168681	CCDS1783.1	2p21	2010-06-29	2005-07-25		ENSG00000150938	ENSG00000150938			2359	protein-coding gene	gene with protein product		606189	"cysteine-rich motor neuron 1"	S52		10642437	Standard	NM_016441		Approved		uc002rpd.3	Q9NZV1	OTTHUMG00000099419	ENST00000280527.2:c.243C>G	chr2.hg19:g.36583678C>G	ENSP00000280527:p.Tyr81*	68.0	0.0	.		72.0	8.0	.	NM_016441	Q2M2G4|Q59GH0|Q7LCQ5|Q9H318	Nonsense_Mutation	SNP	ENST00000280527.2	hg19	CCDS1783.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	36|36	5.673833|5.673833	0.96764|0.96764	.|.	.|.	ENSG00000150938|ENSG00000150938	ENST00000428774|ENST00000280527;ENST00000426856	.|.	.|.	.|.	3.26|3.26	-0.383|-0.383	0.12477|0.12477	.|.	.|0.313844	.|0.28790	.|N	.|0.014130	T|.	0.13157|.	0.0319|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.34527|.	-0.9825|.	3|.	.|0.02654	.|T	.|1	-0.0216|-0.0216	4.367|4.367	0.11228|0.11228	0.0:0.4434:0.1693:0.3873|0.0:0.4434:0.1693:0.3873	.|.	.|.	.|.	.|.	R|X	22|81;31	.|.	.|ENSP00000280527:Y81X	T|Y	+|+	2|3	0|2	CRIM1|CRIM1	36437182|36437182	0.988000|0.988000	0.35896|0.35896	0.948000|0.948000	0.38648|0.38648	0.105000|0.105000	0.19272|0.19272	0.433000|0.433000	0.21477|0.21477	-0.053000|-0.053000	0.13289|0.13289	-0.132000|-0.132000	0.14878|0.14878	ACG|TAC	.	.	.	alt		0.682	CRIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216878.2	NM_016441		G	36583678	C	G	36583678	4	3	124	1	0	0	0	0	0	1	0	0	3875	547	19	4	245	4	CRIM1	2	36583678	Nonsense_Mutation	SNP	C	TCGA-BQ-5889-01A-11D-1589-08		36583678	206615695	7	7764											
SRBD1	55133	hgsc.bcm.edu	37	chr2	45647009	45647009	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacactgtccagtgttgcctTgagtaaagtctgggatacgt	10	12	11	8	1	1	1	0	1	1	0	2	2	2	2	2	1	3	2	2	1	4	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr2:45647009T>C	ENST00000263736.4	-	17	2136	c.2074A>G	c.(2074-2076)Aag>Gag	p.K692E	SRBD1_ENST00000535761.1_Missense_Mutation_p.K211E|SRBD1_ENST00000490133.1_5'UTR	NM_018079.4	NP_060549.4	Q8N5C6	SRBD1_HUMAN	S1 RNA binding domain 1	692					nucleobase-containing compound metabolic process (GO:0006139)		hydrolase activity, acting on ester bonds (GO:0016788)|RNA binding (GO:0003723)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(13)|large_intestine(8)|lung(15)|skin(2)|stomach(1)|urinary_tract(1)	49		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)			AGTGTTGCCTTGAGTAAAGTC	0.383																																					p.K692E		Atlas-SNP	.											.	SRBD1	107	.	0			c.A2074G						PASS	.						151	136	141					2																	45647009		2203	4300	6503	SO:0001583	missense	55133	exon17			TTGCCTTGAGTAA	AK056536	CCDS1823.1	2p21	2008-02-05			ENSG00000068784	ENSG00000068784			25521	protein-coding gene	gene with protein product						12477932	Standard	NM_018079		Approved	FLJ10379	uc002rus.3	Q8N5C6	OTTHUMG00000128814	ENST00000263736.4:c.2074A>G	chr2.hg19:g.45647009T>C	ENSP00000263736:p.Lys692Glu	111.0	0.0	.		170.0	19.0	.	NM_018079	Q53T56|Q96TA4|Q9NW11	Missense_Mutation	SNP	ENST00000263736.4	hg19	CCDS1823.1	.	.	.	.	.	.	.	.	.	.	T	16.11	3.029717	0.54790	.	.	ENSG00000068784	ENST00000263736;ENST00000535761	T;T	0.32272	1.83;1.46	5.74	5.74	0.90152	Tex-like domain (1);	0.000000	0.85682	D	0.000000	T	0.40372	0.1114	L	0.39020	1.185	0.46336	D	0.998999	D	0.67145	0.996	P	0.60609	0.877	T	0.08994	-1.0695	10	0.14656	T	0.56	.	16.0363	0.80631	0.0:0.0:0.0:1.0	.	692	Q8N5C6	SRBD1_HUMAN	E	692;211	ENSP00000263736:K692E;ENSP00000441272:K211E	ENSP00000263736:K692E	K	-	1	0	SRBD1	45500513	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.193000	0.70182	0.460000	0.39030	AAG	.	.	.	none		0.383	SRBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250747.3	NM_018079		C	45647009	T	C	45647009	3	2	124	1	0	0	0	0	1	0	0	0	15145	1821	63	3	933	3	SRBD1	2	45647009	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	9063331	45647009	197552364	8	7765											
EIF5B	9669	hgsc.bcm.edu	37	chr2	99978207	99978207	+	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	aaatttgaagaagaaactgtAaaatccaaagtgactgttga	19	10	8	4	0	0	5	0	3	0	2	1	5	1	5	1	0	1	2	1	0	7	3			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr2:99978207A>T	ENST00000289371.6	+	4	1045	c.843A>T	c.(841-843)gtA>gtT	p.V281V		NM_015904.3	NP_056988.3	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B	281					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|regulation of translational initiation (GO:0006446)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						AAGAAACTGTAAAATCCAAAG	0.388																																					p.V281V	Colon(162;2388 2567 2705 3444)	Atlas-SNP	.											EIF5B,colon,carcinoma,0,1	EIF5B	95	.	0			c.A843T						PASS	.						98	97	97					2																	99978207		1836	4081	5917	SO:0001819	synonymous_variant	9669	exon4			AACTGTAAAATCC	AF078035	CCDS42721.1	2q11.2	2012-09-20			ENSG00000158417	ENSG00000158417			30793	protein-coding gene	gene with protein product	"translation initiation factor IF2"	606086				10200264, 10432305	Standard	XM_005264075		Approved	IF2, KIAA0741, DKFZp434I036, FLJ10524	uc002tab.3	O60841	OTTHUMG00000153242	ENST00000289371.6:c.843A>T	chr2.hg19:g.99978207A>T		185.0	0.0	.		187.0	15.0	.	NM_015904	O95805|Q53RV7|Q53SI8|Q9UF81|Q9UMN7	Silent	SNP	ENST00000289371.6	hg19	CCDS42721.1																																																																																			.	.	.	none		0.388	EIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330364.2	NM_015904		T	99978207	A	T	99978207	2	4	124	1	0	0	0	0	0	0	0	1	5046	349	13	5		5	EIF5B	2	99978207	Silent	SNP	A	TCGA-BQ-5889-01A-11D-1589-08	54331198	99978207	143221166	9	7766											
SLC20A1	6574	hgsc.bcm.edu	37	chr2	113404533	113404533	+	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	attctccgtgggagccaatgAtgtagcaaattcttttggta	10	14	10	7	1	2	1	0	1	2	0	3	2	2	2	2	2	2	3	2	2	4	6			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr2:113404533A>T	ENST00000272542.3	+	2	667	c.128A>T	c.(127-129)gAt>gTt	p.D43V	AC079922.3_ENST00000457336.1_lincRNA	NM_005415.4	NP_005406.3	Q8WUM9	S20A1_HUMAN	solute carrier family 20 (phosphate transporter), member 1	43					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						GGAGCCAATGATGTAGCAAAT	0.502																																					p.D43V		Atlas-SNP	.											.	SLC20A1	59	.	0			c.A128T						PASS	.						110	104	106					2																	113404533		2203	4300	6503	SO:0001583	missense	6574	exon2			CCAATGATGTAGC		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.128A>T	chr2.hg19:g.113404533A>T	ENSP00000272542:p.Asp43Val	96.0	0.0	.		97.0	10.0	.	NM_005415	Q08344|Q6DHX8|Q9UQ82	Missense_Mutation	SNP	ENST00000272542.3	hg19	CCDS2099.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.542663	0.85917	.	.	ENSG00000144136	ENST00000272542	D	0.95412	-3.7	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	D	0.98557	0.9518	H	0.97918	4.105	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99372	1.0920	10	0.87932	D	0	3.1498	13.0754	0.59083	1.0:0.0:0.0:0.0	.	43	Q8WUM9	S20A1_HUMAN	V	43	ENSP00000272542:D43V	ENSP00000272542:D43V	D	+	2	0	SLC20A1	113121004	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.283000	0.95860	2.036000	0.60181	0.482000	0.46254	GAT	.	.	.	none		0.502	SLC20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254086.2	NM_005415		T	113404533	A	T	113404533	3	4	124	1	0	0	0	0	1	0	0	0	14451	333	12	5	130	5	SLC20A1	2	113404533	Missense_Mutation	SNP	A	TCGA-BQ-5889-01A-11D-1589-08	13426326	113404533	129794840	10	7767											
ERCC3	2071	hgsc.bcm.edu	37	chr2	128050232	128050232	+	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	ggactccagtcttgctgagcTtcctgaggtactcggtgatg	6	12	13	10	1	1	3	0	3	1	0	4	4	3	4	2	3	3	3	2	3	1	3			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr2:128050232T>A	ENST00000285398.2	-	3	519	c.425A>T	c.(424-426)aAg>aTg	p.K142M	ERCC3_ENST00000493187.2_Missense_Mutation_p.K78M	NM_000122.1	NP_000113.1	P19447	ERCC3_HUMAN	excision repair cross-complementation group 3	142					7-methylguanosine mRNA capping (GO:0006370)|apoptotic process (GO:0006915)|DNA repair (GO:0006281)|DNA topological change (GO:0006265)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA duplex unwinding (GO:0000717)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein localization (GO:0008104)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|response to UV (GO:0009411)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' DNA helicase activity (GO:0043138)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|damaged DNA binding (GO:0003684)|dATP binding (GO:0032564)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|peptide binding (GO:0042277)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	31	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.073)		CTTGCTGAGCTTCCTGAGGTA	0.493			"Mis, S"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.K142M		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (B)	2	2q21	2071	"excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing)"		E	.	ERCC3	73	.	0			c.A425T						PASS	.						102	92	95					2																	128050232		2203	4300	6503	SO:0001583	missense	2071	exon3	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	CTGAGCTTCCTGA	M31899	CCDS2144.1	2q21	2014-09-17	2014-03-07		ENSG00000163161	ENSG00000163161		"General transcription factors", "General transcription factor IIH complex subunits"	3435	protein-coding gene	gene with protein product	"xeroderma pigmentosum group B complementing"	133510	"excision repair cross-complementing rodent repair deficiency, complementation group 3"			8202161	Standard	NM_000122		Approved	XPB, BTF2, RAD25, TFIIH, GTF2H	uc002toh.1	P19447	OTTHUMG00000131530	ENST00000285398.2:c.425A>T	chr2.hg19:g.128050232T>A	ENSP00000285398:p.Lys142Met	110.0	0.0	.		116.0	12.0	.	NM_000122	Q53QM0	Missense_Mutation	SNP	ENST00000285398.2	hg19	CCDS2144.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.485972	0.84854	.	.	ENSG00000163161	ENST00000285398;ENST00000493187	T;T	0.73363	-0.74;-0.74	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.81356	0.4805	L	0.57536	1.79	0.80722	D	1	B	0.24576	0.106	P	0.46208	0.507	T	0.81722	-0.0803	10	0.72032	D	0.01	-32.2621	14.8747	0.70485	0.0:0.0:0.0:1.0	.	142	P19447	ERCC3_HUMAN	M	142;78	ENSP00000285398:K142M;ENSP00000444796:K78M	ENSP00000285398:K142M	K	-	2	0	ERCC3	127766702	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	1.916000	0.55485	0.528000	0.53228	AAG	.	.	.	none		0.493	ERCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331028.1	NM_000122		A	128050232	T	A	128050232	3	1	124	1	0	0	0	0	1	0	0	0	5216	1609	56	5	1975	5	ERCC3	2	128050232	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	14645699	128050232	115149141	11	7768											
UGT1A1	54658	hgsc.bcm.edu	37	chr2	234669022	234669022	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtgtcccatgctgggaagaTactgttgatcccagtggatg	8	11	14	8	0	0	2	0	1	0	1	2	4	2	4	2	3	2	2	2	3	2	2	rs375204962		TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr2:234669022T>C	ENST00000608383.1	+	1	89	c.89T>C	c.(88-90)aTa>aCa	p.I30T	UGT1A1_ENST00000608381.1_Intron|UGT1A3_ENST00000482026.1_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A1_ENST00000360418.3_Missense_Mutation_p.I30T|UGT1A1_ENST00000609767.1_Intron|UGT1A8_ENST00000305208.5_Missense_Mutation_p.I30T			P22309	UD11_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A1	30					acute-phase response (GO:0006953)|bilirubin conjugation (GO:0006789)|biphenyl catabolic process (GO:0070980)|cellular glucuronidation (GO:0052695)|cellular response to ethanol (GO:0071361)|cellular response to glucocorticoid stimulus (GO:0071385)|digestion (GO:0007586)|drug metabolic process (GO:0017144)|estrogen metabolic process (GO:0008210)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|heme catabolic process (GO:0042167)|heterocycle metabolic process (GO:0046483)|liver development (GO:0001889)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of steroid metabolic process (GO:0045939)|organ regeneration (GO:0031100)|porphyrin-containing compound metabolic process (GO:0006778)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|retinoic acid metabolic process (GO:0042573)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic glucuronidation (GO:0052697)|xenobiotic metabolic process (GO:0006805)	cytochrome complex (GO:0070069)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|steroid binding (GO:0005496)			breast(1)|central_nervous_system(2)|endometrium(7)|large_intestine(5)|lung(9)|skin(4)|urinary_tract(2)	30		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;4.1e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000435)|Lung(119;0.00211)|LUSC - Lung squamous cell carcinoma(224;0.0054)	Abacavir(DB01048)|Acetaminophen(DB00316)|Adenine(DB00173)|Atorvastatin(DB01076)|Axitinib(DB06626)|Diclofenac(DB00586)|Dolutegravir(DB08930)|Eltrombopag(DB06210)|Erlotinib(DB00530)|Estradiol(DB00783)|Etoposide(DB00773)|Ezetimibe(DB00973)|Ezogabine(DB04953)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indacaterol(DB05039)|Indomethacin(DB00328)|Irinotecan(DB00762)|Losartan(DB00678)|Lovastatin(DB00227)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naltrexone(DB00704)|Naproxen(DB00788)|Nilotinib(DB04868)|Pazopanib(DB06589)|Propofol(DB00818)|Raltegravir(DB06817)|Regorafenib(DB08896)|Rifampicin(DB01045)|Simvastatin(DB00641)|Sorafenib(DB00398)|Suprofen(DB00870)|Testosterone Propionate(DB01420)	GCTGGGAAGATACTGTTGATC	0.612																																					p.I30T		Atlas-SNP	.											UGT1A1,NS,carcinoma,0,1	UGT1A1	81	.	0			c.T89C						PASS	.	T	THR/ILE,,,,,,,,,	1,4405	2.1+/-5.4	0,1,2202	66	52	57		89,,,,,,,,,	6.1	0.1	2		57	0,8600		0,0,4300	no	missense,intron,intron,intron,intron,intron,intron,intron,intron,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A6,UGT1A5,UGT1A9,UGT1A4,UGT1A1,UGT1A3	NM_000463.2,NM_001072.3,NM_007120.2,NM_019075.2,NM_019076.4,NM_019077.2,NM_019078.1,NM_019093.2,NM_021027.2,NM_205862.1	89,,,,,,,,,	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign,,,,,,,,,	30/534,,,,,,,,,	234669022	1,13005	2203	4300	6503	SO:0001583	missense	54658	exon1			GGAAGATACTGTT	M57899	CCDS2510.1	2q37.1	2014-09-17	2005-07-20		ENSG00000242366	ENSG00000242366	2.4.1.17	"UDP glucuronosyltransferases"	12530	other	complex locus constituent		191740	"UDP glycosyltransferase 1 family, polypeptide A1"	UGT1, GNT1		9295054, 9535849	Standard	NM_000463		Approved	UGT1A		P22309	OTTHUMG00000059117	ENST00000608383.1:c.89T>C	chr2.hg19:g.234669022T>C	ENSP00000476741:p.Ile30Thr	44.0	1.0	.		52.0	5.0	.	NM_000463	A6NJC3|B8K286	Missense_Mutation	SNP	ENST00000608383.1	hg19	CCDS2510.1	.	.	.	.	.	.	.	.	.	.	T	17.58	3.425296	0.62733	2.27E-4	0.0	ENSG00000241635	ENST00000305208;ENST00000360418	T;T	0.71103	-0.54;-0.54	6.07	6.07	0.98685	.	.	.	.	.	T	0.80076	0.4557	L	0.55990	1.75	0.31696	N	0.641215	P;P	0.46952	0.887;0.537	P;B	0.58266	0.836;0.158	T	0.82948	-0.0204	9	0.87932	D	0	.	16.6277	0.84984	0.0:0.0:0.0:1.0	.	30;30	A6NJC3;P22309	.;UD11_HUMAN	T	30	ENSP00000304845:I30T;ENSP00000353593:I30T	ENSP00000304845:I30T	I	+	2	0	UGT1A1	234333761	0.998000	0.40836	0.056000	0.19401	0.047000	0.14425	8.001000	0.88508	2.330000	0.79161	0.528000	0.53228	ATA	.	.	.	weak		0.612	UGT1A1-203	KNOWN	basic|CCDS	protein_coding	protein_coding				C	234669022	T	C	234669022	3	2	124	1	0	0	0	0	1	0	0	0	16956	1406	49	3	91	3	UGT1A1	2	234669022	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	106618790	234669022	8530351	12	7769											
PLCXD2	257068	hgsc.bcm.edu	37	chr3	111432757	111432757	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttattttctaccactgtccCttctacaagcagtacccctt	8	15	3	15	0	2	0	0	0	2	0	3	0	3	0	4	0	4	2	4	0	5	8	rs372815872		TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr3:111432757C>T	ENST00000477665.1	+	3	972	c.648C>T	c.(646-648)ccC>ccT	p.P216P	PLCXD2_ENST00000393934.3_Silent_p.P216P	NM_001185106.1	NP_001172035.1	Q0VAA5	PLCX2_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 2	216					lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)	p.P216P(1)		endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)	17						ACCACTGTCCCTTCTACAAGC	0.443																																					p.P216P		Atlas-SNP	.											.	PLCXD2	36	.	1	Substitution - coding silent(1)	lung(1)	c.C648T						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	83	82	82		648,648	3.5	1	3		82	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PLCXD2	NM_001185106.1,NM_153268.3	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	216/306,216/305	111432757	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	257068	exon3			CTGTCCCTTCTAC	AK056141	CCDS2961.1, CCDS54619.1	3q13.2	2004-09-09			ENSG00000240891	ENSG00000240891			26462	protein-coding gene	gene with protein product							Standard	NM_001185106		Approved	FLJ31579	uc003dxz.3	Q0VAA5	OTTHUMG00000159279	ENST00000477665.1:c.648C>T	chr3.hg19:g.111432757C>T		142.0	0.0	.		111.0	13.0	.	NM_001185106	Q96N12	Silent	SNP	ENST00000477665.1	hg19	CCDS54619.1																																																																																			.	.	.	weak		0.443	PLCXD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354322.1	NM_153268		T	111432757	C	T	111432757	2	4	124	1	0	0	0	0	0	0	0	1	12049	668	24	2		2	PLCXD2	3	111432757	Silent	SNP	C	TCGA-BQ-5889-01A-11D-1589-08		111432757	86589673	13	7770											
LYAR	55646	hgsc.bcm.edu	37	chr4	4276371	4276375	+	Frame_Shift_Del	DEL	CTTCA	CTTCA	-																															tttctttctcttttattcttCttcacctccccttgctgttc																										TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	CTTCA	CTTCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr4:4276371_4276375delCTTCA	ENST00000343470.4	-	7	791_795	c.551_555delTGAAG	c.(550-555)gtgaagfs	p.VK184fs	LYAR_ENST00000452476.1_Frame_Shift_Del_p.VK184fs	NM_017816.2	NP_060286	Q9NX58	LYAR_HUMAN	Ly1 antibody reactive	184	Lys-rich.					nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(6)|liver(2)|lung(5)|ovary(1)|prostate(1)	17				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		ttttATTCTTCTTCACCTCCCCTTG	0.449																																					p.184_186del		Atlas-INDEL	.											.	LYAR	36	.	0			c.552_556del						PASS	.																																			SO:0001589	frameshift_variant	55646	exon7			.	AL136750	CCDS3374.1	4p16.3	2013-01-10	2012-12-07		ENSG00000145220	ENSG00000145220		"Zinc fingers, C2HC-type containing"	26021	protein-coding gene	gene with protein product			"Ly1 antibody reactive homolog (mouse)"			11230166, 8491376	Standard	NM_001145725		Approved	ZC2HC2, ZLYAR	uc003ght.3	Q9NX58	OTTHUMG00000125477	ENST00000343470.4:c.551_555delTGAAG	chr4.hg19:g.4276371_4276375delCTTCA	ENSP00000345917:p.Val184fs	206.0	0.0	0		175.0	14.0	0.08	NM_001145725	D3DVS4|Q6FI78|Q9NYS1	Frame_Shift_Del	DEL	ENST00000343470.4	hg19	CCDS3374.1																																																																																			.	.	.	none		0.449	LYAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246800.2	NM_017816		-	4276375	CTTCA	-	4276371	7	5	124	1	0	1	0	1	0	0	0	0	9110	912	32	0	600	0	LYAR	4	4276371	Frame_Shift_Del	DEL	CTTCA	TCGA-BQ-5889-01A-11D-1589-08		4276371	186877905	14	7771											
OTUD4	54726	hgsc.bcm.edu	37	chr4	146076795	146076795	+	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	tgagtgacttaagaacctttCtagacaaaggcaggctagta	14	10	10	7	0	1	4	0	2	1	2	1	4	1	4	1	2	1	3	1	2	6	5			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr4:146076795C>A	ENST00000447906.2	-	9	921	c.734G>T	c.(733-735)aGa>aTa	p.R245I	OTUD4_ENST00000455611.2_5'UTR|OTUD4_ENST00000454497.2_Missense_Mutation_p.R180I			Q01804	OTUD4_HUMAN	OTU deubiquitinase 4	245					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)					AAGAACCTTTCTAGACAAAGG	0.358																																					p.R180I		Atlas-SNP	.											.	OTUD4	120	.	0			c.G539T						PASS	.						106	105	105					4																	146076795		2203	4300	6503	SO:0001583	missense	54726	exon9			ACCTTTCTAGACA		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.734G>T	chr4.hg19:g.146076795C>A	ENSP00000395487:p.Arg245Ile	212.0	0.0	.		176.0	11.0	.	NM_001102653	B4DYS4|Q147U2|Q1ZYK1|Q6PG39|Q96MQ5|Q9NT94|Q9UPV6	Missense_Mutation	SNP	ENST00000447906.2	hg19		.	.	.	.	.	.	.	.	.	.	C	16.36	3.101779	0.56183	.	.	ENSG00000164164	ENST00000454497;ENST00000447906;ENST00000514973	T;T;T	0.32753	1.44;1.44;1.45	5.37	5.37	0.77165	.	0.077530	0.56097	D	0.000034	T	0.40448	0.1117	L	0.60455	1.87	0.80722	D	1	D;D	0.65815	0.995;0.985	P;P	0.52217	0.693;0.578	T	0.18777	-1.0326	10	0.54805	T	0.06	-19.7161	11.4953	0.50404	0.0:0.9095:0.0:0.0905	.	245;244	G3V0I6;Q01804	.;OTUD4_HUMAN	I	180;245;179	ENSP00000409279:R180I;ENSP00000395487:R245I;ENSP00000425972:R179I	ENSP00000395487:R245I	R	-	2	0	OTUD4	146296245	1.000000	0.71417	1.000000	0.80357	0.646000	0.38490	0.964000	0.29306	2.669000	0.90835	0.655000	0.94253	AGA	.	.	.	none		0.358	OTUD4-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000365117.2	NM_017493		A	146076795	C	A	146076795	3	1	124	1	0	0	0	0	1	0	0	0	11321	913	32	4	2662	4	OTUD4	4	146076795	Missense_Mutation	SNP	C	TCGA-BQ-5889-01A-11D-1589-08	141800424	146076795	45077481	15	7772											
ARAP3	64411	hgsc.bcm.edu	37	chr5	141033934	141033934	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccctacttcctcatacacTggctcctcgtacacaggctc	7	10	6	18	1	1	0	1	0	0	0	5	0	3	0	4	2	3	3	4	2	3	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr5:141033934T>C	ENST00000239440.4	-	33	4283	c.4218A>G	c.(4216-4218)ccA>ccG	p.P1406P	ARAP3_ENST00000512390.1_5'UTR|FCHSD1_ENST00000522783.1_5'Flank|ARAP3_ENST00000513878.1_Silent_p.P1055P|FCHSD1_ENST00000435817.2_5'Flank|ARAP3_ENST00000508305.1_Silent_p.P1237P|FCHSD1_ENST00000519800.1_5'Flank	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	1406					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						CCTCATACACTGGCTCCTCGT	0.577																																					p.P1406P		Atlas-SNP	.											.	ARAP3	139	.	0			c.A4218G						PASS	.						106	105	105					5																	141033934		2203	4300	6503	SO:0001819	synonymous_variant	64411	exon33			ATACACTGGCTCC	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.4218A>G	chr5.hg19:g.141033934T>C		128.0	0.0	.		144.0	15.0	.	NM_022481	B4DIT1|D3DQE3	Silent	SNP	ENST00000239440.4	hg19	CCDS4266.1																																																																																			.	.	.	none		0.577	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481		C	141033934	T	C	141033934	2	2	124	1	0	0	0	0	0	0	0	1	840	1567	55	3		3	ARAP3	5	141033934	Silent	SNP	T	TCGA-BQ-5889-01A-11D-1589-08		141033934	39881326	16	7773											
RBM27	54439	hgsc.bcm.edu	37	chr5	145613182	145613182	+	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	cctccaatgccaggtccaggCccaggcccgggcccaggtcc	6	4	12	19	1	0	0	0	0	0	0	3	0	3	0	8	5	1	0	8	5	1	0	rs531339624		TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr5:145613182C>T	ENST00000265271.5	+	7	1186	c.1020C>T	c.(1018-1020)ggC>ggT	p.G340G	RBM27_ENST00000506502.1_Silent_p.G340G	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	340	Pro-rich.				mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			caggtccaggcccaggcccgg	0.622													C|||	1	0.000199681	0	0	5008	,	,		12582	0		0.001	False		,,,				2504	0				p.G340G		Atlas-SNP	.											.	RBM27	119	.	0			c.C1020T						PASS	.						72	69	70					5																	145613182		1568	3582	5150	SO:0001819	synonymous_variant	54439	exon7			TCCAGGCCCAGGC	AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	29243	protein-coding gene	gene with protein product	"acidic rich RS domain containing 1"					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.1020C>T	chr5.hg19:g.145613182C>T		101.0	0.0	.		83.0	4.0	.	NM_018989	Q8IYW9	Silent	SNP	ENST00000265271.5	hg19	CCDS43378.1																																																																																			.	.	.	none		0.622	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128		T	145613182	C	T	145613182	2	4	124	1	0	0	0	0	0	0	0	1	13140	726	26	2		2	RBM27	5	145613182	Silent	SNP	C	TCGA-BQ-5889-01A-11D-1589-08	4579248	145613182	35302078	17	7774											
FBXO38	81545	hgsc.bcm.edu	37	chr5	147781650	147781650	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggcgaagagtaaggggccAtgaggcttttagcattccag	11	8	15	7	1	0	2	0	1	0	1	1	4	1	2	2	4	1	3	2	4	3	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr5:147781650A>G	ENST00000340253.5	+	4	536	c.368A>G	c.(367-369)cAt>cGt	p.H123R	FBXO38_ENST00000296701.6_Missense_Mutation_p.H123R|FBXO38_ENST00000394370.3_Missense_Mutation_p.H123R|FBXO38_ENST00000509699.2_3'UTR|FBXO38_ENST00000513826.1_Missense_Mutation_p.H123R			Q6PIJ6	FBX38_HUMAN	F-box protein 38	123					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)			GTAAGGGGCCATGAGGCTTTT	0.458																																					p.H123R		Atlas-SNP	.											.	FBXO38	115	.	0			c.A368G						PASS	.						143	136	139					5																	147781650		2203	4299	6502	SO:0001583	missense	81545	exon4			GGGGCCATGAGGC	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.368A>G	chr5.hg19:g.147781650A>G	ENSP00000342023:p.His123Arg	147.0	0.0	.		143.0	19.0	.	NM_001271723	Q6PK72|Q7Z2U0|Q86VN3|Q9BXY6|Q9H837|Q9HC40	Missense_Mutation	SNP	ENST00000340253.5	hg19		.	.	.	.	.	.	.	.	.	.	A	15.58	2.876042	0.51695	.	.	ENSG00000145868	ENST00000340253;ENST00000296701;ENST00000394370;ENST00000513826	T;T;T;T	0.29917	1.55;1.56;1.55;1.56	5.77	5.77	0.91146	F-box domain, Skp2-like (1);	0.152919	0.64402	D	0.000014	T	0.20373	0.0490	L	0.27053	0.805	0.42393	D	0.992538	B;B;P	0.47677	0.038;0.053;0.899	B;B;B	0.41036	0.023;0.022;0.346	T	0.05683	-1.0870	10	0.02654	T	1	-12.0661	15.2058	0.73177	1.0:0.0:0.0:0.0	.	123;123;123	Q6PIJ6-3;Q6PIJ6-2;Q6PIJ6	.;.;FBX38_HUMAN	R	123	ENSP00000342023:H123R;ENSP00000296701:H123R;ENSP00000377895:H123R;ENSP00000426410:H123R	ENSP00000296701:H123R	H	+	2	0	FBXO38	147761843	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.793000	0.69060	2.326000	0.78906	0.533000	0.62120	CAT	.	.	.	none		0.458	FBXO38-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000252185.2	NM_030793		G	147781650	A	G	147781650	3	3	124	1	0	0	0	0	1	0	0	0	5753	217	8	3	378	3	FBXO38	5	147781650	Missense_Mutation	SNP	A	TCGA-BQ-5889-01A-11D-1589-08	2168468	147781650	33133610	18	7775											
RFX6	222546	hgsc.bcm.edu	37	chr6	117241541	117241541	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctgatattgaaagggttgaTttgaacagcattggctctca	11	14	10	6	0	2	4	1	4	2	0	3	4	2	4	0	2	2	3	0	2	3	5			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr6:117241541T>C	ENST00000332958.2	+	12	1267	c.1251T>C	c.(1249-1251)gaT>gaC	p.D417D		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	417					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						AAAGGGTTGATTTGAACAGCA	0.418																																					p.D417D		Atlas-SNP	.											.	RFX6	141	.	0			c.T1251C						PASS	.						221	197	205					6																	117241541		2203	4300	6503	SO:0001819	synonymous_variant	222546	exon12			GGTTGATTTGAAC	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.1251T>C	chr6.hg19:g.117241541T>C		236.0	0.0	.		264.0	22.0	.	NM_173560	Q5T6B3	Silent	SNP	ENST00000332958.2	hg19	CCDS5113.1																																																																																			.	.	.	none		0.418	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560		C	117241541	T	C	117241541	2	2	124	1	0	0	0	0	0	0	0	1	13280	1490	52	3		3	RFX6	6	117241541	Silent	SNP	T	TCGA-BQ-5889-01A-11D-1589-08		117241541	53873526	19	7776											
MAD1L1	8379	hgsc.bcm.edu	37	chr7	1855740	1855740	+	Missense_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	ggcggctgaagagctcgaggGtgagcgagctgaggaaggca	10	4	20	7	3	0	4	0	3	0	1	1	7	0	5	0	5	3	4	0	5	2	0			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr7:1855740G>A	ENST00000406869.1	-	19	2680	c.2123C>T	c.(2122-2124)aCc>aTc	p.T708I	MAD1L1_ENST00000402746.1_Missense_Mutation_p.T616I|MAD1L1_ENST00000399654.2_Missense_Mutation_p.T708I|MAD1L1_ENST00000265854.7_Missense_Mutation_p.T708I			Q9Y6D9	MD1L1_HUMAN	MAD1 mitotic arrest deficient-like 1 (yeast)	708					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)		GAGCTCGAGGGTGAGCGAGCT	0.667																																					p.T708I		Atlas-SNP	.											.	MAD1L1	81	.	0			c.C2123T						PASS	.						28	35	33					7																	1855740		2040	4207	6247	SO:0001583	missense	8379	exon19			TCGAGGGTGAGCG	U33822	CCDS43539.1	7p22	2013-01-17	2001-11-28		ENSG00000002822	ENSG00000002822			6762	protein-coding gene	gene with protein product		602686	"MAD1 (mitotic arrest deficient, yeast, homolog)-like 1"			10049595, 9546394	Standard	XM_005249876		Approved	HsMAD1, TXBP181, MAD1, PIG9, TP53I9	uc003slg.1	Q9Y6D9	OTTHUMG00000151493	ENST00000406869.1:c.2123C>T	chr7.hg19:g.1855740G>A	ENSP00000385334:p.Thr708Ile	47.0	0.0	.		81.0	15.0	.	NM_003550	B3KR41|Q13312|Q75MI0|Q86UM4|Q9UNH0	Missense_Mutation	SNP	ENST00000406869.1	hg19	CCDS43539.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.679536	0.88542	.	.	ENSG00000002822	ENST00000402746;ENST00000399654;ENST00000406869;ENST00000442131;ENST00000265854;ENST00000450235	T;T;T;T;T	0.54479	0.57;0.57;0.57;0.57;0.57	3.98	3.98	0.46160	.	.	.	.	.	T	0.73628	0.3611	M	0.80616	2.505	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.79671	-0.1706	9	0.87932	D	0	-6.9772	16.1426	0.81536	0.0:0.0:1.0:0.0	.	616;708	B3KR41;Q9Y6D9	.;MD1L1_HUMAN	I	616;708;708;259;708;259	ENSP00000384155:T616I;ENSP00000382562:T708I;ENSP00000385334:T708I;ENSP00000265854:T708I;ENSP00000394886:T259I	ENSP00000265854:T708I	T	-	2	0	MAD1L1	1822266	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.338000	0.90038	1.787000	0.52448	0.456000	0.33151	ACC	.	.	.	none		0.667	MAD1L1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322871.1	NM_003550		A	1855740	G	A	1855740	3	1	124	1	0	0	0	0	1	0	0	0	9154	1261	44	2	37	2	MAD1L1	7	1855740	Missense_Mutation	SNP	G	TCGA-BQ-5889-01A-11D-1589-08		1855740	157282923	20	7777											
GLI3	2737	hgsc.bcm.edu	37	chr7	42004728	42004728	+	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	cccctgtcccactgggtcctGgttctgcatgccattcacca	5	11	8	17	0	2	0	1	0	1	0	4	0	4	0	6	2	2	2	6	2	0	2			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr7:42004728G>T	ENST00000395925.3	-	15	4027	c.3943C>A	c.(3943-3945)Cag>Aag	p.Q1315K	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	1315					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						ACTGGGTCCTGGTTCTGCATG	0.652									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																												p.Q1315K		Atlas-SNP	.											.	GLI3	312	.	0			c.C3943A						PASS	.						37	36	36					7																	42004728		2203	4300	6503	SO:0001583	missense	2737	exon15	Familial Cancer Database	;	GGTCCTGGTTCTG		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.3943C>A	chr7.hg19:g.42004728G>T	ENSP00000379258:p.Gln1315Lys	69.0	0.0	.		89.0	5.0	.	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	hg19	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	G	14.93	2.681803	0.47991	.	.	ENSG00000106571	ENST00000395925	T	0.12569	2.67	5.65	5.65	0.86999	.	0.741669	0.13841	N	0.359041	T	0.09024	0.0223	N	0.22421	0.69	0.23150	N	0.998213	B	0.13145	0.007	B	0.10450	0.005	T	0.34900	-0.9810	10	0.10377	T	0.69	.	9.7991	0.40753	0.0:0.1247:0.6842:0.1911	.	1315	P10071	GLI3_HUMAN	K	1315	ENSP00000379258:Q1315K	ENSP00000379258:Q1315K	Q	-	1	0	GLI3	41971253	0.977000	0.34250	0.012000	0.15200	0.777000	0.43975	2.070000	0.41491	2.655000	0.90218	0.655000	0.94253	CAG	.	.	.	none		0.652	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		T	42004728	G	T	42004728	3	4	124	1	0	0	0	0	1	0	0	0	6446	1357	47	4	803	4	GLI3	7	42004728	Missense_Mutation	SNP	G	TCGA-BQ-5889-01A-11D-1589-08	40148988	42004728	117133935	21	7778											
CALCR	799	hgsc.bcm.edu	37	chr7	93055856	93055856	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcccccaacgctggttccActgaattttgaattgggccc	7	11	8	15	1	0	2	0	2	0	0	2	2	2	2	5	2	1	2	5	2	3	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr7:93055856A>G	ENST00000394441.1	-	13	1552	c.1237T>C	c.(1237-1239)Tgg>Cgg	p.W413R	CALCR_ENST00000421592.1_Missense_Mutation_p.W429R|CALCR_ENST00000360249.4_Missense_Mutation_p.W429R|CALCR_ENST00000426151.1_Missense_Mutation_p.W413R|CALCR_ENST00000359558.2_Missense_Mutation_p.W447R	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor	447					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)	CGCTGGTTCCACTGAATTTTG	0.542																																					p.W447R		Atlas-SNP	.											.	CALCR	200	.	0			c.T1339C						PASS	.						46	51	50					7																	93055856		2203	4300	6503	SO:0001583	missense	799	exon16			GGTTCCACTGAAT	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.1237T>C	chr7.hg19:g.93055856A>G	ENSP00000377959:p.Trp413Arg	154.0	0.0	.		142.0	15.0	.	NM_001164737	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Missense_Mutation	SNP	ENST00000394441.1	hg19	CCDS5631.1	.	.	.	.	.	.	.	.	.	.	A	19.42	3.823645	0.71143	.	.	ENSG00000004948	ENST00000359558;ENST00000360249;ENST00000421592;ENST00000394441;ENST00000426151	T;T;T;T;T	0.62498	0.02;0.02;0.02;0.02;0.02	4.57	4.57	0.56435	.	.	.	.	.	T	0.68659	0.3025	L	0.45228	1.405	0.51482	D	0.999925	D;P	0.71674	0.998;0.613	D;B	0.72075	0.976;0.248	T	0.66106	-0.6006	9	0.33141	T	0.24	.	10.4932	0.44762	1.0:0.0:0.0:0.0	.	447;413	F5H605;A4D1G6	.;.	R	447;429;429;413;413	ENSP00000352561:W447R;ENSP00000353385:W429R;ENSP00000399552:W429R;ENSP00000377959:W413R;ENSP00000389295:W413R	ENSP00000352561:W447R	W	-	1	0	CALCR	92893792	1.000000	0.71417	0.495000	0.27527	0.014000	0.08584	6.514000	0.73746	2.055000	0.61198	0.477000	0.44152	TGG	.	.	.	none		0.542	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742		G	93055856	A	G	93055856	3	3	124	1	0	0	0	0	1	0	0	0	2581	159	6	3	191	3	CALCR	7	93055856	Missense_Mutation	SNP	A	TCGA-BQ-5889-01A-11D-1589-08	51051128	93055856	66082807	22	7779											
EPHB6	2051	hgsc.bcm.edu	37	chr7	142562311	142562311	+	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	acgcaggccagtggggctggGggggcctccctggtggcagc	4	5	20	12	1	0	0	0	0	0	0	1	0	1	0	3	8	1	3	3	8	0	0			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr7:142562311G>T	ENST00000392957.2	+	7	1540	c.753G>T	c.(751-753)ggG>ggT	p.G251G	EPHB6_ENST00000442129.1_Silent_p.G251G|EPHB6_ENST00000411471.2_Intron	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	251	Cys-rich.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					GTGGGGCTGGGGGGGCCTCCC	0.682																																					p.G251G		Atlas-SNP	.											.	EPHB6	168	.	0			c.G753T						PASS	.						47	59	55					7																	142562311		2184	4281	6465	SO:0001819	synonymous_variant	2051	exon7			GGCTGGGGGGGCC	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.753G>T	chr7.hg19:g.142562311G>T		212.0	0.0	.		233.0	37.0	.	NM_004445	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Silent	SNP	ENST00000392957.2	hg19	CCDS5873.2																																																																																			.	.	.	none		0.682	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			T	142562311	G	T	142562311	2	4	124	1	0	0	0	0	0	0	0	1	5180	1219	43	4		4	EPHB6	7	142562311	Silent	SNP	G	TCGA-BQ-5889-01A-11D-1589-08	49506455	142562311	16576352	23	7780											
PDP1	54704	hgsc.bcm.edu	37	chr8	94935503	94935503	+	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	cagaggtaacttaccaccgaTtaaggccacaggataagttt	14	9	9	9	1	0	1	0	0	0	1	0	3	0	2	3	3	2	2	3	3	4	5			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr8:94935503T>A	ENST00000297598.4	+	2	1485	c.1216T>A	c.(1216-1218)Tta>Ata	p.L406I	PDP1_ENST00000520728.1_Missense_Mutation_p.L406I|PDP1_ENST00000396200.3_Missense_Mutation_p.L431I|PDP1_ENST00000517764.1_Missense_Mutation_p.L406I	NM_001161781.1|NM_018444.3	NP_001155253.1|NP_060914.2	Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic subunit 1	406					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						TTACCACCGATTAAGGCCACA	0.458																																					p.L431I		Atlas-SNP	.											.	PDP1	97	.	0			c.T1291A						PASS	.						124	120	121					8																	94935503		2203	4300	6503	SO:0001583	missense	54704	exon3			CACCGATTAAGGC	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.1216T>A	chr8.hg19:g.94935503T>A	ENSP00000297598:p.Leu406Ile	144.0	0.0	.		171.0	13.0	.	NM_001161780	B3KX71|J3KPU0|Q5U5K1	Missense_Mutation	SNP	ENST00000297598.4	hg19	CCDS6259.1	.	.	.	.	.	.	.	.	.	.	T	12.14	1.847623	0.32606	.	.	ENSG00000164951	ENST00000297598;ENST00000520728;ENST00000396200;ENST00000517764	T;T;T;T	0.16897	2.31;2.31;2.31;2.31	6.03	2.5	0.30297	Protein phosphatase 2C-like (5);	0.072136	0.56097	D	0.000026	T	0.20129	0.0484	L	0.28608	0.87	0.58432	D	0.999998	D;P	0.56287	0.975;0.932	P;P	0.57502	0.822;0.725	T	0.02004	-1.1231	10	0.27082	T	0.32	-7.6451	9.7831	0.40660	0.0:0.1882:0.0:0.8118	.	457;406	B4DYX8;Q9P0J1	.;PDP1_HUMAN	I	406;406;431;406	ENSP00000297598:L406I;ENSP00000428317:L406I;ENSP00000379503:L431I;ENSP00000430380:L406I	ENSP00000297598:L406I	L	+	1	2	PDP1	95004679	0.732000	0.28121	1.000000	0.80357	0.993000	0.82548	1.160000	0.31761	1.108000	0.41662	0.533000	0.62120	TTA	.	.	.	none		0.458	PDP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378415.2	NM_018444		A	94935503	T	A	94935503	3	1	124	1	0	0	0	0	1	0	0	0	11692	1490	52	5	1399	5	PDP1	8	94935503	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08		94935503	51428519	24	7781											
SNX30	401548	hgsc.bcm.edu	37	chr9	115567070	115567071	+	Frame_Shift_Ins	INS	-	-	A																															tttaggatctcattttgcccINSaacggtggtactccagcagg																										TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr9:115567070_115567071insA	ENST00000374232.3	+	2	335_336	c.171_172insA	c.(172-174)aacfs	p.N58fs		NM_001012994.1	NP_001013012.1	Q5VWJ9	SNX30_HUMAN	sorting nexin family member 30	58					apoptotic process (GO:0006915)|intracellular protein transport (GO:0006886)	endosome (GO:0005768)	phosphatidylinositol binding (GO:0035091)			large_intestine(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						TCATTTTGCCCAACGGTGGTAC	0.401																																					p.P57fs		Atlas-INDEL	.											.	SNX30	32	.	0			c.171_172insA						PASS	.																																			SO:0001589	frameshift_variant	401548	exon2			.	AK126644	CCDS43865.1	9q33.1	2014-02-12			ENSG00000148158	ENSG00000148158		"Sorting nexins"	23685	protein-coding gene	gene with protein product							Standard	NM_001012994		Approved	ATG24A	uc004bgj.4	Q5VWJ9	OTTHUMG00000020512	ENST00000374232.3:c.173dupA	chr9.hg19:g.115567072_115567072dupA	ENSP00000363349:p.Asn58fs	252.0	0.0	0		265.0	27.0	0.101887	NM_001012994		Frame_Shift_Ins	INS	ENST00000374232.3	hg19	CCDS43865.1																																																																																			.	.	.	none		0.401	SNX30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053700.1			A	115567071	-	A	115567070	7	5	124	1	0	1	1	0	0	0	0	0	14913	581	21	0	177	0	SNX30	9	115567070	Frame_Shift_Ins	INS	-	TCGA-BQ-5889-01A-11D-1589-08		115567070	25646361	25	7782											
STAM	8027	hgsc.bcm.edu	37	chr10	17735224	17735225	+	Missense_Mutation	DNP	GC	GC	AA																															ttcctcttttttgttaggctGcagaacaagcaaaagcaagc																										TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr10:17735224_17735225GC>AA	ENST00000377524.3	+	6	663_664	c.448_449GC>AA	c.(448-450)GCa>AAa	p.A150K	RP11-390B4.3_ENST00000445235.1_RNA|STAM_ENST00000540523.1_Missense_Mutation_p.A39K	NM_003473.3	NP_003464.1	Q92783	STAM1_HUMAN	signal transducing adaptor molecule (SH3 domain and ITAM motif) 1	150					endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	26						TTGTTAGGCTGCAGAACAAGCA	0.406																																					p.A150T|p.A150E		Atlas-SNP	.											.	STAM	60	.	0			c.G448A|c.C449A						PASS	.																																			SO:0001583	missense	8027	exon6			TAGGCTGCAGAAC|AGGCTGCAGAACA	U43899	CCDS7122.1	10p14-p13	2009-04-29			ENSG00000136738	ENSG00000136738			11357	protein-coding gene	gene with protein product	"HSE1 homolog (S. cerevisiae)"	601899				8780729	Standard	NM_003473		Approved	STAM1	uc001ipj.2	Q92783	OTTHUMG00000017749	Exception_encountered	chr10.hg19:g.17735224_17735225delinsAA	ENSP00000366746:p.Ala150Lys	154.0	0.0	.		124.0|122.0	10.0	.	NM_003473	B0YJ99|D3DRU5|Q8N6D9	Missense_Mutation	SNP	ENST00000377524.3	hg19	CCDS7122.1																																																																																			.	.	.	none		0.406	STAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047039.1	NM_003473		AA	17735225	GC	AA	17735224	3	1	124	1	0	0	0	0	1	0	0	0	15260	1319	46	2	470	2	STAM	10	17735224	Missense_Mutation	DNP	GC	TCGA-BQ-5889-01A-11D-1589-08		17735224	117799523	26	7783											
KAT5	10524	hgsc.bcm.edu	37	chr11	65480307	65480307	+	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	tacgtccattacattgactgTgagttctgggcctgaggtgg	7	13	13	8	1	1	3	0	3	1	0	2	3	2	3	2	3	2	1	2	3	2	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr11:65480307T>A	ENST00000377046.3	+	3	420		c.e3+2		KAT5_ENST00000534650.1_Splice_Site|KAT5_ENST00000530446.1_Splice_Site|KAT5_ENST00000525204.1_Splice_Site|KAT5_ENST00000341318.4_Splice_Site|KAT5_ENST00000352980.4_Splice_Site	NM_006388.3	NP_006379.2	Q92993	KAT5_HUMAN	K(lysine) acetyltransferase 5						androgen receptor signaling pathway (GO:0030521)|cellular response to estradiol stimulus (GO:0071392)|chromatin organization (GO:0006325)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|double-strand break repair (GO:0006302)|histone acetylation (GO:0016573)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of growth (GO:0040008)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)|Swr1 complex (GO:0000812)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|histone acetyltransferase activity (GO:0004402)|metal ion binding (GO:0046872)|repressing transcription factor binding (GO:0070491)|transcription coactivator activity (GO:0003713)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)	21						ACATTGACTGTGAGTTCTGGG	0.547																																					.		Atlas-SNP	.											.	KAT5	36	.	0			c.247+2T>A						PASS	.						123	117	119					11																	65480307		2201	4297	6498	SO:0001630	splice_region_variant	10524	exon2			TGACTGTGAGTTC	U74667	CCDS8109.1, CCDS8110.1, CCDS31610.1, CCDS55771.1	11q13	2013-01-10	2008-07-04	2008-07-04	ENSG00000172977	ENSG00000172977		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing"	5275	protein-coding gene	gene with protein product	"Tat interacting protein, 60kDa", "K-acetyltransferase 5"	601409	"HIV-1 Tat interactive protein, 60kDa"	HTATIP		8607265	Standard	NM_006388		Approved	TIP60, PLIP, cPLA2, HTATIP1, ESA1, ZC2HC5	uc001ofk.3	Q92993	OTTHUMG00000166617	ENST00000377046.3:c.148+2T>A	chr11.hg19:g.65480307T>A		83.0	0.0	.		117.0	8.0	.	NM_001206833	B4E3C7|C9JL99|O95624|Q13430|Q17RW5|Q561W3|Q6GSE8|Q9BWK7	Splice_Site	SNP	ENST00000377046.3	hg19	CCDS31610.1	.	.	.	.	.	.	.	.	.	.	t	17.79	3.475097	0.63737	.	.	ENSG00000172977	ENST00000377046;ENST00000352980;ENST00000341318;ENST00000530446;ENST00000530605;ENST00000528198;ENST00000531880	.	.	.	4.3	4.3	0.51218	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.4329	0.50052	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	KAT5	65236883	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.458000	0.66679	1.822000	0.53115	0.459000	0.35465	.	.	.	.	none		0.547	KAT5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390866.2	NM_006388	Intron	A	65480307	T	A	65480307	5	1	124	1	0	0	0	0	0	0	1	0	7990	1710	59	5	255	5	KAT5	11	65480307	Splice_Site	SNP	T	TCGA-BQ-5889-01A-11D-1589-08		65480307	69526209	27	7784											
NDUFV1	4723	hgsc.bcm.edu	37	chr11	67379406	67379406	+	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	atcgcccgcctcattgagttCtataagcacgagagctgtgg	9	10	11	11	3	2	2	1	1	1	1	3	3	2	2	2	1	2	3	2	1	2	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr11:67379406C>A	ENST00000322776.6	+	8	1272	c.1119C>A	c.(1117-1119)ttC>ttA	p.F373L	NDUFV1_ENST00000532303.1_Missense_Mutation_p.F272L|NDUFV1_ENST00000415352.2_Missense_Mutation_p.F366L|NDUFV1_ENST00000526169.1_3'UTR|DOC2GP_ENST00000495263.1_RNA|NDUFV1_ENST00000529927.1_Missense_Mutation_p.F364L	NM_001166102.1|NM_007103.3	NP_001159574.1|NP_009034.2	P49821	NDUV1_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 1, 51kDa	373					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(3)|large_intestine(2)|lung(7)|prostate(1)|skin(2)	16						TCATTGAGTTCTATAAGCACG	0.612																																					p.F373L		Atlas-SNP	.											.	NDUFV1	30	.	0			c.C1119A						PASS	.						130	117	122					11																	67379406		2200	4294	6494	SO:0001583	missense	4723	exon8			TGAGTTCTATAAG	AF092131	CCDS8173.1, CCDS53669.1	11q13	2011-07-04	2002-08-29		ENSG00000167792	ENSG00000167792	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7716	protein-coding gene	gene with protein product	"complex I 51kDa subunit", "NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial"	161015	"NADH dehydrogenase (ubiquinone) flavoprotein 1 (51kD)"			1478657	Standard	NM_007103		Approved	CI-51K	uc001omj.2	P49821	OTTHUMG00000166215	ENST00000322776.6:c.1119C>A	chr11.hg19:g.67379406C>A	ENSP00000322450:p.Phe373Leu	96.0	0.0	.		124.0	12.0	.	NM_007103	O60924|O60940|Q16104|Q6IBR3|Q96BF8|Q96HS7	Missense_Mutation	SNP	ENST00000322776.6	hg19	CCDS8173.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.834500	0.91036	.	.	ENSG00000167792	ENST00000322776;ENST00000532303;ENST00000529927;ENST00000415352;ENST00000453836	D;D;D;D	0.92647	-3.08;-3.08;-3.08;-3.08	4.89	3.98	0.46160	NADH ubiquinone oxidoreductase, F subunit, iron sulphur binding (2);	0.000000	0.85682	D	0.000000	D	0.97495	0.9180	H	0.98370	4.215	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	1.0;1.0;0.999	D	0.97852	1.0275	10	0.87932	D	0	-20.1332	12.1898	0.54264	0.0:0.9151:0.0:0.0849	.	366;364;373	G3V0I5;P49821-2;P49821	.;.;NDUV1_HUMAN	L	373;272;364;366;244	ENSP00000322450:F373L;ENSP00000432015:F272L;ENSP00000436766:F364L;ENSP00000395368:F366L	ENSP00000322450:F373L	F	+	3	2	NDUFV1	67135982	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.801000	0.55545	1.189000	0.43028	0.491000	0.48974	TTC	.	.	.	none		0.612	NDUFV1-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388406.1	NM_007103		A	67379406	C	A	67379406	3	1	124	1	0	0	0	0	1	0	0	0	10306	912	32	4	1149	4	NDUFV1	11	67379406	Missense_Mutation	SNP	C	TCGA-BQ-5889-01A-11D-1589-08	1899099	67379406	67627110	28	7785											
HYLS1	219844	hgsc.bcm.edu	37	chr11	125769383	125769383	+	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	cagggtgaaggagatgtcagGagagaagcccaatctatcca	14	6	13	8	0	2	3	1	1	1	2	3	6	3	4	2	3	1	0	2	3	4	1			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr11:125769383G>T	ENST00000425380.2	+	3	901	c.120G>T	c.(118-120)agG>agT	p.R40S	PUS3_ENST00000227474.3_Intron|HYLS1_ENST00000526028.1_Missense_Mutation_p.R40S|HYLS1_ENST00000356438.3_Missense_Mutation_p.R40S	NM_001134793.1	NP_001128265.1	Q96M11	HYLS1_HUMAN	hydrolethalus syndrome 1	40						centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|skin(3)|upper_aerodigestive_tract(1)	9	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;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0446)		GAGATGTCAGGAGAGAAGCCC	0.488																																					p.R40S	Esophageal Squamous(172;2590 2636 8884 10471)	Atlas-SNP	.											HYLS1,NS,carcinoma,0,1	HYLS1	25	.	0			c.G120T						PASS	.						88	79	82					11																	125769383		2201	4299	6500	SO:0001583	missense	219844	exon3			TGTCAGGAGAGAA	AK057477	CCDS8467.1	11q24	2014-06-18				ENSG00000198331			26558	protein-coding gene	gene with protein product		610693				15843405	Standard	NM_145014		Approved	FLJ32915	uc009zbv.3	Q96M11		ENST00000425380.2:c.120G>T	chr11.hg19:g.125769383G>T	ENSP00000414884:p.Arg40Ser	57.0	0.0	.		81.0	5.0	.	NM_001134793	B3KXI8|Q96BX9	Missense_Mutation	SNP	ENST00000425380.2	hg19	CCDS8467.1	.	.	.	.	.	.	.	.	.	.	G	10.78	1.446536	0.25987	.	.	ENSG00000198331	ENST00000356438;ENST00000425380;ENST00000526028	T;T;T	0.63580	-0.05;-0.05;-0.05	6.17	1.81	0.25067	.	0.207432	0.29501	N	0.011979	T	0.42854	0.1221	L	0.44542	1.39	0.29443	N	0.859016	P	0.41848	0.763	B	0.31101	0.124	T	0.40905	-0.9538	10	0.40728	T	0.16	.	6.3201	0.21213	0.3191:0.162:0.5189:0.0	.	40	Q96M11	HYLS1_HUMAN	S	40	ENSP00000348815:R40S;ENSP00000414884:R40S;ENSP00000436833:R40S	ENSP00000348815:R40S	R	+	3	2	HYLS1	125274593	0.982000	0.34865	0.982000	0.44146	0.989000	0.77384	0.896000	0.28377	0.507000	0.28148	0.655000	0.94253	AGG	.	.	.	none		0.488	HYLS1-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386733.1	NM_145014		T	125769383	G	T	125769383	3	4	124	1	0	0	0	0	1	0	0	0	7476	1165	41	4	122	4	HYLS1	11	125769383	Missense_Mutation	SNP	G	TCGA-BQ-5889-01A-11D-1589-08	58389977	125769383	9237133	29	7786											
SLC26A10	65012	hgsc.bcm.edu	37	chr12	58016635	58016635	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctggctgactcgctgcccaTtgcactggttagttttgcgg	4	14	12	11	2	1	1	0	1	1	0	2	1	1	1	1	3	3	5	1	3	1	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr12:58016635T>C	ENST00000320442.4	+	6	1168	c.857T>C	c.(856-858)aTt>aCt	p.I286T	SLC26A10_ENST00000379218.2_Missense_Mutation_p.I286T	NM_133489.2	NP_597996.2	Q8NG04	S2610_HUMAN	solute carrier family 26, member 10	286						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)					TCGCTGCCCATTGCACTGGTT	0.572																																					p.I286T		Atlas-SNP	.											.	SLC26A10	89	.	0			c.T857C						PASS	.						110	91	98					12																	58016635		2203	4300	6503	SO:0001583	missense	65012	exon6			TGCCCATTGCACT		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.857T>C	chr12.hg19:g.58016635T>C	ENSP00000320217:p.Ile286Thr	88.0	0.0	.		114.0	15.0	.	NM_133489	A6NMJ2|B6ZDQ3|Q6ZWI7	Missense_Mutation	SNP	ENST00000320442.4	hg19	CCDS8949.2	.	.	.	.	.	.	.	.	.	.	.	14.38	2.518982	0.44866	.	.	ENSG00000135502	ENST00000320442;ENST00000379218	D;D	0.93547	-3.24;-3.24	3.76	3.76	0.43208	Sulphate transporter (1);	.	.	.	.	D	0.94850	0.8336	M	0.91090	3.175	0.42787	D	0.993885	P	0.45283	0.855	P	0.46685	0.524	D	0.94723	0.7902	9	0.45353	T	0.12	.	11.1297	0.48339	0.0:0.0:0.0:1.0	.	286	Q8NG04	S2610_HUMAN	T	286	ENSP00000320217:I286T;ENSP00000368520:I286T	ENSP00000320217:I286T	I	+	2	0	SLC26A10	56302902	0.996000	0.38824	0.902000	0.35471	0.457000	0.32468	6.621000	0.74228	1.941000	0.56285	0.523000	0.50628	ATT	.	.	.	none		0.572	SLC26A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250311.2			C	58016635	T	C	58016635	3	2	124	1	0	0	0	0	1	0	0	0	14528	1493	52	3	879	3	SLC26A10	12	58016635	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08		58016635	75835260	30	7787											
ZMYM5	9205	hgsc.bcm.edu	37	chr13	20398872	20398872	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatagacaaaacacagaatcTtttgaggttgaataaagtaa	19	11	7	4	0	1	4	0	2	1	2	1	4	1	4	0	1	1	2	0	1	9	7			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr13:20398872T>C	ENST00000337963.4	-	8	2019	c.1755A>G	c.(1753-1755)aaA>aaG	p.K585K		NM_001142684.1	NP_001136156.1	Q9UJ78	ZMYM5_HUMAN	zinc finger, MYM-type 5	585						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			kidney(1)|large_intestine(5)|lung(9)	15		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)		acacagaatcttttgaggttg	0.333																																					p.K585K		Atlas-SNP	.											.	ZMYM5	73	.	0			c.A1755G						PASS	.						27	23	24					13																	20398872		1567	3581	5148	SO:0001819	synonymous_variant	9205	exon8			AGAATCTTTTGAG	AF161535	CCDS31942.1, CCDS31943.1	13q12	2013-01-08	2005-09-12	2005-09-12	ENSG00000132950	ENSG00000132950		"Zinc fingers, MYM type"	13029	protein-coding gene	gene with protein product			"zinc finger protein 237"	ZNF237			Standard	NM_001039650		Approved	ZNF198L1, MYM	uc010tcn.1	Q9UJ78	OTTHUMG00000016504	ENST00000337963.4:c.1755A>G	chr13.hg19:g.20398872T>C		22.0	0.0	.		35.0	4.0	.	NM_001142684	B2R6V1|Q5T6E1|Q5T6E2|Q5T6E4|Q96IY6|Q9NZY5|Q9UBW0|Q9UJ77	Silent	SNP	ENST00000337963.4	hg19																																																																																				.	.	.	none		0.333	ZMYM5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014242		C	20398872	T	C	20398872	2	2	124	1	0	0	0	0	0	0	0	1	17715	1606	56	3		3	ZMYM5	13	20398872	Silent	SNP	T	TCGA-BQ-5889-01A-11D-1589-08		20398872	94771006	31	7788											
TNFRSF19	55504	hgsc.bcm.edu	37	chr13	24243093	24243093	+	Missense_Mutation	SNP	A	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	cagtccagtctcattctgaaAactttacagcagctactgat	12	12	6	11	0	2	2	1	2	2	0	4	2	3	2	1	0	5	2	1	0	4	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr13:24243093A>C	ENST00000382258.4	+	9	1306	c.1102A>C	c.(1102-1104)Aac>Cac	p.N368H	TNFRSF19_ENST00000248484.4_Missense_Mutation_p.N368H|TNFRSF19_ENST00000403372.2_Missense_Mutation_p.N236H|TNFRSF19_ENST00000382263.3_Missense_Mutation_p.N368H	NM_018647.3	NP_061117.2	Q9NS68	TNR19_HUMAN	tumor necrosis factor receptor superfamily, member 19	368					apoptotic process (GO:0006915)|hair follicle development (GO:0001942)|JNK cascade (GO:0007254)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	integral component of membrane (GO:0016021)	tumor necrosis factor-activated receptor activity (GO:0005031)			breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	22		all_cancers(29;3.4e-22)|all_epithelial(30;8.75e-19)|all_lung(29;5.09e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00193)|Epithelial(112;0.0137)|OV - Ovarian serous cystadenocarcinoma(117;0.0465)|GBM - Glioblastoma multiforme(144;0.184)|Lung(94;0.19)		TCATTCTGAAAACTTTACAGC	0.413																																					p.N368H		Atlas-SNP	.											.	TNFRSF19	52	.	0			c.A1102C						PASS	.						113	115	114					13																	24243093		2203	4300	6503	SO:0001583	missense	55504	exon9			TCTGAAAACTTTA	AB040434	CCDS9301.1, CCDS9302.1, CCDS55893.1	13q12.11-q12.3	2008-07-18			ENSG00000127863	ENSG00000127863		"Tumor necrosis factor receptor superfamily"	11915	protein-coding gene	gene with protein product	"toxicity and JNK inducer"	606122				10764796, 10809768	Standard	NM_018647		Approved	TAJ-alpha, TROY, TAJ, TRADE	uc001uov.2	Q9NS68	OTTHUMG00000016568	ENST00000382258.4:c.1102A>C	chr13.hg19:g.24243093A>C	ENSP00000371693:p.Asn368His	169.0	0.0	.		160.0	14.0	.	NM_018647	A8KA09|A8KA26|B1AM40|B1AM41|B4E2I6|Q9BXZ9|Q9BY00|Q9NZV2	Missense_Mutation	SNP	ENST00000382258.4	hg19	CCDS9302.1	.	.	.	.	.	.	.	.	.	.	A	16.15	3.042549	0.55003	.	.	ENSG00000127863	ENST00000248484;ENST00000403372;ENST00000382258;ENST00000382263	T;T;T;T	0.79749	-1.29;1.32;-1.3;-1.29	5.71	3.22	0.36961	.	0.505867	0.20968	N	0.082460	T	0.78892	0.4355	L	0.27053	0.805	0.09310	N	1	D;D;D	0.63880	0.986;0.993;0.993	P;P;P	0.58873	0.794;0.847;0.847	T	0.69176	-0.5214	10	0.66056	D	0.02	-3.4156	8.9366	0.35704	0.853:0.0:0.147:0.0	.	236;368;368	B4E2I6;Q9NS68;Q9NS68-2	.;TNR19_HUMAN;.	H	368;236;368;368	ENSP00000248484:N368H;ENSP00000385408:N236H;ENSP00000371693:N368H;ENSP00000371698:N368H	ENSP00000248484:N368H	N	+	1	0	TNFRSF19	23141093	0.007000	0.16637	0.000000	0.03702	0.006000	0.05464	0.827000	0.27421	0.422000	0.26005	0.533000	0.62120	AAC	.	.	.	none		0.413	TNFRSF19-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044156.2	NM_018647		C	24243093	A	C	24243093	3	2	124	1	0	0	0	0	1	0	0	0	16304	14	1	5	1132	5	TNFRSF19	13	24243093	Missense_Mutation	SNP	A	TCGA-BQ-5889-01A-11D-1589-08	3844221	24243093	90926785	32	7789											
CKAP2	26586	hgsc.bcm.edu	37	chr13	53042426	53042426	+	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	aattaagcctattgaagagaTgcgacacacgattgtagata	16	10	9	6	2	0	3	0	1	0	2	0	6	0	3	1	0	2	1	1	0	6	6			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr13:53042426T>A	ENST00000378037.5	+	7	1583	c.1493T>A	c.(1492-1494)aTg>aAg	p.M498K	CKAP2_ENST00000258607.5_Missense_Mutation_p.M497K|CKAP2_ENST00000490903.1_Missense_Mutation_p.M449K	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)		ATTGAAGAGATGCGACACACG	0.299																																					p.M498K		Atlas-SNP	.											.	CKAP2	51	.	0			c.T1493A						PASS	.						97	100	99					13																	53042426		2203	4300	6503	SO:0001583	missense	26586	exon7			AAGAGATGCGACA	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.1493T>A	chr13.hg19:g.53042426T>A	ENSP00000367276:p.Met498Lys	57.0	0.0	.		44.0	4.0	.	NM_001098525		Missense_Mutation	SNP	ENST00000378037.5	hg19	CCDS41893.1	.	.	.	.	.	.	.	.	.	.	.	16.76	3.211433	0.58343	.	.	ENSG00000136108	ENST00000258607;ENST00000378037;ENST00000490903	T;T;T	0.26373	1.74;1.74;1.74	5.53	5.53	0.82687	.	0.149392	0.47093	D	0.000251	T	0.32941	0.0846	M	0.74881	2.28	0.43959	D	0.99663	P;P;P	0.42409	0.61;0.61;0.779	B;B;B	0.41036	0.346;0.346;0.346	T	0.23904	-1.0175	10	0.87932	D	0	-5.2435	12.0802	0.53667	0.0:0.0:0.0:1.0	.	449;498;497	E9PD90;Q8WWK9;B2RMQ4	.;CKAP2_HUMAN;.	K	497;498;449	ENSP00000258607:M497K;ENSP00000367276:M498K;ENSP00000417830:M449K	ENSP00000258607:M497K	M	+	2	0	CKAP2	51940427	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.810000	0.55613	2.100000	0.63781	0.533000	0.62120	ATG	.	.	.	none		0.299	CKAP2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355010.2			A	53042426	T	A	53042426	3	1	124	1	0	0	0	0	1	0	0	0	3444	1464	51	5	1519	5	CKAP2	13	53042426	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	28799333	53042426	62127452	33	7790											
CLEC14A	161198	hgsc.bcm.edu	37	chr14	38723829	38723829	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcccgcagatcacagtcccCgactttcaccccattgtttg	7	11	7	16	2	2	1	2	0	0	1	4	2	4	1	5	0	0	2	5	0	0	3			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr14:38723829C>T	ENST00000342213.2	-	1	1745	c.1399G>A	c.(1399-1401)Ggg>Agg	p.G467R		NM_175060.2	NP_778230.1	Q86T13	CLC14_HUMAN	C-type lectin domain family 14, member A	467						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)		TCACAGTCCCCGACTTTCACC	0.597																																					p.G467R		Atlas-SNP	.											.	CLEC14A	83	.	0			c.G1399A						PASS	.						75	77	76					14																	38723829		2203	4300	6503	SO:0001583	missense	161198	exon1			AGTCCCCGACTTT		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.1399G>A	chr14.hg19:g.38723829C>T	ENSP00000353013:p.Gly467Arg	167.0	0.0	.		160.0	22.0	.	NM_175060	Q695G9|Q6PWT6|Q8N5V5	Missense_Mutation	SNP	ENST00000342213.2	hg19	CCDS9667.1	.	.	.	.	.	.	.	.	.	.	C	8.642	0.896202	0.17686	.	.	ENSG00000176435	ENST00000342213	T	0.73681	-0.77	4.19	-6.15	0.02105	.	0.640736	0.12966	N	0.424617	T	0.50343	0.1610	L	0.27053	0.805	0.09310	N	1	B	0.20459	0.045	B	0.09377	0.004	T	0.33624	-0.9861	10	0.87932	D	0	-0.4303	2.5087	0.04652	0.1371:0.2062:0.1279:0.5287	.	467	Q86T13	CLC14_HUMAN	R	467	ENSP00000353013:G467R	ENSP00000353013:G467R	G	-	1	0	CLEC14A	37793580	0.000000	0.05858	0.000000	0.03702	0.097000	0.18754	0.081000	0.14823	-1.071000	0.03145	-0.253000	0.11424	GGG	.	.	.	none		0.597	CLEC14A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276729.1	NM_175060		T	38723829	C	T	38723829	3	4	124	1	0	0	0	0	1	0	0	0	3501	652	23	1	77	1	CLEC14A	14	38723829	Missense_Mutation	SNP	C	TCGA-BQ-5889-01A-11D-1589-08		38723829	68625711	34	7791											
C15orf2	23742	hgsc.bcm.edu	37	chr15	24923231	24923231	+	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	acacaacccagcggcaacacTgcctcagtccaaggctccac	12	4	7	18	1	1	0	1	0	0	0	3	0	3	0	4	2	4	2	4	2	3	0			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr15:24923231T>A	ENST00000329468.2	+	1	2691	c.2217T>A	c.(2215-2217)acT>acA	p.T739T		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	739					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											GCGGCAACACTGCCTCAGTCC	0.557																																					p.T739T		Atlas-SNP	.											.	.	.	.	0			c.T2217A						PASS	.						108	110	109					15																	24923231		2203	4300	6503	SO:0001819	synonymous_variant	23742	exon1			CAACACTGCCTCA	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.2217T>A	chr15.hg19:g.24923231T>A		239.0	0.0	.		231.0	22.0	.	NM_018958		Silent	SNP	ENST00000329468.2	hg19	CCDS10015.1																																																																																			.	.	.	none		0.557	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		A	24923231	T	A	24923231	2	1	124	1	0	0	0	0	0	0	0	1	1786	1567	55	5		5	C15orf2	15	24923231	Silent	SNP	T	TCGA-BQ-5889-01A-11D-1589-08		24923231	77608161	35	7792											
HERC2	8924	hgsc.bcm.edu	37	chr15	28510872	28510872	+	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	cggaatggcctcgtcctcacTggagccttcaaacagatagg	10	8	11	12	2	2	1	2	0	0	1	4	3	3	3	3	4	2	0	3	4	3	2			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr15:28510872T>A	ENST00000261609.7	-	14	1870	c.1762A>T	c.(1762-1764)Agt>Tgt	p.S588C		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)		TCGTCCTCACTGGAGCCTTCA	0.577																																					p.S588C		Atlas-SNP	.											.	HERC2	501	.	0			c.A1762T						PASS	.						123	92	102					15																	28510872		2203	4300	6503	SO:0001583	missense	8924	exon14			CCTCACTGGAGCC	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.1762A>T	chr15.hg19:g.28510872T>A	ENSP00000261609:p.Ser588Cys	73.0	0.0	.		84.0	10.0	.	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	T	31	5.104071	0.94245	.	.	ENSG00000128731	ENST00000261609	D	0.85411	-1.98	5.83	5.83	0.93111	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	D	0.000000	D	0.90202	0.6937	L	0.48986	1.54	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	D	0.90297	0.4327	10	0.52906	T	0.07	.	16.5602	0.84551	0.0:0.0:0.0:1.0	.	588	O95714	HERC2_HUMAN	C	588	ENSP00000261609:S588C	ENSP00000261609:S588C	S	-	1	0	HERC2	26184467	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	7.629000	0.83207	2.367000	0.80283	0.529000	0.55759	AGT	.	.	.	none		0.577	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		A	28510872	T	A	28510872	3	1	124	1	0	0	0	0	1	0	0	0	7065	1580	55	5	13062	5	HERC2	15	28510872	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	3587641	28510872	74020520	36	7793											
TMEM62	80021	hgsc.bcm.edu	37	chr15	43426530	43426530	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaaattctgttctgaaactAttgacatcattcaaccagct	14	13	5	9	0	4	3	2	2	2	1	4	3	4	3	1	0	3	2	1	0	4	5			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr15:43426530A>G	ENST00000260403.2	+	2	535	c.256A>G	c.(256-258)Att>Gtt	p.I86V		NM_024956.3	NP_079232.3	Q0P6H9	TMM62_HUMAN	transmembrane protein 62	86						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)		TTCTGAAACTATTGACATCAT	0.507																																					p.I86V		Atlas-SNP	.											.	TMEM62	47	.	0			c.A256G						PASS	.						110	93	99					15																	43426530		2203	4299	6502	SO:0001583	missense	80021	exon2			GAAACTATTGACA	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.256A>G	chr15.hg19:g.43426530A>G	ENSP00000260403:p.Ile86Val	84.0	0.0	.		83.0	10.0	.	NM_024956	Q6I9Y5|Q9H5J6	Missense_Mutation	SNP	ENST00000260403.2	hg19	CCDS32210.1	.	.	.	.	.	.	.	.	.	.	A	7.057	0.565544	0.13560	.	.	ENSG00000137842	ENST00000260403	T	0.22945	1.93	4.97	2.62	0.31277	.	0.161216	0.53938	D	0.000050	T	0.09379	0.0231	N	0.05259	-0.085	0.43708	D	0.996176	B	0.12630	0.006	B	0.15484	0.013	T	0.18209	-1.0344	10	0.05833	T	0.94	-8.7407	8.1815	0.31313	0.8138:0.0:0.1862:0.0	.	86	Q0P6H9	TMM62_HUMAN	V	86	ENSP00000260403:I86V	ENSP00000260403:I86V	I	+	1	0	TMEM62	41213822	0.969000	0.33509	1.000000	0.80357	0.998000	0.95712	1.160000	0.31761	0.912000	0.36772	0.533000	0.62120	ATT	.	.	.	none		0.507	TMEM62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432227.1	NM_024956		G	43426530	A	G	43426530	3	3	124	1	0	0	0	0	1	0	0	0	16201	449	16	3	262	3	TMEM62	15	43426530	Missense_Mutation	SNP	A	TCGA-BQ-5889-01A-11D-1589-08	14915658	43426530	59104862	37	7794											
FES	2242	hgsc.bcm.edu	37	chr15	91438758	91438758	+	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	ttcagcaccatctaccaggaGctgcagagcatccgaaagcg	12	6	10	13	2	2	1	1	0	1	1	3	3	3	2	3	1	6	4	3	1	2	2			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr15:91438758G>T	ENST00000328850.3	+	19	2581	c.2439G>T	c.(2437-2439)gaG>gaT	p.E813D	FES_ENST00000444422.2_Missense_Mutation_p.E743D|FES_ENST00000450438.2_Missense_Mutation_p.E685D|FES_ENST00000414248.2_Missense_Mutation_p.E685D|FES_ENST00000394300.3_Missense_Mutation_p.E755D|FES_ENST00000394302.1_Missense_Mutation_p.E672D	NM_002005.3	NP_001996.1	P07332	FES_HUMAN	FES proto-oncogene, tyrosine kinase	813	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)			TCTACCAGGAGCTGCAGAGCA	0.642																																					p.E813D		Atlas-SNP	.											.	FES	102	.	0			c.G2439T						PASS	.						60	60	60					15																	91438758		2198	4298	6496	SO:0001583	missense	2242	exon19			CCAGGAGCTGCAG	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.2439G>T	chr15.hg19:g.91438758G>T	ENSP00000331504:p.Glu813Asp	121.0	0.0	.		108.0	8.0	.	NM_002005	B2R6E6|B4DUD0|E9PC94|E9PC95|Q2VXS7|Q2VXS8|Q2VXT0|Q6GTU5	Missense_Mutation	SNP	ENST00000328850.3	hg19	CCDS10365.1	.	.	.	.	.	.	.	.	.	.	G	11.94	1.789274	0.31685	.	.	ENSG00000182511	ENST00000328850;ENST00000414248;ENST00000394302;ENST00000444422;ENST00000394300;ENST00000450438	T;T;T;T;T;T	0.61742	0.08;0.08;0.08;0.08;0.08;0.08	4.18	3.25	0.37280	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.164239	0.53938	D	0.000058	T	0.37999	0.1024	N	0.25031	0.7	0.44780	D	0.997783	B;B;B;B;B;B	0.13594	0.001;0.008;0.001;0.001;0.008;0.001	B;B;B;B;B;B	0.14023	0.004;0.01;0.003;0.002;0.01;0.004	T	0.16394	-1.0404	10	0.19147	T	0.46	-35.8073	9.2926	0.37795	0.0886:0.1513:0.7602:0.0	.	795;685;672;755;743;813	B4DUD9;P07332-2;E7ENM8;P07332-3;P07332-4;P07332	.;.;.;.;.;FES_HUMAN	D	813;685;672;743;755;685	ENSP00000331504:E813D;ENSP00000414629:E685D;ENSP00000377839:E672D;ENSP00000400868:E743D;ENSP00000377837:E755D;ENSP00000409915:E685D	ENSP00000331504:E813D	E	+	3	2	FES	89239762	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	0.776000	0.26704	2.339000	0.79563	0.555000	0.69702	GAG	.	.	.	none		0.642	FES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313497.1	NM_002005		T	91438758	G	T	91438758	3	4	124	1	0	0	0	0	1	0	0	0	5827	962	34	4	2509	4	FES	15	91438758	Missense_Mutation	SNP	G	TCGA-BQ-5889-01A-11D-1589-08	48012228	91438758	11092634	38	7795											
DECR2	26063	hgsc.bcm.edu	37	chr16	457438	457438	+	Missense_Mutation	SNP	T	T	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	cttctaggccgccaggaagcTggctggggccaccggccggc	5	5	16	15	3	1	0	0	0	1	0	1	1	1	1	5	7	1	2	5	7	2	2			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr16:457438T>G	ENST00000219481.5	+	4	353	c.215T>G	c.(214-216)cTg>cGg	p.L72R	DECR2_ENST00000397710.1_Missense_Mutation_p.L123R|DECR2_ENST00000461947.1_Intron|DECR2_ENST00000424398.2_Missense_Mutation_p.L60R	NM_020664.3	NP_065715.1	Q9NUI1	DECR2_HUMAN	2,4-dienoyl CoA reductase 2, peroxisomal	72					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)				GCCAGGAAGCTGGCTGGGGCC	0.652																																					p.L72R		Atlas-SNP	.											.	DECR2	47	.	0			c.T215G						PASS	.						26	31	29					16																	457438		2201	4299	6500	SO:0001583	missense	26063	exon4			GGAAGCTGGCTGG	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.215T>G	chr16.hg19:g.457438T>G	ENSP00000219481:p.Leu72Arg	70.0	0.0	.		109.0	9.0	.	NM_020664	Q6ZRS7|Q96ET0	Missense_Mutation	SNP	ENST00000219481.5	hg19	CCDS10409.1	.	.	.	.	.	.	.	.	.	.	T	16.34	3.096100	0.56075	.	.	ENSG00000242612	ENST00000219481;ENST00000397710;ENST00000424398	T;T	0.54071	0.59;0.59	4.89	4.89	0.63831	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.75332	0.3835	M	0.88181	2.935	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80446	-0.1379	10	0.87932	D	0	.	12.2476	0.54578	0.0:0.0:0.0:1.0	.	72	Q9NUI1	DECR2_HUMAN	R	72;123;60	ENSP00000219481:L72R;ENSP00000400374:L60R	ENSP00000219481:L72R	L	+	2	0	DECR2	397439	1.000000	0.71417	0.987000	0.45799	0.506000	0.33950	7.499000	0.81566	1.831000	0.53308	0.459000	0.35465	CTG	.	.	.	none		0.652	DECR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109069.4	NM_020664		G	457438	T	G	457438	3	3	124	1	0	0	0	0	1	0	0	0	4385	1580	55	5	229	5	DECR2	16	457438	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08		457438	89897315	39	7796											
TSC2	7249	hgsc.bcm.edu	37	chr16	2126139	2126139	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcatcaggtgccgcctgcccTtccggaaggattttgtccct	5	12	10	14	2	2	0	2	0	0	0	4	2	4	2	5	3	2	0	5	3	1	3			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr16:2126139T>C	ENST00000219476.3	+	24	3340	c.2710T>C	c.(2710-2712)Ttc>Ctc	p.F904L	TSC2_ENST00000401874.2_Missense_Mutation_p.F904L|TSC2_ENST00000350773.4_Missense_Mutation_p.F904L|TSC2_ENST00000568454.1_Missense_Mutation_p.F915L|TSC2_ENST00000382538.6_Missense_Mutation_p.F855L|TSC2_ENST00000439673.2_Missense_Mutation_p.F867L|TSC2_ENST00000353929.4_Missense_Mutation_p.F904L	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	904					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)				CCGCCTGCCCTTCCGGAAGGA	0.567			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.F904L		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	.	TSC2	364	.	0			c.T2710C						PASS	.						117	94	102					16																	2126139		2198	4300	6498	SO:0001583	missense	7249	exon24	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	CTGCCCTTCCGGA	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.2710T>C	chr16.hg19:g.2126139T>C	ENSP00000219476:p.Phe904Leu	64.0	0.0	.		104.0	13.0	.	NM_001114382	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Missense_Mutation	SNP	ENST00000219476.3	hg19	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	T	17.02	3.281054	0.59758	.	.	ENSG00000103197	ENST00000219476;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000382538;ENST00000350773	D;D;D;D;D;D	0.85171	-1.95;-1.95;-1.95;-1.95;-1.95;-1.95	5.09	5.09	0.68999	Tuberin-type domain (1);	0.056979	0.64402	D	0.000001	T	0.81221	0.4777	N	0.14661	0.345	0.51012	D	0.999905	B;B;B;B;B;D	0.59357	0.101;0.313;0.176;0.021;0.082;0.985	B;B;B;B;B;D	0.72338	0.147;0.174;0.091;0.132;0.103;0.977	T	0.77351	-0.2620	10	0.02654	T	1	-38.9999	9.422	0.38557	0.0:0.0795:0.0:0.9205	.	855;867;904;904;904;904	B4DIL8;P49815-6;P49815-4;P49815-3;P49815-5;P49815	.;.;.;.;.;TSC2_HUMAN	L	904;904;904;867;855;904	ENSP00000219476:F904L;ENSP00000384468:F904L;ENSP00000248099:F904L;ENSP00000399232:F867L;ENSP00000371978:F855L;ENSP00000344383:F904L	ENSP00000219476:F904L	F	+	1	0	TSC2	2066140	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	5.116000	0.64661	1.919000	0.55581	0.459000	0.35465	TTC	.	.	.	none		0.567	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		C	2126139	T	C	2126139	3	2	124	1	0	0	0	0	1	0	0	0	16618	1609	56	3	2800	3	TSC2	16	2126139	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	1668701	2126139	88228614	40	7797											
PRPF8	10594	hgsc.bcm.edu	37	chr17	1564455	1564455	+	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	agaacggattctgcttcaaaAcctagatggcaaggcaggca	14	7	11	9	1	2	2	1	0	1	2	2	3	2	3	1	4	3	4	1	4	5	3			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr17:1564455A>T	ENST00000572621.1	-	27	4605	c.4340T>A	c.(4339-4341)gTt>gAt	p.V1447D	PRPF8_ENST00000304992.6_Splice_Site_p.V1447D			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	1447	Linker.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		CTGCTTCAAAACCTAGATGGC	0.547																																					p.V1447D		Atlas-SNP	.											.	PRPF8	169	.	0			c.T4340A						PASS	.						82	73	76					17																	1564455		2203	4300	6503	SO:0001630	splice_region_variant	10594	exon28			TTCAAAACCTAGA	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"PRP8 pre-mRNA processing factor 8 homolog (yeast)", "PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.4339-1T>A	chr17.hg19:g.1564455A>T		66.0	0.0	.		79.0	9.0	.	NM_006445	O14547|O75965	Missense_Mutation	SNP	ENST00000572621.1	hg19	CCDS11010.1	.	.	.	.	.	.	.	.	.	.	a	12.99	2.102694	0.37145	.	.	ENSG00000174231	ENST00000304992	T	0.80994	-1.44	6.17	6.17	0.99709	Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.80999	0.4732	L	0.47716	1.5	0.80722	D	1	P	0.42620	0.785	P	0.45794	0.493	T	0.82474	-0.0439	10	0.66056	D	0.02	-2.8406	16.8222	0.85835	1.0:0.0:0.0:0.0	.	1447	Q6P2Q9	PRP8_HUMAN	D	1447	ENSP00000304350:V1447D	ENSP00000304350:V1447D	V	-	2	0	PRPF8	1511205	1.000000	0.71417	1.000000	0.80357	0.193000	0.23685	9.307000	0.96226	2.371000	0.80710	0.533000	0.62120	GTT	.	.	.	none		0.547	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2		Missense_Mutation	T	1564455	A	T	1564455	5	4	124	1	0	0	0	0	0	0	1	0	12585	57	2	5	2731	5	PRPF8	17	1564455	Splice_Site	SNP	A	TCGA-BQ-5889-01A-11D-1589-08		1564455	79630755	41	7798											
NEURL4	84461	hgsc.bcm.edu	37	chr17	7220554	7220554	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggccagggtctccgccccaGcatattgaagggagggggaa	10	5	16	10	1	1	1	0	1	1	0	2	3	1	3	4	5	1	1	4	5	3	2			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr17:7220554G>A	ENST00000399464.2	-	28	4469	c.4454C>T	c.(4453-4455)gCt>gTt	p.A1485V	NEURL4_ENST00000315614.7_Missense_Mutation_p.A1483V|GPS2_ENST00000389167.5_5'Flank|NEURL4_ENST00000570460.1_Missense_Mutation_p.A1461V|GPS2_ENST00000391950.3_5'Flank|NEURL4_ENST00000574120.1_5'Flank|RP11-542C16.2_ENST00000575474.1_Silent_p.L299L|GPS2_ENST00000380728.2_5'Flank	NM_032442.2	NP_115818.2	Q96JN8	NEUL4_HUMAN	neuralized E3 ubiquitin protein ligase 4	1485						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						CTCCGCCCCAGCATATTGAAG	0.647																																					p.A1485V		Atlas-SNP	.											.	NEURL4	192	.	0			c.C4454T						PASS	.						27	29	28					17																	7220554		1909	4108	6017	SO:0001583	missense	84461	exon28			GCCCCAGCATATT		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.4454C>T	chr17.hg19:g.7220554G>A	ENSP00000382390:p.Ala1485Val	54.0	0.0	.		50.0	5.0	.	NM_032442	Q6GPI8|Q96IU9|Q9H0B0	Missense_Mutation	SNP	ENST00000399464.2	hg19	CCDS42251.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.522700	0.85600	.	.	ENSG00000215041	ENST00000315614;ENST00000399464	T;T	0.38722	1.12;1.12	5.02	5.02	0.67125	.	0.068616	0.64402	D	0.000017	T	0.49575	0.1565	M	0.71581	2.175	0.40718	D	0.982632	P;P	0.44139	0.827;0.734	B;B	0.43386	0.418;0.239	T	0.59747	-0.7396	10	0.72032	D	0.01	-10.282	17.1077	0.86668	0.0:0.0:1.0:0.0	.	1483;1485	Q96JN8-2;Q96JN8	.;NEUL4_HUMAN	V	1483;1485	ENSP00000319826:A1483V;ENSP00000382390:A1485V	ENSP00000319826:A1483V	A	-	2	0	NEURL4	7161278	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.975000	0.70475	2.325000	0.78763	0.462000	0.41574	GCT	.	.	.	none		0.647	NEURL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255434.2	NM_032442		A	7220554	G	A	7220554	3	1	124	1	0	0	0	0	1	0	0	0	10354	971	34	2	242	2	NEURL4	17	7220554	Missense_Mutation	SNP	G	TCGA-BQ-5889-01A-11D-1589-08	5656099	7220554	73974656	42	7799											
MYH10	4628	hgsc.bcm.edu	37	chr17	8452026	8452026	+	Frame_Shift_Del	DEL	T	T	-																															atggtctcctggaaattatcTttgtcttgctgtcccggaat																										TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr17:8452026delT	ENST00000269243.4	-	9	1107	c.969delA	c.(967-969)aaafs	p.K323fs	MYH10_ENST00000379980.4_Frame_Shift_Del_p.K339fs|MYH10_ENST00000360416.3_Frame_Shift_Del_p.K333fs|RN7SL129P_ENST00000479993.2_RNA|MYH10_ENST00000396239.1_Frame_Shift_Del_p.K323fs	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	323	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						GGAAATTATCTTTGTCTTGCT	0.383																																					p.D334fs		Atlas-INDEL	.											.	MYH10	148	.	0			c.1000delG						PASS	.						163	160	161					17																	8452026		2203	4300	6503	SO:0001589	frameshift_variant	4628	exon10			.	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.969delA	chr17.hg19:g.8452026delT	ENSP00000269243:p.Lys323fs	197.0	0.0	0		208.0	19.0	0.0913462	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Frame_Shift_Del	DEL	ENST00000269243.4	hg19	CCDS11144.1																																																																																			.	.	.	none		0.383	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			-	8452026	T	-	8452026	7	5	124	1	0	1	0	1	0	0	0	0	10037	1606	56	0	5093	0	MYH10	17	8452026	Frame_Shift_Del	DEL	T	TCGA-BQ-5889-01A-11D-1589-08	1231472	8452026	72743184	43	7800											
SCRN2	90507	hgsc.bcm.edu	37	chr17	45915217	45915217	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaagctatgaagcttacgcaTaagcctggctctccctcttc	9	11	8	13	1	2	1	0	1	2	0	4	2	2	1	2	1	4	4	2	1	5	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr17:45915217T>C	ENST00000290216.9	-	8	1396	c.1271A>G	c.(1270-1272)tAt>tGt	p.Y424C	SCRN2_ENST00000407215.3_3'UTR|SCRN2_ENST00000584123.1_Missense_Mutation_p.Y432C	NM_001145023.1|NM_138355.3	NP_001138495.1|NP_612364.2	Q96FV2	SCRN2_HUMAN	secernin 2	424						extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)			cervix(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	14						AGCTTACGCATAAGCCTGGCT	0.657																																					p.Y424C		Atlas-SNP	.											.	SCRN2	35	.	0			c.A1271G						PASS	.						24	26	25					17																	45915217		2203	4300	6503	SO:0001583	missense	90507	exon8			TACGCATAAGCCT	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.1271A>G	chr17.hg19:g.45915217T>C	ENSP00000290216:p.Tyr424Cys	47.0	0.0	.		45.0	8.0	.	NM_138355	A8K3N1|B7Z8S7|E9PBV5|Q96AC3|Q9BU04	Missense_Mutation	SNP	ENST00000290216.9	hg19	CCDS11519.1	.	.	.	.	.	.	.	.	.	.	T	11.41	1.631333	0.28978	.	.	ENSG00000141295	ENST00000290216	T	0.09817	2.94	5.72	5.72	0.89469	.	0.114320	0.64402	D	0.000008	T	0.37237	0.0996	M	0.83953	2.67	0.53688	D	0.999977	D	0.89917	1.0	D	0.85130	0.997	T	0.26538	-1.0100	10	0.87932	D	0	-1.5376	14.9863	0.71351	0.0:0.0:0.0:1.0	.	424	Q96FV2	SCRN2_HUMAN	C	424	ENSP00000290216:Y424C	ENSP00000290216:Y424C	Y	-	2	0	SCRN2	43270216	1.000000	0.71417	0.037000	0.18230	0.025000	0.11179	5.686000	0.68211	2.184000	0.69523	0.533000	0.62120	TAT	.	.	.	none		0.657	SCRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441383.1	NM_138355		C	45915217	T	C	45915217	3	2	124	1	0	0	0	0	1	0	0	0	13952	1406	49	3	10	3	SCRN2	17	45915217	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08	37463191	45915217	35279993	44	7801											
TEX2	55852	hgsc.bcm.edu	37	chr17	62290509	62290509	+	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	gttggaatcacttccgtagcCatccccctcagaatcacact	10	10	6	15	1	3	1	3	0	0	1	5	2	5	2	4	1	1	2	4	1	3	3			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr17:62290509C>T	ENST00000583097.1	-	2	1241	c.1069G>A	c.(1069-1071)Ggc>Agc	p.G357S	TEX2_ENST00000258991.3_Missense_Mutation_p.G357S|TEX2_ENST00000584379.1_Missense_Mutation_p.G357S			Q8IWB9	TEX2_HUMAN	testis expressed 2	357					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)		CTTCCGTAGCCATCCCCCTCA	0.498																																					p.G357S		Atlas-SNP	.											.	TEX2	89	.	0			c.G1069A						PASS	.						85	76	79					17																	62290509		2203	4300	6503	SO:0001583	missense	55852	exon2			CGTAGCCATCCCC	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.1069G>A	chr17.hg19:g.62290509C>T	ENSP00000462665:p.Gly357Ser	93.0	0.0	.		115.0	12.0	.	NM_018469	Q6AHZ5|Q8N3L0|Q9C0C5	Missense_Mutation	SNP	ENST00000583097.1	hg19		.	.	.	.	.	.	.	.	.	.	C	5.664	0.307054	0.10733	.	.	ENSG00000136478	ENST00000258991	T	0.42513	0.97	6.03	3.96	0.45880	.	0.773939	0.13084	N	0.415036	T	0.20820	0.0501	N	0.08118	0	0.09310	N	1	B;B	0.20261	0.043;0.025	B;B	0.20577	0.03;0.013	T	0.27191	-1.0081	10	0.11485	T	0.65	-0.2203	8.1607	0.31196	0.5291:0.374:0.0969:0.0	.	357;357	Q8IWB9-2;Q8IWB9	.;TEX2_HUMAN	S	357	ENSP00000258991:G357S	ENSP00000258991:G357S	G	-	1	0	TEX2	59644241	0.137000	0.22531	0.007000	0.13788	0.465000	0.32709	1.751000	0.38339	0.809000	0.34255	0.655000	0.94253	GGC	.	.	.	none		0.498	TEX2-003	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000443745.1	NM_018469		T	62290509	C	T	62290509	3	4	124	1	0	0	0	0	1	0	0	0	15793	594	21	2	2379	2	TEX2	17	62290509	Missense_Mutation	SNP	C	TCGA-BQ-5889-01A-11D-1589-08	16375292	62290509	18904701	45	7802											
PRPSAP1	5635	hgsc.bcm.edu	37	chr17	74307703	74307703	+	Frame_Shift_Del	DEL	T	T	-																															ccgaatggcttcagaaagaaTcaaactgatatccacagtct																										TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr17:74307703delT	ENST00000446526.3	-	10	1523	c.1078delA	c.(1078-1080)attfs	p.I360fs	PRPSAP1_ENST00000324684.4_Frame_Shift_Del_p.I257fs|PRPSAP1_ENST00000588364.1_5'UTR	NM_002766.2	NP_002757.2	Q14558	KPRA_HUMAN	phosphoribosyl pyrophosphate synthetase-associated protein 1	331					negative regulation of kinase activity (GO:0033673)|nucleobase-containing compound metabolic process (GO:0006139)|nucleotide biosynthetic process (GO:0009165)	ribose phosphate diphosphokinase complex (GO:0002189)	enzyme inhibitor activity (GO:0004857)|magnesium ion binding (GO:0000287)|ribose phosphate diphosphokinase activity (GO:0004749)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	17						TCAGAAAGAATCAAACTGATA	0.468																																					p.I360fs		Atlas-INDEL	.											.	PRPSAP1	32	.	0			c.1079delT						PASS	.						154	120	131					17																	74307703		2203	4300	6503	SO:0001589	frameshift_variant	5635	exon10			.	D61391	CCDS11743.2	17q24-q25	2008-07-18			ENSG00000161542	ENSG00000161542			9466	protein-coding gene	gene with protein product		601249				8660991	Standard	NM_002766		Approved	PAP39	uc010wta.1	Q14558	OTTHUMG00000155969	ENST00000446526.3:c.1078delA	chr17.hg19:g.74307703delT	ENSP00000414624:p.Ile360fs	55.0	0.0	0		98.0	10.0	0.102041	NM_002766	B2R6M4|Q96H06	Frame_Shift_Del	DEL	ENST00000446526.3	hg19	CCDS11743.2																																																																																			.	.	.	none		0.468	PRPSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342480.2	NM_002766		-	74307703	T	-	74307703	7	5	124	1	0	1	0	1	0	0	0	0	12591	1435	50	0	83	0	PRPSAP1	17	74307703	Frame_Shift_Del	DEL	T	TCGA-BQ-5889-01A-11D-1589-08	12017194	74307703	6887507	46	7803											
MYO1F	4542	hgsc.bcm.edu	37	chr19	8604865	8604865	+	Missense_Mutation	SNP	T	T	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	cggcggtgctggggcgccccTtcttgtctccatccagcttc	2	11	12	16	3	2	0	0	0	2	0	5	0	3	0	4	4	2	2	4	4	0	3			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chr19:8604865T>G	ENST00000338257.8	-	16	1925	c.1658A>C	c.(1657-1659)aAg>aCg	p.K553T		NM_012335.3	NP_036467.2	O00160	MYO1F_HUMAN	myosin IF	553	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						GGGGCGCCCCTTCTTGTCTCC	0.632																																					p.K553T		Atlas-SNP	.											.	MYO1F	128	.	0			c.A1658C						PASS	.						40	43	42					19																	8604865		1904	4113	6017	SO:0001583	missense	4542	exon16			CGCCCCTTCTTGT	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.1658A>C	chr19.hg19:g.8604865T>G	ENSP00000344871:p.Lys553Thr	80.0	0.0	.		87.0	6.0	.	NM_012335	Q8WWN7	Missense_Mutation	SNP	ENST00000338257.8	hg19	CCDS42494.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.577175	0.86645	.	.	ENSG00000142347	ENST00000305795;ENST00000338257	D	0.88201	-2.35	5.01	5.01	0.66863	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.93249	0.7849	M	0.73217	2.22	0.80722	D	1	D	0.71674	0.998	D	0.72625	0.978	D	0.93407	0.6765	10	0.52906	T	0.07	.	13.55	0.61726	0.0:0.0:0.0:1.0	.	553	O00160	MYO1F_HUMAN	T	598;553	ENSP00000344871:K553T	ENSP00000304899:K598T	K	-	2	0	MYO1F	8510865	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	5.902000	0.69869	1.891000	0.54761	0.482000	0.46254	AAG	.	.	.	none		0.632	MYO1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342716.2			G	8604865	T	G	8604865	3	3	124	1	0	0	0	0	1	0	0	0	10080	1609	56	5	1690	5	MYO1F	19	8604865	Missense_Mutation	SNP	T	TCGA-BQ-5889-01A-11D-1589-08		8604865	50524118	47	7804											
GPRASP1	9737	hgsc.bcm.edu	37	chrX	101910683	101910683	+	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	gaggaggagcccattattggGtcctggttttggaccagagt	8	11	15	7	0	0	1	0	0	0	1	1	5	1	4	3	5	1	1	3	5	1	4			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chrX:101910683G>C	ENST00000361600.5	+	5	2643	c.1842G>C	c.(1840-1842)ggG>ggC	p.G614G	GPRASP1_ENST00000444152.1_Silent_p.G614G|GPRASP1_ENST00000415986.1_Silent_p.G614G|GPRASP1_ENST00000537097.1_Silent_p.G614G|RP4-769N13.7_ENST00000602441.1_RNA	NM_014710.4	NP_055525.3	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting protein 1	614	Glu-rich.				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						CCATTATTGGGTCCTGGTTTT	0.512																																					p.G614G		Atlas-SNP	.											.	GPRASP1	140	.	0			c.G1842C						PASS	.						104	103	103					X																	101910683		2203	4300	6503	SO:0001819	synonymous_variant	9737	exon3			TATTGGGTCCTGG	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.1842G>C	chrX.hg19:g.101910683G>C		145.0	0.0	.		160.0	24.0	.	NM_001099411	O43168|Q96LA1	Silent	SNP	ENST00000361600.5	hg19	CCDS35352.1																																																																																			.	.	.	none		0.512	GPRASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057634.2	NM_014710		C	101910683	G	C	101910683	2	2	124	1	0	0	0	0	0	0	0	1	6729	1248	44	4		4	GPRASP1	23	101910683	Silent	SNP	G	TCGA-BQ-5889-01A-11D-1589-08		101910683	53359877	48	7805											
F8	2157	hgsc.bcm.edu	37	chrX	154157883	154157883	+	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	tgagggatgctatgactcctCgtaaggcaatctgataaggg	11	10	13	7	1	1	3	0	3	1	0	3	4	2	4	1	3	1	3	1	3	4	3			TCGA-BQ-5889-01A-11D-1589-08	TCGA-BQ-5889-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	46b1253a-f381-46d3-ad7d-e0ed2bda9eff	fc277028-a6e0-4459-8608-40506e4c36cb	g.chrX:154157883C>T	ENST00000360256.4	-	14	4382	c.4182G>A	c.(4180-4182)acG>acA	p.T1394T		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	1394	B.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	TATGACTCCTCGTAAGGCAAT	0.428																																					p.T1394T		Atlas-SNP	.											.	F8	646	.	0			c.G4182A						PASS	.						166	149	154					X																	154157883		2203	4300	6503	SO:0001819	synonymous_variant	2157	exon14			ACTCCTCGTAAGG	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.4182G>A	chrX.hg19:g.154157883C>T		175.0	0.0	.		137.0	25.0	.	NM_000132	Q14286|Q5HY69	Silent	SNP	ENST00000360256.4	hg19	CCDS35457.1																																																																																			.	.	.	none		0.428	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4			T	154157883	C	T	154157883	2	4	124	1	0	0	0	0	0	0	0	1	5352	871	31	1		1	F8	23	154157883	Silent	SNP	C	TCGA-BQ-5889-01A-11D-1589-08	52247200	154157883	1112677	49	7806											
ATP13A2	23400	hgsc.bcm.edu	37	chr1	17322884	17322884	+	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	tgcagggggccactcacccaGgacagagagggcagccacaa	12	2	14	13	0	1	1	1	0	0	1	1	3	1	2	3	4	2	2	3	4	1	0			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr1:17322884G>T	ENST00000326735.8	-	13	1336	c.1303C>A	c.(1303-1305)Ctg>Atg	p.L435M	ATP13A2_ENST00000452699.1_Missense_Mutation_p.L430M|RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000502860.1_Intron|ATP13A2_ENST00000341676.5_Missense_Mutation_p.L430M			Q9NQ11	AT132_HUMAN	ATPase type 13A2	435					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		CACTCACCCAGGACAGAGAGG	0.612																																					p.L435M		Atlas-SNP	.											.	ATP13A2	85	.	0			c.C1303A						PASS	.						69	78	75					1																	17322884		2203	4300	6503	SO:0001583	missense	23400	exon13			CACCCAGGACAGA	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"ATPases / P-type", "Parkinson disease"	30213	protein-coding gene	gene with protein product		610513	"Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.1303C>A	chr1.hg19:g.17322884G>T	ENSP00000327214:p.Leu435Met	97.0	0.0	.		90.0	35.0	.	NM_022089	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Missense_Mutation	SNP	ENST00000326735.8	hg19	CCDS175.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.879903	0.51801	.	.	ENSG00000159363	ENST00000326735;ENST00000341676;ENST00000452699;ENST00000506174	D;D;D;D	0.92149	-2.98;-2.98;-2.98;-2.98	4.69	2.76	0.32466	ATPase, P-type, ATPase-associated domain (1);	0.545880	0.17421	N	0.174829	D	0.93462	0.7914	M	0.71871	2.18	0.40886	D	0.984039	P;P;D;P	0.53745	0.489;0.898;0.962;0.656	B;P;P;P	0.62491	0.314;0.672;0.903;0.579	D	0.90678	0.4603	10	0.59425	D	0.04	.	4.3183	0.11003	0.2691:0.1732:0.5577:0.0	.	148;430;430;435	Q6ZP48;Q5JXY1;Q6S9Z9;Q9NQ11	.;.;.;AT132_HUMAN	M	435;430;430;149	ENSP00000327214:L435M;ENSP00000341115:L430M;ENSP00000413307:L430M;ENSP00000424393:L149M	ENSP00000327214:L435M	L	-	1	2	ATP13A2	17195471	1.000000	0.71417	0.998000	0.56505	0.886000	0.51366	1.657000	0.37366	0.383000	0.24910	-0.258000	0.10820	CTG	.	.	.	none		0.612	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089		T	17322884	G	T	17322884	3	4	125	1	0	0	0	0	1	0	0	0	1124	991	35	4	2543	4	ATP13A2	1	17322884	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08		17322884	231927737	1	7807											
CACNA1S	779	hgsc.bcm.edu	37	chr1	201030589	201030589	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attggagtctatggccttgtAcagcagcctgggggtgggca	7	10	16	8	0	1	0	0	0	1	0	1	1	1	1	2	5	3	3	2	5	2	4			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr1:201030589A>G	ENST00000362061.3	-	25	3287	c.3061T>C	c.(3061-3063)Tac>Cac	p.Y1021H	CACNA1S_ENST00000367338.3_Missense_Mutation_p.Y1021H	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1021	Dihydropyridine binding. {ECO:0000250}.				axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	ATGGCCTTGTACAGCAGCCTG	0.557																																					p.Y1021H		Atlas-SNP	.											.	CACNA1S	249	.	0			c.T3061C						PASS	.						99	91	94					1																	201030589		2203	4300	6503	SO:0001583	missense	779	exon25			CCTTGTACAGCAG	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.3061T>C	chr1.hg19:g.201030589A>G	ENSP00000355192:p.Tyr1021His	54.0	0.0	.		83.0	17.0	.	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	hg19	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.507446	0.85282	.	.	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.97529	-4.42;-4.42	5.21	5.21	0.72293	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98639	0.9544	M	0.89968	3.075	0.58432	D	0.99999	D	0.89917	1.0	D	0.97110	1.0	D	0.99751	1.1018	10	0.72032	D	0.01	.	15.3483	0.74359	1.0:0.0:0.0:0.0	.	1021	Q13698	CAC1S_HUMAN	H	1021	ENSP00000355192:Y1021H;ENSP00000356307:Y1021H	ENSP00000355192:Y1021H	Y	-	1	0	CACNA1S	199297212	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	8.889000	0.92470	2.087000	0.62958	0.459000	0.35465	TAC	.	.	.	none		0.557	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		G	201030589	A	G	201030589	3	3	125	1	0	0	0	0	1	0	0	0	2549	391	14	3	2640	3	CACNA1S	1	201030589	Missense_Mutation	SNP	A	TCGA-BQ-5890-01A-11D-1589-08	183707705	201030589	48220032	2	7808											
NAV1	89796	hgsc.bcm.edu	37	chr1	201781618	201781618	+	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	tgaccttctccaacaacgtgGagccagccaatggcttcctg	9	9	9	14	1	1	1	0	1	1	0	3	2	2	2	5	2	4	1	5	2	3	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr1:201781618G>T	ENST00000367296.4	+	27	5470	c.5050G>T	c.(5050-5052)Gag>Tag	p.E1684*	NAV1_ENST00000367300.3_Nonsense_Mutation_p.E1624*|IPO9-AS1_ENST00000413035.1_RNA|NAV1_ENST00000367302.1_Nonsense_Mutation_p.E1637*|NAV1_ENST00000295624.6_Nonsense_Mutation_p.E1681*|NAV1_ENST00000367297.4_Nonsense_Mutation_p.E1676*|NAV1_ENST00000367295.1_Nonsense_Mutation_p.E1290*	NM_020443.4	NP_065176.3	Q8NEY1	NAV1_HUMAN	neuron navigator 1	1684					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						CAACAACGTGGAGCCAGCCAA	0.562																																					p.E1684X		Atlas-SNP	.											.	NAV1	143	.	0			c.G5050T						PASS	.						131	108	116					1																	201781618		2203	4300	6503	SO:0001587	stop_gained	89796	exon27			AACGTGGAGCCAG	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.5050G>T	chr1.hg19:g.201781618G>T	ENSP00000356265:p.Glu1684*	107.0	0.0	.		182.0	84.0	.	NM_020443	A8MS88|Q5SVH1|Q5SVH2|Q5SVH3|Q5SVH7|Q5VUY9|Q8IVL2|Q96II1|Q9H7V9|Q9H9S9|Q9H9T5|Q9UGI1|Q9ULK7|Q9ULR9	Nonsense_Mutation	SNP	ENST00000367296.4	hg19	CCDS1414.2	.	.	.	.	.	.	.	.	.	.	G	48	14.566335	0.99801	.	.	ENSG00000134369	ENST00000367302;ENST00000367296;ENST00000295624;ENST00000367297;ENST00000367300;ENST00000367295;ENST00000367301	.	.	.	6.05	6.05	0.98169	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-33.9888	20.2191	0.98319	0.0:0.0:1.0:0.0	.	.	.	.	X	1637;1684;1681;1676;1624;1290;93	.	ENSP00000295624:E1681X	E	+	1	0	NAV1	200048241	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.753000	0.98904	2.866000	0.98385	0.650000	0.86243	GAG	.	.	.	none		0.562	NAV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087013.1	NM_020443		T	201781618	G	T	201781618	4	4	125	1	0	0	0	0	0	1	0	0	10190	1175	41	4	5213	4	NAV1	1	201781618	Nonsense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	751029	201781618	47469003	3	7809											
PLEKHA6	22874	hgsc.bcm.edu	37	chr1	204236626	204236626	+	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	tatagtagaagaggcagcgaTccaccaggacgaaccagcgc	14	4	12	11	3	0	2	0	0	0	2	1	5	1	3	3	2	3	2	3	2	5	3			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr1:204236626T>A	ENST00000272203.3	-	5	573	c.257A>T	c.(256-258)gAt>gTt	p.D86V	PLEKHA6_ENST00000414478.1_Missense_Mutation_p.D86V	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	86	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.									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)			GAGGCAGCGATCCACCAGGAC	0.592																																					p.D86V		Atlas-SNP	.											.	PLEKHA6	115	.	0			c.A257T						PASS	.						114	85	95					1																	204236626		2203	4300	6503	SO:0001583	missense	22874	exon5			CAGCGATCCACCA	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.257A>T	chr1.hg19:g.204236626T>A	ENSP00000272203:p.Asp86Val	73.0	0.0	.		125.0	40.0	.	NM_014935	A7MD51|Q5VTI6	Missense_Mutation	SNP	ENST00000272203.3	hg19	CCDS1444.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.554500	0.86231	.	.	ENSG00000143850	ENST00000272203;ENST00000414478	T;T	0.15017	2.46;2.46	5.51	5.51	0.81932	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.48352	0.1495	M	0.86573	2.825	0.80722	D	1	D	0.71674	0.998	D	0.87578	0.998	T	0.56962	-0.7892	10	0.87932	D	0	-24.5699	15.2951	0.73898	0.0:0.0:0.0:1.0	.	86	Q9Y2H5	PKHA6_HUMAN	V	86	ENSP00000272203:D86V;ENSP00000402046:D86V	ENSP00000272203:D86V	D	-	2	0	PLEKHA6	202503249	1.000000	0.71417	0.997000	0.53966	0.988000	0.76386	6.511000	0.73733	2.086000	0.62901	0.448000	0.29417	GAT	.	.	.	none		0.592	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935		A	204236626	T	A	204236626	3	1	125	1	0	0	0	0	1	0	0	0	12067	1435	50	5	2961	5	PLEKHA6	1	204236626	Missense_Mutation	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	2455008	204236626	45013995	4	7810											
KIAA1804	84451	hgsc.bcm.edu	37	chr1	233518317	233518317	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aattcctcgctgccaaggagAgaactaaatcccatgtgcct	12	9	8	12	1	0	1	0	0	0	1	3	3	2	2	4	1	3	1	4	1	5	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr1:233518317A>G	ENST00000366624.3	+	10	3232	c.2971A>G	c.(2971-2973)Aga>Gga	p.R991G	MLK4_ENST00000366622.1_Missense_Mutation_p.R437G	NM_032435.2	NP_115811.2																					TGCCAAGGAGAGAACTAAATC	0.557																																					p.R991G		Atlas-SNP	.											.	KIAA1804	129	.	0			c.A2971G						PASS	.						118	102	108					1																	233518317		2203	4300	6503	SO:0001583	missense	0	exon10			AAGGAGAGAACTA																												ENST00000366624.3:c.2971A>G	chr1.hg19:g.233518317A>G	ENSP00000355583:p.Arg991Gly	94.0	0.0	.		149.0	39.0	.	NM_032435		Missense_Mutation	SNP	ENST00000366624.3	hg19	CCDS1598.1	.	.	.	.	.	.	.	.	.	.	A	15.19	2.760485	0.49468	.	.	ENSG00000143674	ENST00000366624;ENST00000366622	T;T	0.74947	-0.89;3.17	4.55	4.55	0.56014	.	0.160789	0.30428	U	0.009649	T	0.61236	0.2331	N	0.22421	0.69	0.33546	D	0.59548	P;B	0.40619	0.724;0.029	B;B	0.38500	0.275;0.023	T	0.73569	-0.3941	10	0.48119	T	0.1	.	12.6166	0.56580	1.0:0.0:0.0:0.0	.	438;991	Q5TCX8-3;Q5TCX8	.;M3KL4_HUMAN	G	991;437	ENSP00000355583:R991G;ENSP00000355581:R437G	ENSP00000355581:R437G	R	+	1	2	RP5-862P8.2	231584940	0.995000	0.38212	0.055000	0.19348	0.009000	0.06853	2.656000	0.46716	1.908000	0.55244	0.460000	0.39030	AGA	.	.	.	none		0.557	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1			G	233518317	A	G	233518317	3	3	125	1	0	0	0	0	1	0	0	0	8266	296	11	3	3009	3	KIAA1804	1	233518317	Missense_Mutation	SNP	A	TCGA-BQ-5890-01A-11D-1589-08	29281691	233518317	15732304	5	7811											
TBCE	6905	hgsc.bcm.edu	37	chr1	235599915	235599915	+	Missense_Mutation	SNP	A	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	tggtagtaaacgacaatcagAtatcacaagtaagagctgct	16	9	9	7	1	2	2	2	0	0	2	2	3	2	2	0	1	3	5	0	1	7	4			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr1:235599915A>C	ENST00000366601.3	+	11	1131	c.955A>C	c.(955-957)Ata>Cta	p.I319L	TBCE_ENST00000543662.1_Missense_Mutation_p.I370L|TBCE_ENST00000406207.1_Missense_Mutation_p.I319L|TBCE_ENST00000472011.1_3'UTR			Q15813	TBCE_HUMAN	tubulin folding cofactor E	319					'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)			CGACAATCAGATATCACAAGT	0.428																																					p.I319L		Atlas-SNP	.											.	TBCE	40	.	0			c.A955C						PASS	.						127	121	123					1																	235599915		2203	4300	6503	SO:0001583	missense	6905	exon11			AATCAGATATCAC	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.955A>C	chr1.hg19:g.235599915A>C	ENSP00000355560:p.Ile319Leu	126.0	0.0	.		158.0	34.0	.	NM_003193	A8K8C2|B7Z3P1	Missense_Mutation	SNP	ENST00000366601.3	hg19	CCDS1605.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.163199	0.78226	.	.	ENSG00000116957	ENST00000366601;ENST00000406207;ENST00000543662	T;T;T	0.25414	1.8;1.8;1.8	4.55	4.55	0.56014	.	0.000000	0.85682	D	0.000000	T	0.32466	0.0830	L	0.52823	1.66	0.58432	D	0.999993	D;B;P	0.60575	0.988;0.391;0.538	P;B;P	0.52309	0.695;0.194;0.545	T	0.04723	-1.0931	10	0.15952	T	0.53	-23.5139	12.9072	0.58160	1.0:0.0:0.0:0.0	.	370;319;319	B7Z3P1;A8K8C2;Q15813	.;.;TBCE_HUMAN	L	319;319;370	ENSP00000355560:I319L;ENSP00000384571:I319L;ENSP00000439170:I370L	ENSP00000355560:I319L	I	+	1	0	TBCE	233666538	1.000000	0.71417	0.946000	0.38457	0.879000	0.50718	5.808000	0.69165	2.053000	0.61076	0.533000	0.62120	ATA	.	.	.	none		0.428	TBCE-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000096458.3	NM_003193		C	235599915	A	C	235599915	3	2	125	1	0	0	0	0	1	0	0	0	15646	333	12	5	993	5	TBCE	1	235599915	Missense_Mutation	SNP	A	TCGA-BQ-5890-01A-11D-1589-08	2081598	235599915	13650706	6	7812											
TFCP2L1	29842	hgsc.bcm.edu	37	chr2	121991738	121991738	+	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	gattctgctccagctcctgaCagacataaatggtcatcttt	10	13	7	11	0	3	2	1	1	2	1	5	3	5	2	2	1	2	2	2	1	2	3			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr2:121991738C>T	ENST00000263707.5	-	12	1224	c.1127G>A	c.(1126-1128)tGt>tAt	p.C376Y		NM_014553.2	NP_055368.1	Q9NZI6	TF2L1_HUMAN	transcription factor CP2-like 1	376					cell morphogenesis (GO:0000902)|cytoplasm organization (GO:0007028)|determination of adult lifespan (GO:0008340)|epithelial cell maturation (GO:0002070)|female pregnancy (GO:0007565)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of growth (GO:0045927)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|salivary gland development (GO:0007431)|steroid biosynthetic process (GO:0006694)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(4)|large_intestine(5)|lung(7)|ovary(1)|pancreas(2)|skin(1)|stomach(1)	22	Renal(3;0.01)					CAGCTCCTGACAGACATAAAT	0.532																																					p.C376Y		Atlas-SNP	.											.	TFCP2L1	54	.	0			c.G1127A						PASS	.						103	91	95					2																	121991738		2203	4300	6503	SO:0001583	missense	29842	exon12			TCCTGACAGACAT	AF198488	CCDS2134.1	2q14	2008-02-05			ENSG00000115112	ENSG00000115112			17925	protein-coding gene	gene with protein product		609785				10644752, 11073954	Standard	NM_014553		Approved	LBP-9, CRTR1	uc002tmx.3	Q9NZI6	OTTHUMG00000131443	ENST00000263707.5:c.1127G>A	chr2.hg19:g.121991738C>T	ENSP00000263707:p.Cys376Tyr	90.0	0.0	.		87.0	32.0	.	NM_014553	Q4ZG43	Missense_Mutation	SNP	ENST00000263707.5	hg19	CCDS2134.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.941307	0.73557	.	.	ENSG00000115112	ENST00000263707	T	0.26067	1.76	5.7	4.83	0.62350	.	0.152997	0.64402	D	0.000010	T	0.49677	0.1571	M	0.81942	2.565	0.80722	D	1	D	0.61080	0.989	P	0.60886	0.88	T	0.55730	-0.8095	10	0.56958	D	0.05	.	14.5903	0.68359	0.0:0.93:0.0:0.07	.	376	Q9NZI6	TF2L1_HUMAN	Y	376	ENSP00000263707:C376Y	ENSP00000263707:C376Y	C	-	2	0	TFCP2L1	121708208	1.000000	0.71417	0.994000	0.49952	0.818000	0.46254	6.831000	0.75324	1.426000	0.47256	0.549000	0.68633	TGT	.	.	.	none		0.532	TFCP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338539.1	NM_014553		T	121991738	C	T	121991738	3	4	125	1	0	0	0	0	1	0	0	0	15808	478	17	2	328	2	TFCP2L1	2	121991738	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08		121991738	121207635	7	7813											
C2orf24	27013	hgsc.bcm.edu	37	chr2	220039577	220039577	+	Missense_Mutation	SNP	T	T	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	agcagctccccattcgtcgtTgaagacctcctcctcctccc	6	10	6	19	2	0	2	0	1	0	1	7	2	5	2	7	0	2	3	7	0	1	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr2:220039577T>G	ENST00000409789.1	-	6	860	c.433A>C	c.(433-435)Aac>Cac	p.N145H	CNPPD1_ENST00000360507.5_Missense_Mutation_p.N145H			Q9BV87	CNPD1_HUMAN	cyclin Pas1/PHO80 domain containing 1	145					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						CATTCGTCGTTGAAGACCTCC	0.577																																					p.N145H		Atlas-SNP	.											.	CNPPD1	22	.	0			c.A433C						PASS	.						86	80	82					2																	220039577		2203	4300	6503	SO:0001583	missense	27013	exon5			CGTCGTTGAAGAC	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.433A>C	chr2.hg19:g.220039577T>G	ENSP00000386277:p.Asn145His	77.0	0.0	.		91.0	31.0	.	NM_015680	B2RC77|O75548|Q9H4N0|Q9UQN0	Missense_Mutation	SNP	ENST00000409789.1	hg19	CCDS2433.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.250866	0.80135	.	.	ENSG00000115649	ENST00000360507;ENST00000409789;ENST00000453038;ENST00000451647	T;T;T	0.58940	0.3;0.3;0.3	4.42	4.42	0.53409	.	0.000000	0.85682	D	0.000000	T	0.81192	0.4771	M	0.93638	3.44	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.86432	0.1761	10	0.87932	D	0	-21.9189	13.8616	0.63564	0.0:0.0:0.0:1.0	.	145	Q9BV87	CNPD1_HUMAN	H	145;145;145;172	ENSP00000353698:N145H;ENSP00000386277:N145H;ENSP00000410109:N145H	ENSP00000353698:N145H	N	-	1	0	CNPPD1	219747821	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.766000	0.85320	1.873000	0.54277	0.459000	0.35465	AAC	.	.	.	none		0.577	CNPPD1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336220.1	NM_015680		G	220039577	T	G	220039577	3	3	125	1	0	0	0	0	1	0	0	0	2161	1812	63	5	815	5	C2orf24	2	220039577	Missense_Mutation	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	98047839	220039577	23159796	8	7814											
AGXT	189	hgsc.bcm.edu	37	chr2	241808770	241808770	+	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	agcgagccgtggacatcgggGagcgcataggtaagggagag	11	4	19	7	4	0	1	0	0	0	1	1	5	0	3	1	5	3	2	1	5	2	2	rs180177208		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr2:241808770G>A	ENST00000307503.3	+	2	736	c.349G>A	c.(349-351)Gag>Aag	p.E117K		NM_000030.2	NP_000021.1	P21549	SPYA_HUMAN	alanine-glyoxylate aminotransferase	117					cellular nitrogen compound metabolic process (GO:0034641)|glycine biosynthetic process, by transamination of glyoxylate (GO:0019265)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|L-alanine catabolic process (GO:0042853)|L-cysteine catabolic process (GO:0019448)|oxalic acid secretion (GO:0046724)|pyruvate biosynthetic process (GO:0042866)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	alanine-glyoxylate transaminase activity (GO:0008453)|amino acid binding (GO:0016597)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|receptor binding (GO:0005102)|serine-pyruvate transaminase activity (GO:0004760)|transaminase activity (GO:0008483)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)	18		all_epithelial(40;1.61e-15)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)	Glycine(DB00145)|L-Alanine(DB00160)|L-Serine(DB00133)	GGACATCGGGGAGCGCATAGG	0.657																																					p.E117K		Atlas-SNP	.											.	AGXT	50	.	0			c.G349A						PASS	.						51	52	52					2																	241808770		2203	4300	6503	SO:0001583	missense	189	exon2			ATCGGGGAGCGCA	D13368	CCDS2543.1	2q37.3	2008-02-05	2007-04-13		ENSG00000172482	ENSG00000172482	2.6.1.44, 2.6.1.51		341	protein-coding gene	gene with protein product	"oxalosis I", "primary hyperoxaluria type 1", "L-alanine: glyoxylate aminotransferase 1", "serine:pyruvate aminotransferase", "glycolicaciduria"	604285		SPAT		2039493, 2045108	Standard	NM_000030		Approved	AGXT1, PH1, AGT, SPT, AGT1	uc002waa.4	P21549	OTTHUMG00000133354	ENST00000307503.3:c.349G>A	chr2.hg19:g.241808770G>A	ENSP00000302620:p.Glu117Lys	82.0	0.0	.		87.0	32.0	.	NM_000030	Q53QU6	Missense_Mutation	SNP	ENST00000307503.3	hg19	CCDS2543.1	.	.	.	.	.	.	.	.	.	.	G	6.004	0.369211	0.11352	.	.	ENSG00000172482	ENST00000307503	D	0.85702	-2.02	4.12	4.12	0.48240	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.160335	0.53938	D	0.000048	T	0.80681	0.4669	L	0.60067	1.865	0.49915	D	0.999836	B;B	0.14012	0.004;0.009	B;B	0.17979	0.012;0.02	T	0.75516	-0.3290	10	0.27785	T	0.31	-32.4358	10.2905	0.43592	0.151:0.0:0.849:0.0	.	117;117	B7Z548;P21549	.;SPYA_HUMAN	K	117	ENSP00000302620:E117K	ENSP00000302620:E117K	E	+	1	0	AGXT	241457443	1.000000	0.71417	0.826000	0.32828	0.290000	0.27261	4.798000	0.62510	2.007000	0.58848	0.591000	0.81541	GAG	.	.	.	alt		0.657	AGXT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257186.1	NM_000030		A	241808770	G	A	241808770	3	1	125	1	0	0	0	0	1	0	0	0	404	1175	41	2	355	2	AGXT	2	241808770	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	21769193	241808770	1390603	9	7815											
PASK	23178	hgsc.bcm.edu	37	chr2	242065794	242065794	+	Missense_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	atccaacgtggaaggaacgtGtcctgggctttctctgtcgc	7	11	12	11	3	1	0	0	0	1	0	5	2	3	2	2	3	2	1	2	3	3	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr2:242065794G>A	ENST00000405260.1	-	10	3234	c.2536C>T	c.(2536-2538)Cac>Tac	p.H846Y	PASK_ENST00000539818.1_Missense_Mutation_p.H630Y|PASK_ENST00000358649.4_Missense_Mutation_p.H846Y|PASK_ENST00000403638.3_Missense_Mutation_p.H846Y|PASK_ENST00000234040.4_Missense_Mutation_p.H846Y|PASK_ENST00000544142.1_Missense_Mutation_p.H660Y	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	846					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)		GAAGGAACGTGTCCTGGGCTT	0.572																																					p.H846Y		Atlas-SNP	.											.	PASK	230	.	0			c.C2536T						PASS	.						159	149	152					2																	242065794		2203	4300	6503	SO:0001583	missense	23178	exon10			GAACGTGTCCTGG	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.2536C>T	chr2.hg19:g.242065794G>A	ENSP00000384016:p.His846Tyr	132.0	0.0	.		165.0	59.0	.	NM_015148	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Missense_Mutation	SNP	ENST00000405260.1	hg19	CCDS2545.1	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.619945	0.00828	.	.	ENSG00000115687	ENST00000234040;ENST00000544142;ENST00000405260;ENST00000358649;ENST00000539818;ENST00000403638	T;T;T;T;T;T	0.66280	-0.2;-0.19;-0.2;-0.15;-0.19;0.81	3.24	-6.48	0.01896	.	1.203440	0.06016	N	0.650378	T	0.35856	0.0946	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B	0.32365	0.367;0.011;0.032;0.031;0.09	B;B;B;B;B	0.28385	0.089;0.036;0.009;0.024;0.023	T	0.20773	-1.0265	10	0.31617	T	0.26	.	6.1419	0.20265	0.3709:0.0:0.4891:0.14	.	811;660;846;846;846	B7Z7R6;F5GYW7;Q96RG2-2;G5E9F1;Q96RG2	.;.;.;.;PASK_HUMAN	Y	846;660;846;846;630;846	ENSP00000234040:H846Y;ENSP00000441374:H660Y;ENSP00000384016:H846Y;ENSP00000351475:H846Y;ENSP00000443083:H630Y;ENSP00000384438:H846Y	ENSP00000234040:H846Y	H	-	1	0	PASK	241714467	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.416000	0.02467	-1.226000	0.02574	-1.169000	0.01745	CAC	.	.	.	none		0.572	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148		A	242065794	G	A	242065794	3	1	125	1	0	0	0	0	1	0	0	0	11479	1377	48	2	1471	2	PASK	2	242065794	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	257024	242065794	1133579	10	7816											
ZNF502	91392	hgsc.bcm.edu	37	chr3	44763320	44763320	+	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	actttccaaacaaaggcaaaCctctctcagcatcagagaat	16	8	5	12	0	3	1	2	0	1	1	5	2	4	1	2	1	3	2	2	1	4	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr3:44763320C>G	ENST00000296091.4	+	4	1267	c.1011C>G	c.(1009-1011)aaC>aaG	p.N337K	ZNF502_ENST00000436624.2_Missense_Mutation_p.N337K|ZNF502_ENST00000449836.1_Missense_Mutation_p.N337K	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	337					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|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)		CAAAGGCAAACCTCTCTCAGC	0.403																																					p.N337K		Atlas-SNP	.											.	ZNF502	58	.	0			c.C1011G						PASS	.						57	61	60					3																	44763320		2203	4300	6503	SO:0001583	missense	91392	exon4			GGCAAACCTCTCT	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.1011C>G	chr3.hg19:g.44763320C>G	ENSP00000296091:p.Asn337Lys	124.0	0.0	.		117.0	79.0	.	NM_001134440		Missense_Mutation	SNP	ENST00000296091.4	hg19	CCDS2719.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.31|11.31	1.599882|1.599882	0.28534|0.28534	.|.	.|.	ENSG00000196653|ENSG00000196653	ENST00000449836;ENST00000296091;ENST00000436624|ENST00000427783	T;T;T|.	0.07021|.	3.23;3.23;3.23|.	4.27|4.27	-1.17|-1.17	0.09648|0.09648	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);|.	.|.	.|.	.|.	.|.	T|T	0.14700|0.14700	0.0355|0.0355	N|N	0.20986|0.20986	0.625|0.625	0.09310|0.09310	N|N	1|1	P|.	0.35982|.	0.531|.	B|.	0.24155|.	0.051|.	T|T	0.29119|0.29119	-1.0022|-1.0022	9|6	0.10377|0.02654	T|T	0.69|1	.|.	1.6891|1.6891	0.02848|0.02848	0.1337:0.367:0.1313:0.368|0.1337:0.367:0.1313:0.368	.|.	337|.	Q8TBZ5|.	ZN502_HUMAN|.	K|S	337|337	ENSP00000397390:N337K;ENSP00000296091:N337K;ENSP00000406469:N337K|.	ENSP00000296091:N337K|ENSP00000397812:T337S	N|T	+|+	3|2	2|0	ZNF502|ZNF502	44738324|44738324	0.000000|0.000000	0.05858|0.05858	0.859000|0.859000	0.33776|0.33776	0.997000|0.997000	0.91878|0.91878	-1.664000|-1.664000	0.01966|0.01966	-0.114000|-0.114000	0.11936|0.11936	0.655000|0.655000	0.94253|0.94253	AAC|ACC	.	.	.	none		0.403	ZNF502-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256744.4	NM_033210		G	44763320	C	G	44763320	3	3	125	1	0	0	0	0	1	0	0	0	17962	506	18	4	1017	4	ZNF502	3	44763320	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08		44763320	153259110	11	7817											
NBEAL2	23218	hgsc.bcm.edu	37	chr3	47032943	47032943	+	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	ggctctgtgaagggcctgctGagtgtggtgcggggctggag	4	9	21	7	1	1	2	0	2	1	0	1	3	1	3	1	6	2	3	1	6	1	0	rs181297174		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr3:47032943G>T	ENST00000450053.3	+	8	869	c.690G>T	c.(688-690)ctG>ctT	p.L230L	NBEAL2_ENST00000292309.5_Silent_p.L230L|NBEAL2_ENST00000383740.2_5'UTR	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	230					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)		AGGGCCTGCTGAGTGTGGTGC	0.637																																					p.L230L		Atlas-SNP	.											.	NBEAL2	267	.	0			c.G690T						PASS	.						31	33	32					3																	47032943		2012	4187	6199	SO:0001819	synonymous_variant	23218	exon8			CCTGCTGAGTGTG	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.690G>T	chr3.hg19:g.47032943G>T		20.0	0.0	.		29.0	22.0	.	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Silent	SNP	ENST00000450053.3	hg19	CCDS46817.1																																																																																			.	G|1.000;C|0.000	.	alt		0.637	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		T	47032943	G	T	47032943	2	4	125	1	0	0	0	0	0	0	0	1	10196	1277	45	4		4	NBEAL2	3	47032943	Silent	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	2269623	47032943	150989487	12	7818											
SETD2	29072	hgsc.bcm.edu	37	chr3	47143047	47143047	+	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	gttgtccgttcacagtccacTgagatgatgtttgaaaacaa	12	12	9	8	1	1	3	1	3	0	1	3	4	3	3	2	0	1	3	2	0	3	3			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr3:47143047T>C	ENST00000409792.3	-	8	4960		c.e8-2			NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2						angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.?(2)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CACAGTCCACTGAGATGATGT	0.408			"N, F, S, Mis"		clear cell renal carcinoma																																.		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	SETD2_ENST00000409792,NS,carcinoma,0,2	SETD2	721	.	2	Unknown(2)	kidney(2)	c.4918-2A>G						PASS	.						109	108	108					3																	47143047		2203	4300	6503	SO:0001630	splice_region_variant	29072	exon9			GTCCACTGAGATG	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4918-2A>G	chr3.hg19:g.47143047T>C		115.0	0.0	.		139.0	102.0	.	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Splice_Site	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	T	27.7	4.856990	0.91433	.	.	ENSG00000181555	ENST00000451092;ENST00000543224;ENST00000409792	.	.	.	5.85	5.85	0.93711	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2291	0.82321	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SETD2	47118051	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.955000	0.87856	2.238000	0.73509	0.528000	0.53228	.	.	.	.	none		0.408	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	Intron	C	47143047	T	C	47143047	5	2	125	1	0	0	0	0	0	0	1	0	14144	1594	55	3	2834	3	SETD2	3	47143047	Splice_Site	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	110104	47143047	150879383	13	7819											
PBRM1	55193	hgsc.bcm.edu	37	chr3	52696272	52696272	+	Frame_Shift_Del	DEL	T	T	-																															tcccagagtttgcaagcggcTttatattcaggagaatctgg																										TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr3:52696272delT	ENST00000296302.7	-	4	406	c.405delA	c.(403-405)aaafs	p.K135fs	PBRM1_ENST00000394830.3_Frame_Shift_Del_p.K135fs|PBRM1_ENST00000356770.4_Frame_Shift_Del_p.K135fs|PBRM1_ENST00000337303.4_Frame_Shift_Del_p.K135fs|PBRM1_ENST00000409114.3_Frame_Shift_Del_p.K135fs|PBRM1_ENST00000409057.1_Frame_Shift_Del_p.K135fs|PBRM1_ENST00000409767.1_Frame_Shift_Del_p.K135fs|PBRM1_ENST00000410007.1_Frame_Shift_Del_p.K135fs			Q86U86	PB1_HUMAN	polybromo 1	135					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)		TGCAAGCGGCTTTATATTCAG	0.368			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.A136fs		Atlas-INDEL	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.406delG						PASS	.						110	106	107					3																	52696272		2203	4300	6503	SO:0001589	frameshift_variant	55193	exon5			.	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.405delA	chr3.hg19:g.52696272delT	ENSP00000296302:p.Lys135fs	149.0	0.0	0		91.0	61.0	0.67033	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Frame_Shift_Del	DEL	ENST00000296302.7	hg19																																																																																				.	.	.	none		0.368	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		-	52696272	T	-	52696272	7	5	125	1	0	1	0	1	0	0	0	0	11498	1606	56	0	4603	0	PBRM1	3	52696272	Frame_Shift_Del	DEL	T	TCGA-BQ-5890-01A-11D-1589-08	5553225	52696272	145326158	14	7820											
NPHP3	27031	hgsc.bcm.edu	37	chr3	132410108	132410108	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtggggccttccaggtacTccaatctcactgtttcccaa	8	11	8	14	0	1	0	1	0	1	0	5	0	4	0	4	3	1	2	4	3	3	3			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr3:132410108T>C	ENST00000337331.5	-	18	2584	c.2498A>G	c.(2497-2499)gAg>gGg	p.E833G	NPHP3_ENST00000326682.8_3'UTR	NM_153240.4	NP_694972.3	Q7Z494	NPHP3_HUMAN	nephronophthisis 3 (adolescent)	833					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						TTCCAGGTACTCCAATCTCAC	0.388																																					p.E833G		Atlas-SNP	.											.	NPHP3	110	.	0			c.A2498G						PASS	.						163	169	167					3																	132410108		2203	4300	6503	SO:0001583	missense	27031	exon18			AGGTACTCCAATC	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.2498A>G	chr3.hg19:g.132410108T>C	ENSP00000338766:p.Glu833Gly	251.0	0.0	.		308.0	175.0	.	NM_153240	Q5JPE3|Q5JPE6|Q68D99|Q6NVH3|Q7Z492|Q7Z493|Q8N9R2|Q8NCM5|Q96N70|Q96NK2	Missense_Mutation	SNP	ENST00000337331.5	hg19	CCDS3078.1	.	.	.	.	.	.	.	.	.	.	T	11.05	1.525698	0.27299	.	.	ENSG00000113971	ENST00000393144;ENST00000337331	D	0.91577	-2.87	4.55	3.35	0.38373	.	0.108809	0.64402	D	0.000011	D	0.87977	0.6314	M	0.61703	1.905	0.80722	D	1	B	0.24258	0.1	B	0.24541	0.054	D	0.83643	0.0151	10	0.49607	T	0.09	-10.5568	10.9157	0.47135	0.0:0.0:0.1571:0.8429	.	833	Q7Z494	NPHP3_HUMAN	G	113;833	ENSP00000338766:E833G	ENSP00000338766:E833G	E	-	2	0	NPHP3	133892798	1.000000	0.71417	0.291000	0.24904	0.151000	0.21798	5.118000	0.64673	0.661000	0.30985	0.460000	0.39030	GAG	.	.	.	none		0.388	NPHP3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357020.2	NM_153240		C	132410108	T	C	132410108	3	2	125	1	0	0	0	0	1	0	0	0	10587	1551	54	3	1534	3	NPHP3	3	132410108	Missense_Mutation	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	79713836	132410108	65612322	15	7821											
STX18	53407	hgsc.bcm.edu	37	chr4	4436571	4436571	+	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	tcccaattcaggttgtgtttCagccaaaattttttctgtta	9	18	6	8	0	3	0	2	0	1	0	4	0	4	0	2	1	1	3	2	1	4	7			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr4:4436571C>T	ENST00000306200.2	-	7	691	c.628G>A	c.(628-630)Gaa>Aaa	p.E210K	STX18_ENST00000505286.1_Missense_Mutation_p.E210K	NM_016930.2	NP_058626.1	Q9P2W9	STX18_HUMAN	syntaxin 18	210					ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.0534)		GGTTGTGTTTCAGCCAAAATT	0.353																																					p.E210K		Atlas-SNP	.											.	STX18	16	.	0			c.G628A						PASS	.						80	81	81					4																	4436571		2203	4300	6503	SO:0001583	missense	53407	exon7			GTGTTTCAGCCAA	AB028741	CCDS3377.1	4p16.3-p16.2	2013-09-23			ENSG00000168818	ENSG00000168818			15942	protein-coding gene	gene with protein product		606046				10788491	Standard	NM_016930		Approved	Ufe1	uc003gic.3	Q9P2W9	OTTHUMG00000090331	ENST00000306200.2:c.628G>A	chr4.hg19:g.4436571C>T	ENSP00000305810:p.Glu210Lys	88.0	0.0	.		71.0	18.0	.	NM_016930	Q596L3|Q5TZP5	Missense_Mutation	SNP	ENST00000306200.2	hg19	CCDS3377.1	.	.	.	.	.	.	.	.	.	.	C	9.694	1.152643	0.21371	.	.	ENSG00000168818	ENST00000505286;ENST00000306200;ENST00000512195;ENST00000507908	T;T;T;T	0.50001	0.76;0.76;0.76;0.76	5.19	2.55	0.30701	.	0.372946	0.28388	N	0.015531	T	0.35828	0.0945	L	0.55103	1.725	0.09310	N	0.999999	B	0.06786	0.001	B	0.09377	0.004	T	0.30563	-0.9974	10	0.09338	T	0.73	-1.7145	8.2654	0.31810	0.0:0.7549:0.0:0.2451	.	210	Q9P2W9	STX18_HUMAN	K	210;210;129;129	ENSP00000426648:E210K;ENSP00000305810:E210K;ENSP00000425483:E129K;ENSP00000422376:E129K	ENSP00000305810:E210K	E	-	1	0	STX18	4487472	0.834000	0.29399	0.008000	0.14137	0.804000	0.45430	2.929000	0.48916	0.225000	0.20959	0.655000	0.94253	GAA	.	.	.	none		0.353	STX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206696.1			T	4436571	C	T	4436571	3	4	125	1	0	0	0	0	1	0	0	0	15353	835	29	2	399	2	STX18	4	4436571	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08		4436571	186717705	16	7822											
YTHDC1	91746	hgsc.bcm.edu	37	chr4	69185877	69185877	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcagggggatagtcaatccTtggtttctttctgctgttat	6	17	10	8	0	4	0	2	0	2	0	5	1	5	1	1	3	1	3	1	3	3	5			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr4:69185877T>C	ENST00000344157.4	-	12	1983	c.1648A>G	c.(1648-1650)Agg>Ggg	p.R550G	YTHDC1_ENST00000579690.1_Missense_Mutation_p.R550G|YTHDC1_ENST00000355665.3_Missense_Mutation_p.R532G	NM_001031732.2	NP_001026902.1	Q96MU7	YTDC1_HUMAN	YTH domain containing 1	550	Arg-rich.				mRNA splice site selection (GO:0006376)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	30						TAGTCAATCCTTGGTTTCTTT	0.323																																					p.R550G		Atlas-SNP	.											.	YTHDC1	81	.	0			c.A1648G						PASS	.						66	68	67					4																	69185877		2203	4300	6503	SO:0001583	missense	91746	exon12			CAATCCTTGGTTT	AK098515	CCDS3522.2, CCDS33992.1	4q13.3	2009-01-14			ENSG00000083896	ENSG00000083896			30626	protein-coding gene	gene with protein product						12368078, 10564280	Standard	XM_005265706		Approved	YT521, KIAA1966, YT521-B	uc003hdx.3	Q96MU7	OTTHUMG00000129306	ENST00000344157.4:c.1648A>G	chr4.hg19:g.69185877T>C	ENSP00000339245:p.Arg550Gly	113.0	0.0	.		81.0	25.0	.	NM_001031732	Q4W5Q3|Q7Z622|Q8TF35	Missense_Mutation	SNP	ENST00000344157.4	hg19	CCDS33992.1	.	.	.	.	.	.	.	.	.	.	T	16.05	3.013953	0.54468	.	.	ENSG00000083896	ENST00000344157;ENST00000355665	T;T	0.27557	1.68;1.66	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.44519	0.1297	L	0.27053	0.805	0.58432	D	0.999999	D;D	0.67145	0.989;0.996	D;P	0.75020	0.985;0.867	T	0.41805	-0.9488	10	0.72032	D	0.01	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	532;550	Q96MU7-2;Q96MU7	.;YTDC1_HUMAN	G	550;532	ENSP00000339245:R550G;ENSP00000347888:R532G	ENSP00000339245:R550G	R	-	1	2	YTHDC1	68868472	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.886000	0.69743	2.371000	0.80710	0.533000	0.62120	AGG	.	.	.	none		0.323	YTHDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251437.1	NM_133370		C	69185877	T	C	69185877	3	2	125	1	0	0	0	0	1	0	0	0	17508	1608	56	3	559	3	YTHDC1	4	69185877	Missense_Mutation	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	64749306	69185877	121968399	17	7823											
ELOVL6	79071	hgsc.bcm.edu	37	chr4	111119479	111119479	+	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	atattcttgtaaagtcaacaCtgacatgttcattggggctg	11	14	9	7	0	3	1	2	1	1	0	3	1	3	1	0	2	1	3	0	2	4	6			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr4:111119479C>A	ENST00000394607.3	-	2	176	c.13G>T	c.(13-15)Gtg>Ttg	p.V5L	ELOVL6_ENST00000302274.3_Missense_Mutation_p.V5L|ELOVL6_ENST00000506461.1_5'UTR			Q9H5J4	ELOV6_HUMAN	ELOVL fatty acid elongase 6	5					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)		AAAGTCAACACTGACATGTTC	0.418																																					p.V5L		Atlas-SNP	.											.	ELOVL6	27	.	0			c.G13T						PASS	.						210	182	191					4																	111119479		2203	4300	6503	SO:0001583	missense	79071	exon2			TCAACACTGACAT	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.13G>T	chr4.hg19:g.111119479C>A	ENSP00000378105:p.Val5Leu	204.0	0.0	.		147.0	45.0	.	NM_001130721	Q4W5L0|Q8NCD1	Missense_Mutation	SNP	ENST00000394607.3	hg19	CCDS3690.1	.	.	.	.	.	.	.	.	.	.	C	19.10	3.761175	0.69763	.	.	ENSG00000170522	ENST00000394607;ENST00000302274;ENST00000506625;ENST00000503885	T;T	0.21932	1.98;1.98	5.68	5.68	0.88126	.	0.204024	0.41712	D	0.000835	T	0.16981	0.0408	N	0.22421	0.69	0.48511	D	0.999667	B	0.02656	0.0	B	0.04013	0.001	T	0.06110	-1.0845	10	0.23302	T	0.38	-10.017	18.5758	0.91154	0.0:1.0:0.0:0.0	.	5	Q9H5J4	ELOV6_HUMAN	L	5	ENSP00000378105:V5L;ENSP00000304736:V5L	ENSP00000304736:V5L	V	-	1	0	ELOVL6	111338928	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.795000	0.75140	2.683000	0.91414	0.655000	0.94253	GTG	.	.	.	none		0.418	ELOVL6-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255748.1	NM_024090		A	111119479	C	A	111119479	3	1	125	1	0	0	0	0	1	0	0	0	5080	565	20	4	800	4	ELOVL6	4	111119479	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	41933602	111119479	80034797	18	7824											
INPP4B	8821	hgsc.bcm.edu	37	chr4	143181690	143181690	+	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	ttttccgctcacactttccgGggctgtacattcacatacca	8	13	6	14	2	2	0	2	0	0	0	4	0	4	0	3	2	2	3	3	2	2	6			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr4:143181690G>T	ENST00000513000.1	-	12	1076	c.643C>A	c.(643-645)Ccg>Acg	p.P215T	INPP4B_ENST00000508116.1_Missense_Mutation_p.P215T|INPP4B_ENST00000262992.4_Missense_Mutation_p.P215T|INPP4B_ENST00000308502.4_Missense_Mutation_p.P215T|INPP4B_ENST00000509777.1_Missense_Mutation_p.P215T	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	215					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)	p.P215S(2)		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)					ACACTTTCCGGGGCTGTACAT	0.279																																					p.P215T		Atlas-SNP	.											INPP4B,NS,carcinoma,0,1	INPP4B	132	.	2	Substitution - Missense(2)	lung(2)	c.C643A						PASS	.						53	53	53					4																	143181690		2203	4300	6503	SO:0001583	missense	8821	exon12			TTTCCGGGGCTGT	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.643C>A	chr4.hg19:g.143181690G>T	ENSP00000425487:p.Pro215Thr	47.0	0.0	.		52.0	16.0	.	NM_003866	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Missense_Mutation	SNP	ENST00000513000.1	hg19	CCDS3757.1	.	.	.	.	.	.	.	.	.	.	G	13.81	2.349424	0.41599	.	.	ENSG00000109452	ENST00000513000;ENST00000262992;ENST00000308502;ENST00000543161;ENST00000508116;ENST00000509777;ENST00000511838;ENST00000542702;ENST00000510812;ENST00000514525	T;T;T;T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52	5.52	3.78	0.43462	.	0.221687	0.37219	N	0.002193	T	0.18551	0.0445	N	0.14661	0.345	0.32366	N	0.556496	P;P	0.45531	0.86;0.767	P;B	0.47075	0.536;0.359	T	0.12604	-1.0541	10	0.09843	T	0.71	.	6.5521	0.22440	0.1539:0.0:0.6999:0.1463	.	86;215	B7Z6T2;O15327	.;INP4B_HUMAN	T	215;215;215;86;215;215;30;30;215;86	ENSP00000425487:P215T;ENSP00000262992:P215T;ENSP00000308441:P215T;ENSP00000423954:P215T;ENSP00000422793:P215T;ENSP00000426207:P30T;ENSP00000427250:P215T;ENSP00000421065:P86T	ENSP00000262992:P215T	P	-	1	0	INPP4B	143401140	0.996000	0.38824	0.954000	0.39281	0.988000	0.76386	1.385000	0.34408	0.674000	0.31244	0.655000	0.94253	CCG	.	.	.	none		0.279	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866		T	143181690	G	T	143181690	3	4	125	1	0	0	0	0	1	0	0	0	7760	1232	43	4	2195	4	INPP4B	4	143181690	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	32062211	143181690	47972586	19	7825											
TIGD4	201798	hgsc.bcm.edu	37	chr4	153691640	153691640	+	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	aacatttttaggatgataatCatttaaataataaggaagta	19	14	6	2	0	1	1	1	1	0	0	1	3	1	3	0	2	1	1	0	2	9	9			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr4:153691640C>T	ENST00000304337.2	-	2	1337	c.517G>A	c.(517-519)Gat>Aat	p.D173N		NM_145720.3	NP_663772.1	Q8IY51	TIGD4_HUMAN	tigger transposable element derived 4	173						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.093)					GGATGATAATCATTTAAATAA	0.353																																					p.D173N		Atlas-SNP	.											.	TIGD4	53	.	0			c.G517A						PASS	.						35	38	37					4																	153691640		2172	4288	6460	SO:0001583	missense	201798	exon2			GATAATCATTTAA	AK058054	CCDS34079.1	4q31.23	2008-02-05							18335	protein-coding gene	gene with protein product							Standard	NM_145720		Approved		uc003imy.3	Q8IY51		ENST00000304337.2:c.517G>A	chr4.hg19:g.153691640C>T	ENSP00000355162:p.Asp173Asn	87.0	0.0	.		56.0	18.0	.	NM_145720	Q96LP5	Missense_Mutation	SNP	ENST00000304337.2	hg19	CCDS34079.1	.	.	.	.	.	.	.	.	.	.	C	13.79	2.341226	0.41498	.	.	ENSG00000169989	ENST00000304337	T	0.14893	2.47	5.7	5.7	0.88788	.	0.000000	0.46145	D	0.000301	T	0.16854	0.0405	L	0.35723	1.085	0.38647	D	0.951745	B	0.26744	0.158	B	0.26864	0.074	T	0.09100	-1.0690	10	0.17369	T	0.5	-28.5772	19.8349	0.96652	0.0:1.0:0.0:0.0	.	173	Q8IY51	TIGD4_HUMAN	N	173	ENSP00000355162:D173N	ENSP00000355162:D173N	D	-	1	0	TIGD4	153911090	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.463000	0.66712	2.861000	0.98227	0.655000	0.94253	GAT	.	.	.	none		0.353	TIGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365028.1	NM_145720		T	153691640	C	T	153691640	3	4	125	1	0	0	0	0	1	0	0	0	15910	826	29	2	1025	2	TIGD4	4	153691640	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	10509950	153691640	37462636	20	7826											
SORBS2	8470	hgsc.bcm.edu	37	chr4	186545113	186545114	+	Missense_Mutation	DNP	GT	GT	AG																															caggcgcgcagcaggtccttGtgctgctgctcgctctcgta																										TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G|T	G|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr4:186545113_186545114GT>AG	ENST00000284776.7	-	13	1966_1967	c.1457_1458AC>CT	c.(1456-1458)cAC>cCT	p.H486P	SORBS2_ENST00000498125.1_Intron|SORBS2_ENST00000437304.2_Intron|SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000418609.1_Missense_Mutation_p.H390P|SORBS2_ENST00000355634.5_Missense_Mutation_p.H586P|SORBS2_ENST00000431808.1_Missense_Mutation_p.H486P|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000449407.2_Intron	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	486					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)		GCAGGTCCTTGTGCTGCTGCTC	0.579																																					p.H586H|p.H586P	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-SNP	.											.	SORBS2	300	.	0			c.C1758T|c.A1757C						PASS	.																																			SO:0001583	missense	8470	exon16			GTCCTTGTGCTGC|TCCTTGTGCTGCT		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.1457_1458delinsAG	chr4.hg19:g.186545113_186545114delinsAG	ENSP00000284776:p.His486Pro	106.0|108.0	0.0	.		117.0|114.0	49.0	.	NM_001270771	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Silent|Missense_Mutation	SNP	ENST00000284776.7	hg19	CCDS3845.1																																																																																			.	.	.	none		0.579	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603		AG	186545114	GT	AG	186545113	3	1	125	1	0	0	0	0	1	0	0	0	14941	1368	48	2	1880	2	SORBS2	4	186545113	Missense_Mutation	DNP	GT	TCGA-BQ-5890-01A-11D-1589-08	32853473	186545113	4609163	21	7827											
HEATR7B2	133558	hgsc.bcm.edu	37	chr5	41048530	41048530	+	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	aaagccctattgcaccagccCcacgtaactcccctaaactg	12	7	5	17	1	0	0	0	0	0	0	1	0	1	0	6	0	5	2	6	0	5	4			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr5:41048530C>T	ENST00000399564.4	-	16	2030	c.1580G>A	c.(1579-1581)gGg>gAg	p.G527E	MROH2B_ENST00000506092.2_Missense_Mutation_p.G82E	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	527																	TGCACCAGCCCCACGTAACTC	0.448																																					p.G527E		Atlas-SNP	.											.	.	.	.	0			c.G1580A						PASS	.						92	85	87					5																	41048530		1879	4102	5981	SO:0001583	missense	133558	exon16			CCAGCCCCACGTA		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.1580G>A	chr5.hg19:g.41048530C>T	ENSP00000382476:p.Gly527Glu	63.0	0.0	.		58.0	31.0	.	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Missense_Mutation	SNP	ENST00000399564.4	hg19	CCDS47202.1	.	.	.	.	.	.	.	.	.	.	C	14.39	2.522411	0.44866	.	.	ENSG00000171495	ENST00000506092;ENST00000296803;ENST00000399564	T;T	0.07908	3.15;3.15	4.87	4.87	0.63330	Armadillo-type fold (1);	0.218754	0.32593	N	0.005895	T	0.28167	0.0695	M	0.74647	2.275	0.30027	N	0.813842	D	0.89917	1.0	D	0.97110	1.0	T	0.03202	-1.1061	10	0.66056	D	0.02	.	13.7123	0.62675	0.0:1.0:0.0:0.0	.	527	Q7Z745	HTRB2_HUMAN	E	82;231;527	ENSP00000441504:G82E;ENSP00000382476:G527E	ENSP00000296803:G231E	G	-	2	0	HEATR7B2	41084287	0.914000	0.31030	0.274000	0.24659	0.058000	0.15608	3.303000	0.51858	2.683000	0.91414	0.655000	0.94253	GGG	.	.	.	none		0.448	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489		T	41048530	C	T	41048530	3	4	125	1	0	0	0	0	1	0	0	0	7042	623	22	2	3285	2	HEATR7B2	5	41048530	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08		41048530	139866730	22	7828											
KLHL3	26249	hgsc.bcm.edu	37	chr5	136975648	136975648	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gattgccttgggtgcctggcCgccaaccacaatcatgacct	8	9	10	14	1	1	1	1	1	0	0	1	2	1	1	6	2	3	0	6	2	2	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr5:136975648C>T	ENST00000309755.4	-	9	1365	c.922G>A	c.(922-924)Ggc>Agc	p.G308S	KLHL3_ENST00000541417.1_Intron|KLHL3_ENST00000506491.1_Missense_Mutation_p.G226S|KLHL3_ENST00000508657.1_Missense_Mutation_p.G276S|KLHL3_ENST00000506873.1_5'UTR	NM_017415.2	NP_059111.2	Q9UH77	KLHL3_HUMAN	kelch-like family member 3	308					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)		GGTGCCTGGCCGCCAACCACA	0.542																																					p.G308S		Atlas-SNP	.											.	KLHL3	54	.	0			c.G922A						PASS	.						94	88	90					5																	136975648		2203	4300	6503	SO:0001583	missense	26249	exon9			CCTGGCCGCCAAC	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.922G>A	chr5.hg19:g.136975648C>T	ENSP00000312397:p.Gly308Ser	78.0	0.0	.		90.0	20.0	.	NM_017415	B2RBK7|Q9UH75|Q9UH76|Q9ULU0|Q9Y6V6	Missense_Mutation	SNP	ENST00000309755.4	hg19	CCDS4192.1	.	.	.	.	.	.	.	.	.	.	C	35	5.522061	0.96416	.	.	ENSG00000146021	ENST00000506491;ENST00000508657;ENST00000309755;ENST00000505853	D;D;D;D	0.99494	-6.01;-6.01;-6.01;-6.01	4.54	4.54	0.55810	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	D	0.99701	0.9886	H	0.96048	3.76	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;0.989;0.999	D	0.97261	0.9904	10	0.87932	D	0	.	17.8383	0.88707	0.0:1.0:0.0:0.0	.	77;268;276;308	B7Z6E2;D6RH21;Q9UH77-2;Q9UH77	.;.;.;KLHL3_HUMAN	S	226;276;308;268	ENSP00000424828:G226S;ENSP00000422099:G276S;ENSP00000312397:G308S;ENSP00000426173:G268S	ENSP00000312397:G308S	G	-	1	0	KLHL3	137003547	1.000000	0.71417	0.989000	0.46669	0.995000	0.86356	7.416000	0.80143	2.535000	0.85469	0.655000	0.94253	GGC	.	.	.	none		0.542	KLHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251220.2			T	136975648	C	T	136975648	3	4	125	1	0	0	0	0	1	0	0	0	8390	652	23	1	869	1	KLHL3	5	136975648	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	95927118	136975648	43939612	23	7829											
FAM13B	51306	hgsc.bcm.edu	37	chr5	137289855	137289855	+	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	agtacataaaaatcatatacCtagtaaaagacagtgcttta	19	11	5	6	0	1	1	1	0	0	1	1	1	1	1	1	0	3	3	1	0	10	8			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr5:137289855C>G	ENST00000033079.3	-	14	2103	c.1652G>C	c.(1651-1653)aGa>aCa	p.R551T	FAM13B_ENST00000425075.2_Splice_Site_p.R455T|FAM13B_ENST00000420893.2_Splice_Site_p.R551T	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	551					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						AATCATATACCTAGTAAAAGA	0.388																																					p.R551T		Atlas-SNP	.											.	FAM13B	46	.	0			c.G1652C						PASS	.						67	65	66					5																	137289855		2203	4300	6503	SO:0001630	splice_region_variant	51306	exon14			ATATACCTAGTAA	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.1652+1G>C	chr5.hg19:g.137289855C>G		64.0	0.0	.		77.0	17.0	.	NM_001101800	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Missense_Mutation	SNP	ENST00000033079.3	hg19	CCDS4195.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.148430	0.78001	.	.	ENSG00000031003	ENST00000033079;ENST00000425075;ENST00000420893	T;T;T	0.27104	2.85;1.69;2.85	5.49	5.49	0.81192	.	0.083341	0.64402	D	0.000002	T	0.51550	0.1681	M	0.73217	2.22	0.54753	D	0.999983	D;D;D	0.89917	1.0;0.981;1.0	D;D;D	0.74023	0.982;0.962;0.959	T	0.46978	-0.9152	9	.	.	.	-6.7113	18.3606	0.90372	0.0:1.0:0.0:0.0	.	455;551;551	G3V0H9;Q9NYF5-2;Q9NYF5	.;.;FA13B_HUMAN	T	551;455;551	ENSP00000033079:R551T;ENSP00000394669:R455T;ENSP00000388521:R551T	.	R	-	2	0	FAM13B	137317754	1.000000	0.71417	1.000000	0.80357	0.710000	0.40934	6.298000	0.72763	2.576000	0.86940	0.585000	0.79938	AGA	.	.	.	none		0.388	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1		Missense_Mutation	G	137289855	C	G	137289855	5	3	125	1	0	0	0	0	0	0	1	0	5457	695	24	4	1135	4	FAM13B	5	137289855	Splice_Site	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	314207	137289855	43625405	24	7830											
GABRA1	2554	hgsc.bcm.edu	37	chr5	161281260	161281260	+	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	gatggttatgacaatcgcctGagaccaggattgggaggtag	11	9	15	6	1	0	2	0	2	0	1	1	6	0	4	2	4	0	2	2	4	3	3			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr5:161281260G>A	ENST00000428797.2	+	4	526	c.171G>A	c.(169-171)ctG>ctA	p.L57L	GABRA1_ENST00000444819.1_Silent_p.L57L|GABRA1_ENST00000437025.2_Silent_p.L57L|GABRA1_ENST00000420560.1_Silent_p.L57L|GABRA1_ENST00000023897.6_Silent_p.L57L|GABRA1_ENST00000393943.4_Silent_p.L57L	NM_001127643.1	NP_001121115.1	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 1	57					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)	ACAATCGCCTGAGACCAGGAT	0.383																																					p.L57L		Atlas-SNP	.											.	GABRA1	132	.	0			c.G171A						PASS	.						92	95	94					5																	161281260		2203	4299	6502	SO:0001819	synonymous_variant	2554	exon4			TCGCCTGAGACCA		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.171G>A	chr5.hg19:g.161281260G>A		73.0	0.0	.		112.0	23.0	.	NM_001127643	D3DQK6|Q8N629	Silent	SNP	ENST00000428797.2	hg19	CCDS4357.1																																																																																			.	.	.	none		0.383	GABRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252702.2	NM_000806.5		A	161281260	G	A	161281260	2	1	125	1	0	0	0	0	0	0	0	1	6167	1277	45	2		2	GABRA1	5	161281260	Silent	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	23991405	161281260	19634000	25	7831											
TNXB	7148	hgsc.bcm.edu	37	chr6	32049190	32049190	+	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	ccccacacgctgcctgccacGaagcccgtagaggttcatct	8	7	9	17	3	2	1	1	0	1	1	2	2	2	1	5	1	3	3	5	1	2	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr6:32049190G>A	ENST00000375244.3	-	10	4198	c.3997C>T	c.(3997-3999)Cgt>Tgt	p.R1333C	RNA5SP206_ENST00000516703.1_RNA|TNXB_ENST00000375247.2_Missense_Mutation_p.R1333C			P22105	TENX_HUMAN	tenascin XB	1420	Fibronectin type-III 5. {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						TGCCTGCCACGAAGCCCGTAG	0.647																																					p.R1333C		Atlas-SNP	.											TNXB_ENST00000375247,NS,carcinoma,0,2	TNXB	553	.	0			c.C3997T						PASS	.						23	30	28					6																	32049190		2123	4220	6343	SO:0001583	missense	7148	exon10			TGCCACGAAGCCC	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.3997C>T	chr6.hg19:g.32049190G>A	ENSP00000364393:p.Arg1333Cys	5.0	0.0	.		8.0	5.0	.	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	hg19		.	.	.	.	.	.	.	.	.	.	G	17.37	3.372666	0.61624	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.57595	0.39;0.39	5.23	5.23	0.72850	.	0.950594	0.08613	N	0.919605	T	0.53286	0.1787	M	0.69823	2.125	0.09310	N	1	D	0.53312	0.959	P	0.54924	0.764	T	0.46638	-0.9177	10	0.49607	T	0.09	.	10.2526	0.43377	0.0912:0.0:0.9088:0.0	.	1333	P22105-3	.	C	1333	ENSP00000364393:R1333C;ENSP00000364396:R1333C	ENSP00000364393:R1333C	R	-	1	0	TNXB	32157168	0.365000	0.25006	0.021000	0.16686	0.986000	0.74619	1.552000	0.36244	2.610000	0.88304	0.407000	0.27541	CGT	.	.	.	none		0.647	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		A	32049190	G	A	32049190	3	1	125	1	0	0	0	0	1	0	0	0	16358	1058	37	1	10856	1	TNXB	6	32049190	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08		32049190	139065877	26	7832											
SCUBE3	222663	hgsc.bcm.edu	37	chr6	35213120	35213120	+	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	aacatcaaccccccacccaaGcgcaagatccttatcgtggt	12	7	6	16	2	1	1	1	0	0	1	3	1	2	1	5	1	3	1	5	1	5	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr6:35213120G>A	ENST00000274938.7	+	19	2517	c.2517G>A	c.(2515-2517)aaG>aaA	p.K839K	SCUBE3_ENST00000394681.1_Silent_p.K855K	NM_152753.2	NP_689966.2			signal peptide, CUB domain, EGF-like 3											breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	37						CCCCACCCAAGCGCAAGATCC	0.562																																					p.K839K		Atlas-SNP	.											.	SCUBE3	99	.	0			c.G2517A						PASS	.						111	102	105					6																	35213120		2203	4300	6503	SO:0001819	synonymous_variant	222663	exon19			ACCCAAGCGCAAG	AF452494.1	CCDS4800.1	6p21.3	2008-02-05	2004-05-19	2004-05-21		ENSG00000146197			13655	protein-coding gene	gene with protein product		614708	"CUB domain and EGF-like repeat containing 3"	CEGF3		12270931	Standard	NM_152753		Approved	FLJ34743	uc003okf.1	Q8IX30		ENST00000274938.7:c.2517G>A	chr6.hg19:g.35213120G>A		117.0	0.0	.		122.0	39.0	.	NM_152753		Silent	SNP	ENST00000274938.7	hg19	CCDS4800.1																																																																																			.	.	.	none		0.562	SCUBE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040275.1	NM_152753		A	35213120	G	A	35213120	2	1	125	1	0	0	0	0	0	0	0	1	13959	962	34	2		2	SCUBE3	6	35213120	Silent	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	3163930	35213120	135901947	27	7833											
PEX6	5190	hgsc.bcm.edu	37	chr6	42932546	42932546	+	Missense_Mutation	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	accttcctccaggtcatgaaCcctgcgtttgagggcagctg	7	10	11	13	1	1	2	1	2	0	0	3	2	3	2	4	2	3	3	4	2	1	2	rs61753232		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr6:42932546C>T	ENST00000304611.8	-	16	2857	c.2788G>A	c.(2788-2790)Gtt>Att	p.V930I	PEX6_ENST00000244546.4_3'UTR	NM_000287.3	NP_000278.3	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	930					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)			AGGTCATGAACCCTGCGTTTG	0.587																																					p.V930I		Atlas-SNP	.											.	PEX6	44	.	0			c.G2788A						PASS	.						112	98	103					6																	42932546		2203	4300	6503	SO:0001583	missense	5190	exon16			CATGAACCCTGCG	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.2788G>A	chr6.hg19:g.42932546C>T	ENSP00000303511:p.Val930Ile	143.0	0.0	.		148.0	54.0	.	NM_000287	Q5T8W1|Q8WYQ0|Q8WYQ1|Q8WYQ2|Q99476	Missense_Mutation	SNP	ENST00000304611.8	hg19	CCDS4877.1	.	.	.	.	.	.	.	.	.	.	C	11.86	1.765700	0.31228	.	.	ENSG00000124587	ENST00000304611	D	0.94723	-3.5	5.78	4.92	0.64577	.	0.159370	0.56097	D	0.000024	T	0.79616	0.4476	N	0.13272	0.32	0.80722	D	1	B	0.25667	0.131	B	0.29942	0.109	T	0.76016	-0.3113	10	0.02654	T	1	-14.3262	14.7217	0.69311	0.0:0.9297:0.0:0.0703	.	930	Q13608	PEX6_HUMAN	I	930	ENSP00000303511:V930I	ENSP00000303511:V930I	V	-	1	0	PEX6	43040524	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.850000	0.48294	1.453000	0.47775	-0.143000	0.13931	GTT	.	.	.	none		0.587	PEX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040569.1	NM_000287		T	42932546	C	T	42932546	3	4	125	1	0	0	0	0	1	0	0	0	11757	507	18	2	162	2	PEX6	6	42932546	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	7719426	42932546	128182521	28	7834											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51882414	51882414	+	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	tcacgcttcaggccacacagGaaggccaaggacactgcagg	12	4	12	13	1	2	0	2	0	0	0	2	2	2	2	2	5	1	2	2	5	2	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr6:51882414G>A	ENST00000371117.3	-	34	5669	c.5394C>T	c.(5392-5394)ttC>ttT	p.F1798F	PKHD1_ENST00000340994.4_Silent_p.F1798F	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1798					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)					GGCCACACAGGAAGGCCAAGG	0.522																																					p.F1798F		Atlas-SNP	.											.	PKHD1	927	.	0			c.C5394T						PASS	.						101	89	93					6																	51882414		2203	4300	6503	SO:0001819	synonymous_variant	5314	exon34			ACACAGGAAGGCC	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.5394C>T	chr6.hg19:g.51882414G>A		102.0	0.0	.		103.0	42.0	.	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	hg19	CCDS4935.1																																																																																			.	.	.	none		0.522	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51882414	G	A	51882414	2	1	125	1	0	0	0	0	0	0	0	1	11978	1165	41	2		2	PKHD1	6	51882414	Silent	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	8949868	51882414	119232653	29	7835											
ENPP1	5167	hgsc.bcm.edu	37	chr6	132206107	132206107	+	Missense_Mutation	SNP	A	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	tcatgacaccctactgcgaaAgtatgctgaagaaagaaatg	16	8	9	8	1	1	4	1	2	0	2	1	5	1	4	1	0	3	2	1	0	6	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr6:132206107A>C	ENST00000360971.2	+	23	2368	c.2348A>C	c.(2347-2349)aAg>aCg	p.K783T		NM_006208.2	NP_006199.2	P22413	ENPP1_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 1	783	Nuclease.				3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|ATP catabolic process (GO:0006200)|biomineral tissue development (GO:0031214)|bone remodeling (GO:0046849)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to insulin stimulus (GO:0032869)|generation of precursor metabolites and energy (GO:0006091)|immune response (GO:0006955)|inorganic diphosphate transport (GO:0030505)|negative regulation of cell growth (GO:0030308)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of ossification (GO:0030279)|negative regulation of protein autophosphorylation (GO:0031953)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)|regulation of bone mineralization (GO:0030500)|riboflavin metabolic process (GO:0006771)|sequestering of triglyceride (GO:0030730)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|insulin receptor binding (GO:0005158)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|protein homodimerization activity (GO:0042803)|scavenger receptor activity (GO:0005044)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(22)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	46	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)	CTACTGCGAAAGTATGCTGAA	0.408																																					p.K783T	Colon(104;336 1535 5856 11019 33782)	Atlas-SNP	.											.	ENPP1	108	.	0			c.A2348C						PASS	.						228	208	215					6																	132206107		2203	4300	6503	SO:0001583	missense	5167	exon23			TGCGAAAGTATGC	M57736	CCDS5150.2	6q22-q23	2008-02-07			ENSG00000197594	ENSG00000197594	3.1.4.1, 3.6.1.9		3356	protein-coding gene	gene with protein product		173335		NPPS, M6S1, PDNP1		1315502	Standard	NM_006208		Approved	PC-1, PCA1	uc011ecf.2	P22413	OTTHUMG00000015572	ENST00000360971.2:c.2348A>C	chr6.hg19:g.132206107A>C	ENSP00000354238:p.Lys783Thr	84.0	0.0	.		96.0	34.0	.	NM_006208	Q5T9R6|Q9NPZ3|Q9P1P6|Q9UP61|Q9Y6K3	Missense_Mutation	SNP	ENST00000360971.2	hg19	CCDS5150.2	.	.	.	.	.	.	.	.	.	.	A	12.63	1.996697	0.35226	.	.	ENSG00000197594	ENST00000360971	T	0.69561	-0.41	5.91	-0.54	0.11861	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.445357	0.26013	N	0.026870	T	0.46405	0.1391	L	0.61036	1.89	0.22940	N	0.998539	B	0.24920	0.114	B	0.37833	0.259	T	0.54180	-0.8332	10	0.45353	T	0.12	-2.7243	8.0938	0.30816	0.6341:0.1292:0.2367:0.0	.	783	P22413	ENPP1_HUMAN	T	783	ENSP00000354238:K783T	ENSP00000354238:K783T	K	+	2	0	ENPP1	132247800	1.000000	0.71417	0.005000	0.12908	0.829000	0.46940	1.859000	0.39418	-0.182000	0.10602	-0.242000	0.12053	AAG	.	.	.	none		0.408	ENPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042238.2			C	132206107	A	C	132206107	3	2	125	1	0	0	0	0	1	0	0	0	5131	72	3	5	2438	5	ENPP1	6	132206107	Missense_Mutation	SNP	A	TCGA-BQ-5890-01A-11D-1589-08	80323693	132206107	38908960	30	7836											
TNFAIP3	7128	hgsc.bcm.edu	37	chr6	138200458	138200458	+	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	aaaacaagggcttttgcacaCtgtgtttcatcgagtacaga	13	11	9	8	1	1	1	1	0	0	1	2	2	1	1	0	1	3	4	0	1	4	4			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr6:138200458C>A	ENST00000237289.4	+	7	1942	c.1876C>A	c.(1876-1878)Ctg>Atg	p.L626M		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.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)		CTTTTGCACACTGTGTTTCAT	0.512			"D, N, F"		"marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"																																p.L626M	GBM(130;153 1739 22295 28918 47987)	Atlas-SNP	.		Rec	yes		6	6q23	7128	"tumor necrosis factor, alpha-induced protein 3"		L	.,1	TNFAIP3	340	.	26	Whole gene deletion(25)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(26)	c.C1876A						PASS	.						71	77	75					6																	138200458		2203	4300	6503	SO:0001583	missense	7128	exon7			TGCACACTGTGTT	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.1876C>A	chr6.hg19:g.138200458C>A	ENSP00000237289:p.Leu626Met	85.0	0.0	.		52.0	32.0	.	NM_001270507	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Missense_Mutation	SNP	ENST00000237289.4	hg19	CCDS5187.1	.	.	.	.	.	.	.	.	.	.	C	18.12	3.552844	0.65425	.	.	ENSG00000118503	ENST00000237289;ENST00000535574;ENST00000544646	T	0.43688	0.94	5.82	4.96	0.65561	Zinc finger, A20-type (3);	0.066315	0.64402	D	0.000008	T	0.49406	0.1555	M	0.67953	2.075	0.45837	D	0.9987	D	0.76494	0.999	D	0.75484	0.986	T	0.51934	-0.8642	10	0.41790	T	0.15	-20.5642	11.1227	0.48300	0.0:0.8531:0.0:0.1469	.	626	P21580	TNAP3_HUMAN	M	626	ENSP00000237289:L626M	ENSP00000237289:L626M	L	+	1	2	TNFAIP3	138242151	0.881000	0.30235	0.909000	0.35828	0.972000	0.66771	1.756000	0.38390	1.472000	0.48140	0.655000	0.94253	CTG	.	.	.	none		0.512	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1			A	138200458	C	A	138200458	3	1	125	1	0	0	0	0	1	0	0	0	16286	564	20	4	1898	4	TNFAIP3	6	138200458	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	5994351	138200458	32914609	31	7837											
HOXA2	3199	hgsc.bcm.edu	37	chr7	27140389	27140390	+	Frame_Shift_Ins	INS	-	-	A																															attgtggtgagtgtgtctgtINSaaaaaagtctaagctgtcag																										TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr7:27140389_27140390insA	ENST00000222718.5	-	2	1396_1397	c.1086_1087insT	c.(1084-1089)tttacafs	p.T363fs	HOTAIRM1_ENST00000425358.2_RNA|HOTAIRM1_ENST00000429611.3_RNA|HOTAIRM1_ENST00000434063.3_RNA|HOTAIRM1_ENST00000428939.3_RNA|HOTAIRM1_ENST00000593300.1_RNA	NM_006735.3	NP_006726.1	O43364	HXA2_HUMAN	homeobox A2	363					anterior/posterior pattern specification (GO:0009952)|brain segmentation (GO:0035284)|cell fate determination (GO:0001709)|dorsal/ventral pattern formation (GO:0009953)|embryonic viscerocranium morphogenesis (GO:0048703)|middle ear morphogenesis (GO:0042474)|motor neuron axon guidance (GO:0008045)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast development (GO:0002076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|rhombomere 2 development (GO:0021568)|rhombomere 3 morphogenesis (GO:0021658)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|cervix(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(1)	22						AGTGTGTCTGTAAAAAAGTCTA	0.436																																					p.T363fs		Atlas-INDEL	.											.	HOXA2	56	.	0			c.1087_1088insT						PASS	.																																			SO:0001589	frameshift_variant	3199	exon2			.		CCDS5403.1	7p15.2	2011-06-20	2005-12-22		ENSG00000105996	ENSG00000105996		"Homeoboxes / ANTP class : HOXL subclass"	5103	protein-coding gene	gene with protein product		604685	"homeo box A2"	HOX1K		1358459	Standard	NM_006735		Approved		uc003syh.3	O43364	OTTHUMG00000023208	ENST00000222718.5:c.1087dupT	chr7.hg19:g.27140395_27140395dupA	ENSP00000222718:p.Thr363fs	177.0	0.0	0		177.0	23.0	0.129944	NM_006735	A1L4K3|B2RMW3	Frame_Shift_Ins	INS	ENST00000222718.5	hg19	CCDS5403.1																																																																																			.	.	.	none		0.436	HOXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358508.2			A	27140390	-	A	27140389	7	5	125	1	0	1	1	0	0	0	0	0	7299	1638	57	0	47	0	HOXA2	7	27140389	Frame_Shift_Ins	INS	-	TCGA-BQ-5890-01A-11D-1589-08		27140389	131998274	32	7838											
LRWD1	222229	hgsc.bcm.edu	37	chr7	102110042	102110043	+	Missense_Mutation	DNP	TC	TC	GA																															ggcctcctatgacaagcggaTcatcctctgggacatcgggg																										TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr7:102110042_102110043TC>GA	ENST00000292616.5	+	10	1402_1403	c.1250_1251TC>GA	c.(1249-1251)aTC>aGA	p.I417R	MIR4467_ENST00000578629.1_RNA	NM_152892.1	NP_690852.1	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain containing 1	417					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						GACAAGCGGATCATCCTCTGGG	0.644																																					p.I417S|p.I417I		Atlas-SNP	.											.	LRWD1	41	.	0			c.T1250G|c.C1251A						PASS	.																																			SO:0001583	missense	222229	exon10			AGCGGATCATCCT|GCGGATCATCCTC	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	Exception_encountered	chr7.hg19:g.102110042_102110043delinsGA	ENSP00000292616:p.Ile417Arg	143.0|144.0	0.0	.		127.0	26.0|27.0	.	NM_152892	A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2	Missense_Mutation|Silent	SNP	ENST00000292616.5	hg19	CCDS34715.1																																																																																			.	.	.	none		0.644	LRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349493.1	NM_152892		GA	102110043	TC	GA	102110042	3	3	125	1	0	0	0	0	1	0	0	0	9054	1435	50	5	1288	5	LRWD1	7	102110042	Missense_Mutation	DNP	TC	TCGA-BQ-5890-01A-11D-1589-08	74969653	102110042	57028621	33	7839											
CSMD1	64478	hgsc.bcm.edu	37	chr8	3216707	3216707	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagaggtgcactccacacacGgcggcccccacccaggcagg	9	2	12	18	2	0	1	0	0	0	1	1	1	1	1	4	5	1	2	4	5	0	0			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr8:3216707G>A	ENST00000520002.1	-	22	3829	c.3274C>T	c.(3274-3276)Cgt>Tgt	p.R1092C	CSMD1_ENST00000602723.1_Missense_Mutation_p.R1092C|CSMD1_ENST00000400186.3_Missense_Mutation_p.R1092C|CSMD1_ENST00000539096.1_Missense_Mutation_p.R1091C|CSMD1_ENST00000542608.1_Missense_Mutation_p.R1091C|CSMD1_ENST00000602557.1_Missense_Mutation_p.R1092C|CSMD1_ENST00000537824.1_Missense_Mutation_p.R1091C			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1092	Sushi 6. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CTCCACACACGGCGGCCCCCA	0.557																																					p.R1091C		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C3271T						PASS	.						70	74	73					8																	3216707		2203	4300	6503	SO:0001583	missense	64478	exon21			ACACACGGCGGCC			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.3274C>T	chr8.hg19:g.3216707G>A	ENSP00000430733:p.Arg1092Cys	117.0	0.0	.		120.0	33.0	.	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	20.9|20.9	4.074273|4.074273	0.76415|0.76415	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000335551|ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	.|T;T;T;T;T	.|0.64991	.|-0.13;-0.13;-0.13;-0.13;-0.13	5.34|5.34	5.34|5.34	0.76211|0.76211	.|Complement control module (2);Sushi/SCR/CCP (3);	.|0.000000	.|0.64402	.|D	.|0.000001	D|D	0.83096|0.83096	0.5180|0.5180	M|M	0.92268|0.92268	3.29|3.29	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;0.998	D|D	0.86677|0.86677	0.1914|0.1914	5|10	.|0.66056	.|D	.|0.02	.|.	13.9698|13.9698	0.64233|0.64233	0.0:0.0:0.8484:0.1516|0.0:0.0:0.8484:0.1516	.|.	.|1092;1092;1092	.|E5RIG2;Q96PZ7;Q96PZ7-4	.|.;CSMD1_HUMAN;.	L|C	571|1092;1092;954;1091;1091;1091	.|ENSP00000383047:R1092C;ENSP00000430733:R1092C;ENSP00000441462:R1091C;ENSP00000446243:R1091C;ENSP00000441675:R1091C	.|ENSP00000320445:R954C	P|R	-|-	2|1	0|0	CSMD1|CSMD1	3204114|3204114	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	4.283000|4.283000	0.58977|0.58977	2.489000|2.489000	0.83994|0.83994	0.550000|0.550000	0.68814|0.68814	CCG|CGT	.	.	.	none		0.557	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	3216707	G	A	3216707	3	1	125	1	0	0	0	0	1	0	0	0	3946	1116	39	1	7623	1	CSMD1	8	3216707	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08		3216707	143147315	34	7840											
ADAM7	8756	hgsc.bcm.edu	37	chr8	24357759	24357760	+	Missense_Mutation	DNP	AC	AC	CA																															gtagcctgtgaagaaaccttAcatgttaccagtgagcatcc																										TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr8:24357759_24357760AC>CA	ENST00000175238.6	+	18	2075_2076	c.1992_1993AC>CA	c.(1990-1995)ttACat>ttCAat	p.664_665LH>FN	ADAM7_ENST00000380789.1_Missense_Mutation_p.664_665LH>FN|ADAM7_ENST00000520720.1_Missense_Mutation_p.436_437LH>FN|RP11-624C23.1_ENST00000523578.1_RNA|RP11-561E1.1_ENST00000519364.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	664	Cys-rich.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(24)|ovary(1)|skin(15)	64		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		AAGAAACCTTACATGTTACCAG	0.411																																					p.L664F|p.H665N		Atlas-SNP	.											.	ADAM7	165	.	0			c.A1992C|c.C1993A						PASS	.																																			SO:0001583	missense	8756	exon18			AACCTTACATGTT|ACCTTACATGTTA	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	Exception_encountered	chr8.hg19:g.24357759_24357760delinsCA	ENSP00000175238:p.L664_H665delinsFN	43.0	0.0	.		66.0|68.0	26.0	.	NM_003817	A8K8X7|O75959|Q6PEJ6	Missense_Mutation	SNP	ENST00000175238.6	hg19	CCDS6045.1																																																																																			.	.	.	none		0.411	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817		CA	24357760	AC	CA	24357759	3	2	125	1	0	0	0	0	1	0	0	0	251	388	14	5	2062	5	ADAM7	8	24357759	Missense_Mutation	DNP	AC	TCGA-BQ-5890-01A-11D-1589-08	21141052	24357759	122006263	35	7841											
COL14A1	7373	hgsc.bcm.edu	37	chr8	121219275	121219276	+	Frame_Shift_Ins	INS	-	-	A																															aactggactcatgccccaggINSaaatgtggaaaaatacagag																										TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr8:121219275_121219276insA	ENST00000297848.3	+	10	1403_1404	c.1133_1134insA	c.(1132-1137)ggaaatfs	p.N379fs	COL14A1_ENST00000247781.3_Frame_Shift_Ins_p.N284fs|COL14A1_ENST00000537875.1_Frame_Shift_Ins_p.N379fs|COL14A1_ENST00000309791.4_Frame_Shift_Ins_p.N379fs|COL14A1_ENST00000432943.2_3'UTR	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1											NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			CATGCCCCAGGAAATGTGGAAA	0.436																																					p.G378fs		Atlas-INDEL	.											.	COL14A1	292	.	0			c.1133_1134insA						PASS	.																																			SO:0001589	frameshift_variant	7373	exon10			.		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.1136dupA	chr8.hg19:g.121219278_121219278dupA	ENSP00000297848:p.Asn379fs	49.0	0.0	0		59.0	19.0	0.322034	NM_021110		Frame_Shift_Ins	INS	ENST00000297848.3	hg19	CCDS34938.1																																																																																			.	.	.	none		0.436	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		A	121219276	-	A	121219275	7	5	125	1	0	1	1	0	0	0	0	0	3673	1174	41	0	1167	0	COL14A1	8	121219275	Frame_Shift_Ins	INS	-	TCGA-BQ-5890-01A-11D-1589-08	96861516	121219275	25144747	36	7842											
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84608073	84608073	+	Missense_Mutation	SNP	T	T	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	caggaaatttccttccttagTtccaacaaacaaaagatgtt	15	12	5	9	0	0	1	0	0	0	1	3	2	3	2	3	1	2	2	3	1	6	5			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr9:84608073T>G	ENST00000344803.2	+	4	2735	c.2688T>G	c.(2686-2688)agT>agG	p.S896R		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	896					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CCTTCCTTAGTTCCAACAAAC	0.428																																					p.S896R		Atlas-SNP	.											.	.	.	.	0			c.T2688G						PASS	.						74	65	68					9																	84608073		1843	4100	5943	SO:0001583	missense	389763	exon4			CCTTAGTTCCAAC		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.2688T>G	chr9.hg19:g.84608073T>G	ENSP00000341988:p.Ser896Arg	56.0	0.0	.		66.0	26.0	.	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	hg19	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	T	6.930	0.541227	0.13250	.	.	ENSG00000214929	ENST00000344803	T	0.44482	0.92	3.45	-0.949	0.10376	.	2.375910	0.01543	N	0.019319	T	0.28499	0.0705	L	0.34521	1.04	0.09310	N	1	B	0.29085	0.232	B	0.30251	0.113	T	0.03910	-1.0993	10	0.21540	T	0.41	1.1122	0.6148	0.00767	0.1883:0.1384:0.2367:0.4366	.	896	Q6ZQQ2	F75D1_HUMAN	R	896	ENSP00000341988:S896R	ENSP00000341988:S896R	S	+	3	2	FAM75D1	83797893	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.406000	0.07187	-0.259000	0.09432	-0.417000	0.06048	AGT	.	.	.	none		0.428	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		G	84608073	T	G	84608073	3	3	125	1	0	0	0	0	1	0	0	0	5939	1722	60	5	2702	5	FLJ46321	9	84608073	Missense_Mutation	SNP	T	TCGA-BQ-5890-01A-11D-1589-08		84608073	56605358	37	7843											
TXN	7295	hgsc.bcm.edu	37	chr9	113013695	113013695	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cacgtggctgagaagtcaacTactacaagtttatcacctgc	12	10	8	11	1	2	1	2	1	0	1	2	2	2	1	1	1	4	2	1	1	6	4			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr9:113013695T>C	ENST00000374517.5	-	2	276	c.72A>G	c.(70-72)gtA>gtG	p.V24V	TXN_ENST00000374515.5_Silent_p.V24V	NM_003329.3	NP_003320.2	P10599	THIO_HUMAN	thioredoxin	24	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell proliferation (GO:0008283)|cell redox homeostasis (GO:0045454)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|glycerol ether metabolic process (GO:0006662)|innate immune response (GO:0045087)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|oxidation-reduction process (GO:0055114)|positive regulation of DNA binding (GO:0043388)|regulation of protein import into nucleus, translocation (GO:0033158)|response to radiation (GO:0009314)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	peptide disulfide oxidoreductase activity (GO:0015037)|poly(A) RNA binding (GO:0044822)|protein disulfide oxidoreductase activity (GO:0015035)			kidney(1)|skin(1)	2				OV - Ovarian serous cystadenocarcinoma(323;7.36e-07)		AGAAGTCAACTACTACAAGTT	0.363																																					p.V24V		Atlas-SNP	.											.	TXN	6	.	0			c.A72G						PASS	.						60	60	60					9																	113013695		2203	4300	6503	SO:0001819	synonymous_variant	7295	exon2			GTCAACTACTACA	X77584	CCDS35103.1, CCDS59139.1	9q31	2008-02-05			ENSG00000136810	ENSG00000136810			12435	protein-coding gene	gene with protein product		187700					Standard	NM_003329		Approved	TRX	uc004bep.2	P10599	OTTHUMG00000020480	ENST00000374517.5:c.72A>G	chr9.hg19:g.113013695T>C		41.0	0.0	.		46.0	12.0	.	NM_001244938	B1ALW1|O60744|Q53X69|Q96KI3|Q9UDG5	Silent	SNP	ENST00000374517.5	hg19	CCDS35103.1																																																																																			.	.	.	none		0.363	TXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053614.1			C	113013695	T	C	113013695	2	2	125	1	0	0	0	0	0	0	0	1	16802	1509	53	3		3	TXN	9	113013695	Silent	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	28405622	113013695	28199736	38	7844											
FAM125B	89853	hgsc.bcm.edu	37	chr9	129143362	129143362	+	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	ggttgcacagacagcagatgGtgtggatgctgacctctgga	9	9	15	8	0	1	3	0	1	1	2	1	5	1	5	1	4	3	4	1	4	0	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr9:129143362G>C	ENST00000361171.3	+	3	305	c.224G>C	c.(223-225)gGt>gCt	p.G75A	MVB12B_ENST00000436593.3_Missense_Mutation_p.G60A|MVB12B_ENST00000545391.1_Missense_Mutation_p.G75A|MVB12B_ENST00000535766.1_Missense_Mutation_p.G68A	NM_033446.2	NP_258257.1	Q9H7P6	MB12B_HUMAN	multivesicular body subunit 12B	75	MABP. {ECO:0000255|PROSITE- ProRule:PRU00831}.				protein transport (GO:0015031)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	cytosol (GO:0005829)|early endosome (GO:0005769)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	lipid binding (GO:0008289)										ACAGCAGATGGTGTGGATGCT	0.478																																					p.G75A		Atlas-SNP	.											.	.	.	.	0			c.G224C						PASS	.						131	113	119					9																	129143362		2203	4300	6503	SO:0001583	missense	89853	exon3			CAGATGGTGTGGA	AK000001	CCDS35142.1	9q34.12	2012-12-03	2012-12-03	2012-12-03	ENSG00000196814	ENSG00000196814			23368	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 28", "family with sequence similarity 125, member B"	C9orf28, FAM125B		18005716, 20654576, 22232651	Standard	NM_033446		Approved	FLJ00001	uc004bqh.2	Q9H7P6	OTTHUMG00000020687	ENST00000361171.3:c.224G>C	chr9.hg19:g.129143362G>C	ENSP00000354772:p.Gly75Ala	103.0	0.0	.		93.0	28.0	.	NM_001011703	Q8N6S7	Missense_Mutation	SNP	ENST00000361171.3	hg19	CCDS35142.1	.	.	.	.	.	.	.	.	.	.	G	18.44	3.625105	0.66901	.	.	ENSG00000196814	ENST00000361171;ENST00000545391;ENST00000402437;ENST00000436593;ENST00000535766	T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81	5.15	5.15	0.70609	MABP domain (1);	0.101991	0.64402	D	0.000002	T	0.71937	0.3399	M	0.81497	2.545	0.58432	D	0.999999	D;P;P	0.89917	1.0;0.841;0.675	D;P;B	0.91635	0.999;0.46;0.337	T	0.76542	-0.2921	10	0.87932	D	0	-9.369	18.6946	0.91596	0.0:0.0:1.0:0.0	.	68;60;75	B7Z4X0;B7Z1P9;Q9H7P6	.;.;F125B_HUMAN	A	75;75;60;60;68	ENSP00000354772:G75A;ENSP00000441988:G75A;ENSP00000384751:G60A;ENSP00000401379:G60A;ENSP00000442846:G68A	ENSP00000354772:G75A	G	+	2	0	FAM125B	128183183	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.359000	0.97115	2.418000	0.82041	0.650000	0.86243	GGT	.	.	.	none		0.478	MVB12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054110.1	XM_088525		C	129143362	G	C	129143362	3	2	125	1	0	0	0	0	1	0	0	0	5432	1261	44	4	234	4	FAM125B	9	129143362	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	16129667	129143362	12070069	39	7845											
CYP2C18	1562	hgsc.bcm.edu	37	chr10	96443672	96443672	+	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	agagggaggctcccgtctggCcccactcctctcccgattat	6	9	10	16	2	2	1	0	0	2	1	5	3	4	2	5	3	0	1	5	3	1	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr10:96443672C>A	ENST00000285979.6	+	1	295	c.96C>A	c.(94-96)ggC>ggA	p.G32G	CYP2C18_ENST00000339022.5_Silent_p.G32G	NM_000772.2	NP_000763.1	P33260	CP2CI_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 18	32					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxygen binding (GO:0019825)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	26		Colorectal(252;0.09)		all cancers(201;2.8e-06)|KIRC - Kidney renal clear cell carcinoma(50;0.0646)|Kidney(138;0.0805)	Aminophenazone(DB01424)|Antipyrine(DB01435)|Buprenorphine(DB00921)|Clobazam(DB00349)|Clotiazepam(DB01559)|Cyclophosphamide(DB00531)|Dapsone(DB00250)|Desipramine(DB01151)|Diazepam(DB00829)|Diclofenac(DB00586)|Diphenhydramine(DB01075)|Ifosfamide(DB01181)|Imipramine(DB00458)|Lansoprazole(DB00448)|Lidocaine(DB00281)|Methadone(DB00333)|Omeprazole(DB00338)|Pegvisomant(DB00082)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Propofol(DB00818)|Tolbutamide(DB01124)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vilazodone(DB06684)|Warfarin(DB00682)	TCCCGTCTGGCCCCACTCCTC	0.483																																					p.G32G		Atlas-SNP	.											.	CYP2C18	79	.	0			c.C96A						PASS	.						99	87	91					10																	96443672		2203	4300	6503	SO:0001819	synonymous_variant	1562	exon1			GTCTGGCCCCACT	M61853	CCDS7435.1, CCDS44460.1	10q24	2003-11-12	2003-01-14		ENSG00000108242	ENSG00000108242		"Cytochrome P450s"	2620	protein-coding gene	gene with protein product		601131	"cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 18"	CYP2C17		1896026, 2009263	Standard	NM_000772		Approved	P450IIC17, CPCI, CYP2C		P33260	OTTHUMG00000018796	ENST00000285979.6:c.96C>A	chr10.hg19:g.96443672C>A		52.0	0.0	.		78.0	9.0	.	NM_000772	B2R8K2|Q16703|Q16751|Q4VAT5|Q6GRG1	Silent	SNP	ENST00000285979.6	hg19	CCDS7435.1																																																																																			.	.	.	none		0.483	CYP2C18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049486.1	NM_000772		A	96443672	C	A	96443672	2	1	125	1	0	0	0	0	0	0	0	1	4167	726	26	4		4	CYP2C18	10	96443672	Silent	SNP	C	TCGA-BQ-5890-01A-11D-1589-08		96443672	39091075	40	7846											
DMBT1	1755	hgsc.bcm.edu	37	chr10	124351862	124351862	+	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	gccgagtagaggtcctatacCgaggctcctggggcaccgtg	7	7	15	12	3	0	1	0	0	0	1	2	3	2	1	5	4	1	3	5	4	3	3			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr10:124351862C>A	ENST00000338354.3	+	20	2357	c.2251C>A	c.(2251-2253)Cga>Aga	p.R751R	DMBT1_ENST00000368956.2_Intron|DMBT1_ENST00000330163.4_Intron|DMBT1_ENST00000344338.3_Silent_p.R741R|DMBT1_ENST00000368909.3_Silent_p.R751R|DMBT1_ENST00000368955.3_Silent_p.R741R|DMBT1_ENST00000359586.6_Intron			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	751	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)	p.R751R(3)		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)				GGTCCTATACCGAGGCTCCTG	0.582																																					p.R751R	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	3	Substitution - coding silent(3)	lung(3)	c.C2251A						PASS	.						322	237	265					10																	124351862		2025	4157	6182	SO:0001819	synonymous_variant	1755	exon20			CTATACCGAGGCT		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.2251C>A	chr10.hg19:g.124351862C>A		397.0	1.0	.		437.0	141.0	.	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Silent	SNP	ENST00000338354.3	hg19																																																																																				.	.	.	none		0.582	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		A	124351862	C	A	124351862	2	1	125	1	0	0	0	0	0	0	0	1	4579	644	23	4		4	DMBT1	10	124351862	Silent	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	27908190	124351862	11182885	41	7847											
CD81	975	hgsc.bcm.edu	37	chr11	2417109	2417109	+	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	ctctctgcagcttgactgctGtggctccagcacactgactg	6	11	10	14	0	1	2	0	2	1	0	3	2	2	2	1	1	4	5	1	1	0	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr11:2417109G>T	ENST00000263645.5	+	6	726	c.470G>T	c.(469-471)tGt>tTt	p.C157F	CD81_ENST00000481687.1_Missense_Mutation_p.C163F|CD81_ENST00000381036.3_Missense_Mutation_p.C195F|CD81_ENST00000526072.1_Missense_Mutation_p.C86F|CD81_ENST00000524805.1_3'UTR|CD81_ENST00000492627.1_Missense_Mutation_p.C86F	NM_004356.3	NP_004347.1	P60033	CD81_HUMAN	CD81 molecule	157					activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of 1-phosphatidylinositol 4-kinase activity (GO:0043128)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein localization (GO:0008104)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of immune response (GO:0050776)|viral entry into host cell (GO:0046718)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	MHC class II protein complex binding (GO:0023026)			endometrium(1)|lung(3)|skin(1)	5		all_epithelial(84;0.000161)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.0137)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.000338)|LUSC - Lung squamous cell carcinoma(625;0.191)		CTTGACTGCTGTGGCTCCAGC	0.602																																					p.C157F		Atlas-SNP	.											.	CD81	11	.	0			c.G470T						PASS	.						94	73	80					11																	2417109		2202	4299	6501	SO:0001583	missense	975	exon6			ACTGCTGTGGCTC		CCDS7734.1, CCDS73240.1	11p15.5	2014-09-17	2006-03-28		ENSG00000110651	ENSG00000110651		"CD molecules", "Tetraspanins"	1701	protein-coding gene	gene with protein product		186845	"CD81 antigen (target of antiproliferative antibody 1)"	TAPA1		1650385	Standard	XM_005253260		Approved	TAPA-1, TSPAN28	uc001lwf.1	P60033	OTTHUMG00000009892	ENST00000263645.5:c.470G>T	chr11.hg19:g.2417109G>T	ENSP00000263645:p.Cys157Phe	70.0	0.0	.		75.0	32.0	.	NM_004356	P18582|Q5U0J6	Missense_Mutation	SNP	ENST00000263645.5	hg19	CCDS7734.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.61|11.61	1.691270|1.691270	0.30052|0.30052	.|.	.|.	ENSG00000110651|ENSG00000110651	ENST00000475945;ENST00000263645;ENST00000492627;ENST00000527343;ENST00000381036;ENST00000492252;ENST00000526072;ENST00000481687|ENST00000464784	D;D;D;D;D;D;D;D|.	0.99881|.	-7.47;-7.47;-7.47;-7.47;-7.47;-7.47;-7.47;-7.47|.	3.56|3.56	3.56|3.56	0.40772|0.40772	Tetraspanin, EC2 domain (1);CD81 extracellular domain (1);|.	0.106944|.	0.64402|.	D|.	0.000003|.	D|D	0.85999|0.85999	0.5828|0.5828	H|H	0.96662|0.96662	3.86|3.86	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	0.89124|0.89124	0.3505|0.3505	10|5	0.87932|.	D|.	0|.	.|.	10.8427|10.8427	0.46726|0.46726	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	195;157|.	A6NMH8;P60033|.	.;CD81_HUMAN|.	F|L	86;157;86;146;195;150;86;163|142	ENSP00000433178:C86F;ENSP00000263645:C157F;ENSP00000437242:C86F;ENSP00000433767:C146F;ENSP00000370424:C195F;ENSP00000432249:C150F;ENSP00000431780:C86F;ENSP00000432033:C163F|.	ENSP00000263645:C157F|.	C|V	+|+	2|1	0|0	CD81|CD81	2373685|2373685	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.035000|0.035000	0.12851|0.12851	3.056000|3.056000	0.49923|0.49923	2.011000|2.011000	0.59026|0.59026	0.491000|0.491000	0.48974|0.48974	TGT|GTG	.	.	.	none		0.602	CD81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027357.4	NM_004356		T	2417109	G	T	2417109	3	4	125	1	0	0	0	0	1	0	0	0	3041	1377	48	4	492	4	CD81	11	2417109	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08		2417109	132589407	42	7848											
NELL1	4745	hgsc.bcm.edu	37	chr11	21581738	21581738	+	Missense_Mutation	SNP	T	T	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	tgcttcctatattgcagacaTtgatgaatgtgccttaagaa	12	14	8	7	0	0	4	0	2	0	2	1	4	1	4	2	0	3	2	2	0	5	6			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr11:21581738T>G	ENST00000357134.5	+	17	1942	c.1790T>G	c.(1789-1791)aTt>aGt	p.I597S	NELL1_ENST00000532434.1_Missense_Mutation_p.I550S|NELL1_ENST00000298925.5_Missense_Mutation_p.I625S|NELL1_ENST00000529218.1_Intron|NELL1_ENST00000325319.5_Missense_Mutation_p.I540S	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	597	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|nervous system development (GO:0007399)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						ATTGCAGACATTGATGAATGT	0.478																																					p.I597S		Atlas-SNP	.											.	NELL1	179	.	0			c.T1790G						PASS	.						132	122	125					11																	21581738		2203	4300	6503	SO:0001583	missense	4745	exon17			CAGACATTGATGA	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.1790T>G	chr11.hg19:g.21581738T>G	ENSP00000349654:p.Ile597Ser	181.0	0.0	.		144.0	60.0	.	NM_006157	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Missense_Mutation	SNP	ENST00000357134.5	hg19	CCDS7855.1	.	.	.	.	.	.	.	.	.	.	T	18.34	3.603633	0.66445	.	.	ENSG00000165973	ENST00000298925;ENST00000357134;ENST00000325319;ENST00000532434	D;D;D;D	0.93604	-3.25;-3.25;-3.25;-3.25	5.9	5.9	0.94986	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.067178	0.64402	D	0.000016	D	0.96898	0.8987	M	0.88570	2.965	0.51767	D	0.999934	D;D;D;D	0.64830	0.993;0.994;0.986;0.994	P;D;P;D	0.63192	0.857;0.912;0.885;0.912	D	0.97543	1.0087	10	0.87932	D	0	-6.8617	16.3275	0.82990	0.0:0.0:0.0:1.0	.	540;625;550;597	F5H6I3;B3KXR2;Q92832-2;Q92832	.;.;.;NELL1_HUMAN	S	625;597;540;550	ENSP00000298925:I625S;ENSP00000349654:I597S;ENSP00000317837:I540S;ENSP00000437170:I550S	ENSP00000298925:I625S	I	+	2	0	NELL1	21538314	1.000000	0.71417	1.000000	0.80357	0.528000	0.34623	8.040000	0.89188	2.266000	0.75297	0.528000	0.53228	ATT	.	.	.	none		0.478	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157		G	21581738	T	G	21581738	3	3	125	1	0	0	0	0	1	0	0	0	10340	1493	52	5	1856	5	NELL1	11	21581738	Missense_Mutation	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	19164629	21581738	113424778	43	7849											
SLC5A12	159963	hgsc.bcm.edu	37	chr11	26742996	26742996	+	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	atgttaagaggatgacaaatAggtaagcaatgaagaagact	19	8	11	3	0	0	5	0	2	0	3	0	6	0	6	0	2	1	3	0	2	7	3			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr11:26742996A>T	ENST00000396005.3	-	1	575	c.266T>A	c.(265-267)cTa>cAa	p.L89Q	SLC5A12_ENST00000280467.6_Missense_Mutation_p.L89Q	NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	89					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						GATGACAAATAGGTAAGCAAT	0.468																																					p.L89Q		Atlas-SNP	.											.	SLC5A12	134	.	0			c.T266A						PASS	.						94	95	95					11																	26742996		2203	4299	6502	SO:0001583	missense	159963	exon1			ACAAATAGGTAAG	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.266T>A	chr11.hg19:g.26742996A>T	ENSP00000379326:p.Leu89Gln	81.0	0.0	.		66.0	28.0	.	NM_178498	Q86UC7	Missense_Mutation	SNP	ENST00000396005.3	hg19	CCDS7860.2	.	.	.	.	.	.	.	.	.	.	A	9.586	1.124947	0.20959	.	.	ENSG00000148942	ENST00000396005;ENST00000280467	D;D	0.91686	-2.89;-2.89	5.83	1.3	0.21679	.	1.064190	0.07282	N	0.870876	D	0.91740	0.7388	L	0.58583	1.82	0.09310	N	1	B;P	0.37176	0.204;0.586	P;B	0.45856	0.495;0.436	T	0.81684	-0.0821	10	0.59425	D	0.04	.	6.9268	0.24419	0.1679:0.2534:0.5788:0.0	.	89;89	Q1EHB4-2;Q1EHB4	.;SC5AC_HUMAN	Q	89	ENSP00000379326:L89Q;ENSP00000280467:L89Q	ENSP00000280467:L89Q	L	-	2	0	SLC5A12	26699572	0.018000	0.18449	0.000000	0.03702	0.042000	0.13812	1.941000	0.40233	-0.023000	0.13963	-0.472000	0.04984	CTA	.	.	.	none		0.468	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498		T	26742996	A	T	26742996	3	4	125	1	0	0	0	0	1	0	0	0	14677	420	15	5	1650	5	SLC5A12	11	26742996	Missense_Mutation	SNP	A	TCGA-BQ-5890-01A-11D-1589-08	5161258	26742996	108263520	44	7850											
FLRT1	28992	hgsc.bcm.edu	37	chr11	63884401	63884401	+	Intron	SNP	T	T	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	gctgcatgccttcaagggccTcaacagcctgcggcgcctgg	6	7	13	15	2	2	0	2	0	0	0	2	0	2	0	4	3	5	2	4	3	2	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr11:63884401T>A	ENST00000255681.6	-	3	584				FLRT1_ENST00000246841.3_Missense_Mutation_p.L221H|RP11-21A7A.3_ENST00000543817.1_RNA	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						TTCAAGGGCCTCAACAGCCTG	0.657																																					p.L221H		Atlas-SNP	.											.	FLRT1	46	.	0			c.T662A						PASS	.						37	33	34					11																	63884401		2201	4297	6498	SO:0001627	intron_variant	23769	exon2			AGGGCCTCAACAG	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+34309A>T	chr11.hg19:g.63884401T>A		50.0	0.0	.		44.0	13.0	.	NM_013280	Q9UH96	Missense_Mutation	SNP	ENST00000255681.6	hg19	CCDS8056.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.012781	0.75161	.	.	ENSG00000126500	ENST00000246841	T	0.71222	-0.55	5.56	5.56	0.83823	.	0.000000	0.64402	D	0.000007	D	0.88966	0.6581	H	0.95950	3.745	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92298	0.5847	10	0.87932	D	0	-26.892	14.697	0.69129	0.0:0.0:0.0:1.0	.	193	Q9NZU1	FLRT1_HUMAN	H	221	ENSP00000246841:L221H	ENSP00000246841:L221H	L	+	2	0	FLRT1	63640977	0.997000	0.39634	0.940000	0.37924	0.996000	0.88848	5.163000	0.64948	2.114000	0.64651	0.454000	0.30748	CTC	.	.	.	none		0.657	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067		A	63884401	T	A	63884401	1	1	125	0	1	0	0	0	0	0	0	0	5945	1551	54	5		5	FLRT1	11	63884401	Intron	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	37141405	63884401	71122115	45	7851											
PITPNM1	9600	hgsc.bcm.edu	37	chr11	67265787	67265787	+	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	tccccatcgtggctgtaaggGctcaggctgtaggaggggga	7	8	17	9	1	1	0	1	0	0	0	3	2	2	2	2	6	0	5	2	6	2	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr11:67265787G>A	ENST00000534749.1	-	10	1679	c.1491C>T	c.(1489-1491)agC>agT	p.S497S	PITPNM1_ENST00000436757.2_Silent_p.S497S|PITPNM1_ENST00000356404.3_Silent_p.S497S			O00562	PITM1_HUMAN	phosphatidylinositol transfer protein, membrane-associated 1	497					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						GGCTGTAAGGGCTCAGGCTGT	0.657																																					p.S497S	GBM(28;144 709 4607 5525)	Atlas-SNP	.											.	PITPNM1	84	.	0			c.C1491T						PASS	.						56	55	55					11																	67265787		2196	4291	6487	SO:0001819	synonymous_variant	9600	exon11			GTAAGGGCTCAGG	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.1491C>T	chr11.hg19:g.67265787G>A		24.0	0.0	.		23.0	8.0	.	NM_001130848	A6NME4|Q6T7X3|Q8TBN3|Q9BZ73	Silent	SNP	ENST00000534749.1	hg19	CCDS31620.1																																																																																			.	.	.	none		0.657	PITPNM1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395520.1	NM_004910		A	67265787	G	A	67265787	2	1	125	1	0	0	0	0	0	0	0	1	11957	1194	42	2		2	PITPNM1	11	67265787	Silent	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	3381386	67265787	67740729	46	7852											
WNK1	65125	hgsc.bcm.edu	37	chr12	977170	977170	+	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	aagtagccatttcccagcggCgtaagagcacctccttcctg	9	9	9	14	2	0	1	0	0	0	1	3	1	3	1	5	1	3	3	5	1	3	4	rs200794710		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr12:977170C>T	ENST00000315939.6	+	9	2782				WNK1_ENST00000574564.1_Missense_Mutation_p.R59C|WNK1_ENST00000340908.4_Intron|WNK1_ENST00000537687.1_Missense_Mutation_p.R760C|WNK1_ENST00000530271.2_Missense_Mutation_p.R845C|WNK1_ENST00000535572.1_Intron	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1						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)			TTCCCAGCGGCGTAAGAGCAC	0.512																																					p.R845C	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.C2533T						PASS	.	C	CYS/ARG,CYS/ARG,,	0,3850		0,0,1925	104	105	105		2278,2533,,	5.7	1	12		105	1,8271		0,1,4135	yes	missense,missense,intron,intron	WNK1	NM_001184985.1,NM_213655.4,NM_014823.2,NM_018979.3	180,180,,	0,1,6060	TT,TC,CC		0.0121,0.0,0.0082	probably-damaging,probably-damaging,,	760/2643,845/2635,,	977170	1,12121	1925	4136	6061	SO:0001627	intron_variant	65125	exon10			CAGCGGCGTAAGA	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.2140-3261C>T	chr12.hg19:g.977170C>T		101.0	0.0	.		148.0	7.0	.	NM_213655	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	hg19	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	C	15.95	2.984466	0.53934	0.0	1.21E-4	ENSG00000060237	ENST00000537687;ENST00000530271	T;T	0.15603	2.41;2.41	5.67	5.67	0.87782	.	.	.	.	.	T	0.46795	0.1411	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.39522	-0.9610	8	0.56958	D	0.05	.	19.7725	0.96373	0.0:1.0:0.0:0.0	.	845	F5H2M7	.	C	760;845	ENSP00000444465:R760C;ENSP00000433548:R845C	ENSP00000433548:R845C	R	+	1	0	WNK1	847431	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.487000	0.81328	2.673000	0.90976	0.467000	0.42956	CGT	.	.	.	weak		0.512	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		T	977170	C	T	977170	1	4	125	0	1	0	0	0	0	0	0	0	17389	768	27	1		1	WNK1	12	977170	Intron	SNP	C	TCGA-BQ-5890-01A-11D-1589-08		977170	132874725	47	7853											
KCNC2	3747	hgsc.bcm.edu	37	chr12	75441966	75441966	+	Missense_Mutation	SNP	A	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	tccatcagaagcacacgtgtAatcacctgtcgtcagtagga	12	9	9	11	2	3	1	3	0	0	1	5	2	4	2	2	1	1	3	2	1	3	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr12:75441966A>C	ENST00000549446.1	-	4	2427	c.1747T>G	c.(1747-1749)Tac>Gac	p.Y583D	KCNC2_ENST00000350228.2_Intron|KCNC2_ENST00000548513.1_Missense_Mutation_p.Y583D|KCNC2_ENST00000550433.1_Missense_Mutation_p.Y583D|KCNC2_ENST00000393288.2_Missense_Mutation_p.Y583D|KCNC2_ENST00000341669.3_Missense_Mutation_p.Y583D|KCNC2_ENST00000540018.1_Intron|KCNC2_ENST00000548243.1_5'Flank|KCNC2_ENST00000298972.1_Missense_Mutation_p.Y583D	NM_001260497.1|NM_139137.3	NP_001247426.1|NP_631875.1	Q96PR1	KCNC2_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 2	583					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)	GCACACGTGTAATCACCTGTC	0.463																																					p.Y583D		Atlas-SNP	.											.	KCNC2	239	.	0			c.T1747G						PASS	.						322	257	279					12																	75441966		2203	4300	6503	SO:0001583	missense	3747	exon4			ACGTGTAATCACC	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.1747T>G	chr12.hg19:g.75441966A>C	ENSP00000449253:p.Tyr583Asp	284.0	0.0	.		286.0	108.0	.	NM_139137	B7Z231|F5H030|J3KPP5|Q4LE77|Q86W09|Q8N1V9|Q96PR0	Missense_Mutation	SNP	ENST00000549446.1	hg19	CCDS9007.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.589934	0.86851	.	.	ENSG00000166006	ENST00000550433;ENST00000548513;ENST00000549446;ENST00000341669;ENST00000298972;ENST00000393288	D;D;D;D;D;D	0.97959	-4.52;-4.57;-4.63;-4.52;-4.57;-4.61	5.55	5.55	0.83447	.	1.098430	0.06893	N	0.804679	D	0.98052	0.9358	L	0.55990	1.75	0.58432	D	0.999996	D;P;D	0.57899	0.981;0.895;0.964	P;B;P	0.55871	0.786;0.389;0.745	D	0.93970	0.7248	10	0.72032	D	0.01	.	15.683	0.77388	1.0:0.0:0.0:0.0	.	583;583;583	Q96PR1-2;Q96PR1;Q96PR1-3	.;KCNC2_HUMAN;.	D	583	ENSP00000448301:Y583D;ENSP00000449941:Y583D;ENSP00000449253:Y583D;ENSP00000340121:Y583D;ENSP00000298972:Y583D;ENSP00000376966:Y583D	ENSP00000298972:Y583D	Y	-	1	0	KCNC2	73728233	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.855000	0.75445	2.104000	0.64026	0.477000	0.44152	TAC	.	.	.	none		0.463	KCNC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405581.2	NM_153748		C	75441966	A	C	75441966	3	2	125	1	0	0	0	0	1	0	0	0	8022	362	13	5	243	5	KCNC2	12	75441966	Missense_Mutation	SNP	A	TCGA-BQ-5890-01A-11D-1589-08	74464796	75441966	58409929	48	7854											
NUAK1	9891	hgsc.bcm.edu	37	chr12	106460987	106460987	+	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	cgctgagtatttgctgctgtGtttcaagatgcccttcctcc	5	15	9	12	1	1	2	1	1	0	1	3	2	3	2	3	0	3	5	3	0	2	4			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr12:106460987G>T	ENST00000261402.2	-	7	2958	c.1579C>A	c.(1579-1581)Cac>Aac	p.H527N		NM_014840.2	NP_055655.1	O60285	NUAK1_HUMAN	NUAK family, SNF1-like kinase, 1	527					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						TTGCTGCTGTGTTTCAAGATG	0.627																																					p.H527N		Atlas-SNP	.											.	NUAK1	196	.	0			c.C1579A						PASS	.						68	75	72					12																	106460987		2203	4300	6503	SO:0001583	missense	9891	exon7			TGCTGTGTTTCAA	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.1579C>A	chr12.hg19:g.106460987G>T	ENSP00000261402:p.His527Asn	113.0	0.0	.		121.0	53.0	.	NM_014840	A7MD39|Q96KA8	Missense_Mutation	SNP	ENST00000261402.2	hg19	CCDS31892.1	.	.	.	.	.	.	.	.	.	.	G	18.76	3.692745	0.68271	.	.	ENSG00000074590	ENST00000261402	T	0.73258	-0.73	5.34	5.34	0.76211	.	0.000000	0.64402	D	0.000008	T	0.77239	0.4101	M	0.61703	1.905	0.54753	D	0.999988	P	0.47910	0.902	P	0.50082	0.63	T	0.78411	-0.2214	10	0.51188	T	0.08	.	19.0535	0.93054	0.0:0.0:1.0:0.0	.	527	O60285	NUAK1_HUMAN	N	527	ENSP00000261402:H527N	ENSP00000261402:H527N	H	-	1	0	NUAK1	104985117	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	9.476000	0.97823	2.493000	0.84123	0.462000	0.41574	CAC	.	.	.	none		0.627	NUAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405767.2	NM_014840		T	106460987	G	T	106460987	3	4	125	1	0	0	0	0	1	0	0	0	10719	1377	48	4	410	4	NUAK1	12	106460987	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	31019021	106460987	27390908	49	7855											
RNF17	56163	hgsc.bcm.edu	37	chr13	25352542	25352542	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgaactcatcagctgtaatgTtggtatgaaacatattggtc	12	14	9	6	0	2	2	2	2	0	0	3	2	2	2	0	2	3	4	0	2	5	5			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr13:25352542T>C	ENST00000255324.5	+	4	479	c.427T>C	c.(427-429)Ttg>Ctg	p.L143L	RNF17_ENST00000255326.4_3'UTR|RNF17_ENST00000381921.1_Silent_p.L143L|RNF17_ENST00000255325.6_Silent_p.L143L	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	143					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)		AGCTGTAATGTTGGTATGAAA	0.383																																					p.L143L		Atlas-SNP	.											.	RNF17	259	.	0			c.T427C						PASS	.						158	141	147					13																	25352542		2203	4300	6503	SO:0001819	synonymous_variant	56163	exon4			GTAATGTTGGTAT	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.427T>C	chr13.hg19:g.25352542T>C		171.0	0.0	.		197.0	60.0	.	NM_001184993	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Silent	SNP	ENST00000255324.5	hg19	CCDS9308.2																																																																																			.	.	.	none		0.383	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994		C	25352542	T	C	25352542	2	2	125	1	0	0	0	0	0	0	0	1	13474	1722	60	3		3	RNF17	13	25352542	Silent	SNP	T	TCGA-BQ-5890-01A-11D-1589-08		25352542	89817336	50	7856											
CSPG4	1464	hgsc.bcm.edu	37	chr15	75981607	75981607	+	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	ctcggcgctccacggggaggCcagaggaggtgccaaggacc	8	3	17	13	3	0	1	0	0	0	1	2	4	1	4	4	7	1	1	4	7	1	0			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr15:75981607C>T	ENST00000308508.5	-	3	1891	c.1799G>A	c.(1798-1800)gGc>gAc	p.G600D		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	600	Globular or compact configuration stabilized by disulfide bonds.|Interaction with COL6A2. {ECO:0000250}.|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						CACGGGGAGGCCAGAGGAGGT	0.672																																					p.G600D		Atlas-SNP	.											.	CSPG4	175	.	0			c.G1799A						PASS	.						19	23	21					15																	75981607		2192	4287	6479	SO:0001583	missense	1464	exon3			GGGAGGCCAGAGG	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.1799G>A	chr15.hg19:g.75981607C>T	ENSP00000312506:p.Gly600Asp	47.0	0.0	.		49.0	23.0	.	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	hg19	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	2.636	-0.285218	0.05605	.	.	ENSG00000173546	ENST00000308508	T	0.19938	2.11	5.35	4.4	0.53042	.	0.186703	0.37955	N	0.001879	T	0.15522	0.0374	L	0.53249	1.67	0.09310	N	1	B	0.33583	0.418	B	0.24541	0.054	T	0.18272	-1.0342	10	0.24483	T	0.36	.	6.6414	0.22911	0.1799:0.7302:0.0:0.0899	.	600	Q6UVK1	CSPG4_HUMAN	D	600	ENSP00000312506:G600D	ENSP00000312506:G600D	G	-	2	0	CSPG4	73768662	.	.	0.001000	0.08648	0.417000	0.31264	.	.	1.194000	0.43101	0.555000	0.69702	GGC	.	.	.	none		0.672	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		T	75981607	C	T	75981607	3	4	125	1	0	0	0	0	1	0	0	0	3962	739	26	2	5201	2	CSPG4	15	75981607	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08		75981607	26549785	51	7857											
MCTP2	55784	hgsc.bcm.edu	37	chr15	94884070	94884070	+	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	aacatattttaaaactggaaGatccaaacagtttagaagat	19	11	6	5	0	0	3	0	0	0	3	1	4	1	4	1	1	3	1	1	1	8	5			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr15:94884070G>T	ENST00000357742.4	+	6	886	c.886G>T	c.(886-888)Gat>Tat	p.D296Y	MCTP2_ENST00000543482.1_Missense_Mutation_p.D296Y|MCTP2_ENST00000331706.4_5'UTR|MCTP2_ENST00000451018.3_Missense_Mutation_p.D296Y	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	296					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)			AAAACTGGAAGATCCAAACAG	0.388																																					p.D296Y		Atlas-SNP	.											.	MCTP2	122	.	0			c.G886T						PASS	.						84	82	83					15																	94884070		2197	4298	6495	SO:0001583	missense	55784	exon6			CTGGAAGATCCAA	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.886G>T	chr15.hg19:g.94884070G>T	ENSP00000350377:p.Asp296Tyr	63.0	0.0	.		56.0	25.0	.	NM_001159643	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Missense_Mutation	SNP	ENST00000357742.4	hg19	CCDS32338.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.148823	0.78001	.	.	ENSG00000140563	ENST00000543482;ENST00000556363;ENST00000451018;ENST00000357742	T;T;T	0.10573	2.86;2.86;2.86	5.77	4.86	0.63082	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.29652	0.0740	L	0.60455	1.87	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.99;0.994;0.997;0.999	T	0.02053	-1.1222	10	0.87932	D	0	.	14.4552	0.67411	0.0712:0.0:0.9288:0.0	.	296;296;296;296;296	F5H415;Q6DN12-2;Q6DN12;B7Z6H2;G3V2J2	.;.;MCTP2_HUMAN;.;.	Y	296	ENSP00000438521:D296Y;ENSP00000395109:D296Y;ENSP00000350377:D296Y	ENSP00000350377:D296Y	D	+	1	0	MCTP2	92685074	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.178000	0.94855	1.442000	0.47568	-0.136000	0.14681	GAT	.	.	.	none		0.388	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349		T	94884070	G	T	94884070	3	4	125	1	0	0	0	0	1	0	0	0	9408	942	33	4	908	4	MCTP2	15	94884070	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	18902463	94884070	7647322	52	7858											
PRSS21	10942	hgsc.bcm.edu	37	chr16	2868724	2868724	+	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	ggtggatggtccagtttggcCagctgacttccatgccatcc	6	11	12	12	0	0	1	0	1	0	0	3	2	3	2	5	4	2	2	5	4	0	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr16:2868724C>G	ENST00000005995.3	+	4	346	c.304C>G	c.(304-306)Cag>Gag	p.Q102E	PRSS21_ENST00000450020.3_Missense_Mutation_p.Q102E|PRSS21_ENST00000455114.1_Missense_Mutation_p.Q100E			Q9Y6M0	TEST_HUMAN	protease, serine, 21 (testisin)	102	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				spermatogenesis (GO:0007283)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	15						CCAGTTTGGCCAGCTGACTTC	0.562																																					p.Q102E		Atlas-SNP	.											.	PRSS21	32	.	0			c.C304G						PASS	.						126	101	109					16																	2868724		2198	4300	6498	SO:0001583	missense	10942	exon4			TTTGGCCAGCTGA	AF058300	CCDS10478.1, CCDS45388.1	16p13.3	2010-05-07			ENSG00000007038	ENSG00000007038		"Serine peptidases / Serine peptidases"	9485	protein-coding gene	gene with protein product		608159				10397266, 9826525	Standard	NM_006799		Approved	ESP-1, TEST1, TESTISIN	uc002crt.4	Q9Y6M0	OTTHUMG00000128931	ENST00000005995.3:c.304C>G	chr16.hg19:g.2868724C>G	ENSP00000005995:p.Gln102Glu	98.0	0.0	.		184.0	35.0	.	NM_144957	Q9NS34|Q9P2V6	Missense_Mutation	SNP	ENST00000005995.3	hg19	CCDS10478.1	.	.	.	.	.	.	.	.	.	.	c	0.406	-0.915839	0.02415	.	.	ENSG00000007038	ENST00000455114;ENST00000450020;ENST00000005995	D;D;D	0.87412	-2.25;-2.25;-2.25	4.9	0.325	0.15903	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.253065	0.20623	N	0.088727	T	0.57636	0.2067	N	0.00670	-1.27	0.09310	N	1	B;B;B	0.15930	0.015;0.012;0.012	B;B;B	0.12837	0.008;0.005;0.005	T	0.56220	-0.8015	10	0.02654	T	1	.	10.9331	0.47230	0.0:0.6074:0.267:0.1256	.	102;100;102	Q9Y6M0;Q9Y6M0-2;Q9Y6M0-3	TEST_HUMAN;.;.	E	100;102;102	ENSP00000400632:Q100E;ENSP00000407741:Q102E;ENSP00000005995:Q102E	ENSP00000005995:Q102E	Q	+	1	0	PRSS21	2808725	0.201000	0.23410	0.726000	0.30738	0.199000	0.23934	0.700000	0.25601	0.575000	0.29434	-0.299000	0.09455	CAG	.	.	.	none		0.562	PRSS21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250910.1	NM_006799		G	2868724	C	G	2868724	3	3	125	1	0	0	0	0	1	0	0	0	12628	595	21	4	318	4	PRSS21	16	2868724	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08		2868724	87486029	53	7859											
ZNF597	146434	hgsc.bcm.edu	37	chr16	3487524	3487524	+	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	taactgctgattaatctcagGcttgccttcctctcctgttg	6	16	7	12	0	2	1	1	1	2	0	5	1	3	1	3	1	3	3	3	1	2	5			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr16:3487524G>C	ENST00000301744.4	-	4	410	c.175C>G	c.(175-177)Cct>Gct	p.P59A		NM_152457.1	NP_689670.1	Q96LX8	ZN597_HUMAN	zinc finger protein 597	59	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						TTAATCTCAGGCTTGCCTTCC	0.413																																					p.P59A		Atlas-SNP	.											ZNF597,NS,malignant_melanoma,0,1	ZNF597	41	.	0			c.C175G						PASS	.						49	50	50					16																	3487524		2197	4300	6497	SO:0001583	missense	146434	exon4			TCTCAGGCTTGCC	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.175C>G	chr16.hg19:g.3487524G>C	ENSP00000301744:p.Pro59Ala	82.0	0.0	.		145.0	91.0	.	NM_152457		Missense_Mutation	SNP	ENST00000301744.4	hg19	CCDS10505.1	.	.	.	.	.	.	.	.	.	.	G	0.004	-2.351852	0.00217	.	.	ENSG00000167981	ENST00000301744	T	0.08458	3.09	4.91	-1.26	0.09376	Krueppel-associated box (1);	0.486115	0.17564	N	0.169702	T	0.04227	0.0117	N	0.25201	0.72	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.33929	-0.9849	10	0.62326	D	0.03	-0.9659	1.0959	0.01673	0.1461:0.1764:0.3287:0.3488	.	59	Q96LX8	ZN597_HUMAN	A	59	ENSP00000301744:P59A	ENSP00000301744:P59A	P	-	1	0	ZNF597	3427525	0.000000	0.05858	0.000000	0.03702	0.056000	0.15407	0.183000	0.16919	-0.121000	0.11787	-0.262000	0.10625	CCT	.	.	.	none		0.413	ZNF597-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251511.2	NM_152457		C	3487524	G	C	3487524	3	2	125	1	0	0	0	0	1	0	0	0	18039	1203	42	4	1103	4	ZNF597	16	3487524	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	618800	3487524	86867229	54	7860											
USP31	57478	hgsc.bcm.edu	37	chr16	23083424	23083424	+	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	tcagagagcgacgccagggaGgtgcgtctggaggaagctgc	9	5	18	9	3	2	1	1	0	1	1	2	6	2	4	1	4	4	1	1	4	1	0			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr16:23083424G>T	ENST00000219689.7	-	15	2429	c.2430C>A	c.(2428-2430)acC>acA	p.T810T	USP31_ENST00000567975.1_Silent_p.T103T	NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	0	DUSP 3. {ECO:0000255|PROSITE- ProRule:PRU00613}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		ACGCCAGGGAGGTGCGTCTGG	0.577																																					p.T810T		Atlas-SNP	.											.	USP31	122	.	0			c.C2430A						PASS	.						122	120	121					16																	23083424		2197	4300	6497	SO:0001819	synonymous_variant	57478	exon15			CAGGGAGGTGCGT	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.2430C>A	chr16.hg19:g.23083424G>T		134.0	0.0	.		232.0	20.0	.	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Silent	SNP	ENST00000219689.7	hg19	CCDS10607.1																																																																																			.	.	.	none		0.577	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718		T	23083424	G	T	23083424	2	4	125	1	0	0	0	0	0	0	0	1	17074	987	35	4		4	USP31	16	23083424	Silent	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	19595900	23083424	67271329	55	7861											
NUP93	9688	hgsc.bcm.edu	37	chr16	56792502	56792502	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatcccacatctcccagcgaTtggagagtctgagtgcagcc	9	9	10	13	1	2	2	0	1	2	1	4	4	3	2	3	1	3	1	3	1	1	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr16:56792502T>C	ENST00000308159.5	+	3	353	c.232T>C	c.(232-234)Ttg>Ctg	p.L78L	NUP93_ENST00000569842.1_Silent_p.L78L	NM_014669.4	NP_055484.3	Q8N1F7	NUP93_HUMAN	nucleoporin 93kDa	78					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(2)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						CTCCCAGCGATTGGAGAGTCT	0.512																																					p.L78L	Colon(33;610 796 1305 1705 38917)	Atlas-SNP	.											.	NUP93	75	.	0			c.T232C						PASS	.						108	94	98					16																	56792502		2198	4300	6498	SO:0001819	synonymous_variant	9688	exon3			CAGCGATTGGAGA	D42085	CCDS10769.1, CCDS55996.1	16q13	2008-02-05			ENSG00000102900	ENSG00000102900			28958	protein-coding gene	gene with protein product		614351				9348540, 9531546	Standard	NM_014669		Approved	KIAA0095	uc002eka.3	Q8N1F7	OTTHUMG00000133278	ENST00000308159.5:c.232T>C	chr16.hg19:g.56792502T>C		112.0	0.0	.		98.0	37.0	.	NM_014669	B3KPQ8|Q14705	Silent	SNP	ENST00000308159.5	hg19	CCDS10769.1																																																																																			.	.	.	none		0.512	NUP93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257058.4	NM_014669		C	56792502	T	C	56792502	2	2	125	1	0	0	0	0	0	0	0	1	10779	1490	52	3		3	NUP93	16	56792502	Silent	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	33709078	56792502	33562251	56	7862											
COG8	84342	hgsc.bcm.edu	37	chr16	69368791	69368791	+	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	aggacagcccaaagtacatgCactggcccagcagagagtcc	13	4	11	13	0	0	1	0	0	0	1	1	3	1	2	3	2	4	3	3	2	2	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr16:69368791C>G	ENST00000306875.4	-	3	1160	c.1046G>C	c.(1045-1047)tGc>tCc	p.C349S	RP11-343C2.12_ENST00000562949.1_5'Flank|COG8_ENST00000562081.1_Missense_Mutation_p.C349S	NM_032382.4	NP_115758.3	Q96MW5	COG8_HUMAN	component of oligomeric golgi complex 8	349					protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|kidney(1)|large_intestine(2)|ovary(2)|skin(1)	9						AAAGTACATGCACTGGCCCAG	0.592																																					p.C349S		Atlas-SNP	.											.	COG8	32	.	0			c.G1046C						PASS	.						57	60	59					16																	69368791		2198	4300	6498	SO:0001583	missense	84342	exon3			TACATGCACTGGC	AK025968	CCDS10876.1	16q22.1	2011-05-31			ENSG00000213380	ENSG00000213380		"Components of oligomeric golgi complex"	18623	protein-coding gene	gene with protein product		606979				11980916	Standard	NM_032382		Approved	FLJ22315, DOR1	uc002ewy.2	Q96MW5	OTTHUMG00000154277	ENST00000306875.4:c.1046G>C	chr16.hg19:g.69368791C>G	ENSP00000305459:p.Cys349Ser	103.0	0.0	.		93.0	34.0	.	NM_032382	Q0VAK2|Q8WVV6|Q9H6F8	Missense_Mutation	SNP	ENST00000306875.4	hg19	CCDS10876.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.460053	0.84317	.	.	ENSG00000213380	ENST00000306875	T	0.47528	0.84	5.93	5.93	0.95920	Cullin repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.61489	0.2351	L	0.61218	1.895	0.80722	D	1	B;B	0.33379	0.41;0.41	P;P	0.46917	0.531;0.531	T	0.54330	-0.8310	10	0.35671	T	0.21	-0.7999	20.3363	0.98740	0.0:1.0:0.0:0.0	.	376;349	B4DYU2;Q96MW5	.;COG8_HUMAN	S	349	ENSP00000305459:C349S	ENSP00000305459:C349S	C	-	2	0	COG8	67926292	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.441000	0.80485	2.814000	0.96858	0.563000	0.77884	TGC	.	.	.	none		0.592	COG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268948.2	NM_032382		G	69368791	C	G	69368791	3	3	125	1	0	0	0	0	1	0	0	0	3666	710	25	4	804	4	COG8	16	69368791	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	12576289	69368791	20985962	57	7863											
ZNF778	197320	hgsc.bcm.edu	37	chr16	89294017	89294017	+	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	gtggccttactagacacgtaCgaacacacacgggcgagaag	13	5	12	11	4	0	2	0	0	0	2	0	4	0	2	1	2	3	1	1	2	5	3			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr16:89294017C>T	ENST00000433976.2	+	6	1569	c.1237C>T	c.(1237-1239)Cga>Tga	p.R413*	RP11-46C24.6_ENST00000563182.1_RNA|ZNF778_ENST00000306502.6_Nonsense_Mutation_p.R371*	NM_001201407.1|NM_182531.3	NP_001188336.1|NP_872337.2	Q96MU6	ZN778_HUMAN	zinc finger protein 778	413					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|skin(2)	24				BRCA - Breast invasive adenocarcinoma(80;0.0269)		TAGACACGTACGAACACACAC	0.498																																					p.R441X		Atlas-SNP	.											.	ZNF778	67	.	0			c.C1321T						PASS	.						92	96	94					16																	89294017		2154	4282	6436	SO:0001587	stop_gained	197320	exon7			CACGTACGAACAC	AK056437	CCDS45550.1, CCDS73928.1	16q24.3	2014-09-17			ENSG00000170100	ENSG00000170100		"Zinc fingers, C2H2-type", "-"	26479	protein-coding gene	gene with protein product							Standard	NM_182531		Approved	FLJ31875	uc021tms.1	Q96MU6		ENST00000433976.2:c.1237C>T	chr16.hg19:g.89294017C>T	ENSP00000405289:p.Arg413*	71.0	0.0	.		80.0	23.0	.	NM_001201407	Q08AG0	Nonsense_Mutation	SNP	ENST00000433976.2	hg19	CCDS45550.1	.	.	.	.	.	.	.	.	.	.	C	35	5.468936	0.96274	.	.	ENSG00000170100	ENST00000433976;ENST00000306502	.	.	.	1.13	-0.119	0.13543	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.1288	0.14899	0.6032:0.3967:0.0:0.0	.	.	.	.	X	413;371	.	ENSP00000305203:R371X	R	+	1	2	ZNF778	87821518	0.000000	0.05858	0.002000	0.10522	0.104000	0.19210	-0.846000	0.04336	-0.009000	0.14296	0.558000	0.71614	CGA	.	.	.	none		0.498	ZNF778-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430383.1	NM_182531		T	89294017	C	T	89294017	4	4	125	1	0	0	0	0	0	1	0	0	18163	528	19	1	1255	1	ZNF778	16	89294017	Nonsense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	19925226	89294017	1060736	58	7864											
DEF8	54849	hgsc.bcm.edu	37	chr16	90015887	90015887	+	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	tagaggaatggccatcctgtCcctgcgagcccctgggccct	6	8	12	15	1	0	1	0	0	0	1	2	3	2	2	6	3	2	0	6	3	2	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr16:90015887C>A	ENST00000268676.7	+	2	103	c.14C>A	c.(13-15)tCc>tAc	p.S5Y	DEF8_ENST00000567874.1_5'UTR|DEF8_ENST00000563594.1_5'UTR|DEF8_ENST00000570182.1_5'UTR|DEF8_ENST00000418391.2_5'UTR|DEF8_ENST00000563795.1_5'UTR|DEF8_ENST00000569453.1_5'UTR	NM_207514.2	NP_997397.1	Q6ZN54	DEFI8_HUMAN	differentially expressed in FDCP 8 homolog (mouse)	5					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)		GCCATCCTGTCCCTGCGAGCC	0.672																																					p.S5Y		Atlas-SNP	.											.	DEF8	28	.	0			c.C14A						PASS	.						46	47	47					16																	90015887		2198	4300	6498	SO:0001583	missense	54849	exon2			TCCTGTCCCTGCG	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.14C>A	chr16.hg19:g.90015887C>A	ENSP00000268676:p.Ser5Tyr	86.0	0.0	.		90.0	31.0	.	NM_207514	B3KT65|B4DK62|B4E0S9|B7Z3H6|H3BUG7|Q8N8N3|Q9NXL0	Missense_Mutation	SNP	ENST00000268676.7	hg19	CCDS10989.1	.	.	.	.	.	.	.	.	.	.	C	14.04	2.417522	0.42918	.	.	ENSG00000140995	ENST00000268676	T	0.50001	0.76	2.59	-0.8	0.10897	.	.	.	.	.	T	0.23014	0.0556	N	0.08118	0	0.09310	N	0.999994	B	0.16166	0.016	B	0.16289	0.015	T	0.18745	-1.0327	9	0.87932	D	0	.	3.1996	0.06645	0.0:0.4875:0.226:0.2865	.	5	Q6ZN54	DEFI8_HUMAN	Y	5	ENSP00000268676:S5Y	ENSP00000268676:S5Y	S	+	2	0	DEF8	88543388	0.007000	0.16637	0.000000	0.03702	0.020000	0.10135	1.378000	0.34328	-0.124000	0.11724	0.511000	0.50034	TCC	.	.	.	none		0.672	DEF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000272878.1	NM_207514		A	90015887	C	A	90015887	3	1	125	1	0	0	0	0	1	0	0	0	4389	855	30	4	16	4	DEF8	16	90015887	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08	721870	90015887	338866	59	7865											
KDM6B	23135	hgsc.bcm.edu	37	chr17	7755372	7755372	+	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	tactgggagaccatcagcgcTttctgtgatcggtgcgtgcc	6	11	13	11	3	2	2	1	1	1	1	3	3	2	2	2	2	4	1	2	2	1	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr17:7755372T>G	ENST00000448097.2	+	18	4600	c.4269T>G	c.(4267-4269)gcT>gcG	p.A1423A	KDM6B_ENST00000254846.5_Silent_p.A1423A			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	1423	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				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						CCATCAGCGCTTTCTGTGATC	0.632											OREG0024145	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A1423A		Atlas-SNP	.											.	KDM6B	95	.	0			c.T4269G						PASS	.						95	82	86					17																	7755372		2203	4300	6503	SO:0001819	synonymous_variant	23135	exon18			CAGCGCTTTCTGT	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.4269T>G	chr17.hg19:g.7755372T>G		57.0	0.0	.	644	63.0	19.0	.	NM_001080424	C9IZ40|Q96G33	Silent	SNP	ENST00000448097.2	hg19																																																																																				.	.	.	none		0.632	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272		G	7755372	T	G	7755372	2	3	125	1	0	0	0	0	0	0	0	1	8145	1596	56	5		5	KDM6B	17	7755372	Silent	SNP	T	TCGA-BQ-5890-01A-11D-1589-08		7755372	73439838	60	7866											
ABCA9	10350	hgsc.bcm.edu	37	chr17	66981100	66981100	+	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	accactgacgggttccccagGatgctcagcacaaagcacag	12	5	10	14	1	1	1	1	1	0	0	2	2	2	2	3	2	3	4	3	2	1	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr17:66981100G>A	ENST00000340001.4	-	34	4516	c.4305C>T	c.(4303-4305)atC>atT	p.I1435I	ABCA9_ENST00000453985.2_Silent_p.I1397I|ABCA9_ENST00000370732.2_Intron|ABCA9_ENST00000482072.1_5'Flank	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	1435	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					GGTTCCCCAGGATGCTCAGCA	0.597																																					p.I1435I		Atlas-SNP	.											.	ABCA9	192	.	0			c.C4305T						PASS	.						132	116	121					17																	66981100		2203	4300	6503	SO:0001819	synonymous_variant	10350	exon34			CCCCAGGATGCTC	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.4305C>T	chr17.hg19:g.66981100G>A		116.0	0.0	.		174.0	31.0	.	NM_080283	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Silent	SNP	ENST00000340001.4	hg19	CCDS11681.1																																																																																			.	.	.	none		0.597	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386		A	66981100	G	A	66981100	2	1	125	1	0	0	0	0	0	0	0	1	39	1164	41	2		2	ABCA9	17	66981100	Silent	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	59225728	66981100	14214110	61	7867											
ABCA10	10349	hgsc.bcm.edu	37	chr17	67170778	67170778	+	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	atgagttcccatgaaagctgGaatcccagaaatatgaagta	16	9	9	7	0	0	4	0	3	0	1	2	5	2	5	2	1	1	3	2	1	6	3			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr17:67170778G>T	ENST00000269081.4	-	25	3927	c.3018C>A	c.(3016-3018)ttC>ttA	p.F1006L	ABCA10_ENST00000416101.2_3'UTR|ABCA10_ENST00000519732.1_Intron	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	1006					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)					ATGAAAGCTGGAATCCCAGAA	0.333																																					p.F1006L		Atlas-SNP	.											.	ABCA10	209	.	0			c.C3018A						PASS	.						78	86	83					17																	67170778		2202	4296	6498	SO:0001583	missense	10349	exon25			AAGCTGGAATCCC	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.3018C>A	chr17.hg19:g.67170778G>T	ENSP00000269081:p.Phe1006Leu	143.0	0.0	.		231.0	71.0	.	NM_080282	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Missense_Mutation	SNP	ENST00000269081.4	hg19	CCDS11684.1	.	.	.	.	.	.	.	.	.	.	G	2.023	-0.424331	0.04734	.	.	ENSG00000154263	ENST00000269081	D	0.84944	-1.92	3.1	2.05	0.26809	.	.	.	.	.	T	0.67277	0.2876	N	0.17474	0.49	0.09310	N	1	B	0.25351	0.124	B	0.26614	0.071	T	0.51942	-0.8641	9	0.11485	T	0.65	.	1.6357	0.02741	0.1265:0.2031:0.4424:0.2279	.	1006	Q8WWZ4	ABCAA_HUMAN	L	1006	ENSP00000269081:F1006L	ENSP00000269081:F1006L	F	-	3	2	ABCA10	64682373	0.000000	0.05858	0.001000	0.08648	0.086000	0.17979	-0.664000	0.05292	0.551000	0.29008	0.407000	0.27541	TTC	.	.	.	none		0.333	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282		T	67170778	G	T	67170778	3	4	125	1	0	0	0	0	1	0	0	0	29	1165	41	4	1677	4	ABCA10	17	67170778	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	189678	67170778	14024432	62	7868											
FASN	2194	hgsc.bcm.edu	37	chr17	80050833	80050833	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatggtggcgtacacccgccGggccagggacttcttggtca	6	8	15	12	3	2	0	1	0	1	0	2	2	2	1	3	5	1	1	3	5	1	3	rs200752265		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr17:80050833G>A	ENST00000306749.2	-	6	936	c.718C>T	c.(718-720)Cgg>Tgg	p.R240W		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	240	Beta-ketoacyl synthase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	TACACCCGCCGGGCCAGGGAC	0.682																																					p.R240W	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.C718T						PASS	.						30	31	31					17																	80050833		2183	4296	6479	SO:0001583	missense	2194	exon6			CCCGCCGGGCCAG	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.718C>T	chr17.hg19:g.80050833G>A	ENSP00000304592:p.Arg240Trp	24.0	0.0	.		37.0	12.0	.	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	G	19.51	3.841387	0.71488	.	.	ENSG00000169710	ENST00000306749	T	0.32988	1.43	4.64	2.47	0.30058	Thiolase-like, subgroup (1);Thiolase-like (1);	0.239450	0.32401	N	0.006145	T	0.51873	0.1700	M	0.86028	2.79	0.34231	D	0.676504	D	0.89917	1.0	D	0.66351	0.943	T	0.63350	-0.6657	10	0.87932	D	0	-32.0916	6.8759	0.24147	0.1029:0.0:0.2594:0.6378	.	240	P49327	FAS_HUMAN	W	240	ENSP00000304592:R240W	ENSP00000304592:R240W	R	-	1	2	FASN	77644122	0.246000	0.23909	0.993000	0.49108	0.893000	0.52053	1.570000	0.36439	0.338000	0.23692	0.313000	0.20887	CGG	.	G|0.998;T|0.002	.	alt		0.682	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		A	80050833	G	A	80050833	3	1	125	1	0	0	0	0	1	0	0	0	5690	1115	39	1	6969	1	FASN	17	80050833	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	12880055	80050833	1144377	63	7869											
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-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr19:879943G>C	ENST00000589119.1	-	7	1346	c.1347C>G	c.(1345-1347)caC>caG	p.H449Q	MED16_ENST00000395808.3_Missense_Mutation_p.H449Q|MED16_ENST00000606828.1_Intron|MED16_ENST00000269814.4_Missense_Mutation_p.H449Q|MED16_ENST00000325464.1_Missense_Mutation_p.H449Q|MED16_ENST00000312090.6_Missense_Mutation_p.H449Q			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	.	0			c.C1347G						PASS	.						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	chr19.hg19:g.879943G>C	ENSP00000464810:p.His449Gln	15.0	1.0	.		19.0	2.0	.	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Missense_Mutation	SNP	ENST00000589119.1	hg19	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	125	1	0	0	0	0	1	0	0	0	9441	1136	40	4	1322	4	MED16	19	879943	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08		879943	58249040	64	7870											
CD97	976	hgsc.bcm.edu	37	chr19	14513447	14513447	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctctccatccagaacatgAcgacattgctggccaatgcc	10	9	7	15	1	1	2	0	1	1	1	4	3	3	2	5	1	3	1	5	1	2	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr19:14513447A>G	ENST00000242786.5	+	12	1302	c.1222A>G	c.(1222-1224)Acg>Gcg	p.T408A	CD97_ENST00000357355.3_Missense_Mutation_p.T359A|CD97_ENST00000358600.3_Missense_Mutation_p.T315A|CTC-548K16.5_ENST00000590626.1_RNA	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	408					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						CCAGAACATGACGACATTGCT	0.572																																					p.T408A		Atlas-SNP	.											.	CD97	86	.	0			c.A1222G						PASS	.						120	109	112					19																	14513447		2203	4300	6503	SO:0001583	missense	976	exon12			AACATGACGACAT		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.1222A>G	chr19.hg19:g.14513447A>G	ENSP00000242786:p.Thr408Ala	121.0	0.0	.		91.0	4.0	.	NM_078481	A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	Missense_Mutation	SNP	ENST00000242786.5	hg19	CCDS32929.1	.	.	.	.	.	.	.	.	.	.	A	3.783	-0.045280	0.07452	.	.	ENSG00000123146	ENST00000242786;ENST00000357355;ENST00000358600;ENST00000393059	T;T;T	0.70045	-0.45;-0.37;0.01	5.12	-10.2	0.00374	.	.	.	.	.	T	0.45155	0.1328	N	0.22421	0.69	0.09310	N	1	B;B;B	0.30634	0.288;0.288;0.003	B;B;B	0.26416	0.069;0.069;0.008	T	0.53078	-0.8489	9	0.37606	T	0.19	.	12.7911	0.57534	0.1338:0.4984:0.3678:0.0	.	315;359;408	P48960-2;P48960-3;P48960	.;.;CD97_HUMAN	A	408;359;315;358	ENSP00000242786:T408A;ENSP00000349918:T359A;ENSP00000351413:T315A	ENSP00000242786:T408A	T	+	1	0	CD97	14374447	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-3.355000	0.00500	-4.211000	0.00064	0.374000	0.22700	ACG	.	.	.	none		0.572	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459821.2	NM_078481		G	14513447	A	G	14513447	3	3	125	1	0	0	0	0	1	0	0	0	3051	275	10	3	1268	3	CD97	19	14513447	Missense_Mutation	SNP	A	TCGA-BQ-5890-01A-11D-1589-08	13633504	14513447	44615536	65	7871											
PPP1R15A	23645	hgsc.bcm.edu	37	chr19	49379135	49379135	+	Missense_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	cctctgtcccttcgtccccaGtccagaccacgcccttgagc	5	9	7	20	2	1	2	0	1	1	1	5	2	4	2	7	0	1	0	7	0	0	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr19:49379135G>A	ENST00000200453.5	+	3	2199	c.1930G>A	c.(1930-1932)Gtc>Atc	p.V644I		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	644					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)		TTCGTCCCCAGTCCAGACCAC	0.672																																					p.V644I		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.G1930A						PASS	.						122	120	121					19																	49379135		2203	4300	6503	SO:0001583	missense	23645	exon3			TCCCCAGTCCAGA	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.1930G>A	chr19.hg19:g.49379135G>A	ENSP00000200453:p.Val644Ile	247.0	0.0	.		284.0	91.0	.	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Missense_Mutation	SNP	ENST00000200453.5	hg19	CCDS12738.1	.	.	.	.	.	.	.	.	.	.	G	7.302	0.613292	0.14066	.	.	ENSG00000087074	ENST00000200453;ENST00000540695;ENST00000544084	T	0.05081	3.5	2.9	-5.81	0.02340	.	2.513440	0.01909	N	0.039689	T	0.01905	0.0060	N	0.02916	-0.46	0.09310	N	1	B	0.22346	0.068	B	0.18263	0.021	T	0.35325	-0.9793	10	0.07030	T	0.85	0.3665	0.7652	0.01014	0.2207:0.1394:0.1939:0.446	.	644	O75807	PR15A_HUMAN	I	644;484;602	ENSP00000200453:V644I	ENSP00000200453:V644I	V	+	1	0	PPP1R15A	54070947	0.000000	0.05858	0.000000	0.03702	0.099000	0.18886	-0.505000	0.06367	-1.336000	0.02238	-0.274000	0.10170	GTC	.	.	.	none		0.672	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330		A	49379135	G	A	49379135	3	1	125	1	0	0	0	0	1	0	0	0	12373	1029	36	2	1936	2	PPP1R15A	19	49379135	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	34865688	49379135	9749848	66	7872											
ZNF773	374928	hgsc.bcm.edu	37	chr19	58018434	58018434	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctcatgaaacatcagagagTtcacactggagaaagacctt	15	8	8	10	0	3	4	3	1	0	3	3	6	3	4	2	1	1	1	2	1	2	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr19:58018434T>C	ENST00000282292.4	+	4	1111	c.971T>C	c.(970-972)gTt>gCt	p.V324A	ZNF773_ENST00000593916.1_Intron|ZNF773_ENST00000598770.1_Missense_Mutation_p.V323A|ZNF773_ENST00000599847.1_Intron	NM_198542.1	NP_940944.1	Q6PK81	ZN773_HUMAN	zinc finger protein 773	324					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(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	22		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;0.0254)		CATCAGAGAGTTCACACTGGA	0.428																																					p.V324A		Atlas-SNP	.											.	ZNF773	62	.	0			c.T971C						PASS	.						128	130	130					19																	58018434		2203	4300	6503	SO:0001583	missense	374928	exon4			AGAGAGTTCACAC	BC005167	CCDS33134.1	19q13.43	2013-01-08	2006-12-15	2006-12-15		ENSG00000152439		"Zinc fingers, C2H2-type", "-"	30487	protein-coding gene	gene with protein product			"zinc finger protein 419B"	ZNF419B		12477932	Standard	NM_198542		Approved	MGC4728	uc002qox.3	Q6PK81		ENST00000282292.4:c.971T>C	chr19.hg19:g.58018434T>C	ENSP00000282292:p.Val324Ala	219.0	0.0	.		200.0	47.0	.	NM_198542	Q96DL8	Missense_Mutation	SNP	ENST00000282292.4	hg19	CCDS33134.1	.	.	.	.	.	.	.	.	.	.	T	10.68	1.418764	0.25552	.	.	ENSG00000152439	ENST00000282292	T	0.00976	5.48	1.17	1.17	0.20885	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00906	0.0030	L	0.37850	1.14	0.09310	N	0.999999	P;B	0.39903	0.694;0.429	B;B	0.34652	0.133;0.187	T	0.51521	-0.8695	9	0.87932	D	0	.	5.4406	0.16507	0.0:0.0:0.2844:0.7155	.	323;324	Q6PK81-2;Q6PK81	.;ZN773_HUMAN	A	324	ENSP00000282292:V324A	ENSP00000282292:V324A	V	+	2	0	ZNF773	62710246	0.000000	0.05858	0.990000	0.47175	0.939000	0.58152	0.440000	0.21592	0.785000	0.33685	0.254000	0.18369	GTT	.	.	.	none		0.428	ZNF773-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466475.1	NM_198542		C	58018434	T	C	58018434	3	2	125	1	0	0	0	0	1	0	0	0	18158	1725	60	3	985	3	ZNF773	19	58018434	Missense_Mutation	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	8639299	58018434	1110549	67	7873											
PLCB1	23236	hgsc.bcm.edu	37	chr20	8741054	8741054	+	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	ttttatcttttatattacagGttctgtaaaggcacctgcca	10	17	6	8	0	2	0	0	0	2	0	2	0	2	0	2	2	2	3	2	2	6	8			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr20:8741054G>T	ENST00000338037.6	+	25	2684	c.2657G>T	c.(2656-2658)gGt>gTt	p.G886V	PLCB1_ENST00000378637.2_Splice_Site_p.G886V|PLCB1_ENST00000494924.1_3'UTR|PLCB1_ENST00000378641.3_Splice_Site_p.G886V	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	886					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						TATATTACAGGTTCTGTAAAG	0.348																																					p.Q886L		Atlas-SNP	.											.	PLCB1	394	.	0			c.A2657T						PASS	.						42	42	42					20																	8741054		2203	4300	6503	SO:0001630	splice_region_variant	23236	exon25			TTACAGGTTCTGT	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.2657-1G>T	chr20.hg19:g.8741054G>T		71.0	0.0	.		69.0	21.0	.	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Missense_Mutation	SNP	ENST00000338037.6	hg19	CCDS13102.1	.	.	.	.	.	.	.	.	.	.	G	17.99	3.522308	0.64747	.	.	ENSG00000182621	ENST00000378641;ENST00000338037;ENST00000378637;ENST00000441163;ENST00000535719	T;T;T	0.19250	2.17;2.16;2.17	6.07	6.07	0.98685	.	0.168672	0.52532	D	0.000067	T	0.39384	0.1076	L	0.44542	1.39	0.80722	D	1	D;D	0.65815	0.988;0.995	P;D	0.63113	0.676;0.911	T	0.00559	-1.1671	9	.	.	.	.	20.6593	0.99626	0.0:0.0:1.0:0.0	.	886;886	Q9NQ66;Q9NQ66-2	PLCB1_HUMAN;.	V	886;886;886;806;806	ENSP00000367908:G886V;ENSP00000338185:G886V;ENSP00000367904:G886V	.	G	+	2	0	PLCB1	8689054	1.000000	0.71417	0.996000	0.52242	0.929000	0.56500	8.960000	0.93117	2.885000	0.99019	0.655000	0.94253	GGT	.	.	.	none		0.348	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3		Missense_Mutation	T	8741054	G	T	8741054	5	4	125	1	0	0	0	0	0	0	1	0	12034	1275	44	4	2755	4	PLCB1	20	8741054	Splice_Site	SNP	G	TCGA-BQ-5890-01A-11D-1589-08		8741054	54284466	68	7874											
KCNS1	3787	hgsc.bcm.edu	37	chr20	43726464	43726464	+	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	accagccagcagcgtgagatAgaagggcagcacagacacaa	16	2	12	11	1	0	3	0	1	0	3	0	4	0	3	2	1	4	3	2	1	3	1			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr20:43726464A>T	ENST00000306117.1	-	4	1345	c.949T>A	c.(949-951)Tat>Aat	p.Y317N	KCNS1_ENST00000537075.1_Missense_Mutation_p.Y317N	NM_002251.3	NP_002242.2	Q96KK3	KCNS1_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 1	317					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)			endometrium(1)|lung(3)|ovary(1)|stomach(1)	6		Myeloproliferative disorder(115;0.0122)				AGCGTGAGATAGAAGGGCAGC	0.632																																					p.Y317N		Atlas-SNP	.											.	KCNS1	30	.	0			c.T949A						PASS	.						74	57	62					20																	43726464		2203	4300	6503	SO:0001583	missense	3787	exon4			TGAGATAGAAGGG	AF043473	CCDS13342.1	20q12	2011-07-05			ENSG00000124134	ENSG00000124134		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6300	protein-coding gene	gene with protein product		602905				9305895, 16382104	Standard	NM_002251		Approved	Kv9.1	uc002xnc.3	Q96KK3	OTTHUMG00000033079	ENST00000306117.1:c.949T>A	chr20.hg19:g.43726464A>T	ENSP00000307694:p.Tyr317Asn	32.0	0.0	.		29.0	16.0	.	NM_002251	A2RUL9|B7ZM31|O43652|Q6DJU6	Missense_Mutation	SNP	ENST00000306117.1	hg19	CCDS13342.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.403414	0.83230	.	.	ENSG00000124134	ENST00000306117;ENST00000537075	D;D	0.98701	-5.08;-5.08	5.31	5.31	0.75309	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99336	0.9767	M	0.93283	3.4	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98784	1.0733	10	0.87932	D	0	.	15.2726	0.73717	1.0:0.0:0.0:0.0	.	317	Q96KK3	KCNS1_HUMAN	N	317	ENSP00000307694:Y317N;ENSP00000445595:Y317N	ENSP00000307694:Y317N	Y	-	1	0	KCNS1	43159878	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.220000	0.95180	2.015000	0.59207	0.459000	0.35465	TAT	.	.	.	none		0.632	KCNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080507.3	NM_002251		T	43726464	A	T	43726464	3	4	125	1	0	0	0	0	1	0	0	0	8095	420	15	5	639	5	KCNS1	20	43726464	Missense_Mutation	SNP	A	TCGA-BQ-5890-01A-11D-1589-08	34985410	43726464	19299056	69	7875											
WFDC2	10406	hgsc.bcm.edu	37	chr20	44108666	44108666	+	Missense_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	gtgccaggtggacagccagtGtcctggccagatgaaatgct	9	8	14	10	0	0	2	0	1	0	1	1	3	1	3	4	3	3	1	4	3	1	0			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr20:44108666G>A	ENST00000372676.3	+	3	384	c.308G>A	c.(307-309)tGt>tAt	p.C103Y	WFDC2_ENST00000342873.3_Missense_Mutation_p.C52Y|WFDC2_ENST00000339946.3_Missense_Mutation_p.C55Y|WFDC2_ENST00000488143.1_3'UTR|AL031663.1_ENST00000599747.1_5'Flank	NM_006103.3	NP_006094.3	Q14508	WFDC2_HUMAN	WAP four-disulfide core domain 2	103	WAP 2. {ECO:0000255|PROSITE- ProRule:PRU00722}.				negative regulation of endopeptidase activity (GO:0010951)|proteolysis (GO:0006508)|spermatogenesis (GO:0007283)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	aspartic-type endopeptidase inhibitor activity (GO:0019828)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			lung(1)	1		Myeloproliferative disorder(115;0.0122)				GACAGCCAGTGTCCTGGCCAG	0.537																																					p.C103Y		Atlas-SNP	.											.	WFDC2	8	.	0			c.G308A						PASS	.						107	112	110					20																	44108666		2203	4300	6503	SO:0001583	missense	10406	exon3			GCCAGTGTCCTGG	X63187	CCDS35501.1	20q13.12	2013-01-21			ENSG00000101443	ENSG00000101443		"WAP four-disulfide core domain containing"	15939	protein-coding gene	gene with protein product	"epididymal protein 4"					1686187, 10570965	Standard	NM_006103		Approved	HE4, WAP5, dJ461P17.6, EDDM4	uc002xoo.3	Q14508	OTTHUMG00000032594	ENST00000372676.3:c.308G>A	chr20.hg19:g.44108666G>A	ENSP00000361761:p.Cys103Tyr	217.0	0.0	.		181.0	74.0	.	NM_006103	A2A2A5|A2A2A6|A6PVD5|Q6IB27|Q8WXV9|Q8WXW0|Q8WXW1|Q8WXW2|Q96KJ1	Missense_Mutation	SNP	ENST00000372676.3	hg19	CCDS35501.1	.	.	.	.	.	.	.	.	.	.	G	14.72	2.620538	0.46736	.	.	ENSG00000101443	ENST00000372676;ENST00000339946;ENST00000342873	D;D;D	0.99239	-5.61;-5.61;-5.61	5.26	5.26	0.73747	Whey acidic protein, 4-disulphide core (5);	0.000000	0.64402	D	0.000017	D	0.99670	0.9877	H	0.98276	4.19	0.43947	D	0.996613	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.97440	1.0021	10	0.87932	D	0	-13.7907	14.7141	0.69254	0.0:0.0:1.0:0.0	.	52;55;103	Q14508-2;Q14508-3;Q14508	.;.;WFDC2_HUMAN	Y	103;55;52	ENSP00000361761:C103Y;ENSP00000340215:C55Y;ENSP00000342890:C52Y	ENSP00000340215:C55Y	C	+	2	0	WFDC2	43542080	0.997000	0.39634	0.953000	0.39169	0.096000	0.18686	3.179000	0.50887	2.598000	0.87819	0.655000	0.94253	TGT	.	.	.	none		0.537	WFDC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079476.3			A	44108666	G	A	44108666	3	1	125	1	0	0	0	0	1	0	0	0	17364	1377	48	2	318	2	WFDC2	20	44108666	Missense_Mutation	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	382202	44108666	18916854	70	7876											
DNTTIP1	116092	hgsc.bcm.edu	37	chr20	44424050	44424050	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtggacgcagagcagctgAtccaggaagcctgtcggagc	10	5	16	10	2	0	2	0	1	0	1	2	5	1	5	2	4	4	3	2	4	1	0			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr20:44424050A>G	ENST00000372622.3	+	4	408	c.340A>G	c.(340-342)Atc>Gtc	p.I114V		NM_052951.2	NP_443183.1	Q9H147	TDIF1_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 1	114						nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)	9		Myeloproliferative disorder(115;0.0122)				AGAGCAGCTGATCCAGGAAGC	0.557																																					p.I114V		Atlas-SNP	.											.	DNTTIP1	23	.	0			c.A340G						PASS	.						48	32	38					20																	44424050		2203	4300	6503	SO:0001583	missense	116092	exon4			CAGCTGATCCAGG	AB035676	CCDS13369.1	20q13.12	2003-09-10	2003-09-10	2003-09-12	ENSG00000101457	ENSG00000101457			16160	protein-coding gene	gene with protein product	"novel protein similar to synaptotagmin 1 (SYT1, P65) (isoform 1)", "TdT binding protein"	611388	"chromosome 20 open reading frame 167"	C20orf167		11473582	Standard	NM_052951		Approved	dJ447F3.4, Tdif1	uc002xpk.3	Q9H147	OTTHUMG00000032610	ENST00000372622.3:c.340A>G	chr20.hg19:g.44424050A>G	ENSP00000361705:p.Ile114Val	29.0	0.0	.		18.0	7.0	.	NM_052951	B2RA18|Q96DE3|Q9BQP2|Q9H148	Missense_Mutation	SNP	ENST00000372622.3	hg19	CCDS13369.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	17.46|17.46	3.396221|3.396221	0.62177|0.62177	.|.	.|.	ENSG00000101457|ENSG00000101457	ENST00000372622;ENST00000449078;ENST00000415790|ENST00000435014	T;T|.	0.48201|.	0.92;0.82|.	5.47|5.47	5.47|5.47	0.80525|0.80525	.|.	0.045638|.	0.85682|.	D|.	0.000000|.	T|.	0.60715|.	0.2290|.	L|L	0.42686|0.42686	1.345|1.345	0.44711|0.44711	D|D	0.997702|0.997702	B|.	0.28850|.	0.225|.	B|.	0.30316|.	0.114|.	T|.	0.57551|.	-0.7792|.	10|.	0.35671|.	T|.	0.21|.	-18.7653|-18.7653	14.5366|14.5366	0.67966|0.67966	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	114|.	Q9H147|.	TDIF1_HUMAN|.	V|W	114;109;74|40	ENSP00000361705:I114V;ENSP00000392509:I74V|.	ENSP00000361705:I114V|.	I|X	+|+	1|3	0|0	DNTTIP1|DNTTIP1	43857457|43857457	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.264000|7.264000	0.78432|0.78432	2.304000|2.304000	0.77564|0.77564	0.524000|0.524000	0.50904|0.50904	ATC|TGA	.	.	.	none		0.557	DNTTIP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079502.1	NM_052951		G	44424050	A	G	44424050	3	3	125	1	0	0	0	0	1	0	0	0	4683	333	12	3	354	3	DNTTIP1	20	44424050	Missense_Mutation	SNP	A	TCGA-BQ-5890-01A-11D-1589-08	315384	44424050	18601470	71	7877											
PSMA7	5688	hgsc.bcm.edu	37	chr20	60714841	60714841	+	Missense_Mutation	SNP	T	T	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	gcgggcaggcacccacctgcTtcagactggcgatgtagcgg	7	6	15	13	3	1	1	1	0	0	1	1	2	1	1	2	4	2	4	2	4	1	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr20:60714841T>G	ENST00000370873.4	-	3	470	c.344A>C	c.(343-345)aAg>aCg	p.K115T	PSMA7_ENST00000484488.1_5'UTR|PSMA7_ENST00000370858.3_Missense_Mutation_p.K115T|PSMA7_ENST00000370861.1_Missense_Mutation_p.K45T	NM_002792.3	NP_002783.1	O14818	PSA7_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 7	115					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	identical protein binding (GO:0042802)|threonine-type endopeptidase activity (GO:0004298)			large_intestine(1)|lung(2)	3	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.28e-07)			ACCCACCTGCTTCAGACTGGC	0.617																																					p.K115T		Atlas-SNP	.											.	PSMA7	13	.	0			c.A344C						PASS	.						67	55	59					20																	60714841		2203	4300	6503	SO:0001583	missense	5688	exon3			ACCTGCTTCAGAC	AF022815	CCDS13489.1	20q13.33	2008-07-02			ENSG00000101182	ENSG00000101182		"Proteasome (prosome, macropain) subunits"	9536	protein-coding gene	gene with protein product	"proteasome subunit XAPC7", "proteasome subunit RC6-1"	606607				8764072	Standard	NM_002792		Approved	XAPC7, C6, HSPC, RC6-1	uc002ybx.2	O14818	OTTHUMG00000032895	ENST00000370873.4:c.344A>C	chr20.hg19:g.60714841T>G	ENSP00000359910:p.Lys115Thr	59.0	0.0	.		64.0	21.0	.	NM_002792	B2R515|Q5JXJ2|Q9BR53|Q9H4K5|Q9UEU8	Missense_Mutation	SNP	ENST00000370873.4	hg19	CCDS13489.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	19.47|19.47	3.834596|3.834596	0.71373|0.71373	.|.	.|.	ENSG00000101182|ENSG00000101182	ENST00000370873;ENST00000370861;ENST00000370858|ENST00000442551	T;T;T|.	0.21191|.	2.02;2.02;2.02|.	4.96|4.96	4.96|4.96	0.65561|0.65561	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.80110|0.80110	0.4563|0.4563	M|M	0.88512|0.88512	2.96|2.96	0.80722|0.80722	D|D	1|1	P|.	0.46578|.	0.88|.	P|.	0.55391|.	0.775|.	D|D	0.83890|0.83890	0.0284|0.0284	10|5	0.87932|.	D|.	0|.	.|.	14.9125|14.9125	0.70770|0.70770	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	115|.	O14818|.	PSA7_HUMAN|.	T|R	115;45;115|41	ENSP00000359910:K115T;ENSP00000359898:K45T;ENSP00000359895:K115T|.	ENSP00000359895:K115T|.	K|S	-|-	2|1	0|0	PSMA7|PSMA7	60148236|60148236	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.264000|0.264000	0.26372|0.26372	7.469000|7.469000	0.80959|0.80959	1.974000|1.974000	0.57490|0.57490	0.460000|0.460000	0.39030|0.39030	AAG|AGC	.	.	.	none		0.617	PSMA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079975.1	NM_002792		G	60714841	T	G	60714841	3	3	125	1	0	0	0	0	1	0	0	0	12682	1609	56	5	422	5	PSMA7	20	60714841	Missense_Mutation	SNP	T	TCGA-BQ-5890-01A-11D-1589-08	16290791	60714841	2310679	72	7878											
PRPF6	57473	hgsc.bcm.edu	37	chr20	62642772	62642772	+	Intron	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	gaggaagccaatgggaacacGcagatggtggagaagatcat	15	5	15	6	1	1	3	1	0	0	3	1	7	1	5	1	4	2	1	1	4	4	0	rs199552405		TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr20:62642772G>C	ENST00000450537.1	-	1	56				ZNF512B_ENST00000217130.3_Intron|PRPF6_ENST00000535781.1_Silent_p.T480T			Q96KM6	Z512B_HUMAN	zinc finger protein 512B						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					ATGGGAACACGCAGATGGTGG	0.587																																					p.T480T		Atlas-SNP	.											.	PRPF6	88	.	0			c.G1440C						PASS	.						94	77	83					20																	62642772		2203	4300	6503	SO:0001627	intron_variant	24148	exon11			GAACACGCAGATG	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.4+37285C>G	chr20.hg19:g.62642772G>C		52.0	0.0	.		46.0	12.0	.	NM_012469	Q08AK9|Q9ULM4	Silent	SNP	ENST00000450537.1	hg19	CCDS13548.1																																																																																			.	G|1.000;A|0.000	.	alt		0.587	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713		C	62642772	G	C	62642772	1	2	125	0	1	0	0	0	0	0	0	0	12584	1074	38	4		4	PRPF6	20	62642772	Intron	SNP	G	TCGA-BQ-5890-01A-11D-1589-08	1927931	62642772	382748	73	7879											
SON	6651	hgsc.bcm.edu	37	chr21	34925625	34925625	+	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	tatggctgtcctggagtcttCggctgtgaccgtcctggagt	4	13	14	10	2	1	1	0	1	1	0	4	3	3	3	3	4	0	2	3	4	1	2			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chr21:34925625C>T	ENST00000356577.4	+	3	4563	c.4088C>T	c.(4087-4089)tCg>tTg	p.S1363L	SON_ENST00000290239.6_Missense_Mutation_p.S1363L|SON_ENST00000300278.4_Missense_Mutation_p.S1363L|SON_ENST00000381692.2_Intron|SON_ENST00000381679.4_Missense_Mutation_p.S1363L	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	1363	4 X 8 AA tandem repeats of V-L-E-SS- [AVT]-VT.				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						CTGGAGTCTTCGGCTGTGACC	0.577																																					p.S1363L		Atlas-SNP	.											.	SON	343	.	0			c.C4088T						PASS	.						52	45	48					21																	34925625		2203	4300	6503	SO:0001583	missense	6651	exon3			AGTCTTCGGCTGT	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.4088C>T	chr21.hg19:g.34925625C>T	ENSP00000348984:p.Ser1363Leu	54.0	0.0	.		68.0	17.0	.	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	hg19	CCDS13629.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.86|11.86	1.765064|1.765064	0.31228|0.31228	.|.	.|.	ENSG00000159140|ENSG00000159140	ENST00000436227|ENST00000356577;ENST00000290239;ENST00000300278;ENST00000381679	.|T;T;T;T	.|0.11930	.|2.93;2.93;2.92;2.73	5.08|5.08	4.2|4.2	0.49525|0.49525	.|.	.|0.972270	.|0.08431	.|N	.|0.946875	T|T	0.10035|0.10035	0.0246|0.0246	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	.|B;B;B;B;B	.|0.20780	.|0.048;0.004;0.019;0.007;0.019	.|B;B;B;B;B	.|0.09377	.|0.004;0.001;0.004;0.004;0.004	T|T	0.26360|0.26360	-1.0105|-1.0105	5|10	.|0.36615	.|T	.|0.2	.|.	9.0913|9.0913	0.36612|0.36612	0.0:0.9012:0.0:0.0988|0.0:0.9012:0.0:0.0988	.|.	.|1363;1363;1044;1363;1363	.|P18583-10;P18583;P18583-2;P18583-3;P18583-6	.|.;SON_HUMAN;.;.;.	W|L	358|1363	.|ENSP00000348984:S1363L;ENSP00000290239:S1363L;ENSP00000300278:S1363L;ENSP00000371095:S1363L	.|ENSP00000290239:S1363L	R|S	+|+	1|2	2|0	SON|SON	33847495|33847495	0.001000|0.001000	0.12720|0.12720	0.002000|0.002000	0.10522|0.10522	0.011000|0.011000	0.07611|0.07611	0.354000|0.354000	0.20146|0.20146	1.362000|1.362000	0.46000|0.46000	0.514000|0.514000	0.50259|0.50259	CGG|TCG	.	.	.	none		0.577	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		T	34925625	C	T	34925625	3	4	125	1	0	0	0	0	1	0	0	0	14939	893	31	1	4098	1	SON	21	34925625	Missense_Mutation	SNP	C	TCGA-BQ-5890-01A-11D-1589-08		34925625	13204270	74	7880											
STAG2	10735	hgsc.bcm.edu	37	chrX	123200037	123200037	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttacagtgcccatgacctTtcaaagtgggatttatttgc	9	16	8	8	0	1	1	1	1	0	0	1	2	1	2	2	1	3	0	2	1	3	6			TCGA-BQ-5890-01A-11D-1589-08	TCGA-BQ-5890-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6938c32-20f1-4d04-9939-0c3d217b7c81	7d6403bb-f48a-43e1-9a32-feb3bb9de789	g.chrX:123200037T>C	ENST00000371160.1	+	22	2399	c.2109T>C	c.(2107-2109)ctT>ctC	p.L703L	STAG2_ENST00000371144.3_Silent_p.L703L|STAG2_ENST00000371157.3_Silent_p.L703L|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Silent_p.L703L|STAG2_ENST00000354548.5_Silent_p.L634L|STAG2_ENST00000371145.3_Silent_p.L703L	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	703					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						CCCATGACCTTTCAAAGTGGG	0.294																																					p.L703L		Atlas-SNP	.											.	STAG2	309	.	0			c.T2109C						PASS	.						60	61	61					X																	123200037		2202	4298	6500	SO:0001819	synonymous_variant	10735	exon22			TGACCTTTCAAAG	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.2109T>C	chrX.hg19:g.123200037T>C		76.0	0.0	.		65.0	44.0	.	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Silent	SNP	ENST00000371160.1	hg19	CCDS14607.1																																																																																			.	.	.	none		0.294	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		C	123200037	T	C	123200037	2	2	125	1	0	0	0	0	0	0	0	1	15255	1828	64	3		3	STAG2	23	123200037	Silent	SNP	T	TCGA-BQ-5890-01A-11D-1589-08		123200037	32070523	75	7881											
XPO1	7514	hgsc.bcm.edu	37	chr2	61709536	61709536	+	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	cttgtaggtgagggaaggccGacttaaggagattagccaca	12	8	14	7	1	0	2	0	1	0	1	0	5	0	3	2	4	1	1	2	4	4	4			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr2:61709536G>A	ENST00000401558.2	-	23	3678	c.2951C>T	c.(2950-2952)tCg>tTg	p.S984L	XPO1_ENST00000404992.2_Missense_Mutation_p.S984L|RP11-355B11.2_ENST00000603028.1_RNA|RP11-355B11.2_ENST00000578974.2_RNA|XPO1_ENST00000406957.1_Missense_Mutation_p.S984L|RP11-355B11.2_ENST00000603652.1_RNA|RP11-355B11.2_ENST00000605437.1_RNA|RP11-355B11.2_ENST00000603199.1_RNA	NM_003400.3	NP_003391.1	O14980	XPO1_HUMAN	exportin 1	984					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)			AGGGAAGGCCGACTTAAGGAG	0.398			Mis		CLL																																p.S984L		Atlas-SNP	.	-'	Dom	yes		2	2p15	7514	"exportin 1 (CRM1 homolog, yeast)"		L	.	XPO1	108	.	0			c.C2951T						PASS	.						129	130	129					2																	61709536		2203	4300	6503	SO:0001583	missense	7514	exon23			AAGGCCGACTTAA	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.2951C>T	chr2.hg19:g.61709536G>A	ENSP00000384863:p.Ser984Leu	156.0	0.0	.		128.0	12.0	.	NM_003400	A6NL14|A8K1K5|D6W5E2|Q63HP8|Q68CP3|Q99433	Missense_Mutation	SNP	ENST00000401558.2	hg19	CCDS33205.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.953001	0.73902	.	.	ENSG00000082898	ENST00000401558;ENST00000404992;ENST00000406957	T;T;T	0.68025	-0.3;-0.3;-0.3	5.46	5.46	0.80206	Armadillo-like helical (1);Armadillo-type fold (2);Exportin 1, C-terminal (1);	0.055426	0.85682	D	0.000000	T	0.68366	0.2993	M	0.75615	2.305	0.58432	D	0.999998	B;B	0.31752	0.338;0.233	B;B	0.24848	0.034;0.056	T	0.70883	-0.4751	10	0.66056	D	0.02	-16.6961	19.6691	0.95903	0.0:0.0:1.0:0.0	.	631;984	B3KWD0;O14980	.;XPO1_HUMAN	L	984	ENSP00000384863:S984L;ENSP00000385942:S984L;ENSP00000385559:S984L	ENSP00000384863:S984L	S	-	2	0	XPO1	61563040	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.529000	0.81952	2.721000	0.93114	0.591000	0.81541	TCG	.	.	.	none		0.398	XPO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325872.3	NM_003400		A	61709536	G	A	61709536	3	1	126	1	0	0	0	0	1	0	0	0	17457	1059	37	1	276	1	XPO1	2	61709536	Missense_Mutation	SNP	G	TCGA-BQ-5891-01A-11D-1589-08		61709536	181489837	1	7882											
LRP1B	53353	hgsc.bcm.edu	37	chr2	141643776	141643776	+	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	tgtccaataaagtaaactttGattgaagtgaaaatcaagtg	17	12	8	4	0	1	3	1	3	0	0	2	3	2	3	1	0	1	1	1	0	9	4			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr2:141643776G>C	ENST00000389484.3	-	24	4866	c.3895C>G	c.(3895-3897)Caa>Gaa	p.Q1299E		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1299					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)	p.Q1299K(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		AGTAAACTTTGATTGAAGTGA	0.328										TSP Lung(27;0.18)																											p.Q1299E	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											LRP1B,NS,carcinoma,0,1	LRP1B	1315	.	1	Substitution - Missense(1)	endometrium(1)	c.C3895G						PASS	.						77	79	78					2																	141643776		2202	4299	6501	SO:0001583	missense	53353	exon24			AACTTTGATTGAA	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.3895C>G	chr2.hg19:g.141643776G>C	ENSP00000374135:p.Gln1299Glu	97.0	0.0	.		97.0	80.0	.	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	G	16.51	3.144239	0.57044	.	.	ENSG00000168702	ENST00000389484;ENST00000544579;ENST00000434794	D;D	0.90620	-2.7;-2.7	5.68	5.68	0.88126	Six-bladed beta-propeller, TolB-like (1);	0.140025	0.48767	D	0.000173	T	0.81597	0.4856	N	0.13043	0.29	0.42707	D	0.993639	B;B	0.34015	0.009;0.435	B;B	0.24974	0.009;0.057	T	0.79825	-0.1640	10	0.12430	T	0.62	.	19.7974	0.96491	0.0:0.0:1.0:0.0	.	482;1299	Q96NT6;Q9NZR2	.;LRP1B_HUMAN	E	1299;1237;444	ENSP00000374135:Q1299E;ENSP00000413239:Q444E	ENSP00000374135:Q1299E	Q	-	1	0	LRP1B	141360246	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.640000	0.98453	2.673000	0.90976	0.650000	0.86243	CAA	.	.	.	none		0.328	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		C	141643776	G	C	141643776	3	2	126	1	0	0	0	0	1	0	0	0	8962	1299	45	4	10176	4	LRP1B	2	141643776	Missense_Mutation	SNP	G	TCGA-BQ-5891-01A-11D-1589-08	79934240	141643776	101555597	2	7883											
SETD2	29072	hgsc.bcm.edu	37	chr3	47162849	47162850	+	Frame_Shift_Del	DEL	TT	TT	-																															gtcagaatagtgtctataacTttgactgctccgagaagaac																								rs114327122		TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr3:47162849_47162850delTT	ENST00000409792.3	-	3	3318_3319	c.3276_3277delAA	c.(3274-3279)caaagtfs	p.S1093fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1093					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.S1093R(1)|p.S590R(1)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TGTCTATAACTTTGACTGCTCC	0.416			"N, F, S, Mis"		clear cell renal carcinoma																																p.1093_1093del		Atlas-INDEL	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	2	Substitution - Missense(2)	large_intestine(2)	c.3277_3278del						PASS	.																																			SO:0001589	frameshift_variant	29072	exon3			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.3276_3277delAA	chr3.hg19:g.47162849_47162850delTT	ENSP00000386759:p.Ser1093fs	167.0	0.0	0		141.0	121.0	0.858156	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Del	DEL	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.	.	none		0.416	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		-	47162850	TT	-	47162849	7	5	126	1	0	1	0	1	0	0	0	0	14144	1609	56	0	4493	0	SETD2	3	47162849	Frame_Shift_Del	DEL	TT	TCGA-BQ-5891-01A-11D-1589-08		47162849	150859581	3	7884											
IQCF2	389123	hgsc.bcm.edu	37	chr3	51897176	51897176	+	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	cggcaggcagctctgatcgcCtacgcaaccagagagagggc	10	4	14	13	3	1	3	0	1	1	2	2	4	1	3	2	3	3	4	2	3	2	1			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr3:51897176C>A	ENST00000333127.3	+	3	314	c.285C>A	c.(283-285)gcC>gcA	p.A95A	IQCF2_ENST00000429548.1_3'UTR	NM_203424.1	NP_982248.1	Q8IXL9	IQCF2_HUMAN	IQ motif containing F2	95										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)		CTCTGATCGCCTACGCAACCA	0.582																																					p.A95A		Atlas-SNP	.											.	IQCF2	21	.	0			c.C285A						PASS	.						118	114	115					3																	51897176		2203	4300	6503	SO:0001819	synonymous_variant	389123	exon3			GATCGCCTACGCA	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.285C>A	chr3.hg19:g.51897176C>A		89.0	0.0	.		92.0	4.0	.	NM_203424		Silent	SNP	ENST00000333127.3	hg19	CCDS2835.1																																																																																			.	.	.	none		0.582	IQCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346594.1	NM_203424		A	51897176	C	A	51897176	2	1	126	1	0	0	0	0	0	0	0	1	7815	668	24	4		4	IQCF2	3	51897176	Silent	SNP	C	TCGA-BQ-5891-01A-11D-1589-08	4734327	51897176	146125254	4	7885											
ACTL6A	86	hgsc.bcm.edu	37	chr3	179304341	179304341	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcttctatttcagagtatgcGgttgaaattgattgcaaata	12	16	8	5	1	3	3	1	2	2	1	3	3	3	3	0	1	2	3	0	1	5	8			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr3:179304341G>A	ENST00000429709.2	+	13	1343	c.1130G>A	c.(1129-1131)cGg>cAg	p.R377Q	RP11-15L13.4_ENST00000608818.1_RNA|RP11-145M9.6_ENST00000610007.1_RNA|ACTL6A_ENST00000392662.1_Missense_Mutation_p.R335Q|ACTL6A_ENST00000450518.2_Missense_Mutation_p.R335Q	NM_004301.3	NP_004292.1	O96019	ACL6A_HUMAN	actin-like 6A	377					ATP-dependent chromatin remodeling (GO:0043044)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|nervous system development (GO:0007399)|neural retina development (GO:0003407)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|npBAF complex (GO:0071564)|NuA4 histone acetyltransferase complex (GO:0035267)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|urinary_tract(1)	21	all_cancers(143;3.94e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)			CAGAGTATGCGGTTGAAATTG	0.348																																					p.R377Q		Atlas-SNP	.											.	ACTL6A	43	.	0			c.G1130A						PASS	.						88	88	88					3																	179304341		2203	4300	6503	SO:0001583	missense	86	exon13			GTATGCGGTTGAA	AK098691	CCDS3231.1, CCDS43174.1	3q26.33	2011-07-06			ENSG00000136518	ENSG00000136518		"INO80 complex subunits"	24124	protein-coding gene	gene with protein product	"BAF complex 53 kDa subunit", "BRG1-associated factor", "actin-related protein 4", "INO80 complex subunit K"	604958				9845365, 10380635	Standard	NM_004301		Approved	Actl6, BAF53A, Arp4, Baf53a, INO80K	uc003fjw.3	O96019	OTTHUMG00000157782	ENST00000429709.2:c.1130G>A	chr3.hg19:g.179304341G>A	ENSP00000397552:p.Arg377Gln	75.0	0.0	.		61.0	53.0	.	NM_004301	B3KMN1|D3DNR9|Q8TAE5|Q9BVS8|Q9H0W6	Missense_Mutation	SNP	ENST00000429709.2	hg19	CCDS3231.1	.	.	.	.	.	.	.	.	.	.	G	32	5.140591	0.94560	.	.	ENSG00000136518	ENST00000429709;ENST00000450518;ENST00000392662	D;D;D	0.94687	-3.49;-3.49;-3.49	5.91	4.07	0.47477	.	0.049963	0.85682	D	0.000000	D	0.95984	0.8692	L	0.59436	1.845	0.58432	D	0.999997	D	0.76494	0.999	D	0.64321	0.924	D	0.95826	0.8854	10	0.87932	D	0	.	15.2754	0.73737	0.0:0.0:0.7438:0.2562	.	377	O96019	ACL6A_HUMAN	Q	377;335;335	ENSP00000397552:R377Q;ENSP00000394014:R335Q;ENSP00000376430:R335Q	ENSP00000376430:R335Q	R	+	2	0	ACTL6A	180787035	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.371000	0.97162	0.789000	0.33779	0.655000	0.94253	CGG	.	.	.	none		0.348	ACTL6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349599.1	NM_004301		A	179304341	G	A	179304341	3	1	126	1	0	0	0	0	1	0	0	0	198	1116	39	1	1180	1	ACTL6A	3	179304341	Missense_Mutation	SNP	G	TCGA-BQ-5891-01A-11D-1589-08	127407165	179304341	18718089	5	7886											
KLHL3	26249	hgsc.bcm.edu	37	chr5	136963990	136963990	+	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	agagagcagtcattacctgcGttgcgccggcacatgttcat	9	10	11	11	3	2	1	2	0	0	1	2	2	2	1	2	1	4	4	2	1	1	3	rs562736621		TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr5:136963990G>A	ENST00000309755.4	-	13	2030	c.1587C>T	c.(1585-1587)aaC>aaT	p.N529N	KLHL3_ENST00000541417.1_3'UTR|KLHL3_ENST00000508657.1_Silent_p.N497N|KLHL3_ENST00000506491.1_Silent_p.N447N|KLHL3_ENST00000506873.1_5'UTR	NM_017415.2	NP_059111.2	Q9UH77	KLHL3_HUMAN	kelch-like family member 3	529			N -> K (in PHA2D; impaired interaction with WNK1). {ECO:0000269|PubMed:22406640}.		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)		CATTACCTGCGTTGCGCCGGC	0.537																																					p.N529N		Atlas-SNP	.											.	KLHL3	54	.	0			c.C1587T						PASS	.						219	189	199					5																	136963990		2203	4300	6503	SO:0001819	synonymous_variant	26249	exon13			ACCTGCGTTGCGC	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.1587C>T	chr5.hg19:g.136963990G>A		145.0	0.0	.		260.0	90.0	.	NM_017415	B2RBK7|Q9UH75|Q9UH76|Q9ULU0|Q9Y6V6	Silent	SNP	ENST00000309755.4	hg19	CCDS4192.1																																																																																			.	.	.	none		0.537	KLHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251220.2			A	136963990	G	A	136963990	2	1	126	1	0	0	0	0	0	0	0	1	8390	1136	40	1		1	KLHL3	5	136963990	Silent	SNP	G	TCGA-BQ-5891-01A-11D-1589-08		136963990	43951270	6	7887											
PCDHGA1	56114	hgsc.bcm.edu	37	chr5	140711928	140711928	+	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	ctggaccagaacgacaacgcGcccgagatcctgtaccccgc	10	4	10	17	5	0	2	0	0	0	2	1	5	1	3	5	1	3	1	5	1	3	1			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr5:140711928G>A	ENST00000517417.1	+	1	1677	c.1677G>A	c.(1675-1677)gcG>gcA	p.A559A	PCDHGA1_ENST00000378105.3_Silent_p.A559A	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)			ACGACAACGCGCCCGAGATCC	0.647																																					p.A559A		Atlas-SNP	.											.	PCDHGA1	397	.	0			c.G1677A						PASS	.						130	144	140					5																	140711928		2203	4300	6503	SO:0001819	synonymous_variant	56114	exon1			CAACGCGCCCGAG	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.1677G>A	chr5.hg19:g.140711928G>A		320.0	0.0	.		431.0	204.0	.	NM_018912	Q2M273|Q9Y5D6	Silent	SNP	ENST00000517417.1	hg19	CCDS54922.1																																																																																			.	.	.	none		0.647	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		A	140711928	G	A	140711928	2	1	126	1	0	0	0	0	0	0	0	1	11557	1074	38	1		1	PCDHGA1	5	140711928	Silent	SNP	G	TCGA-BQ-5891-01A-11D-1589-08	3747938	140711928	40203332	7	7888											
DRD1	1812	hgsc.bcm.edu	37	chr5	174870046	174870046	+	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	gtgaggatacgaacagagaaGtccctctccaccaccagccc	12	5	9	15	1	1	2	0	1	1	1	3	5	2	3	5	1	3	0	5	1	3	1			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr5:174870046G>A	ENST00000393752.2	-	2	1049	c.57C>T	c.(55-57)gaC>gaT	p.D19D		NM_000794.3	NP_000785.1	P21728	DRD1_HUMAN	dopamine receptor D1	19					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adult walking behavior (GO:0007628)|astrocyte development (GO:0014002)|behavioral fear response (GO:0001662)|behavioral response to cocaine (GO:0048148)|cellular response to catecholamine stimulus (GO:0071870)|cerebral cortex GABAergic interneuron migration (GO:0021853)|conditioned taste aversion (GO:0001661)|dentate gyrus development (GO:0021542)|dopamine metabolic process (GO:0042417)|dopamine transport (GO:0015872)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose import (GO:0046323)|grooming behavior (GO:0007625)|habituation (GO:0046959)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|maternal behavior (GO:0042711)|mating behavior (GO:0007617)|memory (GO:0007613)|neuronal action potential (GO:0019228)|operant conditioning (GO:0035106)|peristalsis (GO:0030432)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell migration (GO:0030335)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of potassium ion transport (GO:0043268)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|prepulse inhibition (GO:0060134)|protein import into nucleus (GO:0006606)|regulation of dopamine metabolic process (GO:0042053)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|sensitization (GO:0046960)|striatum development (GO:0021756)|synapse assembly (GO:0007416)|synaptic transmission, dopaminergic (GO:0001963)|temperature homeostasis (GO:0001659)|transmission of nerve impulse (GO:0019226)|vasodilation (GO:0042311)|visual learning (GO:0008542)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	23	all_cancers(89;0.00895)|Renal(175;0.000159)|Lung NSC(126;0.00625)|all_lung(126;0.0104)	Medulloblastoma(196;0.0208)|all_neural(177;0.0277)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)		Acepromazine(DB01614)|Acetophenazine(DB01063)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Dopamine(DB00988)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Methylergometrine(DB00353)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Phenylpropanolamine(DB00397)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Promazine(DB00420)|Propericiazine(DB01608)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Triflupromazine(DB00508)|Trimipramine(DB00726)|Ziprasidone(DB00246)	GAACAGAGAAGTCCCTCTCCA	0.572																																					p.D19D		Atlas-SNP	.											.	DRD1	56	.	0			c.C57T						PASS	.						106	108	107					5																	174870046		2203	4300	6503	SO:0001819	synonymous_variant	1812	exon2			AGAGAAGTCCCTC	X55760	CCDS4393.1	5q34-q35	2012-08-08			ENSG00000184845	ENSG00000184845		"GPCR / Class A : Dopamine receptors"	3020	protein-coding gene	gene with protein product		126449					Standard	NM_000794		Approved		uc003mcz.3	P21728	OTTHUMG00000130557	ENST00000393752.2:c.57C>T	chr5.hg19:g.174870046G>A		122.0	0.0	.		190.0	77.0	.	NM_000794	B2RA44|Q4QRJ0	Silent	SNP	ENST00000393752.2	hg19	CCDS4393.1																																																																																			.	.	.	none		0.572	DRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252982.2	NM_000794		A	174870046	G	A	174870046	2	1	126	1	0	0	0	0	0	0	0	1	4758	1020	36	2		2	DRD1	5	174870046	Silent	SNP	G	TCGA-BQ-5891-01A-11D-1589-08	34158118	174870046	6045214	8	7889											
UBR2	23304	hgsc.bcm.edu	37	chr6	42657391	42657391	+	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	taccttgatgactatggggaGaccgaccagggactcaggta	11	8	13	9	1	1	3	1	2	0	1	1	6	1	4	3	4	1	1	3	4	3	4			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr6:42657391G>A	ENST00000372899.1	+	46	5367	c.5109G>A	c.(5107-5109)gaG>gaA	p.E1703E	UBR2_ENST00000372901.1_Silent_p.E1703E|UBR2_ENST00000372883.3_3'UTR	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	1703					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)			ACTATGGGGAGACCGACCAGG	0.517																																					p.E1703E		Atlas-SNP	.											.	UBR2	134	.	0			c.G5109A						PASS	.						254	259	257					6																	42657391		2203	4300	6503	SO:0001819	synonymous_variant	23304	exon46			TGGGGAGACCGAC	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.5109G>A	chr6.hg19:g.42657391G>A		495.0	0.0	.		393.0	351.0	.	NM_015255	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Silent	SNP	ENST00000372899.1	hg19	CCDS4870.1																																																																																			.	.	.	none		0.517	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255		A	42657391	G	A	42657391	2	1	126	1	0	0	0	0	0	0	0	1	16914	933	33	2		2	UBR2	6	42657391	Silent	SNP	G	TCGA-BQ-5891-01A-11D-1589-08		42657391	128457676	9	7890											
DOPEY1	23033	hgsc.bcm.edu	37	chr6	83862077	83862077	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtgtccatgcattgacattActctctgaggtaaatattaa	13	14	7	7	0	1	2	0	2	1	0	3	2	2	2	1	1	2	2	1	1	5	5			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr6:83862077A>G	ENST00000349129.2	+	30	6380	c.6120A>G	c.(6118-6120)ttA>ttG	p.L2040L	DOPEY1_ENST00000484282.1_3'UTR|DOPEY1_ENST00000369739.3_Silent_p.L2031L|DOPEY1_ENST00000237163.5_Intron	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	2040					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)		CATTGACATTACTCTCTGAGG	0.294																																					p.L2040L		Atlas-SNP	.											.	DOPEY1	190	.	0			c.A6120G						PASS	.						62	63	63					6																	83862077		2203	4291	6494	SO:0001819	synonymous_variant	23033	exon30			GACATTACTCTCT	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.6120A>G	chr6.hg19:g.83862077A>G		62.0	0.0	.		66.0	4.0	.	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Silent	SNP	ENST00000349129.2	hg19	CCDS4996.1																																																																																			.	.	.	none		0.294	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018		G	83862077	A	G	83862077	2	3	126	1	0	0	0	0	0	0	0	1	4709	388	14	3		3	DOPEY1	6	83862077	Silent	SNP	A	TCGA-BQ-5891-01A-11D-1589-08	41204686	83862077	87252990	10	7891											
USP45	85015	hgsc.bcm.edu	37	chr6	99930682	99930682	+	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	gaaagtggtcctttttcagtCtccttcatgctgtgaagaaa	10	14	9	8	0	3	2	2	1	1	1	5	3	4	2	2	1	1	1	2	1	3	3			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr6:99930682C>A	ENST00000327681.6	-	8	1324	c.792G>T	c.(790-792)gaG>gaT	p.E264D	USP45_ENST00000329966.6_Missense_Mutation_p.E264D|USP45_ENST00000500704.2_Missense_Mutation_p.E264D|USP45_ENST00000392738.2_Intron|USP45_ENST00000369233.2_Missense_Mutation_p.E264D|USP45_ENST00000472914.2_Missense_Mutation_p.E264D	NM_001080481.1	NP_001073950.1	Q70EL2	UBP45_HUMAN	ubiquitin specific peptidase 45	264	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(2)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	22		all_cancers(76;0.000208)|Acute lymphoblastic leukemia(125;8.41e-11)|all_hematologic(75;2.56e-07)|all_epithelial(107;0.122)|Colorectal(196;0.133)		BRCA - Breast invasive adenocarcinoma(108;0.0718)		CTTTTTCAGTCTCCTTCATGC	0.383																																					p.E264D		Atlas-SNP	.											.	USP45	56	.	0			c.G792T						PASS	.						82	85	84					6																	99930682		2203	4300	6503	SO:0001583	missense	85015	exon8			TTCAGTCTCCTTC	AL832030	CCDS34501.1	6q16.2	2008-02-05	2005-08-08		ENSG00000123552	ENSG00000123552		"Ubiquitin-specific peptidases"	20080	protein-coding gene	gene with protein product			"ubiquitin specific protease 45"			12838346	Standard	NM_001080481		Approved	MGC14793	uc003ppx.2	Q70EL2	OTTHUMG00000015267	ENST00000327681.6:c.792G>T	chr6.hg19:g.99930682C>A	ENSP00000333376:p.Glu264Asp	100.0	0.0	.		86.0	80.0	.	NM_001080481	B2RXG0|Q5T062|Q86T44|Q86TC0|Q9BRU1	Missense_Mutation	SNP	ENST00000327681.6	hg19	CCDS34501.1	.	.	.	.	.	.	.	.	.	.	C	13.19	2.164251	0.38217	.	.	ENSG00000123552	ENST00000500704;ENST00000327681;ENST00000369233;ENST00000511403;ENST00000329966;ENST00000472914	T;T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47;1.47	5.32	3.4	0.38934	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.16257	0.0391	L	0.41961	1.31	0.80722	D	1	B;B	0.30482	0.039;0.281	B;B	0.39185	0.039;0.293	T	0.03630	-1.1018	10	0.42905	T	0.14	.	9.9212	0.41466	0.0:0.7614:0.0:0.2386	.	264;264	D6RBV3;Q70EL2	.;UBP45_HUMAN	D	264;264;264;20;264;264	ENSP00000424372:E264D;ENSP00000333376:E264D;ENSP00000358236:E264D;ENSP00000423374:E20D;ENSP00000330540:E264D;ENSP00000423993:E264D	ENSP00000333376:E264D	E	-	3	2	USP45	100037403	0.155000	0.22806	0.998000	0.56505	0.743000	0.42351	-0.128000	0.10531	0.616000	0.30141	0.557000	0.71058	GAG	.	.	.	none		0.383	USP45-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041609.2	NM_032929		A	99930682	C	A	99930682	3	1	126	1	0	0	0	0	1	0	0	0	17088	912	32	4	1696	4	USP45	6	99930682	Missense_Mutation	SNP	C	TCGA-BQ-5891-01A-11D-1589-08	16068605	99930682	71184385	11	7892											
IRF5	3663	hgsc.bcm.edu	37	chr7	128587532	128587532	+	Missense_Mutation	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	ggcccctgcctgccagcctgCcccctgcaggcgaacagctc	5	5	11	20	1	0	0	0	0	0	0	1	1	0	0	7	2	7	2	7	2	1	0			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr7:128587532C>T	ENST00000402030.2	+	6	754	c.682C>T	c.(682-684)Ccc>Tcc	p.P228S	IRF5_ENST00000249375.4_Missense_Mutation_p.P228S|IRF5_ENST00000473745.1_Missense_Mutation_p.P228S|IRF5_ENST00000477535.1_Intron|IRF5_ENST00000357234.5_Missense_Mutation_p.P244S	NM_001098629.1|NM_001098630.1	NP_001092099.1|NP_001092100.1	Q13568	IRF5_HUMAN	interferon regulatory factor 5	228					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						TGCCAGCCTGCCCCCTGCAGG	0.682																																					p.P244S		Atlas-SNP	.											.	IRF5	40	.	0			c.C730T						PASS	.						15	18	17					7																	128587532		2120	4170	6290	SO:0001583	missense	3663	exon6			AGCCTGCCCCCTG		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.682C>T	chr7.hg19:g.128587532C>T	ENSP00000385352:p.Pro228Ser	40.0	0.0	.		54.0	23.0	.	NM_001098629	A4D1J8|A8DUA8|A8DUA9|E7EQ16|E7EW54|Q1A7B4|Q64GA9|Q64GB1|Q64GB2|Q6RCM8|Q9BQF0	Missense_Mutation	SNP	ENST00000402030.2	hg19	CCDS5808.1	.	.	.	.	.	.	.	.	.	.	C	18.47	3.630932	0.67015	.	.	ENSG00000128604	ENST00000357234;ENST00000402030;ENST00000249375;ENST00000473745;ENST00000412326	D;D;D;D	0.97529	-4.4;-4.42;-4.42;-4.42	5.26	2.02	0.26589	.	0.848323	0.10423	N	0.676477	D	0.95175	0.8436	L	0.53249	1.67	0.36808	D	0.885713	B;B	0.30634	0.043;0.288	B;B	0.35413	0.027;0.202	D	0.93066	0.6478	10	0.56958	D	0.05	-11.2851	8.0991	0.30846	0.1597:0.4338:0.4065:0.0	.	228;244	Q13568;Q13568-2	IRF5_HUMAN;.	S	244;228;228;228;218	ENSP00000349770:P244S;ENSP00000385352:P228S;ENSP00000249375:P228S;ENSP00000419149:P228S	ENSP00000249375:P228S	P	+	1	0	IRF5	128374768	0.309000	0.24518	0.269000	0.24586	0.935000	0.57460	0.974000	0.29436	0.667000	0.31107	0.561000	0.74099	CCC	.	.	.	none		0.682	IRF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350934.1	NM_001098627		T	128587532	C	T	128587532	3	4	126	1	0	0	0	0	1	0	0	0	7840	739	26	2	748	2	IRF5	7	128587532	Missense_Mutation	SNP	C	TCGA-BQ-5891-01A-11D-1589-08		128587532	30551131	12	7893											
SORCS1	114815	hgsc.bcm.edu	37	chr10	108427534	108427534	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgccggcaggcactggccaTtgctgtgtcgctcataacca	8	9	11	13	2	1	0	1	0	0	0	2	0	1	0	3	3	3	4	3	3	1	2			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr10:108427534T>C	ENST00000263054.6	-	17	2223	c.2216A>G	c.(2215-2217)aAt>aGt	p.N739S	SORCS1_ENST00000344440.6_Missense_Mutation_p.N739S|SORCS1_ENST00000369698.1_Missense_Mutation_p.N274S	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	739					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)		GCACTGGCCATTGCTGTGTCG	0.458																																					p.N739S		Atlas-SNP	.											.	SORCS1	534	.	0			c.A2216G						PASS	.						69	62	65					10																	108427534		2203	4300	6503	SO:0001583	missense	114815	exon17			TGGCCATTGCTGT	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.2216A>G	chr10.hg19:g.108427534T>C	ENSP00000263054:p.Asn739Ser	36.0	0.0	.		34.0	31.0	.	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	hg19	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	T	7.105	0.574795	0.13623	.	.	ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440	T;T;T	0.23348	1.91;2.47;2.47	5.49	4.33	0.51752	VPS10 (1);	0.111999	0.64402	N	0.000012	T	0.12433	0.0302	N	0.05031	-0.125	0.39169	D	0.962557	B;B;B;B;B	0.25206	0.073;0.054;0.12;0.073;0.007	B;B;B;B;B	0.25506	0.028;0.061;0.061;0.028;0.02	T	0.13548	-1.0505	9	.	.	.	-18.7721	11.8351	0.52319	0.0:0.0698:0.0:0.9302	.	739;739;739;739;739	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	S	274;739;739	ENSP00000358712:N274S;ENSP00000263054:N739S;ENSP00000345964:N739S	.	N	-	2	0	SORCS1	108417524	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	3.928000	0.56506	0.982000	0.38575	0.379000	0.24179	AAT	.	.	.	none		0.458	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		C	108427534	T	C	108427534	3	2	126	1	0	0	0	0	1	0	0	0	14943	1493	52	3	1564	3	SORCS1	10	108427534	Missense_Mutation	SNP	T	TCGA-BQ-5891-01A-11D-1589-08		108427534	27107213	13	7894											
OR52J3	119679	hgsc.bcm.edu	37	chr11	5068288	5068288	+	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	tcaggctcacataatagcccAttcctactgtgagcacatgg	11	10	8	12	0	2	1	2	1	0	0	3	1	3	1	2	2	3	2	2	2	3	4			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr11:5068288A>T	ENST00000380370.1	+	1	533	c.533A>T	c.(532-534)cAt>cTt	p.H178L		NM_001001916.2	NP_001001916.2	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J, member 3	178						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(6)|large_intestine(6)|lung(19)|ovary(1)|skin(2)	36		Medulloblastoma(188;0.00131)|all_neural(188;0.0189)|Breast(177;0.0204)		Epithelial(150;9.29e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.19)		ATAATAGCCCATTCCTACTGT	0.418																																					p.H178L		Atlas-SNP	.											OR52J3,NS,carcinoma,0,1	OR52J3	77	.	0			c.A533T						PASS	.						191	162	172					11																	5068288		2201	4298	6499	SO:0001583	missense	119679	exon1			TAGCCCATTCCTA	AB065530	CCDS31370.1	11p15.4	2012-08-09			ENSG00000205495	ENSG00000205495		"GPCR / Class A : Olfactory receptors"	14799	protein-coding gene	gene with protein product							Standard	NM_001001916		Approved		uc010qyv.2	Q8NH60	OTTHUMG00000066600	ENST00000380370.1:c.533A>T	chr11.hg19:g.5068288A>T	ENSP00000369728:p.His178Leu	163.0	0.0	.		117.0	112.0	.	NM_001001916	Q6IFE4	Missense_Mutation	SNP	ENST00000380370.1	hg19	CCDS31370.1	.	.	.	.	.	.	.	.	.	.	A	17.43	3.387131	0.61956	.	.	ENSG00000205495	ENST00000380370	T	0.00183	8.6	3.89	3.89	0.44902	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000183	T	0.01061	0.0035	H	0.98769	4.325	0.37287	D	0.908099	D	0.89917	1.0	D	0.97110	1.0	T	0.13019	-1.0525	10	0.87932	D	0	.	11.9816	0.53123	1.0:0.0:0.0:0.0	.	178	Q8NH60	O52J3_HUMAN	L	178	ENSP00000369728:H178L	ENSP00000369728:H178L	H	+	2	0	OR52J3	5024864	0.235000	0.23794	0.989000	0.46669	0.817000	0.46193	3.921000	0.56454	1.742000	0.51746	0.533000	0.62120	CAT	.	.	.	none		0.418	OR52J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142807.1	NM_001001916		T	5068288	A	T	5068288	3	4	126	1	0	0	0	0	1	0	0	0	11129	217	8	5	535	5	OR52J3	11	5068288	Missense_Mutation	SNP	A	TCGA-BQ-5891-01A-11D-1589-08		5068288	129938228	14	7895											
IL10RA	3587	hgsc.bcm.edu	37	chr11	117866403	117866403	+	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	ccagctgtatgtgcggcgccGaaagaagctacccagtgtcc	9	7	12	13	3	0	1	0	0	0	1	1	2	1	1	4	1	4	3	4	1	4	2	rs145975996		TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr11:117866403G>A	ENST00000227752.3	+	6	908	c.788G>A	c.(787-789)cGa>cAa	p.R263Q	IL10RA_ENST00000533700.1_3'UTR|IL10RA_ENST00000545409.1_Missense_Mutation_p.R114Q|IL10RA_ENST00000541785.1_Missense_Mutation_p.R243Q	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	263					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)		GTGCGGCGCCGAAAGAAGCTA	0.602																																					p.R263Q		Atlas-SNP	.											.	IL10RA	46	.	0			c.G788A						PASS	.	G	GLN/ARG	0,4400		0,0,2200	96	76	83		788	-1.2	0	11	dbSNP_134	83	2,8590	2.2+/-6.3	0,2,4294	yes	missense	IL10RA	NM_001558.3	43	0,2,6494	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	263/579	117866403	2,12990	2200	4296	6496	SO:0001583	missense	3587	exon6			GGCGCCGAAAGAA	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.788G>A	chr11.hg19:g.117866403G>A	ENSP00000227752:p.Arg263Gln	43.0	0.0	.		42.0	20.0	.	NM_001558	A8K6I0|B0YJ27	Missense_Mutation	SNP	ENST00000227752.3	hg19	CCDS8388.1	.	.	.	.	.	.	.	.	.	.	G	16.24	3.066789	0.55539	0.0	2.33E-4	ENSG00000110324	ENST00000227752;ENST00000541785;ENST00000545409;ENST00000536858	T;T;T	0.56941	0.43;0.43;1.15	5.16	-1.2	0.09554	.	0.427526	0.16007	N	0.233988	T	0.52757	0.1754	M	0.63428	1.95	0.09310	N	1	D;D	0.69078	0.997;0.995	P;P	0.51945	0.685;0.639	T	0.47420	-0.9119	10	0.45353	T	0.12	-4.5989	7.1947	0.25845	0.1825:0.5157:0.3019:0.0	.	243;263	F5GYV8;Q13651	.;I10R1_HUMAN	Q	263;243;114;243	ENSP00000227752:R263Q;ENSP00000441397:R243Q;ENSP00000443019:R114Q	ENSP00000227752:R263Q	R	+	2	0	IL10RA	117371613	0.000000	0.05858	0.024000	0.17045	0.667000	0.39255	-0.002000	0.12924	0.003000	0.14656	0.563000	0.77884	CGA	.	G|1.000;A|0.000	0.000	weak		0.602	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1			A	117866403	G	A	117866403	3	1	126	1	0	0	0	0	1	0	0	0	7627	1058	37	1	810	1	IL10RA	11	117866403	Missense_Mutation	SNP	G	TCGA-BQ-5891-01A-11D-1589-08	112798115	117866403	17140113	15	7896											
ARHGAP9	64333	hgsc.bcm.edu	37	chr12	57869643	57869643	+	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	tcgatgacagtccgcagcgcGcggtgccaggctcgcagctc	6	6	14	15	6	0	1	0	1	0	0	4	2	1	1	2	2	3	4	2	2	0	0			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr12:57869643G>T	ENST00000356411.2	-	10	1422	c.1284C>A	c.(1282-1284)cgC>cgA	p.R428R	ARHGAP9_ENST00000393797.2_Silent_p.R499R|ARHGAP9_ENST00000550454.1_5'Flank|ARHGAP9_ENST00000550288.1_Silent_p.R507R|ARHGAP9_ENST00000393791.3_Silent_p.R428R|ARHGAP9_ENST00000424809.2_Silent_p.R428R|ARHGAP9_ENST00000430041.2_Silent_p.R244R			Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9	428	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)			TCCGCAGCGCGCGGTGCCAGG	0.672																																					p.R428R		Atlas-SNP	.											.	ARHGAP9	79	.	0			c.C1284A						PASS	.						26	29	28					12																	57869643		2202	4297	6499	SO:0001819	synonymous_variant	64333	exon9			CAGCGCGCGGTGC	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.1284C>A	chr12.hg19:g.57869643G>T		31.0	0.0	.		65.0	4.0	.	NM_001080157	B4DVI3|E9PDX9|Q8NAF3|Q8TCJ3|Q8WYR0|Q96EZ2|Q96S74	Silent	SNP	ENST00000356411.2	hg19																																																																																				.	.	.	none		0.672	ARHGAP9-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_032496		T	57869643	G	T	57869643	2	4	126	1	0	0	0	0	0	0	0	1	889	1074	38	4		4	ARHGAP9	12	57869643	Silent	SNP	G	TCGA-BQ-5891-01A-11D-1589-08		57869643	75982252	16	7897											
EFHA1	221154	hgsc.bcm.edu	37	chr13	22088516	22088516	+	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	tatccagtttcattagttttCactgtcatcaagtcatcttg	9	18	5	9	0	6	0	5	0	1	0	7	0	7	0	1	0	0	2	1	0	3	6			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr13:22088516C>T	ENST00000382374.4	-	7	704	c.639G>A	c.(637-639)gtG>gtA	p.V213V		NM_152726.2	NP_689939.1	Q8IYU8	MICU2_HUMAN	mitochondrial calcium uptake 2	213					mitochondrial calcium ion transport (GO:0006851)|negative regulation of mitochondrial calcium ion concentration (GO:0051562)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)	calcium channel complex (GO:0034704)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|uniplex complex (GO:1990246)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)										CATTAGTTTTCACTGTCATCA	0.318																																					p.V213V		Atlas-SNP	.											.	EFHA1	33	.	0			c.G639A						PASS	.						184	177	179					13																	22088516		2202	4300	6502	SO:0001819	synonymous_variant	221154	exon7			AGTTTTCACTGTC	AK091907	CCDS9297.1	13q12.11	2013-03-13	2013-03-13	2013-03-13	ENSG00000165487	ENSG00000165487		"EF-hand domain containing"	31830	protein-coding gene	gene with protein product		610632	"EF hand domain family A1", "EF-hand domain family, member A1"	EFHA1		23409044	Standard	NM_152726		Approved		uc001uof.3	Q8IYU8	OTTHUMG00000067414	ENST00000382374.4:c.639G>A	chr13.hg19:g.22088516C>T		98.0	0.0	.		93.0	9.0	.	NM_152726	Q8N0T6|Q8NAX8	Silent	SNP	ENST00000382374.4	hg19	CCDS9297.1																																																																																			.	.	.	none		0.318	MICU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144355.1	NM_152726		T	22088516	C	T	22088516	2	4	126	1	0	0	0	0	0	0	0	1	4945	813	29	2		2	EFHA1	13	22088516	Silent	SNP	C	TCGA-BQ-5891-01A-11D-1589-08		22088516	93081362	17	7898											
KL	9365	hgsc.bcm.edu	37	chr13	33591076	33591076	+	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	ggcagcgcgggcgtccccaaCcgcgaggggctgcgctacta	6	4	16	15	6	0	0	0	0	0	0	1	1	1	0	3	4	4	3	3	4	3	2			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr13:33591076C>T	ENST00000380099.3	+	1	506	c.498C>T	c.(496-498)aaC>aaT	p.N166N	KL_ENST00000426690.2_Intron|KL_ENST00000487852.1_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	166	Glycosyl hydrolase-1 1.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)			breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		GCGTCCCCAACCGCGAGGGGC	0.726																																					p.N166N		Atlas-SNP	.											.	KL	106	.	0			c.C498T						PASS	.						11	11	11					13																	33591076		2131	4184	6315	SO:0001819	synonymous_variant	9365	exon1			CCCCAACCGCGAG	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.498C>T	chr13.hg19:g.33591076C>T		23.0	0.0	.		18.0	6.0	.	NM_004795	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Silent	SNP	ENST00000380099.3	hg19	CCDS9347.1																																																																																			.	.	.	none		0.726	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1			T	33591076	C	T	33591076	2	4	126	1	0	0	0	0	0	0	0	1	8338	506	18	2		2	KL	13	33591076	Silent	SNP	C	TCGA-BQ-5891-01A-11D-1589-08	11502560	33591076	81578802	18	7899											
RANBP10	57610	hgsc.bcm.edu	37	chr16	67840335	67840335	+	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	aggcgctgcaagcgccggctCagctcctgctccccagggga	6	5	14	16	3	1	0	1	0	0	0	3	1	3	1	4	4	4	5	4	4	1	0			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr16:67840335C>T	ENST00000317506.3	-	1	220	c.105G>A	c.(103-105)ctG>ctA	p.L35L	RANBP10_ENST00000602677.1_Silent_p.L35L|RANBP10_ENST00000602887.1_5'UTR|RANBP10_ENST00000425512.2_5'UTR|RANBP10_ENST00000448631.2_Silent_p.L35L|TSNAXIP1_ENST00000561639.1_5'Flank|TSNAXIP1_ENST00000415766.3_5'Flank|TSNAXIP1_ENST00000388833.3_5'Flank|RANBP10_ENST00000536251.1_5'UTR|RANBP10_ENST00000411657.2_5'UTR	NM_020850.1	NP_065901.1	Q6VN20	RBP10_HUMAN	RAN binding protein 10	35	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				microtubule cytoskeleton organization (GO:0000226)	cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)	Ran guanyl-nucleotide exchange factor activity (GO:0005087)			endometrium(5)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|skin(1)	23		Acute lymphoblastic leukemia(13;4.34e-06)|all_hematologic(13;0.000643)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00522)|Epithelial(162;0.025)|all cancers(182;0.157)		AGCGCCGGCTCAGCTCCTGCT	0.701																																					p.L35L		Atlas-SNP	.											.	RANBP10	56	.	0			c.G105A						PASS	.						14	15	15					16																	67840335		2183	4253	6436	SO:0001819	synonymous_variant	57610	exon1			CCGGCTCAGCTCC	AB040897	CCDS32469.1	16q22	2008-02-05				ENSG00000141084			29285	protein-coding gene	gene with protein product		614031				14684163	Standard	NM_020850		Approved	KIAA1464	uc002eud.3	Q6VN20		ENST00000317506.3:c.105G>A	chr16.hg19:g.67840335C>T		14.0	0.0	.		18.0	6.0	.	NM_020850	A4FTY2|B4DID0|B4DQH9|E7EW27|Q9P264	Silent	SNP	ENST00000317506.3	hg19	CCDS32469.1																																																																																			.	.	.	none		0.701	RANBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467896.1	NM_020850		T	67840335	C	T	67840335	2	4	126	1	0	0	0	0	0	0	0	1	13039	813	29	2		2	RANBP10	16	67840335	Silent	SNP	C	TCGA-BQ-5891-01A-11D-1589-08		67840335	22514418	19	7900											
AKAP10	11216	hgsc.bcm.edu	37	chr17	19861611	19861611	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tatcaagagaatcagttaaaAaagacgctgtagtttcatgc	16	11	8	6	1	3	2	3	0	0	2	3	3	3	2	0	0	1	4	0	0	7	4			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr17:19861611A>G	ENST00000225737.6	-	4	750	c.593T>C	c.(592-594)tTt>tCt	p.F198S	AKAP10_ENST00000572155.1_5'Flank|AKAP10_ENST00000395536.3_Missense_Mutation_p.F198S	NM_007202.3	NP_009133.2	O43572	AKA10_HUMAN	A kinase (PRKA) anchor protein 10	198	RGS 1. {ECO:0000255|PROSITE- ProRule:PRU00171}.				blood coagulation (GO:0007596)|protein localization (GO:0008104)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)				NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	21	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)					ATCAGTTAAAAAAGACGCTGT	0.418																																					p.F198S		Atlas-SNP	.											.	AKAP10	47	.	0			c.T593C						PASS	.						65	65	65					17																	19861611		2203	4300	6503	SO:0001583	missense	11216	exon4			GTTAAAAAAGACG	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.593T>C	chr17.hg19:g.19861611A>G	ENSP00000225737:p.Phe198Ser	73.0	0.0	.		99.0	49.0	.	NM_007202	B2R650|Q96AJ7	Missense_Mutation	SNP	ENST00000225737.6	hg19	CCDS11214.1	.	.	.	.	.	.	.	.	.	.	A	5.074	0.199347	0.09652	.	.	ENSG00000108599	ENST00000225737;ENST00000395536	T	0.17054	2.3	5.98	3.72	0.42706	Regulator of G protein signalling (2);Regulator of G protein signalling superfamily (1);	0.607188	0.19356	N	0.116264	T	0.05914	0.0154	N	0.03115	-0.41	0.24009	N	0.996183	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.0;0.0	T	0.42068	-0.9473	10	0.06236	T	0.91	-3.1154	7.7403	0.28837	0.6869:0.0:0.3131:0.0	.	198;198;198	E7EMD6;Q2XPN4;O43572	.;.;AKA10_HUMAN	S	198	ENSP00000225737:F198S	ENSP00000225737:F198S	F	-	2	0	AKAP10	19802203	1.000000	0.71417	0.995000	0.50966	0.345000	0.29048	1.891000	0.39738	0.471000	0.27319	0.482000	0.46254	TTT	.	.	.	none		0.418	AKAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132380.2	NM_007202		G	19861611	A	G	19861611	3	3	126	1	0	0	0	0	1	0	0	0	446	14	1	3	1443	3	AKAP10	17	19861611	Missense_Mutation	SNP	A	TCGA-BQ-5891-01A-11D-1589-08		19861611	61333599	20	7901											
MUC16	94025	hgsc.bcm.edu	37	chr19	9065718	9065718	+	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	ccctcaatttagggctcaggGaggaaattgactctttctga	10	12	10	9	0	4	2	2	2	2	0	4	4	4	4	1	3	0	1	1	3	3	4			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr19:9065718G>T	ENST00000397910.4	-	3	21931	c.21728C>A	c.(21727-21729)tCc>tAc	p.S7243Y		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7245	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						AGGGCTCAGGGAGGAAATTGA	0.468																																					p.S7243Y		Atlas-SNP	.											.	MUC16	4315	.	0			c.C21728A						PASS	.						169	161	164					19																	9065718		1979	4157	6136	SO:0001583	missense	94025	exon3			CTCAGGGAGGAAA	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.21728C>A	chr19.hg19:g.9065718G>T	ENSP00000381008:p.Ser7243Tyr	198.0	0.0	.		220.0	16.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	3.932	-0.016036	0.07681	.	.	ENSG00000181143	ENST00000397910	T	0.02737	4.18	2.75	-0.661	0.11417	.	.	.	.	.	T	0.06962	0.0177	L	0.42245	1.32	.	.	.	D	0.65815	0.995	D	0.68943	0.961	T	0.29274	-1.0017	8	0.87932	D	0	.	5.0419	0.14463	0.4634:0.0:0.5366:0.0	.	7243	B5ME49	.	Y	7243	ENSP00000381008:S7243Y	ENSP00000381008:S7243Y	S	-	2	0	MUC16	8926718	0.015000	0.18098	0.000000	0.03702	0.007000	0.05969	2.004000	0.40854	-0.046000	0.13446	0.195000	0.17529	TCC	.	.	.	none		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9065718	G	T	9065718	3	4	126	1	0	0	0	0	1	0	0	0	9980	1174	41	4	22123	4	MUC16	19	9065718	Missense_Mutation	SNP	G	TCGA-BQ-5891-01A-11D-1589-08		9065718	50063265	21	7902											
ZNF761	388561	hgsc.bcm.edu	37	chr19	53958709	53958709	+	RNA	SNP	T	T	A																															aaatcaatacttgaaagacaTaggataattcatactgaaga																										TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr19:53958709T>A	ENST00000454407.1	+	0	1401							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		TTGAAAGACATAGGATAATTC	0.383																																					p.H316Q		Atlas-SNP	.											.	ZNF761	104	.	0			c.T948A						PASS	.						83	85	85					19																	53958709		2203	4300	6503			388561	exon7			AAGACATAGGATA	AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"Zinc fingers, C2H2-type"	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		chr19.hg19:g.53958709T>A		114.0	0.0	.		114.0	97.0	.	NM_001008401	Q6ZNB9	Missense_Mutation	SNP	ENST00000454407.1	hg19																																																																																				.	.	.	none		0.383	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401		A	53958709	T	A	53958709	1	1	126	0	1	0	0	0	0	0	0	0	18148	1403	49	5		5	ZNF761	19	53958709	RNA	SNP	T	TCGA-BQ-5891-01A-11D-1589-08	44892991	53958709	5170274	22	7903	85	2									
ZNF761	388561	hgsc.bcm.edu	37	chr19	53958711	53958711	+	RNA	SNP	G	G	A																															atcaatacttgaaagacataGgataattcatactgaagaga																										TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr19:53958711G>A	ENST00000454407.1	+	0	1403							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		GAAAGACATAGGATAATTCAT	0.383																																					p.R317K		Atlas-SNP	.											.	ZNF761	104	.	0			c.G950A						PASS	.						84	85	85					19																	53958711		2203	4300	6503			388561	exon7			GACATAGGATAAT	AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"Zinc fingers, C2H2-type"	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		chr19.hg19:g.53958711G>A		115.0	0.0	.		114.0	98.0	.	NM_001008401	Q6ZNB9	Missense_Mutation	SNP	ENST00000454407.1	hg19																																																																																				.	.	.	none		0.383	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401		A	53958711	G	A	53958711	1	1	126	0	1	0	0	0	0	0	0	0	18148	1000	35	2		2	ZNF761	19	53958711	RNA	SNP	G	TCGA-BQ-5891-01A-11D-1589-08	2	53958711	5170272	23	7904	85	2									
GGTLC1	92086	hgsc.bcm.edu	37	chr20	23967129	23967129	+	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	ccgtcctctgcgaccacagaCaggtgagcagtgcccccgtc	7	6	11	17	3	1	2	0	1	1	1	3	3	2	2	5	1	3	1	5	1	0	0			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr20:23967129C>T	ENST00000335694.4	-	2	324	c.120G>A	c.(118-120)ctG>ctA	p.L40L	GGTLC1_ENST00000286890.4_Silent_p.L40L|GGTLC1_ENST00000278765.4_Silent_p.L40L	NM_178311.2	NP_842563.1	Q9BX51	GGTL1_HUMAN	gamma-glutamyltransferase light chain 1	40					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						CGACCACAGACAGGTGAGCAG	0.647																																					p.L40L		Atlas-SNP	.											.	GGTLC1	37	.	0			c.G120A						PASS	.						51	45	47					20																	23967129		2203	4300	6503	SO:0001819	synonymous_variant	92086	exon2			CACAGACAGGTGA	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.120G>A	chr20.hg19:g.23967129C>T		56.0	0.0	.		101.0	56.0	.	NM_178311	D3DW43|Q08246	Silent	SNP	ENST00000335694.4	hg19	CCDS13163.1																																																																																			.	.	.	none		0.647	GGTLC1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078366.2	NM_178311.2		T	23967129	C	T	23967129	2	4	126	1	0	0	0	0	0	0	0	1	6372	465	17	2		2	GGTLC1	20	23967129	Silent	SNP	C	TCGA-BQ-5891-01A-11D-1589-08		23967129	39058391	24	7905											
TMPRSS15	5651	hgsc.bcm.edu	37	chr21	19685347	19685347	+	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	atgccatatgctctggattcTgaaccgcactaaaccattgt	11	12	7	11	1	2	1	0	1	2	0	2	2	2	2	3	1	4	2	3	1	4	4	rs111276490		TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr21:19685347T>G	ENST00000284885.3	-	18	2113	c.2080A>C	c.(2080-2082)Aga>Cga	p.R694R		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	694	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						CTCTGGATTCTGAACCGCACT	0.443																																					p.R694R		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.A2080C						PASS	.						149	133	138					21																	19685347		2203	4300	6503	SO:0001819	synonymous_variant	5651	exon18			GGATTCTGAACCG		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.2080A>C	chr21.hg19:g.19685347T>G		119.0	0.0	.		114.0	107.0	.	NM_002772	Q2NKL7	Silent	SNP	ENST00000284885.3	hg19	CCDS13571.1																																																																																			.	T|0.500;C|0.500	.	alt		0.443	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		G	19685347	T	G	19685347	2	3	126	1	0	0	0	0	0	0	0	1	16258	1588	55	5		5	TMPRSS15	21	19685347	Silent	SNP	T	TCGA-BQ-5891-01A-11D-1589-08		19685347	28444548	25	7906											
CCDC116	164592	hgsc.bcm.edu	37	chr22	21989095	21989095	+	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	gttctcagggctgctgggctCaagctctggcgtgcctgaag	5	10	15	11	1	3	1	2	1	2	0	4	1	3	1	1	3	3	5	1	3	2	1			TCGA-BQ-5891-01A-11D-1589-08	TCGA-BQ-5891-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37d4ff42-0161-4f83-bd6f-13eb19d4eabf	28824279-2be9-45db-867a-b165d8191d0c	g.chr22:21989095C>G	ENST00000292779.3	+	4	904	c.743C>G	c.(742-744)tCa>tGa	p.S248*	CCDC116_ENST00000607942.1_Nonsense_Mutation_p.S248*	NM_152612.2	NP_689825.2	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	248										endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(5)	22	Colorectal(54;0.105)					CTGCTGGGCTCAAGCTCTGGC	0.577																																					p.S248X		Atlas-SNP	.											.	CCDC116	56	.	0			c.C743G						PASS	.						85	90	88					22																	21989095		2203	4300	6503	SO:0001587	stop_gained	164592	exon4			TGGGCTCAAGCTC	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.743C>G	chr22.hg19:g.21989095C>G	ENSP00000292779:p.Ser248*	171.0	0.0	.		181.0	8.0	.	NM_152612	Q8N9Y9	Nonsense_Mutation	SNP	ENST00000292779.3	hg19	CCDS13791.1	.	.	.	.	.	.	.	.	.	.	C	18.73	3.687235	0.68157	.	.	ENSG00000161180	ENST00000292779	.	.	.	4.56	4.56	0.56223	.	0.269330	0.27035	N	0.021260	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-55.3163	13.0826	0.59121	0.0:1.0:0.0:0.0	.	.	.	.	X	248	.	ENSP00000292779:S248X	S	+	2	0	CCDC116	20319095	0.644000	0.27277	0.178000	0.23040	0.062000	0.15995	3.279000	0.51670	2.554000	0.86153	0.485000	0.47835	TCA	.	.	.	none		0.577	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612		G	21989095	C	G	21989095	4	3	126	1	0	0	0	0	0	1	0	0	2755	838	29	4	753	4	CCDC116	22	21989095	Nonsense_Mutation	SNP	C	TCGA-BQ-5891-01A-11D-1589-08		21989095	29315471	26	7907											
RCAN3	11123	hgsc.bcm.edu	37	chr1	24840967	24840967	+	Frame_Shift_Del	DEL	T	T	-																															tttggtgaaaatgaagatgaTttggatgagatgatggattt																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr1:24840967delT	ENST00000374395.4	+	2	418	c.105delT	c.(103-105)gatfs	p.D35fs	RCAN3_ENST00000436717.2_Frame_Shift_Del_p.D35fs|RCAN3_ENST00000538532.1_Frame_Shift_Del_p.D35fs|RCAN3_ENST00000374393.2_Frame_Shift_Del_p.D35fs|RCAN3_ENST00000412742.2_Frame_Shift_Del_p.D35fs	NM_001251978.1|NM_001251979.1|NM_001251984.1	NP_001238907.1|NP_001238908.1|NP_001238913.1	Q9UKA8	RCAN3_HUMAN	RCAN family member 3	35					anatomical structure morphogenesis (GO:0009653)|calcium-mediated signaling (GO:0019722)		RNA binding (GO:0003723)|troponin I binding (GO:0031013)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)	7		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00473)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0427)|OV - Ovarian serous cystadenocarcinoma(117;1.13e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;0.000923)|BRCA - Breast invasive adenocarcinoma(304;0.0018)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.00493)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.14)		ATGAAGATGATTTGGATGAGA	0.433																																					p.D35fs		Atlas-INDEL	.											.	RCAN3	22	.	0			c.104delA						PASS	.						206	186	193					1																	24840967		2203	4300	6503	SO:0001589	frameshift_variant	11123	exon1			.		CCDS254.1, CCDS57980.1, CCDS57981.1, CCDS57982.1, CCDS72730.1	1p35.3-p33	2008-02-05	2007-06-26	2007-06-26	ENSG00000117602	ENSG00000117602			3042	protein-coding gene	gene with protein product		605860	"Down syndrome critical region gene 1-like 2"	DSCR1L2		10756093	Standard	NM_001251984		Approved		uc001bjj.3	Q9UKA8	OTTHUMG00000003298	ENST00000374395.4:c.105delT	chr1.hg19:g.24840967delT	ENSP00000363516:p.Asp35fs	93.0	0.0	0		101.0	21.0	0.207921	NM_001251980	A4GU14|A4LA69|E3VWE2|E5L4P0|E5L4P7|E7ENV1|E7EWD8|G1FI66|G1FLF0|Q5ECL3|Q5TGC6|Q9NUC8|Q9UKA7	Frame_Shift_Del	DEL	ENST00000374395.4	hg19	CCDS254.1																																																																																			.	.	.	none		0.433	RCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009176.2			-	24840967	T	-	24840967	7	5	127	1	0	1	0	1	0	0	0	0	13183	1490	52	0	107	0	RCAN3	1	24840967	Frame_Shift_Del	DEL	T	TCGA-BQ-5892-01A-11D-1589-08		24840967	224409654	1	7908											
SFRS4	6429	hgsc.bcm.edu	37	chr1	29475685	29475685	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcttttctctttcttgctcCggctccgactctggctccgg	1	16	9	15	3	3	0	0	0	3	0	7	1	6	0	3	3	2	4	3	3	0	4	rs368357249		TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr1:29475685C>T	ENST00000373795.4	-	6	956	c.722G>A	c.(721-723)cGg>cAg	p.R241Q	SRSF4_ENST00000546138.1_Silent_p.P139P|SRSF4_ENST00000466448.1_5'UTR|RP11-242O24.3_ENST00000413004.1_lincRNA	NM_005626.4	NP_005617.2	Q08170	SRSF4_HUMAN	serine/arginine-rich splicing factor 4	241	Arg/Ser-rich (RS domain).				gene expression (GO:0010467)|hematopoietic progenitor cell differentiation (GO:0002244)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(1)	27						TTTCTTgctccggctccgact	0.592																																					p.R241Q		Atlas-SNP	.											SRSF4,colon,carcinoma,0,1	SRSF4	44	.	0			c.G722A						PASS	.	C	GLN/ARG	2,4398		0,2,2198	50	60	57		722	5.8	1	1		57	0,8596		0,0,4298	no	missense	SRSF4	NM_005626.4	43	0,2,6496	TT,TC,CC		0.0,0.0455,0.0154	probably-damaging	241/495	29475685	2,12994	2200	4298	6498	SO:0001583	missense	6429	exon6			TTGCTCCGGCTCC	BC002781	CCDS333.1	1p35.3	2013-02-12	2010-06-22	2010-06-22	ENSG00000116350	ENSG00000116350		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10786	protein-coding gene	gene with protein product	"SR splicing factor 4"	601940	"splicing factor, arginine/serine-rich 4"	SFRS4		8321209, 20516191	Standard	NM_005626		Approved	SRP75	uc001bro.3	Q08170	OTTHUMG00000003663	ENST00000373795.4:c.722G>A	chr1.hg19:g.29475685C>T	ENSP00000362900:p.Arg241Gln	200.0	1.0	.		162.0	15.0	.	NM_005626	Q5VXP1|Q9BUA4|Q9UEB5	Missense_Mutation	SNP	ENST00000373795.4	hg19	CCDS333.1	.	.	.	.	.	.	.	.	.	.	C	16.47	3.131145	0.56828	4.55E-4	0.0	ENSG00000116350	ENST00000373795;ENST00000434636	T	0.38401	1.14	5.77	5.77	0.91146	.	0.201011	0.34932	N	0.003572	T	0.35189	0.0923	L	0.52573	1.65	0.80722	D	1	D	0.61080	0.989	B	0.42087	0.375	T	0.19778	-1.0295	10	0.59425	D	0.04	.	13.8822	0.63688	0.1522:0.8478:0.0:0.0	.	241	Q08170	SRSF4_HUMAN	Q	241	ENSP00000362900:R241Q	ENSP00000362900:R241Q	R	-	2	0	SRSF4	29348272	0.993000	0.37304	0.999000	0.59377	0.988000	0.76386	3.219000	0.51200	2.723000	0.93209	0.655000	0.94253	CGG	.	.	.	none		0.592	SRSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010392.1	NM_005626		T	29475685	C	T	29475685	3	4	127	1	0	0	0	0	1	0	0	0	14192	652	23	1	766	1	SFRS4	1	29475685	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	4634718	29475685	219774936	2	7909											
ZNF691	51058	hgsc.bcm.edu	37	chr1	43317094	43317094	+	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	tttcggcggcgctcagacctCaccacgcaccagcaagatca	10	6	9	16	4	3	2	3	0	0	2	4	2	3	2	3	2	1	3	3	2	1	1			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr1:43317094C>A	ENST00000372506.1	+	4	805	c.465C>A	c.(463-465)ctC>ctA	p.L155L	ZNF691_ENST00000372502.1_Silent_p.L177L|ZNF691_ENST00000397044.3_Silent_p.L186L|ZNF691_ENST00000372504.1_Silent_p.L177L|ZNF691_ENST00000372508.3_Silent_p.L155L|ZNF691_ENST00000372507.1_Silent_p.L155L	NM_001242739.1	NP_001229668.1	Q5VV52	ZN691_HUMAN	zinc finger protein 691	186						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)				GCTCAGACCTCACCACGCACC	0.597																																					p.L186L		Atlas-SNP	.											.	ZNF691	30	.	0			c.C558A						PASS	.						61	56	58					1																	43317094		2203	4300	6503	SO:0001819	synonymous_variant	51058	exon4			AGACCTCACCACG		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.465C>A	chr1.hg19:g.43317094C>A		89.0	0.0	.		78.0	17.0	.	NM_001242739	A8MXP6|B4DJR7|O95878|Q9NWE8	Silent	SNP	ENST00000372506.1	hg19	CCDS476.1																																																																																			.	.	.	none		0.597	ZNF691-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020192.1	NM_015911		A	43317094	C	A	43317094	2	1	127	1	0	0	0	0	0	0	0	1	18108	813	29	4		4	ZNF691	1	43317094	Silent	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	13841409	43317094	205933527	3	7910											
CACHD1	57685	hgsc.bcm.edu	37	chr1	65143946	65143946	+	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	ccagaaagaatgcttcggggGgattgtgggagccaaaagtc	12	7	15	7	1	0	2	0	0	0	2	2	4	0	4	2	4	2	1	2	4	4	2			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr1:65143946G>A	ENST00000371073.2	+	23	3197	c.3197G>A	c.(3196-3198)gGg>gAg	p.G1066E	CACHD1_ENST00000495994.1_3'UTR|CACHD1_ENST00000290039.5_Missense_Mutation_p.G1015E			Q5VU97	CAHD1_HUMAN	cache domain containing 1	1066					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						TGCTTCGGGGGGATTGTGGGA	0.473																																					p.G1015E		Atlas-SNP	.											.	CACHD1	125	.	0			c.G3044A						PASS	.						94	95	95					1																	65143946		2203	4300	6503	SO:0001583	missense	57685	exon23			TCGGGGGGATTGT	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.3197G>A	chr1.hg19:g.65143946G>A	ENSP00000360113:p.Gly1066Glu	65.0	0.0	.		84.0	6.0	.	NM_020925	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Missense_Mutation	SNP	ENST00000371073.2	hg19		.	.	.	.	.	.	.	.	.	.	G	33	5.284715	0.95517	.	.	ENSG00000158966	ENST00000371073;ENST00000290039	T;T	0.58210	0.35;0.4	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.66839	0.2830	L	0.52905	1.665	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.66056	-0.6018	10	0.87932	D	0	-25.7352	20.8794	0.99867	0.0:0.0:1.0:0.0	.	1066	Q5VU97	CAHD1_HUMAN	E	1066;1015	ENSP00000360113:G1066E;ENSP00000290039:G1015E	ENSP00000290039:G1015E	G	+	2	0	CACHD1	64916534	1.000000	0.71417	0.941000	0.38009	0.996000	0.88848	9.476000	0.97823	2.941000	0.99782	0.655000	0.94253	GGG	.	.	.	none		0.473	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925		A	65143946	G	A	65143946	3	1	127	1	0	0	0	0	1	0	0	0	2539	1232	43	2	3134	2	CACHD1	1	65143946	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08	21826852	65143946	184106675	4	7911											
FMO1	2326	hgsc.bcm.edu	37	chr1	171247924	171247924	+	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	ggcaatataagcatccagatAtatttaaggacaagagagtc	17	9	9	6	0	0	2	0	0	0	2	2	4	1	3	1	2	1	2	1	2	7	6			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr1:171247924A>T	ENST00000354841.4	+	4	672	c.541A>T	c.(541-543)Ata>Tta	p.I181L	FMO1_ENST00000402921.2_Missense_Mutation_p.I118L|FMO1_ENST00000367750.3_Missense_Mutation_p.I181L|FMO1_ENST00000469112.1_3'UTR	NM_001282692.1	NP_001269621.1	Q01740	FMO1_HUMAN	flavin containing monooxygenase 1	181					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)	GCATCCAGATATATTTAAGGA	0.418																																					p.I181L		Atlas-SNP	.											.	FMO1	79	.	0			c.A541T						PASS	.						74	77	76					1																	171247924		2203	4300	6503	SO:0001583	missense	2326	exon5			CCAGATATATTTA	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.541A>T	chr1.hg19:g.171247924A>T	ENSP00000346901:p.Ile181Leu	111.0	0.0	.		137.0	44.0	.	NM_002021	A8K248|B7Z3P4|Q5QPT2|Q9UJC2	Missense_Mutation	SNP	ENST00000354841.4	hg19	CCDS1294.1	.	.	.	.	.	.	.	.	.	.	A	13.08	2.131021	0.37630	.	.	ENSG00000010932	ENST00000367750;ENST00000433267;ENST00000402921;ENST00000354841	T;T;T;T	0.57273	0.41;0.41;0.41;0.41	5.66	1.85	0.25348	.	0.462268	0.24947	N	0.034331	T	0.13243	0.0321	N	0.20610	0.595	0.09310	N	0.999994	B;B;B	0.13145	0.007;0.001;0.002	B;B;B	0.16289	0.015;0.001;0.01	T	0.21621	-1.0240	10	0.31617	T	0.26	-0.8266	5.0708	0.14606	0.5496:0.1475:0.3029:0.0	.	118;181;181	B7Z3P4;B2RCG5;Q01740	.;.;FMO1_HUMAN	L	181;181;118;181	ENSP00000356724:I181L;ENSP00000406982:I181L;ENSP00000385543:I118L;ENSP00000346901:I181L	ENSP00000346901:I181L	I	+	1	0	FMO1	169514548	0.000000	0.05858	0.998000	0.56505	0.998000	0.95712	0.351000	0.20096	0.401000	0.25424	0.460000	0.39030	ATA	.	.	.	none		0.418	FMO1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086212.1	NM_002021		T	171247924	A	T	171247924	3	4	127	1	0	0	0	0	1	0	0	0	5961	449	16	5	555	5	FMO1	1	171247924	Missense_Mutation	SNP	A	TCGA-BQ-5892-01A-11D-1589-08	106103978	171247924	78002697	5	7912											
C1orf9	51430	hgsc.bcm.edu	37	chr1	172558217	172558217	+	Missense_Mutation	SNP	T	T	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	gagtaaaggaaaagattatcTtgtgttagctcaaccaccct	14	11	8	8	0	2	1	1	0	1	1	2	3	2	2	2	1	2	3	2	1	7	4			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr1:172558217T>G	ENST00000263688.3	+	18	2195	c.1976T>G	c.(1975-1977)cTt>cGt	p.L659R	SUCO_ENST00000610051.1_Intron|SUCO_ENST00000367723.4_Missense_Mutation_p.L810R|SUCO_ENST00000608151.1_Missense_Mutation_p.L811R	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	659					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											AAAGATTATCTTGTGTTAGCT	0.383																																					p.L659R		Atlas-SNP	.											.	.	.	.	0			c.T1976G						PASS	.						79	81	81					1																	172558217		2203	4299	6502	SO:0001583	missense	51430	exon18			ATTATCTTGTGTT	AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"SUN-like protein 1", "osteopotentia"		"chromosome 1 open reading frame 9"	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.1976T>G	chr1.hg19:g.172558217T>G	ENSP00000263688:p.Leu659Arg	73.0	0.0	.		88.0	30.0	.	NM_014283	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Missense_Mutation	SNP	ENST00000263688.3	hg19	CCDS1303.1	.	.	.	.	.	.	.	.	.	.	T	3.471	-0.108011	0.06924	.	.	ENSG00000094975	ENST00000367723;ENST00000263688	.	.	.	4.95	2.51	0.30379	.	0.913904	0.09394	N	0.808213	T	0.11324	0.0276	L	0.43152	1.355	0.09310	N	1	B;B;B	0.10296	0.001;0.003;0.001	B;B;B	0.06405	0.001;0.002;0.001	T	0.28170	-1.0052	9	0.18276	T	0.48	-0.0114	2.1827	0.03879	0.4718:0.1619:0.0:0.3663	.	659;811;659	B4DZJ3;Q5H945;Q9UBS9	.;.;OSPT_HUMAN	R	811;659	.	ENSP00000263688:L659R	L	+	2	0	C1orf9	170824840	0.000000	0.05858	0.002000	0.10522	0.610000	0.37248	-0.219000	0.09228	0.693000	0.31634	0.460000	0.39030	CTT	.	.	.	none		0.383	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227		G	172558217	T	G	172558217	3	3	127	1	0	0	0	0	1	0	0	0	2069	1609	56	5	2046	5	C1orf9	1	172558217	Missense_Mutation	SNP	T	TCGA-BQ-5892-01A-11D-1589-08	1310293	172558217	76692404	6	7913											
TMEM81	388730	hgsc.bcm.edu	37	chr1	205053045	205053045	+	Missense_Mutation	SNP	A	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	agttggcttgaaagggtttgAagacctcatcgtcagtggag	10	11	14	6	1	2	3	2	2	0	1	3	4	2	4	1	3	0	3	1	3	2	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr1:205053045A>C	ENST00000367167.3	-	1	600	c.404T>G	c.(403-405)tTc>tGc	p.F135C		NM_203376.1	NP_976310.1	Q6P7N7	TMM81_HUMAN	transmembrane protein 81	135	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)			AAAGGGTTTGAAGACCTCATC	0.468																																					p.F135C		Atlas-SNP	.											.	TMEM81	23	.	0			c.T404G						PASS	.						87	92	90					1																	205053045		2203	4300	6503	SO:0001583	missense	388730	exon1			GGTTTGAAGACCT	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.404T>G	chr1.hg19:g.205053045A>C	ENSP00000356135:p.Phe135Cys	119.0	0.0	.		139.0	32.0	.	NM_203376	Q6UVZ4	Missense_Mutation	SNP	ENST00000367167.3	hg19	CCDS1450.1	.	.	.	.	.	.	.	.	.	.	A	15.50	2.853325	0.51270	.	.	ENSG00000174529	ENST00000367167	T	0.42900	0.96	5.93	5.93	0.95920	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.64216	0.2578	M	0.72894	2.215	0.47245	D	0.999365	D	0.89917	1.0	D	0.91635	0.999	T	0.67562	-0.5639	10	0.87932	D	0	-6.5281	14.6242	0.68608	1.0:0.0:0.0:0.0	.	135	Q6P7N7	TMM81_HUMAN	C	135	ENSP00000356135:F135C	ENSP00000356135:F135C	F	-	2	0	TMEM81	203319668	1.000000	0.71417	0.999000	0.59377	0.171000	0.22731	5.953000	0.70290	2.281000	0.76405	0.533000	0.62120	TTC	.	.	.	none		0.468	TMEM81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090076.1	NM_203376		C	205053045	A	C	205053045	3	2	127	1	0	0	0	0	1	0	0	0	16217	246	9	5	367	5	TMEM81	1	205053045	Missense_Mutation	SNP	A	TCGA-BQ-5892-01A-11D-1589-08	32494828	205053045	44197576	7	7914											
NT5C1B	93034	hgsc.bcm.edu	37	chr2	18767651	18767651	+	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	cttccgcagtgatgattcttGtgatccctgtgatggaaaga	9	13	11	8	1	1	5	0	4	1	1	3	6	3	6	2	1	0	1	2	1	1	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr2:18767651G>C	ENST00000359846.2	-	4	384	c.307C>G	c.(307-309)Caa>Gaa	p.Q103E	NT5C1B_ENST00000304081.4_Missense_Mutation_p.Q43E|RNU6-1215P_ENST00000384441.1_RNA|NT5C1B_ENST00000460052.1_5'UTR|NT5C1B_ENST00000600945.1_Missense_Mutation_p.Q103E|NT5C1B-RDH14_ENST00000532967.1_Missense_Mutation_p.Q103E	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	103	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)				GATGATTCTTGTGATCCCTGT	0.488																																					p.Q120E		Atlas-SNP	.											.	NT5C1B	72	.	0			c.C358G						PASS	.						97	86	89					2																	18767651		2203	4300	6503	SO:0001583	missense	93034	exon4			ATTCTTGTGATCC	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.307C>G	chr2.hg19:g.18767651G>C	ENSP00000352904:p.Gln103Glu	104.0	0.0	.		104.0	11.0	.	NM_001199087	B5MCR0|B7ZVX7|Q53RX2|Q8N9W3|Q8NA26|Q96DU5|Q96KE6|Q96M25|Q96SA3	Missense_Mutation	SNP	ENST00000359846.2	hg19	CCDS33150.1	.	.	.	.	.	.	.	.	.	.	G	11.49	1.655456	0.29425	.	.	ENSG00000250741;ENSG00000250741;ENSG00000185013;ENSG00000185013;ENSG00000185013	ENST00000532967;ENST00000444297;ENST00000304081;ENST00000359846;ENST00000416783	D	0.91124	-2.79	4.79	4.79	0.61399	.	0.287423	0.25604	N	0.029528	D	0.84723	0.5535	L	0.29908	0.895	0.26210	N	0.979313	B;B;B;P;B;B;B;B	0.35745	0.366;0.366;0.278;0.518;0.39;0.264;0.209;0.313	B;B;B;B;B;B;B;B	0.35931	0.156;0.156;0.079;0.156;0.068;0.164;0.106;0.214	T	0.77930	-0.2403	10	0.37606	T	0.19	-30.2005	13.6483	0.62294	0.0:0.0:1.0:0.0	.	86;120;43;86;43;43;103;103	E7EXB7;B4DZ86;B4DXQ9;B4DXZ9;C9J2C7;Q96P26-2;Q96P26;Q96P26-4	.;.;.;.;.;.;5NT1B_HUMAN;.	E	103;43;43;103;120	ENSP00000412639:Q43E	ENSP00000305979:Q43E	Q	-	1	0	NT5C1B-RDH14;NT5C1B	18631132	0.991000	0.36638	0.985000	0.45067	0.092000	0.18411	2.396000	0.44468	2.941000	0.99782	0.655000	0.94253	CAA	.	.	.	none		0.488	NT5C1B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323822.1			C	18767651	G	C	18767651	3	2	127	1	0	0	0	0	1	0	0	0	10693	1386	48	4	1553	4	NT5C1B	2	18767651	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08		18767651	224431722	8	7915											
GPR155	151556	hgsc.bcm.edu	37	chr2	175346653	175346657	+	Frame_Shift_Del	DEL	GTTAA	GTTAA	-																															tggtcatattgactgcaatgGttaagttctctgcaggtaaa																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	GTTAA	GTTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr2:175346653_175346657delGTTAA	ENST00000392552.2	-	2	266_270	c.28_32delTTAAC	c.(28-33)ttaaccfs	p.LT10fs	GPR155_ENST00000295500.4_Frame_Shift_Del_p.LT10fs|GPR155_ENST00000392551.2_Frame_Shift_Del_p.LT10fs	NM_001267051.1|NM_152529.6	NP_001253980.1|NP_689742.4	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155	10					cognition (GO:0050890)|intracellular signal transduction (GO:0035556)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	26						GACTGCAATGGTTAAGTTCTCTGCA	0.4																																					p.10_11del		Atlas-INDEL	.											.	GPR155	76	.	0			c.29_33del						PASS	.																																			SO:0001589	frameshift_variant	151556	exon2			.	AY255528	CCDS2259.1, CCDS74605.1	2q31.1	2012-04-10			ENSG00000163328	ENSG00000163328			22951	protein-coding gene	gene with protein product						12679517	Standard	NM_001033045		Approved	DEPDC3, DEP.7, FLJ31819, PGR22	uc002uiu.4	Q7Z3F1	OTTHUMG00000132336	ENST00000392552.2:c.28_32delTTAAC	chr2.hg19:g.175346653_175346657delGTTAA	ENSP00000376335:p.Leu10fs	161.0	0.0	0		162.0	45.0	0.277778	NM_001267051	B2RCI2|D3DPE2|Q4G0Y6|Q53SJ3|Q53TA8|Q69YG8|Q86SP9|Q8N261|Q8N639|Q8N8K3|Q96MV6	Frame_Shift_Del	DEL	ENST00000392552.2	hg19	CCDS2259.1																																																																																			.	.	.	none		0.4	GPR155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255455.1	NM_152529		-	175346657	GTTAA	-	175346653	7	5	127	1	0	1	0	1	0	0	0	0	6667	1261	44	0	2640	0	GPR155	2	175346653	Frame_Shift_Del	DEL	GTTAA	TCGA-BQ-5892-01A-11D-1589-08	156579002	175346653	67852720	9	7916											
CPO	130749	hgsc.bcm.edu	37	chr2	207827299	207827299	+	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	cagttaattctcacaccttaCggctacaccaaaaataaatc	16	10	3	12	1	1	0	1	0	1	0	3	0	1	0	2	1	2	2	2	1	7	5			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr2:207827299C>T	ENST00000272852.3	+	7	784	c.738C>T	c.(736-738)taC>taT	p.Y246Y		NM_173077.2	NP_775100.1	Q8IVL8	CBPO_HUMAN	carboxypeptidase O	246						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)		TCACACCTTACGGCTACACCA	0.448																																					p.Y246Y		Atlas-SNP	.											.	CPO	42	.	0			c.C738T						PASS	.						170	160	164					2																	207827299		2203	4300	6503	SO:0001819	synonymous_variant	130749	exon7			ACCTTACGGCTAC		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.738C>T	chr2.hg19:g.207827299C>T		179.0	0.0	.		255.0	15.0	.	NM_173077	Q2M277|Q7RTW7	Silent	SNP	ENST00000272852.3	hg19	CCDS2372.1																																																																																			.	.	.	none		0.448	CPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202040.2	NM_173077		T	207827299	C	T	207827299	2	4	127	1	0	0	0	0	0	0	0	1	3822	547	19	1		1	CPO	2	207827299	Silent	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	32480646	207827299	35372074	10	7917											
VHL	7428	hgsc.bcm.edu	37	chr3	10191506	10191506	+	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	agcgatgcctccaggttgtcCggagcctagtcaagcctgag	8	8	13	12	2	1	1	1	1	0	0	3	3	3	2	5	2	4	1	5	2	2	2	rs5030820		TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr3:10191506C>G	ENST00000256474.2	+	3	1339	c.499C>G	c.(499-501)Cgg>Ggg	p.R167G	VHL_ENST00000345392.2_Missense_Mutation_p.R126G|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	167			R -> G (in VHLD; type I-II). {ECO:0000269|PubMed:9829911}.|R -> Q (in pheochromocytoma and VHLD; type II; common mutation; dbSNP:rs5030821). {ECO:0000269|PubMed:12000816, ECO:0000269|PubMed:8956040, ECO:0000269|PubMed:9829912}.|R -> W (in pheochromocytoma and VHLD; type II; common mutation; dbSNP:rs5030820). {ECO:0000269|PubMed:12000816, ECO:0000269|PubMed:8592333, ECO:0000269|PubMed:8956040, ECO:0000269|PubMed:9829912}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|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)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.R167W(8)|p.R167G(2)|p.R167fs*1(1)|p.V166fs*6(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CCAGGTTGTCCGGAGCCTAGT	0.512		1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																												p.R167G		Atlas-SNP	.	yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	VHL,NS,carcinoma,-1,1	VHL	2192	.	12	Substitution - Missense(10)|Deletion - Frameshift(1)|Insertion - Frameshift(1)	kidney(8)|adrenal_gland(2)|large_intestine(1)|endometrium(1)	c.C499G	GRCh37	CM941383|CM941384|HX040002	VHL	M|X	rs5030820	PASS	.						92	84	87					3																	10191506		2203	4300	6503	SO:0001583	missense	7428	exon3	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	GTTGTCCGGAGCC	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.499C>G	chr3.hg19:g.10191506C>G	ENSP00000256474:p.Arg167Gly	47.0	0.0	.		58.0	24.0	.	NM_000551	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	hg19	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	C	18.10	3.548531	0.65311	.	.	ENSG00000134086	ENST00000256474;ENST00000345392;ENST00000450183	D;D	0.99830	-7.01;-7.01	4.86	3.97	0.46021	von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);von Hippel-Lindau disease tumor suppressor, alpha domain (1);	0.000000	0.85682	D	0.000000	D	0.99664	0.9875	M	0.68952	2.095	0.42468	D	0.992812	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.97794	1.0240	10	0.54805	T	0.06	-6.8035	10.4067	0.44260	0.3559:0.6441:0.0:0.0	.	126;167	P40337-2;P40337	.;VHL_HUMAN	G	167;126;85	ENSP00000256474:R167G;ENSP00000344757:R126G	ENSP00000256474:R167G	R	+	1	2	VHL	10166506	0.999000	0.42202	0.908000	0.35775	0.831000	0.47069	2.914000	0.48797	1.375000	0.46248	0.655000	0.94253	CGG	.	C|1.000	.	weak		0.512	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		G	10191506	C	G	10191506	3	3	127	1	0	0	0	0	1	0	0	0	17174	643	23	4	509	4	VHL	3	10191506	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08		10191506	187830924	11	7918											
BAP1	51533	hgsc.bcm.edu	37	chr3	52443866	52443866	+	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	0	0	0	0	0	0	0	0	0	0	tcccctcctcacctgggtcgCtctccagctccagccagccc	4	8	7	22	1	2	0	1	0	1	0	7	0	5	0	8	1	3	2	8	1	0	0			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr3:52443866C>T	ENST00000327906.3	+	0	0				BAP1_ENST00000460680.1_Missense_Mutation_p.S10N|PHF7_ENST00000347025.2_5'Flank|BAP1_ENST00000296288.5_Missense_Mutation_p.S10N	NM_016483.4	NP_057567.3	Q9BWX1	PHF7_HUMAN	PHD finger protein 7							Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)	p.S10T(1)|p.E7_S10delELES(1)		breast(2)|large_intestine(4)|lung(3)	9				BRCA - Breast invasive adenocarcinoma(193;1.71e-05)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)|OV - Ovarian serous cystadenocarcinoma(275;0.0275)		ACCTGGGTCGCTCTCCAGCTC	0.746																																					p.S10N		Atlas-SNP	.											BAP1,NS,carcinoma,0,3	BAP1	371	.	2	Substitution - Missense(1)|Deletion - In frame(1)	kidney(2)	c.G29A						PASS	.						24	30	28					3																	52443866		2203	4298	6501	SO:0001631	upstream_gene_variant	8314	exon1			GGGTCGCTCTCCA	AY014283	CCDS2854.1, CCDS2855.1	3p21.31	2013-01-28			ENSG00000010318	ENSG00000010318		"Zinc fingers, PHD-type"	18458	protein-coding gene	gene with protein product						11042152, 11829468	Standard	NM_016483		Approved	NYD-SP6, HSPC226	uc003ddy.3	Q9BWX1	OTTHUMG00000158495		chr3.hg19:g.52443866C>T	Exception_encountered	59.0	0.0	.		48.0	24.0	.	NM_004656	K4DI82	Missense_Mutation	SNP	ENST00000327906.3	hg19	CCDS2854.1	.	.	.	.	.	.	.	.	.	.	C	35	5.450733	0.96205	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	T;T	0.61627	0.09;0.09	4.93	4.93	0.64822	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (4);	0.000000	0.85682	D	0.000000	T	0.79131	0.4394	M	0.87180	2.865	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.83154	-0.0102	10	0.66056	D	0.02	-4.1481	15.9287	0.79644	0.0:1.0:0.0:0.0	.	10	Q92560	BAP1_HUMAN	N	10	ENSP00000417132:S10N;ENSP00000296288:S10N	ENSP00000296288:S10N	S	-	2	0	BAP1	52418906	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.832000	0.62759	2.289000	0.77006	0.561000	0.74099	AGC	.	.	.	none		0.746	PHF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351155.1	NM_016483		T	52443866	C	T	52443866	1	4	127	0	1	0	0	0	0	0	0	0	1311	797	28	2		2	BAP1	3	52443866	5'Flank	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	42252360	52443866	145578564	12	7919											
HAUS3	79441	hgsc.bcm.edu	37	chr4	2242534	2242534	+	Missense_Mutation	SNP	A	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	acaacacgttctgttcattcAcattcccacaaaaccacttc	13	11	2	15	1	3	0	2	0	1	0	5	0	4	0	2	0	2	2	2	0	3	5			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr4:2242534A>C	ENST00000243706.4	-	2	369	c.140T>G	c.(139-141)gTg>gGg	p.V47G	POLN_ENST00000511885.2_Intron|POLN_ENST00000515357.1_Intron|HAUS3_ENST00000506763.1_Missense_Mutation_p.V47G|HAUS3_ENST00000443786.2_Missense_Mutation_p.V47G	NM_024511.5	NP_078787.2	Q68CZ6	HAUS3_HUMAN	HAUS augmin-like complex, subunit 3	47					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)|endometrium(1)|large_intestine(7)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						CTGTTCATTCACATTCCCACA	0.413																																					p.V47G		Atlas-SNP	.											.	HAUS3	54	.	0			c.T140G						PASS	.						121	110	114					4																	2242534		2203	4300	6503	SO:0001583	missense	79441	exon2			TCATTCACATTCC	AF040964	CCDS33941.1	4p16.3	2013-10-11	2009-04-20	2009-04-20	ENSG00000214367	ENSG00000214367		"HAUS augmin-like complex subunits"	28719	protein-coding gene	gene with protein product		613430	"chromosome 4 open reading frame 15"	C4orf15		19427217, 19812674	Standard	NM_024511		Approved	MGC4701, IT1, dgt3	uc003ges.1	Q68CZ6		ENST00000243706.4:c.140T>G	chr4.hg19:g.2242534A>C	ENSP00000243706:p.Val47Gly	168.0	0.0	.		153.0	13.0	.	NM_024511	B4DF64|O43606|Q8TAZ5|Q9BTJ9	Missense_Mutation	SNP	ENST00000243706.4	hg19	CCDS33941.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.101593	0.76983	.	.	ENSG00000214367	ENST00000506763;ENST00000243706;ENST00000443786	T;T	0.59638	0.25;0.25	4.68	4.68	0.58851	.	0.084524	0.49305	U	0.000154	T	0.70596	0.3242	M	0.78049	2.395	0.80722	D	1	D;D	0.67145	0.996;0.996	P;P	0.62089	0.898;0.898	T	0.74222	-0.3735	10	0.87932	D	0	-17.236	8.3587	0.32346	0.9107:0.0:0.0893:0.0	.	47;47	B4DF64;Q68CZ6	.;HAUS3_HUMAN	G	47	ENSP00000243706:V47G;ENSP00000392903:V47G	ENSP00000243706:V47G	V	-	2	0	HAUS3	2212332	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.993000	0.70616	1.850000	0.53721	0.459000	0.35465	GTG	.	.	.	none		0.413	HAUS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357446.1	NM_024511		C	2242534	A	C	2242534	3	2	127	1	0	0	0	0	1	0	0	0	6974	159	6	5	1687	5	HAUS3	4	2242534	Missense_Mutation	SNP	A	TCGA-BQ-5892-01A-11D-1589-08		2242534	188911742	13	7920											
TMPRSS11A	339967	hgsc.bcm.edu	37	chr4	68777129	68777129	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtagactccaggcttgtcCttttgaccacagttatctcc	7	14	8	12	0	1	2	0	1	1	1	4	2	3	2	4	1	0	3	4	1	2	5	rs376494815		TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr4:68777129C>T	ENST00000334830.7	-	10	1943	c.1197G>A	c.(1195-1197)aaG>aaA	p.K399K	UBA6-AS1_ENST00000500538.2_RNA|TMPRSS11A_ENST00000508048.1_Silent_p.K395K|TMPRSS11A_ENST00000396188.2_Silent_p.K396K			Q6ZMR5	TM11A_HUMAN	transmembrane protease, serine 11A	399	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cell cycle (GO:0007049)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|cervix(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	29						CAGGCTTGTCCTTTTGACCAC	0.403																																					p.K399K	NSCLC(26;2 894 10941 14480 22546)	Atlas-SNP	.											.	TMPRSS11A	74	.	0			c.G1197A						PASS	.	C	,	0,4406		0,0,2203	181	170	174		1188,1197	3.8	1	4		174	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	TMPRSS11A	NM_001114387.1,NM_182606.3	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	396/419,399/422	68777129	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	339967	exon10			CTTGTCCTTTTGA	AF071882	CCDS3519.1	4q13.2	2010-04-13			ENSG00000187054	ENSG00000187054		"Serine peptidases / Transmembrane"	27954	protein-coding gene	gene with protein product		611704				15328353	Standard	NM_182606		Approved	ECRG1	uc003hdr.1	Q6ZMR5	OTTHUMG00000129303	ENST00000334830.7:c.1197G>A	chr4.hg19:g.68777129C>T		150.0	0.0	.		176.0	9.0	.	NM_182606	J3KNQ8|Q2NKI9|Q6JE90|Q7RTY4|Q86TK8	Silent	SNP	ENST00000334830.7	hg19	CCDS3519.1																																																																																			.	.	.	weak		0.403	TMPRSS11A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251433.3	NM_182606		T	68777129	C	T	68777129	2	4	127	1	0	0	0	0	0	0	0	1	16251	680	24	2		2	TMPRSS11A	4	68777129	Silent	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	66534595	68777129	122377147	14	7921											
ALPK1	80216	hgsc.bcm.edu	37	chr4	113333046	113333046	+	Missense_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	cggcggctattgtgttcttgGtggaccggttcctgtatggg	3	14	16	8	3	1	0	0	0	1	0	2	1	2	1	2	6	0	4	2	6	2	6			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr4:113333046G>A	ENST00000458497.1	+	5	619	c.340G>A	c.(340-342)Gtg>Atg	p.V114M	ALPK1_ENST00000505912.1_3'UTR|ALPK1_ENST00000504176.2_Missense_Mutation_p.V36M|ALPK1_ENST00000177648.9_Missense_Mutation_p.V114M	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	114							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		TGTGTTCTTGGTGGACCGGTT	0.622																																					p.V114M		Atlas-SNP	.											.	ALPK1	125	.	0			c.G340A						PASS	.						54	51	52					4																	113333046		2203	4300	6503	SO:0001583	missense	80216	exon5			TTCTTGGTGGACC	AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"lymphocyte alpha-kinase"	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.340G>A	chr4.hg19:g.113333046G>A	ENSP00000398048:p.Val114Met	40.0	0.0	.		39.0	7.0	.	NM_001102406	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Missense_Mutation	SNP	ENST00000458497.1	hg19	CCDS3697.1	.	.	.	.	.	.	.	.	.	.	G	5.078	0.200114	0.09652	.	.	ENSG00000073331	ENST00000458497;ENST00000177648;ENST00000309610;ENST00000504176	T;T;T	0.24151	1.87;1.87;1.87	5.34	-1.67	0.08238	.	0.652897	0.16722	N	0.202210	T	0.05364	0.0142	N	0.00538	-1.39	0.20873	N	0.999835	B;B;B;B	0.18610	0.029;0.023;0.006;0.009	B;B;B;B	0.12837	0.008;0.008;0.005;0.004	T	0.39231	-0.9624	10	0.18276	T	0.48	0.8551	6.1882	0.20510	0.448:0.3512:0.2008:0.0	.	36;89;89;114	F5H138;Q9H623;E7EX13;Q96QP1	.;.;.;ALPK1_HUMAN	M	114;114;89;36	ENSP00000398048:V114M;ENSP00000177648:V114M;ENSP00000426044:V36M	ENSP00000177648:V114M	V	+	1	0	ALPK1	113552495	1.000000	0.71417	0.016000	0.15963	0.097000	0.18754	2.098000	0.41757	-0.525000	0.06391	-0.502000	0.04539	GTG	.	.	.	none		0.622	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144		A	113333046	G	A	113333046	3	1	127	1	0	0	0	0	1	0	0	0	544	1261	44	2	350	2	ALPK1	4	113333046	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08	44555917	113333046	77821230	15	7922											
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123128292	123128292	+	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	tcaagactggtctagtgacaGtcctccagacattttttcat	10	14	7	10	0	3	3	2	1	1	2	5	3	5	3	2	1	0	0	2	1	2	4			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr4:123128292G>C	ENST00000264501.4	+	16	1899	c.1526G>C	c.(1525-1527)aGt>aCt	p.S509T	KIAA1109_ENST00000495260.1_3'UTR|KIAA1109_ENST00000455637.1_Missense_Mutation_p.S509T|KIAA1109_ENST00000388738.3_Missense_Mutation_p.S509T			Q2LD37	K1109_HUMAN	KIAA1109	509					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						TCTAGTGACAGTCCTCCAGAC	0.313																																					p.S509T		Atlas-SNP	.											.	KIAA1109	424	.	0			c.G1526C						PASS	.						117	112	114					4																	123128292		1798	4073	5871	SO:0001583	missense	84162	exon14			GTGACAGTCCTCC	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.1526G>C	chr4.hg19:g.123128292G>C	ENSP00000264501:p.Ser509Thr	300.0	0.0	.		276.0	65.0	.	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.47|11.47	1.647458|1.647458	0.29246|0.29246	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000424425|ENST00000264501;ENST00000388738;ENST00000455637	.|T;T;T	.|0.23147	.|2.51;2.51;1.92	5.67|5.67	4.81|4.81	0.61882|0.61882	.|.	.|0.580238	.|0.15339	.|N	.|0.267600	T|T	0.38983|0.38983	0.1061|0.1061	L|L	0.33485|0.33485	1.01|1.01	0.42164|0.42164	D|D	0.991613|0.991613	.|D	.|0.58268	.|0.982	.|D	.|0.67548	.|0.952	T|T	0.08848|0.08848	-1.0702|-1.0702	5|10	.|0.45353	.|T	.|0.12	.|.	13.7177|13.7177	0.62708|0.62708	0.0749:0.0:0.9251:0.0|0.0749:0.0:0.9251:0.0	.|.	.|509	.|Q2LD37	.|K1109_HUMAN	H|T	341|509	.|ENSP00000264501:S509T;ENSP00000373390:S509T;ENSP00000389925:S509T	.|ENSP00000264501:S509T	Q|S	+|+	3|2	2|0	KIAA1109|KIAA1109	123347742|123347742	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	3.198000|3.198000	0.51035|0.51035	1.349000|1.349000	0.45751|0.45751	0.655000|0.655000	0.94253|0.94253	CAG|AGT	.	.	.	none		0.313	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		C	123128292	G	C	123128292	3	2	127	1	0	0	0	0	1	0	0	0	8215	1029	36	4	1580	4	KIAA1109	4	123128292	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08	9795246	123128292	68025984	16	7923											
MGC42105	167359	hgsc.bcm.edu	37	chr5	43280172	43280172	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtgggcgattttggattcAgcacagtaagcaaaaaaggt	14	9	13	5	1	1	0	1	0	0	0	1	2	1	1	0	4	2	3	0	4	4	4			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr5:43280172A>G	ENST00000512796.1	+	4	2151	c.652A>G	c.(652-654)Agc>Ggc	p.S218G	NIM1_ENST00000326035.2_Missense_Mutation_p.S218G			Q8IY84	NIM1_HUMAN		218	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)										TTTTGGATTCAGCACAGTAAG	0.433																																					p.S218G		Atlas-SNP	.											.	.	.	.	0			c.A652G						PASS	.						93	87	89					5																	43280172		2203	4300	6503	SO:0001583	missense	0	exon4			GGATTCAGCACAG																												ENST00000512796.1:c.652A>G	chr5.hg19:g.43280172A>G	ENSP00000420849:p.Ser218Gly	139.0	0.0	.		120.0	40.0	.	NM_153361	B3KVM1	Missense_Mutation	SNP	ENST00000512796.1	hg19	CCDS3943.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.726016	0.89298	.	.	ENSG00000177453	ENST00000326035;ENST00000512796	T;T	0.30448	1.53;1.53	5.69	5.69	0.88448	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.56819	0.2011	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.56062	-0.8041	10	0.33940	T	0.23	.	15.9442	0.79782	1.0:0.0:0.0:0.0	.	218	Q8IY84	NIM1_HUMAN	G	218	ENSP00000313572:S218G;ENSP00000420849:S218G	ENSP00000313572:S218G	S	+	1	0	AC114947.1	43315929	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.166000	0.68216	0.533000	0.62120	AGC	.	.	.	none		0.433	NIM1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368017.1			G	43280172	A	G	43280172	3	3	127	1	0	0	0	0	1	0	0	0	9559	188	7	3	662	3	MGC42105	5	43280172	Missense_Mutation	SNP	A	TCGA-BQ-5892-01A-11D-1589-08		43280172	137635088	17	7924											
BDP1	55814	hgsc.bcm.edu	37	chr5	70800508	70800508	+	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	aagaggaagatgtcatattaCagcctgagaaaaatgattct	17	10	9	5	0	2	4	1	2	1	3	2	6	2	5	1	1	2	0	1	1	6	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr5:70800508C>T	ENST00000358731.4	+	16	2565	c.2302C>T	c.(2302-2304)Cag>Tag	p.Q768*	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	768					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)		TGTCATATTACAGCCTGAGAA	0.328																																					p.Q768X		Atlas-SNP	.											.	BDP1	204	.	0			c.C2302T						PASS	.						94	86	88					5																	70800508		1839	4090	5929	SO:0001587	stop_gained	55814	exon16			ATATTACAGCCTG	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.2302C>T	chr5.hg19:g.70800508C>T	ENSP00000351575:p.Gln768*	86.0	0.0	.		143.0	42.0	.	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Nonsense_Mutation	SNP	ENST00000358731.4	hg19	CCDS43328.1	.	.	.	.	.	.	.	.	.	.	C	38	7.211890	0.98139	.	.	ENSG00000145734	ENST00000358731;ENST00000437938;ENST00000451951;ENST00000444711	.	.	.	4.86	1.8	0.24995	.	0.592434	0.16073	N	0.230909	.	.	.	.	.	.	0.09310	N	0.999997	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.9453	0.29982	0.165:0.4911:0.3439:0.0	.	.	.	.	X	768;768;348;768	.	ENSP00000351575:Q768X	Q	+	1	0	BDP1	70836264	0.007000	0.16637	0.008000	0.14137	0.007000	0.05969	0.576000	0.23744	0.600000	0.29862	0.603000	0.83216	CAG	.	.	.	none		0.328	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429		T	70800508	C	T	70800508	4	4	127	1	0	0	0	0	0	1	0	0	1395	479	17	2	2364	2	BDP1	5	70800508	Nonsense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	27520336	70800508	110114752	18	7925											
SAR1B	51128	hgsc.bcm.edu	37	chr5	133956720	133956720	+	Frame_Shift_Del	DEL	T	T	-																															tccaatccaagaaataccagTttaccagttttcttatataa																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr5:133956720delT	ENST00000402673.2	-	3	359	c.81delA	c.(79-81)aaafs	p.K27fs	SAR1B_ENST00000507419.1_Intron|SAR1B_ENST00000439578.1_Frame_Shift_Del_p.K27fs	NM_016103.3	NP_057187.1	Q9Y6B6	SAR1B_HUMAN	secretion associated, Ras related GTPase 1B	27					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)			GAAATACCAGTTTACCAGTTT	0.343																																					p.L28fs		Atlas-INDEL	.											.	SAR1B	19	.	0			c.82delC						PASS	.						179	162	168					5																	133956720		2202	4300	6502	SO:0001589	frameshift_variant	51128	exon4			.	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.81delA	chr5.hg19:g.133956720delT	ENSP00000385432:p.Lys27fs	111.0	0.0	0		170.0	41.0	0.241176	NM_001033503	D3DQA4|Q567T4	Frame_Shift_Del	DEL	ENST00000402673.2	hg19	CCDS4177.1																																																																																			.	.	.	none		0.343	SAR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251158.2	NM_016103		-	133956720	T	-	133956720	7	5	127	1	0	1	0	1	0	0	0	0	13853	1722	60	0	535	0	SAR1B	5	133956720	Frame_Shift_Del	DEL	T	TCGA-BQ-5892-01A-11D-1589-08	63156212	133956720	46958540	19	7926											
MAML1	9794	hgsc.bcm.edu	37	chr5	179192969	179192987	+	Frame_Shift_Del	DEL	GGGTCTGCAGGGCAGACCT	GGGTCTGCAGGGCAGACCT	-																															gctctccacaagtgagggccGggtctgcagggcagaccttt																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	GGGTCTGCAGGGCAGACCT	GGGTCTGCAGGGCAGACCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr5:179192969_179192987delGGGTCTGCAGGGCAGACCT	ENST00000292599.3	+	2	1221_1239	c.958_976delGGGTCTGCAGGGCAGACCT	c.(958-978)gggtctgcagggcagacctttfs	p.GSAGQTF320fs	MAML1_ENST00000503050.1_3'UTR	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)											central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGTGAGGGCCGGGTCTGCAGGGCAGACCTTTCTGGGGCC	0.571																																					p.319_325del		Atlas-INDEL	.											.	MAML1	118	.	0			c.957_975del						PASS	.																																			SO:0001589	frameshift_variant	9794	exon2			.	D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"mastermind homolog"	605424	"mastermind (drosophila)-like 1"			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.958_976delGGGTCTGCAGGGCAGACCT	chr5.hg19:g.179192969_179192987delGGGTCTGCAGGGCAGACCT	ENSP00000292599:p.Gly320fs	94.0	0.0	0		89.0	19.0	0.213483	NM_014757		Frame_Shift_Del	DEL	ENST00000292599.3	hg19	CCDS34315.1																																																																																			.	.	.	none		0.571	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757		-	179192987	GGGTCTGCAGGGCAGACCT	-	179192969	7	5	127	1	0	1	0	1	0	0	0	0	9212	1116	39	0	964	0	MAML1	5	179192969	Frame_Shift_Del	DEL	GGGTCTGCAGGGCAGACCT	TCGA-BQ-5892-01A-11D-1589-08	45236249	179192969	1722291	20	7927											
PECI	10455	hgsc.bcm.edu	37	chr6	4128067	4128067	+	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	gcataatttcatgatacatcTgtgtaatgggaagacaagga	15	11	10	5	0	2	2	1	1	1	1	2	4	2	4	0	2	1	2	0	2	5	4			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr6:4128067T>A	ENST00000380118.3	-	5	538		c.e5-2		C6orf201_ENST00000380175.4_Intron|ECI2_ENST00000465828.1_Splice_Site|ECI2_ENST00000361538.2_Splice_Site|ECI2_ENST00000413766.2_Splice_Site|C6orf201_ENST00000333388.5_Intron|ECI2_ENST00000380125.2_Splice_Site			O75521	ECI2_HUMAN	enoyl-CoA delta isomerase 2						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						ATGATACATCTGTGTAATGGG	0.398																																					.		Atlas-SNP	.											.	ECI2	59	.	0			c.412-2A>T						PASS	.						116	118	117					6																	4128067		2203	4300	6503	SO:0001630	splice_region_variant	10455	exon6			TACATCTGTGTAA	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.502-2A>T	chr6.hg19:g.4128067T>A		164.0	0.0	.		194.0	53.0	.	NM_006117	Q5JYK5|Q5JYK7|Q7L124|Q8N0X0|Q9BUE9|Q9H0T9|Q9NQH1|Q9NYH7|Q9UN55	Splice_Site	SNP	ENST00000380118.3	hg19	CCDS43420.2	.	.	.	.	.	.	.	.	.	.	T	12.53	1.966691	0.34659	.	.	ENSG00000198721	ENST00000380118;ENST00000380125;ENST00000361538;ENST00000465828;ENST00000495548	.	.	.	5.64	5.64	0.86602	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6923	0.69096	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	ECI2	4073066	1.000000	0.71417	0.918000	0.36340	0.109000	0.19521	6.484000	0.73621	2.148000	0.66965	0.533000	0.62120	.	.	.	.	none		0.398	ECI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039716.4	NM_006117	Intron	A	4128067	T	A	4128067	5	1	127	1	0	0	0	0	0	0	1	0	11723	1594	55	5	708	5	PECI	6	4128067	Splice_Site	SNP	T	TCGA-BQ-5892-01A-11D-1589-08		4128067	166987000	21	7928											
SKIV2L	6499	hgsc.bcm.edu	37	chr6	31937328	31937328	+	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	cagggctctcagggacccctGagggcctggtggtccgctgc	4	7	16	14	1	1	1	1	1	1	0	3	2	2	2	4	5	1	2	4	5	0	0			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr6:31937328G>A	ENST00000375394.2	+	28	3690	c.3577G>A	c.(3577-3579)Gag>Aag	p.E1193K	DXO_ENST00000478221.1_5'Flank|STK19_ENST00000375333.2_5'Flank|STK19_ENST00000375331.2_5'Flank|SKIV2L_ENST00000544581.1_Missense_Mutation_p.E1000K	NM_006929.4	NP_008860.4	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like (S. cerevisiae)	1193					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						AGGGACCCCTGAGGGCCTGGT	0.662																																					p.E1193K		Atlas-SNP	.											.	SKIV2L	97	.	0			c.G3577A						PASS	.						64	77	72					6																	31937328		1511	2709	4220	SO:0001583	missense	6499	exon28			ACCCCTGAGGGCC		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.3577G>A	chr6.hg19:g.31937328G>A	ENSP00000364543:p.Glu1193Lys	162.0	0.0	.		160.0	41.0	.	NM_006929	O15005|Q12902|Q15476|Q5ST66	Missense_Mutation	SNP	ENST00000375394.2	hg19	CCDS4731.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.946649	0.92593	.	.	ENSG00000204351	ENST00000375394;ENST00000433155;ENST00000544581	T;T	0.39229	1.09;1.09	5.38	5.38	0.77491	DSH, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.71221	0.3314	H	0.94222	3.51	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80353	-0.1418	10	0.87932	D	0	-26.0112	17.9328	0.89004	0.0:0.0:1.0:0.0	.	1193	Q15477	SKIV2_HUMAN	K	1193;1035;1000	ENSP00000364543:E1193K;ENSP00000442645:E1000K	ENSP00000364543:E1193K	E	+	1	0	SKIV2L	32045307	1.000000	0.71417	0.476000	0.27291	0.947000	0.59692	8.247000	0.89830	2.507000	0.84556	0.655000	0.94253	GAG	.	.	.	none		0.662	SKIV2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076264.3			A	31937328	G	A	31937328	3	1	127	1	0	0	0	0	1	0	0	0	14372	1291	45	2	3687	2	SKIV2L	6	31937328	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08	27809261	31937328	139177739	22	7929											
POM121	9883	hgsc.bcm.edu	37	chr7	72412459	72412459	+	Frame_Shift_Del	DEL	G	G	-																															cgctgggtttatcacagtcaGggccgccagggctgctcccc																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr7:72412459delG	ENST00000434423.2	+	11	1927	c.1927delG	c.(1927-1929)gggfs	p.G643fs	POM121_ENST00000446813.1_Frame_Shift_Del_p.G378fs|POM121_ENST00000257622.4_Frame_Shift_Del_p.G378fs|POM121_ENST00000358357.3_Frame_Shift_Del_p.G378fs|POM121_ENST00000395270.1_Frame_Shift_Del_p.G378fs			Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin	643	Pore side. {ECO:0000255}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Lung NSC(55;0.163)				ATCACAGTCAGGGCCGCCAGG	0.597																																					p.S377fs		Atlas-INDEL	.											.	POM121	131	.	0			c.1131delA						PASS	.						1	2	2					7																	72412459		806	2133	2939	SO:0001589	frameshift_variant	9883	exon11			.	AB014518	CCDS5542.1, CCDS59059.1	7q11.23	2013-01-08	2012-03-13		ENSG00000196313	ENSG00000196313		"-"	19702	protein-coding gene	gene with protein product		615753	"POM121 membrane glycoprotein (rat)", "POM121 membrane glycoprotein"			8335683, 9734811, 17900573	Standard	NM_172020		Approved	KIAA0618, DKFZP586G1822, DKFZP586P2220, POM121A	uc003twk.2	Q96HA1	OTTHUMG00000023527	ENST00000434423.2:c.1927delG	chr7.hg19:g.72412459delG	ENSP00000405562:p.Gly643fs	112.0	0.0	0		177.0	11.0	0.0621469	NM_172020	A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	Frame_Shift_Del	DEL	ENST00000434423.2	hg19																																																																																				.	.	.	none		0.597	POM121-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347344.1			-	72412459	G	-	72412459	7	5	127	1	0	1	0	1	0	0	0	0	12246	1000	35	0	1170	0	POM121	7	72412459	Frame_Shift_Del	DEL	G	TCGA-BQ-5892-01A-11D-1589-08		72412459	86726204	23	7930											
C7orf51	222950	hgsc.bcm.edu	37	chr7	100087003	100087003	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgctgtggacctacccagcCacagcagctgggctcaagag	9	5	12	15	1	1	1	1	0	0	1	1	2	1	2	4	2	4	4	4	2	2	1			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr7:100087003C>T	ENST00000300179.2	+	4	1818	c.1659C>T	c.(1657-1659)gcC>gcT	p.A553A	NYAP1_ENST00000423930.1_Silent_p.A553A|NYAP1_ENST00000454988.1_Silent_p.A496A	NM_173564.2	NP_775835.2	Q6ZVC0	NYAP1_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 1	553					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												CCTACCCAGCCACAGCAGCTG	0.682																																					p.A553A		Atlas-SNP	.											.	.	.	.	0			c.C1659T						PASS	.						16	19	18					7																	100087003		2157	4234	6391	SO:0001819	synonymous_variant	222950	exon4			CCCAGCCACAGCA	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.1659C>T	chr7.hg19:g.100087003C>T		43.0	0.0	.		81.0	19.0	.	NM_173564	Q6U9Y3|Q8N1V0	Silent	SNP	ENST00000300179.2	hg19	CCDS5696.1																																																																																			.	.	.	none		0.682	NYAP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339335.2	NM_173564		T	100087003	C	T	100087003	2	4	127	1	0	0	0	0	0	0	0	1	2402	581	21	2		2	C7orf51	7	100087003	Silent	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	27674544	100087003	59051660	24	7931											
CADPS2	93664	hgsc.bcm.edu	37	chr7	122130209	122130210	+	Frame_Shift_Ins	INS	-	-	A																															aattgcaggaactggtttatINSatgattgacctgtggcccta																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr7:122130209_122130210insA	ENST00000449022.2	-	11	1796_1797	c.1777_1778insT	c.(1777-1779)tatfs	p.Y593fs	CADPS2_ENST00000476131.1_5'Flank|CADPS2_ENST00000412584.2_Frame_Shift_Ins_p.Y593fs|CADPS2_ENST00000313070.7_Frame_Shift_Ins_p.Y593fs|CADPS2_ENST00000334010.7_Frame_Shift_Ins_p.Y593fs	NM_017954.10	NP_060424.9	Q86UW7	CAPS2_HUMAN	Ca++-dependent secretion activator 2	593					cellular response to starvation (GO:0009267)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasmic membrane-bounded vesicle (GO:0016023)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(2)	43						AACTGGTTTATATGATTGACCT	0.376																																					p.Y593fs		Atlas-INDEL	.											.	CADPS2	116	.	0			c.1778_1779insT						PASS	.																																			SO:0001589	frameshift_variant	93664	exon11			.		CCDS47691.1, CCDS55158.1	7q31.32	2013-01-10	2008-08-28		ENSG00000081803	ENSG00000081803		"Pleckstrin homology (PH) domain containing"	16018	protein-coding gene	gene with protein product		609978	"Ca++-dependent activator protein for secretion 2"				Standard	NM_017954		Approved		uc010lkq.3	Q86UW7	OTTHUMG00000157093	ENST00000449022.2:c.1778dupT	chr7.hg19:g.122130210_122130210dupA	ENSP00000398481:p.Tyr593fs	120.0	0.0	0		145.0	39.0	0.268966	NM_001009571	A4D0X3|B7ZM56|Q658Q2|Q7Z5T7|Q8IZW9|Q8N7M4|Q9H6P4|Q9HCI1|Q9NWK8	Frame_Shift_Ins	INS	ENST00000449022.2	hg19	CCDS55158.1																																																																																			.	.	.	none		0.376	CADPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347414.2	NM_017954		A	122130210	-	A	122130209	7	5	127	1	0	1	1	0	0	0	0	0	2573	1406	49	0	2236	0	CADPS2	7	122130209	Frame_Shift_Ins	INS	-	TCGA-BQ-5892-01A-11D-1589-08	22043206	122130209	37008454	25	7932											
KIAA1967	57805	hgsc.bcm.edu	37	chr8	22473664	22473664	+	Missense_Mutation	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	ggaggcggccaaggaagaagCcaccaaggaggaagaagcca	16	0	16	9	1	0	2	0	0	0	2	0	6	0	6	4	6	2	0	4	6	6	0			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr8:22473664C>T	ENST00000308511.4	+	14	1997	c.1748C>T	c.(1747-1749)gCc>gTc	p.A583V	CCAR2_ENST00000389279.3_Missense_Mutation_p.A583V|RP11-582J16.5_ENST00000521025.1_RNA|CCAR2_ENST00000520861.1_Missense_Mutation_p.A258V			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	583					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)										AAGGAAGAAGCCACCAAGGAG	0.552																																					p.A583V		Atlas-SNP	.											.	KIAA1967	72	.	0			c.C1748T						PASS	.						94	92	93					8																	22473664		2203	4300	6503	SO:0001583	missense	57805	exon14			AAGAAGCCACCAA	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.1748C>T	chr8.hg19:g.22473664C>T	ENSP00000310670:p.Ala583Val	142.0	0.0	.		133.0	39.0	.	NM_021174	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Missense_Mutation	SNP	ENST00000308511.4	hg19	CCDS34863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	2.012|2.012	-0.426830|-0.426830	0.04701|0.04701	.|.	.|.	ENSG00000158941|ENSG00000158941	ENST00000308511;ENST00000389279;ENST00000520861|ENST00000520738	T;T;T|.	0.31769|.	1.48;1.48;1.48|.	3.18|3.18	0.0872|0.0872	0.14449|0.14449	.|.	0.654422|.	0.13268|.	N|.	0.400758|.	T|T	0.14313|0.14313	0.0346|0.0346	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B;B|.	0.06786|.	0.001;0.0|.	B;B|.	0.04013|.	0.001;0.0|.	T|T	0.24404|0.24404	-1.0161|-1.0161	10|5	0.28530|.	T|.	0.3|.	-1.6537|-1.6537	3.0601|3.0601	0.06197|0.06197	0.1906:0.4477:0.0:0.3617|0.1906:0.4477:0.0:0.3617	.|.	258;583|.	G3V119;Q8N163|.	.;K1967_HUMAN|.	V|S	583;583;258|275	ENSP00000310670:A583V;ENSP00000373930:A583V;ENSP00000429773:A258V|.	ENSP00000310670:A583V|.	A|P	+|+	2|1	0|0	KIAA1967|KIAA1967	22529609|22529609	0.001000|0.001000	0.12720|0.12720	0.050000|0.050000	0.19076|0.19076	0.319000|0.319000	0.28217|0.28217	-0.315000|-0.315000	0.08081|0.08081	-0.013000|-0.013000	0.14199|0.14199	-0.323000|-0.323000	0.08544|0.08544	GCC|CCA	.	.	.	none		0.552	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174		T	22473664	C	T	22473664	3	4	127	1	0	0	0	0	1	0	0	0	8272	739	26	2	1798	2	KIAA1967	8	22473664	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08		22473664	123890358	26	7933											
TEX15	56154	hgsc.bcm.edu	37	chr8	30704070	30704070	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accaaaaggctgggaataaaTgtcaaatcctagaatttctc	16	10	7	8	0	2	1	1	0	1	1	4	2	3	2	2	2	0	1	2	2	8	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr8:30704070T>C	ENST00000256246.2	-	1	2538	c.2464A>G	c.(2464-2466)Att>Gtt	p.I822V	TEX15_ENST00000523186.1_5'Flank	NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	822					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)		TGGGAATAAATGTCAAATCCT	0.373																																					p.I822V		Atlas-SNP	.											.	TEX15	350	.	0			c.A2464G						PASS	.						55	51	53					8																	30704070		2203	4298	6501	SO:0001583	missense	56154	exon1			AATAAATGTCAAA	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.2464A>G	chr8.hg19:g.30704070T>C	ENSP00000256246:p.Ile822Val	108.0	0.0	.		101.0	10.0	.	NM_031271		Missense_Mutation	SNP	ENST00000256246.2	hg19	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	T	0.012	-1.665157	0.00765	.	.	ENSG00000133863	ENST00000256246	T	0.09911	2.93	6.03	3.73	0.42828	.	0.872782	0.10069	N	0.719942	T	0.08846	0.0219	L	0.27053	0.805	0.09310	N	1	B	0.33171	0.4	B	0.33960	0.173	T	0.19224	-1.0312	10	0.87932	D	0	.	7.3269	0.26560	0.0:0.1436:0.0:0.8564	.	822	Q9BXT5	TEX15_HUMAN	V	822	ENSP00000256246:I822V	ENSP00000256246:I822V	I	-	1	0	TEX15	30823612	0.000000	0.05858	0.032000	0.17829	0.027000	0.11550	0.328000	0.19681	2.302000	0.77476	0.533000	0.62120	ATT	.	.	.	none		0.373	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			C	30704070	T	C	30704070	3	2	127	1	0	0	0	0	1	0	0	0	15791	1464	51	3	5921	3	TEX15	8	30704070	Missense_Mutation	SNP	T	TCGA-BQ-5892-01A-11D-1589-08	8230406	30704070	115659952	27	7934											
RORB	6096	hgsc.bcm.edu	37	chr9	77286722	77286722	+	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	cagaccgagcctggcttataGaaccaaggaaagtccagaag	15	5	11	10	1	0	3	0	0	0	3	1	5	1	4	4	2	2	1	4	2	6	2			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr9:77286722G>A	ENST00000396204.2	+	9	1162	c.1162G>A	c.(1162-1164)Gaa>Aaa	p.E388K	RORB_ENST00000376896.3_Missense_Mutation_p.E377K			Q92753	RORB_HUMAN	RAR-related orphan receptor B	388	Ligand-binding. {ECO:0000255}.				amacrine cell differentiation (GO:0035881)|cellular response to retinoic acid (GO:0071300)|eye photoreceptor cell development (GO:0042462)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|rhythmic process (GO:0048511)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.E377Q(2)|p.E377*(1)		breast(2)|large_intestine(4)|lung(1)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	12					Melatonin(DB01065)	CTGGCTTATAGAACCAAGGAA	0.428																																					p.E377K		Atlas-SNP	.											RORB_ENST00000376896,colon,carcinoma,-2,3	RORB	89	.	3	Substitution - Missense(2)|Substitution - Nonsense(1)	breast(2)|ovary(1)	c.G1129A						PASS	.						73	69	70					9																	77286722		2203	4300	6503	SO:0001583	missense	6096	exon9			CTTATAGAACCAA	Y08639	CCDS6646.1	9q22	2013-01-16			ENSG00000198963	ENSG00000198963		"Nuclear hormone receptors"	10259	protein-coding gene	gene with protein product		601972				7926749	Standard	NM_006914		Approved	RZRB, NR1F2, ROR-BETA	uc004ajh.3	Q92753	OTTHUMG00000020026	ENST00000396204.2:c.1162G>A	chr9.hg19:g.77286722G>A	ENSP00000379507:p.Glu388Lys	66.0	0.0	.		96.0	33.0	.	NM_006914	Q8WX73	Missense_Mutation	SNP	ENST00000396204.2	hg19		.	.	.	.	.	.	.	.	.	.	G	22.2	4.255074	0.80135	.	.	ENSG00000198963	ENST00000376896;ENST00000396204	D;D	0.96967	-4.19;-4.19	5.73	5.73	0.89815	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.95834	0.8644	L	0.56280	1.765	0.80722	D	1	B;B	0.27594	0.182;0.01	B;B	0.35813	0.211;0.04	D	0.93462	0.6811	10	0.52906	T	0.07	.	20.2602	0.98440	0.0:0.0:1.0:0.0	.	388;377	Q92753;Q58EY0	RORB_HUMAN;.	K	377;388	ENSP00000366093:E377K;ENSP00000379507:E388K	ENSP00000366093:E377K	E	+	1	0	RORB	76476542	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.807000	0.99171	2.861000	0.98227	0.655000	0.94253	GAA	.	.	.	none		0.428	RORB-201	KNOWN	basic	protein_coding	protein_coding				A	77286722	G	A	77286722	3	1	127	1	0	0	0	0	1	0	0	0	13542	943	33	2	1163	2	RORB	9	77286722	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08		77286722	63926709	28	7935											
SVEP1	79987	hgsc.bcm.edu	37	chr9	113265327	113265327	+	Frame_Shift_Del	DEL	G	G	-																															tagaaacttacccacacaccGgggttctggcccatcccact																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr9:113265327delG	ENST00000401783.2	-	6	1810	c.1474delC	c.(1474-1476)cggfs	p.R492fs	SVEP1_ENST00000302728.8_Frame_Shift_Del_p.R492fs|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374469.1_Frame_Shift_Del_p.R469fs|SVEP1_ENST00000374461.1_Frame_Shift_Del_p.R469fs	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	492	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						CCCACACACCGGGGTTCTGGC	0.443																																					p.R492fs		Atlas-INDEL	.											.	SVEP1	326	.	0			c.1475delG						PASS	.						133	135	134					9																	113265327		1926	4129	6055	SO:0001589	frameshift_variant	79987	exon6			.	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.1474delC	chr9.hg19:g.113265327delG	ENSP00000384917:p.Arg492fs	90.0	0.0	0		110.0	29.0	0.263636	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Frame_Shift_Del	DEL	ENST00000401783.2	hg19	CCDS48004.1																																																																																			.	.	.	none		0.443	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				-	113265327	G	-	113265327	7	5	127	1	0	1	0	1	0	0	0	0	15432	1115	39	0	9413	0	SVEP1	9	113265327	Frame_Shift_Del	DEL	G	TCGA-BQ-5892-01A-11D-1589-08	35978605	113265327	27948104	29	7936											
C10orf90	118611	hgsc.bcm.edu	37	chr10	128193076	128193076	+	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	gtgtctggagaaaaactggtCtctttgtcgtctgcatgggt	7	14	13	7	1	3	1	0	0	3	1	5	2	3	1	0	3	2	1	0	3	2	1			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr10:128193076C>G	ENST00000284694.7	-	3	813	c.693G>C	c.(691-693)gaG>gaC	p.E231D	C10orf90_ENST00000544758.1_Missense_Mutation_p.E328D|C10orf90_ENST00000368674.1_5'UTR|C10orf90_ENST00000392694.1_Missense_Mutation_p.E184D|C10orf90_ENST00000454341.1_Missense_Mutation_p.E231D|C10orf90_ENST00000356858.3_Missense_Mutation_p.E184D	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	231					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)		AAAAACTGGTCTCTTTGTCGT	0.557											OREG0020616	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E231D		Atlas-SNP	.											.	C10orf90	121	.	0			c.G693C						PASS	.						73	78	76					10																	128193076		2203	4300	6503	SO:0001583	missense	118611	exon3			ACTGGTCTCTTTG	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.693G>C	chr10.hg19:g.128193076C>G	ENSP00000284694:p.Glu231Asp	96.0	0.0	.	1563	98.0	24.0	.	NM_001004298	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Missense_Mutation	SNP	ENST00000284694.7	hg19	CCDS31310.1	.	.	.	.	.	.	.	.	.	.	C	12.46	1.944946	0.34283	.	.	ENSG00000154493	ENST00000356858;ENST00000284694;ENST00000454341;ENST00000544758;ENST00000432642;ENST00000368674;ENST00000392694	T;T;T;T;T	0.28255	1.91;1.9;1.94;1.92;1.62	5.27	3.38	0.38709	.	0.457153	0.20722	N	0.086884	T	0.28863	0.0716	L	0.58101	1.795	0.09310	N	1	B;B;B;B;B	0.13594	0.001;0.001;0.008;0.001;0.001	B;B;B;B;B	0.19148	0.003;0.01;0.024;0.01;0.007	T	0.25641	-1.0126	10	0.59425	D	0.04	-3.5758	8.1384	0.31069	0.3227:0.5212:0.1561:0.0	.	328;328;184;231;231	F5GZL2;B4DMQ6;Q5T024;Q96M02;Q96M02-2	.;.;.;CJ090_HUMAN;.	D	184;231;231;328;231;184;184	ENSP00000284694:E231D;ENSP00000398786:E231D;ENSP00000444369:E328D;ENSP00000405995:E231D;ENSP00000376459:E184D	ENSP00000284694:E231D	E	-	3	2	C10orf90	128183066	0.000000	0.05858	0.001000	0.08648	0.061000	0.15899	0.565000	0.23578	0.756000	0.33013	0.655000	0.94253	GAG	.	.	.	none		0.557	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298		G	128193076	C	G	128193076	3	3	127	1	0	0	0	0	1	0	0	0	1625	912	32	4	1434	4	C10orf90	10	128193076	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08		128193076	7341671	30	7937											
OR52B2	255725	hgsc.bcm.edu	37	chr11	6190974	6190974	+	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	gccataccaaatgttaacagTgatgtcagcacaggctaaac	15	8	8	10	0	1	1	1	1	0	0	1	1	1	1	2	1	4	3	2	1	5	3	rs35364339		TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr11:6190974T>A	ENST00000530810.1	-	1	664	c.583A>T	c.(583-585)Act>Tct	p.T195S	RP11-290F24.3_ENST00000529961.1_RNA	NM_001004052.1	NP_001004052.1	Q96RD2	O52B2_HUMAN	olfactory receptor, family 52, subfamily B, 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)			NS(1)|central_nervous_system(3)|endometrium(1)|large_intestine(1)|lung(15)	21		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;3.69e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATGTTAACAGTGATGTCAGCA	0.478																																					p.T195S	NSCLC(5;186 261 1778 7098 14207)	Atlas-SNP	.											.	OR52B2	68	.	0			c.A583T						PASS	.						51	51	51					11																	6190974		2072	4218	6290	SO:0001583	missense	255725	exon1			TAACAGTGATGTC	AB065763	CCDS53598.1	11p15.4	2012-08-09				ENSG00000255307		"GPCR / Class A : Olfactory receptors"	15207	protein-coding gene	gene with protein product							Standard	NM_001004052		Approved		uc010qzy.2	Q96RD2		ENST00000530810.1:c.583A>T	chr11.hg19:g.6190974T>A	ENSP00000432011:p.Thr195Ser	42.0	0.0	.		43.0	11.0	.	NM_001004052	Q8NGM7	Missense_Mutation	SNP	ENST00000530810.1	hg19	CCDS53598.1	.	.	.	.	.	.	.	.	.	.	T	9.208	1.030275	0.19512	.	.	ENSG00000255307	ENST00000530810	T	0.00042	8.84	5.32	4.18	0.49190	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00144	0.0004	N	0.03881	-0.34	0.09310	N	1	D	0.76494	0.999	D	0.83275	0.996	T	0.64347	-0.6429	9	0.26408	T	0.33	.	7.1804	0.25770	0.146:0.0:0.1526:0.7014	.	195	Q96RD2	O52B2_HUMAN	S	195	ENSP00000432011:T195S	ENSP00000432011:T195S	T	-	1	0	OR52B2	6147550	0.000000	0.05858	1.000000	0.80357	0.997000	0.91878	0.367000	0.20382	1.007000	0.39238	0.450000	0.29827	ACT	.	.	.	alt		0.478	OR52B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385977.1	NM_001004052		A	6190974	T	A	6190974	3	1	127	1	0	0	0	0	1	0	0	0	11118	1696	59	5	391	5	OR52B2	11	6190974	Missense_Mutation	SNP	T	TCGA-BQ-5892-01A-11D-1589-08		6190974	128815542	31	7938											
MTCH2	23788	hgsc.bcm.edu	37	chr11	47653227	47653227	+	Frame_Shift_Del	DEL	G	G	-																															atggaagggatgtgtgatgaGggtagcagcagaacgagcga																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr11:47653227delG	ENST00000302503.3	-	6	563	c.406delC	c.(406-408)ctcfs	p.L136fs	MTCH2_ENST00000534074.1_5'Flank|MTCH2_ENST00000542981.1_Intron	NM_014342.3	NP_055157.1	Q9Y6C9	MTCH2_HUMAN	mitochondrial carrier 2	136					protein localization to mitochondrion (GO:0070585)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	11						TGTGTGATGAGGGTAGCAGCA	0.433																																					p.L136fs		Atlas-INDEL	.											.	MTCH2	25	.	0			c.407delT						PASS	.						170	137	148					11																	47653227		2201	4298	6499	SO:0001589	frameshift_variant	23788	exon6			.	AF085361	CCDS7943.1	11p11.2	2013-05-22	2011-05-19		ENSG00000109919	ENSG00000109919		"Solute carriers"	17587	protein-coding gene	gene with protein product	"solute carrier family 25, member 50"	613221	"mitochondrial carrier homolog 2 (C. elegans)"				Standard	NM_014342		Approved	SLC25A50	uc010rho.2	Q9Y6C9	OTTHUMG00000166926	ENST00000302503.3:c.406delC	chr11.hg19:g.47653227delG	ENSP00000303222:p.Leu136fs	68.0	0.0	0		66.0	23.0	0.348485	NM_014342	B2R7L8	Frame_Shift_Del	DEL	ENST00000302503.3	hg19	CCDS7943.1																																																																																			.	.	.	none		0.433	MTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391921.2	NM_014342		-	47653227	G	-	47653227	7	5	127	1	0	1	0	1	0	0	0	0	9921	1000	35	0	537	0	MTCH2	11	47653227	Frame_Shift_Del	DEL	G	TCGA-BQ-5892-01A-11D-1589-08	41462253	47653227	87353289	32	7939											
OR4C11	219429	hgsc.bcm.edu	37	chr11	55371448	55371448	+	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	atgatgcagacctgctggctCatgatggttgggtaacgcaa	10	10	13	8	1	1	3	1	2	0	1	1	3	1	3	1	3	3	6	1	3	2	2	rs373760102		TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr11:55371448C>A	ENST00000302231.4	-	1	426	c.402G>T	c.(400-402)atG>atT	p.M134I		NM_001004700.2	NP_001004700.2	Q6IEV9	OR4CB_HUMAN	olfactory receptor, family 4, subfamily C, member 11	134						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|prostate(1)|skin(1)	33						CCTGCTGGCTCATGATGGTTG	0.463																																					p.M134I		Atlas-SNP	.											.	OR4C11	73	.	0			c.G402T						PASS	.						88	72	78					11																	55371448		2177	4010	6187	SO:0001583	missense	219429	exon1			CTGGCTCATGATG	AB065774	CCDS31503.1	11q11	2012-08-09		2004-03-10	ENSG00000172188	ENSG00000172188		"GPCR / Class A : Olfactory receptors"	15167	protein-coding gene	gene with protein product				OR4C11P			Standard	NM_001004700		Approved		uc010rii.2	Q6IEV9	OTTHUMG00000165290	ENST00000302231.4:c.402G>T	chr11.hg19:g.55371448C>A	ENSP00000306651:p.Met134Ile	110.0	0.0	.		110.0	6.0	.	NM_001004700	B9EIL4|Q8NGL8	Missense_Mutation	SNP	ENST00000302231.4	hg19	CCDS31503.1	.	.	.	.	.	.	.	.	.	.	C	13.71	2.319072	0.41096	.	.	ENSG00000172188	ENST00000302231	T	0.00551	6.65	4.34	3.42	0.39159	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	U	0.000014	T	0.02047	0.0064	M	0.82923	2.615	0.27993	N	0.935588	D	0.69078	0.997	D	0.75020	0.985	T	0.08027	-1.0742	10	0.72032	D	0.01	.	10.4812	0.44695	0.0:0.9023:0.0:0.0977	.	134	Q6IEV9	OR4CB_HUMAN	I	134	ENSP00000306651:M134I	ENSP00000306651:M134I	M	-	3	0	OR4C11	55128024	0.991000	0.36638	0.963000	0.40424	0.237000	0.25408	2.968000	0.49224	1.187000	0.43000	0.478000	0.44815	ATG	.	.	.	alt		0.463	OR4C11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383268.1	NM_001004700		A	55371448	C	A	55371448	3	1	127	1	0	0	0	0	1	0	0	0	11052	826	29	4	532	4	OR4C11	11	55371448	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	7718221	55371448	79635068	33	7940											
DDX47	51202	hgsc.bcm.edu	37	chr12	12974592	12974592	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctttttttctctgtagctgTgattgtaggtggaattgatt	6	21	10	4	0	2	2	0	2	2	0	3	3	2	3	0	2	1	3	0	2	3	8			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr12:12974592T>C	ENST00000358007.3	+	4	396	c.374T>C	c.(373-375)gTg>gCg	p.V125A	DDX47_ENST00000352940.4_Missense_Mutation_p.V125A	NM_016355.3	NP_057439.2	Q9H0S4	DDX47_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47	125	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		Prostate(47;0.0526)		BRCA - Breast invasive adenocarcinoma(232;0.0354)		TCTGTAGCTGTGATTGTAGGT	0.358																																					p.V125A		Atlas-SNP	.											.	DDX47	37	.	0			c.T374C						PASS	.						137	139	139					12																	12974592		2203	4300	6503	SO:0001583	missense	51202	exon4			TAGCTGTGATTGT	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.374T>C	chr12.hg19:g.12974592T>C	ENSP00000350698:p.Val125Ala	84.0	0.0	.		102.0	35.0	.	NM_201224	B3KXP4|G5E955|Q96GM0|Q96NV8|Q9UI98	Missense_Mutation	SNP	ENST00000358007.3	hg19	CCDS8655.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.143646	0.77888	.	.	ENSG00000213782	ENST00000352940;ENST00000358007;ENST00000544400	T;T;T	0.15017	2.46;2.46;2.46	4.87	4.87	0.63330	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.21550	0.0519	N	0.13299	0.325	0.80722	D	1	B;B;D	0.55385	0.398;0.186;0.971	B;B;P	0.59703	0.379;0.121;0.862	T	0.05517	-1.0880	10	0.46703	T	0.11	-19.7359	14.3028	0.66364	0.0:0.0:0.0:1.0	.	125;125;125	Q9H4E3;G5E955;Q9H0S4	.;.;DDX47_HUMAN	A	125;125;62	ENSP00000319578:V125A;ENSP00000350698:V125A;ENSP00000444000:V62A	ENSP00000319578:V125A	V	+	2	0	DDX47	12865859	1.000000	0.71417	1.000000	0.80357	0.795000	0.44927	4.293000	0.59037	2.051000	0.60960	0.454000	0.30748	GTG	.	.	.	none		0.358	DDX47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400674.1	NM_016355		C	12974592	T	C	12974592	3	2	127	1	0	0	0	0	1	0	0	0	4367	1696	59	3	388	3	DDX47	12	12974592	Missense_Mutation	SNP	T	TCGA-BQ-5892-01A-11D-1589-08		12974592	120877303	34	7941											
ANP32D	23519	hgsc.bcm.edu	37	chr12	48866684	48866684	+	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	agtaacagagcctcagtgggCctagaagtattggcagaaaa	15	7	12	7	0	1	3	1	0	0	3	1	3	1	3	2	2	2	3	2	2	6	4			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr12:48866684C>T	ENST00000266594.1	+	1	237	c.237C>T	c.(235-237)ggC>ggT	p.G79G		NM_012404.2	NP_036536.2	O95626	AN32D_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32 family, member D	79						nuclear matrix (GO:0016363)				central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	9						CCTCAGTGGGCCTAGAAGTAT	0.378																																					p.G79G		Atlas-SNP	.											.	ANP32D	15	.	0			c.C237T						PASS	.						91	91	91					12																	48866684		2203	4300	6503	SO:0001819	synonymous_variant	23519	exon1			AGTGGGCCTAGAA	U71084	CCDS31788.1	12q13.12	2008-08-04			ENSG00000139223	ENSG00000139223		"ANP32 acidic nuclear phosphoproteins"	16676	protein-coding gene	gene with protein product	"pp32 related 2"	606878				10086381, 10400610	Standard	NM_012404		Approved	PP32R2	uc010slt.2	O95626	OTTHUMG00000162681	ENST00000266594.1:c.237C>T	chr12.hg19:g.48866684C>T		103.0	0.0	.		112.0	38.0	.	NM_012404	Q6NTC4	Silent	SNP	ENST00000266594.1	hg19	CCDS31788.1																																																																																			.	.	.	none		0.378	ANP32D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370058.1	NM_012404		T	48866684	C	T	48866684	2	4	127	1	0	0	0	0	0	0	0	1	708	726	26	2		2	ANP32D	12	48866684	Silent	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	35892092	48866684	84985211	35	7942											
PPFIA2	8499	hgsc.bcm.edu	37	chr12	81839465	81839465	+	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	ttcttagtgatctttcatgtCgtgacacaaggcactccaaa	11	13	7	10	1	3	2	1	2	2	0	5	2	4	2	1	1	0	1	1	1	3	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr12:81839465C>A	ENST00000549396.1	-	6	600	c.440G>T	c.(439-441)cGa>cTa	p.R147L	PPFIA2_ENST00000550584.2_Missense_Mutation_p.R147L|PPFIA2_ENST00000548586.1_Missense_Mutation_p.R147L|PPFIA2_ENST00000443686.3_Missense_Mutation_p.R73L|PPFIA2_ENST00000407050.4_Missense_Mutation_p.R73L|PPFIA2_ENST00000550359.2_5'UTR|RP11-315E17.1_ENST00000550272.1_RNA|PPFIA2_ENST00000545296.2_5'UTR|PPFIA2_ENST00000552948.1_Missense_Mutation_p.R147L|PPFIA2_ENST00000549325.1_Missense_Mutation_p.R129L|PPFIA2_ENST00000333447.7_Missense_Mutation_p.R129L	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	147	Glu-rich.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)		p.R147Q(1)		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						TCTTTCATGTCGTGACACAAG	0.393																																					p.R147L		Atlas-SNP	.											PPFIA2,rectum,carcinoma,0,1	PPFIA2	207	.	1	Substitution - Missense(1)	large_intestine(1)	c.G440T						PASS	.						98	89	92					12																	81839465		1881	4113	5994	SO:0001583	missense	8499	exon5			TCATGTCGTGACA	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.440G>T	chr12.hg19:g.81839465C>A	ENSP00000450337:p.Arg147Leu	43.0	0.0	.		50.0	3.0	.	NM_001220476	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Missense_Mutation	SNP	ENST00000549396.1	hg19	CCDS55857.1	.	.	.	.	.	.	.	.	.	.	C	36	5.659794	0.96734	.	.	ENSG00000139220	ENST00000549396;ENST00000549325;ENST00000407050;ENST00000541501;ENST00000333447;ENST00000548586;ENST00000443686;ENST00000552948;ENST00000551442	T;T;T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.60958	0.2309	L	0.29908	0.895	0.80722	D	1	D;D	0.67145	0.996;0.987	D;D	0.79108	0.992;0.953	T	0.62348	-0.6873	10	0.87932	D	0	-10.6387	20.3736	0.98901	0.0:1.0:0.0:0.0	.	47;147	B7Z4H8;O75334	.;LIPA2_HUMAN	L	147;129;73;158;129;147;73;147;129	ENSP00000450337:R147L;ENSP00000450298:R129L;ENSP00000385093:R73L;ENSP00000327416:R129L;ENSP00000449338:R147L;ENSP00000388373:R73L;ENSP00000447868:R147L;ENSP00000449469:R129L	ENSP00000327416:R129L	R	-	2	0	PPFIA2	80363596	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	7.818000	0.86416	2.820000	0.97059	0.650000	0.86243	CGA	.	.	.	none		0.393	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1			A	81839465	C	A	81839465	3	1	127	1	0	0	0	0	1	0	0	0	12317	884	31	4	3441	4	PPFIA2	12	81839465	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	32972781	81839465	52012430	36	7943											
CHD8	57680	hgsc.bcm.edu	37	chr14	21862522	21862522	+	Frame_Shift_Del	DEL	T	T	-																															tggtaaggctttcatctgtcTttttgtctagtcgagcaaaa																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr14:21862522delT	ENST00000557364.1	-	31	5776	c.5513delA	c.(5512-5514)aagfs	p.K1838fs	CHD8_ENST00000430710.3_Frame_Shift_Del_p.K1559fs|CHD8_ENST00000399982.2_Frame_Shift_Del_p.K1838fs|SNORD8_ENST00000363915.1_RNA|CHD8_ENST00000555962.1_5'Flank|SNORD9_ENST00000362566.1_RNA			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1838					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)		TTCATCTGTCTTTTTGTCTAG	0.498																																					p.K1838fs		Atlas-INDEL	.											.	CHD8	339	.	0			c.5514delG						PASS	.						76	78	77					14																	21862522		2011	4188	6199	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.5513delA	chr14.hg19:g.21862522delT	ENSP00000451601:p.Lys1838fs	80.0	0.0	0		83.0	24.0	0.289157	NM_001170629	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Frame_Shift_Del	DEL	ENST00000557364.1	hg19	CCDS53885.1																																																																																			.	.	.	none		0.498	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920		-	21862522	T	-	21862522	7	5	127	1	0	1	0	1	0	0	0	0	3333	1609	56	0	2264	0	CHD8	14	21862522	Frame_Shift_Del	DEL	T	TCGA-BQ-5892-01A-11D-1589-08		21862522	85487018	37	7944											
FBXO34	55030	hgsc.bcm.edu	37	chr14	55818351	55818351	+	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	cagatgaactcgttgggttaCctttttcctctcatacctat	8	16	6	11	1	1	2	1	1	1	1	4	2	2	2	3	1	3	2	3	1	4	6			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr14:55818351C>G	ENST00000313833.4	+	2	1488	c.1243C>G	c.(1243-1245)Cct>Gct	p.P415A	FBXO34_ENST00000440021.1_Missense_Mutation_p.P415A	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	415										breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						CGTTGGGTTACCTTTTTCCTC	0.458																																					p.P415A		Atlas-SNP	.											.	FBXO34	61	.	0			c.C1243G						PASS	.						149	132	138					14																	55818351		2203	4300	6503	SO:0001583	missense	55030	exon2			GGGTTACCTTTTT	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.1243C>G	chr14.hg19:g.55818351C>G	ENSP00000313159:p.Pro415Ala	238.0	0.0	.		210.0	57.0	.	NM_017943	Q2VPB5|Q4VBP5|Q86TY4	Missense_Mutation	SNP	ENST00000313833.4	hg19	CCDS32086.1	.	.	.	.	.	.	.	.	.	.	C	0.065	-1.215359	0.01542	.	.	ENSG00000178974	ENST00000313833;ENST00000440021	T;T	0.16897	2.31;2.31	5.48	1.31	0.21738	.	0.732971	0.11730	U	0.535077	T	0.12305	0.0299	L	0.47716	1.5	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.33599	-0.9862	10	0.40728	T	0.16	-21.5592	0.8915	0.01255	0.1775:0.4073:0.173:0.2422	.	415	Q9NWN3	FBX34_HUMAN	A	415	ENSP00000313159:P415A;ENSP00000394117:P415A	ENSP00000313159:P415A	P	+	1	0	FBXO34	54888104	.	.	0.001000	0.08648	0.123000	0.20343	.	.	0.409000	0.25649	-0.156000	0.13503	CCT	.	.	.	none		0.458	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1			G	55818351	C	G	55818351	3	3	127	1	0	0	0	0	1	0	0	0	5751	507	18	4	1245	4	FBXO34	14	55818351	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	33955829	55818351	51531189	38	7945											
DICER1	23405	hgsc.bcm.edu	37	chr14	95562982	95562982	+	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	ggagccctccacatcaggctCtcctcctcctcatcctcctc	5	10	5	21	0	3	0	2	0	1	0	10	1	8	1	7	2	1	1	7	2	0	0			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr14:95562982C>A	ENST00000526495.1	-	25	4566	c.4275G>T	c.(4273-4275)gaG>gaT	p.E1425D	DICER1_ENST00000527414.1_Missense_Mutation_p.E1425D|DICER1_ENST00000393063.1_Missense_Mutation_p.E1425D|DICER1_ENST00000343455.3_Missense_Mutation_p.E1425D|DICER1_ENST00000541352.1_Missense_Mutation_p.E1425D|DICER1_ENST00000556045.1_Missense_Mutation_p.E323D			Q9UPY3	DICER_HUMAN	dicer 1, ribonuclease type III	1425					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)		ACATCAGGCTctcctcctcct	0.478			"Mis F, N"		"sex cord-stromal tumour, TGCT, embryonal rhadomyosarcoma"	pleuropulmonary blastoma			Familial Multinodular Goiter ;DICER 1 syndrome																												p.E1425D		Atlas-SNP	.	yes	Rec	yes	Familial Pleuropulmonary Blastoma	14	14q32.13	23405	"dicer 1, ribonuclease type III "		"E, M, O"	.	DICER1	181	.	0			c.G4275T						PASS	.						60	56	57					14																	95562982		2203	4300	6503	SO:0001583	missense	23405	exon24	Familial Cancer Database	Adolescent Multinodular Goiter, incl. Multinodular Euthyroid Goiter & Non-Medullary Thyroid Cancer;incl. Pleuropulmonary Blastoma, Familial ; Cystic Nephroma, Familial	CAGGCTCTCCTCC	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.4275G>T	chr14.hg19:g.95562982C>A	ENSP00000437256:p.Glu1425Asp	49.0	0.0	.		61.0	24.0	.	NM_030621	A7E2D3|B3KRG4|E0AD28|O95943|Q9UQ02	Missense_Mutation	SNP	ENST00000526495.1	hg19	CCDS9931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.70|11.70	1.715346|1.715346	0.30413|0.30413	.|.	.|.	ENSG00000100697|ENSG00000100697	ENST00000343455;ENST00000526495;ENST00000393063;ENST00000527414;ENST00000556045;ENST00000541352|ENST00000532939	T;T;T;T;D;T|.	0.87103|.	0.36;0.36;0.36;0.36;-2.21;0.67|.	5.32|5.32	1.91|1.91	0.25777|0.25777	Ribonuclease III (3);|.	0.391869|0.391869	0.24366|0.24366	N|N	0.039146|0.039146	T|.	0.38746|.	0.1052|.	L|L	0.38175|0.38175	1.15|1.15	0.39976|0.39976	D|D	0.974854|0.974854	B;B;B|.	0.13594|.	0.008;0.001;0.0|.	B;B;B|.	0.14578|.	0.009;0.011;0.004|.	T|.	0.21075|.	-1.0256|.	10|.	0.30854|.	T|.	0.27|.	-10.9506|-10.9506	0.6205|0.6205	0.00777|0.00777	0.405:0.2239:0.2011:0.17|0.405:0.2239:0.2011:0.17	.|.	323;1425;1425|.	B3KRG4;E0AD28;Q9UPY3|.	.;.;DICER_HUMAN|.	D|X	1425;1425;1425;1425;323;1425|104	ENSP00000343745:E1425D;ENSP00000437256:E1425D;ENSP00000376783:E1425D;ENSP00000435681:E1425D;ENSP00000451041:E323D;ENSP00000444719:E1425D|.	ENSP00000343745:E1425D|.	E|E	-|-	3|1	2|0	DICER1|DICER1	94632735|94632735	0.946000|0.946000	0.32159|0.32159	0.825000|0.825000	0.32803|0.32803	0.882000|0.882000	0.50991|0.50991	0.405000|0.405000	0.21015|0.21015	0.561000|0.561000	0.29186|0.29186	0.561000|0.561000	0.74099|0.74099	GAG|GAG	.	.	.	none		0.478	DICER1-004	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387997.1			A	95562982	C	A	95562982	3	1	127	1	0	0	0	0	1	0	0	0	4523	912	32	4	1513	4	DICER1	14	95562982	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	39744631	95562982	11786558	39	7946											
TELO2	9894	hgsc.bcm.edu	37	chr16	1552985	1552985	+	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	ctcaactacagcctccggcaGcgcatggacatcctggatgt	9	8	10	14	2	1	0	1	0	0	0	3	2	3	2	3	3	4	2	3	3	2	1			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr16:1552985G>T	ENST00000262319.6	+	15	2103	c.1824G>T	c.(1822-1824)caG>caT	p.Q608H	TELO2_ENST00000564507.1_3'UTR	NM_016111.3	NP_057195.2	Q9Y4R8	TELO2_HUMAN	telomere maintenance 2	608					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)				GCCTCCGGCAGCGCATGGACA	0.622																																					p.Q608H		Atlas-SNP	.											.	TELO2	44	.	0			c.G1824T						PASS	.						143	133	137					16																	1552985		2199	4300	6499	SO:0001583	missense	9894	exon15			CCGGCAGCGCATG	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.1824G>T	chr16.hg19:g.1552985G>T	ENSP00000262319:p.Gln608His	155.0	0.0	.		166.0	19.0	.	NM_016111	D3DU73|O75168|Q7LDV4|Q9BR21	Missense_Mutation	SNP	ENST00000262319.6	hg19	CCDS32363.1	.	.	.	.	.	.	.	.	.	.	G	19.15	3.772621	0.69992	.	.	ENSG00000100726	ENST00000262319	T	0.26518	1.73	5.09	5.09	0.68999	Telomere length regulation protein, conserved domain (1);	0.000000	0.85682	D	0.000000	T	0.49660	0.1570	M	0.76938	2.355	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.50734	-0.8793	10	0.54805	T	0.06	-37.6041	10.8668	0.46860	0.0882:0.0:0.9118:0.0	.	608	Q9Y4R8	TELO2_HUMAN	H	608	ENSP00000262319:Q608H	ENSP00000262319:Q608H	Q	+	3	2	TELO2	1492986	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.437000	0.52863	2.391000	0.81399	0.462000	0.41574	CAG	.	.	.	none		0.622	TELO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103602.2	NM_016111		T	1552985	G	T	1552985	3	4	127	1	0	0	0	0	1	0	0	0	15769	962	34	4	1878	4	TELO2	16	1552985	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08		1552985	88801768	40	7947											
CNOT1	23019	hgsc.bcm.edu	37	chr16	58580300	58580300	+	Missense_Mutation	SNP	T	T	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	agagagttgctcatctaaatTcttcaggcgatctttatcct	10	15	7	9	1	5	1	2	0	3	1	6	3	6	1	1	1	1	2	1	1	3	6			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr16:58580300T>G	ENST00000317147.5	-	29	4263	c.3931A>C	c.(3931-3933)Aat>Cat	p.N1311H	CNOT1_ENST00000569240.1_Missense_Mutation_p.N1306H|SNORA46_ENST00000384762.1_RNA|CNOT1_ENST00000441024.2_Missense_Mutation_p.N1311H|CNOT1_ENST00000245138.4_Missense_Mutation_p.N162H	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1311	Interaction with CNOT6, CNOT6L, CNOT7 and CNOT8.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		TCATCTAAATTCTTCAGGCGA	0.413																																					p.N1311H		Atlas-SNP	.											.	CNOT1	359	.	0			c.A3931C						PASS	.						142	128	133					16																	58580300		2198	4300	6498	SO:0001583	missense	23019	exon29			CTAAATTCTTCAG	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.3931A>C	chr16.hg19:g.58580300T>G	ENSP00000320949:p.Asn1311His	131.0	0.0	.		159.0	43.0	.	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	hg19	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	T	15.05	2.719378	0.48728	.	.	ENSG00000125107	ENST00000317147;ENST00000245138;ENST00000394200;ENST00000441024	T;T	0.49432	0.81;0.78	5.39	5.39	0.77823	.	0.219192	0.53938	D	0.000042	T	0.35335	0.0928	N	0.24115	0.695	0.45541	D	0.998496	B;B;B;B	0.31351	0.0;0.32;0.0;0.003	B;B;B;B	0.34138	0.003;0.176;0.001;0.004	T	0.26258	-1.0108	10	0.48119	T	0.1	.	10.6062	0.45396	0.0:0.0753:0.0:0.9247	.	162;1311;1311;1306	B5MDN3;A5YKK6-4;A5YKK6;A5YKK6-2	.;.;CNOT1_HUMAN;.	H	1311;162;1306;1311	ENSP00000320949:N1311H;ENSP00000413113:N1311H	ENSP00000245138:N162H	N	-	1	0	CNOT1	57137801	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.289000	0.72696	2.043000	0.60533	0.528000	0.53228	AAT	.	.	.	none		0.413	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		G	58580300	T	G	58580300	3	3	127	1	0	0	0	0	1	0	0	0	3619	1783	62	5	3505	5	CNOT1	16	58580300	Missense_Mutation	SNP	T	TCGA-BQ-5892-01A-11D-1589-08	57027315	58580300	31774453	41	7948											
NFATC3	4775	hgsc.bcm.edu	37	chr16	68200904	68200904	+	Frame_Shift_Del	DEL	T	T	-																															ttctctgcagatagcctctaTacccgttgagtgctgtaagt																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr16:68200904delT	ENST00000346183.3	+	5	1784	c.1760delT	c.(1759-1761)atafs	p.I587fs	NFATC3_ENST00000575270.1_Frame_Shift_Del_p.I587fs|NFATC3_ENST00000329524.4_Frame_Shift_Del_p.I587fs|NFATC3_ENST00000535127.2_3'UTR|NFATC3_ENST00000349223.5_Frame_Shift_Del_p.I587fs	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	587	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				cellular respiration (GO:0045333)|cellular response to calcium ion (GO:0071277)|cellular response to lithium ion (GO:0071285)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	44		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		ATAGCCTCTATACCCGTTGAG	0.383																																					p.I587fs		Atlas-INDEL	.											.	NFATC3	190	.	0			c.1759delA						PASS	.						223	215	218					16																	68200904		2198	4300	6498	SO:0001589	frameshift_variant	4775	exon5			.	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.1760delT	chr16.hg19:g.68200904delT	ENSP00000300659:p.Ile587fs	152.0	0.0	0		163.0	10.0	0.0613497	NM_173165	O75211|Q14516|Q99840|Q99841|Q99842	Frame_Shift_Del	DEL	ENST00000346183.3	hg19	CCDS10860.1																																																																																			.	.	.	none		0.383	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555		-	68200904	T	-	68200904	7	5	127	1	0	1	0	1	0	0	0	0	10371	1406	49	0	1778	0	NFATC3	16	68200904	Frame_Shift_Del	DEL	T	TCGA-BQ-5892-01A-11D-1589-08	9620604	68200904	22153849	42	7949											
SLC13A5	284111	hgsc.bcm.edu	37	chr17	6597517	6597517	+	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	cagtggcatcggagacatacCtaggtggggaaaagcacagc	13	5	14	9	1	0	1	0	0	0	1	1	3	0	2	1	5	3	2	1	5	4	2	rs113208940		TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr17:6597517C>G	ENST00000433363.2	-	8	1289		c.e8-1		SLC13A5_ENST00000381074.4_Splice_Site|SLC13A5_ENST00000573648.1_Splice_Site|SLC13A5_ENST00000293800.6_Splice_Site	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						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						GGAGACATACCTAGGTGGGGA	0.502																																					.		Atlas-SNP	.											.	SLC13A5	57	.	0			c.1056-1G>C						PASS	.						74	62	66					17																	6597517		2203	4300	6503	SO:0001630	splice_region_variant	284111	exon9			ACATACCTAGGTG	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.1056-1G>C	chr17.hg19:g.6597517C>G		27.0	0.0	.		66.0	17.0	.	NM_001143838	B3KXR0|B7Z4P2|B7ZLB4|F8W7N2|Q6ZMG1	Splice_Site	SNP	ENST00000433363.2	hg19	CCDS11079.1	.	.	.	.	.	.	.	.	.	.	C	12.54	1.969840	0.34754	.	.	ENSG00000141485	ENST00000293800;ENST00000433363;ENST00000381074	.	.	.	5.61	5.61	0.85477	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.5007	0.87731	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC13A5	6538241	1.000000	0.71417	0.947000	0.38551	0.090000	0.18270	6.842000	0.75379	2.815000	0.96918	0.561000	0.74099	.	.	G|1.000	.	weak		0.502	SLC13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219853.2	NM_177550	Intron	G	6597517	C	G	6597517	5	3	127	1	0	0	0	0	0	0	1	0	14408	695	24	4	671	4	SLC13A5	17	6597517	Splice_Site	SNP	C	TCGA-BQ-5892-01A-11D-1589-08		6597517	74597693	43	7950											
ALOX12	239	hgsc.bcm.edu	37	chr17	6899500	6899500	+	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	tctccgggtcgtacaaccgcGtgcagctttggctggtcggg	4	10	15	12	5	1	0	0	0	1	0	4	0	1	0	2	4	4	4	2	4	2	2	rs202195274	byFrequency	TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr17:6899500G>T	ENST00000251535.6	+	1	117	c.64G>T	c.(64-66)Gtg>Ttg	p.V22L	RP11-589P10.5_ENST00000573222.1_lincRNA|RP11-589P10.7_ENST00000572547.1_RNA|AC027763.2_ENST00000399541.2_Intron	NM_000697.2	NP_000688.2	P18054	LOX12_HUMAN	arachidonate 12-lipoxygenase	22	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				aging (GO:0007568)|arachidonic acid metabolic process (GO:0019369)|cellular component movement (GO:0006928)|cellular response to lipid (GO:0071396)|establishment of skin barrier (GO:0061436)|fatty acid oxidation (GO:0019395)|hepoxilin biosynthetic process (GO:0051122)|hepoxilin metabolic process (GO:0051121)|leukotriene A4 metabolic process (GO:1901751)|linoleic acid metabolic process (GO:0043651)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxin B4 biosynthetic process (GO:2001306)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of platelet aggregation (GO:0090331)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|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 endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of gene expression (GO:0010628)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|superoxide anion generation (GO:0042554)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|sarcolemma (GO:0042383)	arachidonate 12-lipoxygenase activity (GO:0004052)|hepoxilin A3 synthase activity (GO:0051120)|hepoxilin-epoxide hydrolase activity (GO:0047977)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(3)|urinary_tract(1)	19						GTACAACCGCGTGCAGCTTTG	0.756													G|||	3	0.000599042	0	0.0014	5008	,	,		9570	0		0.002	False		,,,				2504	0				p.V22L		Atlas-SNP	.											.	ALOX12	49	.	0			c.G64T						PASS	.						4	4	4					17																	6899500		1680	3274	4954	SO:0001583	missense	239	exon1			AACCGCGTGCAGC	M35418	CCDS11084.1	17p13.1	2010-01-14			ENSG00000108839	ENSG00000108839	1.13.11.31	"Arachidonate lipoxygenases"	429	protein-coding gene	gene with protein product	"platelet 12-LOX"	152391				1570320	Standard	NM_000697		Approved	12S-LOX	uc002gdx.4	P18054	OTTHUMG00000102088	ENST00000251535.6:c.64G>T	chr17.hg19:g.6899500G>T	ENSP00000251535:p.Val22Leu	0.0	0.0	.		5.0	4.0	.	NM_000697	O95569|Q6ISF8|Q9UQM4	Missense_Mutation	SNP	ENST00000251535.6	hg19	CCDS11084.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.029860	0.75504	.	.	ENSG00000108839	ENST00000251535	T	0.70282	-0.47	4.89	4.89	0.63831	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	0.077311	0.51477	D	0.000088	T	0.76579	0.4007	M	0.86953	2.85	0.35586	D	0.806715	B	0.27791	0.189	B	0.34385	0.181	T	0.82514	-0.0419	10	0.62326	D	0.03	-9.731	13.7403	0.62845	0.0:0.0:1.0:0.0	.	22	P18054	LOX12_HUMAN	L	22	ENSP00000251535:V22L	ENSP00000251535:V22L	V	+	1	0	ALOX12	6840224	0.936000	0.31750	1.000000	0.80357	0.994000	0.84299	1.345000	0.33953	2.709000	0.92574	0.591000	0.81541	GTG	.	.	.	weak		0.756	ALOX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219922.2			T	6899500	G	T	6899500	3	4	127	1	0	0	0	0	1	0	0	0	536	1145	40	4	66	4	ALOX12	17	6899500	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08	301983	6899500	74295710	44	7951											
GAS7	8522	hgsc.bcm.edu	37	chr17	9846496	9846496	+	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	tttgcccttcagctgtttctGgagcagtagttcaaacccag	8	13	9	11	0	3	0	2	0	1	0	3	1	3	1	2	1	4	5	2	1	2	5			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr17:9846496G>A	ENST00000432992.2	-	7	833	c.673C>T	c.(673-675)Cag>Tag	p.Q225*	GAS7_ENST00000583882.1_Intron|GAS7_ENST00000540214.1_Intron|GAS7_ENST00000542249.1_Nonsense_Mutation_p.Q161*|GAS7_ENST00000579158.1_Nonsense_Mutation_p.Q161*|GAS7_ENST00000396115.2_Intron|GAS7_ENST00000578655.1_5'Flank|GAS7_ENST00000580865.1_Nonsense_Mutation_p.Q85*|GAS7_ENST00000585266.1_Nonsense_Mutation_p.Q165*|GAS7_ENST00000323816.4_Nonsense_Mutation_p.Q165*|GAS7_ENST00000437099.2_Nonsense_Mutation_p.Q161*	NM_201433.1	NP_958839.1	O60861	GAS7_HUMAN	growth arrest-specific 7	225	FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				actin filament bundle assembly (GO:0051017)|actin filament polymerization (GO:0030041)|cell cycle arrest (GO:0007050)|neuron projection morphogenesis (GO:0048812)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)	actin filament (GO:0005884)|cytoplasm (GO:0005737)|ruffle (GO:0001726)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(7)|lung(18)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	39						AGCTGTTTCTGGAGCAGTAGT	0.552			T	MLL	AML*																																p.Q225X		Atlas-SNP	.		Dom	yes		17	17p	8522	growth arrest-specific 7		L	.	GAS7	113	.	0			c.C673T						PASS	.						182	164	170					17																	9846496		2203	4300	6503	SO:0001587	stop_gained	8522	exon7			GTTTCTGGAGCAG	AB007854	CCDS11152.1, CCDS42263.1, CCDS45611.1, CCDS58518.1	17p13.1	2004-02-18							4169	protein-coding gene	gene with protein product		603127				9736752	Standard	NM_001130831		Approved	KIAA0394, MGC1348	uc002gmg.1	O60861		ENST00000432992.2:c.673C>T	chr17.hg19:g.9846496G>A	ENSP00000407552:p.Gln225*	255.0	0.0	.		364.0	18.0	.	NM_201433	A8KAC2|B2RCK9|O43144|Q53Y77|Q7Z571	Nonsense_Mutation	SNP	ENST00000432992.2	hg19	CCDS11152.1	.	.	.	.	.	.	.	.	.	.	G	38	6.925348	0.97940	.	.	ENSG00000007237	ENST00000323816;ENST00000396115;ENST00000437099;ENST00000432992;ENST00000537970;ENST00000541114	.	.	.	5.36	5.36	0.76844	.	0.081859	0.51477	D	0.000091	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-13.6746	18.2231	0.89907	0.0:0.0:1.0:0.0	.	.	.	.	X	225;165;164;85;165;39	.	.	Q	-	1	0	GAS7	9787221	1.000000	0.71417	0.999000	0.59377	0.973000	0.67179	8.955000	0.93058	2.676000	0.91093	0.655000	0.94253	CAG	.	.	.	none		0.552	GAS7-017	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439883.1	NM_003644, NM_201432, NM_201433		A	9846496	G	A	9846496	4	1	127	1	0	0	0	0	0	1	0	0	6257	1357	47	2	789	2	GAS7	17	9846496	Nonsense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08	2946996	9846496	71348714	45	7952											
MYO1D	4642	hgsc.bcm.edu	37	chr17	30932193	30932193	+	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	gaagaggcagacaatgaggtCtttgttgtctttcgtatgga	10	13	13	5	1	2	3	0	1	2	2	3	5	2	4	0	3	0	3	0	3	3	4			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr17:30932193C>T	ENST00000318217.5	-	21	3080	c.2776G>A	c.(2776-2778)Gac>Aac	p.D926N	MYO1D_ENST00000579584.1_Missense_Mutation_p.D926N|MYO1D_ENST00000394649.4_Missense_Mutation_p.D838N	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID	926	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)			ACAATGAGGTCTTTGTTGTCT	0.423																																					p.D926N		Atlas-SNP	.											.	MYO1D	93	.	0			c.G2776A						PASS	.						131	112	119					17																	30932193		2203	4300	6503	SO:0001583	missense	4642	exon21			TGAGGTCTTTGTT	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.2776G>A	chr17.hg19:g.30932193C>T	ENSP00000324527:p.Asp926Asn	67.0	0.0	.		108.0	19.0	.	NM_015194	A6H8V3|Q8NHP9	Missense_Mutation	SNP	ENST00000318217.5	hg19	CCDS32615.1	.	.	.	.	.	.	.	.	.	.	C	32	5.168518	0.94768	.	.	ENSG00000176658	ENST00000318217;ENST00000394649	T	0.61158	0.13	4.88	4.88	0.63580	Myosin tail 2 (1);	0.000000	0.41294	U	0.000917	T	0.77579	0.4151	M	0.83483	2.645	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.80764	0.99;0.994	T	0.81355	-0.0970	10	0.72032	D	0.01	.	15.8776	0.79178	0.0:1.0:0.0:0.0	.	837;926	Q7Z3N6;O94832	.;MYO1D_HUMAN	N	926;118	ENSP00000324527:D926N	ENSP00000324527:D926N	D	-	1	0	MYO1D	27956306	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.445000	0.80570	2.421000	0.82119	0.655000	0.94253	GAC	.	.	.	none		0.423	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1			T	30932193	C	T	30932193	3	4	127	1	0	0	0	0	1	0	0	0	10078	913	32	2	252	2	MYO1D	17	30932193	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	21085697	30932193	50263017	46	7953											
UBTF	7343	hgsc.bcm.edu	37	chr17	42289818	42289818	+	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	agtccttcacctccttcgtaGtggcctgcaaaccaaaagcc	10	9	7	15	1	1	0	1	0	0	0	4	0	3	0	6	1	3	2	6	1	4	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr17:42289818G>C	ENST00000302904.4	-	8	1157	c.665C>G	c.(664-666)aCt>aGt	p.T222S	UBTF_ENST00000527034.1_Intron|UBTF_ENST00000526094.1_Intron|CTB-175E5.7_ENST00000586560.1_RNA|UBTF_ENST00000343638.5_Intron|UBTF_ENST00000533177.1_Intron|UBTF_ENST00000393606.3_Intron|UBTF_ENST00000436088.1_Missense_Mutation_p.T222S|UBTF_ENST00000529383.1_Missense_Mutation_p.T222S|UBTF_ENST00000537550.1_5'Flank			P17480	UBF1_HUMAN	upstream binding transcription factor, RNA polymerase I	222					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)		CTCCTTCGTAGTGGCCTGCAA	0.637																																					p.T222S		Atlas-SNP	.											.	UBTF	65	.	0			c.C665G						PASS	.						78	73	75					17																	42289818		2203	4300	6503	SO:0001583	missense	7343	exon8			TTCGTAGTGGCCT	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.665C>G	chr17.hg19:g.42289818G>C	ENSP00000302640:p.Thr222Ser	136.0	0.0	.		179.0	44.0	.	NM_014233	A8K6R8	Missense_Mutation	SNP	ENST00000302904.4	hg19	CCDS11480.1	.	.	.	.	.	.	.	.	.	.	g	2.112	-0.403562	0.04832	.	.	ENSG00000108312	ENST00000302904;ENST00000436088;ENST00000529383	D;D;D	0.97791	-4.54;-4.54;-4.54	4.9	3.89	0.44902	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.171589	0.50627	N	0.000119	D	0.89853	0.6835	N	0.03050	-0.425	0.33275	D	0.561518	B	0.12630	0.006	B	0.23716	0.048	D	0.84792	0.0779	10	0.02654	T	1	-4.647	10.1054	0.42530	0.0:0.1493:0.696:0.1547	.	222	P17480	UBF1_HUMAN	S	222	ENSP00000302640:T222S;ENSP00000390669:T222S;ENSP00000435708:T222S	ENSP00000302640:T222S	T	-	2	0	UBTF	39645344	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.273000	0.65564	1.135000	0.42183	0.442000	0.29010	ACT	.	.	.	none		0.637	UBTF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395205.1	NM_014233		C	42289818	G	C	42289818	3	2	127	1	0	0	0	0	1	0	0	0	16921	1029	36	4	1685	4	UBTF	17	42289818	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08	11357625	42289818	38905392	47	7954											
MRPL10	124995	hgsc.bcm.edu	37	chr17	45901623	45901623	+	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	tcccattggccgacatgacaGaatccttctcgcgttgctct	7	12	8	14	3	2	2	0	1	2	1	5	3	4	2	3	1	1	2	3	1	1	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr17:45901623G>A	ENST00000351111.2	-	5	739	c.734C>T	c.(733-735)tCt>tTt	p.S245F	OSBPL7_ENST00000392507.3_5'Flank|MRPL10_ENST00000414011.1_Missense_Mutation_p.S255F|MRPL10_ENST00000290208.7_Missense_Mutation_p.S255F|OSBPL7_ENST00000007414.3_5'Flank	NM_145255.3	NP_660298.2	Q7Z7H8	RM10_HUMAN	mitochondrial ribosomal protein L10	245					ribosome biogenesis (GO:0042254)|translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(3)|large_intestine(1)|lung(3)|ovary(1)	8						CGACATGACAGAATCCTTCTC	0.577																																					p.S255F		Atlas-SNP	.											.	MRPL10	24	.	0			c.C764T						PASS	.						119	104	109					17																	45901623		2203	4300	6503	SO:0001583	missense	124995	exon6			ATGACAGAATCCT	AB051618	CCDS11516.1, CCDS11517.1	17q21.3	2012-09-13			ENSG00000159111	ENSG00000159111		"Mitochondrial ribosomal proteins / large subunits"	14055	protein-coding gene	gene with protein product	"39S ribosomal protein L10, mitochondrial"	611825				11551941	Standard	NM_148887		Approved	RPML8, MRP-L8, L10MT, MRP-L10, MRPL8, MGC17973	uc002ily.3	Q7Z7H8	OTTHUMG00000156302	ENST00000351111.2:c.734C>T	chr17.hg19:g.45901623G>A	ENSP00000324100:p.Ser245Phe	110.0	0.0	.		179.0	87.0	.	NM_148887	A6NGJ4|Q96B80|Q96Q55	Missense_Mutation	SNP	ENST00000351111.2	hg19	CCDS11516.1	.	.	.	.	.	.	.	.	.	.	G	15.36	2.809636	0.50421	.	.	ENSG00000159111	ENST00000351111;ENST00000290208;ENST00000414011	T;T;T	0.50813	0.73;1.76;1.76	4.76	2.49	0.30216	.	1.038680	0.07593	N	0.922261	T	0.57286	0.2043	L	0.59436	1.845	0.09310	N	1	P;D	0.56521	0.8;0.976	B;P	0.51016	0.347;0.656	T	0.53034	-0.8495	10	0.72032	D	0.01	-2.0384	13.9408	0.64054	0.0:0.3197:0.6803:0.0	.	245;255	Q7Z7H8;A6NGJ4	RM10_HUMAN;.	F	245;255;255	ENSP00000324100:S245F;ENSP00000290208:S255F;ENSP00000395870:S255F	ENSP00000290208:S255F	S	-	2	0	MRPL10	43256622	0.009000	0.17119	0.001000	0.08648	0.056000	0.15407	1.692000	0.37731	0.954000	0.37851	0.491000	0.48974	TCT	.	.	.	none		0.577	MRPL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343764.1	NM_145255		A	45901623	G	A	45901623	3	1	127	1	0	0	0	0	1	0	0	0	9782	942	33	2	55	2	MRPL10	17	45901623	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08	3611805	45901623	35293587	48	7955											
SHC2	25759	hgsc.bcm.edu	37	chr19	422226	422226	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacatactgcccggggttggTgacgctgtctcgcacaagga	8	8	14	11	3	1	1	0	1	1	0	2	3	1	2	1	4	2	3	1	4	2	2			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr19:422226T>C	ENST00000264554.6	-	11	1539	c.1540A>G	c.(1540-1542)Acc>Gcc	p.T514A		NM_012435.2	NP_036567.2	P98077	SHC2_HUMAN	SHC (Src homology 2 domain containing) transforming protein 2	514	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)		CCGGGGTTGGTGACGCTGTCT	0.677																																					p.T514A		Atlas-SNP	.											.	SHC2	47	.	0			c.A1540G						PASS	.						23	28	27					19																	422226		2196	4298	6494	SO:0001583	missense	25759	exon11			GGTTGGTGACGCT	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.1540A>G	chr19.hg19:g.422226T>C	ENSP00000264554:p.Thr514Ala	16.0	0.0	.		31.0	9.0	.	NM_012435	O60230|Q9NPL5|Q9UCX4	Missense_Mutation	SNP	ENST00000264554.6	hg19	CCDS45891.1	.	.	.	.	.	.	.	.	.	.	T	18.98	3.738320	0.69304	.	.	ENSG00000129946	ENST00000264554	T	0.65178	-0.14	4.76	4.76	0.60689	SH2 motif (5);	0.000000	0.85682	D	0.000000	T	0.67401	0.2889	M	0.65975	2.015	0.54753	D	0.999983	P	0.36495	0.556	P	0.44561	0.453	T	0.71563	-0.4555	10	0.62326	D	0.03	-60.9323	13.7837	0.63097	0.0:0.0:0.0:1.0	.	514	P98077	SHC2_HUMAN	A	514	ENSP00000264554:T514A	ENSP00000264554:T514A	T	-	1	0	SHC2	373226	1.000000	0.71417	1.000000	0.80357	0.530000	0.34684	7.409000	0.80053	2.084000	0.62774	0.533000	0.62120	ACC	.	.	.	none		0.677	SHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451840.3			C	422226	T	C	422226	3	2	127	1	0	0	0	0	1	0	0	0	14284	1696	59	3	216	3	SHC2	19	422226	Missense_Mutation	SNP	T	TCGA-BQ-5892-01A-11D-1589-08		422226	58706757	49	7956											
LRRC8E	80131	hgsc.bcm.edu	37	chr19	7960603	7960603	+	Frame_Shift_Del	DEL	G	G	-																															ccgtggccatgctcatgattGgggtctttggctgcaccctc																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr19:7960603delG	ENST00000306708.6	+	2	216	c.115delG	c.(115-117)gggfs	p.G39fs		NM_001268284.1|NM_001268285.1|NM_025061.4	NP_001255213.1|NP_001255214.1|NP_079337.2	Q6NSJ5	LRC8E_HUMAN	leucine rich repeat containing 8 family, member E	39					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(10)	35						GCTCATGATTGGGGTCTTTGG	0.627																																					p.I38fs		Atlas-INDEL	.											.	LRRC8E	67	.	0			c.114delT						PASS	.						120	90	100					19																	7960603		2203	4300	6503	SO:0001589	frameshift_variant	80131	exon3			.		CCDS12189.1	19p13.2	2008-02-05				ENSG00000171017			26272	protein-coding gene	gene with protein product		612891				12477932	Standard	NM_025061		Approved	FLJ23420	uc002mir.3	Q6NSJ5		ENST00000306708.6:c.115delG	chr19.hg19:g.7960603delG	ENSP00000306524:p.Gly39fs	68.0	0.0	0		68.0	17.0	0.25	NM_001268284	B3KR78|Q2YDY3|Q7L236|Q8N3B0|Q9H5H8	Frame_Shift_Del	DEL	ENST00000306708.6	hg19	CCDS12189.1																																																																																			.	.	.	none		0.627	LRRC8E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461354.1	NM_025061		-	7960603	G	-	7960603	7	5	127	1	0	1	0	1	0	0	0	0	9032	1348	47	0	117	0	LRRC8E	19	7960603	Frame_Shift_Del	DEL	G	TCGA-BQ-5892-01A-11D-1589-08	7538377	7960603	51168380	50	7957											
MUC16	94025	hgsc.bcm.edu	37	chr19	9046479	9046479	+	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	cctaggactggtggccattaCaggtgtggcatctggactac	8	10	13	10	0	1	0	0	0	1	0	1	2	1	2	2	6	2	1	2	6	3	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr19:9046479C>G	ENST00000397910.4	-	5	35355	c.35152G>C	c.(35152-35154)Gta>Cta	p.V11718L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11720	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						GTGGCCATTACAGGTGTGGCA	0.502																																					p.V11718L		Atlas-SNP	.											.	MUC16	4315	.	0			c.G35152C						PASS	.						125	120	121					19																	9046479		1975	4155	6130	SO:0001583	missense	94025	exon5			CCATTACAGGTGT	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.35152G>C	chr19.hg19:g.9046479C>G	ENSP00000381008:p.Val11718Leu	115.0	0.0	.		158.0	44.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	6.049	0.377322	0.11466	.	.	ENSG00000181143	ENST00000397910	T	0.01998	4.51	3.09	-1.82	0.07857	.	.	.	.	.	T	0.00845	0.0028	N	0.01352	-0.895	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.47032	-0.9148	8	0.87932	D	0	.	1.1809	0.01845	0.2598:0.1629:0.1061:0.4712	.	11718	B5ME49	.	L	11718	ENSP00000381008:V11718L	ENSP00000381008:V11718L	V	-	1	0	MUC16	8907479	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.203000	0.09438	-0.527000	0.06374	-0.373000	0.07131	GTA	.	.	.	none		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9046479	C	G	9046479	3	3	127	1	0	0	0	0	1	0	0	0	9980	478	17	4	8691	4	MUC16	19	9046479	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	1085876	9046479	50082504	51	7958											
MUC16	94025	hgsc.bcm.edu	37	chr19	9085838	9085838	+	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	tgtctgcacagaaactttttCtgaagaaactgcatgtagtg	12	13	9	7	0	2	3	0	1	2	2	2	3	2	3	0	0	4	3	0	0	4	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr19:9085838C>A	ENST00000397910.4	-	1	6180	c.5977G>T	c.(5977-5979)Gaa>Taa	p.E1993*		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1993	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						GAAACTTTTTCTGAAGAAACT	0.473																																					p.E1993X		Atlas-SNP	.											.	MUC16	4315	.	0			c.G5977T						PASS	.						139	135	136					19																	9085838		1983	4158	6141	SO:0001587	stop_gained	94025	exon1			CTTTTTCTGAAGA	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.5977G>T	chr19.hg19:g.9085838C>A	ENSP00000381008:p.Glu1993*	93.0	0.0	.		126.0	9.0	.	NM_024690	Q6ZQW5|Q96RK2	Nonsense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	46	12.553061	0.99677	.	.	ENSG00000181143	ENST00000397910	.	.	.	0.235	0.235	0.15431	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	.	.	.	.	.	.	.	X	1993	.	ENSP00000381008:E1993X	E	-	1	0	MUC16	8946838	0.001000	0.12720	0.291000	0.24904	0.292000	0.27327	0.223000	0.17719	0.308000	0.22923	0.313000	0.20887	GAA	.	.	.	none		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9085838	C	A	9085838	4	1	127	1	0	0	0	0	0	1	0	0	9980	922	32	4	37882	4	MUC16	19	9085838	Nonsense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	39359	9085838	50043145	52	7959											
ZNF225	7768	hgsc.bcm.edu	37	chr19	44636328	44636328	+	Frame_Shift_Del	DEL	T	T	-																															gtgaagagtgtgggaaaagaTttactcagaattcacaactt																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr19:44636328delT	ENST00000262894.6	+	5	1841	c.1561delT	c.(1561-1563)tttfs	p.F521fs	ZNF225_ENST00000590612.1_Frame_Shift_Del_p.F521fs|ZNF225_ENST00000592780.1_3'UTR	NM_013362.2	NP_037494.2	Q9UK10	ZN225_HUMAN	zinc finger protein 225	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)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	16		Prostate(69;0.0352)|all_neural(266;0.202)				TGGGAAAAGATTTACTCAGAA	0.388																																					p.R520fs		Atlas-INDEL	.											.	ZNF225	41	.	0			c.1560delA						PASS	.						83	92	89					19																	44636328		2200	4296	6496	SO:0001589	frameshift_variant	7768	exon5			.	AF187991	CCDS46100.1	19q13.31	2013-01-08				ENSG00000256294		"Zinc fingers, C2H2-type", "-"	13018	protein-coding gene	gene with protein product							Standard	NM_013362		Approved		uc002oyj.1	Q9UK10		ENST00000262894.6:c.1561delT	chr19.hg19:g.44636328delT	ENSP00000262894:p.Phe521fs	120.0	0.0	0		127.0	12.0	0.0944882	NM_013362	A8K8S2|Q53F12|Q9NS46|Q9UID8	Frame_Shift_Del	DEL	ENST00000262894.6	hg19	CCDS46100.1																																																																																			.	.	.	none		0.388	ZNF225-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460581.1			-	44636328	T	-	44636328	7	5	127	1	0	1	0	1	0	0	0	0	17791	1493	52	0	1575	0	ZNF225	19	44636328	Frame_Shift_Del	DEL	T	TCGA-BQ-5892-01A-11D-1589-08	35550490	44636328	14492655	53	7960											
ZNF544	27300	hgsc.bcm.edu	37	chr19	58774085	58774085	+	Missense_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	ggcagcaatctcaacttgtaGtgcatcggcggacacatact	11	9	10	11	2	1	0	1	0	1	0	3	1	1	1	0	3	4	4	0	3	4	3			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr19:58774085G>A	ENST00000596652.1	+	6	2347	c.2113G>A	c.(2113-2115)Gtg>Atg	p.V705M	ZNF544_ENST00000596929.1_Intron|CTD-3138B18.4_ENST00000600029.1_Intron|ZNF544_ENST00000600220.1_Missense_Mutation_p.V677M|ZNF544_ENST00000269829.4_Missense_Mutation_p.V705M|ZNF544_ENST00000599953.1_Missense_Mutation_p.V563M|ZNF544_ENST00000595981.1_Intron|ZNF544_ENST00000596825.1_3'UTR|ZNF544_ENST00000415203.2_Missense_Mutation_p.V677M|ZNF544_ENST00000599227.1_3'UTR|ZNF544_ENST00000600044.1_Missense_Mutation_p.V677M|CTD-3138B18.5_ENST00000597230.1_RNA			Q6NX49	ZN544_HUMAN	zinc finger protein 544	705					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|skin(1)|urinary_tract(1)	18		all_cancers(17;4.17e-12)|all_epithelial(17;1.25e-08)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.17)|GBM - Glioblastoma multiforme(193;0.018)		TCAACTTGTAGTGCATCGGCG	0.488																																					p.V705M		Atlas-SNP	.											.	ZNF544	57	.	0			c.G2113A						PASS	.						143	146	145					19																	58774085		2203	4300	6503	SO:0001583	missense	27300	exon7			CTTGTAGTGCATC	AF020591	CCDS12973.1	19q13.43	2013-01-08				ENSG00000198131		"Zinc fingers, C2H2-type", "-"	16759	protein-coding gene	gene with protein product	"zinc finger protein AF020591"						Standard	NM_014480		Approved	AF020591	uc010euo.3	Q6NX49		ENST00000596652.1:c.2113G>A	chr19.hg19:g.58774085G>A	ENSP00000469635:p.Val705Met	282.0	0.0	.		327.0	85.0	.	NM_014480	A8K6J1|Q9UEX4	Missense_Mutation	SNP	ENST00000596652.1	hg19	CCDS12973.1	.	.	.	.	.	.	.	.	.	.	G	7.249	0.602782	0.13939	.	.	ENSG00000198131	ENST00000269829;ENST00000415203;ENST00000441758	T;T	0.36340	1.26;1.26	3.46	-0.182	0.13287	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.24661	0.0598	L	0.49126	1.545	0.09310	N	1	B;B;P	0.39480	0.061;0.235;0.675	B;B;B	0.32677	0.018;0.019;0.15	T	0.12734	-1.0536	9	0.48119	T	0.1	.	4.3215	0.11020	0.411:0.1657:0.4233:0.0	.	677;677;705	B7ZAY1;B4DL50;Q6NX49	.;.;ZN544_HUMAN	M	705;677;257	ENSP00000269829:V705M;ENSP00000394341:V677M	ENSP00000269829:V705M	V	+	1	0	ZNF544	63465897	0.000000	0.05858	0.000000	0.03702	0.507000	0.33981	-0.746000	0.04829	-0.024000	0.13941	0.563000	0.77884	GTG	.	.	.	none		0.488	ZNF544-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466754.1	NM_014480		A	58774085	G	A	58774085	3	1	127	1	0	0	0	0	1	0	0	0	17989	1029	36	2	2127	2	ZNF544	19	58774085	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08	14137757	58774085	354898	54	7961											
JAG1	182	hgsc.bcm.edu	37	chr20	10625851	10625851	+	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	gcacttaaaagcatccccctCatcatagcaggtgccaccgt	11	8	7	15	1	2	0	2	0	0	0	3	0	3	0	4	1	3	3	4	1	3	2			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr20:10625851C>T	ENST00000254958.5	-	17	2682	c.2167G>A	c.(2167-2169)Gag>Aag	p.E723K	JAG1_ENST00000423891.2_Missense_Mutation_p.E564K|JAG1_ENST00000488480.1_RNA	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	723	EGF-like 13. {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)	p.E723fs*6(1)		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						GCATCCCCCTCATCATAGCAG	0.547									Alagille Syndrome																												p.E723K		Atlas-SNP	.											.	JAG1	213	.	1	Insertion - Frameshift(1)	lung(1)	c.G2167A						PASS	.						122	99	107					20																	10625851		2203	4300	6503	SO:0001583	missense	182	exon17	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	CCCCCTCATCATA	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.2167G>A	chr20.hg19:g.10625851C>T	ENSP00000254958:p.Glu723Lys	119.0	0.0	.		142.0	43.0	.	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Missense_Mutation	SNP	ENST00000254958.5	hg19	CCDS13112.1	.	.	.	.	.	.	.	.	.	.	C	13.39	2.224010	0.39300	.	.	ENSG00000101384	ENST00000254958;ENST00000423891	D;D	0.85629	-2.01;-2.01	5.85	5.85	0.93711	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	T	0.74238	0.3690	N	0.12569	0.235	0.58432	D	0.999995	B	0.02656	0.0	B	0.06405	0.002	T	0.68777	-0.5319	10	0.10377	T	0.69	.	20.1577	0.98120	0.0:1.0:0.0:0.0	.	723	P78504	JAG1_HUMAN	K	723;564	ENSP00000254958:E723K;ENSP00000389519:E564K	ENSP00000254958:E723K	E	-	1	0	JAG1	10573851	1.000000	0.71417	0.989000	0.46669	0.978000	0.69477	4.891000	0.63185	2.767000	0.95098	0.655000	0.94253	GAG	.	.	.	none		0.547	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214		T	10625851	C	T	10625851	3	4	127	1	0	0	0	0	1	0	0	0	7941	835	29	2	1529	2	JAG1	20	10625851	Missense_Mutation	SNP	C	TCGA-BQ-5892-01A-11D-1589-08		10625851	52399669	55	7962											
CEP250	11190	hgsc.bcm.edu	37	chr20	34064377	34064378	+	Frame_Shift_Ins	INS	-	-	T																															ctcagtgccttaaatgaggcINStttggcgttagataaagttg																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr20:34064377_34064378insT	ENST00000397527.1	+	16	2540_2541	c.1820_1821insT	c.(1819-1824)gctttgfs	p.L608fs	RP3-477O4.14_ENST00000444933.1_RNA|RP3-477O4.14_ENST00000453914.1_RNA|RP3-477O4.14_ENST00000416260.1_RNA|CEP250_ENST00000342580.4_Frame_Shift_Ins_p.L608fs	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	608	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)			TTAAATGAGGCTTTGGCGTTAG	0.515																																					p.A607fs		Atlas-INDEL	.											.	CEP250	141	.	0			c.1820_1821insT						PASS	.																																			SO:0001589	frameshift_variant	11190	exon16			.	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.1823dupT	chr20.hg19:g.34064380_34064380dupT	ENSP00000380661:p.Leu608fs	68.0	0.0	0		74.0	23.0	0.310811	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Frame_Shift_Ins	INS	ENST00000397527.1	hg19	CCDS13255.1																																																																																			.	.	.	none		0.515	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		T	34064378	-	T	34064377	7	5	127	1	0	1	1	0	0	0	0	0	3254	797	28	0	1870	0	CEP250	20	34064377	Frame_Shift_Ins	INS	-	TCGA-BQ-5892-01A-11D-1589-08	23438526	34064377	28961143	56	7963											
SON	6651	hgsc.bcm.edu	37	chr21	34918555	34918555	+	Missense_Mutation	SNP	T	T	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	cagctgaatggtgaaacaaaTacacccattgaaggaaacca	18	6	8	9	0	0	3	0	3	0	0	0	4	0	4	2	2	4	1	2	2	6	2			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr21:34918555T>G	ENST00000356577.4	+	2	589	c.114T>G	c.(112-114)aaT>aaG	p.N38K	SON_ENST00000300278.4_Missense_Mutation_p.N38K|SON_ENST00000381692.2_Missense_Mutation_p.N38K|SON_ENST00000381679.4_Missense_Mutation_p.N38K|SON_ENST00000290239.6_Missense_Mutation_p.N38K	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	38					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						GTGAAACAAATACACCCATTG	0.393																																					p.N38K		Atlas-SNP	.											.	SON	343	.	0			c.T114G						PASS	.						75	76	76					21																	34918555		2203	4300	6503	SO:0001583	missense	6651	exon2			AACAAATACACCC	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.114T>G	chr21.hg19:g.34918555T>G	ENSP00000348984:p.Asn38Lys	73.0	0.0	.		65.0	23.0	.	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	hg19	CCDS13629.1	.	.	.	.	.	.	.	.	.	.	T	18.69	3.678619	0.68042	.	.	ENSG00000159140	ENST00000356577;ENST00000290239;ENST00000381692;ENST00000300278;ENST00000381679	T;T;T;T;T	0.15139	2.45;2.45;2.45;2.45;2.45	5.68	-2.68	0.06041	.	0.232218	0.30244	N	0.010080	T	0.15003	0.0362	L	0.27053	0.805	0.22639	N	0.998909	B;D;D;D	0.58970	0.003;0.984;0.967;0.967	B;P;P;P	0.50860	0.001;0.449;0.652;0.652	T	0.20571	-1.0271	10	0.66056	D	0.02	.	10.9891	0.47539	0.0:0.578:0.0:0.422	.	38;38;38;38	Q6ZRV7;P18583;P18583-3;P18583-6	.;SON_HUMAN;.;.	K	38	ENSP00000348984:N38K;ENSP00000290239:N38K;ENSP00000371111:N38K;ENSP00000300278:N38K;ENSP00000371095:N38K	ENSP00000290239:N38K	N	+	3	2	SON	33840425	0.995000	0.38212	0.896000	0.35187	0.659000	0.38960	0.152000	0.16302	-0.281000	0.09141	-0.359000	0.07587	AAT	.	.	.	none		0.393	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		G	34918555	T	G	34918555	3	3	127	1	0	0	0	0	1	0	0	0	14939	1403	49	5	120	5	SON	21	34918555	Missense_Mutation	SNP	T	TCGA-BQ-5892-01A-11D-1589-08		34918555	13211340	57	7964											
SON	6651	hgsc.bcm.edu	37	chr21	34922861	34922861	+	Missense_Mutation	SNP	T	T	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	tgcctgagttgccagggcccTctgtgacaccagtgccacag	7	8	12	14	0	1	2	0	2	1	0	1	2	1	2	5	1	3	1	5	1	0	1			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr21:34922861T>G	ENST00000356577.4	+	3	1799	c.1324T>G	c.(1324-1326)Tct>Gct	p.S442A	SON_ENST00000300278.4_Missense_Mutation_p.S442A|SON_ENST00000381692.2_Intron|SON_ENST00000381679.4_Missense_Mutation_p.S442A|SON_ENST00000290239.6_Missense_Mutation_p.S442A	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	442					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						GCCAGGGCCCTCTGTGACACC	0.632																																					p.S442A		Atlas-SNP	.											.	SON	343	.	0			c.T1324G						PASS	.						34	37	36					21																	34922861		2202	4299	6501	SO:0001583	missense	6651	exon3			GGGCCCTCTGTGA	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.1324T>G	chr21.hg19:g.34922861T>G	ENSP00000348984:p.Ser442Ala	88.0	0.0	.		87.0	23.0	.	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	hg19	CCDS13629.1	.	.	.	.	.	.	.	.	.	.	T	15.79	2.937742	0.52972	.	.	ENSG00000159140	ENST00000356577;ENST00000290239;ENST00000300278;ENST00000381679	T;T;T;T	0.14893	2.65;2.66;2.66;2.47	4.92	1.26	0.21427	.	0.404453	0.21839	N	0.068355	T	0.13713	0.0332	N	0.19112	0.55	0.24219	N	0.995448	P;P;P	0.47962	0.844;0.903;0.903	B;P;P	0.50270	0.432;0.636;0.636	T	0.09975	-1.0650	10	0.38643	T	0.18	.	6.7013	0.23227	0.0:0.3711:0.0:0.6289	.	442;442;442	P18583;P18583-3;P18583-6	SON_HUMAN;.;.	A	442	ENSP00000348984:S442A;ENSP00000290239:S442A;ENSP00000300278:S442A;ENSP00000371095:S442A	ENSP00000290239:S442A	S	+	1	0	SON	33844731	.	.	1.000000	0.80357	0.966000	0.64601	.	.	0.427000	0.26145	0.402000	0.26972	TCT	.	.	.	none		0.632	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		G	34922861	T	G	34922861	3	3	127	1	0	0	0	0	1	0	0	0	14939	1551	54	5	1334	5	SON	21	34922861	Missense_Mutation	SNP	T	TCGA-BQ-5892-01A-11D-1589-08	4306	34922861	13207034	58	7965											
PRMT2	3275	hgsc.bcm.edu	37	chr21	48056904	48056905	+	Splice_Site	INS	-	-	AA																															cccagaagtgaatcgcaggtINSaatttccgttccacttccta																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr21:48056904_48056905insAA	ENST00000397637.1	+	2	993		c.e2+2		PRMT2_ENST00000397628.1_Splice_Site|PRMT2_ENST00000451211.2_Splice_Site|PRMT2_ENST00000355680.3_Splice_Site|PRMT2_ENST00000334494.4_Splice_Site|PRMT2_ENST00000458387.2_Splice_Site|PRMT2_ENST00000291705.6_Splice_Site|PRMT2_ENST00000440086.1_Splice_Site|PRMT2_ENST00000397638.2_Splice_Site			P55345	ANM2_HUMAN	protein arginine methyltransferase 2						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)		GAATCGCAGGTAATTTCCGTTC	0.421																																					.		Atlas-INDEL	.											.	PRMT2	48	.	0			c.39+2->AA						PASS	.																																			SO:0001630	splice_region_variant	3275	exon2			.	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.39+2->AA	chr21.hg19:g.48056905_48056906dupAA		38.0	0.0	0		55.0	12.0	0.218182	NM_001535	B7U630|B7U631|B7U632|P78350|Q498Y5|Q5U7D4|Q6FHF0|Q99781|Q9BW15|Q9UMC2	Splice_Site	INS	ENST00000397637.1	hg19	CCDS13737.1																																																																																			.	.	.	none		0.421	PRMT2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207401.1	NM_001535	Intron	AA	48056905	-	AA	48056904	8	5	127	1	0	1	1	0	0	0	1	0	12547	1652	57	0	43	0	PRMT2	21	48056904	Splice_Site	INS	-	TCGA-BQ-5892-01A-11D-1589-08	13134043	48056904	72991	59	7966											
UBE2L3	7332	hgsc.bcm.edu	37	chr22	21975858	21975858	+	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	ccagcctgagcacccgcttcGggctgacctagctgaagaat	9	7	11	14	2	0	4	0	3	0	1	1	4	0	4	4	1	3	4	4	1	3	2			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chr22:21975858G>C	ENST00000342192.4	+	4	563	c.365G>C	c.(364-366)cGg>cCg	p.R122P	UBE2L3_ENST00000545681.1_Missense_Mutation_p.R90P|UBE2L3_ENST00000458578.2_Missense_Mutation_p.R180P	NM_003347.3	NP_003338.1	P68036	UB2L3_HUMAN	ubiquitin-conjugating enzyme E2L 3	122					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)					CACCCGCTTCGGGCTGACCTA	0.478																																					p.R180P		Atlas-SNP	.											.	UBE2L3	11	.	0			c.G539C						PASS	.						34	34	34					22																	21975858		2203	4300	6503	SO:0001583	missense	7332	exon4			CGCTTCGGGCTGA	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.365G>C	chr22.hg19:g.21975858G>C	ENSP00000344259:p.Arg122Pro	64.0	0.0	.		62.0	20.0	.	NM_001256355	B2R4A7|B4DDG1|B4DSZ4|E7EWS7|P51966|P70653|Q9HAV1	Missense_Mutation	SNP	ENST00000342192.4	hg19	CCDS13790.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.485144	0.84854	.	.	ENSG00000185651	ENST00000458578;ENST00000342192;ENST00000545681	T;T;T	0.71934	-0.61;-0.61;1.16	5.66	5.66	0.87406	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.070661	0.53938	D	0.000050	D	0.87103	0.6094	M	0.90814	3.15	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.75484	0.986;0.977	D	0.89031	0.3442	10	0.66056	D	0.02	.	17.2403	0.87011	0.0:0.0:1.0:0.0	.	90;122	B4DDG1;P68036	.;UB2L3_HUMAN	P	180;122;90	ENSP00000400906:R180P;ENSP00000344259:R122P;ENSP00000445931:R90P	ENSP00000344259:R122P	R	+	2	0	UBE2L3	20305858	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	9.848000	0.99507	2.680000	0.91292	0.561000	0.74099	CGG	.	.	.	none		0.478	UBE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320219.1	NM_198157		C	21975858	G	C	21975858	3	2	127	1	0	0	0	0	1	0	0	0	16875	1116	39	4	379	4	UBE2L3	22	21975858	Missense_Mutation	SNP	G	TCGA-BQ-5892-01A-11D-1589-08		21975858	29328708	60	7967											
ATXN3L	92552	hgsc.bcm.edu	37	chrX	13337247	13337248	+	Frame_Shift_Del	DEL	TG	TG	-																															gaagcaggagttacacatgaTgtctttggaagatcttgcga																										TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chrX:13337247_13337248delTG	ENST00000380622.2	-	1	1270_1271	c.806_807delCA	c.(805-807)acafs	p.T269fs	GS1-600G8.3_ENST00000431486.1_RNA	NM_001135995.1	NP_001129467.1	Q9H3M9	ATX3L_HUMAN	ataxin 3-like	269					protein deubiquitination (GO:0016579)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	omega peptidase activity (GO:0008242)|ubiquitin-specific protease activity (GO:0004843)			endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						TTACACATGATGTCTTTGGAAG	0.426																																					p.269_270del		Atlas-INDEL	.											.	ATXN3L	64	.	0			c.807_808del						PASS	.																																			SO:0001589	frameshift_variant	92552	exon1			.		CCDS48080.1	Xp22	2010-09-30			ENSG00000123594	ENSG00000123594			24173	protein-coding gene	gene with protein product		300920					Standard	NM_001135995		Approved	MJDL	uc010ned.3	Q9H3M9	OTTHUMG00000021146	ENST00000380622.2:c.806_807delCA	chrX.hg19:g.13337247_13337248delTG	ENSP00000369996:p.Thr269fs	338.0	0.0	0		360.0	205.0	0.569444	NM_001135995	B2RNY8	Frame_Shift_Del	DEL	ENST00000380622.2	hg19	CCDS48080.1																																																																																			.	.	.	none		0.426	ATXN3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055785.2	NM_001135995		-	13337248	TG	-	13337247	7	5	127	1	0	1	0	1	0	0	0	0	1214	1451	51	0	264	0	ATXN3L	23	13337247	Frame_Shift_Del	DEL	TG	TCGA-BQ-5892-01A-11D-1589-08		13337247	141933313	61	7968											
UTP14A	10813	hgsc.bcm.edu	37	chrX	129045744	129045744	+	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	atgccttgcctgcttcagatCcacagagaagtagcattcaa	12	10	8	11	0	2	2	2	0	0	2	3	3	3	2	3	0	4	3	3	0	3	4			TCGA-BQ-5892-01A-11D-1589-08	TCGA-BQ-5892-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6e208c0a-d4dc-41d8-9f75-740d3fbf33ba	2684973c-b534-4ced-a232-197ba7e30757	g.chrX:129045744C>T	ENST00000394422.3	+	6	412	c.384C>T	c.(382-384)atC>atT	p.I128I	UTP14A_ENST00000425117.2_Intron|UTP14A_ENST00000371042.3_5'Flank|RP4-537K23.4_ENST00000432062.1_RNA|UTP14A_ENST00000371051.5_Silent_p.I74I	NM_006649.3	NP_006640.2	Q9BVJ6	UT14A_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog A (yeast)	128					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						TGCTTCAGATCCACAGAGAAG	0.473																																					p.I128I		Atlas-SNP	.											.	UTP14A	74	.	0			c.C384T						PASS	.						139	133	135					X																	129045744		2203	4300	6503	SO:0001819	synonymous_variant	10813	exon6			TCAGATCCACAGA	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.384C>T	chrX.hg19:g.129045744C>T		138.0	0.0	.		180.0	109.0	.	NM_006649	A8K7A3|A8MVQ1|B4DQ08|E9PEL7|Q5JYF1	Silent	SNP	ENST00000394422.3	hg19	CCDS14615.1																																																																																			.	.	.	none		0.473	UTP14A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058221.1	NM_006649		T	129045744	C	T	129045744	2	4	127	1	0	0	0	0	0	0	0	1	17107	845	30	2		2	UTP14A	23	129045744	Silent	SNP	C	TCGA-BQ-5892-01A-11D-1589-08	115708497	129045744	26224816	62	7969											
JAK1	3716	hgsc.bcm.edu	37	chr1	65344759	65344759	+	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	tgtcatcaacggtgatggtgCgatttggagcataccagagc	10	10	13	8	2	2	2	2	1	0	1	2	4	2	3	1	3	5	1	1	3	2	2			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr1:65344759C>T	ENST00000342505.4	-	4	526	c.278G>A	c.(277-279)cGc>cAc	p.R93H		NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	93	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	GGTGATGGTGCGATTTGGAGC	0.507			Mis		ALL																																p.R93H		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.G278A						PASS	.						134	132	133					1																	65344759		2051	4200	6251	SO:0001583	missense	3716	exon4			ATGGTGCGATTTG	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.278G>A	chr1.hg19:g.65344759C>T	ENSP00000343204:p.Arg93His	53.0	0.0	.		45.0	25.0	.	NM_002227	Q59GQ2|Q9UD26	Missense_Mutation	SNP	ENST00000342505.4	hg19	CCDS41346.1	.	.	.	.	.	.	.	.	.	.	C	0.013	-1.643910	0.00792	.	.	ENSG00000162434	ENST00000342505	T	0.60797	0.16	5.17	-4.45	0.03546	Band 4.1 domain (1);FERM domain (1);	.	.	.	.	T	0.03564	0.0102	N	0.00044	-2.46	0.20926	N	0.999829	B	0.02656	0.0	B	0.01281	0.0	T	0.48091	-0.9065	9	0.02654	T	1	-0.1135	14.8839	0.70553	0.0:0.2045:0.0:0.7955	.	93	P23458	JAK1_HUMAN	H	93	ENSP00000343204:R93H	ENSP00000343204:R93H	R	-	2	0	JAK1	65117347	0.002000	0.14202	0.069000	0.20011	0.073000	0.16967	-0.194000	0.09559	-0.765000	0.04645	-0.794000	0.03295	CGC	.	.	.	none		0.507	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		T	65344759	C	T	65344759	3	4	128	1	0	0	0	0	1	0	0	0	7944	768	27	1	3274	1	JAK1	1	65344759	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08		65344759	183905862	1	7970											
SNX7	51375	hgsc.bcm.edu	37	chr1	99150445	99150445	+	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	atgttttatttcttaggatgCctcattgatggacatgaact	10	17	8	6	0	2	2	1	2	1	0	2	4	2	4	1	2	2	1	1	2	3	5			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr1:99150445C>A	ENST00000306121.3	+	2	194	c.185C>A	c.(184-186)gCc>gAc	p.A62D	SNX7_ENST00000370189.5_5'UTR|SNX7_ENST00000529992.1_Missense_Mutation_p.A62D	NM_015976.4	NP_057060.2	Q9UNH6	SNX7_HUMAN	sorting nexin 7	200	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)		TCTTAGGATGCCTCATTGATG	0.303																																					p.A62D		Atlas-SNP	.											.	SNX7	76	.	0			c.C185A						PASS	.						97	88	91					1																	99150445		2203	4300	6503	SO:0001583	missense	51375	exon2			AGGATGCCTCATT	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.185C>A	chr1.hg19:g.99150445C>A	ENSP00000304429:p.Ala62Asp	110.0	0.0	.		111.0	37.0	.	NM_015976	A8KAF3|D3DT50|Q53FQ3|Q5VT09|Q5VT10|Q86U82|Q8WVD4|Q96FW9|Q9Y3Z7	Missense_Mutation	SNP	ENST00000306121.3	hg19	CCDS755.2	.	.	.	.	.	.	.	.	.	.	C	18.44	3.624884	0.66901	.	.	ENSG00000162627	ENST00000529992;ENST00000306121	T;T	0.32753	2.12;1.44	5.29	4.36	0.52297	.	.	.	.	.	T	0.15522	0.0374	N	0.19112	0.55	0.80722	D	1	B;D	0.53462	0.003;0.96	B;P	0.51229	0.003;0.663	T	0.03221	-1.1059	9	0.16896	T	0.51	.	15.2016	0.73142	0.142:0.858:0.0:0.0	.	62;62	E9PNL2;Q9UNH6-3	.;.	D	62	ENSP00000434731:A62D;ENSP00000304429:A62D	ENSP00000304429:A62D	A	+	2	0	SNX7	98923033	1.000000	0.71417	0.998000	0.56505	0.970000	0.65996	3.677000	0.54619	1.212000	0.43366	0.650000	0.86243	GCC	.	.	.	none		0.303	SNX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029609.2			A	99150445	C	A	99150445	3	1	128	1	0	0	0	0	1	0	0	0	14920	739	26	4	191	4	SNX7	1	99150445	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	33805686	99150445	150100176	2	7971											
SLC9A11	284525	hgsc.bcm.edu	37	chr1	173505010	173505010	+	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	ttttctatacaatattccaaGaaagttaaaacatttttaaa	18	16	2	5	0	1	1	0	0	1	1	2	1	2	1	1	0	2	1	1	0	10	10			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr1:173505010G>T	ENST00000367714.3	-	15	2156	c.1734C>A	c.(1732-1734)ttC>ttA	p.F578L	SLC9C2_ENST00000536496.1_Intron|SLC9C2_ENST00000466087.1_5'UTR	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	578					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)	p.F578L(1)									AATATTCCAAGAAAGTTAAAA	0.259																																					p.F578L		Atlas-SNP	.											SLC9A11,rectum,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1734A						PASS	.						30	36	34					1																	173505010		2143	4195	6338	SO:0001583	missense	284525	exon15			TTCCAAGAAAGTT	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.1734C>A	chr1.hg19:g.173505010G>T	ENSP00000356687:p.Phe578Leu	77.0	0.0	.		113.0	29.0	.	NM_178527	Q86UF3	Missense_Mutation	SNP	ENST00000367714.3	hg19	CCDS1308.1	.	.	.	.	.	.	.	.	.	.	G	1.013	-0.687321	0.03328	.	.	ENSG00000162753	ENST00000367714	T	0.04275	3.66	5.81	2.48	0.30137	.	0.605739	0.15672	N	0.250356	T	0.00967	0.0032	L	0.36672	1.1	0.09310	N	1	B	0.22346	0.068	B	0.15484	0.013	T	0.47898	-0.9081	10	0.11485	T	0.65	-5.8685	3.7288	0.08485	0.2435:0.2051:0.5513:0.0	.	578	Q5TAH2	S9A11_HUMAN	L	578	ENSP00000356687:F578L	ENSP00000356687:F578L	F	-	3	2	SLC9A11	171771633	0.739000	0.28196	0.234000	0.24042	0.083000	0.17756	1.040000	0.30278	0.747000	0.32809	0.603000	0.83216	TTC	.	.	.	none		0.259	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527		T	173505010	G	T	173505010	3	4	128	1	0	0	0	0	1	0	0	0	14724	933	33	4	1696	4	SLC9A11	1	173505010	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	74354565	173505010	75745611	3	7972											
OR13G1	441933	hgsc.bcm.edu	37	chr1	247835611	247835611	+	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	aggagaatagtaaagggtcaCcactgtgagatgagatgagc	15	7	14	5	0	1	4	1	3	0	3	1	7	1	4	1	2	1	1	1	2	4	2			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr1:247835611C>G	ENST00000359688.2	-	1	754	c.733G>C	c.(733-735)Gtg>Ctg	p.V245L	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005487.1	NP_001005487.1	Q8NGZ3	O13G1_HUMAN	olfactory receptor, family 13, subfamily G, member 1	245						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(1)|large_intestine(2)|lung(28)|skin(2)	35	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			TAAAGGGTCACCACTGTGAGA	0.448																																					p.V245L		Atlas-SNP	.											.	OR13G1	78	.	0			c.G733C						PASS	.						162	139	147					1																	247835611		2203	4300	6503	SO:0001583	missense	441933	exon1			GGGTCACCACTGT	AB065623	CCDS31094.1	1q44	2012-08-09			ENSG00000197437	ENSG00000197437		"GPCR / Class A : Olfactory receptors"	14999	protein-coding gene	gene with protein product		611677					Standard	NM_001005487		Approved		uc001idi.1	Q8NGZ3	OTTHUMG00000040212	ENST00000359688.2:c.733G>C	chr1.hg19:g.247835611C>G	ENSP00000352717:p.Val245Leu	122.0	0.0	.		122.0	32.0	.	NM_001005487	B2RN80|Q5T2T2|Q6IF86	Missense_Mutation	SNP	ENST00000359688.2	hg19	CCDS31094.1	.	.	.	.	.	.	.	.	.	.	C	10.52	1.373546	0.24857	.	.	ENSG00000197437	ENST00000359688	T	0.00355	7.91	4.2	3.29	0.37713	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39615	N	0.001320	T	0.00815	0.0027	M	0.86740	2.835	0.09310	N	1	D	0.76494	0.999	D	0.77557	0.99	T	0.26258	-1.0108	10	0.66056	D	0.02	-60.5376	10.2821	0.43545	0.0:0.9016:0.0:0.0984	.	245	Q8NGZ3	O13G1_HUMAN	L	245	ENSP00000352717:V245L	ENSP00000352717:V245L	V	-	1	0	OR13G1	245902234	0.021000	0.18746	0.037000	0.18230	0.096000	0.18686	0.139000	0.16036	1.126000	0.42016	-0.214000	0.12660	GTG	.	.	.	none		0.448	OR13G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096869.1	NM_001005487		G	247835611	C	G	247835611	3	3	128	1	0	0	0	0	1	0	0	0	10949	507	18	4	194	4	OR13G1	1	247835611	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	74330601	247835611	1415010	4	7973											
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178936091	178936091	+	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	atcctctctctgaaatcactGagcaggagaaagattttcta	13	12	7	9	0	4	4	1	2	3	2	6	5	5	4	1	1	1	1	1	1	3	3	rs104886003		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr3:178936091G>A	ENST00000263967.3	+	10	1790	c.1633G>A	c.(1633-1635)Gag>Aag	p.E545K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	545	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> A (in CWS5 and HCC; also found in a glioblastoma multiforme sample). {ECO:0000269|PubMed:15608678, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:23246288}.|E -> G (in KERSEB; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:17673550}.|E -> K (in MCAP, KERSEB, CRC and BC; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N-terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E545K(881)|p.E545Q(18)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TGAAATCACTGAGCAGGAGAA	0.353	E545K(BC3C_URINARY_TRACT)|E545K(BFTC909_KIDNEY)|E545K(DLD1_LARGE_INTESTINE)|E545K(ESS1_ENDOMETRIUM)|E545K(HCC202_BREAST)|E545K(HCT15_LARGE_INTESTINE)|E545K(HSC4_UPPER_AERODIGESTIVE_TRACT)|E545K(HT1197_URINARY_TRACT)|E545K(HUH28_BILIARY_TRACT)|E545K(KYSE510_OESOPHAGUS)|E545K(L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|E545K(MCF7_BREAST)|E545K(MDAMB361_BREAST)|E545K(MKN1_STOMACH)|E545K(NCIH460_LUNG)|E545K(NCIH508_LARGE_INTESTINE)|E545K(NCIH596_LUNG)|E545K(RERFLCSQ1_LUNG)|E545K(TCCSUP_URINARY_TRACT)|E545K(TE5_OESOPHAGUS)	57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.E545K	Colon(199;1504 1750 3362 26421 31210 32040)	Atlas-SNP	.		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	PIK3CA_ENST00000263967,NS,carcinoma,0,1131	PIK3CA	8460	.	899	Substitution - Missense(899)	breast(308)|large_intestine(286)|urinary_tract(97)|lung(44)|endometrium(37)|ovary(25)|stomach(17)|upper_aerodigestive_tract(16)|skin(14)|central_nervous_system(13)|cervix(13)|thyroid(7)|oesophagus(7)|penis(4)|kidney(3)|soft_tissue(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(1)|biliary_tract(1)|NS(1)|pituitary(1)	c.G1633A						PASS	.						61	60	60					3																	178936091		1813	4072	5885	SO:0001583	missense	5290	exon10			ATCACTGAGCAGG		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1633G>A	chr3.hg19:g.178936091G>A	ENSP00000263967:p.Glu545Lys	92.0	0.0	.		68.0	4.0	.	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	hg19	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	36	5.703347	0.96812	.	.	ENSG00000121879	ENST00000263967	T	0.63255	-0.03	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.73822	0.3636	L	0.51914	1.62	0.80722	D	1	D	0.62365	0.991	D	0.62955	0.909	T	0.68872	-0.5294	10	0.32370	T	0.25	-25.7963	20.0024	0.97423	0.0:0.0:1.0:0.0	.	545	P42336	PK3CA_HUMAN	K	545	ENSP00000263967:E545K	ENSP00000263967:E545K	E	+	1	0	PIK3CA	180418785	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAG	.	.	.	weak		0.353	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			A	178936091	G	A	178936091	3	1	128	1	0	0	0	0	1	0	0	0	11920	1291	45	2	1667	2	PIK3CA	3	178936091	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08		178936091	19086339	5	7974											
COL4A3BP	10087	hgsc.bcm.edu	37	chr5	74712823	74712828	+	In_Frame_Del	DEL	TACCAT	TACCAT	-																															cgcttcccctttaaagtctaTaccattaattccttttggtg																										TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	TACCAT	TACCAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr5:74712823_74712828delTACCAT	ENST00000405807.4	-	7	1131_1136	c.710_715delATGGTA	c.(709-717)aatggtata>ata	p.NG237del	COL4A3BP_ENST00000380494.5_In_Frame_Del_p.NG365del|COL4A3BP_ENST00000261415.7_In_Frame_Del_p.NG237del	NM_005713.2	NP_005704.1	Q9Y5P4	C43BP_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen) binding protein	237					cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|ceramide metabolic process (GO:0006672)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi ceramide transport (GO:0035621)|heart morphogenesis (GO:0003007)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lipid homeostasis (GO:0055088)|mitochondrion morphogenesis (GO:0070584)|muscle contraction (GO:0006936)|protein phosphorylation (GO:0006468)|response to endoplasmic reticulum stress (GO:0034976)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ceramide binding (GO:0097001)|ceramide transporter activity (GO:0035620)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein kinase activity (GO:0004672)			breast(1)|kidney(1)|large_intestine(5)|lung(4)|skin(3)|stomach(1)|urinary_tract(1)	16		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;1e-53)		TTAAAGTCTATACCATTAATTCCTTT	0.32																																					p.365_367del		Atlas-INDEL	.											.	COL4A3BP	72	.	0			c.1095_1100del						PASS	.																																			SO:0001651	inframe_deletion	10087	exon8			.	AF136450	CCDS4028.1, CCDS4029.1, CCDS47235.1	5q13.3	2013-01-10	2007-06-08	2007-06-08	ENSG00000113163	ENSG00000113163		"StAR-related lipid transfer (START) domain containing", "Pleckstrin homology (PH) domain containing"	2205	protein-coding gene	gene with protein product	"ceramide transporter", "StAR-related lipid transfer (START) domain containing 11"	604677				10212244	Standard	NM_001130105		Approved	GPBP, STARD11, CERT	uc003kdt.3	Q9Y5P4	OTTHUMG00000102068	ENST00000405807.4:c.710_715delATGGTA	chr5.hg19:g.74712823_74712828delTACCAT	ENSP00000383996:p.Asn237_Gly238del	89.0	0.0	0		73.0	26.0	0.356164	NM_001130105	A8K7S2|B3KUB7|Q53YV1|Q53YV2|Q96Q85|Q96Q88|Q9H2S7|Q9H2S8	In_Frame_Del	DEL	ENST00000405807.4	hg19	CCDS4028.1																																																																																			.	.	.	none		0.32	COL4A3BP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219875.2	NM_005713		-	74712828	TACCAT	-	74712823	7	5	128	1	0	1	0	1	0	0	0	0	3694	1406	49	0	1203	0	COL4A3BP	5	74712823	In_Frame_Del	DEL	TACCAT	TCGA-BQ-5893-01A-11D-1589-08		74712823	106202437	6	7975											
LARS	51520	hgsc.bcm.edu	37	chr5	145533344	145533344	+	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	agcaatatcatcaggggagtCggaaggaacacttgtaacca	15	7	11	8	1	2	0	2	0	0	0	3	3	2	3	1	4	3	2	1	4	5	3			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr5:145533344C>T	ENST00000394434.2	-	12	1349	c.1183G>A	c.(1183-1185)Gac>Aac	p.D395N	LARS_ENST00000545646.1_Missense_Mutation_p.D349N|LARS_ENST00000274562.9_Missense_Mutation_p.D368N|LARS_ENST00000510191.1_Missense_Mutation_p.D341N	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	395	Editing domain.				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)	TCAGGGGAGTCGGAAGGAACA	0.363																																					p.D395N		Atlas-SNP	.											.	LARS	100	.	0			c.G1183A						PASS	.						128	121	123					5																	145533344		2203	4300	6503	SO:0001583	missense	51520	exon12			GGGAGTCGGAAGG	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.1183G>A	chr5.hg19:g.145533344C>T	ENSP00000377954:p.Asp395Asn	35.0	0.0	.		67.0	31.0	.	NM_020117	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	Missense_Mutation	SNP	ENST00000394434.2	hg19	CCDS34265.1	.	.	.	.	.	.	.	.	.	.	C	34	5.346551	0.95807	.	.	ENSG00000133706	ENST00000394434;ENST00000545646;ENST00000510191;ENST00000274562	T;T;T;T	0.35048	1.33;1.33;1.33;1.33	5.59	5.59	0.84812	Valyl/Leucyl/Isoleucyl-tRNA synthetase, class Ia, editing domain (2);Aminoacyl-tRNA synthetase, class Ia (1);	0.000000	0.85682	D	0.000000	T	0.67664	0.2917	M	0.87682	2.9	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.999;0.996;0.948	T	0.70536	-0.4845	10	0.54805	T	0.06	-7.3038	19.956	0.97218	0.0:1.0:0.0:0.0	.	368;349;395	B4DER1;F5H698;Q9P2J5	.;.;SYLC_HUMAN	N	395;349;341;368	ENSP00000377954:D395N;ENSP00000437791:D349N;ENSP00000426005:D341N;ENSP00000274562:D368N	ENSP00000274562:D368N	D	-	1	0	LARS	145513537	1.000000	0.71417	0.998000	0.56505	0.887000	0.51463	5.851000	0.69481	2.788000	0.95919	0.557000	0.71058	GAC	.	.	.	none		0.363	LARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000373367.1	NM_020117		T	145533344	C	T	145533344	3	4	128	1	0	0	0	0	1	0	0	0	8641	884	31	1	2431	1	LARS	5	145533344	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	70820521	145533344	35381916	7	7976											
GRPEL2	134266	hgsc.bcm.edu	37	chr5	148730749	148730749	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gttggggtgcagcctggcacCgtggcattagtaagacaaga	10	8	15	8	1	0	2	0	0	0	2	0	2	0	2	2	4	2	5	2	4	3	3			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr5:148730749C>T	ENST00000329271.3	+	4	692	c.582C>T	c.(580-582)acC>acT	p.T194T	GRPEL2_ENST00000507562.1_3'UTR|GRPEL2_ENST00000416916.2_3'UTR|GRPEL2-AS1_ENST00000521295.1_RNA	NM_152407.3	NP_689620.2	Q8TAA5	GRPE2_HUMAN	GrpE-like 2, mitochondrial (E. coli)	194					cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane (GO:0005743)	adenyl-nucleotide exchange factor activity (GO:0000774)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCCTGGCACCGTGGCATTAG	0.527																																					p.T194T		Atlas-SNP	.											.	GRPEL2	18	.	0			c.C582T						PASS	.						119	111	114					5																	148730749		2203	4300	6503	SO:0001819	synonymous_variant	134266	exon4			TGGCACCGTGGCA	AL832325	CCDS4295.1	5q33.1	2008-02-05			ENSG00000164284	ENSG00000164284			21060	protein-coding gene	gene with protein product							Standard	NM_152407		Approved	DKFZp451C205, Mt-GrpE#2, FLJ23713	uc003lqj.3	Q8TAA5	OTTHUMG00000130048	ENST00000329271.3:c.582C>T	chr5.hg19:g.148730749C>T		150.0	0.0	.		105.0	37.0	.	NM_152407	B4DFA6|Q49AJ6	Silent	SNP	ENST00000329271.3	hg19	CCDS4295.1																																																																																			.	.	.	none		0.527	GRPEL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252327.1	NM_152407		T	148730749	C	T	148730749	2	4	128	1	0	0	0	0	0	0	0	1	6814	639	23	1		1	GRPEL2	5	148730749	Silent	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	3197405	148730749	32184511	8	7977											
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-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	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	203	.	0			c.C107A						PASS	.						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	chr6.hg19:g.136599912G>T	ENSP00000435210:p.Ser36Tyr	37.0	0.0	.		66.0	7.0	.	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	hg19	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	128	1	0	0	0	0	1	0	0	0	1383	942	33	4	2695	4	BCLAF1	6	136599912	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08		136599912	34515155	9	7978											
SAMD5	389432	hgsc.bcm.edu	37	chr6	147830100	147830100	+	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	gtttacgagtggctcaaagcGctgcagcttccgcagtacgc	8	9	12	12	4	1	0	1	0	0	0	2	1	2	0	1	1	5	7	1	1	3	4			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr6:147830100G>A	ENST00000367474.1	+	1	38	c.36G>A	c.(34-36)gcG>gcA	p.A12A		NM_001030060.2	NP_001025231.1	Q5TGI4	SAMD5_HUMAN	sterile alpha motif domain containing 5	12	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.												Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;9.55e-10)|GBM - Glioblastoma multiforme(68;0.112)		GGCTCAAAGCGCTGCAGCTTC	0.637																																					p.A12A		Atlas-SNP	.											.	SAMD5	4	.	0			c.G36A						PASS	.						53	49	50					6																	147830100		2203	4300	6503	SO:0001819	synonymous_variant	389432	exon1			CAAAGCGCTGCAG	AL354880	CCDS34548.1	6q24.3	2013-01-10			ENSG00000203727	ENSG00000203727		"Sterile alpha motif (SAM) domain containing"	21180	protein-coding gene	gene with protein product							Standard	NM_001030060		Approved	dJ875H10.1	uc003qmc.2	Q5TGI4	OTTHUMG00000015767	ENST00000367474.1:c.36G>A	chr6.hg19:g.147830100G>A		73.0	0.0	.		55.0	12.0	.	NM_001030060		Silent	SNP	ENST00000367474.1	hg19	CCDS34548.1																																																																																			.	.	.	none		0.637	SAMD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042610.1	NM_001030060		A	147830100	G	A	147830100	2	1	128	1	0	0	0	0	0	0	0	1	13836	1074	38	1		1	SAMD5	6	147830100	Silent	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	11230188	147830100	23284967	10	7979											
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47970797	47970797	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttggtgggggtctccatcGtgacagtcccaggaagcagc	7	8	14	12	1	1	1	0	1	1	0	4	2	2	2	3	4	2	1	3	4	1	1			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr7:47970797G>A	ENST00000289672.2	-	6	691	c.641C>T	c.(640-642)aCg>aTg	p.T214M		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	214					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						GGTCTCCATCGTGACAGTCCC	0.617																																					p.T214M		Atlas-SNP	.											.	PKD1L1	328	.	0			c.C641T						PASS	.						67	68	68					7																	47970797		2203	4300	6503	SO:0001583	missense	168507	exon6			TCCATCGTGACAG	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.641C>T	chr7.hg19:g.47970797G>A	ENSP00000289672:p.Thr214Met	110.0	0.0	.		85.0	27.0	.	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	hg19	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	G	8.481	0.859718	0.17178	.	.	ENSG00000158683	ENST00000289672	T	0.23147	1.92	3.26	-2.9	0.05648	.	6.156550	0.00725	N	0.000901	T	0.12817	0.0311	N	0.08118	0	0.09310	N	1	B	0.16802	0.019	B	0.08055	0.003	T	0.20505	-1.0273	10	0.46703	T	0.11	.	4.4996	0.11858	0.4273:0.1738:0.3989:0.0	.	214	Q8TDX9	PK1L1_HUMAN	M	214	ENSP00000289672:T214M	ENSP00000289672:T214M	T	-	2	0	PKD1L1	47937322	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.622000	0.02042	-0.610000	0.05716	-0.225000	0.12378	ACG	.	.	.	none		0.617	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		A	47970797	G	A	47970797	3	1	128	1	0	0	0	0	1	0	0	0	11971	1145	40	1	8116	1	PKD1L1	7	47970797	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08		47970797	111167866	11	7980											
TPK1	27010	hgsc.bcm.edu	37	chr7	144245631	144245631	+	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	taacctgcatacaaggctgtCcaacaggaataaggccacac	15	6	8	12	0	0	0	0	0	0	0	1	1	1	1	3	3	4	2	3	3	6	3			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr7:144245631C>A	ENST00000360057.3	-	8	668	c.566G>T	c.(565-567)gGa>gTa	p.G189V	TPK1_ENST00000547966.1_5'UTR|TPK1_ENST00000538212.2_Missense_Mutation_p.G135V|TPK1_ENST00000549981.1_Missense_Mutation_p.G72V|TPK1_ENST00000378099.3_Missense_Mutation_p.G140V	NM_022445.3	NP_071890.2	Q9H3S4	TPK1_HUMAN	thiamin pyrophosphokinase 1	189					small molecule metabolic process (GO:0044281)|thiamine diphosphate biosynthetic process (GO:0009229)|thiamine metabolic process (GO:0006772)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|thiamine binding (GO:0030975)|thiamine diphosphokinase activity (GO:0004788)			large_intestine(3)|lung(12)|ovary(2)|urinary_tract(2)	19					Thiamine(DB00152)	ACAAGGCTGTCCAACAGGAAT	0.418																																					p.G189V	Ovarian(45;88 1034 2073 5829 28455)	Atlas-SNP	.											.	TPK1	41	.	0			c.G566T						PASS	.						200	167	178					7																	144245631		2203	4300	6503	SO:0001583	missense	27010	exon8			GGCTGTCCAACAG	AB028138	CCDS5888.1, CCDS55178.1	7q34-q35	2008-07-18			ENSG00000196511	ENSG00000196511			17358	protein-coding gene	gene with protein product	"placental protein 20", "thiamine pyrophosphokinase 1", "thiamine kinase", "thiamine diphosphokinase"	606370				11342111	Standard	NM_022445		Approved	HTPK1, PP20	uc003weq.3	Q9H3S4	OTTHUMG00000152774	ENST00000360057.3:c.566G>T	chr7.hg19:g.144245631C>A	ENSP00000353165:p.Gly189Val	172.0	0.0	.		145.0	65.0	.	NM_022445	A8K0T7|D3DWG0|I6L9B8|Q6NUR5|Q9H602	Missense_Mutation	SNP	ENST00000360057.3	hg19	CCDS5888.1	.	.	.	.	.	.	.	.	.	.	C	18.00	3.524985	0.64747	.	.	ENSG00000196511	ENST00000360057;ENST00000538212;ENST00000378099;ENST00000549981	T;T;T;T	0.80214	-1.35;-1.35;-1.35;-1.35	5.95	5.95	0.96441	Thiamin pyrophosphokinase, vitamin B1-binding domain (3);	0.000000	0.85682	D	0.000000	D	0.91402	0.7287	M	0.89968	3.075	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.993;1.0;0.999	D	0.92101	0.5688	10	0.59425	D	0.04	-17.4306	15.8749	0.79154	0.0:1.0:0.0:0.0	.	140;189;135	F5GZG6;Q9H3S4;Q6ZQX6	.;TPK1_HUMAN;.	V	189;135;140;72	ENSP00000353165:G189V;ENSP00000438813:G135V;ENSP00000367339:G140V;ENSP00000448698:G72V	ENSP00000353165:G189V	G	-	2	0	TPK1	143876564	1.000000	0.71417	1.000000	0.80357	0.467000	0.32768	5.315000	0.65810	2.817000	0.96982	0.563000	0.77884	GGA	.	.	.	none		0.418	TPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327777.1	NM_022445		A	144245631	C	A	144245631	3	1	128	1	0	0	0	0	1	0	0	0	16416	855	30	4	173	4	TPK1	7	144245631	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	96274834	144245631	14893032	12	7981											
MLL3	58508	hgsc.bcm.edu	37	chr7	151845739	151845739	+	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	gttcaagtggacccacagatCcaagtcaaggttgagtagcc	12	8	11	10	0	2	2	2	1	0	1	3	3	3	3	3	2	1	3	3	2	4	3			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr7:151845739C>A	ENST00000262189.6	-	52	13491	c.13273G>T	c.(13273-13275)Gat>Tat	p.D4425Y	KMT2C_ENST00000355193.2_Missense_Mutation_p.D4482Y	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	4425					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)										ACCCACAGATCCAAGTCAAGG	0.502																																					p.D4425Y		Atlas-SNP	.											MLL3_ENST00000355193,NS,carcinoma,0,2	MLL3	1564	.	0			c.G13273T						PASS	.						97	89	92					7																	151845739		2203	4300	6503	SO:0001583	missense	58508	exon52			ACAGATCCAAGTC	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.13273G>T	chr7.hg19:g.151845739C>A	ENSP00000262189:p.Asp4425Tyr	128.0	0.0	.		102.0	45.0	.	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.05|17.05	3.290706|3.290706	0.59976|0.59976	.|.	.|.	ENSG00000055609|ENSG00000055609	ENST00000262189;ENST00000355193;ENST00000424877|ENST00000360104	D;D;D|.	0.90385|.	-2.0;-1.98;-2.66|.	5.24|5.24	5.24|5.24	0.73138|0.73138	.|.	0.000000|.	0.44285|.	U|.	0.000480|.	T|T	0.78123|0.78123	0.4234|0.4234	M|M	0.78637|0.78637	2.42|2.42	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.91635|.	0.997;0.999;0.999|.	T|T	0.78221|0.78221	-0.2288|-0.2288	10|5	0.49607|.	T|.	0.09|.	.|.	19.1777|19.1777	0.93609|0.93609	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	4425;3543;4482|.	Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3|.	MLL3_HUMAN;.;.|.	Y|V	4425;4482;1042|1985	ENSP00000262189:D4425Y;ENSP00000347325:D4482Y;ENSP00000410411:D1042Y|.	ENSP00000262189:D4425Y|.	D|G	-|-	1|2	0|0	MLL3|MLL3	151476672|151476672	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.957000|0.957000	0.61999|0.61999	7.776000|7.776000	0.85560|0.85560	2.602000|2.602000	0.87976|0.87976	0.557000|0.557000	0.71058|0.71058	GAT|GGA	.	.	.	none		0.502	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			A	151845739	C	A	151845739	3	1	128	1	0	0	0	0	1	0	0	0	9629	855	30	4	1494	4	MLL3	7	151845739	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	7600108	151845739	7292924	13	7982											
MYOM2	9172	hgsc.bcm.edu	37	chr8	2044224	2044224	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acaagcgtgaagttcaccatAaaaactggcacgaggtcaat	16	7	9	9	2	2	1	2	1	0	0	2	2	2	1	1	2	2	2	1	2	6	2			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr8:2044224A>G	ENST00000262113.4	+	18	2404	c.2263A>G	c.(2263-2265)Aaa>Gaa	p.K755E	MYOM2_ENST00000523438.1_Missense_Mutation_p.K180E	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	755	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		AGTTCACCATAAAAACTGGCA	0.517																																					p.K755E		Atlas-SNP	.											.	MYOM2	251	.	0			c.A2263G						PASS	.						104	92	96					8																	2044224		2203	4300	6503	SO:0001583	missense	9172	exon18			CACCATAAAAACT		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.2263A>G	chr8.hg19:g.2044224A>G	ENSP00000262113:p.Lys755Glu	74.0	0.0	.		73.0	23.0	.	NM_003970	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	hg19	CCDS5957.1	.	.	.	.	.	.	.	.	.	.	A	0.005	-2.135743	0.00335	.	.	ENSG00000036448	ENST00000262113;ENST00000523438	T;T	0.54675	0.56;0.56	5.46	0.23	0.15372	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.912312	0.09530	N	0.789730	T	0.32315	0.0825	N	0.25201	0.72	0.09310	N	1	B	0.23540	0.087	B	0.30943	0.122	T	0.31166	-0.9953	10	0.02654	T	1	.	6.2231	0.20693	0.4732:0.3775:0.0689:0.0804	.	755	P54296	MYOM2_HUMAN	E	755;180	ENSP00000262113:K755E;ENSP00000428396:K180E	ENSP00000262113:K755E	K	+	1	0	MYOM2	2031631	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.150000	0.16263	-0.212000	0.10109	-1.477000	0.00996	AAA	.	.	.	none		0.517	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970		G	2044224	A	G	2044224	3	3	128	1	0	0	0	0	1	0	0	0	10099	363	13	3	2329	3	MYOM2	8	2044224	Missense_Mutation	SNP	A	TCGA-BQ-5893-01A-11D-1589-08		2044224	144319798	14	7983											
FAM110B	90362	hgsc.bcm.edu	37	chr8	59059734	59059734	+	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	cgcagcgcaagcatgatcagCtcagactgtgaacagtctca	12	7	10	12	2	3	3	3	2	1	1	4	3	3	3	0	0	4	4	0	0	2	0			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr8:59059734C>T	ENST00000361488.3	+	5	1825	c.945C>T	c.(943-945)agC>agT	p.S315S	FAM110B_ENST00000520369.1_Intron	NM_147189.2	NP_671722.1	Q8TC76	F110B_HUMAN	family with sequence similarity 110, member B	315						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)	26		all_epithelial(80;0.025)|all_lung(136;0.0274)|Lung NSC(129;0.0355)				GCATGATCAGCTCAGACTGTG	0.483																																					p.S315S		Atlas-SNP	.											.	FAM110B	64	.	0			c.C945T						PASS	.						79	75	76					8																	59059734		2203	4300	6503	SO:0001819	synonymous_variant	90362	exon5			GATCAGCTCAGAC	U79298	CCDS6170.1	8q12.1	2007-06-21	2007-03-21	2007-03-21		ENSG00000169122			28587	protein-coding gene	gene with protein product		611394	"chromosome 8 open reading frame 72"	C8orf72		8619474, 9110174, 17499476	Standard	XM_005251324		Approved	MGC39325	uc003xtj.1	Q8TC76		ENST00000361488.3:c.945C>T	chr8.hg19:g.59059734C>T		60.0	0.0	.		45.0	19.0	.	NM_147189	Q5BM08|Q9Y4K2	Silent	SNP	ENST00000361488.3	hg19	CCDS6170.1																																																																																			.	.	.	none		0.483	FAM110B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378095.2	NM_147189		T	59059734	C	T	59059734	2	4	128	1	0	0	0	0	0	0	0	1	5401	796	28	2		2	FAM110B	8	59059734	Silent	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	57015510	59059734	87304288	15	7984											
CSPP1	79848	hgsc.bcm.edu	37	chr8	68087587	68087587	+	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	tggatcctccaagagatcatCacaccttagagattcagcag	13	9	8	11	0	3	2	3	0	0	2	5	5	5	3	3	1	1	1	3	1	2	2			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr8:68087587C>A	ENST00000262210.5	+	24	3041	c.3010C>A	c.(3010-3012)Cac>Aac	p.H1004N	ARFGEF1_ENST00000520381.1_3'UTR|CSPP1_ENST00000412460.1_Missense_Mutation_p.H659N|CSPP1_ENST00000521168.1_3'UTR	NM_024790.6	NP_079066.5	Q1MSJ5	CSPP1_HUMAN	centrosome and spindle pole associated protein 1	1039					positive regulation of cell division (GO:0051781)|positive regulation of cytokinesis (GO:0032467)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|spindle (GO:0005819)|spindle pole (GO:0000922)				NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|prostate(3)|skin(1)|urinary_tract(1)	49	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)			AAGAGATCATCACACCTTAGA	0.363																																					p.H1004N		Atlas-SNP	.											.	CSPP1	129	.	0			c.C3010A						PASS	.						67	66	66					8																	68087587		1874	4104	5978	SO:0001583	missense	79848	exon24			GATCATCACACCT	AJ583433	CCDS43744.1	8q13.2	2014-02-24			ENSG00000104218	ENSG00000104218			26193	protein-coding gene	gene with protein product		611654				15580290, 24360807	Standard	NM_024790		Approved	FLJ22490, CSPP, JBTS21	uc003xxj.3	Q1MSJ5	OTTHUMG00000164564	ENST00000262210.5:c.3010C>A	chr8.hg19:g.68087587C>A	ENSP00000262210:p.His1004Asn	94.0	0.0	.		98.0	5.0	.	NM_024790	A6ND63|Q70F00|Q8TBC1	Missense_Mutation	SNP	ENST00000262210.5	hg19	CCDS43744.1	.	.	.	.	.	.	.	.	.	.	C	12.76	2.034076	0.35893	.	.	ENSG00000104218	ENST00000262210;ENST00000389042;ENST00000412460;ENST00000519668	T;T;T	0.29655	1.56;1.58;1.58	4.8	1.4	0.22301	.	0.673183	0.14117	N	0.340319	T	0.18425	0.0442	L	0.29908	0.895	0.54753	D	0.999989	B;B;B;B	0.25904	0.137;0.102;0.082;0.034	B;B;B;B	0.25140	0.058;0.05;0.037;0.025	T	0.07927	-1.0747	10	0.36615	T	0.2	-2.5735	4.0688	0.09872	0.1755:0.4941:0.2432:0.0872	.	162;659;1004;1039	Q9H688;Q1MSJ5-2;Q1MSJ5-1;Q1MSJ5	.;.;.;CSPP1_HUMAN	N	1004;1039;659;659	ENSP00000262210:H1004N;ENSP00000415782:H659N;ENSP00000430092:H659N	ENSP00000262210:H1004N	H	+	1	0	CSPP1	68250141	0.582000	0.26749	0.987000	0.45799	0.995000	0.86356	0.360000	0.20250	0.541000	0.28827	0.591000	0.81541	CAC	.	.	.	none		0.363	CSPP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379254.1	NM_024790		A	68087587	C	A	68087587	3	1	128	1	0	0	0	0	1	0	0	0	3964	826	29	4	3217	4	CSPP1	8	68087587	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	9027853	68087587	78276435	16	7985											
CSMD3	114788	hgsc.bcm.edu	37	chr8	113249531	113249531	+	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	tgtttccttcctttgaaattGtaagagcctttccatatata	10	18	5	8	0	0	2	0	1	0	1	3	2	3	2	4	0	1	2	4	0	5	9			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr8:113249531G>T	ENST00000297405.5	-	67	10759	c.10515C>A	c.(10513-10515)taC>taA	p.Y3505*	CSMD3_ENST00000455883.2_Nonsense_Mutation_p.Y3336*|CSMD3_ENST00000343508.3_Nonsense_Mutation_p.Y3465*|CSMD3_ENST00000352409.3_Nonsense_Mutation_p.Y3435*	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3505						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CTTTGAAATTGTAAGAGCCTT	0.348										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.Y3505X		Atlas-SNP	.											.	CSMD3	2325	.	0			c.C10515A						PASS	.						157	144	148					8																	113249531		2203	4300	6503	SO:0001587	stop_gained	114788	exon67			GAAATTGTAAGAG	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.10515C>A	chr8.hg19:g.113249531G>T	ENSP00000297405:p.Tyr3505*	99.0	0.0	.		104.0	38.0	.	NM_198123	Q96PZ3	Nonsense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	51	17.550337	0.99888	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	.	.	.	4.77	-1.61	0.08399	.	0.090578	0.46442	D	0.000299	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.6815	0.23123	0.3366:0.1118:0.5516:0.0	.	.	.	.	X	3465;3505;2775;3336;3435	.	ENSP00000297405:Y3505X	Y	-	3	2	CSMD3	113318707	0.982000	0.34865	0.993000	0.49108	0.533000	0.34776	0.213000	0.17521	-0.254000	0.09500	-0.499000	0.04595	TAC	.	.	.	none		0.348	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113249531	G	T	113249531	4	4	128	1	0	0	0	0	0	1	0	0	3948	1372	48	4	628	4	CSMD3	8	113249531	Nonsense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	45161944	113249531	33114491	17	7986			1	17		2	2	36	N	G_C	5.313724e-05
CSMD3	114788	hgsc.bcm.edu	37	chr8	113249566	113249566	+	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	tatataattttgggcaaataCatcatcaggaactgtgaata	16	13	7	5	0	2	1	2	1	0	0	2	2	2	2	0	2	2	1	0	2	8	7			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr8:113249566C>A	ENST00000297405.5	-	67	10724	c.10480G>T	c.(10480-10482)Gta>Tta	p.V3494L	CSMD3_ENST00000455883.2_Missense_Mutation_p.V3325L|CSMD3_ENST00000343508.3_Missense_Mutation_p.V3454L|CSMD3_ENST00000352409.3_Missense_Mutation_p.V3424L	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3494						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						TGGGCAAATACATCATCAGGA	0.303										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.V3494L		Atlas-SNP	.											.	CSMD3	2325	.	0			c.G10480T						PASS	.						110	103	105					8																	113249566		2203	4300	6503	SO:0001583	missense	114788	exon67			CAAATACATCATC	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.10480G>T	chr8.hg19:g.113249566C>A	ENSP00000297405:p.Val3494Leu	82.0	0.0	.		80.0	25.0	.	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	14.53	2.563747	0.45694	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.33865	1.71;1.7;1.78;1.39;1.76	4.77	4.77	0.60923	.	0.000000	0.64402	D	0.000010	T	0.55417	0.1919	M	0.71206	2.165	0.48087	D	0.999581	D;D;B	0.61080	0.989;0.961;0.038	D;P;B	0.63033	0.91;0.741;0.07	T	0.50432	-0.8829	10	0.16896	T	0.51	.	17.9788	0.89134	0.0:1.0:0.0:0.0	.	3325;3494;3454	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	L	3454;3494;2764;3325;3424	ENSP00000345799:V3454L;ENSP00000297405:V3494L;ENSP00000341558:V2764L;ENSP00000412263:V3325L;ENSP00000343124:V3424L	ENSP00000297405:V3494L	V	-	1	0	CSMD3	113318742	1.000000	0.71417	1.000000	0.80357	0.431000	0.31685	7.627000	0.83176	2.467000	0.83353	0.467000	0.42956	GTA	.	.	.	none		0.303	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113249566	C	A	113249566	3	1	128	1	0	0	0	0	1	0	0	0	3948	478	17	4	663	4	CSMD3	8	113249566	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	35	113249566	33114456	18	7987			1	17		2	2	36	N	G_C	5.313724e-05
DENND3	22898	hgsc.bcm.edu	37	chr8	142186773	142186773	+	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	gcgtccaagaaagaagtcttCgaagccaacctgaaaaccga	16	5	9	11	3	1	3	0	1	1	2	3	5	2	3	4	0	3	0	4	0	7	1	rs374490803		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr8:142186773C>T	ENST00000262585.2	+	15	2657	c.2379C>T	c.(2377-2379)ttC>ttT	p.F793F	DENND3_ENST00000424248.1_Silent_p.F741F|DENND3_ENST00000519811.1_Silent_p.F873F	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	793					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)			AAGAAGTCTTCGAAGCCAACC	0.512																																					p.F793F		Atlas-SNP	.											.	DENND3	127	.	0			c.C2379T						PASS	.	C		0,4406		0,0,2203	117	105	109		2379	-8	0.4	8		109	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	DENND3	NM_014957.2		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		793/1199	142186773	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	22898	exon15			AGTCTTCGAAGCC	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.2379C>T	chr8.hg19:g.142186773C>T		121.0	0.0	.		91.0	40.0	.	NM_014957	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Silent	SNP	ENST00000262585.2	hg19	CCDS34947.1	.	.	.	.	.	.	.	.	.	.	C	9.548	1.115101	0.20795	0.0	2.33E-4	ENSG00000105339	ENST00000518668	.	.	.	5.37	-7.98	0.01135	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-17.7694	14.5506	0.68065	0.0:0.5424:0.0:0.4576	.	.	.	.	X	798	.	.	R	+	1	2	DENND3	142255955	0.831000	0.29352	0.363000	0.25875	0.894000	0.52154	-0.115000	0.10741	-1.794000	0.01256	-1.124000	0.02001	CGA	.	.	.	weak		0.512	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957		T	142186773	C	T	142186773	2	4	128	1	0	0	0	0	0	0	0	1	4434	883	31	1		1	DENND3	8	142186773	Silent	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	28937207	142186773	4177249	19	7988											
FAM83H	286077	hgsc.bcm.edu	37	chr8	144809117	144809117	+	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	ggggacgttgagtggctctgGgcagagaggaagcgggaagg	9	5	22	5	2	1	2	0	1	1	1	1	6	1	5	0	7	1	3	0	7	2	1			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr8:144809117G>C	ENST00000388913.3	-	5	2639	c.2514C>G	c.(2512-2514)gcC>gcG	p.A838A		NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	838					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)			AGTGGCTCTGGGCAGAGAGGA	0.701																																					p.A838A		Atlas-SNP	.											.	FAM83H	68	.	0			c.C2514G						PASS	.						10	11	11					8																	144809117		1984	4151	6135	SO:0001819	synonymous_variant	286077	exon5			GCTCTGGGCAGAG	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.2514C>G	chr8.hg19:g.144809117G>C		28.0	0.0	.		22.0	8.0	.	NM_198488	A0JLS2|Q8N4W0	Silent	SNP	ENST00000388913.3	hg19	CCDS6410.2																																																																																			.	.	.	none		0.701	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488		C	144809117	G	C	144809117	2	2	128	1	0	0	0	0	0	0	0	1	5647	1219	43	4		4	FAM83H	8	144809117	Silent	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	2622344	144809117	1554905	20	7989											
SMARCA2	6595	hgsc.bcm.edu	37	chr9	2110312	2110312	+	Silent	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	aaattcaatgaacctggatcCcagtatttcattttcttgct	11	16	5	9	0	3	1	2	1	1	0	4	2	4	2	2	1	2	2	2	1	4	6			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr9:2110312C>T	ENST00000382203.1	+	24	3560	c.3351C>T	c.(3349-3351)tcC>tcT	p.S1117S	SMARCA2_ENST00000349721.2_Silent_p.S1117S|SMARCA2_ENST00000357248.2_Silent_p.S1117S|SMARCA2_ENST00000382194.1_Silent_p.S1117S			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	1117	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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)		AACCTGGATCCCAGTATTTCA	0.453																																					p.S1117S		Atlas-SNP	.											.	SMARCA2	313	.	0			c.C3351T						PASS	.						94	88	90					9																	2110312		2203	4300	6503	SO:0001819	synonymous_variant	6595	exon24			TGGATCCCAGTAT	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.3351C>T	chr9.hg19:g.2110312C>T		64.0	0.0	.		102.0	32.0	.	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Silent	SNP	ENST00000382203.1	hg19	CCDS34977.1																																																																																			.	.	.	none		0.453	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070		T	2110312	C	T	2110312	2	4	128	1	0	0	0	0	0	0	0	1	14782	610	22	2		2	SMARCA2	9	2110312	Silent	SNP	C	TCGA-BQ-5893-01A-11D-1589-08		2110312	139103119	21	7990											
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84607771	84607771	+	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	cggagacttcttcagacaagGatctgaggtctaactctgag	11	10	11	9	1	5	4	1	2	4	2	5	6	5	5	0	3	1	0	0	3	2	3			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr9:84607771G>T	ENST00000344803.2	+	4	2433	c.2386G>T	c.(2386-2388)Gat>Tat	p.D796Y		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	796					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TTCAGACAAGGATCTGAGGTC	0.463																																					p.D796Y		Atlas-SNP	.											.	.	.	.	0			c.G2386T						PASS	.						102	99	100					9																	84607771		1908	4112	6020	SO:0001583	missense	389763	exon4			GACAAGGATCTGA		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.2386G>T	chr9.hg19:g.84607771G>T	ENSP00000341988:p.Asp796Tyr	157.0	0.0	.		102.0	37.0	.	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	hg19	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	G	11.52	1.664689	0.29604	.	.	ENSG00000214929	ENST00000344803	T	0.07114	3.22	2.85	1.93	0.25924	.	3.256700	0.00687	N	0.000704	T	0.16896	0.0406	L	0.54323	1.7	0.09310	N	1	D	0.57571	0.98	P	0.60012	0.867	T	0.48234	-0.9053	10	0.02654	T	1	1.3602	5.6289	0.17499	0.1558:0.0:0.8442:0.0	.	796	Q6ZQQ2	F75D1_HUMAN	Y	796	ENSP00000341988:D796Y	ENSP00000341988:D796Y	D	+	1	0	FAM75D1	83797591	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.442000	0.21628	0.762000	0.33152	0.462000	0.41574	GAT	.	.	.	none		0.463	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		T	84607771	G	T	84607771	3	4	128	1	0	0	0	0	1	0	0	0	5939	1174	41	4	2400	4	FLJ46321	9	84607771	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	82497459	84607771	56605660	22	7991											
SVEP1	79987	hgsc.bcm.edu	37	chr9	113141740	113141740	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgatcatgtctccatattgaTaatgtacgcctcgagcaatt	11	14	7	9	2	2	2	1	2	1	0	4	3	2	2	2	0	2	2	2	0	4	5			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr9:113141740T>C	ENST00000401783.2	-	44	10631	c.10295A>G	c.(10294-10296)tAt>tGt	p.Y3432C	SVEP1_ENST00000374469.1_Missense_Mutation_p.Y3409C|SVEP1_ENST00000297826.5_Missense_Mutation_p.Y1358C	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	3432	Sushi 34. {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						TCCATATTGATAATGTACGCC	0.403																																					p.Y3432C		Atlas-SNP	.											.	SVEP1	326	.	0			c.A10295G						PASS	.						112	100	104					9																	113141740		1940	4146	6086	SO:0001583	missense	79987	exon44			TATTGATAATGTA	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.10295A>G	chr9.hg19:g.113141740T>C	ENSP00000384917:p.Tyr3432Cys	79.0	0.0	.		71.0	33.0	.	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	T	17.46	3.394554	0.62066	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826	T;T;T	0.69926	-0.44;-0.44;-0.44	5.87	5.87	0.94306	Complement control module (2);Sushi/SCR/CCP (3);	0.240647	0.43416	D	0.000575	D	0.83912	0.5357	M	0.93720	3.45	0.80722	D	1	D	0.69078	0.997	D	0.63113	0.911	D	0.86941	0.2079	10	0.52906	T	0.07	.	11.9508	0.52954	0.1299:0.0:0.0:0.8701	.	3432	Q4LDE5	SVEP1_HUMAN	C	3432;3409;1358	ENSP00000384917:Y3432C;ENSP00000363593:Y3409C;ENSP00000297826:Y1358C	ENSP00000297826:Y1358C	Y	-	2	0	SVEP1	112181561	1.000000	0.71417	0.989000	0.46669	0.666000	0.39218	4.371000	0.59523	2.248000	0.74166	0.533000	0.62120	TAT	.	.	.	none		0.403	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	113141740	T	C	113141740	3	2	128	1	0	0	0	0	1	0	0	0	15432	1406	49	3	440	3	SVEP1	9	113141740	Missense_Mutation	SNP	T	TCGA-BQ-5893-01A-11D-1589-08	28533969	113141740	28071691	23	7992											
OR1B1	347169	hgsc.bcm.edu	37	chr9	125391500	125391500	+	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	gtaaccccaaatgcatagaaGaaaaagaactgagccaagca	20	4	8	9	0	0	4	0	1	0	3	0	4	0	4	3	0	5	3	3	0	8	2			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr9:125391500G>A	ENST00000304833.3	-	1	352	c.315C>T	c.(313-315)ttC>ttT	p.F105F	RP11-64P14.7_ENST00000419604.1_RNA|RP11-64P14.7_ENST00000431442.1_RNA	NM_001004450.1	NP_001004450.1	Q8NGR6	OR1B1_HUMAN	olfactory receptor, family 1, subfamily B, member 1	105						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)	16						ATGCATAGAAGAAAAAGAACT	0.502																																					p.F105F		Atlas-SNP	.											.	OR1B1	48	.	0			c.C315T						PASS	.						85	77	79					9																	125391500		2203	4300	6503	SO:0001819	synonymous_variant	347169	exon1			ATAGAAGAAAAAG	AC006313	CCDS35126.1	9q33.2	2012-08-09			ENSG00000171484	ENSG00000171484		"GPCR / Class A : Olfactory receptors"	8181	protein-coding gene	gene with protein product							Standard	NM_001004450		Approved	OR9-B	uc011lyz.2	Q8NGR6	OTTHUMG00000020616	ENST00000304833.3:c.315C>T	chr9.hg19:g.125391500G>A		60.0	0.0	.		55.0	21.0	.	NM_001004450	Q6IFN3	Silent	SNP	ENST00000304833.3	hg19	CCDS35126.1																																																																																			.	.	.	none		0.502	OR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053947.2	NM_001004450		A	125391500	G	A	125391500	2	1	128	1	0	0	0	0	0	0	0	1	10958	933	33	2		2	OR1B1	9	125391500	Silent	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	12249760	125391500	15821931	24	7993											
OR13A1	79290	hgsc.bcm.edu	37	chr10	45799786	45799786	+	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	aaagccctgcaggatgaactCggttaccaacgtctggttac	11	9	10	11	2	1	1	0	1	1	0	2	2	1	2	2	3	6	3	2	3	5	2	rs200530280		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr10:45799786C>T	ENST00000553795.1	-	4	393	c.85G>A	c.(85-87)Gag>Aag	p.E29K	OR13A1_ENST00000374401.2_Missense_Mutation_p.E29K|OR13A1_ENST00000536058.1_Missense_Mutation_p.E29K	NM_001004297.2	NP_001004297.2	Q8NGR1	O13A1_HUMAN	olfactory receptor, family 13, subfamily A, member 1	29						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.E29K(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(2)|urinary_tract(1)	19						AGGATGAACTCGGTTACCAAC	0.517																																					p.E29K		Atlas-SNP	.											OR13A1,ear,carcinoma,0,1	OR13A1	49	.	1	Substitution - Missense(1)	skin(1)	c.G85A						PASS	.						70	81	77					10																	45799786		2203	4300	6503	SO:0001583	missense	79290	exon4			TGAACTCGGTTAC	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.85G>A	chr10.hg19:g.45799786C>T	ENSP00000451950:p.Glu29Lys	95.0	0.0	.		84.0	38.0	.	NM_001004297	Q2M3M4|Q5VV57|Q6IFH5|Q6ZMN6	Missense_Mutation	SNP	ENST00000553795.1	hg19	CCDS31188.1	.	.	.	.	.	.	.	.	.	.	c	10.75	1.438543	0.25900	.	.	ENSG00000256574	ENST00000553795;ENST00000536058;ENST00000374401	T;T;T	0.01119	5.31;5.31;5.31	5.09	3.18	0.36537	.	0.350510	0.20650	N	0.088225	T	0.02380	0.0073	M	0.80028	2.48	0.29732	N	0.837839	B	0.25743	0.133	B	0.27715	0.082	T	0.04678	-1.0934	10	0.72032	D	0.01	-21.4609	8.6395	0.33968	0.0:0.7602:0.1539:0.0858	.	29	Q8NGR1	O13A1_HUMAN	K	29	ENSP00000451950:E29K;ENSP00000438657:E29K;ENSP00000363522:E29K	ENSP00000311379:E29K	E	-	1	0	OR13A1	45119792	0.008000	0.16893	0.368000	0.25939	0.065000	0.16274	0.141000	0.16076	0.625000	0.30304	0.603000	0.83216	GAG	.	C|0.999;A|0.001	.	alt		0.517	OR13A1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047779.2	NM_001004297		T	45799786	C	T	45799786	3	4	128	1	0	0	0	0	1	0	0	0	10940	893	31	1	905	1	OR13A1	10	45799786	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08		45799786	89734961	25	7994											
PPFIBP2	8495	hgsc.bcm.edu	37	chr11	7618800	7618800	+	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	tcctggaacaggtgagtgtcCtcacagaccaagtagaagcc	12	7	11	11	0	1	3	1	1	0	2	3	4	3	4	4	2	2	1	4	2	4	1	rs17851928		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr11:7618800C>G	ENST00000299492.4	+	5	770	c.382C>G	c.(382-384)Ctc>Gtc	p.L128V	PPFIBP2_ENST00000533792.1_5'UTR|PPFIBP2_ENST00000528883.1_Missense_Mutation_p.L16V	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	128				L -> I (in Ref. 2; AAH21714). {ECO:0000305}.	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)		GGTGAGTGTCCTCACAGACCA	0.512																																					p.L128V		Atlas-SNP	.											.	PPFIBP2	87	.	0			c.C382G						PASS	.						63	58	60					11																	7618800		2201	4296	6497	SO:0001583	missense	8495	exon5			AGTGTCCTCACAG	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.382C>G	chr11.hg19:g.7618800C>G	ENSP00000299492:p.Leu128Val	33.0	0.0	.		19.0	9.0	.	NM_003621	B7Z433|E9PK77|O75337|Q8WW26	Missense_Mutation	SNP	ENST00000299492.4	hg19	CCDS31419.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.718828	0.89205	.	.	ENSG00000166387	ENST00000299492;ENST00000527790;ENST00000541115;ENST00000528883	T;T;T	0.49720	2.55;2.55;0.77	5.5	5.5	0.81552	.	0.000000	0.53938	D	0.000044	T	0.70202	0.3197	M	0.78344	2.41	0.80722	D	1	D;D;D;D	0.89917	1.0;0.996;1.0;1.0	D;D;D;D	0.91635	0.999;0.929;0.999;0.997	T	0.72626	-0.4236	10	0.59425	D	0.04	-6.6607	16.8778	0.86056	0.0:1.0:0.0:0.0	.	16;16;51;128	E9PK77;B7Z433;F5GWB0;Q8ND30	.;.;.;LIPB2_HUMAN	V	128;128;51;16	ENSP00000299492:L128V;ENSP00000434981:L128V;ENSP00000435469:L16V	ENSP00000299492:L128V	L	+	1	0	PPFIBP2	7575376	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.639000	0.61361	2.600000	0.87896	0.655000	0.94253	CTC	.	.	.	alt		0.512	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621		G	7618800	C	G	7618800	3	3	128	1	0	0	0	0	1	0	0	0	12321	681	24	4	396	4	PPFIBP2	11	7618800	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08		7618800	127387716	26	7995											
TTC17	55761	hgsc.bcm.edu	37	chr11	43380551	43380551	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccggtacgagctgccgccttGctccggcccaggctggctcc	3	7	13	18	4	0	0	0	0	0	0	2	1	2	0	6	4	4	5	6	4	1	2			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr11:43380551G>A	ENST00000039989.4	+	1	61	c.47G>A	c.(46-48)tGc>tAc	p.C16Y	RP11-484D2.2_ENST00000526220.1_RNA|TTC17_ENST00000299240.6_Missense_Mutation_p.C16Y	NM_018259.5	NP_060729.2	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17	16					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						CTGCCGCCTTGCTCCGGCCCA	0.711																																					p.C16Y		Atlas-SNP	.											.	TTC17	112	.	0			c.G47A						PASS	.						10	13	12					11																	43380551		2188	4280	6468	SO:0001583	missense	55761	exon1			CGCCTTGCTCCGG	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.47G>A	chr11.hg19:g.43380551G>A	ENSP00000039989:p.Cys16Tyr	25.0	0.0	.		20.0	10.0	.	NM_018259	G3XAB3|Q8NEC0	Missense_Mutation	SNP	ENST00000039989.4	hg19	CCDS31466.1	.	.	.	.	.	.	.	.	.	.	G	15.19	2.759055	0.49468	.	.	ENSG00000052841	ENST00000299240;ENST00000039989	T;T	0.30981	1.51;1.52	5.5	5.5	0.81552	.	0.471757	0.22070	N	0.065056	T	0.13114	0.0318	N	0.08118	0	0.23611	N	0.99729	B;B	0.33379	0.41;0.021	B;B	0.26094	0.066;0.037	T	0.17623	-1.0363	10	0.17832	T	0.49	-0.8355	9.4046	0.38453	0.0:0.1538:0.6866:0.1596	.	16;16	Q96AE7;G3XAB3	TTC17_HUMAN;.	Y	16	ENSP00000299240:C16Y;ENSP00000039989:C16Y	ENSP00000039989:C16Y	C	+	2	0	TTC17	43337127	0.979000	0.34478	0.972000	0.41901	0.951000	0.60555	3.441000	0.52893	2.868000	0.98415	0.555000	0.69702	TGC	.	.	.	none		0.711	TTC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389577.2	NM_018259		A	43380551	G	A	43380551	3	1	128	1	0	0	0	0	1	0	0	0	16696	1319	46	2	49	2	TTC17	11	43380551	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	35761751	43380551	91625965	27	7996											
PICALM	8301	hgsc.bcm.edu	37	chr11	85714416	85714416	+	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	aagaatgatatacctgcttgCagctgtagaatctttgattt	12	15	8	6	0	1	4	0	2	1	2	1	4	1	4	1	0	4	4	1	0	6	6			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr11:85714416C>A	ENST00000393346.3	-	9	1034	c.886G>T	c.(886-888)Gca>Tca	p.A296S	PICALM_ENST00000526033.1_Missense_Mutation_p.A296S|PICALM_ENST00000528398.1_Missense_Mutation_p.A245S|PICALM_ENST00000356360.5_Missense_Mutation_p.A296S|PICALM_ENST00000532317.1_Missense_Mutation_p.A296S			Q13492	PICAL_HUMAN	phosphatidylinositol binding clathrin assembly protein	296					axonogenesis (GO:0007409)|cargo loading into vesicle (GO:0035459)|cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|hemopoiesis (GO:0030097)|iron ion homeostasis (GO:0055072)|iron ion import into cell (GO:0097459)|negative regulation of gene expression (GO:0010629)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of receptor-mediated endocytosis (GO:0048261)|positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902961)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902959)|regulation of endocytosis (GO:0030100)|regulation of protein localization (GO:0032880)|synaptic vesicle maturation (GO:0016188)|vesicle-mediated transport (GO:0016192)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neurofibrillary tangle (GO:0097418)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|vesicle (GO:0031982)	1-phosphatidylinositol binding (GO:0005545)|clathrin adaptor activity (GO:0035615)|clathrin binding (GO:0030276)|clathrin heavy chain binding (GO:0032050)			endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)				TACCTGCTTGCAGCTGTAGAA	0.388			T	"MLLT10, MLL"	"TALL, AML, "																																p.A296S		Atlas-SNP	.		Dom	yes		11	11q14	8301	phosphatidylinositol binding clathrin assembly protein (CALM)		L	.	PICALM	82	.	0			c.G886T						PASS	.						97	93	94					11																	85714416		2203	4299	6502	SO:0001583	missense	8301	exon9			TGCTTGCAGCTGT	BC048259	CCDS8272.1, CCDS31653.1, CCDS55783.1, CCDS55784.1	11q14	2008-02-01			ENSG00000073921	ENSG00000073921			15514	protein-coding gene	gene with protein product		603025				8643484	Standard	NM_001206947		Approved	CALM, CLTH	uc001pbm.3	Q13492	OTTHUMG00000166981	ENST00000393346.3:c.886G>T	chr11.hg19:g.85714416C>A	ENSP00000377015:p.Ala296Ser	74.0	0.0	.		99.0	27.0	.	NM_007166	B4DTM3|E9PN05|F8VPG7|O60700|Q4LE54|Q6GMQ6|Q86XZ9	Missense_Mutation	SNP	ENST00000393346.3	hg19	CCDS8272.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.559328	0.86335	.	.	ENSG00000073921	ENST00000532317;ENST00000526033;ENST00000447890;ENST00000393346;ENST00000528398;ENST00000356360	T;T;T;T;T	0.58210	0.35;0.35;0.35;0.35;0.35	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.72574	0.3477	M	0.71036	2.16	0.80722	D	1	D;D;B;P	0.69078	0.997;0.968;0.356;0.95	D;P;B;P	0.75020	0.985;0.854;0.178;0.716	T	0.71533	-0.4564	9	.	.	.	-9.5668	19.5037	0.95106	0.0:1.0:0.0:0.0	.	245;296;296;296	E9PN05;F8VPG7;Q13492;Q13492-3	.;.;PICAL_HUMAN;.	S	296;296;296;296;245;296	ENSP00000436958:A296S;ENSP00000433846:A296S;ENSP00000377015:A296S;ENSP00000434884:A245S;ENSP00000348718:A296S	.	A	-	1	0	PICALM	85392064	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.818000	0.86416	2.596000	0.87737	0.655000	0.94253	GCA	.	.	.	none		0.388	PICALM-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392224.1	NM_007166		A	85714416	C	A	85714416	3	1	128	1	0	0	0	0	1	0	0	0	11887	710	25	4	1148	4	PICALM	11	85714416	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	42333865	85714416	49292100	28	7997											
SPATA13	221178	hgsc.bcm.edu	37	chr13	24825881	24825881	+	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	ttccaggccgcccatgcctgCtcaccaggtgccaccctaca	7	7	8	19	1	1	0	1	0	0	0	2	0	2	0	7	2	4	1	7	2	1	2			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr13:24825881C>A	ENST00000382095.4	+	3	577	c.170C>A	c.(169-171)gCt>gAt	p.A57D	SPATA13_ENST00000382108.3_Missense_Mutation_p.A682D|SPATA13-AS1_ENST00000430733.1_RNA|SPATA13_ENST00000424834.2_Missense_Mutation_p.A682D|RP11-307N16.6_ENST00000382141.4_Missense_Mutation_p.A560D	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13	57					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)		CCCATGCCTGCTCACCAGGTG	0.622																																					p.A682D		Atlas-SNP	.											.	SPATA13	92	.	0			c.C2045A						PASS	.						60	65	63					13																	24825881		2203	4300	6503	SO:0001583	missense	221178	exon4			TGCCTGCTCACCA	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.170C>A	chr13.hg19:g.24825881C>A	ENSP00000371527:p.Ala57Asp	117.0	0.0	.		118.0	49.0	.	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Missense_Mutation	SNP	ENST00000382095.4	hg19	CCDS9305.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.7|25.7	4.662502|4.662502	0.88251|0.88251	.|.	.|.	ENSG00000182957|ENSG00000182957	ENST00000382108;ENST00000382095;ENST00000434675;ENST00000438694|ENST00000424834	T;T;T|.	0.35789|.	1.29;1.29;1.29|.	5.97|5.97	5.13|5.13	0.70059|0.70059	.|.	0.125113|.	0.56097|.	D|.	0.000034|.	T|.	0.61173|.	0.2326|.	L|L	0.46157|0.46157	1.445|1.445	0.80722|0.80722	D|D	1|1	P;D;B|.	0.53462|.	0.634;0.96;0.361|.	B;P;B|.	0.48795|.	0.3;0.59;0.074|.	T|.	0.55866|.	-0.8073|.	10|.	0.46703|.	T|.	0.11|.	.|.	13.7166|13.7166	0.62700|0.62700	0.0:0.927:0.0:0.073|0.0:0.927:0.0:0.073	.|.	3;3;57|.	Q96N96-5;Q96N96-4;Q96N96|.	.;.;SPT13_HUMAN|.	D|X	682;57;17;3|719	ENSP00000371542:A682D;ENSP00000371527:A57D;ENSP00000401605:A17D|.	ENSP00000371527:A57D|.	A|C	+|+	2|3	0|2	SPATA13|SPATA13	23723881|23723881	1.000000|1.000000	0.71417|0.71417	0.636000|0.636000	0.29352|0.29352	0.775000|0.775000	0.43874|0.43874	5.552000|5.552000	0.67281|0.67281	2.836000|2.836000	0.97738|0.97738	0.655000|0.655000	0.94253|0.94253	GCT|TGC	.	.	.	none		0.622	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023		A	24825881	C	A	24825881	3	1	128	1	0	0	0	0	1	0	0	0	15012	797	28	4	2055	4	SPATA13	13	24825881	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08		24825881	90343997	29	7998											
SHISA2	387914	hgsc.bcm.edu	37	chr13	26620708	26620708	+	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	ttggtgtgagggaagggggaCtgaatctgcctgtagccagg	8	9	18	6	0	1	2	0	2	1	0	1	4	1	4	2	5	2	1	2	5	3	2			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr13:26620708C>G	ENST00000319420.3	-	2	886	c.831G>C	c.(829-831)caG>caC	p.Q277H		NM_001007538.1	NP_001007539.1	Q6UWI4	SHSA2_HUMAN	shisa family member 2	277					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(2)|skin(1)	17						GGAAGGGGGACTGAATCTGCC	0.567																																					p.Q277H		Atlas-SNP	.											.	SHISA2	43	.	0			c.G831C						PASS	.						104	91	96					13																	26620708		2203	4300	6503	SO:0001583	missense	387914	exon2			GGGGGACTGAATC		CCDS31951.1	13q12.13	2013-07-31	2013-07-31	2008-04-01	ENSG00000180730	ENSG00000180730		"Shisa homologs"	20366	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 13", "transmembrane protein 46", "shisa homolog 2 (Xenopus laevis)"	C13orf13, TMEM46			Standard	NM_001007538		Approved	bA398O19.2, PRO28631, WGAR9166, hShisa	uc001uqm.1	Q6UWI4	OTTHUMG00000016612	ENST00000319420.3:c.831G>C	chr13.hg19:g.26620708C>G	ENSP00000313079:p.Gln277His	87.0	0.0	.		85.0	30.0	.	NM_001007538	B9EH70|Q5W0G8	Missense_Mutation	SNP	ENST00000319420.3	hg19	CCDS31951.1	.	.	.	.	.	.	.	.	.	.	C	18.33	3.599692	0.66332	.	.	ENSG00000180730	ENST00000319420	T	0.52057	0.68	5.58	4.74	0.60224	.	0.149265	0.46758	D	0.000272	T	0.55924	0.1951	L	0.27053	0.805	0.80722	D	1	D	0.71674	0.998	D	0.79784	0.993	T	0.60530	-0.7245	10	0.66056	D	0.02	-21.8958	14.6091	0.68504	0.0:0.9296:0.0:0.0704	.	277	Q6UWI4	SHSA2_HUMAN	H	277	ENSP00000313079:Q277H	ENSP00000313079:Q277H	Q	-	3	2	SHISA2	25518708	1.000000	0.71417	0.996000	0.52242	0.854000	0.48673	2.473000	0.45145	1.364000	0.46038	0.650000	0.86243	CAG	.	.	.	none		0.567	SHISA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044239.2	NM_001007538		G	26620708	C	G	26620708	3	3	128	1	0	0	0	0	1	0	0	0	14293	564	20	4	60	4	SHISA2	13	26620708	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	1794827	26620708	88549170	30	7999											
DENND4A	10260	hgsc.bcm.edu	37	chr15	65983020	65983020	+	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	cttttagatttggtaagtctCactggcttaggagaattagg	10	15	11	5	0	1	2	1	0	1	2	2	3	1	2	0	4	0	2	0	4	5	6			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr15:65983020C>T	ENST00000431932.2	-	22	3988	c.3780G>A	c.(3778-3780)gtG>gtA	p.V1260V	DENND4A_ENST00000443035.3_Silent_p.V1303V|DENND4A_ENST00000567323.1_5'Flank	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	1260					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						TGGTAAGTCTCACTGGCTTAG	0.413																																					p.V1303V		Atlas-SNP	.											.	DENND4A	217	.	0			c.G3909A						PASS	.						101	104	103					15																	65983020		1893	4107	6000	SO:0001819	synonymous_variant	10260	exon23			AAGTCTCACTGGC	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.3780G>A	chr15.hg19:g.65983020C>T		133.0	0.0	.		100.0	29.0	.	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Silent	SNP	ENST00000431932.2	hg19	CCDS45285.1																																																																																			.	.	.	none		0.413	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		T	65983020	C	T	65983020	2	4	128	1	0	0	0	0	0	0	0	1	4435	813	29	2		2	DENND4A	15	65983020	Silent	SNP	C	TCGA-BQ-5893-01A-11D-1589-08		65983020	36548372	31	8000											
SIN3A	25942	hgsc.bcm.edu	37	chr15	75692465	75692465	+	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	aaggtagagtcctcagaccaCgaagggaaggaaacccaggt	15	4	13	9	1	1	2	1	0	0	2	2	5	2	4	3	4	1	1	3	4	5	1	rs373830836		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr15:75692465C>T	ENST00000394947.3	-	12	2084	c.1770G>A	c.(1768-1770)tcG>tcA	p.S590S	SIN3A_ENST00000360439.4_Silent_p.S590S|SIN3A_ENST00000394949.4_Silent_p.S590S	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						CCTCAGACCACGAAGGGAAGG	0.393																																					p.S590S		Atlas-SNP	.											.	SIN3A	152	.	0			c.G1770A						PASS	.	C	,,	0,4394		0,0,2197	96	91	93		1770,1770,1770	-12.2	0.2	15		93	1,8587	1.2+/-3.3	0,1,4293	no	coding-synonymous,coding-synonymous,coding-synonymous	SIN3A	NM_001145357.1,NM_001145358.1,NM_015477.2	,,	0,1,6490	TT,TC,CC		0.0116,0.0,0.0077	,,	590/1274,590/1274,590/1274	75692465	1,12981	2197	4294	6491	SO:0001819	synonymous_variant	25942	exon12			AGACCACGAAGGG	AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"SIN3 homolog A, transcription regulator (yeast)", "SIN3 transcription regulator homolog A (yeast)"			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.1770G>A	chr15.hg19:g.75692465C>T		86.0	0.0	.		87.0	32.0	.	NM_001145358		Silent	SNP	ENST00000394947.3	hg19	CCDS10279.1																																																																																			.	.	.	weak		0.393	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477		T	75692465	C	T	75692465	2	4	128	1	0	0	0	0	0	0	0	1	14338	523	19	1		1	SIN3A	15	75692465	Silent	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	9709445	75692465	26838927	32	8001											
CIITA	4261	hgsc.bcm.edu	37	chr16	10992850	10992850	+	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	cagaagttgggcagaaaagtCagaaaagacgtgagtgagcc	16	5	14	6	1	1	6	1	2	0	4	1	6	1	6	1	1	1	2	1	1	5	1			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr16:10992850C>A	ENST00000324288.8	+	5	560	c.427C>A	c.(427-429)Cag>Aag	p.Q143K	CIITA_ENST00000537380.1_3'UTR|CIITA_ENST00000381835.5_Missense_Mutation_p.Q143K	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	143					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						GCAGAAAAGTCAGAAAAGACG	0.507			T	"FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"	"PMBL, Hodgkin Lymphona, "																																p.Q143K		Atlas-SNP	.		Dom	yes		16	16p13	4261	"class II, major histocompatibility complex, transactivator"		L	.	CIITA	92	.	0			c.C427A						PASS	.						159	151	154					16																	10992850		2197	4300	6497	SO:0001583	missense	4261	exon5			AAAAGTCAGAAAA	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.427C>A	chr16.hg19:g.10992850C>A	ENSP00000316328:p.Gln143Lys	115.0	0.0	.		137.0	29.0	.	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Missense_Mutation	SNP	ENST00000324288.8	hg19	CCDS10544.1	.	.	.	.	.	.	.	.	.	.	C	14.14	2.446255	0.43429	.	.	ENSG00000179583	ENST00000324288;ENST00000381835;ENST00000388910;ENST00000537380	T;T	0.74842	-0.88;1.54	3.81	3.81	0.43845	.	0.428781	0.17282	N	0.179967	T	0.66626	0.2808	L	0.50333	1.59	0.25966	N	0.982563	P;P;B;B;P;B	0.40398	0.649;0.455;0.126;0.126;0.716;0.323	B;B;B;B;B;B	0.36567	0.228;0.094;0.049;0.049;0.228;0.079	T	0.64118	-0.6482	10	0.54805	T	0.06	.	11.3836	0.49771	0.0:1.0:0.0:0.0	.	143;143;143;143;144;143	F5H2J4;E9PFE0;A0N0N9;P33076;F2Z2G8;Q96KL4	.;.;.;C2TA_HUMAN;.;.	K	143;143;144;143	ENSP00000316328:Q143K;ENSP00000371257:Q143K	ENSP00000316328:Q143K	Q	+	1	0	CIITA	10900351	0.989000	0.36119	0.889000	0.34880	0.900000	0.52787	3.160000	0.50739	2.134000	0.65973	0.557000	0.71058	CAG	.	.	.	none		0.507	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246		A	10992850	C	A	10992850	3	1	128	1	0	0	0	0	1	0	0	0	3430	827	29	4	445	4	CIITA	16	10992850	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08		10992850	79361903	33	8002											
ANKRD11	29123	hgsc.bcm.edu	37	chr16	89349917	89349917	+	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	tccttatcggggccatccttCttctccttctctcgtgctgg	2	16	8	15	2	3	0	0	0	3	0	9	0	5	0	4	3	1	1	4	3	1	4			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr16:89349917C>G	ENST00000301030.4	-	9	3493	c.3033G>C	c.(3031-3033)aaG>aaC	p.K1011N	ANKRD11_ENST00000378330.2_Missense_Mutation_p.K1011N	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1011	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)		GGCCATCCTTCTTCTCCTTCT	0.517																																					p.K1011N		Atlas-SNP	.											.	ANKRD11	195	.	0			c.G3033C						PASS	.						142	139	140					16																	89349917		2198	4300	6498	SO:0001583	missense	29123	exon9			ATCCTTCTTCTCC	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.3033G>C	chr16.hg19:g.89349917C>G	ENSP00000301030:p.Lys1011Asn	187.0	0.0	.		122.0	69.0	.	NM_001256183	Q6NTG1|Q6QMF8	Missense_Mutation	SNP	ENST00000301030.4	hg19	CCDS32513.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.26|16.26	3.072498|3.072498	0.55646|0.55646	.|.	.|.	ENSG00000167522|ENSG00000167522	ENST00000301030;ENST00000378330|ENST00000330736	T;T|.	0.54071|.	0.59;0.59|.	5.5|5.5	3.5|3.5	0.40072|0.40072	.|.	0.059984|.	0.64402|.	D|.	0.000004|.	T|T	0.69324|0.69324	0.3098|0.3098	M|M	0.64997|0.64997	1.995|1.995	0.80722|0.80722	D|D	1|1	D|.	0.59767|.	0.986|.	P|.	0.62435|.	0.902|.	T|T	0.71626|0.71626	-0.4536|-0.4536	10|6	0.51188|0.54805	T|T	0.08|0.06	.|.	12.1739|12.1739	0.54173|0.54173	0.0:0.8519:0.0:0.1481|0.0:0.8519:0.0:0.1481	.|.	1011|.	Q6UB99|.	ANR11_HUMAN|.	N|T	1011|562	ENSP00000301030:K1011N;ENSP00000367581:K1011N|.	ENSP00000301030:K1011N|ENSP00000330815:R562T	K|R	-|-	3|2	2|0	ANKRD11|ANKRD11	87877418|87877418	1.000000|1.000000	0.71417|0.71417	0.967000|0.967000	0.41034|0.41034	0.198000|0.198000	0.23893|0.23893	4.656000|4.656000	0.61483|0.61483	1.425000|1.425000	0.47237|0.47237	0.655000|0.655000	0.94253|0.94253	AAG|AGA	.	.	.	none		0.517	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		G	89349917	C	G	89349917	3	3	128	1	0	0	0	0	1	0	0	0	639	912	32	4	4978	4	ANKRD11	16	89349917	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08	78357067	89349917	1004836	34	8003											
TP53	7157	hgsc.bcm.edu	37	chr17	7574002	7574002	+	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	ccaaggcctcattcagctctCggaacatctcgaagcgctca	10	8	8	15	3	5	0	3	0	2	0	7	2	5	1	2	2	3	2	2	2	3	1	rs375338359		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr17:7574002C>A	ENST00000269305.4	-	10	1214	c.1025G>T	c.(1024-1026)cGa>cTa	p.R342L	TP53_ENST00000359597.4_Intron|TP53_ENST00000420246.2_3'UTR|TP53_ENST00000445888.2_Missense_Mutation_p.R342L|TP53_ENST00000413465.2_Intron|TP53_ENST00000455263.2_3'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	342	Interaction with CARM1.|Interaction with HIPK1. {ECO:0000250}.|Interaction with HIPK2.|Oligomerization.		R -> L (in a sporadic cancer; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.R342P(3)|p.R342Q(2)|p.?(1)|p.R342_N345delRELN(1)|p.E343fs*3(1)|p.R342fs*3(1)|p.I332fs*5(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ATTCAGCTCTCGGAACATCTC	0.557		111	"Mis, N, F"		"breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"	"breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R342L	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,malignant_melanoma,-1,10	TP53	33396	.	18	Whole gene deletion(8)|Substitution - Missense(5)|Deletion - Frameshift(3)|Unknown(1)|Deletion - In frame(1)	upper_aerodigestive_tract(4)|bone(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|breast(2)|ovary(2)|large_intestine(1)|stomach(1)	c.G1025T						PASS	.						62	48	53					17																	7574002		2203	4300	6503	SO:0001583	missense	7157	exon10	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AGCTCTCGGAACA	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.1025G>T	chr17.hg19:g.7574002C>A	ENSP00000269305:p.Arg342Leu	81.0	1.0	.		58.0	3.0	.	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	10.19	1.280933	0.23392	.	.	ENSG00000141510	ENST00000269305;ENST00000445888;ENST00000396473	D;D	0.92595	-3.07;-3.07	5.43	2.35	0.29111	p53, tetramerisation domain (3);	0.217683	0.37906	N	0.001893	D	0.85349	0.5676	L	0.42581	1.335	0.19575	N	0.999965	B	0.10296	0.003	B	0.18871	0.023	T	0.70898	-0.4747	10	0.29301	T	0.29	-0.3792	4.3338	0.11076	0.1588:0.5914:0.0:0.2498	.	342	P04637	P53_HUMAN	L	342;342;331	ENSP00000269305:R342L;ENSP00000391478:R342L	ENSP00000269305:R342L	R	-	2	0	TP53	7514727	0.035000	0.19736	0.264000	0.24511	0.867000	0.49689	-0.268000	0.08607	0.271000	0.22005	0.561000	0.74099	CGA	.	.	.	alt		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7574002	C	A	7574002	3	1	128	1	0	0	0	0	1	0	0	0	16393	884	31	4	164	4	TP53	17	7574002	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08		7574002	73621208	35	8004											
KIAA1468	57614	hgsc.bcm.edu	37	chr18	59888685	59888685	+	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	gaatttttattgaagaataaCtataagcttacatcaataac	18	14	4	5	0	1	2	1	1	0	1	1	3	1	2	0	0	4	1	0	0	10	9			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr18:59888685C>T	ENST00000398130.2	+	5	1045	c.813C>T	c.(811-813)aaC>aaT	p.N271N	KIAA1468_ENST00000256858.6_Silent_p.N271N	NM_020854.3	NP_065905.2	Q9P260	K1468_HUMAN	KIAA1468	271	LisH. {ECO:0000255|PROSITE- ProRule:PRU00126}.									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)				TGAAGAATAACTATAAGCTTA	0.303																																					p.N271N		Atlas-SNP	.											.	KIAA1468	93	.	0			c.C813T						PASS	.						52	49	50					18																	59888685		1803	4062	5865	SO:0001819	synonymous_variant	57614	exon5			GAATAACTATAAG	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.813C>T	chr18.hg19:g.59888685C>T		68.0	0.0	.		98.0	28.0	.	NM_020854		Silent	SNP	ENST00000398130.2	hg19	CCDS11979.2																																																																																			.	.	.	none		0.303	KIAA1468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256187.1	NM_020854		T	59888685	C	T	59888685	2	4	128	1	0	0	0	0	0	0	0	1	8243	564	20	2		2	KIAA1468	18	59888685	Silent	SNP	C	TCGA-BQ-5893-01A-11D-1589-08		59888685	18188563	36	8005											
RHPN2	85415	hgsc.bcm.edu	37	chr19	33503622	33503622	+	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	tcttcactgtaatgttccagGataaaatccttaaagaaaaa	17	12	5	7	0	2	1	1	0	1	1	4	2	4	2	2	1	0	2	2	1	7	5			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr19:33503622G>C	ENST00000254260.3	-	5	434	c.399C>G	c.(397-399)atC>atG	p.I133M	RHPN2_ENST00000400226.4_De_novo_Start_InFrame	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	133	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)					AATGTTCCAGGATAAAATCCT	0.348																																					p.I133M		Atlas-SNP	.											.	RHPN2	107	.	0			c.C399G						PASS	.						64	63	64					19																	33503622		2203	4300	6503	SO:0001583	missense	85415	exon5			TTCCAGGATAAAA	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.399C>G	chr19.hg19:g.33503622G>C	ENSP00000254260:p.Ile133Met	50.0	0.0	.		54.0	24.0	.	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	hg19	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	G	12.80	2.045171	0.36085	.	.	ENSG00000131941	ENST00000254260	T	0.36340	1.26	4.67	-0.356	0.12583	BRO1 domain (3);	0.000000	0.85682	D	0.000000	T	0.65407	0.2688	H	0.95151	3.63	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.69316	-0.5177	10	0.87932	D	0	4.3606	9.4837	0.38917	0.5257:0.0:0.4743:0.0	.	133	Q8IUC4	RHPN2_HUMAN	M	133	ENSP00000254260:I133M	ENSP00000254260:I133M	I	-	3	3	RHPN2	38195462	1.000000	0.71417	0.998000	0.56505	0.408000	0.30992	0.918000	0.28678	0.003000	0.14656	0.455000	0.32223	ATC	.	.	.	none		0.348	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103		C	33503622	G	C	33503622	3	2	128	1	0	0	0	0	1	0	0	0	13364	1164	41	4	1705	4	RHPN2	19	33503622	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08		33503622	25625361	37	8006											
KIAA0355	9710	hgsc.bcm.edu	37	chr19	34832921	34832921	+	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	caaccacagcagccgtcactGcctgtgccccctccaccacg	8	5	7	21	2	1	0	1	0	0	0	2	0	2	0	7	0	5	1	7	0	1	0			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr19:34832921G>A	ENST00000299505.6	+	10	2955	c.2082G>A	c.(2080-2082)ctG>ctA	p.L694L		NM_014686.3	NP_055501.2	O15063	K0355_HUMAN	KIAA0355	694										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)					AGCCGTCACTGCCTGTGCCCC	0.632																																					p.L694L		Atlas-SNP	.											.	KIAA0355	105	.	0			c.G2082A						PASS	.						69	72	71					19																	34832921		2203	4299	6502	SO:0001819	synonymous_variant	9710	exon10			GTCACTGCCTGTG		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.2082G>A	chr19.hg19:g.34832921G>A		133.0	0.0	.		111.0	35.0	.	NM_014686	Q2M3W4	Silent	SNP	ENST00000299505.6	hg19	CCDS12436.1																																																																																			.	.	.	none		0.632	KIAA0355-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451678.4	NM_014686		A	34832921	G	A	34832921	2	1	128	1	0	0	0	0	0	0	0	1	8177	1306	46	2		2	KIAA0355	19	34832921	Silent	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	1329299	34832921	24296062	38	8007											
TMEM149	79713	hgsc.bcm.edu	37	chr19	36230750	36230750	+	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	ccaggatagggataggggtcGgctttctccttgggccagca	7	9	15	10	1	1	0	0	0	1	0	3	2	1	2	3	6	1	2	3	6	2	4			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr19:36230750G>C	ENST00000592537.1	-	4	682	c.582C>G	c.(580-582)gcC>gcG	p.A194A	IGFLR1_ENST00000246532.1_Silent_p.A194A|AD000671.6_ENST00000589807.1_3'UTR|IGFLR1_ENST00000588992.1_Intron|KMT2B_ENST00000607650.1_RNA|IGFLR1_ENST00000592889.1_Intron|IGFLR1_ENST00000587101.1_5'UTR|IGFLR1_ENST00000344990.3_Intron			Q9H665	IGFR1_HUMAN	IGF-like family receptor 1	194						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(3)|large_intestine(1)|lung(8)|prostate(1)	15						GATAGGGGTCGGCTTTCTCCT	0.617																																					p.A194A		Atlas-SNP	.											.	IGFLR1	28	.	0			c.C582G						PASS	.						88	91	90					19																	36230750		2203	4300	6503	SO:0001819	synonymous_variant	79713	exon4			GGGGTCGGCTTTC	AK026226	CCDS12472.1	19q13.12	2012-10-02	2011-04-04	2011-04-04	ENSG00000126246	ENSG00000126246			23620	protein-coding gene	gene with protein product		614143	"U2(RNU2) small nuclear RNA auxiliary factor 1-like 4", "transmembrane protein 149"	U2AF1L4, TMEM149		21454693	Standard	NM_024660		Approved	FLJ22573	uc002obd.4	Q9H665		ENST00000592537.1:c.582C>G	chr19.hg19:g.36230750G>C		197.0	0.0	.		159.0	66.0	.	NM_024660	Q8N5X0	Silent	SNP	ENST00000592537.1	hg19	CCDS12472.1																																																																																			.	.	.	none		0.617	IGFLR1-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459077.1	NM_024660		C	36230750	G	C	36230750	2	2	128	1	0	0	0	0	0	0	0	1	16074	1103	39	4		4	TMEM149	19	36230750	Silent	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	1397829	36230750	22898233	39	8008											
CNFN	84518	hgsc.bcm.edu	37	chr19	42893120	42893120	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccgtgagacctgtgtgccAgtcactgagctgggtctggt	5	11	15	10	1	2	2	1	2	1	1	3	3	3	2	3	2	2	1	3	2	0	0			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr19:42893120A>G	ENST00000222032.5	-	2	119	c.70T>C	c.(70-72)Tgg>Cgg	p.W24R	CNFN_ENST00000597255.1_Missense_Mutation_p.W24R	NM_032488.3	NP_115877.2	Q9BYD5	CNFN_HUMAN	cornifelin	24					keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				lung(1)|prostate(1)	2		Prostate(69;0.00899)				CCTGTGTGCCAGTCACTGAGC	0.617																																					p.W24R		Atlas-SNP	.											.	CNFN	5	.	0			c.T70C						PASS	.						133	99	111					19																	42893120		2203	4300	6503	SO:0001583	missense	84518	exon2			TGTGCCAGTCACT	AB049591	CCDS12606.1	19q13.31	2006-01-11				ENSG00000105427			30183	protein-coding gene	gene with protein product		611764					Standard	NM_032488		Approved	PLAC8L2	uc002otp.4	Q9BYD5		ENST00000222032.5:c.70T>C	chr19.hg19:g.42893120A>G	ENSP00000222032:p.Trp24Arg	50.0	0.0	.		37.0	22.0	.	NM_032488	B2R569	Missense_Mutation	SNP	ENST00000222032.5	hg19	CCDS12606.1	.	.	.	.	.	.	.	.	.	.	A	16.88	3.244613	0.59103	.	.	ENSG00000105427	ENST00000222032	T	0.29655	1.56	5.0	3.97	0.46021	.	0.000000	0.85682	D	0.000000	T	0.53738	0.1815	M	0.89658	3.05	0.46078	D	0.998858	D	0.56746	0.977	P	0.56612	0.802	T	0.60702	-0.7211	10	0.72032	D	0.01	-18.0017	10.0235	0.42057	0.8298:0.1702:0.0:0.0	.	24	Q9BYD5	CNFN_HUMAN	R	24	ENSP00000222032:W24R	ENSP00000222032:W24R	W	-	1	0	CNFN	47584960	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.707000	0.68370	0.847000	0.35167	-0.471000	0.05019	TGG	.	.	.	none		0.617	CNFN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463859.1	NM_032488		G	42893120	A	G	42893120	3	3	128	1	0	0	0	0	1	0	0	0	3597	188	7	3	280	3	CNFN	19	42893120	Missense_Mutation	SNP	A	TCGA-BQ-5893-01A-11D-1589-08	6662370	42893120	16235863	40	8009											
DMPK	1760	hgsc.bcm.edu	37	chr19	46280763	46280763	+	Missense_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	ctccaccccggcccagccgtGtctccgggggacacagcaac	7	4	11	19	3	1	0	0	0	1	0	3	1	2	1	6	3	3	1	6	3	1	0			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr19:46280763G>A	ENST00000291270.4	-	8	1093	c.968C>T	c.(967-969)aCa>aTa	p.T323I	DMPK_ENST00000343373.4_Missense_Mutation_p.T333I|DMPK_ENST00000458663.2_Missense_Mutation_p.T323I|DMPK_ENST00000600757.1_Missense_Mutation_p.T333I|DMPK_ENST00000354227.5_Missense_Mutation_p.T323I|DMPK_ENST00000595361.1_5'Flank|DMPK_ENST00000447742.2_Missense_Mutation_p.T323I	NM_004409.3	NP_004400.4	Q09013	DMPK_HUMAN	dystrophia myotonica-protein kinase	323	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		GCCCAGCCGTGTCTCCGGGGG	0.647																																					p.T333I	Esophageal Squamous(35;307 869 9153 24033 28903)	Atlas-SNP	.											.	DMPK	74	.	0			c.C998T						PASS	.						39	41	40					19																	46280763		2203	4300	6503	SO:0001583	missense	1760	exon7			AGCCGTGTCTCCG	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.968C>T	chr19.hg19:g.46280763G>A	ENSP00000291270:p.Thr323Ile	82.0	0.0	.		76.0	31.0	.	NM_001081563	E5KR08|Q16205|Q6P5Z6	Missense_Mutation	SNP	ENST00000291270.4	hg19	CCDS12674.1	.	.	.	.	.	.	.	.	.	.	g	6.239	0.412186	0.11812	.	.	ENSG00000104936	ENST00000458663;ENST00000342805;ENST00000291270;ENST00000447742;ENST00000377750;ENST00000343373;ENST00000348168;ENST00000354227	T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2	4.63	-1.42	0.08913	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.960065	0.08582	N	0.924432	T	0.47985	0.1475	L	0.48935	1.535	0.09310	N	1	B;B;B;B;B;B;B;B	0.10296	0.001;0.0;0.003;0.001;0.001;0.001;0.001;0.0	B;B;B;B;B;B;B;B	0.12156	0.005;0.002;0.003;0.007;0.007;0.004;0.001;0.001	T	0.31392	-0.9945	10	0.21014	T	0.42	.	4.9214	0.13871	0.5892:0.0:0.2497:0.1611	.	323;323;349;323;323;323;370;333	Q09013-12;Q09013-16;G5E982;E5KR07;E5KR05;Q09013;Q59FU6;E5KR08	.;.;.;.;.;DMPK_HUMAN;.;.	I	323;349;323;323;323;333;333;323	ENSP00000401753:T323I;ENSP00000291270:T323I;ENSP00000413417:T323I;ENSP00000345997:T333I;ENSP00000346168:T323I	ENSP00000291270:T323I	T	-	2	0	DMPK	50972603	0.000000	0.05858	0.091000	0.20842	0.655000	0.38815	-1.221000	0.02968	-0.044000	0.13491	-0.254000	0.11334	ACA	.	.	.	none		0.647	DMPK-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460572.1	NM_004409		A	46280763	G	A	46280763	3	1	128	1	0	0	0	0	1	0	0	0	4586	1377	48	2	960	2	DMPK	19	46280763	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	3387643	46280763	12848220	41	8010											
PRKCG	5582	hgsc.bcm.edu	37	chr19	54385815	54385815	+	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	ggcccctgttttgcagaaagGgggccctgaggcagaaggtg	8	7	17	9	0	0	3	0	1	0	2	0	3	0	3	3	5	1	3	3	5	2	2			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr19:54385815G>T	ENST00000263431.3	+	1	349	c.67G>T	c.(67-69)Ggg>Tgg	p.G23W	PRKCG_ENST00000540413.1_Missense_Mutation_p.G23W|PRKCG_ENST00000536044.1_Missense_Mutation_p.G23W|PRKCG_ENST00000542049.1_5'Flank	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	23					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)	TTGCAGAAAGGGGGCCCTGAG	0.627																																					p.G23W		Atlas-SNP	.											.	PRKCG	246	.	0			c.G67T						PASS	.						66	74	71					19																	54385815		2203	4300	6503	SO:0001583	missense	5582	exon1			AGAAAGGGGGCCC	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.67G>T	chr19.hg19:g.54385815G>T	ENSP00000263431:p.Gly23Trp	175.0	0.0	.		156.0	72.0	.	NM_002739	B7Z8Q0	Missense_Mutation	SNP	ENST00000263431.3	hg19	CCDS12867.1	.	.	.	.	.	.	.	.	.	.	G	19.99	3.929442	0.73327	.	.	ENSG00000126583	ENST00000536044;ENST00000540413;ENST00000263431;ENST00000419486	D;D;D	0.95069	-3.6;-3.6;-3.6	4.08	4.08	0.47627	.	.	.	.	.	D	0.96830	0.8965	M	0.77820	2.39	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.999;0.999	D	0.97398	0.9994	9	0.87932	D	0	.	14.1554	0.65415	0.0:0.0:1.0:0.0	.	23;23;23;23	F5H5C4;B7Z870;B7Z3W6;P05129	.;.;.;KPCG_HUMAN	W	23;23;23;46	ENSP00000440541:G23W;ENSP00000443493:G23W;ENSP00000263431:G23W	ENSP00000263431:G23W	G	+	1	0	PRKCG	59077627	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.851000	0.92205	1.996000	0.58369	0.491000	0.48974	GGG	.	.	.	none		0.627	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739		T	54385815	G	T	54385815	3	4	128	1	0	0	0	0	1	0	0	0	12522	1232	43	4	69	4	PRKCG	19	54385815	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	8105052	54385815	4743168	42	8011											
KIR3DL3	115653	hgsc.bcm.edu	37	chr19	55239373	55239373	+	Missense_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	accctctggacatcgtggtcGtaggtgagagaatacagacc	11	8	12	10	2	1	3	0	1	1	2	3	5	1	4	2	3	1	1	2	3	3	2			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr19:55239373G>A	ENST00000291860.1	+	4	670	c.652G>A	c.(652-654)Gta>Ata	p.V218I	KIR3DL1_ENST00000402254.2_Intron|KIR2DL4_ENST00000396284.2_Intron|KIR3DL1_ENST00000538269.1_Intron|KIR3DL1_ENST00000541392.1_Intron|CTB-61M7.1_ENST00000400864.3_RNA	NM_153443.3	NP_703144.2	Q8N743	KI3L3_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 3	218						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(3)|prostate(1)|skin(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		CATCGTGGTCGTAGGTGAGAG	0.542																																					p.V218I		Atlas-SNP	.											KIR3DL3,colon,carcinoma,0,1	KIR3DL3	46	.	0			c.G652A						PASS	.						8	8	8					19																	55239373		1846	3121	4967	SO:0001583	missense	115653	exon4			GTGGTCGTAGGTG	AF352324	CCDS12903.1	19q13.4	2014-05-22			ENSG00000242019	ENSG00000242019		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	16312	protein-coding gene	gene with protein product		610095				11513144	Standard	NM_153443		Approved	KIRC1, KIR3DL7, KIR44, CD158z	uc002qgu.1	Q8N743	OTTHUMG00000065884	ENST00000291860.1:c.652G>A	chr19.hg19:g.55239373G>A	ENSP00000291860:p.Val218Ile	181.0	0.0	.		146.0	65.0	.	NM_153443	A9PL62|A9PL64|A9PL65|A9PL66|A9PL67|A9PL68|A9PZV4|A9PZV7|A9PZV8|A9Q066|A9Q0R5|A9Q242|A9Q250|A9Q251|O95056|Q1X775|Q1X777|Q1X778|Q1X779|Q1X780|Q1X781|Q1X782|Q1X783|Q7Z7N4|Q8NHI2|Q8NHI3|Q9UEI4	Missense_Mutation	SNP	ENST00000291860.1	hg19	CCDS12903.1	.	.	.	.	.	.	.	.	.	.	-	4.693	0.128795	0.08981	.	.	ENSG00000242019	ENST00000291860	T	0.00730	5.77	1.38	0.293	0.15742	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.958988	0.08407	N	0.950530	T	0.00328	0.0010	N	0.00436	-1.5	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.44345	-0.9334	10	0.45353	T	0.12	.	4.3253	0.11038	0.5511:0.0:0.4489:0.0	.	218	Q8N743	KI3L3_HUMAN	I	218	ENSP00000291860:V218I	ENSP00000291860:V218I	V	+	1	0	KIR3DL3	59931185	0.003000	0.15002	0.002000	0.10522	0.002000	0.02628	-0.697000	0.05098	-0.402000	0.07633	-1.140000	0.01884	GTA	.	.	.	none		0.542	KIR3DL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141147.1	NM_153443		A	55239373	G	A	55239373	3	1	128	1	0	0	0	0	1	0	0	0	8329	1145	40	1	666	1	KIR3DL3	19	55239373	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08	853558	55239373	3889610	43	8012											
SAMHD1	25939	hgsc.bcm.edu	37	chr20	35563508	35563508	+	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	tcccagctgtttgatgtatcGaagacgttgaaattgaggtg	10	13	12	6	2	0	4	0	3	0	1	2	5	1	4	1	1	1	4	1	1	3	4	rs121434517		TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chr20:35563508G>C	ENST00000262878.4	-	4	632	c.433C>G	c.(433-435)Cga>Gga	p.R145G	SAMHD1_ENST00000373694.5_5'UTR	NM_015474.3	NP_056289.2	Q9Y3Z3	SAMH1_HUMAN	SAM domain and HD domain 1	145			R -> Q (in AGS5). {ECO:0000269|PubMed:19525956}.		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)				TTGATGTATCGAAGACGTTGA	0.433																																					p.R145G		Atlas-SNP	.											.	SAMHD1	62	.	0			c.C433G						PASS	.						135	125	129					20																	35563508		2203	4300	6503	SO:0001583	missense	25939	exon4			TGTATCGAAGACG	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.433C>G	chr20.hg19:g.35563508G>C	ENSP00000262878:p.Arg145Gly	114.0	0.0	.		73.0	4.0	.	NM_015474	B4E2A5|E1P5V2|Q5JXG8|Q8N491|Q9H004|Q9H005|Q9H3U9	Missense_Mutation	SNP	ENST00000262878.4	hg19	CCDS13288.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.343156	0.82022	.	.	ENSG00000101347	ENST00000262878	D	0.96522	-4.04	6.05	4.04	0.47022	HD domain (1);	0.000000	0.85682	D	0.000000	D	0.98327	0.9445	H	0.94222	3.51	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.98576	1.0648	10	0.87932	D	0	-16.0364	9.3019	0.37851	0.0657:0.0:0.6789:0.2553	.	145	Q9Y3Z3	SAMH1_HUMAN	G	145	ENSP00000262878:R145G	ENSP00000262878:R145G	R	-	1	2	SAMHD1	34996922	1.000000	0.71417	0.967000	0.41034	0.983000	0.72400	3.147000	0.50639	1.571000	0.49722	0.650000	0.86243	CGA	.	.	.	alt		0.433	SAMHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079062.2	NM_015474		C	35563508	G	C	35563508	3	2	128	1	0	0	0	0	1	0	0	0	13841	1066	37	4	1499	4	SAMHD1	20	35563508	Missense_Mutation	SNP	G	TCGA-BQ-5893-01A-11D-1589-08		35563508	27462012	44	8013											
EIF1AX	1964	hgsc.bcm.edu	37	chrX	20152121	20152121	+	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	taatgtccgaggtatttatcCaaacctacaaaagaaaagtc	17	10	6	8	1	0	1	0	0	0	1	3	2	2	1	3	1	2	1	3	1	9	5			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chrX:20152121C>A	ENST00000379607.5	-	4	412	c.209G>T	c.(208-210)tGg>tTg	p.W70L	EIF1AX_ENST00000379593.1_Missense_Mutation_p.W42L|snoU2_19_ENST00000364722.1_RNA|snoU2-30_ENST00000365012.1_RNA	NM_001412.3	NP_001403.1	P47813	IF1AX_HUMAN	eukaryotic translation initiation factor 1A, X-linked	70	S1-like.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(2)|lung(1)|ovary(1)|prostate(1)	5						GGTATTTATCCAAACCTACAA	0.323																																					p.W70L		Atlas-SNP	.											.	EIF1AX	21	.	0			c.G209T						PASS	.						56	47	50					X																	20152121		2203	4300	6503	SO:0001583	missense	1964	exon4			TTTATCCAAACCT	L18960	CCDS14196.1	Xp22.13	2014-02-19	2002-11-28	2004-05-26	ENSG00000173674	ENSG00000173674			3250	protein-coding gene	gene with protein product		300186	"eukaryotic translation initiation factor 1A, X chromosome"	EIF4C, EIF1A		8106356, 9381176	Standard	NM_001412		Approved	eIF-1A, eIF-4C	uc004czt.3	P47813	OTTHUMG00000022704	ENST00000379607.5:c.209G>T	chrX.hg19:g.20152121C>A	ENSP00000368927:p.Trp70Leu	37.0	0.0	.		33.0	20.0	.	NM_001412	B2R5U5|Q0VGC2|Q5JPS5|Q5JPS6	Missense_Mutation	SNP	ENST00000379607.5	hg19	CCDS14196.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.803652	0.90623	.	.	ENSG00000173674	ENST00000379607;ENST00000379593	T;T	0.58652	0.32;0.32	5.64	5.64	0.86602	Nucleic acid-binding, OB-fold-like (1);RNA-binding domain, S1, IF1 type (2);Nucleic acid-binding, OB-fold (1);	.	.	.	.	D	0.86653	0.5984	H	0.99090	4.425	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.92362	0.5898	9	0.87932	D	0	-3.1686	16.8722	0.86043	0.0:1.0:0.0:0.0	.	70	P47813	IF1AX_HUMAN	L	70;42	ENSP00000368927:W70L;ENSP00000368912:W42L	ENSP00000368912:W42L	W	-	2	0	EIF1AX	20062042	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.076000	0.76806	2.361000	0.80049	0.600000	0.82982	TGG	.	.	.	none		0.323	EIF1AX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058913.1			A	20152121	C	A	20152121	3	1	128	1	0	0	0	0	1	0	0	0	4994	595	21	4	241	4	EIF1AX	23	20152121	Missense_Mutation	SNP	C	TCGA-BQ-5893-01A-11D-1589-08		20152121	135118439	45	8014											
GPR34	2857	hgsc.bcm.edu	37	chrX	41555435	41555435	+	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	atagtatggatgcttgctctTggtggattcctaactatgat	9	16	10	6	0	1	1	0	1	1	0	2	3	2	3	1	3	3	3	1	3	4	7			TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chrX:41555435T>A	ENST00000378142.4	+	3	833	c.549T>A	c.(547-549)ctT>ctA	p.L183L	CASK_ENST00000442742.2_Intron|CASK_ENST00000318588.9_Intron|GPR34_ENST00000378138.5_Silent_p.L183L|CASK_ENST00000378154.1_Intron|CASK_ENST00000378158.1_Intron|CASK_ENST00000378163.1_Intron|CASK_ENST00000378166.4_Intron|CASK_ENST00000361962.4_Intron|CASK_ENST00000421587.2_Intron	NM_001097579.1|NM_005300.3	NP_001091048.1|NP_005291.1	Q9UPC5	GPR34_HUMAN	G protein-coupled receptor 34	183					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						TGCTTGCTCTTGGTGGATTCC	0.353																																					p.L183L		Atlas-SNP	.											.	GPR34	42	.	0			c.T549A						PASS	.						63	59	60					X																	41555435		2203	4300	6503	SO:0001819	synonymous_variant	2857	exon3			TGCTCTTGGTGGA	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.549T>A	chrX.hg19:g.41555435T>A		60.0	0.0	.		58.0	49.0	.	NM_001097579	O95853	Silent	SNP	ENST00000378142.4	hg19	CCDS14258.1																																																																																			.	.	.	none		0.353	GPR34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056264.1	NM_005300		A	41555435	T	A	41555435	2	1	128	1	0	0	0	0	0	0	0	1	6696	1799	63	5		5	GPR34	23	41555435	Silent	SNP	T	TCGA-BQ-5893-01A-11D-1589-08	21403314	41555435	113715125	46	8015											
BCORL1	63035	hgsc.bcm.edu	37	chrX	129173153	129173154	+	Frame_Shift_Ins	INS	-	-	CTGG																															aatgacaacctggagaccatINSctggctcctgctgtcctatg																										TCGA-BQ-5893-01A-11D-1589-08	TCGA-BQ-5893-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c3f8ab09-b776-4ca3-9b9d-f9848542f3dd	bbfe1ddb-1749-401c-b2f8-9b0854ae7d23	g.chrX:129173153_129173154insCTGG	ENST00000218147.7	+	10	4711_4712	c.4514_4515insCTGG	c.(4513-4518)atctggfs	p.-1509fs	BCORL1_ENST00000303743.5_Frame_Shift_Ins_p.-1583fs|BCORL1_ENST00000540052.1_Frame_Shift_Ins_p.-1509fs|BCORL1_ENST00000359304.2_Frame_Shift_Ins_p.-1379fs			Q5H9F3	BCORL_HUMAN	BCL6 corepressor-like 1						chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|liver(3)|lung(30)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	75						CTGGAGACCATCTGGCTCCTGC	0.574																																					p.I1505fs		Atlas-INDEL	.											.	BCORL1	213	.	0			c.4514_4515insCTGG						PASS	.																																			SO:0001589	frameshift_variant	63035	exon9			.	AL136450	CCDS14616.1	Xq25-q26.1	2014-09-17	2010-06-10		ENSG00000085185	ENSG00000085185		"Ankyrin repeat domain containing"	25657	protein-coding gene	gene with protein product		300688	"chromosome X open reading frame 10", "BCL6 co-repressor-like 1"	CXorf10			Standard	NM_021946		Approved	FLJ11362	uc022cdu.1	Q5H9F3	OTTHUMG00000022379	ENST00000218147.7:c.4515_4518dupCTGG	chrX.hg19:g.129173154_129173157dupCTGG	ENSP00000218147:p.Leu1509fs	74.0	0.0	0		38.0	22.0	0.578947	NM_021946	B5MDQ8|Q5H9F2|Q5H9F4|Q6ZVE0|Q8TEN3|Q9Y528	Frame_Shift_Ins	INS	ENST00000218147.7	hg19	CCDS14616.1																																																																																			.	.	.	none		0.574	BCORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058223.1	NM_021946		CTGG	129173154	-	CTGG	129173153	7	5	128	1	0	1	1	0	0	0	0	0	1387	1435	50	0	4774	0	BCORL1	23	129173153	Frame_Shift_Ins	INS	-	TCGA-BQ-5893-01A-11D-1589-08	87617718	129173153	26097407	47	8016											
DUSP12	11266	hgsc.bcm.edu	37	chr1	161726704	161726704	+	Frame_Shift_Del	DEL	G	G	-																															gtggatgaaatgaaaatattGcctgttttgggatcacaaac																										TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr1:161726704delG	ENST00000367943.4	+	6	1022	c.990delG	c.(988-990)ttgfs	p.L330fs		NM_007240.1	NP_009171.1	Q9UNI6	DUS12_HUMAN	dual specificity phosphatase 12	330					cellular protein modification process (GO:0006464)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of glucokinase activity (GO:0033133)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|lung(1)	5	all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00634)			TGAAAATATTGCCTGTTTTGG	0.373																																					p.L330fs		Atlas-INDEL	.											.	DUSP12	20	.	0			c.989delT						PASS	.																																			SO:0001589	frameshift_variant	11266	exon6			.	AF119226	CCDS1234.1	1q21-q22	2011-06-09			ENSG00000081721	ENSG00000081721		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	3067	protein-coding gene	gene with protein product	"serine/threonine specific protein phosphatase", "YVH1 protein-tyrosine phosphatase (S. cerevisiae) ortholog"	604835				10446167	Standard	XM_005244862		Approved	YVH1, DUSP1	uc001gbo.3	Q9UNI6	OTTHUMG00000034540	ENST00000367943.4:c.990delG	chr1.hg19:g.161726704delG	ENSP00000356920:p.Leu330fs	82.0	0.0	0		68.0	23.0	0.338235	NM_007240	Q5VXA8	Frame_Shift_Del	DEL	ENST00000367943.4	hg19	CCDS1234.1																																																																																			.	.	.	none		0.373	DUSP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083588.1	NM_007240		-	161726704	G	-	161726704	7	5	129	1	0	1	0	1	0	0	0	0	4814	1310	46	0	1012	0	DUSP12	1	161726704	Frame_Shift_Del	DEL	G	TCGA-BQ-5894-01A-11D-1589-08		161726704	87523917	1	8017											
PLXNA2	5362	hgsc.bcm.edu	37	chr1	208270156	208270156	+	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	cccggacacctgcccctccaCctctgtcaggttcccaaagg	7	7	8	19	1	2	0	1	0	1	0	4	1	4	1	7	3	1	1	7	3	1	1			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr1:208270156C>A	ENST00000367033.3	-	7	2561	c.1804G>T	c.(1804-1806)Gtg>Ttg	p.V602L		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	602					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)		TGCCCCTCCACCTCTGTCAGG	0.562																																					p.V602L		Atlas-SNP	.											.	PLXNA2	178	.	0			c.G1804T						PASS	.						76	63	67					1																	208270156		2203	4300	6503	SO:0001583	missense	5362	exon7			CCTCCACCTCTGT	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.1804G>T	chr1.hg19:g.208270156C>A	ENSP00000356000:p.Val602Leu	82.0	0.0	.		63.0	20.0	.	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	hg19	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	C	11.86	1.764098	0.31228	.	.	ENSG00000076356	ENST00000367033	T	0.00856	5.61	4.92	4.92	0.64577	.	0.309702	0.38837	N	0.001558	T	0.01695	0.0054	L	0.57536	1.79	0.58432	D	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.61272	-0.7096	10	0.22109	T	0.4	.	18.3153	0.90218	0.0:1.0:0.0:0.0	.	602	O75051	PLXA2_HUMAN	L	602	ENSP00000356000:V602L	ENSP00000356000:V602L	V	-	1	0	PLXNA2	206336779	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	5.321000	0.65846	2.563000	0.86464	0.655000	0.94253	GTG	.	.	.	none		0.562	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		A	208270156	C	A	208270156	3	1	129	1	0	0	0	0	1	0	0	0	12127	507	18	4	3984	4	PLXNA2	1	208270156	Missense_Mutation	SNP	C	TCGA-BQ-5894-01A-11D-1589-08	46543452	208270156	40980465	2	8018											
MBD5	55777	hgsc.bcm.edu	37	chr2	149226038	149226038	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agttaatgattggatcatcaAatgccatgggaaggctatat	14	12	10	5	0	2	1	2	1	0	0	2	3	2	3	1	3	1	2	1	3	5	4			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr2:149226038A>G	ENST00000407073.1	+	9	1523	c.526A>G	c.(526-528)Aat>Gat	p.N176D	MBD5_ENST00000404807.1_Missense_Mutation_p.N176D	NM_018328.4	NP_060798.2	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	176					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)		TGGATCATCAAATGCCATGGG	0.423																																					p.N176D		Atlas-SNP	.											.	MBD5	164	.	0			c.A526G						PASS	.						77	73	74					2																	149226038		2203	4300	6503	SO:0001583	missense	55777	exon9			TCATCAAATGCCA	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.526A>G	chr2.hg19:g.149226038A>G	ENSP00000386049:p.Asn176Asp	94.0	0.0	.		99.0	24.0	.	NM_018328	A5HMQ4|A7E2B1|Q53SR1|Q9NUV6	Missense_Mutation	SNP	ENST00000407073.1	hg19	CCDS33302.1	.	.	.	.	.	.	.	.	.	.	A	16.82	3.227484	0.58668	.	.	ENSG00000204406	ENST00000407073;ENST00000404807	T;T	0.45668	0.89;0.89	5.16	5.16	0.70880	.	0.088275	0.49305	D	0.000155	T	0.30070	0.0753	N	0.08118	0	0.33054	D	0.533103	D	0.56968	0.978	P	0.47528	0.549	T	0.43015	-0.9417	10	0.40728	T	0.16	-3.4654	13.8586	0.63545	1.0:0.0:0.0:0.0	.	176	Q9P267	MBD5_HUMAN	D	176	ENSP00000386049:N176D;ENSP00000384672:N176D	ENSP00000384672:N176D	N	+	1	0	MBD5	148942508	1.000000	0.71417	0.909000	0.35828	0.972000	0.66771	4.483000	0.60264	2.079000	0.62486	0.482000	0.46254	AAT	.	.	.	none		0.423	MBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318111.2			G	149226038	A	G	149226038	3	3	129	1	0	0	0	0	1	0	0	0	9354	14	1	3	540	3	MBD5	2	149226038	Missense_Mutation	SNP	A	TCGA-BQ-5894-01A-11D-1589-08		149226038	93973335	3	8019											
CYTIP	9595	hgsc.bcm.edu	37	chr2	158287080	158287080	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagatagttacgttagcaggTttccggacgatctgatcagg	10	11	12	8	3	2	2	1	1	1	1	3	4	3	3	1	3	2	4	1	3	3	4			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr2:158287080T>C	ENST00000264192.3	-	5	588	c.467A>G	c.(466-468)aAc>aGc	p.N156S	CYTIP_ENST00000540637.1_Missense_Mutation_p.N50S|CYTIP_ENST00000497432.1_5'Flank	NM_004288.4	NP_004279.3	O60759	CYTIP_HUMAN	cytohesin 1 interacting protein	156	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				regulation of cell adhesion (GO:0030155)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|endosome (GO:0005768)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	15						CGTTAGCAGGTTTCCGGACGA	0.428																																					p.N156S		Atlas-SNP	.											.	CYTIP	45	.	0			c.A467G						PASS	.						173	152	159					2																	158287080		2203	4300	6503	SO:0001583	missense	9595	exon5			AGCAGGTTTCCGG	L06633	CCDS2204.1	2q11.2	2011-09-08	2008-08-14	2008-08-19	ENSG00000115165	ENSG00000115165			9506	protein-coding gene	gene with protein product	"cytohesin binding protein HE", "cytohesin binder and regulator"	604448	"pleckstrin homology, Sec7 and coiled-coil domains, binding protein"	PSCDBP		18926288, 10343115, 11867758, 20530790, 21562043	Standard	NM_004288		Approved	B3-1, HE, CYBR, CASP, CYTHIP	uc002tzj.1	O60759	OTTHUMG00000154551	ENST00000264192.3:c.467A>G	chr2.hg19:g.158287080T>C	ENSP00000264192:p.Asn156Ser	78.0	0.0	.		87.0	17.0	.	NM_004288	B4DWH9|Q15630|Q8NE32	Missense_Mutation	SNP	ENST00000264192.3	hg19	CCDS2204.1	.	.	.	.	.	.	.	.	.	.	T	17.59	3.427467	0.62733	.	.	ENSG00000115165	ENST00000264192;ENST00000540637;ENST00000418920	T;T;T	0.24908	1.83;1.83;1.83	5.87	4.71	0.59529	PDZ/DHR/GLGF (4);	0.040138	0.85682	N	0.000000	T	0.34366	0.0895	N	0.26162	0.8	0.40568	D	0.981273	D	0.61080	0.989	D	0.77557	0.99	T	0.15838	-1.0423	10	0.59425	D	0.04	-24.1417	8.8383	0.35126	0.0:0.0847:0.0:0.9153	.	156	O60759	CYTIP_HUMAN	S	156;50;50	ENSP00000264192:N156S;ENSP00000440801:N50S;ENSP00000394308:N50S	ENSP00000264192:N156S	N	-	2	0	CYTIP	157995326	1.000000	0.71417	0.994000	0.49952	0.973000	0.67179	2.314000	0.43743	1.149000	0.42402	0.533000	0.62120	AAC	.	.	.	none		0.428	CYTIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254926.1	NM_004288		C	158287080	T	C	158287080	3	2	129	1	0	0	0	0	1	0	0	0	4209	1725	60	3	628	3	CYTIP	2	158287080	Missense_Mutation	SNP	T	TCGA-BQ-5894-01A-11D-1589-08	9061042	158287080	84912293	4	8020											
PDZD2	23037	hgsc.bcm.edu	37	chr5	32108131	32108131	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagatgaaattcttgctattAatgggaaacctctggttggg	11	13	12	5	0	2	2	0	1	2	1	2	4	2	3	1	3	2	2	1	3	4	5			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr5:32108131A>G	ENST00000438447.1	+	25	8798	c.8410A>G	c.(8410-8412)Aat>Gat	p.N2804D	CTD-2152M20.2_ENST00000503441.1_RNA|PDZD2_ENST00000282493.3_Missense_Mutation_p.N2804D|PDZD2_ENST00000513490.1_3'UTR			O15018	PDZD2_HUMAN	PDZ domain containing 2	2804	PDZ 6. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						TCTTGCTATTAATGGGAAACC	0.403																																					p.N2804D		Atlas-SNP	.											.	PDZD2	306	.	0			c.A8410G						PASS	.						134	139	137					5																	32108131		2203	4300	6503	SO:0001583	missense	23037	exon24			GCTATTAATGGGA	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.8410A>G	chr5.hg19:g.32108131A>G	ENSP00000402033:p.Asn2804Asp	159.0	0.0	.		126.0	53.0	.	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	hg19	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.233379	0.79688	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.56776	0.44;0.44	5.88	5.88	0.94601	PDZ/DHR/GLGF (4);	0.097034	0.45867	D	0.000337	T	0.59742	0.2216	L	0.41415	1.275	0.35013	D	0.757058	D	0.76494	0.999	D	0.71870	0.975	T	0.68269	-0.5453	10	0.39692	T	0.17	.	8.7229	0.34452	0.9164:0.0:0.0836:0.0	.	2804	O15018	PDZD2_HUMAN	D	2804;2605;2804	ENSP00000402033:N2804D;ENSP00000282493:N2804D	ENSP00000282493:N2804D	N	+	1	0	PDZD2	32143888	1.000000	0.71417	0.995000	0.50966	0.975000	0.68041	3.761000	0.55242	2.242000	0.73789	0.533000	0.62120	AAT	.	.	.	none		0.403	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			G	32108131	A	G	32108131	3	3	129	1	0	0	0	0	1	0	0	0	11708	362	13	3	8504	3	PDZD2	5	32108131	Missense_Mutation	SNP	A	TCGA-BQ-5894-01A-11D-1589-08		32108131	148807129	5	8021											
SLIT3	6586	hgsc.bcm.edu	37	chr5	168098301	168098301	+	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	ctgtccttctccacggagcgGcacaggccgtgcttgcacac	6	8	11	16	3	1	0	0	0	1	0	3	1	2	1	3	3	3	3	3	3	0	2			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr5:168098301G>C	ENST00000519560.1	-	34	4448	c.4029C>G	c.(4027-4029)tgC>tgG	p.C1343W	SLIT3_ENST00000332966.8_Missense_Mutation_p.C1350W|SLIT3_ENST00000404867.3_Missense_Mutation_p.C1343W	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	1343	EGF-like 7. {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)	p.C1343*(1)		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)			CCACGGAGCGGCACAGGCCGT	0.677																																					p.C1350W	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											SLIT3,NS,carcinoma,0,1	SLIT3	224	.	1	Substitution - Nonsense(1)	lung(1)	c.C4050G						PASS	.						43	35	37					5																	168098301		2203	4300	6503	SO:0001583	missense	6586	exon34			GGAGCGGCACAGG	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.4029C>G	chr5.hg19:g.168098301G>C	ENSP00000430333:p.Cys1343Trp	50.0	0.0	.		36.0	2.0	.	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Missense_Mutation	SNP	ENST00000519560.1	hg19	CCDS4369.1	.	.	.	.	.	.	.	.	.	.	G	14.96	2.692168	0.48202	.	.	ENSG00000184347	ENST00000519560;ENST00000332966;ENST00000404867	D;D;D	0.82433	-1.6;-1.61;-1.59	5.16	-3.59	0.04583	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.91952	0.7451	H	0.95004	3.61	0.80722	D	1	D	0.69078	0.997	D	0.75484	0.986	D	0.91550	0.5256	10	0.72032	D	0.01	.	15.2185	0.73288	0.6215:0.0:0.3785:0.0	.	1343	O75094	SLIT3_HUMAN	W	1343;1350;1343	ENSP00000430333:C1343W;ENSP00000332164:C1350W;ENSP00000384890:C1343W	ENSP00000332164:C1350W	C	-	3	2	SLIT3	168030879	0.999000	0.42202	0.356000	0.25785	0.910000	0.53928	0.533000	0.23082	-0.956000	0.03631	-1.598000	0.00824	TGC	.	.	.	none		0.677	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062		C	168098301	G	C	168098301	3	2	129	1	0	0	0	0	1	0	0	0	14754	1195	42	4	554	4	SLIT3	5	168098301	Missense_Mutation	SNP	G	TCGA-BQ-5894-01A-11D-1589-08	135990170	168098301	12816959	6	8022											
GMDS	2762	hgsc.bcm.edu	37	chr6	1930387	1930387	+	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	tcgtttggcatccagatttcCcaaactgaaacattccagtt	11	13	6	11	1	0	2	0	1	0	1	4	2	3	2	3	1	2	3	3	1	2	4			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr6:1930387C>T	ENST00000380815.4	-	7	990	c.721G>A	c.(721-723)Gga>Aga	p.G241R	GMDS_ENST00000530927.1_Missense_Mutation_p.G211R	NM_001500.3	NP_001491.1	O60547	GMDS_HUMAN	GDP-mannose 4,6-dehydratase	241					'de novo' GDP-L-fucose biosynthetic process (GO:0042351)|GDP-mannose metabolic process (GO:0019673)|Notch signaling pathway (GO:0007219)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	GDP-mannose 4,6-dehydratase activity (GO:0008446)|NADP+ binding (GO:0070401)		GMDS/PDE8B(2)	breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|prostate(1)	21	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)		TCCAGATTTCCCAAACTGAAA	0.408																																					p.G241R		Atlas-SNP	.											.	GMDS	44	.	0			c.G721A						PASS	.						143	124	131					6																	1930387		2203	4300	6503	SO:0001583	missense	2762	exon7			GATTTCCCAAACT	AF042377	CCDS4474.1, CCDS58994.1	6p25	2011-09-14			ENSG00000112699	ENSG00000112699	4.2.1.47	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	4369	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 3E, member 1"	602884				9525924, 19027726	Standard	NM_001500		Approved	GMD, SDR3E1	uc003mtq.3	O60547	OTTHUMG00000016143	ENST00000380815.4:c.721G>A	chr6.hg19:g.1930387C>T	ENSP00000370194:p.Gly241Arg	163.0	0.0	.		134.0	33.0	.	NM_001500	E9PI88|O75357|Q5T954|Q6FH09|Q9UGZ3|Q9UJK9	Missense_Mutation	SNP	ENST00000380815.4	hg19	CCDS4474.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.953109	0.92660	.	.	ENSG00000112699	ENST00000530927;ENST00000380815	D;D	0.95656	-3.77;-3.77	5.63	5.63	0.86233	NAD-dependent epimerase/dehydratase (1);	0.000000	0.85682	D	0.000000	D	0.99042	0.9672	H	0.99415	4.555	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99198	1.0872	10	0.87932	D	0	-19.5481	19.6914	0.96002	0.0:1.0:0.0:0.0	.	241	O60547	GMDS_HUMAN	R	211;241	ENSP00000436726:G211R;ENSP00000370194:G241R	ENSP00000370194:G241R	G	-	1	0	GMDS	1875386	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.487000	0.81328	2.644000	0.89710	0.563000	0.77884	GGA	.	.	.	none		0.408	GMDS-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000043380.3			T	1930387	C	T	1930387	3	4	129	1	0	0	0	0	1	0	0	0	6493	632	22	2	417	2	GMDS	6	1930387	Missense_Mutation	SNP	C	TCGA-BQ-5894-01A-11D-1589-08		1930387	169184680	7	8023											
MEP1A	4224	hgsc.bcm.edu	37	chr6	46801054	46801054	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctcgattctacaattcggAgggatatggttttggggtaa	9	13	12	7	2	1	0	0	0	1	0	3	3	1	2	1	5	1	2	1	5	4	7			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr6:46801054A>G	ENST00000230588.4	+	11	1397	c.1388A>G	c.(1387-1389)gAg>gGg	p.E463G		NM_005588.2	NP_005579.2	Q16819	MEP1A_HUMAN	meprin A, alpha (PABA peptide hydrolase)	463	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				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)			TACAATTCGGAGGGATATGGT	0.498																																					p.E463G		Atlas-SNP	.											.	MEP1A	93	.	0			c.A1388G						PASS	.						74	76	75					6																	46801054		2203	4300	6503	SO:0001583	missense	4224	exon11			ATTCGGAGGGATA		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.1388A>G	chr6.hg19:g.46801054A>G	ENSP00000230588:p.Glu463Gly	157.0	0.0	.		130.0	19.0	.	NM_005588	A2RRM4|B0AZP9|B2RCS2|Q8TDC9|Q9H1R1	Missense_Mutation	SNP	ENST00000230588.4	hg19	CCDS4918.1	.	.	.	.	.	.	.	.	.	.	A	15.89	2.965894	0.53507	.	.	ENSG00000112818	ENST00000230588	T	0.42900	0.96	5.72	5.72	0.89469	TRAF-type (1);TRAF-like (1);MATH (3);	0.000000	0.85682	D	0.000000	T	0.65059	0.2655	M	0.88906	2.99	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.73269	-0.4036	10	0.72032	D	0.01	-31.3608	15.9995	0.80280	1.0:0.0:0.0:0.0	.	491;463	B7ZL91;Q16819	.;MEP1A_HUMAN	G	463	ENSP00000230588:E463G	ENSP00000230588:E463G	E	+	2	0	MEP1A	46909013	1.000000	0.71417	0.998000	0.56505	0.073000	0.16967	9.339000	0.96797	2.186000	0.69663	0.528000	0.53228	GAG	.	.	.	none		0.498	MEP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040803.1	NM_005588		G	46801054	A	G	46801054	3	3	129	1	0	0	0	0	1	0	0	0	9482	304	11	3	1430	3	MEP1A	6	46801054	Missense_Mutation	SNP	A	TCGA-BQ-5894-01A-11D-1589-08	44870667	46801054	124314013	8	8024											
OPN5	221391	hgsc.bcm.edu	37	chr6	47754339	47754339	+	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	cccgctgaaataatgactatCaatttagcagtctgtgatct	12	13	7	9	1	3	3	1	3	2	0	3	3	3	3	1	0	1	2	1	0	5	4			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr6:47754339C>A	ENST00000371211.2	+	2	247	c.219C>A	c.(217-219)atC>atA	p.I73I	OPN5_ENST00000489301.2_Silent_p.I73I|OPN5_ENST00000393699.2_Silent_p.I73I	NM_181744.3	NP_859528.1	Q6U736	OPN5_HUMAN	opsin 5	73					phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)	p.I73I(1)		endometrium(1)|large_intestine(3)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	29						TAATGACTATCAATTTAGCAG	0.403																																					p.I73I	Melanoma(28;740 973 10870 42660 45347)	Atlas-SNP	.											OPN5,NS,carcinoma,0,1	OPN5	58	.	1	Substitution - coding silent(1)	lung(1)	c.C219A						PASS	.						139	128	132					6																	47754339		2203	4300	6503	SO:0001819	synonymous_variant	221391	exon2			GACTATCAATTTA	AY288419	CCDS4923.1	6p12.3	2012-08-08	2004-01-23		ENSG00000124818	ENSG00000124818		"GPCR / Class A : Opsin receptors"	19992	protein-coding gene	gene with protein product	"neuropsin"	609042	"transmembrane protein 13"	TMEM13		14623103, 14623098	Standard	NR_033806		Approved	neuropsin, dJ402H5.1	uc003ozc.3	Q6U736	OTTHUMG00000014803	ENST00000371211.2:c.219C>A	chr6.hg19:g.47754339C>A		137.0	1.0	.		123.0	43.0	.	NM_181744	A0AV33|Q5T5B9|Q5T886|Q7Z603|Q86SL5	Silent	SNP	ENST00000371211.2	hg19	CCDS4923.1																																																																																			.	.	.	none		0.403	OPN5-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359451.1	NM_181744		A	47754339	C	A	47754339	2	1	129	1	0	0	0	0	0	0	0	1	10890	816	29	4		4	OPN5	6	47754339	Silent	SNP	C	TCGA-BQ-5894-01A-11D-1589-08	953285	47754339	123360728	9	8025											
COL19A1	1310	hgsc.bcm.edu	37	chr6	70639518	70639518	+	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	taattgcgaggaggcagactGatgaaaaggacactgtggat	14	8	14	5	1	0	3	0	2	0	1	0	7	0	6	0	4	1	1	0	4	3	2			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr6:70639518G>T	ENST00000322773.4	+	6	694	c.592G>T	c.(592-594)Gat>Tat	p.D198Y		NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	198	Laminin G-like.				cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						GAGGCAGACTGATGAAAAGGA	0.423																																					p.D198Y		Atlas-SNP	.											.	COL19A1	232	.	0			c.G592T						PASS	.						111	106	108					6																	70639518		2203	4300	6503	SO:0001583	missense	1310	exon6			CAGACTGATGAAA		CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"Collagens"	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.592G>T	chr6.hg19:g.70639518G>T	ENSP00000316030:p.Asp198Tyr	150.0	0.0	.		93.0	16.0	.	NM_001858	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Missense_Mutation	SNP	ENST00000322773.4	hg19	CCDS4970.1	.	.	.	.	.	.	.	.	.	.	G	3.418	-0.118699	0.06838	.	.	ENSG00000082293	ENST00000322773	T	0.02525	4.26	5.64	3.86	0.44501	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	0.564051	0.17635	N	0.167232	T	0.01800	0.0057	L	0.50333	1.59	0.80722	D	1	P	0.52842	0.956	B	0.41723	0.365	T	0.57648	-0.7775	10	0.66056	D	0.02	.	11.8431	0.52366	0.1408:0.0:0.8592:0.0	.	198	Q14993	COJA1_HUMAN	Y	198	ENSP00000316030:D198Y	ENSP00000316030:D198Y	D	+	1	0	COL19A1	70696239	0.997000	0.39634	0.001000	0.08648	0.020000	0.10135	5.263000	0.65507	0.732000	0.32470	0.655000	0.94253	GAT	.	.	.	none		0.423	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1			T	70639518	G	T	70639518	3	4	129	1	0	0	0	0	1	0	0	0	3678	1290	45	4	610	4	COL19A1	6	70639518	Missense_Mutation	SNP	G	TCGA-BQ-5894-01A-11D-1589-08	22885179	70639518	100475549	10	8026											
KIAA2026	158358	hgsc.bcm.edu	37	chr9	5922386	5922386	+	Missense_Mutation	SNP	T	T	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	ttttcctgcctcactctggcTagtcttaactgatggtgtta	6	17	8	10	0	3	1	1	1	2	0	4	1	4	1	2	2	2	2	2	2	3	5			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr9:5922386T>G	ENST00000399933.3	-	8	3609	c.3610A>C	c.(3610-3612)Agc>Cgc	p.S1204R	KIAA2026_ENST00000381461.2_Missense_Mutation_p.S1174R	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	1204										breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		TCACTCTGGCTAGTCTTAACT	0.453																																					p.S1204R		Atlas-SNP	.											.	KIAA2026	231	.	0			c.A3610C						PASS	.						115	112	113					9																	5922386		2013	4183	6196	SO:0001583	missense	158358	exon8			TCTGGCTAGTCTT	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.3610A>C	chr9.hg19:g.5922386T>G	ENSP00000382815:p.Ser1204Arg	115.0	0.0	.		97.0	32.0	.	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Missense_Mutation	SNP	ENST00000399933.3	hg19		.	.	.	.	.	.	.	.	.	.	T	14.67	2.603738	0.46423	.	.	ENSG00000183354	ENST00000399933;ENST00000381461	.	.	.	4.99	4.99	0.66335	.	0.365571	0.26975	N	0.021550	T	0.30665	0.0772	L	0.27053	0.805	0.28046	N	0.933557	P	0.35908	0.527	B	0.35470	0.203	T	0.32214	-0.9915	9	0.62326	D	0.03	-2.703	11.277	0.49172	0.1362:0.0:0.0:0.8638	.	1204	Q5HYC2	K2026_HUMAN	R	1204;1174	.	ENSP00000370870:S1174R	S	-	1	0	KIAA2026	5912386	0.984000	0.35163	0.997000	0.53966	0.663000	0.39108	3.354000	0.52254	2.102000	0.63906	0.454000	0.30748	AGC	.	.	.	none		0.453	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969		G	5922386	T	G	5922386	3	3	129	1	0	0	0	0	1	0	0	0	8277	1522	53	5	2705	5	KIAA2026	9	5922386	Missense_Mutation	SNP	T	TCGA-BQ-5894-01A-11D-1589-08		5922386	135291045	11	8027											
STAM	8027	hgsc.bcm.edu	37	chr10	17747670	17747670	+	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	gttaatgaacgaagatccgaTgtattccatgtatgcaaagt	14	12	9	6	2	0	2	0	1	0	1	2	4	2	2	2	0	2	4	2	0	6	4			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr10:17747670T>A	ENST00000377524.3	+	12	1354	c.1139T>A	c.(1138-1140)aTg>aAg	p.M380K	STAM_ENST00000540523.1_Missense_Mutation_p.M269K	NM_003473.3	NP_003464.1	Q92783	STAM1_HUMAN	signal transducing adaptor molecule (SH3 domain and ITAM motif) 1	380	ITAM.				endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	26						GAAGATCCGATGTATTCCATG	0.368																																					p.M380K		Atlas-SNP	.											.	STAM	60	.	0			c.T1139A						PASS	.						160	153	156					10																	17747670		2203	4300	6503	SO:0001583	missense	8027	exon12			ATCCGATGTATTC	U43899	CCDS7122.1	10p14-p13	2009-04-29			ENSG00000136738	ENSG00000136738			11357	protein-coding gene	gene with protein product	"HSE1 homolog (S. cerevisiae)"	601899				8780729	Standard	NM_003473		Approved	STAM1	uc001ipj.2	Q92783	OTTHUMG00000017749	ENST00000377524.3:c.1139T>A	chr10.hg19:g.17747670T>A	ENSP00000366746:p.Met380Lys	228.0	0.0	.		166.0	48.0	.	NM_003473	B0YJ99|D3DRU5|Q8N6D9	Missense_Mutation	SNP	ENST00000377524.3	hg19	CCDS7122.1	.	.	.	.	.	.	.	.	.	.	T	16.28	3.077571	0.55753	.	.	ENSG00000136738	ENST00000377524;ENST00000540523	T;T	0.38722	1.47;1.12	5.64	4.49	0.54785	.	0.132590	0.64402	D	0.000002	T	0.33089	0.0851	L	0.48642	1.525	0.52501	D	0.999957	P;B	0.36048	0.534;0.173	B;B	0.32211	0.142;0.031	T	0.11494	-1.0585	10	0.28530	T	0.3	-5.6897	11.8463	0.52387	0.0:0.0697:0.0:0.9303	.	269;380	B4DZT2;Q92783	.;STAM1_HUMAN	K	380;269	ENSP00000366746:M380K;ENSP00000438073:M269K	ENSP00000366746:M380K	M	+	2	0	STAM	17787676	1.000000	0.71417	0.968000	0.41197	0.992000	0.81027	7.698000	0.84413	2.152000	0.67230	0.533000	0.62120	ATG	.	.	.	none		0.368	STAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047039.1	NM_003473		A	17747670	T	A	17747670	3	1	129	1	0	0	0	0	1	0	0	0	15260	1464	51	5	1185	5	STAM	10	17747670	Missense_Mutation	SNP	T	TCGA-BQ-5894-01A-11D-1589-08		17747670	117787077	12	8028											
OR52N5	390075	hgsc.bcm.edu	37	chr11	5799428	5799428	+	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	ccttggcaatgatagggttgGtgagtgtggtagcataacgc	9	11	15	6	1	0	2	0	2	0	0	0	2	0	2	1	4	2	4	1	4	4	5			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr11:5799428G>T	ENST00000317093.2	-	1	469	c.437C>A	c.(436-438)aCc>aAc	p.T146N	TRIM5_ENST00000380027.1_Intron	NM_001001922.2	NP_001001922.2	Q8NH56	O52N5_HUMAN	olfactory receptor, family 52, subfamily N, member 5	146						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(3)|liver(1)|lung(17)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.05e-11)|LUSC - Lung squamous cell carcinoma(625;0.112)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.195)		GATAGGGTTGGTGAGTGTGGT	0.507																																					p.T146N		Atlas-SNP	.											.	OR52N5	58	.	0			c.C437A						PASS	.						146	115	126					11																	5799428		2125	4095	6220	SO:0001583	missense	390075	exon1			GGGTTGGTGAGTG	AB065535	CCDS31397.1	11p15.4	2012-08-09			ENSG00000181009	ENSG00000181009		"GPCR / Class A : Olfactory receptors"	15231	protein-coding gene	gene with protein product							Standard	NM_001001922		Approved	OR52N5Q	uc010qzn.2	Q8NH56	OTTHUMG00000168799	ENST00000317093.2:c.437C>A	chr11.hg19:g.5799428G>T	ENSP00000322866:p.Thr146Asn	54.0	0.0	.		34.0	11.0	.	NM_001001922	B9EH12|Q6IFG2	Missense_Mutation	SNP	ENST00000317093.2	hg19	CCDS31397.1	.	.	.	.	.	.	.	.	.	.	G	13.46	2.245082	0.39697	.	.	ENSG00000181009	ENST00000317093	T	0.01051	5.4	3.49	3.49	0.39957	GPCR, rhodopsin-like superfamily (1);	0.000000	0.31697	U	0.007215	T	0.04048	0.0113	L	0.50919	1.6	0.38487	D	0.947868	D	0.62365	0.991	D	0.65010	0.931	T	0.54715	-0.8252	10	0.51188	T	0.08	.	14.1011	0.65056	0.0:0.0:1.0:0.0	.	146	Q8NH56	O52N5_HUMAN	N	146	ENSP00000322866:T146N	ENSP00000322866:T146N	T	-	2	0	OR52N5	5756004	0.994000	0.37717	0.771000	0.31576	0.554000	0.35429	2.842000	0.48230	1.952000	0.56665	0.494000	0.49563	ACC	.	.	.	none		0.507	OR52N5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401141.1	NM_001001922		T	5799428	G	T	5799428	3	4	129	1	0	0	0	0	1	0	0	0	11137	1261	44	4	541	4	OR52N5	11	5799428	Missense_Mutation	SNP	G	TCGA-BQ-5894-01A-11D-1589-08		5799428	129207088	13	8029											
BUD13	84811	hgsc.bcm.edu	37	chr11	116633298	116633298	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caagctgcttcttgtctccaAaatgggattttgcttgcttt	7	17	8	9	0	2	0	0	0	2	0	3	1	2	1	1	1	4	4	1	1	3	6			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr11:116633298A>G	ENST00000260210.4	-	4	1030	c.1007T>C	c.(1006-1008)tTt>tCt	p.F336S	BUD13_ENST00000375445.3_Intron	NM_032725.3	NP_116114.1	Q9BRD0	BUD13_HUMAN	BUD13 homolog (S. cerevisiae)	336					mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)	nucleus (GO:0005634)|RES complex (GO:0070274)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|pancreas(2)|skin(1)|urinary_tract(1)	22	all_hematologic(175;0.0487)	all_cancers(61;1.72e-06)|all_epithelial(67;0.000735)|Melanoma(852;0.022)|Acute lymphoblastic leukemia(157;0.0255)|Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(158;0.0588)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;5.81e-06)|all cancers(92;0.000144)|OV - Ovarian serous cystadenocarcinoma(223;0.154)		CTTGTCTCCAAAATGGGATTT	0.443																																					p.F336S		Atlas-SNP	.											.	BUD13	41	.	0			c.T1007C						PASS	.						134	120	125					11																	116633298		2201	4296	6497	SO:0001583	missense	84811	exon4			TCTCCAAAATGGG	BC006350	CCDS8374.1, CCDS53712.1	11q23.3	2012-06-07	2007-01-12		ENSG00000137656	ENSG00000137656			28199	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 71"		"BUD13 homolog (yeast)"			12477932	Standard	NM_032725		Approved	MGC13125, fSAP71, Cwc26	uc001ppn.3	Q9BRD0	OTTHUMG00000045136	ENST00000260210.4:c.1007T>C	chr11.hg19:g.116633298A>G	ENSP00000260210:p.Phe336Ser	267.0	0.0	.		213.0	66.0	.	NM_032725	A8K0S0|Q96LS7	Missense_Mutation	SNP	ENST00000260210.4	hg19	CCDS8374.1	.	.	.	.	.	.	.	.	.	.	A	14.33	2.503865	0.44558	.	.	ENSG00000137656	ENST00000260210	T	0.16597	2.33	4.83	-1.94	0.07571	.	1.189750	0.05897	N	0.629384	T	0.12008	0.0292	L	0.31926	0.97	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.41502	-0.9505	10	0.87932	D	0	-0.611	3.4276	0.07416	0.4025:0.0:0.1998:0.3978	.	336;336	A8K4Z6;Q9BRD0	.;BUD13_HUMAN	S	336	ENSP00000260210:F336S	ENSP00000260210:F336S	F	-	2	0	BUD13	116138508	0.000000	0.05858	0.276000	0.24689	0.974000	0.67602	0.121000	0.15667	0.010000	0.14839	0.533000	0.62120	TTT	.	.	.	none		0.443	BUD13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000104864.1	NM_032725		G	116633298	A	G	116633298	3	3	129	1	0	0	0	0	1	0	0	0	1575	14	1	3	880	3	BUD13	11	116633298	Missense_Mutation	SNP	A	TCGA-BQ-5894-01A-11D-1589-08	110833870	116633298	18373218	14	8030											
C12orf51	283450	hgsc.bcm.edu	37	chr12	112694159	112694159	+	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	ttgcgaagagcatctgctatCaaatctaaggtacaggcagc	13	9	10	9	1	3	1	1	0	2	1	3	2	3	1	0	2	5	4	0	2	5	4			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr12:112694159C>T	ENST00000430131.2	-	20	3141	c.1996G>A	c.(1996-1998)Gat>Aat	p.D666N	HECTD4_ENST00000550722.1_Missense_Mutation_p.D952N|HECTD4_ENST00000377560.5_Missense_Mutation_p.D916N|RP3-521E19.2_ENST00000547401.1_RNA			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	666					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)										CATCTGCTATCAAATCTAAGG	0.423																																					p.D954N		Atlas-SNP	.											.	.	.	.	0			c.G2860A						PASS	.						126	129	128					12																	112694159		2203	4300	6503	SO:0001583	missense	283450	exon21			TGCTATCAAATCT	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.1996G>A	chr12.hg19:g.112694159C>T	ENSP00000404379:p.Asp666Asn	191.0	0.0	.		177.0	55.0	.	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	C	36	5.948543	0.97134	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	T;T;T	0.65178	-0.02;0.0;-0.14	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.70919	0.3279	L	0.27053	0.805	0.58432	D	0.999995	D;D;D	0.67145	0.996;0.993;0.996	D;D;D	0.73708	0.981;0.971;0.981	T	0.73202	-0.4057	10	0.87932	D	0	.	19.4096	0.94665	0.0:1.0:0.0:0.0	.	666;666;666	Q9Y4D8-2;Q9Y4D8;Q9Y4D8-3	.;K0614_HUMAN;.	N	916;666;952	ENSP00000366783:D916N;ENSP00000404379:D666N;ENSP00000449784:D952N	ENSP00000366783:D916N	D	-	1	0	C12orf51	111178542	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.298000	0.78815	2.820000	0.97059	0.655000	0.94253	GAT	.	.	.	none		0.423	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		T	112694159	C	T	112694159	3	4	129	1	0	0	0	0	1	0	0	0	1698	826	29	2	10218	2	C12orf51	12	112694159	Missense_Mutation	SNP	C	TCGA-BQ-5894-01A-11D-1589-08		112694159	21157736	15	8031											
WDR45L	56270	hgsc.bcm.edu	37	chr17	80579499	80579499	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acttactttctcggatgcagTtgcaattcttgttccctgca	7	16	7	11	1	2	0	0	0	2	0	4	1	3	1	1	1	4	5	1	1	2	6			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr17:80579499T>C	ENST00000392325.4	-	6	798	c.604A>G	c.(604-606)Act>Gct	p.T202A	WDR45B_ENST00000571835.1_5'UTR	NM_019613.3	NP_062559.2	Q5MNZ6	WIPI3_HUMAN	WD repeat domain 45B	202																	TCGGATGCAGTTGCAATTCTT	0.542																																					p.T202A		Atlas-SNP	.											.	.	.	.	0			c.A604G						PASS	.						127	97	107					17																	80579499		2203	4300	6503	SO:0001583	missense	56270	exon6			ATGCAGTTGCAAT	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.604A>G	chr17.hg19:g.80579499T>C	ENSP00000376139:p.Thr202Ala	103.0	0.0	.		81.0	11.0	.	NM_019613	O95328|Q2MCP6|Q6IBN2	Missense_Mutation	SNP	ENST00000392325.4	hg19	CCDS11815.2	.	.	.	.	.	.	.	.	.	.	T	18.41	3.618375	0.66787	.	.	ENSG00000141580	ENST00000392325;ENST00000539012	T	0.57907	0.37	4.82	4.82	0.62117	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.81327	0.4799	H	0.96777	3.88	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87771	0.2605	10	0.72032	D	0.01	-25.7216	14.6708	0.68942	0.0:0.0:0.0:1.0	.	202	Q5MNZ6	WIPI3_HUMAN	A	202;174	ENSP00000376139:T202A	ENSP00000376139:T202A	T	-	1	0	WDR45L	78172788	1.000000	0.71417	0.910000	0.35882	0.534000	0.34807	7.503000	0.81632	1.935000	0.56089	0.460000	0.39030	ACT	.	.	.	none		0.542	WDR45B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316536.1	NM_019613		C	80579499	T	C	80579499	3	2	129	1	0	0	0	0	1	0	0	0	17310	1725	60	3	450	3	WDR45L	17	80579499	Missense_Mutation	SNP	T	TCGA-BQ-5894-01A-11D-1589-08		80579499	615711	16	8032											
KLK3	354	hgsc.bcm.edu	37	chr19	51359636	51359636	+	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	acccccagtgggtcctcacaGctgcccactgcatcaggaag	9	6	10	16	0	2	0	2	0	0	0	3	1	3	1	4	2	3	2	4	2	1	0			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr19:51359636G>T	ENST00000326003.2	+	2	228	c.187G>T	c.(187-189)Gct>Tct	p.A63S	KLK3_ENST00000593997.1_Missense_Mutation_p.A63S|KLK3_ENST00000595952.1_Missense_Mutation_p.A63S|KLK3_ENST00000597483.1_Missense_Mutation_p.A63S|KLK3_ENST00000360617.3_Missense_Mutation_p.A63S	NM_001030047.1|NM_001030048.1|NM_001648.2	NP_001025218.1|NP_001025219.1|NP_001639.1	P07288	KLK3_HUMAN	kallikrein-related peptidase 3	63	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular protein metabolic process (GO:0044267)|negative regulation of angiogenesis (GO:0016525)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|cervix(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00763)|GBM - Glioblastoma multiforme(134;0.0144)		GGTCCTCACAGCTGCCCACTG	0.617																																					p.A63S	Colon(185;1767 2023 13025 30120 37630)	Atlas-SNP	.											.	KLK3	76	.	0			c.G187T						PASS	.						76	77	77					19																	51359636		2203	4300	6503	SO:0001583	missense	354	exon2			CTCACAGCTGCCC	X14810	CCDS12807.1, CCDS33083.1, CCDS46155.1	19q13.41	2012-10-02	2006-10-27			ENSG00000142515		"Kallikreins"	6364	protein-coding gene	gene with protein product		176820	"kallikrein 3, (prostate specific antigen)"	APS		2456523, 2436946, 16800724, 16800723	Standard	NM_001648		Approved	PSA	uc021uyi.1	P07288		ENST00000326003.2:c.187G>T	chr19.hg19:g.51359636G>T	ENSP00000314151:p.Ala63Ser	172.0	0.0	.		144.0	42.0	.	NM_001030050	C9JXH3|G3V0H4|G3XAE3|Q15096|Q16272|Q86TG8|Q8IXI4	Missense_Mutation	SNP	ENST00000326003.2	hg19	CCDS12807.1	.	.	.	.	.	.	.	.	.	.	G	13.59	2.281163	0.40394	.	.	ENSG00000142515	ENST00000326003;ENST00000422986;ENST00000360617;ENST00000435152;ENST00000326052	D;D;D	0.95272	-3.66;-3.66;-3.66	2.91	1.81	0.25067	.	0.000000	0.32041	N	0.006661	D	0.96231	0.8771	M	0.77486	2.375	0.27490	N	0.952326	D;D;D;D	0.89917	0.998;0.987;0.999;1.0	D;D;D;D	0.91635	0.951;0.923;0.976;0.999	D	0.90785	0.4682	10	0.87932	D	0	.	8.8252	0.35050	0.0:0.0:0.7734:0.2266	.	63;63;63;63	Q8NCW4;G3XAE3;G3V0H4;C9JXH3	.;.;.;.	S	63	ENSP00000314151:A63S;ENSP00000393628:A63S;ENSP00000353829:A63S	ENSP00000314151:A63S	A	+	1	0	KLK3	56051448	0.999000	0.42202	0.987000	0.45799	0.256000	0.26092	6.780000	0.75063	0.516000	0.28340	0.436000	0.28706	GCT	.	.	.	none		0.617	KLK3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464067.1	NM_145864		T	51359636	G	T	51359636	3	4	129	1	0	0	0	0	1	0	0	0	8412	971	34	4	193	4	KLK3	19	51359636	Missense_Mutation	SNP	G	TCGA-BQ-5894-01A-11D-1589-08		51359636	7769347	17	8033											
SLC23A2	9962	hgsc.bcm.edu	37	chr20	4854628	4854628	+	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	gctaccagaagcacgccttgCctggcatctgtgcgagcata	9	8	11	13	2	1	1	0	0	1	1	1	2	1	1	3	1	5	4	3	1	3	3			TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr20:4854628C>T	ENST00000379333.1	-	11	1448	c.1056G>A	c.(1054-1056)agG>agA	p.R352R	SLC23A2_ENST00000338244.1_Silent_p.R352R|SLC23A2_ENST00000424750.2_Silent_p.R238R|SLC23A2_ENST00000468355.1_5'UTR	NM_203327.1	NP_976072.1	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 2	352					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						GCACGCCTTGCCTGGCATCTG	0.547																																					p.R352R		Atlas-SNP	.											.	SLC23A2	62	.	0			c.G1056A						PASS	.						117	103	108					20																	4854628		2203	4300	6503	SO:0001819	synonymous_variant	9962	exon11			GCCTTGCCTGGCA	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.1056G>A	chr20.hg19:g.4854628C>T		176.0	0.0	.		161.0	7.0	.	NM_203327	B4DJZ1|Q8WWR4|Q92512|Q96D54|Q9UNU1|Q9UP85	Silent	SNP	ENST00000379333.1	hg19	CCDS13085.1	.	.	.	.	.	.	.	.	.	.	C	0.340	-0.951260	0.02285	.	.	ENSG00000089057	ENST00000423430	.	.	.	5.72	-2.31	0.06765	.	.	.	.	.	T	0.50650	0.1628	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.46721	-0.9171	4	.	.	.	-23.1993	6.8431	0.23973	0.0:0.4114:0.1221:0.4665	.	.	.	.	T	109	.	.	A	-	1	0	SLC23A2	4802628	0.430000	0.25538	0.065000	0.19835	0.002000	0.02628	-0.233000	0.09041	-0.035000	0.13691	-0.140000	0.14226	GCA	.	.	.	none		0.547	SLC23A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077832.1			T	4854628	C	T	4854628	2	4	129	1	0	0	0	0	0	0	0	1	14476	738	26	2		2	SLC23A2	20	4854628	Silent	SNP	C	TCGA-BQ-5894-01A-11D-1589-08		4854628	58170892	18	8034											
JAG1	182	hgsc.bcm.edu	37	chr20	10621489	10621489	+	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	tctgcaacggcagcaatcagCgagctgtttccatcacgttt	9	11	9	12	3	3	0	2	0	1	0	4	1	4	0	1	1	5	6	1	1	2	2	rs202075581	byFrequency	TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr20:10621489C>A	ENST00000254958.5	-	25	3656	c.3141G>T	c.(3139-3141)tcG>tcT	p.S1047S	JAG1_ENST00000423891.2_Silent_p.S888S	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	1047					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						CAGCAATCAGCGAGCTGTTTC	0.448									Alagille Syndrome																												p.S1047S		Atlas-SNP	.											.	JAG1	213	.	0			c.G3141T						PASS	.						113	100	104					20																	10621489		2203	4300	6503	SO:0001819	synonymous_variant	182	exon25	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AATCAGCGAGCTG	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.3141G>T	chr20.hg19:g.10621489C>A		101.0	0.0	.		74.0	5.0	.	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Silent	SNP	ENST00000254958.5	hg19	CCDS13112.1																																																																																			.	C|0.999;T|0.001	.	alt		0.448	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214		A	10621489	C	A	10621489	2	1	129	1	0	0	0	0	0	0	0	1	7941	755	27	4		4	JAG1	20	10621489	Silent	SNP	C	TCGA-BQ-5894-01A-11D-1589-08	5766861	10621489	52404031	19	8035											
KCNJ4	3761	hgsc.bcm.edu	37	chr22	38823432	38823433	+	In_Frame_Ins	INS	-	-	GGA																															aggtcccgctggtccaggggINScaggtactcgccctcctggg																										TCGA-BQ-5894-01A-11D-1589-08	TCGA-BQ-5894-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91c4ab90-4133-4ba6-a47b-c71a8401b3eb	2cdd7b73-3fff-470a-81b6-2d03e2025874	g.chr22:38823432_38823433insGGA	ENST00000303592.3	-	2	963_964	c.705_706insTCC	c.(703-708)ctgccc>ctgTCCccc	p.235_236LP>LSP	RP3-434P1.6_ENST00000433230.1_RNA	NM_004981.1|NM_152868.2	NP_004972.1|NP_690607.1	P48050	KCNJ4_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 4	235					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)|PDZ domain binding (GO:0030165)			endometrium(7)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23	Melanoma(58;0.0286)					TGGTCCAGGGGCAGGTACTCGC	0.629																																					p.P236delinsSP		Atlas-INDEL	.											.	KCNJ4	74	.	0			c.706_707insTCC						PASS	.																																			SO:0001652	inframe_insertion	3761	exon2			.	U07364	CCDS13971.1	22q13.1	2011-07-05			ENSG00000168135	ENSG00000168135		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6265	protein-coding gene	gene with protein product		600504				8016146, 16382105	Standard	NM_152868		Approved	Kir2.3, HIR, HRK1, hIRK2, IRK3	uc003avs.1	P48050	OTTHUMG00000151131	ENST00000303592.3:c.705_706insTCC	chr22.hg19:g.38823432_38823433insGGA	ENSP00000306497:p.Leu235_Pro236insSer	72.0	0.0	0		54.0	13.0	0.240741	NM_004981	Q14D44	In_Frame_Ins	INS	ENST00000303592.3	hg19	CCDS13971.1																																																																																			.	.	.	none		0.629	KCNJ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321447.1	NM_004981		GGA	38823433	-	GGA	38823432	7	5	129	1	0	1	1	0	0	0	0	0	8060	1203	42	0	635	0	KCNJ4	22	38823432	In_Frame_Ins	INS	-	TCGA-BQ-5894-01A-11D-1589-08		38823432	12481134	20	8036											
CSMD2	114784	hgsc.bcm.edu	37	chr1	34180229	34180229	+	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	gctccacaggcgccgtctgcCccccaggcacgtgatgcggg	5	5	14	17	4	1	1	0	1	1	0	2	1	2	1	5	3	2	2	5	3	0	0			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr1:34180229C>T	ENST00000373381.4	-	21	3540	c.3364G>A	c.(3364-3366)Ggc>Agc	p.G1122S		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1082	CUB 7. {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)				CGCCGTCTGCCCCCCAGGCAC	0.607																																					p.G1082S		Atlas-SNP	.											.	CSMD2	946	.	0			c.G3244A						PASS	.						120	136	131					1																	34180229		2203	4300	6503	SO:0001583	missense	114784	exon21			GTCTGCCCCCCAG	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.3364G>A	chr1.hg19:g.34180229C>T	ENSP00000362479:p.Gly1122Ser	302.0	0.0	.		106.0	71.0	.	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	hg19		.	.	.	.	.	.	.	.	.	.	C	36	5.810255	0.96975	.	.	ENSG00000121904	ENST00000373381	T	0.24151	1.87	5.85	5.85	0.93711	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	T	0.48040	0.1478	L	0.51422	1.61	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	0.998;1.0	T	0.21075	-1.0256	10	0.46703	T	0.11	.	19.1531	0.93496	0.0:1.0:0.0:0.0	.	1082;1122	Q7Z408;E7EUA6	CSMD2_HUMAN;.	S	1122	ENSP00000362479:G1122S	ENSP00000241312:G1082S	G	-	1	0	CSMD2	33952816	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	7.818000	0.86416	2.753000	0.94483	0.655000	0.94253	GGC	.	.	.	none		0.607	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		T	34180229	C	T	34180229	3	4	130	1	0	0	0	0	1	0	0	0	3947	623	22	2	7415	2	CSMD2	1	34180229	Missense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08		34180229	215070392	1	8037											
ENSA	2029	hgsc.bcm.edu	37	chr1	150601936	150601936	+	Missense_Mutation	SNP	T	T	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	cagggttctcttcttcttgtTtctgggacatggcgggaccg	4	14	13	10	2	4	0	0	0	4	0	5	2	4	2	1	4	0	2	1	4	0	5	rs148754482		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr1:150601936T>G	ENST00000369014.5	-	1	136	c.11A>C	c.(10-12)aAa>aCa	p.K4T	ENSA_ENST00000503345.1_Missense_Mutation_p.K4T|ENSA_ENST00000362052.7_Missense_Mutation_p.K4T|ENSA_ENST00000339643.5_Missense_Mutation_p.K4T|ENSA_ENST00000369016.4_Missense_Mutation_p.K4T|ENSA_ENST00000361532.5_5'Flank|ENSA_ENST00000503241.1_Missense_Mutation_p.K4T|ENSA_ENST00000354702.3_5'Flank|ENSA_ENST00000361631.5_5'Flank|ENSA_ENST00000271690.8_Missense_Mutation_p.K4T|ENSA_ENST00000513281.1_5'Flank|ENSA_ENST00000356527.5_Missense_Mutation_p.K4T|ENSA_ENST00000369009.3_Missense_Mutation_p.K4T			O43768	ENSA_HUMAN	endosulfine alpha	4					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of catalytic activity (GO:0043086)|regulation of catalytic activity (GO:0050790)|regulation of insulin secretion (GO:0050796)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|transport (GO:0006810)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ion channel inhibitor activity (GO:0008200)|phosphatase inhibitor activity (GO:0019212)|potassium channel inhibitor activity (GO:0019870)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase inhibitor activity (GO:0004864)|protein phosphatase type 2A regulator activity (GO:0008601)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(1)	4	all_cancers(9;3.09e-52)|all_epithelial(9;4.47e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-31)|Breast(34;0.000615)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;9.85e-23)|all cancers(9;5.06e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.67e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000701)|LUSC - Lung squamous cell carcinoma(543;0.171)			TTCTTCTTGTTTCTGGGACAT	0.662																																					p.K4T	Esophageal Squamous(188;763 2078 3002 3411 26027)	Atlas-SNP	.											.	ENSA	41	.	0			c.A11C						PASS	.						59	61	60					1																	150601936		2203	4300	6503	SO:0001583	missense	2029	exon1			TCTTGTTTCTGGG	X99906	CCDS958.1, CCDS959.1, CCDS960.1, CCDS961.1, CCDS962.1, CCDS963.1, CCDS964.1, CCDS965.1	1q21.3	2010-03-11			ENSG00000143420	ENSG00000143420			3360	protein-coding gene	gene with protein product		603061				9653196	Standard	NM_004436		Approved	MGC4319, MGC8394, MGC78563, ARPP-19e	uc001eve.3	O43768	OTTHUMG00000035004	ENST00000369014.5:c.11A>C	chr1.hg19:g.150601936T>G	ENSP00000358010:p.Lys4Thr	108.0	0.0	.		76.0	35.0	.	NM_004436	A8K1Z9|E9PB69|Q5T5H2|Q68D48|Q6FHW0|Q6IAM4|Q6NUL2|Q6VUC6|Q6VUC7|Q6VUC8|Q6VUC9|Q6VUD0|Q6VUD1|Q9NRZ0	Missense_Mutation	SNP	ENST00000369014.5	hg19	CCDS958.1	.	.	.	.	.	.	.	.	.	.	T	18.08	3.543606	0.65198	.	.	ENSG00000143420	ENST00000369016;ENST00000369014;ENST00000369009;ENST00000339643;ENST00000271690;ENST00000356527;ENST00000502246;ENST00000503345;ENST00000503241;ENST00000362052	T	0.46063	0.88	5.78	3.46	0.39613	.	0.177686	0.48286	D	0.000183	T	0.26702	0.0653	L	0.40543	1.245	0.33054	D	0.533083	D;P;D;P;D	0.76494	0.999;0.728;0.982;0.534;0.99	P;B;P;B;P	0.60012	0.867;0.372;0.628;0.154;0.794	T	0.06679	-1.0813	10	0.16420	T	0.52	.	5.8762	0.18830	0.1492:0.0804:0.0:0.7704	.	4;4;4;4;4	A6NMQ3;O43768-8;E9PB69;O43768;O43768-3	.;.;.;ENSA_HUMAN;.	T	4	ENSP00000358012:K4T	ENSP00000271690:K4T	K	-	2	0	ENSA	148868560	1.000000	0.71417	0.998000	0.56505	0.671000	0.39405	3.104000	0.50306	1.004000	0.39156	-0.710000	0.03640	AAA	.	T|1.000;C|0.000	.	alt		0.662	ENSA-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000084720.2	NM_207042		G	150601936	T	G	150601936	3	3	130	1	0	0	0	0	1	0	0	0	5138	1841	64	5	610	5	ENSA	1	150601936	Missense_Mutation	SNP	T	TCGA-BQ-7044-01A-11D-1961-08	116421707	150601936	98648685	2	8038											
C2orf16	84226	hgsc.bcm.edu	37	chr2	27802751	27802751	+	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	ttaaggagtcaaatacccccCgatgtgcctccacctctagc	10	9	7	15	1	2	0	1	0	1	0	3	2	3	1	6	1	3	0	6	1	4	3	rs375978019	byFrequency	TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr2:27802751C>A	ENST00000408964.2	+	1	3363	c.3312C>A	c.(3310-3312)ccC>ccA	p.P1104P	AC074091.1_ENST00000408604.1_RNA	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1104						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)		p.P1104P(2)		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)					AAATACCCCCCGATGTGCCTC	0.448																																					p.P1104P		Atlas-SNP	.											C2orf16_ENST00000408964,NS,carcinoma,0,2	C2orf16	357	.	2	Substitution - coding silent(2)	lung(2)	c.C3312A						PASS	.						83	85	85					2																	27802751		1910	4127	6037	SO:0001819	synonymous_variant	84226	exon1			ACCCCCCGATGTG	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.3312C>A	chr2.hg19:g.27802751C>A		159.0	2.0	.		155.0	9.0	.	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Silent	SNP	ENST00000408964.2	hg19	CCDS42666.1																																																																																			.	.	.	alt		0.448	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		A	27802751	C	A	27802751	2	1	130	1	0	0	0	0	0	0	0	1	2159	639	23	4		4	C2orf16	2	27802751	Silent	SNP	C	TCGA-BQ-7044-01A-11D-1961-08		27802751	215396622	3	8039											
HEATR5B	54497	hgsc.bcm.edu	37	chr2	37235951	37235951	+	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	taattgctctttttggttttGactctgcttcctttttaata	6	23	5	7	0	2	1	0	1	2	0	3	1	3	1	1	1	2	3	1	1	3	11			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr2:37235951G>A	ENST00000233099.5	-	28	4420	c.4325C>T	c.(4324-4326)tCa>tTa	p.S1442L	HEATR5B_ENST00000354531.2_Missense_Mutation_p.S1442L	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1442						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)				TTTTGGTTTTGACTCTGCTTC	0.323																																					p.S1442L		Atlas-SNP	.											.	HEATR5B	185	.	0			c.C4325T						PASS	.						275	252	260					2																	37235951		2203	4300	6503	SO:0001583	missense	54497	exon28			GGTTTTGACTCTG	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.4325C>T	chr2.hg19:g.37235951G>A	ENSP00000233099:p.Ser1442Leu	243.0	0.0	.		196.0	83.0	.	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Missense_Mutation	SNP	ENST00000233099.5	hg19	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	G	16.34	3.096063	0.56075	.	.	ENSG00000008869	ENST00000233099;ENST00000354531	T;T	0.48201	0.82;0.82	5.75	4.87	0.63330	Armadillo-like helical (1);Armadillo-type fold (1);	0.421246	0.25753	N	0.028524	T	0.31071	0.0785	L	0.29908	0.895	0.35398	D	0.79138	B;B	0.28933	0.228;0.0	B;B	0.21546	0.035;0.002	T	0.33059	-0.9883	10	0.23891	T	0.37	-16.3124	9.1639	0.37038	0.0727:0.0:0.7809:0.1464	.	1442;1442	Q9P2D3-3;Q9P2D3	.;HTR5B_HUMAN	L	1442	ENSP00000233099:S1442L;ENSP00000346531:S1442L	ENSP00000233099:S1442L	S	-	2	0	HEATR5B	37089455	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.382000	0.66213	2.716000	0.92895	0.655000	0.94253	TCA	.	.	.	none		0.323	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		A	37235951	G	A	37235951	3	1	130	1	0	0	0	0	1	0	0	0	7039	1294	45	2	1926	2	HEATR5B	2	37235951	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	9433200	37235951	205963422	4	8040											
CLASP1	23332	hgsc.bcm.edu	37	chr2	122122716	122122716	+	Missense_Mutation	SNP	A	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	gcaggagcagaatggtcttgAagtgctcctcccagacacca	11	7	11	12	0	1	3	0	1	1	2	3	4	3	4	3	2	2	3	3	2	2	1			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr2:122122716A>C	ENST00000263710.4	-	36	4420	c.4031T>G	c.(4030-4032)tTc>tGc	p.F1344C	CLASP1_ENST00000397587.3_Missense_Mutation_p.F1284C|CLASP1_ENST00000545861.1_Missense_Mutation_p.F1051C|CLASP1_ENST00000409078.3_Missense_Mutation_p.F1277C|CLASP1_ENST00000541377.1_Missense_Mutation_p.F1283C|CLASP1_ENST00000541859.1_Missense_Mutation_p.F1061C|CLASP1_ENST00000455322.2_Missense_Mutation_p.F1300C	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	1344	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)					AATGGTCTTGAAGTGCTCCTC	0.557																																					p.F1344C		Atlas-SNP	.											.	CLASP1	135	.	0			c.T4031G						PASS	.						69	75	73					2																	122122716		2086	4216	6302	SO:0001583	missense	23332	exon35			GTCTTGAAGTGCT	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.4031T>G	chr2.hg19:g.122122716A>C	ENSP00000263710:p.Phe1344Cys	40.0	0.0	.		39.0	20.0	.	NM_015282	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Missense_Mutation	SNP	ENST00000263710.4	hg19		.	.	.	.	.	.	.	.	.	.	a	27.0	4.794213	0.90453	.	.	ENSG00000074054	ENST00000263710;ENST00000455322;ENST00000397587;ENST00000541377;ENST00000541859;ENST00000409078;ENST00000545861	T;T;T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3	5.57	5.57	0.84162	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.82678	0.5089	M	0.80616	2.505	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.91635	0.995;0.999;0.997;0.997	D	0.85278	0.1060	10	0.87932	D	0	-10.7425	16.0196	0.80472	1.0:0.0:0.0:0.0	.	1277;1284;1285;1344	E7EUA5;F5GWS0;A2RU21;Q7Z460	.;.;.;CLAP1_HUMAN	C	1344;1300;1284;1283;1061;1277;1051	ENSP00000263710:F1344C;ENSP00000389372:F1300C;ENSP00000380717:F1284C;ENSP00000441625:F1283C;ENSP00000441770:F1061C;ENSP00000386442:F1277C;ENSP00000438620:F1051C	ENSP00000263710:F1344C	F	-	2	0	CLASP1	121839186	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.927000	0.92846	2.249000	0.74217	0.454000	0.30748	TTC	.	.	.	none		0.557	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282		C	122122716	A	C	122122716	3	2	130	1	0	0	0	0	1	0	0	0	3456	246	9	5	605	5	CLASP1	2	122122716	Missense_Mutation	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	84886765	122122716	121076657	5	8041											
NFE2L2	4780	hgsc.bcm.edu	37	chr2	178098800	178098800	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggctgaattgggagaaatTcacctgtctcttcatctagt	9	14	9	9	0	4	2	2	1	2	1	5	3	4	2	1	2	0	1	1	2	3	4			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr2:178098800T>C	ENST00000397062.3	-	2	799	c.245A>G	c.(244-246)gAa>gGa	p.E82G	NFE2L2_ENST00000423513.1_Missense_Mutation_p.E66G|NFE2L2_ENST00000446151.2_Missense_Mutation_p.E66G|NFE2L2_ENST00000464747.1_Missense_Mutation_p.E66G|NFE2L2_ENST00000397063.4_Missense_Mutation_p.E66G	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	82					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E82G(3)|p.G81_F83delGEF(1)|p.E82V(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			TGGGAGAAATTCACCTGTCTC	0.433			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.E82G		Atlas-SNP	.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	NFE2L2,NS,carcinoma,+1,7	NFE2L2	225	.	5	Substitution - Missense(4)|Deletion - In frame(1)	liver(3)|lung(1)|oesophagus(1)	c.A245G						PASS	.						137	137	137					2																	178098800		1900	4105	6005	SO:0001583	missense	4780	exon2			AGAAATTCACCTG		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.245A>G	chr2.hg19:g.178098800T>C	ENSP00000380252:p.Glu82Gly	118.0	0.0	.		99.0	41.0	.	NM_006164	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	hg19	CCDS42782.1	.	.	.	.	.	.	.	.	.	.	T	29.9	5.048793	0.93740	.	.	ENSG00000116044	ENST00000397063;ENST00000397062;ENST00000446151;ENST00000448782;ENST00000421929;ENST00000423513	T;T;T;T;T;T	0.38077	1.57;1.57;1.57;1.16;1.16;1.57	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.66287	0.2774	M	0.87180	2.865	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.87578	0.997;0.994;0.998;0.997	T	0.72959	-0.4133	10	0.87932	D	0	.	16.098	0.81144	0.0:0.0:0.0:1.0	.	66;66;66;82	E9PGJ7;B4DNB0;C9JFL6;Q16236	.;.;.;NF2L2_HUMAN	G	66;82;66;66;66;66	ENSP00000380253:E66G;ENSP00000380252:E82G;ENSP00000411575:E66G;ENSP00000400073:E66G;ENSP00000412191:E66G;ENSP00000410015:E66G	ENSP00000380252:E82G	E	-	2	0	NFE2L2	177807046	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.503000	0.81632	2.210000	0.71456	0.460000	0.39030	GAA	.	.	.	none		0.433	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		C	178098800	T	C	178098800	3	2	130	1	0	0	0	0	1	0	0	0	10375	1783	62	3	1588	3	NFE2L2	2	178098800	Missense_Mutation	SNP	T	TCGA-BQ-7044-01A-11D-1961-08	55976084	178098800	65100573	6	8042											
ATIC	471	hgsc.bcm.edu	37	chr2	216211585	216211585	+	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	acaccatccacaagtgctttCgatgaagtttaaaacaggag	15	9	8	9	1	0	1	0	1	0	0	2	3	1	2	2	1	2	2	2	1	4	3	rs139340343	byFrequency	TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr2:216211585C>A	ENST00000236959.9	+	14	1750	c.1424C>A	c.(1423-1425)tCg>tAg	p.S475*	ATIC_ENST00000540518.1_Nonsense_Mutation_p.S416*|ATIC_ENST00000435675.1_Nonsense_Mutation_p.S474*	NM_004044.6	NP_004035.2	P31939	PUR9_HUMAN	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	475					'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|dihydrofolate metabolic process (GO:0046452)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	IMP cyclohydrolase activity (GO:0003937)|phosphoribosylaminoimidazolecarboxamide formyltransferase activity (GO:0004643)|protein homodimerization activity (GO:0042803)		ATIC/ALK(24)	large_intestine(2)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	8		Renal(323;0.229)		Epithelial(149;2.02e-06)|all cancers(144;0.000316)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.0097)	Methotrexate(DB00563)|Pemetrexed(DB00642)|Tetrahydrofolic acid(DB00116)	CAAGTGCTTTCGATGAAGTTT	0.473			T	ALK	ALCL																																p.S475X		Atlas-SNP	.		Dom	yes		2	2q35	471	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase		L	ATIC_ENST00000236959,NS,carcinoma,-1,1	ATIC	84	.	0			c.C1424A						PASS	.						163	146	152					2																	216211585		2203	4300	6503	SO:0001587	stop_gained	471	exon14			TGCTTTCGATGAA		CCDS2398.1	2q35	2010-04-27			ENSG00000138363	ENSG00000138363	2.1.2.3, 3.5.4.10		794	protein-coding gene	gene with protein product	"phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase"	601731				8567683, 9378707	Standard	NM_004044		Approved	PURH, AICARFT, IMPCHASE	uc002vex.4	P31939	OTTHUMG00000133023	ENST00000236959.9:c.1424C>A	chr2.hg19:g.216211585C>A	ENSP00000236959:p.Ser475*	147.0	1.0	.		121.0	5.0	.	NM_004044	A8K202|E9PBU3|Q13856|Q53S28	Nonsense_Mutation	SNP	ENST00000236959.9	hg19	CCDS2398.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.03|19.03	3.747041|3.747041	0.69418|0.69418	.|.	.|.	ENSG00000138363|ENSG00000138363	ENST00000446622;ENST00000426233|ENST00000236959;ENST00000540518;ENST00000435675	.|.	.|.	.|.	5.8|5.8	4.93|4.93	0.64822|0.64822	.|.	.|0.384948	.|0.29602	.|N	.|0.011699	T|.	0.44477|.	0.1295|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.52139|.	-0.8615|.	3|.	.|0.13853	.|T	.|0.58	-11.5275|-11.5275	10.9721|10.9721	0.47444|0.47444	0.0:0.8039:0.1284:0.0676|0.0:0.8039:0.1284:0.0676	.|.	.|.	.|.	.|.	L|X	168;143|475;416;474	.|.	.|ENSP00000236959:S475X	F|S	+|+	3|2	2|0	ATIC|ATIC	215919830|215919830	0.821000|0.821000	0.29204|0.29204	0.383000|0.383000	0.26132|0.26132	0.933000|0.933000	0.57130|0.57130	1.281000|1.281000	0.33214|0.33214	1.608000|1.608000	0.50180|0.50180	-0.128000|-0.128000	0.14901|0.14901	TTC|TCG	.	C|1.000;T|0.000	.	alt		0.473	ATIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256610.1	NM_004044		A	216211585	C	A	216211585	4	1	130	1	0	0	0	0	0	1	0	0	1105	893	31	4	1478	4	ATIC	2	216211585	Nonsense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08	38112785	216211585	26987788	7	8043											
FN1	2335	hgsc.bcm.edu	37	chr2	216289927	216289927	+	Missense_Mutation	SNP	A	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	agaccacaccactgtctgtgAcacagtggccatagggagga	12	6	12	11	0	1	2	0	1	1	1	1	4	1	4	3	3	0	0	3	3	1	1			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr2:216289927A>C	ENST00000359671.1	-	7	1191	c.926T>G	c.(925-927)gTc>gGc	p.V309G	FN1_ENST00000443816.1_Missense_Mutation_p.V309G|FN1_ENST00000357009.2_Missense_Mutation_p.V309G|FN1_ENST00000426059.1_Missense_Mutation_p.V309G|FN1_ENST00000346544.3_Missense_Mutation_p.V309G|FN1_ENST00000421182.1_Missense_Mutation_p.V309G|FN1_ENST00000345488.5_Missense_Mutation_p.V309G|FN1_ENST00000357867.4_Missense_Mutation_p.V309G|FN1_ENST00000446046.1_Missense_Mutation_p.V309G|FN1_ENST00000356005.4_Missense_Mutation_p.V309G|FN1_ENST00000354785.4_Missense_Mutation_p.V309G|FN1_ENST00000323926.6_Missense_Mutation_p.V309G|FN1_ENST00000336916.4_Missense_Mutation_p.V309G|FN1_ENST00000432072.2_Missense_Mutation_p.V309G			P02751	FINC_HUMAN	fibronectin 1	309	Collagen-binding.|Fibronectin type-I 6. {ECO:0000255|PROSITE-ProRule:PRU00478}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	ACTGTCTGTGACACAGTGGCC	0.557																																					p.V309G		Atlas-SNP	.											.	FN1	521	.	0			c.T926G						PASS	.						138	138	138					2																	216289927		2203	4300	6503	SO:0001583	missense	2335	exon7			TCTGTGACACAGT		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.926T>G	chr2.hg19:g.216289927A>C	ENSP00000352696:p.Val309Gly	267.0	1.0	.		224.0	90.0	.	NM_212476	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	hg19		.	.	.	.	.	.	.	.	.	.	A	21.6	4.179602	0.78564	.	.	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	0.44881	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;0.91	5.83	4.69	0.59074	.	0.187265	0.36303	N	0.002672	T	0.52108	0.1714	L	0.36672	1.1	0.80722	D	1	B;D;B;P;B;B;P;D;B;B;P	0.69078	0.055;0.997;0.09;0.891;0.25;0.294;0.593;0.97;0.25;0.25;0.935	B;D;B;P;B;B;B;P;B;B;P	0.80764	0.092;0.994;0.072;0.621;0.092;0.149;0.21;0.839;0.092;0.092;0.736	T	0.54609	-0.8268	10	0.87932	D	0	.	11.3208	0.49421	0.9296:0.0:0.0704:0.0	.	309;309;309;309;309;309;309;309;309;309;309	E9PG29;P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.;.	G	309	ENSP00000394423:V309G;ENSP00000323534:V309G;ENSP00000338200:V309G;ENSP00000350534:V309G;ENSP00000346839:V309G;ENSP00000352696:V309G;ENSP00000265312:V309G;ENSP00000273049:V309G;ENSP00000349509:V309G;ENSP00000410422:V309G;ENSP00000415018:V309G;ENSP00000399538:V309G;ENSP00000348285:V309G;ENSP00000398907:V309G	ENSP00000265313:V309G	V	-	2	0	FN1	215998172	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.190000	0.58365	2.231000	0.72958	0.460000	0.39030	GTC	.	.	.	none		0.557	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		C	216289927	A	C	216289927	3	2	130	1	0	0	0	0	1	0	0	0	5969	275	10	5	6700	5	FN1	2	216289927	Missense_Mutation	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	78342	216289927	26909446	8	8044											
SCN5A	6331	hgsc.bcm.edu	37	chr3	38645417	38645417	+	Missense_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	gccagggcaccagcagtgatGtgtggtggctctcgctctcc	5	9	14	13	1	2	1	0	1	2	0	4	1	2	1	3	3	1	4	3	3	0	0	rs199473575		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr3:38645417G>A	ENST00000333535.4	-	12	1825	c.1676C>T	c.(1675-1677)aCa>aTa	p.T559I	SCN5A_ENST00000449557.2_Missense_Mutation_p.T559I|SCN5A_ENST00000451551.2_Missense_Mutation_p.T559I|SCN5A_ENST00000413689.1_Missense_Mutation_p.T559I|SCN5A_ENST00000423572.2_Missense_Mutation_p.T559I|SCN5A_ENST00000443581.1_Missense_Mutation_p.T559I|SCN5A_ENST00000425664.1_Missense_Mutation_p.T559I|SCN5A_ENST00000450102.2_Missense_Mutation_p.T559I|SCN5A_ENST00000414099.2_Missense_Mutation_p.T559I|SCN5A_ENST00000455624.2_Missense_Mutation_p.T559I			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	559					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)	CAGCAGTGATGTGTGGTGGCT	0.622																																					p.T559I		Atlas-SNP	.											.	SCN5A	634	.	0			c.C1676T						PASS	.						49	55	53					3																	38645417		2086	4212	6298	SO:0001583	missense	6331	exon12			AGTGATGTGTGGT	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.1676C>T	chr3.hg19:g.38645417G>A	ENSP00000328968:p.Thr559Ile	77.0	0.0	.		67.0	35.0	.	NM_001160160	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Missense_Mutation	SNP	ENST00000333535.4	hg19	CCDS46796.1	.	.	.	.	.	.	.	.	.	.	G	15.26	2.780662	0.49891	.	.	ENSG00000183873	ENST00000414099;ENST00000423572;ENST00000413689;ENST00000451551;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624;ENST00000450102;ENST00000449557	D;D;D;D;D;D;D;D;D;D	0.90844	-2.74;-2.74;-2.74;-2.74;-2.74;-2.74;-2.74;-2.74;-2.74;-2.74	4.27	2.43	0.29744	Domain of unknown function DUF3451 (1);	0.879266	0.09862	N	0.746040	D	0.87014	0.6072	L	0.44542	1.39	0.29849	N	0.828558	B;P;B;B;P;P;P	0.43231	0.259;0.801;0.418;0.259;0.801;0.799;0.763	B;B;B;B;B;B;B	0.43360	0.041;0.417;0.051;0.059;0.192;0.371;0.293	T	0.81636	-0.0843	10	0.72032	D	0.01	.	6.1048	0.20067	0.1921:0.2795:0.5284:0.0	.	559;559;559;559;559;559;559	E9PEF3;E9PHB6;Q14524-6;E9PG18;Q14524;Q14524-2;E9PEK2	.;.;.;.;SCN5A_HUMAN;.;.	I	559	ENSP00000398962:T559I;ENSP00000398266:T559I;ENSP00000410257:T559I;ENSP00000388797:T559I;ENSP00000397915:T559I;ENSP00000416634:T559I;ENSP00000328968:T559I;ENSP00000399524:T559I;ENSP00000403355:T559I;ENSP00000413996:T559I	ENSP00000328968:T559I	T	-	2	0	SCN5A	38620421	0.911000	0.30947	0.896000	0.35187	0.619000	0.37552	1.714000	0.37961	1.020000	0.39573	-0.224000	0.12420	ACA	.	.	.	weak		0.622	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056		A	38645417	G	A	38645417	3	1	130	1	0	0	0	0	1	0	0	0	13935	1377	48	2	4442	2	SCN5A	3	38645417	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08		38645417	159377013	9	8045											
AFAP1	60312	hgsc.bcm.edu	37	chr4	7857226	7857226	+	Missense_Mutation	SNP	T	T	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	ttccggagcttttccggggcTcagcggcacagcttcctcat	5	11	11	14	3	2	0	2	0	0	0	5	1	5	1	3	4	3	4	3	4	0	4			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr4:7857226T>G	ENST00000360265.4	-	3	535	c.301A>C	c.(301-303)Agc>Cgc	p.S101R	AFAP1_ENST00000382543.3_Missense_Mutation_p.S101R|AFAP1_ENST00000358461.2_Missense_Mutation_p.S101R|AFAP1_ENST00000420658.1_Missense_Mutation_p.S101R			Q8N556	AFAP1_HUMAN	actin filament associated protein 1	101	Pro-rich.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(4)|stomach(2)	32						TTTCCGGGGCTCAGCGGCACA	0.562																																					p.S101R		Atlas-SNP	.											.	AFAP1	93	.	0			c.A301C						PASS	.						89	76	81					4																	7857226		2203	4300	6503	SO:0001583	missense	60312	exon4			CGGGGCTCAGCGG	AB209676	CCDS3397.1, CCDS47010.1	4p16	2014-02-12	2007-02-07		ENSG00000196526	ENSG00000196526		"Pleckstrin homology (PH) domain containing"	24017	protein-coding gene	gene with protein product		608252				14755689, 11641786, 11607843	Standard	NM_198595		Approved	AFAP-110, AFAP	uc011bwk.1	Q8N556	OTTHUMG00000125515	ENST00000360265.4:c.301A>C	chr4.hg19:g.7857226T>G	ENSP00000353402:p.Ser101Arg	88.0	0.0	.		60.0	26.0	.	NM_001134647	A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Missense_Mutation	SNP	ENST00000360265.4	hg19	CCDS3397.1	.	.	.	.	.	.	.	.	.	.	T	19.26	3.793690	0.70452	.	.	ENSG00000196526	ENST00000360265;ENST00000420658;ENST00000358461;ENST00000382543	T;T;T;T	0.47177	0.85;0.85;0.85;0.85	4.79	4.79	0.61399	.	0.087086	0.85682	D	0.000000	T	0.52403	0.1732	L	0.34521	1.04	0.43326	D	0.995356	D;D	0.67145	0.996;0.99	P;P	0.58577	0.719;0.841	T	0.56347	-0.7994	10	0.66056	D	0.02	-20.9708	13.3262	0.60461	0.0:0.0:0.0:1.0	.	101;101	E9PDT7;Q8N556	.;AFAP1_HUMAN	R	101	ENSP00000353402:S101R;ENSP00000410689:S101R;ENSP00000351245:S101R;ENSP00000371983:S101R	ENSP00000351245:S101R	S	-	1	0	AFAP1	7908126	1.000000	0.71417	0.975000	0.42487	0.988000	0.76386	3.466000	0.53071	1.780000	0.52325	0.459000	0.35465	AGC	.	.	.	none		0.562	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2	NM_021638		G	7857226	T	G	7857226	3	3	130	1	0	0	0	0	1	0	0	0	353	1551	54	5	2203	5	AFAP1	4	7857226	Missense_Mutation	SNP	T	TCGA-BQ-7044-01A-11D-1961-08		7857226	183297050	10	8046											
SLC10A4	201780	hgsc.bcm.edu	37	chr4	48490947	48490948	+	Frame_Shift_Ins	INS	-	-	TC																															tgatggaaaccgctcagactINStctctctaaatgtggagata																										TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr4:48490947_48490948insTC	ENST00000273861.4	+	3	1524_1525	c.1305_1306insTC	c.(1306-1308)tctfs	p.S436fs	ZAR1_ENST00000327939.4_5'Flank	NM_152679.3	NP_689892.1	Q96EP9	NTCP4_HUMAN	solute carrier family 10, member 4	436						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						CCGCTCAGACTTCTCTCTAAAT	0.351																																					p.T435fs		Atlas-INDEL	.											.,1	SLC10A4	23	.	0			c.1305_1306insTC						PASS	.																																			SO:0001589	frameshift_variant	201780	exon3			.	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.1310_1311dupTC	chr4.hg19:g.48490952_48490953dupTC	ENSP00000273861:p.Ser436fs	63.0	0.0	0		67.0	16.0	0.238806	NM_152679	Q8WUZ2	Frame_Shift_Ins	INS	ENST00000273861.4	hg19	CCDS3482.1																																																																																			.	.	.	none		0.351	SLC10A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219926.3	NM_152679		TC	48490948	-	TC	48490947	7	5	130	1	0	1	1	0	0	0	0	0	14389	1596	56	0	1315	0	SLC10A4	4	48490947	Frame_Shift_Ins	INS	-	TCGA-BQ-7044-01A-11D-1961-08	40633721	48490947	142663329	11	8047											
SMARCAD1	56916	hgsc.bcm.edu	37	chr4	95191935	95191935	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttggctggcattggtacataAacatggacttaatggcattt	11	14	10	6	0	0	0	0	0	0	0	0	1	0	1	0	5	2	4	0	5	4	6			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr4:95191935A>G	ENST00000354268.4	+	11	1611	c.1538A>G	c.(1537-1539)aAa>aGa	p.K513R	SMARCAD1_ENST00000509418.1_Missense_Mutation_p.K83R|SMARCAD1_ENST00000457823.2_Missense_Mutation_p.K513R			Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	513	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|chromosome separation (GO:0051304)|DNA double-strand break processing (GO:0000729)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|nucleotide metabolic process (GO:0009117)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|regulation of DNA recombination (GO:0000018)	heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|liver(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)		TTGGTACATAAACATGGACTT	0.343																																					p.K513R		Atlas-SNP	.											.	SMARCAD1	97	.	0			c.A1538G						PASS	.						198	186	190					4																	95191935		2203	4300	6503	SO:0001583	missense	56916	exon11			TACATAAACATGG	AB032948	CCDS3639.1, CCDS47101.1, CCDS58914.1	4q22-q23	2008-02-05			ENSG00000163104	ENSG00000163104			18398	protein-coding gene	gene with protein product		612761				11031099	Standard	NM_001128430		Approved	ETL1, DKFZP762K2015, KIAA1122, DKFZp762K2015	uc003htb.4	Q9H4L7	OTTHUMG00000130971	ENST00000354268.4:c.1538A>G	chr4.hg19:g.95191935A>G	ENSP00000346217:p.Lys513Arg	164.0	0.0	.		123.0	47.0	.	NM_001128429	B7Z799|Q05D56|Q96SX1|Q9H017|Q9H860|Q9NPU9|Q9ULU7	Missense_Mutation	SNP	ENST00000354268.4	hg19	CCDS3639.1	.	.	.	.	.	.	.	.	.	.	A	17.84	3.488315	0.64074	.	.	ENSG00000163104	ENST00000359052;ENST00000457823;ENST00000354268;ENST00000509418	D;D;D;D	0.93247	-3.19;-3.19;-3.19;-3.19	5.86	5.86	0.93980	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.46442	D	0.000282	D	0.85660	0.5748	N	0.03294	-0.36	0.54753	D	0.999987	B;B	0.32753	0.256;0.383	B;B	0.37091	0.241;0.155	D	0.84661	0.0706	10	0.23302	T	0.38	-27.7438	16.2652	0.82574	1.0:0.0:0.0:0.0	.	513;513	Q9H4L7;Q9H4L7-2	SMRCD_HUMAN;.	R	513;513;513;83	ENSP00000351947:K513R;ENSP00000415576:K513R;ENSP00000346217:K513R;ENSP00000423286:K83R	ENSP00000346217:K513R	K	+	2	0	SMARCAD1	95410958	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.861000	0.75478	2.241000	0.73720	0.528000	0.53228	AAA	.	.	.	none		0.343	SMARCAD1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253583.1	NM_020159		G	95191935	A	G	95191935	3	3	130	1	0	0	0	0	1	0	0	0	14785	14	1	3	1576	3	SMARCAD1	4	95191935	Missense_Mutation	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	46700988	95191935	95962341	12	8048											
PDZD2	23037	hgsc.bcm.edu	37	chr5	32108145	32108145	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctattaatgggaaacctctGgttgggctcatgcactttga	9	13	11	8	0	2	1	1	1	1	0	2	2	2	2	1	3	2	4	1	3	3	4			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr5:32108145G>A	ENST00000438447.1	+	25	8812	c.8424G>A	c.(8422-8424)ctG>ctA	p.L2808L	PDZD2_ENST00000282493.3_Silent_p.L2808L|CTD-2152M20.2_ENST00000503441.1_RNA|PDZD2_ENST00000513490.1_3'UTR			O15018	PDZD2_HUMAN	PDZ domain containing 2	2808	PDZ 6. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						GGAAACCTCTGGTTGGGCTCA	0.388																																					p.L2808L		Atlas-SNP	.											.	PDZD2	306	.	0			c.G8424A						PASS	.						129	134	133					5																	32108145		2203	4300	6503	SO:0001819	synonymous_variant	23037	exon24			ACCTCTGGTTGGG	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.8424G>A	chr5.hg19:g.32108145G>A		125.0	0.0	.		125.0	54.0	.	NM_178140	Q9BXD4	Silent	SNP	ENST00000438447.1	hg19	CCDS34137.1																																																																																			.	.	.	none		0.388	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			A	32108145	G	A	32108145	2	1	130	1	0	0	0	0	0	0	0	1	11708	1335	47	2		2	PDZD2	5	32108145	Silent	SNP	G	TCGA-BQ-7044-01A-11D-1961-08		32108145	148807115	13	8049											
POLK	51426	hgsc.bcm.edu	37	chr5	74872636	74872636	+	Missense_Mutation	SNP	A	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	acttgctgattatgatcccaAttttatggccatgagtcttg	9	16	8	8	0	1	3	0	3	1	0	2	3	2	3	2	1	1	1	2	1	3	5			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr5:74872636A>C	ENST00000241436.4	+	6	744	c.572A>C	c.(571-573)aAt>aCt	p.N191T	POLK_ENST00000506928.1_3'UTR|POLK_ENST00000515295.1_Missense_Mutation_p.N191T|POLK_ENST00000352007.5_Missense_Mutation_p.N191T|POLK_ENST00000508526.1_Missense_Mutation_p.N191T|POLK_ENST00000380481.3_Missense_Mutation_p.N101T|POLK_ENST00000504026.1_Missense_Mutation_p.N191T	NM_016218.2	NP_057302.1	Q9UBT6	POLK_HUMAN	polymerase (DNA directed) kappa	191	UmuC.				DNA repair (GO:0006281)|nucleotide-excision repair, DNA gap filling (GO:0006297)	nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)			endometrium(1)|kidney(4)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	27		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;2.9e-54)|all cancers(79;1.27e-42)		TATGATCCCAATTTTATGGCC	0.328								DNA polymerases (catalytic subunits)																													p.N191T		Atlas-SNP	.											.	POLK	123	.	0			c.A572C						PASS	.						72	70	71					5																	74872636		2203	4299	6502	SO:0001583	missense	51426	exon6			ATCCCAATTTTAT	AB027564	CCDS4030.1	5q13	2012-05-18			ENSG00000122008	ENSG00000122008		"DNA polymerases"	9183	protein-coding gene	gene with protein product	"polymerase (DNA-directed) kappa", "DINB protein", "DNA polymerase kappa"	605650		DINB1		10887153, 10518552	Standard	NM_016218		Approved	POLQ, DINP	uc003kdw.3	Q9UBT6	OTTHUMG00000102107	ENST00000241436.4:c.572A>C	chr5.hg19:g.74872636A>C	ENSP00000241436:p.Asn191Thr	79.0	0.0	.		54.0	24.0	.	NM_016218	B2RBD2|Q5Q9G5|Q5Q9G6|Q5Q9G7|Q5Q9G8|Q86VJ8|Q8IZY0|Q8IZY1|Q8NB30|Q96L01|Q96Q86|Q96Q87|Q9UHC5	Missense_Mutation	SNP	ENST00000241436.4	hg19	CCDS4030.1	.	.	.	.	.	.	.	.	.	.	A	19.74	3.883355	0.72410	.	.	ENSG00000122008	ENST00000241436;ENST00000352007;ENST00000515295;ENST00000504026;ENST00000508526;ENST00000380481	T;T;T;T;T;T	0.76060	-0.99;-0.99;-0.99;-0.99;-0.99;-0.99	5.34	5.34	0.76211	DNA-repair protein, UmuC-like, N-terminal (1);DNA-repair protein, UmuC-like (1);	0.296696	0.40064	N	0.001200	T	0.77987	0.4213	L	0.38175	1.15	0.42098	D	0.991328	P;P;P;D	0.53885	0.804;0.607;0.597;0.963	P;P;P;P	0.62740	0.663;0.653;0.624;0.906	T	0.80415	-0.1392	10	0.87932	D	0	-10.8466	11.291	0.49250	0.9266:0.0:0.0734:0.0	.	191;191;191;191	Q9UBT6-3;Q5Q9G5;Q9UBT6-2;Q9UBT6	.;.;.;POLK_HUMAN	T	191;191;191;191;191;101	ENSP00000241436:N191T;ENSP00000342256:N191T;ENSP00000424174:N191T;ENSP00000425075:N191T;ENSP00000426853:N191T;ENSP00000369848:N101T	ENSP00000241436:N191T	N	+	2	0	POLK	74908392	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.254000	0.65457	2.018000	0.59344	0.460000	0.39030	AAT	.	.	.	none		0.328	POLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219945.3	NM_016218		C	74872636	A	C	74872636	3	2	130	1	0	0	0	0	1	0	0	0	12211	101	4	5	590	5	POLK	5	74872636	Missense_Mutation	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	42764491	74872636	106042624	14	8050											
MAML1	9794	hgsc.bcm.edu	37	chr5	179192887	179192887	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctgccacacaaacccccttGgcacaggacattaatattaa	14	9	5	13	0	1	0	0	0	1	0	1	1	1	1	3	2	2	1	3	2	4	4			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr5:179192887G>A	ENST00000292599.3	+	2	1139	c.876G>A	c.(874-876)ttG>ttA	p.L292L	MAML1_ENST00000503050.1_3'UTR	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)											central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AAACCCCCTTGGCACAGGACA	0.527																																					p.L292L		Atlas-SNP	.											.	MAML1	118	.	0			c.G876A						PASS	.						63	71	68					5																	179192887		2203	4300	6503	SO:0001819	synonymous_variant	9794	exon2			CCCCTTGGCACAG	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.876G>A	chr5.hg19:g.179192887G>A		164.0	0.0	.		146.0	68.0	.	NM_014757		Silent	SNP	ENST00000292599.3	hg19	CCDS34315.1																																																																																			.	.	.	none		0.527	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757		A	179192887	G	A	179192887	2	1	130	1	0	0	0	0	0	0	0	1	9212	1339	47	2		2	MAML1	5	179192887	Silent	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	104320251	179192887	1722373	15	8051											
BAT2	7916	hgsc.bcm.edu	37	chr6	31595867	31595867	+	Missense_Mutation	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	agctccacctccagcatcagCcccaacaccagagacagaac	14	3	6	18	0	1	2	1	0	0	2	3	3	3	2	6	0	5	2	6	0	2	0			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr6:31595867C>T	ENST00000376033.2	+	12	1850	c.1616C>T	c.(1615-1617)gCc>gTc	p.A539V	PRRC2A_ENST00000376007.4_Missense_Mutation_p.A539V	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	539	2 X type B repeats.|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						CCAGCATCAGCCCCAACACCA	0.627																																					p.A539V		Atlas-SNP	.											.	PRRC2A	152	.	0			c.C1616T						PASS	.						127	114	119					6																	31595867		1511	2709	4220	SO:0001583	missense	7916	exon12			CATCAGCCCCAAC	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.1616C>T	chr6.hg19:g.31595867C>T	ENSP00000365201:p.Ala539Val	159.0	0.0	.		136.0	55.0	.	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	hg19	CCDS4708.1	.	.	.	.	.	.	.	.	.	.	C	9.670	1.146580	0.21288	.	.	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033	T;T	0.08102	3.13;3.13	4.62	0.771	0.18504	.	0.843533	0.10340	N	0.686385	T	0.00967	0.0032	N	0.02011	-0.69	0.24306	N	0.995104	B	0.02656	0.0	B	0.04013	0.001	T	0.48269	-0.9050	10	0.87932	D	0	-0.1078	6.2328	0.20744	0.0:0.5543:0.0:0.4457	.	539	P48634	PRC2A_HUMAN	V	539;528;539;539	ENSP00000365175:A539V;ENSP00000365201:A539V	ENSP00000365175:A539V	A	+	2	0	PRRC2A	31703846	0.098000	0.21812	0.464000	0.27143	0.840000	0.47671	1.319000	0.33655	0.269000	0.21961	0.561000	0.74099	GCC	.	.	.	none		0.627	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686		T	31595867	C	T	31595867	3	4	130	1	0	0	0	0	1	0	0	0	1319	739	26	2	1658	2	BAT2	6	31595867	Missense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08		31595867	139519200	16	8052											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51917922	51917922	+	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	ttcatccacatagaacaggcCcgtctcctgggccagaggga	10	7	11	13	1	2	2	1	0	1	2	4	3	3	3	4	3	1	0	4	3	2	2			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr6:51917922C>T	ENST00000371117.3	-	21	2367	c.2092G>A	c.(2092-2094)Ggc>Agc	p.G698S	PKHD1_ENST00000340994.4_Missense_Mutation_p.G698S	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	698					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)					TAGAACAGGCCCGTCTCCTGG	0.517																																					p.G698S		Atlas-SNP	.											.	PKHD1	927	.	0			c.G2092A						PASS	.						72	73	73					6																	51917922		2203	4300	6503	SO:0001583	missense	5314	exon21			ACAGGCCCGTCTC	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.2092G>A	chr6.hg19:g.51917922C>T	ENSP00000360158:p.Gly698Ser	85.0	0.0	.		62.0	25.0	.	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	14.36	2.511891	0.44660	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.86865	-1.97;-2.18	5.63	3.77	0.43336	.	0.810468	0.11546	N	0.553288	T	0.63141	0.2486	L	0.33485	1.01	0.09310	N	1	B;B	0.20887	0.047;0.049	B;B	0.16289	0.015;0.012	T	0.50734	-0.8793	10	0.13108	T	0.6	.	9.2695	0.37661	0.0:0.7612:0.0:0.2388	.	698;698	P08F94-2;P08F94	.;PKHD1_HUMAN	S	698	ENSP00000360158:G698S;ENSP00000341097:G698S	ENSP00000341097:G698S	G	-	1	0	PKHD1	52025881	0.000000	0.05858	0.012000	0.15200	0.396000	0.30629	0.272000	0.18644	1.462000	0.47948	0.655000	0.94253	GGC	.	.	.	none		0.517	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		T	51917922	C	T	51917922	3	4	130	1	0	0	0	0	1	0	0	0	11978	623	22	2	10359	2	PKHD1	6	51917922	Missense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08	20322055	51917922	119197145	17	8053											
CLIP2	7461	hgsc.bcm.edu	37	chr7	73752800	73752800	+	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	tccccactgcacaaacagtcAtctggaccctcctcctcccc	8	8	4	21	0	2	0	1	0	1	0	6	1	6	1	7	1	2	1	7	1	1	0			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr7:73752800A>T	ENST00000395060.1	+	2	144	c.144A>T	c.(142-144)tcA>tcT	p.S48S	CLIP2_ENST00000223398.6_Silent_p.S48S|CLIP2_ENST00000361545.5_Silent_p.S48S			Q9UDT6	CLIP2_HUMAN	CAP-GLY domain containing linker protein 2	48						cytoplasmic microtubule (GO:0005881)|microtubule associated complex (GO:0005875)|microtubule plus-end (GO:0035371)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|pancreas(1)|prostate(2)|skin(3)	30						ACAAACAGTCATCTGGACCCT	0.657																																					p.S48S		Atlas-SNP	.											.	CLIP2	134	.	0			c.A144T						PASS	.						21	17	18					7																	73752800		2195	4292	6487	SO:0001819	synonymous_variant	7461	exon3			ACAGTCATCTGGA	AB006629	CCDS5569.1, CCDS5570.1	7q11.23	2008-06-12	2007-01-04	2007-01-04	ENSG00000106665	ENSG00000106665			2586	protein-coding gene	gene with protein product		603432	"cytoplasmic linker 2", "Williams-Beuren syndrome chromosome region 3"	WBSCR4, CYLN2, WBSCR3		8812460, 9799601	Standard	NM_003388		Approved	CLIP-115, KIAA0291, WSCR4, CLIP, WSCR3	uc003uam.3	Q9UDT6	OTTHUMG00000022980	ENST00000395060.1:c.144A>T	chr7.hg19:g.73752800A>T		19.0	0.0	.		29.0	18.0	.	NM_032421	O14527|O43611	Silent	SNP	ENST00000395060.1	hg19	CCDS5569.1																																																																																			.	.	.	none		0.657	CLIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252556.1	NM_003388		T	73752800	A	T	73752800	2	4	130	1	0	0	0	0	0	0	0	1	3535	204	8	5		5	CLIP2	7	73752800	Silent	SNP	A	TCGA-BQ-7044-01A-11D-1961-08		73752800	85385863	18	8054											
UFSP1	402682	hgsc.bcm.edu	37	chr7	100486530	100486530	+	Frame_Shift_Del	DEL	G	G	-																															cacaggttgtagaaggagttGgggtcaaaggctgcactcac																								rs372960530		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr7:100486530delG	ENST00000388761.2	-	1	809	c.363delC	c.(361-363)cccfs	p.P121fs		NM_001015072.3	NP_001015072.2	Q6NVU6	UFSP1_HUMAN	UFM1-specific peptidase 1 (non-functional)	121						extracellular vesicular exosome (GO:0070062)	thiolester hydrolase activity (GO:0016790)|UFM1 hydrolase activity (GO:0071567)			lung(1)|stomach(1)	2	Lung NSC(181;0.041)|all_lung(186;0.0581)					AGAAGGAGTTGGGGTCAAAGG	0.567																																					p.N122fs		Atlas-INDEL	.											.	UFSP1	8	.	0			c.364delA						PASS	.						181	154	163					7																	100486530		2203	4300	6503	SO:0001589	frameshift_variant	402682	exon1			.	AF312032	CCDS34710.1	7q22.1	2008-03-25			ENSG00000176125	ENSG00000176125			33821	protein-coding gene	gene with protein product		611481				17182609, 18321862	Standard	NM_001015072		Approved	UFSP	uc003uxc.4	Q6NVU6	OTTHUMG00000159662	ENST00000388761.2:c.363delC	chr7.hg19:g.100486530delG	ENSP00000373413:p.Pro121fs	153.0	0.0	0		197.0	106.0	0.538071	NM_001015072	A4D2E4|A8K8V2|B6ZDG6|Q9BXP6	Frame_Shift_Del	DEL	ENST00000388761.2	hg19	CCDS34710.1																																																																																			.	.	.	none		0.567	UFSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356751.1	NM_001015072		-	100486530	G	-	100486530	7	5	130	1	0	1	0	1	0	0	0	0	16949	1335	47	0	69	0	UFSP1	7	100486530	Frame_Shift_Del	DEL	G	TCGA-BQ-7044-01A-11D-1961-08	26733730	100486530	58652133	19	8055											
CHCHD3	54927	hgsc.bcm.edu	37	chr7	132754922	132754922	+	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	ctgaggcaccataagcaccaGaataccgctgagacttcgaa	14	6	9	12	2	0	3	0	2	0	2	1	5	0	3	3	1	2	3	3	1	4	3			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr7:132754922G>A	ENST00000262570.5	-	2	293	c.149C>T	c.(148-150)tCt>tTt	p.S50F	CHCHD3_ENST00000542753.1_Missense_Mutation_p.S50F|CHCHD3_ENST00000476546.1_Intron|CHCHD3_ENST00000448878.1_Missense_Mutation_p.S50F	NM_017812.2	NP_060282.1	Q9NX63	MIC19_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 3	50					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						ATAAGCACCAGAATACCGCTG	0.353																																					p.S50F		Atlas-SNP	.											.	CHCHD3	21	.	0			c.C149T						PASS	.						79	69	72					7																	132754922		2203	4300	6503	SO:0001583	missense	54927	exon2			GCACCAGAATACC	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.149C>T	chr7.hg19:g.132754922G>A	ENSP00000262570:p.Ser50Phe	71.0	0.0	.		82.0	17.0	.	NM_017812		Missense_Mutation	SNP	ENST00000262570.5	hg19	CCDS5828.1	.	.	.	.	.	.	.	.	.	.	G	12.56	1.975118	0.34848	.	.	ENSG00000106554	ENST00000262570;ENST00000448878;ENST00000542753	T;T;T	0.46451	0.87;0.87;0.87	6.03	6.03	0.97812	.	0.483083	0.24301	N	0.039727	T	0.55513	0.1925	L	0.43152	1.355	0.23841	N	0.996695	B;D;B	0.65815	0.006;0.995;0.004	B;D;B	0.63283	0.006;0.913;0.007	T	0.51553	-0.8691	10	0.66056	D	0.02	-0.3383	16.0569	0.80812	0.0:0.0:1.0:0.0	.	50;50;50	G3V1K1;C9JRZ6;Q9NX63	.;.;CHCH3_HUMAN	F	50	ENSP00000262570:S50F;ENSP00000389297:S50F;ENSP00000440267:S50F	ENSP00000262570:S50F	S	-	2	0	CHCHD3	132405462	1.000000	0.71417	0.739000	0.30968	0.676000	0.39594	3.255000	0.51484	2.861000	0.98227	0.655000	0.94253	TCT	.	.	.	none		0.353	CHCHD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000338899.1	NM_017812		A	132754922	G	A	132754922	3	1	130	1	0	0	0	0	1	0	0	0	3319	942	33	2	562	2	CHCHD3	7	132754922	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	32268392	132754922	26383741	20	8056											
EXOC4	60412	hgsc.bcm.edu	37	chr7	133692515	133692515	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctggcatcaagaaaatgtgtAggaacatttttgttcttcag	12	14	9	6	0	3	1	2	0	1	1	3	2	3	2	0	2	1	3	0	2	5	5			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr7:133692515A>G	ENST00000253861.4	+	17	2643	c.2614A>G	c.(2614-2616)Agg>Ggg	p.R872G	EXOC4_ENST00000539845.1_Missense_Mutation_p.R771G|EXOC4_ENST00000545148.1_Missense_Mutation_p.R482G|EXOC4_ENST00000541309.1_Missense_Mutation_p.R160G	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	872					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)				GAAAATGTGTAGGAACATTTT	0.502																																					p.R872G		Atlas-SNP	.											.	EXOC4	118	.	0			c.A2614G						PASS	.						85	71	76					7																	133692515		2203	4300	6503	SO:0001583	missense	60412	exon17			ATGTGTAGGAACA	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.2614A>G	chr7.hg19:g.133692515A>G	ENSP00000253861:p.Arg872Gly	63.0	0.0	.		83.0	36.0	.	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Missense_Mutation	SNP	ENST00000253861.4	hg19	CCDS5829.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.958834	0.74016	.	.	ENSG00000131558	ENST00000253861;ENST00000546185;ENST00000539845;ENST00000545148;ENST00000541309	.	.	.	5.45	2.87	0.33458	.	0.000000	0.85682	D	0.000000	T	0.78020	0.4218	M	0.84082	2.675	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.984;0.998;0.996	T	0.81075	-0.1097	9	0.66056	D	0.02	.	11.6561	0.51320	0.7492:0.2508:0.0:0.0	.	404;482;872	B7Z689;F5GZT1;Q96A65	.;.;EXOC4_HUMAN	G	872;491;771;482;160	.	ENSP00000253861:R872G	R	+	1	2	EXOC4	133343055	0.966000	0.33281	0.990000	0.47175	0.984000	0.73092	1.330000	0.33781	2.078000	0.62432	0.482000	0.46254	AGG	.	.	.	none		0.502	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807		G	133692515	A	G	133692515	3	3	130	1	0	0	0	0	1	0	0	0	5308	411	15	3	2689	3	EXOC4	7	133692515	Missense_Mutation	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	937593	133692515	25446148	21	8057											
MGAM	8972	hgsc.bcm.edu	37	chr7	141750617	141750617	+	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	ttacagtgaaacacaatggtGtcccaagtcagacttctcct	12	11	7	11	0	2	2	1	1	1	1	4	2	3	2	2	1	2	0	2	1	4	2			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr7:141750617G>T	ENST00000549489.2	+	24	2853	c.2758G>T	c.(2758-2760)Gtc>Ttc	p.V920F	MGAM_ENST00000475668.2_Missense_Mutation_p.V920F	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	920					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)	ACACAATGGTGTCCCAAGTCA	0.388																																					p.V920F		Atlas-SNP	.											.	MGAM	767	.	0			c.G2758T						PASS	.						105	95	98					7																	141750617		1869	4101	5970	SO:0001583	missense	8972	exon24			AATGGTGTCCCAA	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.2758G>T	chr7.hg19:g.141750617G>T	ENSP00000447378:p.Val920Phe	147.0	0.0	.		196.0	41.0	.	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	hg19	CCDS47727.1	.	.	.	.	.	.	.	.	.	.	G	11.17	1.560136	0.27827	.	.	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	D	0.89681	-2.55	5.81	0.962	0.19643	.	1.575090	0.03884	N	0.277575	D	0.86464	0.5939	M	0.62266	1.93	0.09310	N	1	B	0.27791	0.189	B	0.18561	0.022	T	0.66296	-0.5959	10	0.24483	T	0.36	.	9.7694	0.40580	0.4125:0.0:0.5875:0.0	.	920	O43451	MGA_HUMAN	F	920;920;797	ENSP00000447378:V920F	ENSP00000316431:V797F	V	+	1	0	MGAM	141397086	0.000000	0.05858	0.000000	0.03702	0.389000	0.30415	0.254000	0.18314	-0.105000	0.12132	-0.336000	0.08194	GTC	.	.	.	none		0.388	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			T	141750617	G	T	141750617	3	4	130	1	0	0	0	0	1	0	0	0	9548	1377	48	4	2848	4	MGAM	7	141750617	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	8058102	141750617	17388046	22	8058											
LZTS1	11178	hgsc.bcm.edu	37	chr8	20107305	20107305	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcaacctccaagggctccccGgcgctgtccccacgtgccag	6	6	10	19	3	1	0	1	0	0	0	4	0	4	0	7	2	2	2	7	2	2	0			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr8:20107305G>A	ENST00000381569.1	-	4	2076	c.1719C>T	c.(1717-1719)gcC>gcT	p.A573A	LZTS1_ENST00000265801.6_Silent_p.A573A|LZTS1_ENST00000522290.1_Silent_p.A514A			Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1	573					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)		AGGGCTCCCCGGCGCTGTCCC	0.632																																					p.A573A		Atlas-SNP	.											.	LZTS1	72	.	0			c.C1719T						PASS	.						83	82	82					8																	20107305		2203	4300	6503	SO:0001819	synonymous_variant	11178	exon3			CTCCCCGGCGCTG	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.1719C>T	chr8.hg19:g.20107305G>A		132.0	0.0	.		124.0	56.0	.	NM_021020	D3DSQ6|Q9Y5V7|Q9Y5V8|Q9Y5V9|Q9Y5W0|Q9Y5W1|Q9Y5W2	Silent	SNP	ENST00000381569.1	hg19	CCDS6015.1																																																																																			.	.	.	none		0.632	LZTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214122.1	NM_021020		A	20107305	G	A	20107305	2	1	130	1	0	0	0	0	0	0	0	1	9145	1103	39	1		1	LZTS1	8	20107305	Silent	SNP	G	TCGA-BQ-7044-01A-11D-1961-08		20107305	126256717	23	8059											
PPP2R2A	5520	hgsc.bcm.edu	37	chr8	26227846	26227849	+	Frame_Shift_Del	DEL	CACA	CACA	-																															acttcaataagaaaatccttCacacagcctggcaccccaag																										TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	CACA	CACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr8:26227846_26227849delCACA	ENST00000380737.3	+	10	1590_1593	c.1261_1264delCACA	c.(1261-1266)cacacafs	p.HT421fs	PPP2R2A_ENST00000315985.7_Frame_Shift_Del_p.HT431fs	NM_002717.3	NP_002708.1	P63151	2ABA_HUMAN	protein phosphatase 2, regulatory subunit B, alpha	421					G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|response to morphine (GO:0043278)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			kidney(1)|large_intestine(2)|ovary(1)	4		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		GAAAATCCTTCACACAGCCTGGCA	0.426																																					p.430_431del		Atlas-INDEL	.											.	PPP2R2A	44	.	0			c.1290_1293del						PASS	.																																			SO:0001589	frameshift_variant	5520	exon10			.	M64929	CCDS34867.1, CCDS55213.1	8p21.2	2013-01-10	2010-04-14		ENSG00000221914	ENSG00000221914	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "WD repeat domain containing"	9304	protein-coding gene	gene with protein product	"PP2A subunit B isoform alpha"	604941	"protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), alpha isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B, alpha isoform"			1849734	Standard	NM_001177591		Approved	PR52A, PR55A, B55A		P63151	OTTHUMG00000163850	ENST00000380737.3:c.1261_1264delCACA	chr8.hg19:g.26227846_26227849delCACA	ENSP00000370113:p.His421fs	51.0	0.0	0		45.0	11.0	0.244444	NM_001177591	B2RBU8|B4E1T7|P50409|Q00007	Frame_Shift_Del	DEL	ENST00000380737.3	hg19	CCDS34867.1																																																																																			.	.	.	none		0.426	PPP2R2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375954.2	NM_002717		-	26227849	CACA	-	26227846	7	5	130	1	0	1	0	1	0	0	0	0	12394	826	29	0	1340	0	PPP2R2A	8	26227846	Frame_Shift_Del	DEL	CACA	TCGA-BQ-7044-01A-11D-1961-08	6120541	26227846	120136176	24	8060											
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110451259	110451259	+	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	attagatgccttttgcccaaGttgtctcctggaaaacatga	11	13	8	9	0	1	2	0	1	1	1	2	3	1	3	3	1	3	1	3	1	4	4			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr8:110451259G>A	ENST00000378402.5	+	32	3998	c.3894G>A	c.(3892-3894)aaG>aaA	p.K1298K		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1298	IPT/TIG 6.				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)			TTTTGCCCAAGTTGTCTCCTG	0.393										HNSCC(38;0.096)																											p.K1298K		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.G3894A						PASS	.						141	137	138					8																	110451259		1844	4085	5929	SO:0001819	synonymous_variant	93035	exon32			GCCCAAGTTGTCT	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.3894G>A	chr8.hg19:g.110451259G>A		249.0	0.0	.		212.0	81.0	.	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	hg19	CCDS47911.1																																																																																			.	.	.	none		0.393	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		A	110451259	G	A	110451259	2	1	130	1	0	0	0	0	0	0	0	1	11979	1020	36	2		2	PKHD1L1	8	110451259	Silent	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	84223413	110451259	35912763	25	8061											
NMT2	9397	hgsc.bcm.edu	37	chr10	15154953	15154953	+	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	caggaaatcagtcagtttacCgttggggctctaggagcaaa	12	9	12	8	1	3	0	2	0	1	0	3	2	3	2	1	4	2	4	1	4	4	4	rs201047504		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr10:15154953C>A	ENST00000378165.4	-	10	1260	c.1180G>T	c.(1180-1182)Ggt>Tgt	p.G394C	RPP38_ENST00000451677.1_Intron|NMT2_ENST00000535341.1_Missense_Mutation_p.G381C|NMT2_ENST00000540259.1_Missense_Mutation_p.G206C|NMT2_ENST00000378150.1_Missense_Mutation_p.G381C	NM_004808.2	NP_004799.1	O60551	NMT2_HUMAN	N-myristoyltransferase 2	394					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)	p.G394S(1)		breast(3)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(3)	21						GTCAGTTTACCGTTGGGGCTC	0.512																																					p.G394C	Melanoma(117;1345 1645 4130 12688 30625)	Atlas-SNP	.											NMT2,NS,carcinoma,0,1	NMT2	44	.	1	Substitution - Missense(1)	lung(1)	c.G1180T						PASS	.						153	150	151					10																	15154953		2203	4300	6503	SO:0001583	missense	9397	exon10			GTTTACCGTTGGG	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.1180G>T	chr10.hg19:g.15154953C>A	ENSP00000367407:p.Gly394Cys	144.0	2.0	.		121.0	8.0	.	NM_004808	B0YJ49|Q53Y38|Q5VUC8|Q9BRB4	Missense_Mutation	SNP	ENST00000378165.4	hg19	CCDS7109.1	.	.	.	.	.	.	.	.	.	.	C	18.14	3.557561	0.65425	.	.	ENSG00000152465	ENST00000378165;ENST00000378150;ENST00000378143;ENST00000540259;ENST00000535341	T	0.50813	0.73	5.74	5.74	0.90152	Acyl-CoA N-acyltransferase (2);Myristoyl-CoA:protein N-myristoyltransferase, C-terminal (1);	0.095052	0.64402	D	0.000001	T	0.77718	0.4172	M	0.92169	3.28	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.76071	0.987;0.984;0.984	T	0.82653	-0.0351	10	0.87932	D	0	-20.1679	19.9332	0.97128	0.0:1.0:0.0:0.0	.	394;381;394	B2RCF3;Q5VUC6;O60551	.;.;NMT2_HUMAN	C	394;381;425;206;381	ENSP00000367407:G394C	ENSP00000367385:G425C	G	-	1	0	NMT2	15194959	1.000000	0.71417	0.995000	0.50966	0.124000	0.20399	7.380000	0.79704	2.702000	0.92279	0.655000	0.94253	GGT	.	.	.	alt		0.512	NMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046958.2	NM_004808		A	15154953	C	A	15154953	3	1	130	1	0	0	0	0	1	0	0	0	10511	652	23	4	328	4	NMT2	10	15154953	Missense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08		15154953	120379794	26	8062											
SLC16A9	220963	hgsc.bcm.edu	37	chr10	61413807	61413807	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcttgctacatcttccataAgtaatgaaggtggaaaccct	12	13	7	9	0	2	1	0	1	2	0	3	2	3	2	2	2	3	2	2	2	5	6			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr10:61413807A>G	ENST00000395348.3	-	5	1613	c.977T>C	c.(976-978)cTt>cCt	p.L326P	SLC16A9_ENST00000395347.1_Missense_Mutation_p.L326P	NM_194298.2	NP_919274.1	Q7RTY1	MOT9_HUMAN	solute carrier family 16, member 9	326					urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			kidney(3)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	23						ATCTTCCATAAGTAATGAAGG	0.363																																					p.L326P		Atlas-SNP	.											.	SLC16A9	58	.	0			c.T977C						PASS	.						55	52	53					10																	61413807		2203	4300	6503	SO:0001583	missense	220963	exon5			TCCATAAGTAATG	AK125791	CCDS7256.1	10q21.3	2013-07-18	2013-07-18	2004-01-21	ENSG00000165449	ENSG00000165449		"Solute carriers"	23520	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 9"	614242	"chromosome 10 open reading frame 36", "solute carrier family 16 (monocarboxylic acid transporters), member 9", "solute carrier family 16, member 9 (monocarboxylic acid transporter 9)"	C10orf36			Standard	NM_194298		Approved	FLJ43803, MCT9	uc010qig.1	Q7RTY1	OTTHUMG00000018283	ENST00000395348.3:c.977T>C	chr10.hg19:g.61413807A>G	ENSP00000378757:p.Leu326Pro	55.0	0.0	.		77.0	29.0	.	NM_194298	Q6ZMI2|Q9UFH8	Missense_Mutation	SNP	ENST00000395348.3	hg19	CCDS7256.1	.	.	.	.	.	.	.	.	.	.	A	17.33	3.362232	0.61403	.	.	ENSG00000165449	ENST00000395348;ENST00000395347	T;T	0.34472	1.36;1.36	4.73	4.73	0.59995	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.164197	0.56097	D	0.000037	T	0.51534	0.1680	L	0.44542	1.39	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	T	0.54186	-0.8331	10	0.66056	D	0.02	.	14.2093	0.65755	1.0:0.0:0.0:0.0	.	326	Q7RTY1	MOT9_HUMAN	P	326	ENSP00000378757:L326P;ENSP00000378756:L326P	ENSP00000378756:L326P	L	-	2	0	SLC16A9	61083813	1.000000	0.71417	0.974000	0.42286	0.984000	0.73092	8.962000	0.93254	1.751000	0.51876	0.482000	0.46254	CTT	.	.	.	none		0.363	SLC16A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048174.2	NM_194298		G	61413807	A	G	61413807	3	3	130	1	0	0	0	0	1	0	0	0	14428	72	3	3	560	3	SLC16A9	10	61413807	Missense_Mutation	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	46258854	61413807	74120940	27	8063											
PDLIM1	9124	hgsc.bcm.edu	37	chr10	96998413	96998413	+	Missense_Mutation	SNP	T	T	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	agtgacaggagctttaacacTtctgaatcctgagggcttgt	10	12	11	8	0	1	3	0	3	1	0	2	4	2	4	1	2	2	2	1	2	2	4			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr10:96998413T>G	ENST00000329399.6	-	6	823	c.715A>C	c.(715-717)Agt>Cgt	p.S239R	PDLIM1_ENST00000477757.1_5'UTR	NM_020992.2	NP_066272.1	O00151	PDLI1_HUMAN	PDZ and LIM domain 1	239					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)		GCTTTAACACTTCTGAATCCT	0.468																																					p.S239R		Atlas-SNP	.											.	PDLIM1	33	.	0			c.A715C						PASS	.						94	84	87					10																	96998413		2203	4300	6503	SO:0001583	missense	9124	exon6			TAACACTTCTGAA	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.715A>C	chr10.hg19:g.96998413T>G	ENSP00000360305:p.Ser239Arg	64.0	0.0	.		66.0	26.0	.	NM_020992	B2RBS6|Q5VZH5|Q9BPZ9	Missense_Mutation	SNP	ENST00000329399.6	hg19	CCDS7441.1	.	.	.	.	.	.	.	.	.	.	T	29.2	4.985379	0.93044	.	.	ENSG00000107438	ENST00000329399	T	0.22134	1.97	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.45337	0.1337	M	0.85859	2.78	0.80722	D	1	D	0.61697	0.99	P	0.57101	0.813	T	0.53578	-0.8419	10	0.66056	D	0.02	-13.9009	14.2967	0.66318	0.0:0.0:0.0:1.0	.	239	O00151	PDLI1_HUMAN	R	239	ENSP00000360305:S239R	ENSP00000360305:S239R	S	-	1	0	PDLIM1	96988403	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.927000	0.87577	1.978000	0.57642	0.454000	0.30748	AGT	.	.	.	none		0.468	PDLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049508.1			G	96998413	T	G	96998413	3	3	130	1	0	0	0	0	1	0	0	0	11686	1609	56	5	282	5	PDLIM1	10	96998413	Missense_Mutation	SNP	T	TCGA-BQ-7044-01A-11D-1961-08	35584606	96998413	38536334	28	8064											
DNMBP	23268	hgsc.bcm.edu	37	chr10	101646325	101646325	+	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	gtttctgtaccagcttatggGgccctgtaaacatgctcagt	8	13	10	10	0	2	0	1	0	1	0	2	0	2	0	2	2	4	5	2	2	4	4			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr10:101646325G>C	ENST00000324109.4	-	13	3441	c.3350C>G	c.(3349-3351)cCc>cGc	p.P1117R	DNMBP_ENST00000540316.1_Missense_Mutation_p.P53R|DNMBP_ENST00000472036.1_5'UTR|DNMBP_ENST00000342239.3_Missense_Mutation_p.P1141R|DNMBP_ENST00000543621.1_Missense_Mutation_p.P363R	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	1117	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		CAGCTTATGGGGCCCTGTAAA	0.502																																					p.P1117R		Atlas-SNP	.											.	DNMBP	173	.	0			c.C3350G						PASS	.						116	115	115					10																	101646325		2203	4300	6503	SO:0001583	missense	23268	exon13			TTATGGGGCCCTG	AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554		"Rho guanine nucleotide exchange factors"	30373	protein-coding gene	gene with protein product	"scaffold protein TUBA"	611282				10231032, 14506234	Standard	NM_015221		Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.3350C>G	chr10.hg19:g.101646325G>C	ENSP00000315659:p.Pro1117Arg	256.0	0.0	.		236.0	80.0	.	NM_015221	Q8IVY3|Q9Y2L3	Missense_Mutation	SNP	ENST00000324109.4	hg19	CCDS7485.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.990069	0.93106	.	.	ENSG00000107554	ENST00000342239;ENST00000324109;ENST00000393570;ENST00000543621;ENST00000540316	T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1	5.82	5.82	0.92795	BAR (3);	0.000000	0.48286	D	0.000199	T	0.82019	0.4946	M	0.83483	2.645	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.83050	-0.0153	10	0.62326	D	0.03	-22.7596	19.7034	0.96065	0.0:0.0:1.0:0.0	.	1117;363;1141	Q6XZF7;Q6XZF7-2;Q5SVK8	DNMBP_HUMAN;.;.	R	1141;1117;363;363;53	ENSP00000344914:P1141R;ENSP00000315659:P1117R;ENSP00000443657:P363R;ENSP00000443573:P53R	ENSP00000315659:P1117R	P	-	2	0	DNMBP	101636315	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.866000	0.99616	2.756000	0.94617	0.561000	0.74099	CCC	.	.	.	none		0.502	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221		C	101646325	G	C	101646325	3	2	130	1	0	0	0	0	1	0	0	0	4676	1232	43	4	1403	4	DNMBP	10	101646325	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	4647912	101646325	33888422	29	8065											
SLK	9748	hgsc.bcm.edu	37	chr10	105750528	105750528	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tacatggtagagattgacatAttagcatcttgtgatcaccc	12	13	8	8	0	2	3	1	2	1	1	2	4	2	3	1	1	2	2	1	1	4	6			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr10:105750528A>G	ENST00000369755.3	+	2	791	c.246A>G	c.(244-246)atA>atG	p.I82M	SLK_ENST00000335753.4_Missense_Mutation_p.I82M	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	82	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		AGATTGACATATTAGCATCTT	0.363																																					p.I82M	NSCLC(111;540 1651 1927 4474 17706)	Atlas-SNP	.											.	SLK	107	.	0			c.A246G						PASS	.						132	123	126					10																	105750528		2203	4300	6503	SO:0001583	missense	9748	exon2			TGACATATTAGCA		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.246A>G	chr10.hg19:g.105750528A>G	ENSP00000358770:p.Ile82Met	75.0	0.0	.		69.0	29.0	.	NM_014720	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Missense_Mutation	SNP	ENST00000369755.3	hg19	CCDS7553.1	.	.	.	.	.	.	.	.	.	.	A	17.81	3.480734	0.63849	.	.	ENSG00000065613	ENST00000335753;ENST00000369755	T;T	0.69435	-0.4;-0.4	6.17	-1.34	0.09143	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	0.68467	0.3004	L	0.41961	1.31	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.64067	-0.6494	10	0.42905	T	0.14	.	7.0526	0.25081	0.3492:0.3447:0.0:0.3061	.	82;82	Q9H2G2-2;Q9H2G2	.;SLK_HUMAN	M	82	ENSP00000336824:I82M;ENSP00000358770:I82M	ENSP00000336824:I82M	I	+	3	3	SLK	105740518	0.793000	0.28825	0.997000	0.53966	0.966000	0.64601	-0.030000	0.12308	-0.051000	0.13334	-0.313000	0.08912	ATA	.	.	.	none		0.363	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720		G	105750528	A	G	105750528	3	3	130	1	0	0	0	0	1	0	0	0	14761	439	16	3	252	3	SLK	10	105750528	Missense_Mutation	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	4104203	105750528	29784219	30	8066											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1247945	1247945	+	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	cgcttccctggcctttgcaaCtacgtgttctctgagcactg	5	13	9	14	2	1	1	0	1	1	0	3	1	2	1	2	1	4	4	2	1	2	4			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr11:1247945C>G	ENST00000529681.1	+	4	358	c.300C>G	c.(298-300)aaC>aaG	p.N100K	MUC5B_ENST00000447027.1_Missense_Mutation_p.N100K	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	100	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.			FPGLCN -> LPCLCK (in Ref. 2; AAC67545). {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)		GCCTTTGCAACTACGTGTTCT	0.632																																					p.N100K		Atlas-SNP	.											.	MUC5B	473	.	0			c.C300G						PASS	.						43	45	44					11																	1247945		2150	4262	6412	SO:0001583	missense	727897	exon4			TTGCAACTACGTG	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.300C>G	chr11.hg19:g.1247945C>G	ENSP00000436812:p.Asn100Lys	37.0	0.0	.		36.0	7.0	.	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	hg19	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	C	11.67	1.708565	0.30322	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.58797	0.31;0.31	3.68	0.662	0.17880	von Willebrand factor, type D domain (3);	.	.	.	.	T	0.67515	0.2901	L	0.59912	1.85	0.36644	D	0.876996	D;D;D	0.89917	0.997;1.0;1.0	D;D;D	0.79784	0.958;0.993;0.993	T	0.70513	-0.4851	9	0.87932	D	0	.	8.7992	0.34898	0.0:0.6325:0.0:0.3675	.	100;756;100	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	K	100;100;100;133	ENSP00000436812:N100K;ENSP00000415793:N100K	ENSP00000343037:N100K	N	+	3	2	MUC5B	1204521	1.000000	0.71417	0.993000	0.49108	0.927000	0.56198	0.972000	0.29409	0.261000	0.21753	0.561000	0.74099	AAC	.	.	.	none		0.632	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		G	1247945	C	G	1247945	3	3	130	1	0	0	0	0	1	0	0	0	9986	564	20	4	314	4	MUC5B	11	1247945	Missense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08		1247945	133758571	31	8067											
PRKRIR	5612	hgsc.bcm.edu	37	chr11	76063689	76063689	+	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	cagaatcaagatttcaaataGagattttaggtattctttgt	14	16	7	4	0	3	3	2	0	1	3	3	4	3	3	0	1	0	1	0	1	6	7			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr11:76063689G>C	ENST00000260045.3	-	5	610	c.505C>G	c.(505-507)Cta>Gta	p.L169V	PRKRIR_ENST00000531878.1_5'Flank	NM_004705.2	NP_004696.2	O43422	P52K_HUMAN	protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor)	169					negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)|signal transduction (GO:0007165)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|large_intestine(4)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	25						ATTTCAAATAGAGATTTTAGG	0.413																																					p.L169V		Atlas-SNP	.											.	PRKRIR	65	.	0			c.C505G						PASS	.						44	39	40					11																	76063689		2200	4292	6492	SO:0001583	missense	5612	exon5			CAAATAGAGATTT	AF007393	CCDS8243.1	11q13.5	2013-01-25			ENSG00000137492	ENSG00000137492		"THAP (C2CH-type zinc finger) domain containing"	9440	protein-coding gene	gene with protein product	"THAP domain containing 12"	607374				9447982	Standard	NM_004705		Approved	P52rIPK, DAP4, THAP12	uc001oxh.1	O43422	OTTHUMG00000165280	ENST00000260045.3:c.505C>G	chr11.hg19:g.76063689G>C	ENSP00000260045:p.Leu169Val	54.0	0.0	.		29.0	21.0	.	NM_004705	A8K728|Q17RY9|Q8WTW1|Q9Y3Z4	Missense_Mutation	SNP	ENST00000260045.3	hg19	CCDS8243.1	.	.	.	.	.	.	.	.	.	.	G	12.33	1.904821	0.33628	.	.	ENSG00000137492	ENST00000260045	.	.	.	4.99	-0.031	0.13911	.	0.157256	0.45606	D	0.000351	T	0.52948	0.1766	M	0.67953	2.075	0.34998	D	0.755717	P	0.46277	0.875	P	0.50082	0.63	T	0.59306	-0.7479	9	0.23302	T	0.38	.	9.0537	0.36392	0.5611:0.0:0.4389:0.0	.	169	O43422	P52K_HUMAN	V	169	.	ENSP00000260045:L169V	L	-	1	2	PRKRIR	75741337	0.470000	0.25854	0.991000	0.47740	0.952000	0.60782	1.098000	0.31000	0.038000	0.15604	0.586000	0.80456	CTA	.	.	.	none		0.413	PRKRIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383188.1	NM_004705		C	76063689	G	C	76063689	3	2	130	1	0	0	0	0	1	0	0	0	12536	933	33	4	1784	4	PRKRIR	11	76063689	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	74815744	76063689	58942827	32	8068											
DIP2B	57609	hgsc.bcm.edu	37	chr12	51019819	51019819	+	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	actcctatctccttacagccCgcagacacaaggtaggcaat	12	8	7	14	1	1	1	0	0	1	1	3	1	2	1	3	2	2	3	3	2	5	3			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr12:51019819C>A	ENST00000301180.5	+	2	195	c.161C>A	c.(160-162)cCg>cAg	p.P54Q		NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	54	DMAP-interaction.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.P54Q(1)		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						CCTTACAGCCCGCAGACACAA	0.378																																					p.P54Q		Atlas-SNP	.											DIP2B,NS,carcinoma,0,1	DIP2B	167	.	1	Substitution - Missense(1)	lung(1)	c.C161A						PASS	.						107	105	105					12																	51019819		2203	4300	6503	SO:0001583	missense	57609	exon2			ACAGCCCGCAGAC	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.161C>A	chr12.hg19:g.51019819C>A	ENSP00000301180:p.Pro54Gln	128.0	2.0	.		142.0	10.0	.	NM_173602	Q6B011|Q8N1L5|Q8NB38	Missense_Mutation	SNP	ENST00000301180.5	hg19	CCDS31799.1	.	.	.	.	.	.	.	.	.	.	c	14.24	2.476710	0.44044	.	.	ENSG00000066084	ENST00000455310;ENST00000301180	T	0.46819	0.86	4.75	3.87	0.44632	DMAP1-binding (1);	0.212294	0.49916	D	0.000135	T	0.46756	0.1409	L	0.49350	1.555	0.37755	D	0.926104	B;B	0.32800	0.385;0.182	B;B	0.41723	0.365;0.147	T	0.54430	-0.8295	10	0.56958	D	0.05	-5.0148	9.2742	0.37690	0.0:0.9016:0.0:0.0984	.	54;54	Q9P265;E9PHD6	DIP2B_HUMAN;.	Q	54	ENSP00000301180:P54Q	ENSP00000301180:P54Q	P	+	2	0	DIP2B	49306086	0.994000	0.37717	0.994000	0.49952	0.851000	0.48451	3.511000	0.53400	1.369000	0.46134	-0.213000	0.12676	CCG	.	.	.	none		0.378	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602		A	51019819	C	A	51019819	3	1	130	1	0	0	0	0	1	0	0	0	4530	652	23	4	167	4	DIP2B	12	51019819	Missense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08		51019819	82832076	33	8069											
MON2	23041	hgsc.bcm.edu	37	chr12	62959064	62959064	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagataatgtatccagctatAtttgaccagttgttggcatt	11	15	8	7	0	0	2	0	1	0	1	1	2	1	2	2	1	1	5	2	1	4	8			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr12:62959064A>G	ENST00000393632.2	+	27	4471	c.4080A>G	c.(4078-4080)atA>atG	p.I1360M	MON2_ENST00000280379.6_Missense_Mutation_p.I1361M|MON2_ENST00000393629.2_Missense_Mutation_p.I1360M|MON2_ENST00000552738.1_Missense_Mutation_p.I1337M|MON2_ENST00000393630.3_Missense_Mutation_p.I1361M|MON2_ENST00000546600.1_Missense_Mutation_p.I1360M	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	1360					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)		ATCCAGCTATATTTGACCAGT	0.348																																					p.I1360M		Atlas-SNP	.											.	MON2	160	.	0			c.A4080G						PASS	.						193	193	193					12																	62959064		2203	4300	6503	SO:0001583	missense	23041	exon27			AGCTATATTTGAC		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.4080A>G	chr12.hg19:g.62959064A>G	ENSP00000377252:p.Ile1360Met	227.0	1.0	.		199.0	91.0	.	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	ENST00000393632.2	hg19	CCDS31849.1	.	.	.	.	.	.	.	.	.	.	A	15.23	2.770800	0.49680	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000552738;ENST00000393629	T;T;T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.46;-0.46;-0.46	5.44	3.0	0.34707	.	0.000000	0.85682	D	0.000000	T	0.71358	0.3330	L	0.48642	1.525	0.58432	D	0.999998	D;D;D;P;D	0.76494	0.998;0.998;0.998;0.655;0.999	D;D;D;B;D	0.67900	0.919;0.954;0.954;0.295;0.954	T	0.66921	-0.5801	9	.	.	.	-21.3568	8.7848	0.34814	0.4208:0.4646:0.0:0.1146	.	1360;1337;1360;235;1360	B9EGP5;F8VWA6;F8W1Z6;Q7Z3U7-3;Q7Z3U7-4	.;.;.;.;.	M	1360;1361;1361;1360;1337;1360	ENSP00000377252:I1360M;ENSP00000377250:I1361M;ENSP00000280379:I1361M;ENSP00000447407:I1360M;ENSP00000449215:I1337M;ENSP00000377249:I1360M	.	I	+	3	3	MON2	61245331	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.341000	0.43983	0.409000	0.25649	-0.316000	0.08728	ATA	.	.	.	none		0.348	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		G	62959064	A	G	62959064	3	3	130	1	0	0	0	0	1	0	0	0	9707	439	16	3	4186	3	MON2	12	62959064	Missense_Mutation	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	11939245	62959064	70892831	34	8070											
LNX2	222484	hgsc.bcm.edu	37	chr13	28136573	28136575	+	In_Frame_Del	DEL	CCG	CCG	-																															aataatctgggcagcaagctCcggagttccatacttcaggt																								rs377695945		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	CCG	CCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr13:28136573_28136575delCCG	ENST00000316334.3	-	5	1328_1330	c.1199_1201delCGG	c.(1198-1203)ccggag>cag	p.400_401PE>Q		NM_153371.3	NP_699202.1	Q8N448	LNX2_HUMAN	ligand of numb-protein X 2	400	PDZ 2. {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)		GCAGCAAGCTCCGGAGTTCCATA	0.512																																					p.400_401del		Atlas-INDEL	.											.	LNX2	70	.	0			c.1200_1202del						PASS	.																																			SO:0001651	inframe_deletion	222484	exon5			.	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.1199_1201delCGG	chr13.hg19:g.28136573_28136575delCCG	ENSP00000325929:p.Pro400_Glu401delinsGln	175.0	0.0	0		143.0	58.0	0.405594	NM_153371	Q5W0P0|Q6ZMH2|Q96SH4	In_Frame_Del	DEL	ENST00000316334.3	hg19	CCDS9323.1																																																																																			.	.	.	none		0.512	LNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044302.2			-	28136575	CCG	-	28136573	7	5	130	1	0	1	0	1	0	0	0	0	8873	864	30	0	895	0	LNX2	13	28136573	In_Frame_Del	DEL	CCG	TCGA-BQ-7044-01A-11D-1961-08		28136573	87033305	35	8071											
DOCK9	23348	hgsc.bcm.edu	37	chr13	99540613	99540613	+	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	aacctccatcttcacactcaCcttggcaaaagacttctgac	12	10	4	15	0	4	2	2	1	2	1	5	2	5	2	3	1	1	1	3	1	3	3			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr13:99540613C>T	ENST00000376460.1	-	17	2058		c.e17+1		DOCK9_ENST00000448493.2_Splice_Site|DOCK9_ENST00000339416.2_Splice_Site|DOCK9_ENST00000442173.1_Splice_Site	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9						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)					TTCACACTCACCTTGGCAAAA	0.398																																					.		Atlas-SNP	.											.	DOCK9	311	.	0			c.1980+1G>A						PASS	.						167	158	161					13																	99540613		1931	4118	6049	SO:0001630	splice_region_variant	23348	exon18			CACTCACCTTGGC	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.1977+1G>A	chr13.hg19:g.99540613C>T		227.0	0.0	.		224.0	24.0	.	NM_015296	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Splice_Site	SNP	ENST00000376460.1	hg19	CCDS45062.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.474160	0.84640	.	.	ENSG00000088387	ENST00000376460;ENST00000357329;ENST00000376455;ENST00000400235;ENST00000428223;ENST00000339416;ENST00000448493;ENST00000442173	.	.	.	5.67	5.67	0.87782	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.7775	0.96400	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DOCK9	98338614	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.438000	0.80431	2.680000	0.91292	0.655000	0.94253	.	.	.	.	none		0.398	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296	Intron	T	99540613	C	T	99540613	5	4	130	1	0	0	0	0	0	0	1	0	4696	521	18	2	4449	2	DOCK9	13	99540613	Splice_Site	SNP	C	TCGA-BQ-7044-01A-11D-1961-08	71404040	99540613	15629265	36	8072											
FAM71D	161142	hgsc.bcm.edu	37	chr14	67688507	67688507	+	3'UTR	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	tttttacaggagcttgagaaCtgaatcaaacacttcaggta	14	12	8	7	0	2	2	2	2	0	1	2	4	2	3	0	2	4	2	0	2	5	6			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr14:67688507C>A	ENST00000556046.1	+	0	1713							Q8N9W8	FA71D_HUMAN	family with sequence similarity 71, member D							cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|large_intestine(1)|lung(9)|ovary(1)	13		all_hematologic(31;0.0116)		all cancers(60;0.00107)|BRCA - Breast invasive adenocarcinoma(234;0.00993)|OV - Ovarian serous cystadenocarcinoma(108;0.012)		AGCTTGAGAACTGAATCAAAC	0.353																																					p.T391N		Atlas-SNP	.											.	FAM71D	33	.	0			c.C1172A						PASS	.						87	82	84					14																	67688507		2203	4300	6503	SO:0001624	3_prime_UTR_variant	161142	exon7			TGAGAACTGAATC		CCDS9778.1	14q23.3	2007-11-20	2007-11-20	2007-11-20		ENSG00000172717			20101	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 54"	C14orf54			Standard	NM_173526		Approved		uc001xja.2	Q8N9W8		ENST00000556046.1:c.*1228C>A	chr14.hg19:g.67688507C>A		63.0	0.0	.		54.0	11.0	.	NM_173526	Q86VN4	Missense_Mutation	SNP	ENST00000556046.1	hg19		.	.	.	.	.	.	.	.	.	.	C	6.948	0.544670	0.13312	.	.	ENSG00000172717	ENST00000556117;ENST00000557671	.	.	.	5.95	1.59	0.23543	.	.	.	.	.	T	0.25306	0.0615	N	0.24115	0.695	.	.	.	.	.	.	.	.	.	T	0.25082	-1.0142	4	.	.	.	0.0	2.5085	0.04651	0.3418:0.4102:0.1494:0.0986	.	.	.	.	M	52;49	.	.	L	+	1	2	FAM71D	66758260	1.000000	0.71417	0.283000	0.24790	0.059000	0.15707	0.853000	0.27777	0.750000	0.32877	-0.345000	0.07892	CTG	.	.	.	none		0.353	FAM71D-009	KNOWN	not_organism_supported|basic|appris_candidate	nonsense_mediated_decay	protein_coding	OTTHUMT00000412390.1	NM_173526		A	67688507	C	A	67688507	1	1	130	0	1	0	0	0	0	0	0	0	5617	565	20	4		4	FAM71D	14	67688507	3'UTR	SNP	C	TCGA-BQ-7044-01A-11D-1961-08		67688507	39661033	37	8073											
DPF3	8110	hgsc.bcm.edu	37	chr14	73238479	73238479	+	Missense_Mutation	SNP	T	T	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	tctccatccagatgtagcagTtgttctgggccaccccagtc	7	11	9	14	0	2	1	0	0	2	1	5	1	3	1	5	1	1	4	5	1	1	3			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr14:73238479T>G	ENST00000556509.1	-	2	154	c.155A>C	c.(154-156)aAc>aCc	p.N52T	DPF3_ENST00000546183.1_Missense_Mutation_p.N62T|DPF3_ENST00000541685.1_Missense_Mutation_p.N52T	NM_001280542.1	NP_001267471.1	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3	52					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)		GATGTAGCAGTTGTTCTGGGC	0.622																																					p.N52T		Atlas-SNP	.											DPF3_ENST00000541685,NS,carcinoma,0,3	DPF3	117	.	0			c.A155C						PASS	.						87	95	92					14																	73238479		2195	4299	6494	SO:0001583	missense	8110	exon2			TAGCAGTTGTTCT	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.155A>C	chr14.hg19:g.73238479T>G	ENSP00000450518:p.Asn52Thr	158.0	1.0	.		90.0	38.0	.	NM_012074	A8MSI3|B7Z276|F5H575|Q32UJ0|Q6P9E6|Q6ZT41|Q9H7Y5	Missense_Mutation	SNP	ENST00000556509.1	hg19		.	.	.	.	.	.	.	.	.	.	t	30	5.056952	0.93846	.	.	ENSG00000205683	ENST00000540281;ENST00000556509;ENST00000398816;ENST00000541685;ENST00000546183	D;T;T	0.91068	-2.78;-0.26;-0.26	5.54	5.54	0.83059	.	.	.	.	.	D	0.94251	0.8154	M	0.64997	1.995	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.991	D;D;D	0.74023	0.97;0.958;0.982	D	0.94833	0.7998	9	0.87932	D	0	.	15.693	0.77469	0.0:0.0:0.0:1.0	.	62;52;52	F5H575;Q92784-2;Q92784	.;.;DPF3_HUMAN	T	52;52;51;52;62	ENSP00000450518:N52T;ENSP00000441640:N52T;ENSP00000444662:N62T	ENSP00000381791:N107T	N	-	2	0	DPF3	72308232	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.026000	0.88783	2.116000	0.64780	0.529000	0.55759	AAC	.	.	.	none		0.622	DPF3-004	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000413152.2			G	73238479	T	G	73238479	3	3	130	1	0	0	0	0	1	0	0	0	4720	1725	60	5	950	5	DPF3	14	73238479	Missense_Mutation	SNP	T	TCGA-BQ-7044-01A-11D-1961-08	5549972	73238479	34111061	38	8074											
PPP4R4	57718	hgsc.bcm.edu	37	chr14	94741788	94741788	+	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	ctcccttaccgagtacttccCgtgggacaggtaactcagtt	8	11	9	13	2	1	0	1	0	0	0	3	2	3	1	3	2	3	3	3	2	3	5	rs550716897		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr14:94741788C>A	ENST00000304338.3	+	24	2681	c.2527C>A	c.(2527-2529)Cgt>Agt	p.R843S		NM_058237.1	NP_478144.1	Q6NUP7	PP4R4_HUMAN	protein phosphatase 4, regulatory subunit 4	843					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						GAGTACTTCCCGTGGGACAGG	0.448																																					p.R843S		Atlas-SNP	.											.	PPP4R4	107	.	0			c.C2527A						PASS	.						206	193	197					14																	94741788		2203	4300	6503	SO:0001583	missense	57718	exon24			ACTTCCCGTGGGA	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.2527C>A	chr14.hg19:g.94741788C>A	ENSP00000305924:p.Arg843Ser	204.0	0.0	.		186.0	9.0	.	NM_058237	Q9BUF8|Q9HCF0	Missense_Mutation	SNP	ENST00000304338.3	hg19	CCDS9921.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.200451	0.79015	.	.	ENSG00000119698	ENST00000304338	.	.	.	6.02	6.02	0.97574	.	0.066833	0.64402	D	0.000017	T	0.55226	0.1907	L	0.34521	1.04	0.80722	D	1	P	0.48016	0.904	B	0.44108	0.441	T	0.56872	-0.7907	9	0.56958	D	0.05	-13.6956	20.5373	0.99239	0.0:1.0:0.0:0.0	.	843	Q6NUP7	PP4R4_HUMAN	S	843	.	ENSP00000305924:R843S	R	+	1	0	PPP4R4	93811541	1.000000	0.71417	0.998000	0.56505	0.905000	0.53344	5.457000	0.66672	2.857000	0.98124	0.650000	0.86243	CGT	.	.	.	none		0.448	PPP4R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413056.1	NM_058237		A	94741788	C	A	94741788	3	1	130	1	0	0	0	0	1	0	0	0	12415	652	23	4	2694	4	PPP4R4	14	94741788	Missense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08	21503309	94741788	12607752	39	8075											
ITPKA	3706	hgsc.bcm.edu	37	chr15	41794669	41794670	+	Frame_Shift_Ins	INS	-	-	A																															gcaggtgcttcgcgtctttgINSaagagtttgtgcaaggagat																										TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr15:41794669_41794670insA	ENST00000260386.5	+	5	1131_1132	c.1078_1079insA	c.(1078-1080)gaafs	p.E360fs		NM_002220.2	NP_002211.1	P23677	IP3KA_HUMAN	inositol-trisphosphate 3-kinase A	360					actin cytoskeleton organization (GO:0030036)|dendritic spine maintenance (GO:0097062)|inositol metabolic process (GO:0006020)|inositol phosphate metabolic process (GO:0043647)|positive regulation of dendritic spine morphogenesis (GO:0061003)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendritic spine (GO:0043197)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			kidney(1)|lung(3)|skin(1)	5		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;7.63e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		TCGCGTCTTTGAAGAGTTTGTG	0.604																																					p.E360fs		Atlas-INDEL	.											.	ITPKA	19	.	0			c.1078_1079insA						PASS	.																																			SO:0001589	frameshift_variant	3706	exon5			.	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.1080dupA	chr15.hg19:g.41794671_41794671dupA	ENSP00000260386:p.Glu360fs	67.0	0.0	0		80.0	29.0	0.3625	NM_002220	Q8TAN3	Frame_Shift_Ins	INS	ENST00000260386.5	hg19	CCDS10076.1																																																																																			.	.	.	none		0.604	ITPKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252695.3	NM_002220		A	41794670	-	A	41794669	7	5	130	1	0	1	1	0	0	0	0	0	7924	1291	45	0	1096	0	ITPKA	15	41794669	Frame_Shift_Ins	INS	-	TCGA-BQ-7044-01A-11D-1961-08		41794669	60736723	40	8076											
C15orf43	145645	hgsc.bcm.edu	37	chr15	45270783	45270783	+	Frame_Shift_Del	DEL	A	A	-																															ggcatatcatgttcaaaatgAaattaatatgtctgctataa																										TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr15:45270783delA	ENST00000340827.3	+	7	637	c.620delA	c.(619-621)gaafs	p.E207fs		NM_152448.2	NP_689661.1	Q8NHR7	CO043_HUMAN	chromosome 15 open reading frame 43	207										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)		GTTCAAAATGAAATTAATATG	0.294																																					p.E207fs		Atlas-INDEL	.											.	C15orf43	19	.	0			c.619delG						PASS	.						40	43	42					15																	45270783		2193	4282	6475	SO:0001589	frameshift_variant	145645	exon7			.	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.620delA	chr15.hg19:g.45270783delA	ENSP00000340644:p.Glu207fs	52.0	0.0	0		44.0	18.0	0.409091	NM_152448		Frame_Shift_Del	DEL	ENST00000340827.3	hg19	CCDS10115.1																																																																																			.	.	.	none		0.294	C15orf43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254032.1	NM_152448		-	45270783	A	-	45270783	7	5	130	1	0	1	0	1	0	0	0	0	1799	246	9	0	646	0	C15orf43	15	45270783	Frame_Shift_Del	DEL	A	TCGA-BQ-7044-01A-11D-1961-08	3476114	45270783	57260609	41	8077											
ZNF609	23060	hgsc.bcm.edu	37	chr15	64966235	64966235	+	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	acagcctctgacagcaaaggGaccagtaacagcagcaaaac	17	3	9	12	0	1	1	0	1	1	0	1	2	1	2	2	1	6	4	2	1	4	1			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr15:64966235G>T	ENST00000326648.3	+	4	1310	c.1182G>T	c.(1180-1182)ggG>ggT	p.G394G	RNU6-549P_ENST00000384433.1_RNA|ZNF609_ENST00000559364.1_3'UTR	NM_015042.1	NP_055857.1	O15014	ZN609_HUMAN	zinc finger protein 609	394						nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						ACAGCAAAGGGACCAGTAACA	0.577																																					p.G394G		Atlas-SNP	.											.	ZNF609	106	.	0			c.G1182T						PASS	.						96	97	97					15																	64966235		2203	4299	6502	SO:0001819	synonymous_variant	23060	exon4			CAAAGGGACCAGT	BC014251	CCDS32270.1	15q22.1	2008-05-02				ENSG00000180357		"Zinc fingers, C2H2-type"	29003	protein-coding gene	gene with protein product						9205841	Standard	NM_015042		Approved	KIAA0295	uc002ann.3	O15014		ENST00000326648.3:c.1182G>T	chr15.hg19:g.64966235G>T		191.0	0.0	.		150.0	55.0	.	NM_015042	Q0D2I2	Silent	SNP	ENST00000326648.3	hg19	CCDS32270.1																																																																																			.	.	.	none		0.577	ZNF609-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418130.1	XM_042833		T	64966235	G	T	64966235	2	4	130	1	0	0	0	0	0	0	0	1	18047	1161	41	4		4	ZNF609	15	64966235	Silent	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	19695452	64966235	37565157	42	8078											
THSD4	79875	hgsc.bcm.edu	37	chr15	72063439	72063439	+	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	agggtggctttcgggtccggGaagtgcggtgtctgtctgat	4	12	18	7	3	2	1	0	1	2	0	4	2	3	2	1	5	1	1	1	5	1	1			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr15:72063439G>C	ENST00000355327.3	+	17	2940	c.2806G>C	c.(2806-2808)Gaa>Caa	p.E936Q	THSD4_ENST00000261862.6_Missense_Mutation_p.E936Q|THSD4_ENST00000357769.4_Missense_Mutation_p.E576Q			Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4	936	TSP type-1 6. {ECO:0000255|PROSITE- ProRule:PRU00210}.				elastic fiber assembly (GO:0048251)	extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						TCGGGTCCGGGAAGTGCGGTG	0.507																																					p.E936Q		Atlas-SNP	.											.	THSD4	75	.	0			c.G2806C						PASS	.						157	149	151					15																	72063439		1899	4126	6025	SO:0001583	missense	79875	exon16			GTCCGGGAAGTGC	AK023772	CCDS10238.2, CCDS66817.1	15q23	2009-11-09			ENSG00000187720	ENSG00000187720			25835	protein-coding gene	gene with protein product		614476				19734141	Standard	NM_001286429		Approved	FVSY9334, PRO34005, FLJ13710, ADAMTSL6	uc002atb.1	Q6ZMP0	OTTHUMG00000133389	ENST00000355327.3:c.2806G>C	chr15.hg19:g.72063439G>C	ENSP00000347484:p.Glu936Gln	172.0	0.0	.		143.0	63.0	.	NM_024817	B2RTY3|B4DR13|Q6MZI3|Q6UXZ8|Q9H8E4	Missense_Mutation	SNP	ENST00000355327.3	hg19	CCDS10238.2	.	.	.	.	.	.	.	.	.	.	G	18.91	3.724411	0.68959	.	.	ENSG00000187720	ENST00000355327;ENST00000261862;ENST00000357769	T;T;T	0.50813	0.73;0.73;0.73	5.05	5.05	0.67936	.	.	.	.	.	T	0.56761	0.2007	L	0.28649	0.875	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.54596	-0.8270	9	0.35671	T	0.21	.	15.9236	0.79592	0.0:0.0:1.0:0.0	.	576;936	B4DR13;Q6ZMP0	.;THSD4_HUMAN	Q	936;936;576	ENSP00000347484:E936Q;ENSP00000261862:E936Q;ENSP00000350413:E576Q	ENSP00000261862:E936Q	E	+	1	0	THSD4	69850493	1.000000	0.71417	1.000000	0.80357	0.252000	0.25951	9.638000	0.98445	2.353000	0.79882	0.557000	0.71058	GAA	.	.	.	none		0.507	THSD4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257253.2	NM_024817		C	72063439	G	C	72063439	3	2	130	1	0	0	0	0	1	0	0	0	15890	1175	41	4	2868	4	THSD4	15	72063439	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	7097204	72063439	30467953	43	8079											
BNC1	646	hgsc.bcm.edu	37	chr15	83932666	83932666	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggcctacagtctggggacGtcactgtgaaacctgggcac	9	7	14	11	1	2	1	1	1	1	0	2	3	2	2	2	4	2	1	2	4	2	1	rs377611889		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr15:83932666G>A	ENST00000345382.2	-	4	1422	c.1337C>T	c.(1336-1338)aCg>aTg	p.T446M	BNC1_ENST00000569704.1_Missense_Mutation_p.T439M|RP11-382A20.4_ENST00000565495.1_RNA	NM_001717.3	NP_001708.3	Q01954	BNC1_HUMAN	basonuclin 1	446					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						GTCTGGGGACGTCACTGTGAA	0.527																																					p.T446M		Atlas-SNP	.											.	BNC1	149	.	0			c.C1337T						PASS	.	G	MET/THR	1,4405	2.1+/-5.4	0,1,2202	129	118	122		1337	0.3	0	15		122	0,8600		0,0,4300	no	missense	BNC1	NM_001717.3	81	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	446/995	83932666	1,13005	2203	4300	6503	SO:0001583	missense	646	exon4			GGGGACGTCACTG	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.1337C>T	chr15.hg19:g.83932666G>A	ENSP00000307041:p.Thr446Met	92.0	0.0	.		71.0	27.0	.	NM_001717	Q15840	Missense_Mutation	SNP	ENST00000345382.2	hg19	CCDS10324.1	.	.	.	.	.	.	.	.	.	.	G	0.574	-0.839807	0.02692	2.27E-4	0.0	ENSG00000169594	ENST00000345382;ENST00000541809	T	0.47869	0.83	4.98	0.334	0.15948	.	0.605786	0.17317	N	0.178658	T	0.32376	0.0827	L	0.39397	1.21	0.09310	N	1	B;B	0.23806	0.008;0.091	B;B	0.16289	0.004;0.015	T	0.16958	-1.0385	10	0.51188	T	0.08	-1.7277	5.5626	0.17152	0.2685:0.4447:0.2868:0.0	.	439;446	F5GY04;Q01954	.;BNC1_HUMAN	M	446;439	ENSP00000307041:T446M	ENSP00000307041:T446M	T	-	2	0	BNC1	81723670	0.001000	0.12720	0.001000	0.08648	0.136000	0.21042	0.733000	0.26087	-0.119000	0.11830	0.655000	0.94253	ACG	.	.	.	weak		0.527	BNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304006.1	NM_001717		A	83932666	G	A	83932666	3	1	130	1	0	0	0	0	1	0	0	0	1474	1145	40	1	1655	1	BNC1	15	83932666	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	11869227	83932666	18598726	44	8080											
AKAP13	11214	hgsc.bcm.edu	37	chr15	86125257	86125257	+	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	gtactcctgaggaagccacgGggagccttgcaggatgtttt	8	10	14	9	1	0	1	0	1	0	0	1	4	1	4	3	4	4	3	3	4	2	4			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr15:86125257G>C	ENST00000394518.2	+	7	4053	c.3958G>C	c.(3958-3960)Ggg>Cgg	p.G1320R	AKAP13_ENST00000361243.2_Missense_Mutation_p.G1320R|RP11-815J21.2_ENST00000561409.1_RNA	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	1320					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						GGAAGCCACGGGGAGCCTTGC	0.507																																					p.G1320R	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.G3958C						PASS	.						55	53	53					15																	86125257		2202	4299	6501	SO:0001583	missense	11214	exon7			GCCACGGGGAGCC	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.3958G>C	chr15.hg19:g.86125257G>C	ENSP00000378026:p.Gly1320Arg	115.0	0.0	.		89.0	4.0	.	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	hg19	CCDS32319.1	.	.	.	.	.	.	.	.	.	.	G	13.67	2.305937	0.40795	.	.	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540	T;T	0.16597	2.33;2.33	4.87	2.96	0.34315	.	.	.	.	.	T	0.19446	0.0467	M	0.62723	1.935	0.09310	N	0.999996	P;P	0.49090	0.718;0.919	B;B	0.43052	0.168;0.406	T	0.13442	-1.0509	9	0.87932	D	0	.	6.6634	0.23027	0.0987:0.1806:0.7206:0.0	.	1320;1320	Q12802;Q12802-2	AKP13_HUMAN;.	R	1320;1320;1319;1319	ENSP00000354718:G1320R;ENSP00000378026:G1320R	ENSP00000354718:G1320R	G	+	1	0	AKAP13	83926261	0.000000	0.05858	0.003000	0.11579	0.007000	0.05969	0.156000	0.16382	0.448000	0.26722	-0.176000	0.13171	GGG	.	.	.	none		0.507	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		C	86125257	G	C	86125257	3	2	130	1	0	0	0	0	1	0	0	0	449	1232	43	4	3980	4	AKAP13	15	86125257	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	2192591	86125257	16406135	45	8081											
ADAMTS17	170691	hgsc.bcm.edu	37	chr15	100871170	100871170	+	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	gtcaaggaccatttgcgcctGatcagatgttctcgtccact	8	12	9	12	2	3	2	2	1	1	1	5	3	4	3	3	1	1	1	3	1	1	2			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr15:100871170G>A	ENST00000268070.4	-	3	645	c.540C>T	c.(538-540)atC>atT	p.I180I		NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	180						proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)	50	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		ATTTGCGCCTGATCAGATGTT	0.582																																					p.I180I		Atlas-SNP	.											.	ADAMTS17	127	.	0			c.C540T						PASS	.						129	122	125					15																	100871170		2203	4300	6503	SO:0001819	synonymous_variant	170691	exon3			GCGCCTGATCAGA	AJ315735	CCDS10383.1	15q24	2014-01-28	2005-08-19		ENSG00000140470	ENSG00000140470		"ADAM metallopeptidases with thrombospondin type 1 motif"	17109	protein-coding gene	gene with protein product		607511	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17"			11867212	Standard	NM_139057		Approved	FLJ32769, FLJ16363	uc002bvv.1	Q8TE56	OTTHUMG00000149867	ENST00000268070.4:c.540C>T	chr15.hg19:g.100871170G>A		99.0	0.0	.		87.0	47.0	.	NM_139057	Q2I7G4|Q6ZN75	Silent	SNP	ENST00000268070.4	hg19	CCDS10383.1																																																																																			.	.	.	none		0.582	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1	NM_139057		A	100871170	G	A	100871170	2	1	130	1	0	0	0	0	0	0	0	1	262	1280	45	2		2	ADAMTS17	15	100871170	Silent	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	14745913	100871170	1660222	46	8082											
PDILT	204474	hgsc.bcm.edu	37	chr16	20410442	20410442	+	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	gaaaagcaccatgaggaagcGggtctggttcagcatctggg	11	7	15	8	1	3	1	1	1	2	0	3	3	3	2	1	4	3	3	1	4	3	1	rs368369154		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr16:20410442G>T	ENST00000302451.4	-	2	429	c.181C>A	c.(181-183)Cgc>Agc	p.R61S		NM_174924.1	NP_777584.1	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis expressed	61					cell migration (GO:0016477)|cell redox homeostasis (GO:0045454)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|spermatid development (GO:0007286)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)	p.R61S(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(33)|prostate(3)|skin(1)|urinary_tract(1)	61						ATGAGGAAGCGGGTCTGGTTC	0.562																																					p.R61S		Atlas-SNP	.											PDILT,NS,carcinoma,+1,1	PDILT	120	.	1	Substitution - Missense(1)	lung(1)	c.C181A						PASS	.						100	91	94					16																	20410442		2203	4300	6503	SO:0001583	missense	204474	exon2			GGAAGCGGGTCTG		CCDS10584.1	16p12.3	2011-11-10	2009-02-23		ENSG00000169340	ENSG00000169340		"Protein disulfide isomerases"	27338	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 7", "protein disulfide isomerase-like protein of the testis"					15475357	Standard	NM_174924		Approved	PDIA7	uc002dhc.1	Q8N807	OTTHUMG00000131487	ENST00000302451.4:c.181C>A	chr16.hg19:g.20410442G>T	ENSP00000305465:p.Arg61Ser	68.0	1.0	.		105.0	7.0	.	NM_174924	Q8IVQ5	Missense_Mutation	SNP	ENST00000302451.4	hg19	CCDS10584.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.027180	0.75390	.	.	ENSG00000169340	ENST00000302451	T	0.03212	4.01	4.21	4.21	0.49690	Thioredoxin domain (1);Thioredoxin-like fold (2);	0.357715	0.30134	N	0.010336	T	0.05135	0.0137	L	0.34521	1.04	0.33941	D	0.643194	P	0.48834	0.916	P	0.48454	0.578	T	0.46034	-0.9220	10	0.21014	T	0.42	.	12.3542	0.55165	0.0:0.0:1.0:0.0	.	61	Q8N807	PDILT_HUMAN	S	61	ENSP00000305465:R61S	ENSP00000305465:R61S	R	-	1	0	PDILT	20317943	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	3.640000	0.54350	2.623000	0.88846	0.591000	0.81541	CGC	.	.	.	alt		0.562	PDILT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254332.1	NM_174924		T	20410442	G	T	20410442	3	4	130	1	0	0	0	0	1	0	0	0	11681	1116	39	4	1617	4	PDILT	16	20410442	Missense_Mutation	SNP	G	TCGA-BQ-7044-01A-11D-1961-08		20410442	69944311	47	8083											
IRX6	79190	hgsc.bcm.edu	37	chr16	55360382	55360382	+	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	agtcgactgctgggcagtgcGcgaccggagctgggcgccgc	5	5	18	13	6	0	0	0	0	0	0	1	3	0	1	2	3	3	3	2	3	0	0			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr16:55360382G>A	ENST00000290552.7	+	2	1512	c.180G>A	c.(178-180)gcG>gcA	p.A60A	IRX6_ENST00000558315.1_3'UTR|RP11-26L20.3_ENST00000558730.2_RNA	NM_024335.2	NP_077311.2	P78412	IRX6_HUMAN	iroquois homeobox 6	60					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						TGGGCAGTGCGCGACCGGAGC	0.657																																					p.A60A		Atlas-SNP	.											.	IRX6	66	.	0			c.G180A						PASS	.						26	24	25					16																	55360382		2198	4300	6498	SO:0001819	synonymous_variant	79190	exon2			CAGTGCGCGACCG	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.180G>A	chr16.hg19:g.55360382G>A		40.0	0.0	.		48.0	28.0	.	NM_024335	B2RN06|Q7Z2K0	Silent	SNP	ENST00000290552.7	hg19	CCDS32449.1																																																																																			.	.	.	none		0.657	IRX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417445.4	NM_024335		A	55360382	G	A	55360382	2	1	130	1	0	0	0	0	0	0	0	1	7855	1074	38	1		1	IRX6	16	55360382	Silent	SNP	G	TCGA-BQ-7044-01A-11D-1961-08	34949940	55360382	34994371	48	8084											
CDH5	1003	hgsc.bcm.edu	37	chr16	66413245	66413245	+	Missense_Mutation	SNP	A	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	tgttcctcctgggaagatgcAgaggctcatgatgctcctcg	7	11	12	11	1	1	3	1	1	0	2	5	4	4	4	3	2	2	4	3	2	1	1			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr16:66413245A>C	ENST00000341529.3	+	2	153	c.5A>C	c.(4-6)cAg>cCg	p.Q2P	CDH5_ENST00000563425.2_Missense_Mutation_p.Q2P	NM_001795.3	NP_001786.2	P33151	CADH5_HUMAN	cadherin 5, type 2 (vascular endothelium)	2					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)	GGGAAGATGCAGAGGCTCATG	0.572																																					p.Q2P		Atlas-SNP	.											.	CDH5	111	.	0			c.A5C						PASS	.						79	83	82					16																	66413245		2200	4299	6499	SO:0001583	missense	1003	exon2			AGATGCAGAGGCT	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.5A>C	chr16.hg19:g.66413245A>C	ENSP00000344115:p.Gln2Pro	231.0	0.0	.		268.0	61.0	.	NM_001795	Q4VAI5|Q4VAI6	Missense_Mutation	SNP	ENST00000341529.3	hg19	CCDS10804.1	.	.	.	.	.	.	.	.	.	.	A	11.95	1.791839	0.31685	.	.	ENSG00000179776	ENST00000341529;ENST00000379531	T	0.56103	0.48	4.38	2.03	0.26663	.	.	.	.	.	T	0.27169	0.0666	N	0.08118	0	0.42316	D	0.992239	B	0.11235	0.004	B	0.06405	0.002	T	0.04386	-1.0955	9	0.42905	T	0.14	.	4.3874	0.11323	0.6928:0.2005:0.1067:0.0	.	2	P33151	CADH5_HUMAN	P	2	ENSP00000344115:Q2P	ENSP00000344115:Q2P	Q	+	2	0	CDH5	64970746	0.837000	0.29446	0.481000	0.27354	0.805000	0.45488	1.348000	0.33987	0.204000	0.20548	0.379000	0.24179	CAG	.	.	.	none		0.572	CDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268767.1	NM_001795		C	66413245	A	C	66413245	3	2	130	1	0	0	0	0	1	0	0	0	3115	188	7	5	7	5	CDH5	16	66413245	Missense_Mutation	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	11052863	66413245	23941508	49	8085											
ZC3H18	124245	hgsc.bcm.edu	37	chr16	88666335	88666335	+	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	agattggaattctcggatccCgagagatgtcagagacacag	13	8	12	8	2	2	3	1	0	1	3	4	8	3	5	1	2	0	0	1	2	1	2			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr16:88666335C>A	ENST00000301011.5	+	6	1267	c.1067C>A	c.(1066-1068)cCg>cAg	p.P356Q	ZC3H18_ENST00000452588.2_Missense_Mutation_p.P380Q	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	356						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)		TCTCGGATCCCGAGAGATGTC	0.517																																					p.P356Q	Ovarian(121;375 2276 20373 38669)	Atlas-SNP	.											.	ZC3H18	90	.	0			c.C1067A						PASS	.						97	105	102					16																	88666335		2198	4300	6498	SO:0001583	missense	124245	exon6			GGATCCCGAGAGA	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.1067C>A	chr16.hg19:g.88666335C>A	ENSP00000301011:p.Pro356Gln	153.0	0.0	.		184.0	9.0	.	NM_144604	Q96DG4|Q96MP7	Missense_Mutation	SNP	ENST00000301011.5	hg19	CCDS10967.1	.	.	.	.	.	.	.	.	.	.	C	13.01	2.108621	0.37242	.	.	ENSG00000158545	ENST00000301011;ENST00000289509;ENST00000452588;ENST00000545404	T;T	0.30448	1.53;1.56	5.16	5.16	0.70880	.	0.103761	0.64402	D	0.000003	T	0.30727	0.0774	L	0.34521	1.04	0.37331	D	0.909979	P;P;P	0.41569	0.755;0.459;0.755	B;B;B	0.43360	0.417;0.299;0.417	T	0.21621	-1.0240	10	0.46703	T	0.11	-3.6361	16.815	0.85732	0.0:1.0:0.0:0.0	.	380;380;356	E7ERS3;B4DTK7;Q86VM9	.;.;ZCH18_HUMAN	Q	356;380;380;239	ENSP00000301011:P356Q;ENSP00000416951:P380Q	ENSP00000289509:P380Q	P	+	2	0	ZC3H18	87193836	1.000000	0.71417	0.028000	0.17463	0.747000	0.42532	5.110000	0.64622	2.390000	0.81377	0.561000	0.74099	CCG	.	.	.	none		0.517	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1	NM_144604		A	88666335	C	A	88666335	3	1	130	1	0	0	0	0	1	0	0	0	17580	652	23	4	1085	4	ZC3H18	16	88666335	Missense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08	22253090	88666335	1688418	50	8086											
SREBF1	6720	hgsc.bcm.edu	37	chr17	17722461	17722461	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagaggccggggccttgcTgccagctgcgagccggttga	5	6	18	12	3	0	2	0	1	0	1	0	3	0	2	4	5	5	4	4	5	0	2			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr17:17722461T>C	ENST00000261646.5	-	5	1118	c.934A>G	c.(934-936)Agc>Ggc	p.S312G	SREBF1_ENST00000338854.5_Missense_Mutation_p.S312G|SREBF1_ENST00000395757.1_Missense_Mutation_p.S58G|SREBF1_ENST00000583732.1_5'UTR|SREBF1_ENST00000355815.4_Missense_Mutation_p.S342G|SREBF1_ENST00000435530.2_Missense_Mutation_p.S312G	NM_004176.4	NP_004167.3	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription factor 1	312	Interaction with LMNA. {ECO:0000250}.				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						GGGGCCTTGCTGCCAGCTGCG	0.607																																					p.S342G		Atlas-SNP	.											.	SREBF1	47	.	0			c.A1024G						PASS	.						62	60	60					17																	17722461		2203	4300	6503	SO:0001583	missense	6720	exon6			CCTTGCTGCCAGC	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.934A>G	chr17.hg19:g.17722461T>C	ENSP00000261646:p.Ser312Gly	92.0	0.0	.		83.0	34.0	.	NM_001005291	B0I4X3|B0I4X4|D3DXC4|Q16062|Q59F52|Q6P4R7|Q6PFW7|Q6PJ36|Q8TAK9	Missense_Mutation	SNP	ENST00000261646.5	hg19	CCDS11189.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.54|11.54	1.668371|1.668371	0.29604|0.29604	.|.	.|.	ENSG00000072310|ENSG00000072310	ENST00000395751|ENST00000338854;ENST00000355815;ENST00000261646;ENST00000395757;ENST00000418712;ENST00000423161;ENST00000435530	.|T;T;T;T;T	.|0.76578	.|0.66;0.65;0.66;1.02;-1.03	4.41|4.41	0.985|0.985	0.19779|0.19779	.|.	.|0.390138	.|0.18906	.|N	.|0.127893	T|T	0.43809|0.43809	0.1264|0.1264	N|N	0.01091|0.01091	-1.02|-1.02	0.27003|0.27003	N|N	0.964868|0.964868	.|B;B;B;B	.|0.02656	.|0.0;0.0;0.0;0.0	.|B;B;B;B	.|0.04013	.|0.001;0.001;0.0;0.001	T|T	0.37150|0.37150	-0.9718|-0.9718	5|10	.|0.14656	.|T	.|0.56	-6.3745|-6.3745	8.5495|8.5495	0.33442|0.33442	0.0:0.7314:0.0:0.2686|0.0:0.7314:0.0:0.2686	.|.	.|312;288;312;342	.|B0I4X3;B0I4X4;P36956;P36956-4	.|.;.;SRBP1_HUMAN;.	R|G	319|312;342;312;58;149;238;312	.|ENSP00000345822:S312G;ENSP00000348069:S342G;ENSP00000261646:S312G;ENSP00000379106:S58G;ENSP00000413389:S312G	.|ENSP00000261646:S312G	Q|S	-|-	2|1	0|0	SREBF1|SREBF1	17663186|17663186	0.654000|0.654000	0.27367|0.27367	0.484000|0.484000	0.27391|0.27391	0.781000|0.781000	0.44180|0.44180	1.287000|1.287000	0.33284|0.33284	-0.124000|-0.124000	0.11724|0.11724	0.459000|0.459000	0.35465|0.35465	CAG|AGC	.	.	.	none		0.607	SREBF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131771.1	NM_004176		C	17722461	T	C	17722461	3	2	130	1	0	0	0	0	1	0	0	0	15153	1580	55	3	2569	3	SREBF1	17	17722461	Missense_Mutation	SNP	T	TCGA-BQ-7044-01A-11D-1961-08		17722461	63472749	51	8087											
NF1	4763	hgsc.bcm.edu	37	chr17	29490388	29490388	+	Frame_Shift_Del	DEL	C	C	-																															tgcagtctttagtcgcatttCtaccaggttagtgtgtaaat																										TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr17:29490388delC	ENST00000358273.4	+	4	856	c.473delC	c.(472-474)tctfs	p.S158fs	NF1_ENST00000431387.4_Frame_Shift_Del_p.S158fs|NF1_ENST00000356175.3_Frame_Shift_Del_p.S158fs	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	158					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AGTCGCATTTCTACCAGGTTA	0.368			"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.S158fs		Atlas-INDEL	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(3)|central_nervous_system(2)	c.472delT						PASS	.						53	52	52					17																	29490388		2203	4300	6503	SO:0001589	frameshift_variant	4763	exon4	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.473delC	chr17.hg19:g.29490388delC	ENSP00000351015:p.Ser158fs	110.0	0.0	0		104.0	56.0	0.538462	NM_001042492	O00662|Q14284|Q14930|Q14931|Q9UMK3	Frame_Shift_Del	DEL	ENST00000358273.4	hg19	CCDS42292.1																																																																																			.	.	.	none		0.368	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		-	29490388	C	-	29490388	7	5	130	1	0	1	0	1	0	0	0	0	10363	913	32	0	487	0	NF1	17	29490388	Frame_Shift_Del	DEL	C	TCGA-BQ-7044-01A-11D-1961-08	11767927	29490388	51704822	52	8088											
NF1	4763	hgsc.bcm.edu	37	chr17	29552188	29552189	+	Frame_Shift_Del	DEL	AG	AG	-																															ttccttctagtggaaataccAgtcaaatgtccatggatcat																										TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr17:29552188_29552189delAG	ENST00000358273.4	+	17	2304_2305	c.1921_1922delAG	c.(1921-1923)agtfs	p.S641fs	NF1_ENST00000356175.3_Frame_Shift_Del_p.S641fs	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	641					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TGGAAATACCAGTCAAATGTCC	0.406			"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.640_641del		Atlas-INDEL	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)	c.1920_1921del						PASS	.																																			SO:0001589	frameshift_variant	4763	exon17	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.1921_1922delAG	chr17.hg19:g.29552188_29552189delAG	ENSP00000351015:p.Ser641fs	171.0	0.0	0		177.0	70.0	0.39548	NM_001042492	O00662|Q14284|Q14930|Q14931|Q9UMK3	Frame_Shift_Del	DEL	ENST00000358273.4	hg19	CCDS42292.1																																																																																			.	.	.	none		0.406	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		-	29552189	AG	-	29552188	7	5	130	1	0	1	0	1	0	0	0	0	10363	188	7	0	2048	0	NF1	17	29552188	Frame_Shift_Del	DEL	AG	TCGA-BQ-7044-01A-11D-1961-08	61800	29552188	51643022	53	8089											
POLG2	11232	hgsc.bcm.edu	37	chr17	62486981	62486981	+	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	tcctaggttccacagggtttCtattaactcctttccccagg	7	14	7	13	0	1	0	0	0	1	0	5	0	5	0	5	3	1	2	5	3	3	6			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr17:62486981C>G	ENST00000539111.2	-	4	968	c.901G>C	c.(901-903)Gaa>Caa	p.E301Q		NM_007215.3	NP_009146.2	Q9UHN1	DPOG2_HUMAN	polymerase (DNA directed), gamma 2, accessory subunit	301					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)	extracellular vesicular exosome (GO:0070062)|mitochondrial chromosome (GO:0000262)|mitochondrial nucleoid (GO:0042645)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(4)|skin(2)|stomach(1)|urinary_tract(1)	15	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;4.97e-11)			CACAGGGTTTCTATTAACTCC	0.408																																					p.E301Q	Colon(3;18 21 435 17652 48887)	Atlas-SNP	.											.	POLG2	29	.	0			c.G901C						PASS	.						118	105	110					17																	62486981		2203	4300	6503	SO:0001583	missense	11232	exon4			GGGTTTCTATTAA	U94703	CCDS32706.1	17q23.3	2012-05-18			ENSG00000256525	ENSG00000256525		"DNA polymerases"	9180	protein-coding gene	gene with protein product		604983				9153213	Standard	NM_007215		Approved	MTPOLB, HP55	uc002jei.3	Q9UHN1		ENST00000539111.2:c.901G>C	chr17.hg19:g.62486981C>G	ENSP00000442563:p.Glu301Gln	86.0	0.0	.		81.0	39.0	.	NM_007215	O00419|Q0IJ81|Q96GW2|Q9UK35|Q9UK94	Missense_Mutation	SNP	ENST00000539111.2	hg19	CCDS32706.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.048199	0.75846	.	.	ENSG00000256525	ENST00000539111	T	0.79554	-1.28	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	D	0.88194	0.6371	M	0.81341	2.54	0.58432	D	0.999998	D;D	0.71674	0.998;0.998	P;P	0.55713	0.782;0.782	D	0.88758	0.3255	10	0.51188	T	0.08	-11.7483	19.247	0.93906	0.0:1.0:0.0:0.0	.	301;301	E5KS15;Q9UHN1	.;DPOG2_HUMAN	Q	301	ENSP00000442563:E301Q	ENSP00000442563:E301Q	E	-	1	0	POLG2	59917443	1.000000	0.71417	0.997000	0.53966	0.239000	0.25481	6.697000	0.74603	2.516000	0.84829	0.655000	0.94253	GAA	.	.	.	none		0.408	POLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443820.1	NM_007215		G	62486981	C	G	62486981	3	3	130	1	0	0	0	0	1	0	0	0	12208	922	32	4	576	4	POLG2	17	62486981	Missense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08	32934793	62486981	18708229	54	8090											
RNF213	57674	hgsc.bcm.edu	37	chr17	78293016	78293016	+	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	cccctctcccagatcactgcCtactgcaatagttgctggga	8	10	8	15	0	2	1	1	0	1	1	3	2	2	2	4	1	4	3	4	1	3	3			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr17:78293016C>G	ENST00000582970.1	+	17	3071	c.2928C>G	c.(2926-2928)gcC>gcG	p.A976A	RNF213_ENST00000319921.4_Silent_p.A976A|RNF213_ENST00000508628.2_Silent_p.A1025A|RNF213_ENST00000456466.1_Silent_p.A976A|CTD-2047H16.2_ENST00000576808.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	976					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)			AGATCACTGCCTACTGCAATA	0.522																																					p.A976A		Atlas-SNP	.											.	RNF213	766	.	0			c.C2928G						PASS	.						122	122	122					17																	78293016		2203	4300	6503	SO:0001819	synonymous_variant	57674	exon17			CACTGCCTACTGC	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.2928C>G	chr17.hg19:g.78293016C>G		217.0	0.0	.		218.0	79.0	.	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	hg19	CCDS58606.1																																																																																			.	.	.	none		0.522	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		G	78293016	C	G	78293016	2	3	130	1	0	0	0	0	0	0	0	1	13490	668	24	4		4	RNF213	17	78293016	Silent	SNP	C	TCGA-BQ-7044-01A-11D-1961-08	15806035	78293016	2902194	55	8091											
C19orf45	374877	hgsc.bcm.edu	37	chr19	7570473	7570475	+	In_Frame_Del	DEL	CGG	CGG	-																															ggaaattggtgccccggcccCggcagtctggacaccttcat																								rs568541151		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	CGG	CGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr19:7570473_7570475delCGG	ENST00000361664.2	+	6	1107_1109	c.966_968delCGG	c.(964-969)cccggc>ccc	p.G323del	CTD-2207O23.12_ENST00000599312.1_5'Flank	NM_198534.2	NP_940936.2	Q8NA69	CS045_HUMAN	chromosome 19 open reading frame 45	323										endometrium(1)|kidney(1)|liver(1)|lung(2)|ovary(2)|stomach(1)	8						GCCCCGGCCCCGGCAGTCTGGAC	0.571																																					p.322_323del		Atlas-INDEL	.											.	C19orf45	36	.	0			c.965_967del						PASS	.																																			SO:0001651	inframe_deletion	374877	exon6			.	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.966_968delCGG	chr19.hg19:g.7570473_7570475delCGG	ENSP00000355241:p.Gly323del	97.0	0.0	0		71.0	25.0	0.352113	NM_198534	Q8N115	In_Frame_Del	DEL	ENST00000361664.2	hg19	CCDS12179.2																																																																																			.	.	.	none		0.571	C19orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347808.1	NM_198534		-	7570475	CGG	-	7570473	7	5	130	1	0	1	0	1	0	0	0	0	1930	639	23	0	984	0	C19orf45	19	7570473	In_Frame_Del	DEL	CGG	TCGA-BQ-7044-01A-11D-1961-08		7570473	51558510	56	8092											
LPHN1	22859	hgsc.bcm.edu	37	chr19	14268166	14268166	+	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	tgcggtcggtctgcagccccCgcaggaagcagaaggtggag	8	5	17	11	3	1	1	0	0	1	1	2	3	1	3	2	5	4	3	2	5	2	0			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr19:14268166C>A	ENST00000340736.6	-	15	2954	c.2657G>T	c.(2656-2658)cGg>cTg	p.R886L	CTB-55O6.12_ENST00000592086.1_RNA|CTB-55O6.12_ENST00000588387.1_RNA|CTB-55O6.12_ENST00000588658.1_RNA|LPHN1_ENST00000361434.3_Missense_Mutation_p.R881L	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	886					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)	p.R886L(1)		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						CTGCAGCCCCCGCAGGAAGCA	0.587																																					p.R886L		Atlas-SNP	.											LPHN1,NS,carcinoma,0,1	LPHN1	107	.	1	Substitution - Missense(1)	endometrium(1)	c.G2657T						PASS	.						138	126	130					19																	14268166		2203	4300	6503	SO:0001583	missense	22859	exon15			AGCCCCCGCAGGA	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.2657G>T	chr19.hg19:g.14268166C>A	ENSP00000340688:p.Arg886Leu	113.0	1.0	.		135.0	7.0	.	NM_001008701	Q96IE7|Q9BU07|Q9HAR3	Missense_Mutation	SNP	ENST00000340736.6	hg19	CCDS32928.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.275126	0.80580	.	.	ENSG00000072071	ENST00000340736;ENST00000361434	T;T	0.58652	0.32;0.32	4.62	3.57	0.40892	GPCR, family 2-like (1);	0.000000	0.64402	D	0.000001	T	0.80059	0.4554	M	0.92555	3.32	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.85130	0.992;0.997	D	0.84354	0.0534	10	0.87932	D	0	.	12.6877	0.56956	0.0:0.8322:0.1678:0.0	.	881;886	O94910-2;O94910	.;LPHN1_HUMAN	L	886;881	ENSP00000340688:R886L;ENSP00000355328:R881L	ENSP00000340688:R886L	R	-	2	0	LPHN1	14129166	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.754000	0.85163	1.038000	0.40049	0.491000	0.48974	CGG	.	.	.	none		0.587	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921		A	14268166	C	A	14268166	3	1	130	1	0	0	0	0	1	0	0	0	8922	652	23	4	1807	4	LPHN1	19	14268166	Missense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08	6697693	14268166	44860817	57	8093											
EPS15L1	58513	hgsc.bcm.edu	37	chr19	16503123	16503124	+	Missense_Mutation	DNP	GT	GT	AA																															caccccactcaccttcgaagGtaaggaagggtttttcgtga																										TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G|T	G|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr19:16503123_16503124GT>AA	ENST00000248070.6	-	19	2233_2234	c.2094_2095AC>TT	c.(2092-2097)ttACct>ttTTct	p.698_699LP>FS	EPS15L1_ENST00000594975.1_Missense_Mutation_p.700_701LP>FS|EPS15L1_ENST00000455140.2_Missense_Mutation_p.698_699LP>FS|EPS15L1_ENST00000535753.2_Missense_Mutation_p.698_699LP>FS	NM_021235.2	NP_067058.1	Q9UBC2	EP15R_HUMAN	epidermal growth factor receptor pathway substrate 15-like 1	698	15 X 3 AA repeats of D-P-F.				endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	clathrin coat of coated pit (GO:0030132)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(4)|skin(2)	30						ACCTTCGAAGGTAAGGAAGGGT	0.559																																					p.P699S|p.L698F		Atlas-SNP	.											.	EPS15L1	81	.	0			c.C2095T|c.A2094T						PASS	.																																			SO:0001583	missense	58513	exon19			TCGAAGGTAAGGA|CGAAGGTAAGGAA	AF110265	CCDS32944.1, CCDS58653.1, CCDS58654.1, CCDS59363.1	19p13.12	2013-01-10				ENSG00000127527		"EF-hand domain containing"	24634	protein-coding gene	gene with protein product							Standard	NM_001258374		Approved	eps15R	uc002ndx.4	Q9UBC2		ENST00000248070.6:c.2094_2095delinsAA	chr19.hg19:g.16503123_16503124delinsAA	ENSP00000248070:p.L698_P699delinsFS	82.0|84.0	0.0	.		80.0|79.0	43.0	.	NM_021235	A2RRF3|A5PL29|B4DKA3	Missense_Mutation	SNP	ENST00000248070.6	hg19	CCDS32944.1																																																																																			.	.	.	none		0.559	EPS15L1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461040.1	NM_021235		AA	16503124	GT	AA	16503123	3	1	130	1	0	0	0	0	1	0	0	0	5195	1261	44	2	519	2	EPS15L1	19	16503123	Missense_Mutation	DNP	GT	TCGA-BQ-7044-01A-11D-1961-08	2234957	16503123	42625860	58	8094											
EPS15L1	58513	hgsc.bcm.edu	37	chr19	16551694	16551694	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtttgtccaagaaccctttAccttctggatcggccaagtc	8	13	8	12	1	1	1	0	0	1	1	4	2	2	2	4	2	2	1	4	2	4	4			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr19:16551694A>G	ENST00000248070.6	-	4	331	c.192T>C	c.(190-192)ggT>ggC	p.G64G	CTD-2013N17.4_ENST00000587343.1_RNA|EPS15L1_ENST00000594975.1_Silent_p.G64G|EPS15L1_ENST00000455140.2_Silent_p.G64G|EPS15L1_ENST00000535753.2_Silent_p.G64G|EPS15L1_ENST00000597937.1_Silent_p.G64G	NM_021235.2	NP_067058.1	Q9UBC2	EP15R_HUMAN	epidermal growth factor receptor pathway substrate 15-like 1	64	EH 1. {ECO:0000255|PROSITE- ProRule:PRU00077}.|Interaction with DAB2. {ECO:0000250}.				endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	clathrin coat of coated pit (GO:0030132)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(4)|skin(2)	30						AGAACCCTTTACCTTCTGGAT	0.527																																					p.G64G		Atlas-SNP	.											.	EPS15L1	81	.	0			c.T192C						PASS	.						270	276	274					19																	16551694		2203	4300	6503	SO:0001819	synonymous_variant	58513	exon4			CCCTTTACCTTCT	AF110265	CCDS32944.1, CCDS58653.1, CCDS58654.1, CCDS59363.1	19p13.12	2013-01-10				ENSG00000127527		"EF-hand domain containing"	24634	protein-coding gene	gene with protein product							Standard	NM_001258374		Approved	eps15R	uc002ndx.4	Q9UBC2		ENST00000248070.6:c.192T>C	chr19.hg19:g.16551694A>G		541.0	1.0	.		503.0	186.0	.	NM_021235	A2RRF3|A5PL29|B4DKA3	Silent	SNP	ENST00000248070.6	hg19	CCDS32944.1																																																																																			.	.	.	none		0.527	EPS15L1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461040.1	NM_021235		G	16551694	A	G	16551694	2	3	130	1	0	0	0	0	0	0	0	1	5195	378	14	3		3	EPS15L1	19	16551694	Silent	SNP	A	TCGA-BQ-7044-01A-11D-1961-08	48571	16551694	42577289	59	8095											
BCAM	4059	hgsc.bcm.edu	37	chr19	45322619	45322619	+	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	atagcccgcagagccaatccCcggacggcagggttgggtga	9	5	15	12	3	0	2	0	1	0	1	1	3	1	3	4	4	2	3	4	4	2	2			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr19:45322619C>T	ENST00000270233.6	+	12	1512	c.1490C>T	c.(1489-1491)cCc>cTc	p.P497L	BCAM_ENST00000589651.1_Missense_Mutation_p.P497L	NM_001013257.2|NM_005581.4	NP_001013275.1|NP_005572.2	P50895	BCAM_HUMAN	basal cell adhesion molecule (Lutheran blood group)	497	Ig-like C2-type 3.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	laminin binding (GO:0043236)|laminin receptor activity (GO:0005055)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				GAGCCAATCCCCGGACGGCAG	0.662																																					p.P497L		Atlas-SNP	.											.	BCAM	53	.	0			c.C1490T						PASS	.						59	64	62					19																	45322619		2203	4300	6503	SO:0001583	missense	4059	exon12			CAATCCCCGGACG	X83425	CCDS12644.1, CCDS42575.1	19q12-q13	2014-07-18	2006-02-23	2006-01-12		ENSG00000187244		"CD molecules", "Blood group antigens", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6722	protein-coding gene	gene with protein product		612773	"Lutheran blood group (Auberger b antigen included)", "basal cell adhesion molecule (Lu and Au blood groups)"	LU			Standard	NM_005581		Approved	CD239	uc002ozu.4	P50895		ENST00000270233.6:c.1490C>T	chr19.hg19:g.45322619C>T	ENSP00000270233:p.Pro497Leu	84.0	0.0	.		46.0	22.0	.	NM_001013257	A8MYF9|A9YWT5|A9YWT6|Q86VC7	Missense_Mutation	SNP	ENST00000270233.6	hg19	CCDS12644.1	.	.	.	.	.	.	.	.	.	.	.	0.017	-1.487632	0.01018	.	.	ENSG00000187244	ENST00000270233;ENST00000391955	T;T	0.03124	4.04;4.04	4.31	0.796	0.18648	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.02533	0.0077	L	0.28694	0.88	0.09310	N	1	B	0.12013	0.005	B	0.12156	0.007	T	0.49532	-0.8930	9	0.13853	T	0.58	-6.5334	3.4865	0.07622	0.1986:0.5733:0.0:0.2281	.	497	P50895	BCAM_HUMAN	L	497	ENSP00000270233:P497L;ENSP00000375817:P497L	ENSP00000270233:P497L	P	+	2	0	BCAM	50014459	0.003000	0.15002	0.001000	0.08648	0.113000	0.19764	-0.023000	0.12456	0.031000	0.15407	0.543000	0.68304	CCC	.	.	.	none		0.662	BCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453220.1	NM_005581		T	45322619	C	T	45322619	3	4	130	1	0	0	0	0	1	0	0	0	1344	623	22	2	1536	2	BCAM	19	45322619	Missense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08	28770925	45322619	13806364	60	8096											
FCAR	2204	hgsc.bcm.edu	37	chr19	55385758	55385758	+	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	tcagcacgatggaccccaaaCagaccaccctcctgtgtctt	10	8	7	16	1	2	1	1	0	1	1	3	3	3	2	5	1	2	1	5	1	1	1			TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr19:55385758C>T	ENST00000355524.3	+	1	23	c.13C>T	c.(13-15)Cag>Tag	p.Q5*	FCAR_ENST00000391725.3_Nonsense_Mutation_p.Q5*|FCAR_ENST00000353758.4_Nonsense_Mutation_p.Q5*|FCAR_ENST00000345937.4_Nonsense_Mutation_p.Q5*|FCAR_ENST00000391726.3_Nonsense_Mutation_p.Q5*|FCAR_ENST00000469767.1_Nonsense_Mutation_p.Q5*|FCAR_ENST00000391724.3_Nonsense_Mutation_p.Q5*|FCAR_ENST00000482092.2_3'UTR|FCAR_ENST00000391723.3_Nonsense_Mutation_p.Q5*|FCAR_ENST00000359272.4_Nonsense_Mutation_p.Q5*	NM_002000.2	NP_001991.1	P24071	FCAR_HUMAN	Fc fragment of IgA, receptor for	5					immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(2)	24				GBM - Glioblastoma multiforme(193;0.0443)		GGACCCCAAACAGACCACCCT	0.483																																					p.Q5X		Atlas-SNP	.											.	FCAR	110	.	0			c.C13T						PASS	.						135	122	127					19																	55385758		2203	4300	6503	SO:0001587	stop_gained	2204	exon1			CCCAAACAGACCA	X54150	CCDS12907.1, CCDS12908.1, CCDS12909.1, CCDS12910.1, CCDS42622.1, CCDS42623.1, CCDS42624.1, CCDS42625.1, CCDS46180.1	19q13.42	2013-01-29			ENSG00000186431	ENSG00000186431		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3608	protein-coding gene	gene with protein product		147045				1577457	Standard	NM_133269		Approved	CD89	uc002qhr.1	P24071	OTTHUMG00000065936	ENST00000355524.3:c.13C>T	chr19.hg19:g.55385758C>T	ENSP00000347714:p.Gln5*	138.0	0.0	.		136.0	59.0	.	NM_133279	Q13603|Q13604|Q15727|Q15728|Q1AJL7|Q1AJL8|Q1AJL9|Q53X38|Q53X39|Q92587|Q92588|Q92590|Q92592|Q92593|Q9UEK0	Nonsense_Mutation	SNP	ENST00000355524.3	hg19	CCDS12907.1	.	.	.	.	.	.	.	.	.	.	C	18.11	3.549835	0.65311	.	.	ENSG00000186431	ENST00000433231;ENST00000391726;ENST00000355524;ENST00000391725;ENST00000345937;ENST00000353758;ENST00000359272;ENST00000391723;ENST00000391724	.	.	.	2.76	1.72	0.24424	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	.	7.8266	0.29318	0.0:0.2588:0.7412:0.0	.	.	.	.	X	5	.	ENSP00000338257:Q5X	Q	+	1	0	FCAR	60077570	0.000000	0.05858	0.001000	0.08648	0.021000	0.10359	-0.054000	0.11826	0.725000	0.32318	-0.226000	0.12346	CAG	.	.	.	none		0.483	FCAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000141243.1	NM_002000		T	55385758	C	T	55385758	4	4	130	1	0	0	0	0	0	1	0	0	5780	479	17	2	15	2	FCAR	19	55385758	Nonsense_Mutation	SNP	C	TCGA-BQ-7044-01A-11D-1961-08	10063139	55385758	3743225	61	8097											
PARD6B	84612	hgsc.bcm.edu	37	chr20	49366983	49366991	+	In_Frame_Del	DEL	TCAAAAACT	TCAAAAACT	-																															tttgaaacacatgctccagaTcaaaaactcttagaagaaga																										TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	TCAAAAACT	TCAAAAACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chr20:49366983_49366991delTCAAAAACT	ENST00000371610.2	+	3	1320_1328	c.1077_1085delTCAAAAACT	c.(1075-1086)gatcaaaaactc>gac	p.QKL360del	PARD6B_ENST00000396039.1_Intron	NM_032521.2	NP_115910.1	Q9BYG5	PAR6B_HUMAN	par-6 family cell polarity regulator beta	360					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						ATGCTCCAGATCAAAAACTCTTAGAAGAA	0.397																																					p.359_362del		Atlas-INDEL	.											.	PARD6B	31	.	0			c.1076_1084del						PASS	.																																			SO:0001651	inframe_deletion	84612	exon3			.	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.1077_1085delTCAAAAACT	chr20.hg19:g.49366983_49366991delTCAAAAACT	ENSP00000360672:p.Gln360_Leu362del	66.0	0.0	0		74.0	22.0	0.297297	NM_032521	A2A2A7|Q9Y510	In_Frame_Del	DEL	ENST00000371610.2	hg19	CCDS33485.1																																																																																			.	.	.	none		0.397	PARD6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079697.2	NM_032521		-	49366991	TCAAAAACT	-	49366983	7	5	130	1	0	1	0	1	0	0	0	0	11453	1432	50	0	1087	0	PARD6B	20	49366983	In_Frame_Del	DEL	TCAAAAACT	TCGA-BQ-7044-01A-11D-1961-08		49366983	13658537	62	8098											
PORCN	64840	hgsc.bcm.edu	37	chrX	48371012	48371012	+	Frame_Shift_Del	DEL	G	G	-																															cagaaggtggcccggagcctGgcactggccctgctgtgcct																										TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	g.chrX:48371012delG	ENST00000326194.6	+	5	634	c.591delG	c.(589-591)ctgfs	p.L197fs	PORCN_ENST00000537758.1_Frame_Shift_Del_p.L197fs|PORCN_ENST00000361988.3_Frame_Shift_Del_p.L197fs|PORCN_ENST00000359882.4_Frame_Shift_Del_p.L197fs|PORCN_ENST00000355092.3_Frame_Shift_Del_p.L197fs|PORCN_ENST00000355961.4_Frame_Shift_Del_p.L197fs|PORCN_ENST00000367574.4_Frame_Shift_Del_p.L126fs	NM_203475.1	NP_982301.1	Q9H237	PORCN_HUMAN	porcupine homolog (Drosophila)	197					glycoprotein metabolic process (GO:0009100)|Wnt signaling pathway (GO:0016055)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|integral component of endoplasmic reticulum membrane (GO:0030176)	transferase activity, transferring acyl groups (GO:0016746)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CCCGGAGCCTGGCACTGGCCC	0.647																																					p.L197fs		Atlas-INDEL	.											.	PORCN	61	.	0			c.590delT						PASS	.						54	48	50					X																	48371012		2203	4300	6503	SO:0001589	frameshift_variant	64840	exon5			.	AF317058	CCDS14296.1, CCDS14297.1, CCDS14298.1, CCDS14299.1	Xp11.23	2014-02-05			ENSG00000102312	ENSG00000102312			17652	protein-coding gene	gene with protein product		300651	"dermal hypoplasia, focal"	DHOF		10866835, 12034504, 17546030	Standard	NM_203474		Approved	MG61, PORC, PPN, por	uc004djv.1	Q9H237	OTTHUMG00000024116	ENST00000326194.6:c.591delG	chrX.hg19:g.48371012delG	ENSP00000322304:p.Leu197fs	15.0	0.0	0		11.0	11.0	1	NM_203475	B2RBN8|B7ZAR3|Q14829|Q9H234|Q9H235|Q9H236|Q9UJU7	Frame_Shift_Del	DEL	ENST00000326194.6	hg19	CCDS14299.1																																																																																			.	.	.	none		0.647	PORCN-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356990.1	NM_022825		-	48371012	G	-	48371012	7	5	130	1	0	1	0	1	0	0	0	0	12265	1335	47	0	609	0	PORCN	23	48371012	Frame_Shift_Del	DEL	G	TCGA-BQ-7044-01A-11D-1961-08		48371012	106899548	63	8099											
KIAA1522	57648	hgsc.bcm.edu	37	chr1	33236795	33236795	+	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	ggtgcctgcccccttctcccCacctccctccaagcccagga	5	7	7	22	0	1	0	0	0	1	0	4	1	3	1	9	2	3	0	9	2	1	1			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr1:33236795C>A	ENST00000373480.1	+	6	1941	c.1838C>A	c.(1837-1839)cCa>cAa	p.P613Q	KIAA1522_ENST00000373481.3_Missense_Mutation_p.P624Q|KIAA1522_ENST00000294521.3_Intron|KIAA1522_ENST00000401073.2_Missense_Mutation_p.P672Q	NM_001198972.1	NP_001185901.1	Q9P206	K1522_HUMAN	KIAA1522	613	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)				CCCTTCTCCCCACCTCCCTCC	0.647																																					p.P672Q		Atlas-SNP	.											.	KIAA1522	68	.	0			c.C2015A						PASS	.						58	64	62					1																	33236795		1901	4107	6008	SO:0001583	missense	57648	exon6			TCTCCCCACCTCC	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.1838C>A	chr1.hg19:g.33236795C>A	ENSP00000362579:p.Pro613Gln	134.0	0.0	.		141.0	46.0	.	NM_020888	B4DQU8|B5MDY0|C9JH84|Q8TCQ0	Missense_Mutation	SNP	ENST00000373480.1	hg19	CCDS55588.1	.	.	.	.	.	.	.	.	.	.	C	12.84	2.057475	0.36277	.	.	ENSG00000162522	ENST00000401073;ENST00000373481;ENST00000373480	T;T;T	0.18502	2.21;2.21;2.24	4.07	4.07	0.47477	.	0.000000	0.56097	D	0.000038	T	0.33673	0.0871	L	0.56769	1.78	0.38739	D	0.95385	D;D;D	0.76494	0.99;0.99;0.999	P;P;D	0.67548	0.901;0.901;0.952	T	0.16217	-1.0410	10	0.59425	D	0.04	-5.8801	11.0055	0.47631	0.0:0.9058:0.0:0.0942	.	624;613;672	Q9P206-3;Q9P206;Q9P206-2	.;K1522_HUMAN;.	Q	672;624;613	ENSP00000383851:P672Q;ENSP00000362580:P624Q;ENSP00000362579:P613Q	ENSP00000362579:P613Q	P	+	2	0	KIAA1522	33009382	0.814000	0.29104	0.958000	0.39756	0.821000	0.46438	3.744000	0.55112	1.954000	0.56735	0.563000	0.77884	CCA	.	.	.	none		0.647	KIAA1522-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022130.1			A	33236795	C	A	33236795	3	1	131	1	0	0	0	0	1	0	0	0	8245	594	21	4	2037	4	KIAA1522	1	33236795	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08		33236795	216013826	1	8100											
SLC5A9	200010	hgsc.bcm.edu	37	chr1	48708165	48708165	+	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	ggtggactcggaactgccccCtctctgagctggagaaggag	8	7	15	11	1	1	2	0	1	1	1	3	6	1	5	2	5	3	1	2	5	2	0			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr1:48708165C>T	ENST00000438567.2	+	13	1766	c.1714C>T	c.(1714-1716)Ctc>Ttc	p.L572F	SLC5A9_ENST00000471020.1_3'UTR|SLC5A9_ENST00000533824.1_Missense_Mutation_p.L593F|SLC5A9_ENST00000236495.5_Missense_Mutation_p.L597F	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	572					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						GAACTGCCCCCTCTCTGAGCT	0.597																																					p.L597F		Atlas-SNP	.											.	SLC5A9	82	.	0			c.C1789T						PASS	.						73	73	73					1																	48708165		2203	4300	6503	SO:0001583	missense	200010	exon14			TGCCCCCTCTCTG	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.1714C>T	chr1.hg19:g.48708165C>T	ENSP00000401730:p.Leu572Phe	129.0	0.0	.		162.0	9.0	.	NM_001135181	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Missense_Mutation	SNP	ENST00000438567.2	hg19	CCDS30709.2	.	.	.	.	.	.	.	.	.	.	C	2.600	-0.293103	0.05568	.	.	ENSG00000117834	ENST00000533824;ENST00000438567;ENST00000236495	T;T;T	0.63255	-0.03;-0.03;-0.03	4.42	2.25	0.28309	.	2.354250	0.01631	N	0.023545	T	0.51381	0.1671	L	0.29908	0.895	0.09310	N	1	B;B;B	0.25521	0.128;0.023;0.112	B;B;B	0.29716	0.04;0.058;0.106	T	0.35649	-0.9780	10	0.44086	T	0.13	.	2.3723	0.04333	0.2782:0.4525:0.1682:0.1011	.	593;572;597	E9PJ08;Q2M3M2;E9PAK4	.;SC5A9_HUMAN;.	F	593;572;597	ENSP00000431900:L593F;ENSP00000401730:L572F;ENSP00000236495:L597F	ENSP00000236495:L597F	L	+	1	0	SLC5A9	48480752	0.000000	0.05858	0.002000	0.10522	0.032000	0.12392	-2.295000	0.01143	0.283000	0.22279	0.655000	0.94253	CTC	.	.	.	none		0.597	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174		T	48708165	C	T	48708165	3	4	131	1	0	0	0	0	1	0	0	0	14685	681	24	2	1843	2	SLC5A9	1	48708165	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	15471370	48708165	200542456	2	8101											
CTH	1491	hgsc.bcm.edu	37	chr1	70895506	70895506	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctctgggagctgatatttcTatgtattctgcaacaaaata	12	14	8	7	0	3	1	0	1	3	0	3	2	3	2	0	1	3	4	0	1	7	6			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr1:70895506T>C	ENST00000370938.3	+	6	762	c.618T>C	c.(616-618)tcT>tcC	p.S206S	CTH_ENST00000346806.2_Silent_p.S162S|CTH_ENST00000411986.2_Silent_p.S174S|CTH_ENST00000464926.1_3'UTR	NM_001902.5	NP_001893.2	Q96IQ7	VSIG2_HUMAN	cystathionine gamma-lyase	0	Ig-like C2-type.					integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						CTGATATTTCTATGTATTCTG	0.353																																					p.S206S		Atlas-SNP	.											.	CTH	48	.	0			c.T618C						PASS	.						103	97	99					1																	70895506		2203	4300	6503	SO:0001819	synonymous_variant	1491	exon6			TATTTCTATGTAT	BC015807	CCDS650.1, CCDS651.1, CCDS53333.1	1p31.1	2014-06-24	2014-06-24		ENSG00000116761	ENSG00000116761	4.4.1.1		2501	protein-coding gene	gene with protein product		607657	"cystathionase (cystathionine gamma-lyase)"			1339280	Standard	NM_001902		Approved		uc001dfd.3	P32929	OTTHUMG00000009352	ENST00000370938.3:c.618T>C	chr1.hg19:g.70895506T>C		76.0	0.0	.		79.0	26.0	.	NM_001902	O95791|Q9NX42	Silent	SNP	ENST00000370938.3	hg19	CCDS650.1																																																																																			.	.	.	none		0.353	CTH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025918.1	NM_001902		C	70895506	T	C	70895506	2	2	131	1	0	0	0	0	0	0	0	1	4011	1509	53	3		3	CTH	1	70895506	Silent	SNP	T	TCGA-BQ-7045-01A-31D-1961-08	22187341	70895506	178355115	3	8102											
ABCA4	24	hgsc.bcm.edu	37	chr1	94528186	94528186	+	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	tggaggtagattccaactggAgcctccgcctgcacctggct	7	9	12	13	1	0	1	0	0	0	1	2	3	2	3	5	4	3	3	5	4	2	2			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr1:94528186A>T	ENST00000370225.3	-	13	1970	c.1884T>A	c.(1882-1884)gcT>gcA	p.A628A	ABCA4_ENST00000535735.1_Silent_p.A628A	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	628					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)		TTCCAACTGGAGCCTCCGCCT	0.572																																					p.A628A		Atlas-SNP	.											.	ABCA4	275	.	0			c.T1884A						PASS	.						76	74	75					1																	94528186		2203	4300	6503	SO:0001819	synonymous_variant	24	exon13			AACTGGAGCCTCC	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.1884T>A	chr1.hg19:g.94528186A>T		63.0	0.0	.		59.0	16.0	.	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	hg19	CCDS747.1																																																																																			.	.	.	none		0.572	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		T	94528186	A	T	94528186	2	4	131	1	0	0	0	0	0	0	0	1	34	291	11	5		5	ABCA4	1	94528186	Silent	SNP	A	TCGA-BQ-7045-01A-31D-1961-08	23632680	94528186	154722435	4	8103											
SEMA6C	10500	hgsc.bcm.edu	37	chr1	151112138	151112138	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgggcaccagcccctccccTtcttcttcggcttgaagatc	5	12	8	16	1	2	2	0	1	2	1	5	2	3	2	5	2	1	2	5	2	1	5	rs200312578		TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr1:151112138T>C	ENST00000341697.3	-	5	1964	c.273A>G	c.(271-273)gaA>gaG	p.E91E				Q9H3T2	SEM6C_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	91	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	28	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			GCCCCTCCCCTTCTTCTTCGG	0.582																																					p.E91E		Atlas-SNP	.											.	SEMA6C	70	.	0			c.A273G						PASS	.						55	53	54					1																	151112138		2203	4300	6503	SO:0001819	synonymous_variant	10500	exon5			CTCCCCTTCTTCT	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.273A>G	chr1.hg19:g.151112138T>C		50.0	0.0	.		62.0	4.0	.	NM_001178061	D3DV15|Q5JR71|Q5JR72|Q5JR73|Q8WXT8|Q8WXT9|Q8WXU0|Q96JF8	Silent	SNP	ENST00000341697.3	hg19	CCDS984.1																																																																																			.	T|0.999;G|0.001	.	alt		0.582	SEMA6C-004	KNOWN	alternative_5_UTR|mRNA_start_NF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034074.1	NM_030913		C	151112138	T	C	151112138	2	2	131	1	0	0	0	0	0	0	0	1	14054	1606	56	3		3	SEMA6C	1	151112138	Silent	SNP	T	TCGA-BQ-7045-01A-31D-1961-08	56583952	151112138	98138483	5	8104											
PROX1	5629	hgsc.bcm.edu	37	chr1	214170437	214170438	+	Frame_Shift_Ins	INS	-	-	AT																															cagtgtggcattaaggggcaINSatgaaaatgaaagagagatg																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr1:214170437_214170438insAT	ENST00000366958.4	+	2	1167_1168	c.559_560insAT	c.(559-561)aatfs	p.N187fs	PROX1_ENST00000498508.2_Frame_Shift_Ins_p.N187fs|PROX1_ENST00000435016.1_Frame_Shift_Ins_p.N187fs|PROX1_ENST00000261454.4_Frame_Shift_Ins_p.N187fs	NM_001270616.1	NP_001257545.1	Q92786	PROX1_HUMAN	prospero homeobox 1	187					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)		ATTAAGGGGCAATGAAAATGAA	0.505																																					p.N187fs		Atlas-INDEL	.											.	PROX1	124	.	0			c.559_560insAT						PASS	.																																			SO:0001589	frameshift_variant	5629	exon2			.	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.560_561dupAT	chr1.hg19:g.214170438_214170439dupAT	ENSP00000355925:p.Asn187fs	79.0	0.0	0		74.0	21.0	0.283784	NM_001270616	A6NK29|A8K2B1|Q5SW76|Q8TB91	Frame_Shift_Ins	INS	ENST00000366958.4	hg19	CCDS31021.1																																																																																			.	.	.	none		0.505	PROX1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089727.6	NM_002763		AT	214170438	-	AT	214170437	7	5	131	1	0	1	1	0	0	0	0	0	12570	130	5	0	561	0	PROX1	1	214170437	Frame_Shift_Ins	INS	-	TCGA-BQ-7045-01A-31D-1961-08	63058299	214170437	35080184	6	8105											
ADD2	119	hgsc.bcm.edu	37	chr2	70900055	70900055	+	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	taaagggctctttgtctctgCctccttcgctgggctctgca	4	14	10	13	1	3	0	0	0	3	0	6	0	4	0	2	2	2	4	2	2	2	3	rs138503054		TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr2:70900055C>A	ENST00000264436.4	-	15	2269	c.1825G>T	c.(1825-1827)Gca>Tca	p.A609S	ADD2_ENST00000407644.2_Missense_Mutation_p.A609S|ADD2_ENST00000355733.3_Missense_Mutation_p.R637S	NM_001617.3	NP_001608.1	P35612	ADDB_HUMAN	adducin 2 (beta)	609					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						TTTGTCTCTGCCTCCTTCGCT	0.547																																					p.R637S		Atlas-SNP	.											.	ADD2	261	.	0			c.G1911T						PASS	.						43	40	41					2																	70900055		2203	4300	6503	SO:0001583	missense	119	exon16			TCTCTGCCTCCTT	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.1825G>T	chr2.hg19:g.70900055C>A	ENSP00000264436:p.Ala609Ser	41.0	0.0	.		52.0	17.0	.	NM_017488	A8K4P2|B4DM17|D6W5G7|D6W5G8|Q13482|Q16412|Q59G82|Q5U5P4|Q6P0P2|Q6PGQ4|Q7Z688|Q7Z689|Q7Z690|Q7Z691	Missense_Mutation	SNP	ENST00000264436.4	hg19	CCDS1906.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.858|0.858	-0.736122|-0.736122	0.03111|0.03111	.|.	.|.	ENSG00000075340|ENSG00000075340	ENST00000264436;ENST00000407644;ENST00000456320|ENST00000355733	T;T|T	0.19938|0.07908	2.11;2.11|3.15	5.97|5.97	-0.847|-0.847	0.10730|0.10730	.|.	0.549745|.	0.16787|.	N|.	0.199546|.	T|T	0.06554|0.06554	0.0168|0.0168	.|.	.|.	.|.	0.28924|0.28924	N|N	0.891981|0.891981	B;B|P	0.02656|0.37500	0.0;0.0|0.597	B;B|B	0.08055|0.42916	0.0;0.003|0.402	T|T	0.33954|0.33954	-0.9848|-0.9848	9|7	0.05351|.	T|.	0.99|.	-0.0968|-0.0968	1.2149|1.2149	0.01912|0.01912	0.2:0.3933:0.2045:0.2022|0.2:0.3933:0.2045:0.2022	.|.	609;609|637	Q05DK5;P35612|P35612-3	.;ADDB_HUMAN|.	S|S	609;609;361|637	ENSP00000264436:A609S;ENSP00000384677:A609S|ENSP00000347972:R637S	ENSP00000264436:A609S|.	A|R	-|-	1|3	0|2	ADD2|ADD2	70753563|70753563	0.012000|0.012000	0.17670|0.17670	0.453000|0.453000	0.27007|0.27007	0.423000|0.423000	0.31445|0.31445	-0.223000|-0.223000	0.09177|0.09177	0.306000|0.306000	0.22856|0.22856	0.655000|0.655000	0.94253|0.94253	GCA|AGG	.	C|1.000;T|0.000	.	alt		0.547	ADD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251918.4	NM_001617		A	70900055	C	A	70900055	3	1	131	1	0	0	0	0	1	0	0	0	305	739	26	4	363	4	ADD2	2	70900055	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08		70900055	172299318	7	8106											
PLEKHB2	55041	hgsc.bcm.edu	37	chr2	131904282	131904282	+	Frame_Shift_Del	DEL	C	C	-																															agacaacgacagcgacctggCactgggcatgctggcaggag																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr2:131904282delC	ENST00000403716.1	+	8	1165	c.605delC	c.(604-606)gcafs	p.A202fs	PLEKHB2_ENST00000438882.2_Frame_Shift_Del_p.H166fs|PLEKHB2_ENST00000234115.6_Frame_Shift_Del_p.A201fs|PLEKHB2_ENST00000409612.1_Frame_Shift_Del_p.A202fs|PLEKHB2_ENST00000439822.2_Frame_Shift_Del_p.H158fs|PLEKHB2_ENST00000538982.1_Frame_Shift_Del_p.A154fs|PLEKHB2_ENST00000409279.1_Frame_Shift_Del_p.A202fs|PLEKHB2_ENST00000303908.3_Intron|PLEKHB2_ENST00000404460.1_Intron|PLEKHB2_ENST00000409158.1_Frame_Shift_Del_p.A210fs	NM_001100623.1|NM_001267062.1|NM_001267063.1|NM_001267064.1|NM_001267065.1|NM_001267066.1|NM_017958.2	NP_001094093.1|NP_001253991.1|NP_001253992.1|NP_001253993.1|NP_001253994.1|NP_001253995.1|NP_060428.2	Q96CS7	PKHB2_HUMAN	pleckstrin homology domain containing, family B (evectins) member 2	202						endosome (GO:0005768)|membrane (GO:0016020)				large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.0828)		AGCGACCTGGCACTGGGCATG	0.507																																					p.A216fs		Atlas-INDEL	.											.	PLEKHB2	47	.	0			c.646delG						PASS	.						160	166	164					2																	131904282		2203	4300	6503	SO:0001589	frameshift_variant	55041	exon9			.		CCDS2166.1, CCDS46413.1, CCDS58729.1, CCDS58730.1, CCDS74576.1, CCDS74577.1	2q22.1	2013-01-10			ENSG00000115762	ENSG00000115762		"Pleckstrin homology (PH) domain containing"	19236	protein-coding gene	gene with protein product						10200314	Standard	NM_017958		Approved	EVT2, FLJ20783	uc031rpd.1	Q96CS7	OTTHUMG00000131656	ENST00000403716.1:c.605delC	chr2.hg19:g.131904282delC	ENSP00000385892:p.Ala202fs	293.0	0.0	0		311.0	83.0	0.266881	NM_001267062	B4DF08|B4DZ66|B8ZZN1|Q53FF1|Q53TH7|Q86W37|Q9BV75|Q9NWK1	Frame_Shift_Del	DEL	ENST00000403716.1	hg19	CCDS46413.1																																																																																			.	.	.	none		0.507	PLEKHB2-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331304.2	NM_017958		-	131904282	C	-	131904282	7	5	131	1	0	1	0	1	0	0	0	0	12072	710	25	0	631	0	PLEKHB2	2	131904282	Frame_Shift_Del	DEL	C	TCGA-BQ-7045-01A-31D-1961-08	61004227	131904282	111295091	8	8107	86	2									
PLEKHB2	55041	hgsc.bcm.edu	37	chr2	131904284	131904284	+	Missense_Mutation	SNP	C	C	G																															acaacgacagcgacctggcaCtgggcatgctggcaggagca																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr2:131904284C>G	ENST00000403716.1	+	8	1167	c.607C>G	c.(607-609)Ctg>Gtg	p.L203V	PLEKHB2_ENST00000438882.2_Missense_Mutation_p.H166Q|PLEKHB2_ENST00000234115.6_Missense_Mutation_p.L202V|PLEKHB2_ENST00000409612.1_Missense_Mutation_p.L203V|PLEKHB2_ENST00000439822.2_Missense_Mutation_p.H158Q|PLEKHB2_ENST00000538982.1_Missense_Mutation_p.L155V|PLEKHB2_ENST00000409279.1_Missense_Mutation_p.L203V|PLEKHB2_ENST00000303908.3_Intron|PLEKHB2_ENST00000404460.1_Intron|PLEKHB2_ENST00000409158.1_Missense_Mutation_p.L211V	NM_001100623.1|NM_001267062.1|NM_001267063.1|NM_001267064.1|NM_001267065.1|NM_001267066.1|NM_017958.2	NP_001094093.1|NP_001253991.1|NP_001253992.1|NP_001253993.1|NP_001253994.1|NP_001253995.1|NP_060428.2	Q96CS7	PKHB2_HUMAN	pleckstrin homology domain containing, family B (evectins) member 2	203						endosome (GO:0005768)|membrane (GO:0016020)				large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.0828)		CGACCTGGCACTGGGCATGCT	0.512																																					p.L217V		Atlas-SNP	.											.	PLEKHB2	47	.	0			c.C649G						PASS	.						158	165	162					2																	131904284		2203	4300	6503	SO:0001583	missense	55041	exon9			CTGGCACTGGGCA		CCDS2166.1, CCDS46413.1, CCDS58729.1, CCDS58730.1, CCDS74576.1, CCDS74577.1	2q22.1	2013-01-10			ENSG00000115762	ENSG00000115762		"Pleckstrin homology (PH) domain containing"	19236	protein-coding gene	gene with protein product						10200314	Standard	NM_017958		Approved	EVT2, FLJ20783	uc031rpd.1	Q96CS7	OTTHUMG00000131656	ENST00000403716.1:c.607C>G	chr2.hg19:g.131904284C>G	ENSP00000385892:p.Leu203Val	305.0	0.0	.		310.0	84.0	.	NM_001267062	B4DF08|B4DZ66|B8ZZN1|Q53FF1|Q53TH7|Q86W37|Q9BV75|Q9NWK1	Missense_Mutation	SNP	ENST00000403716.1	hg19	CCDS46413.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.09|15.09	2.730380|2.730380	0.48939|0.48939	.|.	.|.	ENSG00000115762|ENSG00000115762	ENST00000439822;ENST00000438882|ENST00000409158;ENST00000403716;ENST00000234115;ENST00000538982;ENST00000409612;ENST00000409279	.|.	.|.	.|.	5.59|5.59	4.72|4.72	0.59763|0.59763	.|.	.|.	.|.	.|.	.|.	T|T	0.54615|0.54615	0.1869|0.1869	M|M	0.63843|0.63843	1.955|1.955	0.43448|0.43448	D|D	0.995636|0.995636	B;B|P;P;P;P	0.21381|0.52316	0.055;0.011|0.921;0.952;0.921;0.921	B;B|B;P;B;B	0.12156|0.49301	0.006;0.007|0.401;0.606;0.401;0.401	T|T	0.57081|0.57081	-0.7872|-0.7872	8|8	0.51188|0.52906	T|T	0.08|0.07	.|.	7.4489|7.4489	0.27227|0.27227	0.1648:0.751:0.0:0.0842|0.1648:0.751:0.0:0.0842	.|.	158;166|202;202;203;211	B4DZ66;B4DF08|Q53FF1;Q96CS7-3;Q96CS7;B8ZZN1	.;.|.;.;PKHB2_HUMAN;.	Q|V	158;166|211;203;202;155;203;203	.|.	ENSP00000401193:H166Q|ENSP00000234115:L202V	H|L	+|+	3|1	2|2	PLEKHB2|PLEKHB2	131620754|131620754	0.798000|0.798000	0.28890|0.28890	0.831000|0.831000	0.32960|0.32960	0.808000|0.808000	0.45660|0.45660	1.295000|1.295000	0.33377|0.33377	1.386000|1.386000	0.46466|0.46466	-0.151000|-0.151000	0.13558|0.13558	CAC|CTG	.	.	.	none		0.512	PLEKHB2-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331304.2	NM_017958		G	131904284	C	G	131904284	3	3	131	1	0	0	0	0	1	0	0	0	12072	564	20	4	633	4	PLEKHB2	2	131904284	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	2	131904284	111295089	9	8108	86	2									
HTR2B	3357	hgsc.bcm.edu	37	chr2	231988374	231988374	+	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	tcctctggtattgattctgtCtgtaatccagaccagttaga	9	15	8	9	0	3	3	0	1	3	2	5	3	5	3	3	1	0	3	3	1	3	5			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr2:231988374C>A	ENST00000258400.3	-	2	617	c.105G>T	c.(103-105)caG>caT	p.Q35H	PSMD1_ENST00000409643.1_Intron|PSMD1_ENST00000373635.4_Intron|PSMD1_ENST00000308696.6_Intron	NM_000867.4	NP_000858.3	P41595	5HT2B_HUMAN	5-hydroxytryptamine (serotonin) receptor 2B, G protein-coupled	35					activation of phospholipase C activity (GO:0007202)|behavior (GO:0007610)|calcium-mediated signaling (GO:0019722)|cardiac muscle hypertrophy (GO:0003300)|cellular calcium ion homeostasis (GO:0006874)|cellular response to temperature stimulus (GO:0071502)|cGMP biosynthetic process (GO:0006182)|embryonic morphogenesis (GO:0048598)|ERK1 and ERK2 cascade (GO:0070371)|G-protein coupled receptor internalization (GO:0002031)|G-protein coupled receptor signaling pathway (GO:0007186)|heart morphogenesis (GO:0003007)|intestine smooth muscle contraction (GO:0014827)|negative regulation of apoptotic process (GO:0043066)|negative regulation of autophagy (GO:0010507)|negative regulation of cell death (GO:0060548)|neural crest cell differentiation (GO:0014033)|neural crest cell migration (GO:0001755)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphorylation (GO:0016310)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|protein kinase C signaling (GO:0070528)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of behavior (GO:0050795)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|serotonin receptor signaling pathway (GO:0007210)|vasoconstriction (GO:0042310)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	drug binding (GO:0008144)|G-protein alpha-subunit binding (GO:0001965)|Ras GTPase activator activity (GO:0005099)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|urinary_tract(1)	11		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)|Medulloblastoma(418;0.232)		Epithelial(121;4.48e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0141)	Amoxapine(DB00543)|Apomorphine(DB00714)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Clomipramine(DB01242)|Dihydroergotamine(DB00320)|Doxepin(DB01142)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ketamine(DB01221)|Lisuride(DB00589)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Ropinirole(DB00268)|Triflupromazine(DB00508)|Yohimbine(DB01392)	TTGATTCTGTCTGTAATCCAG	0.418																																					p.Q35H	Ovarian(155;1331 1891 12853 14038 34991)	Atlas-SNP	.											.	HTR2B	33	.	0			c.G105T						PASS	.						192	179	183					2																	231988374		2203	4300	6503	SO:0001583	missense	3357	exon2			TTCTGTCTGTAAT		CCDS2483.1	2q36.3-q37.1	2012-08-08	2012-02-03		ENSG00000135914	ENSG00000135914		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5294	protein-coding gene	gene with protein product		601122	"5-hydroxytryptamine (serotonin) receptor 2B"			8143856	Standard	NM_000867		Approved	5-HT(2B), 5-HT2B	uc002vro.3	P41595	OTTHUMG00000133222	ENST00000258400.3:c.105G>T	chr2.hg19:g.231988374C>A	ENSP00000258400:p.Gln35His	132.0	0.0	.		144.0	48.0	.	NM_000867	B2R9D5|Q53TI1|Q62221|Q6P523	Missense_Mutation	SNP	ENST00000258400.3	hg19	CCDS2483.1	.	.	.	.	.	.	.	.	.	.	C	13.05	2.121899	0.37436	.	.	ENSG00000135914	ENST00000258400	T	0.36878	1.23	5.52	1.53	0.23141	.	0.500549	0.19422	N	0.114664	T	0.27349	0.0671	L	0.44542	1.39	0.23144	N	0.998224	B	0.33379	0.41	B	0.35510	0.204	T	0.14504	-1.0470	10	0.22706	T	0.39	.	8.4754	0.33009	0.0:0.4476:0.4023:0.1501	.	35	P41595	5HT2B_HUMAN	H	35	ENSP00000258400:Q35H	ENSP00000258400:Q35H	Q	-	3	2	HTR2B	231696618	1.000000	0.71417	0.999000	0.59377	0.953000	0.61014	1.887000	0.39698	0.297000	0.22615	-0.237000	0.12165	CAG	.	.	.	none		0.418	HTR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256957.2	NM_000867		A	231988374	C	A	231988374	3	1	131	1	0	0	0	0	1	0	0	0	7449	912	32	4	1352	4	HTR2B	2	231988374	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	100084090	231988374	11210999	10	8109											
AZI2	64343	hgsc.bcm.edu	37	chr3	28382066	28382066	+	Frame_Shift_Del	DEL	C	C	-																															atctctcttatgggctttttCatgattcagaatacagatat																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr3:28382066delC	ENST00000479665.1	-	2	574	c.43delG	c.(43-45)gaafs	p.E15fs	AZI2_ENST00000420543.2_Frame_Shift_Del_p.E15fs|AZI2_ENST00000295748.3_5'UTR|AZI2_ENST00000334100.6_Frame_Shift_Del_p.E15fs|AZI2_ENST00000457172.1_Frame_Shift_Del_p.E15fs	NM_022461.3	NP_071906.1	Q9H6S1	AZI2_HUMAN	5-azacytidine induced 2	15	Homodimerization. {ECO:0000250}.				dendritic cell differentiation (GO:0097028)|dendritic cell proliferation (GO:0044565)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|interferon-alpha production (GO:0032607)|interferon-gamma production (GO:0032609)|interleukin-6 production (GO:0032635)|mitotic cell cycle (GO:0000278)|T cell activation (GO:0042110)|tumor necrosis factor production (GO:0032640)	cytoplasm (GO:0005737)				cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15						TGGGCTTTTTCATGATTCAGA	0.348																																					p.E15fs		Atlas-INDEL	.											.	AZI2	33	.	0			c.44delA						PASS	.						104	107	106					3																	28382066		2203	4300	6503	SO:0001589	frameshift_variant	64343	exon2			.	AC093142	CCDS2647.1, CCDS46782.1, CCDS46783.1	3p23	2006-03-01			ENSG00000163512	ENSG00000163512			24002	protein-coding gene	gene with protein product		609916				10580148	Standard	NM_001134432		Approved	NAP1, FLJ21939, AZ2	uc003ceb.4	Q9H6S1	OTTHUMG00000130573	ENST00000479665.1:c.43delG	chr3.hg19:g.28382066delC	ENSP00000419371:p.Glu15fs	121.0	0.0	0		127.0	50.0	0.393701	NM_001134432	A8K3M2|C9JB40|H7BXU6|Q86W99|Q9BQF1	Frame_Shift_Del	DEL	ENST00000479665.1	hg19	CCDS2647.1																																																																																			.	.	.	none		0.348	AZI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252998.2	NM_203326		-	28382066	C	-	28382066	7	5	131	1	0	1	0	1	0	0	0	0	1241	835	29	0	1252	0	AZI2	3	28382066	Frame_Shift_Del	DEL	C	TCGA-BQ-7045-01A-31D-1961-08		28382066	169640364	11	8110											
CRTAP	10491	hgsc.bcm.edu	37	chr3	33156008	33156008	+	Missense_Mutation	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	cggacttccagcgccgcgagCcctacaagttcctgcagttc	7	8	10	16	4	0	0	0	0	0	0	3	2	2	1	4	1	4	3	4	1	2	4			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr3:33156008C>T	ENST00000320954.6	+	1	538	c.439C>T	c.(439-441)Ccc>Tcc	p.P147S	CRTAP_ENST00000449224.1_Missense_Mutation_p.P147S	NM_006371.4	NP_006362.1	O75718	CRTAP_HUMAN	cartilage associated protein	147					chaperone-mediated protein folding (GO:0061077)|extracellular matrix organization (GO:0030198)|negative regulation of post-translational protein modification (GO:1901874)|peptidyl-proline hydroxylation to 3-hydroxy-L-proline (GO:0018400)|protein stabilization (GO:0050821)|spermatogenesis (GO:0007283)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular space (GO:0005615)|macromolecular complex (GO:0032991)|proteinaceous extracellular matrix (GO:0005578)	protein complex binding (GO:0032403)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	9						GCGCCGCGAGCCCTACAAGTT	0.726																																					p.P147S		Atlas-SNP	.											.	CRTAP	16	.	0			c.C439T						PASS	.						7	8	8					3																	33156008		1469	3247	4716	SO:0001583	missense	10491	exon1			CGCGAGCCCTACA	AJ006470	CCDS2657.1	3p22	2014-09-17			ENSG00000170275	ENSG00000170275			2379	protein-coding gene	gene with protein product	"leprecan-like 3"	605497				9217321, 10429950	Standard	NM_006371		Approved	CASP, LEPREL3	uc003cfl.4	O75718	OTTHUMG00000130746	ENST00000320954.6:c.439C>T	chr3.hg19:g.33156008C>T	ENSP00000323696:p.Pro147Ser	20.0	0.0	.		42.0	14.0	.	NM_006371	B2RBL6	Missense_Mutation	SNP	ENST00000320954.6	hg19	CCDS2657.1	.	.	.	.	.	.	.	.	.	.	C	32	5.124174	0.94429	.	.	ENSG00000170275	ENST00000320954;ENST00000509775;ENST00000539684;ENST00000449224;ENST00000423366	T;T	0.78003	-1.14;-1.14	4.31	4.31	0.51392	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	D	0.89698	0.6790	M	0.88310	2.945	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.91955	0.5574	10	0.87932	D	0	-10.8094	16.9301	0.86188	0.0:1.0:0.0:0.0	.	147;147	C9JP16;O75718	.;CRTAP_HUMAN	S	147;147;134;147;147	ENSP00000323696:P147S;ENSP00000409997:P147S	ENSP00000323696:P147S	P	+	1	0	CRTAP	33131012	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.262000	0.78410	2.398000	0.81561	0.467000	0.42956	CCC	.	.	.	none		0.726	CRTAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253246.3			T	33156008	C	T	33156008	3	4	131	1	0	0	0	0	1	0	0	0	3900	739	26	2	441	2	CRTAP	3	33156008	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	4773942	33156008	164866422	12	8111											
USP19	10869	hgsc.bcm.edu	37	chr3	49148708	49148709	+	Missense_Mutation	DNP	TC	TC	AT																															ctttgtcctctagccgctgcTctcggttggatgaatcaatt																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr3:49148708_49148709TC>AT	ENST00000398888.2	-	21	3316_3317	c.2998_2999GA>AT	c.(2998-3000)GAg>ATg	p.E1000M	USP19_ENST00000398896.1_Missense_Mutation_p.E808M|USP19_ENST00000417901.1_Missense_Mutation_p.E1103M|USP19_ENST00000398892.3_Missense_Mutation_p.E1040M|USP19_ENST00000434032.2_Missense_Mutation_p.E1101M|USP19_ENST00000398898.2_Missense_Mutation_p.E1040M|USP19_ENST00000453664.1_Missense_Mutation_p.E1091M	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	1000	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)		TAGCCGCTGCTCTCGGTTGGAT	0.545																																					p.E1103V|p.E1103K		Atlas-SNP	.											.	USP19	158	.	0			c.A3308T|c.G3307A						PASS	.																																			SO:0001583	missense	10869	exon22			CGCTGCTCTCGGT|GCTGCTCTCGGTT	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.2998_2999delinsAT	chr3.hg19:g.49148708_49148709delinsAT	ENSP00000381863:p.Glu1000Met	87.0|88.0	0.0	.		117.0|115.0	58.0	.	NM_001199161	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Missense_Mutation	SNP	ENST00000398888.2	hg19	CCDS43090.1																																																																																			.	.	.	none		0.545	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677		AT	49148709	TC	AT	49148708	3	1	131	1	0	0	0	0	1	0	0	0	17062	1551	54	5	981	5	USP19	3	49148708	Missense_Mutation	DNP	TC	TCGA-BQ-7045-01A-31D-1961-08	15992700	49148708	148873722	13	8112											
CISH	1154	hgsc.bcm.edu	37	chr3	50645554	50645554	+	Frame_Shift_Del	DEL	A	A	-																															tgtcgggcctcgctggccgtAatggaaccccaataccagcc																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr3:50645554delA	ENST00000348721.3	-	3	441	c.261delT	c.(259-261)attfs	p.I87fs	CISH_ENST00000443053.2_Frame_Shift_Del_p.I104fs	NM_145071.2	NP_659508.1	Q9NSE2	CISH_HUMAN	cytokine inducible SH2-containing protein	87	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				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)		CGCTGGCCGTAATGGAACCCC	0.562																																					p.T105fs		Atlas-INDEL	.											.	CISH	27	.	0			c.313delA						PASS	.						38	38	38					3																	50645554		2203	4300	6503	SO:0001589	frameshift_variant	1154	exon4			.	Z77852	CCDS2831.1, CCDS46834.1	3p21.3	2013-02-14			ENSG00000114737	ENSG00000114737		"Suppressors of cytokine signaling", "SH2 domain containing"	1984	protein-coding gene	gene with protein product		602441				9465889, 7796808	Standard	NM_013324		Approved	CIS, G18, CIS-1, SOCS	uc003dax.3	Q9NSE2	OTTHUMG00000156853	ENST00000348721.3:c.261delT	chr3.hg19:g.50645554delA	ENSP00000294173:p.Ile87fs	67.0	0.0	0		71.0	10.0	0.140845	NM_013324	B2R9N1|G5E9R1|Q9NS38|Q9Y5R1	Frame_Shift_Del	DEL	ENST00000348721.3	hg19	CCDS2831.1																																																																																			.	.	.	none		0.562	CISH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346245.1	NM_145071		-	50645554	A	-	50645554	7	5	131	1	0	1	0	1	0	0	0	0	3439	358	13	0	519	0	CISH	3	50645554	Frame_Shift_Del	DEL	A	TCGA-BQ-7045-01A-31D-1961-08	1496846	50645554	147376876	14	8113											
MITF	4286	hgsc.bcm.edu	37	chr3	69988260	69988261	+	Frame_Shift_Ins	INS	-	-	T																															ttttgcagggattttataagINStttgaagagcaaaacagggc																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr3:69988260_69988261insT	ENST00000448226.2	+	4	721_722	c.594_595insT	c.(595-597)tttfs	p.F199fs	MITF_ENST00000394355.2_Frame_Shift_Ins_p.F174fs|MITF_ENST00000352241.4_Frame_Shift_Ins_p.F199fs|MITF_ENST00000314589.5_Frame_Shift_Ins_p.F183fs|MITF_ENST00000314557.6_Frame_Shift_Ins_p.F92fs|MITF_ENST00000472437.1_Frame_Shift_Ins_p.F147fs|MITF_ENST00000394351.3_Frame_Shift_Ins_p.F92fs|MITF_ENST00000531774.1_Frame_Shift_Ins_p.F36fs|MITF_ENST00000328528.6_Frame_Shift_Ins_p.F198fs			O75030	MITF_HUMAN	microphthalmia-associated transcription factor	199					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)	p.K91N(1)		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)		GATTTTATAAGTTTGAAGAGCA	0.441			A		melanoma		"Waardenburg syndrome type 2, Tietz syndrome"																														p.K198fs	Melanoma(29;269 969 31479 41502 42961)	Atlas-INDEL	.		Dom	yes		3	3p14.1	4286	microphthalmia-associated transcription factor	yes	E	MITF,rectum,carcinoma,0,1	MITF	156	.	1	Substitution - Missense(1)	large_intestine(1)	c.594_595insT						PASS	.																																			SO:0001589	frameshift_variant	4286	exon4			.		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.597dupT	chr3.hg19:g.69988263_69988263dupT	ENSP00000391803:p.Phe199fs	47.0	0.0	0		75.0	38.0	0.506667	NM_198159	B4DJL2|D3K197|E9PFN0|Q14841|Q9P2V0|Q9P2V1|Q9P2V2|Q9P2Y8	Frame_Shift_Ins	INS	ENST00000448226.2	hg19																																																																																				.	.	.	none		0.441	MITF-007	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000313947.1	NM_198159		T	69988261	-	T	69988260	7	5	131	1	0	1	1	0	0	0	0	0	9603	1020	36	0	829	0	MITF	3	69988260	Frame_Shift_Ins	INS	-	TCGA-BQ-7045-01A-31D-1961-08	19342706	69988260	128034170	15	8114											
DZIP1L	199221	hgsc.bcm.edu	37	chr3	137805834	137805834	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagccatgtgctcttcatgcAgttccttcacttttcttttc	5	18	5	13	0	4	0	2	0	2	0	6	0	5	0	2	0	3	3	2	0	0	7			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr3:137805834A>G	ENST00000327532.2	-	7	1393	c.1031T>C	c.(1030-1032)cTg>cCg	p.L344P	DZIP1L_ENST00000488595.1_5'UTR|DZIP1L_ENST00000469243.1_Missense_Mutation_p.L344P	NM_173543.2	NP_775814.2	Q8IYY4	DZI1L_HUMAN	DAZ interacting zinc finger protein 1-like	344					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						CTCTTCATGCAGTTCCTTCAC	0.423																																					p.L344P		Atlas-SNP	.											.	DZIP1L	88	.	0			c.T1031C						PASS	.						227	199	209					3																	137805834		2203	4300	6503	SO:0001583	missense	199221	exon8			TCATGCAGTTCCT	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.1031T>C	chr3.hg19:g.137805834A>G	ENSP00000332148:p.Leu344Pro	102.0	0.0	.		133.0	31.0	.	NM_001170538	C9JUG5|Q96M38	Missense_Mutation	SNP	ENST00000327532.2	hg19	CCDS3096.1	.	.	.	.	.	.	.	.	.	.	A	11.33	1.607713	0.28623	.	.	ENSG00000158163	ENST00000327532;ENST00000469243;ENST00000536706	T;T	0.50277	0.75;0.75	5.1	3.92	0.45320	.	0.353745	0.21368	N	0.075699	T	0.61788	0.2375	M	0.65975	2.015	0.44136	D	0.996925	D;D	0.89917	0.999;1.0	D;D	0.73380	0.974;0.98	T	0.58934	-0.7548	10	0.42905	T	0.14	-4.3459	8.3577	0.32340	0.8247:0.0:0.0:0.1753	.	344;344	Q8IYY4-2;Q8IYY4	.;DZI1L_HUMAN	P	344	ENSP00000332148:L344P;ENSP00000419486:L344P	ENSP00000332148:L344P	L	-	2	0	DZIP1L	139288524	0.829000	0.29322	0.156000	0.22583	0.039000	0.13416	4.330000	0.59266	0.859000	0.35456	-0.333000	0.08304	CTG	.	.	.	none		0.423	DZIP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357548.1	NM_173543		G	137805834	A	G	137805834	3	3	131	1	0	0	0	0	1	0	0	0	4866	188	7	3	1321	3	DZIP1L	3	137805834	Missense_Mutation	SNP	A	TCGA-BQ-7045-01A-31D-1961-08	67817574	137805834	60216596	16	8115											
EIF4G1	1981	hgsc.bcm.edu	37	chr3	184041746	184041746	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctgtggcctatgccaacaTgtgccgctgcctcatggcgg	5	10	12	14	2	2	0	1	0	1	0	2	0	2	0	4	3	4	1	4	3	2	1			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr3:184041746T>C	ENST00000346169.2	+	16	2724	c.2453T>C	c.(2452-2454)aTg>aCg	p.M818T	EIF4G1_ENST00000352767.3_Missense_Mutation_p.M825T|EIF4G1_ENST00000441154.1_Missense_Mutation_p.M655T|EIF4G1_ENST00000434061.2_Missense_Mutation_p.M623T|EIF4G1_ENST00000424196.1_Missense_Mutation_p.M825T|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000350481.5_Missense_Mutation_p.M654T|EIF4G1_ENST00000435046.2_Missense_Mutation_p.M622T|EIF4G1_ENST00000382330.3_Missense_Mutation_p.M825T|EIF4G1_ENST00000411531.1_Missense_Mutation_p.M779T|EIF4G1_ENST00000414031.1_Missense_Mutation_p.M778T|EIF4G1_ENST00000427845.1_Missense_Mutation_p.M732T|EIF4G1_ENST00000392537.2_Missense_Mutation_p.M731T|EIF4G1_ENST00000342981.4_Missense_Mutation_p.M819T|SNORD66_ENST00000390856.1_RNA|EIF4G1_ENST00000319274.6_Missense_Mutation_p.M818T	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	818	eIF3/EIF4A-binding.				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)			TATGCCAACATGTGCCGCTGC	0.517																																					p.M825T		Atlas-SNP	.											.	EIF4G1	151	.	0			c.T2474C						PASS	.						66	63	64					3																	184041746		2203	4300	6503	SO:0001583	missense	1981	exon17			CCAACATGTGCCG	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.2453T>C	chr3.hg19:g.184041746T>C	ENSP00000316879:p.Met818Thr	104.0	0.0	.		124.0	33.0	.	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Missense_Mutation	SNP	ENST00000346169.2	hg19	CCDS3259.1	.	.	.	.	.	.	.	.	.	.	T	18.37	3.609064	0.66558	.	.	ENSG00000114867	ENST00000346169;ENST00000414031;ENST00000392537;ENST00000450424;ENST00000421110;ENST00000382330;ENST00000426123;ENST00000350481;ENST00000352767;ENST00000427845;ENST00000342981;ENST00000319274;ENST00000424196;ENST00000411531;ENST00000444861;ENST00000441154;ENST00000434061;ENST00000435046	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.24151	1.87;1.87;1.87;1.87;1.87;1.87;1.87;1.87;1.87;1.87;1.87;1.87;1.87;1.87;1.87;1.87;1.87;1.87	5.92	5.92	0.95590	MIF4G-like, type 3 (2);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.038518	0.85682	D	0.000000	T	0.52517	0.1739	M	0.86805	2.84	0.80722	D	1	P;P;P;P	0.49862	0.929;0.929;0.929;0.929	P;P;P;P	0.56216	0.794;0.794;0.794;0.794	T	0.60692	-0.7213	10	0.87932	D	0	-18.7766	16.3634	0.83296	0.0:0.0:0.0:1.0	.	825;819;818;825	E9PFM1;D3DNT2;Q04637;B2RU10	.;.;IF4G1_HUMAN;.	T	818;778;731;819;826;825;759;654;825;732;819;818;825;779;654;655;623;622	ENSP00000316879:M818T;ENSP00000391935:M778T;ENSP00000376320:M731T;ENSP00000391412:M819T;ENSP00000413159:M826T;ENSP00000371767:M825T;ENSP00000403269:M759T;ENSP00000317600:M654T;ENSP00000338020:M825T;ENSP00000407682:M732T;ENSP00000343450:M819T;ENSP00000323737:M818T;ENSP00000416255:M825T;ENSP00000395974:M779T;ENSP00000398145:M654T;ENSP00000399858:M655T;ENSP00000411826:M623T;ENSP00000404754:M622T	ENSP00000323737:M818T	M	+	2	0	EIF4G1	185524440	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.270000	0.75569	0.459000	0.35465	ATG	.	.	.	none		0.517	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917		C	184041746	T	C	184041746	3	2	131	1	0	0	0	0	1	0	0	0	5038	1464	51	3	2507	3	EIF4G1	3	184041746	Missense_Mutation	SNP	T	TCGA-BQ-7045-01A-31D-1961-08	46235912	184041746	13980684	17	8116											
LAP3	51056	hgsc.bcm.edu	37	chr4	17590497	17590497	+	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	cattcctcagtgtggccaaaGgatctgacgagcccccagtc	9	8	10	14	1	2	1	1	1	1	0	4	3	3	2	4	2	1	0	4	2	1	1			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr4:17590497G>A	ENST00000226299.4	+	7	1034	c.760G>A	c.(760-762)Gga>Aga	p.G254R	LAP3_ENST00000503467.1_3'UTR|AC006160.5_ENST00000511010.1_RNA|LAP3_ENST00000606142.1_Missense_Mutation_p.G223R	NM_015907.2	NP_056991.2	P28838	AMPL_HUMAN	leucine aminopeptidase 3	254					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						TGTGGCCAAAGGATCTGACGA	0.453																																					p.G254R		Atlas-SNP	.											.	LAP3	50	.	0			c.G760A						PASS	.						110	108	108					4																	17590497		2203	4300	6503	SO:0001583	missense	51056	exon7			GCCAAAGGATCTG	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.760G>A	chr4.hg19:g.17590497G>A	ENSP00000226299:p.Gly254Arg	121.0	0.0	.		134.0	50.0	.	NM_015907	B3KMQ3|Q6IAM6|Q6P0L6|Q9UQE3	Missense_Mutation	SNP	ENST00000226299.4	hg19	CCDS3422.1	.	.	.	.	.	.	.	.	.	.	G	31	5.103254	0.94245	.	.	ENSG00000002549	ENST00000226299;ENST00000513105	T;T	0.58506	0.44;0.33	5.12	5.12	0.69794	Peptidase M17, leucyl aminopeptidase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.87390	0.6165	H	0.99415	4.555	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93090	0.6499	10	0.87932	D	0	-22.9866	18.9237	0.92536	0.0:0.0:1.0:0.0	.	254	P28838	AMPL_HUMAN	R	254;88	ENSP00000226299:G254R;ENSP00000424724:G88R	ENSP00000226299:G254R	G	+	1	0	LAP3	17199595	1.000000	0.71417	0.994000	0.49952	0.922000	0.55478	9.673000	0.98631	2.534000	0.85438	0.557000	0.71058	GGA	.	.	.	none		0.453	LAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250365.1			A	17590497	G	A	17590497	3	1	131	1	0	0	0	0	1	0	0	0	8630	1001	35	2	786	2	LAP3	4	17590497	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08		17590497	173563779	18	8117											
KDR	3791	hgsc.bcm.edu	37	chr4	55981041	55981042	+	Splice_Site	INS	-	-	T																															aaaggaaatgtcctcttaccINStacaacgacaactatgtaca																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr4:55981041_55981042insT	ENST00000263923.4	-	5	952_953	c.657_658insA	c.(655-660)gtaggg>gtaAggg	p.G220fs		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	220					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)	GTCCTCTTACCTACAACGACAA	0.347			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)																											p.G220fs		Atlas-INDEL	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	.	KDR	307	.	0			c.658_659insA						PASS	.																																			SO:0001630	splice_region_variant	3791	exon5			.	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.658+1->A	chr4.hg19:g.55981042_55981042dupT		83.0	0.0	0		93.0	27.0	0.290323	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Frame_Shift_Ins	INS	ENST00000263923.4	hg19	CCDS3497.1																																																																																			.	.	.	none		0.347	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1		Frame_Shift_Ins	T	55981042	-	T	55981041	8	5	131	1	0	1	1	0	0	0	1	0	8146	695	24	0	3516	0	KDR	4	55981041	Splice_Site	INS	-	TCGA-BQ-7045-01A-31D-1961-08	38390544	55981041	135173235	19	8118											
KIAA1211	57482	hgsc.bcm.edu	37	chr4	57182080	57182080	+	Frame_Shift_Del	DEL	T	T	-																															ttccttgtcccaagccttccTtaccctccgcagaaagtggt																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr4:57182080delT	ENST00000504228.1	+	6	2517	c.2412delT	c.(2410-2412)cctfs	p.P804fs	KIAA1211_ENST00000541073.1_Frame_Shift_Del_p.P797fs|KIAA1211_ENST00000264229.6_Frame_Shift_Del_p.P804fs			Q6ZU35	K1211_HUMAN	KIAA1211	804										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)					CAAGCCTTCCTTACCCTCCGC	0.592																																					p.P804fs		Atlas-INDEL	.											.	KIAA1211	178	.	0			c.2411delC						PASS	.						81	89	86					4																	57182080		2023	4206	6229	SO:0001589	frameshift_variant	57482	exon8			.	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.2412delT	chr4.hg19:g.57182080delT	ENSP00000423366:p.Pro804fs	94.0	0.0	0		65.0	22.0	0.338462	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Frame_Shift_Del	DEL	ENST00000504228.1	hg19	CCDS43230.1																																																																																			.	.	.	none		0.592	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722		-	57182080	T	-	57182080	7	5	131	1	0	1	0	1	0	0	0	0	8222	1596	56	0	2430	0	KIAA1211	4	57182080	Frame_Shift_Del	DEL	T	TCGA-BQ-7045-01A-31D-1961-08	1201039	57182080	133972196	20	8119											
PRKG2	5593	hgsc.bcm.edu	37	chr4	82074809	82074809	+	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	aatagttacctttccttttgCcaaaatgaaaaaggtacttc	14	14	5	8	0	0	1	0	1	0	0	2	1	1	1	3	1	3	2	3	1	8	7			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr4:82074809C>A	ENST00000395578.1	-	7	1095	c.979G>T	c.(979-981)Gca>Tca	p.A327S	PRKG2_ENST00000509169.1_5'UTR|PRKG2_ENST00000418486.2_Missense_Mutation_p.A327S|PRKG2_ENST00000545647.1_5'UTR|PRKG2_ENST00000264399.1_Missense_Mutation_p.A327S			Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	327					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						TTTCCTTTTGCCAAAATGAAA	0.328																																					p.A327S		Atlas-SNP	.											.	PRKG2	195	.	0			c.G979T						PASS	.						76	73	74					4																	82074809		2203	4300	6503	SO:0001583	missense	5593	exon6			CTTTTGCCAAAAT	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.979G>T	chr4.hg19:g.82074809C>A	ENSP00000378945:p.Ala327Ser	57.0	0.0	.		55.0	10.0	.	NM_006259	B4DMX3|E7EPE6|O00125|O60916	Missense_Mutation	SNP	ENST00000395578.1	hg19	CCDS3589.1	.	.	.	.	.	.	.	.	.	.	C	6.115	0.389407	0.11581	.	.	ENSG00000138669	ENST00000395578;ENST00000264399;ENST00000418486	D;D;D	0.92699	-3.09;-3.09;-3.09	6.08	6.08	0.98989	Cyclic nucleotide-binding, conserved site (1);Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.049240	0.85682	D	0.000000	D	0.84701	0.5530	L	0.28192	0.835	0.80722	D	1	B;B	0.10296	0.003;0.002	B;B	0.16289	0.015;0.01	T	0.77000	-0.2750	10	0.02654	T	1	-21.5253	14.3009	0.66352	0.1487:0.8513:0.0:0.0	.	327;327	E7EPE6;Q13237	.;KGP2_HUMAN	S	327	ENSP00000378945:A327S;ENSP00000264399:A327S;ENSP00000389038:A327S	ENSP00000264399:A327S	A	-	1	0	PRKG2	82293833	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.691000	0.61738	2.894000	0.99253	0.591000	0.81541	GCA	.	.	.	none		0.328	PRKG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252639.1	NM_006259		A	82074809	C	A	82074809	3	1	131	1	0	0	0	0	1	0	0	0	12533	739	26	4	1361	4	PRKG2	4	82074809	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	24892729	82074809	109079467	21	8120											
OSTC	58505	hgsc.bcm.edu	37	chr4	109571838	109571838	+	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	actttgtaccgtgtcccgttCttagtgctcgaatgtcccaa	7	14	8	12	3	1	0	0	0	1	0	4	1	3	0	3	0	2	3	3	0	4	4			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr4:109571838C>T	ENST00000361564.4	+	1	99	c.27C>T	c.(25-27)ttC>ttT	p.F9F	OSTC_ENST00000505745.1_3'UTR|OSTC_ENST00000512478.2_Silent_p.F9F|RNU6-431P_ENST00000383874.1_RNA	NM_021227.3	NP_067050.1	Q9NRP0	OSTC_HUMAN	oligosaccharyltransferase complex subunit (non-catalytic)	9			F -> L (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)|oligosaccharyltransferase complex (GO:0008250)		p.F9L(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(3)	6						GTGTCCCGTTCTTAGTGCTCG	0.597																																					p.F9F		Atlas-SNP	.											OSTC,NS,carcinoma,0,1	OSTC	9	.	1	Substitution - Missense(1)	breast(1)	c.C27T						PASS	.						74	73	74					4																	109571838		2203	4300	6503	SO:0001819	synonymous_variant	58505	exon1			CCCGTTCTTAGTG	AF201937	CCDS3681.1, CCDS58921.1, CCDS75177.1	4q25	2013-03-06	2013-03-06		ENSG00000198856	ENSG00000198856			24448	protein-coding gene	gene with protein product	"DC2 protein"		"oligosaccharyltransferase complex subunit"			15835887	Standard	NM_021227		Approved	DC2	uc031sgt.1	Q9NRP0	OTTHUMG00000161031	ENST00000361564.4:c.27C>T	chr4.hg19:g.109571838C>T		90.0	0.0	.		131.0	42.0	.	NM_001267818	A8MYS2|B2R5H1|D6RH22|Q9P075|Q9P1R4	Silent	SNP	ENST00000361564.4	hg19	CCDS3681.1																																																																																			.	.	.	none		0.597	OSTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363485.1	NM_021227		T	109571838	C	T	109571838	2	4	131	1	0	0	0	0	0	0	0	1	11303	912	32	2		2	OSTC	4	109571838	Silent	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	27497029	109571838	81582438	22	8121											
NDUFS6	4726	hgsc.bcm.edu	37	chr5	1801592	1801592	+	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	gtggcgaggcggcgcggagcCtgcccctgggcgccaggtgt	3	5	20	13	5	0	0	0	0	0	0	0	2	0	1	4	6	2	0	4	6	0	0			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr5:1801592C>A	ENST00000274137.5	+	1	79	c.61C>A	c.(61-63)Ctg>Atg	p.L21M	MRPL36_ENST00000505818.1_5'Flank|MRPL36_ENST00000505059.2_5'Flank|MRPL36_ENST00000508987.1_5'Flank|NDUFS6_ENST00000469176.1_Missense_Mutation_p.L21M|MRPL36_ENST00000382647.7_5'Flank|NDUFS6_ENST00000510329.1_3'UTR	NM_004553.4	NP_004544.1	O75380	NDUS6_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 6, 13kDa (NADH-coenzyme Q reductase)	21					cardiovascular system development (GO:0072358)|cellular metabolic process (GO:0044237)|fatty acid metabolic process (GO:0006631)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|mitochondrion morphogenesis (GO:0070584)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|muscle contraction (GO:0006936)|reproductive system development (GO:0061458)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	electron carrier activity (GO:0009055)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|prostate(1)	7						GGCGCGGAGCCTGCCCCTGGG	0.701																																					p.L21M		Atlas-SNP	.											.	NDUFS6	11	.	0			c.C61A						PASS	.						13	16	15					5																	1801592		2169	4256	6425	SO:0001583	missense	4726	exon1			CGGAGCCTGCCCC	BC038664	CCDS3866.1	5p15.33	2011-07-04	2002-08-29		ENSG00000145494	ENSG00000145494	1.6.99.3, 1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7713	protein-coding gene	gene with protein product	"complex I 13kDa subunit A", "NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial"	603848	"NADH dehydrogenase (ubiquinone) Fe-S protein 6 (13kD) (NADH-coenzyme Q reductase)"			9763677	Standard	NM_004553		Approved	CI-13kA	uc003jcy.3	O75380	OTTHUMG00000090372	ENST00000274137.5:c.61C>A	chr5.hg19:g.1801592C>A	ENSP00000274137:p.Leu21Met	32.0	0.0	.		44.0	21.0	.	NM_004553		Missense_Mutation	SNP	ENST00000274137.5	hg19	CCDS3866.1	.	.	.	.	.	.	.	.	.	.	C	11.76	1.733559	0.30684	.	.	ENSG00000145494	ENST00000274137;ENST00000469176	T	0.77750	-1.12	4.23	0.315	0.15852	.	1.107710	0.06942	N	0.813089	T	0.72676	0.3490	M	0.75447	2.3	0.09310	N	1	P	0.34837	0.472	B	0.33295	0.161	T	0.57676	-0.7770	10	0.33940	T	0.23	-2.3227	3.9905	0.09535	0.0:0.3596:0.377:0.2635	.	21	O75380	NDUS6_HUMAN	M	21	ENSP00000274137:L21M	ENSP00000274137:L21M	L	+	1	2	NDUFS6	1854592	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	0.256000	0.18351	0.156000	0.19299	-0.171000	0.13296	CTG	.	.	.	none		0.701	NDUFS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206744.2	NM_004553		A	1801592	C	A	1801592	3	1	131	1	0	0	0	0	1	0	0	0	10303	680	24	4	63	4	NDUFS6	5	1801592	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08		1801592	179113668	23	8122											
C6orf195	154386	hgsc.bcm.edu	37	chr6	2623684	2623684	+	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	ggagagacgtcagaaagcttCattgctaatctccctctgac	11	10	9	11	1	4	3	2	1	2	2	5	5	4	4	1	1	2	2	1	1	2	3			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr6:2623684C>A	ENST00000296847.3	-	3	896	c.373G>T	c.(373-375)Gaa>Taa	p.E125*		NM_152554.2	NP_689767.2	Q96MT4	CF195_HUMAN	chromosome 6 open reading frame 195	125										cervix(1)|endometrium(1)|lung(2)|skin(1)	5	Ovarian(93;0.0412)	all_hematologic(90;0.0895)				CAGAAAGCTTCATTGCTAATC	0.493																																					p.E125X		Atlas-SNP	.											.	C6orf195	10	.	0			c.G373T						PASS	.						65	67	67					6																	2623684		1977	4166	6143	SO:0001587	stop_gained	154386	exon3			AAGCTTCATTGCT	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.373G>T	chr6.hg19:g.2623684C>A	ENSP00000296847:p.Glu125*	64.0	0.0	.		75.0	27.0	.	NM_152554	Q3SY08|Q3SY09|Q3SY10|Q5TAW4	Nonsense_Mutation	SNP	ENST00000296847.3	hg19	CCDS43416.1	.	.	.	.	.	.	.	.	.	.	C	36	5.801906	0.96960	.	.	ENSG00000164385	ENST00000296847	.	.	.	4.52	0.877	0.19145	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	3.3228	0.07056	0.192:0.5359:0.0:0.2721	.	.	.	.	X	125	.	ENSP00000296847:E125X	E	-	1	0	C6orf195	2568683	0.000000	0.05858	0.000000	0.03702	0.073000	0.16967	0.349000	0.20055	0.064000	0.16427	-0.136000	0.14681	GAA	.	.	.	none		0.493	C6orf195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039633.1	NM_152554		A	2623684	C	A	2623684	4	1	131	1	0	0	0	0	0	1	0	0	2352	835	29	4	14	4	C6orf195	6	2623684	Nonsense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08		2623684	168491383	24	8123											
C6orf223	221416	hgsc.bcm.edu	37	chr6	43970795	43970795	+	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	ttgcaggggcacggctaatgCgctctaattacccaccgccg	8	8	11	14	4	1	0	0	0	1	0	1	0	1	0	3	3	3	4	3	3	3	4			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr6:43970795C>T	ENST00000336600.5	+	4	681	c.661C>T	c.(661-663)Cgc>Tgc	p.R221C	C6orf223_ENST00000442114.2_Missense_Mutation_p.R201C|RP5-1120P11.1_ENST00000422059.1_RNA|C6orf223_ENST00000439969.2_3'UTR|C6orf223_ENST00000448947.2_3'UTR|RP5-1120P11.1_ENST00000607590.1_RNA	NM_001171992.1|NM_153246.4	NP_001165463.1|NP_694978.2	Q8N319	CF223_HUMAN	chromosome 6 open reading frame 223	221										central_nervous_system(1)|lung(2)|pancreas(1)|prostate(1)|urinary_tract(1)	6	all_cancers(18;2.28e-07)|all_epithelial(2;1.62e-08)|Lung NSC(15;0.000172)|all_lung(25;0.000533)|Hepatocellular(11;0.00309)|Ovarian(13;0.0437)		all cancers(41;0.00141)|Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.217)			ACGGCTAATGCGCTCTAATTA	0.637																																					p.R221C		Atlas-SNP	.											.	C6orf223	14	.	0			c.C661T						PASS	.						25	31	29					6																	43970795		2202	4295	6497	SO:0001583	missense	221416	exon4			CTAATGCGCTCTA	BC032706	CCDS34459.1, CCDS55016.1	6p21.1	2012-09-05			ENSG00000181577	ENSG00000181577			28692	protein-coding gene	gene with protein product						12477932	Standard	NM_153246		Approved	MGC45491	uc003own.3	Q8N319	OTTHUMG00000014753	ENST00000336600.5:c.661C>T	chr6.hg19:g.43970795C>T	ENSP00000426159:p.Arg221Cys	88.0	0.0	.		88.0	37.0	.	NM_153246	E9PB59|Q8N575	Missense_Mutation	SNP	ENST00000336600.5	hg19	CCDS34459.1	.	.	.	.	.	.	.	.	.	.	C	12.55	1.973119	0.34848	.	.	ENSG00000181577	ENST00000336600	T	0.40756	1.02	3.26	2.39	0.29439	.	0.205916	0.24638	N	0.036836	T	0.08133	0.0203	N	0.08118	0	0.80722	D	1	P	0.36599	0.56	B	0.27262	0.078	T	0.08722	-1.0708	10	0.87932	D	0	.	6.5098	0.22216	0.0:0.865:0.0:0.135	.	221	Q8N319	CF223_HUMAN	C	221	ENSP00000426159:R221C	ENSP00000426159:R221C	R	+	1	0	C6orf223	44078773	0.337000	0.24766	1.000000	0.80357	0.994000	0.84299	0.280000	0.18790	0.963000	0.38082	0.491000	0.48974	CGC	.	.	.	none		0.637	C6orf223-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040702.3	NM_153246		T	43970795	C	T	43970795	3	4	131	1	0	0	0	0	1	0	0	0	2359	768	27	1	718	1	C6orf223	6	43970795	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	41347111	43970795	127144272	25	8124											
GFRAL	389400	hgsc.bcm.edu	37	chr6	55223709	55223709	+	Frame_Shift_Del	DEL	C	C	-																															gcactatagaacatttcagtCaaaatgctggcagcgtgtga																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr6:55223709delC	ENST00000340465.2	+	6	811	c.725delC	c.(724-726)tcafs	p.S242fs		NM_207410.2	NP_997293.2	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like	242					negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|stress-activated protein kinase signaling cascade (GO:0031098)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|kidney(5)|large_intestine(2)|liver(1)|lung(31)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	48	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			ACATTTCAGTCAAAATGCTGG	0.398																																					p.S242fs		Atlas-INDEL	.											.	GFRAL	91	.	0			c.724delT						PASS	.						115	106	109					6																	55223709		2203	4300	6503	SO:0001589	frameshift_variant	389400	exon6			.	AY358198	CCDS4957.1	6p12.1	2007-06-22			ENSG00000187871	ENSG00000187871			32789	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 144"	C6orf144		16086688	Standard	NM_207410		Approved	GRAL, UNQ9356, bA360D14.1	uc003pcm.1	Q6UXV0	OTTHUMG00000014900	ENST00000340465.2:c.725delC	chr6.hg19:g.55223709delC	ENSP00000343636:p.Ser242fs	112.0	0.0	0		130.0	46.0	0.353846	NM_207410	Q5VTF6	Frame_Shift_Del	DEL	ENST00000340465.2	hg19	CCDS4957.1																																																																																			.	.	.	none		0.398	GFRAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040995.2	NM_207410		-	55223709	C	-	55223709	7	5	131	1	0	1	0	1	0	0	0	0	6358	838	29	0	747	0	GFRAL	6	55223709	Frame_Shift_Del	DEL	C	TCGA-BQ-7045-01A-31D-1961-08	11252914	55223709	115891358	26	8125											
KIAA1919	91749	hgsc.bcm.edu	37	chr6	111587895	111587895	+	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	tgcagtcattggaattcttcAaggaaaataccctgatttgc	12	13	8	8	0	3	1	2	1	1	0	3	3	3	3	1	2	3	1	1	2	5	5			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr6:111587895A>T	ENST00000368847.4	+	4	1483	c.1130A>T	c.(1129-1131)cAa>cTa	p.Q377L		NM_153369.2	NP_699200.2	Q5TF39	NAGT1_HUMAN	KIAA1919	377					carbohydrate transport (GO:0008643)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			large_intestine(3)|lung(2)|ovary(4)|skin(3)	12		all_cancers(87;2.35e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.0209)		OV - Ovarian serous cystadenocarcinoma(136;0.055)|all cancers(137;0.0871)|Epithelial(106;0.0884)		GGAATTCTTCAAGGAAAATAC	0.403																																					p.Q377L		Atlas-SNP	.											.	KIAA1919	54	.	0			c.A1130T						PASS	.						111	115	114					6																	111587895		2203	4300	6503	SO:0001583	missense	91749	exon4			TTCTTCAAGGAAA	BC036115	CCDS5090.1	6q22	2013-10-02			ENSG00000173214	ENSG00000173214			21053	protein-coding gene	gene with protein product							Standard	NM_153369		Approved	MGC33953, MFSD4B	uc003puv.4	Q5TF39	OTTHUMG00000015372	ENST00000368847.4:c.1130A>T	chr6.hg19:g.111587895A>T	ENSP00000357840:p.Gln377Leu	205.0	0.0	.		220.0	67.0	.	NM_153369	A8K9M0|Q8IYB6|Q96PW9|Q9P0D6	Missense_Mutation	SNP	ENST00000368847.4	hg19	CCDS5090.1	.	.	.	.	.	.	.	.	.	.	A	0.017	-1.496996	0.01001	.	.	ENSG00000173214	ENST00000368847	T	0.78481	-1.18	5.92	5.92	0.95590	Major facilitator superfamily domain, general substrate transporter (1);	0.239924	0.43110	D	0.000612	T	0.54367	0.1854	L	0.49640	1.575	0.36102	D	0.844223	B	0.28378	0.209	B	0.25987	0.065	T	0.57522	-0.7797	10	0.02654	T	1	-15.1619	16.3615	0.83270	1.0:0.0:0.0:0.0	.	377	Q5TF39	NAGT1_HUMAN	L	377	ENSP00000357840:Q377L	ENSP00000357840:Q377L	Q	+	2	0	KIAA1919	111694588	0.984000	0.35163	0.981000	0.43875	0.149000	0.21700	3.380000	0.52448	2.264000	0.75181	0.450000	0.29827	CAA	.	.	.	none		0.403	KIAA1919-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041827.1	NM_153369		T	111587895	A	T	111587895	3	4	131	1	0	0	0	0	1	0	0	0	8269	130	5	5	1144	5	KIAA1919	6	111587895	Missense_Mutation	SNP	A	TCGA-BQ-7045-01A-31D-1961-08	56364186	111587895	59527172	27	8126											
THBS2	7058	hgsc.bcm.edu	37	chr6	169622311	169622311	+	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	cctgccccggcgtgttccccGtgtgccacagcgcgttcctc	2	9	11	19	5	0	0	0	0	0	0	3	0	2	0	7	1	3	2	7	1	0	2			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr6:169622311G>T	ENST00000366787.3	-	20	3503	c.3254C>A	c.(3253-3255)aCg>aAg	p.T1085K	THBS2_ENST00000488355.1_5'UTR|XXyac-YX65C7_A.2_ENST00000444188.1_RNA	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	1085	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.T1085M(1)		NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		CGTGTTCCCCGTGTGCCACAG	0.662																																					p.T1085K	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-SNP	.											THBS2,NS,carcinoma,+1,1	THBS2	230	.	1	Substitution - Missense(1)	endometrium(1)	c.C3254A						PASS	.						58	58	58					6																	169622311		2203	4300	6503	SO:0001583	missense	7058	exon20			TTCCCCGTGTGCC		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.3254C>A	chr6.hg19:g.169622311G>T	ENSP00000355751:p.Thr1085Lys	150.0	0.0	.		102.0	25.0	.	NM_003247	A6H8N1|A7E232|Q5RI52	Missense_Mutation	SNP	ENST00000366787.3	hg19	CCDS34574.1	.	.	.	.	.	.	.	.	.	.	G	17.05	3.290586	0.59976	.	.	ENSG00000186340	ENST00000366787;ENST00000392099	D	0.91996	-2.95	4.21	4.21	0.49690	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.000000	0.42172	U	0.000748	D	0.94453	0.8215	M	0.66939	2.045	0.58432	D	0.999992	D	0.89917	1.0	D	0.72075	0.976	D	0.95110	0.8237	10	0.66056	D	0.02	-24.5393	16.5686	0.84605	0.0:0.0:1.0:0.0	.	1085	P35442	TSP2_HUMAN	K	1085;343	ENSP00000355751:T1085K	ENSP00000355751:T1085K	T	-	2	0	THBS2	169364236	1.000000	0.71417	1.000000	0.80357	0.244000	0.25665	9.166000	0.94766	1.887000	0.54652	0.297000	0.19635	ACG	.	.	.	none		0.662	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247		T	169622311	G	T	169622311	3	4	131	1	0	0	0	0	1	0	0	0	15866	1145	40	4	280	4	THBS2	6	169622311	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08	58034416	169622311	1492756	28	8127											
CCM2	83605	hgsc.bcm.edu	37	chr7	45104062	45104062	+	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	tgccctgtggttccttccagAgagcccaccagcttccggga	6	9	11	15	1	0	1	0	0	0	1	3	3	3	2	6	2	3	2	6	2	0	3			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr7:45104062A>G	ENST00000258781.6	+	4	438	c.289A>G	c.(289-291)Aga>Gga	p.R97G	CCM2_ENST00000475551.1_Splice_Site_p.R91G|CCM2_ENST00000544363.1_Splice_Site_p.R97G|CCM2_ENST00000381112.3_Splice_Site_p.R118G|CCM2_ENST00000461377.1_3'UTR|CCM2_ENST00000541586.1_Splice_Site_p.R39G|CCM2_ENST00000474617.1_Splice_Site_p.R91G	NM_031443.3	NP_113631.1	Q9BSQ5	CCM2_HUMAN	cerebral cavernous malformation 2	97	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				blood vessel endothelial cell differentiation (GO:0060837)|cell-cell junction organization (GO:0045216)|endothelial cell development (GO:0001885)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|inner ear development (GO:0048839)|integrin-mediated signaling pathway (GO:0007229)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|stress-activated MAPK cascade (GO:0051403)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)	cytoplasm (GO:0005737)|protein complex (GO:0043234)				NS(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						TTCCTTCCAGAGAGCCCACCA	0.567																																					p.R118G		Atlas-SNP	.											.	CCM2	42	.	0			c.A352G						PASS	.						43	37	39					7																	45104062		2203	4300	6503	SO:0001630	splice_region_variant	83605	exon4			TTCCAGAGAGCCC	BC004903	CCDS5500.1, CCDS34630.1, CCDS55108.1, CCDS55109.1	7p13	2014-09-17	2004-02-13	2004-02-18	ENSG00000136280	ENSG00000136280			21708	protein-coding gene	gene with protein product	"malcavernin"	607929	"chromosome 7 open reading frame 22"	C7orf22		9811928	Standard	NM_001029835		Approved	MGC4607	uc003tms.3	Q9BSQ5	OTTHUMG00000129246	ENST00000258781.6:c.289-1A>G	chr7.hg19:g.45104062A>G		41.0	0.0	.		75.0	11.0	.	NM_001029835	A4D2L4|B3KUV0|D3DVL4|E9PDJ3|F5H0E1|F5H551|Q71RE5|Q8TAT4	Missense_Mutation	SNP	ENST00000258781.6	hg19	CCDS5500.1	.	.	.	.	.	.	.	.	.	.	A	16.21	3.058731	0.55325	.	.	ENSG00000136280	ENST00000258781;ENST00000541586;ENST00000544363;ENST00000475551;ENST00000381112;ENST00000474617	T;T;T;T;T;T	0.49432	0.78;0.78;0.78;0.78;0.78;0.78	5.32	4.24	0.50183	Phosphotyrosine interaction domain (1);	0.051158	0.85682	D	0.000000	T	0.55130	0.1901	M	0.67953	2.075	0.48901	D	0.999727	B;P;P;P;P;P	0.49559	0.118;0.923;0.925;0.873;0.617;0.873	B;P;P;B;B;P	0.52159	0.075;0.578;0.691;0.385;0.173;0.461	T	0.54476	-0.8288	9	.	.	.	-18.4128	10.5848	0.45275	0.7713:0.2287:0.0:0.0	.	90;60;118;97;39;97	B7Z5A6;B7Z8D5;E9PDJ3;F5H0E1;F5H551;Q9BSQ5	.;.;.;.;.;CCM2_HUMAN	G	97;39;97;91;118;91	ENSP00000258781:R97G;ENSP00000444725:R39G;ENSP00000438035:R97G;ENSP00000417180:R91G;ENSP00000370503:R118G;ENSP00000419474:R91G	.	R	+	1	2	CCM2	45070587	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	3.295000	0.51794	0.976000	0.38417	0.533000	0.62120	AGA	.	.	.	none		0.567	CCM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251348.1	NM_031443	Missense_Mutation	G	45104062	A	G	45104062	5	3	131	1	0	0	0	0	0	0	1	0	2910	318	11	3	400	3	CCM2	7	45104062	Splice_Site	SNP	A	TCGA-BQ-7045-01A-31D-1961-08		45104062	114034601	29	8128											
PCLO	27445	hgsc.bcm.edu	37	chr7	82532016	82532016	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttatttttatccttgcgtgAggaaagatgtagtgcatagt	10	16	11	4	1	0	2	0	1	0	1	1	3	1	3	1	1	2	3	1	1	5	7			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr7:82532016A>G	ENST00000333891.9	-	9	13816	c.13479T>C	c.(13477-13479)ccT>ccC	p.P4493P	PCLO_ENST00000423517.2_Silent_p.P4493P	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						TCCTTGCGTGAGGAAAGATGT	0.299																																					p.P4493P		Atlas-SNP	.											.	PCLO	1506	.	0			c.T13479C						PASS	.						198	180	186					7																	82532016		1833	4089	5922	SO:0001819	synonymous_variant	27445	exon9			TGCGTGAGGAAAG	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.13479T>C	chr7.hg19:g.82532016A>G		89.0	0.0	.		111.0	63.0	.	NM_014510		Silent	SNP	ENST00000333891.9	hg19	CCDS47630.1																																																																																			.	.	.	none		0.299	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		G	82532016	A	G	82532016	2	3	131	1	0	0	0	0	0	0	0	1	11590	291	11	3		3	PCLO	7	82532016	Silent	SNP	A	TCGA-BQ-7045-01A-31D-1961-08	37427954	82532016	76606647	30	8129											
CHCHD3	54927	hgsc.bcm.edu	37	chr7	132523165	132523165	+	Missense_Mutation	SNP	T	T	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	tattaaaaacttacttgaacTttgcttccacctcttcagca	12	15	3	11	0	2	1	1	1	1	0	3	1	3	1	2	0	5	2	2	0	6	7			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr7:132523165T>G	ENST00000262570.5	-	6	662	c.518A>C	c.(517-519)aAg>aCg	p.K173T	CHCHD3_ENST00000476546.1_5'UTR|AC009518.8_ENST00000453078.1_RNA|CHCHD3_ENST00000448878.1_Missense_Mutation_p.K178T	NM_017812.2	NP_060282.1	Q9NX63	MIC19_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 3	173					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						TTACTTGAACTTTGCTTCCAC	0.333																																					p.K173T		Atlas-SNP	.											.	CHCHD3	21	.	0			c.A518C						PASS	.						73	73	73					7																	132523165		2203	4300	6503	SO:0001583	missense	54927	exon6			TTGAACTTTGCTT	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.518A>C	chr7.hg19:g.132523165T>G	ENSP00000262570:p.Lys173Thr	69.0	0.0	.		75.0	39.0	.	NM_017812		Missense_Mutation	SNP	ENST00000262570.5	hg19	CCDS5828.1	.	.	.	.	.	.	.	.	.	.	T	17.27	3.346334	0.61073	.	.	ENSG00000106554	ENST00000262570;ENST00000448878	T;T	0.45668	0.89;0.89	5.97	5.97	0.96955	.	0.165073	0.51477	D	0.000084	T	0.48390	0.1497	L	0.33137	0.985	0.80722	D	1	D;B	0.76494	0.999;0.294	D;B	0.72982	0.979;0.21	T	0.44065	-0.9352	10	0.30078	T	0.28	-29.5969	8.416	0.32672	0.0:0.1479:0.0:0.8521	.	178;173	C9JRZ6;Q9NX63	.;CHCH3_HUMAN	T	173;178	ENSP00000262570:K173T;ENSP00000389297:K178T	ENSP00000262570:K173T	K	-	2	0	CHCHD3	132173705	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.637000	0.46553	2.288000	0.76882	0.533000	0.62120	AAG	.	.	.	none		0.333	CHCHD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000338899.1	NM_017812		G	132523165	T	G	132523165	3	3	131	1	0	0	0	0	1	0	0	0	3319	1609	56	5	177	5	CHCHD3	7	132523165	Missense_Mutation	SNP	T	TCGA-BQ-7045-01A-31D-1961-08	49991149	132523165	26615498	31	8130											
KCNV1	27012	hgsc.bcm.edu	37	chr8	110986410	110986410	+	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	gcggtaggaagccaccaccaCggccagcttgccaaggcgcg	9	3	14	15	4	0	0	0	0	0	0	0	1	0	1	5	4	3	2	5	4	3	2			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr8:110986410C>A	ENST00000524391.1	-	2	1240	c.208G>T	c.(208-210)Gtg>Ttg	p.V70L	RP11-696P8.2_ENST00000530667.1_RNA|KCNV1_ENST00000297404.1_Missense_Mutation_p.V70L			Q6PIU1	KCNV1_HUMAN	potassium channel, subfamily V, member 1	70					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)			GCCACCACCACGGCCAGCTTG	0.692																																					p.V70L		Atlas-SNP	.											.	KCNV1	101	.	0			c.G208T						PASS	.						14	13	13					8																	110986410		2190	4286	6476	SO:0001583	missense	27012	exon1			CCACCACGGCCAG	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.208G>T	chr8.hg19:g.110986410C>A	ENSP00000435954:p.Val70Leu	18.0	0.0	.		15.0	8.0	.	NM_014379	Q9UHJ4	Missense_Mutation	SNP	ENST00000524391.1	hg19	CCDS6314.1	.	.	.	.	.	.	.	.	.	.	C	9.543	1.113775	0.20795	.	.	ENSG00000164794	ENST00000524391;ENST00000297404	T;T	0.76448	-1.02;-1.02	4.95	4.07	0.47477	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.406801	0.24251	N	0.040174	T	0.56659	0.2000	N	0.02225	-0.63	0.33369	D	0.573278	B	0.26195	0.144	B	0.30646	0.118	T	0.64816	-0.6318	10	0.45353	T	0.12	.	12.8935	0.58084	0.0:0.8369:0.1631:0.0	.	70	Q6PIU1	KCNV1_HUMAN	L	70	ENSP00000435954:V70L;ENSP00000297404:V70L	ENSP00000297404:V70L	V	-	1	0	KCNV1	111055586	0.764000	0.28473	0.999000	0.59377	0.995000	0.86356	1.510000	0.35790	1.285000	0.44548	0.655000	0.94253	GTG	.	.	.	none		0.692	KCNV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385525.1	NM_014379		A	110986410	C	A	110986410	3	1	131	1	0	0	0	0	1	0	0	0	8101	536	19	4	1306	4	KCNV1	8	110986410	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08		110986410	35377612	32	8131											
GOLGA2	2801	hgsc.bcm.edu	37	chr9	131028577	131028577	+	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	tcacgttacttcttccaactGatccgtaatttcttggttct	7	18	5	11	2	4	1	1	1	3	0	6	1	6	1	2	1	2	3	2	1	3	7			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr9:131028577G>A	ENST00000421699.2	-	8	601	c.589C>T	c.(589-591)Cag>Tag	p.Q197*	GOLGA2_ENST00000609374.1_Nonsense_Mutation_p.Q185*	NM_004486.4	NP_004477.3	Q08379	GOGA2_HUMAN	golgin A2	197					mitotic cell cycle (GO:0000278)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34						TCTTCCAACTGATCCGTAATT	0.498																																					p.Q197X		Atlas-SNP	.											.	GOLGA2	69	.	0			c.C589T						PASS	.						133	126	128					9																	131028577		2203	4300	6503	SO:0001587	stop_gained	2801	exon8			CCAACTGATCCGT	L06147	CCDS6896.2	9q34.13	2010-06-28	2010-02-12		ENSG00000167110	ENSG00000167110			4425	protein-coding gene	gene with protein product	"Golgi matrix protein GM130", "SY11 protein"	602580	"golgi autoantigen, golgin subfamily a, 2"			8315394	Standard	NM_004486		Approved	GM130, golgin-95	uc011maw.2	Q08379	OTTHUMG00000020732	ENST00000421699.2:c.589C>T	chr9.hg19:g.131028577G>A	ENSP00000416097:p.Gln197*	124.0	0.0	.		107.0	39.0	.	NM_004486	Q6GRM9|Q9BRB0|Q9NYF9	Nonsense_Mutation	SNP	ENST00000421699.2	hg19	CCDS6896.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	18.14|18.14	3.556608|3.556608	0.65425|0.65425	.|.	.|.	ENSG00000167110|ENSG00000167110	ENST00000421699;ENST00000450617|ENST00000458730	.|.	.|.	.|.	5.33|5.33	5.33|5.33	0.75918|0.75918	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.76227	.|0.3958	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.74842	.|-0.3527	.|3	0.45353|.	T|.	0.12|.	.|.	19.4623|19.4623	0.94922|0.94922	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|L	197;224|129	.|.	ENSP00000416097:Q197X|.	Q|S	-|-	1|2	0|0	GOLGA2|GOLGA2	130068398|130068398	1.000000|1.000000	0.71417|0.71417	0.612000|0.612000	0.29024|0.29024	0.034000|0.034000	0.12701|0.12701	6.353000|6.353000	0.73032|0.73032	2.663000|2.663000	0.90544|0.90544	0.558000|0.558000	0.71614|0.71614	CAG|TCA	.	.	.	none		0.498	GOLGA2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054358.2	NM_004486		A	131028577	G	A	131028577	4	1	131	1	0	0	0	0	0	1	0	0	6559	1299	45	2	2495	2	GOLGA2	9	131028577	Nonsense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08		131028577	10184854	33	8132											
UBAC1	10422	hgsc.bcm.edu	37	chr9	138839743	138839743	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttatctggagctttctggtcTtgttttttctacacagaaac	8	18	7	8	0	4	1	0	0	4	1	4	2	4	2	0	2	3	2	0	2	3	7			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr9:138839743T>C	ENST00000371756.3	-	4	559	c.342A>G	c.(340-342)caA>caG	p.Q114Q	UBAC1_ENST00000465873.1_5'Flank	NM_016172.2	NP_057256.2	Q9BSL1	UBAC1_HUMAN	UBA domain containing 1	114					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				NS(1)|biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.1e-06)|Epithelial(140;7.79e-06)		CTTTCTGGTCTTGTTTTTTCT	0.517																																					p.Q114Q	NSCLC(78;973 1398 27381 29552 42415)	Atlas-SNP	.											.	UBAC1	40	.	0			c.A342G						PASS	.						82	81	81					9																	138839743		2203	4300	6503	SO:0001819	synonymous_variant	10422	exon4			CTGGTCTTGTTTT	AF176796	CCDS35177.1	9q34.3	2008-02-05	2007-04-20	2007-04-20	ENSG00000130560	ENSG00000130560			30221	protein-coding gene	gene with protein product		608129	"ubiquitin associated domain containing 1"	UBADC1		10857748, 8619474	Standard	NM_016172		Approved	GBDR1	uc004cgt.3	Q9BSL1	OTTHUMG00000020920	ENST00000371756.3:c.342A>G	chr9.hg19:g.138839743T>C		30.0	0.0	.		34.0	15.0	.	NM_016172	O75500|Q9UMW7	Silent	SNP	ENST00000371756.3	hg19	CCDS35177.1																																																																																			.	.	.	none		0.517	UBAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055034.1	NM_016172		C	138839743	T	C	138839743	2	2	131	1	0	0	0	0	0	0	0	1	16846	1606	56	3		3	UBAC1	9	138839743	Silent	SNP	T	TCGA-BQ-7045-01A-31D-1961-08	7811166	138839743	2373688	34	8133											
OR4C15	81309	hgsc.bcm.edu	37	chr11	55322355	55322355	+	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	tactcttctatcatgaacagGaggctctgtggcattctgat	9	14	9	9	0	5	2	1	2	4	0	5	3	5	3	0	3	2	2	0	3	3	4			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr11:55322355G>C	ENST00000314644.2	+	1	573	c.573G>C	c.(571-573)agG>agC	p.R191S		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15	137						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						TCATGAACAGGAGGCTCTGTG	0.498										HNSCC(20;0.049)																											p.R191S		Atlas-SNP	.											.	OR4C15	145	.	0			c.G573C						PASS	.						103	99	100					11																	55322355		2201	4296	6497	SO:0001583	missense	81309	exon1			GAACAGGAGGCTC	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.573G>C	chr11.hg19:g.55322355G>C	ENSP00000324958:p.Arg191Ser	138.0	0.0	.		175.0	53.0	.	NM_001001920	Q6IFE2	Missense_Mutation	SNP	ENST00000314644.2	hg19	CCDS31501.1	.	.	.	.	.	.	.	.	.	.	G	10.36	1.328725	0.24167	.	.	ENSG00000181939	ENST00000314644	T	0.01347	4.99	5.12	1.75	0.24633	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.02083	0.0065	L	0.56769	1.78	0.09310	N	1	B	0.30584	0.286	B	0.32677	0.15	T	0.42068	-0.9473	9	0.87932	D	0	.	4.8871	0.13708	0.2199:0.3168:0.4633:0.0	.	137	Q8NGM1	OR4CF_HUMAN	S	191	ENSP00000324958:R191S	ENSP00000324958:R191S	R	+	3	2	OR4C15	55078931	0.000000	0.05858	0.500000	0.27589	0.181000	0.23173	-1.112000	0.03299	0.549000	0.28973	0.385000	0.25706	AGG	.	.	.	none		0.498	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1	NM_001001920		C	55322355	G	C	55322355	3	2	131	1	0	0	0	0	1	0	0	0	11055	1165	41	4	575	4	OR4C15	11	55322355	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08		55322355	79684161	35	8134											
C2CD3	26005	hgsc.bcm.edu	37	chr11	73745646	73745646	+	Intron	DEL	G	G	-																															tcatgcttccagttacttcaGtaactacctatattaaaaat																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr11:73745646delG	ENST00000334126.7	-	31	6108				C2CD3_ENST00000313663.7_Frame_Shift_Del_p.Y1963fs|C2CD3_ENST00000542452.1_5'Flank			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3						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)					AGTTACTTCAGTAACTACCTA	0.368																																					p.X1964E		Atlas-INDEL	.											.	C2CD3	288	.	0			c.5890delT						PASS	.						74	74	74					11																	73745646		2200	4293	6493	SO:0001627	intron_variant	26005	exon31			.	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.5882-323C>-	chr11.hg19:g.73745646delG		51.0	0.0	0		40.0	10.0	0.25	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Frame_Shift_Del	DEL	ENST00000334126.7	hg19																																																																																				.	.	.	none		0.368	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		-	73745646	G	-	73745646	6	5	131	0	1	1	0	1	0	0	0	0	2156	1024	36	0		0	C2CD3	11	73745646	Intron	DEL	G	TCGA-BQ-7045-01A-31D-1961-08	18423291	73745646	61260870	36	8135											
LRIG3	121227	hgsc.bcm.edu	37	chr12	59283874	59283874	+	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	ggagtgtgttggccaaattgTcaaaatacccaggttccatt	11	12	10	8	0	1	0	1	0	0	0	2	1	2	1	3	3	1	2	3	3	4	5			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr12:59283874T>A	ENST00000320743.3	-	5	849	c.563A>T	c.(562-564)gAc>gTc	p.D188V	LRIG3_ENST00000379141.4_Missense_Mutation_p.D128V	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	188					otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)			LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			GGCCAAATTGTCAAAATACCC	0.413			T	ROS1	NSCLC																																p.D188V		Atlas-SNP	.		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	.	LRIG3	120	.	0			c.A563T						PASS	.						247	238	241					12																	59283874		2203	4300	6503	SO:0001583	missense	121227	exon5			AAATTGTCAAAAT	AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"Immunoglobulin superfamily / I-set domain containing"	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.563A>T	chr12.hg19:g.59283874T>A	ENSP00000326759:p.Asp188Val	253.0	0.0	.		257.0	80.0	.	NM_153377	Q6UXL7|Q8NC72	Missense_Mutation	SNP	ENST00000320743.3	hg19	CCDS8960.1	.	.	.	.	.	.	.	.	.	.	T	15.87	2.961782	0.53400	.	.	ENSG00000139263	ENST00000379141;ENST00000320743;ENST00000552267	T;T;T	0.57273	0.41;0.41;0.41	5.55	5.55	0.83447	.	0.000000	0.39020	N	0.001494	T	0.52041	0.1710	L	0.39692	1.235	0.80722	D	1	P;P	0.50528	0.593;0.936	B;P	0.48304	0.406;0.573	T	0.49312	-0.8953	9	.	.	.	.	15.6961	0.77499	0.0:0.0:0.0:1.0	.	128;188	Q6UXM1-2;Q6UXM1	.;LRIG3_HUMAN	V	128;188;95	ENSP00000368436:D128V;ENSP00000326759:D188V;ENSP00000449109:D95V	.	D	-	2	0	LRIG3	57570141	1.000000	0.71417	0.997000	0.53966	0.322000	0.28314	4.225000	0.58600	2.110000	0.64415	0.460000	0.39030	GAC	.	.	.	none		0.413	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377		A	59283874	T	A	59283874	3	1	131	1	0	0	0	0	1	0	0	0	8953	1667	58	5	2856	5	LRIG3	12	59283874	Missense_Mutation	SNP	T	TCGA-BQ-7045-01A-31D-1961-08		59283874	74568021	37	8136											
GPC6	10082	hgsc.bcm.edu	37	chr13	94482740	94482740	+	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	tacccgcgccttcattgctgCcaggacctttgtccaggggc	5	10	11	15	2	1	0	1	0	0	0	2	1	2	1	5	3	3	1	5	3	1	4			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr13:94482740C>G	ENST00000377047.4	+	3	1268	c.653C>G	c.(652-654)gCc>gGc	p.A218G	GPC6-AS2_ENST00000445540.1_RNA	NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6	218					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)				TTCATTGCTGCCAGGACCTTT	0.498																																					p.A218G		Atlas-SNP	.											.	GPC6	102	.	0			c.C653G						PASS	.						50	49	49					13																	94482740		2203	4300	6503	SO:0001583	missense	10082	exon3			TTGCTGCCAGGAC	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.653C>G	chr13.hg19:g.94482740C>G	ENSP00000366246:p.Ala218Gly	85.0	0.0	.		53.0	18.0	.	NM_005708	A8K279|Q96SG5|Q96SG8|Q9H1P4	Missense_Mutation	SNP	ENST00000377047.4	hg19	CCDS9469.1	.	.	.	.	.	.	.	.	.	.	C	32	5.161612	0.94727	.	.	ENSG00000183098	ENST00000377047	T	0.57907	0.37	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.77377	0.4121	M	0.87097	2.86	0.53688	D	0.999974	D;D	0.89917	1.0;0.999	D;D	0.81914	0.983;0.995	T	0.78288	-0.2262	10	0.46703	T	0.11	.	19.8022	0.96513	0.0:1.0:0.0:0.0	.	218;218	B4E2M1;Q9Y625	.;GPC6_HUMAN	G	218	ENSP00000366246:A218G	ENSP00000366246:A218G	A	+	2	0	GPC6	93280741	1.000000	0.71417	0.932000	0.37286	0.943000	0.58893	7.442000	0.80503	2.771000	0.95319	0.644000	0.83932	GCC	.	.	.	none		0.498	GPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045460.4	NM_005708		G	94482740	C	G	94482740	3	3	131	1	0	0	0	0	1	0	0	0	6609	739	26	4	663	4	GPC6	13	94482740	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08		94482740	20687138	38	8137											
RAP2A	5911	hgsc.bcm.edu	37	chr13	98086836	98086836	+	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	aatacgaccccaccatcgagGacttctaccgcaaggagatc	13	6	8	14	3	1	1	0	0	1	1	3	5	1	2	4	2	2	1	4	2	4	3			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr13:98086836G>A	ENST00000245304.4	+	1	361	c.112G>A	c.(112-114)Gac>Aac	p.D38N		NM_021033.6	NP_066361.1	P10114	RAP2A_HUMAN	RAP2A, member of RAS oncogene family	38					actin cytoskeleton reorganization (GO:0031532)|cellular protein localization (GO:0034613)|establishment of protein localization (GO:0045184)|negative regulation of cell migration (GO:0030336)|positive regulation of protein autophosphorylation (GO:0031954)|Rap protein signal transduction (GO:0032486)|regulation of dendrite morphogenesis (GO:0048814)|regulation of JNK cascade (GO:0046328)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|recycling endosome (GO:0055037)|recycling endosome membrane (GO:0055038)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	5	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.166)			CACCATCGAGGACTTCTACCG	0.627																																					p.D38N		Atlas-SNP	.											.	RAP2A	15	.	0			c.G112A						PASS	.						114	107	109					13																	98086836		2203	4300	6503	SO:0001583	missense	5911	exon1			ATCGAGGACTTCT	AF205602	CCDS9485.1	13q34	2014-05-09			ENSG00000125249	ENSG00000125249			9861	protein-coding gene	gene with protein product		179540		RAP2			Standard	NM_021033		Approved	K-REV	uc001vnd.3	P10114	OTTHUMG00000017240	ENST00000245304.4:c.112G>A	chr13.hg19:g.98086836G>A	ENSP00000245304:p.Asp38Asn	149.0	0.0	.		174.0	57.0	.	NM_021033	B2RCJ1|Q5JSC1|Q5JSC2	Missense_Mutation	SNP	ENST00000245304.4	hg19	CCDS9485.1	.	.	.	.	.	.	.	.	.	.	G	34	5.299548	0.95574	.	.	ENSG00000125249	ENST00000245304	D	0.83335	-1.71	2.95	2.95	0.34219	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.89111	0.6622	M	0.68593	2.085	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.90284	0.4317	10	0.66056	D	0.02	.	13.9659	0.64209	0.0:0.0:1.0:0.0	.	38	P10114	RAP2A_HUMAN	N	38	ENSP00000245304:D38N	ENSP00000245304:D38N	D	+	1	0	RAP2A	96884837	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.055000	0.93873	1.673000	0.50895	0.484000	0.47621	GAC	.	.	.	none		0.627	RAP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045528.4			A	98086836	G	A	98086836	3	1	131	1	0	0	0	0	1	0	0	0	13053	1174	41	2	114	2	RAP2A	13	98086836	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08	3604096	98086836	17083042	39	8138											
GPR18	2841	hgsc.bcm.edu	37	chr13	99907879	99907879	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caaatggccattcatcttttGcataataaaacattcgaaag	16	12	5	8	1	2	0	1	0	1	0	3	1	2	0	1	1	2	1	1	1	5	6			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr13:99907879G>A	ENST00000340807.3	-	3	804	c.248C>T	c.(247-249)gCa>gTa	p.A83V	UBAC2_ENST00000403766.3_Intron|GPR18_ENST00000397470.2_Missense_Mutation_p.A83V|GPR18_ENST00000397473.2_Missense_Mutation_p.A83V|UBAC2_ENST00000376440.2_Intron			Q14330	GPR18_HUMAN	G protein-coupled receptor 18	83					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(2)|lung(6)	10	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Glycine(DB00145)	TTCATCTTTTGCATAATAAAA	0.383																																					p.A83V		Atlas-SNP	.											.	GPR18	23	.	0			c.C248T						PASS	.						71	71	71					13																	99907879		2203	4300	6503	SO:0001583	missense	2841	exon2			TCTTTTGCATAAT	L42324	CCDS9491.1	13q32	2014-01-30			ENSG00000125245	ENSG00000125245		"GPCR / Class A : Orphans"	4472	protein-coding gene	gene with protein product		602042				9205118	Standard	NM_005292		Approved		uc010afv.3	Q14330	OTTHUMG00000017266	ENST00000340807.3:c.248C>T	chr13.hg19:g.99907879G>A	ENSP00000343428:p.Ala83Val	79.0	0.0	.		69.0	18.0	.	NM_001098200	Q6GTM3|Q96HI6|Q9H2L2	Missense_Mutation	SNP	ENST00000340807.3	hg19	CCDS9491.1	.	.	.	.	.	.	.	.	.	.	G	5.690	0.311943	0.10789	.	.	ENSG00000125245	ENST00000397473;ENST00000397470;ENST00000340807;ENST00000416594	T;T;T;T	0.35973	1.28;1.28;1.28;1.28	6.07	1.18	0.20946	GPCR, rhodopsin-like superfamily (1);	0.322518	0.32328	N	0.006250	T	0.23054	0.0557	L	0.34521	1.04	0.09310	N	0.999999	B	0.06786	0.001	B	0.08055	0.003	T	0.18555	-1.0333	9	.	.	.	-5.3997	8.9019	0.35499	0.2064:0.3912:0.4024:0.0	.	83	Q14330	GPR18_HUMAN	V	83	ENSP00000380613:A83V;ENSP00000380610:A83V;ENSP00000343428:A83V;ENSP00000401611:A83V	.	A	-	2	0	GPR18	98705880	0.888000	0.30383	0.430000	0.26722	0.894000	0.52154	0.767000	0.26575	0.138000	0.18790	-0.137000	0.14449	GCA	.	.	.	none		0.383	GPR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045585.1			A	99907879	G	A	99907879	3	1	131	1	0	0	0	0	1	0	0	0	6682	1319	46	2	751	2	GPR18	13	99907879	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08	1821043	99907879	15261999	40	8139											
SNX6	58533	hgsc.bcm.edu	37	chr14	35062276	35062276	+	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	tgggatcttgtcattctatcAgatttagcagatgcatcctt	9	16	8	8	0	4	2	2	0	2	2	5	3	5	3	1	1	2	2	1	1	2	6			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr14:35062276A>T	ENST00000362031.4	-	8	759	c.729T>A	c.(727-729)tcT>tcA	p.S243S	SNX6_ENST00000355110.5_Silent_p.S119S|SNX6_ENST00000396526.3_Silent_p.S115S|SNX6_ENST00000396534.3_Silent_p.S115S	NM_152233.2	NP_689419.2	Q9UNH7	SNX6_HUMAN	sorting nexin 6	231					intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|intracellular (GO:0005622)|nucleus (GO:0005634)	phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)			endometrium(4)|lung(1)|ovary(1)	6	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00199)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.0245)		TCATTCTATCAGATTTAGCAG	0.299																																					p.S243S		Atlas-SNP	.											.	SNX6	21	.	0			c.T729A						PASS	.						73	71	72					14																	35062276		2203	4299	6502	SO:0001819	synonymous_variant	58533	exon8			TCTATCAGATTTA	AF121856	CCDS9648.1, CCDS41942.1	14q13	2010-08-05			ENSG00000129515	ENSG00000129515		"Sorting nexins"	14970	protein-coding gene	gene with protein product		606098				11279102	Standard	XM_006720224		Approved		uc001wsf.1	Q9UNH7	OTTHUMG00000140213	ENST00000362031.4:c.729T>A	chr14.hg19:g.35062276A>T		96.0	0.0	.		61.0	18.0	.	NM_152233	C0H5W9|Q9Y449	Silent	SNP	ENST00000362031.4	hg19	CCDS41942.1																																																																																			.	.	.	none		0.299	SNX6-002	KNOWN	downstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276642.3			T	35062276	A	T	35062276	2	4	131	1	0	0	0	0	0	0	0	1	14919	175	7	5		5	SNX6	14	35062276	Silent	SNP	A	TCGA-BQ-7045-01A-31D-1961-08		35062276	72287264	41	8140											
CLEC14A	161198	hgsc.bcm.edu	37	chr14	38724316	38724316	+	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	gttgcagtggccggcgggcgCctggtgggcaccccggtccc	2	6	18	15	4	0	0	0	0	0	0	1	0	1	0	5	6	1	3	5	6	0	1			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr14:38724316C>T	ENST00000342213.2	-	1	1258	c.912G>A	c.(910-912)agG>agA	p.R304R		NM_175060.2	NP_778230.1	Q86T13	CLC14_HUMAN	C-type lectin domain family 14, member A	304						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)		CCGGCGGGCGCCTGGTGGGCA	0.657																																					p.R304R		Atlas-SNP	.											.	CLEC14A	83	.	0			c.G912A						PASS	.						44	48	47					14																	38724316		2198	4289	6487	SO:0001819	synonymous_variant	161198	exon1			CGGGCGCCTGGTG		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.912G>A	chr14.hg19:g.38724316C>T		135.0	0.0	.		139.0	50.0	.	NM_175060	Q695G9|Q6PWT6|Q8N5V5	Silent	SNP	ENST00000342213.2	hg19	CCDS9667.1																																																																																			.	.	.	none		0.657	CLEC14A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276729.1	NM_175060		T	38724316	C	T	38724316	2	4	131	1	0	0	0	0	0	0	0	1	3501	738	26	2		2	CLEC14A	14	38724316	Silent	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	3662040	38724316	68625224	42	8141											
FERMT2	10979	hgsc.bcm.edu	37	chr14	53386065	53386065	+	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	gagcatggtcagaccaatctTtttttacatctataaaaaac	15	13	5	8	0	3	1	1	0	2	1	3	2	3	1	1	1	3	1	1	1	6	6			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr14:53386065T>A	ENST00000395631.2	-	3	383	c.167A>T	c.(166-168)aAa>aTa	p.K56I	FERMT2_ENST00000399304.3_Missense_Mutation_p.K56I|FERMT2_ENST00000343279.4_Missense_Mutation_p.K56I|FERMT2_ENST00000341590.3_Missense_Mutation_p.K56I|FERMT2_ENST00000553373.1_Missense_Mutation_p.K56I			Q96AC1	FERM2_HUMAN	fermitin family member 2	56	Interaction with membranes containing phosphatidylinositol phosphate.				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|focal adhesion assembly (GO:0048041)|integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|protein localization to membrane (GO:0072657)|regulation of cell shape (GO:0008360)|substrate adhesion-dependent cell spreading (GO:0034446)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|stress fiber (GO:0001725)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)		ERO1L/FERMT2(2)	NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	20	Breast(41;0.0342)					AGACCAATCTTTTTTTACATC	0.333																																					p.K56I		Atlas-SNP	.											.	FERMT2	59	.	0			c.A167T						PASS	.						73	72	73					14																	53386065		2203	4300	6503	SO:0001583	missense	10979	exon3			CAATCTTTTTTTA	Z24725	CCDS9713.1, CCDS45107.1, CCDS45108.1	14q22.1	2013-01-10	2010-06-24	2007-12-14	ENSG00000073712	ENSG00000073712		"Fermitins", "Pleckstrin homology (PH) domain containing"	15767	protein-coding gene	gene with protein product	"kindlin-2"	607746	"pleckstrin homology domain containing, family C (with FERM domain) member 1", "fermitin family homolog 2 (Drosophila)"	PLEKHC1		8175911, 12697302	Standard	NM_006832		Approved	mig-2, KIND2, UNC112B	uc001xac.3	Q96AC1	OTTHUMG00000140309	ENST00000395631.2:c.167A>T	chr14.hg19:g.53386065T>A	ENSP00000378993:p.Lys56Ile	107.0	0.0	.		99.0	27.0	.	NM_001135000	B5TJY2|Q14840|Q86TY7	Missense_Mutation	SNP	ENST00000395631.2	hg19	CCDS9713.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.478457	0.84747	.	.	ENSG00000073712	ENST00000395631;ENST00000341590;ENST00000343279;ENST00000553373;ENST00000399304;ENST00000555692;ENST00000554712	T;T;T;T;T;T;T	0.11712	2.75;2.75;2.75;2.75;2.75;2.75;2.75	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.22513	0.0543	M	0.62723	1.935	0.80722	D	1	P;B;B	0.35542	0.508;0.375;0.078	P;B;B	0.45998	0.5;0.248;0.042	T	0.00621	-1.1640	10	0.42905	T	0.14	.	16.1966	0.82029	0.0:0.0:0.0:1.0	.	56;56;56	Q96AC1-2;Q96AC1;B5TJY2	.;FERM2_HUMAN;.	I	56;56;56;56;56;12;56	ENSP00000378993:K56I;ENSP00000340391:K56I;ENSP00000342858:K56I;ENSP00000451084:K56I;ENSP00000382243:K56I;ENSP00000452472:K12I;ENSP00000450506:K56I	ENSP00000340391:K56I	K	-	2	0	FERMT2	52455815	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.291000	0.72719	2.232000	0.73038	0.528000	0.53228	AAA	.	.	.	none		0.333	FERMT2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276907.2	NM_006832		A	53386065	T	A	53386065	3	1	131	1	0	0	0	0	1	0	0	0	5825	1841	64	5	1964	5	FERMT2	14	53386065	Missense_Mutation	SNP	T	TCGA-BQ-7045-01A-31D-1961-08	14661749	53386065	53963475	43	8142											
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102466716	102466716	+	Missense_Mutation	SNP	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	agatgaaggagcaaccctggGtttcagtacagcctcgaaag	13	7	12	9	1	1	2	1	1	0	1	2	4	1	3	2	2	4	3	2	2	4	2			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr14:102466716G>A	ENST00000360184.4	+	18	4218	c.4054G>A	c.(4054-4056)Gtt>Att	p.V1352I		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	1352	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						GCAACCCTGGGTTTCAGTACA	0.428																																					p.V1352I		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.G4054A						PASS	.						115	116	116					14																	102466716		2203	4300	6503	SO:0001583	missense	1778	exon18			CCCTGGGTTTCAG	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.4054G>A	chr14.hg19:g.102466716G>A	ENSP00000348965:p.Val1352Ile	85.0	0.0	.		87.0	28.0	.	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	hg19	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	G	16.32	3.089051	0.55968	.	.	ENSG00000197102	ENST00000360184	T	0.28666	1.6	5.64	5.64	0.86602	Dynein heavy chain, domain-2 (1);	0.000000	0.85682	D	0.000000	T	0.18635	0.0447	N	0.03983	-0.305	0.80722	D	1	B	0.29646	0.253	B	0.33960	0.173	T	0.14755	-1.0461	10	0.16896	T	0.51	.	20.0769	0.97748	0.0:0.0:1.0:0.0	.	1352	Q14204	DYHC1_HUMAN	I	1352	ENSP00000348965:V1352I	ENSP00000348965:V1352I	V	+	1	0	DYNC1H1	101536469	1.000000	0.71417	0.999000	0.59377	0.942000	0.58702	8.001000	0.88508	2.820000	0.97059	0.650000	0.86243	GTT	.	.	.	none		0.428	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		A	102466716	G	A	102466716	3	1	131	1	0	0	0	0	1	0	0	0	4843	1261	44	2	4124	2	DYNC1H1	14	102466716	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08	49080651	102466716	4882824	44	8143											
ATP10A	57194	hgsc.bcm.edu	37	chr15	25924510	25924510	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actgtgaccgccttgaagatGctcctataagtagtctgtgg	9	12	11	9	1	1	3	0	2	1	1	2	3	2	3	3	1	1	2	3	1	4	4			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr15:25924510G>A	ENST00000356865.6	-	21	4589	c.4478C>T	c.(4477-4479)gCa>gTa	p.A1493V		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	1493					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)		CCTTGAAGATGCTCCTATAAG	0.423																																					p.A1493V		Atlas-SNP	.											.	ATP10A	270	.	0			c.C4478T						PASS	.						57	61	60					15																	25924510		2203	4300	6503	SO:0001583	missense	57194	exon21			GAAGATGCTCCTA	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.4478C>T	chr15.hg19:g.25924510G>A	ENSP00000349325:p.Ala1493Val	74.0	0.0	.		100.0	25.0	.	NM_024490	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	hg19	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	G	13.94	2.386201	0.42308	.	.	ENSG00000206190	ENST00000356865	T	0.10477	2.87	4.74	3.76	0.43208	.	10.878000	0.00166	N	0.000006	T	0.07954	0.0199	N	0.08118	0	0.09310	N	1	B	0.30482	0.281	B	0.22601	0.04	T	0.16129	-1.0413	10	0.46703	T	0.11	-3.4971	12.1728	0.54167	0.0:0.0:0.7797:0.2203	.	1493	O60312	AT10A_HUMAN	V	1493	ENSP00000349325:A1493V	ENSP00000349325:A1493V	A	-	2	0	ATP10A	23475603	0.618000	0.27051	0.010000	0.14722	0.250000	0.25880	1.852000	0.39348	2.475000	0.83589	0.655000	0.94253	GCA	.	.	.	none		0.423	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		A	25924510	G	A	25924510	3	1	131	1	0	0	0	0	1	0	0	0	1116	1319	46	2	25	2	ATP10A	15	25924510	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08		25924510	76606882	45	8144											
HAPLN3	145864	hgsc.bcm.edu	37	chr15	89422488	89422488	+	Frame_Shift_Del	DEL	G	G	-																															gcccgttgggggactggtaaGgaaagaccacacctgcaggg																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr15:89422488delG	ENST00000359595.3	-	4	720	c.506delC	c.(505-507)cctfs	p.P169fs	HAPLN3_ENST00000562889.1_Frame_Shift_Del_p.P231fs	NM_178232.2	NP_839946.1	Q96S86	HPLN3_HUMAN	hyaluronan and proteoglycan link protein 3	169	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)	GGACTGGTAAGGAAAGACCAC	0.632											OREG0023445	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P169fs		Atlas-INDEL	.											.	HAPLN3	43	.	0			c.507delT						PASS	.						36	41	39					15																	89422488		2200	4299	6499	SO:0001589	frameshift_variant	145864	exon4			.	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.506delC	chr15.hg19:g.89422488delG	ENSP00000352606:p.Pro169fs	68.0	0.0	0	1267	65.0	19.0	0.292308	NM_178232	A8K7P0	Frame_Shift_Del	DEL	ENST00000359595.3	hg19	CCDS10346.1																																																																																			.	.	.	none		0.632	HAPLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309070.1	NM_178232		-	89422488	G	-	89422488	7	5	131	1	0	1	0	1	0	0	0	0	6963	1000	35	0	584	0	HAPLN3	15	89422488	Frame_Shift_Del	DEL	G	TCGA-BQ-7045-01A-31D-1961-08	63497978	89422488	13108904	46	8145											
ZNF598	90850	hgsc.bcm.edu	37	chr16	2052644	2052644	+	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	cagaacttgcagagcgggtgCccacggtgcgacgtgtcatc	8	7	14	12	4	1	2	1	0	0	2	2	3	1	2	1	2	5	1	1	2	1	1			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr16:2052644C>T	ENST00000563630.1	-	4	632	c.390G>A	c.(388-390)ggG>ggA	p.G130G	ZNF598_ENST00000431526.1_Silent_p.G185G|ZNF598_ENST00000562103.1_Silent_p.G130G			Q86UK7	ZN598_HUMAN	zinc finger protein 598	185							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						AGAGCGGGTGCCCACGGTGCG	0.602																																					p.G185G		Atlas-SNP	.											.	ZNF598	55	.	0			c.G555A						PASS	.						50	58	55					16																	2052644		2169	4266	6435	SO:0001819	synonymous_variant	90850	exon6			CGGGTGCCCACGG	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.390G>A	chr16.hg19:g.2052644C>T		40.0	0.0	.		50.0	10.0	.	NM_178167	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Silent	SNP	ENST00000563630.1	hg19																																																																																				.	.	.	none		0.602	ZNF598-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000434439.1	NM_178167		T	2052644	C	T	2052644	2	4	131	1	0	0	0	0	0	0	0	1	18040	726	26	2		2	ZNF598	16	2052644	Silent	SNP	C	TCGA-BQ-7045-01A-31D-1961-08		2052644	88302109	47	8146											
CLUAP1	23059	hgsc.bcm.edu	37	chr16	3554721	3554721	+	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	tgtatttttccttggacagaTttcacagagatgatgagagc	11	14	10	6	0	1	4	1	2	0	3	2	7	2	5	1	1	1	1	1	1	1	5			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr16:3554721T>C	ENST00000576634.1	+	2	168	c.24T>C	c.(22-24)aaT>aaC	p.N8N	CLUAP1_ENST00000571025.1_Splice_Site_p.N8N|CLUAP1_ENST00000417763.2_5'UTR|CLUAP1_ENST00000341633.5_Splice_Site_p.N8N|LA16c-306E5.3_ENST00000574423.2_RNA	NM_015041.2	NP_055856.1	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1	8					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						CTTGGACAGATTTCACAGAGA	0.383																																					p.N8N		Atlas-SNP	.											.	CLUAP1	32	.	0			c.T24C						PASS	.						106	103	104					16																	3554721		2197	4300	6497	SO:0001630	splice_region_variant	23059	exon2			GACAGATTTCACA	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.23-1T>C	chr16.hg19:g.3554721T>C		60.0	0.0	.		105.0	21.0	.	NM_015041	O75138|Q65ZA3|Q9H8R4|Q9H8T1	Silent	SNP	ENST00000576634.1	hg19	CCDS32381.1																																																																																			.	.	.	none		0.383	CLUAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437883.2	NM_024793	Silent	C	3554721	T	C	3554721	5	2	131	1	0	0	0	0	0	0	1	0	3571	1507	52	3	30	3	CLUAP1	16	3554721	Splice_Site	SNP	T	TCGA-BQ-7045-01A-31D-1961-08	1502077	3554721	86800032	48	8147											
TIAF1	9220	hgsc.bcm.edu	37	chr17	27400954	27400954	+	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	gaggcagtgcttggatcagcCctgaactgctgtagttggaa	9	10	14	8	0	1	1	1	1	0	0	1	4	1	3	1	3	4	5	1	3	3	3			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr17:27400954C>G	ENST00000359450.6	-	1	4921	c.264G>C	c.(262-264)agG>agC	p.R88S	MYO18A_ENST00000527372.1_3'UTR|MYO18A_ENST00000533112.1_3'UTR|MYO18A_ENST00000529578.1_5'UTR|MYO18A_ENST00000531253.1_3'UTR|TIAF1_ENST00000408971.2_Missense_Mutation_p.R88S|MYO18A_ENST00000354329.4_3'UTR	NM_004740.3	NP_004731.2	O95411	TIAF1_HUMAN	TGFB1-induced anti-apoptotic factor 1	88					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)			TTGGATCAGCCCTGAACTGCT	0.532																																					p.R88S		Atlas-SNP	.											.	TIAF1	9	.	0			c.G264C						PASS	.						166	140	149					17																	27400954		2203	4300	6503	SO:0001583	missense	9220	exon1			ATCAGCCCTGAAC	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.264G>C	chr17.hg19:g.27400954C>G	ENSP00000352424:p.Arg88Ser	206.0	0.0	.		251.0	129.0	.	NM_004740	A2RRE2|Q6PEG2	Missense_Mutation	SNP	ENST00000359450.6	hg19	CCDS32599.1	.	.	.	.	.	.	.	.	.	.	C	13.16	2.152934	0.38021	.	.	ENSG00000221995	ENST00000408971;ENST00000511177	.	.	.	5.55	5.55	0.83447	.	.	.	.	.	T	0.22666	0.0547	N	0.08118	0	0.23577	N	0.997377	P	0.35363	0.497	B	0.31016	0.123	T	0.26985	-1.0087	8	0.87932	D	0	.	16.3692	0.83347	0.0:1.0:0.0:0.0	.	88	O95411	TIAF1_HUMAN	S	88	.	ENSP00000386130:R88S	R	-	3	2	TIAF1	24425080	0.786000	0.28738	0.969000	0.41365	0.843000	0.47879	3.603000	0.54074	2.894000	0.99253	0.655000	0.94253	AGG	.	.	.	none		0.532	TIAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372394.2	NM_004740		G	27400954	C	G	27400954	3	3	131	1	0	0	0	0	1	0	0	0	15900	622	22	4	87	4	TIAF1	17	27400954	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08		27400954	53794256	49	8148											
TMEM101	84336	hgsc.bcm.edu	37	chr17	42089524	42089524	+	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	atgccatacagcacgaagaaCagctggatcatcagctcccc	13	6	8	14	1	2	1	2	0	0	1	3	3	3	2	3	1	6	3	3	1	3	1			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr17:42089524C>T	ENST00000589334.1	-	5	861	c.546G>A	c.(544-546)ctG>ctA	p.L182L	TMEM101_ENST00000206380.3_Silent_p.L182L|TMEM101_ENST00000542039.1_Silent_p.L124L			Q96IK0	TM101_HUMAN	transmembrane protein 101	182					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)		GCACGAAGAACAGCTGGATCA	0.587																																					p.L182L		Atlas-SNP	.											.	TMEM101	18	.	0			c.G546A						PASS	.						112	95	100					17																	42089524		2203	4300	6503	SO:0001819	synonymous_variant	84336	exon4			GAAGAACAGCTGG	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.546G>A	chr17.hg19:g.42089524C>T		97.0	0.0	.		122.0	27.0	.	NM_032376	B2R9N6	Silent	SNP	ENST00000589334.1	hg19	CCDS11474.1																																																																																			.	.	.	none		0.587	TMEM101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457665.1	NM_032376		T	42089524	C	T	42089524	2	4	131	1	0	0	0	0	0	0	0	1	16028	465	17	2		2	TMEM101	17	42089524	Silent	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	14688570	42089524	39105686	50	8149											
BZRAP1	9256	hgsc.bcm.edu	37	chr17	56386306	56386306	+	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	cctctcccgtgtggggcccaGtcgtccagaggcctggggcc	3	7	15	16	2	1	1	0	0	1	1	4	1	2	1	6	5	0	0	6	5	0	0			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr17:56386306G>T	ENST00000343736.4	-	22	4490	c.4327C>A	c.(4327-4329)Ctg>Atg	p.L1443M	BZRAP1_ENST00000355701.3_Missense_Mutation_p.L1443M|BZRAP1_ENST00000268893.6_Missense_Mutation_p.L1383M			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1443						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)					GTGGGGCCCAGTCGTCCAGAG	0.692																																					p.L1443M		Atlas-SNP	.											.	BZRAP1	287	.	0			c.C4327A						PASS	.						27	34	32					17																	56386306		2173	4260	6433	SO:0001583	missense	9256	exon22			GGCCCAGTCGTCC	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.4327C>A	chr17.hg19:g.56386306G>T	ENSP00000345824:p.Leu1443Met	89.0	0.0	.		149.0	36.0	.	NM_004758	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	hg19	CCDS11605.1	.	.	.	.	.	.	.	.	.	.	G	7.586	0.669756	0.14776	.	.	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	T;T;T	0.04758	3.56;3.56;3.56	5.31	2.94	0.34122	.	0.632124	0.16677	N	0.204129	T	0.02888	0.0086	N	0.08118	0	0.09310	N	1	B;B;B	0.31519	0.327;0.106;0.064	B;B;B	0.28232	0.087;0.015;0.006	T	0.42899	-0.9424	10	0.72032	D	0.01	.	10.1566	0.42827	0.1877:0.0:0.8123:0.0	.	1443;1383;1443	B7ZVZ7;O95153-2;O95153	.;.;RIMB1_HUMAN	M	1443;1443;1383	ENSP00000347929:L1443M;ENSP00000345824:L1443M;ENSP00000268893:L1383M	ENSP00000268893:L1383M	L	-	1	2	BZRAP1	53741305	1.000000	0.71417	0.155000	0.22561	0.518000	0.34316	2.879000	0.48522	1.233000	0.43693	0.563000	0.77884	CTG	.	.	.	none		0.692	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758		T	56386306	G	T	56386306	3	4	131	1	0	0	0	0	1	0	0	0	1579	1020	36	4	1286	4	BZRAP1	17	56386306	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08	14296782	56386306	24808904	51	8150											
KCNH6	81033	hgsc.bcm.edu	37	chr17	61623123	61623123	+	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	ggccacccctagcctcacctCtacatcccctggaagtacaa	10	7	6	18	0	2	0	1	0	1	0	3	1	3	1	7	2	3	1	7	2	5	3			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr17:61623123C>T	ENST00000583023.1	+	14	2856	c.2845C>T	c.(2845-2847)Cta>Tta	p.L949L	KCNH6_ENST00000581784.1_Silent_p.L860L|KCNH6_ENST00000314672.5_Silent_p.L913L|KCNH6_ENST00000456941.2_Silent_p.L860L	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	949					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)	p.L949V(1)|p.L949I(1)		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)	AGCCTCACCTCTACATCCCCT	0.587																																					p.L949L		Atlas-SNP	.											KCNH6,bladder,carcinoma,0,2	KCNH6	122	.	2	Substitution - Missense(2)	urinary_tract(1)|lung(1)	c.C2845T						PASS	.						122	113	116					17																	61623123		2203	4300	6503	SO:0001819	synonymous_variant	81033	exon14			TCACCTCTACATC	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.2845C>T	chr17.hg19:g.61623123C>T		126.0	0.0	.		169.0	33.0	.	NM_030779	Q9BRD7	Silent	SNP	ENST00000583023.1	hg19	CCDS11638.1																																																																																			.	.	.	none		0.587	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779		T	61623123	C	T	61623123	2	4	131	1	0	0	0	0	0	0	0	1	8043	912	32	2		2	KCNH6	17	61623123	Silent	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	5236817	61623123	19572087	52	8151											
THOC1	9984	hgsc.bcm.edu	37	chr18	214909	214909	+	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	ctgttacaggtttgtctcgcCgaacatcaggacctagaaaa	12	10	9	10	2	2	1	1	0	1	1	3	3	2	2	2	2	2	2	2	2	5	3			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr18:214909C>A	ENST00000261600.6	-	21	1698	c.1691G>T	c.(1690-1692)cGg>cTg	p.R564L		NM_005131.2	NP_005122.2	Q96FV9	THOC1_HUMAN	THO complex 1	564					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)				TTTGTCTCGCCGAACATCAGG	0.388																																					p.R564L		Atlas-SNP	.											.	THOC1	43	.	0			c.G1691T						PASS	.						140	136	137					18																	214909		1844	4089	5933	SO:0001583	missense	9984	exon21			TCTCGCCGAACAT	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.1691G>T	chr18.hg19:g.214909C>A	ENSP00000261600:p.Arg564Leu	157.0	0.0	.		171.0	8.0	.	NM_005131	B2RBP6|Q15219|Q64I72|Q64I73	Missense_Mutation	SNP	ENST00000261600.6	hg19	CCDS45820.1	.	.	.	.	.	.	.	.	.	.	C	8.710	0.911843	0.17907	.	.	ENSG00000079134	ENST00000261600	D	0.92699	-3.09	6.03	4.23	0.50019	Death (1);DEATH-like (2);	0.111699	0.64402	D	0.000009	D	0.84902	0.5575	L	0.29908	0.895	0.38420	D	0.946166	B	0.09022	0.002	B	0.10450	0.005	T	0.79827	-0.1639	10	0.29301	T	0.29	-8.2798	8.0093	0.30344	0.0:0.6786:0.0:0.3213	.	564	Q96FV9	THOC1_HUMAN	L	564	ENSP00000261600:R564L	ENSP00000261600:R564L	R	-	2	0	THOC1	204909	0.998000	0.40836	0.997000	0.53966	0.995000	0.86356	2.971000	0.49248	1.560000	0.49568	-0.150000	0.13652	CGG	.	.	.	none		0.388	THOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440348.5	NM_005131		A	214909	C	A	214909	3	1	131	1	0	0	0	0	1	0	0	0	15876	652	23	4	286	4	THOC1	18	214909	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08		214909	77862339	53	8152											
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9257291	9257291	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttaactgtgccaggagatacTagtccttctcccaaacctga	11	11	7	12	0	1	2	0	1	1	1	3	3	2	2	4	1	4	0	4	1	4	4			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr18:9257291T>C	ENST00000262126.4	+	9	4266	c.4026T>C	c.(4024-4026)acT>acC	p.T1342T	RP11-888D10.4_ENST00000609701.1_RNA|ANKRD12_ENST00000400020.3_Silent_p.T1319T|ANKRD12_ENST00000383440.2_Silent_p.T1319T	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1342						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						CAGGAGATACTAGTCCTTCTC	0.398																																					p.T1342T		Atlas-SNP	.											.	ANKRD12	167	.	0			c.T4026C						PASS	.						122	117	119					18																	9257291		2203	4300	6503	SO:0001819	synonymous_variant	23253	exon9			AGATACTAGTCCT	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.4026T>C	chr18.hg19:g.9257291T>C		132.0	0.0	.		120.0	43.0	.	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Silent	SNP	ENST00000262126.4	hg19	CCDS11843.1																																																																																			.	.	.	none		0.398	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		C	9257291	T	C	9257291	2	2	131	1	0	0	0	0	0	0	0	1	640	1509	53	3		3	ANKRD12	18	9257291	Silent	SNP	T	TCGA-BQ-7045-01A-31D-1961-08	9042382	9257291	68819957	54	8153											
ASXL3	80816	hgsc.bcm.edu	37	chr18	31263418	31263418	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgacatagaaaccccaggAtctattcttgtcaacactaa	15	11	5	10	0	3	2	1	1	2	1	3	3	3	3	2	1	2	0	2	1	5	6			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr18:31263418A>G	ENST00000269197.5	+	8	765	c.765A>G	c.(763-765)ggA>ggG	p.G255G		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	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)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						AAACCCCAGGATCTATTCTTG	0.418																																					p.G255G		Atlas-SNP	.											.	ASXL3	405	.	0			c.A765G						PASS	.						109	106	107					18																	31263418		1872	4099	5971	SO:0001819	synonymous_variant	80816	exon8			CCCAGGATCTATT	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.765A>G	chr18.hg19:g.31263418A>G		53.0	0.0	.		54.0	14.0	.	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Silent	SNP	ENST00000269197.5	hg19	CCDS45847.1																																																																																			.	.	.	none		0.418	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			G	31263418	A	G	31263418	2	3	131	1	0	0	0	0	0	0	0	1	1068	320	12	3		3	ASXL3	18	31263418	Silent	SNP	A	TCGA-BQ-7045-01A-31D-1961-08	22006127	31263418	46813830	55	8154											
ELAC1	55520	hgsc.bcm.edu	37	chr18	48513160	48513160	+	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	tgatggaggagtaaaactgtGctttgaagcagacctgttga	12	11	13	5	0	0	4	0	3	0	1	0	6	0	6	1	2	3	4	1	2	3	3			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr18:48513160G>C	ENST00000269466.3	+	4	904	c.797G>C	c.(796-798)tGc>tCc	p.C266S	RP11-729L2.2_ENST00000588256.1_Intron|SMAD4_ENST00000452201.2_Intron|ELAC1_ENST00000588577.1_3'UTR|RP11-729L2.2_ENST00000590722.2_Intron	NM_018696.2	NP_061166.1	Q9H777	RNZ1_HUMAN	elaC ribonuclease Z 1	266					tRNA 3'-trailer cleavage (GO:0042779)	cytosol (GO:0005829)|nucleus (GO:0005634)	endoribonuclease activity, producing 5'-phosphomonoesters (GO:0016891)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(4)|prostate(1)	6		Colorectal(6;0.0269)|all_epithelial(6;0.0729)		Colorectal(21;0.000943)|COAD - Colon adenocarcinoma(17;0.0398)|READ - Rectum adenocarcinoma(32;0.0894)|STAD - Stomach adenocarcinoma(97;0.18)		GTAAAACTGTGCTTTGAAGCA	0.478																																					p.C266S		Atlas-SNP	.											.	ELAC1	17	.	0			c.G797C						PASS	.						96	85	89					18																	48513160		2203	4300	6503	SO:0001583	missense	55520	exon4			AACTGTGCTTTGA	AB029151	CCDS11949.1	18q21	2013-05-24	2013-05-24		ENSG00000141642	ENSG00000141642	3.1.26.11		14197	protein-coding gene	gene with protein product	"tRNA Z (short form)", "RNaseZ(S)"	608079	"elaC (E. coli) homolog 1", "elaC homolog 1 (E. coli)"			12711671, 21559454	Standard	NM_018696		Approved	D29	uc002lez.3	Q9H777	OTTHUMG00000132695	ENST00000269466.3:c.797G>C	chr18.hg19:g.48513160G>C	ENSP00000269466:p.Cys266Ser	55.0	0.0	.		48.0	14.0	.	NM_018696	Q9NS99	Missense_Mutation	SNP	ENST00000269466.3	hg19	CCDS11949.1	.	.	.	.	.	.	.	.	.	.	G	18.92	3.725203	0.68959	.	.	ENSG00000141642	ENST00000269466	T	0.76060	-0.99	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.70430	0.3223	L	0.28458	0.855	0.80722	D	1	P	0.37423	0.594	B	0.42959	0.403	T	0.69300	-0.5181	10	0.37606	T	0.19	.	18.233	0.89939	0.0:0.0:1.0:0.0	.	266	Q9H777	RNZ1_HUMAN	S	266	ENSP00000269466:C266S	ENSP00000269466:C266S	C	+	2	0	ELAC1	46767158	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	8.916000	0.92745	2.597000	0.87782	0.655000	0.94253	TGC	.	.	.	none		0.478	ELAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255992.2			C	48513160	G	C	48513160	3	2	131	1	0	0	0	0	1	0	0	0	5048	1319	46	4	807	4	ELAC1	18	48513160	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08	17249742	48513160	29564088	56	8155											
ZNF763	284390	hgsc.bcm.edu	37	chr19	12089881	12089881	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaaagcattatcttataagtTttcaaacacacctaagaatg	17	12	5	7	0	2	1	1	0	1	1	2	2	2	1	1	0	2	2	1	0	7	6			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr19:12089881T>C	ENST00000358987.3	+	4	1269	c.1142T>C	c.(1141-1143)tTt>tCt	p.F381S	ZNF763_ENST00000545530.1_Missense_Mutation_p.F259S|ZNF763_ENST00000590798.1_Missense_Mutation_p.F401S|ZNF763_ENST00000343949.5_Missense_Mutation_p.F384S|ZNF763_ENST00000538752.1_Missense_Mutation_p.F401S			Q0D2J5	ZN763_HUMAN	zinc finger protein 763	381					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						TCTTATAAGTTTTCAAACACA	0.398																																					p.F384S		Atlas-SNP	.											.	ZNF763	31	.	0			c.T1151C						PASS	.						67	73	71					19																	12089881		2180	4294	6474	SO:0001583	missense	284390	exon4			ATAAGTTTTCAAA	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.1142T>C	chr19.hg19:g.12089881T>C	ENSP00000402017:p.Phe381Ser	121.0	0.0	.		143.0	55.0	.	NM_001012753	B3KRU3|B4DRE7	Missense_Mutation	SNP	ENST00000358987.3	hg19		.	.	.	.	.	.	.	.	.	.	t	0	-2.724828	0.00091	.	.	ENSG00000197054	ENST00000538752;ENST00000343949;ENST00000545530;ENST00000358987	T;T;T;T	0.06068	3.45;3.44;3.35;3.45	0.855	-1.71	0.08133	.	.	.	.	.	T	0.01254	0.0041	N	0.00060	-2.34	0.09310	N	1	B;P;B	0.35774	0.018;0.519;0.018	B;P;B	0.45449	0.004;0.481;0.004	T	0.22695	-1.0209	9	0.02654	T	1	.	2.0667	0.03604	0.2548:0.2103:0.0:0.5349	.	401;381;384	F5H0A9;Q0D2J5;Q0D2J5-2	.;ZN763_HUMAN;.	S	401;384;259;381	ENSP00000438117:F401S;ENSP00000369774:F384S;ENSP00000446166:F259S;ENSP00000402017:F381S	ENSP00000369774:F384S	F	+	2	0	ZNF763	11950881	0.000000	0.05858	0.000000	0.03702	0.049000	0.14656	0.148000	0.16224	-1.202000	0.02655	0.155000	0.16302	TTT	.	.	.	none		0.398	ZNF763-002	KNOWN	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000344158.1	NM_001012753		C	12089881	T	C	12089881	3	2	131	1	0	0	0	0	1	0	0	0	18149	1841	64	3	1165	3	ZNF763	19	12089881	Missense_Mutation	SNP	T	TCGA-BQ-7045-01A-31D-1961-08		12089881	47039102	57	8156											
ZSWIM4	65249	hgsc.bcm.edu	37	chr19	13915960	13915960	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctccgagatcaacttggtgaAtggtaagggcaccccggggg	9	7	15	10	2	1	2	1	1	0	1	2	3	2	2	3	5	1	2	3	5	3	2			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr19:13915960A>G	ENST00000254323.2	+	3	899	c.710A>G	c.(709-711)aAt>aGt	p.N237S	ZSWIM4_ENST00000440752.2_5'UTR	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	237							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)			AACTTGGTGAATGGTAAGGGC	0.607											OREG0025298	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N237S		Atlas-SNP	.											.	ZSWIM4	69	.	0			c.A710G						PASS	.						35	34	34					19																	13915960		2203	4299	6502	SO:0001583	missense	65249	exon3			TGGTGAATGGTAA	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.710A>G	chr19.hg19:g.13915960A>G	ENSP00000254323:p.Asn237Ser	73.0	0.0	.	691	64.0	17.0	.	NM_023072		Missense_Mutation	SNP	ENST00000254323.2	hg19	CCDS32924.1	.	.	.	.	.	.	.	.	.	.	A	7.710	0.695019	0.15039	.	.	ENSG00000132003	ENST00000254323	T	0.21191	2.02	4.81	4.81	0.61882	.	0.093972	0.43747	D	0.000522	T	0.10337	0.0253	N	0.05441	-0.05	0.80722	D	1	B	0.16802	0.019	B	0.18561	0.022	T	0.14144	-1.0483	10	0.10377	T	0.69	-33.1503	12.3201	0.54979	1.0:0.0:0.0:0.0	.	237	Q9H7M6	ZSWM4_HUMAN	S	237	ENSP00000254323:N237S	ENSP00000254323:N237S	N	+	2	0	ZSWIM4	13776960	1.000000	0.71417	0.941000	0.38009	0.192000	0.23643	8.632000	0.90995	1.806000	0.52798	0.459000	0.35465	AAT	.	.	.	none		0.607	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342		G	13915960	A	G	13915960	3	3	131	1	0	0	0	0	1	0	0	0	18255	101	4	3	720	3	ZSWIM4	19	13915960	Missense_Mutation	SNP	A	TCGA-BQ-7045-01A-31D-1961-08	1826079	13915960	45213023	58	8157											
JAK3	3718	hgsc.bcm.edu	37	chr19	17946018	17946018	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgccatggggcaggccttTgtcctcctaagggggccaga	7	9	14	11	0	0	1	0	0	0	1	2	1	2	1	5	5	1	1	5	5	1	3			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr19:17946018T>C	ENST00000527670.1	-	14	1950	c.1921A>G	c.(1921-1923)Aaa>Gaa	p.K641E	JAK3_ENST00000534444.1_Missense_Mutation_p.K641E|JAK3_ENST00000458235.1_Missense_Mutation_p.K641E			P52333	JAK3_HUMAN	Janus kinase 3	641	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell differentiation (GO:0030183)|enzyme linked receptor protein signaling pathway (GO:0007167)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of dendritic cell cytokine production (GO:0002731)|negative regulation of FasL biosynthetic process (GO:0045221)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of thymocyte apoptotic process (GO:0070244)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of T cell apoptotic process (GO:0070232)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-9 (GO:0071104)|STAT protein import into nucleus (GO:0007262)|T cell homeostasis (GO:0043029)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147					Tofacitinib(DB08895)	GGCAGGCCTTTGTCCTCCTAA	0.577		2	Mis		"acute megakaryocytic leukemia, ETP ALL"																																p.K641E		Atlas-SNP	.		Dom	yes		19	19p13.1	3718	Janus kinase 3		L	.	JAK3	341	.	0			c.A1921G						PASS	.						24	27	26					19																	17946018		2203	4300	6503	SO:0001583	missense	3718	exon15			GGCCTTTGTCCTC	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.1921A>G	chr19.hg19:g.17946018T>C	ENSP00000432511:p.Lys641Glu	52.0	0.0	.		50.0	13.0	.	NM_000215	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Missense_Mutation	SNP	ENST00000527670.1	hg19	CCDS12366.1	.	.	.	.	.	.	.	.	.	.	T	18.16	3.561092	0.65538	.	.	ENSG00000105639	ENST00000458235;ENST00000527670;ENST00000534444	D;D;D	0.83837	-1.77;-1.77;-1.77	5.32	5.32	0.75619	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.244952	0.39985	N	0.001215	D	0.88998	0.6590	M	0.67569	2.06	0.45439	D	0.998412	D;P	0.65815	0.995;0.931	D;P	0.66497	0.944;0.816	D	0.90111	0.4192	10	0.87932	D	0	-10.7087	13.227	0.59921	0.0:0.0:0.0:1.0	.	641;641	P52333-2;P52333	.;JAK3_HUMAN	E	641	ENSP00000391676:K641E;ENSP00000432511:K641E;ENSP00000436421:K641E	ENSP00000391676:K641E	K	-	1	0	JAK3	17807018	1.000000	0.71417	1.000000	0.80357	0.547000	0.35210	5.606000	0.67641	2.009000	0.58944	0.454000	0.30748	AAA	.	.	.	none		0.577	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215		C	17946018	T	C	17946018	3	2	131	1	0	0	0	0	1	0	0	0	7946	1821	63	3	1493	3	JAK3	19	17946018	Missense_Mutation	SNP	T	TCGA-BQ-7045-01A-31D-1961-08	4030058	17946018	41182965	59	8158											
ZNF566	84924	hgsc.bcm.edu	37	chr19	36940231	36940231	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttccccagtatgaattctcTgatgttgagtaaagtttgag	10	16	9	6	0	1	4	0	4	1	0	3	4	2	4	2	0	0	4	2	0	4	6			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr19:36940231T>C	ENST00000434377.2	-	5	986	c.905A>G	c.(904-906)cAg>cGg	p.Q302R	ZNF566_ENST00000493391.1_Missense_Mutation_p.Q198R|ZNF566_ENST00000392170.2_Missense_Mutation_p.Q303R|ZNF566_ENST00000454319.1_Missense_Mutation_p.Q303R|ZNF566_ENST00000424129.2_Missense_Mutation_p.Q302R	NM_032838.4	NP_116227.1	Q969W8	ZN566_HUMAN	zinc finger protein 566	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)			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)					ATGAATTCTCTGATGTTGAGT	0.403																																					p.Q303R		Atlas-SNP	.											.	ZNF566	40	.	0			c.A908G						PASS	.						80	81	80					19																	36940231		2203	4300	6503	SO:0001583	missense	84924	exon5			ATTCTCTGATGTT	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.905A>G	chr19.hg19:g.36940231T>C	ENSP00000415520:p.Gln302Arg	92.0	0.0	.		119.0	5.0	.	NM_001145343	B7ZL95|Q2M3J1	Missense_Mutation	SNP	ENST00000434377.2	hg19	CCDS12494.1	.	.	.	.	.	.	.	.	.	.	T	13.03	2.116877	0.37339	.	.	ENSG00000186017	ENST00000454319;ENST00000434377;ENST00000392170;ENST00000424129	T;T;T;T	0.17691	2.26;2.26;2.26;2.26	3.9	3.9	0.45041	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.42548	D	0.000695	T	0.15089	0.0364	N	0.02345	-0.59	0.26120	N	0.980568	D;D	0.63880	0.981;0.993	P;D	0.72338	0.816;0.977	T	0.04976	-1.0914	10	0.62326	D	0.03	.	7.8932	0.29691	0.1845:0.0:0.0:0.8155	.	303;302	B7ZL95;Q969W8	.;ZN566_HUMAN	R	303;302;303;302	ENSP00000394207:Q303R;ENSP00000415520:Q302R;ENSP00000376010:Q303R;ENSP00000401259:Q302R	ENSP00000376010:Q303R	Q	-	2	0	ZNF566	41632071	0.888000	0.30383	1.000000	0.80357	0.985000	0.73830	1.423000	0.34837	1.775000	0.52247	0.454000	0.30748	CAG	.	.	.	none		0.403	ZNF566-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000341054.1	NM_032838		C	36940231	T	C	36940231	3	2	131	1	0	0	0	0	1	0	0	0	18009	1580	55	3	355	3	ZNF566	19	36940231	Missense_Mutation	SNP	T	TCGA-BQ-7045-01A-31D-1961-08	18994213	36940231	22188752	60	8159											
ZNF787	126208	hgsc.bcm.edu	37	chr19	56599455	56599455	+	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	gcctcgtcgtcgtcgtcgtcCtcctcctccccgcccgcgcg	0	9	10	22	9	0	0	0	0	0	0	9	0	4	0	7	0	0	0	7	0	0	0	rs202243737	byFrequency	TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr19:56599455C>G	ENST00000270459.3	-	3	1204	c.1086G>C	c.(1084-1086)gaG>gaC	p.E362D		NM_001002836.2	NP_001002836	Q6DD87	ZN787_HUMAN	zinc finger protein 787	362					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|lung(2)|pancreas(1)	5		Colorectal(82;3.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0559)		CGTCGTCGTCCTCCTCCTCCC	0.786													c|||	31	0.0061901	0.0174	0.0086	5008	,	,		3491	0		0.002	False		,,,				2504	0				p.E362D		Atlas-SNP	.											.	ZNF787	20	.	0			c.G1086C						PASS	.						5	6	6					19																	56599455		1716	3706	5422	SO:0001583	missense	126208	exon3			GTCGTCCTCCTCC	BC077728, AF000560	CCDS42634.1	19q13.42	2013-01-08				ENSG00000142409		"Zinc fingers, C2H2-type"	26998	protein-coding gene	gene with protein product							Standard	NM_001002836		Approved		uc010eth.1	Q6DD87		ENST00000270459.3:c.1086G>C	chr19.hg19:g.56599455C>G	ENSP00000270459:p.Glu362Asp	11.0	0.0	.		26.0	14.0	.	NM_001002836	O00455	Missense_Mutation	SNP	ENST00000270459.3	hg19	CCDS42634.1	.	.	.	.	.	.	.	.	.	.	c	2.272	-0.366767	0.05069	.	.	ENSG00000142409	ENST00000270459	T	0.06687	3.27	1.38	0.235	0.15431	.	.	.	.	.	T	0.02688	0.0081	N	0.02539	-0.55	0.09310	N	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.48222	-0.9054	9	0.15066	T	0.55	-9.261	5.3742	0.16156	0.0:0.4529:0.5471:0.0	.	362	Q6DD87	ZN787_HUMAN	D	362	ENSP00000270459:E362D	ENSP00000270459:E362D	E	-	3	2	ZNF787	61291267	0.001000	0.12720	0.020000	0.16555	0.393000	0.30537	-0.022000	0.12480	0.167000	0.19631	0.494000	0.49563	GAG	.	C|0.996;G|0.004	0.004	weak		0.786	ZNF787-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457498.1	NM_001002836		G	56599455	C	G	56599455	3	3	131	1	0	0	0	0	1	0	0	0	18171	680	24	4	69	4	ZNF787	19	56599455	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	19659224	56599455	2529528	61	8160											
SALL4	57167	hgsc.bcm.edu	37	chr20	50405586	50405586	+	Silent	SNP	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	aacaaaggggtcatccctggGgacaatgtcgagggtcccac	11	6	13	11	1	1	0	1	0	0	0	4	2	3	1	2	5	1	0	2	5	3	0			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr20:50405586G>A	ENST00000217086.4	-	3	2667	c.2556C>T	c.(2554-2556)tcC>tcT	p.S852S	SALL4_ENST00000395997.3_Silent_p.S415S|SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000371539.3_Silent_p.S75S	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	852					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						TCATCCCTGGGGACAATGTCG	0.577																																					p.S852S		Atlas-SNP	.											.	SALL4	168	.	0			c.C2556T						PASS	.						57	54	55					20																	50405586		2203	4300	6503	SO:0001819	synonymous_variant	57167	exon3			CCCTGGGGACAAT	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.2556C>T	chr20.hg19:g.50405586G>A		73.0	0.0	.		59.0	19.0	.	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	hg19	CCDS13438.1																																																																																			.	.	.	none		0.577	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			A	50405586	G	A	50405586	2	1	131	1	0	0	0	0	0	0	0	1	13826	1219	43	2		2	SALL4	20	50405586	Silent	SNP	G	TCGA-BQ-7045-01A-31D-1961-08		50405586	12619934	62	8161											
KRTAP13-1	140258	hgsc.bcm.edu	37	chr21	31768620	31768620	+	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	tgccagacatcctatgtggaGtccagcccctgccagacctc	8	8	9	16	0	0	2	0	0	0	2	3	3	2	3	7	1	3	0	7	1	1	1			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr21:31768620G>T	ENST00000355459.2	+	1	229	c.216G>T	c.(214-216)gaG>gaT	p.E72D		NM_181599.2	NP_853630.2	Q8IUC0	KR131_HUMAN	keratin associated protein 13-1	72	5 X 10 AA approximate repeats.					intermediate filament (GO:0005882)				endometrium(1)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CCTATGTGGAGTCCAGCCCCT	0.602																																					p.E72D		Atlas-SNP	.											.	KRTAP13-1	48	.	0			c.G216T						PASS	.						60	61	61					21																	31768620		2203	4300	6503	SO:0001583	missense	140258	exon1			TGTGGAGTCCAGC	AJ457066	CCDS13590.2	21q22.11	2013-06-20			ENSG00000198390	ENSG00000198390		"Keratin associated proteins"	18924	protein-coding gene	gene with protein product		608718				12359730	Standard	NM_181599		Approved	KAP13.1	uc002yoa.3	Q8IUC0	OTTHUMG00000057800	ENST00000355459.2:c.216G>T	chr21.hg19:g.31768620G>T	ENSP00000347635:p.Glu72Asp	89.0	0.0	.		83.0	26.0	.	NM_181599	Q14D20|Q3LI79	Missense_Mutation	SNP	ENST00000355459.2	hg19	CCDS13590.2	.	.	.	.	.	.	.	.	.	.	G	12.28	1.890413	0.33348	.	.	ENSG00000198390	ENST00000355459	T	0.03982	3.74	4.51	0.568	0.17333	.	1.594350	0.04748	N	0.423995	T	0.09158	0.0226	M	0.68317	2.08	0.09310	N	1	P	0.46784	0.884	P	0.48334	0.574	T	0.32079	-0.9920	10	0.20046	T	0.44	.	3.3017	0.06985	0.2615:0.0:0.4305:0.308	.	72	Q8IUC0	KR131_HUMAN	D	72	ENSP00000347635:E72D	ENSP00000347635:E72D	E	+	3	2	KRTAP13-1	30690491	0.000000	0.05858	0.002000	0.10522	0.045000	0.14185	0.172000	0.16704	0.089000	0.17243	0.557000	0.71058	GAG	.	.	.	none		0.602	KRTAP13-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128252.3			T	31768620	G	T	31768620	3	4	131	1	0	0	0	0	1	0	0	0	8529	1020	36	4	218	4	KRTAP13-1	21	31768620	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08		31768620	16361275	63	8162											
DNAJC28	54943	hgsc.bcm.edu	37	chr21	34861049	34861050	+	Frame_Shift_Ins	INS	-	-	A																															cctttcccactgagattgtcINSaaagtctccttttgccatgg																										TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr21:34861049_34861050insA	ENST00000314399.3	-	2	1089_1090	c.651_652insT	c.(649-654)tttgacfs	p.D218fs	DNAJC28_ENST00000402202.1_Frame_Shift_Ins_p.D218fs|DNAJC28_ENST00000381947.3_Frame_Shift_Ins_p.D218fs	NM_017833.3	NP_060303.2	Q9NX36	DJC28_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 28	218										endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(5)|skin(1)|urinary_tract(1)	18						CTGAGATTGTCAAAGTCTCCTT	0.386																																					p.D218_N219delinsX		Atlas-INDEL	.											DNAJC28,right_lower_lobe,carcinoma,0,1	DNAJC28	47	.	0			c.652_653insT						PASS	.																																			SO:0001589	frameshift_variant	54943	exon2			.	AK000468	CCDS13626.1	21q22.11	2011-09-02	2008-06-17	2008-06-17	ENSG00000177692	ENSG00000177692		"Heat shock proteins / DNAJ (HSP40)"	1297	protein-coding gene	gene with protein product	"Orf28"		"chromosome 21 open reading frame 55"	C21orf55			Standard	NM_017833		Approved	C21orf78	uc002yrw.3	Q9NX36	OTTHUMG00000065531	ENST00000314399.3:c.652dupT	chr21.hg19:g.34861052_34861052dupA	ENSP00000320303:p.Asp218fs	202.0	0.0	0		202.0	51.0	0.252475	NM_001040192	D3DSF2	Frame_Shift_Ins	INS	ENST00000314399.3	hg19	CCDS13626.1																																																																																			.	.	.	none		0.386	DNAJC28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140454.3			A	34861050	-	A	34861049	7	5	131	1	0	1	1	0	0	0	0	0	4648	826	29	0	518	0	DNAJC28	21	34861049	Frame_Shift_Ins	INS	-	TCGA-BQ-7045-01A-31D-1961-08	3092429	34861049	13268846	64	8163											
NDUFV3	4731	hgsc.bcm.edu	37	chr21	44317078	44317078	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgtttcgaggacttgcttcTacggtttctttgtctgcgga	4	17	12	8	3	3	0	0	0	3	0	4	3	3	2	0	3	3	3	0	3	1	6			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr21:44317078T>C	ENST00000340344.4	+	2	156	c.90T>C	c.(88-90)tcT>tcC	p.S30S	NDUFV3_ENST00000460259.1_3'UTR|NDUFV3_ENST00000354250.2_Silent_p.S30S	NM_001001503.1	NP_001001503.1	P56181	NDUV3_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 3, 10kDa	30					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|skin(1)	10				STAD - Stomach adenocarcinoma(101;0.0606)		GACTTGCTTCTACGGTTTCTT	0.413																																					p.S30S		Atlas-SNP	.											.	NDUFV3	23	.	0			c.T90C						PASS	.						87	86	86					21																	44317078		2203	4300	6503	SO:0001819	synonymous_variant	4731	exon2			TGCTTCTACGGTT		CCDS33572.1, CCDS33573.1	21q22.3	2011-07-04	2002-08-29		ENSG00000160194	ENSG00000160194	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7719	protein-coding gene	gene with protein product	"complex I 10kDa subunit"	602184	"NADH dehydrogenase (ubiquinone) flavoprotein 3 (10kD)"			9344673	Standard	NM_021075		Approved	CI-10k	uc002zcm.3	P56181	OTTHUMG00000086823	ENST00000340344.4:c.90T>C	chr21.hg19:g.44317078T>C		121.0	0.0	.		94.0	27.0	.	NM_001001503	A8K0M1|J3KNX7|Q6FGD3|Q8WU60|Q9HCR5	Silent	SNP	ENST00000340344.4	hg19	CCDS33573.1																																																																																			.	.	.	none		0.413	NDUFV3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195448.2			C	44317078	T	C	44317078	2	2	131	1	0	0	0	0	0	0	0	1	10308	1509	53	3		3	NDUFV3	21	44317078	Silent	SNP	T	TCGA-BQ-7045-01A-31D-1961-08	9456029	44317078	3812817	65	8164											
PPM1F	9647	hgsc.bcm.edu	37	chr22	22287929	22287929	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgtgaccatcaaacacagcaAagtaggcgcggttcacaggg	13	5	12	11	3	2	1	2	1	0	0	2	1	2	1	1	3	2	3	1	3	3	2			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr22:22287929A>G	ENST00000263212.5	-	5	686	c.581T>C	c.(580-582)tTt>tCt	p.F194S	PPM1F_ENST00000407142.1_Missense_Mutation_p.F26S|PPM1F_ENST00000397495.4_Missense_Mutation_p.F194S|PPM1F_ENST00000538191.1_Missense_Mutation_p.F90S	NM_014634.3	NP_055449.1	P49593	PPM1F_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1F	194					cellular response to drug (GO:0035690)|histone dephosphorylation (GO:0016576)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of growth (GO:0045927)|positive regulation of stress fiber assembly (GO:0051496)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	calmodulin-dependent protein phosphatase activity (GO:0033192)|metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	12	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.155)		AAACACAGCAAAGTAGGCGCG	0.667																																					p.F194S		Atlas-SNP	.											.	PPM1F	34	.	0			c.T581C						PASS	.						61	52	55					22																	22287929		2203	4300	6503	SO:0001583	missense	9647	exon5			ACAGCAAAGTAGG	D13640	CCDS13796.1	22q11.22	2012-04-17	2010-03-05		ENSG00000100034	ENSG00000100034	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	19388	protein-coding gene	gene with protein product	"partner of PIX 2", "Ca(2+)/calmodulin-dependent protein kinase phosphatase"		"protein phosphatase 1F (PP2C domain containing)"			11864573, 11559703	Standard	NM_014634		Approved	FEM-2, KIAA0015, POPX2, CaMKPase, CAMKP	uc002zvp.2	P49593	OTTHUMG00000150835	ENST00000263212.5:c.581T>C	chr22.hg19:g.22287929A>G	ENSP00000263212:p.Phe194Ser	47.0	0.0	.		57.0	25.0	.	NM_014634	A8K6G3|B7Z2C3|Q96PM2	Missense_Mutation	SNP	ENST00000263212.5	hg19	CCDS13796.1	.	.	.	.	.	.	.	.	.	.	A	15.29	2.789526	0.50102	.	.	ENSG00000100034	ENST00000263212;ENST00000407142;ENST00000406981;ENST00000538191;ENST00000397495;ENST00000445205	T;T;T;T;T	0.12465	2.68;2.68;2.68;2.68;2.68	4.95	4.95	0.65309	Protein phosphatase 2C-like (5);	0.052935	0.85682	D	0.000000	T	0.46678	0.1405	M	0.92555	3.32	0.48040	D	0.999577	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.995;0.995;0.995	T	0.60131	-0.7323	10	0.87932	D	0	-0.6926	14.4382	0.67296	1.0:0.0:0.0:0.0	.	90;194;194	B7Z2C3;A8MX49;P49593	.;.;PPM1F_HUMAN	S	194;26;26;90;194;26	ENSP00000263212:F194S;ENSP00000384930:F26S;ENSP00000439915:F90S;ENSP00000380632:F194S;ENSP00000392372:F26S	ENSP00000263212:F194S	F	-	2	0	PPM1F	20617929	1.000000	0.71417	0.992000	0.48379	0.088000	0.18126	3.605000	0.54088	2.077000	0.62373	0.454000	0.30748	TTT	.	.	.	none		0.667	PPM1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320267.2	NM_014634		G	22287929	A	G	22287929	3	3	131	1	0	0	0	0	1	0	0	0	12349	14	1	3	799	3	PPM1F	22	22287929	Missense_Mutation	SNP	A	TCGA-BQ-7045-01A-31D-1961-08		22287929	29016637	66	8165											
SFI1	9814	hgsc.bcm.edu	37	chr22	31924806	31924806	+	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	tagtgcagtatcgtggcacaCatacttgtacccgacagggc	10	9	11	11	2	0	0	0	0	0	0	1	1	0	0	1	2	3	4	1	2	4	5			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr22:31924806C>T	ENST00000400288.2	+	3	328	c.223C>T	c.(223-225)Cat>Tat	p.H75Y	SFI1_ENST00000443326.1_Intron|SFI1_ENST00000400289.1_Intron|SFI1_ENST00000443011.1_Intron|SFI1_ENST00000414585.1_Intron|SFI1_ENST00000432498.1_Missense_Mutation_p.H75Y|SFI1_ENST00000540643.1_Missense_Mutation_p.H75Y	NM_001007467.2	NP_001007468.1	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	75					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						TCGTGGCACACATACTTGTAC	0.483																																					p.H75Y		Atlas-SNP	.											.	SFI1	78	.	0			c.C223T						PASS	.						121	114	116					22																	31924806		1992	4175	6167	SO:0001583	missense	9814	exon3			GGCACACATACTT	AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089			29064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 139"	612765				14504268	Standard	NM_001007467		Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000400288.2:c.223C>T	chr22.hg19:g.31924806C>T	ENSP00000383145:p.His75Tyr	110.0	0.0	.		130.0	41.0	.	NM_001007467	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	Missense_Mutation	SNP	ENST00000400288.2	hg19	CCDS43004.1	.	.	.	.	.	.	.	.	.	.	C	6.278	0.419420	0.11928	.	.	ENSG00000198089	ENST00000432498;ENST00000540643;ENST00000421060;ENST00000444859;ENST00000400288;ENST00000450787	T;T;T;T;T	0.32515	3.32;3.02;1.45;3.33;2.1	4.26	-0.0926	0.13656	.	0.718935	0.12712	N	0.445472	T	0.12135	0.0295	N	0.08118	0	0.09310	N	1	B;B;B;B	0.22746	0.005;0.012;0.004;0.074	B;B;B;B	0.23018	0.004;0.009;0.006;0.043	T	0.36335	-0.9752	10	0.10377	T	0.69	.	6.4426	0.21859	0.0:0.5881:0.0:0.4119	.	75;75;75;75	A8K8P3-9;A8K8P3-2;A8K8P3;A8K8P3-5	.;.;SFI1_HUMAN;.	Y	75;75;75;75;75;26	ENSP00000402679:H75Y;ENSP00000443025:H75Y;ENSP00000411793:H75Y;ENSP00000383145:H75Y;ENSP00000389364:H26Y	ENSP00000383145:H75Y	H	+	1	0	SFI1	30254806	0.000000	0.05858	0.000000	0.03702	0.063000	0.16089	0.236000	0.17967	0.079000	0.16929	-0.237000	0.12165	CAT	.	.	.	none		0.483	SFI1-023	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337180.3	NM_014775		T	31924806	C	T	31924806	3	4	131	1	0	0	0	0	1	0	0	0	14169	478	17	2	229	2	SFI1	22	31924806	Missense_Mutation	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	9636877	31924806	19379760	67	8166											
APOL1	8542	hgsc.bcm.edu	37	chr22	36661665	36661665	+	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	agggagtttttgggtgagaaCatatccaactttctttcctt	9	16	9	7	0	1	1	0	1	1	1	3	3	3	2	2	2	2	1	2	2	3	6			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chr22:36661665C>T	ENST00000397278.3	+	6	1012	c.783C>T	c.(781-783)aaC>aaT	p.N261N	APOL1_ENST00000319136.4_Silent_p.N277N|APOL1_ENST00000347595.7_Silent_p.N140N|APOL1_ENST00000422706.1_Silent_p.N261N|APOL1_ENST00000426053.1_Silent_p.N243N|APOL1_ENST00000397279.4_Silent_p.N261N	NM_003661.3	NP_003652.2	O14791	APOL1_HUMAN	apolipoprotein L, 1	261					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|cholesterol metabolic process (GO:0008203)|cytolysis (GO:0019835)|innate immune response (GO:0045087)|killing of cells of other organism (GO:0031640)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|high-density lipoprotein particle (GO:0034364)|intrinsic component of membrane (GO:0031224)|very-low-density lipoprotein particle (GO:0034361)	chloride channel activity (GO:0005254)|lipid binding (GO:0008289)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	14						TGGGTGAGAACATATCCAACT	0.498																																					p.N277N		Atlas-SNP	.											.	APOL1	35	.	0			c.C831T						PASS	.						123	114	117					22																	36661665		2203	4300	6503	SO:0001819	synonymous_variant	8542	exon7			TGAGAACATATCC	AF019225	CCDS13925.1, CCDS13926.1, CCDS46702.1	22q13.1	2014-09-17			ENSG00000100342	ENSG00000100342		"Apolipoproteins"	618	protein-coding gene	gene with protein product		603743		APOL		9325276, 11374903, 16020735	Standard	NM_003661		Approved		uc011amp.2	O14791	OTTHUMG00000030427	ENST00000397278.3:c.783C>T	chr22.hg19:g.36661665C>T		66.0	0.0	.		60.0	18.0	.	NM_145343	A5PLQ4|B4DU12|E9PF24|O60804|Q5R3P7|Q5R3P8|Q96AB8|Q96PM4|Q9BQ03	Silent	SNP	ENST00000397278.3	hg19	CCDS13926.1																																																																																			.	.	.	none		0.498	APOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319100.4	NM_145343		T	36661665	C	T	36661665	2	4	131	1	0	0	0	0	0	0	0	1	805	477	17	2		2	APOL1	22	36661665	Silent	SNP	C	TCGA-BQ-7045-01A-31D-1961-08	4736859	36661665	14642901	68	8167											
RPL10	6134	hgsc.bcm.edu	37	chrX	153627911	153627911	+	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	gtggccacatggtgtcagatGaatatgagcagctgtcctct	9	11	12	9	0	2	3	1	2	1	1	3	3	3	3	2	2	2	2	2	2	2	1			TCGA-BQ-7045-01A-31D-1961-08	TCGA-BQ-7045-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	413a9e10-cac7-4b6c-91cd-b58fd4499c07	0ed1c015-2f52-4269-98d4-b78e9323f29c	g.chrX:153627911G>A	ENST00000369817.2	+	5	742	c.166G>A	c.(166-168)Gaa>Aaa	p.E56K	RPL10_ENST00000406022.2_Missense_Mutation_p.E5K|RPL10_ENST00000424325.2_Missense_Mutation_p.E56K|SNORA70_ENST00000384436.1_RNA			P27635	RL10_HUMAN	ribosomal protein L10	56					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)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8	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)					GGTGTCAGATGAATATGAGCA	0.507																																					p.E56K		Atlas-SNP	.											.	RPL10	22	.	0			c.G166A						PASS	.						112	110	111					X																	153627911		2203	4300	6503	SO:0001583	missense	6134	exon4			TCAGATGAATATG	AB007170	CCDS14746.1, CCDS76059.1	Xq28	2011-04-06			ENSG00000147403	ENSG00000147403		"L ribosomal proteins"	10298	protein-coding gene	gene with protein product		312173				9582194	Standard	NM_006013		Approved	NOV, QM, DXS648E, DXS648, FLJ23544, L10	uc004fkm.2	P27635	OTTHUMG00000033189	ENST00000369817.2:c.166G>A	chrX.hg19:g.153627911G>A	ENSP00000358832:p.Glu56Lys	91.0	0.0	.		89.0	50.0	.	NM_001256577	A3KQT0|D3DWW6|Q16470|Q2HXT7|Q53FH7|Q6FGN8|Q8TDA5	Missense_Mutation	SNP	ENST00000369817.2	hg19	CCDS14746.1	.	.	.	.	.	.	.	.	.	.	G	35	5.435565	0.96150	.	.	ENSG00000147403	ENST00000369817;ENST00000424325;ENST00000436473;ENST00000344746;ENST00000458500;ENST00000406022;ENST00000451365	T;T;T;T	0.79940	-0.98;-0.98;-0.98;-1.32	4.77	4.77	0.60923	Ribosomal protein L10e/L16 (2);	0.150767	0.42420	U	0.000704	D	0.92616	0.7654	H	0.96720	3.87	0.80722	D	1	P;D	0.65815	0.912;0.995	P;D	0.69654	0.876;0.965	D	0.94917	0.8070	10	0.87932	D	0	-16.8236	14.3504	0.66697	0.0:0.0:1.0:0.0	.	56;56	A6QRI9;P27635	.;RL10_HUMAN	K	56;56;56;56;56;5;39	ENSP00000358832:E56K;ENSP00000413436:E56K;ENSP00000341730:E56K;ENSP00000385621:E5K	ENSP00000341730:E56K	E	+	1	0	RPL10	153281105	1.000000	0.71417	0.996000	0.52242	0.891000	0.51852	8.919000	0.92770	1.963000	0.57068	0.600000	0.82982	GAA	.	.	.	none		0.507	RPL10-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127774.5	NM_006013		A	153627911	G	A	153627911	3	1	131	1	0	0	0	0	1	0	0	0	13567	1291	45	2	176	2	RPL10	23	153627911	Missense_Mutation	SNP	G	TCGA-BQ-7045-01A-31D-1961-08		153627911	1642649	69	8168											
ADAR	103	hgsc.bcm.edu	37	chr1	154562826	154562826	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttcctgcttgccttgcttcTtgctgtgtgcgcagacggct	2	15	11	13	2	1	1	0	0	1	1	2	1	2	1	2	1	5	5	2	1	0	5			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr1:154562826T>C	ENST00000368474.4	-	7	2529	c.2330A>G	c.(2329-2331)aAg>aGg	p.K777R	ADAR_ENST00000292205.5_Missense_Mutation_p.K820R|ADAR_ENST00000368471.3_Missense_Mutation_p.K482R	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	777	DRBM 3. {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)		GCCTTGCTTCTTGCTGTGTGC	0.542																																					p.K777R		Atlas-SNP	.											.	ADAR	113	.	0			c.A2330G						PASS	.						99	92	94					1																	154562826		2203	4300	6503	SO:0001583	missense	103	exon7			TGCTTCTTGCTGT	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.2330A>G	chr1.hg19:g.154562826T>C	ENSP00000357459:p.Lys777Arg	117.0	0.0	.		129.0	22.0	.	NM_015840	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Missense_Mutation	SNP	ENST00000368474.4	hg19	CCDS1071.1	.	.	.	.	.	.	.	.	.	.	T	34	5.404549	0.96051	.	.	ENSG00000160710	ENST00000292205;ENST00000368474;ENST00000368471;ENST00000529168	D;D;D;D	0.87334	-2.24;-2.24;-2.24;-2.24	5.94	5.94	0.96194	Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1);	0.000000	0.85682	D	0.000000	D	0.93038	0.7784	M	0.83223	2.63	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.992;0.997;0.999	D	0.94043	0.7311	10	0.87932	D	0	-29.5181	16.3951	0.83601	0.0:0.0:0.0:1.0	.	758;777;777	P55265-3;P55265-2;P55265	.;.;DSRAD_HUMAN	R	820;777;482;772	ENSP00000292205:K820R;ENSP00000357459:K777R;ENSP00000357456:K482R;ENSP00000431794:K772R	ENSP00000292205:K820R	K	-	2	0	ADAR	152829450	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.424000	0.80242	2.272000	0.75746	0.460000	0.39030	AAG	.	.	.	none		0.542	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111		C	154562826	T	C	154562826	3	2	132	1	0	0	0	0	1	0	0	0	281	1609	56	3	1386	3	ADAR	1	154562826	Missense_Mutation	SNP	T	TCGA-BQ-7046-01A-11D-1961-08		154562826	94687795	1	8169											
CACNA1S	779	hgsc.bcm.edu	37	chr1	201034981	201034981	+	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	ctcaccttgaagagctggacGccgatgcaggcaaacatgaa	13	6	11	11	2	1	3	1	2	0	1	1	5	1	4	2	2	3	3	2	2	3	1			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr1:201034981G>T	ENST00000362061.3	-	22	3064	c.2838C>A	c.(2836-2838)ggC>ggA	p.G946G	CACNA1S_ENST00000367338.3_Silent_p.G946G	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	946					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)	AGAGCTGGACGCCGATGCAGG	0.622																																					p.G946G		Atlas-SNP	.											.	CACNA1S	249	.	0			c.C2838A						PASS	.						85	70	75					1																	201034981		2203	4300	6503	SO:0001819	synonymous_variant	779	exon22			CTGGACGCCGATG	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.2838C>A	chr1.hg19:g.201034981G>T		40.0	0.0	.		30.0	10.0	.	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Silent	SNP	ENST00000362061.3	hg19	CCDS1407.1																																																																																			.	.	.	none		0.622	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		T	201034981	G	T	201034981	2	4	132	1	0	0	0	0	0	0	0	1	2549	1074	38	4		4	CACNA1S	1	201034981	Silent	SNP	G	TCGA-BQ-7046-01A-11D-1961-08	46472155	201034981	48215640	2	8170											
PARP9	83666	hgsc.bcm.edu	37	chr3	122247353	122247353	+	Missense_Mutation	SNP	A	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	gtatagcctgcatgccactaAaaataacaaaggtttcaggg	15	9	9	8	0	1	0	1	0	0	0	1	0	1	0	2	2	4	3	2	2	7	5			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr3:122247353A>C	ENST00000360356.2	-	11	2650	c.2423T>G	c.(2422-2424)tTt>tGt	p.F808C	PARP9_ENST00000471785.1_Missense_Mutation_p.F773C|PARP9_ENST00000492382.1_Missense_Mutation_p.F353C|PARP9_ENST00000477522.2_Missense_Mutation_p.F773C	NM_001146102.1|NM_031458.2	NP_001139574.1|NP_113646.2	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	808	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)		CATGCCACTAAAAATAACAAA	0.453																																					p.F808C		Atlas-SNP	.											.	PARP9	72	.	0			c.T2423G						PASS	.						118	108	111					3																	122247353		2203	4300	6503	SO:0001583	missense	83666	exon11			CCACTAAAAATAA	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.2423T>G	chr3.hg19:g.122247353A>C	ENSP00000353512:p.Phe808Cys	82.0	0.0	.		138.0	6.0	.	NM_031458	A8KA94|B2R8S9|E9PFM7|Q8TCP3|Q9BZL8|Q9BZL9	Missense_Mutation	SNP	ENST00000360356.2	hg19	CCDS3014.1	.	.	.	.	.	.	.	.	.	.	A	15.59	2.879929	0.51801	.	.	ENSG00000138496	ENST00000360356;ENST00000492382;ENST00000477522;ENST00000471785;ENST00000452457	T;T;T;T	0.31769	1.8;1.48;1.69;1.69	4.7	4.7	0.59300	Poly(ADP-ribose) polymerase, catalytic domain (1);	0.000000	0.52532	D	0.000063	T	0.48295	0.1492	M	0.80746	2.51	0.80722	D	1	D;D;D	0.64830	0.99;0.994;0.994	P;P;P	0.57468	0.796;0.766;0.821	T	0.51810	-0.8658	10	0.54805	T	0.06	.	8.7045	0.34345	0.8079:0.1921:0.0:0.0	.	808;353;773	Q8IXQ6;G5E9U8;Q8IXQ6-2	PARP9_HUMAN;.;.	C	808;353;773;773;731	ENSP00000353512:F808C;ENSP00000417664:F353C;ENSP00000419506:F773C;ENSP00000419001:F773C	ENSP00000353512:F808C	F	-	2	0	PARP9	123730043	1.000000	0.71417	1.000000	0.80357	0.744000	0.42396	3.138000	0.50570	2.108000	0.64289	0.533000	0.62120	TTT	.	.	.	none		0.453	PARP9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355957.1	NM_031458		C	122247353	A	C	122247353	3	2	132	1	0	0	0	0	1	0	0	0	11473	14	1	5	145	5	PARP9	3	122247353	Missense_Mutation	SNP	A	TCGA-BQ-7046-01A-11D-1961-08		122247353	75775077	3	8171											
HPS3	84343	hgsc.bcm.edu	37	chr3	148872995	148872995	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcaccagtgcagctgtacaAagagatggtactcttttcaa	12	11	8	10	0	3	1	2	0	1	1	3	2	3	1	1	1	4	4	1	1	4	4			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr3:148872995A>G	ENST00000296051.2	+	8	1642	c.1502A>G	c.(1501-1503)aAa>aGa	p.K501R	HPS3_ENST00000460120.1_Missense_Mutation_p.K336R	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	501					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)			CAGCTGTACAAAGAGATGGTA	0.348									Hermansky-Pudlak syndrome																												p.K501R		Atlas-SNP	.											.	HPS3	104	.	0			c.A1502G						PASS	.						136	141	140					3																	148872995		2203	4300	6503	SO:0001583	missense	84343	exon8	Familial Cancer Database	HPS, HPS1-8	TGTACAAAGAGAT	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.1502A>G	chr3.hg19:g.148872995A>G	ENSP00000296051:p.Lys501Arg	102.0	0.0	.		96.0	29.0	.	NM_032383	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Missense_Mutation	SNP	ENST00000296051.2	hg19	CCDS3140.1	.	.	.	.	.	.	.	.	.	.	A	1.459	-0.562938	0.03939	.	.	ENSG00000163755	ENST00000296051;ENST00000460120	T;T	0.64260	-0.09;-0.09	4.89	3.74	0.42951	.	0.205149	0.44902	N	0.000404	T	0.49474	0.1559	L	0.43923	1.385	0.25950	N	0.982762	B;B	0.22746	0.074;0.027	B;B	0.22386	0.039;0.013	T	0.35992	-0.9766	10	0.28530	T	0.3	-8.4607	7.6211	0.28185	0.8276:0.0:0.1724:0.0	.	336;501	G5E9V4;Q969F9	.;HPS3_HUMAN	R	501;336	ENSP00000296051:K501R;ENSP00000418230:K336R	ENSP00000296051:K501R	K	+	2	0	HPS3	150355685	1.000000	0.71417	0.999000	0.59377	0.018000	0.09664	2.513000	0.45494	1.000000	0.39049	-0.250000	0.11733	AAA	.	.	.	none		0.348	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383		G	148872995	A	G	148872995	3	3	132	1	0	0	0	0	1	0	0	0	7347	14	1	3	1532	3	HPS3	3	148872995	Missense_Mutation	SNP	A	TCGA-BQ-7046-01A-11D-1961-08	26625642	148872995	49149435	4	8172											
C4orf37	285555	hgsc.bcm.edu	37	chr4	98633942	98633942	+	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	tatggggcaagatttccttaAaacaggattgtatgctgcag	12	12	11	6	0	0	1	0	0	0	1	1	2	1	2	1	3	3	4	1	3	5	5			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr4:98633942A>T	ENST00000295268.3	-	10	1317	c.1228T>A	c.(1228-1230)Tta>Ata	p.L410I	STPG2_ENST00000506482.1_5'UTR	NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	410																	GATTTCCTTAAAACAGGATTG	0.348																																					p.L410I		Atlas-SNP	.											.	.	.	.	0			c.T1228A						PASS	.						98	101	100					4																	98633942		2203	4300	6503	SO:0001583	missense	285555	exon10			TCCTTAAAACAGG	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.1228T>A	chr4.hg19:g.98633942A>T	ENSP00000295268:p.Leu410Ile	136.0	0.0	.		112.0	39.0	.	NM_174952		Missense_Mutation	SNP	ENST00000295268.3	hg19	CCDS3645.1	.	.	.	.	.	.	.	.	.	.	A	10.61	1.397643	0.25205	.	.	ENSG00000163116	ENST00000522676;ENST00000295268	T;T	0.49139	0.79;2.73	4.85	2.3	0.28687	.	0.854661	0.09752	N	0.760480	T	0.32704	0.0838	L	0.27053	0.805	0.09310	N	0.999998	P	0.38300	0.626	B	0.40782	0.34	T	0.14868	-1.0457	10	0.23302	T	0.38	-8.0438	4.5761	0.12234	0.4933:0.3146:0.192:0.0	.	410	Q8N412	CD037_HUMAN	I	124;410	ENSP00000428346:L124I;ENSP00000295268:L410I	ENSP00000295268:L410I	L	-	1	2	C4orf37	98852965	0.779000	0.28652	0.948000	0.38648	0.774000	0.43823	0.556000	0.23438	1.930000	0.55929	0.528000	0.53228	TTA	.	.	.	none		0.348	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952		T	98633942	A	T	98633942	3	4	132	1	0	0	0	0	1	0	0	0	2269	11	1	5	159	5	C4orf37	4	98633942	Missense_Mutation	SNP	A	TCGA-BQ-7046-01A-11D-1961-08		98633942	92520334	5	8173											
RAB24	53917	hgsc.bcm.edu	37	chr5	176729807	176729807	+	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	gtagattctactcatggcctCatagcgctcagagcctgctg	8	11	10	12	1	4	2	3	0	1	2	4	2	4	2	2	1	4	3	2	1	3	4			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr5:176729807C>G	ENST00000303251.6	-	3	630	c.211G>C	c.(211-213)Gag>Cag	p.E71Q	PRELID1_ENST00000303204.4_5'Flank|RAB24_ENST00000393611.2_Missense_Mutation_p.E71Q|RAB24_ENST00000303270.6_Missense_Mutation_p.E42Q|PRELID1_ENST00000503216.1_5'Flank	NM_001031677.2	NP_001026847.1	Q969Q5	RAB24_HUMAN	RAB24, member RAS oncogene family	71					autophagy (GO:0006914)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	autophagic vacuole (GO:0005776)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)					all_cancers(89;2.49e-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)			CTCATGGCCTCATAGCGCTCA	0.537																																					p.E71Q		Atlas-SNP	.											.	RAB24	19	.	0			c.G211C						PASS	.						98	93	95					5																	176729807		2203	4300	6503	SO:0001583	missense	53917	exon3			TGGCCTCATAGCG	AF087904	CCDS34300.1	5q35.3	2009-10-06			ENSG00000169228	ENSG00000169228		"RAB, member RAS oncogene"	9765	protein-coding gene	gene with protein product		612415					Standard	NM_001031677		Approved		uc003mfw.3	Q969Q5	OTTHUMG00000130849	ENST00000303251.6:c.211G>C	chr5.hg19:g.176729807C>G	ENSP00000304376:p.Glu71Gln	109.0	0.0	.		97.0	4.0	.	NM_001031677	Q7Z4Z7	Missense_Mutation	SNP	ENST00000303251.6	hg19	CCDS34300.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.064810	0.76187	.	.	ENSG00000169228	ENST00000393611;ENST00000303251;ENST00000303270	T;T;T	0.76968	-1.06;-1.06;-1.06	5.49	5.49	0.81192	Small GTP-binding protein domain (1);	0.000000	0.85682	U	0.000000	T	0.60637	0.2284	N	0.02765	-0.5	0.80722	D	1	P;P	0.39181	0.536;0.663	B;B	0.37833	0.223;0.259	T	0.70019	-0.4987	10	0.59425	D	0.04	1.7456	18.9659	0.92695	0.0:1.0:0.0:0.0	.	71;42	Q969Q5;F8W8H5	RAB24_HUMAN;.	Q	71;71;42	ENSP00000377235:E71Q;ENSP00000304376:E71Q;ENSP00000302085:E42Q	ENSP00000304376:E71Q	E	-	1	0	RAB24	176662413	1.000000	0.71417	0.996000	0.52242	0.990000	0.78478	7.185000	0.77714	2.576000	0.86940	0.555000	0.69702	GAG	.	.	.	none		0.537	RAB24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253416.1	NM_130781		G	176729807	C	G	176729807	3	3	132	1	0	0	0	0	1	0	0	0	12924	835	29	4	424	4	RAB24	5	176729807	Missense_Mutation	SNP	C	TCGA-BQ-7046-01A-11D-1961-08		176729807	4185453	6	8174											
KIAA0319	9856	hgsc.bcm.edu	37	chr6	24578370	24578370	+	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	ttaccaggatcaaggttagaCaagcgtaagacgggagagtc	14	7	13	7	2	1	3	1	0	0	3	2	5	1	4	1	3	2	2	1	3	5	3			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr6:24578370C>G	ENST00000378214.3	-	9	1997	c.1473G>C	c.(1471-1473)ttG>ttC	p.L491F	KIAA0319_ENST00000543707.1_Missense_Mutation_p.L491F|KIAA0319_ENST00000537886.1_Missense_Mutation_p.L491F|KIAA0319_ENST00000430948.2_Missense_Mutation_p.L446F|KIAA0319_ENST00000535378.1_Missense_Mutation_p.L482F	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	491	PKD 2. {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						CAAGGTTAGACAAGCGTAAGA	0.408																																					p.L491F		Atlas-SNP	.											.	KIAA0319	117	.	0			c.G1473C						PASS	.						144	138	140					6																	24578370		2203	4300	6503	SO:0001583	missense	9856	exon9			GTTAGACAAGCGT	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.1473G>C	chr6.hg19:g.24578370C>G	ENSP00000367459:p.Leu491Phe	116.0	0.0	.		131.0	44.0	.	NM_001168377	A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Missense_Mutation	SNP	ENST00000378214.3	hg19	CCDS34348.1	.	.	.	.	.	.	.	.	.	.	C	14.51	2.558223	0.45590	.	.	ENSG00000137261	ENST00000537886;ENST00000535378;ENST00000430948;ENST00000378214;ENST00000543707	T;T;T;T;T	0.14144	2.53;2.53;2.53;2.53;2.53	4.12	3.14	0.36123	PKD/Chitinase domain (1);Fibronectin, type III (1);PKD/REJ-like protein (1);PKD domain (2);	0.101129	0.41396	D	0.000885	T	0.20981	0.0505	M	0.64080	1.96	0.43628	D	0.99601	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.00518	-1.1693	10	0.72032	D	0.01	-0.9176	8.9471	0.35764	0.0:0.8102:0.0:0.1898	.	491;482;491	F5H123;Q5VV43-2;Q5VV43	.;.;K0319_HUMAN	F	491;482;446;491;491	ENSP00000439700:L491F;ENSP00000442403:L482F;ENSP00000401086:L446F;ENSP00000367459:L491F;ENSP00000437656:L491F	ENSP00000367459:L491F	L	-	3	2	KIAA0319	24686349	1.000000	0.71417	0.460000	0.27093	0.015000	0.08874	0.975000	0.29449	2.105000	0.64084	0.555000	0.69702	TTG	.	.	.	none		0.408	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040009.1	NM_014809		G	24578370	C	G	24578370	3	3	132	1	0	0	0	0	1	0	0	0	8175	477	17	4	1797	4	KIAA0319	6	24578370	Missense_Mutation	SNP	C	TCGA-BQ-7046-01A-11D-1961-08		24578370	146536697	7	8175											
FGL2	10875	hgsc.bcm.edu	37	chr7	76828725	76828726	+	Frame_Shift_Ins	INS	-	-	T																															actctctaattctctaactcINStgttatcaccaacctctccc																										TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr7:76828725_76828726insT	ENST00000248598.5	-	1	417_418	c.385_386insA	c.(385-387)agafs	p.R129fs	CCDC146_ENST00000285871.4_Intron|RP11-467H10.2_ENST00000459742.1_RNA|CCDC146_ENST00000431197.1_Intron	NM_006682.2	NP_006673.1	Q14314	FGL2_HUMAN	fibrinogen-like 2	129						extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)				breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(2)	13						TTCTCTAACTCTGTTATCACCA	0.495																																					p.R129fs		Atlas-INDEL	.											.	FGL2	40	.	0			c.386_387insA						PASS	.																																			SO:0001589	frameshift_variant	10875	exon1			.	Z36531	CCDS5591.1	7q11.23	2013-02-06			ENSG00000127951	ENSG00000127951		"Fibrinogen C domain containing"	3696	protein-coding gene	gene with protein product		605351				7642106	Standard	NM_006682		Approved	pT49, T49	uc003ugb.3	Q14314	OTTHUMG00000130681	ENST00000248598.5:c.386dupA	chr7.hg19:g.76828726_76828726dupT	ENSP00000248598:p.Arg129fs	129.0	0.0	0		164.0	33.0	0.20122	NM_006682		Frame_Shift_Ins	INS	ENST00000248598.5	hg19	CCDS5591.1																																																																																			.	.	.	none		0.495	FGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253176.1	NM_006682		T	76828726	-	T	76828725	7	5	132	1	0	1	1	0	0	0	0	0	5880	913	32	0	941	0	FGL2	7	76828725	Frame_Shift_Ins	INS	-	TCGA-BQ-7046-01A-11D-1961-08		76828725	82309938	8	8176											
MYST3	7994	hgsc.bcm.edu	37	chr8	41836161	41836161	+	Splice_Site	DEL	C	C	-																															tgccacaagtacaacttacaCcgtgttttgtttctttaacc																										TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr8:41836161delC	ENST00000396930.3	-	7	1585	c.1042delG	c.(1042-1044)gta>ta	p.V348fs	KAT6A_ENST00000265713.2_Splice_Site_p.V348fs|KAT6A_ENST00000406337.1_Splice_Site_p.V348fs|KAT6A_ENST00000485568.1_Splice_Site_p.V348fs	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	348	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)										ACAACTTACACCGTGTTTTGT	0.383																																					p.V348fs		Atlas-INDEL	.											.	.	.	.	0			c.1043delT						PASS	.						338	340	340					8																	41836161		2203	4300	6503	SO:0001630	splice_region_variant	7994	exon7			.	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.1043+1G>-	chr8.hg19:g.41836161delC		420.0	0.0	0		379.0	105.0	0.277045	NM_001099412	Q76L81	Frame_Shift_Del	DEL	ENST00000396930.3	hg19	CCDS6124.1																																																																																			.	.	.	none		0.383	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766	Frame_Shift_Del	-	41836161	C	-	41836161	8	5	132	1	0	1	0	1	0	0	1	0	10111	521	18	0	5020	0	MYST3	8	41836161	Splice_Site	DEL	C	TCGA-BQ-7046-01A-11D-1961-08		41836161	104527861	9	8177											
CNTLN	54875	hgsc.bcm.edu	37	chr9	17462949	17462949	+	Frame_Shift_Del	DEL	T	T	-																															ctcactaaacagtcatcaaaTgtgaagactttgaaatttga																										TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr9:17462949delT	ENST00000380647.3	+	20	3426	c.3342delT	c.(3340-3342)aatfs	p.N1114fs	CNTLN_ENST00000262360.5_Frame_Shift_Del_p.N1114fs|CNTLN_ENST00000425824.1_Frame_Shift_Del_p.N1114fs			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	1114					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)		AGTCATCAAATGTGAAGACTT	0.299																																					p.N1114fs		Atlas-INDEL	.											.	CNTLN	128	.	0			c.3341delA						PASS	.						83	81	81					9																	17462949		1809	4069	5878	SO:0001589	frameshift_variant	54875	exon20			.	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.3342delT	chr9.hg19:g.17462949delT	ENSP00000370021:p.Asn1114fs	114.0	0.0	0		97.0	29.0	0.298969	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Frame_Shift_Del	DEL	ENST00000380647.3	hg19	CCDS43789.1																																																																																			.	.	.	none		0.299	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		-	17462949	T	-	17462949	7	5	132	1	0	1	0	1	0	0	0	0	3641	1461	51	0	3450	0	CNTLN	9	17462949	Frame_Shift_Del	DEL	T	TCGA-BQ-7046-01A-11D-1961-08		17462949	123750482	10	8178											
SVIL	6840	hgsc.bcm.edu	37	chr10	29811367	29811367	+	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	aatagacatggttttgctggGtgagtcaagaaggccctccc	10	10	12	9	0	1	3	1	1	0	2	2	3	2	3	2	3	1	2	2	3	4	3			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr10:29811367G>C	ENST00000355867.4	-	16	4113	c.3361C>G	c.(3361-3363)Ccc>Gcc	p.P1121A	SVIL_ENST00000535393.1_Missense_Mutation_p.P19A|SVIL_ENST00000375400.3_Missense_Mutation_p.P695A|SVIL_ENST00000375398.2_Missense_Mutation_p.P1121A	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1121					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)				GTTTTGCTGGGTGAGTCAAGA	0.468																																					p.P1121A		Atlas-SNP	.											.	SVIL	226	.	0			c.C3361G						PASS	.						70	70	70					10																	29811367		2203	4300	6503	SO:0001583	missense	6840	exon16			TGCTGGGTGAGTC	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.3361C>G	chr10.hg19:g.29811367G>C	ENSP00000348128:p.Pro1121Ala	101.0	0.0	.		86.0	29.0	.	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	hg19	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	G	9.477	1.097117	0.20552	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867;ENST00000535393;ENST00000535994	T;T;T;T	0.12255	2.79;2.83;2.83;2.7	5.82	2.6	0.31112	.	0.415737	0.28482	N	0.015187	T	0.07863	0.0197	L	0.32530	0.975	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	0.21827	-1.0234	10	0.12430	T	0.62	-11.1568	4.4588	0.11656	0.2785:0.2093:0.5123:0.0	.	19;695;1121	F5H2Q5;O95425-2;O95425	.;.;SVIL_HUMAN	A	695;1121;1121;19;75	ENSP00000364549:P695A;ENSP00000364547:P1121A;ENSP00000348128:P1121A;ENSP00000445472:P19A	ENSP00000348128:P1121A	P	-	1	0	SVIL	29851373	0.955000	0.32602	0.678000	0.29963	0.512000	0.34134	1.769000	0.38522	0.798000	0.33994	0.563000	0.77884	CCC	.	.	.	none		0.468	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			C	29811367	G	C	29811367	3	2	132	1	0	0	0	0	1	0	0	0	15433	1261	44	4	3375	4	SVIL	10	29811367	Missense_Mutation	SNP	G	TCGA-BQ-7046-01A-11D-1961-08		29811367	105723380	11	8179											
PARD3	56288	hgsc.bcm.edu	37	chr10	34648076	34648076	+	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	acttttttgcatttcttaccTcattgcacttgcttattctc	6	21	3	11	0	3	0	1	0	2	0	4	0	3	0	1	0	4	3	1	0	2	9			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr10:34648076T>C	ENST00000374789.3	-	14	2391	c.2066A>G	c.(2065-2067)gAg>gGg	p.E689G	PARD3_ENST00000374794.3_Splice_Site_p.E632G|PARD3_ENST00000374773.1_Splice_Site_p.E689G|PARD3_ENST00000374768.1_Splice_Site_p.E127G|PARD3_ENST00000544292.1_Splice_Site_p.E406G|PARD3_ENST00000374776.1_Splice_Site_p.E676G|PARD3_ENST00000545693.1_Splice_Site_p.E676G|PARD3_ENST00000340077.5_Splice_Site_p.E689G|PARD3_ENST00000374790.3_Splice_Site_p.E632G|PARD3_ENST00000374788.3_Splice_Site_p.E689G|PARD3_ENST00000346874.4_Splice_Site_p.E689G|PARD3_ENST00000350537.4_Splice_Site_p.E676G|PARD3_ENST00000545260.1_Splice_Site_p.E632G	NM_019619.3	NP_062565.2	Q8TEW0	PARD3_HUMAN	par-3 family cell polarity regulator	689					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)				ATTTCTTACCTCATTGCACTT	0.378																																					p.E689G		Atlas-SNP	.											.	PARD3	131	.	0			c.A2066G						PASS	.						167	156	160					10																	34648076		2203	4300	6503	SO:0001630	splice_region_variant	56288	exon14			CTTACCTCATTGC	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.2067+1A>G	chr10.hg19:g.34648076T>C		171.0	0.0	.		161.0	47.0	.	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	hg19	CCDS7178.1	.	.	.	.	.	.	.	.	.	.	T	13.74	2.328750	0.41197	.	.	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	0.20332	2.43;2.43;2.49;2.49;2.52;2.45;2.42;2.43;2.1;2.08;2.16;2.12;2.25	5.56	5.56	0.83823	PDZ/DHR/GLGF (1);	0.414096	0.28706	N	0.014403	T	0.30916	0.0780	L	0.50333	1.59	0.80722	D	1	P;P;B;P;B;P;P;B;B;P;P;B;B;P;B	0.46512	0.719;0.879;0.391;0.719;0.391;0.82;0.719;0.236;0.023;0.597;0.825;0.069;0.076;0.506;0.085	B;B;B;B;B;P;B;B;B;B;P;B;B;P;B	0.49502	0.377;0.409;0.304;0.377;0.304;0.613;0.377;0.076;0.013;0.209;0.533;0.113;0.078;0.502;0.113	T	0.01508	-1.1337	10	0.45353	T	0.12	.	15.7055	0.77577	0.0:0.0:0.0:1.0	.	632;632;676;676;676;689;689;689;632;676;689;689;676;689;406	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;.;.;.;.;.;.;.	G	676;632;689;689;689;632;676;632;676;689;689;406;127	ENSP00000443147:E676G;ENSP00000440857:E632G;ENSP00000363921:E689G;ENSP00000363920:E689G;ENSP00000340591:E689G;ENSP00000363926:E632G;ENSP00000311986:E676G;ENSP00000363922:E632G;ENSP00000363908:E676G;ENSP00000341844:E689G;ENSP00000363905:E689G;ENSP00000444429:E406G;ENSP00000363900:E127G	ENSP00000341844:E689G	E	-	2	0	PARD3	34688082	1.000000	0.71417	0.990000	0.47175	0.190000	0.23558	6.186000	0.72026	2.114000	0.64651	0.533000	0.62120	GAG	.	.	.	none		0.378	PARD3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047527.1	NM_019619	Missense_Mutation	C	34648076	T	C	34648076	5	2	132	1	0	0	0	0	0	0	1	0	11450	1565	54	3	2087	3	PARD3	10	34648076	Splice_Site	SNP	T	TCGA-BQ-7046-01A-11D-1961-08	4836709	34648076	100886671	12	8180											
TMEM26	219623	hgsc.bcm.edu	37	chr10	63212836	63212836	+	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	gttaaggaagaccagtccctCcatgctggccggagcactct	9	8	11	13	1	1	1	0	0	1	1	3	3	3	3	4	3	2	3	4	3	2	1			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr10:63212836C>T	ENST00000399298.3	-	1	372	c.4G>A	c.(4-6)Gag>Aag	p.E2K	TMEM26_ENST00000399293.1_Missense_Mutation_p.E2K|RP11-809M12.1_ENST00000389640.4_RNA	NM_178505.6	NP_848600.2	Q6ZUK4	TMM26_HUMAN	transmembrane protein 26	2						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	18	Prostate(12;0.0112)					ACCAGTCCCTCCATGCTGGCC	0.667																																					p.E2K		Atlas-SNP	.											.	TMEM26	47	.	0			c.G4A						PASS	.						45	54	51					10																	63212836		2126	4227	6353	SO:0001583	missense	219623	exon1			GTCCCTCCATGCT	BC042872	CCDS41530.1	10q21.3	2008-10-20			ENSG00000196932	ENSG00000196932			28550	protein-coding gene	gene with protein product						12477932	Standard	NM_178505		Approved	MGC35010, Em:AC068892.1	uc001jlo.2	Q6ZUK4	OTTHUMG00000018293	ENST00000399298.3:c.4G>A	chr10.hg19:g.63212836C>T	ENSP00000382237:p.Glu2Lys	71.0	0.0	.		75.0	28.0	.	NM_178505	Q6ZVM0|Q8IVN9	Missense_Mutation	SNP	ENST00000399298.3	hg19	CCDS41530.1	.	.	.	.	.	.	.	.	.	.	C	15.18	2.755604	0.49362	.	.	ENSG00000196932	ENST00000399298;ENST00000399293	.	.	.	5.01	4.1	0.47936	.	0.902018	0.09509	N	0.792586	T	0.46132	0.1377	L	0.50333	1.59	0.34559	D	0.71215	P	0.43392	0.805	B	0.34722	0.188	T	0.53373	-0.8448	9	0.24483	T	0.36	-18.3363	14.8814	0.70537	0.1446:0.8554:0.0:0.0	.	2	Q6ZUK4	TMM26_HUMAN	K	2	.	ENSP00000382232:E2K	E	-	1	0	TMEM26	62882842	1.000000	0.71417	1.000000	0.80357	0.204000	0.24138	4.777000	0.62361	1.315000	0.45114	-0.182000	0.12963	GAG	.	.	.	none		0.667	TMEM26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359121.1	NM_178505		T	63212836	C	T	63212836	3	4	132	1	0	0	0	0	1	0	0	0	16163	864	30	2	1126	2	TMEM26	10	63212836	Missense_Mutation	SNP	C	TCGA-BQ-7046-01A-11D-1961-08	28564760	63212836	72321911	13	8181											
DNAJB12	54788	hgsc.bcm.edu	37	chr10	74100871	74100871	+	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	ggctcttgtcatcgccgaacTggtcatactgcttcctcttc	5	14	8	14	2	4	0	2	0	2	0	7	1	5	0	2	2	3	2	2	2	2	4			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr10:74100871T>A	ENST00000444643.2	-	4	847	c.515A>T	c.(514-516)cAg>cTg	p.Q172L	DNAJB12_ENST00000394903.2_Missense_Mutation_p.Q206L|DNAJB12_ENST00000338820.3_Missense_Mutation_p.Q206L|DNAJB12_ENST00000461919.1_5'UTR			Q9NXW2	DJB12_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 12	172	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.					integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|skin(1)	4						ATCGCCGAACTGGTCATACTG	0.602																																					p.Q206L		Atlas-SNP	.											.	DNAJB12	22	.	0			c.A617T						PASS	.						75	67	69					10																	74100871		2203	4300	6503	SO:0001583	missense	54788	exon4			CCGAACTGGTCAT	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.515A>T	chr10.hg19:g.74100871T>A	ENSP00000403313:p.Gln172Leu	79.0	0.0	.		69.0	24.0	.	NM_017626	B7Z7I3|Q9H6H0	Missense_Mutation	SNP	ENST00000444643.2	hg19		.	.	.	.	.	.	.	.	.	.	T	8.916	0.959878	0.18507	.	.	ENSG00000148719	ENST00000338820;ENST00000394903;ENST00000444643	T;T;T	0.73258	-0.73;-0.73;-0.73	5.48	5.48	0.80851	Heat shock protein DnaJ, N-terminal (3);	0.122950	0.64402	D	0.000020	T	0.59528	0.2200	N	0.17474	0.49	0.58432	D	0.999999	D;P	0.54207	0.965;0.879	P;B	0.49887	0.625;0.227	T	0.59721	-0.7401	10	0.02654	T	1	-6.3488	15.622	0.76813	0.0:0.0:0.0:1.0	.	172;172	Q9NXW2-2;Q9NXW2	.;DJB12_HUMAN	L	206;206;172	ENSP00000345575:Q206L;ENSP00000378363:Q206L;ENSP00000403313:Q172L	ENSP00000345575:Q206L	Q	-	2	0	DNAJB12	73770877	1.000000	0.71417	1.000000	0.80357	0.754000	0.42855	5.015000	0.64035	2.086000	0.62901	0.529000	0.55759	CAG	.	.	.	none		0.602	DNAJB12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048581.2			A	74100871	T	A	74100871	3	1	132	1	0	0	0	0	1	0	0	0	4619	1580	55	5	632	5	DNAJB12	10	74100871	Missense_Mutation	SNP	T	TCGA-BQ-7046-01A-11D-1961-08	10888035	74100871	61433876	14	8182											
EML3	256364	hgsc.bcm.edu	37	chr11	62376458	62376458	+	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	gaacgcagtctgtgtgccccCggtaatgtctctggccgcca	6	9	12	14	3	2	0	0	0	2	0	3	1	2	0	4	2	2	2	4	2	2	1			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr11:62376458C>A	ENST00000394773.2	-	7	1212	c.905G>T	c.(904-906)cGg>cTg	p.R302L	EML3_ENST00000278845.4_Missense_Mutation_p.R303L|RP11-831H9.3_ENST00000532626.1_RNA|EML3_ENST00000494176.2_Missense_Mutation_p.R274L|EML3_ENST00000531557.1_Missense_Mutation_p.R85L|EML3_ENST00000438258.1_5'Flank|EML3_ENST00000529309.1_Missense_Mutation_p.R302L|ROM1_ENST00000534093.1_5'Flank	NM_153265.2	NP_694997.2	Q32P44	EMAL3_HUMAN	echinoderm microtubule associated protein like 3	302						cytoplasm (GO:0005737)|microtubule (GO:0005874)				biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						TGTGTGCCCCCGGTAATGTCT	0.637																																					p.R302L		Atlas-SNP	.											.	EML3	61	.	0			c.G905T						PASS	.						134	149	144					11																	62376458		2202	4299	6501	SO:0001583	missense	256364	exon7			TGCCCCCGGTAAT	AK093146	CCDS8023.2	11q12.3	2013-01-10			ENSG00000149499	ENSG00000149499		"WD repeat domain containing"	26666	protein-coding gene	gene with protein product						15225882, 14744259	Standard	NM_153265		Approved	FLJ35827, ELP95	uc001ntu.1	Q32P44	OTTHUMG00000149817	ENST00000394773.2:c.905G>T	chr11.hg19:g.62376458C>A	ENSP00000378254:p.Arg302Leu	286.0	0.0	.		325.0	16.0	.	NM_153265	Q6ZQW7|Q8NA55	Missense_Mutation	SNP	ENST00000394773.2	hg19	CCDS8023.2	.	.	.	.	.	.	.	.	.	.	C	3.507	-0.100684	0.06967	.	.	ENSG00000149499	ENST00000394773;ENST00000278845;ENST00000531557;ENST00000494176;ENST00000529309	T;T;T;T;T	0.60920	0.15;0.15;0.15;0.15;0.15	5.69	4.69	0.59074	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.290099	0.31199	N	0.008070	T	0.27241	0.0668	N	0.02403	-0.565	0.39947	D	0.974484	B;B;B;B;B	0.11235	0.003;0.001;0.0;0.004;0.002	B;B;B;B;B	0.12156	0.006;0.007;0.0;0.006;0.003	T	0.28776	-1.0033	10	0.02654	T	1	-16.8234	12.6609	0.56813	0.2364:0.7636:0.0:0.0	.	302;302;85;303;274	Q32P44-2;Q32P44;G3V195;B7WPE2;G3V1D0	.;EMAL3_HUMAN;.;.;.	L	302;303;85;274;302	ENSP00000378254:R302L;ENSP00000278845:R303L;ENSP00000433417:R85L;ENSP00000435064:R274L;ENSP00000434513:R302L	ENSP00000278845:R303L	R	-	2	0	EML3	62133034	0.991000	0.36638	1.000000	0.80357	0.981000	0.71138	1.076000	0.30729	2.676000	0.91093	0.655000	0.94253	CGG	.	.	.	none		0.637	EML3-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313432.1	NM_153265		A	62376458	C	A	62376458	3	1	132	1	0	0	0	0	1	0	0	0	5100	652	23	4	1849	4	EML3	11	62376458	Missense_Mutation	SNP	C	TCGA-BQ-7046-01A-11D-1961-08		62376458	72630058	15	8183											
NRXN2	9379	hgsc.bcm.edu	37	chr11	64453122	64453122	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctcactcctcctacctggCgcaggtttcgggtgacccgg	4	11	11	15	3	1	1	1	1	1	0	5	1	3	1	4	4	1	2	4	4	1	3			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr11:64453122C>T	ENST00000377551.1	-	5	1359	c.1148G>A	c.(1147-1149)cGc>cAc	p.R383H	NRXN2_ENST00000409571.1_Missense_Mutation_p.R383H|NRXN2_ENST00000265459.6_Missense_Mutation_p.R383H|NRXN2_ENST00000377559.3_Missense_Mutation_p.R359H			Q9P2S2	NRX2A_HUMAN	neurexin 2	383	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|gephyrin clustering (GO:0097116)|neuroligin clustering (GO:0097118)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	calcium channel regulator activity (GO:0005246)|cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|neuroligin family protein binding (GO:0097109)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	71						TCCTACCTGGCGCAGGTTTCG	0.602																																					p.R383H		Atlas-SNP	.											.	NRXN2	247	.	0			c.G1148A						PASS	.						86	87	86					11																	64453122		2201	4297	6498	SO:0001583	missense	9379	exon6			ACCTGGCGCAGGT		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.1148G>A	chr11.hg19:g.64453122C>T	ENSP00000366774:p.Arg383His	112.0	0.0	.		124.0	40.0	.	NM_015080	A7E2C1|Q9Y2D6	Missense_Mutation	SNP	ENST00000377551.1	hg19	CCDS8077.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.9|25.9	4.684359|4.684359	0.88639|0.88639	.|.	.|.	ENSG00000110076|ENSG00000110076	ENST00000417749|ENST00000377551;ENST00000377559;ENST00000265459;ENST00000345863;ENST00000409571;ENST00000442300	.|T;T;T;T;T	.|0.78481	.|-1.18;-1.18;-1.18;-1.18;-1.18	4.0|4.0	4.0|4.0	0.46444|0.46444	.|Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.|0.000000	.|0.44097	.|U	.|0.000496	D|D	0.84969|0.84969	0.5590|0.5590	M|M	0.62088|0.62088	1.915|1.915	0.58432|0.58432	D|D	0.999998|0.999998	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.87578	.|0.998;0.987;0.998	D|D	0.86396|0.86396	0.1739|0.1739	5|10	.|0.87932	.|D	.|0	.|.	11.9853|11.9853	0.53145|0.53145	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|359;383;136	.|Q9P2S2-2;Q9P2S2;E7EV67	.|.;NRX2A_HUMAN;.	T|H	144|383;359;383;359;383;154	.|ENSP00000366774:R383H;ENSP00000366782:R359H;ENSP00000265459:R383H;ENSP00000386416:R383H;ENSP00000388971:R154H	.|ENSP00000265459:R383H	A|R	-|-	1|2	0|0	NRXN2|NRXN2	64209698|64209698	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	7.814000|7.814000	0.86154|0.86154	1.951000|1.951000	0.56629|0.56629	0.467000|0.467000	0.42956|0.42956	GCC|CGC	.	.	.	none		0.602	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104967.3	NM_015080		T	64453122	C	T	64453122	3	4	132	1	0	0	0	0	1	0	0	0	10673	768	27	1	4331	1	NRXN2	11	64453122	Missense_Mutation	SNP	C	TCGA-BQ-7046-01A-11D-1961-08	2076664	64453122	70553394	16	8184											
ROBO4	54538	hgsc.bcm.edu	37	chr11	124765531	124765531	+	Silent	SNP	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	tggcctcccggggcagtctgGgtcctgaacaaggccgtgta	6	8	15	12	2	1	1	0	1	1	0	3	1	3	1	4	5	1	2	4	5	3	1			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr11:124765531G>A	ENST00000306534.3	-	6	1343	c.858C>T	c.(856-858)acC>acT	p.T286T	ROBO4_ENST00000533054.1_Silent_p.T141T|ROBO4_ENST00000526899.1_5'Flank	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	286	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)		GGGCAGTCTGGGTCCTGAACA	0.672																																					p.T286T		Atlas-SNP	.											.	ROBO4	130	.	0			c.C858T						PASS	.						36	44	41					11																	124765531		2193	4283	6476	SO:0001819	synonymous_variant	54538	exon6			AGTCTGGGTCCTG	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.858C>T	chr11.hg19:g.124765531G>A		89.0	0.0	.		117.0	36.0	.	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Silent	SNP	ENST00000306534.3	hg19	CCDS8455.1																																																																																			.	.	.	none		0.672	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055		A	124765531	G	A	124765531	2	1	132	1	0	0	0	0	0	0	0	1	13529	1219	43	2		2	ROBO4	11	124765531	Silent	SNP	G	TCGA-BQ-7046-01A-11D-1961-08	60312409	124765531	10240985	17	8185											
CAND1	55832	hgsc.bcm.edu	37	chr12	67691215	67691215	+	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	gacttcttgttaatttccatCcttcaattctgacctgtcta	8	18	4	11	0	4	1	1	1	3	0	6	2	6	1	3	0	0	1	3	0	3	7			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr12:67691215C>A	ENST00000545606.1	+	5	957	c.520C>A	c.(520-522)Cct>Act	p.P174T		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	174					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)		TAATTTCCATCCTTCAATTCT	0.408																																					p.P174T		Atlas-SNP	.											.	CAND1	100	.	0			c.C520A						PASS	.						119	122	121					12																	67691215		2203	4300	6503	SO:0001583	missense	55832	exon5			TTCCATCCTTCAA		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.520C>A	chr12.hg19:g.67691215C>A	ENSP00000442318:p.Pro174Thr	141.0	0.0	.		154.0	35.0	.	NM_018448	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Missense_Mutation	SNP	ENST00000545606.1	hg19	CCDS8977.1	.	.	.	.	.	.	.	.	.	.	C	15.16	2.751582	0.49257	.	.	ENSG00000111530	ENST00000545606;ENST00000299218;ENST00000540047	T	0.66099	-0.19	5.34	5.34	0.76211	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.63546	0.2520	M	0.65498	2.005	0.80722	D	1	B	0.25521	0.128	B	0.27380	0.079	T	0.59968	-0.7354	9	.	.	.	-15.7741	19.057	0.93069	0.0:1.0:0.0:0.0	.	174	Q86VP6	CAND1_HUMAN	T	174;174;16	ENSP00000442318:P174T	.	P	+	1	0	CAND1	65977482	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.879000	0.69690	2.508000	0.84585	0.655000	0.94253	CCT	.	.	.	none		0.408	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448		A	67691215	C	A	67691215	3	1	132	1	0	0	0	0	1	0	0	0	2617	855	30	4	538	4	CAND1	12	67691215	Missense_Mutation	SNP	C	TCGA-BQ-7046-01A-11D-1961-08		67691215	66160680	18	8186											
NR2F2	7026	hgsc.bcm.edu	37	chr15	96875635	96875635	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacgtgcgagggctgcaagAgcttcttcaagcgcagcgtg	8	8	14	11	4	3	1	2	0	1	1	3	2	3	1	0	1	5	4	0	1	2	2			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr15:96875635A>G	ENST00000394166.3	+	1	1690	c.301A>G	c.(301-303)Agc>Ggc	p.S101G	NR2F2_ENST00000421109.2_Intron|NR2F2_ENST00000453270.2_5'Flank|NR2F2_ENST00000394171.2_5'Flank|MIR1469_ENST00000410719.1_RNA	NM_021005.3	NP_066285.1	P24468	COT2_HUMAN	nuclear receptor subfamily 2, group F, member 2	101					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)			GGGCTGCAAGAGCTTCTTCAA	0.612																																					p.S101G		Atlas-SNP	.											.	NR2F2	35	.	0			c.A301G						PASS	.						66	53	57					15																	96875635		2197	4298	6495	SO:0001583	missense	7026	exon1			TGCAAGAGCTTCT	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.301A>G	chr15.hg19:g.96875635A>G	ENSP00000377721:p.Ser101Gly	29.0	0.0	.		35.0	14.0	.	NM_021005	B4DQJ2|B6ZGU1|Q03754|Q3KQR7	Missense_Mutation	SNP	ENST00000394166.3	hg19	CCDS10375.1	.	.	.	.	.	.	.	.	.	.	A	17.76	3.468861	0.63625	.	.	ENSG00000185551	ENST00000394166	D	0.96745	-4.11	4.61	4.61	0.57282	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (5);	0.187668	0.42821	N	0.000656	D	0.91784	0.7401	N	0.01235	-0.94	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.88109	0.2824	10	0.02654	T	1	.	12.8472	0.57837	1.0:0.0:0.0:0.0	.	101	P24468	COT2_HUMAN	G	101	ENSP00000377721:S101G	ENSP00000377721:S101G	S	+	1	0	NR2F2	94676639	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.257000	0.72480	1.705000	0.51264	0.379000	0.24179	AGC	.	.	.	none		0.612	NR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313534.1			G	96875635	A	G	96875635	3	3	132	1	0	0	0	0	1	0	0	0	10635	304	11	3	350	3	NR2F2	15	96875635	Missense_Mutation	SNP	A	TCGA-BQ-7046-01A-11D-1961-08		96875635	5655757	19	8187											
RSPRY1	89970	hgsc.bcm.edu	37	chr16	57261323	57261323	+	Frame_Shift_Del	DEL	A	A	-																															gccggcagctgatttggtacAatgccagaagtaagcctcac																										TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr16:57261323delA	ENST00000537866.1	+	11	2104	c.1231delA	c.(1231-1233)aatfs	p.N411fs	RSPRY1_ENST00000394420.4_Frame_Shift_Del_p.N411fs|RSPRY1_ENST00000563073.1_3'UTR			Q96DX4	RSPRY_HUMAN	ring finger and SPRY domain containing 1	411	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					extracellular region (GO:0005576)	zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|urinary_tract(3)	27						GATTTGGTACAATGCCAGAAG	0.453																																					p.Y410X		Atlas-INDEL	.											.	RSPRY1	49	.	0			c.1230delC						PASS	.						122	104	110					16																	57261323		2198	4300	6498	SO:0001589	frameshift_variant	89970	exon11			.	AB075852	CCDS10775.1	16q13	2014-02-12			ENSG00000159579	ENSG00000159579		"RING-type (C3HC4) zinc fingers"	29420	protein-coding gene	gene with protein product						11853319	Standard	NM_133368		Approved	KIAA1972	uc002elb.3	Q96DX4	OTTHUMG00000133462	ENST00000537866.1:c.1231delA	chr16.hg19:g.57261323delA	ENSP00000443176:p.Asn411fs	85.0	0.0	0		99.0	54.0	0.545455	NM_133368	Q6UX21|Q8ND53	Frame_Shift_Del	DEL	ENST00000537866.1	hg19	CCDS10775.1																																																																																			.	.	.	none		0.453	RSPRY1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432953.1	NM_133368		-	57261323	A	-	57261323	7	5	132	1	0	1	0	1	0	0	0	0	13726	130	5	0	1269	0	RSPRY1	16	57261323	Frame_Shift_Del	DEL	A	TCGA-BQ-7046-01A-11D-1961-08		57261323	33093430	20	8188											
MYBBP1A	10514	hgsc.bcm.edu	37	chr17	4451584	4451584	+	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	cccggtgcctgcttgaactgCgtgctgagggtctgcaacag	6	9	14	12	2	1	2	0	2	1	0	1	2	1	2	2	2	7	3	2	2	2	1			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr17:4451584C>T	ENST00000254718.4	-	12	1884	c.1578G>A	c.(1576-1578)acG>acA	p.T526T	MYBBP1A_ENST00000381556.2_Silent_p.T526T			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	526	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						GCTTGAACTGCGTGCTGAGGG	0.637																																					p.T526T		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.G1578A						PASS	.						64	64	64					17																	4451584		2203	4300	6503	SO:0001819	synonymous_variant	10514	exon12			GAACTGCGTGCTG	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.1578G>A	chr17.hg19:g.4451584C>T		136.0	0.0	.		198.0	111.0	.	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	hg19	CCDS11046.1																																																																																			.	.	.	none		0.637	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520		T	4451584	C	T	4451584	2	4	132	1	0	0	0	0	0	0	0	1	10015	755	27	1		1	MYBBP1A	17	4451584	Silent	SNP	C	TCGA-BQ-7046-01A-11D-1961-08		4451584	76743626	21	8189											
GPRC5C	55890	hgsc.bcm.edu	37	chr17	72436053	72436053	+	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	tacaacctgtgtgaccgctcTggggcgtggggcatcgtcct	5	10	14	12	3	1	1	0	1	1	0	3	1	2	1	3	4	2	2	3	4	2	1			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr17:72436053T>A	ENST00000481232.1	+	2	784	c.273T>A	c.(271-273)tcT>tcA	p.S91S	GPRC5C_ENST00000342648.5_Intron|GPRC5C_ENST00000392629.2_Silent_p.S58S|GPRC5C_ENST00000392627.1_Silent_p.S91S			Q9NQ84	GPC5C_HUMAN	G protein-coupled receptor, class C, group 5, member C	46					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						GTGACCGCTCTGGGGCGTGGG	0.662																																					p.S91S		Atlas-SNP	.											.	GPRC5C	92	.	0			c.T273A						PASS	.						62	59	60					17																	72436053		2203	4299	6502	SO:0001819	synonymous_variant	55890	exon2			CCGCTCTGGGGCG	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.273T>A	chr17.hg19:g.72436053T>A		95.0	0.0	.		178.0	98.0	.	NM_022036	B5BUN4|Q2NL85|Q9NZG5	Silent	SNP	ENST00000481232.1	hg19																																																																																				.	.	.	none		0.662	GPRC5C-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000145095.2			A	72436053	T	A	72436053	2	1	132	1	0	0	0	0	0	0	0	1	6733	1567	55	5		5	GPRC5C	17	72436053	Silent	SNP	T	TCGA-BQ-7046-01A-11D-1961-08	67984469	72436053	8759157	22	8190											
C20orf3	57136	hgsc.bcm.edu	37	chr20	24944513	24944513	+	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	aagagcccaggtacaggtgcCcatcgtgttcgtgcacctcg	8	8	12	13	3	0	1	0	0	0	1	3	1	0	1	3	2	4	3	3	2	2	2			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr20:24944513C>T	ENST00000217456.2	-	9	1477	c.1187G>A	c.(1186-1188)gGg>gAg	p.G396E	APMAP_ENST00000447138.1_3'UTR	NM_020531.2	NP_065392.1	Q9HDC9	APMAP_HUMAN	adipocyte plasma membrane associated protein	396					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)										GTACAGGTGCCCATCGTGTTC	0.627																																					p.G396E		Atlas-SNP	.											.	APMAP	3	.	0			c.G1187A						PASS	.						103	94	97					20																	24944513		2203	4300	6503	SO:0001583	missense	57136	exon9			AGGTGCCCATCGT	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.1187G>A	chr20.hg19:g.24944513C>T	ENSP00000217456:p.Gly396Glu	109.0	0.0	.		139.0	24.0	.	NM_020531	A8K514|B4DXG1|Q6UVZ8|Q9GZS8|Q9NUB2	Missense_Mutation	SNP	ENST00000217456.2	hg19	CCDS13166.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.06|17.06	3.291373|3.291373	0.59976|0.59976	.|.	.|.	ENSG00000101474|ENSG00000101474	ENST00000217456|ENST00000451442	T|T	0.36520|0.35605	1.25|1.3	4.86|4.86	4.86|4.86	0.63082|0.63082	Six-bladed beta-propeller, TolB-like (1);|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.58708|0.58708	0.2141|0.2141	M|M	0.82132|0.82132	2.575|2.575	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.999;0.973|.	D;P|.	0.68192|.	0.956;0.685|.	T|T	0.64643|0.64643	-0.6359|-0.6359	10|8	0.44086|0.62326	T|D	0.13|0.03	-18.3321|-18.3321	15.4972|15.4972	0.75662|0.75662	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	388;396|.	A2A2F9;Q9HDC9|.	.;APMAP_HUMAN|.	E|S	396|389	ENSP00000217456:G396E|ENSP00000395874:G389S	ENSP00000217456:G396E|ENSP00000395874:G389S	G|G	-|-	2|1	0|0	C20orf3|C20orf3	24892513|24892513	1.000000|1.000000	0.71417|0.71417	0.502000|0.502000	0.27614|0.27614	0.164000|0.164000	0.22412|0.22412	7.726000|7.726000	0.84824|0.84824	2.216000|2.216000	0.71823|0.71823	0.561000|0.561000	0.74099|0.74099	GGG|GGC	.	.	.	none		0.627	APMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078380.2	NM_020531		T	24944513	C	T	24944513	3	4	132	1	0	0	0	0	1	0	0	0	2111	623	22	2	67	2	C20orf3	20	24944513	Missense_Mutation	SNP	C	TCGA-BQ-7046-01A-11D-1961-08		24944513	38081007	23	8191											
BACH1	571	hgsc.bcm.edu	37	chr21	30698866	30698866	+	Frame_Shift_Del	DEL	A	A	-																															ttggaactgacagagtccgtActggggaatctagtgtcaaa																										TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr21:30698866delA	ENST00000399921.1	+	3	964	c.721delA	c.(721-723)actfs	p.T241fs	BACH1_ENST00000286800.3_Frame_Shift_Del_p.T241fs	NM_206866.1	NP_996749.1	Q9BX63	FANCJ_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 1	0	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|urinary_tract(2)	27						CAGAGTCCGTACTGGGGAATC	0.453																																					p.R240fs		Atlas-INDEL	.											.	BACH1	66	.	0			c.720delT						PASS	.						57	59	58					21																	30698866		2203	4300	6503	SO:0001589	frameshift_variant	571	exon3			.	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.721delA	chr21.hg19:g.30698866delA	ENSP00000382805:p.Thr241fs	92.0	0.0	0		113.0	38.0	0.336283	NM_206866	Q3MJE2|Q8NCI5	Frame_Shift_Del	DEL	ENST00000399921.1	hg19	CCDS13585.1																																																																																			.	.	.	none		0.453	BACH1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171974.1	NM_206866		-	30698866	A	-	30698866	7	5	132	1	0	1	0	1	0	0	0	0	1283	391	14	0	727	0	BACH1	21	30698866	Frame_Shift_Del	DEL	A	TCGA-BQ-7046-01A-11D-1961-08		30698866	17431029	24	8192											
DSCAM	1826	hgsc.bcm.edu	37	chr21	41459172	41459172	+	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	agacaatgtctttcatccatGgagtagtcactgtcccactg	10	12	8	11	0	3	1	2	0	1	1	5	2	5	2	2	1	0	1	2	1	2	2			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr21:41459172G>A	ENST00000400454.1	-	22	4370	c.3893C>T	c.(3892-3894)cCa>cTa	p.P1298L		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1298	Ig-like C2-type 10.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				TTTCATCCATGGAGTAGTCAC	0.488																																					p.P1298L	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.C3893T						PASS	.						152	147	149					21																	41459172		1995	4169	6164	SO:0001583	missense	1826	exon22			ATCCATGGAGTAG	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.3893C>T	chr21.hg19:g.41459172G>A	ENSP00000383303:p.Pro1298Leu	165.0	0.0	.		137.0	14.0	.	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	hg19	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.670051	0.88348	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.25912	1.77;1.77	4.71	4.71	0.59529	Fibronectin, type III (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.41488	0.1161	L	0.33339	1.005	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	T	0.35226	-0.9797	10	0.59425	D	0.04	.	18.0505	0.89347	0.0:0.0:1.0:0.0	.	1298	O60469	DSCAM_HUMAN	L	1298;1050	ENSP00000383303:P1298L;ENSP00000385342:P1050L	ENSP00000383303:P1298L	P	-	2	0	DSCAM	40381042	1.000000	0.71417	0.262000	0.24481	0.988000	0.76386	9.633000	0.98432	2.316000	0.78162	0.563000	0.77884	CCA	.	.	.	none		0.488	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		A	41459172	G	A	41459172	3	1	132	1	0	0	0	0	1	0	0	0	4770	1348	47	2	2193	2	DSCAM	21	41459172	Missense_Mutation	SNP	G	TCGA-BQ-7046-01A-11D-1961-08	10760306	41459172	6670723	25	8193											
SNAP29	9342	hgsc.bcm.edu	37	chr22	21237785	21237785	+	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	tccccagaggggctggttctGccatgagtactgatgcttac	7	11	12	11	0	1	3	0	2	1	1	2	3	2	3	3	3	4	4	3	3	2	3			TCGA-BQ-7046-01A-11D-1961-08	TCGA-BQ-7046-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1fa8122c-c3e4-4e48-a47a-82feb79f1dc0	ea85b7f0-e214-4d27-80c1-c254338b6b0c	g.chr22:21237785G>C	ENST00000215730.7	+	4	675	c.547G>C	c.(547-549)Gcc>Ccc	p.A183P		NM_004782.3	NP_004773.1	O95721	SNP29_HUMAN	synaptosomal-associated protein, 29kDa	183					autophagic vacuole fusion (GO:0000046)|exocytosis (GO:0006887)|membrane fusion (GO:0061025)|protein transport (GO:0015031)|vesicle targeting (GO:0006903)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|SNARE complex (GO:0031201)|synapse (GO:0045202)	SNAP receptor activity (GO:0005484)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|upper_aerodigestive_tract(1)	9	all_cancers(11;2.77e-25)|all_epithelial(7;8.92e-24)|Lung NSC(8;1.49e-15)|all_lung(8;2.54e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000592)|Lung(15;0.0117)			GGCTGGTTCTGCCATGAGTAC	0.498																																					p.A183P		Atlas-SNP	.											SNAP29,right_lower_lobe,carcinoma,0,1	SNAP29	22	.	0			c.G547C						PASS	.						218	198	205					22																	21237785		2203	4300	6503	SO:0001583	missense	9342	exon4			GGTTCTGCCATGA	AF115436	CCDS13784.1	22q11.21	2008-06-10	2002-08-29		ENSG00000099940	ENSG00000099940			11133	protein-coding gene	gene with protein product	"soluble 29 kDa NSF attachment protein"	604202	"synaptosomal-associated protein, 29kD"			9852078, 10591208	Standard	NM_004782		Approved	SNAP-29, CEDNIK	uc011ahw.2	O95721	OTTHUMG00000150765	ENST00000215730.7:c.547G>C	chr22.hg19:g.21237785G>C	ENSP00000215730:p.Ala183Pro	385.0	1.0	.		327.0	100.0	.	NM_004782		Missense_Mutation	SNP	ENST00000215730.7	hg19	CCDS13784.1	.	.	.	.	.	.	.	.	.	.	G	12.46	1.944634	0.34283	.	.	ENSG00000099940	ENST00000215730;ENST00000439214	.	.	.	4.17	-2.31	0.06765	SNAP-25 (1);	0.598056	0.18243	N	0.147169	T	0.17408	0.0418	N	0.22421	0.69	0.09310	N	1	P	0.41524	0.753	P	0.44921	0.464	T	0.12319	-1.0552	9	0.33141	T	0.24	-0.0293	2.763	0.05312	0.3197:0.0:0.3417:0.3386	.	183	O95721	SNP29_HUMAN	P	183;90	.	ENSP00000215730:A183P	A	+	1	0	SNAP29	19567785	0.014000	0.17966	0.001000	0.08648	0.009000	0.06853	0.143000	0.16115	-0.176000	0.10707	-0.218000	0.12543	GCC	.	.	.	none		0.498	SNAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320000.4	NM_004782		C	21237785	G	C	21237785	3	2	132	1	0	0	0	0	1	0	0	0	14844	1319	46	4	561	4	SNAP29	22	21237785	Missense_Mutation	SNP	G	TCGA-BQ-7046-01A-11D-1961-08		21237785	30066781	26	8194											
KIAA0090	23065	hgsc.bcm.edu	37	chr1	19566346	19566346	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taagcaaactcagcgttccaTaatggtactgcagcagagca	14	8	9	10	1	1	1	1	0	0	1	2	1	2	1	1	1	7	6	1	1	4	4			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr1:19566346T>C	ENST00000477853.1	-	8	962	c.920A>G	c.(919-921)tAt>tGt	p.Y307C	EMC1_ENST00000375199.3_Missense_Mutation_p.Y307C|EMC1_ENST00000375208.3_Missense_Mutation_p.Y285C|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	307						ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)											CAGCGTTCCATAATGGTACTG	0.547																																					p.Y307C		Atlas-SNP	.											.	.	.	.	0			c.A920G						PASS	.						81	83	82					1																	19566346		2203	4300	6503	SO:0001583	missense	23065	exon8			GTTCCATAATGGT		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.920A>G	chr1.hg19:g.19566346T>C	ENSP00000420608:p.Tyr307Cys	91.0	0.0	.		81.0	28.0	.	NM_001271427	A8K6F3|Q14700|Q5TG62|Q63HL0|Q63HL3|Q8NBH8	Missense_Mutation	SNP	ENST00000477853.1	hg19	CCDS190.1	.	.	.	.	.	.	.	.	.	.	T	6.476	0.456042	0.12283	.	.	ENSG00000127463	ENST00000477853;ENST00000375199;ENST00000375208	T;T;T	0.21932	1.98;1.98;1.98	5.63	3.3	0.37823	.	0.510435	0.24343	N	0.039353	T	0.10252	0.0251	N	0.08118	0	0.09310	N	0.999998	B;P;P;B	0.35456	0.218;0.502;0.502;0.369	B;B;B;B	0.36418	0.161;0.161;0.224;0.112	T	0.17653	-1.0362	10	0.36615	T	0.2	-5.9075	8.4851	0.33067	0.1216:0.0:0.1381:0.7404	.	285;307;307;307	Q8N766-4;Q8N766-2;Q8N766-3;Q8N766	.;.;.;K0090_HUMAN	C	307;307;285	ENSP00000420608:Y307C;ENSP00000364345:Y307C;ENSP00000364354:Y285C	ENSP00000364345:Y307C	Y	-	2	0	KIAA0090	19438933	0.998000	0.40836	0.449000	0.26957	0.158000	0.22134	3.412000	0.52679	2.137000	0.66172	0.533000	0.62120	TAT	.	.	.	none		0.547	EMC1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007076.2	NM_015047		C	19566346	T	C	19566346	3	2	133	1	0	0	0	0	1	0	0	0	8160	1406	49	3	2125	3	KIAA0090	1	19566346	Missense_Mutation	SNP	T	TCGA-BQ-7048-01A-11D-1961-08		19566346	229684275	1	8195											
GFI1	2672	hgsc.bcm.edu	37	chr1	92948601	92948601	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgcctgcatttgaagtgcTgtctgcaaagaggaggcagg	9	8	14	10	1	1	2	0	1	1	1	1	3	1	3	2	3	3	4	2	3	2	1			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr1:92948601T>C	ENST00000370332.1	-	3	436	c.118A>G	c.(118-120)Agc>Ggc	p.S40G	GFI1_ENST00000294702.5_Missense_Mutation_p.S40G|GFI1_ENST00000483490.1_5'UTR|GFI1_ENST00000427103.1_Missense_Mutation_p.S40G	NM_001127215.1	NP_001120687.1	Q99684	GFI1_HUMAN	growth factor independent 1 transcription repressor	40					auditory receptor cell differentiation (GO:0042491)|cell fate commitment (GO:0045165)|cellular response to lipopolysaccharide (GO:0071222)|inner ear morphogenesis (GO:0042472)|mechanosensory behavior (GO:0007638)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cell fate specification (GO:0009996)|negative regulation of neuron projection development (GO:0010977)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vitamin D biosynthetic process (GO:0010957)|positive regulation of cell fate specification (GO:0042660)|positive regulation of interleukin-6-mediated signaling pathway (GO:0070105)|regulation of toll-like receptor signaling pathway (GO:0034121)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|viral process (GO:0016032)	nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15		all_lung(203;0.00292)|Lung NSC(277;0.0115)|all_neural(321;0.185)|Glioma(108;0.203)		OV - Ovarian serous cystadenocarcinoma(397;9.04e-07)|Epithelial(280;1.17e-05)|all cancers(265;5.61e-05)|GBM - Glioblastoma multiforme(16;0.0191)		TTTGAAGTGCTGTCTGCAAAG	0.667																																					p.S40G		Atlas-SNP	.											.	GFI1	41	.	0			c.A118G						PASS	.						26	32	30					1																	92948601		2200	4294	6494	SO:0001583	missense	2672	exon3			AAGTGCTGTCTGC	U67369	CCDS30773.1	1p22	2014-09-17	2007-10-04		ENSG00000162676	ENSG00000162676		"Zinc fingers, C2H2-type"	4237	protein-coding gene	gene with protein product		600871	"growth factor independent 1"	ZNF163		7789186	Standard	NM_005263		Approved	GFI1A, GFI-1	uc001dov.4	Q99684	OTTHUMG00000010897	ENST00000370332.1:c.118A>G	chr1.hg19:g.92948601T>C	ENSP00000359357:p.Ser40Gly	76.0	0.0	.		55.0	22.0	.	NM_005263	Q8N564	Missense_Mutation	SNP	ENST00000370332.1	hg19	CCDS30773.1	.	.	.	.	.	.	.	.	.	.	T	8.861	0.946887	0.18356	.	.	ENSG00000162676	ENST00000370332;ENST00000427103;ENST00000294702	T;T;T	0.09255	3.0;3.0;3.0	5.18	-2.98	0.05513	.	0.726593	0.13857	N	0.357995	T	0.01029	0.0034	N	0.12182	0.205	0.19775	N	0.999954	B	0.02656	0.0	B	0.01281	0.0	T	0.46133	-0.9213	10	0.06891	T	0.86	-6.9644	7.2257	0.26014	0.1163:0.4299:0.0:0.4538	.	40	Q99684	GFI1_HUMAN	G	40	ENSP00000359357:S40G;ENSP00000399719:S40G;ENSP00000294702:S40G	ENSP00000294702:S40G	S	-	1	0	GFI1	92721189	0.003000	0.15002	0.979000	0.43373	0.161000	0.22273	-0.880000	0.04183	-0.481000	0.06792	-0.379000	0.06801	AGC	.	.	.	none		0.667	GFI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030054.1	NM_005263		C	92948601	T	C	92948601	3	2	133	1	0	0	0	0	1	0	0	0	6346	1580	55	3	1170	3	GFI1	1	92948601	Missense_Mutation	SNP	T	TCGA-BQ-7048-01A-11D-1961-08	73382255	92948601	156302020	2	8196											
MR1	3140	hgsc.bcm.edu	37	chr1	181019230	181019230	+	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	ttctgcagtatgcatatgacGggcaggatttcctgatcttc	8	14	10	9	1	2	2	0	2	2	0	4	3	3	3	1	2	2	4	1	2	2	5			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr1:181019230G>T	ENST00000367580.5	+	3	417	c.412G>T	c.(412-414)Ggg>Tgg	p.G138W	MR1_ENST00000438435.2_3'UTR|MR1_ENST00000282990.6_Missense_Mutation_p.G138W|MR1_ENST00000367579.3_Intron|MR1_ENST00000434571.2_Missense_Mutation_p.G138W	NM_001531.2	NP_001522.1	Q95460	HMR1_HUMAN	major histocompatibility complex, class I-related	138	Alpha-2.|Ligand-binding.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	MHC class I receptor activity (GO:0032393)|peptide antigen binding (GO:0042605)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	18					Antithymocyte globulin(DB00098)	TGCATATGACGGGCAGGATTT	0.502																																					p.G138W	Colon(174;1412 1962 45296 46549 47110)	Atlas-SNP	.											.	MR1	46	.	0			c.G412T						PASS	.						128	115	120					1																	181019230		2203	4300	6503	SO:0001583	missense	3140	exon4			TATGACGGGCAGG	AF010446	CCDS1342.1, CCDS53440.1, CCDS53441.1, CCDS53442.1	1q25.3	2013-01-11	2003-03-05	2003-03-07	ENSG00000153029	ENSG00000153029		"Immunoglobulin superfamily / C1-set domain containing"	4975	protein-coding gene	gene with protein product		600764	"major histocompatibility complex, class I-like sequence"	HLALS		7624800, 9784382	Standard	NM_001194999		Approved		uc001goq.2	Q95460	OTTHUMG00000035175	ENST00000367580.5:c.412G>T	chr1.hg19:g.181019230G>T	ENSP00000356552:p.Gly138Trp	112.0	0.0	.		99.0	7.0	.	NM_001195035	A8K2V9|B4E3B1|O97985|O97986|Q53GM1|Q95HB8|Q9MY23|Q9NPL2|Q9TQB3|Q9TQB9|Q9TQK3	Missense_Mutation	SNP	ENST00000367580.5	hg19	CCDS1342.1	.	.	.	.	.	.	.	.	.	.	G	17.73	3.460730	0.63513	.	.	ENSG00000153029	ENST00000434571;ENST00000367580;ENST00000282990	T;T;T	0.00468	7.22;7.22;7.22	4.27	4.27	0.50696	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.317505	0.27270	N	0.020131	T	0.03136	0.0092	H	0.98426	4.23	0.42493	D	0.992906	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	0.03773	-1.1005	9	0.87932	D	0	.	14.5586	0.68120	0.0:0.0:1.0:0.0	.	138;138;138;138	B4E3B1;Q95460-3;Q95460;Q95460-4	.;.;HMR1_HUMAN;.	W	138	ENSP00000388504:G138W;ENSP00000356552:G138W;ENSP00000282990:G138W	ENSP00000282990:G138W	G	+	1	0	MR1	179285853	1.000000	0.71417	0.997000	0.53966	0.623000	0.37688	4.723000	0.61965	2.362000	0.80069	0.460000	0.39030	GGG	.	.	.	none		0.502	MR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085134.2	NM_001531		T	181019230	G	T	181019230	3	4	133	1	0	0	0	0	1	0	0	0	9759	1116	39	4	422	4	MR1	1	181019230	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	88070629	181019230	68231391	3	8197											
NPL	80896	hgsc.bcm.edu	37	chr1	182775301	182775301	+	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	gaatggcacaacaggagaagGcctgtccctgagcgtctcag	11	6	13	11	1	1	2	1	1	1	1	3	4	2	2	2	3	2	1	2	3	3	0			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr1:182775301G>C	ENST00000367553.1	+	4	208	c.164G>C	c.(163-165)gGc>gCc	p.G55A	NPL_ENST00000367552.2_Missense_Mutation_p.G55A|NPL_ENST00000258317.2_Missense_Mutation_p.G55A|NPL_ENST00000367554.3_5'UTR|NPL_ENST00000367550.2_Missense_Mutation_p.G55A|NPL_ENST00000367555.1_Missense_Mutation_p.G55A|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)	55					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						ACAGGAGAAGGCCTGTCCCTG	0.532																																					p.G55A		Atlas-SNP	.											.	NPL	55	.	0			c.G164C						PASS	.						111	109	110					1																	182775301		2203	4300	6503	SO:0001583	missense	80896	exon5			GAGAAGGCCTGTC	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.164G>C	chr1.hg19:g.182775301G>C	ENSP00000356524:p.Gly55Ala	77.0	0.0	.		85.0	13.0	.	NM_001200052	B2R839|Q4G0Q8|Q4G0Z2|Q64L88|Q6PEL0	Missense_Mutation	SNP	ENST00000367553.1	hg19	CCDS1350.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.482498	0.84747	.	.	ENSG00000135838	ENST00000367555;ENST00000367553;ENST00000367552;ENST00000258317;ENST00000367550	D;D;D;D;D	0.94897	-3.55;-1.53;-3.55;-1.53;-3.55	5.26	5.26	0.73747	Aldolase-type TIM barrel (1);	0.050750	0.85682	D	0.000000	D	0.95695	0.8600	M	0.62723	1.935	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.969	D;D;P	0.74023	0.957;0.982;0.671	D	0.93397	0.6757	10	0.06625	T	0.88	-14.9114	15.7916	0.78369	0.0:0.0:1.0:0.0	.	55;55;55	Q9BXD5-4;Q9BXD5;Q9BXD5-3	.;NPL_HUMAN;.	A	55	ENSP00000356526:G55A;ENSP00000356524:G55A;ENSP00000356523:G55A;ENSP00000258317:G55A;ENSP00000356521:G55A	ENSP00000258317:G55A	G	+	2	0	NPL	181041924	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	6.722000	0.74735	2.451000	0.82905	0.563000	0.77884	GGC	.	.	.	none		0.532	NPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085463.1	NM_030769		C	182775301	G	C	182775301	3	2	133	1	0	0	0	0	1	0	0	0	10592	1203	42	4	174	4	NPL	1	182775301	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	1756071	182775301	66475320	4	8198											
CYP1B1	1545	hgsc.bcm.edu	37	chr2	38302357	38302357	+	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	cgccgccgcgtttccgatcaGtggccacgcaaacgggcccg	6	5	13	17	8	1	0	1	0	0	0	2	1	2	0	5	2	1	2	5	2	1	1			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr2:38302357G>C	ENST00000260630.3	-	2	576	c.175C>G	c.(175-177)Ctg>Gtg	p.L59V	CYP1B1-AS1_ENST00000589303.1_RNA|CYP1B1_ENST00000494864.1_Intron|CYP1B1_ENST00000407341.1_Missense_Mutation_p.L59V|CYP1B1-AS1_ENST00000431999.1_RNA	NM_000104.3	NP_000095	Q16678	CP1B1_HUMAN	cytochrome P450, family 1, subfamily B, polypeptide 1	59					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)	TTTCCGATCAGTGGCCACGCA	0.721																																					p.L59V		Atlas-SNP	.											.	CYP1B1	39	.	0			c.C175G						PASS	.						8	10	9					2																	38302357		2147	4207	6354	SO:0001583	missense	1545	exon2			CGATCAGTGGCCA	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.175C>G	chr2.hg19:g.38302357G>C	ENSP00000260630:p.Leu59Val	18.0	0.0	.		12.0	6.0	.	NM_000104	Q5TZW8|Q93089|Q9H316	Missense_Mutation	SNP	ENST00000260630.3	hg19	CCDS1793.1	.	.	.	.	.	.	.	.	.	.	G	5.939	0.357214	0.11239	.	.	ENSG00000138061	ENST00000260630;ENST00000407341	T;T	0.69561	-0.41;-0.41	4.29	2.42	0.29668	.	0.389391	0.24269	N	0.040011	T	0.50292	0.1607	N	0.20574	0.59	0.26804	N	0.969141	B	0.27910	0.193	B	0.38378	0.272	T	0.41627	-0.9498	10	0.14656	T	0.56	.	7.627	0.28218	0.0953:0.1661:0.7386:0.0	.	59	Q53TK1	.	V	59	ENSP00000260630:L59V;ENSP00000384972:L59V	ENSP00000260630:L59V	L	-	1	2	CYP1B1	38155861	0.008000	0.16893	0.990000	0.47175	0.027000	0.11550	0.123000	0.15708	0.415000	0.25817	-0.479000	0.04858	CTG	.	.	.	none		0.721	CYP1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218580.3	NM_000104		C	38302357	G	C	38302357	3	2	133	1	0	0	0	0	1	0	0	0	4153	1020	36	4	1464	4	CYP1B1	2	38302357	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08		38302357	204897016	5	8199											
BCL2L11	10018	hgsc.bcm.edu	37	chr2	111921708	111921716	+	Splice_Site	DEL	AGGTATTTT	AGGTATTTT	-																															agctttccttttgttgtttcAggtatttttgaataattacc																								rs142125092		TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	AGGTATTTT	AGGTATTTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr2:111921708_111921716delAGGTATTTT	ENST00000393256.3	+	4	771_778	c.498_505delAGGTATTTT	c.(496-507)agaggtattttt>agtt	p.166_169RGIF>S	BCL2L11_ENST00000308659.8_Splice_Site_p.106_109RGIF>S	NM_001204106.1|NM_006538.4|NM_138621.4|NM_138627.3	NP_001191035.1|NP_006529.1|NP_619527.1|NP_619533.1	O43521	B2L11_HUMAN	BCL2-like 11 (apoptosis facilitator)	166					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|apoptotic signaling pathway (GO:0097190)|B cell apoptotic process (GO:0001783)|B cell homeostasis (GO:0001782)|brain development (GO:0007420)|cell-matrix adhesion (GO:0007160)|cellular process regulating host cell cycle in response to virus (GO:0060154)|developmental pigmentation (GO:0048066)|ear development (GO:0043583)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|kidney development (GO:0001822)|male gonad development (GO:0008584)|mammary gland development (GO:0030879)|myeloid cell homeostasis (GO:0002262)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic process by virus (GO:0060139)|positive regulation of cell cycle (GO:0045787)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902110)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein homooligomerization (GO:0032464)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|post-embryonic organ morphogenesis (GO:0048563)|regulation of developmental pigmentation (GO:0048070)|regulation of organ growth (GO:0046620)|response to endoplasmic reticulum stress (GO:0034976)|spermatogenesis (GO:0007283)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|thymocyte apoptotic process (GO:0070242)|thymus development (GO:0048538)|tube formation (GO:0035148)	BIM-BCL-2 complex (GO:0097141)|BIM-BCL-xl complex (GO:0097140)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|mitochondrial outer membrane (GO:0005741)				endometrium(4)|large_intestine(3)|lung(2)|prostate(2)	11						TTGTTGTTTCAGGTATTTTTGAATAATTA	0.445																																					p.167_168del		Atlas-INDEL	.											.	BCL2L11	36	.	0			c.499_504del						PASS	.																																			SO:0001630	splice_region_variant	10018	exon4			.	AF032458	CCDS2089.1, CCDS2092.1, CCDS42731.1, CCDS56131.1, CCDS56132.1, CCDS56133.1, CCDS56134.1, CCDS56135.1, CCDS56136.1, CCDS74560.1, CCDS74561.1, CCDS74559.1	2q13	2014-09-17			ENSG00000153094	ENSG00000153094			994	protein-coding gene	gene with protein product		603827				9731710, 9430630	Standard	NM_006538		Approved	BOD, BimL, BimEL, BimS, BIM	uc002tgv.1	O43521	OTTHUMG00000131256	ENST00000393256.3:c.499-1AGGTATTTT>-	chr2.hg19:g.111921708_111921716delAGGTATTTT		97.0	0.0	0		58.0	13.0	0.224138	NM_138621	A8K2W2|O43522|Q0MSE7|Q0MSE8|Q0MSE9|Q53R28|Q6JTU6|Q6T851|Q6TE14|Q6TE15|Q6TE16|Q6V402|Q8WYL6|Q8WYL7|Q8WYL8|Q8WYL9|Q8WYM0|Q8WYM1	In_Frame_Del	DEL	ENST00000393256.3	hg19	CCDS2089.1																																																																																			.	.	.	none		0.445	BCL2L11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254022.3		In_Frame_Del	-	111921716	AGGTATTTT	-	111921708	8	5	133	1	0	1	0	1	0	0	1	0	1369	202	7	0	636	0	BCL2L11	2	111921708	Splice_Site	DEL	AGGTATTTT	TCGA-BQ-7048-01A-11D-1961-08	73619351	111921708	131277665	6	8200											
WDR33	55339	hgsc.bcm.edu	37	chr2	128526506	128526506	+	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	tatgacacatcatgtacttaCatcattgtaataacctgcat	14	14	4	9	0	2	1	2	1	0	0	2	1	2	1	1	0	4	3	1	0	5	6			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr2:128526506C>A	ENST00000322313.4	-	3	432		c.e3+1		WDR33_ENST00000393006.1_Splice_Site|WDR33_ENST00000409658.3_Splice_Site	NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33						mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		CATGTACTTACATCATTGTAA	0.323																																					.		Atlas-SNP	.											.	WDR33	136	.	0			c.273+1G>T						PASS	.						138	126	130					2																	128526506		2203	4300	6503	SO:0001630	splice_region_variant	55339	exon4			TACTTACATCATT		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.273+1G>T	chr2.hg19:g.128526506C>A		142.0	0.0	.		126.0	48.0	.	NM_018383	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Splice_Site	SNP	ENST00000322313.4	hg19	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.530432	0.85706	.	.	ENSG00000136709	ENST00000322313;ENST00000436787;ENST00000393006;ENST00000409658;ENST00000408998	.	.	.	5.29	5.29	0.74685	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.8826	0.92362	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	WDR33	128242976	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	7.506000	0.81665	2.627000	0.88993	0.655000	0.94253	.	.	.	.	none		0.323	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383	Intron	A	128526506	C	A	128526506	5	1	133	1	0	0	0	0	0	0	1	0	17299	492	17	4	4225	4	WDR33	2	128526506	Splice_Site	SNP	C	TCGA-BQ-7048-01A-11D-1961-08	16604798	128526506	114672867	7	8201											
TRIP12	9320	hgsc.bcm.edu	37	chr2	230701700	230701702	+	Splice_Site	DEL	ACT	ACT	-																															cccaggccagagcctcgccgActacaacagaaaaatgtcat																										TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	ACT	ACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr2:230701700_230701702delACT	ENST00000283943.5	-	5	1186	c.1008delAGT	c.(1006-1008)aga>ag	p.R338del	TRIP12_ENST00000409677.1_Splice_Site_p.R380del|TRIP12_ENST00000543084.1_Intron|TRIP12_ENST00000389045.3_Splice_Site_p.R35del|TRIP12_ENST00000389044.4_Splice_Site_p.R380del	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	338					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		AGCCTCGCCGACTACAACAGAAA	0.483																																					p.336_337del		Atlas-INDEL	.											TRIP12,colon,carcinoma,0,1	TRIP12	207	.	0			c.1008_1009del						PASS	.																																			SO:0001630	splice_region_variant	9320	exon5			.	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.1008-1AGT>-	chr2.hg19:g.230701700_230701702delACT		54.0	0.0	0		47.0	23.0	0.489362	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Frame_Shift_Del	DEL	ENST00000283943.5	hg19	CCDS33391.1																																																																																			.	.	.	none		0.483	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238	In_Frame_Del	-	230701702	ACT	-	230701700	8	5	133	1	0	1	0	1	0	0	1	0	16568	289	10	0	5118	0	TRIP12	2	230701700	Splice_Site	DEL	ACT	TCGA-BQ-7048-01A-11D-1961-08	102175194	230701700	12497673	8	8202											
PRICKLE2	166336	hgsc.bcm.edu	37	chr3	64084893	64084893	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggggatgggttctcctaggAaatagccctcgttgtcagac	8	10	14	9	1	2	1	1	0	1	1	4	3	2	3	2	4	1	2	2	4	3	4			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr3:64084893A>G	ENST00000295902.6	-	8	2954	c.2369T>C	c.(2368-2370)tTc>tCc	p.F790S	RP11-129B22.1_ENST00000482609.1_RNA|PRICKLE2-AS1_ENST00000460946.1_RNA|PRICKLE2-AS1_ENST00000476308.1_RNA|PRICKLE2_ENST00000564377.1_Missense_Mutation_p.F846S	NM_198859.3	NP_942559.1	Q7Z3G6	PRIC2_HUMAN	prickle homolog 2 (Drosophila)	790					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)		TTCTCCTAGGAAATAGCCCTC	0.567																																					p.F790S		Atlas-SNP	.											.	PRICKLE2	88	.	0			c.T2369C						PASS	.						76	77	77					3																	64084893		2203	4300	6503	SO:0001583	missense	166336	exon8			CCTAGGAAATAGC	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.2369T>C	chr3.hg19:g.64084893A>G	ENSP00000295902:p.Phe790Ser	82.0	0.0	.		84.0	39.0	.	NM_198859	Q0VF44	Missense_Mutation	SNP	ENST00000295902.6	hg19	CCDS2902.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.039965	0.75732	.	.	ENSG00000163637	ENST00000295902	D	0.88046	-2.33	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.92004	0.7467	M	0.68317	2.08	0.80722	D	1	D	0.76494	0.999	D	0.63488	0.915	D	0.92874	0.6317	10	0.87932	D	0	-40.9764	15.8395	0.78835	1.0:0.0:0.0:0.0	.	790	Q7Z3G6	PRIC2_HUMAN	S	790	ENSP00000295902:F790S	ENSP00000295902:F790S	F	-	2	0	PRICKLE2	64059933	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.962000	0.93254	2.152000	0.67230	0.533000	0.62120	TTC	.	.	.	none		0.567	PRICKLE2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352219.1	NM_198859		G	64084893	A	G	64084893	3	3	133	1	0	0	0	0	1	0	0	0	12497	246	9	3	169	3	PRICKLE2	3	64084893	Missense_Mutation	SNP	A	TCGA-BQ-7048-01A-11D-1961-08		64084893	133937537	9	8203											
PLD1	5337	hgsc.bcm.edu	37	chr3	171394619	171394619	+	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	ggcgtggagtacctgtcaatGaaatctgcccgggtgcacca	9	8	13	11	2	2	1	1	1	1	0	2	2	2	2	3	3	3	2	3	3	3	1			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr3:171394619G>A	ENST00000351298.4	-	18	2127	c.2001C>T	c.(1999-2001)ttC>ttT	p.F667F	PLD1_ENST00000340989.4_Silent_p.F667F|PLD1_ENST00000342215.6_Missense_Mutation_p.S558L|PLD1_ENST00000356327.5_Silent_p.F629F	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific	667	Catalytic.				chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	ACCTGTCAATGAAATCTGCCC	0.542																																					p.F667F	NSCLC(149;2174 3517 34058)	Atlas-SNP	.											.	PLD1	134	.	0			c.C2001T						PASS	.						52	46	48					3																	171394619		2203	4300	6503	SO:0001819	synonymous_variant	5337	exon18			GTCAATGAAATCT	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.2001C>T	chr3.hg19:g.171394619G>A		39.0	0.0	.		47.0	19.0	.	NM_002662		Silent	SNP	ENST00000351298.4	hg19	CCDS3216.1	.	.	.	.	.	.	.	.	.	.	G	17.91	3.505561	0.64410	.	.	ENSG00000075651	ENST00000342215	T	0.34275	1.37	5.81	4.94	0.65067	.	.	.	.	.	T	0.46073	0.1374	.	.	.	0.28598	N	0.90932	.	.	.	.	.	.	T	0.42515	-0.9447	6	0.49607	T	0.09	-20.5851	14.4529	0.67397	0.0699:0.0:0.9301:0.0	.	.	.	.	L	558	ENSP00000339936:S558L	ENSP00000339936:S558L	S	-	2	0	PLD1	172877313	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.889000	0.56212	1.464000	0.47987	0.557000	0.71058	TCA	.	.	.	none		0.542	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662		A	171394619	G	A	171394619	2	1	133	1	0	0	0	0	0	0	0	1	12052	1281	45	2		2	PLD1	3	171394619	Silent	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	107309726	171394619	26627811	10	8204											
SEL1L3	23231	hgsc.bcm.edu	37	chr4	25806261	25806261	+	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	gcagctggaatccgtcagaaAggggacgatagagctaattt	13	8	13	7	2	1	2	1	0	0	2	2	5	2	4	1	3	2	3	1	3	4	3			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr4:25806261A>T	ENST00000399878.3	-	10	1800	c.1678T>A	c.(1678-1680)Ttt>Att	p.F560I	SEL1L3_ENST00000264868.5_Missense_Mutation_p.F525I|SEL1L3_ENST00000502949.1_Missense_Mutation_p.F407I	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	560						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						TCCGTCAGAAAGGGGACGATA	0.433																																					p.F560I		Atlas-SNP	.											.	SEL1L3	62	.	0			c.T1678A						PASS	.						93	89	90					4																	25806261		1896	4134	6030	SO:0001583	missense	23231	exon10			TCAGAAAGGGGAC	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.1678T>A	chr4.hg19:g.25806261A>T	ENSP00000382767:p.Phe560Ile	55.0	0.0	.		55.0	23.0	.	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Missense_Mutation	SNP	ENST00000399878.3	hg19	CCDS47037.1	.	.	.	.	.	.	.	.	.	.	A	12.90	2.076787	0.36662	.	.	ENSG00000091490	ENST00000399878;ENST00000264868;ENST00000502949	T;T;T	0.13538	2.79;2.8;2.58	6.02	2.18	0.27775	Tetratricopeptide-like helical (1);	0.882014	0.10506	N	0.666713	T	0.12732	0.0309	L	0.47716	1.5	0.26551	N	0.973918	B	0.19445	0.036	B	0.12837	0.008	T	0.35375	-0.9791	10	0.20519	T	0.43	-0.7039	10.2524	0.43377	0.7466:0.0:0.2534:0.0	.	560	Q68CR1	SE1L3_HUMAN	I	560;525;407	ENSP00000382767:F560I;ENSP00000264868:F525I;ENSP00000425438:F407I	ENSP00000264868:F525I	F	-	1	0	SEL1L3	25415359	0.998000	0.40836	0.775000	0.31657	0.911000	0.54048	2.508000	0.45450	0.151000	0.19162	0.533000	0.62120	TTT	.	.	.	none		0.433	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187		T	25806261	A	T	25806261	3	4	133	1	0	0	0	0	1	0	0	0	14025	72	3	5	1780	5	SEL1L3	4	25806261	Missense_Mutation	SNP	A	TCGA-BQ-7048-01A-11D-1961-08		25806261	165348015	11	8205											
C4orf39	152756	hgsc.bcm.edu	37	chr4	165878576	165878576	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accaccatcaggtcccagccTctttttgtgacaaggactag	10	10	8	13	0	2	1	1	1	1	0	3	2	3	2	4	2	1	0	4	2	2	3			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr4:165878576T>C	ENST00000513876.2	+	1	477	c.402T>C	c.(400-402)ccT>ccC	p.P134P	TRIM61_ENST00000329314.5_Intron	NM_153027.1	NP_694572.1	Q96MZ4	F218A_HUMAN	family with sequence similarity 218, member A	134																	GGTCCCAGCCTCTTTTTGTGA	0.572																																					p.P134P		Atlas-SNP	.											C4orf39,right_upper_lobe,carcinoma,0,1	.	.	.	0			c.T402C						PASS	.						73	74	74					4																	165878576		2203	4300	6503	SO:0001819	synonymous_variant	152756	exon1			CCAGCCTCTTTTT	AK056221	CCDS3807.1	4q32.3	2012-03-01	2012-03-01	2012-03-01	ENSG00000250486	ENSG00000250486			26466	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 39"	C4orf39		12477932	Standard	NM_153027		Approved	FLJ31659	uc003iqx.1	Q96MZ4	OTTHUMG00000161252	ENST00000513876.2:c.402T>C	chr4.hg19:g.165878576T>C		79.0	1.0	.		93.0	4.0	.	NM_153027		Silent	SNP	ENST00000513876.2	hg19	CCDS3807.1																																																																																			.	.	.	none		0.572	FAM218A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364308.1	NM_153027		C	165878576	T	C	165878576	2	2	133	1	0	0	0	0	0	0	0	1	2270	1538	54	3		3	C4orf39	4	165878576	Silent	SNP	T	TCGA-BQ-7048-01A-11D-1961-08	140072315	165878576	25275700	12	8206											
CTNND2	1501	hgsc.bcm.edu	37	chr5	11117619	11117619	+	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	atcacgtacagcaaggcatcCgtaagcccatcacactctct	12	8	6	15	2	3	0	2	0	1	0	5	0	4	0	2	1	3	4	2	1	3	2			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr5:11117619C>A	ENST00000304623.8	-	13	2409	c.2220G>T	c.(2218-2220)acG>acT	p.T740T	CTNND2_ENST00000458100.2_Silent_p.T307T|CTNND2_ENST00000503622.1_Silent_p.T403T|CTNND2_ENST00000359640.2_Silent_p.T740T|CTNND2_ENST00000511377.1_Silent_p.T649T|CTNND2_ENST00000495388.2_5'UTR	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	740					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.T740T(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						GCAAGGCATCCGTAAGCCCAT	0.507																																					p.T740T		Atlas-SNP	.											CTNND2,caecum,carcinoma,0,1	CTNND2	289	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2220T						PASS	.						215	174	188					5																	11117619		2203	4300	6503	SO:0001819	synonymous_variant	1501	exon13			GGCATCCGTAAGC	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.2220G>T	chr5.hg19:g.11117619C>A		205.0	1.0	.		198.0	9.0	.	NM_001332	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Silent	SNP	ENST00000304623.8	hg19	CCDS3881.1																																																																																			.	.	.	none		0.507	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332		A	11117619	C	A	11117619	2	1	133	1	0	0	0	0	0	0	0	1	4022	639	23	4		4	CTNND2	5	11117619	Silent	SNP	C	TCGA-BQ-7048-01A-11D-1961-08		11117619	169797641	13	8207											
TNPO1	3842	hgsc.bcm.edu	37	chr5	72151675	72151675	+	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	actttcagaacttcccaaatGgtgtaacagactttattaaa	15	13	5	8	0	1	2	1	0	0	2	2	2	2	2	1	1	2	1	1	1	6	6			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr5:72151675G>A	ENST00000337273.5	+	4	706	c.280G>A	c.(280-282)Ggt>Agt	p.G94S	TNPO1_ENST00000506351.2_Missense_Mutation_p.G86S|TNPO1_ENST00000454282.1_Intron|TNPO1_ENST00000513944.1_3'UTR|TNPO1_ENST00000523768.1_Intron|TNPO1_ENST00000447967.2_Missense_Mutation_p.G86S	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1	94	Importin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00115}.				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)		CTTCCCAAATGGTGTAACAGA	0.328																																					p.G94S		Atlas-SNP	.											TNPO1,colon,carcinoma,0,1	TNPO1	90	.	0			c.G280A						PASS	.						62	62	62					5																	72151675		2203	4297	6500	SO:0001583	missense	3842	exon4			CCAAATGGTGTAA	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.280G>A	chr5.hg19:g.72151675G>A	ENSP00000336712:p.Gly94Ser	95.0	0.0	.		81.0	20.0	.	NM_002270	B4DVC6|Q92957|Q92975	Missense_Mutation	SNP	ENST00000337273.5	hg19	CCDS43329.1	.	.	.	.	.	.	.	.	.	.	G	15.11	2.737401	0.49045	.	.	ENSG00000083312	ENST00000337273;ENST00000447967;ENST00000506351	T;T;T	0.65549	-0.16;-0.16;-0.16	4.89	4.89	0.63831	Armadillo-like helical (1);Armadillo-type fold (1);Importin-beta, N-terminal (3);	0.095869	0.64402	D	0.000001	T	0.43255	0.1239	N	0.10685	0.025	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.29852	-0.9998	10	0.18276	T	0.48	-2.9577	18.4554	0.90718	0.0:0.0:1.0:0.0	.	94	Q92973	TNPO1_HUMAN	S	94;86;86	ENSP00000336712:G94S;ENSP00000415164:G86S;ENSP00000425118:G86S	ENSP00000336712:G94S	G	+	1	0	TNPO1	72187431	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.320000	0.96346	2.430000	0.82344	0.650000	0.86243	GGT	.	.	.	none		0.328	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	NM_002270		A	72151675	G	A	72151675	3	1	133	1	0	0	0	0	1	0	0	0	16347	1348	47	2	294	2	TNPO1	5	72151675	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	61034056	72151675	108763585	14	8208											
FNIP1	96459	hgsc.bcm.edu	37	chr5	131007378	131007379	+	Frame_Shift_Del	DEL	CT	CT	-																															cagcaatttttttatctgaaCtctctttatccccatggggg																										TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr5:131007378_131007379delCT	ENST00000510461.1	-	14	2853_2854	c.2758_2759delAG	c.(2758-2760)agtfs	p.S921fs	FNIP1_ENST00000307968.7_Frame_Shift_Del_p.S893fs|CTC-432M15.3_ENST00000514667.1_Intron|FNIP1_ENST00000307954.8_Frame_Shift_Del_p.S876fs	NM_133372.2	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1	921					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)		TTTATCTGAACTCTCTTTATCC	0.416																																					p.920_920del		Atlas-INDEL	.											.	FNIP1	104	.	0			c.2759_2760del						PASS	.																																			SO:0001589	frameshift_variant	96459	exon14			.	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.2758_2759delAG	chr5.hg19:g.131007382_131007383delCT	ENSP00000421985:p.Ser921fs	139.0	0.0	0		144.0	61.0	0.423611	NM_133372	D6RJH5|Q86T47|Q9BUT0	Frame_Shift_Del	DEL	ENST00000510461.1	hg19	CCDS34227.1																																																																																			.	.	.	none		0.416	FNIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370077.1	NM_133372		-	131007379	CT	-	131007378	7	5	133	1	0	1	0	1	0	0	0	0	5982	565	20	0	761	0	FNIP1	5	131007378	Frame_Shift_Del	DEL	CT	TCGA-BQ-7048-01A-11D-1961-08	58855703	131007378	49907882	15	8209											
FGF1	2246	hgsc.bcm.edu	37	chr5	141974869	141974869	+	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	atctctttaatcagaagagaCtggcagggggagaaacaaga	16	7	12	6	0	2	4	1	0	1	4	3	6	2	4	0	3	1	1	0	3	4	2			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr5:141974869C>A	ENST00000359370.6	-	4	533	c.454G>T	c.(454-456)Gtc>Ttc	p.V152F	FGF1_ENST00000337706.2_Missense_Mutation_p.V152F|FGF1_ENST00000378046.1_Missense_Mutation_p.V152F|FGF1_ENST00000360966.5_3'UTR|AC005592.2_ENST00000414314.1_RNA|AC005592.2_ENST00000443800.1_RNA|FGF1_ENST00000407758.1_3'UTR|FGF1_ENST00000419524.2_Missense_Mutation_p.V152F|FGF1_ENST00000494579.1_5'UTR	NM_000800.4|NM_001144892.2|NM_001144934.1|NM_001144935.1|NM_001257205.1|NM_001257206.1|NM_001257207.1|NM_001257210.1|NM_001257212.1|NM_033137.2	NP_000791.1|NP_001138364.1|NP_001138406.1|NP_001138407.1|NP_001244134.1|NP_001244135.1|NP_001244136.1|NP_001244139.1|NP_001244141.1|NP_149128.1	P05230	FGF1_HUMAN	fibroblast growth factor 1 (acidic)	152					anatomical structure morphogenesis (GO:0009653)|angiogenesis (GO:0001525)|branch elongation involved in ureteric bud branching (GO:0060681)|cell differentiation (GO:0030154)|cellular response to heat (GO:0034605)|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)|mesonephric epithelium development (GO:0072163)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)	fibroblast growth factor receptor binding (GO:0005104)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|S100 protein binding (GO:0044548)			large_intestine(1)|lung(2)	3		all_neural(839;0.0416)|Ovarian(839;0.0955)|all_hematologic(541;0.1)|Prostate(461;0.157)|Lung NSC(810;0.21)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.00032)	Amlexanox(DB01025)|Pazopanib(DB06589)|Pentosan Polysulfate(DB00686)	TCAGAAGAGACTGGCAGGGGG	0.493																																					p.V152F		Atlas-SNP	.											.	FGF1	9	.	0			c.G454T						PASS	.						65	66	66					5																	141974869		2203	4300	6503	SO:0001583	missense	2246	exon4			AAGAGACTGGCAG	X59065	CCDS4275.1, CCDS4276.1	5q31.3-q33.2	2014-01-30			ENSG00000113578	ENSG00000113578		"Endogenous ligands"	3665	protein-coding gene	gene with protein product	"heparin-binding growth factor 1", "endothelial cell growth factor, alpha", "endothelial cell growth factor, beta"	131220		FGFA		1697263, 3523756	Standard	NM_033137		Approved	AFGF, ECGF, ECGFA, ECGFB, HBGF1, ECGF-beta, FGF-alpha, GLIO703	uc031slo.1	P05230	OTTHUMG00000059703	ENST00000359370.6:c.454G>T	chr5.hg19:g.141974869C>A	ENSP00000352329:p.Val152Phe	104.0	0.0	.		105.0	36.0	.	NM_001257209	B2R5T0|D3DQF2|P07502|Q16588	Missense_Mutation	SNP	ENST00000359370.6	hg19	CCDS4275.1	.	.	.	.	.	.	.	.	.	.	C	18.77	3.694692	0.68386	.	.	ENSG00000113578	ENST00000359370;ENST00000378046;ENST00000337706;ENST00000441680;ENST00000419524	T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87	5.87	5.87	0.94306	.	0.081539	0.51477	D	0.000089	T	0.58133	0.2101	M	0.80982	2.52	0.54753	D	0.999984	P;D	0.53745	0.465;0.962	B;P	0.48189	0.132;0.57	T	0.64495	-0.6394	10	0.87932	D	0	.	20.2084	0.98285	0.0:1.0:0.0:0.0	.	151;152	A8K147;P05230	.;FGF1_HUMAN	F	152	ENSP00000352329:V152F;ENSP00000367285:V152F;ENSP00000338548:V152F;ENSP00000404742:V152F;ENSP00000396195:V152F	ENSP00000338548:V152F	V	-	1	0	FGF1	141955053	0.996000	0.38824	0.940000	0.37924	0.841000	0.47740	4.573000	0.60893	2.774000	0.95407	0.650000	0.86243	GTC	.	.	.	none		0.493	FGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132735.2	NM_000800		A	141974869	C	A	141974869	3	1	133	1	0	0	0	0	1	0	0	0	5845	565	20	4	17	4	FGF1	5	141974869	Missense_Mutation	SNP	C	TCGA-BQ-7048-01A-11D-1961-08	10967491	141974869	38940391	16	8210											
XPO5	57510	hgsc.bcm.edu	37	chr6	43541219	43541219	+	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	tgtccaagagctccttacttGacaacgtgttccaggatctg	9	12	9	11	1	1	2	0	1	1	1	4	3	4	3	3	1	3	2	3	1	3	3			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr6:43541219G>C	ENST00000265351.7	-	2	435	c.225C>G	c.(223-225)gtC>gtG	p.V75V	POLH_ENST00000372236.4_5'Flank|POLH_ENST00000372226.1_5'Flank|POLH_ENST00000535400.1_5'Flank	NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	75	Necessary for interaction with Ran.				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)			CTCCTTACTTGACAACGTGTT	0.433																																					p.V75V		Atlas-SNP	.											.	XPO5	79	.	0			c.C225G						PASS	.						87	85	86					6																	43541219		1910	4111	6021	SO:0001819	synonymous_variant	57510	exon2			TTACTTGACAACG	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.225C>G	chr6.hg19:g.43541219G>C		84.0	0.0	.		433.0	223.0	.	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Silent	SNP	ENST00000265351.7	hg19	CCDS47430.1																																																																																			.	.	.	none		0.433	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750		C	43541219	G	C	43541219	2	2	133	1	0	0	0	0	0	0	0	1	17459	1277	45	4		4	XPO5	6	43541219	Silent	SNP	G	TCGA-BQ-7048-01A-11D-1961-08		43541219	127573848	17	8211											
LATS1	9113	hgsc.bcm.edu	37	chr6	150005370	150005370	+	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	gggacaggagagattcgggaGattacgtattccatgtttcc	10	11	13	7	2	0	2	0	0	0	2	3	6	2	4	2	3	1	2	2	3	2	5			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr6:150005370G>T	ENST00000543571.1	-	4	1402	c.855C>A	c.(853-855)atC>atA	p.I285I	LATS1_ENST00000253339.5_Silent_p.I285I|LATS1_ENST00000392273.3_Silent_p.I285I|LATS1_ENST00000542747.1_5'UTR	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1											central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		AGATTCGGGAGATTACGTATT	0.532																																					p.I285I		Atlas-SNP	.											.	LATS1	241	.	0			c.C855A						PASS	.						153	144	147					6																	150005370		2203	4300	6503	SO:0001819	synonymous_variant	9113	exon4			TCGGGAGATTACG	AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"LATS (large tumor suppressor, Drosophila) homolog 1", "LATS, large tumor suppressor, homolog 1 (Drosophila)"			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000543571.1:c.855C>A	chr6.hg19:g.150005370G>T		179.0	0.0	.		172.0	77.0	.	NM_001270519		Silent	SNP	ENST00000543571.1	hg19	CCDS34551.1																																																																																			.	.	.	none		0.532	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043923.4	NM_004690		T	150005370	G	T	150005370	2	4	133	1	0	0	0	0	0	0	0	1	8653	932	33	4		4	LATS1	6	150005370	Silent	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	106464151	150005370	21109697	18	8212											
ESR1	2099	hgsc.bcm.edu	37	chr6	152201893	152201893	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtaaatgctacgaagtgggAatgatgaaaggtggtaggta	14	9	15	3	2	0	2	0	2	0	0	0	4	0	3	0	4	2	4	0	4	8	4			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr6:152201893A>G	ENST00000206249.3	+	3	1109	c.747A>G	c.(745-747)ggA>ggG	p.G249G	ESR1_ENST00000440973.1_Silent_p.G249G|ESR1_ENST00000456483.2_Silent_p.G249G|ESR1_ENST00000406599.1_Intron|ESR1_ENST00000338799.5_Silent_p.G249G|ESR1_ENST00000427531.2_Silent_p.G76G|ESR1_ENST00000443427.1_Silent_p.G249G	NM_000125.3	NP_000116.2	P03372	ESR1_HUMAN	estrogen receptor 1	249	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)	ACGAAGTGGGAATGATGAAAG	0.547																																					p.G249G		Atlas-SNP	.											.	ESR1	94	.	0			c.A747G						PASS	.						50	50	50					6																	152201893		2203	4300	6503	SO:0001819	synonymous_variant	2099	exon3			AGTGGGAATGATG	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.747A>G	chr6.hg19:g.152201893A>G		52.0	0.0	.		41.0	13.0	.	NM_000125	Q13511|Q14276|Q5T5H7|Q6MZQ9|Q9NU51|Q9UDZ7|Q9UIS7	Silent	SNP	ENST00000206249.3	hg19	CCDS5234.1	.	.	.	.	.	.	.	.	.	.	A	9.711	1.157115	0.21454	.	.	ENSG00000091831	ENST00000427531	.	.	.	5.42	-10.8	0.00216	.	.	.	.	.	T	0.33089	0.0851	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58918	-0.7551	4	.	.	.	.	11.1314	0.48349	0.3958:0.3957:0.2085:0.0	.	.	.	.	G	154	.	.	E	+	2	0	ESR1	152243586	0.000000	0.05858	0.469000	0.27204	0.972000	0.66771	-2.223000	0.01214	-2.121000	0.00825	-1.074000	0.02243	GAA	.	.	.	none		0.547	ESR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043308.1			G	152201893	A	G	152201893	2	3	133	1	0	0	0	0	0	0	0	1	5258	233	9	3		3	ESR1	6	152201893	Silent	SNP	A	TCGA-BQ-7048-01A-11D-1961-08	2196523	152201893	18913174	19	8213											
MYCT1	80177	hgsc.bcm.edu	37	chr6	153043198	153043198	+	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	tttccatccctttctgcaatGtccaccacttcctgtggaaa	8	14	5	14	0	1	0	0	0	1	0	5	1	5	1	5	1	1	1	5	1	2	3			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr6:153043198G>T	ENST00000367245.5	+	2	526	c.518G>T	c.(517-519)tGt>tTt	p.C173F	MYCT1_ENST00000529453.1_Intron	NM_025107.2	NP_079383.2	Q8N699	MYCT1_HUMAN	myc target 1	173						nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	20		Ovarian(120;0.0654)		OV - Ovarian serous cystadenocarcinoma(155;1.33e-10)|BRCA - Breast invasive adenocarcinoma(81;0.143)		TTTCTGCAATGTCCACCACTT	0.498																																					p.C173F		Atlas-SNP	.											.	MYCT1	48	.	0			c.G518T						PASS	.						89	87	88					6																	153043198		2203	4300	6503	SO:0001583	missense	80177	exon2			TGCAATGTCCACC	AF527367	CCDS5239.1	6q25.1	2008-02-05			ENSG00000120279	ENSG00000120279			23172	protein-coding gene	gene with protein product						12477932	Standard	NM_025107		Approved	MTLC, FLJ21269	uc003qpc.4	Q8N699	OTTHUMG00000015850	ENST00000367245.5:c.518G>T	chr6.hg19:g.153043198G>T	ENSP00000356214:p.Cys173Phe	117.0	0.0	.		103.0	46.0	.	NM_025107	Q8N396|Q8TBE8|Q9H763	Missense_Mutation	SNP	ENST00000367245.5	hg19	CCDS5239.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.28|18.28	3.589712|3.589712	0.66105|0.66105	.|.	.|.	ENSG00000120279|ENSG00000120279	ENST00000367245|ENST00000532295	T|.	0.32753|.	1.44|.	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	0.364348|.	0.35838|.	N|.	0.002941|.	T|T	0.64875|0.64875	0.2638|0.2638	L|L	0.60455|0.60455	1.87|1.87	0.80722|0.80722	D|D	1|1	P;P|.	0.50617|.	0.937;0.853|.	P;P|.	0.49999|.	0.628;0.628|.	T|T	0.61907|0.61907	-0.6966|-0.6966	10|5	0.51188|.	T|.	0.08|.	-9.8469|-9.8469	16.985|16.985	0.86338|0.86338	0.0:0.1271:0.8729:0.0|0.0:0.1271:0.8729:0.0	.|.	125;173|.	D6Q1S4;Q8N699|.	.;MYCT1_HUMAN|.	F|F	173|154	ENSP00000356214:C173F|.	ENSP00000356214:C173F|.	C|V	+|+	2|1	0|0	MYCT1|MYCT1	153084891|153084891	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.964000|0.964000	0.63967|0.63967	5.162000|5.162000	0.64942|0.64942	2.727000|2.727000	0.93392|0.93392	0.579000|0.579000	0.79373|0.79373	TGT|GTC	.	.	.	none		0.498	MYCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042750.2	NM_025107		T	153043198	G	T	153043198	3	4	133	1	0	0	0	0	1	0	0	0	10029	1377	48	4	524	4	MYCT1	6	153043198	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	841305	153043198	18071869	20	8214											
TTLL2	83887	hgsc.bcm.edu	37	chr6	167755036	167755036	+	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	cagaccgtggcaaagctccaGatccccaagcaggcaacttt	12	6	9	14	1	0	2	0	0	0	2	2	2	2	2	4	2	3	4	4	2	3	1			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr6:167755036G>T	ENST00000239587.5	+	3	1736	c.1648G>T	c.(1648-1650)Gat>Tat	p.D550Y		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	550					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)		CAAAGCTCCAGATCCCCAAGC	0.502																																					p.D550Y		Atlas-SNP	.											.	TTLL2	82	.	0			c.G1648T						PASS	.						113	104	107					6																	167755036		2203	4300	6503	SO:0001583	missense	83887	exon3			GCTCCAGATCCCC	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.1648G>T	chr6.hg19:g.167755036G>T	ENSP00000239587:p.Asp550Tyr	142.0	0.0	.		135.0	51.0	.	NM_031949	B2RB11|B3KS77|Q7Z6R8|Q86X22	Missense_Mutation	SNP	ENST00000239587.5	hg19	CCDS5301.1	.	.	.	.	.	.	.	.	.	.	G	4.684	0.127134	0.08981	.	.	ENSG00000120440	ENST00000239587;ENST00000540954	T	0.02395	4.31	4.04	-7.0	0.01599	.	2.486670	0.01433	N	0.014832	T	0.00552	0.0018	N	0.14661	0.345	0.09310	N	1	B	0.23185	0.081	B	0.16722	0.016	T	0.45659	-0.9246	10	0.56958	D	0.05	.	3.3015	0.06984	0.368:0.3942:0.1298:0.108	.	550	Q9BWV7	TTLL2_HUMAN	Y	550;477	ENSP00000239587:D550Y	ENSP00000239587:D550Y	D	+	1	0	TTLL2	167675026	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	0.123000	0.15708	-1.248000	0.02503	0.491000	0.48974	GAT	.	.	.	none		0.502	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949		T	167755036	G	T	167755036	3	4	133	1	0	0	0	0	1	0	0	0	16739	942	33	4	1658	4	TTLL2	6	167755036	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	14711838	167755036	3360031	21	8215											
FOXK1	221937	hgsc.bcm.edu	37	chr7	4780549	4780549	+	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	agaagaggccccagcctcccCgctgcggccactgtaccccc	7	4	10	20	2	0	2	0	0	0	2	1	2	1	2	8	2	3	2	8	2	2	1			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr7:4780549C>A	ENST00000328914.4	+	2	641	c.641C>A	c.(640-642)cCg>cAg	p.P214Q	FOXK1_ENST00000446823.1_Missense_Mutation_p.P51Q	NM_001037165.1	NP_001032242.1			forkhead box K1									p.P40L(1)|p.P214L(1)|p.P40Q(1)|p.P214Q(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		CCAGCCTCCCCGCTGCGGCCA	0.647																																					p.P214Q		Atlas-SNP	.											KIAA0415_ENST00000450194,colon,carcinoma,0,2	FOXK1	64	.	4	Substitution - Missense(4)	large_intestine(2)|lung(2)	c.C641A						PASS	.						105	113	110					7																	4780549		2203	4300	6503	SO:0001583	missense	221937	exon2			CCTCCCCGCTGCG	BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916		"Forkhead boxes"	23480	protein-coding gene	gene with protein product						15202027	Standard	NM_001037165		Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000328914.4:c.641C>A	chr7.hg19:g.4780549C>A	ENSP00000328720:p.Pro214Gln	199.0	1.0	.		174.0	10.0	.	NM_001037165		Missense_Mutation	SNP	ENST00000328914.4	hg19	CCDS34591.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.240773	0.79912	.	.	ENSG00000164916	ENST00000446823;ENST00000328914;ENST00000545598	D;D	0.96136	-3.63;-3.92	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.97284	0.9112	M	0.68317	2.08	0.80722	D	1	D;D;P	0.89917	1.0;1.0;0.845	D;D;P	0.91635	0.999;0.995;0.513	D	0.97390	0.9988	10	0.51188	T	0.08	.	17.8708	0.88810	0.0:1.0:0.0:0.0	.	214;97;51	P85037;F5H8G8;P85037-2	FOXK1_HUMAN;.;.	Q	51;214;97	ENSP00000394442:P51Q;ENSP00000328720:P214Q	ENSP00000328720:P214Q	P	+	2	0	FOXK1	4747075	1.000000	0.71417	0.679000	0.29978	0.718000	0.41266	7.684000	0.84104	2.449000	0.82847	0.563000	0.77884	CCG	.	.	.	none		0.647	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2			A	4780549	C	A	4780549	3	1	133	1	0	0	0	0	1	0	0	0	6021	652	23	4	647	4	FOXK1	7	4780549	Missense_Mutation	SNP	C	TCGA-BQ-7048-01A-11D-1961-08		4780549	154358114	22	8216											
AUTS2	26053	hgsc.bcm.edu	37	chr7	70255838	70255838	+	Frame_Shift_Del	DEL	T	T	-																															ggactcctcaacaagaccccTccgacagcagcgctgagcgc																										TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr7:70255838delT	ENST00000342771.4	+	19	3957	c.3636delT	c.(3634-3636)cctfs	p.P1213fs	AUTS2_ENST00000406775.2_Frame_Shift_Del_p.P1189fs	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	1213										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)		ACAAGACCCCTCCGACAGCAG	0.677																																					p.P1212fs		Atlas-INDEL	.											.	AUTS2	173	.	0			c.3635delC						PASS	.						43	48	46					7																	70255838		2203	4299	6502	SO:0001589	frameshift_variant	26053	exon19			.	AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.3636delT	chr7.hg19:g.70255838delT	ENSP00000344087:p.Pro1213fs	45.0	0.0	0		45.0	13.0	0.288889	NM_015570	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Frame_Shift_Del	DEL	ENST00000342771.4	hg19	CCDS5539.1																																																																																			.	.	.	none		0.677	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			-	70255838	T	-	70255838	7	5	133	1	0	1	0	1	0	0	0	0	1225	1538	54	0	3855	0	AUTS2	7	70255838	Frame_Shift_Del	DEL	T	TCGA-BQ-7048-01A-11D-1961-08	65475289	70255838	88882825	23	8217											
TBL2	26608	hgsc.bcm.edu	37	chr7	72988278	72988278	+	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	cttgtcccacctgcagtcagGgctgaagcgcaccagggtgg	7	7	14	13	1	1	1	1	1	0	0	2	1	2	1	3	3	2	3	3	3	1	1			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr7:72988278G>A	ENST00000305632.5	-	3	677	c.436C>T	c.(436-438)Cct>Tct	p.P146S	TBL2_ENST00000459913.1_5'UTR|TBL2_ENST00000452475.1_Missense_Mutation_p.P146S|TBL2_ENST00000432538.1_Missense_Mutation_p.P110S	NM_012453.2	NP_036585.1	Q9Y4P3	TBL2_HUMAN	transducin (beta)-like 2	146							poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	19		Lung NSC(55;0.0659)|all_lung(88;0.152)				CTGCAGTCAGGGCTGAAGCGC	0.612																																					p.P146S		Atlas-SNP	.											.	TBL2	47	.	0			c.C436T						PASS	.						95	75	82					7																	72988278		2203	4300	6503	SO:0001583	missense	26608	exon3			AGTCAGGGCTGAA	AF056183	CCDS5551.1	7q11.23	2013-01-10			ENSG00000106638	ENSG00000106638		"WD repeat domain containing"	11586	protein-coding gene	gene with protein product	"Williams-Beuren syndrome chromosome region 13"	605842				9860302, 10575226	Standard	XM_006715923		Approved	WS-betaTRP, WBSCR13, DKFZP43N024	uc003tyh.3	Q9Y4P3	OTTHUMG00000023427	ENST00000305632.5:c.436C>T	chr7.hg19:g.72988278G>A	ENSP00000307260:p.Pro146Ser	110.0	0.0	.		89.0	27.0	.	NM_012453	Q9UQE2	Missense_Mutation	SNP	ENST00000305632.5	hg19	CCDS5551.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.841121	0.91197	.	.	ENSG00000106638	ENST00000305632;ENST00000541783;ENST00000432538;ENST00000452475	T;T;T	0.38077	1.16;1.16;1.16	5.3	5.3	0.74995	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.63803	0.2542	M	0.82323	2.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.66701	-0.5857	10	0.49607	T	0.09	-9.9847	16.4333	0.83861	0.0:0.0:1.0:0.0	.	110;146	E9PF19;Q9Y4P3	.;TBL2_HUMAN	S	146;146;110;146	ENSP00000307260:P146S;ENSP00000413979:P110S;ENSP00000407371:P146S	ENSP00000307260:P146S	P	-	1	0	TBL2	72626214	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.735000	0.98825	2.491000	0.84063	0.561000	0.74099	CCT	.	.	.	none		0.612	TBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252233.3	NM_012453		A	72988278	G	A	72988278	3	1	133	1	0	0	0	0	1	0	0	0	15654	1232	43	2	927	2	TBL2	7	72988278	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	2732440	72988278	86150385	24	8218											
MFHAS1	9258	hgsc.bcm.edu	37	chr8	8750559	8750559	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcaggttgccactgtccaTcccagccatggcggggcccc	5	8	11	17	1	1	0	1	0	0	0	3	0	3	0	6	4	2	1	6	4	0	2			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr8:8750559T>C	ENST00000276282.6	-	1	596	c.10A>G	c.(10-12)Atg>Gtg	p.M4V	RNU6-682P_ENST00000363843.1_RNA	NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	4										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)		CCACTGTCCATCCCAGCCATG	0.756																																					p.M4V	Melanoma(103;1201 2045 17515 28966)	Atlas-SNP	.											.	MFHAS1	58	.	0			c.A10G						PASS	.						3	3	3					8																	8750559		1577	3199	4776	SO:0001583	missense	9258	exon1			TGTCCATCCCAGC	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.10A>G	chr8.hg19:g.8750559T>C	ENSP00000276282:p.Met4Val	3.0	0.0	.		15.0	5.0	.	NM_004225	Q96CI0	Missense_Mutation	SNP	ENST00000276282.6	hg19	CCDS34844.1	.	.	.	.	.	.	.	.	.	.	T	12.24	1.878455	0.33162	.	.	ENSG00000147324	ENST00000276282	T	0.33216	1.42	3.87	2.66	0.31614	.	1.223050	0.06260	N	0.693747	T	0.17152	0.0412	N	0.08118	0	0.21105	N	0.99978	B	0.02656	0.0	B	0.01281	0.0	T	0.28744	-1.0034	10	0.23891	T	0.37	.	8.696	0.34296	0.0:0.0:0.1918:0.8082	.	4	Q9Y4C4	MFHA1_HUMAN	V	4	ENSP00000276282:M4V	ENSP00000276282:M4V	M	-	1	0	MFHAS1	8787969	0.980000	0.34600	0.977000	0.42913	0.611000	0.37282	2.561000	0.45905	0.513000	0.28278	0.369000	0.22263	ATG	.	.	.	none		0.756	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225		C	8750559	T	C	8750559	3	2	133	1	0	0	0	0	1	0	0	0	9528	1435	50	3	3160	3	MFHAS1	8	8750559	Missense_Mutation	SNP	T	TCGA-BQ-7048-01A-11D-1961-08		8750559	137613463	25	8219											
MTUS1	57509	hgsc.bcm.edu	37	chr8	17581310	17581310	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctaggcaaattcacccatgAcgactgtgcagttttcaagg	11	11	9	10	1	3	1	2	1	1	0	3	2	3	1	1	2	1	3	1	2	3	4			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr8:17581310A>G	ENST00000262102.6	-	4	2544	c.2320T>C	c.(2320-2322)Tca>Cca	p.S774P	MTUS1_ENST00000381869.3_Intron|MTUS1_ENST00000544260.1_5'Flank|MTUS1_ENST00000381861.3_5'Flank|MTUS1_ENST00000519263.1_Intron	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	774					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)		TTCACCCATGACGACTGTGCA	0.463																																					p.S774P		Atlas-SNP	.											.	MTUS1	144	.	0			c.T2320C						PASS	.						152	141	144					8																	17581310		1865	4099	5964	SO:0001583	missense	57509	exon4			CCCATGACGACTG	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.2320T>C	chr8.hg19:g.17581310A>G	ENSP00000262102:p.Ser774Pro	235.0	1.0	.		137.0	59.0	.	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	hg19	CCDS43717.1	.	.	.	.	.	.	.	.	.	.	A	15.94	2.980872	0.53827	.	.	ENSG00000129422	ENST00000262102	T	0.42900	0.96	3.8	3.8	0.43715	.	2.627820	0.01895	N	0.038843	T	0.55081	0.1898	L	0.32530	0.975	0.53688	D	0.999979	D	0.69078	0.997	D	0.64410	0.925	T	0.44528	-0.9322	10	0.29301	T	0.29	-2.2162	12.137	0.53977	1.0:0.0:0.0:0.0	.	774	Q9ULD2	MTUS1_HUMAN	P	774	ENSP00000262102:S774P	ENSP00000262102:S774P	S	-	1	0	MTUS1	17625590	0.099000	0.21834	0.064000	0.19789	0.885000	0.51271	2.939000	0.48995	1.933000	0.56026	0.533000	0.62120	TCA	.	.	.	none		0.463	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		G	17581310	A	G	17581310	3	3	133	1	0	0	0	0	1	0	0	0	9972	275	10	3	1859	3	MTUS1	8	17581310	Missense_Mutation	SNP	A	TCGA-BQ-7048-01A-11D-1961-08	8830751	17581310	128782712	26	8220											
CLTA	1211	hgsc.bcm.edu	37	chr9	36211662	36211662	+	Frame_Shift_Del	DEL	G	G	-																															cccaggcactgagtgggaacGggtggcccggctgtgtgact																								rs192679731		TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr9:36211662delG	ENST00000242285.6	+	7	758	c.638delG	c.(637-639)cggfs	p.R213fs	CLTA_ENST00000345519.5_Frame_Shift_Del_p.R183fs|CLTA_ENST00000538225.1_Frame_Shift_Del_p.R195fs|CLTA_ENST00000433436.2_Frame_Shift_Del_p.R213fs|CLTA_ENST00000470744.1_Frame_Shift_Del_p.R195fs|CLTA_ENST00000466396.1_Frame_Shift_Del_p.R161fs|CLTA_ENST00000540080.1_Frame_Shift_Del_p.R131fs|CLTA_ENST00000396603.2_Frame_Shift_Del_p.R201fs			P09496	CLCA_HUMAN	clathrin, light chain A	213					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)			GAGTGGGAACGGGTGGCCCGG	0.542																																					p.R213fs		Atlas-INDEL	.											CLTA,NS,carcinoma,0,1	CLTA	18	.	0			c.637delC						PASS	.						99	94	96					9																	36211662		2203	4300	6503	SO:0001589	frameshift_variant	1211	exon7			.		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.638delG	chr9.hg19:g.36211662delG	ENSP00000242285:p.Arg213fs	153.0	0.0	0		111.0	41.0	0.369369	NM_007096	A8K4W3|B4DIN1|F5H6N3|Q2XPN5|Q53XZ1	Frame_Shift_Del	DEL	ENST00000242285.6	hg19	CCDS6601.1																																																																																			.	.	.	none		0.542	CLTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052405.1	NM_007096		-	36211662	G	-	36211662	7	5	133	1	0	1	0	1	0	0	0	0	3566	1116	39	0	664	0	CLTA	9	36211662	Frame_Shift_Del	DEL	G	TCGA-BQ-7048-01A-11D-1961-08		36211662	105001769	27	8221											
TGFBR1	7046	hgsc.bcm.edu	37	chr9	101894937	101894937	+	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	gagtgccaaatgaagaggacCcttcattagatcgccctttt	11	11	9	10	1	1	3	1	1	0	2	2	5	1	4	3	1	1	0	3	1	3	4			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr9:101894937C>G	ENST00000374994.4	+	3	607	c.490C>G	c.(490-492)Cct>Gct	p.P164A	TGFBR1_ENST00000550253.1_Missense_Mutation_p.P95A|TGFBR1_ENST00000374990.2_Intron|TGFBR1_ENST00000552516.1_Missense_Mutation_p.P168A	NM_004612.2	NP_004603.1	P36897	TGFR1_HUMAN	transforming growth factor, beta receptor 1	164					activation of MAPKK activity (GO:0000186)|angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|artery morphogenesis (GO:0048844)|blastocyst development (GO:0001824)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen fibril organization (GO:0030199)|embryonic cranial skeleton morphogenesis (GO:0048701)|endothelial cell migration (GO:0043542)|epithelial to mesenchymal transition (GO:0001837)|extracellular structure organization (GO:0043062)|germ cell migration (GO:0008354)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|mesenchymal cell differentiation (GO:0048762)|negative regulation of apoptotic process (GO:0043066)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|parathyroid gland development (GO:0060017)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|pharyngeal system development (GO:0060037)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of protein binding (GO:0043393)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|response to cholesterol (GO:0070723)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|thymus development (GO:0048538)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	endosome (GO:0005768)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|tight junction (GO:0005923)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	ATP binding (GO:0005524)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transforming growth factor beta-activated receptor activity (GO:0005024)|type II transforming growth factor beta receptor binding (GO:0005114)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	27		Acute lymphoblastic leukemia(62;0.0559)				TGAAGAGGACCCTTCATTAGA	0.438																																					p.P164A		Atlas-SNP	.											.	TGFBR1	70	.	0			c.C490G						PASS	.						160	135	144					9																	101894937		2203	4300	6503	SO:0001583	missense	7046	exon3			GAGGACCCTTCAT		CCDS6738.1, CCDS47998.1	9q22	2014-01-30	2008-07-31		ENSG00000106799	ENSG00000106799			11772	protein-coding gene	gene with protein product	"activin A receptor type II-like kinase, 53kDa"	190181	"transforming growth factor, beta receptor I (activin A receptor type II-like kinase, 53kD)", "multiple self-healing squamous epithelioma"	MSSE, ESS1		1319842, 8530052, 21358634	Standard	NM_001130916		Approved	ALK-5, ACVRLK4	uc004azc.3	P36897	OTTHUMG00000020353	ENST00000374994.4:c.490C>G	chr9.hg19:g.101894937C>G	ENSP00000364133:p.Pro164Ala	161.0	0.0	.		137.0	43.0	.	NM_004612	Q6IR47|Q706C0|Q706C1	Missense_Mutation	SNP	ENST00000374994.4	hg19	CCDS6738.1	.	.	.	.	.	.	.	.	.	.	C	15.54	2.864541	0.51482	.	.	ENSG00000106799	ENST00000547314;ENST00000552573;ENST00000374994;ENST00000540092;ENST00000552516;ENST00000548365;ENST00000550253;ENST00000546584	T;T;T;T;T;T;T	0.70282	-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.68495	0.3007	L	0.58583	1.82	0.80722	D	1	B	0.28850	0.225	B	0.31290	0.127	T	0.63310	-0.6666	10	0.11182	T	0.66	.	19.3122	0.94192	0.0:1.0:0.0:0.0	.	164	P36897	TGFR1_HUMAN	A	95;99;164;164;168;99;95;161	ENSP00000449934:P95A;ENSP00000447182:P99A;ENSP00000364133:P164A;ENSP00000447297:P168A;ENSP00000448518:P99A;ENSP00000450052:P95A;ENSP00000447707:P161A	ENSP00000364133:P164A	P	+	1	0	TGFBR1	100934758	1.000000	0.71417	0.993000	0.49108	0.981000	0.71138	7.818000	0.86416	2.865000	0.98341	0.655000	0.94253	CCT	.	.	.	none		0.438	TGFBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053390.3			G	101894937	C	G	101894937	3	3	133	1	0	0	0	0	1	0	0	0	15833	623	22	4	500	4	TGFBR1	9	101894937	Missense_Mutation	SNP	C	TCGA-BQ-7048-01A-11D-1961-08	65683275	101894937	39318494	28	8222											
ANK3	288	hgsc.bcm.edu	37	chr10	61829643	61829643	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctagattggtttctacagTggtgtcccctgactgtggct	5	15	11	10	0	2	2	0	1	2	1	3	2	3	2	2	3	1	2	2	3	2	4			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr10:61829643T>C	ENST00000280772.2	-	37	11187	c.10996A>G	c.(10996-10998)Act>Gct	p.T3666A	ANK3_ENST00000503366.1_Intron|ANK3_ENST00000373827.2_Intron|ANK3_ENST00000355288.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3666					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						GTTTCTACAGTGGTGTCCCCT	0.532																																					p.T3666A		Atlas-SNP	.											.	ANK3	703	.	0			c.A10996G						PASS	.						105	110	108					10																	61829643		2203	4300	6503	SO:0001583	missense	288	exon37			CTACAGTGGTGTC	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.10996A>G	chr10.hg19:g.61829643T>C	ENSP00000280772:p.Thr3666Ala	70.0	0.0	.		69.0	32.0	.	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	hg19	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	T	7.641	0.680808	0.14907	.	.	ENSG00000151150	ENST00000280772	T	0.18016	2.24	5.67	1.95	0.26073	.	0.170468	0.27831	N	0.017678	T	0.09730	0.0239	L	0.27053	0.805	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16748	-1.0392	10	0.41790	T	0.15	.	4.0495	0.09788	0.2679:0.1431:0.0:0.589	.	3666	Q12955	ANK3_HUMAN	A	3666	ENSP00000280772:T3666A	ENSP00000280772:T3666A	T	-	1	0	ANK3	61499649	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.468000	0.35332	0.366000	0.24427	0.533000	0.62120	ACT	.	.	.	none		0.532	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		C	61829643	T	C	61829643	3	2	133	1	0	0	0	0	1	0	0	0	622	1696	59	3	2478	3	ANK3	10	61829643	Missense_Mutation	SNP	T	TCGA-BQ-7048-01A-11D-1961-08		61829643	73705104	29	8223											
SFTPD	6441	hgsc.bcm.edu	37	chr10	81702148	81702148	+	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	cagaccagccacctacctttGggcccagcttctccttttgg	6	11	8	16	0	1	1	0	0	1	1	2	1	1	1	6	2	3	1	6	2	1	5	rs2077117		TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr10:81702148G>C	ENST00000372292.3	-	4	469	c.429C>G	c.(427-429)ccC>ccG	p.P143P		NM_003019.4	NP_003010.4	P35247	SFTPD_HUMAN	surfactant protein D	143	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)			ACCTACCTTTGGGCCCAGCTT	0.607																																					p.P143P		Atlas-SNP	.											.	SFTPD	43	.	0			c.C429G						PASS	.						82	75	77					10																	81702148		2203	4300	6503	SO:0001819	synonymous_variant	6441	exon4			ACCTTTGGGCCCA	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.429C>G	chr10.hg19:g.81702148G>C		74.0	0.0	.		59.0	22.0	.	NM_003019	Q5T0M3|Q6FH08|Q86YK9|Q8TCD8|Q9UCJ2|Q9UCJ3	Silent	SNP	ENST00000372292.3	hg19	CCDS7362.1																																																																																			.	.	.	alt		0.607	SFTPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049011.1			C	81702148	G	C	81702148	2	2	133	1	0	0	0	0	0	0	0	1	14206	1335	47	4		4	SFTPD	10	81702148	Silent	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	19872505	81702148	53832599	30	8224											
CALHM2	51063	hgsc.bcm.edu	37	chr10	105209181	105209181	+	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	gcctgcggctgacctcctccCggaagtctgacaggttgtca	6	9	12	14	2	2	2	1	2	1	0	4	3	4	3	4	3	1	2	4	3	1	1			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr10:105209181C>A	ENST00000260743.5	-	3	1041	c.518G>T	c.(517-519)cGg>cTg	p.R173L	CALHM2_ENST00000393235.1_Missense_Mutation_p.R173L|RP11-225H22.7_ENST00000608063.1_RNA|CALHM2_ENST00000369788.3_Missense_Mutation_p.R173L|CALHM2_ENST00000494180.1_5'Flank	NM_015916.4	NP_057000.2	Q9HA72	CAHM2_HUMAN	calcium homeostasis modulator 2	173					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						GACCTCCTCCCGGAAGTCTGA	0.602																																					p.R173L		Atlas-SNP	.											CALHM2,NS,carcinoma,0,1	CALHM2	30	.	0			c.G518T						PASS	.						63	65	64					10																	105209181		2202	4298	6500	SO:0001583	missense	51063	exon3			TCCTCCCGGAAGT	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.518G>T	chr10.hg19:g.105209181C>A	ENSP00000260743:p.Arg173Leu	110.0	0.0	.		111.0	8.0	.	NM_015916	D3DR94|O95893|Q6ZUV9	Missense_Mutation	SNP	ENST00000260743.5	hg19	CCDS7549.1	.	.	.	.	.	.	.	.	.	.	C	14.73	2.623943	0.46840	.	.	ENSG00000138172	ENST00000369788;ENST00000260743;ENST00000393235	T;T;T	0.19394	2.15;2.15;2.15	5.45	2.22	0.28083	.	0.419984	0.23239	N	0.050361	T	0.19287	0.0463	L	0.56199	1.76	0.30873	N	0.732274	P;B;B	0.37573	0.6;0.312;0.267	B;B;B	0.37304	0.193;0.103;0.246	T	0.11842	-1.0571	10	0.56958	D	0.05	-35.5257	7.6922	0.28575	0.0:0.5628:0.0:0.4372	.	173;173;173	Q9HA72-2;Q9HA72-3;Q9HA72	.;.;CAHM2_HUMAN	L	173	ENSP00000358803:R173L;ENSP00000260743:R173L;ENSP00000376927:R173L	ENSP00000260743:R173L	R	-	2	0	CALHM2	105199171	0.974000	0.33945	1.000000	0.80357	0.887000	0.51463	0.723000	0.25939	0.689000	0.31550	-0.215000	0.12644	CGG	.	.	.	none		0.602	CALHM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050159.1	NM_015916		A	105209181	C	A	105209181	3	1	133	1	0	0	0	0	1	0	0	0	2585	652	23	4	461	4	CALHM2	10	105209181	Missense_Mutation	SNP	C	TCGA-BQ-7048-01A-11D-1961-08	23507033	105209181	30325566	31	8225											
ADD3	120	hgsc.bcm.edu	37	chr10	111878343	111878343	+	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	atgtccttctgattttttccAggtgaaagtcaatataatag	12	16	7	6	0	2	2	1	2	1	0	4	2	4	2	2	1	0	0	2	1	5	7			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr10:111878343A>G	ENST00000356080.4	+	6	934		c.e6-1		ADD3_ENST00000497125.1_Splice_Site|ADD3_ENST00000360162.3_Splice_Site|ADD3_ENST00000277900.8_Splice_Site	NM_016824.3	NP_058432.1	Q9UEY8	ADDG_HUMAN	adducin 3 (gamma)							cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	29		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)		GATTTTTTCCAGGTGAAAGTC	0.378																																					.		Atlas-SNP	.											.	ADD3	89	.	0			c.568-2A>G						PASS	.						102	104	103					10																	111878343		2203	4300	6503	SO:0001630	splice_region_variant	120	exon6			TTTTCCAGGTGAA	U37122	CCDS7561.1, CCDS7562.1	10q25.2	2005-11-08			ENSG00000148700	ENSG00000148700			245	protein-coding gene	gene with protein product		601568		ADDL		8893809	Standard	XM_005269529		Approved		uc001kyv.3	Q9UEY8	OTTHUMG00000019032	ENST00000356080.4:c.568-1A>G	chr10.hg19:g.111878343A>G		102.0	0.0	.		82.0	35.0	.	NM_019903	D3DRA8|O43243|Q5VU09|Q92773|Q9UEY7	Splice_Site	SNP	ENST00000356080.4	hg19	CCDS7561.1	.	.	.	.	.	.	.	.	.	.	A	16.87	3.241968	0.58995	.	.	ENSG00000148700	ENST00000360162;ENST00000356080;ENST00000277900	.	.	.	5.28	4.11	0.48088	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8604	0.52463	0.8691:0.0:0.0:0.1309	.	.	.	.	.	-1	.	.	.	+	.	.	ADD3	111868333	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	7.423000	0.80229	0.905000	0.36596	0.460000	0.39030	.	.	.	.	none		0.378	ADD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050289.1	NM_019903	Intron	G	111878343	A	G	111878343	5	3	133	1	0	0	0	0	0	0	1	0	306	202	7	3	584	3	ADD3	10	111878343	Splice_Site	SNP	A	TCGA-BQ-7048-01A-11D-1961-08	6669162	111878343	23656404	32	8226											
MICALCL	84953	hgsc.bcm.edu	37	chr11	12316190	12316190	+	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	tcctccctcagactcaaagaCaaatcttttgagagtttcct	11	13	5	12	0	3	3	2	1	1	3	6	4	6	3	3	0	0	1	3	0	2	3			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr11:12316190C>T	ENST00000256186.2	+	3	1503	c.1212C>T	c.(1210-1212)gaC>gaT	p.D404D		NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	404					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)		GACTCAAAGACAAATCTTTTG	0.468																																					p.D404D		Atlas-SNP	.											.	MICALCL	59	.	0			c.C1212T						PASS	.						121	123	122					11																	12316190		1848	4097	5945	SO:0001819	synonymous_variant	84953	exon3			CAAAGACAAATCT	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.1212C>T	chr11.hg19:g.12316190C>T		238.0	0.0	.		181.0	65.0	.	NM_032867	Q7RTP7|Q96JU6	Silent	SNP	ENST00000256186.2	hg19	CCDS41620.1																																																																																			.	.	.	none		0.468	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1	NM_032867		T	12316190	C	T	12316190	2	4	133	1	0	0	0	0	0	0	0	1	9579	477	17	2		2	MICALCL	11	12316190	Silent	SNP	C	TCGA-BQ-7048-01A-11D-1961-08		12316190	122690326	33	8227											
OR8U8	219417	hgsc.bcm.edu	37	chr11	56143937	56143937	+	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	tggcctctgtcttctacacaGtgatcattcccatgttgaat	8	15	7	11	0	4	2	1	2	3	0	5	2	5	2	2	1	1	1	2	1	2	4			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr11:56143937G>C	ENST00000302270.1	+	1	838	c.838G>C	c.(838-840)Gtg>Ctg	p.V280L		NM_001005204.1	NP_001005204.1	Q8NH10	OR8U1_HUMAN	olfactory receptor, family 8, subfamily U, member 1	280						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)					CTTCTACACAGTGATCATTCC	0.413																																					p.V280L		Atlas-SNP	.											.	OR8U1	59	.	0			c.G838C						PASS	.						143	148	146					11																	56143937		2044	4227	6271	SO:0001583	missense	219417	exon1			TACACAGTGATCA	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.838G>C	chr11.hg19:g.56143937G>C	ENSP00000304188:p.Val280Leu	337.0	0.0	.		303.0	13.0	.	NM_001005204		Missense_Mutation	SNP	ENST00000302270.1	hg19	CCDS41647.1	.	.	.	.	.	.	.	.	.	.	G	0.050	-1.254672	0.01457	.	.	ENSG00000172199	ENST00000302270	T	0.00279	8.33	5.69	2.69	0.31865	GPCR, rhodopsin-like superfamily (1);	0.174841	0.27411	N	0.019484	T	0.00178	0.0005	N	0.21448	0.665	0.09310	N	1	B	0.28933	0.228	B	0.41666	0.363	T	0.23940	-1.0174	10	0.11794	T	0.64	.	7.9511	0.30014	0.1954:0.1192:0.6855:0.0	.	280	Q8NH10	OR8U1_HUMAN	L	280	ENSP00000304188:V280L	ENSP00000304188:V280L	V	+	1	0	OR8U1	55900513	0.061000	0.20836	0.998000	0.56505	0.181000	0.23173	0.606000	0.24194	1.425000	0.47237	-0.245000	0.11935	GTG	.	.	.	none		0.413	OR8U1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391607.1	NM_001005204		C	56143937	G	C	56143937	3	2	133	1	0	0	0	0	1	0	0	0	11254	1029	36	4	32	4	OR8U8	11	56143937	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	43827747	56143937	78862579	34	8228											
C1QTNF5	114902	hgsc.bcm.edu	37	chr11	119210071	119210071	+	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	actggggagctgtgccagtcGgagtacaccagaaatccgga	11	6	14	10	2	0	1	0	0	0	1	2	4	1	4	3	4	3	2	3	4	2	1			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr11:119210071G>C	ENST00000528368.1	-	3	933	c.702C>G	c.(700-702)tcC>tcG	p.S234S	C1QTNF5_ENST00000445041.2_Silent_p.S234S|RP11-334E6.10_ENST00000501918.2_RNA|MFRP_ENST00000555262.1_3'UTR|MFRP_ENST00000530681.1_3'UTR|C1QTNF5_ENST00000525657.1_5'UTR	NM_001278431.1	NP_001265360.1	Q9BXJ0	C1QT5_HUMAN	C1q and tumor necrosis factor related protein 5	234	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.					collagen trimer (GO:0005581)|extracellular vesicular exosome (GO:0070062)				endometrium(1)|lung(2)	3		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.78e-05)		TGTGCCAGTCGGAGTACACCA	0.552																																					p.S234S		Atlas-SNP	.											.	C1QTNF5	12	.	0			c.C702G						PASS	.						100	93	96					11																	119210071		2199	4295	6494	SO:0001819	synonymous_variant	114902	exon15			CCAGTCGGAGTAC	AF329841	CCDS8420.1	11q23.3	2013-05-10				ENSG00000223953			14344	protein-coding gene	gene with protein product	"complement-c1q tumor necrosis factor-related protein 5", "complement C1q tumor necrosis factor-related protein 5 precursor variant 3"	608752				12944416	Standard	NM_015645		Approved	CTRP5, DKFZp586B0621, LORD		Q9BXJ0	OTTHUMG00000166198	ENST00000528368.1:c.702C>G	chr11.hg19:g.119210071G>C		79.0	0.0	.		75.0	26.0	.	NM_015645	A6NDD3|B0YJ35|Q335M2|Q8N6P2|Q9UFX4	Silent	SNP	ENST00000528368.1	hg19	CCDS8420.1																																																																																			.	.	.	none		0.552	C1QTNF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388354.1	NM_015645		C	119210071	G	C	119210071	2	2	133	1	0	0	0	0	0	0	0	1	1968	1103	39	4		4	C1QTNF5	11	119210071	Silent	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	63066134	119210071	15796445	35	8229											
LRP6	4040	hgsc.bcm.edu	37	chr12	12302076	12302076	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcggaactgagctcacaacCacagtaaagccctagggaaa	15	5	9	12	1	1	1	1	1	0	0	2	3	1	3	2	2	4	2	2	2	6	2			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr12:12302076C>T	ENST00000261349.4	-	14	3082	c.3006G>A	c.(3004-3006)gtG>gtA	p.V1002V	LRP6_ENST00000543091.1_Silent_p.V1002V	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1002	Beta-propeller 4.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				AGCTCACAACCACAGTAAAGC	0.453																																					p.V1002V		Atlas-SNP	.											.	LRP6	170	.	0			c.G3006A						PASS	.						135	137	136					12																	12302076		2203	4300	6503	SO:0001819	synonymous_variant	4040	exon14			CACAACCACAGTA	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.3006G>A	chr12.hg19:g.12302076C>T		282.0	0.0	.		262.0	115.0	.	NM_002336	Q17RZ2	Silent	SNP	ENST00000261349.4	hg19	CCDS8647.1																																																																																			.	.	.	none		0.453	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			T	12302076	C	T	12302076	2	4	133	1	0	0	0	0	0	0	0	1	8969	581	21	2		2	LRP6	12	12302076	Silent	SNP	C	TCGA-BQ-7048-01A-11D-1961-08		12302076	121549819	36	8230											
C12orf54	121273	hgsc.bcm.edu	37	chr12	48888593	48888593	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcacagaagcataaggccTccagattccttgatgacccc	11	8	9	13	0	0	4	0	2	0	2	2	4	2	4	5	2	1	2	5	2	2	3			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr12:48888593T>C	ENST00000548364.1	+	7	312	c.255T>C	c.(253-255)ccT>ccC	p.P85P	RP11-722P11.4_ENST00000551847.1_RNA|C12orf54_ENST00000314014.2_Silent_p.P85P			Q6X4T0	CL054_HUMAN	chromosome 12 open reading frame 54	85										endometrium(1)|large_intestine(4)	5						GCATAAGGCCTCCAGATTCCT	0.488																																					p.P85P		Atlas-SNP	.											.	C12orf54	11	.	0			c.T255C						PASS	.						114	116	116					12																	48888593		2203	4300	6503	SO:0001819	synonymous_variant	121273	exon8			AAGGCCTCCAGAT	BC031670	CCDS8764.1	12q13.11	2011-01-31			ENSG00000177627	ENSG00000177627			28553	protein-coding gene	gene with protein product						12477932	Standard	NM_152319		Approved	MGC35033	uc001rrr.3	Q6X4T0	OTTHUMG00000170019	ENST00000548364.1:c.255T>C	chr12.hg19:g.48888593T>C		186.0	0.0	.		183.0	75.0	.	NM_152319	Q6X4S9|Q8N5S2	Silent	SNP	ENST00000548364.1	hg19	CCDS8764.1																																																																																			.	.	.	none		0.488	C12orf54-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406875.1	NM_152319		C	48888593	T	C	48888593	2	2	133	1	0	0	0	0	0	0	0	1	1701	1538	54	3		3	C12orf54	12	48888593	Silent	SNP	T	TCGA-BQ-7048-01A-11D-1961-08	36586517	48888593	84963302	37	8231											
MLL2	8085	hgsc.bcm.edu	37	chr12	49437679	49437679	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcagggaacatgtcctccAgtttgctcttcttgcgccct	7	12	9	13	1	2	0	0	0	2	0	4	1	4	1	3	1	4	3	3	1	2	3			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr12:49437679A>G	ENST00000301067.7	-	22	5290	c.5291T>C	c.(5290-5292)cTg>cCg	p.L1764P		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1764					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)										CATGTCCTCCAGTTTGCTCTT	0.567											OREG0021780	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L1764P		Atlas-SNP	.											.	MLL2	1173	.	0			c.T5291C						PASS	.						166	177	174					12																	49437679		2147	4242	6389	SO:0001583	missense	8085	exon22			TCCTCCAGTTTGC	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.5291T>C	chr12.hg19:g.49437679A>G	ENSP00000301067:p.Leu1764Pro	147.0	0.0	.	962	119.0	38.0	.	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	A	14.19	2.462524	0.43736	.	.	ENSG00000167548	ENST00000301067	D	0.92199	-2.99	4.93	4.93	0.64822	.	.	.	.	.	D	0.94925	0.8359	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.95361	0.8455	9	0.87932	D	0	.	13.5598	0.61782	1.0:0.0:0.0:0.0	.	1764	O14686	MLL2_HUMAN	P	1764	ENSP00000301067:L1764P	ENSP00000301067:L1764P	L	-	2	0	MLL2	47723946	1.000000	0.71417	0.941000	0.38009	0.935000	0.57460	9.259000	0.95561	1.846000	0.53633	0.260000	0.18958	CTG	.	.	.	none		0.567	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			G	49437679	A	G	49437679	3	3	133	1	0	0	0	0	1	0	0	0	9628	188	7	3	11454	3	MLL2	12	49437679	Missense_Mutation	SNP	A	TCGA-BQ-7048-01A-11D-1961-08	549086	49437679	84414216	38	8232											
KCTD4	386618	hgsc.bcm.edu	37	chr13	45768267	45768269	+	In_Frame_Del	DEL	TTA	TTA	-																															tgaacgatcgtggttatctgTtatttccaagaaagtagtct																										TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	TTA	TTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr13:45768267_45768269delTTA	ENST00000379108.1	-	1	583_585	c.434_436delTAA	c.(433-438)ataaca>aca	p.I145del	GTF2F2_ENST00000340473.6_Intron|KCTD4_ENST00000405872.1_In_Frame_Del_p.I145del			Q8WVF5	KCTD4_HUMAN	potassium channel tetramerization domain containing 4	145					protein homooligomerization (GO:0051260)					breast(1)|endometrium(1)|large_intestine(2)|lung(4)	8		Lung NSC(96;6.55e-05)|Breast(139;0.00378)|Prostate(109;0.00438)|Lung SC(185;0.0262)|Hepatocellular(98;0.0524)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000249)|BRCA - Breast invasive adenocarcinoma(63;0.207)		TGGTTATCTGTTATTTCCAAGAA	0.414																																					p.145_146del		Atlas-INDEL	.											.	KCTD4	18	.	0			c.435_437del						PASS	.																																			SO:0001651	inframe_deletion	386618	exon2			.	BC018063	CCDS9396.1	13q14.12-q14.13	2013-06-20	2013-06-20		ENSG00000180332	ENSG00000180332			23227	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 4"				Standard	NM_198404		Approved	bA321C24.3	uc001uzx.4	Q8WVF5	OTTHUMG00000016844	ENST00000379108.1:c.434_436delTAA	chr13.hg19:g.45768267_45768269delTTA	ENSP00000368402:p.Ile145del	173.0	0.0	0		162.0	15.0	0.0925926	NM_198404	Q5W0P9	In_Frame_Del	DEL	ENST00000379108.1	hg19	CCDS9396.1																																																																																			.	.	.	none		0.414	KCTD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044757.1			-	45768269	TTA	-	45768267	7	5	133	1	0	1	0	1	0	0	0	0	8118	1725	60	0	347	0	KCTD4	13	45768267	In_Frame_Del	DEL	TTA	TCGA-BQ-7048-01A-11D-1961-08		45768267	69401611	39	8233											
KLHDC1	122773	hgsc.bcm.edu	37	chr14	50196254	50196254	+	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	tctaaacctagacacctggaCttggtctggaaggtaagttt	11	12	10	8	0	2	1	0	0	2	1	2	3	2	3	2	4	1	2	2	4	5	5			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr14:50196254C>G	ENST00000359332.2	+	8	788	c.698C>G	c.(697-699)aCt>aGt	p.T233S	KLHDC1_ENST00000554512.1_3'UTR	NM_172193.2	NP_751943.1	Q8N7A1	KLDC1_HUMAN	kelch domain containing 1	233						cytoplasm (GO:0005737)				kidney(1)|large_intestine(1)|liver(2)|lung(5)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	12	all_epithelial(31;0.00244)|Breast(41;0.00964)					GACACCTGGACTTGGTCTGGA	0.348																																					p.T233S		Atlas-SNP	.											.	KLHDC1	24	.	0			c.C698G						PASS	.						115	104	108					14																	50196254		2203	4299	6502	SO:0001583	missense	122773	exon8			CCTGGACTTGGTC	AF111806	CCDS9692.1	14q21.3	2007-08-01			ENSG00000197776	ENSG00000197776			19836	protein-coding gene	gene with protein product		611281					Standard	NM_172193		Approved	MST025	uc001www.3	Q8N7A1	OTTHUMG00000140295	ENST00000359332.2:c.698C>G	chr14.hg19:g.50196254C>G	ENSP00000352282:p.Thr233Ser	80.0	0.0	.		61.0	24.0	.	NM_172193	B3KXD9|Q8WYI1	Missense_Mutation	SNP	ENST00000359332.2	hg19	CCDS9692.1	.	.	.	.	.	.	.	.	.	.	C	9.838	1.190260	0.21954	.	.	ENSG00000197776	ENST00000359332;ENST00000557128	T;T	0.67523	-0.27;-0.27	5.78	1.34	0.21922	Galactose oxidase/kelch, beta-propeller (1);Kelch-type beta propeller (1);	0.164679	0.53938	D	0.000057	T	0.48241	0.1489	N	0.25485	0.75	0.23636	N	0.997233	B;B	0.30361	0.277;0.085	B;B	0.31547	0.132;0.038	T	0.30297	-0.9983	10	0.21014	T	0.42	-0.3182	9.4425	0.38677	0.0:0.5979:0.0:0.4021	.	104;233	G3V3T1;Q8N7A1	.;KLDC1_HUMAN	S	233;104	ENSP00000352282:T233S;ENSP00000451407:T104S	ENSP00000352282:T233S	T	+	2	0	KLHDC1	49266004	0.933000	0.31639	0.991000	0.47740	0.956000	0.61745	0.163000	0.16520	-0.028000	0.13850	-0.237000	0.12165	ACT	.	.	.	none		0.348	KLHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276882.2	NM_172193		G	50196254	C	G	50196254	3	3	133	1	0	0	0	0	1	0	0	0	8361	565	20	4	728	4	KLHDC1	14	50196254	Missense_Mutation	SNP	C	TCGA-BQ-7048-01A-11D-1961-08		50196254	57153286	40	8234											
ENTPD5	957	hgsc.bcm.edu	37	chr14	74443764	74443765	+	Splice_Site	INS	-	-	A																															taacccaagctaatatgcctINSaaaaagaaagaaagacaagg																										TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr14:74443764_74443765insA	ENST00000334696.6	-	8	837		c.e8-2		ENTPD5_ENST00000557325.1_Splice_Site	NM_001249.2	NP_001240.1	O75356	ENTP5_HUMAN	ectonucleoside triphosphate diphosphohydrolase 5						'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)		CTAATATGCCTAAAAAGAAAGA	0.366																																					.		Atlas-INDEL	.											.	ENTPD5	26	.	0			c.518-2->T						PASS	.																																			SO:0001630	splice_region_variant	957	exon9			.	AF039918	CCDS9825.1	14q24	2003-10-03	2003-10-03			ENSG00000187097			3367	protein-coding gene	gene with protein product		603162	"proto-oncogene CPH"	CD39L4, PCPH		9271669, 9676430	Standard	NM_001249		Approved	NTPDase-5	uc010tuo.2	O75356		ENST00000334696.6:c.518-2->T	chr14.hg19:g.74443769_74443769dupA		144.0	0.0	0		100.0	38.0	0.38	NM_001249	A1L4C5|Q96RX0	Splice_Site	INS	ENST00000334696.6	hg19	CCDS9825.1																																																																																			.	.	.	none		0.366	ENTPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412637.1	NM_001249	Intron	A	74443765	-	A	74443764	8	5	133	1	0	1	1	0	0	0	1	0	5144	1536	53	0	806	0	ENTPD5	14	74443764	Splice_Site	INS	-	TCGA-BQ-7048-01A-11D-1961-08	24247510	74443764	32905776	41	8235											
GABRG3	2567	hgsc.bcm.edu	37	chr15	27777965	27777965	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggactcgtactcccgggtcTttttccccacgtccttcctg	3	14	8	16	3	1	0	0	0	1	0	6	1	5	1	5	2	1	1	5	2	1	4			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr15:27777965T>C	ENST00000333743.6	+	10	1596	c.1342T>C	c.(1342-1344)Ttt>Ctt	p.F448L	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	448					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)	CTCCCGGGTCTTTTTCCCCAC	0.473																																					p.F448L	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											GABRG3,right_upper_lobe,carcinoma,0,1	GABRG3	115	.	0			c.T1342C						PASS	.						72	73	73					15																	27777965		1952	4142	6094	SO:0001583	missense	2567	exon10			CGGGTCTTTTTCC		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.1342T>C	chr15.hg19:g.27777965T>C	ENSP00000331912:p.Phe448Leu	65.0	0.0	.		62.0	3.0	.	NM_033223	G3V594|Q9HD46|Q9NYT2	Missense_Mutation	SNP	ENST00000333743.6	hg19	CCDS45195.1	.	.	.	.	.	.	.	.	.	.	T	15.85	2.954120	0.53293	.	.	ENSG00000182256	ENST00000333743	T	0.80824	-1.42	5.75	3.4	0.38934	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.175067	0.50627	D	0.000109	T	0.65080	0.2657	N	0.20401	0.57	0.80722	D	1	B	0.25206	0.12	B	0.33196	0.159	T	0.49504	-0.8933	10	0.08837	T	0.75	.	7.9945	0.30261	0.0:0.0709:0.1369:0.7922	.	448	Q99928	GBRG3_HUMAN	L	448	ENSP00000331912:F448L	ENSP00000331912:F448L	F	+	1	0	GABRG3	25451560	1.000000	0.71417	0.319000	0.25293	0.894000	0.52154	4.846000	0.62860	0.422000	0.26005	0.528000	0.53228	TTT	.	.	.	none		0.473	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2			C	27777965	T	C	27777965	3	2	133	1	0	0	0	0	1	0	0	0	6180	1609	56	3	1380	3	GABRG3	15	27777965	Missense_Mutation	SNP	T	TCGA-BQ-7048-01A-11D-1961-08		27777965	74753427	42	8236											
MESDC2	23184	hgsc.bcm.edu	37	chr15	81282037	81282037	+	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	ccgggcgagccttcggccgcGcaggacccaggcggtggtag	5	4	18	14	6	0	0	0	0	0	0	1	2	0	1	4	6	1	2	4	6	1	2			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr15:81282037G>A	ENST00000261758.4	-	1	182	c.96C>T	c.(94-96)tgC>tgT	p.C32C	RP11-775C24.3_ENST00000563737.1_lincRNA	NM_015154.1	NP_055969.1	Q14696	MESD_HUMAN	mesoderm development candidate 2	32	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						CTTCGGCCGCGCAGGACCCAG	0.637																																					p.C32C		Atlas-SNP	.											.	MESDC2	23	.	0			c.C96T						PASS	.						35	35	35					15																	81282037		2203	4298	6501	SO:0001819	synonymous_variant	23184	exon1			GGCCGCGCAGGAC	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.96C>T	chr15.hg19:g.81282037G>A		64.0	0.0	.		68.0	33.0	.	NM_015154	B4DW84|D3DW96|Q969U1	Silent	SNP	ENST00000261758.4	hg19	CCDS32308.1																																																																																			.	.	.	none		0.637	MESDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417673.2	NM_015154		A	81282037	G	A	81282037	2	1	133	1	0	0	0	0	0	0	0	1	9488	1079	38	1		1	MESDC2	15	81282037	Silent	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	53504072	81282037	21249355	43	8237											
RNF157	114804	hgsc.bcm.edu	37	chr17	74158077	74158077	+	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	gttatcactcacttcgtcttCagccacctggccaaggagaa	10	10	8	13	1	4	1	3	0	1	1	5	2	4	1	3	2	1	1	3	2	3	3			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr17:74158077C>A	ENST00000269391.6	-	10	931	c.799G>T	c.(799-801)Gaa>Taa	p.E267*	RNF157_ENST00000319945.6_Nonsense_Mutation_p.E267*	NM_052916.2	NP_443148.1	Q96PX1	RN157_HUMAN	ring finger protein 157	267							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)			ACTTCGTCTTCAGCCACCTGG	0.527																																					p.E267X	GBM(186;507 2120 27388 27773 52994)	Atlas-SNP	.											.	RNF157	66	.	0			c.G799T						PASS	.						96	68	78					17																	74158077		2203	4300	6503	SO:0001587	stop_gained	114804	exon10			CGTCTTCAGCCAC	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.799G>T	chr17.hg19:g.74158077C>A	ENSP00000269391:p.Glu267*	89.0	0.0	.		67.0	31.0	.	NM_052916	Q8NB72|Q96N56	Nonsense_Mutation	SNP	ENST00000269391.6	hg19	CCDS32740.1	.	.	.	.	.	.	.	.	.	.	C	38	6.984953	0.97983	.	.	ENSG00000141576	ENST00000269391;ENST00000319945;ENST00000301610	.	.	.	5.73	5.73	0.89815	.	0.044080	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-18.6068	19.893	0.96937	0.0:1.0:0.0:0.0	.	.	.	.	X	267;267;229	.	ENSP00000269391:E267X	E	-	1	0	RNF157	71669672	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.782000	0.85680	2.693000	0.91896	0.655000	0.94253	GAA	.	.	.	none		0.527	RNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255874.2	XM_290732		A	74158077	C	A	74158077	4	1	133	1	0	0	0	0	0	1	0	0	13467	835	29	4	1280	4	RNF157	17	74158077	Nonsense_Mutation	SNP	C	TCGA-BQ-7048-01A-11D-1961-08		74158077	7037133	44	8238											
TMC6	11322	hgsc.bcm.edu	37	chr17	76115385	76115385	+	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	agaggaccctcaccaggtcaGagtctgcccataaatcagct	12	7	9	13	0	4	2	3	0	1	2	4	3	4	3	3	2	2	1	3	2	2	1			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr17:76115385G>C	ENST00000590602.1	-	14	1963	c.1804C>G	c.(1804-1806)Ctg>Gtg	p.L602V	TMC6_ENST00000592076.1_Intron|TMC6_ENST00000322933.4_Missense_Mutation_p.L181V|TMC6_ENST00000306591.7_Intron|TMC6_ENST00000322914.3_Missense_Mutation_p.L602V|TMC6_ENST00000591436.1_Missense_Mutation_p.L181V|TMC6_ENST00000392467.3_Missense_Mutation_p.L602V			Q7Z403	TMC6_HUMAN	transmembrane channel-like 6	602					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)			CACCAGGTCAGAGTCTGCCCA	0.622																																					p.L602V		Atlas-SNP	.											.	TMC6	42	.	0			c.C1804G						PASS	.						133	117	123					17																	76115385		2203	4300	6503	SO:0001583	missense	11322	exon14			AGGTCAGAGTCTG	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.1804C>G	chr17.hg19:g.76115385G>C	ENSP00000465261:p.Leu602Val	130.0	0.0	.		100.0	31.0	.	NM_001127198	O43284|Q45VJ2|Q8IU98|Q8IUI7|Q8IWU8|Q8TEQ7|Q9HAG5	Missense_Mutation	SNP	ENST00000590602.1	hg19	CCDS32748.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.992746	0.74703	.	.	ENSG00000141524	ENST00000322914;ENST00000392467;ENST00000322933;ENST00000392466	T;T;T	0.67698	-0.28;-0.28;-0.28	4.72	4.72	0.59763	.	0.000000	0.64402	D	0.000002	T	0.79707	0.4492	L	0.60904	1.88	0.47994	D	0.999565	D;D	0.89917	0.998;1.0	D;D	0.83275	0.98;0.996	T	0.82232	-0.0559	10	0.72032	D	0.01	-16.0397	17.6365	0.88123	0.0:0.0:1.0:0.0	.	602;181	Q7Z403;Q7Z403-3	TMC6_HUMAN;.	V	602;602;181;68	ENSP00000313408:L602V;ENSP00000376260:L602V;ENSP00000313479:L181V	ENSP00000313408:L602V	L	-	1	2	TMC6	73626980	1.000000	0.71417	0.980000	0.43619	0.951000	0.60555	3.385000	0.52485	2.164000	0.68074	0.555000	0.69702	CTG	.	.	.	none		0.622	TMC6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437146.1			C	76115385	G	C	76115385	3	2	133	1	0	0	0	0	1	0	0	0	16001	933	33	4	641	4	TMC6	17	76115385	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08	1957308	76115385	5079825	45	8239											
LGI4	163175	hgsc.bcm.edu	37	chr19	35617832	35617832	+	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	caggcagcggccggcgaaggGctgtgccagcacaatgtgag	9	4	17	11	3	0	1	0	1	0	0	0	2	0	1	2	4	3	3	2	4	2	0			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr19:35617832G>T	ENST00000310123.3	-	7	1237	c.718C>A	c.(718-720)Ccc>Acc	p.P240T	LGI4_ENST00000392225.3_Missense_Mutation_p.P240T|LGI4_ENST00000493050.1_5'UTR	NM_139284.2	NP_644813.1	Q8N135	LGI4_HUMAN	leucine-rich repeat LGI family, member 4	240					adult locomotory behavior (GO:0008344)|glial cell proliferation (GO:0014009)|myelination in peripheral nervous system (GO:0022011)|neuron maturation (GO:0042551)	extracellular space (GO:0005615)				endometrium(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			CCGGCGAAGGGCTGTGCCAGC	0.662																																					p.P240T		Atlas-SNP	.											.	LGI4	32	.	0			c.C718A						PASS	.						40	46	44					19																	35617832		2203	4300	6503	SO:0001583	missense	163175	exon7			CGAAGGGCTGTGC	AJ487519	CCDS12444.1	19q13.13	2008-07-03			ENSG00000153902	ENSG00000153902			18712	protein-coding gene	gene with protein product		608303				12023020	Standard	NM_139284		Approved		uc002nxx.2	Q8N135	OTTHUMG00000044558	ENST00000310123.3:c.718C>A	chr19.hg19:g.35617832G>T	ENSP00000312273:p.Pro240Thr	87.0	0.0	.		334.0	26.0	.	NM_139284	B2RN53|B9EGS7|Q5M8T1	Missense_Mutation	SNP	ENST00000310123.3	hg19	CCDS12444.1	.	.	.	.	.	.	.	.	.	.	G	16.80	3.222746	0.58668	.	.	ENSG00000153902	ENST00000310123;ENST00000392225;ENST00000437421	D;D	0.81579	-1.51;-1.51	3.94	3.94	0.45596	.	0.000000	0.64402	D	0.000013	D	0.87245	0.6129	M	0.64170	1.965	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.88525	0.3099	10	0.72032	D	0.01	.	13.5039	0.61474	0.0:0.0:1.0:0.0	.	151;240	Q658V8;Q8N135	.;LGI4_HUMAN	T	240	ENSP00000312273:P240T;ENSP00000376059:P240T	ENSP00000312273:P240T	P	-	1	0	LGI4	40309672	1.000000	0.71417	1.000000	0.80357	0.325000	0.28411	7.564000	0.82326	2.025000	0.59659	0.313000	0.20887	CCC	.	.	.	none		0.662	LGI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103963.1			T	35617832	G	T	35617832	3	4	133	1	0	0	0	0	1	0	0	0	8761	1203	42	4	907	4	LGI4	19	35617832	Missense_Mutation	SNP	G	TCGA-BQ-7048-01A-11D-1961-08		35617832	23511151	46	8240											
ZNF335	63925	hgsc.bcm.edu	37	chr20	44579218	44579218	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtggggccgtaggcttgagTgctgtgccatgtgcgcctgc	3	10	18	10	2	0	1	0	1	0	0	0	1	0	1	3	4	4	3	3	4	1	2			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr20:44579218T>C	ENST00000322927.2	-	21	3306	c.3206A>G	c.(3205-3207)cAc>cGc	p.H1069R	ZNF335_ENST00000426788.1_Missense_Mutation_p.H914R	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	1069					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				TAGGCTTGAGTGCTGTGCCAT	0.592																																					p.H1069R		Atlas-SNP	.											.	ZNF335	115	.	0			c.A3206G						PASS	.						126	137	133					20																	44579218		2203	4300	6503	SO:0001583	missense	63925	exon21			CTTGAGTGCTGTG	AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"Zinc fingers, C2H2-type"	15807	protein-coding gene	gene with protein product	"NRC-interacting factor 1"	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.3206A>G	chr20.hg19:g.44579218T>C	ENSP00000325326:p.His1069Arg	256.0	0.0	.		229.0	25.0	.	NM_022095	B4DLG7|Q548D0|Q9H684	Missense_Mutation	SNP	ENST00000322927.2	hg19	CCDS13389.1	.	.	.	.	.	.	.	.	.	.	T	18.39	3.613272	0.66672	.	.	ENSG00000198026	ENST00000322927;ENST00000243961;ENST00000426788	D;D	0.88975	-2.45;-2.45	4.82	4.82	0.62117	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.97235	0.9096	H	0.99783	4.775	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.98479	1.0604	10	0.87932	D	0	-30.0634	14.0159	0.64523	0.0:0.0:0.0:1.0	.	914;1069	Q9H4Z2-2;Q9H4Z2	.;ZN335_HUMAN	R	1069;846;914	ENSP00000325326:H1069R;ENSP00000397098:H914R	ENSP00000243961:H846R	H	-	2	0	ZNF335	44012625	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	7.442000	0.80503	2.166000	0.68216	0.460000	0.39030	CAC	.	.	.	none		0.592	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095		C	44579218	T	C	44579218	3	2	133	1	0	0	0	0	1	0	0	0	17864	1696	59	3	854	3	ZNF335	20	44579218	Missense_Mutation	SNP	T	TCGA-BQ-7048-01A-11D-1961-08		44579218	18446302	47	8241											
ZBTB46	140685	hgsc.bcm.edu	37	chr20	62421455	62421455	+	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	gaggcccgtagcccacgtctCcaggccatagaggctgtgaa	9	6	13	13	2	1	2	0	1	1	1	2	3	1	2	4	3	1	2	4	3	3	2			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr20:62421455C>G	ENST00000245663.4	-	2	806	c.656G>C	c.(655-657)gGa>gCa	p.G219A	ZBTB46_ENST00000395104.1_Missense_Mutation_p.G219A|ZBTB46_ENST00000302995.2_Missense_Mutation_p.G219A|ZBTB46_ENST00000480766.1_5'Flank	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	219					negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					GCCCACGTCTCCAGGCCATAG	0.602																																					p.G219A		Atlas-SNP	.											.	ZBTB46	72	.	0			c.G656C						PASS	.						65	61	62					20																	62421455		2203	4300	6503	SO:0001583	missense	140685	exon2			ACGTCTCCAGGCC	AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16094	protein-coding gene	gene with protein product	"BTB-ZF protein expressed in effector lymphocytes"	614639	"BTB (POZ) domain containing 4"	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.656G>C	chr20.hg19:g.62421455C>G	ENSP00000245663:p.Gly219Ala	84.0	0.0	.		59.0	23.0	.	NM_025224	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Missense_Mutation	SNP	ENST00000245663.4	hg19	CCDS13538.1	.	.	.	.	.	.	.	.	.	.	C	7.452	0.642959	0.14451	.	.	ENSG00000130584	ENST00000245663;ENST00000302995;ENST00000395104	T;T;T	0.08807	3.05;3.05;3.05	5.53	5.53	0.82687	.	0.168310	0.53938	D	0.000060	T	0.08846	0.0219	L	0.40543	1.245	0.26386	N	0.976659	B	0.12630	0.006	B	0.10450	0.005	T	0.34428	-0.9829	10	0.08837	T	0.75	.	18.4243	0.90604	0.0:1.0:0.0:0.0	.	219	Q86UZ6	ZBT46_HUMAN	A	219	ENSP00000245663:G219A;ENSP00000303102:G219A;ENSP00000378536:G219A	ENSP00000245663:G219A	G	-	2	0	ZBTB46	61891899	0.511000	0.26179	0.923000	0.36655	0.092000	0.18411	3.313000	0.51935	2.609000	0.88269	0.650000	0.86243	GGA	.	.	.	none		0.602	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224		G	62421455	C	G	62421455	3	3	133	1	0	0	0	0	1	0	0	0	17559	855	30	4	1129	4	ZBTB46	20	62421455	Missense_Mutation	SNP	C	TCGA-BQ-7048-01A-11D-1961-08	17842237	62421455	604065	48	8242											
KRTAP27-1	643812	hgsc.bcm.edu	37	chr21	31709825	31709825	+	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	tggcagctggtggtttcattGcaggtttcttgaaagttgtc	6	16	13	6	0	2	1	1	1	1	0	3	1	2	1	0	4	2	6	0	4	1	5			TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr21:31709825G>A	ENST00000382835.2	-	1	187	c.162C>T	c.(160-162)tgC>tgT	p.C54C		NM_001077711.1	NP_001071179.1	Q3LI81	KR271_HUMAN	keratin associated protein 27-1	54						intermediate filament (GO:0005882)				endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(1)	18						TGGTTTCATTGCAGGTTTCTT	0.448																																					p.C54C		Atlas-SNP	.											.	KRTAP27-1	53	.	0			c.C162T						PASS	.						159	150	153					21																	31709825		2203	4300	6503	SO:0001819	synonymous_variant	643812	exon1			TTCATTGCAGGTT	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.162C>T	chr21.hg19:g.31709825G>A		150.0	0.0	.		145.0	50.0	.	NM_001077711		Silent	SNP	ENST00000382835.2	hg19	CCDS33532.1																																																																																			.	.	.	none		0.448	KRTAP27-1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132470.3	NM_001077711		A	31709825	G	A	31709825	2	1	133	1	0	0	0	0	0	0	0	1	8551	1311	46	2		2	KRTAP27-1	21	31709825	Silent	SNP	G	TCGA-BQ-7048-01A-11D-1961-08		31709825	16420070	49	8243											
SMARCB1	6598	hgsc.bcm.edu	37	chr22	24145544	24145544	+	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	tcagcccgaggtgctggtccCcatccggctggacatggaga	7	7	14	13	2	1	1	1	0	0	1	3	4	3	2	4	5	2	2	4	5	0	0	rs137986695		TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr22:24145544C>T	ENST00000263121.7	+	5	759	c.563C>T	c.(562-564)cCc>cTc	p.P188L	SMARCB1_ENST00000407422.3_Missense_Mutation_p.P179L|SMARCB1_ENST00000407082.3_Missense_Mutation_p.P142L|SMARCB1_ENST00000344921.6_Missense_Mutation_p.P197L	NM_003073.3	NP_003064.2	Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	188	2 X approximate tandem repeats.|HIV-1 integrase-binding.|MYC-binding.				ATP-dependent chromatin remodeling (GO:0043044)|blastocyst hatching (GO:0001835)|cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|DNA integration (GO:0015074)|DNA repair (GO:0006281)|mitotic cell cycle phase transition (GO:0044772)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	p53 binding (GO:0002039)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)	p.?(6)|p.P188L(1)|p.V185_M193del(1)		bone(4)|central_nervous_system(198)|endometrium(4)|haematopoietic_and_lymphoid_tissue(25)|kidney(3)|large_intestine(5)|liver(2)|lung(5)|meninges(5)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|soft_tissue(194)	458		Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05)				GTGCTGGTCCCCATCCGGCTG	0.592			"D, N, F, S"		malignant rhabdoid	malignant rhabdoid																															p.P188L		Atlas-SNP	.	yes	Rec	yes	Rhabdoid predisposition syndrome	22	22q11	6598	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1"		M	SMARCB1,arm,malignant_melanoma,0,1	SMARCB1	586	.	8	Unknown(3)|Deletion - Frameshift(3)|Substitution - Missense(1)|Deletion - In frame(1)	soft_tissue(5)|central_nervous_system(2)|skin(1)	c.C563T						PASS	.						114	103	107					22																	24145544		2203	4300	6503	SO:0001583	missense	6598	exon5			TGGTCCCCATCCG	U04847	CCDS13817.1, CCDS46671.1	22q11.23	2014-09-17			ENSG00000099956	ENSG00000099956			11103	protein-coding gene	gene with protein product	"sucrose nonfermenting, yeast, homolog-like 1", "integrase interactor 1", "malignant rhabdoid tumor suppressor", "protein phosphatase 1, regulatory subunit 144"	601607		SNF5L1		7801128, 10319872, 10365963	Standard	NM_003073		Approved	BAF47, Ini1, Snr1, hSNFS, Sfh1p, RDT, PPP1R144	uc002zyb.3	Q12824	OTTHUMG00000150737	ENST00000263121.7:c.563C>T	chr22.hg19:g.24145544C>T	ENSP00000263121:p.Pro188Leu	127.0	0.0	.		114.0	10.0	.	NM_003073	O75784|O95474|Q17S11|Q38GA1|Q76N08|Q9UBH2	Missense_Mutation	SNP	ENST00000263121.7	hg19	CCDS13817.1	.	.	.	.	.	.	.	.	.	.	C	34	5.321447	0.95682	.	.	ENSG00000099956	ENST00000417137;ENST00000344921;ENST00000263121;ENST00000407422;ENST00000407082	D;D;D;D;D	0.95447	-3.71;-3.71;-3.71;-3.71;-3.71	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	D	0.98251	0.9421	M	0.92784	3.345	0.80722	D	1	D;D;D;D	0.89917	0.998;1.0;0.993;0.999	D;D;D;D	0.97110	0.982;1.0;0.983;0.997	D	0.99323	1.0907	10	0.72032	D	0.01	-25.3436	17.5295	0.87810	0.0:1.0:0.0:0.0	.	197;179;188;206	G5E975;Q17S11;Q12824;C9JTA6	.;.;SNF5_HUMAN;.	L	206;197;188;179;142	ENSP00000388489:P206L;ENSP00000340883:P197L;ENSP00000263121:P188L;ENSP00000383984:P179L;ENSP00000385226:P142L	ENSP00000263121:P188L	P	+	2	0	SMARCB1	22475544	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.810000	0.86072	2.472000	0.83506	0.644000	0.83932	CCC	.	.	.	weak		0.592	SMARCB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319872.1	NM_003073		T	24145544	C	T	24145544	3	4	133	1	0	0	0	0	1	0	0	0	14787	623	22	2	581	2	SMARCB1	22	24145544	Missense_Mutation	SNP	C	TCGA-BQ-7048-01A-11D-1961-08		24145544	27159022	50	8244											
MKL1	57591	hgsc.bcm.edu	37	chr22	40816560	40816562	+	In_Frame_Del	DEL	CCC	CCC	-																															ctgggggggtcccgctgcttCccagggcctcgcctgctgac																										TCGA-BQ-7048-01A-11D-1961-08	TCGA-BQ-7048-11A-01D-1961-08	CCC	CCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ee5ae28-9eb8-4f46-b9d9-13c5246297eb	71fbff51-4f0d-4d4f-8083-f64c0ac772b8	g.chr22:40816560_40816562delCCC	ENST00000355630.3	-	11	1490_1492	c.900_902delGGG	c.(898-903)ctggga>cta	p.G301del	MKL1_ENST00000402042.1_In_Frame_Del_p.G251del|MKL1_ENST00000396617.3_In_Frame_Del_p.G301del|MKL1_ENST00000407029.1_In_Frame_Del_p.G301del	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	301					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						CCCGCTGCTTCCCAGGGCCTCGC	0.665			T	RBM15	acute megakaryocytic leukemia																																p.301_301del		Atlas-INDEL	.		Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	.	MKL1	69	.	0			c.901_903del						PASS	.																																			SO:0001651	inframe_deletion	57591	exon11			.	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.900_902delGGG	chr22.hg19:g.40816560_40816562delCCC	ENSP00000347847:p.Gly301del	139.0	0.0	0		97.0	39.0	0.402062	NM_020831	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	In_Frame_Del	DEL	ENST00000355630.3	hg19	CCDS14003.1																																																																																			.	.	.	none		0.665	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831		-	40816562	CCC	-	40816560	7	5	133	1	0	1	0	1	0	0	0	0	9608	855	30	0	1913	0	MKL1	22	40816560	In_Frame_Del	DEL	CCC	TCGA-BQ-7048-01A-11D-1961-08	16671016	40816560	10488006	51	8245											
MKI67IP	84365	hgsc.bcm.edu	37	chr2	122488590	122488590	+	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	gtgtccgattccgattatacCgtttcactgatggatatgat	9	15	9	8	3	1	2	1	2	0	0	3	5	3	3	3	1	1	1	3	1	3	5			TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr2:122488590C>A	ENST00000285814.4	-	4	515	c.443G>T	c.(442-444)cGg>cTg	p.R148L	AC018737.1_ENST00000419902.1_RNA	NM_032390.4	NP_115766.3	Q9BYG3	MK67I_HUMAN		148					negative regulation of phosphatase activity (GO:0010923)|protein complex assembly (GO:0006461)|rRNA metabolic process (GO:0016072)|rRNA transcription (GO:0009303)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|pancreas(1)|urinary_tract(1)	12						CCGATTATACCGTTTCACTGA	0.343																																					p.R148L		Atlas-SNP	.											.	MKI67IP	27	.	0			c.G443T						PASS	.						107	103	105					2																	122488590		2203	4299	6502	SO:0001583	missense	84365	exon4			TTATACCGTTTCA																												ENST00000285814.4:c.443G>T	chr2.hg19:g.122488590C>A	ENSP00000285814:p.Arg148Leu	125.0	0.0	.		160.0	8.0	.	NM_032390	A8K788|Q8TB66|Q96ED4	Missense_Mutation	SNP	ENST00000285814.4	hg19	CCDS2135.1	.	.	.	.	.	.	.	.	.	.	C	18.59	3.657638	0.67586	.	.	ENSG00000155438	ENST00000285814;ENST00000409201;ENST00000447132;ENST00000451734	T;T;T	0.54071	2.13;0.59;1.33	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.68686	0.3028	M	0.72894	2.215	0.80722	D	1	D;D	0.67145	0.996;0.994	P;P	0.61132	0.884;0.687	T	0.71823	-0.4476	10	0.87932	D	0	-11.903	15.2323	0.73401	0.0:1.0:0.0:0.0	.	148;148	B4DSM4;Q9BYG3	.;MK67I_HUMAN	L	148;148;43;116	ENSP00000285814:R148L;ENSP00000406227:R43L;ENSP00000398116:R116L	ENSP00000285814:R148L	R	-	2	0	MKI67IP	122205060	1.000000	0.71417	0.922000	0.36590	0.325000	0.28411	5.870000	0.69620	2.668000	0.90789	0.655000	0.94253	CGG	.	.	.	none		0.343	MKI67IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254239.2			A	122488590	C	A	122488590	3	1	134	1	0	0	0	0	1	0	0	0	9606	652	23	4	454	4	MKI67IP	2	122488590	Missense_Mutation	SNP	C	TCGA-BQ-7049-01A-11D-1961-08		122488590	120710783	1	8246											
RFTN2	130132	hgsc.bcm.edu	37	chr2	198511301	198511301	+	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	tataacaggatgaatagcccCgacaatatatcctttaagat	16	11	6	8	1	0	2	0	1	0	1	1	4	1	3	3	1	2	0	3	1	8	7			TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr2:198511301C>A	ENST00000295049.4	-	2	765	c.229G>T	c.(229-231)Ggg>Tgg	p.G77W		NM_144629.2	NP_653230.2	Q52LD8	RFTN2_HUMAN	raftlin family member 2	77					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						TGAATAGCCCCGACAATATAT	0.378																																					p.G77W		Atlas-SNP	.											.	RFTN2	68	.	0			c.G229T						PASS	.						116	117	116					2																	198511301		2203	4300	6503	SO:0001583	missense	130132	exon2			TAGCCCCGACAAT	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.229G>T	chr2.hg19:g.198511301C>A	ENSP00000295049:p.Gly77Trp	166.0	0.0	.		197.0	9.0	.	NM_144629	Q14DH4|Q2TA69|Q53QE0|Q53SE1|Q96NM3	Missense_Mutation	SNP	ENST00000295049.4	hg19	CCDS2323.1	.	.	.	.	.	.	.	.	.	.	C	19.38	3.815785	0.70912	.	.	ENSG00000162944	ENST00000295049;ENST00000429081	T;T	0.32753	1.44;1.44	5.39	4.5	0.54988	.	0.474569	0.23536	N	0.047134	T	0.47948	0.1473	L	0.51422	1.61	0.40875	D	0.983944	D	0.89917	1.0	D	0.87578	0.998	T	0.46911	-0.9157	10	0.87932	D	0	-13.4825	12.182	0.54218	0.0:0.9205:0.0:0.0795	.	77	Q52LD8	RFTN2_HUMAN	W	77	ENSP00000295049:G77W;ENSP00000398128:G77W	ENSP00000295049:G77W	G	-	1	0	RFTN2	198219546	0.387000	0.25188	0.999000	0.59377	0.943000	0.58893	2.256000	0.43231	2.687000	0.91594	0.585000	0.79938	GGG	.	.	.	none		0.378	RFTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256106.2	NM_144629		A	198511301	C	A	198511301	3	1	134	1	0	0	0	0	1	0	0	0	13272	652	23	4	1308	4	RFTN2	2	198511301	Missense_Mutation	SNP	C	TCGA-BQ-7049-01A-11D-1961-08	76022711	198511301	44688072	2	8247											
SEPT2	4735	hgsc.bcm.edu	37	chr2	242277178	242277178	+	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	aaagctgacactctcaccctGaaggaacgggagcggctgaa	13	5	12	11	2	1	3	1	3	1	0	2	5	1	5	1	3	3	2	1	3	4	0			TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr2:242277178G>C	ENST00000391973.2	+	7	1095	c.567G>C	c.(565-567)ctG>ctC	p.L189L	SEPT2_ENST00000360051.3_Silent_p.L189L|SEPT2_ENST00000402092.2_Silent_p.L189L|SEPT2_ENST00000391971.2_Silent_p.L189L|SEPT2_ENST00000407971.1_Silent_p.L149L|SEPT2_ENST00000401990.1_Silent_p.L199L	NM_006155.1	NP_006146.1	Q15019	SEPT2_HUMAN	septin 2	189	Septin-type G.				cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|neuron projection development (GO:0031175)|regulation of L-glutamate transport (GO:0002036)|regulation of protein localization (GO:0032880)|smoothened signaling pathway (GO:0007224)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|exocyst (GO:0000145)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|synapse (GO:0045202)	enzyme regulator activity (GO:0030234)|GTP binding (GO:0005525)			central_nervous_system(2)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12		all_cancers(19;7.62e-41)|all_epithelial(40;1.71e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.24e-34)|all cancers(36;7.15e-32)|OV - Ovarian serous cystadenocarcinoma(60;1.21e-15)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;3.16e-06)|Lung(119;7.81e-05)|LUSC - Lung squamous cell carcinoma(224;0.000742)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0889)		CTCTCACCCTGAAGGAACGGG	0.507																																					p.L189L		Atlas-SNP	.											.	SEPT2	33	.	0			c.G567C						PASS	.						76	71	73					2																	242277178		2203	4300	6503	SO:0001819	synonymous_variant	4735	exon8			CACCCTGAAGGAA	D28540	CCDS2548.1, CCDS63195.1, CCDS74682.1	2q37.3	2013-01-21	2005-01-11	2005-01-12	ENSG00000168385	ENSG00000168385		"Septins"	7729	protein-coding gene	gene with protein product		601506	"neural precursor cell expressed, developmentally down-regulated 5"	DIFF6, NEDD5		8697812	Standard	XM_005247011		Approved	KIAA0158, hNedd5, Pnutl3	uc002wbd.3	Q15019	OTTHUMG00000133394	ENST00000391973.2:c.567G>C	chr2.hg19:g.242277178G>C		104.0	0.0	.		87.0	4.0	.	NM_001008491	B4DGE8|Q14132|Q53QU3|Q8IUK9|Q96CB0	Silent	SNP	ENST00000391973.2	hg19	CCDS2548.1	.	.	.	.	.	.	.	.	.	.	G	10.65	1.408628	0.25378	.	.	ENSG00000168385	ENST00000457874	.	.	.	5.23	4.35	0.52113	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.7547	0.62928	0.074:0.0:0.926:0.0	.	.	.	.	S	161	.	.	X	+	2	2	SEPT2	241925851	1.000000	0.71417	0.999000	0.59377	0.977000	0.68977	3.609000	0.54117	1.215000	0.43411	0.655000	0.94253	TGA	.	.	.	none		0.507	SEPT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323177.3	NM_006155		C	242277178	G	C	242277178	2	2	134	1	0	0	0	0	0	0	0	1	14077	1277	45	4		4	SEPT2	2	242277178	Silent	SNP	G	TCGA-BQ-7049-01A-11D-1961-08	43765877	242277178	922195	3	8248											
CCDC13	152206	hgsc.bcm.edu	37	chr3	42777251	42777251	+	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	gctgtcgcactttggcctccCgctcagctaccatggcctgc	4	10	10	17	2	1	0	1	0	0	0	3	0	2	0	4	2	3	4	4	2	1	2			TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr3:42777251C>A	ENST00000310232.6	-	10	1402	c.1319G>T	c.(1318-1320)cGg>cTg	p.R440L	CCDC13-AS1_ENST00000418161.1_RNA|CCDC13-AS1_ENST00000446950.1_RNA	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	440										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						TTTGGCCTCCCGCTCAGCTAC	0.602																																					p.R440L		Atlas-SNP	.											.	CCDC13	71	.	0			c.G1319T						PASS	.						119	104	109					3																	42777251		2203	4300	6503	SO:0001583	missense	152206	exon10			GCCTCCCGCTCAG	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.1319G>T	chr3.hg19:g.42777251C>A	ENSP00000309836:p.Arg440Leu	169.0	0.0	.		163.0	10.0	.	NM_144719		Missense_Mutation	SNP	ENST00000310232.6	hg19	CCDS2705.1	.	.	.	.	.	.	.	.	.	.	C	18.80	3.700694	0.68501	.	.	ENSG00000244607	ENST00000310232	T	0.27720	1.65	5.03	5.03	0.67393	.	0.085006	0.47852	D	0.000217	T	0.55353	0.1915	M	0.75447	2.3	0.38311	D	0.943263	D	0.89917	1.0	D	0.76071	0.987	T	0.57207	-0.7851	10	0.30078	T	0.28	.	17.144	0.86761	0.0:1.0:0.0:0.0	.	440	Q8IYE1	CCD13_HUMAN	L	440	ENSP00000309836:R440L	ENSP00000309836:R440L	R	-	2	0	CCDC13	42752255	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	4.131000	0.57970	2.345000	0.79718	0.511000	0.50034	CGG	.	.	.	none		0.602	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719		A	42777251	C	A	42777251	3	1	134	1	0	0	0	0	1	0	0	0	2767	652	23	4	856	4	CCDC13	3	42777251	Missense_Mutation	SNP	C	TCGA-BQ-7049-01A-11D-1961-08		42777251	155245179	4	8249											
KIAA1407	57577	hgsc.bcm.edu	37	chr3	113737705	113737705	+	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	tgtgccaggcagcgaaatacCgtttttgacactgcagcgga	10	9	12	10	3	0	1	0	1	0	0	0	3	0	2	2	2	5	3	2	2	2	3	rs149867008	byFrequency	TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr3:113737705C>A	ENST00000295878.3	-	8	1129	c.983G>T	c.(982-984)cGg>cTg	p.R328L	KIAA1407_ENST00000545063.1_Missense_Mutation_p.R159L	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	328								p.R328L(1)		endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						AGCGAAATACCGTTTTTGACA	0.483																																					p.R328L		Atlas-SNP	.											.	KIAA1407	80	.	1	Substitution - Missense(1)	lung(1)	c.G983T						PASS	.						174	176	175					3																	113737705		2203	4300	6503	SO:0001583	missense	57577	exon8			AAATACCGTTTTT	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.983G>T	chr3.hg19:g.113737705C>A	ENSP00000295878:p.Arg328Leu	391.0	0.0	.		348.0	14.0	.	NM_020817	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	hg19	CCDS2977.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.984892	0.74474	.	.	ENSG00000163617	ENST00000295878;ENST00000545063;ENST00000491000	T;T;T	0.51574	1.35;0.73;0.7	5.76	4.78	0.61160	.	0.269718	0.36034	N	0.002833	T	0.59101	0.2169	M	0.64997	1.995	0.80722	D	1	D;D;D	0.76494	0.99;0.999;0.995	P;D;P	0.70487	0.796;0.969;0.879	T	0.61501	-0.7050	10	0.62326	D	0.03	.	5.5084	0.16866	0.0:0.6308:0.2044:0.1648	.	315;204;328	C9JA89;B4DIZ9;Q8NCU4	.;.;K1407_HUMAN	L	328;159;315	ENSP00000295878:R328L;ENSP00000446381:R159L;ENSP00000418099:R315L	ENSP00000295878:R328L	R	-	2	0	KIAA1407	115220395	0.420000	0.25457	1.000000	0.80357	0.990000	0.78478	0.674000	0.25218	2.726000	0.93360	0.655000	0.94253	CGG	.	C|1.000;T|0.000	.	alt		0.483	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817		A	113737705	C	A	113737705	3	1	134	1	0	0	0	0	1	0	0	0	8236	652	23	4	1867	4	KIAA1407	3	113737705	Missense_Mutation	SNP	C	TCGA-BQ-7049-01A-11D-1961-08	70960454	113737705	84284725	5	8250											
AFAP1	60312	hgsc.bcm.edu	37	chr4	7840357	7840357	+	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	tcttctttttgctgtctttcGggatgtacgtaatgttacag	6	19	9	7	2	3	0	0	0	3	0	4	1	3	1	0	1	3	4	0	1	3	7			TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr4:7840357G>T	ENST00000360265.4	-	5	854	c.620C>A	c.(619-621)cCg>cAg	p.P207Q	AFAP1_ENST00000358461.2_Missense_Mutation_p.P207Q|AFAP1_ENST00000420658.1_Missense_Mutation_p.P207Q|AFAP1_ENST00000382543.3_Missense_Mutation_p.P207Q			Q8N556	AFAP1_HUMAN	actin filament associated protein 1	207	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(4)|stomach(2)	32						GCTGTCTTTCGGGATGTACGT	0.507																																					p.P207Q		Atlas-SNP	.											.	AFAP1	93	.	0			c.C620A						PASS	.						209	191	197					4																	7840357		2203	4300	6503	SO:0001583	missense	60312	exon6			TCTTTCGGGATGT	AB209676	CCDS3397.1, CCDS47010.1	4p16	2014-02-12	2007-02-07		ENSG00000196526	ENSG00000196526		"Pleckstrin homology (PH) domain containing"	24017	protein-coding gene	gene with protein product		608252				14755689, 11641786, 11607843	Standard	NM_198595		Approved	AFAP-110, AFAP	uc011bwk.1	Q8N556	OTTHUMG00000125515	ENST00000360265.4:c.620C>A	chr4.hg19:g.7840357G>T	ENSP00000353402:p.Pro207Gln	166.0	0.0	.		174.0	9.0	.	NM_001134647	A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Missense_Mutation	SNP	ENST00000360265.4	hg19	CCDS3397.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.981112	0.74474	.	.	ENSG00000196526	ENST00000360265;ENST00000420658;ENST00000358461;ENST00000382543	T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98	4.46	4.46	0.54185	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.056876	0.64402	D	0.000001	D	0.85852	0.5793	M	0.79123	2.44	0.58432	D	0.999998	D;D	0.69078	0.997;0.988	D;D	0.70016	0.967;0.963	D	0.87651	0.2528	10	0.59425	D	0.04	-44.5193	17.4002	0.87458	0.0:0.0:1.0:0.0	.	207;207	E9PDT7;Q8N556	.;AFAP1_HUMAN	Q	207	ENSP00000353402:P207Q;ENSP00000410689:P207Q;ENSP00000351245:P207Q;ENSP00000371983:P207Q	ENSP00000351245:P207Q	P	-	2	0	AFAP1	7891257	1.000000	0.71417	0.836000	0.33094	0.629000	0.37895	7.154000	0.77437	2.344000	0.79699	0.650000	0.86243	CCG	.	.	.	none		0.507	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2	NM_021638		T	7840357	G	T	7840357	3	4	134	1	0	0	0	0	1	0	0	0	353	1116	39	4	1876	4	AFAP1	4	7840357	Missense_Mutation	SNP	G	TCGA-BQ-7049-01A-11D-1961-08		7840357	183313919	6	8251											
SDHA	6389	hgsc.bcm.edu	37	chr5	224586	224586	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgaggcagggtttaatacaGcatgtgttaccaagctgttt	10	13	11	7	0	0	1	0	1	0	0	0	1	0	1	1	2	4	6	1	2	4	5			TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr5:224586G>A	ENST00000264932.6	+	3	377	c.262G>A	c.(262-264)Gca>Aca	p.A88T	SDHA_ENST00000504309.1_Missense_Mutation_p.A88T|SDHA_ENST00000510361.1_Missense_Mutation_p.A88T	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	88					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)	GTTTAATACAGCATGTGTTAC	0.547									Familial Paragangliomas																												p.A88T		Atlas-SNP	.											.	SDHA	80	.	0			c.G262A						PASS	.						111	110	110					5																	224586		2203	4300	6503	SO:0001583	missense	6389	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	AATACAGCATGTG	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.262G>A	chr5.hg19:g.224586G>A	ENSP00000264932:p.Ala88Thr	215.0	0.0	.		165.0	27.0	.	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Missense_Mutation	SNP	ENST00000264932.6	hg19	CCDS3853.1	.	.	.	.	.	.	.	.	.	.	g	25.0	4.594697	0.86953	.	.	ENSG00000073578	ENST00000264932;ENST00000327872;ENST00000504309;ENST00000510361	T;T;T	0.72282	-0.64;-0.64;-0.09	5.56	5.56	0.83823	Fumarate reductase/succinate dehydrogenase flavoprotein, N-terminal (1);	0.000000	0.85682	U	0.000000	D	0.84192	0.5418	M	0.75264	2.295	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;0.997;0.998	D	0.85385	0.1122	10	0.87932	D	0	.	17.4364	0.87553	0.0:0.0:1.0:0.0	.	88;88;88;88;94	E9PBJ5;B4DYN5;D6RFM5;P31040;Q59GW8	.;.;.;DHSA_HUMAN;.	T	88	ENSP00000264932:A88T;ENSP00000426514:A88T;ENSP00000427703:A88T	ENSP00000264932:A88T	A	+	1	0	SDHA	277586	1.000000	0.71417	0.200000	0.23457	0.418000	0.31294	9.385000	0.97223	2.794000	0.96219	0.539000	0.68188	GCA	.	.	.	none		0.547	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168		A	224586	G	A	224586	3	1	134	1	0	0	0	0	1	0	0	0	13976	971	34	2	272	2	SDHA	5	224586	Missense_Mutation	SNP	G	TCGA-BQ-7049-01A-11D-1961-08		224586	180690674	7	8252											
ADAMTS12	81792	hgsc.bcm.edu	37	chr5	33596055	33596055	+	Missense_Mutation	SNP	T	T	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	ttacctgggtggacaagcctTttcatggcacttcttctgtc	6	15	9	11	0	3	0	1	0	2	0	4	1	3	1	2	3	2	1	2	3	2	5			TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr5:33596055T>G	ENST00000504830.1	-	17	2973	c.2638A>C	c.(2638-2640)Aag>Cag	p.K880Q	ADAMTS12_ENST00000352040.3_Missense_Mutation_p.K795Q|ADAMTS12_ENST00000504582.1_5'UTR	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	880	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						GGACAAGCCTTTTCATGGCAC	0.507										HNSCC(64;0.19)																											p.K880Q		Atlas-SNP	.											.	ADAMTS12	464	.	0			c.A2638C						PASS	.						225	189	201					5																	33596055		2203	4300	6503	SO:0001583	missense	81792	exon17			AAGCCTTTTCATG	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.2638A>C	chr5.hg19:g.33596055T>G	ENSP00000422554:p.Lys880Gln	181.0	0.0	.		168.0	30.0	.	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	hg19	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	T	11.21	1.571445	0.28003	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.52526	0.66;0.66	5.77	3.29	0.37713	.	0.320980	0.41500	N	0.000878	T	0.20861	0.0502	N	0.03891	-0.335	0.80722	D	1	B;B	0.15473	0.013;0.001	B;B	0.13407	0.007;0.009	T	0.04178	-1.0971	10	0.15066	T	0.55	.	8.4354	0.32784	0.0:0.0654:0.3833:0.5514	.	795;880	P58397-3;P58397	.;ATS12_HUMAN	Q	880;795	ENSP00000422554:K880Q;ENSP00000344847:K795Q	ENSP00000344847:K795Q	K	-	1	0	ADAMTS12	33631812	0.975000	0.34042	1.000000	0.80357	0.993000	0.82548	0.949000	0.29109	0.494000	0.27859	0.477000	0.44152	AAG	.	.	.	none		0.507	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		G	33596055	T	G	33596055	3	3	134	1	0	0	0	0	1	0	0	0	257	1850	64	5	2178	5	ADAMTS12	5	33596055	Missense_Mutation	SNP	T	TCGA-BQ-7049-01A-11D-1961-08	33371469	33596055	147319205	8	8253											
DBN1	1627	hgsc.bcm.edu	37	chr5	176895199	176895199	+	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	ttctggttctcaaagtgtccCgaaagctcctgcaagccccc	8	10	8	15	1	2	0	1	0	2	0	5	1	4	0	4	1	3	3	4	1	3	2			TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr5:176895199C>A	ENST00000309007.5	-	3	384	c.165G>T	c.(163-165)tcG>tcT	p.S55S	DBN1_ENST00000292385.5_Silent_p.S57S|DBN1_ENST00000393565.1_Silent_p.S55S	NM_004395.3	NP_004386	Q16643	DREB_HUMAN	drebrin 1	55	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				actin filament organization (GO:0007015)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|maintenance of protein location in cell (GO:0032507)|neural precursor cell proliferation (GO:0061351)|regulation of dendrite development (GO:0050773)|regulation of neuronal synaptic plasticity (GO:0048168)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|gap junction (GO:0005921)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|profilin binding (GO:0005522)	p.S55S(1)|p.S57S(1)		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)			CAAAGTGTCCCGAAAGCTCCT	0.522																																					p.S57S		Atlas-SNP	.											.	DBN1	122	.	2	Substitution - coding silent(2)	kidney(2)	c.G171T						PASS	.						153	158	156					5																	176895199		2203	4300	6503	SO:0001819	synonymous_variant	1627	exon4			GTGTCCCGAAAGC		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.165G>T	chr5.hg19:g.176895199C>A		306.0	0.0	.		227.0	11.0	.	NM_080881	A8MV58|B2RBG0|Q9UFZ5	Silent	SNP	ENST00000309007.5	hg19	CCDS4420.1																																																																																			.	.	.	none		0.522	DBN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253429.2	NM_080881		A	176895199	C	A	176895199	2	1	134	1	0	0	0	0	0	0	0	1	4254	639	23	4		4	DBN1	5	176895199	Silent	SNP	C	TCGA-BQ-7049-01A-11D-1961-08	143299144	176895199	4020061	9	8254											
HIST1H2BC	8347	hgsc.bcm.edu	37	chr6	26123936	26123936	+	Missense_Mutation	SNP	A	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	gctcaaatatgtcgttaacgAaagaattcatgatgcccatg	14	11	8	8	2	2	2	2	1	0	1	3	3	2	2	1	0	2	2	1	0	5	3			TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr6:26123936A>C	ENST00000314332.5	-	1	202	c.197T>G	c.(196-198)tTc>tGc	p.F66C	HIST1H2AC_ENST00000377791.2_5'Flank|HIST1H2BC_ENST00000396984.1_Missense_Mutation_p.F66C|HIST1H2AC_ENST00000602637.1_5'Flank			P62807	H2B1C_HUMAN	histone cluster 1, H2bc	66					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						GTCGTTAACGAAAGAATTCAT	0.557																																					p.F66C		Atlas-SNP	.											.	HIST1H2BC	35	.	0			c.T197G						PASS	.						157	149	151					6																	26123936		2203	4300	6503	SO:0001583	missense	8347	exon1			TTAACGAAAGAAT	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.197T>G	chr6.hg19:g.26123936A>C	ENSP00000321744:p.Phe66Cys	279.0	0.0	.		226.0	15.0	.	NM_003526	P02278|Q3B872|Q4VB69|Q93078|Q93080	Missense_Mutation	SNP	ENST00000314332.5	hg19	CCDS4584.1	.	.	.	.	.	.	.	.	.	.	.	20.7	4.033354	0.75504	.	.	ENSG00000180596	ENST00000314332;ENST00000396984	T;T	0.27557	1.66;1.66	5.61	5.61	0.85477	Histone-fold (2);Histone core (1);	.	.	.	.	T	0.40932	0.1137	.	.	.	0.41896	D	0.990396	P	0.47253	0.892	P	0.55749	0.783	T	0.38457	-0.9660	8	0.72032	D	0.01	.	15.2833	0.73806	1.0:0.0:0.0:0.0	.	66	P62807	H2B1C_HUMAN	C	66	ENSP00000321744:F66C;ENSP00000380180:F66C	ENSP00000321744:F66C	F	-	2	0	HIST1H2BC	26231915	1.000000	0.71417	0.998000	0.56505	0.277000	0.26821	9.051000	0.93849	2.259000	0.74868	0.528000	0.53228	TTC	.	.	.	none		0.557	HIST1H2BC-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468022.1	NM_003526		C	26123936	A	C	26123936	3	2	134	1	0	0	0	0	1	0	0	0	7149	246	9	5	187	5	HIST1H2BC	6	26123936	Missense_Mutation	SNP	A	TCGA-BQ-7049-01A-11D-1961-08		26123936	144991131	10	8255											
SYNJ2	8871	hgsc.bcm.edu	37	chr6	158516906	158516906	+	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	tcttgtgcccaaggtaccccCgaggaggaagaagtcagccc	10	6	12	13	1	2	1	1	0	1	1	2	4	2	3	4	3	3	1	4	3	4	2			TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr6:158516906C>A	ENST00000355585.4	+	27	4076	c.4001C>A	c.(4000-4002)cCg>cAg	p.P1334Q	SYNJ2_ENST00000367112.1_Missense_Mutation_p.P419Q|SYNJ2_ENST00000367122.2_Missense_Mutation_p.P1289Q	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	1334	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)	p.P1334L(1)		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)		AAGGTACCCCCGAGGAGGAAG	0.642																																					p.P1334Q		Atlas-SNP	.											SYNJ2,NS,carcinoma,0,1	SYNJ2	111	.	1	Substitution - Missense(1)	ovary(1)	c.C4001A						PASS	.						37	45	42					6																	158516906		2203	4300	6503	SO:0001583	missense	8871	exon27			TACCCCCGAGGAG	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.4001C>A	chr6.hg19:g.158516906C>A	ENSP00000347792:p.Pro1334Gln	102.0	0.0	.		74.0	7.0	.	NM_003898	Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	Missense_Mutation	SNP	ENST00000355585.4	hg19	CCDS5254.1	.	.	.	.	.	.	.	.	.	.	C	16.64	3.178918	0.57692	.	.	ENSG00000078269	ENST00000367122;ENST00000355585;ENST00000367112	D;D;T	0.96104	-3.78;-3.91;-0.54	5.79	4.92	0.64577	.	0.093328	0.47852	D	0.000213	D	0.95598	0.8569	L	0.59436	1.845	0.44908	D	0.997928	D;D	0.89917	1.0;1.0	D;D	0.91635	0.988;0.999	D	0.88909	0.3358	10	0.87932	D	0	.	14.599	0.68427	0.0:0.9306:0.0:0.0694	.	729;1334	B4DLC4;O15056	.;SYNJ2_HUMAN	Q	1289;1334;419	ENSP00000356089:P1289Q;ENSP00000347792:P1334Q;ENSP00000356079:P419Q	ENSP00000347792:P1334Q	P	+	2	0	SYNJ2	158436894	0.985000	0.35326	0.029000	0.17559	0.304000	0.27724	4.827000	0.62723	-2.585000	0.00460	-0.781000	0.03364	CCG	.	.	.	none		0.642	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2			A	158516906	C	A	158516906	3	1	134	1	0	0	0	0	1	0	0	0	15465	652	23	4	4107	4	SYNJ2	6	158516906	Missense_Mutation	SNP	C	TCGA-BQ-7049-01A-11D-1961-08	132392970	158516906	12598161	11	8256											
ELN	2006	hgsc.bcm.edu	37	chr7	73474352	73474352	+	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	cctggcgttggcgtggctccCggcattggccctggtggagt	2	10	17	12	3	0	0	0	0	0	0	1	1	1	1	3	7	0	3	3	7	0	2			TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr7:73474352C>A	ENST00000252034.7	+	23	1950	c.1551C>A	c.(1549-1551)ccC>ccA	p.P517P	ELN_ENST00000380553.4_Silent_p.P381P|ELN_ENST00000380575.4_Silent_p.P488P|ELN_ENST00000458204.1_Silent_p.P507P|ELN_ENST00000380562.4_Silent_p.P523P|ELN_ENST00000357036.5_Silent_p.P522P|ELN_ENST00000320492.7_Silent_p.P436P|ELN_ENST00000380584.4_Silent_p.P484P|ELN_ENST00000380576.5_Silent_p.P498P|ELN_ENST00000429192.1_Silent_p.P503P|CTB-51J22.1_ENST00000435932.1_RNA|ELN_ENST00000320399.6_Silent_p.P517P|ELN_ENST00000414324.1_Silent_p.P493P|ELN_ENST00000445912.1_Silent_p.P517P|ELN_ENST00000358929.4_Silent_p.P552P	NM_000501.2|NM_001278915.1	NP_000492.2|NP_001265844.1	P15502	ELN_HUMAN	elastin	0	Ala-rich.				blood circulation (GO:0008015)|blood vessel remodeling (GO:0001974)|cell proliferation (GO:0008283)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|organ morphogenesis (GO:0009887)|regulation of actin filament polymerization (GO:0030833)|respiratory gaseous exchange (GO:0007585)|skeletal muscle tissue development (GO:0007519)|stress fiber assembly (GO:0043149)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(4)|pancreas(2)|prostate(1)|skin(2)|stomach(1)	32		Lung NSC(55;0.159)				GCGTGGCTCCCGGCATTGGCC	0.647			T	PAX5	B-ALL		"Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome"																														p.P522P		Atlas-SNP	.		Dom	yes		7	7q11.23	2006	elastin	yes	L	.	ELN	81	.	0			c.C1566A						PASS	.						109	104	105					7																	73474352		2203	4300	6503	SO:0001819	synonymous_variant	2006	exon23			GGCTCCCGGCATT		CCDS5562.2, CCDS43598.1, CCDS43599.1, CCDS47611.1, CCDS47612.1, CCDS64673.1, CCDS64674.1, CCDS64675.1, CCDS64676.1, CCDS64677.1, CCDS64678.1, CCDS75616.1, CCDS75617.1	7q11.1-q21.1	2008-08-01	2008-08-01		ENSG00000049540	ENSG00000049540			3327	protein-coding gene	gene with protein product	"tropoelastin", "supravalvular aortic stenosis", "Williams-Beuren syndrome"	130160				8096434	Standard	NM_001278939		Approved	WBS, WS, SVAS	uc003tzn.3	P15502	OTTHUMG00000150229	ENST00000252034.7:c.1551C>A	chr7.hg19:g.73474352C>A		227.0	0.0	.		182.0	9.0	.	NM_001081754	B3KTS6|O15336|O15337|Q14233|Q14234|Q14235|Q14238|Q6P0L4|Q6ZWJ6|Q75MU5|Q7Z316|Q7Z3F5|Q9UMF5	Silent	SNP	ENST00000252034.7	hg19	CCDS5562.2																																																																																			.	.	.	none		0.647	ELN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316913.1	NM_000501		A	73474352	C	A	73474352	2	1	134	1	0	0	0	0	0	0	0	1	5073	639	23	4		4	ELN	7	73474352	Silent	SNP	C	TCGA-BQ-7049-01A-11D-1961-08		73474352	85664311	12	8257											
ELAVL2	1993	hgsc.bcm.edu	37	chr9	23762205	23762205	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attggctgtgttattgcaagTtggcccattagacagttgtg	8	15	12	6	0	0	1	0	0	0	1	0	1	0	1	1	2	1	5	1	2	3	6			TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr9:23762205T>C	ENST00000397312.2	-	2	302	c.28A>G	c.(28-30)Act>Gct	p.T10A	ELAVL2_ENST00000380110.4_Missense_Mutation_p.T39A|ELAVL2_ENST00000223951.6_Missense_Mutation_p.T10A|ELAVL2_ENST00000462649.1_5'Flank|ELAVL2_ENST00000380117.1_Missense_Mutation_p.T10A|ELAVL2_ENST00000544538.1_Missense_Mutation_p.T10A	NM_004432.3	NP_004423.2	Q12926	ELAV2_HUMAN	ELAV like neuron-specific RNA binding protein 2	10					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)		TTATTGCAAGTTGGCCCATTA	0.403																																					p.T10A		Atlas-SNP	.											.	ELAVL2	80	.	0			c.A28G						PASS	.						296	273	281					9																	23762205		2203	4299	6502	SO:0001583	missense	1993	exon2			TGCAAGTTGGCCC	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.28A>G	chr9.hg19:g.23762205T>C	ENSP00000380479:p.Thr10Ala	388.0	0.0	.		433.0	83.0	.	NM_001171195	D3DRK3|Q13235|Q59G15|Q8NEM4|Q9H1Q8	Missense_Mutation	SNP	ENST00000397312.2	hg19	CCDS6515.1	.	.	.	.	.	.	.	.	.	.	T	11.52	1.662813	0.29515	.	.	ENSG00000107105	ENST00000223951;ENST00000397312;ENST00000544538;ENST00000380110;ENST00000380117;ENST00000359598;ENST00000440102	T;T;T;T;T	0.13196	2.61;3.01;3.01;3.01;2.92	5.92	5.92	0.95590	.	0.225320	0.44688	D	0.000426	T	0.07728	0.0194	N	0.04508	-0.205	0.50039	D	0.999841	B;B	0.02656	0.0;0.0	B;B	0.12156	0.001;0.007	T	0.38112	-0.9676	10	0.19147	T	0.46	.	16.371	0.83361	0.0:0.0:0.0:1.0	.	10;10	Q12926;Q12926-2	ELAV2_HUMAN;.	A	10;10;10;10;10;38;10	ENSP00000223951:T10A;ENSP00000380479:T10A;ENSP00000440998:T10A;ENSP00000369460:T10A;ENSP00000412602:T10A	ENSP00000223951:T10A	T	-	1	0	ELAVL2	23752205	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.014000	0.64029	2.267000	0.75376	0.477000	0.44152	ACT	.	.	.	none		0.403	ELAVL2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051943.2	NM_004432		C	23762205	T	C	23762205	3	2	134	1	0	0	0	0	1	0	0	0	5052	1725	60	3	1075	3	ELAVL2	9	23762205	Missense_Mutation	SNP	T	TCGA-BQ-7049-01A-11D-1961-08		23762205	117451226	13	8258											
ZNF618	114991	hgsc.bcm.edu	37	chr9	116812343	116812343	+	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	cggccgtgggcgccagaagcGggtgtgtaaatatgtgtgaa	9	8	17	7	4	0	2	0	1	0	1	0	2	0	2	2	3	1	1	2	3	5	2			TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr9:116812343G>T	ENST00000374126.5	+	15	2860	c.2761G>T	c.(2761-2763)Ggg>Tgg	p.G921W	ZNF618_ENST00000470105.1_3'UTR|ZNF618_ENST00000288466.7_Missense_Mutation_p.G828W			Q5T7W0	ZN618_HUMAN	zinc finger protein 618	921					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						CGCCAGAAGCGGGTGTGTAAA	0.512																																					p.G828W		Atlas-SNP	.											ZNF618_ENST00000374126,NS,carcinoma,0,3	ZNF618	184	.	0			c.G2482T						PASS	.						56	62	60					9																	116812343		1833	4080	5913	SO:0001583	missense	114991	exon14			AGAAGCGGGTGTG	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.2761G>T	chr9.hg19:g.116812343G>T	ENSP00000363241:p.Gly921Trp	155.0	0.0	.		179.0	8.0	.	NM_133374	B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49	Missense_Mutation	SNP	ENST00000374126.5	hg19		.	.	.	.	.	.	.	.	.	.	G	20.8	4.056794	0.76074	.	.	ENSG00000157657	ENST00000374126;ENST00000288466	T;T	0.21734	1.99;1.99	5.93	5.93	0.95920	Ribonuclease H-like (1);	0.099558	0.64402	D	0.000002	T	0.46308	0.1386	.	.	.	0.52501	D	0.999958	P;D;D	0.62365	0.953;0.981;0.991	P;P;P	0.59424	0.739;0.652;0.857	T	0.38499	-0.9658	9	0.87932	D	0	-36.171	19.3319	0.94293	0.0:0.0:1.0:0.0	.	888;921;828	B9EG82;Q5T7W0;Q5T7W0-2	.;ZN618_HUMAN;.	W	921;828	ENSP00000363241:G921W;ENSP00000288466:G828W	ENSP00000288466:G828W	G	+	1	0	ZNF618	115852164	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	7.265000	0.78442	2.815000	0.96918	0.561000	0.74099	GGG	.	.	.	none		0.512	ZNF618-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000053749.1	XM_054983		T	116812343	G	T	116812343	3	4	134	1	0	0	0	0	1	0	0	0	18054	1116	39	4	2536	4	ZNF618	9	116812343	Missense_Mutation	SNP	G	TCGA-BQ-7049-01A-11D-1961-08	93050138	116812343	24401088	14	8259											
PDCD11	22984	hgsc.bcm.edu	37	chr10	105202030	105202030	+	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	aggcagagaaggaactgtccCgcattgaggaggcgctgatg	11	6	16	8	2	0	3	0	2	0	1	1	6	1	5	1	4	1	3	1	4	2	1	rs576894256		TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr10:105202030C>A	ENST00000369797.3	+	32	4862	c.4768C>A	c.(4768-4770)Cgc>Agc	p.R1590S		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	1590					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)		GGAACTGTCCCGCATTGAGGA	0.537																																					p.R1590S		Atlas-SNP	.											.	PDCD11	160	.	0			c.C4768A						PASS	.						107	109	109					10																	105202030		2203	4300	6503	SO:0001583	missense	22984	exon32			CTGTCCCGCATTG	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.4768C>A	chr10.hg19:g.105202030C>A	ENSP00000358812:p.Arg1590Ser	180.0	0.0	.		187.0	11.0	.	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	hg19	CCDS31276.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.002691	0.74932	.	.	ENSG00000148843	ENST00000369797	T	0.40756	1.02	5.27	5.27	0.74061	.	0.110569	0.64402	D	0.000014	T	0.41396	0.1157	N	0.25485	0.75	0.40880	D	0.983985	D	0.60160	0.987	P	0.55577	0.779	T	0.10382	-1.0632	10	0.20519	T	0.43	-15.7903	12.4343	0.55590	0.2802:0.7198:0.0:0.0	.	1590	Q14690	RRP5_HUMAN	S	1590	ENSP00000358812:R1590S	ENSP00000358812:R1590S	R	+	1	0	PDCD11	105192020	0.998000	0.40836	1.000000	0.80357	0.849000	0.48306	2.898000	0.48672	2.619000	0.88677	0.561000	0.74099	CGC	.	.	.	none		0.537	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1			A	105202030	C	A	105202030	3	1	134	1	0	0	0	0	1	0	0	0	11624	652	23	4	4890	4	PDCD11	10	105202030	Missense_Mutation	SNP	C	TCGA-BQ-7049-01A-11D-1961-08		105202030	30332717	15	8260											
NLRX1	79671	hgsc.bcm.edu	37	chr11	119051968	119051968	+	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	gccaaattaccacactgcggTgagtgacctgggagtggggc	9	7	15	10	1	0	2	0	2	0	0	0	3	0	3	3	4	2	0	3	4	2	1			TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr11:119051968T>A	ENST00000409109.1	+	8	2941		c.e8+2		NLRX1_ENST00000292199.2_Splice_Site|NLRX1_ENST00000409991.1_Splice_Site|NLRX1_ENST00000409265.4_Splice_Site|NLRX1_ENST00000525863.1_Splice_Site	NM_001282144.1	NP_001269073.1	Q86UT6	NLRX1_HUMAN	NLR family member X1						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)		CACACTGCGGTGAGTGACCTG	0.582																																					.		Atlas-SNP	.											.	NLRX1	128	.	0			c.2354+2T>A						PASS	.						85	68	74					11																	119051968		2200	4295	6495	SO:0001630	splice_region_variant	79671	exon8			CTGCGGTGAGTGA	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.2354+2T>A	chr11.hg19:g.119051968T>A		55.0	0.0	.		59.0	16.0	.	NM_024618	A8K6Q1|B3KPK2|B3KTA2|Q7RTR3|Q96D51|Q9H724	Splice_Site	SNP	ENST00000409109.1	hg19	CCDS8416.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.200656	0.79015	.	.	ENSG00000160703	ENST00000409991;ENST00000292199;ENST00000409265;ENST00000409109;ENST00000525863	.	.	.	5.36	5.36	0.76844	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.9739	0.58527	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	NLRX1	118557178	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	5.819000	0.69243	2.246000	0.74042	0.533000	0.62120	.	.	.	.	none		0.582	NLRX1-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335403.1	NM_170722	Intron	A	119051968	T	A	119051968	5	1	134	1	0	0	0	0	0	0	1	0	10492	1710	59	5	2382	5	NLRX1	11	119051968	Splice_Site	SNP	T	TCGA-BQ-7049-01A-11D-1961-08		119051968	15954548	16	8261											
UTP20	27340	hgsc.bcm.edu	37	chr12	101693787	101693787	+	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	aaggtgataccactcgtcacCggcttcatagaggcactctt	10	10	9	12	2	3	2	2	1	1	1	4	2	3	2	2	3	1	2	2	3	3	4			TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr12:101693787C>A	ENST00000261637.4	+	14	1797	c.1623C>A	c.(1621-1623)acC>acA	p.T541T		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	541					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						CACTCGTCACCGGCTTCATAG	0.438																																					p.T541T		Atlas-SNP	.											.	UTP20	222	.	0			c.C1623A						PASS	.						207	200	203					12																	101693787		2203	4300	6503	SO:0001819	synonymous_variant	27340	exon14			CGTCACCGGCTTC	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.1623C>A	chr12.hg19:g.101693787C>A		310.0	0.0	.		368.0	17.0	.	NM_014503	Q9H3H4	Silent	SNP	ENST00000261637.4	hg19	CCDS9081.1																																																																																			.	.	.	none		0.438	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		A	101693787	C	A	101693787	2	1	134	1	0	0	0	0	0	0	0	1	17111	639	23	4		4	UTP20	12	101693787	Silent	SNP	C	TCGA-BQ-7049-01A-11D-1961-08		101693787	32158108	17	8262											
TSC2	7249	hgsc.bcm.edu	37	chr16	2129191	2129191	+	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	ctccaacttcacggctgtccCgaagaggtccaggcggcact	8	7	11	15	3	1	1	1	0	0	1	4	2	4	1	3	4	1	2	3	4	2	1			TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr16:2129191C>A	ENST00000219476.3	+	27	3755	c.3125C>A	c.(3124-3126)cCg>cAg	p.P1042Q	TSC2_ENST00000568454.1_Missense_Mutation_p.P1009Q|TSC2_ENST00000382538.6_Missense_Mutation_p.P950Q|TSC2_ENST00000439673.2_Missense_Mutation_p.P962Q|TSC2_ENST00000353929.4_Missense_Mutation_p.P999Q|TSC2_ENST00000350773.4_Missense_Mutation_p.P1042Q|TSC2_ENST00000401874.2_Missense_Mutation_p.P998Q|TSC2_ENST00000568366.1_3'UTR	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	1042					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)				ACGGCTGTCCCGAAGAGGTCC	0.617			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.P1042Q		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	.	TSC2	364	.	0			c.C3125A						PASS	.						84	71	75					16																	2129191		2198	4300	6498	SO:0001583	missense	7249	exon27	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	CTGTCCCGAAGAG	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.3125C>A	chr16.hg19:g.2129191C>A	ENSP00000219476:p.Pro1042Gln	149.0	0.0	.		101.0	7.0	.	NM_001114382	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Missense_Mutation	SNP	ENST00000219476.3	hg19	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	C	18.22	3.576568	0.65878	.	.	ENSG00000103197	ENST00000219476;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000382538;ENST00000350773	D;D;D;D;D	0.93076	-3.16;-3.02;-3.03;-3.03;-3.08	4.97	4.97	0.65823	.	0.125602	0.53938	D	0.000046	D	0.96531	0.8868	M	0.75615	2.305	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;0.998;0.999;0.999;1.0;1.0	D;D;D;D;D;D	0.97110	0.989;0.979;0.993;0.993;1.0;0.997	D	0.97151	0.9831	10	0.87932	D	0	-37.0385	18.23	0.89931	0.0:1.0:0.0:0.0	.	950;962;1042;998;998;1042	B4DIL8;P49815-6;P49815-4;P49815-3;P49815-5;P49815	.;.;.;.;.;TSC2_HUMAN	Q	1042;999;999;962;950;1042	ENSP00000219476:P1042Q;ENSP00000248099:P999Q;ENSP00000399232:P962Q;ENSP00000371978:P950Q;ENSP00000344383:P1042Q	ENSP00000219476:P1042Q	P	+	2	0	TSC2	2069192	1.000000	0.71417	0.992000	0.48379	0.052000	0.14988	7.755000	0.85180	2.306000	0.77630	0.655000	0.94253	CCG	.	.	.	none		0.617	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		A	2129191	C	A	2129191	3	1	134	1	0	0	0	0	1	0	0	0	16618	652	23	4	3227	4	TSC2	16	2129191	Missense_Mutation	SNP	C	TCGA-BQ-7049-01A-11D-1961-08		2129191	88225562	18	8263											
CDR2	1039	hgsc.bcm.edu	37	chr16	22360668	22360668	+	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	ttctcctggtcacactttccCgggctccttctcccttggcc	2	14	7	18	1	3	0	1	0	2	0	7	0	5	0	5	3	0	1	5	3	0	4	rs374733638		TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr16:22360668C>A	ENST00000268383.2	-	4	745	c.438G>T	c.(436-438)ccG>ccT	p.P146P		NM_001802.1	NP_001793.1	Q01850	CDR2_HUMAN	cerebellar degeneration-related protein 2, 62kDa	146						cytoplasm (GO:0005737)				endometrium(3)|large_intestine(3)|lung(3)|skin(1)|urinary_tract(1)	11				GBM - Glioblastoma multiforme(48;0.0188)		CACACTTTCCCGGGCTCCTTC	0.537																																					p.P146P		Atlas-SNP	.											.	CDR2	34	.	0			c.G438T						PASS	.						112	113	113					16																	22360668		2197	4300	6497	SO:0001819	synonymous_variant	1039	exon4			CTTTCCCGGGCTC	M63256	CCDS32404.1	16p13.1-p12	2008-02-05	2002-08-29			ENSG00000140743			1799	protein-coding gene	gene with protein product	"Yo paraneoplastic antigen"	117340	"cerebellar degeneration-related protein (62kD)"			2014264	Standard	NM_001802		Approved	CDR62, Yo	uc002dkn.3	Q01850		ENST00000268383.2:c.438G>T	chr16.hg19:g.22360668C>A		230.0	0.0	.		211.0	10.0	.	NM_001802	A8K8A8|Q13977	Silent	SNP	ENST00000268383.2	hg19	CCDS32404.1																																																																																			.	.	.	alt		0.537	CDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430081.1			A	22360668	C	A	22360668	2	1	134	1	0	0	0	0	0	0	0	1	3174	639	23	4		4	CDR2	16	22360668	Silent	SNP	C	TCGA-BQ-7049-01A-11D-1961-08	20231477	22360668	67994085	19	8264											
ZNF404	342908	hgsc.bcm.edu	37	chr19	44378055	44378055	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatttgactaaaacatcccActttaggtctctgttgtctc	9	16	5	11	0	3	1	1	1	2	0	6	1	4	1	1	1	1	1	1	1	3	5			TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr19:44378055A>G	ENST00000587539.1	-	3	310	c.311T>C	c.(310-312)gTg>gCg	p.V104A	ZNF404_ENST00000324394.6_Missense_Mutation_p.V102A	NM_001033719.2	NP_001028891.2	Q494X3	ZN404_HUMAN	zinc finger protein 404	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)			NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|skin(1)|stomach(2)|urinary_tract(1)	17		Prostate(69;0.0352)				AAAACATCCCACTTTAGGTCT	0.333																																					p.V101A		Atlas-SNP	.											.	ZNF404	46	.	0			c.T302C						PASS	.						137	146	143					19																	44378055		1838	4087	5925	SO:0001583	missense	342908	exon2			CATCCCACTTTAG	XM_092027	CCDS59394.1	19q13.31	2013-01-08				ENSG00000176222		"Zinc fingers, C2H2-type", "-"	19417	protein-coding gene	gene with protein product							Standard	NM_001033719		Approved		uc002oxs.5	Q494X3		ENST00000587539.1:c.311T>C	chr19.hg19:g.44378055A>G	ENSP00000466051:p.Val104Ala	264.0	0.0	.		343.0	16.0	.	NM_001033719	A4FU30|K7ELF2	Missense_Mutation	SNP	ENST00000587539.1	hg19	CCDS59394.1	.	.	.	.	.	.	.	.	.	.	A	0	-2.730337	0.00089	.	.	ENSG00000176222	ENST00000324394	T	0.06142	3.34	2.99	0.516	0.17019	.	.	.	.	.	T	0.03695	0.0105	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.45116	-0.9283	9	0.27082	T	0.32	.	7.3893	0.26901	0.6601:0.0:0.0:0.3399	.	104	Q494X3	ZN404_HUMAN	A	102	ENSP00000319479:V102A	ENSP00000319479:V102A	V	-	2	0	ZNF404	49069895	0.355000	0.24921	0.001000	0.08648	0.012000	0.07955	1.127000	0.31357	0.341000	0.23771	-0.898000	0.02899	GTG	.	.	.	none		0.333	ZNF404-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460019.1	NM_001033719		G	44378055	A	G	44378055	3	3	134	1	0	0	0	0	1	0	0	0	17898	159	6	3	1351	3	ZNF404	19	44378055	Missense_Mutation	SNP	A	TCGA-BQ-7049-01A-11D-1961-08		44378055	14750928	20	8265											
C19orf63	284361	hgsc.bcm.edu	37	chr19	50981244	50981244	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtggggctgctgctggagcActcatttgagatcggtgagt	6	11	17	7	1	1	2	1	2	0	1	2	4	1	3	0	5	3	4	0	5	0	1			TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr19:50981244A>G	ENST00000334976.6	+	2	219	c.173A>G	c.(172-174)cAc>cGc	p.H58R	EMC10_ENST00000598585.1_Missense_Mutation_p.H58R|FAM71E1_ENST00000600100.1_5'Flank|CTD-2545M3.2_ENST00000598194.1_RNA|FAM71E1_ENST00000595790.1_5'Flank|EMC10_ENST00000376918.3_Missense_Mutation_p.H58R	NM_206538.2	NP_996261.1	Q5UCC4	EMC10_HUMAN	ER membrane protein complex subunit 10	58						ER membrane protein complex (GO:0072546)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)											CTGCTGGAGCACTCATTTGAG	0.607																																					p.H58R		Atlas-SNP	.											.	.	.	.	0			c.A173G						PASS	.						115	107	110					19																	50981244		2203	4300	6503	SO:0001583	missense	284361	exon2			TGGAGCACTCATT	BC062607	CCDS12796.1, CCDS42594.1	19q13.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000161671	ENSG00000161671			27609	protein-coding gene	gene with protein product	"hematopoietic signal peptide-containing secreted 1", "hematopoietic signal peptide-containing membrane domain-containing 1"	614545	"chromosome 19 open reading frame 63"	C19orf63		12975309, 22119785	Standard	NM_175063		Approved	INM02, HSS1, HSM1	uc002psl.3	Q5UCC4		ENST00000334976.6:c.173A>G	chr19.hg19:g.50981244A>G	ENSP00000334037:p.His58Arg	132.0	0.0	.		101.0	22.0	.	NM_175063	Q5UCC6|Q69YT5|Q6UWP3|Q86YL4|Q8N541	Missense_Mutation	SNP	ENST00000334976.6	hg19	CCDS12796.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.991013	0.74703	.	.	ENSG00000161671	ENST00000334976;ENST00000376918;ENST00000376920	.	.	.	4.4	4.4	0.53042	.	0.108519	0.64402	D	0.000008	T	0.75788	0.3897	M	0.71036	2.16	0.80722	D	1	D;D;D	0.89917	1.0;0.989;0.999	D;D;D	0.75020	0.984;0.985;0.961	T	0.78797	-0.2063	9	0.87932	D	0	-17.5433	11.7796	0.52006	1.0:0.0:0.0:0.0	.	58;58;58	Q5UCC4;Q5UCC4-2;Q5UCC4-3	INM02_HUMAN;.;.	R	58	.	ENSP00000334037:H58R	H	+	2	0	C19orf63	55673056	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.415000	0.66411	1.909000	0.55274	0.402000	0.26972	CAC	.	.	.	none		0.607	EMC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464760.2	NM_175063		G	50981244	A	G	50981244	3	3	134	1	0	0	0	0	1	0	0	0	1947	159	6	3	179	3	C19orf63	19	50981244	Missense_Mutation	SNP	A	TCGA-BQ-7049-01A-11D-1961-08	6603189	50981244	8147739	21	8266											
ZNF761	388561	hgsc.bcm.edu	37	chr19	53959648	53959648	+	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	tgccatcgtagacttcatacCggagagaaaccttacaaatg	14	9	8	10	2	1	2	1	0	0	2	2	4	1	3	3	1	4	1	3	1	5	4	rs373072898		TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr19:53959648C>A	ENST00000454407.1	+	0	2340							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		GACTTCATACCGGAGAGAAAC	0.408																																					p.T629T		Atlas-SNP	.											ZNF761,NS,carcinoma,0,1	ZNF761	104	.	0			c.C1887A						PASS	.						112	116	115					19																	53959648		2202	4300	6502			388561	exon7			TCATACCGGAGAG	AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"Zinc fingers, C2H2-type"	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		chr19.hg19:g.53959648C>A		160.0	0.0	.		163.0	7.0	.	NM_001008401	Q6ZNB9	Silent	SNP	ENST00000454407.1	hg19																																																																																				.	.	.	alt		0.408	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401		A	53959648	C	A	53959648	1	1	134	0	1	0	0	0	0	0	0	0	18148	639	23	4		4	ZNF761	19	53959648	RNA	SNP	C	TCGA-BQ-7049-01A-11D-1961-08	2978404	53959648	5169335	22	8267											
TM9SF4	9777	hgsc.bcm.edu	37	chr20	30723909	30723909	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	accagctctcgaacccagctAccttatgaatactattcact	12	11	4	14	1	2	1	1	1	1	0	3	2	2	1	3	0	5	2	3	0	6	5			TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr20:30723909A>G	ENST00000398022.2	+	3	397	c.162A>G	c.(160-162)ctA>ctG	p.L54L	TM9SF4_ENST00000217315.5_Silent_p.L37L	NM_014742.3	NP_055557.2	Q92544	TM9S4_HUMAN	transmembrane 9 superfamily protein member 4	54						integral component of membrane (GO:0016021)				central_nervous_system(2)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			GAACCCAGCTACCTTATGAAT	0.483																																					p.L54L		Atlas-SNP	.											.	TM9SF4	65	.	0			c.A162G						PASS	.						120	99	106					20																	30723909		2203	4300	6503	SO:0001819	synonymous_variant	9777	exon3			CCAGCTACCTTAT	BC021107	CCDS13196.2	20q11.21	2004-04-19			ENSG00000101337	ENSG00000101337			30797	protein-coding gene	gene with protein product						9039502	Standard	NM_014742		Approved	KIAA0255, dJ836N17.2	uc002wxj.2	Q92544	OTTHUMG00000032206	ENST00000398022.2:c.162A>G	chr20.hg19:g.30723909A>G		84.0	0.0	.		109.0	5.0	.	NM_014742	B0QYT7|Q9NUA3	Silent	SNP	ENST00000398022.2	hg19	CCDS13196.2																																																																																			.	.	.	none		0.483	TM9SF4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323568.1	NM_014742		G	30723909	A	G	30723909	2	3	134	1	0	0	0	0	0	0	0	1	15992	378	14	3		3	TM9SF4	20	30723909	Silent	SNP	A	TCGA-BQ-7049-01A-11D-1961-08		30723909	32301611	23	8268											
IFT52	51098	hgsc.bcm.edu	37	chr20	42265804	42265804	+	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	ggtttttcctcccagtttccGggagttaccacctcctcctc	4	14	7	16	1	0	0	0	0	0	0	6	1	5	1	7	2	1	3	7	2	1	4	rs145627647	byFrequency	TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr20:42265804G>T	ENST00000373030.3	+	12	1161	c.1031G>T	c.(1030-1032)cGg>cTg	p.R344L	IFT52_ENST00000373039.4_Missense_Mutation_p.R344L	NM_016004.2	NP_057088.2	Q9Y366	IFT52_HUMAN	intraflagellar transport 52	344					cilium morphogenesis (GO:0060271)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|intraciliary transport (GO:0042073)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube formation (GO:0001841)|regulation of protein processing (GO:0070613)|smoothened signaling pathway (GO:0007224)	centriole (GO:0005814)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|dendrite terminus (GO:0044292)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|photoreceptor connecting cilium (GO:0032391)	protein C-terminus binding (GO:0008022)			endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			CCCAGTTTCCGGGAGTTACCA	0.418																																					p.R344L		Atlas-SNP	.											.	IFT52	40	.	0			c.G1031T						PASS	.						83	83	83					20																	42265804		2203	4300	6503	SO:0001583	missense	51098	exon12			GTTTCCGGGAGTT	AF151811	CCDS33470.1	20q12-q13.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000101052	ENSG00000101052		"Intraflagellar transport homologs"	15901	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 9", "intraflagellar transport 52 homolog (Chlamydomonas)"	C20orf9		10810093	Standard	NM_016004		Approved	CGI-53, NGD5, dJ1028D15.1, NGD2	uc002xkw.3	Q9Y366	OTTHUMG00000032513	ENST00000373030.3:c.1031G>T	chr20.hg19:g.42265804G>T	ENSP00000362121:p.Arg344Leu	138.0	0.0	.		191.0	9.0	.	NM_016004	B3KMA1|E1P5W9|Q5H8Z0|Q9H1G3|Q9H1G4|Q9H1H2	Missense_Mutation	SNP	ENST00000373030.3	hg19	CCDS33470.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.203933	0.79127	.	.	ENSG00000101052	ENST00000373030;ENST00000373039	.	.	.	5.27	5.27	0.74061	.	0.048064	0.85682	D	0.000000	T	0.66954	0.2842	M	0.84683	2.71	0.80722	D	1	P	0.43094	0.799	B	0.37198	0.243	T	0.74618	-0.3605	9	0.52906	T	0.07	-17.1501	18.0301	0.89281	0.0:0.0:1.0:0.0	.	344	Q9Y366	IFT52_HUMAN	L	344	.	ENSP00000362121:R344L	R	+	2	0	IFT52	41699218	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	6.421000	0.73353	2.628000	0.89032	0.655000	0.94253	CGG	.	G|0.999;A|0.001	.	alt		0.418	IFT52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079317.1	NM_016004		T	42265804	G	T	42265804	3	4	134	1	0	0	0	0	1	0	0	0	7568	1116	39	4	1073	4	IFT52	20	42265804	Missense_Mutation	SNP	G	TCGA-BQ-7049-01A-11D-1961-08	11541895	42265804	20759716	24	8269											
MYH9	4627	hgsc.bcm.edu	37	chr22	36714304	36714304	+	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	cccgtcccaccttgatgcgcGgggtgaggattcctctggtg	4	10	14	13	3	1	2	0	2	1	0	3	3	3	3	4	4	1	0	4	4	0	2			TCGA-BQ-7049-01A-11D-1961-08	TCGA-BQ-7049-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	91478a08-9bea-426b-bd0c-ca7cc87297b1	fd0fcf99-b8da-43e8-9ccb-9c792ac32047	g.chr22:36714304G>T	ENST00000216181.5	-	11	1405	c.1175C>A	c.(1174-1176)cCg>cAg	p.P392Q	RN7SL349P_ENST00000582364.1_RNA	NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	392	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						CTTGATGCGCGGGGTGAGGAT	0.532			T	ALK	ALCL		"Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"		Hereditary Macrothrombocytopenia, MYH9-associated																												p.P392Q		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"myosin, heavy polypeptide 9, non-muscle"	yes	L	.	MYH9	225	.	0			c.C1175A						PASS	.						203	197	199					22																	36714304		2203	4300	6503	SO:0001583	missense	4627	exon11	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	ATGCGCGGGGTGA		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.1175C>A	chr22.hg19:g.36714304G>T	ENSP00000216181:p.Pro392Gln	322.0	0.0	.		284.0	12.0	.	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Missense_Mutation	SNP	ENST00000216181.5	hg19	CCDS13927.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.032337	0.93575	.	.	ENSG00000100345	ENST00000337818;ENST00000216181	D	0.87729	-2.29	4.96	4.96	0.65561	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.94791	0.8318	M	0.90369	3.11	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95721	0.8766	10	0.87932	D	0	.	18.2503	0.90000	0.0:0.0:1.0:0.0	.	392	P35579	MYH9_HUMAN	Q	256;392	ENSP00000216181:P392Q	ENSP00000216181:P392Q	P	-	2	0	MYH9	35044250	1.000000	0.71417	0.979000	0.43373	0.987000	0.75469	9.813000	0.99286	2.475000	0.83589	0.650000	0.86243	CCG	.	.	.	none		0.532	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473		T	36714304	G	T	36714304	3	4	134	1	0	0	0	0	1	0	0	0	10049	1116	39	4	4831	4	MYH9	22	36714304	Missense_Mutation	SNP	G	TCGA-BQ-7049-01A-11D-1961-08		36714304	14590262	25	8270											
ASH1L	55870	hgsc.bcm.edu	37	chr1	155317614	155317614	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatctcatcaatctgggctgAtgcctcatgccgggcattgt	8	12	10	11	1	4	1	3	1	2	0	5	1	4	1	2	2	2	2	2	2	2	1			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr1:155317614A>G	ENST00000368346.3	-	20	8290	c.7651T>C	c.(7651-7653)Tca>Cca	p.S2551P	ASH1L_ENST00000392403.3_Missense_Mutation_p.S2546P|MIR555_ENST00000384987.1_RNA			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	2551					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)			ATCTGGGCTGATGCCTCATGC	0.488																																					p.S2546P		Atlas-SNP	.											.	ASH1L	279	.	0			c.T7636C						PASS	.						197	160	173					1																	155317614		2203	4300	6503	SO:0001583	missense	55870	exon20			GGGCTGATGCCTC	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.7651T>C	chr1.hg19:g.155317614A>G	ENSP00000357330:p.Ser2551Pro	146.0	0.0	.		137.0	59.0	.	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	hg19		.	.	.	.	.	.	.	.	.	.	A	17.35	3.367145	0.61513	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	T;T	0.16743	2.32;2.32	5.4	5.4	0.78164	Bromodomain (3);	0.058282	0.64402	D	0.000002	T	0.07007	0.0178	N	0.08118	0	0.80722	D	1	P;P	0.50272	0.89;0.933	B;P	0.49752	0.417;0.621	T	0.21177	-1.0253	10	0.45353	T	0.12	.	10.9753	0.47463	0.7253:0.2747:0.0:0.0	.	2551;2546	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	P	2551;2546	ENSP00000357330:S2551P;ENSP00000376204:S2546P	ENSP00000357330:S2551P	S	-	1	0	ASH1L	153584238	0.923000	0.31300	1.000000	0.80357	0.998000	0.95712	2.017000	0.40981	2.266000	0.75297	0.533000	0.62120	TCA	.	.	.	none		0.488	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		G	155317614	A	G	155317614	3	3	135	1	0	0	0	0	1	0	0	0	1041	333	12	3	1294	3	ASH1L	1	155317614	Missense_Mutation	SNP	A	TCGA-BQ-7050-01A-11D-1961-08		155317614	93933007	1	8271											
ATP1B1	481	hgsc.bcm.edu	37	chr1	169076130	169076130	+	Frame_Shift_Del	DEL	G	G	-																															ttcatctggaactcagagaaGaaggagtttctgggcaggac																										TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr1:169076130delG	ENST00000367816.1	+	2	592	c.63delG	c.(61-63)aagfs	p.K22fs	RP5-1018K9.1_ENST00000415637.1_RNA|ATP1B1_ENST00000367815.4_Frame_Shift_Del_p.K22fs|ATP1B1_ENST00000499679.3_5'Flank			P05026	AT1B1_HUMAN	ATPase, Na+/K+ transporting, beta 1 polypeptide	22					blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular potassium ion homeostasis (GO:0030007)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|leukocyte migration (GO:0050900)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|positive regulation of ATP catabolic process (GO:1903291)|positive regulation of ATPase activity (GO:0032781)|positive regulation of calcium:sodium antiporter activity (GO:1903281)|positive regulation of potassium ion import (GO:1903288)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of sodium ion export from cell (GO:1903278)|potassium ion import (GO:0010107)|protein localization to plasma membrane (GO:0072659)|protein stabilization (GO:0050821)|protein transport into plasma membrane raft (GO:0044861)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression (GO:0010468)|relaxation of cardiac muscle (GO:0055119)|response to hypoxia (GO:0001666)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|vesicle (GO:0031982)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|MHC class II protein complex binding (GO:0023026)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	14	all_hematologic(923;0.208)					ACTCAGAGAAGAAGGAGTTTC	0.657																																					p.K21fs		Atlas-INDEL	.											.	ATP1B1	29	.	0			c.62delA						PASS	.						51	57	55					1																	169076130		2203	4300	6503	SO:0001589	frameshift_variant	481	exon1			.	U16799	CCDS1276.1	1q24.2	2012-10-22			ENSG00000143153	ENSG00000143153		"ATPases / P-type"	804	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit beta-1", "sodium pump subunit beta-1", "sodium-potassium ATPase subunit beta 1 (non-catalytic)"	182330		ATP1B			Standard	NM_001677		Approved		uc001gfr.1	P05026	OTTHUMG00000034590	ENST00000367816.1:c.63delG	chr1.hg19:g.169076130delG	ENSP00000356790:p.Lys22fs	44.0	0.0	0		42.0	10.0	0.238095	NM_001677	Q5TGZ3	Frame_Shift_Del	DEL	ENST00000367816.1	hg19	CCDS1276.1																																																																																			.	.	.	none		0.657	ATP1B1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083696.1			-	169076130	G	-	169076130	7	5	135	1	0	1	0	1	0	0	0	0	1132	933	33	0	65	0	ATP1B1	1	169076130	Frame_Shift_Del	DEL	G	TCGA-BQ-7050-01A-11D-1961-08	13758516	169076130	80174491	2	8272											
NEK7	140609	hgsc.bcm.edu	37	chr1	198231718	198231718	+	Missense_Mutation	SNP	T	T	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	tttttagatatttgatttaaTggatgccaaagcacgtgctg	11	16	9	5	1	0	2	0	1	0	1	0	3	0	3	1	1	3	2	1	1	4	7			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr1:198231718T>G	ENST00000367385.4	+	4	554	c.212T>G	c.(211-213)aTg>aGg	p.M71R	NEK7_ENST00000538004.1_Missense_Mutation_p.M71R	NM_133494.2	NP_598001.1	Q8TDX7	NEK7_HUMAN	NIMA-related kinase 7	71	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)			endometrium(3)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21						TTTGATTTAATGGATGCCAAA	0.289																																					p.M71R		Atlas-SNP	.											.	NEK7	42	.	0			c.T212G						PASS	.						125	134	131					1																	198231718		2203	4292	6495	SO:0001583	missense	140609	exon4			ATTTAATGGATGC	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.212T>G	chr1.hg19:g.198231718T>G	ENSP00000356355:p.Met71Arg	208.0	0.0	.		173.0	28.0	.	NM_133494	A6NGT8	Missense_Mutation	SNP	ENST00000367385.4	hg19	CCDS1394.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.394506	0.83011	.	.	ENSG00000151414	ENST00000367385;ENST00000538004;ENST00000391974	T;T;T	0.63913	-0.07;-0.07;3.21	5.46	5.46	0.80206	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.67924	0.2945	L	0.28192	0.835	0.80722	D	1	D	0.57257	0.979	D	0.65573	0.936	T	0.71751	-0.4498	10	0.66056	D	0.02	.	15.4982	0.75673	0.0:0.0:0.0:1.0	.	71	Q8TDX7	NEK7_HUMAN	R	71	ENSP00000356355:M71R;ENSP00000444621:M71R;ENSP00000375835:M71R	ENSP00000356355:M71R	M	+	2	0	NEK7	196498341	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.506000	0.81665	2.198000	0.70561	0.528000	0.53228	ATG	.	.	.	none		0.289	NEK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086550.2	NM_133494		G	198231718	T	G	198231718	3	3	135	1	0	0	0	0	1	0	0	0	10336	1464	51	5	222	5	NEK7	1	198231718	Missense_Mutation	SNP	T	TCGA-BQ-7050-01A-11D-1961-08	29155588	198231718	51018903	3	8273											
LRRC3B	116135	hgsc.bcm.edu	37	chr3	26751861	26751861	+	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	gcaaaatcaggaggatgcccGgagacacctcgaatacttga	14	6	11	10	2	1	2	1	1	0	1	2	6	1	4	2	3	2	1	2	3	4	2			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr3:26751861G>T	ENST00000396641.2	+	2	1290	c.698G>T	c.(697-699)cGg>cTg	p.R233L	AC114877.3_ENST00000446601.1_lincRNA|LRRC3B_ENST00000456208.2_Missense_Mutation_p.R233L|LRRC3B_ENST00000417744.1_Missense_Mutation_p.R233L	NM_052953.2	NP_443185.1	Q96PB8	LRC3B_HUMAN	leucine rich repeat containing 3B	233						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	21						GAGGATGCCCGGAGACACCTC	0.448																																					p.R233L		Atlas-SNP	.											.	LRRC3B	51	.	0			c.G698T						PASS	.						78	76	76					3																	26751861		2203	4300	6503	SO:0001583	missense	116135	exon2			ATGCCCGGAGACA	AF396933	CCDS2644.1	3p24	2004-07-12			ENSG00000179796	ENSG00000179796			28105	protein-coding gene	gene with protein product							Standard	NM_052953		Approved	LRP15	uc003cdp.3	Q96PB8	OTTHUMG00000130572	ENST00000396641.2:c.698G>T	chr3.hg19:g.26751861G>T	ENSP00000379880:p.Arg233Leu	35.0	0.0	.		42.0	4.0	.	NM_052953	Q5M8T0	Missense_Mutation	SNP	ENST00000396641.2	hg19	CCDS2644.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.309657	0.81247	.	.	ENSG00000179796	ENST00000396641;ENST00000417744;ENST00000456208	T;T;T	0.64803	-0.12;-0.12;-0.12	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.79667	0.4485	M	0.75777	2.31	0.80722	D	1	D	0.76494	0.999	D	0.68765	0.96	T	0.80641	-0.1292	10	0.87932	D	0	-10.319	19.2859	0.94069	0.0:0.0:1.0:0.0	.	233	Q96PB8	LRC3B_HUMAN	L	233	ENSP00000379880:R233L;ENSP00000406370:R233L;ENSP00000394940:R233L	ENSP00000379880:R233L	R	+	2	0	LRRC3B	26726865	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.813000	0.99286	2.873000	0.98535	0.563000	0.77884	CGG	.	.	.	none		0.448	LRRC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252997.2	NM_052953		T	26751861	G	T	26751861	3	4	135	1	0	0	0	0	1	0	0	0	9003	1116	39	4	700	4	LRRC3B	3	26751861	Missense_Mutation	SNP	G	TCGA-BQ-7050-01A-11D-1961-08		26751861	171270569	4	8274											
DNAJC13	23317	hgsc.bcm.edu	37	chr3	132184844	132184844	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtctgcttttttcagacagcTaagtagacatttagtgggac	10	14	10	7	0	2	2	1	0	1	2	2	3	2	3	0	1	2	3	0	1	3	7			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr3:132184844T>C	ENST00000260818.6	+	18	2146	c.1898T>C	c.(1897-1899)cTa>cCa	p.L633P	DNAJC13_ENST00000486798.1_3'UTR	NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	633					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						TTCAGACAGCTAAGTAGACAT	0.338																																					p.L633P		Atlas-SNP	.											.	DNAJC13	253	.	0			c.T1898C						PASS	.						72	70	70					3																	132184844		2203	4300	6503	SO:0001583	missense	23317	exon18			GACAGCTAAGTAG	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.1898T>C	chr3.hg19:g.132184844T>C	ENSP00000260818:p.Leu633Pro	38.0	0.0	.		42.0	12.0	.	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	hg19	CCDS33857.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.419736	0.83559	.	.	ENSG00000138246	ENST00000260818	T	0.34859	1.34	5.53	5.53	0.82687	Armadillo-type fold (1);	0.000000	0.64402	D	0.000007	T	0.64159	0.2573	M	0.82193	2.58	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.997	T	0.70226	-0.4930	10	0.87932	D	0	.	15.6649	0.77221	0.0:0.0:0.0:1.0	.	633;633	A7E2Y5;O75165	.;DJC13_HUMAN	P	633	ENSP00000260818:L633P	ENSP00000260818:L633P	L	+	2	0	DNAJC13	133667534	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.813000	0.86123	2.103000	0.63969	0.528000	0.53228	CTA	.	.	.	none		0.338	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		C	132184844	T	C	132184844	3	2	135	1	0	0	0	0	1	0	0	0	4634	1522	53	3	1964	3	DNAJC13	3	132184844	Missense_Mutation	SNP	T	TCGA-BQ-7050-01A-11D-1961-08	105432983	132184844	65837586	5	8275											
XRN1	54464	hgsc.bcm.edu	37	chr3	142141468	142141468	+	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	catatgttccataaagaagaGgcagtgcatcatgattaata	16	11	8	6	0	1	3	1	1	0	2	2	3	2	3	1	1	1	3	1	1	6	5			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr3:142141468G>C	ENST00000264951.4	-	8	1040	c.923C>G	c.(922-924)cCt>cGt	p.P308R	XRN1_ENST00000392981.2_Missense_Mutation_p.P308R|XRN1_ENST00000463916.1_Missense_Mutation_p.P308R|RNU1-100P_ENST00000365255.1_RNA|XRN1_ENST00000544157.1_Missense_Mutation_p.P98R	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	308					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						ATAAAGAAGAGGCAGTGCATC	0.358																																					p.P308R		Atlas-SNP	.											.	XRN1	138	.	0			c.C923G						PASS	.						84	86	85					3																	142141468		2203	4298	6501	SO:0001583	missense	54464	exon8			AGAAGAGGCAGTG	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.923C>G	chr3.hg19:g.142141468G>C	ENSP00000264951:p.Pro308Arg	99.0	0.0	.		118.0	10.0	.	NM_001042604	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Missense_Mutation	SNP	ENST00000264951.4	hg19	CCDS3123.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.716498	0.89205	.	.	ENSG00000114127	ENST00000264951;ENST00000392981;ENST00000463916;ENST00000544157	T;T	0.30448	1.53;1.53	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.63534	0.2519	M	0.87682	2.9	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.997;0.997;0.994	D;D;P;D;D	0.87578	0.998;0.998;0.887;0.984;0.963	T	0.68659	-0.5350	10	0.59425	D	0.04	-9.0623	19.3082	0.94173	0.0:0.0:1.0:0.0	.	98;308;169;308;308	B4E2K3;Q8IZH2-3;B3KW17;Q8IZH2-2;Q8IZH2	.;.;.;.;XRN1_HUMAN	R	308;308;308;98	ENSP00000264951:P308R;ENSP00000376707:P308R	ENSP00000264951:P308R	P	-	2	0	XRN1	143624158	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.363000	0.97131	2.572000	0.86782	0.650000	0.86243	CCT	.	.	.	none		0.358	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001		C	142141468	G	C	142141468	3	2	135	1	0	0	0	0	1	0	0	0	17471	1000	35	4	4337	4	XRN1	3	142141468	Missense_Mutation	SNP	G	TCGA-BQ-7050-01A-11D-1961-08	9956624	142141468	55880962	6	8276											
TCERG1	10915	hgsc.bcm.edu	37	chr5	145836845	145836845	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgactgctcctggtactccaGcactacctcctacggaggag	8	9	10	14	1	0	1	0	1	0	0	3	3	3	3	4	3	5	3	4	3	3	3			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr5:145836845G>A	ENST00000296702.5	+	3	423	c.385G>A	c.(385-387)Gca>Aca	p.A129T	TCERG1_ENST00000394421.2_Missense_Mutation_p.A129T	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	129	Pro-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)			TGGTACTCCAGCACTACCTCC	0.458																																					p.A129T		Atlas-SNP	.											.	TCERG1	148	.	0			c.G385A						PASS	.						101	95	97					5																	145836845		2203	4300	6503	SO:0001583	missense	10915	exon3			ACTCCAGCACTAC	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.385G>A	chr5.hg19:g.145836845G>A	ENSP00000296702:p.Ala129Thr	145.0	0.0	.		120.0	41.0	.	NM_006706	Q2NKN2|Q59EA1	Missense_Mutation	SNP	ENST00000296702.5	hg19	CCDS4282.1	.	.	.	.	.	.	.	.	.	.	G	15.13	2.742261	0.49151	.	.	ENSG00000113649	ENST00000296702;ENST00000394421	T;T	0.25912	1.77;1.77	5.28	4.29	0.51040	.	0.308756	0.35124	N	0.003438	T	0.15392	0.0371	N	0.21282	0.65	0.33542	D	0.595008	B;B;B	0.17038	0.02;0.003;0.001	B;B;B	0.09377	0.004;0.004;0.002	T	0.11324	-1.0592	10	0.27082	T	0.32	-18.8301	9.1164	0.36760	0.1984:0.0:0.8016:0.0	.	129;129;129	B7Z921;O14776-2;O14776	.;.;TCRG1_HUMAN	T	129	ENSP00000296702:A129T;ENSP00000377943:A129T	ENSP00000296702:A129T	A	+	1	0	TCERG1	145817038	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.771000	0.38542	2.463000	0.83235	0.491000	0.48974	GCA	.	.	.	none		0.458	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006		A	145836845	G	A	145836845	3	1	135	1	0	0	0	0	1	0	0	0	15697	971	34	2	395	2	TCERG1	5	145836845	Missense_Mutation	SNP	G	TCGA-BQ-7050-01A-11D-1961-08		145836845	35078415	7	8277											
DSP	1832	hgsc.bcm.edu	37	chr6	7579570	7579570	+	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	ctggcccgagatgccaactcGgaaaactgtaataagaacaa	16	6	9	10	2	0	2	0	0	0	2	1	4	0	3	2	2	4	1	2	2	7	2			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr6:7579570G>T	ENST00000379802.3	+	23	3488	c.3147G>T	c.(3145-3147)tcG>tcT	p.S1049S	DSP_ENST00000418664.2_Silent_p.S1049S	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	1049	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)	p.S1049S(1)		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)		ATGCCAACTCGGAAAACTGTA	0.448																																					p.S1049S		Atlas-SNP	.											DSP,colon,NS,0,1	DSP	306	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3147T						PASS	.						41	46	44					6																	7579570		2203	4300	6503	SO:0001819	synonymous_variant	1832	exon23			CAACTCGGAAAAC	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.3147G>T	chr6.hg19:g.7579570G>T		58.0	1.0	.		65.0	3.0	.	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	hg19	CCDS4501.1																																																																																			.	.	.	none		0.448	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		T	7579570	G	T	7579570	2	4	135	1	0	0	0	0	0	0	0	1	4783	1103	39	4		4	DSP	6	7579570	Silent	SNP	G	TCGA-BQ-7050-01A-11D-1961-08		7579570	163535497	8	8278											
EPHB6	2051	hgsc.bcm.edu	37	chr7	142568111	142568111	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtggctgcatttgacaagAtgatccgcaagccagatacc	11	9	11	10	1	0	4	0	2	0	2	1	4	1	4	3	2	3	3	3	2	3	2			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr7:142568111A>G	ENST00000392957.2	+	18	3539	c.2752A>G	c.(2752-2754)Atg>Gtg	p.M918V	EPHB6_ENST00000411471.2_Missense_Mutation_p.M641V|EPHB6_ENST00000442129.1_Missense_Mutation_p.M918V|EPHB6_ENST00000476059.1_3'UTR	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	918	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					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)					ATTTGACAAGATGATCCGCAA	0.577																																					p.M918V		Atlas-SNP	.											.	EPHB6	168	.	0			c.A2752G						PASS	.						65	75	72					7																	142568111		2203	4300	6503	SO:0001583	missense	2051	exon18			GACAAGATGATCC	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.2752A>G	chr7.hg19:g.142568111A>G	ENSP00000376684:p.Met918Val	190.0	0.0	.		190.0	19.0	.	NM_004445	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Missense_Mutation	SNP	ENST00000392957.2	hg19	CCDS5873.2	.	.	.	.	.	.	.	.	.	.	A	16.64	3.180826	0.57800	.	.	ENSG00000106123	ENST00000392957;ENST00000442129;ENST00000411471	T;T;T	0.61392	0.11;0.11;0.11	5.58	5.58	0.84498	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000016	T	0.60625	0.2283	L	0.49126	1.545	0.42496	D	0.992913	P;P	0.52463	0.953;0.946	P;P	0.51101	0.458;0.659	T	0.65561	-0.6138	10	0.87932	D	0	.	11.0016	0.47609	0.8441:0.1559:0.0:0.0	.	918;641	O15197;O15197-2	EPHB6_HUMAN;.	V	918;918;641	ENSP00000376684:M918V;ENSP00000410789:M918V;ENSP00000409061:M641V	ENSP00000376684:M918V	M	+	1	0	EPHB6	142278233	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.307000	0.33516	2.107000	0.64212	0.533000	0.62120	ATG	.	.	.	none		0.577	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			G	142568111	A	G	142568111	3	3	135	1	0	0	0	0	1	0	0	0	5180	333	12	3	2806	3	EPHB6	7	142568111	Missense_Mutation	SNP	A	TCGA-BQ-7050-01A-11D-1961-08		142568111	16570552	9	8279											
ASB10	136371	hgsc.bcm.edu	37	chr7	150878332	150878332	+	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	cagcgggcggtggtggcctcGgcatcggtgatggactggca	5	7	19	10	4	0	1	0	1	0	0	2	2	0	2	1	8	1	2	1	8	0	0	rs61743170	byFrequency	TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr7:150878332G>T	ENST00000420175.2	-	3	822	c.798C>A	c.(796-798)gcC>gcA	p.A266A	ASB10_ENST00000275838.1_Silent_p.A266A|ASB10_ENST00000434669.1_Silent_p.A311A|ASB10_ENST00000377867.3_Silent_p.A251A|ASB10_ENST00000422024.1_Silent_p.A311A			Q8WXI3	ASB10_HUMAN	ankyrin repeat and SOCS box containing 10	266					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|lung(7)|skin(2)	12			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGGTGGCCTCGGCATCGGTGA	0.657																																					p.A266A		Atlas-SNP	.											.	ASB10	99	.	0			c.C798A						PASS	.						31	33	32					7																	150878332		2203	4298	6501	SO:0001819	synonymous_variant	136371	exon3			GGCCTCGGCATCG	AK055536	CCDS5921.2, CCDS47749.1, CCDS47750.1, CCDS47749.2, CCDS47750.2	7q35	2014-02-04	2011-01-25		ENSG00000146926	ENSG00000146926		"Ankyrin repeat domain containing"	17185	protein-coding gene	gene with protein product		615054	"ankyrin repeat and SOCS box-containing 10", "glaucoma 1, open angle, F (adult-onset)"	GLC1F		22156576	Standard	NM_080871		Approved		uc003wjm.1	Q8WXI3	OTTHUMG00000157013	ENST00000420175.2:c.798C>A	chr7.hg19:g.150878332G>T		66.0	0.0	.		63.0	6.0	.	NM_001142459	A0AVH0|Q6ZUL6	Silent	SNP	ENST00000420175.2	hg19	CCDS47750.2																																																																																			.	G|0.914;A|0.086	.	alt		0.657	ASB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347096.3	NM_080871		T	150878332	G	T	150878332	2	4	135	1	0	0	0	0	0	0	0	1	1014	1103	39	4		4	ASB10	7	150878332	Silent	SNP	G	TCGA-BQ-7050-01A-11D-1961-08	8310221	150878332	8260331	10	8280											
EPPK1	83481	hgsc.bcm.edu	37	chr8	144940482	144940482	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggagatctgctgcccggtgtAggggtcggtgtagccggtga	5	9	19	8	3	1	2	0	1	1	1	2	3	1	2	2	6	3	3	2	6	2	2			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr8:144940482A>G	ENST00000525985.1	-	2	7011	c.6940T>C	c.(6940-6942)Tac>Cac	p.Y2314H				P58107	EPIPL_HUMAN	epiplakin 1	2314						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)			TGCCCGGTGTAGGGGTCGGTG	0.711																																					p.Y2314H		Atlas-SNP	.											.	EPPK1	199	.	0			c.T6940C						PASS	.						190	184	186					8																	144940482		2184	4264	6448	SO:0001583	missense	83481	exon1			CGGTGTAGGGGTC	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.6940T>C	chr8.hg19:g.144940482A>G	ENSP00000436337:p.Tyr2314His	352.0	0.0	.		336.0	27.0	.	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	hg19		.	.	.	.	.	.	.	.	.	.	A	19.61	3.860098	0.71834	.	.	ENSG00000227184	ENST00000525985	T	0.69040	-0.37	4.63	4.63	0.57726	.	.	.	.	.	T	0.78666	0.4319	M	0.74881	2.28	0.27571	N	0.949888	D	0.60575	0.988	D	0.74674	0.984	T	0.69289	-0.5184	9	0.20046	T	0.44	.	12.1078	0.53821	1.0:0.0:0.0:0.0	.	2314	E9PPU0	.	H	2314	ENSP00000436337:Y2314H	ENSP00000436337:Y2314H	Y	-	1	0	EPPK1	145012470	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.597000	0.54031	1.957000	0.56846	0.477000	0.44152	TAC	.	.	.	none		0.711	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		G	144940482	A	G	144940482	3	3	135	1	0	0	0	0	1	0	0	0	5192	420	15	3	326	3	EPPK1	8	144940482	Missense_Mutation	SNP	A	TCGA-BQ-7050-01A-11D-1961-08		144940482	1423540	11	8281											
NTRK2	4915	hgsc.bcm.edu	37	chr9	87342656	87342656	+	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	gaaaggcaaccccaaaccagCgcttcagtggttctataacg	13	7	9	12	2	2	0	1	0	1	0	2	1	2	0	3	2	4	3	3	2	5	4			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr9:87342656C>G	ENST00000323115.4	+	8	1294	c.941C>G	c.(940-942)gCg>gGg	p.A314G	NTRK2_ENST00000359847.3_Missense_Mutation_p.A314G|NTRK2_ENST00000376213.1_Missense_Mutation_p.A314G|NTRK2_ENST00000395866.2_Missense_Mutation_p.A158G|NTRK2_ENST00000304053.6_Missense_Mutation_p.A314G|NTRK2_ENST00000376208.1_Missense_Mutation_p.A314G|NTRK2_ENST00000376214.1_Missense_Mutation_p.A314G|NTRK2_ENST00000395882.1_Missense_Mutation_p.A314G|NTRK2_ENST00000277120.3_Missense_Mutation_p.A314G			Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2	314	Ig-like C2-type 2.				activation of adenylate cyclase activity (GO:0007190)|aging (GO:0007568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|circadian rhythm (GO:0007623)|feeding behavior (GO:0007631)|glutamate secretion (GO:0014047)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mechanoreceptor differentiation (GO:0042490)|negative regulation of anoikis (GO:2000811)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular junction development (GO:0007528)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system neuron development (GO:0048935)|positive regulation of axonogenesis (GO:0050772)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|regulation of dendrite development (GO:0050773)|regulation of neurotransmitter secretion (GO:0046928)|regulation of protein kinase B signaling (GO:0051896)|regulation of Rac GTPase activity (GO:0032314)|response to auditory stimulus (GO:0010996)|retinal rod cell development (GO:0046548)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasculogenesis (GO:0001570)	cell surface (GO:0009986)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endosome (GO:0005768)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|brain-derived neurotrophic factor binding (GO:0048403)|brain-derived neurotrophic factor-activated receptor activity (GO:0060175)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	46					Amitriptyline(DB00321)	CCCAAACCAGCGCTTCAGTGG	0.443										TSP Lung(25;0.17)																											p.A314G		Atlas-SNP	.											.	NTRK2	331	.	0			c.C941G						PASS	.						94	96	95					9																	87342656		2203	4300	6503	SO:0001583	missense	4915	exon9			AACCAGCGCTTCA	AF410902	CCDS6671.1, CCDS35050.1, CCDS35051.1, CCDS35052.1, CCDS35053.1	9q22.1	2013-01-11			ENSG00000148053	ENSG00000148053	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8032	protein-coding gene	gene with protein product		600456				7789988	Standard	NM_001018065		Approved	TRKB	uc004anz.1	Q16620	OTTHUMG00000020120	ENST00000323115.4:c.941C>G	chr9.hg19:g.87342656C>G	ENSP00000314586:p.Ala314Gly	94.0	0.0	.		87.0	33.0	.	NM_001018065	B1ANZ4|B4DFV9|Q16675|Q59GJ1|Q8WXJ5|Q8WXJ6|Q8WXJ7	Missense_Mutation	SNP	ENST00000323115.4	hg19	CCDS35050.1	.	.	.	.	.	.	.	.	.	.	C	17.17	3.321558	0.60634	.	.	ENSG00000148053	ENST00000376214;ENST00000376213;ENST00000395882;ENST00000376208;ENST00000304053;ENST00000277120;ENST00000323115;ENST00000359847;ENST00000395866	T;T;T;T;T;T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27	5.91	5.91	0.95273	Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.385251	0.29900	N	0.010905	T	0.58090	0.2098	N	0.14661	0.345	0.30052	N	0.811719	B;B;B;B;B;B;B;B	0.27316	0.045;0.009;0.009;0.011;0.11;0.011;0.175;0.009	B;B;B;B;B;B;B;B	0.36766	0.064;0.022;0.022;0.039;0.232;0.043;0.148;0.023	T	0.52351	-0.8587	10	0.23891	T	0.37	.	20.2873	0.98536	0.0:1.0:0.0:0.0	.	158;314;314;314;314;314;360;314	B4DFV9;Q16620-3;Q16620-5;Q5VWE5;Q16620;Q16620-4;Q59GJ1;Q16620-2	.;.;.;.;NTRK2_HUMAN;.;.;.	G	314;314;314;314;314;314;314;314;158	ENSP00000365387:A314G;ENSP00000365386:A314G;ENSP00000379221:A314G;ENSP00000365381:A314G;ENSP00000306167:A314G;ENSP00000277120:A314G;ENSP00000314586:A314G;ENSP00000352906:A314G;ENSP00000379207:A158G	ENSP00000277120:A314G	A	+	2	0	NTRK2	86532476	0.561000	0.26578	1.000000	0.80357	0.998000	0.95712	2.910000	0.48766	2.799000	0.96334	0.585000	0.79938	GCG	.	.	.	none		0.443	NTRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052882.1			G	87342656	C	G	87342656	3	3	135	1	0	0	0	0	1	0	0	0	10714	768	27	4	971	4	NTRK2	9	87342656	Missense_Mutation	SNP	C	TCGA-BQ-7050-01A-11D-1961-08		87342656	53870775	12	8282											
CYLC2	1539	hgsc.bcm.edu	37	chr9	105767702	105767702	+	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	tcgaaggatgccaagaaagaTgcaaaggagattaaaaaagg	20	5	12	4	1	0	3	0	0	0	3	1	6	0	4	1	3	2	1	1	3	7	1	rs2298052	byFrequency	TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr9:105767702T>A	ENST00000374798.3	+	5	859	c.789T>A	c.(787-789)gaT>gaA	p.D263E	CYLC2_ENST00000487798.1_Missense_Mutation_p.D263E	NM_001340.3	NP_001331.1	Q14093	CYLC2_HUMAN	cylicin, basic protein of sperm head cytoskeleton 2	263	31 X 3 AA repeats of K-K-X.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)	p.D263D(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)	41		all_hematologic(171;0.125)				CCAAGAAAGATGCAAAGGAGA	0.388																																					p.D263E		Atlas-SNP	.											CYLC2,NS,carcinoma,0,1	CYLC2	109	.	1	Substitution - coding silent(1)	stomach(1)	c.T789A						PASS	.						117	112	114					9																	105767702		2203	4300	6503	SO:0001583	missense	1539	exon5			GAAAGATGCAAAG	Z46788	CCDS35085.1	9q31.2	2008-07-21			ENSG00000155833	ENSG00000155833			2583	protein-coding gene	gene with protein product		604035				7737358	Standard	NM_001340		Approved		uc004bbs.2	Q14093	OTTHUMG00000020396	ENST00000374798.3:c.789T>A	chr9.hg19:g.105767702T>A	ENSP00000420256:p.Asp263Glu	71.0	0.0	.		70.0	14.0	.	NM_001340	B2R8F4|Q5VVJ9	Missense_Mutation	SNP	ENST00000374798.3	hg19	CCDS35085.1	.	.	.	.	.	.	.	.	.	.	T	2.261	-0.369199	0.05069	.	.	ENSG00000155833	ENST00000374798;ENST00000487798	T;T	0.14022	2.54;2.54	4.21	-5.98	0.02220	.	1.421110	0.04878	N	0.447237	T	0.06050	0.0157	L	0.29908	0.895	0.80722	P	0.0	B	0.23891	0.093	B	0.23574	0.047	T	0.37244	-0.9714	9	0.02654	T	1	-0.742	0.3139	0.00292	0.3842:0.1819:0.2128:0.221	.	263	Q14093	CYLC2_HUMAN	E	263	ENSP00000420256:D263E;ENSP00000417674:D263E	ENSP00000420256:D263E	D	+	3	2	CYLC2	104807523	0.000000	0.05858	0.000000	0.03702	0.104000	0.19210	-0.647000	0.05397	-0.974000	0.03550	0.477000	0.44152	GAT	.	T|0.972;C|0.028	.	alt		0.388	CYLC2-001	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053463.3	NM_001340		A	105767702	T	A	105767702	3	1	135	1	0	0	0	0	1	0	0	0	4144	1461	51	5	807	5	CYLC2	9	105767702	Missense_Mutation	SNP	T	TCGA-BQ-7050-01A-11D-1961-08	18425046	105767702	35445729	13	8283											
DDB1	1642	hgsc.bcm.edu	37	chr11	61077796	61077796	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtgttggtcaatgataagtAggttgtgcacctccacctct	8	14	10	9	0	2	1	1	1	1	0	3	1	3	1	3	2	1	4	3	2	3	4			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr11:61077796A>G	ENST00000301764.7	-	19	2769	c.2372T>C	c.(2371-2373)cTa>cCa	p.L791P	DDB1_ENST00000450997.2_Missense_Mutation_p.L102P	NM_001923.4	NP_001914.3	Q16531	DDB1_HUMAN	damage-specific DNA binding protein 1, 127kDa	791	Interaction with CDT1 and CUL4A.|WD repeat beta-propeller C.				DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of mitotic cell cycle phase transition (GO:1901990)|UV-damage excision repair (GO:0070914)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	48						AATGATAAGTAGGTTGTGCAC	0.507								Nucleotide excision repair (NER)																													p.L791P		Atlas-SNP	.											.	DDB1	100	.	0			c.T2372C						PASS	.						137	119	125					11																	61077796		2203	4299	6502	SO:0001583	missense	1642	exon19			ATAAGTAGGTTGT	AJ002955	CCDS31576.1	11q12-q13	2014-09-17	2002-08-29		ENSG00000167986	ENSG00000167986			2717	protein-coding gene	gene with protein product		600045	"damage-specific DNA binding protein 1 (127kD)"			8530102, 10574459	Standard	NM_001923		Approved	XPE	uc001nrc.5	Q16531	OTTHUMG00000168209	ENST00000301764.7:c.2372T>C	chr11.hg19:g.61077796A>G	ENSP00000301764:p.Leu791Pro	103.0	0.0	.		95.0	4.0	.	NM_001923	A6NG77|B2R648|B4DG00|O15176|Q13289|Q58F96	Missense_Mutation	SNP	ENST00000301764.7	hg19	CCDS31576.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.963370	0.92791	.	.	ENSG00000167986	ENST00000301764;ENST00000450997;ENST00000543658;ENST00000535147	T;T;T	0.50813	0.73;1.23;0.73	5.87	5.87	0.94306	Cleavage/polyadenylation specificity factor, A subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.72145	0.3424	M	0.83953	2.67	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.76509	-0.2933	10	0.87932	D	0	-20.9791	16.5764	0.84681	1.0:0.0:0.0:0.0	.	102;791	B4DG00;Q16531	.;DDB1_HUMAN	P	791;102;102;258	ENSP00000301764:L791P;ENSP00000388705:L102P;ENSP00000445844:L102P	ENSP00000301764:L791P	L	-	2	0	DDB1	60834372	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.287000	0.95975	2.371000	0.80710	0.533000	0.62120	CTA	.	.	.	none		0.507	DDB1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398816.1	NM_001923		G	61077796	A	G	61077796	3	3	135	1	0	0	0	0	1	0	0	0	4325	420	15	3	1086	3	DDB1	11	61077796	Missense_Mutation	SNP	A	TCGA-BQ-7050-01A-11D-1961-08		61077796	73928720	14	8284											
PCF11	51585	hgsc.bcm.edu	37	chr11	82875304	82875304	+	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	ttcccctagcatctccactcCtccaattgttcctgatatac	8	14	3	16	0	1	1	0	1	1	0	6	1	5	1	6	0	2	2	6	0	4	6			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr11:82875304C>T	ENST00000298281.4	+	4	1015	c.563C>T	c.(562-564)cCt>cTt	p.P188L		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	188					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						ATCTCCACTCCTCCAATTGTT	0.393																																					p.P188L		Atlas-SNP	.											.	PCF11	220	.	0			c.C563T						PASS	.						64	59	60					11																	82875304		1868	4092	5960	SO:0001583	missense	51585	exon4			CCACTCCTCCAAT	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.563C>T	chr11.hg19:g.82875304C>T	ENSP00000298281:p.Pro188Leu	57.0	0.0	.		53.0	14.0	.	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	hg19	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	C	17.74	3.462969	0.63513	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.49432	1.74;0.78;0.79	5.73	5.73	0.89815	.	0.118143	0.39687	N	0.001292	T	0.36580	0.0972	L	0.36672	1.1	0.80722	D	1	P;B	0.35328	0.495;0.421	B;B	0.28849	0.095;0.058	T	0.13176	-1.0519	9	.	.	.	.	15.3998	0.74830	0.0:0.8614:0.1386:0.0	.	188;188	E9PQ01;O94913	.;PCF11_HUMAN	L	188	ENSP00000298281:P188L;ENSP00000434540:P188L;ENSP00000431567:P188L	.	P	+	2	0	PCF11	82552952	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.304000	0.65744	2.710000	0.92621	0.650000	0.86243	CCT	.	.	.	none		0.393	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		T	82875304	C	T	82875304	3	4	135	1	0	0	0	0	1	0	0	0	11580	681	24	2	577	2	PCF11	11	82875304	Missense_Mutation	SNP	C	TCGA-BQ-7050-01A-11D-1961-08	21797508	82875304	52131212	15	8285											
RIMKLB	57494	hgsc.bcm.edu	37	chr12	8906675	8906675	+	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	aacagatgggagaatgcaaaGcaactgctcattaggtaaaa	18	7	10	6	0	1	2	1	0	0	2	1	3	1	2	0	2	5	4	0	2	7	2			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr12:8906675G>T	ENST00000538135.1	+	5	1508	c.683G>T	c.(682-684)aGc>aTc	p.S228I	RIMKLB_ENST00000535829.1_Missense_Mutation_p.S228I|RIMKLB_ENST00000357529.3_Missense_Mutation_p.S228I|RIMKLB_ENST00000299673.5_3'UTR			Q9ULI2	RIMKB_HUMAN	ribosomal modification protein rimK-like family member B	228	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						AGAATGCAAAGCAACTGCTCA	0.383																																					p.S228I		Atlas-SNP	.											.	RIMKLB	47	.	0			c.G683T						PASS	.						155	137	143					12																	8906675		1908	4124	6032	SO:0001583	missense	57494	exon6			TGCAAAGCAACTG	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.683G>T	chr12.hg19:g.8906675G>T	ENSP00000440943:p.Ser228Ile	158.0	0.0	.		139.0	7.0	.	NM_020734	B7Z834|D3DUV2|Q8N4P4|Q8WTW6	Missense_Mutation	SNP	ENST00000538135.1	hg19	CCDS41748.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.477042	0.84640	.	.	ENSG00000166532	ENST00000535829;ENST00000357529;ENST00000538135	.	.	.	4.82	4.82	0.62117	ATP-grasp fold (1);ATP-grasp fold, RimK-type (1);ATP-grasp fold, subdomain 2 (1);	0.000000	0.85682	U	0.000000	D	0.84584	0.5504	M	0.89534	3.04	0.80722	D	1	D;D	0.69078	0.997;0.993	D;D	0.69824	0.966;0.94	D	0.88278	0.2934	9	0.87932	D	0	.	16.8175	0.85738	0.0:0.0:1.0:0.0	.	228;228	Q9ULI2-2;Q9ULI2	.;RIMKB_HUMAN	I	228	.	ENSP00000350136:S228I	S	+	2	0	RIMKLB	8797942	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.835000	0.92100	2.375000	0.81037	0.585000	0.79938	AGC	.	.	.	none		0.383	RIMKLB-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398874.1	NM_020734		T	8906675	G	T	8906675	3	4	135	1	0	0	0	0	1	0	0	0	13379	971	34	4	697	4	RIMKLB	12	8906675	Missense_Mutation	SNP	G	TCGA-BQ-7050-01A-11D-1961-08		8906675	124945220	16	8286											
PAN2	9924	hgsc.bcm.edu	37	chr12	56720460	56720460	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaagtgtgtcagtggtgagTgggacagggatgagggaaag	12	7	20	2	0	1	3	1	2	0	1	1	6	1	6	0	4	0	0	0	4	2	0			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr12:56720460T>C	ENST00000425394.2	-	7	1579	c.1203A>G	c.(1201-1203)ccA>ccG	p.P401P	PAN2_ENST00000548043.1_Silent_p.P401P|PAN2_ENST00000257931.5_Silent_p.P401P|PAN2_ENST00000440411.3_Silent_p.P401P	NM_001127460.2	NP_001120932	Q9HBH5	RDH14_HUMAN	PAN2 poly(A) specific ribonuclease subunit	0					osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	41					Vitamin A(DB00162)	CAGTGGTGAGTGGGACAGGGA	0.597																																					p.P401P		Atlas-SNP	.											.	PAN2	107	.	0			c.A1203G						PASS	.						70	61	64					12																	56720460		2203	4300	6503	SO:0001819	synonymous_variant	9924	exon7			GGTGAGTGGGACA	AB014610	CCDS8915.1, CCDS44922.1, CCDS53802.1	12q13.2	2014-03-27	2014-03-27	2008-01-08		ENSG00000135473		"Ubiquitin-specific peptidases"	20074	protein-coding gene	gene with protein product	"PAN2 homolog, PABP1 dependent poly A specific ribonuclease subunit (S. cerevisiae)"		"ubiquitin specific protease 52", "ubiquitin specific peptidase 52", "PAN2 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"	USP52		12838346, 14583602	Standard	NM_014871		Approved	KIAA0710, hPAN2	uc001skx.3	Q504Q3	OTTHUMG00000170412	ENST00000425394.2:c.1203A>G	chr12.hg19:g.56720460T>C		51.0	0.0	.		47.0	22.0	.	NM_014871		Silent	SNP	ENST00000425394.2	hg19	CCDS44922.1																																																																																			.	.	.	none		0.597	PAN2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409024.1	NM_014871		C	56720460	T	C	56720460	2	2	135	1	0	0	0	0	0	0	0	1	11421	1683	59	3		3	PAN2	12	56720460	Silent	SNP	T	TCGA-BQ-7050-01A-11D-1961-08	47813785	56720460	77131435	17	8287											
ZFC3H1	196441	hgsc.bcm.edu	37	chr12	72017888	72017888	+	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	tgtaccaagtgcttacctgtAaaattgccagtgcactttgg	10	13	9	9	0	0	0	0	0	0	0	0	0	0	0	3	1	5	4	3	1	5	5			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr12:72017888A>T	ENST00000378743.3	-	23	4860	c.4502T>A	c.(4501-4503)tTa>tAa	p.L1501*		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	1501					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						GCTTACCTGTAAAATTGCCAG	0.358																																					p.L1501X		Atlas-SNP	.											.	ZFC3H1	172	.	0			c.T4502A						PASS	.						153	145	147					12																	72017888		1838	4095	5933	SO:0001587	stop_gained	196441	exon23			ACCTGTAAAATTG	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.4502T>A	chr12.hg19:g.72017888A>T	ENSP00000368017:p.Leu1501*	243.0	0.0	.		218.0	40.0	.	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Nonsense_Mutation	SNP	ENST00000378743.3	hg19	CCDS41813.1	.	.	.	.	.	.	.	.	.	.	A	45	11.914642	0.99617	.	.	ENSG00000133858	ENST00000378743	.	.	.	5.39	5.39	0.77823	.	0.000000	0.64402	D	0.000013	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.4122	0.74937	1.0:0.0:0.0:0.0	.	.	.	.	X	1501	.	ENSP00000368017:L1501X	L	-	2	0	ZFC3H1	70304155	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	8.262000	0.89862	2.038000	0.60285	0.533000	0.62120	TTA	.	.	.	none		0.358	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		T	72017888	A	T	72017888	4	4	135	1	0	0	0	0	0	1	0	0	17645	372	13	5	1519	5	ZFC3H1	12	72017888	Nonsense_Mutation	SNP	A	TCGA-BQ-7050-01A-11D-1961-08	15297428	72017888	61834007	18	8288											
THBS1	7057	hgsc.bcm.edu	37	chr15	39882095	39882095	+	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	ctgggccactatagcgacccCatgtaccgctgcgagtgcaa	9	7	11	14	3	0	0	0	0	0	0	0	2	0	0	4	1	4	3	4	1	4	3			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr15:39882095C>G	ENST00000260356.5	+	13	2181	c.2016C>G	c.(2014-2016)ccC>ccG	p.P672P		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	672	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)		ATAGCGACCCCATGTACCGCT	0.607																																					p.P672P		Atlas-SNP	.											.	THBS1	106	.	0			c.C2016G						PASS	.						111	92	99					15																	39882095		2200	4297	6497	SO:0001819	synonymous_variant	7057	exon13			CGACCCCATGTAC		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.2016C>G	chr15.hg19:g.39882095C>G		48.0	0.0	.		48.0	9.0	.	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	hg19	CCDS32194.1																																																																																			.	.	.	none		0.607	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		G	39882095	C	G	39882095	2	3	135	1	0	0	0	0	0	0	0	1	15865	581	21	4		4	THBS1	15	39882095	Silent	SNP	C	TCGA-BQ-7050-01A-11D-1961-08		39882095	62649297	19	8289											
ZNF532	55205	hgsc.bcm.edu	37	chr18	56586514	56586514	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaaccatccctgaagcaacCggatagtcccagaagcatct	15	6	7	13	1	1	2	0	1	1	1	3	3	3	3	4	1	4	2	4	1	6	1			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr18:56586514C>T	ENST00000336078.4	+	4	1771	c.995C>T	c.(994-996)cCg>cTg	p.P332L	ZNF532_ENST00000589288.1_Missense_Mutation_p.P332L|ZNF532_ENST00000591808.1_Missense_Mutation_p.P332L|ZNF532_ENST00000591083.1_Missense_Mutation_p.P332L|ZNF532_ENST00000591230.1_Missense_Mutation_p.P332L	NM_018181.4	NP_060651.2	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	332					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(14)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(4)|urinary_tract(1)	52						CTGAAGCAACCGGATAGTCCC	0.522																																					p.P332L		Atlas-SNP	.											.	ZNF532	108	.	0			c.C995T						PASS	.						97	100	99					18																	56586514		2203	4300	6503	SO:0001583	missense	55205	exon4			AGCAACCGGATAG	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.995C>T	chr18.hg19:g.56586514C>T	ENSP00000338217:p.Pro332Leu	139.0	0.0	.		152.0	61.0	.	NM_018181	Q4G0V6|Q7L7Z7|Q96QR7|Q9NVJ6	Missense_Mutation	SNP	ENST00000336078.4	hg19	CCDS11969.1	.	.	.	.	.	.	.	.	.	.	c	14.64	2.595026	0.46318	.	.	ENSG00000074657	ENST00000336078	T	0.02158	4.42	4.97	4.97	0.65823	.	0.114354	0.64402	N	0.000009	T	0.05456	0.0144	M	0.76574	2.34	0.80722	D	1	D	0.58620	0.983	B	0.41135	0.348	T	0.24657	-1.0154	10	0.87932	D	0	-11.3748	17.8864	0.88856	0.0:1.0:0.0:0.0	.	332	Q9HCE3	ZN532_HUMAN	L	332	ENSP00000338217:P332L	ENSP00000338217:P332L	P	+	2	0	ZNF532	54737494	1.000000	0.71417	0.494000	0.27515	0.027000	0.11550	7.737000	0.84957	2.320000	0.78422	0.550000	0.68814	CCG	.	.	.	none		0.522	ZNF532-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256130.1	NM_018181		T	56586514	C	T	56586514	3	4	135	1	0	0	0	0	1	0	0	0	17984	652	23	1	997	1	ZNF532	18	56586514	Missense_Mutation	SNP	C	TCGA-BQ-7050-01A-11D-1961-08		56586514	21490734	20	8290											
LMNB2	84823	hgsc.bcm.edu	37	chr19	2435072	2435072	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtgctggctccgcagctccTccagcgcctgtgccatcttg	3	10	11	17	3	1	0	0	0	1	0	4	0	4	0	5	1	4	4	5	1	0	1			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr19:2435072T>C	ENST00000582871.1	-	5	808	c.722A>G	c.(721-723)gAg>gGg	p.E241G	LMNB2_ENST00000325327.3_Missense_Mutation_p.E261G	NM_032737.3	NP_116126.3	Q03252	LMNB2_HUMAN	lamin B2	241	Coil 2.|Rod.					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)		CCGCAGCTCCTCCAGCGCCTG	0.701																																					p.E261G		Atlas-SNP	.											.	LMNB2	40	.	0			c.A782G						PASS	.						37	39	38					19																	2435072		2200	4299	6499	SO:0001583	missense	84823	exon5			AGCTCCTCCAGCG	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.722A>G	chr19.hg19:g.2435072T>C	ENSP00000462730:p.Glu241Gly	101.0	0.0	.		90.0	4.0	.	NM_032737	O75292|Q14734|Q96DF6	Missense_Mutation	SNP	ENST00000582871.1	hg19		.	.	.	.	.	.	.	.	.	.	T	16.18	3.050050	0.55218	.	.	ENSG00000176619	ENST00000325327	.	.	.	4.83	4.83	0.62350	Filament (1);	0.116455	0.64402	D	0.000017	T	0.56529	0.1991	L	0.47016	1.485	0.46149	D	0.998892	B	0.09022	0.002	B	0.16722	0.016	T	0.57505	-0.7800	9	0.72032	D	0.01	.	13.2379	0.59979	0.0:0.0:0.0:1.0	.	241	Q03252	LMNB2_HUMAN	G	241	.	ENSP00000327054:E241G	E	-	2	0	LMNB2	2386072	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.335000	0.52105	1.807000	0.52817	0.459000	0.35465	GAG	.	.	.	none		0.701	LMNB2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032737		C	2435072	T	C	2435072	3	2	135	1	0	0	0	0	1	0	0	0	8857	1551	54	3	1112	3	LMNB2	19	2435072	Missense_Mutation	SNP	T	TCGA-BQ-7050-01A-11D-1961-08		2435072	56693911	21	8291											
ZNF440	126070	hgsc.bcm.edu	37	chr19	11943483	11943485	+	In_Frame_Del	DEL	GTT	GTT	-																															gttcagtagttccttcagtaGttccagttccttttgatatc																										TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	GTT	GTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr19:11943483_11943485delGTT	ENST00000304060.5	+	4	1656_1658	c.1492_1494delGTT	c.(1492-1494)gttdel	p.V498del		NM_152357.2	NP_689570.2	Q8IYI8	ZN440_HUMAN	zinc finger protein 440	498					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(9)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						TCCTTCAGTAGTTCCAGTTCCTT	0.404																																					p.497_498del		Atlas-INDEL	.											.	ZNF440	56	.	0			c.1491_1493del						PASS	.																																			SO:0001651	inframe_deletion	126070	exon4			.	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.1492_1494delGTT	chr19.hg19:g.11943483_11943485delGTT	ENSP00000305373:p.Val498del	81.0	0.0	0		45.0	18.0	0.4	NM_152357	Q8N1R9	In_Frame_Del	DEL	ENST00000304060.5	hg19	CCDS42503.1																																																																																			.	.	.	none		0.404	ZNF440-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344508.1	NM_152357		-	11943485	GTT	-	11943483	7	5	135	1	0	1	0	1	0	0	0	0	17925	1029	36	0	1506	0	ZNF440	19	11943483	In_Frame_Del	DEL	GTT	TCGA-BQ-7050-01A-11D-1961-08	9508411	11943483	47185500	22	8292											
ZFP36	7538	hgsc.bcm.edu	37	chr19	39898403	39898403	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcctcctgtcgctgagcccTgacgtgcccgtgccatccga	5	8	11	17	4	0	2	0	2	0	0	3	3	2	2	6	0	4	1	6	0	0	0			TCGA-BQ-7050-01A-11D-1961-08	TCGA-BQ-7050-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b6b349c-fb1d-44a6-abcf-da2951066a9b	ecae3b13-cf72-4058-8385-cb3bf34bec83	g.chr19:39898403T>C	ENST00000248673.3	+	2	103	c.45T>C	c.(43-45)ccT>ccC	p.P15P	ZFP36_ENST00000594045.1_3'UTR|ZFP36_ENST00000597629.1_Silent_p.P21P|MIR4530_ENST00000581459.1_RNA	NM_003407.3	NP_003398.2	P26651	TTP_HUMAN	ZFP36 ring finger protein	15					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)			CGCTGAGCCCTGACGTGCCCG	0.667																																					p.P21P	NSCLC(67;1164 1324 12056 21056 30097)	Atlas-SNP	.											.	ZFP36	19	.	0			c.T63C						PASS	.						102	114	110					19																	39898403		2202	4298	6500	SO:0001819	synonymous_variant	7538	exon2			GAGCCCTGACGTG	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.45T>C	chr19.hg19:g.39898403T>C		331.0	0.0	.		295.0	105.0	.	NM_003407	B2RA54	Silent	SNP	ENST00000248673.3	hg19																																																																																				.	.	.	none		0.667	ZFP36-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding				C	39898403	T	C	39898403	2	2	135	1	0	0	0	0	0	0	0	1	17657	1567	55	3		3	ZFP36	19	39898403	Silent	SNP	T	TCGA-BQ-7050-01A-11D-1961-08	27954920	39898403	19230580	23	8293											
PLCH2	9651	hgsc.bcm.edu	37	chr1	2436173	2436173	+	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	ctgccaagtccaagagcctgGgcgacctcactgctgatgac	9	7	11	14	1	1	3	1	2	0	1	2	4	2	3	4	1	3	1	4	1	2	0			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr1:2436173G>A	ENST00000419816.2	+	22	4046	c.3772G>A	c.(3772-3774)Ggc>Agc	p.G1258S	PLCH2_ENST00000449969.1_3'UTR|PLCH2_ENST00000378486.3_Missense_Mutation_p.G1258S|PLCH2_ENST00000378488.3_Missense_Mutation_p.G1222S			O75038	PLCH2_HUMAN	phospholipase C, eta 2	1258					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)		CAAGAGCCTGGGCGACCTCAC	0.701																																					p.G1258S		Atlas-SNP	.											.	PLCH2	131	.	0			c.G3772A						PASS	.						28	34	32					1																	2436173		2066	4170	6236	SO:0001583	missense	9651	exon22			AGCCTGGGCGACC	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.3772G>A	chr1.hg19:g.2436173G>A	ENSP00000389803:p.Gly1258Ser	46.0	0.0	.		48.0	19.0	.	NM_014638	A2VCM3|B9DI80|Q3LUA8|Q86XJ2|Q86XU1|Q86YU7|Q8TEH5|Q8WUS6	Missense_Mutation	SNP	ENST00000419816.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.88|18.88	3.718362|3.718362	0.68844|0.68844	.|.	.|.	ENSG00000149527|ENSG00000149527	ENST00000378486;ENST00000378488;ENST00000278878|ENST00000419816	T;T|.	0.76578|.	-0.69;-1.03|.	4.41|4.41	4.41|4.41	0.53225|0.53225	.|.	1.629000|.	0.03724|.	N|.	0.252361|.	T|.	0.74504|.	0.3725|.	M|M	0.73962|0.73962	2.25|2.25	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.87578|.	0.998;0.998|.	T|.	0.76214|.	-0.3041|.	10|.	0.87932|.	D|.	0|.	.|.	15.9517|15.9517	0.79843|0.79843	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1010;1258|.	B9DI82;O75038|.	.;PLCH2_HUMAN|.	S|X	1258;1222;1010|552	ENSP00000367747:G1258S;ENSP00000367749:G1222S|.	ENSP00000278878:G1010S|.	G|W	+|+	1|3	0|0	PLCH2|PLCH2	2426033|2426033	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.712000|0.712000	0.41017|0.41017	5.901000|5.901000	0.69861|0.69861	1.999000|1.999000	0.58509|0.58509	0.491000|0.491000	0.48974|0.48974	GGC|TGG	.	.	.	none		0.701	PLCH2-009	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467514.1	NM_014638		A	2436173	G	A	2436173	3	1	136	1	0	0	0	0	1	0	0	0	12045	1232	43	2	3858	2	PLCH2	1	2436173	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08		2436173	246814448	1	8294											
MFN2	9927	hgsc.bcm.edu	37	chr1	12061548	12061549	+	Frame_Shift_Del	DEL	TT	TT	-																															aggccggggaccgcatcttcTttgtgtctgctaaggaggtg																										TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr1:12061548_12061549delTT	ENST00000235329.5	+	9	1229_1230	c.907_908delTT	c.(907-909)tttfs	p.F303fs	MFN2_ENST00000444836.1_Frame_Shift_Del_p.F303fs	NM_014874.3	NP_055689.1	O95140	MFN2_HUMAN	mitofusin 2	303	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)		CCGCATCTTCTTTGTGTCTGCT	0.574																																					p.302_303del		Atlas-INDEL	.											.	MFN2	83	.	0			c.906_907del						PASS	.																																			SO:0001589	frameshift_variant	9927	exon9			.	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.907_908delTT	chr1.hg19:g.12061548_12061549delTT	ENSP00000235329:p.Phe303fs	48.0	0.0	0		47.0	26.0	0.553191	NM_014874	A8K1B3|O95572|Q5JXC3|Q5JXC4|Q9H131|Q9NSX8	Frame_Shift_Del	DEL	ENST00000235329.5	hg19	CCDS30587.1																																																																																			.	.	.	none		0.574	MFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006859.2	NM_014874		-	12061549	TT	-	12061548	7	5	136	1	0	1	0	1	0	0	0	0	9531	1609	56	0	933	0	MFN2	1	12061548	Frame_Shift_Del	DEL	TT	TCGA-BQ-7051-01A-12D-1961-08	9625375	12061548	237189073	2	8295											
HSPG2	3339	hgsc.bcm.edu	37	chr1	22214014	22214014	+	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	ggcatgcggcctcctggggcCcacagggcaggggcctgacg	5	4	18	14	2	0	1	0	1	0	0	1	1	1	1	4	7	1	2	4	7	0	0			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr1:22214014C>A	ENST00000374695.3	-	8	936	c.857G>T	c.(856-858)gGg>gTg	p.G286V		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	286	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.				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)	CTCCTGGGGCCCACAGGGCAG	0.657																																					p.G286V		Atlas-SNP	.											.	HSPG2	311	.	0			c.G857T						PASS	.						67	82	77					1																	22214014		2203	4299	6502	SO:0001583	missense	3339	exon8			TGGGGCCCACAGG	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.857G>T	chr1.hg19:g.22214014C>A	ENSP00000363827:p.Gly286Val	70.0	0.0	.		80.0	37.0	.	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.61|18.61	3.661500|3.661500	0.67700|0.67700	.|.	.|.	ENSG00000142798|ENSG00000142798	ENST00000412328;ENST00000374673|ENST00000374695	T;D|D	0.95918|0.95853	0.35;-3.85|-3.83	5.09|5.09	3.22|3.22	0.36961|0.36961	.|.	0.178923|0.178923	0.27027|0.27027	N|N	0.021295|0.021295	D|D	0.94771|0.94771	0.8312|0.8312	M|M	0.80183|0.80183	2.485|2.485	0.52501|0.52501	D|D	0.999955|0.999955	D|P	0.89917|0.36683	1.0|0.565	D|B	0.69479|0.41374	0.964|0.355	D|D	0.91702|0.91702	0.5374|0.5374	10|10	0.59425|0.38643	D|T	0.04|0.18	.|.	9.1776|9.1776	0.37120|0.37120	0.0:0.8213:0.0:0.1787|0.0:0.8213:0.0:0.1787	.|.	209|286	Q5SZI5|P98160	.|PGBM_HUMAN	C|V	209;113|286	ENSP00000405412:G209C;ENSP00000363805:G113C|ENSP00000363827:G286V	ENSP00000363805:G113C|ENSP00000363827:G286V	G|G	-|-	1|2	0|0	HSPG2|HSPG2	22086601|22086601	0.001000|0.001000	0.12720|0.12720	0.995000|0.995000	0.50966|0.50966	0.549000|0.549000	0.35272|0.35272	0.204000|0.204000	0.17335|0.17335	0.566000|0.566000	0.29273|0.29273	0.462000|0.462000	0.41574|0.41574	GGC|GGG	.	.	.	none		0.657	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		A	22214014	C	A	22214014	3	1	136	1	0	0	0	0	1	0	0	0	7437	623	22	4	12678	4	HSPG2	1	22214014	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	10152466	22214014	227036607	3	8296											
HIVEP3	59269	hgsc.bcm.edu	37	chr1	42048585	42048585	+	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	cccttcttggtctttttggtAagctcgctttccttgggttc	2	19	9	11	1	2	0	0	0	2	0	5	0	3	0	2	3	1	4	2	3	1	8			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr1:42048585A>T	ENST00000372583.1	-	4	2769	c.1884T>A	c.(1882-1884)ctT>ctA	p.L628L	HIVEP3_ENST00000429157.2_Silent_p.L628L|HIVEP3_ENST00000247584.5_Silent_p.L628L|HIVEP3_ENST00000372584.1_Silent_p.L628L	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	628	No DNA binding activity or transactivation activity, but complete prevention of TRAF-dependent NF-Kappa-B activation; associates with TRAF2 and JUN. {ECO:0000250}.				positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				TCTTTTTGGTAAGCTCGCTTT	0.493																																					p.L628L		Atlas-SNP	.											.	HIVEP3	235	.	0			c.T1884A						PASS	.						123	120	121					1																	42048585		2203	4300	6503	SO:0001819	synonymous_variant	59269	exon4			TTTGGTAAGCTCG	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.1884T>A	chr1.hg19:g.42048585A>T		183.0	0.0	.		152.0	61.0	.	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Silent	SNP	ENST00000372583.1	hg19	CCDS463.1																																																																																			.	.	.	none		0.493	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		T	42048585	A	T	42048585	2	4	136	1	0	0	0	0	0	0	0	1	7195	349	13	5		5	HIVEP3	1	42048585	Silent	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	19834571	42048585	207202036	4	8297											
CYP4A11	1579	hgsc.bcm.edu	37	chr1	47402352	47402352	+	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	tcaccagcatcactcgtacaGagtctgccatgagccccaca	11	7	7	16	1	3	2	2	1	1	1	4	2	3	2	4	0	4	2	4	0	1	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr1:47402352G>C	ENST00000310638.4	-	4	525	c.494C>G	c.(493-495)tCt>tGt	p.S165C	CYP4A11_ENST00000371905.1_Missense_Mutation_p.S165C|CYP4A11_ENST00000496519.1_5'Flank|CYP4A11_ENST00000371904.4_Missense_Mutation_p.S165C|CYP4A11_ENST00000457840.2_Missense_Mutation_p.S61C|CYP4A11_ENST00000462347.1_Missense_Mutation_p.S165C	NM_000778.3	NP_000769.2	Q02928	CP4AB_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 11	165					arachidonic acid metabolic process (GO:0019369)|cellular lipid metabolic process (GO:0044255)|epoxygenase P450 pathway (GO:0019373)|fatty acid metabolic process (GO:0006631)|leukotriene B4 catabolic process (GO:0036101)|leukotriene metabolic process (GO:0006691)|long-chain fatty acid metabolic process (GO:0001676)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of icosanoid secretion (GO:0032305)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)			endometrium(2)|kidney(5)|large_intestine(6)|lung(6)|ovary(5)|prostate(3)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	36					Cisplatin(DB00515)|Clofibrate(DB00636)|Dexamethasone(DB01234)|Estrone(DB00655)|Ethanol(DB00898)|Lansoprazole(DB00448)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Rifampicin(DB01045)|Tretinoin(DB00755)	CACTCGTACAGAGTCTGCCAT	0.562																																					p.S165C		Atlas-SNP	.											CYP4A11,NS,carcinoma,0,1	CYP4A11	77	.	0			c.C494G						PASS	.						88	70	76					1																	47402352		2203	4300	6503	SO:0001583	missense	1579	exon4			CGTACAGAGTCTG	L04751	CCDS543.1	1p33	2008-02-05	2003-01-14		ENSG00000187048	ENSG00000187048		"Cytochrome P450s"	2642	protein-coding gene	gene with protein product		601310	"cytochrome P450, subfamily IVA, polypeptide 11"	CYP4A2		7679927	Standard	NM_000778		Approved	CYP4AII	uc001cqp.4	Q02928	OTTHUMG00000008020	ENST00000310638.4:c.494C>G	chr1.hg19:g.47402352G>C	ENSP00000311095:p.Ser165Cys	79.0	0.0	.		62.0	23.0	.	NM_000778	Q06766|Q16865|Q16866|Q5VSP8|Q86SU6|Q8IWY5	Missense_Mutation	SNP	ENST00000310638.4	hg19	CCDS543.1	.	.	.	.	.	.	.	.	.	.	N	18.30	3.593520	0.66219	.	.	ENSG00000187048	ENST00000310638;ENST00000371904;ENST00000371905;ENST00000457840	T;T;T;T	0.69806	-0.43;-0.43;-0.43;-0.43	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.71753	0.3377	L	0.48642	1.525	0.41496	D	0.988252	P	0.45768	0.866	P	0.53988	0.739	T	0.71517	-0.4569	10	0.45353	T	0.12	.	15.1292	0.72507	0.0:0.1409:0.859:0.0	.	165	Q02928	CP4AB_HUMAN	C	165;165;165;61	ENSP00000311095:S165C;ENSP00000360971:S165C;ENSP00000360972:S165C;ENSP00000406272:S61C	ENSP00000311095:S165C	S	-	2	0	CYP4A11	47174939	1.000000	0.71417	0.448000	0.26945	0.053000	0.15095	4.950000	0.63603	2.640000	0.89533	0.644000	0.83932	TCT	.	.	.	none		0.562	CYP4A11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022022.1	NM_000778		C	47402352	G	C	47402352	3	2	136	1	0	0	0	0	1	0	0	0	4185	942	33	4	1101	4	CYP4A11	1	47402352	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	5353767	47402352	201848269	5	8298											
ZCCHC11	23318	hgsc.bcm.edu	37	chr1	52902541	52902541	+	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	tctcgggtctctaaagtctcGagtatcgtggaggtctcggg	6	12	14	9	4	4	0	0	0	4	0	9	2	4	1	0	4	0	1	0	4	3	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr1:52902541G>T	ENST00000371544.3	-	26	4307	c.4045C>A	c.(4045-4047)Cga>Aga	p.R1349R	ZCCHC11_ENST00000257177.4_Silent_p.R1350R	NM_001009881.2|NM_015269.2	NP_001009881.1|NP_056084.1	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11	1349					cytokine production (GO:0001816)|miRNA catabolic process (GO:0010587)|miRNA metabolic process (GO:0010586)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|pre-miRNA processing (GO:0031054)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|RNA 3'-end processing (GO:0031123)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(17)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	58						CTAAAGTCTCGAGTATCGTGG	0.483																																					p.R1350R		Atlas-SNP	.											.	ZCCHC11	151	.	0			c.C4048A						PASS	.						185	188	187					1																	52902541		2203	4300	6503	SO:0001819	synonymous_variant	23318	exon26			AGTCTCGAGTATC	D83776	CCDS30715.1, CCDS30716.1	1p32.3	2014-03-05			ENSG00000134744	ENSG00000134744		"Zinc fingers, CCHC domain containing"	28981	protein-coding gene	gene with protein product	"TUTase4"	613692				8724849, 12239557	Standard	NM_015269		Approved	KIAA0191, PAPD3, TUT4	uc001cty.2	Q5TAX3	OTTHUMG00000008200	ENST00000371544.3:c.4045C>A	chr1.hg19:g.52902541G>T		178.0	0.0	.		160.0	72.0	.	NM_001009881	A2RRP0|B7Z8J5|D3DQ35|Q12764|Q5TAX2|Q5TAX4|Q86XZ3	Silent	SNP	ENST00000371544.3	hg19	CCDS30716.1	.	.	.	.	.	.	.	.	.	.	G	8.051	0.765950	0.15983	.	.	ENSG00000134744	ENST00000474453	.	.	.	3.77	2.84	0.33178	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.7235	0.34456	0.0:0.0:0.7739:0.2261	.	.	.	.	X	194	.	.	S	-	2	0	ZCCHC11	52675129	1.000000	0.71417	0.958000	0.39756	0.893000	0.52053	1.976000	0.40579	1.155000	0.42497	0.655000	0.94253	TCG	.	.	.	none		0.483	ZCCHC11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022462.1	XM_038288		T	52902541	G	T	52902541	2	4	136	1	0	0	0	0	0	0	0	1	17592	1066	37	4		4	ZCCHC11	1	52902541	Silent	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	5500189	52902541	196348080	6	8299											
CEP350	9857	hgsc.bcm.edu	37	chr1	180000535	180000535	+	Missense_Mutation	SNP	A	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	gtggctcccatcaaggaaagAaatctgggaccagcagcaaa	15	5	11	10	0	2	1	1	0	1	1	3	3	3	3	2	3	2	3	2	3	4	0			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr1:180000535A>C	ENST00000367607.3	+	15	4049	c.3631A>C	c.(3631-3633)Aaa>Caa	p.K1211Q		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	1211	Ser-rich.				microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						TCAAGGAAAGAAATCTGGGAC	0.398																																					p.K1211Q		Atlas-SNP	.											.	CEP350	418	.	0			c.A3631C						PASS	.						50	52	51					1																	180000535		2203	4300	6503	SO:0001583	missense	9857	exon15			GGAAAGAAATCTG	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.3631A>C	chr1.hg19:g.180000535A>C	ENSP00000356579:p.Lys1211Gln	36.0	0.0	.		38.0	16.0	.	NM_014810	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	hg19	CCDS1336.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.816051	0.90790	.	.	ENSG00000135837	ENST00000367607	T	0.59906	0.23	6.02	6.02	0.97574	.	0.000000	0.49916	D	0.000133	T	0.66616	0.2807	L	0.32530	0.975	0.42214	D	0.991828	D;D	0.76494	0.999;0.998	D;P	0.78314	0.991;0.796	T	0.64884	-0.6302	9	.	.	.	.	16.2108	0.82158	1.0:0.0:0.0:0.0	.	1211;1211	E7EU22;Q5VT06	.;CE350_HUMAN	Q	1211	ENSP00000356579:K1211Q	.	K	+	1	0	CEP350	178267158	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	6.354000	0.73036	2.299000	0.77371	0.528000	0.53228	AAA	.	.	.	none		0.398	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		C	180000535	A	C	180000535	3	2	136	1	0	0	0	0	1	0	0	0	3256	247	9	5	3685	5	CEP350	1	180000535	Missense_Mutation	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	127097994	180000535	69250086	7	8300											
PTPN14	5784	hgsc.bcm.edu	37	chr1	214556993	214556993	+	Silent	SNP	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	gccagggccgcctgcagctgGgcactgtactccatcttctc	5	9	11	16	1	2	0	0	0	2	0	4	0	3	0	4	2	3	4	4	2	1	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr1:214556993G>A	ENST00000366956.5	-	13	2399	c.2205C>T	c.(2203-2205)gcC>gcT	p.A735A	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	735					lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)			NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		CCTGCAGCTGGGCACTGTACT	0.632																																					p.A735A	Colon(92;557 1424 24372 34121 40073)	Atlas-SNP	.											.	PTPN14	168	.	0			c.C2205T						PASS	.						35	41	39					1																	214556993		2201	4295	6496	SO:0001819	synonymous_variant	5784	exon13			CAGCTGGGCACTG	X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.2205C>T	chr1.hg19:g.214556993G>A		78.0	0.0	.		67.0	30.0	.	NM_005401	Q5VSI0	Silent	SNP	ENST00000366956.5	hg19	CCDS1514.1																																																																																			.	.	.	none		0.632	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401		A	214556993	G	A	214556993	2	1	136	1	0	0	0	0	0	0	0	1	12794	1219	43	2		2	PTPN14	1	214556993	Silent	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	34556458	214556993	34693628	8	8301											
SULT1C4	27233	hgsc.bcm.edu	37	chr2	109002781	109002781	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatggcaaactattcatcgaTtcctgctgaaatcatggacc	13	11	7	10	1	2	1	2	1	0	0	4	3	3	2	2	2	2	2	2	2	4	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr2:109002781T>C	ENST00000272452.2	+	6	1075	c.749T>C	c.(748-750)aTt>aCt	p.I250T	SULT1C4_ENST00000409309.3_Missense_Mutation_p.I175T	NM_006588.2	NP_006579.2	O75897	ST1C4_HUMAN	sulfotransferase family, cytosolic, 1C, member 4	250					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	sulfotransferase activity (GO:0008146)			endometrium(1)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	12						TATTCATCGATTCCTGCTGAA	0.299																																					p.I250T		Atlas-SNP	.											.	SULT1C4	41	.	0			c.T749C						PASS	.						92	89	90					2																	109002781		2203	4300	6503	SO:0001583	missense	27233	exon6			CATCGATTCCTGC	AF055584	CCDS2077.1	2q12.3	2008-09-04	2007-03-16	2007-03-16	ENSG00000198075	ENSG00000198075		"Sulfotransferases, cytosolic"	11457	protein-coding gene	gene with protein product		608357	"sulfotransferase family, cytosolic, 1C, member 2"	SULT1C2		10783263, 9852044	Standard	NM_006588		Approved	SULT1C	uc002tea.1	O75897	OTTHUMG00000130958	ENST00000272452.2:c.749T>C	chr2.hg19:g.109002781T>C	ENSP00000272452:p.Ile250Thr	111.0	0.0	.		119.0	59.0	.	NM_006588	Q069I8|Q08AS5|Q53S63	Missense_Mutation	SNP	ENST00000272452.2	hg19	CCDS2077.1	.	.	.	.	.	.	.	.	.	.	T	10.97	1.502652	0.26949	.	.	ENSG00000198075	ENST00000272452;ENST00000409309	D;D	0.82344	-1.6;-1.6	4.69	3.51	0.40186	Sulfotransferase domain (1);	0.823783	0.10424	N	0.676268	T	0.81034	0.4739	L	0.39147	1.195	0.09310	N	1	P;B	0.39480	0.675;0.05	P;B	0.47603	0.551;0.131	T	0.69650	-0.5088	10	0.54805	T	0.06	.	6.7246	0.23348	0.1598:0.0:0.1461:0.6941	.	175;250	Q08AS5;O75897	.;ST1C4_HUMAN	T	250;175	ENSP00000272452:I250T;ENSP00000387225:I175T	ENSP00000272452:I250T	I	+	2	0	SULT1C4	108369213	0.086000	0.21541	0.001000	0.08648	0.087000	0.18053	3.039000	0.49791	0.904000	0.36572	0.496000	0.49642	ATT	.	.	.	none		0.299	SULT1C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253561.1	NM_006588		C	109002781	T	C	109002781	3	2	136	1	0	0	0	0	1	0	0	0	15391	1493	52	3	771	3	SULT1C4	2	109002781	Missense_Mutation	SNP	T	TCGA-BQ-7051-01A-12D-1961-08		109002781	134196592	9	8302											
NFE2L2	4780	hgsc.bcm.edu	37	chr2	178098803	178098803	+	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	gctgaattgggagaaattcaCctgtctcttcatctagttgt	9	15	9	8	0	4	2	2	1	2	1	5	3	4	2	1	1	0	2	1	1	3	5			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr2:178098803C>A	ENST00000397062.3	-	2	796	c.242G>T	c.(241-243)gGt>gTt	p.G81V	NFE2L2_ENST00000446151.2_Missense_Mutation_p.G65V|NFE2L2_ENST00000464747.1_Missense_Mutation_p.G65V|NFE2L2_ENST00000397063.4_Missense_Mutation_p.G65V|NFE2L2_ENST00000423513.1_Missense_Mutation_p.G65V	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	81					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G81D(5)|p.G81V(4)|p.G81_F83delGEF(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			GAGAAATTCACCTGTCTCTTC	0.433			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.G81V		Atlas-SNP	.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	NFE2L2,NS,carcinoma,-1,11	NFE2L2	225	.	10	Substitution - Missense(9)|Deletion - In frame(1)	lung(4)|oesophagus(2)|liver(2)|endometrium(1)|kidney(1)	c.G242T						PASS	.						143	142	142					2																	178098803		1901	4105	6006	SO:0001583	missense	4780	exon2			AATTCACCTGTCT		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.242G>T	chr2.hg19:g.178098803C>A	ENSP00000380252:p.Gly81Val	68.0	0.0	.		98.0	51.0	.	NM_006164	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	hg19	CCDS42782.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.0|28.0	4.883817|4.883817	0.91814|0.91814	.|.	.|.	ENSG00000116044|ENSG00000116044	ENST00000449627|ENST00000397063;ENST00000397062;ENST00000446151;ENST00000448782;ENST00000421929;ENST00000423513	.|T;T;T;T;T;T	.|0.52983	.|1.19;1.19;1.19;0.64;0.64;1.19	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.75110	.|0.3805	M|M	0.87180|0.87180	2.865|2.865	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.97110	.|0.999;0.999;1.0;0.999	.|T	.|0.78563	.|-0.2156	.|10	.|0.87932	.|D	.|0	.|.	19.9976|19.9976	0.97389|0.97389	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|65;65;65;81	.|E9PGJ7;B4DNB0;C9JFL6;Q16236	.|.;.;.;NF2L2_HUMAN	.|V	-1|65;81;65;65;65;65	.|ENSP00000380253:G65V;ENSP00000380252:G81V;ENSP00000411575:G65V;ENSP00000400073:G65V;ENSP00000412191:G65V;ENSP00000410015:G65V	.|ENSP00000380252:G81V	.|G	-|-	.|2	.|0	NFE2L2|NFE2L2	177807049|177807049	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.993000|0.993000	0.82548|0.82548	7.298000|7.298000	0.78815|0.78815	2.737000|2.737000	0.93849|0.93849	0.563000|0.563000	0.77884|0.77884	.|GGT	.	.	.	none		0.433	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		A	178098803	C	A	178098803	3	1	136	1	0	0	0	0	1	0	0	0	10375	507	18	4	1591	4	NFE2L2	2	178098803	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	69096022	178098803	65100570	10	8303											
SLC22A13	9390	hgsc.bcm.edu	37	chr3	38317429	38317429	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaagtgggggacttcggccTggacgtctatctgacgcagc	7	8	14	12	3	2	1	0	1	2	0	3	3	2	3	2	4	1	1	2	4	2	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr3:38317429T>C	ENST00000311856.4	+	7	1128	c.1079T>C	c.(1078-1080)cTg>cCg	p.L360P	SLC22A13_ENST00000450935.2_3'UTR	NM_004256.3	NP_004247.2	Q9Y226	S22AD_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 13	360					nicotinate transport (GO:2001142)|organic cation transport (GO:0015695)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	nicotinate transporter activity (GO:0090416)|organic cation transmembrane transporter activity (GO:0015101)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|urinary_tract(1)	20				KIRC - Kidney renal clear cell carcinoma(284;0.0533)|Kidney(284;0.067)		GACTTCGGCCTGGACGTCTAT	0.572																																					p.L360P		Atlas-SNP	.											.	SLC22A13	42	.	0			c.T1079C						PASS	.						80	77	78					3																	38317429		2203	4300	6503	SO:0001583	missense	9390	exon7			TCGGCCTGGACGT	AB010438	CCDS2676.1	3p22.2	2013-07-18	2013-07-18	2003-10-15	ENSG00000172940	ENSG00000172940		"Solute carriers"	8494	protein-coding gene	gene with protein product		604047	"organic cationic transporter-like 3", "solute carrier family 22 (organic anion transporter), member 13"	ORCTL3		10072596, 18411268	Standard	NM_004256		Approved	OCTL1, OCTL3, OAT10	uc003chz.3	Q9Y226	OTTHUMG00000131086	ENST00000311856.4:c.1079T>C	chr3.hg19:g.38317429T>C	ENSP00000310241:p.Leu360Pro	77.0	0.0	.		77.0	29.0	.	NM_004256	B2RCV9|Q8IYG1	Missense_Mutation	SNP	ENST00000311856.4	hg19	CCDS2676.1	.	.	.	.	.	.	.	.	.	.	T	18.57	3.652783	0.67472	.	.	ENSG00000172940	ENST00000311856	T	0.62639	0.01	5.04	5.04	0.67666	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.64402	D	0.000001	T	0.81408	0.4816	M	0.91196	3.185	0.80722	D	1	D;D	0.69078	0.996;0.997	D;D	0.70227	0.945;0.968	T	0.82623	-0.0366	10	0.28530	T	0.3	.	14.2827	0.66224	0.0:0.0:0.0:1.0	.	360;360	Q9Y226-2;Q9Y226	.;S22AD_HUMAN	P	360	ENSP00000310241:L360P	ENSP00000310241:L360P	L	+	2	0	SLC22A13	38292433	1.000000	0.71417	1.000000	0.80357	0.438000	0.31896	5.806000	0.69150	2.040000	0.60383	0.533000	0.62120	CTG	.	.	.	none		0.572	SLC22A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253746.2	NM_004256		C	38317429	T	C	38317429	3	2	136	1	0	0	0	0	1	0	0	0	14457	1580	55	3	1105	3	SLC22A13	3	38317429	Missense_Mutation	SNP	T	TCGA-BQ-7051-01A-12D-1961-08		38317429	159705001	11	8304											
SACM1L	22908	hgsc.bcm.edu	37	chr3	45773632	45773632	+	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	gatcaggtagcagaaatgcaAgatgaattaaggtaagctat	17	9	11	4	0	1	3	1	1	0	2	1	4	1	3	0	2	3	5	0	2	7	4			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr3:45773632A>T	ENST00000389061.5	+	13	1293	c.1089A>T	c.(1087-1089)caA>caT	p.Q363H	SACM1L_ENST00000541314.1_Missense_Mutation_p.Q302H|SACM1L_ENST00000418611.1_Missense_Mutation_p.Q260H	NM_014016.3	NP_054735.3	Q9NTJ5	SAC1_HUMAN	SAC1 suppressor of actin mutations 1-like (yeast)	363	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)	phosphatase activity (GO:0016791)|phosphatidylinositol bisphosphate phosphatase activity (GO:0034593)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)		CAGAAATGCAAGATGAATTAA	0.338																																					p.Q363H		Atlas-SNP	.											.	SACM1L	38	.	0			c.A1089T						PASS	.						105	115	112					3																	45773632		2203	4299	6502	SO:0001583	missense	22908	exon13			AATGCAAGATGAA	AB020658	CCDS33745.1	3p21.3	2010-03-11			ENSG00000211456	ENSG00000211456			17059	protein-coding gene	gene with protein product		606569				10048485, 11352561	Standard	NM_014016		Approved	SAC1, KIAA0851	uc003cos.2	Q9NTJ5	OTTHUMG00000156653	ENST00000389061.5:c.1089A>T	chr3.hg19:g.45773632A>T	ENSP00000373713:p.Gln363His	151.0	0.0	.		146.0	69.0	.	NM_014016	A8K527|B4DK71|O94935|Q7LA14|Q7LA22|Q96AX7|Q9NQ46|Q9NQ57	Missense_Mutation	SNP	ENST00000389061.5	hg19	CCDS33745.1	.	.	.	.	.	.	.	.	.	.	A	13.96	2.391717	0.42410	.	.	ENSG00000211456	ENST00000418611;ENST00000389061;ENST00000541314;ENST00000433336	T;T;T;T	0.43294	0.95;0.95;0.95;1.53	5.99	-5.27	0.02763	Synaptojanin, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.61714	0.2369	M	0.88031	2.925	0.52501	D	0.999958	D;D	0.76494	0.999;0.998	D;D	0.65987	0.94;0.912	T	0.68716	-0.5335	10	0.36615	T	0.2	-3.4019	15.7038	0.77563	0.4825:0.0:0.5175:0.0	.	302;363	B4DK71;Q9NTJ5	.;SAC1_HUMAN	H	260;363;302;40	ENSP00000396387:Q260H;ENSP00000373713:Q363H;ENSP00000443373:Q302H;ENSP00000412883:Q40H	ENSP00000373713:Q363H	Q	+	3	2	SACM1L	45748636	0.993000	0.37304	0.874000	0.34290	0.998000	0.95712	0.423000	0.21313	-1.249000	0.02500	0.533000	0.62120	CAA	.	.	.	none		0.338	SACM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345065.2	NM_014016		T	45773632	A	T	45773632	3	4	136	1	0	0	0	0	1	0	0	0	13816	69	3	5	1139	5	SACM1L	3	45773632	Missense_Mutation	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	7456203	45773632	152248798	12	8305											
SLC38A3	10991	hgsc.bcm.edu	37	chr3	50252997	50252997	+	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	catccgtgcctatgagcagcTgggctaccgtgcctttggga	6	10	13	12	2	0	1	0	1	0	0	1	2	1	2	4	2	5	3	4	2	2	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr3:50252997T>C	ENST00000420502.1	+	0	548									solute carrier family 38, member 3											breast(1)|cervix(1)|endometrium(1)|lung(3)	6				BRCA - Breast invasive adenocarcinoma(193;0.000275)|KIRC - Kidney renal clear cell carcinoma(197;0.00548)|Kidney(197;0.00615)		TATGAGCAGCTGGGCTACCGT	0.622																																					p.L132P		Atlas-SNP	.											.	SLC38A3	22	.	0			c.T395C						PASS	.						47	51	50					3																	50252997		2095	4216	6311			10991	exon6			AGCAGCTGGGCTA	U49082	CCDS74940.1	3p21.3	2013-05-22			ENSG00000188338	ENSG00000188338		"Solute carriers"	18044	protein-coding gene	gene with protein product		604437				10619430, 10823827	Standard	XM_006712954		Approved	G17, SN1	uc003cyn.4	Q99624	OTTHUMG00000156764		chr3.hg19:g.50252997T>C		85.0	0.0	.		65.0	29.0	.	NM_006841		Missense_Mutation	SNP	ENST00000420502.1	hg19																																																																																				.	.	.	none		0.622	SLC38A3-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000345635.2	NM_006841		C	50252997	T	C	50252997	1	2	136	0	1	0	0	0	0	0	0	0	14618	1580	55	3		3	SLC38A3	3	50252997	RNA	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	4479365	50252997	147769433	13	8306											
PPM1M	132160	hgsc.bcm.edu	37	chr3	52282683	52282683	+	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	cgtgtggagaaatcggatctCaagtacccactgatccatgg	11	9	11	10	2	1	2	1	1	1	1	4	4	2	3	2	3	1	1	2	3	3	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr3:52282683C>T	ENST00000296487.4	+	7	866	c.462C>T	c.(460-462)ctC>ctT	p.L154L	PPM1M_ENST00000323588.4_Silent_p.L154L|PPM1M_ENST00000457351.2_Silent_p.L315L|PPM1M_ENST00000409502.3_Silent_p.L103L			Q96MI6	PPM1M_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1M	154	PP2C-like.				protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|manganese ion binding (GO:0030145)			prostate(1)|urinary_tract(1)	2				BRCA - Breast invasive adenocarcinoma(193;2.4e-05)|Kidney(197;0.00171)|KIRC - Kidney renal clear cell carcinoma(197;0.00194)		AATCGGATCTCAAGTACCCAC	0.572																																					p.L315L	NSCLC(151;810 2688 34365 49863)	Atlas-SNP	.											.	PPM1M	9	.	0			c.C945T						PASS	.						156	139	145					3																	52282683		2203	4300	6503	SO:0001819	synonymous_variant	132160	exon7			GGATCTCAAGTAC	AK096681	CCDS46840.1	3p21.31	2012-04-17	2010-03-05		ENSG00000164088	ENSG00000164088		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	26506	protein-coding gene	gene with protein product	"protein phosphatase 2C eta"	608979	"protein phosphatase 1M (PP2C domain containing)"			12477932	Standard	NM_001122870		Approved	PP2Ceta, FLJ32332	uc011bed.2	Q96MI6	OTTHUMG00000153046	ENST00000296487.4:c.462C>T	chr3.hg19:g.52282683C>T		140.0	0.0	.		150.0	70.0	.	NM_144641	Q8N8J9|Q96DB8	Silent	SNP	ENST00000296487.4	hg19		.	.	.	.	.	.	.	.	.	.	C	9.454	1.091407	0.20471	.	.	ENSG00000164088	ENST00000457454	.	.	.	4.78	3.9	0.45041	.	.	.	.	.	T	0.58337	0.2115	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54957	-0.8215	4	.	.	.	.	8.0844	0.30762	0.0:0.7542:0.1611:0.0848	.	.	.	.	L	210	.	.	S	+	2	0	PPM1M	52257723	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	0.991000	0.29654	1.205000	0.43262	0.561000	0.74099	TCA	.	.	.	none		0.572	PPM1M-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000329230.2	NM_144641		T	52282683	C	T	52282683	2	4	136	1	0	0	0	0	0	0	0	1	12355	813	29	2		2	PPM1M	3	52282683	Silent	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	2029686	52282683	145739747	14	8307											
SLMAP	7871	hgsc.bcm.edu	37	chr3	57827089	57827089	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatggtatggaagcccggcTccgctcagagtgagtataat	11	9	13	8	2	1	3	1	1	0	2	2	4	2	4	2	3	1	4	2	3	4	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr3:57827089T>C	ENST00000428312.1	+	3	504	c.410T>C	c.(409-411)cTc>cCc	p.L137P	SLMAP_ENST00000295951.3_Missense_Mutation_p.L137P|SLMAP_ENST00000449503.2_Missense_Mutation_p.L137P|SLMAP_ENST00000416870.1_5'UTR|SLMAP_ENST00000295952.3_Missense_Mutation_p.L137P|SLMAP_ENST00000383718.3_Missense_Mutation_p.L137P			Q14BN4	SLMAP_HUMAN	sarcolemma associated protein	137	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)		GAAGCCCGGCTCCGCTCAGAG	0.338																																					p.L137P		Atlas-SNP	.											.	SLMAP	46	.	0			c.T410C						PASS	.						67	70	69					3																	57827089		2203	4300	6503	SO:0001583	missense	7871	exon3			CCCGGCTCCGCTC	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.410T>C	chr3.hg19:g.57827089T>C	ENSP00000398661:p.Leu137Pro	73.0	0.0	.		81.0	39.0	.	NM_007159	Q14C95|Q6AI54|Q6UXC9|Q6ZVQ8|Q8NCW9|Q9H297|Q9HCH1|Q9Y681	Missense_Mutation	SNP	ENST00000428312.1	hg19		.	.	.	.	.	.	.	.	.	.	T	11.27	1.589587	0.28357	.	.	ENSG00000163681	ENST00000295951;ENST00000295952;ENST00000383718;ENST00000428312;ENST00000449503	T;T;T;T;T	0.47177	1.45;1.45;0.85;1.44;1.49	4.85	4.85	0.62838	.	0.259220	0.31438	N	0.007646	T	0.24586	0.0596	N	0.01874	-0.695	0.80722	D	1	P;P;P;B	0.50369	0.816;0.934;0.898;0.002	P;B;B;B	0.45712	0.491;0.418;0.434;0.005	T	0.11299	-1.0593	10	0.26408	T	0.33	-2.0339	10.587	0.45288	0.0:0.0:0.1615:0.8385	.	137;137;137;137	Q14BN4-2;Q14BN4;Q14BN4-3;Q14BN4-6	.;SLMAP_HUMAN;.;.	P	137	ENSP00000295951:L137P;ENSP00000295952:L137P;ENSP00000373224:L137P;ENSP00000398661:L137P;ENSP00000412945:L137P	ENSP00000295951:L137P	L	+	2	0	SLMAP	57802129	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.864000	0.69575	1.799000	0.52666	0.533000	0.62120	CTC	.	.	.	none		0.338	SLMAP-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351584.1	NM_007159		C	57827089	T	C	57827089	3	2	136	1	0	0	0	0	1	0	0	0	14762	1551	54	3	420	3	SLMAP	3	57827089	Missense_Mutation	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	5544406	57827089	140195341	15	8308											
ADAMTS9	56999	hgsc.bcm.edu	37	chr3	64536694	64536703	+	Frame_Shift_Del	DEL	CACCACCTTG	CACCACCTTG	-																															tttttgttgtcatccacacaCaccaccttgcggtacctgga																								rs17071010|rs146412036|rs138988394	byFrequency	TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	CACCACCTTG	CACCACCTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr3:64536694_64536703delCACCACCTTG	ENST00000498707.1	-	31	5076_5085	c.4734_4743delCAAGGTGGTG	c.(4732-4743)cgcaaggtggtgfs	p.RKVV1578fs	ADAMTS9_ENST00000295903.4_Frame_Shift_Del_p.RKVV1550fs	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	1578	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)	p.V1581M(1)		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)		CATCCACACACACCACCTTGCGGTACCTGG	0.5																																					p.1579_1582del		Atlas-INDEL	.											.	ADAMTS9	206	.	1	Substitution - Missense(1)	large_intestine(1)	c.4735_4744del						PASS	.																																			SO:0001589	frameshift_variant	56999	exon31			.	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.4734_4743delCAAGGTGGTG	chr3.hg19:g.64536694_64536703delCACCACCTTG	ENSP00000418735:p.Arg1578fs	237.0	0.0	0		135.0	26.0	0.192593	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Frame_Shift_Del	DEL	ENST00000498707.1	hg19	CCDS2903.1																																																																																			.	.	.	none		0.5	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1			-	64536703	CACCACCTTG	-	64536694	7	5	136	1	0	1	0	1	0	0	0	0	273	465	17	0	1100	0	ADAMTS9	3	64536694	Frame_Shift_Del	DEL	CACCACCTTG	TCGA-BQ-7051-01A-12D-1961-08	6709605	64536694	133485736	16	8309											
KIAA1524	57650	hgsc.bcm.edu	37	chr3	108282018	108282018	+	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	gagcagcctccaataatattCtcagtccagactgtacttgt	11	12	7	11	0	1	1	1	0	1	1	4	2	3	1	3	0	3	2	3	0	4	5			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr3:108282018C>A	ENST00000295746.8	-	13	1665	c.1589G>T	c.(1588-1590)aGa>aTa	p.R530I	KIAA1524_ENST00000487834.1_5'UTR|KIAA1524_ENST00000491772.1_Missense_Mutation_p.R371I	NM_020890.2	NP_065941.2	Q8TCG1	CIP2A_HUMAN	KIAA1524	530					positive regulation of neural precursor cell proliferation (GO:2000179)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R530T(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(21)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CAATAATATTCTCAGTCCAGA	0.393																																					p.R530I		Atlas-SNP	.											KIAA1524,colon,carcinoma,+1,1	KIAA1524	82	.	1	Substitution - Missense(1)	ovary(1)	c.G1589T						PASS	.						154	159	158					3																	108282018		2203	4300	6503	SO:0001583	missense	57650	exon13			AATATTCTCAGTC	AB040957	CCDS33812.1	3q13.13	2014-01-14			ENSG00000163507	ENSG00000163507			29302	protein-coding gene	gene with protein product	"cancerous inhibitor of protein phosphatase 2A"	610643				10819331, 24214971	Standard	NM_020890		Approved	CIP2A	uc003dxb.4	Q8TCG1	OTTHUMG00000159233	ENST00000295746.8:c.1589G>T	chr3.hg19:g.108282018C>A	ENSP00000295746:p.Arg530Ile	252.0	0.0	.		204.0	74.0	.	NM_020890	A1L4J7|B9EGC3|Q6P4G6|Q8WVP8|Q96PI2|Q9H9C6|Q9P204	Missense_Mutation	SNP	ENST00000295746.8	hg19	CCDS33812.1	.	.	.	.	.	.	.	.	.	.	C	19.14	3.770678	0.69992	.	.	ENSG00000163507	ENST00000491772;ENST00000295746	T;T	0.35048	1.33;1.33	5.3	4.43	0.53597	.	0.494865	0.23127	N	0.051633	T	0.40067	0.1102	L	0.53249	1.67	0.53005	D	0.999964	P	0.46706	0.883	P	0.46172	0.506	T	0.31024	-0.9958	10	0.62326	D	0.03	-4.6479	11.7182	0.51666	0.0:0.8541:0.0:0.1459	.	530	Q8TCG1	CIP2A_HUMAN	I	371;530	ENSP00000419487:R371I;ENSP00000295746:R530I	ENSP00000295746:R530I	R	-	2	0	KIAA1524	109764708	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.617000	0.46385	1.237000	0.43756	0.563000	0.77884	AGA	.	.	.	none		0.393	KIAA1524-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353975.2	NM_020890		A	108282018	C	A	108282018	3	1	136	1	0	0	0	0	1	0	0	0	8246	913	32	4	1164	4	KIAA1524	3	108282018	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	43745324	108282018	89740412	17	8310											
ZNF721	170960	hgsc.bcm.edu	37	chr4	436019	436019	+	Missense_Mutation	SNP	A	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	agagtttatctccagtatgaAttttcttatattcgttcagg	10	18	7	6	1	3	2	1	1	2	1	5	2	3	2	1	1	0	3	1	1	5	9			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr4:436019A>C	ENST00000338977.5	-	2	2249	c.2201T>G	c.(2200-2202)aTt>aGt	p.I734S	ZNF721_ENST00000507078.1_Intron|ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000511833.2_Missense_Mutation_p.I746S|ZNF721_ENST00000506646.1_Intron			Q8TF20	ZN721_HUMAN	zinc finger protein 721	734					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						TCCAGTATGAATTTTCTTATA	0.378																																					p.T746R		Atlas-SNP	.											.	ZNF721	205	.	0			c.C2237G						PASS	.						31	33	32					4																	436019		1990	4173	6163	SO:0001583	missense	170960	exon3			GTATGAATTTTCT	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.2201T>G	chr4.hg19:g.436019A>C	ENSP00000340524:p.Ile734Ser	29.0	0.0	.		33.0	12.0	.	NM_133474	Q69YG7	Missense_Mutation	SNP	ENST00000338977.5	hg19		.	.	.	.	.	.	.	.	.	.	A	10.61	1.397775	0.25205	.	.	ENSG00000182903	ENST00000338977;ENST00000511833	T;T	0.00949	5.51;5.51	1.28	-0.782	0.10961	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01558	0.0050	L	0.52266	1.64	0.09310	N	1	P;P;P	0.41569	0.65;0.755;0.711	P;B;B	0.47102	0.537;0.239;0.154	T	0.44651	-0.9314	9	0.56958	D	0.05	.	4.9522	0.14021	0.6885:0.3115:0.0:0.0	.	734;746;746	Q8TF20;D9N162;Q8TF20-2	ZN721_HUMAN;.;.	S	734;746	ENSP00000340524:I734S;ENSP00000428878:I746S	ENSP00000340524:I734S	I	-	2	0	ZNF721	426019	0.000000	0.05858	0.003000	0.11579	0.055000	0.15305	0.796000	0.26986	-0.422000	0.07405	0.155000	0.16302	ATT	.	.	.	none		0.378	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474		C	436019	A	C	436019	3	2	136	1	0	0	0	0	1	0	0	0	18134	101	4	5	538	5	ZNF721	4	436019	Missense_Mutation	SNP	A	TCGA-BQ-7051-01A-12D-1961-08		436019	190718257	18	8311											
NSUN7	79730	hgsc.bcm.edu	37	chr4	40778094	40778094	+	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	tcgaagtcttgctgtccattCtgtaaaggctttattaaata	11	16	7	7	1	2	0	0	0	2	0	4	1	3	0	1	1	1	3	1	1	7	7			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr4:40778094C>A	ENST00000381782.2	+	7	1349	c.854C>A	c.(853-855)tCt>tAt	p.S285Y	NSUN7_ENST00000316607.5_Missense_Mutation_p.S285Y|NSUN7_ENST00000463952.1_3'UTR	NM_024677.4	NP_078953	Q8NE18	NSUN7_HUMAN	NOP2/Sun domain family, member 7	285							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|cervix(1)|large_intestine(1)|lung(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	12						GCTGTCCATTCTGTAAAGGCT	0.333																																					p.S285Y		Atlas-SNP	.											.	NSUN7	70	.	0			c.C854A						PASS	.						92	92	92					4																	40778094		2202	4298	6500	SO:0001583	missense	79730	exon7			TCCATTCTGTAAA	BC036568	CCDS3461.2	4p14	2013-10-11	2009-11-23		ENSG00000179299	ENSG00000179299		"NOP2/Sun domain containing"	25857	protein-coding gene	gene with protein product			"NOL1/NOP2/Sun domain family, member 7"			17442852	Standard	NM_024677		Approved	FLJ14001	uc003gvj.4	Q8NE18	OTTHUMG00000128597	ENST00000381782.2:c.854C>A	chr4.hg19:g.40778094C>A	ENSP00000371201:p.Ser285Tyr	52.0	0.0	.		41.0	19.0	.	NM_024677	C9JI19|Q8N9K8|Q9H815	Missense_Mutation	SNP	ENST00000381782.2	hg19	CCDS3461.2	.	.	.	.	.	.	.	.	.	.	C	22.7	4.318911	0.81469	.	.	ENSG00000179299	ENST00000381782;ENST00000316607	T;T	0.09163	3.01;3.01	5.61	5.61	0.85477	.	0.180007	0.49305	D	0.000151	T	0.31918	0.0812	L	0.59436	1.845	0.51767	D	0.999938	D;D	0.71674	0.997;0.998	D;D	0.72075	0.931;0.976	T	0.00666	-1.1619	10	0.66056	D	0.02	-20.3807	19.2661	0.93985	0.0:1.0:0.0:0.0	.	285;285	Q8NE18;Q8NE18-2	NSUN7_HUMAN;.	Y	285	ENSP00000371201:S285Y;ENSP00000319127:S285Y	ENSP00000319127:S285Y	S	+	2	0	NSUN7	40472851	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.610000	0.67668	2.643000	0.89663	0.557000	0.71058	TCT	.	.	.	none		0.333	NSUN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250454.2	NM_024677		A	40778094	C	A	40778094	3	1	136	1	0	0	0	0	1	0	0	0	10690	913	32	4	876	4	NSUN7	4	40778094	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	40342075	40778094	150376182	19	8312											
POLR2B	5431	hgsc.bcm.edu	37	chr4	57891054	57891054	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tacttttttttttaaaaggtAtcggctaacaagggtgaaat	13	16	8	4	1	0	1	0	1	0	0	1	1	0	1	0	3	2	2	0	3	7	8			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr4:57891054A>G	ENST00000381227.1	+	23	3380	c.2967A>G	c.(2965-2967)gtA>gtG	p.V989V	POLR2B_ENST00000314595.5_Silent_p.V989V|POLR2B_ENST00000431623.2_Silent_p.V914V|POLR2B_ENST00000441246.2_Silent_p.V982V			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	989					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					TTTAAAAGGTATCGGCTAACA	0.313																																					p.V989V		Atlas-SNP	.											.	POLR2B	108	.	0			c.A2967G						PASS	.						118	119	119					4																	57891054		2203	4300	6503	SO:0001819	synonymous_variant	5431	exon22			AAAGGTATCGGCT		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.2967A>G	chr4.hg19:g.57891054A>G		91.0	0.0	.		86.0	38.0	.	NM_000938	A8K1A8|Q8IZ61	Silent	SNP	ENST00000381227.1	hg19	CCDS3511.1																																																																																			.	.	.	none		0.313	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938		G	57891054	A	G	57891054	2	3	136	1	0	0	0	0	0	0	0	1	12222	436	16	3		3	POLR2B	4	57891054	Silent	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	17112960	57891054	133263222	20	8313											
DHX29	54505	hgsc.bcm.edu	37	chr5	54591351	54591351	+	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	ctgaatccttcaggaagtgcAtcttaaaataaaagaaacta	18	10	6	7	0	2	2	1	1	1	1	3	3	3	3	1	1	2	1	1	1	8	4			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr5:54591351A>G	ENST00000251636.5	-	5	655	c.507T>C	c.(505-507)gaT>gaC	p.D169D	RP11-506H20.1_ENST00000506435.1_RNA	NM_019030.2	NP_061903.2	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29	169						eukaryotic 43S preinitiation complex (GO:0016282)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation initiation factor activity (GO:0003743)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|lung(6)|ovary(4)|prostate(1)|skin(3)|urinary_tract(2)	46		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)				CAGGAAGTGCATCTTAAAATA	0.348																																					p.D169D		Atlas-SNP	.											.	DHX29	116	.	0			c.T507C						PASS	.						73	74	74					5																	54591351		2203	4300	6503	SO:0001630	splice_region_variant	54505	exon5			AAGTGCATCTTAA	AY036974	CCDS34158.1	5q11.2	2008-02-05	2003-06-13	2003-06-20	ENSG00000067248	ENSG00000067248		"DEAH-boxes"	15815	protein-coding gene	gene with protein product		612720	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 29"	DDX29			Standard	XM_005248544		Approved		uc003jpx.3	Q7Z478	OTTHUMG00000162313	ENST00000251636.5:c.506-1T>C	chr5.hg19:g.54591351A>G		67.0	0.0	.		58.0	24.0	.	NM_019030	O75549|Q63HN0|Q63HN3|Q8IWW2|Q8N3A1|Q9UMH2	Silent	SNP	ENST00000251636.5	hg19	CCDS34158.1	.	.	.	.	.	.	.	.	.	.	A	11.92	1.781171	0.31502	.	.	ENSG00000067248	ENST00000508346	.	.	.	5.95	3.44	0.39384	.	.	.	.	.	T	0.57873	0.2083	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53746	-0.8395	4	.	.	.	.	8.1903	0.31363	0.7953:0.1348:0.07:0.0	.	.	.	.	R	134	.	.	C	-	1	0	DHX29	54627108	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	1.848000	0.39309	1.075000	0.40932	0.528000	0.53228	TGC	.	.	.	none		0.348	DHX29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368532.1	NM_019030	Silent	G	54591351	A	G	54591351	5	3	136	1	0	0	0	0	0	0	1	0	4505	231	8	3	3694	3	DHX29	5	54591351	Splice_Site	SNP	A	TCGA-BQ-7051-01A-12D-1961-08		54591351	126323909	21	8314											
CTNNA1	1495	hgsc.bcm.edu	37	chr5	138268291	138268291	+	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	ccgactcggcttgcaagcagGacctgctggcctacctgcaa	8	7	11	15	2	0	0	0	0	0	0	1	2	0	1	4	3	5	5	4	3	3	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr5:138268291G>A	ENST00000302763.7	+	17	2413	c.2323G>A	c.(2323-2325)Gac>Aac	p.D775N	CTNNA1_ENST00000355078.5_Missense_Mutation_p.D672N|CTNNA1_ENST00000518825.1_Missense_Mutation_p.D775N|CTNNA1_ENST00000540387.1_Missense_Mutation_p.D405N	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	775					adherens junction organization (GO:0034332)|aging (GO:0007568)|apical junction assembly (GO:0043297)|axon regeneration (GO:0031103)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular protein localization (GO:0034613)|cellular response to indole-3-methanol (GO:0071681)|epithelial cell-cell adhesion (GO:0090136)|establishment or maintenance of cell polarity (GO:0007163)|gap junction assembly (GO:0016264)|male gonad development (GO:0008584)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell motility (GO:2000146)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|negative regulation of neuroblast proliferation (GO:0007406)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of smoothened signaling pathway (GO:0045880)|protein heterooligomerization (GO:0051291)|response to estrogen (GO:0043627)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|catenin complex (GO:0016342)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|gamma-catenin binding (GO:0045295)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|vinculin binding (GO:0017166)			NS(1)|breast(7)|cervix(2)|endometrium(4)|kidney(6)|large_intestine(16)|lung(9)|oesophagus(2)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	52			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TTGCAAGCAGGACCTGCTGGC	0.607																																					p.D775N		Atlas-SNP	.											.	CTNNA1	114	.	0			c.G2323A						PASS	.						53	46	49					5																	138268291		2203	4300	6503	SO:0001583	missense	1495	exon17			AAGCAGGACCTGC	D13866	CCDS34243.1, CCDS75315.1	5q31.2	2008-02-05	2002-08-29			ENSG00000044115			2509	protein-coding gene	gene with protein product		116805	"catenin (cadherin-associated protein), alpha 1 (102kD)"			1924379	Standard	XM_005271898		Approved	CAP102	uc003ldh.3	P35221		ENST00000302763.7:c.2323G>A	chr5.hg19:g.138268291G>A	ENSP00000304669:p.Asp775Asn	43.0	0.0	.		34.0	19.0	.	NM_001903	Q12795|Q8N1C0	Missense_Mutation	SNP	ENST00000302763.7	hg19	CCDS34243.1	.	.	.	.	.	.	.	.	.	.	G	35	5.472975	0.96274	.	.	ENSG00000044115	ENST00000355078;ENST00000302763;ENST00000537034;ENST00000541863;ENST00000518825;ENST00000540387	T;T;T;T	0.36878	1.23;1.23;1.23;1.23	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.57695	0.2071	M	0.65677	2.01	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.977	D;D;P	0.87578	0.996;0.998;0.893	T	0.45614	-0.9249	10	0.13108	T	0.6	-22.7863	19.2223	0.93803	0.0:0.0:1.0:0.0	.	775;652;775	G3XAM7;B4DKT9;P35221	.;.;CTNA1_HUMAN	N	672;775;775;760;775;405	ENSP00000347190:D672N;ENSP00000304669:D775N;ENSP00000427821:D775N;ENSP00000438476:D405N	ENSP00000304669:D775N	D	+	1	0	CTNNA1	138296190	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.635000	0.98437	2.873000	0.98535	0.563000	0.77884	GAC	.	.	.	none		0.607	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903		A	138268291	G	A	138268291	3	1	136	1	0	0	0	0	1	0	0	0	4014	1174	41	2	2385	2	CTNNA1	5	138268291	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	83676940	138268291	42646969	22	8315											
ANKHD1	54882	hgsc.bcm.edu	37	chr5	139864824	139864824	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catggggctgaccctactcaTcgactcaaggtagtctactt	9	11	9	12	1	3	1	2	1	1	0	4	2	3	1	1	3	2	2	1	3	4	4			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr5:139864824T>C	ENST00000360839.2	+	12	2143	c.1989T>C	c.(1987-1989)caT>caC	p.H663H	ANKHD1-EIF4EBP3_ENST00000532219.1_Silent_p.H663H|ANKHD1_ENST00000297183.6_Silent_p.H663H	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	663						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)			ACCCTACTCATCGACTCAAGG	0.498																																					p.H663H		Atlas-SNP	.											.	ANKHD1	233	.	0			c.T1989C						PASS	.						85	75	78					5																	139864824		2203	4300	6503	SO:0001819	synonymous_variant	54882	exon12			TACTCATCGACTC	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.1989T>C	chr5.hg19:g.139864824T>C		49.0	0.0	.		46.0	18.0	.	NM_017747	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Silent	SNP	ENST00000360839.2	hg19	CCDS4225.1	.	.	.	.	.	.	.	.	.	.	T	9.851	1.193672	0.22037	.	.	ENSG00000131503	ENST00000246149	.	.	.	5.29	2.6	0.31112	.	.	.	.	.	T	0.58864	0.2152	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54807	-0.8238	4	.	.	.	.	9.6999	0.40180	0.0:0.2399:0.0:0.7601	.	.	.	.	T	158	.	.	I	+	2	0	ANKHD1	139845008	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.439000	0.44846	0.939000	0.37446	0.459000	0.35465	ATC	.	.	.	none		0.498	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		C	139864824	T	C	139864824	2	2	136	1	0	0	0	0	0	0	0	1	628	1432	50	3		3	ANKHD1	5	139864824	Silent	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	1596533	139864824	41050436	23	8316											
TMCO6	55374	hgsc.bcm.edu	37	chr5	140021512	140021512	+	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	accagcaaccaggccctgctGcagcttgaggcggctcggtg	7	6	14	14	2	0	1	0	1	0	0	1	1	0	1	3	4	5	5	3	4	1	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr5:140021512G>A	ENST00000394671.3	+	4	473	c.372G>A	c.(370-372)ctG>ctA	p.L124L	TMCO6_ENST00000511410.1_3'UTR|TMCO6_ENST00000252100.6_Silent_p.L124L|NDUFA2_ENST00000510680.1_Intron|TMCO6_ENST00000537378.1_Intron	NM_018502.3	NP_060972.3	Q96DC7	TMCO6_HUMAN	transmembrane and coiled-coil domains 6	124					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|urinary_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGCCCTGCTGCAGCTTGAGG	0.622																																					p.L124L		Atlas-SNP	.											.	TMCO6	30	.	0			c.G372A						PASS	.						40	45	44					5																	140021512		2033	4188	6221	SO:0001819	synonymous_variant	55374	exon4			CCTGCTGCAGCTT	BC001910	CCDS4233.2, CCDS75320.1	5q31.3	2008-11-06			ENSG00000113119	ENSG00000113119			28814	protein-coding gene	gene with protein product						12477932	Standard	XM_005268476		Approved	FLJ39769, PRO1580	uc003lgl.3	Q96DC7	OTTHUMG00000129497	ENST00000394671.3:c.372G>A	chr5.hg19:g.140021512G>A		88.0	0.0	.		89.0	37.0	.	NM_018502	Q9BUU0|Q9P198	Silent	SNP	ENST00000394671.3	hg19	CCDS4233.2																																																																																			.	.	.	none		0.622	TMCO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251666.2	NM_018502		A	140021512	G	A	140021512	2	1	136	1	0	0	0	0	0	0	0	1	16012	1306	46	2		2	TMCO6	5	140021512	Silent	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	156688	140021512	40893748	24	8317											
C6orf47	57827	hgsc.bcm.edu	37	chr6	31627425	31627425	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagtctcccagactcttgAgtgctagagataggctggtc	8	11	11	11	0	2	3	0	1	2	2	5	4	3	3	2	2	1	2	2	2	2	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr6:31627425A>G	ENST00000375911.1	-	1	1124	c.300T>C	c.(298-300)acT>acC	p.T100T	C6orf47-AS1_ENST00000422049.1_RNA	NM_021184.3	NP_067007.3	O95873	CF047_HUMAN	chromosome 6 open reading frame 47	100						cytoplasm (GO:0005737)				NS(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9						CAGACTCTTGAGTGCTAGAGA	0.577																																					p.T100T		Atlas-SNP	.											.	C6orf47	15	.	0			c.T300C						PASS	.						61	65	64					6																	31627425		1510	2708	4218	SO:0001819	synonymous_variant	57827	exon1			CTCTTGAGTGCTA	AF129756	CCDS34399.1	6p21.3	2011-12-13			ENSG00000204439	ENSG00000204439			19076	protein-coding gene	gene with protein product						2477242	Standard	NM_021184		Approved	D6S53E, G4	uc003nvm.1	O95873	OTTHUMG00000031172	ENST00000375911.1:c.300T>C	chr6.hg19:g.31627425A>G		83.0	0.0	.		86.0	35.0	.	NM_021184	B0UXA1|B0UZ50|Q5SSS6|Q95IG0	Silent	SNP	ENST00000375911.1	hg19	CCDS34399.1																																																																																			.	.	.	none		0.577	C6orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076324.1	NM_021184		G	31627425	A	G	31627425	2	3	136	1	0	0	0	0	0	0	0	1	2366	291	11	3		3	C6orf47	6	31627425	Silent	SNP	A	TCGA-BQ-7051-01A-12D-1961-08		31627425	139487642	25	8318											
PHF1	5252	hgsc.bcm.edu	37	chr6	33380325	33380325	+	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	gtgtctggtccagtttgaggAtgattcgcagtttctggttc	5	16	13	7	1	2	2	0	2	2	0	5	3	3	3	1	3	0	4	1	3	0	4			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr6:33380325A>T	ENST00000374516.3	+	3	471	c.200A>T	c.(199-201)gAt>gTt	p.D67V	PHF1_ENST00000374512.3_Missense_Mutation_p.D67V|PHF1_ENST00000459809.1_3'UTR	NM_024165.2	NP_077084.1	O43189	PHF1_HUMAN	PHD finger protein 1	67	Tudor.				cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of histone H3-K27 methylation (GO:0061087)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	methylated histone binding (GO:0035064)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(5)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19		Ovarian(999;0.0443)				CAGTTTGAGGATGATTCGCAG	0.478																																					p.D67V		Atlas-SNP	.											.	PHF1	42	.	0			c.A200T						PASS	.						166	162	163					6																	33380325		2203	4300	6503	SO:0001583	missense	5252	exon3			TTGAGGATGATTC	AF029678	CCDS4777.1, CCDS4778.1	6p21.3	2013-01-28			ENSG00000112511	ENSG00000112511		"Tudor domain containing", "Zinc fingers, PHD-type"	8919	protein-coding gene	gene with protein product	"tudor domain containing 19C"	602881				9545646, 18385154	Standard	NM_024165		Approved	MTF2L2, TDRD19C	uc003oeh.3	O43189	OTTHUMG00000031105	ENST00000374516.3:c.200A>T	chr6.hg19:g.33380325A>T	ENSP00000363640:p.Asp67Val	146.0	0.0	.		114.0	45.0	.	NM_024165	B1AZX2|B1AZX3|O60929|Q5SU07|Q5SU08|Q96KM7	Missense_Mutation	SNP	ENST00000374516.3	hg19	CCDS4777.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.967657	0.74131	.	.	ENSG00000112511	ENST00000427004;ENST00000428274;ENST00000374512;ENST00000374516	T;T;T;T	0.68479	-0.33;-0.33;-0.33;-0.33	4.58	4.58	0.56647	Tudor domain (1);	0.000000	0.85682	D	0.000000	T	0.73651	0.3614	M	0.68952	2.095	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;0.99	T	0.77910	-0.2411	10	0.87932	D	0	-21.3302	11.944	0.52918	1.0:0.0:0.0:0.0	.	67;67	O43189-2;O43189	.;PHF1_HUMAN	V	67	ENSP00000410494:D67V;ENSP00000392697:D67V;ENSP00000363636:D67V;ENSP00000363640:D67V	ENSP00000363636:D67V	D	+	2	0	PHF1	33488303	1.000000	0.71417	0.998000	0.56505	0.969000	0.65631	8.976000	0.93442	1.928000	0.55862	0.460000	0.39030	GAT	.	.	.	none		0.478	PHF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076175.3			T	33380325	A	T	33380325	3	4	136	1	0	0	0	0	1	0	0	0	11827	333	12	5	206	5	PHF1	6	33380325	Missense_Mutation	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	1752900	33380325	137734742	26	8319											
GUCA1B	2979	hgsc.bcm.edu	37	chr6	42152609	42152609	+	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	ccagctgctgggattcatgtCcatctgcagcatcttcatca	8	12	8	13	0	5	0	3	0	2	0	6	1	6	1	2	1	4	4	2	1	0	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr6:42152609C>A	ENST00000230361.3	-	4	642	c.547G>T	c.(547-549)Gac>Tac	p.D183Y		NM_002098.5	NP_002089.4	Q9UMX6	GUC1B_HUMAN	guanylate cyclase activator 1B (retina)	183					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)			GGATTCATGTCCATCTGCAGC	0.587																																					p.D183Y		Atlas-SNP	.											.	GUCA1B	19	.	0			c.G547T						PASS	.						131	112	118					6																	42152609		2203	4300	6503	SO:0001583	missense	2979	exon4			TCATGTCCATCTG	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.547G>T	chr6.hg19:g.42152609C>A	ENSP00000230361:p.Asp183Tyr	112.0	0.0	.		89.0	46.0	.	NM_002098	Q9NU15	Missense_Mutation	SNP	ENST00000230361.3	hg19	CCDS4865.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.274245	0.80580	.	.	ENSG00000112599	ENST00000230361	T	0.53640	0.61	4.36	4.36	0.52297	EF-hand-like domain (1);	0.102162	0.64402	D	0.000004	T	0.38719	0.1051	N	0.08118	0	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.52711	-0.8539	10	0.54805	T	0.06	.	15.1849	0.72993	0.0:1.0:0.0:0.0	.	183	Q9UMX6	GUC1B_HUMAN	Y	183	ENSP00000230361:D183Y	ENSP00000230361:D183Y	D	-	1	0	GUCA1B	42260587	1.000000	0.71417	0.992000	0.48379	0.874000	0.50279	5.791000	0.69045	2.361000	0.80049	0.655000	0.94253	GAC	.	.	.	none		0.587	GUCA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040550.1	NM_002098		A	42152609	C	A	42152609	3	1	136	1	0	0	0	0	1	0	0	0	6896	855	30	4	59	4	GUCA1B	6	42152609	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	8772284	42152609	128962458	27	8320											
SYNJ2	8871	hgsc.bcm.edu	37	chr6	158450005	158450005	+	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	tctcgctttgacctgactgtCcgcacgcagaagcaggggga	8	8	13	12	3	1	3	0	2	1	1	3	4	2	4	2	2	1	4	2	2	1	1	rs372960799		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr6:158450005C>T	ENST00000355585.4	+	3	507	c.432C>T	c.(430-432)gtC>gtT	p.V144V	SYNJ2_ENST00000367122.2_Silent_p.V144V|SYNJ2_ENST00000367121.3_Silent_p.V144V|SYNJ2_ENST00000449859.2_Silent_p.V93V	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	144	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	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)		ACCTGACTGTCCGCACGCAGA	0.582													C|||	1	0.000199681	8e-04	0	5008	,	,		16943	0		0	False		,,,				2504	0				p.V144V		Atlas-SNP	.											.	SYNJ2	111	.	0			c.C432T						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	65	67	66		,432	-0.5	0.7	6		66	0,8600		0,0,4300	no	utr-5,coding-synonymous	SYNJ2	NM_001178088.1,NM_003898.3	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	,144/1497	158450005	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8871	exon3			GACTGTCCGCACG	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.432C>T	chr6.hg19:g.158450005C>T		76.0	0.0	.		89.0	34.0	.	NM_003898	Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	Silent	SNP	ENST00000355585.4	hg19	CCDS5254.1	.	.	.	.	.	.	.	.	.	.	C	0.979	-0.697726	0.03279	2.27E-4	0.0	ENSG00000078269	ENST00000367113	.	.	.	4.62	-0.532	0.11890	.	.	.	.	.	T	0.45875	0.1364	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51857	-0.8652	4	.	.	.	.	11.4359	0.50068	0.0:0.2478:0.6114:0.1408	.	.	.	.	F	119	.	.	S	+	2	0	SYNJ2	158369993	0.753000	0.28349	0.672000	0.29872	0.084000	0.17831	0.009000	0.13219	1.108000	0.41662	0.655000	0.94253	TCC	.	.	.	weak		0.582	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2			T	158450005	C	T	158450005	2	4	136	1	0	0	0	0	0	0	0	1	15465	842	30	2		2	SYNJ2	6	158450005	Silent	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	116297396	158450005	12665062	28	8321											
ARMC10	83787	hgsc.bcm.edu	37	chr7	102724230	102724230	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggatcctgtaattattgaaAgagctttgattactttgggt	11	16	10	4	0	0	3	0	2	0	1	1	4	1	4	1	2	2	2	1	2	4	6			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr7:102724230A>G	ENST00000323716.3	+	3	738	c.346A>G	c.(346-348)Aga>Gga	p.R116G	ARMC10_ENST00000441711.2_Missense_Mutation_p.R81G|ARMC10_ENST00000454559.1_Missense_Mutation_p.R81G|ARMC10_ENST00000541300.1_Missense_Mutation_p.R81G|ARMC10_ENST00000428183.2_Missense_Mutation_p.R116G|ARMC10_ENST00000425331.1_Missense_Mutation_p.R81G	NM_031905.4	NP_114111.2	Q8N2F6	ARM10_HUMAN	armadillo repeat containing 10	116					regulation of growth (GO:0040008)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	11						AATTATTGAAAGAGCTTTGAT	0.398																																					p.R116G		Atlas-SNP	.											.	ARMC10	25	.	0			c.A346G						PASS	.						94	96	95					7																	102724230		2203	4300	6503	SO:0001583	missense	83787	exon3			ATTGAAAGAGCTT	AY150853	CCDS5728.1, CCDS55145.1, CCDS55146.1, CCDS55147.1, CCDS55148.1, CCDS55149.1	7q22.1	2013-02-14			ENSG00000170632	ENSG00000170632		"Armadillo repeat containing"	21706	protein-coding gene	gene with protein product	"specific Splicing Variant involved in Hepatocarcinogenesis"	611864				12839973	Standard	NM_031905		Approved	MGC3195, SVH	uc003vaw.2	Q8N2F6	OTTHUMG00000157201	ENST00000323716.3:c.346A>G	chr7.hg19:g.102724230A>G	ENSP00000319412:p.Arg116Gly	76.0	0.0	.		98.0	32.0	.	NM_031905	A8K703|B4DWJ8|F5GX65|Q75K91|Q75MG6|Q75ML8|Q8IZC1|Q8IZC2|Q8IZC3|Q9BTM6	Missense_Mutation	SNP	ENST00000323716.3	hg19	CCDS5728.1	.	.	.	.	.	.	.	.	.	.	A	16.07	3.017384	0.54576	.	.	ENSG00000170632	ENST00000323716;ENST00000428183;ENST00000441711;ENST00000454559;ENST00000425331;ENST00000541300;ENST00000434153	T;T;T;T;T;T;T	0.47869	1.5;1.6;1.5;1.6;1.5;1.6;0.83	5.28	4.11	0.48088	Armadillo-like helical (1);Armadillo-type fold (1);	0.413848	0.28209	N	0.016195	T	0.54464	0.1860	L	0.59436	1.845	0.23809	N	0.996789	P;B;B;D;P;P	0.58268	0.741;0.039;0.096;0.982;0.852;0.863	P;B;B;P;B;P	0.54889	0.497;0.05;0.073;0.763;0.436;0.627	T	0.47799	-0.9089	10	0.49607	T	0.09	-8.0575	9.962	0.41701	0.6711:0.3289:0.0:0.0	.	81;81;81;116;81;116	B4DWJ8;F5GX65;Q8N2F6-4;Q8N2F6-3;Q8N2F6-2;Q8N2F6	.;.;.;.;.;ARM10_HUMAN	G	116;116;81;81;81;81;116	ENSP00000319412:R116G;ENSP00000396654:R116G;ENSP00000413619:R81G;ENSP00000405612:R81G;ENSP00000397969:R81G;ENSP00000440463:R81G;ENSP00000398201:R116G	ENSP00000319412:R116G	R	+	1	2	ARMC10	102511466	0.988000	0.35896	0.991000	0.47740	0.941000	0.58515	1.811000	0.38942	0.948000	0.37687	0.456000	0.33151	AGA	.	.	.	none		0.398	ARMC10-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347882.1	NM_031905		G	102724230	A	G	102724230	3	3	136	1	0	0	0	0	1	0	0	0	950	64	3	3	356	3	ARMC10	7	102724230	Missense_Mutation	SNP	A	TCGA-BQ-7051-01A-12D-1961-08		102724230	56414433	29	8322											
MLL3	58508	hgsc.bcm.edu	37	chr7	151880116	151880116	+	Frame_Shift_Del	DEL	A	A	-																															ctttgctttaaaggatctttAaaaagctccgaatcaatacg																										TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr7:151880116delA	ENST00000262189.6	-	35	5426	c.5208delT	c.(5206-5208)tttfs	p.F1736fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.F1736fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1736	Gln-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)										AAGGATCTTTAAAAAGCTCCG	0.343																																					p.K1737fs		Atlas-INDEL	.											.	MLL3	1564	.	0			c.5209delA						PASS	.						216	218	217					7																	151880116		2203	4300	6503	SO:0001589	frameshift_variant	58508	exon35			.	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.5208delT	chr7.hg19:g.151880116delA	ENSP00000262189:p.Phe1736fs	340.0	0.0	0		463.0	289.0	0.62419	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	hg19	CCDS5931.1																																																																																			.	.	.	none		0.343	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			-	151880116	A	-	151880116	7	5	136	1	0	1	0	1	0	0	0	0	9629	359	13	0	9627	0	MLL3	7	151880116	Frame_Shift_Del	DEL	A	TCGA-BQ-7051-01A-12D-1961-08	49155886	151880116	7258547	30	8323											
RP1	6101	hgsc.bcm.edu	37	chr8	55534829	55534829	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtaccccaagggaaatgcAaagtcagaaagcagaaagag	18	4	12	7	0	1	3	1	0	0	3	1	4	1	4	2	1	3	3	2	1	6	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr8:55534829A>G	ENST00000220676.1	+	3	916	c.768A>G	c.(766-768)gcA>gcG	p.A256A		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	256					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)			AGGGAAATGCAAAGTCAGAAA	0.403																																					p.A256A	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.A768G						PASS	.						78	80	80					8																	55534829		2203	4300	6503	SO:0001819	synonymous_variant	6101	exon3			AAATGCAAAGTCA	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.768A>G	chr8.hg19:g.55534829A>G		51.0	0.0	.		51.0	18.0	.	NM_006269		Silent	SNP	ENST00000220676.1	hg19	CCDS6160.1																																																																																			.	.	.	none		0.403	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		G	55534829	A	G	55534829	2	3	136	1	0	0	0	0	0	0	0	1	13545	117	5	3		3	RP1	8	55534829	Silent	SNP	A	TCGA-BQ-7051-01A-12D-1961-08		55534829	90829193	31	8324											
MATN2	4147	hgsc.bcm.edu	37	chr8	98943606	98943609	+	Frame_Shift_Del	DEL	CTAA	CTAA	-																															aggcacgggacacgggcatcCtaatctttgccattggtgtg																										TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	CTAA	CTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr8:98943606_98943609delCTAA	ENST00000520016.1	+	2	692_695	c.568_571delCTAA	c.(568-573)ctaatcfs	p.LI190fs	MATN2_ENST00000521689.1_Frame_Shift_Del_p.LI190fs|MATN2_ENST00000524308.1_Frame_Shift_Del_p.LI190fs|MATN2_ENST00000522025.2_Intron|MATN2_ENST00000254898.5_Frame_Shift_Del_p.LI190fs			O00339	MATN2_HUMAN	matrilin 2	190	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			CACGGGCATCCTAATCTTTGCCAT	0.559																																					p.189_190del		Atlas-INDEL	.											.	MATN2	165	.	0			c.567_570del						PASS	.																																			SO:0001589	frameshift_variant	4147	exon3			.	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.568_571delCTAA	chr8.hg19:g.98943606_98943609delCTAA	ENSP00000430487:p.Leu190fs	53.0	0.0	0		44.0	19.0	0.431818	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Frame_Shift_Del	DEL	ENST00000520016.1	hg19	CCDS55264.1																																																																																			.	.	.	none		0.559	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1			-	98943609	CTAA	-	98943606	7	5	136	1	0	1	0	1	0	0	0	0	9341	680	24	0	574	0	MATN2	8	98943606	Frame_Shift_Del	DEL	CTAA	TCGA-BQ-7051-01A-12D-1961-08	43408777	98943606	47420416	32	8325											
SLC45A4	57210	hgsc.bcm.edu	37	chr8	142238284	142238284	+	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	ttgagcattctaacctttctGaagactccattgatttgacc	10	15	6	10	0	2	5	0	4	2	1	3	5	3	5	3	0	2	1	3	0	2	6			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr8:142238284G>A	ENST00000024061.3	-	1	389	c.82C>T	c.(82-84)Cag>Tag	p.Q28*	SLC45A4_ENST00000519067.1_Nonsense_Mutation_p.Q28*|SLC45A4_ENST00000517878.1_Intron|SLC45A4_ENST00000433583.2_Intron	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)			TAACCTTTCTGAAGACTCCAT	0.537																																					p.Q28X		Atlas-SNP	.											.	SLC45A4	71	.	0			c.C82T						PASS	.						191	177	181					8																	142238284		2203	4300	6503	SO:0001587	stop_gained	57210	exon1			CTTTCTGAAGACT	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.82C>T	chr8.hg19:g.142238284G>A	ENSP00000024061:p.Gln28*	217.0	0.0	.		187.0	83.0	.	NM_001080431	Q6ZRI2|Q9ULU3	Nonsense_Mutation	SNP	ENST00000024061.3	hg19	CCDS34948.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.134082	0.77662	.	.	ENSG00000022567	ENST00000519067;ENST00000024061	.	.	.	1.79	-1.83	0.07833	.	0.589005	0.15260	U	0.271852	.	.	.	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	.	4.245	0.10667	0.1675:0.4643:0.3682:0.0	.	.	.	.	X	28	.	ENSP00000024061:Q28X	Q	-	1	0	SLC45A4	142307466	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.632000	0.02024	-0.542000	0.06249	0.556000	0.70494	CAG	.	.	.	none		0.537	SLC45A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378571.3	XM_050325		A	142238284	G	A	142238284	4	1	136	1	0	0	0	0	0	1	0	0	14656	1299	45	2	2346	2	SLC45A4	8	142238284	Nonsense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	43294678	142238284	4125738	33	8326											
PITRM1	10531	hgsc.bcm.edu	37	chr10	3206029	3206029	+	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	cactgagtacgtgtggtcagGaagaagtctgttctgaaggt	10	11	14	6	1	3	3	1	2	2	1	3	4	3	4	0	3	1	2	0	3	4	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr10:3206029G>A	ENST00000224949.4	-	7	713	c.679C>T	c.(679-681)Cct>Tct	p.P227S	PITRM1-AS1_ENST00000601046.1_RNA|PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000380989.2_Missense_Mutation_p.P227S|PITRM1_ENST00000451104.2_Missense_Mutation_p.P195S			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	227					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						GTGTGGTCAGGAAGAAGTCTG	0.448																																					p.P227S		Atlas-SNP	.											.	PITRM1	109	.	0			c.C679T						PASS	.						124	122	123					10																	3206029		1934	4132	6066	SO:0001583	missense	10531	exon7			GGTCAGGAAGAAG	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.679C>T	chr10.hg19:g.3206029G>A	ENSP00000224949:p.Pro227Ser	79.0	0.0	.		63.0	28.0	.	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	hg19	CCDS59208.1	.	.	.	.	.	.	.	.	.	.	g	19.62	3.860856	0.71834	.	.	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000451104	T;T;T	0.31247	1.5;1.5;1.5	5.7	5.7	0.88788	Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.000000	0.85682	D	0.000000	T	0.65091	0.2658	M	0.88241	2.94	0.80722	D	1	D;D;D;D;D;D	0.89917	0.998;0.995;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.927;0.947;1.0;0.998;0.998;0.998	T	0.70960	-0.4730	10	0.87932	D	0	.	19.8478	0.96722	0.0:0.0:1.0:0.0	.	220;195;227;227;227;220	E9PDX6;E7ES23;Q5JRX3-2;C9JSL2;Q5JRX3;B4DH07	.;.;.;.;PREP_HUMAN;.	S	227;220;227;195	ENSP00000224949:P227S;ENSP00000370377:P227S;ENSP00000401201:P195S	ENSP00000224949:P227S	P	-	1	0	PITRM1	3196029	1.000000	0.71417	0.997000	0.53966	0.075000	0.17131	9.162000	0.94745	2.698000	0.92095	0.655000	0.94253	CCT	.	.	.	none		0.448	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2			A	3206029	G	A	3206029	3	1	136	1	0	0	0	0	1	0	0	0	11960	1174	41	2	2518	2	PITRM1	10	3206029	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08		3206029	132328718	34	8327											
NCOA4	8031	hgsc.bcm.edu	37	chr10	51586276	51586276	+	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	tttcttttattgcaggaagtAttacttaattcacctctaca	11	18	4	8	0	3	0	1	0	2	0	3	1	3	1	1	1	3	2	1	1	6	9			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr10:51586276A>T	ENST00000443446.1	+	9	1933	c.1704A>T	c.(1702-1704)gtA>gtT	p.V568V	NCOA4_ENST00000344348.6_Silent_p.V568V|NCOA4_ENST00000430396.2_Silent_p.V468V|NCOA4_ENST00000374082.1_Missense_Mutation_p.Y523F|NCOA4_ENST00000414907.2_Silent_p.V402V|NCOA4_ENST00000374087.4_Silent_p.V568V|NCOA4_ENST00000438493.1_Silent_p.V584V|NCOA4_ENST00000452682.1_Silent_p.V584V	NM_001145262.1	NP_001138734.1	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4	568					androgen receptor signaling pathway (GO:0030521)|male gonad development (GO:0008584)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|skin(1)	5						TGCAGGAAGTATTACTTAATT	0.398			T	RET	papillary thyroid																																p.V584V		Atlas-SNP	.		Dom	yes		10	10q11.2	8031	nuclear receptor coactivator 4 - PTC3 (ELE1)		E	.	NCOA4	58	.	0			c.A1752T						PASS	.						114	111	112					10																	51586276		2203	4300	6503	SO:0001819	synonymous_variant	8031	exon10			GGAAGTATTACTT	L49399	CCDS73092.1, CCDS73093.1, CCDS73094.1	10q11.2	2014-04-10			ENSG00000138293	ENSG00000266412			7671	protein-coding gene	gene with protein product	"RET-activating gene ELE1"	601984				8290261, 8643607, 24695223	Standard	NM_001145260		Approved	ARA70, RFG, ELE1, PTC3, DKFZp762E1112	uc009xon.3	Q13772	OTTHUMG00000188314	ENST00000443446.1:c.1704A>T	chr10.hg19:g.51586276A>T		137.0	0.0	.		127.0	48.0	.	NM_001145261	A8K8W5|B4E260|E9PAV7|J3KQN8|Q14239	Silent	SNP	ENST00000443446.1	hg19	CCDS7237.1	.	.	.	.	.	.	.	.	.	.	A	3.664	-0.068949	0.07228	.	.	ENSG00000138293	ENST00000374082	T	0.26223	1.75	5.41	1.78	0.24846	.	.	.	.	.	T	0.08670	0.0215	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29181	-1.0020	6	0.02654	T	1	-2.9612	2.9009	0.05705	0.482:0.309:0.077:0.132	.	.	.	.	F	523	ENSP00000363195:Y523F	ENSP00000363195:Y523F	Y	+	2	0	NCOA4	51256282	0.994000	0.37717	0.999000	0.59377	0.958000	0.62258	0.292000	0.19011	0.141000	0.18875	0.533000	0.62120	TAT	.	.	.	none		0.398	NCOA4-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048052.1	NM_005437		T	51586276	A	T	51586276	2	4	136	1	0	0	0	0	0	0	0	1	10238	436	16	5		5	NCOA4	10	51586276	Silent	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	48380247	51586276	83948471	35	8328											
PTEN	5728	hgsc.bcm.edu	37	chr10	89717669	89717669	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attcctccaattcaggacccAcacgacgggaagacaagttc	13	7	8	13	2	1	1	1	0	0	1	4	4	3	3	3	2	0	1	3	2	3	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr10:89717669A>G	ENST00000371953.3	+	7	2051	c.694A>G	c.(694-696)Aca>Gca	p.T232A	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	232	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.?(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)		TTCAGGACCCACACGACGGGA	0.423		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.T232A		Atlas-SNP	.	yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	.,1	PTEN	3652	.	48	Whole gene deletion(37)|Deletion - Frameshift(9)|Deletion - In frame(1)|Unknown(1)	prostate(16)|central_nervous_system(10)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)	c.A694G						PASS	.						155	133	140					10																	89717669		2203	4300	6503	SO:0001583	missense	5728	exon7	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	GGACCCACACGAC	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.694A>G	chr10.hg19:g.89717669A>G	ENSP00000361021:p.Thr232Ala	116.0	1.0	.		91.0	30.0	.	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	hg19	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	12.75	2.030305	0.35797	.	.	ENSG00000171862	ENST00000371953	D	0.85773	-2.03	5.15	5.15	0.70609	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.158008	0.56097	D	0.000030	T	0.74711	0.3752	N	0.25647	0.755	0.51482	D	0.999926	B	0.16802	0.019	B	0.16289	0.015	T	0.68519	-0.5387	9	.	.	.	-10.0511	10.8662	0.46856	0.8504:0.0:0.0:0.1496	.	232	P60484	PTEN_HUMAN	A	232	ENSP00000361021:T232A	.	T	+	1	0	PTEN	89707649	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.612000	0.67681	1.928000	0.55862	0.477000	0.44152	ACA	.	.	.	none		0.423	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89717669	A	G	89717669	3	3	136	1	0	0	0	0	1	0	0	0	12748	159	6	3	720	3	PTEN	10	89717669	Missense_Mutation	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	38131393	89717669	45817078	36	8329											
DRD4	1815	hgsc.bcm.edu	37	chr11	639919	639919	+	Missense_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	gcggcctgcagcgctgggagGtggcacgtcgcgccaagctg	5	5	18	13	5	0	0	0	0	0	0	1	1	0	1	2	4	3	4	2	4	1	0			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr11:639919G>A	ENST00000176183.5	+	3	682	c.670G>A	c.(670-672)Gtg>Atg	p.V224M		NM_000797.3	NP_000788.2	P21917	DRD4_HUMAN	dopamine receptor D4	224					activation of MAPK activity (GO:0000187)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adult locomotory behavior (GO:0008344)|arachidonic acid secretion (GO:0050482)|behavioral fear response (GO:0001662)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|cellular calcium ion homeostasis (GO:0006874)|circadian rhythm (GO:0007623)|dopamine metabolic process (GO:0042417)|dopamine receptor signaling pathway (GO:0007212)|fear response (GO:0042596)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of protein secretion (GO:0050709)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|olfactory learning (GO:0008355)|photoperiodism (GO:0009648)|positive regulation of dopamine uptake involved in synaptic transmission (GO:0051586)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of kinase activity (GO:0033674)|positive regulation of penile erection (GO:0060406)|positive regulation of sodium:proton antiporter activity (GO:0032417)|regulation of calcium-mediated signaling (GO:0050848)|regulation of circadian rhythm (GO:0042752)|regulation of dopamine metabolic process (GO:0042053)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of neurotransmitter secretion (GO:0046928)|response to amphetamine (GO:0001975)|response to histamine (GO:0034776)|response to steroid hormone (GO:0048545)|retina development in camera-type eye (GO:0060041)|short-term memory (GO:0007614)|social behavior (GO:0035176)|synaptic transmission, dopaminergic (GO:0001963)	cell cortex (GO:0005938)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|vesicle membrane (GO:0012506)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gi/Go (GO:0001591)|drug binding (GO:0008144)|identical protein binding (GO:0042802)|potassium channel regulator activity (GO:0015459)|SH3 domain binding (GO:0017124)			NS(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	4		all_cancers(49;1.69e-08)|all_epithelial(84;1.65e-05)|Breast(177;0.000231)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.36e-28)|Epithelial(43;2.59e-27)|OV - Ovarian serous cystadenocarcinoma(40;3.53e-21)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Dopamine(DB00988)|Iloperidone(DB04946)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Pramipexole(DB00413)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Ziprasidone(DB00246)	GCGCTGGGAGGTGGCACGTCG	0.741																																					p.V224M		Atlas-SNP	.											.	DRD4	17	.	0			c.G670A						PASS	.						30	23	25					11																	639919		2194	4290	6484	SO:0001583	missense	1815	exon3			TGGGAGGTGGCAC	L12398	CCDS7710.1	11p15.5	2012-08-08			ENSG00000069696	ENSG00000069696		"GPCR / Class A : Dopamine receptors"	3025	protein-coding gene	gene with protein product		126452					Standard	NM_000797		Approved		uc001lqp.2	P21917	OTTHUMG00000133312	ENST00000176183.5:c.670G>A	chr11.hg19:g.639919G>A	ENSP00000176183:p.Val224Met	39.0	0.0	.		33.0	15.0	.	NM_000797	B0M0J7|Q7Z7Q5|Q8NGM5	Missense_Mutation	SNP	ENST00000176183.5	hg19	CCDS7710.1	.	.	.	.	.	.	.	.	.	.	G	14.34	2.506330	0.44558	.	.	ENSG00000069696	ENST00000176183	T	0.37915	1.17	2.79	1.81	0.25067	GPCR, rhodopsin-like superfamily (1);	0.391968	0.24476	N	0.038200	T	0.30916	0.0780	.	.	.	0.24791	N	0.992753	P	0.47604	0.898	B	0.42138	0.377	T	0.14811	-1.0459	9	0.56958	D	0.05	.	10.3373	0.43858	0.0:0.2038:0.7962:0.0	.	224	P21917	DRD4_HUMAN	M	224	ENSP00000176183:V224M	ENSP00000176183:V224M	V	+	1	0	DRD4	629919	1.000000	0.71417	0.365000	0.25901	0.758000	0.43043	4.570000	0.60872	0.461000	0.27071	0.313000	0.20887	GTG	.	.	.	none		0.741	DRD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257109.1	NM_000797		A	639919	G	A	639919	3	1	136	1	0	0	0	0	1	0	0	0	4761	1261	44	2	680	2	DRD4	11	639919	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08		639919	134366597	37	8330											
OR4A16	81327	hgsc.bcm.edu	37	chr11	55110978	55110978	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgcatgggtcagctcttcaTagaacacttacttggtggtg	8	14	11	8	0	3	1	2	0	1	1	3	1	3	1	0	3	4	2	0	3	3	5			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr11:55110978T>C	ENST00000314721.2	+	1	352	c.302T>C	c.(301-303)aTa>aCa	p.I101T		NM_001005274.1	NP_001005274.1	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A, member 16	101						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						CAGCTCTTCATAGAACACTTA	0.443																																					p.I101T		Atlas-SNP	.											.	OR4A16	120	.	0			c.T302C						PASS	.						203	189	193					11																	55110978		2201	4296	6497	SO:0001583	missense	81327	exon1			TCTTCATAGAACA	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.302T>C	chr11.hg19:g.55110978T>C	ENSP00000325128:p.Ile101Thr	317.0	0.0	.		268.0	22.0	.	NM_001005274	Q6IFL3	Missense_Mutation	SNP	ENST00000314721.2	hg19	CCDS31499.1	.	.	.	.	.	.	.	.	.	.	t	0.119	-1.128496	0.01756	.	.	ENSG00000181961	ENST00000314721	T	0.00864	5.6	2.57	1.45	0.22620	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00906	0.0030	L	0.39085	1.19	0.09310	N	1	B	0.16802	0.019	B	0.15484	0.013	T	0.46317	-0.9200	9	0.20519	T	0.43	.	5.5053	0.16850	0.0:0.1562:0.0:0.8438	.	101	Q8NH70	O4A16_HUMAN	T	101	ENSP00000325128:I101T	ENSP00000325128:I101T	I	+	2	0	OR4A16	54867554	0.000000	0.05858	0.009000	0.14445	0.018000	0.09664	0.028000	0.13644	1.186000	0.42985	0.346000	0.21813	ATA	.	.	.	none		0.443	OR4A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391160.1	NM_001005274		C	55110978	T	C	55110978	3	2	136	1	0	0	0	0	1	0	0	0	11048	1406	49	3	304	3	OR4A16	11	55110978	Missense_Mutation	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	54471059	55110978	79895538	38	8331											
PAK1	5058	hgsc.bcm.edu	37	chr11	77047284	77047284	+	Frame_Shift_Del	DEL	T	T	-																															gttcctaccatggtgctccgTttgctctgctctggggttat																										TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr11:77047284delT	ENST00000356341.3	-	13	1791	c.1260delA	c.(1258-1260)aaafs	p.K420fs	PAK1_ENST00000530617.1_Frame_Shift_Del_p.K420fs|PAK1_ENST00000525542.1_5'UTR|PAK1_ENST00000528203.1_Frame_Shift_Del_p.K322fs|PAK1_ENST00000278568.4_Frame_Shift_Del_p.K420fs	NM_002576.4	NP_002567.3	Q13153	PAK1_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 1	420	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cellular response to insulin stimulus (GO:0032869)|dendrite development (GO:0016358)|exocytosis (GO:0006887)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor clustering (GO:0043113)|response to hypoxia (GO:0001666)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|wound healing (GO:0042060)	axon (GO:0030424)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|intercalated disc (GO:0014704)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|Z disc (GO:0030018)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(13)|skin(2)|stomach(1)	29	all_cancers(14;1.75e-18)					TGGTGCTCCGTTTGCTCTGCT	0.473																																					p.R421fs		Atlas-INDEL	.											.	PAK1	89	.	0			c.1261delC						PASS	.						148	145	146					11																	77047284		2200	4292	6492	SO:0001589	frameshift_variant	5058	exon13			.	U51120	CCDS8250.1, CCDS44687.1	11q13-q14	2008-06-17	2008-06-17						8590	protein-coding gene	gene with protein product	"STE20 homolog, yeast"	602590	"p21/Cdc42/Rac1-activated kinase 1 (yeast Ste20-related)", "p21/Cdc42/Rac1-activated kinase 1 (STE20 homolog, yeast)"			8805275, 9533029	Standard	NM_002576		Approved		uc001oyg.4	Q13153		ENST00000356341.3:c.1260delA	chr11.hg19:g.77047284delT	ENSP00000348696:p.Lys420fs	121.0	0.0	0		104.0	43.0	0.413462	NM_001128620	O75561|Q13567|Q32M53|Q32M54|Q86W79	Frame_Shift_Del	DEL	ENST00000356341.3	hg19	CCDS8250.1																																																																																			.	.	.	none		0.473	PAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382083.2	NM_002576		-	77047284	T	-	77047284	7	5	136	1	0	1	0	1	0	0	0	0	11406	1722	60	0	442	0	PAK1	11	77047284	Frame_Shift_Del	DEL	T	TCGA-BQ-7051-01A-12D-1961-08	21936306	77047284	57959232	39	8332											
UBE4A	9354	hgsc.bcm.edu	37	chr11	118250228	118250228	+	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	aggttgcctggcgggatgctCagcaaagttctagccctgct	7	10	13	11	1	2	0	1	0	1	0	2	1	2	1	2	3	5	5	2	3	2	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr11:118250228C>T	ENST00000431736.2	+	11	1732	c.1660C>T	c.(1660-1662)Cag>Tag	p.Q554*	UBE4A_ENST00000252108.3_Nonsense_Mutation_p.Q547*|UBE4A_ENST00000545354.1_Nonsense_Mutation_p.Q19*					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)		GCGGGATGCTCAGCAAAGTTC	0.493																																					p.Q554X		Atlas-SNP	.											.	UBE4A	97	.	0			c.C1660T						PASS	.						107	101	103					11																	118250228		2200	4296	6496	SO:0001587	stop_gained	9354	exon11			GATGCTCAGCAAA	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.1660C>T	chr11.hg19:g.118250228C>T	ENSP00000387362:p.Gln554*	144.0	0.0	.		97.0	51.0	.	NM_004788		Nonsense_Mutation	SNP	ENST00000431736.2	hg19	CCDS8396.1	.	.	.	.	.	.	.	.	.	.	C	40	8.417745	0.98803	.	.	ENSG00000110344	ENST00000252108;ENST00000431736;ENST00000545354	.	.	.	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.2921	19.4627	0.94924	0.0:1.0:0.0:0.0	.	.	.	.	X	547;554;19	.	ENSP00000252108:Q547X	Q	+	1	0	UBE4A	117755438	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.487000	0.81328	2.588000	0.87417	0.655000	0.94253	CAG	.	.	.	none		0.493	UBE4A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398143.1	NM_004788		T	118250228	C	T	118250228	4	4	136	1	0	0	0	0	0	1	0	0	16894	827	29	2	1698	2	UBE4A	11	118250228	Nonsense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	41202944	118250228	16756288	40	8333											
NLRX1	79671	hgsc.bcm.edu	37	chr11	119044337	119044337	+	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	ctgatgagctacttcgcccaCccgcggagctggccctggag	6	7	13	15	3	0	2	0	2	0	0	1	4	0	4	3	3	3	2	3	3	1	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr11:119044337C>T	ENST00000409109.1	+	5	966	c.379C>T	c.(379-381)Ccc>Tcc	p.P127S	NLRX1_ENST00000474751.2_3'UTR|NLRX1_ENST00000409991.1_Missense_Mutation_p.P127S|NLRX1_ENST00000409265.4_Missense_Mutation_p.P127S|NLRX1_ENST00000292199.2_Missense_Mutation_p.P127S|NLRX1_ENST00000525863.1_Missense_Mutation_p.P127S	NM_001282144.1	NP_001269073.1	Q86UT6	NLRX1_HUMAN	NLR family member X1	127	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)		ACTTCGCCCACCCGCGGAGCT	0.667																																					p.P127S		Atlas-SNP	.											.	NLRX1	128	.	0			c.C379T						PASS	.						43	44	44					11																	119044337		2200	4295	6495	SO:0001583	missense	79671	exon5			CGCCCACCCGCGG	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.379C>T	chr11.hg19:g.119044337C>T	ENSP00000387334:p.Pro127Ser	71.0	0.0	.		46.0	18.0	.	NM_024618	A8K6Q1|B3KPK2|B3KTA2|Q7RTR3|Q96D51|Q9H724	Missense_Mutation	SNP	ENST00000409109.1	hg19	CCDS8416.1	.	.	.	.	.	.	.	.	.	.	C	0.005	-2.139675	0.00335	.	.	ENSG00000160703	ENST00000454811;ENST00000449394;ENST00000422249;ENST00000409991;ENST00000292199;ENST00000409265;ENST00000409109;ENST00000525863	T;T;T;T;T;T;T;T	0.69561	1.73;1.73;1.17;-0.31;-0.31;-0.41;-0.31;-0.41	5.6	-7.76	0.01232	.	1.215480	0.05625	N	0.580711	T	0.32406	0.0828	N	0.03608	-0.345	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.13953	-1.0490	10	0.18710	T	0.47	.	3.4574	0.07521	0.0971:0.1552:0.1941:0.5535	.	127;127	Q86UT6-2;Q86UT6	.;NLRX1_HUMAN	S	127	ENSP00000400268:P127S;ENSP00000402801:P127S;ENSP00000402381:P127S;ENSP00000386851:P127S;ENSP00000292199:P127S;ENSP00000386858:P127S;ENSP00000387334:P127S;ENSP00000433442:P127S	ENSP00000292199:P127S	P	+	1	0	NLRX1	118549547	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.553000	0.06012	-1.611000	0.01581	-0.459000	0.05422	CCC	.	.	.	none		0.667	NLRX1-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335403.1	NM_170722		T	119044337	C	T	119044337	3	4	136	1	0	0	0	0	1	0	0	0	10492	507	18	2	393	2	NLRX1	11	119044337	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	794109	119044337	15962179	41	8334											
TRIM29	23650	hgsc.bcm.edu	37	chr11	119988941	119988941	+	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	gcaagctcacctttcagggaGaaggaggagctgccttggac	10	7	14	10	0	2	1	2	0	0	1	2	5	2	4	2	4	3	3	2	4	2	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr11:119988941G>A	ENST00000341846.5	-	7	2038	c.1617C>T	c.(1615-1617)ttC>ttT	p.F539F	TRIM29_ENST00000529044.1_Silent_p.F278F|TRIM29_ENST00000528870.1_Silent_p.F72F|TRIM29_ENST00000524816.3_Silent_p.F105F|TRIM29_ENST00000541857.1_Silent_p.F272F|TRIM29_ENST00000525887.1_5'UTR	NM_012101.3	NP_036233.2	Q14134	TRI29_HUMAN	tripartite motif containing 29	539					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)		CTTTCAGGGAGAAGGAGGAGC	0.592																																					p.F539F		Atlas-SNP	.											.	TRIM29	78	.	0			c.C1617T						PASS	.						100	85	90					11																	119988941		2199	4295	6494	SO:0001819	synonymous_variant	23650	exon7			CAGGGAGAAGGAG	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.1617C>T	chr11.hg19:g.119988941G>A		37.0	0.0	.		33.0	12.0	.	NM_012101	Q96AA9|Q9BZY7	Silent	SNP	ENST00000341846.5	hg19	CCDS8428.1	.	.	.	.	.	.	.	.	.	.	G	9.447	1.089611	0.20390	.	.	ENSG00000137699	ENST00000525327;ENST00000524956	.	.	.	5.04	5.04	0.67666	.	.	.	.	.	T	0.69187	0.3083	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68135	-0.5489	4	.	.	.	.	13.87	0.63612	0.0:0.0:1.0:0.0	.	.	.	.	F	132;77	.	.	L	-	1	0	TRIM29	119494151	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	3.287000	0.51732	2.343000	0.79666	0.407000	0.27541	CTC	.	.	.	none		0.592	TRIM29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277108.2	NM_012101		A	119988941	G	A	119988941	2	1	136	1	0	0	0	0	0	0	0	1	16515	933	33	2		2	TRIM29	11	119988941	Silent	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	944604	119988941	15017575	42	8335											
FKBP4	2288	hgsc.bcm.edu	37	chr12	2909052	2909052	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttgggaaggaaaagttccaAatcccaccaaatgctgagct	14	8	10	9	0	0	1	0	1	0	0	2	3	2	3	3	2	2	4	3	2	5	2	rs201311104		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr12:2909052A>G	ENST00000001008.4	+	6	895	c.708A>G	c.(706-708)caA>caG	p.Q236Q	RP4-816N1.7_ENST00000547042.1_RNA|RP4-816N1.6_ENST00000547834.1_RNA	NM_002014.3	NP_002005.1	Q02790	FKBP4_HUMAN	FK506 binding protein 4, 59kDa	236	PPIase FKBP-type 2. {ECO:0000255|PROSITE- ProRule:PRU00277}.				androgen receptor signaling pathway (GO:0030521)|chaperone-mediated protein folding (GO:0061077)|copper ion transport (GO:0006825)|embryo implantation (GO:0007566)|male sex differentiation (GO:0046661)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)|negative regulation of neuron projection development (GO:0010977)|prostate gland development (GO:0030850)|protein complex localization (GO:0031503)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|steroid hormone receptor complex assembly (GO:0006463)	axonal growth cone (GO:0044295)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|FK506 binding (GO:0005528)|GTP binding (GO:0005525)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(1)	14			OV - Ovarian serous cystadenocarcinoma(31;0.00105)			AAAAGTTCCAAATCCCACCAA	0.438																																					p.Q236Q		Atlas-SNP	.											.	FKBP4	29	.	0			c.A708G						PASS	.						86	89	88					12																	2909052		2203	4300	6503	SO:0001819	synonymous_variant	2288	exon6			GTTCCAAATCCCA	M88279	CCDS8512.1	12p13.33	2013-01-10	2002-08-29		ENSG00000004478	ENSG00000004478		"Tetratricopeptide (TTC) repeat domain containing"	3720	protein-coding gene	gene with protein product		600611	"FK506-binding protein 4 (59kD)"			1279700	Standard	NM_002014		Approved	FKBP59, FKBP52	uc001qkz.3	Q02790	OTTHUMG00000090429	ENST00000001008.4:c.708A>G	chr12.hg19:g.2909052A>G		39.0	0.0	.		33.0	19.0	.	NM_002014	D3DUQ1|Q9UCP1|Q9UCV7	Silent	SNP	ENST00000001008.4	hg19	CCDS8512.1																																																																																			.	A|0.999;G|0.001	0.001	weak		0.438	FKBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206861.1			G	2909052	A	G	2909052	2	3	136	1	0	0	0	0	0	0	0	1	5917	11	1	3		3	FKBP4	12	2909052	Silent	SNP	A	TCGA-BQ-7051-01A-12D-1961-08		2909052	130942843	43	8336											
DPPA3	359787	hgsc.bcm.edu	37	chr12	7867786	7867786	+	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	ccttctctttcaggggcctcTcaaatctcctccgagacgtt	6	13	7	15	2	4	1	2	0	3	1	8	2	5	1	4	2	0	1	4	2	1	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr12:7867786T>A	ENST00000345088.2	+	2	207	c.90T>A	c.(88-90)tcT>tcA	p.S30S		NM_199286.2	NP_954980.1	Q6W0C5	DPPA3_HUMAN	developmental pluripotency associated 3	30					chromatin modification (GO:0016568)|embryonic cleavage (GO:0040016)|negative regulation of DNA demethylation (GO:1901536)|protection of DNA demethylation of female pronucleus (GO:0044726)|regulation of genetic imprinting (GO:2000653)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|nucleus (GO:0005634)	methylated histone binding (GO:0035064)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(2)	8				Kidney(36;0.0887)		CAGGGGCCTCTCAAATCTCCT	0.468																																					p.S30S		Atlas-SNP	.											.	DPPA3	26	.	0			c.T90A						PASS	.						122	136	131					12																	7867786		2203	4300	6503	SO:0001819	synonymous_variant	359787	exon2			GGCCTCTCAAATC	AY317075	CCDS8582.1	12p13.31	2012-10-02			ENSG00000187569	ENSG00000187569			19199	protein-coding gene	gene with protein product		608408					Standard	NM_199286		Approved	Stella	uc001qtf.3	Q6W0C5	OTTHUMG00000168434	ENST00000345088.2:c.90T>A	chr12.hg19:g.7867786T>A		235.0	0.0	.		223.0	102.0	.	NM_199286	Q0P5U3|Q6JZS6	Silent	SNP	ENST00000345088.2	hg19	CCDS8582.1																																																																																			.	.	.	none		0.468	DPPA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399718.1	NM_199286		A	7867786	T	A	7867786	2	1	136	1	0	0	0	0	0	0	0	1	4737	1538	54	5		5	DPPA3	12	7867786	Silent	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	4958734	7867786	125984109	44	8337											
CNTN1	1272	hgsc.bcm.edu	37	chr12	41323760	41323760	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttccagtccttctattacaaAgagcgtgttcagcaaattca	12	13	6	10	1	3	1	2	0	1	1	5	1	5	1	2	0	3	2	2	0	4	6			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr12:41323760A>G	ENST00000551295.2	+	7	776	c.659A>G	c.(658-660)aAg>aGg	p.K220R	CNTN1_ENST00000360099.3_Missense_Mutation_p.K220R|CNTN1_ENST00000547849.1_Missense_Mutation_p.K220R|CNTN1_ENST00000547702.1_Missense_Mutation_p.K220R|CNTN1_ENST00000347616.1_Missense_Mutation_p.K220R|CNTN1_ENST00000348761.2_Missense_Mutation_p.K209R	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	220	Ig-like C2-type 2.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				TCTATTACAAAGAGCGTGTTC	0.383																																					p.K220R		Atlas-SNP	.											.	CNTN1	207	.	0			c.A659G						PASS	.						174	169	171					12																	41323760		2203	4300	6503	SO:0001583	missense	1272	exon7			TTACAAAGAGCGT	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.659A>G	chr12.hg19:g.41323760A>G	ENSP00000447006:p.Lys220Arg	219.0	0.0	.		210.0	85.0	.	NM_001256063	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Missense_Mutation	SNP	ENST00000551295.2	hg19	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	A	17.38	3.375898	0.61735	.	.	ENSG00000018236	ENST00000547702;ENST00000551295;ENST00000547849;ENST00000347616;ENST00000360099;ENST00000348761	T;T;T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0;-1.0;-1.0	5.39	5.39	0.77823	Immunoglobulin subtype (1);Immunoglobulin-like (1);	0.000000	0.85682	D	0.000000	T	0.78534	0.4298	L	0.53671	1.685	0.58432	D	0.99999	P;P;D	0.53151	0.61;0.948;0.958	B;P;P	0.53593	0.298;0.611;0.73	T	0.77059	-0.2728	10	0.33141	T	0.24	.	15.7149	0.77661	1.0:0.0:0.0:0.0	.	220;209;220	Q12860-3;Q12860-2;Q12860	.;.;CNTN1_HUMAN	R	220;220;220;220;220;209	ENSP00000448004:K220R;ENSP00000447006:K220R;ENSP00000448653:K220R;ENSP00000325660:K220R;ENSP00000353213:K220R;ENSP00000261160:K209R	ENSP00000325660:K220R	K	+	2	0	CNTN1	39610027	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.962000	0.93254	2.180000	0.69256	0.533000	0.62120	AAG	.	.	.	none		0.383	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		G	41323760	A	G	41323760	3	3	136	1	0	0	0	0	1	0	0	0	3642	72	3	3	681	3	CNTN1	12	41323760	Missense_Mutation	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	33455974	41323760	92528135	45	8338											
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43823478	43823478	+	Frame_Shift_Del	DEL	A	A	-																															ttatgagaacagttggtaatAaagcggtctcaagtttagaa																										TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr12:43823478delA	ENST00000389420.3	-	24	3430	c.3431delT	c.(3430-3432)ttafs	p.L1145fs	ADAMTS20_ENST00000395541.2_Intron|ADAMTS20_ENST00000553158.1_Frame_Shift_Del_p.L1145fs	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1145					extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		AGTTGGTAATAAAGCGGTCTC	0.343																																					p.L1144fs		Atlas-INDEL	.											.	ADAMTS20	635	.	0			c.3432delA						PASS	.						60	56	57					12																	43823478		2203	4298	6501	SO:0001589	frameshift_variant	80070	exon24			.	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.3431delT	chr12.hg19:g.43823478delA	ENSP00000374071:p.Leu1145fs	19.0	0.0	0		27.0	12.0	0.444444	NM_025003	A6NNC9|J3QT00	Frame_Shift_Del	DEL	ENST00000389420.3	hg19	CCDS31778.2																																																																																			.	.	.	none		0.343	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		-	43823478	A	-	43823478	7	5	136	1	0	1	0	1	0	0	0	0	266	372	13	0	2364	0	ADAMTS20	12	43823478	Frame_Shift_Del	DEL	A	TCGA-BQ-7051-01A-12D-1961-08	2499718	43823478	90028417	46	8339											
CCNT1	904	hgsc.bcm.edu	37	chr12	49087909	49087909	+	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	ttgaaccatcctgtggtaagGaatgatcaactcctgtaagt	12	12	9	8	0	1	2	1	2	0	0	3	3	3	3	3	2	2	2	3	2	5	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr12:49087909G>T	ENST00000261900.3	-	9	1310	c.1088C>A	c.(1087-1089)tCc>tAc	p.S363Y		NM_001240.3	NP_001231.2	O60563	CCNT1_HUMAN	cyclin T1	363					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|snRNA binding (GO:0017069)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|skin(2)	27						CTGTGGTAAGGAATGATCAAC	0.458																																					p.S363Y		Atlas-SNP	.											.	CCNT1	55	.	0			c.C1088A						PASS	.						177	170	172					12																	49087909		2203	4300	6503	SO:0001583	missense	904	exon9			GGTAAGGAATGAT	AF048730	CCDS8766.1, CCDS61109.1	12q13.11	2010-11-15			ENSG00000129315	ENSG00000129315			1599	protein-coding gene	gene with protein product		143055	"human immunodeficiency virus type 1 (HIV-1) expression (elevated) 1"	HIVE1		9491887, 9499409	Standard	NM_001240		Approved	CCNT, CYCT1	uc001rsd.4	O60563	OTTHUMG00000170393	ENST00000261900.3:c.1088C>A	chr12.hg19:g.49087909G>T	ENSP00000261900:p.Ser363Tyr	154.0	0.0	.		176.0	78.0	.	NM_001240	A9XU13|E7EX76|O60581	Missense_Mutation	SNP	ENST00000261900.3	hg19	CCDS8766.1	.	.	.	.	.	.	.	.	.	.	G	14.46	2.543525	0.45280	.	.	ENSG00000129315	ENST00000261900	T	0.52057	0.68	5.49	4.54	0.55810	.	0.669254	0.16281	N	0.221349	T	0.44623	0.1302	N	0.22421	0.69	0.37399	D	0.912769	D	0.63880	0.993	P	0.50440	0.641	T	0.52815	-0.8525	10	0.56958	D	0.05	-7.9232	14.673	0.68958	0.0:0.1463:0.8536:0.0	.	363	O60563	CCNT1_HUMAN	Y	363	ENSP00000261900:S363Y	ENSP00000261900:S363Y	S	-	2	0	CCNT1	47374176	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	3.968000	0.56809	2.587000	0.87381	0.491000	0.48974	TCC	.	.	.	none		0.458	CCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408853.1	NM_001240		T	49087909	G	T	49087909	3	4	136	1	0	0	0	0	1	0	0	0	2936	1174	41	4	1096	4	CCNT1	12	49087909	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	5264431	49087909	84763986	47	8340											
FREM2	341640	hgsc.bcm.edu	37	chr13	39450406	39450406	+	Missense_Mutation	SNP	T	T	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	tacgtgactactcagggaccTatactgtgaagctggtgcca	10	10	11	10	1	1	2	1	2	0	0	1	3	1	3	2	2	5	1	2	2	5	4			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr13:39450406T>G	ENST00000280481.7	+	20	8647	c.8431T>G	c.(8431-8433)Tat>Gat	p.Y2811D		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2811					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)		CTCAGGGACCTATACTGTGAA	0.448																																					p.Y2811D		Atlas-SNP	.											.	FREM2	385	.	0			c.T8431G						PASS	.						124	112	116					13																	39450406		2203	4300	6503	SO:0001583	missense	341640	exon20			GGGACCTATACTG	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.8431T>G	chr13.hg19:g.39450406T>G	ENSP00000280481:p.Tyr2811Asp	97.0	0.0	.		82.0	42.0	.	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	hg19	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	T	18.86	3.712772	0.68730	.	.	ENSG00000150893	ENST00000280481	T	0.47528	0.84	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.73853	0.3640	M	0.89095	3.005	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.79769	-0.1664	10	0.87932	D	0	.	15.9477	0.79806	0.0:0.0:0.0:1.0	.	2811	Q5SZK8	FREM2_HUMAN	D	2811	ENSP00000280481:Y2811D	ENSP00000280481:Y2811D	Y	+	1	0	FREM2	38348406	1.000000	0.71417	0.984000	0.44739	0.366000	0.29705	7.967000	0.87967	2.179000	0.69175	0.460000	0.39030	TAT	.	.	.	none		0.448	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		G	39450406	T	G	39450406	3	3	136	1	0	0	0	0	1	0	0	0	6052	1522	53	5	8509	5	FREM2	13	39450406	Missense_Mutation	SNP	T	TCGA-BQ-7051-01A-12D-1961-08		39450406	75719472	48	8341											
KBTBD6	89890	hgsc.bcm.edu	37	chr13	41705610	41705612	+	In_Frame_Del	DEL	CAC	CAC	-																															ctggggtgtccaaagaagatCaccatctccttggcacacat																										TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	CAC	CAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr13:41705610_41705612delCAC	ENST00000379485.1	-	1	1270_1272	c.1036_1038delGTG	c.(1036-1038)gtgdel	p.V346del	KBTBD6_ENST00000499385.2_In_Frame_Del_p.V280del	NM_152903.4	NP_690867.3	Q86V97	KBTB6_HUMAN	kelch repeat and BTB (POZ) domain containing 6	346										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)		CAAAGAAGATCACCATCTCCTTG	0.527																																					p.346_347del		Atlas-INDEL	.											.	KBTBD6	83	.	0			c.1037_1039del						PASS	.																																			SO:0001651	inframe_deletion	89890	exon1			.	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.1036_1038delGTG	chr13.hg19:g.41705610_41705612delCAC	ENSP00000368799:p.Val346del	152.0	0.0	0		94.0	29.0	0.308511	NM_152903	Q5T6Y8|Q8N8L0|Q8NDM5|Q96MP6	In_Frame_Del	DEL	ENST00000379485.1	hg19	CCDS9376.1																																																																																			.	.	.	none		0.527	KBTBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044657.1	NM_152903		-	41705612	CAC	-	41705610	7	5	136	1	0	1	0	1	0	0	0	0	8004	813	29	0	990	0	KBTBD6	13	41705610	In_Frame_Del	DEL	CAC	TCGA-BQ-7051-01A-12D-1961-08	2255204	41705610	73464268	49	8342											
TEP1	7011	hgsc.bcm.edu	37	chr14	20845481	20845481	+	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	ctgggaagtggccagtcctaGcacaggcttctggaatctgg	8	9	14	10	0	2	0	0	0	2	0	3	2	3	2	2	5	1	2	2	5	3	2	rs375172392		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr14:20845481G>A	ENST00000262715.5	-	41	6086	c.6046C>T	c.(6046-6048)Cta>Tta	p.L2016L	TEP1_ENST00000556935.1_Silent_p.L1908L|TEP1_ENST00000545983.1_Silent_p.L354L	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	2016					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)		GCCAGTCCTAGCACAGGCTTC	0.507																																					p.L2016L		Atlas-SNP	.											.	TEP1	224	.	0			c.C6046T						PASS	.						36	36	36					14																	20845481		2203	4300	6503	SO:0001819	synonymous_variant	7011	exon41			GTCCTAGCACAGG		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.6046C>T	chr14.hg19:g.20845481G>A		41.0	0.0	.		49.0	22.0	.	NM_007110	A0AUV9	Silent	SNP	ENST00000262715.5	hg19	CCDS9548.1																																																																																			.	.	.	alt		0.507	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		A	20845481	G	A	20845481	2	1	136	1	0	0	0	0	0	0	0	1	15771	962	34	2		2	TEP1	14	20845481	Silent	SNP	G	TCGA-BQ-7051-01A-12D-1961-08		20845481	86504059	50	8343											
PNP	4860	hgsc.bcm.edu	37	chr14	20944608	20944608	+	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	ttcgagtctttggcttctcaCtcatcactaacaaggtcatc	9	14	6	12	1	5	0	4	0	2	0	8	1	5	0	0	2	1	1	0	2	2	4			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr14:20944608C>T	ENST00000361505.5	+	6	864	c.718C>T	c.(718-720)Ctc>Ttc	p.L240F	RP11-203M5.8_ENST00000554678.1_lincRNA	NM_000270.3	NP_000261.2	P01298	PAHO_HUMAN	purine nucleoside phosphorylase	0					digestion (GO:0007586)|protein secretion (GO:0009306)	extracellular region (GO:0005576)	hormone activity (GO:0005179)|receptor binding (GO:0005102)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|stomach(2)	10						TGGCTTCTCACTCATCACTAA	0.458																																					p.L240F		Atlas-SNP	.											.	PNP	21	.	0			c.C718T						PASS	.						150	128	135					14																	20944608		2203	4300	6503	SO:0001583	missense	4860	exon6			TTCTCACTCATCA		CCDS9552.1	14q11.2	2014-09-17	2009-12-02	2009-12-02	ENSG00000198805	ENSG00000198805	2.4.2.1		7892	protein-coding gene	gene with protein product		164050	"nucleoside phosphorylase"	NP		6087295	Standard	NM_000270		Approved	PUNP	uc001vxo.4	P00491	OTTHUMG00000029546	ENST00000361505.5:c.718C>T	chr14.hg19:g.20944608C>T	ENSP00000354532:p.Leu240Phe	94.0	0.0	.		93.0	43.0	.	NM_000270		Missense_Mutation	SNP	ENST00000361505.5	hg19	CCDS9552.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.542982	0.86022	.	.	ENSG00000198805	ENST00000361505	D	0.88046	-2.33	4.88	4.88	0.63580	Nucleoside phosphorylase domain (1);	0.064044	0.64402	D	0.000003	D	0.93762	0.8006	M	0.83603	2.65	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94473	0.7686	10	0.72032	D	0.01	-21.5214	16.9641	0.86281	0.0:1.0:0.0:0.0	.	240	P00491	PNPH_HUMAN	F	240	ENSP00000354532:L240F	ENSP00000354532:L240F	L	+	1	0	PNP	20014448	0.999000	0.42202	0.994000	0.49952	0.951000	0.60555	4.327000	0.59247	2.528000	0.85240	0.655000	0.94253	CTC	.	.	.	none		0.458	PNP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073646.2	NM_000270.2		T	20944608	C	T	20944608	3	4	136	1	0	0	0	0	1	0	0	0	12170	565	20	2	740	2	PNP	14	20944608	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	99127	20944608	86404932	51	8344											
RNF31	55072	hgsc.bcm.edu	37	chr14	24626550	24626550	+	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	aggacttccagaactggaaaCgcatgaacgacccagaatac	16	5	9	11	2	0	3	0	1	0	2	1	6	1	5	2	2	4	1	2	2	5	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr14:24626550C>T	ENST00000324103.6	+	15	2865	c.2545C>T	c.(2545-2547)Cgc>Tgc	p.R849C	RP11-468E2.4_ENST00000558468.1_Missense_Mutation_p.R324C|RNF31_ENST00000559275.1_Missense_Mutation_p.R698C|RNF31_ENST00000382687.3_Missense_Mutation_p.R698C|RNA5SP383_ENST00000362934.1_RNA	NM_017999.4	NP_060469.4	Q96EP0	RNF31_HUMAN	ring finger protein 31	849					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)		GAACTGGAAACGCATGAACGA	0.567																																					p.R849C		Atlas-SNP	.											.	RNF31	95	.	0			c.C2545T						PASS	.						75	81	79					14																	24626550		1988	4157	6145	SO:0001583	missense	55072	exon15			TGGAAACGCATGA	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.2545C>T	chr14.hg19:g.24626550C>T	ENSP00000315112:p.Arg849Cys	37.0	0.0	.		28.0	16.0	.	NM_017999	A0A962|Q86VI2|Q8TEI0|Q96GB4|Q96NF1|Q9H5F1|Q9NWD2	Missense_Mutation	SNP	ENST00000324103.6	hg19	CCDS41931.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.997602	0.54147	.	.	ENSG00000092098	ENST00000382682;ENST00000324103;ENST00000382687	T;T	0.77877	-1.13;-1.13	5.34	4.44	0.53790	.	0.000000	0.85682	D	0.000000	D	0.85296	0.5664	L	0.61218	1.895	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;0.951;0.996;0.998	D	0.86555	0.1837	10	0.87932	D	0	-19.6302	12.2841	0.54783	0.308:0.692:0.0:0.0	.	849;608;849;698	A0A962;B3KV71;Q96EP0;Q96EP0-3	.;.;RNF31_HUMAN;.	C	282;849;698	ENSP00000315112:R849C;ENSP00000372134:R698C	ENSP00000315112:R849C	R	+	1	0	RNF31	23696390	1.000000	0.71417	1.000000	0.80357	0.592000	0.36648	0.675000	0.25232	1.467000	0.48044	-0.203000	0.12734	CGC	.	.	.	none		0.567	RNF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071921.3	NM_017999		T	24626550	C	T	24626550	3	4	136	1	0	0	0	0	1	0	0	0	13500	536	19	1	2603	1	RNF31	14	24626550	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	3681942	24626550	82722990	52	8345											
KIAA0391	9692	hgsc.bcm.edu	37	chr14	35592664	35592664	+	Missense_Mutation	SNP	T	T	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	gccagatatctcaggaaagaTgagggcagtaataagcaagt	16	7	12	6	0	1	3	1	1	1	2	2	4	1	4	1	2	1	3	1	2	5	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr14:35592664T>G	ENST00000557565.1	+	2	594	c.213T>G	c.(211-213)gaT>gaG	p.D71E	KIAA0391_ENST00000603544.1_Missense_Mutation_p.D71E|KIAA0391_ENST00000250377.7_De_novo_Start_OutOfFrame|KIAA0391_ENST00000321130.10_Missense_Mutation_p.D71E|KIAA0391_ENST00000605870.1_Intron|PPP2R3C_ENST00000261475.5_5'Flank|KIAA0391_ENST00000534898.4_Missense_Mutation_p.D71E|KIAA0391_ENST00000603588.1_Intron|PPP2R3C_ENST00000555644.1_5'Flank|KIAA0391_ENST00000604948.1_Intron	NM_001282234.1	NP_001269163.1	O15091	MRRP3_HUMAN	KIAA0391	71					tRNA processing (GO:0008033)	mitochondrion (GO:0005739)				central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	14	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)		TCAGGAAAGATGAGGGCAGTA	0.408																																					p.D71E		Atlas-SNP	.											.	KIAA0391	35	.	0			c.T213G						PASS	.						65	62	63					14																	35592664		2203	4300	6503	SO:0001583	missense	9692	exon2			GAAAGATGAGGGC	AB002389	CCDS32063.1, CCDS58312.1, CCDS58313.1, CCDS58314.1	14q13.2	2013-06-18			ENSG00000100890	ENSG00000100890			19958	protein-coding gene	gene with protein product	"mitochondrial RNase P subunit 3", "proteinaceous RNase P"	609947				9205841, 18984158	Standard	NM_001256678		Approved	MRPP3, PRORP	uc001wsy.2	O15091		ENST00000557565.1:c.213T>G	chr14.hg19:g.35592664T>G	ENSP00000454657:p.Asp71Glu	61.0	0.0	.		52.0	25.0	.	NM_014672	B4DXD9|B4E0S8|B4E211|C4AM93|D3DS99|D3DSA1|Q86SZ4|Q86YB5|Q8N5L5	Missense_Mutation	SNP	ENST00000557565.1	hg19	CCDS32063.1	.	.	.	.	.	.	.	.	.	.	T	2.705	-0.270055	0.05716	.	.	ENSG00000100890	ENST00000321130;ENST00000534898;ENST00000556121	T;T	0.40756	1.03;1.02	5.25	-5.42	0.02640	.	0.854894	0.10131	N	0.712121	T	0.21509	0.0518	N	0.22421	0.69	0.09310	N	0.999997	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18116	-1.0347	10	0.25751	T	0.34	-0.2169	6.1442	0.20276	0.2948:0.0:0.2418:0.4635	.	71;71	O15091-2;O15091	.;MRRP3_HUMAN	E	71	ENSP00000324697:D71E;ENSP00000440915:D71E	ENSP00000324697:D71E	D	+	3	2	KIAA0391	34662415	0.000000	0.05858	0.000000	0.03702	0.115000	0.19883	-0.292000	0.08332	-1.164000	0.02790	-1.783000	0.00646	GAT	.	.	.	none		0.408	KIAA0391-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000411280.1	NM_014672		G	35592664	T	G	35592664	3	3	136	1	0	0	0	0	1	0	0	0	8179	1461	51	5	215	5	KIAA0391	14	35592664	Missense_Mutation	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	10966114	35592664	71756876	53	8346											
VTI1B	10490	hgsc.bcm.edu	37	chr14	68118141	68118141	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtagtaaaccaggcctccCaggatggcgagctccagtaa	11	8	11	11	1	0	0	0	0	0	0	2	2	2	1	4	3	2	4	4	3	4	4			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr14:68118141C>T	ENST00000554659.1	-	6	1001	c.660G>A	c.(658-660)ctG>ctA	p.L220L	ARG2_ENST00000261783.3_3'UTR	NM_006370.2	NP_006361.1	Q9UEU0	VTI1B_HUMAN	vesicle transport through interaction with t-SNAREs 1B	220					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)		CCAGGCCTCCCAGGATGGCGA	0.453																																					p.L220L		Atlas-SNP	.											.	VTI1B	15	.	0			c.G660A						PASS	.						69	71	70					14																	68118141		2203	4300	6503	SO:0001819	synonymous_variant	10490	exon6			GCCTCCCAGGATG	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.660G>A	chr14.hg19:g.68118141C>T		98.0	0.0	.		89.0	48.0	.	NM_006370	O43547|Q96J28	Silent	SNP	ENST00000554659.1	hg19	CCDS9786.1	.	.	.	.	.	.	.	.	.	.	C	19.30	3.801303	0.70567	.	.	ENSG00000100568	ENST00000554636	.	.	.	6.17	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.6819	0.28518	0.1315:0.7266:0.0:0.1419	.	.	.	.	X	98	.	.	W	-	2	0	VTI1B	67187894	0.123000	0.22298	1.000000	0.80357	0.996000	0.88848	-0.529000	0.06186	1.560000	0.49568	0.655000	0.94253	TGG	.	.	.	none		0.453	VTI1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412558.2			T	68118141	C	T	68118141	2	4	136	1	0	0	0	0	0	0	0	1	17248	581	21	2		2	VTI1B	14	68118141	Silent	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	32525477	68118141	39231399	54	8347											
COX5A	9377	hgsc.bcm.edu	37	chr15	75221461	75221461	+	Frame_Shift_Del	DEL	A	A	-																															tttatgttccaattacctttAcgcaattcccaggcatctat																										TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr15:75221461delA	ENST00000322347.6	-	2	366	c.213delT	c.(211-213)cgtfs	p.R71fs	COX5A_ENST00000568783.1_Frame_Shift_Del_p.R71fs|COX5A_ENST00000567270.1_Intron|COX5A_ENST00000568517.1_5'UTR|COX5A_ENST00000562233.1_Frame_Shift_Del_p.R71fs|COX5A_ENST00000564811.1_Frame_Shift_Del_p.R71fs	NM_004255.3	NP_004246.2	P20674	COX5A_HUMAN	cytochrome c oxidase subunit Va	71					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)	cytochrome-c oxidase activity (GO:0004129)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|pancreas(1)	3						AATTACCTTTACGCAATTCCC	0.413																																					p.K72fs		Atlas-INDEL	.											.	COX5A	9	.	0			c.214delA						PASS	.						140	129	133					15																	75221461		2197	4295	6492	SO:0001589	frameshift_variant	9377	exon2			.	M22760	CCDS10273.1	15q25	2011-07-04			ENSG00000178741	ENSG00000178741	1.9.3.1	"Mitochondrial respiratory chain complex / Complex IV"	2267	protein-coding gene	gene with protein product		603773				10072584, 2853101	Standard	NM_004255		Approved		uc002azi.4	P20674	OTTHUMG00000142825	ENST00000322347.6:c.213delT	chr15.hg19:g.75221461delA	ENSP00000317780:p.Arg71fs	174.0	0.0	0		108.0	34.0	0.314815	NM_004255	P30045|Q8TB65	Frame_Shift_Del	DEL	ENST00000322347.6	hg19	CCDS10273.1																																																																																			.	.	.	none		0.413	COX5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286417.1	NM_004255		-	75221461	A	-	75221461	7	5	136	1	0	1	0	1	0	0	0	0	3774	378	14	0	251	0	COX5A	15	75221461	Frame_Shift_Del	DEL	A	TCGA-BQ-7051-01A-12D-1961-08		75221461	27309931	55	8348											
SIN3A	25942	hgsc.bcm.edu	37	chr15	75664533	75664533	+	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	aatctctgatgtagacgcttGcttacacgctcatgggactg	9	12	10	10	2	2	2	1	1	1	1	3	3	2	3	0	1	2	4	0	1	3	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr15:75664533G>A	ENST00000394947.3	-	21	3923	c.3609C>T	c.(3607-3609)agC>agT	p.S1203S	RP11-817O13.8_ENST00000563278.1_lincRNA|SIN3A_ENST00000394949.4_Silent_p.S1203S|SIN3A_ENST00000360439.4_Silent_p.S1203S	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						GTAGACGCTTGCTTACACGCT	0.433																																					p.S1203S		Atlas-SNP	.											.	SIN3A	152	.	0			c.C3609T						PASS	.						109	105	106					15																	75664533		2197	4294	6491	SO:0001819	synonymous_variant	25942	exon21			ACGCTTGCTTACA	AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"SIN3 homolog A, transcription regulator (yeast)", "SIN3 transcription regulator homolog A (yeast)"			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.3609C>T	chr15.hg19:g.75664533G>A		151.0	0.0	.		135.0	47.0	.	NM_001145358		Silent	SNP	ENST00000394947.3	hg19	CCDS10279.1																																																																																			.	.	.	none		0.433	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477		A	75664533	G	A	75664533	2	1	136	1	0	0	0	0	0	0	0	1	14338	1310	46	2		2	SIN3A	15	75664533	Silent	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	443072	75664533	26866859	56	8349											
C15orf42	90381	hgsc.bcm.edu	37	chr15	90138745	90138745	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catccagatggcagtccggaTgtggctggggagaaaggaat	11	7	16	7	1	0	2	0	0	0	2	2	5	2	4	2	6	0	2	2	6	2	0			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr15:90138745T>C	ENST00000268138.7	+	7	1908	c.1803T>C	c.(1801-1803)gaT>gaC	p.D601D	TICRR_ENST00000560985.1_Silent_p.D600D			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	601					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)										GCAGTCCGGATGTGGCTGGGG	0.443																																					p.D601D		Atlas-SNP	.											.	.	.	.	0			c.T1803C						PASS	.						112	107	108					15																	90138745		1888	4113	6001	SO:0001819	synonymous_variant	90381	exon7			TCCGGATGTGGCT	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.1803T>C	chr15.hg19:g.90138745T>C		119.0	0.0	.		88.0	40.0	.	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Silent	SNP	ENST00000268138.7	hg19	CCDS10352.2																																																																																			.	.	.	none		0.443	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259		C	90138745	T	C	90138745	2	2	136	1	0	0	0	0	0	0	0	1	1798	1461	51	3		3	C15orf42	15	90138745	Silent	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	14474212	90138745	12392647	57	8350											
SLC46A1	113235	hgsc.bcm.edu	37	chr17	26731859	26731859	+	Frame_Shift_Del	DEL	C	C	-																															ttcataaagggttaagatgtCctgggccccaaagtgcacag																										TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr17:26731859delC	ENST00000440501.1	-	2	951	c.856delG	c.(856-858)gacfs	p.D286fs	SLC46A1_ENST00000321666.5_Frame_Shift_Del_p.D286fs|SLC46A1_ENST00000584729.1_5'UTR|CTD-2350C19.2_ENST00000580714.1_RNA|CTD-2350C19.1_ENST00000583956.1_RNA	NM_080669.4	NP_542400.2	Q96NT5	PCFT_HUMAN	solute carrier family 46 (folate transporter), member 1	286					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)	GTTAAGATGTCCTGGGCCCCA	0.542																																					p.D286fs		Atlas-INDEL	.											.	SLC46A1	17	.	0			c.857delA						PASS	.						109	118	115					17																	26731859		2022	4180	6202	SO:0001589	frameshift_variant	113235	exon2			.	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.856delG	chr17.hg19:g.26731859delC	ENSP00000395653:p.Asp286fs	88.0	0.0	0		112.0	70.0	0.625	NM_001242366	Q1HE20|Q86T92|Q8TEG3|Q96FL0	Frame_Shift_Del	DEL	ENST00000440501.1	hg19																																																																																				.	.	.	none		0.542	SLC46A1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_080669		-	26731859	C	-	26731859	7	5	136	1	0	1	0	1	0	0	0	0	14657	855	30	0	540	0	SLC46A1	17	26731859	Frame_Shift_Del	DEL	C	TCGA-BQ-7051-01A-12D-1961-08		26731859	54463351	58	8351											
SPAG5	10615	hgsc.bcm.edu	37	chr17	26911390	26911390	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctctgggtaagctggcagAgtaactcatccttcatagcc	9	11	10	11	0	3	1	2	0	1	1	4	1	4	1	2	2	4	5	2	2	3	4			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr17:26911390A>G	ENST00000321765.5	-	12	2602	c.2270T>C	c.(2269-2271)cTc>cCc	p.L757P		NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	757	Gln-rich.|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)					AAGCTGGCAGAGTAACTCATC	0.522																																					p.L757P		Atlas-SNP	.											.	SPAG5	92	.	0			c.T2270C						PASS	.						218	200	206					17																	26911390		2203	4300	6503	SO:0001583	missense	10615	exon12			TGGCAGAGTAACT	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.2270T>C	chr17.hg19:g.26911390A>G	ENSP00000323300:p.Leu757Pro	291.0	0.0	.		368.0	253.0	.	NM_006461	O95213|Q9BWE8|Q9NT17|Q9UFE6	Missense_Mutation	SNP	ENST00000321765.5	hg19	CCDS32594.1	.	.	.	.	.	.	.	.	.	.	A	16.00	2.998487	0.54147	.	.	ENSG00000076382	ENST00000321765;ENST00000536674	.	.	.	6.02	6.02	0.97574	.	0.363685	0.23744	N	0.044981	T	0.64394	0.2594	L	0.34521	1.04	0.48901	D	0.999721	D	0.76494	0.999	D	0.66497	0.944	T	0.65030	-0.6267	9	0.49607	T	0.09	-0.4993	12.9338	0.58303	1.0:0.0:0.0:0.0	.	757	Q96R06	SPAG5_HUMAN	P	757;254	.	ENSP00000323300:L757P	L	-	2	0	SPAG5	23935517	0.987000	0.35691	1.000000	0.80357	0.573000	0.36030	4.247000	0.58750	2.304000	0.77564	0.528000	0.53228	CTC	.	.	.	none		0.522	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461		G	26911390	A	G	26911390	3	3	136	1	0	0	0	0	1	0	0	0	14994	304	11	3	1363	3	SPAG5	17	26911390	Missense_Mutation	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	179531	26911390	54283820	59	8352											
KRT27	342574	hgsc.bcm.edu	37	chr17	38938378	38938378	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacggcaagaaccaggtccaAatttctcataccaccccttg	12	8	6	15	1	1	1	1	0	1	1	3	1	2	1	5	2	2	1	5	2	4	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr17:38938378A>G	ENST00000301656.3	-	1	408	c.368T>C	c.(367-369)tTt>tCt	p.F123S		NM_181537.3	NP_853515.2			keratin 27											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				ACCAGGTCCAAATTTCTCATA	0.498																																					p.F123S		Atlas-SNP	.											.	KRT27	41	.	0			c.T368C						PASS	.						154	135	141					17																	38938378		2203	4300	6503	SO:0001583	missense	342574	exon1			GGTCCAAATTTCT	AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"-", "Intermediate filaments type I, keratins (acidic)"	30841	protein-coding gene	gene with protein product			"keratin 25C"	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.368T>C	chr17.hg19:g.38938378A>G	ENSP00000301656:p.Phe123Ser	129.0	0.0	.		190.0	10.0	.	NM_181537		Missense_Mutation	SNP	ENST00000301656.3	hg19	CCDS11375.1	.	.	.	.	.	.	.	.	.	.	A	6.807	0.517981	0.13005	.	.	ENSG00000171446	ENST00000301656	D	0.87729	-2.29	5.66	1.89	0.25635	Filament (1);	0.279078	0.31290	N	0.007902	T	0.74030	0.3663	N	0.12182	0.205	0.30019	N	0.814529	B	0.13145	0.007	B	0.15870	0.014	T	0.67496	-0.5656	10	0.49607	T	0.09	.	10.0469	0.42192	0.5272:0.0:0.0:0.4728	.	123	Q7Z3Y8	K1C27_HUMAN	S	123	ENSP00000301656:F123S	ENSP00000301656:F123S	F	-	2	0	KRT27	36191904	0.001000	0.12720	0.987000	0.45799	0.444000	0.32077	0.662000	0.25038	0.449000	0.26747	-0.344000	0.07964	TTT	.	.	.	none		0.498	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537		G	38938378	A	G	38938378	3	3	136	1	0	0	0	0	1	0	0	0	8471	14	1	3	1043	3	KRT27	17	38938378	Missense_Mutation	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	12026988	38938378	42256832	60	8353											
HEXDC	284004	hgsc.bcm.edu	37	chr17	80382347	80382347	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtttccctacgagggcccTctgaggctgctgagggccaa	7	9	13	12	1	1	2	0	2	1	0	2	3	2	2	3	3	2	3	3	3	2	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr17:80382347T>C	ENST00000327949.9	+	2	173	c.162T>C	c.(160-162)ccT>ccC	p.P54P	HEXDC_ENST00000577944.1_Silent_p.P54P|HEXDC_ENST00000337014.6_Silent_p.P54P			Q8WVB3	HEXDC_HUMAN	hexosaminidase (glycosyl hydrolase family 20, catalytic domain) containing	54					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)			ACGAGGGCCCTCTGAGGCTGC	0.612																																					p.P54P		Atlas-SNP	.											.	HEXDC	43	.	0			c.T162C						PASS	.						97	92	94					17																	80382347		1940	4131	6071	SO:0001819	synonymous_variant	284004	exon3			GGGCCCTCTGAGG	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.162T>C	chr17.hg19:g.80382347T>C		115.0	0.0	.		139.0	38.0	.	NM_173620	B7UUP6|Q8IYN4|Q8TE81	Silent	SNP	ENST00000327949.9	hg19																																																																																				.	.	.	none		0.612	HEXDC-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000443513.1	NM_173620		C	80382347	T	C	80382347	2	2	136	1	0	0	0	0	0	0	0	1	7082	1538	54	3		3	HEXDC	17	80382347	Silent	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	41443969	80382347	812863	61	8354											
C18orf55	29090	hgsc.bcm.edu	37	chr18	71816322	71816322	+	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	aggagtcagagagggggaacCgccgtcccaacatcacaaaa	15	3	12	11	2	2	1	2	0	0	1	3	4	3	3	3	3	2	0	3	3	4	0			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr18:71816322C>G	ENST00000169551.6	+	1	577	c.279C>G	c.(277-279)acC>acG	p.T93T	FBXO15_ENST00000269500.5_5'Flank|TIMM21_ENST00000580087.1_Silent_p.T93T|FBXO15_ENST00000419743.2_5'Flank	NM_014177.2	NP_054896.2	Q9BVV7	TIM21_HUMAN	translocase of inner mitochondrial membrane 21 homolog (yeast)	93					cellular protein metabolic process (GO:0044267)|mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex IV assembly (GO:0033617)|protein import into mitochondrial matrix (GO:0030150)|protein targeting to mitochondrion (GO:0006626)	integral component of membrane (GO:0016021)|mitochondrial inner membrane presequence translocase complex (GO:0005744)											GAGGGGGAACCGCCGTCCCAA	0.498																																					p.T93T		Atlas-SNP	.											.	.	.	.	0			c.C279G						PASS	.						57	58	58					18																	71816322		2203	4300	6503	SO:0001819	synonymous_variant	29090	exon1			GGGAACCGCCGTC	BC000892	CCDS12003.1	18q22.3	2011-11-25	2011-11-25	2011-11-25	ENSG00000075336	ENSG00000075336			25010	protein-coding gene	gene with protein product		615180	"chromosome 18 open reading frame 55"	C18orf55		11042152	Standard	NM_014177		Approved	HSPC154, TIM21	uc010dqr.1	Q9BVV7	OTTHUMG00000132844	ENST00000169551.6:c.279C>G	chr18.hg19:g.71816322C>G		72.0	0.0	.		67.0	32.0	.	NM_014177	Q9P010	Silent	SNP	ENST00000169551.6	hg19	CCDS12003.1																																																																																			.	.	.	none		0.498	TIMM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256318.1	NM_014177		G	71816322	C	G	71816322	2	3	136	1	0	0	0	0	0	0	0	1	1907	639	23	4		4	C18orf55	18	71816322	Silent	SNP	C	TCGA-BQ-7051-01A-12D-1961-08		71816322	6260926	62	8355											
STXBP2	6813	hgsc.bcm.edu	37	chr19	7712265	7712265	+	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	gcttcggtcactggcacaagAacaaggctggcatagaagcc	12	6	12	11	1	1	2	1	0	0	2	2	2	1	2	1	4	2	4	1	4	5	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr19:7712265A>T	ENST00000221283.5	+	18	1595	c.1564A>T	c.(1564-1566)Aac>Tac	p.N522Y	STXBP2_ENST00000441779.2_Missense_Mutation_p.N533Y|STXBP2_ENST00000414284.2_Missense_Mutation_p.N519Y|STXBP2_ENST00000602355.1_Missense_Mutation_p.N57Y	NM_006949.2	NP_008880.2	Q15833	STXB2_HUMAN	syntaxin binding protein 2	522					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						CTGGCACAAGAACAAGGCTGG	0.662																																					p.N533Y		Atlas-SNP	.											.	STXBP2	63	.	0			c.A1597T						PASS	.						24	33	30					19																	7712265		2192	4284	6476	SO:0001583	missense	6813	exon18			CACAAGAACAAGG	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.1564A>T	chr19.hg19:g.7712265A>T	ENSP00000221283:p.Asn522Tyr	57.0	0.0	.		52.0	21.0	.	NM_001272034	B4E175|E7EQD5|Q9BU65	Missense_Mutation	SNP	ENST00000221283.5	hg19	CCDS12181.1	.	.	.	.	.	.	.	.	.	.	A	19.54	3.846916	0.71603	.	.	ENSG00000076944	ENST00000221283;ENST00000414284;ENST00000441779;ENST00000543902	T;T;T	0.80480	-1.38;-1.38;-1.38	5.26	4.18	0.49190	.	0.112112	0.64402	D	0.000017	D	0.82761	0.5107	L	0.55481	1.735	0.44611	D	0.997588	P;P;P;P	0.48407	0.91;0.91;0.889;0.91	P;P;P;P	0.55161	0.689;0.77;0.562;0.689	D	0.84034	0.0361	10	0.72032	D	0.01	-1.3267	10.063	0.42286	0.8312:0.1688:0.0:0.0	.	533;488;519;522	E7EQD5;B4DY46;Q15833-2;Q15833	.;.;.;STXB2_HUMAN	Y	522;519;533;522	ENSP00000221283:N522Y;ENSP00000409471:N519Y;ENSP00000413606:N533Y	ENSP00000221283:N522Y	N	+	1	0	STXBP2	7618265	1.000000	0.71417	1.000000	0.80357	0.644000	0.38419	5.775000	0.68915	2.003000	0.58678	0.454000	0.30748	AAC	.	.	.	none		0.662	STXBP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460963.1	NM_006949		T	7712265	A	T	7712265	3	4	136	1	0	0	0	0	1	0	0	0	15365	246	9	5	1634	5	STXBP2	19	7712265	Missense_Mutation	SNP	A	TCGA-BQ-7051-01A-12D-1961-08		7712265	51416718	63	8356											
DOCK6	57572	hgsc.bcm.edu	37	chr19	11312640	11312640	+	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	gtgctgagcagcgtcttacgCttgtgttgctcgggcagctc	4	12	14	11	3	1	1	0	1	1	0	3	1	1	1	0	1	6	7	0	1	1	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr19:11312640C>A	ENST00000294618.7	-	44	5624	c.5613G>T	c.(5611-5613)aaG>aaT	p.K1871N	DOCK6_ENST00000319867.7_Missense_Mutation_p.K1210N|DOCK6_ENST00000586702.1_5'UTR|CTC-510F12.2_ENST00000588634.1_RNA	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1871	DHR-2.				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						GCGTCTTACGCTTGTGTTGCT	0.637																																					p.K1871N		Atlas-SNP	.											.	DOCK6	104	.	0			c.G5613T						PASS	.						75	82	80					19																	11312640		2150	4243	6393	SO:0001583	missense	57572	exon44			CTTACGCTTGTGT		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.5613G>T	chr19.hg19:g.11312640C>A	ENSP00000294618:p.Lys1871Asn	16.0	0.0	.		20.0	11.0	.	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Missense_Mutation	SNP	ENST00000294618.7	hg19	CCDS45975.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.205580	0.79127	.	.	ENSG00000130158	ENST00000294618;ENST00000319867	T;T	0.20200	2.09;2.09	4.98	2.85	0.33270	.	0.000000	0.85682	D	0.000000	T	0.48750	0.1517	M	0.90082	3.085	0.58432	D	0.999999	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.85130	0.988;0.99;0.997	T	0.49153	-0.8969	10	0.87932	D	0	-31.2742	7.885	0.29644	0.0:0.7188:0.0:0.2812	.	1210;1871;1210	C9IZV6;Q96HP0;B4DIL4	.;DOCK6_HUMAN;.	N	1871;1210	ENSP00000294618:K1871N;ENSP00000321556:K1210N	ENSP00000294618:K1871N	K	-	3	2	DOCK6	11173640	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	1.212000	0.32394	0.478000	0.27488	0.491000	0.48974	AAG	.	.	.	none		0.637	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812		A	11312640	C	A	11312640	3	1	136	1	0	0	0	0	1	0	0	0	4693	796	28	4	550	4	DOCK6	19	11312640	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	3600375	11312640	47816343	64	8357											
DOCK6	57572	hgsc.bcm.edu	37	chr19	11312680	11312680	+	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	ccccgtgtgcgcgcccatccGgcgtgaacggcgtgcagaac	6	5	14	16	7	0	2	0	1	0	1	1	2	1	2	4	2	4	1	4	2	2	0			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr19:11312680G>C	ENST00000294618.7	-	44	5584	c.5573C>G	c.(5572-5574)cCg>cGg	p.P1858R	DOCK6_ENST00000319867.7_Missense_Mutation_p.P1197R|DOCK6_ENST00000586702.1_5'UTR|CTC-510F12.2_ENST00000588634.1_RNA	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1858	DHR-2.				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						GCGCCCATCCGGCGTGAACGG	0.597																																					p.P1858R		Atlas-SNP	.											.	DOCK6	104	.	0			c.C5573G						PASS	.						85	91	89					19																	11312680		2135	4244	6379	SO:0001583	missense	57572	exon44			CCATCCGGCGTGA		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.5573C>G	chr19.hg19:g.11312680G>C	ENSP00000294618:p.Pro1858Arg	42.0	0.0	.		35.0	10.0	.	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Missense_Mutation	SNP	ENST00000294618.7	hg19	CCDS45975.1	.	.	.	.	.	.	.	.	.	.	G	4.448	0.083033	0.08533	.	.	ENSG00000130158	ENST00000294618;ENST00000319867	T;T	0.16457	2.34;2.34	4.84	3.8	0.43715	.	0.164262	0.43747	D	0.000521	T	0.09686	0.0238	N	0.20986	0.625	0.34097	D	0.661381	B;B;B	0.23058	0.026;0.079;0.055	B;B;B	0.32149	0.017;0.141;0.064	T	0.19063	-1.0317	10	0.07325	T	0.83	-15.5866	5.6208	0.17455	0.2773:0.0:0.7227:0.0	.	1197;1858;1197	C9IZV6;Q96HP0;B4DIL4	.;DOCK6_HUMAN;.	R	1858;1197	ENSP00000294618:P1858R;ENSP00000321556:P1197R	ENSP00000294618:P1858R	P	-	2	0	DOCK6	11173680	1.000000	0.71417	0.710000	0.30468	0.153000	0.21895	5.138000	0.64795	2.213000	0.71641	0.491000	0.48974	CCG	.	.	.	none		0.597	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812		C	11312680	G	C	11312680	3	2	136	1	0	0	0	0	1	0	0	0	4693	1116	39	4	590	4	DOCK6	19	11312680	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	40	11312680	47816303	65	8358											
OR7A17	26333	hgsc.bcm.edu	37	chr19	14991895	14991895	+	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	atgcagcctgcataggtgatGactctgctctgtgtctggat	7	13	12	9	0	3	2	0	2	3	0	3	3	3	3	1	2	4	3	1	2	1	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr19:14991895G>A	ENST00000327462.2	-	1	369	c.273C>T	c.(271-273)gtC>gtT	p.V91V		NM_030901.1	NP_112163.1	O14581	OR7AH_HUMAN	olfactory receptor, family 7, subfamily A, member 17	91						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)	12	Ovarian(108;0.203)					CATAGGTGATGACTCTGCTCT	0.468																																					p.V91V		Atlas-SNP	.											.	OR7A17	37	.	0			c.C273T						PASS	.						151	131	138					19																	14991895		2203	4300	6503	SO:0001819	synonymous_variant	26333	exon1			GGTGATGACTCTG	X64993	CCDS12319.1	19p13.12	2012-08-09				ENSG00000185385		"GPCR / Class A : Olfactory receptors"	8363	protein-coding gene	gene with protein product						1370859	Standard	NM_030901		Approved	HTPCRX19	uc010xob.2	O14581		ENST00000327462.2:c.273C>T	chr19.hg19:g.14991895G>A		95.0	0.0	.		126.0	59.0	.	NM_030901	Q6IFQ6|Q96R98	Silent	SNP	ENST00000327462.2	hg19	CCDS12319.1																																																																																			.	.	.	none		0.468	OR7A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466523.1	NM_030901		A	14991895	G	A	14991895	2	1	136	1	0	0	0	0	0	0	0	1	11222	1277	45	2		2	OR7A17	19	14991895	Silent	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	3679215	14991895	44137088	66	8359											
USHBP1	83878	hgsc.bcm.edu	37	chr19	17362478	17362478	+	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	ccacctgttccagctccctgCgcagagactgcagctgctcc	6	8	9	18	1	0	1	0	0	0	1	3	2	3	1	5	0	5	6	5	0	0	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr19:17362478C>G	ENST00000252597.3	-	12	2008	c.1835G>C	c.(1834-1836)cGc>cCc	p.R612P	AC010646.3_ENST00000594059.1_5'UTR|USHBP1_ENST00000431146.2_Missense_Mutation_p.R548P	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						CAGCTCCCTGCGCAGAGACTG	0.602																																					p.R612P		Atlas-SNP	.											.	USHBP1	85	.	0			c.G1835C						PASS	.						75	74	74					19																	17362478		2203	4300	6503	SO:0001583	missense	83878	exon12			TCCCTGCGCAGAG	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.1835G>C	chr19.hg19:g.17362478C>G	ENSP00000252597:p.Arg612Pro	96.0	0.0	.		104.0	48.0	.	NM_031941		Missense_Mutation	SNP	ENST00000252597.3	hg19	CCDS12353.1	.	.	.	.	.	.	.	.	.	.	C	5.320	0.244414	0.10077	.	.	ENSG00000130307	ENST00000252597;ENST00000431146	T;T	0.19250	2.17;2.16	4.28	1.98	0.26296	.	0.610995	0.13794	N	0.362329	T	0.19927	0.0479	L	0.57536	1.79	0.09310	N	1	P;P	0.45240	0.854;0.854	B;B	0.43301	0.415;0.415	T	0.13845	-1.0494	10	0.49607	T	0.09	-11.2307	4.0967	0.09995	0.234:0.6445:0.0:0.1215	.	548;612	B4DUE8;Q8N6Y0	.;USBP1_HUMAN	P	612;548	ENSP00000252597:R612P;ENSP00000407902:R548P	ENSP00000252597:R612P	R	-	2	0	USHBP1	17223478	0.000000	0.05858	0.005000	0.12908	0.023000	0.10783	0.206000	0.17375	2.108000	0.64289	0.561000	0.74099	CGC	.	.	.	none		0.602	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941		G	17362478	C	G	17362478	3	3	136	1	0	0	0	0	1	0	0	0	17049	768	27	4	284	4	USHBP1	19	17362478	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	2370583	17362478	41766505	67	8360											
CRTC1	23373	hgsc.bcm.edu	37	chr19	18876245	18876245	+	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	cctggctcctctccacagcaCcgcccagctggcgtcagccc	5	6	9	21	2	2	0	1	0	1	0	4	0	3	0	6	2	3	3	6	2	0	0			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr19:18876245C>G	ENST00000321949.8	+	9	944	c.918C>G	c.(916-918)caC>caG	p.H306Q	CRTC1_ENST00000338797.6_Missense_Mutation_p.H322Q|CRTC1_ENST00000594658.1_Missense_Mutation_p.H265Q|CRTC1_ENST00000601916.1_Missense_Mutation_p.H231Q	NM_015321.2	NP_056136.2			CREB regulated transcription coactivator 1										CRTC1/MAML2(516)	NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	19						CTCCACAGCACCGCCCAGCTG	0.622																																					p.H322Q		Atlas-SNP	.											.	CRTC1	88	.	0			c.C966G						PASS	.						131	128	129					19																	18876245		2203	4300	6503	SO:0001583	missense	23373	exon10			ACAGCACCGCCCA	AY040323	CCDS32963.1, CCDS42525.1	19p13	2012-07-31	2005-11-24	2005-11-24					16062	protein-coding gene	gene with protein product	"transducer of regulated cAMP response element-binding protein"	607536	"mucoepidermoid carcinoma translocated 1"	MECT1		12539049, 14536081, 14506290	Standard	NM_015321		Approved	KIAA0616, FLJ14027, TORC1	uc010ebv.3	Q6UUV9		ENST00000321949.8:c.918C>G	chr19.hg19:g.18876245C>G	ENSP00000323332:p.His306Gln	199.0	0.0	.		180.0	66.0	.	NM_001098482		Missense_Mutation	SNP	ENST00000321949.8	hg19	CCDS32963.1	.	.	.	.	.	.	.	.	.	.	C	4.850	0.158062	0.09236	.	.	ENSG00000105662	ENST00000262813;ENST00000338797;ENST00000321949	T;T	0.11495	2.77;2.77	4.23	3.18	0.36537	.	0.533386	0.19393	N	0.115375	T	0.07548	0.0190	L	0.46157	1.445	0.41761	D	0.989719	P;B;B	0.35348	0.496;0.284;0.112	B;B;B	0.27608	0.081;0.071;0.037	T	0.22208	-1.0223	10	0.17832	T	0.49	-19.0333	7.3343	0.26601	0.0:0.7971:0.0:0.2029	.	306;322;306	Q6UUV9-3;Q6UUV9-2;Q6UUV9	.;.;CRTC1_HUMAN	Q	306;322;306	ENSP00000345001:H322Q;ENSP00000323332:H306Q	ENSP00000262813:H306Q	H	+	3	2	CRTC1	18737245	0.713000	0.27926	0.992000	0.48379	0.498000	0.33706	0.107000	0.15375	2.077000	0.62373	0.561000	0.74099	CAC	.	.	.	none		0.622	CRTC1-002	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465151.3	NM_025021		G	18876245	C	G	18876245	3	3	136	1	0	0	0	0	1	0	0	0	3901	506	18	4	1004	4	CRTC1	19	18876245	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	1513767	18876245	40252738	68	8361											
ZNF253	56242	hgsc.bcm.edu	37	chr19	20003291	20003291	+	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	tacctggccctcaatcctctCcaaacataaaagaactcata	15	9	3	14	0	3	1	2	0	1	1	5	1	4	1	4	1	3	0	4	1	7	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr19:20003291C>T	ENST00000589717.1	+	4	1327	c.1235C>T	c.(1234-1236)tCc>tTc	p.S412F	AC011477.1_ENST00000578823.1_RNA|ZNF253_ENST00000355650.4_Missense_Mutation_p.S336F|CTC-559E9.8_ENST00000585571.1_RNA	NM_021047.2	NP_066385.2	O75346	ZN253_HUMAN	zinc finger protein 253	412				Missing (in Ref. 1; AAC26844). {ECO:0000305}.	negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TCAATCCTCTCCAAACATAAA	0.388																																					p.S412F		Atlas-SNP	.											.	ZNF253	99	.	0			c.C1235T						PASS	.						39	43	42					19																	20003291		2087	4250	6337	SO:0001583	missense	56242	exon4			TCCTCTCCAAACA	AF038951	CCDS42532.1	19p12	2014-02-12	2003-12-17		ENSG00000256771	ENSG00000256771		"Zinc fingers, C2H2-type", "-"	13497	protein-coding gene	gene with protein product		606954	"zinc finger protein 411"	ZNF411		10585455	Standard	NM_021047		Approved	BMZF-1, FLJ90391	uc002noj.3	O75346	OTTHUMG00000182369	ENST00000589717.1:c.1235C>T	chr19.hg19:g.20003291C>T	ENSP00000468720:p.Ser412Phe	37.0	0.0	.		38.0	19.0	.	NM_021047	A4FVA7|Q0P6G3|Q6P0L2|Q8NCA3|Q8NCF9	Missense_Mutation	SNP	ENST00000589717.1	hg19	CCDS42532.1	.	.	.	.	.	.	.	.	.	.	c	3.372	-0.128115	0.06753	.	.	ENSG00000256771	ENST00000355650	.	.	.	0.876	0.876	0.19138	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.25938	0.0632	L	0.35542	1.07	0.09310	N	1	P	0.34562	0.457	B	0.39299	0.296	T	0.21415	-1.0246	7	.	.	.	.	3.9875	0.09522	0.409:0.591:0.0:0.0	.	412	O75346	ZN253_HUMAN	F	412	.	.	S	+	2	0	ZNF253	19864291	0.000000	0.05858	0.004000	0.12327	0.004000	0.04260	0.021000	0.13489	0.293000	0.22520	0.298000	0.19748	TCC	.	.	.	none		0.388	ZNF253-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460802.1	NM_021047		T	20003291	C	T	20003291	3	4	136	1	0	0	0	0	1	0	0	0	17809	855	30	2	1249	2	ZNF253	19	20003291	Missense_Mutation	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	1127046	20003291	39125692	69	8362											
ZNF471	57573	hgsc.bcm.edu	37	chr19	57037192	57037192	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttttagtgatagctcatccTgtgctcagcatcaaagactc	10	13	7	11	0	3	2	3	1	0	1	5	2	4	2	1	0	3	3	1	0	3	3			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr19:57037192T>C	ENST00000308031.5	+	5	1889	c.1756T>C	c.(1756-1758)Tgt>Cgt	p.C586R	ZNF471_ENST00000593197.1_3'UTR|ZNF471_ENST00000591537.1_3'UTR	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	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)|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)		TAGCTCATCCTGTGCTCAGCA	0.408																																					p.C586R	Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)	Atlas-SNP	.											.	ZNF471	99	.	0			c.T1756C						PASS	.						78	74	75					19																	57037192		2203	4300	6503	SO:0001583	missense	57573	exon5			TCATCCTGTGCTC	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.1756T>C	chr19.hg19:g.57037192T>C	ENSP00000309161:p.Cys586Arg	62.0	0.0	.		76.0	33.0	.	NM_020813	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Missense_Mutation	SNP	ENST00000308031.5	hg19	CCDS12945.1	.	.	.	.	.	.	.	.	.	.	T	4.114	0.019231	0.08006	.	.	ENSG00000196263	ENST00000308031	T	0.00949	5.51	3.68	-2.53	0.06326	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00724	0.0024	N	0.11789	0.175	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.45498	-0.9257	9	0.87932	D	0	.	9.1979	0.37240	0.0:0.4048:0.0:0.5952	.	586	Q9BX82	ZN471_HUMAN	R	586	ENSP00000309161:C586R	ENSP00000309161:C586R	C	+	1	0	ZNF471	61729004	0.000000	0.05858	0.017000	0.16124	0.514000	0.34195	-1.549000	0.02182	-0.322000	0.08615	-0.464000	0.05259	TGT	.	.	.	none		0.408	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813		C	57037192	T	C	57037192	3	2	136	1	0	0	0	0	1	0	0	0	17942	1580	55	3	1770	3	ZNF471	19	57037192	Missense_Mutation	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	37033901	57037192	2091791	70	8363											
PTPRT	11122	hgsc.bcm.edu	37	chr20	41100970	41100970	+	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	ccctcggggttagacagcaaGagtcgcagccggatggtcat	9	7	14	11	3	1	2	1	0	0	2	3	3	1	3	2	4	2	3	2	4	2	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr20:41100970G>A	ENST00000373187.1	-	8	1385	c.1386C>T	c.(1384-1386)ctC>ctT	p.L462L	PTPRT_ENST00000356100.2_Silent_p.L462L|PTPRT_ENST00000373198.4_Silent_p.L462L|PTPRT_ENST00000373201.1_Silent_p.L462L|PTPRT_ENST00000373193.3_Silent_p.L462L|PTPRT_ENST00000373184.1_Silent_p.L462L|PTPRT_ENST00000373190.1_Silent_p.L462L			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	462	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				TAGACAGCAAGAGTCGCAGCC	0.612																																					p.L462L		Atlas-SNP	.											.	PTPRT	372	.	0			c.C1386T						PASS	.						57	62	60					20																	41100970		2134	4245	6379	SO:0001819	synonymous_variant	11122	exon8			CAGCAAGAGTCGC	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.1386C>T	chr20.hg19:g.41100970G>A		103.0	0.0	.		147.0	51.0	.	NM_007050	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Silent	SNP	ENST00000373187.1	hg19	CCDS42874.1																																																																																			.	.	.	none		0.612	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			A	41100970	G	A	41100970	2	1	136	1	0	0	0	0	0	0	0	1	12825	929	33	2		2	PTPRT	20	41100970	Silent	SNP	G	TCGA-BQ-7051-01A-12D-1961-08		41100970	21924550	71	8364											
ZGPAT	84619	hgsc.bcm.edu	37	chr20	62366823	62366823	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagagtgccaagcgggcccTgagcctgcggctcttccaga	8	6	13	14	2	1	3	0	1	1	2	2	3	2	3	4	2	4	1	4	2	2	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr20:62366823T>C	ENST00000328969.5	+	6	1491	c.1364T>C	c.(1363-1365)cTg>cCg	p.L455P	ZGPAT_ENST00000369967.3_Missense_Mutation_p.L435P|ZGPAT_ENST00000448100.2_Missense_Mutation_p.L435P|LIME1_ENST00000309546.3_5'Flank|RP4-583P15.14_ENST00000467211.1_5'Flank|ZGPAT_ENST00000357119.4_Missense_Mutation_p.L426P|ZGPAT_ENST00000355969.6_Missense_Mutation_p.L435P|RP4-583P15.15_ENST00000490623.2_Nonstop_Mutation_p.*341R	NM_032527.4	NP_115916.3	Q8N5A5	ZGPAT_HUMAN	zinc finger, CCCH-type with G patch domain	455					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)					AAGCGGGCCCTGAGCCTGCGG	0.667																																					p.L455P		Atlas-SNP	.											.	ZGPAT	57	.	0			c.T1364C						PASS	.						23	27	26					20																	62366823		2200	4300	6500	SO:0001583	missense	84619	exon6			GGGCCCTGAGCCT	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.1364T>C	chr20.hg19:g.62366823T>C	ENSP00000332013:p.Leu455Pro	32.0	0.0	.		51.0	30.0	.	NM_032527	E1P5K1|Q4VXN9|Q5JWI9|Q5JWJ0|Q8NC55|Q8WUV4|Q96JI0|Q96JU4|Q9H401	Missense_Mutation	SNP	ENST00000328969.5	hg19	CCDS13534.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.234362	0.79800	.	.	ENSG00000197114	ENST00000448100;ENST00000355969;ENST00000357119;ENST00000369967;ENST00000328969	T;T;T;T;T	0.32988	1.45;1.45;1.47;1.45;1.43	5.69	4.57	0.56435	.	0.072010	0.56097	D	0.000022	T	0.53738	0.1815	M	0.76328	2.33	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	0.54490	-0.8286	10	0.52906	T	0.07	-25.847	11.8041	0.52143	0.1318:0.0:0.0:0.8682	.	426;455;435	Q8N5A5-3;Q8N5A5;Q8N5A5-2	.;ZGPAT_HUMAN;.	P	435;435;426;435;455	ENSP00000391176:L435P;ENSP00000348242:L435P;ENSP00000349634:L426P;ENSP00000358984:L435P;ENSP00000332013:L455P	ENSP00000332013:L455P	L	+	2	0	ZGPAT	61837267	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	5.891000	0.69782	0.955000	0.37878	0.460000	0.39030	CTG	.	.	.	none		0.667	ZGPAT-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080214.1	NM_181484		C	62366823	T	C	62366823	3	2	136	1	0	0	0	0	1	0	0	0	17686	1580	55	3	1382	3	ZGPAT	20	62366823	Missense_Mutation	SNP	T	TCGA-BQ-7051-01A-12D-1961-08	21265853	62366823	658697	72	8365											
SFI1	9814	hgsc.bcm.edu	37	chr22	32002357	32002357	+	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	agaacaccatggcccgagtgGatgaagccaaaaaaaccttt	16	6	9	10	1	0	2	0	1	0	1	0	4	0	3	4	2	3	0	4	2	5	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr22:32002357G>C	ENST00000400288.2	+	21	2203	c.2098G>C	c.(2098-2100)Gat>Cat	p.D700H	SFI1_ENST00000414585.1_Missense_Mutation_p.D547H|SFI1_ENST00000432498.1_Missense_Mutation_p.D669H|SFI1_ENST00000400289.1_Missense_Mutation_p.D618H|SFI1_ENST00000443011.1_Missense_Mutation_p.D547H|SFI1_ENST00000443326.1_Missense_Mutation_p.D618H|SFI1_ENST00000540643.1_Missense_Mutation_p.D645H	NM_001007467.2	NP_001007468.1	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	700					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						GGCCCGAGTGGATGAAGCCAA	0.517																																					p.D700H		Atlas-SNP	.											.	SFI1	78	.	0			c.G2098C						PASS	.						88	88	88					22																	32002357		2023	4185	6208	SO:0001583	missense	9814	exon21			CGAGTGGATGAAG	AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089			29064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 139"	612765				14504268	Standard	NM_001007467		Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000400288.2:c.2098G>C	chr22.hg19:g.32002357G>C	ENSP00000383145:p.Asp700His	61.0	0.0	.		63.0	25.0	.	NM_001007467	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	Missense_Mutation	SNP	ENST00000400288.2	hg19	CCDS43004.1	.	.	.	.	.	.	.	.	.	.	G	8.780	0.928003	0.18131	.	.	ENSG00000198089	ENST00000432498;ENST00000540643;ENST00000443326;ENST00000414585;ENST00000443011;ENST00000400289;ENST00000400288;ENST00000417682	T;T;T;T;T;T;T;T	0.14266	3.1;3.1;2.94;2.93;2.93;2.94;3.1;2.52	5.06	0.509	0.16977	.	0.751926	0.13001	N	0.421651	T	0.10035	0.0246	N	0.08118	0	0.09310	N	1	P;P;P;P;P	0.42757	0.789;0.603;0.603;0.789;0.573	P;B;B;P;B	0.49922	0.626;0.366;0.277;0.626;0.366	T	0.28364	-1.0046	10	0.40728	T	0.16	.	6.8814	0.24174	0.4019:0.0:0.5981:0.0	.	645;618;618;669;700	A8K8P3-9;A8K8P3-10;A8K8P3-3;A8K8P3-2;A8K8P3	.;.;.;.;SFI1_HUMAN	H	669;645;618;547;547;618;700;283	ENSP00000402679:D669H;ENSP00000443025:D645H;ENSP00000416469:D618H;ENSP00000397148:D547H;ENSP00000401199:D547H;ENSP00000383146:D618H;ENSP00000383145:D700H;ENSP00000398871:D283H	ENSP00000383145:D700H	D	+	1	0	SFI1	30332357	0.001000	0.12720	0.033000	0.17914	0.025000	0.11179	0.187000	0.16998	0.237000	0.21200	-0.995000	0.02519	GAT	.	.	.	none		0.517	SFI1-023	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337180.3	NM_014775		C	32002357	G	C	32002357	3	2	136	1	0	0	0	0	1	0	0	0	14169	1174	41	4	2176	4	SFI1	22	32002357	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08		32002357	19302209	73	8366											
C1QTNF6	114904	hgsc.bcm.edu	37	chr22	37578251	37578251	+	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	gtcgtcctcggccttgatgaGgtggccgctgaaggtgatgt	5	11	16	9	3	0	4	0	4	0	0	3	4	1	4	3	4	0	1	3	4	1	1			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr22:37578251G>C	ENST00000337843.2	-	3	889	c.814C>G	c.(814-816)Ctc>Gtc	p.L272V	C1QTNF6_ENST00000397110.2_Missense_Mutation_p.L272V|RP1-151B14.6_ENST00000419128.1_RNA|C1QTNF6_ENST00000255836.6_Missense_Mutation_p.L148V|C1QTNF6_ENST00000470655.1_5'UTR	NM_031910.3	NP_114116.3	Q9BXI9	C1QT6_HUMAN	C1q and tumor necrosis factor related protein 6	253					protein heterotrimerization (GO:0070208)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)				breast(1)|large_intestine(2)|lung(6)|stomach(1)|upper_aerodigestive_tract(1)	11						GCCTTGATGAGGTGGCCGCTG	0.657																																					p.L272V		Atlas-SNP	.											.	C1QTNF6	32	.	0			c.C814G						PASS	.						61	57	58					22																	37578251		2203	4300	6503	SO:0001583	missense	114904	exon3			TGATGAGGTGGCC	AF329842	CCDS13943.1	22q13.1	2014-02-21			ENSG00000133466	ENSG00000133466			14343	protein-coding gene	gene with protein product		614910				12975309	Standard	NM_031910		Approved	CTRP6, ZACRP6	uc003aqy.1	Q9BXI9	OTTHUMG00000150538	ENST00000337843.2:c.814C>G	chr22.hg19:g.37578251G>C	ENSP00000338812:p.Leu272Val	48.0	0.0	.		35.0	18.0	.	NM_182486	Q5H9G8|Q6ZRM7	Missense_Mutation	SNP	ENST00000337843.2	hg19	CCDS13943.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.981527	0.74474	.	.	ENSG00000133466	ENST00000397110;ENST00000337843;ENST00000255836	T;T;T	0.51574	0.7;0.7;0.7	4.84	4.84	0.62591	Tumour necrosis factor-like (2);Complement C1q protein (3);	0.000000	0.64402	D	0.000001	T	0.78444	0.4284	H	0.97265	3.97	0.58432	D	0.999997	D;D	0.76494	0.999;0.998	D;D	0.72075	0.976;0.971	D	0.85842	0.1398	10	0.87932	D	0	.	13.3544	0.60619	0.0787:0.0:0.9213:0.0	.	272;253	Q9BXI9-2;Q9BXI9	.;C1QT6_HUMAN	V	272;272;148	ENSP00000380299:L272V;ENSP00000338812:L272V;ENSP00000255836:L148V	ENSP00000255836:L148V	L	-	1	0	C1QTNF6	35908197	1.000000	0.71417	1.000000	0.80357	0.829000	0.46940	5.704000	0.68347	2.238000	0.73509	0.491000	0.48974	CTC	.	.	.	none		0.657	C1QTNF6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318807.1	NM_182486		C	37578251	G	C	37578251	3	2	136	1	0	0	0	0	1	0	0	0	1969	1000	35	4	26	4	C1QTNF6	22	37578251	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	5575894	37578251	13726315	74	8367											
ARFGAP3	26286	hgsc.bcm.edu	37	chr22	43213794	43213794	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcaacattttttttgccactAatgttcatcttttcgtcttt	7	22	3	9	1	4	0	2	0	2	0	5	0	4	0	1	0	2	1	1	0	2	9			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chr22:43213794A>G	ENST00000263245.5	-	10	1101	c.882T>C	c.(880-882)atT>atC	p.I294I	ARFGAP3_ENST00000437119.2_Silent_p.I250I|ARFGAP3_ENST00000429508.2_Silent_p.I222I	NM_001142293.1|NM_014570.4	NP_001135765.1|NP_055385.3	Q9NP61	ARFG3_HUMAN	ADP-ribosylation factor GTPase activating protein 3	294					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						TTTTGCCACtaatgttcatct	0.348																																					p.I294I	GBM(58;544 1030 21460 27159 48838)	Atlas-SNP	.											.	ARFGAP3	48	.	0			c.T882C						PASS	.						296	266	276					22																	43213794		2203	4300	6503	SO:0001819	synonymous_variant	26286	exon10			GCCACTAATGTTC	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.882T>C	chr22.hg19:g.43213794A>G		174.0	0.0	.		139.0	63.0	.	NM_014570	E9PB03|Q9BSC6|Q9H9J0|Q9NT10|Q9NUP5|Q9Y4V3|Q9Y4V4	Silent	SNP	ENST00000263245.5	hg19	CCDS14042.1	.	.	.	.	.	.	.	.	.	.	A	7.151	0.583739	0.13749	.	.	ENSG00000242247	ENST00000453516	.	.	.	5.35	-2.94	0.05581	.	.	.	.	.	.	.	.	.	.	.	0.32559	N	0.531383	.	.	.	.	.	.	.	.	.	.	.	.	.	-8.1118	4.5685	0.12198	0.2139:0.5126:0.1904:0.0831	.	.	.	.	Q	141	.	.	X	-	1	0	ARFGAP3	41543738	0.000000	0.05858	0.062000	0.19696	0.849000	0.48306	-0.717000	0.04986	-0.307000	0.08804	-0.291000	0.09656	TAG	.	.	.	none		0.348	ARFGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319747.2	NM_014570		G	43213794	A	G	43213794	2	3	136	1	0	0	0	0	0	0	0	1	851	358	13	3		3	ARFGAP3	22	43213794	Silent	SNP	A	TCGA-BQ-7051-01A-12D-1961-08	5635543	43213794	8090772	75	8368											
SYN1	6853	hgsc.bcm.edu	37	chrX	47432308	47432308	+	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	gacttcctcaggctgcggatGgtctcagctttcacctcgtc	5	12	10	14	2	3	0	3	0	1	0	7	2	4	1	2	3	2	2	2	3	0	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chrX:47432308G>C	ENST00000295987.7	-	13	2197	c.2073C>G	c.(2071-2073)acC>acG	p.T691T	SYN1_ENST00000340666.4_3'UTR	NM_006950.3	NP_008881.2	P17600	SYN1_HUMAN	synapsin I	691	E.				neurotransmitter secretion (GO:0007269)|regulation of neurotransmitter secretion (GO:0046928)|regulation of synaptic vesicle exocytosis (GO:2000300)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|protein kinase binding (GO:0019901)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(6)|lung(6)|ovary(1)	21						GGCTGCGGATGGTCTCAGCTT	0.582																																					p.T691T		Atlas-SNP	.											.	SYN1	84	.	0			c.C2073G						PASS	.						108	91	97					X																	47432308		2203	4300	6503	SO:0001819	synonymous_variant	6853	exon13			GCGGATGGTCTCA		CCDS14280.1, CCDS35233.1	Xp11.2	2012-10-02			ENSG00000008056	ENSG00000008056			11494	protein-coding gene	gene with protein product		313440					Standard	NM_133499		Approved		uc004die.3	P17600	OTTHUMG00000021454	ENST00000295987.7:c.2073C>G	chrX.hg19:g.47432308G>C		74.0	0.0	.		58.0	56.0	.	NM_006950	B1AJQ1|O75825|Q5H9A9	Silent	SNP	ENST00000295987.7	hg19	CCDS14280.1																																																																																			.	.	.	none		0.582	SYN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056445.1	NM_006950		C	47432308	G	C	47432308	2	2	136	1	0	0	0	0	0	0	0	1	15452	1335	47	4		4	SYN1	23	47432308	Silent	SNP	G	TCGA-BQ-7051-01A-12D-1961-08		47432308	107838252	76	8369											
HEPH	9843	hgsc.bcm.edu	37	chrX	65390505	65390505	+	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	actcgagtctactacctgggCatccgggatgtgcagtggaa	9	9	13	10	2	1	0	0	0	1	0	3	3	2	2	2	3	3	2	2	3	3	2			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chrX:65390505C>T	ENST00000343002.2	+	1	757	c.93C>T	c.(91-93)ggC>ggT	p.G31G	HEPH_ENST00000519389.1_Silent_p.G85G|HEPH_ENST00000419594.1_Silent_p.G34G|HEPH_ENST00000441993.2_Silent_p.G34G|HEPH_ENST00000374727.3_Silent_p.G34G|HEPH_ENST00000336279.5_Intron			Q9BQS7	HEPH_HUMAN	hephaestin	31	Plastocyanin-like 1.				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						ACTACCTGGGCATCCGGGATG	0.527																																					p.G85G		Atlas-SNP	.											.	HEPH	224	.	0			c.C255T						PASS	.						94	64	74					X																	65390505		2203	4300	6503	SO:0001819	synonymous_variant	9843	exon2			CCTGGGCATCCGG	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.93C>T	chrX.hg19:g.65390505C>T		25.0	0.0	.		23.0	19.0	.	NM_138737	B1AJX8|D3DVT7|E9PHN8|O75180|Q6UW45|Q9C058	Silent	SNP	ENST00000343002.2	hg19																																																																																				.	.	.	none		0.527	HEPH-002	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000056995.1	NM_138737		T	65390505	C	T	65390505	2	4	136	1	0	0	0	0	0	0	0	1	7061	697	25	2		2	HEPH	23	65390505	Silent	SNP	C	TCGA-BQ-7051-01A-12D-1961-08	17958197	65390505	89880055	77	8370											
ARHGAP36	158763	hgsc.bcm.edu	37	chrX	130215818	130215818	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcctctctgagctggagcGtctgaagctgcaagagactg	9	8	13	11	1	2	3	0	2	2	1	3	5	2	4	1	1	5	3	1	1	2	0			TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	g.chrX:130215818G>A	ENST00000276211.5	+	2	524	c.179G>A	c.(178-180)cGt>cAt	p.R60H	ARHGAP36_ENST00000370921.1_5'Flank|ARHGAP36_ENST00000370922.1_Missense_Mutation_p.R48H	NM_144967.3	NP_659404.2	Q6ZRI8	RHG36_HUMAN	Rho GTPase activating protein 36	60					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.R60H(1)		breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(16)|lung(31)|ovary(4)|prostate(4)|skin(3)|urinary_tract(2)	71						GAGCTGGAGCGTCTGAAGCTG	0.532																																					p.R60H		Atlas-SNP	.											.	ARHGAP36	171	.	1	Substitution - Missense(1)	large_intestine(1)	c.G179A						PASS	.						125	107	113					X																	130215818		2203	4300	6503	SO:0001583	missense	158763	exon2			TGGAGCGTCTGAA		CCDS14628.1, CCDS65320.1	Xq26.1	2011-06-29			ENSG00000147256	ENSG00000147256		"Rho GTPase activating proteins"	26388	protein-coding gene	gene with protein product							Standard	NM_144967		Approved	FLJ30058	uc004evz.3	Q6ZRI8	OTTHUMG00000022402	ENST00000276211.5:c.179G>A	chrX.hg19:g.130215818G>A	ENSP00000276211:p.Arg60His	127.0	0.0	.		96.0	87.0	.	NM_144967	B7Z234|B7Z439|Q5JRL9|Q5JRM0|Q5JRM1|Q96NU6	Missense_Mutation	SNP	ENST00000276211.5	hg19	CCDS14628.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.358508	0.82243	.	.	ENSG00000147256	ENST00000276211;ENST00000370922;ENST00000423277;ENST00000412432	T;T;T	0.28666	1.6;1.61;1.68	4.16	4.16	0.48862	.	0.000000	0.47455	D	0.000238	T	0.40886	0.1135	L	0.29908	0.895	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.997;0.994	T	0.30387	-0.9980	10	0.87932	D	0	.	10.8111	0.46547	0.0:0.0:1.0:0.0	.	29;48;60	Q6ZRI8-2;Q6ZRI8-4;Q6ZRI8	.;.;RHG36_HUMAN	H	60;48;12;29	ENSP00000276211:R60H;ENSP00000359960:R48H;ENSP00000408515:R29H	ENSP00000276211:R60H	R	+	2	0	ARHGAP36	130043499	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.627000	0.67784	2.315000	0.78130	0.544000	0.68410	CGT	.	.	.	none		0.532	ARHGAP36-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355073.1	NM_144967		A	130215818	G	A	130215818	3	1	136	1	0	0	0	0	1	0	0	0	883	1145	40	1	181	1	ARHGAP36	23	130215818	Missense_Mutation	SNP	G	TCGA-BQ-7051-01A-12D-1961-08	64825313	130215818	25054742	78	8371											
MYSM1	114803	hgsc.bcm.edu	37	chr1	59125680	59125680	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttaaaataatcacattaacaAttcctttgtacagttctctt	14	17	2	8	0	2	0	1	0	1	0	4	0	3	0	1	0	2	2	1	0	6	8			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr1:59125680A>G	ENST00000472487.1	-	20	2515	c.2476T>C	c.(2476-2478)Ttg>Ctg	p.L826L	MYSM1_ENST00000493821.1_5'UTR	NM_001085487.2	NP_001078956.1	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1	826					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)					CACATTAACAATTCCTTTGTA	0.299																																					p.L826L		Atlas-SNP	.											.	MYSM1	50	.	0			c.T2476C						PASS	.						77	75	76					1																	59125680		1805	4073	5878	SO:0001819	synonymous_variant	114803	exon20			TTAACAATTCCTT	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.2476T>C	chr1.hg19:g.59125680A>G		84.0	0.0	.		88.0	4.0	.	NM_001085487	A8KA54|B3KX65|Q68DD3|Q6AI53|Q7Z3G8|Q96PX3	Silent	SNP	ENST00000472487.1	hg19	CCDS41343.1																																																																																			.	.	.	none		0.299	MYSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026343.2	XM_055481		G	59125680	A	G	59125680	2	3	137	1	0	0	0	0	0	0	0	1	10108	98	4	3		3	MYSM1	1	59125680	Silent	SNP	A	TCGA-BQ-7053-01A-11D-1961-08		59125680	190124941	1	8372											
TTN	7273	hgsc.bcm.edu	37	chr2	179611917	179611917	+	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	gggggtgtggagtatctctcTagagtctctcctggaggtgt	5	13	16	7	0	3	1	0	0	3	1	6	3	4	3	1	5	0	1	1	5	2	2	rs578160962		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr2:179611917T>C	ENST00000591111.1	-	46	10585				TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000589042.1_Intron|TTN_ENST00000360870.5_Silent_p.L5070L			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)			AGTATCTCTCTAGAGTCTCTC	0.522													T|||	1	0.000199681	0	0.0014	5008	,	,		15437	0		0	False		,,,				2504	0				p.L5070L		Atlas-SNP	.											TTN_ENST00000360870,NS,carcinoma,0,1	TTN	18412	.	0			c.A15210G						PASS	.						70	74	72					2																	179611917		2203	4300	6503	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.10361-5269A>G	chr2.hg19:g.179611917T>C		123.0	1.0	.		133.0	8.0	.	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.	.	none		0.522	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179611917	T	C	179611917	1	2	137	0	1	0	0	0	0	0	0	0	16747	1509	53	3		3	TTN	2	179611917	Intron	SNP	T	TCGA-BQ-7053-01A-11D-1961-08		179611917	63587456	2	8373											
PGAP1	80055	hgsc.bcm.edu	37	chr2	197767380	197767380	+	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	tcctgaacgaacttggtaatCccggaatcctccagctacag	11	9	8	13	2	0	1	0	1	0	0	4	3	4	2	4	2	4	2	4	2	5	3			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr2:197767380C>T	ENST00000354764.4	-	5	850	c.736G>A	c.(736-738)Gat>Aat	p.D246N	PGAP1_ENST00000485830.1_5'UTR|PGAP1_ENST00000409475.1_Missense_Mutation_p.D246N|PGAP1_ENST00000409188.1_Missense_Mutation_p.D204N	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	246					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						ACTTGGTAATCCCGGAATCCT	0.353																																					p.D246N		Atlas-SNP	.											.	PGAP1	84	.	0			c.G736A						PASS	.						89	96	94					2																	197767380		2203	4300	6503	SO:0001583	missense	80055	exon5			GGTAATCCCGGAA		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.736G>A	chr2.hg19:g.197767380C>T	ENSP00000346809:p.Asp246Asn	98.0	0.0	.		90.0	32.0	.	NM_024989	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Missense_Mutation	SNP	ENST00000354764.4	hg19	CCDS2318.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.812990	0.90707	.	.	ENSG00000197121	ENST00000354764;ENST00000409475;ENST00000409188	D;D;D	0.96491	-4.03;-4.03;-4.03	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	D	0.98585	0.9527	M	0.92122	3.275	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;0.999	D	0.99628	1.0985	10	0.87932	D	0	-16.6327	18.3788	0.90443	0.0:1.0:0.0:0.0	.	204;246;246	B4DYY6;Q75T13-3;Q75T13	.;.;PGAP1_HUMAN	N	246;246;204	ENSP00000346809:D246N;ENSP00000387028:D246N;ENSP00000386802:D204N	ENSP00000346809:D246N	D	-	1	0	PGAP1	197475625	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.144000	0.64832	2.568000	0.86640	0.650000	0.86243	GAT	.	.	.	none		0.353	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989		T	197767380	C	T	197767380	3	4	137	1	0	0	0	0	1	0	0	0	11784	855	30	2	2124	2	PGAP1	2	197767380	Missense_Mutation	SNP	C	TCGA-BQ-7053-01A-11D-1961-08	18155463	197767380	45431993	3	8374											
LRRFIP1	9208	hgsc.bcm.edu	37	chr2	238636568	238636568	+	Intron	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	atcacagtccctgaatagaaGatctggcagggttagtatag	13	10	11	7	0	2	3	1	1	1	2	3	3	3	3	1	2	0	3	1	2	6	4			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr2:238636568G>C	ENST00000392000.4	+	4	366				LRRFIP1_ENST00000308482.9_Missense_Mutation_p.R145T|LRRFIP1_ENST00000244815.5_Intron|LRRFIP1_ENST00000289175.6_Intron	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1						innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|protein homodimerization activity (GO:0042803)			NS(1)|breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	29		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)		CTGAATAGAAGATCTGGCAGG	0.318																																					p.R145T		Atlas-SNP	.											.	LRRFIP1	171	.	0			c.G434C						PASS	.						204	199	201					2																	238636568		1568	3582	5150	SO:0001627	intron_variant	9208	exon8			ATAGAAGATCTGG	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.249+7103G>C	chr2.hg19:g.238636568G>C		194.0	0.0	.		189.0	66.0	.	NM_001137550	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Missense_Mutation	SNP	ENST00000392000.4	hg19	CCDS46552.1	.	.	.	.	.	.	.	.	.	.	G	15.82	2.945238	0.53079	.	.	ENSG00000124831	ENST00000308482;ENST00000391999;ENST00000420665	T	0.48201	0.82	5.3	4.2	0.49525	.	.	.	.	.	T	0.29288	0.0729	N	0.24115	0.695	0.80722	D	1	B	0.31318	0.319	B	0.32624	0.149	T	0.08207	-1.0733	9	0.23891	T	0.37	.	5.5337	0.16999	0.2308:0.0:0.7692:0.0	.	145	E9PGZ2	.	T	145;135;100	ENSP00000310109:R145T	ENSP00000310109:R145T	R	+	2	0	LRRFIP1	238301307	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.587000	0.53957	2.652000	0.90054	0.655000	0.94253	AGA	.	.	.	none		0.318	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735		C	238636568	G	C	238636568	1	2	137	0	1	0	0	0	0	0	0	0	9034	942	33	4		4	LRRFIP1	2	238636568	Intron	SNP	G	TCGA-BQ-7053-01A-11D-1961-08	40869188	238636568	4562805	4	8375											
PRRT3	285368	hgsc.bcm.edu	37	chr3	9990555	9990555	+	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	cctccacagctcctctcaccCgctggggggagatggggtct	5	8	13	15	1	2	1	1	0	2	1	5	2	4	1	4	5	1	2	4	5	0	0	rs187203537		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr3:9990555C>A	ENST00000412055.1	-	3	1187	c.1058G>T	c.(1057-1059)cGg>cTg	p.R353L	PRRT3-AS1_ENST00000431558.1_RNA|PRRT3_ENST00000411976.2_Missense_Mutation_p.R353L	NM_207351.3	NP_997234.3	Q5FWE3	PRRT3_HUMAN	proline-rich transmembrane protein 3	353	Pro-rich.					integral component of membrane (GO:0016021)				NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(1)|skin(1)|stomach(2)	13						TCCTCTCACCCGCTGGGGGGA	0.592																																					p.R353L		Atlas-SNP	.											.	PRRT3	35	.	0			c.G1058T						PASS	.						59	65	63					3																	9990555		1927	4137	6064	SO:0001583	missense	285368	exon3			CTCACCCGCTGGG	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.1058G>T	chr3.hg19:g.9990555C>A	ENSP00000392511:p.Arg353Leu	131.0	0.0	.		146.0	6.0	.	NM_207351	Q49AD0|Q6UXY6|Q8NBC9	Missense_Mutation	SNP	ENST00000412055.1	hg19	CCDS43049.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.468603	0.84533	.	.	ENSG00000163704	ENST00000412055;ENST00000411976	T;T	0.33654	1.66;1.4	5.17	5.17	0.71159	.	0.000000	0.50627	D	0.000103	T	0.48840	0.1522	L	0.36672	1.1	0.37495	D	0.916543	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.49204	-0.8964	9	.	.	.	-10.5905	14.1662	0.65477	0.0:1.0:0.0:0.0	.	353;353	Q5FWE3-3;Q5FWE3	.;PRRT3_HUMAN	L	353	ENSP00000392511:R353L;ENSP00000404512:R353L	.	R	-	2	0	PRRT3	9965555	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	1.604000	0.36804	2.403000	0.81681	0.655000	0.94253	CGG	.	C|0.999;T|0.001	.	alt		0.592	PRRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339322.1	NM_207351		A	9990555	C	A	9990555	3	1	137	1	0	0	0	0	1	0	0	0	12621	652	23	4	1895	4	PRRT3	3	9990555	Missense_Mutation	SNP	C	TCGA-BQ-7053-01A-11D-1961-08		9990555	188031875	5	8376											
VPRBP	9730	hgsc.bcm.edu	37	chr3	51457622	51457622	+	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	gctagcggaccctgggggggCcgtggctgaggatgagcagt	6	6	20	9	2	0	2	0	2	0	0	0	4	0	4	2	6	2	3	2	6	1	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr3:51457622C>G	ENST00000335891.5	-	7	1464	c.1455G>C	c.(1453-1455)cgG>cgC	p.R485R				Q9Y4B6	VPRBP_HUMAN	Vpr (HIV-1) binding protein	934	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)		CCTGGGGGGGCCGTGGCTGAG	0.592																																					p.R881R		Atlas-SNP	.											.	VPRBP	107	.	0			c.G2643C						PASS	.						44	47	46					3																	51457622		1981	4163	6144	SO:0001819	synonymous_variant	9730	exon14			GGGGGGCCGTGGC	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.1455G>C	chr3.hg19:g.51457622C>G		78.0	0.0	.		60.0	27.0	.	NM_014703	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Silent	SNP	ENST00000335891.5	hg19																																																																																				.	.	.	none		0.592	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014703		G	51457622	C	G	51457622	2	3	137	1	0	0	0	0	0	0	0	1	17197	726	26	4		4	VPRBP	3	51457622	Silent	SNP	C	TCGA-BQ-7053-01A-11D-1961-08	41467067	51457622	146564808	6	8377											
GMPS	8833	hgsc.bcm.edu	37	chr3	155654202	155654202	+	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	tcgggacccacttcaaaagcAgccttcatgccagagatctg	11	8	9	13	1	3	1	2	0	1	1	4	3	3	2	3	1	3	1	3	1	2	2			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr3:155654202A>T	ENST00000496455.2	+	15	2218	c.1883A>T	c.(1882-1884)cAg>cTg	p.Q628L	GMPS_ENST00000295920.7_Missense_Mutation_p.Q529L	NM_003875.2	NP_003866.1	P49915	GUAA_HUMAN	guanine monphosphate synthase	628					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)	CTTCAAAAGCAGCCTTCATGC	0.443			T	MLL	AML																																p.Q628L	Ovarian(153;896 1876 4149 15499 28134)	Atlas-SNP	.		Dom	yes		3	3q24	8833	guanine monphosphate synthetase		L	.	GMPS	70	.	0			c.A1883T						PASS	.						128	120	122					3																	155654202		1870	4103	5973	SO:0001583	missense	8833	exon15			AAAAGCAGCCTTC	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.1883A>T	chr3.hg19:g.155654202A>T	ENSP00000419851:p.Gln628Leu	169.0	0.0	.		165.0	49.0	.	NM_003875	A8K639|B4DXV7|F8W720	Missense_Mutation	SNP	ENST00000496455.2	hg19	CCDS46941.1	.	.	.	.	.	.	.	.	.	.	A	14.40	2.524899	0.44969	.	.	ENSG00000163655	ENST00000496455;ENST00000295920;ENST00000537975;ENST00000541628	.	.	.	5.53	5.53	0.82687	GMP synthase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.58308	0.2113	L	0.55990	1.75	0.80722	D	1	B;B	0.09022	0.001;0.002	B;B	0.06405	0.001;0.002	T	0.53954	-0.8365	9	0.30854	T	0.27	-12.4699	15.6641	0.77213	1.0:0.0:0.0:0.0	.	529;628	F8W720;P49915	.;GUAA_HUMAN	L	628;529;577;628	.	ENSP00000295920:Q529L	Q	+	2	0	GMPS	157136896	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.800000	0.91900	2.086000	0.62901	0.459000	0.35465	CAG	.	.	.	none		0.443	GMPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351260.2			T	155654202	A	T	155654202	3	4	137	1	0	0	0	0	1	0	0	0	6505	188	7	5	1941	5	GMPS	3	155654202	Missense_Mutation	SNP	A	TCGA-BQ-7053-01A-11D-1961-08	104196580	155654202	42368228	7	8378											
MAP3K13	9175	hgsc.bcm.edu	37	chr3	185146747	185146747	+	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	ttcagcaggtcaggcagtggCagtggtgggtttcttgaagg	7	11	17	6	0	3	1	2	1	1	0	3	1	3	1	0	6	1	4	0	6	1	3			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr3:185146747C>T	ENST00000265026.3	+	2	712	c.378C>T	c.(376-378)ggC>ggT	p.G126G	MAP3K13_ENST00000446828.1_Intron|MAP3K13_ENST00000424227.1_Silent_p.G126G|MAP3K13_ENST00000535426.1_Intron|MAP3K13_ENST00000443863.1_Intron	NM_004721.4	NP_004712.1			mitogen-activated protein kinase kinase kinase 13											NS(1)|biliary_tract(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(13)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			CAGGCAGTGGCAGTGGTGGGT	0.493																																					p.G126G		Atlas-SNP	.											.	MAP3K13	209	.	0			c.C378T						PASS	.						93	94	94					3																	185146747		2203	4300	6503	SO:0001819	synonymous_variant	9175	exon2			CAGTGGCAGTGGT	BC031677	CCDS3270.1, CCDS56298.1	3q27	2011-06-09			ENSG00000073803	ENSG00000073803		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6852	protein-coding gene	gene with protein product	"leucine zipper-bearing kinase"	604915				9353328	Standard	NM_004721		Approved	LZK, MEKK13	uc003fpi.3	O43283	OTTHUMG00000156673	ENST00000265026.3:c.378C>T	chr3.hg19:g.185146747C>T		80.0	0.0	.		94.0	27.0	.	NM_004721		Silent	SNP	ENST00000265026.3	hg19	CCDS3270.1																																																																																			.	.	.	none		0.493	MAP3K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345268.1	NM_004721		T	185146747	C	T	185146747	2	4	137	1	0	0	0	0	0	0	0	1	9254	697	25	2		2	MAP3K13	3	185146747	Silent	SNP	C	TCGA-BQ-7053-01A-11D-1961-08	29492545	185146747	12875683	8	8379											
WFS1	7466	hgsc.bcm.edu	37	chr4	6303094	6303094	+	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	atggcacagctgaggaatttCaagggcacctactgctacct	11	9	10	11	0	1	1	1	1	0	0	1	2	1	2	2	3	4	4	2	3	4	3			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr4:6303094C>T	ENST00000226760.1	+	8	1742	c.1572C>T	c.(1570-1572)ttC>ttT	p.F524F	WFS1_ENST00000503569.1_Silent_p.F524F	NM_001145853.1|NM_006005.3	NP_001139325.1|NP_005996.2	O76024	WFS1_HUMAN	Wolfram syndrome 1 (wolframin)	524					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|calcium ion homeostasis (GO:0055074)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glucose homeostasis (GO:0042593)|kidney development (GO:0001822)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of programmed cell death (GO:0043069)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurological system process (GO:0050877)|olfactory behavior (GO:0042048)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of growth (GO:0045927)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of proteolysis (GO:0045862)|protein maturation by protein folding (GO:0022417)|protein stabilization (GO:0050821)|renal water homeostasis (GO:0003091)|response to endoplasmic reticulum stress (GO:0034976)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	activating transcription factor binding (GO:0033613)|ATPase binding (GO:0051117)|transporter activity (GO:0005215)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	21				Colorectal(103;0.0512)		TGAGGAATTTCAAGGGCACCT	0.597																																					p.F524F		Atlas-SNP	.											.	WFS1	71	.	0			c.C1572T						PASS	.						119	105	109					4																	6303094		2203	4300	6503	SO:0001819	synonymous_variant	7466	exon8			GAATTTCAAGGGC	AF084481	CCDS3386.1	4p16.1	2014-06-18			ENSG00000109501	ENSG00000109501			12762	protein-coding gene	gene with protein product		606201		DFNA6, DFNA14, DFNA38		7987399, 9771706	Standard	NM_006005		Approved	DIDMOAD, WFS	uc003gix.3	O76024	OTTHUMG00000090431	ENST00000226760.1:c.1572C>T	chr4.hg19:g.6303094C>T		223.0	0.0	.		196.0	79.0	.	NM_001145853	B2R797|D3DVT1|Q8N6I3|Q9UNW6	Silent	SNP	ENST00000226760.1	hg19	CCDS3386.1																																																																																			.	.	.	none		0.597	WFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206863.1			T	6303094	C	T	6303094	2	4	137	1	0	0	0	0	0	0	0	1	17372	825	29	2		2	WFS1	4	6303094	Silent	SNP	C	TCGA-BQ-7053-01A-11D-1961-08		6303094	184851182	9	8380											
LRBA	987	hgsc.bcm.edu	37	chr4	151935707	151935707	+	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	tttcagagacaatgcaccccCttcagtaggggtttcttctc	8	13	8	12	0	4	1	2	0	2	1	5	2	4	1	2	2	1	3	2	2	2	5			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr4:151935707C>A	ENST00000357115.3	-	2	331	c.88G>T	c.(88-90)Ggg>Tgg	p.G30W	LRBA_ENST00000535741.1_Missense_Mutation_p.G30W|LRBA_ENST00000507224.1_Missense_Mutation_p.G30W|LRBA_ENST00000510413.1_Missense_Mutation_p.G30W	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	30						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)					AATGCACCCCCTTCAGTAGGG	0.537																																					p.G30W		Atlas-SNP	.											.	LRBA	253	.	0			c.G88T						PASS	.						63	53	56					4																	151935707		2203	4300	6503	SO:0001583	missense	987	exon2			CACCCCCTTCAGT	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.88G>T	chr4.hg19:g.151935707C>A	ENSP00000349629:p.Gly30Trp	47.0	0.0	.		60.0	23.0	.	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	hg19	CCDS3773.1	.	.	.	.	.	.	.	.	.	.	C	18.02	3.529711	0.64860	.	.	ENSG00000198589	ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224	T;T;T;T	0.56444	0.88;1.03;0.88;0.46	5.33	5.33	0.75918	.	1.239200	0.06405	U	0.719521	T	0.52386	0.1731	L	0.47716	1.5	0.37618	D	0.921196	P;P;P	0.49447	0.876;0.924;0.924	B;B;B	0.43360	0.219;0.417;0.391	T	0.50432	-0.8829	10	0.48119	T	0.1	.	11.3073	0.49342	0.0:0.9149:0.0:0.0851	.	30;30;30	P50851;Q6P1X2;P50851-2	LRBA_HUMAN;.;.	W	30	ENSP00000446299:G30W;ENSP00000421552:G30W;ENSP00000349629:G30W;ENSP00000422180:G30W	ENSP00000349629:G30W	G	-	1	0	LRBA	152155157	0.031000	0.19500	0.961000	0.40146	0.587000	0.36485	1.159000	0.31749	2.514000	0.84764	0.555000	0.69702	GGG	.	.	.	none		0.537	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			A	151935707	C	A	151935707	3	1	137	1	0	0	0	0	1	0	0	0	8938	681	24	4	8731	4	LRBA	4	151935707	Missense_Mutation	SNP	C	TCGA-BQ-7053-01A-11D-1961-08	145632613	151935707	39218569	10	8381											
TRIM2	23321	hgsc.bcm.edu	37	chr4	154237027	154237027	+	Frame_Shift_Del	DEL	G	G	-																															caaaagtcgttttggcatacGgggacgctctccggggcagc																										TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr4:154237027delG	ENST00000437508.2	+	8	1778	c.1577delG	c.(1576-1578)cggfs	p.R526fs	TRIM2_ENST00000338700.5_Frame_Shift_Del_p.R553fs	NM_001130067.1	NP_001123539.1	Q9C040	TRIM2_HUMAN	tripartite motif containing 2	526					cell death (GO:0008219)|regulation of neuron apoptotic process (GO:0043523)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)	19	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)		TTTGGCATACGGGGACGCTCT	0.463																																					p.R553fs		Atlas-INDEL	.											.	TRIM2	105	.	0			c.1657delC						PASS	.						80	90	87					4																	154237027		2203	4300	6503	SO:0001589	frameshift_variant	23321	exon8			.	AF220018	CCDS3781.2, CCDS47147.1	4q31.3	2013-01-09	2011-01-25		ENSG00000109654	ENSG00000109654		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	15974	protein-coding gene	gene with protein product		614141	"tripartite motif-containing 2"			9628581, 11331580	Standard	NM_015271		Approved	KIAA0517, RNF86	uc003inh.2	Q9C040	OTTHUMG00000155991	ENST00000437508.2:c.1577delG	chr4.hg19:g.154237027delG	ENSP00000415812:p.Arg526fs	162.0	0.0	0		136.0	52.0	0.382353	NM_015271	D3DP09|O60272|Q9BSI9|Q9UFZ1	Frame_Shift_Del	DEL	ENST00000437508.2	hg19	CCDS47147.1																																																																																			.	.	.	none		0.463	TRIM2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342652.1			-	154237027	G	-	154237027	7	5	137	1	0	1	0	1	0	0	0	0	16506	1116	39	0	1688	0	TRIM2	4	154237027	Frame_Shift_Del	DEL	G	TCGA-BQ-7053-01A-11D-1961-08	2301320	154237027	36917249	11	8382											
EGFLAM	133584	hgsc.bcm.edu	37	chr5	38407020	38407020	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctaacccaaagaccatttctAggctcatcccccctacctca	11	9	3	18	0	3	1	2	0	1	1	4	1	4	1	6	1	2	1	6	1	4	4			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr5:38407020A>G	ENST00000354891.3	+	8	1265	c.919A>G	c.(919-921)Agg>Ggg	p.R307G	EGFLAM_ENST00000397202.2_Intron|EGFLAM_ENST00000336740.6_Missense_Mutation_p.R73G|EGFLAM_ENST00000322350.5_Missense_Mutation_p.R307G	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	307					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)					GACCATTTCTAGGCTCATCCC	0.483																																					p.R307G	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.A919G						PASS	.						155	147	149					5																	38407020		2203	4300	6503	SO:0001583	missense	133584	exon8			ATTTCTAGGCTCA	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.919A>G	chr5.hg19:g.38407020A>G	ENSP00000346964:p.Arg307Gly	101.0	0.0	.		99.0	4.0	.	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Missense_Mutation	SNP	ENST00000354891.3	hg19	CCDS56363.1	.	.	.	.	.	.	.	.	.	.	A	11.67	1.706602	0.30232	.	.	ENSG00000164318	ENST00000354891;ENST00000322350;ENST00000336740;ENST00000339580	T;T;T	0.80123	0.77;0.6;-1.34	5.69	1.96	0.26148	.	0.293605	0.35320	N	0.003289	T	0.70263	0.3204	M	0.72118	2.19	0.09310	N	1	B;P;P	0.40834	0.196;0.611;0.73	B;B;B	0.32980	0.067;0.075;0.156	T	0.64833	-0.6314	10	0.52906	T	0.07	-20.3281	2.0497	0.03568	0.416:0.32:0.1499:0.114	.	73;307;307	Q63HQ2-4;Q63HQ2;Q63HQ2-2	.;EGFLA_HUMAN;.	G	307;307;73;73	ENSP00000346964:R307G;ENSP00000313084:R307G;ENSP00000337607:R73G	ENSP00000313084:R307G	R	+	1	2	EGFLAM	38442777	0.487000	0.25988	0.030000	0.17652	0.190000	0.23558	1.133000	0.31430	0.102000	0.17638	-0.256000	0.11100	AGG	.	.	.	none		0.483	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403		G	38407020	A	G	38407020	3	3	137	1	0	0	0	0	1	0	0	0	4968	411	15	3	963	3	EGFLAM	5	38407020	Missense_Mutation	SNP	A	TCGA-BQ-7053-01A-11D-1961-08		38407020	142508240	12	8383											
XRCC4	7518	hgsc.bcm.edu	37	chr5	82406899	82406899	+	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	gacatggcaatggaaaaaggGaaatatgttggtgaactgag	16	8	14	3	0	0	2	0	2	0	0	0	5	0	4	0	4	1	2	0	4	6	2			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr5:82406899G>T	ENST00000511817.1	+	3	272	c.192G>T	c.(190-192)ggG>ggT	p.G64G	XRCC4_ENST00000509268.1_3'UTR|XRCC4_ENST00000396027.4_Silent_p.G64G|XRCC4_ENST00000282268.3_Silent_p.G64G|XRCC4_ENST00000338635.6_Silent_p.G64G			Q13426	XRCC4_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 4	64					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)		TGGAAAAAGGGAAATATGTTG	0.338								Non-homologous end-joining																													p.G64G		Atlas-SNP	.											.	XRCC4	37	.	0			c.G192T						PASS	.						98	95	96					5																	82406899		2203	4300	6503	SO:0001819	synonymous_variant	7518	exon3			AAAAGGGAAATAT	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.192G>T	chr5.hg19:g.82406899G>T		65.0	0.0	.		53.0	22.0	.	NM_003401	A8K3X4|Q9BS72|Q9UP94	Silent	SNP	ENST00000511817.1	hg19	CCDS4059.1																																																																																			.	.	.	none		0.338	XRCC4-003	NOVEL	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369624.1	NM_022550		T	82406899	G	T	82406899	2	4	137	1	0	0	0	0	0	0	0	1	17467	1161	41	4		4	XRCC4	5	82406899	Silent	SNP	G	TCGA-BQ-7053-01A-11D-1961-08	43999879	82406899	98508361	13	8384											
ERAP1	51752	hgsc.bcm.edu	37	chr5	96139212	96139212	+	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	tgtgtacgggagcccgacaaGgaggggctcgggagccagca	9	4	18	10	3	0	0	0	0	0	0	1	4	0	3	2	5	4	3	2	5	2	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr5:96139212G>A	ENST00000443439.2	-	2	484	c.418C>T	c.(418-420)Ctt>Ttt	p.L140F	ERAP1_ENST00000296754.3_Missense_Mutation_p.L140F|CTD-2260A17.3_ENST00000606656.1_RNA|CTD-2260A17.3_ENST00000606346.1_RNA	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	140					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)		AGCCCGACAAGGAGGGGCTCG	0.557																																					p.L140F		Atlas-SNP	.											.	ERAP1	59	.	0			c.C418T						PASS	.						63	70	68					5																	96139212		2203	4300	6503	SO:0001583	missense	51752	exon2			CGACAAGGAGGGG	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.418C>T	chr5.hg19:g.96139212G>A	ENSP00000406304:p.Leu140Phe	107.0	0.0	.		101.0	40.0	.	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Missense_Mutation	SNP	ENST00000443439.2	hg19	CCDS47250.1	.	.	.	.	.	.	.	.	.	.	G	4.542	0.100606	0.08731	.	.	ENSG00000164307	ENST00000296754;ENST00000443439;ENST00000414384	T;T	0.02763	4.17;4.17	5.51	2.68	0.31781	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.757856	0.12763	N	0.441158	T	0.03564	0.0102	L	0.52011	1.625	0.09310	N	1	B;B	0.15719	0.014;0.004	B;B	0.23852	0.049;0.019	T	0.48456	-0.9034	10	0.11182	T	0.66	.	9.253	0.37566	0.0:0.2989:0.4675:0.2337	.	140;140	Q9NZ08;Q9NZ08-2	ERAP1_HUMAN;.	F	140	ENSP00000296754:L140F;ENSP00000406304:L140F	ENSP00000296754:L140F	L	-	1	0	ERAP1	96164968	0.156000	0.22821	0.002000	0.10522	0.010000	0.07245	0.894000	0.28350	0.243000	0.21327	0.561000	0.74099	CTT	.	.	.	none		0.557	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442		A	96139212	G	A	96139212	3	1	137	1	0	0	0	0	1	0	0	0	5205	1000	35	2	2512	2	ERAP1	5	96139212	Missense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08	13732313	96139212	84776048	14	8385											
LY6G6F	259215	hgsc.bcm.edu	37	chr6	31677862	31677862	+	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	cgggctgggacatgccttggAttctgatgctgctgctcaca	6	11	13	11	1	2	1	1	1	1	0	2	3	2	3	1	3	4	4	1	3	0	2			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr6:31677862A>T	ENST00000375832.4	+	4	728	c.706A>T	c.(706-708)Att>Ttt	p.I236F	LY6G6F_ENST00000556581.1_Missense_Mutation_p.I236F|MEGT1_ENST00000503322.1_Missense_Mutation_p.I236F|XXbac-BPG32J3.20_ENST00000461287.1_Intron	NM_001003693.1	NP_001003693.1	Q5SQ64	LY66F_HUMAN	lymphocyte antigen 6 complex, locus G6F	236						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						CATGCCTTGGATTCTGATGCT	0.617																																					p.I236F		Atlas-SNP	.											.	LY6G6F	23	.	0			c.A706T						PASS	.						93	67	76					6																	31677862		1511	2708	4219	SO:0001583	missense	259215	exon4			CCTTGGATTCTGA		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.706A>T	chr6.hg19:g.31677862A>T	ENSP00000364992:p.Ile236Phe	71.0	0.0	.		54.0	17.0	.	NM_001003693	B0UXB7|O95869|Q7Z5H2|Q96QC7|Q9NZJ1	Missense_Mutation	SNP	ENST00000375832.4	hg19	CCDS34403.1	.	.	.	.	.	.	.	.	.	.	A	12.70	2.015117	0.35511	.	.	ENSG00000204424;ENSG00000204424;ENSG00000250641	ENST00000556581;ENST00000375832;ENST00000503322	T;T;T	0.26957	1.99;1.7;1.99	5.25	4.09	0.47781	.	0.098536	0.44688	D	0.000436	T	0.20981	0.0505	M	0.66939	2.045	0.32179	N	0.580661	D;P	0.54047	0.964;0.906	P;P	0.51101	0.659;0.546	T	0.12319	-1.0552	10	0.87932	D	0	-13.2059	7.687	0.28546	0.9038:0.0:0.0962:0.0	.	236;236	Q9NZJ1;Q5SQ64	.;LY66F_HUMAN	F	236	ENSP00000452432:I236F;ENSP00000364992:I236F;ENSP00000421232:I236F	ENSP00000364992:I236F	I	+	1	0	XXbac-BPG32J3.19;LY6G6F	31785841	1.000000	0.71417	1.000000	0.80357	0.262000	0.26303	1.214000	0.32419	0.844000	0.35094	0.477000	0.44152	ATT	.	.	.	none		0.617	LY6G6F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076532.2	NM_001003693		T	31677862	A	T	31677862	3	4	137	1	0	0	0	0	1	0	0	0	9103	333	12	5	720	5	LY6G6F	6	31677862	Missense_Mutation	SNP	A	TCGA-BQ-7053-01A-11D-1961-08		31677862	139437205	15	8386											
GSTA2	2939	hgsc.bcm.edu	37	chr6	52617715	52617715	+	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	atcaaggcaagcttggcatcTtgttcctcaggttgactaaa	11	12	9	9	0	3	1	2	1	1	0	4	1	4	1	1	3	1	5	1	3	4	5	rs200252041		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr6:52617715T>A	ENST00000493422.1	-	5	506	c.351A>T	c.(349-351)caA>caT	p.Q117H		NM_000846.4	NP_000837.3	P09210	GSTA2_HUMAN	glutathione S-transferase alpha 2	117	GST C-terminal.				epithelial cell differentiation (GO:0030855)|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)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Lung NSC(77;0.118)				Azathioprine(DB00993)|Busulfan(DB01008)|Chloroquine(DB00608)|Clofibrate(DB00636)|Ethacrynic acid(DB00903)|Glutathione(DB00143)|Vitamin E(DB00163)	GCTTGGCATCTTGTTCCTCAG	0.393																																					p.Q117H		Atlas-SNP	.											.	GSTA2	33	.	0			c.A351T						PASS	.						240	229	233					6																	52617715		2203	4300	6503	SO:0001583	missense	2939	exon5			GGCATCTTGTTCC	AL109918	CCDS4944.1	6p12.2	2012-06-21	2008-11-26		ENSG00000244067	ENSG00000244067	2.5.1.18	"Glutathione S-transferases / Soluble"	4627	protein-coding gene	gene with protein product		138360	"glutathione S-transferase A2"	GST2			Standard	NM_000846		Approved		uc003pay.3	P09210	OTTHUMG00000016263	ENST00000493422.1:c.351A>T	chr6.hg19:g.52617715T>A	ENSP00000420168:p.Gln117His	329.0	0.0	.		366.0	132.0	.	NM_000846	Q12759|Q16491|Q9NTY6	Missense_Mutation	SNP	ENST00000493422.1	hg19	CCDS4944.1	.	.	.	.	.	.	.	.	.	.	t	10.44	1.349542	0.24426	.	.	ENSG00000244067	ENST00000493422	T	0.02067	4.47	2.26	2.26	0.28386	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.539313	0.17882	N	0.158839	T	0.01092	0.0036	L	0.31926	0.97	0.09310	N	1	B	0.28233	0.204	B	0.38056	0.264	T	0.45775	-0.9238	10	0.87932	D	0	.	8.464	0.32944	0.0:0.0:0.0:1.0	.	117	P09210	GSTA2_HUMAN	H	117	ENSP00000420168:Q117H	ENSP00000420168:Q117H	Q	-	3	2	GSTA2	52725674	0.000000	0.05858	0.030000	0.17652	0.008000	0.06430	-0.493000	0.06459	1.310000	0.45006	0.254000	0.18369	CAA	.	T|1.000;C|0.000	.	alt		0.393	GSTA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043589.1	NM_000846		A	52617715	T	A	52617715	3	1	137	1	0	0	0	0	1	0	0	0	6838	1606	56	5	329	5	GSTA2	6	52617715	Missense_Mutation	SNP	T	TCGA-BQ-7053-01A-11D-1961-08	20939853	52617715	118497352	16	8387											
TMEM30A	55754	hgsc.bcm.edu	37	chr6	75975041	75975042	+	Frame_Shift_Del	DEL	AT	AT	-																															aattagacagtccataatacAtaaacacgttgccctagaga																										TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr6:75975041_75975042delAT	ENST00000230461.6	-	3	687_688	c.358_359delAT	c.(358-360)atgfs	p.M120fs	TMEM30A_ENST00000370050.5_Start_Codon_Del|TMEM30A_ENST00000475111.2_Frame_Shift_Del_p.M84fs	NM_018247.3	NP_060717.1	Q9NV96	CC50A_HUMAN	transmembrane protein 30A	120					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						TCCATAATACATAAACACGTTG	0.327																																					p.120_120del		Atlas-INDEL	.											.	TMEM30A	40	.	0			c.359_360del						PASS	.																																			SO:0001589	frameshift_variant	55754	exon3			.	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.358_359delAT	chr6.hg19:g.75975041_75975042delAT	ENSP00000230461:p.Met120fs	39.0	0.0	0		35.0	14.0	0.4	NM_018247	A8K9V8|E1P539|Q658Z3|Q96H09|Q9NSL9	Frame_Shift_Del	DEL	ENST00000230461.6	hg19	CCDS4983.1																																																																																			.	.	.	none		0.327	TMEM30A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041248.2	NM_018247		-	75975042	AT	-	75975041	7	5	137	1	0	1	0	1	0	0	0	0	16165	217	8	0	746	0	TMEM30A	6	75975041	Frame_Shift_Del	DEL	AT	TCGA-BQ-7053-01A-11D-1961-08	23357326	75975041	95140026	17	8388											
SOBP	55084	hgsc.bcm.edu	37	chr6	107955224	107955224	+	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	gtgatgaccaaccgcggcccGgtgccgctgcccatcttcat	6	8	11	16	4	2	2	1	2	1	0	2	2	2	2	5	2	3	1	5	2	1	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr6:107955224G>T	ENST00000317357.5	+	6	1835	c.1176G>T	c.(1174-1176)ccG>ccT	p.P392P		NM_018013.3	NP_060483.3			sine oculis binding protein homolog (Drosophila)											endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	26		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)		ACCGCGGCCCGGTGCCGCTGC	0.672																																					p.P392P		Atlas-SNP	.											.	SOBP	53	.	0			c.G1176T						PASS	.						63	70	68					6																	107955224		2018	4170	6188	SO:0001819	synonymous_variant	55084	exon6			CGGCCCGGTGCCG	AK001021	CCDS43488.1	6q21	2007-03-15			ENSG00000112320	ENSG00000112320			29256	protein-coding gene	gene with protein product		613667					Standard	NM_018013		Approved	FLJ10159	uc003prx.3	A7XYQ1	OTTHUMG00000015312	ENST00000317357.5:c.1176G>T	chr6.hg19:g.107955224G>T		148.0	0.0	.		141.0	6.0	.	NM_018013		Silent	SNP	ENST00000317357.5	hg19	CCDS43488.1																																																																																			.	.	.	none		0.672	SOBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041693.2	NM_018013		T	107955224	G	T	107955224	2	4	137	1	0	0	0	0	0	0	0	1	14925	1103	39	4		4	SOBP	6	107955224	Silent	SNP	G	TCGA-BQ-7053-01A-11D-1961-08	31980183	107955224	63159843	18	8389											
CPVL	54504	hgsc.bcm.edu	37	chr7	29135764	29135764	+	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	aggcccatgttccacaaagaGtccaaacatggatgaacctc	14	7	8	12	0	0	2	0	1	0	1	3	3	2	3	4	2	2	1	4	2	3	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr7:29135764G>T	ENST00000409850.1	-	8	1004	c.358C>A	c.(358-360)Ctc>Atc	p.L120I	CPVL_ENST00000488891.2_5'UTR|CPVL_ENST00000396276.3_Missense_Mutation_p.L120I|CPVL_ENST00000265394.5_Missense_Mutation_p.L120I			Q9H3G5	CPVL_HUMAN	carboxypeptidase, vitellogenic-like	120						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						TCCACAAAGAGTCCAAACATG	0.468																																					p.L120I		Atlas-SNP	.											.	CPVL	60	.	0			c.C358A						PASS	.						177	165	169					7																	29135764		2203	4300	6503	SO:0001583	missense	54504	exon4			CAAAGAGTCCAAA	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.358C>A	chr7.hg19:g.29135764G>T	ENSP00000387164:p.Leu120Ile	216.0	0.0	.		218.0	71.0	.	NM_019029	A4D1A4|Q6UX20|Q8NBL7|Q96AR7|Q9HB41	Missense_Mutation	SNP	ENST00000409850.1	hg19	CCDS5419.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.911407	0.92178	.	.	ENSG00000106066	ENST00000265394;ENST00000396276;ENST00000409850;ENST00000542995;ENST00000448959;ENST00000458405;ENST00000447426	D;D;D;D;D;D	0.87571	-2.27;-2.27;-2.27;-2.27;-2.27;-2.27	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	D	0.93789	0.8014	M	0.85777	2.775	0.80722	D	1	D	0.69078	0.997	D	0.65573	0.936	D	0.93612	0.6940	10	0.46703	T	0.11	-0.6878	18.7662	0.91874	0.0:0.0:1.0:0.0	.	120	Q9H3G5	CPVL_HUMAN	I	120;120;120;4;50;4;50	ENSP00000265394:L120I;ENSP00000379572:L120I;ENSP00000387164:L120I;ENSP00000409036:L50I;ENSP00000417015:L4I;ENSP00000395690:L50I	ENSP00000265394:L120I	L	-	1	0	CPVL	29102289	1.000000	0.71417	0.998000	0.56505	0.918000	0.54935	6.732000	0.74790	2.519000	0.84933	0.491000	0.48974	CTC	.	.	.	none		0.468	CPVL-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328305.1	NM_019029		T	29135764	G	T	29135764	3	4	137	1	0	0	0	0	1	0	0	0	3837	1029	36	4	1112	4	CPVL	7	29135764	Missense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08		29135764	130002899	19	8390											
EIF3E	3646	hgsc.bcm.edu	37	chr8	109215296	109215296	+	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	gaaaggcttttggtcttttcAatcacttgctgatagggtga	9	15	11	6	0	3	2	2	2	1	0	3	3	3	2	0	3	1	2	0	3	3	6			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr8:109215296A>T	ENST00000220849.5	-	12	1277	c.1215T>A	c.(1213-1215)atT>atA	p.I405I	EIF3E_ENST00000519517.1_5'Flank|EIF3E_ENST00000519030.1_Silent_p.I312I	NM_001568.2	NP_001559.1			eukaryotic translation initiation factor 3, subunit E										EIF3E/RSPO2(6)	NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(57;6.84e-10)			TGGTCTTTTCAATCACTTGCT	0.393																																					p.I405I	GBM(15;360 410 8460 34179 52246)	Atlas-SNP	.											.	EIF3E	73	.	0			c.T1215A						PASS	.						157	141	147					8																	109215296		2203	4297	6500	SO:0001819	synonymous_variant	3646	exon12			CTTTTCAATCACT	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.1215T>A	chr8.hg19:g.109215296A>T		88.0	0.0	.		112.0	41.0	.	NM_001568		Silent	SNP	ENST00000220849.5	hg19	CCDS6308.1	.	.	.	.	.	.	.	.	.	.	A	10.72	1.431022	0.25726	.	.	ENSG00000104408	ENST00000522352	.	.	.	5.7	3.26	0.37387	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-23.5683	7.9818	0.30188	0.8114:0.0:0.0671:0.1214	.	.	.	.	R	116	.	.	X	-	1	0	EIF3E	109284472	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.959000	0.40412	0.964000	0.38108	0.477000	0.44152	TGA	.	.	.	none		0.393	EIF3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380612.2	NM_001568		T	109215296	A	T	109215296	2	4	137	1	0	0	0	0	0	0	0	1	5017	126	5	5		5	EIF3E	8	109215296	Silent	SNP	A	TCGA-BQ-7053-01A-11D-1961-08		109215296	37148726	20	8391											
CNTNAP3	79937	hgsc.bcm.edu	37	chr9	39140600	39140600	+	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	aagcccagacgggttccctcGgtgcttgtgggcttcacaag	7	9	13	12	2	1	1	1	0	0	1	3	1	2	1	2	3	2	3	2	3	2	3			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr9:39140600G>A	ENST00000297668.6	-	12	1865	c.1792C>T	c.(1792-1794)Cga>Tga	p.R598*	CNTNAP3_ENST00000377659.1_Nonsense_Mutation_p.R598*|CNTNAP3_ENST00000377656.2_Nonsense_Mutation_p.R598*|CNTNAP3_ENST00000358144.2_Nonsense_Mutation_p.R510*|CNTNAP3_ENST00000323947.7_Nonsense_Mutation_p.R505*	NM_033655.3	NP_387504.2	Q9BZ76	CNTP3_HUMAN	contactin associated protein-like 3	598	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				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)		GGGTTCCCTCGGTGCTTGTGG	0.468																																					p.R598X		Atlas-SNP	.											.	CNTNAP3	82	.	0			c.C1792T						PASS	.						38	44	42					9																	39140600		2203	4300	6503	SO:0001587	stop_gained	79937	exon12			TCCCTCGGTGCTT	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.1792C>T	chr9.hg19:g.39140600G>A	ENSP00000297668:p.Arg598*	107.0	0.0	.		98.0	32.0	.	NM_033655	B1AMA0|Q9C0E9	Nonsense_Mutation	SNP	ENST00000297668.6	hg19	CCDS6616.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.384365	0.82792	.	.	ENSG00000106714	ENST00000297668;ENST00000377656;ENST00000358144;ENST00000323947;ENST00000377659	.	.	.	2.85	1.69	0.24217	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	.	7.9696	0.30119	0.0:0.0:0.2419:0.7581	.	.	.	.	X	598;598;510;505;598	.	ENSP00000297668:R598X	R	-	1	2	CNTNAP3	39130600	0.593000	0.26840	0.377000	0.26055	0.034000	0.12701	0.720000	0.25896	0.328000	0.23435	0.440000	0.28878	CGA	.	.	.	none		0.468	CNTNAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052511.1	NM_033655		A	39140600	G	A	39140600	4	1	137	1	0	0	0	0	0	1	0	0	3650	1124	39	1	2126	1	CNTNAP3	9	39140600	Nonsense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08		39140600	102072831	21	8392											
INVS	27130	hgsc.bcm.edu	37	chr9	103059359	103059359	+	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	ccactgcagtaagcaaggccCccaagagtccatccaagggc	12	4	10	15	0	0	1	0	0	0	1	2	1	2	1	5	2	2	3	5	2	4	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr9:103059359C>A	ENST00000262457.2	+	15	3132	c.2947C>A	c.(2947-2949)Ccc>Acc	p.P983T	INVS_ENST00000541287.1_Missense_Mutation_p.P887T|INVS_ENST00000262456.2_Missense_Mutation_p.P813T	NM_014425.3	NP_055240.2	Q9Y283	INVS_HUMAN	inversin	983					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)				AAGCAAGGCCCCCAAGAGTCC	0.498																																					p.P983T		Atlas-SNP	.											.	INVS	81	.	0			c.C2947A						PASS	.						89	83	85					9																	103059359		2203	4300	6503	SO:0001583	missense	27130	exon15			AAGGCCCCCAAGA	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.2947C>A	chr9.hg19:g.103059359C>A	ENSP00000262457:p.Pro983Thr	50.0	0.0	.		53.0	31.0	.	NM_014425	A2A2Y2|Q2NKL0|Q5W0T6|Q8IVX8|Q9BRB9|Q9Y488|Q9Y498	Missense_Mutation	SNP	ENST00000262457.2	hg19	CCDS6746.1	.	.	.	.	.	.	.	.	.	.	C	0.007	-1.983872	0.00443	.	.	ENSG00000119509	ENST00000262457;ENST00000541287;ENST00000262456	T;T;T	0.38722	1.15;1.15;1.12	5.25	-0.716	0.11212	.	0.687064	0.14809	N	0.297151	T	0.16854	0.0405	N	0.04508	-0.205	0.09310	N	1	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.11329	0.006;0.001;0.0	T	0.13899	-1.0492	10	0.56958	D	0.05	.	3.4624	0.07537	0.1837:0.4859:0.231:0.0995	.	887;983;813	F5GZH2;Q9Y283;Q9Y283-2	.;INVS_HUMAN;.	T	983;887;813	ENSP00000262457:P983T;ENSP00000444454:P887T;ENSP00000262456:P813T	ENSP00000262456:P813T	P	+	1	0	INVS	102099180	0.023000	0.18921	0.222000	0.23844	0.317000	0.28152	0.424000	0.21330	0.160000	0.19432	0.650000	0.86243	CCC	.	.	.	none		0.498	INVS-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053407.1	NM_014425		A	103059359	C	A	103059359	3	1	137	1	0	0	0	0	1	0	0	0	7794	623	22	4	3001	4	INVS	9	103059359	Missense_Mutation	SNP	C	TCGA-BQ-7053-01A-11D-1961-08	63918759	103059359	38154072	22	8393											
PRKG1	5592	hgsc.bcm.edu	37	chr10	53227571	53227571	+	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	gaattggctattctttacaaCtgtacccggacagcgaccgt	10	11	9	11	3	1	0	0	0	1	0	1	3	1	1	2	2	4	2	2	2	5	6			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr10:53227571C>G	ENST00000401604.2	+	3	716	c.522C>G	c.(520-522)aaC>aaG	p.N174K	PRKG1_ENST00000373985.1_Missense_Mutation_p.N162K|PRKG1_ENST00000373980.4_Missense_Mutation_p.N189K			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	174	cGMP-binding, high affinity.				actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		TTCTTTACAACTGTACCCGGA	0.383																																					p.N189K		Atlas-SNP	.											.	PRKG1	167	.	0			c.C567G						PASS	.						154	141	145					10																	53227571		2203	4300	6503	SO:0001583	missense	5592	exon3			TTACAACTGTACC		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.522C>G	chr10.hg19:g.53227571C>G	ENSP00000384200:p.Asn174Lys	94.0	0.0	.		119.0	40.0	.	NM_006258	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Missense_Mutation	SNP	ENST00000401604.2	hg19	CCDS44399.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.475767	0.84640	.	.	ENSG00000185532	ENST00000401604;ENST00000373985;ENST00000373980;ENST00000373976	D;D;D;D	0.96940	-4.18;-4.18;-1.92;-1.92	5.79	4.89	0.63831	Cyclic nucleotide-binding, conserved site (1);Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.115539	0.56097	D	0.000027	D	0.97983	0.9336	M	0.85462	2.755	0.80722	D	1	D;D;D	0.89917	0.983;1.0;0.998	P;D;D	0.75484	0.82;0.985;0.986	D	0.98576	1.0648	10	0.87932	D	0	-19.8616	12.5809	0.56390	0.0:0.9197:0.0:0.0803	.	174;189;174	B4DT93;Q13976-2;Q13976	.;.;KGP1_HUMAN	K	174;162;189;47	ENSP00000384200:N174K;ENSP00000363097:N162K;ENSP00000363092:N189K;ENSP00000363087:N47K	ENSP00000363087:N47K	N	+	3	2	PRKG1	52897577	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.118000	0.31246	1.450000	0.47717	0.563000	0.77884	AAC	.	.	.	none		0.383	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	53227571	C	G	53227571	3	3	137	1	0	0	0	0	1	0	0	0	12532	564	20	4	847	4	PRKG1	10	53227571	Missense_Mutation	SNP	C	TCGA-BQ-7053-01A-11D-1961-08		53227571	82307176	23	8394											
CDH23	64072	hgsc.bcm.edu	37	chr10	73406335	73406335	+	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	ctgtacaacatcagcctgtaCgagaacgtcaccgtggggac	11	7	11	12	3	2	1	2	0	0	1	2	3	2	2	2	2	5	2	2	2	4	2	rs549569431	byFrequency	TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr10:73406335C>T	ENST00000224721.6	+	13	1430	c.1425C>T	c.(1423-1425)taC>taT	p.Y475Y	CDH23_ENST00000299366.7_Silent_p.Y515Y|CDH23_ENST00000398809.4_Silent_p.Y470Y|CDH23_ENST00000398842.3_Silent_p.Y470Y|CDH23_ENST00000461841.3_Silent_p.Y515Y	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	470	Cadherin 5. {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						TCAGCCTGTACGAGAACGTCA	0.577													C|||	2	0.000399361	0	0	5008	,	,		19433	0		0	False		,,,				2504	0.002				p.Y470Y		Atlas-SNP	.											.	CDH23	365	.	0			c.C1410T						PASS	.						160	169	166					10																	73406335		2132	4248	6380	SO:0001819	synonymous_variant	64072	exon13			CCTGTACGAGAAC	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.1425C>T	chr10.hg19:g.73406335C>T		235.0	0.0	.		219.0	64.0	.	NM_052836	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	hg19																																																																																				.	.	.	none		0.577	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		T	73406335	C	T	73406335	2	4	137	1	0	0	0	0	0	0	0	1	3110	547	19	1		1	CDH23	10	73406335	Silent	SNP	C	TCGA-BQ-7053-01A-11D-1961-08	20178764	73406335	62128412	24	8395											
HNRNPUL2	221092	hgsc.bcm.edu	37	chr11	62491826	62491826	+	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	catgttcatccttctcatccCgctgtctctttaccccccgc	4	14	4	19	2	3	0	2	0	2	0	7	0	5	0	5	0	1	2	5	0	1	4	rs577159200		TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr11:62491826C>A	ENST00000301785.5	-	2	803	c.611G>T	c.(610-612)cGg>cTg	p.R204L	HNRNPUL2-BSCL2_ENST00000403734.2_Missense_Mutation_p.R204L	NM_001079559.2	NP_001073027.1	Q1KMD3	HNRL2_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 2	204	Glu-rich. {ECO:0000255}.					membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						CTTCTCATCCCGCTGTCTCTT	0.512																																					p.R204L		Atlas-SNP	.											.	HNRNPUL2	41	.	0			c.G611T						PASS	.						132	133	133					11																	62491826		1970	4165	6135	SO:0001583	missense	221092	exon2			TCATCCCGCTGTC		CCDS41659.1	11q12	2013-07-16		2008-04-18	ENSG00000214753	ENSG00000214753			25451	protein-coding gene	gene with protein product				HNRPUL2			Standard	NM_001079559		Approved	DKFZp762N1910	uc001nuw.3	Q1KMD3	OTTHUMG00000167773	ENST00000301785.5:c.611G>T	chr11.hg19:g.62491826C>A	ENSP00000301785:p.Arg204Leu	175.0	0.0	.		177.0	12.0	.	NM_001079559	Q8N3B3	Missense_Mutation	SNP	ENST00000301785.5	hg19	CCDS41659.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.454369	0.84209	.	.	ENSG00000214753	ENST00000301785	T	0.65178	-0.14	4.9	4.9	0.64082	.	0.423150	0.24037	N	0.042138	T	0.68686	0.3028	L	0.36672	1.1	0.45284	D	0.998283	D	0.60160	0.987	D	0.65010	0.931	T	0.70974	-0.4726	10	0.72032	D	0.01	-11.7379	13.4322	0.61062	0.0:1.0:0.0:0.0	.	204	Q1KMD3	HNRL2_HUMAN	L	204	ENSP00000301785:R204L	ENSP00000301785:R204L	R	-	2	0	HNRNPUL2	62248402	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	6.879000	0.75572	2.547000	0.85894	0.655000	0.94253	CGG	.	.	.	none		0.512	HNRNPUL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396208.2	XM_495877		A	62491826	C	A	62491826	3	1	137	1	0	0	0	0	1	0	0	0	7282	652	23	4	1684	4	HNRNPUL2	11	62491826	Missense_Mutation	SNP	C	TCGA-BQ-7053-01A-11D-1961-08		62491826	72514690	25	8396											
PC	5091	hgsc.bcm.edu	37	chr11	66636376	66636376	+	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	cgggagttgacctcgatgaaGtagtgcttgccgtgcctgtc	6	11	14	10	3	0	2	0	2	0	0	2	4	0	3	3	1	3	3	3	1	2	3			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr11:66636376G>T	ENST00000393958.2	-	9	1056	c.963C>A	c.(961-963)taC>taA	p.Y321*	PC_ENST00000393955.2_Nonsense_Mutation_p.Y321*|PC_ENST00000524491.1_Nonsense_Mutation_p.Y281*|PC_ENST00000355677.3_Nonsense_Mutation_p.Y321*|PC_ENST00000393960.1_Nonsense_Mutation_p.Y321*	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	321	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)	CCTCGATGAAGTAGTGCTTGC	0.677																																					p.Y321X		Atlas-SNP	.											.	PC	116	.	0			c.C963A						PASS	.						90	79	83					11																	66636376		2200	4295	6495	SO:0001587	stop_gained	5091	exon9			GATGAAGTAGTGC	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.963C>A	chr11.hg19:g.66636376G>T	ENSP00000377530:p.Tyr321*	94.0	0.0	.		123.0	38.0	.	NM_000920	B4DN00|Q16705	Nonsense_Mutation	SNP	ENST00000393958.2	hg19	CCDS8152.1	.	.	.	.	.	.	.	.	.	.	G	36	5.754004	0.96890	.	.	ENSG00000173599	ENST00000393955;ENST00000393958;ENST00000393960;ENST00000524491;ENST00000355677	.	.	.	4.65	2.37	0.29283	.	0.000000	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-22.0017	6.9367	0.24470	0.3253:0.0:0.6747:0.0	.	.	.	.	X	321;321;321;281;321	.	ENSP00000347900:Y321X	Y	-	3	2	PC	66392952	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.978000	0.49305	0.954000	0.37851	0.561000	0.74099	TAC	.	.	.	none		0.677	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716		T	66636376	G	T	66636376	4	4	137	1	0	0	0	0	0	1	0	0	11504	1024	36	4	2629	4	PC	11	66636376	Nonsense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08	4144550	66636376	68370140	26	8397											
MMP27	64066	hgsc.bcm.edu	37	chr11	102573542	102573542	+	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	tgagtgtcaccacccagaccCggaccaggaggaaaggcatg	12	4	13	12	1	1	2	1	1	0	1	1	5	1	5	4	4	0	1	4	4	1	0			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr11:102573542C>A	ENST00000260229.4	-	4	652	c.561G>T	c.(559-561)ccG>ccT	p.P187P		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	187					collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.P187P(2)		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)	CACCCAGACCCGGACCAGGAG	0.443																																					p.P187P		Atlas-SNP	.											MMP27,NS,carcinoma,0,2	MMP27	84	.	2	Substitution - coding silent(2)	lung(1)|central_nervous_system(1)	c.G561T						PASS	.						84	88	86					11																	102573542		2203	4299	6502	SO:0001819	synonymous_variant	64066	exon4			CAGACCCGGACCA	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.561G>T	chr11.hg19:g.102573542C>A		134.0	1.0	.		160.0	8.0	.	NM_022122	Q6UWK6	Silent	SNP	ENST00000260229.4	hg19	CCDS8319.1																																																																																			.	.	.	none		0.443	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122		A	102573542	C	A	102573542	2	1	137	1	0	0	0	0	0	0	0	1	9671	639	23	4		4	MMP27	11	102573542	Silent	SNP	C	TCGA-BQ-7053-01A-11D-1961-08	35937166	102573542	32432974	27	8398											
GNPTAB	79158	hgsc.bcm.edu	37	chr12	102147162	102147162	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatttaccattcctgcagcTcatgcatatgaaggaaacgg	13	10	9	9	1	1	1	1	1	0	0	2	3	2	2	2	2	5	3	2	2	5	4			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr12:102147162T>C	ENST00000299314.7	-	19	3852	c.3590A>G	c.(3589-3591)gAg>gGg	p.E1197G		NM_024312.4	NP_077288.2	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	1197					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						TTCCTGCAGCTCATGCATATG	0.383																																					p.E1197G		Atlas-SNP	.											.	GNPTAB	120	.	0			c.A3590G						PASS	.						126	114	118					12																	102147162		2203	4300	6503	SO:0001583	missense	79158	exon19			TGCAGCTCATGCA	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.3590A>G	chr12.hg19:g.102147162T>C	ENSP00000299314:p.Glu1197Gly	68.0	0.0	.		77.0	28.0	.	NM_024312	A2RRQ9|Q3ZQK2|Q6IPW5|Q86TQ2|Q96N13|Q9ULL2	Missense_Mutation	SNP	ENST00000299314.7	hg19	CCDS9088.1	.	.	.	.	.	.	.	.	.	.	T	17.85	3.490528	0.64074	.	.	ENSG00000111670	ENST00000299314	D	0.83163	-1.69	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.89196	0.6646	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.88424	0.3030	10	0.39692	T	0.17	-26.24	15.9351	0.79698	0.0:0.0:0.0:1.0	.	1197	Q3T906	GNPTA_HUMAN	G	1197	ENSP00000299314:E1197G	ENSP00000299314:E1197G	E	-	2	0	GNPTAB	100671293	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.694000	0.84235	2.167000	0.68274	0.482000	0.46254	GAG	.	.	.	none		0.383	GNPTAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409182.1			C	102147162	T	C	102147162	3	2	137	1	0	0	0	0	1	0	0	0	6552	1551	54	3	192	3	GNPTAB	12	102147162	Missense_Mutation	SNP	T	TCGA-BQ-7053-01A-11D-1961-08		102147162	31704733	28	8399											
RASAL1	8437	hgsc.bcm.edu	37	chr12	113565934	113565934	+	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	atccagaggcaggtgcaccgTgtactcctccccccagaagg	9	6	11	15	1	0	2	0	0	0	2	3	2	3	2	6	3	2	3	6	3	2	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr12:113565934T>A	ENST00000261729.5	-	4	487	c.172A>T	c.(172-174)Acg>Tcg	p.T58S	RASAL1_ENST00000418411.2_5'UTR|RASAL1_ENST00000548055.1_Missense_Mutation_p.T58S|RASAL1_ENST00000446861.3_Missense_Mutation_p.T58S|RASAL1_ENST00000546530.1_Missense_Mutation_p.T58S			O95294	RASL1_HUMAN	RAS protein activator like 1 (GAP1 like)	58	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.		T -> M (in dbSNP:rs34598602). {ECO:0000269|PubMed:15489334}.		intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|phospholipid binding (GO:0005543)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(3)|prostate(2)|skin(2)	43						AGGTGCACCGTGTACTCCTCC	0.617																																					p.T58S		Atlas-SNP	.											.	RASAL1	89	.	0			c.A172T						PASS	.						197	195	196					12																	113565934		2203	4300	6503	SO:0001583	missense	8437	exon4			GCACCGTGTACTC	AF086713	CCDS9165.1, CCDS55888.1, CCDS55889.1, CCDS73529.1	12q23-q24	2013-01-10			ENSG00000111344	ENSG00000111344		"Pleckstrin homology (PH) domain containing"	9873	protein-coding gene	gene with protein product		604118				9751798	Standard	NM_001193520		Approved	RASAL	uc001tul.3	O95294	OTTHUMG00000169705	ENST00000261729.5:c.172A>T	chr12.hg19:g.113565934T>A	ENSP00000261729:p.Thr58Ser	327.0	0.0	.		349.0	118.0	.	NM_004658	B7ZKM4|C9JFK5|F8VQX1|Q52M03|Q59H24|Q96CC7	Missense_Mutation	SNP	ENST00000261729.5	hg19	CCDS9165.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.130000	0.77549	.	.	ENSG00000111344	ENST00000546530;ENST00000261729;ENST00000446861;ENST00000548055	T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39	5.12	5.12	0.69794	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	0.74846	0.3770	L	0.45137	1.4	0.41650	D	0.98912	D;D;D;P;D;D	0.89917	1.0;1.0;1.0;0.698;0.994;1.0	D;D;D;P;D;D	0.91635	0.999;0.999;0.999;0.503;0.932;0.999	T	0.74191	-0.3745	10	0.36615	T	0.2	.	13.8909	0.63738	0.0:0.0:0.0:1.0	.	58;58;70;58;58;58	B4DG06;F8VRH9;Q59H24;F8VQX1;O95294;O95294-2	.;.;.;.;RASL1_HUMAN;.	S	58	ENSP00000450244:T58S;ENSP00000261729:T58S;ENSP00000395920:T58S;ENSP00000448510:T58S	ENSP00000261729:T58S	T	-	1	0	RASAL1	112050317	1.000000	0.71417	0.993000	0.49108	0.930000	0.56654	7.259000	0.78381	1.939000	0.56221	0.402000	0.26972	ACG	.	.	.	none		0.617	RASAL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405522.2	NM_004658		A	113565934	T	A	113565934	3	1	137	1	0	0	0	0	1	0	0	0	13076	1696	59	5	2318	5	RASAL1	12	113565934	Missense_Mutation	SNP	T	TCGA-BQ-7053-01A-11D-1961-08	11418772	113565934	20285961	29	8400											
SACS	26278	hgsc.bcm.edu	37	chr13	23906994	23906994	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttataagaggaagtgttccaTttacctcttgatattgagga	12	15	9	5	0	1	3	0	2	1	1	2	5	2	5	2	2	1	1	2	2	5	8			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr13:23906994T>C	ENST00000382292.3	-	9	11294	c.11021A>G	c.(11020-11022)aAt>aGt	p.N3674S	SACS_ENST00000402364.1_Missense_Mutation_p.N2924S|SACS_ENST00000382298.3_Missense_Mutation_p.N3674S			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3674					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)		AAGTGTTCCATTTACCTCTTG	0.393																																					p.N3674S		Atlas-SNP	.											.	SACS	871	.	0			c.A11021G						PASS	.						85	85	85					13																	23906994		2203	4300	6503	SO:0001583	missense	26278	exon10			GTTCCATTTACCT	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.11021A>G	chr13.hg19:g.23906994T>C	ENSP00000371729:p.Asn3674Ser	82.0	0.0	.		102.0	43.0	.	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	hg19	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	T	11.44	1.639656	0.29157	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.87571	-2.12;-2.27;-2.12	5.8	5.8	0.92144	.	0.045544	0.85682	D	0.000000	T	0.79118	0.4392	N	0.17082	0.46	0.33015	D	0.528049	B	0.17465	0.022	B	0.14023	0.01	T	0.78450	-0.2199	10	0.33940	T	0.23	.	16.1429	0.81539	0.0:0.0:0.0:1.0	.	3674	Q9NZJ4	SACS_HUMAN	S	3674;2924;3674	ENSP00000371729:N3674S;ENSP00000385844:N2924S;ENSP00000371735:N3674S	ENSP00000371729:N3674S	N	-	2	0	SACS	22804994	1.000000	0.71417	0.981000	0.43875	0.722000	0.41435	4.970000	0.63742	2.209000	0.71365	0.460000	0.39030	AAT	.	.	.	none		0.393	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		C	23906994	T	C	23906994	3	2	137	1	0	0	0	0	1	0	0	0	13817	1493	52	3	2722	3	SACS	13	23906994	Missense_Mutation	SNP	T	TCGA-BQ-7053-01A-11D-1961-08		23906994	91262884	30	8401											
CHRFAM7A	89832	hgsc.bcm.edu	37	chr15	30665308	30665308	+	Frame_Shift_Del	DEL	A	A	-																															cagtgctgcacatcaaagggAaaccagcgtacatcgatgta																										TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr15:30665308delA	ENST00000299847.2	-	6	654	c.201delT	c.(199-201)tttfs	p.F67fs	CHRFAM7A_ENST00000567722.1_5'Flank|CHRFAM7A_ENST00000397827.3_5'UTR|CHRFAM7A_ENST00000401522.3_5'UTR	NM_139320.1	NP_647536.1	Q494W8	CRFM7_HUMAN	CHRNA7 (cholinergic receptor, nicotinic, alpha 7, exons 5-10) and FAM7A (family with sequence similarity 7A, exons A-E) fusion	67						integral component of membrane (GO:0016021)	extracellular ligand-gated ion channel activity (GO:0005230)			large_intestine(3)|lung(1)|skin(2)	6		all_lung(180;3.42e-11)|Breast(32;0.000153)		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)		CATCAAAGGGAAACCAGCGTA	0.483																																					p.P68fs		Atlas-INDEL	.											.	CHRFAM7A	15	.	0			c.202delC						PASS	.						61	60	61					15																	30665308		2176	4256	6432	SO:0001589	frameshift_variant	89832	exon6			.	AF029838	CCDS32184.1, CCDS42008.1	15q13.2	2013-04-24	2006-02-01		ENSG00000166664	ENSG00000166664			15781	protein-coding gene	gene with protein product		609756				11829490	Standard	NM_139320		Approved	D-10, CHRNA7-DR1	uc001zdt.1	Q494W8	OTTHUMG00000175645	ENST00000299847.2:c.201delT	chr15.hg19:g.30665308delA	ENSP00000299847:p.Phe67fs	779.0	0.0	0		732.0	118.0	0.161202	NM_139320	A8KAB9	Frame_Shift_Del	DEL	ENST00000299847.2	hg19	CCDS32184.1																																																																																			.	.	.	none		0.483	CHRFAM7A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430700.1	NM_148911		-	30665308	A	-	30665308	7	5	137	1	0	1	0	1	0	0	0	0	3377	243	9	0	1057	0	CHRFAM7A	15	30665308	Frame_Shift_Del	DEL	A	TCGA-BQ-7053-01A-11D-1961-08		30665308	71866084	31	8402											
IQGAP1	8826	hgsc.bcm.edu	37	chr15	91009552	91009552	+	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	agtagaaagtggtgatgttgGcaaaacactgagtgcccttc	12	10	12	7	0	0	3	0	2	0	1	1	3	0	3	1	2	2	3	1	2	4	3			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr15:91009552G>T	ENST00000268182.5	+	17	2043	c.1919G>T	c.(1918-1920)gGc>gTc	p.G640V	IQGAP1_ENST00000560738.1_Missense_Mutation_p.G68V	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	640					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)			GGTGATGTTGGCAAAACACTG	0.443																																					p.G640V		Atlas-SNP	.											.	IQGAP1	140	.	0			c.G1919T						PASS	.						148	124	132					15																	91009552		2198	4298	6496	SO:0001583	missense	8826	exon17			ATGTTGGCAAAAC	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.1919G>T	chr15.hg19:g.91009552G>T	ENSP00000268182:p.Gly640Val	147.0	0.0	.		123.0	33.0	.	NM_003870	A7MBM3	Missense_Mutation	SNP	ENST00000268182.5	hg19	CCDS10362.1	.	.	.	.	.	.	.	.	.	.	G	10.86	1.470092	0.26423	.	.	ENSG00000140575	ENST00000268182	D	0.95171	-3.63	5.29	3.3	0.37823	.	0.339619	0.31268	N	0.007960	D	0.88444	0.6438	N	0.16478	0.41	0.33977	D	0.647533	B	0.02656	0.0	B	0.04013	0.001	D	0.87361	0.2344	10	0.35671	T	0.21	-7.5112	14.694	0.69107	0.0:0.4098:0.5901:0.0	.	640	P46940	IQGA1_HUMAN	V	640	ENSP00000268182:G640V	ENSP00000268182:G640V	G	+	2	0	IQGAP1	88810556	0.653000	0.27358	0.946000	0.38457	0.974000	0.67602	2.180000	0.42537	1.438000	0.47492	0.655000	0.94253	GGC	.	.	.	none		0.443	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870		T	91009552	G	T	91009552	3	4	137	1	0	0	0	0	1	0	0	0	7821	1203	42	4	1985	4	IQGAP1	15	91009552	Missense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08	60344244	91009552	11521840	32	8403											
CNOT1	23019	hgsc.bcm.edu	37	chr16	58620607	58620607	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cactgacgtctgcgtcaatgTaagaacgcagaagatctgga	13	8	11	9	3	3	4	1	1	2	3	3	5	3	5	0	1	2	2	0	1	4	1			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr16:58620607T>C	ENST00000317147.5	-	7	811	c.479A>G	c.(478-480)tAc>tGc	p.Y160C	CNOT1_ENST00000441024.2_Missense_Mutation_p.Y160C|CNOT1_ENST00000569240.1_Missense_Mutation_p.Y160C	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	160					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)		TGCGTCAATGTAAGAACGCAG	0.458																																					p.Y160C		Atlas-SNP	.											.	CNOT1	359	.	0			c.A479G						PASS	.						218	225	223					16																	58620607		2198	4300	6498	SO:0001583	missense	23019	exon7			TCAATGTAAGAAC	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.479A>G	chr16.hg19:g.58620607T>C	ENSP00000320949:p.Tyr160Cys	397.0	0.0	.		385.0	106.0	.	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	hg19	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.651332	0.88056	.	.	ENSG00000125107	ENST00000317147;ENST00000394200;ENST00000441024	T;T	0.24350	1.86;1.86	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.49813	0.1579	M	0.71206	2.165	0.80722	D	1	D;D;D	0.76494	0.999;0.997;0.999	D;P;P	0.81914	0.995;0.808;0.871	T	0.49380	-0.8946	9	.	.	.	-13.1581	15.1793	0.72941	0.0:0.0:0.0:1.0	.	160;160;160	A5YKK6-4;A5YKK6;A5YKK6-2	.;CNOT1_HUMAN;.	C	160	ENSP00000320949:Y160C;ENSP00000413113:Y160C	.	Y	-	2	0	CNOT1	57178108	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.997000	0.88414	2.041000	0.60428	0.454000	0.30748	TAC	.	.	.	none		0.458	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		C	58620607	T	C	58620607	3	2	137	1	0	0	0	0	1	0	0	0	3619	1638	57	3	7045	3	CNOT1	16	58620607	Missense_Mutation	SNP	T	TCGA-BQ-7053-01A-11D-1961-08		58620607	31734146	33	8404											
BCMO1	53630	hgsc.bcm.edu	37	chr16	81298288	81298288	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtaaatctggcaacgtcacAtccccattatgatgaggctg	11	10	10	10	1	2	2	1	2	1	0	3	2	3	2	2	3	1	3	2	3	4	2			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr16:81298288A>G	ENST00000258168.2	+	5	976	c.515A>G	c.(514-516)cAt>cGt	p.H172R	BCMO1_ENST00000425577.2_Missense_Mutation_p.H103R	NM_017429.2	NP_059125.2														breast(2)|endometrium(1)|large_intestine(4)|lung(9)|prostate(3)|skin(3)|stomach(1)	23						GCAACGTCACATCCCCATTAT	0.403																																					p.H172R		Atlas-SNP	.											.	BCMO1	53	.	0			c.A515G						PASS	.						160	135	143					16																	81298288		2202	4300	6502	SO:0001583	missense	53630	exon5			CGTCACATCCCCA																												ENST00000258168.2:c.515A>G	chr16.hg19:g.81298288A>G	ENSP00000258168:p.His172Arg	115.0	0.0	.		102.0	31.0	.	NM_017429		Missense_Mutation	SNP	ENST00000258168.2	hg19	CCDS10934.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.125684	0.77436	.	.	ENSG00000135697	ENST00000258168;ENST00000425577	D;D	0.99545	-6.13;-6.13	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	D	0.99715	0.9890	H	0.94658	3.565	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.76575	0.988;0.971	D	0.97280	0.9917	10	0.87932	D	0	-25.987	14.8045	0.69942	1.0:0.0:0.0:0.0	.	103;172	E7EM88;Q9HAY6	.;BCDO1_HUMAN	R	172;103	ENSP00000258168:H172R;ENSP00000400586:H103R	ENSP00000258168:H172R	H	+	2	0	BCMO1	79855789	1.000000	0.71417	0.989000	0.46669	0.843000	0.47879	8.759000	0.91667	1.896000	0.54893	0.449000	0.29647	CAT	.	.	.	none		0.403	BCMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269056.1			G	81298288	A	G	81298288	3	3	137	1	0	0	0	0	1	0	0	0	1384	217	8	3	533	3	BCMO1	16	81298288	Missense_Mutation	SNP	A	TCGA-BQ-7053-01A-11D-1961-08	22677681	81298288	9056465	34	8405											
MED13	9969	hgsc.bcm.edu	37	chr17	60040331	60040331	+	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	cactttatcccgatccatcgTgctaaaatttaaggtagaaa	14	12	6	9	2	0	1	0	0	0	1	3	2	2	1	2	1	1	2	2	1	6	6			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr17:60040331T>G	ENST00000397786.2	-	21	4922	c.4846A>C	c.(4846-4848)Acg>Ccg	p.T1616P		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1616					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						CGATCCATCGTGCTAAAATTT	0.398																																					p.T1616P		Atlas-SNP	.											.	MED13	181	.	0			c.A4846C						PASS	.						62	60	60					17																	60040331		1850	4094	5944	SO:0001630	splice_region_variant	9969	exon21			CCATCGTGCTAAA	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.4845-1A>C	chr17.hg19:g.60040331T>G		91.0	0.0	.		131.0	34.0	.	NM_005121	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	hg19	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.199056	0.79015	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	T	0.76060	-0.99	5.44	4.34	0.51931	.	0.045205	0.85682	D	0.000000	T	0.76786	0.4036	M	0.64997	1.995	0.80722	D	1	D	0.57899	0.981	P	0.52109	0.69	T	0.73544	-0.3949	10	0.29301	T	0.29	-33.0615	11.6656	0.51372	0.1329:0.0:0.0:0.8671	.	1616	Q9UHV7	MED13_HUMAN	P	1616;1615	ENSP00000380888:T1616P	ENSP00000262436:T1615P	T	-	1	0	MED13	57395113	1.000000	0.71417	0.989000	0.46669	0.957000	0.61999	5.940000	0.70187	0.864000	0.35578	0.533000	0.62120	ACG	.	.	.	none		0.398	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121	Missense_Mutation	G	60040331	T	G	60040331	5	3	137	1	0	0	0	0	0	0	1	0	9437	1710	59	5	1718	5	MED13	17	60040331	Splice_Site	SNP	T	TCGA-BQ-7053-01A-11D-1961-08		60040331	21154879	35	8406											
ITGB4	3691	hgsc.bcm.edu	37	chr17	73746316	73746316	+	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	aggaagatccatttcaactgGctgcccccttctggcaagcc	9	9	9	14	0	2	1	1	0	1	1	3	2	3	2	4	3	3	2	4	3	3	2			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr17:73746316G>A	ENST00000200181.3	+	28	3628	c.3441G>A	c.(3439-3441)tgG>tgA	p.W1147*	ITGB4_ENST00000449880.2_Nonsense_Mutation_p.W1147*|ITGB4_ENST00000450894.3_Nonsense_Mutation_p.W1147*|ITGB4_ENST00000579662.1_Nonsense_Mutation_p.W1147*|ITGB4_ENST00000339591.3_Nonsense_Mutation_p.W1147*	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	1147	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			ATTTCAACTGGCTGCCCCCTT	0.632											OREG0024739	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.W1147X		Atlas-SNP	.											.	ITGB4	165	.	0			c.G3441A						PASS	.						33	34	33					17																	73746316		2203	4300	6503	SO:0001587	stop_gained	3691	exon28			CAACTGGCTGCCC		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.3441G>A	chr17.hg19:g.73746316G>A	ENSP00000200181:p.Trp1147*	58.0	0.0	.	1147	90.0	46.0	.	NM_001005731	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Nonsense_Mutation	SNP	ENST00000200181.3	hg19	CCDS11727.1	.	.	.	.	.	.	.	.	.	.	G	45	11.812557	0.99605	.	.	ENSG00000132470	ENST00000200181;ENST00000339591;ENST00000449880	.	.	.	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.7383	0.96217	0.0:0.0:1.0:0.0	.	.	.	.	X	1147	.	ENSP00000200181:W1147X	W	+	3	0	ITGB4	71257911	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.280000	0.89903	2.675000	0.91044	0.655000	0.94253	TGG	.	.	.	none		0.632	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			A	73746316	G	A	73746316	4	1	137	1	0	0	0	0	0	1	0	0	7904	1212	42	2	3547	2	ITGB4	17	73746316	Nonsense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08	13705985	73746316	7448894	36	8407											
ABCA7	10347	hgsc.bcm.edu	37	chr19	1061844	1061844	+	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	cgtttcgcatggtgacggggGacacattggccagcaggggc	7	7	17	10	3	0	1	0	1	0	0	1	2	0	2	1	6	1	3	1	6	0	2			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr19:1061844G>A	ENST00000263094.6	+	41	5758	c.5527G>A	c.(5527-5529)Gac>Aac	p.D1843N	ABCA7_ENST00000433129.1_Missense_Mutation_p.D1843N|ABCA7_ENST00000435683.2_Missense_Mutation_p.D1705N	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1843	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)		GGTGACGGGGGACACATTGGC	0.642																																					p.D1843N		Atlas-SNP	.											.	ABCA7	174	.	0			c.G5527A						PASS	.						98	83	88					19																	1061844		2203	4299	6502	SO:0001583	missense	10347	exon41			ACGGGGGACACAT	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.5527G>A	chr19.hg19:g.1061844G>A	ENSP00000263094:p.Asp1843Asn	72.0	0.0	.		60.0	16.0	.	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	hg19	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	G	15.92	2.975956	0.53720	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.96200	-3.94;-3.94	3.57	2.52	0.30459	ATPase, AAA+ type, core (1);ABC transporter-like (2);	.	.	.	.	D	0.94837	0.8332	L	0.27053	0.805	0.43133	D	0.994875	D;D	0.76494	0.999;0.978	D;P	0.79784	0.993;0.906	D	0.93757	0.7063	9	0.87932	D	0	.	9.6422	0.39846	0.1075:0.0:0.8925:0.0	.	968;1843	D6W5Y0;Q8IZY2	.;ABCA7_HUMAN	N	1843	ENSP00000263094:D1843N;ENSP00000414062:D1843N	ENSP00000263094:D1843N	D	+	1	0	ABCA7	1012844	1.000000	0.71417	0.969000	0.41365	0.089000	0.18198	7.374000	0.79633	0.692000	0.31613	-0.258000	0.10820	GAC	.	.	.	none		0.642	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		A	1061844	G	A	1061844	3	1	137	1	0	0	0	0	1	0	0	0	37	1174	41	2	5685	2	ABCA7	19	1061844	Missense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08		1061844	58067139	37	8408											
SH2D3A	10045	hgsc.bcm.edu	37	chr19	6760836	6760836	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgctcatcctccagttgaaAgagggctgtgggtcggcctg	6	11	14	10	1	1	2	1	1	0	1	4	2	3	2	3	3	1	3	3	3	1	2			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr19:6760836A>G	ENST00000245908.6	-	3	501	c.232T>C	c.(232-234)Ttt>Ctt	p.F78L	SH2D3A_ENST00000599563.1_5'UTR|SH2D3A_ENST00000437152.3_Intron	NM_005490.2	NP_005481.2	Q9BRG2	SH23A_HUMAN	SH2 domain containing 3A	78	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|urinary_tract(1)	24						TCCAGTTGAAAGAGGGCTGTG	0.642																																					p.F78L		Atlas-SNP	.											.	SH2D3A	53	.	0			c.T232C						PASS	.						64	63	64					19																	6760836		2203	4300	6503	SO:0001583	missense	10045	exon3			GTTGAAAGAGGGC	AF124249	CCDS12173.1	19p13.3	2013-02-14	2002-01-14			ENSG00000125731		"SH2 domain containing"	16885	protein-coding gene	gene with protein product		604721	"SH2 domain-containing 3A"			10187783	Standard	NM_005490		Approved	NSP1	uc002mft.3	Q9BRG2		ENST00000245908.6:c.232T>C	chr19.hg19:g.6760836A>G	ENSP00000245908:p.Phe78Leu	95.0	0.0	.		99.0	32.0	.	NM_005490	A8K9R6|B4DRS7|Q9Y2X4	Missense_Mutation	SNP	ENST00000245908.6	hg19	CCDS12173.1	.	.	.	.	.	.	.	.	.	.	A	17.60	3.431070	0.62844	.	.	ENSG00000125731	ENST00000245908	T	0.65178	-0.14	4.88	4.88	0.63580	SH2 motif (4);	0.000000	0.43747	D	0.000537	T	0.66366	0.2782	M	0.74546	2.27	0.80722	D	1	B	0.33883	0.43	B	0.39876	0.312	T	0.71310	-0.4631	10	0.87932	D	0	-15.1205	12.5273	0.56093	1.0:0.0:0.0:0.0	.	78	Q9BRG2	SH23A_HUMAN	L	78	ENSP00000245908:F78L	ENSP00000245908:F78L	F	-	1	0	SH2D3A	6711836	1.000000	0.71417	1.000000	0.80357	0.318000	0.28184	7.241000	0.78201	2.062000	0.61559	0.454000	0.30748	TTT	.	.	.	none		0.642	SH2D3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458016.1	NM_005490		G	6760836	A	G	6760836	3	3	137	1	0	0	0	0	1	0	0	0	14246	72	3	3	1530	3	SH2D3A	19	6760836	Missense_Mutation	SNP	A	TCGA-BQ-7053-01A-11D-1961-08	5698992	6760836	52368147	38	8409											
MAP2K7	5609	hgsc.bcm.edu	37	chr19	7976338	7976338	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggtggagctggcaacaggAcagtttccctacaagaactg	12	7	12	10	0	0	1	0	0	0	1	1	3	1	3	1	4	4	3	1	4	4	2			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr19:7976338A>G	ENST00000397979.3	+	9	1008	c.954A>G	c.(952-954)ggA>ggG	p.G318G	MAP2K7_ENST00000545011.1_Silent_p.G360G|MAP2K7_ENST00000397981.3_Silent_p.G325G|MAP2K7_ENST00000397983.3_Silent_p.G334G|CTD-3193O13.13_ENST00000595655.1_RNA	NM_145185.2	NP_660186.1	O14733	MP2K7_HUMAN	mitogen-activated protein kinase kinase 7	318	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of neuron apoptotic process (GO:0043525)|response to heat (GO:0009408)|response to osmotic stress (GO:0006970)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|magnesium ion binding (GO:0000287)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(2)|central_nervous_system(3)|endometrium(1)|large_intestine(8)|lung(4)|ovary(1)	19						TGGCAACAGGACAGTTTCCCT	0.607																																					p.G318G		Atlas-SNP	.											.	MAP2K7	66	.	0			c.A954G						PASS	.						44	49	47					19																	7976338		1939	4121	6060	SO:0001819	synonymous_variant	5609	exon9			AACAGGACAGTTT	AF006689	CCDS42491.1, CCDS74277.1, CCDS74278.1	19p13.3-p13.2	2011-06-09			ENSG00000076984	ENSG00000076984	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6847	protein-coding gene	gene with protein product		603014		PRKMK7		9312068	Standard	XM_005272489		Approved	MKK7, Jnkk2	uc002mit.3	O14733	OTTHUMG00000137368	ENST00000397979.3:c.954A>G	chr19.hg19:g.7976338A>G		76.0	0.0	.		40.0	12.0	.	NM_145185	B2R9S5|D6W659|O14648|O14816|O60452|O60453|Q1PG43|Q8IY10	Silent	SNP	ENST00000397979.3	hg19	CCDS42491.1																																																																																			.	.	.	none		0.607	MAP2K7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000267980.1			G	7976338	A	G	7976338	2	3	137	1	0	0	0	0	0	0	0	1	9249	262	10	3		3	MAP2K7	19	7976338	Silent	SNP	A	TCGA-BQ-7053-01A-11D-1961-08	1215502	7976338	51152645	39	8410											
ZNF613	79898	hgsc.bcm.edu	37	chr19	52448014	52448014	+	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	gtcatatatatgcagtgattGtggaaaaggcttcatcaaga	14	12	10	5	0	3	2	3	1	0	1	3	3	3	3	0	2	1	2	0	2	6	5			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr19:52448014G>T	ENST00000293471.6	+	6	1557	c.878G>T	c.(877-879)tGt>tTt	p.C293F	ZNF613_ENST00000391794.4_Missense_Mutation_p.C257F	NM_001031721.3	NP_001026891.2	Q6PF04	ZN613_HUMAN	zinc finger protein 613	293					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	19		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.0183)		TGCAGTGATTGTGGAAAAGGC	0.438																																					p.C293F		Atlas-SNP	.											.	ZNF613	62	.	0			c.G878T						PASS	.						67	73	71					19																	52448014		2203	4300	6503	SO:0001583	missense	79898	exon6			GTGATTGTGGAAA	AK027565	CCDS12844.1, CCDS33089.1	19q13.41	2013-01-08						"Zinc fingers, C2H2-type", "-"	25827	protein-coding gene	gene with protein product						12477932	Standard	NM_001031721		Approved	FLJ13590	uc002pxz.2	Q6PF04		ENST00000293471.6:c.878G>T	chr19.hg19:g.52448014G>T	ENSP00000293471:p.Cys293Phe	91.0	0.0	.		107.0	30.0	.	NM_001031721	Q96SS9	Missense_Mutation	SNP	ENST00000293471.6	hg19	CCDS33089.1	.	.	.	.	.	.	.	.	.	.	G	16.63	3.176698	0.57692	.	.	ENSG00000176024	ENST00000293471;ENST00000391794	D;D	0.85861	-2.04;-2.04	3.1	3.1	0.35709	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36034	N	0.002824	D	0.94673	0.8282	H	0.97415	4	0.43662	D	0.99608	D	0.89917	1.0	D	0.91635	0.999	D	0.96089	0.9060	10	0.87932	D	0	.	13.4498	0.61163	0.0:0.0:1.0:0.0	.	293	Q6PF04	ZN613_HUMAN	F	293;257	ENSP00000293471:C293F;ENSP00000375671:C257F	ENSP00000293471:C293F	C	+	2	0	ZNF613	57139826	1.000000	0.71417	0.876000	0.34364	0.804000	0.45430	8.406000	0.90216	1.730000	0.51580	0.655000	0.94253	TGT	.	.	.	none		0.438	ZNF613-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461104.2	NM_024840		T	52448014	G	T	52448014	3	4	137	1	0	0	0	0	1	0	0	0	18050	1377	48	4	892	4	ZNF613	19	52448014	Missense_Mutation	SNP	G	TCGA-BQ-7053-01A-11D-1961-08	44471676	52448014	6680969	40	8411											
KCNJ15	3772	hgsc.bcm.edu	37	chr21	39672237	39672239	+	In_Frame_Del	DEL	GAG	GAG	-																															attctgagaaacagcaactcGaggagaagtacaggcaggag																										TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr21:39672237_39672239delGAG	ENST00000328656.4	+	4	1357_1359	c.1054_1056delGAG	c.(1054-1056)gagdel	p.E353del	KCNJ15_ENST00000398930.1_In_Frame_Del_p.E353del|KCNJ15_ENST00000398932.1_In_Frame_Del_p.E353del|KCNJ15_ENST00000398938.2_In_Frame_Del_p.E353del|KCNJ15_ENST00000398934.1_In_Frame_Del_p.E353del	NM_001276437.1|NM_001276438.1|NM_001276439.1|NM_002243.3	NP_001263366.1|NP_001263367.1|NP_001263368.1|NP_002234.2	Q99712	KCJ15_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 15	353					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	24					Yohimbine(DB01392)	ACAGCAACTCGAGGAGAAGTACA	0.443																																					p.351_352del		Atlas-INDEL	.											.	KCNJ15	43	.	0			c.1053_1055del						PASS	.																																			SO:0001651	inframe_deletion	3772	exon3			.	Y10745	CCDS13656.1	21q22.2	2011-07-05			ENSG00000157551	ENSG00000157551		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6261	protein-coding gene	gene with protein product		602106				9299242, 8995301, 16382105	Standard	NM_170736		Approved	Kir4.2, Kir1.3, IRKK	uc002ywx.4	Q99712	OTTHUMG00000090609	ENST00000328656.4:c.1054_1056delGAG	chr21.hg19:g.39672240_39672242delGAG	ENSP00000331698:p.Glu353del	74.0	0.0	0		66.0	18.0	0.272727	NM_170736	D3DSH5|O00564|Q96L28|Q99446	In_Frame_Del	DEL	ENST00000328656.4	hg19	CCDS13656.1																																																																																			.	.	.	none		0.443	KCNJ15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207181.2	NM_002243		-	39672239	GAG	-	39672237	7	5	137	1	0	1	0	1	0	0	0	0	8056	1059	37	0	1056	0	KCNJ15	21	39672237	In_Frame_Del	DEL	GAG	TCGA-BQ-7053-01A-11D-1961-08		39672237	8457658	41	8412											
SGSM3	57591	hgsc.bcm.edu	37	chr22	40803806	40803806	+	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	1	0	0	0	0	0	0	0	tgtgcagatcgtgtctcagaAggacgagcactgctgggtgg	8	9	16	8	2	1	2	1	0	1	2	3	4	1	3	0	3	3	3	0	3	1	0			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chr22:40803806A>C	ENST00000355630.3	-	0	4496				SGSM3_ENST00000248929.9_Missense_Mutation_p.K513T|SGSM3_ENST00000454798.2_Missense_Mutation_p.K446T	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1						negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						GTGTCTCAGAAGGACGAGCAC	0.622			T	RBM15	acute megakaryocytic leukemia																																p.K513T		Atlas-SNP	.		Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	.	SGSM3	48	.	0			c.A1538C						PASS	.						60	61	60					22																	40803806		2203	4300	6503	SO:0001628	intergenic_variant	27352	exon14			CTCAGAAGGACGA	AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588			14334	protein-coding gene	gene with protein product	"megakaryocytic acute leukemia", "myocardin-related transcription factor A", "basic, SAP and coiled-coil domain"	606078				11431691, 12019265, 14970199	Standard	XM_005261692		Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146		chr22.hg19:g.40803806A>C		83.0	0.0	.		108.0	31.0	.	NM_015705	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Missense_Mutation	SNP	ENST00000355630.3	hg19	CCDS14003.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.958990	0.92726	.	.	ENSG00000100359	ENST00000248929;ENST00000454798	T;T	0.49720	0.77;0.77	5.23	5.23	0.72850	Src homology-3 domain (4);	0.045898	0.85682	D	0.000000	T	0.47911	0.1471	N	0.04820	-0.15	0.80722	D	1	D;D;D;D	0.65815	0.985;0.958;0.981;0.995	P;P;P;D	0.69479	0.876;0.904;0.905;0.964	T	0.61222	-0.7106	10	0.87932	D	0	.	15.4205	0.75006	1.0:0.0:0.0:0.0	.	450;446;541;513	B4DVE3;B4DMS2;Q96HU1-2;Q96HU1	.;.;.;SGSM3_HUMAN	T	513;446	ENSP00000248929:K513T;ENSP00000390998:K446T	ENSP00000248929:K513T	K	+	2	0	SGSM3	39133752	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	8.528000	0.90598	2.109000	0.64355	0.459000	0.35465	AAG	.	.	.	none		0.622	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831		C	40803806	A	C	40803806	1	2	137	0	1	0	0	0	0	0	0	0	14237	72	3	5		5	SGSM3	22	40803806	IGR	SNP	A	TCGA-BQ-7053-01A-11D-1961-08		40803806	10500760	42	8413											
TEX11	56159	hgsc.bcm.edu	37	chrX	69898664	69898664	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	attctcaaacctcaaaactaCtggcagcttgtctccacaga	13	10	5	13	0	3	1	2	0	2	1	5	1	3	1	2	1	4	2	2	1	4	3			TCGA-BQ-7053-01A-11D-1961-08	TCGA-BQ-7053-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	95c43067-a2b1-4cdb-b018-47b3210fd396	d525dfc6-e5f2-40a6-b090-ecfc5e8c5f18	g.chrX:69898664C>T	ENST00000395889.2	-	16	1432	c.1277G>A	c.(1276-1278)aGt>aAt	p.S426N	TEX11_ENST00000374320.2_Missense_Mutation_p.S101N|TEX11_ENST00000344304.3_Missense_Mutation_p.S426N|TEX11_ENST00000374333.2_Missense_Mutation_p.S411N	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	426					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					CTCAAAACTACTGGCAGCTTG	0.338																																					p.S426N		Atlas-SNP	.											.	TEX11	132	.	0			c.G1277A						PASS	.						111	97	102					X																	69898664		2203	4300	6503	SO:0001583	missense	56159	exon16			AAACTACTGGCAG	AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"testis expressed sequence 11"			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.1277G>A	chrX.hg19:g.69898664C>T	ENSP00000379226:p.Ser426Asn	56.0	0.0	.		48.0	17.0	.	NM_001003811	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Missense_Mutation	SNP	ENST00000395889.2	hg19	CCDS35323.1	.	.	.	.	.	.	.	.	.	.	C	4.605	0.112373	0.08831	.	.	ENSG00000120498	ENST00000374333;ENST00000395889;ENST00000374320;ENST00000344304	T;T;T;T	0.74002	-0.8;-0.8;-0.8;-0.8	4.58	-1.09	0.09904	Tetratricopeptide-like helical (1);	0.437979	0.23803	N	0.044403	T	0.45875	0.1364	N	0.08118	0	0.09310	N	1	B;B	0.26195	0.119;0.144	B;B	0.30251	0.069;0.113	T	0.30416	-0.9979	9	.	.	.	0.0168	3.6866	0.08331	0.1899:0.282:0.0:0.5281	.	411;426	Q8IYF3-3;Q8IYF3	.;TEX11_HUMAN	N	411;426;101;426	ENSP00000363453:S411N;ENSP00000379226:S426N;ENSP00000363440:S101N;ENSP00000340995:S426N	.	S	-	2	0	TEX11	69815389	0.996000	0.38824	0.062000	0.19696	0.495000	0.33615	0.274000	0.18680	-0.223000	0.09943	-0.371000	0.07208	AGT	.	.	.	none		0.338	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1			T	69898664	C	T	69898664	3	4	137	1	0	0	0	0	1	0	0	0	15786	565	20	2	1609	2	TEX11	23	69898664	Missense_Mutation	SNP	C	TCGA-BQ-7053-01A-11D-1961-08		69898664	85371896	43	8414											
TGFBRAP1	9392	hgsc.bcm.edu	37	chr2	105886051	105886051	+	Missense_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	acaggcagtagtcctcggccGctgcaaagtcctgcagctcg	8	7	12	14	3	0	0	0	0	0	0	4	0	2	0	3	2	3	6	3	2	2	1			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr2:105886051G>A	ENST00000393359.2	-	11	2510	c.2084C>T	c.(2083-2085)gCg>gTg	p.A695V	TGFBRAP1_ENST00000258449.1_Missense_Mutation_p.A695V			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	695					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						GTCCTCGGCCGCTGCAAAGTC	0.657																																					p.A695V	Esophageal Squamous(183;794 2019 9730 21801 48859)	Atlas-SNP	.											.	TGFBRAP1	70	.	0			c.C2084T						PASS	.						26	27	27					2																	105886051		2203	4300	6503	SO:0001583	missense	9392	exon11			TCGGCCGCTGCAA	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.2084C>T	chr2.hg19:g.105886051G>A	ENSP00000377027:p.Ala695Val	45.0	0.0	.		35.0	6.0	.	NM_004257	A8K5R7|D3DVJ8|O60466	Missense_Mutation	SNP	ENST00000393359.2	hg19	CCDS2067.1	.	.	.	.	.	.	.	.	.	.	G	18.44	3.625045	0.66901	.	.	ENSG00000135966	ENST00000393359;ENST00000258449;ENST00000543724	T;T	0.19806	2.12;2.12	5.54	4.64	0.57946	.	0.053015	0.85682	D	0.000000	T	0.49406	0.1555	M	0.86178	2.8	0.54753	D	0.999985	D;D	0.89917	1.0;0.992	D;D	0.68039	0.955;0.909	T	0.56098	-0.8035	10	0.46703	T	0.11	-29.6428	15.5761	0.76387	0.0:0.0:0.8611:0.1389	.	150;695	B3KMM9;Q8WUH2	.;TGFA1_HUMAN	V	695;695;150	ENSP00000377027:A695V;ENSP00000258449:A695V	ENSP00000258449:A695V	A	-	2	0	TGFBRAP1	105252483	1.000000	0.71417	0.404000	0.26397	0.158000	0.22134	9.470000	0.97683	1.293000	0.44690	0.462000	0.41574	GCG	.	.	.	none		0.657	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257		A	105886051	G	A	105886051	3	1	138	1	0	0	0	0	1	0	0	0	15836	1087	38	1	506	1	TGFBRAP1	2	105886051	Missense_Mutation	SNP	G	TCGA-BQ-7055-01A-11D-1961-08		105886051	137313322	1	8415											
CCDC71	64925	hgsc.bcm.edu	37	chr3	49200861	49200862	+	Frame_Shift_Del	DEL	CT	CT	-																															gacactgggggacccagtggCtctgttggttttgctctggt																										TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr3:49200861_49200862delCT	ENST00000321895.6	-	2	886_887	c.780_781delAG	c.(778-783)agagccfs	p.RA260fs		NM_022903.3	NP_075054.3	Q8IV32	CCD71_HUMAN	coiled-coil domain containing 71	260										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)		GACCCAGTGGCTCTGTTGGTTT	0.624																																					p.261_261del		Atlas-INDEL	.											.	CCDC71	33	.	0			c.781_782del						PASS	.																																			SO:0001589	frameshift_variant	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.780_781delAG	chr3.hg19:g.49200863_49200864delCT	ENSP00000319006:p.Arg260fs	194.0	0.0	0		152.0	43.0	0.282895	NM_022903	Q6IPE2|Q9H8H4|Q9H9F1	Frame_Shift_Del	DEL	ENST00000321895.6	hg19	CCDS2790.1																																																																																			.	.	.	none		0.624	CCDC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345980.1	NM_022903		-	49200862	CT	-	49200861	7	5	138	1	0	1	0	1	0	0	0	0	2846	797	28	0	626	0	CCDC71	3	49200861	Frame_Shift_Del	DEL	CT	TCGA-BQ-7055-01A-11D-1961-08		49200861	148821569	2	8416											
DEFB114	245928	hgsc.bcm.edu	37	chr6	49931770	49931770	+	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	gacatctatcttacctggtaGaatgaaggtcacataacaca	15	10	7	9	0	3	2	1	1	2	1	3	3	3	2	1	2	2	1	1	2	6	4			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr6:49931770G>A	ENST00000322066.3	-	1	48	c.49C>T	c.(49-51)Cta>Tta	p.L17L		NM_001037499.1	NP_001032588.1	Q30KQ6	DB114_HUMAN	defensin, beta 114	17					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)					TTACCTGGTAGAATGAAGGTC	0.284																																					p.L17L		Atlas-SNP	.											.	DEFB114	12	.	0			c.C49T						PASS	.						69	68	68					6																	49931770		2202	4293	6495	SO:0001819	synonymous_variant	245928	exon1			CTGGTAGAATGAA	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.49C>T	chr6.hg19:g.49931770G>A		71.0	0.0	.		60.0	11.0	.	NM_001037499	Q8NES9	Silent	SNP	ENST00000322066.3	hg19	CCDS34474.1																																																																																			.	.	.	none		0.284	DEFB114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359665.1	NM_001037499		A	49931770	G	A	49931770	2	1	138	1	0	0	0	0	0	0	0	1	4405	933	33	2		2	DEFB114	6	49931770	Silent	SNP	G	TCGA-BQ-7055-01A-11D-1961-08		49931770	121183297	3	8417											
CRY1	1407	hgsc.bcm.edu	37	chr12	107399011	107399011	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atcatactcaattgaaagttTagtaatgttccattcctaaa	15	15	4	7	0	2	1	2	1	0	0	4	1	4	1	2	0	1	3	2	0	7	8			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr12:107399011T>C	ENST00000008527.5	-	3	1150	c.283A>G	c.(283-285)Aaa>Gaa	p.K95E		NM_004075.4	NP_004066.1	Q16526	CRY1_HUMAN	cryptochrome circadian clock 1	95	Photolyase/cryptochrome alpha/beta.				blue light signaling pathway (GO:0009785)|circadian regulation of gene expression (GO:0032922)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|entrainment of circadian clock by photoperiod (GO:0043153)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|lipid storage (GO:0019915)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of glucocorticoid secretion (GO:2000850)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|regulation of DNA damage checkpoint (GO:2000001)|response to glucagon (GO:0033762)|response to insulin (GO:0032868)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	blue light photoreceptor activity (GO:0009882)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|DNA photolyase activity (GO:0003913)|double-stranded DNA binding (GO:0003690)|nuclear hormone receptor binding (GO:0035257)|nucleotide binding (GO:0000166)|phosphatase binding (GO:0019902)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin binding (GO:0043130)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|skin(1)	29						ATTGAAAGTTTAGTAATGTTC	0.343																																					p.K95E		Atlas-SNP	.											.	CRY1	74	.	0			c.A283G						PASS	.						137	132	134					12																	107399011		2203	4300	6503	SO:0001583	missense	1407	exon3			AAAGTTTAGTAAT	BC030519	CCDS9112.1	12q23-q24.1	2014-01-17	2014-01-17		ENSG00000008405	ENSG00000008405			2384	protein-coding gene	gene with protein product		601933	"cryptochrome 1 (photolyase-like)"	PHLL1		8921389	Standard	NM_004075		Approved		uc001tmi.4	Q16526	OTTHUMG00000170005	ENST00000008527.5:c.283A>G	chr12.hg19:g.107399011T>C	ENSP00000008527:p.Lys95Glu	149.0	0.0	.		167.0	64.0	.	NM_004075		Missense_Mutation	SNP	ENST00000008527.5	hg19	CCDS9112.1	.	.	.	.	.	.	.	.	.	.	T	15.48	2.847284	0.51164	.	.	ENSG00000008405	ENST00000008527	.	.	.	5.61	5.61	0.85477	Rossmann-like alpha/beta/alpha sandwich fold (1);DNA photolyase, N-terminal (2);	0.160218	0.53938	D	0.000048	T	0.54319	0.1851	L	0.49640	1.575	0.41632	D	0.989029	B	0.19073	0.033	B	0.19666	0.026	T	0.52472	-0.8571	9	0.06757	T	0.87	-12.0027	15.8086	0.78538	0.0:0.0:0.0:1.0	.	95	Q16526	CRY1_HUMAN	E	95	.	ENSP00000008527:K95E	K	-	1	0	CRY1	105923141	1.000000	0.71417	0.996000	0.52242	0.955000	0.61496	5.296000	0.65698	2.147000	0.66899	0.477000	0.44152	AAA	.	.	.	none		0.343	CRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406827.1	NM_004075		C	107399011	T	C	107399011	3	2	138	1	0	0	0	0	1	0	0	0	3905	1763	61	3	1517	3	CRY1	12	107399011	Missense_Mutation	SNP	T	TCGA-BQ-7055-01A-11D-1961-08		107399011	26452884	4	8418											
SYT3	84258	hgsc.bcm.edu	37	chr19	51135675	51135675	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctcaggggatgtttggctcGgtttgaccccagcggccact	5	10	14	12	2	1	1	1	1	0	0	2	2	1	2	3	5	1	4	3	5	0	2			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr19:51135675G>A	ENST00000338916.4	-	2	1175	c.542C>T	c.(541-543)cCg>cTg	p.P181L	SYT3_ENST00000544769.1_Missense_Mutation_p.P181L|SYT3_ENST00000600079.1_Missense_Mutation_p.P181L|SYT3_ENST00000593901.1_Missense_Mutation_p.P181L	NM_032298.2	NP_115674.1	Q9BQG1	SYT3_HUMAN	synaptotagmin III	181					calcium ion-dependent exocytosis (GO:0017156)|positive regulation of vesicle fusion (GO:0031340)|response to calcium ion (GO:0051592)	cell junction (GO:0030054)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(2)|skin(3)|urinary_tract(2)	35		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00462)|GBM - Glioblastoma multiforme(134;0.0188)		TGTTTGGCTCGGTTTGACCCC	0.657																																					p.P181L		Atlas-SNP	.											.	SYT3	85	.	0			c.C542T						PASS	.						33	34	34					19																	51135675		2203	4300	6503	SO:0001583	missense	84258	exon2			TGGCTCGGTTTGA	AL136594	CCDS12798.1	19q13.33	2014-07-02			ENSG00000213023	ENSG00000213023		"Synaptotagmins"	11511	protein-coding gene	gene with protein product		600327				7749232	Standard	NM_032298		Approved		uc002psv.3	Q9BQG1	OTTHUMG00000183064	ENST00000338916.4:c.542C>T	chr19.hg19:g.51135675G>A	ENSP00000340914:p.Pro181Leu	71.0	0.0	.		74.0	23.0	.	NM_032298	Q8N5Z1|Q8N640	Missense_Mutation	SNP	ENST00000338916.4	hg19	CCDS12798.1	.	.	.	.	.	.	.	.	.	.	G	12.34	1.907284	0.33628	.	.	ENSG00000213023	ENST00000338916;ENST00000544769	T;T	0.54479	0.57;0.57	5.24	5.24	0.73138	.	0.715640	0.12228	U	0.487701	T	0.29355	0.0731	N	0.03608	-0.345	0.09310	N	0.999994	B	0.09022	0.002	B	0.04013	0.001	T	0.06110	-1.0845	10	0.49607	T	0.09	.	8.4467	0.32847	0.169:0.0:0.831:0.0	.	181	Q9BQG1	SYT3_HUMAN	L	181	ENSP00000340914:P181L;ENSP00000438883:P181L	ENSP00000340914:P181L	P	-	2	0	SYT3	55827487	0.978000	0.34361	0.974000	0.42286	0.996000	0.88848	3.207000	0.51106	2.605000	0.88082	0.655000	0.94253	CCG	.	.	.	none		0.657	SYT3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464910.1	NM_032298		A	51135675	G	A	51135675	3	1	138	1	0	0	0	0	1	0	0	0	15487	1116	39	1	1258	1	SYT3	19	51135675	Missense_Mutation	SNP	G	TCGA-BQ-7055-01A-11D-1961-08		51135675	7993308	5	8419											
ZNF304	57343	hgsc.bcm.edu	37	chr19	57869057	57869057	+	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	tggcctcattctgcaccagaGggttcacactggagaaaagc	11	8	11	11	0	3	2	2	0	1	2	3	3	3	2	2	3	2	2	2	3	2	2			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr19:57869057G>A	ENST00000282286.5	+	3	1993	c.1820G>A	c.(1819-1821)aGg>aAg	p.R607K	ZNF304_ENST00000443917.2_Missense_Mutation_p.R654K|ZNF304_ENST00000598744.1_Missense_Mutation_p.R565K|ZNF304_ENST00000391705.3_Missense_Mutation_p.R607K			Q9HCX3	ZN304_HUMAN	zinc finger protein 304	607					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)		CTGCACCAGAGGGTTCACACT	0.478																																					p.R607K		Atlas-SNP	.											.	ZNF304	74	.	0			c.G1820A						PASS	.						84	81	82					19																	57869057		2203	4300	6503	SO:0001583	missense	57343	exon3			ACCAGAGGGTTCA	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.1820G>A	chr19.hg19:g.57869057G>A	ENSP00000282286:p.Arg607Lys	90.0	0.0	.		106.0	23.0	.	NM_020657		Missense_Mutation	SNP	ENST00000282286.5	hg19	CCDS12950.1	.	.	.	.	.	.	.	.	.	.	G	19.37	3.814001	0.70912	.	.	ENSG00000131845	ENST00000282286;ENST00000391705;ENST00000443917	T;T;T	0.18338	2.22;2.22;2.22	3.89	1.75	0.24633	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.29126	0.0724	L	0.42744	1.35	0.23056	N	0.998366	P;D	0.58970	0.898;0.984	P;D	0.69142	0.483;0.962	T	0.07462	-1.0771	9	0.45353	T	0.12	.	9.2462	0.37527	0.1894:0.0:0.8106:0.0	.	607;654	Q9HCX3;E7EQD3	ZN304_HUMAN;.	K	607;607;654	ENSP00000282286:R607K;ENSP00000375586:R607K;ENSP00000401642:R654K	ENSP00000282286:R607K	R	+	2	0	ZNF304	62560869	0.892000	0.30473	0.763000	0.31416	0.981000	0.71138	5.266000	0.65525	0.600000	0.29862	0.650000	0.86243	AGG	.	.	.	none		0.478	ZNF304-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465785.1			A	57869057	G	A	57869057	3	1	138	1	0	0	0	0	1	0	0	0	17845	1000	35	2	1830	2	ZNF304	19	57869057	Missense_Mutation	SNP	G	TCGA-BQ-7055-01A-11D-1961-08	6733382	57869057	1259926	6	8420											
ZYG11B	79699	hgsc.bcm.edu	37	chr1	53287196	53287196	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgaacatactgatccccaTgtccaacagattgctgtggc	11	10	8	12	0	0	3	0	2	0	1	2	3	2	3	3	1	4	1	3	1	3	2	rs368928161		TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr1:53287196T>C	ENST00000294353.6	+	14	2275	c.2130T>C	c.(2128-2130)caT>caC	p.H710H	ZYG11B_ENST00000443756.2_Silent_p.H640H	NM_024646.2	NP_078922.1	Q9C0D3	ZY11B_HUMAN	zyg-11 family member B, cell cycle regulator	710										breast(1)|endometrium(1)|kidney(6)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	30						CTGATCCCCATGTCCAACAGA	0.433																																					p.H710H		Atlas-SNP	.											.	ZYG11B	61	.	0			c.T2130C						PASS	.	T		0,4406		0,0,2203	98	85	90		2130	-5	0.9	1		90	1,8599		0,1,4299	no	coding-synonymous	ZYG11B	NM_024646.2		0,1,6502	CC,CT,TT		0.0116,0.0,0.0077		710/745	53287196	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	79699	exon14			TCCCCATGTCCAA	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.2130T>C	chr1.hg19:g.53287196T>C		71.0	0.0	.		75.0	35.0	.	NM_024646	Q8N2X3|Q9H8L8	Silent	SNP	ENST00000294353.6	hg19	CCDS30717.1																																																																																			.	.	.	none		0.433	ZYG11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024749.1	NM_024646		C	53287196	T	C	53287196	2	2	139	1	0	0	0	0	0	0	0	1	18265	1461	51	3		3	ZYG11B	1	53287196	Silent	SNP	T	TCGA-BQ-7056-01A-11D-1961-08		53287196	195963425	1	8421											
PYCR2	29920	hgsc.bcm.edu	37	chr1	226109611	226109611	+	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	ggcatcgatgaggtcctcttCcacctcagtgcagaagccca	9	8	10	14	1	2	2	1	1	1	1	5	3	4	2	4	2	2	2	4	2	1	1			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr1:226109611C>G	ENST00000343818.6	-	4	635	c.487G>C	c.(487-489)Gaa>Caa	p.E163Q	PYCR2_ENST00000478402.1_5'UTR|RP4-559A3.7_ENST00000432920.2_Intron	NM_013328.2	NP_037460.2	Q96C36	P5CR2_HUMAN	pyrroline-5-carboxylate reductase family, member 2	163					L-proline biosynthetic process (GO:0055129)	cytoplasm (GO:0005737)	pyrroline-5-carboxylate reductase activity (GO:0004735)			kidney(1)|lung(3)	4	Breast(184;0.197)				L-Proline(DB00172)	AGGTCCTCTTCCACCTCAGTG	0.637																																					p.E163Q		Atlas-SNP	.											.	PYCR2	13	.	0			c.G487C						PASS	.						56	43	48					1																	226109611		2203	4300	6503	SO:0001583	missense	29920	exon4			CCTCTTCCACCTC	AF151351	CCDS31043.1, CCDS73039.1	1q42.13	2008-02-05			ENSG00000143811	ENSG00000143811			30262	protein-coding gene	gene with protein product						12477932	Standard	NM_013328		Approved	P5CR2	uc001hpq.4	Q96C36	OTTHUMG00000037506	ENST00000343818.6:c.487G>C	chr1.hg19:g.226109611C>G	ENSP00000342502:p.Glu163Gln	31.0	0.0	.		35.0	7.0	.	NM_013328	A8K798|Q7Z515|Q9Y5J4	Missense_Mutation	SNP	ENST00000343818.6	hg19	CCDS31043.1	.	.	.	.	.	.	.	.	.	.	c	15.98	2.994034	0.54041	.	.	ENSG00000143811	ENST00000343818;ENST00000316940;ENST00000316918	D	0.85088	-1.94	4.67	4.67	0.58626	6-phosphogluconate dehydrogenase, C-terminal-like (1);	0.000000	0.85682	D	0.000000	D	0.86723	0.6001	M	0.63169	1.94	0.52501	D	0.999958	P;D	0.59767	0.954;0.986	B;P	0.50825	0.442;0.651	D	0.85792	0.1368	10	0.34782	T	0.22	.	15.4503	0.75268	0.0:1.0:0.0:0.0	.	163;162	Q96C36;E7EUS9	P5CR2_HUMAN;.	Q	163;162;116	ENSP00000342502:E163Q	ENSP00000321499:E116Q	E	-	1	0	PYCR2	224176234	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	5.801000	0.69115	2.570000	0.86706	0.655000	0.94253	GAA	.	.	.	none		0.637	PYCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091314.1	NM_013328		G	226109611	C	G	226109611	3	3	139	1	0	0	0	0	1	0	0	0	12869	864	30	4	491	4	PYCR2	1	226109611	Missense_Mutation	SNP	C	TCGA-BQ-7056-01A-11D-1961-08	172822415	226109611	23141010	2	8422											
DLX1	1745	hgsc.bcm.edu	37	chr2	172950598	172950598	+	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	gctcagcctcgtccttctccCgaccgctgggctacccctac	4	9	8	20	3	2	0	1	0	1	0	5	1	3	0	6	1	3	3	6	1	2	3			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr2:172950598C>A	ENST00000361725.4	+	1	645	c.193C>A	c.(193-195)Cga>Aga	p.R65R	DLX1_ENST00000341900.6_Silent_p.R65R	NM_178120.4	NP_835221.2	P56177	DLX1_HUMAN	distal-less homeobox 1	65					cerebral cortex GABAergic interneuron fate commitment (GO:0021893)|embryonic skeletal system development (GO:0048706)|hippocampus development (GO:0021766)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|proximal/distal pattern formation (GO:0009954)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|subpallium development (GO:0021544)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|lung(4)|prostate(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.216)			GTCCTTCTCCCGACCGCTGGG	0.652																																					p.R65R		Atlas-SNP	.											.	DLX1	23	.	0			c.C193A						PASS	.						90	89	89					2																	172950598		2203	4300	6503	SO:0001819	synonymous_variant	1745	exon1			TTCTCCCGACCGC	BC013010	CCDS2247.2, CCDS33328.1	2q31.1	2011-06-20	2005-12-22		ENSG00000144355	ENSG00000144355		"Homeoboxes / ANTP class : NKL subclass"	2914	protein-coding gene	gene with protein product		600029	"distal-less homeo box 1"			7907794	Standard	NM_001038493		Approved		uc002uhl.3	P56177	OTTHUMG00000073951	ENST00000361725.4:c.193C>A	chr2.hg19:g.172950598C>A		186.0	0.0	.		163.0	8.0	.	NM_178120	D3DPD7|Q53ZU4|Q7Z724|Q8IYB2	Silent	SNP	ENST00000361725.4	hg19	CCDS2247.2																																																																																			.	.	.	none		0.652	DLX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405916.1	XM_087198		A	172950598	C	A	172950598	2	1	139	1	0	0	0	0	0	0	0	1	4572	644	23	4		4	DLX1	2	172950598	Silent	SNP	C	TCGA-BQ-7056-01A-11D-1961-08		172950598	70248775	3	8423											
TTN	7273	hgsc.bcm.edu	37	chr2	179443931	179443931	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atttttggcaatcgtacactAtaagagttgtgttaaccgca	12	14	8	7	2	0	1	0	0	0	1	1	1	0	1	1	1	2	5	1	1	5	7			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr2:179443931A>G	ENST00000591111.1	-	270	63127	c.62903T>C	c.(62902-62904)aTa>aCa	p.I20968T	RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I13736T|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590807.1_RNA|RP11-171I2.5_ENST00000604215.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.I22609T|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I13544T|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.I20041T|TTN_ENST00000359218.5_Missense_Mutation_p.I13669T|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000591332.1_RNA			Q8WZ42	TITIN_HUMAN	titin	20968	Ig-like 112.				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)			ATCGTACACTATAAGAGTTGT	0.448																																					p.I22609T		Atlas-SNP	.											.	TTN	18412	.	0			c.T67826C						PASS	.						129	125	126					2																	179443931		1936	4122	6058	SO:0001583	missense	7273	exon320			TACACTATAAGAG	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.62903T>C	chr2.hg19:g.179443931A>G	ENSP00000465570:p.Ile20968Thr	204.0	0.0	.		199.0	45.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	10.40	1.340192	0.24339	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08	5.98	4.82	0.62117	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.45196	0.1330	N	0.16166	0.38	0.22666	N	0.998875	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;0.001	T	0.40608	-0.9554	9	0.87932	D	0	.	9.2435	0.37511	0.8612:0.0:0.1388:0.0	.	13544;13669;13736;20968	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	20041;13544;13736;13669;13542	ENSP00000343764:I20041T;ENSP00000434586:I13544T;ENSP00000340554:I13736T;ENSP00000352154:I13669T	ENSP00000340554:I13736T	I	-	2	0	TTN	179152177	0.996000	0.38824	0.972000	0.41901	0.977000	0.68977	5.187000	0.65087	1.075000	0.40932	0.533000	0.62120	ATA	.	.	.	none		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179443931	A	G	179443931	3	3	139	1	0	0	0	0	1	0	0	0	16747	449	16	3	40325	3	TTN	2	179443931	Missense_Mutation	SNP	A	TCGA-BQ-7056-01A-11D-1961-08	6493333	179443931	63755442	4	8424											
COL7A1	1294	hgsc.bcm.edu	37	chr3	48602253	48602253	+	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	accacccggggtgggcagcgGcgctcgcaggcctcacgggt	5	4	17	15	5	1	0	1	0	0	0	2	0	1	0	3	6	1	3	3	6	0	0			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr3:48602253G>A	ENST00000328333.8	-	117	8888	c.8781C>T	c.(8779-8781)cgC>cgT	p.R2927R	UCN2_ENST00000273610.3_5'Flank|COL7A1_ENST00000470076.1_5'UTR|COL7A1_ENST00000454817.1_Silent_p.R2895R	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2927	BPTI/Kunitz inhibitor. {ECO:0000255|PROSITE-ProRule:PRU00031}.|Nonhelical region (NC2).				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GTGGGCAGCGGCGCTCGCAGG	0.662																																					p.R2927R		Atlas-SNP	.											.	COL7A1	320	.	0			c.C8781T						PASS	.						32	33	33					3																	48602253		2202	4299	6501	SO:0001819	synonymous_variant	1294	exon117			GCAGCGGCGCTCG	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.8781C>T	chr3.hg19:g.48602253G>A		55.0	0.0	.		56.0	26.0	.	NM_000094	Q14054|Q16507	Silent	SNP	ENST00000328333.8	hg19	CCDS2773.1																																																																																			.	.	.	none		0.662	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		A	48602253	G	A	48602253	2	1	139	1	0	0	0	0	0	0	0	1	3706	1190	42	2		2	COL7A1	3	48602253	Silent	SNP	G	TCGA-BQ-7056-01A-11D-1961-08		48602253	149420177	5	8425											
RBM15B	29890	hgsc.bcm.edu	37	chr3	51431021	51431021	+	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	ggcttctggtgttgaaaaacAgctgcttccccacgtctatg	8	12	10	11	1	2	1	0	1	2	0	3	1	3	1	2	2	3	4	2	2	3	4			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr3:51431021A>T	ENST00000323686.4	+	1	2291	c.2191A>T	c.(2191-2193)Agc>Tgc	p.S731C		NM_013286.4	NP_037418.3	Q8NDT2	RB15B_HUMAN	RNA binding motif protein 15B	731	Interaction with Epstein-Barr virus BMLF1.|SPOC. {ECO:0000255|PROSITE- ProRule:PRU00249}.				mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|large_intestine(5)|lung(3)	12				BRCA - Breast invasive adenocarcinoma(193;0.000224)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GTTGAAAAACAGCTGCTTCCC	0.512																																					p.S731C		Atlas-SNP	.											.	RBM15B	47	.	0			c.A2191T						PASS	.						88	89	88					3																	51431021		2203	4300	6503	SO:0001583	missense	29890	exon1			AAAAACAGCTGCT	AL831838	CCDS33764.1	3p21.1	2013-02-12			ENSG00000179837	ENSG00000259956		"RNA binding motif (RRM) containing"	24303	protein-coding gene	gene with protein product		612602				16129689	Standard	NM_013286		Approved	HUMAGCGB, OTT3	uc003dbd.3	Q8NDT2	OTTHUMG00000156896	ENST00000323686.4:c.2191A>T	chr3.hg19:g.51431021A>T	ENSP00000313890:p.Ser731Cys	126.0	0.0	.		104.0	10.0	.	NM_013286	A4QPG7|Q6QE19|Q9BV96	Missense_Mutation	SNP	ENST00000323686.4	hg19	CCDS33764.1	.	.	.	.	.	.	.	.	.	.	A	17.46	3.394518	0.62066	.	.	ENSG00000179837	ENST00000323686;ENST00000540284;ENST00000541145;ENST00000536338	T	0.18338	2.22	5.75	5.75	0.90469	Spen Paralogue and Orthologue SPOC, C-terminal-like (2);Spen paralogue/orthologue C-terminal, metazoa (1);Spen paralogue and orthologue SPOC, C-terminal (1);	.	.	.	.	T	0.46718	0.1407	M	0.83953	2.67	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.52034	-0.8629	9	0.87932	D	0	-23.1168	16.0623	0.80847	1.0:0.0:0.0:0.0	.	731	Q8NDT2	RB15B_HUMAN	C	731;52;404;150	ENSP00000313890:S731C	ENSP00000313890:S731C	S	+	1	0	RBM15B	51406061	1.000000	0.71417	1.000000	0.80357	0.655000	0.38815	9.307000	0.96226	2.195000	0.70347	0.533000	0.62120	AGC	.	.	.	none		0.512	RBM15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346489.1	NM_013286		T	51431021	A	T	51431021	3	4	139	1	0	0	0	0	1	0	0	0	13130	188	7	5	2193	5	RBM15B	3	51431021	Missense_Mutation	SNP	A	TCGA-BQ-7056-01A-11D-1961-08	2828768	51431021	146591409	6	8426											
WDR52	55779	hgsc.bcm.edu	37	chr3	113128125	113128125	+	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	aacagaggccagcaagttacCgctgtagttaaagtccacat	14	8	9	10	1	0	1	0	0	0	1	1	1	1	1	3	1	3	5	3	1	6	3			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr3:113128125C>A	ENST00000295868.2	-	7	880	c.718G>T	c.(718-720)Ggt>Tgt	p.G240C	WDR52-AS1_ENST00000473329.1_RNA|WDR52_ENST00000393845.2_Missense_Mutation_p.G240C|WDR52-AS1_ENST00000498480.1_RNA	NM_018338.3	NP_060808.2												p.G240C(1)		breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						AGCAAGTTACCGCTGTAGTTA	0.393																																					p.G240C		Atlas-SNP	.											.	WDR52	151	.	1	Substitution - Missense(1)	lung(1)	c.G718T						PASS	.						126	118	121					3																	113128125		2203	4300	6503	SO:0001583	missense	55779	exon7			AGTTACCGCTGTA																												ENST00000295868.2:c.718G>T	chr3.hg19:g.113128125C>A	ENSP00000295868:p.Gly240Cys	141.0	0.0	.		136.0	7.0	.	NM_001164496		Missense_Mutation	SNP	ENST00000295868.2	hg19	CCDS2972.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.675005	0.88445	.	.	ENSG00000206530	ENST00000393845;ENST00000295868	T;T	0.73897	-0.79;2.77	6.04	6.04	0.98038	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	.	.	.	.	D	0.90614	0.7057	M	0.93638	3.44	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91830	0.5474	9	0.87932	D	0	.	20.5948	0.99439	0.0:1.0:0.0:0.0	.	240	Q96MT7	WDR52_HUMAN	C	240	ENSP00000377428:G240C;ENSP00000295868:G240C	ENSP00000295868:G240C	G	-	1	0	WDR52	114610815	1.000000	0.71417	0.218000	0.23776	0.028000	0.11728	7.223000	0.78033	2.873000	0.98535	0.563000	0.77884	GGT	.	.	.	none		0.393	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3			A	113128125	C	A	113128125	3	1	139	1	0	0	0	0	1	0	0	0	17316	652	23	4	4977	4	WDR52	3	113128125	Missense_Mutation	SNP	C	TCGA-BQ-7056-01A-11D-1961-08	61697104	113128125	84894305	7	8427											
UGT2A1	10941	hgsc.bcm.edu	37	chr4	70513331	70513331	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggttcctatgagacttatcTgaagggagaacagcagaagg	13	9	13	6	0	1	4	0	2	1	3	2	6	2	4	1	3	2	2	1	3	5	3			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr4:70513331T>C	ENST00000503640.1	-	1	87	c.32A>G	c.(31-33)cAg>cGg	p.Q11R	UGT2A1_ENST00000286604.4_Missense_Mutation_p.Q11R|UGT2A1_ENST00000514019.1_Missense_Mutation_p.Q11R|UGT2A1_ENST00000512704.1_Missense_Mutation_p.Q11R	NM_006798.3	NP_006789.2	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A1, complex locus	11					cellular glucuronidation (GO:0052695)|detection of chemical stimulus (GO:0009593)|metabolic process (GO:0008152)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						GAGACTTATCTGAAGGGAGAA	0.363																																					p.Q11R		Atlas-SNP	.											.	UGT2A1	131	.	0			c.A32G						PASS	.						43	41	42					4																	70513331		2202	4298	6500	SO:0001583	missense	10941	exon2			CTTATCTGAAGGG	AJ006054	CCDS3529.1, CCDS58901.1, CCDS58902.1	4q13	2013-03-28	2010-12-02					"UDP glucuronosyltransferases"	12542	protein-coding gene	gene with protein product		604716	"UDP glycosyltransferase 2 family, polypeptide A1", "UDP glucuronosyltransferase 2 family, polypeptide A1"			10359671	Standard	NM_001252274		Approved		uc011caq.2	Q9Y4X1	OTTHUMG00000184942	ENST00000503640.1:c.32A>G	chr4.hg19:g.70513331T>C	ENSP00000424478:p.Gln11Arg	40.0	0.0	.		45.0	13.0	.	NM_001252274	B4E2F4|D3GER1|D3GER2|E9PDM7|J3KNA3	Missense_Mutation	SNP	ENST00000503640.1	hg19	CCDS3529.1	.	.	.	.	.	.	.	.	.	.	T	10.08	1.251452	0.22880	.	.	ENSG00000173610	ENST00000503640;ENST00000512704;ENST00000514019;ENST00000286604;ENST00000505512	T;T;T;T;T	0.60424	0.2;0.27;0.21;0.19;1.99	5.93	4.69	0.59074	.	1.385230	0.04777	N	0.429078	T	0.50990	0.1648	L	0.34521	1.04	.	.	.	B;B;B;B	0.25772	0.047;0.134;0.047;0.047	B;B;B;B	0.28784	0.022;0.094;0.022;0.022	T	0.38929	-0.9638	9	0.25106	T	0.35	.	11.0455	0.47857	0.0:0.0:0.1554:0.8446	.	11;11;11;11	E9PDM7;B4E2F4;D6RFW5;Q9Y4X1	.;.;.;UD2A1_HUMAN	R	11	ENSP00000424478:Q11R;ENSP00000421432:Q11R;ENSP00000425497:Q11R;ENSP00000286604:Q11R;ENSP00000427709:Q11R	ENSP00000286604:Q11R	Q	-	2	0	UGT2A1	70547920	0.908000	0.30866	1.000000	0.80357	0.292000	0.27327	1.859000	0.39418	2.281000	0.76405	0.533000	0.62120	CAG	.	.	.	none		0.363	UGT2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251554.3	NM_006798		C	70513331	T	C	70513331	3	2	139	1	0	0	0	0	1	0	0	0	16965	1580	55	3	1575	3	UGT2A1	4	70513331	Missense_Mutation	SNP	T	TCGA-BQ-7056-01A-11D-1961-08		70513331	120640945	8	8428											
SLC4A4	8671	hgsc.bcm.edu	37	chr4	72412140	72412140	+	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	atgctccctcatggctcttcCgtggtatgtagctgctacgg	5	13	11	12	2	2	0	1	0	1	0	4	0	4	0	2	3	4	6	2	3	3	4			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr4:72412140C>A	ENST00000264485.5	+	19	2633	c.2516C>A	c.(2515-2517)cCg>cAg	p.P839Q	SLC4A4_ENST00000425175.1_Missense_Mutation_p.P839Q|SLC4A4_ENST00000340595.3_Missense_Mutation_p.P795Q|SLC4A4_ENST00000351898.6_Intron	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	839					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)	ATGGCTCTTCCGTGGTATGTA	0.463																																					p.P839Q		Atlas-SNP	.											.	SLC4A4	269	.	0			c.C2516A						PASS	.						251	196	214					4																	72412140		2203	4299	6502	SO:0001583	missense	8671	exon19			CTCTTCCGTGGTA	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.2516C>A	chr4.hg19:g.72412140C>A	ENSP00000264485:p.Pro839Gln	169.0	0.0	.		184.0	8.0	.	NM_001098484	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	hg19	CCDS43236.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.417192	0.83449	.	.	ENSG00000080493	ENST00000264485;ENST00000425175;ENST00000340595	D;D;D	0.89050	-2.46;-2.46;-2.46	5.75	5.75	0.90469	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.96803	0.8956	H	0.96633	3.855	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97617	1.0133	10	0.87932	D	0	.	19.9564	0.97221	0.0:1.0:0.0:0.0	.	839;795;839	A5JJ20;Q9Y6R1-2;Q9Y6R1	.;.;S4A4_HUMAN	Q	839;839;795	ENSP00000264485:P839Q;ENSP00000393557:P839Q;ENSP00000344272:P795Q	ENSP00000264485:P839Q	P	+	2	0	SLC4A4	72631004	1.000000	0.71417	0.328000	0.25416	0.600000	0.36913	7.818000	0.86416	2.708000	0.92522	0.650000	0.86243	CCG	.	.	.	none		0.463	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		A	72412140	C	A	72412140	3	1	139	1	0	0	0	0	1	0	0	0	14669	652	23	4	2707	4	SLC4A4	4	72412140	Missense_Mutation	SNP	C	TCGA-BQ-7056-01A-11D-1961-08	1898809	72412140	118742136	9	8429											
C4orf26	152816	hgsc.bcm.edu	37	chr4	76489342	76489342	+	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	aggacaagaagaggtatttaCgcctcctggagattcacaaa	15	8	10	8	1	1	3	1	0	0	3	2	5	2	4	2	3	1	1	2	3	5	4			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr4:76489342C>T	ENST00000311623.4	+	2	121	c.86C>T	c.(85-87)aCg>aTg	p.T29M	C4orf26_ENST00000435974.2_Missense_Mutation_p.R44C	NM_001257072.1|NM_178497.3	NP_001244001.1|NP_848592.2	Q17RF5	CD026_HUMAN	chromosome 4 open reading frame 26	29						extracellular region (GO:0005576)				kidney(1)|large_intestine(4)|stomach(1)	6			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			GAGGTATTTACGCCTCCTGGA	0.527																																					p.R44C		Atlas-SNP	.											C4orf26_ENST00000435974,rectum,carcinoma,-1,2	C4orf26	24	.	0			c.C130T						PASS	.						67	71	70					4																	76489342		2203	4300	6503	SO:0001583	missense	152816	exon3			TATTTACGCCTCC	AK074237	CCDS3569.1, CCDS56334.1, CCDS75142.1	4q21.1	2012-10-31			ENSG00000174792	ENSG00000174792			26300	protein-coding gene	gene with protein product		614829				22901946	Standard	NM_001206981		Approved	FLJ23657	uc011cbo.2	Q17RF5	OTTHUMG00000130104	ENST00000311623.4:c.86C>T	chr4.hg19:g.76489342C>T	ENSP00000311307:p.Thr29Met	114.0	0.0	.		106.0	48.0	.	NM_001206981	B4DTI3|E7ETQ0|Q8TEC3	Missense_Mutation	SNP	ENST00000311623.4	hg19	CCDS3569.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.382|7.382	0.628915|0.628915	0.14257|0.14257	.|.	.|.	ENSG00000174792|ENSG00000174792	ENST00000435974|ENST00000311623	T|T	0.50813|0.39592	0.73|1.07	4.6|4.6	1.05|1.05	0.20165|0.20165	.|.	.|0.365474	.|0.21557	.|N	.|0.072634	T|T	0.39384|0.39384	0.1076|0.1076	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	1|1	B|D	0.06786|0.89917	0.001|1.0	B|P	0.04013|0.58660	0.001|0.843	T|T	0.19418|0.19418	-1.0306|-1.0306	9|10	0.87932|0.87932	D|D	0|0	.|.	4.1083|4.1083	0.10047|0.10047	0.181:0.61:0.0:0.209|0.181:0.61:0.0:0.209	.|.	44|29	E7ETQ0|Q17RF5	.|CD026_HUMAN	C|M	44|29	ENSP00000406925:R44C|ENSP00000311307:T29M	ENSP00000406925:R44C|ENSP00000311307:T29M	R|T	+|+	1|2	0|0	C4orf26|C4orf26	76708366|76708366	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.212000|0.212000	0.24457|0.24457	-0.328000|-0.328000	0.07945|0.07945	0.054000|0.054000	0.16065|0.16065	0.551000|0.551000	0.68910|0.68910	CGC|ACG	.	.	.	none		0.527	C4orf26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252410.1	NM_178497		T	76489342	C	T	76489342	3	4	139	1	0	0	0	0	1	0	0	0	2259	536	19	1	92	1	C4orf26	4	76489342	Missense_Mutation	SNP	C	TCGA-BQ-7056-01A-11D-1961-08	4077202	76489342	114664934	10	8430											
UGT3A2	167127	hgsc.bcm.edu	37	chr5	36035804	36035804	+	Missense_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	aaggctgcacctggccttatGtctccttcacctttctggcc	5	13	8	15	0	3	0	1	0	2	0	4	0	3	0	5	3	1	2	5	3	2	3			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr5:36035804G>A	ENST00000282507.3	-	7	1669	c.1568C>T	c.(1567-1569)aCa>aTa	p.T523I	UGT3A2_ENST00000545528.1_Missense_Mutation_p.T221I|UGT3A2_ENST00000513300.1_Missense_Mutation_p.T489I	NM_174914.3	NP_777574.2	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2	523					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)			CTGGCCTTATGTCTCCTTCAC	0.582																																					p.T523I		Atlas-SNP	.											.	UGT3A2	117	.	0			c.C1568T						PASS	.						53	48	50					5																	36035804		2203	4300	6503	SO:0001583	missense	167127	exon7			CCTTATGTCTCCT		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.1568C>T	chr5.hg19:g.36035804G>A	ENSP00000282507:p.Thr523Ile	64.0	0.0	.		61.0	23.0	.	NM_174914	B4DUQ7|E9PFK7|Q6UXC4|Q8NBP2	Missense_Mutation	SNP	ENST00000282507.3	hg19	CCDS3914.1	.	.	.	.	.	.	.	.	.	.	G	10.17	1.276110	0.23307	.	.	ENSG00000168671	ENST00000282507;ENST00000513300;ENST00000545528	T;T;D	0.83992	0.02;-0.22;-1.79	2.74	-0.134	0.13481	.	2.665640	0.03471	U	0.213729	T	0.67636	0.2914	N	0.08118	0	0.09310	N	1	P;P	0.50272	0.933;0.933	B;B	0.42386	0.386;0.386	T	0.62120	-0.6921	10	0.87932	D	0	.	3.4564	0.07516	0.3405:0.0:0.479:0.1806	.	489;523	E9PFK7;Q3SY77	.;UD3A2_HUMAN	I	523;489;221	ENSP00000282507:T523I;ENSP00000427404:T489I;ENSP00000445367:T221I	ENSP00000282507:T523I	T	-	2	0	UGT3A2	36071561	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	0.200000	0.17257	-0.057000	0.13199	0.563000	0.77884	ACA	.	.	.	none		0.582	UGT3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253771.2	NM_174914		A	36035804	G	A	36035804	3	1	139	1	0	0	0	0	1	0	0	0	16976	1377	48	2	7	2	UGT3A2	5	36035804	Missense_Mutation	SNP	G	TCGA-BQ-7056-01A-11D-1961-08		36035804	144879456	11	8431											
DDX4	54514	hgsc.bcm.edu	37	chr5	55088515	55088515	+	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	agttttggatgaagctgatcGcatgttggatatgggttttg	8	16	14	3	1	0	2	0	2	0	0	1	4	0	4	0	3	1	5	0	3	2	6			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr5:55088515G>T	ENST00000505374.1	+	17	1441	c.1349G>T	c.(1348-1350)cGc>cTc	p.R450L	DDX4_ENST00000511853.1_Missense_Mutation_p.R301L|DDX4_ENST00000354991.5_Missense_Mutation_p.R416L|DDX4_ENST00000514278.2_Missense_Mutation_p.R430L|DDX4_ENST00000353507.5_Missense_Mutation_p.R416L	NM_024415.2	NP_077726.1	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	450	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				male meiosis I (GO:0007141)|multicellular organismal development (GO:0007275)|regulation of protein localization (GO:0032880)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pi-body (GO:0071546)|piP-body (GO:0071547)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	24		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				GAAGCTGATCGCATGTTGGAT	0.353																																					p.R450L		Atlas-SNP	.											DDX4_ENST00000511853,NS,carcinoma,0,3	DDX4	194	.	0			c.G1349T						PASS	.						75	74	74					5																	55088515		2203	4300	6503	SO:0001583	missense	54514	exon17			CTGATCGCATGTT	AF262962	CCDS3969.1, CCDS47208.1, CCDS54854.1, CCDS54855.1	5p15.2-p13.1	2008-02-05	2003-06-13		ENSG00000152670	ENSG00000152670		"DEAD-boxes"	18700	protein-coding gene	gene with protein product		605281	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 4"			10920202, 11850529	Standard	NM_001142549		Approved	VASA	uc003jqg.4	Q9NQI0	OTTHUMG00000097044	ENST00000505374.1:c.1349G>T	chr5.hg19:g.55088515G>T	ENSP00000424838:p.Arg450Leu	78.0	0.0	.		63.0	27.0	.	NM_024415	A8K8Q2|B3KSF4|D6RDK4|E9PCD8|Q5M7Z3|Q86VX0|Q9NT92|Q9NYB1	Missense_Mutation	SNP	ENST00000505374.1	hg19	CCDS3969.1	.	.	.	.	.	.	.	.	.	.	G	33	5.250592	0.95305	.	.	ENSG00000152670	ENST00000353507;ENST00000514278;ENST00000505374;ENST00000506511;ENST00000354991;ENST00000511853	D;D;D;T;D;D	0.93247	-3.19;-3.19;-3.19;0.92;-3.19;-3.19	5.39	5.39	0.77823	RNA helicase, ATP-dependent, DEAD-box, conserved site (1);DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.061968	0.64402	D	0.000017	D	0.96904	0.8989	M	0.81341	2.54	0.80722	D	1	D;D;D;D	0.89917	0.998;0.968;0.992;1.0	P;P;P;D	0.85130	0.901;0.717;0.842;0.997	D	0.97158	0.9836	10	0.87932	D	0	-27.4782	19.5193	0.95179	0.0:0.0:1.0:0.0	.	430;301;416;450	D6RDK4;E9PCD8;Q9NQI0-2;Q9NQI0	.;.;.;DDX4_HUMAN	L	416;430;450;430;416;301	ENSP00000334167:R416L;ENSP00000425359:R430L;ENSP00000424838:R450L;ENSP00000427167:R430L;ENSP00000347087:R416L;ENSP00000423123:R301L	ENSP00000334167:R416L	R	+	2	0	DDX4	55124272	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.405000	0.97313	2.687000	0.91594	0.561000	0.74099	CGC	.	.	.	none		0.353	DDX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214147.2	NM_024415		T	55088515	G	T	55088515	3	4	139	1	0	0	0	0	1	0	0	0	4362	1087	38	4	1452	4	DDX4	5	55088515	Missense_Mutation	SNP	G	TCGA-BQ-7056-01A-11D-1961-08	19052711	55088515	125826745	12	8432											
TNPO3	23534	hgsc.bcm.edu	37	chr7	128641219	128641219	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttagtctccacattctcaaTggcatagagagctgagcata	12	11	9	9	0	2	2	1	1	2	1	4	3	2	2	1	1	2	4	1	1	4	4			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr7:128641219T>C	ENST00000265388.5	-	6	909	c.766A>G	c.(766-768)Att>Gtt	p.I256V	TNPO3_ENST00000471166.1_Missense_Mutation_p.I256V|TNPO3_ENST00000471234.1_Missense_Mutation_p.I256V|TNPO3_ENST00000482320.1_Missense_Mutation_p.I190V|TNPO3_ENST00000393245.1_Missense_Mutation_p.I256V			Q9Y5L0	TNPO3_HUMAN	transportin 3	256					splicing factor protein import into nucleus (GO:0035048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(3)	22						ACATTCTCAATGGCATAGAGA	0.483																																					p.I256V	Pancreas(147;583 2585 39696 52331)	Atlas-SNP	.											.	TNPO3	148	.	0			c.A766G						PASS	.						264	229	241					7																	128641219		2203	4300	6503	SO:0001583	missense	23534	exon6			TCTCAATGGCATA	AF145029	CCDS5809.1, CCDS55162.1	7q32.2	2014-02-03			ENSG00000064419	ENSG00000064419		"Importins"	17103	protein-coding gene	gene with protein product	"importin 12"	610032	"limb girdle muscular dystrophy 1F (autosomal dominant)"	LGMD1F		10366588, 10713112, 23543484, 23667635	Standard	NM_012470		Approved	TRN-SR, MTR10A, TRN-SR2, IPO12	uc003vol.2	Q9Y5L0	OTTHUMG00000158409	ENST00000265388.5:c.766A>G	chr7.hg19:g.128641219T>C	ENSP00000265388:p.Ile256Val	348.0	0.0	.		328.0	120.0	.	NM_012470	A4D1K9|C9IZM0|Q6NUM1|Q96G71|Q96GU9|Q9Y3R2	Missense_Mutation	SNP	ENST00000265388.5	hg19	CCDS5809.1	.	.	.	.	.	.	.	.	.	.	T	10.42	1.346233	0.24426	.	.	ENSG00000064419	ENST00000393245;ENST00000265388;ENST00000482320;ENST00000471234;ENST00000471166	.	.	.	5.57	5.57	0.84162	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.41604	0.1166	N	0.22421	0.69	0.48511	D	0.999669	B;B;B	0.27450	0.039;0.179;0.063	B;B;B	0.22386	0.018;0.039;0.039	T	0.30592	-0.9973	9	0.17369	T	0.5	.	13.9666	0.64213	0.0:0.0:0.0:1.0	.	256;256;256	C9IZM0;C9J7E5;Q9Y5L0	.;.;TNPO3_HUMAN	V	256;256;190;256;256	.	ENSP00000265388:I256V	I	-	1	0	TNPO3	128428455	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.088000	0.71371	2.247000	0.74100	0.528000	0.53228	ATT	.	.	.	none		0.483	TNPO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350929.1	NM_012470		C	128641219	T	C	128641219	3	2	139	1	0	0	0	0	1	0	0	0	16349	1464	51	3	2073	3	TNPO3	7	128641219	Missense_Mutation	SNP	T	TCGA-BQ-7056-01A-11D-1961-08		128641219	30497444	13	8433											
RBP3	5949	hgsc.bcm.edu	37	chr10	48390462	48390462	+	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	tgctcagcacctcctggcccGggacgctgtccacccgcagg	5	6	12	18	3	1	0	1	0	0	0	3	1	3	1	5	3	2	4	5	3	0	0	rs147118201	byFrequency	TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr10:48390462G>T	ENST00000224600.4	-	1	529	c.416C>A	c.(415-417)cCg>cAg	p.P139Q	AL731561.2_ENST00000581861.1_RNA	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	139	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)	CTCCTGGCCCGGGACGCTGTC	0.637																																					p.P139Q		Atlas-SNP	.											.	RBP3	152	.	0			c.C416A						PASS	.						69	76	74					10																	48390462		2203	4300	6503	SO:0001583	missense	5949	exon1			TGGCCCGGGACGC	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.416C>A	chr10.hg19:g.48390462G>T	ENSP00000224600:p.Pro139Gln	167.0	0.0	.		149.0	8.0	.	NM_002900	Q0QD34|Q5VSR0|Q8IXN0	Missense_Mutation	SNP	ENST00000224600.4	hg19	CCDS7218.1	.	.	.	.	.	.	.	.	.	.	G	14.12	2.440090	0.43326	.	.	ENSG00000107618	ENST00000224600	T	0.63417	-0.04	5.7	5.7	0.88788	Interphotoreceptor retinol-binding (2);	0.268394	0.38272	N	0.001741	T	0.80460	0.4627	M	0.89601	3.045	0.35549	D	0.803682	D	0.89917	1.0	D	0.97110	1.0	D	0.86547	0.1832	10	0.72032	D	0.01	-37.5679	8.3623	0.32365	0.1656:0.0:0.8344:0.0	.	139	P10745	RET3_HUMAN	Q	139	ENSP00000224600:P139Q	ENSP00000224600:P139Q	P	-	2	0	RBP3	48010468	1.000000	0.71417	0.847000	0.33407	0.010000	0.07245	5.910000	0.69931	2.705000	0.92388	0.650000	0.86243	CCG	.	G|1.000;A|0.000	.	alt		0.637	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900		T	48390462	G	T	48390462	3	4	139	1	0	0	0	0	1	0	0	0	13170	1116	39	4	3343	4	RBP3	10	48390462	Missense_Mutation	SNP	G	TCGA-BQ-7056-01A-11D-1961-08		48390462	87144285	14	8434											
DUSP13	142891	hgsc.bcm.edu	37	chr10	76868897	76868897	+	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	gtcctctccccccagctctgGgagagaggtctcagccatgg	6	8	12	15	0	3	1	1	0	3	1	6	3	4	2	5	3	2	1	5	3	0	0			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr10:76868897G>A	ENST00000542569.1	+	0	0				SAMD8_ENST00000372687.4_5'Flank|DUSP13_ENST00000491677.2_5'UTR|DUSP13_ENST00000607009.1_5'UTR|SAMD8_ENST00000372690.3_5'Flank|DUSP13_ENST00000372700.3_Missense_Mutation_p.P7S|DUSP13_ENST00000607131.1_5'UTR|DUSP13_ENST00000372702.3_Missense_Mutation_p.P7S	NM_001174156.1|NM_144660.2	NP_001167627.1|NP_653261.1	Q96LT4	SAMD8_HUMAN	sterile alpha motif domain containing 8						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)					CCCAGCTCTGGGAGAGAGGTC	0.627																																					p.P7S		Atlas-SNP	.											.	DUSP13	82	.	0			c.C19T						PASS	.						43	43	43					10																	76868897		2203	4300	6503	SO:0001631	upstream_gene_variant	51207	exon1			GCTCTGGGAGAGA	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		chr10.hg19:g.76868897G>A	Exception_encountered	49.0	0.0	.		58.0	25.0	.	NM_001007272	Q5JSC5|Q5JSC8|Q66K52	Missense_Mutation	SNP	ENST00000542569.1	hg19	CCDS53543.1	.	.	.	.	.	.	.	.	.	.	G	10.27	1.302638	0.23736	.	.	ENSG00000079393	ENST00000372702;ENST00000372700	T;T	0.11495	3.76;2.77	5.91	-0.569	0.11756	.	.	.	.	.	T	0.06142	0.0159	N	0.22421	0.69	0.20703	N	0.999863	B;B	0.06786	0.0;0.001	B;B	0.09377	0.004;0.003	T	0.39014	-0.9634	9	0.87932	D	0	.	1.8802	0.03226	0.2904:0.1258:0.4545:0.1293	.	7;7	Q9UII6-4;Q6B8I1	.;MDSP_HUMAN	S	7	ENSP00000361787:P7S;ENSP00000361785:P7S	ENSP00000361785:P7S	P	-	1	0	DUSP13	76538903	0.461000	0.25783	0.168000	0.22838	0.265000	0.26407	0.801000	0.27055	0.117000	0.18138	-0.136000	0.14681	CCA	.	.	.	none		0.627	SAMD8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_144660		A	76868897	G	A	76868897	1	1	139	0	1	0	0	0	0	0	0	0	4815	1232	43	2		2	DUSP13	10	76868897	5'Flank	SNP	G	TCGA-BQ-7056-01A-11D-1961-08	28478435	76868897	58665850	15	8435											
ATM	472	hgsc.bcm.edu	37	chr11	108206609	108206609	+	Missense_Mutation	SNP	A	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	acaagatgctgtcatgcaacAggtcttccagatgtgtaata	13	11	9	8	0	2	2	1	0	1	2	3	2	3	2	1	1	3	3	1	1	4	3			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr11:108206609A>C	ENST00000452508.2	+	57	8378	c.8189A>C	c.(8188-8190)cAg>cCg	p.Q2730P	C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Missense_Mutation_p.Q2730P			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2730	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	GTCATGCAACAGGTCTTCCAG	0.348			"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.Q2730P		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	.	ATM	1657	.	0			c.A8189C						PASS	.						114	106	108					11																	108206609		2201	4298	6499	SO:0001583	missense	472	exon56	Familial Cancer Database	AT, Louis-Bar syndrome	TGCAACAGGTCTT	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.8189A>C	chr11.hg19:g.108206609A>C	ENSP00000388058:p.Gln2730Pro	73.0	0.0	.		57.0	20.0	.	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	hg19	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	A	27.0	4.787127	0.90367	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	D;D	0.88896	-2.44;-2.44	5.56	5.56	0.83823	Protein kinase-like domain (1);Armadillo-type fold (1);Phosphatidylinositol 3/4-kinase, conserved site (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	D	0.96605	0.8892	H	0.97758	4.07	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98083	1.0405	10	0.87932	D	0	.	15.7045	0.77565	1.0:0.0:0.0:0.0	.	2730	Q13315	ATM_HUMAN	P	2730	ENSP00000278616:Q2730P;ENSP00000388058:Q2730P	ENSP00000278616:Q2730P	Q	+	2	0	ATM	107711819	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.809000	0.91944	2.125000	0.65367	0.533000	0.62120	CAG	.	.	.	none		0.348	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		C	108206609	A	C	108206609	3	2	139	1	0	0	0	0	1	0	0	0	1109	188	7	5	8407	5	ATM	11	108206609	Missense_Mutation	SNP	A	TCGA-BQ-7056-01A-11D-1961-08		108206609	26799907	16	8436											
C11orf1	64776	hgsc.bcm.edu	37	chr11	111753250	111753250	+	Silent	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	aatacctattcaaaccgtacCctgatgggcaactggaacca	14	8	7	12	1	1	1	1	1	0	0	1	2	1	2	4	2	5	2	4	2	7	4			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr11:111753250C>T	ENST00000260276.3	+	2	541	c.204C>T	c.(202-204)acC>acT	p.T68T	C11orf1_ENST00000528125.1_Silent_p.T22T|C11orf1_ENST00000530214.1_Silent_p.T68T|C11orf1_ENST00000529270.1_Silent_p.T108T	NM_022761.2	NP_073598.1	Q9H5F2	CK001_HUMAN	chromosome 11 open reading frame 1	68						nucleus (GO:0005634)				kidney(2)|lung(3)	5		all_cancers(61;1.26e-15)|all_epithelial(67;9.52e-10)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|Medulloblastoma(222;0.0228)|all_neural(223;0.0281)		all cancers(92;6.28e-09)|Epithelial(105;4.11e-08)|OV - Ovarian serous cystadenocarcinoma(223;1.52e-07)|BRCA - Breast invasive adenocarcinoma(274;1.1e-06)		CAAACCGTACCCTGATGGGCA	0.438																																					p.T68T		Atlas-SNP	.											.	C11orf1	15	.	0			c.C204T						PASS	.						129	117	121					11																	111753250		2201	4297	6498	SO:0001819	synonymous_variant	64776	exon2			CCGTACCCTGATG	AJ250229	CCDS8350.1	11q23.1	2012-05-30			ENSG00000137720	ENSG00000137720			1163	protein-coding gene	gene with protein product						10873569	Standard	NM_022761		Approved	FLJ23499	uc001pmd.3	Q9H5F2	OTTHUMG00000166884	ENST00000260276.3:c.204C>T	chr11.hg19:g.111753250C>T		61.0	0.0	.		83.0	30.0	.	NM_022761	Q6I9X7|Q9NQC6	Silent	SNP	ENST00000260276.3	hg19	CCDS8350.1																																																																																			.	.	.	none		0.438	C11orf1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391650.1	NM_022761		T	111753250	C	T	111753250	2	4	139	1	0	0	0	0	0	0	0	1	1631	610	22	2		2	C11orf1	11	111753250	Silent	SNP	C	TCGA-BQ-7056-01A-11D-1961-08	3546641	111753250	23253266	17	8437											
FKBP11	51303	hgsc.bcm.edu	37	chr12	49319118	49319118	+	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	gagggtccggacgggactttCggtttcgagcccagcctcag	6	8	15	12	4	1	0	1	0	0	0	4	4	2	2	3	4	2	1	3	4	0	2			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr12:49319118C>G	ENST00000550765.1	-	1	492	c.94G>C	c.(94-96)Gaa>Caa	p.E32Q	FKBP11_ENST00000444214.2_5'Flank|RP11-302B13.5_ENST00000398092.4_Intron|FKBP11_ENST00000552878.1_Missense_Mutation_p.E32Q|FKBP11_ENST00000453172.2_Missense_Mutation_p.E32Q|CCDC65_ENST00000266984.5_Intron|AC073610.5_ENST00000537495.1_Intron|Y_RNA_ENST00000364808.1_RNA	NM_016594.2	NP_057678.1	Q9NYL4	FKB11_HUMAN	FK506 binding protein 11, 19 kDa	32					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						ACGGGACTTTCGGTTTCGAGC	0.662																																					p.E32Q		Atlas-SNP	.											.	FKBP11	12	.	0			c.G94C						PASS	.						31	32	32					12																	49319118		2203	4298	6501	SO:0001583	missense	51303	exon1			GACTTTCGGTTTC	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.94G>C	chr12.hg19:g.49319118C>G	ENSP00000449751:p.Glu32Gln	51.0	0.0	.		40.0	14.0	.	NM_016594	B4DWB7	Missense_Mutation	SNP	ENST00000550765.1	hg19	CCDS8773.1	.	.	.	.	.	.	.	.	.	.	C	11.20	1.568652	0.28003	.	.	ENSG00000134285	ENST00000550765;ENST00000552878;ENST00000453172	T;T;T	0.56611	0.46;1.2;0.45	4.58	3.69	0.42338	.	0.561459	0.16287	N	0.221075	T	0.43277	0.1240	L	0.29908	0.895	0.38062	D	0.9361	P;P	0.44690	0.841;0.746	B;B	0.43155	0.218;0.41	T	0.50792	-0.8786	10	0.87932	D	0	-14.2492	10.3341	0.43839	0.0:0.9065:0.0:0.0935	.	32;32	B4DWB7;Q9NYL4	.;FKB11_HUMAN	Q	32	ENSP00000449751:E32Q;ENSP00000447911:E32Q;ENSP00000396874:E32Q	ENSP00000256680:E32Q	E	-	1	0	FKBP11	47605385	1.000000	0.71417	1.000000	0.80357	0.472000	0.32918	4.451000	0.60047	1.299000	0.44798	0.561000	0.74099	GAA	.	.	.	none		0.662	FKBP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408927.1	NM_016594		G	49319118	C	G	49319118	3	3	139	1	0	0	0	0	1	0	0	0	5910	893	31	4	592	4	FKBP11	12	49319118	Missense_Mutation	SNP	C	TCGA-BQ-7056-01A-11D-1961-08		49319118	84532777	18	8438											
TARBP2	7786	hgsc.bcm.edu	37	chr12	53895924	53895925	+	5'Flank	INS	-	-	T																															gagggccaagcccaccagccINStaatttcaccttccgggtca																										TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr12:53895924_53895925insT	ENST00000267079.2	-	0	0				TARBP2_ENST00000456234.2_Frame_Shift_Ins_p.N40fs|TARBP2_ENST00000549028.1_3'UTR|MAP3K12_ENST00000547488.1_5'Flank|RP11-793H13.11_ENST00000602306.1_RNA|TARBP2_ENST00000394357.2_Frame_Shift_Ins_p.N40fs|MAP3K12_ENST00000547151.1_5'Flank|TARBP2_ENST00000552857.1_Intron|TARBP2_ENST00000266987.2_Frame_Shift_Ins_p.N61fs	NM_001193511.1|NM_006301.3	NP_001180440.1|NP_006292.3	Q12852	M3K12_HUMAN	mitogen-activated protein kinase kinase kinase 12						histone phosphorylation (GO:0016572)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	37						GCCCACCAGCCTAATTTCACCT	0.599																																					p.P60fs		Atlas-INDEL	.											.	TARBP2	35	.	0			c.179_180insT						PASS	.																																			SO:0001631	upstream_gene_variant	6895	exon2			.	U07358	CCDS8860.1, CCDS55831.1	12q13.13	2013-10-30			ENSG00000139625	ENSG00000139625		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6851	protein-coding gene	gene with protein product	"dual leucine zipper kinase DLK"	600447		ZPK		8037767	Standard	NM_006301		Approved	MUK, DLK, ZPKP1, MEKK12	uc001sdn.2	Q12852	OTTHUMG00000169854		chr12.hg19:g.53895925_53895925dupT	Exception_encountered	67.0	0.0	0		67.0	25.0	0.373134	NM_134323	B3KSS9|G3V1Y2|Q86VQ5|Q8WY25	Frame_Shift_Ins	INS	ENST00000267079.2	hg19	CCDS8860.1																																																																																			.	.	.	none		0.599	MAP3K12-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406267.1	NM_006301		T	53895925	-	T	53895924	6	5	139	0	1	1	1	0	0	0	0	0	15568	681	24	0		0	TARBP2	12	53895924	5'Flank	INS	-	TCGA-BQ-7056-01A-11D-1961-08	4576806	53895924	79955971	19	8439											
C12orf64	283310	hgsc.bcm.edu	37	chr12	80626779	80626779	+	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	ggcttgggacgggatatctgGgatctacctcaagctgtctg	7	11	14	9	1	4	0	1	0	3	0	4	3	4	3	1	4	2	2	1	4	3	3			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr12:80626779G>A	ENST00000547103.1	+	8	698	c.692G>A	c.(691-693)gGg>gAg	p.G231E	OTOGL_ENST00000458043.2_Missense_Mutation_p.G231E			Q3ZCN5	OTOGL_HUMAN	otogelin-like	231	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						GGGATATCTGGGATCTACCTC	0.413																																					p.G231E		Atlas-SNP	.											.	OTOGL	235	.	0			c.G692A						PASS	.						92	89	90					12																	80626779		1872	4109	5981	SO:0001583	missense	283310	exon8			TATCTGGGATCTA	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.692G>A	chr12.hg19:g.80626779G>A	ENSP00000447211:p.Gly231Glu	90.0	0.0	.		80.0	34.0	.	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	hg19		.	.	.	.	.	.	.	.	.	.	G	23.5	4.419978	0.83559	.	.	ENSG00000165899	ENST00000547103;ENST00000458043	T;T	0.58506	0.33;0.33	5.92	5.02	0.67125	.	.	.	.	.	T	0.67429	0.2892	L	0.52905	1.665	0.58432	D	0.999999	.	.	.	.	.	.	T	0.68720	-0.5334	7	0.51188	T	0.08	.	17.0842	0.86606	0.0:0.1269:0.873:0.0	.	.	.	.	E	231	ENSP00000447211:G231E;ENSP00000400895:G231E	ENSP00000400895:G231E	G	+	2	0	OTOGL	79150910	1.000000	0.71417	0.999000	0.59377	0.979000	0.70002	6.419000	0.73345	1.480000	0.48289	0.650000	0.86243	GGG	.	.	.	none		0.413	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591		A	80626779	G	A	80626779	3	1	139	1	0	0	0	0	1	0	0	0	1709	1232	43	2	722	2	C12orf64	12	80626779	Missense_Mutation	SNP	G	TCGA-BQ-7056-01A-11D-1961-08	26730855	80626779	53225116	20	8440											
TCL1B	9623	hgsc.bcm.edu	37	chr14	96152848	96152848	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctaggggtgccccctggccGtctgtggatccagaggcctg	4	9	15	13	1	2	1	0	0	2	1	3	2	3	2	5	5	1	0	5	5	1	1			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr14:96152848G>A	ENST00000340722.7	+	1	95	c.44G>A	c.(43-45)cGt>cAt	p.R15H	RP11-1070N10.6_ENST00000461160.1_RNA	NM_004918.3	NP_004909.1	O95988	TCL1B_HUMAN	T-cell leukemia/lymphoma 1B	15										cervix(1)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		all_cancers(154;0.103)		COAD - Colon adenocarcinoma(157;0.205)|Epithelial(152;0.248)		CCCCCTGGCCGTCTGTGGATC	0.627																																					p.R15H		Atlas-SNP	.											.	TCL1B	30	.	0			c.G44A						PASS	.						93	95	94					14																	96152848		2203	4300	6503	SO:0001583	missense	9623	exon1			CTGGCCGTCTGTG	AB018563	CCDS32151.1	14q32.1	2008-09-05			ENSG00000213231	ENSG00000213231			11649	protein-coding gene	gene with protein product		603769				10077617	Standard	NM_004918		Approved	TML1	uc001yez.3	O95988	OTTHUMG00000028912	ENST00000340722.7:c.44G>A	chr14.hg19:g.96152848G>A	ENSP00000343223:p.Arg15His	134.0	0.0	.		128.0	57.0	.	NM_004918	A6NEK7|Q6IAR7|Q9UBQ4	Missense_Mutation	SNP	ENST00000340722.7	hg19	CCDS32151.1	.	.	.	.	.	.	.	.	.	.	G	11.66	1.705553	0.30232	.	.	ENSG00000213231	ENST00000340722;ENST00000538038	T	0.32272	1.46	2.78	-0.328	0.12690	.	.	.	.	.	T	0.27798	0.0684	L	0.31664	0.95	0.09310	N	1	D	0.64830	0.994	P	0.58520	0.84	T	0.18713	-1.0328	9	0.15499	T	0.54	.	3.386	0.07272	0.1377:0.0:0.411:0.4513	.	15	O95988	TCL1B_HUMAN	H	15	ENSP00000343223:R15H	ENSP00000343223:R15H	R	+	2	0	TCL1B	95222601	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.684000	0.05173	-0.071000	0.12886	0.455000	0.32223	CGT	.	.	.	none		0.627	TCL1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315123.2			A	96152848	G	A	96152848	3	1	139	1	0	0	0	0	1	0	0	0	15717	1145	40	1	46	1	TCL1B	14	96152848	Missense_Mutation	SNP	G	TCGA-BQ-7056-01A-11D-1961-08		96152848	11196692	21	8441											
HERC1	8925	hgsc.bcm.edu	37	chr15	63978661	63978661	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattctccactaggcaacacTgagctttctccgggtcaaag	10	10	8	13	1	3	1	1	1	2	0	5	1	3	1	2	2	2	2	2	2	3	3			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr15:63978661T>C	ENST00000443617.2	-	34	6209	c.6122A>G	c.(6121-6123)cAg>cGg	p.Q2041R	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	2041	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						TAGGCAACACTGAGCTTTCTC	0.473																																					p.Q2041R		Atlas-SNP	.											.	HERC1	624	.	0			c.A6122G						PASS	.						177	178	178					15																	63978661		1955	4150	6105	SO:0001583	missense	8925	exon34			CAACACTGAGCTT	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.6122A>G	chr15.hg19:g.63978661T>C	ENSP00000390158:p.Gln2041Arg	333.0	0.0	.		299.0	125.0	.	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	T	18.96	3.733306	0.69189	.	.	ENSG00000103657	ENST00000443617	T	0.60040	0.22	5.63	5.63	0.86233	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	0.000000	0.64402	D	0.000001	T	0.37320	0.0999	N	0.08118	0	0.47698	D	0.999492	P	0.38978	0.652	B	0.33295	0.161	T	0.42749	-0.9433	10	0.48119	T	0.1	.	15.8367	0.78805	0.0:0.0:0.0:1.0	.	2041	Q15751	HERC1_HUMAN	R	2041	ENSP00000390158:Q2041R	ENSP00000390158:Q2041R	Q	-	2	0	HERC1	61765714	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	3.268000	0.51585	2.142000	0.66516	0.533000	0.62120	CAG	.	.	.	none		0.473	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		C	63978661	T	C	63978661	3	2	139	1	0	0	0	0	1	0	0	0	7064	1580	55	3	8643	3	HERC1	15	63978661	Missense_Mutation	SNP	T	TCGA-BQ-7056-01A-11D-1961-08		63978661	38552731	22	8442											
ALPK3	57538	hgsc.bcm.edu	37	chr15	85400008	85400009	+	Frame_Shift_Ins	INS	-	-	A																															acacaggcaggtgagaagatINSacaggaagacaggaaggccc																										TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr15:85400008_85400009insA	ENST00000258888.5	+	6	2812_2813	c.2645_2646insA	c.(2644-2649)atacagfs	p.Q883fs		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	883					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)			GGTGAGAAGATACAGGAAGACA	0.554																																					p.I882fs		Atlas-INDEL	.											.	ALPK3	289	.	0			c.2645_2646insA						PASS	.																																			SO:0001589	frameshift_variant	57538	exon6			.	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.2646dupA	chr15.hg19:g.85400009_85400009dupA	ENSP00000258888:p.Gln883fs	48.0	0.0	0		51.0	26.0	0.509804	NM_020778	Q9P2L6	Frame_Shift_Ins	INS	ENST00000258888.5	hg19	CCDS10333.1																																																																																			.	.	.	none		0.554	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778		A	85400009	-	A	85400008	7	5	139	1	0	1	1	0	0	0	0	0	546	1406	49	0	2667	0	ALPK3	15	85400008	Frame_Shift_Ins	INS	-	TCGA-BQ-7056-01A-11D-1961-08	21421347	85400008	17131384	23	8443											
NFAT5	10725	hgsc.bcm.edu	37	chr16	69718811	69718811	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcagctggtgctttgaatgTaaatgtgaagaaggaaatat	15	11	12	3	0	0	3	0	2	0	1	0	4	0	4	0	2	3	4	0	2	7	3			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr16:69718811T>C	ENST00000354436.2	+	10	1976	c.1658T>C	c.(1657-1659)gTa>gCa	p.V553A	NFAT5_ENST00000349945.1_Missense_Mutation_p.V477A|NFAT5_ENST00000567239.1_Missense_Mutation_p.V570A|NFAT5_ENST00000432919.1_Missense_Mutation_p.V571A|NFAT5_ENST00000393742.2_Missense_Mutation_p.V477A|NFAT5_ENST00000566899.1_Missense_Mutation_p.V477A	NM_006599.3	NP_006590.1	O94916	NFAT5_HUMAN	nuclear factor of activated T-cells 5, tonicity-responsive	553					cytokine production (GO:0001816)|excretion (GO:0007588)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of calcineurin-NFAT signaling cascade (GO:0070884)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						GCTTTGAATGTAAATGTGAAG	0.323																																					p.V571A		Atlas-SNP	.											.	NFAT5	184	.	0			c.T1712C						PASS	.						67	72	70					16																	69718811		2197	4300	6497	SO:0001583	missense	10725	exon11			TGAATGTAAATGT	AF134870	CCDS10881.1, CCDS10882.1, CCDS45519.1	16q22.1	2009-11-24			ENSG00000102908	ENSG00000102908		"Nuclear factor of activated T-cells"	7774	protein-coding gene	gene with protein product		604708				10377394	Standard	NM_173214		Approved	TONEBP, KIAA0827, NFATL1, OREBP, NFATZ, NF-AT5	uc002exl.2	O94916	OTTHUMG00000137572	ENST00000354436.2:c.1658T>C	chr16.hg19:g.69718811T>C	ENSP00000346420:p.Val553Ala	91.0	0.0	.		98.0	5.0	.	NM_138713	A2RRB4|A6H8V5|E9PHR7|O95693|Q7LA65|Q969Q8|Q96QH3|Q9UN18	Missense_Mutation	SNP	ENST00000354436.2	hg19	CCDS10881.1	.	.	.	.	.	.	.	.	.	.	T	16.60	3.169644	0.57584	.	.	ENSG00000102908	ENST00000432919;ENST00000426654;ENST00000349945;ENST00000354436;ENST00000393742	T;T;T;T	0.46451	0.88;0.88;0.87;0.88	5.31	5.31	0.75309	Immunoglobulin E-set (1);	0.122950	0.53938	D	0.000041	T	0.48484	0.1502	L	0.56769	1.78	0.58432	D	0.999999	B;P;B;P	0.49185	0.001;0.92;0.021;0.907	B;B;B;P	0.50490	0.003;0.439;0.013;0.642	T	0.39014	-0.9634	10	0.16896	T	0.51	.	15.2702	0.73696	0.0:0.0:0.0:1.0	.	570;553;571;477	A2RRB4;O94916;E9PHR7;O94916-2	.;NFAT5_HUMAN;.;.	A	571;570;477;553;477	ENSP00000396538:V571A;ENSP00000338806:V477A;ENSP00000346420:V553A;ENSP00000377343:V477A	ENSP00000338806:V477A	V	+	2	0	NFAT5	68276312	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.036000	0.64164	2.011000	0.59026	0.528000	0.53228	GTA	.	.	.	none		0.323	NFAT5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268952.2	NM_138714		C	69718811	T	C	69718811	3	2	139	1	0	0	0	0	1	0	0	0	10367	1638	57	3	1754	3	NFAT5	16	69718811	Missense_Mutation	SNP	T	TCGA-BQ-7056-01A-11D-1961-08		69718811	20635942	24	8444											
DNAH9	1770	hgsc.bcm.edu	37	chr17	11520831	11520831	+	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	gaggtgaagccccagctgcgGcccctgctccacgtggtctg	5	7	14	15	2	1	1	0	1	1	0	2	2	2	1	5	3	4	2	5	3	1	0			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr17:11520831G>C	ENST00000262442.4	+	5	1076	c.1008G>C	c.(1006-1008)cgG>cgC	p.R336R	DNAH9_ENST00000454412.2_Silent_p.R336R	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	336	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)		CCCAGCTGCGGCCCCTGCTCC	0.592																																					p.R336R		Atlas-SNP	.											.	DNAH9	695	.	0			c.G1008C						PASS	.						57	53	54					17																	11520831		2203	4300	6503	SO:0001819	synonymous_variant	1770	exon5			GCTGCGGCCCCTG	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.1008G>C	chr17.hg19:g.11520831G>C		73.0	0.0	.		60.0	17.0	.	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	hg19	CCDS11160.1																																																																																			.	.	.	none		0.592	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		C	11520831	G	C	11520831	2	2	139	1	0	0	0	0	0	0	0	1	4610	1190	42	4		4	DNAH9	17	11520831	Silent	SNP	G	TCGA-BQ-7056-01A-11D-1961-08		11520831	69674379	25	8445											
DDX5	1655	hgsc.bcm.edu	37	chr17	62498660	62498660	+	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	catgatctcttccattagacGaataagtctaataataggag	15	12	7	7	1	2	2	0	1	2	1	4	4	3	3	1	1	0	0	1	1	6	6			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr17:62498660G>C	ENST00000225792.5	-	9	1392	c.991C>G	c.(991-993)Cgt>Ggt	p.R331G	DDX5_ENST00000450599.2_Missense_Mutation_p.R252G|DDX5_ENST00000580026.1_5'Flank|MIR3064_ENST00000581130.1_RNA|MIR5047_ENST00000579212.1_RNA|DDX5_ENST00000578804.1_Missense_Mutation_p.R331G	NM_004396.3	NP_004387.1	P17844	DDX5_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 5	331	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cell growth (GO:0016049)|circadian rhythm (GO:0007623)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of osteoblast differentiation (GO:0045667)|regulation of skeletal muscle cell differentiation (GO:2001014)|regulation of viral genome replication (GO:0045069)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA helicase activity (GO:0003724)|transcription coactivator activity (GO:0003713)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	19	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)			TCCATTAGACGAATAAGTCTA	0.353			T	ETV4	prostate																																p.R331G	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.C991G						PASS	.						86	82	83					17																	62498660		2203	4300	6503	SO:0001583	missense	1655	exon9			TTAGACGAATAAG	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.991C>G	chr17.hg19:g.62498660G>C	ENSP00000225792:p.Arg331Gly	81.0	0.0	.		85.0	4.0	.	NM_004396	B4DLW8|B5BU21|D3DU32|E7ETL9|O75681|Q53Y61	Missense_Mutation	SNP	ENST00000225792.5	hg19	CCDS11659.1	.	.	.	.	.	.	.	.	.	.	G	15.73	2.918794	0.52546	.	.	ENSG00000108654	ENST00000540698;ENST00000450599;ENST00000225792	.	.	.	5.91	5.91	0.95273	Helicase, C-terminal (1);	0.096682	0.85682	D	0.000000	T	0.54078	0.1836	N	0.25060	0.705	0.80722	D	1	B;B;B;B	0.14012	0.001;0.009;0.009;0.009	B;B;B;B	0.17979	0.008;0.02;0.02;0.02	T	0.48681	-0.9014	9	0.62326	D	0.03	-11.1323	20.2985	0.98592	0.0:0.0:1.0:0.0	.	252;331;320;331	B4DLW8;B5BUE6;B4DN41;P17844	.;.;.;DDX5_HUMAN	G	331;261;320	.	ENSP00000225792:R320G	R	-	1	0	DDX5	59929122	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	9.292000	0.96076	2.793000	0.96121	0.655000	0.94253	CGT	.	.	.	none		0.353	DDX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444030.1	NM_004396		C	62498660	G	C	62498660	3	2	139	1	0	0	0	0	1	0	0	0	4369	1058	37	4	873	4	DDX5	17	62498660	Missense_Mutation	SNP	G	TCGA-BQ-7056-01A-11D-1961-08	50977829	62498660	18696550	26	8446											
RALBP1	10928	hgsc.bcm.edu	37	chr18	9535719	9535719	+	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	catgaggagcgcgaggccatCatcgagctgcgcgtgcagct	8	6	15	12	5	1	1	1	1	0	0	2	4	1	2	1	2	5	3	1	2	0	0			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr18:9535719C>G	ENST00000019317.4	+	10	1975	c.1752C>G	c.(1750-1752)atC>atG	p.I584M	RALBP1_ENST00000383432.3_Missense_Mutation_p.I584M			Q15311	RBP1_HUMAN	ralA binding protein 1	584					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)	GCGAGGCCATCATCGAGCTGC	0.582																																					p.I584M		Atlas-SNP	.											.	RALBP1	48	.	0			c.C1752G						PASS	.						20	18	18					18																	9535719		2203	4299	6502	SO:0001583	missense	10928	exon10			GGCCATCATCGAG	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.1752C>G	chr18.hg19:g.9535719C>G	ENSP00000019317:p.Ile584Met	29.0	0.0	.		18.0	10.0	.	NM_006788	D3DUI0	Missense_Mutation	SNP	ENST00000019317.4	hg19	CCDS11845.1	.	.	.	.	.	.	.	.	.	.	C	17.13	3.311613	0.60414	.	.	ENSG00000017797	ENST00000019317;ENST00000383432	T;T	0.12879	2.64;2.64	5.01	4.14	0.48551	.	0.000000	0.85682	D	0.000000	T	0.17916	0.0430	L	0.59436	1.845	0.58432	D	0.999995	P	0.45474	0.859	B	0.42653	0.394	T	0.01935	-1.1244	10	0.66056	D	0.02	-13.417	13.4422	0.61119	0.0:0.9242:0.0:0.0758	.	584	Q15311	RBP1_HUMAN	M	584	ENSP00000019317:I584M;ENSP00000372924:I584M	ENSP00000019317:I584M	I	+	3	3	RALBP1	9525719	1.000000	0.71417	0.998000	0.56505	0.953000	0.61014	2.717000	0.47227	1.237000	0.43756	0.655000	0.94253	ATC	.	.	.	none		0.582	RALBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254479.1	NM_006788		G	9535719	C	G	9535719	3	3	139	1	0	0	0	0	1	0	0	0	13025	816	29	4	1786	4	RALBP1	18	9535719	Missense_Mutation	SNP	C	TCGA-BQ-7056-01A-11D-1961-08		9535719	68541529	27	8447											
ADAMTS10	81794	hgsc.bcm.edu	37	chr19	8661946	8661946	+	Missense_Mutation	SNP	A	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	tgccatggccgctgtggttcAcgatggatttctgccactta	6	13	11	11	2	2	0	1	0	1	0	2	2	2	1	3	3	2	2	3	3	1	3			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr19:8661946A>C	ENST00000597188.1	-	8	1235	c.965T>G	c.(964-966)gTg>gGg	p.V322G	ADAMTS10_ENST00000270328.4_Missense_Mutation_p.V322G|ADAMTS10_ENST00000596709.1_5'Flank	NM_030957.2	NP_112219.3	Q9H324	ATS10_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 10	322	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					extracellular matrix (GO:0031012)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(16)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(3)|skin(10)|urinary_tract(1)	53						GCTGTGGTTCACGATGGATTT	0.572																																					p.V322G		Atlas-SNP	.											.	ADAMTS10	132	.	0			c.T965G						PASS	.						102	89	93					19																	8661946		2203	4300	6503	SO:0001583	missense	81794	exon8			TGGTTCACGATGG	AF163762	CCDS12206.1, CCDS62529.1	19p13.2	2014-08-12	2005-08-19		ENSG00000142303	ENSG00000142303		"ADAM metallopeptidases with thrombospondin type 1 motif"	13201	protein-coding gene	gene with protein product		608990	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 10"				Standard	XM_005272499		Approved	ADAM-TS10	uc002mkj.1	Q9H324	OTTHUMG00000182216	ENST00000597188.1:c.965T>G	chr19.hg19:g.8661946A>C	ENSP00000471851:p.Val322Gly	108.0	0.0	.		98.0	39.0	.	NM_030957	M0QZE4	Missense_Mutation	SNP	ENST00000597188.1	hg19	CCDS12206.1	.	.	.	.	.	.	.	.	.	.	A	16.27	3.074561	0.55646	.	.	ENSG00000142303	ENST00000270328;ENST00000393912	T	0.64438	-0.1	5.4	5.4	0.78164	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.175593	0.38663	U	0.001601	T	0.49236	0.1545	N	0.20685	0.6	0.80722	D	1	P	0.38729	0.644	B	0.39771	0.309	T	0.47837	-0.9086	10	0.26408	T	0.33	.	14.5981	0.68422	1.0:0.0:0.0:0.0	.	322	Q9H324	ATS10_HUMAN	G	322;76	ENSP00000270328:V322G	ENSP00000270328:V322G	V	-	2	0	ADAMTS10	8567946	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.354000	0.66040	2.036000	0.60181	0.460000	0.39030	GTG	.	.	.	none		0.572	ADAMTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460085.3	NM_030957		C	8661946	A	C	8661946	3	2	139	1	0	0	0	0	1	0	0	0	256	159	6	5	2422	5	ADAMTS10	19	8661946	Missense_Mutation	SNP	A	TCGA-BQ-7056-01A-11D-1961-08		8661946	50467037	28	8448											
SIPA1L3	23094	hgsc.bcm.edu	37	chr19	38621327	38621327	+	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	tggccgtggtcacactgaccCacgaccagatgatcgacctg	9	7	11	14	3	1	3	1	2	0	1	2	5	1	3	4	2	0	0	4	2	0	0			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr19:38621327C>G	ENST00000222345.6	+	10	3567	c.3058C>G	c.(3058-3060)Cac>Gac	p.H1020D		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	1020	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)			CACACTGACCCACGACCAGAT	0.642																																					p.H1020D		Atlas-SNP	.											.	SIPA1L3	150	.	0			c.C3058G						PASS	.						72	63	66					19																	38621327		2203	4300	6503	SO:0001583	missense	23094	exon10			CTGACCCACGACC	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.3058C>G	chr19.hg19:g.38621327C>G	ENSP00000222345:p.His1020Asp	111.0	0.0	.		88.0	4.0	.	NM_015073	Q2TV87	Missense_Mutation	SNP	ENST00000222345.6	hg19	CCDS33007.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.849035	0.91277	.	.	ENSG00000105738	ENST00000222345	T	0.64085	-0.08	5.21	5.21	0.72293	PDZ/DHR/GLGF (3);	0.000000	0.85682	D	0.000000	D	0.83635	0.5297	M	0.91663	3.23	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	D	0.87360	0.2343	10	0.87932	D	0	-32.8671	17.8767	0.88827	0.0:1.0:0.0:0.0	.	1020	O60292	SI1L3_HUMAN	D	1020	ENSP00000222345:H1020D	ENSP00000222345:H1020D	H	+	1	0	SIPA1L3	43313167	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.770000	0.85390	2.590000	0.87494	0.563000	0.77884	CAC	.	.	.	none		0.642	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278		G	38621327	C	G	38621327	3	3	139	1	0	0	0	0	1	0	0	0	14344	594	21	4	3088	4	SIPA1L3	19	38621327	Missense_Mutation	SNP	C	TCGA-BQ-7056-01A-11D-1961-08	29959381	38621327	20507656	29	8449											
ZNF404	342908	hgsc.bcm.edu	37	chr19	44377748	44377748	+	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	ttcataccagtatgaattatCtgatgctgaataagctgtga	13	14	8	6	0	2	4	1	4	1	0	2	4	2	4	1	0	3	3	1	0	6	5			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr19:44377748C>G	ENST00000587539.1	-	3	617	c.618G>C	c.(616-618)caG>caC	p.Q206H	ZNF404_ENST00000324394.6_Missense_Mutation_p.Q204H	NM_001033719.2	NP_001028891.2	Q494X3	ZN404_HUMAN	zinc finger protein 404	206					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|skin(1)|stomach(2)|urinary_tract(1)	17		Prostate(69;0.0352)				TATGAATTATCTGATGCTGAA	0.368																																					p.Q203H		Atlas-SNP	.											.	ZNF404	46	.	0			c.G609C						PASS	.						87	92	90					19																	44377748		2095	4252	6347	SO:0001583	missense	342908	exon2			AATTATCTGATGC	XM_092027	CCDS59394.1	19q13.31	2013-01-08				ENSG00000176222		"Zinc fingers, C2H2-type", "-"	19417	protein-coding gene	gene with protein product							Standard	NM_001033719		Approved		uc002oxs.5	Q494X3		ENST00000587539.1:c.618G>C	chr19.hg19:g.44377748C>G	ENSP00000466051:p.Gln206His	174.0	0.0	.		151.0	60.0	.	NM_001033719	A4FU30|K7ELF2	Missense_Mutation	SNP	ENST00000587539.1	hg19	CCDS59394.1	.	.	.	.	.	.	.	.	.	.	C	13.49	2.252356	0.39797	.	.	ENSG00000176222	ENST00000324394	T	0.18502	2.21	2.71	2.71	0.32032	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.31949	0.0813	M	0.77820	2.39	0.23351	N	0.997856	D	0.54207	0.965	P	0.58928	0.848	T	0.14254	-1.0479	9	0.52906	T	0.07	.	3.4705	0.07565	0.2546:0.6054:0.0:0.1399	.	206	Q494X3	ZN404_HUMAN	H	204	ENSP00000319479:Q204H	ENSP00000319479:Q204H	Q	-	3	2	ZNF404	49069588	0.564000	0.26602	1.000000	0.80357	0.979000	0.70002	1.602000	0.36783	1.519000	0.48950	0.404000	0.27445	CAG	.	.	.	none		0.368	ZNF404-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460019.1	NM_001033719		G	44377748	C	G	44377748	3	3	139	1	0	0	0	0	1	0	0	0	17898	912	32	4	1044	4	ZNF404	19	44377748	Missense_Mutation	SNP	C	TCGA-BQ-7056-01A-11D-1961-08	5756421	44377748	14751235	30	8450											
ZNF578	147660	hgsc.bcm.edu	37	chr19	53014896	53014896	+	Missense_Mutation	SNP	A	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	ttcacgtcatcatagacttcAtactggagagaaaccttaca	14	11	6	10	1	4	2	4	0	0	2	4	4	4	3	1	1	3	0	1	1	4	5			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr19:53014896A>C	ENST00000421239.2	+	6	1506	c.1262A>C	c.(1261-1263)cAt>cCt	p.H421P	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	421					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		CATAGACTTCATACTGGAGAG	0.383																																					p.H421P		Atlas-SNP	.											.	.	.	.	0			c.A1262C						PASS	.						81	85	84					19																	53014896		2203	4300	6503	SO:0001583	missense	147660	exon6			GACTTCATACTGG	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.1262A>C	chr19.hg19:g.53014896A>C	ENSP00000459216:p.His421Pro	149.0	0.0	.		153.0	10.0	.	NM_001099694	B4DR51|I3L1Y6	Missense_Mutation	SNP	ENST00000421239.2	hg19	CCDS54310.1	.	.	.	.	.	.	.	.	.	.	-	14.26	2.481441	0.44147	.	.	ENSG00000258405	ENST00000553364	.	.	.	1.48	1.48	0.22813	.	.	.	.	.	T	0.77685	0.4167	H	0.95950	3.745	0.30406	N	0.779575	D	0.57571	0.98	D	0.77004	0.989	T	0.72912	-0.4148	7	.	.	.	.	7.9426	0.29967	1.0:0.0:0.0:0.0	.	421	G3V4F6	.	P	421	.	.	H	+	2	0	ZNF578	57706708	0.998000	0.40836	0.005000	0.12908	0.050000	0.14768	6.983000	0.76180	0.696000	0.31696	0.246000	0.17985	CAT	.	.	.	none		0.383	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472		C	53014896	A	C	53014896	3	2	139	1	0	0	0	0	1	0	0	0	18022	217	8	5	1272	5	ZNF578	19	53014896	Missense_Mutation	SNP	A	TCGA-BQ-7056-01A-11D-1961-08	8637148	53014896	6114087	31	8451											
CHD6	84181	hgsc.bcm.edu	37	chr20	40053940	40053940	+	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	cggcacagttccttgcggttGcagcgctggtaaacagtgac	8	9	13	11	3	0	1	0	1	0	0	1	1	1	1	1	3	4	6	1	3	2	4			TCGA-BQ-7056-01A-11D-1961-08	TCGA-BQ-7056-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8030657c-5a4c-49c4-a1c4-87344411c96f	5f202358-ec0a-45aa-b346-79d9e4f5b268	g.chr20:40053940G>C	ENST00000373233.3	-	29	4401	c.4224C>G	c.(4222-4224)tgC>tgG	p.C1408W		NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1408					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)				CCTTGCGGTTGCAGCGCTGGT	0.552																																					p.C1408W		Atlas-SNP	.											.	CHD6	312	.	0			c.C4224G						PASS	.						85	76	79					20																	40053940		2203	4300	6503	SO:0001583	missense	84181	exon29			GCGGTTGCAGCGC	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.4224C>G	chr20.hg19:g.40053940G>C	ENSP00000362330:p.Cys1408Trp	88.0	0.0	.		77.0	4.0	.	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	hg19	CCDS13317.1	.	.	.	.	.	.	.	.	.	.	G	19.03	3.748438	0.69533	.	.	ENSG00000124177	ENST00000373233	T	0.79352	-1.26	5.66	-0.168	0.13343	.	0.000000	0.64402	D	0.000003	T	0.80742	0.4681	M	0.63428	1.95	0.80722	D	1	D	0.57257	0.979	P	0.57776	0.827	T	0.78790	-0.2066	10	0.51188	T	0.08	-12.621	10.7656	0.46292	0.3652:0.0:0.6348:0.0	.	1408	Q8TD26	CHD6_HUMAN	W	1408	ENSP00000362330:C1408W	ENSP00000362330:C1408W	C	-	3	2	CHD6	39487354	1.000000	0.71417	0.998000	0.56505	0.917000	0.54804	3.947000	0.56652	0.047000	0.15862	-0.136000	0.14681	TGC	.	.	.	none		0.552	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			C	40053940	G	C	40053940	3	2	139	1	0	0	0	0	1	0	0	0	3331	1311	46	4	3959	4	CHD6	20	40053940	Missense_Mutation	SNP	G	TCGA-BQ-7056-01A-11D-1961-08		40053940	22971580	32	8452											
TRIT1	54802	hgsc.bcm.edu	37	chr1	40307511	40307511	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaaacactctgactttctaTggtgttgacagcatctgagt	10	13	10	8	0	3	3	0	3	3	0	3	4	3	4	0	2	2	2	0	2	2	3			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr1:40307511T>C	ENST00000316891.5	-	11	1323	c.1309A>G	c.(1309-1311)Ata>Gta	p.I437V	TRIT1_ENST00000541099.1_Missense_Mutation_p.I55V|TRIT1_ENST00000372818.1_Missense_Mutation_p.I411V|TRIT1_ENST00000537440.1_Missense_Mutation_p.I133V|TRIT1_ENST00000537223.1_Missense_Mutation_p.I133V|TRIT1_ENST00000441669.2_Missense_Mutation_p.I355V|TRIT1_ENST00000545233.1_Missense_Mutation_p.I191V|TRIT1_ENST00000491865.1_5'UTR	NM_017646.4	NP_060116.2	Q9H3H1	MOD5_HUMAN	tRNA isopentenyltransferase 1	437					tRNA processing (GO:0008033)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|tRNA dimethylallyltransferase activity (GO:0052381)			breast(1)|large_intestine(5)|liver(1)|lung(3)|ovary(2)|pancreas(1)|stomach(1)|urinary_tract(1)	15	all_cancers(7;4.55e-14)|all_lung(5;1.23e-16)|all_epithelial(6;2.17e-16)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;3.29e-18)|Epithelial(16;3.07e-17)|all cancers(16;6.21e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			TGACTTTCTATGGTGTTGACA	0.418																																					p.I437V		Atlas-SNP	.											.	TRIT1	40	.	0			c.A1309G						PASS	.						266	252	257					1																	40307511		2203	4300	6503	SO:0001583	missense	54802	exon11			TTTCTATGGTGTT	AF074918	CCDS30681.1	1p34.2	2012-10-05			ENSG00000043514	ENSG00000043514	2.5.1.8		20286	protein-coding gene	gene with protein product						11111046, 15870694	Standard	NM_017646		Approved	FLJ20061, IPT	uc021olz.1	Q9H3H1	OTTHUMG00000009245	ENST00000316891.5:c.1309A>G	chr1.hg19:g.40307511T>C	ENSP00000321810:p.Ile437Val	259.0	0.0	.		249.0	99.0	.	NM_017646	A1A4X7|Q3T7B5|Q5QPK5|Q5QPK6|Q6IAC9|Q96FJ3|Q96L45|Q9NXT7	Missense_Mutation	SNP	ENST00000316891.5	hg19	CCDS30681.1	.	.	.	.	.	.	.	.	.	.	T	0.782	-0.761836	0.02996	.	.	ENSG00000043514	ENST00000046894;ENST00000372825;ENST00000441669;ENST00000316891;ENST00000372818;ENST00000534869;ENST00000545233;ENST00000537440;ENST00000537223;ENST00000541099	T;T	0.41065	1.02;1.01	5.67	-5.07	0.02938	.	2.410530	0.01192	N	0.007346	T	0.21761	0.0524	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.04013	0.0;0.001;0.001;0.0	T	0.06463	-1.0825	10	0.20519	T	0.43	0.246	1.1747	0.01832	0.3107:0.2806:0.0931:0.3157	.	437;411;355;133	Q9H3H1;Q9H3H1-4;Q9H3H1-5;Q3T7B5	MOD5_HUMAN;.;.;.	V	411;355;349;437;411;330;191;133;133;55	ENSP00000321810:I437V;ENSP00000361905:I411V	ENSP00000046894:I411V	I	-	1	0	TRIT1	40080098	0.000000	0.05858	0.000000	0.03702	0.102000	0.19082	-0.878000	0.04192	-0.471000	0.06891	-0.242000	0.12053	ATA	.	.	.	none		0.418	TRIT1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025627.2	NM_017646		C	40307511	T	C	40307511	3	2	140	1	0	0	0	0	1	0	0	0	16572	1464	51	3	98	3	TRIT1	1	40307511	Missense_Mutation	SNP	T	TCGA-BQ-7058-01A-11D-1961-08		40307511	208943110	1	8453											
MIER1	57708	hgsc.bcm.edu	37	chr1	67423741	67423741	+	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	cttttattttgatttatttaGgaaggcgacatgccaattca	11	17	7	6	1	1	1	1	1	0	0	1	3	1	2	1	2	1	0	1	2	5	9			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr1:67423741G>C	ENST00000355356.3	+	4	329		c.e4-1		MIER1_ENST00000371014.1_Splice_Site|MIER1_ENST00000401041.1_Splice_Site|MIER1_ENST00000357692.2_Splice_Site|MIER1_ENST00000355977.6_Splice_Site|MIER1_ENST00000479067.1_Splice_Site|MIER1_ENST00000371016.1_Splice_Site|MIER1_ENST00000371018.3_Splice_Site|MIER1_ENST00000401042.3_Splice_Site	NM_001077701.2|NM_001077704.2	NP_001071169.1|NP_001071172.1	Q8N108	MIER1_HUMAN	mesoderm induction early response 1, transcriptional regulator						positive regulation of chromatin silencing (GO:0031937)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(3)	15						GATTTATTTAGGAAGGCGACA	0.373																																					.		Atlas-SNP	.											.	MIER1	86	.	0			c.232-1G>C						PASS	.						87	80	82					1																	67423741		1874	4116	5990	SO:0001630	splice_region_variant	57708	exon6			TATTTAGGAAGGC		CCDS41347.1, CCDS41348.1, CCDS53325.1, CCDS53326.1, CCDS53327.1, CCDS53328.1, CCDS53329.1, CCDS53330.1, CCDS60163.1	1p31.2	2013-07-23	2013-07-23		ENSG00000198160	ENSG00000198160			29657	protein-coding gene	gene with protein product			"mesoderm induction early response 1 homolog (Xenopus laevis)"			12242014, 12482978	Standard	NM_020948		Approved	hMI-ER1, MI-ER1, KIAA1610	uc001dde.2	Q8N108	OTTHUMG00000009194	ENST00000355356.3:c.181-1G>C	chr1.hg19:g.67423741G>C		88.0	0.0	.		53.0	15.0	.	NM_001146111	C9JFD4|Q08AE0|Q32NC4|Q5T104|Q5TAD1|Q5TAD2|Q5TAD4|Q5TAD5|Q6AHY8|Q86TB4|Q8N156|Q8N161|Q8NC37|Q8NES4|Q8NES5|Q8NES6|Q8WWG2|Q9HCG2	Splice_Site	SNP	ENST00000355356.3	hg19	CCDS41348.1	.	.	.	.	.	.	.	.	.	.	G	17.76	3.468581	0.63625	.	.	ENSG00000198160	ENST00000371017;ENST00000371018;ENST00000357692;ENST00000401041;ENST00000371016;ENST00000371014;ENST00000401042;ENST00000355356	.	.	.	5.56	5.56	0.83823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8992	0.96978	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MIER1	67196329	1.000000	0.71417	1.000000	0.80357	0.692000	0.40212	8.843000	0.92142	2.789000	0.95967	0.591000	0.81541	.	.	.	.	none		0.373	MIER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025491.2	NM_020948	Intron	C	67423741	G	C	67423741	5	2	140	1	0	0	0	0	0	0	1	0	9587	1014	35	4	434	4	MIER1	1	67423741	Splice_Site	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	27116230	67423741	181826880	2	8454											
ARHGAP29	9411	hgsc.bcm.edu	37	chr1	94668261	94668261	+	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	ttgcatgcataataattttgCctttttgagagcattctctg	9	18	7	7	0	1	1	0	1	1	1	2	2	1	1	1	0	4	3	1	0	2	8			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr1:94668261C>A	ENST00000260526.6	-	11	1164	c.982G>T	c.(982-984)Gca>Tca	p.A328S	ARHGAP29_ENST00000370217.3_Missense_Mutation_p.A328S	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	328					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)		AATAATTTTGCCTTTTTGAGA	0.388																																					p.A328S		Atlas-SNP	.											.	ARHGAP29	132	.	0			c.G982T						PASS	.						145	130	135					1																	94668261		2203	4300	6503	SO:0001583	missense	9411	exon11			ATTTTGCCTTTTT		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.982G>T	chr1.hg19:g.94668261C>A	ENSP00000260526:p.Ala328Ser	100.0	0.0	.		77.0	26.0	.	NM_004815	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Missense_Mutation	SNP	ENST00000260526.6	hg19	CCDS748.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.652915	0.88056	.	.	ENSG00000137962	ENST00000260526;ENST00000370217	T;T	0.47869	0.83;0.83	6.06	5.16	0.70880	.	0.000000	0.38381	N	0.001718	T	0.58278	0.2111	M	0.69358	2.11	0.58432	D	0.999999	P;D	0.89917	0.944;1.0	P;D	0.83275	0.646;0.996	T	0.60622	-0.7227	10	0.41790	T	0.15	-25.713	15.6619	0.77193	0.0:0.9344:0.0:0.0656	.	328;328	Q52LW3-2;Q52LW3	.;RHG29_HUMAN	S	328	ENSP00000260526:A328S;ENSP00000359237:A328S	ENSP00000260526:A328S	A	-	1	0	ARHGAP29	94440849	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.054000	0.76649	1.578000	0.49821	0.650000	0.86243	GCA	.	.	.	none		0.388	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815		A	94668261	C	A	94668261	3	1	140	1	0	0	0	0	1	0	0	0	878	739	26	4	2855	4	ARHGAP29	1	94668261	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08	27244520	94668261	154582360	3	8455											
BCL9	607	hgsc.bcm.edu	37	chr1	147086309	147086309	+	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	catcaaatgctacagcccccAggtcttctaccccctcccat	9	9	4	19	0	3	0	1	0	2	0	4	0	4	0	5	1	4	1	5	1	3	3			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr1:147086309A>C	ENST00000234739.3	+	6	1194	c.454A>C	c.(454-456)Agg>Cgg	p.R152R	BCL9_ENST00000473292.1_3'UTR	NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	152					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)					TACAGCCCCCAGGTCTTCTAC	0.498			T	"IGH@, IGL@"	B-ALL																																p.R152R		Atlas-SNP	.		Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	.	BCL9	150	.	0			c.A454C						PASS	.						118	119	119					1																	147086309		2203	4300	6503	SO:0001819	synonymous_variant	607	exon6			GCCCCCAGGTCTT	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.454A>C	chr1.hg19:g.147086309A>C		98.0	0.0	.		76.0	30.0	.	NM_004326	Q5T489	Silent	SNP	ENST00000234739.3	hg19	CCDS30833.1																																																																																			.	.	.	none		0.498	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326		C	147086309	A	C	147086309	2	2	140	1	0	0	0	0	0	0	0	1	1381	179	7	5		5	BCL9	1	147086309	Silent	SNP	A	TCGA-BQ-7058-01A-11D-1961-08	52418048	147086309	102164312	4	8456											
BCL9	607	hgsc.bcm.edu	37	chr1	147086367	147086367	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agagcccacacctgctcagaAgactccagccaaagtggtgt	12	6	10	13	0	1	3	1	0	0	3	2	3	2	3	4	1	3	1	4	1	2	0			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr1:147086367A>G	ENST00000234739.3	+	6	1252	c.512A>G	c.(511-513)aAg>aGg	p.K171R	BCL9_ENST00000473292.1_3'UTR	NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	171					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)					CCTGCTCAGAAGACTCCAGCC	0.537			T	"IGH@, IGL@"	B-ALL																																p.K171R		Atlas-SNP	.		Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	.	BCL9	150	.	0			c.A512G						PASS	.						106	100	102					1																	147086367		2203	4300	6503	SO:0001583	missense	607	exon6			CTCAGAAGACTCC	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.512A>G	chr1.hg19:g.147086367A>G	ENSP00000234739:p.Lys171Arg	72.0	0.0	.		63.0	34.0	.	NM_004326	Q5T489	Missense_Mutation	SNP	ENST00000234739.3	hg19	CCDS30833.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.492914	0.84962	.	.	ENSG00000116128	ENST00000234739	T	0.63580	-0.05	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.64382	0.2593	L	0.41824	1.3	0.58432	D	0.999993	D;D	0.63880	0.993;0.993	D;D	0.72625	0.978;0.978	T	0.63598	-0.6601	10	0.36615	T	0.2	-20.3683	15.8615	0.79026	1.0:0.0:0.0:0.0	.	171;171	Q1JQ81;O00512	.;BCL9_HUMAN	R	171	ENSP00000234739:K171R	ENSP00000234739:K171R	K	+	2	0	BCL9	145552991	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.962000	0.76048	2.333000	0.79357	0.533000	0.62120	AAG	.	.	.	none		0.537	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326		G	147086367	A	G	147086367	3	3	140	1	0	0	0	0	1	0	0	0	1381	72	3	3	522	3	BCL9	1	147086367	Missense_Mutation	SNP	A	TCGA-BQ-7058-01A-11D-1961-08	58	147086367	102164254	5	8457											
KPRP	448834	hgsc.bcm.edu	37	chr1	152733695	152733695	+	Missense_Mutation	SNP	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	ggggcaagagagtggtgctgGctgtgggcctggtgatgtgt	5	10	21	5	0	0	2	0	1	0	1	0	3	0	2	1	6	1	3	1	6	1	0			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr1:152733695G>A	ENST00000606109.1	+	1	1659	c.1631G>A	c.(1630-1632)gGc>gAc	p.G544D	KPRP_ENST00000368773.1_Missense_Mutation_p.G544D			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	544						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)			AGTGGTGCTGGCTGTGGGCCT	0.577																																					p.G544D		Atlas-SNP	.											.	KPRP	152	.	0			c.G1631A						PASS	.						78	72	74					1																	152733695		2203	4300	6503	SO:0001583	missense	448834	exon2			GTGCTGGCTGTGG	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.1631G>A	chr1.hg19:g.152733695G>A	ENSP00000475216:p.Gly544Asp	98.0	0.0	.		117.0	52.0	.	NM_001025231		Missense_Mutation	SNP	ENST00000606109.1	hg19	CCDS30862.1	.	.	.	.	.	.	.	.	.	.	G	16.80	3.224172	0.58668	.	.	ENSG00000203786	ENST00000368773	T	0.12672	2.66	3.95	3.03	0.35002	.	0.773292	0.11405	N	0.567368	T	0.05181	0.0138	L	0.40543	1.245	0.09310	N	1	P	0.44044	0.825	B	0.41691	0.364	T	0.28170	-1.0052	10	0.51188	T	0.08	-1.4837	7.7874	0.29099	0.114:0.0:0.886:0.0	.	544	Q5T749	KPRP_HUMAN	D	544	ENSP00000357762:G544D	ENSP00000357762:G544D	G	+	2	0	KPRP	151000319	0.168000	0.22989	0.022000	0.16811	0.516000	0.34256	0.680000	0.25306	1.243000	0.43853	0.313000	0.20887	GGC	.	.	.	none		0.577	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231		A	152733695	G	A	152733695	3	1	140	1	0	0	0	0	1	0	0	0	8443	1203	42	2	1633	2	KPRP	1	152733695	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	5647328	152733695	96516926	6	8458											
NLRP3	114548	hgsc.bcm.edu	37	chr1	247597496	247597496	+	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	tggtggagctggacctgagtGacaacgccctcggtgacttc	7	9	14	11	2	0	3	0	3	0	0	2	5	0	5	2	4	2	1	2	4	1	1			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr1:247597496G>T	ENST00000336119.3	+	5	3165	c.2419G>T	c.(2419-2421)Gac>Tac	p.D807Y	NLRP3_ENST00000391827.2_Missense_Mutation_p.D750Y|NLRP3_ENST00000348069.2_Missense_Mutation_p.D750Y|NLRP3_ENST00000366496.2_Missense_Mutation_p.D807Y|NLRP3_ENST00000366497.2_Missense_Mutation_p.D807Y|NLRP3_ENST00000391828.3_Missense_Mutation_p.D807Y	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	807					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)			GGACCTGAGTGACAACGCCCT	0.577																																					p.D807Y		Atlas-SNP	.											.	NLRP3	286	.	0			c.G2419T						PASS	.						136	123	127					1																	247597496		2203	4300	6503	SO:0001583	missense	114548	exon5			CTGAGTGACAACG	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.2419G>T	chr1.hg19:g.247597496G>T	ENSP00000337383:p.Asp807Tyr	116.0	0.0	.		121.0	38.0	.	NM_004895	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Missense_Mutation	SNP	ENST00000336119.3	hg19	CCDS1632.1	.	.	.	.	.	.	.	.	.	.	g	1.230	-0.624429	0.03636	.	.	ENSG00000162711	ENST00000391828;ENST00000366497;ENST00000336119;ENST00000348069;ENST00000366496;ENST00000391827	T;T;T;D;T;D	0.87729	0.56;0.63;0.56;-2.29;0.63;-2.29	3.44	1.55	0.23275	.	0.684628	0.12798	N	0.438274	T	0.69369	0.3103	N	0.13198	0.31	0.09310	N	0.999996	B;B;B;B;B	0.33826	0.427;0.004;0.279;0.013;0.015	B;B;B;B;B	0.34301	0.179;0.01;0.086;0.043;0.012	T	0.61153	-0.7120	10	0.02654	T	1	.	4.9238	0.13883	0.1408:0.2854:0.5737:0.0	.	787;750;750;807;807	B7ZKS9;Q96P20-4;Q96P20-2;Q96P20-5;Q96P20	.;.;.;.;NALP3_HUMAN	Y	807;807;807;750;807;750	ENSP00000375704:D807Y;ENSP00000355453:D807Y;ENSP00000337383:D807Y;ENSP00000294752:D750Y;ENSP00000355452:D807Y;ENSP00000375703:D750Y	ENSP00000337383:D807Y	D	+	1	0	NLRP3	245664119	0.000000	0.05858	0.947000	0.38551	0.104000	0.19210	-1.135000	0.03225	0.475000	0.27415	0.472000	0.43445	GAC	.	.	.	none		0.577	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895		T	247597496	G	T	247597496	3	4	140	1	0	0	0	0	1	0	0	0	10485	1290	45	4	2437	4	NLRP3	1	247597496	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	94863801	247597496	1653125	7	8459											
HEATR5B	54497	hgsc.bcm.edu	37	chr2	37280725	37280725	+	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	tttagcttgtttaacacattCagcaaagtgatccaacattt	13	15	5	8	0	1	1	1	1	0	0	2	1	2	1	1	0	4	3	1	0	4	7			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr2:37280725C>A	ENST00000233099.5	-	17	2520	c.2425G>T	c.(2425-2427)Gaa>Taa	p.E809*	HEATR5B_ENST00000354531.2_Nonsense_Mutation_p.E809*	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	809						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)				TTAACACATTCAGCAAAGTGA	0.328																																					p.E809X		Atlas-SNP	.											.	HEATR5B	185	.	0			c.G2425T						PASS	.						51	52	52					2																	37280725		2203	4300	6503	SO:0001587	stop_gained	54497	exon17			CACATTCAGCAAA	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.2425G>T	chr2.hg19:g.37280725C>A	ENSP00000233099:p.Glu809*	46.0	0.0	.		28.0	8.0	.	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Nonsense_Mutation	SNP	ENST00000233099.5	hg19	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	C	42	9.667231	0.99233	.	.	ENSG00000008869	ENST00000233099;ENST00000354531	.	.	.	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	-27.7923	20.1736	0.98170	0.0:1.0:0.0:0.0	.	.	.	.	X	809	.	ENSP00000233099:E809X	E	-	1	0	HEATR5B	37134229	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.771000	0.85420	2.767000	0.95098	0.557000	0.71058	GAA	.	.	.	none		0.328	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		A	37280725	C	A	37280725	4	1	140	1	0	0	0	0	0	1	0	0	7039	835	29	4	3870	4	HEATR5B	2	37280725	Nonsense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08		37280725	205918648	8	8460											
RANBP2	5903	hgsc.bcm.edu	37	chr2	109379713	109379713	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggcccagtctatggcatgaaTaggcttccaccccaacagca	11	7	9	14	0	1	1	0	1	1	0	2	1	2	1	4	3	2	3	4	3	4	3			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr2:109379713T>C	ENST00000283195.6	+	20	2844	c.2718T>C	c.(2716-2718)aaT>aaC	p.N906N		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	906					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						ATGGCATGAATAGGCTTCCAC	0.413																																					p.N906N		Atlas-SNP	.											.	RANBP2	488	.	0			c.T2718C						PASS	.						76	72	73					2																	109379713		2203	4300	6503	SO:0001819	synonymous_variant	5903	exon20			CATGAATAGGCTT	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.2718T>C	chr2.hg19:g.109379713T>C		92.0	0.0	.		93.0	29.0	.	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Silent	SNP	ENST00000283195.6	hg19	CCDS2079.1																																																																																			.	.	.	none		0.413	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		C	109379713	T	C	109379713	2	2	140	1	0	0	0	0	0	0	0	1	13041	1403	49	3		3	RANBP2	2	109379713	Silent	SNP	T	TCGA-BQ-7058-01A-11D-1961-08	72098988	109379713	133819660	9	8461											
SLC40A1	30061	hgsc.bcm.edu	37	chr2	190428774	190428774	+	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	tcatataaaggaaagcaagaCccatgccagccagaaacaca	19	4	7	11	0	1	2	1	0	0	2	1	3	1	3	3	1	4	1	3	1	6	2			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr2:190428774C>G	ENST00000261024.2	-	7	1364	c.938G>C	c.(937-939)gGt>gCt	p.G313A		NM_014585.5	NP_055400.1	Q9NP59	S40A1_HUMAN	solute carrier family 40 (iron-regulated transporter), member 1	313					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)			GAAAGCAAGACCCATGCCAGC	0.527																																					p.G313A		Atlas-SNP	.											.	SLC40A1	51	.	0			c.G938C						PASS	.						109	88	95					2																	190428774		2203	4300	6503	SO:0001583	missense	30061	exon7			GCAAGACCCATGC	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.938G>C	chr2.hg19:g.190428774C>G	ENSP00000261024:p.Gly313Ala	53.0	0.0	.		68.0	28.0	.	NM_014585	Q6FI62|Q7Z4F8|Q8IVB2|Q9NRL0	Missense_Mutation	SNP	ENST00000261024.2	hg19	CCDS2299.1	.	.	.	.	.	.	.	.	.	.	C	16.89	3.246458	0.59103	.	.	ENSG00000138449	ENST00000261024;ENST00000544056	D	0.92752	-3.1	6.16	3.02	0.34903	Major facilitator superfamily domain, general substrate transporter (1);	0.199649	0.53938	N	0.000049	T	0.82102	0.4964	N	0.16903	0.455	0.49915	D	0.999833	P	0.34826	0.471	B	0.35470	0.203	T	0.79320	-0.1852	10	0.02654	T	1	-15.2428	12.8928	0.58082	0.1134:0.5621:0.3246:0.0	.	313	Q9NP59	S40A1_HUMAN	A	313;48	ENSP00000261024:G313A	ENSP00000261024:G313A	G	-	2	0	SLC40A1	190137019	0.713000	0.27926	1.000000	0.80357	0.999000	0.98932	1.166000	0.31834	1.561000	0.49584	0.650000	0.86243	GGT	.	.	.	none		0.527	SLC40A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255916.2			G	190428774	C	G	190428774	3	3	140	1	0	0	0	0	1	0	0	0	14641	507	18	4	785	4	SLC40A1	2	190428774	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08	81049061	190428774	52770599	10	8462											
VPRBP	9730	hgsc.bcm.edu	37	chr3	51456171	51456171	+	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	gtgatggctgagttgtgacaGttatagctggcctcctcctg	6	13	13	9	0	0	3	0	3	0	0	2	3	2	3	3	2	1	4	3	2	2	3			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr3:51456171G>T	ENST00000335891.5	-	8	2058	c.2049C>A	c.(2047-2049)aaC>aaA	p.N683K				Q9Y4B6	VPRBP_HUMAN	Vpr (HIV-1) binding protein	1132					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)		AGTTGTGACAGTTATAGCTGG	0.502																																					p.N1079K		Atlas-SNP	.											.	VPRBP	107	.	0			c.C3237A						PASS	.						135	138	137					3																	51456171		2033	4194	6227	SO:0001583	missense	9730	exon15			GTGACAGTTATAG	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.2049C>A	chr3.hg19:g.51456171G>T	ENSP00000338857:p.Asn683Lys	198.0	0.0	.		208.0	171.0	.	NM_014703	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Missense_Mutation	SNP	ENST00000335891.5	hg19		.	.	.	.	.	.	.	.	.	.	G	13.79	2.340869	0.41498	.	.	ENSG00000145041	ENST00000423656;ENST00000335891	T;T	0.01240	5.12;5.12	5.99	4.03	0.46877	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.127622	0.64402	D	0.000001	T	0.01156	0.0038	L	0.31926	0.97	0.58432	D	0.999997	B	0.02656	0.0	B	0.04013	0.001	T	0.45614	-0.9249	10	0.07175	T	0.84	-19.5801	6.0918	0.19999	0.2259:0.1364:0.6376:0.0	.	1132	Q9Y4B6	VPRBP_HUMAN	K	703;683	ENSP00000393183:N703K;ENSP00000338857:N683K	ENSP00000338857:N683K	N	-	3	2	VPRBP	51431211	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.575000	0.46025	1.377000	0.46286	0.655000	0.94253	AAC	.	.	.	none		0.502	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014703		T	51456171	G	T	51456171	3	4	140	1	0	0	0	0	1	0	0	0	17197	1020	36	4	1167	4	VPRBP	3	51456171	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08		51456171	146566259	11	8463											
PBRM1	55193	hgsc.bcm.edu	37	chr3	52584609	52584609	+	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	ccagctggatgtgggccgggAtatggaggtggtgcctgctg	5	9	19	8	1	0	0	0	0	0	0	0	3	0	3	3	6	3	2	3	6	1	1			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr3:52584609A>T	ENST00000296302.7	-	29	4726	c.4725T>A	c.(4723-4725)taT>taA	p.Y1575*	PBRM1_ENST00000394830.3_Nonsense_Mutation_p.Y1468*|PBRM1_ENST00000356770.4_Nonsense_Mutation_p.Y1488*|RNU6-856P_ENST00000516959.1_RNA|SMIM4_ENST00000476842.1_Intron|PBRM1_ENST00000409767.1_Nonsense_Mutation_p.Y1483*|PBRM1_ENST00000410007.1_Nonsense_Mutation_p.Y1495*|PBRM1_ENST00000337303.4_Nonsense_Mutation_p.Y1468*|PBRM1_ENST00000409114.3_Nonsense_Mutation_p.Y1538*|PBRM1_ENST00000409057.1_Nonsense_Mutation_p.Y1520*			Q86U86	PB1_HUMAN	polybromo 1	1575	Pro-rich.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		GTGGGCCGGGATATGGAGGTG	0.572			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.Y1468X		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.T4404A						PASS	.						81	84	83					3																	52584609		2203	4300	6503	SO:0001587	stop_gained	55193	exon29			GCCGGGATATGGA	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.4725T>A	chr3.hg19:g.52584609A>T	ENSP00000296302:p.Tyr1575*	87.0	0.0	.		95.0	68.0	.	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Nonsense_Mutation	SNP	ENST00000296302.7	hg19		.	.	.	.	.	.	.	.	.	.	A	43	9.940619	0.99300	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767	.	.	.	5.93	4.78	0.61160	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.079	8.842	0.35148	0.7955:0.0:0.2045:0.0	.	.	.	.	X	1488;1468;1575;1468;1520;1495;1538;1483	.	ENSP00000296302:Y1575X	Y	-	3	2	PBRM1	52559649	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.050000	0.30404	1.087000	0.41251	-0.250000	0.11733	TAT	.	.	.	none		0.572	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		T	52584609	A	T	52584609	4	4	140	1	0	0	0	0	0	1	0	0	11498	340	12	5	352	5	PBRM1	3	52584609	Nonsense_Mutation	SNP	A	TCGA-BQ-7058-01A-11D-1961-08	1128438	52584609	145437821	12	8464											
COL8A1	1295	hgsc.bcm.edu	37	chr3	99513269	99513269	+	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	gccaggagccatgggcatgcCtggggcaaaaggagaaattg	12	5	16	8	0	0	1	0	0	0	1	0	3	0	2	3	5	2	2	3	5	3	1			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr3:99513269C>T	ENST00000261037.3	+	5	904	c.524C>T	c.(523-525)cCt>cTt	p.P175L	COL8A1_ENST00000273342.4_Missense_Mutation_p.P175L	NM_001850.4	NP_001841.2	P27658	CO8A1_HUMAN	collagen, type VIII, alpha 1	175	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						ATGGGCATGCCTGGGGCAAAA	0.552																																					p.P175L		Atlas-SNP	.											.	COL8A1	68	.	0			c.C524T						PASS	.						44	48	46					3																	99513269		2203	4300	6503	SO:0001583	missense	1295	exon5			GCATGCCTGGGGC	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.524C>T	chr3.hg19:g.99513269C>T	ENSP00000261037:p.Pro175Leu	49.0	0.0	.		52.0	44.0	.	NM_001850	D3DN42|Q53XI6|Q96D07	Missense_Mutation	SNP	ENST00000261037.3	hg19	CCDS2934.1	.	.	.	.	.	.	.	.	.	.	C	13.63	2.294831	0.40594	.	.	ENSG00000144810	ENST00000261037;ENST00000273342	D;D	0.96685	-4.09;-4.09	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	D	0.97945	0.9324	M	0.88450	2.955	0.58432	D	0.999999	P;P	0.51449	0.945;0.945	P;P	0.57204	0.815;0.815	D	0.98294	1.0515	10	0.54805	T	0.06	.	16.849	0.85988	0.0:1.0:0.0:0.0	.	176;175	E7EPK9;P27658	.;CO8A1_HUMAN	L	175	ENSP00000261037:P175L;ENSP00000273342:P175L	ENSP00000261037:P175L	P	+	2	0	COL8A1	100995959	0.976000	0.34144	0.960000	0.40013	0.992000	0.81027	2.529000	0.45632	2.583000	0.87209	0.655000	0.94253	CCT	.	.	.	none		0.552	COL8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309001.1	NM_001850		T	99513269	C	T	99513269	3	4	140	1	0	0	0	0	1	0	0	0	3707	681	24	2	530	2	COL8A1	3	99513269	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08	46928660	99513269	98509161	13	8465											
PDIA5	10954	hgsc.bcm.edu	37	chr3	122821610	122821610	+	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	tttgacagggatggtgcattTcatactgaatataaccgagc	12	12	10	7	1	1	2	1	2	0	0	1	4	1	3	1	2	4	1	1	2	4	5			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr3:122821610T>A	ENST00000316218.7	+	5	449	c.354T>A	c.(352-354)ttT>ttA	p.F118L		NM_006810.3	NP_006801.1	Q14554	PDIA5_HUMAN	protein disulfide isomerase family A, member 5	118					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|oxidation-reduction process (GO:0055114)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	oxidoreductase activity (GO:0016491)|protein disulfide isomerase activity (GO:0003756)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	21				GBM - Glioblastoma multiforme(114;0.0427)		ATGGTGCATTTCATACTGAAT	0.393																																					p.F118L		Atlas-SNP	.											.	PDIA5	66	.	0			c.T354A						PASS	.						138	121	127					3																	122821610		2203	4300	6503	SO:0001583	missense	10954	exon5			TGCATTTCATACT	AK054963	CCDS3020.1	3q21.1	2009-11-20	2005-06-29		ENSG00000065485	ENSG00000065485	5.3.4.1	"Protein disulfide isomerases"	24811	protein-coding gene	gene with protein product			"protein disulfide isomerase-associated 5"			7556671	Standard	NM_006810		Approved	PDIR, FLJ30401	uc003egc.2	Q14554	OTTHUMG00000159558	ENST00000316218.7:c.354T>A	chr3.hg19:g.122821610T>A	ENSP00000323313:p.Phe118Leu	37.0	0.0	.		27.0	24.0	.	NM_006810	D3DN95|Q9BV43	Missense_Mutation	SNP	ENST00000316218.7	hg19	CCDS3020.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.148995	0.78001	.	.	ENSG00000065485	ENST00000316218;ENST00000484644	T	0.20598	2.06	4.97	4.97	0.65823	Thioredoxin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.41903	0.1179	M	0.76574	2.34	0.53688	D	0.999974	D	0.76494	0.999	D	0.75484	0.986	T	0.30621	-0.9972	10	0.14656	T	0.56	.	12.261	0.54651	0.0:0.0:0.0:1.0	.	118	Q14554	PDIA5_HUMAN	L	118;22	ENSP00000323313:F118L	ENSP00000323313:F118L	F	+	3	2	PDIA5	124304300	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.656000	0.46716	2.080000	0.62538	0.460000	0.39030	TTT	.	.	.	none		0.393	PDIA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356192.1	NM_006810		A	122821610	T	A	122821610	3	1	140	1	0	0	0	0	1	0	0	0	11678	1780	62	5	372	5	PDIA5	3	122821610	Missense_Mutation	SNP	T	TCGA-BQ-7058-01A-11D-1961-08	23308341	122821610	75200820	14	8466											
AFM	173	hgsc.bcm.edu	37	chr4	74364944	74364944	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgtacgctaagtgaagagtTtgcctgtgttgataatttgg	9	15	12	5	1	0	3	0	2	0	1	0	3	0	3	1	1	2	4	1	1	4	6			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr4:74364944T>C	ENST00000226355.3	+	11	1496	c.1403T>C	c.(1402-1404)tTt>tCt	p.F468S		NM_001133.2	NP_001124.1	P43652	AFAM_HUMAN	afamin	468	Albumin 3. {ECO:0000255|PROSITE- ProRule:PRU00769}.				vitamin transport (GO:0051180)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	vitamin E binding (GO:0008431)			breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	Breast(15;0.00102)		Epithelial(6;5.69e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|all cancers(17;0.000555)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AGTGAAGAGTTTGCCTGTGTT	0.403																																					p.F468S		Atlas-SNP	.											.	AFM	101	.	0			c.T1403C						PASS	.						184	158	167					4																	74364944		2203	4300	6503	SO:0001583	missense	173	exon11			AAGAGTTTGCCTG	L32140	CCDS3557.1	4q13.3	2008-06-11			ENSG00000079557	ENSG00000079557			316	protein-coding gene	gene with protein product		104145				7517938	Standard	NM_001133		Approved	ALB2, ALBA	uc003hhb.3	P43652	OTTHUMG00000130004	ENST00000226355.3:c.1403T>C	chr4.hg19:g.74364944T>C	ENSP00000226355:p.Phe468Ser	66.0	0.0	.		49.0	18.0	.	NM_001133	A8K3E1|Q32MR3|Q4W5C5	Missense_Mutation	SNP	ENST00000226355.3	hg19	CCDS3557.1	.	.	.	.	.	.	.	.	.	.	T	11.29	1.595211	0.28445	.	.	ENSG00000079557	ENST00000226355	T	0.57107	0.42	5.55	4.38	0.52667	Serum albumin-like (1);Serum albumin, N-terminal (3);	0.351548	0.26931	N	0.021779	T	0.55401	0.1918	L	0.41356	1.27	0.29327	N	0.866933	D	0.69078	0.997	D	0.65773	0.938	T	0.49000	-0.8984	10	0.21014	T	0.42	.	7.4141	0.27034	0.0:0.0943:0.0:0.9057	.	468	P43652	AFAM_HUMAN	S	468	ENSP00000226355:F468S	ENSP00000226355:F468S	F	+	2	0	AFM	74583808	1.000000	0.71417	1.000000	0.80357	0.122000	0.20287	2.017000	0.40981	2.111000	0.64477	0.533000	0.62120	TTT	.	.	.	none		0.403	AFM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252275.2			C	74364944	T	C	74364944	3	2	140	1	0	0	0	0	1	0	0	0	361	1841	64	3	1445	3	AFM	4	74364944	Missense_Mutation	SNP	T	TCGA-BQ-7058-01A-11D-1961-08		74364944	116789332	15	8467											
LEF1	51176	hgsc.bcm.edu	37	chr4	109084775	109084775	+	Missense_Mutation	SNP	A	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	tttgacatgtatgggtcgttAttcatatttggcatcattat	9	19	8	5	1	2	1	2	1	0	0	3	1	2	1	0	2	0	3	0	2	4	7			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr4:109084775A>C	ENST00000265165.1	-	3	1017	c.363T>G	c.(361-363)aaT>aaG	p.N121K	LEF1_ENST00000510624.1_Missense_Mutation_p.N53K|LEF1_ENST00000438313.2_Missense_Mutation_p.N121K|LEF1_ENST00000379951.2_Missense_Mutation_p.N121K|LEF1_ENST00000512172.1_Missense_Mutation_p.N53K	NM_016269.4	NP_057353.1	Q9UJU2	LEF1_HUMAN	lymphoid enhancer-binding factor 1	121	Pro-rich.				alpha-beta T cell differentiation (GO:0046632)|anatomical structure regression (GO:0060033)|apoptotic process involved in morphogenesis (GO:0060561)|apoptotic process involved in patterning of blood vessels (GO:1902262)|B cell proliferation (GO:0042100)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cell chemotaxis (GO:0060326)|cellular response to cytokine stimulus (GO:0071345)|cellular response to interleukin-4 (GO:0071353)|chorio-allantoic fusion (GO:0060710)|dentate gyrus development (GO:0021542)|embryonic limb morphogenesis (GO:0030326)|epithelial to mesenchymal transition (GO:0001837)|eye pigmentation (GO:0048069)|face morphogenesis (GO:0060325)|forebrain neuroblast division (GO:0021873)|forebrain neuron differentiation (GO:0021879)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|mammary gland development (GO:0030879)|muscle fiber development (GO:0048747)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic process in bone marrow (GO:0071866)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA binding (GO:0043392)|negative regulation of estrogen receptor binding (GO:0071899)|negative regulation of interleukin-13 production (GO:0032696)|negative regulation of interleukin-4 production (GO:0032713)|negative regulation of interleukin-5 production (GO:0032714)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|neutrophil differentiation (GO:0030223)|odontoblast differentiation (GO:0071895)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|paraxial mesoderm formation (GO:0048341)|patterning of blood vessels (GO:0001569)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of cell cycle process (GO:0090068)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation in bone marrow (GO:0071864)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of gene expression (GO:0010628)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell-cell adhesion (GO:0022407)|regulation of striated muscle tissue development (GO:0016202)|sensory perception of taste (GO:0050909)|somitogenesis (GO:0001756)|sprouting angiogenesis (GO:0002040)|steroid hormone mediated signaling pathway (GO:0043401)|T cell receptor V(D)J recombination (GO:0033153)|T-helper 1 cell differentiation (GO:0045063)|tongue development (GO:0043586)|trachea gland development (GO:0061153)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|C2H2 zinc finger domain binding (GO:0070742)|chromatin binding (GO:0003682)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|enhancer binding (GO:0035326)|estrogen receptor activity (GO:0030284)|estrogen receptor binding (GO:0030331)|gamma-catenin binding (GO:0045295)|histone binding (GO:0042393)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(14)|prostate(1)|urinary_tract(1)	25				OV - Ovarian serous cystadenocarcinoma(123;0.000224)		ATGGGTCGTTATTCATATTTG	0.428																																					p.N121K		Atlas-SNP	.											.	LEF1	93	.	0			c.T363G						PASS	.						196	173	181					4																	109084775		2203	4300	6503	SO:0001583	missense	51176	exon3			GTCGTTATTCATA		CCDS3679.1, CCDS47122.1, CCDS47123.1, CCDS54791.1	4q23-q25	2011-07-08			ENSG00000138795	ENSG00000138795			6551	protein-coding gene	gene with protein product		153245				1783375	Standard	NM_016269		Approved	TCF1ALPHA, TCF10, TCF7L3	uc003hyt.2	Q9UJU2	OTTHUMG00000131809	ENST00000265165.1:c.363T>G	chr4.hg19:g.109084775A>C	ENSP00000265165:p.Asn121Lys	169.0	0.0	.		103.0	40.0	.	NM_001130714	B4DG38|B7Z8E2|E9PDK3|Q3ZCU4|Q9HAZ0	Missense_Mutation	SNP	ENST00000265165.1	hg19	CCDS3679.1	.	.	.	.	.	.	.	.	.	.	A	9.451	1.090605	0.20471	.	.	ENSG00000138795	ENST00000265165;ENST00000379951;ENST00000438313;ENST00000510624;ENST00000515500;ENST00000512172	D;D;D;D	0.99113	-5.42;-5.42;-5.42;-5.44	5.74	-3.28	0.05033	CTNNB1 binding, N-teminal (1);	0.187580	0.53938	D	0.000050	D	0.96728	0.8932	L	0.47716	1.5	0.32383	N	0.554276	P;P;P;P;B	0.42078	0.77;0.643;0.728;0.732;0.322	B;B;B;B;B	0.40901	0.184;0.132;0.156;0.343;0.216	D	0.94059	0.7325	10	0.28530	T	0.3	-19.1486	13.7994	0.63190	0.4778:0.0:0.5222:0.0	.	53;6;121;121;121	E9PDK3;B4DZY5;Q9UJU2-6;Q9UJU2-5;Q9UJU2	.;.;.;.;LEF1_HUMAN	K	121;121;121;53;53;53	ENSP00000265165:N121K;ENSP00000369284:N121K;ENSP00000406176:N121K;ENSP00000422840:N53K	ENSP00000265165:N121K	N	-	3	2	LEF1	109304224	0.997000	0.39634	0.018000	0.16275	0.994000	0.84299	0.624000	0.24462	-0.783000	0.04534	0.460000	0.39030	AAT	.	.	.	none		0.428	LEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254749.2			C	109084775	A	C	109084775	3	2	140	1	0	0	0	0	1	0	0	0	8721	446	16	5	956	5	LEF1	4	109084775	Missense_Mutation	SNP	A	TCGA-BQ-7058-01A-11D-1961-08	34719831	109084775	82069501	16	8468											
LRBA	987	hgsc.bcm.edu	37	chr4	151827549	151827549	+	Frame_Shift_Del	DEL	A	A	-																															attccatgataaaggccagcAaggttgaactagaatttttt																										TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr4:151827549delA	ENST00000357115.3	-	12	1745	c.1502delT	c.(1501-1503)ttgfs	p.L502fs	LRBA_ENST00000510413.1_Frame_Shift_Del_p.L502fs|LRBA_ENST00000507224.1_Frame_Shift_Del_p.L502fs|LRBA_ENST00000535741.1_Frame_Shift_Del_p.L502fs	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	502						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)					AAAGGCCAGCAAGGTTGAACT	0.333																																					p.L501fs		Atlas-INDEL	.											.	LRBA	253	.	0			c.1503delG						PASS	.						85	89	88					4																	151827549		2203	4300	6503	SO:0001589	frameshift_variant	987	exon12			.	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.1502delT	chr4.hg19:g.151827549delA	ENSP00000349629:p.Leu502fs	145.0	0.0	0		120.0	36.0	0.3	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Frame_Shift_Del	DEL	ENST00000357115.3	hg19	CCDS3773.1																																																																																			.	.	.	none		0.333	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			-	151827549	A	-	151827549	7	5	140	1	0	1	0	1	0	0	0	0	8938	131	5	0	7277	0	LRBA	4	151827549	Frame_Shift_Del	DEL	A	TCGA-BQ-7058-01A-11D-1961-08	42742774	151827549	39326727	17	8469											
FAM105A	54491	hgsc.bcm.edu	37	chr5	14609077	14609077	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcctctgatcctttgagctTcatgatgaatcacctgaatt	10	15	6	10	0	3	5	2	5	1	0	5	5	5	5	3	0	1	1	3	0	2	3			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr5:14609077T>C	ENST00000274217.3	+	7	968	c.848T>C	c.(847-849)tTc>tCc	p.F283S		NM_019018.2	NP_061891.1	Q9NUU6	F105A_HUMAN	family with sequence similarity 105, member A	283	OTU.									large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	Lung NSC(4;0.00592)					CCTTTGAGCTTCATGATGAAT	0.433																																					p.F283S		Atlas-SNP	.											.	FAM105A	32	.	0			c.T848C						PASS	.						149	153	152					5																	14609077		2203	4300	6503	SO:0001583	missense	54491	exon7			TGAGCTTCATGAT		CCDS3884.1	5p15.2	2014-02-24			ENSG00000145569	ENSG00000145569		"OTU domain containing"	25629	protein-coding gene	gene with protein product						12477932	Standard	NM_019018		Approved	FLJ11127, NET20	uc003jfj.3	Q9NUU6	OTTHUMG00000131056	ENST00000274217.3:c.848T>C	chr5.hg19:g.14609077T>C	ENSP00000274217:p.Phe283Ser	217.0	0.0	.		222.0	83.0	.	NM_019018	Q53H50|Q9H037	Missense_Mutation	SNP	ENST00000274217.3	hg19	CCDS3884.1	.	.	.	.	.	.	.	.	.	.	T	19.07	3.756651	0.69648	.	.	ENSG00000145569	ENST00000274217	T	0.16743	2.32	4.89	4.89	0.63831	.	0.000000	0.64402	D	0.000001	T	0.37625	0.1010	M	0.72894	2.215	0.41254	D	0.986734	D	0.76494	0.999	D	0.68943	0.961	T	0.23691	-1.0181	10	0.87932	D	0	-22.3388	10.4145	0.44314	0.1462:0.0:0.0:0.8538	.	283	Q9NUU6	F105A_HUMAN	S	283	ENSP00000274217:F283S	ENSP00000274217:F283S	F	+	2	0	FAM105A	14662077	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.702000	0.61817	1.819000	0.53055	0.477000	0.44152	TTC	.	.	.	none		0.433	FAM105A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253710.1	NM_019018		C	14609077	T	C	14609077	3	2	140	1	0	0	0	0	1	0	0	0	5391	1783	62	3	874	3	FAM105A	5	14609077	Missense_Mutation	SNP	T	TCGA-BQ-7058-01A-11D-1961-08		14609077	166306183	18	8470											
TXNDC5	81567	hgsc.bcm.edu	37	chr6	7889004	7889004	+	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	gtgacggtctccgtcgctccAgtctctgtgcgctgcagctg	3	11	13	14	4	2	1	0	1	2	0	6	1	3	1	2	1	3	4	2	1	0	0			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr6:7889004A>C	ENST00000379757.4	-	7	934	c.897T>G	c.(895-897)acT>acG	p.T299T	TXNDC5_ENST00000473453.1_Silent_p.T191T|TXNDC5_ENST00000539054.1_Silent_p.T227T|BLOC1S5-TXNDC5_ENST00000439343.2_3'UTR	NM_030810.3	NP_110437.2	Q8NBS9	TXND5_HUMAN	thioredoxin domain containing 5 (endoplasmic reticulum)	299					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)					CCGTCGCTCCAGTCTCTGTGC	0.642																																					p.T299T	Ovarian(119;1430 1625 3928 26125 34589)	Atlas-SNP	.											.	TXNDC5	33	.	0			c.T897G						PASS	.						136	131	132					6																	7889004		2203	4300	6503	SO:0001819	synonymous_variant	81567	exon7			CGCTCCAGTCTCT	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.897T>G	chr6.hg19:g.7889004A>C		250.0	0.0	.		275.0	114.0	.	NM_030810	B2RDM2|Q5TCQ0|Q8ND33|Q8TCT2|Q9BVH9	Silent	SNP	ENST00000379757.4	hg19	CCDS4505.1																																																																																			.	.	.	none		0.642	TXNDC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039792.1	NM_030810		C	7889004	A	C	7889004	2	2	140	1	0	0	0	0	0	0	0	1	16811	175	7	5		5	TXNDC5	6	7889004	Silent	SNP	A	TCGA-BQ-7058-01A-11D-1961-08		7889004	163226063	19	8471											
UNC5D	137970	hgsc.bcm.edu	37	chr8	35541184	35541184	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcggactcaggaaattacacCtgcatggcagccaacatcgt	12	8	9	12	2	1	0	1	0	0	0	3	2	1	2	2	3	4	2	2	3	3	1			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr8:35541184C>T	ENST00000404895.2	+	5	1018	c.690C>T	c.(688-690)acC>acT	p.T230T	UNC5D_ENST00000287272.2_Silent_p.T230T|UNC5D_ENST00000420357.1_Silent_p.T230T|UNC5D_ENST00000416672.1_Silent_p.T230T|UNC5D_ENST00000453357.2_Silent_p.T225T	NM_080872.2	NP_543148.2	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)	230	Ig-like C2-type.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|pyramidal neuron differentiation (GO:0021859)|regulation of neuron migration (GO:2001222)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)		p.T225T(1)		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)		GAAATTACACCTGCATGGCAG	0.537																																					p.T230T		Atlas-SNP	.											.	UNC5D	393	.	1	Substitution - coding silent(1)	lung(1)	c.C690T						PASS	.						86	72	77					8																	35541184		2203	4300	6503	SO:0001819	synonymous_variant	137970	exon5			TTACACCTGCATG	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.690C>T	chr8.hg19:g.35541184C>T		55.0	0.0	.		58.0	22.0	.	NM_080872	Q8WYP7	Silent	SNP	ENST00000404895.2	hg19	CCDS6093.2																																																																																			.	.	.	none		0.537	UNC5D-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347586.2			T	35541184	C	T	35541184	2	4	140	1	0	0	0	0	0	0	0	1	17007	668	24	2		2	UNC5D	8	35541184	Silent	SNP	C	TCGA-BQ-7058-01A-11D-1961-08		35541184	110822838	20	8472											
CDH17	1015	hgsc.bcm.edu	37	chr8	95158391	95158391	+	Frame_Shift_Del	DEL	C	C	-																															gacacagagctcaaggaagaCccccctaaggaattgaatga																								rs537643053	byFrequency	TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr8:95158391delC	ENST00000027335.3	-	15	2056	c.1932delG	c.(1930-1932)gggfs	p.G644fs	CDH17_ENST00000441892.2_Frame_Shift_Del_p.G430fs|CDH17_ENST00000450165.2_Frame_Shift_Del_p.G644fs	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	644	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)			NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			TCAAGGAAGACCCCCCTAAGG	0.438																																					p.S645fs		Atlas-INDEL	.											.	CDH17	119	.	0			c.1933delT						PASS	.						80	74	76					8																	95158391		2203	4300	6503	SO:0001589	frameshift_variant	1015	exon15			.	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"Cadherins / Major cadherins"	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.1932delG	chr8.hg19:g.95158391delC	ENSP00000027335:p.Gly644fs	81.0	0.0	0		76.0	24.0	0.315789	NM_004063	Q15336|Q2M2E0	Frame_Shift_Del	DEL	ENST00000027335.3	hg19	CCDS6260.1																																																																																			.	.	.	none		0.438	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063		-	95158391	C	-	95158391	7	5	140	1	0	1	0	1	0	0	0	0	3104	494	18	0	582	0	CDH17	8	95158391	Frame_Shift_Del	DEL	C	TCGA-BQ-7058-01A-11D-1961-08	59617207	95158391	51205631	21	8473											
NOV	4856	hgsc.bcm.edu	37	chr8	120429171	120429171	+	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	cagtggcctctactgtgatcGcagcgcggaccccagcaacc	8	6	11	16	3	1	1	0	1	1	0	2	2	1	2	4	2	4	2	4	2	2	1			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr8:120429171G>C	ENST00000259526.3	+	2	499	c.272G>C	c.(271-273)cGc>cCc	p.R91P	RP11-775B15.2_ENST00000519786.1_RNA	NM_002514.3	NP_002505.1	Q9UIW2	PLXA1_HUMAN	nephroblastoma overexpressed	0	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|skin(3)	21	all_cancers(13;3.84e-26)|Lung NSC(37;1.19e-08)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000507)			TACTGTGATCGCAGCGCGGAC	0.612											OREG0018940	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R91P		Atlas-SNP	.											.	NOV	51	.	0			c.G272C						PASS	.						48	44	46					8																	120429171		2203	4300	6503	SO:0001583	missense	4856	exon2			GTGATCGCAGCGC	X96584	CCDS6328.1	8q24.12	2012-02-27	2012-02-27		ENSG00000136999	ENSG00000136999			7885	protein-coding gene	gene with protein product		164958	"nephroblastoma overexpressed gene"			1334251	Standard	NM_002514		Approved	IGFBP9, CCN3	uc003yoq.2	P48745	OTTHUMG00000164984	ENST00000259526.3:c.272G>C	chr8.hg19:g.120429171G>C	ENSP00000259526:p.Arg91Pro	44.0	0.0	.	1503	49.0	23.0	.	NM_002514		Missense_Mutation	SNP	ENST00000259526.3	hg19	CCDS6328.1	.	.	.	.	.	.	.	.	.	.	G	19.27	3.796255	0.70567	.	.	ENSG00000136999	ENST00000259526	T	0.61274	0.12	4.93	4.05	0.47172	Insulin-like growth factor-binding protein, IGFBP (2);	0.205916	0.45126	D	0.000394	T	0.50497	0.1619	N	0.11313	0.125	0.37745	D	0.925773	D	0.71674	0.998	P	0.61132	0.884	T	0.56932	-0.7897	10	0.45353	T	0.12	-42.0353	8.4948	0.33121	0.0773:0.0:0.7703:0.1525	.	91	P48745	NOV_HUMAN	P	91	ENSP00000259526:R91P	ENSP00000259526:R91P	R	+	2	0	NOV	120498352	0.151000	0.22747	1.000000	0.80357	0.990000	0.78478	0.194000	0.17135	1.436000	0.47453	0.561000	0.74099	CGC	.	.	.	none		0.612	NOV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381301.1	NM_002514		C	120429171	G	C	120429171	3	2	140	1	0	0	0	0	1	0	0	0	10560	1087	38	4	278	4	NOV	8	120429171	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	25270780	120429171	25934851	22	8474											
RASEF	158158	hgsc.bcm.edu	37	chr9	85597649	85597649	+	Missense_Mutation	SNP	A	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	ttggaattggtcccggttagAttggtaatggatctgctgtc	7	15	13	6	1	1	1	0	0	1	1	3	3	2	3	1	5	1	3	1	5	3	5			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr9:85597649A>C	ENST00000376447.3	-	17	2426	c.2166T>G	c.(2164-2166)aaT>aaG	p.N722K		NM_152573.2	NP_689786.2	Q8IZ41	RASEF_HUMAN	RAS and EF-hand domain containing	722					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						TCCCGGTTAGATTGGTAATGG	0.433																																					p.N722K		Atlas-SNP	.											.	RASEF	69	.	0			c.T2166G						PASS	.						391	359	370					9																	85597649		2203	4300	6503	SO:0001583	missense	158158	exon17			GGTTAGATTGGTA	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.2166T>G	chr9.hg19:g.85597649A>C	ENSP00000365630:p.Asn722Lys	252.0	0.0	.		273.0	87.0	.	NM_152573	A6NC29|Q96N04	Missense_Mutation	SNP	ENST00000376447.3	hg19	CCDS6662.1	.	.	.	.	.	.	.	.	.	.	A	8.015	0.758440	0.15846	.	.	ENSG00000165105	ENST00000376447	T	0.60797	0.16	5.05	-4.07	0.03975	.	0.378995	0.27640	N	0.018471	T	0.26774	0.0655	N	0.12746	0.255	0.20563	N	0.999889	B	0.09022	0.002	B	0.04013	0.001	T	0.36138	-0.9760	10	0.05721	T	0.95	.	9.4599	0.38778	0.2492:0.0:0.6328:0.118	.	722	Q8IZ41	RASEF_HUMAN	K	722	ENSP00000365630:N722K	ENSP00000365630:N722K	N	-	3	2	RASEF	84787469	0.953000	0.32496	0.062000	0.19696	0.834000	0.47266	0.266000	0.18534	-0.671000	0.05274	-0.353000	0.07706	AAT	.	.	.	none		0.433	RASEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052825.1	NM_152573		C	85597649	A	C	85597649	3	2	140	1	0	0	0	0	1	0	0	0	13081	330	12	5	60	5	RASEF	9	85597649	Missense_Mutation	SNP	A	TCGA-BQ-7058-01A-11D-1961-08		85597649	55615782	23	8475											
LOC645961	645961	hgsc.bcm.edu	37	chr9	90747533	90747533	+	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	1	0	0	0	0	0	0	0	0	gctcatgagaggaccgggagGctccatcaggtgttcttttg	7	11	14	9	1	3	1	2	1	1	1	4	4	4	3	2	4	0	3	2	4	0	3			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr9:90747533G>T								U6 (134283 upstream) : U3 (241650 downstream)																							GGACCGGGAGGCTCCATCAGG	0.597																																					p.A140D		Atlas-SNP	.											.	.	.	.	0			c.C419A						PASS	.						86	104	99					9																	90747533		692	1591	2283	SO:0001628	intergenic_variant	645961	exon4			CGGGAGGCTCCAT																													chr9.hg19:g.90747533G>T		201.0	0.0	.		230.0	25.0	.	NM_001166137		Missense_Mutation	SNP		hg19																																																																																				.	.	.	none	0	0.597									T	90747533	G	T	90747533	1	4	140	0	1	0	0	0	0	0	0	0	8890	1203	42	4		4	LOC645961	9	90747533	IGR	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	5149884	90747533	50465898	24	8476											
PAPPA	5069	hgsc.bcm.edu	37	chr9	118969850	118969850	+	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	tggcaggagtagcaacttggCcatgggacaaggaggccctg	10	6	16	9	0	0	0	0	0	0	0	0	3	0	3	2	6	2	3	2	6	3	2			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr9:118969850C>T	ENST00000328252.3	+	3	1963	c.1594C>T	c.(1594-1596)Cca>Tca	p.P532S	PAPPA_ENST00000534838.1_Intron	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	532	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						AGCAACTTGGCCATGGGACAA	0.433																																					p.P532S		Atlas-SNP	.											.	PAPPA	243	.	0			c.C1594T						PASS	.						72	68	69					9																	118969850		2203	4300	6503	SO:0001583	missense	5069	exon3			ACTTGGCCATGGG		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.1594C>T	chr9.hg19:g.118969850C>T	ENSP00000330658:p.Pro532Ser	96.0	0.0	.		74.0	23.0	.	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Missense_Mutation	SNP	ENST00000328252.3	hg19	CCDS6813.1	.	.	.	.	.	.	.	.	.	.	C	35	5.509017	0.96386	.	.	ENSG00000182752	ENST00000328252;ENST00000443904	T	0.05258	3.47	6.07	6.07	0.98685	Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.44030	0.1274	H	0.97315	3.98	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.61826	-0.6983	10	0.87932	D	0	-9.2416	20.6439	0.99570	0.0:1.0:0.0:0.0	.	74;532	E7EMD3;Q13219	.;PAPP1_HUMAN	S	532;74	ENSP00000330658:P532S	ENSP00000330658:P532S	P	+	1	0	PAPPA	118009671	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.786000	0.85741	2.884000	0.98904	0.655000	0.94253	CCA	.	.	.	none		0.433	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		T	118969850	C	T	118969850	3	4	140	1	0	0	0	0	1	0	0	0	11439	739	26	2	1604	2	PAPPA	9	118969850	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08	28222317	118969850	22243581	25	8477											
ASTN2	23245	hgsc.bcm.edu	37	chr9	119495750	119495750	+	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	ctcctccaccggcagcgggaTcaccaacagcccatcggcca	9	4	9	19	3	1	0	1	0	0	0	4	1	3	1	6	3	3	1	6	3	1	0	rs150944935	byFrequency	TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr9:119495750T>A	ENST00000313400.4	-	14	2549	c.2449A>T	c.(2449-2451)Atc>Ttc	p.I817F	ASTN2_ENST00000361209.2_Missense_Mutation_p.I766F|ASTN2_ENST00000373996.3_Missense_Mutation_p.I813F|ASTN2_ENST00000361477.3_5'UTR			O75129	ASTN2_HUMAN	astrotactin 2	817					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						GGCAGCGGGATCACCAACAGC	0.602																																					p.I766F		Atlas-SNP	.											.	ASTN2	307	.	0			c.A2296T						PASS	.						73	78	76					9																	119495750		2203	4300	6503	SO:0001583	missense	23245	exon13			GCGGGATCACCAA	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.2449A>T	chr9.hg19:g.119495750T>A	ENSP00000314038:p.Ile817Phe	115.0	0.0	.		165.0	16.0	.	NM_014010	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	hg19		.	.	.	.	.	.	.	.	.	.	T	19.46	3.831645	0.71258	.	.	ENSG00000148219	ENST00000313400;ENST00000373996;ENST00000373986;ENST00000361209	T;T;T;T	0.15372	2.75;2.74;2.43;2.77	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.21801	0.0525	N	0.14661	0.345	0.80722	D	1	D;D;D	0.71674	0.991;0.998;0.978	P;P;P	0.61874	0.791;0.895;0.877	T	0.08351	-1.0726	9	.	.	.	-20.5951	14.7786	0.69749	0.0:0.0:0.0:1.0	.	766;817;813	O75129-2;O75129;O75129-3	.;ASTN2_HUMAN;.	F	817;813;540;766	ENSP00000314038:I817F;ENSP00000363108:I813F;ENSP00000363098:I540F;ENSP00000354504:I766F	.	I	-	1	0	ASTN2	118535571	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.962000	0.87912	1.890000	0.54733	0.459000	0.35465	ATC	.	T|1.000;C|0.000	.	alt		0.602	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010		A	119495750	T	A	119495750	3	1	140	1	0	0	0	0	1	0	0	0	1065	1435	50	5	1842	5	ASTN2	9	119495750	Missense_Mutation	SNP	T	TCGA-BQ-7058-01A-11D-1961-08	525900	119495750	21717681	26	8478											
ECD	11319	hgsc.bcm.edu	37	chr10	74906091	74906091	+	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	ctgccatttctagcctttccCggtactgagcagaaccttct	7	13	7	14	1	2	2	0	1	2	1	3	2	3	2	4	1	5	2	4	1	3	5	rs147908494	byFrequency	TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr10:74906091C>G	ENST00000372979.4	-	9	1276	c.1070G>C	c.(1069-1071)cGg>cCg	p.R357P	ECD_ENST00000454759.2_Missense_Mutation_p.R314P|ECD_ENST00000430082.2_Missense_Mutation_p.R357P	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	357					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)					TAGCCTTTCCCGGTACTGAGC	0.388																																					p.R357P		Atlas-SNP	.											.	ECD	50	.	0			c.G1070C						PASS	.						70	60	64					10																	74906091		2203	4300	6503	SO:0001583	missense	11319	exon9			CTTTCCCGGTACT	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.1070G>C	chr10.hg19:g.74906091C>G	ENSP00000362070:p.Arg357Pro	37.0	0.0	.		40.0	7.0	.	NM_001135752	C9JX46|E9PAW8	Missense_Mutation	SNP	ENST00000372979.4	hg19	CCDS7321.1	.	.	.	.	.	.	.	.	.	.	c	16.22	3.061911	0.55432	.	.	ENSG00000122882	ENST00000372979;ENST00000430082;ENST00000454759	T;T;T	0.18657	2.2;2.2;2.2	5.86	3.46	0.39613	.	0.479204	0.25307	N	0.031608	T	0.22704	0.0548	L	0.46157	1.445	0.25782	N	0.984718	P;P;P	0.48694	0.583;0.719;0.914	P;P;P	0.52793	0.511;0.518;0.709	T	0.11397	-1.0589	10	0.36615	T	0.2	-20.0372	1.3395	0.02151	0.2109:0.0988:0.1488:0.5415	.	314;357;357	E9PAW8;C9JX46;O95905	.;.;SGT1_HUMAN	P	357;357;314	ENSP00000362070:R357P;ENSP00000401566:R357P;ENSP00000395786:R314P	ENSP00000362070:R357P	R	-	2	0	ECD	74576097	0.515000	0.26210	1.000000	0.80357	0.871000	0.50021	0.390000	0.20768	1.054000	0.40438	-0.310000	0.09108	CGG	.	C|0.999;T|0.001	.	alt		0.388	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265		G	74906091	C	G	74906091	3	3	140	1	0	0	0	0	1	0	0	0	4890	652	23	4	991	4	ECD	10	74906091	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08		74906091	60628656	27	8479											
ADK	132	hgsc.bcm.edu	37	chr10	76468112	76468112	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actggtctctgacaagcctcTgactgaatgtatccgtgctg	8	12	10	11	1	2	3	0	3	2	0	4	3	3	3	2	1	2	2	2	1	3	1			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr10:76468112T>C	ENST00000286621.2	+	11	1048	c.998T>C	c.(997-999)cTg>cCg	p.L333P	ADK_ENST00000539909.1_Missense_Mutation_p.L276P|ADK_ENST00000541550.1_Missense_Mutation_p.L298P|ADK_ENST00000372734.3_Missense_Mutation_p.L316P	NM_006721.3	NP_006712.2	P55263	ADK_HUMAN	adenosine kinase	333					adenosine metabolic process (GO:0046085)|AMP salvage (GO:0044209)|circadian regulation of gene expression (GO:0032922)|dATP biosynthetic process (GO:0006175)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of T cell proliferation (GO:0042102)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|ribonucleoside monophosphate biosynthetic process (GO:0009156)|small molecule metabolic process (GO:0044281)|type B pancreatic cell proliferation (GO:0044342)	cytosol (GO:0005829)|nucleus (GO:0005634)	adenosine kinase activity (GO:0004001)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)|poly(A) RNA binding (GO:0044822)			breast(1)|large_intestine(2)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	8	Prostate(51;0.0112)|Ovarian(15;0.148)				Abacavir(DB01048)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Adenosine(DB00640)|Ribavirin(DB00811)	GACAAGCCTCTGACTGAATGT	0.453																																					p.L333P		Atlas-SNP	.											.	ADK	28	.	0			c.T998C						PASS	.						148	145	146					10																	76468112		2203	4300	6503	SO:0001583	missense	132	exon11			AGCCTCTGACTGA	U50196	CCDS7343.1, CCDS7344.1, CCDS55716.1, CCDS55717.1	10q22.2	2006-02-21			ENSG00000156110	ENSG00000156110	2.7.1.20		257	protein-coding gene	gene with protein product	"adenosine 5'-phosphotransferase"	102750				8577746	Standard	NM_001123		Approved	AK	uc001jwi.3	P55263	OTTHUMG00000018506	ENST00000286621.2:c.998T>C	chr10.hg19:g.76468112T>C	ENSP00000286621:p.Leu333Pro	201.0	0.0	.		184.0	67.0	.	NM_006721	B7Z783|B7Z800|O00741|O00742|Q16710|Q5JQ10|Q5JQ11|Q9BTN2	Missense_Mutation	SNP	ENST00000286621.2	hg19	CCDS7343.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.992018	0.74703	.	.	ENSG00000156110	ENST00000539909;ENST00000286621;ENST00000372734;ENST00000541550	D;D;D;D	0.90620	-2.7;-1.54;-1.54;-1.54	5.48	5.48	0.80851	Carbohydrate/purine kinase (1);	0.220948	0.39210	N	0.001422	D	0.94656	0.8277	M	0.79011	2.435	0.80722	D	1	D;B;D;B	0.69078	0.997;0.226;0.997;0.042	D;B;D;B	0.66847	0.947;0.275;0.947;0.173	D	0.94816	0.7983	10	0.54805	T	0.06	-6.7191	14.538	0.67973	0.0:0.0:0.0:1.0	.	298;276;316;333	B7Z800;B7Z783;Q5JQ10;P55263	.;.;.;ADK_HUMAN	P	276;333;316;298	ENSP00000443965:L276P;ENSP00000286621:L333P;ENSP00000361819:L316P;ENSP00000438321:L298P	ENSP00000286621:L333P	L	+	2	0	ADK	76138118	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.195000	0.77798	2.078000	0.62432	0.533000	0.62120	CTG	.	.	.	none		0.453	ADK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048763.1	NM_001123, NM_006721		C	76468112	T	C	76468112	3	2	140	1	0	0	0	0	1	0	0	0	320	1580	55	3	1058	3	ADK	10	76468112	Missense_Mutation	SNP	T	TCGA-BQ-7058-01A-11D-1961-08	1562021	76468112	59066635	28	8480											
OR1S1	219959	hgsc.bcm.edu	37	chr11	57982376	57982376	+	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	tgtacctggtcactgtgattGggaacgggctcatcattgtg	7	13	13	8	1	3	1	3	1	0	0	3	2	3	2	1	3	2	2	1	3	2	3			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr11:57982376G>A	ENST00000309433.6	+	1	160	c.160G>A	c.(160-162)Ggg>Agg	p.G54R		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	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)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				CACTGTGATTGGGAACGGGCT	0.448																																					p.G54R		Atlas-SNP	.											.	OR1S1	139	.	0			c.G160A						PASS	.						323	297	306					11																	57982376		2201	4296	6497	SO:0001583	missense	219959	exon1			GTGATTGGGAACG	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"GPCR / Class A : Olfactory receptors"	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.160G>A	chr11.hg19:g.57982376G>A	ENSP00000311688:p.Gly54Arg	322.0	0.0	.		229.0	90.0	.	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	hg19	CCDS31546.1	.	.	.	.	.	.	.	.	.	.	G	14.57	2.576223	0.45902	.	.	ENSG00000172774	ENST00000309433	T	0.15256	2.44	3.45	3.45	0.39498	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49916	D	0.000137	T	0.49558	0.1564	H	0.95328	3.655	0.09310	N	0.999999	D	0.89917	1.0	D	0.70935	0.971	T	0.50406	-0.8832	10	0.87932	D	0	.	10.0621	0.42282	0.1064:0.0:0.8936:0.0	.	54	Q8NH92	OR1S1_HUMAN	R	54	ENSP00000311688:G54R	ENSP00000311688:G54R	G	+	1	0	OR1S1	57738952	0.784000	0.28713	0.803000	0.32268	0.673000	0.39480	2.153000	0.42282	1.770000	0.52166	0.479000	0.44913	GGG	.	.	.	none		0.448	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458		A	57982376	G	A	57982376	3	1	140	1	0	0	0	0	1	0	0	0	10979	1348	47	2	162	2	OR1S1	11	57982376	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08		57982376	77024140	29	8481											
TRMT112	51504	hgsc.bcm.edu	37	chr11	64084953	64084953	+	Frame_Shift_Del	DEL	C	C	-																															ggggaagccacgggaccccaCcccccgcacatgcgagctca																										TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr11:64084953delC	ENST00000544844.1	-	1	603	c.46delG	c.(46-48)gtgfs	p.V16fs	PRDX5_ENST00000347941.4_5'Flank|TRMT112_ENST00000308774.2_Frame_Shift_Del_p.V16fs|TRMT112_ENST00000535750.1_5'UTR|PRDX5_ENST00000265462.4_5'Flank|TRMT112_ENST00000535126.1_Frame_Shift_Del_p.G4fs|PRDX5_ENST00000352435.4_5'Flank|TRMT112_ENST00000539854.1_Frame_Shift_Del_p.V16fs			Q9UI30	TR112_HUMAN	tRNA methyltransferase 11-2 homolog (S. cerevisiae)	16	TRM112.				peptidyl-glutamine methylation (GO:0018364)	extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	protein methyltransferase activity (GO:0008276)			large_intestine(1)|upper_aerodigestive_tract(1)	2						CGGGACCCCACCCCCCGCACA	0.657																																					p.V16fs		Atlas-INDEL	.											.	TRMT112	9	.	0			c.47delT						PASS	.						22	22	22					11																	64084953		2200	4294	6494	SO:0001589	frameshift_variant	51504	exon1			.	AF110774	CCDS8068.1, CCDS66113.1, CCDS73312.1	11q13.1	2013-07-23			ENSG00000173113	ENSG00000173113			26940	protein-coding gene	gene with protein product						11042152	Standard	NM_001286082		Approved	HSPC152, HSPC170, TRM112, TRMT11-2	uc001nzt.3	Q9UI30	OTTHUMG00000167848	ENST00000544844.1:c.46delG	chr11.hg19:g.64084953delC	ENSP00000438349:p.Val16fs	16.0	0.0	0		34.0	11.0	0.323529	NM_016404	B2R539|J3KNG5|Q3MHC7|Q8N2Z4	Frame_Shift_Del	DEL	ENST00000544844.1	hg19	CCDS8068.1																																																																																			.	.	.	none		0.657	TRMT112-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396598.2	NM_016404		-	64084953	C	-	64084953	7	5	140	1	0	1	0	1	0	0	0	0	16575	507	18	0	347	0	TRMT112	11	64084953	Frame_Shift_Del	DEL	C	TCGA-BQ-7058-01A-11D-1961-08	6102577	64084953	70921563	30	8482											
DPF2	5977	hgsc.bcm.edu	37	chr11	65113439	65113439	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gattggccttgcccaacaacTactgtgacttctgcctgggg	7	11	11	12	0	1	1	0	1	1	0	1	2	1	1	3	3	5	0	3	3	3	4			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr11:65113439T>C	ENST00000528416.1	+	8	947	c.814T>C	c.(814-816)Tac>Cac	p.Y272H	DPF2_ENST00000532264.1_3'UTR|DPF2_ENST00000415073.2_Intron|DPF2_ENST00000252268.4_Missense_Mutation_p.Y286H	NM_006268.4	NP_006259.1	Q92785	REQU_HUMAN	D4, zinc and double PHD fingers family 2	272					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						GCCCAACAACTACTGTGACTT	0.537																																					p.Y272H		Atlas-SNP	.											.	DPF2	54	.	0			c.T814C						PASS	.						123	125	124					11																	65113439		2201	4297	6498	SO:0001583	missense	5977	exon8			AACAACTACTGTG	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.814T>C	chr11.hg19:g.65113439T>C	ENSP00000436901:p.Tyr272His	176.0	0.0	.		220.0	95.0	.	NM_006268	A8K7C9|B4DT58	Missense_Mutation	SNP	ENST00000528416.1	hg19	CCDS8100.1	.	.	.	.	.	.	.	.	.	.	T	29.7	5.025345	0.93518	.	.	ENSG00000133884	ENST00000528416;ENST00000252268	D;D	0.91011	-2.75;-2.77	5.92	5.92	0.95590	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.34338	N	0.004057	D	0.95739	0.8614	M	0.87900	2.915	0.54753	D	0.999988	D	0.63046	0.992	D	0.87578	0.998	D	0.96274	0.9201	10	0.87932	D	0	-23.8316	14.3154	0.66446	0.0:0.0:0.0:1.0	.	272	Q92785	REQU_HUMAN	H	272;286	ENSP00000436901:Y272H;ENSP00000252268:Y286H	ENSP00000252268:Y286H	Y	+	1	0	DPF2	64870015	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.946000	0.87746	2.270000	0.75569	0.459000	0.35465	TAC	.	.	.	none		0.537	DPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387293.3	NM_006268		C	65113439	T	C	65113439	3	2	140	1	0	0	0	0	1	0	0	0	4719	1522	53	3	844	3	DPF2	11	65113439	Missense_Mutation	SNP	T	TCGA-BQ-7058-01A-11D-1961-08	1028486	65113439	69893077	31	8483											
SPTBN2	6712	hgsc.bcm.edu	37	chr11	66488565	66488565	+	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	ctgacctcacctgccagagcCttaatgcgagacctctcaaa	11	8	7	15	1	2	3	2	1	1	2	3	4	2	3	5	0	3	0	5	0	2	1			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr11:66488565C>G	ENST00000533211.1	-	3	478	c.147G>C	c.(145-147)aaG>aaC	p.K49N	SPTBN2_ENST00000529997.1_Missense_Mutation_p.K49N|SPTBN2_ENST00000309996.2_Missense_Mutation_p.K49N			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	49	Actin-binding.				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						CTGCCAGAGCCTTAATGCGAG	0.572																																					p.K49N		Atlas-SNP	.											.	SPTBN2	188	.	0			c.G147C						PASS	.						76	65	68					11																	66488565		2200	4295	6495	SO:0001583	missense	6712	exon2			CAGAGCCTTAATG	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.147G>C	chr11.hg19:g.66488565C>G	ENSP00000432568:p.Lys49Asn	64.0	0.0	.		74.0	37.0	.	NM_006946	O14872|O14873	Missense_Mutation	SNP	ENST00000533211.1	hg19	CCDS8150.1	.	.	.	.	.	.	.	.	.	.	C	18.22	3.576172	0.65878	.	.	ENSG00000173898	ENST00000533211;ENST00000309996;ENST00000529997;ENST00000443262;ENST00000527010	T;T;T;T	0.61274	0.12;0.12;0.12;0.12	4.58	3.67	0.42095	Calponin homology domain (2);	0.000000	0.85682	D	0.000000	T	0.76133	0.3945	M	0.92169	3.28	0.52099	D	0.999946	D	0.67145	0.996	P	0.61477	0.889	T	0.79100	-0.1942	10	0.87932	D	0	.	8.4196	0.32692	0.0:0.8157:0.0:0.1843	.	49	O15020	SPTN2_HUMAN	N	49	ENSP00000432568:K49N;ENSP00000311489:K49N;ENSP00000433593:K49N;ENSP00000433631:K49N	ENSP00000311489:K49N	K	-	3	2	SPTBN2	66245141	0.999000	0.42202	1.000000	0.80357	0.959000	0.62525	0.667000	0.25112	1.062000	0.40625	0.561000	0.74099	AAG	.	.	.	none		0.572	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946		G	66488565	C	G	66488565	3	3	140	1	0	0	0	0	1	0	0	0	15132	680	24	4	7169	4	SPTBN2	11	66488565	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08	1375126	66488565	68517951	32	8484											
PCF11	51585	hgsc.bcm.edu	37	chr11	82877707	82877707	+	Missense_Mutation	SNP	A	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	agaatgtagaaaactggcaaAgttccaagtctgccaaaaga	18	7	9	7	0	1	3	0	0	1	3	2	3	2	3	2	1	2	3	2	1	8	2			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr11:82877707A>C	ENST00000298281.4	+	5	2220	c.1768A>C	c.(1768-1770)Agt>Cgt	p.S590R		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	590					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						AAACTGGCAAAGTTCCAAGTC	0.373																																					p.S590R		Atlas-SNP	.											PCF11_ENST00000298281,NS,carcinoma,0,2	PCF11	220	.	0			c.A1768C						PASS	.						69	70	70					11																	82877707		1801	3982	5783	SO:0001583	missense	51585	exon5			TGGCAAAGTTCCA	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.1768A>C	chr11.hg19:g.82877707A>C	ENSP00000298281:p.Ser590Arg	170.0	0.0	.		151.0	57.0	.	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	hg19	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	A	13.31	2.199720	0.38905	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.46063	1.89;0.89;0.88	6.07	4.96	0.65561	.	0.165679	0.43747	D	0.000537	T	0.27063	0.0663	N	0.19112	0.55	0.28203	N	0.927278	P;B	0.50528	0.936;0.244	P;B	0.45099	0.469;0.143	T	0.13072	-1.0523	9	.	.	.	.	4.9308	0.13916	0.7534:0.0:0.2466:0.0	.	590;590	E9PQ01;O94913	.;PCF11_HUMAN	R	590	ENSP00000298281:S590R;ENSP00000434540:S590R;ENSP00000431567:S590R	.	S	+	1	0	PCF11	82555355	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.144000	0.64832	2.326000	0.78906	0.533000	0.62120	AGT	.	.	.	none		0.373	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		C	82877707	A	C	82877707	3	2	140	1	0	0	0	0	1	0	0	0	11580	72	3	5	1786	5	PCF11	11	82877707	Missense_Mutation	SNP	A	TCGA-BQ-7058-01A-11D-1961-08	16389142	82877707	52128809	33	8485											
B4GALNT3	283358	hgsc.bcm.edu	37	chr12	662534	662534	+	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	gcggaaactcctggctcagcCccgggagggcctgctggccc	5	5	15	16	2	1	0	1	0	0	0	2	2	2	2	5	5	3	2	5	5	1	0			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr12:662534C>A	ENST00000266383.5	+	14	1458	c.1445C>A	c.(1444-1446)cCc>cAc	p.P482H		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	482					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)			CTGGCTCAGCCCCGGGAGGGC	0.627																																					p.P482H		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.C1445A						PASS	.						55	63	60					12																	662534		2203	4300	6503	SO:0001583	missense	283358	exon14			CTCAGCCCCGGGA	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.1445C>A	chr12.hg19:g.662534C>A	ENSP00000266383:p.Pro482His	128.0	0.0	.		132.0	40.0	.	NM_173593	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	hg19	CCDS8504.1	.	.	.	.	.	.	.	.	.	.	C	13.94	2.387397	0.42308	.	.	ENSG00000139044	ENST00000266383;ENST00000322843	T;T	0.32988	3.47;1.43	5.75	1.75	0.24633	.	0.694092	0.14730	N	0.301809	T	0.20861	0.0502	L	0.36672	1.1	0.09310	N	1	P;P	0.41265	0.744;0.61	B;B	0.39027	0.288;0.167	T	0.08249	-1.0731	10	0.39692	T	0.17	-7.1623	5.6204	0.17453	0.0:0.6186:0.1433:0.238	.	385;482	E9PHD9;Q6L9W6	.;B4GN3_HUMAN	H	482;385	ENSP00000266383:P482H;ENSP00000322953:P385H	ENSP00000266383:P482H	P	+	2	0	B4GALNT3	532795	0.000000	0.05858	0.001000	0.08648	0.072000	0.16883	-0.111000	0.10807	0.790000	0.33803	0.650000	0.86243	CCC	.	.	.	none		0.627	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593		A	662534	C	A	662534	3	1	140	1	0	0	0	0	1	0	0	0	1268	623	22	4	1499	4	B4GALNT3	12	662534	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08		662534	133189361	34	8486											
TMTC3	160418	hgsc.bcm.edu	37	chr12	88548132	88548132	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctagcagcttttttgtcatAtaccagatcaaaaggaccag	13	12	7	9	0	3	1	2	0	1	1	3	2	3	2	2	1	3	2	2	1	5	6			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr12:88548132A>G	ENST00000266712.6	+	4	696	c.476A>G	c.(475-477)tAt>tGt	p.Y159C		NM_181783.3	NP_861448.2	Q6ZXV5	TMTC3_HUMAN	transmembrane and tetratricopeptide repeat containing 3	159					bud outgrowth involved in lung branching (GO:0060447)|lung alveolus development (GO:0048286)|muscle fiber development (GO:0048747)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(5)|liver(1)|lung(12)|prostate(4)|skin(1)	31						TTTTTGTCATATACCAGATCA	0.318																																					p.Y159C		Atlas-SNP	.											.	TMTC3	75	.	0			c.A476G						PASS	.						82	80	81					12																	88548132		2203	4296	6499	SO:0001583	missense	160418	exon4			TGTCATATACCAG		CCDS9032.1	12q21.32	2014-09-04			ENSG00000139324	ENSG00000139324		"Tetratricopeptide (TTC) repeat domain containing"	26899	protein-coding gene	gene with protein product							Standard	NM_181783		Approved	FLJ90492, SMILE	uc001tau.3	Q6ZXV5	OTTHUMG00000169887	ENST00000266712.6:c.476A>G	chr12.hg19:g.88548132A>G	ENSP00000266712:p.Tyr159Cys	103.0	0.0	.		82.0	30.0	.	NM_181783	Q5CZ86|Q5H9T6|Q68DQ6|Q68DX0|Q7Z332|Q8NC50	Missense_Mutation	SNP	ENST00000266712.6	hg19	CCDS9032.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.221546	0.79464	.	.	ENSG00000139324	ENST00000266712;ENST00000551088	T	0.71698	-0.59	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	D	0.86682	0.5991	M	0.90145	3.09	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.89279	0.3610	9	.	.	.	-14.1188	15.2357	0.73430	1.0:0.0:0.0:0.0	.	159	Q6ZXV5-2	.	C	159;86	ENSP00000266712:Y159C	.	Y	+	2	0	TMTC3	87072263	1.000000	0.71417	0.995000	0.50966	0.908000	0.53690	6.888000	0.75622	1.998000	0.58463	0.455000	0.32223	TAT	.	.	.	none		0.318	TMTC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406421.1	NM_181783		G	88548132	A	G	88548132	3	3	140	1	0	0	0	0	1	0	0	0	16274	449	16	3	486	3	TMTC3	12	88548132	Missense_Mutation	SNP	A	TCGA-BQ-7058-01A-11D-1961-08	87885598	88548132	45303763	35	8487											
NID2	22795	hgsc.bcm.edu	37	chr14	52474565	52474565	+	Frame_Shift_Del	DEL	A	A	-																															agcagtttagagaaagggtcAaaggttaagccattgggcaa																										TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr14:52474565delA	ENST00000216286.5	-	19	3842	c.3843delT	c.(3841-3843)tttfs	p.F1281fs	NID2_ENST00000541773.1_Frame_Shift_Del_p.F1180fs	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	1281					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)					agaaagggtcaaaggttaagc	0.403																																					p.D1282fs		Atlas-INDEL	.											.	NID2	201	.	0			c.3844delG						PASS	.						126	116	120					14																	52474565		2203	4300	6503	SO:0001589	frameshift_variant	22795	exon19			.	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.3843delT	chr14.hg19:g.52474565delA	ENSP00000216286:p.Phe1281fs	72.0	0.0	0		61.0	21.0	0.344262	NM_007361	A8K6I7|B4DU19|O43710	Frame_Shift_Del	DEL	ENST00000216286.5	hg19	CCDS9706.1																																																																																			.	.	.	none		0.403	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			-	52474565	A	-	52474565	7	5	140	1	0	1	0	1	0	0	0	0	10422	127	5	0	300	0	NID2	14	52474565	Frame_Shift_Del	DEL	A	TCGA-BQ-7058-01A-11D-1961-08		52474565	54874975	36	8488											
PCNX	22990	hgsc.bcm.edu	37	chr14	71413816	71413816	+	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	acaaggcaactgttcaaccaGgagaaaagacagcaatggac	18	4	10	9	0	1	2	1	0	0	2	1	4	1	3	1	3	3	3	1	3	6	1			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr14:71413816G>T	ENST00000304743.2	+	2	784	c.338G>T	c.(337-339)aGg>aTg	p.R113M	PCNX_ENST00000439984.3_Missense_Mutation_p.R113M|PCNX_ENST00000238570.5_Missense_Mutation_p.R113M	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	113						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)		TGTTCAACCAGGAGAAAAGAC	0.398																																					p.R113M		Atlas-SNP	.											.	PCNX	198	.	0			c.G338T						PASS	.						108	94	99					14																	71413816		2203	4300	6503	SO:0001583	missense	22990	exon2			CAACCAGGAGAAA	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.338G>T	chr14.hg19:g.71413816G>T	ENSP00000304192:p.Arg113Met	31.0	0.0	.		24.0	9.0	.	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	hg19	CCDS9806.1	.	.	.	.	.	.	.	.	.	.	G	16.53	3.149085	0.57151	.	.	ENSG00000100731	ENST00000304743;ENST00000238570;ENST00000439984	T;T;T	0.42513	0.97;0.97;0.97	5.87	5.87	0.94306	.	0.248009	0.40144	N	0.001174	T	0.54013	0.1832	L	0.48642	1.525	0.47737	D	0.999505	D;D;D	0.71674	0.99;0.99;0.998	P;P;P	0.61592	0.707;0.707;0.891	T	0.52124	-0.8617	10	0.56958	D	0.05	.	13.8269	0.63357	0.0783:0.0:0.9217:0.0	.	113;113;113	B2RTR6;Q96RV3;Q96RV3-2	.;PCX1_HUMAN;.	M	113	ENSP00000304192:R113M;ENSP00000238570:R113M;ENSP00000396617:R113M	ENSP00000238570:R113M	R	+	2	0	PCNX	70483569	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.762000	0.68809	2.779000	0.95612	0.655000	0.94253	AGG	.	.	.	none		0.398	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		T	71413816	G	T	71413816	3	4	140	1	0	0	0	0	1	0	0	0	11598	1000	35	4	344	4	PCNX	14	71413816	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	18939251	71413816	35935724	37	8489											
HERC1	8925	hgsc.bcm.edu	37	chr15	64005696	64005696	+	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	ggatcacggagttgcatgcaGcagtgtacacatcctgaccc	10	8	11	12	1	1	1	1	1	0	0	2	3	2	3	2	2	4	5	2	2	1	2			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr15:64005696G>C	ENST00000443617.2	-	23	4406	c.4319C>G	c.(4318-4320)gCt>gGt	p.A1440G	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	1440					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						GTTGCATGCAGCAGTGTACAC	0.537																																					p.A1440G		Atlas-SNP	.											.	HERC1	624	.	0			c.C4319G						PASS	.						104	101	102					15																	64005696		2101	4230	6331	SO:0001583	missense	8925	exon23			CATGCAGCAGTGT	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.4319C>G	chr15.hg19:g.64005696G>C	ENSP00000390158:p.Ala1440Gly	104.0	0.0	.		96.0	33.0	.	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	G	15.50	2.853473	0.51270	.	.	ENSG00000103657	ENST00000443617;ENST00000425434	T	0.34859	1.34	5.53	5.53	0.82687	.	0.069961	0.56097	D	0.000037	T	0.22513	0.0543	N	0.08118	0	0.44417	D	0.997336	B;B	0.09022	0.002;0.0	B;B	0.11329	0.006;0.003	T	0.04678	-1.0934	10	0.49607	T	0.09	.	14.9975	0.71443	0.0:0.1421:0.8579:0.0	.	424;1440	B4DKS2;Q15751	.;HERC1_HUMAN	G	1440;424	ENSP00000390158:A1440G	ENSP00000389613:A424G	A	-	2	0	HERC1	61792749	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.377000	0.79668	2.599000	0.87857	0.655000	0.94253	GCT	.	.	.	none		0.537	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		C	64005696	G	C	64005696	3	2	140	1	0	0	0	0	1	0	0	0	7064	971	34	4	10490	4	HERC1	15	64005696	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08		64005696	38525696	38	8490											
CILP	8483	hgsc.bcm.edu	37	chr15	65496681	65496681	+	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	tgtgagtacaatgggggcaaActtgacctttgtgatcttca	10	13	11	7	0	2	3	1	3	1	0	2	3	2	3	1	2	2	2	1	2	3	4			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr15:65496681A>T	ENST00000261883.4	-	6	1010	c.844T>A	c.(844-846)Ttt>Att	p.F282I		NM_003613.3	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	282					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						ATGGGGGCAAACTTGACCTTT	0.527																																					p.F282I		Atlas-SNP	.											.	CILP	124	.	0			c.T844A						PASS	.						119	105	110					15																	65496681		2201	4299	6500	SO:0001583	missense	8483	exon6			GGGCAAACTTGAC	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.844T>A	chr15.hg19:g.65496681A>T	ENSP00000261883:p.Phe282Ile	143.0	0.0	.		128.0	53.0	.	NM_003613	B2R8F7|Q6UW99|Q8IYI5	Missense_Mutation	SNP	ENST00000261883.4	hg19	CCDS10203.1	.	.	.	.	.	.	.	.	.	.	A	18.07	3.541043	0.65085	.	.	ENSG00000138615	ENST00000261883	T	0.38722	1.12	5.63	5.63	0.86233	Carboxypeptidase-like, regulatory domain (1);	0.095383	0.64402	D	0.000001	T	0.45337	0.1337	M	0.69358	2.11	0.36495	D	0.868693	B	0.29341	0.242	B	0.29942	0.109	T	0.56414	-0.7983	10	0.72032	D	0.01	-4.1505	15.024	0.71653	1.0:0.0:0.0:0.0	.	282	O75339	CILP1_HUMAN	I	282	ENSP00000261883:F282I	ENSP00000261883:F282I	F	-	1	0	CILP	63283734	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.410000	0.73294	2.148000	0.66965	0.460000	0.39030	TTT	.	.	.	none		0.527	CILP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256829.1	NM_003613		T	65496681	A	T	65496681	3	4	140	1	0	0	0	0	1	0	0	0	3431	43	2	5	2726	5	CILP	15	65496681	Missense_Mutation	SNP	A	TCGA-BQ-7058-01A-11D-1961-08	1490985	65496681	37034711	39	8491											
SRL	6345	hgsc.bcm.edu	37	chr16	4245669	4245669	+	Missense_Mutation	SNP	A	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	ttctctaggaaattctggccAaacttctcaaggggtgagaa	12	11	10	8	0	3	1	1	1	3	1	5	3	3	2	1	4	1	0	1	4	5	4			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr16:4245669A>C	ENST00000399609.3	-	5	507	c.495T>G	c.(493-495)ttT>ttG	p.F165L	SRL_ENST00000537996.1_Missense_Mutation_p.F123L	NM_001098814.1	NP_001092284.1	Q86TD4	SRCA_HUMAN	sarcalumenin	624	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						AATTCTGGCCAAACTTCTCAA	0.527																																					p.F165L		Atlas-SNP	.											.	SRL	56	.	0			c.T495G						PASS	.						92	93	93					16																	4245669		1908	4134	6042	SO:0001583	missense	6345	exon5			CTGGCCAAACTTC	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.495T>G	chr16.hg19:g.4245669A>C	ENSP00000382518:p.Phe165Leu	104.0	0.0	.		217.0	154.0	.	NM_001098814		Missense_Mutation	SNP	ENST00000399609.3	hg19	CCDS42113.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.436347	0.83885	.	.	ENSG00000185739	ENST00000399609;ENST00000330063;ENST00000537996	D;D	0.96041	-3.89;-3.89	5.1	4.01	0.46588	.	0.000000	0.85682	U	0.000000	D	0.95475	0.8530	M	0.75264	2.295	0.80722	D	1	P	0.51147	0.942	P	0.49953	0.627	D	0.94708	0.7889	10	0.87932	D	0	-10.1449	9.749	0.40464	0.8549:0.0:0.1451:0.0	.	165	Q86TD4-2	.	L	165;623;123	ENSP00000382518:F165L;ENSP00000440350:F123L	ENSP00000333285:F623L	F	-	3	2	SRL	4185670	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.492000	0.45311	1.065000	0.40693	0.533000	0.62120	TTT	.	.	.	none		0.527	SRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438087.1	XM_064152		C	4245669	A	C	4245669	3	2	140	1	0	0	0	0	1	0	0	0	15162	127	5	5	934	5	SRL	16	4245669	Missense_Mutation	SNP	A	TCGA-BQ-7058-01A-11D-1961-08		4245669	86109084	40	8492											
NLK	51701	hgsc.bcm.edu	37	chr17	26490600	26490600	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctccattcagctggcattttAcatcgagacattaagccagg	11	11	8	11	1	1	1	1	0	0	1	3	2	2	1	2	2	3	2	2	2	2	4			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr17:26490600A>G	ENST00000407008.3	+	5	1501	c.783A>G	c.(781-783)ttA>ttG	p.L261L		NM_016231.4	NP_057315.3	Q9UBE8	NLK_HUMAN	nemo-like kinase	261	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|Required for interaction with TAB2. {ECO:0000250}.|Sufficient for interaction with DAPK3.				intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of Wnt signaling pathway (GO:0030178)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|serine phosphorylation of STAT3 protein (GO:0033136)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase activity (GO:0004707)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|SH2 domain binding (GO:0042169)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(1)	14	all_lung(13;0.000343)|Lung NSC(42;0.00184)			UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		CTGGCATTTTACATCGAGACA	0.318																																					p.L261L		Atlas-SNP	.											.	NLK	88	.	0			c.A783G						PASS	.						85	83	83					17																	26490600		2203	4300	6503	SO:0001819	synonymous_variant	51701	exon5			CATTTTACATCGA	AF197898	CCDS11224.2	17q11.2	2005-12-22	2005-12-22		ENSG00000087095	ENSG00000087095			29858	protein-coding gene	gene with protein product		609476	"nemo like kinase"			9448268, 10863097	Standard	NM_016231		Approved		uc010crj.3	Q9UBE8	OTTHUMG00000132451	ENST00000407008.3:c.783A>G	chr17.hg19:g.26490600A>G		59.0	0.0	.		46.0	17.0	.	NM_016231	B2RCX1|Q2PNI9|Q6P2A3	Silent	SNP	ENST00000407008.3	hg19	CCDS11224.2																																																																																			.	.	.	none		0.318	NLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255607.3	NM_016231		G	26490600	A	G	26490600	2	3	140	1	0	0	0	0	0	0	0	1	10473	388	14	3		3	NLK	17	26490600	Silent	SNP	A	TCGA-BQ-7058-01A-11D-1961-08		26490600	54704610	41	8493											
COX11	1353	hgsc.bcm.edu	37	chr17	53045784	53045784	+	Missense_Mutation	SNP	T	T	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	gtgtgaaagggttcgagctcTtaggccgccgcggcggctgc	5	8	17	11	5	1	1	0	1	1	0	2	2	1	1	2	4	2	3	2	4	2	2			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr17:53045784T>G	ENST00000299335.3	-	1	362	c.224A>C	c.(223-225)aAg>aCg	p.K75T	STXBP4_ENST00000299341.4_5'Flank|COX11_ENST00000571584.1_Missense_Mutation_p.K75T|STXBP4_ENST00000434978.2_5'Flank|STXBP4_ENST00000376352.2_5'Flank|STXBP4_ENST00000398391.2_5'Flank|STXBP4_ENST00000405898.1_5'Flank	NM_004375.3	NP_004366.1	Q9Y6N1	COX11_HUMAN	cytochrome c oxidase assembly homolog 11 (yeast)	75					hydrogen ion transmembrane transport (GO:1902600)|negative regulation of glucokinase activity (GO:0033132)|respiratory chain complex IV assembly (GO:0008535)|respiratory gaseous exchange (GO:0007585)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	copper ion binding (GO:0005507)|cytochrome-c oxidase activity (GO:0004129)|electron carrier activity (GO:0009055)			endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|prostate(1)	9						GTTCGAGCTCTTAGGCCGCCG	0.677																																					p.K75T		Atlas-SNP	.											.	COX11	16	.	0			c.A224C						PASS	.						36	39	38					17																	53045784		2193	4279	6472	SO:0001583	missense	1353	exon1			GAGCTCTTAGGCC	AF044321	CCDS11583.1, CCDS58579.1	17q22	2012-10-15	2012-10-15			ENSG00000166260		"Mitochondrial respiratory chain complex assembly factors"	2261	protein-coding gene	gene with protein product	"cytochrome c oxidase subunit 11", "cytochrome c oxidase assembly protein COX11"	603648	"COX11 (yeast) homolog, cytochrome c oxidase assembly protein", "COX11 cytochrome c oxidase assembly homolog (yeast)"			9878253	Standard	NM_004375		Approved	COX11P	uc010wng.1	Q9Y6N1		ENST00000299335.3:c.224A>C	chr17.hg19:g.53045784T>G	ENSP00000299335:p.Lys75Thr	108.0	0.0	.		149.0	75.0	.	NM_001162861	D3DTY5|I3L220|Q6FHB7|Q9BRX0|Q9UME8	Missense_Mutation	SNP	ENST00000299335.3	hg19	CCDS11583.1	.	.	.	.	.	.	.	.	.	.	T	8.726	0.915585	0.17907	.	.	ENSG00000166260	ENST00000299335	T	0.46451	0.87	5.02	2.75	0.32379	.	0.295867	0.40728	N	0.001025	T	0.34890	0.0913	M	0.61703	1.905	0.29814	N	0.831394	B;B	0.18863	0.031;0.007	B;B	0.14023	0.01;0.003	T	0.27468	-1.0073	10	0.22706	T	0.39	-11.5209	7.4832	0.27417	0.0:0.2509:0.0:0.7491	.	75;75	B4DI26;Q9Y6N1	.;COX11_HUMAN	T	75	ENSP00000299335:K75T	ENSP00000299335:K75T	K	-	2	0	COX11	50400783	0.913000	0.31002	0.971000	0.41717	0.013000	0.08279	1.102000	0.31050	0.364000	0.24374	-0.250000	0.11733	AAG	.	.	.	none		0.677	COX11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439182.1	NM_004375		G	53045784	T	G	53045784	3	3	140	1	0	0	0	0	1	0	0	0	3765	1609	56	5	688	5	COX11	17	53045784	Missense_Mutation	SNP	T	TCGA-BQ-7058-01A-11D-1961-08	26555184	53045784	28149426	42	8494											
DDX5	1655	hgsc.bcm.edu	37	chr17	62500170	62500170	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacttagagcaactggccaTccctgagcttgaatagcagt	11	9	9	12	0	0	3	0	2	0	1	1	3	1	3	3	1	4	3	3	1	4	3			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr17:62500170T>C	ENST00000225792.5	-	4	773	c.372A>G	c.(370-372)ggA>ggG	p.G124G	MIR5047_ENST00000579212.1_RNA|DDX5_ENST00000578804.1_Silent_p.G124G|CEP95_ENST00000581056.1_5'Flank|DDX5_ENST00000450599.2_Intron|CEP95_ENST00000553412.1_5'Flank|CEP95_ENST00000556440.2_5'Flank|DDX5_ENST00000580026.1_5'Flank	NM_004396.3	NP_004387.1	P17844	DDX5_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 5	124					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)			CAACTGGCCATCCCTGAGCTT	0.398			T	ETV4	prostate																																p.G124G	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.A372G						PASS	.						143	136	138					17																	62500170		2203	4300	6503	SO:0001819	synonymous_variant	1655	exon4			TGGCCATCCCTGA	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.372A>G	chr17.hg19:g.62500170T>C		173.0	1.0	.		172.0	103.0	.	NM_004396	B4DLW8|B5BU21|D3DU32|E7ETL9|O75681|Q53Y61	Silent	SNP	ENST00000225792.5	hg19	CCDS11659.1																																																																																			.	.	.	none		0.398	DDX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444030.1	NM_004396		C	62500170	T	C	62500170	2	2	140	1	0	0	0	0	0	0	0	1	4369	1422	50	3		3	DDX5	17	62500170	Silent	SNP	T	TCGA-BQ-7058-01A-11D-1961-08	9454386	62500170	18695040	43	8495											
SLC9A3R1	9368	hgsc.bcm.edu	37	chr17	72745286	72745286	+	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	agacggacgagcagctgcagAagctcggcgtccaggtccga	10	4	15	12	5	0	2	0	0	0	2	3	5	2	3	2	3	4	4	2	3	1	0			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr17:72745286A>T	ENST00000262613.5	+	1	496	c.301A>T	c.(301-303)Aag>Tag	p.K101*	MIR3615_ENST00000585285.1_RNA|MIR3615_ENST00000581999.1_RNA	NM_004252.4	NP_004243.1	O14745	NHRF1_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3 regulator 1	101					actin cytoskeleton organization (GO:0030036)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|bile acid secretion (GO:0032782)|cellular phosphate ion homeostasis (GO:0030643)|cellular protein localization (GO:0034613)|glutathione transport (GO:0034635)|microvillus assembly (GO:0030033)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sodium ion transport (GO:0010766)|negative regulation of sodium:proton antiporter activity (GO:0032416)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|protein complex assembly (GO:0006461)|regulation of excretion (GO:0044062)|regulation of protein kinase activity (GO:0045859)|regulation of sodium:proton antiporter activity (GO:0032415)|renal absorption (GO:0070293)|renal phosphate ion absorption (GO:0097291)|renal sodium ion transport (GO:0003096)|Wnt signaling pathway (GO:0016055)	actin cytoskeleton (GO:0015629)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell periphery (GO:0071944)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|membrane raft (GO:0045121)|microvillus (GO:0005902)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)|vesicle (GO:0031982)	beta-2 adrenergic receptor binding (GO:0031698)|beta-catenin binding (GO:0008013)|chloride channel regulator activity (GO:0017081)|growth factor receptor binding (GO:0070851)|PDZ domain binding (GO:0030165)|phosphatase binding (GO:0019902)|protein self-association (GO:0043621)|receptor binding (GO:0005102)			large_intestine(4)	4						GCAGCTGCAGAAGCTCGGCGT	0.736																																					p.K101X		Atlas-SNP	.											.	SLC9A3R1	12	.	0			c.A301T						PASS	.						3	5	4					17																	72745286		1866	3862	5728	SO:0001587	stop_gained	9368	exon1			CTGCAGAAGCTCG	AF015926	CCDS11705.1	17q25.1	2014-09-04	2012-03-22		ENSG00000109062	ENSG00000109062			11075	protein-coding gene	gene with protein product		604990	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulatory factor 1", "solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulator 1", "solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1"			9314537, 9430655	Standard	NM_004252		Approved	NHERF, EBP50	uc002jlo.4	O14745	OTTHUMG00000178863	ENST00000262613.5:c.301A>T	chr17.hg19:g.72745286A>T	ENSP00000262613:p.Lys101*	19.0	0.0	.		28.0	15.0	.	NM_004252	B3KY21|O43552|Q86WQ5	Nonsense_Mutation	SNP	ENST00000262613.5	hg19	CCDS11705.1	.	.	.	.	.	.	.	.	.	.	A	39	7.293378	0.98192	.	.	ENSG00000109062	ENST00000262613;ENST00000413388	.	.	.	4.34	4.34	0.51931	.	0.194752	0.44097	D	0.000484	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-35.2354	7.5228	0.27637	0.901:0.0:0.099:0.0	.	.	.	.	X	101;51	.	ENSP00000262613:K101X	K	+	1	0	SLC9A3R1	70256881	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	3.636000	0.54317	1.831000	0.53308	0.402000	0.26972	AAG	.	.	.	none		0.736	SLC9A3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443671.1			T	72745286	A	T	72745286	4	4	140	1	0	0	0	0	0	1	0	0	14727	247	9	5	303	5	SLC9A3R1	17	72745286	Nonsense_Mutation	SNP	A	TCGA-BQ-7058-01A-11D-1961-08	10245116	72745286	8449924	44	8496											
FASN	2194	hgsc.bcm.edu	37	chr17	80038618	80038618	+	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	tgctgagccgggaggccaggCtgtggaacacggtggtggag	7	6	20	8	2	0	1	0	1	0	0	0	4	0	4	2	7	3	2	2	7	1	0			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr17:80038618C>T	ENST00000306749.2	-	39	6994	c.6776G>A	c.(6775-6777)aGc>aAc	p.S2259N	FASN_ENST00000579758.1_Intron	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	2259	Thioesterase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	GGAGGCCAGGCTGTGGAACAC	0.687																																					p.S2259N	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.G6776A						PASS	.						45	45	45					17																	80038618		2191	4290	6481	SO:0001583	missense	2194	exon39			GCCAGGCTGTGGA	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.6776G>A	chr17.hg19:g.80038618C>T	ENSP00000304592:p.Ser2259Asn	28.0	0.0	.		32.0	7.0	.	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	C	10.05	1.242946	0.22796	.	.	ENSG00000169710	ENST00000306749	T	0.26067	1.76	4.47	2.3	0.28687	Thioesterase (1);	0.302769	0.35407	N	0.003229	T	0.10252	0.0251	N	0.08118	0	0.34398	D	0.694932	B	0.06786	0.001	B	0.06405	0.002	T	0.16541	-1.0399	10	0.19147	T	0.46	-34.0126	6.0153	0.19598	0.0:0.6205:0.1749:0.2047	.	2259	P49327	FAS_HUMAN	N	2259	ENSP00000304592:S2259N	ENSP00000304592:S2259N	S	-	2	0	FASN	77631907	1.000000	0.71417	1.000000	0.80357	0.670000	0.39368	0.914000	0.28624	1.091000	0.41335	0.591000	0.81541	AGC	.	.	.	none		0.687	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		T	80038618	C	T	80038618	3	4	140	1	0	0	0	0	1	0	0	0	5690	797	28	2	779	2	FASN	17	80038618	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08	7293332	80038618	1156592	45	8497											
METTL4	64863	hgsc.bcm.edu	37	chr18	2554953	2554953	+	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	gggcttactacccttgtcctGtttttcaaaaagtggataaa	11	14	8	8	0	1	0	1	0	0	0	2	1	2	1	2	2	2	2	2	2	6	6			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr18:2554953G>C	ENST00000574538.1	-	4	1319	c.544C>G	c.(544-546)Cag>Gag	p.Q182E	snoU109_ENST00000459316.1_RNA|METTL4_ENST00000319888.6_Missense_Mutation_p.Q182E	NM_022840.3	NP_073751.3	Q8N3J2	METL4_HUMAN	methyltransferase like 4	182					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						CCCTTGTCCTGTTTTTCAAAA	0.388																																					p.Q182E		Atlas-SNP	.											.	METTL4	40	.	0			c.C544G						PASS	.						119	124	122					18																	2554953		2203	4300	6503	SO:0001583	missense	64863	exon4			TGTCCTGTTTTTC		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.544C>G	chr18.hg19:g.2554953G>C	ENSP00000458290:p.Gln182Glu	219.0	0.0	.		104.0	61.0	.	NM_022840	B2RNA1|Q2TAA7|Q9H5U9	Missense_Mutation	SNP	ENST00000574538.1	hg19	CCDS11826.1	.	.	.	.	.	.	.	.	.	.	G	7.036	0.561490	0.13498	.	.	ENSG00000101574	ENST00000319888	T	0.21031	2.03	5.85	0.516	0.17019	.	1.312720	0.04780	N	0.429705	T	0.14743	0.0356	L	0.42245	1.32	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.26744	-1.0094	10	0.02654	T	1	0.1066	4.6714	0.12691	0.2571:0.2993:0.4436:0.0	.	182	Q8N3J2	METL4_HUMAN	E	182	ENSP00000320349:Q182E	ENSP00000320349:Q182E	Q	-	1	0	METTL4	2544953	0.000000	0.05858	0.000000	0.03702	0.916000	0.54674	0.407000	0.21049	0.055000	0.16094	0.655000	0.94253	CAG	.	.	.	none		0.388	METTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254326.3	NM_022840		C	2554953	G	C	2554953	3	2	140	1	0	0	0	0	1	0	0	0	9509	1386	48	4	898	4	METTL4	18	2554953	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08		2554953	75522295	46	8498											
PALM	5064	hgsc.bcm.edu	37	chr19	746543	746543	+	Missense_Mutation	SNP	T	T	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	gcccggccaggagcccccggTcacaatgatcttcatgggtt	7	8	12	14	2	3	1	2	1	1	0	3	2	3	2	4	4	1	1	4	4	1	2			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr19:746543T>G	ENST00000338448.5	+	9	939	c.893T>G	c.(892-894)gTc>gGc	p.V298G	PALM_ENST00000264560.7_Missense_Mutation_p.V254G|PALM_ENST00000593172.1_3'UTR	NM_002579.2	NP_002570.2	O75781	PALM_HUMAN	paralemmin	298					cellular component movement (GO:0006928)|cellular response to electrical stimulus (GO:0071257)|cytoskeleton organization (GO:0007010)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of filopodium assembly (GO:0051491)|protein targeting to plasma membrane (GO:0072661)|regulation of cell shape (GO:0008360)|synapse maturation (GO:0060074)	apicolateral plasma membrane (GO:0016327)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cytoplasmic membrane-bounded vesicle (GO:0016023)|dendrite membrane (GO:0032590)|dendritic spine membrane (GO:0032591)|filopodium membrane (GO:0031527)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(1)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_epithelial(18;2.19e-21)|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)|Lung(535;0.201)		GAGCCCCCGGTCACAATGATC	0.667																																					p.V298G		Atlas-SNP	.											.	PALM	26	.	0			c.T893G						PASS	.						34	32	32					19																	746543		2203	4299	6502	SO:0001583	missense	5064	exon9			CCCCGGTCACAAT	Y16270	CCDS32857.1, CCDS32858.1	19p13.3	2008-07-17				ENSG00000099864			8594	protein-coding gene	gene with protein product		608134				9615234, 9813098	Standard	XM_005259565		Approved	KIAA0270	uc002lpm.1	O75781		ENST00000338448.5:c.893T>G	chr19.hg19:g.746543T>G	ENSP00000341911:p.Val298Gly	49.0	0.0	.		56.0	19.0	.	NM_002579	O43359|O95673|Q92559|Q9UPJ4|Q9UQS2|Q9UQS3	Missense_Mutation	SNP	ENST00000338448.5	hg19	CCDS32857.1	.	.	.	.	.	.	.	.	.	.	T	18.83	3.706659	0.68615	.	.	ENSG00000099864	ENST00000338448;ENST00000264560;ENST00000538247	T;T	0.28666	1.6;1.6	4.92	3.83	0.44106	.	0.000000	0.85682	D	0.000000	T	0.55049	0.1896	M	0.82630	2.6	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.60627	-0.7226	10	0.87932	D	0	-41.4159	9.8074	0.40801	0.1538:0.0:0.0:0.8462	.	254;298	O75781-2;O75781	.;PALM_HUMAN	G	298;254;163	ENSP00000341911:V298G;ENSP00000264560:V254G	ENSP00000264560:V254G	V	+	2	0	PALM	697543	1.000000	0.71417	0.998000	0.56505	0.546000	0.35178	5.847000	0.69451	1.839000	0.53478	0.379000	0.24179	GTC	.	.	.	none		0.667	PALM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457592.1	NM_002579		G	746543	T	G	746543	3	3	140	1	0	0	0	0	1	0	0	0	11415	1667	58	5	927	5	PALM	19	746543	Missense_Mutation	SNP	T	TCGA-BQ-7058-01A-11D-1961-08		746543	58382440	47	8499											
PIAS4	51588	hgsc.bcm.edu	37	chr19	4013072	4013072	+	Missense_Mutation	SNP	A	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	gctgttcaagaagatcaaggAgctgtacgagacccgctacg	12	7	12	10	3	2	3	2	0	0	3	2	5	2	4	1	1	3	5	1	1	5	3			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr19:4013072A>C	ENST00000262971.2	+	2	294	c.179A>C	c.(178-180)gAg>gCg	p.E60A		NM_015897.2	NP_056981.2	Q8N2W9	PIAS4_HUMAN	protein inhibitor of activated STAT, 4	60					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)		AAGATCAAGGAGCTGTACGAG	0.632																																					p.E60A		Atlas-SNP	.											.	PIAS4	40	.	0			c.A179C						PASS	.						58	57	57					19																	4013072		2203	4300	6503	SO:0001583	missense	51588	exon2			TCAAGGAGCTGTA	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.179A>C	chr19.hg19:g.4013072A>C	ENSP00000262971:p.Glu60Ala	55.0	0.0	.		86.0	38.0	.	NM_015897	O75926|Q96G19|Q9UN16	Missense_Mutation	SNP	ENST00000262971.2	hg19	CCDS12118.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.769648	0.90020	.	.	ENSG00000105229	ENST00000262971	T	0.39592	1.07	5.14	5.14	0.70334	DNA-binding SAP (1);	0.053905	0.85682	D	0.000000	T	0.60444	0.2269	L	0.61036	1.89	0.53688	D	0.999975	D	0.69078	0.997	D	0.68765	0.96	T	0.64571	-0.6376	10	0.87932	D	0	-35.6334	14.1251	0.65215	1.0:0.0:0.0:0.0	.	60	Q8N2W9	PIAS4_HUMAN	A	60	ENSP00000262971:E60A	ENSP00000262971:E60A	E	+	2	0	PIAS4	3964072	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.283000	0.95860	1.938000	0.56188	0.459000	0.35465	GAG	.	.	.	none		0.632	PIAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457496.1	NM_015897		C	4013072	A	C	4013072	3	2	140	1	0	0	0	0	1	0	0	0	11885	304	11	5	185	5	PIAS4	19	4013072	Missense_Mutation	SNP	A	TCGA-BQ-7058-01A-11D-1961-08	3266529	4013072	55115911	48	8500											
FBXW9	84261	hgsc.bcm.edu	37	chr19	12807385	12807385	+	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	aatcatcgcaccgccctaggGgaagctccattgcgaccggg	9	6	12	14	4	1	0	1	0	0	0	3	2	2	1	4	3	2	2	4	3	3	2			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr19:12807385G>T	ENST00000380339.3	-	1	47	c.11C>A	c.(10-12)cCc>cAc	p.P4H	FBXW9_ENST00000393261.3_Missense_Mutation_p.P4H|FBXW9_ENST00000544494.1_5'UTR|FBXW9_ENST00000587955.1_Missense_Mutation_p.P4H			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	4					SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						CCGCCCTAGGGGAAGCTCCAT	0.662																																					p.P4H		Atlas-SNP	.											.	FBXW9	30	.	0			c.C11A						PASS	.						34	36	35					19																	12807385		1899	3937	5836	SO:0001583	missense	84261	exon1			CCTAGGGGAAGCT	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.11C>A	chr19.hg19:g.12807385G>T	ENSP00000369696:p.Pro4His	75.0	0.0	.		99.0	31.0	.	NM_032301	B3KVP7|Q9BT89	Missense_Mutation	SNP	ENST00000380339.3	hg19		.	.	.	.	.	.	.	.	.	.	G	12.20	1.867154	0.32977	.	.	ENSG00000132004	ENST00000393261;ENST00000380339	T;T	0.47869	1.86;0.83	3.77	1.64	0.23874	.	0.182213	0.26646	N	0.023231	T	0.42810	0.1219	L	0.27053	0.805	0.22142	N	0.999336	D;D	0.61697	0.99;0.99	P;P	0.55824	0.785;0.785	T	0.20605	-1.0270	10	0.87932	D	0	-7.2791	6.1222	0.20159	0.2273:0.0:0.7727:0.0	.	4;4	Q5XUX1-2;Q5XUX1-3	.;.	H	4	ENSP00000376945:P4H;ENSP00000369696:P4H	ENSP00000369696:P4H	P	-	2	0	FBXW9	12668385	0.169000	0.23002	0.087000	0.20705	0.044000	0.14063	2.195000	0.42677	0.575000	0.29434	0.462000	0.41574	CCC	.	.	.	none		0.662	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301		T	12807385	G	T	12807385	3	4	140	1	0	0	0	0	1	0	0	0	5778	1232	43	4	1405	4	FBXW9	19	12807385	Missense_Mutation	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	8794313	12807385	46321598	49	8501											
RYR1	6261	hgsc.bcm.edu	37	chr19	38976604	38976604	+	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	gggagttggagtcaccacttCgctgaggcccccgcatcatt	7	9	12	13	2	2	1	2	1	0	0	3	3	2	3	3	3	0	3	3	3	0	3	rs398123472		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr19:38976604C>T	ENST00000359596.3	+	34	5309	c.5309C>T	c.(5308-5310)tCg>tTg	p.S1770L	RYR1_ENST00000360985.3_Missense_Mutation_p.S1770L|RYR1_ENST00000355481.4_Missense_Mutation_p.S1770L			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1770	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GTCACCACTTCGCTGAGGCCC	0.682																																					p.S1770L		Atlas-SNP	.											RYR1,lower_third,carcinoma,0,1	RYR1	708	.	0			c.C5309T						PASS	.						41	40	40					19																	38976604		2203	4300	6503	SO:0001583	missense	6261	exon34			CCACTTCGCTGAG	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.5309C>T	chr19.hg19:g.38976604C>T	ENSP00000352608:p.Ser1770Leu	67.0	0.0	.		87.0	41.0	.	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	C	10.53	1.376736	0.24857	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.73469	-0.75;-0.75;-0.75	3.62	3.62	0.41486	.	0.079974	0.50627	U	0.000120	T	0.68311	0.2987	M	0.62723	1.935	0.32730	N	0.509105	P;P	0.52170	0.945;0.951	B;B	0.40134	0.273;0.32	T	0.79472	-0.1789	10	0.72032	D	0.01	.	10.3775	0.44090	0.0:0.612:0.388:0.0	.	1770;1770	P21817-2;P21817	.;RYR1_HUMAN	L	1770	ENSP00000352608:S1770L;ENSP00000347667:S1770L;ENSP00000354254:S1770L	ENSP00000347667:S1770L	S	+	2	0	RYR1	43668444	0.864000	0.29904	1.000000	0.80357	0.159000	0.22180	1.096000	0.30976	1.850000	0.53721	0.585000	0.79938	TCG	.	.	.	none		0.682	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	38976604	C	T	38976604	3	4	140	1	0	0	0	0	1	0	0	0	13781	893	31	1	5443	1	RYR1	19	38976604	Missense_Mutation	SNP	C	TCGA-BQ-7058-01A-11D-1961-08	26169219	38976604	20152379	50	8502											
PSG3	5671	hgsc.bcm.edu	37	chr19	43237192	43237192	+	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	gggtataagttgctgctggaGatggagggcttgggagtctc	7	11	18	5	0	1	1	0	0	1	1	2	4	1	3	0	5	2	5	0	5	2	4			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr19:43237192G>T	ENST00000327495.5	-	3	637	c.453C>A	c.(451-453)atC>atA	p.I151I	PSG3_ENST00000490592.1_5'Flank|PSG3_ENST00000595140.1_Silent_p.I151I	NM_021016.3	NP_066296.2	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	151	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)				TGCTGCTGGAGATGGAGGGCT	0.522																																					p.I151I		Atlas-SNP	.											.	PSG3	82	.	0			c.C453A						PASS	.						160	160	160					19																	43237192		2203	4300	6503	SO:0001819	synonymous_variant	5671	exon3			GCTGGAGATGGAG		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.453C>A	chr19.hg19:g.43237192G>T		341.0	1.0	.		310.0	117.0	.	NM_021016	Q08265|Q9BRW2|Q9UPL4|Q9UQ77	Silent	SNP	ENST00000327495.5	hg19	CCDS12611.1																																																																																			.	.	.	none		0.522	PSG3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321423.2	NM_021016		T	43237192	G	T	43237192	2	4	140	1	0	0	0	0	0	0	0	1	12666	932	33	4		4	PSG3	19	43237192	Silent	SNP	G	TCGA-BQ-7058-01A-11D-1961-08	4260588	43237192	15891791	51	8503											
PCBP3	54039	hgsc.bcm.edu	37	chr21	47333926	47333926	+	Missense_Mutation	SNP	T	T	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	cgcctccacccctgtcatttTtgcaggtggtcaggtaagag	7	11	11	12	1	2	1	2	0	0	1	3	1	3	1	4	3	1	2	4	3	1	3			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chr21:47333926T>G	ENST00000400314.1	+	10	1000	c.662T>G	c.(661-663)tTt>tGt	p.F221C	PCBP3_ENST00000400308.1_Intron|PCBP3_ENST00000400309.1_Missense_Mutation_p.F221C|PCBP3_ENST00000400304.1_Missense_Mutation_p.F189C|PCBP3_ENST00000400310.1_Missense_Mutation_p.F221C|PCBP3_ENST00000449640.1_Missense_Mutation_p.F221C			P57721	PCBP3_HUMAN	poly(rC) binding protein 3	221					mRNA metabolic process (GO:0016071)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(3)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)		CCTGTCATTTTTGCAGGTGGT	0.602																																					p.F221C		Atlas-SNP	.											.	PCBP3	82	.	0			c.T662G						PASS	.						64	72	69					21																	47333926		1987	4167	6154	SO:0001583	missense	54039	exon8			TCATTTTTGCAGG	AF176329	CCDS42974.2, CCDS46652.1	21q22.3	2013-07-16	2001-11-28		ENSG00000183570	ENSG00000183570			8651	protein-coding gene	gene with protein product		608502	"poly(rC)-binding protein 3"			10936052	Standard	NM_020528		Approved		uc002zhq.2	P57721	OTTHUMG00000090399	ENST00000400314.1:c.662T>G	chr21.hg19:g.47333926T>G	ENSP00000383168:p.Phe221Cys	78.0	0.0	.		100.0	39.0	.	NM_020528	A8MPS2|A8MQ26|B7WNN9|B7WPC1|Q8N9K6|Q96EP6	Missense_Mutation	SNP	ENST00000400314.1	hg19	CCDS42974.2	.	.	.	.	.	.	.	.	.	.	T	22.1	4.250671	0.80135	.	.	ENSG00000183570	ENST00000400314;ENST00000400310;ENST00000400309;ENST00000449640;ENST00000346743;ENST00000400304	T;T;T;T;T	0.47177	1.49;1.41;1.43;1.49;0.85	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.58206	0.2106	L	0.52364	1.645	0.80722	D	1	D;B;D;B	0.67145	0.986;0.039;0.996;0.004	P;B;P;B	0.58391	0.838;0.099;0.784;0.029	T	0.59445	-0.7453	10	0.48119	T	0.1	-3.3437	14.9659	0.71193	0.0:0.0:0.0:1.0	.	189;221;221;221	E9PFP8;P57721-4;P57721;P57721-5	.;.;PCBP3_HUMAN;.	C	221;221;221;221;221;189	ENSP00000383168:F221C;ENSP00000383165:F221C;ENSP00000383164:F221C;ENSP00000401198:F221C;ENSP00000383159:F189C	ENSP00000330225:F221C	F	+	2	0	PCBP3	46158354	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.577000	0.82486	1.933000	0.56026	0.460000	0.39030	TTT	.	.	.	none		0.602	PCBP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206808.2			G	47333926	T	G	47333926	3	3	140	1	0	0	0	0	1	0	0	0	11509	1841	64	5	692	5	PCBP3	21	47333926	Missense_Mutation	SNP	T	TCGA-BQ-7058-01A-11D-1961-08		47333926	795969	52	8504											
FAM123B	139285	hgsc.bcm.edu	37	chrX	63412033	63412033	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcttcttcctcctcgtcAtcatcatctggcaaggccat	6	14	5	16	1	6	0	3	0	3	0	10	0	9	0	4	2	0	1	4	2	1	2			TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chrX:63412033A>G	ENST00000330258.3	-	2	1406	c.1134T>C	c.(1132-1134)gaT>gaC	p.D378D	AMER1_ENST00000403336.1_Silent_p.D378D|AMER1_ENST00000374869.3_Silent_p.D378D	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	378	Glu-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)									cctcctcGTCATCATCATCTG	0.522																																					p.D378D		Atlas-SNP	.											.	.	.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.T1134C						PASS	.						153	142	146					X																	63412033		2203	4300	6503	SO:0001819	synonymous_variant	139285	exon2			CTCGTCATCATCA	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.1134T>C	chrX.hg19:g.63412033A>G		88.0	0.0	.		85.0	7.0	.	NM_152424	A2IB86|Q8N885	Silent	SNP	ENST00000330258.3	hg19	CCDS14377.2																																																																																			.	.	.	none		0.522	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		G	63412033	A	G	63412033	2	3	140	1	0	0	0	0	0	0	0	1	5427	214	8	3		3	FAM123B	23	63412033	Silent	SNP	A	TCGA-BQ-7058-01A-11D-1961-08		63412033	91858527	53	8505											
GPRASP1	9737	hgsc.bcm.edu	37	chrX	101912417	101912418	+	Frame_Shift_Del	DEL	TC	TC	-																															caatttacccgagatttcatTcgagattcaggtgttgtctc																										TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	TC	TC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	g.chrX:101912417_101912418delTC	ENST00000361600.5	+	5	4377_4378	c.3576_3577delTC	c.(3574-3579)attcgafs	p.IR1192fs	RP4-769N13.7_ENST00000602441.1_RNA|GPRASP1_ENST00000415986.1_Frame_Shift_Del_p.IR1192fs|GPRASP1_ENST00000444152.1_Frame_Shift_Del_p.IR1192fs|GPRASP1_ENST00000537097.1_Frame_Shift_Del_p.IR1192fs	NM_014710.4	NP_055525.3	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting protein 1	1192	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						GAGATTTCATTCGAGATTCAGG	0.371																																					p.1192_1192del		Atlas-INDEL	.											.	GPRASP1	140	.	0			c.3575_3576del						PASS	.																																			SO:0001589	frameshift_variant	9737	exon6			.	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.3576_3577delTC	chrX.hg19:g.101912417_101912418delTC	ENSP00000355146:p.Ile1192fs	76.0	0.0	0		69.0	52.0	0.753623	NM_001184727	O43168|Q96LA1	Frame_Shift_Del	DEL	ENST00000361600.5	hg19	CCDS35352.1																																																																																			.	.	.	none		0.371	GPRASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057634.2	NM_014710		-	101912418	TC	-	101912417	7	5	140	1	0	1	0	1	0	0	0	0	6729	1771	62	0	3578	0	GPRASP1	23	101912417	Frame_Shift_Del	DEL	TC	TCGA-BQ-7058-01A-11D-1961-08	38500384	101912417	53358143	54	8506											
PEX10	5192	hgsc.bcm.edu	37	chr1	2340282	2340282	+	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	tgatgctgacgtactcctccCccagggtctggtagcctgcg	5	10	12	14	2	1	2	0	2	1	0	3	2	3	2	4	2	4	3	4	2	2	2			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr1:2340282C>G	ENST00000447513.2	-	3	277	c.209G>C	c.(208-210)gGg>gCg	p.G70A	PEX10_ENST00000507596.1_Missense_Mutation_p.G70A|PEX10_ENST00000288774.3_Missense_Mutation_p.G70A|PEX10_ENST00000515760.1_5'UTR	NM_002617.3	NP_002608.1	O60683	PEX10_HUMAN	peroxisomal biogenesis factor 10	70					peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)	integral component of peroxisomal membrane (GO:0005779)|intracellular (GO:0005622)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(2)	7	all_cancers(77;0.000247)|all_epithelial(69;9.96e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;5.35e-20)|all_lung(118;2.78e-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)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.1e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.02e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00102)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0169)|Lung(427;0.199)		GTACTCCTCCCCCAGGGTCTG	0.677																																					p.G70A	GBM(12;9 508 1649 13619)	Atlas-SNP	.											.	PEX10	18	.	0			c.G209C						PASS	.						94	95	95					1																	2340282		2203	4300	6503	SO:0001583	missense	5192	exon3			TCCTCCCCCAGGG	AF060502	CCDS41.1, CCDS44045.1	1p36.32	2013-01-09	2008-08-26		ENSG00000157911	ENSG00000157911		"RING-type (C3HC4) zinc fingers"	8851	protein-coding gene	gene with protein product		602859	"peroxisome biogenesis factor 10"			9683594	Standard	NM_002617		Approved	RNF69	uc001ajg.3	O60683	OTTHUMG00000001637	ENST00000447513.2:c.209G>C	chr1.hg19:g.2340282C>G	ENSP00000407922:p.Gly70Ala	54.0	0.0	.		58.0	14.0	.	NM_002617	B3KWD8|Q5T095|Q9BW90	Missense_Mutation	SNP	ENST00000447513.2	hg19	CCDS44045.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.210641	0.79240	.	.	ENSG00000157911	ENST00000288774;ENST00000447513;ENST00000507596	D;D;D	0.88201	-2.35;-2.35;-2.35	4.48	4.48	0.54585	Pex, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.95661	0.8589	M	0.92833	3.35	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96912	0.9668	10	0.87932	D	0	2.6652	16.1137	0.81283	0.0:1.0:0.0:0.0	.	70;70	O60683;O60683-2	PEX10_HUMAN;.	A	70	ENSP00000288774:G70A;ENSP00000407922:G70A;ENSP00000424291:G70A	ENSP00000288774:G70A	G	-	2	0	PEX10	2330142	1.000000	0.71417	1.000000	0.80357	0.668000	0.39293	5.505000	0.66981	2.035000	0.60131	0.462000	0.41574	GGG	.	.	.	none		0.677	PEX10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367454.1	NM_153818		G	2340282	C	G	2340282	3	3	141	1	0	0	0	0	1	0	0	0	11743	623	22	4	847	4	PEX10	1	2340282	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08		2340282	246910339	1	8507											
PER3	8863	hgsc.bcm.edu	37	chr1	7887456	7887456	+	Missense_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	cctcacccggaagagaatacGcagcccccggaactgcaccg	11	3	10	17	4	1	1	1	0	0	1	1	4	1	3	5	2	4	2	5	2	4	1			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr1:7887456G>A	ENST00000361923.2	+	17	2618	c.2443G>A	c.(2443-2445)Gca>Aca	p.A815T	RP3-467L1.4_ENST00000451646.1_RNA|PER3_ENST00000377532.3_Missense_Mutation_p.A823T	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	815	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)		AAGAGAATACGCAGCCCCCGG	0.622																																					p.A815T		Atlas-SNP	.											.	PER3	95	.	0			c.G2443A						PASS	.						67	69	68					1																	7887456		2203	4300	6503	SO:0001583	missense	8863	exon17			GAATACGCAGCCC	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.2443G>A	chr1.hg19:g.7887456G>A	ENSP00000355031:p.Ala815Thr	162.0	0.0	.		112.0	28.0	.	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	hg19	CCDS89.1	.	.	.	.	.	.	.	.	.	.	G	7.390	0.630557	0.14322	.	.	ENSG00000049246	ENST00000377532;ENST00000361923;ENST00000539773	T;T	0.10192	2.9;2.9	3.68	-2.56	0.06268	.	2.865610	0.00841	N	0.001740	T	0.04003	0.0112	N	0.11427	0.14	0.09310	N	1	B;P;B;B	0.34662	0.07;0.462;0.41;0.07	B;B;B;B	0.24541	0.011;0.054;0.053;0.011	T	0.20009	-1.0288	10	0.17369	T	0.5	.	0.9429	0.01359	0.3343:0.3073:0.2098:0.1487	.	815;823;823;815	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	T	823;815;26	ENSP00000366755:A823T;ENSP00000355031:A815T	ENSP00000355031:A815T	A	+	1	0	PER3	7810043	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	0.918000	0.28678	-0.394000	0.07727	0.561000	0.74099	GCA	.	.	.	none		0.622	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831		A	7887456	G	A	7887456	3	1	141	1	0	0	0	0	1	0	0	0	11738	1087	38	1	2509	1	PER3	1	7887456	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	5547174	7887456	241363165	2	8508											
YARS	8565	hgsc.bcm.edu	37	chr1	33246690	33246690	+	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	ccccacacggatatccagccGggatgggatgacctcctctg	8	7	11	15	2	1	1	0	1	1	0	3	4	3	4	6	3	1	0	6	3	1	1	rs376054085		TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr1:33246690G>T	ENST00000373477.4	-	10	2007	c.1099C>A	c.(1099-1101)Cgg>Agg	p.R367R	YARS_ENST00000469100.1_5'UTR	NM_003680.3	NP_003671.1	P54577	SYYC_HUMAN	tyrosyl-tRNA synthetase	367	tRNA-binding. {ECO:0000255|PROSITE- ProRule:PRU00209}.				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)	p.R367W(1)		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)	ATATCCAGCCGGGATGGGATG	0.507																																					p.R367R		Atlas-SNP	.											YARS,caecum,carcinoma,0,1	YARS	34	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1099A						PASS	.						135	123	127					1																	33246690		2203	4300	6503	SO:0001819	synonymous_variant	8565	exon10			CCAGCCGGGATGG	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.1099C>A	chr1.hg19:g.33246690G>T		194.0	0.0	.		185.0	8.0	.	NM_003680	B3KWK4|D3DPQ4|O43276|Q53EN1	Silent	SNP	ENST00000373477.4	hg19	CCDS368.1																																																																																			.	.	.	none		0.507	YARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011225.1	NM_003680		T	33246690	G	T	33246690	2	4	141	1	0	0	0	0	0	0	0	1	17479	1115	39	4		4	YARS	1	33246690	Silent	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	25359234	33246690	216003931	3	8509											
THRAP3	9967	hgsc.bcm.edu	37	chr1	36767245	36767245	+	Frame_Shift_Del	DEL	G	G	-																															cgattttcaaaaaagaaaccGggaagaggagtgggacccag																								rs566092059		TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr1:36767245delG	ENST00000354618.5	+	11	2818	c.2594delG	c.(2593-2595)cggfs	p.R865fs	THRAP3_ENST00000469141.2_Frame_Shift_Del_p.R865fs	NM_005119.3	NP_005110.2	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	865	Required for mRNA decay activity.				androgen receptor signaling pathway (GO:0030521)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|phosphoprotein binding (GO:0051219)|poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(5)|stomach(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				AAAAGAAACCGGGAAGAGGAG	0.478			T	USP6	aneurysmal bone cysts																																p.R865fs	Pancreas(129;785 1795 20938 23278 32581)	Atlas-INDEL	.		Dom	yes		1	1p34.3	9967	thyroid hormone receptor associated protein 3 (TRAP150)		M	.	THRAP3	93	.	0			c.2593delC						PASS	.						66	68	67					1																	36767245		2203	4300	6503	SO:0001589	frameshift_variant	9967	exon11			.	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.2594delG	chr1.hg19:g.36767245delG	ENSP00000346634:p.Arg865fs	75.0	0.0	0		78.0	21.0	0.269231	NM_005119	D3DPS5|Q5VTK6	Frame_Shift_Del	DEL	ENST00000354618.5	hg19	CCDS405.1																																																																																			.	.	.	none		0.478	THRAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021688.2	NM_005119		-	36767245	G	-	36767245	7	5	141	1	0	1	0	1	0	0	0	0	15886	1116	39	0	2628	0	THRAP3	1	36767245	Frame_Shift_Del	DEL	G	TCGA-BQ-7059-01A-11D-1961-08	3520555	36767245	212483376	4	8510											
ATXN7L2	127002	hgsc.bcm.edu	37	chr1	110034064	110034064	+	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	gagtgaagcgggcagggcccCtggactgtcgtggctcccct	5	7	16	13	2	0	1	0	1	0	0	2	3	1	2	4	4	1	2	4	4	1	0			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr1:110034064C>A	ENST00000369870.3	+	10	1894	c.1879C>A	c.(1879-1881)Ctg>Atg	p.L627M	CYB561D1_ENST00000496961.1_5'Flank|CYB561D1_ENST00000369868.3_5'Flank|CYB561D1_ENST00000430195.2_5'Flank|CYB561D1_ENST00000533024.1_5'Flank|CYB561D1_ENST00000420578.2_5'Flank|CYB561D1_ENST00000528785.1_5'Flank|CYB561D1_ENST00000393709.3_5'Flank|ATXN7L2_ENST00000459635.1_3'UTR|CYB561D1_ENST00000527072.1_5'Flank|CYB561D1_ENST00000310611.4_5'Flank	NM_153340.4	NP_699171.3	Q5T6C5	AT7L2_HUMAN	ataxin 7-like 2	627										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)	17		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0426)|Epithelial(280;0.0675)|READ - Rectum adenocarcinoma(129;0.0693)|all cancers(265;0.071)|LUSC - Lung squamous cell carcinoma(189;0.228)		GGCAGGGCCCCTGGACTGTCG	0.622																																					p.L627M		Atlas-SNP	.											.	ATXN7L2	60	.	0			c.C1879A						PASS	.						35	40	38					1																	110034064		2203	4300	6503	SO:0001583	missense	127002	exon10			GGGCCCCTGGACT	BC037582	CCDS30794.1	1p13.2	2008-02-05			ENSG00000162650	ENSG00000162650			28713	protein-coding gene	gene with protein product						12477932	Standard	NM_153340		Approved	MGC46534, FLJ00381	uc001dxr.3	Q5T6C5	OTTHUMG00000011027	ENST00000369870.3:c.1879C>A	chr1.hg19:g.110034064C>A	ENSP00000358886:p.Leu627Met	85.0	0.0	.		52.0	20.0	.	NM_153340		Missense_Mutation	SNP	ENST00000369870.3	hg19	CCDS30794.1	.	.	.	.	.	.	.	.	.	.	C	14.37	2.514316	0.44763	.	.	ENSG00000162650	ENST00000369870;ENST00000369869	T	0.38560	1.13	5.36	3.26	0.37387	.	0.440276	0.19115	N	0.122331	T	0.23451	0.0567	N	0.24115	0.695	0.25930	N	0.983008	P;D	0.64830	0.946;0.994	P;P	0.55222	0.714;0.771	T	0.04678	-1.0934	10	0.72032	D	0.01	-0.0215	7.9316	0.29905	0.0:0.7788:0.0:0.2212	.	254;627	Q5T6C4;Q5T6C5	.;AT7L2_HUMAN	M	627;254	ENSP00000358886:L627M	ENSP00000358885:L254M	L	+	1	2	ATXN7L2	109835587	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	2.056000	0.41355	0.647000	0.30713	-0.258000	0.10820	CTG	.	.	.	none		0.622	ATXN7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030331.1	NM_153340		A	110034064	C	A	110034064	3	1	141	1	0	0	0	0	1	0	0	0	1217	680	24	4	1917	4	ATXN7L2	1	110034064	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	73266819	110034064	139216557	5	8511											
INSRR	3645	hgsc.bcm.edu	37	chr1	156811976	156811976	+	Missense_Mutation	SNP	T	T	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	atctcggtgcacaaacttgtTggcagcaaggtaggccatgc	10	9	12	10	1	1	0	0	0	1	0	2	0	1	0	1	4	4	5	1	4	3	3			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr1:156811976T>G	ENST00000368195.3	-	19	3721	c.3325A>C	c.(3325-3327)Aac>Cac	p.N1109H	NTRK1_ENST00000392302.2_Missense_Mutation_p.L38W	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	1109	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)					ACAAACTTGTTGGCAGCAAGG	0.572																																					p.N1109H		Atlas-SNP	.											.	INSRR	309	.	0			c.A3325C						PASS	.						104	95	98					1																	156811976		2203	4300	6503	SO:0001583	missense	3645	exon19			ACTTGTTGGCAGC	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.3325A>C	chr1.hg19:g.156811976T>G	ENSP00000357178:p.Asn1109His	58.0	0.0	.		41.0	12.0	.	NM_014215	O60724|Q5VZS3	Missense_Mutation	SNP	ENST00000368195.3	hg19	CCDS1160.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.4|23.4	4.413045|4.413045	0.83449|0.83449	.|.	.|.	ENSG00000198400|ENSG00000027644	ENST00000392302|ENST00000368195	T|D	0.76839|0.82803	-1.05|-1.65	4.83|4.83	4.83|4.83	0.62350|0.62350	.|Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.|0.260110	.|0.27223	.|N	.|0.020345	T|T	0.67664|0.67664	0.2917|0.2917	N|N	0.17594|0.17594	0.5|0.5	0.37606|0.37606	D|D	0.920732|0.920732	D|P	0.76494|0.41102	0.999|0.738	D|P	0.64042|0.44623	0.921|0.455	T|T	0.76490|0.76490	-0.2940|-0.2940	9|10	0.87932|0.72032	D|D	0|0.01	.|.	13.364|13.364	0.60674|0.60674	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	38|1109	A6NF12|P14616	.|INSRR_HUMAN	W|H	38|1109	ENSP00000376120:L38W|ENSP00000357178:N1109H	ENSP00000376120:L38W|ENSP00000357178:N1109H	L|N	+|-	2|1	0|0	NTRK1|INSRR	155078600|155078600	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.968000|0.968000	0.65278|0.65278	7.868000|7.868000	0.87116|0.87116	2.041000|2.041000	0.60428|0.60428	0.459000|0.459000	0.35465|0.35465	TTG|AAC	.	.	.	none		0.572	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		G	156811976	T	G	156811976	3	3	141	1	0	0	0	0	1	0	0	0	7781	1821	63	5	583	5	INSRR	1	156811976	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	46777912	156811976	92438645	6	8512											
PLEKHA6	22874	hgsc.bcm.edu	37	chr1	204198070	204198070	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctggctccactcacctcctTattgatgtccacgtcataat	8	13	5	15	1	2	1	2	1	0	0	5	1	5	1	5	1	0	1	5	1	2	3			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr1:204198070T>C	ENST00000272203.3	-	19	3062	c.2746A>G	c.(2746-2748)Aag>Gag	p.K916E	PLEKHA6_ENST00000414478.1_Missense_Mutation_p.K936E	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	916										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)			CTCACCTCCTTATTGATGTCC	0.587																																					p.K916E		Atlas-SNP	.											.	PLEKHA6	115	.	0			c.A2746G						PASS	.						116	112	113					1																	204198070		2203	4300	6503	SO:0001583	missense	22874	exon19			CCTCCTTATTGAT	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.2746A>G	chr1.hg19:g.204198070T>C	ENSP00000272203:p.Lys916Glu	163.0	0.0	.		187.0	49.0	.	NM_014935	A7MD51|Q5VTI6	Missense_Mutation	SNP	ENST00000272203.3	hg19	CCDS1444.1	.	.	.	.	.	.	.	.	.	.	T	16.53	3.148801	0.57151	.	.	ENSG00000143850	ENST00000272203;ENST00000414478	T;T	0.45276	0.9;0.9	5.3	5.3	0.74995	.	0.265846	0.36628	N	0.002497	T	0.59649	0.2209	M	0.72894	2.215	0.35019	D	0.757628	D	0.58268	0.982	D	0.67548	0.952	T	0.71002	-0.4718	10	0.49607	T	0.09	-32.3486	10.459	0.44567	0.0:0.0786:0.0:0.9214	.	916	Q9Y2H5	PKHA6_HUMAN	E	916;936	ENSP00000272203:K916E;ENSP00000402046:K936E	ENSP00000272203:K916E	K	-	1	0	PLEKHA6	202464693	1.000000	0.71417	0.875000	0.34327	0.332000	0.28634	5.520000	0.67080	1.995000	0.58328	0.460000	0.39030	AAG	.	.	.	none		0.587	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935		C	204198070	T	C	204198070	3	2	141	1	0	0	0	0	1	0	0	0	12067	1763	61	3	416	3	PLEKHA6	1	204198070	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	47386094	204198070	45052551	7	8513											
TP53BP2	7159	hgsc.bcm.edu	37	chr1	223984099	223984099	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcactctggtttcggtaaggAttagataagaaaggcagtaa	14	11	11	5	1	2	2	1	0	1	2	3	3	2	3	0	4	0	4	0	4	5	5			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr1:223984099A>G	ENST00000343537.7	-	13	2433	c.2142T>C	c.(2140-2142)aaT>aaC	p.N714N	TP53BP2_ENST00000391879.2_5'UTR|TP53BP2_ENST00000391878.2_Silent_p.N585N|TP53BP2_ENST00000498843.1_5'UTR	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	708					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)		TTCGGTAAGGATTAGATAAGA	0.438																																					p.N714N		Atlas-SNP	.											.	TP53BP2	144	.	0			c.T2142C						PASS	.						143	139	140					1																	223984099		2203	4300	6503	SO:0001819	synonymous_variant	7159	exon13			GTAAGGATTAGAT	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.2142T>C	chr1.hg19:g.223984099A>G		208.0	0.0	.		228.0	52.0	.	NM_001031685	B4DG66|Q12892|Q86X75|Q96KQ3	Silent	SNP	ENST00000343537.7	hg19	CCDS44319.1																																																																																			.	.	.	none		0.438	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3	NM_001031685, NM_005426		G	223984099	A	G	223984099	2	3	141	1	0	0	0	0	0	0	0	1	16396	330	12	3		3	TP53BP2	1	223984099	Silent	SNP	A	TCGA-BQ-7059-01A-11D-1961-08	19786029	223984099	25266522	8	8514											
DUSP11	8446	hgsc.bcm.edu	37	chr2	74007101	74007101	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggatgatgccactggctcaTgtgggtcccaagaagccgcc	8	7	14	12	1	1	2	1	1	0	1	2	3	2	3	4	3	2	1	4	3	2	0			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr2:74007101T>C	ENST00000272444.3	-	1	183	c.142A>G	c.(142-144)Atg>Gtg	p.M48V	DUSP11_ENST00000377706.4_Start_Codon_SNP_p.M1V|DUSP11_ENST00000443070.1_Missense_Mutation_p.M48V|DUSP11_ENST00000480948.1_5'Flank	NM_003584.2	NP_003575.2	O75319	DUS11_HUMAN	dual specificity phosphatase 11 (RNA/RNP complex 1-interacting)	1					peptidyl-tyrosine dephosphorylation (GO:0035335)|polynucleotide 5' dephosphorylation (GO:0098507)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)	nucleus (GO:0005634)	nucleotide phosphatase activity, acting on free nucleotides (GO:0098519)|phosphatase activity (GO:0016791)|poly(A) RNA binding (GO:0044822)|polynucleotide 5'-phosphatase activity (GO:0004651)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(4)|skin(1)	12						CACTGGCTCATGTGGGTCCCA	0.607											OREG0014714	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.M48V		Atlas-SNP	.											.	DUSP11	35	.	0			c.A142G						PASS	.						61	61	61					2																	74007101		2203	4300	6503	SO:0001583	missense	8446	exon1			GGCTCATGTGGGT	AF023917	CCDS1928.2	2p13.1	2011-06-09			ENSG00000144048	ENSG00000144048		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	3066	protein-coding gene	gene with protein product		603092				9685386	Standard	NM_003584		Approved	PIR1	uc002sjp.3	O75319	OTTHUMG00000129816	ENST00000272444.3:c.142A>G	chr2.hg19:g.74007101T>C	ENSP00000272444:p.Met48Val	108.0	0.0	.	1149	82.0	24.0	.	NM_003584	B2RCT8|Q6AI47|Q9BWE3	Missense_Mutation	SNP	ENST00000272444.3	hg19	CCDS1928.2	.	.	.	.	.	.	.	.	.	.	T	15.13	2.742276	0.49151	.	.	ENSG00000144048	ENST00000272444;ENST00000443070;ENST00000377706	T;T	0.32988	1.43;2.01	4.6	4.6	0.57074	.	0.059637	0.56097	D	0.000024	T	0.35008	0.0917	.	.	.	0.80722	D	1	P;D	0.55172	0.882;0.97	B;P	0.48627	0.428;0.584	T	0.10291	-1.0636	9	0.51188	T	0.08	-4.2088	10.6571	0.45682	0.0:0.0:0.0:1.0	.	48;1	C9JYA6;O75319	.;DUS11_HUMAN	V	48;48;1	ENSP00000413444:M48V;ENSP00000366935:M1V	ENSP00000272444:M48V	M	-	1	0	DUSP11	73860609	1.000000	0.71417	0.998000	0.56505	0.013000	0.08279	3.027000	0.49697	2.285000	0.76669	0.533000	0.62120	ATG	.	.	.	none		0.607	DUSP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252047.3			C	74007101	T	C	74007101	3	2	141	1	0	0	0	0	1	0	0	0	4813	1464	51	3	1027	3	DUSP11	2	74007101	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08		74007101	169192272	9	8515											
RAPGEF4	11069	hgsc.bcm.edu	37	chr2	173885421	173885421	+	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	tggacgcctgtttgcttgccCgcgagagcaattcgattcac	7	11	11	12	4	1	1	1	0	0	1	2	4	1	2	2	1	3	3	2	1	1	4			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr2:173885421C>A	ENST00000397081.3	+	23	2374	c.2231C>A	c.(2230-2232)cCg>cAg	p.P744Q	RAPGEF4_ENST00000538974.1_Missense_Mutation_p.P573Q|RAPGEF4_ENST00000397087.3_Missense_Mutation_p.P600Q|RAPGEF4_ENST00000540783.1_Missense_Mutation_p.P591Q|RAPGEF4_ENST00000264111.6_Missense_Mutation_p.P743Q|RAPGEF4_ENST00000409036.1_Missense_Mutation_p.P744Q|RAPGEF4_ENST00000535187.1_Missense_Mutation_p.P524Q|RAPGEF4_ENST00000539331.1_Missense_Mutation_p.P591Q	NM_007023.3	NP_008954.2	Q8WZA2	RPGF4_HUMAN	Rap guanine nucleotide exchange factor (GEF) 4	744					blood coagulation (GO:0007596)|calcium ion-dependent exocytosis (GO:0017156)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|insulin secretion (GO:0030073)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of exocytosis (GO:0017157)|regulation of insulin secretion (GO:0050796)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(14)|lung(13)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47			OV - Ovarian serous cystadenocarcinoma(117;0.194)			TTTGCTTGCCCGCGAGAGCAA	0.448																																					p.P744Q		Atlas-SNP	.											.	RAPGEF4	103	.	0			c.C2231A						PASS	.						179	166	170					2																	173885421		1902	4125	6027	SO:0001583	missense	11069	exon23			CTTGCCCGCGAGA	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.2231C>A	chr2.hg19:g.173885421C>A	ENSP00000380271:p.Pro744Gln	216.0	0.0	.		198.0	9.0	.	NM_007023	B2R7R3|B7Z283|B7Z3T6|B7Z912|O95636|Q8IXK6|Q8TAA4	Missense_Mutation	SNP	ENST00000397081.3	hg19	CCDS42775.1	.	.	.	.	.	.	.	.	.	.	C	19.31	3.803308	0.70682	.	.	ENSG00000091428	ENST00000264111;ENST00000397081;ENST00000409036;ENST00000397087;ENST00000538974;ENST00000540783;ENST00000539331;ENST00000535187	T;T;T;T;T;T;T;T	0.63913	0.15;0.15;-0.07;0.04;0.04;0.16;0.16;-0.05	5.77	5.77	0.91146	Ras-association (1);Ras guanine nucleotide exchange factor, domain (1);	0.054509	0.85682	D	0.000000	T	0.71476	0.3344	M	0.62723	1.935	0.80722	D	1	P;B	0.52463	0.953;0.297	P;B	0.52646	0.705;0.239	T	0.67300	-0.5705	10	0.30854	T	0.27	.	19.9915	0.97366	0.0:1.0:0.0:0.0	.	600;744	Q8WZA2-3;Q8WZA2	.;RPGF4_HUMAN	Q	743;744;744;600;573;591;591;524	ENSP00000264111:P743Q;ENSP00000380271:P744Q;ENSP00000387104:P744Q;ENSP00000380276:P600Q;ENSP00000440135:P573Q;ENSP00000440250:P591Q;ENSP00000437384:P591Q;ENSP00000438011:P524Q	ENSP00000264111:P743Q	P	+	2	0	RAPGEF4	173593667	1.000000	0.71417	0.994000	0.49952	0.980000	0.70556	4.812000	0.62613	2.723000	0.93209	0.655000	0.94253	CCG	.	.	.	none		0.448	RAPGEF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257864.2	NM_007023		A	173885421	C	A	173885421	3	1	141	1	0	0	0	0	1	0	0	0	13059	652	23	4	2337	4	RAPGEF4	2	173885421	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	99878320	173885421	69313952	10	8516											
CNTN6	27255	hgsc.bcm.edu	37	chr3	1371578	1371578	+	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	gcttttcccagggcagctatCtcttggaaaagaggaacgga	11	9	12	9	1	1	1	0	0	1	1	3	4	2	4	1	4	2	3	1	4	4	4			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr3:1371578C>G	ENST00000446702.2	+	11	1950	c.1323C>G	c.(1321-1323)atC>atG	p.I441M	CNTN6_ENST00000539053.1_Missense_Mutation_p.I369M|CNTN6_ENST00000350110.2_Missense_Mutation_p.I441M			Q9UQ52	CNTN6_HUMAN	contactin 6	441	Ig-like C2-type 5.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		GGGCAGCTATCTCTTGGAAAA	0.333																																					p.I441M		Atlas-SNP	.											.	CNTN6	245	.	0			c.C1323G						PASS	.						57	59	58					3																	1371578		2202	4299	6501	SO:0001583	missense	27255	exon11			AGCTATCTCTTGG	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	2176	protein-coding gene	gene with protein product	"neural adhesion molecule"	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.1323C>G	chr3.hg19:g.1371578C>G	ENSP00000407822:p.Ile441Met	50.0	0.0	.		59.0	14.0	.	NM_014461	Q2KHM2	Missense_Mutation	SNP	ENST00000446702.2	hg19	CCDS2557.1	.	.	.	.	.	.	.	.	.	.	C	15.76	2.929637	0.52759	.	.	ENSG00000134115	ENST00000446702;ENST00000539053;ENST00000350110	T;T;T	0.72282	-0.64;-0.64;-0.64	5.71	0.115	0.14643	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.491996	0.18537	N	0.138338	T	0.81128	0.4758	M	0.92604	3.325	0.09310	N	1	P	0.48350	0.909	P	0.57371	0.819	T	0.70901	-0.4746	10	0.72032	D	0.01	.	4.4769	0.11748	0.0:0.2343:0.1888:0.5769	.	441	Q9UQ52	CNTN6_HUMAN	M	441;369;441	ENSP00000407822:I441M;ENSP00000442791:I369M;ENSP00000341882:I441M	ENSP00000341882:I441M	I	+	3	3	CNTN6	1346578	0.000000	0.05858	0.482000	0.27366	0.987000	0.75469	-0.078000	0.11375	0.093000	0.17368	0.563000	0.77884	ATC	.	.	.	none		0.333	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461		G	1371578	C	G	1371578	3	3	141	1	0	0	0	0	1	0	0	0	3647	903	32	4	1361	4	CNTN6	3	1371578	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08		1371578	196650852	11	8517											
OGG1	8536	hgsc.bcm.edu	37	chr3	9800959	9800960	+	Intron	INS	-	-	T																															gaattacagacttcttcctcINStagacttggaggtgagggac																										TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr3:9800959_9800960insT	ENST00000256460.3	-	10	1090				OGG1_ENST00000302008.8_Frame_Shift_Ins_p.R347fs|OGG1_ENST00000349503.5_Intron|OGG1_ENST00000449570.2_3'UTR|OGG1_ENST00000383826.5_Intron|OGG1_ENST00000302036.7_Intron	NM_003656.4	NP_003647.1	Q14012	KCC1A_HUMAN	calcium/calmodulin-dependent protein kinase I						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)		ACTTCTTCCTCTAGACTTGGAG	0.46																																					p.S346fs		Atlas-INDEL	.											.	OGG1	57	.	0			c.1037_1038insT						PASS	.																																			SO:0001627	intron_variant	4968	exon7			.	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.912+211->A	chr3.hg19:g.9800960_9800960dupT		172.0	0.0	0		157.0	32.0	0.203822	NM_016828	Q3KPF6	Frame_Shift_Ins	INS	ENST00000256460.3	hg19	CCDS2582.1																																																																																			.	.	.	none		0.46	CAMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250206.1	NM_003656		T	9800960	-	T	9800959	6	5	141	0	1	1	1	0	0	0	0	0	10852	913	32	0		0	OGG1	3	9800959	Intron	INS	-	TCGA-BQ-7059-01A-11D-1961-08	8429381	9800959	188221471	12	8518											
CHDH	55349	hgsc.bcm.edu	37	chr3	53857341	53857341	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagaccactaccttcatggAtggtcatgtccatccagccg	9	9	10	13	1	2	1	2	0	0	1	4	3	4	2	5	3	2	0	5	3	1	2			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr3:53857341A>G	ENST00000315251.6	-	3	1132	c.695T>C	c.(694-696)aTc>aCc	p.I232T		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	232					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)	ACCTTCATGGATGGTCATGTC	0.612																																					p.I232T		Atlas-SNP	.											.	CHDH	34	.	0			c.T695C						PASS	.						46	48	47					3																	53857341		2203	4300	6503	SO:0001583	missense	55349	exon3			TCATGGATGGTCA	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.695T>C	chr3.hg19:g.53857341A>G	ENSP00000319851:p.Ile232Thr	18.0	0.0	.		17.0	5.0	.	NM_018397	Q9NY17	Missense_Mutation	SNP	ENST00000315251.6	hg19	CCDS2873.1	.	.	.	.	.	.	.	.	.	.	A	15.66	2.898970	0.52227	.	.	ENSG00000016391	ENST00000315251	T	0.39592	1.07	5.72	5.72	0.89469	Glucose-methanol-choline oxidoreductase, N-terminal (1);	0.161948	0.52532	D	0.000066	T	0.56046	0.1959	L	0.55103	1.725	0.53688	D	0.999973	D	0.63046	0.992	D	0.66084	0.941	T	0.57106	-0.7868	10	0.52906	T	0.07	-30.1407	11.1366	0.48378	0.8624:0.0:0.0:0.1376	.	232	Q8NE62	CHDH_HUMAN	T	232	ENSP00000319851:I232T	ENSP00000319851:I232T	I	-	2	0	CHDH	53832381	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.882000	0.92420	2.182000	0.69389	0.455000	0.32223	ATC	.	.	.	none		0.612	CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397		G	53857341	A	G	53857341	3	3	141	1	0	0	0	0	1	0	0	0	3335	333	12	3	1117	3	CHDH	3	53857341	Missense_Mutation	SNP	A	TCGA-BQ-7059-01A-11D-1961-08	44056382	53857341	144165089	13	8519											
PDS5A	23244	hgsc.bcm.edu	37	chr4	39978137	39978137	+	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	cggagggtaagcgatcttccCgtcggcactcacgacgccac	8	6	12	15	6	2	0	1	0	1	0	4	3	3	1	2	3	1	2	2	3	1	2			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr4:39978137C>A	ENST00000303538.8	-	2	600	c.61G>T	c.(61-63)Ggg>Tgg	p.G21W	PDS5A_ENST00000503396.1_Missense_Mutation_p.G21W	NM_001100399.1	NP_001093869.1			PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)											breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						GCGATCTTCCCGTCGGCACTC	0.572											OREG0016159	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G21W		Atlas-SNP	.											PDS5A_ENST00000503396,NS,carcinoma,0,2	PDS5A	114	.	0			c.G61T						PASS	.						108	119	116					4																	39978137		1980	4154	6134	SO:0001583	missense	23244	exon2			TCTTCCCGTCGGC	AF294791	CCDS47045.1, CCDS54759.1	4p14	2007-06-20			ENSG00000121892	ENSG00000121892			29088	protein-coding gene	gene with protein product		613200				11076961, 15855230	Standard	NM_001100399		Approved	KIAA0648, PIG54, SCC-112	uc003guv.4	Q29RF7	OTTHUMG00000160582	ENST00000303538.8:c.61G>T	chr4.hg19:g.39978137C>A	ENSP00000303427:p.Gly21Trp	161.0	1.0	.	890	140.0	8.0	.	NM_001100399		Missense_Mutation	SNP	ENST00000303538.8	hg19	CCDS47045.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.561627	0.86335	.	.	ENSG00000121892	ENST00000303538;ENST00000503396	.	.	.	4.0	4.0	0.46444	.	0.249770	0.26453	U	0.024297	T	0.74935	0.3782	M	0.62723	1.935	0.80722	D	1	D;D	0.76494	0.996;0.999	D;D	0.79784	0.98;0.993	T	0.75519	-0.3289	8	.	.	.	-4.2139	14.4859	0.67616	0.0:1.0:0.0:0.0	.	21;21	Q29RF7-3;Q29RF7	.;PDS5A_HUMAN	W	21	.	.	G	-	1	0	PDS5A	39654532	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.320000	0.79064	2.077000	0.62373	0.591000	0.81541	GGG	.	.	.	none		0.572	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200		A	39978137	C	A	39978137	3	1	141	1	0	0	0	0	1	0	0	0	11698	652	23	4	4113	4	PDS5A	4	39978137	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08		39978137	151176139	14	8520											
SLC30A9	10463	hgsc.bcm.edu	37	chr4	42072612	42072612	+	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	aggcatggtctcagcattccTcatctacactaacacagaag	13	9	7	12	0	3	1	2	0	2	1	5	1	4	1	1	2	3	2	1	2	3	3			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr4:42072612T>A	ENST00000264451.7	+	15	1502	c.1322T>A	c.(1321-1323)cTc>cAc	p.L441H		NM_006345.3	NP_006336.3	Q6PML9	ZNT9_HUMAN	solute carrier family 30 (zinc transporter), member 9	441					nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|zinc ion transport (GO:0006829)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cation transmembrane transporter activity (GO:0008324)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TCAGCATTCCTCATCTACACT	0.458																																					p.L441H		Atlas-SNP	.											.	SLC30A9	58	.	0			c.T1322A						PASS	.						211	177	188					4																	42072612		2203	4300	6503	SO:0001583	missense	10463	exon15			CATTCCTCATCTA	AF006621	CCDS3465.1	4p13	2013-05-22	2003-09-09	2003-09-10	ENSG00000014824	ENSG00000014824		"Solute carriers"	1329	protein-coding gene	gene with protein product	"GRIP1-dependent nuclear receptor coactivator"	604604	"chromosome 4 open reading frame 1"	C4orf1		10409434, 11906820	Standard	NM_006345		Approved	HUEL, ZNT9, GAC63	uc003gwl.3	Q6PML9	OTTHUMG00000099387	ENST00000264451.7:c.1322T>A	chr4.hg19:g.42072612T>A	ENSP00000264451:p.Leu441His	110.0	0.0	.		133.0	43.0	.	NM_006345	Q4W5B6|Q7Z5I7|Q8TBB2|Q9Y6R2	Missense_Mutation	SNP	ENST00000264451.7	hg19	CCDS3465.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.512256	0.85389	.	.	ENSG00000014824	ENST00000264451;ENST00000536881	T	0.71817	-0.6	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	D	0.87188	0.6115	M	0.91459	3.21	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.90228	0.4277	10	0.87932	D	0	-6.7973	15.4439	0.75213	0.0:0.0:0.0:1.0	.	441	Q6PML9	ZNT9_HUMAN	H	441;269	ENSP00000264451:L441H	ENSP00000264451:L441H	L	+	2	0	SLC30A9	41767369	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	7.951000	0.87819	2.099000	0.63709	0.533000	0.62120	CTC	.	.	.	none		0.458	SLC30A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216842.3			A	42072612	T	A	42072612	3	1	141	1	0	0	0	0	1	0	0	0	14575	1551	54	5	1380	5	SLC30A9	4	42072612	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	2094475	42072612	149081664	15	8521											
WDFY3	23001	hgsc.bcm.edu	37	chr4	85781624	85781624	+	Missense_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	ttgttccttctgagtcatgtGccggggaggatggcacaact	7	12	13	9	1	2	1	1	1	1	0	3	3	3	3	2	4	2	2	2	4	1	3			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr4:85781624G>A	ENST00000295888.4	-	4	528	c.121C>T	c.(121-123)Cac>Tac	p.H41Y	WDFY3_ENST00000322366.6_Missense_Mutation_p.H41Y	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	41					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)		TGAGTCATGTGCCGGGGAGGA	0.577																																					p.H41Y		Atlas-SNP	.											.	WDFY3	314	.	0			c.C121T						PASS	.						140	129	133					4																	85781624		2203	4300	6503	SO:0001583	missense	23001	exon4			TCATGTGCCGGGG	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.121C>T	chr4.hg19:g.85781624G>A	ENSP00000295888:p.His41Tyr	128.0	0.0	.		156.0	30.0	.	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	hg19	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.238404	0.79800	.	.	ENSG00000163625	ENST00000322366;ENST00000295888;ENST00000509172	T;T	0.63744	-0.06;-0.06	5.72	5.72	0.89469	.	0.045076	0.85682	D	0.000000	T	0.43255	0.1239	N	0.08118	0	0.80722	D	1	D;D	0.52996	0.957;0.957	B;B	0.43575	0.402;0.424	T	0.48364	-0.9042	10	0.02654	T	1	.	19.8968	0.96969	0.0:0.0:1.0:0.0	.	41;41	E2QRK8;Q8IZQ1	.;WDFY3_HUMAN	Y	41	ENSP00000318466:H41Y;ENSP00000295888:H41Y	ENSP00000295888:H41Y	H	-	1	0	WDFY3	86000648	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	9.580000	0.98207	2.691000	0.91804	0.655000	0.94253	CAC	.	.	.	none		0.577	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		A	85781624	G	A	85781624	3	1	141	1	0	0	0	0	1	0	0	0	17282	1319	46	2	10762	2	WDFY3	4	85781624	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	43709012	85781624	105372652	16	8522											
NR3C2	4306	hgsc.bcm.edu	37	chr4	149357285	149357285	+	Frame_Shift_Del	DEL	T	T	-																															tgtgcgacctggagcctcgaTtttcaacattaggggagcat																										TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr4:149357285delT	ENST00000358102.3	-	2	1090	c.728delA	c.(727-729)aatfs	p.N243fs	NR3C2_ENST00000355292.3_Frame_Shift_Del_p.N243fs|NR3C2_ENST00000512865.1_Frame_Shift_Del_p.N243fs|NR3C2_ENST00000344721.4_Frame_Shift_Del_p.N243fs|NR3C2_ENST00000511528.1_Frame_Shift_Del_p.N243fs	NM_000901.4|NM_001166104.1	NP_000892.2|NP_001159576.1	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	243	Modulating.				gene expression (GO:0010467)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|receptor complex (GO:0043235)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Drospirenone(DB01395)|Eplerenone(DB00700)|Felodipine(DB01023)|Fludrocortisone(DB00687)|Fluticasone Propionate(DB00588)|Nimodipine(DB00393)|Progesterone(DB00396)|Spironolactone(DB00421)	GGAGCCTCGATTTTCAACATT	0.527																																					p.N243fs	Melanoma(27;428 957 40335 51025 51111)	Atlas-INDEL	.											.	NR3C2	94	.	0			c.729delT						PASS	.						74	76	75					4																	149357285		2203	4300	6503	SO:0001589	frameshift_variant	4306	exon2			.	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.728delA	chr4.hg19:g.149357285delT	ENSP00000350815:p.Asn243fs	147.0	0.0	0		149.0	46.0	0.308725	NM_001166104	B0ZBF5|B0ZBF7|Q2NKL1|Q96KQ8|Q96KQ9	Frame_Shift_Del	DEL	ENST00000358102.3	hg19	CCDS3772.1																																																																																			.	.	.	none		0.527	NR3C2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364986.1			-	149357285	T	-	149357285	7	5	141	1	0	1	0	1	0	0	0	0	10638	1493	52	0	2258	0	NR3C2	4	149357285	Frame_Shift_Del	DEL	T	TCGA-BQ-7059-01A-11D-1961-08	63575661	149357285	41796991	17	8523											
RAD50	10111	hgsc.bcm.edu	37	chr5	131976367	131976367	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taggggcttttttccaggtaTtagcctcactcatcattcgc	7	15	8	11	1	3	0	3	0	0	0	5	0	4	0	2	3	1	2	2	3	3	7			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr5:131976367T>C	ENST00000265335.6	+	24	4009	c.3622T>C	c.(3622-3624)Tta>Cta	p.L1208L	AC004041.2_ENST00000457489.1_RNA|AC004041.2_ENST00000435042.1_RNA|AC004041.2_ENST00000458509.1_RNA|AC004041.2_ENST00000417516.1_RNA|RAD50_ENST00000378823.3_Silent_p.L1069L			Q92878	RAD50_HUMAN	RAD50 homolog (S. cerevisiae)	1208	Ala/Asp-rich (DA-box).				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)			TTTCCAGGTATTAGCCTCACT	0.498								Homologous recombination																													p.L1208L		Atlas-SNP	.											.	RAD50	246	.	0			c.T3622C						PASS	.						168	156	160					5																	131976367		2203	4300	6503	SO:0001819	synonymous_variant	10111	exon24			CAGGTATTAGCCT	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.3622T>C	chr5.hg19:g.131976367T>C		186.0	0.0	.		177.0	36.0	.	NM_005732	B9EGF5|O43254|Q6GMT7|Q6P5X3|Q9UP86	Silent	SNP	ENST00000265335.6	hg19	CCDS34233.1	.	.	.	.	.	.	.	.	.	.	T	12.52	1.963735	0.34659	.	.	ENSG00000113522	ENST00000455677	.	.	.	5.94	1.0	0.19881	.	.	.	.	.	T	0.55226	0.1907	.	.	.	0.58432	D	0.999996	.	.	.	.	.	.	T	0.46275	-0.9203	4	.	.	.	-7.5964	8.3809	0.32470	0.0:0.5216:0.0:0.4784	.	.	.	.	T	86	.	.	I	+	2	0	RAD50	132004266	0.068000	0.21057	0.032000	0.17829	0.920000	0.55202	0.417000	0.21214	0.177000	0.19895	0.528000	0.53228	ATT	.	.	.	none		0.498	RAD50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132566.5	NM_005732		C	131976367	T	C	131976367	2	2	141	1	0	0	0	0	0	0	0	1	12997	1490	52	3		3	RAD50	5	131976367	Silent	SNP	T	TCGA-BQ-7059-01A-11D-1961-08		131976367	48938893	18	8524											
MAML1	9794	hgsc.bcm.edu	37	chr5	179193559	179193560	+	Frame_Shift_Ins	INS	-	-	C																															tggactacggcaatacaaaaINScccctttctcattacaaagc																										TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr5:179193559_179193560insC	ENST00000292599.3	+	2	1811_1812	c.1548_1549insC	c.(1549-1551)cccfs	p.P517fs	MAML1_ENST00000503050.1_3'UTR	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)											central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCAATACAAAACCCCTTTCTCA	0.559																																					p.K516fs		Atlas-INDEL	.											.	MAML1	118	.	0			c.1548_1549insC						PASS	.																																			SO:0001589	frameshift_variant	9794	exon2			.	D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"mastermind homolog"	605424	"mastermind (drosophila)-like 1"			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.1552dupC	chr5.hg19:g.179193563_179193563dupC	ENSP00000292599:p.Pro517fs	103.0	0.0	0		80.0	19.0	0.2375	NM_014757		Frame_Shift_Ins	INS	ENST00000292599.3	hg19	CCDS34315.1																																																																																			.	.	.	none		0.559	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757		C	179193560	-	C	179193559	7	5	141	1	0	1	1	0	0	0	0	0	9212	40	2	0	1554	0	MAML1	5	179193559	Frame_Shift_Ins	INS	-	TCGA-BQ-7059-01A-11D-1961-08	47217192	179193559	1721701	19	8525											
TBC1D9B	23061	hgsc.bcm.edu	37	chr5	179318454	179318455	+	Frame_Shift_Ins	INS	-	-	A																															tgtagttgttggagatgaacINSatctggccagggatgtgcag																										TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr5:179318454_179318455insA	ENST00000356834.3	-	6	1005_1006	c.968_969insT	c.(967-969)atgfs	p.M323fs	TBC1D9B_ENST00000355235.3_Frame_Shift_Ins_p.M323fs	NM_198868.2	NP_942568.2	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	323	GRAM 2.					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)			TGGAGATGAACATCTGGCCAGG	0.599																																					p.M323fs		Atlas-INDEL	.											.	TBC1D9B	157	.	0			c.969_970insT						PASS	.																																			SO:0001589	frameshift_variant	23061	exon6			.	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.969dupT	chr5.hg19:g.179318455_179318455dupA	ENSP00000349291:p.Met323fs	184.0	0.0	0		176.0	41.0	0.232955	NM_198868	D3DWQ5|D3DWQ6|O75163|Q53EY0|Q6MZI2|Q96H49	Frame_Shift_Ins	INS	ENST00000356834.3	hg19	CCDS43408.1																																																																																			.	.	.	none		0.599	TBC1D9B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253501.3	NM_015043		A	179318455	-	A	179318454	7	5	141	1	0	1	1	0	0	0	0	0	15640	478	17	0	2851	0	TBC1D9B	5	179318454	Frame_Shift_Ins	INS	-	TCGA-BQ-7059-01A-11D-1961-08	124895	179318454	1596806	20	8526											
TRIM38	10475	hgsc.bcm.edu	37	chr6	25967011	25967011	+	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	attgaagccctcaaagagacGgatcaagaaatgtcatgtga	16	8	10	7	1	3	4	3	2	0	2	3	6	3	5	1	1	1	0	1	1	4	1			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr6:25967011G>C	ENST00000357085.3	+	3	737	c.261G>C	c.(259-261)acG>acC	p.T87T	TRIM38_ENST00000349458.3_Silent_p.T87T	NM_006355.3	NP_006346.1	O00635	TRI38_HUMAN	tripartite motif containing 38	87					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)	p.T87T(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	23						TCAAAGAGACGGATCAAGAAA	0.562																																					p.T87T		Atlas-SNP	.											TRIM38,NS,carcinoma,0,1	TRIM38	50	.	1	Substitution - coding silent(1)	lung(1)	c.G261C						PASS	.						61	58	59					6																	25967011		2203	4300	6503	SO:0001819	synonymous_variant	10475	exon3			AGAGACGGATCAA	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.261G>C	chr6.hg19:g.25967011G>C		54.0	0.0	.		54.0	17.0	.	NM_006355	B2R862	Silent	SNP	ENST00000357085.3	hg19	CCDS4568.1																																																																																			.	.	.	none		0.562	TRIM38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040076.2			C	25967011	G	C	25967011	2	2	141	1	0	0	0	0	0	0	0	1	16524	1103	39	4		4	TRIM38	6	25967011	Silent	SNP	G	TCGA-BQ-7059-01A-11D-1961-08		25967011	145148056	21	8527											
ITPR3	3710	hgsc.bcm.edu	37	chr6	33644599	33644599	+	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	actacaaggtgatcaagtcgGagctggaccggctgcggacc	10	6	14	11	3	1	1	1	1	0	0	2	4	1	4	2	5	3	2	2	5	3	1			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr6:33644599G>A	ENST00000374316.5	+	27	4397	c.3337G>A	c.(3337-3339)Gag>Aag	p.E1113K	ITPR3_ENST00000605930.1_Missense_Mutation_p.E1113K			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	1113					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)	GATCAAGTCGGAGCTGGACCG	0.622																																					p.E1113K		Atlas-SNP	.											.	ITPR3	409	.	0			c.G3337A						PASS	.						93	80	85					6																	33644599		2203	4300	6503	SO:0001583	missense	3710	exon26			AAGTCGGAGCTGG	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.3337G>A	chr6.hg19:g.33644599G>A	ENSP00000363435:p.Glu1113Lys	94.0	0.0	.		67.0	19.0	.	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	hg19	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.587672	0.86851	.	.	ENSG00000096433	ENST00000374316	D	0.91237	-2.81	5.22	5.22	0.72569	.	0.111019	0.64402	D	0.000010	D	0.85822	0.5786	L	0.44542	1.39	0.58432	D	0.999993	P	0.45594	0.862	B	0.41917	0.37	D	0.88575	0.3132	10	0.87932	D	0	-36.8399	18.8137	0.92070	0.0:0.0:1.0:0.0	.	1113	Q14573	ITPR3_HUMAN	K	1113	ENSP00000363435:E1113K	ENSP00000363435:E1113K	E	+	1	0	ITPR3	33752577	1.000000	0.71417	0.943000	0.38184	0.927000	0.56198	8.010000	0.88615	2.435000	0.82474	0.655000	0.94253	GAG	.	.	.	none		0.622	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224		A	33644599	G	A	33644599	3	1	141	1	0	0	0	0	1	0	0	0	7929	1175	41	2	3439	2	ITPR3	6	33644599	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	7677588	33644599	137470468	22	8528											
DOPEY1	23033	hgsc.bcm.edu	37	chr6	83839062	83839062	+	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	caaaatgggacagaaattcaCaaggagatgtaaaagagaaa	22	5	10	4	0	1	3	1	0	0	3	1	6	1	4	0	2	0	1	0	2	7	2			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr6:83839062C>A	ENST00000349129.2	+	16	2436	c.2176C>A	c.(2176-2178)Caa>Aaa	p.Q726K	DOPEY1_ENST00000237163.5_Missense_Mutation_p.Q707K|DOPEY1_ENST00000369739.3_Missense_Mutation_p.Q717K	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	726					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)		CAGAAATTCACAAGGAGATGT	0.398																																					p.Q726K		Atlas-SNP	.											.	DOPEY1	190	.	0			c.C2176A						PASS	.						78	77	78					6																	83839062		2203	4300	6503	SO:0001583	missense	23033	exon16			AATTCACAAGGAG	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.2176C>A	chr6.hg19:g.83839062C>A	ENSP00000195654:p.Gln726Lys	56.0	0.0	.		85.0	16.0	.	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	hg19	CCDS4996.1	.	.	.	.	.	.	.	.	.	.	C	13.15	2.151734	0.38021	.	.	ENSG00000083097	ENST00000349129;ENST00000237163;ENST00000369739	T;T	0.21734	1.99;1.99	5.68	5.68	0.88126	.	0.594531	0.18093	N	0.151930	T	0.15392	0.0371	L	0.57536	1.79	0.80722	D	1	B;B;B	0.15473	0.004;0.013;0.004	B;B;B	0.13407	0.006;0.009;0.006	T	0.02610	-1.1134	10	0.32370	T	0.25	.	19.7974	0.96491	0.0:1.0:0.0:0.0	.	617;717;726	E1P545;B2RWN9;Q5JWR5	.;.;DOP1_HUMAN	K	726;707;707	ENSP00000195654:Q726K;ENSP00000237163:Q707K	ENSP00000237163:Q707K	Q	+	1	0	DOPEY1	83895781	0.879000	0.30193	0.997000	0.53966	0.964000	0.63967	3.092000	0.50207	2.673000	0.90976	0.650000	0.86243	CAA	.	.	.	none		0.398	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018		A	83839062	C	A	83839062	3	1	141	1	0	0	0	0	1	0	0	0	4709	479	17	4	2230	4	DOPEY1	6	83839062	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	50194463	83839062	87276005	23	8529											
FAM120B	84498	hgsc.bcm.edu	37	chr6	170700175	170700175	+	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	atgaaggagaacagacgcatCactggccgagcccactgggg	12	4	14	11	2	1	3	1	1	0	2	1	5	1	3	2	4	2	1	2	4	2	0			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr6:170700175C>G	ENST00000476287.1	+	8	2673	c.2565C>G	c.(2563-2565)atC>atG	p.I855M	FAM120B_ENST00000252510.9_Missense_Mutation_p.I187M|FAM120B_ENST00000540480.1_Missense_Mutation_p.I867M|FAM120B_ENST00000537664.1_Missense_Mutation_p.I878M	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	855					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)		ACAGACGCATCACTGGCCGAG	0.562																																					p.I855M		Atlas-SNP	.											.	FAM120B	108	.	0			c.C2565G						PASS	.						72	62	65					6																	170700175		2203	4300	6503	SO:0001583	missense	84498	exon8			ACGCATCACTGGC	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.2565C>G	chr6.hg19:g.170700175C>G	ENSP00000417970:p.Ile855Met	60.0	0.0	.		58.0	4.0	.	NM_032448	B4DL34|Q86V68|Q96JI9	Missense_Mutation	SNP	ENST00000476287.1	hg19	CCDS5314.1	.	.	.	.	.	.	.	.	.	.	C	10.97	1.500782	0.26861	.	.	ENSG00000112584	ENST00000540480;ENST00000537664;ENST00000476287;ENST00000252510	T;T;T	0.09723	2.96;2.95;2.97	5.5	-3.03	0.05429	.	0.167917	0.40469	N	0.001099	T	0.06371	0.0164	L	0.27053	0.805	0.09310	N	1	D;D	0.76494	0.999;0.999	D;D	0.71656	0.967;0.974	T	0.22382	-1.0218	10	0.56958	D	0.05	-19.2842	7.8011	0.29174	0.1064:0.3727:0.0:0.5209	.	855;855	Q96EK7;F2Z2E1	F120B_HUMAN;.	M	867;878;855;187	ENSP00000444125:I867M;ENSP00000440125:I878M;ENSP00000417970:I855M	ENSP00000252510:I187M	I	+	3	3	FAM120B	170542100	0.002000	0.14202	0.000000	0.03702	0.051000	0.14879	-0.226000	0.09139	-0.631000	0.05560	0.655000	0.94253	ATC	.	.	.	none		0.562	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448		G	170700175	C	G	170700175	3	3	141	1	0	0	0	0	1	0	0	0	5421	816	29	4	2591	4	FAM120B	6	170700175	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	86861113	170700175	414892	24	8530											
KLHL7	55975	hgsc.bcm.edu	37	chr7	23163475	23163476	+	Frame_Shift_Ins	INS	-	-	T																															gttcttgctgcagccagtcaINStttttttaacttaatgttca																										TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr7:23163475_23163476insT	ENST00000339077.5	+	2	443_444	c.200_201insT	c.(199-204)cattttfs	p.HF67fs	KLHL7_ENST00000545771.1_Frame_Shift_Ins_p.HF45fs|KLHL7_ENST00000322231.7_Frame_Shift_Ins_p.HF45fs|KLHL7_ENST00000539124.1_Intron|KLHL7_ENST00000545443.1_Frame_Shift_Ins_p.HF45fs|KLHL7_ENST00000409689.1_Frame_Shift_Ins_p.HF19fs|KLHL7_ENST00000542558.1_Intron|KLHL7_ENST00000322275.5_Frame_Shift_Ins_p.HF67fs|KLHL7_ENST00000410047.1_Frame_Shift_Ins_p.HF45fs|KLHL7_ENST00000479288.1_Intron	NM_001031710.2	NP_001026880.2	Q8IXQ5	KLHL7_HUMAN	kelch-like family member 7	67	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GCAGCCAGTCATTTTTTTAACT	0.332																																					p.H67fs		Atlas-INDEL	.											.	KLHL7	102	.	0			c.200_201insT						PASS	.																																			SO:0001589	frameshift_variant	55975	exon2			.		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.207dupT	chr7.hg19:g.23163482_23163482dupT	ENSP00000343273:p.His67fs	49.0	0.0	0		94.0	30.0	0.319149	NM_001031710	A4D144|B7Z5I9|G5E9G3|Q7Z765|Q96MV2|Q9BQF8|Q9UDQ9	Frame_Shift_Ins	INS	ENST00000339077.5	hg19	CCDS34609.1																																																																																			.	.	.	none		0.332	KLHL7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326860.3	NM_018846		T	23163476	-	T	23163475	7	5	141	1	0	1	1	0	0	0	0	0	8401	217	8	0	206	0	KLHL7	7	23163475	Frame_Shift_Ins	INS	-	TCGA-BQ-7059-01A-11D-1961-08		23163475	135975188	25	8531											
OGDH	4967	hgsc.bcm.edu	37	chr7	44685022	44685022	+	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	gccgaggctccctggctgctGtggcccatgcacagtccctg	4	8	13	16	1	0	0	0	0	0	0	2	1	2	0	4	3	2	4	4	3	0	0			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr7:44685022G>T	ENST00000222673.5	+	3	361	c.319G>T	c.(319-321)Gtg>Ttg	p.V107L	OGDH_ENST00000543843.1_Missense_Mutation_p.V47L|OGDH_ENST00000447398.1_Missense_Mutation_p.V107L|OGDH_ENST00000444676.1_Missense_Mutation_p.V107L|OGDH_ENST00000449767.1_Missense_Mutation_p.V107L|OGDH_ENST00000443864.2_Missense_Mutation_p.V107L|OGDH_ENST00000439616.2_Intron	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	107					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)	CCTGGCTGCTGTGGCCCATGC	0.597																																					p.V107L		Atlas-SNP	.											.	OGDH	145	.	0			c.G319T						PASS	.						85	83	83					7																	44685022		2203	4300	6503	SO:0001583	missense	4967	exon3			GCTGCTGTGGCCC	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.319G>T	chr7.hg19:g.44685022G>T	ENSP00000222673:p.Val107Leu	159.0	0.0	.		169.0	35.0	.	NM_001165036	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Missense_Mutation	SNP	ENST00000222673.5	hg19	CCDS34627.1	.	.	.	.	.	.	.	.	.	.	G	11.90	1.775197	0.31411	.	.	ENSG00000105953	ENST00000443864;ENST00000449767;ENST00000447398;ENST00000419661;ENST00000444676;ENST00000222673;ENST00000543843	T;T;T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94;0.94;0.94	5.81	-4.96	0.03038	.	1.033080	0.07585	N	0.921017	T	0.10680	0.0261	N	0.02181	-0.65	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.0;0.0;0.001	T	0.27054	-1.0085	10	0.05620	T	0.96	-2.8184	1.8649	0.03196	0.4868:0.1815:0.1602:0.1715	.	107;107;107;107	E9PBM1;E9PDF2;Q02218;Q96DD3	.;.;ODO1_HUMAN;.	L	107;107;107;107;107;107;47	ENSP00000388084:V107L;ENSP00000392878:V107L;ENSP00000388183:V107L;ENSP00000411830:V107L;ENSP00000414662:V107L;ENSP00000222673:V107L;ENSP00000443821:V47L	ENSP00000222673:V107L	V	+	1	0	OGDH	44651547	0.003000	0.15002	0.000000	0.03702	0.974000	0.67602	0.473000	0.22132	-0.618000	0.05656	0.655000	0.94253	GTG	.	.	.	none		0.597	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1			T	44685022	G	T	44685022	3	4	141	1	0	0	0	0	1	0	0	0	10846	1377	48	4	325	4	OGDH	7	44685022	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	21521547	44685022	114453641	26	8532											
MET	4233	hgsc.bcm.edu	37	chr7	116423407	116423407	+	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	ctgattttggtcttgccagaGacatgtatgataaagaatac	13	13	9	6	0	1	4	0	2	1	2	1	5	1	4	1	1	2	1	1	1	5	6	rs121913671		TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr7:116423407G>C	ENST00000318493.6	+	19	3923	c.3736G>C	c.(3736-3738)Gac>Cac	p.D1246H	MET_ENST00000539704.1_Missense_Mutation_p.D98H|MET_ENST00000397752.3_Missense_Mutation_p.D1228H			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.D1246H(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)			TCTTGCCAGAGACATGTATGA	0.378			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.D1246H		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,colon,carcinoma,-2,1	MET	412	.	1	Substitution - Missense(1)	kidney(1)	c.G3736C	GRCh37	CM970946	MET	M	rs121913671	PASS	.						106	99	102					7																	116423407		1841	4093	5934	SO:0001583	missense	4233	exon19	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	GCCAGAGACATGT	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.3736G>C	chr7.hg19:g.116423407G>C	ENSP00000317272:p.Asp1246His	67.0	1.0	.		101.0	30.0	.	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.285616	0.80803	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000539704	D;D;D	0.83837	-1.77;-1.77;-1.77	5.46	5.46	0.80206	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.91327	0.7265	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	D	0.91745	0.5407	10	0.87932	D	0	.	19.6667	0.95895	0.0:0.0:1.0:0.0	.	1246;1228	P08581-2;P08581	.;MET_HUMAN	H	1228;1246;98	ENSP00000380860:D1228H;ENSP00000317272:D1246H;ENSP00000445020:D98H	ENSP00000317272:D1246H	D	+	1	0	MET	116210643	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.813000	0.99286	2.721000	0.93114	0.563000	0.77884	GAC	.	.	.	alt		0.378	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			C	116423407	G	C	116423407	3	2	141	1	0	0	0	0	1	0	0	0	9492	942	33	4	3806	4	MET	7	116423407	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	71738385	116423407	42715256	27	8533											
MCPH1	79648	hgsc.bcm.edu	37	chr8	6335132	6335133	+	Frame_Shift_Ins	INS	-	-	A																															agccaacaagaacattagtcINSatgacaagcatgccatctga																										TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr8:6335132_6335133insA	ENST00000344683.5	+	10	2029_2030	c.1953_1954insA	c.(1954-1956)atgfs	p.M652fs		NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	652	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.				cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)		AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		GAACATTAGTCATGACAAGCAT	0.317																																					p.V651fs	Colon(95;1448 1467 8277 34473 35819)	Atlas-INDEL	.											.	MCPH1	65	.	0			c.1953_1954insA						PASS	.																																			SO:0001589	frameshift_variant	79648	exon10			.	AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"BRCT-repeat inhibitor of TERT expression 1"	607117	"microcephaly, primary autosomal recessive 1"			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.1954dupA	chr8.hg19:g.6335133_6335133dupA	ENSP00000342924:p.Met652fs	159.0	0.0	0		281.0	77.0	0.274021	NM_024596	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Frame_Shift_Ins	INS	ENST00000344683.5	hg19	CCDS43689.1																																																																																			.	.	.	none		0.317	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596		A	6335133	-	A	6335132	7	5	141	1	0	1	1	0	0	0	0	0	9405	813	29	0	1999	0	MCPH1	8	6335132	Frame_Shift_Ins	INS	-	TCGA-BQ-7059-01A-11D-1961-08		6335132	140028890	28	8534											
ADAM32	203102	hgsc.bcm.edu	37	chr8	39044454	39044454	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggagataactctggaggcAtttgcagttattgtcaccca	12	11	10	8	0	2	1	1	0	1	1	2	3	2	2	1	3	2	3	1	3	3	4			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr8:39044454A>G	ENST00000379907.4	+	11	1069	c.942A>G	c.(940-942)gcA>gcG	p.A314A	ADAM32_ENST00000519315.1_Intron|ADAM32_ENST00000437682.2_Intron	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	314	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)			CTCTGGAGGCATTTGCAGTTA	0.358																																					p.A314A		Atlas-SNP	.											.	ADAM32	70	.	0			c.A942G						PASS	.						79	76	77					8																	39044454		1814	4076	5890	SO:0001819	synonymous_variant	203102	exon11			GGAGGCATTTGCA	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.942A>G	chr8.hg19:g.39044454A>G		83.0	0.0	.		139.0	34.0	.	NM_145004	Q8TC42	Silent	SNP	ENST00000379907.4	hg19	CCDS47846.1																																																																																			.	.	.	none		0.358	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004		G	39044454	A	G	39044454	2	3	141	1	0	0	0	0	0	0	0	1	249	204	8	3		3	ADAM32	8	39044454	Silent	SNP	A	TCGA-BQ-7059-01A-11D-1961-08	32709322	39044454	107319568	29	8535											
OSGIN2	734	hgsc.bcm.edu	37	chr8	90936955	90936955	+	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	caagagaaactgggaaattaGgggttatcagcgaatagctg	15	8	13	5	1	1	1	1	0	0	1	1	4	1	2	0	3	3	2	0	3	7	3			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr8:90936955G>C	ENST00000297438.2	+	6	1068	c.713G>C	c.(712-714)aGg>aCg	p.R238T	OSGIN2_ENST00000451899.2_Missense_Mutation_p.R282T	NM_004337.2	NP_004328.1	Q9Y236	OSGI2_HUMAN	oxidative stress induced growth inhibitor family member 2	238					meiotic nuclear division (GO:0007126)					breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|urinary_tract(1)	17			BRCA - Breast invasive adenocarcinoma(11;0.0344)			TGGGAAATTAGGGGTTATCAG	0.418																																					p.R282T		Atlas-SNP	.											.	OSGIN2	73	.	0			c.G845C						PASS	.						75	77	76					8																	90936955		2203	4300	6503	SO:0001583	missense	734	exon6			AAATTAGGGGTTA	AF061326	CCDS6248.1, CCDS47888.1	8q21	2006-10-05	2006-10-05	2006-10-05	ENSG00000164823	ENSG00000164823			1355	protein-coding gene	gene with protein product		604598	"chromosome 8 open reading frame 1"	C8orf1		9933573	Standard	NM_004337		Approved	hT41	uc003yeh.3	Q9Y236	OTTHUMG00000163811	ENST00000297438.2:c.713G>C	chr8.hg19:g.90936955G>C	ENSP00000297438:p.Arg238Thr	84.0	0.0	.		95.0	30.0	.	NM_001126111		Missense_Mutation	SNP	ENST00000297438.2	hg19	CCDS6248.1	.	.	.	.	.	.	.	.	.	.	G	10.74	1.436313	0.25813	.	.	ENSG00000164823	ENST00000297438;ENST00000451899	T;T	0.22539	1.95;1.95	5.25	5.25	0.73442	.	0.041552	0.85682	D	0.000000	T	0.16769	0.0403	L	0.43152	1.355	0.80722	D	1	B;B	0.31077	0.307;0.163	B;B	0.26416	0.069;0.068	T	0.05209	-1.0899	10	0.17832	T	0.49	-3.8246	12.2313	0.54490	0.0783:0.0:0.9217:0.0	.	282;238	Q9Y236-2;Q9Y236	.;OSGI2_HUMAN	T	238;282	ENSP00000297438:R238T;ENSP00000396445:R282T	ENSP00000297438:R238T	R	+	2	0	OSGIN2	91006130	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.061000	0.89467	2.461000	0.83175	0.555000	0.69702	AGG	.	.	.	none		0.418	OSGIN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375691.1	NM_004337		C	90936955	G	C	90936955	3	2	141	1	0	0	0	0	1	0	0	0	11297	1000	35	4	867	4	OSGIN2	8	90936955	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	51892501	90936955	55427067	30	8536											
GSN	2934	hgsc.bcm.edu	37	chr9	124089637	124089638	+	Frame_Shift_Ins	INS	-	-	C																															cgatgcctttgttctgaaaaINSccccctcagccgcctacctg																								rs376326631		TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr9:124089637_124089638insC	ENST00000373818.4	+	13	1861_1862	c.1792_1793insC	c.(1792-1794)accfs	p.T598fs	GSN_ENST00000394353.2_Frame_Shift_Ins_p.T558fs|GSN_ENST00000341272.2_Frame_Shift_Ins_p.T547fs|GSN_ENST00000436847.1_Frame_Shift_Ins_p.T558fs|GSN_ENST00000373823.3_Frame_Shift_Ins_p.T547fs|GSN_ENST00000545652.1_Frame_Shift_Ins_p.T555fs|GSN_ENST00000373807.1_Frame_Shift_Ins_p.T329fs|GSN_ENST00000449733.1_Frame_Shift_Ins_p.T547fs|GSN_ENST00000373806.1_Frame_Shift_Ins_p.T23fs|GSN_ENST00000412819.1_Frame_Shift_Ins_p.T547fs|GSN_ENST00000373808.2_Frame_Shift_Ins_p.T547fs	NM_000177.4|NM_001258029.1	NP_000168.1|NP_001244958.1	P06396	GELS_HUMAN	gelsolin	598	Actin-binding, Ca-sensitive. {ECO:0000255}.				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						TGTTCTGAAAACCCCCTCAGCC	0.594																																					p.T598fs		Atlas-INDEL	.											.	GSN	81	.	0			c.1792_1793insC						PASS	.																																			SO:0001589	frameshift_variant	2934	exon13			.	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.1797dupC	chr9.hg19:g.124089642_124089642dupC	ENSP00000362924:p.Thr598fs	83.0	0.0	0		85.0	16.0	0.188235	NM_000177	A2A418|A8MUD1|A8MYN7|B7Z373|B7Z5V1|F5H1A8|Q5T0I2|Q8WVV7	Frame_Shift_Ins	INS	ENST00000373818.4	hg19	CCDS6828.1																																																																																			.	.	.	none		0.594	GSN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053861.1	NM_000177		C	124089638	-	C	124089637	7	5	141	1	0	1	1	0	0	0	0	0	6832	43	2	0	1870	0	GSN	9	124089637	Frame_Shift_Ins	INS	-	TCGA-BQ-7059-01A-11D-1961-08		124089637	17123794	31	8537											
DNAJC1	64215	hgsc.bcm.edu	37	chr10	22171214	22171214	+	Frame_Shift_Del	DEL	T	T	-																															ttataaagcttatttacctgTtttttctgtgttcggttcct																										TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr10:22171214delT	ENST00000376980.3	-	8	1265	c.975delA	c.(973-975)aaafs	p.K325fs		NM_022365.3	NP_071760.2	Q96KC8	DNJC1_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 1	325	SANT 1. {ECO:0000255|PROSITE- ProRule:PRU00624}.				negative regulation of proteolysis (GO:0045861)|positive regulation of ATPase activity (GO:0032781)|protein folding (GO:0006457)|regulation of protein secretion (GO:0050708)|regulation of translation (GO:0006417)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(2)|lung(13)|skin(2)|upper_aerodigestive_tract(2)	21		Breast(68;0.00869)|Prostate(175;0.0181)|Lung SC(717;0.0262)				TATTTACCTGTTTTTTCTGTG	0.323																																					p.Q326fs		Atlas-INDEL	.											.	DNAJC1	42	.	0			c.976delC						PASS	.						142	132	135					10																	22171214		2202	4300	6502	SO:0001589	frameshift_variant	64215	exon8			.	AK026062	CCDS7136.1	10p11.23	2011-09-02			ENSG00000136770	ENSG00000136770		"Heat shock proteins / DNAJ (HSP40)"	20090	protein-coding gene	gene with protein product		611207					Standard	NM_022365		Approved	DNAJL1, ERdj1, MTJ1	uc001irc.3	Q96KC8	OTTHUMG00000017800	ENST00000376980.3:c.975delA	chr10.hg19:g.22171214delT	ENSP00000366179:p.Lys325fs	66.0	0.0	0		77.0	16.0	0.207792	NM_022365	B0YIZ8|Q5VX89|Q9H6B8	Frame_Shift_Del	DEL	ENST00000376980.3	hg19	CCDS7136.1																																																																																			.	.	.	none		0.323	DNAJC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047149.1	NM_022365		-	22171214	T	-	22171214	7	5	141	1	0	1	0	1	0	0	0	0	4630	1722	60	0	709	0	DNAJC1	10	22171214	Frame_Shift_Del	DEL	T	TCGA-BQ-7059-01A-11D-1961-08		22171214	113363533	32	8538											
PTCHD3	374308	hgsc.bcm.edu	37	chr10	27687672	27687673	+	In_Frame_Ins	INS	-	-	GTATAT																															tcctgcacatggaaacacccINSatatatactgcttatgatgt																										TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr10:27687672_27687673insGTATAT	ENST00000438700.3	-	4	1971_1972	c.1854_1855insATATAC	c.(1852-1857)tatggg>tatATATACggg	p.617_618insYI		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	617					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						TGGAAACACCCATATATACTGC	0.361																																					p.G619delinsIYG		Atlas-INDEL	.											.	PTCHD3	140	.	0			c.1855_1856insATATAC						PASS	.																																			SO:0001652	inframe_insertion	374308	exon4			.	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.1854_1855insATATAC	chr10.hg19:g.27687672_27687673insGTATAT	ENSP00000417658:p.Ile617_Tyr618insTyrIle	130.0	0.0	0		107.0	13.0	0.121495	NM_001034842	I3L499|Q6ZU28	In_Frame_Ins	INS	ENST00000438700.3	hg19	CCDS31173.1																																																																																			.	.	.	none		0.361	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541		GTATAT	27687673	-	GTATAT	27687672	7	5	141	1	0	1	1	0	0	0	0	0	12744	594	21	0	452	0	PTCHD3	10	27687672	In_Frame_Ins	INS	-	TCGA-BQ-7059-01A-11D-1961-08	5516458	27687672	107847075	33	8539											
TMEM133	83935	hgsc.bcm.edu	37	chr11	100863392	100863392	+	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	tcaaaatgtgccagttccacTtggtaataacgttgggaaaa	14	11	9	7	1	1	0	1	0	0	0	2	1	2	1	2	2	2	3	2	2	6	5			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr11:100863392T>A	ENST00000303130.2	+	1	582	c.353T>A	c.(352-354)cTt>cAt	p.L118H		NM_032021.2	NP_114410.1	Q9H2Q1	TM133_HUMAN	transmembrane protein 133	118						integral component of membrane (GO:0016021)				kidney(2)|large_intestine(1)|lung(1)|prostate(1)	5		Acute lymphoblastic leukemia(157;0.000869)|all_hematologic(158;0.014)		BRCA - Breast invasive adenocarcinoma(274;0.0675)		CCAGTTCCACTTGGTAATAAC	0.388																																					p.L118H		Atlas-SNP	.											.	TMEM133	9	.	0			c.T353A						PASS	.						142	137	138					11																	100863392		2203	4299	6502	SO:0001583	missense	83935	exon1			TTCCACTTGGTAA	AF247167	CCDS8309.1	11q22.1	2006-03-09				ENSG00000170647			24033	protein-coding gene	gene with protein product						12477932	Standard	NM_032021		Approved	AD031	uc001pgf.3	Q9H2Q1		ENST00000303130.2:c.353T>A	chr11.hg19:g.100863392T>A	ENSP00000303999:p.Leu118His	177.0	0.0	.		153.0	28.0	.	NM_032021		Missense_Mutation	SNP	ENST00000303130.2	hg19	CCDS8309.1	.	.	.	.	.	.	.	.	.	.	T	8.089	0.774082	0.16051	.	.	ENSG00000170647	ENST00000303130	.	.	.	2.67	-1.16	0.09678	.	.	.	.	.	T	0.22704	0.0548	N	0.08118	0	0.09310	N	1	D	0.65815	0.995	P	0.56398	0.797	T	0.14448	-1.0472	8	0.87932	D	0	.	4.3705	0.11246	0.1931:0.0:0.4529:0.3539	.	118	Q9H2Q1	TM133_HUMAN	H	118	.	ENSP00000303999:L118H	L	+	2	0	TMEM133	100368602	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.318000	0.08050	-0.257000	0.09459	-0.329000	0.08387	CTT	.	.	.	none		0.388	TMEM133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395137.1	NM_032021		A	100863392	T	A	100863392	3	1	141	1	0	0	0	0	1	0	0	0	16061	1609	56	5	355	5	TMEM133	11	100863392	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08		100863392	34143124	34	8540											
PHLDB1	23187	hgsc.bcm.edu	37	chr11	118516164	118516164	+	Frame_Shift_Del	DEL	A	A	-																															gtgccagtgggatgcccttcAcggggcagcacccttcccag																										TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr11:118516164delA	ENST00000361417.2	+	17	3623	c.3212delA	c.(3211-3213)cacfs	p.H1071fs	PHLDB1_ENST00000356063.5_Frame_Shift_Del_p.H1024fs|PHLDB1_ENST00000534672.1_3'UTR|PHLDB1_ENST00000524713.1_Frame_Shift_Del_p.H214fs|PHLDB1_ENST00000527898.1_Frame_Shift_Del_p.H122fs	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	1071										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)		GATGCCCTTCACGGGGCAGCA	0.652																																					p.H1071fs		Atlas-INDEL	.											.	PHLDB1	103	.	0			c.3211delC						PASS	.						42	51	48					11																	118516164		2200	4295	6495	SO:0001589	frameshift_variant	23187	exon16			.		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.3212delA	chr11.hg19:g.118516164delA	ENSP00000354498:p.His1071fs	143.0	0.0	0		92.0	27.0	0.293478	NM_001144758	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Frame_Shift_Del	DEL	ENST00000361417.2	hg19	CCDS8401.1																																																																																			.	.	.	none		0.652	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157		-	118516164	A	-	118516164	7	5	141	1	0	1	0	1	0	0	0	0	11858	159	6	0	3270	0	PHLDB1	11	118516164	Frame_Shift_Del	DEL	A	TCGA-BQ-7059-01A-11D-1961-08	17652772	118516164	16490352	35	8541	87	2									
PHLDB1	23187	hgsc.bcm.edu	37	chr11	118516166	118516166	+	Missense_Mutation	SNP	G	G	C																															gccagtgggatgcccttcacGgggcagcacccttcccagcg																										TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr11:118516166G>C	ENST00000361417.2	+	17	3625	c.3214G>C	c.(3214-3216)Ggg>Cgg	p.G1072R	PHLDB1_ENST00000356063.5_Missense_Mutation_p.G1025R|PHLDB1_ENST00000534672.1_3'UTR|PHLDB1_ENST00000524713.1_Missense_Mutation_p.G215R|PHLDB1_ENST00000527898.1_Missense_Mutation_p.G123R	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	1072										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)		TGCCCTTCACGGGGCAGCACC	0.657																																					p.G1072R		Atlas-SNP	.											.	PHLDB1	103	.	0			c.G3214C						PASS	.						43	52	49					11																	118516166		2200	4295	6495	SO:0001583	missense	23187	exon16			CTTCACGGGGCAG		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.3214G>C	chr11.hg19:g.118516166G>C	ENSP00000354498:p.Gly1072Arg	152.0	0.0	.		90.0	26.0	.	NM_001144758	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Missense_Mutation	SNP	ENST00000361417.2	hg19	CCDS8401.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.268966	0.80469	.	.	ENSG00000019144	ENST00000361417;ENST00000361465;ENST00000358191;ENST00000356063;ENST00000527898;ENST00000524713	T;T;T;T	0.50277	1.41;1.48;0.75;0.76	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.65883	0.2734	L	0.59436	1.845	0.58432	D	0.999997	D;D;D;D;D	0.89917	1.0;0.997;0.999;0.995;0.991	D;D;D;D;D	0.97110	1.0;0.966;0.989;0.976;0.922	T	0.57124	-0.7865	10	0.21014	T	0.42	-37.8382	19.9036	0.96999	0.0:0.0:1.0:0.0	.	215;436;831;1025;1072	B4DK17;B0YJ65;Q5W9G0;Q86UU1-2;Q86UU1	.;.;.;.;PHLB1_HUMAN	R	1072;846;436;1025;123;215	ENSP00000354498:G1072R;ENSP00000348359:G1025R;ENSP00000435388:G123R;ENSP00000434905:G215R	ENSP00000348359:G1025R	G	+	1	0	PHLDB1	118021376	1.000000	0.71417	0.821000	0.32701	0.728000	0.41692	5.896000	0.69822	2.706000	0.92434	0.655000	0.94253	GGG	.	.	.	none		0.657	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157		C	118516166	G	C	118516166	3	2	141	1	0	0	0	0	1	0	0	0	11858	1116	39	4	3272	4	PHLDB1	11	118516166	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	2	118516166	16490350	36	8542	87	2									
GRIK4	2900	hgsc.bcm.edu	37	chr11	120745883	120745883	+	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	cttaccggccacattgaattCaacagcaaaggccagaggtc	13	7	9	12	1	1	2	1	1	0	1	2	2	1	2	3	3	3	1	3	3	4	3			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr11:120745883C>T	ENST00000527524.2	+	11	1382	c.1095C>T	c.(1093-1095)ttC>ttT	p.F365F	GRIK4_ENST00000438375.2_Silent_p.F365F|RP11-640N11.2_ENST00000505153.2_RNA	NM_001282470.1	NP_001269399.1	Q16099	GRIK4_HUMAN	glutamate receptor, ionotropic, kainate 4	365					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)		ACATTGAATTCAACAGCAAAG	0.502																																					p.F365F		Atlas-SNP	.											.	GRIK4	149	.	0			c.C1095T						PASS	.						130	112	118					11																	120745883		2203	4299	6502	SO:0001819	synonymous_variant	2900	exon9			TGAATTCAACAGC	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.1095C>T	chr11.hg19:g.120745883C>T		111.0	0.0	.		136.0	24.0	.	NM_014619	A8K9L1	Silent	SNP	ENST00000527524.2	hg19	CCDS8433.1																																																																																			.	.	.	none		0.502	GRIK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109760.4	NM_014619		T	120745883	C	T	120745883	2	4	141	1	0	0	0	0	0	0	0	1	6783	825	29	2		2	GRIK4	11	120745883	Silent	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	2229717	120745883	14260633	37	8543											
CDON	50937	hgsc.bcm.edu	37	chr11	125880565	125880565	+	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	ttgcacttactggtgccgtaAttataactggcttgaatcca	10	14	8	9	1	0	1	0	1	0	0	1	1	1	1	2	2	4	3	2	2	5	6			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr11:125880565A>T	ENST00000392693.3	-	8	1350	c.1223T>A	c.(1222-1224)aTt>aAt	p.I408N	CDON_ENST00000263577.7_Missense_Mutation_p.I408N	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	408	Ig-like C2-type 5.				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)		TGGTGCCGTAATTATAACTGG	0.428																																					p.I408N		Atlas-SNP	.											.	CDON	137	.	0			c.T1223A						PASS	.						63	61	62					11																	125880565		2201	4299	6500	SO:0001583	missense	50937	exon8			GCCGTAATTATAA	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.1223T>A	chr11.hg19:g.125880565A>T	ENSP00000376458:p.Ile408Asn	87.0	0.0	.		75.0	18.0	.	NM_016952	O14631	Missense_Mutation	SNP	ENST00000392693.3	hg19	CCDS58192.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	7.259|7.259	0.604826|0.604826	0.14002|0.14002	.|.	.|.	ENSG00000064309|ENSG00000064309	ENST00000392693;ENST00000263577|ENST00000534661	T;T|.	0.29142|.	1.58;1.58|.	5.01|5.01	2.7|2.7	0.31948|0.31948	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.421653|.	0.19358|.	N|.	0.116221|.	T|T	0.38612|0.38612	0.1047|0.1047	L|L	0.43923|0.43923	1.385|1.385	0.09310|0.09310	N|N	0.999999|0.999999	P;P|.	0.36392|.	0.551;0.496|.	B;B|.	0.39738|.	0.308;0.205|.	T|T	0.21965|0.21965	-1.0230|-1.0230	10|5	0.66056|.	D|.	0.02|.	-2.7576|-2.7576	8.6995|8.6995	0.34316|0.34316	0.7929:0.0:0.2071:0.0|0.7929:0.0:0.2071:0.0	.|.	408;408|.	Q4KMG0;Q4KMG0-2|.	CDON_HUMAN;.|.	N|K	408|383	ENSP00000376458:I408N;ENSP00000263577:I408N|.	ENSP00000263577:I408N|.	I|N	-|-	2|3	0|2	CDON|CDON	125385775|125385775	0.210000|0.210000	0.23517|0.23517	0.307000|0.307000	0.25127|0.25127	0.339000|0.339000	0.28857|0.28857	1.941000|1.941000	0.40233|0.40233	0.272000|0.272000	0.22027|0.22027	0.482000|0.482000	0.46254|0.46254	ATT|AAT	.	.	.	none		0.428	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952		T	125880565	A	T	125880565	3	4	141	1	0	0	0	0	1	0	0	0	3172	101	4	5	2623	5	CDON	11	125880565	Missense_Mutation	SNP	A	TCGA-BQ-7059-01A-11D-1961-08	5134682	125880565	9125951	38	8544											
SLC2A14	144195	hgsc.bcm.edu	37	chr12	7982586	7982586	+	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	ggcagccaacaggttgacaaTcagcattgaattgcgcctgt	11	9	11	10	1	1	2	1	2	0	0	1	2	1	2	2	2	4	3	2	2	3	3			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr12:7982586T>A	ENST00000543909.1	-	10	1117	c.358A>T	c.(358-360)Att>Ttt	p.I120F	SLC2A14_ENST00000431042.2_Missense_Mutation_p.I97F|SLC2A14_ENST00000396589.2_Missense_Mutation_p.I120F|SLC2A14_ENST00000340749.5_Missense_Mutation_p.I97F|SLC2A14_ENST00000542505.1_Intron|SLC2A14_ENST00000542546.1_Missense_Mutation_p.I11F|SLC2A14_ENST00000539924.1_Missense_Mutation_p.I135F|SLC2A14_ENST00000535295.1_Missense_Mutation_p.I11F			Q8TDB8	GTR14_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 14	120					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)		AGGTTGACAATCAGCATTGAA	0.458																																					p.I120F		Atlas-SNP	.											.	SLC2A14	78	.	0			c.A358T						PASS	.						62	61	61					12																	7982586		2203	4300	6503	SO:0001583	missense	144195	exon6			TGACAATCAGCAT	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.358A>T	chr12.hg19:g.7982586T>A	ENSP00000440480:p.Ile120Phe	63.0	0.0	.		81.0	16.0	.	NM_153449	B3KVB5|B3KWW7|B7Z844|B7ZAC3|Q6UY84|Q8TDB9	Missense_Mutation	SNP	ENST00000543909.1	hg19	CCDS8585.1	.	.	.	.	.	.	.	.	.	.	t	10.42	1.346517	0.24426	.	.	ENSG00000173262	ENST00000340749;ENST00000543909;ENST00000431042;ENST00000396589;ENST00000535295;ENST00000542546;ENST00000539924;ENST00000546234;ENST00000542782;ENST00000535344;ENST00000537557;ENST00000535266	T;T;T;T;T;T;T;T;T;T;T;T	0.74632	-0.86;-0.86;-0.86;-0.86;-0.86;-0.86;-0.86;-0.86;-0.86;-0.86;-0.86;-0.86	3.11	1.89	0.25635	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.451473	0.22797	N	0.055529	T	0.63094	0.2482	L	0.49455	1.56	0.09310	N	1	B;B;B;B	0.17852	0.02;0.006;0.002;0.024	B;B;B;B	0.24394	0.049;0.049;0.013;0.053	T	0.46076	-0.9217	10	0.15499	T	0.54	.	7.3787	0.26843	0.0:0.0:0.4716:0.5284	.	135;11;97;120	B7ZAC3;B7Z844;Q8TDB8-2;Q8TDB8	.;.;.;GTR14_HUMAN	F	97;120;97;120;11;11;135;97;97;97;120;120	ENSP00000340450:I97F;ENSP00000440480:I120F;ENSP00000407287:I97F;ENSP00000379834:I120F;ENSP00000440492:I11F;ENSP00000443903:I11F;ENSP00000445929:I135F;ENSP00000440043:I97F;ENSP00000438312:I97F;ENSP00000443217:I97F;ENSP00000440044:I120F;ENSP00000437653:I120F	ENSP00000340450:I97F	I	-	1	0	SLC2A14	7873853	0.000000	0.05858	0.522000	0.27862	0.249000	0.25844	-0.458000	0.06737	0.201000	0.20466	0.377000	0.23210	ATT	.	.	.	none		0.458	SLC2A14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399836.2	NM_153449		A	7982586	T	A	7982586	3	1	141	1	0	0	0	0	1	0	0	0	14556	1435	50	5	1232	5	SLC2A14	12	7982586	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08		7982586	125869309	39	8545											
H2AFJ	55766	hgsc.bcm.edu	37	chr12	14927683	14927684	+	Frame_Shift_Ins	INS	-	-	T																															ccatccgcaacgacgaggagINSttaaacaagctgctgggcaa																										TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr12:14927683_14927684insT	ENST00000544848.1	+	1	414_415	c.279_280insT	c.(280-282)ttafs	p.L94fs		NM_177925.2	NP_808760.1	Q9BTM1	H2AJ_HUMAN	H2A histone family, member J	94						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E93D(1)		NS(1)|central_nervous_system(1)|kidney(1)|ovary(1)|skin(1)	5						ACGACGAGGAGTTAAACAAGCT	0.614																																					p.E93fs		Atlas-INDEL	.											H2AFJ,caecum,carcinoma,+1,1	H2AFJ	14	.	1	Substitution - Missense(1)	ovary(1)	c.279_280insT						PASS	.																																			SO:0001589	frameshift_variant	55766	exon1			.	AK001765	CCDS31752.1	12p12.3	2012-09-11			ENSG00000246705	ENSG00000246705		"Histones / Replication-independent"	14456	protein-coding gene	gene with protein product							Standard	NM_177925		Approved	FLJ10903, MGC921	uc009zia.3	Q9BTM1	OTTHUMG00000168736	ENST00000544848.1:c.281dupT	chr12.hg19:g.14927685_14927685dupT	ENSP00000438553:p.Leu94fs	131.0	0.0	0		159.0	58.0	0.36478	NM_177925	Q9NV63	Frame_Shift_Ins	INS	ENST00000544848.1	hg19	CCDS31752.1																																																																																			.	.	.	none		0.614	H2AFJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400845.1	NM_177925		T	14927684	-	T	14927683	7	5	141	1	0	1	1	0	0	0	0	0	6933	1020	36	0	281	0	H2AFJ	12	14927683	Frame_Shift_Ins	INS	-	TCGA-BQ-7059-01A-11D-1961-08	6945097	14927683	118924212	40	8546											
ANO6	196527	hgsc.bcm.edu	37	chr12	45695869	45695869	+	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	tcagcatgattttcgaacccCggagtttgtgagtactattc	9	14	9	9	2	1	2	1	2	0	0	3	4	1	3	2	1	3	3	2	1	3	6			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr12:45695869C>A	ENST00000320560.8	+	2	345	c.143C>A	c.(142-144)cCg>cAg	p.P48Q	ANO6_ENST00000441606.2_Missense_Mutation_p.P30Q|ANO6_ENST00000426898.2_Intron|ANO6_ENST00000435642.1_Missense_Mutation_p.P48Q|ANO6_ENST00000425752.2_Missense_Mutation_p.P48Q|ANO6_ENST00000423947.3_Missense_Mutation_p.P69Q	NM_001025356.2	NP_001020527.2	Q4KMQ2	ANO6_HUMAN	anoctamin 6	48					activation of blood coagulation via clotting cascade (GO:0002543)|blood coagulation (GO:0007596)|bone mineralization involved in bone maturation (GO:0035630)|calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|phosphatidylserine exposure on blood platelet (GO:0097045)|phospholipid scrambling (GO:0017121)|positive regulation of endothelial cell apoptotic process (GO:2000353)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)|voltage-gated chloride channel activity (GO:0005247)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						TTTCGAACCCCGGAGTTTGTG	0.328																																					p.P69Q		Atlas-SNP	.											.	ANO6	163	.	0			c.C206A						PASS	.						140	138	138					12																	45695869		2203	4300	6503	SO:0001583	missense	196527	exon3			GAACCCCGGAGTT	AL832340	CCDS31782.1, CCDS44865.1, CCDS44866.1, CCDS55819.1	12q12-q13.11	2014-09-17	2008-08-28	2008-08-28				"Ion channels / Chloride channels : Calcium activated : Anoctamins"	25240	protein-coding gene	gene with protein product		608663	"transmembrane protein 16F"	TMEM16F		15067359, 24692353	Standard	NM_001025356		Approved	DKFZp313M0720	uc010slf.2	Q4KMQ2	OTTHUMG00000169564	ENST00000320560.8:c.143C>A	chr12.hg19:g.45695869C>A	ENSP00000320087:p.Pro48Gln	102.0	0.0	.		152.0	7.0	.	NM_001204803	A6NNM6|B9EGG0|E7ENK4|E9PB30|E9PCT2|Q8N3Q2	Missense_Mutation	SNP	ENST00000320560.8	hg19	CCDS31782.1	.	.	.	.	.	.	.	.	.	.	C	15.34	2.805266	0.50315	.	.	ENSG00000177119	ENST00000425752;ENST00000423947;ENST00000435642;ENST00000320560;ENST00000441606	T;T;T;T;T	0.70516	-0.49;-0.36;-0.49;-0.34;-0.33	4.83	4.83	0.62350	.	0.193850	0.31450	N	0.007636	T	0.81054	0.4743	L	0.61218	1.895	0.34896	D	0.745981	B;P;D;B	0.89917	0.089;0.622;1.0;0.171	B;B;D;B	0.85130	0.057;0.222;0.997;0.14	D	0.84674	0.0713	10	0.42905	T	0.14	.	14.1386	0.65303	0.0:1.0:0.0:0.0	.	30;69;48;48	E9PB30;B9EGG0;E9PCT2;Q4KMQ2	.;.;.;ANO6_HUMAN	Q	48;69;48;48;30	ENSP00000391417:P48Q;ENSP00000409126:P69Q;ENSP00000413840:P48Q;ENSP00000320087:P48Q;ENSP00000413137:P30Q	ENSP00000320087:P48Q	P	+	2	0	ANO6	43982136	0.223000	0.23663	0.737000	0.30932	0.994000	0.84299	3.434000	0.52841	2.611000	0.88343	0.643000	0.83706	CCG	.	.	.	none		0.328	ANO6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404822.1	XM_113743		A	45695869	C	A	45695869	3	1	141	1	0	0	0	0	1	0	0	0	701	652	23	4	169	4	ANO6	12	45695869	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	30768186	45695869	88156026	41	8547											
SLC38A1	81539	hgsc.bcm.edu	37	chr12	46633478	46633478	+	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	tcacctatttatctgaccatTttctacttcggtgaaatcat	10	17	4	10	1	4	2	2	2	2	0	5	2	4	2	2	1	1	0	2	1	4	7			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr12:46633478T>A	ENST00000398637.5	-	3	800	c.106A>T	c.(106-108)Aat>Tat	p.N36Y	SLC38A1_ENST00000439706.1_Missense_Mutation_p.N36Y|SLC38A1_ENST00000546893.1_Missense_Mutation_p.N36Y|SLC38A1_ENST00000552197.1_Missense_Mutation_p.N36Y|SLC38A1_ENST00000549049.1_Missense_Mutation_p.N36Y|SLC38A1_ENST00000549633.1_Intron	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	36					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)			ATCTGACCATTTTCTACTTCG	0.413																																					p.N36Y		Atlas-SNP	.											.	SLC38A1	58	.	0			c.A106T						PASS	.						159	147	151					12																	46633478		1872	4125	5997	SO:0001583	missense	81539	exon3			GACCATTTTCTAC	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.106A>T	chr12.hg19:g.46633478T>A	ENSP00000381634:p.Asn36Tyr	88.0	0.0	.		171.0	33.0	.	NM_030674	Q8NC61|Q8NCF8|Q96JX2|Q9H2Q2	Missense_Mutation	SNP	ENST00000398637.5	hg19	CCDS41774.1	.	.	.	.	.	.	.	.	.	.	T	19.53	3.844471	0.71488	.	.	ENSG00000111371	ENST00000549049;ENST00000439706;ENST00000398637;ENST00000546893;ENST00000552197;ENST00000550173	T;T;T;T;T	0.07688	3.33;3.33;3.33;3.33;3.17	4.93	4.93	0.64822	.	0.000000	0.56097	D	0.000026	T	0.13457	0.0326	N	0.08118	0	0.46437	D	0.999046	D;P	0.89917	1.0;0.871	D;B	0.87578	0.998;0.327	T	0.35076	-0.9803	10	0.66056	D	0.02	-24.0257	14.896	0.70644	0.0:0.0:0.0:1.0	.	36;36	F8VX04;Q9H2H9	.;S38A1_HUMAN	Y	36	ENSP00000449607:N36Y;ENSP00000398142:N36Y;ENSP00000381634:N36Y;ENSP00000447853:N36Y;ENSP00000449756:N36Y	ENSP00000381634:N36Y	N	-	1	0	SLC38A1	44919745	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	4.732000	0.62029	1.975000	0.57531	0.477000	0.44152	AAT	.	.	.	none		0.413	SLC38A1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404218.2			A	46633478	T	A	46633478	3	1	141	1	0	0	0	0	1	0	0	0	14614	1841	64	5	1417	5	SLC38A1	12	46633478	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	937609	46633478	87218417	42	8548											
TCTN1	79600	hgsc.bcm.edu	37	chr12	111070319	111070319	+	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	cagattcgtttctgagatttCcttcgtccctgacatcatct	7	16	6	12	2	3	3	1	2	2	2	7	4	5	3	2	0	0	1	2	0	0	4			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr12:111070319C>T	ENST00000551590.1	+	5	823	c.667C>T	c.(667-669)Cct>Tct	p.P223S	TCTN1_ENST00000397655.3_Missense_Mutation_p.P223S|TCTN1_ENST00000397659.4_Missense_Mutation_p.P223S|AC144522.1_ENST00000408319.1_RNA|HVCN1_ENST00000548312.1_Intron|TCTN1_ENST00000551555.2_3'UTR|TCTN1_ENST00000377654.3_Missense_Mutation_p.P45S			Q2MV58	TECT1_HUMAN	tectonic family member 1	223					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						TCTGAGATTTCCTTCGTCCCT	0.398																																					p.P223S		Atlas-SNP	.											TCTN1,NS,lymphoid_neoplasm,0,1	TCTN1	37	.	0			c.C667T						PASS	.						197	184	188					12																	111070319		1898	4131	6029	SO:0001583	missense	79600	exon5			AGATTTCCTTCGT	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.667C>T	chr12.hg19:g.111070319C>T	ENSP00000448735:p.Pro223Ser	182.0	1.0	.		244.0	52.0	.	NM_024549	A8MX11|Q49A60|Q6P5X1|Q6UXW2|Q8NAE9|Q96N72|Q9H798	Missense_Mutation	SNP	ENST00000551590.1	hg19	CCDS41835.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.656513	0.88154	.	.	ENSG00000204852	ENST00000397650;ENST00000551590;ENST00000397655;ENST00000377654;ENST00000547868;ENST00000548095;ENST00000397657;ENST00000397659;ENST00000397652	D;D;D;D	0.98313	-4.86;-4.86;-4.86;-4.86	5.97	5.97	0.96955	Domain of unknown function DUF1619 (1);	0.000000	0.85682	D	0.000000	D	0.99099	0.9690	M	0.87180	2.865	0.58432	D	0.999993	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.99716	1.1008	10	0.87932	D	0	-15.0486	18.9916	0.92794	0.0:1.0:0.0:0.0	.	223;223;223;163;167	Q2MV58;Q2MV58-3;Q2MV58-2;C9J1H5;C9J1H4	TECT1_HUMAN;.;.;.;.	S	163;223;223;45;45;223;45;223;167	ENSP00000448735:P223S;ENSP00000380775:P223S;ENSP00000366882:P45S;ENSP00000380779:P223S	ENSP00000366882:P45S	P	+	1	0	TCTN1	109554702	1.000000	0.71417	0.767000	0.31495	0.782000	0.44232	4.913000	0.63341	2.835000	0.97688	0.591000	0.81541	CCT	.	.	.	none		0.398	TCTN1-001	KNOWN	non_canonical_TEC|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316016.2	NM_024549		T	111070319	C	T	111070319	3	4	141	1	0	0	0	0	1	0	0	0	15734	855	30	2	785	2	TCTN1	12	111070319	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	64436841	111070319	22781576	43	8549											
ATXN2	6311	hgsc.bcm.edu	37	chr12	111908459	111908459	+	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	tggagtaagctggtggggtgGctgcaatcggtgggcccgct	5	9	19	8	2	0	0	0	0	0	0	1	1	0	1	1	7	2	5	1	7	2	1			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr12:111908459G>C	ENST00000377617.3	-	19	3247	c.3086C>G	c.(3085-3087)gCc>gGc	p.A1029G	ATXN2_ENST00000608853.1_Missense_Mutation_p.A869G|ATXN2_ENST00000389153.4_Missense_Mutation_p.A766G|ATXN2_ENST00000542287.2_Missense_Mutation_p.A764G|ATXN2_ENST00000535949.1_Missense_Mutation_p.A740G|ATXN2_ENST00000550104.1_3'UTR	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	1029	Pro-rich.				cell death (GO:0008219)|cerebellar Purkinje cell differentiation (GO:0021702)|cytoplasmic mRNA processing body assembly (GO:0033962)|homeostasis of number of cells (GO:0048872)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of receptor internalization (GO:0002091)|neuromuscular process (GO:0050905)|neuron projection morphogenesis (GO:0048812)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA transport (GO:0050658)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|trans-Golgi network (GO:0005802)	epidermal growth factor receptor binding (GO:0005154)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						TGGTGGGGTGGCTGCAATCGG	0.532																																					p.A1029G		Atlas-SNP	.											.	ATXN2	99	.	0			c.C3086G						PASS	.						139	128	132					12																	111908459		2203	4300	6503	SO:0001583	missense	6311	exon19			GGGGTGGCTGCAA	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.3086C>G	chr12.hg19:g.111908459G>C	ENSP00000366843:p.Ala1029Gly	149.0	0.0	.		179.0	63.0	.	NM_002973	A6NLD4|Q6ZQZ7|Q99493	Missense_Mutation	SNP	ENST00000377617.3	hg19	CCDS31902.1	.	.	.	.	.	.	.	.	.	.	G	34	5.351916	0.95830	.	.	ENSG00000204842	ENST00000389154;ENST00000389153;ENST00000377617;ENST00000482777;ENST00000542287;ENST00000535949	T	0.77620	-1.11	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.85444	0.5698	L	0.52573	1.65	0.80722	D	1	D;D;D;D;D	0.76494	0.998;0.997;0.993;0.999;0.998	D;D;D;D;D	0.85130	0.994;0.985;0.978;0.997;0.994	T	0.81564	-0.0875	10	0.27082	T	0.32	-9.4636	19.888	0.96917	0.0:0.0:1.0:0.0	.	48;1029;740;764;766	Q99700-3;Q99700;Q24JQ7;F8VQP2;F8WB06	.;ATX2_HUMAN;.;.;.	G	84;766;1029;48;764;740	ENSP00000366843:A1029G	ENSP00000366843:A1029G	A	-	2	0	ATXN2	110392842	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.476000	0.97823	2.720000	0.93068	0.591000	0.81541	GCC	.	.	.	none		0.532	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973		C	111908459	G	C	111908459	3	2	141	1	0	0	0	0	1	0	0	0	1211	1203	42	4	883	4	ATXN2	12	111908459	Missense_Mutation	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	838140	111908459	21943436	44	8550											
SBNO1	55206	hgsc.bcm.edu	37	chr12	123806180	123806180	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctcatagtcactttcttcaTtatcagaggcatcagattca	11	15	5	10	0	7	2	6	0	2	2	8	2	7	2	0	1	0	1	0	1	2	5			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr12:123806180T>C	ENST00000602398.1	-	17	2352	c.2225A>G	c.(2224-2226)aAt>aGt	p.N742S	SBNO1_ENST00000267176.4_Missense_Mutation_p.N741S|SBNO1_ENST00000602750.1_Missense_Mutation_p.N741S|SBNO1_ENST00000420886.2_Missense_Mutation_p.N742S			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	742					regulation of transcription, DNA-templated (GO:0006355)					NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		ACTTTCTTCATTATCAGAGGC	0.403																																					p.N742S		Atlas-SNP	.											.	SBNO1	138	.	0			c.A2225G						PASS	.						193	173	180					12																	123806180		2203	4300	6503	SO:0001583	missense	55206	exon16			TCTTCATTATCAG	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"sno, strawberry notch homolog 1 (Drosophila)"				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.2225A>G	chr12.hg19:g.123806180T>C	ENSP00000473665:p.Asn742Ser	132.0	0.0	.		218.0	90.0	.	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Missense_Mutation	SNP	ENST00000602398.1	hg19	CCDS53844.1	.	.	.	.	.	.	.	.	.	.	T	3.761	-0.049616	0.07407	.	.	ENSG00000139697	ENST00000420886;ENST00000267176	T;T	0.28666	1.6;1.6	5.33	4.15	0.48705	.	0.449012	0.24209	N	0.040557	T	0.09949	0.0244	N	0.00926	-1.1	0.35755	D	0.819721	B;B;B	0.19200	0.0;0.001;0.034	B;B;B	0.21917	0.001;0.001;0.037	T	0.20538	-1.0272	10	0.06365	T	0.9	-14.1214	12.2297	0.54480	0.0:0.0:0.1426:0.8574	.	742;741;740	A3KN83;A3KN83-2;A3KN83-3	SBNO1_HUMAN;.;.	S	742;741	ENSP00000387361:N742S;ENSP00000267176:N741S	ENSP00000267176:N741S	N	-	2	0	SBNO1	122372133	0.996000	0.38824	0.986000	0.45419	0.996000	0.88848	1.100000	0.31025	0.819000	0.34492	0.460000	0.39030	AAT	.	.	.	none		0.403	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183		C	123806180	T	C	123806180	3	2	141	1	0	0	0	0	1	0	0	0	13875	1493	52	3	2020	3	SBNO1	12	123806180	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	11897721	123806180	10045715	45	8551											
MTHFD1	4522	hgsc.bcm.edu	37	chr14	64915025	64915025	+	Missense_Mutation	SNP	A	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	ttccagtagtagtggccgtgAatgcattcaagtaagtgtag	11	12	12	6	1	1	1	1	1	0	0	2	1	2	1	2	1	1	5	2	1	6	6			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr14:64915025A>C	ENST00000545908.1	+	23	2666	c.2437A>C	c.(2437-2439)Aat>Cat	p.N813H	MTHFD1_ENST00000216605.8_Missense_Mutation_p.N757H|CTD-2555O16.2_ENST00000556640.1_RNA			P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	757	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)	AGTGGCCGTGAATGCATTCAA	0.383																																					p.N757H	Colon(18;220 581 13419 18191 31512)|GBM(126;343 1658 28700 44425 52519)	Atlas-SNP	.											.	MTHFD1	61	.	0			c.A2269C						PASS	.						79	78	78					14																	64915025		2203	4300	6503	SO:0001583	missense	4522	exon23			GCCGTGAATGCAT	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.2437A>C	chr14.hg19:g.64915025A>C	ENSP00000438588:p.Asn813His	43.0	0.0	.		59.0	12.0	.	NM_005956	B2R5Y2|G3V2B8|Q86VC9|Q9BVP5	Missense_Mutation	SNP	ENST00000545908.1	hg19		.	.	.	.	.	.	.	.	.	.	A	21.0	4.077868	0.76528	.	.	ENSG00000100714	ENST00000545908;ENST00000555709;ENST00000216605	T;T;T	0.47177	0.85;0.85;0.85	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	D	0.82898	0.5137	H	0.99573	4.635	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.90598	0.4542	10	0.87932	D	0	-21.8056	16.1926	0.82004	1.0:0.0:0.0:0.0	.	813;757	F5H2F4;G3V2B8	.;.	H	813;757;813	ENSP00000438588:N813H;ENSP00000450560:N757H;ENSP00000216605:N813H	ENSP00000216605:N757H	N	+	1	0	MTHFD1	63984778	1.000000	0.71417	0.914000	0.36105	0.594000	0.36715	9.339000	0.96797	2.219000	0.72066	0.533000	0.62120	AAT	.	.	.	none		0.383	MTHFD1-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000412167.1			C	64915025	A	C	64915025	3	2	141	1	0	0	0	0	1	0	0	0	9934	246	9	5	2359	5	MTHFD1	14	64915025	Missense_Mutation	SNP	A	TCGA-BQ-7059-01A-11D-1961-08		64915025	42434515	46	8552											
ATG2B	55102	hgsc.bcm.edu	37	chr14	96784101	96784101	+	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	agtattaatgagctgactggCtactgaaagcccaatgccat	13	10	9	9	0	0	3	0	3	0	0	0	3	0	3	2	1	4	3	2	1	5	3			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr14:96784101C>G	ENST00000359933.4	-	19	3864	c.2971G>C	c.(2971-2973)Gcc>Ccc	p.A991P		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	991					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)		AGCTGACTGGCTACTGAAAGC	0.343																																					p.A991P		Atlas-SNP	.											.	ATG2B	169	.	0			c.G2971C						PASS	.						101	96	98					14																	96784101		1833	4104	5937	SO:0001583	missense	55102	exon19			GACTGGCTACTGA	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.2971G>C	chr14.hg19:g.96784101C>G	ENSP00000353010:p.Ala991Pro	134.0	0.0	.		189.0	35.0	.	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	hg19	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	C	20.5	3.998612	0.74818	.	.	ENSG00000066739	ENST00000359933	T	0.39997	1.05	5.54	5.54	0.83059	.	0.164574	0.39759	U	0.001274	T	0.63034	0.2477	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.54576	-0.8273	10	0.25751	T	0.34	.	19.8585	0.96775	0.0:1.0:0.0:0.0	.	991	Q96BY7	ATG2B_HUMAN	P	991	ENSP00000353010:A991P	ENSP00000353010:A991P	A	-	1	0	ATG2B	95853854	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.496000	0.81526	2.760000	0.94817	0.655000	0.94253	GCC	.	.	.	none		0.343	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		G	96784101	C	G	96784101	3	3	141	1	0	0	0	0	1	0	0	0	1094	797	28	4	3361	4	ATG2B	14	96784101	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	31869076	96784101	10565439	47	8553											
TMED3	23423	hgsc.bcm.edu	37	chr15	79606106	79606106	+	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	ttatggttgtcaggtcatcaCtggaggccactacgatgttg	8	13	12	8	1	3	0	3	0	0	0	3	2	3	1	1	4	1	2	1	4	2	4			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr15:79606106C>G	ENST00000299705.5	+	2	364	c.176C>G	c.(175-177)aCt>aGt	p.T59S	TMED3_ENST00000424155.2_Missense_Mutation_p.T59S|TMED3_ENST00000536821.1_Missense_Mutation_p.T59S	NM_007364.2	NP_031390.1	Q9Y3Q3	TMED3_HUMAN	transmembrane emp24 protein transport domain containing 3	59	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.				protein transport (GO:0015031)	COPI vesicle coat (GO:0030126)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				large_intestine(3)|lung(4)|ovary(1)|skin(1)	9						CAGGTCATCACTGGAGGCCAC	0.478																																					p.T59S		Atlas-SNP	.											.	TMED3	19	.	0			c.C176G						PASS	.						94	82	86					15																	79606106		2196	4293	6489	SO:0001583	missense	23423	exon2			TCATCACTGGAGG	BC022232	CCDS10310.1, CCDS73768.1	15q24-q25	2011-02-09	2005-08-26	2005-01-07	ENSG00000166557	ENSG00000166557			28889	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 22", "transmembrane emp24 domain containing 3"	C15orf22		12975309	Standard	XM_005254263		Approved	p24B	uc002beu.3	Q9Y3Q3	OTTHUMG00000144170	ENST00000299705.5:c.176C>G	chr15.hg19:g.79606106C>G	ENSP00000299705:p.Thr59Ser	42.0	0.0	.		51.0	8.0	.	NM_007364	A8K069|B4DN05|Q2T9F8	Missense_Mutation	SNP	ENST00000299705.5	hg19	CCDS10310.1	.	.	.	.	.	.	.	.	.	.	C	16.79	3.220785	0.58560	.	.	ENSG00000166557	ENST00000299705;ENST00000424155;ENST00000536821;ENST00000543455	T;T;T;T	0.14766	2.48;2.48;2.48;2.48	4.88	4.88	0.63580	GOLD (3);	0.258714	0.39407	N	0.001373	T	0.12220	0.0297	L	0.28694	0.88	0.47698	D	0.999498	B;B	0.29085	0.232;0.004	B;B	0.35607	0.206;0.01	T	0.06954	-1.0798	10	0.08599	T	0.76	-25.4826	15.9067	0.79436	0.0:1.0:0.0:0.0	.	59;59	B4DN05;Q9Y3Q3	.;TMED3_HUMAN	S	59	ENSP00000299705:T59S;ENSP00000414983:T59S;ENSP00000446062:T59S;ENSP00000440228:T59S	ENSP00000299705:T59S	T	+	2	0	TMED3	77393161	0.995000	0.38212	0.976000	0.42696	0.985000	0.73830	3.616000	0.54174	2.680000	0.91292	0.655000	0.94253	ACT	.	.	.	none		0.478	TMED3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291369.1	NM_007364		G	79606106	C	G	79606106	3	3	141	1	0	0	0	0	1	0	0	0	16017	565	20	4	182	4	TMED3	15	79606106	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08		79606106	22925286	48	8554											
SRRM2	23524	hgsc.bcm.edu	37	chr16	2808492	2808492	+	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	cttgttcgggagtctagcagTtctcgctcaccaaccccaaa	9	10	8	14	2	3	0	1	0	2	0	5	1	3	1	3	1	2	4	3	1	3	4			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr16:2808492T>A	ENST00000301740.8	+	5	1086	c.537T>A	c.(535-537)agT>agA	p.S179R		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	179	Ser-rich.			SS -> NN (in Ref. 2; AAF21439). {ECO:0000305}.	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						AGTCTAGCAGTTCTCGCTCAC	0.423																																					p.S179R		Atlas-SNP	.											.	SRRM2	263	.	0			c.T537A						PASS	.						161	166	165					16																	2808492		2198	4300	6498	SO:0001583	missense	23524	exon5			TAGCAGTTCTCGC	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.537T>A	chr16.hg19:g.2808492T>A	ENSP00000301740:p.Ser179Arg	268.0	0.0	.		274.0	50.0	.	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	hg19	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	T	16.70	3.195477	0.58126	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000396975;ENST00000426305	T	0.25250	1.81	5.15	2.81	0.32909	.	0.000000	0.64402	D	0.000006	T	0.29749	0.0743	N	0.19112	0.55	0.32407	N	0.551109	D	0.71674	0.998	D	0.76071	0.987	T	0.32955	-0.9887	10	0.87932	D	0	-4.3082	6.3143	0.21182	0.0:0.2621:0.0:0.7379	.	179	Q9UQ35	SRRM2_HUMAN	R	179;179;83;144	ENSP00000301740:S179R	ENSP00000301740:S179R	S	+	3	2	SRRM2	2748493	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	0.382000	0.20635	0.797000	0.33971	0.528000	0.53228	AGT	.	.	.	none		0.423	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			A	2808492	T	A	2808492	3	1	141	1	0	0	0	0	1	0	0	0	15181	1722	60	5	551	5	SRRM2	16	2808492	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08		2808492	87546261	49	8555											
ZNF23	7571	hgsc.bcm.edu	37	chr16	71483580	71483580	+	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	ctaaaaaaacactcctccacGgggcttgtctcatctttcac	11	11	5	14	1	3	0	2	0	2	0	6	0	5	0	2	2	1	1	2	2	4	3	rs376275643		TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr16:71483580G>T	ENST00000393539.2	-	6	1161	c.348C>A	c.(346-348)ccC>ccA	p.P116P	ZNF23_ENST00000497160.1_3'UTR|ZNF23_ENST00000428724.2_Silent_p.P58P|ZNF23_ENST00000417828.1_Silent_p.P116P|AC010547.9_ENST00000561908.1_3'UTR|ZNF23_ENST00000357254.4_Silent_p.P116P|ZNF23_ENST00000358700.2_3'UTR|ZNF23_ENST00000539742.1_5'UTR|ZNF23_ENST00000564528.1_Silent_p.P58P	NM_145911.1	NP_666016.1	P17027	ZNF23_HUMAN	zinc finger protein 23	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P116P(1)		NS(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(14)|stomach(1)|urinary_tract(1)	29		Ovarian(137;0.00768)		BRCA - Breast invasive adenocarcinoma(221;0.0686)		ACTCCTCCACGGGGCTTGTCT	0.448																																					p.P116P		Atlas-SNP	.											.	ZNF23	65	.	1	Substitution - coding silent(1)	lung(1)	c.C348A						PASS	.						167	173	171					16																	71483580		2198	4300	6498	SO:0001819	synonymous_variant	7571	exon6			CTCCACGGGGCTT	X52347	CCDS10900.1	16q22.2	2013-03-28	2012-07-12		ENSG00000167377	ENSG00000167377		"Zinc fingers, C2H2-type"	13023	protein-coding gene	gene with protein product		194527	"zinc finger protein 359"	ZNF359			Standard	NM_145911		Approved	KOX16, Zfp612, ZNF612	uc002faf.3	P17027	OTTHUMG00000176797	ENST00000393539.2:c.348C>A	chr16.hg19:g.71483580G>T		232.0	0.0	.		242.0	10.0	.	NM_145911	Q8NDP5|Q96IT3|Q9UG42	Silent	SNP	ENST00000393539.2	hg19	CCDS10900.1																																																																																			.	.	.	alt		0.448	ZNF23-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268985.23	NM_145911		T	71483580	G	T	71483580	2	4	141	1	0	0	0	0	0	0	0	1	17795	1103	39	4		4	ZNF23	16	71483580	Silent	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	68675088	71483580	18871173	50	8556											
DHX38	9785	hgsc.bcm.edu	37	chr16	72138441	72138441	+	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	acatcagccacgatggatgcGgagaagtttgctgccttttt	9	12	11	9	2	1	1	1	0	0	1	1	4	1	2	2	2	4	2	2	2	1	3	rs199994362	byFrequency	TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr16:72138441G>T	ENST00000268482.3	+	15	2576	c.2067G>T	c.(2065-2067)gcG>gcT	p.A689A	DHX38_ENST00000536867.1_Intron	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	689	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)	p.A689A(1)		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)				CGATGGATGCGGAGAAGTTTG	0.572																																					p.A689A	Melanoma(97;711 1442 7855 13832 28836)	Atlas-SNP	.											DHX38,rectum,carcinoma,0,1	DHX38	91	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2067T						PASS	.						242	177	199					16																	72138441		2198	4300	6498	SO:0001819	synonymous_variant	9785	exon15			GGATGCGGAGAAG	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.2067G>T	chr16.hg19:g.72138441G>T		114.0	0.0	.		128.0	7.0	.	NM_014003	B4DVG8|D3DWS7|O75212|Q96HN7	Silent	SNP	ENST00000268482.3	hg19	CCDS10907.1																																																																																			.	G|0.999;A|0.001	.	alt		0.572	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003		T	72138441	G	T	72138441	2	4	141	1	0	0	0	0	0	0	0	1	4513	1103	39	4		4	DHX38	16	72138441	Silent	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	654861	72138441	18216312	51	8557											
WSCD1	23302	hgsc.bcm.edu	37	chr17	6012935	6012935	+	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	gttccctggcaggagttcccCttggccattctcaggggctg	4	11	13	13	0	1	0	1	0	1	0	4	1	3	1	4	5	0	4	4	5	0	4			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr17:6012935C>G	ENST00000574946.1	+	6	1248	c.858C>G	c.(856-858)ccC>ccG	p.P286P	WSCD1_ENST00000539421.1_Silent_p.P286P|WSCD1_ENST00000574232.1_Silent_p.P286P|WSCD1_ENST00000317744.5_Silent_p.P286P|WSCD1_ENST00000573634.1_Silent_p.P170P			Q658N2	WSCD1_HUMAN	WSC domain containing 1	286	WSC 2. {ECO:0000255|PROSITE- ProRule:PRU00558}.					integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)	p.P286P(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)	35						AGGAGTTCCCCTTGGCCATTC	0.557																																					p.P286P		Atlas-SNP	.											WSCD1,NS,carcinoma,0,1	WSCD1	84	.	1	Substitution - coding silent(1)	endometrium(1)	c.C858G						PASS	.						260	245	250					17																	6012935		2203	4300	6503	SO:0001819	synonymous_variant	23302	exon6			GTTCCCCTTGGCC		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.858C>G	chr17.hg19:g.6012935C>G		483.0	1.0	.		392.0	87.0	.	NM_015253	A8K0N8|D3DTM3|O60276|Q96G45	Silent	SNP	ENST00000574946.1	hg19	CCDS32538.1																																																																																			.	.	.	none		0.557	WSCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438965.4	NM_015253		G	6012935	C	G	6012935	2	3	141	1	0	0	0	0	0	0	0	1	17418	668	24	4		4	WSCD1	17	6012935	Silent	SNP	C	TCGA-BQ-7059-01A-11D-1961-08		6012935	75182275	52	8558											
ZNF830	91603	hgsc.bcm.edu	37	chr17	33289281	33289281	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgagaaagcagaaatacaTgaaaaagtggtggaaaggag	20	6	13	2	0	0	3	0	2	0	2	0	6	0	5	0	3	2	1	0	3	6	2			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr17:33289281T>C	ENST00000361952.3	+	1	733	c.696T>C	c.(694-696)caT>caC	p.H232H	CCT6B_ENST00000314144.5_5'Flank|CCT6B_ENST00000421975.3_5'Flank|CCT6B_ENST00000436961.3_5'Flank	NM_052857.3	NP_443089.3	Q96NB3	ZN830_HUMAN	zinc finger protein 830	232					blastocyst growth (GO:0001832)|mitotic nuclear division (GO:0007067)|nuclear cell cycle DNA replication (GO:0033260)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|large_intestine(1)|liver(2)|lung(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Ovarian(249;0.17)				CAGAAATACATGAAAAAGTGG	0.448																																					p.H232H		Atlas-SNP	.											.	ZNF830	26	.	0			c.T696C						PASS	.						49	48	48					17																	33289281		2203	4300	6503	SO:0001819	synonymous_variant	91603	exon1			AATACATGAAAAA	AK055707	CCDS32618.1	17q12	2013-10-23	2008-03-25	2008-03-25	ENSG00000198783	ENSG00000198783			28291	protein-coding gene	gene with protein product	"orphan maintenance of genome 1"		"coiled-coil domain containing 16"	CCDC16		23066043	Standard	NM_052857		Approved	MGC20398, OMCG1	uc002hih.4	Q96NB3	OTTHUMG00000179771	ENST00000361952.3:c.696T>C	chr17.hg19:g.33289281T>C		63.0	0.0	.		59.0	16.0	.	NM_052857	Q96F60|Q96GZ5|Q9BU38	Silent	SNP	ENST00000361952.3	hg19	CCDS32618.1																																																																																			.	.	.	none		0.448	ZNF830-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448018.1	NM_052857		C	33289281	T	C	33289281	2	2	141	1	0	0	0	0	0	0	0	1	18196	1461	51	3		3	ZNF830	17	33289281	Silent	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	27276346	33289281	47905929	53	8559											
NR1D1	9572	hgsc.bcm.edu	37	chr17	38253601	38253601	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtcactatagagggattcAgggctggtgcggcttgggga	7	11	17	6	1	2	1	2	0	0	1	2	3	2	3	0	6	1	2	0	6	2	5			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr17:38253601A>G	ENST00000246672.3	-	2	717	c.87T>C	c.(85-87)ccT>ccC	p.P29P		NM_021724.3	NP_068370.1	P20393	NR1D1_HUMAN	nuclear receptor subfamily 1, group D, member 1	29	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)					AGAGGGATTCAGGGCTGGTGC	0.592																																					p.P29P		Atlas-SNP	.											.	NR1D1	45	.	0			c.T87C						PASS	.						57	62	60					17																	38253601		2203	4300	6503	SO:0001819	synonymous_variant	9572	exon2			GGATTCAGGGCTG	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.87T>C	chr17.hg19:g.38253601A>G		47.0	0.0	.		30.0	12.0	.	NM_021724	Q0P5Z4|Q15304	Silent	SNP	ENST00000246672.3	hg19	CCDS11361.1																																																																																			.	.	.	none		0.592	NR1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257135.1			G	38253601	A	G	38253601	2	3	141	1	0	0	0	0	0	0	0	1	10622	175	7	3		3	NR1D1	17	38253601	Silent	SNP	A	TCGA-BQ-7059-01A-11D-1961-08	4964320	38253601	42941609	54	8560											
NAGS	162417	hgsc.bcm.edu	37	chr17	42083544	42083544	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcgtcgctggccaaggcgcTgcggcccaccaaaatcatct	8	6	11	16	5	2	0	1	0	1	0	3	0	2	0	3	3	1	2	3	3	3	0			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr17:42083544T>C	ENST00000293404.3	+	3	972	c.854T>C	c.(853-855)cTg>cCg	p.L285P	PYY_ENST00000360085.2_5'Flank	NM_153006.2	NP_694551.1	Q8N159	NAGS_HUMAN	N-acetylglutamate synthase	285	Amino-acid kinase domain (AAK).				arginine biosynthetic process (GO:0006526)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	mitochondrial matrix (GO:0005759)	acetyl-CoA:L-glutamate N-acetyltransferase activity (GO:0004042)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8		Breast(137;0.00536)|Prostate(33;0.0724)		BRCA - Breast invasive adenocarcinoma(366;0.113)		GCCAAGGCGCTGCGGCCCACC	0.662																																					p.L285P		Atlas-SNP	.											.	NAGS	25	.	0			c.T854C						PASS	.						29	29	29					17																	42083544		2200	4297	6497	SO:0001583	missense	162417	exon3			AGGCGCTGCGGCC	AY116537	CCDS11473.1	17q21.31	2008-02-05				ENSG00000161653			17996	protein-coding gene	gene with protein product		608300				15050968, 12459178	Standard	NM_153006		Approved	AGAS, ARGA, NAT7	uc002ies.3	Q8N159		ENST00000293404.3:c.854T>C	chr17.hg19:g.42083544T>C	ENSP00000293404:p.Leu285Pro	82.0	0.0	.		60.0	14.0	.	NM_153006	B2RAZ9|Q8IWR4	Missense_Mutation	SNP	ENST00000293404.3	hg19	CCDS11473.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.478496	0.84747	.	.	ENSG00000161653	ENST00000541745;ENST00000293404	D	0.94576	-3.46	4.49	4.49	0.54785	Aspartate/glutamate/uridylate kinase (2);	0.000000	0.64402	D	0.000014	D	0.96815	0.8960	M	0.79926	2.475	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.98	D	0.97143	0.9826	10	0.87932	D	0	-18.0769	11.7799	0.52008	0.0:0.0:0.0:1.0	.	119;285	Q2NKP2;Q8N159	.;NAGS_HUMAN	P	119;285	ENSP00000293404:L285P	ENSP00000293404:L285P	L	+	2	0	NAGS	39439070	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	6.544000	0.73878	1.883000	0.54544	0.374000	0.22700	CTG	.	.	.	none		0.662	NAGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457660.1	NM_153006		C	42083544	T	C	42083544	3	2	141	1	0	0	0	0	1	0	0	0	10152	1580	55	3	864	3	NAGS	17	42083544	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08	3829943	42083544	39111666	55	8561											
TMEM146	257062	hgsc.bcm.edu	37	chr19	5744442	5744442	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgtttgtttcataggcagAaatcattgggtctttaggcg	8	16	11	6	1	4	1	2	0	2	1	4	1	4	1	0	3	0	3	0	3	3	6			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr19:5744442A>G	ENST00000381624.3	+	8	639	c.578A>G	c.(577-579)gAa>gGa	p.E193G	CATSPERD_ENST00000381614.2_5'UTR	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	193					multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)											TCATAGGCAGAAATCATTGGG	0.368																																					p.E193G		Atlas-SNP	.											.	.	.	.	0			c.A578G						PASS	.						177	156	162					19																	5744442		1821	4093	5914	SO:0001583	missense	257062	exon8			AGGCAGAAATCAT	BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898			28598	protein-coding gene	gene with protein product			"transmembrane protein 146"	TMEM146		21224844	Standard	NM_152784		Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036	ENST00000381624.3:c.578A>G	chr19.hg19:g.5744442A>G	ENSP00000371037:p.Glu193Gly	112.0	0.0	.		125.0	16.0	.	NM_152784	Q6ZRP1	Missense_Mutation	SNP	ENST00000381624.3	hg19	CCDS12149.2	.	.	.	.	.	.	.	.	.	.	A	11.28	1.590905	0.28357	.	.	ENSG00000174898	ENST00000394548;ENST00000381624	T	0.16597	2.33	2.61	-0.961	0.10337	.	1.018470	0.07916	U	0.975045	T	0.14227	0.0344	L	0.60455	1.87	0.09310	N	0.999999	P	0.46512	0.879	B	0.40009	0.316	T	0.20974	-1.0259	10	0.66056	D	0.02	.	0.3749	0.00385	0.3898:0.2527:0.1457:0.2118	.	193	Q86XM0	TM146_HUMAN	G	119;193	ENSP00000371037:E193G	ENSP00000371037:E193G	E	+	2	0	TMEM146	5695442	0.000000	0.05858	0.000000	0.03702	0.094000	0.18550	0.059000	0.14322	-0.283000	0.09115	0.260000	0.18958	GAA	.	.	.	none		0.368	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784		G	5744442	A	G	5744442	3	3	141	1	0	0	0	0	1	0	0	0	16072	246	9	3	608	3	TMEM146	19	5744442	Missense_Mutation	SNP	A	TCGA-BQ-7059-01A-11D-1961-08		5744442	53384541	56	8562											
C3	718	hgsc.bcm.edu	37	chr19	6711075	6711075	+	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	gttgacgttgagggtctcccCgggtctgagctctgtacgta	5	12	14	10	3	3	3	0	3	3	0	4	3	3	3	2	2	2	5	2	2	2	4	rs148820222		TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr19:6711075C>A	ENST00000245907.6	-	12	1494	c.1402G>T	c.(1402-1404)Ggg>Tgg	p.G468W		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	468					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)	AGGGTCTCCCCGGGTCTGAGC	0.597																																					p.G468W		Atlas-SNP	.											.	C3	192	.	0			c.G1402T						PASS	.						232	206	215					19																	6711075		2203	4300	6503	SO:0001583	missense	718	exon12			TCTCCCCGGGTCT	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.1402G>T	chr19.hg19:g.6711075C>A	ENSP00000245907:p.Gly468Trp	234.0	0.0	.		176.0	8.0	.	NM_000064	A7E236	Missense_Mutation	SNP	ENST00000245907.6	hg19	CCDS32883.1	.	.	.	.	.	.	.	.	.	.	C	13.98	2.399751	0.42512	.	.	ENSG00000125730	ENST00000245907	T	0.78707	-1.2	5.03	5.03	0.67393	Alpha-2-macroglobulin, N-terminal 2 (1);	0.273635	0.41194	D	0.000922	D	0.91126	0.7206	M	0.94021	3.485	0.41715	D	0.989475	D	0.89917	1.0	D	0.91635	0.999	D	0.93675	0.6993	10	0.87932	D	0	.	17.1311	0.86726	0.0:1.0:0.0:0.0	.	468	P01024	CO3_HUMAN	W	468	ENSP00000245907:G468W	ENSP00000245907:G468W	G	-	1	0	C3	6662075	0.672000	0.27530	0.279000	0.24732	0.004000	0.04260	3.025000	0.49681	2.344000	0.79699	0.557000	0.71058	GGG	.	C|1.000;T|0.000	.	alt		0.597	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		A	6711075	C	A	6711075	3	1	141	1	0	0	0	0	1	0	0	0	2206	652	23	4	3709	4	C3	19	6711075	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	966633	6711075	52417908	57	8563											
QTRT1	81890	hgsc.bcm.edu	37	chr19	10823458	10823458	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggctctgccctggtgcccActgggaacctgcagttgagg	5	10	14	12	0	1	1	0	1	1	0	1	2	1	2	3	4	4	3	3	4	1	2	rs568561273		TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr19:10823458A>G	ENST00000250237.5	+	8	896	c.886A>G	c.(886-888)Act>Gct	p.T296A		NM_031209.2	NP_112486.1	Q9BXR0	TGT_HUMAN	queuine tRNA-ribosyltransferase 1	296					queuosine biosynthetic process (GO:0008616)|tRNA modification (GO:0006400)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|queuine tRNA-ribosyltransferase activity (GO:0008479)			large_intestine(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	12			Epithelial(33;1.55e-05)|all cancers(31;3.42e-05)			CCTGGTGCCCACTGGGAACCT	0.622																																					p.T296A		Atlas-SNP	.											.	QTRT1	25	.	0			c.A886G						PASS	.						118	111	113					19																	10823458		2203	4300	6503	SO:0001583	missense	81890	exon8			GTGCCCACTGGGA	AF302783	CCDS12248.1	19p13.3	2014-06-11	2008-07-31		ENSG00000213339	ENSG00000213339	2.4.2.29		23797	protein-coding gene	gene with protein product	"tRNA-guanine transglycosylase"	609615				20354154	Standard	NM_031209		Approved	TGT	uc002mpr.3	Q9BXR0		ENST00000250237.5:c.886A>G	chr19.hg19:g.10823458A>G	ENSP00000250237:p.Thr296Ala	249.0	0.0	.		228.0	44.0	.	NM_031209	B4DFM7|Q96BQ4|Q9BXQ9	Missense_Mutation	SNP	ENST00000250237.5	hg19	CCDS12248.1	.	.	.	.	.	.	.	.	.	.	A	0.571	-0.841326	0.02692	.	.	ENSG00000213339	ENST00000250237	.	.	.	3.87	3.87	0.44632	.	0.163748	0.42821	U	0.000652	T	0.28067	0.0692	L	0.43923	1.385	0.26123	N	0.980526	B	0.14805	0.011	B	0.17433	0.018	T	0.21143	-1.0254	9	0.07990	T	0.79	-8.686	6.4838	0.22077	0.7837:0.0:0.0:0.2163	.	296	Q9BXR0	TGT_HUMAN	A	296	.	ENSP00000250237:T296A	T	+	1	0	QTRT1	10684458	1.000000	0.71417	0.998000	0.56505	0.601000	0.36947	5.570000	0.67398	1.631000	0.50456	0.379000	0.24179	ACT	.	.	.	none		0.622	QTRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452086.1	NM_031209		G	10823458	A	G	10823458	3	3	141	1	0	0	0	0	1	0	0	0	12898	159	6	3	916	3	QTRT1	19	10823458	Missense_Mutation	SNP	A	TCGA-BQ-7059-01A-11D-1961-08	4112383	10823458	48305525	58	8564											
NOTCH3	4854	hgsc.bcm.edu	37	chr19	15289675	15289675	+	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	ggtcagcccacccccaggacCcgggctaggacggcactggc	7	3	14	17	2	1	0	1	0	0	0	1	2	1	2	4	6	1	2	4	6	1	1			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr19:15289675C>G	ENST00000263388.2	-	23	3871	c.3796G>C	c.(3796-3798)Ggt>Cgt	p.G1266R		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	1266	EGF-like 32. {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)			CCCCCAGGACCCGGGCTAGGA	0.652																																					p.G1266R		Atlas-SNP	.											.	NOTCH3	340	.	0			c.G3796C						PASS	.						36	32	33					19																	15289675		2198	4296	6494	SO:0001583	missense	4854	exon23			CAGGACCCGGGCT	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.3796G>C	chr19.hg19:g.15289675C>G	ENSP00000263388:p.Gly1266Arg	25.0	0.0	.		17.0	5.0	.	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	hg19	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	C	13.76	2.333583	0.41297	.	.	ENSG00000074181	ENST00000263388;ENST00000539383	D	0.92099	-2.97	3.54	2.41	0.29592	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.94016	0.8083	M	0.72894	2.215	0.09310	N	1	P;D	0.89917	0.566;1.0	B;D	0.87578	0.131;0.998	D	0.84646	0.0698	9	0.54805	T	0.06	.	4.1418	0.10196	0.0:0.7058:0.0:0.2942	.	1217;1266	Q59FL3;Q9UM47	.;NOTC3_HUMAN	R	1266;1216	ENSP00000263388:G1266R	ENSP00000263388:G1266R	G	-	1	0	NOTCH3	15150675	0.011000	0.17503	0.110000	0.21437	0.729000	0.41735	0.970000	0.29383	1.813000	0.52934	0.561000	0.74099	GGT	.	.	.	none		0.652	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		G	15289675	C	G	15289675	3	3	141	1	0	0	0	0	1	0	0	0	10557	623	22	4	3213	4	NOTCH3	19	15289675	Missense_Mutation	SNP	C	TCGA-BQ-7059-01A-11D-1961-08	4466217	15289675	43839308	59	8565											
GPR32	2854	hgsc.bcm.edu	37	chr19	51273914	51273914	+	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	gacaggcaacctggggtcctGacacgtgatcgctcttgttc	7	10	12	12	2	1	2	0	2	1	0	4	3	2	2	2	3	1	3	2	3	1	2			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr19:51273914G>C	ENST00000270590.4	+	1	194	c.57G>C	c.(55-57)ctG>ctC	p.L19L		NM_001506.1	NP_001497.1	O75388	GPR32_HUMAN	G protein-coupled receptor 32	19					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(4)|endometrium(4)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	29		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		CTGGGGTCCTGACACGTGATC	0.512																																					p.L19L	Esophageal Squamous(113;152 1581 5732 15840 44398)	Atlas-SNP	.											.	GPR32	68	.	0			c.G57C						PASS	.						80	65	70					19																	51273914		2203	4300	6503	SO:0001819	synonymous_variant	2854	exon1			GGTCCTGACACGT	AF045764	CCDS12801.1	19q13.33	2012-08-20			ENSG00000142511	ENSG00000142511		"GPCR / Class A : Resolvin receptors"	4487	protein-coding gene	gene with protein product	"resolvin D1 receptor"	603195				9653656	Standard	NM_001506		Approved	RVDR1	uc010ycf.3	O75388		ENST00000270590.4:c.57G>C	chr19.hg19:g.51273914G>C		51.0	0.0	.		45.0	8.0	.	NM_001506	Q502U7|Q6NWS5	Silent	SNP	ENST00000270590.4	hg19	CCDS12801.1																																																																																			.	.	.	none		0.512	GPR32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465016.1			C	51273914	G	C	51273914	2	2	141	1	0	0	0	0	0	0	0	1	6695	1277	45	4		4	GPR32	19	51273914	Silent	SNP	G	TCGA-BQ-7059-01A-11D-1961-08	35984239	51273914	7855069	60	8566											
ZNF416	55659	hgsc.bcm.edu	37	chr19	58084258	58084258	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caatgttcaataaggttggaActttggctaaaagatttccc	13	13	8	7	0	1	1	1	0	0	1	2	2	2	2	1	3	1	3	1	3	6	6			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr19:58084258A>G	ENST00000196489.3	-	4	1236	c.1014T>C	c.(1012-1014)agT>agC	p.S338S		NM_017879.1	NP_060349.1	Q9BWM5	ZN416_HUMAN	zinc finger protein 416	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)			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)		TAAGGTTGGAACTTTGGCTAA	0.428																																					p.S338S		Atlas-SNP	.											.	ZNF416	50	.	0			c.T1014C						PASS	.						96	93	94					19																	58084258		2203	4300	6503	SO:0001819	synonymous_variant	55659	exon4			GTTGGAACTTTGG	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.1014T>C	chr19.hg19:g.58084258A>G		74.0	0.0	.		75.0	15.0	.	NM_017879	Q9NWW8	Silent	SNP	ENST00000196489.3	hg19	CCDS12954.1																																																																																			.	.	.	none		0.428	ZNF416-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466787.1	NM_017879		G	58084258	A	G	58084258	2	3	141	1	0	0	0	0	0	0	0	1	17905	40	2	3		3	ZNF416	19	58084258	Silent	SNP	A	TCGA-BQ-7059-01A-11D-1961-08	6810344	58084258	1044725	61	8567											
CSE1L	1434	hgsc.bcm.edu	37	chr20	47691344	47691344	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctgatgaagaagcatttgaAgataattctgaggagtacat	15	11	11	4	0	1	6	0	4	1	2	1	7	1	7	0	1	2	3	0	1	5	4			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr20:47691344A>G	ENST00000262982.2	+	11	1212	c.1089A>G	c.(1087-1089)gaA>gaG	p.E363E	CSE1L_ENST00000542325.1_Silent_p.E146E|CSE1L_ENST00000396192.3_Silent_p.E307E	NM_001256135.1|NM_001316.3	NP_001243064.1|NP_001307.2	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like (yeast)	363					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	importin-alpha export receptor activity (GO:0008262)			breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(11)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	35			BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)			AAGCATTTGAAGATAATTCTG	0.383																																					p.E363E		Atlas-SNP	.											.	CSE1L	83	.	0			c.A1089G						PASS	.						172	158	163					20																	47691344		2203	4300	6503	SO:0001819	synonymous_variant	1434	exon11			ATTTGAAGATAAT	U33286	CCDS13412.1, CCDS58773.1	20q13	2013-05-01	2001-11-28		ENSG00000124207	ENSG00000124207		"Exportins"	2431	protein-coding gene	gene with protein product	"cellular apoptosis susceptibility"	601342	"chromosome segregation 1 (yeast homolog)-like"			8963895, 7479798	Standard	NM_001316		Approved	CAS, XPO2, CSE1	uc002xty.4	P55060	OTTHUMG00000033046	ENST00000262982.2:c.1089A>G	chr20.hg19:g.47691344A>G		48.0	0.0	.		58.0	12.0	.	NM_001316	A3RLL6|B2R5T4|E1P5Y0|F8W904|O75432|Q32M40|Q9H5B7|Q9NTS0|Q9UP98|Q9UP99|Q9UPA0	Silent	SNP	ENST00000262982.2	hg19	CCDS13412.1																																																																																			.	.	.	none		0.383	CSE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080345.2	NM_001316		G	47691344	A	G	47691344	2	3	141	1	0	0	0	0	0	0	0	1	3932	69	3	3		3	CSE1L	20	47691344	Silent	SNP	A	TCGA-BQ-7059-01A-11D-1961-08		47691344	15334176	62	8568											
TXN2	25828	hgsc.bcm.edu	37	chr22	36876727	36876727	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcaaggagatcctcgtggtgTatattgtccgggctgggttg	6	13	15	7	2	1	1	1	0	0	1	4	2	3	1	2	4	0	3	2	4	3	4			TCGA-BQ-7059-01A-11D-1961-08	TCGA-BQ-7059-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9beec2fe-169d-4c3d-b177-f0d7bd9e5e96	bdab2c62-1568-47e5-b8f6-99ada040a736	g.chr22:36876727T>C	ENST00000216185.2	-	2	624	c.158A>G	c.(157-159)tAc>tGc	p.Y53C	TXN2_ENST00000487725.1_5'UTR|TXN2_ENST00000416967.1_De_novo_Start_OutOfFrame|TXN2_ENST00000403313.1_Missense_Mutation_p.Y53C			Q99757	THIOM_HUMAN	thioredoxin 2	53					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						CCTCGTGGTGTATATTGTCCG	0.542																																					p.Y53C		Atlas-SNP	.											.	TXN2	15	.	0			c.A158G						PASS	.						162	137	145					22																	36876727		2203	4300	6503	SO:0001583	missense	25828	exon2			GTGGTGTATATTG	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.158A>G	chr22.hg19:g.36876727T>C	ENSP00000216185:p.Tyr53Cys	117.0	0.0	.		117.0	24.0	.	NM_012473	Q5JZA0|Q6FH60|Q9UH29	Missense_Mutation	SNP	ENST00000216185.2	hg19	CCDS13928.1	.	.	.	.	.	.	.	.	.	.	t	4.360	0.066374	0.08388	.	.	ENSG00000100348	ENST00000216185;ENST00000403313	T;T	0.11495	2.77;2.77	5.59	-4.59	0.03400	Thioredoxin-like fold (1);	1.054490	0.07330	N	0.879042	T	0.07413	0.0187	L	0.47716	1.5	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44559	-0.9320	10	0.38643	T	0.18	.	0.2548	0.00210	0.3331:0.1924:0.2444:0.2301	.	53	Q99757	THIOM_HUMAN	C	53	ENSP00000216185:Y53C;ENSP00000385393:Y53C	ENSP00000216185:Y53C	Y	-	2	0	TXN2	35206673	0.001000	0.12720	0.004000	0.12327	0.028000	0.11728	-0.205000	0.09411	-0.499000	0.06623	-0.459000	0.05422	TAC	.	.	.	none		0.542	TXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319016.1	NM_012473		C	36876727	T	C	36876727	3	2	141	1	0	0	0	0	1	0	0	0	16803	1638	57	3	354	3	TXN2	22	36876727	Missense_Mutation	SNP	T	TCGA-BQ-7059-01A-11D-1961-08		36876727	14427839	63	8569											
MUL1	79594	hgsc.bcm.edu	37	chr1	20827614	20827614	+	Frame_Shift_Del	DEL	G	G	-																															gccttgtttgggcggctgcaGgcggacagagttgttgtcca																										TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr1:20827614delG	ENST00000264198.3	-	4	764	c.628delC	c.(628-630)ctgfs	p.L210fs		NM_024544.2	NP_078820.2	Q969V5	MUL1_HUMAN	mitochondrial E3 ubiquitin protein ligase 1	210					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|cellular response to exogenous dsRNA (GO:0071360)|mitochondrial fission (GO:0000266)|mitochondrion localization (GO:0051646)|negative regulation of cell growth (GO:0030308)|negative regulation of chemokine (C-C motif) ligand 5 production (GO:0071650)|negative regulation of defense response to virus by host (GO:0050689)|negative regulation of innate immune response (GO:0045824)|negative regulation of mitochondrial fusion (GO:0010637)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein sumoylation (GO:0033235)|protein stabilization (GO:0050821)|protein sumoylation (GO:0016925)|protein ubiquitination (GO:0016567)|regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901028)	cytoplasm (GO:0005737)|integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	identical protein binding (GO:0042802)|signal transducer activity (GO:0004871)|SUMO ligase activity (GO:0019789)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(5)	11		Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00748)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000137)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.00124)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)		GGCGGCTGCAGGCGGACAGAG	0.607																																					p.L210fs		Atlas-INDEL	.											.	MUL1	34	.	0			c.629delT						PASS	.						87	84	85					1																	20827614		2203	4300	6503	SO:0001589	frameshift_variant	79594	exon4			.	BC014010	CCDS208.1	1p36.12	2013-01-11	2010-09-17	2008-03-26	ENSG00000090432	ENSG00000090432		"RING-type (C3HC4) zinc fingers"	25762	protein-coding gene	gene with protein product	"ring finger protein 218", "mitochondria-anchored protein ligase", "growth inhibition and death E3 ligase", "mitochondrial ubiquitin ligase activator of NFKB 1"	612037	"chromosome 1 open reading frame 166"	C1orf166		18591963, 12761501, 18213395, 18207745	Standard	NM_024544		Approved	FLJ12875, MULAN, RNF218, MAPL, GIDE	uc001bdi.4	Q969V5	OTTHUMG00000002838	ENST00000264198.3:c.628delC	chr1.hg19:g.20827614delG	ENSP00000264198:p.Leu210fs	145.0	0.0	0		142.0	45.0	0.316901	NM_024544	B5M497|Q7Z431|Q9H9B5	Frame_Shift_Del	DEL	ENST00000264198.3	hg19	CCDS208.1																																																																																			.	.	.	none		0.607	MUL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007951.1	NM_024544		-	20827614	G	-	20827614	7	5	142	1	0	1	0	1	0	0	0	0	9991	991	35	0	434	0	MUL1	1	20827614	Frame_Shift_Del	DEL	G	TCGA-BQ-7060-01A-11D-1961-08		20827614	228423007	1	8570											
EPHA8	2046	hgsc.bcm.edu	37	chr1	22903099	22903099	+	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	agcaagcgcggcttctacctGgccttccaggacataggtgc	8	8	12	13	2	1	0	0	0	1	0	2	1	2	1	3	4	4	2	3	4	3	4			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr1:22903099G>T	ENST00000166244.3	+	3	621	c.549G>T	c.(547-549)ctG>ctT	p.L183L	EPHA8_ENST00000374644.4_Silent_p.L183L|EPHA8_ENST00000538803.1_Silent_p.L183L	NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	183	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GCTTCTACCTGGCCTTCCAGG	0.617																																					p.L183L		Atlas-SNP	.											.	EPHA8	221	.	0			c.G549T						PASS	.						73	66	69					1																	22903099		2203	4300	6503	SO:0001819	synonymous_variant	2046	exon3			CTACCTGGCCTTC	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.549G>T	chr1.hg19:g.22903099G>T		74.0	0.0	.		69.0	25.0	.	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Silent	SNP	ENST00000166244.3	hg19	CCDS225.1																																																																																			.	.	.	none		0.617	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526		T	22903099	G	T	22903099	2	4	142	1	0	0	0	0	0	0	0	1	5175	1335	47	4		4	EPHA8	1	22903099	Silent	SNP	G	TCGA-BQ-7060-01A-11D-1961-08	2075485	22903099	226347522	2	8571											
ZNF619	285267	hgsc.bcm.edu	37	chr3	40529349	40529349	+	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	tggttcagcatcagcgagttCacactggggagaaaccttat	11	10	11	9	1	3	1	3	0	0	1	3	3	3	1	1	3	3	3	1	3	2	3			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr3:40529349C>T	ENST00000314686.5	+	6	1705	c.1300C>T	c.(1300-1302)Cac>Tac	p.H434Y	ZNF619_ENST00000522736.1_Missense_Mutation_p.H441Y|ZNF619_ENST00000432264.2_Missense_Mutation_p.H450Y|ZNF619_ENST00000456778.1_Missense_Mutation_p.H406Y|ZNF619_ENST00000521353.1_Missense_Mutation_p.H490Y|ZNF619_ENST00000520737.1_3'UTR|ZNF619_ENST00000429348.2_Missense_Mutation_p.H450Y|ZNF619_ENST00000447116.2_Missense_Mutation_p.H490Y			Q8N2I2	ZN619_HUMAN	zinc finger protein 619	434					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		TCAGCGAGTTCACACTGGGGA	0.463																																					p.H490Y		Atlas-SNP	.											.	ZNF619	57	.	0			c.C1468T						PASS	.						92	95	94					3																	40529349		2203	4300	6503	SO:0001583	missense	285267	exon6			CGAGTTCACACTG	AK075245	CCDS46801.1, CCDS46802.1, CCDS46803.1	3p21.33	2013-01-08			ENSG00000177873	ENSG00000177873		"Zinc fingers, C2H2-type", "-"	26910	protein-coding gene	gene with protein product							Standard	NM_001145083		Approved	FLJ90764	uc011azb.2	Q8N2I2	OTTHUMG00000131391	ENST00000314686.5:c.1300C>T	chr3.hg19:g.40529349C>T	ENSP00000322529:p.His434Tyr	84.0	0.0	.		115.0	64.0	.	NM_001145082	B4E271|C9JRN5|D4PHA2|E9PCD9	Missense_Mutation	SNP	ENST00000314686.5	hg19		.	.	.	.	.	.	.	.	.	.	C	16.06	3.017099	0.54576	.	.	ENSG00000177873	ENST00000314686;ENST00000447116;ENST00000429348;ENST00000456778;ENST00000442066;ENST00000522736;ENST00000521353;ENST00000432264	T;T;T;T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27	2.44	2.44	0.29823	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.82010	0.4944	M	0.87269	2.87	0.30841	N	0.735643	D;D;D;D;D;D	0.89917	0.999;0.998;0.998;1.0;0.998;0.999	D;D;D;D;D;D	0.91635	0.996;0.982;0.976;0.999;0.976;0.996	T	0.79495	-0.1780	9	0.87932	D	0	.	10.5917	0.45314	0.0:1.0:0.0:0.0	.	406;450;490;392;441;434	B4E271;C9JRN5;E9PCD9;B7Z9B3;Q17RW3;Q8N2I2	.;.;.;.;.;ZN619_HUMAN	Y	434;490;450;406;71;441;490;450	ENSP00000322529:H434Y;ENSP00000411132:H490Y;ENSP00000398024:H450Y;ENSP00000397232:H406Y;ENSP00000428004:H441Y;ENSP00000430705:H490Y;ENSP00000388710:H450Y	ENSP00000322529:H434Y	H	+	1	0	ZNF619	40504353	0.998000	0.40836	0.972000	0.41901	0.869000	0.49853	3.961000	0.56759	1.376000	0.46267	0.563000	0.77884	CAC	.	.	.	none		0.463	ZNF619-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000254180.2	NM_173656		T	40529349	C	T	40529349	3	4	142	1	0	0	0	0	1	0	0	0	18055	826	29	2	1508	2	ZNF619	3	40529349	Missense_Mutation	SNP	C	TCGA-BQ-7060-01A-11D-1961-08		40529349	157493081	3	8572											
RPL29	6159	hgsc.bcm.edu	37	chr3	52029445	52029445	+	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	ggcccaaaaaacttacactgGttgtgtgtggtgtggttctt	8	14	12	7	0	1	0	0	0	1	0	1	0	1	0	1	4	2	2	1	4	4	4			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr3:52029445G>A	ENST00000466397.1	-	2	173	c.33C>T	c.(31-33)aaC>aaT	p.N11N	RPL29_ENST00000475248.1_Silent_p.N11N|RPL29_ENST00000481629.1_Silent_p.N11N|RPL29_ENST00000294189.6_Silent_p.N11N|RPL29_ENST00000495383.1_Silent_p.N11N|RPL29_ENST00000479017.1_Silent_p.N11N			P47914	RL29_HUMAN	ribosomal protein L29	11					cellular protein metabolic process (GO:0044267)|embryo implantation (GO:0007566)|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)	heparin binding (GO:0008201)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		ACTTACACTGGTTGTGTGTGG	0.567																																					p.N11N		Atlas-SNP	.											.	RPL29	8	.	0			c.C33T						PASS	.						130	106	114					3																	52029445		2203	4300	6503	SO:0001819	synonymous_variant	6159	exon2			ACACTGGTTGTGT	U10248	CCDS2845.1	3p21.3-p21.2	2013-03-11			ENSG00000162244	ENSG00000162244		"L ribosomal proteins"	10331	protein-coding gene	gene with protein product	"60S ribosomal protein L29", "heparin/heparan sulfate-interacting protein", "HP/HS-interacting protein", "heparin/heparan sulfate-binding protein", "cell surface heparin-binding protein HIP"	601832	"ribosomal protein L29 pseudogene 10"	RPL29P10		8597591	Standard	NM_000992		Approved	HIP, HUMRPL29, L29	uc003dcs.3	P47914	OTTHUMG00000155262	ENST00000466397.1:c.33C>T	chr3.hg19:g.52029445G>A		106.0	0.0	.		116.0	26.0	.	NM_000992	A8K0H3|B2R4M8|Q6IPY3	Silent	SNP	ENST00000466397.1	hg19	CCDS2845.1																																																																																			.	.	.	none		0.567	RPL29-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349680.2	NM_000992		A	52029445	G	A	52029445	2	1	142	1	0	0	0	0	0	0	0	1	13591	1252	44	2		2	RPL29	3	52029445	Silent	SNP	G	TCGA-BQ-7060-01A-11D-1961-08	11500096	52029445	145992985	4	8573											
POLQ	10721	hgsc.bcm.edu	37	chr3	121168266	121168266	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccattccataaatgatcccaTagcaaatctgaaagggagtc	15	9	7	10	0	1	2	0	2	1	0	4	3	3	3	3	1	1	1	3	1	5	3			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr3:121168266T>C	ENST00000264233.5	-	26	7288	c.7160A>G	c.(7159-7161)tAt>tGt	p.Y2387C		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	2387					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)		AATGATCCCATAGCAAATCTG	0.358								DNA polymerases (catalytic subunits)																													p.Y2387C	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.A7160G						PASS	.						166	164	164					3																	121168266		2203	4300	6503	SO:0001583	missense	10721	exon26			ATCCCATAGCAAA	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.7160A>G	chr3.hg19:g.121168266T>C	ENSP00000264233:p.Tyr2387Cys	343.0	1.0	.		395.0	195.0	.	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	hg19	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.113078	0.77210	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	D	0.98221	-4.8	5.26	5.26	0.73747	DNA-directed DNA polymerase, family A, palm domain (2);DNA-directed DNA polymerase, family A, conserved site (1);	0.061290	0.64402	D	0.000002	D	0.99184	0.9717	M	0.93854	3.465	0.45502	D	0.99846	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.99211	1.0876	10	0.87932	D	0	.	14.8334	0.70164	0.0:0.0:0.0:1.0	.	2387;1559	O75417;O75417-2	DPOLQ_HUMAN;.	C	2010;2387;2523	ENSP00000264233:Y2387C	ENSP00000264233:Y2387C	Y	-	2	0	POLQ	122650956	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.345000	0.79337	1.968000	0.57251	0.533000	0.62120	TAT	.	.	.	none		0.358	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		C	121168266	T	C	121168266	3	2	142	1	0	0	0	0	1	0	0	0	12215	1406	49	3	632	3	POLQ	3	121168266	Missense_Mutation	SNP	T	TCGA-BQ-7060-01A-11D-1961-08	69138821	121168266	76854164	5	8574											
KPNA4	3840	hgsc.bcm.edu	37	chr3	160249255	160249255	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaataatgtactcacttgtcAtctctttcaagacaatggac	14	13	5	9	0	4	1	3	0	1	1	5	2	4	2	0	1	1	1	0	1	5	4			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr3:160249255A>G	ENST00000334256.4	-	6	683	c.378T>C	c.(376-378)gaT>gaC	p.D126D		NM_002268.4	NP_002259.1	O00629	IMA3_HUMAN	karyopherin alpha 4 (importin alpha 3)	126					cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	protein transporter activity (GO:0008565)			breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)	22			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)			CTCACTTGTCATCTCTTTCAA	0.303																																					p.D126D		Atlas-SNP	.											.	KPNA4	50	.	0			c.T378C						PASS	.						78	85	83					3																	160249255		2202	4296	6498	SO:0001819	synonymous_variant	3840	exon6			CTTGTCATCTCTT	AB002533	CCDS3191.1	3q25.33	2013-02-14			ENSG00000186432	ENSG00000186432		"Importins", "Armadillo repeat containing"	6397	protein-coding gene	gene with protein product		602970				9168958, 9395085	Standard	NM_002268		Approved	QIP1, SRP3, IPOA3, MGC12217, MGC26703	uc003fdn.3	O00629	OTTHUMG00000159033	ENST00000334256.4:c.378T>C	chr3.hg19:g.160249255A>G		182.0	0.0	.		235.0	128.0	.	NM_002268	A8K4S6|D3DNM2|O00190	Silent	SNP	ENST00000334256.4	hg19	CCDS3191.1																																																																																			.	.	.	none		0.303	KPNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352960.1	NM_002268		G	160249255	A	G	160249255	2	3	142	1	0	0	0	0	0	0	0	1	8439	214	8	3		3	KPNA4	3	160249255	Silent	SNP	A	TCGA-BQ-7060-01A-11D-1961-08	39080989	160249255	37773175	6	8575											
DGKG	1608	hgsc.bcm.edu	37	chr3	186006591	186006591	+	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	ctggggattccgagcttgaaGaccgagggacggggggttcc	7	7	18	9	3	0	2	0	1	0	1	2	6	2	4	3	6	1	2	3	6	1	3			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr3:186006591G>A	ENST00000265022.3	-	6	991	c.452C>T	c.(451-453)tCt>tTt	p.S151F	DGKG_ENST00000344484.4_Missense_Mutation_p.S151F|DGKG_ENST00000544847.1_Missense_Mutation_p.S151F|DGKG_ENST00000382164.4_Missense_Mutation_p.S151F	NM_001080744.1|NM_001080745.1|NM_001346.2	NP_001074213.1|NP_001074214.1|NP_001337.2	P49619	DGKG_HUMAN	diacylglycerol kinase, gamma 90kDa	151	Poly-Ser.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|neuron development (GO:0048666)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	42	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	CGAGCTTGAAGACCGAGGGAC	0.552																																					p.S151F		Atlas-SNP	.											.	DGKG	98	.	0			c.C452T						PASS	.						138	151	147					3																	186006591		2203	4300	6503	SO:0001583	missense	1608	exon6			CTTGAAGACCGAG	AF020945	CCDS3274.1, CCDS43181.1, CCDS43182.1	3q27-q28	2013-01-10	2002-08-29		ENSG00000058866	ENSG00000058866	2.7.1.107	"EF-hand domain containing"	2853	protein-coding gene	gene with protein product		601854	"diacylglycerol kinase, gamma (90kD)"	DAGK3		8034597	Standard	NM_001080744		Approved		uc003fqa.3	P49619	OTTHUMG00000156617	ENST00000265022.3:c.452C>T	chr3.hg19:g.186006591G>A	ENSP00000265022:p.Ser151Phe	346.0	0.0	.		420.0	97.0	.	NM_001346	B2RAH4|Q2M1H4|Q5FWG1	Missense_Mutation	SNP	ENST00000265022.3	hg19	CCDS3274.1	.	.	.	.	.	.	.	.	.	.	G	14.12	2.439692	0.43326	.	.	ENSG00000058866	ENST00000265022;ENST00000344484;ENST00000382164;ENST00000544847;ENST00000538691	T;T;T;T	0.48522	0.81;0.81;0.81;0.81	5.74	1.92	0.25849	.	2.306020	0.01541	N	0.019244	T	0.42765	0.1217	L	0.38175	1.15	0.09310	N	1	B;B;B;B	0.31435	0.323;0.219;0.323;0.217	B;B;B;B	0.38378	0.272;0.188;0.272;0.092	T	0.20273	-1.0280	10	0.34782	T	0.22	.	3.4838	0.07611	0.1475:0.1347:0.5782:0.1396	.	151;151;151;151	F5GX27;P49619-2;P49619-3;P49619	.;.;.;DGKG_HUMAN	F	151;151;151;151;154	ENSP00000265022:S151F;ENSP00000339777:S151F;ENSP00000371599:S151F;ENSP00000440507:S151F	ENSP00000265022:S151F	S	-	2	0	DGKG	187489285	0.974000	0.33945	0.001000	0.08648	0.025000	0.11179	3.286000	0.51724	0.139000	0.18822	0.563000	0.77884	TCT	.	.	.	none		0.552	DGKG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344800.3			A	186006591	G	A	186006591	3	1	142	1	0	0	0	0	1	0	0	0	4471	942	33	2	2003	2	DGKG	3	186006591	Missense_Mutation	SNP	G	TCGA-BQ-7060-01A-11D-1961-08	25757336	186006591	12015839	7	8576											
LRBA	987	hgsc.bcm.edu	37	chr4	151271258	151271259	+	Frame_Shift_Ins	INS	-	-	AT																															cttgctgtttatagccaaaaINSatgagatcaatccattggtg																										TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr4:151271258_151271259insAT	ENST00000357115.3	-	49	7523_7524	c.7280_7281insAT	c.(7279-7281)attfs	p.I2427fs	LRBA_ENST00000510413.1_Frame_Shift_Ins_p.I2416fs|LRBA_ENST00000503716.1_5'UTR|LRBA_ENST00000535741.1_Frame_Shift_Ins_p.I2416fs|LRBA_ENST00000507224.1_Frame_Shift_Ins_p.I2416fs	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	2427	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)					TATAGCCAAAAATGAGATCAAT	0.391																																					p.I2427fs		Atlas-INDEL	.											.	LRBA	253	.	0			c.7281_7282insAT						PASS	.																																			SO:0001589	frameshift_variant	987	exon49			.	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.7279_7280dupAT	chr4.hg19:g.151271259_151271260dupAT	ENSP00000349629:p.Ile2427fs	81.0	0.0	0		70.0	12.0	0.171429	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Frame_Shift_Ins	INS	ENST00000357115.3	hg19	CCDS3773.1																																																																																			.	.	.	none		0.391	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			AT	151271259	-	AT	151271258	7	5	142	1	0	1	1	0	0	0	0	0	8938	10	1	0	1350	0	LRBA	4	151271258	Frame_Shift_Ins	INS	-	TCGA-BQ-7060-01A-11D-1961-08		151271258	39883018	8	8577											
NSD1	64324	hgsc.bcm.edu	37	chr5	176637880	176637880	+	Frame_Shift_Del	DEL	T	T	-																															aggctctcctttggccagcaTttctaaaagtgggaaagtgg																										TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr5:176637880delT	ENST00000439151.2	+	5	2525	c.2480delT	c.(2479-2481)attfs	p.I827fs	NSD1_ENST00000361032.4_Frame_Shift_Del_p.I724fs|NSD1_ENST00000347982.4_Frame_Shift_Del_p.I558fs|NSD1_ENST00000354179.4_Frame_Shift_Del_p.I558fs	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	827					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)		TTGGCCAGCATTTCTAAAAGT	0.413			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.I827fs		Atlas-INDEL	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.2479delA						PASS	.						69	70	69					5																	176637880		2203	4300	6503	SO:0001589	frameshift_variant	64324	exon5	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	.	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.2480delT	chr5.hg19:g.176637880delT	ENSP00000395929:p.Ile827fs	61.0	0.0	0		49.0	13.0	0.265306	NM_022455	Q96PD8|Q96RN7	Frame_Shift_Del	DEL	ENST00000439151.2	hg19	CCDS4412.1																																																																																			.	.	.	none		0.413	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		-	176637880	T	-	176637880	7	5	142	1	0	1	0	1	0	0	0	0	10676	1493	52	0	2494	0	NSD1	5	176637880	Frame_Shift_Del	DEL	T	TCGA-BQ-7060-01A-11D-1961-08		176637880	4277380	9	8578											
HSPA1A	3303	hgsc.bcm.edu	37	chr6	31784255	31784256	+	Frame_Shift_Ins	INS	-	-	CC																															aacaggctggtgaaccacttINScgtggaggagttcaagagaa																										TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr6:31784255_31784256insCC	ENST00000375651.5	+	1	965_966	c.722_723insCC	c.(721-726)ttcgtgfs	p.V242fs	HSPA1L_ENST00000375654.4_5'Flank|HSPA1A_ENST00000608703.1_Frame_Shift_Ins_p.V77fs|HSPA1L_ENST00000417199.3_5'Flank|HSPA1A_ENST00000458062.2_Frame_Shift_Ins_p.V151fs	NM_005345.5	NP_005336.3	P08107	HSP71_HUMAN	heat shock 70kDa protein 1A	242					ATP catabolic process (GO:0006200)|cellular heat acclimation (GO:0070370)|cellular response to heat (GO:0034605)|gene expression (GO:0010467)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of inclusion body assembly (GO:0090084)|negative regulation of protein ubiquitination (GO:0031397)|positive regulation of erythrocyte differentiation (GO:0045648)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)	aggresome (GO:0016235)|blood microparticle (GO:0072562)|centriole (GO:0005814)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|inclusion body (GO:0016234)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|double-stranded RNA binding (GO:0003725)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|poly(A) RNA binding (GO:0044822)|protein binding involved in protein folding (GO:0044183)|protein N-terminus binding (GO:0047485)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)|virus receptor activity (GO:0001618)			endometrium(1)|ovary(1)|stomach(1)	3						GTGAACCACTTCGTGGAGGAGT	0.609																																					p.F241fs		Atlas-INDEL	.											.	HSPA1A	9	.	0			c.722_723insCC						PASS	.																																			SO:0001589	frameshift_variant	3303	exon1			.	BC002453	CCDS34414.1	6p21.3	2012-10-02	2002-08-29		ENSG00000204389	ENSG00000204389		"Heat shock proteins / HSP70"	5232	protein-coding gene	gene with protein product		140550	"heat shock 70kD protein 1A"	HSPA1			Standard	NM_005345		Approved	HSP70-1	uc003nxj.3	P08107	OTTHUMG00000031201	Exception_encountered	chr6.hg19:g.31784255_31784256insCC	ENSP00000364802:p.Val242fs	132.0	0.0	0		116.0	13.0	0.112069	NM_005345	B4E3B6|P19790|Q5JQI4|Q5SP17|Q9UQL9|Q9UQM0	Frame_Shift_Ins	INS	ENST00000375651.5	hg19	CCDS34414.1																																																																																			.	.	.	none		0.609	HSPA1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076401.2			CC	31784256	-	CC	31784255	7	5	142	1	0	1	1	0	0	0	0	0	7415	1783	62	0	724	0	HSPA1A	6	31784255	Frame_Shift_Ins	INS	-	TCGA-BQ-7060-01A-11D-1961-08		31784255	139330812	10	8579											
HSPA1B	3304	hgsc.bcm.edu	37	chr6	31796449	31796450	+	Frame_Shift_Ins	INS	-	-	CC																															aacaggctggtgaaccacttINScgtggaggagttcaagagaa																										TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr6:31796449_31796450insCC	ENST00000375650.3	+	1	938_939	c.722_723insCC	c.(721-726)ttcgtgfs	p.V242fs	HSPA1B_ENST00000545241.1_Frame_Shift_Ins_p.V151fs	NM_005346.4	NP_005337.2	P08107	HSP71_HUMAN	heat shock 70kDa protein 1B	242					ATP catabolic process (GO:0006200)|cellular heat acclimation (GO:0070370)|cellular response to heat (GO:0034605)|gene expression (GO:0010467)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of inclusion body assembly (GO:0090084)|negative regulation of protein ubiquitination (GO:0031397)|positive regulation of erythrocyte differentiation (GO:0045648)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)	aggresome (GO:0016235)|blood microparticle (GO:0072562)|centriole (GO:0005814)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|inclusion body (GO:0016234)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|double-stranded RNA binding (GO:0003725)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|poly(A) RNA binding (GO:0044822)|protein binding involved in protein folding (GO:0044183)|protein N-terminus binding (GO:0047485)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)|virus receptor activity (GO:0001618)			breast(1)|large_intestine(1)|prostate(1)	3						GTGAACCACTTCGTGGAGGAGT	0.609																																					p.F241fs		Atlas-INDEL	.											.	HSPA1B	5	.	0			c.722_723insCC						PASS	.																																			SO:0001589	frameshift_variant	3304	exon1			.		CCDS34415.1	6p21.3	2011-09-02	2002-08-29		ENSG00000204388	ENSG00000204388		"Heat shock proteins / HSP70"	5233	protein-coding gene	gene with protein product		603012	"heat shock 70kD protein 1B"			1700760	Standard	NM_005346		Approved	HSP70-2	uc003nxk.2	P08107	OTTHUMG00000031202	Exception_encountered	chr6.hg19:g.31796449_31796450insCC	ENSP00000364801:p.Val242fs	111.0	0.0	0		96.0	14.0	0.145833	NM_005346	B4E3B6|P19790|Q5JQI4|Q5SP17|Q9UQL9|Q9UQM0	Frame_Shift_Ins	INS	ENST00000375650.3	hg19	CCDS34415.1																																																																																			.	.	.	none		0.609	HSPA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076402.2			CC	31796450	-	CC	31796449	7	5	142	1	0	1	1	0	0	0	0	0	7416	1783	62	0	724	0	HSPA1B	6	31796449	Frame_Shift_Ins	INS	-	TCGA-BQ-7060-01A-11D-1961-08	12194	31796449	139318618	11	8580											
MYO6	4646	hgsc.bcm.edu	37	chr6	76542650	76542650	+	Frame_Shift_Del	DEL	A	A	-																															gccggcaaaacagaaaatacAaaatttgttctaaggtgagt																										TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr6:76542650delA	ENST00000369977.3	+	6	622	c.483delA	c.(481-483)acafs	p.T161fs	MYO6_ENST00000369975.1_Frame_Shift_Del_p.T161fs|MYO6_ENST00000369985.4_Frame_Shift_Del_p.T161fs|MYO6_ENST00000369981.3_Frame_Shift_Del_p.T161fs	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	161	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)		CAGAAAATACAAAATTTGTTC	0.413																																					p.T161fs		Atlas-INDEL	.											.	MYO6	124	.	0			c.482delC						PASS	.						74	80	78					6																	76542650		2203	4300	6503	SO:0001589	frameshift_variant	4646	exon6			.	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.483delA	chr6.hg19:g.76542650delA	ENSP00000358994:p.Thr161fs	107.0	0.0	0		140.0	43.0	0.307143	NM_004999	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Frame_Shift_Del	DEL	ENST00000369977.3	hg19	CCDS34487.1																																																																																			.	.	.	none		0.413	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999		-	76542650	A	-	76542650	7	5	142	1	0	1	0	1	0	0	0	0	10088	117	5	0	501	0	MYO6	6	76542650	Frame_Shift_Del	DEL	A	TCGA-BQ-7060-01A-11D-1961-08	44746201	76542650	94572417	12	8581											
C7orf57	136288	hgsc.bcm.edu	37	chr7	48081007	48081007	+	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	gcgtcccagatcccaggtctCagcaatttgggagactcaca	10	8	10	13	1	2	2	2	0	1	2	5	3	4	2	2	2	1	1	2	2	1	1			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr7:48081007C>A	ENST00000348904.3	+	3	344	c.132C>A	c.(130-132)ctC>ctA	p.L44L	C7orf57_ENST00000430738.1_Silent_p.L89L|C7orf57_ENST00000420324.1_Silent_p.L89L|C7orf57_ENST00000539619.1_Silent_p.L44L|C7orf57_ENST00000435376.1_5'UTR	NM_001100159.2	NP_001093629.1	Q8NEG2	CG057_HUMAN	chromosome 7 open reading frame 57	44										breast(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	9						TCCCAGGTCTCAGCAATTTGG	0.542																																					p.L44L		Atlas-SNP	.											.	C7orf57	59	.	0			c.C132A						PASS	.						51	55	54					7																	48081007		1920	4141	6061	SO:0001819	synonymous_variant	136288	exon3			AGGTCTCAGCAAT	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.132C>A	chr7.hg19:g.48081007C>A		88.0	0.0	.		100.0	46.0	.	NM_001100159	C9JBJ8	Silent	SNP	ENST00000348904.3	hg19	CCDS47583.1																																																																																			.	.	.	none		0.542	C7orf57-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341745.1	NM_001100159		A	48081007	C	A	48081007	2	1	142	1	0	0	0	0	0	0	0	1	2406	813	29	4		4	C7orf57	7	48081007	Silent	SNP	C	TCGA-BQ-7060-01A-11D-1961-08		48081007	111057656	13	8582											
ST7	7982	hgsc.bcm.edu	37	chr7	116863027	116863027	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctcaatctcaacatttccAaaactgaactcatcacccct	14	10	1	16	0	4	1	4	1	1	0	6	1	5	1	4	0	3	0	4	0	5	1			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr7:116863027A>G	ENST00000265437.5	+	16	1965	c.1751A>G	c.(1750-1752)cAa>cGa	p.Q584R	ST7_ENST00000393451.3_Intron|ST7_ENST00000393443.1_Intron|ST7_ENST00000393444.3_Intron|ST7_ENST00000393449.1_Intron|ST7_ENST00000393446.2_Intron|ST7_ENST00000393447.4_Intron|ST7_ENST00000432298.1_Intron|ST7_ENST00000422922.1_Intron|ST7_ENST00000323984.3_Intron	NM_021908.2	NP_068708.1	Q9Y561	LRP12_HUMAN	suppression of tumorigenicity 7	0					endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(1)	21	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		caacatttccaaaactgaact	0.517																																					p.Q584R		Atlas-SNP	.											.	ST7	64	.	0			c.A1751G						PASS	.						86	86	86					7																	116863027		2203	4300	6503	SO:0001583	missense	7982	exon16			ATTTCCAAAACTG	AJ277291	CCDS5769.1, CCDS5770.1	7q31.2	2008-06-06			ENSG00000004866	ENSG00000004866			11351	protein-coding gene	gene with protein product		600833		FAM4A1		8105370, 8938430	Standard	NM_021908		Approved	TSG7, SEN4, ETS7q, HELG, RAY1, FAM4A	uc003vin.3	Q9NRC1	OTTHUMG00000023888	ENST00000265437.5:c.1751A>G	chr7.hg19:g.116863027A>G	ENSP00000265437:p.Gln584Arg	66.0	0.0	.		84.0	42.0	.	NM_021908	A8K137|B4DRQ2	Missense_Mutation	SNP	ENST00000265437.5	hg19	CCDS5770.1	.	.	.	.	.	.	.	.	.	.	A	11.22	1.575245	0.28092	.	.	ENSG00000004866	ENST00000265437	T	0.18174	2.23	4.5	-2.45	0.06481	.	0.926145	0.09155	N	0.840984	T	0.07548	0.0190	N	0.08118	0	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.16394	-1.0404	10	0.48119	T	0.1	-0.0371	5.8835	0.18868	0.2864:0.5195:0.1941:0.0	.	561;584	B7Z573;Q9NRC1	.;ST7_HUMAN	R	584	ENSP00000265437:Q584R	ENSP00000265437:Q584R	Q	+	2	0	ST7	116650263	0.048000	0.20356	0.982000	0.44146	0.470000	0.32858	-0.930000	0.03972	-0.261000	0.09405	-0.331000	0.08364	CAA	.	.	.	none		0.517	ST7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000141622.1	NM_021908		G	116863027	A	G	116863027	3	3	142	1	0	0	0	0	1	0	0	0	15241	130	5	3	1813	3	ST7	7	116863027	Missense_Mutation	SNP	A	TCGA-BQ-7060-01A-11D-1961-08	68782020	116863027	42275636	14	8583											
POP1	10940	hgsc.bcm.edu	37	chr8	99161148	99161148	+	Missense_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	tgattcagcagccaggaaaaGtgactggtgaagatcgacta	14	8	12	7	1	1	4	1	3	0	1	2	6	1	5	1	2	2	1	1	2	4	2			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr8:99161148G>A	ENST00000401707.2	+	13	1897	c.1816G>A	c.(1816-1818)Gtg>Atg	p.V606M	POP1_ENST00000349693.3_Missense_Mutation_p.V606M	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)	606					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)			GCCAGGAAAAGTGACTGGTGA	0.478																																					p.V606M		Atlas-SNP	.											.	POP1	85	.	0			c.G1816A						PASS	.						83	72	76					8																	99161148		2203	4300	6503	SO:0001583	missense	10940	exon13			GGAAAAGTGACTG	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.1816G>A	chr8.hg19:g.99161148G>A	ENSP00000385787:p.Val606Met	52.0	0.0	.		47.0	16.0	.	NM_001145860	A8K5W9|Q15037	Missense_Mutation	SNP	ENST00000401707.2	hg19	CCDS6277.1	.	.	.	.	.	.	.	.	.	.	G	12.90	2.075851	0.36662	.	.	ENSG00000104356	ENST00000401707;ENST00000349693	T;T	0.37411	1.2;1.2	5.46	4.58	0.56647	.	0.468009	0.23298	N	0.049711	T	0.25232	0.0613	L	0.38838	1.175	0.33165	D	0.54748	B	0.28233	0.204	B	0.21151	0.033	T	0.31420	-0.9944	10	0.41790	T	0.15	-5.9978	7.3479	0.26674	0.2299:0.0:0.7701:0.0	.	606	Q99575	POP1_HUMAN	M	606	ENSP00000385787:V606M;ENSP00000339529:V606M	ENSP00000339529:V606M	V	+	1	0	POP1	99230324	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	3.436000	0.52856	1.311000	0.45024	-0.150000	0.13652	GTG	.	.	.	none		0.478	POP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379470.1	NM_015029		A	99161148	G	A	99161148	3	1	142	1	0	0	0	0	1	0	0	0	12258	1029	36	2	1862	2	POP1	8	99161148	Missense_Mutation	SNP	G	TCGA-BQ-7060-01A-11D-1961-08		99161148	47202874	15	8584											
KBTBD4	55709	hgsc.bcm.edu	37	chr11	47597183	47597183	+	Frame_Shift_Del	DEL	T	T	-																															tgactctgcaaaagcctctcTttcctctttattaaagttga																										TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr11:47597183delT	ENST00000526005.1	-	3	811	c.658delA	c.(658-660)agafs	p.R220fs	KBTBD4_ENST00000395288.2_Frame_Shift_Del_p.R220fs|NDUFS3_ENST00000533507.1_Intron|KBTBD4_ENST00000450908.1_5'Flank|KBTBD4_ENST00000430070.2_Frame_Shift_Del_p.R236fs|KBTBD4_ENST00000525720.1_Frame_Shift_Del_p.R269fs|RNU5E-10P_ENST00000363506.1_RNA|KBTBD4_ENST00000533290.1_Frame_Shift_Del_p.R245fs			Q9NVX7	KBTB4_HUMAN	kelch repeat and BTB (POZ) domain containing 4	220	BACK.									NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	24						AAAGCCTCTCTTTCCTCTTTA	0.443																																					p.R236fs		Atlas-INDEL	.											KBTBD4,face,carcinoma,0,1	KBTBD4	55	.	0			c.707delG						PASS	.						164	158	160					11																	47597183		2201	4298	6499	SO:0001589	frameshift_variant	55709	exon3			.	AF151086	CCDS7940.1, CCDS44594.1	11p11.2	2013-01-08	2003-12-12	2003-12-17	ENSG00000123444	ENSG00000123444		"BTB/POZ domain containing"	23761	protein-coding gene	gene with protein product			"BTB and kelch domain containing 4"	BKLHD4		11042152	Standard	NM_018095		Approved	FLJ10450, HSPC252	uc001nfz.3	Q9NVX7	OTTHUMG00000166894	ENST00000526005.1:c.658delA	chr11.hg19:g.47597183delT	ENSP00000433340:p.Arg220fs	182.0	0.0	0		176.0	44.0	0.25	NM_018095	D3DQS1|D3DQS2|Q6IA85|Q9BUC3|Q9NV76	Frame_Shift_Del	DEL	ENST00000526005.1	hg19	CCDS7940.1																																																																																			.	.	.	none		0.443	KBTBD4-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000391763.1	NM_016506		-	47597183	T	-	47597183	7	5	142	1	0	1	0	1	0	0	0	0	8002	1617	56	0	906	0	KBTBD4	11	47597183	Frame_Shift_Del	DEL	T	TCGA-BQ-7060-01A-11D-1961-08		47597183	87409333	16	8585											
NAA16	79612	hgsc.bcm.edu	37	chr13	41905433	41905433	+	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	ctttagaagagaggcttcaaAtttatgaagaaattagtaag	17	12	9	3	0	1	4	1	1	0	3	1	5	1	4	0	1	0	2	0	1	8	7			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr13:41905433A>T	ENST00000379406.3	+	8	1159	c.835A>T	c.(835-837)Att>Ttt	p.I279F	NAA16_ENST00000403412.3_Missense_Mutation_p.I279F|NAA16_ENST00000379367.3_Missense_Mutation_p.I279F	NM_024561.4	NP_078837.3	Q6N069	NAA16_HUMAN	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	279					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						GAGGCTTCAAATTTATGAAGA	0.318																																					p.I279F		Atlas-SNP	.											.,1	NAA16	74	.	0			c.A835T						PASS	.						73	81	78					13																	41905433		2203	4296	6499	SO:0001583	missense	79612	exon8			CTTCAAATTTATG	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.835A>T	chr13.hg19:g.41905433A>T	ENSP00000368716:p.Ile279Phe	187.0	0.0	.		148.0	47.0	.	NM_001110798	B0QZ59|Q5VSP9|Q6P2D5|Q8N5J3|Q8N870	Missense_Mutation	SNP	ENST00000379406.3	hg19	CCDS9379.1	.	.	.	.	.	.	.	.	.	.	A	13.46	2.242909	0.39598	.	.	ENSG00000172766	ENST00000379367;ENST00000379406;ENST00000403412	T;T;T	0.45276	0.9;0.9;0.9	5.53	1.72	0.24424	.	0.233772	0.36167	N	0.002755	T	0.35008	0.0917	L	0.47716	1.5	0.49915	D	0.999832	B;P;B	0.37423	0.031;0.594;0.002	B;P;B	0.44860	0.049;0.462;0.008	T	0.09443	-1.0674	10	0.13470	T	0.59	-3.7053	5.4616	0.16619	0.647:0.1367:0.2163:0.0	.	279;279;279	Q6N069;Q6N069-4;Q6N069-5	NAA16_HUMAN;.;.	F	279	ENSP00000368674:I279F;ENSP00000368716:I279F;ENSP00000386103:I279F	ENSP00000368674:I279F	I	+	1	0	NAA16	40803433	1.000000	0.71417	0.989000	0.46669	0.977000	0.68977	2.768000	0.47645	0.070000	0.16634	0.459000	0.35465	ATT	.	.	.	none		0.318	NAA16-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044672.2	NM_018527		T	41905433	A	T	41905433	3	4	142	1	0	0	0	0	1	0	0	0	10126	101	4	5	865	5	NAA16	13	41905433	Missense_Mutation	SNP	A	TCGA-BQ-7060-01A-11D-1961-08		41905433	73264445	17	8586											
TEP1	7011	hgsc.bcm.edu	37	chr14	20841196	20841196	+	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	tgtggccacagccttagcttCctgccacaagattagttccc	8	11	8	14	0	0	1	0	0	0	1	2	1	2	1	5	1	3	2	5	1	3	4			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr14:20841196C>T	ENST00000262715.5	-	48	6965	c.6925G>A	c.(6925-6927)Gaa>Aaa	p.E2309K	TEP1_ENST00000556935.1_Missense_Mutation_p.E2201K|TEP1_ENST00000545983.1_Missense_Mutation_p.E647K	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	2309					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)		GCCTTAGCTTCCTGCCACAAG	0.517																																					p.E2309K		Atlas-SNP	.											.	TEP1	224	.	0			c.G6925A						PASS	.						77	78	78					14																	20841196		2203	4300	6503	SO:0001583	missense	7011	exon48			TAGCTTCCTGCCA		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.6925G>A	chr14.hg19:g.20841196C>T	ENSP00000262715:p.Glu2309Lys	115.0	0.0	.		103.0	41.0	.	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	hg19	CCDS9548.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.58|12.58	1.981914|1.981914	0.34942|0.34942	.|.	.|.	ENSG00000129566|ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935;ENST00000545983|ENST00000553984	T;T;T|.	0.56103|.	2.26;2.26;0.48|.	5.77|5.77	2.31|2.31	0.28768|0.28768	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.860064|.	0.10567|.	N|.	0.659553|.	T|T	0.19485|0.19485	0.0468|0.0468	N|N	0.14661|0.14661	0.345|0.345	0.20638|0.20638	N|N	0.999872|0.999872	B;B;B;B|.	0.14805|.	0.007;0.004;0.011;0.002|.	B;B;B;B|.	0.13407|.	0.006;0.007;0.009;0.003|.	T|T	0.25467|0.25467	-1.0131|-1.0131	10|5	0.06757|.	T|.	0.87|.	0.0511|0.0511	5.2313|5.2313	0.15424|0.15424	0.0:0.62:0.1541:0.2259|0.0:0.62:0.1541:0.2259	.|.	647;2201;1652;2309|.	B4E0B6;G3V5X7;G3V2A4;Q99973|.	.;.;.;TEP1_HUMAN|.	K|E	2309;2309;2201;647|15	ENSP00000262715:E2309K;ENSP00000452574:E2201K;ENSP00000438849:E647K|.	ENSP00000262715:E2309K|.	E|G	-|-	1|2	0|0	TEP1|TEP1	19911036|19911036	0.182000|0.182000	0.23173|0.23173	0.350000|0.350000	0.25708|0.25708	0.972000|0.972000	0.66771|0.66771	0.105000|0.105000	0.15333|0.15333	0.154000|0.154000	0.19237|0.19237	-0.150000|-0.150000	0.13652|0.13652	GAA|GGA	.	.	.	none		0.517	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		T	20841196	C	T	20841196	3	4	142	1	0	0	0	0	1	0	0	0	15771	864	30	2	990	2	TEP1	14	20841196	Missense_Mutation	SNP	C	TCGA-BQ-7060-01A-11D-1961-08		20841196	86508344	18	8587											
NDNL2	56160	hgsc.bcm.edu	37	chr15	29561225	29561225	+	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	gtattccaggtaacgctgtcGcacaaagtcctcagtaatga	12	10	9	10	2	1	1	1	1	0	0	4	1	3	1	2	1	1	5	2	1	4	4			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr15:29561225G>C	ENST00000332303.4	-	1	808	c.685C>G	c.(685-687)Cga>Gga	p.R229G	FAM189A1_ENST00000261275.4_Intron	NM_138704.3	NP_619649.1	Q96MG7	MAGG1_HUMAN	necdin-like 2	229	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)		p.R229*(1)		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)		TAACGCTGTCGCACAAAGTCC	0.532																																					p.R229G		Atlas-SNP	.											NDNL2,colon,carcinoma,0,1	NDNL2	19	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C685G						PASS	.						68	75	73					15																	29561225		2203	4300	6503	SO:0001583	missense	56160	exon1			GCTGTCGCACAAA	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.685C>G	chr15.hg19:g.29561225G>C	ENSP00000330694:p.Arg229Gly	149.0	0.0	.		134.0	50.0	.	NM_138704	Q8IW16|Q8TEI6|Q9H214	Missense_Mutation	SNP	ENST00000332303.4	hg19	CCDS10023.1	.	.	.	.	.	.	.	.	.	.	G	17.45	3.392428	0.62066	.	.	ENSG00000185115	ENST00000332303	T	0.06142	3.34	4.1	3.16	0.36331	.	0.069228	0.56097	D	0.000039	T	0.24470	0.0593	M	0.86864	2.845	0.41871	D	0.990272	D	0.64830	0.994	D	0.68483	0.958	T	0.02150	-1.1205	10	0.87932	D	0	.	9.1001	0.36662	0.0:0.0:0.7819:0.2181	.	229	Q96MG7	MAGG1_HUMAN	G	229	ENSP00000330694:R229G	ENSP00000330694:R229G	R	-	1	2	NDNL2	27348517	0.989000	0.36119	0.984000	0.44739	0.885000	0.51271	1.680000	0.37607	1.262000	0.44165	0.563000	0.77884	CGA	.	.	.	none		0.532	NDNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251370.1	NM_138704		C	29561225	G	C	29561225	3	2	142	1	0	0	0	0	1	0	0	0	10255	1095	38	4	233	4	NDNL2	15	29561225	Missense_Mutation	SNP	G	TCGA-BQ-7060-01A-11D-1961-08		29561225	72970167	19	8588											
ARHGAP11A	9824	hgsc.bcm.edu	37	chr15	32928906	32928906	+	Missense_Mutation	SNP	T	T	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	agcccagaggaaaatctattTgaaactaatgatttgactat	16	12	7	6	0	1	4	0	3	1	1	1	5	1	5	1	1	2	0	1	1	6	5			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr15:32928906T>G	ENST00000361627.3	+	12	2654	c.1932T>G	c.(1930-1932)ttT>ttG	p.F644L	ARHGAP11A_ENST00000565905.1_Missense_Mutation_p.F455L|ARHGAP11A_ENST00000543522.1_Missense_Mutation_p.F455L	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	644					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)		AAAATCTATTTGAAACTAATG	0.358																																					p.F644L	Colon(45;757 1134 30003 36652)	Atlas-SNP	.											.	ARHGAP11A	84	.	0			c.T1932G						PASS	.						30	32	31					15																	32928906		2197	4296	6493	SO:0001583	missense	9824	exon12			TCTATTTGAAACT	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.1932T>G	chr15.hg19:g.32928906T>G	ENSP00000355090:p.Phe644Leu	59.0	0.0	.		46.0	25.0	.	NM_014783	B4DZN9|Q6PI96|Q9Y3S6	Missense_Mutation	SNP	ENST00000361627.3	hg19	CCDS10028.1	.	.	.	.	.	.	.	.	.	.	.	3.671	-0.067535	0.07273	.	.	ENSG00000198826	ENST00000361627;ENST00000543522	T	0.08370	3.1	4.68	0.799	0.18667	.	0.649114	0.13886	N	0.355958	T	0.05686	0.0149	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.40869	-0.9540	10	0.27785	T	0.31	.	6.2376	0.20772	0.2542:0.0:0.2632:0.4826	.	644	Q6P4F7	RHGBA_HUMAN	L	644;455	ENSP00000355090:F644L	ENSP00000355090:F644L	F	+	3	2	ARHGAP11A	30716198	0.999000	0.42202	0.595000	0.28798	0.557000	0.35523	1.332000	0.33805	-0.039000	0.13602	0.455000	0.32223	TTT	.	.	.	none		0.358	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783		G	32928906	T	G	32928906	3	3	142	1	0	0	0	0	1	0	0	0	863	1809	63	5	2001	5	ARHGAP11A	15	32928906	Missense_Mutation	SNP	T	TCGA-BQ-7060-01A-11D-1961-08	3367681	32928906	69602486	20	8589											
TMC5	79838	hgsc.bcm.edu	37	chr16	19490814	19490814	+	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	tctgatggattttgtgttctCtttagtcaattccttcctgg	5	20	8	8	0	3	1	1	1	2	0	6	2	5	2	2	2	0	1	2	2	2	7			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr16:19490814C>G	ENST00000396229.2	+	14	2980	c.2231C>G	c.(2230-2232)tCt>tGt	p.S744C	TMC5_ENST00000542583.2_Missense_Mutation_p.S744C|TMC5_ENST00000564959.1_Missense_Mutation_p.S427C|TMC5_ENST00000381414.4_Missense_Mutation_p.S744C|TMC5_ENST00000541464.1_Missense_Mutation_p.S692C|CTA-363E6.6_ENST00000561762.1_RNA|TMC5_ENST00000561503.1_Missense_Mutation_p.S385C|TMC5_ENST00000219821.5_Missense_Mutation_p.S498C	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	744					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						TTTGTGTTCTCTTTAGTCAAT	0.473																																					p.S744C		Atlas-SNP	.											.	TMC5	169	.	0			c.C2231G						PASS	.						246	253	250					16																	19490814		2197	4300	6497	SO:0001583	missense	79838	exon14			TGTTCTCTTTAGT	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.2231C>G	chr16.hg19:g.19490814C>G	ENSP00000379531:p.Ser744Cys	344.0	1.0	.		389.0	116.0	.	NM_001105249	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Missense_Mutation	SNP	ENST00000396229.2	hg19	CCDS45431.1	.	.	.	.	.	.	.	.	.	.	C	11.59	1.684070	0.29872	.	.	ENSG00000103534	ENST00000541464;ENST00000381414;ENST00000396229;ENST00000542583;ENST00000219821;ENST00000440743	T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16	5.15	5.15	0.70609	.	0.292700	0.35207	N	0.003365	T	0.49864	0.1582	N	0.26042	0.785	0.34863	D	0.742852	B;B;B;B;B;B	0.31548	0.068;0.12;0.008;0.01;0.328;0.281	B;B;B;B;B;B	0.30401	0.07;0.081;0.023;0.026;0.115;0.07	T	0.62973	-0.6740	10	0.48119	T	0.1	-9.1731	14.3209	0.66487	0.0:0.8051:0.1949:0.0	.	692;427;498;498;744;744	F5GYU8;E7EU57;Q6UXY8-3;B3KUQ8;Q6UXY8;Q6UXY8-2	.;.;.;.;TMC5_HUMAN;.	C	692;744;744;744;498;427	ENSP00000441227:S692C;ENSP00000370822:S744C;ENSP00000379531:S744C;ENSP00000446274:S744C;ENSP00000219821:S498C	ENSP00000219821:S498C	S	+	2	0	TMC5	19398315	0.525000	0.26290	0.987000	0.45799	0.873000	0.50193	0.913000	0.28611	2.387000	0.81309	0.555000	0.69702	TCT	.	.	.	none		0.473	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780		G	19490814	C	G	19490814	3	3	142	1	0	0	0	0	1	0	0	0	16000	913	32	4	2591	4	TMC5	16	19490814	Missense_Mutation	SNP	C	TCGA-BQ-7060-01A-11D-1961-08		19490814	70863939	21	8590											
C16orf70	80262	hgsc.bcm.edu	37	chr16	67168085	67168085	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgcagcccaattttgcccaTggcctggcttctctccagat	6	13	8	14	0	1	1	0	0	1	1	3	1	2	1	4	2	3	2	4	2	1	4			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr16:67168085T>C	ENST00000219139.3	+	7	653	c.465T>C	c.(463-465)caT>caC	p.H155H	C16orf70_ENST00000569683.1_3'UTR|C16orf70_ENST00000569600.1_Silent_p.H155H	NM_025187.3	NP_079463.2	Q9BSU1	CP070_HUMAN	chromosome 16 open reading frame 70	155										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)		ATTTTGCCCATGGCCTGGCTT	0.483																																					p.H155H		Atlas-SNP	.											.	C16orf70	38	.	0			c.T465C						PASS	.						107	100	102					16																	67168085		2200	4300	6500	SO:0001819	synonymous_variant	80262	exon7			TGCCCATGGCCTG	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.465T>C	chr16.hg19:g.67168085T>C		109.0	0.0	.		175.0	52.0	.	NM_025187	Q9HA86	Silent	SNP	ENST00000219139.3	hg19	CCDS10828.1																																																																																			.	.	.	none		0.483	C16orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268829.2	NM_025187		C	67168085	T	C	67168085	2	2	142	1	0	0	0	0	0	0	0	1	1831	1461	51	3		3	C16orf70	16	67168085	Silent	SNP	T	TCGA-BQ-7060-01A-11D-1961-08	47677271	67168085	23186668	22	8591											
ERAL1	26284	hgsc.bcm.edu	37	chr17	27182278	27182278	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccctggaccacttcctcggaTtctctcagcccgacagttcg	6	10	8	17	3	2	0	1	0	1	0	6	3	3	2	4	2	1	1	4	2	0	3			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr17:27182278T>C	ENST00000254928.5	+	1	323	c.226T>C	c.(226-228)Ttc>Ctc	p.F76L	ERAL1_ENST00000578001.1_3'UTR|FAM222B_ENST00000583953.1_5'Flank	NM_005702.2	NP_005693.1	O75616	ERAL1_HUMAN	Era-like 12S mitochondrial rRNA chaperone 1	76					ribosomal small subunit assembly (GO:0000028)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|rRNA binding (GO:0019843)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(2)	11	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)		Epithelial(11;1.12e-05)|all cancers(11;5.32e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000272)|OV - Ovarian serous cystadenocarcinoma(11;0.105)			CTTCCTCGGATTCTCTCAGCC	0.602																																					p.F76L		Atlas-SNP	.											.	ERAL1	28	.	0			c.T226C						PASS	.						41	43	42					17																	27182278		2203	4300	6503	SO:0001583	missense	26284	exon1			CTCGGATTCTCTC	AF082657	CCDS11244.1	17q11.2	2013-05-22	2013-05-22		ENSG00000132591	ENSG00000132591			3424	protein-coding gene	gene with protein product		607435	"Era (E. coli G-protein homolog)-like 1", "Era G-protein-like 1 (E. coli)"			10945472, 20604745	Standard	NM_005702		Approved	HERA-B	uc002hcy.1	O75616	OTTHUMG00000132675	ENST00000254928.5:c.226T>C	chr17.hg19:g.27182278T>C	ENSP00000254928:p.Phe76Leu	85.0	0.0	.		95.0	56.0	.	NM_005702	B3KN21|C9JEC6|O75617|Q8WUY4|Q96LE2|Q96TC0	Missense_Mutation	SNP	ENST00000254928.5	hg19	CCDS11244.1	.	.	.	.	.	.	.	.	.	.	T	9.501	1.103237	0.20632	.	.	ENSG00000132591	ENST00000254928	.	.	.	5.25	-1.46	0.08800	.	0.850078	0.10643	N	0.650826	T	0.07188	0.0182	N	0.02011	-0.69	0.09310	N	0.999995	B;B	0.06786	0.0;0.001	B;B	0.08055	0.001;0.003	T	0.33904	-0.9850	9	0.02654	T	1	-3.854	1.1254	0.01734	0.3213:0.163:0.3615:0.1542	.	76;76	O75616;O75616-2	ERAL1_HUMAN;.	L	76	.	ENSP00000254928:F76L	F	+	1	0	ERAL1	24206404	0.113000	0.22115	0.236000	0.24074	0.049000	0.14656	-0.256000	0.08757	-0.052000	0.13311	0.459000	0.35465	TTC	.	.	.	none		0.602	ERAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255937.2			C	27182278	T	C	27182278	3	2	142	1	0	0	0	0	1	0	0	0	5204	1493	52	3	228	3	ERAL1	17	27182278	Missense_Mutation	SNP	T	TCGA-BQ-7060-01A-11D-1961-08		27182278	54012932	23	8592											
SYNGR2	9144	hgsc.bcm.edu	37	chr17	76167099	76167099	+	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	agatcagcaacgccactgacCgcaagtacctggtcattggt	11	8	10	12	2	2	2	2	1	0	1	2	2	2	2	3	2	3	3	3	2	3	2	rs147752279		TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr17:76167099C>A	ENST00000225777.3	+	2	360	c.301C>A	c.(301-303)Cgc>Agc	p.R101S	SYNGR2_ENST00000590201.1_Missense_Mutation_p.R45S|SYNGR2_ENST00000588282.1_Missense_Mutation_p.R101S|SYNGR2_ENST00000585591.1_Missense_Mutation_p.R101S|SYNGR2_ENST00000589711.1_Intron|SYNGR2_ENST00000592456.1_3'UTR			O43760	SNG2_HUMAN	synaptogyrin 2	101	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				protein targeting (GO:0006605)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)				endometrium(2)|large_intestine(1)|liver(1)|lung(1)|skin(1)|urinary_tract(1)	7			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)|OV - Ovarian serous cystadenocarcinoma(97;0.0994)			CGCCACTGACCGCAAGTACCT	0.587																																					p.R101S		Atlas-SNP	.											.	SYNGR2	17	.	0			c.C301A						PASS	.						100	82	88					17																	76167099		2203	4300	6503	SO:0001583	missense	9144	exon2			ACTGACCGCAAGT	AJ002308	CCDS11753.1	17q25.3	2014-09-11			ENSG00000108639	ENSG00000108639			11499	protein-coding gene	gene with protein product	"cellugyrin"	603926				9760194	Standard	NM_004710		Approved		uc002juu.1	O43760	OTTHUMG00000177457	ENST00000225777.3:c.301C>A	chr17.hg19:g.76167099C>A	ENSP00000225777:p.Arg101Ser	70.0	0.0	.		90.0	7.0	.	NM_004710	O43762|Q3KQZ2|Q658S7	Missense_Mutation	SNP	ENST00000225777.3	hg19	CCDS11753.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.576506	0.86645	.	.	ENSG00000108639	ENST00000225777	T	0.22134	1.97	4.91	4.91	0.64330	Marvel (1);MARVEL-like domain (1);	0.000000	0.85682	D	0.000000	T	0.50548	0.1622	M	0.81682	2.555	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.992;0.994	T	0.57254	-0.7843	10	0.87932	D	0	-26.581	18.0587	0.89370	0.0:1.0:0.0:0.0	.	101;101	O43760;Q3KQZ2	SNG2_HUMAN;.	S	101	ENSP00000225777:R101S	ENSP00000225777:R101S	R	+	1	0	SYNGR2	73678694	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.576000	0.60915	2.428000	0.82296	0.561000	0.74099	CGC	.	C|1.000;T|0.000	.	alt		0.587	SYNGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437009.2			A	76167099	C	A	76167099	3	1	142	1	0	0	0	0	1	0	0	0	15461	652	23	4	307	4	SYNGR2	17	76167099	Missense_Mutation	SNP	C	TCGA-BQ-7060-01A-11D-1961-08	48984821	76167099	5028111	24	8593											
ZNF559	84527	hgsc.bcm.edu	37	chr19	9453288	9453288	+	Silent	SNP	A	A	G																															tatcaatgtaaggaatgtggAaaagcctttattaattcctc																										TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr19:9453288A>G	ENST00000393883.2	+	6	1809	c.1161A>G	c.(1159-1161)ggA>ggG	p.G387G	ZNF559_ENST00000317221.7_3'UTR|ZNF559_ENST00000538743.1_Silent_p.G307G|ZNF177_ENST00000541595.2_Intron|CTC-325H20.2_ENST00000592371.1_lincRNA|ZNF177_ENST00000446085.4_Intron|ZNF177_ENST00000602738.1_Intron|ZNF559_ENST00000586255.1_Intron|ZNF559_ENST00000603380.1_Silent_p.G387G|ZNF177_ENST00000605471.1_Intron|ZNF559_ENST00000587557.1_Silent_p.G451G|ZNF177_ENST00000602856.1_Intron	NM_001202412.1	NP_001189341.1	Q9BR84	ZN559_HUMAN	zinc finger protein 559	387					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|large_intestine(7)|lung(15)|ovary(1)|urinary_tract(1)	26						AGGAATGTGGAAAAGCCTTTA	0.393																																					p.G451G		Atlas-SNP	.											.	ZNF559	77	.	0			c.A1353G						PASS	.						62	57	59					19																	9453288		2203	4300	6503	SO:0001819	synonymous_variant	84527	exon6			ATGTGGAAAAGCC	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.1161A>G	chr19.hg19:g.9453288A>G		72.0	0.0	.		74.0	28.0	.	NM_001202406	K7EMG6	Silent	SNP	ENST00000393883.2	hg19	CCDS12211.1																																																																																			.	.	.	none		0.393	ZNF559-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449021.1	NM_032497		G	9453288	A	G	9453288	2	3	142	1	0	0	0	0	0	0	0	1	18002	233	9	3		3	ZNF559	19	9453288	Silent	SNP	A	TCGA-BQ-7060-01A-11D-1961-08		9453288	49675695	25	8594	88	2									
ZNF559	84527	hgsc.bcm.edu	37	chr19	9453293	9453293	+	Missense_Mutation	SNP	C	C	G																															atgtaaggaatgtggaaaagCctttattaattcctcttcct																										TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr19:9453293C>G	ENST00000393883.2	+	6	1814	c.1166C>G	c.(1165-1167)gCc>gGc	p.A389G	ZNF559_ENST00000317221.7_3'UTR|ZNF559_ENST00000538743.1_Missense_Mutation_p.A309G|ZNF177_ENST00000541595.2_Intron|CTC-325H20.2_ENST00000592371.1_lincRNA|ZNF177_ENST00000446085.4_Intron|ZNF177_ENST00000602738.1_Intron|ZNF559_ENST00000586255.1_Intron|ZNF559_ENST00000603380.1_Missense_Mutation_p.A389G|ZNF177_ENST00000605471.1_Intron|ZNF559_ENST00000587557.1_Missense_Mutation_p.A453G|ZNF177_ENST00000602856.1_Intron	NM_001202412.1	NP_001189341.1	Q9BR84	ZN559_HUMAN	zinc finger protein 559	389					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						TGTGGAAAAGCCTTTATTAAT	0.403																																					p.A453G		Atlas-SNP	.											.	ZNF559	77	.	0			c.C1358G						PASS	.						63	58	60					19																	9453293		2203	4300	6503	SO:0001583	missense	84527	exon6			GAAAAGCCTTTAT	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.1166C>G	chr19.hg19:g.9453293C>G	ENSP00000377461:p.Ala389Gly	71.0	0.0	.		74.0	26.0	.	NM_001202406	K7EMG6	Missense_Mutation	SNP	ENST00000393883.2	hg19	CCDS12211.1	.	.	.	.	.	.	.	.	.	.	C	14.65	2.599554	0.46318	.	.	ENSG00000188321	ENST00000317221;ENST00000538743;ENST00000393883	T;T	0.13901	2.55;2.55	2.22	-0.134	0.13481	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10766	0.0263	N	0.21324	0.655	0.09310	N	1	B;B;B	0.25441	0.028;0.126;0.108	B;B;B	0.38500	0.035;0.275;0.114	T	0.44682	-0.9312	9	0.72032	D	0.01	.	2.8735	0.05624	0.0:0.4172:0.241:0.3417	.	389;389;309	B3KPL8;Q9BR84;B4DP29	.;ZN559_HUMAN;.	G	389;309;389	ENSP00000442832:A309G;ENSP00000377461:A389G	ENSP00000325393:A389G	A	+	2	0	ZNF559	9314293	0.000000	0.05858	0.051000	0.19133	0.916000	0.54674	-0.790000	0.04604	0.024000	0.15214	0.313000	0.20887	GCC	.	.	.	none		0.403	ZNF559-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449021.1	NM_032497		G	9453293	C	G	9453293	3	3	142	1	0	0	0	0	1	0	0	0	18002	739	26	4	1180	4	ZNF559	19	9453293	Missense_Mutation	SNP	C	TCGA-BQ-7060-01A-11D-1961-08	5	9453293	49675690	26	8595	88	2									
ZNRF3	84133	hgsc.bcm.edu	37	chr22	29445350	29445350	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggactcccacggcaaccccgTcaccttgctgaccatggacc	8	6	9	18	2	1	1	1	1	0	0	2	3	2	3	6	3	2	2	6	3	1	1			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chr22:29445350T>C	ENST00000544604.2	+	8	1356	c.1181T>C	c.(1180-1182)gTc>gCc	p.V394A	ZNRF3_ENST00000402174.1_Missense_Mutation_p.V294A|ZNRF3_ENST00000332811.4_Missense_Mutation_p.V294A|ZNRF3_ENST00000406323.3_Missense_Mutation_p.V294A	NM_001206998.1	NP_001193927.1	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	394					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						GGCAACCCCGTCACCTTGCTG	0.667																																					p.V394A		Atlas-SNP	.											.	ZNRF3	75	.	0			c.T1181C						PASS	.						56	64	61					22																	29445350		2180	4280	6460	SO:0001583	missense	84133	exon8			ACCCCGTCACCTT	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.1181T>C	chr22.hg19:g.29445350T>C	ENSP00000443824:p.Val394Ala	69.0	0.0	.		55.0	15.0	.	NM_001206998	B3KU18|Q6ICH1|Q6NTF8|Q8WU18	Missense_Mutation	SNP	ENST00000544604.2	hg19	CCDS56225.1	.	.	.	.	.	.	.	.	.	.	T	10.42	1.345420	0.24426	.	.	ENSG00000183579	ENST00000544604;ENST00000332811;ENST00000462485;ENST00000402174;ENST00000406323	T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32	5.53	4.5	0.54988	.	0.316033	0.36665	N	0.002471	T	0.67702	0.2921	L	0.44542	1.39	0.34781	D	0.734712	P	0.45531	0.86	B	0.37692	0.256	T	0.70029	-0.4984	10	0.07325	T	0.83	-5.454	10.3398	0.43870	0.0:0.0764:0.0:0.9236	.	394	Q9ULT6	ZNRF3_HUMAN	A	394;294;101;294;294	ENSP00000443824:V394A;ENSP00000328614:V294A;ENSP00000384456:V294A;ENSP00000384553:V294A	ENSP00000328614:V294A	V	+	2	0	ZNRF3	27775350	1.000000	0.71417	0.291000	0.24904	0.272000	0.26649	7.390000	0.79816	0.945000	0.37605	0.533000	0.62120	GTC	.	.	.	none		0.667	ZNRF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320943.2	XM_290972		C	29445350	T	C	29445350	3	2	142	1	0	0	0	0	1	0	0	0	18225	1667	58	3	907	3	ZNRF3	22	29445350	Missense_Mutation	SNP	T	TCGA-BQ-7060-01A-11D-1961-08		29445350	21859216	27	8596											
BEND2	139105	hgsc.bcm.edu	37	chrX	18195783	18195783	+	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	aggatttccttggagaacaaAatacgaaccaagtagcaggc	16	7	10	8	1	0	1	0	0	0	1	1	4	1	2	2	3	4	2	2	3	7	4			TCGA-BQ-7060-01A-11D-1961-08	TCGA-BQ-7060-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3a023a28-7d8a-4390-995a-a2a91db99ceb	4a037b1b-bb44-4cec-83b6-2c926f8e4859	g.chrX:18195783A>T	ENST00000380033.4	-	10	1668	c.1536T>A	c.(1534-1536)atT>atA	p.I512I	BEND2_ENST00000380030.3_Silent_p.I421I	NM_153346.4	NP_699177.2	Q8NDZ0	BEND2_HUMAN	BEN domain containing 2	512	BEN 1. {ECO:0000255|PROSITE- ProRule:PRU00784}.									NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(11)|liver(1)|lung(21)|ovary(3)|prostate(1)	49						TGGAGAACAAAATACGAACCA	0.428																																					p.I512I		Atlas-SNP	.											.	BEND2	108	.	0			c.T1536A						PASS	.						267	253	258					X																	18195783		2203	4300	6503	SO:0001819	synonymous_variant	139105	exon10			GAACAAAATACGA	AK128155	CCDS14184.1, CCDS55375.1	Xp22.22	2012-11-22	2008-10-03	2008-10-03	ENSG00000177324	ENSG00000177324		"BEN domain containing"	28509	protein-coding gene	gene with protein product			"chromosome X open reading frame 20"	CXorf20		12477932	Standard	NM_153346		Approved	MGC33653	uc004cyj.4	Q8NDZ0	OTTHUMG00000021211	ENST00000380033.4:c.1536T>A	chrX.hg19:g.18195783A>T		265.0	0.0	.		291.0	207.0	.	NM_153346	E9PFY2|Q4V9S2|Q5JXE5	Silent	SNP	ENST00000380033.4	hg19	CCDS14184.1																																																																																			.	.	.	none		0.428	BEND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055940.1	NM_153346		T	18195783	A	T	18195783	2	4	142	1	0	0	0	0	0	0	0	1	1398	10	1	5		5	BEND2	23	18195783	Silent	SNP	A	TCGA-BQ-7060-01A-11D-1961-08		18195783	137074777	28	8597											
MTOR	2475	hgsc.bcm.edu	37	chr1	11307790	11307790	+	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	tttcagcacccactggcacaCctgagagaggaaggataaag	14	6	11	10	0	1	2	1	1	0	1	1	5	1	4	2	3	1	2	2	3	3	2			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr1:11307790C>A	ENST00000361445.4	-	8	1193	c.1117G>T	c.(1117-1119)Gtg>Ttg	p.V373L		NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	373	Interaction with NBN.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	CACTGGCACACCTGAGAGAGG	0.498																																					p.V373L		Atlas-SNP	.											.	MTOR	327	.	0			c.G1117T						PASS	.						95	94	94					1																	11307790		2203	4300	6503	SO:0001630	splice_region_variant	2475	exon8			GGCACACCTGAGA	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.1117-1G>T	chr1.hg19:g.11307790C>A		114.0	0.0	.		90.0	18.0	.	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	hg19	CCDS127.1	.	.	.	.	.	.	.	.	.	.	C	15.31	2.796328	0.50208	.	.	ENSG00000198793	ENST00000361445;ENST00000539766	T	0.57273	0.41	5.74	5.74	0.90152	Armadillo-like helical (1);Armadillo-type fold (2);	0.000000	0.85682	D	0.000000	T	0.52075	0.1712	M	0.69823	2.125	0.80722	D	1	B	0.26744	0.158	B	0.19391	0.025	T	0.53092	-0.8487	10	0.56958	D	0.05	-0.496	13.1719	0.59604	0.0:0.9275:0.0:0.0725	.	373	P42345	MTOR_HUMAN	L	373	ENSP00000354558:V373L	ENSP00000354558:V373L	V	-	1	0	MTOR	11230377	1.000000	0.71417	1.000000	0.80357	0.730000	0.41778	5.752000	0.68728	2.712000	0.92718	0.650000	0.86243	GTG	.	.	.	none		0.498	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	Missense_Mutation	A	11307790	C	A	11307790	5	1	143	1	0	0	0	0	0	0	1	0	9961	521	18	4	6736	4	MTOR	1	11307790	Splice_Site	SNP	C	TCGA-BQ-7061-01A-11D-1961-08		11307790	237942831	1	8598											
ZMYM6	9204	hgsc.bcm.edu	37	chr1	35476600	35476600	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccctgagacaggggcaccGccgaagagtttgttcctttt	7	10	13	11	2	0	2	0	1	0	2	1	4	1	2	4	3	0	3	4	3	1	4			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr1:35476600G>A	ENST00000357182.4	-	9	1327	c.1100C>T	c.(1099-1101)gCg>gTg	p.A367V	ZMYM6_ENST00000373340.2_Missense_Mutation_p.A367V|ZMYM6_ENST00000487874.1_Missense_Mutation_p.A367V|ZMYM6_ENST00000493328.1_5'UTR	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6	367					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)	p.A367V(1)|p.A367E(1)		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)				CAGGGGCACCGCCGAAGAGTT	0.458																																					p.A367V		Atlas-SNP	.											ZMYM6,NS,carcinoma,0,2	ZMYM6	110	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.C1100T						PASS	.						53	53	53					1																	35476600		2203	4300	6503	SO:0001583	missense	9204	exon9			GGCACCGCCGAAG	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.1100C>T	chr1.hg19:g.35476600G>A	ENSP00000349708:p.Ala367Val	87.0	1.0	.		95.0	37.0	.	NM_007167	B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	Missense_Mutation	SNP	ENST00000357182.4	hg19	CCDS387.2	.	.	.	.	.	.	.	.	.	.	G	0.993	-0.693458	0.03303	.	.	ENSG00000163867	ENST00000373340;ENST00000357182	T;T	0.21191	2.02;3.19	5.2	-0.779	0.10973	.	0.649416	0.15854	N	0.241338	T	0.05181	0.0138	N	0.00926	-1.1	0.19575	N	0.999966	B;B;B	0.16166	0.016;0.004;0.001	B;B;B	0.08055	0.002;0.001;0.003	T	0.42716	-0.9435	10	0.07644	T	0.81	-7.0E-4	10.0213	0.42044	0.749:0.0:0.251:0.0	.	270;367;367	B4DWC0;O95789;O95789-1	.;ZMYM6_HUMAN;.	V	367	ENSP00000362437:A367V;ENSP00000349708:A367V	ENSP00000349708:A367V	A	-	2	0	ZMYM6	35249187	0.006000	0.16342	0.025000	0.17156	0.615000	0.37417	0.331000	0.19733	-0.009000	0.14296	0.655000	0.94253	GCG	.	.	.	none		0.458	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011999.1	NM_007167		A	35476600	G	A	35476600	3	1	143	1	0	0	0	0	1	0	0	0	17716	1087	38	1	2909	1	ZMYM6	1	35476600	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	24168810	35476600	213774021	2	8599											
LCE2A	353139	hgsc.bcm.edu	37	chr1	152671691	152671691	+	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	ctgccacagctctggggactGctgctgaccagacctcgaac	8	7	11	15	1	1	2	0	1	1	1	2	4	1	3	3	2	5	3	3	2	1	0			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr1:152671691G>C	ENST00000368779.1	+	2	365	c.314G>C	c.(313-315)tGc>tCc	p.C105S		NM_178428.3	NP_848515.1	Q5TA79	LCE2A_HUMAN	late cornified envelope 2A	105	Cys-rich.				keratinization (GO:0031424)					breast(1)|large_intestine(1)|liver(2)|lung(4)	8	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCTGGGGACTGCTGCTGACCA	0.587																																					p.C105S		Atlas-SNP	.											.	LCE2A	22	.	0			c.G314C						PASS	.						41	46	45					1																	152671691		2203	4300	6503	SO:0001583	missense	353139	exon2			GGGACTGCTGCTG		CCDS1021.1	1q21.3	2008-02-05			ENSG00000187173	ENSG00000187173		"Late cornified envelopes"	29469	protein-coding gene	gene with protein product		612609				11698679	Standard	NM_178428		Approved	LEP9	uc001faj.3	Q5TA79	OTTHUMG00000012392	ENST00000368779.1:c.314G>C	chr1.hg19:g.152671691G>C	ENSP00000357768:p.Cys105Ser	121.0	0.0	.		127.0	32.0	.	NM_178428	A4QMZ9	Missense_Mutation	SNP	ENST00000368779.1	hg19	CCDS1021.1	.	.	.	.	.	.	.	.	.	.	G	10.23	1.291835	0.23564	.	.	ENSG00000187173	ENST00000368779	T	0.03496	3.91	4.41	4.41	0.53225	.	.	.	.	.	T	0.09069	0.0224	M	0.71206	2.165	0.27116	N	0.962263	D	0.76494	0.999	D	0.78314	0.991	T	0.02691	-1.1123	9	0.87932	D	0	.	12.3335	0.55054	0.0:0.0:1.0:0.0	.	105	Q5TA79	LCE2A_HUMAN	S	105	ENSP00000357768:C105S	ENSP00000357768:C105S	C	+	2	0	LCE2A	150938315	0.999000	0.42202	1.000000	0.80357	0.737000	0.42083	1.350000	0.34010	2.253000	0.74438	0.650000	0.86243	TGC	.	.	.	none		0.587	LCE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034512.1	NM_178428		C	152671691	G	C	152671691	3	2	143	1	0	0	0	0	1	0	0	0	8672	1319	46	4	316	4	LCE2A	1	152671691	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	117195091	152671691	96578930	3	8600											
TNN	63923	hgsc.bcm.edu	37	chr1	175086172	175086172	+	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	gccaccattgacaggtatgtGgtgcgctacacctctgccaa	9	9	10	13	1	1	1	0	1	1	0	1	1	1	1	4	2	3	2	4	2	3	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr1:175086172G>C	ENST00000239462.4	+	10	2330	c.2217G>C	c.(2215-2217)gtG>gtC	p.V739V		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	739	Fibronectin type-III 6. {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)		ACAGGTATGTGGTGCGCTACA	0.622																																					p.V739V		Atlas-SNP	.											TNN,NS,carcinoma,0,1	TNN	297	.	0			c.G2217C						PASS	.						78	77	77					1																	175086172		2203	4300	6503	SO:0001819	synonymous_variant	63923	exon10			GTATGTGGTGCGC	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.2217G>C	chr1.hg19:g.175086172G>C		91.0	1.0	.		120.0	5.0	.	NM_022093	B9EGP3|Q5R360	Silent	SNP	ENST00000239462.4	hg19	CCDS30943.1																																																																																			.	.	.	none		0.622	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527		C	175086172	G	C	175086172	2	2	143	1	0	0	0	0	0	0	0	1	16335	1335	47	4		4	TNN	1	175086172	Silent	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	22414481	175086172	74164449	4	8601											
DHX9	1660	hgsc.bcm.edu	37	chr1	182850707	182850707	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtgagcacaaaagacttaatAtggctacactaagaatgact	17	9	8	7	0	0	4	0	2	0	2	0	4	0	4	0	1	2	2	0	1	7	4			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr1:182850707A>G	ENST00000367549.3	+	24	2949	c.2839A>G	c.(2839-2841)Atg>Gtg	p.M947V	DHX9_ENST00000485081.1_3'UTR	NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	947					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						AAGACTTAATATGGCTACACT	0.363																																					p.M947V	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.A2839G						PASS	.						111	103	105					1																	182850707		1829	4080	5909	SO:0001583	missense	1660	exon24			CTTAATATGGCTA	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.2839A>G	chr1.hg19:g.182850707A>G	ENSP00000356520:p.Met947Val	144.0	0.0	.		105.0	76.0	.	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Missense_Mutation	SNP	ENST00000367549.3	hg19	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	A	9.958	1.221960	0.22457	.	.	ENSG00000135829	ENST00000367549	T	0.03468	3.92	5.94	5.94	0.96194	.	0.041899	0.85682	D	0.000000	T	0.05593	0.0147	L	0.52126	1.63	0.52501	D	0.999959	B;B	0.16396	0.002;0.017	B;B	0.10450	0.005;0.005	T	0.41197	-0.9522	10	0.17369	T	0.5	.	16.3945	0.83586	1.0:0.0:0.0:0.0	.	226;947	B3KU66;Q08211	.;DHX9_HUMAN	V	947	ENSP00000356520:M947V	ENSP00000356520:M947V	M	+	1	0	DHX9	181117330	1.000000	0.71417	0.999000	0.59377	0.825000	0.46686	6.735000	0.74806	2.265000	0.75225	0.482000	0.46254	ATG	.	.	.	none		0.363	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		G	182850707	A	G	182850707	3	3	143	1	0	0	0	0	1	0	0	0	4518	449	16	3	2929	3	DHX9	1	182850707	Missense_Mutation	SNP	A	TCGA-BQ-7061-01A-11D-1961-08	7764535	182850707	66399914	5	8602											
ASPM	259266	hgsc.bcm.edu	37	chr1	197073973	197073974	+	Frame_Shift_Ins	INS	-	-	A																															ctataccatgattgtatgatINSaatagcagaattttcttctt																										TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr1:197073973_197073974insA	ENST00000367409.4	-	18	4663_4664	c.4407_4408insT	c.(4405-4410)attatcfs	p.I1470fs	ASPM_ENST00000294732.7_Intron|ASPM_ENST00000367408.1_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	1470					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						GATTGTATGATAATAGCAGAAT	0.292																																					p.I1470fs		Atlas-INDEL	.											.	ASPM	444	.	0			c.4408_4409insT						PASS	.																																			SO:0001589	frameshift_variant	259266	exon18			.	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"microcephaly, primary autosomal recessive 5", "asp (abnormal spindle)-like, microcephaly associated (Drosophila)"	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.4408dupT	chr1.hg19:g.197073975_197073975dupA	ENSP00000356379:p.Ile1470fs	69.0	0.0	0		58.0	45.0	0.775862	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Frame_Shift_Ins	INS	ENST00000367409.4	hg19	CCDS1389.1																																																																																			.	.	.	none		0.292	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		A	197073974	-	A	197073973	7	5	143	1	0	1	1	0	0	0	0	0	1056	1406	49	0	6069	0	ASPM	1	197073973	Frame_Shift_Ins	INS	-	TCGA-BQ-7061-01A-11D-1961-08	14223266	197073973	52176648	6	8603											
USP34	9736	hgsc.bcm.edu	37	chr2	61450209	61450209	+	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	acttacatgttctgcaagtcGattattgtatcgacacaggc	11	13	8	9	2	1	0	0	0	1	0	3	2	1	0	0	1	2	3	0	1	4	5			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr2:61450209G>C	ENST00000398571.2	-	64	7811	c.7735C>G	c.(7735-7737)Cga>Gga	p.R2579G	USP34_ENST00000472689.1_5'Flank	NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	2579					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)			TCTGCAAGTCGATTATTGTAT	0.383																																					p.R2579G		Atlas-SNP	.											.	USP34	334	.	0			c.C7735G						PASS	.						76	66	69					2																	61450209		1841	4093	5934	SO:0001583	missense	9736	exon64			CAAGTCGATTATT	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.7735C>G	chr2.hg19:g.61450209G>C	ENSP00000381577:p.Arg2579Gly	46.0	0.0	.		38.0	10.0	.	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	hg19	CCDS42686.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.54|16.54	3.151332|3.151332	0.57151|0.57151	.|.	.|.	ENSG00000115464|ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571|ENST00000411912	T|.	0.64803|.	-0.12|.	6.06|6.06	5.17|5.17	0.71159|0.71159	Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.67702|0.67702	0.2921|0.2921	L|L	0.50333|0.50333	1.59|1.59	0.80722|0.80722	D|D	1|1	D|.	0.60160|.	0.987|.	D|.	0.67725|.	0.953|.	T|T	0.65598|0.65598	-0.6129|-0.6129	10|5	0.72032|.	D|.	0.01|.	.|.	15.4863|15.4863	0.75571|0.75571	0.0:0.0:0.6762:0.3238|0.0:0.0:0.6762:0.3238	.|.	2579|.	Q70CQ2|.	UBP34_HUMAN|.	G|W	2427;2427;2579|338	ENSP00000381577:R2579G|.	ENSP00000263989:R2427G|.	R|S	-|-	1|2	2|0	USP34|USP34	61303713|61303713	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	5.187000|5.187000	0.65087|0.65087	1.558000|1.558000	0.49541|0.49541	0.650000|0.650000	0.86243|0.86243	CGA|TCG	.	.	.	none		0.383	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			C	61450209	G	C	61450209	3	2	143	1	0	0	0	0	1	0	0	0	17077	1066	37	4	2973	4	USP34	2	61450209	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08		61450209	181749164	7	8604											
C2orf3	6936	hgsc.bcm.edu	37	chr2	75921529	75921529	+	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	tactccctcaggtgtgagcgGtgagtttcctgtagtaatgt	7	14	12	8	1	1	2	1	2	0	0	3	2	3	2	2	2	2	3	2	2	3	4			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr2:75921529G>C	ENST00000321027.3	-	6	991	c.858C>G	c.(856-858)caC>caG	p.H286Q	GCFC2_ENST00000409857.3_Missense_Mutation_p.H248Q|GCFC2_ENST00000541687.1_Missense_Mutation_p.P248A	NM_001201334.1|NM_003203.4	NP_001188263.1|NP_003194.3	P16383	GCFC2_HUMAN	GC-rich sequence DNA-binding factor 2	286					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)|U2-type post-mRNA release spliceosomal complex (GO:0071008)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)										GGTGTGAGCGGTGAGTTTCCT	0.294																																					p.H286Q		Atlas-SNP	.											.	.	.	.	0			c.C858G						PASS	.						148	150	149					2																	75921529		2203	4300	6503	SO:0001583	missense	6936	exon6			TGAGCGGTGAGTT	AB026911	CCDS1961.1, CCDS62943.1	2p12	2014-01-17	2011-11-24	2011-11-24	ENSG00000005436	ENSG00000005436			1317	protein-coding gene	gene with protein product	"GC binding factor"	189901	"transcription factor 9 (binds GC-rich sequences)", "chromosome 2 open reading frame 3"	TCF9, C2orf3		1370479, 2556218, 17309879, 24304693	Standard	NM_003203		Approved	DNABF, GCF	uc002sno.3	P16383	OTTHUMG00000129989	ENST00000321027.3:c.858C>G	chr2.hg19:g.75921529G>C	ENSP00000318690:p.His286Gln	125.0	0.0	.		98.0	40.0	.	NM_003203	A4UHQ8|O95032|Q53TY0|Q6P2F2	Missense_Mutation	SNP	ENST00000321027.3	hg19	CCDS1961.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.83|17.83	3.486559|3.486559	0.63962|0.63962	.|.	.|.	ENSG00000005436|ENSG00000005436	ENST00000321027;ENST00000409857|ENST00000541687	T;T|T	0.19105|0.39229	2.17;2.28|1.09	5.29|5.29	0.803|0.803	0.18691|0.18691	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.41282|0.41282	0.1152|0.1152	M|M	0.80982|0.80982	2.52|2.52	0.20926|0.20926	N|N	0.999823|0.999823	D|.	0.64830|.	0.994|.	P|.	0.59288|.	0.855|.	T|T	0.43877|0.43877	-0.9364|-0.9364	10|7	0.42905|0.02654	T|T	0.14|1	-15.9173|-15.9173	7.4758|7.4758	0.27376|0.27376	0.5377:0.0:0.4623:0.0|0.5377:0.0:0.4623:0.0	.|.	286|.	P16383|.	GCF_HUMAN|.	Q|A	286;248|248	ENSP00000318690:H286Q;ENSP00000386552:H248Q|ENSP00000437767:P248A	ENSP00000318690:H286Q|ENSP00000437767:P248A	H|P	-|-	3|1	2|0	C2orf3|C2orf3	75775037|75775037	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.944000|0.944000	0.59088|0.59088	1.338000|1.338000	0.33873|0.33873	0.152000|0.152000	0.19188|0.19188	-0.140000|-0.140000	0.14226|0.14226	CAC|CCG	.	.	.	none		0.294	GCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252255.2	NM_003203		C	75921529	G	C	75921529	3	2	143	1	0	0	0	0	1	0	0	0	2164	1252	44	4	1535	4	C2orf3	2	75921529	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	14471320	75921529	167277844	8	8605											
C2orf55	343990	hgsc.bcm.edu	37	chr2	99411105	99411105	+	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	ggctctcttcagctgatgcaGttccttctccatcatcactg	6	14	7	14	0	5	1	3	1	2	0	8	1	6	1	2	1	2	4	2	1	0	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr2:99411105G>C	ENST00000397899.2	-	10	3110	c.2779C>G	c.(2779-2781)Ctg>Gtg	p.L927V		NM_207362.2	NP_997245.2	Q6NV74	K121L_HUMAN	KIAA1211-like	927																	AGCTGATGCAGTTCCTTCTCC	0.478																																					p.L927V		Atlas-SNP	.											.	.	.	.	0			c.C2779G						PASS	.						109	107	108					2																	99411105		1996	4184	6180	SO:0001583	missense	343990	exon10			GATGCAGTTCCTT	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.2779C>G	chr2.hg19:g.99411105G>C	ENSP00000380996:p.Leu927Val	125.0	0.0	.		144.0	60.0	.	NM_207362		Missense_Mutation	SNP	ENST00000397899.2	hg19	CCDS42720.1	.	.	.	.	.	.	.	.	.	.	G	12.84	2.057396	0.36277	.	.	ENSG00000196872	ENST00000397899	T	0.46819	0.86	5.27	0.764	0.18465	.	.	.	.	.	T	0.55449	0.1921	L	0.59436	1.845	0.24768	N	0.992884	D	0.76494	0.999	D	0.80764	0.994	T	0.49532	-0.8930	9	0.08599	T	0.76	-7.2777	8.2997	0.32006	0.3464:0.0:0.6536:0.0	.	927	Q6NV74	CB055_HUMAN	V	927	ENSP00000380996:L927V	ENSP00000380996:L927V	L	-	1	2	C2orf55	98777537	0.018000	0.18449	0.911000	0.35937	0.969000	0.65631	-0.303000	0.08210	-0.047000	0.13423	-0.255000	0.11280	CTG	.	.	.	none		0.478	KIAA1211L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329933.1	NM_207362		C	99411105	G	C	99411105	3	2	143	1	0	0	0	0	1	0	0	0	2178	1020	36	4	113	4	C2orf55	2	99411105	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	23489576	99411105	143788268	9	8606											
XIRP2	129446	hgsc.bcm.edu	37	chr2	168103542	168103542	+	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	tcacttaaagaatcaagccaTcgatggaaagaatctaaaca	19	8	6	8	1	3	2	2	0	1	2	4	4	3	3	1	1	2	0	1	1	8	2			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr2:168103542T>A	ENST00000409195.1	+	9	5729	c.5640T>A	c.(5638-5640)caT>caA	p.H1880Q	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.H1880Q|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.H1658Q|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000420519.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1705					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						AATCAAGCCATCGATGGAAAG	0.383																																					p.H1880Q		Atlas-SNP	.											.	XIRP2	914	.	0			c.T5640A						PASS	.						83	75	77					2																	168103542		1885	4124	6009	SO:0001583	missense	129446	exon9			AAGCCATCGATGG	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.5640T>A	chr2.hg19:g.168103542T>A	ENSP00000386840:p.His1880Gln	73.0	0.0	.		72.0	18.0	.	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	T	0.007	-1.991182	0.00439	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.02280	4.36;4.36;4.36	5.46	-10.9	0.00192	.	1.270260	0.04947	N	0.459528	T	0.01254	0.0041	L	0.27053	0.805	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	0.45279	-0.9272	10	0.20519	T	0.43	4.4394	1.0633	0.01605	0.3314:0.095:0.2197:0.3539	.	1705;1705;1658	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	Q	1880;1880;1658	ENSP00000386840:H1880Q;ENSP00000295237:H1880Q;ENSP00000387255:H1658Q	ENSP00000295237:H1880Q	H	+	3	2	XIRP2	167811788	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.516000	0.00222	-2.709000	0.00395	-1.577000	0.00868	CAT	.	.	.	none		0.383	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		A	168103542	T	A	168103542	3	1	143	1	0	0	0	0	1	0	0	0	17442	1432	50	5	5670	5	XIRP2	2	168103542	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	68692437	168103542	75095831	10	8607											
SPEG	10290	hgsc.bcm.edu	37	chr2	220309733	220309733	+	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	acaggcaaccggggccgggcCacggcacctgggggtggagc	7	2	19	13	3	0	0	0	0	0	0	0	1	0	1	4	8	2	2	4	8	1	0			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr2:220309733C>G	ENST00000312358.7	+	3	797	c.665C>G	c.(664-666)cCa>cGa	p.P222R	SPEG_ENST00000396695.2_Intron|SPEG_ENST00000396698.1_Missense_Mutation_p.P118R	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	222					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)		GGGGCCGGGCCACGGCACCTG	0.716																																					p.P222R		Atlas-SNP	.											.	SPEG	272	.	0			c.C665G						PASS	.						10	14	13					2																	220309733		1928	4078	6006	SO:0001583	missense	10290	exon3			CCGGGCCACGGCA	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.665C>G	chr2.hg19:g.220309733C>G	ENSP00000311684:p.Pro222Arg	16.0	0.0	.		22.0	9.0	.	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	hg19	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	C	14.61	2.587755	0.46110	.	.	ENSG00000072195	ENST00000312358;ENST00000265327;ENST00000396698	T;T	0.69175	-0.38;-0.11	4.86	4.86	0.63082	.	0.000000	0.36932	U	0.002335	T	0.61739	0.2371	N	0.14661	0.345	0.80722	D	1	D	0.59357	0.985	P	0.58077	0.832	T	0.61058	-0.7139	10	0.31617	T	0.26	.	11.9491	0.52944	0.0:0.9075:0.0:0.0925	.	222	Q15772	SPEG_HUMAN	R	222;222;118	ENSP00000311684:P222R;ENSP00000379926:P118R	ENSP00000265327:P222R	P	+	2	0	SPEG	220017977	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.189000	0.42621	2.227000	0.72691	0.442000	0.29010	CCA	.	.	.	none		0.716	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		G	220309733	C	G	220309733	3	3	143	1	0	0	0	0	1	0	0	0	15048	594	21	4	675	4	SPEG	2	220309733	Missense_Mutation	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	52206191	220309733	22889640	11	8608											
MRPL44	65080	hgsc.bcm.edu	37	chr2	224824513	224824513	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgaagacgagtacccagacAtgcccactgaaggcataaaa	16	6	9	10	1	0	4	0	2	0	2	0	5	0	4	2	1	2	2	2	1	5	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr2:224824513A>G	ENST00000258383.3	+	2	511	c.442A>G	c.(442-444)Atg>Gtg	p.M148V		NM_022915.3	NP_075066.1	Q9H9J2	RM44_HUMAN	mitochondrial ribosomal protein L44	148	RNase III.				mitochondrial translational elongation (GO:0070125)|RNA processing (GO:0006396)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		all_lung(227;0.00679)|Lung NSC(271;0.00855)|Renal(207;0.0112)|all_hematologic(139;0.189)		Epithelial(121;2.51e-10)|all cancers(144;7.89e-08)|Lung(261;0.00705)|LUSC - Lung squamous cell carcinoma(224;0.008)		GTACCCAGACATGCCCACTGA	0.428																																					p.M148V		Atlas-SNP	.											.	MRPL44	31	.	0			c.A442G						PASS	.						76	80	79					2																	224824513		2203	4300	6503	SO:0001583	missense	65080	exon2			CCAGACATGCCCA	AK022763	CCDS2459.1	2p24.3-p24.1	2012-09-13			ENSG00000135900	ENSG00000135900		"Mitochondrial ribosomal proteins / large subunits"	16650	protein-coding gene	gene with protein product	"39S ribosomal protein L44, mitochondrial"	611849					Standard	NM_022915		Approved	FLJ12701, FLJ13990	uc002vnr.4	Q9H9J2	OTTHUMG00000133164	ENST00000258383.3:c.442A>G	chr2.hg19:g.224824513A>G	ENSP00000258383:p.Met148Val	114.0	0.0	.		106.0	47.0	.	NM_022915	Q53S16|Q6IA62|Q9H821	Missense_Mutation	SNP	ENST00000258383.3	hg19	CCDS2459.1	.	.	.	.	.	.	.	.	.	.	A	3.222	-0.159303	0.06544	.	.	ENSG00000135900	ENST00000258383	T	0.39997	1.05	5.42	-3.5	0.04710	Ribonuclease III (3);	0.216533	0.40222	N	0.001151	T	0.15046	0.0363	N	0.04880	-0.145	0.21020	N	0.9998	B	0.02656	0.0	B	0.06405	0.002	T	0.07539	-1.0767	10	0.38643	T	0.18	-2.8434	4.3393	0.11101	0.5634:0.2199:0.0:0.2166	.	148	Q9H9J2	RM44_HUMAN	V	148	ENSP00000258383:M148V	ENSP00000258383:M148V	M	+	1	0	MRPL44	224532757	0.005000	0.15991	0.981000	0.43875	0.030000	0.12068	0.015000	0.13355	-0.206000	0.10203	-2.558000	0.00175	ATG	.	.	.	none		0.428	MRPL44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256866.2	NM_022915		G	224824513	A	G	224824513	3	3	143	1	0	0	0	0	1	0	0	0	9815	217	8	3	448	3	MRPL44	2	224824513	Missense_Mutation	SNP	A	TCGA-BQ-7061-01A-11D-1961-08	4514780	224824513	18374860	12	8609											
GOLGA4	2803	hgsc.bcm.edu	37	chr3	37365472	37365472	+	Missense_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	aactgtcagaagtattaaaaGcccgtcacaaactagaagag	18	7	8	8	1	2	3	2	0	0	3	2	3	2	3	1	0	3	1	1	0	8	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr3:37365472G>A	ENST00000361924.2	+	14	2469	c.2095G>A	c.(2095-2097)Gcc>Acc	p.A699T	GOLGA4_ENST00000356847.4_Missense_Mutation_p.A721T|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	699	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						AGTATTAAAAGCCCGTCACAA	0.358																																					p.A721T		Atlas-SNP	.											.	GOLGA4	173	.	0			c.G2161A						PASS	.						32	35	34					3																	37365472		2195	4266	6461	SO:0001583	missense	2803	exon15			TTAAAAGCCCGTC	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.2095G>A	chr3.hg19:g.37365472G>A	ENSP00000354486:p.Ala699Thr	44.0	0.0	.		39.0	29.0	.	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	hg19	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	G	6.302	0.423898	0.11928	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000429018;ENST00000437131	T;T;T	0.22539	1.99;1.99;1.95	5.22	3.44	0.39384	.	0.449282	0.16613	N	0.206829	T	0.13329	0.0323	N	0.25890	0.77	0.09310	N	1	B;B;B;B	0.12013	0.005;0.001;0.001;0.002	B;B;B;B	0.09377	0.004;0.004;0.004;0.003	T	0.30563	-0.9974	10	0.15066	T	0.55	.	10.028	0.42083	0.2751:0.0:0.7249:0.0	.	699;699;721;699	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	T	699;721;260;570	ENSP00000354486:A699T;ENSP00000349305:A721T;ENSP00000405842:A570T	ENSP00000349305:A721T	A	+	1	0	GOLGA4	37340476	0.002000	0.14202	0.168000	0.22838	0.683000	0.39861	0.601000	0.24119	0.721000	0.32231	0.655000	0.94253	GCC	.	.	.	none		0.358	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		A	37365472	G	A	37365472	3	1	143	1	0	0	0	0	1	0	0	0	6562	971	34	2	2219	2	GOLGA4	3	37365472	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08		37365472	160656958	13	8610											
SETD2	29072	hgsc.bcm.edu	37	chr3	47164114	47164114	+	Frame_Shift_Del	DEL	A	A	-																															caggagatccatttatatttAattctatgggacaaaaactt																										TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr3:47164114delA	ENST00000409792.3	-	3	2054	c.2012delT	c.(2011-2013)ttafs	p.L671fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	671					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		ATTTATATTTAATTCTATGGG	0.328			"N, F, S, Mis"		clear cell renal carcinoma																																p.L671fs		Atlas-INDEL	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.2013delA						PASS	.						58	63	61					3																	47164114		2203	4299	6502	SO:0001589	frameshift_variant	29072	exon3			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.2012delT	chr3.hg19:g.47164114delA	ENSP00000386759:p.Leu671fs	102.0	0.0	0		85.0	70.0	0.823529	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Del	DEL	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.	.	none		0.328	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		-	47164114	A	-	47164114	7	5	143	1	0	1	0	1	0	0	0	0	14144	372	13	0	5758	0	SETD2	3	47164114	Frame_Shift_Del	DEL	A	TCGA-BQ-7061-01A-11D-1961-08	9798642	47164114	150858316	14	8611											
ACY1	95	hgsc.bcm.edu	37	chr3	52023049	52023049	+	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	gacatatatacacgcctgctGcctgcccttgccagtgtgcc	7	10	9	15	1	0	0	0	0	0	0	0	1	0	0	5	0	6	1	5	0	3	4			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr3:52023049G>C	ENST00000404366.2	+	15	1331	c.1185G>C	c.(1183-1185)ctG>ctC	p.L395L	ACY1_ENST00000476351.1_Silent_p.L360L|ACY1_ENST00000476854.1_Silent_p.L330L|ACY1_ENST00000458031.2_Silent_p.L485L|ACY1_ENST00000494103.1_Silent_p.L323L|ABHD14A-ACY1_ENST00000463937.1_Silent_p.L496L	NM_000666.2|NM_001198895.1	NP_000657.1|NP_001185824.1	Q03154	ACY1_HUMAN	aminoacylase 1	395					cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aminoacylase activity (GO:0004046)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Acetylcysteine(DB06151)|L-Aspartic Acid(DB00128)	CACGCCTGCTGCCTGCCCTTG	0.607																																					p.L395L		Atlas-SNP	.											.	ACY1	35	.	0			c.G1185C						PASS	.						116	102	107					3																	52023049		2203	4300	6503	SO:0001819	synonymous_variant	95	exon15			CCTGCTGCCTGCC	L07548	CCDS2844.1, CCDS56261.1, CCDS56262.1, CCDS56263.1	3p21.2	2006-02-02			ENSG00000243989	ENSG00000243989	3.5.1.14		177	protein-coding gene	gene with protein product		104620				1707030, 6948533	Standard	NM_000666		Approved		uc003dcq.3	Q03154	OTTHUMG00000157815	ENST00000404366.2:c.1185G>C	chr3.hg19:g.52023049G>C		167.0	1.0	.		125.0	98.0	.	NM_001198895	C9J6I6|C9J9D8|C9JWD4	Silent	SNP	ENST00000404366.2	hg19	CCDS2844.1																																																																																			.	.	.	none		0.607	ACY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349657.1	NM_000666		C	52023049	G	C	52023049	2	2	143	1	0	0	0	0	0	0	0	1	226	1306	46	4		4	ACY1	3	52023049	Silent	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	4858935	52023049	145999381	15	8612											
PBRM1	55193	hgsc.bcm.edu	37	chr3	52651555	52651555	+	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	gctttcttatgttctttttaCtgttgagggggaggtagaaa	8	17	12	4	0	2	2	0	1	2	1	2	3	2	3	0	3	1	4	0	3	4	8			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr3:52651555C>T	ENST00000296302.7	-	14	1543		c.e14-1		PBRM1_ENST00000337303.4_Splice_Site|PBRM1_ENST00000356770.4_Splice_Site|PBRM1_ENST00000409767.1_Splice_Site|PBRM1_ENST00000409114.3_Splice_Site|PBRM1_ENST00000409057.1_Splice_Site|PBRM1_ENST00000394830.3_Splice_Site|PBRM1_ENST00000410007.1_Splice_Site			Q86U86	PB1_HUMAN	polybromo 1						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)		GTTCTTTTTACTGTTGAGGGG	0.348			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																.		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.1542-1G>A						PASS	.						52	52	52					3																	52651555		2202	4300	6502	SO:0001630	splice_region_variant	55193	exon16			TTTTTACTGTTGA	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.1542-1G>A	chr3.hg19:g.52651555C>T		38.0	0.0	.		35.0	23.0	.	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Splice_Site	SNP	ENST00000296302.7	hg19		.	.	.	.	.	.	.	.	.	.	C	21.4	4.147027	0.77888	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.139	0.98050	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PBRM1	52626595	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	3.810000	0.55613	2.764000	0.94973	0.655000	0.94253	.	.	.	.	none		0.348	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165	Intron	T	52651555	C	T	52651555	5	4	143	1	0	0	0	0	0	0	1	0	11498	579	20	2	3427	2	PBRM1	3	52651555	Splice_Site	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	628506	52651555	145370875	16	8613											
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113377559	113377559	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgtggtttgcattgtatcTgatgaatcttgctcaactct	7	17	8	9	0	4	2	1	2	3	0	4	2	4	2	1	1	3	4	1	1	3	4			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr3:113377559T>C	ENST00000478658.1	-	5	2987	c.2970A>G	c.(2968-2970)tcA>tcG	p.S990S	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Silent_p.S990S			Q68DE3	K2018_HUMAN	KIAA2018	990						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						GCATTGTATCTGATGAATCTT	0.393																																					p.S990S		Atlas-SNP	.											.	KIAA2018	180	.	0			c.A2970G						PASS	.						113	106	108					3																	113377559		1870	4096	5966	SO:0001819	synonymous_variant	205717	exon7			TGTATCTGATGAA	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.2970A>G	chr3.hg19:g.113377559T>C		152.0	0.0	.		134.0	104.0	.	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	hg19	CCDS43133.1																																																																																			.	.	.	none		0.393	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		C	113377559	T	C	113377559	2	2	143	1	0	0	0	0	0	0	0	1	8275	1567	55	3		3	KIAA2018	3	113377559	Silent	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	60726004	113377559	84644871	17	8614											
CD86	942	hgsc.bcm.edu	37	chr3	121822644	121822644	+	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	tatcatccatcacaaaaagcCcacaggaatgattcgcatcc	15	8	5	13	1	2	1	2	1	0	0	5	2	4	2	3	1	1	1	3	1	4	2			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr3:121822644C>G	ENST00000330540.2	+	3	466	c.350C>G	c.(349-351)cCc>cGc	p.P117R	CD86_ENST00000393627.2_Missense_Mutation_p.P111R|CD86_ENST00000469710.1_Missense_Mutation_p.P35R|CD86_ENST00000493101.1_Intron|CD86_ENST00000264468.5_Intron	NM_175862.4	NP_787058	P42081	CD86_HUMAN	CD86 molecule	117	Ig-like V-type.				aging (GO:0007568)|B cell activation (GO:0042113)|cell-cell signaling (GO:0007267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to metal ion (GO:0071248)|defense response to virus (GO:0051607)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|immune response (GO:0006955)|innate immune response (GO:0045087)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of T cell anergy (GO:0002668)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 biosynthetic process (GO:0045404)|positive regulation of lymphotoxin A biosynthetic process (GO:0043017)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|response to interferon-gamma (GO:0034341)|response to yeast (GO:0001878)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell proliferation involved in immune response (GO:0002309)|toll-like receptor signaling pathway (GO:0002224)|viral process (GO:0016032)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)|receptor activity (GO:0004872)			breast(2)|endometrium(1)|kidney(1)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	23				GBM - Glioblastoma multiforme(114;0.156)	Abatacept(DB01281)|Antithymocyte globulin(DB00098)|Belatacept(DB06681)	CACAAAAAGCCCACAGGAATG	0.453																																					p.P117R	GBM(67;1379 1389 36064 39806)	Atlas-SNP	.											.	CD86	43	.	0			c.C350G						PASS	.						129	134	132					3																	121822644		2203	4300	6503	SO:0001583	missense	942	exon3			AAAAGCCCACAGG		CCDS3009.1, CCDS43138.1, CCDS56272.1, CCDS56273.1, CCDS74991.1	3q21	2013-01-29	2006-03-28		ENSG00000114013	ENSG00000114013		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1705	protein-coding gene	gene with protein product	"B-lymphocyte antigen B7-2"	601020	"CD86 antigen (CD28 antigen ligand 2, B7-2 antigen)"	CD28LG2		7513726	Standard	NM_006889		Approved	B7.2, B7-2	uc003eet.3	P42081	OTTHUMG00000159482	ENST00000330540.2:c.350C>G	chr3.hg19:g.121822644C>G	ENSP00000332049:p.Pro117Arg	125.0	0.0	.		77.0	64.0	.	NM_175862	A0N0P0|B7Z2F3|B7Z702|E7ETN5|E9PC27|Q13655|Q6FHB1|Q6GTS4|Q7M4L5	Missense_Mutation	SNP	ENST00000330540.2	hg19	CCDS3009.1	.	.	.	.	.	.	.	.	.	.	C	15.22	2.769867	0.49680	.	.	ENSG00000114013	ENST00000469710;ENST00000330540;ENST00000482356;ENST00000393627	T;T;T;T	0.30182	1.54;1.54;1.54;1.54	5.54	4.67	0.58626	Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.828917	0.10874	N	0.624588	T	0.55768	0.1941	M	0.82630	2.6	0.25045	N	0.991176	D	0.64830	0.994	D	0.65987	0.94	T	0.44574	-0.9319	10	0.41790	T	0.15	-0.8312	10.1893	0.43017	0.0:0.9112:0.0:0.0888	.	117	P42081	CD86_HUMAN	R	35;117;111;111	ENSP00000418988:P35R;ENSP00000332049:P117R;ENSP00000419116:P111R;ENSP00000377248:P111R	ENSP00000332049:P117R	P	+	2	0	CD86	123305334	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	0.065000	0.14466	1.578000	0.49821	0.655000	0.94253	CCC	.	.	.	none		0.453	CD86-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000355671.1	NM_006889		G	121822644	C	G	121822644	3	3	143	1	0	0	0	0	1	0	0	0	3045	623	22	4	360	4	CD86	3	121822644	Missense_Mutation	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	8445085	121822644	76199786	18	8615											
USP38	84640	hgsc.bcm.edu	37	chr4	144141548	144141548	+	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	caacgacccaccaggaagctGtggaccaactggtggagggg	11	4	15	11	1	0	0	0	0	0	0	0	4	0	3	3	6	3	1	3	6	3	0			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr4:144141548G>C	ENST00000307017.4	+	10	3574	c.3068G>C	c.(3067-3069)tGt>tCt	p.C1023S		NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	1023					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	33	all_hematologic(180;0.158)					CCAGGAAGCTGTGGACCAACT	0.512																																					p.C1023S		Atlas-SNP	.											.	USP38	92	.	0			c.G3068C						PASS	.						92	94	93					4																	144141548		2203	4300	6503	SO:0001583	missense	84640	exon10			GAAGCTGTGGACC	AF211481	CCDS3758.1	4q31.1	2008-02-05	2005-08-08		ENSG00000170185	ENSG00000170185		"Ubiquitin-specific peptidases"	20067	protein-coding gene	gene with protein product			"ubiquitin specific protease 38"			12838346	Standard	NM_032557		Approved	KIAA1891, HP43.8KD	uc003ijb.3	Q8NB14	OTTHUMG00000161420	ENST00000307017.4:c.3068G>C	chr4.hg19:g.144141548G>C	ENSP00000303434:p.Cys1023Ser	92.0	0.0	.		71.0	4.0	.	NM_032557	B3KX93|Q3ZCV1|Q8NDF5|Q96DK6|Q96PZ6|Q9BY55	Missense_Mutation	SNP	ENST00000307017.4	hg19	CCDS3758.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.312440	0.81358	.	.	ENSG00000170185	ENST00000307017	T	0.10477	2.87	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.35799	0.0944	M	0.71581	2.175	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.01452	-1.1351	10	0.62326	D	0.03	-13.0776	20.1294	0.97995	0.0:0.0:1.0:0.0	.	1023	Q8NB14	UBP38_HUMAN	S	1023	ENSP00000303434:C1023S	ENSP00000303434:C1023S	C	+	2	0	USP38	144360998	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.835000	0.99442	2.758000	0.94735	0.591000	0.81541	TGT	.	.	.	none		0.512	USP38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364869.1	NM_032557		C	144141548	G	C	144141548	3	2	143	1	0	0	0	0	1	0	0	0	17081	1377	48	4	3106	4	USP38	4	144141548	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08		144141548	47012728	19	8616											
SMAD1	4086	hgsc.bcm.edu	37	chr4	146475084	146475084	+	Missense_Mutation	SNP	T	T	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	agtgggtgtagtctgaaaatTtttaacaaccaagaatttgc	14	13	9	5	0	1	2	0	1	1	1	1	2	1	2	1	1	3	1	1	1	7	5			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr4:146475084T>G	ENST00000515385.1	+	6	1688	c.1146T>G	c.(1144-1146)atT>atG	p.I382M	SMAD1_ENST00000394092.2_Missense_Mutation_p.I382M|SMAD1_ENST00000302085.4_Missense_Mutation_p.I382M			Q15797	SMAD1_HUMAN	SMAD family member 1	382	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cardiac muscle cell proliferation (GO:0060038)|cartilage development (GO:0051216)|cellular response to BMP stimulus (GO:0071773)|embryonic pattern specification (GO:0009880)|gamete generation (GO:0007276)|hindbrain development (GO:0030902)|homeostatic process (GO:0042592)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|mesodermal cell fate commitment (GO:0001710)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|negative regulation of muscle cell apoptotic process (GO:0010656)|osteoblast fate commitment (GO:0002051)|positive regulation of cartilage development (GO:0061036)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of gene expression (GO:0010628)|positive regulation of osteoblast differentiation (GO:0045669)|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)|primary miRNA processing (GO:0031053)|protein phosphorylation (GO:0006468)|response to drug (GO:0042493)|response to organonitrogen compound (GO:0010243)|signal transduction (GO:0007165)|SMAD protein complex assembly (GO:0007183)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|mitochondrion (GO:0005739)|nuclear inner membrane (GO:0005637)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	co-SMAD binding (GO:0070410)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)			endometrium(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	17	all_hematologic(180;0.151)					GTCTGAAAATTTTTAACAACC	0.398																																					p.I382M	Pancreas(182;1287 2092 10326 35158 50562)	Atlas-SNP	.											.	SMAD1	48	.	0			c.T1146G						PASS	.						165	158	160					4																	146475084		2203	4300	6503	SO:0001583	missense	4086	exon6			GAAAATTTTTAAC	U59423	CCDS3765.1	4q31.21	2013-10-22	2006-11-06	2004-05-26	ENSG00000170365	ENSG00000170365		"SMADs"	6767	protein-coding gene	gene with protein product		601595	"MAD, mothers against decapentaplegic homolog 1 (Drosophila)", "SMAD, mothers against DPP homolog 1 (Drosophila)"	MADH1		8653785, 8673135	Standard	NM_005900		Approved	MADR1, JV4-1	uc003ikc.3	Q15797	OTTHUMG00000161592	ENST00000515385.1:c.1146T>G	chr4.hg19:g.146475084T>G	ENSP00000426568:p.Ile382Met	141.0	0.0	.		101.0	36.0	.	NM_005900	A8KAJ0|D3DNZ9|Q16636|Q9UFT8	Missense_Mutation	SNP	ENST00000515385.1	hg19	CCDS3765.1	.	.	.	.	.	.	.	.	.	.	T	19.20	3.782414	0.70222	.	.	ENSG00000170365	ENST00000302085;ENST00000394092;ENST00000515385	D;D;D	0.97811	-4.55;-4.55;-4.55	5.73	2.08	0.27032	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.98836	0.9607	H	0.95712	3.71	0.80722	D	1	D	0.54397	0.966	D	0.73708	0.981	D	0.98389	1.0562	10	0.87932	D	0	.	9.1222	0.36795	0.0:0.1974:0.0:0.8026	.	382	Q15797	SMAD1_HUMAN	M	382	ENSP00000305769:I382M;ENSP00000377652:I382M;ENSP00000426568:I382M	ENSP00000305769:I382M	I	+	3	3	SMAD1	146694534	0.995000	0.38212	1.000000	0.80357	0.983000	0.72400	0.316000	0.19469	0.136000	0.18733	0.528000	0.53228	ATT	.	.	.	none		0.398	SMAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365467.1	NM_005900		G	146475084	T	G	146475084	3	3	143	1	0	0	0	0	1	0	0	0	14770	1829	64	5	1164	5	SMAD1	4	146475084	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	2333536	146475084	44679192	20	8617											
IRF2	3660	hgsc.bcm.edu	37	chr4	185339324	185339324	+	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	gaatcacccaagattaccttGatgtgcttaactttgtcttc	10	15	6	10	0	2	2	1	1	1	1	3	3	2	2	2	0	3	1	2	0	4	5			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr4:185339324G>C	ENST00000393593.3	-	5	615	c.408C>G	c.(406-408)atC>atG	p.I136M	IRF2_ENST00000512020.1_5'UTR	NM_002199.3	NP_002190.2	P14316	IRF2_HUMAN	interferon regulatory factor 2	136					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)		AGATTACCTTGATGTGCTTAA	0.398																																					p.I136M		Atlas-SNP	.											.	IRF2	53	.	0			c.C408G						PASS	.						317	261	280					4																	185339324		2203	4300	6503	SO:0001583	missense	3660	exon5			TACCTTGATGTGC		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.408C>G	chr4.hg19:g.185339324G>C	ENSP00000377218:p.Ile136Met	187.0	0.0	.		186.0	64.0	.	NM_002199	D6RCK5|H0Y8S3|Q6IAS7|Q96B99	Missense_Mutation	SNP	ENST00000393593.3	hg19	CCDS3835.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.31|11.31	1.601714|1.601714	0.28534|0.28534	.|.	.|.	ENSG00000168310|ENSG00000168310	ENST00000393593;ENST00000507523;ENST00000510814;ENST00000506230;ENST00000505316|ENST00000505067	D;D;D;D|.	0.98090|.	-4.66;-4.65;-4.63;-4.71|.	6.17|6.17	5.17|5.17	0.71159|0.71159	.|.	0.584493|.	0.19685|.	N|.	0.108406|.	T|T	0.49047|0.49047	0.1534|0.1534	L|L	0.44542|0.44542	1.39|1.39	0.42544|0.42544	D|D	0.993085|0.993085	B|.	0.23854|.	0.092|.	B|.	0.18263|.	0.021|.	T|T	0.44205|0.44205	-0.9343|-0.9343	10|5	0.45353|.	T|.	0.12|.	-20.7082|-20.7082	5.7421|5.7421	0.18100|0.18100	0.129:0.0:0.6708:0.2002|0.129:0.0:0.6708:0.2002	.|.	136|.	P14316|.	IRF2_HUMAN|.	M|E	136|35	ENSP00000377218:I136M;ENSP00000427204:I136M;ENSP00000424552:I136M;ENSP00000422860:I136M|.	ENSP00000377218:I136M|.	I|Q	-|-	3|1	3|0	IRF2|IRF2	185576318|185576318	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	0.647000|0.647000	0.24812|0.24812	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	ATC|CAA	.	.	.	none		0.398	IRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361393.1			C	185339324	G	C	185339324	3	2	143	1	0	0	0	0	1	0	0	0	7835	1280	45	4	661	4	IRF2	4	185339324	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	38864240	185339324	5814952	21	8618											
UGT3A2	167127	hgsc.bcm.edu	37	chr5	36039694	36039694	+	Missense_Mutation	SNP	A	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	accccttggggtaggtgagcAaaggcattgttcatctcctt	8	12	11	10	0	2	1	1	1	1	0	3	1	2	1	3	4	1	4	3	4	2	5			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr5:36039694A>C	ENST00000282507.3	-	5	1061	c.960T>G	c.(958-960)ttT>ttG	p.F320L	UGT3A2_ENST00000513300.1_Missense_Mutation_p.F286L|UGT3A2_ENST00000504954.1_5'Flank|UGT3A2_ENST00000545528.1_Missense_Mutation_p.F18L	NM_174914.3	NP_777574.2	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2	320					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)			GTAGGTGAGCAAAGGCATTGT	0.493																																					p.F320L		Atlas-SNP	.											.	UGT3A2	117	.	0			c.T960G						PASS	.						142	130	134					5																	36039694		2203	4300	6503	SO:0001583	missense	167127	exon5			GTGAGCAAAGGCA		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.960T>G	chr5.hg19:g.36039694A>C	ENSP00000282507:p.Phe320Leu	122.0	0.0	.		126.0	46.0	.	NM_174914	B4DUQ7|E9PFK7|Q6UXC4|Q8NBP2	Missense_Mutation	SNP	ENST00000282507.3	hg19	CCDS3914.1	.	.	.	.	.	.	.	.	.	.	A	8.718	0.913757	0.17907	.	.	ENSG00000168671	ENST00000282507;ENST00000513300;ENST00000545528	T;T;T	0.50001	0.76;0.76;4.06	3.18	3.18	0.36537	.	0.000000	0.85682	D	0.000000	T	0.46210	0.1381	L	0.35414	1.06	0.36452	D	0.866122	D;D	0.89917	0.998;1.0	D;D	0.91635	0.986;0.999	T	0.54543	-0.8278	10	0.02654	T	1	.	6.7806	0.23643	0.8835:0.0:0.1165:0.0	.	286;320	E9PFK7;Q3SY77	.;UD3A2_HUMAN	L	320;286;18	ENSP00000282507:F320L;ENSP00000427404:F286L;ENSP00000445367:F18L	ENSP00000282507:F320L	F	-	3	2	UGT3A2	36075451	0.999000	0.42202	0.882000	0.34594	0.212000	0.24457	0.703000	0.25646	1.689000	0.51079	0.482000	0.46254	TTT	.	.	.	none		0.493	UGT3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253771.2	NM_174914		C	36039694	A	C	36039694	3	2	143	1	0	0	0	0	1	0	0	0	16976	127	5	5	623	5	UGT3A2	5	36039694	Missense_Mutation	SNP	A	TCGA-BQ-7061-01A-11D-1961-08		36039694	144875566	22	8619											
GFRA3	2676	hgsc.bcm.edu	37	chr5	137610073	137610073	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcagcagcaacatcaggActacgggcggcagcggtcgc	10	3	15	13	4	1	0	1	0	0	0	2	1	1	1	0	4	6	5	0	4	2	1			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr5:137610073A>G	ENST00000274721.3	-	1	287	c.41T>C	c.(40-42)gTc>gCc	p.V14A	GFRA3_ENST00000378362.3_Missense_Mutation_p.V14A	NM_001496.3	NP_001487.2	O60609	GFRA3_HUMAN	GDNF family receptor alpha 3	14					nervous system development (GO:0007399)|neuron migration (GO:0001764)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extrinsic component of membrane (GO:0019898)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|receptor binding (GO:0005102)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			caacatcaggactacgggcgg	0.731																																					p.V14A		Atlas-SNP	.											.	GFRA3	36	.	0			c.T41C						PASS	.						6	10	8					5																	137610073		2055	4108	6163	SO:0001583	missense	2676	exon1			ATCAGGACTACGG	AY358997	CCDS4201.1	5q31.1-q31.3	2008-02-05			ENSG00000146013	ENSG00000146013			4245	protein-coding gene	gene with protein product		605710				9407096	Standard	NM_001496		Approved	GFRa-3	uc003lcn.3	O60609	OTTHUMG00000129200	ENST00000274721.3:c.41T>C	chr5.hg19:g.137610073A>G	ENSP00000274721:p.Val14Ala	8.0	0.0	.		9.0	6.0	.	NM_001496	B2RA36|B4DMY9|Q6UW20|Q8IUZ2	Missense_Mutation	SNP	ENST00000274721.3	hg19	CCDS4201.1	.	.	.	.	.	.	.	.	.	.	A	10.66	1.413148	0.25465	.	.	ENSG00000146013	ENST00000274721;ENST00000378362	T;T	0.49139	1.38;0.79	3.8	2.63	0.31362	.	2.674420	0.01678	N	0.025995	T	0.31071	0.0785	N	0.08118	0	0.09310	N	1	B;B	0.16396	0.017;0.01	B;B	0.18263	0.021;0.009	T	0.24261	-1.0165	10	0.51188	T	0.08	0.3298	5.8269	0.18558	0.879:0.0:0.121:0.0	.	14;14	O60609-2;O60609	.;GFRA3_HUMAN	A	14	ENSP00000274721:V14A;ENSP00000367613:V14A	ENSP00000274721:V14A	V	-	2	0	GFRA3	137637972	0.015000	0.18098	0.128000	0.21923	0.007000	0.05969	1.017000	0.29989	0.799000	0.34018	0.477000	0.44152	GTC	.	.	.	none		0.731	GFRA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251277.1	NM_001496		G	137610073	A	G	137610073	3	3	143	1	0	0	0	0	1	0	0	0	6356	275	10	3	1193	3	GFRA3	5	137610073	Missense_Mutation	SNP	A	TCGA-BQ-7061-01A-11D-1961-08	101570379	137610073	43305187	23	8620											
SNRPC	6631	hgsc.bcm.edu	37	chr6	34730469	34730469	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agagcaggctcagagcctgaTtgacaaaacaagtatgtttc	14	9	10	8	0	1	4	1	2	0	2	2	4	1	4	1	1	3	4	1	1	4	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr6:34730469T>C	ENST00000244520.5	+	3	287	c.149T>C	c.(148-150)aTt>aCt	p.I50T	SNRPC_ENST00000374017.3_Missense_Mutation_p.I71T|SNRPC_ENST00000374018.1_Missense_Mutation_p.I9T|SNRPC_ENST00000474635.1_3'UTR	NM_003093.2	NP_003084.1			small nuclear ribonucleoprotein polypeptide C											endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|pancreas(1)	6						CAGAGCCTGATTGACAAAACA	0.413																																					p.I50T	NSCLC(131;576 1831 5287 11175 13324)	Atlas-SNP	.											.	SNRPC	16	.	0			c.T149C						PASS	.						81	72	75					6																	34730469		2203	4300	6503	SO:0001583	missense	6631	exon3			GCCTGATTGACAA		CCDS34436.1	6p21	2014-03-06			ENSG00000124562	ENSG00000124562			11157	protein-coding gene	gene with protein product		603522				2971157, 8532530	Standard	NR_029472		Approved	U1-C, Yhc1	uc003ojt.2	P09234	OTTHUMG00000014555	ENST00000244520.5:c.149T>C	chr6.hg19:g.34730469T>C	ENSP00000244520:p.Ile50Thr	25.0	0.0	.		22.0	6.0	.	NM_003093		Missense_Mutation	SNP	ENST00000244520.5	hg19	CCDS34436.1	.	.	.	.	.	.	.	.	.	.	T	17.21	3.330727	0.60853	.	.	ENSG00000124562	ENST00000244520;ENST00000374018;ENST00000374017	T;T;T	0.32988	1.43;1.43;1.43	6.17	4.99	0.66335	.	0.093403	0.64402	N	0.000001	T	0.20170	0.0485	M	0.80422	2.495	0.80722	D	1	P	0.36144	0.539	B	0.28709	0.093	T	0.05273	-1.0895	10	0.52906	T	0.07	.	12.5154	0.56030	0.1252:0.0:0.0:0.8748	.	50	P09234	RU1C_HUMAN	T	50;9;71	ENSP00000244520:I50T;ENSP00000363130:I9T;ENSP00000363129:I71T	ENSP00000244520:I50T	I	+	2	0	SNRPC	34838447	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.602000	0.82796	1.111000	0.41721	0.533000	0.62120	ATT	.	.	.	none		0.413	SNRPC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040255.1	NM_003093		C	34730469	T	C	34730469	3	2	143	1	0	0	0	0	1	0	0	0	14876	1493	52	3	159	3	SNRPC	6	34730469	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08		34730469	136384598	24	8621											
PPARD	5467	hgsc.bcm.edu	37	chr6	35392132	35392132	+	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	gtgatccacgacatcgagacAttgtggcaggcagagaaggg	12	6	15	8	2	0	3	0	1	0	2	2	6	1	3	1	3	0	2	1	3	1	1			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr6:35392132A>C	ENST00000311565.4	+	8	1003	c.654A>C	c.(652-654)acA>acC	p.T218T	PPARD_ENST00000540939.1_Silent_p.T115T|PPARD_ENST00000448077.2_Silent_p.T179T|PPARD_ENST00000444397.1_Silent_p.T218T|PPARD_ENST00000337400.2_Silent_p.T218T|PPARD_ENST00000418635.2_Silent_p.T120T|PPARD_ENST00000360694.3_Silent_p.T218T	NM_001171818.1	NP_001165289.1	Q03181	PPARD_HUMAN	peroxisome proliferator-activated receptor delta	218					adipose tissue development (GO:0060612)|anagen (GO:0042640)|apoptotic signaling pathway (GO:0097190)|axon ensheathment (GO:0008366)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cell-substrate adhesion (GO:0031589)|cellular response to hypoxia (GO:0071456)|cholesterol metabolic process (GO:0008203)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|fatty acid beta-oxidation (GO:0006635)|fatty acid catabolic process (GO:0009062)|fatty acid transport (GO:0015908)|gene expression (GO:0010467)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|heart development (GO:0007507)|intracellular receptor signaling pathway (GO:0030522)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)|lipid metabolic process (GO:0006629)|mRNA transcription (GO:0009299)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of inflammatory response (GO:0050728)|negative regulation of smooth muscle cell migration (GO:0014912)|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)|phospholipid biosynthetic process (GO:0008654)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epidermis development (GO:0045684)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of insulin secretion (GO:0032024)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasodilation (GO:0045909)|proteoglycan metabolic process (GO:0006029)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to activity (GO:0014823)|response to glucose (GO:0009749)|response to vitamin A (GO:0033189)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vitamin A metabolic process (GO:0006776)|wound healing (GO:0042060)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|linoleic acid binding (GO:0070539)|lipid binding (GO:0008289)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(4)|liver(2)|lung(9)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23					Bezafibrate(DB01393)|Icosapent(DB00159)|Sulindac(DB00605)|Treprostinil(DB00374)	ACATCGAGACATTGTGGCAGG	0.597																																					p.T218T		Atlas-SNP	.											.	PPARD	46	.	0			c.A654C						PASS	.						56	54	55					6																	35392132		2203	4300	6503	SO:0001819	synonymous_variant	5467	exon8			CGAGACATTGTGG	L07592	CCDS4803.1, CCDS4804.1, CCDS54994.1, CCDS54995.1	6p21.2	2013-01-16	2006-10-17		ENSG00000112033	ENSG00000112033		"Nuclear hormone receptors"	9235	protein-coding gene	gene with protein product		600409	"peroxisome proliferative activated receptor, delta"			1333051	Standard	NM_177435		Approved	NUC1, NUCII, FAAR, NR1C2	uc003okm.3	Q03181	OTTHUMG00000014567	ENST00000311565.4:c.654A>C	chr6.hg19:g.35392132A>C		67.0	0.0	.		62.0	22.0	.	NM_001171818	A8K6J6|B4E3V3|B6ZGS1|B7Z3W1|E9PE18|Q5D1P0|Q7Z5K0|Q9BUD4	Silent	SNP	ENST00000311565.4	hg19	CCDS4803.1																																																																																			.	.	.	none		0.597	PPARD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040288.1	NM_006238		C	35392132	A	C	35392132	2	2	143	1	0	0	0	0	0	0	0	1	12305	204	8	5		5	PPARD	6	35392132	Silent	SNP	A	TCGA-BQ-7061-01A-11D-1961-08	661663	35392132	135722935	25	8622											
TCTE1	202500	hgsc.bcm.edu	37	chr6	44254102	44254102	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaacatgcgtttccagctgcCgccatggtgggccacgtggc	6	8	14	13	3	0	0	0	0	0	0	1	1	1	0	4	3	4	2	4	3	1	1	rs149566851		TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr6:44254102C>T	ENST00000371505.4	-	3	567	c.445G>A	c.(445-447)Ggc>Agc	p.G149S	TCTE1_ENST00000371504.1_5'Flank|TCTE1_ENST00000371503.3_5'UTR|TMEM151B_ENST00000438774.2_Intron|RP11-444E17.6_ENST00000505802.1_Intron	NM_182539.3	NP_872345.2	Q5JU00	TCTE1_HUMAN	t-complex-associated-testis-expressed 1	149										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)			TTCCAGCTGCCGCCATGGTGG	0.612																																					p.G149S		Atlas-SNP	.											.	TCTE1	77	.	0			c.G445A						PASS	.						69	62	64					6																	44254102		2203	4300	6503	SO:0001583	missense	202500	exon3			AGCTGCCGCCATG	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.445G>A	chr6.hg19:g.44254102C>T	ENSP00000360560:p.Gly149Ser	91.0	0.0	.		108.0	22.0	.	NM_182539	B4DX59|Q8IYS6	Missense_Mutation	SNP	ENST00000371505.4	hg19	CCDS4910.1	.	.	.	.	.	.	.	.	.	.	C	13.22	2.172677	0.38413	.	.	ENSG00000146221	ENST00000371505	T	0.53857	0.6	4.95	0.751	0.18392	.	0.494509	0.24332	N	0.039444	T	0.22666	0.0547	M	0.66939	2.045	0.31913	N	0.614463	B	0.29508	0.246	B	0.15484	0.013	T	0.02698	-1.1122	10	0.42905	T	0.14	-22.0618	3.2087	0.06675	0.1282:0.533:0.1253:0.2135	.	149	Q5JU00	TCTE1_HUMAN	S	149	ENSP00000360560:G149S	ENSP00000360560:G149S	G	-	1	0	TCTE1	44362080	0.194000	0.23325	0.977000	0.42913	0.826000	0.46750	1.144000	0.31565	1.073000	0.40885	0.563000	0.77884	GGC	.	C|1.000;A|0.000	.	alt		0.612	TCTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040736.1	NM_182539		T	44254102	C	T	44254102	3	4	143	1	0	0	0	0	1	0	0	0	15729	652	23	1	1072	1	TCTE1	6	44254102	Missense_Mutation	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	8861970	44254102	126860965	26	8623											
TDRD6	221400	hgsc.bcm.edu	37	chr6	46660547	46660547	+	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	tggagaacaggtagcagacaGgagaaattgtatcccatgtc	14	8	12	7	0	0	3	0	0	0	3	2	5	1	3	1	3	2	3	1	3	4	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr6:46660547G>C	ENST00000316081.6	+	1	4682	c.4682G>C	c.(4681-4683)aGg>aCg	p.R1561T	TDRD6_ENST00000544460.1_Missense_Mutation_p.R1561T	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	1561					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)			GTAGCAGACAGGAGAAATTGT	0.383																																					p.R1561T		Atlas-SNP	.											.	TDRD6	205	.	0			c.G4682C						PASS	.						143	136	139					6																	46660547		2203	4300	6503	SO:0001583	missense	221400	exon1			CAGACAGGAGAAA	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.4682G>C	chr6.hg19:g.46660547G>C	ENSP00000346065:p.Arg1561Thr	86.0	0.0	.		70.0	30.0	.	NM_001168359	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Missense_Mutation	SNP	ENST00000316081.6	hg19	CCDS34470.1	.	.	.	.	.	.	.	.	.	.	G	4.125	0.021357	0.08006	.	.	ENSG00000180113	ENST00000544460;ENST00000316081	T;T	0.14640	2.49;2.49	5.77	1.57	0.23409	Maternal tudor protein (1);	2.015520	0.01660	N	0.025077	T	0.01870	0.0059	N	0.17082	0.46	0.09310	N	1	B;B	0.20550	0.037;0.046	B;B	0.16289	0.009;0.015	T	0.36040	-0.9764	10	0.14252	T	0.57	-1.2406	1.4939	0.02462	0.3025:0.1233:0.4278:0.1465	.	1561;1561	F5H5M3;O60522	.;TDRD6_HUMAN	T	1561	ENSP00000443299:R1561T;ENSP00000346065:R1561T	ENSP00000346065:R1561T	R	+	2	0	TDRD6	46768506	0.000000	0.05858	0.002000	0.10522	0.009000	0.06853	0.037000	0.13840	-0.027000	0.13873	-0.345000	0.07892	AGG	.	.	.	none		0.383	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443		C	46660547	G	C	46660547	3	2	143	1	0	0	0	0	1	0	0	0	15746	1000	35	4	4684	4	TDRD6	6	46660547	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	2406445	46660547	124454520	27	8624											
FAM46A	55603	hgsc.bcm.edu	37	chr6	82461531	82461531	+	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	gcggacgccaatgcgcttctCggccaggcgccgccgcacca	6	4	13	18	7	1	0	0	0	1	0	2	1	1	1	5	3	1	2	5	3	1	1			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr6:82461531C>T	ENST00000320172.6	-	2	642	c.328G>A	c.(328-330)Gag>Aag	p.E110K	FAM46A_ENST00000369754.3_Missense_Mutation_p.E129K|FAM46A_ENST00000369756.3_Missense_Mutation_p.E191K	NM_017633.2	NP_060103.2	Q96IP4	FA46A_HUMAN	family with sequence similarity 46, member A	110					regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)		poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	12		all_cancers(76;6.74e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000282)|all_epithelial(107;0.0104)		BRCA - Breast invasive adenocarcinoma(397;0.0428)		ATGCGCTTCTCGGCCAGGCGC	0.672																																					p.E110K		Atlas-SNP	.											.	FAM46A	37	.	0			c.G328A						PASS	.						33	33	33					6																	82461531		2199	4296	6495	SO:0001583	missense	55603	exon2			GCTTCTCGGCCAG	AF350451	CCDS34489.1	6q14	2008-07-03	2004-08-19	2004-08-26	ENSG00000112773	ENSG00000112773			18345	protein-coding gene	gene with protein product		611357	"chromosome 6 open reading frame 37"	C6orf37		12054608, 17803723	Standard	NM_017633		Approved	FLJ20037	uc003pjg.3	Q96IP4	OTTHUMG00000015097	ENST00000320172.6:c.328G>A	chr6.hg19:g.82461531C>T	ENSP00000318298:p.Glu110Lys	71.0	0.0	.		67.0	31.0	.	NM_017633	A8K7U4|Q5TF86|Q8NFZ9|Q9BW32|Q9NXV5	Missense_Mutation	SNP	ENST00000320172.6	hg19	CCDS34489.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.133356	0.77662	.	.	ENSG00000112773	ENST00000369754;ENST00000320172;ENST00000369756	T;T;T	0.24538	1.85;1.85;1.85	5.38	5.38	0.77491	Domain of unknown function DUF1693 (1);	0.093645	0.64402	D	0.000001	T	0.12902	0.0313	L	0.39514	1.22	0.80722	D	1	P;P	0.41748	0.524;0.761	B;B	0.35413	0.202;0.128	T	0.03268	-1.1054	9	.	.	.	-16.9061	18.9095	0.92477	0.0:1.0:0.0:0.0	.	110;129	Q96IP4;Q96IP4-2	FA46A_HUMAN;.	K	129;110;191	ENSP00000358769:E129K;ENSP00000318298:E110K;ENSP00000358771:E191K	.	E	-	1	0	FAM46A	82518250	0.983000	0.35010	0.952000	0.39060	0.004000	0.04260	2.564000	0.45931	2.786000	0.95864	0.563000	0.77884	GAG	.	.	.	none		0.672	FAM46A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041331.1			T	82461531	C	T	82461531	3	4	143	1	0	0	0	0	1	0	0	0	5572	893	31	1	1008	1	FAM46A	6	82461531	Missense_Mutation	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	35800984	82461531	88653536	28	8625											
ROS1	6098	hgsc.bcm.edu	37	chr6	117706858	117706858	+	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	taactcaccacatatgtcttTccagcccagtagagaaagtg	13	10	7	11	0	2	1	1	0	1	1	3	2	3	1	3	0	2	1	3	0	4	4			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr6:117706858T>A	ENST00000368508.3	-	15	2490	c.2292A>T	c.(2290-2292)ggA>ggT	p.G764G	ROS1_ENST00000368507.3_Silent_p.G759G|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	764					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)		CATATGTCTTTCCAGCCCAGT	0.423			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																p.G764G		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	.	ROS1	728	.	0			c.A2292T						PASS	.						94	87	89					6																	117706858		2203	4300	6503	SO:0001819	synonymous_variant	6098	exon15			TGTCTTTCCAGCC	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.2292A>T	chr6.hg19:g.117706858T>A		143.0	0.0	.		118.0	53.0	.	NM_002944	Q15368|Q5TDB5	Silent	SNP	ENST00000368508.3	hg19	CCDS5116.1																																																																																			.	.	.	none		0.423	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			A	117706858	T	A	117706858	2	1	143	1	0	0	0	0	0	0	0	1	13544	1770	62	5		5	ROS1	6	117706858	Silent	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	35245327	117706858	53408209	29	8626											
PDE7B	27115	hgsc.bcm.edu	37	chr6	136512787	136512788	+	Frame_Shift_Ins	INS	-	-	A																															cgtggagccgctcttccgggINSaatgggcccatttcacgggt																										TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr6:136512787_136512788insA	ENST00000308191.6	+	13	1465_1466	c.1162_1163insA	c.(1162-1164)gaafs	p.E388fs	RP13-143G15.4_ENST00000417643.1_RNA|RP13-143G15.4_ENST00000585946.1_RNA|RP13-143G15.4_ENST00000591521.1_RNA	NM_018945.3	NP_061818.1	Q9NP56	PDE7B_HUMAN	phosphodiesterase 7B	388	Catalytic. {ECO:0000250}.				cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)	p.E388*(1)		breast(1)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Colorectal(23;0.24)			OV - Ovarian serous cystadenocarcinoma(155;0.0136)|GBM - Glioblastoma multiforme(68;0.0147)	Caffeine(DB00201)|Dyphylline(DB00651)|Ketotifen(DB00920)	GCTCTTCCGGGAATGGGCCCAT	0.589																																					p.E388fs		Atlas-INDEL	.											PDE7B,NS,carcinoma,0,1	PDE7B	55	.	1	Substitution - Nonsense(1)	lung(1)	c.1162_1163insA						PASS	.																																			SO:0001589	frameshift_variant	27115	exon13			.	AB038040	CCDS5175.1	6q23-q24	2008-03-18			ENSG00000171408	ENSG00000171408	3.1.4.17	"Phosphodiesterases"	8792	protein-coding gene	gene with protein product		604645				10618442	Standard	XM_005266931		Approved		uc003qgp.3	Q9NP56	OTTHUMG00000015641	ENST00000308191.6:c.1164dupA	chr6.hg19:g.136512789_136512789dupA	ENSP00000310661:p.Glu388fs	38.0	0.0	0		35.0	12.0	0.342857	NM_018945	Q5W154	Frame_Shift_Ins	INS	ENST00000308191.6	hg19	CCDS5175.1																																																																																			.	.	.	none		0.589	PDE7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042371.1			A	136512788	-	A	136512787	7	5	143	1	0	1	1	0	0	0	0	0	11659	1175	41	0	1212	0	PDE7B	6	136512787	Frame_Shift_Ins	INS	-	TCGA-BQ-7061-01A-11D-1961-08	18805929	136512787	34602280	30	8627											
RAET1G	353091	hgsc.bcm.edu	37	chr6	150240371	150240371	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagtcaaagaggaggaagaTctgtccatcgaaactgagct	14	8	12	7	1	2	4	1	2	1	2	4	7	3	6	1	2	2	1	1	2	3	0			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr6:150240371T>C	ENST00000367360.2	-	3	506	c.439A>G	c.(439-441)Atc>Gtc	p.I147V	RAET1G_ENST00000479265.1_Missense_Mutation_p.I147V|RP11-244K5.8_ENST00000606915.1_RNA|RAET1E-AS1_ENST00000605899.1_RNA|RAET1E-AS1_ENST00000446954.2_RNA	NM_001001788.2	NP_001001788.2			retinoic acid early transcript 1G											NS(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|urinary_tract(1)	13		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.73e-12)		AGGAGGAAGATCTGTCCATCG	0.507																																					p.I147V		Atlas-SNP	.											.	RAET1G	31	.	0			c.A439G						PASS	.						210	194	200					6																	150240371		2203	4300	6503	SO:0001583	missense	353091	exon3			GGAAGATCTGTCC	AY172579	CCDS43514.1	6q24.1-25.1	2009-04-29	2004-11-22		ENSG00000203722	ENSG00000203722			16795	protein-coding gene	gene with protein product		609244	"retinoic acid early transcript 1G pseudogene"			11827464, 15240696	Standard	NM_001001788		Approved	ULBP5	uc010kii.1	Q6H3X3	OTTHUMG00000015802	ENST00000367360.2:c.439A>G	chr6.hg19:g.150240371T>C	ENSP00000356329:p.Ile147Val	142.0	0.0	.		130.0	59.0	.	NM_001001788		Missense_Mutation	SNP	ENST00000367360.2	hg19	CCDS43514.1	.	.	.	.	.	.	.	.	.	.	T	2.316	-0.356879	0.05138	.	.	ENSG00000203722	ENST00000367360;ENST00000479265	T;T	0.00695	5.83;5.83	2.4	-0.116	0.13555	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	0.00356	0.0011	L	0.39898	1.24	0.09310	N	1	B	0.24043	0.096	B	0.37091	0.241	T	0.33650	-0.9860	9	0.22706	T	0.39	.	6.0143	0.19594	0.0:0.1591:0.0:0.8409	.	147	Q6H3X3	RET1G_HUMAN	V	147	ENSP00000356329:I147V;ENSP00000417503:I147V	ENSP00000356329:I147V	I	-	1	0	RAET1G	150282064	0.000000	0.05858	0.005000	0.12908	0.001000	0.01503	-1.019000	0.03622	-0.018000	0.14079	-1.493000	0.00968	ATC	.	.	.	none		0.507	RAET1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042668.2			C	150240371	T	C	150240371	3	2	143	1	0	0	0	0	1	0	0	0	13013	1435	50	3	577	3	RAET1G	6	150240371	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	13727584	150240371	20874696	31	8628											
GNAI1	2770	hgsc.bcm.edu	37	chr7	79842142	79842142	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaggatctctttgaagaaaaAatcaaaaagagccctctcac	18	8	6	9	0	3	3	2	1	2	2	5	4	3	4	1	1	1	0	1	1	7	1			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr7:79842142A>G	ENST00000351004.3	+	7	1204	c.831A>G	c.(829-831)aaA>aaG	p.K277K	GNAI1_ENST00000457358.2_Silent_p.K225K	NM_002069.5	NP_002060.4	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	277					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						TTGAAGAAAAAATCAAAAAGA	0.323																																					p.K277K		Atlas-SNP	.											.	GNAI1	44	.	0			c.A831G						PASS	.						67	74	71					7																	79842142		2203	4294	6497	SO:0001819	synonymous_variant	2770	exon7			AGAAAAAATCAAA	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.831A>G	chr7.hg19:g.79842142A>G		198.0	0.0	.		263.0	74.0	.	NM_002069	A8KA88|B4E2V1|C9J3A4|P04898|P11015|P31871|Q5U074|Q8TAN5|Q9UGA4	Silent	SNP	ENST00000351004.3	hg19	CCDS5595.1																																																																																			.	.	.	none		0.323	GNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253254.1	NM_002069		G	79842142	A	G	79842142	2	3	143	1	0	0	0	0	0	0	0	1	6511	11	1	3		3	GNAI1	7	79842142	Silent	SNP	A	TCGA-BQ-7061-01A-11D-1961-08		79842142	79296521	32	8629											
SAMD9	54809	hgsc.bcm.edu	37	chr7	92734539	92734539	+	Missense_Mutation	SNP	T	T	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	tactatttggcagtaaaactTccacaaatcttggctctcga	12	13	6	10	1	2	0	0	0	2	0	4	1	3	0	1	2	2	3	1	2	5	6			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr7:92734539T>G	ENST00000379958.2	-	3	1141	c.872A>C	c.(871-873)gAa>gCa	p.E291A		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	291						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)			CAGTAAAACTTCCACAAATCT	0.353																																					p.E291A		Atlas-SNP	.											.	SAMD9	239	.	0			c.A872C						PASS	.						122	121	121					7																	92734539		2203	4300	6503	SO:0001583	missense	54809	exon2			AAAACTTCCACAA	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.872A>C	chr7.hg19:g.92734539T>G	ENSP00000369292:p.Glu291Ala	88.0	0.0	.		95.0	52.0	.	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	hg19	CCDS34680.1	.	.	.	.	.	.	.	.	.	.	T	17.37	3.372223	0.61624	.	.	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.16324	2.35;2.35	4.34	4.34	0.51931	.	0.190136	0.33127	U	0.005253	T	0.20700	0.0498	M	0.73598	2.24	0.30798	N	0.740149	P	0.40970	0.734	B	0.35114	0.196	T	0.33111	-0.9881	10	0.72032	D	0.01	-8.454	12.7423	0.57259	0.0:0.0:0.0:1.0	.	291	Q5K651	SAMD9_HUMAN	A	291	ENSP00000369292:E291A;ENSP00000414529:E291A	ENSP00000369292:E291A	E	-	2	0	SAMD9	92572475	1.000000	0.71417	0.998000	0.56505	0.879000	0.50718	2.498000	0.45363	1.948000	0.56530	0.491000	0.48974	GAA	.	.	.	none		0.353	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		G	92734539	T	G	92734539	3	3	143	1	0	0	0	0	1	0	0	0	13839	1783	62	5	3901	5	SAMD9	7	92734539	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	12892397	92734539	66404124	33	8630											
SLC26A5	375611	hgsc.bcm.edu	37	chr7	103029511	103029511	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcacagcagtgatcaaaccAtagtccaatcccaggaacaa	17	6	6	12	0	2	1	2	1	0	0	4	2	4	2	3	1	3	1	3	1	5	1			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr7:103029511A>G	ENST00000306312.3	-	14	1719	c.1458T>C	c.(1456-1458)taT>taC	p.Y486Y	SLC26A5_ENST00000356767.4_Intron|SLC26A5_ENST00000393730.1_Silent_p.Y454Y|SLC26A5_ENST00000393735.2_Silent_p.Y486Y|SLC26A5_ENST00000393729.1_Silent_p.Y449Y|SLC26A5_ENST00000432958.2_Silent_p.Y454Y|SLC26A5_ENST00000339444.6_Silent_p.Y486Y|SLC26A5_ENST00000393727.1_Silent_p.Y486Y|SLC26A5_ENST00000393723.1_Silent_p.Y454Y|SLC26A5_ENST00000354356.4_5'UTR	NM_198999.2	NP_945350.1	P58743	S26A5_HUMAN	solute carrier family 26 (anion exchanger), member 5	486					regulation of cell shape (GO:0008360)|regulation of membrane potential (GO:0042391)|sensory perception of sound (GO:0007605)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)	secondary active sulfate transmembrane transporter activity (GO:0008271)			endometrium(5)|kidney(2)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)	43						TGATCAAACCATAGTCCAATC	0.458																																					p.Y486Y		Atlas-SNP	.											.	SLC26A5	231	.	0			c.T1458C						PASS	.						141	108	119					7																	103029511		2203	4300	6503	SO:0001819	synonymous_variant	375611	exon14			CAAACCATAGTCC	AC005064	CCDS5733.1, CCDS43630.1, CCDS55150.1, CCDS5732.1, CCDS43629.1	7q22	2013-07-18	2013-07-18	2005-09-13	ENSG00000170615	ENSG00000170615		"Solute carriers"	9359	protein-coding gene	gene with protein product	"deafness, neurosensory, autosomal recessive, 61"	604943	"prestin (motor protein)"	PRES		10821263	Standard	NM_206883		Approved	DFNB61	uc003vbz.3	P58743	OTTHUMG00000149911	ENST00000306312.3:c.1458T>C	chr7.hg19:g.103029511A>G		54.0	0.0	.		78.0	17.0	.	NM_206883	Q496J2|Q7Z7F3|Q86UF8|Q86UF9|Q86UG0	Silent	SNP	ENST00000306312.3	hg19	CCDS5733.1																																																																																			.	.	.	none		0.458	SLC26A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313860.1	NM_198999		G	103029511	A	G	103029511	2	3	143	1	0	0	0	0	0	0	0	1	14533	224	8	3		3	SLC26A5	7	103029511	Silent	SNP	A	TCGA-BQ-7061-01A-11D-1961-08	10294972	103029511	56109152	34	8631											
KIAA1549	57670	hgsc.bcm.edu	37	chr7	138602963	138602963	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcctcaaattcagagaagTctgctacgacgctactcatt	11	12	6	12	2	4	1	3	0	1	1	5	3	5	1	1	0	3	2	1	0	4	5			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr7:138602963T>C	ENST00000422774.1	-	2	1457	c.1409A>G	c.(1408-1410)gAc>gGc	p.D470G	KIAA1549_ENST00000440172.1_Missense_Mutation_p.D470G|KIAA1549_ENST00000242365.4_Missense_Mutation_p.D420G			Q9HCM3	K1549_HUMAN	KIAA1549	470						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						TTCAGAGAAGTCTGCTACGAC	0.483			O	BRAF	pilocytic astrocytoma																																p.D470G	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549	314	.	0			c.A1409G						PASS	.						39	40	40					7																	138602963		2029	4193	6222	SO:0001583	missense	57670	exon2			GAGAAGTCTGCTA		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.1409A>G	chr7.hg19:g.138602963T>C	ENSP00000416040:p.Asp470Gly	66.0	0.0	.		77.0	23.0	.	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	hg19	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	T	11.54	1.669378	0.29693	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.41065	1.01;1.03;1.03	4.75	3.59	0.41128	.	0.100076	0.43579	N	0.000548	T	0.26448	0.0646	N	0.20986	0.625	0.20703	N	0.999861	B;B	0.23540	0.053;0.087	B;B	0.23018	0.019;0.043	T	0.14476	-1.0471	10	0.33141	T	0.24	.	8.3927	0.32537	0.0:0.089:0.0:0.911	.	470;470	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	G	470;420;470	ENSP00000406661:D470G;ENSP00000242365:D420G;ENSP00000416040:D470G	ENSP00000242365:D420G	D	-	2	0	KIAA1549	138253503	0.991000	0.36638	0.195000	0.23364	0.070000	0.16714	1.352000	0.34033	0.846000	0.35142	0.533000	0.62120	GAC	.	.	.	none		0.483	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			C	138602963	T	C	138602963	3	2	143	1	0	0	0	0	1	0	0	0	8251	1667	58	3	4519	3	KIAA1549	7	138602963	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	35573452	138602963	20535700	35	8632											
TMEM176B	28959	hgsc.bcm.edu	37	chr7	150493608	150493608	+	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	tgacgtgggtgggctgggatGgcctagaggccatagcaact	8	8	17	8	1	0	2	0	1	0	1	0	3	0	3	2	5	2	2	2	5	3	2			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr7:150493608G>C	ENST00000447204.2	-	2	422	c.50C>G	c.(49-51)cCa>cGa	p.P17R	TMEM176B_ENST00000450753.2_Missense_Mutation_p.P17R|TMEM176B_ENST00000492607.1_Missense_Mutation_p.P17R|TMEM176B_ENST00000429904.2_Missense_Mutation_p.P17R|TMEM176B_ENST00000326442.5_Missense_Mutation_p.P17R|TMEM176B_ENST00000434545.1_Missense_Mutation_p.P17R	NM_014020.3	NP_054739.3	Q3YBM2	T176B_HUMAN	transmembrane protein 176B	17				PS -> HA (in Ref. 1; AAD23440). {ECO:0000305}.	cell differentiation (GO:0030154)|negative regulation of dendritic cell differentiation (GO:2001199)|organ morphogenesis (GO:0009887)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				cervix(1)|large_intestine(4)|lung(10)|ovary(1)|skin(3)	19			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GGGCTGGGATGGCCTAGAGGC	0.522																																					p.P17R		Atlas-SNP	.											.	TMEM176B	36	.	0			c.C50G						PASS	.						91	82	85					7																	150493608		2203	4300	6503	SO:0001583	missense	28959	exon2			TGGGATGGCCTAG	AF115384	CCDS5908.1, CCDS47746.1	7q36.1	2006-09-04			ENSG00000106565	ENSG00000106565			29596	protein-coding gene	gene with protein product		610385				9922225	Standard	NM_014020		Approved	LR8	uc003whu.4	Q3YBM2	OTTHUMG00000157577	ENST00000447204.2:c.50C>G	chr7.hg19:g.150493608G>C	ENSP00000410269:p.Pro17Arg	72.0	0.0	.		129.0	6.0	.	NM_014020	B2RDK2|D3DWZ7|E9PAV4|Q5BJI2|Q9BT42|Q9Y609	Missense_Mutation	SNP	ENST00000447204.2	hg19	CCDS5908.1	.	.	.	.	.	.	.	.	.	.	G	4.944	0.175328	0.09391	.	.	ENSG00000106565	ENST00000492607;ENST00000326442;ENST00000447204;ENST00000434545;ENST00000429904;ENST00000450753;ENST00000528038	T;T;T;T;T;T	0.07327	3.35;3.35;3.35;3.35;3.35;3.2	4.92	-6.03	0.02185	.	2.014350	0.02708	N	0.112490	T	0.03564	0.0102	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.0	T	0.37197	-0.9716	10	0.14252	T	0.57	2.0728	0.9199	0.01312	0.193:0.1221:0.2552:0.4297	.	17;17	E9PAV4;Q3YBM2	.;T176B_HUMAN	R	17	ENSP00000419258:P17R;ENSP00000318409:P17R;ENSP00000410269:P17R;ENSP00000413531:P17R;ENSP00000397810:P17R;ENSP00000404831:P17R	ENSP00000318409:P17R	P	-	2	0	TMEM176B	150124541	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.663000	0.05299	-0.721000	0.04929	0.467000	0.42956	CCA	.	.	.	none		0.522	TMEM176B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349204.1	NM_014020		C	150493608	G	C	150493608	3	2	143	1	0	0	0	0	1	0	0	0	16105	1348	47	4	786	4	TMEM176B	7	150493608	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	11890645	150493608	8645055	36	8633											
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77617295	77617296	+	Missense_Mutation	DNP	GA	GA	TT																															gtctccgccataatacagggGattggcaaagacaaagaacc																										TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr8:77617295_77617296GA>TT	ENST00000521891.2	+	2	1420_1421	c.972_973GA>TT	c.(970-975)ggGAtt>ggTTtt	p.I325F	ZFHX4_ENST00000050961.6_Missense_Mutation_p.I325F|ZFHX4_ENST00000517683.1_Intron|ZFHX4_ENST00000455469.2_Missense_Mutation_p.I325F|ZFHX4_ENST00000518282.1_Missense_Mutation_p.I325F	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	325					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.G324G(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)			TAATACAGGGGATTGGCAAAGA	0.441										HNSCC(33;0.089)																											p.G324G|p.I325F		Atlas-SNP	.											ZFHX4,NS,carcinoma,0,1|.	ZFHX4	878	.	1	Substitution - coding silent(1)	lung(1)	c.G972T|c.A973T						PASS	.																																			SO:0001583	missense	79776	exon2			ACAGGGGATTGGC|CAGGGGATTGGCA		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	Exception_encountered	chr8.hg19:g.77617295_77617296delinsTT	ENSP00000430497:p.Ile325Phe	143.0|142.0	0.0	.		158.0|161.0	61.0|63.0	.	NM_024721	G3V138|Q18PS0|Q6ZN20	Silent|Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2																																																																																			.	.	.	none		0.441	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		TT	77617296	GA	TT	77617295	3	4	143	1	0	0	0	0	1	0	0	0	17647	1161	41	4	974	4	ZFHX4	8	77617295	Missense_Mutation	DNP	GA	TCGA-BQ-7061-01A-11D-1961-08		77617295	68746727	37	8634											
ANKRD26	22852	hgsc.bcm.edu	37	chr10	27349330	27349331	+	In_Frame_Ins	INS	-	-	TCA																															tttatttggaacagaatcttINStcatttcaatggtaggctga																										TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr10:27349330_27349331insTCA	ENST00000376087.4	-	15	1672_1673	c.1507_1508insTGA	c.(1507-1509)aaa>aTGAaa	p.502_503insM	ANKRD26_ENST00000436985.2_In_Frame_Ins_p.518_519insM	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	502					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						AACAGAATCTTTCATTTCAATG	0.277																																					p.K503delinsMK		Atlas-INDEL	.											.	ANKRD26	179	.	0			c.1508_1509insTGA						PASS	.																																			SO:0001652	inframe_insertion	22852	exon15			.	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.1505_1507dupTGA	chr10.hg19:g.27349331_27349333dupTCA	ENSP00000365255:p.Met502_Met502dup	171.0	0.0	0		143.0	44.0	0.307692	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	In_Frame_Ins	INS	ENST00000376087.4	hg19	CCDS41499.1																																																																																			.	.	.	none		0.277	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			TCA	27349331	-	TCA	27349330	7	5	143	1	0	1	1	0	0	0	0	0	654	1841	64	0	3704	0	ANKRD26	10	27349330	In_Frame_Ins	INS	-	TCGA-BQ-7061-01A-11D-1961-08		27349330	108185417	38	8635											
NCAPD3	23310	hgsc.bcm.edu	37	chr11	134038822	134038822	+	Frame_Shift_Del	DEL	G	G	-																															cttcactgacctctctgactGggggaacttgttgtacttct																										TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr11:134038822delG	ENST00000534548.2	-	25	3293	c.3229delC	c.(3229-3231)cagfs	p.Q1077fs		NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	1077					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)		CTCTCTGACTGGGGGAACTTG	0.443																																					p.Q1077fs		Atlas-INDEL	.											.	NCAPD3	141	.	0			c.3230delA						PASS	.						115	107	110					11																	134038822		2201	4297	6498	SO:0001589	frameshift_variant	23310	exon25			.	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.3229delC	chr11.hg19:g.134038822delG	ENSP00000433681:p.Gln1077fs	110.0	0.0	0		91.0	35.0	0.384615	NM_015261	A6NFS2|Q4KMQ9	Frame_Shift_Del	DEL	ENST00000534548.2	hg19	CCDS31723.1																																																																																			.	.	.	none		0.443	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261		-	134038822	G	-	134038822	7	5	143	1	0	1	0	1	0	0	0	0	10213	1357	47	0	1311	0	NCAPD3	11	134038822	Frame_Shift_Del	DEL	G	TCGA-BQ-7061-01A-11D-1961-08		134038822	967694	39	8636											
SLC6A13	6540	hgsc.bcm.edu	37	chr12	346409	346409	+	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	acagagccagctcccagcgcAgggcccccaggtgctggatc	8	4	13	16	1	0	1	0	0	0	1	2	2	1	2	4	3	4	3	4	3	0	0			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr12:346409A>T	ENST00000343164.4	-	6	663	c.611T>A	c.(610-612)cTg>cAg	p.L204Q	SLC6A13_ENST00000445055.2_Missense_Mutation_p.L112Q	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	204					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)			CTCCCAGCGCAGGGCCCCCAG	0.602																																					p.L204Q		Atlas-SNP	.											.	SLC6A13	62	.	0			c.T611A						PASS	.						66	69	68					12																	346409		2203	4300	6503	SO:0001583	missense	6540	exon6			CAGCGCAGGGCCC	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.611T>A	chr12.hg19:g.346409A>T	ENSP00000339260:p.Leu204Gln	133.0	0.0	.		164.0	41.0	.	NM_016615	B4DJL1|Q8TCC2|Q8WW56	Missense_Mutation	SNP	ENST00000343164.4	hg19	CCDS8502.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.892851	0.91889	.	.	ENSG00000010379	ENST00000445055;ENST00000313154;ENST00000343164;ENST00000546319	T;T;T	0.78003	-1.14;-1.14;-1.14	5.5	5.5	0.81552	.	0.070471	0.64402	D	0.000018	D	0.90428	0.7003	M	0.92317	3.295	0.80722	D	1	D;D;D	0.76494	0.976;0.999;0.996	D;D;D	0.71414	0.964;0.973;0.964	D	0.92683	0.6160	10	0.87932	D	0	.	15.8304	0.78745	1.0:0.0:0.0:0.0	.	112;183;204	B4DJL1;B4DJS3;Q9NSD5	.;.;S6A13_HUMAN	Q	112;183;204;112	ENSP00000407104:L112Q;ENSP00000339260:L204Q;ENSP00000444606:L112Q	ENSP00000318097:L183Q	L	-	2	0	SLC6A13	216670	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.127000	0.94417	2.322000	0.78497	0.529000	0.55759	CTG	.	.	.	none		0.602	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615		T	346409	A	T	346409	3	4	143	1	0	0	0	0	1	0	0	0	14689	188	7	5	1237	5	SLC6A13	12	346409	Missense_Mutation	SNP	A	TCGA-BQ-7061-01A-11D-1961-08		346409	133505486	40	8637											
ATN1	1822	hgsc.bcm.edu	37	chr12	7046365	7046365	+	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	tacggaaagagagccccgtcCccgggggcctacaagacagc	11	3	13	14	3	0	2	0	0	0	2	1	4	1	3	5	3	4	0	5	3	4	2			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr12:7046365C>G	ENST00000356654.4	+	5	2172	c.1935C>G	c.(1933-1935)tcC>tcG	p.S645S	ATN1_ENST00000396684.2_Silent_p.S645S	NM_001007026.1	NP_001007027.1	P54259	ATN1_HUMAN	atrophin 1	645					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						GAGCCCCGTCCCCGGGGGCCT	0.672																																					p.S645S		Atlas-SNP	.											.	ATN1	95	.	0			c.C1935G						PASS	.						22	27	25					12																	7046365		2201	4291	6492	SO:0001819	synonymous_variant	1822	exon5			CCCGTCCCCGGGG	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.1935C>G	chr12.hg19:g.7046365C>G		76.0	0.0	.		95.0	54.0	.	NM_001007026	Q99495|Q99621|Q9UEK7	Silent	SNP	ENST00000356654.4	hg19	CCDS31734.1																																																																																			.	.	.	none		0.672	ATN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401948.2	NM_001940		G	7046365	C	G	7046365	2	3	143	1	0	0	0	0	0	0	0	1	1111	610	22	4		4	ATN1	12	7046365	Silent	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	6699956	7046365	126805530	41	8638											
TAS2R13	50838	hgsc.bcm.edu	37	chr12	11061866	11061866	+	Missense_Mutation	SNP	A	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	tgaattctgcaattattacaAgagtgaagatactcggcagg	14	11	10	6	1	1	4	0	2	1	2	2	4	1	4	0	2	3	2	0	2	7	4			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr12:11061866A>C	ENST00000390677.2	-	1	295	c.32T>G	c.(31-33)cTt>cGt	p.L11R	PRR4_ENST00000536668.1_Intron	NM_023920.2	NP_076409.1	Q9NYV9	T2R13_HUMAN	taste receptor, type 2, member 13	11					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|positive regulation of cytokinesis (GO:0032467)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9						AATTATTACAAGAGTGAAGAT	0.388																																					p.L11R		Atlas-SNP	.											.	TAS2R13	29	.	0			c.T32G						PASS	.						39	38	39					12																	11061866		2202	4298	6500	SO:0001583	missense	50838	exon1			ATTACAAGAGTGA	AF227137	CCDS8635.1	12p13	2012-08-22			ENSG00000212128	ENSG00000212128		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14919	protein-coding gene	gene with protein product		604792				10761934, 10766242	Standard	NM_023920		Approved	T2R13, TRB3	uc001qzg.1	Q9NYV9		ENST00000390677.2:c.32T>G	chr12.hg19:g.11061866A>C	ENSP00000375095:p.Leu11Arg	41.0	0.0	.		54.0	31.0	.	NM_023920	Q4G0I5|Q502V8|Q645X2	Missense_Mutation	SNP	ENST00000390677.2	hg19	CCDS8635.1	.	.	.	.	.	.	.	.	.	.	A	12.87	2.068962	0.36470	.	.	ENSG00000212128	ENST00000390677	T	0.00922	5.54	3.3	2.14	0.27477	.	0.745999	0.10446	U	0.673619	T	0.02888	0.0086	M	0.76328	2.33	0.09310	N	1	P	0.48834	0.916	P	0.54026	0.74	T	0.42582	-0.9443	10	0.87932	D	0	.	5.1506	0.15007	0.8598:0.0:0.1402:0.0	.	11	Q9NYV9	T2R13_HUMAN	R	11	ENSP00000375095:L11R	ENSP00000375095:L11R	L	-	2	0	TAS2R13	10953133	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	0.614000	0.24314	0.456000	0.26937	0.533000	0.62120	CTT	.	.	.	none		0.388	TAS2R13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400229.1			C	11061866	A	C	11061866	3	2	143	1	0	0	0	0	1	0	0	0	15579	72	3	5	883	5	TAS2R13	12	11061866	Missense_Mutation	SNP	A	TCGA-BQ-7061-01A-11D-1961-08	4015501	11061866	122790029	42	8639											
DPY19L2	283417	hgsc.bcm.edu	37	chr12	64041138	64041138	+	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	atgtgcaataccaggaggctAtgattaccttaaaaaagata	17	10	8	6	0	0	2	0	1	0	1	0	3	0	3	2	2	3	2	2	2	8	5			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr12:64041138A>T	ENST00000324472.4	-	5	779	c.596T>A	c.(595-597)aTa>aAa	p.I199K	RP11-415I12.3_ENST00000509615.2_RNA	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	199					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)			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)		CCAGGAGGCTATGATTACCTT	0.299																																					p.I199K		Atlas-SNP	.											.	DPY19L2	97	.	0			c.T596A						PASS	.						60	65	63					12																	64041138		2203	4297	6500	SO:0001583	missense	283417	exon5			GAGGCTATGATTA		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.596T>A	chr12.hg19:g.64041138A>T	ENSP00000315988:p.Ile199Lys	148.0	0.0	.		189.0	40.0	.	NM_173812	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Missense_Mutation	SNP	ENST00000324472.4	hg19	CCDS31851.1	.	.	.	.	.	.	.	.	.	.	A	10.54	1.378802	0.24944	.	.	ENSG00000177990	ENST00000324472	T	0.56275	0.47	2.35	2.35	0.29111	.	0.184092	0.34828	U	0.003648	T	0.59046	0.2165	M	0.66939	2.045	0.58432	D	0.999995	D	0.53619	0.961	P	0.57009	0.811	T	0.57808	-0.7747	9	.	.	.	.	6.5488	0.22420	1.0:0.0:0.0:0.0	.	199	Q6NUT2	D19L2_HUMAN	K	199	ENSP00000315988:I199K	.	I	-	2	0	DPY19L2	62327405	0.987000	0.35691	0.069000	0.20011	0.326000	0.28443	5.607000	0.67648	1.080000	0.41073	0.155000	0.16302	ATA	.	.	.	none		0.299	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812		T	64041138	A	T	64041138	3	4	143	1	0	0	0	0	1	0	0	0	4743	449	16	5	1752	5	DPY19L2	12	64041138	Missense_Mutation	SNP	A	TCGA-BQ-7061-01A-11D-1961-08	52979272	64041138	69810757	43	8640											
RFX4	5992	hgsc.bcm.edu	37	chr12	107154995	107154995	+	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	tacccttttaatagccccacTtcccggatggaaccttgttt	8	14	6	13	1	0	0	0	0	0	0	1	2	1	2	5	2	3	1	5	2	4	7			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr12:107154995T>A	ENST00000392842.1	+	18	2370	c.1956T>A	c.(1954-1956)acT>acA	p.T652T	RFX4_ENST00000357881.4_Silent_p.T661T|RP11-144F15.1_ENST00000551505.1_Intron|RFX4_ENST00000229387.5_Silent_p.T558T	NM_213594.2	NP_998759.1	Q33E94	RFX4_HUMAN	regulatory factor X, 4 (influences HLA class II expression)	652					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						ATAGCCCCACTTCCCGGATGG	0.468																																					p.T661T		Atlas-SNP	.											.	RFX4	218	.	0			c.T1983A						PASS	.						190	205	200					12																	107154995		2203	4300	6503	SO:0001819	synonymous_variant	5992	exon18			CCCCACTTCCCGG	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.1956T>A	chr12.hg19:g.107154995T>A		430.0	1.0	.		528.0	282.0	.	NM_001206691	A8K5Y0|B2RDW4|Q33DW6|Q33DW7|Q33E95|Q6YM53|Q8MHQ1|Q8NC78|Q8NDF9|Q8SNA1|Q96S80|Q9BXI0	Silent	SNP	ENST00000392842.1	hg19	CCDS9106.1																																																																																			.	.	.	none		0.468	RFX4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402707.1	NM_032491		A	107154995	T	A	107154995	2	1	143	1	0	0	0	0	0	0	0	1	13278	1596	56	5		5	RFX4	12	107154995	Silent	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	43113857	107154995	26696900	44	8641											
NOS1	4842	hgsc.bcm.edu	37	chr12	117655909	117655909	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggactcagatctaaggcggtTggtcacttcgtacgttcgca	8	11	12	10	4	3	1	2	0	1	1	5	2	3	2	0	4	1	4	0	4	2	5			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr12:117655909T>C	ENST00000338101.4	-	28	4337	c.4333A>G	c.(4333-4335)Aac>Gac	p.N1445D	NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Missense_Mutation_p.N1411D			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)		CTAAGGCGGTTGGTCACTTCG	0.498																																					p.N1445D	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.A4333G						PASS	.						312	309	310					12																	117655909		1986	4167	6153	SO:0001583	missense	4842	exon29			GGCGGTTGGTCAC		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.4333A>G	chr12.hg19:g.117655909T>C	ENSP00000337459:p.Asn1445Asp	458.0	0.0	.		603.0	135.0	.	NM_001204218		Missense_Mutation	SNP	ENST00000338101.4	hg19	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	T	17.40	3.379742	0.61845	.	.	ENSG00000089250	ENST00000397605;ENST00000317775;ENST00000338101	T;T	0.01397	4.94;4.99	4.57	4.57	0.56435	.	0.093612	0.85682	D	0.000000	T	0.02342	0.0072	L	0.59436	1.845	0.80722	D	1	P	0.36412	0.552	B	0.35039	0.194	T	0.60393	-0.7272	10	0.38643	T	0.18	-42.2525	14.0843	0.64944	0.0:0.0:0.0:1.0	.	1411	P29475	NOS1_HUMAN	D	1306;1411;1445	ENSP00000320758:N1411D;ENSP00000337459:N1445D	ENSP00000320758:N1411D	N	-	1	0	NOS1	116140292	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.501000	0.81600	1.914000	0.55421	0.459000	0.35465	AAC	.	.	.	none		0.498	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			C	117655909	T	C	117655909	3	2	143	1	0	0	0	0	1	0	0	0	10548	1812	63	3	81	3	NOS1	12	117655909	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	10500914	117655909	16195986	45	8642											
RIMBP2	23504	hgsc.bcm.edu	37	chr12	130919339	130919339	+	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	gaggcgcccctcctcttgaaGtctggagagtcataggcgtc	7	9	13	12	2	3	2	1	1	2	1	5	4	4	2	3	3	0	0	3	3	2	2			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr12:130919339G>A	ENST00000261655.4	-	11	2305	c.2142C>T	c.(2140-2142)gaC>gaT	p.D714D	RIMBP2_ENST00000536002.1_Silent_p.D622D|RIMBP2_ENST00000535703.1_Silent_p.D622D	NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	714					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)		TCCTCTTGAAGTCTGGAGAGT	0.597																																					p.D714D		Atlas-SNP	.											.	RIMBP2	220	.	0			c.C2142T						PASS	.						74	81	79					12																	130919339		2203	4300	6503	SO:0001819	synonymous_variant	23504	exon11			CTTGAAGTCTGGA	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.2142C>T	chr12.hg19:g.130919339G>A		167.0	0.0	.		206.0	30.0	.	NM_015347	Q96ID2	Silent	SNP	ENST00000261655.4	hg19	CCDS31925.1																																																																																			.	.	.	none		0.597	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347		A	130919339	G	A	130919339	2	1	143	1	0	0	0	0	0	0	0	1	13376	1020	36	2		2	RIMBP2	12	130919339	Silent	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	13263430	130919339	2932556	46	8643											
MGA	23269	hgsc.bcm.edu	37	chr15	42041819	42041837	+	Frame_Shift_Del	DEL	CTAATGTAATAAAACAAAA	CTAATGTAATAAAACAAAA	-																															agaggctgtagaccctgaggCtaatgtaataaaacaaaact																								rs373448335		TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	CTAATGTAATAAAACAAAA	CTAATGTAATAAAACAAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr15:42041819_42041837delCTAATGTAATAAAACAAAA	ENST00000570161.1	+	16	6014_6032	c.6014_6032delCTAATGTAATAAAACAAAA	c.(6013-6033)gctaatgtaataaaacaaaacfs	p.ANVIKQN2005fs	MGA_ENST00000389936.4_Frame_Shift_Del_p.ANVIKQN1966fs|MGA_ENST00000545763.1_Frame_Shift_Del_p.ANVIKQN1796fs|MGA_ENST00000219905.7_Frame_Shift_Del_p.ANVIKQN2005fs|MGA_ENST00000566586.1_Frame_Shift_Del_p.ANVIKQN1796fs			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GACCCTGAGGCTAATGTAATAAAACAAAACTCAGGAGCT	0.416																																					p.2005_2011del		Atlas-INDEL	.											.	MGA	264	.	0			c.6013_6031del						PASS	.																																			SO:0001589	frameshift_variant	23269	exon17			.	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.6014_6032delCTAATGTAATAAAACAAAA	chr15.hg19:g.42041819_42041837delCTAATGTAATAAAACAAAA	ENSP00000457035:p.Ala2005fs	153.0	0.0	0		111.0	24.0	0.216216	NM_001164273	Q0VAX6|Q75ME7|Q86UM5	Frame_Shift_Del	DEL	ENST00000570161.1	hg19	CCDS55959.1																																																																																			.	.	.	none		0.416	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		-	42041837	CTAATGTAATAAAACAAAA	-	42041819	7	5	143	1	0	1	0	1	0	0	0	0	9547	797	28	0	6076	0	MGA	15	42041819	Frame_Shift_Del	DEL	CTAATGTAATAAAACAAAA	TCGA-BQ-7061-01A-11D-1961-08		42041819	60489573	47	8644											
TP53BP1	7158	hgsc.bcm.edu	37	chr15	43749140	43749140	+	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	agaattgagaactggagacaTgggttccgtatcctcaatct	12	11	10	8	1	2	3	1	1	1	3	4	5	4	3	2	2	1	2	2	2	4	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr15:43749140T>A	ENST00000263801.3	-	12	1903	c.1651A>T	c.(1651-1653)Atg>Ttg	p.M551L	TP53BP1_ENST00000382044.4_Missense_Mutation_p.M556L|TP53BP1_ENST00000450115.2_Missense_Mutation_p.M556L|TP53BP1_ENST00000382039.3_Missense_Mutation_p.M556L|TP53BP1_ENST00000605155.1_5'Flank	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	551					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)		ACTGGAGACATGGGTTCCGTA	0.403								Other conserved DNA damage response genes																													p.M556L		Atlas-SNP	.											.	TP53BP1	157	.	0			c.A1666T						PASS	.						152	135	141					15																	43749140		2201	4298	6499	SO:0001583	missense	7158	exon12			GAGACATGGGTTC	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.1651A>T	chr15.hg19:g.43749140T>A	ENSP00000263801:p.Met551Leu	108.0	0.0	.		66.0	27.0	.	NM_001141980	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Missense_Mutation	SNP	ENST00000263801.3	hg19	CCDS10096.1	.	.	.	.	.	.	.	.	.	.	T	4.082	0.013103	0.07912	.	.	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115;ENST00000413546	T;T;T;T;T	0.15017	2.46;2.46;2.46;2.46;2.46	5.04	1.11	0.20524	.	0.534882	0.20646	N	0.088301	T	0.09730	0.0239	L	0.36672	1.1	0.19775	N	0.999951	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	0.37361	-0.9709	10	0.10377	T	0.69	-0.7027	5.1031	0.14770	0.3274:0.0823:0.0:0.5903	.	556;551;556;556	B7Z3E7;Q12888;Q12888-2;F8VY86	.;TP53B_HUMAN;.;.	L	551;556;556;556;556	ENSP00000263801:M551L;ENSP00000371475:M556L;ENSP00000371470:M556L;ENSP00000393497:M556L;ENSP00000388028:M556L	ENSP00000263801:M551L	M	-	1	0	TP53BP1	41536432	0.005000	0.15991	0.993000	0.49108	0.768000	0.43524	0.173000	0.16724	0.321000	0.23259	-0.371000	0.07208	ATG	.	.	.	none		0.403	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			A	43749140	T	A	43749140	3	1	143	1	0	0	0	0	1	0	0	0	16395	1464	51	5	4335	5	TP53BP1	15	43749140	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	1707321	43749140	58782252	48	8645											
MYO1E	4643	hgsc.bcm.edu	37	chr15	59501015	59501015	+	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	gcatgcatcgtggcgcacacGtcatccaggatgctcatgat	9	9	11	12	3	2	1	2	1	0	0	4	2	3	2	1	2	2	4	1	2	0	0			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr15:59501015G>A	ENST00000288235.4	-	14	1794	c.1395C>T	c.(1393-1395)gaC>gaT	p.D465D		NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	465	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)		TGGCGCACACGTCATCCAGGA	0.542																																					p.D465D		Atlas-SNP	.											.	MYO1E	99	.	0			c.C1395T						PASS	.						118	99	105					15																	59501015		2191	4290	6481	SO:0001819	synonymous_variant	4643	exon14			GCACACGTCATCC	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.1395C>T	chr15.hg19:g.59501015G>A		73.0	0.0	.		71.0	16.0	.	NM_004998	Q14778	Silent	SNP	ENST00000288235.4	hg19	CCDS32254.1																																																																																			.	.	.	none		0.542	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1	NM_004998		A	59501015	G	A	59501015	2	1	143	1	0	0	0	0	0	0	0	1	10079	1136	40	1		1	MYO1E	15	59501015	Silent	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	15751875	59501015	43030377	49	8646											
TLN2	83660	hgsc.bcm.edu	37	chr15	63011987	63011987	+	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	cagtggctgatcacatccctCagctggtccagggagtgagg	8	8	14	11	0	2	2	2	2	0	0	4	3	4	3	2	4	1	2	2	4	0	0			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr15:63011987C>G	ENST00000561311.1	+	24	3129	c.2899C>G	c.(2899-2901)Cag>Gag	p.Q967E	TLN2_ENST00000306829.6_Missense_Mutation_p.Q967E			Q9Y4G6	TLN2_HUMAN	talin 2	967	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						TCACATCCCTCAGCTGGTCCA	0.547																																					p.Q967E		Atlas-SNP	.											.	TLN2	253	.	0			c.C2899G						PASS	.						65	51	56					15																	63011987		2203	4300	6503	SO:0001583	missense	83660	exon22			ATCCCTCAGCTGG	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.2899C>G	chr15.hg19:g.63011987C>G	ENSP00000453508:p.Gln967Glu	52.0	0.0	.		36.0	13.0	.	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	hg19	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	C	16.18	3.050280	0.55218	.	.	ENSG00000171914	ENST00000306829	T	0.67865	-0.29	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.63153	0.2487	L	0.47716	1.5	0.80722	D	1	B	0.24882	0.113	B	0.25987	0.065	T	0.56745	-0.7928	10	0.22706	T	0.39	-16.8653	19.9103	0.97024	0.0:1.0:0.0:0.0	.	967	Q9Y4G6	TLN2_HUMAN	E	967	ENSP00000303476:Q967E	ENSP00000303476:Q967E	Q	+	1	0	TLN2	60799279	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.887000	0.63156	2.765000	0.95021	0.650000	0.86243	CAG	.	.	.	none		0.547	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			G	63011987	C	G	63011987	3	3	143	1	0	0	0	0	1	0	0	0	15960	827	29	4	2985	4	TLN2	15	63011987	Missense_Mutation	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	3510972	63011987	39519405	50	8647											
RASGRF1	5923	hgsc.bcm.edu	37	chr15	79264261	79264261	+	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	ttgaaactggcgaatctctcGgataatatgggatatctgtg	11	13	11	6	2	2	1	0	1	2	0	4	4	2	3	0	3	1	0	0	3	5	4			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr15:79264261G>A	ENST00000419573.3	-	27	3950	c.3676C>T	c.(3676-3678)Cga>Tga	p.R1226*	RASGRF1_ENST00000558480.2_Nonsense_Mutation_p.R1210*|RASGRF1_ENST00000394745.3_Nonsense_Mutation_p.R442*	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	1226	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						CGAATCTCTCGGATAATATGG	0.473																																					p.R1226X		Atlas-SNP	.											.	RASGRF1	168	.	0			c.C3676T						PASS	.						268	228	242					15																	79264261		2196	4293	6489	SO:0001587	stop_gained	5923	exon27			TCTCTCGGATAAT	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.3676C>T	chr15.hg19:g.79264261G>A	ENSP00000405963:p.Arg1226*	233.0	0.0	.		216.0	75.0	.	NM_002891	F8VPA5|H0YKF2|J3KQP9|Q16027	Nonsense_Mutation	SNP	ENST00000419573.3	hg19	CCDS10309.1	.	.	.	.	.	.	.	.	.	.	G	42	9.264118	0.99118	.	.	ENSG00000058335	ENST00000419573;ENST00000394741;ENST00000394745	.	.	.	4.23	3.23	0.37069	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.9463	0.47301	0.0:0.0:0.8013:0.1987	.	.	.	.	X	1226;1210;442	.	ENSP00000378224:R1210X	R	-	1	2	RASGRF1	77051316	1.000000	0.71417	0.999000	0.59377	0.806000	0.45545	1.206000	0.32321	2.169000	0.68431	0.561000	0.74099	CGA	.	.	.	none		0.473	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891		A	79264261	G	A	79264261	4	1	143	1	0	0	0	0	0	1	0	0	13085	1124	39	1	153	1	RASGRF1	15	79264261	Nonsense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08	16252274	79264261	23267131	51	8648											
C16orf62	57020	hgsc.bcm.edu	37	chr16	19711796	19711797	+	Stop_Codon_Ins	INS	-	-	G																															ccctctgcaaacaaggacctINSgacccccgggcccatcccca																										TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr16:19711796_19711797insG	ENST00000251143.5	+	0	2902_2903				C16orf62_ENST00000448695.1_Stop_Codon_Ins|C16orf62_ENST00000542263.1_Stop_Codon_Ins|C16orf62_ENST00000543152.1_Stop_Codon_Ins|C16orf62_ENST00000438132.3_Stop_Codon_Ins|C16orf62_ENST00000417362.2_Stop_Codon_Ins			Q7Z3J2	CP062_HUMAN	chromosome 16 open reading frame 62							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						AACAAGGACCTGACCCCCGGGC	0.51																																					p.X1053delinsW		Atlas-INDEL	.											.	C16orf62	164	.	0			c.3157_3158insG						PASS	.																																			SO:0001567	stop_retained_variant	57020	exon31			.		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.2890dupG	chr16.hg19:g.19711797_19711797dupG	ENSP00000251143:p.*964Trpext*54	99.0	0.0	0		85.0	28.0	0.329412	NM_020314	A8K2M1|O43329|Q69YI1|Q6PDA0|Q7L371|Q86W66|Q8WXA5|Q9H0L7|Q9H7C8	Frame_Shift_Ins	INS	ENST00000251143.5	hg19																																																																																				.	.	.	none		0.51	C16orf62-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_020314		G	19711797	-	G	19711796	7	5	143	1	0	1	1	0	0	0	0	0	1827	1593	55	0	3012	0	C16orf62	16	19711796	Stop_Codon_Ins	INS	-	TCGA-BQ-7061-01A-11D-1961-08		19711796	70642957	52	8649											
ZP2	7783	hgsc.bcm.edu	37	chr16	21215430	21215430	+	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	caattccattgtcatgcagcTggctcacatcaatgttctgg	9	13	8	11	0	4	0	3	0	1	0	5	0	5	0	1	2	2	4	1	2	2	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr16:21215430T>A	ENST00000574002.1	-	10	1375	c.893A>T	c.(892-894)cAg>cTg	p.Q298L	ZP2_ENST00000219593.4_Missense_Mutation_p.Q298L|AF001550.7_ENST00000572747.1_RNA|ZP2_ENST00000574091.1_Missense_Mutation_p.Q298L			Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 (sperm receptor)	298					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)		GTCATGCAGCTGGCTCACATC	0.428																																					p.Q298L		Atlas-SNP	.											.	ZP2	92	.	0			c.A893T						PASS	.						161	137	145					16																	21215430		2200	4300	6500	SO:0001583	missense	7783	exon9			TGCAGCTGGCTCA	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.893A>T	chr16.hg19:g.21215430T>A	ENSP00000460971:p.Gln298Leu	102.0	0.0	.		88.0	33.0	.	NM_003460	B2R7J2|Q4VAN9|Q4VAP0|Q4VAP1	Missense_Mutation	SNP	ENST00000574002.1	hg19	CCDS10596.1	.	.	.	.	.	.	.	.	.	.	T	13.43	2.233434	0.39498	.	.	ENSG00000103310	ENST00000219593	T	0.78816	-1.21	6.08	3.74	0.42951	.	0.574315	0.17910	N	0.157889	D	0.84938	0.5583	M	0.73962	2.25	0.09310	N	1	D;B;B	0.89917	1.0;0.223;0.223	D;B;B	0.91635	0.999;0.143;0.053	T	0.73563	-0.3943	10	0.28530	T	0.3	-5.929	9.6718	0.40017	0.1165:0.0:0.1209:0.7626	.	298;298;298	B4DEV1;Q4VAP1;Q05996	.;.;ZP2_HUMAN	L	298	ENSP00000219593:Q298L	ENSP00000219593:Q298L	Q	-	2	0	ZP2	21122931	0.975000	0.34042	0.255000	0.24374	0.042000	0.13812	2.912000	0.48782	2.330000	0.79161	0.533000	0.62120	CAG	.	.	.	none		0.428	ZP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207365.2			A	21215430	T	A	21215430	3	1	143	1	0	0	0	0	1	0	0	0	18228	1580	55	5	1388	5	ZP2	16	21215430	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	1503634	21215430	69139323	53	8650											
FOXC2	2303	hgsc.bcm.edu	37	chr16	86601010	86601010	+	Missense_Mutation	SNP	T	T	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	ccctacctgagcgagcagaaTtactaccgggctgcgggcag	9	6	13	13	3	0	2	0	1	0	1	0	3	0	2	3	2	6	3	3	2	4	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr16:86601010T>G	ENST00000320354.4	+	1	154	c.69T>G	c.(67-69)aaT>aaG	p.N23K	RP11-463O9.5_ENST00000563280.1_RNA	NM_005251.2	NP_005242.1	Q99958	FOXC2_HUMAN	forkhead box C2 (MFH-1, mesenchyme forkhead 1)	23					artery morphogenesis (GO:0048844)|blood vessel remodeling (GO:0001974)|camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|collagen fibril organization (GO:0030199)|embryonic heart tube development (GO:0035050)|embryonic viscerocranium morphogenesis (GO:0048703)|glomerular endothelium development (GO:0072011)|glomerular mesangial cell development (GO:0072144)|glomerular visceral epithelial cell differentiation (GO:0072112)|heart development (GO:0007507)|insulin receptor signaling pathway (GO:0008286)|lymphangiogenesis (GO:0001946)|mesoderm development (GO:0007498)|metanephros development (GO:0001656)|negative regulation of apoptotic process involved in outflow tract morphogenesis (GO:1902257)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell development (GO:0014032)|Notch signaling pathway (GO:0007219)|ossification (GO:0001503)|paraxial mesodermal cell fate commitment (GO:0048343)|patterning of blood vessels (GO:0001569)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular wound healing (GO:0035470)|regulation of blood vessel size (GO:0050880)|regulation of organ growth (GO:0046620)|response to hormone (GO:0009725)|somitogenesis (GO:0001756)|ureteric bud development (GO:0001657)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	15						GCGAGCAGAATTACTACCGGG	0.701									Late-onset Hereditary Lymphedema																												p.N23K		Atlas-SNP	.											.	FOXC2	46	.	0			c.T69G						PASS	.						34	38	37					16																	86601010		2196	4296	6492	SO:0001583	missense	2303	exon1	Familial Cancer Database	Hereditary Lymphedema type II, Meige Lymphedema	GCAGAATTACTAC	Y08223	CCDS10958.1	16q24.1	2008-04-10			ENSG00000176692	ENSG00000176692		"Forkhead boxes"	3801	protein-coding gene	gene with protein product		602402		FKHL14		9169153, 8674414	Standard	NM_005251		Approved	MFH-1	uc002fjq.3	Q99958	OTTHUMG00000137652	ENST00000320354.4:c.69T>G	chr16.hg19:g.86601010T>G	ENSP00000326371:p.Asn23Lys	93.0	0.0	.		85.0	32.0	.	NM_005251	C6KMR9|Q14DA6	Missense_Mutation	SNP	ENST00000320354.4	hg19	CCDS10958.1	.	.	.	.	.	.	.	.	.	.	T	18.41	3.618182	0.66787	.	.	ENSG00000176692	ENST00000320354	D	0.94862	-3.54	3.49	-4.32	0.03688	.	0.351583	0.22692	U	0.056809	D	0.91768	0.7396	L	0.46157	1.445	0.37017	D	0.896014	P	0.47409	0.895	P	0.47573	0.55	D	0.88376	0.2998	10	0.39692	T	0.17	.	14.3409	0.66624	0.0:0.8175:0.0:0.1825	.	23	Q99958	FOXC2_HUMAN	K	23	ENSP00000326371:N23K	ENSP00000326371:N23K	N	+	3	2	FOXC2	85158511	0.974000	0.33945	0.948000	0.38648	0.973000	0.67179	0.371000	0.20450	-1.237000	0.02539	-0.689000	0.03729	AAT	.	.	.	none		0.701	FOXC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269104.2	NM_005251		G	86601010	T	G	86601010	3	3	143	1	0	0	0	0	1	0	0	0	6002	1490	52	5	71	5	FOXC2	16	86601010	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	65385580	86601010	3753743	54	8651											
TSR1	55720	hgsc.bcm.edu	37	chr17	2232753	2232753	+	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	cagggtcacgcctcaccaccAtattcaatactgacatctgg	11	9	7	14	1	4	1	3	1	1	0	4	1	4	1	3	2	1	0	3	2	3	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr17:2232753A>T	ENST00000301364.5	-	11	2866	c.1787T>A	c.(1786-1788)aTg>aAg	p.M596K	SNORD91A_ENST00000390861.1_RNA|SNORD91B_ENST00000391250.1_RNA	NM_018128.4	NP_060598.3	Q2NL82	TSR1_HUMAN	TSR1, 20S rRNA accumulation, homolog (S. cerevisiae)	596					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						CCTCACCACCATATTCAATAC	0.438																																					p.M596K		Atlas-SNP	.											.	TSR1	57	.	0			c.T1787A						PASS	.						89	80	83					17																	2232753		2203	4300	6503	SO:0001583	missense	55720	exon11			ACCACCATATTCA	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.1787T>A	chr17.hg19:g.2232753A>T	ENSP00000301364:p.Met596Lys	68.0	0.0	.		75.0	26.0	.	NM_018128	Q8WUY5|Q9NVT0|Q9P2E6	Missense_Mutation	SNP	ENST00000301364.5	hg19	CCDS32525.1	.	.	.	.	.	.	.	.	.	.	A	17.23	3.337499	0.60963	.	.	ENSG00000167721	ENST00000301364	T	0.18016	2.24	5.34	5.34	0.76211	Ribosome biogenesis protein BMS1/TSR1, C-terminal (1);	0.225116	0.52532	D	0.000063	T	0.23649	0.0572	M	0.69185	2.1	0.53688	D	0.999979	B	0.25667	0.131	B	0.29440	0.102	T	0.02533	-1.1145	10	0.54805	T	0.06	-17.0729	14.4964	0.67691	1.0:0.0:0.0:0.0	.	596	Q2NL82	TSR1_HUMAN	K	596	ENSP00000301364:M596K	ENSP00000301364:M596K	M	-	2	0	TSR1	2179503	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.017000	0.93651	2.014000	0.59158	0.459000	0.35465	ATG	.	.	.	none		0.438	TSR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438180.2	NM_018128		T	2232753	A	T	2232753	3	4	143	1	0	0	0	0	1	0	0	0	16676	217	8	5	647	5	TSR1	17	2232753	Missense_Mutation	SNP	A	TCGA-BQ-7061-01A-11D-1961-08		2232753	78962457	55	8652											
PITPNM3	83394	hgsc.bcm.edu	37	chr17	6375990	6375990	+	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	aacctaccgaggaggagggaCtgcccatcgcccagtgggaa	11	4	14	12	2	0	0	0	0	0	0	1	5	0	4	4	4	3	0	4	4	3	1			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr17:6375990C>T	ENST00000262483.8	-	11	1503	c.1416G>A	c.(1414-1416)caG>caA	p.Q472Q	PITPNM3_ENST00000421306.3_Silent_p.Q436Q|PITPNM3_ENST00000576664.1_5'UTR	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	472	DDHD. {ECO:0000255|PROSITE- ProRule:PRU00378}.				phosphatidylinositol metabolic process (GO:0046488)|phospholipid transport (GO:0015914)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)|receptor tyrosine kinase binding (GO:0030971)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(3)|skin(2)	36				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		GGAGGAGGGACTGCCCATCGC	0.652																																					p.Q472Q		Atlas-SNP	.											.	PITPNM3	91	.	0			c.G1416A						PASS	.						57	57	57					17																	6375990		2202	4300	6502	SO:0001819	synonymous_variant	83394	exon11			GAGGGACTGCCCA	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.1416G>A	chr17.hg19:g.6375990C>T		33.0	0.0	.		28.0	15.0	.	NM_031220	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Silent	SNP	ENST00000262483.8	hg19	CCDS11076.1																																																																																			.	.	.	none		0.652	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219824.2	NM_031220		T	6375990	C	T	6375990	2	4	143	1	0	0	0	0	0	0	0	1	11959	564	20	2		2	PITPNM3	17	6375990	Silent	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	4143237	6375990	74819220	56	8653											
ST6GALNAC2	10610	hgsc.bcm.edu	37	chr17	74570497	74570497	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggctttgtgttggctcaggCggtcccagagcgctggggtg	3	10	19	9	2	1	1	1	0	0	1	2	1	2	1	1	6	1	4	1	6	0	2			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr17:74570497C>T	ENST00000225276.5	-	3	630	c.311G>A	c.(310-312)cGc>cAc	p.R104H	ST6GALNAC2_ENST00000586520.1_5'UTR	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	104					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						TTGGCTCAGGCGGTCCCAGAG	0.637																																					p.R104H		Atlas-SNP	.											ST6GALNAC2,colon,carcinoma,0,1	ST6GALNAC2	29	.	0			c.G311A						PASS	.						38	35	36					17																	74570497		2203	4300	6503	SO:0001583	missense	10610	exon3			CTCAGGCGGTCCC	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.311G>A	chr17.hg19:g.74570497C>T	ENSP00000225276:p.Arg104His	40.0	0.0	.		44.0	16.0	.	NM_006456	Q12971	Missense_Mutation	SNP	ENST00000225276.5	hg19	CCDS11747.1	.	.	.	.	.	.	.	.	.	.	c	14.90	2.674158	0.47781	.	.	ENSG00000070731	ENST00000225276	T	0.32272	1.46	4.47	-0.561	0.11785	.	0.749066	0.12928	N	0.427572	T	0.24392	0.0591	L	0.55017	1.72	0.18873	N	0.999984	B	0.29301	0.241	B	0.25884	0.064	T	0.19353	-1.0308	10	0.56958	D	0.05	-1.9719	6.7032	0.23236	0.0:0.3692:0.0:0.6308	.	104	Q9UJ37	SIA7B_HUMAN	H	104	ENSP00000225276:R104H	ENSP00000225276:R104H	R	-	2	0	ST6GALNAC2	72082092	0.001000	0.12720	0.960000	0.40013	0.859000	0.49053	0.361000	0.20267	0.093000	0.17368	-0.258000	0.10820	CGC	.	.	.	none		0.637	ST6GALNAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450650.1	NM_006456		T	74570497	C	T	74570497	3	4	143	1	0	0	0	0	1	0	0	0	15236	768	27	1	841	1	ST6GALNAC2	17	74570497	Missense_Mutation	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	68194507	74570497	6624713	57	8654											
ZNF564	163050	hgsc.bcm.edu	37	chr19	12639496	12639497	+	Frame_Shift_Del	DEL	AG	AG	-																															aagttcacagccacatcctcAgaggccactgagtcctaaaa																										TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr19:12639496_12639497delAG	ENST00000339282.7	-	2	213_214	c.17_18delCT	c.(16-18)tctfs	p.S6fs	CTD-2192J16.20_ENST00000593682.1_3'UTR|CTD-2192J16.21_ENST00000601420.1_RNA|ZNF709_ENST00000428311.1_Intron	NM_144976.3	NP_659413.1	Q8TBZ8	ZN564_HUMAN	zinc finger protein 564	6	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(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18						CCACATCCTCAGAGGCCACTGA	0.45																																					p.6_7del		Atlas-INDEL	.											.	ZNF564	55	.	0			c.18_19del						PASS	.																																			SO:0001589	frameshift_variant	163050	exon2			.	BC028367	CCDS42505.1	19p13.2	2013-09-19			ENSG00000249709	ENSG00000249709		"Zinc fingers, C2H2-type", "-"	31106	protein-coding gene	gene with protein product							Standard	NM_144976		Approved	MGC26914		Q8TBZ8	OTTHUMG00000156418	ENST00000339282.7:c.17_18delCT	chr19.hg19:g.12639498_12639499delAG	ENSP00000340004:p.Ser6fs	140.0	0.0	0		146.0	54.0	0.369863	NM_144976	B9EGT4|Q6P1K6	Frame_Shift_Del	DEL	ENST00000339282.7	hg19	CCDS42505.1																																																																																			.	.	.	none		0.45	ZNF564-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344120.2	NM_144976		-	12639497	AG	-	12639496	7	5	143	1	0	1	0	1	0	0	0	0	18007	175	7	0	1655	0	ZNF564	19	12639496	Frame_Shift_Del	DEL	AG	TCGA-BQ-7061-01A-11D-1961-08		12639496	46489487	58	8655											
TRMT1	55621	hgsc.bcm.edu	37	chr19	13226494	13226494	+	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	tggtctcctgaggccaggttTtcactctctttcagttcaac	6	15	8	12	0	5	1	3	1	2	0	7	1	5	1	2	3	1	2	2	3	1	4			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr19:13226494T>A	ENST00000592062.1	-	5	969	c.399A>T	c.(397-399)gaA>gaT	p.E133D	TRMT1_ENST00000592892.1_5'UTR|TRMT1_ENST00000221504.8_Missense_Mutation_p.E133D|NACC1_ENST00000292431.4_5'Flank|TRMT1_ENST00000357720.4_Missense_Mutation_p.E133D|TRMT1_ENST00000437766.1_Missense_Mutation_p.E133D			Q9NXH9	TRM1_HUMAN	tRNA methyltransferase 1 homolog (S. cerevisiae)	133	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)		AGGCCAGGTTTTCACTCTCTT	0.572																																					p.E133D		Atlas-SNP	.											.	TRMT1	31	.	0			c.A399T						PASS	.						166	168	168					19																	13226494		2203	4300	6503	SO:0001583	missense	55621	exon4			CAGGTTTTCACTC	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.399A>T	chr19.hg19:g.13226494T>A	ENSP00000466967:p.Glu133Asp	280.0	0.0	.		299.0	114.0	.	NM_001136035	O76103|Q548Y5|Q8WVA6	Missense_Mutation	SNP	ENST00000592062.1	hg19	CCDS12293.1	.	.	.	.	.	.	.	.	.	.	T	9.755	1.168481	0.21621	.	.	ENSG00000104907	ENST00000357720;ENST00000437766;ENST00000221504	.	.	.	3.89	2.82	0.32997	.	0.227351	0.35677	N	0.003045	T	0.31979	0.0814	N	0.19112	0.55	0.36296	D	0.856722	B;B	0.09022	0.001;0.002	B;B	0.08055	0.002;0.003	T	0.18650	-1.0330	9	0.17369	T	0.5	-2.7274	8.7051	0.34349	0.0:0.0:0.1926:0.8074	.	133;133	Q9NXH9-2;Q9NXH9	.;TRM1_HUMAN	D	133	.	ENSP00000221504:E133D	E	-	3	2	TRMT1	13087494	0.311000	0.24536	0.324000	0.25361	0.593000	0.36681	1.442000	0.35046	0.797000	0.33971	0.460000	0.39030	GAA	.	.	.	none		0.572	TRMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452780.2	NM_017722		A	13226494	T	A	13226494	3	1	143	1	0	0	0	0	1	0	0	0	16573	1838	64	5	1636	5	TRMT1	19	13226494	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	586998	13226494	45902489	59	8656											
SIN3B	23309	hgsc.bcm.edu	37	chr19	16964967	16964967	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgcaggtccgccgggtgcTgaagagccaggaggtgtatg	7	8	17	9	2	1	2	0	1	1	1	2	3	2	3	3	4	3	3	3	4	2	1			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr19:16964967T>C	ENST00000248054.5	+	8	974	c.953T>C	c.(952-954)cTg>cCg	p.L318P	SIN3B_ENST00000596802.1_Missense_Mutation_p.L318P|SIN3B_ENST00000379803.1_Missense_Mutation_p.L318P					SIN3 transcription regulator family member B											endometrium(4)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26						CGCCGGGTGCTGAAGAGCCAG	0.597																																					p.L318P		Atlas-SNP	.											.	SIN3B	90	.	0			c.T953C						PASS	.						56	53	54					19																	16964967		2203	4300	6503	SO:0001583	missense	23309	exon8			GGGTGCTGAAGAG	AB014600	CCDS32946.1, CCDS74308.1	19p13.12	2013-08-21	2013-08-21						19354	protein-coding gene	gene with protein product		607777	"SIN3 homolog B, transcription regulator (yeast)", "SIN3 transcription regulator homolog B (yeast)"			9734811	Standard	XM_005259832		Approved	KIAA0700	uc002ney.2	O75182		ENST00000248054.5:c.953T>C	chr19.hg19:g.16964967T>C	ENSP00000248054:p.Leu318Pro	64.0	0.0	.		65.0	28.0	.	NM_015260		Missense_Mutation	SNP	ENST00000248054.5	hg19		.	.	.	.	.	.	.	.	.	.	T	21.4	4.138166	0.77775	.	.	ENSG00000127511	ENST00000379803;ENST00000248054	T;T	0.63580	-0.05;0.13	5.19	5.19	0.71726	.	0.064314	0.64402	D	0.000004	D	0.83275	0.5219	M	0.92923	3.36	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.987;0.988	D	0.87560	0.2471	10	0.87932	D	0	-38.9141	14.2256	0.65858	0.0:0.0:0.0:1.0	.	318;318;318	O75182-2;O75182;O75182-3	.;SIN3B_HUMAN;.	P	318	ENSP00000369131:L318P;ENSP00000248054:L318P	ENSP00000248054:L318P	L	+	2	0	SIN3B	16825967	1.000000	0.71417	0.993000	0.49108	0.870000	0.49936	7.837000	0.86796	1.958000	0.56883	0.459000	0.35465	CTG	.	.	.	none		0.597	SIN3B-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000462846.1	NM_015260		C	16964967	T	C	16964967	3	2	143	1	0	0	0	0	1	0	0	0	14339	1580	55	3	983	3	SIN3B	19	16964967	Missense_Mutation	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	3738473	16964967	42164016	60	8657											
LSR	51599	hgsc.bcm.edu	37	chr19	35757260	35757260	+	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	cctgttgattgtgtcctcacAgtgtatgccgccggcaaagc	7	11	11	12	2	1	1	1	1	0	0	2	1	2	1	4	1	2	3	4	1	2	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr19:35757260A>G	ENST00000361790.3	+	6	1081		c.e6-1		USF2_ENST00000594064.1_5'Flank|LSR_ENST00000427250.1_Splice_Site|LSR_ENST00000354900.3_Splice_Site|LSR_ENST00000347609.4_Splice_Site|USF2_ENST00000343550.5_5'Flank|LSR_ENST00000602122.1_Splice_Site|USF2_ENST00000222305.3_5'Flank|USF2_ENST00000379134.3_5'Flank|LSR_ENST00000360798.3_Splice_Site|AD000684.2_ENST00000602262.1_RNA|USF2_ENST00000595068.1_5'Flank	NM_205834.3	NP_991403.1	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor						embryo development (GO:0009790)|liver development (GO:0001889)	chylomicron (GO:0042627)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	13	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			GTGTCCTCACAGTGTATGCCG	0.627																																					.		Atlas-SNP	.											.	LSR	60	.	0			c.866-2A>G						PASS	.						76	78	77					19																	35757260		2203	4300	6503	SO:0001630	splice_region_variant	51599	exon5			CCTCACAGTGTAT	AF130366	CCDS12449.1, CCDS12450.1, CCDS12451.1, CCDS59376.1	19q13.12	2013-01-11			ENSG00000105699	ENSG00000105699		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29572	protein-coding gene	gene with protein product	"lipolysis-stimulated remnant", "immunoglobulin-like domain containing receptor 3"					10224102	Standard	NM_015925		Approved	LISCH7, ILDR3	uc002nyl.3	Q86X29		ENST00000361790.3:c.923-1A>G	chr19.hg19:g.35757260A>G		175.0	0.0	.		140.0	39.0	.	NM_015925	A6NDW3|B4DKL4|E9PHD4|O00112|O00426|Q6ZT80|Q8NBM0|Q9BT33|Q9UQL3	Splice_Site	SNP	ENST00000361790.3	hg19	CCDS12450.1	.	.	.	.	.	.	.	.	.	.	A	12.74	2.029984	0.35797	.	.	ENSG00000105699	ENST00000361790;ENST00000354900;ENST00000360798;ENST00000347609;ENST00000427250	.	.	.	3.99	2.94	0.34122	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.7508	0.28896	0.8124:0.0:0.0:0.1876	.	.	.	.	.	-1	.	.	.	+	.	.	LSR	40449100	1.000000	0.71417	0.489000	0.27452	0.523000	0.34469	7.126000	0.77201	0.540000	0.28808	0.379000	0.24179	.	.	.	.	none		0.627	LSR-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465513.2	NM_015925	Intron	G	35757260	A	G	35757260	5	3	143	1	0	0	0	0	0	0	1	0	9071	202	7	3	943	3	LSR	19	35757260	Splice_Site	SNP	A	TCGA-BQ-7061-01A-11D-1961-08	18792293	35757260	23371723	61	8658											
ZSCAN4	201516	hgsc.bcm.edu	37	chr19	58187881	58187881	+	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	gagattcatagaagacctgaCtgatgacagcataaatccac	16	8	8	9	0	1	6	1	3	0	3	2	7	2	6	2	0	1	1	2	0	4	3			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr19:58187881C>G	ENST00000318203.5	+	3	1065	c.368C>G	c.(367-369)aCt>aGt	p.T123S		NM_152677.2	NP_689890.1	Q8NAM6	ZSCA4_HUMAN	zinc finger and SCAN domain containing 4	123	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				telomere maintenance via telomere lengthening (GO:0010833)|transcription, DNA-templated (GO:0006351)	nuclear chromosome, telomeric region (GO:0000784)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|large_intestine(5)|liver(2)|lung(17)|ovary(1)|skin(1)|stomach(1)	30		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;0.026)		GAAGACCTGACTGATGACAGC	0.418																																					p.T123S		Atlas-SNP	.											.	ZSCAN4	72	.	0			c.C368G						PASS	.						83	81	81					19																	58187881		2203	4300	6503	SO:0001583	missense	201516	exon3			ACCTGACTGATGA	AK092424	CCDS12958.1	19q13.43	2013-01-08	2004-11-01	2004-11-02		ENSG00000180532		"-", "Zinc fingers, C2H2-type"	23709	protein-coding gene	gene with protein product		613419	"zinc finger protein 494"	ZNF494			Standard	NM_152677		Approved	FLJ35105	uc002qpu.3	Q8NAM6		ENST00000318203.5:c.368C>G	chr19.hg19:g.58187881C>G	ENSP00000321963:p.Thr123Ser	73.0	0.0	.		73.0	26.0	.	NM_152677	Q3MIQ2	Missense_Mutation	SNP	ENST00000318203.5	hg19	CCDS12958.1	.	.	.	.	.	.	.	.	.	.	C	9.547	1.114797	0.20795	.	.	ENSG00000180532	ENST00000318203	T	0.04317	3.65	4.42	-8.83	0.00806	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (1);	1.418230	0.04476	N	0.376945	T	0.04363	0.0120	L	0.53671	1.685	0.09310	N	1	B	0.14805	0.011	B	0.22386	0.039	T	0.40021	-0.9585	10	0.11794	T	0.64	0.036	5.2622	0.15580	0.3993:0.1301:0.3976:0.073	.	123	Q8NAM6	ZSCA4_HUMAN	S	123	ENSP00000321963:T123S	ENSP00000321963:T123S	T	+	2	0	ZSCAN4	62879693	0.006000	0.16342	0.000000	0.03702	0.016000	0.09150	-0.007000	0.12810	-2.018000	0.00943	-0.140000	0.14226	ACT	.	.	.	none		0.418	ZSCAN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466812.1	NM_152677		G	58187881	C	G	58187881	3	3	143	1	0	0	0	0	1	0	0	0	18249	565	20	4	370	4	ZSCAN4	19	58187881	Missense_Mutation	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	22430621	58187881	941102	62	8659											
ENTPD6	955	hgsc.bcm.edu	37	chr20	25198149	25198149	+	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	cttctccagggcaccctgcaGgcctccccacccggctacct	5	7	8	21	1	1	0	0	0	1	0	3	0	2	0	7	3	2	3	7	3	1	2			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chr20:25198149G>C	ENST00000376652.4	+	9	973	c.810G>C	c.(808-810)caG>caC	p.Q270H	ENTPD6_ENST00000433259.2_Missense_Mutation_p.Q270H|Y_RNA_ENST00000365544.1_RNA|ENTPD6_ENST00000360031.2_Missense_Mutation_p.Q269H|ENTPD6_ENST00000354989.5_Missense_Mutation_p.Q253H			O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6 (putative)	270					response to calcium ion (GO:0051592)|response to magnesium ion (GO:0032026)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity (GO:0008894)|nucleoside-triphosphatase activity (GO:0017111)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|prostate(1)|skin(1)	27						GCACCCTGCAGGCCTCCCCAC	0.537																																					p.Q270H		Atlas-SNP	.											ENTPD6,right_upper_lobe,carcinoma,0,1	ENTPD6	57	.	0			c.G810C						PASS	.						93	91	92					20																	25198149		2203	4300	6503	SO:0001583	missense	955	exon9			CCTGCAGGCCTCC	AF039916	CCDS13170.1, CCDS46586.1	20p11.21	2010-06-24	2010-06-24		ENSG00000197586	ENSG00000197586			3368	protein-coding gene	gene with protein product		603160	"interleukin 6 signal transducer-2"	CD39L2, IL6ST2		9676430	Standard	NM_001247		Approved	NTPDase-6, dJ738P15.3	uc002wuj.2	O75354	OTTHUMG00000032116	ENST00000376652.4:c.810G>C	chr20.hg19:g.25198149G>C	ENSP00000365840:p.Gln270His	132.0	0.0	.		131.0	32.0	.	NM_001247	A6NCX6|D3DW49|Q5QPJ2|Q5QPJ5|Q7Z5B5|Q8N3H3|Q8TAS7|Q9UJD1	Missense_Mutation	SNP	ENST00000376652.4	hg19	CCDS13170.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	7.510|7.510|7.510	0.654527|0.654527|0.654527	0.14580|0.14580|0.14580	.|.|.	.|.|.	ENSG00000197586|ENSG00000197586|ENSG00000197586	ENST00000376666|ENST00000354989;ENST00000360031;ENST00000525986;ENST00000376641;ENST00000376652;ENST00000439162;ENST00000417467;ENST00000433259;ENST00000425813|ENST00000433417;ENST00000427553;ENST00000447877	.|T;T;T;T;T;T;T|.	.|0.11495|.	.|2.77;2.77;2.77;2.77;2.77;2.77;2.77|.	5.71|5.71|5.71	2.69|2.69|2.69	0.31865|0.31865|0.31865	.|.|.	.|0.866486|.	.|0.10745|.	.|N|.	.|0.638962|.	T|T|T	0.51686|0.51686|0.51686	0.1689|0.1689|0.1689	L|L|L	0.58925|0.58925|0.58925	1.835|1.835|1.835	0.33639|0.33639|0.33639	D|D|D	0.607014|0.607014|0.607014	.|B;B;B;B;B;B;B;B;B|.	.|0.20459|.	.|0.004;0.045;0.045;0.027;0.045;0.004;0.006;0.022;0.012|.	.|B;B;B;B;B;B;B;B;B|.	.|0.30105|.	.|0.021;0.076;0.076;0.049;0.111;0.029;0.033;0.037;0.037|.	T|T|T	0.58047|0.58047|0.58047	-0.7705|-0.7705|-0.7705	5|10|5	.|0.46703|.	.|T|.	.|0.11|.	-8.1099|-8.1099|-8.1099	5.5882|5.5882|5.5882	0.17287|0.17287|0.17287	0.1474:0.0:0.5745:0.2781|0.1474:0.0:0.5745:0.2781|0.1474:0.0:0.5745:0.2781	.|.|.	.|52;252;270;270;270;253;269;269;270|.	.|B4DHS2;B4DDM7;B4DNK6;E7EP89;Q5QPI9;O75354-2;D3DW49;Q5QPJ2;O75354|.	.|.;.;.;.;.;.;.;.;ENTP6_HUMAN|.	R|H|T	94|253;269;190;166;270;252;204;270;222|191;128;163	.|ENSP00000347084:Q253H;ENSP00000353131:Q269H;ENSP00000365840:Q270H;ENSP00000408098:Q252H;ENSP00000395064:Q204H;ENSP00000401895:Q270H;ENSP00000390646:Q222H|.	.|ENSP00000347084:Q253H|.	G|Q|R	+|+|+	1|3|2	0|2|0	ENTPD6|ENTPD6|ENTPD6	25146149|25146149|25146149	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.038000|0.038000|0.038000	0.18304|0.18304|0.18304	0.058000|0.058000|0.058000	0.15608|0.15608|0.15608	1.836000|1.836000|1.836000	0.39191|0.39191|0.39191	0.346000|0.346000|0.346000	0.23899|0.23899|0.23899	0.462000|0.462000|0.462000	0.41574|0.41574|0.41574	GGC|CAG|AGG	.	.	.	none		0.537	ENTPD6-020	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078414.2			C	25198149	G	C	25198149	3	2	143	1	0	0	0	0	1	0	0	0	5145	991	35	4	847	4	ENTPD6	20	25198149	Missense_Mutation	SNP	G	TCGA-BQ-7061-01A-11D-1961-08		25198149	37827371	63	8660											
GSPT2	23708	hgsc.bcm.edu	37	chrX	51486959	51486960	+	Missense_Mutation	DNP	GC	GC	TT																															ctgcggggcccgactcagccGcccaccctcccggccggctc																										TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chrX:51486959_51486960GC>TT	ENST00000340438.4	+	1	479_480	c.237_238GC>TT	c.(235-240)ccGCcc>ccTTcc	p.P80S		NM_018094.4	NP_060564.2	Q8IYD1	ERF3B_HUMAN	G1 to S phase transition 2	80					cell cycle (GO:0007049)|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)|translation (GO:0006412)|translational termination (GO:0006415)	cytosol (GO:0005829)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	20	Ovarian(276;0.236)					CGACTCAGCCGCCCACCCTCCC	0.658																																					p.P79P|p.P80S		Atlas-SNP	.											.	GSPT2	57	.	0			c.G237T|c.C238T						PASS	.																																			SO:0001583	missense	23708	exon1			TCAGCCGCCCACC|CAGCCGCCCACCC	AI285711	CCDS14336.1	Xp11.22	2008-05-14			ENSG00000189369	ENSG00000189369			4622	protein-coding gene	gene with protein product		300418				10575220	Standard	NM_018094		Approved	eRF3b, FLJ10441	uc004dpl.3	Q8IYD1	OTTHUMG00000021538	Exception_encountered	chrX.hg19:g.51486959_51486960delinsTT	ENSP00000341247:p.Pro80Ser	21.0|20.0	0.0	.		28.0	9.0	.	NM_018094	Q9H909|Q9NVY0|Q9NY44	Silent|Missense_Mutation	SNP	ENST00000340438.4	hg19	CCDS14336.1																																																																																			.	.	.	none		0.658	GSPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056587.1			TT	51486960	GC	TT	51486959	3	4	143	1	0	0	0	0	1	0	0	0	6834	1074	38	4	239	4	GSPT2	23	51486959	Missense_Mutation	DNP	GC	TCGA-BQ-7061-01A-11D-1961-08		51486959	103783601	64	8661											
LAS1L	81887	hgsc.bcm.edu	37	chrX	64749564	64749564	+	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	atcggcctttacatctgactCcgtacttttcccatcatcct	7	15	4	15	2	2	1	1	1	1	0	6	1	5	1	4	1	2	1	4	1	2	5			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chrX:64749564C>A	ENST00000374811.3	-	5	749	c.709G>T	c.(709-711)Gag>Tag	p.E237*	LAS1L_ENST00000374807.5_Nonsense_Mutation_p.E237*|LAS1L_ENST00000374804.5_Nonsense_Mutation_p.E195*|LAS1L_ENST00000312391.8_Nonsense_Mutation_p.E237*	NM_031206.4	NP_112483.1	Q9Y4W2	LAS1L_HUMAN	LAS1-like (S. cerevisiae)	237					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(3)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	33						ACATCTGACTCCGTACTTTTC	0.453																																					p.E237X		Atlas-SNP	.											.	LAS1L	72	.	0			c.G709T						PASS	.						219	177	191					X																	64749564		2203	4300	6503	SO:0001587	stop_gained	81887	exon5			CTGACTCCGTACT	BC014545	CCDS14381.1, CCDS55433.1, CCDS55434.1	Xq12	2008-02-05			ENSG00000001497	ENSG00000001497			25726	protein-coding gene	gene with protein product						12477932	Standard	NM_031206		Approved	FLJ12525	uc004dwa.2	Q9Y4W2	OTTHUMG00000021720	ENST00000374811.3:c.709G>T	chrX.hg19:g.64749564C>A	ENSP00000363944:p.Glu237*	235.0	0.0	.		218.0	75.0	.	NM_031206	A9X410|Q5JXQ0|Q8TEN5|Q9H9V5	Nonsense_Mutation	SNP	ENST00000374811.3	hg19	CCDS14381.1	.	.	.	.	.	.	.	.	.	.	C	13.89	2.371792	0.42003	.	.	ENSG00000001497	ENST00000374807;ENST00000374811;ENST00000374804;ENST00000312391	.	.	.	5.18	4.29	0.51040	.	0.478134	0.21197	N	0.078537	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	10.8918	0.47000	0.0:0.8136:0.1864:0.0	.	.	.	.	X	237;237;195;237	.	ENSP00000308649:E237X	E	-	1	0	LAS1L	64666289	0.369000	0.25039	0.062000	0.19696	0.007000	0.05969	1.842000	0.39250	1.194000	0.43101	0.600000	0.82982	GAG	.	.	.	none		0.453	LAS1L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056974.1	NM_031206		A	64749564	C	A	64749564	4	1	143	1	0	0	0	0	0	1	0	0	8643	864	30	4	1535	4	LAS1L	23	64749564	Nonsense_Mutation	SNP	C	TCGA-BQ-7061-01A-11D-1961-08	13262605	64749564	90520996	65	8662											
KIF4A	24137	hgsc.bcm.edu	37	chrX	69637856	69637856	+	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	gaaccgccagcaaggcaaggTaggatcagggctgtttcctc	10	7	13	11	1	1	0	1	0	0	0	3	2	2	1	3	4	2	5	3	4	4	2			TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chrX:69637856T>C	ENST00000374403.3	+	29	3454		c.e29+2			NM_012310.4	NP_036442.3	O95239	KIF4A_HUMAN	kinesin family member 4A						anterograde axon cargo transport (GO:0008089)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle organization (GO:0006996)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(6)|endometrium(9)|kidney(3)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	51						CAAGGCAAGGTAGGATCAGGG	0.537																																					.		Atlas-SNP	.											.	KIF4A	118	.	0			c.3372+2T>C						PASS	.						139	96	111					X																	69637856		2203	4300	6503	SO:0001630	splice_region_variant	24137	exon29			GCAAGGTAGGATC	AF179308	CCDS14401.1	Xq13.1	2008-08-11			ENSG00000090889	ENSG00000090889		"Kinesins"	13339	protein-coding gene	gene with protein product	"chromokinesin"	300521				10773663	Standard	NM_012310		Approved	KIF4-G1, KIF4, HSA271784, FLJ12530, FLJ12655, FLJ14204, FLJ20631	uc004dyg.3	O95239	OTTHUMG00000021775	ENST00000374403.3:c.3372+2T>C	chrX.hg19:g.69637856T>C		134.0	0.0	.		115.0	44.0	.	NM_012310	B2R7V5|D3DVU4|Q86TN3|Q86XX7|Q9NNY6|Q9NY24|Q9UMW3	Splice_Site	SNP	ENST00000374403.3	hg19	CCDS14401.1	.	.	.	.	.	.	.	.	.	.	t	12.71	2.020554	0.35606	.	.	ENSG00000090889	ENST00000374403;ENST00000544650	.	.	.	5.3	4.14	0.48551	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.5846	0.27985	0.0:0.0:0.2369:0.7631	.	.	.	.	.	-1	.	.	.	+	.	.	KIF4A	69554581	1.000000	0.71417	0.998000	0.56505	0.414000	0.31173	2.056000	0.41355	1.974000	0.57490	0.427000	0.28365	.	.	.	.	none		0.537	KIF4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057068.1	NM_012310	Intron	C	69637856	T	C	69637856	5	2	143	1	0	0	0	0	0	0	1	0	8310	1652	57	3	3484	3	KIF4A	23	69637856	Splice_Site	SNP	T	TCGA-BQ-7061-01A-11D-1961-08	4888292	69637856	85632704	66	8663											
SLITRK2	84631	hgsc.bcm.edu	37	chrX	144904633	144904634	+	Missense_Mutation	DNP	GC	GC	CT																															ttacttcctctcaaggcctgGctagacaccataactgtttt																										TCGA-BQ-7061-01A-11D-1961-08	TCGA-BQ-7061-11A-01D-1961-08	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ae48a526-0daa-42b6-b98e-1453e9dc631a	4968c132-2d26-4a31-ab07-6d7c154551de	g.chrX:144904633_144904634GC>CT	ENST00000370490.1	+	1	4945_4946	c.690_691GC>CT	c.(688-693)tgGCta>tgCTta	p.W230C	SLITRK2_ENST00000428560.2_Missense_Mutation_p.W230C|SLITRK2_ENST00000447897.2_Missense_Mutation_p.W230C|SLITRK2_ENST00000434188.2_Missense_Mutation_p.W230C|SLITRK2_ENST00000413937.2_Missense_Mutation_p.W230C			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	230	LRRCT 1.				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)					TCAAGGCCTGGCTAGACACCAT	0.49																																					p.W230C|p.L231L		Atlas-SNP	.											.	SLITRK2	221	.	0			c.G690C|c.C691T						PASS	.																																			SO:0001583	missense	84631	exon5			GGCCTGGCTAGAC|GCCTGGCTAGACA	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	Exception_encountered	chrX.hg19:g.144904633_144904634delinsCT	ENSP00000359521:p.Trp230Cys	188.0|187.0	0.0	.		171.0	36.0|37.0	.	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Missense_Mutation|Silent	SNP	ENST00000370490.1	hg19	CCDS14680.1																																																																																			.	.	.	none		0.49	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		CT	144904634	GC	CT	144904633	3	2	143	1	0	0	0	0	1	0	0	0	14756	1212	42	4	692	4	SLITRK2	23	144904633	Missense_Mutation	DNP	GC	TCGA-BQ-7061-01A-11D-1961-08	75266777	144904633	10365927	67	8664											
NADK	65220	hgsc.bcm.edu	37	chr1	1686870	1686870	+	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	aaagctgaatggggtcaggaAgcccagggagcccaggtgga	12	4	17	8	0	1	1	1	1	0	0	1	4	1	4	2	6	3	1	2	6	3	0			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr1:1686870A>T	ENST00000341426.5	-	7	852	c.631T>A	c.(631-633)Ttc>Atc	p.F211I	NADK_ENST00000342348.5_Missense_Mutation_p.F179I|NADK_ENST00000341991.3_Missense_Mutation_p.F211I|NADK_ENST00000492768.1_5'Flank|NADK_ENST00000378625.1_Missense_Mutation_p.F356I|NADK_ENST00000344463.4_Missense_Mutation_p.F356I	NM_023018.4	NP_075394.3	O95544	NADK_HUMAN	NAD kinase	211					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)		GGGGTCAGGAAGCCCAGGGAG	0.607																																					p.F356I		Atlas-SNP	.											.	NADK	79	.	0			c.T1066A						PASS	.						156	158	157					1																	1686870		2203	4300	6503	SO:0001583	missense	65220	exon9			TCAGGAAGCCCAG	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.631T>A	chr1.hg19:g.1686870A>T	ENSP00000341679:p.Phe211Ile	259.0	0.0	.		268.0	48.0	.	NM_001198994	A6NNN3|A8K296|B7Z434|F5GXR5|Q5QPS4|Q9H2P2|Q9H931	Missense_Mutation	SNP	ENST00000341426.5	hg19	CCDS30565.1	.	.	.	.	.	.	.	.	.	.	A	33	5.256937	0.95336	.	.	ENSG00000008130	ENST00000341426;ENST00000341991;ENST00000378625;ENST00000344463;ENST00000342348;ENST00000400922	T;T;T;T;T;T	0.61158	0.13;0.13;0.13;0.13;0.13;0.13	5.25	5.25	0.73442	ATP-NAD kinase, PpnK-type, alpha/beta (1);ATP-NAD kinase, PpnK-type (1);	0.000000	0.85682	D	0.000000	D	0.84502	0.5486	H	0.98199	4.17	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;0.997;0.995;0.994	D	0.90129	0.4205	10	0.87932	D	0	-34.481	14.2701	0.66147	1.0:0.0:0.0:0.0	.	179;356;356;211	F5GXR5;Q9H2P2;Q5QPS4;O95544	.;.;.;NADK_HUMAN	I	211;211;356;356;179;179	ENSP00000341679:F211I;ENSP00000344340:F211I;ENSP00000367890:F356I;ENSP00000340925:F356I;ENSP00000339727:F179I;ENSP00000383713:F179I	ENSP00000341679:F211I	F	-	1	0	NADK	1676730	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.884000	0.92432	2.119000	0.64992	0.379000	0.24179	TTC	.	.	.	none		0.607	NADK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002769.1	NM_023018		T	1686870	A	T	1686870	3	4	144	1	0	0	0	0	1	0	0	0	10144	72	3	5	733	5	NADK	1	1686870	Missense_Mutation	SNP	A	TCGA-BQ-7062-01A-11D-1961-08		1686870	247563751	1	8665											
RPL11	6135	hgsc.bcm.edu	37	chr1	24021204	24021204	+	Missense_Mutation	SNP	T	T	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	cagatactggaaactttggtTttgggatccaggaacacatc	12	11	10	8	0	0	1	0	0	0	1	2	4	1	4	1	4	3	1	1	4	3	4			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr1:24021204T>G	ENST00000374550.3	+	4	364	c.319T>G	c.(319-321)Ttt>Gtt	p.F107V	RPL11_ENST00000482370.1_3'UTR	NM_000975.3|NM_001199802.1	NP_000966.2|NP_001186731.1	P62913	RL11_HUMAN	ribosomal protein L11	107					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein localization to nucleus (GO:0034504)|protein targeting (GO:0006605)|ribosomal large subunit biogenesis (GO:0042273)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)	6		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.13e-24)|Colorectal(126;5.06e-08)|COAD - Colon adenocarcinoma(152;2.92e-06)|GBM - Glioblastoma multiforme(114;4.4e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|KIRC - Kidney renal clear cell carcinoma(1967;0.00322)|STAD - Stomach adenocarcinoma(196;0.0124)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0837)|LUSC - Lung squamous cell carcinoma(448;0.185)		AAACTTTGGTTTTGGGATCCA	0.403																																					p.F107V		Atlas-SNP	.											.	RPL11	21	.	0			c.T319G						PASS	.						146	143	144					1																	24021204		2203	4300	6503	SO:0001583	missense	6135	exon4			TTTGGTTTTGGGA	L05092	CCDS238.1	1p36.1-p35	2011-04-06			ENSG00000142676	ENSG00000142676		"L ribosomal proteins"	10301	protein-coding gene	gene with protein product		604175				9582194, 10343117	Standard	NM_000975		Approved	L11	uc001bhk.3	P62913	OTTHUMG00000002926	ENST00000374550.3:c.319T>G	chr1.hg19:g.24021204T>G	ENSP00000363676:p.Phe107Val	127.0	0.0	.		131.0	43.0	.	NM_000975	P25121|P39026|Q8TDH2|Q9Y674	Missense_Mutation	SNP	ENST00000374550.3	hg19	CCDS238.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.400589	0.83120	.	.	ENSG00000142676	ENST00000374550;ENST00000443624;ENST00000458455	D;D;D	0.82344	-1.6;-1.6;-1.6	5.85	5.85	0.93711	Ribosomal protein L5 domain (2);	0.000000	0.85682	D	0.000000	D	0.94159	0.8126	H	0.96301	3.8	0.80722	D	1	P;P	0.52061	0.938;0.95	D;D	0.80764	0.974;0.994	D	0.95729	0.8773	10	0.87932	D	0	-9.5649	16.233	0.82357	0.0:0.0:0.0:1.0	.	106;107	P62913-2;P62913	.;RL11_HUMAN	V	107;105;105	ENSP00000363676:F107V;ENSP00000390839:F105V;ENSP00000398888:F105V	ENSP00000363676:F107V	F	+	1	0	RPL11	23893791	1.000000	0.71417	0.993000	0.49108	0.476000	0.33039	7.874000	0.87199	2.239000	0.73571	0.529000	0.55759	TTT	.	.	.	none		0.403	RPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008168.1	NM_000975		G	24021204	T	G	24021204	3	3	144	1	0	0	0	0	1	0	0	0	13570	1841	64	5	333	5	RPL11	1	24021204	Missense_Mutation	SNP	T	TCGA-BQ-7062-01A-11D-1961-08	22334334	24021204	225229417	2	8666											
ZSCAN20	7579	hgsc.bcm.edu	37	chr1	33956714	33956714	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttataaattctgggaaaaggAgcactgcagattacagcctg	14	10	10	7	0	1	1	0	0	1	1	1	3	1	3	1	2	4	2	1	2	6	4			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr1:33956714A>G	ENST00000361328.3	+	6	1009	c.856A>G	c.(856-858)Agc>Ggc	p.S286G	ZSCAN20_ENST00000373413.2_Missense_Mutation_p.S232G	NM_145238.3	NP_660281	P17040	ZSC20_HUMAN	zinc finger and SCAN domain containing 20	286					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)				TGGGAAAAGGAGCACTGCAGA	0.468																																					p.S286G		Atlas-SNP	.											.	ZSCAN20	107	.	0			c.A856G						PASS	.						55	55	55					1																	33956714		1886	4113	5999	SO:0001583	missense	7579	exon6			AAAAGGAGCACTG	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.856A>G	chr1.hg19:g.33956714A>G	ENSP00000355053:p.Ser286Gly	82.0	0.0	.		86.0	4.0	.	NM_145238	A8K2D0|B1ALI4|B1ALI5|B1ALI6|Q6ZN23|Q96FA9|Q96H84	Missense_Mutation	SNP	ENST00000361328.3	hg19	CCDS41300.1	.	.	.	.	.	.	.	.	.	.	A	6.309	0.425166	0.11987	.	.	ENSG00000121903	ENST00000373411;ENST00000326544;ENST00000373413;ENST00000361328;ENST00000401072	T	0.02140	4.43	5.64	3.3	0.37823	.	1.076990	0.06981	N	0.819956	T	0.02267	0.0070	L	0.29908	0.895	0.09310	N	1	B;B;B	0.29988	0.0;0.264;0.0	B;B;B	0.28011	0.001;0.085;0.0	T	0.50583	-0.8811	10	0.26408	T	0.33	-4.0623	5.892	0.18919	0.7468:0.1676:0.0855:0.0	.	286;232;286	P17040-3;P17040-4;P17040	.;.;ZSC20_HUMAN	G	232;286;232;220;220	ENSP00000362512:S232G	ENSP00000324450:S286G	S	+	1	0	ZSCAN20	33729301	0.934000	0.31675	0.009000	0.14445	0.304000	0.27724	1.295000	0.33377	0.495000	0.27882	0.533000	0.62120	AGC	.	.	.	none		0.468	ZSCAN20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277003.2	NM_145238		G	33956714	A	G	33956714	3	3	144	1	0	0	0	0	1	0	0	0	18244	304	11	3	874	3	ZSCAN20	1	33956714	Missense_Mutation	SNP	A	TCGA-BQ-7062-01A-11D-1961-08	9935510	33956714	215293907	3	8667											
LMO4	8543	hgsc.bcm.edu	37	chr1	87805263	87805263	+	Frame_Shift_Del	DEL	T	T	-																															cagcgcttgcggacagtcgaTtcctgcgagtgaactcgtca																										TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr1:87805263delT	ENST00000370544.5	+	3	1061	c.281delT	c.(280-282)attfs	p.I94fs	LMO4_ENST00000489303.1_3'UTR|LMO4_ENST00000370542.1_Frame_Shift_Del_p.I94fs	NM_006769.3	NP_006760.1	P61968	LMO4_HUMAN	LIM domain only 4	94	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				negative regulation of protein complex assembly (GO:0031333)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell activation (GO:0050865)|regulation of cell fate specification (GO:0042659)|spinal cord association neuron differentiation (GO:0021527)|spinal cord motor neuron differentiation (GO:0021522)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)|ventral spinal cord interneuron differentiation (GO:0021514)|ventricular septum development (GO:0003281)	transcription factor complex (GO:0005667)	enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(1)	9		Lung NSC(277;0.179)		all cancers(265;0.00456)|Epithelial(280;0.0148)|BRCA - Breast invasive adenocarcinoma(282;0.153)		GGACAGTCGATTCCTGCGAGT	0.388																																					p.I94fs		Atlas-INDEL	.											.	LMO4	21	.	0			c.280delA						PASS	.						95	95	95					1																	87805263		2203	4300	6503	SO:0001589	frameshift_variant	8543	exon3			.	U24576	CCDS713.1	1p22.3	2008-02-05			ENSG00000143013	ENSG00000143013			6644	protein-coding gene	gene with protein product		603129					Standard	NM_006769		Approved		uc001dmi.3	P61968	OTTHUMG00000010248	ENST00000370544.5:c.281delT	chr1.hg19:g.87805263delT	ENSP00000359575:p.Ile94fs	54.0	0.0	0		58.0	17.0	0.293103	NM_006769	D3DT23|O00158|O88894	Frame_Shift_Del	DEL	ENST00000370544.5	hg19	CCDS713.1																																																																																			.	.	.	none		0.388	LMO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028264.2	NM_006769		-	87805263	T	-	87805263	7	5	144	1	0	1	0	1	0	0	0	0	8861	1493	52	0	287	0	LMO4	1	87805263	Frame_Shift_Del	DEL	T	TCGA-BQ-7062-01A-11D-1961-08	53848549	87805263	161445358	4	8668											
ZBTB37	84614	hgsc.bcm.edu	37	chr1	173839638	173839638	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttctgttacacagggcggaTatgcctgcaactggcagata	10	11	11	9	1	1	1	0	0	1	1	1	2	1	2	1	3	4	3	1	3	4	4			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr1:173839638T>C	ENST00000367701.5	+	2	466	c.275T>C	c.(274-276)aTa>aCa	p.I92T	ZBTB37_ENST00000432989.1_Missense_Mutation_p.I92T|GAS5_ENST00000364084.1_RNA|ZBTB37_ENST00000367702.1_Missense_Mutation_p.I92T|ZBTB37_ENST00000367704.1_Missense_Mutation_p.I92T|ZBTB37_ENST00000427304.1_Missense_Mutation_p.I92T			Q5TC79	ZBT37_HUMAN	zinc finger and BTB domain containing 37	92	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(4)	13						ACAGGGCGGATATGCCTGCAA	0.433																																					p.I92T		Atlas-SNP	.											.	ZBTB37	38	.	0			c.T275C						PASS	.						74	74	74					1																	173839638		2203	4300	6503	SO:0001583	missense	84614	exon3			GGCGGATATGCCT	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.275T>C	chr1.hg19:g.173839638T>C	ENSP00000356674:p.Ile92Thr	71.0	0.0	.		80.0	19.0	.	NM_032522	Q5TC80|Q96M87|Q9BQ88	Missense_Mutation	SNP	ENST00000367701.5	hg19	CCDS44278.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.123564	0.77436	.	.	ENSG00000185278	ENST00000367704;ENST00000427304;ENST00000432989;ENST00000367702;ENST00000367701	T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3	5.85	5.85	0.93711	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.044936	0.85682	D	0.000000	T	0.71358	0.3330	L	0.48174	1.505	0.58432	D	0.999993	D;P	0.63880	0.993;0.941	D;P	0.68039	0.955;0.736	T	0.75639	-0.3248	10	0.87932	D	0	.	16.2271	0.82306	0.0:0.0:0.0:1.0	.	92;92	Q5TC79;Q5TC79-2	ZBT37_HUMAN;.	T	92	ENSP00000356677:I92T;ENSP00000415293:I92T;ENSP00000409408:I92T;ENSP00000356675:I92T;ENSP00000356674:I92T	ENSP00000356674:I92T	I	+	2	0	ZBTB37	172106261	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	7.698000	0.84413	2.234000	0.73211	0.460000	0.39030	ATA	.	.	.	none		0.433	ZBTB37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090729.2	NM_032522		C	173839638	T	C	173839638	3	2	144	1	0	0	0	0	1	0	0	0	17550	1406	49	3	277	3	ZBTB37	1	173839638	Missense_Mutation	SNP	T	TCGA-BQ-7062-01A-11D-1961-08	86034375	173839638	75410983	5	8669											
NFASC	23114	hgsc.bcm.edu	37	chr1	204923960	204923960	+	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	tgtccacttctctccagaatCtcctctgtggcccaaggaaa	9	11	7	14	0	3	1	0	0	3	1	7	2	5	2	4	2	0	0	4	2	3	1			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr1:204923960C>A	ENST00000401399.1	+	6	615	c.416C>A	c.(415-417)tCt>tAt	p.S139Y	NFASC_ENST00000367169.4_Missense_Mutation_p.S139Y|NFASC_ENST00000403080.1_Missense_Mutation_p.S139Y|NFASC_ENST00000404076.1_Missense_Mutation_p.S133Y|NFASC_ENST00000360049.4_Missense_Mutation_p.S133Y|NFASC_ENST00000339876.6_Missense_Mutation_p.S139Y|NFASC_ENST00000404907.1_Missense_Mutation_p.S133Y|NFASC_ENST00000513543.1_Missense_Mutation_p.S133Y|NFASC_ENST00000539706.1_Missense_Mutation_p.S133Y|NFASC_ENST00000367171.4_Missense_Mutation_p.S139Y|NFASC_ENST00000338515.6_Missense_Mutation_p.S139Y|NFASC_ENST00000367170.4_Missense_Mutation_p.S139Y|NFASC_ENST00000338586.6_Missense_Mutation_p.S139Y|NFASC_ENST00000367172.4_Missense_Mutation_p.S139Y			O94856	NFASC_HUMAN	neurofascin	139					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)			TCTCCAGAATCTCCTCTGTGG	0.597																																					p.S139Y		Atlas-SNP	.											.	NFASC	396	.	0			c.C416A						PASS	.						105	107	106					1																	204923960		2203	4300	6503	SO:0001583	missense	23114	exon7			CAGAATCTCCTCT	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.416C>A	chr1.hg19:g.204923960C>A	ENSP00000385637:p.Ser139Tyr	190.0	0.0	.		213.0	51.0	.	NM_001005388	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Missense_Mutation	SNP	ENST00000401399.1	hg19	CCDS53460.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.3|29.3	4.998077|4.998077	0.93227|0.93227	.|.	.|.	ENSG00000163531|ENSG00000163531	ENST00000367173|ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000446412;ENST00000403080;ENST00000404076;ENST00000401399;ENST00000404907;ENST00000513543;ENST00000430393	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.72282	.|1.09;-0.64;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09	5.37|5.37	5.37|5.37	0.77165|0.77165	.|.	.|0.000000	.|0.52532	.|D	.|0.000064	D|D	0.83069|0.83069	0.5174|0.5174	M|M	0.64260|0.64260	1.97|1.97	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D;D	.|0.87578	.|0.998;0.977;0.992;0.977;0.99;0.976	D|D	0.84410|0.84410	0.0565|0.0565	5|10	.|0.72032	.|D	.|0.01	.|.	18.6966|18.6966	0.91603|0.91603	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|133;133;235;139;133;139	.|O94856-11;O94856-8;B4DRH7;O94856-9;O94856-3;O94856-2	.|.;.;.;.;.;.	I|Y	109|139;139;139;139;139;139;133;133;133;139;139;139;133;139;133;133;109	.|ENSP00000356140:S139Y;ENSP00000356139:S139Y;ENSP00000356138:S139Y;ENSP00000342128:S139Y;ENSP00000344786:S139Y;ENSP00000343509:S139Y;ENSP00000438614:S133Y;ENSP00000353154:S133Y;ENSP00000356137:S139Y;ENSP00000412161:S139Y;ENSP00000384875:S139Y;ENSP00000385676:S133Y;ENSP00000385637:S139Y;ENSP00000384061:S133Y;ENSP00000425908:S133Y;ENSP00000415031:S109Y	.|ENSP00000295776:S133Y	L|S	+|+	1|2	0|0	NFASC|NFASC	203190583|203190583	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	7.797000|7.797000	0.85911|0.85911	2.516000|2.516000	0.84829|0.84829	0.655000|0.655000	0.94253|0.94253	CTC|TCT	.	.	.	none		0.597	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388		A	204923960	C	A	204923960	3	1	144	1	0	0	0	0	1	0	0	0	10366	913	32	4	434	4	NFASC	1	204923960	Missense_Mutation	SNP	C	TCGA-BQ-7062-01A-11D-1961-08	31084322	204923960	44326661	6	8670											
ALPI	248	hgsc.bcm.edu	37	chr2	233322816	233322816	+	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	gcgcctgctgagcaggaaccCccgcggcttctacctctttg	5	9	11	16	3	2	1	0	1	2	0	2	2	2	2	4	2	4	3	4	2	2	3			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr2:233322816C>T	ENST00000295463.3	+	8	1042	c.965C>T	c.(964-966)cCc>cTc	p.P322L		NM_001631.3	NP_001622.2	P09923	PPBI_HUMAN	alkaline phosphatase, intestinal	322					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)		AGCAGGAACCCCCGCGGCTTC	0.662																																					p.P322L		Atlas-SNP	.											.	ALPI	64	.	0			c.C965T						PASS	.						58	65	63					2																	233322816		2203	4300	6503	SO:0001583	missense	248	exon8			GGAACCCCCGCGG	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.965C>T	chr2.hg19:g.233322816C>T	ENSP00000295463:p.Pro322Leu	105.0	0.0	.		108.0	26.0	.	NM_001631	B2R7Y4|Q53S80|Q9UBV5|Q9UCL2	Missense_Mutation	SNP	ENST00000295463.3	hg19	CCDS2492.1	.	.	.	.	.	.	.	.	.	.	C	13.56	2.273284	0.40194	.	.	ENSG00000163295	ENST00000295463	D	0.96300	-3.97	4.46	4.46	0.54185	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.106561	0.64402	D	0.000003	D	0.97238	0.9097	M	0.93328	3.405	0.58432	D	0.999999	P	0.38223	0.623	B	0.40741	0.339	D	0.98720	1.0708	10	0.62326	D	0.03	.	16.2794	0.82664	0.0:1.0:0.0:0.0	.	322	P09923	PPBI_HUMAN	L	322	ENSP00000295463:P322L	ENSP00000295463:P322L	P	+	2	0	ALPI	233031060	1.000000	0.71417	0.784000	0.31847	0.009000	0.06853	7.289000	0.78701	2.318000	0.78349	0.561000	0.74099	CCC	.	.	.	none		0.662	ALPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257035.2	NM_001631		T	233322816	C	T	233322816	3	4	144	1	0	0	0	0	1	0	0	0	543	623	22	2	995	2	ALPI	2	233322816	Missense_Mutation	SNP	C	TCGA-BQ-7062-01A-11D-1961-08		233322816	9876557	7	8671											
PLXNB1	5364	hgsc.bcm.edu	37	chr3	48459373	48459373	+	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	gcacagggcactccagccacCgtgaccatgcccagcacatc	10	4	9	18	1	0	1	0	1	0	0	2	1	1	1	5	1	3	3	5	1	0	0			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr3:48459373C>A	ENST00000358536.4	-	16	3590	c.3321G>T	c.(3319-3321)acG>acT	p.T1107T	PLXNB1_ENST00000465117.1_5'Flank|PLXNB1_ENST00000448774.2_Intron|PLXNB1_ENST00000358459.4_Silent_p.T924T|PLXNB1_ENST00000456774.1_Silent_p.T924T|PLXNB1_ENST00000296440.6_Silent_p.T1107T	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	1107	IPT/TIG 1.				axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CTCCAGCCACCGTGACCATGC	0.662																																					p.T1107T		Atlas-SNP	.											.	PLXNB1	150	.	0			c.G3321T						PASS	.						60	58	59					3																	48459373		2203	4300	6503	SO:0001819	synonymous_variant	5364	exon16			AGCCACCGTGACC	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"Plexins"	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.3321G>T	chr3.hg19:g.48459373C>A		87.0	0.0	.		94.0	20.0	.	NM_001130082	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Silent	SNP	ENST00000358536.4	hg19	CCDS2765.1																																																																																			.	.	.	none		0.662	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673		A	48459373	C	A	48459373	2	1	144	1	0	0	0	0	0	0	0	1	12130	639	23	4		4	PLXNB1	3	48459373	Silent	SNP	C	TCGA-BQ-7062-01A-11D-1961-08		48459373	149563057	8	8672											
NDUFAF3	25915	hgsc.bcm.edu	37	chr3	49059877	49059877	+	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	cgaggccgctcaggcaatgtAcatcgacagctacaacagcc	12	5	10	14	3	1	0	1	0	0	0	2	2	1	0	2	2	5	4	2	2	4	2			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr3:49059877A>T	ENST00000326925.6	+	2	1310	c.176A>T	c.(175-177)tAc>tTc	p.Y59F	MIR191_ENST00000384873.1_RNA|NDUFAF3_ENST00000395458.2_Missense_Mutation_p.Y2F|NDUFAF3_ENST00000451378.2_Missense_Mutation_p.Y2F|DALRD3_ENST00000440857.1_5'Flank|MIR425_ENST00000362162.1_RNA|DALRD3_ENST00000496568.1_5'Flank|DALRD3_ENST00000313778.5_5'Flank|NDUFAF3_ENST00000326912.4_Missense_Mutation_p.Y2F	NM_199069.1	NP_951032.1	Q9BU61	NDUF3_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 3	59					mitochondrial respiratory chain complex I assembly (GO:0032981)	mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(4)	8						CAGGCAATGTACATCGACAGC	0.652																																					p.Y59F		Atlas-SNP	.											.	NDUFAF3	9	.	0			c.A176T						PASS	.						23	24	23					3																	49059877		2200	4299	6499	SO:0001583	missense	25915	exon2			CAATGTACATCGA		CCDS2784.1, CCDS2785.1	3p21.31	2012-10-12	2012-05-08	2009-03-18	ENSG00000178057	ENSG00000178057		"Mitochondrial respiratory chain complex assembly factors"	29918	protein-coding gene	gene with protein product		612911	"chromosome 3 open reading frame 60", "NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 3"	C3orf60		12653254, 9349717	Standard	NM_199069		Approved	MGC10527, DKFZP564J0123, E3-3, 2P1	uc003cvq.3	Q9BU61	OTTHUMG00000156773	ENST00000326925.6:c.176A>T	chr3.hg19:g.49059877A>T	ENSP00000323076:p.Tyr59Phe	66.0	0.0	.		106.0	23.0	.	NM_199069		Missense_Mutation	SNP	ENST00000326925.6	hg19	CCDS2784.1	.	.	.	.	.	.	.	.	.	.	A	15.90	2.970503	0.53614	.	.	ENSG00000178057	ENST00000326912;ENST00000326925;ENST00000395458;ENST00000451378	D;D;D;D	0.85629	-2.01;-2.01;-2.01;-2.01	5.29	2.73	0.32206	.	0.264355	0.36665	N	0.002471	T	0.70885	0.3275	L	0.33485	1.01	0.31716	N	0.638898	B	0.02656	0.0	B	0.06405	0.002	T	0.58493	-0.7627	10	0.11182	T	0.66	-8.5232	4.4326	0.11535	0.598:0.0:0.09:0.312	.	59	Q9BU61	NDUF3_HUMAN	F	2;59;2;2	ENSP00000323003:Y2F;ENSP00000323076:Y59F;ENSP00000378843:Y2F;ENSP00000402465:Y2F	ENSP00000323003:Y2F	Y	+	2	0	NDUFAF3	49034881	1.000000	0.71417	0.997000	0.53966	0.638000	0.38207	4.002000	0.57053	0.833000	0.34828	0.533000	0.62120	TAC	.	.	.	none		0.652	NDUFAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345683.2	NM_199069		T	49059877	A	T	49059877	3	4	144	1	0	0	0	0	1	0	0	0	10283	391	14	5	182	5	NDUFAF3	3	49059877	Missense_Mutation	SNP	A	TCGA-BQ-7062-01A-11D-1961-08	600504	49059877	148962553	9	8673											
DNAH1	25981	hgsc.bcm.edu	37	chr3	52432935	52432935	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaggcactcaaggggctggtAgtgatgtcctctcagctgga	9	9	14	9	0	2	1	2	1	1	0	4	2	3	2	1	5	1	4	1	5	3	1			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr3:52432935A>G	ENST00000420323.2	+	76	12420	c.12159A>G	c.(12157-12159)gtA>gtG	p.V4053V		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	4118					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)		AGGGGCTGGTAGTGATGTCCT	0.552																																					p.V4053V		Atlas-SNP	.											.	DNAH1	534	.	0			c.A12159G						PASS	.						48	54	52					3																	52432935		2092	4227	6319	SO:0001819	synonymous_variant	25981	exon76			GCTGGTAGTGATG	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.12159A>G	chr3.hg19:g.52432935A>G		36.0	0.0	.		49.0	11.0	.	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Silent	SNP	ENST00000420323.2	hg19	CCDS46842.1																																																																																			.	.	.	none		0.552	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		G	52432935	A	G	52432935	2	3	144	1	0	0	0	0	0	0	0	1	4599	407	15	3		3	DNAH1	3	52432935	Silent	SNP	A	TCGA-BQ-7062-01A-11D-1961-08	3373058	52432935	145589495	10	8674											
PDGFRB	5159	hgsc.bcm.edu	37	chr5	149515196	149515213	+	In_Frame_Del	DEL	CCGTGTCTAGCCCAGTGA	CCGTGTCTAGCCCAGTGA	-																															gtgggtgcaaaagtattctcCcgtgtctagcccagtgaggt																								rs141870925|rs188981582|rs556826386	byFrequency	TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	CCGTGTCTAGCCCAGTGA	CCGTGTCTAGCCCAGTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr5:149515196_149515213delCCGTGTCTAGCCCAGTGA	ENST00000261799.4	-	3	738_755	c.269_286delTCACTGGGCTAGACACGG	c.(268-288)ctcactgggctagacacggga>cga	p.90_96LTGLDTG>R		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	90	Ig-like C2-type 1.				adrenal gland development (GO:0030325)|aorta morphogenesis (GO:0035909)|cardiac myofibril assembly (GO:0055003)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in coronary angiogenesis (GO:0060981)|cell migration involved in vasculogenesis (GO:0035441)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glycosaminoglycan biosynthetic process (GO:0006024)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerular capillary formation (GO:0072277)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|metanephric mesenchymal cell migration (GO:0035789)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to estradiol (GO:0032355)|response to fluid shear stress (GO:0034405)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to retinoic acid (GO:0032526)|response to toxic substance (GO:0009636)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|smooth muscle cell chemotaxis (GO:0071670)|smooth muscle tissue development (GO:0048745)|tissue homeostasis (GO:0001894)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|platelet-derived growth factor-activated receptor activity (GO:0005017)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|vascular endothelial growth factor binding (GO:0038085)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(3)|prostate(3)|skin(3)|stomach(6)|urinary_tract(1)	75		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AAGTATTCTCCCGTGTCTAGCCCAGTGAGGTTGGTCAG	0.592			T	"ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"	"MPD, AML, CMML, CML"																																p.90_96del		Atlas-INDEL	.		Dom	yes		5	5q31-q32	5159	"platelet-derived growth factor receptor, beta polypeptide"		L	.	PDGFRB	142	.	0			c.270_287del						PASS	.																																			SO:0001651	inframe_deletion	5159	exon3			.	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.269_286delTCACTGGGCTAGACACGG	chr5.hg19:g.149515196_149515213delCCGTGTCTAGCCCAGTGA	ENSP00000261799:p.Leu90_Gly96delinsArg	153.0	0.0	0		120.0	19.0	0.158333	NM_002609	B5A957|Q8N5L4	In_Frame_Del	DEL	ENST00000261799.4	hg19	CCDS4303.1																																																																																			.	.	.	none		0.592	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609		-	149515213	CCGTGTCTAGCCCAGTGA	-	149515196	7	5	144	1	0	1	0	1	0	0	0	0	11669	632	22	0	3118	0	PDGFRB	5	149515196	In_Frame_Del	DEL	CCGTGTCTAGCCCAGTGA	TCGA-BQ-7062-01A-11D-1961-08		149515196	31400064	11	8675											
ASCC3	10973	hgsc.bcm.edu	37	chr6	101296249	101296249	+	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	aacttcttataatctaggctTatagttttctgagtttcacc	10	18	5	8	0	4	1	1	1	3	0	4	1	4	1	1	1	1	3	1	1	6	9			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr6:101296249T>A	ENST00000369162.2	-	4	920	c.576A>T	c.(574-576)atA>atT	p.I192I	ASCC3_ENST00000522650.1_Silent_p.I192I	NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	192					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)		AATCTAGGCTTATAGTTTTCT	0.378																																					p.I192I		Atlas-SNP	.											.	ASCC3	205	.	0			c.A576T						PASS	.						59	58	58					6																	101296249		2203	4300	6503	SO:0001819	synonymous_variant	10973	exon4			TAGGCTTATAGTT	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.576A>T	chr6.hg19:g.101296249T>A		67.0	0.0	.		70.0	16.0	.	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Silent	SNP	ENST00000369162.2	hg19	CCDS5046.1																																																																																			.	.	.	none		0.378	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		A	101296249	T	A	101296249	2	1	144	1	0	0	0	0	0	0	0	1	1033	1744	61	5		5	ASCC3	6	101296249	Silent	SNP	T	TCGA-BQ-7062-01A-11D-1961-08		101296249	69818818	12	8676											
NOM1	64434	hgsc.bcm.edu	37	chr7	156752614	156752614	+	Frame_Shift_Del	DEL	A	A	-																															ataaatacggaagcgaagggAaagagtgtgacaacctgttc																										TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr7:156752614delA	ENST00000275820.3	+	4	1393	c.1378delA	c.(1378-1380)aaafs	p.K460fs	NOM1_ENST00000460332.1_3'UTR	NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	460	MIF4G. {ECO:0000255|PROSITE- ProRule:PRU00698}.					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)		AAGCGAAGGGAAAGAGTGTGA	0.443																																					p.G459fs		Atlas-INDEL	.											.	NOM1	73	.	0			c.1377delG						PASS	.						128	109	115					7																	156752614		2203	4300	6503	SO:0001589	frameshift_variant	64434	exon4			.	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.1378delA	chr7.hg19:g.156752614delA	ENSP00000275820:p.Lys460fs	58.0	0.0	0		61.0	16.0	0.262295	NM_138400	Q96I08	Frame_Shift_Del	DEL	ENST00000275820.3	hg19	CCDS34787.1																																																																																			.	.	.	none		0.443	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400		-	156752614	A	-	156752614	7	5	144	1	0	1	0	1	0	0	0	0	10537	247	9	0	1392	0	NOM1	7	156752614	Frame_Shift_Del	DEL	A	TCGA-BQ-7062-01A-11D-1961-08		156752614	2386049	13	8677											
C8orf41	80185	hgsc.bcm.edu	37	chr8	33369560	33369560	+	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	cttcattttctccatgtaggAatcctgccacagaaccgcat	10	12	6	13	1	2	1	1	0	1	1	4	2	3	2	4	1	2	2	4	1	3	4			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr8:33369560A>T	ENST00000431156.2	-	2	1190	c.572T>A	c.(571-573)tTc>tAc	p.F191Y	TTI2_ENST00000519356.1_5'Flank|TTI2_ENST00000360742.5_Missense_Mutation_p.F191Y|TTI2_ENST00000520636.1_Missense_Mutation_p.F191Y|SNORD13_ENST00000459299.1_RNA	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	191																	TCCATGTAGGAATCCTGCCAC	0.502																																					p.F191Y		Atlas-SNP	.											.	.	.	.	0			c.T572A						PASS	.						191	196	194					8																	33369560		2203	4300	6503	SO:0001583	missense	80185	exon2			TGTAGGAATCCTG	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.572T>A	chr8.hg19:g.33369560A>T	ENSP00000411169:p.Phe191Tyr	353.0	0.0	.		363.0	95.0	.	NM_001265581	D3DSV7|Q96IM2|Q9H5N4	Missense_Mutation	SNP	ENST00000431156.2	hg19	CCDS6090.1	.	.	.	.	.	.	.	.	.	.	A	18.29	3.592154	0.66219	.	.	ENSG00000129696	ENST00000360742;ENST00000431156;ENST00000522668;ENST00000520636;ENST00000520397	T;T;T	0.76709	-1.04;-1.04;-1.04	4.66	4.66	0.58398	.	0.101991	0.43579	D	0.000544	D	0.85102	0.5620	M	0.76838	2.35	0.25824	N	0.984245	D;D;D	0.63880	0.993;0.993;0.993	P;P;P	0.60012	0.867;0.867;0.867	T	0.79057	-0.1959	10	0.72032	D	0.01	-23.4405	11.5884	0.50931	1.0:0.0:0.0:0.0	.	191;191;191	E5RH83;Q6NXR4;E5RIH5	.;TTI2_HUMAN;.	Y	191	ENSP00000353971:F191Y;ENSP00000411169:F191Y;ENSP00000428401:F191Y	ENSP00000353971:F191Y	F	-	2	0	C8orf41	33489102	1.000000	0.71417	0.326000	0.25389	0.530000	0.34684	5.556000	0.67307	1.954000	0.56735	0.533000	0.62120	TTC	.	.	.	none		0.502	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115		T	33369560	A	T	33369560	3	4	144	1	0	0	0	0	1	0	0	0	2429	246	9	5	982	5	C8orf41	8	33369560	Missense_Mutation	SNP	A	TCGA-BQ-7062-01A-11D-1961-08		33369560	112994462	14	8678											
PSCA	8000	hgsc.bcm.edu	37	chr8	143762846	143762846	+	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	gggagcagtgctggaccgcgCgcatccgtgagtggggggac	6	5	20	10	4	0	1	0	1	0	0	1	4	1	4	2	5	2	3	2	5	0	0			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr8:143762846C>G	ENST00000301258.4	+	2	210	c.127C>G	c.(127-129)Cgc>Ggc	p.R43G	PSCA_ENST00000505305.1_3'UTR|PSCA_ENST00000513264.1_Missense_Mutation_p.R43G	NM_005672.4	NP_005663.2	O43653	PSCA_HUMAN	prostate stem cell antigen	52	UPAR/Ly6.					anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)	2	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)					CTGGACCGCGCGCATCCGTGA	0.607																																					p.R43G		Atlas-SNP	.											.	PSCA	9	.	0			c.C127G						PASS	.						12	16	15					8																	143762846		2125	4209	6334	SO:0001583	missense	8000	exon2			ACCGCGCGCATCC	AF043498	CCDS47925.1, CCDS47925.2	8q24.2	2004-02-03				ENSG00000167653			9500	protein-coding gene	gene with protein product		602470				9465086	Standard	NM_005672		Approved		uc022bcd.1	O43653		ENST00000301258.4:c.127C>G	chr8.hg19:g.143762846C>G	ENSP00000301258:p.Arg43Gly	14.0	0.0	.		16.0	6.0	.	NM_005672	Q6UW92	Missense_Mutation	SNP	ENST00000301258.4	hg19	CCDS47925.2	.	.	.	.	.	.	.	.	.	.	C	11.60	1.686883	0.29962	.	.	ENSG00000167653	ENST00000301258;ENST00000513264	T	0.70399	-0.48	2.97	2.09	0.27110	Ly-6 antigen / uPA receptor -like (1);CD59 antigen (1);	1.295300	0.05740	N	0.601212	T	0.75079	0.3801	M	0.72894	2.215	0.09310	N	1	P	0.43169	0.8	P	0.50162	0.633	T	0.57837	-0.7742	10	0.26408	T	0.33	.	6.0755	0.19913	0.0:0.8561:0.0:0.1439	.	52	O43653	PSCA_HUMAN	G	52	ENSP00000426508:R52G	ENSP00000301258:R52G	R	+	1	0	PSCA	143759848	0.001000	0.12720	0.001000	0.08648	0.176000	0.22953	1.247000	0.32815	0.837000	0.34925	0.456000	0.33151	CGC	.	.	.	none		0.607	PSCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367112.2	NM_005672		G	143762846	C	G	143762846	3	3	144	1	0	0	0	0	1	0	0	0	12655	768	27	4	133	4	PSCA	8	143762846	Missense_Mutation	SNP	C	TCGA-BQ-7062-01A-11D-1961-08	110393286	143762846	2601176	15	8679											
TLN1	7094	hgsc.bcm.edu	37	chr9	35698169	35698169	+	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	cttcactgcgttgccagcagCctgggcagagagaaagtggc	9	7	14	11	1	1	2	1	0	0	2	1	3	1	2	2	2	4	3	2	2	1	2	rs555751291		TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr9:35698169C>G	ENST00000314888.9	-	56	7725	c.7372G>C	c.(7372-7374)Gct>Cct	p.A2458P	TLN1_ENST00000540444.1_Splice_Site_p.A2346P	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	2458	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TTGCCAGCAGCCTGGGCAGAG	0.512																																					p.A2458P		Atlas-SNP	.											.	TLN1	185	.	0			c.G7372C						PASS	.						74	68	70					9																	35698169		2203	4300	6503	SO:0001630	splice_region_variant	7094	exon56			CAGCAGCCTGGGC	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.7372-1G>C	chr9.hg19:g.35698169C>G		70.0	0.0	.		83.0	14.0	.	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	hg19	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.417660	0.83449	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.31769	1.48;1.48	4.83	4.83	0.62350	I/LWEQ (4);	0.053747	0.85682	D	0.000000	T	0.56441	0.1985	M	0.79258	2.445	0.80722	D	1	D	0.63880	0.993	D	0.65323	0.934	T	0.60747	-0.7202	10	0.56958	D	0.05	-4.1588	18.0913	0.89476	0.0:1.0:0.0:0.0	.	2458	Q9Y490	TLN1_HUMAN	P	2458;2346	ENSP00000316029:A2458P;ENSP00000442981:A2346P	ENSP00000316029:A2458P	A	-	1	0	TLN1	35688169	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.752000	0.62176	2.509000	0.84616	0.655000	0.94253	GCT	.	.	.	none		0.512	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	Missense_Mutation	G	35698169	C	G	35698169	5	3	144	1	0	0	0	0	0	0	1	0	15959	753	26	4	261	4	TLN1	9	35698169	Splice_Site	SNP	C	TCGA-BQ-7062-01A-11D-1961-08		35698169	105515262	16	8680											
IFIT5	24138	hgsc.bcm.edu	37	chr10	91177427	91177427	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttggaggaaagtattatcaAaaggctaaagcggcttttga	14	12	11	4	1	1	1	1	1	0	0	1	3	1	3	0	4	1	3	0	4	7	6			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr10:91177427A>G	ENST00000371795.4	+	2	684	c.471A>G	c.(469-471)caA>caG	p.Q157Q	IFIT5_ENST00000416601.1_Silent_p.Q157Q	NM_012420.2	NP_036552.1	Q13325	IFIT5_HUMAN	interferon-induced protein with tetratricopeptide repeats 5	157					defense response to virus (GO:0051607)|innate immune response (GO:0045087)	actin cytoskeleton (GO:0015629)|apical part of cell (GO:0045177)|ruffle membrane (GO:0032587)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)|tRNA binding (GO:0000049)			endometrium(1)|large_intestine(4)|lung(4)	9						AGTATTATCAAAAGGCTAAAG	0.443																																					p.Q157Q		Atlas-SNP	.											.	IFIT5	32	.	0			c.A471G						PASS	.						71	74	73					10																	91177427		2203	4300	6503	SO:0001819	synonymous_variant	24138	exon2			TTATCAAAAGGCT	U34605	CCDS7403.1	10q23.31	2013-01-10			ENSG00000152778	ENSG00000152778		"Tetratricopeptide (TTC) repeat domain containing"	13328	protein-coding gene	gene with protein product	"retinoic acid- and interferon-inducible protein (58kD)"					9398535	Standard	NM_012420		Approved	RI58	uc010qnh.2	Q13325	OTTHUMG00000018713	ENST00000371795.4:c.471A>G	chr10.hg19:g.91177427A>G		94.0	0.0	.		102.0	24.0	.	NM_012420	B2R5X9|B4DDV1|Q5T7I9|Q6IAX3	Silent	SNP	ENST00000371795.4	hg19	CCDS7403.1																																																																																			.	.	.	none		0.443	IFIT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049303.1	NM_012420		G	91177427	A	G	91177427	2	3	144	1	0	0	0	0	0	0	0	1	7532	11	1	3		3	IFIT5	10	91177427	Silent	SNP	A	TCGA-BQ-7062-01A-11D-1961-08		91177427	44357320	17	8681											
DMBT1	1755	hgsc.bcm.edu	37	chr10	124352013	124352013	+	Missense_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	cattgttctggatgatgtgcGctgctcaggacacgagtcct	7	12	12	10	2	2	1	1	1	1	0	3	4	3	3	1	2	2	3	1	2	0	2			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr10:124352013G>A	ENST00000338354.3	+	20	2508	c.2402G>A	c.(2401-2403)cGc>cAc	p.R801H	DMBT1_ENST00000368909.3_Missense_Mutation_p.R801H|DMBT1_ENST00000368956.2_Intron|DMBT1_ENST00000344338.3_Missense_Mutation_p.R791H|DMBT1_ENST00000368955.3_Missense_Mutation_p.R791H|DMBT1_ENST00000330163.4_Intron|DMBT1_ENST00000359586.6_Intron			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	801	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)				GATGATGTGCGCTGCTCAGGA	0.607																																					p.R801H	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											DMBT1_ENST00000368915,NS,carcinoma,0,3	DMBT1	677	.	0			c.G2402A						PASS	.						155	114	127					10																	124352013		2023	4110	6133	SO:0001583	missense	1755	exon20			ATGTGCGCTGCTC		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.2402G>A	chr10.hg19:g.124352013G>A	ENSP00000342210:p.Arg801His	254.0	1.0	.		321.0	21.0	.	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	hg19		.	.	.	.	.	.	.	.	.	.	G	0.015	-1.564805	0.00903	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000344338;ENST00000368909;ENST00000368955	T;T;T;T	0.44881	0.91;0.91;0.91;0.91	3.9	-0.752	0.11072	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	.	.	.	.	T	0.43233	0.1238	L	0.42008	1.315	0.09310	N	1	D;B;B;B	0.76494	0.999;0.098;0.098;0.119	D;B;B;B	0.63033	0.91;0.005;0.005;0.008	T	0.26224	-1.0109	9	0.33141	T	0.24	.	1.6023	0.02676	0.3222:0.1635:0.395:0.1192	.	562;801;791;801	Q9UGM3-4;Q9UGM3-6;Q9UGM3-3;Q9UGM3	.;.;.;DMBT1_HUMAN	H	801;801;801;801;801;801;791;801;791	ENSP00000342210:R801H;ENSP00000343175:R791H;ENSP00000357905:R801H;ENSP00000357951:R791H	ENSP00000342210:R801H	R	+	2	0	DMBT1	124342003	0.000000	0.05858	0.023000	0.16930	0.017000	0.09413	-1.614000	0.02057	-0.442000	0.07190	-0.219000	0.12488	CGC	.	.	.	none		0.607	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		A	124352013	G	A	124352013	3	1	144	1	0	0	0	0	1	0	0	0	4579	1087	38	1	2480	1	DMBT1	10	124352013	Missense_Mutation	SNP	G	TCGA-BQ-7062-01A-11D-1961-08	33174586	124352013	11182734	18	8682											
AGBL2	79841	hgsc.bcm.edu	37	chr11	47726183	47726183	+	Frame_Shift_Del	DEL	G	G	-																															ttggtagacaaaatggaaaaGagctcttggggttctcgaag																								rs373862581		TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr11:47726183delG	ENST00000525123.1	-	7	783	c.498delC	c.(496-498)ctcfs	p.L166fs	AGBL2_ENST00000298861.4_Frame_Shift_Del_p.L166fs|AGBL2_ENST00000528244.1_Frame_Shift_Del_p.L128fs|AGBL2_ENST00000357610.3_Frame_Shift_Del_p.L166fs|AGBL2_ENST00000529712.1_5'UTR	NM_024783.3	NP_079059.2	Q5U5Z8	CBPC2_HUMAN	ATP/GTP binding protein-like 2	166						cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)	34						AAATGGAAAAGAGCTCTTGGG	0.428																																					p.F167fs		Atlas-INDEL	.											.	AGBL2	73	.	0			c.499delT						PASS	.						141	132	135					11																	47726183		2201	4298	6499	SO:0001589	frameshift_variant	79841	exon7			.		CCDS7944.1	11p11.2	2014-06-23			ENSG00000165923	ENSG00000165923			26296	protein-coding gene	gene with protein product	"cytoplasmic carboxypeptidase 2"					12738998, 21303978	Standard	NM_024783		Approved	FLJ23598, CCP2	uc001ngg.3	Q5U5Z8	OTTHUMG00000165368	ENST00000525123.1:c.498delC	chr11.hg19:g.47726183delG	ENSP00000435582:p.Leu166fs	112.0	0.0	0		98.0	24.0	0.244898	NM_024783	A8MPX2|Q53FV5|Q8IV57|Q9H5C0	Frame_Shift_Del	DEL	ENST00000525123.1	hg19	CCDS7944.1																																																																																			.	.	.	none		0.428	AGBL2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383726.2	NM_024783		-	47726183	G	-	47726183	7	5	144	1	0	1	0	1	0	0	0	0	376	929	33	0	2262	0	AGBL2	11	47726183	Frame_Shift_Del	DEL	G	TCGA-BQ-7062-01A-11D-1961-08		47726183	87280333	19	8683											
MS4A8B	83661	hgsc.bcm.edu	37	chr11	60482801	60482801	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggtgagtgtcatctatccaAacatctatgcagcaaaccca	14	9	7	11	0	3	1	1	1	2	0	4	1	4	1	2	1	4	2	2	1	4	2			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr11:60482801A>G	ENST00000300226.2	+	7	870	c.667A>G	c.(667-669)Aac>Gac	p.N223D		NM_031457.1	NP_113645.1	Q9BY19	M4A8_HUMAN	membrane-spanning 4-domains, subfamily A, member 8	223						integral component of membrane (GO:0016021)											CATCTATCCAAACATCTATGC	0.512																																					p.N223D		Atlas-SNP	.											.	.	.	.	0			c.A667G						PASS	.						139	119	126					11																	60482801		2203	4300	6503	SO:0001583	missense	83661	exon7			TATCCAAACATCT	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.667A>G	chr11.hg19:g.60482801A>G	ENSP00000300226:p.Asn223Asp	79.0	0.0	.		75.0	6.0	.	NM_031457	Q8TCA5	Missense_Mutation	SNP	ENST00000300226.2	hg19	CCDS7990.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	5.374|5.374	0.254305|0.254305	0.10185|0.10185	.|.	.|.	ENSG00000166959|ENSG00000166959	ENST00000529752|ENST00000300226	T|T	0.18016|0.08008	2.24|3.14	4.21|4.21	1.87|1.87	0.25490|0.25490	.|.	.|.	.|.	.|.	.|.	T|T	0.05318|0.05318	0.0141|0.0141	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	1|1	.|P	.|0.37466	.|0.596	.|B	.|0.32864	.|0.154	T|T	0.39251|0.39251	-0.9623|-0.9623	7|9	0.15499|0.30078	T|T	0.54|0.28	-8.3887|-8.3887	5.7024|5.7024	0.17889|0.17889	0.7776:0.0:0.2223:0.0|0.7776:0.0:0.2223:0.0	.|.	.|223	.|Q9BY19	.|M4A8B_HUMAN	R|D	205|223	ENSP00000436857:K205R|ENSP00000300226:N223D	ENSP00000436857:K205R|ENSP00000300226:N223D	K|N	+|+	2|1	0|0	MS4A8B|MS4A8B	60239377|60239377	0.001000|0.001000	0.12720|0.12720	0.002000|0.002000	0.10522|0.10522	0.004000|0.004000	0.04260|0.04260	1.017000|1.017000	0.29989|0.29989	0.279000|0.279000	0.22186|0.22186	-0.290000|-0.290000	0.09829|0.09829	AAA|AAC	.	.	.	none		0.512	MS4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395605.1			G	60482801	A	G	60482801	3	3	144	1	0	0	0	0	1	0	0	0	9874	14	1	3	689	3	MS4A8B	11	60482801	Missense_Mutation	SNP	A	TCGA-BQ-7062-01A-11D-1961-08	12756618	60482801	74523715	20	8684											
HNRNPUL2	221092	hgsc.bcm.edu	37	chr11	62489600	62489600	+	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	ttggcatacctcacattcctCtatggtcttgggagggactg	7	13	11	10	0	3	0	1	0	2	0	4	2	4	2	2	4	1	1	2	4	2	5			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr11:62489600C>A	ENST00000301785.5	-	7	1540	c.1348G>T	c.(1348-1350)Gag>Tag	p.E450*	HNRNPUL2-BSCL2_ENST00000403734.2_Nonsense_Mutation_p.E450*	NM_001079559.2	NP_001073027.1	Q1KMD3	HNRL2_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 2	450						membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						TCACATTCCTCTATGGTCTTG	0.517																																					p.E450X		Atlas-SNP	.											.	HNRNPUL2	41	.	0			c.G1348T						PASS	.						72	71	71					11																	62489600		2062	4209	6271	SO:0001587	stop_gained	221092	exon7			ATTCCTCTATGGT		CCDS41659.1	11q12	2013-07-16		2008-04-18	ENSG00000214753	ENSG00000214753			25451	protein-coding gene	gene with protein product				HNRPUL2			Standard	NM_001079559		Approved	DKFZp762N1910	uc001nuw.3	Q1KMD3	OTTHUMG00000167773	ENST00000301785.5:c.1348G>T	chr11.hg19:g.62489600C>A	ENSP00000301785:p.Glu450*	74.0	0.0	.		101.0	25.0	.	NM_001079559	Q8N3B3	Nonsense_Mutation	SNP	ENST00000301785.5	hg19	CCDS41659.1	.	.	.	.	.	.	.	.	.	.	C	38	7.037044	0.98017	.	.	ENSG00000214753	ENST00000301785	.	.	.	5.55	5.55	0.83447	.	0.262799	0.38217	N	0.001774	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.715	17.0466	0.86505	0.0:1.0:0.0:0.0	.	.	.	.	X	450	.	ENSP00000301785:E450X	E	-	1	0	HNRNPUL2	62246176	0.998000	0.40836	0.996000	0.52242	0.992000	0.81027	1.869000	0.39519	2.894000	0.99253	0.655000	0.94253	GAG	.	.	.	none		0.517	HNRNPUL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396208.2	XM_495877		A	62489600	C	A	62489600	4	1	144	1	0	0	0	0	0	1	0	0	7282	922	32	4	927	4	HNRNPUL2	11	62489600	Nonsense_Mutation	SNP	C	TCGA-BQ-7062-01A-11D-1961-08	2006799	62489600	72516916	21	8685											
RAD51AP1	10635	hgsc.bcm.edu	37	chr12	4657343	4657343	+	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	agtgtagccagtgattatttAggtaagttttttatattaat	12	19	8	2	0	0	1	0	1	0	0	0	1	0	1	1	1	1	3	1	1	7	10			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr12:4657343A>T	ENST00000544927.1	+	5	415	c.405A>T	c.(403-405)ttA>ttT	p.L135F	RAD51AP1_ENST00000321524.7_Splice_Site_p.L152F|RAD51AP1_ENST00000543041.1_Splice_Site_p.L17F|RAD51AP1_ENST00000352618.4_Splice_Site_p.L135F|RAD51AP1_ENST00000228843.9_Splice_Site_p.L152F					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)			GTGATTATTTAGGTAAGtttt	0.289																																					p.L152F		Atlas-SNP	.											.	RAD51AP1	30	.	0			c.A456T						PASS	.						59	67	64					12																	4657343		2202	4298	6500	SO:0001630	splice_region_variant	10635	exon6			TTATTTAGGTAAG	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	ENST00000544927.1:c.406+1A>T	chr12.hg19:g.4657343A>T		82.0	0.0	.		108.0	46.0	.	NM_001130862		Missense_Mutation	SNP	ENST00000544927.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.48|17.48	3.400705|3.400705	0.62177|0.62177	.|.	.|.	ENSG00000111247|ENSG00000111247	ENST00000321524;ENST00000543041;ENST00000228843;ENST00000352618;ENST00000544927|ENST00000536117	T;T;T;T;T|.	0.37058|.	1.22;1.22;1.22;1.22;1.22|.	4.97|4.97	3.82|3.82	0.43975|0.43975	.|.	0.645832|.	0.14584|.	N|.	0.310677|.	T|.	0.48223|.	0.1488|.	L|L	0.41710|0.41710	1.295|1.295	0.34395|0.34395	D|D	0.694667|0.694667	D;B;P;B|.	0.89917|.	1.0;0.185;0.492;0.047|.	D;B;B;B|.	0.85130|.	0.997;0.171;0.171;0.032|.	T|.	0.57306|.	-0.7834|.	10|.	0.46703|.	T|.	0.11|.	-1.5623|-1.5623	8.1351|8.1351	0.31050|0.31050	0.7774:0.2226:0.0:0.0|0.7774:0.2226:0.0:0.0	.|.	17;152;152;135|.	B4DUS5;Q96B01;A8K313;Q96B01-2|.	.;R51A1_HUMAN;.;.|.	F|X	152;17;152;135;135|130	ENSP00000323750:L152F;ENSP00000439960:L17F;ENSP00000228843:L152F;ENSP00000309479:L135F;ENSP00000446296:L135F|.	ENSP00000228843:L152F|.	L|R	+|+	3|1	2|2	RAD51AP1|RAD51AP1	4527604|4527604	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	1.882000|1.882000	0.39648|0.39648	2.085000|2.085000	0.62840|0.62840	0.482000|0.482000	0.46254|0.46254	TTA|AGA	.	.	.	none		0.289	RAD51AP1-012	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000399208.1	NM_006479	Missense_Mutation	T	4657343	A	T	4657343	5	4	144	1	0	0	0	0	0	0	1	0	12999	434	15	5	478	5	RAD51AP1	12	4657343	Splice_Site	SNP	A	TCGA-BQ-7062-01A-11D-1961-08		4657343	129194552	22	8686											
LMBR1L	55716	hgsc.bcm.edu	37	chr12	49500795	49500795	+	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	ggtcaggaagatgtggcagaGgatgtacagtgttgcaaaca	13	8	15	5	0	1	2	1	0	0	2	1	4	1	4	0	4	3	4	0	4	3	2			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr12:49500795G>T	ENST00000267102.8	-	2	448	c.106C>A	c.(106-108)Ctc>Atc	p.L36I	LMBR1L_ENST00000547382.1_Missense_Mutation_p.L36I|LMBR1L_ENST00000553204.1_5'UTR|LMBR1L_ENST00000395141.4_5'Flank	NM_018113.2	NP_060583.2	Q6UX01	LMBRL_HUMAN	limb development membrane protein 1-like	36	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						ATGTGGCAGAGGATGTACAGT	0.512																																					p.L36I		Atlas-SNP	.											.	LMBR1L	61	.	0			c.C106A						PASS	.						141	161	154					12																	49500795		2105	4230	6335	SO:0001583	missense	55716	exon2			GGCAGAGGATGTA	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.106C>A	chr12.hg19:g.49500795G>T	ENSP00000267102:p.Leu36Ile	219.0	0.0	.		317.0	136.0	.	NM_018113	Q969J4|Q96BY8|Q96HN8|Q9NT09|Q9NVE1|Q9NVU9|Q9ULP6	Missense_Mutation	SNP	ENST00000267102.8	hg19	CCDS8780.2	.	.	.	.	.	.	.	.	.	.	G	9.092	1.001902	0.19121	.	.	ENSG00000139636	ENST00000267102;ENST00000547382;ENST00000547675;ENST00000550137;ENST00000551854;ENST00000551782	T;T;T;T;T	0.34472	1.36;1.36;1.36;1.36;1.36	5.25	3.45	0.39498	LMBR1-like membrane protein (1);	0.130135	0.52532	D	0.000077	T	0.19685	0.0473	N	0.16368	0.405	0.80722	D	1	P;P	0.36412	0.496;0.552	B;B	0.38428	0.126;0.273	T	0.06625	-1.0816	10	0.02654	T	1	-2.6499	10.8004	0.46485	0.1557:0.0:0.8443:0.0	.	36;36	Q6UX01-3;Q6UX01	.;LMBRL_HUMAN	I	36;36;36;36;41;36	ENSP00000267102:L36I;ENSP00000447329:L36I;ENSP00000447240:L36I;ENSP00000446641:L41I;ENSP00000449633:L36I	ENSP00000267102:L36I	L	-	1	0	LMBR1L	47787062	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	1.966000	0.40481	0.813000	0.34350	0.563000	0.77884	CTC	.	.	.	none		0.512	LMBR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318696.1	NM_018113		T	49500795	G	T	49500795	3	4	144	1	0	0	0	0	1	0	0	0	8848	1000	35	4	1427	4	LMBR1L	12	49500795	Missense_Mutation	SNP	G	TCGA-BQ-7062-01A-11D-1961-08	44843452	49500795	84351100	23	8687											
PAH	5053	hgsc.bcm.edu	37	chr12	103234258	103234258	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggtgtatgggtcgtagcgaActgagaagggccgaggtatt	9	9	18	5	3	0	1	0	1	0	1	1	4	0	1	1	4	2	3	1	4	5	4			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr12:103234258A>G	ENST00000553106.1	-	12	1707	c.1235T>C	c.(1234-1236)gTt>gCt	p.V412A	PAH_ENST00000307000.2_Missense_Mutation_p.V407A	NM_000277.1	NP_000268.1	P00439	PH4H_HUMAN	phenylalanine hydroxylase	412					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)	GTCGTAGCGAACTGAGAAGGG	0.448																																					p.V412A		Atlas-SNP	.											.	PAH	77	.	0			c.T1235C						PASS	.						168	151	157					12																	103234258		2203	4300	6503	SO:0001583	missense	5053	exon12			TAGCGAACTGAGA	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.1235T>C	chr12.hg19:g.103234258A>G	ENSP00000448059:p.Val412Ala	140.0	0.0	.		144.0	64.0	.	NM_000277	Q16717|Q8TC14	Missense_Mutation	SNP	ENST00000553106.1	hg19	CCDS9092.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.379312	0.82682	.	.	ENSG00000171759	ENST00000553106;ENST00000307000	D;D	0.99755	-6.64;-6.64	5.63	5.63	0.86233	Aromatic amino acid hydroxylase, C-terminal (4);	0.000000	0.85682	D	0.000000	D	0.99405	0.9790	M	0.78637	2.42	0.80722	D	1	P	0.39748	0.686	B	0.42422	0.387	D	0.98750	1.0720	10	0.56958	D	0.05	-29.1046	14.8162	0.70036	1.0:0.0:0.0:0.0	.	412	P00439	PH4H_HUMAN	A	412;407	ENSP00000448059:V412A;ENSP00000303500:V407A	ENSP00000303500:V407A	V	-	2	0	PAH	101758388	1.000000	0.71417	0.993000	0.49108	0.729000	0.41735	8.471000	0.90403	2.152000	0.67230	0.459000	0.35465	GTT	.	.	.	none		0.448	PAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406692.1			G	103234258	A	G	103234258	3	3	144	1	0	0	0	0	1	0	0	0	11401	43	2	3	131	3	PAH	12	103234258	Missense_Mutation	SNP	A	TCGA-BQ-7062-01A-11D-1961-08	53733463	103234258	30617637	24	8688											
GPR109A	338442	hgsc.bcm.edu	37	chr12	123187395	123187395	+	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	ccacagaaggcaagagatgaTggctgctgtccgattggaga	12	7	14	8	1	0	4	0	1	0	3	1	7	1	4	2	3	1	3	2	3	2	1			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr12:123187395T>A	ENST00000328880.5	-	1	495	c.436A>T	c.(436-438)Atc>Ttc	p.I146F	RP11-324E6.6_ENST00000543611.1_lincRNA|HCAR1_ENST00000356987.2_Intron	NM_177551.3	NP_808219.1	Q8TDS4	HCAR2_HUMAN	hydroxycarboxylic acid receptor 2	146					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)	CAAGAGATGATGGCTGCTGTC	0.557																																					p.I146F		Atlas-SNP	.											.	HCAR2	36	.	0			c.A436T						PASS	.						128	113	118					12																	123187395		2203	4300	6503	SO:0001583	missense	338442	exon1			AGATGATGGCTGC	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.436A>T	chr12.hg19:g.123187395T>A	ENSP00000375066:p.Ile146Phe	139.0	0.0	.		167.0	36.0	.	NM_177551	A0PJL5|A7LGG3	Missense_Mutation	SNP	ENST00000328880.5	hg19	CCDS9235.1	.	.	.	.	.	.	.	.	.	.	T	7.211	0.595394	0.13875	.	.	ENSG00000182782	ENST00000328880;ENST00000536970	T	0.72615	-0.67	5.55	-6.58	0.01836	GPCR, rhodopsin-like superfamily (1);	0.529882	0.18506	N	0.139204	T	0.47783	0.1464	L	0.33189	0.99	0.09310	N	1	B	0.14438	0.01	B	0.19946	0.027	T	0.45454	-0.9260	10	0.10902	T	0.67	-17.8896	9.0102	0.36137	0.0:0.4452:0.345:0.2098	.	146	Q8TDS4	HCAR2_HUMAN	F	146	ENSP00000375066:I146F	ENSP00000375066:I146F	I	-	1	0	HCAR2	121753348	0.001000	0.12720	0.001000	0.08648	0.954000	0.61252	-0.487000	0.06505	-0.941000	0.03700	0.533000	0.62120	ATC	.	.	.	none		0.557	HCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370202.1	NM_177551		A	123187395	T	A	123187395	3	1	144	1	0	0	0	0	1	0	0	0	6632	1464	51	5	659	5	GPR109A	12	123187395	Missense_Mutation	SNP	T	TCGA-BQ-7062-01A-11D-1961-08	19953137	123187395	10664500	25	8689											
CHRNA5	1138	hgsc.bcm.edu	37	chr15	78885562	78885562	+	Missense_Mutation	SNP	A	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	tataaatgggcaaatatattAataccagttcatattggaaa	18	13	6	4	0	1	0	1	0	0	0	1	1	1	1	1	2	1	2	1	2	10	9	rs558115871		TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr15:78885562A>C	ENST00000299565.5	+	6	1574	c.1374A>C	c.(1372-1374)ttA>ttC	p.L458F	CHRNA5_ENST00000559554.1_3'UTR|RP11-650L12.2_ENST00000567141.1_RNA|CHRNA3_ENST00000348639.3_Intron	NM_000745.3	NP_000736.2	P30532	ACHA5_HUMAN	cholinergic receptor, nicotinic, alpha 5 (neuronal)	458					behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)|skin(3)	15					Galantamine(DB00674)|Nicotine(DB00184)	CAAATATATTAATACCAGTTC	0.338																																					p.L458F		Atlas-SNP	.											.	CHRNA5	48	.	0			c.A1374C						PASS	.						104	94	97					15																	78885562		2196	4293	6489	SO:0001583	missense	1138	exon6			TATATTAATACCA		CCDS10304.1	15q24	2012-02-11	2012-02-07		ENSG00000169684	ENSG00000169684		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1959	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 5 (neuronal)"	118505	"cholinergic receptor, nicotinic, alpha polypeptide 5"			2004777	Standard	NM_000745		Approved		uc002bdy.3	P30532	OTTHUMG00000143858	ENST00000299565.5:c.1374A>C	chr15.hg19:g.78885562A>C	ENSP00000299565:p.Leu458Phe	57.0	0.0	.		59.0	13.0	.	NM_000745	Q15824|Q99554	Missense_Mutation	SNP	ENST00000299565.5	hg19	CCDS10304.1	.	.	.	.	.	.	.	.	.	.	A	12.30	1.895619	0.33442	.	.	ENSG00000169684	ENST00000299565	T	0.78481	-1.18	5.23	-1.75	0.08031	.	0.287773	0.35870	N	0.002933	T	0.50188	0.1601	N	0.08118	0	0.47065	D	0.999304	B	0.18461	0.028	B	0.14023	0.01	T	0.08994	-1.0695	10	0.54805	T	0.06	.	3.7176	0.08444	0.5096:0.0946:0.0656:0.3301	.	458	P30532	ACHA5_HUMAN	F	458	ENSP00000299565:L458F	ENSP00000299565:L458F	L	+	3	2	CHRNA5	76672617	0.756000	0.28383	0.039000	0.18376	0.834000	0.47266	0.062000	0.14389	-0.290000	0.09025	-1.450000	0.01041	TTA	.	.	.	none		0.338	CHRNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290106.1			C	78885562	A	C	78885562	3	2	144	1	0	0	0	0	1	0	0	0	3388	359	13	5	1396	5	CHRNA5	15	78885562	Missense_Mutation	SNP	A	TCGA-BQ-7062-01A-11D-1961-08		78885562	23645830	26	8690											
ADCY9	115	hgsc.bcm.edu	37	chr16	4029168	4029168	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgggagtagacggccagtgcGggaagcgacaccaggatggc	10	4	18	9	3	0	1	0	0	0	1	0	5	0	4	2	5	2	1	2	5	2	1			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr16:4029168G>A	ENST00000294016.3	-	8	3166	c.2628C>T	c.(2626-2628)ccC>ccT	p.P876P		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	876					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						CGGCCAGTGCGGGAAGCGACA	0.582																																					p.P876P		Atlas-SNP	.											.	ADCY9	151	.	0			c.C2628T						PASS	.						128	121	124					16																	4029168		2197	4300	6497	SO:0001819	synonymous_variant	115	exon8			CAGTGCGGGAAGC	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.2628C>T	chr16.hg19:g.4029168G>A		140.0	0.0	.		157.0	30.0	.	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Silent	SNP	ENST00000294016.3	hg19	CCDS32382.1																																																																																			.	.	.	none		0.582	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1			A	4029168	G	A	4029168	2	1	144	1	0	0	0	0	0	0	0	1	301	1103	39	1		1	ADCY9	16	4029168	Silent	SNP	G	TCGA-BQ-7062-01A-11D-1961-08		4029168	86325585	27	8691											
ACSM3	6296	hgsc.bcm.edu	37	chr16	20787239	20787239	+	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	tgcgatggagttttgaggaaCtgggatctctgtccagaaaa	11	11	13	6	1	1	2	0	1	1	1	3	6	2	5	1	3	2	1	1	3	3	2			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr16:20787239C>T	ENST00000289416.5	+	3	773	c.298C>T	c.(298-300)Ctg>Ttg	p.L100L	ACSM3_ENST00000450120.2_Silent_p.L55L|ACSM3_ENST00000440284.2_Silent_p.L100L	NM_005622.3	NP_005613.2	Q53FZ2	ACSM3_HUMAN	acyl-CoA synthetase medium-chain family member 3	100			L -> P (in dbSNP:rs5713).		cholesterol homeostasis (GO:0042632)|fatty acid biosynthetic process (GO:0006633)|regulation of blood pressure (GO:0008217)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	21						TTTTGAGGAACTGGGATCTCT	0.458																																					p.L100L		Atlas-SNP	.											.	ACSM3	113	.	0			c.C298T						PASS	.						119	127	125					16																	20787239		2201	4300	6501	SO:0001819	synonymous_variant	6296	exon3			GAGGAACTGGGAT	D16350	CCDS10589.1, CCDS45435.1	16p13.11	2006-02-08	2005-09-08	2005-09-08	ENSG00000005187	ENSG00000005187		"Acyl-CoA synthetase family"	10522	protein-coding gene	gene with protein product		145505	"SA (rat hypertension-associated) homolog", "SA hypertension-associated homolog (rat)"	SAH		7843754, 7907320, 11470804	Standard	NM_005622		Approved	SA	uc002dhr.3	Q53FZ2	OTTHUMG00000131552	ENST00000289416.5:c.298C>T	chr16.hg19:g.20787239C>T		188.0	0.0	.		248.0	53.0	.	NM_005622	O60363|Q13732|Q15425|Q7KYM6|Q9BUA2	Silent	SNP	ENST00000289416.5	hg19	CCDS10589.1																																																																																			.	.	.	none		0.458	ACSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254414.2	NM_005622		T	20787239	C	T	20787239	2	4	144	1	0	0	0	0	0	0	0	1	185	564	20	2		2	ACSM3	16	20787239	Silent	SNP	C	TCGA-BQ-7062-01A-11D-1961-08	16758071	20787239	69567514	28	8692											
WDR81	124997	hgsc.bcm.edu	37	chr17	1631524	1631524	+	Missense_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	acttccaagccgggctctatGtgactgagtctccccagccc	7	9	9	16	1	2	2	0	2	2	0	4	2	3	2	5	1	2	1	5	1	2	2			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr17:1631524G>A	ENST00000409644.1	+	1	3271	c.3271G>A	c.(3271-3273)Gtg>Atg	p.V1091M	WDR81_ENST00000309182.5_Missense_Mutation_p.V40M|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000419248.1_Intron|WDR81_ENST00000437219.2_Intron|WDR81_ENST00000446363.1_Intron|WDR81_ENST00000545662.1_5'Flank	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1091					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)		CGGGCTCTATGTGACTGAGTC	0.662																																					p.V1091M		Atlas-SNP	.											.	WDR81	180	.	0			c.G3271A						PASS	.						38	45	43					17																	1631524		2202	4299	6501	SO:0001583	missense	124997	exon1			CTCTATGTGACTG	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.3271G>A	chr17.hg19:g.1631524G>A	ENSP00000386609:p.Val1091Met	102.0	0.0	.		152.0	25.0	.	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Missense_Mutation	SNP	ENST00000409644.1	hg19	CCDS54062.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.473006	0.84640	.	.	ENSG00000167716	ENST00000309182;ENST00000409644;ENST00000354680	T;T	0.56103	2.09;0.48	5.65	5.65	0.86999	.	0.060024	0.64402	D	0.000003	T	0.65481	0.2695	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76071	0.987;0.987	T	0.67589	-0.5632	10	0.87932	D	0	.	19.7221	0.96147	0.0:0.0:1.0:0.0	.	218;40	Q8TEL1;Q562E7	.;WDR81_HUMAN	M	40;1091;40	ENSP00000312074:V40M;ENSP00000386609:V1091M	ENSP00000312074:V40M	V	+	1	0	WDR81	1578274	1.000000	0.71417	0.962000	0.40283	0.655000	0.38815	9.327000	0.96396	2.679000	0.91253	0.655000	0.94253	GTG	.	.	.	none		0.662	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348		A	1631524	G	A	1631524	3	1	144	1	0	0	0	0	1	0	0	0	17342	1377	48	2	3335	2	WDR81	17	1631524	Missense_Mutation	SNP	G	TCGA-BQ-7062-01A-11D-1961-08		1631524	79563686	29	8693											
MYO19	80179	hgsc.bcm.edu	37	chr17	34871758	34871758	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgttctatcctctctgcaaTcttgtggctctcccaagatg	6	15	7	13	0	4	1	0	0	4	1	7	1	5	1	2	1	1	3	2	1	3	3			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr17:34871758T>C	ENST00000431794.3	-	7	1012	c.490A>G	c.(490-492)Att>Gtt	p.I164V	MYO19_ENST00000586007.1_Missense_Mutation_p.I164V|MYO19_ENST00000544606.1_Missense_Mutation_p.I30V|MYO19_ENST00000268852.9_Missense_Mutation_p.I164V	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX	164	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)		CTCTCTGCAATCTTGTGGCTC	0.522																																					p.I164V		Atlas-SNP	.											.	MYO19	130	.	0			c.A490G						PASS	.						78	81	80					17																	34871758		1998	4151	6149	SO:0001583	missense	80179	exon8			CTGCAATCTTGTG	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.490A>G	chr17.hg19:g.34871758T>C	ENSP00000409936:p.Ile164Val	54.0	0.0	.		74.0	13.0	.	NM_001163735	Q59GS4|Q9H5X2	Missense_Mutation	SNP	ENST00000431794.3	hg19	CCDS54112.1	.	.	.	.	.	.	.	.	.	.	T	4.263	0.047870	0.08243	.	.	ENSG00000141140	ENST00000431794;ENST00000268852;ENST00000544606	D;D;D	0.87103	-2.21;-2.21;-2.21	5.72	1.64	0.23874	Myosin head, motor domain (2);	0.524811	0.15805	N	0.243761	T	0.68632	0.3022	N	0.02736	-0.51	0.24560	N	0.993978	B;B;B;B	0.15473	0.0;0.0;0.0;0.013	B;B;B;B	0.12837	0.003;0.002;0.0;0.008	T	0.56679	-0.7939	10	0.30078	T	0.28	.	9.161	0.37023	0.0:0.3696:0.0:0.6304	.	30;164;164;164	B4DSL5;Q96H55;Q96H55-2;Q96H55-4	.;MYO19_HUMAN;.;.	V	164;164;30	ENSP00000409936:I164V;ENSP00000268852:I164V;ENSP00000438365:I30V	ENSP00000268852:I164V	I	-	1	0	MYO19	31945871	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	1.767000	0.38501	0.098000	0.17522	0.383000	0.25322	ATT	.	.	.	none		0.522	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109		C	34871758	T	C	34871758	3	2	144	1	0	0	0	0	1	0	0	0	10074	1435	50	3	2562	3	MYO19	17	34871758	Missense_Mutation	SNP	T	TCGA-BQ-7062-01A-11D-1961-08	33240234	34871758	46323452	30	8694											
DGKE	8526	hgsc.bcm.edu	37	chr17	54926211	54926211	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagatggaattaaactagAtcggtaagttacgtttcccc	13	11	9	8	2	0	2	0	0	0	2	2	3	1	3	2	2	3	4	2	2	6	5			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr17:54926211A>G	ENST00000284061.3	+	6	1223	c.1043A>G	c.(1042-1044)gAt>gGt	p.D348G		NM_003647.2	NP_003638.1	P52429	DGKE_HUMAN	diacylglycerol kinase, epsilon 64kDa	348	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|phospholipid biosynthetic process (GO:0008654)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25	Breast(9;3.59e-07)					ATTAAACTAGATCGGTAAGTT	0.378																																					p.D348G		Atlas-SNP	.											.	DGKE	47	.	0			c.A1043G						PASS	.						118	114	115					17																	54926211		2203	4300	6503	SO:0001583	missense	8526	exon6			AACTAGATCGGTA	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.1043A>G	chr17.hg19:g.54926211A>G	ENSP00000284061:p.Asp348Gly	93.0	0.0	.		112.0	26.0	.	NM_003647	Q8TBM4|Q9UKQ3	Missense_Mutation	SNP	ENST00000284061.3	hg19	CCDS11590.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.750777	0.89753	.	.	ENSG00000153933	ENST00000284061	T	0.60672	0.17	5.59	5.59	0.84812	Diacylglycerol kinase, catalytic domain (3);	0.090430	0.85682	D	0.000000	T	0.81692	0.4876	M	0.92880	3.355	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.86463	0.1780	10	0.87932	D	0	.	15.7661	0.78128	1.0:0.0:0.0:0.0	.	348;348	A1L4Q0;P52429	.;DGKE_HUMAN	G	348	ENSP00000284061:D348G	ENSP00000284061:D348G	D	+	2	0	DGKE	52281210	1.000000	0.71417	0.993000	0.49108	0.990000	0.78478	8.532000	0.90613	2.134000	0.65973	0.460000	0.39030	GAT	.	.	.	none		0.378	DGKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440601.1	NM_003647		G	54926211	A	G	54926211	3	3	144	1	0	0	0	0	1	0	0	0	4470	333	12	3	1061	3	DGKE	17	54926211	Missense_Mutation	SNP	A	TCGA-BQ-7062-01A-11D-1961-08	20054453	54926211	26268999	31	8695											
ZNF407	55628	hgsc.bcm.edu	37	chr18	72344119	72344120	+	Frame_Shift_Ins	INS	-	-	TA																															tgaaaaccagagtagaaagcINStagacaccttagtaacctca																										TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr18:72344119_72344120insTA	ENST00000299687.5	+	1	1144_1145	c.1144_1145insTA	c.(1144-1146)ctafs	p.L382fs	ZNF407_ENST00000309902.6_Frame_Shift_Ins_p.L382fs|ZNF407_ENST00000582337.1_Frame_Shift_Ins_p.L382fs|ZNF407_ENST00000577538.1_Frame_Shift_Ins_p.L382fs	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	382					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)		GAGTAGAAAGCTAGACACCTTA	0.431																																					p.L382fs		Atlas-INDEL	.											.	ZNF407	231	.	0			c.1144_1145insTA						PASS	.																																			SO:0001589	frameshift_variant	55628	exon1			.	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.1145_1146dupTA	chr18.hg19:g.72344120_72344121dupTA	ENSP00000299687:p.Leu382fs	75.0	0.0	0		94.0	26.0	0.276596	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Frame_Shift_Ins	INS	ENST00000299687.5	hg19	CCDS45885.1																																																																																			.	.	.	none		0.431	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		TA	72344120	-	TA	72344119	7	5	144	1	0	1	1	0	0	0	0	0	17899	796	28	0	1146	0	ZNF407	18	72344119	Frame_Shift_Ins	INS	-	TCGA-BQ-7062-01A-11D-1961-08		72344119	5733129	32	8696											
STAP2	55620	hgsc.bcm.edu	37	chr19	4328673	4328673	+	Splice_Site	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	tccagacgcgcatgcgcaccCgttgtgcatctgccgcgtgg	5	8	13	15	6	1	1	0	0	1	1	2	1	2	1	3	1	3	4	3	1	0	1			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr19:4328673C>G	ENST00000594605.1	-	6	712	c.589G>C	c.(589-591)Ggg>Cgg	p.G197R	STAP2_ENST00000600324.1_Splice_Site_p.G197R|STAP2_ENST00000597593.1_5'Flank	NM_001013841.1	NP_001013863.1	Q9UGK3	STAP2_HUMAN	signal transducing adaptor family member 2	197	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)		CATGCGCACCCGTTGTGCATC	0.726																																					p.G197R		Atlas-SNP	.											.	STAP2	38	.	0			c.G589C						PASS	.						12	13	12					19																	4328673		2187	4277	6464	SO:0001630	splice_region_variant	55620	exon6			CGCACCCGTTGTG	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.590+1G>C	chr19.hg19:g.4328673C>G		19.0	0.0	.		23.0	10.0	.	NM_001013841	A6NKK3|Q9NXI2	Missense_Mutation	SNP	ENST00000594605.1	hg19	CCDS45926.1	.	.	.	.	.	.	.	.	.	.	C	12.70	2.017070	0.35606	.	.	ENSG00000178078	ENST00000314714;ENST00000424810	.	.	.	4.47	3.42	0.39159	SH2 motif (3);	0.167039	0.37261	N	0.002172	T	0.62196	0.2408	M	0.77103	2.36	0.43160	D	0.99494	B;B	0.28258	0.205;0.119	B;B	0.29176	0.066;0.099	T	0.64605	-0.6368	9	0.87932	D	0	-9.4374	10.5452	0.45056	0.0:0.9014:0.0:0.0986	.	197;197	Q9UGK3-2;Q9UGK3	.;STAP2_HUMAN	R	197	.	ENSP00000317912:G197R	G	-	1	0	STAP2	4279673	0.703000	0.27826	0.790000	0.31976	0.373000	0.29922	1.145000	0.31577	0.866000	0.35629	0.479000	0.44913	GGG	.	.	.	none		0.726	STAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458114.2	NM_001013841	Missense_Mutation	G	4328673	C	G	4328673	5	3	144	1	0	0	0	0	0	0	1	0	15265	666	23	4	792	4	STAP2	19	4328673	Splice_Site	SNP	C	TCGA-BQ-7062-01A-11D-1961-08		4328673	54800310	33	8697											
PPP1R16B	26051	hgsc.bcm.edu	37	chr20	37536822	37536822	+	Nonsense_Mutation	SNP	G	G	T																															gggagaccaggacagaccaaGagaataaggaccctgtgagt																										TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr20:37536822G>T	ENST00000299824.1	+	10	1369	c.1180G>T	c.(1180-1182)Gag>Tag	p.E394*	PPP1R16B_ENST00000373331.2_Nonsense_Mutation_p.E352*	NM_015568.2	NP_056383.1	Q96T49	PP16B_HUMAN	protein phosphatase 1, regulatory subunit 16B	394					regulation of filopodium assembly (GO:0051489)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(23)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	49		Myeloproliferative disorder(115;0.00878)				GACAGACCAAGAGAATAAGGA	0.607																																					p.E394X		Atlas-SNP	.											.	PPP1R16B	103	.	0			c.G1180T						PASS	.						88	81	84					20																	37536822		2203	4300	6503	SO:0001587	stop_gained	26051	exon10			GACCAAGAGAATA	AB020630	CCDS13309.1, CCDS54462.1	20q11.23	2013-01-10	2011-10-04		ENSG00000101445	ENSG00000101445		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	15850	protein-coding gene	gene with protein product	"TGF-beta-inhibited membrane-associated protein", "ankyrin repeat domain protein 4"	613275	"protein phosphatase 1, regulatory (inhibitor) subunit 16B"			10048485, 12055102	Standard	NM_001172735		Approved	KIAA0823, TIMAP, ANKRD4	uc002xje.3	Q96T49	OTTHUMG00000032465	ENST00000299824.1:c.1180G>T	chr20.hg19:g.37536822G>T	ENSP00000299824:p.Glu394*	49.0	0.0	.		84.0	14.0	.	NM_015568	A2RRR6|E9PFS8|O94912|Q5W9G4|Q9NQG4	Nonsense_Mutation	SNP	ENST00000299824.1	hg19	CCDS13309.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	39|39	7.556183|7.556183	0.98355|0.98355	.|.	.|.	ENSG00000101445|ENSG00000101445	ENST00000299824;ENST00000373331|ENST00000438192	.|.	.|.	.|.	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	0.154659|.	0.56097|.	D|.	0.000027|.	.|T	.|0.71341	.|0.3328	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.68953	.|-0.5273	.|4	0.34782|.	T|.	0.22|.	.|.	14.8843|14.8843	0.70555|0.70555	0.0:0.0:0.8566:0.1433|0.0:0.0:0.8566:0.1433	.|.	.|.	.|.	.|.	X|N	394;352|294	.|.	ENSP00000299824:E394X|.	E|K	+|+	1|3	0|2	PPP1R16B|PPP1R16B	36970236|36970236	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	6.369000|6.369000	0.73109|0.73109	2.771000|2.771000	0.95319|0.95319	0.644000|0.644000	0.83932|0.83932	GAG|AAG	.	.	.	none		0.607	PPP1R16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079220.2	NM_015568		T	37536822	G	T	37536822	4	4	144	1	0	0	0	0	0	1	0	0	12376	943	33	4	1214	4	PPP1R16B	20	37536822	Nonsense_Mutation	SNP	G	TCGA-BQ-7062-01A-11D-1961-08		37536822	25488698	34	8698	89	2									
PPP1R16B	26051	hgsc.bcm.edu	37	chr20	37536828	37536828	+	Missense_Mutation	SNP	A	A	G																															ccaggacagaccaagagaatAaggaccctgtgagtggcctc																										TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr20:37536828A>G	ENST00000299824.1	+	10	1375	c.1186A>G	c.(1186-1188)Aag>Gag	p.K396E	PPP1R16B_ENST00000373331.2_Missense_Mutation_p.K354E	NM_015568.2	NP_056383.1	Q96T49	PP16B_HUMAN	protein phosphatase 1, regulatory subunit 16B	396					regulation of filopodium assembly (GO:0051489)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(23)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	49		Myeloproliferative disorder(115;0.00878)				CCAAGAGAATAAGGACCCTGT	0.607																																					p.K396E		Atlas-SNP	.											.	PPP1R16B	103	.	0			c.A1186G						PASS	.						82	77	79					20																	37536828		2203	4300	6503	SO:0001583	missense	26051	exon10			GAGAATAAGGACC	AB020630	CCDS13309.1, CCDS54462.1	20q11.23	2013-01-10	2011-10-04		ENSG00000101445	ENSG00000101445		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	15850	protein-coding gene	gene with protein product	"TGF-beta-inhibited membrane-associated protein", "ankyrin repeat domain protein 4"	613275	"protein phosphatase 1, regulatory (inhibitor) subunit 16B"			10048485, 12055102	Standard	NM_001172735		Approved	KIAA0823, TIMAP, ANKRD4	uc002xje.3	Q96T49	OTTHUMG00000032465	ENST00000299824.1:c.1186A>G	chr20.hg19:g.37536828A>G	ENSP00000299824:p.Lys396Glu	43.0	0.0	.		73.0	12.0	.	NM_015568	A2RRR6|E9PFS8|O94912|Q5W9G4|Q9NQG4	Missense_Mutation	SNP	ENST00000299824.1	hg19	CCDS13309.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.38|13.38	2.219266|2.219266	0.39201|0.39201	.|.	.|.	ENSG00000101445|ENSG00000101445	ENST00000438192|ENST00000299824;ENST00000373331	.|T;T	.|0.70869	.|-0.31;-0.52	5.79|5.79	4.7|4.7	0.59300|0.59300	.|.	.|0.210830	.|0.50627	.|D	.|0.000114	T|T	0.54806|0.54806	0.1881|0.1881	L|L	0.36672|0.36672	1.1|1.1	0.25150|0.25150	N|N	0.990439|0.990439	.|B;B	.|0.19445	.|0.017;0.036	.|B;B	.|0.20767	.|0.007;0.031	T|T	0.36163|0.36163	-0.9759|-0.9759	5|10	.|0.07990	.|T	.|0.79	.|.	9.383|9.383	0.38325|0.38325	0.8649:0.0:0.1351:0.0|0.8649:0.0:0.1351:0.0	.|.	.|354;396	.|E9PFS8;Q96T49	.|.;PP16B_HUMAN	M|E	296|396;354	.|ENSP00000299824:K396E;ENSP00000362428:K354E	.|ENSP00000299824:K396E	I|K	+|+	3|1	3|0	PPP1R16B|PPP1R16B	36970242|36970242	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.946000|0.946000	0.59487|0.59487	4.056000|4.056000	0.57448|0.57448	2.236000|2.236000	0.73375|0.73375	0.524000|0.524000	0.50904|0.50904	ATA|AAG	.	.	.	none		0.607	PPP1R16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079220.2	NM_015568		G	37536828	A	G	37536828	3	3	144	1	0	0	0	0	1	0	0	0	12376	363	13	3	1220	3	PPP1R16B	20	37536828	Missense_Mutation	SNP	A	TCGA-BQ-7062-01A-11D-1961-08	6	37536828	25488692	35	8699	89	2									
APOL6	80830	hgsc.bcm.edu	37	chr22	36055619	36055619	+	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	ctgtgtgtgtgtctgtgtgtCtgtgtgtatgtacagtttac	4	19	13	5	0	2	0	0	0	2	0	2	0	2	0	0	0	2	3	0	0	3	4			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr22:36055619C>G	ENST00000409652.4	+	3	1284	c.1008C>G	c.(1006-1008)gtC>gtG	p.V336V		NM_030641.3	NP_085144.1	Q9BWW8	APOL6_HUMAN	apolipoprotein L, 6	336					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						gtctgtgtgtctgtgtgtatg	0.483																																					p.V336V		Atlas-SNP	.											APOL6,NS,carcinoma,0,1	APOL6	26	.	0			c.C1008G						PASS	.						94	61	72					22																	36055619		2203	4300	6503	SO:0001819	synonymous_variant	80830	exon3			GTGTGTCTGTGTG	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.1008C>G	chr22.hg19:g.36055619C>G		27.0	0.0	.		32.0	3.0	.	NM_030641	Q5R3S1|Q658J1|Q8IXX6|Q9UGG1	Silent	SNP	ENST00000409652.4	hg19	CCDS13919.1																																																																																			.	.	.	none		0.483	APOL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319081.2	NM_030641		G	36055619	C	G	36055619	2	3	144	1	0	0	0	0	0	0	0	1	810	900	32	4		4	APOL6	22	36055619	Silent	SNP	C	TCGA-BQ-7062-01A-11D-1961-08		36055619	15248947	36	8700											
MICALL1	85377	hgsc.bcm.edu	37	chr22	38313744	38313744	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gccacccagaaagggccttgCaccctgttccccgccgtctg	6	7	10	18	2	1	1	0	0	1	1	2	1	2	1	7	1	1	2	7	1	1	2			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chr22:38313744C>T	ENST00000215957.6	+	4	494	c.368C>T	c.(367-369)gCa>gTa	p.A123V		NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1	123					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)					AAGGGCCTTGCACCCTGTTCC	0.622																																					p.A123V		Atlas-SNP	.											.	MICALL1	53	.	0			c.C368T						PASS	.						80	66	71					22																	38313744		2203	4300	6503	SO:0001583	missense	85377	exon4			GCCTTGCACCCTG	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.368C>T	chr22.hg19:g.38313744C>T	ENSP00000215957:p.Ala123Val	110.0	0.0	.		117.0	28.0	.	NM_033386	Q5TI16|Q7RTP5|Q8N3N8|Q9BVL9|Q9BY92|Q9UH43|Q9UH44|Q9UH45	Missense_Mutation	SNP	ENST00000215957.6	hg19	CCDS13961.1	.	.	.	.	.	.	.	.	.	.	C	13.00	2.105894	0.37145	.	.	ENSG00000100139	ENST00000445494;ENST00000215957	T;T	0.73363	-0.74;0.52	3.8	2.78	0.32641	.	0.408833	0.20490	N	0.091317	T	0.55986	0.1955	N	0.19112	0.55	0.19775	N	0.999952	B	0.06786	0.001	B	0.06405	0.002	T	0.48833	-0.9000	10	0.48119	T	0.1	.	7.2373	0.26077	0.0:0.8793:0.0:0.1207	.	123	Q8N3F8	MILK1_HUMAN	V	39;123	ENSP00000404543:A39V;ENSP00000215957:A123V	ENSP00000215957:A123V	A	+	2	0	MICALL1	36643690	0.000000	0.05858	0.005000	0.12908	0.609000	0.37215	0.091000	0.15046	1.176000	0.42840	0.455000	0.32223	GCA	.	.	.	none		0.622	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319545.4	NM_033386		T	38313744	C	T	38313744	3	4	144	1	0	0	0	0	1	0	0	0	9580	710	25	2	382	2	MICALL1	22	38313744	Missense_Mutation	SNP	C	TCGA-BQ-7062-01A-11D-1961-08	2258125	38313744	12990822	37	8701											
MORC4	79710	hgsc.bcm.edu	37	chrX	106201626	106201626	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caggtaacatggatggatcaAtcttcccaggaagctttctc	11	11	9	10	0	3	0	1	0	2	0	5	3	4	3	1	4	2	2	1	4	3	3			TCGA-BQ-7062-01A-11D-1961-08	TCGA-BQ-7062-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8017a612-f39d-4ab8-bd99-55f6568c4bd8	46dc5965-f675-4a6a-8374-017cd8873bb9	g.chrX:106201626A>G	ENST00000355610.4	-	11	1599	c.1325T>C	c.(1324-1326)aTt>aCt	p.I442T	MORC4_ENST00000255495.7_Missense_Mutation_p.I442T|MORC4_ENST00000535534.1_Missense_Mutation_p.I190T	NM_001085354.2|NM_024657.4	NP_001078823.1|NP_078933.3	Q8TE76	MORC4_HUMAN	MORC family CW-type zinc finger 4	442						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						GGATGGATCAATCTTCCCAGG	0.423																																					p.I442T		Atlas-SNP	.											.	MORC4	155	.	0			c.T1325C						PASS	.						132	111	118					X																	106201626		2203	4300	6503	SO:0001583	missense	79710	exon11			GGATCAATCTTCC	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.1325T>C	chrX.hg19:g.106201626A>G	ENSP00000347821:p.Ile442Thr	50.0	0.0	.		59.0	32.0	.	NM_001085354	A1YR23|A1YR24|H7BXF1|Q5JUK7|Q96MZ2|Q9HAI7	Missense_Mutation	SNP	ENST00000355610.4	hg19	CCDS14525.2	.	.	.	.	.	.	.	.	.	.	A	11.41	1.630627	0.28978	.	.	ENSG00000133131	ENST00000355610;ENST00000535534;ENST00000255495	T;T;T	0.30981	2.76;1.51;2.75	5.93	5.93	0.95920	Zinc finger, CW-type (2);	0.519296	0.19062	N	0.123746	T	0.27278	0.0669	L	0.37466	1.105	0.24268	N	0.995258	B;B;B	0.26975	0.165;0.042;0.042	B;B;B	0.28385	0.089;0.055;0.055	T	0.26815	-1.0092	10	0.72032	D	0.01	-5.7895	11.5626	0.50785	1.0:0.0:0.0:0.0	.	190;442;442	A1YR24;A1YR23;Q8TE76	.;.;MORC4_HUMAN	T	442;190;442	ENSP00000347821:I442T;ENSP00000440359:I190T;ENSP00000255495:I442T	ENSP00000255495:I442T	I	-	2	0	MORC4	106088282	0.305000	0.24481	0.911000	0.35937	0.454000	0.32378	1.929000	0.40114	2.004000	0.58718	0.441000	0.28932	ATT	.	.	.	none		0.423	MORC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057816.3	NM_024657		G	106201626	A	G	106201626	3	3	144	1	0	0	0	0	1	0	0	0	9711	101	4	3	1516	3	MORC4	23	106201626	Missense_Mutation	SNP	A	TCGA-BQ-7062-01A-11D-1961-08		106201626	49068934	38	8702											
FGGY	55277	hgsc.bcm.edu	37	chr1	60133071	60133091	+	Splice_Site	DEL	TACTGGTAAGTCTGGGAAAGA	TACTGGTAAGTCTGGGAAAGA	-																															gtgcaaatgcatgcggacatTactggtaagtctgggaaaga																								rs115318188	byFrequency	TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	TACTGGTAAGTCTGGGAAAGA	TACTGGTAAGTCTGGGAAAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr1:60133071_60133091delTACTGGTAAGTCTGGGAAAGA	ENST00000303721.7	+	13	1587_1591	c.1413_1417delTACTGGTAAGTCTGGGAAAGA	c.(1411-1419)attactggt>atgt	p.471_473ITG>M	FGGY_ENST00000371218.4_Splice_Site_p.495_497ITG>M|FGGY_ENST00000371210.1_Splice_Site_p.172_174ITG>M|FGGY_ENST00000371212.1_Splice_Site_p.383_385ITG>M	NM_018291.3	NP_060761.3	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing	471					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)	p.G361C(1)|p.G473C(1)		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)					ATGCGGACATTACTGGTAAGTCTGGGAAAGAGGAGAGAAGG	0.466																																					p.495_497del		Atlas-INDEL	.											.	FGGY	99	.	2	Substitution - Missense(2)	lung(2)	c.1484_1489del						PASS	.																																			SO:0001630	splice_region_variant	55277	exon14			.		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.1417+1TACTGGTAAGTCTGGGAAAGA>-	chr1.hg19:g.60133071_60133091delTACTGGTAAGTCTGGGAAAGA		252.0	0.0	0		119.0	19.0	0.159664	NM_001113411	B1AK92|B1AK93|B1AK94|B2RDR8|D3DQ56|Q9HA63|Q9NV20	In_Frame_Del	DEL	ENST00000303721.7	hg19	CCDS611.2																																																																																			.	.	.	none		0.466	FGGY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023210.2	NM_001113411	In_Frame_Del	-	60133091	TACTGGTAAGTCTGGGAAAGA	-	60133071	8	5	145	1	0	1	0	1	0	0	1	0	5878	1742	61	0	1535	0	FGGY	1	60133071	Splice_Site	DEL	TACTGGTAAGTCTGGGAAAGA	TCGA-DW-5560-01A-01D-1589-08		60133071	189117550	1	8703											
FRRS1	391059	hgsc.bcm.edu	37	chr1	100214268	100214268	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccattgggataattagccacAtaactaatgtgcaacagaag	16	9	8	8	0	0	1	0	0	0	1	0	2	0	2	2	1	4	1	2	1	6	5			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr1:100214268A>G	ENST00000414213.1	-	3	658	c.57T>C	c.(55-57)taT>taC	p.Y19Y	FRRS1_ENST00000287474.5_Silent_p.Y19Y			Q6ZNA5	FRRS1_HUMAN	ferric-chelate reductase 1	19	Reelin. {ECO:0000255|PROSITE- ProRule:PRU00363}.					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)		AATTAGCCACATAACTAATGT	0.378																																					p.Y19Y		Atlas-SNP	.											.	FRRS1	50	.	0			c.T57C						PASS	.						154	132	139					1																	100214268		2203	4300	6503	SO:0001819	synonymous_variant	391059	exon3			AGCCACATAACTA	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.57T>C	chr1.hg19:g.100214268A>G		112.0	0.0	.		107.0	38.0	.	NM_001013660	A6NLN7	Silent	SNP	ENST00000414213.1	hg19																																																																																				.	.	.	none		0.378	FRRS1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001013660		G	100214268	A	G	100214268	2	3	145	1	0	0	0	0	0	0	0	1	6067	224	8	3		3	FRRS1	1	100214268	Silent	SNP	A	TCGA-DW-5560-01A-01D-1589-08	40081197	100214268	149036353	2	8704											
ALX3	257	hgsc.bcm.edu	37	chr1	110604111	110604111	+	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	atgtcataggcagccgtgaaGgggttccgcccctcctggat	7	9	13	12	2	1	1	1	1	0	0	3	2	3	2	5	4	1	2	5	4	2	2			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr1:110604111G>T	ENST00000369792.4	-	3	756	c.669C>A	c.(667-669)ccC>ccA	p.P223P	RP4-773N10.4_ENST00000596959.1_RNA|RP4-773N10.4_ENST00000554749.1_RNA	NM_006492.2	NP_006483.2	O95076	ALX3_HUMAN	ALX homeobox 3	223					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)		CAGCCGTGAAGGGGTTCCGCC	0.622																																					p.P223P		Atlas-SNP	.											.	ALX3	16	.	0			c.C669A						PASS	.						79	78	78					1																	110604111		2203	4300	6503	SO:0001819	synonymous_variant	257	exon3			CGTGAAGGGGTTC	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.669C>A	chr1.hg19:g.110604111G>T		106.0	0.0	.		101.0	34.0	.	NM_006492	O95075|Q5T8M4	Silent	SNP	ENST00000369792.4	hg19	CCDS819.1																																																																																			.	.	.	none		0.622	ALX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032232.2	NM_006492		T	110604111	G	T	110604111	2	4	145	1	0	0	0	0	0	0	0	1	557	987	35	4		4	ALX3	1	110604111	Silent	SNP	G	TCGA-DW-5560-01A-01D-1589-08	10389843	110604111	138646510	3	8705											
DSTYK	25778	hgsc.bcm.edu	37	chr1	205132867	205132867	+	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	ctacctgtttgagataattaCtggtgatgtgaactgagaca	12	13	10	6	0	0	4	0	4	0	2	0	6	0	4	1	1	3	1	1	1	4	4			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr1:205132867C>G	ENST00000367162.3	-	4	1571	c.1541G>C	c.(1540-1542)aGt>aCt	p.S514T	DSTYK_ENST00000367160.4_Intron|DSTYK_ENST00000367161.3_Missense_Mutation_p.S514T	NM_015375.2	NP_056190.1	Q6XUX3	DUSTY_HUMAN	dual serine/threonine and tyrosine protein kinase	514					cellular response to fibroblast growth factor stimulus (GO:0044344)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of kinase activity (GO:0033674)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(2)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(2)	14						GAGATAATTACTGGTGATGTG	0.433																																					p.S514T		Atlas-SNP	.											DSTYK_ENST00000367162,colon,carcinoma,0,1	DSTYK	87	.	0			c.G1541C						PASS	.						80	72	75					1																	205132867		2203	4300	6503	SO:0001583	missense	25778	exon4			TAATTACTGGTGA	AF068286	CCDS1451.1, CCDS1452.1	1q32	2008-12-18	2008-12-18	2008-12-18	ENSG00000133059	ENSG00000133059			29043	protein-coding gene	gene with protein product		612666	"receptor interacting protein kinase 5"	RIPK5		15178406	Standard	NM_015375		Approved	KIAA0472, DustyPK, RIP5	uc001hbw.3	Q6XUX3	OTTHUMG00000037102	ENST00000367162.3:c.1541G>C	chr1.hg19:g.205132867C>G	ENSP00000356130:p.Ser514Thr	35.0	0.0	.		31.0	2.0	.	NM_199462	B7ZL64|O75060|Q17R94|Q5RKT0|Q6IN87|Q6P997|Q86Y03|Q9P1S5	Missense_Mutation	SNP	ENST00000367162.3	hg19	CCDS1451.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.245935	0.80024	.	.	ENSG00000133059	ENST00000367161;ENST00000367162	T;T	0.81163	-1.41;-1.46	5.8	5.8	0.92144	.	0.090598	0.85682	D	0.000000	D	0.84047	0.5386	L	0.35723	1.085	0.80722	D	1	D;D	0.63880	0.993;0.977	P;P	0.58454	0.839;0.751	D	0.83764	0.0216	10	0.49607	T	0.09	-13.2589	19.6644	0.95887	0.0:1.0:0.0:0.0	.	514;514	Q6XUX3-2;Q6XUX3	.;DUSTY_HUMAN	T	514	ENSP00000356129:S514T;ENSP00000356130:S514T	ENSP00000356129:S514T	S	-	2	0	DSTYK	203399490	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.108000	0.71522	2.758000	0.94735	0.563000	0.77884	AGT	.	.	.	none		0.433	DSTYK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090345.1	NM_015375		G	205132867	C	G	205132867	3	3	145	1	0	0	0	0	1	0	0	0	4787	565	20	4	1288	4	DSTYK	1	205132867	Missense_Mutation	SNP	C	TCGA-DW-5560-01A-01D-1589-08	94528756	205132867	44117754	4	8706											
BIN1	274	hgsc.bcm.edu	37	chr2	127828371	127828371	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggtaggtccggagatcctTctgcagccgggtgccctccg	5	8	14	14	3	1	1	0	0	1	1	4	2	4	1	5	4	3	2	5	4	1	2			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr2:127828371T>C	ENST00000316724.5	-	3	598	c.187A>G	c.(187-189)Aag>Gag	p.K63E	BIN1_ENST00000393041.3_Missense_Mutation_p.K63E|BIN1_ENST00000351659.3_Missense_Mutation_p.K63E|BIN1_ENST00000348750.4_Missense_Mutation_p.K63E|BIN1_ENST00000357970.3_Missense_Mutation_p.K63E|BIN1_ENST00000352848.3_Missense_Mutation_p.K63E|BIN1_ENST00000346226.3_Missense_Mutation_p.K63E|BIN1_ENST00000409400.1_Missense_Mutation_p.K63E|BIN1_ENST00000393040.3_Missense_Mutation_p.K63E|BIN1_ENST00000259238.4_Missense_Mutation_p.K63E|BIN1_ENST00000376113.2_Missense_Mutation_p.K63E	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	63	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.|Interaction with BIN2.				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)		CGGAGATCCTTCTGCAGCCGG	0.647																																					p.K63E		Atlas-SNP	.											.	BIN1	85	.	0			c.A187G						PASS	.						45	44	44					2																	127828371		2203	4300	6503	SO:0001583	missense	274	exon3			GATCCTTCTGCAG	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.187A>G	chr2.hg19:g.127828371T>C	ENSP00000316779:p.Lys63Glu	31.0	0.0	.		56.0	24.0	.	NM_139346	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Missense_Mutation	SNP	ENST00000316724.5	hg19	CCDS2138.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.331702	0.81690	.	.	ENSG00000136717	ENST00000376113;ENST00000357970;ENST00000393040;ENST00000348750;ENST00000259238;ENST00000346226;ENST00000393041;ENST00000351659;ENST00000352848;ENST00000316724;ENST00000409400	T;T;T;T;T;T;T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07	4.49	3.3	0.37823	BAR (3);	0.101360	0.64402	D	0.000002	T	0.71558	0.3354	M	0.66939	2.045	0.54753	D	0.999988	P;D;P;P;P;P;P;P;B;P;P;B;P	0.60575	0.947;0.988;0.457;0.942;0.606;0.952;0.938;0.884;0.432;0.837;0.941;0.047;0.929	P;D;B;P;B;P;P;B;B;B;B;B;P	0.65010	0.879;0.931;0.286;0.528;0.286;0.611;0.804;0.346;0.177;0.287;0.357;0.017;0.794	T	0.73697	-0.3901	10	0.87932	D	0	-23.223	8.0196	0.30402	0.0:0.0991:0.0:0.9009	.	63;39;63;63;63;63;63;63;63;63;63;63;63	B7Z2Z2;B7Z6Y2;O00499-4;O00499-7;O00499-6;O00499-2;O00499-3;O00499-8;O00499-11;O00499-5;O00499-10;O00499-9;O00499	.;.;.;.;.;.;.;.;.;.;.;.;BIN1_HUMAN	E	63	ENSP00000365281:K63E;ENSP00000350654:K63E;ENSP00000376760:K63E;ENSP00000259237:K63E;ENSP00000259238:K63E;ENSP00000315411:K63E;ENSP00000376761:K63E;ENSP00000315388:K63E;ENSP00000315284:K63E;ENSP00000316779:K63E;ENSP00000386797:K63E	ENSP00000259238:K63E	K	-	1	0	BIN1	127544841	1.000000	0.71417	1.000000	0.80357	0.767000	0.43475	4.533000	0.60615	1.884000	0.54569	0.459000	0.35465	AAG	.	.	.	none		0.647	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343		C	127828371	T	C	127828371	3	2	145	1	0	0	0	0	1	0	0	0	1432	1792	62	3	1711	3	BIN1	2	127828371	Missense_Mutation	SNP	T	TCGA-DW-5560-01A-01D-1589-08		127828371	115371002	5	8707											
NEB	4703	hgsc.bcm.edu	37	chr2	152512859	152512859	+	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	ttctcatagtttttcttgtaCtcccgatcagattgcatctt	7	19	5	10	1	4	1	2	0	3	1	6	2	5	1	1	0	2	3	1	0	2	8			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr2:152512859C>T	ENST00000172853.10	-	49	6450	c.6303G>A	c.(6301-6303)gaG>gaA	p.E2101E	NEB_ENST00000427231.2_Silent_p.E2101E|NEB_ENST00000409198.1_Silent_p.E2101E|NEB_ENST00000604864.1_Silent_p.E2101E|NEB_ENST00000603639.1_Silent_p.E2101E|NEB_ENST00000397345.3_Silent_p.E2101E			P20929	NEBU_HUMAN	nebulin	2101					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)		TTTTCTTGTACTCCCGATCAG	0.483																																					p.E2101E		Atlas-SNP	.											.	NEB	1697	.	0			c.G6303A						PASS	.						239	236	237					2																	152512859		2046	4199	6245	SO:0001819	synonymous_variant	4703	exon49			CTTGTACTCCCGA	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.6303G>A	chr2.hg19:g.152512859C>T		191.0	0.0	.		155.0	66.0	.	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	hg19																																																																																				.	.	.	none		0.483	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152512859	C	T	152512859	2	4	145	1	0	0	0	0	0	0	0	1	10309	564	20	2		2	NEB	2	152512859	Silent	SNP	C	TCGA-DW-5560-01A-01D-1589-08	24684488	152512859	90686514	6	8708											
PRKRA	8575	hgsc.bcm.edu	37	chr2	179306336	179306336	+	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	atagctgtcaacattactcaCtaaagaaatgtggttctctg	13	13	7	8	0	3	1	2	0	1	1	4	1	3	1	0	1	3	2	0	1	6	4			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr2:179306336C>T	ENST00000325748.4	-	6	810		c.e6+1		PRKRA_ENST00000432031.2_Splice_Site|PRKRA_ENST00000487082.1_Splice_Site|AC009948.5_ENST00000453026.2_RNA|PRKRA_ENST00000438687.3_Splice_Site	NM_003690.4	NP_003681.1	O75569	PRKRA_HUMAN	protein kinase, interferon-inducible double stranded RNA dependent activator						cellular response to oxidative stress (GO:0034599)|gene expression (GO:0010467)|immune response (GO:0006955)|middle ear morphogenesis (GO:0042474)|negative regulation of cell proliferation (GO:0008285)|outer ear morphogenesis (GO:0042473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|production of siRNA involved in RNA interference (GO:0030422)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	enzyme activator activity (GO:0008047)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.?(1)		central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.00634)|all cancers(119;0.0265)			ACATTACTCACTAAAGAAATG	0.353																																					.	Melanoma(200;68 3001 23825 48764)	Atlas-SNP	.											PRKRA,NS,carcinoma,0,1	PRKRA	56	.	1	Unknown(1)	lung(1)	c.534+1G>A						PASS	.						70	74	73					2																	179306336		2203	4300	6503	SO:0001630	splice_region_variant	8575	exon7			TACTCACTAAAGA	AF072860	CCDS2279.1, CCDS46460.1, CCDS46461.1	2q31.2	2009-08-25			ENSG00000180228	ENSG00000180228			9438	protein-coding gene	gene with protein product	"protein activator of the interferon-induced protein kinase"	603424				9687506, 10336432	Standard	NM_003690		Approved	PACT, RAX, HSD14, DYT16	uc002umf.3	O75569	OTTHUMG00000132576	ENST00000325748.4:c.609+1G>A	chr2.hg19:g.179306336C>T		61.0	1.0	.		80.0	5.0	.	NM_001139518	A8K3I6|Q53G24|Q6X7T5|Q8NDK4	Splice_Site	SNP	ENST00000325748.4	hg19	CCDS2279.1	.	.	.	.	.	.	.	.	.	.	C	18.75	3.689950	0.68271	.	.	ENSG00000180228	ENST00000325748;ENST00000438687;ENST00000487082;ENST00000432031	.	.	.	5.55	5.55	0.83447	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.5111	0.44862	0.0:0.9114:0.0:0.0886	.	.	.	.	.	-1	.	.	.	-	.	.	PRKRA	179014582	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	4.492000	0.60334	2.618000	0.88619	0.591000	0.81541	.	.	.	.	none		0.353	PRKRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255782.2	NM_003690	Intron	T	179306336	C	T	179306336	5	4	145	1	0	0	0	0	0	0	1	0	12534	579	20	2	343	2	PRKRA	2	179306336	Splice_Site	SNP	C	TCGA-DW-5560-01A-01D-1589-08	26793477	179306336	63893037	7	8709											
TTN	7273	hgsc.bcm.edu	37	chr2	179433843	179433843	+	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	0	0	0	0	0	0	0	0	0	ttctcagctgtgactctaaaGtaataactgcaaccttcttg	11	14	6	10	0	3	1	1	1	3	0	4	1	3	1	1	0	4	3	1	0	5	6			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr2:179433843G>C	ENST00000591111.1	-	276	72317	c.72093C>G	c.(72091-72093)taC>taG	p.Y24031*	TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342175.6_Nonsense_Mutation_p.Y16799*|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000359218.5_Nonsense_Mutation_p.Y16732*|TTN_ENST00000460472.2_Nonsense_Mutation_p.Y16607*|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Nonsense_Mutation_p.Y25672*|TTN_ENST00000342992.6_Nonsense_Mutation_p.Y23104*|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586707.1_RNA			Q8WZ42	TITIN_HUMAN	titin	24031	Fibronectin type-III 74. {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)			TGACTCTAAAGTAATAACTGC	0.418																																					p.Y25672X		Atlas-SNP	.											.	TTN	18412	.	0			c.C77016G						PASS	.						171	169	170					2																	179433843		1958	4136	6094	SO:0001587	stop_gained	7273	exon326			TCTAAAGTAATAA	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.72093C>G	chr2.hg19:g.179433843G>C	ENSP00000465570:p.Tyr24031*	200.0	0.0	.		231.0	99.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	63	76.472557	0.99993	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.5208	0.61566	0.071:0.0:0.929:0.0	.	.	.	.	X	23104;16607;16799;16732;16605	.	ENSP00000340554:Y16799X	Y	-	3	2	TTN	179142089	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.714000	0.68422	2.803000	0.96430	0.650000	0.86243	TAC	.	.	.	none		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179433843	G	C	179433843	4	2	145	1	0	0	0	0	0	1	0	0	16747	1024	36	4	31111	4	TTN	2	179433843	Nonsense_Mutation	SNP	G	TCGA-DW-5560-01A-01D-1589-08	127507	179433843	63765530	8	8710											
RBM6	10180	hgsc.bcm.edu	37	chr3	50005960	50005960	+	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	aaagtccagttcaagaccaaGataagtcacagctttctgga	15	9	8	9	0	3	2	2	0	1	2	4	3	4	3	2	1	1	2	2	1	4	3			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr3:50005960G>T	ENST00000266022.4	+	3	1361	c.1102G>T	c.(1102-1104)Gat>Tat	p.D368Y	RBM6_ENST00000422955.1_Intron|RBM6_ENST00000441115.1_Intron|RBM6_ENST00000442092.1_Intron|RBM6_ENST00000443081.1_Missense_Mutation_p.D236Y|RBM6_ENST00000539992.1_Intron	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	368					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)		TCAAGACCAAGATAAGTCACA	0.463																																					p.D368Y		Atlas-SNP	.											.	RBM6	85	.	0			c.G1102T						PASS	.						80	76	78					3																	50005960		2203	4300	6503	SO:0001583	missense	10180	exon3			GACCAAGATAAGT	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.1102G>T	chr3.hg19:g.50005960G>T	ENSP00000266022:p.Asp368Tyr	72.0	0.0	.		96.0	43.0	.	NM_005777	O60549|O75524|Q86SS3	Missense_Mutation	SNP	ENST00000266022.4	hg19	CCDS2809.1	.	.	.	.	.	.	.	.	.	.	G	12.79	2.043431	0.36085	.	.	ENSG00000004534	ENST00000266022;ENST00000443081	T;T	0.36878	1.23;1.25	5.85	3.97	0.46021	.	0.614854	0.16479	N	0.212625	T	0.29389	0.0732	N	0.24115	0.695	0.80722	D	1	D	0.59767	0.986	P	0.49752	0.621	T	0.01988	-1.1234	9	.	.	.	-4.7397	7.5857	0.27991	0.1421:0.1365:0.7214:0.0	.	368	P78332	RBM6_HUMAN	Y	368;236	ENSP00000266022:D368Y;ENSP00000396466:D236Y	.	D	+	1	0	RBM6	49980964	1.000000	0.71417	0.999000	0.59377	0.735000	0.41995	2.640000	0.46579	1.495000	0.48549	0.491000	0.48974	GAT	.	.	.	none		0.463	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777		T	50005960	G	T	50005960	3	4	145	1	0	0	0	0	1	0	0	0	13157	942	33	4	1108	4	RBM6	3	50005960	Missense_Mutation	SNP	G	TCGA-DW-5560-01A-01D-1589-08		50005960	148016470	9	8711											
PET112L	5188	hgsc.bcm.edu	37	chr4	152592364	152592364	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccaggatctcctttatcaTgactggatctgctcggcttt	6	15	8	12	1	3	1	1	1	2	0	6	3	4	3	2	3	1	2	2	3	1	3			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr4:152592364T>C	ENST00000515812.1	-	12	1529	c.1513A>G	c.(1513-1515)Atg>Gtg	p.M505V	PET112_ENST00000263985.6_Missense_Mutation_p.M546V|RP11-164P12.4_ENST00000508664.1_RNA|PET112_ENST00000507592.1_5'UTR																breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	23						TCCTTTATCATGACTGGATCT	0.483																																					p.M546V		Atlas-SNP	.											.	PET112	43	.	0			c.A1636G						PASS	.						178	163	168					4																	152592364		2203	4300	6503	SO:0001583	missense	5188	exon13			TTATCATGACTGG																												ENST00000515812.1:c.1513A>G	chr4.hg19:g.152592364T>C	ENSP00000426859:p.Met505Val	156.0	0.0	.		187.0	88.0	.	NM_004564		Missense_Mutation	SNP	ENST00000515812.1	hg19		.	.	.	.	.	.	.	.	.	.	T	0.061	-1.224008	0.01530	.	.	ENSG00000059691	ENST00000263985;ENST00000515812	T;T	0.39592	1.07;1.08	5.8	-5.06	0.02946	Asn/Gln amidotransferase (2);	0.986159	0.08279	N	0.970181	T	0.13286	0.0322	N	0.02181	-0.65	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39961	-0.9588	10	0.06365	T	0.9	0.2792	10.1442	0.42753	0.0:0.1381:0.5532:0.3086	.	546	O75879	GATB_HUMAN	V	546;505	ENSP00000263985:M546V;ENSP00000426859:M505V	ENSP00000263985:M546V	M	-	1	0	PET112	152811814	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.347000	0.07750	-0.814000	0.04352	-0.904000	0.02843	ATG	.	.	.	none		0.483	PET112-002	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365672.1			C	152592364	T	C	152592364	3	2	145	1	0	0	0	0	1	0	0	0	11741	1464	51	3	41	3	PET112L	4	152592364	Missense_Mutation	SNP	T	TCGA-DW-5560-01A-01D-1589-08		152592364	38561912	10	8712											
F12	2161	hgsc.bcm.edu	37	chr5	176831341	176831341	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggggtctggcactgtgccaGgtcgcagtactcccagctca	6	9	13	13	1	2	0	1	0	1	0	4	0	3	0	2	4	3	4	2	4	1	1			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr5:176831341G>A	ENST00000253496.3	-	9	922	c.874C>T	c.(874-876)Ctg>Ttg	p.L292L	F12_ENST00000514943.1_5'Flank	NM_000505.3	NP_000496.2	P00748	FA12_HUMAN	coagulation factor XII (Hageman factor)	292	Kringle. {ECO:0000255|PROSITE- ProRule:PRU00121}.				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)	CACTGTGCCAGGTCGCAGTAC	0.692									Hereditary Angioedema		OREG0017088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L292L		Atlas-SNP	.											.	F12	35	.	0			c.C874T						PASS	.						17	21	19					5																	176831341		2201	4296	6497	SO:0001819	synonymous_variant	2161	exon9	Familial Cancer Database	HAE, type I-III, Hereditary Angioneurotic Edema, HANE,	GTGCCAGGTCGCA	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.874C>T	chr5.hg19:g.176831341G>A		50.0	0.0	.	1934	35.0	15.0	.	NM_000505	P78339	Silent	SNP	ENST00000253496.3	hg19	CCDS34302.1																																																																																			.	.	.	none		0.692	F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373217.1			A	176831341	G	A	176831341	2	1	145	1	0	0	0	0	0	0	0	1	5341	991	35	2		2	F12	5	176831341	Silent	SNP	G	TCGA-DW-5560-01A-01D-1589-08		176831341	4083919	11	8713											
VPS37D	155382	hgsc.bcm.edu	37	chr7	73083798	73083798	+	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	ctgcctggcctccaactacgCgctggccaaggagaacctgg	8	6	12	15	2	0	1	0	0	0	1	1	2	1	1	5	4	4	1	5	4	4	1	rs370705512		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr7:73083798C>G	ENST00000324941.4	+	2	322	c.188C>G	c.(187-189)gCg>gGg	p.A63G	VPS37D_ENST00000451519.1_Intron	NM_001077621.1	NP_001071089.1			vacuolar protein sorting 37 homolog D (S. cerevisiae)											central_nervous_system(1)|ovary(1)	2		Lung NSC(55;0.0908)|all_lung(88;0.198)				TCCAACTACGCGCTGGCCAAG	0.677																																					p.A63G		Atlas-SNP	.											.	VPS37D	10	.	0			c.C188G						PASS	.						7	9	8					7																	73083798		1885	4067	5952	SO:0001583	missense	155382	exon2			ACTACGCGCTGGC	AY081952	CCDS43596.1	7q11.23	2007-07-27	2006-04-04	2005-08-18	ENSG00000176428	ENSG00000176428			18287	protein-coding gene	gene with protein product		610039	"Williams Beuren syndrome chromosome region 24", "vacuolar protein sorting 37D (yeast)"	WBSCR24		15218037	Standard	NM_001077621		Approved	MGC35352	uc003tyr.3	Q86XT2	OTTHUMG00000157227	ENST00000324941.4:c.188C>G	chr7.hg19:g.73083798C>G	ENSP00000320416:p.Ala63Gly	7.0	0.0	.		10.0	4.0	.	NM_001077621		Missense_Mutation	SNP	ENST00000324941.4	hg19	CCDS43596.1	.	.	.	.	.	.	.	.	.	.	C	13.77	2.336561	0.41398	.	.	ENSG00000176428	ENST00000324941	T	0.77229	-1.08	4.3	3.41	0.39046	Modifier of rudimentary, Modr (1);	0.335218	0.24041	U	0.042099	T	0.64438	0.2598	N	0.14661	0.345	0.80722	D	1	P	0.49090	0.919	P	0.46172	0.506	T	0.66002	-0.6031	10	0.66056	D	0.02	.	8.0448	0.30542	0.0:0.8859:0.0:0.1141	.	63	Q86XT2	VP37D_HUMAN	G	63	ENSP00000320416:A63G	ENSP00000320416:A63G	A	+	2	0	VPS37D	72721734	0.015000	0.18098	0.868000	0.34077	0.570000	0.35934	1.008000	0.29872	1.024000	0.39682	0.563000	0.77884	GCG	.	.	.	alt		0.677	VPS37D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348064.1	NM_152560		G	73083798	C	G	73083798	3	3	145	1	0	0	0	0	1	0	0	0	17220	768	27	4	194	4	VPS37D	7	73083798	Missense_Mutation	SNP	C	TCGA-DW-5560-01A-01D-1589-08		73083798	86054865	12	8714											
EDF1	8721	hgsc.bcm.edu	37	chr9	139757816	139757816	+	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	tgcccacctccagggtcaccCtgtcatggtgcagctcctct	5	10	9	17	0	3	0	2	0	1	0	5	0	5	0	5	2	3	2	5	2	0	0			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr9:139757816C>A	ENST00000224073.1	-	3	242	c.215G>T	c.(214-216)aGg>aTg	p.R72M	EDF1_ENST00000371649.1_Missense_Mutation_p.R72M|EDF1_ENST00000371648.4_Missense_Mutation_p.R72M	NM_003792.2	NP_003783.1	O60869	EDF1_HUMAN	endothelial differentiation-related factor 1	72	Interaction with NR5A2, PPARG and NR1H3.|Interaction with TBP and NR5A1.				endothelial cell differentiation (GO:0045446)|multicellular organismal development (GO:0007275)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of lipid metabolic process (GO:0019216)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			lung(1)	1	all_cancers(76;0.0841)|all_epithelial(76;0.217)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)		CAGGGTCACCCTGTCATGGTG	0.617																																					p.R72M		Atlas-SNP	.											.	EDF1	9	.	0			c.G215T						PASS	.						150	112	125					9																	139757816		2203	4300	6503	SO:0001583	missense	8721	exon3			GTCACCCTGTCAT	AJ005259	CCDS7011.1, CCDS7012.1, CCDS65193.1	9q34.3	2009-11-06			ENSG00000107223	ENSG00000107223			3164	protein-coding gene	gene with protein product	"multiprotein bridging factor-1"	605107				9813014, 15112053	Standard	NM_003792		Approved	EDF-1	uc004cjt.1	O60869	OTTHUMG00000020948	ENST00000224073.1:c.215G>T	chr9.hg19:g.139757816C>A	ENSP00000224073:p.Arg72Met	69.0	0.0	.		48.0	19.0	.	NM_003792	Q5T5T2|Q9UIM1	Missense_Mutation	SNP	ENST00000224073.1	hg19	CCDS7011.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.877120	0.91664	.	.	ENSG00000107223	ENST00000371649;ENST00000224073;ENST00000371648	.	.	.	5.79	4.9	0.64082	Lambda repressor-like, DNA-binding (1);Multiprotein bridging factor 1, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.76877	0.4049	M	0.80847	2.515	0.80722	D	1	P;P	0.48407	0.897;0.91	P;P	0.57425	0.725;0.82	T	0.80741	-0.1247	9	0.87932	D	0	-10.8624	14.6074	0.68489	0.0:0.9301:0.0:0.0699	.	72;72	O60869-2;O60869	.;EDF1_HUMAN	M	72	.	ENSP00000224073:R72M	R	-	2	0	EDF1	138877637	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.317000	0.79018	1.463000	0.47967	0.655000	0.94253	AGG	.	.	.	none		0.617	EDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055143.1			A	139757816	C	A	139757816	3	1	145	1	0	0	0	0	1	0	0	0	4916	681	24	4	278	4	EDF1	9	139757816	Missense_Mutation	SNP	C	TCGA-DW-5560-01A-01D-1589-08		139757816	1455615	13	8715											
OR52H1	390067	hgsc.bcm.edu	37	chr11	5566652	5566652	+	Frame_Shift_Del	DEL	C	C	-																															atacagaagggaattccaatCcacacatggaattgctccag																								rs565760908		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr11:5566652delC	ENST00000322653.4	-	1	127	c.102delG	c.(100-102)tggfs	p.W34fs	HBG2_ENST00000380259.2_Intron	NM_001005289.1	NP_001005289.1	Q8NGJ2	O52H1_HUMAN	olfactory receptor, family 52, subfamily H, member 1	34						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)		GAATTCCAATCCACACATGGA	0.473																																					p.I35fs		Atlas-INDEL	.											.	OR52H1	46	.	0			c.103delA						PASS	.						88	80	83					11																	5566652		2201	4297	6498	SO:0001589	frameshift_variant	390067	exon1			.	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.102delG	chr11.hg19:g.5566652delC	ENSP00000326259:p.Trp34fs	99.0	0.0	0		72.0	27.0	0.375	NM_001005289	B9EH26|Q6IF79	Frame_Shift_Del	DEL	ENST00000322653.4	hg19	CCDS31386.1																																																																																			.	.	.	none		0.473	OR52H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143400.1	NM_001005289		-	5566652	C	-	5566652	7	5	145	1	0	1	0	1	0	0	0	0	11126	856	30	0	863	0	OR52H1	11	5566652	Frame_Shift_Del	DEL	C	TCGA-DW-5560-01A-01D-1589-08		5566652	129439864	14	8716											
SAPS3	55291	hgsc.bcm.edu	37	chr11	68318634	68318637	+	Frame_Shift_Del	DEL	CATC	CATC	-																															agaggcttgtggaaatagttCatccatcgcaagaagaagat																										TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	CATC	CATC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr11:68318634_68318637delCATC	ENST00000393800.2	+	6	852_855	c.598_601delCATC	c.(598-603)catccafs	p.HP200fs	PPP6R3_ENST00000527403.2_Frame_Shift_Del_p.HP200fs|PPP6R3_ENST00000534534.1_Intron|PPP6R3_ENST00000265636.5_Frame_Shift_Del_p.HP200fs|PPP6R3_ENST00000393799.2_Frame_Shift_Del_p.HP200fs|PPP6R3_ENST00000393801.3_Frame_Shift_Del_p.HP200fs|PPP6R3_ENST00000529710.1_Frame_Shift_Del_p.HP200fs|PPP6R3_ENST00000524904.1_Frame_Shift_Del_p.HP200fs|PPP6R3_ENST00000265637.4_Frame_Shift_Del_p.HP200fs|PPP6R3_ENST00000524845.1_Frame_Shift_Del_p.HP200fs	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	200					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						GGAAATAGTTCATCCATCGCAAGA	0.348																																					p.199_200del		Atlas-INDEL	.											.	PPP6R3	159	.	0			c.597_600del						PASS	.																																			SO:0001589	frameshift_variant	55291	exon6			.	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.598_601delCATC	chr11.hg19:g.68318638_68318641delCATC	ENSP00000377389:p.His200fs	79.0	0.0	0		55.0	25.0	0.454545	NM_001164161	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Frame_Shift_Del	DEL	ENST00000393800.2	hg19	CCDS53672.1																																																																																			.	.	.	none		0.348	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1	NM_018312		-	68318637	CATC	-	68318634	7	5	145	1	0	1	0	1	0	0	0	0	13851	826	29	0	612	0	SAPS3	11	68318634	Frame_Shift_Del	DEL	CATC	TCGA-DW-5560-01A-01D-1589-08	62751982	68318634	66687882	15	8717											
RPL6	6128	hgsc.bcm.edu	37	chr12	112843158	112843158	+	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	cagctttctgatcaatcttgCgctgctccgtaatctcatat	8	15	6	12	2	4	1	2	1	3	0	6	1	5	1	1	0	3	4	1	0	3	4			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr12:112843158C>T	ENST00000424576.2	-	7	922	c.737G>A	c.(736-738)cGc>cAc	p.R246H	RPL6_ENST00000202773.9_Missense_Mutation_p.R246H	NM_001024662.1	NP_001019833.1	Q02878	RL6_HUMAN	ribosomal protein L6	246					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						ATCAATCTTGCGCTGCTCCGT	0.393																																					p.R246H		Atlas-SNP	.											.	RPL6	20	.	0			c.G737A						PASS	.						23	25	24					12																	112843158		2187	4288	6475	SO:0001583	missense	6128	exon7			ATCTTGCGCTGCT	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.737G>A	chr12.hg19:g.112843158C>T	ENSP00000403172:p.Arg246His	49.0	0.0	.		59.0	16.0	.	NM_001024662	Q2M3Q3|Q8WW97	Missense_Mutation	SNP	ENST00000424576.2	hg19	CCDS9162.1	.	.	.	.	.	.	.	.	.	.	C	17.88	3.498413	0.64298	.	.	ENSG00000089009	ENST00000202773;ENST00000424576;ENST00000549923	T;T	0.34072	1.38;1.38	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.40645	0.1125	M	0.66297	2.02	0.80722	D	1	B	0.30439	0.279	B	0.29524	0.103	T	0.40572	-0.9556	10	0.62326	D	0.03	.	16.8348	0.85954	0.0:1.0:0.0:0.0	.	246	Q02878	RL6_HUMAN	H	246;246;186	ENSP00000202773:R246H;ENSP00000403172:R246H	ENSP00000202773:R246H	R	-	2	0	RPL6	111327541	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	6.919000	0.75793	2.408000	0.81797	0.591000	0.81541	CGC	.	.	.	none		0.393	RPL6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405422.1			T	112843158	C	T	112843158	3	4	145	1	0	0	0	0	1	0	0	0	13611	768	27	1	133	1	RPL6	12	112843158	Missense_Mutation	SNP	C	TCGA-DW-5560-01A-01D-1589-08		112843158	21008737	16	8718											
SBNO1	55206	hgsc.bcm.edu	37	chr12	123801801	123801802	+	Frame_Shift_Ins	INS	-	-	T																															gctctatcagcgctccaaggINStaattctaaagtcatatgaa																										TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr12:123801801_123801802insT	ENST00000602398.1	-	21	3028_3029	c.2901_2902insA	c.(2899-2904)ttacctfs	p.P968fs	SBNO1_ENST00000420886.2_Frame_Shift_Ins_p.P968fs|SBNO1_ENST00000267176.4_Frame_Shift_Ins_p.P967fs|SBNO1_ENST00000602750.1_Frame_Shift_Ins_p.P967fs			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	968					regulation of transcription, DNA-templated (GO:0006355)					NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		GCGCTCCAAGGTAATTCTAAAG	0.396																																					p.P968fs		Atlas-INDEL	.											.	SBNO1	138	.	0			c.2902_2903insA						PASS	.																																			SO:0001589	frameshift_variant	55206	exon20			.	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"sno, strawberry notch homolog 1 (Drosophila)"				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.2902dupA	chr12.hg19:g.123801802_123801802dupT	ENSP00000473665:p.Pro968fs	91.0	0.0	0		115.0	36.0	0.313043	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Frame_Shift_Ins	INS	ENST00000602398.1	hg19	CCDS53844.1																																																																																			.	.	.	none		0.396	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183		T	123801802	-	T	123801801	7	5	145	1	0	1	1	0	0	0	0	0	13875	1261	44	0	1327	0	SBNO1	12	123801801	Frame_Shift_Ins	INS	-	TCGA-DW-5560-01A-01D-1589-08	10958643	123801801	10050094	17	8719											
INF2	64423	hgsc.bcm.edu	37	chr14	105174895	105174896	+	Frame_Shift_Ins	INS	-	-	C																															caaggagcccaccatggtggINSccccccgggccaggaaggag																										TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr14:105174895_105174896insC	ENST00000392634.4	+	9	1970_1971	c.1858_1859insC	c.(1858-1860)gccfs	p.A620fs	INF2_ENST00000330634.7_Frame_Shift_Ins_p.A620fs	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	620	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)		CACCATGGTGGCCCCCCGGGCC	0.703											OREG0022959	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A620fs		Atlas-INDEL	.											.	INF2	148	.	0			c.1858_1859insC						PASS	.																																			SO:0001589	frameshift_variant	64423	exon9			.	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.1864dupC	chr14.hg19:g.105174901_105174901dupC	ENSP00000376410:p.Ala620fs	44.0	0.0	0	1387	43.0	22.0	0.511628	NM_001031714	Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	Frame_Shift_Ins	INS	ENST00000392634.4	hg19	CCDS9989.2																																																																																			.	.	.	none		0.703	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	NM_022489		C	105174896	-	C	105174895	7	5	145	1	0	1	1	0	0	0	0	0	7741	1203	42	0	1892	0	INF2	14	105174895	Frame_Shift_Ins	INS	-	TCGA-DW-5560-01A-01D-1589-08		105174895	2174645	18	8720											
CHD2	1106	hgsc.bcm.edu	37	chr15	93567925	93567925	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agattataactggaatgttcGgaaaacataaaggacagctc	17	9	9	6	1	0	1	0	0	0	1	2	4	0	4	0	3	3	2	0	3	7	4			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr15:93567925G>A	ENST00000394196.4	+	39	6545	c.5477G>A	c.(5476-5478)cGg>cAg	p.R1826Q		NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1826					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)			TGGAATGTTCGGAAAACATAA	0.428																																					p.R1826Q		Atlas-SNP	.											CHD2_ENST00000394196,NS,carcinoma,0,1	CHD2	280	.	0			c.G5477A						PASS	.						50	47	48					15																	93567925		1887	4107	5994	SO:0001583	missense	1106	exon39			ATGTTCGGAAAAC	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.5477G>A	chr15.hg19:g.93567925G>A	ENSP00000377747:p.Arg1826Gln	59.0	0.0	.		44.0	4.0	.	NM_001271	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	hg19	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	G	36	5.643949	0.96704	.	.	ENSG00000173575	ENST00000394196	D	0.92647	-3.08	5.56	5.56	0.83823	.	.	.	.	.	D	0.93485	0.7921	L	0.27053	0.805	0.80722	D	1	D	0.69078	0.997	D	0.70227	0.968	D	0.94151	0.7405	9	0.72032	D	0.01	-0.1389	19.8965	0.96963	0.0:0.0:1.0:0.0	.	1826	O14647	CHD2_HUMAN	Q	1826	ENSP00000377747:R1826Q	ENSP00000377747:R1826Q	R	+	2	0	CHD2	91368929	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.932000	0.75869	2.771000	0.95319	0.563000	0.77884	CGG	.	.	.	none		0.428	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		A	93567925	G	A	93567925	3	1	145	1	0	0	0	0	1	0	0	0	3327	1116	39	1	5631	1	CHD2	15	93567925	Missense_Mutation	SNP	G	TCGA-DW-5560-01A-01D-1589-08		93567925	8963467	19	8721											
PLEKHG4	25894	hgsc.bcm.edu	37	chr16	67315014	67315014	+	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	gcccgaagtacaggcactggGactgacagtgctagttgatg	10	8	14	9	1	0	2	0	2	0	0	0	4	0	3	1	2	2	4	1	2	3	3			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr16:67315014G>C	ENST00000360461.5	+	4	3275	c.740G>C	c.(739-741)gGa>gCa	p.G247A	PLEKHG4_ENST00000379344.3_Missense_Mutation_p.G247A|PLEKHG4_ENST00000427155.2_Missense_Mutation_p.G247A|PLEKHG4_ENST00000450733.1_Missense_Mutation_p.G166A	NM_001129727.1|NM_015432.3	NP_001123199.1|NP_056247.1	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4	247							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)		CAGGCACTGGGACTGACAGTG	0.552																																					p.G247A		Atlas-SNP	.											.	PLEKHG4	94	.	0			c.G740C						PASS	.						138	123	128					16																	67315014		2198	4300	6498	SO:0001583	missense	25894	exon5			CACTGGGACTGAC	AK024475	CCDS32466.1, CCDS45512.1	16q22.1	2013-01-11						"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	24501	protein-coding gene	gene with protein product	"puratrophin-1"	609526	"spinocerebellar ataxia 4"	SCA4		16491300, 16001362	Standard	NM_015432		Approved	DKFZP434I216, ARHGEF44	uc010cef.3	Q58EX7		ENST00000360461.5:c.740G>C	chr16.hg19:g.67315014G>C	ENSP00000353646:p.Gly247Ala	155.0	0.0	.		118.0	62.0	.	NM_001129728	Q4G0J8|Q4H485|Q56A69|Q9H7K4|Q9UFW0	Missense_Mutation	SNP	ENST00000360461.5	hg19	CCDS32466.1	.	.	.	.	.	.	.	.	.	.	G	34	5.393426	0.96009	.	.	ENSG00000196155	ENST00000360461;ENST00000427155;ENST00000379344;ENST00000450733	T;T;T;T	0.37058	1.22;1.22;1.22;1.22	5.71	5.71	0.89125	.	0.000000	0.32802	N	0.005631	T	0.66366	0.2782	M	0.88570	2.965	0.35318	D	0.78447	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.998	T	0.78059	-0.2352	10	0.62326	D	0.03	.	15.3559	0.74425	0.0:0.0:1.0:0.0	.	166;54;247	Q58EX7-2;B4E3H4;Q58EX7	.;.;PKHG4_HUMAN	A	247;247;247;166	ENSP00000353646:G247A;ENSP00000401118:G247A;ENSP00000368649:G247A;ENSP00000398030:G166A	ENSP00000353646:G247A	G	+	2	0	PLEKHG4	65872515	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	5.887000	0.69751	2.688000	0.91661	0.591000	0.81541	GGA	.	.	.	none		0.552	PLEKHG4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421395.2	NM_015432		C	67315014	G	C	67315014	3	2	145	1	0	0	0	0	1	0	0	0	12078	1174	41	4	754	4	PLEKHG4	16	67315014	Missense_Mutation	SNP	G	TCGA-DW-5560-01A-01D-1589-08		67315014	23039739	20	8722											
ABR	29	hgsc.bcm.edu	37	chr17	975901	975901	+	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	ccggcgggggtcgatgtcctCgttgatgctggacaggaagt	6	9	17	9	4	0	1	0	1	0	0	3	4	1	3	2	5	1	2	2	5	1	1			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr17:975901C>A	ENST00000302538.5	-	8	993	c.847G>T	c.(847-849)Gag>Tag	p.E283*	ABR_ENST00000574437.1_Nonsense_Mutation_p.E237*|ABR_ENST00000536794.2_Nonsense_Mutation_p.E65*|ABR_ENST00000544583.2_Nonsense_Mutation_p.E237*|ABR_ENST00000291107.2_Nonsense_Mutation_p.E246*	NM_001282149.1|NM_021962.3	NP_001269078.1|NP_068781.2	Q12979	ABR_HUMAN	active BCR-related	283	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phagocytosis (GO:0050766)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.E283K(1)		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)		TCGATGTCCTCGTTGATGCTG	0.642																																					p.E283X	Esophageal Squamous(197;2016 2115 4129 29033 46447)	Atlas-SNP	.											ABR,NS,carcinoma,0,1	ABR	119	.	1	Substitution - Missense(1)	breast(1)	c.G847T						PASS	.						99	78	85					17																	975901		2203	4300	6503	SO:0001587	stop_gained	29	exon8			TGTCCTCGTTGAT	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.847G>T	chr17.hg19:g.975901C>A	ENSP00000303909:p.Glu283*	41.0	0.0	.		30.0	2.0	.	NM_021962	B3KW89|B7Z6H7|D3DTH3|D3DTH4|F5H3S2|F5H8B3|Q13693|Q13694	Nonsense_Mutation	SNP	ENST00000302538.5	hg19	CCDS10999.1	.	.	.	.	.	.	.	.	.	.	C	37	6.326444	0.97476	.	.	ENSG00000159842	ENST00000302538;ENST00000544583;ENST00000291107;ENST00000536794;ENST00000382259	.	.	.	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	.	19.0001	0.92830	0.0:1.0:0.0:0.0	.	.	.	.	X	283;237;246;65;167	.	ENSP00000291107:E246X	E	-	1	0	ABR	922651	1.000000	0.71417	0.987000	0.45799	0.996000	0.88848	7.751000	0.85126	2.712000	0.92718	0.650000	0.86243	GAG	.	.	.	none		0.642	ABR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206675.4			A	975901	C	A	975901	4	1	145	1	0	0	0	0	0	1	0	0	99	893	31	4	1796	4	ABR	17	975901	Nonsense_Mutation	SNP	C	TCGA-DW-5560-01A-01D-1589-08		975901	80219309	21	8723											
CDK12	51755	hgsc.bcm.edu	37	chr17	37627488	37627488	+	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	actggtgaatgtaacacatcTaaacacagaggtaaaaaatt	19	9	7	6	0	1	2	0	1	1	1	1	2	1	2	0	2	2	2	0	2	7	4			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr17:37627488T>A	ENST00000447079.4	+	2	1436	c.1403T>A	c.(1402-1404)cTa>cAa	p.L468Q	CDK12_ENST00000430627.2_Missense_Mutation_p.L468Q	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	468					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						GTAACACATCTAAACACAGAG	0.383			"Mis, N, F"		serous ovarian					TCGA Ovarian(9;0.13)																											p.L468Q		Atlas-SNP	.		Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	.	CDK12	161	.	0			c.T1403A						PASS	.						98	103	101					17																	37627488		2203	4300	6503	SO:0001583	missense	51755	exon2			CACATCTAAACAC	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.1403T>A	chr17.hg19:g.37627488T>A	ENSP00000398880:p.Leu468Gln	159.0	0.0	.		187.0	50.0	.	NM_016507	A7E2B2|B4DYX4|B9EIQ6|O94978	Missense_Mutation	SNP	ENST00000447079.4	hg19	CCDS11337.1	.	.	.	.	.	.	.	.	.	.	T	12.44	1.939975	0.34283	.	.	ENSG00000167258	ENST00000430627;ENST00000447079	T;T	0.39787	1.06;1.06	5.76	3.58	0.41010	.	0.608641	0.12825	N	0.436065	T	0.22589	0.0545	N	0.14661	0.345	0.21220	N	0.99976	B;B;B	0.16603	0.01;0.01;0.018	B;B;B	0.25291	0.026;0.026;0.059	T	0.18967	-1.0320	10	0.25106	T	0.35	-0.9823	2.5375	0.04717	0.2138:0.3455:0.0:0.4407	.	467;468;468	E7EUM9;Q9NYV4;Q9NYV4-2	.;CDK12_HUMAN;.	Q	468	ENSP00000407720:L468Q;ENSP00000398880:L468Q	ENSP00000407720:L468Q	L	+	2	0	CDK12	34881014	0.002000	0.14202	1.000000	0.80357	0.998000	0.95712	0.584000	0.23864	1.076000	0.40961	0.528000	0.53228	CTA	.	.	.	none		0.383	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507		A	37627488	T	A	37627488	3	1	145	1	0	0	0	0	1	0	0	0	3130	1522	53	5	1409	5	CDK12	17	37627488	Missense_Mutation	SNP	T	TCGA-DW-5560-01A-01D-1589-08	36651587	37627488	43567722	22	8724											
JUP	3728	hgsc.bcm.edu	37	chr17	39914006	39914006	+	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	cagcaccccggcagccacgcGctggatgttctccaccgacg	7	5	11	18	5	1	0	0	0	1	0	2	2	1	1	5	2	2	4	5	2	0	1	rs199511559		TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr17:39914006G>T	ENST00000393931.3	-	11	1922	c.1804C>A	c.(1804-1806)Cgc>Agc	p.R602S	JUP_ENST00000540235.1_Intron|JUP_ENST00000393930.1_Missense_Mutation_p.R602S|JUP_ENST00000310706.5_Missense_Mutation_p.R602S	NM_002230.2	NP_002221.1	P14923	PLAK_HUMAN	junction plakoglobin	602	Interaction with DSC1.				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)	p.R602C(1)		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)		GCAGCCACGCGCTGGATGTTC	0.667																																					p.R602S	Colon(16;42 520 6044 17852 28530)	Atlas-SNP	.											JUP,NS,carcinoma,0,1	JUP	64	.	1	Substitution - Missense(1)	endometrium(1)	c.C1804A						PASS	.						25	24	25					17																	39914006		2203	4297	6500	SO:0001583	missense	3728	exon11			CCACGCGCTGGAT	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.1804C>A	chr17.hg19:g.39914006G>T	ENSP00000377508:p.Arg602Ser	47.0	0.0	.		56.0	4.0	.	NM_021991	Q15093|Q15151|Q7L3S5|Q86W21|Q9BWC4|Q9HCX9	Missense_Mutation	SNP	ENST00000393931.3	hg19	CCDS11407.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.128863	0.77549	.	.	ENSG00000173801	ENST00000393930;ENST00000310706;ENST00000393931	T;T;T	0.70869	-0.52;-0.52;-0.52	4.83	4.83	0.62350	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.80899	0.4712	M	0.64404	1.975	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82339	-0.0506	10	0.87932	D	0	-13.1972	12.2188	0.54423	0.0:0.0:0.83:0.17	.	602	P14923	PLAK_HUMAN	S	602	ENSP00000377507:R602S;ENSP00000311113:R602S;ENSP00000377508:R602S	ENSP00000311113:R602S	R	-	1	0	JUP	37167532	1.000000	0.71417	0.998000	0.56505	0.634000	0.38068	4.360000	0.59455	2.518000	0.84900	0.561000	0.74099	CGC	.	.	.	alt		0.667	JUP-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257406.1			T	39914006	G	T	39914006	3	4	145	1	0	0	0	0	1	0	0	0	7979	1087	38	4	449	4	JUP	17	39914006	Missense_Mutation	SNP	G	TCGA-DW-5560-01A-01D-1589-08	2286518	39914006	41281204	23	8725											
CLTC	1213	hgsc.bcm.edu	37	chr17	57754485	57754485	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgttggaaagtattgtgagaAgagagatccacatctggcct	12	11	12	6	0	1	3	0	1	1	3	2	6	2	4	2	2	0	2	2	2	3	3			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr17:57754485A>G	ENST00000269122.3	+	17	3006	c.2732A>G	c.(2731-2733)aAg>aGg	p.K911R	CLTC_ENST00000393043.1_Missense_Mutation_p.K911R|CLTC_ENST00000579815.1_3'UTR|CLTC_ENST00000579456.1_Intron	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	911	Heavy chain arm.|Proximal segment.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					TATTGTGAGAAGAGAGATCCA	0.423			T	"ALK, TFE3"	"ALCL, renal "																																p.K911R		Atlas-SNP	.		Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	.	CLTC	124	.	0			c.A2732G						PASS	.						118	116	116					17																	57754485		2203	4300	6503	SO:0001583	missense	1213	exon17			GTGAGAAGAGAGA	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.2732A>G	chr17.hg19:g.57754485A>G	ENSP00000269122:p.Lys911Arg	82.0	0.0	.		127.0	82.0	.	NM_004859	D3DU00|Q6N0A0|Q86TF2	Missense_Mutation	SNP	ENST00000269122.3	hg19	CCDS32696.1	.	.	.	.	.	.	.	.	.	.	A	34	5.330051	0.95733	.	.	ENSG00000141367	ENST00000269122;ENST00000393043	T;T	0.23552	1.9;1.9	5.69	5.69	0.88448	Tetratricopeptide-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.56156	0.1966	M	0.85945	2.785	0.80722	D	1	D;B	0.69078	0.997;0.139	D;B	0.83275	0.996;0.394	T	0.60707	-0.7210	10	0.48119	T	0.1	.	15.9483	0.79809	1.0:0.0:0.0:0.0	.	911;911	Q00610;Q00610-2	CLH1_HUMAN;.	R	911	ENSP00000269122:K911R;ENSP00000376763:K911R	ENSP00000269122:K911R	K	+	2	0	CLTC	55109267	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.228000	0.95250	2.168000	0.68352	0.455000	0.32223	AAG	.	.	.	none		0.423	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859		G	57754485	A	G	57754485	3	3	145	1	0	0	0	0	1	0	0	0	3568	72	3	3	2798	3	CLTC	17	57754485	Missense_Mutation	SNP	A	TCGA-DW-5560-01A-01D-1589-08	17840479	57754485	23440725	24	8726											
SLC16A6	9120	hgsc.bcm.edu	37	chr17	66267173	66267173	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagaattcagtagcaaaagtAaaggcaaacagagacacagt	20	5	9	7	0	1	2	1	0	0	2	1	3	1	2	0	1	2	4	0	1	7	3			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr17:66267173A>G	ENST00000327268.4	-	6	1292	c.1128T>C	c.(1126-1128)ttT>ttC	p.F376F	SLC16A6_ENST00000580666.1_Silent_p.F376F|ARSG_ENST00000448504.2_Intron	NM_001174166.1	NP_001167637.1	O15403	MOT7_HUMAN	solute carrier family 16, member 6	376					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)	TAGCAAAAGTAAAGGCAAACA	0.443																																					p.F376F		Atlas-SNP	.											.	SLC16A6	56	.	0			c.T1128C						PASS	.						120	112	115					17																	66267173		2203	4300	6503	SO:0001819	synonymous_variant	9120	exon6			AAAAGTAAAGGCA	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.1128T>C	chr17.hg19:g.66267173A>G		94.0	0.0	.		130.0	85.0	.	NM_001174166	Q6P1X3	Silent	SNP	ENST00000327268.4	hg19	CCDS11675.1																																																																																			.	.	.	none		0.443	SLC16A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448323.1	NM_004694		G	66267173	A	G	66267173	2	3	145	1	0	0	0	0	0	0	0	1	14425	359	13	3		3	SLC16A6	17	66267173	Silent	SNP	A	TCGA-DW-5560-01A-01D-1589-08	8512688	66267173	14928037	25	8727											
NCOA3	8202	hgsc.bcm.edu	37	chr20	46252817	46252817	+	Frame_Shift_Del	DEL	A	A	-																															gtaagacagatacgtcaaatAaaagagcaaggtaataaaaa																										TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr20:46252817delA	ENST00000371998.3	+	4	437	c.246delA	c.(244-246)atafs	p.I82fs	NCOA3_ENST00000341724.6_Frame_Shift_Del_p.I82fs|NCOA3_ENST00000372004.3_Frame_Shift_Del_p.I82fs|NCOA3_ENST00000371997.3_Frame_Shift_Del_p.I82fs			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	82	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				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						TACGTCAAATAAAAGAGCAAG	0.378																																					p.I82fs		Atlas-INDEL	.											.	NCOA3	156	.	0			c.245delT						PASS	.						61	58	59					20																	46252817		2203	4300	6503	SO:0001589	frameshift_variant	8202	exon4			.	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.246delA	chr20.hg19:g.46252817delA	ENSP00000361066:p.Ile82fs	38.0	0.0	0		89.0	17.0	0.191011	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Frame_Shift_Del	DEL	ENST00000371998.3	hg19	CCDS13407.1																																																																																			.	.	.	none		0.378	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		-	46252817	A	-	46252817	7	5	145	1	0	1	0	1	0	0	0	0	10237	352	13	0	252	0	NCOA3	20	46252817	Frame_Shift_Del	DEL	A	TCGA-DW-5560-01A-01D-1589-08		46252817	16772703	26	8728											
FBXO7	25793	hgsc.bcm.edu	37	chr22	32889131	32889131	+	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	atttgggttggtcgtcctccCattggaactgaaactacgga	9	12	11	9	2	0	1	0	1	0	0	3	3	2	3	2	4	3	1	2	4	3	4			TCGA-DW-5560-01A-01D-1589-08	TCGA-DW-5560-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5a6ec0d8-cd0a-4f81-b981-27efdc14709c	e5457299-318e-451f-8658-07ea29ecbd40	g.chr22:32889131C>A	ENST00000266087.7	+	7	1334	c.1007C>A	c.(1006-1008)cCa>cAa	p.P336Q	FBXO7_ENST00000397426.1_Missense_Mutation_p.P222Q|FBXO7_ENST00000382058.3_Missense_Mutation_p.P257Q	NM_012179.3	NP_036311.3	Q9Y3I1	FBX7_HUMAN	F-box protein 7	336	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				cell death (GO:0008219)|mitochondrion degradation (GO:0000422)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of lymphocyte differentiation (GO:0045620)|protein targeting to mitochondrion (GO:0006626)|protein ubiquitination (GO:0016567)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GTCGTCCTCCCATTGGAACTG	0.438																																					p.P336Q		Atlas-SNP	.											.	FBXO7	131	.	0			c.C1007A						PASS	.						371	310	330					22																	32889131		2203	4300	6503	SO:0001583	missense	25793	exon7			TCCTCCCATTGGA	AF129537	CCDS13907.1, CCDS58806.1	22q12.3	2013-09-19	2004-06-15		ENSG00000100225	ENSG00000100225		"F-boxes /  "other"", "Parkinson disease"	13586	protein-coding gene	gene with protein product		605648	"F-box only protein 7"			10531035, 10531037, 19038853	Standard	NM_001257990		Approved	FBX7, Fbx, PARK15	uc003amq.3	Q9Y3I1	OTTHUMG00000030674	ENST00000266087.7:c.1007C>A	chr22.hg19:g.32889131C>A	ENSP00000266087:p.Pro336Gln	270.0	1.0	.		278.0	111.0	.	NM_012179	B4DNB3|B4DWX5|Q5TGC4|Q5TI86|Q96HM6|Q9UF21|Q9UKT2	Missense_Mutation	SNP	ENST00000266087.7	hg19	CCDS13907.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.192232	0.78902	.	.	ENSG00000100225	ENST00000266087;ENST00000382058;ENST00000397426	D;D;D	0.99709	-6.48;-6.48;-6.48	6.08	6.08	0.98989	F-box domain, cyclin-like (3);F-box domain, Skp2-like (1);	0.000000	0.85682	D	0.000000	D	0.99799	0.9914	M	0.91459	3.21	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.996;1.0	D	0.97617	1.0133	10	0.87932	D	0	-17.0815	20.6634	0.99662	0.0:1.0:0.0:0.0	.	336;257;336	A8K7F7;Q9Y3I1-2;Q9Y3I1	.;.;FBX7_HUMAN	Q	336;257;222	ENSP00000266087:P336Q;ENSP00000371490:P257Q;ENSP00000380571:P222Q	ENSP00000266087:P336Q	P	+	2	0	FBXO7	31219131	1.000000	0.71417	0.815000	0.32552	0.630000	0.37929	5.980000	0.70516	2.894000	0.99253	0.655000	0.94253	CCA	.	.	.	none		0.438	FBXO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129001.1			A	32889131	C	A	32889131	3	1	145	1	0	0	0	0	1	0	0	0	5767	594	21	4	1074	4	FBXO7	22	32889131	Missense_Mutation	SNP	C	TCGA-DW-5560-01A-01D-1589-08		32889131	18415435	27	8729											
UBIAD1	29914	hgsc.bcm.edu	37	chr1	11346095	11346095	+	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	agccaggccttcaacaaactGccccagaggactgccaagct	12	5	9	15	0	1	1	1	0	0	1	1	2	1	2	5	2	6	1	5	2	3	1			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr1:11346095G>C	ENST00000376810.5	+	2	1250	c.924G>C	c.(922-924)ctG>ctC	p.L308L	UBIAD1_ENST00000376804.2_Intron	NM_013319.2	NP_037451.1	Q9Y5Z9	UBIA1_HUMAN	UbiA prenyltransferase domain containing 1	308					menaquinone biosynthetic process (GO:0009234)|ubiquinone biosynthetic process (GO:0006744)|vitamin K biosynthetic process (GO:0042371)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	antioxidant activity (GO:0016209)|prenyltransferase activity (GO:0004659)			endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|prostate(3)	12	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.000818)|all_lung(284;0.00105)|Colorectal(325;0.0062)|Breast(348;0.012)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.52e-06)|COAD - Colon adenocarcinoma(227;0.000254)|BRCA - Breast invasive adenocarcinoma(304;0.000299)|Kidney(185;0.000754)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0487)		TCAACAAACTGCCCCAGAGGA	0.547																																					p.L308L		Atlas-SNP	.											.	UBIAD1	27	.	0			c.G924C						PASS	.						110	107	108					1																	11346095		2203	4300	6503	SO:0001819	synonymous_variant	29914	exon2			CAAACTGCCCCAG		CCDS129.1	1p36.22	2012-05-02			ENSG00000120942	ENSG00000120942			30791	protein-coding gene	gene with protein product	"transitional epithelia response protein"	611632	"Schnyder crystalline corneal dystrophy"	SCCD		20953171, 12497587, 11314041, 17668063, 17962451, 8894705	Standard	NM_013319		Approved	TERE1	uc001asg.3	Q9Y5Z9	OTTHUMG00000002075	ENST00000376810.5:c.924G>C	chr1.hg19:g.11346095G>C		157.0	0.0	.		152.0	62.0	.	NM_013319	B3KQG3|Q53GX3|Q5THD4	Silent	SNP	ENST00000376810.5	hg19	CCDS129.1																																																																																			.	.	.	none		0.547	UBIAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005773.1	NM_013319		C	11346095	G	C	11346095	2	2	146	1	0	0	0	0	0	0	0	1	16897	1306	46	4		4	UBIAD1	1	11346095	Silent	SNP	G	TCGA-DW-5561-01A-01D-1589-08		11346095	237904526	1	8730											
PADI3	51702	hgsc.bcm.edu	37	chr1	17609568	17609568	+	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	ttcaagtggtggaacatggtGccctgagacagctcccaccc	9	8	11	13	0	1	1	1	1	0	1	2	3	2	2	3	3	3	1	3	3	2	1			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr1:17609568G>A	ENST00000375460.3	+	16	2029	c.1989G>A	c.(1987-1989)gtG>gtA	p.V663V		NM_016233.2	NP_057317.2	Q9ULW8	PADI3_HUMAN	peptidyl arginine deiminase, type III	663					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|liver(2)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;1.17e-05)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	GGAACATGGTGCCCTGAGACA	0.572																																					p.V663V		Atlas-SNP	.											.	PADI3	81	.	0			c.G1989A						PASS	.						90	74	79					1																	17609568		2203	4300	6503	SO:0001819	synonymous_variant	51702	exon16			CATGGTGCCCTGA	AB026831	CCDS179.1	1p36.13	2008-02-05			ENSG00000142619	ENSG00000142619	3.5.3.15	"Peptidyl arginine deiminases"	18337	protein-coding gene	gene with protein product		606755				11069618	Standard	NM_016233		Approved	PDI3	uc001bai.3	Q9ULW8	OTTHUMG00000002373	ENST00000375460.3:c.1989G>A	chr1.hg19:g.17609568G>A		53.0	0.0	.		62.0	13.0	.	NM_016233	Q58EY7|Q70SX5	Silent	SNP	ENST00000375460.3	hg19	CCDS179.1																																																																																			.	.	.	none		0.572	PADI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006805.1			A	17609568	G	A	17609568	2	1	146	1	0	0	0	0	0	0	0	1	11386	1306	46	2		2	PADI3	1	17609568	Silent	SNP	G	TCGA-DW-5561-01A-01D-1589-08	6263473	17609568	231641053	2	8731											
ZDHHC18	84243	hgsc.bcm.edu	37	chr1	27176925	27176925	+	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	tgtgtggtcacccacctgacGttgcgtgagttgtgggtgag	5	12	16	8	2	1	3	1	3	0	0	1	3	1	3	2	2	1	2	2	2	0	2	rs373583803		TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr1:27176925G>A	ENST00000374142.4	+	4	875	c.780G>A	c.(778-780)acG>acA	p.T260T		NM_032283.2	NP_115659.1	Q9NUE0	ZDH18_HUMAN	zinc finger, DHHC-type containing 18	260					cellular protein localization (GO:0034613)|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)			endometrium(1)|large_intestine(2)	3		all_cancers(24;5.82e-22)|all_epithelial(13;9.91e-20)|Colorectal(325;0.000147)|Breast(348;0.000706)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;5.71e-53)|Epithelial(14;4.73e-52)|OV - Ovarian serous cystadenocarcinoma(117;1.53e-29)|Colorectal(126;1.9e-09)|COAD - Colon adenocarcinoma(152;4.2e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000548)|STAD - Stomach adenocarcinoma(196;0.00065)|KIRC - Kidney renal clear cell carcinoma(1967;0.000779)|GBM - Glioblastoma multiforme(114;0.0265)|READ - Rectum adenocarcinoma(331;0.0455)|Lung(427;0.163)|LUSC - Lung squamous cell carcinoma(448;0.237)		CCCACCTGACGTTGCGTGAGT	0.567																																					p.T260T		Atlas-SNP	.											.	ZDHHC18	20	.	0			c.G780A						PASS	.	G		0,4406		0,0,2203	159	139	145		780	-3.6	1	1		145	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZDHHC18	NM_032283.2		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		260/389	27176925	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	84243	exon4			CCTGACGTTGCGT	AK056427	CCDS30650.1	1p36.11	2008-05-02			ENSG00000204160	ENSG00000204160		"Zinc fingers, DHHC-type"	20712	protein-coding gene	gene with protein product							Standard	NM_032283		Approved	DKFZp667O2416	uc001bnb.3	Q9NUE0	OTTHUMG00000004092	ENST00000374142.4:c.780G>A	chr1.hg19:g.27176925G>A		201.0	0.0	.		185.0	76.0	.	NM_032283	A6NHY9|B4DQ84|Q5JYH0|Q9H020	Silent	SNP	ENST00000374142.4	hg19	CCDS30650.1	.	.	.	.	.	.	.	.	.	.	G	8.860	0.946706	0.18356	0.0	2.33E-4	ENSG00000204160	ENST00000488397	.	.	.	5.05	-3.58	0.04597	.	.	.	.	.	T	0.36496	0.0969	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35968	-0.9767	4	.	.	.	-4.0065	0.8159	0.01102	0.389:0.2593:0.1417:0.21	.	.	.	.	I	25	.	.	V	+	1	0	ZDHHC18	27049512	0.000000	0.05858	0.965000	0.40720	0.894000	0.52154	-1.818000	0.01717	-0.387000	0.07809	-0.215000	0.12644	GTT	.	.	.	none		0.567	ZDHHC18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011706.3	NM_032283		A	27176925	G	A	27176925	2	1	146	1	0	0	0	0	0	0	0	1	17620	1132	40	1		1	ZDHHC18	1	27176925	Silent	SNP	G	TCGA-DW-5561-01A-01D-1589-08	9567357	27176925	222073696	3	8732											
KIAA1522	57648	hgsc.bcm.edu	37	chr1	33237745	33237745	+	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	agctggagcggcccgtgtccCctgagacccaggctgacctc	6	6	13	16	2	0	2	0	2	0	1	2	4	1	3	5	3	2	2	5	3	0	0			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr1:33237745C>A	ENST00000373480.1	+	6	2891	c.2788C>A	c.(2788-2790)Cct>Act	p.P930T	KIAA1522_ENST00000294521.3_Intron|KIAA1522_ENST00000401073.2_Missense_Mutation_p.P989T|KIAA1522_ENST00000373481.3_Missense_Mutation_p.P941T	NM_001198972.1	NP_001185901.1	Q9P206	K1522_HUMAN	KIAA1522	930	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)				GCCCGTGTCCCCTGAGACCCA	0.647																																					p.P989T		Atlas-SNP	.											.	KIAA1522	68	.	0			c.C2965A						PASS	.						20	27	25					1																	33237745		1981	4161	6142	SO:0001583	missense	57648	exon6			GTGTCCCCTGAGA	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.2788C>A	chr1.hg19:g.33237745C>A	ENSP00000362579:p.Pro930Thr	31.0	0.0	.		40.0	13.0	.	NM_020888	B4DQU8|B5MDY0|C9JH84|Q8TCQ0	Missense_Mutation	SNP	ENST00000373480.1	hg19	CCDS55588.1	.	.	.	.	.	.	.	.	.	.	C	19.26	3.793037	0.70452	.	.	ENSG00000162522	ENST00000401073;ENST00000373481;ENST00000373480	T;T;T	0.17054	2.3;2.33;2.35	4.85	4.85	0.62838	.	0.315683	0.28011	N	0.016953	T	0.36358	0.0964	L	0.59436	1.845	0.32817	D	0.502245	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.76575	0.988;0.988;0.988	T	0.33394	-0.9870	10	0.37606	T	0.19	-12.0197	14.185	0.65601	0.0:0.8504:0.1496:0.0	.	941;930;989	Q9P206-3;Q9P206;Q9P206-2	.;K1522_HUMAN;.	T	989;941;930	ENSP00000383851:P989T;ENSP00000362580:P941T;ENSP00000362579:P930T	ENSP00000362579:P930T	P	+	1	0	KIAA1522	33010332	0.987000	0.35691	1.000000	0.80357	0.799000	0.45148	2.754000	0.47532	2.682000	0.91365	0.650000	0.86243	CCT	.	.	.	none		0.647	KIAA1522-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022130.1			A	33237745	C	A	33237745	3	1	146	1	0	0	0	0	1	0	0	0	8245	623	22	4	2987	4	KIAA1522	1	33237745	Missense_Mutation	SNP	C	TCGA-DW-5561-01A-01D-1589-08	6060820	33237745	216012876	4	8733											
MACF1	23499	hgsc.bcm.edu	37	chr1	39835802	39835802	+	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	aaactgaagggagtattccaCctacggaaacttctatgagt	14	10	9	8	1	1	2	0	2	1	0	2	4	2	4	2	2	3	1	2	2	6	5			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr1:39835802C>G	ENST00000372915.3	+	50	13141	c.13054C>G	c.(13054-13056)Cct>Gct	p.P4352A	MACF1_ENST00000564288.1_Missense_Mutation_p.P4347A|MACF1_ENST00000361689.2_Missense_Mutation_p.P2285A|MACF1_ENST00000317713.7_Missense_Mutation_p.P2285A|MACF1_ENST00000289893.4_Missense_Mutation_p.P2787A|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000545844.1_Missense_Mutation_p.P2285A|MACF1_ENST00000539005.1_Missense_Mutation_p.P2285A|MACF1_ENST00000567887.1_Missense_Mutation_p.P4384A			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	4352					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)			GAGTATTCCACCTACGGAAAC	0.448																																					p.P2285A		Atlas-SNP	.											.	MACF1	909	.	0			c.C6853G						PASS	.						75	76	76					1																	39835802		2203	4300	6503	SO:0001583	missense	23499	exon47			ATTCCACCTACGG	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.13054C>G	chr1.hg19:g.39835802C>G	ENSP00000362006:p.Pro4352Ala	48.0	0.0	.		35.0	18.0	.	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.632|0.632	-0.816867|-0.816867	0.02776|0.02776	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893|ENST00000372925	T;T;T;T;T;T|.	0.32023|.	1.47;1.47;1.47;1.47;1.47;1.47|.	5.37|5.37	-0.194|-0.194	0.13240|0.13240	.|.	0.900226|.	0.09361|.	N|.	0.812758|.	T|T	0.20292|0.20292	0.0488|0.0488	N|N	0.16368|0.16368	0.405|0.405	0.09310|0.09310	N|N	1|1	B;B;B;B|.	0.15141|.	0.012;0.003;0.002;0.001|.	B;B;B;B|.	0.25759|.	0.063;0.004;0.007;0.006|.	T|T	0.29518|0.29518	-1.0009|-1.0009	10|5	0.07175|.	T|.	0.84|.	.|.	6.3552|6.3552	0.21397|0.21397	0.0:0.4709:0.249:0.28|0.0:0.4709:0.249:0.28	.|.	4352;2285;2285;2250|.	Q9UPN3;F8W8Q1;Q9UPN3-2;Q9UPN3-3|.	MACF1_HUMAN;.;.;.|.	A|S	2285;4352;2285;2285;2285;2787|1418	ENSP00000439537:P2285A;ENSP00000362006:P4352A;ENSP00000354573:P2285A;ENSP00000313438:P2285A;ENSP00000444364:P2285A;ENSP00000289893:P2787A|.	ENSP00000289893:P2787A|.	P|T	+|+	1|2	0|0	MACF1|MACF1	39608389|39608389	0.000000|0.000000	0.05858|0.05858	0.116000|0.116000	0.21606|0.21606	0.992000|0.992000	0.81027|0.81027	0.181000|0.181000	0.16880|0.16880	0.245000|0.245000	0.21373|0.21373	0.655000|0.655000	0.94253|0.94253	CCT|ACC	.	.	.	none		0.448	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		G	39835802	C	G	39835802	3	3	146	1	0	0	0	0	1	0	0	0	9151	507	18	4	13186	4	MACF1	1	39835802	Missense_Mutation	SNP	C	TCGA-DW-5561-01A-01D-1589-08	6598057	39835802	209414819	5	8734											
TMEM81	388730	hgsc.bcm.edu	37	chr1	205052751	205052751	+	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	cgccaccaaccactccaatgGcaattcctattcccaaggct	11	8	5	17	1	0	0	0	0	0	0	3	0	3	0	6	2	1	2	6	2	5	3			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr1:205052751G>T	ENST00000367167.3	-	1	894	c.698C>A	c.(697-699)gCc>gAc	p.A233D		NM_203376.1	NP_976310.1	Q6P7N7	TMM81_HUMAN	transmembrane protein 81	233						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)			CACTCCAATGGCAATTCCTAT	0.512																																					p.A233D		Atlas-SNP	.											.	TMEM81	23	.	0			c.C698A						PASS	.						133	120	124					1																	205052751		2203	4300	6503	SO:0001583	missense	388730	exon1			CCAATGGCAATTC	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.698C>A	chr1.hg19:g.205052751G>T	ENSP00000356135:p.Ala233Asp	123.0	0.0	.		113.0	37.0	.	NM_203376	Q6UVZ4	Missense_Mutation	SNP	ENST00000367167.3	hg19	CCDS1450.1	.	.	.	.	.	.	.	.	.	.	G	18.19	3.569050	0.65765	.	.	ENSG00000174529	ENST00000367167	T	0.35605	1.3	5.79	-0.62	0.11567	.	1.790840	0.02843	N	0.128129	T	0.37183	0.0994	L	0.57536	1.79	0.09310	N	1	P	0.37276	0.589	B	0.38616	0.277	T	0.34354	-0.9832	10	0.66056	D	0.02	-30.4547	5.7266	0.18017	0.3683:0.291:0.3406:0.0	.	233	Q6P7N7	TMM81_HUMAN	D	233	ENSP00000356135:A233D	ENSP00000356135:A233D	A	-	2	0	TMEM81	203319374	0.000000	0.05858	0.000000	0.03702	0.083000	0.17756	0.115000	0.15540	-0.133000	0.11537	0.655000	0.94253	GCC	.	.	.	none		0.512	TMEM81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090076.1	NM_203376		T	205052751	G	T	205052751	3	4	146	1	0	0	0	0	1	0	0	0	16217	1203	42	4	73	4	TMEM81	1	205052751	Missense_Mutation	SNP	G	TCGA-DW-5561-01A-01D-1589-08	165216949	205052751	44197870	6	8735											
CR2	1380	hgsc.bcm.edu	37	chr1	207642031	207642031	+	Missense_Mutation	SNP	A	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	taactgtttgtcttcgggaaAatggagtgctgtccccccca	8	12	10	11	1	1	0	0	0	1	0	3	2	2	2	3	2	2	2	3	2	3	3			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr1:207642031A>C	ENST00000367058.3	+	3	794	c.605A>C	c.(604-606)aAa>aCa	p.K202T	CR2_ENST00000367057.3_Missense_Mutation_p.K202T|CR2_ENST00000485707.1_3'UTR|CR2_ENST00000458541.2_Missense_Mutation_p.K202T|CR2_ENST00000367059.3_Missense_Mutation_p.K202T	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	202	Sushi 3. {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						TCTTCGGGAAAATGGAGTGCT	0.413																																					p.K202T		Atlas-SNP	.											.	CR2	164	.	0			c.A605C						PASS	.						270	250	257					1																	207642031		2203	4300	6503	SO:0001583	missense	1380	exon3			CGGGAAAATGGAG	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.605A>C	chr1.hg19:g.207642031A>C	ENSP00000356025:p.Lys202Thr	288.0	0.0	.		195.0	85.0	.	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	hg19	CCDS1478.1	.	.	.	.	.	.	.	.	.	.	A	1.073	-0.669450	0.03403	.	.	ENSG00000117322	ENST00000367058;ENST00000367057;ENST00000367059;ENST00000458541	T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01	5.82	-5.11	0.02901	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.25121	0.0610	N	0.02158	-0.66	0.09310	N	1	B;B;B	0.13594	0.008;0.004;0.002	B;B;B	0.17979	0.02;0.015;0.007	T	0.24870	-1.0148	9	0.13470	T	0.59	.	3.9575	0.09396	0.2886:0.4405:0.0679:0.203	.	202;202;202	Q5SR47;P20023;P20023-3	.;CR2_HUMAN;.	T	202	ENSP00000356025:K202T;ENSP00000356024:K202T;ENSP00000356026:K202T;ENSP00000404222:K202T	ENSP00000356024:K202T	K	+	2	0	CR2	205708654	0.000000	0.05858	0.013000	0.15412	0.042000	0.13812	-0.669000	0.05262	-0.440000	0.07211	-0.445000	0.05633	AAA	.	.	.	none		0.413	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877		C	207642031	A	C	207642031	3	2	146	1	0	0	0	0	1	0	0	0	3844	14	1	5	615	5	CR2	1	207642031	Missense_Mutation	SNP	A	TCGA-DW-5561-01A-01D-1589-08	2589280	207642031	41608590	7	8736											
SPEG	10290	hgsc.bcm.edu	37	chr2	220338577	220338577	+	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	gggccctcacctgcaccgccCgaaaccgtcacggcacacag	9	3	10	19	4	2	0	2	0	0	0	2	1	2	0	5	2	2	2	5	2	1	0			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr2:220338577C>A	ENST00000312358.7	+	18	4531	c.4399C>A	c.(4399-4401)Cga>Aga	p.R1467R	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1467	Ig-like 7.				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)		CTGCACCGCCCGAAACCGTCA	0.647																																					p.R1467R		Atlas-SNP	.											.	SPEG	272	.	0			c.C4399A						PASS	.						56	66	63					2																	220338577		2052	4184	6236	SO:0001819	synonymous_variant	10290	exon18			ACCGCCCGAAACC	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.4399C>A	chr2.hg19:g.220338577C>A		156.0	0.0	.		157.0	86.0	.	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Silent	SNP	ENST00000312358.7	hg19	CCDS42824.1																																																																																			.	.	.	none		0.647	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		A	220338577	C	A	220338577	2	1	146	1	0	0	0	0	0	0	0	1	15048	644	23	4		4	SPEG	2	220338577	Silent	SNP	C	TCGA-DW-5561-01A-01D-1589-08		220338577	22860796	8	8737											
ATG7	10533	hgsc.bcm.edu	37	chr3	11356947	11356947	+	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	ttaaacactacagtgatttcTtccaaggtcaaaggacgaag	15	10	8	8	1	2	1	1	1	1	0	3	3	3	2	1	2	2	0	1	2	6	4			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr3:11356947T>A	ENST00000354449.3	+	7	683	c.658T>A	c.(658-660)Ttc>Atc	p.F220I	ATG7_ENST00000354956.5_Missense_Mutation_p.F220I|ATG7_ENST00000446450.2_Missense_Mutation_p.F181I	NM_006395.2	NP_006386.1	O95352	ATG7_HUMAN	autophagy related 7	220					adult walking behavior (GO:0007628)|C-terminal protein lipidation (GO:0006501)|cardiac muscle cell development (GO:0055013)|cellular amino acid metabolic process (GO:0006520)|cellular protein modification process (GO:0006464)|cellular response to hyperoxia (GO:0071455)|cellular response to nitrogen starvation (GO:0006995)|cellular response to starvation (GO:0009267)|central nervous system neuron axonogenesis (GO:0021955)|cerebellar Purkinje cell layer development (GO:0021680)|cerebral cortex development (GO:0021987)|late nucleophagy (GO:0044805)|liver development (GO:0001889)|membrane fusion (GO:0061025)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of apoptotic process (GO:0043066)|negative stranded viral RNA replication (GO:0039689)|neurological system process (GO:0050877)|piecemeal microautophagy of nucleus (GO:0034727)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein modification process (GO:0031401)|post-embryonic development (GO:0009791)|protein catabolic process (GO:0030163)|protein lipidation (GO:0006497)|protein modification by small protein conjugation (GO:0032446)|protein transport (GO:0015031)|pyramidal neuron development (GO:0021860)|regulation of protein ubiquitination (GO:0031396)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|pre-autophagosomal structure (GO:0000407)	Atg12 activating enzyme activity (GO:0019778)|Atg8 activating enzyme (GO:0019779)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)|ubiquitin activating enzyme activity (GO:0004839)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(14)|prostate(1)|skin(2)|urinary_tract(1)	34						CAGTGATTTCTTCCAAGGTCA	0.348																																					p.F220I		Atlas-SNP	.											.	ATG7	56	.	0			c.T658A						PASS	.						110	97	101					3																	11356947		2203	4300	6503	SO:0001583	missense	10533	exon7			GATTTCTTCCAAG	AF094516	CCDS2605.1, CCDS46752.1, CCDS46753.1	3p25.3-p25.2	2014-02-18	2012-06-06	2005-09-11	ENSG00000197548	ENSG00000197548		"Ubiquitin-like modifier activating enzymes"	16935	protein-coding gene	gene with protein product	"ubiquitin-activating enzyme E1-like protein"	608760	"APG7 autophagy 7-like (S. cerevisiae)", "ATG7 autophagy related 7 homolog (S. cerevisiae)"	APG7L		10233149	Standard	NM_006395		Approved	GSA7, DKFZp434N0735	uc003bwc.3	O95352	OTTHUMG00000129740	ENST00000354449.3:c.658T>A	chr3.hg19:g.11356947T>A	ENSP00000346437:p.Phe220Ile	66.0	0.0	.		71.0	30.0	.	NM_001136031	B4E170|E9PB95|Q7L8L0|Q9BWP2|Q9UFH4	Missense_Mutation	SNP	ENST00000354449.3	hg19	CCDS2605.1	.	.	.	.	.	.	.	.	.	.	T	17.89	3.499788	0.64298	.	.	ENSG00000197548	ENST00000446450;ENST00000354956;ENST00000354449	T;T;T	0.48522	0.81;0.81;0.81	4.67	4.67	0.58626	.	0.069886	0.64402	D	0.000020	T	0.50429	0.1615	M	0.88105	2.93	0.43381	D	0.995487	P;B;B	0.36086	0.536;0.134;0.083	B;B;B	0.29598	0.104;0.028;0.02	T	0.57751	-0.7757	9	.	.	.	-13.2176	11.6384	0.51217	0.0:0.0:0.0:1.0	.	181;220;220	E9PB95;O95352-2;O95352	.;.;ATG7_HUMAN	I	181;220;220	ENSP00000412580:F181I;ENSP00000347042:F220I;ENSP00000346437:F220I	.	F	+	1	0	ATG7	11331947	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.439000	0.59968	1.726000	0.51525	0.482000	0.46254	TTC	.	.	.	none		0.348	ATG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251951.3	NM_006395		A	11356947	T	A	11356947	3	1	146	1	0	0	0	0	1	0	0	0	1101	1609	56	5	680	5	ATG7	3	11356947	Missense_Mutation	SNP	T	TCGA-DW-5561-01A-01D-1589-08		11356947	186665483	9	8738											
DHX30	22907	hgsc.bcm.edu	37	chr3	47882520	47882520	+	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	agctgaatccagagagtattCgaccagggggacctgggggc	10	6	16	9	1	0	2	0	1	0	1	2	5	1	3	3	4	1	2	3	4	2	2			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr3:47882520C>A	ENST00000445061.1	+	7	927	c.520C>A	c.(520-522)Cga>Aga	p.R174R	DHX30_ENST00000446256.2_Silent_p.R135R|DHX30_ENST00000348968.4_Silent_p.R146R|DHX30_ENST00000457607.1_Silent_p.R202R	NM_138615.2	NP_619520.1	Q7L2E3	DHX30_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 30	174						cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|large_intestine(11)|lung(13)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	37				BRCA - Breast invasive adenocarcinoma(193;0.000696)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		AGAGAGTATTCGACCAGGGGG	0.597																																					p.R174R		Atlas-SNP	.											DHX30,NS,carcinoma,0,1	DHX30	101	.	0			c.C520A						PASS	.						34	34	34					3																	47882520		2203	4300	6503	SO:0001819	synonymous_variant	22907	exon7			AGTATTCGACCAG	AB020697	CCDS2759.1	3p24.3-p22.1	2013-07-16	2013-07-16	2003-06-13	ENSG00000132153	ENSG00000132153		"DEAH-boxes"	16716	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 30", "DEAH (Asp-Glu-Ala-His) box polypeptide 30"	DDX30		10048485, 18022663	Standard	NM_138615		Approved	KIAA0890, FLJ11214	uc003cru.3	Q7L2E3	OTTHUMG00000133522	ENST00000445061.1:c.520C>A	chr3.hg19:g.47882520C>A		39.0	0.0	.		46.0	4.0	.	NM_138615	A8K5F1|O94965|Q7Z753|Q96CH4|Q9NUQ0	Silent	SNP	ENST00000445061.1	hg19	CCDS2759.1																																																																																			.	.	.	none		0.597	DHX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257495.2	NM_138615		A	47882520	C	A	47882520	2	1	146	1	0	0	0	0	0	0	0	1	4506	876	31	4		4	DHX30	3	47882520	Silent	SNP	C	TCGA-DW-5561-01A-01D-1589-08	36525573	47882520	150139910	10	8739											
ATP13A4	84239	hgsc.bcm.edu	37	chr3	193132518	193132518	+	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	gtctgaaaggcaccagcttaGggtaggcaccattcagattc	11	9	11	10	0	2	2	1	1	1	1	3	2	2	2	2	3	1	4	2	3	3	4			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr3:193132518G>C	ENST00000342695.4	-	26	3186	c.2864C>G	c.(2863-2865)cCt>cGt	p.P955R	ATP13A4_ENST00000482964.1_5'Flank|ATP13A4_ENST00000400270.2_5'UTR|ATP13A4_ENST00000392443.3_Missense_Mutation_p.P936R	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	955						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)		CACCAGCTTAGGGTAGGCACC	0.408																																					p.P955R		Atlas-SNP	.											.	ATP13A4	154	.	0			c.C2864G						PASS	.						76	69	72					3																	193132518		2203	4300	6503	SO:0001583	missense	84239	exon26			AGCTTAGGGTAGG	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.2864C>G	chr3.hg19:g.193132518G>C	ENSP00000339182:p.Pro955Arg	89.0	0.0	.		68.0	23.0	.	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Missense_Mutation	SNP	ENST00000342695.4	hg19	CCDS3304.2	.	.	.	.	.	.	.	.	.	.	G	19.55	3.847905	0.71603	.	.	ENSG00000127249	ENST00000392443;ENST00000342695	D;D	0.89485	-2.52;-2.52	6.02	6.02	0.97574	.	0.000000	0.64402	D	0.000001	D	0.94082	0.8103	M	0.78637	2.42	0.80722	D	1	D	0.69078	0.997	D	0.67103	0.949	D	0.92892	0.6332	10	0.40728	T	0.16	-24.9732	18.0311	0.89285	0.0:0.0:1.0:0.0	.	955	Q4VNC1	AT134_HUMAN	R	936;955	ENSP00000376238:P936R;ENSP00000339182:P955R	ENSP00000339182:P955R	P	-	2	0	ATP13A4	194615212	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.191000	0.65110	2.857000	0.98124	0.650000	0.86243	CCT	.	.	.	none		0.408	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279		C	193132518	G	C	193132518	3	2	146	1	0	0	0	0	1	0	0	0	1126	1000	35	4	746	4	ATP13A4	3	193132518	Missense_Mutation	SNP	G	TCGA-DW-5561-01A-01D-1589-08	145249998	193132518	4889912	11	8740											
PARM1	25849	hgsc.bcm.edu	37	chr4	75937687	75937687	+	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	cctttgtctgtttctcttccGacaaacattgtaccaccgac	8	14	5	14	2	2	0	0	0	2	0	4	2	3	0	4	0	2	2	4	0	2	5			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr4:75937687G>C	ENST00000307428.7	+	2	308	c.96G>C	c.(94-96)ccG>ccC	p.P32P	PARM1_ENST00000513238.1_Intron|RP11-44F21.2_ENST00000513770.1_RNA	NM_015393.3	NP_056208.2	Q6UWI2	PARM1_HUMAN	prostate androgen-regulated mucin-like protein 1	32					positive regulation of telomerase activity (GO:0051973)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|plasma membrane (GO:0005886)				cervix(1)|endometrium(2)|lung(4)|ovary(1)	8						TTTCTCTTCCGACAAACATTG	0.488																																					p.P32P		Atlas-SNP	.											PARM1_ENST00000307428,colon,carcinoma,0,3	PARM1	52	.	0			c.G96C						PASS	.																																			SO:0001819	synonymous_variant	25849	exon2			TCTTCCGACAAAC	AK022311	CCDS47077.1	4q13.3-q21.3	2010-02-17	2009-09-28		ENSG00000169116	ENSG00000169116			24536	protein-coding gene	gene with protein product	"Prostatic androgen-repressed message 1", "Castration-induced prostatic apoptosis-related protein 1", "WSC4, cell wall integrity and stress response component 4 homolog (S. cerevisiae)"					10499539, 12772192, 18027867	Standard	NM_015393		Approved	DKFZP564O0823, Cipar1, WSC4	uc003hih.2	Q6UWI2	OTTHUMG00000160827	ENST00000307428.7:c.96G>C	chr4.hg19:g.75937687G>C		81.0	0.0	.		67.0	32.0	.	NM_015393	B3KMQ9|Q96DV8|Q9Y4S1	Silent	SNP	ENST00000307428.7	hg19	CCDS47077.1																																																																																			.	.	.	none		0.488	PARM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362494.1	NM_015393		C	75937687	G	C	75937687	2	2	146	1	0	0	0	0	0	0	0	1	11459	1045	37	4		4	PARM1	4	75937687	Silent	SNP	G	TCGA-DW-5561-01A-01D-1589-08		75937687	115216589	12	8741											
ENPEP	2028	hgsc.bcm.edu	37	chr4	111397845	111397845	+	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	cggacagtggaaaaactttcGactgccggacttcgtcaacc	11	8	10	12	4	1	0	1	0	0	0	3	4	1	3	2	3	3	0	2	3	3	2			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr4:111397845G>A	ENST00000265162.5	+	1	617	c.275G>A	c.(274-276)cGa>cAa	p.R92Q		NM_001977.3	NP_001968.3	Q07075	AMPE_HUMAN	glutamyl aminopeptidase (aminopeptidase A)	92					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)		AAAAACTTTCGACTGCCGGAC	0.612																																					p.R92Q		Atlas-SNP	.											.	ENPEP	149	.	0			c.G275A						PASS	.						75	80	78					4																	111397845		2203	4300	6503	SO:0001583	missense	2028	exon1			ACTTTCGACTGCC	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.275G>A	chr4.hg19:g.111397845G>A	ENSP00000265162:p.Arg92Gln	133.0	0.0	.		93.0	36.0	.	NM_001977	Q504U2	Missense_Mutation	SNP	ENST00000265162.5	hg19	CCDS3691.1	.	.	.	.	.	.	.	.	.	.	G	19.64	3.865651	0.71949	.	.	ENSG00000138792	ENST00000265162	T	0.03181	4.02	5.83	5.83	0.93111	.	0.098719	0.64402	D	0.000003	T	0.23210	0.0561	M	0.89785	3.06	0.58432	D	0.999999	D	0.89917	1.0	D	0.76575	0.988	T	0.00599	-1.1651	10	0.87932	D	0	.	14.2874	0.66254	0.0708:0.0:0.9292:0.0	.	92	Q07075	AMPE_HUMAN	Q	92	ENSP00000265162:R92Q	ENSP00000265162:R92Q	R	+	2	0	ENPEP	111617294	1.000000	0.71417	1.000000	0.80357	0.002000	0.02628	7.579000	0.82511	2.758000	0.94735	0.561000	0.74099	CGA	.	.	.	none		0.612	ENPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255747.2			A	111397845	G	A	111397845	3	1	146	1	0	0	0	0	1	0	0	0	5130	1058	37	1	277	1	ENPEP	4	111397845	Missense_Mutation	SNP	G	TCGA-DW-5561-01A-01D-1589-08	35460158	111397845	79756431	13	8742											
ADCY2	108	hgsc.bcm.edu	37	chr5	7820695	7820695	+	Missense_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	caggtattaaccatggacctGtgatagctggtgtgattgga	10	12	13	6	0	0	2	0	2	0	0	0	4	0	4	2	4	2	2	2	4	3	4			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr5:7820695G>A	ENST00000338316.4	+	24	3105	c.3016G>A	c.(3016-3018)Gtg>Atg	p.V1006M	ADCY2_ENST00000537121.1_Missense_Mutation_p.V826M	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	1006					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						CCATGGACCTGTGATAGCTGG	0.428																																					p.V1006M		Atlas-SNP	.											.	ADCY2	337	.	0			c.G3016A						PASS	.						107	95	99					5																	7820695		2203	4300	6503	SO:0001583	missense	108	exon24			GGACCTGTGATAG	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.3016G>A	chr5.hg19:g.7820695G>A	ENSP00000342952:p.Val1006Met	54.0	0.0	.		63.0	33.0	.	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	hg19	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	G	25.4	4.632738	0.87660	.	.	ENSG00000078295	ENST00000338316;ENST00000541993;ENST00000537121	T;T	0.48522	0.81;0.81	5.19	5.19	0.71726	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.85682	D	0.000000	T	0.81437	0.4822	H	0.98178	4.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.88857	0.3323	10	0.87932	D	0	.	18.7434	0.91782	0.0:0.0:1.0:0.0	.	826;1006	B7Z2C1;Q08462	.;ADCY2_HUMAN	M	1006;839;826	ENSP00000342952:V1006M;ENSP00000444803:V826M	ENSP00000342952:V1006M	V	+	1	0	ADCY2	7873695	1.000000	0.71417	0.968000	0.41197	0.900000	0.52787	9.565000	0.98154	2.430000	0.82344	0.655000	0.94253	GTG	.	.	.	none		0.428	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		A	7820695	G	A	7820695	3	1	146	1	0	0	0	0	1	0	0	0	294	1377	48	2	3110	2	ADCY2	5	7820695	Missense_Mutation	SNP	G	TCGA-DW-5561-01A-01D-1589-08		7820695	173094565	14	8743											
CMBL	134147	hgsc.bcm.edu	37	chr5	10288604	10288609	+	In_Frame_Del	DEL	AAGGCT	AAGGCT	-																															ccagtcgccagaggggtcccAaggctcttgccctacaaaga																										TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	AAGGCT	AAGGCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr5:10288604_10288609delAAGGCT	ENST00000296658.3	-	3	668_673	c.248_253delAGCCTT	c.(247-255)gagccttgg>ggg	p.83_85EPW>G	CMBL_ENST00000510532.1_5'UTR	NM_138809.3	NP_620164.1	Q96DG6	CMBL_HUMAN	carboxymethylenebutenolidase homolog (Pseudomonas)	83						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(1)|lung(9)|skin(1)|stomach(1)	13						GAGGGGTCCCAAGGCTCTTGCCCTAC	0.456																																					p.83_85del		Atlas-INDEL	.											.	CMBL	24	.	0			c.249_254del						PASS	.																																			SO:0001651	inframe_deletion	134147	exon3			.		CCDS3878.1	5p15.2	2010-06-25	2006-09-12		ENSG00000164237	ENSG00000164237	3.1.-.-		25090	protein-coding gene	gene with protein product		613379	"carboxymethylenebutenolidase-like (Pseudomonas)"			3804974, 20177059	Standard	NM_138809		Approved	FLJ23617	uc003jes.3	Q96DG6	OTTHUMG00000131043	ENST00000296658.3:c.248_253delAGCCTT	chr5.hg19:g.10288604_10288609delAAGGCT	ENSP00000296658:p.Glu83_Trp85delinsGly	131.0	0.0	0		101.0	32.0	0.316832	NM_138809	D3DTC7|Q8TED6	In_Frame_Del	DEL	ENST00000296658.3	hg19	CCDS3878.1																																																																																			.	.	.	none		0.456	CMBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253689.1	NM_138809		-	10288609	AAGGCT	-	10288604	7	5	146	1	0	1	0	1	0	0	0	0	3578	130	5	0	500	0	CMBL	5	10288604	In_Frame_Del	DEL	AAGGCT	TCGA-DW-5561-01A-01D-1589-08	2467909	10288604	170626656	15	8744											
RPS14	6208	hgsc.bcm.edu	37	chr5	149827271	149827271	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgatgacctgttcttccttcTtttccttcccctttcgaggt	3	19	6	13	1	2	2	0	2	2	0	6	3	5	2	5	1	0	1	5	1	0	7			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr5:149827271T>C	ENST00000401695.3	-	2	72	c.26A>G	c.(25-27)aAg>aGg	p.K9R	RPS14_ENST00000407193.1_Missense_Mutation_p.K9R|RPS14_ENST00000312037.5_Missense_Mutation_p.K9R			P62263	RS14_HUMAN	ribosomal protein S14	9					cellular protein metabolic process (GO:0044267)|erythrocyte differentiation (GO:0030218)|gene expression (GO:0010467)|maturation of SSU-rRNA (GO:0030490)|mRNA metabolic process (GO:0016071)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translation (GO:0006417)|ribosomal small subunit assembly (GO:0000028)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	mRNA 5'-UTR binding (GO:0048027)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)|translation regulator activity (GO:0045182)			central_nervous_system(1)|lung(1)|skin(1)	3		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTCTTCCTTCTTTTCCTTCCC	0.443																																					p.K9R		Atlas-SNP	.											.	RPS14	11	.	0			c.A26G						PASS	.						125	111	116					5																	149827271		2203	4300	6503	SO:0001583	missense	6208	exon2			TCCTTCTTTTCCT		CCDS4307.1	5q31-q33	2012-10-02			ENSG00000164587	ENSG00000164587		"S ribosomal proteins"	10387	protein-coding gene	gene with protein product	"emetine resistance", "40S ribosomal protein S14"	130620				3785212, 1549121	Standard	XM_006714790		Approved	EMTB, S14	uc003lsj.3	P62263	OTTHUMG00000130080	ENST00000401695.3:c.26A>G	chr5.hg19:g.149827271T>C	ENSP00000385958:p.Lys9Arg	143.0	0.0	.		148.0	67.0	.	NM_001025071	B2R5G5|D3DQG5|P06366|Q5BJI0	Missense_Mutation	SNP	ENST00000401695.3	hg19	CCDS4307.1	.	.	.	.	.	.	.	.	.	.	T	16.51	3.142739	0.57044	.	.	ENSG00000164587	ENST00000401695;ENST00000407193;ENST00000521466;ENST00000312037	.	.	.	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.43656	0.1257	N	0.22421	0.69	0.80722	D	1	B	0.10296	0.003	B	0.08055	0.003	T	0.28332	-1.0047	9	0.23891	T	0.37	.	15.1102	0.72349	0.0:0.0:0.0:1.0	.	9	P62263	RS14_HUMAN	R	9	.	ENSP00000311028:K9R	K	-	2	0	RPS14	149807464	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.649000	0.83500	2.023000	0.59567	0.455000	0.32223	AAG	.	.	.	none		0.443	RPS14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252373.1	NM_001025071		C	149827271	T	C	149827271	3	2	146	1	0	0	0	0	1	0	0	0	13637	1609	56	3	445	3	RPS14	5	149827271	Missense_Mutation	SNP	T	TCGA-DW-5561-01A-01D-1589-08	139538667	149827271	31087989	16	8745											
CPEB4	80315	hgsc.bcm.edu	37	chr5	173317605	173317605	+	Frame_Shift_Del	DEL	G	G	-																															tccgtggagcagctaccagaGtccgtcaccaacaccctcct																								rs372054497		TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr5:173317605delG	ENST00000265085.5	+	1	2323	c.869delG	c.(868-870)agtfs	p.S290fs	CPEB4_ENST00000517880.1_5'Flank|CPEB4_ENST00000334035.5_Frame_Shift_Del_p.S290fs|CPEB4_ENST00000522336.1_5'Flank|CPEB4_ENST00000519835.1_Frame_Shift_Del_p.S290fs|CPEB4_ENST00000520867.1_Frame_Shift_Del_p.S290fs	NM_030627.2	NP_085130.2	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding protein 4	290					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)			AGCTACCAGAGTCCGTCACCA	0.572																																					p.S290fs		Atlas-INDEL	.											.	CPEB4	54	.	0			c.868delA						PASS	.						148	161	157					5																	173317605		2203	4300	6503	SO:0001589	frameshift_variant	80315	exon1			.	BX538213	CCDS4390.1	5q21	2013-02-12			ENSG00000113742	ENSG00000113742		"RNA binding motif (RRM) containing"	21747	protein-coding gene	gene with protein product		610607				11214970, 12672660	Standard	NM_030627		Approved	KIAA1673	uc003mcs.4	Q17RY0	OTTHUMG00000130541	ENST00000265085.5:c.869delG	chr5.hg19:g.173317605delG	ENSP00000265085:p.Ser290fs	376.0	0.0	0		277.0	108.0	0.389892	NM_030627	B7ZLQ7|Q7Z310|Q8N405|Q9C0J0	Frame_Shift_Del	DEL	ENST00000265085.5	hg19	CCDS4390.1																																																																																			.	.	.	none		0.572	CPEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252964.2	NM_030627		-	173317605	G	-	173317605	7	5	146	1	0	1	0	1	0	0	0	0	3805	1029	36	0	871	0	CPEB4	5	173317605	Frame_Shift_Del	DEL	G	TCGA-DW-5561-01A-01D-1589-08	23490334	173317605	7597655	17	8746											
PRPF4B	8899	hgsc.bcm.edu	37	chr6	4047415	4047415	+	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	taatttcctttaaggttcatCtcagaagaagttgttggcac	11	15	8	7	0	2	2	2	0	1	2	4	2	3	2	1	2	0	4	1	2	4	7			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr6:4047415C>G	ENST00000337659.6	+	7	1968	c.1868C>G	c.(1867-1869)tCt>tGt	p.S623C	PRPF4B_ENST00000538861.1_Missense_Mutation_p.S609C	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN	pre-mRNA processing factor 4B	623					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)				TAAGGTTCATCTCAGAAGAAG	0.284																																					p.S623C		Atlas-SNP	.											.	PRPF4B	140	.	0			c.C1868G						PASS	.						154	146	148					6																	4047415		2202	4298	6500	SO:0001583	missense	8899	exon7			GTTCATCTCAGAA	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.1868C>G	chr6.hg19:g.4047415C>G	ENSP00000337194:p.Ser623Cys	128.0	0.0	.		195.0	67.0	.	NM_003913	A8K5C9|Q5D0F6|Q5TAY8|Q8IVC3|Q8TDP2|Q96QT7|Q9UEE6	Missense_Mutation	SNP	ENST00000337659.6	hg19	CCDS4488.1	.	.	.	.	.	.	.	.	.	.	C	18.21	3.572647	0.65765	.	.	ENSG00000112739	ENST00000337659;ENST00000538861	T;T	0.68479	-0.33;-0.32	5.51	4.63	0.57726	.	0.380183	0.25372	N	0.031153	T	0.31167	0.0788	N	0.14661	0.345	0.34271	D	0.681056	B	0.20164	0.042	B	0.21917	0.037	T	0.19582	-1.0301	10	0.51188	T	0.08	.	9.3135	0.37919	0.1456:0.7823:0.0:0.0721	.	623	Q13523	PRP4B_HUMAN	C	623;609	ENSP00000337194:S623C;ENSP00000439331:S609C	ENSP00000337194:S623C	S	+	2	0	PRPF4B	3992414	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.825000	0.48096	1.424000	0.47217	0.650000	0.86243	TCT	.	.	.	none		0.284	PRPF4B-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314018.2			G	4047415	C	G	4047415	3	3	146	1	0	0	0	0	1	0	0	0	12583	913	32	4	1894	4	PRPF4B	6	4047415	Missense_Mutation	SNP	C	TCGA-DW-5561-01A-01D-1589-08		4047415	167067652	18	8747											
KCND2	3751	hgsc.bcm.edu	37	chr7	119915491	119915491	+	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	tgagtatcatcgacgtggtgGccatcctgccttattacatt	8	14	9	10	2	1	1	1	1	0	0	3	2	2	1	3	2	2	1	3	2	3	4			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr7:119915491G>T	ENST00000331113.4	+	1	1770	c.805G>T	c.(805-807)Gcc>Tcc	p.A269S		NM_012281.2	NP_036413.1	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 2	269					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)	CGACGTGGTGGCCATCCTGCC	0.512																																					p.A269S		Atlas-SNP	.											.	KCND2	194	.	0			c.G805T						PASS	.						172	142	152					7																	119915491		2203	4300	6503	SO:0001583	missense	3751	exon1			GTGGTGGCCATCC	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.805G>T	chr7.hg19:g.119915491G>T	ENSP00000333496:p.Ala269Ser	82.0	0.0	.		102.0	28.0	.	NM_012281	O95012|O95021|Q2TBD3|Q9UBY7|Q9UN98|Q9UNH9	Missense_Mutation	SNP	ENST00000331113.4	hg19	CCDS5776.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.348475	0.82132	.	.	ENSG00000184408	ENST00000331113	D	0.98493	-4.96	5.27	5.27	0.74061	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.97084	0.9047	N	0.16166	0.38	0.80722	D	1	P	0.46578	0.88	P	0.57620	0.824	D	0.96477	0.9353	9	.	.	.	.	19.2668	0.93990	0.0:0.0:1.0:0.0	.	269	Q9NZV8	KCND2_HUMAN	S	269	ENSP00000333496:A269S	.	A	+	1	0	KCND2	119702727	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.813000	0.99286	2.636000	0.89361	0.557000	0.71058	GCC	.	.	.	none		0.512	KCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346996.1	NM_012281		T	119915491	G	T	119915491	3	4	146	1	0	0	0	0	1	0	0	0	8026	1203	42	4	807	4	KCND2	7	119915491	Missense_Mutation	SNP	G	TCGA-DW-5561-01A-01D-1589-08		119915491	39223172	19	8748											
CDKN2B	1030	hgsc.bcm.edu	37	chr9	22006244	22006244	+	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	cgggcgctgcccatcatcatGacctgccagagagagcagag	10	5	13	13	2	2	4	2	1	0	3	2	5	2	4	3	1	3	2	3	1	0	0			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr9:22006244G>A	ENST00000276925.6	-	2	568	c.159C>T	c.(157-159)gtC>gtT	p.V53V	CDKN2B-AS1_ENST00000582072.1_RNA|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2B-AS1_ENST00000428597.1_RNA|CDKN2B-AS1_ENST00000582301.1_RNA|CDKN2B-AS1_ENST00000577551.1_RNA|CDKN2B-AS1_ENST00000580576.1_RNA|CDKN2B-AS1_ENST00000584816.1_RNA|CDKN2B-AS1_ENST00000455933.2_RNA|CDKN2B-AS1_ENST00000585267.1_RNA|CDKN2B-AS1_ENST00000581051.1_RNA|CDKN2B-AS1_ENST00000584351.1_RNA|CDKN2B-AS1_ENST00000584020.1_RNA|CDKN2B-AS1_ENST00000583719.1_RNA|CDKN2B-AS1_ENST00000468603.2_RNA|CDKN2B-AS1_ENST00000580467.1_RNA|CDKN2B_ENST00000380142.4_3'UTR|CDKN2B-AS1_ENST00000584637.1_RNA	NM_004936.3|NM_078487.2	NP_004927.2|NP_511042.1	P42772	CDN2B_HUMAN	cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)	53					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)		CCATCATCATGACCTGCCAGA	0.647																																					p.V53V		Atlas-SNP	.											.	CDKN2B	12	.	2	Whole gene deletion(2)	lung(2)	c.C159T						PASS	.						14	17	16					9																	22006244		2175	4259	6434	SO:0001819	synonymous_variant	1030	exon2			CATCATGACCTGC	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.159C>T	chr9.hg19:g.22006244G>A		49.0	0.0	.		22.0	8.0	.	NM_004936	O15125|Q6FI09	Silent	SNP	ENST00000276925.6	hg19	CCDS6512.1																																																																																			.	.	.	none		0.647	CDKN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051932.2	NM_004936		A	22006244	G	A	22006244	2	1	146	1	0	0	0	0	0	0	0	1	3166	1277	45	2		2	CDKN2B	9	22006244	Silent	SNP	G	TCGA-DW-5561-01A-01D-1589-08		22006244	119207187	20	8749											
NIPSNAP3B	55335	hgsc.bcm.edu	37	chr9	107531256	107531256	+	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	gataaacaagagacggaaatTacttacctgataccatggtc	16	9	8	8	1	0	2	0	1	0	1	1	5	0	3	2	2	4	0	2	2	7	4			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr9:107531256T>A	ENST00000374762.3	+	3	455	c.384T>A	c.(382-384)atT>atA	p.I128I	NIPSNAP3B_ENST00000461177.1_3'UTR	NM_018376.2	NP_060846.2	Q9BS92	NPS3B_HUMAN	nipsnap homolog 3B (C. elegans)	128										breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	11						AGACGGAAATTACTTACCTGA	0.383																																					p.I128I		Atlas-SNP	.											.	NIPSNAP3B	22	.	0			c.T384A						PASS	.						79	76	77					9																	107531256		2203	4300	6503	SO:0001819	synonymous_variant	55335	exon3			GGAAATTACTTAC	BC017914	CCDS6761.1	9q31.3	2003-11-27			ENSG00000165028	ENSG00000165028			23641	protein-coding gene	gene with protein product		608872				12477932	Standard	NM_018376		Approved	FLJ11275	uc004bci.3	Q9BS92	OTTHUMG00000020414	ENST00000374762.3:c.384T>A	chr9.hg19:g.107531256T>A		95.0	0.0	.		77.0	38.0	.	NM_018376	Q5VX30|Q9NUM2	Silent	SNP	ENST00000374762.3	hg19	CCDS6761.1																																																																																			.	.	.	none		0.383	NIPSNAP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053486.1	NM_018376		A	107531256	T	A	107531256	2	1	146	1	0	0	0	0	0	0	0	1	10438	1742	61	5		5	NIPSNAP3B	9	107531256	Silent	SNP	T	TCGA-DW-5561-01A-01D-1589-08	85525012	107531256	33682175	21	8750											
CEP110	11064	hgsc.bcm.edu	37	chr9	123888062	123888062	+	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	tcagtgggttgcaagaatacCtggggaccattaaaggccag	12	8	13	8	0	1	1	1	0	0	1	1	2	1	2	3	4	2	2	3	4	5	3			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr9:123888062C>A	ENST00000373855.1	+	14	2133	c.1873C>A	c.(1873-1875)Ctg>Atg	p.L625M	CNTRL_ENST00000373847.1_Missense_Mutation_p.L73M|CNTRL_ENST00000238341.5_Missense_Mutation_p.L625M|CNTRL_ENST00000373850.1_Missense_Mutation_p.L73M			Q7Z7A1	CNTRL_HUMAN	centriolin	625					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						GCAAGAATACCTGGGGACCAT	0.458																																					p.L625M		Atlas-SNP	.											.	CNTRL	161	.	0			c.C1873A						PASS	.						120	123	122					9																	123888062		2203	4300	6503	SO:0001583	missense	11064	exon12			GAATACCTGGGGA	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.1873C>A	chr9.hg19:g.123888062C>A	ENSP00000362962:p.Leu625Met	146.0	0.0	.		124.0	5.0	.	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	hg19	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.944003	0.73672	.	.	ENSG00000119397	ENST00000373855;ENST00000238341;ENST00000454238;ENST00000373851;ENST00000373850;ENST00000373847	T;T;T;T	0.65549	0.25;0.25;-0.16;0.05	5.59	4.69	0.59074	.	.	.	.	.	T	0.69214	0.3086	L	0.34521	1.04	0.37252	D	0.906593	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.998;0.999;0.997	T	0.74237	-0.3730	9	0.51188	T	0.08	.	13.301	0.60326	0.0:0.9245:0.0:0.0755	.	625;625;625	B2RP65;F5GZN0;Q7Z7A1	.;.;CNTRL_HUMAN	M	625;625;625;107;73;73	ENSP00000362962:L625M;ENSP00000238341:L625M;ENSP00000362956:L73M;ENSP00000362953:L73M	ENSP00000238341:L625M	L	+	1	2	CNTRL	122927883	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.004000	0.40854	1.349000	0.45751	0.650000	0.86243	CTG	.	.	.	none		0.458	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018		A	123888062	C	A	123888062	3	1	146	1	0	0	0	0	1	0	0	0	3247	680	24	4	1919	4	CEP110	9	123888062	Missense_Mutation	SNP	C	TCGA-DW-5561-01A-01D-1589-08	16356806	123888062	17325369	22	8751											
C10orf95	79946	hgsc.bcm.edu	37	chr10	104211148	104211149	+	Frame_Shift_Ins	INS	-	-	C																															gactccccactcacttgtctINSccttcagccttggggagccg																								rs144830667		TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr10:104211148_104211149insC	ENST00000239125.1	-	1	151_152	c.77_78insG	c.(76-78)ggafs	p.G26fs	RP11-18I14.10_ENST00000473970.2_RNA|RP11-18I14.10_ENST00000594818.1_RNA|RP11-18I14.10_ENST00000596045.1_RNA|RP11-18I14.10_ENST00000596366.1_RNA|RP11-18I14.10_ENST00000494270.2_RNA|RP11-18I14.10_ENST00000492465.2_RNA	NM_024886.1	NP_079162.1	Q9H7T3	CJ095_HUMAN	chromosome 10 open reading frame 95	26										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)		CTCACTTGTCTCCTTCAGCCTT	0.639																																					p.G26fs		Atlas-INDEL	.											.	C10orf95	5	.	0			c.78_79insG						PASS	.																																			SO:0001589	frameshift_variant	79946	exon1			.	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.78dupG	chr10.hg19:g.104211150_104211150dupC	ENSP00000239125:p.Gly26fs	55.0	0.0	0		42.0	18.0	0.428571	NM_024886	A0AVQ7	Frame_Shift_Ins	INS	ENST00000239125.1	hg19	CCDS7534.1																																																																																			.	.	.	none		0.639	C10orf95-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050065.1	NM_024886		C	104211149	-	C	104211148	7	5	146	1	0	1	1	0	0	0	0	0	1628	1538	54	0	703	0	C10orf95	10	104211148	Frame_Shift_Ins	INS	-	TCGA-DW-5561-01A-01D-1589-08		104211148	31323599	23	8752											
OR4A16	81327	hgsc.bcm.edu	37	chr11	55110797	55110797	+	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	ttgtgacaatggtgggaaacCtcctcatttgggtgactact	9	13	11	8	0	1	2	1	2	0	0	2	3	2	3	2	3	2	0	2	3	3	3			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr11:55110797C>T	ENST00000314721.2	+	1	171	c.121C>T	c.(121-123)Ctc>Ttc	p.L41F		NM_001005274.1	NP_001005274.1	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A, member 16	41						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						GGTGGGAAACCTCCTCATTTG	0.428																																					p.L41F		Atlas-SNP	.											OR4A16,right_upper_lobe,carcinoma,0,1	OR4A16	120	.	0			c.C121T						PASS	.						122	115	117					11																	55110797		2201	4296	6497	SO:0001583	missense	81327	exon1			GGAAACCTCCTCA	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.121C>T	chr11.hg19:g.55110797C>T	ENSP00000325128:p.Leu41Phe	202.0	0.0	.		180.0	64.0	.	NM_001005274	Q6IFL3	Missense_Mutation	SNP	ENST00000314721.2	hg19	CCDS31499.1	.	.	.	.	.	.	.	.	.	.	c	7.100	0.573809	0.13623	.	.	ENSG00000181961	ENST00000314721	T	0.00438	7.42	2.41	1.46	0.22682	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00637	0.0021	L	0.55017	1.72	0.09310	N	0.999999	D	0.57899	0.981	D	0.63597	0.916	T	0.56938	-0.7896	9	0.37606	T	0.19	.	6.7077	0.23260	0.0:0.8361:0.0:0.1639	.	41	Q8NH70	O4A16_HUMAN	F	41	ENSP00000325128:L41F	ENSP00000325128:L41F	L	+	1	0	OR4A16	54867373	0.000000	0.05858	0.772000	0.31596	0.023000	0.10783	-0.898000	0.04105	1.353000	0.45828	0.185000	0.17295	CTC	.	.	.	none		0.428	OR4A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391160.1	NM_001005274		T	55110797	C	T	55110797	3	4	146	1	0	0	0	0	1	0	0	0	11048	681	24	2	123	2	OR4A16	11	55110797	Missense_Mutation	SNP	C	TCGA-DW-5561-01A-01D-1589-08		55110797	79895719	24	8753											
ETS1	2113	hgsc.bcm.edu	37	chr11	128360461	128360461	+	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	gttaatagtgggacatctgcAcattccatatctgcatgaaa	13	12	8	8	0	2	1	0	1	2	0	3	2	3	2	1	1	2	3	1	1	4	4			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr11:128360461A>T	ENST00000319397.6	-	2	402	c.93T>A	c.(91-93)tgT>tgA	p.C31*	ETS1_ENST00000345075.4_Nonsense_Mutation_p.C31*|ETS1_ENST00000531611.1_Nonsense_Mutation_p.C31*|ETS1_ENST00000535549.1_Intron|ETS1_ENST00000392668.4_Nonsense_Mutation_p.C75*|ETS1_ENST00000526145.2_Nonsense_Mutation_p.C31*	NM_005238.3	NP_005229.1	P14921	ETS1_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 1	31					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)		GGACATCTGCACATTCCATAT	0.363																																					p.C75X		Atlas-SNP	.											.	ETS1	123	.	0			c.T225A						PASS	.						110	104	106					11																	128360461		2201	4297	6498	SO:0001587	stop_gained	2113	exon4			ATCTGCACATTCC		CCDS8475.1, CCDS44767.1, CCDS53724.1	11q23.3	2013-07-09	2013-07-09		ENSG00000134954	ENSG00000134954			3488	protein-coding gene	gene with protein product	"Avian erythroblastosis virus E26 (v-ets) oncogene homolog-1", "ets protein"	164720		EWSR2		1522903	Standard	NM_005238		Approved	FLJ10768, ETS-1	uc001qej.2	P14921	OTTHUMG00000165799	ENST00000319397.6:c.93T>A	chr11.hg19:g.128360461A>T	ENSP00000324578:p.Cys31*	76.0	0.0	.		68.0	26.0	.	NM_001143820	A9UL17|F5GYX9|Q14278|Q16080|Q6N087|Q96AC5	Nonsense_Mutation	SNP	ENST00000319397.6	hg19	CCDS8475.1	.	.	.	.	.	.	.	.	.	.	A	38	6.929848	0.97944	.	.	ENSG00000134954	ENST00000345075;ENST00000392668;ENST00000531611;ENST00000319397;ENST00000526145	.	.	.	5.65	2.0	0.26442	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	9.4666	0.38817	0.796:0.0:0.204:0.0	.	.	.	.	X	31;75;31;31;31	.	ENSP00000324578:C31X	C	-	3	2	ETS1	127865671	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.583000	0.36579	0.084000	0.17077	-0.376000	0.06991	TGT	.	.	.	none		0.363	ETS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386269.2	NM_005238		T	128360461	A	T	128360461	4	4	146	1	0	0	0	0	0	1	0	0	5277	157	6	5	1260	5	ETS1	11	128360461	Nonsense_Mutation	SNP	A	TCGA-DW-5561-01A-01D-1589-08	73249664	128360461	6646055	25	8754											
SLC6A13	6540	hgsc.bcm.edu	37	chr12	335609	335609	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcctgagacatgaagcccAggatggagaagatggcaaag	14	5	14	8	0	0	4	0	2	0	3	1	7	1	5	2	3	1	2	2	3	3	0			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr12:335609A>G	ENST00000343164.4	-	9	1059	c.1007T>C	c.(1006-1008)cTg>cCg	p.L336P	SLC6A13_ENST00000539668.1_5'Flank|SLC6A13_ENST00000445055.2_Missense_Mutation_p.L244P	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	336					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)			CATGAAGCCCAGGATGGAGAA	0.622																																					p.L336P		Atlas-SNP	.											.	SLC6A13	62	.	0			c.T1007C						PASS	.						64	58	60					12																	335609		2203	4300	6503	SO:0001583	missense	6540	exon9			AAGCCCAGGATGG	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.1007T>C	chr12.hg19:g.335609A>G	ENSP00000339260:p.Leu336Pro	58.0	0.0	.		77.0	46.0	.	NM_016615	B4DJL1|Q8TCC2|Q8WW56	Missense_Mutation	SNP	ENST00000343164.4	hg19	CCDS8502.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.496459	0.85069	.	.	ENSG00000010379	ENST00000445055;ENST00000313154;ENST00000343164	D;D	0.83075	-1.68;-1.68	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	D	0.95462	0.8526	H	0.99634	4.67	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.995;0.998;0.996	D	0.97664	1.0162	10	0.87932	D	0	.	15.3028	0.73966	1.0:0.0:0.0:0.0	.	244;315;336	B4DJL1;B4DJS3;Q9NSD5	.;.;S6A13_HUMAN	P	244;315;336	ENSP00000407104:L244P;ENSP00000339260:L336P	ENSP00000318097:L315P	L	-	2	0	SLC6A13	205870	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.260000	0.95568	2.010000	0.58986	0.402000	0.26972	CTG	.	.	.	none		0.622	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615		G	335609	A	G	335609	3	3	146	1	0	0	0	0	1	0	0	0	14689	188	7	3	829	3	SLC6A13	12	335609	Missense_Mutation	SNP	A	TCGA-DW-5561-01A-01D-1589-08		335609	133516286	26	8755											
GAPDH	2597	hgsc.bcm.edu	37	chr12	6646478	6646485	+	Frame_Shift_Del	DEL	TGCCTCCT	TGCCTCCT	-																															tccctctttctttgcagcaaTgcctcctgcaccaccaactg																										TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	TGCCTCCT	TGCCTCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr12:6646478_6646485delTGCCTCCT	ENST00000229239.5	+	7	1113_1120	c.447_454delTGCCTCCT	c.(445-456)aatgcctcctgcfs	p.NASC149fs	GAPDH_ENST00000396856.1_Frame_Shift_Del_p.NASC74fs|RP5-940J5.9_ENST00000602946.1_RNA|GAPDH_ENST00000396861.1_Frame_Shift_Del_p.NASC149fs|GAPDH_ENST00000396859.1_Frame_Shift_Del_p.NASC149fs|GAPDH_ENST00000396858.1_Frame_Shift_Del_p.NASC107fs	NM_002046.4	NP_002037.2	P04406	G3P_HUMAN	glyceraldehyde-3-phosphate dehydrogenase	149					carbohydrate metabolic process (GO:0005975)|cellular response to interferon-gamma (GO:0071346)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of translation (GO:0017148)|neuron apoptotic process (GO:0051402)|peptidyl-cysteine S-trans-nitrosylation (GO:0035606)|protein stabilization (GO:0050821)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|GAIT complex (GO:0097452)|lipid particle (GO:0005811)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)|vesicle (GO:0031982)	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity (GO:0004365)|identical protein binding (GO:0042802)|microtubule binding (GO:0008017)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|peptidyl-cysteine S-nitrosylase activity (GO:0035605)			central_nervous_system(1)|cervix(1)|endometrium(1)|lung(4)	7						TTTGCAGCAATGCCTCCTGCACCACCAA	0.596																																					p.149_151del		Atlas-INDEL	.											.	GAPDH	20	.	0			c.446_453del						PASS	.																																			SO:0001589	frameshift_variant	2597	exon7			.	AF261085	CCDS8549.1, CCDS58201.1	12p13.31	2012-10-02		2005-05-06	ENSG00000111640	ENSG00000111640	1.2.1.12		4141	protein-coding gene	gene with protein product		138400		GAPD		3170585	Standard	NM_002046		Approved		uc001qop.2	P04406	OTTHUMG00000137379	ENST00000229239.5:c.447_454delTGCCTCCT	chr12.hg19:g.6646478_6646485delTGCCTCCT	ENSP00000229239:p.Asn149fs	37.0	0.0	0		43.0	10.0	0.232558	NM_002046	E7EUT4|P00354|Q53X65	Frame_Shift_Del	DEL	ENST00000229239.5	hg19	CCDS8549.1																																																																																			.	.	.	none		0.596	GAPDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268059.1	NM_002046		-	6646485	TGCCTCCT	-	6646478	7	5	146	1	0	1	0	1	0	0	0	0	6243	1461	51	0	469	0	GAPDH	12	6646478	Frame_Shift_Del	DEL	TGCCTCCT	TCGA-DW-5561-01A-01D-1589-08	6310869	6646478	127205417	27	8756											
TAS2R20	259295	hgsc.bcm.edu	37	chr12	11150353	11150353	+	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	taatttgatcagctgaggagAtcttttgtctcttgacccag	9	15	9	8	0	3	4	1	3	2	1	4	5	3	4	1	1	1	1	1	1	1	5			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr12:11150353A>T	ENST00000538986.1	-	1	121	c.122T>A	c.(121-123)aTc>aAc	p.I41N	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	41					sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						AGCTGAGGAGATCTTTTGTCT	0.378																																					p.I41N		Atlas-SNP	.											.	TAS2R20	17	.	0			c.T122A						PASS	.						42	47	45					12																	11150353		2203	4300	6503	SO:0001583	missense	259295	exon1			GAGGAGATCTTTT	AX097732, AF494236	CCDS8639.1	12p13.2	2012-08-22			ENSG00000255837	ENSG00000255837		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	19109	protein-coding gene	gene with protein product		613962	"taste receptor, type 2, member 49"	TAS2R49			Standard	NM_176889		Approved	T2R20, T2R56	uc001qzm.2	P59543	OTTHUMG00000162695	ENST00000538986.1:c.122T>A	chr12.hg19:g.11150353A>T	ENSP00000441624:p.Ile41Asn	75.0	0.0	.		100.0	63.0	.	NM_176889	P59549|Q2HIZ4|Q496D8|Q645X9	Missense_Mutation	SNP	ENST00000538986.1	hg19	CCDS8639.1	.	.	.	.	.	.	.	.	.	.	A	13.23	2.174148	0.38413	.	.	ENSG00000255837	ENST00000538986	T	0.00966	5.49	2.77	2.77	0.32553	.	2.834990	0.02303	U	0.071363	T	0.10252	0.0251	H	0.95437	3.67	0.09310	N	1	D	0.67145	0.996	D	0.75020	0.985	T	0.13469	-1.0508	10	0.87932	D	0	.	8.9683	0.35890	1.0:0.0:0.0:0.0	.	41	P59543	T2R20_HUMAN	N	41	ENSP00000441624:I41N	ENSP00000441624:I41N	I	-	2	0	TAS2R20	11041620	0.002000	0.14202	0.015000	0.15790	0.002000	0.02628	1.473000	0.35387	1.279000	0.44446	0.482000	0.46254	ATC	.	.	.	none		0.378	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	NM_176889		T	11150353	A	T	11150353	3	4	146	1	0	0	0	0	1	0	0	0	15583	333	12	5	811	5	TAS2R20	12	11150353	Missense_Mutation	SNP	A	TCGA-DW-5561-01A-01D-1589-08	4503875	11150353	122701542	28	8757											
TBC1D15	64786	hgsc.bcm.edu	37	chr12	72288466	72288466	+	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	tttttcttcctactgcatagAaaattaaaaaggacccttat	14	15	4	8	0	1	1	0	0	1	1	2	2	2	2	2	1	2	1	2	1	8	7			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr12:72288466A>T	ENST00000550746.1	+	8	773	c.709A>T	c.(709-711)Aaa>Taa	p.K237*	TBC1D15_ENST00000393309.3_5'UTR|TBC1D15_ENST00000319106.8_Splice_Site_p.K228*|TBC1D15_ENST00000485960.2_Splice_Site_p.K220*	NM_001146213.1|NM_022771.4	NP_001139685.2|NP_073608.4	Q8TC07	TBC15_HUMAN	TBC1 domain family, member 15	237					positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab GTPase activity (GO:0032313)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	Rab GTPase activator activity (GO:0005097)			NS(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						TACTGCATAGAAAATTAAAAA	0.323																																					p.K237X		Atlas-SNP	.											.	TBC1D15	99	.	0			c.A709T						PASS	.						39	42	41					12																	72288466		2199	4297	6496	SO:0001630	splice_region_variant	64786	exon8			GCATAGAAAATTA	AL157464	CCDS31858.1, CCDS53814.1, CCDS55849.1	12q15	2013-07-09			ENSG00000121749	ENSG00000121749			25694	protein-coding gene	gene with protein product		612662				16055087	Standard	NM_022771		Approved	FLJ12085, DKFZp761D0223	uc001swu.3	Q8TC07	OTTHUMG00000158553	ENST00000550746.1:c.709-1A>T	chr12.hg19:g.72288466A>T		90.0	0.0	.		97.0	51.0	.	NM_022771	B4DMT9|B9A6L6|J3KNI9|Q9HA83	Nonsense_Mutation	SNP	ENST00000550746.1	hg19	CCDS31858.1	.	.	.	.	.	.	.	.	.	.	A	37	6.212367	0.97380	.	.	ENSG00000121749	ENST00000550746;ENST00000491063;ENST00000319106;ENST00000485960	.	.	.	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-23.4381	15.2064	0.73183	1.0:0.0:0.0:0.0	.	.	.	.	X	237;121;228;220	.	.	K	+	1	0	TBC1D15	70574733	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	9.336000	0.96533	1.999000	0.58509	0.473000	0.43528	AAA	.	.	.	none		0.323	TBC1D15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351266.2	NM_022771	Nonsense_Mutation	T	72288466	A	T	72288466	5	4	146	1	0	0	0	0	0	0	1	0	15616	260	9	5	863	5	TBC1D15	12	72288466	Splice_Site	SNP	A	TCGA-DW-5561-01A-01D-1589-08	61138113	72288466	61563429	29	8758											
GALNT4	8693	hgsc.bcm.edu	37	chr12	89918277	89918277	+	Missense_Mutation	SNP	A	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	agatataggccactgttaaaAacgccagcagcaggcagctc	14	6	10	11	1	0	1	0	0	0	1	1	1	0	1	2	2	4	5	2	2	5	3			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr12:89918277A>C	ENST00000529983.2	-	1	306	c.50T>G	c.(49-51)tTt>tGt	p.F17C	POC1B-GALNT4_ENST00000547474.1_Intron|GALNT4_ENST00000413530.1_Intron|POC1B_ENST00000313546.3_Intron|POC1B_ENST00000549504.1_Intron|POC1B_ENST00000549035.1_Intron|RP11-734K2.4_ENST00000605233.1_RNA|POC1B_ENST00000541909.1_Intron|POC1B_ENST00000393179.4_Intron|POC1B-GALNT4_ENST00000548729.1_Intron	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	17					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						CACTGTTAAAAACGCCAGCAG	0.617											OREG0022018	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F17C		Atlas-SNP	.											.	GALNT4	38	.	0			c.T50G						PASS	.						27	30	29					12																	89918277		1943	4137	6080	SO:0001583	missense	8693	exon1			GTTAAAAACGCCA	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.50T>G	chr12.hg19:g.89918277A>C	ENSP00000436604:p.Phe17Cys	59.0	0.0	.	1271	56.0	24.0	.	NM_003774	B2R775|B4DMX6|O00208	Missense_Mutation	SNP	ENST00000529983.2	hg19	CCDS53817.1	.	.	.	.	.	.	.	.	.	.	A	12.83	2.054156	0.36277	.	.	ENSG00000257594	ENST00000529983	T	0.54071	0.59	5.68	1.85	0.25348	.	.	.	.	.	T	0.30135	0.0755	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16630	-1.0396	8	.	.	.	.	6.3543	0.21393	0.7004:0.1382:0.1614:0.0	.	17	Q8N4A0	GALT4_HUMAN	C	17	ENSP00000436604:F17C	.	F	-	2	0	GALNT4	88442408	0.499000	0.26083	0.374000	0.26016	0.715000	0.41141	3.427000	0.52785	0.991000	0.38814	0.482000	0.46254	TTT	.	.	.	none		0.617	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2	NM_003774		C	89918277	A	C	89918277	3	2	146	1	0	0	0	0	1	0	0	0	6222	14	1	5	1690	5	GALNT4	12	89918277	Missense_Mutation	SNP	A	TCGA-DW-5561-01A-01D-1589-08	17629811	89918277	43933618	30	8759											
SLC7A1	6541	hgsc.bcm.edu	37	chr13	30091728	30091728	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctatgaggctggttgaaaTgttcacaattagcccagaga	13	10	10	8	0	1	3	1	2	0	1	1	4	1	3	2	2	1	3	2	2	4	4			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr13:30091728T>C	ENST00000380752.5	-	10	1878	c.1492A>G	c.(1492-1494)Att>Gtt	p.I498V	SLC7A1_ENST00000473577.1_5'UTR	NM_003045.4	NP_003036.1	P30825	CTR1_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	498					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)	CTGGTTGAAATGTTCACAATT	0.498																																					p.I498V		Atlas-SNP	.											.	SLC7A1	64	.	0			c.A1492G						PASS	.						158	156	156					13																	30091728		2203	4300	6503	SO:0001583	missense	6541	exon10			TTGAAATGTTCAC	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.1492A>G	chr13.hg19:g.30091728T>C	ENSP00000370128:p.Ile498Val	293.0	0.0	.		323.0	93.0	.	NM_003045	Q5JR50	Missense_Mutation	SNP	ENST00000380752.5	hg19	CCDS9333.1	.	.	.	.	.	.	.	.	.	.	T	2.607	-0.291568	0.05568	.	.	ENSG00000139514	ENST00000380752	D	0.85861	-2.04	5.24	-1.65	0.08291	.	0.538057	0.20369	N	0.093684	T	0.69459	0.3113	N	0.17312	0.475	0.41573	D	0.988693	B	0.02656	0.0	B	0.04013	0.001	T	0.52859	-0.8519	10	0.17369	T	0.5	.	12.2085	0.54365	0.0:0.4844:0.0:0.5156	.	498	P30825	CTR1_HUMAN	V	498	ENSP00000370128:I498V	ENSP00000370128:I498V	I	-	1	0	SLC7A1	28989728	0.018000	0.18449	0.984000	0.44739	0.561000	0.35649	-0.909000	0.04058	-0.145000	0.11294	-0.264000	0.10439	ATT	.	.	.	none		0.498	SLC7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044337.2	NM_003045		C	30091728	T	C	30091728	3	2	146	1	0	0	0	0	1	0	0	0	14705	1464	51	3	413	3	SLC7A1	13	30091728	Missense_Mutation	SNP	T	TCGA-DW-5561-01A-01D-1589-08		30091728	85078150	31	8760											
TRIP4	9325	hgsc.bcm.edu	37	chr15	64702017	64702017	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagaaaattcactagcagagTatcatagcaggtaagtgagc	17	8	10	6	0	2	3	2	1	0	2	2	3	2	3	0	1	3	4	0	1	7	5			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr15:64702017T>C	ENST00000261884.3	+	7	1093	c.1033T>C	c.(1033-1035)Tat>Cat	p.Y345H		NM_016213.4	NP_057297.2	Q15650	TRIP4_HUMAN	thyroid hormone receptor interactor 4	345					positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21						ACTAGCAGAGTATCATAGCAG	0.428																																					p.Y345H		Atlas-SNP	.											.	TRIP4	43	.	0			c.T1033C						PASS	.						77	77	77					15																	64702017		2203	4300	6503	SO:0001583	missense	9325	exon7			GCAGAGTATCATA	L40371	CCDS10194.1	15q22.1	2014-02-17			ENSG00000103671	ENSG00000103671		"-"	12310	protein-coding gene	gene with protein product	"zinc finger, C2HC5-type"	604501				7776974	Standard	NM_016213		Approved	HsT17391, ZC2HC5	uc002anm.3	Q15650	OTTHUMG00000133033	ENST00000261884.3:c.1033T>C	chr15.hg19:g.64702017T>C	ENSP00000261884:p.Tyr345His	83.0	0.0	.		75.0	25.0	.	NM_016213	B2RAS0|Q96ED7|Q9UKH0	Missense_Mutation	SNP	ENST00000261884.3	hg19	CCDS10194.1	.	.	.	.	.	.	.	.	.	.	T	18.65	3.668883	0.67814	.	.	ENSG00000103671	ENST00000261884	.	.	.	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.77705	0.4170	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	T	0.74805	-0.3540	9	0.17369	T	0.5	-24.5764	16.1616	0.81721	0.0:0.0:0.0:1.0	.	345	Q15650	TRIP4_HUMAN	H	345	.	ENSP00000261884:Y345H	Y	+	1	0	TRIP4	62489070	1.000000	0.71417	0.980000	0.43619	0.327000	0.28475	7.628000	0.83189	2.221000	0.72209	0.454000	0.30748	TAT	.	.	.	none		0.428	TRIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256635.2	NM_016213		C	64702017	T	C	64702017	3	2	146	1	0	0	0	0	1	0	0	0	16570	1638	57	3	1059	3	TRIP4	15	64702017	Missense_Mutation	SNP	T	TCGA-DW-5561-01A-01D-1589-08		64702017	37829375	32	8761											
ADCY9	115	hgsc.bcm.edu	37	chr16	4165346	4165346	+	Missense_Mutation	SNP	T	T	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	tggaggacagctgcttggggTtgatcttgacgcgcacgctg	6	10	16	9	3	1	2	0	2	1	0	1	4	1	4	0	4	2	5	0	4	0	3			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr16:4165346T>G	ENST00000294016.3	-	2	636	c.98A>C	c.(97-99)aAc>aCc	p.N33T		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	33					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						CTGCTTGGGGTTGATCTTGAC	0.637																																					p.N33T		Atlas-SNP	.											.	ADCY9	151	.	0			c.A98C						PASS	.						91	66	75					16																	4165346		2197	4300	6497	SO:0001583	missense	115	exon2			TTGGGGTTGATCT	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.98A>C	chr16.hg19:g.4165346T>G	ENSP00000294016:p.Asn33Thr	23.0	0.0	.		29.0	12.0	.	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Missense_Mutation	SNP	ENST00000294016.3	hg19	CCDS32382.1	.	.	.	.	.	.	.	.	.	.	T	7.635	0.679628	0.14907	.	.	ENSG00000162104	ENST00000294016	T	0.27402	1.67	4.98	3.87	0.44632	.	0.478928	0.24490	N	0.038068	T	0.23094	0.0558	L	0.34521	1.04	0.37612	D	0.920957	B	0.23442	0.085	B	0.16289	0.015	T	0.07501	-1.0769	10	0.49607	T	0.09	.	11.1518	0.48464	0.0:0.0:0.1549:0.8451	.	33	O60503	ADCY9_HUMAN	T	33	ENSP00000294016:N33T	ENSP00000294016:N33T	N	-	2	0	ADCY9	4105347	1.000000	0.71417	0.997000	0.53966	0.064000	0.16182	4.786000	0.62425	0.728000	0.32382	-0.477000	0.04895	AAC	.	.	.	none		0.637	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1			G	4165346	T	G	4165346	3	3	146	1	0	0	0	0	1	0	0	0	301	1725	60	5	4003	5	ADCY9	16	4165346	Missense_Mutation	SNP	T	TCGA-DW-5561-01A-01D-1589-08		4165346	86189407	33	8762											
SUPT6H	6830	hgsc.bcm.edu	37	chr17	27002076	27002076	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaacatgaaaaagaagctaTtgcggaagaaatcttccagg	17	7	11	6	1	1	3	0	1	1	2	2	5	2	5	1	3	3	1	1	3	7	3			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr17:27002076T>C	ENST00000314616.6	+	5	717	c.434T>C	c.(433-435)aTt>aCt	p.I145T	SUPT6H_ENST00000347486.4_Missense_Mutation_p.I145T|AC010761.13_ENST00000578819.1_RNA	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	145	Asp/Glu-rich.|Interaction with IWS1. {ECO:0000250}.|Interaction with PAAF1.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					AAAGAAGCTATTGCGGAAGAA	0.527																																					p.I145T		Atlas-SNP	.											.	SUPT6H	165	.	0			c.T434C						PASS	.						86	80	82					17																	27002076		2203	4300	6503	SO:0001583	missense	6830	exon5			AAGCTATTGCGGA	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.434T>C	chr17.hg19:g.27002076T>C	ENSP00000319104:p.Ile145Thr	49.0	0.0	.		82.0	25.0	.	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	hg19	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	T	16.67	3.186987	0.57909	.	.	ENSG00000109111	ENST00000314616;ENST00000347486	.	.	.	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.75889	0.3911	M	0.79693	2.465	0.80722	D	1	P	0.50156	0.932	P	0.58520	0.84	T	0.73655	-0.3914	9	0.17832	T	0.49	-10.4269	15.9812	0.80111	0.0:0.0:0.0:1.0	.	145	Q7KZ85	SPT6H_HUMAN	T	145	.	ENSP00000319104:I145T	I	+	2	0	SUPT6H	24026203	1.000000	0.71417	0.995000	0.50966	0.833000	0.47200	7.328000	0.79160	2.178000	0.69098	0.533000	0.62120	ATT	.	.	.	none		0.527	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		C	27002076	T	C	27002076	3	2	146	1	0	0	0	0	1	0	0	0	15412	1493	52	3	448	3	SUPT6H	17	27002076	Missense_Mutation	SNP	T	TCGA-DW-5561-01A-01D-1589-08		27002076	54193134	34	8763											
SF3A2	8175	hgsc.bcm.edu	37	chr19	2248401	2248401	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctcccggggtccatccgtcGgctcctggggtccaccctca	3	8	11	19	3	1	0	1	0	0	0	7	0	6	0	7	5	0	1	7	5	0	0	rs375562170	byFrequency	TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr19:2248401G>A	ENST00000221494.5	+	9	1669	c.1251G>A	c.(1249-1251)tcG>tcA	p.S417S	AMH_ENST00000221496.4_5'Flank|MIR4321_ENST00000592276.1_RNA	NM_007165.4	NP_009096.2	Q15428	SF3A2_HUMAN	splicing factor 3a, subunit 2, 66kDa	417	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)		TCCATCCGTCGGCTCCTGGGG	0.711													G|||	6	0.00119808	0.0045	0	5008	,	,		7987	0		0	False		,,,				2504	0				p.S417S		Atlas-SNP	.											.	SF3A2	22	.	0			c.G1251A						PASS	.	G		29,3801		0,29,1886	5	6	6		1251	-3.8	0.1	19		6	0,8044		0,0,4022	no	coding-synonymous	SF3A2	NM_007165.4		0,29,5908	AA,AG,GG		0.0,0.7572,0.2442		417/465	2248401	29,11845	1915	4022	5937	SO:0001819	synonymous_variant	8175	exon9			TCCGTCGGCTCCT	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.1251G>A	chr19.hg19:g.2248401G>A		1.0	0.0	.		9.0	4.0	.	NM_007165	B2RBU1|D6W605|O75245	Silent	SNP	ENST00000221494.5	hg19	CCDS12084.1																																																																																			.	.	.	weak		0.711	SF3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451268.3			A	2248401	G	A	2248401	2	1	146	1	0	0	0	0	0	0	0	1	14160	1103	39	1		1	SF3A2	19	2248401	Silent	SNP	G	TCGA-DW-5561-01A-01D-1589-08		2248401	56880582	35	8764											
NDUFB7	4713	hgsc.bcm.edu	37	chr19	14677078	14677078	+	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	ccttcatgcgcatcacatagCtgggggaaaagcacgagagg	12	6	13	10	2	2	1	2	0	0	1	2	3	2	2	1	3	3	3	1	3	3	2			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr19:14677078C>A	ENST00000215565.2	-	3	343		c.e3-1			NM_004146.5	NP_004137.2	P17568	NDUB7_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7, 18kDa						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			endometrium(3)|large_intestine(2)|lung(2)|ovary(1)	8						CATCACATAGCTGGGGGAAAA	0.667																																					.		Atlas-SNP	.											.	NDUFB7	14	.	0			c.282-1G>T						PASS	.						38	42	40					19																	14677078		2202	4300	6502	SO:0001630	splice_region_variant	4713	exon4			ACATAGCTGGGGG		CCDS12314.1	19p13.12	2011-07-04	2002-08-29		ENSG00000099795	ENSG00000099795		"Mitochondrial respiratory chain complex / Complex I"	7702	protein-coding gene	gene with protein product	"NADH-ubiquinone oxidoreductase B18 subunit", "complex I B18 subunit"	603842	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7 (18kD, B18)"			9763677, 10830904	Standard	NM_004146		Approved	B18, CI-B18, MGC2480	uc002mzg.3	P17568		ENST00000215565.2:c.282-1G>T	chr19.hg19:g.14677078C>A		97.0	0.0	.		78.0	35.0	.	NM_004146	Q6ICN9|Q9UI16	Splice_Site	SNP	ENST00000215565.2	hg19	CCDS12314.1	.	.	.	.	.	.	.	.	.	.	C	16.68	3.190561	0.58017	.	.	ENSG00000099795	ENST00000215565	.	.	.	5.31	5.31	0.75309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4537	0.84003	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NDUFB7	14538078	1.000000	0.71417	0.999000	0.59377	0.454000	0.32378	7.184000	0.77705	2.493000	0.84123	0.460000	0.39030	.	.	.	.	none		0.667	NDUFB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466025.1	NM_004146	Intron	A	14677078	C	A	14677078	5	1	146	1	0	0	0	0	0	0	1	0	10293	811	28	4	136	4	NDUFB7	19	14677078	Splice_Site	SNP	C	TCGA-DW-5561-01A-01D-1589-08	12428677	14677078	44451905	36	8765											
ZNF681	148213	hgsc.bcm.edu	37	chr19	23927477	23927484	+	Frame_Shift_Del	DEL	TTAAAGGC	TTAAAGGC	-																															tagtaagggttaaggactgaTtaaaggctttgtcacattct																										TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	TTAAAGGC	TTAAAGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr19:23927477_23927484delTTAAAGGC	ENST00000402377.3	-	4	1009_1016	c.868_875delGCCTTTAA	c.(868-876)gcctttaatfs	p.AFN290fs	ZNF681_ENST00000395385.3_Frame_Shift_Del_p.AFN221fs	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	290					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			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)				TAAGGACTGATTAAAGGCTTTGTCACAT	0.375																																					p.290_292del		Atlas-INDEL	.											.	ZNF681	76	.	0			c.869_876del						PASS	.																																			SO:0001589	frameshift_variant	148213	exon4			.	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.868_875delGCCTTTAA	chr19.hg19:g.23927477_23927484delTTAAAGGC	ENSP00000384000:p.Ala290fs	165.0	0.0	0		108.0	28.0	0.259259	NM_138286	B3KVF7	Frame_Shift_Del	DEL	ENST00000402377.3	hg19	CCDS12414.2																																																																																			.	.	.	none		0.375	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286		-	23927484	TTAAAGGC	-	23927477	7	5	146	1	0	1	0	1	0	0	0	0	18100	1493	52	0	1066	0	ZNF681	19	23927477	Frame_Shift_Del	DEL	TTAAAGGC	TCGA-DW-5561-01A-01D-1589-08	9250399	23927477	35201506	37	8766											
SFRS6	6431	hgsc.bcm.edu	37	chr20	42087023	42087023	+	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	acggcttcgtggagttcgagGactcccgcgacgccgacgac	7	6	14	14	8	0	0	0	0	0	0	3	6	1	2	2	3	0	2	2	3	0	2			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr20:42087023G>A	ENST00000244020.3	+	2	236	c.130G>A	c.(130-132)Gac>Aac	p.D44N		NM_006275.5	NP_006266.2	Q13247	SRSF6_HUMAN	serine/arginine-rich splicing factor 6	44	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell death (GO:0060548)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of keratinocyte proliferation (GO:0010837)|regulation of wound healing (GO:0061041)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)	p.D44N(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|upper_aerodigestive_tract(2)	5						GGAGTTCGAGGACTCCCGCGA	0.716																																					p.D44N		Atlas-SNP	.											SRSF6_ENST00000244020,NS,carcinoma,0,1	SRSF6	37	.	1	Substitution - Missense(1)	lung(1)	c.G130A						PASS	.						8	7	8					20																	42087023		2096	4170	6266	SO:0001583	missense	6431	exon2			TTCGAGGACTCCC	U30883	CCDS13318.1	20q12-q13.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000124193	ENSG00000124193		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10788	protein-coding gene	gene with protein product	"pre-mRNA splicing factor SRP55", "SR splicing factor 6"	601944	"splicing factor, arginine/serine-rich 6"	SFRS6		7556075, 20516191	Standard	NM_006275		Approved	SRP55, B52	uc010zwg.2	Q13247	OTTHUMG00000032502	ENST00000244020.3:c.130G>A	chr20.hg19:g.42087023G>A	ENSP00000244020:p.Asp44Asn	14.0	0.0	.		17.0	9.0	.	NM_006275	B7Z6J3|E1P5W6|Q13244|Q13245|Q96J06|Q9UJB8|Q9Y3N7	Missense_Mutation	SNP	ENST00000244020.3	hg19	CCDS13318.1	.	.	.	.	.	.	.	.	.	.	g	26.3	4.719681	0.89205	.	.	ENSG00000124193	ENST00000244020	T	0.75050	-0.9	3.59	3.59	0.41128	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.054648	0.64402	D	0.000001	T	0.79581	0.4470	L	0.43598	1.365	0.80722	D	1	D;D	0.65815	0.995;0.986	D;P	0.63597	0.916;0.838	T	0.82418	-0.0467	10	0.87932	D	0	.	14.2003	0.65699	0.0:0.0:1.0:0.0	.	44;44	Q13247;A8K588	SRSF6_HUMAN;.	N	44	ENSP00000244020:D44N	ENSP00000244020:D44N	D	+	1	0	SRSF6	41520437	1.000000	0.71417	1.000000	0.80357	0.336000	0.28762	8.758000	0.91663	1.838000	0.53458	0.552000	0.68991	GAC	.	.	.	none		0.716	SRSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079292.1	NM_006275		A	42087023	G	A	42087023	3	1	146	1	0	0	0	0	1	0	0	0	14194	1174	41	2	136	2	SFRS6	20	42087023	Missense_Mutation	SNP	G	TCGA-DW-5561-01A-01D-1589-08		42087023	20938497	38	8767											
SEC14L4	284904	hgsc.bcm.edu	37	chr22	30891293	30891293	+	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	gcagctcacagactttgatgCgcttccggatcatatcctgc	8	11	9	13	2	2	2	2	1	0	1	4	3	4	3	2	1	3	3	2	1	1	3			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr22:30891293C>T	ENST00000255858.7	-	5	454	c.371G>A	c.(370-372)cGc>cAc	p.R124H	RP4-539M6.14_ENST00000442126.1_RNA|SEC14L4_ENST00000381982.3_Missense_Mutation_p.R124H|SEC14L4_ENST00000392772.2_Missense_Mutation_p.R70H|SEC14L4_ENST00000540456.1_Missense_Mutation_p.R109H|RP4-539M6.14_ENST00000610156.1_RNA	NM_001161368.1|NM_174977.3	NP_001154840.1|NP_777637.1	Q9UDX3	S14L4_HUMAN	SEC14-like 4 (S. cerevisiae)	124	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.		R -> G (in dbSNP:rs9606739).			integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|pancreas(1)|skin(1)	21					Vitamin E(DB00163)	GACTTTGATGCGCTTCCGGAT	0.572																																					p.R124H		Atlas-SNP	.											.	SEC14L4	43	.	0			c.G371A						PASS	.						72	62	65					22																	30891293		2203	4300	6503	SO:0001583	missense	284904	exon5			TTGATGCGCTTCC	AY158085	CCDS13878.1, CCDS54517.1	22q12.1	2003-03-10			ENSG00000133488	ENSG00000133488			20627	protein-coding gene	gene with protein product		612825					Standard	NM_174977		Approved	TAP3, dJ130H16.5	uc003aid.2	Q9UDX3	OTTHUMG00000151258	ENST00000255858.7:c.371G>A	chr22.hg19:g.30891293C>T	ENSP00000255858:p.Arg124His	52.0	0.0	.		40.0	17.0	.	NM_001161368	A5D6W7|A6NCV4	Missense_Mutation	SNP	ENST00000255858.7	hg19	CCDS13878.1	.	.	.	.	.	.	.	.	.	.	c	18.44	3.623875	0.66901	.	.	ENSG00000133488	ENST00000255858;ENST00000540456;ENST00000392772;ENST00000381982	T;T;T;T	0.75704	-0.96;-0.96;-0.96;-0.96	4.9	2.77	0.32553	Cellular retinaldehyde-binding/triple function, C-terminal (5);	0.077270	0.52532	D	0.000077	T	0.65954	0.2741	N	0.16790	0.44	0.80722	D	1	D;D;D	0.65815	0.991;0.995;0.985	P;P;P	0.61397	0.871;0.888;0.75	T	0.60796	-0.7192	10	0.14252	T	0.57	-11.5328	5.6156	0.17430	0.0:0.6061:0.0:0.3939	.	70;109;124	B3KSF0;G3V1L4;Q9UDX3	.;.;S14L4_HUMAN	H	124;109;70;124	ENSP00000255858:R124H;ENSP00000440848:R109H;ENSP00000376525:R70H;ENSP00000371412:R124H	ENSP00000255858:R124H	R	-	2	0	SEC14L4	29221293	0.996000	0.38824	0.131000	0.22000	0.495000	0.33615	2.090000	0.41682	1.169000	0.42739	0.655000	0.94253	CGC	.	.	.	none		0.572	SEC14L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321946.1	NM_174977		T	30891293	C	T	30891293	3	4	146	1	0	0	0	0	1	0	0	0	13997	768	27	1	887	1	SEC14L4	22	30891293	Missense_Mutation	SNP	C	TCGA-DW-5561-01A-01D-1589-08		30891293	20413273	39	8768											
YWHAH	7533	hgsc.bcm.edu	37	chr22	32352660	32352660	+	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	tcgatgatgccatagctgagCtggacacactaaacgaggat	13	8	11	9	2	0	2	0	2	0	0	1	6	0	4	1	2	4	2	1	2	3	2			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chr22:32352660C>T	ENST00000248975.5	+	2	895	c.622C>T	c.(622-624)Ctg>Ttg	p.L208L	YWHAH_ENST00000471374.1_3'UTR|YWHAH_ENST00000397492.1_3'UTR	NM_003405.3	NP_003396.1	Q04917	1433F_HUMAN	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta	208					apoptotic process (GO:0006915)|glucocorticoid catabolic process (GO:0006713)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular protein transport (GO:0006886)|intrinsic apoptotic signaling pathway (GO:0097193)|membrane depolarization during action potential (GO:0086010)|membrane organization (GO:0061024)|negative regulation of dendrite morphogenesis (GO:0050774)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of sodium ion transport (GO:0002028)|regulation of synaptic plasticity (GO:0048167)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|glucocorticoid receptor binding (GO:0035259)|insulin-like growth factor receptor binding (GO:0005159)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|sodium channel regulator activity (GO:0017080)			breast(1)|central_nervous_system(1)|large_intestine(1)|upper_aerodigestive_tract(1)	4						CATAGCTGAGCTGGACACACT	0.527																																					p.L208L	Ovarian(98;460 2060 9263 44007)	Atlas-SNP	.											.	YWHAH	14	.	0			c.C622T						PASS	.						72	55	61					22																	32352660		2203	4300	6503	SO:0001819	synonymous_variant	7533	exon2			GCTGAGCTGGACA	X78138	CCDS13901.1	22q12.1-q13.1	2013-12-03	2013-12-03		ENSG00000128245	ENSG00000128245			12853	protein-coding gene	gene with protein product	"14-3-3 eta"	113508	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide"	YWHA1			Standard	NM_003405		Approved		uc003alz.3	Q04917	OTTHUMG00000030833	ENST00000248975.5:c.622C>T	chr22.hg19:g.32352660C>T		43.0	0.0	.		34.0	18.0	.	NM_003405		Silent	SNP	ENST00000248975.5	hg19	CCDS13901.1																																																																																			.	.	.	none		0.527	YWHAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075721.2	NM_003405		T	32352660	C	T	32352660	2	4	146	1	0	0	0	0	0	0	0	1	17516	796	28	2		2	YWHAH	22	32352660	Silent	SNP	C	TCGA-DW-5561-01A-01D-1589-08	1461367	32352660	18951906	40	8769											
WNK3	65267	hgsc.bcm.edu	37	chrX	54319393	54319393	+	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	acaactgtcggtccaaggacAtgtacaggtaaaacagtgga	15	7	11	8	1	0	0	0	0	0	0	2	2	1	2	1	4	3	2	1	4	5	2			TCGA-DW-5561-01A-01D-1589-08	TCGA-DW-5561-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7722e078-7471-43c1-85f8-2a36938fe489	2c3eb624-d770-4d82-b225-1b58054242b7	g.chrX:54319393A>T	ENST00000375159.2	-	9	1964	c.1965T>A	c.(1963-1965)caT>caA	p.H655Q	WNK3_ENST00000354646.2_Missense_Mutation_p.H655Q|WNK3_ENST00000375169.3_Missense_Mutation_p.H655Q			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	655					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						GTCCAAGGACATGTACAGGTA	0.418																																					p.H655Q		Atlas-SNP	.											.	WNK3	218	.	0			c.T1965A						PASS	.						100	87	92					X																	54319393		2203	4300	6503	SO:0001583	missense	65267	exon10			AAGGACATGTACA	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.1965T>A	chrX.hg19:g.54319393A>T	ENSP00000364301:p.His655Gln	46.0	0.0	.		28.0	21.0	.	NM_001002838	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Missense_Mutation	SNP	ENST00000375159.2	hg19	CCDS14357.1	.	.	.	.	.	.	.	.	.	.	A	1.564	-0.535847	0.04082	.	.	ENSG00000196632	ENST00000375169;ENST00000354646;ENST00000375159	T;T;T	0.42131	0.98;0.98;0.98	5.21	2.73	0.32206	.	0.631512	0.14072	N	0.343324	T	0.23054	0.0557	N	0.19112	0.55	0.09310	N	1	B;B	0.12013	0.0;0.005	B;B	0.10450	0.003;0.005	T	0.22312	-1.0220	10	0.22109	T	0.4	-0.9144	4.0626	0.09846	0.7167:0.0:0.1006:0.1826	.	655;655	Q9BYP7-3;Q9BYP7	.;WNK3_HUMAN	Q	655	ENSP00000364312:H655Q;ENSP00000346667:H655Q;ENSP00000364301:H655Q	ENSP00000346667:H655Q	H	-	3	2	WNK3	54336118	0.769000	0.28531	0.170000	0.22879	0.756000	0.42949	1.264000	0.33015	0.220000	0.20860	0.451000	0.29950	CAT	.	.	.	none		0.418	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922		T	54319393	A	T	54319393	3	4	146	1	0	0	0	0	1	0	0	0	17391	214	8	5	3497	5	WNK3	23	54319393	Missense_Mutation	SNP	A	TCGA-DW-5561-01A-01D-1589-08		54319393	100951167	41	8770											
PEF1	553115	hgsc.bcm.edu	37	chr1	32100955	32100955	+	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	catcccaggattggggtgtcCatagggccctccaccagctg	7	8	12	14	0	0	0	0	0	0	0	3	1	3	1	5	4	1	1	5	4	1	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr1:32100955C>A	ENST00000373703.4	-	2	215	c.193G>T	c.(193-195)Gga>Tga	p.G65*	PEF1_ENST00000440872.2_Nonsense_Mutation_p.G65*|PEF1_ENST00000492061.1_5'UTR	NM_012392.3	NP_036524.1	Q9UBV8	PEF1_HUMAN	penta-EF-hand domain containing 1	65	9 X 9 AA approximate tandem repeat of [AP]-P-G-G-P-Y-G-G-P-P.				proteolysis (GO:0006508)|response to calcium ion (GO:0051592)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|poly(A) RNA binding (GO:0044822)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(2)|upper_aerodigestive_tract(1)	7		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)|all_neural(195;0.186)		STAD - Stomach adenocarcinoma(196;0.0546)		TTGGGGTGTCCATAGGGCCCT	0.627																																					p.G65X		Atlas-SNP	.											.	PEF1	20	.	0			c.G193T						PASS	.						23	25	25					1																	32100955		2203	4299	6502	SO:0001587	stop_gained	553115	exon2			GGTGTCCATAGGG		CCDS345.1	1p34	2013-01-10			ENSG00000162517	ENSG00000162517		"EF-hand domain containing"	30009	protein-coding gene	gene with protein product	"peflin"	610033				10486255, 11883899	Standard	NM_012392		Approved	PEF1A	uc001bth.2	Q9UBV8	OTTHUMG00000003877	ENST00000373703.4:c.193G>T	chr1.hg19:g.32100955C>A	ENSP00000362807:p.Gly65*	45.0	0.0	.		51.0	18.0	.	NM_012392		Nonsense_Mutation	SNP	ENST00000373703.4	hg19	CCDS345.1	.	.	.	.	.	.	.	.	.	.	C	34	5.384325	0.95967	.	.	ENSG00000162517	ENST00000373703;ENST00000440872	.	.	.	4.71	4.71	0.59529	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	.	17.2908	0.87156	0.0:1.0:0.0:0.0	.	.	.	.	X	65	.	ENSP00000362807:G65X	G	-	1	0	PEF1	31873542	1.000000	0.71417	0.998000	0.56505	0.930000	0.56654	6.128000	0.71650	2.541000	0.85698	0.561000	0.74099	GGA	.	.	.	none		0.627	PEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011046.1	NM_012392		A	32100955	C	A	32100955	4	1	147	1	0	0	0	0	0	1	0	0	11725	603	21	4	677	4	PEF1	1	32100955	Nonsense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08		32100955	217149666	1	8771											
DEDD	9191	hgsc.bcm.edu	37	chr1	161092019	161092019	+	Missense_Mutation	SNP	A	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	cctcgtctacatttaccagcAgcttgatggcttcatggccc	7	12	8	14	1	2	1	1	1	1	0	3	1	2	1	3	2	4	3	3	2	2	5			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr1:161092019A>C	ENST00000368006.3	-	6	1089	c.875T>G	c.(874-876)cTg>cGg	p.L292R	DEDD_ENST00000490843.2_Missense_Mutation_p.L292R|DEDD_ENST00000392188.1_Missense_Mutation_p.L322R|DEDD_ENST00000458050.2_Missense_Mutation_p.L292R|DEDD_ENST00000489249.1_5'UTR|DEDD_ENST00000368005.1_Missense_Mutation_p.L322R|NIT1_ENST00000368008.1_Intron|DEDD_ENST00000545495.1_Missense_Mutation_p.L292R	NM_032998.2	NP_127491.1	O75618	DEDD_HUMAN	death effector domain containing	292					decidualization (GO:0046697)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|regulation of apoptotic process (GO:0042981)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	DNA binding (GO:0003677)			cervix(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|skin(1)	10	all_cancers(52;3.39e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			ATTTACCAGCAGCTTGATGGC	0.498																																					p.L292R		Atlas-SNP	.											.	DEDD	22	.	0			c.T875G						PASS	.						100	93	95					1																	161092019		2203	4300	6503	SO:0001583	missense	9191	exon5			ACCAGCAGCTTGA	AF043733	CCDS1219.1	1q23.1	2008-02-05	2002-01-14		ENSG00000158796	ENSG00000158796			2755	protein-coding gene	gene with protein product		606841	"death effector domain-containing"			9774341, 9832420	Standard	XM_005245597		Approved	DEFT, FLDED1, CASP8IP1, KE05, DEDD1	uc001fxz.3	O75618	OTTHUMG00000033104	ENST00000368006.3:c.875T>G	chr1.hg19:g.161092019A>C	ENSP00000356985:p.Leu292Arg	95.0	0.0	.		95.0	32.0	.	NM_001039711	D3DVF5|O60737	Missense_Mutation	SNP	ENST00000368006.3	hg19	CCDS1219.1	.	.	.	.	.	.	.	.	.	.	A	19.68	3.871963	0.72180	.	.	ENSG00000158796	ENST00000368006;ENST00000392188;ENST00000545495;ENST00000458050;ENST00000541906;ENST00000368005;ENST00000535389	.	.	.	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.70386	0.3218	M	0.64997	1.995	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.87578	0.998;0.997;0.996	T	0.74948	-0.3490	9	0.87932	D	0	.	13.2065	0.59800	1.0:0.0:0.0:0.0	.	249;322;292	B4DKM1;B1AQP5;O75618	.;.;DEDD_HUMAN	R	292;322;292;292;292;322;249	.	ENSP00000356984:L322R	L	-	2	0	DEDD	159358643	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.135000	0.94478	2.209000	0.71365	0.533000	0.62120	CTG	.	.	.	none		0.498	DEDD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080582.1	NM_004216		C	161092019	A	C	161092019	3	2	147	1	0	0	0	0	1	0	0	0	4386	188	7	5	85	5	DEDD	1	161092019	Missense_Mutation	SNP	A	TCGA-DW-7834-01A-11D-2136-08	128991064	161092019	88158602	2	8772											
RGS1	5996	hgsc.bcm.edu	37	chr1	192547354	192547354	+	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	cccctcgtttctttttagctGgtcaaaatgtctttggaagt	7	17	8	9	1	3	0	1	0	2	0	4	1	3	1	2	2	1	2	2	2	4	5			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr1:192547354G>C	ENST00000367459.3	+	4	349	c.283G>C	c.(283-285)Ggt>Cgt	p.G95R	RGS1_ENST00000469578.2_Missense_Mutation_p.G95R	NM_002922.3	NP_002913.3	Q08116	RGS1_HUMAN	regulator of G-protein signaling 1	95	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				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)				CTTTTTAGCTGGTCAAAATGT	0.343																																					p.G95R		Atlas-SNP	.											.	RGS1	75	.	0			c.G283C						PASS	.						122	130	127					1																	192547354		2203	4300	6503	SO:0001583	missense	5996	exon4			TTAGCTGGTCAAA	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.283G>C	chr1.hg19:g.192547354G>C	ENSP00000356429:p.Gly95Arg	187.0	0.0	.		151.0	40.0	.	NM_002922	B2RDM9|B4DZY0|Q07918|Q9H1W2	Missense_Mutation	SNP	ENST00000367459.3	hg19	CCDS1375.2	.	.	.	.	.	.	.	.	.	.	G	13.87	2.365805	0.41902	.	.	ENSG00000090104	ENST00000367459	T	0.02944	4.1	5.91	5.91	0.95273	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);Regulator of G-protein signaling, domain 1 (1);	0.000000	0.85682	D	0.000000	T	0.25680	0.0625	H	0.94886	3.595	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.12319	-1.0552	10	0.87932	D	0	.	18.8649	0.92287	0.0:0.0:1.0:0.0	.	95;95	Q08116-2;Q08116	.;RGS1_HUMAN	R	95	ENSP00000356429:G95R	ENSP00000356429:G95R	G	+	1	0	RGS1	190813977	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	7.640000	0.83355	2.804000	0.96469	0.650000	0.86243	GGT	.	.	.	none		0.343	RGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086391.1	NM_002922		C	192547354	G	C	192547354	3	2	147	1	0	0	0	0	1	0	0	0	13305	1348	47	4	297	4	RGS1	1	192547354	Missense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08	31455335	192547354	56703267	3	8773											
ELF3	1999	hgsc.bcm.edu	37	chr1	201980419	201980420	+	Frame_Shift_Ins	INS	-	-	G																															aacccccagatgtcattggaINSgggtacaggtgggtctcagc																										TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr1:201980419_201980420insG	ENST00000359651.3	+	1	3347_3348	c.155_156insG	c.(154-159)gagggtfs	p.EG52fs	ELF3_ENST00000495848.1_3'UTR|RP11-465N4.4_ENST00000419190.1_RNA|ELF3_ENST00000367284.5_Frame_Shift_Ins_p.EG52fs|ELF3_ENST00000367283.3_Frame_Shift_Ins_p.EG52fs|RP11-510N19.5_ENST00000504773.1_RNA					E74-like factor 3 (ets domain transcription factor, epithelial-specific )									p.E52G(2)		breast(2)|endometrium(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	20						ATGTCATTGGAGGGTACAGGTG	0.609																																					p.E52fs		Atlas-INDEL	.											ELF3_ENST00000359651,NS,carcinoma,0,2	ELF3	92	.	2	Substitution - Missense(2)	lung(2)	c.155_156insG						PASS	.																																			SO:0001589	frameshift_variant	1999	exon2			.	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.158dupG	chr1.hg19:g.201980422_201980422dupG	ENSP00000352673:p.Glu52fs	135.0	0.0	0		144.0	11.0	0.0763889	NM_004433		Frame_Shift_Ins	INS	ENST00000359651.3	hg19	CCDS1419.1																																																																																			.	.	.	none		0.609	ELF3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087360.1	NM_004433		G	201980420	-	G	201980419	7	5	147	1	0	1	1	0	0	0	0	0	5057	304	11	0	157	0	ELF3	1	201980419	Frame_Shift_Ins	INS	-	TCGA-DW-7834-01A-11D-2136-08	9433065	201980419	47270202	4	8774											
PLXNA2	5362	hgsc.bcm.edu	37	chr1	208215581	208215581	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcgaagccacgttgcccCggtcgcgcatggagaaactg	9	6	14	12	5	0	2	0	1	0	1	1	4	0	2	3	2	4	2	3	2	2	1			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr1:208215581C>T	ENST00000367033.3	-	22	4905	c.4148G>A	c.(4147-4149)cGg>cAg	p.R1383Q		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	1383					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)		CACGTTGCCCCGGTCGCGCAT	0.582																																					p.R1383Q		Atlas-SNP	.											.	PLXNA2	178	.	0			c.G4148A						PASS	.						94	92	92					1																	208215581		2203	4300	6503	SO:0001583	missense	5362	exon22			TTGCCCCGGTCGC	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.4148G>A	chr1.hg19:g.208215581C>T	ENSP00000356000:p.Arg1383Gln	91.0	0.0	.		91.0	30.0	.	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	hg19	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	C	35	5.504221	0.96371	.	.	ENSG00000076356	ENST00000367033	T	0.15718	2.4	5.15	5.15	0.70609	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.46092	0.1375	M	0.78456	2.415	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.49916	-0.8888	10	0.87932	D	0	.	18.6381	0.91385	0.0:1.0:0.0:0.0	.	1383	O75051	PLXA2_HUMAN	Q	1383	ENSP00000356000:R1383Q	ENSP00000356000:R1383Q	R	-	2	0	PLXNA2	206282204	1.000000	0.71417	0.980000	0.43619	0.826000	0.46750	7.480000	0.81109	2.391000	0.81399	0.455000	0.32223	CGG	.	.	.	none		0.582	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		T	208215581	C	T	208215581	3	4	147	1	0	0	0	0	1	0	0	0	12127	652	23	1	1580	1	PLXNA2	1	208215581	Missense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08	6235162	208215581	41035040	5	8775											
NUP133	55746	hgsc.bcm.edu	37	chr1	229631732	229631732	+	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	tcatctaattcccatttactGatgtttgaactcgtcaggct	9	16	6	10	1	3	2	2	2	1	0	5	2	4	2	1	1	2	2	1	1	3	5			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr1:229631732G>T	ENST00000261396.3	-	7	973	c.882C>A	c.(880-882)atC>atA	p.I294I	NUP133_ENST00000537506.1_Silent_p.I278I	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	294			I -> V (in dbSNP:rs11805194).		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)				CCCATTTACTGATGTTTGAAC	0.363																																					p.I294I		Atlas-SNP	.											.	NUP133	111	.	0			c.C882A						PASS	.						105	101	103					1																	229631732		2203	4299	6502	SO:0001819	synonymous_variant	55746	exon7			TTTACTGATGTTT		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.882C>A	chr1.hg19:g.229631732G>T		65.0	0.0	.		74.0	31.0	.	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Silent	SNP	ENST00000261396.3	hg19	CCDS1579.1																																																																																			.	.	.	none		0.363	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230		T	229631732	G	T	229631732	2	4	147	1	0	0	0	0	0	0	0	1	10761	1280	45	4		4	NUP133	1	229631732	Silent	SNP	G	TCGA-DW-7834-01A-11D-2136-08	21416151	229631732	19618889	6	8776											
LPIN1	23175	hgsc.bcm.edu	37	chr2	11913751	11913751	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttttttcctccagaactcTtcctaatgatatacctccat	9	18	2	12	0	1	2	0	1	1	1	5	2	5	2	5	0	2	0	5	0	4	8			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr2:11913751T>C	ENST00000256720.2	+	5	695	c.602T>C	c.(601-603)cTt>cCt	p.L201P	LPIN1_ENST00000425416.2_Missense_Mutation_p.L207P|LPIN1_ENST00000449576.2_Missense_Mutation_p.L250P|LPIN1_ENST00000396098.1_Missense_Mutation_p.L207P|LPIN1_ENST00000396099.1_Missense_Mutation_p.L207P	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	201					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)		TCCAGAACTCTTCCTAATGAT	0.358																																					p.L250P		Atlas-SNP	.											.	LPIN1	99	.	0			c.T749C						PASS	.						81	88	86					2																	11913751		2203	4300	6503	SO:0001583	missense	23175	exon6			GAACTCTTCCTAA	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.602T>C	chr2.hg19:g.11913751T>C	ENSP00000256720:p.Leu201Pro	127.0	0.0	.		113.0	35.0	.	NM_001261428	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Missense_Mutation	SNP	ENST00000256720.2	hg19	CCDS1682.1	.	.	.	.	.	.	.	.	.	.	T	5.891	0.348519	0.11126	.	.	ENSG00000134324	ENST00000449576;ENST00000396098;ENST00000396099;ENST00000425416;ENST00000256720	T;D;T;T;T	0.89270	-1.47;-2.49;-1.45;-1.47;-1.47	5.6	3.27	0.37495	.	0.457402	0.18485	N	0.139836	T	0.80884	0.4709	L	0.31926	0.97	0.09310	N	0.999998	B;B;B	0.11235	0.002;0.0;0.004	B;B;B	0.11329	0.006;0.002;0.006	T	0.66929	-0.5799	10	0.31617	T	0.26	-5.5606	7.3106	0.26473	0.0:0.2849:0.0:0.7151	.	250;201;207	F5GY24;Q14693;A8MU38	.;LPIN1_HUMAN;.	P	250;207;207;207;201	ENSP00000397908:L250P;ENSP00000379405:L207P;ENSP00000379406:L207P;ENSP00000401522:L207P;ENSP00000256720:L201P	ENSP00000256720:L201P	L	+	2	0	LPIN1	11831202	0.012000	0.17670	0.131000	0.22000	0.489000	0.33432	1.405000	0.34635	0.974000	0.38366	0.482000	0.46254	CTT	.	.	.	none		0.358	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693		C	11913751	T	C	11913751	3	2	147	1	0	0	0	0	1	0	0	0	8925	1609	56	3	616	3	LPIN1	2	11913751	Missense_Mutation	SNP	T	TCGA-DW-7834-01A-11D-2136-08		11913751	231285622	7	8777											
IFIH1	64135	hgsc.bcm.edu	37	chr2	163167397	163167397	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctgcacaatcctttttagtAgctctcttacacctgattca	9	16	4	12	0	3	1	1	1	2	0	5	1	4	1	2	0	3	3	2	0	4	6			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr2:163167397A>G	ENST00000263642.2	-	2	895	c.500T>C	c.(499-501)cTa>cCa	p.L167P	IFIH1_ENST00000421365.2_Missense_Mutation_p.L167P	NM_022168.3	NP_071451.2	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	167	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 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						CCTTTTTAGTAGCTCTCTTAC	0.358																																					p.L167P		Atlas-SNP	.											.	IFIH1	102	.	0			c.T500C						PASS	.						81	72	75					2																	163167397		2203	4299	6502	SO:0001583	missense	64135	exon2			TTTAGTAGCTCTC	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.500T>C	chr2.hg19:g.163167397A>G	ENSP00000263642:p.Leu167Pro	55.0	0.0	.		54.0	15.0	.	NM_022168	Q2NKL6|Q6DC96|Q86X56|Q96MX8|Q9H3G6	Missense_Mutation	SNP	ENST00000263642.2	hg19	CCDS2217.1	.	.	.	.	.	.	.	.	.	.	A	17.16	3.318793	0.60524	.	.	ENSG00000115267	ENST00000263642;ENST00000543192;ENST00000421365	T;T	0.63255	-0.03;-0.03	5.81	5.81	0.92471	DEATH-like (2);Caspase Recruitment (1);	0.140170	0.48286	D	0.000192	T	0.79411	0.4441	M	0.76574	2.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.81874	-0.0732	10	0.87932	D	0	-10.3294	16.1677	0.81782	1.0:0.0:0.0:0.0	.	167;167	Q9BYX4-2;Q9BYX4	.;IFIH1_HUMAN	P	167	ENSP00000263642:L167P;ENSP00000408450:L167P	ENSP00000263642:L167P	L	-	2	0	IFIH1	162875643	0.991000	0.36638	0.999000	0.59377	0.237000	0.25408	6.182000	0.71995	2.218000	0.71995	0.528000	0.53228	CTA	.	.	.	none		0.358	IFIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255078.2	NM_022168		G	163167397	A	G	163167397	3	3	147	1	0	0	0	0	1	0	0	0	7527	420	15	3	2637	3	IFIH1	2	163167397	Missense_Mutation	SNP	A	TCGA-DW-7834-01A-11D-2136-08	151253646	163167397	80031976	8	8778											
OBFC2A	64859	hgsc.bcm.edu	37	chr2	192543405	192543405	+	Missense_Mutation	SNP	A	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	gcccggactgaaaaacttaaAtgtcgtctttattgtcctgg	10	13	9	9	2	1	1	0	1	1	0	3	2	2	2	2	2	1	0	2	2	5	4			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr2:192543405A>C	ENST00000425611.2	+	1	148	c.65A>C	c.(64-66)aAt>aCt	p.N22T	NABP1_ENST00000410026.2_Intron|NABP1_ENST00000409510.1_Intron	NM_001031716.2	NP_001026886.1	Q96AH0	SOSB2_HUMAN	nucleic acid binding protein 1	22					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SOSS complex (GO:0070876)	RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)										AAAAACTTAAATGTCGTCTTT	0.562																																					p.N22T		Atlas-SNP	.											.	.	.	.	0			c.A65C						PASS	.						42	50	47					2																	192543405		2203	4300	6503	SO:0001583	missense	64859	exon1			ACTTAAATGTCGT	BC017114	CCDS33352.1, CCDS58745.1	2q32.3	2012-06-19	2012-06-19	2012-06-19	ENSG00000173559	ENSG00000173559			26232	protein-coding gene	gene with protein product	"single-stranded DNA-binding protein 2", "sensor of single-strand DNA complex subunit B2"	612103	"oligonucleotide/oligosaccharide-binding fold containing 2A"	OBFC2A			Standard	NM_001031716		Approved	FLJ22833, DKFZp667M1322, FLJ13624, MGC111163, SSB2, hSSB2, SOSS-B2	uc002usx.3	Q96AH0	OTTHUMG00000132720	ENST00000425611.2:c.65A>C	chr2.hg19:g.192543405A>C	ENSP00000403683:p.Asn22Thr	113.0	0.0	.		100.0	32.0	.	NM_001031716	Q658Y8|Q9H5X6	Missense_Mutation	SNP	ENST00000425611.2	hg19	CCDS33352.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.527945	0.85706	.	.	ENSG00000173559	ENST00000425611	T	0.28255	1.62	5.51	5.51	0.81932	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);	0.107337	0.64402	D	0.000007	T	0.46927	0.1418	M	0.68728	2.09	0.54753	D	0.999989	D	0.63046	0.992	P	0.59487	0.858	T	0.47522	-0.9111	10	0.56958	D	0.05	.	9.7659	0.40561	0.9219:0.0:0.0781:0.0	.	22	Q96AH0	SOSB2_HUMAN	T	22	ENSP00000403683:N22T	ENSP00000307968:N22T	N	+	2	0	OBFC2A	192251650	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.953000	0.70290	2.080000	0.62538	0.533000	0.62120	AAT	.	.	.	none		0.562	NABP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256060.1	NM_022837		C	192543405	A	C	192543405	3	2	147	1	0	0	0	0	1	0	0	0	10815	101	4	5	67	5	OBFC2A	2	192543405	Missense_Mutation	SNP	A	TCGA-DW-7834-01A-11D-2136-08	29376008	192543405	50655968	9	8779											
SF3B1	23451	hgsc.bcm.edu	37	chr2	198274598	198274598	+	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	gtgtatcacctcgtccaggaGtagcagctcccgctggtgtg	6	10	13	12	2	1	0	1	0	0	0	4	1	3	1	3	2	2	5	3	2	2	2	rs1044635		TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr2:198274598G>T	ENST00000335508.6	-	7	891	c.800C>A	c.(799-801)aCt>aAt	p.T267N		NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	267	Interaction with PPP1R8.|U2AF homology region; mediates interaction with RMB39.				anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			TCGTCCAGGAGTAGCAGCTCC	0.562			Mis		myelodysplastic syndrome																																p.T267N		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1	1038	.	0			c.C800A						PASS	.						170	167	168					2																	198274598		2203	4300	6503	SO:0001583	missense	23451	exon7			CCAGGAGTAGCAG	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.800C>A	chr2.hg19:g.198274598G>T	ENSP00000335321:p.Thr267Asn	197.0	0.0	.		222.0	78.0	.	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	hg19	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	G	32	5.179984	0.94846	.	.	ENSG00000115524	ENST00000335508	.	.	.	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.57562	0.2062	L	0.44542	1.39	0.80722	D	1	D	0.55800	0.973	P	0.47346	0.544	T	0.53954	-0.8365	9	0.27082	T	0.32	.	19.0839	0.93194	0.0:0.0:1.0:0.0	.	267	O75533	SF3B1_HUMAN	N	267	.	ENSP00000335321:T267N	T	-	2	0	SF3B1	197982843	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.750000	0.98875	2.502000	0.84385	0.655000	0.94253	ACT	.	G|1.000;A|0.000	.	alt		0.562	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			T	198274598	G	T	198274598	3	4	147	1	0	0	0	0	1	0	0	0	14162	1029	36	4	3190	4	SF3B1	2	198274598	Missense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08	5731193	198274598	44924775	10	8780											
DNAJB2	3300	hgsc.bcm.edu	37	chr2	220150708	220150708	+	3'UTR	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	ccgcccctgctctctccccaGatgtgttctgagctggatgc	4	11	10	16	1	2	2	0	1	2	1	4	3	3	3	5	1	3	3	5	1	0	1			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr2:220150708G>T	ENST00000336576.5	+	0	2262				DNAJB2_ENST00000392086.4_Splice_Site	NM_006736.5	NP_006727.2	P25686	DNJB2_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 2						cell death (GO:0008219)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of inclusion body assembly (GO:0090084)|negative regulation of protein deubiquitination (GO:0090086)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein folding (GO:0006457)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|inclusion body (GO:0016234)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|polyubiquitin binding (GO:0031593)|proteasome binding (GO:0070628)|unfolded protein binding (GO:0051082)			endometrium(4)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	14		Renal(207;0.0474)		Epithelial(149;1.97e-06)|all cancers(144;0.00028)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCTCTCCCCAGATGTGTTCTG	0.647																																					.		Atlas-SNP	.											.	DNAJB2	31	.	0			c.824-1G>T						PASS	.						56	63	61					2																	220150708		2002	4166	6168	SO:0001624	3_prime_UTR_variant	3300	exon10			TCCCCAGATGTGT		CCDS2439.1, CCDS46519.1	2q32-q34	2011-09-02			ENSG00000135924	ENSG00000135924		"Heat shock proteins / DNAJ (HSP40)"	5228	protein-coding gene	gene with protein product		604139		HSJ1		1599432, 10516435	Standard	NM_006736		Approved	HSPF3	uc002vkx.1	P25686	OTTHUMG00000133134	ENST00000336576.5:c.*999G>T	chr2.hg19:g.220150708G>T		69.0	0.0	.		67.0	4.0	.	NM_001039550	A8K9P6|Q8IUK1|Q8IUK2|Q96F52	Splice_Site	SNP	ENST00000336576.5	hg19	CCDS2439.1	.	.	.	.	.	.	.	.	.	.	G	19.20	3.782364	0.70222	.	.	ENSG00000135924	ENST00000392086	.	.	.	6.08	6.08	0.98989	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.3963	0.87446	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DNAJB2	219858952	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.413000	0.59795	2.894000	0.99253	0.655000	0.94253	.	.	.	.	none		0.647	DNAJB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256823.2			T	220150708	G	T	220150708	1	4	147	0	1	0	0	0	0	0	0	0	4622	956	33	4		4	DNAJB2	2	220150708	3'UTR	SNP	G	TCGA-DW-7834-01A-11D-2136-08	21876110	220150708	23048665	11	8781											
DDX60	55601	hgsc.bcm.edu	37	chr4	169172121	169172121	+	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	ctaccctaagatatccttttCtaaagaggatttcaactaat	14	14	4	9	0	2	2	1	0	1	2	3	3	3	3	2	1	2	0	2	1	7	8			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr4:169172121C>T	ENST00000393743.3	-	28	4133	c.3842G>A	c.(3841-3843)aGa>aAa	p.R1281K	DDX60_ENST00000505393.1_5'Flank	NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	1281	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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)		ATATCCTTTTCTAAAGAGGAT	0.338																																					p.R1281K		Atlas-SNP	.											.	DDX60	304	.	0			c.G3842A						PASS	.						76	79	78					4																	169172121		2201	4297	6498	SO:0001583	missense	55601	exon28			CCTTTTCTAAAGA	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.3842G>A	chr4.hg19:g.169172121C>T	ENSP00000377344:p.Arg1281Lys	53.0	0.0	.		64.0	16.0	.	NM_017631	Q6PK35|Q9NVE3	Missense_Mutation	SNP	ENST00000393743.3	hg19	CCDS34097.1	.	.	.	.	.	.	.	.	.	.	C	12.97	2.096722	0.36952	.	.	ENSG00000137628	ENST00000393743	T	0.26957	1.7	5.4	5.4	0.78164	Helicase, C-terminal (3);	0.075985	0.56097	D	0.000034	T	0.27098	0.0664	L	0.39020	1.185	0.39934	D	0.974326	P	0.36768	0.569	B	0.38880	0.284	T	0.05750	-1.0866	10	0.52906	T	0.07	.	18.7821	0.91937	0.0:1.0:0.0:0.0	.	1281	Q8IY21	DDX60_HUMAN	K	1281	ENSP00000377344:R1281K	ENSP00000377344:R1281K	R	-	2	0	DDX60	169408696	1.000000	0.71417	0.408000	0.26446	0.120000	0.20174	4.958000	0.63660	2.549000	0.85964	0.467000	0.42956	AGA	.	.	.	none		0.338	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631		T	169172121	C	T	169172121	3	4	147	1	0	0	0	0	1	0	0	0	4380	913	32	2	1340	2	DDX60	4	169172121	Missense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08		169172121	21982155	12	8782											
PALLD	23022	hgsc.bcm.edu	37	chr4	169433375	169433375	+	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	gtcaagtcccctggggccagGcattgctaccaggacaacca	10	6	11	14	0	1	0	1	0	0	0	2	1	2	1	5	4	3	2	5	4	3	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr4:169433375G>A	ENST00000505667.1	+	2	893	c.720G>A	c.(718-720)agG>agA	p.R240R	PALLD_ENST00000333488.4_Silent_p.R117R|PALLD_ENST00000335742.7_5'UTR|PALLD_ENST00000261509.6_Silent_p.R240R			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	240					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)		CTGGGGCCAGGCATTGCTACC	0.597									Pancreatic Cancer, Familial Clustering of																												p.R240R	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.G720A						PASS	.						89	86	87					4																	169433375		2203	4300	6503	SO:0001819	synonymous_variant	23022	exon2	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	GGCCAGGCATTGC	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.720G>A	chr4.hg19:g.169433375G>A		119.0	0.0	.		121.0	5.0	.	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Silent	SNP	ENST00000505667.1	hg19	CCDS54818.1																																																																																			.	.	.	none		0.597	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081		A	169433375	G	A	169433375	2	1	147	1	0	0	0	0	0	0	0	1	11414	1194	42	2		2	PALLD	4	169433375	Silent	SNP	G	TCGA-DW-7834-01A-11D-2136-08	261254	169433375	21720901	13	8783											
WWC2	80014	hgsc.bcm.edu	37	chr4	184166688	184166688	+	Missense_Mutation	SNP	A	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	aggagaaaaagaaaaacaagAtctgatgcaggtacattata	21	7	9	4	0	1	4	0	1	1	3	1	5	1	4	0	2	3	2	0	2	8	3			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr4:184166688A>C	ENST00000403733.3	+	6	921	c.722A>C	c.(721-723)gAt>gCt	p.D241A	WWC2_ENST00000504005.1_Intron|WWC2_ENST00000378925.3_Missense_Mutation_p.D143A|WWC2_ENST00000448232.2_Missense_Mutation_p.D241A|WWC2_ENST00000513834.1_Missense_Mutation_p.D241A	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	241					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)		GAAAAACAAGATCTGATGCAG	0.433																																					p.D241A		Atlas-SNP	.											.	WWC2	78	.	0			c.A722C						PASS	.						50	50	50					4																	184166688		2203	4300	6503	SO:0001583	missense	80014	exon6			AACAAGATCTGAT	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.722A>C	chr4.hg19:g.184166688A>C	ENSP00000384222:p.Asp241Ala	54.0	0.0	.		50.0	14.0	.	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Missense_Mutation	SNP	ENST00000403733.3	hg19	CCDS34109.2	.	.	.	.	.	.	.	.	.	.	A	25.0	4.591096	0.86851	.	.	ENSG00000151718	ENST00000403733;ENST00000378925;ENST00000513834;ENST00000448232	T;T;T;T	0.15256	3.17;2.44;3.23;3.03	5.08	5.08	0.68730	.	0.000000	0.64402	D	0.000001	T	0.38904	0.1058	M	0.77820	2.39	0.58432	D	0.999999	D	0.67145	0.996	P	0.60609	0.877	T	0.15925	-1.0420	10	0.33940	T	0.23	-24.0084	15.3161	0.74078	1.0:0.0:0.0:0.0	.	241	Q6AWC2	WWC2_HUMAN	A	241;143;241;241	ENSP00000384222:D241A;ENSP00000368205:D143A;ENSP00000425054:D241A;ENSP00000398577:D241A	ENSP00000368205:D143A	D	+	2	0	WWC2	184403682	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	8.856000	0.92245	2.254000	0.74563	0.533000	0.62120	GAT	.	.	.	none		0.433	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949		C	184166688	A	C	184166688	3	2	147	1	0	0	0	0	1	0	0	0	17424	333	12	5	744	5	WWC2	4	184166688	Missense_Mutation	SNP	A	TCGA-DW-7834-01A-11D-2136-08	14733313	184166688	6987588	14	8784											
PDZD2	23037	hgsc.bcm.edu	37	chr5	32074625	32074625	+	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	cgaggctgaggccaagcccaGtggctcacagacagtgaacc	11	4	13	13	1	1	3	1	2	0	1	1	4	1	3	3	3	2	2	3	3	2	0			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr5:32074625G>T	ENST00000438447.1	+	18	3801	c.3413G>T	c.(3412-3414)aGt>aTt	p.S1138I	PDZD2_ENST00000282493.3_Missense_Mutation_p.S1138I			O15018	PDZD2_HUMAN	PDZ domain containing 2	1138					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						GCCAAGCCCAGTGGCTCACAG	0.587																																					p.S1138I		Atlas-SNP	.											.	PDZD2	306	.	0			c.G3413T						PASS	.						42	42	42					5																	32074625		2203	4300	6503	SO:0001583	missense	23037	exon17			AGCCCAGTGGCTC	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.3413G>T	chr5.hg19:g.32074625G>T	ENSP00000402033:p.Ser1138Ile	64.0	0.0	.		49.0	19.0	.	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	hg19	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	G	12.67	2.006840	0.35415	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.06933	3.24;3.24	5.21	1.07	0.20283	.	1.010820	0.07935	N	0.978210	T	0.06325	0.0163	L	0.51422	1.61	0.09310	N	1	P;B	0.37864	0.61;0.01	B;B	0.28139	0.086;0.014	T	0.38436	-0.9661	10	0.20519	T	0.43	.	4.0787	0.09916	0.1583:0.1285:0.5814:0.1318	.	964;1138	B4E3P2;O15018	.;PDZD2_HUMAN	I	1138;940;1138	ENSP00000402033:S1138I;ENSP00000282493:S1138I	ENSP00000282493:S1138I	S	+	2	0	PDZD2	32110382	0.002000	0.14202	0.001000	0.08648	0.005000	0.04900	1.151000	0.31651	0.543000	0.28864	0.655000	0.94253	AGT	.	.	.	none		0.587	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			T	32074625	G	T	32074625	3	4	147	1	0	0	0	0	1	0	0	0	11708	1029	36	4	3479	4	PDZD2	5	32074625	Missense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08		32074625	148840635	15	8785											
FCHO2	115548	hgsc.bcm.edu	37	chr5	72383545	72383545	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgaacttgtgggcactggctAtaggctttccttaataaaga	11	12	10	8	1	0	1	0	0	0	1	1	2	1	1	1	3	1	3	1	3	6	6			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr5:72383545A>G	ENST00000430046.2	+	25	2491	c.2375A>G	c.(2374-2376)tAt>tGt	p.Y792C	FCHO2_ENST00000341845.6_Missense_Mutation_p.Y792C|FCHO2_ENST00000512348.1_Missense_Mutation_p.Y759C	NM_001146032.1|NM_138782.2	NP_001139504.1|NP_620137.2	Q0JRZ9	FCHO2_HUMAN	FCH domain only 2	792	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.|Mediates interaction with DAB2, EPS15, EPS15R and ITSN1.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|membrane invagination (GO:0010324)|protein localization to plasma membrane (GO:0072659)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	17		Lung NSC(167;0.0465)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;4.6e-53)		GGCACTGGCTATAGGCTTTCC	0.398																																					p.Y792C		Atlas-SNP	.											.	FCHO2	96	.	0			c.A2375G						PASS	.						128	126	127					5																	72383545		1836	4085	5921	SO:0001583	missense	115548	exon25			CTGGCTATAGGCT	AL831971	CCDS47230.1, CCDS54868.1	5q13.2	2005-08-15			ENSG00000157107	ENSG00000157107			25180	protein-coding gene	gene with protein product		613438				15254787	Standard	NM_138782		Approved		uc003kcl.3	Q0JRZ9	OTTHUMG00000162413	ENST00000430046.2:c.2375A>G	chr5.hg19:g.72383545A>G	ENSP00000393776:p.Tyr792Cys	213.0	0.0	.		229.0	61.0	.	NM_138782	A8K6W7|B2RNQ9|B4DHK0|E9PG79|Q0JTJ3|Q96CF5	Missense_Mutation	SNP	ENST00000430046.2	hg19	CCDS47230.1	.	.	.	.	.	.	.	.	.	.	A	15.49	2.849389	0.51270	.	.	ENSG00000157107	ENST00000430046;ENST00000341845;ENST00000512348	T;T;T	0.54675	0.56;0.56;0.56	4.77	4.77	0.60923	Muniscin C-terminal mu homology domain (1);	0.000000	0.85682	D	0.000000	T	0.75591	0.3870	M	0.87682	2.9	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.81024	-0.1120	10	0.87932	D	0	-11.6205	14.7503	0.69519	1.0:0.0:0.0:0.0	.	759;792	E9PG79;Q0JRZ9	.;FCHO2_HUMAN	C	792;792;759	ENSP00000393776:Y792C;ENSP00000344034:Y792C;ENSP00000427296:Y759C	ENSP00000344034:Y792C	Y	+	2	0	FCHO2	72419301	1.000000	0.71417	0.960000	0.40013	0.262000	0.26303	8.705000	0.91357	2.124000	0.65301	0.528000	0.53228	TAT	.	.	.	none		0.398	FCHO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368795.3	XM_291142		G	72383545	A	G	72383545	3	3	147	1	0	0	0	0	1	0	0	0	5795	449	16	3	2473	3	FCHO2	5	72383545	Missense_Mutation	SNP	A	TCGA-DW-7834-01A-11D-2136-08	40308920	72383545	108531715	16	8786											
VCAN	1462	hgsc.bcm.edu	37	chr5	82785943	82785943	+	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	tgggaaaaagcccaccggtgAggggctccctctctggaaaa	11	6	13	11	1	1	1	0	1	1	0	3	3	2	3	3	5	1	1	3	5	4	0			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr5:82785943A>T	ENST00000265077.3	+	3	662	c.97A>T	c.(97-99)Agg>Tgg	p.R33W	VCAN_ENST00000513984.1_Missense_Mutation_p.R33W|VCAN_ENST00000512590.2_De_novo_Start_InFrame|VCAN_ENST00000342785.4_Missense_Mutation_p.R33W|VCAN_ENST00000343200.5_Missense_Mutation_p.R33W|VCAN_ENST00000502527.2_Missense_Mutation_p.R33W	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	33	Ig-like V-type.				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)	CCCACCGGTGAGGGGCTCCCT	0.403																																					p.R33W		Atlas-SNP	.											.	VCAN	498	.	0			c.A97T						PASS	.						51	51	51					5																	82785943		2202	4293	6495	SO:0001583	missense	1462	exon3			CCGGTGAGGGGCT	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.97A>T	chr5.hg19:g.82785943A>T	ENSP00000265077:p.Arg33Trp	102.0	0.0	.		115.0	32.0	.	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	hg19	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	A	14.90	2.672502	0.47781	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000342785;ENST00000513960;ENST00000513984;ENST00000502527	T;T;T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24;-0.24;-0.24	5.99	2.17	0.27698	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.395914	0.24213	N	0.040512	T	0.72220	0.3433	L	0.50333	1.59	0.21064	N	0.999792	P;P;D;D;D	0.63880	0.804;0.857;0.986;0.993;0.965	P;P;P;D;P	0.66602	0.87;0.641;0.702;0.945;0.838	T	0.62613	-0.6817	10	0.72032	D	0.01	.	8.4359	0.32786	0.6885:0.2476:0.0639:0.0	.	33;33;33;33;33	P13611-3;P13611-4;P13611-2;P13611;Q86W61	.;.;.;CSPG2_HUMAN;.	W	33	ENSP00000265077:R33W;ENSP00000340062:R33W;ENSP00000342768:R33W;ENSP00000426251:R33W;ENSP00000426715:R33W;ENSP00000421362:R33W	ENSP00000265077:R33W	R	+	1	2	VCAN	82821699	0.054000	0.20591	0.027000	0.17364	0.046000	0.14306	1.559000	0.36320	0.134000	0.18681	-0.316000	0.08728	AGG	.	.	.	none		0.403	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		T	82785943	A	T	82785943	3	4	147	1	0	0	0	0	1	0	0	0	17150	295	11	5	103	5	VCAN	5	82785943	Missense_Mutation	SNP	A	TCGA-DW-7834-01A-11D-2136-08	10402398	82785943	98129317	17	8787											
VARS2	57176	hgsc.bcm.edu	37	chr6	30888201	30888201	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagaaccaccccatggtacTgcccatctgcaggtaacctc	10	7	7	17	0	1	1	0	0	1	1	2	1	1	1	6	2	5	3	6	2	3	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr6:30888201T>C	ENST00000321897.5	+	13	2017	c.1385T>C	c.(1384-1386)cTg>cCg	p.L462P	VARS2_ENST00000416670.2_Missense_Mutation_p.L462P|VARS2_ENST00000476162.1_3'UTR|VARS2_ENST00000542001.1_Missense_Mutation_p.L322P|VARS2_ENST00000541562.1_Missense_Mutation_p.L492P			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	462					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						CCCATGGTACTGCCCATCTGC	0.527																																					p.L492P		Atlas-SNP	.											.	VARS2	60	.	0			c.T1475C						PASS	.						41	43	42					6																	30888201		2203	4300	6503	SO:0001583	missense	57176	exon14			TGGTACTGCCCAT	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.1385T>C	chr6.hg19:g.30888201T>C	ENSP00000316092:p.Leu462Pro	48.0	0.0	.		61.0	19.0	.	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Missense_Mutation	SNP	ENST00000321897.5	hg19	CCDS34387.1	.	.	.	.	.	.	.	.	.	.	T	19.18	3.777854	0.70107	.	.	ENSG00000137411	ENST00000321897;ENST00000416670;ENST00000542001;ENST00000541562	T;T;T;T	0.37752	1.18;1.18;1.18;1.18	4.26	4.26	0.50523	Valyl/Leucyl/Isoleucyl-tRNA synthetase, class Ia, editing domain (1);Aminoacyl-tRNA synthetase, class Ia (1);	0.000000	0.64402	D	0.000002	T	0.56077	0.1961	M	0.88450	2.955	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.996	T	0.65923	-0.6050	10	0.87932	D	0	-11.1733	11.6463	0.51263	0.0:0.0:0.0:1.0	.	460;492;462	B7ZL25;F5GXJ0;Q5ST30	.;.;SYVM_HUMAN	P	462;462;322;492	ENSP00000316092:L462P;ENSP00000394802:L462P;ENSP00000438200:L322P;ENSP00000441000:L492P	ENSP00000316092:L462P	L	+	2	0	VARS2	30996180	1.000000	0.71417	0.999000	0.59377	0.982000	0.71751	7.008000	0.76341	1.708000	0.51301	0.374000	0.22700	CTG	.	.	.	none		0.527	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442		C	30888201	T	C	30888201	3	2	147	1	0	0	0	0	1	0	0	0	17136	1580	55	3	1529	3	VARS2	6	30888201	Missense_Mutation	SNP	T	TCGA-DW-7834-01A-11D-2136-08		30888201	140226866	18	8788											
ZNF76	7629	hgsc.bcm.edu	37	chr6	35260658	35260658	+	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	ccttggctctcctctcccagCcgcctctgcagccgaggaga	5	8	10	18	2	3	1	0	0	3	1	5	3	3	1	6	2	3	2	6	2	0	1			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr6:35260658C>T	ENST00000373953.3	+	11	1432	c.1166C>T	c.(1165-1167)gCc>gTc	p.A389V	ZNF76_ENST00000339411.5_Splice_Site_p.A389V|ZNF76_ENST00000440666.2_Splice_Site_p.A363V	NM_003427.3	NP_003418.2	P36508	ZNF76_HUMAN	zinc finger protein 76	389					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						CCTCTCCCAGCCGCCTCTGCA	0.622																																					p.A389V	Esophageal Squamous(52;92 1039 20612 23956 34676)	Atlas-SNP	.											.	ZNF76	37	.	0			c.C1166T						PASS	.						54	58	57					6																	35260658		2203	4300	6503	SO:0001630	splice_region_variant	7629	exon11			TCCCAGCCGCCTC	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.1166-1C>T	chr6.hg19:g.35260658C>T		129.0	0.0	.		148.0	45.0	.	NM_003427	Q9BQB2	Missense_Mutation	SNP	ENST00000373953.3	hg19	CCDS4801.1	.	.	.	.	.	.	.	.	.	.	C	14.71	2.615788	0.46631	.	.	ENSG00000065029	ENST00000373953;ENST00000440666;ENST00000339411	T;T;T	0.10668	2.88;2.88;2.85	4.83	4.83	0.62350	.	0.000000	0.36740	N	0.002424	T	0.01835	0.0058	N	0.08118	0	0.26011	N	0.981989	B;B	0.33135	0.392;0.399	B;B	0.34452	0.115;0.183	T	0.43196	-0.9406	9	.	.	.	.	8.2836	0.31915	0.176:0.6542:0.1698:0.0	.	389;389	P36508-2;P36508	.;ZNF76_HUMAN	V	389;363;389	ENSP00000363064:A389V;ENSP00000392243:A363V;ENSP00000344097:A389V	.	A	+	2	0	ZNF76	35368636	0.001000	0.12720	1.000000	0.80357	0.876000	0.50452	1.026000	0.30103	2.487000	0.83934	0.491000	0.48974	GCC	.	.	.	none		0.622	ZNF76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040279.2	NM_003427	Missense_Mutation	T	35260658	C	T	35260658	5	4	147	1	0	0	0	0	0	0	1	0	18147	753	26	2	1204	2	ZNF76	6	35260658	Splice_Site	SNP	C	TCGA-DW-7834-01A-11D-2136-08	4372457	35260658	135854409	19	8789											
DNAH8	1769	hgsc.bcm.edu	37	chr6	38709565	38709565	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aattggaacactggaaacgcAtgtcagccaagttcaactat	15	9	8	9	1	2	0	2	0	0	0	2	2	2	2	1	2	4	2	1	2	6	3			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr6:38709565A>G	ENST00000359357.3	+	6	798	c.544A>G	c.(544-546)Atg>Gtg	p.M182V	DNAH8_ENST00000449981.2_Missense_Mutation_p.M399V|RN7SL465P_ENST00000468411.2_RNA|DNAH8_ENST00000441566.1_Missense_Mutation_p.M182V			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	182					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						CTGGAAACGCATGTCAGCCAA	0.398																																					p.M399V		Atlas-SNP	.											.	DNAH8	1239	.	0			c.A1195G						PASS	.						121	105	110					6																	38709565		2203	4300	6503	SO:0001583	missense	1769	exon8			AAACGCATGTCAG	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.544A>G	chr6.hg19:g.38709565A>G	ENSP00000352312:p.Met182Val	83.0	0.0	.		77.0	27.0	.	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	A	16.47	3.131132	0.56828	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.56611	0.45;0.45;0.45	5.91	5.91	0.95273	Dynein heavy chain, domain-1 (1);	0.047100	0.85682	D	0.000000	T	0.36276	0.0961	L	0.29908	0.895	0.40827	D	0.983553	B	0.27765	0.188	B	0.36608	0.229	T	0.42965	-0.9420	10	0.66056	D	0.02	.	16.3429	0.83101	1.0:0.0:0.0:0.0	.	182	Q96JB1	DYH8_HUMAN	V	387;387;182;182	ENSP00000333363:M387V;ENSP00000352312:M182V;ENSP00000402294:M182V	ENSP00000333363:M387V	M	+	1	0	DNAH8	38817543	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.248000	0.72418	2.256000	0.74724	0.523000	0.50628	ATG	.	.	.	none		0.398	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		G	38709565	A	G	38709565	3	3	147	1	0	0	0	0	1	0	0	0	4609	217	8	3	558	3	DNAH8	6	38709565	Missense_Mutation	SNP	A	TCGA-DW-7834-01A-11D-2136-08	3448907	38709565	132405502	20	8790											
BAI3	577	hgsc.bcm.edu	37	chr6	69943243	69943243	+	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	ctgtgcttaccgatgcatccCatacgaaatgcttatgtgat	10	13	8	10	2	0	1	0	1	0	0	1	3	1	1	2	0	5	3	2	0	4	3			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr6:69943243C>T	ENST00000370598.1	+	18	3363	c.2542C>T	c.(2542-2544)Cat>Tat	p.H848Y	BAI3_ENST00000238918.8_Missense_Mutation_p.H54Y	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	848	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.				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)				CGATGCATCCCATACGAAATG	0.473																																					p.H848Y		Atlas-SNP	.											.	BAI3	451	.	0			c.C2542T						PASS	.						203	180	188					6																	69943243		2203	4300	6503	SO:0001583	missense	577	exon18			GCATCCCATACGA	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.2542C>T	chr6.hg19:g.69943243C>T	ENSP00000359630:p.His848Tyr	266.0	0.0	.		215.0	68.0	.	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	hg19	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	C	15.82	2.946496	0.53186	.	.	ENSG00000135298	ENST00000370598;ENST00000238918	T;T	0.69175	-0.38;-0.38	5.37	5.37	0.77165	GPS domain (3);	0.000000	0.85682	D	0.000000	T	0.75953	0.3920	L	0.54863	1.705	0.80722	D	1	D;D	0.89917	0.982;1.0	P;D	0.87578	0.824;0.998	T	0.77230	-0.2664	10	0.62326	D	0.03	.	19.1872	0.93648	0.0:1.0:0.0:0.0	.	54;848	B7Z356;O60242	.;BAI3_HUMAN	Y	848;54	ENSP00000359630:H848Y;ENSP00000238918:H54Y	ENSP00000238918:H54Y	H	+	1	0	BAI3	69999964	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.889000	0.69766	2.539000	0.85634	0.454000	0.30748	CAT	.	.	.	none		0.473	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			T	69943243	C	T	69943243	3	4	147	1	0	0	0	0	1	0	0	0	1300	594	21	2	2604	2	BAI3	6	69943243	Missense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08	31233678	69943243	101171824	21	8791											
RFX6	222546	hgsc.bcm.edu	37	chr6	117245902	117245902	+	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	atggagacccagtttaataaTgacaaagagcaggagttaca	17	8	10	6	0	0	3	0	1	0	2	0	5	0	4	1	2	2	3	1	2	4	4			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr6:117245902T>A	ENST00000332958.2	+	15	1642	c.1626T>A	c.(1624-1626)aaT>aaA	p.N542K		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	542					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						AGTTTAATAATGACAAAGAGC	0.338																																					p.N542K		Atlas-SNP	.											.	RFX6	141	.	0			c.T1626A						PASS	.						100	99	99					6																	117245902		2203	4300	6503	SO:0001583	missense	222546	exon15			TAATAATGACAAA	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.1626T>A	chr6.hg19:g.117245902T>A	ENSP00000332208:p.Asn542Lys	97.0	0.0	.		92.0	20.0	.	NM_173560	Q5T6B3	Missense_Mutation	SNP	ENST00000332958.2	hg19	CCDS5113.1	.	.	.	.	.	.	.	.	.	.	T	17.98	3.521372	0.64747	.	.	ENSG00000185002	ENST00000332958	T	0.57107	0.42	5.32	4.15	0.48705	.	0.000000	0.85682	D	0.000000	T	0.46229	0.1382	L	0.49640	1.575	0.53688	D	0.999972	D	0.59357	0.985	P	0.53360	0.724	T	0.50508	-0.8820	10	0.56958	D	0.05	-21.9444	10.8185	0.46591	0.0:0.0743:0.0:0.9257	.	542	Q8HWS3	RFX6_HUMAN	K	542	ENSP00000332208:N542K	ENSP00000332208:N542K	N	+	3	2	RFX6	117352595	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.890000	0.39728	2.138000	0.66242	0.533000	0.62120	AAT	.	.	.	none		0.338	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560		A	117245902	T	A	117245902	3	1	147	1	0	0	0	0	1	0	0	0	13280	1461	51	5	1684	5	RFX6	6	117245902	Missense_Mutation	SNP	T	TCGA-DW-7834-01A-11D-2136-08	47302659	117245902	53869165	22	8792											
AEBP1	165	hgsc.bcm.edu	37	chr7	44152208	44152208	+	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	ggatggagaagaaccccttcGtgctgggagcaaatctgaac	12	7	13	9	1	1	3	0	1	1	2	2	6	1	5	2	3	4	2	2	3	4	1			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr7:44152208G>C	ENST00000223357.3	+	18	2574	c.2269G>C	c.(2269-2271)Gtg>Ctg	p.V757L	MIR4649_ENST00000582839.1_RNA|AEBP1_ENST00000450684.2_Missense_Mutation_p.V332L	NM_001129.3	NP_001120.3	Q8IUX7	AEBP1_HUMAN	AE binding protein 1	757	Interaction with PTEN. {ECO:0000250}.				cell adhesion (GO:0007155)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(13)|upper_aerodigestive_tract(2)	33						GAACCCCTTCGTGCTGGGAGC	0.642																																					p.V757L		Atlas-SNP	.											.	AEBP1	102	.	0			c.G2269C						PASS	.						48	52	51					7																	44152208		2203	4299	6502	SO:0001583	missense	165	exon18			CCCTTCGTGCTGG	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.2269G>C	chr7.hg19:g.44152208G>C	ENSP00000223357:p.Val757Leu	117.0	0.0	.		151.0	40.0	.	NM_001129	Q14113|Q59ER7|Q6ZSC7|Q7KZ79	Missense_Mutation	SNP	ENST00000223357.3	hg19	CCDS5476.1	.	.	.	.	.	.	.	.	.	.	G	32	5.147205	0.94603	.	.	ENSG00000106624	ENST00000223357;ENST00000450684	T;T	0.03524	3.9;3.9	5.08	5.08	0.68730	Peptidase M14, carboxypeptidase A (2);	0.000000	0.85682	D	0.000000	T	0.20981	0.0505	M	0.83953	2.67	0.80722	D	1	D;P	0.76494	0.999;0.887	D;P	0.81914	0.995;0.796	T	0.00473	-1.1718	10	0.62326	D	0.03	-39.5208	17.5863	0.87982	0.0:0.0:1.0:0.0	.	332;757	Q8IUX7-2;Q8IUX7	.;AEBP1_HUMAN	L	757;332	ENSP00000223357:V757L;ENSP00000398878:V332L	ENSP00000223357:V757L	V	+	1	0	AEBP1	44118733	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.597000	0.74118	2.533000	0.85409	0.491000	0.48974	GTG	.	.	.	none		0.642	AEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250993.2	NM_001129		C	44152208	G	C	44152208	3	2	147	1	0	0	0	0	1	0	0	0	349	1145	40	4	2339	4	AEBP1	7	44152208	Missense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08		44152208	114986455	23	8793											
OGDH	4967	hgsc.bcm.edu	37	chr7	44714122	44714122	+	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	ttgacaagtctagtgagaatGgcgtggactacgtgatcatg	11	11	13	6	2	2	3	1	3	1	1	2	5	2	4	0	2	1	0	0	2	4	3			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr7:44714122G>A	ENST00000222673.5	+	7	943	c.901G>A	c.(901-903)Ggc>Agc	p.G301S	OGDH_ENST00000443864.2_Missense_Mutation_p.G301S|OGDH_ENST00000543843.1_Missense_Mutation_p.G252S|OGDH_ENST00000439616.2_Missense_Mutation_p.G151S|OGDH_ENST00000447398.1_Missense_Mutation_p.G312S|OGDH_ENST00000444676.1_Missense_Mutation_p.G316S|OGDH_ENST00000449767.1_Missense_Mutation_p.G297S|OGDH_ENST00000459672.1_3'UTR	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	301					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)	TAGTGAGAATGGCGTGGACTA	0.572																																					p.G301S		Atlas-SNP	.											.	OGDH	145	.	0			c.G901A						PASS	.						136	110	119					7																	44714122		2203	4300	6503	SO:0001583	missense	4967	exon7			GAGAATGGCGTGG	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.901G>A	chr7.hg19:g.44714122G>A	ENSP00000222673:p.Gly301Ser	104.0	0.0	.		126.0	55.0	.	NM_002541	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Missense_Mutation	SNP	ENST00000222673.5	hg19	CCDS34627.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.996894	0.93167	.	.	ENSG00000105953	ENST00000439616;ENST00000443864;ENST00000449767;ENST00000447398;ENST00000444676;ENST00000222673;ENST00000543843	D;T;D;D;D;D;D	0.95788	-3.81;2.48;-3.81;-3.81;-3.81;-3.81;-3.81	4.97	4.97	0.65823	Dehydrogenase, E1 component (1);	0.000000	0.85682	D	0.000000	D	0.98061	0.9361	M	0.88570	2.965	0.80722	D	1	D;D;D;D;D;D;D	0.76494	0.999;0.999;0.998;0.998;0.998;0.998;0.999	D;D;D;D;D;D;D	0.87578	0.995;0.996;0.995;0.996;0.992;0.995;0.998	D	0.99091	1.0840	10	0.87932	D	0	-17.2819	18.1993	0.89833	0.0:0.0:1.0:0.0	.	96;151;297;312;203;301;301	B4E3E9;E9PFG7;E9PBM1;E9PDF2;A2VCT2;Q02218;Q96DD3	.;.;.;.;.;ODO1_HUMAN;.	S	151;301;297;312;316;301;252	ENSP00000398576:G151S;ENSP00000388084:G301S;ENSP00000392878:G297S;ENSP00000388183:G312S;ENSP00000414662:G316S;ENSP00000222673:G301S;ENSP00000443821:G252S	ENSP00000222673:G301S	G	+	1	0	OGDH	44680647	1.000000	0.71417	0.169000	0.22859	0.771000	0.43674	9.609000	0.98334	2.462000	0.83206	0.561000	0.74099	GGC	.	.	.	none		0.572	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1			A	44714122	G	A	44714122	3	1	147	1	0	0	0	0	1	0	0	0	10846	1348	47	2	1018	2	OGDH	7	44714122	Missense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08	561914	44714122	114424541	24	8794											
VSTM2A	222008	hgsc.bcm.edu	37	chr7	54617692	54617692	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaatgccaacagccatgccCgcagaatgcaggccttcgaa	12	6	9	14	2	1	1	1	0	0	1	2	2	1	1	4	1	5	2	4	1	4	1			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr7:54617692C>T	ENST00000407838.3	+	4	869	c.463C>T	c.(463-465)Cgc>Tgc	p.R155C	VSTM2A_ENST00000402026.2_Missense_Mutation_p.R154C|VSTM2A_ENST00000404951.1_Missense_Mutation_p.R155C|VSTM2A_ENST00000498834.1_3'UTR|VSTM2A_ENST00000302287.3_Missense_Mutation_p.R155C|VSTM2A_ENST00000402613.3_Missense_Mutation_p.R155C	NM_182546.2	NP_872352.2	Q8TAG5	VTM2A_HUMAN	V-set and transmembrane domain containing 2A	155						extracellular region (GO:0005576)		p.R155C(1)|p.R154C(1)		endometrium(1)|large_intestine(2)|lung(12)|prostate(1)	16			STAD - Stomach adenocarcinoma(5;0.0525)			CAGCCATGCCCGCAGAATGCA	0.577																																					p.R155C		Atlas-SNP	.											VSTM2A,NS,carcinoma,0,2	VSTM2A	53	.	2	Substitution - Missense(2)	endometrium(2)	c.C463T						PASS	.						57	54	55					7																	54617692		2203	4299	6502	SO:0001583	missense	222008	exon4			CATGCCCGCAGAA	BC028404	CCDS5512.2, CCDS75604.1	7p11.2	2013-01-11	2007-08-10	2007-08-10	ENSG00000170419	ENSG00000170419		"Immunoglobulin superfamily / V-set domain containing"	28499	protein-coding gene	gene with protein product			"V-set and transmembrane domain containing 2"	VSTM2		12477932	Standard	XM_006715663		Approved	MGC33530	uc010kzf.3	Q8TAG5	OTTHUMG00000129271	ENST00000407838.3:c.463C>T	chr7.hg19:g.54617692C>T	ENSP00000384967:p.Arg155Cys	30.0	0.0	.		32.0	13.0	.	NM_182546	A4D2E9|B5MC94	Missense_Mutation	SNP	ENST00000407838.3	hg19	CCDS5512.2	.	.	.	.	.	.	.	.	.	.	C	20.2	3.950503	0.73787	.	.	ENSG00000170419	ENST00000302287;ENST00000407838;ENST00000404951;ENST00000402026;ENST00000402613	T;T;T;T;T	0.50277	0.75;0.78;0.75;0.75;0.78	5.06	3.17	0.36434	.	0.000000	0.85682	D	0.000000	T	0.64080	0.2566	M	0.68952	2.095	0.52501	D	0.999954	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.996;0.998;0.993	T	0.63440	-0.6637	10	0.51188	T	0.08	-25.8697	11.9552	0.52976	0.334:0.666:0.0:0.0	.	155;155;155	Q8TAG5;Q8TAG5-2;B5MCX6	VTM2A_HUMAN;.;.	C	155;155;155;154;155	ENSP00000303108:R155C;ENSP00000384967:R155C;ENSP00000384701:R155C;ENSP00000385933:R154C;ENSP00000384103:R155C	ENSP00000303108:R155C	R	+	1	0	VSTM2A	54585186	0.357000	0.24938	0.524000	0.27887	0.981000	0.71138	0.571000	0.23669	0.566000	0.29273	0.655000	0.94253	CGC	.	.	.	none		0.577	VSTM2A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318694.1	NM_182546		T	54617692	C	T	54617692	3	4	147	1	0	0	0	0	1	0	0	0	17241	652	23	1	477	1	VSTM2A	7	54617692	Missense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08	9903570	54617692	104520971	25	8795											
LUC7L2	100996928	hgsc.bcm.edu	37	chr7	139107032	139107032	+	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	cggtcctatgagagtgctaaTggcagatcagaagacaggag	13	7	14	7	1	1	4	1	1	0	4	2	6	2	5	1	3	1	2	1	3	3	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr7:139107032T>A	ENST00000354926.4	+	10	1479	c.1125T>A	c.(1123-1125)aaT>aaA	p.N375K	C7orf55-LUC7L2_ENST00000482860.1_3'UTR|C7orf55-LUC7L2_ENST00000541170.3_Missense_Mutation_p.N372K|LUC7L2_ENST00000541515.3_Missense_Mutation_p.N441K|C7orf55-LUC7L2_ENST00000263545.6_Missense_Mutation_p.N374K	NM_001270643.1|NM_016019.4	NP_001257572.1|NP_057103.2			C7orf55-LUC7L2 readthrough																		AGAGTGCTAATGGCAGATCAG	0.478																																					p.N441K		Atlas-SNP	.											.	.	.	.	0			c.T1323A						PASS	.						133	136	135					7																	139107032		1945	4137	6082	SO:0001583	missense	100996928	exon11			TGCTAATGGCAGA		CCDS59084.1	7q34	2013-02-14			ENSG00000146963	ENSG00000146963			44671	other	readthrough							Standard	NM_001244584		Approved		uc011kqt.3		OTTHUMG00000151717	ENST00000354926.4:c.1125T>A	chr7.hg19:g.139107032T>A	ENSP00000347005:p.Asn375Lys	170.0	0.0	.		200.0	102.0	.	NM_001244584		Missense_Mutation	SNP	ENST00000354926.4	hg19	CCDS43656.1	.	.	.	.	.	.	.	.	.	.	T	15.60	2.880250	0.51801	.	.	ENSG00000146963	ENST00000541170;ENST00000541515;ENST00000545899;ENST00000354926;ENST00000263545	T;T;T;T	0.41400	1.59;1.59;1.59;1.0	6.03	3.72	0.42706	.	0.255682	0.45126	D	0.000400	T	0.33702	0.0872	L	0.58810	1.83	0.42902	D	0.994235	P;P;P;P	0.40731	0.608;0.608;0.728;0.608	B;B;B;B	0.36186	0.109;0.109;0.219;0.109	T	0.46898	-0.9158	9	0.23891	T	0.37	-21.4412	8.941	0.35729	0.0:0.2436:0.0:0.7564	.	441;372;374;375	B7Z4Q3;B7Z500;Q9Y383-2;Q9Y383	.;.;.;LC7L2_HUMAN	K	372;441;375;375;374	ENSP00000441604:N372K;ENSP00000440222:N441K;ENSP00000347005:N375K;ENSP00000263545:N374K	ENSP00000263545:N374K	N	+	3	2	LUC7L2	138757572	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	0.312000	0.19397	1.117000	0.41842	0.455000	0.32223	AAT	.	.	.	none		0.478	C7orf55-LUC7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323618.2			A	139107032	T	A	139107032	3	1	147	1	0	0	0	0	1	0	0	0	9090	1461	51	5	1163	5	LUC7L2	7	139107032	Missense_Mutation	SNP	T	TCGA-DW-7834-01A-11D-2136-08	84489340	139107032	20031631	26	8796											
PRSS55	203074	hgsc.bcm.edu	37	chr8	10390473	10390473	+	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	gccaatggtcatcatggactGggaggagtgttcaaagatgt	11	10	14	6	0	3	1	3	0	0	1	3	4	3	4	1	4	0	1	1	4	2	1	rs150767306		TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr8:10390473G>A	ENST00000328655.3	+	4	696	c.656G>A	c.(655-657)tGg>tAg	p.W219*	PRSS55_ENST00000522210.1_Nonsense_Mutation_p.W219*|PRSS51_ENST00000523024.1_RNA	NM_198464.3	NP_940866.2	Q6UWB4	PRS55_HUMAN	protease, serine, 55	219	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)	31						ATCATGGACTGGGAGGAGTGT	0.473																																					p.W219X		Atlas-SNP	.											.	PRSS55	67	.	0			c.G656A						PASS	.						124	112	116					8																	10390473		2203	4300	6503	SO:0001587	stop_gained	203074	exon4			TGGACTGGGAGGA	AY358867	CCDS5976.1, CCDS56523.1	8p23.1	2014-01-21			ENSG00000184647	ENSG00000184647		"Serine peptidases / Serine peptidases"	30824	protein-coding gene	gene with protein product		615144				12975309, 18844450	Standard	NM_198464		Approved	T-SP1, UNQ9391, CT153	uc003wta.3	Q6UWB4	OTTHUMG00000129345	ENST00000328655.3:c.656G>A	chr8.hg19:g.10390473G>A	ENSP00000333003:p.Trp219*	109.0	0.0	.		95.0	34.0	.	NM_001197020	E5RJX5	Nonsense_Mutation	SNP	ENST00000328655.3	hg19	CCDS5976.1	.	.	.	.	.	.	.	.	.	.	G	19.40	3.820578	0.71028	.	.	ENSG00000184647	ENST00000328655;ENST00000522210	.	.	.	5.27	4.39	0.52855	.	0.259915	0.20629	N	0.088631	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	.	10.0857	0.42417	0.094:0.0:0.906:0.0	.	.	.	.	X	219	.	ENSP00000333003:W219X	W	+	2	0	PRSS55	10427883	0.948000	0.32251	0.056000	0.19401	0.063000	0.16089	1.788000	0.38714	1.344000	0.45657	0.591000	0.81541	TGG	.	G|1.000;T|0.000	.	alt		0.473	PRSS55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251493.3	NM_198464		A	10390473	G	A	10390473	4	1	147	1	0	0	0	0	0	1	0	0	12644	1357	47	2	670	2	PRSS55	8	10390473	Nonsense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08		10390473	135973549	27	8797											
C8orf80	389643	hgsc.bcm.edu	37	chr8	27888815	27888815	+	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	atttccagccacttcttatcCcaatttctgtcattttctcc	7	18	2	14	0	4	0	1	0	3	0	7	0	6	0	4	0	1	0	4	0	2	6			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr8:27888815C>G	ENST00000413272.2	-	15	1995	c.1853G>C	c.(1852-1854)gGg>gCg	p.G618A	NUGGC_ENST00000341513.6_Missense_Mutation_p.G618A	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	618					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)										ACTTCTTATCCCAATTTCTGT	0.468																																					p.G618A		Atlas-SNP	.											.	.	.	.	0			c.G1853C						PASS	.						139	140	140					8																	27888815		1863	4103	5966	SO:0001583	missense	389643	exon15			CTTATCCCAATTT	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.1853G>C	chr8.hg19:g.27888815C>G	ENSP00000408697:p.Gly618Ala	202.0	0.0	.		192.0	49.0	.	NM_001010906	Q6ZP73	Missense_Mutation	SNP	ENST00000413272.2	hg19	CCDS47833.1	.	.	.	.	.	.	.	.	.	.	C	10.38	1.333721	0.24167	.	.	ENSG00000189233	ENST00000413272;ENST00000341513	T;T	0.32753	1.44;1.44	5.23	4.26	0.50523	.	0.580298	0.17797	N	0.161690	T	0.18002	0.0432	L	0.27053	0.805	0.09310	N	1	B	0.27229	0.172	B	0.22386	0.039	T	0.14309	-1.0477	10	0.06625	T	0.88	-16.0958	11.7736	0.51972	0.1875:0.8125:0.0:0.0	.	618	Q68CJ6	SLIP_HUMAN	A	618	ENSP00000408697:G618A;ENSP00000345031:G618A	ENSP00000345031:G618A	G	-	2	0	C8orf80	27944734	0.006000	0.16342	0.846000	0.33378	0.810000	0.45777	1.525000	0.35953	2.441000	0.82636	0.655000	0.94253	GGG	.	.	.	none		0.468	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906		G	27888815	C	G	27888815	3	3	147	1	0	0	0	0	1	0	0	0	2441	623	22	4	557	4	C8orf80	8	27888815	Missense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08	17498342	27888815	118475207	28	8798											
NR5A1	2516	hgsc.bcm.edu	37	chr9	127262609	127262609	+	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	aagggctctgggtagccgtaCggcagcccaggctgtggggg	6	6	19	10	2	1	0	0	0	1	0	1	0	1	0	2	6	3	5	2	6	3	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr9:127262609C>A	ENST00000373588.4	-	4	826	c.630G>T	c.(628-630)ccG>ccT	p.P210P		NM_004959.4	NP_004950.2	Q13285	STF1_HUMAN	nuclear receptor subfamily 5, group A, member 1	210					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						GGTAGCCGTACGGCAGCCCAG	0.667																																					p.P210P		Atlas-SNP	.											NR5A1,colon,carcinoma,0,1	NR5A1	32	.	0			c.G630T						PASS	.						5	6	6					9																	127262609		2112	4146	6258	SO:0001819	synonymous_variant	2516	exon4			GCCGTACGGCAGC	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.630G>T	chr9.hg19:g.127262609C>A		6.0	2.0	.		9.0	5.0	.	NM_004959	O15196|Q5T6F5	Silent	SNP	ENST00000373588.4	hg19	CCDS6856.1																																																																																			.	.	.	none		0.667	NR5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054029.1	NM_004959		A	127262609	C	A	127262609	2	1	147	1	0	0	0	0	0	0	0	1	10642	523	19	4		4	NR5A1	9	127262609	Silent	SNP	C	TCGA-DW-7834-01A-11D-2136-08		127262609	13950822	29	8799											
KIF20B	9585	hgsc.bcm.edu	37	chr10	91498338	91498338	+	Missense_Mutation	SNP	A	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	acatttacttcaattaaaagAagaagaagaagaaaccaaca	23	7	5	6	0	1	5	1	0	0	5	1	5	1	5	1	0	3	0	1	0	10	4			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr10:91498338A>C	ENST00000371728.3	+	20	3805	c.3740A>C	c.(3739-3741)gAa>gCa	p.E1247A	KIF20B_ENST00000394289.2_Missense_Mutation_p.E1247A|KIF20B_ENST00000416354.1_Missense_Mutation_p.E1277A|KIF20B_ENST00000478929.1_3'UTR|KIF20B_ENST00000260753.4_Missense_Mutation_p.E1207A	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	1247	Poly-Glu.				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						CAATTAAAAGAAGAAGAAGAA	0.279																																					p.E1207A		Atlas-SNP	.											.	KIF20B	191	.	0			c.A3620C						PASS	.						33	35	34					10																	91498338		2006	4193	6199	SO:0001583	missense	9585	exon20			TAAAAGAAGAAGA	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.3740A>C	chr10.hg19:g.91498338A>C	ENSP00000360793:p.Glu1247Ala	46.0	0.0	.		59.0	23.0	.	NM_016195	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Missense_Mutation	SNP	ENST00000371728.3	hg19		.	.	.	.	.	.	.	.	.	.	A	12.72	2.021492	0.35701	.	.	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	T;T;T;T	0.71341	-0.46;-0.48;-0.56;-0.48	5.82	4.62	0.57501	.	0.125962	0.36167	N	0.002752	T	0.65375	0.2685	M	0.62723	1.935	0.32524	N	0.535885	P;P	0.52316	0.919;0.952	B;B	0.43916	0.253;0.436	T	0.75419	-0.3324	10	0.56958	D	0.05	-24.2326	5.4057	0.16320	0.6693:0.0:0.073:0.2577	.	1247;1207	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	A	1207;1277;1247;1247	ENSP00000260753:E1207A;ENSP00000411545:E1277A;ENSP00000377830:E1247A;ENSP00000360793:E1247A	ENSP00000260753:E1207A	E	+	2	0	KIF20B	91488318	1.000000	0.71417	1.000000	0.80357	0.278000	0.26855	4.090000	0.57693	2.222000	0.72286	0.383000	0.25322	GAA	.	.	.	none		0.279	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195		C	91498338	A	C	91498338	3	2	147	1	0	0	0	0	1	0	0	0	8294	246	9	5	3694	5	KIF20B	10	91498338	Missense_Mutation	SNP	A	TCGA-DW-7834-01A-11D-2136-08		91498338	44036409	30	8800											
TRIM8	81603	hgsc.bcm.edu	37	chr10	104404881	104404881	+	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	gtgtgccagtactgctgctaCtacagcggcgcgcatcaggg	7	8	14	12	3	1	0	1	0	0	0	1	0	1	0	1	2	7	4	1	2	3	3			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr10:104404881C>T	ENST00000302424.7	+	1	629	c.507C>T	c.(505-507)taC>taT	p.Y169Y	RP11-47A8.5_ENST00000607967.1_lincRNA	NM_030912.2	NP_112174.2	Q9BZR9	TRIM8_HUMAN	tripartite motif containing 8	169					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|PML body (GO:0016605)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		ACTGCTGCTACTACAGCGGCG	0.662																																					p.Y169Y		Atlas-SNP	.											.	TRIM8	35	.	0			c.C507T						PASS	.						14	15	15					10																	104404881		1665	3276	4941	SO:0001819	synonymous_variant	81603	exon1			CTGCTACTACAGC	AF281046	CCDS31274.1	10q24.3	2013-01-09	2011-01-25	2002-06-14	ENSG00000171206	ENSG00000171206		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	15579	protein-coding gene	gene with protein product	"glioblastoma expressed ring finger protein"	606125	"ring finger protein 27", "tripartite motif-containing 8"	RNF27		11118312, 12163497	Standard	NM_030912		Approved	GERP	uc001kvz.2	Q9BZR9	OTTHUMG00000018964	ENST00000302424.7:c.507C>T	chr10.hg19:g.104404881C>T		42.0	0.0	.		46.0	9.0	.	NM_030912	A6NI31|Q9C028	Silent	SNP	ENST00000302424.7	hg19	CCDS31274.1																																																																																			.	.	.	none		0.662	TRIM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050084.3	NM_030912		T	104404881	C	T	104404881	2	4	147	1	0	0	0	0	0	0	0	1	16560	576	20	2		2	TRIM8	10	104404881	Silent	SNP	C	TCGA-DW-7834-01A-11D-2136-08	12906543	104404881	31129866	31	8801											
PTPRJ	5795	hgsc.bcm.edu	37	chr11	48149503	48149503	+	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	tgagcctcgcgctgtcatccCcggactccgctccagcacct	5	8	9	19	4	1	1	1	1	0	0	5	2	4	2	6	1	2	3	6	1	0	0			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr11:48149503C>T	ENST00000418331.2	+	7	1617	c.1265C>T	c.(1264-1266)cCc>cTc	p.P422L	PTPRJ_ENST00000440289.2_Missense_Mutation_p.P422L	NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	422	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						GCTGTCATCCCCGGACTCCGC	0.552																																					p.P422L		Atlas-SNP	.											.	PTPRJ	225	.	0			c.C1265T						PASS	.						137	112	121					11																	48149503		2201	4298	6499	SO:0001583	missense	5795	exon7			TCATCCCCGGACT	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.1265C>T	chr11.hg19:g.48149503C>T	ENSP00000400010:p.Pro422Leu	116.0	0.0	.		124.0	42.0	.	NM_001098503	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	hg19	CCDS7945.1	.	.	.	.	.	.	.	.	.	.	C	10.36	1.329627	0.24167	.	.	ENSG00000149177	ENST00000278456;ENST00000418331;ENST00000440289	T;T	0.57752	0.38;0.38	6.17	-3.83	0.04269	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	T	0.18635	0.0447	N	0.01352	-0.895	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.09377	0.004;0.004	T	0.18272	-1.0342	9	0.25106	T	0.35	.	6.2032	0.20587	0.0:0.2896:0.327:0.3835	.	422;422	Q12913;Q6P4H4	PTPRJ_HUMAN;.	L	422	ENSP00000400010:P422L;ENSP00000409733:P422L	ENSP00000278456:P422L	P	+	2	0	PTPRJ	48106079	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.846000	0.04336	-1.113000	0.02981	-0.751000	0.03497	CCC	.	.	.	none		0.552	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1			T	48149503	C	T	48149503	3	4	147	1	0	0	0	0	1	0	0	0	12817	623	22	2	1291	2	PTPRJ	11	48149503	Missense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08		48149503	86857013	32	8802											
NAALADL1	10004	hgsc.bcm.edu	37	chr11	64822081	64822081	+	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	ctcgtagtaggagcctcgctCcactcctgaggggggcaggt	6	8	15	12	2	0	1	0	1	0	0	4	2	2	2	3	5	1	4	3	5	2	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr11:64822081C>T	ENST00000358658.3	-	5	760	c.733G>A	c.(733-735)Gag>Aag	p.E245K	NAALADL1_ENST00000355721.3_Missense_Mutation_p.E204K|NAALADL1_ENST00000355369.2_Missense_Mutation_p.E245K|NAALADL1_ENST00000356632.3_Missense_Mutation_p.E245K|NAALADL1_ENST00000340252.4_Missense_Mutation_p.E245K|NAALADL1_ENST00000339885.2_Missense_Mutation_p.E245K	NM_005468.2	NP_005459.2	Q9UQQ1	NALDL_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 1	245						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	29						GAGCCTCGCTCCACTCCTGAG	0.597											OREG0032001	type=REGULATORY REGION|TFbs=RELA|Dataset=RELA (p65) ChIP-PET Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with paired-end diTag sequencing (ChIP-PET)																									p.E245K		Atlas-SNP	.											.	NAALADL1	58	.	0			c.G733A						PASS	.						56	55	55					11																	64822081		2201	4297	6498	SO:0001583	missense	10004	exon5			CTCGCTCCACTCC	AF010141	CCDS31604.1	11q12	2011-08-16			ENSG00000168060	ENSG00000168060			23536	protein-coding gene	gene with protein product	"ileal peptidase I100"	602640				10085079	Standard	NM_005468		Approved		uc001ocn.3	Q9UQQ1	OTTHUMG00000165595	ENST00000358658.3:c.733G>A	chr11.hg19:g.64822081C>T	ENSP00000351484:p.Glu245Lys	39.0	0.0	.	1079	35.0	8.0	.	NM_005468	C9J8A1|C9J964|C9JL35|C9JSN0|O43176	Missense_Mutation	SNP	ENST00000358658.3	hg19	CCDS31604.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.798953	0.90538	.	.	ENSG00000168060	ENST00000358658;ENST00000355369;ENST00000339885;ENST00000453486;ENST00000340252;ENST00000355721;ENST00000356632	T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93	4.7	3.78	0.43462	.	0.000000	0.85682	D	0.000000	T	0.60508	0.2274	M	0.81802	2.56	0.50632	D	0.999881	P	0.51240	0.943	P	0.57720	0.826	T	0.66842	-0.5821	10	0.87932	D	0	-32.0749	12.6604	0.56811	0.0:0.8326:0.1674:0.0	.	245	Q9UQQ1	NALDL_HUMAN	K	245;245;245;245;245;204;245	ENSP00000351484:E245K;ENSP00000347530:E245K;ENSP00000340111:E245K;ENSP00000344244:E245K;ENSP00000347955:E204K;ENSP00000349045:E245K	ENSP00000340111:E245K	E	-	1	0	NAALADL1	64578657	1.000000	0.71417	0.979000	0.43373	0.757000	0.42996	6.561000	0.73955	1.196000	0.43129	0.655000	0.94253	GAG	.	.	.	none		0.597	NAALADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385162.1	NM_005468		T	64822081	C	T	64822081	3	4	147	1	0	0	0	0	1	0	0	0	10136	864	30	2	1545	2	NAALADL1	11	64822081	Missense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08	16672578	64822081	70184435	33	8803											
PZP	5858	hgsc.bcm.edu	37	chr12	9356427	9356427	+	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	tcagtgaagaggctcctgttTtccctgccagactccaagga	9	10	10	12	0	1	3	1	1	0	2	4	4	4	4	4	2	1	2	4	2	2	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr12:9356427T>A	ENST00000261336.2	-	2	232	c.204A>T	c.(202-204)gaA>gaT	p.E68D	PZP_ENST00000381997.2_5'Flank	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	68					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						GGCTCCTGTTTTCCCTGCCAG	0.557																																					p.E68D	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											.	PZP	422	.	0			c.A204T						PASS	.						114	104	107					12																	9356427		2203	4300	6503	SO:0001583	missense	5858	exon2			CCTGTTTTCCCTG	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.204A>T	chr12.hg19:g.9356427T>A	ENSP00000261336:p.Glu68Asp	141.0	0.0	.		154.0	51.0	.	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	hg19	CCDS8600.1	.	.	.	.	.	.	.	.	.	.	T	0.086	-1.175971	0.01646	.	.	ENSG00000126838	ENST00000261336	T	0.08282	3.11	2.08	-0.306	0.12780	.	1.942830	0.04105	U	0.313539	T	0.10121	0.0248	M	0.70275	2.135	0.09310	N	1	B	0.22683	0.073	B	0.19946	0.027	T	0.42378	-0.9455	10	0.12766	T	0.61	.	4.2572	0.10722	0.0:0.3652:0.0:0.6348	.	68	P20742	PZP_HUMAN	D	68	ENSP00000261336:E68D	ENSP00000261336:E68D	E	-	3	2	PZP	9247694	0.000000	0.05858	0.002000	0.10522	0.396000	0.30629	-1.538000	0.02204	-0.076000	0.12775	0.383000	0.25322	GAA	.	.	.	none		0.557	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864		A	9356427	T	A	9356427	3	1	147	1	0	0	0	0	1	0	0	0	12882	1838	64	5	4384	5	PZP	12	9356427	Missense_Mutation	SNP	T	TCGA-DW-7834-01A-11D-2136-08		9356427	124495468	34	8804											
DNAJC22	79962	hgsc.bcm.edu	37	chr12	49743366	49743366	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcatggagtttgtcctcctTctgccttaccggatctggag	5	14	10	12	1	3	0	1	0	2	0	5	3	5	3	4	3	2	1	4	3	1	3			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr12:49743366T>C	ENST00000549441.2	+	3	1915	c.711T>C	c.(709-711)ctT>ctC	p.L237L	DNAJC22_ENST00000395069.3_Silent_p.L237L			Q8N4W6	DJC22_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 22	237						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(2)|lung(1)|ovary(1)|pancreas(1)	10						TTGTCCTCCTTCTGCCTTACC	0.532																																					p.L237L		Atlas-SNP	.											.	DNAJC22	29	.	0			c.T711C						PASS	.						162	163	163					12																	49743366		2203	4300	6503	SO:0001819	synonymous_variant	79962	exon2			CCTCCTTCTGCCT	AK055747	CCDS8785.1	12q13.12	2011-09-02		2008-07-08	ENSG00000178401	ENSG00000178401		"Heat shock proteins / DNAJ (HSP40)"	25802	protein-coding gene	gene with protein product	"wurst homolog (Drosophila)"					17558392	Standard	NM_024902		Approved	wus, FLJ13236	uc001rua.3	Q8N4W6		ENST00000549441.2:c.711T>C	chr12.hg19:g.49743366T>C		307.0	0.0	.		277.0	87.0	.	NM_024902	B3KP54	Silent	SNP	ENST00000549441.2	hg19	CCDS8785.1																																																																																			.	.	.	none		0.532	DNAJC22-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404302.2	NM_024902		C	49743366	T	C	49743366	2	2	147	1	0	0	0	0	0	0	0	1	4643	1770	62	3		3	DNAJC22	12	49743366	Silent	SNP	T	TCGA-DW-7834-01A-11D-2136-08	40386939	49743366	84108529	35	8805											
GPR18	2841	hgsc.bcm.edu	37	chr13	99908051	99908051	+	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	gatacagctatagaagacaaGggctgcaattttgtattcat	14	12	9	6	0	1	2	1	0	0	2	1	3	1	2	0	1	3	4	0	1	7	7			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr13:99908051G>C	ENST00000340807.3	-	3	632	c.76C>G	c.(76-78)Ctt>Gtt	p.L26V	UBAC2_ENST00000376440.2_Intron|UBAC2_ENST00000403766.3_Intron|GPR18_ENST00000397470.2_Missense_Mutation_p.L26V|GPR18_ENST00000397473.2_Missense_Mutation_p.L26V			Q14330	GPR18_HUMAN	G protein-coupled receptor 18	26					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(2)|lung(6)	10	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Glycine(DB00145)	TAGAAGACAAGGGCTGCAATT	0.388																																					p.L26V		Atlas-SNP	.											GPR18,NS,carcinoma,0,1	GPR18	23	.	0			c.C76G						PASS	.						131	130	131					13																	99908051		2203	4300	6503	SO:0001583	missense	2841	exon2			AGACAAGGGCTGC	L42324	CCDS9491.1	13q32	2014-01-30			ENSG00000125245	ENSG00000125245		"GPCR / Class A : Orphans"	4472	protein-coding gene	gene with protein product		602042				9205118	Standard	NM_005292		Approved		uc010afv.3	Q14330	OTTHUMG00000017266	ENST00000340807.3:c.76C>G	chr13.hg19:g.99908051G>C	ENSP00000343428:p.Leu26Val	142.0	0.0	.		140.0	31.0	.	NM_001098200	Q6GTM3|Q96HI6|Q9H2L2	Missense_Mutation	SNP	ENST00000340807.3	hg19	CCDS9491.1	.	.	.	.	.	.	.	.	.	.	G	15.10	2.732792	0.48939	.	.	ENSG00000125245	ENST00000397473;ENST00000397470;ENST00000340807;ENST00000416594	T;T;T;T	0.37058	1.22;1.22;1.22;1.22	5.95	5.08	0.68730	.	0.078514	0.52532	D	0.000062	T	0.20047	0.0482	N	0.08118	0	0.58432	D	0.999996	B	0.30605	0.287	B	0.25987	0.065	T	0.05451	-1.0884	9	.	.	.	-16.1138	16.3083	0.82859	0.0:0.0:0.8666:0.1334	.	26	Q14330	GPR18_HUMAN	V	26	ENSP00000380613:L26V;ENSP00000380610:L26V;ENSP00000343428:L26V;ENSP00000401611:L26V	.	L	-	1	0	GPR18	98706052	1.000000	0.71417	0.847000	0.33407	0.750000	0.42670	5.384000	0.66225	1.475000	0.48197	0.563000	0.77884	CTT	.	.	.	none		0.388	GPR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045585.1			C	99908051	G	C	99908051	3	2	147	1	0	0	0	0	1	0	0	0	6682	1000	35	4	923	4	GPR18	13	99908051	Missense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08		99908051	15261827	36	8806											
SLC7A8	23428	hgsc.bcm.edu	37	chr14	23607203	23607203	+	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	agaaatgggcatgatccaggCcatgactcctaggagcttct	11	9	11	10	0	1	3	0	2	1	1	3	4	3	4	3	3	1	2	3	3	2	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr14:23607203C>T	ENST00000316902.7	-	7	1668	c.943G>A	c.(943-945)Gcc>Acc	p.A315T	SLC7A8_ENST00000529705.2_Missense_Mutation_p.A210T|SLC7A8_ENST00000453702.1_Missense_Mutation_p.A112T|SLC7A8_ENST00000469263.1_Intron|SLC7A8_ENST00000532568.1_5'Flank|SLC7A8_ENST00000422941.2_Missense_Mutation_p.A91T	NM_012244.3	NP_036376.2	Q9UHI5	LAT2_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 8	315					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|metal ion homeostasis (GO:0055065)|neutral amino acid transport (GO:0015804)|organic cation transport (GO:0015695)|response to toxic substance (GO:0009636)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|organic cation transmembrane transporter activity (GO:0015101)|peptide antigen binding (GO:0042605)|toxin transporter activity (GO:0019534)			autonomic_ganglia(1)|endometrium(6)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|skin(1)	24	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00809)	L-Alanine(DB00160)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	ATGATCCAGGCCATGACTCCT	0.567																																					p.A315T		Atlas-SNP	.											.	SLC7A8	54	.	0			c.G943A						PASS	.						112	104	107					14																	23607203		2203	4300	6503	SO:0001583	missense	23428	exon7			TCCAGGCCATGAC	Y18483	CCDS9590.1, CCDS41924.1, CCDS58304.1, CCDS58305.1	14q11.2	2013-05-22	2011-07-12		ENSG00000092068	ENSG00000092068		"Solute carriers"	11066	protein-coding gene	gene with protein product		604235				10080183, 10391915	Standard	NM_001267036		Approved	LPI-PC1, LAT2	uc001wiz.4	Q9UHI5	OTTHUMG00000028720	ENST00000316902.7:c.943G>A	chr14.hg19:g.23607203C>T	ENSP00000320378:p.Ala315Thr	119.0	0.0	.		113.0	26.0	.	NM_012244	B2R8Q4|B4DKT4|B4DTV6|D3DS46|F2Z2J4|Q86U05|Q9UKQ6|Q9UKQ7|Q9UKQ8|Q9Y445	Missense_Mutation	SNP	ENST00000316902.7	hg19	CCDS9590.1	.	.	.	.	.	.	.	.	.	.	C	16.80	3.222325	0.58560	.	.	ENSG00000092068	ENST00000316902;ENST00000334354;ENST00000453702;ENST00000529705;ENST00000422941;ENST00000206514	D;D;D;D	0.90133	-2.62;-2.62;-2.62;-2.62	5.44	4.54	0.55810	Amino acid permease domain (1);	0.306262	0.35772	N	0.002981	D	0.87815	0.6272	L	0.48877	1.53	0.49213	D	0.999763	B;B;B	0.28128	0.201;0.118;0.07	B;B;B	0.28305	0.088;0.088;0.038	D	0.86389	0.1734	10	0.72032	D	0.01	.	14.7754	0.69729	0.1459:0.8541:0.0:0.0	.	210;91;315	B4DKT4;B4DTV6;Q9UHI5	.;.;LAT2_HUMAN	T	315;112;112;210;91;112	ENSP00000320378:A315T;ENSP00000391577:A112T;ENSP00000434345:A210T;ENSP00000416398:A91T	ENSP00000206514:A112T	A	-	1	0	SLC7A8	22677043	0.979000	0.34478	1.000000	0.80357	0.997000	0.91878	0.137000	0.15995	1.409000	0.46915	0.563000	0.77884	GCC	.	.	.	none		0.567	SLC7A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071718.3			T	23607203	C	T	23607203	3	4	147	1	0	0	0	0	1	0	0	0	14717	739	26	2	684	2	SLC7A8	14	23607203	Missense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08		23607203	83742337	37	8807											
C14orf50	145376	hgsc.bcm.edu	37	chr14	65032084	65032084	+	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	ttccaaaacaggttgacagaTaaaagacttgctgcaaaaga	18	8	8	7	0	0	4	0	1	0	3	1	4	1	4	1	1	3	3	1	1	6	4			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr14:65032084T>A	ENST00000298705.1	+	5	375	c.279T>A	c.(277-279)gaT>gaA	p.D93E	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	93					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										GGTTGACAGATAAAAGACTTG	0.338																																					p.D93E		Atlas-SNP	.											.	.	.	.	0			c.T279A						PASS	.						91	80	83					14																	65032084		2203	4300	6503	SO:0001583	missense	145376	exon5			GACAGATAAAAGA		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.279T>A	chr14.hg19:g.65032084T>A	ENSP00000298705:p.Asp93Glu	64.0	0.0	.		37.0	13.0	.	NM_172365	Q6NTH6	Missense_Mutation	SNP	ENST00000298705.1	hg19	CCDS9767.1	.	.	.	.	.	.	.	.	.	.	T	8.979	0.974851	0.18736	.	.	ENSG00000165807	ENST00000298705	T	0.31247	1.5	5.79	2.16	0.27623	.	0.198907	0.35320	N	0.003286	T	0.17109	0.0411	L	0.39898	1.24	0.25922	N	0.983102	B	0.24721	0.11	B	0.17433	0.018	T	0.30119	-0.9989	10	0.05959	T	0.93	-17.5714	5.9771	0.19387	0.0:0.0945:0.4215:0.4839	.	93	Q96LQ0	PPR36_HUMAN	E	93	ENSP00000298705:D93E	ENSP00000298705:D93E	D	+	3	2	C14orf50	64101837	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	0.518000	0.22847	0.433000	0.26313	0.533000	0.62120	GAT	.	.	.	none		0.338	PPP1R36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280667.1	NM_172365		A	65032084	T	A	65032084	3	1	147	1	0	0	0	0	1	0	0	0	1779	1403	49	5	297	5	C14orf50	14	65032084	Missense_Mutation	SNP	T	TCGA-DW-7834-01A-11D-2136-08	41424881	65032084	42317456	38	8808											
EIF2S1	1965	hgsc.bcm.edu	37	chr14	67848335	67848335	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagtggcttgttatggttaTgaaggcattgatgctgtaaa	11	14	13	3	0	0	2	0	2	0	0	0	3	0	2	0	3	1	6	0	3	6	5			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr14:67848335T>C	ENST00000256383.4	+	6	1067	c.606T>C	c.(604-606)taT>taC	p.Y202Y	EIF2S1_ENST00000466499.2_Silent_p.Y202Y	NM_004094.4	NP_004085.1	P05198	IF2A_HUMAN	eukaryotic translation initiation factor 2, subunit 1 alpha, 35kDa	202					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|protein autophosphorylation (GO:0046777)|regulation of translational initiation in response to stress (GO:0043558)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2 complex (GO:0005850)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|polysome (GO:0005844)	poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|translation initiation factor activity (GO:0003743)			breast(1)|cervix(2)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	9				all cancers(60;0.000683)|OV - Ovarian serous cystadenocarcinoma(108;0.00579)|BRCA - Breast invasive adenocarcinoma(234;0.00937)		GTTATGGTTATGAAGGCATTG	0.343																																					p.Y202Y		Atlas-SNP	.											.	EIF2S1	17	.	0			c.T606C						PASS	.						89	93	91					14																	67848335		2203	4300	6503	SO:0001819	synonymous_variant	1965	exon6			TGGTTATGAAGGC	J02645	CCDS9781.1	14q21.3	2011-01-07	2002-08-29		ENSG00000134001	ENSG00000134001			3265	protein-coding gene	gene with protein product		603907	"eukaryotic translation initiation factor 2, subunit 1 (alpha, 35kD )"	EIF2		2948954	Standard	NM_004094		Approved	EIF-2alpha, EIF2A	uc001xjg.3	P05198	OTTHUMG00000029800	ENST00000256383.4:c.606T>C	chr14.hg19:g.67848335T>C		117.0	0.0	.		166.0	58.0	.	NM_004094		Silent	SNP	ENST00000256383.4	hg19	CCDS9781.1	.	.	.	.	.	.	.	.	.	.	T	9.345	1.063966	0.20067	.	.	ENSG00000134001	ENST00000555876	.	.	.	6.0	2.3	0.28687	.	.	.	.	.	T	0.58779	0.2146	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51052	-0.8754	4	.	.	.	-12.7575	9.7872	0.40684	0.0:0.196:0.0:0.804	.	.	.	.	T	159	.	.	M	+	2	0	EIF2S1	66918088	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	1.756000	0.38390	0.149000	0.19098	0.528000	0.53228	ATG	.	.	.	none		0.343	EIF2S1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074342.3	NM_004094		C	67848335	T	C	67848335	2	2	147	1	0	0	0	0	0	0	0	1	5011	1471	51	3		3	EIF2S1	14	67848335	Silent	SNP	T	TCGA-DW-7834-01A-11D-2136-08	2816251	67848335	39501205	39	8809											
KIAA0556	23247	hgsc.bcm.edu	37	chr16	27720066	27720066	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agacgagatcaaagatgccaTctacgtgaccatggagatcc	14	7	10	10	2	2	5	1	1	1	4	3	7	3	5	3	1	2	0	3	1	2	1			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr16:27720066T>C	ENST00000261588.4	+	13	1449	c.1430T>C	c.(1429-1431)aTc>aCc	p.I477T	CTD-2049O4.1_ENST00000568831.1_RNA|KIAA0556_ENST00000567894.1_3'UTR|CTD-2049O4.1_ENST00000563052.1_RNA|CTD-2049O4.1_ENST00000564893.1_RNA	NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	477						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						AAAGATGCCATCTACGTGACC	0.453																																					p.I477T		Atlas-SNP	.											.	KIAA0556	348	.	0			c.T1430C						PASS	.						120	105	110					16																	27720066		2197	4300	6497	SO:0001583	missense	23247	exon13			ATGCCATCTACGT	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.1430T>C	chr16.hg19:g.27720066T>C	ENSP00000261588:p.Ile477Thr	110.0	0.0	.		139.0	28.0	.	NM_015202	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	hg19	CCDS32415.1	.	.	.	.	.	.	.	.	.	.	T	15.39	2.818111	0.50633	.	.	ENSG00000047578	ENST00000261588;ENST00000327217	T	0.13778	2.56	5.49	4.4	0.53042	.	0.797554	0.11412	N	0.566654	T	0.19886	0.0478	M	0.75264	2.295	0.09310	N	0.999996	B	0.21071	0.051	B	0.19391	0.025	T	0.14008	-1.0488	10	0.51188	T	0.08	-4.828	10.5152	0.44885	0.0:0.0775:0.0:0.9225	.	477	O60303	K0556_HUMAN	T	477;384	ENSP00000261588:I477T	ENSP00000261588:I477T	I	+	2	0	KIAA0556	27627567	0.986000	0.35501	0.001000	0.08648	0.582000	0.36321	3.571000	0.53841	0.912000	0.36772	0.379000	0.24179	ATC	.	.	.	none		0.453	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202		C	27720066	T	C	27720066	3	2	147	1	0	0	0	0	1	0	0	0	8190	1435	50	3	1480	3	KIAA0556	16	27720066	Missense_Mutation	SNP	T	TCGA-DW-7834-01A-11D-2136-08		27720066	62634687	40	8810											
TOP3A	7156	hgsc.bcm.edu	37	chr17	18212208	18212208	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacctacctggccatacagAtgataatcaaattcatagat	15	10	6	10	0	2	3	2	1	0	2	2	3	2	3	3	1	2	1	3	1	5	5			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr17:18212208A>G	ENST00000321105.5	-	2	442	c.228T>C	c.(226-228)caT>caC	p.H76H	TOP3A_ENST00000582230.1_5'UTR|TOP3A_ENST00000542570.1_Missense_Mutation_p.I6T	NM_004618.3	NP_004609.1	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	76	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						GGCCATACAGATGATAATCAA	0.289																																					p.H76H		Atlas-SNP	.											.	TOP3A	85	.	0			c.T228C						PASS	.						36	33	34					17																	18212208		2201	4295	6496	SO:0001819	synonymous_variant	7156	exon2			ATACAGATGATAA	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.228T>C	chr17.hg19:g.18212208A>G		35.0	0.0	.		46.0	15.0	.	NM_004618	A8KA61|B4DK80|D3DXC7|Q13473	Silent	SNP	ENST00000321105.5	hg19	CCDS11194.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.18|13.18	2.161482|2.161482	0.38119|0.38119	.|.	.|.	ENSG00000177302|ENSG00000177302	ENST00000542570|ENST00000412083	T|.	0.08282|.	3.11|.	5.04|5.04	-5.1|-5.1	0.02911|0.02911	.|.	.|.	.|.	.|.	.|.	T|T	0.50616|0.50616	0.1626|0.1626	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.53258|0.53258	-0.8464|-0.8464	6|4	0.21014|.	T|.	0.42|.	-4.7873|-4.7873	8.3168|8.3168	0.32104|0.32104	0.5159:0.1661:0.3181:0.0|0.5159:0.1661:0.3181:0.0	.|.	.|.	.|.	.|.	T|P	6|56	ENSP00000442336:I6T|.	ENSP00000442336:I6T|.	I|S	-|-	2|1	0|0	TOP3A|TOP3A	18152933|18152933	0.817000|0.817000	0.29147|0.29147	0.469000|0.469000	0.27204|0.27204	0.893000|0.893000	0.52053|0.52053	-0.001000|-0.001000	0.12947|0.12947	-0.503000|-0.503000	0.06586|0.06586	-0.220000|-0.220000	0.12472|0.12472	ATC|TCT	.	.	.	none		0.289	TOP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132052.2			G	18212208	A	G	18212208	2	3	147	1	0	0	0	0	0	0	0	1	16379	330	12	3		3	TOP3A	17	18212208	Silent	SNP	A	TCGA-DW-7834-01A-11D-2136-08		18212208	62983002	41	8811											
EFTUD2	9343	hgsc.bcm.edu	37	chr17	42945230	42945230	+	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	actccacgaaacttctctggGagctgctagttggggccttt	7	12	11	11	1	1	0	0	0	1	0	3	2	2	1	2	3	3	3	2	3	2	4			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr17:42945230G>A	ENST00000426333.2	-	13	1391	c.1094C>T	c.(1093-1095)tCc>tTc	p.S365F	EFTUD2_ENST00000592576.1_Missense_Mutation_p.S355F|EFTUD2_ENST00000591382.1_Missense_Mutation_p.S365F|EFTUD2_ENST00000402521.3_Missense_Mutation_p.S330F	NM_001142605.1|NM_001258354.1|NM_004247.3	NP_001136077.1|NP_001245283.1|NP_004238.3	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain containing 2	365	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	32		Prostate(33;0.109)				ACTTCTCTGGGAGCTGCTAGT	0.483																																					p.S365F	Ovarian(10;65 485 10258 29980 30707)	Atlas-SNP	.											.	EFTUD2	85	.	0			c.C1094T						PASS	.						48	47	48					17																	42945230		2203	4300	6503	SO:0001583	missense	9343	exon13			CTCTGGGAGCTGC	D21163	CCDS11489.1, CCDS45707.1, CCDS59295.1	17q21.31	2014-08-12			ENSG00000108883	ENSG00000108883			30858	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 116 kD"	603892				9233818	Standard	NM_004247		Approved	U5-116KD, Snrp116, Snu114, SNRNP116	uc002ihn.2	Q15029	OTTHUMG00000179865	ENST00000426333.2:c.1094C>T	chr17.hg19:g.42945230G>A	ENSP00000392094:p.Ser365Phe	20.0	0.0	.		29.0	17.0	.	NM_004247	B4DK30|B4DMC0|D3DX58|K7EJ81|Q9BUR0	Missense_Mutation	SNP	ENST00000426333.2	hg19	CCDS11489.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.231134	0.79688	.	.	ENSG00000108883	ENST00000426333;ENST00000262414;ENST00000402521	T;T	0.76839	-1.05;-1.05	6.17	6.17	0.99709	Protein synthesis factor, GTP-binding (1);	0.000000	0.85682	D	0.000000	T	0.81964	0.4934	L	0.56769	1.78	0.80722	D	1	P;P	0.41710	0.76;0.76	P;P	0.47891	0.56;0.56	T	0.77477	-0.2573	10	0.32370	T	0.25	0.1139	20.8794	0.99867	0.0:0.0:1.0:0.0	.	355;365	B4DMC0;Q15029	.;U5S1_HUMAN	F	365;355;330	ENSP00000392094:S365F;ENSP00000385873:S330F	ENSP00000262414:S355F	S	-	2	0	EFTUD2	40300756	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.406000	0.97321	2.941000	0.99782	0.655000	0.94253	TCC	.	.	.	none		0.483	EFTUD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448672.1	NM_004247		A	42945230	G	A	42945230	3	1	147	1	0	0	0	0	1	0	0	0	4963	1174	41	2	1888	2	EFTUD2	17	42945230	Missense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08	24733022	42945230	38249980	42	8812											
WNT3	7473	hgsc.bcm.edu	37	chr17	44845986	44845986	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tacttggcccggagggtctcCacccagcctcgggactcacg	6	7	12	16	3	2	0	1	0	1	0	4	2	2	2	4	4	2	0	4	4	1	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr17:44845986C>T	ENST00000225512.5	-	4	930	c.768G>A	c.(766-768)gtG>gtA	p.V256V		NM_030753.4	NP_110380.1	P56703	WNT3_HUMAN	wingless-type MMTV integration site family, member 3	256					anterior/posterior axis specification (GO:0009948)|axon guidance (GO:0007411)|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 fate commitment (GO:0045165)|cell morphogenesis (GO:0000902)|cellular response to retinoic acid (GO:0071300)|dorsal/ventral axis specification (GO:0009950)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|gamete generation (GO:0007276)|head morphogenesis (GO:0060323)|limb bud formation (GO:0060174)|mammary gland epithelium development (GO:0061180)|mesoderm formation (GO:0001707)|negative regulation of axon extension involved in axon guidance (GO:0048843)|neuron differentiation (GO:0030182)|positive regulation of collateral sprouting in absence of injury (GO:0048697)|positive regulation of gene expression (GO:0010628)|Spemann organizer formation at the anterior end of the primitive streak (GO:0060064)	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)			endometrium(2)|large_intestine(6)|lung(4)|prostate(1)	13			BRCA - Breast invasive adenocarcinoma(9;0.0257)			GGAGGGTCTCCACCCAGCCTC	0.592																																					p.G256G		Atlas-SNP	.											.	WNT3	34	.	0			c.A768A						PASS	.						85	91	89					17																	44845986		2203	4300	6503	SO:0001819	synonymous_variant	7473	exon4			GGTCTCCACCCAG	AY009397	CCDS11505.1	17q21-q22	2013-02-28				ENSG00000108379		"Wingless-type MMTV integration sites", "Endogenous ligands"	12782	protein-coding gene	gene with protein product	"WNT-3 proto-oncogene protein"	165330		INT4		8244403	Standard	NM_030753		Approved	MGC131950, MGC138321, MGC138323	uc002ikv.3	P56703		ENST00000225512.5:c.768G>A	chr17.hg19:g.44845986C>T		146.0	0.0	.		174.0	79.0	.	NM_030753	Q2M237|Q9H1J9	Silent	SNP	ENST00000225512.5	hg19	CCDS11505.1																																																																																			.	.	.	none		0.592	WNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440427.1	NM_030753		T	44845986	C	T	44845986	2	4	147	1	0	0	0	0	0	0	0	1	17400	581	21	2		2	WNT3	17	44845986	Silent	SNP	C	TCGA-DW-7834-01A-11D-2136-08	1900756	44845986	36349224	43	8813											
RNF213	57674	hgsc.bcm.edu	37	chr17	78321576	78321576	+	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	cgggttcaccccaacttccgCctgattgtcattgaagagaa	10	10	9	12	2	2	3	2	2	0	1	3	4	3	3	4	1	1	1	4	1	3	4			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr17:78321576C>T	ENST00000582970.1	+	29	9584	c.9441C>T	c.(9439-9441)cgC>cgT	p.R3147R	RNF213_ENST00000336301.6_Silent_p.R1220R|RNF213_ENST00000508628.2_Silent_p.R3196R	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3147					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)			CCAACTTCCGCCTGATTGTCA	0.552																																					p.R3147R		Atlas-SNP	.											.	RNF213	766	.	0			c.C9441T						PASS	.						55	53	54					17																	78321576		2203	4300	6503	SO:0001819	synonymous_variant	57674	exon29			CTTCCGCCTGATT	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.9441C>T	chr17.hg19:g.78321576C>T		79.0	0.0	.		88.0	6.0	.	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	hg19	CCDS58606.1																																																																																			.	.	.	none		0.552	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		T	78321576	C	T	78321576	2	4	147	1	0	0	0	0	0	0	0	1	13490	726	26	2		2	RNF213	17	78321576	Silent	SNP	C	TCGA-DW-7834-01A-11D-2136-08	33475590	78321576	2873634	44	8814											
AP3D1	8943	hgsc.bcm.edu	37	chr19	2151253	2151253	+	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	ctcacctcgtcctccttgtgGttacggatgccgcggaccaa	6	10	10	15	4	1	0	1	0	0	0	4	2	3	2	5	3	2	1	5	3	2	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr19:2151253G>C	ENST00000345016.5	-	1	312	c.81C>G	c.(79-81)aaC>aaG	p.N27K	AP3D1_ENST00000355272.6_Missense_Mutation_p.N27K|AP3D1_ENST00000350812.6_Missense_Mutation_p.N27K|AP3D1_ENST00000356926.4_Missense_Mutation_p.N27K	NM_003938.6	NP_003929.4	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1 subunit	27					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)		CCTCCTTGTGGTTACGGATGC	0.682																																					p.N27K		Atlas-SNP	.											.	AP3D1	81	.	0			c.C81G						PASS	.						29	32	31					19																	2151253		1958	4139	6097	SO:0001583	missense	8943	exon1			CTTGTGGTTACGG	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.81C>G	chr19.hg19:g.2151253G>C	ENSP00000344055:p.Asn27Lys	29.0	0.0	.		34.0	16.0	.	NM_001261826	O00202|O75262|Q59HF5|Q96G11|Q9H3C6	Missense_Mutation	SNP	ENST00000345016.5	hg19	CCDS42459.1	.	.	.	.	.	.	.	.	.	.	G	15.05	2.717231	0.48622	.	.	ENSG00000065000	ENST00000356926;ENST00000345016;ENST00000355272;ENST00000343722;ENST00000350812	T;T;T;T	0.18657	2.2;2.65;2.62;2.21	3.89	2.85	0.33270	Armadillo-like helical (1);	0.000000	0.85682	D	0.000000	T	0.32436	0.0829	L	0.40543	1.245	0.25610	N	0.986508	B;B;D	0.67145	0.264;0.058;0.996	B;B;D	0.78314	0.033;0.067;0.991	T	0.02860	-1.1101	10	0.52906	T	0.07	-55.1245	9.2068	0.37293	0.1883:0.0:0.8117:0.0	.	27;27;27	O14617-5;O14617;G5E988	.;AP3D1_HUMAN;.	K	27	ENSP00000349398:N27K;ENSP00000344055:N27K;ENSP00000347416:N27K;ENSP00000342321:N27K	ENSP00000341579:N27K	N	-	3	2	AP3D1	2102253	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.691000	0.37721	0.971000	0.38288	0.436000	0.28706	AAC	.	.	.	none		0.682	AP3D1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450912.1			C	2151253	G	C	2151253	3	2	147	1	0	0	0	0	1	0	0	0	746	1252	44	4	3658	4	AP3D1	19	2151253	Missense_Mutation	SNP	G	TCGA-DW-7834-01A-11D-2136-08		2151253	56977730	45	8815											
PSMC4	5704	hgsc.bcm.edu	37	chr19	40478461	40478461	+	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	gccatcgtgggctctaccacAggtgtgctaaggacacctca	9	8	11	13	1	2	0	1	0	1	0	3	1	2	1	3	3	2	2	3	3	2	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr19:40478461A>G	ENST00000157812.2	+	3	519	c.321A>G	c.(319-321)acA>acG	p.T107T	PSMC4_ENST00000455878.2_Splice_Site_p.T76T	NM_006503.3|NM_153001.2	NP_006494.1|NP_694546.1	P43686	PRS6B_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 4	107					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)					GCTCTACCACAGGTGTGCTAA	0.512																																					p.T107T	Colon(105;1478 1543 4034 6132 38638)	Atlas-SNP	.											.	PSMC4	48	.	0			c.A321G						PASS	.						41	36	38					19																	40478461		2203	4300	6503	SO:0001630	splice_region_variant	5704	exon3			TACCACAGGTGTG	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.322+1A>G	chr19.hg19:g.40478461A>G		30.0	0.0	.		46.0	11.0	.	NM_006503	Q96FV5|Q9UBM3|Q9UEX3	Silent	SNP	ENST00000157812.2	hg19	CCDS12547.1																																																																																			.	.	.	none		0.512	PSMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462485.1	NM_006503	Silent	G	40478461	A	G	40478461	5	3	147	1	0	0	0	0	0	0	1	0	12699	202	7	3	331	3	PSMC4	19	40478461	Splice_Site	SNP	A	TCGA-DW-7834-01A-11D-2136-08	38327208	40478461	18650522	46	8816											
MEGF8	1954	hgsc.bcm.edu	37	chr19	42861598	42861598	+	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	cagccgttgctggtcacaccCttactgcccgccgaggcctg	5	8	11	17	3	1	0	1	0	0	0	1	1	1	0	5	2	4	2	5	2	1	2			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr19:42861598C>G	ENST00000251268.6	+	28	4873	c.4873C>G	c.(4873-4875)Ctt>Gtt	p.L1625V	MEGF8_ENST00000334370.4_Missense_Mutation_p.L1558V	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	1625					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)				TGGTCACACCCTTACTGCCCG	0.652																																					p.L1625V		Atlas-SNP	.											.	MEGF8	358	.	0			c.C4873G						PASS	.						67	68	67					19																	42861598		2203	4300	6503	SO:0001583	missense	1954	exon28			CACACCCTTACTG	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.4873C>G	chr19.hg19:g.42861598C>G	ENSP00000251268:p.Leu1625Val	182.0	0.0	.		163.0	44.0	.	NM_001271938	A8KAY0|O75097	Missense_Mutation	SNP	ENST00000251268.6	hg19		.	.	.	.	.	.	.	.	.	.	C	22.5	4.302490	0.81136	.	.	ENSG00000105429	ENST00000334370;ENST00000251268	T;T	0.64438	-0.1;-0.1	5.21	5.21	0.72293	Galactose oxidase/kelch, beta-propeller (1);Kelch-type beta propeller (1);	0.000000	0.56097	D	0.000038	T	0.74913	0.3779	L	0.50333	1.59	0.80722	D	1	D;D	0.63046	0.992;0.99	P;D	0.72982	0.792;0.979	T	0.76110	-0.3079	10	0.56958	D	0.05	-13.3833	17.5358	0.87830	0.0:1.0:0.0:0.0	.	1625;1558	Q7Z7M0;Q7Z7M0-2	MEGF8_HUMAN;.	V	1558;1625	ENSP00000334219:L1558V;ENSP00000251268:L1625V	ENSP00000251268:L1625V	L	+	1	0	MEGF8	47553438	1.000000	0.71417	0.980000	0.43619	0.985000	0.73830	4.334000	0.59291	2.453000	0.82957	0.563000	0.77884	CTT	.	.	.	none		0.652	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		G	42861598	C	G	42861598	3	3	147	1	0	0	0	0	1	0	0	0	9470	681	24	4	4778	4	MEGF8	19	42861598	Missense_Mutation	SNP	C	TCGA-DW-7834-01A-11D-2136-08	2383137	42861598	16267385	47	8817											
NRIP1	8204	hgsc.bcm.edu	37	chr21	16337670	16337670	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttacttctgtgcggggacaaAtctcgcacacagttttctga	9	13	9	10	2	3	1	0	1	3	0	4	2	3	2	0	2	2	2	0	2	2	4			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr21:16337670A>G	ENST00000400202.1	-	3	3556	c.2844T>C	c.(2842-2844)gaT>gaC	p.D948D	NRIP1_ENST00000400199.1_Silent_p.D948D|NRIP1_ENST00000318948.4_Silent_p.D948D|AF127577.10_ENST00000446301.1_RNA			P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	948	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)		GCGGGGACAAATCTCGCACAC	0.428																																					p.D948D		Atlas-SNP	.											.	NRIP1	103	.	0			c.T2844C						PASS	.						82	82	82					21																	16337670		2203	4299	6502	SO:0001819	synonymous_variant	8204	exon4			GGACAAATCTCGC	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.2844T>C	chr21.hg19:g.16337670A>G		150.0	0.0	.		157.0	44.0	.	NM_003489	Q8IWE8	Silent	SNP	ENST00000400202.1	hg19	CCDS13568.1																																																																																			.	.	.	none		0.428	NRIP1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157926.1	NM_003489		G	16337670	A	G	16337670	2	3	147	1	0	0	0	0	0	0	0	1	10659	98	4	3		3	NRIP1	21	16337670	Silent	SNP	A	TCGA-DW-7834-01A-11D-2136-08		16337670	31792225	48	8818											
NCAM2	4685	hgsc.bcm.edu	37	chr21	22658662	22658662	+	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	gatgcagaagtggtttgccgAgttagcagttcacctgcacc	9	10	12	10	1	1	1	1	0	0	1	1	3	1	1	3	1	4	6	3	1	2	3			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr21:22658662A>T	ENST00000400546.1	+	4	660	c.411A>T	c.(409-411)cgA>cgT	p.R137R	NCAM2_ENST00000486367.1_3'UTR|NCAM2_ENST00000535285.1_Silent_p.R162R|NCAM2_ENST00000284894.7_Intron	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	137	Ig-like C2-type 2.				axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		TGGTTTGCCGAGTTAGCAGTT	0.398																																					p.R137R		Atlas-SNP	.											.	NCAM2	220	.	0			c.A411T						PASS	.						119	114	116					21																	22658662		2019	4192	6211	SO:0001819	synonymous_variant	4685	exon4			TTGCCGAGTTAGC		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.411A>T	chr21.hg19:g.22658662A>T		64.0	0.0	.		55.0	15.0	.	NM_004540	A8MQ06|B7Z841|Q7Z7F2	Silent	SNP	ENST00000400546.1	hg19	CCDS42910.1																																																																																			.	.	.	none		0.398	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		T	22658662	A	T	22658662	2	4	147	1	0	0	0	0	0	0	0	1	10210	291	11	5		5	NCAM2	21	22658662	Silent	SNP	A	TCGA-DW-7834-01A-11D-2136-08	6320992	22658662	25471233	49	8819											
SON	6651	hgsc.bcm.edu	37	chr21	34932382	34932382	+	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	ggaaggtagtccaaggtacaActatttagcttcccgatttg	11	12	10	8	1	0	0	0	0	0	0	2	2	2	1	2	3	3	3	2	3	7	7			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr21:34932382A>G	ENST00000356577.4	+	6	7132				SON_ENST00000290239.6_Intron|SON_ENST00000381692.2_Intron|SON_ENST00000300278.4_Missense_Mutation_p.N2286S	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein						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						CCAAGGTACAACTATTTAGCT	0.473																																					p.N2286S		Atlas-SNP	.											.	SON	343	.	0			c.A6857G						PASS	.						149	142	145					21																	34932382		2203	4300	6503	SO:0001627	intron_variant	6651	exon7			GGTACAACTATTT	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.6657+301A>G	chr21.hg19:g.34932382A>G		200.0	0.0	.		180.0	55.0	.	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	hg19	CCDS13629.1	.	.	.	.	.	.	.	.	.	.	A	12.33	1.907015	0.33628	.	.	ENSG00000159140	ENST00000300278	T	0.09630	2.96	5.58	5.58	0.84498	.	.	.	.	.	T	0.32071	0.0817	.	.	.	0.80722	D	1	D	0.67145	0.996	D	0.77557	0.99	T	0.03922	-1.0992	8	0.87932	D	0	.	12.1393	0.53989	1.0:0.0:0.0:0.0	.	2286	P18583-3	.	S	2286	ENSP00000300278:N2286S	ENSP00000300278:N2286S	N	+	2	0	SON	33854252	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.247000	0.58750	2.124000	0.65301	0.460000	0.39030	AAC	.	.	.	none		0.473	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		G	34932382	A	G	34932382	1	3	147	0	1	0	0	0	0	0	0	0	14939	43	2	3		3	SON	21	34932382	Intron	SNP	A	TCGA-DW-7834-01A-11D-2136-08	12273720	34932382	13197513	50	8820											
RHBDD3	25807	hgsc.bcm.edu	37	chr22	29656765	29656765	+	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	aggagcctcaggggccagcaCcccgccaaggtcctgcacaa	10	3	12	16	1	1	0	1	0	0	0	2	1	2	1	6	4	3	2	6	4	2	0			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chr22:29656765C>A	ENST00000216085.7	-	5	1045	c.621G>T	c.(619-621)ggG>ggT	p.G207G	CTA-984G1.5_ENST00000433125.1_RNA	NM_012265.1	NP_036397.1	Q9Y3P4	RHBD3_HUMAN	rhomboid domain containing 3	207					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						GGGGCCAGCACCCCGCCAAGG	0.692																																					p.G207G		Atlas-SNP	.											.	RHBDD3	17	.	0			c.G621T						PASS	.						17	17	17					22																	29656765		2198	4291	6489	SO:0001819	synonymous_variant	25807	exon5			CCAGCACCCCGCC	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.621G>T	chr22.hg19:g.29656765C>A		23.0	0.0	.		29.0	9.0	.	NM_012265	Q6I9X3|Q9UGQ7	Silent	SNP	ENST00000216085.7	hg19	CCDS13850.1																																																																																			.	.	.	none		0.692	RHBDD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321085.1	NM_012265		A	29656765	C	A	29656765	2	1	147	1	0	0	0	0	0	0	0	1	13331	494	18	4		4	RHBDD3	22	29656765	Silent	SNP	C	TCGA-DW-7834-01A-11D-2136-08		29656765	21647801	51	8821											
MAP7D3	79649	hgsc.bcm.edu	37	chrX	135314169	135314169	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggacgcttccatgcttgtgTtgcagaatacttccacattc	8	13	9	11	1	0	1	0	0	0	1	3	2	2	2	2	1	3	4	2	1	2	6			TCGA-DW-7834-01A-11D-2136-08	TCGA-DW-7834-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7f7db203-247b-49e1-a80e-c8be4047bc17	1354f438-e892-40c1-84b6-cd15f786a963	g.chrX:135314169T>C	ENST00000316077.9	-	8	1167	c.947A>G	c.(946-948)aAc>aGc	p.N316S	MAP7D3_ENST00000370661.1_Missense_Mutation_p.N281S|MAP7D3_ENST00000370663.5_Missense_Mutation_p.N298S	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	316					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)					CATGCTTGTGTTGCAGAATAC	0.567																																					p.N316S		Atlas-SNP	.											.	MAP7D3	102	.	0			c.A947G						PASS	.						167	168	168					X																	135314169		2132	4212	6344	SO:0001583	missense	79649	exon8			CTTGTGTTGCAGA	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.947A>G	chrX.hg19:g.135314169T>C	ENSP00000318086:p.Asn316Ser	209.0	0.0	.		192.0	23.0	.	NM_024597	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Missense_Mutation	SNP	ENST00000316077.9	hg19	CCDS44004.1	.	.	.	.	.	.	.	.	.	.	T	4.011	-0.000557	0.07819	.	.	ENSG00000129680	ENST00000370661;ENST00000316077;ENST00000370663;ENST00000370660	T;T;T;T	0.11930	2.73;2.73;2.73;2.73	3.62	-1.54	0.08584	.	.	.	.	.	T	0.07773	0.0195	N	0.22421	0.69	0.09310	N	1	B;B;B;B	0.26258	0.09;0.126;0.09;0.145	B;B;B;B	0.26614	0.032;0.039;0.032;0.071	T	0.44467	-0.9326	9	0.13108	T	0.6	0.3015	8.6543	0.34053	0.0:0.6237:0.0:0.3763	.	298;275;316;281	B4DWD2;Q8IWC1-2;Q8IWC1;Q8IWC1-3	.;.;MA7D3_HUMAN;.	S	281;316;298;275	ENSP00000359695:N281S;ENSP00000318086:N316S;ENSP00000359697:N298S;ENSP00000359694:N275S	ENSP00000318086:N316S	N	-	2	0	MAP7D3	135141835	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.087000	0.14958	-0.273000	0.09246	-0.463000	0.05309	AAC	.	.	.	none		0.567	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2			C	135314169	T	C	135314169	3	2	147	1	0	0	0	0	1	0	0	0	9276	1725	60	3	1727	3	MAP7D3	23	135314169	Missense_Mutation	SNP	T	TCGA-DW-7834-01A-11D-2136-08		135314169	19956391	52	8822											
NUDC	10726	hgsc.bcm.edu	37	chr1	27271886	27271886	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgttctcttcacagatcaaTaagatggagtggtggagccg	10	12	12	7	1	3	2	2	0	1	2	4	4	3	4	1	3	1	1	1	3	2	4			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr1:27271886T>C	ENST00000321265.5	+	7	870	c.747T>C	c.(745-747)aaT>aaC	p.N249N	NUDC_ENST00000484772.1_3'UTR	NM_006600.3	NP_006591.1	Q9Y266	NUDC_HUMAN	nudC nuclear distribution protein	249	CS. {ECO:0000255|PROSITE- ProRule:PRU00547}.				cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)				cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|ovary(1)	8				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;6.1e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.87e-29)|Colorectal(126;5.74e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000281)|STAD - Stomach adenocarcinoma(196;0.000604)|KIRC - Kidney renal clear cell carcinoma(1967;0.000739)|READ - Rectum adenocarcinoma(331;0.0421)		CACAGATCAATAAGATGGAGT	0.537																																					p.N249N		Atlas-SNP	.											.	NUDC	15	.	0			c.T747C						PASS	.						59	53	55					1																	27271886		2203	4300	6503	SO:0001819	synonymous_variant	10726	exon7			GATCAATAAGATG		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.747T>C	chr1.hg19:g.27271886T>C		51.0	0.0	.		44.0	19.0	.	NM_006600	Q5QP31|Q5QP35|Q9H0N2|Q9Y2B6	Silent	SNP	ENST00000321265.5	hg19	CCDS292.1																																																																																			.	.	.	none		0.537	NUDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012172.2			C	27271886	T	C	27271886	2	2	148	1	0	0	0	0	0	0	0	1	10728	1403	49	3		3	NUDC	1	27271886	Silent	SNP	T	TCGA-DW-7836-01A-11D-2136-08		27271886	221978735	1	8823											
DUSP23	54935	hgsc.bcm.edu	37	chr1	159752041	159752041	+	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	ttggctgcaggagatgccatTgctgaaatccgacgactacg	10	9	12	10	3	0	2	0	1	0	1	1	5	1	2	2	2	4	3	2	2	2	3			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr1:159752041T>A	ENST00000368107.1	+	2	464	c.366T>A	c.(364-366)atT>atA	p.I122I	DUSP23_ENST00000368109.1_Silent_p.I122I|DUSP23_ENST00000368108.3_Silent_p.I122I			Q9BVJ7	DUS23_HUMAN	dual specificity phosphatase 23	122	Tyrosine-protein phosphatase.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			lung(1)	1	all_hematologic(112;0.0537)					GAGATGCCATTGCTGAAATCC	0.577																																					p.I122I		Atlas-SNP	.											.	DUSP23	9	.	0			c.T366A						PASS	.						119	108	112					1																	159752041		2203	4300	6503	SO:0001819	synonymous_variant	54935	exon3			TGCCATTGCTGAA		CCDS1187.1	1q23.1	2011-06-09			ENSG00000158716	ENSG00000158716		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	21480	protein-coding gene	gene with protein product						15147733	Standard	XM_005245289		Approved	FLJ20442, DUSP25	uc001ftz.1	Q9BVJ7	OTTHUMG00000022795	ENST00000368107.1:c.366T>A	chr1.hg19:g.159752041T>A		92.0	0.0	.		80.0	40.0	.	NM_017823	Q9NX48	Silent	SNP	ENST00000368107.1	hg19	CCDS1187.1																																																																																			.	.	.	none		0.577	DUSP23-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085552.1	NM_017823		A	159752041	T	A	159752041	2	1	148	1	0	0	0	0	0	0	0	1	4824	1800	63	5		5	DUSP23	1	159752041	Silent	SNP	T	TCGA-DW-7836-01A-11D-2136-08	132480155	159752041	89498580	2	8824											
TOMM40L	84134	hgsc.bcm.edu	37	chr1	161197494	161197494	+	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	gcccaggtcttgctcctcttGgcagagcggctccgagctaa	6	9	12	14	2	2	1	0	0	2	1	4	2	4	1	3	3	3	4	3	3	1	3			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr1:161197494G>T	ENST00000367988.3	+	5	614	c.345G>T	c.(343-345)ttG>ttT	p.L115F	TOMM40L_ENST00000474486.1_Intron|TOMM40L_ENST00000545897.1_Intron|NR1I3_ENST00000479324.1_5'Flank|MIR5187_ENST00000583479.1_RNA|TOMM40L_ENST00000367987.1_Missense_Mutation_p.L115F	NM_032174.4	NP_115550.2	Q969M1	TM40L_HUMAN	translocase of outer mitochondrial membrane 40 homolog (yeast)-like	115					ion transport (GO:0006811)|protein transport (GO:0015031)	mitochondrial outer membrane (GO:0005741)|pore complex (GO:0046930)|protein complex (GO:0043234)	porin activity (GO:0015288)			large_intestine(2)|liver(4)|lung(4)	10	all_cancers(52;1.86e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			TGCTCCTCTTGGCAGAGCGGC	0.582											OREG0013943	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L115F		Atlas-SNP	.											.	TOMM40L	19	.	0			c.G345T						PASS	.						60	54	56					1																	161197494		2203	4300	6503	SO:0001583	missense	84134	exon5			CCTCTTGGCAGAG		CCDS1227.1, CCDS65700.1	1q23.3	2008-02-05	2007-01-12		ENSG00000158882	ENSG00000158882			25756	protein-coding gene	gene with protein product			"translocase of outer mitochondrial membrane 40 homolog-like (yeast)"				Standard	NM_032174		Approved	FLJ12770, TOMM40B	uc001fzd.3	Q969M1	OTTHUMG00000034345	ENST00000367988.3:c.345G>T	chr1.hg19:g.161197494G>T	ENSP00000356967:p.Leu115Phe	87.0	0.0	.	1814	66.0	35.0	.	NM_032174	B7Z4U0|D3DVG9	Missense_Mutation	SNP	ENST00000367988.3	hg19	CCDS1227.1	.	.	.	.	.	.	.	.	.	.	G	14.57	2.574862	0.45902	.	.	ENSG00000158882	ENST00000367988;ENST00000542686;ENST00000367987	T;T	0.50001	0.76;0.76	5.49	4.52	0.55395	.	0.140087	0.48767	D	0.000176	T	0.20659	0.0497	L	0.29908	0.895	0.43971	D	0.996654	B	0.13145	0.007	B	0.20955	0.032	T	0.04427	-1.0952	9	0.24483	T	0.36	-10.7345	13.4834	0.61351	0.0:0.1581:0.8419:0.0	.	115	Q969M1	TM40L_HUMAN	F	115;62;115	ENSP00000356967:L115F;ENSP00000356966:L115F	ENSP00000356966:L115F	L	+	3	2	TOMM40L	159464118	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.926000	0.28804	2.578000	0.87016	0.655000	0.94253	TTG	.	.	.	none		0.582	TOMM40L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083029.1	NM_032174		T	161197494	G	T	161197494	3	4	148	1	0	0	0	0	1	0	0	0	16371	1339	47	4	359	4	TOMM40L	1	161197494	Missense_Mutation	SNP	G	TCGA-DW-7836-01A-11D-2136-08	1445453	161197494	88053127	3	8825											
CACNA1S	779	hgsc.bcm.edu	37	chr1	201013478	201013478	+	Missense_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	ggaatattccctcctccatcGcagcctccaccatggctctc	7	10	6	18	1	1	0	0	0	1	0	7	1	5	1	6	2	1	2	6	2	2	2			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr1:201013478G>A	ENST00000362061.3	-	39	5001	c.4775C>T	c.(4774-4776)gCg>gTg	p.A1592V	RP11-168O16.2_ENST00000415359.1_RNA|CACNA1S_ENST00000367338.3_Missense_Mutation_p.A1573V	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1592					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)	CTCCTCCATCGCAGCCTCCAC	0.622																																					p.A1592V		Atlas-SNP	.											.	CACNA1S	249	.	0			c.C4775T						PASS	.						86	72	77					1																	201013478		2203	4300	6503	SO:0001583	missense	779	exon39			TCCATCGCAGCCT	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.4775C>T	chr1.hg19:g.201013478G>A	ENSP00000355192:p.Ala1592Val	90.0	0.0	.		96.0	43.0	.	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	hg19	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	.	18.25	3.581852	0.65992	.	.	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.96334	-3.98;-3.89	4.98	4.98	0.66077	.	0.913156	0.09136	N	0.843670	D	0.94974	0.8374	M	0.69358	2.11	0.46011	D	0.99881	P	0.36909	0.573	B	0.25759	0.063	D	0.91638	0.5324	10	0.38643	T	0.18	.	18.2653	0.90050	0.0:0.0:1.0:0.0	.	1592	Q13698	CAC1S_HUMAN	V	1592;1573	ENSP00000355192:A1592V;ENSP00000356307:A1573V	ENSP00000355192:A1592V	A	-	2	0	CACNA1S	199280101	1.000000	0.71417	0.604000	0.28916	0.956000	0.61745	5.418000	0.66429	2.304000	0.77564	0.555000	0.69702	GCG	.	.	.	none		0.622	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		A	201013478	G	A	201013478	3	1	148	1	0	0	0	0	1	0	0	0	2549	1087	38	1	870	1	CACNA1S	1	201013478	Missense_Mutation	SNP	G	TCGA-DW-7836-01A-11D-2136-08	39815984	201013478	48237143	4	8826											
ERO1LB	56605	hgsc.bcm.edu	37	chr1	236385229	236385229	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agacaacacatatacctgtaAttttccccataatctgcatt	14	13	3	11	0	1	1	0	0	1	1	2	1	2	1	3	0	3	2	3	0	5	7			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr1:236385229A>G	ENST00000354619.5	-	14	1405	c.1204T>C	c.(1204-1206)Tta>Cta	p.L402L		NM_019891.3	NP_063944.3	Q86YB8	ERO1B_HUMAN	ERO1-like beta (S. cerevisiae)	402					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)	TATACCTGTAATTTTCCCCAT	0.343																																					p.L402L		Atlas-SNP	.											.	ERO1LB	48	.	0			c.T1204C						PASS	.						103	101	102					1																	236385229		2202	4300	6502	SO:0001819	synonymous_variant	56605	exon14			CCTGTAATTTTCC	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.1204T>C	chr1.hg19:g.236385229A>G		78.0	0.0	.		39.0	22.0	.	NM_019891	B4DF57|Q5T1H4|Q8IZ11|Q9NR62	Silent	SNP	ENST00000354619.5	hg19	CCDS31064.1																																																																																			.	.	.	none		0.343	ERO1LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096371.1	NM_019891		G	236385229	A	G	236385229	2	3	148	1	0	0	0	0	0	0	0	1	5242	98	4	3		3	ERO1LB	1	236385229	Silent	SNP	A	TCGA-DW-7836-01A-11D-2136-08	35371751	236385229	12865392	5	8827											
OR2AK2	391191	hgsc.bcm.edu	37	chr1	248129596	248129596	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagtgaggagactgttgggAtattggatatgctgtagaaa	12	11	15	3	0	0	3	0	1	0	2	0	6	0	5	0	3	1	4	0	3	4	5			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr1:248129596A>G	ENST00000366480.3	+	1	1062	c.963A>G	c.(961-963)ggA>ggG	p.G321G	OR2L13_ENST00000366478.2_Intron	NM_001004491.1	NP_001004491.1	Q8NG84	O2AK2_HUMAN	olfactory receptor, family 2, subfamily AK, member 2	321						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)			GACTGTTGGGATATTGGATAT	0.393																																					p.G321G	Melanoma(45;390 1181 23848 28461 41504)	Atlas-SNP	.											.	OR2AK2	90	.	0			c.A963G						PASS	.						99	96	97					1																	248129596		2203	4300	6503	SO:0001819	synonymous_variant	391191	exon1			GTTGGGATATTGG	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.963A>G	chr1.hg19:g.248129596A>G		113.0	0.0	.		69.0	31.0	.	NM_001004491	B2RND1|Q6IF05	Silent	SNP	ENST00000366480.3	hg19	CCDS31102.1																																																																																			.	.	.	none		0.393	OR2AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096858.2	NM_001004491		G	248129596	A	G	248129596	2	3	148	1	0	0	0	0	0	0	0	1	10993	320	12	3		3	OR2AK2	1	248129596	Silent	SNP	A	TCGA-DW-7836-01A-11D-2136-08	11744367	248129596	1121025	6	8828											
LTBP1	4052	hgsc.bcm.edu	37	chr2	33246142	33246142	+	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	gctgcttcctcgtggggcccTcctgagcaagcagcaaagca	8	7	12	14	1	0	1	0	1	0	0	3	1	2	1	3	2	5	6	3	2	2	1			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr2:33246142T>A	ENST00000404816.2	+	3	1085	c.732T>A	c.(730-732)ccT>ccA	p.P244P	LTBP1_ENST00000354476.3_Silent_p.P244P			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	244					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)				CGTGGGGCCCTCCTGAGCAAG	0.567																																					p.P244P		Atlas-SNP	.											.	LTBP1	317	.	0			c.T732A						PASS	.						109	111	110					2																	33246142		2203	4300	6503	SO:0001819	synonymous_variant	4052	exon3			GGGCCCTCCTGAG		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.732T>A	chr2.hg19:g.33246142T>A		219.0	0.0	.		169.0	60.0	.	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Silent	SNP	ENST00000404816.2	hg19	CCDS33177.2																																																																																			.	.	.	none		0.567	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		A	33246142	T	A	33246142	2	1	148	1	0	0	0	0	0	0	0	1	9080	1538	54	5		5	LTBP1	2	33246142	Silent	SNP	T	TCGA-DW-7836-01A-11D-2136-08		33246142	209953231	7	8829											
LYG2	254773	hgsc.bcm.edu	37	chr2	99861757	99861757	+	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	aaatttaagtcccctgtggtCccagccgtcttgcaggacag	9	10	10	12	1	1	0	0	0	1	0	3	1	3	1	4	2	2	1	4	2	2	3			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr2:99861757C>A	ENST00000409238.1	-	3	369	c.349G>T	c.(349-351)Gac>Tac	p.D117Y	LYG2_ENST00000409679.1_Missense_Mutation_p.D117Y|LYG2_ENST00000423800.1_Missense_Mutation_p.D117Y|LYG2_ENST00000333017.2_Missense_Mutation_p.D117Y			Q86SG7	LYG2_HUMAN	lysozyme G-like 2	117					cell wall macromolecule catabolic process (GO:0016998)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)			large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(1)|stomach(1)	12						CCCCTGTGGTCCCAGCCGTCT	0.522																																					p.D117Y		Atlas-SNP	.											.	LYG2	26	.	0			c.G349T						PASS	.						102	94	97					2																	99861757		2203	4300	6503	SO:0001583	missense	254773	exon4			TGTGGTCCCAGCC	AF323919	CCDS2042.1	2q11.2	2008-02-05			ENSG00000185674	ENSG00000185674			29615	protein-coding gene	gene with protein product						8889548, 12574869	Standard	NM_175735		Approved	LYGH	uc002szw.1	Q86SG7	OTTHUMG00000130643	ENST00000409238.1:c.349G>T	chr2.hg19:g.99861757C>A	ENSP00000386939:p.Asp117Tyr	126.0	0.0	.		102.0	42.0	.	NM_175735	Q496G2|Q53RW0	Missense_Mutation	SNP	ENST00000409238.1	hg19	CCDS2042.1	.	.	.	.	.	.	.	.	.	.	C	18.28	3.589375	0.66105	.	.	ENSG00000185674	ENST00000409238;ENST00000333017;ENST00000409679;ENST00000423306	.	.	.	5.78	4.91	0.64330	Lytic transglycosylase-like, catalytic (1);Lysozyme-like domain (1);	0.174545	0.40728	N	0.001027	T	0.69450	0.3112	M	0.63428	1.95	0.37969	D	0.933212	D;D;D	0.71674	0.998;0.998;0.998	D;D;D	0.66847	0.947;0.947;0.947	T	0.73113	-0.4085	8	.	.	.	-2.2835	10.7149	0.46006	0.0:0.9126:0.0:0.0874	.	117;117;117	Q496G2;C9J4J0;Q86SG7	.;.;LYG2_HUMAN	Y	117	.	.	D	-	1	0	LYG2	99228189	1.000000	0.71417	1.000000	0.80357	0.772000	0.43724	2.364000	0.44187	1.465000	0.48006	0.555000	0.69702	GAC	.	.	.	none		0.522	LYG2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330307.1	NM_175735		A	99861757	C	A	99861757	3	1	148	1	0	0	0	0	1	0	0	0	9112	855	30	4	301	4	LYG2	2	99861757	Missense_Mutation	SNP	C	TCGA-DW-7836-01A-11D-2136-08	66615615	99861757	143337616	8	8830											
ALS2	57679	hgsc.bcm.edu	37	chr2	202606404	202606404	+	Frame_Shift_Del	DEL	A	A	-																															actggatacttgctctgtatAactatccaagaagagacttg																										TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr2:202606404delA	ENST00000264276.6	-	11	2716	c.2344delT	c.(2344-2346)tatfs	p.Y782fs	ALS2_ENST00000457679.2_Frame_Shift_Del_p.Y94fs	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	782	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						TGCTCTGTATAACTATCCAAG	0.463																																					p.Y782fs		Atlas-Indel,Pindel	.											.	ALS2	172	.	0			c.2345delA						PASS	.						63	60	61					2																	202606404		1893	4121	6014	SO:0001589	frameshift_variant	57679	exon11			.	AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"Rho guanine nucleotide exchange factors"	443	protein-coding gene	gene with protein product	"alsin"	606352	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.2344delT	chr2.hg19:g.202606404delA	ENSP00000264276:p.Tyr782fs	78.0	0.0	0		39.0	17.0	0.435897	NM_020919	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Frame_Shift_Del	DEL	ENST00000264276.6	hg19	CCDS42800.1																																																																																			.	.	.	none		0.463	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919		-	202606404	A	-	202606404	7	5	148	1	0	1	0	1	0	0	0	0	550	362	13	0	2725	0	ALS2	2	202606404	Frame_Shift_Del	DEL	A	TCGA-DW-7836-01A-11D-2136-08	102744647	202606404	40592969	9	8831											
TNS1	7145	hgsc.bcm.edu	37	chr2	218749811	218749811	+	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	agacaacccccaggtcatggAtggcacaggtgtggaactgc	11	6	13	11	0	1	1	1	0	0	1	1	3	1	3	2	5	3	1	2	5	2	0			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr2:218749811A>T	ENST00000171887.4	-	14	1270	c.818T>A	c.(817-819)aTc>aAc	p.I273N	TNS1_ENST00000419504.1_Missense_Mutation_p.I273N|TNS1_ENST00000430930.1_Missense_Mutation_p.I273N|TNS1_ENST00000310858.6_Missense_Mutation_p.I304N	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	273	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		CAGGTCATGGATGGCACAGGT	0.592																																					p.I273N		Atlas-SNP	.											.	TNS1	251	.	0			c.T818A						PASS	.						140	113	122					2																	218749811		2203	4300	6503	SO:0001583	missense	7145	exon14			TCATGGATGGCAC	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.818T>A	chr2.hg19:g.218749811A>T	ENSP00000171887:p.Ile273Asn	104.0	0.0	.		88.0	39.0	.	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	hg19	CCDS2407.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.9|22.9	4.347781|4.347781	0.82022|0.82022	.|.	.|.	ENSG00000079308|ENSG00000079308	ENST00000453356|ENST00000171887;ENST00000419504;ENST00000430930;ENST00000446903;ENST00000413554;ENST00000310858	.|D;D;D;D;D;D	.|0.89270	.|-2.49;-2.49;-2.49;-2.49;-2.49;-2.49	4.83|4.83	4.83|4.83	0.62350|0.62350	.|Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	.|0.358725	.|0.30227	.|N	.|0.010111	D|D	0.94019|0.94019	0.8084|0.8084	M|M	0.79805|0.79805	2.47|2.47	0.47276|0.47276	D|D	0.999373|0.999373	.|D;D;D;D;D;D	.|0.76494	.|0.999;0.995;0.961;0.993;0.999;0.999	.|D;D;P;D;D;D	.|0.71184	.|0.972;0.961;0.828;0.942;0.972;0.972	D|D	0.94788|0.94788	0.7959|0.7959	5|10	.|0.87932	.|D	.|0	.|.	14.2677|14.2677	0.66129|0.66129	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|273;327;304;273;273;273	.|B2RU35;A1L0S7;Q6IPI5;Q9HBL0;E9PGF5;E9PF55	.|.;.;.;TENS1_HUMAN;.;.	Q|N	48|273;273;273;398;341;304	.|ENSP00000171887:I273N;ENSP00000408724:I273N;ENSP00000406016:I273N;ENSP00000405460:I398N;ENSP00000400383:I341N;ENSP00000308321:I304N	.|ENSP00000171887:I273N	H|I	-|-	3|2	2|0	TNS1|TNS1	218458056|218458056	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	9.004000|9.004000	0.93583|0.93583	2.021000|2.021000	0.59480|0.59480	0.460000|0.460000	0.39030|0.39030	CAT|ATC	.	.	.	none		0.592	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		T	218749811	A	T	218749811	3	4	148	1	0	0	0	0	1	0	0	0	16355	333	12	5	4469	5	TNS1	2	218749811	Missense_Mutation	SNP	A	TCGA-DW-7836-01A-11D-2136-08	16143407	218749811	24449562	10	8832											
RBM5	10181	hgsc.bcm.edu	37	chr3	50129618	50129618	+	Missense_Mutation	SNP	T	T	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	ggggtgatagatatgatgacTaccgagactatgacagtcca	13	9	12	7	1	0	6	0	4	0	2	1	7	1	6	2	2	1	0	2	2	4	4			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr3:50129618T>G	ENST00000347869.3	+	3	335	c.160T>G	c.(160-162)Tac>Gac	p.Y54D	RBM5_ENST00000469838.1_Missense_Mutation_p.Y54D	NM_005778.3	NP_005769.1	P52756	RBM5_HUMAN	RNA binding motif protein 5	54				DY -> GS (in Ref. 1; AAA99715). {ECO:0000305}.	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)		ATATGATGACTACCGAGACTA	0.498																																					p.Y54D		Atlas-SNP	.											.	RBM5	76	.	0			c.T160G						PASS	.						102	94	97					3																	50129618		2203	4300	6503	SO:0001583	missense	10181	exon3			GATGACTACCGAG	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.160T>G	chr3.hg19:g.50129618T>G	ENSP00000343054:p.Tyr54Asp	56.0	0.0	.		64.0	36.0	.	NM_005778	B2RA45|B4DM16|B4DMF9|B4DZ63|Q93021|Q9BU14|Q9HDA6|Q9UKY8|Q9UL24	Missense_Mutation	SNP	ENST00000347869.3	hg19	CCDS2810.1	.	.	.	.	.	.	.	.	.	.	T	10.29	1.310260	0.23821	.	.	ENSG00000003756	ENST00000347869;ENST00000469838;ENST00000404526;ENST00000536082;ENST00000441305;ENST00000437500;ENST00000417905;ENST00000543047;ENST00000539538	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	4.83	3.63	0.41609	.	0.293852	0.33610	N	0.004734	T	0.26122	0.0637	N	0.22421	0.69	0.44523	D	0.997476	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.06499	-1.0823	9	.	.	.	-8.6199	10.5358	0.45002	0.0:0.0795:0.0:0.9204	.	54;54	P52756;E1CJT4	RBM5_HUMAN;.	D	54;54;54;54;54;54;54;53;53	ENSP00000343054:Y54D;ENSP00000419534:Y54D;ENSP00000390711:Y54D;ENSP00000406119:Y54D	.	Y	+	1	0	RBM5	50104622	0.998000	0.40836	1.000000	0.80357	0.820000	0.46376	1.836000	0.39191	2.037000	0.60232	0.450000	0.29827	TAC	.	.	.	none		0.498	RBM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345797.3	NM_005778		G	50129618	T	G	50129618	3	3	148	1	0	0	0	0	1	0	0	0	13156	1522	53	5	166	5	RBM5	3	50129618	Missense_Mutation	SNP	T	TCGA-DW-7836-01A-11D-2136-08		50129618	147892812	11	8833											
NPY2R	4887	hgsc.bcm.edu	37	chr4	156136064	156136064	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttttgccaatccccttctcTatggctggatgaacagcaac	9	12	7	13	0	1	1	0	1	1	0	3	2	2	2	3	2	4	2	3	2	4	4			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr4:156136064T>C	ENST00000329476.3	+	2	1462	c.973T>C	c.(973-975)Tat>Cat	p.Y325H	NPY2R_ENST00000506608.1_Missense_Mutation_p.Y325H	NM_000910.2	NP_000901.1	P49146	NPY2R_HUMAN	neuropeptide Y receptor Y2	325					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)	TCCCCTTCTCTATGGCTGGAT	0.512																																					p.Y325H		Atlas-SNP	.											.	NPY2R	87	.	0			c.T973C						PASS	.						114	96	102					4																	156136064		2203	4300	6503	SO:0001583	missense	4887	exon2			CTTCTCTATGGCT	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.973T>C	chr4.hg19:g.156136064T>C	ENSP00000332591:p.Tyr325His	153.0	0.0	.		87.0	37.0	.	NM_000910	Q13281|Q13457|Q4W5G7|Q6AZZ6|Q9UE67	Missense_Mutation	SNP	ENST00000329476.3	hg19	CCDS3791.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.198384	0.79015	.	.	ENSG00000185149	ENST00000329476;ENST00000506608	D;D	0.93247	-3.19;-3.19	5.74	5.74	0.90152	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.98353	0.9453	H	0.99487	4.59	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99659	1.0993	10	0.87932	D	0	.	15.2138	0.73247	0.0:0.0:0.0:1.0	.	325	P49146	NPY2R_HUMAN	H	325	ENSP00000332591:Y325H;ENSP00000426366:Y325H	ENSP00000332591:Y325H	Y	+	1	0	NPY2R	156355514	1.000000	0.71417	0.976000	0.42696	0.970000	0.65996	8.040000	0.89188	2.189000	0.69895	0.523000	0.50628	TAT	.	.	.	none		0.512	NPY2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365128.1	NM_000910		C	156136064	T	C	156136064	3	2	148	1	0	0	0	0	1	0	0	0	10616	1522	53	3	975	3	NPY2R	4	156136064	Missense_Mutation	SNP	T	TCGA-DW-7836-01A-11D-2136-08		156136064	35018212	12	8834											
KCNQ5	56479	hgsc.bcm.edu	37	chr6	73904447	73904447	+	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	ttcagtgcccagactttctaCgcgcttagccctactatgca	8	12	7	14	2	2	1	1	0	1	1	2	1	2	1	2	0	5	2	2	0	4	6			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr6:73904447C>T	ENST00000370398.1	+	14	2218	c.2109C>T	c.(2107-2109)taC>taT	p.Y703Y	KCNQ5_ENST00000414165.2_Silent_p.Y593Y|KCNQ5_ENST00000342056.2_Silent_p.Y722Y|KCNQ5_ENST00000403813.2_Silent_p.Y694Y|KCNQ5_ENST00000402622.2_Silent_p.Y713Y|KCNQ5_ENST00000355635.3_Silent_p.Y704Y|KCNQ5_ENST00000355194.4_Silent_p.Y703Y	NM_019842.3	NP_062816.2	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 5	703					protein complex assembly (GO:0006461)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|cervix(1)|endometrium(6)|kidney(7)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	57		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)	Ezogabine(DB04953)	AGACTTTCTACGCGCTTAGCC	0.493																																					p.Y722Y	GBM(142;1375 1859 14391 23261 44706)	Atlas-SNP	.											.	KCNQ5	153	.	0			c.C2166T						PASS	.						132	131	132					6																	73904447		2203	4300	6503	SO:0001819	synonymous_variant	56479	exon15			TTTCTACGCGCTT	AF202977	CCDS4976.1, CCDS55034.1	6q14	2012-07-05			ENSG00000185760	ENSG00000185760		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6299	protein-coding gene	gene with protein product		607357				10787416, 10816588, 16382104	Standard	NM_019842		Approved	Kv7.5	uc011dyh.2	Q9NR82	OTTHUMG00000015020	ENST00000370398.1:c.2109C>T	chr6.hg19:g.73904447C>T		205.0	0.0	.		174.0	80.0	.	NM_001160133	A6NKT6|A6PVT6|A8MSQ5|B4DS33|B5MC83|B7ZL37|F5GZV0|Q17RE1|Q5VVP3|Q86W40|Q9NRN0|Q9NYA6	Silent	SNP	ENST00000370398.1	hg19	CCDS4976.1																																																																																			.	.	.	none		0.493	KCNQ5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041198.3	NM_019842		T	73904447	C	T	73904447	2	4	148	1	0	0	0	0	0	0	0	1	8093	547	19	1		1	KCNQ5	6	73904447	Silent	SNP	C	TCGA-DW-7836-01A-11D-2136-08		73904447	97210620	13	8835											
SLC26A4	5172	hgsc.bcm.edu	37	chr7	107335130	107335130	+	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	tatgcagctgtgtgacattcCtcgtctgtggagacagaata	10	12	11	8	1	1	3	0	1	1	2	3	4	2	3	1	1	2	2	1	1	3	3			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr7:107335130C>A	ENST00000265715.3	+	12	1630	c.1406C>A	c.(1405-1407)cCt>cAt	p.P469H	SLC26A4_ENST00000480841.1_3'UTR|SLC26A4_ENST00000541474.1_Missense_Mutation_p.P30H|SLC26A4_ENST00000544569.1_Missense_Mutation_p.P56H|SLC26A4_ENST00000543100.1_Missense_Mutation_p.P38H	NM_000441.1	NP_000432.1	O43511	S26A4_HUMAN	solute carrier family 26 (anion exchanger), member 4	469					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						TGTGACATTCCTCGTCTGTGG	0.428									Pendred syndrome																												p.P469H		Atlas-SNP	.											.	SLC26A4	117	.	0			c.C1406A						PASS	.						174	156	162					7																	107335130		2203	4300	6503	SO:0001583	missense	5172	exon12	Familial Cancer Database	Goiter-Deafness syndrome	ACATTCCTCGTCT	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.1406C>A	chr7.hg19:g.107335130C>A	ENSP00000265715:p.Pro469His	107.0	0.0	.		124.0	79.0	.	NM_000441	B7Z266|O43170	Missense_Mutation	SNP	ENST00000265715.3	hg19	CCDS5746.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657406	0.88154	.	.	ENSG00000091137	ENST00000265715;ENST00000541474;ENST00000544569;ENST00000543100	D;D;D;D	0.94897	-3.13;-3.55;-3.13;-3.13	5.66	5.66	0.87406	Sulphate transporter (1);	0.000000	0.85682	D	0.000000	D	0.97835	0.9289	M	0.89904	3.07	0.58432	D	0.999998	D;D;P	0.89917	1.0;1.0;0.932	D;D;P	0.97110	0.999;1.0;0.599	D	0.97207	0.9868	10	0.42905	T	0.14	.	20.1041	0.97884	0.0:1.0:0.0:0.0	.	30;56;469	F5H104;B7Z6M6;O43511	.;.;S26A4_HUMAN	H	469;30;56;38	ENSP00000265715:P469H;ENSP00000439743:P30H;ENSP00000437427:P56H;ENSP00000441209:P38H	ENSP00000265715:P469H	P	+	2	0	SLC26A4	107122366	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.145000	0.77365	2.826000	0.97356	0.655000	0.94253	CCT	.	.	.	none		0.428	SLC26A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337148.1	NM_000441		A	107335130	C	A	107335130	3	1	148	1	0	0	0	0	1	0	0	0	14532	681	24	4	1448	4	SLC26A4	7	107335130	Missense_Mutation	SNP	C	TCGA-DW-7836-01A-11D-2136-08		107335130	51803533	14	8836											
ADAM32	203102	hgsc.bcm.edu	37	chr8	39068760	39068760	+	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	aatgtcttcagaataagccaCaaatgcaaaaaaaatctccg	19	8	5	9	1	3	1	1	0	2	1	4	1	3	1	2	0	2	1	2	0	8	2			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr8:39068760C>T	ENST00000379907.4	+	12	1277	c.1150C>T	c.(1150-1152)Caa>Taa	p.Q384*	ADAM32_ENST00000519315.1_Intron|ADAM32_ENST00000437682.2_Intron	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	384						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)			GAATAAGCCACAAATGCAAAA	0.393																																					p.Q384X		Atlas-SNP	.											.	ADAM32	70	.	0			c.C1150T						PASS	.						82	78	79					8																	39068760		1816	4089	5905	SO:0001587	stop_gained	203102	exon12			AAGCCACAAATGC	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.1150C>T	chr8.hg19:g.39068760C>T	ENSP00000369238:p.Gln384*	24.0	0.0	.		17.0	11.0	.	NM_145004	Q8TC42	Nonsense_Mutation	SNP	ENST00000379907.4	hg19	CCDS47846.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.618144	0.87359	.	.	ENSG00000197140	ENST00000379907	.	.	.	5.23	4.3	0.51218	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	.	11.6429	0.51244	0.177:0.823:0.0:0.0	.	.	.	.	X	384	.	ENSP00000369238:Q384X	Q	+	1	0	ADAM32	39187917	0.013000	0.17824	0.987000	0.45799	0.438000	0.31896	0.452000	0.21795	2.585000	0.87301	0.650000	0.86243	CAA	.	.	.	none		0.393	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004		T	39068760	C	T	39068760	4	4	148	1	0	0	0	0	0	1	0	0	249	479	17	2	1196	2	ADAM32	8	39068760	Nonsense_Mutation	SNP	C	TCGA-DW-7836-01A-11D-2136-08		39068760	107295262	15	8837											
CSMD3	114788	hgsc.bcm.edu	37	chr8	113697849	113697849	+	Frame_Shift_Del	DEL	C	C	-																															aaagaaagatgtatccggctCcctggatcagagattatcgt																										TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr8:113697849delC	ENST00000297405.5	-	15	2512	c.2268delG	c.(2266-2268)gggfs	p.G756fs	CSMD3_ENST00000352409.3_Frame_Shift_Del_p.G756fs|CSMD3_ENST00000343508.3_Frame_Shift_Del_p.G716fs|CSMD3_ENST00000455883.2_Frame_Shift_Del_p.G652fs	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	756	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GTATCCGGCTCCCTGGATCAG	0.413										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.S757fs		Atlas-INDEL	.											.	CSMD3	2325	.	0			c.2269delA						PASS	.						100	107	105					8																	113697849		2203	4300	6503	SO:0001589	frameshift_variant	114788	exon15			.	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.2268delG	chr8.hg19:g.113697849delC	ENSP00000297405:p.Gly756fs	148.0	0.0	0		104.0	51.0	0.490385	NM_198123	Q96PZ3	Frame_Shift_Del	DEL	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.	.	none		0.413	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		-	113697849	C	-	113697849	7	5	148	1	0	1	0	1	0	0	0	0	3948	842	30	0	9083	0	CSMD3	8	113697849	Frame_Shift_Del	DEL	C	TCGA-DW-7836-01A-11D-2136-08	74629089	113697849	32666173	16	8838	90	3									
CSMD3	114788	hgsc.bcm.edu	37	chr8	113697851	113697852	+	Frame_Shift_Del	DEL	CT	CT	-																															agaaagatgtatccggctccCtggatcagagattatcgtcc																										TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr8:113697851_113697852delCT	ENST00000297405.5	-	15	2509_2510	c.2265_2266delAG	c.(2263-2268)ccagggfs	p.G756fs	CSMD3_ENST00000352409.3_Frame_Shift_Del_p.G756fs|CSMD3_ENST00000343508.3_Frame_Shift_Del_p.G716fs|CSMD3_ENST00000455883.2_Frame_Shift_Del_p.G652fs	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	756	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						ATCCGGCTCCCTGGATCAGAGA	0.416										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.756_756del		Pindel	.											CSMD3_ENST00000343508,right_upper_lobe,carcinoma,+1,1	CSMD3	2325	.	0			c.2266_2267del						PASS	.																																			SO:0001589	frameshift_variant	114788	exon15			.	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.2265_2266delAG	chr8.hg19:g.113697851_113697852delCT	ENSP00000297405:p.Gly756fs	155.0	0.0	.		107.0	36.0	0.336	NM_198123	Q96PZ3	Frame_Shift_Del	DEL	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.	.	none		0.416	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		-	113697852	CT	-	113697851	7	5	148	1	0	1	0	1	0	0	0	0	3948	681	24	0	9085	0	CSMD3	8	113697851	Frame_Shift_Del	DEL	CT	TCGA-DW-7836-01A-11D-2136-08	2	113697851	32666171	17	8839	90	3									
CSMD3	114788	hgsc.bcm.edu	37	chr8	113697852	113697852	+	Silent	SNP	T	T	G																															gaaagatgtatccggctcccTggatcagagattatcgtcca																										TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr8:113697852T>G	ENST00000297405.5	-	15	2509	c.2265A>C	c.(2263-2265)ccA>ccC	p.P755P	CSMD3_ENST00000352409.3_Silent_p.P755P|CSMD3_ENST00000343508.3_Silent_p.P715P|CSMD3_ENST00000455883.2_Silent_p.P651P	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	755	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TCCGGCTCCCTGGATCAGAGA	0.413										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.P755P		Atlas-SNP	.											.	CSMD3	2325	.	0			c.A2265C						PASS	.						100	108	105					8																	113697852		2203	4300	6503	SO:0001819	synonymous_variant	114788	exon15			GCTCCCTGGATCA	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.2265A>C	chr8.hg19:g.113697852T>G		158.0	0.0	.		106.0	52.0	.	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.	.	none		0.413	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		G	113697852	T	G	113697852	2	3	148	1	0	0	0	0	0	0	0	1	3948	1567	55	5		5	CSMD3	8	113697852	Silent	SNP	T	TCGA-DW-7836-01A-11D-2136-08	1	113697852	32666170	18	8840	90	3									
MRC1	4360	hgsc.bcm.edu	37	chr10	17891759	17891759	+	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	tcgactttattatctcccagCtaggatatggtgagaaactt	11	14	8	8	1	1	1	0	1	1	1	3	4	1	2	1	2	2	1	1	2	5	6			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr10:17891759C>T	ENST00000331429.2	+	7	1343	c.1240C>T	c.(1240-1242)Cta>Tta	p.L414L	MRC1L1_ENST00000457317.1_Silent_p.L414L																breast(1)|endometrium(1)|large_intestine(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						TATCTCCCAGCTAGGATATGG	0.438																																					p.L414L		Atlas-SNP	.											.	MRC1	13	.	0			c.C1240T						PASS	.						161	174	170					10																	17891759		2158	4135	6293	SO:0001819	synonymous_variant	4360	exon7			TCCCAGCTAGGAT																												ENST00000331429.2:c.1240C>T	chr10.hg19:g.17891759C>T		318.0	1.0	.		243.0	92.0	.	NM_002438		Silent	SNP	ENST00000331429.2	hg19																																																																																				.	.	.	none		0.438	MRC1L1-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047054.1			T	17891759	C	T	17891759	2	4	148	1	0	0	0	0	0	0	0	1	9763	796	28	2		2	MRC1	10	17891759	Silent	SNP	C	TCGA-DW-7836-01A-11D-2136-08		17891759	117642988	19	8841											
PPP3CB	5532	hgsc.bcm.edu	37	chr10	75214208	75214208	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcagtcattagttcatcaTcagagcaaatactcagaaca	15	11	5	10	0	6	2	6	0	0	2	6	2	6	2	0	0	3	2	0	0	4	4			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr10:75214208T>C	ENST00000360663.5	-	10	1259	c.1148A>G	c.(1147-1149)gAt>gGt	p.D383G	PPP3CB_ENST00000544628.1_Missense_Mutation_p.D11G|PPP3CB_ENST00000394822.2_Missense_Mutation_p.D401G|PPP3CB_ENST00000342558.3_Missense_Mutation_p.D383G|PPP3CB_ENST00000394829.2_Missense_Mutation_p.D383G|PPP3CB_ENST00000545874.1_Missense_Mutation_p.D297G|PPP3CB_ENST00000394828.2_Missense_Mutation_p.D383G			P16298	PP2BB_HUMAN	protein phosphatase 3, catalytic subunit, beta isozyme	383					axon extension (GO:0048675)|calcium ion-dependent exocytosis (GO:0017156)|cellular response to drug (GO:0035690)|dephosphorylation (GO:0016311)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|innate immune response (GO:0045087)|learning (GO:0007612)|locomotion involved in locomotory behavior (GO:0031987)|memory (GO:0007613)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of transcription, DNA-templated (GO:0045893)|protein dephosphorylation (GO:0006470)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of synaptic plasticity (GO:0048167)|response to cytokine (GO:0034097)|signal transduction (GO:0007165)|social behavior (GO:0035176)|T cell activation (GO:0042110)|T cell differentiation (GO:0030217)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)	calcineurin complex (GO:0005955)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein phosphatase activity (GO:0033192)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|protein dimerization activity (GO:0046983)|protein phosphatase 2B binding (GO:0030346)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(7)|skin(1)|urinary_tract(1)	22	Prostate(51;0.0119)					TAGTTCATCATCAGAGCAAAT	0.313																																					p.D383G		Atlas-SNP	.											.	PPP3CB	68	.	0			c.A1148G						PASS	.						143	136	138					10																	75214208		2203	4298	6501	SO:0001583	missense	5532	exon10			TCATCATCAGAGC	M29551	CCDS7328.1, CCDS44436.1, CCDS44437.1	10q22.2	2010-03-17	2010-03-05		ENSG00000107758	ENSG00000107758	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9315	protein-coding gene	gene with protein product	"calcineurin A beta", "protein phosphatase 2B, catalytic subunit, beta isoform"	114106	"protein phosphatase 3 (formerly 2B), catalytic subunit, beta isoform (calcineurin A beta)", "protein phosphatase 3 (formerly 2B), catalytic subunit, beta isoform"	CALNB		1659808, 2558868	Standard	XM_005269944		Approved	CALNA2, CNA2, PP2Bbeta	uc001juf.3	P16298	OTTHUMG00000018472	ENST00000360663.5:c.1148A>G	chr10.hg19:g.75214208T>C	ENSP00000353881:p.Asp383Gly	156.0	0.0	.		88.0	28.0	.	NM_001142354	P16299|Q5F2F9|Q8N1F0|Q8N3W4	Missense_Mutation	SNP	ENST00000360663.5	hg19	CCDS7328.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.368061	0.82463	.	.	ENSG00000107758	ENST00000360663;ENST00000394829;ENST00000394828;ENST00000394823;ENST00000544628;ENST00000430762;ENST00000342558;ENST00000545874;ENST00000394822	T;T;T;T;T;T;T	0.05786	3.39;3.39;3.39;3.39;3.39;3.39;3.39	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	T	0.18923	0.0454	M	0.64676	1.99	0.80722	D	1	D;P;B;P;B	0.54047	0.964;0.586;0.052;0.819;0.022	P;P;B;B;B	0.56127	0.792;0.46;0.029;0.345;0.018	T	0.00057	-1.2173	10	0.56958	D	0.05	.	16.4943	0.84223	0.0:0.0:0.0:1.0	.	401;297;383;383;383	P16298-2;F5H0F8;P16298-3;Q8N1F0;P16298	.;.;.;.;PP2BB_HUMAN	G	383;383;383;46;11;36;383;297;401	ENSP00000353881:D383G;ENSP00000378306:D383G;ENSP00000378305:D383G;ENSP00000437596:D11G;ENSP00000343147:D383G;ENSP00000439876:D297G;ENSP00000378299:D401G	ENSP00000343147:D383G	D	-	2	0	PPP3CB	74884214	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.841000	0.86834	2.291000	0.77112	0.533000	0.62120	GAT	.	.	.	none		0.313	PPP3CB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048669.1	NM_021132		C	75214208	T	C	75214208	3	2	148	1	0	0	0	0	1	0	0	0	12408	1435	50	3	449	3	PPP3CB	10	75214208	Missense_Mutation	SNP	T	TCGA-DW-7836-01A-11D-2136-08	57322449	75214208	60320539	20	8842											
AHNAK	79026	hgsc.bcm.edu	37	chr11	62298802	62298802	+	Missense_Mutation	SNP	A	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	gtatctacttttggtgcagaAatgtccacattcgctttgga	9	15	9	8	1	1	1	0	0	1	1	3	2	2	2	1	2	2	3	1	2	3	6			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr11:62298802A>C	ENST00000378024.4	-	5	3361	c.3087T>G	c.(3085-3087)atT>atG	p.I1029M	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	1029					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)				TTGGTGCAGAAATGTCCACAT	0.453																																					p.I1029M		Atlas-SNP	.											.	AHNAK	532	.	0			c.T3087G						PASS	.						98	95	96					11																	62298802		2202	4299	6501	SO:0001583	missense	79026	exon5			TGCAGAAATGTCC	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.3087T>G	chr11.hg19:g.62298802A>C	ENSP00000367263:p.Ile1029Met	141.0	0.0	.		77.0	39.0	.	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	hg19	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	-	12.64	1.997934	0.35226	.	.	ENSG00000124942	ENST00000378024	T	0.01527	4.8	4.63	3.5	0.40072	.	0.822488	0.10918	N	0.619768	T	0.04497	0.0123	M	0.83953	2.67	0.28015	N	0.934744	P	0.48089	0.905	P	0.45971	0.499	T	0.30504	-0.9976	10	0.33940	T	0.23	-2.6022	5.0819	0.14661	0.7519:0.0:0.0886:0.1594	.	1029	Q09666	AHNK_HUMAN	M	1029	ENSP00000367263:I1029M	ENSP00000367263:I1029M	I	-	3	3	AHNAK	62055378	1.000000	0.71417	1.000000	0.80357	0.739000	0.42172	0.982000	0.29539	0.734000	0.32515	0.454000	0.30748	ATT	.	.	.	none		0.453	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		C	62298802	A	C	62298802	3	2	148	1	0	0	0	0	1	0	0	0	414	10	1	5	14705	5	AHNAK	11	62298802	Missense_Mutation	SNP	A	TCGA-DW-7836-01A-11D-2136-08		62298802	72707714	21	8843											
C12orf59	120939	hgsc.bcm.edu	37	chr12	10342575	10342575	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctccctgggccagctgcccTcctctttggacaccctccca	4	9	8	20	0	1	0	0	0	1	0	4	1	4	1	6	2	2	2	6	2	0	1			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr12:10342575T>C	ENST00000381923.2	+	6	792	c.388T>C	c.(388-390)Tcc>Ccc	p.S130P	TMEM52B_ENST00000298530.3_Missense_Mutation_p.S110P|TMEM52B_ENST00000536952.1_Missense_Mutation_p.S130P			Q4KMG9	TM52B_HUMAN	transmembrane protein 52B	130						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											CCAGCTGCCCTCCTCTTTGGA	0.582																																					p.S110P		Atlas-SNP	.											.	.	.	.	0			c.T328C						PASS	.						66	61	63					12																	10342575		2203	4300	6503	SO:0001583	missense	120939	exon4			CTGCCCTCCTCTT	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.388T>C	chr12.hg19:g.10342575T>C	ENSP00000371348:p.Ser130Pro	75.0	0.0	.		53.0	30.0	.	NM_153022	Q96NA7	Missense_Mutation	SNP	ENST00000381923.2	hg19		.	.	.	.	.	.	.	.	.	.	T	2.193	-0.384873	0.04966	.	.	ENSG00000165685	ENST00000381923;ENST00000298530;ENST00000536952	T;T;T	0.32272	1.46;1.46;1.46	4.39	-1.11	0.09840	.	0.546525	0.17750	N	0.163267	T	0.17831	0.0428	L	0.43152	1.355	0.09310	N	0.999998	B;B	0.06786	0.0;0.001	B;B	0.08055	0.003;0.002	T	0.14615	-1.0466	10	0.33141	T	0.24	-7.7347	0.9089	0.01290	0.1631:0.3042:0.1683:0.3644	.	130;110	Q4KMG9;Q4KMG9-2	CL059_HUMAN;.	P	130;110;130	ENSP00000371348:S130P;ENSP00000298530:S110P;ENSP00000446102:S130P	ENSP00000298530:S110P	S	+	1	0	C12orf59	10233842	0.000000	0.05858	0.260000	0.24451	0.195000	0.23768	-0.335000	0.07873	-0.279000	0.09167	-0.399000	0.06403	TCC	.	.	.	none		0.582	TMEM52B-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000399645.1	NM_153022		C	10342575	T	C	10342575	3	2	148	1	0	0	0	0	1	0	0	0	1704	1551	54	3	342	3	C12orf59	12	10342575	Missense_Mutation	SNP	T	TCGA-DW-7836-01A-11D-2136-08		10342575	123509320	22	8844											
KRT3	3850	hgsc.bcm.edu	37	chr12	53188038	53188038	+	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	tcaaggttgtttgtgcctgaGatggaacttgtgccctgctg	6	14	13	8	0	1	1	1	1	0	1	1	3	1	2	2	2	4	3	2	2	2	3			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr12:53188038G>C	ENST00000417996.2	-	2	797	c.723C>G	c.(721-723)atC>atG	p.I241M	KRT3_ENST00000309505.3_Missense_Mutation_p.I241M	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	241	Linker 1.|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						TTGTGCCTGAGATGGAACTTG	0.547																																					p.I241M		Atlas-SNP	.											.	KRT3	65	.	0			c.C723G						PASS	.						140	159	152					12																	53188038		2190	4299	6489	SO:0001583	missense	3850	exon2			GCCTGAGATGGAA		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.723C>G	chr12.hg19:g.53188038G>C	ENSP00000413479:p.Ile241Met	171.0	0.0	.		139.0	56.0	.	NM_057088	A6NIS2|Q701L8	Missense_Mutation	SNP	ENST00000417996.2	hg19	CCDS44895.1	.	.	.	.	.	.	.	.	.	.	G	11.80	1.747661	0.30955	.	.	ENSG00000186442	ENST00000417996;ENST00000309505	T;T	0.77358	-1.09;-1.09	4.84	3.03	0.35002	Filament (1);	0.796636	0.10927	N	0.618820	T	0.65015	0.2651	N	0.14661	0.345	0.09310	N	0.999997	D	0.54207	0.965	P	0.44518	0.452	T	0.55010	-0.8207	10	0.59425	D	0.04	.	9.7916	0.40708	0.171:0.0:0.829:0.0	.	241	P12035	K2C3_HUMAN	M	241	ENSP00000413479:I241M;ENSP00000312206:I241M	ENSP00000312206:I241M	I	-	3	3	KRT3	51474305	0.543000	0.26434	0.057000	0.19452	0.311000	0.27955	1.403000	0.34612	0.770000	0.33336	-0.137000	0.14449	ATC	.	.	.	none		0.547	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1	NM_057088		C	53188038	G	C	53188038	3	2	148	1	0	0	0	0	1	0	0	0	8473	932	33	4	1195	4	KRT3	12	53188038	Missense_Mutation	SNP	G	TCGA-DW-7836-01A-11D-2136-08	42845463	53188038	80663857	23	8845											
EFS	10278	hgsc.bcm.edu	37	chr14	23830017	23830017	+	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	ggggggactcagcggtgttgTcatacagtgcccgggccagc	6	7	17	11	2	2	0	2	0	0	0	2	1	2	1	2	5	4	1	2	5	1	2			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr14:23830017T>A	ENST00000216733.3	-	2	651	c.44A>T	c.(43-45)gAc>gTc	p.D15V	EFS_ENST00000429593.2_Intron|EFS_ENST00000351354.3_Intron	NM_005864.2	NP_005855.1	O43281	EFS_HUMAN	embryonal Fyn-associated substrate	15	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			endometrium(2)|kidney(1)|large_intestine(1)|liver(1)|lung(5)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)	16	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00649)		AGCGGTGTTGTCATACAGTGC	0.647																																					p.D15V		Atlas-SNP	.											.	EFS	37	.	0			c.A44T						PASS	.						23	24	24					14																	23830017		2203	4299	6502	SO:0001583	missense	10278	exon2			GTGTTGTCATACA	AB001466	CCDS9595.1, CCDS9596.1, CCDS61404.1	14q11.2-q12	2011-04-13			ENSG00000100842	ENSG00000100842		"Cas scaffolding proteins"	16898	protein-coding gene	gene with protein product	"Cas scaffolding protein family member 3"	609906				9349509	Standard	NM_005864		Approved	EFS2, EFS1, HEFS, SIN, CASS3	uc001wjo.4	O43281	OTTHUMG00000028741	ENST00000216733.3:c.44A>T	chr14.hg19:g.23830017T>A	ENSP00000216733:p.Asp15Val	51.0	0.0	.		67.0	23.0	.	NM_005864	B2RAJ7|B4DJ56|E9PGU2|O43282	Missense_Mutation	SNP	ENST00000216733.3	hg19	CCDS9595.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.776984	0.90195	.	.	ENSG00000100842	ENST00000216733	T	0.57907	0.37	4.99	4.99	0.66335	Src homology-3 domain (5);	0.000000	0.85682	D	0.000000	T	0.82176	0.4980	H	0.98446	4.235	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.88428	0.3033	10	0.87932	D	0	-29.2596	12.9697	0.58505	0.0:0.0:0.0:1.0	.	15	O43281	EFS_HUMAN	V	15	ENSP00000216733:D15V	ENSP00000216733:D15V	D	-	2	0	EFS	22899857	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.888000	0.75622	2.234000	0.73211	0.460000	0.39030	GAC	.	.	.	none		0.647	EFS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071770.2			A	23830017	T	A	23830017	3	1	148	1	0	0	0	0	1	0	0	0	4961	1667	58	5	1661	5	EFS	14	23830017	Missense_Mutation	SNP	T	TCGA-DW-7836-01A-11D-2136-08		23830017	83519523	24	8846											
SYNE2	23224	hgsc.bcm.edu	37	chr14	64587724	64587724	+	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	taacctttctgaattggaatCcattgtaactgaaaggccac	13	12	7	9	0	1	2	0	2	1	0	2	3	2	3	3	2	2	1	3	2	5	5			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr14:64587724C>T	ENST00000344113.4	+	68	13315	c.13103C>T	c.(13102-13104)tCc>tTc	p.S4368F	ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000358025.3_Missense_Mutation_p.S4368F|SYNE2_ENST00000554584.1_Missense_Mutation_p.S4383F|SYNE2_ENST00000553455.1_Missense_Mutation_p.S87F|SYNE2_ENST00000357395.3_Missense_Mutation_p.S753F|SYNE2_ENST00000394768.2_Missense_Mutation_p.S753F|SYNE2_ENST00000555002.1_Missense_Mutation_p.S1002F	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	4368					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)		GAATTGGAATCCATTGTAACT	0.403																																					p.S4368F		Atlas-SNP	.											.	SYNE2	577	.	0			c.C13103T						PASS	.						97	89	92					14																	64587724		2203	4300	6503	SO:0001583	missense	23224	exon68			TGGAATCCATTGT	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.13103C>T	chr14.hg19:g.64587724C>T	ENSP00000341781:p.Ser4368Phe	110.0	0.0	.		45.0	24.0	.	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	C	7.349	0.622515	0.14193	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768;ENST00000553455	T;T;T;T;T;T	0.58652	0.73;4.03;0.73;0.32;4.08;4.03	5.4	3.57	0.40892	.	0.605748	0.15778	N	0.245095	T	0.49626	0.1568	L	0.57536	1.79	0.09310	N	0.999999	B;B;B	0.14438	0.003;0.006;0.01	B;B;B	0.17722	0.019;0.007;0.015	T	0.48636	-0.9018	10	0.56958	D	0.05	.	4.7178	0.12903	0.0:0.6119:0.1734:0.2147	.	753;4368;4368	Q8WXH0-7;Q8WXH0;Q8WXH0-2	.;SYNE2_HUMAN;.	F	4368;753;4368;4383;4383;1002;753;87	ENSP00000350719:S4368F;ENSP00000349969:S753F;ENSP00000341781:S4368F;ENSP00000452570:S4383F;ENSP00000450831:S1002F;ENSP00000378249:S753F	ENSP00000261678:S4383F	S	+	2	0	SYNE2	63657477	0.000000	0.05858	0.001000	0.08648	0.060000	0.15804	0.304000	0.19228	0.829000	0.34733	0.655000	0.94253	TCC	.	.	.	none		0.403	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		T	64587724	C	T	64587724	3	4	148	1	0	0	0	0	1	0	0	0	15458	855	30	2	13369	2	SYNE2	14	64587724	Missense_Mutation	SNP	C	TCGA-DW-7836-01A-11D-2136-08	40757707	64587724	42761816	25	8847											
SMG1	23049	hgsc.bcm.edu	37	chr16	18937327	18937327	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgccgccgccgccgccgcCgctgctcagccgagaccccg	3	3	14	21	8	1	1	1	0	0	1	1	2	1	1	9	1	3	2	9	1	0	0			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr16:18937327C>T	ENST00000446231.2	-	1	449	c.37G>A	c.(37-39)Ggc>Agc	p.G13S	SMG1_ENST00000567737.1_5'UTR|SMG1_ENST00000389467.3_Missense_Mutation_p.G13S|CTD-2288F12.1_ENST00000565782.1_RNA			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	13	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						ccgccgccgccgctgcTCAGC	0.736																																					p.G13S		Atlas-SNP	.											.	SMG1	401	.	0			c.G37A						PASS	.						2	3	3					16																	18937327		1046	2801	3847	SO:0001583	missense	23049	exon1			CGCCGCCGCTGCT	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.37G>A	chr16.hg19:g.18937327C>T	ENSP00000402515:p.Gly13Ser	13.0	0.0	.		38.0	5.0	.	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	hg19	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	c	16.19	3.051895	0.55218	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.01240	5.12;5.12	4.27	3.31	0.37934	.	0.832224	0.10596	N	0.656220	T	0.00998	0.0033	N	0.14661	0.345	0.31512	N	0.663496	B	0.22346	0.068	B	0.08055	0.003	T	0.29912	-0.9996	10	0.12766	T	0.61	.	6.0417	0.19738	0.0:0.7231:0.0:0.2769	.	13	Q96Q15	SMG1_HUMAN	S	13	ENSP00000402515:G13S;ENSP00000374118:G13S	ENSP00000374118:G13S	G	-	1	0	SMG1	18844828	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.149000	0.42244	0.999000	0.39023	0.455000	0.32223	GGC	.	.	.	none		0.736	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		T	18937327	C	T	18937327	3	4	148	1	0	0	0	0	1	0	0	0	14808	652	23	1	11200	1	SMG1	16	18937327	Missense_Mutation	SNP	C	TCGA-DW-7836-01A-11D-2136-08		18937327	71417426	26	8848											
POLR3E	55718	hgsc.bcm.edu	37	chr16	22324995	22324995	+	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	gcagctgcggcccagcttctCctacctggataaggctgacg	7	8	12	14	2	1	1	0	1	1	0	2	2	1	2	3	3	4	4	3	3	2	3			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr16:22324995C>A	ENST00000299853.5	+	7	586	c.419C>A	c.(418-420)tCc>tAc	p.S140Y	POLR3E_ENST00000418581.2_Missense_Mutation_p.S104Y|POLR3E_ENST00000359210.4_Missense_Mutation_p.S140Y|POLR3E_ENST00000564209.1_Missense_Mutation_p.S140Y	NM_001258033.1|NM_001258035.1|NM_018119.3	NP_001244962.1|NP_001244964.1|NP_060589.1	Q9NVU0	RPC5_HUMAN	polymerase (RNA) III (DNA directed) polypeptide E (80kD)	140					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|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)	centrosome (GO:0005813)|cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.012)		CCCAGCTTCTCCTACCTGGAT	0.632																																					p.S140Y		Atlas-SNP	.											.	POLR3E	62	.	0			c.C419A						PASS	.						49	50	50					16																	22324995		2197	4300	6497	SO:0001583	missense	55718	exon7			GCTTCTCCTACCT	AY092085	CCDS10605.1, CCDS58432.1, CCDS58433.1, CCDS58434.1, CCDS73845.1	16p12	2013-01-21			ENSG00000058600	ENSG00000058600		"RNA polymerase subunits"	30347	protein-coding gene	gene with protein product						10819331, 10521666	Standard	NM_018119		Approved	RPC5, SIN, FLJ10509	uc002dkk.4	Q9NVU0	OTTHUMG00000094779	ENST00000299853.5:c.419C>A	chr16.hg19:g.22324995C>A	ENSP00000299853:p.Ser140Tyr	78.0	0.0	.		119.0	75.0	.	NM_001258033	B4DL24|B4DUP6|H3BT11|Q9BWF7|Q9H8W8|Q9H907|Q9P276	Missense_Mutation	SNP	ENST00000299853.5	hg19	CCDS10605.1	.	.	.	.	.	.	.	.	.	.	C	34	5.371103	0.95923	.	.	ENSG00000058600	ENST00000299853;ENST00000359210;ENST00000418581	T;T;T	0.48201	0.82;0.82;0.82	5.47	5.47	0.80525	.	0.117597	0.64402	D	0.000020	T	0.62865	0.2463	L	0.52011	1.625	0.52501	D	0.99995	D;D;D;D;D;D	0.65815	0.993;0.993;0.993;0.995;0.993;0.991	D;P;D;P;P;P	0.63381	0.914;0.879;0.914;0.807;0.879;0.861	T	0.64939	-0.6289	10	0.87932	D	0	-20.1214	18.0983	0.89498	0.0:1.0:0.0:0.0	.	84;104;140;140;140;140	B4DDR0;B4DL24;B4DUP6;Q9NVU0-2;Q9NVU0;Q9NVU0-3	.;.;.;.;RPC5_HUMAN;.	Y	140;140;104	ENSP00000299853:S140Y;ENSP00000352140:S140Y;ENSP00000399254:S104Y	ENSP00000299853:S140Y	S	+	2	0	POLR3E	22232496	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.513000	0.67037	2.563000	0.86464	0.561000	0.74099	TCC	.	.	.	none		0.632	POLR3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211590.1	NM_018119		A	22324995	C	A	22324995	3	1	148	1	0	0	0	0	1	0	0	0	12239	855	30	4	441	4	POLR3E	16	22324995	Missense_Mutation	SNP	C	TCGA-DW-7836-01A-11D-2136-08	3387668	22324995	68029758	27	8849											
SNTB2	6645	hgsc.bcm.edu	37	chr16	69294139	69294139	+	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	ggaggcagtaaagaggtgaaGcatattgcctggctggcaga	12	7	16	6	0	0	3	0	1	0	2	0	4	0	4	1	5	2	5	1	5	4	3			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr16:69294139G>A	ENST00000336278.4	+	3	1019	c.981G>A	c.(979-981)aaG>aaA	p.K327K	SNTB2_ENST00000528525.1_3'UTR	NM_006750.3	NP_006741.1	Q13425	SNTB2_HUMAN	syntrophin, beta 2 (dystrophin-associated protein A1, 59kDa, basic component 2)	327	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|microtubule (GO:0005874)|protein complex (GO:0043234)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	13		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.208)		AAGAGGTGAAGCATATTGCCT	0.522																																					p.K327K	NSCLC(58;1458 1722 3262 39967)|Melanoma(111;1698 2173 25379 28738)	Atlas-SNP	.											.	SNTB2	22	.	0			c.G981A						PASS	.						114	90	98					16																	69294139		2198	4300	6498	SO:0001819	synonymous_variant	6645	exon3			GGTGAAGCATATT	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.981G>A	chr16.hg19:g.69294139G>A		72.0	0.0	.		71.0	44.0	.	NM_006750	Q9BY09	Silent	SNP	ENST00000336278.4	hg19	CCDS10873.1																																																																																			.	.	.	none		0.522	SNTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268945.1			A	69294139	G	A	69294139	2	1	148	1	0	0	0	0	0	0	0	1	14886	962	34	2		2	SNTB2	16	69294139	Silent	SNP	G	TCGA-DW-7836-01A-11D-2136-08	46969144	69294139	21060614	28	8850											
SLC7A5	8140	hgsc.bcm.edu	37	chr16	87868146	87868146	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcttccagaaggagacggCgatcaggaagaggcaggcca	12	5	15	9	2	2	3	1	0	1	3	3	6	3	4	2	5	0	1	2	5	2	1			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr16:87868146C>T	ENST00000261622.4	-	9	1407	c.1342G>A	c.(1342-1344)Gcc>Acc	p.A448T	RP4-536B24.2_ENST00000563687.1_RNA|SLC7A5_ENST00000565644.1_Missense_Mutation_p.A182T	NM_003486.5	NP_003477.4	Q01650	LAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 5	448					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)	AAGGAGACGGCGATCAGGAAG	0.617																																					p.A448T		Atlas-SNP	.											SLC7A5,colon,carcinoma,0,1	SLC7A5	28	.	0			c.G1342A						PASS	.																																			SO:0001583	missense	8140	exon9			AGACGGCGATCAG	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.1342G>A	chr16.hg19:g.87868146C>T	ENSP00000261622:p.Ala448Thr	10.0	1.0	.		21.0	10.0	.	NM_003486	Q8IV97|Q9UBN8|Q9UP15|Q9UQC0	Missense_Mutation	SNP	ENST00000261622.4	hg19	CCDS10964.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.018259	0.75275	.	.	ENSG00000103257	ENST00000261622	D	0.90620	-2.7	5.45	5.45	0.79879	.	0.120057	0.64402	D	0.000017	D	0.86916	0.6048	N	0.20986	0.625	0.44976	D	0.997999	D	0.54601	0.967	P	0.45167	0.472	D	0.88309	0.2955	10	0.52906	T	0.07	.	18.3254	0.90252	0.0:1.0:0.0:0.0	.	448	Q01650	LAT1_HUMAN	T	448	ENSP00000261622:A448T	ENSP00000261622:A448T	A	-	1	0	SLC7A5	86425647	0.998000	0.40836	1.000000	0.80357	0.976000	0.68499	2.919000	0.48836	2.578000	0.87016	0.456000	0.33151	GCC	.	.	.	none		0.617	SLC7A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269110.2	NM_003486		T	87868146	C	T	87868146	3	4	148	1	0	0	0	0	1	0	0	0	14713	768	27	1	189	1	SLC7A5	16	87868146	Missense_Mutation	SNP	C	TCGA-DW-7836-01A-11D-2136-08	18574007	87868146	2486607	29	8851											
MYO1C	4641	hgsc.bcm.edu	37	chr17	1386297	1386297	+	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	tctccccagagatcatcacaGcctggtcccgacgctccgtg	7	8	9	17	3	3	1	2	0	1	1	6	3	5	1	5	1	1	1	5	1	0	0			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr17:1386297G>C	ENST00000575158.1	-	4	475	c.299C>G	c.(298-300)gCt>gGt	p.A100G	MYO1C_ENST00000573198.1_5'Flank|MYO1C_ENST00000545534.2_Missense_Mutation_p.A111G|MYO1C_ENST00000361007.2_Missense_Mutation_p.A100G|MYO1C_ENST00000359786.5_Missense_Mutation_p.A135G|MYO1C_ENST00000438665.2_Missense_Mutation_p.A116G			Q12965	MYO1E_HUMAN	myosin IC	107	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)		GATCATCACAGCCTGGTCCCG	0.677																																					p.A135G		Atlas-SNP	.											.	MYO1C	57	.	0			c.C404G						PASS	.						29	28	29					17																	1386297		2203	4300	6503	SO:0001583	missense	4641	exon4			ATCACAGCCTGGT	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.299C>G	chr17.hg19:g.1386297G>C	ENSP00000459174:p.Ala100Gly	38.0	0.0	.		58.0	8.0	.	NM_001080779	Q14778	Missense_Mutation	SNP	ENST00000575158.1	hg19	CCDS11003.1	.	.	.	.	.	.	.	.	.	.	G	18.49	3.636053	0.67130	.	.	ENSG00000197879	ENST00000359786;ENST00000438665;ENST00000535856;ENST00000361007;ENST00000545534;ENST00000535421	D;D;D;D	0.88124	-2.34;-2.34;-2.34;-2.34	5.45	5.45	0.79879	Myosin head, motor domain (3);	0.140578	0.64402	D	0.000005	D	0.86944	0.6055	L	0.58354	1.805	0.39738	D	0.97171	P;B;P	0.36647	0.563;0.43;0.508	B;B;B	0.41894	0.369;0.266;0.253	D	0.88555	0.3119	10	0.87932	D	0	.	13.3051	0.60347	0.0:0.2668:0.7332:0.0	.	111;135;116	B7Z3E5;O00159;O00159-3	.;MYO1C_HUMAN;.	G	135;116;116;100;111;100	ENSP00000352834:A135G;ENSP00000412197:A116G;ENSP00000354283:A100G;ENSP00000437685:A111G	ENSP00000352834:A135G	A	-	2	0	MYO1C	1333047	1.000000	0.71417	0.959000	0.39883	0.696000	0.40369	4.738000	0.62073	2.548000	0.85928	0.462000	0.41574	GCT	.	.	.	none		0.677	MYO1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438694.2			C	1386297	G	C	1386297	3	2	148	1	0	0	0	0	1	0	0	0	10077	971	34	4	2903	4	MYO1C	17	1386297	Missense_Mutation	SNP	G	TCGA-DW-7836-01A-11D-2136-08		1386297	79808913	30	8852											
NLRP1	22861	hgsc.bcm.edu	37	chr17	5461735	5461735	+	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	aagcttcttcacgtggcggcTgaatttaatgcagaaagtgc	11	11	11	8	2	2	2	1	1	1	1	2	2	2	2	0	2	3	3	0	2	4	4			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr17:5461735T>A	ENST00000572272.1	-	4	2280	c.2281A>T	c.(2281-2283)Agc>Tgc	p.S761C	NLRP1_ENST00000269280.4_Missense_Mutation_p.S761C|NLRP1_ENST00000354411.3_Missense_Mutation_p.S761C|NLRP1_ENST00000577119.1_Missense_Mutation_p.S761C|NLRP1_ENST00000571307.1_5'UTR|NLRP1_ENST00000345221.3_Missense_Mutation_p.S761C|NLRP1_ENST00000262467.5_Missense_Mutation_p.S761C			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	761					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)				ACGTGGCGGCTGAATTTAATG	0.498																																					p.S761C		Atlas-SNP	.											.	NLRP1	358	.	0			c.A2281T						PASS	.						96	96	96					17																	5461735		2203	4300	6503	SO:0001583	missense	22861	exon4			GGCGGCTGAATTT	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.2281A>T	chr17.hg19:g.5461735T>A	ENSP00000460475:p.Ser761Cys	123.0	0.0	.		116.0	33.0	.	NM_033007	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	hg19	CCDS42246.1	.	.	.	.	.	.	.	.	.	.	T	1.036	-0.680260	0.03353	.	.	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221;ENST00000537069	T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74	4.02	1.81	0.25067	.	0.336093	0.21989	N	0.066194	T	0.07503	0.0189	N	0.00055	-2.375	0.09310	N	0.999994	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.04013	0.001;0.0;0.0;0.0;0.0;0.0	T	0.39014	-0.9634	10	0.02654	T	1	.	3.4335	0.07437	0.6926:0.0:0.1074:0.2	.	27;761;761;761;761;761	F5H042;Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;.;NALP1_HUMAN;.;.	C	761;761;761;761;761;27	ENSP00000442029:S761C;ENSP00000262467:S761C;ENSP00000269280:S761C;ENSP00000346390:S761C;ENSP00000324366:S761C	ENSP00000262467:S761C	S	-	1	0	NLRP1	5402459	0.002000	0.14202	0.392000	0.26245	0.340000	0.28889	0.623000	0.24447	0.372000	0.24591	-1.045000	0.02358	AGC	.	.	.	none		0.498	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004		A	5461735	T	A	5461735	3	1	148	1	0	0	0	0	1	0	0	0	10478	1580	55	5	2271	5	NLRP1	17	5461735	Missense_Mutation	SNP	T	TCGA-DW-7836-01A-11D-2136-08	4075438	5461735	75733475	31	8853											
FOXN1	8456	hgsc.bcm.edu	37	chr17	26864406	26864406	+	Frame_Shift_Del	DEL	C	C	-																															ccccccacggcccctgcaggCccctctgtgtacctcagccc																										TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr17:26864406delC	ENST00000226247.2	+	8	1928	c.1899delC	c.(1897-1899)ggcfs	p.G633fs	FOXN1_ENST00000579795.1_Frame_Shift_Del_p.G633fs	NM_003593.2	NP_003584.2	O15353	FOXN1_HUMAN	forkhead box N1	633					defense response (GO:0006952)|epidermis development (GO:0008544)|epithelial cell proliferation (GO:0050673)|hair follicle development (GO:0001942)|keratinocyte differentiation (GO:0030216)|lymphocyte homeostasis (GO:0002260)|nail development (GO:0035878)|organ morphogenesis (GO:0009887)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(8)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Lung NSC(42;0.00431)					CCCCTGCAGGCCCCTCTGTGT	0.677																																					p.G633fs		Atlas-Indel,Pindel	.											.	FOXN1	51	.	0			c.1898delG						PASS	.						23	27	26					17																	26864406		2203	4298	6501	SO:0001589	frameshift_variant	8456	exon8			.	Y11739	CCDS11232.1	17q11-q12	2014-09-17	2003-06-12	2003-06-13	ENSG00000109101	ENSG00000109101		"Forkhead boxes"	12765	protein-coding gene	gene with protein product		600838	"winged-helix nude", "Rowett nude"	WHN, RONU		9321431	Standard	NM_003593		Approved	FKHL20	uc002hbj.3	O15353	OTTHUMG00000132603	ENST00000226247.2:c.1899delC	chr17.hg19:g.26864406delC	ENSP00000226247:p.Gly633fs	65.0	0.0	0		100.0	24.0	0.24	NM_003593	B2R9Q7|O15352	Frame_Shift_Del	DEL	ENST00000226247.2	hg19	CCDS11232.1																																																																																			.	.	.	none		0.677	FOXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255832.1			-	26864406	C	-	26864406	7	5	148	1	0	1	0	1	0	0	0	0	6026	726	26	0	1929	0	FOXN1	17	26864406	Frame_Shift_Del	DEL	C	TCGA-DW-7836-01A-11D-2136-08	21402671	26864406	54330804	32	8854											
SUPT6H	6830	hgsc.bcm.edu	37	chr17	27005892	27005892	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acacggctgtttgagaagatGcaggcttatcagtatgaaca	13	10	11	7	1	1	3	1	2	0	2	1	4	1	3	0	2	2	5	0	2	4	3			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr17:27005892G>A	ENST00000314616.6	+	11	1543	c.1260G>A	c.(1258-1260)atG>atA	p.M420I	SUPT6H_ENST00000347486.4_Missense_Mutation_p.M420I	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	420	Interaction with IWS1. {ECO:0000250}.|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)					TTGAGAAGATGCAGGCTTATC	0.517																																					p.M420I		Atlas-SNP	.											.	SUPT6H	165	.	0			c.G1260A						PASS	.						135	128	131					17																	27005892		2203	4300	6503	SO:0001583	missense	6830	exon11			GAAGATGCAGGCT	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.1260G>A	chr17.hg19:g.27005892G>A	ENSP00000319104:p.Met420Ile	152.0	0.0	.		162.0	99.0	.	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	hg19	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.643321	0.87859	.	.	ENSG00000109111	ENST00000314616;ENST00000347486	T;T	0.41400	1.0;1.0	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.50309	0.1608	M	0.62088	1.915	0.80722	D	1	P	0.41929	0.765	P	0.44359	0.447	T	0.35649	-0.9780	10	0.32370	T	0.25	-21.3743	20.428	0.99075	0.0:0.0:1.0:0.0	.	420	Q7KZ85	SPT6H_HUMAN	I	420	ENSP00000319104:M420I;ENSP00000338143:M420I	ENSP00000319104:M420I	M	+	3	0	SUPT6H	24030019	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.283000	0.95860	2.837000	0.97791	0.655000	0.94253	ATG	.	.	.	none		0.517	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		A	27005892	G	A	27005892	3	1	148	1	0	0	0	0	1	0	0	0	15412	1319	46	2	1298	2	SUPT6H	17	27005892	Missense_Mutation	SNP	G	TCGA-DW-7836-01A-11D-2136-08	141486	27005892	54189318	33	8855											
LRRC59	55379	hgsc.bcm.edu	37	chr17	48462617	48462617	+	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	ttcccgctcctgagcttcctTagctcgctgcttagcctcac	4	13	7	17	2	1	1	1	1	0	0	5	1	4	1	4	0	4	5	4	0	2	4			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr17:48462617T>A	ENST00000225972.7	-	6	773	c.538A>T	c.(538-540)Aag>Tag	p.K180*	Y_RNA_ENST00000384097.1_RNA	NM_018509.3	NP_060979.2	Q96AG4	LRC59_HUMAN	leucine rich repeat containing 59	180						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.K180E(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	13	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)			TGAGCTTCCTTAGCTCGCTGC	0.527																																					p.K180X		Atlas-SNP	.											LRRC59,NS,carcinoma,0,1	LRRC59	23	.	1	Substitution - Missense(1)	lung(1)	c.A538T						PASS	.						110	110	110					17																	48462617		2203	4300	6503	SO:0001587	stop_gained	55379	exon6			CTTCCTTAGCTCG	AK025328	CCDS11566.1	17q21.33	2014-02-12	2006-01-12		ENSG00000108829	ENSG00000108829			28817	protein-coding gene	gene with protein product		614854				12477932	Standard	NM_018509		Approved	PRO1855, FLJ21675	uc002iqt.3	Q96AG4	OTTHUMG00000162079	ENST00000225972.7:c.538A>T	chr17.hg19:g.48462617T>A	ENSP00000225972:p.Lys180*	206.0	0.0	.		231.0	64.0	.	NM_018509	B2RE83|D3DTX8|Q9P189	Nonsense_Mutation	SNP	ENST00000225972.7	hg19	CCDS11566.1	.	.	.	.	.	.	.	.	.	.	T	39	7.478468	0.98309	.	.	ENSG00000108829	ENST00000225972	.	.	.	5.87	4.73	0.59995	.	0.206543	0.47093	D	0.000244	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.0564	0.58982	0.0:0.0:0.1338:0.8661	.	.	.	.	X	180	.	ENSP00000225972:K180X	K	-	1	0	LRRC59	45817616	0.994000	0.37717	0.985000	0.45067	0.993000	0.82548	2.417000	0.44653	2.371000	0.80710	0.533000	0.62120	AAG	.	.	.	none		0.527	LRRC59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367117.2	NM_018509		A	48462617	T	A	48462617	4	1	148	1	0	0	0	0	0	1	0	0	9022	1763	61	5	393	5	LRRC59	17	48462617	Nonsense_Mutation	SNP	T	TCGA-DW-7836-01A-11D-2136-08	21456725	48462617	32732593	34	8856											
METTL4	64863	hgsc.bcm.edu	37	chr18	2552727	2552727	+	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	taactgatttgttctgccatGgtggatctatcacaattaca	11	15	7	8	0	3	1	1	1	2	0	3	2	3	2	1	2	3	1	1	2	4	5			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr18:2552727G>A	ENST00000574538.1	-	5	1641	c.866C>T	c.(865-867)cCa>cTa	p.P289L	METTL4_ENST00000319888.6_Missense_Mutation_p.P289L|snoU109_ENST00000459316.1_RNA	NM_022840.3	NP_073751.3	Q8N3J2	METL4_HUMAN	methyltransferase like 4	289					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						GTTCTGCCATGGTGGATCTAT	0.284																																					p.P289L		Atlas-SNP	.											.	METTL4	40	.	0			c.C866T						PASS	.						100	95	97					18																	2552727		2201	4297	6498	SO:0001583	missense	64863	exon5			TGCCATGGTGGAT		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.866C>T	chr18.hg19:g.2552727G>A	ENSP00000458290:p.Pro289Leu	44.0	0.0	.		22.0	13.0	.	NM_022840	B2RNA1|Q2TAA7|Q9H5U9	Missense_Mutation	SNP	ENST00000574538.1	hg19	CCDS11826.1	.	.	.	.	.	.	.	.	.	.	G	18.07	3.542180	0.65198	.	.	ENSG00000101574	ENST00000319888	D	0.88741	-2.42	5.44	5.44	0.79542	DNA methylase, N-6 adenine-specific, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.96491	0.8855	H	0.95437	3.67	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97268	0.9909	10	0.87932	D	0	-10.0395	19.6271	0.95682	0.0:0.0:1.0:0.0	.	289;289	A8K1T6;Q8N3J2	.;METL4_HUMAN	L	289	ENSP00000320349:P289L	ENSP00000320349:P289L	P	-	2	0	METTL4	2542727	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	7.974000	0.88039	2.712000	0.92718	0.650000	0.86243	CCA	.	.	.	none		0.284	METTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254326.3	NM_022840		A	2552727	G	A	2552727	3	1	148	1	0	0	0	0	1	0	0	0	9509	1348	47	2	572	2	METTL4	18	2552727	Missense_Mutation	SNP	G	TCGA-DW-7836-01A-11D-2136-08		2552727	75524521	35	8857											
DUS3L	56931	hgsc.bcm.edu	37	chr19	5789679	5789679	+	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	ggtctccaggtagcgccccaCgtcgtgcagaaagcggcagc	8	5	14	14	4	1	1	0	0	1	1	3	1	1	1	3	3	4	3	3	3	2	1			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr19:5789679C>A	ENST00000309061.7	-	3	535	c.439G>T	c.(439-441)Gtg>Ttg	p.V147L	DUS3L_ENST00000320699.8_Intron|DUS3L_ENST00000590681.1_5'UTR	NM_020175.2	NP_064560.2	Q96G46	DUS3L_HUMAN	dihydrouridine synthase 3-like (S. cerevisiae)	147							flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA dihydrouridine synthase activity (GO:0017150)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|skin(2)	14						TAGCGCCCCACGTCGTGCAGA	0.677																																					p.V147L		Atlas-SNP	.											.	DUS3L	42	.	0			c.G439T						PASS	.						12	18	16					19																	5789679		2120	4219	6339	SO:0001583	missense	56931	exon3			GCCCCACGTCGTG		CCDS32880.1, CCDS54202.1	19p13.3	2014-02-12			ENSG00000141994	ENSG00000141994			26920	protein-coding gene	gene with protein product						12477932	Standard	NM_020175		Approved	DUS3, FLJ13896	uc002mdc.3	Q96G46	OTTHUMG00000162311	ENST00000309061.7:c.439G>T	chr19.hg19:g.5789679C>A	ENSP00000311977:p.Val147Leu	24.0	0.0	.		28.0	9.0	.	NM_020175	Q96HM5|Q9BSU4|Q9H877|Q9NPR1	Missense_Mutation	SNP	ENST00000309061.7	hg19	CCDS32880.1	.	.	.	.	.	.	.	.	.	.	C	0.236	-1.017044	0.02078	.	.	ENSG00000141994	ENST00000309061	T	0.15603	2.41	4.51	-0.951	0.10369	Zinc finger, CCCH-type (1);	0.454534	0.20607	N	0.089046	T	0.08088	0.0202	N	0.19112	0.55	0.20074	N	0.999939	B	0.09022	0.002	B	0.11329	0.006	T	0.40979	-0.9534	10	0.10636	T	0.68	2.778	8.3861	0.32501	0.0:0.4616:0.4471:0.0913	.	147	Q96G46	DUS3L_HUMAN	L	147	ENSP00000311977:V147L	ENSP00000311977:V147L	V	-	1	0	DUS3L	5740679	0.042000	0.20092	0.001000	0.08648	0.013000	0.08279	0.424000	0.21330	0.063000	0.16370	0.561000	0.74099	GTG	.	.	.	none		0.677	DUS3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451870.2	NM_020175		A	5789679	C	A	5789679	3	1	148	1	0	0	0	0	1	0	0	0	4809	536	19	4	1557	4	DUS3L	19	5789679	Missense_Mutation	SNP	C	TCGA-DW-7836-01A-11D-2136-08		5789679	53339304	36	8858											
ZNF559	84527	hgsc.bcm.edu	37	chr19	9452847	9452848	+	Missense_Mutation	DNP	CT	CT	AA																															actcaagatggagaaaaattCtatgaatgtaaagcatgtgg																										TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr19:9452847_9452848CT>AA	ENST00000393883.2	+	6	1368_1369	c.720_721CT>AA	c.(718-723)ttCTat>ttAAat	p.240_241FY>LN	CTC-325H20.2_ENST00000592371.1_lincRNA|ZNF559_ENST00000587557.1_Missense_Mutation_p.304_305FY>LN|ZNF177_ENST00000605471.1_Intron|ZNF559_ENST00000317221.7_3'UTR|ZNF559_ENST00000586255.1_Intron|ZNF177_ENST00000446085.4_Intron|ZNF559_ENST00000603380.1_Missense_Mutation_p.240_241FY>LN|ZNF177_ENST00000602856.1_Intron|ZNF559_ENST00000538743.1_Missense_Mutation_p.160_161FY>LN|ZNF177_ENST00000541595.2_Intron|ZNF559_ENST00000592896.1_3'UTR|ZNF177_ENST00000602738.1_Intron	NM_001202412.1	NP_001189341.1	Q9BR84	ZN559_HUMAN	zinc finger protein 559	240					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|large_intestine(7)|lung(15)|ovary(1)|urinary_tract(1)	26						GAGAAAAATTCTATGAATGTAA	0.361																																					p.F304L|p.Y305N		Atlas-SNP	.											.	ZNF559	77	.	0			c.C912A|c.T913A						PASS	.																																			SO:0001583	missense	84527	exon6			AAAATTCTATGAA|AAATTCTATGAAT	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	Exception_encountered	chr19.hg19:g.9452847_9452848delinsAA	ENSP00000377461:p.F240_Y241delinsLN	126.0|127.0	0.0	.		54.0|53.0	26.0|25.0	.	NM_001202406	K7EMG6	Missense_Mutation	SNP	ENST00000393883.2	hg19	CCDS12211.1																																																																																			.	.	.	none		0.361	ZNF559-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449021.1	NM_032497		AA	9452848	CT	AA	9452847	3	1	148	1	0	0	0	0	1	0	0	0	18002	912	32	4	734	4	ZNF559	19	9452847	Missense_Mutation	DNP	CT	TCGA-DW-7836-01A-11D-2136-08	3663168	9452847	49676136	37	8859											
ACTN4	81	hgsc.bcm.edu	37	chr19	39219691	39219691	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgaccccaaccatagcggccTtgtgaccttccaagccttca	9	8	7	17	2	1	1	1	1	0	0	2	2	2	1	7	1	3	0	7	1	3	4			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr19:39219691T>C	ENST00000252699.2	+	20	2550	c.2474T>C	c.(2473-2475)cTt>cCt	p.L825P	ACTN4_ENST00000497637.1_3'UTR|ACTN4_ENST00000424234.2_Missense_Mutation_p.L435P|ACTN4_ENST00000390009.3_Missense_Mutation_p.L606P	NM_004924.4	NP_004915.2	O43707	ACTN4_HUMAN	actinin, alpha 4	825	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.|Mediates interaction with MICALL2. {ECO:0000250}.				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)			CATAGCGGCCTTGTGACCTTC	0.607																																					p.L825P	Colon(168;199 1940 10254 46213 46384)	Atlas-SNP	.											.	ACTN4	69	.	0			c.T2474C						PASS	.						132	102	112					19																	39219691		2203	4300	6503	SO:0001583	missense	81	exon20			GCGGCCTTGTGAC	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.2474T>C	chr19.hg19:g.39219691T>C	ENSP00000252699:p.Leu825Pro	140.0	0.0	.		221.0	101.0	.	NM_004924	A4K467|D6PXK4|O76048	Missense_Mutation	SNP	ENST00000252699.2	hg19	CCDS12518.1	.	.	.	.	.	.	.	.	.	.	T	14.29	2.491189	0.44249	.	.	ENSG00000130402	ENST00000252699;ENST00000424234;ENST00000390009;ENST00000440400	T;T;T;T	0.78924	-0.07;-0.07;-0.07;-1.22	3.62	3.62	0.41486	EF-hand-like domain (1);	0.328967	0.28327	N	0.015757	T	0.64416	0.2596	N	0.22421	0.69	0.58432	D	0.999999	B	0.23316	0.083	B	0.23716	0.048	T	0.62483	-0.6845	10	0.40728	T	0.16	.	11.6505	0.51286	0.0:0.0:0.0:1.0	.	825	O43707	ACTN4_HUMAN	P	825;435;606;256	ENSP00000252699:L825P;ENSP00000411187:L435P;ENSP00000439497:L606P;ENSP00000398393:L256P	ENSP00000252699:L825P	L	+	2	0	ACTN4	43911531	0.930000	0.31532	0.999000	0.59377	0.976000	0.68499	3.892000	0.56235	1.656000	0.50722	0.459000	0.35465	CTT	.	.	.	none		0.607	ACTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268091.1			C	39219691	T	C	39219691	3	2	148	1	0	0	0	0	1	0	0	0	207	1609	56	3	2552	3	ACTN4	19	39219691	Missense_Mutation	SNP	T	TCGA-DW-7836-01A-11D-2136-08	29766844	39219691	19909292	38	8860											
GAB4	128954	hgsc.bcm.edu	37	chr22	17444670	17444670	+	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	tgttaccagtgctcctcggcGgggctgaactgctggtgcca	5	10	14	12	2	0	1	0	1	0	0	2	1	1	1	3	4	5	4	3	4	2	1			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr22:17444670G>C	ENST00000400588.1	-	9	1633	c.1526C>G	c.(1525-1527)cCg>cGg	p.P509R		NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	509										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)				GCTCCTCGGCGGGGCTGAACT	0.612																																					p.P509R		Atlas-SNP	.											.	GAB4	95	.	0			c.C1526G						PASS	.						47	54	52					22																	17444670		1991	4192	6183	SO:0001583	missense	128954	exon9			CTCGGCGGGGCTG	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.1526C>G	chr22.hg19:g.17444670G>C	ENSP00000383431:p.Pro509Arg	71.0	0.0	.		65.0	22.0	.	NM_001037814		Missense_Mutation	SNP	ENST00000400588.1	hg19	CCDS42976.1	.	.	.	.	.	.	.	.	.	.	G	0.264	-0.997244	0.02145	.	.	ENSG00000215568	ENST00000400588	T	0.21543	2.0	2.3	-0.182	0.13287	.	0.250153	0.41097	D	0.000958	T	0.09862	0.0242	L	0.38175	1.15	0.09310	N	0.999994	P	0.39157	0.662	B	0.34138	0.176	T	0.34551	-0.9824	10	0.08179	T	0.78	.	4.6103	0.12399	0.13:0.0:0.5111:0.3589	.	509	Q2WGN9	GAB4_HUMAN	R	509	ENSP00000383431:P509R	ENSP00000383431:P509R	P	-	2	0	GAB4	15824670	1.000000	0.71417	0.085000	0.20634	0.002000	0.02628	4.484000	0.60271	-0.257000	0.09459	-1.465000	0.01017	CCG	.	.	.	none		0.612	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882		C	17444670	G	C	17444670	3	2	148	1	0	0	0	0	1	0	0	0	6158	1116	39	4	206	4	GAB4	22	17444670	Missense_Mutation	SNP	G	TCGA-DW-7836-01A-11D-2136-08		17444670	33859896	39	8861											
SEC14L2	23541	hgsc.bcm.edu	37	chr22	30805245	30805245	+	Missense_Mutation	SNP	A	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	ttggcctcaagcatctctggAagcctgctgtggaggcctat	7	11	12	11	0	2	0	1	0	1	0	3	2	2	2	3	4	3	2	3	4	3	2			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chr22:30805245A>C	ENST00000312932.9	+	6	753	c.493A>C	c.(493-495)Aag>Cag	p.K165Q	SEC14L2_ENST00000405717.3_Missense_Mutation_p.K165Q|SEC14L2_ENST00000403484.1_Missense_Mutation_p.K91Q|SEC14L2_ENST00000402592.3_Missense_Mutation_p.K82Q|RP4-539M6.19_ENST00000439838.1_5'Flank|SEC14L2_ENST00000459728.1_3'UTR	NM_012429.3	NP_036561.1	O76054	S14L2_HUMAN	SEC14-like 2 (S. cerevisiae)	165	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cholesterol biosynthetic process (GO:0045540)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	phospholipid binding (GO:0005543)|transporter activity (GO:0005215)|vitamin E binding (GO:0008431)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|urinary_tract(1)	10					Vitamin E(DB00163)	GCATCTCTGGAAGCCTGCTGT	0.592																																					p.K165Q		Atlas-SNP	.											.	SEC14L2	24	.	0			c.A493C						PASS	.						58	63	61					22																	30805245		2203	4300	6503	SO:0001583	missense	23541	exon6			CTCTGGAAGCCTG	AL096881	CCDS13876.1, CCDS46685.1, CCDS56228.1	22q12.2	2010-08-19	2001-11-28		ENSG00000100003	ENSG00000100003			10699	protein-coding gene	gene with protein product	"supernatant protein factor"	607558	"SEC14 (S. cerevisiae)-like 2"	C22orf6		10591208	Standard	NM_033382		Approved	TAP, SPF, KIAA1186, KIAA1658	uc003ahr.3	O76054	OTTHUMG00000151024	ENST00000312932.9:c.493A>C	chr22.hg19:g.30805245A>C	ENSP00000316203:p.Lys165Gln	76.0	0.0	.		60.0	32.0	.	NM_012429	B7Z8Q1|F5H3U4|Q53EQ2|Q6PD61|Q9ULN4	Missense_Mutation	SNP	ENST00000312932.9	hg19	CCDS13876.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.716174	0.89205	.	.	ENSG00000100003	ENST00000312932;ENST00000428195;ENST00000403484;ENST00000405717;ENST00000402592	T;T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05;-1.05	4.79	4.79	0.61399	Cellular retinaldehyde-binding/triple function, C-terminal (5);	0.000000	0.85682	D	0.000000	D	0.86406	0.5925	M	0.72353	2.195	0.80722	D	1	D;P;D;P	0.89917	1.0;0.933;0.996;0.88	D;P;D;B	0.74674	0.984;0.711;0.949;0.383	D	0.88014	0.2764	10	0.72032	D	0.01	-0.6938	14.1425	0.65329	1.0:0.0:0.0:0.0	.	82;91;165;165	F5H3U4;B3KRD8;O76054;O76054-4	.;.;S14L2_HUMAN;.	Q	165;111;91;165;82	ENSP00000316203:K165Q;ENSP00000387781:K111Q;ENSP00000383993:K91Q;ENSP00000385186:K165Q;ENSP00000383882:K82Q	ENSP00000316203:K165Q	K	+	1	0	SEC14L2	29135245	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.622000	0.90953	2.018000	0.59344	0.533000	0.62120	AAG	.	.	.	none		0.592	SEC14L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321018.4	NM_012429		C	30805245	A	C	30805245	3	2	148	1	0	0	0	0	1	0	0	0	13995	247	9	5	515	5	SEC14L2	22	30805245	Missense_Mutation	SNP	A	TCGA-DW-7836-01A-11D-2136-08	13360575	30805245	20499321	40	8862											
ARSE	415	hgsc.bcm.edu	37	chrX	2867409	2867409	+	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	tctttggaagcacatgggctGctccgtgatggtgtggtttc	5	14	14	8	1	1	1	0	1	1	0	3	2	2	2	1	4	2	4	1	4	1	2			TCGA-DW-7836-01A-11D-2136-08	TCGA-DW-7836-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1cca814c-40fe-426c-b494-86a634031f4c	22c58020-f91d-4657-99ae-53bd869ee210	g.chrX:2867409G>A	ENST00000381134.3	-	6	856	c.790C>T	c.(790-792)Cag>Tag	p.Q264*	ARSE_ENST00000545496.1_Nonsense_Mutation_p.Q289*|ARSE_ENST00000540563.1_Nonsense_Mutation_p.Q219*	NM_000047.2	NP_000038.2	P51690	ARSE_HUMAN	arylsulfatase E (chondrodysplasia punctata 1)	264					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)				CACATGGGCTGCTCCGTGATG	0.527																																					p.Q264X		Atlas-SNP	.											.	ARSE	43	.	0			c.C790T						PASS	.						92	73	79					X																	2867409		2203	4300	6503	SO:0001587	stop_gained	415	exon6			TGGGCTGCTCCGT	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.790C>T	chrX.hg19:g.2867409G>A	ENSP00000370526:p.Gln264*	70.0	0.0	.		42.0	38.0	.	NM_000047	Q53FT2|Q53FU8	Nonsense_Mutation	SNP	ENST00000381134.3	hg19	CCDS14122.1	.	.	.	.	.	.	.	.	.	.	g	21.9	4.216506	0.79352	.	.	ENSG00000157399	ENST00000540563;ENST00000545496;ENST00000381134	.	.	.	3.54	3.54	0.40534	.	0.139687	0.51477	D	0.000095	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	14.5415	0.67999	0.0:0.0:1.0:0.0	.	.	.	.	X	219;289;264	.	ENSP00000370526:Q264X	Q	-	1	0	ARSE	2877409	1.000000	0.71417	0.267000	0.24556	0.056000	0.15407	5.631000	0.67812	1.395000	0.46643	0.591000	0.81541	CAG	.	.	.	none		0.527	ARSE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055643.1	NM_000047		A	2867409	G	A	2867409	4	1	148	1	0	0	0	0	0	1	0	0	990	1328	46	2	1003	2	ARSE	23	2867409	Nonsense_Mutation	SNP	G	TCGA-DW-7836-01A-11D-2136-08		2867409	152403151	41	8863											
DNAJC16	23341	hgsc.bcm.edu	37	chr1	15890499	15890500	+	Frame_Shift_Del	DEL	GA	GA	-																															aagacccttggattgggagtGagagtgacaaatttatcctc																										TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	GA	GA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr1:15890499_15890500delGA	ENST00000375847.3	+	10	1578_1579	c.1414_1415delGA	c.(1414-1416)gagfs	p.E472fs	DNAJC16_ENST00000375849.1_Frame_Shift_Del_p.E472fs|RP4-680D5.8_ENST00000606186.1_RNA|DNAJC16_ENST00000483270.1_3'UTR|DNAJC16_ENST00000375838.1_Frame_Shift_Del_p.E472fs	NM_015291.2	NP_056106.1	Q9Y2G8	DJC16_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 16	472					cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(7)|urinary_tract(1)	18		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		GATTGGGAGTGAGAGTGACAAA	0.465																																					p.471_472del		Atlas-INDEL	.											.	DNAJC16	59	.	0			c.1413_1414del						PASS	.																																			SO:0001589	frameshift_variant	23341	exon10			.	AB023179	CCDS30606.1, CCDS72710.1	1p36.1	2011-09-02			ENSG00000116138	ENSG00000116138		"Heat shock proteins / DNAJ (HSP40)"	29157	protein-coding gene	gene with protein product							Standard	NM_015291		Approved	KIAA0962	uc001aws.3	Q9Y2G8	OTTHUMG00000002358	ENST00000375847.3:c.1414_1415delGA	chr1.hg19:g.15890501_15890502delGA	ENSP00000365007:p.Glu472fs	308.0	0.0	0		306.0	86.0	0.281046	NM_015291	Q68D57|Q86X32|Q8N5P4	Frame_Shift_Del	DEL	ENST00000375847.3	hg19	CCDS30606.1																																																																																			.	.	.	none		0.465	DNAJC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006764.1	NM_015291		-	15890500	GA	-	15890499	7	5	149	1	0	1	0	1	0	0	0	0	4637	1291	45	0	1448	0	DNAJC16	1	15890499	Frame_Shift_Del	DEL	GA	TCGA-DW-7837-01A-11D-2136-08		15890499	233360122	1	8864											
ST6GALNAC5	81849	hgsc.bcm.edu	37	chr1	77528824	77528824	+	Missense_Mutation	SNP	T	T	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	acggacattcaatattcactTttttcaaccagactggaaac	14	12	5	10	1	3	1	3	0	0	1	3	3	3	3	1	2	2	0	1	2	4	6			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr1:77528824T>G	ENST00000477717.1	+	5	1179	c.944T>G	c.(943-945)tTt>tGt	p.F315C		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	315					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						AATATTCACTTTTTTCAACCA	0.438																																					p.F315C		Atlas-SNP	.											.	ST6GALNAC5	59	.	0			c.T944G						PASS	.						116	110	112					1																	77528824		2203	4300	6503	SO:0001583	missense	81849	exon5			TTCACTTTTTTCA		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.944T>G	chr1.hg19:g.77528824T>G	ENSP00000417583:p.Phe315Cys	139.0	0.0	.		153.0	49.0	.	NM_030965	B1AK82	Missense_Mutation	SNP	ENST00000477717.1	hg19	CCDS673.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.359557	0.82353	.	.	ENSG00000117069	ENST00000477717;ENST00000438953	T	0.58358	0.34	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.73210	0.3558	M	0.89095	3.005	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79562	-0.1752	10	0.87932	D	0	-36.7448	16.3789	0.83431	0.0:0.0:0.0:1.0	.	315	Q9BVH7	SIA7E_HUMAN	C	315;225	ENSP00000417583:F315C	ENSP00000406658:F225C	F	+	2	0	ST6GALNAC5	77301412	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.649000	0.83500	2.267000	0.75376	0.533000	0.62120	TTT	.	.	.	none		0.438	ST6GALNAC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026692.2	NM_030965		G	77528824	T	G	77528824	3	3	149	1	0	0	0	0	1	0	0	0	15239	1841	64	5	962	5	ST6GALNAC5	1	77528824	Missense_Mutation	SNP	T	TCGA-DW-7837-01A-11D-2136-08	61638325	77528824	171721797	2	8865			1	18		2	2	12	N	T_G	1.385795e-05
ST6GALNAC5	81849	hgsc.bcm.edu	37	chr1	77528835	77528835	+	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	atattcacttttttcaaccaGactggaaaccagaatcactt	14	13	4	10	0	3	2	3	0	0	2	3	3	3	3	2	1	2	0	2	1	4	6			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr1:77528835G>A	ENST00000477717.1	+	5	1190	c.955G>A	c.(955-957)Gac>Aac	p.D319N		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	319					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						TTTTCAACCAGACTGGAAACC	0.438																																					p.D319N		Atlas-SNP	.											.	ST6GALNAC5	59	.	0			c.G955A						PASS	.						113	106	109					1																	77528835		2203	4300	6503	SO:0001583	missense	81849	exon5			CAACCAGACTGGA		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.955G>A	chr1.hg19:g.77528835G>A	ENSP00000417583:p.Asp319Asn	136.0	0.0	.		153.0	46.0	.	NM_030965	B1AK82	Missense_Mutation	SNP	ENST00000477717.1	hg19	CCDS673.1	.	.	.	.	.	.	.	.	.	.	G	15.10	2.733083	0.48939	.	.	ENSG00000117069	ENST00000477717;ENST00000438953	T	0.30714	1.52	5.93	2.92	0.33932	.	0.140018	0.64402	N	0.000006	T	0.12475	0.0303	L	0.49350	1.555	0.50467	D	0.999873	B	0.18166	0.026	B	0.16289	0.015	T	0.05022	-1.0911	10	0.23302	T	0.38	-15.1218	11.5508	0.50719	0.0636:0.2339:0.7025:0.0	.	319	Q9BVH7	SIA7E_HUMAN	N	319;229	ENSP00000417583:D319N	ENSP00000406658:D229N	D	+	1	0	ST6GALNAC5	77301423	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.553000	0.60753	0.830000	0.34757	0.655000	0.94253	GAC	.	.	.	none		0.438	ST6GALNAC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026692.2	NM_030965		A	77528835	G	A	77528835	3	1	149	1	0	0	0	0	1	0	0	0	15239	942	33	2	973	2	ST6GALNAC5	1	77528835	Missense_Mutation	SNP	G	TCGA-DW-7837-01A-11D-2136-08	11	77528835	171721786	3	8866			1	18		2	2	12	N	T_G	1.385795e-05
EGLN1	54583	hgsc.bcm.edu	37	chr1	231556782	231556782	+	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	tttgtagctgcccagcttccCgttacagtggcgtatcaggt	6	13	11	11	2	1	0	1	0	0	0	2	0	2	0	2	2	4	5	2	2	3	5			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr1:231556782C>A	ENST00000366641.3	-	1	4008	c.853G>T	c.(853-855)Ggg>Tgg	p.G285W	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)				CCCAGCTTCCCGTTACAGTGG	0.607																																					p.G285W		Atlas-SNP	.											.	EGLN1	38	.	0			c.G853T						PASS	.						118	114	115					1																	231556782		2203	4300	6503	SO:0001583	missense	54583	exon1			GCTTCCCGTTACA	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.853G>T	chr1.hg19:g.231556782C>A	ENSP00000355601:p.Gly285Trp	181.0	0.0	.		158.0	7.0	.	NM_022051		Missense_Mutation	SNP	ENST00000366641.3	hg19	CCDS1595.1	.	.	.	.	.	.	.	.	.	.	C	35	5.558127	0.96514	.	.	ENSG00000135766	ENST00000366641	D	0.87103	-2.21	4.76	4.76	0.60689	Prolyl 4-hydroxylase, alpha subunit (1);	0.000000	0.85682	D	0.000000	D	0.93690	0.7984	M	0.85041	2.73	0.80722	D	1	D	0.71674	0.998	D	0.64410	0.925	D	0.94830	0.7995	10	0.87932	D	0	-8.1275	18.1409	0.89639	0.0:1.0:0.0:0.0	.	285	Q9GZT9	EGLN1_HUMAN	W	285	ENSP00000355601:G285W	ENSP00000355601:G285W	G	-	1	0	EGLN1	229623405	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.924000	0.70054	2.304000	0.77564	0.563000	0.77884	GGG	.	.	.	none		0.607	EGLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092879.1	NM_022051		A	231556782	C	A	231556782	3	1	149	1	0	0	0	0	1	0	0	0	4970	652	23	4	447	4	EGLN1	1	231556782	Missense_Mutation	SNP	C	TCGA-DW-7837-01A-11D-2136-08	154027947	231556782	17693839	4	8867											
IFT172	26160	hgsc.bcm.edu	37	chr2	27685657	27685657	+	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	ataaaagtctgttccttctcCgccctgtgggggaaaaagga	11	10	11	9	1	2	0	0	0	2	0	4	2	3	2	3	3	0	1	3	3	4	3			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr2:27685657C>A	ENST00000260570.3	-	20	2129	c.2026G>T	c.(2026-2028)Gga>Tga	p.G676*		NM_015662.1	NP_056477.1	Q9UG01	IF172_HUMAN	intraflagellar transport 172	676					bone development (GO:0060348)|brain development (GO:0007420)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|epidermis development (GO:0008544)|heart looping (GO:0001947)|hindgut development (GO:0061525)|left/right axis specification (GO:0070986)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)	axoneme (GO:0005930)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(17)|lung(17)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	43	Acute lymphoblastic leukemia(172;0.155)					GTTCCTTCTCCGCCCTGTGGG	0.448																																					p.G676X		Atlas-SNP	.											.	IFT172	119	.	0			c.G2026T						PASS	.						94	99	97					2																	27685657		2203	4300	6503	SO:0001587	stop_gained	26160	exon20			CTTCTCCGCCCTG	AB033005	CCDS1755.1	2p23.3	2014-07-03	2014-07-03		ENSG00000138002	ENSG00000138002		"Intraflagellar transport homologs", "WD repeat domain containing"	30391	protein-coding gene	gene with protein product	"wimple homolog"	607386	"intraflagellar transport 172 homolog (Chlamydomonas)"			10788441, 10574461, 24140113	Standard	XM_005264254		Approved	SLB, wim, osm-1, NPHP17	uc002rku.3	Q9UG01	OTTHUMG00000128425	ENST00000260570.3:c.2026G>T	chr2.hg19:g.27685657C>A	ENSP00000260570:p.Gly676*	142.0	0.0	.		118.0	6.0	.	NM_015662	A5PKZ0|B2RNU5|Q86X44|Q96HW4|Q9UFJ9|Q9ULP1	Nonsense_Mutation	SNP	ENST00000260570.3	hg19	CCDS1755.1	.	.	.	.	.	.	.	.	.	.	C	40	8.188732	0.98696	.	.	ENSG00000138002	ENST00000260570	.	.	.	5.54	5.54	0.83059	.	0.099543	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	-12.2619	18.0587	0.89370	0.0:1.0:0.0:0.0	.	.	.	.	X	676	.	ENSP00000260570:G676X	G	-	1	0	IFT172	27539161	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.355000	0.79434	2.601000	0.87937	0.655000	0.94253	GGA	.	.	.	none		0.448	IFT172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250213.2	NM_015662		A	27685657	C	A	27685657	4	1	149	1	0	0	0	0	0	1	0	0	7564	661	23	4	3339	4	IFT172	2	27685657	Nonsense_Mutation	SNP	C	TCGA-DW-7837-01A-11D-2136-08		27685657	215513716	5	8868											
CLASP1	23332	hgsc.bcm.edu	37	chr2	122206659	122206659	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggtgtggtacaagtgctctgCttctctgctgaagtgactgt	6	14	13	8	0	2	2	0	2	2	0	3	2	2	2	0	2	4	4	0	2	3	2			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr2:122206659C>T	ENST00000263710.4	-	17	1950	c.1561G>A	c.(1561-1563)Gca>Aca	p.A521T	CLASP1_ENST00000541859.1_Missense_Mutation_p.A290T|CLASP1_ENST00000409078.3_Missense_Mutation_p.A521T|CLASP1_ENST00000541377.1_Missense_Mutation_p.A521T|CLASP1_ENST00000455322.2_Missense_Mutation_p.A521T|CLASP1_ENST00000397587.3_Missense_Mutation_p.A521T|CLASP1_ENST00000545861.1_Missense_Mutation_p.A289T	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	521					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)					AAGTGCTCTGCTTCTCTGCTG	0.493																																					p.A521T		Atlas-SNP	.											.	CLASP1	135	.	0			c.G1561A						PASS	.						100	99	99					2																	122206659		1961	4153	6114	SO:0001583	missense	23332	exon17			GCTCTGCTTCTCT	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.1561G>A	chr2.hg19:g.122206659C>T	ENSP00000263710:p.Ala521Thr	39.0	0.0	.		39.0	12.0	.	NM_001207051	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Missense_Mutation	SNP	ENST00000263710.4	hg19		.	.	.	.	.	.	.	.	.	.	C	36	5.877189	0.97055	.	.	ENSG00000074054	ENST00000263710;ENST00000455322;ENST00000397587;ENST00000541377;ENST00000541859;ENST00000409078;ENST00000545861	T;T;T;T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08;-0.08;-0.08;-0.08	6.04	6.04	0.98038	Armadillo-like helical (1);Armadillo-type fold (2);CLASP N-terminal domain (1);	0.000000	0.85682	D	0.000000	D	0.83889	0.5352	M	0.88377	2.95	0.80722	D	1	D;D;D;D	0.76494	0.999;0.998;0.999;0.999	D;D;D;D	0.91635	0.997;0.995;0.998;0.999	D	0.85446	0.1158	10	0.87932	D	0	-19.0221	20.5948	0.99439	0.0:1.0:0.0:0.0	.	521;521;521;521	E7EUA5;F5GWS0;B7ZLX3;Q7Z460	.;.;.;CLAP1_HUMAN	T	521;521;521;521;290;521;289	ENSP00000263710:A521T;ENSP00000389372:A521T;ENSP00000380717:A521T;ENSP00000441625:A521T;ENSP00000441770:A290T;ENSP00000386442:A521T;ENSP00000438620:A289T	ENSP00000263710:A521T	A	-	1	0	CLASP1	121923129	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.818000	0.86416	2.873000	0.98535	0.563000	0.77884	GCA	.	.	.	none		0.493	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282		T	122206659	C	T	122206659	3	4	149	1	0	0	0	0	1	0	0	0	3456	797	28	2	3203	2	CLASP1	2	122206659	Missense_Mutation	SNP	C	TCGA-DW-7837-01A-11D-2136-08	94521002	122206659	120992714	6	8869											
C3orf19	51244	hgsc.bcm.edu	37	chr3	14695999	14695999	+	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	aacaagaaaaacttctaaaaGattctggagtttttggaaaa	19	11	7	4	0	2	2	0	0	2	2	2	4	2	4	0	2	2	1	0	2	8	5			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr3:14695999G>C	ENST00000383794.3	+	2	182	c.109G>C	c.(109-111)Gat>Cat	p.D37H	CCDC174_ENST00000303688.7_Missense_Mutation_p.D37H	NM_016474.4	NP_057558.3	Q6PII3	CC174_HUMAN	coiled-coil domain containing 174	37						cytoplasm (GO:0005737)|nucleus (GO:0005634)											ACTTCTAAAAGATTCTGGAGT	0.299																																					p.D37H		Atlas-SNP	.											.	.	.	.	0			c.G109C						PASS	.						26	26	26					3																	14695999		1779	4049	5828	SO:0001583	missense	51244	exon2			CTAAAAGATTCTG	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.109G>C	chr3.hg19:g.14695999G>C	ENSP00000373304:p.Asp37His	30.0	0.0	.		38.0	17.0	.	NM_016474	Q96CS5	Missense_Mutation	SNP	ENST00000383794.3	hg19	CCDS2620.2	.	.	.	.	.	.	.	.	.	.	G	15.54	2.862642	0.51482	.	.	ENSG00000154781	ENST00000383794;ENST00000303688	T;T	0.46063	0.88;0.89	5.58	4.7	0.59300	.	0.057430	0.64402	D	0.000001	T	0.61048	0.2316	M	0.70275	2.135	0.46981	D	0.999278	D	0.89917	1.0	D	0.71184	0.972	T	0.63005	-0.6733	10	0.59425	D	0.04	-12.7651	12.8107	0.57637	0.08:0.0:0.92:0.0	.	37	Q6PII3	CC019_HUMAN	H	37	ENSP00000373304:D37H;ENSP00000302344:D37H	ENSP00000302344:D37H	D	+	1	0	C3orf19	14671003	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	6.367000	0.73099	2.620000	0.88729	0.491000	0.48974	GAT	.	.	.	none		0.299	CCDC174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252077.2	NM_016474		C	14695999	G	C	14695999	3	2	149	1	0	0	0	0	1	0	0	0	2214	942	33	4	115	4	C3orf19	3	14695999	Missense_Mutation	SNP	G	TCGA-DW-7837-01A-11D-2136-08		14695999	183326431	7	8870											
DPH3	285381	hgsc.bcm.edu	37	chr3	16302327	16302327	+	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	tgggactgtttctccacacaCaaactgatcctaagacagag	13	9	8	11	0	1	3	0	1	1	2	3	4	2	4	2	1	1	1	2	1	2	2			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr3:16302327C>G	ENST00000488423.1	-	3	288	c.193G>C	c.(193-195)Gtg>Ctg	p.V65L	DPH3_ENST00000285082.4_5'UTR|DPH3_ENST00000383775.4_Missense_Mutation_p.V40L	NM_206831.2	NP_996662.1	Q96FX2	DPH3_HUMAN	diphthamide biosynthesis 3	65					negative regulation of protein secretion (GO:0050709)|peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)|positive regulation of binding (GO:0051099)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			large_intestine(2)	2						TCTCCACACACAAACTGATCC	0.388																																					p.V65L		Atlas-SNP	.											.	DPH3	7	.	0			c.G193C						PASS	.						98	87	91					3																	16302327		2203	4300	6503	SO:0001583	missense	285381	exon3			CACACACAAACTG	BC010181	CCDS2629.1, CCDS43058.1	3p25.1	2013-06-19	2013-06-19	2006-10-25	ENSG00000154813	ENSG00000154813			27717	protein-coding gene	gene with protein product	"DPH3A, KTI11 homolog A (S. cerevisiae)"	608959	"zinc finger, CSL-type containing 2", "DPH3 homolog (KTI11, S. cerevisiae)", "DPH3, KTI11 homolog (S. cerevisiae)"	ZCSL2		14527407, 14980502, 15485916, 16648478	Standard	NM_001047434		Approved	DESR1, DELGIP1, MGC20197, KTI11, DELGIP, DPH3A	uc003cau.3	Q96FX2	OTTHUMG00000129866	ENST00000488423.1:c.193G>C	chr3.hg19:g.16302327C>G	ENSP00000419599:p.Val65Leu	49.0	0.0	.		68.0	4.0	.	NM_206831		Missense_Mutation	SNP	ENST00000488423.1	hg19	CCDS2629.1	.	.	.	.	.	.	.	.	.	.	C	10.30	1.311440	0.23821	.	.	ENSG00000154813	ENST00000488423;ENST00000383775	.	.	.	5.73	3.22	0.36961	.	0.175580	0.64402	D	0.000016	T	0.16128	0.0388	.	.	.	0.24129	N	0.995778	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.30563	-0.9974	8	0.07990	T	0.79	-32.8775	7.2848	0.26333	0.0:0.2036:0.0:0.7964	.	40;65	Q96FX2-2;Q96FX2	.;DPH3_HUMAN	L	65;40	.	ENSP00000373285:V40L	V	-	1	0	DPH3	16277331	1.000000	0.71417	0.996000	0.52242	0.992000	0.81027	1.606000	0.36826	0.362000	0.24319	0.491000	0.48974	GTG	.	.	.	none		0.388	DPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252108.2	NM_206831		G	16302327	C	G	16302327	3	3	149	1	0	0	0	0	1	0	0	0	4723	478	17	4	59	4	DPH3	3	16302327	Missense_Mutation	SNP	C	TCGA-DW-7837-01A-11D-2136-08	1606328	16302327	181720103	8	8871											
SLC22A13	9390	hgsc.bcm.edu	37	chr3	38317479	38317479	+	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	gagctgttgaggtgcctgccCgctgttccagcatcttcatg	5	12	12	12	1	2	1	1	1	1	0	3	2	3	1	3	1	4	5	3	1	0	3	rs117371763	byFrequency	TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr3:38317479C>A	ENST00000311856.4	+	7	1178	c.1129C>A	c.(1129-1131)Cgc>Agc	p.R377S	SLC22A13_ENST00000450935.2_3'UTR	NM_004256.3	NP_004247.2	Q9Y226	S22AD_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 13	377					nicotinate transport (GO:2001142)|organic cation transport (GO:0015695)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	nicotinate transporter activity (GO:0090416)|organic cation transmembrane transporter activity (GO:0015101)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|urinary_tract(1)	20				KIRC - Kidney renal clear cell carcinoma(284;0.0533)|Kidney(284;0.067)		GGTGCCTGCCCGCTGTTCCAG	0.567																																					p.R377S		Atlas-SNP	.											.	SLC22A13	42	.	0			c.C1129A						PASS	.						80	68	72					3																	38317479		2203	4300	6503	SO:0001583	missense	9390	exon7			CCTGCCCGCTGTT	AB010438	CCDS2676.1	3p22.2	2013-07-18	2013-07-18	2003-10-15	ENSG00000172940	ENSG00000172940		"Solute carriers"	8494	protein-coding gene	gene with protein product		604047	"organic cationic transporter-like 3", "solute carrier family 22 (organic anion transporter), member 13"	ORCTL3		10072596, 18411268	Standard	NM_004256		Approved	OCTL1, OCTL3, OAT10	uc003chz.3	Q9Y226	OTTHUMG00000131086	ENST00000311856.4:c.1129C>A	chr3.hg19:g.38317479C>A	ENSP00000310241:p.Arg377Ser	55.0	0.0	.		75.0	5.0	.	NM_004256	B2RCV9|Q8IYG1	Missense_Mutation	SNP	ENST00000311856.4	hg19	CCDS2676.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.101702	0.76983	.	.	ENSG00000172940	ENST00000311856	T	0.72942	-0.7	5.16	3.37	0.38596	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.048082	0.85682	D	0.000000	T	0.76579	0.4007	L	0.59967	1.855	0.80722	D	1	D;P	0.61697	0.99;0.946	D;P	0.64776	0.929;0.726	T	0.71642	-0.4531	10	0.21540	T	0.41	.	10.7573	0.46245	0.0:0.846:0.0:0.154	.	377;377	Q9Y226-2;Q9Y226	.;S22AD_HUMAN	S	377	ENSP00000310241:R377S	ENSP00000310241:R377S	R	+	1	0	SLC22A13	38292483	0.991000	0.36638	0.943000	0.38184	0.893000	0.52053	2.927000	0.48900	0.696000	0.31696	0.655000	0.94253	CGC	.	C|0.999;T|0.001	.	alt		0.567	SLC22A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253746.2	NM_004256		A	38317479	C	A	38317479	3	1	149	1	0	0	0	0	1	0	0	0	14457	652	23	4	1155	4	SLC22A13	3	38317479	Missense_Mutation	SNP	C	TCGA-DW-7837-01A-11D-2136-08	22015152	38317479	159704951	9	8872											
PCDH7	5099	hgsc.bcm.edu	37	chr4	30724425	30724425	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaacggggtggtcacctgcAccgtggtgggcgacgtgccc	6	6	17	12	4	1	1	1	0	0	1	1	2	1	1	3	5	3	1	3	5	1	0			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr4:30724425A>G	ENST00000361762.2	+	1	2389	c.1381A>G	c.(1381-1383)Acc>Gcc	p.T461A	PCDH7_ENST00000543491.1_Missense_Mutation_p.T461A	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	461	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T414P(1)|p.T461P(1)		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						GGTCACCTGCACCGTGGTGGG	0.642																																					p.T461A		Atlas-SNP	.											PCDH7_ENST00000361762,NS,carcinoma,0,1	PCDH7	215	.	2	Substitution - Missense(2)	lung(2)	c.A1381G						PASS	.						74	56	62					4																	30724425		2203	4300	6503	SO:0001583	missense	5099	exon1			ACCTGCACCGTGG	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.1381A>G	chr4.hg19:g.30724425A>G	ENSP00000355243:p.Thr461Ala	62.0	1.0	.		62.0	3.0	.	NM_032457	O60246|O60247|Q4W5C4	Missense_Mutation	SNP	ENST00000361762.2	hg19	CCDS33971.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.21|14.21	2.465990|2.465990	0.43839|0.43839	.|.	.|.	ENSG00000169851|ENSG00000169851	ENST00000511884|ENST00000361762;ENST00000543491;ENST00000333135	.|T;T	.|0.48836	.|0.8;0.8	5.16|5.16	5.16|5.16	0.70880|0.70880	.|Cadherin (4);Cadherin-like (1);	.|.	.|.	.|.	.|.	T|T	0.47002|0.47002	0.1422|0.1422	L|L	0.28694|0.28694	0.88|0.88	0.47819|0.47819	D|D	0.999523|0.999523	.|B;B;B	.|0.32653	.|0.328;0.328;0.379	.|B;B;P	.|0.44447	.|0.321;0.321;0.45	T|T	0.44174|0.44174	-0.9345|-0.9345	5|9	.|0.35671	.|T	.|0.21	.|.	15.1585|15.1585	0.72761|0.72761	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|461;414;461	.|F5GWJ1;O60245-3;O60245	.|.;.;PCDH7_HUMAN	R|A	150|461;461;414	.|ENSP00000355243:T461A;ENSP00000441802:T461A	.|ENSP00000330302:T414A	H|T	+|+	2|1	0|0	PCDH7|PCDH7	30333523|30333523	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	5.956000|5.956000	0.70315|0.70315	2.164000|2.164000	0.68074|0.68074	0.533000|0.533000	0.62120|0.62120	CAC|ACC	.	.	.	none		0.642	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589		G	30724425	A	G	30724425	3	3	149	1	0	0	0	0	1	0	0	0	11523	159	6	3	1383	3	PCDH7	4	30724425	Missense_Mutation	SNP	A	TCGA-DW-7837-01A-11D-2136-08		30724425	160429851	10	8873											
DDX60L	91351	hgsc.bcm.edu	37	chr4	169337906	169337906	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcgaataatgacaaggaggaGctcccaaaattttgctccaa	15	9	8	9	1	0	1	0	1	0	0	3	4	2	3	2	2	2	2	2	2	6	3			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr4:169337906G>A	ENST00000511577.1	-	20	2900	c.2653C>T	c.(2653-2655)Ctc>Ttc	p.L885F	DDX60L_ENST00000260184.7_Missense_Mutation_p.L885F|DDX60L_ENST00000505890.1_Missense_Mutation_p.L885F			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	885	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)		ACAAGGAGGAGCTCCCAAAAT	0.343																																					p.L885F		Atlas-SNP	.											.	DDX60L	116	.	0			c.C2653T						PASS	.						107	102	104					4																	169337906		1833	4116	5949	SO:0001583	missense	91351	exon20			GGAGGAGCTCCCA	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.2653C>T	chr4.hg19:g.169337906G>A	ENSP00000422423:p.Leu885Phe	82.0	0.0	.		111.0	33.0	.	NM_001012967	Q96ND6	Missense_Mutation	SNP	ENST00000511577.1	hg19		.	.	.	.	.	.	.	.	.	.	G	15.04	2.714600	0.48622	.	.	ENSG00000181381	ENST00000260184;ENST00000511577;ENST00000505890;ENST00000505863	T;T;T;T	0.74526	-0.85;-0.85;1.2;1.2	3.42	3.42	0.39159	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.183055	0.25361	U	0.031226	T	0.69124	0.3076	L	0.49640	1.575	0.25638	N	0.986238	P;P;P	0.45283	0.855;0.769;0.855	B;B;B	0.41510	0.359;0.288;0.359	T	0.66164	-0.5992	10	0.66056	D	0.02	.	13.027	0.58821	0.0:0.0:1.0:0.0	.	885;885;885	E9PAP8;D6R906;Q5H9U9	.;.;DDX6L_HUMAN	F	885;885;885;581	ENSP00000260184:L885F;ENSP00000422423:L885F;ENSP00000422202:L885F;ENSP00000421026:L581F	ENSP00000260184:L885F	L	-	1	0	DDX60L	169574481	1.000000	0.71417	0.896000	0.35187	0.943000	0.58893	5.558000	0.67319	1.619000	0.50296	0.461000	0.40582	CTC	.	.	.	none		0.343	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		A	169337906	G	A	169337906	3	1	149	1	0	0	0	0	1	0	0	0	4381	971	34	2	2543	2	DDX60L	4	169337906	Missense_Mutation	SNP	G	TCGA-DW-7837-01A-11D-2136-08	138613481	169337906	21816370	11	8874											
MAP3K1	4214	hgsc.bcm.edu	37	chr5	56177037	56177037	+	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	agactgttgttggaatttccTgctgaattttatcctcatat	9	18	7	7	0	1	2	1	1	0	1	3	3	3	3	2	1	1	3	2	1	4	6			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr5:56177037T>A	ENST00000399503.3	+	13	2307	c.2307T>A	c.(2305-2307)ccT>ccA	p.P769P		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	769					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)		TGGAATTTCCTGCTGAATTTT	0.348																																					p.P769P		Atlas-SNP	.											.	MAP3K1	355	.	0			c.T2307A						PASS	.						164	147	152					5																	56177037		1836	4079	5915	SO:0001819	synonymous_variant	4214	exon13			ATTTCCTGCTGAA	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.2307T>A	chr5.hg19:g.56177037T>A		48.0	0.0	.		76.0	25.0	.	NM_005921		Silent	SNP	ENST00000399503.3	hg19	CCDS43318.1																																																																																			.	.	.	none		0.348	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066		A	56177037	T	A	56177037	2	1	149	1	0	0	0	0	0	0	0	1	9250	1567	55	5		5	MAP3K1	5	56177037	Silent	SNP	T	TCGA-DW-7837-01A-11D-2136-08		56177037	124738223	12	8875											
PPP1R9A	55607	hgsc.bcm.edu	37	chr7	94827675	94827675	+	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	ccacagatttgttattgggcGggaaaaaccaggacaagtga	14	8	12	7	1	0	2	0	1	0	1	0	4	0	4	2	3	1	1	2	3	4	3			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr7:94827675G>T	ENST00000433881.1	+	6	2301	c.1769G>T	c.(1768-1770)cGg>cTg	p.R590L	PPP1R9A_ENST00000456331.2_Missense_Mutation_p.R590L|PPP1R9A_ENST00000340694.4_Missense_Mutation_p.R590L|AC002429.5_ENST00000417881.2_RNA|PPP1R9A_ENST00000289495.5_Missense_Mutation_p.R590L|PPP1R9A_ENST00000424654.1_Missense_Mutation_p.R590L|PPP1R9A_ENST00000433360.1_Missense_Mutation_p.R590L			Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory subunit 9A	590	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				actin filament organization (GO:0007015)|calcium-mediated signaling (GO:0019722)|neuron projection development (GO:0031175)	cell junction (GO:0030054)|cortical actin cytoskeleton (GO:0030864)|dendritic spine (GO:0043197)|filopodium (GO:0030175)|growth cone (GO:0030426)|synapse (GO:0045202)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(11)|liver(2)|lung(22)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(8)|urinary_tract(5)	71	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)			GTTATTGGGCGGGAAAAACCA	0.453										HNSCC(28;0.073)																											p.R590L		Atlas-SNP	.											.	PPP1R9A	264	.	0			c.G1769T						PASS	.						75	75	75					7																	94827675		2203	4300	6503	SO:0001583	missense	55607	exon6			TTGGGCGGGAAAA	AB033048	CCDS34683.1, CCDS55127.1, CCDS55128.1	7q21.3	2013-01-10	2011-10-04		ENSG00000158528	ENSG00000158528		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Sterile alpha motif (SAM) domain containing"	14946	protein-coding gene	gene with protein product		602468	"protein phosphatase 1, regulatory (inhibitor) subunit 9A"			10574462	Standard	NM_001166160		Approved	Neurabin-I, KIAA1222, FLJ20068	uc010lfj.3	Q9ULJ8	OTTHUMG00000155566	ENST00000433881.1:c.1769G>T	chr7.hg19:g.94827675G>T	ENSP00000398870:p.Arg590Leu	81.0	0.0	.		152.0	12.0	.	NM_017650	A1L494|B2RWQ1|E9PCA0|E9PCK6|E9PDX1|F8W7J9|O76059|Q9NXT2	Missense_Mutation	SNP	ENST00000433881.1	hg19	CCDS34683.1	.	.	.	.	.	.	.	.	.	.	G	19.09	3.759811	0.69763	.	.	ENSG00000158528	ENST00000433360;ENST00000340694;ENST00000424654;ENST00000433881;ENST00000289495;ENST00000456331	T;T;T;T;T;T	0.55234	0.53;0.53;0.53;0.53;0.53;0.53	5.61	5.61	0.85477	PDZ/DHR/GLGF (3);	0.000000	0.85682	D	0.000000	D	0.83603	0.5290	H	0.97758	4.07	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	0.998;0.999;0.999;0.987;0.997	D	0.88812	0.3292	10	0.87932	D	0	.	20.0173	0.97481	0.0:0.0:1.0:0.0	.	590;590;590;590;590	B7ZLX4;F8W7J9;E9PDX1;E9PCK6;Q9ULJ8	.;.;.;.;NEB1_HUMAN	L	590	ENSP00000405514:R590L;ENSP00000344524:R590L;ENSP00000411342:R590L;ENSP00000398870:R590L;ENSP00000289495:R590L;ENSP00000402893:R590L	ENSP00000289495:R590L	R	+	2	0	PPP1R9A	94665611	1.000000	0.71417	0.992000	0.48379	0.038000	0.13279	9.718000	0.98758	2.814000	0.96858	0.591000	0.81541	CGG	.	.	.	none		0.453	PPP1R9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340662.1	NM_001166160		T	94827675	G	T	94827675	3	4	149	1	0	0	0	0	1	0	0	0	12388	1116	39	4	1787	4	PPP1R9A	7	94827675	Missense_Mutation	SNP	G	TCGA-DW-7837-01A-11D-2136-08		94827675	64310988	13	8876											
DUS4L	11062	hgsc.bcm.edu	37	chr7	107216872	107216872	+	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	aggctgaagcaacaggagttTcatggattacagtccatgga	13	9	12	7	0	1	1	1	1	0	0	2	4	2	4	1	4	3	3	1	4	3	2			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr7:107216872T>A	ENST00000265720.3	+	7	903	c.541T>A	c.(541-543)Tca>Aca	p.S181T	DUS4L_ENST00000402620.1_Missense_Mutation_p.S60T	NM_001270419.1|NM_181581.2	NP_001257348.1|NP_853559.1	O95620	DUS4L_HUMAN	dihydrouridine synthase 4-like (S. cerevisiae)	181							flavin adenine dinucleotide binding (GO:0050660)|tRNA dihydrouridine synthase activity (GO:0017150)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	8						AACAGGAGTTTCATGGATTAC	0.353																																					p.S181T		Atlas-SNP	.											.	DUS4L	27	.	0			c.T541A						PASS	.						81	76	78					7																	107216872		2203	4300	6503	SO:0001583	missense	11062	exon7			GGAGTTTCATGGA	U62767	CCDS5745.1	7q22-q31	2007-12-04			ENSG00000105865	ENSG00000105865			21517	protein-coding gene	gene with protein product	"protein similar to E.coli yhdg and R. capsulatus nifR3"						Standard	NM_181581		Approved	PP35, DUS4	uc031syv.1	O95620	OTTHUMG00000154763	ENST00000265720.3:c.541T>A	chr7.hg19:g.107216872T>A	ENSP00000265720:p.Ser181Thr	69.0	0.0	.		114.0	30.0	.	NM_001270419	B4DLX0|Q2NKK1	Missense_Mutation	SNP	ENST00000265720.3	hg19	CCDS5745.1	.	.	.	.	.	.	.	.	.	.	T	8.361	0.833117	0.16820	.	.	ENSG00000105865	ENST00000265720;ENST00000402620	T;T	0.22539	1.95;1.95	6.01	3.59	0.41128	Aldolase-type TIM barrel (1);	0.166724	0.56097	D	0.000035	T	0.18130	0.0435	L	0.48935	1.535	0.51233	D	0.99991	B;B	0.16396	0.017;0.017	B;B	0.25291	0.059;0.059	T	0.05468	-1.0883	10	0.26408	T	0.33	.	8.1312	0.31029	0.1207:0.0651:0.0:0.8142	.	181;181	A4D0R5;O95620	.;DUS4L_HUMAN	T	181;60	ENSP00000265720:S181T;ENSP00000385274:S60T	ENSP00000265720:S181T	S	+	1	0	DUS4L	107004108	1.000000	0.71417	0.680000	0.29994	0.052000	0.14988	5.909000	0.69923	0.489000	0.27749	-0.297000	0.09499	TCA	.	.	.	none		0.353	DUS4L-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336967.2	NM_181581		A	107216872	T	A	107216872	3	1	149	1	0	0	0	0	1	0	0	0	4810	1783	62	5	559	5	DUS4L	7	107216872	Missense_Mutation	SNP	T	TCGA-DW-7837-01A-11D-2136-08	12389197	107216872	51921791	14	8877											
TRIM24	8805	hgsc.bcm.edu	37	chr7	138145434	138145434	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcggagcgcggcggcgaggcGgcccggctcaacctgttgga	5	5	18	13	7	1	0	1	0	0	0	2	3	1	2	2	7	2	2	2	7	1	1			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr7:138145434G>A	ENST00000343526.4	+	1	356	c.141G>A	c.(139-141)gcG>gcA	p.A47A	TRIM24_ENST00000415680.2_Silent_p.A47A			O15164	TIF1A_HUMAN	tripartite motif containing 24	47					calcium ion homeostasis (GO:0055074)|cellular response to estrogen stimulus (GO:0071391)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of protein stability (GO:0031647)|regulation of signal transduction by p53 class mediator (GO:1901796)|regulation of vitamin D receptor signaling pathway (GO:0070562)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nuclear euchromatin (GO:0005719)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|ligase activity (GO:0016874)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(5)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	40						GCGGCGAGGCGGCCCGGCTCA	0.746																																					p.A47A	Pancreas(179;936 2074 16128 47811 50326)|Colon(136;168 1735 9344 12243 52014)	Atlas-SNP	.											.	TRIM24	131	.	0			c.G141A						PASS	.						5	7	6					7																	138145434		1615	3579	5194	SO:0001819	synonymous_variant	8805	exon1			CGAGGCGGCCCGG	AF009353	CCDS5847.1, CCDS47720.1	7q32-q34	2013-01-28	2011-01-25	2005-06-02	ENSG00000122779	ENSG00000122779		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	11812	protein-coding gene	gene with protein product		603406	"transcriptional intermediary factor 1", "tripartite motif-containing 24"	TIF1		9115274, 9191165	Standard	NM_003852		Approved	hTIF1, Tif1a, RNF82, TIF1A	uc003vuc.3	O15164	OTTHUMG00000155820	ENST00000343526.4:c.141G>A	chr7.hg19:g.138145434G>A		23.0	0.0	.		29.0	12.0	.	NM_003852	A4D1R7|A4D1R8|O95854	Silent	SNP	ENST00000343526.4	hg19	CCDS5847.1																																																																																			.	.	.	none		0.746	TRIM24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341814.1	NM_015905		A	138145434	G	A	138145434	2	1	149	1	0	0	0	0	0	0	0	1	16510	1103	39	1		1	TRIM24	7	138145434	Silent	SNP	G	TCGA-DW-7837-01A-11D-2136-08	30928562	138145434	20993229	15	8878											
CLU	1191	hgsc.bcm.edu	37	chr8	27457323	27457323	+	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	gacccgcagatagtactggtCttcgccttgcgtgaggtttg	6	12	13	10	3	1	2	0	1	1	1	2	3	1	2	2	2	2	3	2	2	2	5			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr8:27457323C>G	ENST00000316403.10	-	7	1543	c.1138G>C	c.(1138-1140)Gac>Cac	p.D380H	CLU_ENST00000405140.3_Missense_Mutation_p.D380H|CLU_ENST00000560366.1_Missense_Mutation_p.D432H|CLU_ENST00000546343.1_Missense_Mutation_p.D391H|CLU_ENST00000523500.1_Missense_Mutation_p.D380H			P10909	CLUS_HUMAN	clusterin	380					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)		TAGTACTGGTCTTCGCCTTGC	0.602																																					p.D380H		Atlas-SNP	.											.	CLU	54	.	0			c.G1138C						PASS	.						71	57	62					8																	27457323		2203	4300	6503	SO:0001583	missense	1191	exon7			ACTGGTCTTCGCC	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.1138G>C	chr8.hg19:g.27457323C>G	ENSP00000315130:p.Asp380His	33.0	0.0	.		27.0	10.0	.	NM_001831	B2R9Q1|B3KSE6|P11380|P11381|Q2TU75|Q5HYC1|Q7Z5B9	Missense_Mutation	SNP	ENST00000316403.10	hg19	CCDS47832.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	17.93|17.93|17.93	3.509052|3.509052|3.509052	0.64410|0.64410|0.64410	.|.|.	.|.|.	ENSG00000120885|ENSG00000120885|ENSG00000120885	ENST00000316403;ENST00000546343;ENST00000405140;ENST00000523500;ENST00000380446;ENST00000520012|ENST00000521770|ENST00000522098	T;T;T|.|.	0.23754|.|.	1.89;1.89;1.89|.|.	5.62|5.62|5.62	3.57|3.57|3.57	0.40892|0.40892|0.40892	Clusterin, C-terminal (1);|.|.	0.252635|.|.	0.44688|.|.	D|.|.	0.000435|.|.	T|T|T	0.55768|0.55768|0.55768	0.1941|0.1941|0.1941	M|M|M	0.81942|0.81942|0.81942	2.565|2.565|2.565	0.19300|0.19300|0.19300	N|N|N	0.999975|0.999975|0.999975	D;D;D;D|.|.	0.89917|.|.	1.0;1.0;1.0;0.99|.|.	D;D;D;D|.|.	0.91635|.|.	0.995;0.999;0.999;0.912|.|.	T|T|T	0.51988|0.51988|0.51988	-0.8635|-0.8635|-0.8635	10|5|5	0.87932|.|.	D|.|.	0|.|.	-20.387|-20.387|-20.387	5.2925|5.2925|5.2925	0.15735|0.15735|0.15735	0.0:0.6574:0.0:0.3426|0.0:0.6574:0.0:0.3426|0.0:0.6574:0.0:0.3426	.|.|.	245;432;391;380|.|.	E7ETA7;P10909-2;P10909-5;P10909|.|.	.;.;.;CLUS_HUMAN|.|.	H|N|T	432;391;380;380;205;245|70|242	ENSP00000446413:D391H;ENSP00000385419:D380H;ENSP00000429620:D380H|.|.	ENSP00000315130:D432H|.|.	D|K|R	-|-|-	1|3|2	0|2|0	CLU|CLU|CLU	27513240|27513240|27513240	0.048000|0.048000|0.048000	0.20356|0.20356|0.20356	0.005000|0.005000|0.005000	0.12908|0.12908|0.12908	0.275000|0.275000|0.275000	0.26752|0.26752|0.26752	1.118000|1.118000|1.118000	0.31246|0.31246|0.31246	1.363000|1.363000|1.363000	0.46019|0.46019|0.46019	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GAC|AAG|AGA	.	.	.	none		0.602	CLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219953.3	NM_001831		G	27457323	C	G	27457323	3	3	149	1	0	0	0	0	1	0	0	0	3570	913	32	4	223	4	CLU	8	27457323	Missense_Mutation	SNP	C	TCGA-DW-7837-01A-11D-2136-08		27457323	118906699	16	8879											
MYST3	7994	hgsc.bcm.edu	37	chr8	41791942	41791942	+	Missense_Mutation	SNP	T	T	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	ctcctccacctcaggctcctTggtttcggtctcaggactat	5	13	8	15	1	2	0	2	0	1	0	7	1	5	1	4	4	0	2	4	4	1	3			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr8:41791942T>G	ENST00000396930.3	-	18	4339	c.3796A>C	c.(3796-3798)Aag>Cag	p.K1266Q	KAT6A_ENST00000265713.2_Missense_Mutation_p.K1266Q|KAT6A_ENST00000406337.1_Missense_Mutation_p.K1266Q	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1266					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)										tcAGGCTCCTTGGTTTCGGTC	0.582																																					p.K1266Q		Atlas-SNP	.											.	.	.	.	0			c.A3796C						PASS	.						70	57	61					8																	41791942		2203	4300	6503	SO:0001583	missense	7994	exon18			GCTCCTTGGTTTC	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.3796A>C	chr8.hg19:g.41791942T>G	ENSP00000380136:p.Lys1266Gln	28.0	0.0	.		12.0	4.0	.	NM_001099412	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	hg19	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	T	5.700	0.313720	0.10789	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930	T;T;T	0.59772	0.24;0.24;0.24	5.95	5.95	0.96441	.	0.067727	0.64402	D	0.000010	T	0.59582	0.2204	L	0.27053	0.805	0.33409	D	0.578344	D	0.71674	0.998	P	0.59115	0.852	T	0.63382	-0.6650	10	0.18710	T	0.47	-26.6212	16.4159	0.83738	0.0:0.0:0.0:1.0	.	1266	Q92794	KAT6A_HUMAN	Q	1266	ENSP00000265713:K1266Q;ENSP00000385888:K1266Q;ENSP00000380136:K1266Q	ENSP00000265713:K1266Q	K	-	1	0	KAT6A	41911099	0.647000	0.27304	0.108000	0.21378	0.021000	0.10359	1.215000	0.32431	2.279000	0.76181	0.533000	0.62120	AAG	.	.	.	none		0.582	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		G	41791942	T	G	41791942	3	3	149	1	0	0	0	0	1	0	0	0	10111	1821	63	5	2222	5	MYST3	8	41791942	Missense_Mutation	SNP	T	TCGA-DW-7837-01A-11D-2136-08	14334619	41791942	104572080	17	8880											
TRPM3	80036	hgsc.bcm.edu	37	chr9	73213442	73213442	+	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	cacgcagtagatgaccctccCgtcactcctgaagggctggt	8	8	11	14	2	1	3	1	2	0	1	3	3	3	3	3	2	0	3	3	2	2	1			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr9:73213442C>A	ENST00000377111.2	-	20	3148	c.2905G>T	c.(2905-2907)Ggg>Tgg	p.G969W	TRPM3_ENST00000377105.1_Missense_Mutation_p.G828W|TRPM3_ENST00000377106.1_Missense_Mutation_p.G841W|TRPM3_ENST00000408909.2_Missense_Mutation_p.G828W|TRPM3_ENST00000377110.3_Missense_Mutation_p.G969W|TRPM3_ENST00000358082.3_Missense_Mutation_p.G831W|TRPM3_ENST00000357533.2_Missense_Mutation_p.G973W|TRPM3_ENST00000396280.5_Missense_Mutation_p.G818W|TRPM3_ENST00000396285.1_Missense_Mutation_p.G816W|TRPM3_ENST00000423814.3_Missense_Mutation_p.G996W|TRPM3_ENST00000360823.2_Missense_Mutation_p.G831W|TRPM3_ENST00000396292.4_Missense_Mutation_p.G841W	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	994					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)	p.G973W(1)|p.G841W(1)|p.G969W(1)		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						ATGACCCTCCCGTCACTCCTG	0.498																																					p.G969W		Atlas-SNP	.											TRPM3_ENST00000423814,colon,carcinoma,0,3	TRPM3	700	.	3	Substitution - Missense(3)	lung(3)	c.G2905T						PASS	.						138	125	129					9																	73213442		2203	4300	6503	SO:0001583	missense	80036	exon20			CCCTCCCGTCACT	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.2905G>T	chr9.hg19:g.73213442C>A	ENSP00000366315:p.Gly969Trp	161.0	1.0	.		169.0	8.0	.	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377111.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.0|24.0	4.478419|4.478419	0.84747|0.84747	.|.	.|.	ENSG00000083067|ENSG00000083067	ENST00000377111;ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814|ENST00000396280	T;T;T;T;T;T;T;T;T;T;T|.	0.74842|.	-0.88;-0.88;-0.88;-0.88;-0.88;-0.88;-0.88;-0.88;-0.88;-0.88;-0.88|.	4.87|4.87	4.87|4.87	0.63330|0.63330	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.86752|0.86752	0.6008|0.6008	M|M	0.93720|0.93720	3.45|3.45	0.58432|0.58432	D|D	0.999994|0.999994	D;P;D;D;D;D;D;D|.	0.89917|.	1.0;0.813;1.0;1.0;0.999;0.999;1.0;0.994|.	D;B;D;D;D;D;D;D|.	0.97110|.	0.987;0.415;1.0;1.0;0.997;0.993;1.0;0.989|.	D|D	0.90516|0.90516	0.4485|0.4485	10|5	0.87932|.	D|.	0|.	-17.254|-17.254	18.3586|18.3586	0.90367|0.90367	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	969;969;959;973;831;828;941;816|.	Q9HCF6-2;Q9HCF6-10;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1;Q9HCF6-8;A2A3F3|.	.;.;.;.;.;.;.;.|.	W|L	969;969;841;831;828;973;828;816;841;831;996|817	ENSP00000366315:G969W;ENSP00000366314:G969W;ENSP00000366310:G841W;ENSP00000354066:G831W;ENSP00000366309:G828W;ENSP00000350140:G973W;ENSP00000386127:G828W;ENSP00000379581:G816W;ENSP00000379587:G841W;ENSP00000350791:G831W;ENSP00000389542:G996W|.	ENSP00000350140:G973W|.	G|R	-|-	1|2	0|0	TRPM3|TRPM3	72403262|72403262	1.000000|1.000000	0.71417|0.71417	0.935000|0.935000	0.37517|0.37517	0.958000|0.958000	0.62258|0.62258	7.479000|7.479000	0.81095|0.81095	2.405000|2.405000	0.81733|0.81733	0.573000|0.573000	0.79308|0.79308	GGG|CGG	.	.	.	none		0.498	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945		A	73213442	C	A	73213442	3	1	149	1	0	0	0	0	1	0	0	0	16599	652	23	4	2242	4	TRPM3	9	73213442	Missense_Mutation	SNP	C	TCGA-DW-7837-01A-11D-2136-08		73213442	67999989	18	8881											
PRPF18	8559	hgsc.bcm.edu	37	chr10	13658431	13658431	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atcttcagatggccattggaAatgcgccttggcccatcggt	8	11	11	11	2	2	1	1	0	1	1	3	2	2	2	3	4	1	0	3	4	1	3			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr10:13658431A>G	ENST00000378572.3	+	9	986	c.826A>G	c.(826-828)Aat>Gat	p.N276D		NM_003675.3	NP_003666.1	Q99633	PRP18_HUMAN	pre-mRNA processing factor 18	276					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						GGCCATTGGAAATGCGCCTTG	0.413																																					p.N276D		Atlas-SNP	.											.	PRPF18	32	.	0			c.A826G						PASS	.						152	141	145					10																	13658431		2203	4300	6503	SO:0001583	missense	8559	exon9			ATTGGAAATGCGC	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.826A>G	chr10.hg19:g.13658431A>G	ENSP00000367835:p.Asn276Asp	153.0	0.0	.		159.0	46.0	.	NM_003675	Q5T9P9|Q9BUI9	Missense_Mutation	SNP	ENST00000378572.3	hg19	CCDS7100.1	.	.	.	.	.	.	.	.	.	.	A	27.0	4.790746	0.90367	.	.	ENSG00000165630	ENST00000378572;ENST00000298451	.	.	.	5.3	5.3	0.74995	Prp18 (3);	0.000000	0.85682	D	0.000000	D	0.86356	0.5913	H	0.94886	3.595	0.80722	D	1	D	0.65815	0.995	D	0.75020	0.985	D	0.90319	0.4343	9	0.87932	D	0	-32.2513	15.2507	0.73542	1.0:0.0:0.0:0.0	.	276	Q99633	PRP18_HUMAN	D	276;38	.	ENSP00000298451:N38D	N	+	1	0	PRPF18	13698437	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.320000	0.96346	2.006000	0.58801	0.528000	0.53228	AAT	.	.	.	none		0.413	PRPF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046879.1			G	13658431	A	G	13658431	3	3	149	1	0	0	0	0	1	0	0	0	12573	14	1	3	860	3	PRPF18	10	13658431	Missense_Mutation	SNP	A	TCGA-DW-7837-01A-11D-2136-08		13658431	121876316	19	8882											
CUBN	8029	hgsc.bcm.edu	37	chr10	16957909	16957910	+	Frame_Shift_Ins	INS	-	-	A																															ttcaaaagagatggtgagatINSagtgtccagagagcccctgg																										TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr10:16957909_16957910insA	ENST00000377833.4	-	46	7185_7186	c.7120_7121insT	c.(7120-7122)tatfs	p.Y2374fs		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2374	CUB 17. {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)	GATGGTGAGATAGTGTCCAGAG	0.436																																					p.Y2374fs		Atlas-INDEL	.											.	CUBN	515	.	0			c.7121_7122insT						PASS	.																																			SO:0001589	frameshift_variant	8029	exon46			.	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.7121dupT	chr10.hg19:g.16957910_16957910dupA	ENSP00000367064:p.Tyr2374fs	128.0	0.0	0		141.0	51.0	0.361702	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Frame_Shift_Ins	INS	ENST00000377833.4	hg19	CCDS7113.1																																																																																			.	.	.	none		0.436	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		A	16957910	-	A	16957909	7	5	149	1	0	1	1	0	0	0	0	0	4053	1406	49	0	3838	0	CUBN	10	16957909	Frame_Shift_Ins	INS	-	TCGA-DW-7837-01A-11D-2136-08	3299478	16957909	118576838	20	8883											
CYP26A1	1592	hgsc.bcm.edu	37	chr10	94834144	94834144	+	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	gttcgggcggcccaccgtacGggtgatgggcgcggacaatg	6	6	18	11	6	0	1	0	1	0	0	1	2	0	2	2	5	1	2	2	5	2	2			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr10:94834144G>T	ENST00000224356.4	+	2	314	c.269G>T	c.(268-270)cGg>cTg	p.R90L	CYP26A1_ENST00000394139.1_Missense_Mutation_p.R21L|CYP26A1_ENST00000371531.1_Missense_Mutation_p.R21L	NM_000783.3	NP_000774.2	O43174	CP26A_HUMAN	cytochrome P450, family 26, subfamily A, polypeptide 1	90					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)	p.R21L(1)		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)	CCCACCGTACGGGTGATGGGC	0.632																																					p.R90L		Atlas-SNP	.											.	CYP26A1	59	.	1	Substitution - Missense(1)	lung(1)	c.G269T						PASS	.						88	93	91					10																	94834144		2203	4300	6503	SO:0001583	missense	1592	exon2			CCGTACGGGTGAT	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.269G>T	chr10.hg19:g.94834144G>T	ENSP00000224356:p.Arg90Leu	285.0	0.0	.		219.0	10.0	.	NM_000783	B3KNI4|Q5VXH9|Q5VXI0	Missense_Mutation	SNP	ENST00000224356.4	hg19	CCDS7426.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.461853	0.84425	.	.	ENSG00000095596	ENST00000371531;ENST00000224356;ENST00000394139	T;T;T	0.65916	-0.18;-0.18;-0.18	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.68201	0.2975	L	0.45228	1.405	0.80722	D	1	P	0.43412	0.806	P	0.53649	0.731	T	0.61792	-0.6990	10	0.25751	T	0.34	-20.5899	18.8725	0.92320	0.0:0.0:1.0:0.0	.	90	O43174	CP26A_HUMAN	L	21;90;21	ENSP00000360586:R21L;ENSP00000224356:R90L;ENSP00000377695:R21L	ENSP00000224356:R90L	R	+	2	0	CYP26A1	94824134	1.000000	0.71417	1.000000	0.80357	0.581000	0.36288	9.187000	0.94912	2.711000	0.92665	0.561000	0.74099	CGG	.	.	.	none		0.632	CYP26A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049408.3			T	94834144	G	T	94834144	3	4	149	1	0	0	0	0	1	0	0	0	4157	1116	39	4	275	4	CYP26A1	10	94834144	Missense_Mutation	SNP	G	TCGA-DW-7837-01A-11D-2136-08	77876235	94834144	40700603	21	8884											
ARHGEF17	9828	hgsc.bcm.edu	37	chr11	73066676	73066676	+	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	gccaaggaggcgaggcctgcCtttctcaagttcctagaggt	8	9	13	11	1	1	1	1	0	1	1	3	3	2	2	4	4	1	1	4	4	3	3			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr11:73066676C>G	ENST00000263674.3	+	4	3902	c.3552C>G	c.(3550-3552)gcC>gcG	p.A1184A	AP002761.1_ENST00000582555.1_RNA	NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	1184	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						CGAGGCCTGCCTTTCTCAAGT	0.557																																					p.A1184A		Atlas-SNP	.											.	ARHGEF17	117	.	0			c.C3552G						PASS	.						92	88	90					11																	73066676		2200	4293	6493	SO:0001819	synonymous_variant	9828	exon4			GCCTGCCTTTCTC	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.3552C>G	chr11.hg19:g.73066676C>G		58.0	0.0	.		77.0	29.0	.	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Silent	SNP	ENST00000263674.3	hg19	CCDS8221.1																																																																																			.	.	.	none		0.557	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		G	73066676	C	G	73066676	2	3	149	1	0	0	0	0	0	0	0	1	900	668	24	4		4	ARHGEF17	11	73066676	Silent	SNP	C	TCGA-DW-7837-01A-11D-2136-08		73066676	61939840	22	8885											
FAT3	120114	hgsc.bcm.edu	37	chr11	92568207	92568207	+	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	cagccaagacgtctacagtgCggttatcagtgaagacgcct	11	8	11	11	3	2	3	1	1	1	2	2	3	2	3	2	1	3	1	2	1	4	2	rs376234071		TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr11:92568207C>G	ENST00000298047.6	+	14	10060	c.10043C>G	c.(10042-10044)gCg>gGg	p.A3348G	FAT3_ENST00000409404.2_Missense_Mutation_p.A3348G|FAT3_ENST00000525166.1_Missense_Mutation_p.A3198G			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3348	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)	p.A3348V(2)		NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GTCTACAGTGCGGTTATCAGT	0.517										TCGA Ovarian(4;0.039)																											p.A3348G		Atlas-SNP	.											FAT3_ENST00000409404,caecum,carcinoma,0,6	FAT3	1822	.	2	Substitution - Missense(2)	endometrium(2)	c.C10043G						PASS	.						53	53	53					11																	92568207		1941	4149	6090	SO:0001583	missense	120114	exon14			ACAGTGCGGTTAT	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.10043C>G	chr11.hg19:g.92568207C>G	ENSP00000298047:p.Ala3348Gly	45.0	0.0	.		41.0	2.0	.	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	C	17.79	3.475779	0.63737	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.54479	0.57;0.57;0.57	5.46	5.46	0.80206	.	.	.	.	.	T	0.66636	0.2809	L	0.46819	1.47	0.80722	D	1	D	0.71674	0.998	D	0.64410	0.925	T	0.66296	-0.5959	9	0.51188	T	0.08	.	19.3231	0.94250	0.0:1.0:0.0:0.0	.	3348	Q8TDW7-3	.	G	3348;3348;3198	ENSP00000298047:A3348G;ENSP00000387040:A3348G;ENSP00000432586:A3198G	ENSP00000298047:A3348G	A	+	2	0	FAT3	92207855	0.998000	0.40836	0.060000	0.19600	0.269000	0.26545	4.891000	0.63185	2.539000	0.85634	0.655000	0.94253	GCG	.	.	.	alt		0.517	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		G	92568207	C	G	92568207	3	3	149	1	0	0	0	0	1	0	0	0	5698	768	27	4	10097	4	FAT3	11	92568207	Missense_Mutation	SNP	C	TCGA-DW-7837-01A-11D-2136-08	19501531	92568207	42438309	23	8886											
R3HDM2	22864	hgsc.bcm.edu	37	chr12	57652719	57652719	+	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	ggtctccaggcttctgccccCgctggtccatgctgtagtat	4	12	11	14	1	2	0	0	0	2	0	4	0	3	0	4	3	2	5	4	3	2	3	rs199873508		TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr12:57652719C>A	ENST00000347140.3	-	20	2603	c.2213G>T	c.(2212-2214)cGg>cTg	p.R738L	R3HDM2_ENST00000546843.1_5'UTR|R3HDM2_ENST00000403821.2_Missense_Mutation_p.R772L|R3HDM2_ENST00000402412.1_Missense_Mutation_p.R752L|R3HDM2_ENST00000441731.2_Missense_Mutation_p.R433L|R3HDM2_ENST00000358907.2_Missense_Mutation_p.R738L|R3HDM2_ENST00000413953.2_Missense_Mutation_p.R465L|RP11-123K3.4_ENST00000548184.1_3'UTR			Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	738						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						CTTCTGCCCCCGCTGGTCCAT	0.567																																					p.R738L		Atlas-SNP	.											.	R3HDM2	125	.	0			c.G2213T						PASS	.						81	75	77					12																	57652719		2203	4300	6503	SO:0001583	missense	22864	exon18			TGCCCCCGCTGGT	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.2213G>T	chr12.hg19:g.57652719C>A	ENSP00000317903:p.Arg738Leu	189.0	0.0	.		193.0	8.0	.	NM_014925	Q2M1T9|Q3ZCT5	Missense_Mutation	SNP	ENST00000347140.3	hg19	CCDS8937.2	.	.	.	.	.	.	.	.	.	.	C	33	5.206223	0.95033	.	.	ENSG00000179912	ENST00000413953;ENST00000393811;ENST00000347140;ENST00000402412;ENST00000358907;ENST00000441731;ENST00000429355;ENST00000403821;ENST00000548161	T;T;T;T;T;T;T;T	0.69561	-0.24;-0.41;0.45;0.5;0.45;-0.34;0.27;0.51	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.79616	0.4476	L	0.58810	1.83	0.51012	D	0.999908	D;D;D;D	0.69078	0.997;0.997;0.993;0.996	D;D;D;D	0.79108	0.987;0.987;0.982;0.992	T	0.79443	-0.1801	10	0.56958	D	0.05	-20.7023	18.0941	0.89483	0.0:1.0:0.0:0.0	.	772;752;738;465	B5MCG9;B5MCU0;Q9Y2K5;E9PAL1	.;.;R3HD2_HUMAN;.	L	465;465;738;752;738;433;503;772;127	ENSP00000409146:R465L;ENSP00000377400:R465L;ENSP00000317903:R738L;ENSP00000385839:R752L;ENSP00000351784:R738L;ENSP00000408536:R433L;ENSP00000394676:R503L;ENSP00000385169:R772L	ENSP00000317903:R738L	R	-	2	0	R3HDM2	55938986	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	5.027000	0.64109	2.885000	0.99019	0.655000	0.94253	CGG	.	C|0.999;T|0.001	.	alt		0.567	R3HDM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326570.2	NM_014925		A	57652719	C	A	57652719	3	1	149	1	0	0	0	0	1	0	0	0	12901	652	23	4	737	4	R3HDM2	12	57652719	Missense_Mutation	SNP	C	TCGA-DW-7837-01A-11D-2136-08		57652719	76199176	24	8887											
CENPJ	55835	hgsc.bcm.edu	37	chr13	25466977	25466977	+	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	cctttcttttcaaatcttccCgtaaatctgctatttgctgt	7	19	4	11	1	4	0	1	0	3	0	5	0	5	0	2	0	2	3	2	0	4	7			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr13:25466977C>A	ENST00000381884.4	-	10	3205	c.3020G>T	c.(3019-3021)cGg>cTg	p.R1007L	CENPJ_ENST00000545981.1_Missense_Mutation_p.R1007L	NM_018451.4	NP_060921.3	Q9HC77	CENPJ_HUMAN	centromere protein J	1007					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)		CAAATCTTCCCGTAAATCTGC	0.348																																					p.R1007L		Atlas-SNP	.											.	CENPJ	116	.	0			c.G3020T						PASS	.						141	138	139					13																	25466977		2203	4300	6503	SO:0001583	missense	55835	exon10			TCTTCCCGTAAAT	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.3020G>T	chr13.hg19:g.25466977C>A	ENSP00000371308:p.Arg1007Leu	146.0	0.0	.		146.0	6.0	.	NM_018451	Q2KHM6|Q5JPD5|Q5T6R5|Q96KS5|Q9C067	Missense_Mutation	SNP	ENST00000381884.4	hg19	CCDS9310.1	.	.	.	.	.	.	.	.	.	.	C	15.17	2.753145	0.49362	.	.	ENSG00000151849	ENST00000381884;ENST00000545981;ENST00000445729	T;T	0.35973	1.28;1.86	5.22	2.78	0.32641	.	0.113214	0.64402	D	0.000008	T	0.23330	0.0564	N	0.19112	0.55	0.32091	N	0.591866	B;B	0.25563	0.129;0.0	B;B	0.25614	0.062;0.0	T	0.18618	-1.0331	10	0.66056	D	0.02	.	9.9179	0.41446	0.0:0.1055:0.0:0.8945	.	88;1007	Q5T6R6;Q9HC77	.;CENPJ_HUMAN	L	1007	ENSP00000371308:R1007L;ENSP00000441090:R1007L	ENSP00000371308:R1007L	R	-	2	0	CENPJ	24364977	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.540000	0.60664	0.381000	0.24851	-0.263000	0.10527	CGG	.	.	.	none		0.348	CENPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044209.1	NM_018451		A	25466977	C	A	25466977	3	1	149	1	0	0	0	0	1	0	0	0	3236	652	23	4	1028	4	CENPJ	13	25466977	Missense_Mutation	SNP	C	TCGA-DW-7837-01A-11D-2136-08		25466977	89702901	25	8888											
KCNH5	27133	hgsc.bcm.edu	37	chr14	63483656	63483656	+	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	tccacaatctgggcatttccCagtaagaaacttgattctga	12	12	7	10	0	2	3	0	2	2	1	4	3	4	3	2	1	1	2	2	1	3	4			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr14:63483656C>G	ENST00000322893.7	-	2	358	c.90G>C	c.(88-90)ctG>ctC	p.L30L	KCNH5_ENST00000394968.1_5'UTR|KCNH5_ENST00000394964.2_5'UTR|KCNH5_ENST00000420622.2_Silent_p.L30L	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	30	PAS.				potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		GGGCATTTCCCAGTAAGAAAC	0.363																																					p.L30L		Atlas-SNP	.											.	KCNH5	320	.	0			c.G90C						PASS	.						85	80	82					14																	63483656		2203	4299	6502	SO:0001819	synonymous_variant	27133	exon2			ATTTCCCAGTAAG	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.90G>C	chr14.hg19:g.63483656C>G		99.0	0.0	.		121.0	5.0	.	NM_172375	C9JP98	Silent	SNP	ENST00000322893.7	hg19	CCDS9756.1																																																																																			.	.	.	none		0.363	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		G	63483656	C	G	63483656	2	3	149	1	0	0	0	0	0	0	0	1	8042	581	21	4		4	KCNH5	14	63483656	Silent	SNP	C	TCGA-DW-7837-01A-11D-2136-08		63483656	43865884	26	8889											
OR4N4	283694	hgsc.bcm.edu	37	chr15	22383017	22383017	+	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	caacttcttctgtgatgtccGacaggtcatcaagctggctt	8	13	9	11	1	4	1	2	1	2	0	5	2	5	1	1	2	2	2	1	2	2	3	rs150038016	byFrequency	TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr15:22383017G>C	ENST00000328795.4	+	1	636	c.545G>C	c.(544-546)cGa>cCa	p.R182P	RP11-69H14.6_ENST00000558896.1_RNA	NM_001005241.2	NP_001005241.2	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N, member 4	182						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|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)		TGTGATGTCCGACAGGTCATC	0.527																																					p.R182P		Atlas-SNP	.											OR4N4,NS,carcinoma,+1,1	OR4N4	108	.	0			c.G545C						PASS	.						96	79	84					15																	22383017		2189	4257	6446	SO:0001583	missense	283694	exon1			ATGTCCGACAGGT	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.545G>C	chr15.hg19:g.22383017G>C	ENSP00000332500:p.Arg182Pro	155.0	2.0	.		182.0	8.0	.	NM_001005241	Q6IEY3|Q6IF56	Missense_Mutation	SNP	ENST00000328795.4	hg19	CCDS32173.1	.	.	.	.	.	.	.	.	.	.	.	0.004	-2.362066	0.00214	.	.	ENSG00000183706	ENST00000328795	T	0.00026	8.94	3.37	3.37	0.38596	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48767	N	0.000173	T	0.00039	0.0001	N	0.00014	-2.915	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30563	-0.9974	10	0.09084	T	0.74	-0.3003	6.2571	0.20879	0.2138:0.5784:0.2077:0.0	.	182	Q8N0Y3	OR4N4_HUMAN	P	182	ENSP00000332500:R182P	ENSP00000332500:R182P	R	+	2	0	OR4N4	19884381	0.000000	0.05858	0.995000	0.50966	0.462000	0.32619	-0.407000	0.07178	0.750000	0.32877	-0.499000	0.04595	CGA	.	G|0.999;A|0.001	.	alt		0.527	OR4N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414922.1			C	22383017	G	C	22383017	3	2	149	1	0	0	0	0	1	0	0	0	11085	1058	37	4	547	4	OR4N4	15	22383017	Missense_Mutation	SNP	G	TCGA-DW-7837-01A-11D-2136-08		22383017	80148375	27	8890											
RAB11A	8766	hgsc.bcm.edu	37	chr15	66180113	66180113	+	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	tgtctccaagcaacaatgtgGttcctattcatgttccacca	10	13	6	12	0	2	0	1	0	1	0	5	0	4	0	4	1	2	3	4	1	4	4			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr15:66180113G>C	ENST00000261890.2	+	5	714	c.586G>C	c.(586-588)Gtt>Ctt	p.V196L	RAB11A_ENST00000569896.1_3'UTR|RAB11A_ENST00000564910.1_Missense_Mutation_p.V126L|RAB11A_ENST00000565075.1_Missense_Mutation_p.V178L	NM_001206836.1|NM_004663.4	NP_001193765.1|NP_004654.1	P62491	RB11A_HUMAN	RAB11A, member RAS oncogene family	196					cytokinesis (GO:0000910)|establishment of protein localization to membrane (GO:0090150)|exosomal secretion (GO:1990182)|GTP catabolic process (GO:0006184)|melanosome transport (GO:0032402)|multivesicular body assembly (GO:0036258)|neuron projection development (GO:0031175)|plasma membrane to endosome transport (GO:0048227)|positive regulation of axon extension (GO:0045773)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of multivesicular body size (GO:0010796)|regulation of protein transport (GO:0051223)|small GTPase mediated signal transduction (GO:0007264)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	axon (GO:0030424)|cleavage furrow (GO:0032154)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|multivesicular body (GO:0005771)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)|syntaxin binding (GO:0019905)			kidney(1)|large_intestine(2)|lung(1)|prostate(1)	5						CAACAATGTGGTTCCTATTCA	0.428																																					p.V196L		Atlas-SNP	.											.	RAB11A	14	.	0			c.G586C						PASS	.						137	123	128					15																	66180113		2201	4299	6500	SO:0001583	missense	8766	exon5			AATGTGGTTCCTA	X56740	CCDS10212.1, CCDS58373.1	15q22.31	2008-05-14			ENSG00000103769	ENSG00000103769		"RAB, member RAS oncogene"	9760	protein-coding gene	gene with protein product		605570				1704119, 9662449	Standard	NM_004663		Approved	YL8	uc002apk.3	P62491	OTTHUMG00000133162	ENST00000261890.2:c.586G>C	chr15.hg19:g.66180113G>C	ENSP00000261890:p.Val196Leu	122.0	0.0	.		130.0	15.0	.	NM_004663	B2R4B6|B4DT13|P24410|Q5TZN9|Q9JLX1	Missense_Mutation	SNP	ENST00000261890.2	hg19	CCDS10212.1	.	.	.	.	.	.	.	.	.	.	G	15.27	2.783421	0.49891	.	.	ENSG00000103769	ENST00000261890	T	0.63744	-0.06	5.45	5.45	0.79879	.	0.056657	0.64402	D	0.000001	T	0.45316	0.1336	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.29397	-1.0013	10	0.29301	T	0.29	.	19.3	0.94140	0.0:0.0:1.0:0.0	.	196	P62491	RB11A_HUMAN	L	196	ENSP00000261890:V196L	ENSP00000261890:V196L	V	+	1	0	RAB11A	63967167	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.547000	0.85894	0.655000	0.94253	GTT	.	.	.	none		0.428	RAB11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256864.1			C	66180113	G	C	66180113	3	2	149	1	0	0	0	0	1	0	0	0	12904	1261	44	4	604	4	RAB11A	15	66180113	Missense_Mutation	SNP	G	TCGA-DW-7837-01A-11D-2136-08	43797096	66180113	36351279	28	8891											
RSPRY1	89970	hgsc.bcm.edu	37	chr16	57265132	57265132	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atatcaacaatgtgagttcaAttttggagcaaaaccattca	16	12	6	7	0	3	1	3	1	0	0	3	2	3	2	1	1	3	2	1	1	6	5	rs368309991		TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr16:57265132A>G	ENST00000537866.1	+	13	2303	c.1430A>G	c.(1429-1431)aAt>aGt	p.N477S	RSPRY1_ENST00000394420.4_Missense_Mutation_p.N477S|RSPRY1_ENST00000563073.1_3'UTR			Q96DX4	RSPRY_HUMAN	ring finger and SPRY domain containing 1	477	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					extracellular region (GO:0005576)	zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|urinary_tract(3)	27						TGTGAGTTCAATTTTGGAGCA	0.333																																					p.N477S		Atlas-SNP	.											.	RSPRY1	49	.	0			c.A1430G						PASS	.	A	SER/ASN	1,4395	2.1+/-5.4	0,1,2197	108	104	105		1430	5.8	1	16		105	0,8600		0,0,4300	no	missense	RSPRY1	NM_133368.1	46	0,1,6497	GG,GA,AA		0.0,0.0227,0.0077	probably-damaging	477/577	57265132	1,12995	2198	4300	6498	SO:0001583	missense	89970	exon13			AGTTCAATTTTGG	AB075852	CCDS10775.1	16q13	2014-02-12			ENSG00000159579	ENSG00000159579		"RING-type (C3HC4) zinc fingers"	29420	protein-coding gene	gene with protein product						11853319	Standard	NM_133368		Approved	KIAA1972	uc002elb.3	Q96DX4	OTTHUMG00000133462	ENST00000537866.1:c.1430A>G	chr16.hg19:g.57265132A>G	ENSP00000443176:p.Asn477Ser	72.0	0.0	.		89.0	27.0	.	NM_133368	Q6UX21|Q8ND53	Missense_Mutation	SNP	ENST00000537866.1	hg19	CCDS10775.1	.	.	.	.	.	.	.	.	.	.	A	27.8	4.863491	0.91511	2.27E-4	0.0	ENSG00000159579	ENST00000394420;ENST00000537866	T;T	0.75704	-0.96;-0.96	5.78	5.78	0.91487	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.85682	D	0.000000	D	0.89777	0.6813	M	0.93197	3.39	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92360	0.5896	10	0.87932	D	0	.	16.1167	0.81309	1.0:0.0:0.0:0.0	.	477	Q96DX4	RSPRY_HUMAN	S	477	ENSP00000377942:N477S;ENSP00000443176:N477S	ENSP00000377942:N477S	N	+	2	0	RSPRY1	55822633	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.204000	0.70986	0.528000	0.53228	AAT	.	.	.	weak		0.333	RSPRY1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432953.1	NM_133368		G	57265132	A	G	57265132	3	3	149	1	0	0	0	0	1	0	0	0	13726	101	4	3	1476	3	RSPRY1	16	57265132	Missense_Mutation	SNP	A	TCGA-DW-7837-01A-11D-2136-08		57265132	33089621	29	8892											
FAM57A	79850	hgsc.bcm.edu	37	chr17	643752	643752	+	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	tcgtcatccgcagaggctccGgggagaccttggggacttct	6	9	14	12	3	2	2	1	0	1	2	5	4	4	3	3	5	0	2	3	5	0	2			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr17:643752G>T	ENST00000308278.8	+	4	652	c.416G>T	c.(415-417)cGg>cTg	p.R139L	FAM57A_ENST00000572018.1_Intron|FAM57A_ENST00000301324.8_Intron	NM_024792.1	NP_079068.1	Q8TBR7	FA57A_HUMAN	family with sequence similarity 57, member A	139	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(2)|large_intestine(1)|lung(2)|prostate(2)|urinary_tract(2)	10				UCEC - Uterine corpus endometrioid carcinoma (25;0.0217)		CAGAGGCTCCGGGGAGACCTT	0.512																																					p.R139L		Atlas-SNP	.											.	FAM57A	17	.	0			c.G416T						PASS	.						103	100	101					17																	643752		2203	4300	6503	SO:0001583	missense	79850	exon4			GGCTCCGGGGAGA	AK025935	CCDS10996.1	17p13.3	2014-08-14				ENSG00000167695			29646	protein-coding gene	gene with protein product		611627				12270127	Standard	NM_024792		Approved	FLJ22282, CT120	uc002frp.3	Q8TBR7		ENST00000308278.8:c.416G>T	chr17.hg19:g.643752G>T	ENSP00000312017:p.Arg139Leu	141.0	0.0	.		188.0	8.0	.	NM_024792	A8K7Q0|Q7Z464|Q96D97|Q9H6H3	Missense_Mutation	SNP	ENST00000308278.8	hg19	CCDS10996.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.780072	0.90195	.	.	ENSG00000167695	ENST00000308278;ENST00000451373	.	.	.	6.17	6.17	0.99709	TRAM/LAG1/CLN8 homology domain (3);	0.043459	0.85682	D	0.000000	D	0.83949	0.5365	M	0.88775	2.98	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79320	-0.1852	9	0.11182	T	0.66	-23.056	19.8676	0.96824	0.0:0.0:1.0:0.0	.	139	Q8TBR7	FA57A_HUMAN	L	139;212	.	ENSP00000312017:R139L	R	+	2	0	FAM57A	590502	1.000000	0.71417	0.989000	0.46669	0.242000	0.25591	9.718000	0.98758	2.941000	0.99782	0.655000	0.94253	CGG	.	.	.	none		0.512	FAM57A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437155.2	NM_024792		T	643752	G	T	643752	3	4	149	1	0	0	0	0	1	0	0	0	5595	1116	39	4	430	4	FAM57A	17	643752	Missense_Mutation	SNP	G	TCGA-DW-7837-01A-11D-2136-08		643752	80551458	30	8893											
PER1	5187	hgsc.bcm.edu	37	chr17	8045244	8045244	+	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	gcatggctcggagccgctccCgatcctgcttcagcacagag	7	7	12	15	3	1	1	1	0	0	1	4	3	3	2	3	2	3	5	3	2	0	1	rs373929413		TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr17:8045244C>A	ENST00000317276.4	-	22	3716	c.3479G>T	c.(3478-3480)cGg>cTg	p.R1160L	PER1_ENST00000581082.1_Missense_Mutation_p.R1137L|PER1_ENST00000578089.1_5'Flank	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	1160	CRY binding domain. {ECO:0000250}.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)	p.R1160L(1)		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						GAGCCGCTCCCGATCCTGCTT	0.632			T	ETV6	"AML, CMML"			Other conserved DNA damage response genes																													p.R1160L		Atlas-SNP	.		Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	.	PER1	104	.	1	Substitution - Missense(1)	lung(1)	c.G3479T						PASS	.						50	54	53					17																	8045244		2203	4300	6503	SO:0001583	missense	5187	exon22			CGCTCCCGATCCT	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.3479G>T	chr17.hg19:g.8045244C>A	ENSP00000314420:p.Arg1160Leu	118.0	0.0	.		142.0	6.0	.	NM_002616	B2RPA8|B4DI49|D3DTR3	Missense_Mutation	SNP	ENST00000317276.4	hg19	CCDS11131.1	.	.	.	.	.	.	.	.	.	.	C	32	5.155795	0.94686	.	.	ENSG00000179094	ENST00000317276	T	0.14022	2.54	5.67	4.64	0.57946	Period circadian-like, C-terminal (1);	0.066928	0.64402	D	0.000009	T	0.16085	0.0387	L	0.28649	0.875	0.80722	D	1	D;P	0.58268	0.982;0.951	P;B	0.51516	0.672;0.429	T	0.01013	-1.1481	10	0.33141	T	0.24	-21.4261	13.1256	0.59354	0.1607:0.8393:0.0:0.0	.	1151;1160	A2I2P6;O15534	.;PER1_HUMAN	L	1160	ENSP00000314420:R1160L	ENSP00000314420:R1160L	R	-	2	0	PER1	7985969	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.309000	0.43699	2.697000	0.92050	0.655000	0.94253	CGG	.	.	.	alt		0.632	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2			A	8045244	C	A	8045244	3	1	149	1	0	0	0	0	1	0	0	0	11736	652	23	4	401	4	PER1	17	8045244	Missense_Mutation	SNP	C	TCGA-DW-7837-01A-11D-2136-08	7401492	8045244	73149966	31	8894											
NCOR1	9611	hgsc.bcm.edu	37	chr17	15935762	15935762	+	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	tggagtactgctgagcatccGcatagtcagagggttataag	11	10	13	7	1	1	2	1	1	0	1	2	3	2	3	1	2	3	5	1	2	4	4			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr17:15935762G>C	ENST00000268712.3	-	46	7428	c.7171C>G	c.(7171-7173)Cgg>Ggg	p.R2391G	NCOR1_ENST00000395851.1_Missense_Mutation_p.R2288G|NCOR1_ENST00000395857.3_Missense_Mutation_p.R975G	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	2391	Interaction with C1D. {ECO:0000250}.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)	p.R2391W(1)		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)		CTGAGCATCCGCATAGTCAGA	0.468																																					p.R2391G		Atlas-SNP	.											NCOR1,colon,carcinoma,+1,1	NCOR1	240	.	1	Substitution - Missense(1)	prostate(1)	c.C7171G						PASS	.						117	106	110					17																	15935762		2203	4300	6503	SO:0001583	missense	9611	exon46			GCATCCGCATAGT	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.7171C>G	chr17.hg19:g.15935762G>C	ENSP00000268712:p.Arg2391Gly	139.0	0.0	.		214.0	41.0	.	NM_006311	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	hg19	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	G	14.64	2.596051	0.46318	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849;ENST00000395857	T;T;T	0.61040	0.14;0.75;0.25	5.96	3.9	0.45041	.	0.048575	0.85682	D	0.000000	T	0.53367	0.1792	L	0.60455	1.87	0.58432	D	0.999992	B;B;B;B;B	0.29341	0.036;0.013;0.242;0.132;0.06	B;B;B;B;B	0.31614	0.022;0.01;0.133;0.089;0.05	T	0.52990	-0.8501	10	0.56958	D	0.05	-9.7742	10.6076	0.45402	0.0:0.1166:0.4874:0.3961	.	2294;2391;2288;910;404	E7EVK1;O75376;O75376-2;Q86YY1;Q86YY2	.;NCOR1_HUMAN;.;.;.	G	2391;2288;2294;975	ENSP00000268712:R2391G;ENSP00000379192:R2288G;ENSP00000379198:R975G	ENSP00000268712:R2391G	R	-	1	2	NCOR1	15876487	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.109000	0.50345	0.780000	0.33566	-0.181000	0.13052	CGG	.	.	.	none		0.468	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		C	15935762	G	C	15935762	3	2	149	1	0	0	0	0	1	0	0	0	10242	1086	38	4	155	4	NCOR1	17	15935762	Missense_Mutation	SNP	G	TCGA-DW-7837-01A-11D-2136-08	7890518	15935762	65259448	32	8895											
RND2	8153	hgsc.bcm.edu	37	chr17	41180521	41180521	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccggtcctctgagcgcagcGtcagggatgtcttccatgtg	5	10	13	13	3	3	1	1	1	2	0	5	2	5	2	3	2	2	1	3	2	0	1			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr17:41180521G>A	ENST00000587250.2	+	5	615	c.508G>A	c.(508-510)Gtc>Atc	p.V170I	RND2_ENST00000544533.1_Missense_Mutation_p.V171I|CTD-3199J23.4_ENST00000225973.5_lincRNA			P52198	RND2_HUMAN	Rho family GTPase 2	170					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)		TGAGCGCAGCGTCAGGGATGT	0.622																																					p.V170I		Atlas-SNP	.											.	RND2	10	.	0			c.G508A						PASS	.						67	63	65					17																	41180521		2203	4300	6503	SO:0001583	missense	8153	exon5			CGCAGCGTCAGGG	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	ENST00000587250.2:c.508G>A	chr17.hg19:g.41180521G>A	ENSP00000466680:p.Val170Ile	112.0	0.0	.		113.0	30.0	.	NM_005440	A8K2D4|O00690|O00734|Q5U0P6|Q99535	Missense_Mutation	SNP	ENST00000587250.2	hg19	CCDS11452.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.941209	0.92526	.	.	ENSG00000108830	ENST00000544533;ENST00000225973	T	0.80653	-1.4	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.81621	0.4861	L	0.36672	1.1	0.80722	D	1	P	0.41643	0.758	P	0.48704	0.587	T	0.82420	-0.0466	10	0.66056	D	0.02	.	19.2909	0.94098	0.0:0.0:1.0:0.0	.	170	P52198	RND2_HUMAN	I	171;170	ENSP00000439328:V171I	ENSP00000225973:V170I	V	+	1	0	RND2	38434047	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.623000	0.98386	2.894000	0.99253	0.655000	0.94253	GTC	.	.	.	none		0.622	RND2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453111.2	NM_005440		A	41180521	G	A	41180521	3	1	149	1	0	0	0	0	1	0	0	0	13433	1145	40	1	526	1	RND2	17	41180521	Missense_Mutation	SNP	G	TCGA-DW-7837-01A-11D-2136-08	25244759	41180521	40014689	33	8896											
EVPL	2125	hgsc.bcm.edu	37	chr17	74005355	74005355	+	Missense_Mutation	SNP	T	T	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	cacctccttgctcaccgtctTggtctccaccttggcccgct	3	12	7	19	2	3	0	1	0	2	0	5	0	4	0	6	2	1	2	6	2	0	3			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr17:74005355T>G	ENST00000301607.3	-	22	4184	c.3931A>C	c.(3931-3933)Aag>Cag	p.K1311Q	EVPL_ENST00000586740.1_Missense_Mutation_p.K1333Q	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1311	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						CTCACCGTCTTGGTCTCCACC	0.682																																					p.K1311Q		Atlas-SNP	.											.	EVPL	155	.	0			c.A3931C						PASS	.						105	114	111					17																	74005355		2202	4300	6502	SO:0001583	missense	2125	exon22			CCGTCTTGGTCTC	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.3931A>C	chr17.hg19:g.74005355T>G	ENSP00000301607:p.Lys1311Gln	451.0	0.0	.		432.0	94.0	.	NM_001988	A0AUV5	Missense_Mutation	SNP	ENST00000301607.3	hg19	CCDS11737.1	.	.	.	.	.	.	.	.	.	.	T	11.83	1.755797	0.31046	.	.	ENSG00000167880	ENST00000301607	T	0.56611	0.45	5.41	4.32	0.51571	.	0.092795	0.64402	D	0.000001	T	0.53384	0.1793	M	0.75777	2.31	0.37299	D	0.908594	P;B	0.39759	0.687;0.142	B;B	0.37731	0.257;0.048	T	0.63479	-0.6628	10	0.72032	D	0.01	-43.3057	12.5545	0.56246	0.0:0.0:0.1392:0.8608	.	1333;1311	B7ZLH8;Q92817	.;EVPL_HUMAN	Q	1311	ENSP00000301607:K1311Q	ENSP00000301607:K1311Q	K	-	1	0	EVPL	71516950	1.000000	0.71417	1.000000	0.80357	0.581000	0.36288	2.654000	0.46699	0.875000	0.35847	0.459000	0.35465	AAG	.	.	.	none		0.682	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988		G	74005355	T	G	74005355	3	3	149	1	0	0	0	0	1	0	0	0	5294	1821	63	5	2174	5	EVPL	17	74005355	Missense_Mutation	SNP	T	TCGA-DW-7837-01A-11D-2136-08	32824834	74005355	7189855	34	8897											
GPR32	2854	hgsc.bcm.edu	37	chr19	51274070	51274070	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgtggatgactgtcttccgTatggcacgcacggtctccac	6	11	11	13	3	2	1	0	1	2	0	4	2	3	2	2	3	0	3	2	3	1	2			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr19:51274070T>C	ENST00000270590.4	+	1	350	c.213T>C	c.(211-213)cgT>cgC	p.R71R		NM_001506.1	NP_001497.1	O75388	GPR32_HUMAN	G protein-coupled receptor 32	71					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(4)|endometrium(4)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	29		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		CTGTCTTCCGTATGGCACGCA	0.572																																					p.R71R	Esophageal Squamous(113;152 1581 5732 15840 44398)	Atlas-SNP	.											.	GPR32	68	.	0			c.T213C						PASS	.						225	169	188					19																	51274070		2203	4300	6503	SO:0001819	synonymous_variant	2854	exon1			CTTCCGTATGGCA	AF045764	CCDS12801.1	19q13.33	2012-08-20			ENSG00000142511	ENSG00000142511		"GPCR / Class A : Resolvin receptors"	4487	protein-coding gene	gene with protein product	"resolvin D1 receptor"	603195				9653656	Standard	NM_001506		Approved	RVDR1	uc010ycf.3	O75388		ENST00000270590.4:c.213T>C	chr19.hg19:g.51274070T>C		101.0	0.0	.		74.0	4.0	.	NM_001506	Q502U7|Q6NWS5	Silent	SNP	ENST00000270590.4	hg19	CCDS12801.1																																																																																			.	.	.	none		0.572	GPR32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465016.1			C	51274070	T	C	51274070	2	2	149	1	0	0	0	0	0	0	0	1	6695	1625	57	3		3	GPR32	19	51274070	Silent	SNP	T	TCGA-DW-7837-01A-11D-2136-08		51274070	7854913	35	8898											
NLRP5	126206	hgsc.bcm.edu	37	chr19	56539072	56539072	+	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	gacgtggtgggggagagcgtCgcccccttcaaccaaacgct	8	6	14	13	4	1	1	1	0	0	1	2	3	1	1	3	3	3	1	3	3	2	1			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr19:56539072C>T	ENST00000390649.3	+	7	1473	c.1473C>T	c.(1471-1473)gtC>gtT	p.V491V		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	491	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)		GGGAGAGCGTCGCCCCCTTCA	0.632																																					p.V491V		Atlas-SNP	.											.	NLRP5	217	.	0			c.C1473T						PASS	.						31	34	33					19																	56539072		2140	4237	6377	SO:0001819	synonymous_variant	126206	exon7			GAGCGTCGCCCCC	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.1473C>T	chr19.hg19:g.56539072C>T		49.0	0.0	.		56.0	25.0	.	NM_153447	A8MTY4|Q86W29	Silent	SNP	ENST00000390649.3	hg19	CCDS12938.1																																																																																			.	.	.	none		0.632	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447		T	56539072	C	T	56539072	2	4	149	1	0	0	0	0	0	0	0	1	10487	871	31	1		1	NLRP5	19	56539072	Silent	SNP	C	TCGA-DW-7837-01A-11D-2136-08	5265002	56539072	2589911	36	8899											
TRPC4AP	26133	hgsc.bcm.edu	37	chr20	33591257	33591257	+	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	gtccttgtgcaggtagtgctGctgccagaagcgcagcaggt	7	9	15	10	1	0	1	0	0	0	1	1	1	1	1	2	2	6	6	2	2	2	2			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr20:33591257G>T	ENST00000252015.2	-	18	2301	c.2212C>A	c.(2212-2214)Cag>Aag	p.Q738K	TRPC4AP_ENST00000432634.2_Missense_Mutation_p.Q699K|TRPC4AP_ENST00000451813.2_Missense_Mutation_p.Q730K|TRPC4AP_ENST00000539834.1_Missense_Mutation_p.Q340K			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein	738					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)			AGGTAGTGCTGCTGCCAGAAG	0.632																																					p.Q738K		Atlas-SNP	.											.	TRPC4AP	64	.	0			c.C2212A						PASS	.						59	59	59					20																	33591257		2203	4300	6503	SO:0001583	missense	26133	exon18			AGTGCTGCTGCCA	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.2212C>A	chr20.hg19:g.33591257G>T	ENSP00000252015:p.Gln738Lys	129.0	0.0	.		126.0	36.0	.	NM_015638	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Missense_Mutation	SNP	ENST00000252015.2	hg19	CCDS13246.1	.	.	.	.	.	.	.	.	.	.	G	6.251	0.414503	0.11870	.	.	ENSG00000100991	ENST00000252015;ENST00000451813;ENST00000539834;ENST00000432634;ENST00000541994	.	.	.	4.65	4.65	0.58169	.	0.189321	0.48767	D	0.000179	T	0.51517	0.1679	L	0.36672	1.1	0.50632	D	0.999882	B;B;B	0.20164	0.042;0.042;0.042	B;B;B	0.16289	0.015;0.015;0.015	T	0.47586	-0.9106	9	0.12766	T	0.61	.	17.7234	0.88358	0.0:0.0:1.0:0.0	.	699;730;738	B4E0Q1;E1P5Q0;Q8TEL6	.;.;TP4AP_HUMAN	K	738;730;340;699;723	.	ENSP00000252015:Q738K	Q	-	1	0	TRPC4AP	33054918	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.652000	0.83633	2.398000	0.81561	0.462000	0.41574	CAG	.	.	.	none		0.632	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638		T	33591257	G	T	33591257	3	4	149	1	0	0	0	0	1	0	0	0	16593	1328	46	4	189	4	TRPC4AP	20	33591257	Missense_Mutation	SNP	G	TCGA-DW-7837-01A-11D-2136-08		33591257	29434263	37	8900											
KCNQ2	3785	hgsc.bcm.edu	37	chr20	62078166	62078166	+	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	gtggaaaacacagacagcacGaggcaggagaaaaccaggag	18	1	14	8	1	0	2	0	0	0	2	0	6	0	4	1	4	3	2	1	4	4	0			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chr20:62078166G>C	ENST00000359125.2	-	2	495	c.321C>G	c.(319-321)ctC>ctG	p.L107L	KCNQ2_ENST00000344462.4_Silent_p.L107L|RP11-358D14.2_ENST00000436263.1_RNA|KCNQ2_ENST00000359689.1_Silent_p.L107L|KCNQ2_ENST00000344425.5_Silent_p.L107L|KCNQ2_ENST00000354587.3_Silent_p.L107L|KCNQ2_ENST00000360480.3_Silent_p.L107L|KCNQ2_ENST00000357249.2_Silent_p.L107L|KCNQ2_ENST00000370224.1_Silent_p.L107L	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	107					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)	CAGACAGCACGAGGCAGGAGA	0.632																																					p.L107L		Atlas-SNP	.											.	KCNQ2	201	.	0			c.C321G						PASS	.						85	80	82					20																	62078166		2203	4300	6503	SO:0001819	synonymous_variant	3785	exon2			CAGCACGAGGCAG	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.321C>G	chr20.hg19:g.62078166G>C		202.0	0.0	.		172.0	51.0	.	NM_172106	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Silent	SNP	ENST00000359125.2	hg19	CCDS13520.1																																																																																			.	.	.	none		0.632	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109		C	62078166	G	C	62078166	2	2	149	1	0	0	0	0	0	0	0	1	8090	1045	37	4		4	KCNQ2	20	62078166	Silent	SNP	G	TCGA-DW-7837-01A-11D-2136-08	28486909	62078166	947354	38	8901											
RPS6KA3	6197	hgsc.bcm.edu	37	chrX	20195138	20195138	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgtttgcaggatttcgctTgaaaagcattcgtaaaagac	12	13	9	7	2	1	2	0	1	1	1	3	3	1	3	0	1	2	5	0	1	4	5			TCGA-DW-7837-01A-11D-2136-08	TCGA-DW-7837-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ec9b4fb0-c3b1-4a2b-a3e7-393b27f961da	5a082628-cf8e-4550-812a-28faf2a1735e	g.chrX:20195138T>C	ENST00000379565.3	-	11	1117	c.910A>G	c.(910-912)Aag>Gag	p.K304E	RPS6KA3_ENST00000540702.1_Missense_Mutation_p.K276E|RPS6KA3_ENST00000544447.1_Missense_Mutation_p.K276E|RPS6KA3_ENST00000379548.4_Missense_Mutation_p.K275E	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	304	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	GGATTTCGCTTGAAAAGCATT	0.318																																					p.K304E		Atlas-SNP	.											.	RPS6KA3	110	.	0			c.A910G						PASS	.						60	62	61					X																	20195138		2203	4300	6503	SO:0001583	missense	6197	exon11			TTCGCTTGAAAAG	U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"ribosomal protein S6 kinase, 90kD, polypeptide 3", "mental retardation, X-linked 19", "Coffin-Lowry syndrome"	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.910A>G	chrX.hg19:g.20195138T>C	ENSP00000368884:p.Lys304Glu	39.0	0.0	.		68.0	4.0	.	NM_004586	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Missense_Mutation	SNP	ENST00000379565.3	hg19	CCDS14197.1	.	.	.	.	.	.	.	.	.	.	T	16.85	3.237629	0.58886	.	.	ENSG00000177189	ENST00000379565;ENST00000544447;ENST00000379548;ENST00000540702	T;T;T;T	0.52754	0.65;0.65;0.65;0.65	5.64	5.64	0.86602	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	0.39091	0.1065	N	0.01817	-0.705	0.80722	D	1	B;B;P;B	0.52842	0.17;0.165;0.956;0.198	B;B;P;B	0.59546	0.134;0.034;0.859;0.084	T	0.55418	-0.8144	10	0.37606	T	0.19	.	14.8754	0.70491	0.0:0.0:0.0:1.0	.	276;275;276;304	B4DG22;F5GYC4;B7ZB17;P51812	.;.;.;KS6A3_HUMAN	E	304;276;275;276	ENSP00000368884:K304E;ENSP00000440220:K276E;ENSP00000368865:K275E;ENSP00000444837:K276E	ENSP00000368865:K275E	K	-	1	0	RPS6KA3	20105059	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.215000	0.72206	1.894000	0.54839	0.417000	0.27973	AAG	.	.	.	none		0.318	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586		C	20195138	T	C	20195138	3	2	149	1	0	0	0	0	1	0	0	0	13665	1821	63	3	1360	3	RPS6KA3	23	20195138	Missense_Mutation	SNP	T	TCGA-DW-7837-01A-11D-2136-08		20195138	135075422	39	8902											
TRIM63	84676	hgsc.bcm.edu	37	chr1	26386776	26386776	+	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	ccttggtcactcgacgggaaTcctccagctgagtgatgatg	8	10	12	11	2	1	3	1	3	0	0	4	5	3	4	3	2	1	1	3	2	1	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr1:26386776T>A	ENST00000374272.3	-	4	716	c.578A>T	c.(577-579)gAt>gTt	p.D193V	TRIM63_ENST00000483052.1_5'Flank	NM_032588.3	NP_115977.2	Q969Q1	TRI63_HUMAN	tripartite motif containing 63, E3 ubiquitin protein ligase	193	Interaction with TTN.				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)		TCGACGGGAATCCTCCAGCTG	0.572																																					p.D193V		Atlas-SNP	.											.	TRIM63	33	.	0			c.A578T						PASS	.						122	113	116					1																	26386776		2203	4300	6503	SO:0001583	missense	84676	exon4			CGGGAATCCTCCA	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.578A>T	chr1.hg19:g.26386776T>A	ENSP00000363390:p.Asp193Val	156.0	0.0	.		125.0	25.0	.	NM_032588	B4DN95|Q5T2I1|Q96BD3|Q96KD9|Q9BYV4	Missense_Mutation	SNP	ENST00000374272.3	hg19	CCDS273.1	.	.	.	.	.	.	.	.	.	.	T	18.01	3.528379	0.64860	.	.	ENSG00000158022	ENST00000374272	T	0.39787	1.06	5.21	5.21	0.72293	.	0.086183	0.85682	D	0.000000	T	0.50222	0.1603	M	0.68593	2.085	0.80722	D	1	B	0.32893	0.389	B	0.40741	0.339	T	0.55792	-0.8085	10	0.87932	D	0	.	15.0417	0.71796	0.0:0.0:0.0:1.0	.	193	Q969Q1	TRI63_HUMAN	V	193	ENSP00000363390:D193V	ENSP00000363390:D193V	D	-	2	0	TRIM63	26259363	1.000000	0.71417	1.000000	0.80357	0.774000	0.43823	5.828000	0.69307	2.081000	0.62600	0.379000	0.24179	GAT	.	.	.	none		0.572	TRIM63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019750.1	NM_032588		A	26386776	T	A	26386776	3	1	150	1	0	0	0	0	1	0	0	0	16550	1435	50	5	507	5	TRIM63	1	26386776	Missense_Mutation	SNP	T	TCGA-DW-7838-01A-11D-2136-08		26386776	222863845	1	8903											
KIF2C	11004	hgsc.bcm.edu	37	chr1	45206651	45206651	+	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	ctgtgtttcagtggaatgggCagaaggaggtgccacaaagg	11	8	16	6	0	1	1	1	0	0	1	1	3	1	3	1	5	1	2	1	5	3	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr1:45206651C>A	ENST00000372224.4	+	2	250	c.137C>A	c.(136-138)gCa>gAa	p.A46E	KIF2C_ENST00000372218.4_Missense_Mutation_p.A46E|KIF2C_ENST00000493027.1_3'UTR	NM_006845.3	NP_006836.2	Q99661	KIF2C_HUMAN	kinesin family member 2C	46	Globular. {ECO:0000255}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|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)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|microtubule motor activity (GO:0003777)|microtubule plus-end binding (GO:0051010)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|ovary(1)|skin(1)|urinary_tract(1)	34	Acute lymphoblastic leukemia(166;0.155)					GTGGAATGGGCAGAAGGAGGT	0.413																																					p.A46E		Atlas-SNP	.											.	KIF2C	68	.	0			c.C137A						PASS	.						106	102	103					1																	45206651		2203	4300	6503	SO:0001583	missense	11004	exon2			AATGGGCAGAAGG	U63743	CCDS512.1, CCDS72774.1	1p34.1	2014-01-21	2003-01-13	2003-01-17	ENSG00000142945	ENSG00000142945		"Kinesins"	6393	protein-coding gene	gene with protein product		604538	"kinesin-like 6 (mitotic centromere-associated kinesin)"	KNSL6		9434124	Standard	NM_006845		Approved	MCAK, CT139	uc001cmg.4	Q99661	OTTHUMG00000008416	ENST00000372224.4:c.137C>A	chr1.hg19:g.45206651C>A	ENSP00000361298:p.Ala46Glu	69.0	0.0	.		75.0	8.0	.	NM_006845	B3ITR9|Q5JR88|Q6ICU1|Q96C18|Q96HB8|Q9BWV8	Missense_Mutation	SNP	ENST00000372224.4	hg19	CCDS512.1	.	.	.	.	.	.	.	.	.	.	c	15.02	2.708022	0.48412	.	.	ENSG00000142945	ENST00000452259;ENST00000372224;ENST00000372218;ENST00000455186	T;T;T;T	0.74947	1.14;-0.89;-0.72;0.9	5.95	0.825	0.18824	.	1.230180	0.05208	N	0.506277	T	0.64864	0.2637	L	0.43152	1.355	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.17098	0.017;0.017	T	0.55554	-0.8123	10	0.52906	T	0.07	.	2.3087	0.04181	0.1215:0.4871:0.1181:0.2733	.	46;46	B7Z6Q6;Q99661	.;KIF2C_HUMAN	E	46;46;46;37	ENSP00000410346:A46E;ENSP00000361298:A46E;ENSP00000361292:A46E;ENSP00000395050:A37E	ENSP00000361292:A46E	A	+	2	0	KIF2C	44979238	0.981000	0.34729	0.990000	0.47175	0.995000	0.86356	-0.030000	0.12308	-0.083000	0.12618	0.655000	0.94253	GCA	.	.	.	none		0.413	KIF2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023180.1	NM_006845		A	45206651	C	A	45206651	3	1	150	1	0	0	0	0	1	0	0	0	8306	710	25	4	143	4	KIF2C	1	45206651	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	18819875	45206651	204043970	2	8904											
TXNDC12	51060	hgsc.bcm.edu	37	chr1	52494277	52494277	+	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	agctccacaccaggatttatGaataatcaccatcaggggca	14	8	8	11	0	2	1	2	1	0	0	3	2	3	2	3	3	1	2	3	3	3	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr1:52494277G>T	ENST00000371626.4	-	3	1258	c.184C>A	c.(184-186)Cat>Aat	p.H62N		NM_015913.3	NP_056997.1	O95881	TXD12_HUMAN	thioredoxin domain containing 12 (endoplasmic reticulum)	62					cell redox homeostasis (GO:0045454)	endoplasmic reticulum (GO:0005783)	protein-disulfide reductase (glutathione) activity (GO:0019153)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	7					Glutathione(DB00143)	CAGGATTTATGAATAATCACC	0.299																																					p.H62N		Atlas-SNP	.											.	TXNDC12	18	.	0			c.C184A						PASS	.						86	85	85					1																	52494277		2203	4300	6503	SO:0001583	missense	51060	exon3			ATTTATGAATAAT	AF131758	CCDS561.1	1p32.3	2011-10-19			ENSG00000117862	ENSG00000117862		"Protein disulfide isomerases"	24626	protein-coding gene	gene with protein product	"endoplasmic reticulum thioredoxin superfamily member, 18 kDa", "anterior gradient homolog 1 (Xenopus laevis)", "protein disulfide isomerase family A, member 16"	609448				8619474, 9110174	Standard	NM_015913		Approved	TLP19, ERP18, ERP19, hAG-1, AGR1, PDIA16	uc001cti.4	O95881	OTTHUMG00000008629	ENST00000371626.4:c.184C>A	chr1.hg19:g.52494277G>T	ENSP00000360688:p.His62Asn	103.0	0.0	.		69.0	9.0	.	NM_015913	B3KQS0|Q5T1T4|Q96H50	Missense_Mutation	SNP	ENST00000371626.4	hg19	CCDS561.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.570676	0.86542	.	.	ENSG00000117862	ENST00000371626	T	0.52754	0.65	5.6	5.6	0.85130	Thioredoxin domain (1);Thioredoxin, conserved site (1);Thioredoxin-like fold (3);	0.000000	0.85682	D	0.000000	T	0.73682	0.3618	M	0.87269	2.87	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	T	0.76705	-0.2861	10	0.52906	T	0.07	.	17.7823	0.88527	0.0:0.0:1.0:0.0	.	62	O95881	TXD12_HUMAN	N	62	ENSP00000360688:H62N	ENSP00000360688:H62N	H	-	1	0	TXNDC12	52266865	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	8.150000	0.89634	2.622000	0.88805	0.655000	0.94253	CAT	.	.	.	none		0.299	TXNDC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023818.1	NM_015913		T	52494277	G	T	52494277	3	4	150	1	0	0	0	0	1	0	0	0	16805	1290	45	4	354	4	TXNDC12	1	52494277	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	7287626	52494277	196756344	3	8905											
WDR47	22911	hgsc.bcm.edu	37	chr1	109554105	109554105	+	Frame_Shift_Del	DEL	T	T	-																															ataaacgattgttactagccTtaaaaccagcttcacttagc																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr1:109554105delT	ENST00000369962.3	-	5	785	c.563delA	c.(562-564)aagfs	p.K188fs	WDR47_ENST00000369965.4_Frame_Shift_Del_p.K188fs|WDR47_ENST00000357672.3_Frame_Shift_Del_p.K160fs|WDR47_ENST00000361054.3_Frame_Shift_Del_p.K160fs|WDR47_ENST00000400794.3_Frame_Shift_Del_p.K195fs			O94967	WDR47_HUMAN	WD repeat domain 47	188					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)		GTTACTAGCCTTAAAACCAGC	0.413																																					p.K195fs		Atlas-INDEL	.											.	WDR47	56	.	0			c.585delG						PASS	.						206	212	210					1																	109554105		2203	4296	6499	SO:0001589	frameshift_variant	22911	exon5			.	AB020700	CCDS30787.1, CCDS44186.1, CCDS44187.1	1p13.3	2013-01-09			ENSG00000085433	ENSG00000085433		"WD repeat domain containing"	29141	protein-coding gene	gene with protein product		615734				10048485	Standard	NM_014969		Approved	KIAA0893	uc001dwl.3	O94967	OTTHUMG00000011734	ENST00000369962.3:c.563delA	chr1.hg19:g.109554105delT	ENSP00000358979:p.Lys188fs	435.0	0.0	0		342.0	55.0	0.160819	NM_001142550	A8MX09|Q5TYV7|Q5TYV8|Q5TYV9|Q8IXT7|Q8IYU9	Frame_Shift_Del	DEL	ENST00000369962.3	hg19	CCDS44187.1																																																																																			.	.	.	none		0.413	WDR47-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000032414.2	NM_014969		-	109554105	T	-	109554105	7	5	150	1	0	1	0	1	0	0	0	0	17312	1609	56	0	2243	0	WDR47	1	109554105	Frame_Shift_Del	DEL	T	TCGA-DW-7838-01A-11D-2136-08	57059828	109554105	139696516	4	8906											
ANKRD35	148741	hgsc.bcm.edu	37	chr1	145561665	145561665	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actaccaatggggcacagacCtttggccctgatcatgctga	10	9	10	12	0	1	3	1	2	0	1	1	3	1	3	3	3	2	2	3	3	2	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr1:145561665C>T	ENST00000355594.4	+	10	1440	c.1353C>T	c.(1351-1353)acC>acT	p.T451T		NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	451										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)					GGGCACAGACCTTTGGCCCTG	0.587																																					p.T451T	Melanoma(9;127 754 22988 51047)	Atlas-SNP	.											.	ANKRD35	96	.	0			c.C1353T						PASS	.						59	67	64					1																	145561665		2203	4300	6503	SO:0001819	synonymous_variant	148741	exon10			ACAGACCTTTGGC	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.1353C>T	chr1.hg19:g.145561665C>T		113.0	0.0	.		97.0	22.0	.	NM_144698	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Silent	SNP	ENST00000355594.4	hg19	CCDS919.1																																																																																			.	.	.	none		0.587	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698		T	145561665	C	T	145561665	2	4	150	1	0	0	0	0	0	0	0	1	664	668	24	2		2	ANKRD35	1	145561665	Silent	SNP	C	TCGA-DW-7838-01A-11D-2136-08	36007560	145561665	103688956	5	8907											
FLAD1	80308	hgsc.bcm.edu	37	chr1	154961016	154961016	+	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	gggtgctggaggggatgaagGgactattccaaaacccagct	11	7	15	8	0	0	1	0	1	0	0	1	4	1	4	2	5	3	2	2	5	4	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr1:154961016G>A	ENST00000292180.3	+	2	1130	c.808G>A	c.(808-810)Gga>Aga	p.G270R	FLAD1_ENST00000368432.1_Missense_Mutation_p.G173R|FLAD1_ENST00000368433.1_Missense_Mutation_p.G270R|FLAD1_ENST00000368428.1_5'Flank|FLAD1_ENST00000295530.2_Missense_Mutation_p.G3R|FLAD1_ENST00000405236.2_Missense_Mutation_p.G171R|FLAD1_ENST00000368431.3_Missense_Mutation_p.G171R|FLAD1_ENST00000315144.10_Missense_Mutation_p.G173R	NM_025207.4	NP_079483.3	Q8NFF5	FAD1_HUMAN	flavin adenine dinucleotide synthetase 1	270					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)			GGGGATGAAGGGACTATTCCA	0.572																																					p.G270R		Atlas-SNP	.											.	FLAD1	52	.	0			c.G808A						PASS	.						43	41	42					1																	154961016		2203	4300	6503	SO:0001583	missense	80308	exon2			ATGAAGGGACTAT		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.808G>A	chr1.hg19:g.154961016G>A	ENSP00000292180:p.Gly270Arg	69.0	0.0	.		69.0	9.0	.	NM_025207	Q8N5J1|Q8N686|Q8WU93|Q8WUJ4|Q96CR8|Q99764|Q9HBN6	Missense_Mutation	SNP	ENST00000292180.3	hg19	CCDS1078.1	.	.	.	.	.	.	.	.	.	.	G	10.59	1.391696	0.25118	.	.	ENSG00000160688	ENST00000368433;ENST00000315144;ENST00000368432;ENST00000368431;ENST00000292180;ENST00000405236;ENST00000295530	.	.	.	5.51	1.43	0.22495	Molybdopterin binding (2);	0.470755	0.24384	N	0.038987	T	0.05777	0.0151	N	0.25890	0.77	0.09310	N	1	P;B;P	0.45474	0.859;0.05;0.491	B;B;B	0.37304	0.246;0.124;0.076	T	0.32188	-0.9916	9	0.21014	T	0.42	-1.0E-4	6.7182	0.23314	0.2278:0.3684:0.4038:0.0	.	3;270;171	Q5T191;Q8NFF5;Q8NFF5-4	.;FAD1_HUMAN;.	R	270;173;173;171;270;171;3	.	ENSP00000292180:G270R	G	+	1	0	FLAD1	153227640	0.089000	0.21612	0.069000	0.20011	0.879000	0.50718	1.889000	0.39718	0.419000	0.25927	0.561000	0.74099	GGA	.	.	.	none		0.572	FLAD1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091089.1	NM_025207		A	154961016	G	A	154961016	3	1	150	1	0	0	0	0	1	0	0	0	5927	1233	43	2	889	2	FLAD1	1	154961016	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	9399351	154961016	94289605	6	8908											
LOXL3	84695	hgsc.bcm.edu	37	chr2	74761483	74761483	+	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	tcgagacagaaactagctttGtggccctcagccaccttggt	9	10	10	12	1	1	2	1	0	0	2	2	3	1	2	3	2	3	1	3	2	2	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr2:74761483G>A	ENST00000264094.3	-	11	1970	c.1899C>T	c.(1897-1899)caC>caT	p.H633H	LOXL3_ENST00000393937.2_Silent_p.H488H|LOXL3_ENST00000409986.1_Silent_p.H488H|LOXL3_ENST00000409549.1_Silent_p.H577H|LOXL3_ENST00000409249.1_Intron	NM_032603.2	NP_115992.1	P58215	LOXL3_HUMAN	lysyl oxidase-like 3	633	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						AACTAGCTTTGTGGCCCTCAG	0.502																																					p.H633H		Atlas-SNP	.											.	LOXL3	73	.	0			c.C1899T						PASS	.						190	183	185					2																	74761483		2203	4300	6503	SO:0001819	synonymous_variant	84695	exon11			AGCTTTGTGGCCC	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.1899C>T	chr2.hg19:g.74761483G>A		117.0	0.0	.		121.0	20.0	.	NM_032603	D6W5J1|Q2EHP2|Q6IPL7|Q96RS1	Silent	SNP	ENST00000264094.3	hg19	CCDS1953.1																																																																																			.	.	.	none		0.502	LOXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252215.1	NM_032603		A	74761483	G	A	74761483	2	1	150	1	0	0	0	0	0	0	0	1	8908	1368	48	2		2	LOXL3	2	74761483	Silent	SNP	G	TCGA-DW-7838-01A-11D-2136-08		74761483	168437890	7	8909											
TUBA3D	113457	hgsc.bcm.edu	37	chr2	132236969	132236969	+	Silent	SNP	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	gcagccaataattacgccagGggccattacaccatcggcaa	13	6	9	13	2	0	0	0	0	0	0	1	0	0	0	4	3	3	2	4	3	5	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr2:132236969G>A	ENST00000321253.6	+	3	422	c.315G>A	c.(313-315)agG>agA	p.R105R	TUBA3D_ENST00000409047.2_3'UTR	NM_080386.3	NP_525125.2	Q13748	TBA3C_HUMAN	tubulin, alpha 3d	105					'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)		ATTACGCCAGGGGCCATTACA	0.527																																					p.R105R	Ovarian(137;2059 2432 35543 39401)	Atlas-SNP	.											.	TUBA3D	60	.	0			c.G315A						PASS	.						209	172	184					2																	132236969		2203	4300	6503	SO:0001819	synonymous_variant	113457	exon3			CGCCAGGGGCCAT	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.315G>A	chr2.hg19:g.132236969G>A		273.0	0.0	.		256.0	40.0	.	NM_080386	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Silent	SNP	ENST00000321253.6	hg19	CCDS33290.1																																																																																			.	.	.	none		0.527	TUBA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331800.2	NM_080386		A	132236969	G	A	132236969	2	1	150	1	0	0	0	0	0	0	0	1	16759	1223	43	2		2	TUBA3D	2	132236969	Silent	SNP	G	TCGA-DW-7838-01A-11D-2136-08	57475486	132236969	110962404	8	8910											
FIGN	55137	hgsc.bcm.edu	37	chr2	164466515	164466515	+	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	acagtgtccagttgcatcagAaattcggttctcatccgact	10	12	8	11	2	2	1	2	0	1	1	6	2	4	1	2	1	1	3	2	1	1	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr2:164466515A>T	ENST00000333129.3	-	3	2141	c.1827T>A	c.(1825-1827)ttT>ttA	p.F609L	FIGN_ENST00000482917.1_5'Flank|FIGN_ENST00000409634.1_Intron	NM_018086.2	NP_060556.2	Q5HY92	FIGN_HUMAN	fidgetin	609					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						GTTGCATCAGAAATTCGGTTC	0.458																																					p.F609L		Atlas-SNP	.											.	FIGN	106	.	0			c.T1827A						PASS	.						105	99	101					2																	164466515		1948	4151	6099	SO:0001583	missense	55137	exon3			CATCAGAAATTCG	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.1827T>A	chr2.hg19:g.164466515A>T	ENSP00000333836:p.Phe609Leu	153.0	0.0	.		105.0	23.0	.	NM_018086	B3KWM0|Q9H6M5|Q9NVZ9	Missense_Mutation	SNP	ENST00000333129.3	hg19	CCDS2221.2	.	.	.	.	.	.	.	.	.	.	A	12.72	2.023844	0.35701	.	.	ENSG00000182263	ENST00000333129	D	0.86865	-2.18	5.47	2.81	0.32909	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.055714	0.64402	D	0.000001	T	0.74504	0.3725	N	0.00771	-1.2	0.58432	D	0.999996	B	0.32324	0.364	P	0.51999	0.687	T	0.66767	-0.5840	10	0.21014	T	0.42	-19.2916	5.9791	0.19397	0.6913:0.0:0.3087:0.0	.	609	Q5HY92	FIGN_HUMAN	L	609	ENSP00000333836:F609L	ENSP00000333836:F609L	F	-	3	2	FIGN	164174761	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	1.691000	0.37721	1.009000	0.39289	0.383000	0.25322	TTT	.	.	.	none		0.458	FIGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157220.2	NM_018086		T	164466515	A	T	164466515	3	4	150	1	0	0	0	0	1	0	0	0	5898	243	9	5	456	5	FIGN	2	164466515	Missense_Mutation	SNP	A	TCGA-DW-7838-01A-11D-2136-08	32229546	164466515	78732858	9	8911											
TTN	7273	hgsc.bcm.edu	37	chr2	179650403	179650403	+	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	tgaaacagtaaagtgagggcTagctgtgcgggggcgtttat	10	10	16	5	2	0	2	0	2	0	0	0	2	0	2	0	3	3	4	0	3	5	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr2:179650403T>A	ENST00000591111.1	-	15	2661	c.2437A>T	c.(2437-2439)Agc>Tgc	p.S813C	TTN_ENST00000359218.5_Missense_Mutation_p.S767C|TTN_ENST00000360870.5_Missense_Mutation_p.S813C|TTN_ENST00000460472.2_Missense_Mutation_p.S767C|TTN_ENST00000589042.1_Missense_Mutation_p.S813C|TTN_ENST00000342175.6_Missense_Mutation_p.S767C|TTN_ENST00000342992.6_Missense_Mutation_p.S813C			Q8WZ42	TITIN_HUMAN	titin	33644					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)			AAGTGAGGGCTAGCTGTGCGG	0.373																																					p.S813C		Atlas-SNP	.											.	TTN	18412	.	0			c.A2437T						PASS	.						172	167	169					2																	179650403		2203	4300	6503	SO:0001583	missense	7273	exon15			GAGGGCTAGCTGT	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.2437A>T	chr2.hg19:g.179650403T>A	ENSP00000465570:p.Ser813Cys	94.0	0.0	.		88.0	16.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	12.88	2.071468	0.36566	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.67523	-0.27;-0.03;-0.03;-0.04;0.15	5.51	5.51	0.81932	Ribonuclease H-like (1);	.	.	.	.	T	0.70159	0.3192	L	0.27053	0.805	0.24564	N	0.993953	D;D;D;D;D	0.89917	0.993;0.993;0.993;0.993;1.0	P;P;P;P;D	0.69479	0.628;0.628;0.628;0.628;0.964	T	0.62699	-0.6799	9	0.87932	D	0	.	10.3027	0.43661	0.0:0.0737:0.0:0.9263	.	767;767;767;813;813	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	C	813;767;767;767;767;813	ENSP00000343764:S813C;ENSP00000434586:S767C;ENSP00000340554:S767C;ENSP00000352154:S767C;ENSP00000354117:S813C	ENSP00000340554:S767C	S	-	1	0	TTN	179358648	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	2.566000	0.45948	2.210000	0.71456	0.533000	0.62120	AGC	.	.	.	none		0.373	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179650403	T	A	179650403	3	1	150	1	0	0	0	0	1	0	0	0	16747	1522	53	5	108943	5	TTN	2	179650403	Missense_Mutation	SNP	T	TCGA-DW-7838-01A-11D-2136-08	15183888	179650403	63548970	10	8912											
COL6A3	1293	hgsc.bcm.edu	37	chr2	238303376	238303376	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tattgagcggttcacttgctAtttcttttaacgctccttca	7	18	6	10	2	3	1	2	1	1	0	4	1	4	1	1	1	3	3	1	1	3	9			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr2:238303376A>G	ENST00000295550.4	-	3	1015	c.563T>C	c.(562-564)aTa>aCa	p.I188T	COL6A3_ENST00000472056.1_Intron|COL6A3_ENST00000347401.3_Missense_Mutation_p.I188T|COL6A3_ENST00000346358.4_Missense_Mutation_p.I188T|COL6A3_ENST00000409809.1_Intron|COL6A3_ENST00000353578.4_Intron|COL6A3_ENST00000392003.2_Intron|COL6A3_ENST00000392004.3_Intron	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	188	Nonhelical region.|VWFA 1. {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)		TTCACTTGCTATTTCTTTTAA	0.433																																					p.I188T		Atlas-SNP	.											.	COL6A3	608	.	0			c.T563C						PASS	.						127	124	125					2																	238303376		2203	4300	6503	SO:0001583	missense	1293	exon3			CTTGCTATTTCTT	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.563T>C	chr2.hg19:g.238303376A>G	ENSP00000295550:p.Ile188Thr	122.0	0.0	.		85.0	13.0	.	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	A	6.536	0.467096	0.12402	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000346358;ENST00000433762	D;D;D;D	0.84146	-1.81;-1.81;-1.81;-1.81	4.9	3.72	0.42706	von Willebrand factor, type A (3);	0.267710	0.25584	U	0.029678	D	0.88437	0.6436	H	0.94886	3.595	0.47778	D	0.999513	B;B	0.19445	0.009;0.036	B;B	0.20767	0.021;0.031	D	0.85506	0.1194	10	0.62326	D	0.03	.	10.6923	0.45877	0.9233:0.0:0.0766:0.0	.	188;188	E9PCV6;P12111	.;CO6A3_HUMAN	T	188	ENSP00000295550:I188T;ENSP00000315609:I188T;ENSP00000295546:I188T;ENSP00000389539:I188T	ENSP00000295550:I188T	I	-	2	0	COL6A3	237968115	1.000000	0.71417	0.997000	0.53966	0.219000	0.24729	6.121000	0.71602	0.699000	0.31761	0.374000	0.22700	ATA	.	.	.	none		0.433	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		G	238303376	A	G	238303376	3	3	150	1	0	0	0	0	1	0	0	0	3703	449	16	3	9185	3	COL6A3	2	238303376	Missense_Mutation	SNP	A	TCGA-DW-7838-01A-11D-2136-08	58652973	238303376	4895997	11	8913											
RNPEPL1	57140	hgsc.bcm.edu	37	chr2	241516157	241516157	+	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	gcactcttcctggaccggctCctggatgggtccccgctgcc	3	9	12	17	2	1	0	0	0	1	0	4	2	4	2	6	4	1	3	6	4	0	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr2:241516157C>T	ENST00000270357.4	+	9	1616	c.1023C>T	c.(1021-1023)ctC>ctT	p.L341L	RNPEPL1_ENST00000464550.1_3'UTR	NM_018226.4	NP_060696.4	Q9HAU8	RNPL1_HUMAN	arginyl aminopeptidase (aminopeptidase B)-like 1	341					leukotriene biosynthetic process (GO:0019370)		aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	13		all_epithelial(40;1.13e-11)|Breast(86;0.000169)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.204)|Melanoma(123;0.238)		Epithelial(32;3.05e-31)|all cancers(36;8.2e-29)|OV - Ovarian serous cystadenocarcinoma(60;8.55e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;5.12e-06)|Lung(119;0.00168)|Colorectal(34;0.005)|LUSC - Lung squamous cell carcinoma(224;0.00813)|COAD - Colon adenocarcinoma(134;0.0322)		TGGACCGGCTCCTGGATGGGT	0.687																																					p.L572L		Atlas-SNP	.											.	RNPEPL1	32	.	0			c.C1716T						PASS	.						29	33	32					2																	241516157		2196	4289	6485	SO:0001819	synonymous_variant	57140	exon9			CCGGCTCCTGGAT			2q37.3	2012-03-06			ENSG00000142327	ENSG00000142327			10079	protein-coding gene	gene with protein product		605287				19508204	Standard	NM_018226		Approved		uc002vzi.4	Q9HAU8	OTTHUMG00000133357	ENST00000270357.4:c.1023C>T	chr2.hg19:g.241516157C>T		99.0	0.0	.		83.0	11.0	.	NM_018226	Q5XKC3|Q6NX56|Q96AC9|Q9H033|Q9NVD0	Silent	SNP	ENST00000270357.4	hg19																																																																																				.	.	.	none		0.687	RNPEPL1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257190.4	NM_018226		T	241516157	C	T	241516157	2	4	150	1	0	0	0	0	0	0	0	1	13523	842	30	2		2	RNPEPL1	2	241516157	Silent	SNP	C	TCGA-DW-7838-01A-11D-2136-08	3212781	241516157	1683216	12	8914											
SCAP	22937	hgsc.bcm.edu	37	chr3	47456625	47456625	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgagggcagtgtgggtctcCaaggagaagaaatcaaggga	13	6	16	6	0	2	3	1	1	1	2	3	5	2	4	1	4	0	1	1	4	4	0			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr3:47456625C>T	ENST00000265565.5	-	19	3514	c.3102G>A	c.(3100-3102)ttG>ttA	p.L1034L	SCAP_ENST00000441517.2_Silent_p.L778L|SCAP_ENST00000545718.1_Silent_p.L641L	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone	1034	Interaction with SREBF2. {ECO:0000250}.				aging (GO:0007568)|cholesterol metabolic process (GO:0008203)|negative regulation of cholesterol biosynthetic process (GO:0045541)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of fatty acid biosynthetic process (GO:0042304)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	26				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		TGTGGGTCTCCAAGGAGAAGA	0.632																																					p.L1034L	Pancreas(149;978 1908 29304 37806 46700)	Atlas-SNP	.											.	SCAP	88	.	0			c.G3102A						PASS	.						51	53	52					3																	47456625		2202	4299	6501	SO:0001819	synonymous_variant	22937	exon19			GGTCTCCAAGGAG	BC020987	CCDS2755.2	3p21.31	2013-01-10			ENSG00000114650	ENSG00000114650		"WD repeat domain containing"	30634	protein-coding gene	gene with protein product	"SREBP cleavage activating protein"	601510				8898195, 8724849, 10570913	Standard	XM_005264967		Approved	KIAA0199	uc003crh.1	Q12770	OTTHUMG00000125539	ENST00000265565.5:c.3102G>A	chr3.hg19:g.47456625C>T		65.0	0.0	.		69.0	17.0	.	NM_012235	Q8N2E0|Q8WUA1	Silent	SNP	ENST00000265565.5	hg19	CCDS2755.2																																																																																			.	.	.	none		0.632	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246872.2	NM_012235		T	47456625	C	T	47456625	2	4	150	1	0	0	0	0	0	0	0	1	13890	593	21	2		2	SCAP	3	47456625	Silent	SNP	C	TCGA-DW-7838-01A-11D-2136-08		47456625	150565805	13	8915											
C3orf18	51161	hgsc.bcm.edu	37	chr3	50602964	50602964	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatggtacccacgccggccGtgccaccagctgcatcaggg	7	5	13	16	3	1	0	1	0	0	0	1	0	1	0	5	3	4	4	5	3	1	1	rs559763162		TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr3:50602964G>A	ENST00000357203.3	-	3	706	c.167C>T	c.(166-168)aCg>aTg	p.T56M	C3orf18_ENST00000441239.1_Missense_Mutation_p.T56M|C3orf18_ENST00000449241.1_Missense_Mutation_p.T56M|C3orf18_ENST00000486175.1_Intron|C3orf18_ENST00000426034.1_Missense_Mutation_p.T56M	NM_016210.4	NP_057294.2	Q9UK00	CC018_HUMAN	chromosome 3 open reading frame 18	56						integral component of membrane (GO:0016021)				lung(1)|pancreas(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.0175)|Kidney(197;0.0207)		CACGCCGGCCGTGCCACCAGC	0.607																																					p.T56M		Atlas-SNP	.											.	C3orf18	12	.	0			c.C167T						PASS	.						88	76	80					3																	50602964		2202	4300	6502	SO:0001583	missense	51161	exon3			CCGGCCGTGCCAC	AF188706	CCDS2829.1, CCDS54589.1	3p21.3	2006-01-11			ENSG00000088543	ENSG00000088543			24837	protein-coding gene	gene with protein product						12477932	Standard	NM_016210		Approved	G20	uc010hlp.3	Q9UK00	OTTHUMG00000156854	ENST00000357203.3:c.167C>T	chr3.hg19:g.50602964G>A	ENSP00000349732:p.Thr56Met	67.0	0.0	.		65.0	13.0	.	NM_016210	C9JNP0	Missense_Mutation	SNP	ENST00000357203.3	hg19	CCDS2829.1	.	.	.	.	.	.	.	.	.	.	G	10.95	1.495028	0.26774	.	.	ENSG00000088543	ENST00000426034;ENST00000357203;ENST00000449241;ENST00000441239	T;T;T;T	0.42513	2.52;2.52;2.52;0.97	5.24	3.36	0.38483	.	0.821587	0.11279	N	0.580514	T	0.24851	0.0603	N	0.19112	0.55	0.21105	N	0.999781	P;P	0.52577	0.89;0.954	B;B	0.37780	0.258;0.251	T	0.05920	-1.0856	10	0.52906	T	0.07	-12.7022	7.5988	0.28065	0.0:0.3237:0.5385:0.1378	.	56;56	C9JNP0;Q9UK00	.;CC018_HUMAN	M	56	ENSP00000387606:T56M;ENSP00000349732:T56M;ENSP00000404913:T56M;ENSP00000414124:T56M	ENSP00000349732:T56M	T	-	2	0	C3orf18	50577968	0.019000	0.18553	0.001000	0.08648	0.388000	0.30384	2.265000	0.43311	1.193000	0.43086	0.462000	0.41574	ACG	.	.	.	none		0.607	C3orf18-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346260.2	NM_016210		A	50602964	G	A	50602964	3	1	150	1	0	0	0	0	1	0	0	0	2213	1145	40	1	337	1	C3orf18	3	50602964	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	3146339	50602964	147419466	14	8916											
BBX	56987	hgsc.bcm.edu	37	chr3	107491690	107491690	+	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	aaggaattgagaaattttgaGgcattgcaaatagatgacat	17	11	10	3	0	0	4	0	3	0	2	0	6	0	5	0	2	1	2	0	2	5	5			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr3:107491690G>C	ENST00000325805.8	+	11	1409	c.1122G>C	c.(1120-1122)gaG>gaC	p.E374D	BBX_ENST00000406780.1_Missense_Mutation_p.E374D|BBX_ENST00000416476.2_Intron|BBX_ENST00000402543.1_Missense_Mutation_p.E374D|BBX_ENST00000415149.2_Missense_Mutation_p.E374D			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	374					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)			GAAATTTTGAGGCATTGCAAA	0.323																																					p.E374D		Atlas-SNP	.											.	BBX	156	.	0			c.G1122C						PASS	.						58	68	64					3																	107491690		2203	4298	6501	SO:0001583	missense	56987	exon11			TTTTGAGGCATTG	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.1122G>C	chr3.hg19:g.107491690G>C	ENSP00000319974:p.Glu374Asp	99.0	0.0	.		109.0	48.0	.	NM_001142568	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	Missense_Mutation	SNP	ENST00000325805.8	hg19	CCDS46881.1	.	.	.	.	.	.	.	.	.	.	G	4.952	0.176823	0.09443	.	.	ENSG00000114439	ENST00000415149;ENST00000325767;ENST00000402543;ENST00000325805;ENST00000402163;ENST00000406780	D;D;D;D;D	0.98747	-4.6;-4.6;-4.61;-5.11;-4.6	6.16	-0.709	0.11237	.	0.342008	0.33253	N	0.005119	D	0.94486	0.8225	N	0.24115	0.695	0.28521	N	0.91307	B;B;B	0.18461	0.012;0.028;0.009	B;B;B	0.14023	0.004;0.01;0.009	D	0.88666	0.3192	10	0.45353	T	0.12	-10.7263	7.4111	0.27017	0.5975:0.0:0.282:0.1205	.	374;374;374	C9JA69;Q8WY36;Q8WY36-2	.;BBX_HUMAN;.	D	374;225;374;374;374;374	ENSP00000408358:E374D;ENSP00000385317:E374D;ENSP00000319974:E374D;ENSP00000385518:E374D;ENSP00000385530:E374D	ENSP00000319742:E225D	E	+	3	2	BBX	108974380	0.991000	0.36638	0.873000	0.34254	0.130000	0.20726	0.223000	0.17719	-0.449000	0.07117	-1.871000	0.00553	GAG	.	.	.	none		0.323	BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235		C	107491690	G	C	107491690	3	2	150	1	0	0	0	0	1	0	0	0	1343	991	35	4	1152	4	BBX	3	107491690	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	56888726	107491690	90530740	15	8917											
EHHADH	1962	hgsc.bcm.edu	37	chr3	184922367	184922367	+	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	aacagctcctcctccttcttGatgcccacttcatagggata	9	12	6	14	0	2	1	1	1	1	0	5	2	5	2	4	1	3	1	4	1	3	5	rs149294851		TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr3:184922367G>A	ENST00000231887.3	-	6	822	c.747C>T	c.(745-747)atC>atT	p.I249I	EHHADH_ENST00000456310.1_Silent_p.I153I	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	249	Enoyl-CoA hydratase / isomerase.				fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			CCTCCTTCTTGATGCCCACTT	0.517																																					p.I249I		Atlas-SNP	.											.	EHHADH	73	.	0			c.C747T						PASS	.						131	128	129					3																	184922367		2203	4300	6503	SO:0001819	synonymous_variant	1962	exon6			CTTCTTGATGCCC	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.747C>T	chr3.hg19:g.184922367G>A		234.0	0.0	.		289.0	88.0	.	NM_001966	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Silent	SNP	ENST00000231887.3	hg19	CCDS33901.1																																																																																			.	G|1.000;C|0.000	.	alt		0.517	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1			A	184922367	G	A	184922367	2	1	150	1	0	0	0	0	0	0	0	1	4984	1280	45	2		2	EHHADH	3	184922367	Silent	SNP	G	TCGA-DW-7838-01A-11D-2136-08	77430677	184922367	13100063	16	8918											
MFSD10	10227	hgsc.bcm.edu	37	chr4	2934901	2934901	+	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	cccagtgagtggcgcacacaGaaactgcaggacagagaatg	14	4	13	10	1	0	3	0	1	0	2	0	5	0	4	1	2	2	2	1	2	2	0			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr4:2934901G>C	ENST00000329687.4	-	3	838	c.304C>G	c.(304-306)Ctg>Gtg	p.L102V	MFSD10_ENST00000514800.1_Missense_Mutation_p.L102V|MFSD10_ENST00000355443.4_Missense_Mutation_p.L102V|NOP14-AS1_ENST00000507999.1_RNA|NOP14-AS1_ENST00000505731.1_RNA|MFSD10_ENST00000508221.1_Missense_Mutation_p.L102V|NOP14-AS1_ENST00000515194.1_RNA|NOP14-AS1_ENST00000512712.2_RNA|MFSD10_ENST00000507555.1_Missense_Mutation_p.L102V	NM_001120.4	NP_001111.3	Q14728	MFS10_HUMAN	major facilitator superfamily domain containing 10	102					apoptotic process (GO:0006915)|tetracycline transport (GO:0015904)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)	tetracycline transporter activity (GO:0008493)			breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		GGCGCACACAGAAACTGCAGG	0.617																																					p.L102V		Atlas-SNP	.											MFSD10,bladder,carcinoma,0,1	MFSD10	22	.	0			c.C304G						PASS	.						53	53	53					4																	2934901		2202	4299	6501	SO:0001583	missense	10227	exon3			CACACAGAAACTG	L11669	CCDS3365.1	4p16.3	2008-03-03			ENSG00000109736	ENSG00000109736			16894	protein-coding gene	gene with protein product	"tetracycline transporter like protein"	610977				8353488, 17362938	Standard	NM_001120		Approved	TETRAN, IT10C3	uc003gfz.3	Q14728	OTTHUMG00000122081	ENST00000329687.4:c.304C>G	chr4.hg19:g.2934901G>C	ENSP00000332646:p.Leu102Val	38.0	0.0	.		54.0	9.0	.	NM_001120	Q07706	Missense_Mutation	SNP	ENST00000329687.4	hg19	CCDS3365.1	.	.	.	.	.	.	.	.	.	.	G	5.826	0.336718	0.11013	.	.	ENSG00000109736	ENST00000514800;ENST00000355443;ENST00000329687;ENST00000508221;ENST00000507555	T;T;T;T;T	0.57107	0.42;0.42;0.42;0.42;0.42	4.19	-0.214	0.13161	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.370891	0.28062	N	0.016760	T	0.33585	0.0868	L	0.45422	1.42	0.20307	N	0.999916	B;B;B;B	0.23735	0.012;0.022;0.09;0.007	B;B;B;B	0.29267	0.042;0.078;0.1;0.032	T	0.09796	-1.0658	10	0.14656	T	0.56	-10.5579	0.8156	0.01102	0.2667:0.3381:0.2238:0.1713	.	102;102;102;102	D6RIZ4;D6RE79;D6RA47;Q14728	.;.;.;MFS10_HUMAN	V	102	ENSP00000426907:L102V;ENSP00000347619:L102V;ENSP00000332646:L102V;ENSP00000425757:L102V;ENSP00000423402:L102V	ENSP00000332646:L102V	L	-	1	2	MFSD10	2904699	0.985000	0.35326	0.153000	0.22517	0.211000	0.24417	0.178000	0.16820	0.045000	0.15804	0.561000	0.74099	CTG	.	.	.	none		0.617	MFSD10-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358072.2	NM_001120		C	2934901	G	C	2934901	3	2	150	1	0	0	0	0	1	0	0	0	9535	933	33	4	1103	4	MFSD10	4	2934901	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08		2934901	188219375	17	8919											
JAKMIP1	152789	hgsc.bcm.edu	37	chr4	6066676	6066676	+	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	gtgttgtaggatgtttcggaCaacgtttctgagtccacaga	9	13	12	7	2	1	2	0	1	1	1	3	4	2	4	1	2	1	4	1	2	2	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr4:6066676C>T	ENST00000282924.5	-	9	1847	c.1362G>A	c.(1360-1362)ttG>ttA	p.L454L	JAKMIP1_ENST00000409371.3_Silent_p.L269L|JAKMIP1_ENST00000457227.2_5'UTR|JAKMIP1_ENST00000409831.1_Silent_p.L454L|JAKMIP1_ENST00000410077.2_Silent_p.L289L|JAKMIP1_ENST00000409021.3_Silent_p.L454L	NM_144720.3	NP_653321.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	454	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						ATGTTTCGGACAACGTTTCTG	0.488																																					p.L454L		Atlas-SNP	.											.	JAKMIP1	250	.	0			c.G1362A						PASS	.						192	163	173					4																	6066676		2203	4300	6503	SO:0001819	synonymous_variant	152789	exon9			TTCGGACAACGTT	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.1362G>A	chr4.hg19:g.6066676C>T		125.0	0.0	.		92.0	6.0	.	NM_001099433	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Silent	SNP	ENST00000282924.5	hg19	CCDS3385.1																																																																																			.	.	.	none		0.488	JAKMIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246816.2	NM_144720		T	6066676	C	T	6066676	2	4	150	1	0	0	0	0	0	0	0	1	7947	477	17	2		2	JAKMIP1	4	6066676	Silent	SNP	C	TCGA-DW-7838-01A-11D-2136-08	3131775	6066676	185087600	18	8920											
BOD1L	259282	hgsc.bcm.edu	37	chr4	13601157	13601157	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttctcttctgcatttatgAggtgtaaagtgctctctttc	6	19	7	9	0	4	1	0	1	4	0	7	1	4	1	0	1	2	3	0	1	3	6			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr4:13601157A>G	ENST00000040738.5	-	10	7502	c.7367T>C	c.(7366-7368)cTc>cCc	p.L2456P		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	2456						nucleus (GO:0005634)	DNA binding (GO:0003677)										TGCATTTATGAGGTGTAAAGT	0.468											OREG0016115	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L2456P		Atlas-SNP	.											.	.	.	.	0			c.T7367C						PASS	.						164	147	153					4																	13601157		2203	4300	6503	SO:0001583	missense	259282	exon10			TTTATGAGGTGTA	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.7367T>C	chr4.hg19:g.13601157A>G	ENSP00000040738:p.Leu2456Pro	112.0	0.0	.	688	108.0	5.0	.	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	hg19	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	A	13.05	2.120234	0.37436	.	.	ENSG00000038219	ENST00000040738	T	0.09350	2.99	4.17	-0.642	0.11486	.	0.433636	0.16546	N	0.209707	T	0.06781	0.0173	L	0.27053	0.805	0.09310	N	1	B	0.12630	0.006	B	0.08055	0.003	T	0.30937	-0.9961	10	0.40728	T	0.16	.	8.0002	0.30293	0.597:0.0:0.403:0.0	.	2456	Q8NFC6	BOD1L_HUMAN	P	2456	ENSP00000040738:L2456P	ENSP00000040738:L2456P	L	-	2	0	BOD1L	13210255	0.000000	0.05858	0.003000	0.11579	0.018000	0.09664	0.222000	0.17699	-0.013000	0.14199	0.454000	0.30748	CTC	.	.	.	none		0.468	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		G	13601157	A	G	13601157	3	3	150	1	0	0	0	0	1	0	0	0	1483	304	11	3	1856	3	BOD1L	4	13601157	Missense_Mutation	SNP	A	TCGA-DW-7838-01A-11D-2136-08	7534481	13601157	177553119	19	8921											
GPR98	84059	hgsc.bcm.edu	37	chr5	89953910	89953915	+	In_Frame_Del	DEL	AAATCA	AAATCA	-																															tcagacagggagaaactaacAaatcattcattatttctgca																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	AAATCA	AAATCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr5:89953910_89953915delAAATCA	ENST00000405460.2	+	21	4663_4668	c.4567_4572delAAATCA	c.(4567-4572)aaatcadel	p.KS1523del		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1523	Calx-beta 10. {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)		AGAAACTAACAAATCATTCATTATTT	0.374																																					p.1522_1524del		Atlas-INDEL	.											.	GPR98	605	.	0			c.4566_4571del						PASS	.																																			SO:0001651	inframe_deletion	84059	exon21			.	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.4567_4572delAAATCA	chr5.hg19:g.89953910_89953915delAAATCA	ENSP00000384582:p.Lys1523_Ser1524del	124.0	0.0	0		126.0	30.0	0.238095	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	In_Frame_Del	DEL	ENST00000405460.2	hg19	CCDS47246.1																																																																																			.	.	.	none		0.374	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		-	89953915	AAATCA	-	89953910	7	5	150	1	0	1	0	1	0	0	0	0	6728	131	5	0	4649	0	GPR98	5	89953910	In_Frame_Del	DEL	AAATCA	TCGA-DW-7838-01A-11D-2136-08		89953910	90961350	20	8922											
C5orf36	285600	hgsc.bcm.edu	37	chr5	93856481	93856481	+	Missense_Mutation	SNP	A	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	agaggaattatcttcaacagAatgaagagacgtcctagaga	17	8	10	6	1	2	5	1	1	1	4	3	8	3	6	1	1	1	0	1	1	6	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr5:93856481A>C	ENST00000329378.7	-	5	691	c.442T>G	c.(442-444)Tct>Gct	p.S148A	KIAA0825_ENST00000427991.2_Missense_Mutation_p.S148A|KIAA0825_ENST00000513200.3_Missense_Mutation_p.S148A|KIAA0825_ENST00000312498.7_Missense_Mutation_p.S148A	NM_173665.2	NP_775936.1	Q8IV33	K0825_HUMAN	KIAA0825	148										breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(1)	13						TCTTCAACAGAATGAAGAGAC	0.418																																					p.S148A		Atlas-SNP	.											.	KIAA0825	172	.	0			c.T442G						PASS	.						68	68	68					5																	93856481		2203	4299	6502	SO:0001583	missense	285600	exon5			CAACAGAATGAAG	BX648338	CCDS4070.1	5q15	2011-02-23	2011-02-23	2011-02-23	ENSG00000185261	ENSG00000185261			28532	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 36"	C5orf36		12477932	Standard	NM_173665		Approved	DKFZp686F0372, MGC34713	uc011cuk.2	Q8IV33	OTTHUMG00000131331	ENST00000329378.7:c.442T>G	chr5.hg19:g.93856481A>C	ENSP00000331385:p.Ser148Ala	55.0	0.0	.		60.0	15.0	.	NM_173665	O94914|Q6ZNN2	Missense_Mutation	SNP	ENST00000329378.7	hg19	CCDS4070.1	.	.	.	.	.	.	.	.	.	.	A	0.007	-1.938185	0.00484	.	.	ENSG00000185261	ENST00000513200;ENST00000427991;ENST00000312498;ENST00000329378	T;T;T;T	0.38077	1.18;1.18;1.16;1.18	5.27	4.16	0.48862	.	1.670800	0.02660	N	0.107410	T	0.19644	0.0472	N	0.11560	0.145	0.21445	N	0.999683	B;B	0.11235	0.001;0.004	B;B	0.08055	0.002;0.003	T	0.37197	-0.9716	10	0.05436	T	0.98	.	6.5441	0.22397	0.4544:0.4284:0.0:0.1172	.	148;148	Q8IV33;Q8IV33-2	K0825_HUMAN;.	A	148	ENSP00000424618:S148A;ENSP00000400288:S148A;ENSP00000312205:S148A;ENSP00000331385:S148A	ENSP00000312205:S148A	S	-	1	0	KIAA0825	93882237	1.000000	0.71417	0.939000	0.37840	0.025000	0.11179	2.208000	0.42797	1.984000	0.57885	0.477000	0.44152	TCT	.	.	.	none		0.418	KIAA0825-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371180.2	NM_173665		C	93856481	A	C	93856481	3	2	150	1	0	0	0	0	1	0	0	0	2297	246	9	5	3458	5	C5orf36	5	93856481	Missense_Mutation	SNP	A	TCGA-DW-7838-01A-11D-2136-08	3902571	93856481	87058779	21	8923											
HSD17B4	3295	hgsc.bcm.edu	37	chr5	118824931	118824931	+	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	agtatgtggcacctcttgtcCtttggctttgtcacgagagt	6	15	11	9	1	2	1	1	0	1	1	3	2	3	1	2	2	0	3	2	2	1	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr5:118824931C>T	ENST00000256216.6	+	9	800	c.667C>T	c.(667-669)Ctt>Ttt	p.L223F	HSD17B4_ENST00000504811.1_Missense_Mutation_p.L248F|HSD17B4_ENST00000515320.1_Missense_Mutation_p.L205F|HSD17B4_ENST00000414835.2_Missense_Mutation_p.L83F|HSD17B4_ENST00000509514.1_5'UTR|HSD17B4_ENST00000513628.1_Missense_Mutation_p.L86F|HSD17B4_ENST00000510025.1_Missense_Mutation_p.L199F	NM_000414.3	NP_000405.1	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4	223	(3R)-hydroxyacyl-CoA dehydrogenase.				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)		ACCTCTTGTCCTTTGGCTTTG	0.378																																					p.L248F	Colon(35;490 801 34689 41394 43344)	Atlas-SNP	.											.	HSD17B4	63	.	0			c.C742T						PASS	.						221	214	217					5																	118824931		2202	4300	6502	SO:0001583	missense	3295	exon10			CTTGTCCTTTGGC		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.667C>T	chr5.hg19:g.118824931C>T	ENSP00000256216:p.Leu223Phe	87.0	0.0	.		186.0	61.0	.	NM_001199291	B4DNV1|B4DVS5|E9PB82|F5HE57	Missense_Mutation	SNP	ENST00000256216.6	hg19	CCDS4126.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.490542	0.64074	.	.	ENSG00000133835	ENST00000256216;ENST00000515320;ENST00000510025;ENST00000504811;ENST00000414835;ENST00000513628	D;D;D;D;D;D	0.90955	-2.76;-2.76;-2.76;-2.76;-2.76;-2.76	5.97	5.97	0.96955	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.95262	0.8463	M	0.87381	2.88	0.80722	D	1	D;P;P;P	0.71674	0.998;0.891;0.746;0.891	D;B;B;B	0.71414	0.973;0.266;0.266;0.194	D	0.94345	0.7574	10	0.39692	T	0.17	-19.2226	13.265	0.60128	0.0:0.9271:0.0:0.0729	.	248;205;199;223	F5HE57;E9PB82;E7EWE5;P51659	.;.;.;DHB4_HUMAN	F	223;205;199;248;83;86	ENSP00000256216:L223F;ENSP00000424613:L205F;ENSP00000424940:L199F;ENSP00000420914:L248F;ENSP00000411960:L83F;ENSP00000425993:L86F	ENSP00000256216:L223F	L	+	1	0	HSD17B4	118852830	0.999000	0.42202	1.000000	0.80357	0.393000	0.30537	3.986000	0.56937	2.834000	0.97654	0.650000	0.86243	CTT	.	.	.	none		0.378	HSD17B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250863.3	NM_000414		T	118824931	C	T	118824931	3	4	150	1	0	0	0	0	1	0	0	0	7393	681	24	2	701	2	HSD17B4	5	118824931	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	24968450	118824931	62090329	22	8924											
ZNF608	57507	hgsc.bcm.edu	37	chr5	123980011	123980011	+	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	ggtcgtacatctgtgggtaaGgataagcatgcaagtactgt	11	11	13	6	1	1	0	0	0	1	0	2	1	1	1	0	3	4	5	0	3	5	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr5:123980011G>A	ENST00000306315.5	-	5	4484	c.4049C>T	c.(4048-4050)cCt>cTt	p.P1350L	ZNF608_ENST00000513985.1_5'UTR|ZNF608_ENST00000504926.1_Missense_Mutation_p.P923L	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	1350							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)		CTGTGGGTAAGGATAAGCATG	0.502																																					p.P1350L		Atlas-SNP	.											.	ZNF608	117	.	0			c.C4049T						PASS	.						216	161	179					5																	123980011		2203	4300	6503	SO:0001583	missense	57507	exon5			GGGTAAGGATAAG	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.4049C>T	chr5.hg19:g.123980011G>A	ENSP00000307746:p.Pro1350Leu	86.0	0.0	.		105.0	17.0	.	NM_020747	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Missense_Mutation	SNP	ENST00000306315.5	hg19	CCDS34219.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.704307	0.88924	.	.	ENSG00000168916	ENST00000504926;ENST00000306315	T;T	0.50813	0.78;0.73	5.55	5.55	0.83447	.	0.063529	0.64402	D	0.000002	T	0.68961	0.3058	M	0.65498	2.005	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	T	0.70439	-0.4871	10	0.87932	D	0	-13.536	19.8645	0.96799	0.0:0.0:1.0:0.0	.	1350	Q9ULD9	ZN608_HUMAN	L	923;1350	ENSP00000427657:P923L;ENSP00000307746:P1350L	ENSP00000307746:P1350L	P	-	2	0	ZNF608	124007910	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.896000	0.87350	2.766000	0.95052	0.643000	0.83706	CCT	.	.	.	none		0.502	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432		A	123980011	G	A	123980011	3	1	150	1	0	0	0	0	1	0	0	0	18046	1000	35	2	509	2	ZNF608	5	123980011	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	5155080	123980011	56935249	23	8925											
GPR116	221395	hgsc.bcm.edu	37	chr6	46867766	46867766	+	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	ccaagcaagagtttacatacCggctcgtttttgcctcagtg	9	12	9	11	2	1	1	1	0	0	1	2	1	1	1	3	1	4	4	3	1	4	5	rs145334563	byFrequency	TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr6:46867766C>A	ENST00000283296.7	-	3	445	c.157G>T	c.(157-159)Gtt>Ttt	p.V53F	GPR116_ENST00000362015.4_Splice_Site_p.V53F|GPR116_ENST00000265417.7_Splice_Site_p.V53F|GPR116_ENST00000456426.2_Splice_Site_p.V53F	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	53					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)			GTTTACATACCGGCTCGTTTT	0.383																																					p.V53F	NSCLC(59;410 1274 8751 36715 50546)	Atlas-SNP	.											.	GPR116	133	.	0			c.G157T						PASS	.						109	98	102					6																	46867766		2203	4300	6503	SO:0001630	splice_region_variant	221395	exon3			ACATACCGGCTCG	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.157+1G>T	chr6.hg19:g.46867766C>A		119.0	0.0	.		100.0	22.0	.	NM_015234	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Missense_Mutation	SNP	ENST00000283296.7	hg19	CCDS4919.1	.	.	.	.	.	.	.	.	.	.	C	14.20	2.464871	0.43839	.	.	ENSG00000069122	ENST00000452370;ENST00000283296;ENST00000362015;ENST00000456426;ENST00000265417	T;T;T;T	0.29655	1.62;2.0;1.56;1.62	4.96	4.96	0.65561	.	0.286307	0.24695	N	0.036356	T	0.36082	0.0954	M	0.64997	1.995	0.80722	D	1	P;P;P	0.52842	0.956;0.911;0.956	P;P;P	0.56474	0.632;0.799;0.632	T	0.05468	-1.0883	9	.	.	.	-3.8272	14.057	0.64776	0.0:1.0:0.0:0.0	.	53;53;53	A8K0D8;Q8IZF2-3;Q8IZF2	.;.;GP116_HUMAN	F	53	ENSP00000283296:V53F;ENSP00000354563:V53F;ENSP00000412866:V53F;ENSP00000265417:V53F	.	V	-	1	0	GPR116	46975725	0.983000	0.35010	0.886000	0.34754	0.036000	0.12997	3.364000	0.52328	2.479000	0.83701	0.462000	0.41574	GTT	.	C|0.999;T|0.001	.	alt		0.383	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234	Missense_Mutation	A	46867766	C	A	46867766	5	1	150	1	0	0	0	0	0	0	1	0	6640	666	23	4	3959	4	GPR116	6	46867766	Splice_Site	SNP	C	TCGA-DW-7838-01A-11D-2136-08		46867766	124247301	24	8926											
COL9A1	1297	hgsc.bcm.edu	37	chr6	70944522	70944522	+	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	ggccctggacaccaggcaggCcggtggcaccctgttctccc	5	6	13	17	1	1	0	0	0	1	0	2	1	1	1	5	6	0	3	5	6	0	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr6:70944522C>A	ENST00000357250.6	-	34	2392	c.2234G>T	c.(2233-2235)gGc>gTc	p.G745V	RP1-149L1.1_ENST00000522264.1_RNA|COL9A1_ENST00000489611.1_5'UTR|COL9A1_ENST00000370499.4_Missense_Mutation_p.G502V|COL9A1_ENST00000320755.7_Missense_Mutation_p.G502V	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	745	Collagen-like 8.|Triple-helical region (COL2).				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						ACCAGGCAGGCCGGTGGCACC	0.647																																					p.G745V		Atlas-SNP	.											.	COL9A1	228	.	0			c.G2234T						PASS	.						36	38	37					6																	70944522		2203	4300	6503	SO:0001583	missense	1297	exon34			GGCAGGCCGGTGG		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.2234G>T	chr6.hg19:g.70944522C>A	ENSP00000349790:p.Gly745Val	55.0	0.0	.		53.0	5.0	.	NM_001851	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Missense_Mutation	SNP	ENST00000357250.6	hg19	CCDS4971.1	.	.	.	.	.	.	.	.	.	.	C	19.89	3.911377	0.72983	.	.	ENSG00000112280	ENST00000357250;ENST00000320755;ENST00000370499	D;D;D	0.99637	-6.29;-6.29;-6.29	5.74	5.74	0.90152	.	0.149132	0.64402	D	0.000011	D	0.99846	0.9929	H	0.97758	4.07	0.80722	D	1	D;D;P	0.76494	0.999;0.996;0.918	D;D;P	0.75484	0.986;0.941;0.806	D	0.96911	0.9667	10	0.87932	D	0	.	19.9077	0.97014	0.0:1.0:0.0:0.0	.	745;502;294	P20849;P20849-2;B3KWS8	CO9A1_HUMAN;.;.	V	745;502;502	ENSP00000349790:G745V;ENSP00000315252:G502V;ENSP00000359530:G502V	ENSP00000315252:G502V	G	-	2	0	COL9A1	71001243	1.000000	0.71417	0.988000	0.46212	0.907000	0.53573	7.556000	0.82233	2.714000	0.92807	0.585000	0.79938	GGC	.	.	.	none		0.647	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2			A	70944522	C	A	70944522	3	1	150	1	0	0	0	0	1	0	0	0	3709	739	26	4	551	4	COL9A1	6	70944522	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	24076756	70944522	100170545	25	8927											
PMS2	5395	hgsc.bcm.edu	37	chr7	6035170	6035170	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaaaattttaaatacctttgCtgggtcacaaggccgccggt	12	11	9	9	2	1	0	1	0	0	0	1	0	1	0	3	3	2	1	3	3	6	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:6035170C>T	ENST00000265849.7	-	8	1003	c.898G>A	c.(898-900)Gca>Aca	p.A300T	PMS2_ENST00000441476.2_Missense_Mutation_p.A194T|PMS2_ENST00000406569.3_Missense_Mutation_p.A300T|PMS2_ENST00000469652.1_Intron|PMS2_ENST00000382321.4_Intron	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	300					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)		AATACCTTTGCTGGGTCACAA	0.383			"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.A300T		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.G898A						PASS	.						89	84	86					7																	6035170		2203	4300	6503	SO:0001583	missense	5395	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	CCTTTGCTGGGTC		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.898G>A	chr7.hg19:g.6035170C>T	ENSP00000265849:p.Ala300Thr	95.0	0.0	.		104.0	31.0	.	NM_000535	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Missense_Mutation	SNP	ENST00000265849.7	hg19	CCDS5343.1	.	.	.	.	.	.	.	.	.	.	c	15.72	2.917497	0.52546	.	.	ENSG00000122512	ENST00000265849;ENST00000382322;ENST00000441476;ENST00000406569	D;D;D	0.83992	-1.79;-1.79;-1.79	5.85	4.96	0.65561	Ribosomal protein S5 domain 2-type fold (1);DNA mismatch repair protein, N-terminal (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);DNA mismatch repair protein, C-terminal (1);	0.410133	0.26345	N	0.024920	T	0.73969	0.3655	L	0.49350	1.555	0.42490	D	0.992891	B;B;B	0.34241	0.012;0.068;0.444	B;B;B	0.27262	0.007;0.013;0.078	T	0.69367	-0.5164	10	0.14656	T	0.56	-8.6094	10.6468	0.45626	0.1337:0.7984:0.0:0.0678	.	300;300;194	P54278-3;P54278;C9J167	.;PMS2_HUMAN;.	T	300;253;194;300	ENSP00000265849:A300T;ENSP00000392843:A194T;ENSP00000384308:A300T	ENSP00000265849:A300T	A	-	1	0	PMS2	6001696	0.544000	0.26441	1.000000	0.80357	0.989000	0.77384	0.265000	0.18515	1.469000	0.48083	0.650000	0.86243	GCA	.	.	.	none		0.383	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535		T	6035170	C	T	6035170	3	4	150	1	0	0	0	0	1	0	0	0	12150	797	28	2	1722	2	PMS2	7	6035170	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08		6035170	153103493	26	8928											
POU6F2	11281	hgsc.bcm.edu	37	chr7	39446255	39446255	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcagcagccatgagctcCatagcaagctcacaggcctt	10	7	10	14	0	1	1	1	1	0	0	2	1	2	1	3	1	6	6	3	1	2	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:39446255C>T	ENST00000403058.1	+	7	1096	c.942C>T	c.(940-942)tcC>tcT	p.S314S	POU6F2_ENST00000559001.1_Intron|POU6F2_ENST00000518318.2_Silent_p.S314S|POU6F2-AS1_ENST00000433519.1_RNA	NM_001166018.1|NM_007252.3	NP_001159490.1|NP_009183.3	P78424	PO6F2_HUMAN	POU class 6 homeobox 2	314	Gln-rich.				central nervous system development (GO:0007417)|ganglion mother cell fate determination (GO:0007402)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42						CCATGAGCTCCATAGCAAGCT	0.532																																					p.S314S		Atlas-SNP	.											.	POU6F2	117	.	0			c.C942T						PASS	.						57	57	57					7																	39446255		2203	4300	6503	SO:0001819	synonymous_variant	11281	exon7			GAGCTCCATAGCA	U91934	CCDS34620.2, CCDS55103.1	7p14.1	2011-06-20	2007-07-13		ENSG00000106536	ENSG00000106536		"Homeoboxes / POU class"	21694	protein-coding gene	gene with protein product	"Retina-derived POU-domain factor-1"	609062	"POU domain, class 6, transcription factor 2"			8601806	Standard	NM_007252		Approved	RPF-1	uc003thb.2	P78424	OTTHUMG00000150803	ENST00000403058.1:c.942C>T	chr7.hg19:g.39446255C>T		103.0	0.0	.		99.0	31.0	.	NM_007252	A4D1W2|C4AMB9|P78425|Q75ME8|Q86UM6|Q9UDS7	Silent	SNP	ENST00000403058.1	hg19	CCDS34620.2																																																																																			.	.	.	none		0.532	POU6F2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320146.3	NM_007252		T	39446255	C	T	39446255	2	4	150	1	0	0	0	0	0	0	0	1	12292	581	21	2		2	POU6F2	7	39446255	Silent	SNP	C	TCGA-DW-7838-01A-11D-2136-08	33411085	39446255	119692408	27	8929											
ZMIZ2	83637	hgsc.bcm.edu	37	chr7	44805818	44805818	+	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	tccttcccacccaccacgccCagcaccccaacccttgctga	8	6	4	23	1	0	1	0	1	0	0	2	1	2	1	8	0	3	2	8	0	1	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:44805818C>G	ENST00000309315.4	+	17	2421	c.2298C>G	c.(2296-2298)ccC>ccG	p.P766P	ZMIZ2_ENST00000413916.1_Silent_p.P708P|ZMIZ2_ENST00000433667.1_Silent_p.P734P|ZMIZ2_ENST00000265346.7_Silent_p.P740P|ZMIZ2_ENST00000463931.1_3'UTR|ZMIZ2_ENST00000441627.1_Silent_p.P766P	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2	766	Pro-rich.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						CCACCACGCCCAGCACCCCAA	0.632																																					p.P766P	NSCLC(20;604 852 1948 16908 50522)	Atlas-SNP	.											.	ZMIZ2	82	.	0			c.C2298G						PASS	.						58	66	64					7																	44805818		1960	4127	6087	SO:0001819	synonymous_variant	83637	exon17			CACGCCCAGCACC	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.2298C>G	chr7.hg19:g.44805818C>G		113.0	0.0	.		138.0	19.0	.	NM_031449	A4D2K7|D3DVL1|O94790|Q0VGB4|Q659A8|Q6JKL5|Q8WTX8|Q96Q01|Q9BQH7	Silent	SNP	ENST00000309315.4	hg19	CCDS43576.1																																																																																			.	.	.	none		0.632	ZMIZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341790.1	NM_031449		G	44805818	C	G	44805818	2	3	150	1	0	0	0	0	0	0	0	1	17709	581	21	4		4	ZMIZ2	7	44805818	Silent	SNP	C	TCGA-DW-7838-01A-11D-2136-08	5359563	44805818	114332845	28	8930											
DMTF1	9988	hgsc.bcm.edu	37	chr7	86808890	86808890	+	Frame_Shift_Del	DEL	C	C	-																															ataaaagatgctacagaaatCatctttgagatgtcaaaaga																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:86808890delC	ENST00000394703.5	+	10	1112	c.549delC	c.(547-549)atcfs	p.I184fs	DMTF1_ENST00000411766.2_Frame_Shift_Del_p.I143fs|DMTF1_ENST00000331242.7_Frame_Shift_Del_p.I184fs|DMTF1_ENST00000413276.2_Frame_Shift_Del_p.I184fs|DMTF1_ENST00000432937.2_Frame_Shift_Del_p.I96fs|DMTF1_ENST00000394702.3_Frame_Shift_Del_p.I184fs|DMTF1_ENST00000414194.2_5'UTR	NM_021145.3	NP_066968.3	Q9Y222	DMTF1_HUMAN	cyclin D binding myb-like transcription factor 1	184	Interaction with CCND1, CCND2 and CCND3. {ECO:0000250}.|Interaction with CCND2. {ECO:0000250}.|Required for DNA-binding. {ECO:0000250}.				cell cycle (GO:0007049)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)	16	Esophageal squamous(14;0.0058)					CTACAGAAATCATCTTTGAGA	0.363																																					p.I183fs		Atlas-INDEL	.											.	DMTF1	48	.	0			c.548delT						PASS	.						63	58	60					7																	86808890		2203	4300	6503	SO:0001589	frameshift_variant	9988	exon10			.	AF084530	CCDS5601.1, CCDS47633.1	7q21	2014-06-25			ENSG00000135164	ENSG00000135164			14603	protein-coding gene	gene with protein product	"cyclin D-binding Myb-like protein"	608491				10095122, 24958102	Standard	NR_024549		Approved	DMP1, DMTF, hDMP1, MRUL	uc003uih.3	Q9Y222	OTTHUMG00000154135	ENST00000394703.5:c.549delC	chr7.hg19:g.86808890delC	ENSP00000378193:p.Ile184fs	39.0	0.0	0		51.0	10.0	0.196078	NM_021145	B2RBE1|B4DJS5|Q05C48|Q59G79|Q6IS13|Q969T2|Q9H2Z2|Q9H2Z3	Frame_Shift_Del	DEL	ENST00000394703.5	hg19	CCDS5601.1																																																																																			.	.	.	none		0.363	DMTF1-002	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334025.5	NM_021145		-	86808890	C	-	86808890	7	5	150	1	0	1	0	1	0	0	0	0	4594	816	29	0	571	0	DMTF1	7	86808890	Frame_Shift_Del	DEL	C	TCGA-DW-7838-01A-11D-2136-08	42003072	86808890	72329773	29	8931											
ABCB4	5244	hgsc.bcm.edu	37	chr7	87051487	87051487	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcccagaaataagaaaatcaAagagaatatgttgcacttct	18	10	6	7	0	2	3	1	0	1	3	3	4	3	3	1	0	1	2	1	0	7	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:87051487A>G	ENST00000265723.4	-	18	2377	c.2266T>C	c.(2266-2268)Ttg>Ctg	p.L756L	ABCB4_ENST00000359206.3_Silent_p.L756L|ABCB4_ENST00000453593.1_Silent_p.L756L|ABCB4_ENST00000545634.1_Silent_p.L756L|ABCB4_ENST00000358400.3_Silent_p.L756L	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	756	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	AAGAAAATCAAAGAGAATATG	0.338																																					p.L756L		Atlas-SNP	.											.	ABCB4	177	.	0			c.T2266C						PASS	.						56	56	56					7																	87051487		2203	4300	6503	SO:0001819	synonymous_variant	5244	exon18			AAATCAAAGAGAA	M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"ATP binding cassette transporters / subfamily B"	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.2266T>C	chr7.hg19:g.87051487A>G		59.0	0.0	.		58.0	4.0	.	NM_018850	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Silent	SNP	ENST00000265723.4	hg19	CCDS5606.1																																																																																			.	.	.	none		0.338	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443		G	87051487	A	G	87051487	2	3	150	1	0	0	0	0	0	0	0	1	43	11	1	3		3	ABCB4	7	87051487	Silent	SNP	A	TCGA-DW-7838-01A-11D-2136-08	242597	87051487	72087176	30	8932											
CYP3A43	64816	hgsc.bcm.edu	37	chr7	99454477	99454477	+	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	atcgagtagatttctttcaaCagatgatcgactcccagaat	13	12	7	9	2	2	4	1	1	1	3	5	6	3	4	1	0	1	1	1	0	3	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:99454477C>A	ENST00000354829.2	+	9	923	c.820C>A	c.(820-822)Cag>Aag	p.Q274K	CYP3A43_ENST00000415413.1_Missense_Mutation_p.Q63K|CYP3A43_ENST00000477658.1_3'UTR|CYP3A43_ENST00000417625.1_Missense_Mutation_p.Q164K|CYP3A43_ENST00000444905.1_Missense_Mutation_p.Q21K|CYP3A43_ENST00000312017.5_Missense_Mutation_p.Q274K|CYP3A43_ENST00000222382.5_Missense_Mutation_p.Q274K|CYP3A43_ENST00000342499.4_Missense_Mutation_p.Q134K	NM_022820.3|NM_057095.1	NP_073731.1|NP_476436.1	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 43	274			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)	TTTCTTTCAACAGATGATCGA	0.438																																					p.Q274K		Atlas-SNP	.											.	CYP3A43	52	.	0			c.C820A						PASS	.						92	99	97					7																	99454477		2203	4300	6503	SO:0001583	missense	64816	exon9			TTTCAACAGATGA	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.820C>A	chr7.hg19:g.99454477C>A	ENSP00000346887:p.Gln274Lys	215.0	0.0	.		188.0	18.0	.	NM_057096	Q495Y1|Q75MK2|Q75MK3|Q9HB52|Q9HB53|Q9HB54|Q9HB57	Missense_Mutation	SNP	ENST00000354829.2	hg19	CCDS5676.1	.	.	.	.	.	.	.	.	.	.	C	11.75	1.731904	0.30684	.	.	ENSG00000021461	ENST00000354829;ENST00000417625;ENST00000342499;ENST00000444905;ENST00000415413;ENST00000312017;ENST00000222382	T;T;T;T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28;-0.23;-0.28;-0.28	2.26	0.94	0.19513	.	0.176318	0.37623	U	0.002017	T	0.55625	0.1932	L	0.37697	1.125	0.20873	N	0.999837	B;P;B;B;B	0.39094	0.048;0.659;0.023;0.029;0.012	B;P;B;B;B	0.44732	0.067;0.459;0.006;0.011;0.011	T	0.50742	-0.8792	10	0.87932	D	0	.	4.1559	0.10260	0.0:0.6974:0.0:0.3026	.	164;134;274;274;274	Q495Y1;F8W6L8;Q9HB55-3;Q75MK2;Q9HB55	.;.;.;.;CP343_HUMAN	K	274;164;134;21;63;274;274	ENSP00000346887:Q274K;ENSP00000416581:Q164K;ENSP00000345351:Q134K;ENSP00000405557:Q21K;ENSP00000401521:Q63K;ENSP00000312110:Q274K;ENSP00000222382:Q274K	ENSP00000222382:Q274K	Q	+	1	0	CYP3A43	99292413	0.985000	0.35326	0.730000	0.30809	0.247000	0.25773	0.188000	0.17018	0.257000	0.21650	0.195000	0.17529	CAG	.	.	.	none		0.438	CYP3A43-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000344379.1			A	99454477	C	A	99454477	3	1	150	1	0	0	0	0	1	0	0	0	4181	479	17	4	854	4	CYP3A43	7	99454477	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	12402990	99454477	59684186	31	8933											
CPA4	51200	hgsc.bcm.edu	37	chr7	129962495	129962495	+	Silent	SNP	T	T	C																															ctgaagaccatcatggagcaTgtgcgggacaacctctacta																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:129962495T>C	ENST00000222482.4	+	11	1273	c.1245T>C	c.(1243-1245)caT>caC	p.H415H	CPA4_ENST00000493259.1_Silent_p.H311H|CPA4_ENST00000445470.2_Silent_p.H382H	NM_016352.3	NP_057436.2	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4	415					histone acetylation (GO:0016573)	extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Melanoma(18;0.0435)					TCATGGAGCATGTGCGGGACA	0.537																																					p.H415H		Atlas-SNP	.											.	CPA4	47	.	0			c.T1245C						PASS	.						198	161	173					7																	129962495		2203	4300	6503	SO:0001819	synonymous_variant	51200	exon11			GGAGCATGTGCGG	AF095719	CCDS5818.1, CCDS55163.1	7q32	2008-07-18			ENSG00000128510	ENSG00000128510			15740	protein-coding gene	gene with protein product	"carboxypeptidase A3"	607635				10383164, 10860668	Standard	NM_016352		Approved	CPA3	uc003vpr.3	Q9UI42	OTTHUMG00000157825	ENST00000222482.4:c.1245T>C	chr7.hg19:g.129962495T>C		159.0	0.0	.		188.0	39.0	.	NM_016352	B7Z576|Q86UY9	Silent	SNP	ENST00000222482.4	hg19	CCDS5818.1																																																																																			.	.	.	none		0.537	CPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349725.1	NM_016352		C	129962495	T	C	129962495	2	2	150	1	0	0	0	0	0	0	0	1	3794	1461	51	3		3	CPA4	7	129962495	Silent	SNP	T	TCGA-DW-7838-01A-11D-2136-08	30508018	129962495	29176168	32	8934	91	2									
CPA4	51200	hgsc.bcm.edu	37	chr7	129962499	129962499	+	Missense_Mutation	SNP	C	C	T																															agaccatcatggagcatgtgCgggacaacctctactaggcg																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:129962499C>T	ENST00000222482.4	+	11	1277	c.1249C>T	c.(1249-1251)Cgg>Tgg	p.R417W	CPA4_ENST00000493259.1_Missense_Mutation_p.R313W|CPA4_ENST00000445470.2_Missense_Mutation_p.R384W	NM_016352.3	NP_057436.2	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4	417					histone acetylation (GO:0016573)	extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Melanoma(18;0.0435)					GGAGCATGTGCGGGACAACCT	0.542																																					p.R417W		Atlas-SNP	.											.	CPA4	47	.	0			c.C1249T						PASS	.						193	157	169					7																	129962499		2203	4300	6503	SO:0001583	missense	51200	exon11			CATGTGCGGGACA	AF095719	CCDS5818.1, CCDS55163.1	7q32	2008-07-18			ENSG00000128510	ENSG00000128510			15740	protein-coding gene	gene with protein product	"carboxypeptidase A3"	607635				10383164, 10860668	Standard	NM_016352		Approved	CPA3	uc003vpr.3	Q9UI42	OTTHUMG00000157825	ENST00000222482.4:c.1249C>T	chr7.hg19:g.129962499C>T	ENSP00000222482:p.Arg417Trp	154.0	0.0	.		185.0	42.0	.	NM_016352	B7Z576|Q86UY9	Missense_Mutation	SNP	ENST00000222482.4	hg19	CCDS5818.1	.	.	.	.	.	.	.	.	.	.	C	13.60	2.286285	0.40494	.	.	ENSG00000128510	ENST00000445470;ENST00000222482;ENST00000538687;ENST00000493259	T;T;T	0.03468	3.92;3.92;3.92	5.75	2.87	0.33458	.	0.218110	0.40908	D	0.000989	T	0.13970	0.0338	M	0.79475	2.455	0.09310	N	1	D;D	0.89917	0.999;1.0	P;D	0.65443	0.827;0.935	T	0.01956	-1.1240	10	0.56958	D	0.05	.	9.1872	0.37178	0.2596:0.6719:0.0:0.0685	.	384;417	B7Z576;Q9UI42	.;CBPA4_HUMAN	W	384;417;222;313	ENSP00000412947:R384W;ENSP00000222482:R417W;ENSP00000419660:R313W	ENSP00000222482:R417W	R	+	1	2	CPA4	129749735	0.000000	0.05858	0.981000	0.43875	0.111000	0.19643	0.043000	0.13971	0.763000	0.33175	0.563000	0.77884	CGG	.	.	.	none		0.542	CPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349725.1	NM_016352		T	129962499	C	T	129962499	3	4	150	1	0	0	0	0	1	0	0	0	3794	759	27	1	1291	1	CPA4	7	129962499	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	4	129962499	29176164	33	8935	91	2									
AKR1B15	441282	hgsc.bcm.edu	37	chr7	134260620	134260620	+	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	gagaaactgatccagtactgCcactccaagggcatcaccgt	12	7	9	13	1	1	2	1	1	0	1	3	3	3	2	4	1	3	2	4	1	3	1	rs267601304		TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:134260620C>T	ENST00000457545.2	+	8	944	c.684C>T	c.(682-684)tgC>tgT	p.C228C	AKR1B15_ENST00000423958.1_Silent_p.C200C	NM_001080538.2	NP_001074007.2	C9JRZ8	AK1BF_HUMAN	aldo-keto reductase family 1, member B15	228							oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|urinary_tract(1)	18						TCCAGTACTGCCACTCCAAGG	0.532																																					p.C228C		Atlas-SNP	.											.	AKR1B15	105	.	0			c.C684T						PASS	.						111	88	96					7																	134260620		2203	4300	6503	SO:0001819	synonymous_variant	441282	exon8			GTACTGCCACTCC		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.684C>T	chr7.hg19:g.134260620C>T		129.0	0.0	.		105.0	20.0	.	NM_001080538	C9J3V2	Silent	SNP	ENST00000457545.2	hg19	CCDS47715.2																																																																																			.	.	.	none		0.532	AKR1B15-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339726.2			T	134260620	C	T	134260620	2	4	150	1	0	0	0	0	0	0	0	1	468	747	26	2		2	AKR1B15	7	134260620	Silent	SNP	C	TCGA-DW-7838-01A-11D-2136-08	4298121	134260620	24878043	34	8936											
SVOPL	136306	hgsc.bcm.edu	37	chr7	138281232	138281232	+	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	cgcatacaacacagacagatGagaagagacacagggccccc	16	2	10	13	1	0	4	0	1	0	4	0	6	0	4	2	1	2	1	2	1	3	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:138281232G>A	ENST00000419765.3	-	14	1430	c.1397C>T	c.(1396-1398)tCa>tTa	p.S466L	SVOPL_ENST00000421622.1_Missense_Mutation_p.S346L|SVOPL_ENST00000288513.5_Missense_Mutation_p.S314L|SVOPL_ENST00000463557.1_5'UTR|SVOPL_ENST00000436657.1_Missense_Mutation_p.S314L	NM_001139456.1	NP_001132928.1	Q8N434	SVOPL_HUMAN	SVOP-like	466						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	19						ACAGACAGATGAGAAGAGACA	0.463																																					p.S466L		Atlas-SNP	.											.	SVOPL	111	.	0			c.C1397T						PASS	.						117	111	113					7																	138281232		2203	4300	6503	SO:0001583	missense	136306	exon14			ACAGATGAGAAGA	BC036796	CCDS5848.1, CCDS47721.1	7q34	2011-07-12	2007-04-04		ENSG00000157703	ENSG00000157703			27034	protein-coding gene	gene with protein product		611700	"SV2 related protein homolog (rat)-like"				Standard	NM_001139456		Approved	MGC46715	uc011kqh.2	Q8N434	OTTHUMG00000155870	ENST00000419765.3:c.1397C>T	chr7.hg19:g.138281232G>A	ENSP00000405482:p.Ser466Leu	80.0	0.0	.		107.0	14.0	.	NM_001139456		Missense_Mutation	SNP	ENST00000419765.3	hg19	CCDS47721.1	.	.	.	.	.	.	.	.	.	.	G	12.07	1.826903	0.32329	.	.	ENSG00000157703	ENST00000288513;ENST00000421622;ENST00000436657;ENST00000419765	T;T;T;T	0.58210	0.35;0.35;0.35;0.35	5.48	5.48	0.80851	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.260251	0.37483	N	0.002067	T	0.40145	0.1105	N	0.22421	0.69	0.35878	D	0.828749	B;B	0.33171	0.012;0.4	B;B	0.28011	0.055;0.085	T	0.51317	-0.8721	10	0.45353	T	0.12	-3.3112	17.1313	0.86727	0.0:0.0:1.0:0.0	.	466;314	Q8N434;Q8N434-2	SVOPL_HUMAN;.	L	314;346;314;466	ENSP00000288513:S314L;ENSP00000412830:S346L;ENSP00000417018:S314L;ENSP00000405482:S466L	ENSP00000288513:S314L	S	-	2	0	SVOPL	137931772	1.000000	0.71417	0.821000	0.32701	0.024000	0.10985	5.924000	0.70054	2.563000	0.86464	0.655000	0.94253	TCA	.	.	.	none		0.463	SVOPL-005	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342092.4	NM_174959		A	138281232	G	A	138281232	3	1	150	1	0	0	0	0	1	0	0	0	15436	1294	45	2	89	2	SVOPL	7	138281232	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	4020612	138281232	20857431	35	8937											
ZNF777	27153	hgsc.bcm.edu	37	chr7	149152518	149152518	+	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	gcctcatggcctgggcctccAgcttcctctccactgcttgg	3	11	10	17	0	2	0	1	0	1	0	5	0	4	0	6	3	2	2	6	3	0	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:149152518A>T	ENST00000247930.4	-	2	919	c.596T>A	c.(595-597)cTg>cAg	p.L199Q		NM_015694.2	NP_056509.2	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	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(5)|lung(17)|ovary(1)|skin(2)|urinary_tract(1)	26	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			CTGGGCCTCCAGCTTCCTCTC	0.597																																					p.L199Q		Atlas-SNP	.											.	ZNF777	63	.	0			c.T596A						PASS	.						67	76	73					7																	149152518		2188	4291	6479	SO:0001583	missense	27153	exon2			GCCTCCAGCTTCC	AB033111	CCDS43675.1	7q36.1	2013-01-08			ENSG00000196453	ENSG00000196453		"Zinc fingers, C2H2-type", "-"	22213	protein-coding gene	gene with protein product							Standard	NM_015694		Approved	KIAA1285	uc003wfv.3	Q9ULD5	OTTHUMG00000158967	ENST00000247930.4:c.596T>A	chr7.hg19:g.149152518A>T	ENSP00000247930:p.Leu199Gln	204.0	0.0	.		209.0	46.0	.	NM_015694	Q8N2R2|Q8N659	Missense_Mutation	SNP	ENST00000247930.4	hg19	CCDS43675.1	.	.	.	.	.	.	.	.	.	.	A	19.31	3.802961	0.70682	.	.	ENSG00000196453	ENST00000247930	T	0.06294	3.32	4.93	4.93	0.64822	.	0.234968	0.21936	N	0.066956	T	0.06554	0.0168	N	0.08118	0	0.33892	D	0.637431	D	0.54207	0.965	P	0.51355	0.667	T	0.32322	-0.9911	10	0.72032	D	0.01	-14.7997	11.0022	0.47614	1.0:0.0:0.0:0.0	.	199	Q9ULD5-2	.	Q	199	ENSP00000247930:L199Q	ENSP00000247930:L199Q	L	-	2	0	ZNF777	148783451	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	5.489000	0.66875	1.856000	0.53863	0.533000	0.62120	CTG	.	.	.	none		0.597	ZNF777-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352708.1	NM_015694		T	149152518	A	T	149152518	3	4	150	1	0	0	0	0	1	0	0	0	18162	188	7	5	1919	5	ZNF777	7	149152518	Missense_Mutation	SNP	A	TCGA-DW-7838-01A-11D-2136-08	10871286	149152518	9986145	36	8938											
TSNARE1	203062	hgsc.bcm.edu	37	chr8	143381927	143381927	+	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	gtccgggagcagcgcctgctCctggccctgccacatgttgt	4	9	13	15	2	0	0	0	0	0	0	2	1	2	1	5	2	4	3	5	2	0	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr8:143381927C>G	ENST00000307180.3	-	10	1327	c.1210G>C	c.(1210-1212)Gag>Cag	p.E404Q	TSNARE1_ENST00000519651.1_Missense_Mutation_p.E185Q|TSNARE1_ENST00000524325.1_Missense_Mutation_p.E403Q|TSNARE1_ENST00000518928.1_5'UTR|TSNARE1_ENST00000520166.1_Missense_Mutation_p.E404Q	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	404					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)					AGCGCCTGCTCCTGGCCCTGC	0.617																																					p.E404Q		Atlas-SNP	.											.	TSNARE1	59	.	0			c.G1210C						PASS	.						73	66	69					8																	143381927		2203	4300	6503	SO:0001583	missense	203062	exon10			CCTGCTCCTGGCC			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.1210G>C	chr8.hg19:g.143381927C>G	ENSP00000303437:p.Glu404Gln	109.0	0.0	.		103.0	14.0	.	NM_145003	B7ZLB0|Q14D03	Missense_Mutation	SNP	ENST00000307180.3	hg19	CCDS6384.1	.	.	.	.	.	.	.	.	.	.	C	7.933	0.741084	0.15642	.	.	ENSG00000171045	ENST00000524325;ENST00000307180;ENST00000520166;ENST00000519651	T;T;T;T	0.20463	2.07;2.07;2.07;2.07	4.76	3.89	0.44902	t-SNARE (1);	0.233173	0.21158	U	0.079203	T	0.16214	0.0390	L	0.37630	1.12	0.23254	N	0.998034	P;B;P;P	0.47409	0.895;0.421;0.895;0.895	B;B;B;B	0.41299	0.353;0.058;0.353;0.353	T	0.08351	-1.0726	10	0.27082	T	0.32	-20.6332	10.2182	0.43182	0.0:0.9055:0.0:0.0945	.	403;185;404;405	B7ZLB0;E5RHT3;Q96NA8;A0AVG3	.;.;TSNA1_HUMAN;.	Q	403;404;404;185	ENSP00000428763:E403Q;ENSP00000303437:E404Q;ENSP00000427770:E404Q;ENSP00000429679:E185Q	ENSP00000303437:E404Q	E	-	1	0	TSNARE1	143379834	0.970000	0.33590	0.175000	0.22980	0.206000	0.24218	1.184000	0.32053	1.001000	0.39076	-0.137000	0.14449	GAG	.	.	.	none		0.617	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_145003		G	143381927	C	G	143381927	3	3	150	1	0	0	0	0	1	0	0	0	16642	864	30	4	347	4	TSNARE1	8	143381927	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08		143381927	2982095	37	8939											
TSTD2	158427	hgsc.bcm.edu	37	chr9	100368460	100368460	+	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	gaagtttctgcaatcaagaaGgatagtatcactttgttctt	12	15	8	6	0	4	1	2	0	2	1	4	3	4	2	0	1	1	4	0	1	6	6			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr9:100368460G>T	ENST00000341170.4	-	7	1301	c.919C>A	c.(919-921)Ctt>Att	p.L307I	TSTD2_ENST00000354801.2_Missense_Mutation_p.L47I	NM_139246.4	NP_640339.4	Q5T7W7	TSTD2_HUMAN	thiosulfate sulfurtransferase (rhodanese)-like domain containing 2	307	Rhodanese. {ECO:0000255|PROSITE- ProRule:PRU00173}.							p.L307I(1)		large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	15						CAATCAAGAAGGATAGTATCA	0.353																																					p.L307I		Atlas-SNP	.											TSTD2,NS,carcinoma,0,1	TSTD2	42	.	1	Substitution - Missense(1)	ovary(1)	c.C919A						PASS	.						117	116	117					9																	100368460		2203	4300	6503	SO:0001583	missense	158427	exon7			CAAGAAGGATAGT	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.919C>A	chr9.hg19:g.100368460G>T	ENSP00000342499:p.Leu307Ile	103.0	0.0	.		72.0	9.0	.	NM_139246	A6NMJ4|A8K584|Q6ZQZ6|Q8IYM3|Q8WY73|Q96ML6|Q96MU1	Missense_Mutation	SNP	ENST00000341170.4	hg19	CCDS6727.2	.	.	.	.	.	.	.	.	.	.	G	14.49	2.552202	0.45487	.	.	ENSG00000136925	ENST00000375172;ENST00000341170;ENST00000375165;ENST00000354801	T;T;T	0.27104	1.69;1.69;1.69	5.18	3.31	0.37934	Rhodanese-like (5);	0.066943	0.64402	N	0.000014	T	0.17916	0.0430	L	0.41492	1.28	0.32895	D	0.512421	B;B	0.33477	0.013;0.413	B;B	0.35607	0.032;0.206	T	0.14172	-1.0482	10	0.20046	T	0.44	-5.0176	5.6795	0.17767	0.1448:0.0:0.666:0.1892	.	81;307	B3KVC7;Q5T7W7	.;TSTD2_HUMAN	I	81;307;47;47	ENSP00000342499:L307I;ENSP00000364308:L47I;ENSP00000346856:L47I	ENSP00000342499:L307I	L	-	1	0	TSTD2	99408281	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	1.989000	0.40707	1.490000	0.48466	0.655000	0.94253	CTT	.	.	.	none		0.353	TSTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053325.4	NM_139246		T	100368460	G	T	100368460	3	4	150	1	0	0	0	0	1	0	0	0	16687	1000	35	4	647	4	TSTD2	9	100368460	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08		100368460	40844971	38	8940											
SLC31A1	1317	hgsc.bcm.edu	37	chr9	116018468	116018469	+	Frame_Shift_Ins	INS	-	-	C																															ggggatgagctatatggactINSccaacagtaccatgcaacct																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr9:116018468_116018469insC	ENST00000374212.4	+	2	192_193	c.40_41insC	c.(40-42)tccfs	p.S14fs	CDC26_ENST00000490408.1_Intron|SLC31A1_ENST00000374210.6_Frame_Shift_Ins_p.S14fs	NM_001859.3	NP_001850.1	O15431	COPT1_HUMAN	solute carrier family 31 (copper transporter), member 1	14					cellular copper ion homeostasis (GO:0006878)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	copper ion transmembrane transporter activity (GO:0005375)|copper uptake transmembrane transporter activity (GO:0015088)			breast(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	7					Bortezomib(DB00188)|Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	CTATATGGACTCCAACAGTACC	0.436																																					p.S14fs	Ovarian(135;1049 1799 4519 17564 28677)	Atlas-INDEL	.											.	SLC31A1	12	.	0			c.40_41insC						PASS	.																																			SO:0001589	frameshift_variant	1317	exon2			.	U83460	CCDS6789.1	9q32	2013-07-17	2013-07-17		ENSG00000136868	ENSG00000136868		"Solute carriers"	11016	protein-coding gene	gene with protein product	copper transport 1 homolog (S. cerevisiae)	603085		COPT1		9207117	Standard	NM_001859		Approved	hCTR1, CTR1	uc004bgu.3	O15431	OTTHUMG00000020519	ENST00000374212.4:c.42dupC	chr9.hg19:g.116018470_116018470dupC	ENSP00000363329:p.Ser14fs	134.0	0.0	0		118.0	18.0	0.152542	NM_001859	A8K8Z6|Q53GR5|Q5T1M4	Frame_Shift_Ins	INS	ENST00000374212.4	hg19	CCDS6789.1																																																																																			.	.	.	none		0.436	SLC31A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053715.1	NM_001859		C	116018469	-	C	116018468	7	5	150	1	0	1	1	0	0	0	0	0	14576	1551	54	0	42	0	SLC31A1	9	116018468	Frame_Shift_Ins	INS	-	TCGA-DW-7838-01A-11D-2136-08	15650008	116018468	25194963	39	8941											
OR1N2	138882	hgsc.bcm.edu	37	chr9	125316283	125316283	+	Frame_Shift_Del	DEL	C	C	-																															ttatgggtgtgtatttacttCctccatcaacttactctaca																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr9:125316283delC	ENST00000373688.2	+	1	893	c.835delC	c.(835-837)cctfs	p.P280fs		NM_001004457.1	NP_001004457.1	Q8NGR9	OR1N2_HUMAN	olfactory receptor, family 1, subfamily N, member 2	280						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(3)	26						GTATTTACTTCCTCCATCAAC	0.463																																					p.L278fs		Atlas-INDEL	.											.	OR1N2	51	.	0			c.834delT						PASS	.						196	199	198					9																	125316283		2203	4300	6503	SO:0001589	frameshift_variant	138882	exon1			.		CCDS35123.1	9q33.2	2013-09-20			ENSG00000171501	ENSG00000171501		"GPCR / Class A : Olfactory receptors"	15111	protein-coding gene	gene with protein product							Standard	NM_001004457		Approved		uc011lyx.2	Q8NGR9	OTTHUMG00000020607	ENST00000373688.2:c.835delC	chr9.hg19:g.125316283delC	ENSP00000362792:p.Pro280fs	115.0	0.0	0		140.0	21.0	0.15	NM_001004457	A3KFM2|B2RNY4|Q6IF17|Q96RA3	Frame_Shift_Del	DEL	ENST00000373688.2	hg19	CCDS35123.1																																																																																			.	.	.	none		0.463	OR1N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053937.2			-	125316283	C	-	125316283	7	5	150	1	0	1	0	1	0	0	0	0	10977	855	30	0	837	0	OR1N2	9	125316283	Frame_Shift_Del	DEL	C	TCGA-DW-7838-01A-11D-2136-08	9297815	125316283	15897148	40	8942											
HSPA5	3309	hgsc.bcm.edu	37	chr9	128001454	128001454	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctggtcaaagtcttctccAcccagatgagtatctccatt	9	12	7	13	1	4	2	1	1	3	1	6	2	4	2	3	1	0	2	3	1	2	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr9:128001454A>G	ENST00000324460.6	-	5	965	c.762T>C	c.(760-762)ggT>ggC	p.G254G	RP11-65N13.8_ENST00000468244.1_RNA	NM_005347.4	NP_005338.1	P11021	GRP78_HUMAN	heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa)	254					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular response to antibiotic (GO:0071236)|cellular response to glucose starvation (GO:0042149)|cellular response to interleukin-4 (GO:0071353)|cerebellar Purkinje cell layer development (GO:0021680)|cerebellum structural organization (GO:0021589)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|maintenance of protein localization in endoplasmic reticulum (GO:0035437)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell migration (GO:0030335)|positive regulation of protein ubiquitination (GO:0031398)|regulation of protein folding in endoplasmic reticulum (GO:0060904)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum chaperone complex (GO:0034663)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|chaperone binding (GO:0051087)|enzyme binding (GO:0019899)|glycoprotein binding (GO:0001948)|misfolded protein binding (GO:0051787)|protein domain specific binding (GO:0019904)|ribosome binding (GO:0043022)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(4)|prostate(2)|skin(1)	23					Acetylsalicylic acid(DB00945)|Antihemophilic Factor(DB00025)	AGTCTTCTCCACCCAGATGAG	0.468										Prostate(1;0.17)																											p.G254G		Atlas-SNP	.											.	HSPA5	41	.	0			c.T762C						PASS	.						58	57	57					9																	128001454		2203	4300	6503	SO:0001819	synonymous_variant	3309	exon5			TTCTCCACCCAGA		CCDS6863.1	9q33.3	2011-09-02	2002-08-29		ENSG00000044574	ENSG00000044574		"Heat shock proteins / HSP70"	5238	protein-coding gene	gene with protein product		138120	"heat shock 70kD protein 5 (glucose-regulated protein, 78kD)"	GRP78			Standard	NM_005347		Approved	BiP	uc004bpn.3	P11021	OTTHUMG00000020672	ENST00000324460.6:c.762T>C	chr9.hg19:g.128001454A>G		68.0	0.0	.		52.0	7.0	.	NM_005347	B0QZ61|Q2EF78|Q9NPF1|Q9UK02	Silent	SNP	ENST00000324460.6	hg19	CCDS6863.1																																																																																			.	.	.	none		0.468	HSPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054062.1			G	128001454	A	G	128001454	2	3	150	1	0	0	0	0	0	0	0	1	7421	146	6	3		3	HSPA5	9	128001454	Silent	SNP	A	TCGA-DW-7838-01A-11D-2136-08	2685171	128001454	13211977	41	8943											
PKN3	29941	hgsc.bcm.edu	37	chr9	131476565	131476565	+	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	tgctgcccccctgcagctccCcgagcacaatcagcccccct	6	6	7	22	1	1	0	1	0	0	0	2	1	2	0	8	0	6	4	8	0	1	0			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr9:131476565C>A	ENST00000291906.4	+	11	1795	c.1402C>A	c.(1402-1404)Ccg>Acg	p.P468T		NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	468	Pro-rich.				epithelial cell migration (GO:0010631)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24						CTGCAGCTCCCCGAGCACAAT	0.647																																					p.P468T		Atlas-SNP	.											.	PKN3	62	.	0			c.C1402A						PASS	.						62	70	67					9																	131476565		2203	4300	6503	SO:0001583	missense	29941	exon11			AGCTCCCCGAGCA	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.1402C>A	chr9.hg19:g.131476565C>A	ENSP00000291906:p.Pro468Thr	243.0	0.0	.		240.0	42.0	.	NM_013355	Q9UM03	Missense_Mutation	SNP	ENST00000291906.4	hg19	CCDS6908.1	.	.	.	.	.	.	.	.	.	.	C	6.729	0.503216	0.12822	.	.	ENSG00000160447	ENST00000291906	T	0.27256	1.68	5.3	4.36	0.52297	.	.	.	.	.	T	0.22742	0.0549	L	0.51422	1.61	0.26351	N	0.977203	P	0.42827	0.791	B	0.40901	0.343	T	0.05616	-1.0874	9	0.09590	T	0.72	.	11.1984	0.48726	0.3181:0.6818:0.0:0.0	.	468	Q6P5Z2	PKN3_HUMAN	T	468	ENSP00000291906:P468T	ENSP00000291906:P468T	P	+	1	0	PKN3	130516386	0.031000	0.19500	0.911000	0.35937	0.516000	0.34256	1.330000	0.33781	2.478000	0.83669	0.563000	0.77884	CCG	.	.	.	none		0.647	PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054487.1	NM_013355		A	131476565	C	A	131476565	3	1	150	1	0	0	0	0	1	0	0	0	11988	623	22	4	1444	4	PKN3	9	131476565	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	3475111	131476565	9736866	42	8944											
ZER1	10444	hgsc.bcm.edu	37	chr9	131512978	131512978	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacactctgctctgagcggtActcggaatttgttaggtaga	9	12	11	9	2	2	2	0	1	2	1	3	3	2	3	0	3	3	4	0	3	4	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr9:131512978A>G	ENST00000291900.2	-	8	1682	c.1276T>C	c.(1276-1278)Tac>Cac	p.Y426H	ZER1_ENST00000494461.1_5'Flank|snoU13_ENST00000459043.1_RNA	NM_006336.2	NP_006327.2	Q7Z7L7	ZER1_HUMAN	zyg-11 related, cell cycle regulator	426					protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein transferase activity (GO:0051438)	Cul2-RING ubiquitin ligase complex (GO:0031462)	ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	15						TCTGAGCGGTACTCGGAATTT	0.562																																					p.Y426H		Atlas-SNP	.											.	ZER1	49	.	0			c.T1276C						PASS	.						102	89	94					9																	131512978		2203	4300	6503	SO:0001583	missense	10444	exon8			AGCGGTACTCGGA	X99802	CCDS6910.1	9q33.3	2013-01-17	2012-12-10	2007-01-04	ENSG00000160445	ENSG00000160445		"ZYG11 cell cycle regulator family"	30960	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 60", "zyg-11 homolog B (C. elegans)-like", "zer-1 homolog (C. elegans)"	C9orf60, ZYG11BL		11719588	Standard	NM_006336		Approved	ZYG, Hzyg	uc004bwa.2	Q7Z7L7	OTTHUMG00000020759	ENST00000291900.2:c.1276T>C	chr9.hg19:g.131512978A>G	ENSP00000291900:p.Tyr426His	82.0	0.0	.		100.0	16.0	.	NM_006336	O00156|Q5T272|Q5T273	Missense_Mutation	SNP	ENST00000291900.2	hg19	CCDS6910.1	.	.	.	.	.	.	.	.	.	.	A	12.92	2.082101	0.36758	.	.	ENSG00000160445	ENST00000291900	T	0.06218	3.33	4.35	4.35	0.52113	Armadillo-like helical (1);Armadillo-type fold (1);	0.146987	0.47455	D	0.000229	T	0.07234	0.0183	L	0.44542	1.39	0.58432	D	0.999999	B	0.26258	0.145	B	0.31191	0.125	T	0.29181	-1.0020	10	0.15499	T	0.54	-31.0091	12.8828	0.58026	1.0:0.0:0.0:0.0	.	426	Q7Z7L7	ZER1_HUMAN	H	426	ENSP00000291900:Y426H	ENSP00000291900:Y426H	Y	-	1	0	ZER1	130552799	1.000000	0.71417	1.000000	0.80357	0.583000	0.36354	8.478000	0.90428	1.832000	0.53329	0.383000	0.25322	TAC	.	.	.	none		0.562	ZER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054491.1	NM_006336		G	131512978	A	G	131512978	3	3	150	1	0	0	0	0	1	0	0	0	17637	391	14	3	1060	3	ZER1	9	131512978	Missense_Mutation	SNP	A	TCGA-DW-7838-01A-11D-2136-08	36413	131512978	9700453	43	8945											
AKR1C3	8644	hgsc.bcm.edu	37	chr10	5139633	5139633	+	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	ttaacctctgcagctttggtCcacttttcatcgaccagagt	8	14	7	12	1	2	1	1	0	1	1	4	2	3	1	3	1	3	2	3	1	1	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr10:5139633C>G	ENST00000380554.3	+	3	912	c.260C>G	c.(259-261)tCc>tGc	p.S87C	AKR1C3_ENST00000439082.2_5'UTR|AKR1C3_ENST00000470862.2_3'UTR|AKR1C3_ENST00000605149.1_Missense_Mutation_p.S64C	NM_001253908.1|NM_003739.5	NP_001240837.1|NP_003730.4	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3	87					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)	CAGCTTTGGTCCACTTTTCAT	0.393																																					p.S87C		Atlas-SNP	.											.	AKR1C3	21	.	0			c.C260G						PASS	.						134	128	130					10																	5139633		2203	4300	6503	SO:0001583	missense	8644	exon3			TTTGGTCCACTTT	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.260C>G	chr10.hg19:g.5139633C>G	ENSP00000369927:p.Ser87Cys	137.0	0.0	.		134.0	28.0	.	NM_001253908	A8K2V0|B4DL37|Q5T2L1|Q96DJ1|Q96KI8|Q99530|Q9UCX1|Q9UII3|Q9UKL9	Missense_Mutation	SNP	ENST00000380554.3	hg19	CCDS7063.1	.	.	.	.	.	.	.	.	.	.	C	0.010	-1.788233	0.00628	.	.	ENSG00000196139	ENST00000380554	T	0.26373	1.74	1.93	-3.27	0.05048	NADP-dependent oxidoreductase domain (3);	1.227770	0.05968	N	0.641929	T	0.11153	0.0272	N	0.11651	0.15	0.58432	D	0.999999	B;B	0.15473	0.011;0.013	B;B	0.23852	0.049;0.048	T	0.47045	-0.9147	10	0.05833	T	0.94	.	7.0923	0.25291	0.0:0.392:0.4898:0.1181	.	87;87	B4DKT3;P42330	.;AK1C3_HUMAN	C	87	ENSP00000369927:S87C	ENSP00000369927:S87C	S	+	2	0	AKR1C3	5129633	0.000000	0.05858	0.013000	0.15412	0.934000	0.57294	-1.103000	0.03329	-0.933000	0.03737	-0.458000	0.05436	TCC	.	.	.	none		0.393	AKR1C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046533.2	NM_003739		G	5139633	C	G	5139633	3	3	150	1	0	0	0	0	1	0	0	0	471	855	30	4	270	4	AKR1C3	10	5139633	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08		5139633	130395114	44	8946											
IL15RA	3601	hgsc.bcm.edu	37	chr10	6008174	6008174	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgttcaacacgcactccgTcaggctggacgtgccggctt	6	10	11	14	4	2	0	2	0	0	0	3	1	3	1	2	3	2	4	2	3	1	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr10:6008174T>C	ENST00000379977.3	-	2	314	c.217A>G	c.(217-219)Acg>Gcg	p.T73A	IL15RA_ENST00000528354.1_Missense_Mutation_p.T73A|IL15RA_ENST00000525219.2_Missense_Mutation_p.T37A|IL15RA_ENST00000397248.2_Missense_Mutation_p.T37A|IL15RA_ENST00000397250.2_Intron|IL15RA_ENST00000534292.1_5'UTR|IL15RA_ENST00000397255.3_Missense_Mutation_p.T73A|IL15RA_ENST00000530685.1_Missense_Mutation_p.T73A|IL15RA_ENST00000397251.3_Intron|IL15RA_ENST00000379971.1_Intron			Q13261	I15RA_HUMAN	interleukin 15 receptor, alpha	73	Sushi. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|negative regulation of neuron projection development (GO:0010977)|positive regulation of natural killer cell differentiation (GO:0032825)|response to nutrient levels (GO:0031667)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|signal transducer activity (GO:0004871)			cervix(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	5						ACGCACTCCGTCAGGCTGGAC	0.557																																					p.T159A		Atlas-SNP	.											.	IL15RA	17	.	0			c.A475G						PASS	.						91	78	82					10																	6008174		2203	4300	6503	SO:0001583	missense	3601	exon3			ACTCCGTCAGGCT	U31628	CCDS7074.1, CCDS7075.1, CCDS7075.2, CCDS58069.1, CCDS73065.1	10p15.1	2012-02-27			ENSG00000134470	ENSG00000134470		"Interleukins and interleukin receptors", "CD molecules"	5978	protein-coding gene	gene with protein product		601070				8530383	Standard	NM_002189		Approved	CD215, IL-15RA	uc021pmo.1	Q13261	OTTHUMG00000017612	ENST00000379977.3:c.217A>G	chr10.hg19:g.6008174T>C	ENSP00000369312:p.Thr73Ala	65.0	0.0	.		40.0	6.0	.	NM_001256765	B4E2C2|Q3B769|Q5JVA1|Q5JVA2|Q5JVA4|Q6B0J2|Q7LDR4|Q7Z609	Missense_Mutation	SNP	ENST00000379977.3	hg19	CCDS7074.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.76|15.76	2.927337|2.927337	0.52759|0.52759	.|.	.|.	ENSG00000134470|ENSG00000134470	ENST00000397246;ENST00000379977;ENST00000397248;ENST00000319465;ENST00000528354;ENST00000530685;ENST00000397255;ENST00000429135;ENST00000453922|ENST00000532039	T;T;T;T;T;T;T;T|.	0.29397|.	1.92;1.57;1.57;1.92;1.92;1.57;1.92;1.57|.	4.8|4.8	4.8|4.8	0.61643|0.61643	Complement control module (2);Sushi/SCR/CCP (2);|.	0.149436|.	0.43747|.	D|.	0.000539|.	T|.	0.47414|.	0.1444|.	L|L	0.57536|0.57536	1.79|1.79	0.24971|0.24971	N|N	0.991666|0.991666	D;D|.	0.64830|.	0.994;0.994|.	P;P|.	0.61328|.	0.887;0.887|.	T|.	0.38714|.	-0.9648|.	10|.	0.51188|.	T|.	0.08|.	-16.2672|-16.2672	10.7393|10.7393	0.46143|0.46143	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	73;73|.	Q13261-3;Q13261|.	.;I15RA_HUMAN|.	A|W	37;73;37;37;73;73;73;73;37|43	ENSP00000380420:T37A;ENSP00000369312:T73A;ENSP00000380421:T37A;ENSP00000435454:T73A;ENSP00000435995:T73A;ENSP00000380426:T73A;ENSP00000395113:T73A;ENSP00000405107:T37A|.	ENSP00000322245:T37A|.	T|X	-|-	1|3	0|0	IL15RA|IL15RA	6048180|6048180	0.998000|0.998000	0.40836|0.40836	0.968000|0.968000	0.41197|0.41197	0.304000|0.304000	0.27724|0.27724	3.427000|3.427000	0.52785|0.52785	1.783000|1.783000	0.52377|0.52377	0.379000|0.379000	0.24179|0.24179	ACG|TGA	.	.	.	none		0.557	IL15RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046615.2	NM_172200, NM_002189		C	6008174	T	C	6008174	3	2	150	1	0	0	0	0	1	0	0	0	7639	1667	58	3	610	3	IL15RA	10	6008174	Missense_Mutation	SNP	T	TCGA-DW-7838-01A-11D-2136-08	868541	6008174	129526573	45	8947											
VDAC2	7417	hgsc.bcm.edu	37	chr10	76980587	76980587	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctttgattttgctggacctgCaatccatggttcagctgtct	6	16	9	10	0	2	1	1	1	1	0	3	2	3	2	2	2	3	4	2	2	1	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr10:76980587C>T	ENST00000332211.6	+	7	656	c.443C>T	c.(442-444)gCa>gTa	p.A148V	VDAC2_ENST00000313132.4_Missense_Mutation_p.A163V|VDAC2_ENST00000543351.1_Missense_Mutation_p.A148V|VDAC2_ENST00000535553.1_Missense_Mutation_p.A109V|VDAC2_ENST00000472137.1_3'UTR	NM_003375.3	NP_003366.2	P45880	VDAC2_HUMAN	voltage-dependent anion channel 2	148					anion transport (GO:0006820)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of protein polymerization (GO:0032272)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|pore complex (GO:0046930)	nucleotide binding (GO:0000166)|porin activity (GO:0015288)|voltage-gated anion channel activity (GO:0008308)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(1)|ovary(1)|pancreas(2)|prostate(1)|urinary_tract(1)	10	all_cancers(46;0.0642)|all_epithelial(25;0.00604)|Prostate(51;0.0112)|Ovarian(15;0.183)				Dihydroxyaluminium(DB01375)	GCTGGACCTGCAATCCATGGT	0.418																																					p.A163V		Atlas-SNP	.											.	VDAC2	27	.	0			c.C488T						PASS	.						97	95	95					10																	76980587		2203	4297	6500	SO:0001583	missense	7417	exon8			GACCTGCAATCCA	BC000165	CCDS7348.1, CCDS53544.1	10q22	2011-11-15			ENSG00000165637	ENSG00000165637		"Voltage-dependent anion channels"	12672	protein-coding gene	gene with protein product		193245				7517385, 10049775	Standard	NM_003375		Approved		uc021ptp.1	P45880	OTTHUMG00000018517	ENST00000332211.6:c.443C>T	chr10.hg19:g.76980587C>T	ENSP00000361686:p.Ala148Val	165.0	0.0	.		129.0	20.0	.	NM_001184783	Q5VWK1|Q5VWK3|Q6IB40|Q7L3J5|Q9BWK8|Q9Y5I6	Missense_Mutation	SNP	ENST00000332211.6	hg19	CCDS7348.1	.	.	.	.	.	.	.	.	.	.	C	14.32	2.501060	0.44455	.	.	ENSG00000165637	ENST00000298468;ENST00000543351;ENST00000344036;ENST00000332211;ENST00000535553;ENST00000313132;ENST00000447677	T;T;T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02;1.02;1.02	5.48	5.48	0.80851	.	0.050056	0.85682	D	0.000000	T	0.26304	0.0642	N	0.05441	-0.05	0.58432	D	0.999999	B;B;B	0.21520	0.025;0.036;0.057	B;B;B	0.22880	0.019;0.036;0.042	T	0.10474	-1.0628	10	0.12766	T	0.61	.	19.3533	0.94401	0.0:1.0:0.0:0.0	.	109;163;148	B4DKM5;P45880-1;P45880	.;.;VDAC2_HUMAN	V	148;148;148;148;109;163;148	ENSP00000298468:A148V;ENSP00000443092:A148V;ENSP00000344876:A148V;ENSP00000361686:A148V;ENSP00000445901:A109V;ENSP00000361635:A163V;ENSP00000401492:A148V	ENSP00000298468:A148V	A	+	2	0	VDAC2	76650593	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.013000	0.70776	2.588000	0.87417	0.563000	0.77884	GCA	.	.	.	none		0.418	VDAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048792.1	NM_003375		T	76980587	C	T	76980587	3	4	150	1	0	0	0	0	1	0	0	0	17159	710	25	2	545	2	VDAC2	10	76980587	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	70972413	76980587	58554160	46	8948											
BTAF1	9044	hgsc.bcm.edu	37	chr10	93773747	93773747	+	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	ttgcaggatcttccacctaaAattattcaagactattattg	13	15	5	8	0	2	1	1	0	1	1	3	2	3	2	2	1	1	1	2	1	6	8			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr10:93773747A>T	ENST00000265990.6	+	32	4853	c.4545A>T	c.(4543-4545)aaA>aaT	p.K1515N	BTAF1_ENST00000544642.1_Missense_Mutation_p.K343N	NM_003972.2	NP_003963.1	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170kDa	1515					negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(6)	59		Colorectal(252;0.0846)				TTCCACCTAAAATTATTCAAG	0.368																																					p.K1515N		Atlas-SNP	.											.	BTAF1	148	.	0			c.A4545T						PASS	.						134	144	140					10																	93773747		2203	4300	6503	SO:0001583	missense	9044	exon32			ACCTAAAATTATT	AJ001017	CCDS7419.1	10q22-q23	2013-05-01	2013-05-01		ENSG00000095564	ENSG00000095564			17307	protein-coding gene	gene with protein product	"Mot1 homolog (S. cerevisiae)"	605191	"BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170 kD (Mot1 homolog, S. cerevisiae)"			9342322, 9488487	Standard	NM_003972		Approved	TAFII170, TAF172, MOT1, TAF-172, TAF(II)170	uc001khr.3	O14981	OTTHUMG00000018752	ENST00000265990.6:c.4545A>T	chr10.hg19:g.93773747A>T	ENSP00000265990:p.Lys1515Asn	262.0	0.0	.		184.0	23.0	.	NM_003972	B4E0W6|O43578	Missense_Mutation	SNP	ENST00000265990.6	hg19	CCDS7419.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.299734	0.81136	.	.	ENSG00000095564	ENST00000265990;ENST00000544642;ENST00000538688	D;D	0.94723	-3.5;-3.5	5.8	5.8	0.92144	SNF2-related (1);	0.050554	0.85682	D	0.000000	D	0.98726	0.9572	H	0.99719	4.725	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99525	1.0959	10	0.87932	D	0	-21.227	16.2031	0.82102	1.0:0.0:0.0:0.0	.	1515	O14981	BTAF1_HUMAN	N	1515;343;365	ENSP00000265990:K1515N;ENSP00000439924:K343N	ENSP00000265990:K1515N	K	+	3	2	BTAF1	93763727	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.660000	0.68018	2.231000	0.72958	0.524000	0.50904	AAA	.	.	.	none		0.368	BTAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049380.4	NM_003972		T	93773747	A	T	93773747	3	4	150	1	0	0	0	0	1	0	0	0	1538	11	1	5	4671	5	BTAF1	10	93773747	Missense_Mutation	SNP	A	TCGA-DW-7838-01A-11D-2136-08	16793160	93773747	41761000	47	8949											
PSD	5662	hgsc.bcm.edu	37	chr10	104176443	104176443	+	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	gactcaagccccctggagcaGgtagcccattcagtggcctc	8	7	11	15	0	2	0	2	0	0	0	3	2	2	1	4	3	3	2	4	3	2	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr10:104176443G>C	ENST00000020673.5	-	2	879	c.353C>G	c.(352-354)cCt>cGt	p.P118R	PSD_ENST00000492902.2_5'Flank|PSD_ENST00000406432.1_Missense_Mutation_p.P118R	NM_001270966.1|NM_002779.4	NP_001257895.1|NP_002770.3	A5PKW4	PSD1_HUMAN	pleckstrin and Sec7 domain containing	118	Pro-rich.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)		CCCTGGAGCAGGTAGCCCATT	0.657																																					p.P118R		Atlas-SNP	.											.	PSD	164	.	0			c.C353G						PASS	.						29	33	32					10																	104176443		2203	4296	6499	SO:0001583	missense	5662	exon3			GGAGCAGGTAGCC	X99688	CCDS31272.1, CCDS73187.1	10q24	2013-01-10	2004-04-28		ENSG00000059915	ENSG00000059915		"Pleckstrin homology (PH) domain containing"	9507	protein-coding gene	gene with protein product		602327	"pleckstrin and Sec7 domain protein"			9417912	Standard	NM_002779		Approved	KIAA2011, TYL, PSD1	uc009xxd.2	A5PKW4	OTTHUMG00000018954	ENST00000020673.5:c.353C>G	chr10.hg19:g.104176443G>C	ENSP00000020673:p.Pro118Arg	90.0	0.0	.		81.0	17.0	.	NM_001270965	B1AKX7|D3DR87|Q15673|Q8IVG0	Missense_Mutation	SNP	ENST00000020673.5	hg19	CCDS31272.1	.	.	.	.	.	.	.	.	.	.	G	18.29	3.592108	0.66219	.	.	ENSG00000059915	ENST00000020673;ENST00000406432	T;T	0.28666	1.6;1.6	4.36	4.36	0.52297	.	0.109296	0.37483	N	0.002079	T	0.30665	0.0772	N	0.08118	0	0.35207	D	0.774816	D	0.62365	0.991	P	0.58013	0.831	T	0.51068	-0.8752	10	0.66056	D	0.02	.	15.5617	0.76253	0.0:0.0:1.0:0.0	.	118	A5PKW4	PSD1_HUMAN	R	118	ENSP00000020673:P118R;ENSP00000384830:P118R	ENSP00000020673:P118R	P	-	2	0	PSD	104166433	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	2.473000	0.45145	2.375000	0.81037	0.561000	0.74099	CCT	.	.	.	none		0.657	PSD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050041.2			C	104176443	G	C	104176443	3	2	150	1	0	0	0	0	1	0	0	0	12656	1000	35	4	2785	4	PSD	10	104176443	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	10402696	104176443	31358304	48	8950											
BRSK2	9024	hgsc.bcm.edu	37	chr11	1459605	1459605	+	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	taaagctgcacgacgtttatGaaaacaaaaaatatttgtag	18	11	7	5	2	0	1	0	1	0	0	0	2	0	1	0	0	3	4	0	0	10	6			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr11:1459605G>A	ENST00000528841.1	+	3	640	c.256G>A	c.(256-258)Gaa>Aaa	p.E86K	BRSK2_ENST00000308230.5_Missense_Mutation_p.E86K|BRSK2_ENST00000382179.1_Missense_Mutation_p.E132K|BRSK2_ENST00000531197.1_Missense_Mutation_p.E86K|BRSK2_ENST00000528710.1_Missense_Mutation_p.E26K|BRSK2_ENST00000526678.1_Missense_Mutation_p.E86K|BRSK2_ENST00000308219.9_Missense_Mutation_p.E86K			Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2	86	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)		CGACGTTTATGAAAACAAAAA	0.567																																					p.E132K		Atlas-SNP	.											.	BRSK2	97	.	0			c.G394A						PASS	.						94	104	101					11																	1459605		2156	4273	6429	SO:0001583	missense	9024	exon3			GTTTATGAAAACA	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.256G>A	chr11.hg19:g.1459605G>A	ENSP00000432000:p.Glu86Lys	136.0	0.0	.		127.0	15.0	.	NM_001256630	B3KVE9|E9PLM7|O60843|O95099|Q5J5B4|Q6ZMQ4|Q8TB60	Missense_Mutation	SNP	ENST00000528841.1	hg19	CCDS58107.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.766637	0.90020	.	.	ENSG00000174672	ENST00000308219;ENST00000531197;ENST00000308230;ENST00000528841;ENST00000526678;ENST00000528596;ENST00000524702;ENST00000528710;ENST00000382179	T;T;T;T;T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21	2.57	2.57	0.30868	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.063288	0.64402	U	0.000008	T	0.78457	0.4286	M	0.71581	2.175	0.80722	D	1	P;D;B;D;D	0.71674	0.64;0.998;0.411;0.966;0.958	P;D;B;D;P	0.78314	0.602;0.991;0.354;0.923;0.875	T	0.81289	-0.1000	10	0.87932	D	0	.	12.2615	0.54652	0.0:0.0:1.0:0.0	.	86;132;86;86;86	Q8IWQ3-4;Q8IWQ3-5;Q8IWQ3-3;Q8IWQ3;Q8IWQ3-2	.;.;.;BRSK2_HUMAN;.	K	86;86;86;86;86;26;26;26;132	ENSP00000310697:E86K;ENSP00000431152:E86K;ENSP00000310805:E86K;ENSP00000432000:E86K;ENSP00000433370:E86K;ENSP00000434075:E26K;ENSP00000432672:E26K;ENSP00000433235:E26K;ENSP00000371614:E132K	ENSP00000310697:E86K	E	+	1	0	BRSK2	1416181	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.575000	0.74018	1.455000	0.47813	0.313000	0.20887	GAA	.	.	.	none		0.567	BRSK2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393033.1	NM_003957		A	1459605	G	A	1459605	3	1	150	1	0	0	0	0	1	0	0	0	1526	1291	45	2	266	2	BRSK2	11	1459605	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08		1459605	133546911	49	8951											
FBXO3	26273	hgsc.bcm.edu	37	chr11	33770334	33770334	+	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	gttccataccaactactccaGgtccttgaacttcttccacg	9	12	5	15	1	1	1	0	1	1	0	5	1	5	1	5	1	4	1	5	1	4	6			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr11:33770334G>T	ENST00000265651.3	-	9	1055	c.1037C>A	c.(1036-1038)cCt>cAt	p.P346H	FBXO3_ENST00000534136.1_Missense_Mutation_p.P346H|FBXO3_ENST00000448981.2_Missense_Mutation_p.P346H|FBXO3_ENST00000531080.1_Missense_Mutation_p.P33H|FBXO3_ENST00000532057.1_Missense_Mutation_p.P33H|FBXO3_ENST00000526785.1_Missense_Mutation_p.P233H|FBXO3_ENST00000530401.1_Missense_Mutation_p.P341H	NM_012175.3	NP_036307.2	Q9UK99	FBX3_HUMAN	F-box protein 3	346	ApaG. {ECO:0000255|PROSITE- ProRule:PRU00412}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|pancreas(1)|stomach(1)	13		Lung NSC(402;0.0804)		BRCA - Breast invasive adenocarcinoma(625;0.00315)|Lung(977;0.00488)|LUSC - Lung squamous cell carcinoma(625;0.008)		AACTACTCCAGGTCCTTGAAC	0.368																																					p.P346H		Atlas-SNP	.											.	FBXO3	37	.	0			c.C1037A						PASS	.						103	102	102					11																	33770334		2202	4298	6500	SO:0001583	missense	26273	exon9			ACTCCAGGTCCTT	AK001943	CCDS7887.1, CCDS44566.1	11p13	2006-07-07	2004-06-15		ENSG00000110429	ENSG00000110429		"F-boxes /  "other""	13582	protein-coding gene	gene with protein product		609089	"F-box only protein 3"			10531037	Standard	NM_033406		Approved	FBX3, FBA	uc001muz.3	Q9UK99	OTTHUMG00000166244	ENST00000265651.3:c.1037C>A	chr11.hg19:g.33770334G>T	ENSP00000265651:p.Pro346His	103.0	0.0	.		79.0	17.0	.	NM_012175	B3KY16|D3DR05|Q86X90|Q9H0V2|Q9NUX2	Missense_Mutation	SNP	ENST00000265651.3	hg19	CCDS7887.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.768020	0.90020	.	.	ENSG00000110429	ENST00000526785;ENST00000265651;ENST00000530401;ENST00000531080;ENST00000532057;ENST00000534136;ENST00000448981	T;T;T;T;T	0.47869	0.84;0.83;0.86;0.86;0.87	5.61	5.61	0.85477	ApaG domain (4);	0.000000	0.85682	D	0.000000	T	0.70859	0.3272	M	0.77486	2.375	0.80722	D	1	P;P;D	0.89917	0.936;0.936;1.0	P;P;D	0.77004	0.64;0.64;0.989	T	0.69636	-0.5092	10	0.41790	T	0.15	-16.4467	19.6304	0.95699	0.0:0.0:1.0:0.0	.	341;346;346	Q9UK99-3;Q9UK99-2;Q9UK99	.;.;FBX3_HUMAN	H	233;346;341;33;33;346;346	ENSP00000435680:P233H;ENSP00000265651:P346H;ENSP00000433781:P341H;ENSP00000431745:P346H;ENSP00000408836:P346H	ENSP00000265651:P346H	P	-	2	0	FBXO3	33726910	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.230000	0.95299	2.663000	0.90544	0.491000	0.48974	CCT	.	.	.	none		0.368	FBXO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388665.1	NM_012175		T	33770334	G	T	33770334	3	4	150	1	0	0	0	0	1	0	0	0	5746	1000	35	4	399	4	FBXO3	11	33770334	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	32310729	33770334	101236182	50	8952											
USP5	8078	hgsc.bcm.edu	37	chr12	6968684	6968684	+	Missense_Mutation	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	gaatgccccgacggaccctaCccaggatttcagcacccagg	10	5	10	16	2	1	0	1	0	0	0	1	4	1	2	5	3	3	1	5	3	2	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr12:6968684C>T	ENST00000229268.8	+	9	1161	c.1109C>T	c.(1108-1110)aCc>aTc	p.T370I	USP5_ENST00000389231.5_Missense_Mutation_p.T370I	NM_001098536.1	NP_001092006.1	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 (isopeptidase T)	370	USP.				positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin thiolesterase activity (GO:0004221)|zinc ion binding (GO:0008270)			breast(6)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|skin(2)|urinary_tract(2)	36						ACGGACCCTACCCAGGATTTC	0.562																																					p.T370I		Atlas-SNP	.											.	USP5	124	.	0			c.C1109T						PASS	.						91	83	86					12																	6968684		2203	4300	6503	SO:0001583	missense	8078	exon9			ACCCTACCCAGGA	U35116	CCDS31733.1, CCDS41743.1	12p13	2007-03-02	2005-08-08		ENSG00000111667	ENSG00000111667		"Ubiquitin-specific peptidases"	12628	protein-coding gene	gene with protein product		601447	"ubiquitin specific protease 5 (isopeptidase T)"			12838346, 8723724	Standard	NM_003481		Approved	IsoT	uc001qri.4	P45974	OTTHUMG00000169233	ENST00000229268.8:c.1109C>T	chr12.hg19:g.6968684C>T	ENSP00000229268:p.Thr370Ile	124.0	0.0	.		116.0	27.0	.	NM_003481	D3DUS7|D3DUS8|Q96J22	Missense_Mutation	SNP	ENST00000229268.8	hg19	CCDS41743.1	.	.	.	.	.	.	.	.	.	.	C	31	5.072808	0.93950	.	.	ENSG00000111667	ENST00000229268;ENST00000389231	T;T	0.29655	1.56;1.56	5.38	5.38	0.77491	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.046637	0.85682	D	0.000000	T	0.56232	0.1971	M	0.74546	2.27	0.80722	D	1	D;P	0.57899	0.981;0.534	D;P	0.66497	0.944;0.454	T	0.51560	-0.8690	10	0.39692	T	0.17	-8.4151	19.3333	0.94303	0.0:1.0:0.0:0.0	.	370;370	P45974;P45974-2	UBP5_HUMAN;.	I	370	ENSP00000229268:T370I;ENSP00000373883:T370I	ENSP00000229268:T370I	T	+	2	0	USP5	6838945	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.609000	0.82925	2.793000	0.96121	0.655000	0.94253	ACC	.	.	.	none		0.562	USP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402982.1			T	6968684	C	T	6968684	3	4	150	1	0	0	0	0	1	0	0	0	17093	507	18	2	1143	2	USP5	12	6968684	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08		6968684	126883211	51	8953											
CGRRF1	10668	hgsc.bcm.edu	37	chr14	55005042	55005042	+	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	tgtgcaggcagtttgttcagGaatcttttgcactttgcagt	7	16	11	7	0	2	0	1	0	1	0	2	1	2	1	0	2	3	6	0	2	1	5			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr14:55005042G>C	ENST00000216420.7	+	6	1072	c.940G>C	c.(940-942)Gaa>Caa	p.E314Q		NM_006568.2	NP_006559.1	Q99675	CGRF1_HUMAN	cell growth regulator with ring finger domain 1	314					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						GTTTGTTCAGGAATCTTTTGC	0.423																																					p.E314Q		Atlas-SNP	.											.	CGRRF1	30	.	0			c.G940C						PASS	.						97	89	92					14																	55005042		2203	4300	6503	SO:0001583	missense	10668	exon6			GTTCAGGAATCTT	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.940G>C	chr14.hg19:g.55005042G>C	ENSP00000216420:p.Glu314Gln	82.0	0.0	.		89.0	4.0	.	NM_006568	Q96BX2	Missense_Mutation	SNP	ENST00000216420.7	hg19	CCDS9719.1	.	.	.	.	.	.	.	.	.	.	G	19.56	3.850667	0.71719	.	.	ENSG00000100532	ENST00000216420	T	0.67523	-0.27	5.23	3.42	0.39159	Zinc finger, RING/FYVE/PHD-type (1);	0.046947	0.85682	D	0.000000	T	0.60064	0.2240	N	0.25094	0.71	0.43088	D	0.994752	D	0.54601	0.967	P	0.52159	0.691	T	0.57329	-0.7830	10	0.33141	T	0.24	-14.1511	11.656	0.51318	0.143:0.0:0.857:0.0	.	314	Q99675	CGRF1_HUMAN	Q	314	ENSP00000216420:E314Q	ENSP00000216420:E314Q	E	+	1	0	CGRRF1	54074792	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.236000	0.78154	0.794000	0.33899	0.462000	0.41574	GAA	.	.	.	none		0.423	CGRRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276905.2	NM_006568		C	55005042	G	C	55005042	3	2	150	1	0	0	0	0	1	0	0	0	3308	1175	41	4	962	4	CGRRF1	14	55005042	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08		55005042	52344498	52	8954											
CLMN	79789	hgsc.bcm.edu	37	chr14	95670344	95670344	+	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	ctttgccactcttgggctccCttcaaagcaaagggacaggt	9	10	10	12	0	2	0	1	0	1	0	3	1	3	1	2	3	2	2	2	3	2	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr14:95670344C>T	ENST00000298912.4	-	9	1455	c.1342G>A	c.(1342-1344)Ggg>Agg	p.G448R		NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	448					negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		CTTGGGCTCCCTTCAAAGCAA	0.483																																					p.G448R		Atlas-SNP	.											.	CLMN	103	.	0			c.G1342A						PASS	.						87	82	84					14																	95670344		2203	4300	6503	SO:0001583	missense	79789	exon9			GGCTCCCTTCAAA	AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.1342G>A	chr14.hg19:g.95670344C>T	ENSP00000298912:p.Gly448Arg	109.0	0.0	.		102.0	22.0	.	NM_024734	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Missense_Mutation	SNP	ENST00000298912.4	hg19	CCDS9933.1	.	.	.	.	.	.	.	.	.	.	C	11.56	1.673672	0.29693	.	.	ENSG00000165959	ENST00000298912	D	0.94537	-3.45	5.63	3.66	0.41972	.	0.000000	0.38837	N	0.001556	D	0.90896	0.7139	M	0.66939	2.045	0.18873	N	0.999986	P	0.37122	0.583	B	0.32342	0.144	D	0.86083	0.1545	10	0.87932	D	0	.	5.9466	0.19221	0.3449:0.5687:0.0:0.0864	.	448	Q96JQ2	CLMN_HUMAN	R	448	ENSP00000298912:G448R	ENSP00000298912:G448R	G	-	1	0	CLMN	94740097	0.137000	0.22531	0.209000	0.23619	0.021000	0.10359	0.357000	0.20199	1.337000	0.45525	0.655000	0.94253	GGG	.	.	.	none		0.483	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2			T	95670344	C	T	95670344	3	4	150	1	0	0	0	0	1	0	0	0	3544	681	24	2	1686	2	CLMN	14	95670344	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	40665302	95670344	11679196	53	8955											
SPTBN5	51332	hgsc.bcm.edu	37	chr15	42149779	42149779	+	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	gcacaacctcacctcacaggCcttctggagcttggccacct	8	8	8	17	0	3	0	2	0	1	0	3	1	3	1	5	3	2	2	5	3	1	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr15:42149779C>G	ENST00000320955.6	-	50	8583	c.8356G>C	c.(8356-8358)Gcc>Ccc	p.A2786P		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	2786					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)		ACCTCACAGGCCTTCTGGAGC	0.652																																					p.A2751P		Atlas-SNP	.											.	SPTBN5	171	.	0			c.G8251C						PASS	.						28	34	32					15																	42149779		2004	4170	6174	SO:0001583	missense	51332	exon50			CACAGGCCTTCTG	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.8356G>C	chr15.hg19:g.42149779C>G	ENSP00000317790:p.Ala2786Pro	21.0	0.0	.		23.0	8.0	.	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	hg19		.	.	.	.	.	.	.	.	.	.	.	15.93	2.979532	0.53827	.	.	ENSG00000137877	ENST00000320955	T	0.39787	1.06	4.2	3.28	0.37604	.	0.000000	0.56097	D	0.000023	T	0.62720	0.2451	M	0.78049	2.395	0.19300	N	0.99998	D	0.89917	1.0	D	0.77004	0.989	T	0.56463	-0.7975	10	0.72032	D	0.01	.	12.048	0.53491	0.0:0.916:0.0:0.084	.	2786	Q9NRC6	SPTN5_HUMAN	P	2786	ENSP00000317790:A2786P	ENSP00000317790:A2786P	A	-	1	0	SPTBN5	39937071	0.983000	0.35010	0.020000	0.16555	0.009000	0.06853	2.620000	0.46410	0.977000	0.38444	0.467000	0.42956	GCC	.	.	.	none		0.652	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		G	42149779	C	G	42149779	3	3	150	1	0	0	0	0	1	0	0	0	15134	739	26	4	2744	4	SPTBN5	15	42149779	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08		42149779	60381613	54	8956											
C16orf92	146378	hgsc.bcm.edu	37	chr16	30035201	30035219	+	Splice_Site	DEL	ACTCAGGTATGAACCAGCT	ACTCAGGTATGAACCAGCT	-																															gaaacccatcgtgttcattaActcaggtatgaaccagcttg																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	ACTCAGGTATGAACCAGCT	ACTCAGGTATGAACCAGCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr16:30035201_30035219delACTCAGGTATGAACCAGCT	ENST00000300575.2	+	2	305_310	c.284_289delACTCAGGTATGAACCAGCT	c.(283-291)aactcaggt>agt	p.NSG95fs	DOC2A_ENST00000567824.1_5'Flank	NM_001109659.1|NM_001109660.1	NP_001103129.1|NP_001103130.1	Q96LL3	CP092_HUMAN	chromosome 16 open reading frame 92	95						integral component of membrane (GO:0016021)				breast(3)|lung(3)	6						GTGTTCATTAACTCAGGTATGAACCAGCTTGAGAAGGGA	0.543																																					p.95_97del		Atlas-INDEL	.											.	C16orf92	11	.	0			c.283_289del						PASS	.																																			SO:0001630	splice_region_variant	146378	exon2			.	AK058133	CCDS42146.1	16p11.2	2012-05-30			ENSG00000167194	ENSG00000167194			26346	protein-coding gene	gene with protein product							Standard	NM_001109659		Approved	FLJ25404	uc002dvs.2	Q96LL3	OTTHUMG00000177107	ENST00000300575.2:c.289+1ACTCAGGTATGAACCAGCT>-	chr16.hg19:g.30035201_30035219delACTCAGGTATGAACCAGCT		81.0	0.0	0		62.0	10.0	0.16129	NM_001109660	Q494R8	Frame_Shift_Del	DEL	ENST00000300575.2	hg19	CCDS42146.1																																																																																			.	.	.	none		0.543	C16orf92-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435351.1	NM_001109659	Frame_Shift_Del	-	30035219	ACTCAGGTATGAACCAGCT	-	30035201	8	5	150	1	0	1	0	1	0	0	1	0	1847	43	2	0	304	0	C16orf92	16	30035201	Splice_Site	DEL	ACTCAGGTATGAACCAGCT	TCGA-DW-7838-01A-11D-2136-08		30035201	60319552	55	8957											
SALL1	6299	hgsc.bcm.edu	37	chr16	51172851	51172851	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttactgtcctgaggagaaacAtgcacgaagccgttgacctc	11	9	10	11	2	0	3	0	2	0	1	2	5	1	3	3	1	4	2	3	1	3	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr16:51172851A>G	ENST00000251020.4	-	2	3315	c.3282T>C	c.(3280-3282)caT>caC	p.H1094H	SALL1_ENST00000541611.1_Intron|SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Silent_p.H997H	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	1094					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)			GAGGAGAAACATGCACGAAGC	0.572																																					p.H1094H	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.T3282C						PASS	.						116	104	108					16																	51172851		2198	4300	6498	SO:0001819	synonymous_variant	6299	exon2			AGAAACATGCACG	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.3282T>C	chr16.hg19:g.51172851A>G		96.0	0.0	.		123.0	18.0	.	NM_002968	Q99881|Q9NSC3|Q9P1R0	Silent	SNP	ENST00000251020.4	hg19	CCDS10747.1																																																																																			.	.	.	none		0.572	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		G	51172851	A	G	51172851	2	3	150	1	0	0	0	0	0	0	0	1	13823	214	8	3		3	SALL1	16	51172851	Silent	SNP	A	TCGA-DW-7838-01A-11D-2136-08	21137650	51172851	39181902	56	8958											
FAM65A	79567	hgsc.bcm.edu	37	chr16	67577079	67577079	+	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	ggaggaggcactgggggcccTaatggctgccctggatgact	7	7	17	10	0	0	1	0	1	0	0	0	4	0	4	2	7	1	2	2	7	1	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr16:67577079T>A	ENST00000379312.3	+	13	2523	c.2402T>A	c.(2401-2403)cTa>cAa	p.L801Q	FAM65A_ENST00000042381.4_Missense_Mutation_p.L797Q|FAM65A_ENST00000540839.3_Missense_Mutation_p.L817Q|CTD-2012K14.4_ENST00000564717.1_RNA|FAM65A_ENST00000422602.2_Missense_Mutation_p.L817Q|FAM65A_ENST00000428437.2_Missense_Mutation_p.L811Q|CTD-2012K14.3_ENST00000563083.1_RNA	NM_001193522.1|NM_024519.3	NP_001180451.1|NP_078795.2	Q6ZS17	FA65A_HUMAN	family with sequence similarity 65, member A	801						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0474)|Epithelial(162;0.117)		CTGGGGGCCCTAATGGCTGCC	0.642																																					p.L817Q		Atlas-SNP	.											.	FAM65A	104	.	0			c.T2450A						PASS	.						17	16	17					16																	67577079		2198	4298	6496	SO:0001583	missense	79567	exon13			GGGCCCTAATGGC	AK127792	CCDS10840.1, CCDS54026.1, CCDS54027.1, CCDS54028.1	16q22.1	2008-02-05			ENSG00000039523	ENSG00000039523			25836	protein-coding gene	gene with protein product						11572484	Standard	NM_001193522		Approved	FLJ13725	uc010vjp.2	Q6ZS17	OTTHUMG00000137536	ENST00000379312.3:c.2402T>A	chr16.hg19:g.67577079T>A	ENSP00000368614:p.Leu801Gln	39.0	0.0	.		40.0	14.0	.	NM_001193523	B4DEQ9|B4DIM2|E9PBS3|Q4G0A4|Q7Z5R7|Q8NDA4|Q96J39|Q96PV8|Q9H8D9	Missense_Mutation	SNP	ENST00000379312.3	hg19	CCDS54028.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.237952	0.79800	.	.	ENSG00000039523	ENST00000379312;ENST00000042381;ENST00000422602;ENST00000540839	T;T;T	0.49432	0.78;0.78;0.78	5.52	5.52	0.82312	.	0.070064	0.56097	D	0.000022	T	0.67258	0.2874	M	0.72894	2.215	0.09310	N	0.999991	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.68765	0.96;0.96;0.96;0.96	T	0.63664	-0.6586	10	0.87932	D	0	-9.5432	15.6534	0.77115	0.0:0.0:0.0:1.0	.	811;817;801;817	B4DIM2;E9PBS3;Q6ZS17;B4DEQ9	.;.;FA65A_HUMAN;.	Q	801;797;817;811	ENSP00000368614:L801Q;ENSP00000042381:L797Q;ENSP00000400099:L817Q	ENSP00000042381:L797Q	L	+	2	0	FAM65A	66134580	0.901000	0.30685	0.994000	0.49952	0.920000	0.55202	4.728000	0.62000	2.120000	0.65058	0.454000	0.30748	CTA	.	.	.	none		0.642	FAM65A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268866.3	NM_024519		A	67577079	T	A	67577079	3	1	150	1	0	0	0	0	1	0	0	0	5606	1522	53	5	2436	5	FAM65A	16	67577079	Missense_Mutation	SNP	T	TCGA-DW-7838-01A-11D-2136-08	16404228	67577079	22777674	57	8959											
ZZEF1	23140	hgsc.bcm.edu	37	chr17	3919676	3919676	+	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	cctcacttgcacctccattcCtggctcctccatgaactggc	6	11	6	18	0	1	1	1	1	0	0	5	1	5	1	6	2	2	2	6	2	1	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:3919676C>A	ENST00000381638.2	-	49	8210	c.8086G>T	c.(8086-8088)Gga>Tga	p.G2696*		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	2696							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						ACCTCCATTCCTGGCTCCTCC	0.597																																					p.G2696X		Atlas-SNP	.											.	ZZEF1	195	.	0			c.G8086T						PASS	.						154	114	127					17																	3919676		2203	4300	6503	SO:0001587	stop_gained	23140	exon49			CCATTCCTGGCTC	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.8086G>T	chr17.hg19:g.3919676C>A	ENSP00000371051:p.Gly2696*	154.0	0.0	.		162.0	39.0	.	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Nonsense_Mutation	SNP	ENST00000381638.2	hg19	CCDS11043.1	.	.	.	.	.	.	.	.	.	.	C	50	17.192008	0.99881	.	.	ENSG00000074755	ENST00000381638	.	.	.	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-14.3127	20.0271	0.97525	0.0:1.0:0.0:0.0	.	.	.	.	X	2696	.	ENSP00000371051:G2696X	G	-	1	0	ZZEF1	3866425	1.000000	0.71417	0.961000	0.40146	0.948000	0.59901	7.487000	0.81328	2.744000	0.94065	0.650000	0.86243	GGA	.	.	.	none		0.597	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		A	3919676	C	A	3919676	4	1	150	1	0	0	0	0	0	1	0	0	18267	690	24	4	827	4	ZZEF1	17	3919676	Nonsense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08		3919676	77275534	58	8960											
ZFP3	124961	hgsc.bcm.edu	37	chr17	4995909	4995909	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctatgtatgtaaggaatgTgggaaggccttcagggggaa	11	9	15	6	0	1	0	1	0	0	0	1	3	1	3	2	5	0	2	2	5	6	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:4995909T>C	ENST00000318833.3	+	2	1446	c.1110T>C	c.(1108-1110)tgT>tgC	p.C370C		NM_153018.2	NP_694563.1	Q96NJ6	ZFP3_HUMAN	ZFP3 zinc finger protein	370					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(3)|prostate(1)	20						GTAAGGAATGTGGGAAGGCCT	0.413																																					p.C370C		Atlas-SNP	.											.	ZFP3	54	.	0			c.T1110C						PASS	.						46	48	48					17																	4995909		2203	4300	6503	SO:0001819	synonymous_variant	124961	exon2			GGAATGTGGGAAG	BX647638	CCDS11067.1	17p13.2	2013-01-08	2012-11-27		ENSG00000180787	ENSG00000180787		"Zinc fingers, C2H2-type"	12861	protein-coding gene	gene with protein product		194480	"zinc finger protein homologous to Zfp-3 in mouse", "zinc finger protein 3 homolog (mouse)"				Standard	NM_153018		Approved	FLJ30726, ZNF752	uc002gaq.3	Q96NJ6		ENST00000318833.3:c.1110T>C	chr17.hg19:g.4995909T>C		85.0	0.0	.		72.0	4.0	.	NM_153018	A5PLL4	Silent	SNP	ENST00000318833.3	hg19	CCDS11067.1																																																																																			.	.	.	none		0.413	ZFP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438979.1	NM_153018		C	4995909	T	C	4995909	2	2	150	1	0	0	0	0	0	0	0	1	17655	1702	59	3		3	ZFP3	17	4995909	Silent	SNP	T	TCGA-DW-7838-01A-11D-2136-08	1076233	4995909	76199301	59	8961											
WIPF2	147179	hgsc.bcm.edu	37	chr17	38420795	38420800	+	In_Frame_Del	DEL	CCAAGG	CCAAGG	-																															ccagttctcgagctgctgccCcaaggcctccagtatctgcc																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	CCAAGG	CCAAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:38420795_38420800delCCAAGG	ENST00000323571.4	+	5	607_612	c.367_372delCCAAGG	c.(367-372)ccaaggdel	p.PR123del	WIPF2_ENST00000394103.3_Intron|WIPF2_ENST00000494757.1_3'UTR|WIPF2_ENST00000585043.1_In_Frame_Del_p.PR123del|WIPF2_ENST00000536600.1_Intron|WIPF2_ENST00000583130.1_In_Frame_Del_p.PR123del	NM_133264.4	NP_573571.1	Q8TF74	WIPF2_HUMAN	WAS/WASL interacting protein family, member 2	123					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)		p.R124G(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	30						AGCTGCTGCCCCAAGGCCTCCAGTAT	0.573										HNSCC(43;0.11)																											p.122_124del		Atlas-INDEL	.											.	WIPF2	55	.	1	Substitution - Missense(1)	kidney(1)	c.366_371del						PASS	.																																			SO:0001651	inframe_deletion	147179	exon5			.	BC025965	CCDS11364.1	17q21.2	2006-10-12			ENSG00000171475	ENSG00000171475			30923	protein-coding gene	gene with protein product		609692				12213210, 11829459	Standard	XM_005257083		Approved	WICH, WIRE	uc002hug.1	Q8TF74	OTTHUMG00000133331	ENST00000323571.4:c.367_372delCCAAGG	chr17.hg19:g.38420795_38420800delCCAAGG	ENSP00000320924:p.Pro123_Arg124del	163.0	0.0	0		141.0	24.0	0.170213	NM_133264	A8K0L3|Q658J8|Q71RE1|Q8TE44	In_Frame_Del	DEL	ENST00000323571.4	hg19	CCDS11364.1																																																																																			.	.	.	none		0.573	WIPF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257157.2	NM_133264		-	38420800	CCAAGG	-	38420795	7	5	150	1	0	1	0	1	0	0	0	0	17380	623	22	0	381	0	WIPF2	17	38420795	In_Frame_Del	DEL	CCAAGG	TCGA-DW-7838-01A-11D-2136-08	33424886	38420795	42774415	60	8962			1	19		2	2	12	N	CCAAGG_A	2.736039e-05
WIPF2	147179	hgsc.bcm.edu	37	chr17	38420806	38420806	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgctgccccaaggcctccAgtatctgccgccagcgggcg	5	6	13	17	3	1	0	0	0	1	0	2	0	2	0	6	2	4	3	6	2	2	1	rs139121244		TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:38420806A>G	ENST00000323571.4	+	5	618	c.378A>G	c.(376-378)ccA>ccG	p.P126P	WIPF2_ENST00000394103.3_Intron|WIPF2_ENST00000494757.1_3'UTR|WIPF2_ENST00000585043.1_Silent_p.P126P|WIPF2_ENST00000536600.1_Intron|WIPF2_ENST00000583130.1_Silent_p.P126P	NM_133264.4	NP_573571.1	Q8TF74	WIPF2_HUMAN	WAS/WASL interacting protein family, member 2	126					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	30						CAAGGCCTCCAGTATCTGCCG	0.582										HNSCC(43;0.11)																											p.P126P		Atlas-SNP	.											.	WIPF2	55	.	0			c.A378G						PASS	.			1,4405	2.1+/-5.4	0,1,2202	60	69	66		378	-5.5	0.3	17	dbSNP_134	66	0,8600		0,0,4300	no	coding-synonymous	WIPF2	NM_133264.4		0,1,6502	GG,GA,AA		0.0,0.0227,0.0077		126/441	38420806	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	147179	exon5			GCCTCCAGTATCT	BC025965	CCDS11364.1	17q21.2	2006-10-12			ENSG00000171475	ENSG00000171475			30923	protein-coding gene	gene with protein product		609692				12213210, 11829459	Standard	XM_005257083		Approved	WICH, WIRE	uc002hug.1	Q8TF74	OTTHUMG00000133331	ENST00000323571.4:c.378A>G	chr17.hg19:g.38420806A>G		168.0	0.0	.		151.0	35.0	.	NM_133264	A8K0L3|Q658J8|Q71RE1|Q8TE44	Silent	SNP	ENST00000323571.4	hg19	CCDS11364.1																																																																																			.	A|1.000;G|0.000	0.000	weak		0.582	WIPF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257157.2	NM_133264		G	38420806	A	G	38420806	2	3	150	1	0	0	0	0	0	0	0	1	17380	175	7	3		3	WIPF2	17	38420806	Silent	SNP	A	TCGA-DW-7838-01A-11D-2136-08	11	38420806	42774404	61	8963			1	19		2	2	12	N	CCAAGG_A	2.736039e-05
KRT37	8688	hgsc.bcm.edu	37	chr17	39577782	39577782	+	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	aatgaggctctgcatctgggCcagctctgtgccgtagcggt	6	10	14	11	2	3	1	0	1	3	0	3	1	3	1	2	3	4	4	2	3	2	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:39577782C>G	ENST00000225550.3	-	6	1077	c.1078G>C	c.(1078-1080)Gcc>Ccc	p.A360P	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	360	Coil 2.|Rod.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	25		Breast(137;0.000496)				TGCATCTGGGCCAGCTCTGTG	0.567																																					p.A360P		Atlas-SNP	.											.	KRT37	61	.	0			c.G1078C						PASS	.						66	63	64					17																	39577782		2203	4300	6503	SO:0001583	missense	8688	exon6			TCTGGGCCAGCTC	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.1078G>C	chr17.hg19:g.39577782C>G	ENSP00000225550:p.Ala360Pro	89.0	0.0	.		101.0	13.0	.	NM_003770		Missense_Mutation	SNP	ENST00000225550.3	hg19	CCDS32653.1	.	.	.	.	.	.	.	.	.	.	C	16.14	3.037494	0.54896	.	.	ENSG00000108417	ENST00000225550	T	0.14640	2.49	5.44	2.17	0.27698	Filament (1);	0.000000	0.49305	D	0.000155	T	0.32763	0.0840	H	0.96861	3.895	0.28206	N	0.92715	B	0.34349	0.45	B	0.37239	0.244	T	0.42582	-0.9443	10	0.66056	D	0.02	.	13.3764	0.60741	0.5453:0.4547:0.0:0.0	.	360	O76014	KRT37_HUMAN	P	360	ENSP00000225550:A360P	ENSP00000225550:A360P	A	-	1	0	KRT37	36831308	0.000000	0.05858	1.000000	0.80357	0.990000	0.78478	-0.196000	0.09532	0.197000	0.20387	0.655000	0.94253	GCC	.	.	.	none		0.567	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770		G	39577782	C	G	39577782	3	3	150	1	0	0	0	0	1	0	0	0	8481	739	26	4	279	4	KRT37	17	39577782	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	1156976	39577782	41617428	62	8964											
MED13	9969	hgsc.bcm.edu	37	chr17	60023946	60023946	+	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	agccaggagagtgcattgtaCtgttccaaaacaaacctgaa	15	8	9	9	0	0	2	0	1	0	1	1	3	1	2	3	1	5	3	3	1	5	3			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:60023946C>G	ENST00000397786.2	-	30	6484	c.6408G>C	c.(6406-6408)caG>caC	p.Q2136H		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	2136					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						GTGCATTGTACTGTTCCAAAA	0.378																																					p.Q2136H		Atlas-SNP	.											.	MED13	181	.	0			c.G6408C						PASS	.						79	74	76					17																	60023946		1866	4104	5970	SO:0001583	missense	9969	exon30			ATTGTACTGTTCC	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.6408G>C	chr17.hg19:g.60023946C>G	ENSP00000380888:p.Gln2136His	49.0	0.0	.		77.0	24.0	.	NM_005121	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	hg19	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	C	14.58	2.576706	0.45902	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	D	0.83837	-1.77	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	D	0.90748	0.7096	M	0.75447	2.3	0.80722	D	1	D	0.67145	0.996	D	0.81914	0.995	D	0.90884	0.4756	10	0.48119	T	0.1	-4.4995	18.2754	0.90081	0.0:1.0:0.0:0.0	.	2136	Q9UHV7	MED13_HUMAN	H	2136;2135	ENSP00000380888:Q2136H	ENSP00000262436:Q2135H	Q	-	3	2	MED13	57378728	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.403000	0.79983	2.315000	0.78130	0.591000	0.81541	CAG	.	.	.	none		0.378	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		G	60023946	C	G	60023946	3	3	150	1	0	0	0	0	1	0	0	0	9437	564	20	4	120	4	MED13	17	60023946	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	20446164	60023946	21171264	63	8965											
RNF157	114804	hgsc.bcm.edu	37	chr17	74163165	74163165	+	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	tgacacactcctcgcttgtaCtgcacagtctccgactggag	8	10	9	14	2	1	1	0	1	1	0	4	3	2	2	2	1	2	3	2	1	1	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:74163165C>A	ENST00000269391.6	-	5	618	c.486G>T	c.(484-486)caG>caT	p.Q162H	RNF157_ENST00000319945.6_Missense_Mutation_p.Q162H	NM_052916.2	NP_443148.1	Q96PX1	RN157_HUMAN	ring finger protein 157	162							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)			CTCGCTTGTACTGCACAGTCT	0.567																																					p.Q162H	GBM(186;507 2120 27388 27773 52994)	Atlas-SNP	.											.	RNF157	66	.	0			c.G486T						PASS	.						127	114	118					17																	74163165		2203	4300	6503	SO:0001583	missense	114804	exon5			CTTGTACTGCACA	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.486G>T	chr17.hg19:g.74163165C>A	ENSP00000269391:p.Gln162His	215.0	0.0	.		219.0	29.0	.	NM_052916	Q8NB72|Q96N56	Missense_Mutation	SNP	ENST00000269391.6	hg19	CCDS32740.1	.	.	.	.	.	.	.	.	.	.	C	4.577	0.107271	0.08780	.	.	ENSG00000141576	ENST00000269391;ENST00000319945;ENST00000301610	T;T	0.27890	1.64;1.64	5.43	2.38	0.29361	.	0.131468	0.64402	N	0.000001	T	0.05593	0.0147	N	0.00152	-1.975	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40757	-0.9546	10	0.02654	T	1	-4.6639	10.0104	0.41984	0.0971:0.1243:0.7785:0.0	.	162;162	Q96PX1-2;Q96PX1	.;RN157_HUMAN	H	162;162;124	ENSP00000269391:Q162H;ENSP00000321837:Q162H	ENSP00000269391:Q162H	Q	-	3	2	RNF157	71674760	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.577000	0.23758	0.271000	0.22005	-0.128000	0.14901	CAG	.	.	.	none		0.567	RNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255874.2	XM_290732		A	74163165	C	A	74163165	3	1	150	1	0	0	0	0	1	0	0	0	13467	564	20	4	1613	4	RNF157	17	74163165	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	14139219	74163165	7032045	64	8966											
BIRC5	332	hgsc.bcm.edu	37	chr17	76212806	76212806	+	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	ctgtcaagaagcagtttgaaGaattaacccttggtgaattt	13	13	9	6	0	1	4	1	2	0	2	1	4	1	4	1	1	2	2	1	1	6	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:76212806G>A	ENST00000350051.3	+	3	402	c.283G>A	c.(283-285)Gaa>Aaa	p.E95K	AC087645.1_ENST00000600484.1_Missense_Mutation_p.S264F|BIRC5_ENST00000301633.4_Missense_Mutation_p.E118K|BIRC5_ENST00000592734.1_Intron|BIRC5_ENST00000374948.2_Intron|BIRC5_ENST00000589892.1_3'UTR	NM_001168.2	NP_001159.2	O15392	BIRC5_HUMAN	baculoviral IAP repeat containing 5	95					apoptotic process (GO:0006915)|cell division (GO:0051301)|chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|establishment of chromosome localization (GO:0051303)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of exit from mitosis (GO:0031536)|positive regulation of mitotic cell cycle (GO:0045931)|protein complex localization (GO:0031503)|protein phosphorylation (GO:0006468)|spindle checkpoint (GO:0031577)|transcription, DNA-templated (GO:0006351)	centriole (GO:0005814)|chromosome passenger complex (GO:0032133)|chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|interphase microtubule organizing center (GO:0031021)|microtubule (GO:0005874)|midbody (GO:0030496)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	chaperone binding (GO:0051087)|cobalt ion binding (GO:0050897)|cofactor binding (GO:0048037)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|microtubule binding (GO:0008017)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|Ran GTPase binding (GO:0008536)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			kidney(1)|urinary_tract(1)	2			BRCA - Breast invasive adenocarcinoma(99;0.00269)|OV - Ovarian serous cystadenocarcinoma(97;0.153)			GCAGTTTGAAGAATTAACCCT	0.398																																					p.E118K		Atlas-SNP	.											.	BIRC5	32	.	0			c.G352A						PASS	.						72	79	77					17																	76212806		2203	4300	6503	SO:0001583	missense	332	exon4			TTTGAAGAATTAA	U75285	CCDS11755.1, CCDS32751.1, CCDS32752.1	17q25.3	2013-01-17	2011-01-25		ENSG00000089685	ENSG00000089685		"Baculoviral IAP repeat containing"	593	protein-coding gene	gene with protein product	"survivin variant 3 alpha"	603352	"apoptosis inhibitor 4", "baculoviral IAP repeat-containing 5"	API4		8106347, 7947793	Standard	XR_243654		Approved	EPR-1, survivin	uc002jvf.3	O15392		ENST00000350051.3:c.283G>A	chr17.hg19:g.76212806G>A	ENSP00000324180:p.Glu95Lys	126.0	0.0	.		117.0	29.0	.	NM_001012271	A2SUH6|B2R4R1|Q2I3N8|Q4VGX0|Q53F61|Q5MGC6|Q6FHL2|Q75SP2|Q9P2W8	Missense_Mutation	SNP	ENST00000350051.3	hg19	CCDS11755.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.456362	0.84317	.	.	ENSG00000089685	ENST00000301633;ENST00000350051;ENST00000432014	T;T	0.03920	3.76;3.76	5.62	5.62	0.85841	Baculoviral inhibition of apoptosis protein repeat (1);	0.384181	0.30762	N	0.008935	T	0.07728	0.0194	L	0.59436	1.845	0.80722	D	1	B;B;B;P	0.50617	0.18;0.118;0.415;0.937	B;B;B;B	0.39590	0.053;0.036;0.202;0.304	T	0.18335	-1.0340	10	0.40728	T	0.16	-19.2617	17.1223	0.86705	0.0:0.0:1.0:0.0	.	95;95;118;95	O15392-4;O15392;O15392-2;A3E0Z5	.;BIRC5_HUMAN;.;.	K	118;95;118	ENSP00000301633:E118K;ENSP00000324180:E95K	ENSP00000301633:E118K	E	+	1	0	BIRC5	73724401	1.000000	0.71417	0.995000	0.50966	0.987000	0.75469	4.796000	0.62496	2.648000	0.89879	0.462000	0.41574	GAA	.	.	.	none		0.398	BIRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437231.2	NM_001168		A	76212806	G	A	76212806	3	1	150	1	0	0	0	0	1	0	0	0	1437	943	33	2	366	2	BIRC5	17	76212806	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	2049641	76212806	4982404	65	8967											
APCDD1	147495	hgsc.bcm.edu	37	chr18	10471914	10471914	+	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	tttgccatgcatgaacttcaGctcatccgggtggagaagca	10	10	11	10	1	2	2	2	1	0	1	3	3	3	2	2	2	5	3	2	2	2	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr18:10471914G>A	ENST00000355285.5	+	3	984	c.630G>A	c.(628-630)caG>caA	p.Q210Q	APCDD1_ENST00000578882.1_Intron	NM_153000.4	NP_694545.1			adenomatosis polyposis coli down-regulated 1											NS(1)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				READ - Rectum adenocarcinoma(15;0.08)		ATGAACTTCAGCTCATCCGGG	0.582																																					p.Q210Q		Atlas-SNP	.											.	APCDD1	57	.	0			c.G630A						PASS	.						145	132	136					18																	10471914		2203	4300	6503	SO:0001819	synonymous_variant	147495	exon3			ACTTCAGCTCATC	AB056722	CCDS11849.1	18p11.21	2006-07-07			ENSG00000154856	ENSG00000154856			15718	protein-coding gene	gene with protein product		607479				12384519	Standard	NM_153000		Approved	B7323	uc002kom.4	Q8J025	OTTHUMG00000131635	ENST00000355285.5:c.630G>A	chr18.hg19:g.10471914G>A		271.0	0.0	.		219.0	38.0	.	NM_153000		Silent	SNP	ENST00000355285.5	hg19	CCDS11849.1																																																																																			.	.	.	none		0.582	APCDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254529.2	NM_153000		A	10471914	G	A	10471914	2	1	150	1	0	0	0	0	0	0	0	1	765	962	34	2		2	APCDD1	18	10471914	Silent	SNP	G	TCGA-DW-7838-01A-11D-2136-08		10471914	67605334	66	8968											
CEP192	55125	hgsc.bcm.edu	37	chr18	13071144	13071144	+	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	tgtcacctggaccttgcttaGatattccatcgattttgtcc	7	16	7	11	1	1	1	1	0	0	1	4	3	3	2	4	1	1	1	4	1	2	6			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr18:13071144G>T	ENST00000325971.8	+	26	5086	c.3493G>T	c.(3493-3495)Gat>Tat	p.D1165Y	CEP192_ENST00000506447.1_Missense_Mutation_p.D1761Y|CEP192_ENST00000430049.2_Missense_Mutation_p.D1286Y			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	1165					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						ACCTTGCTTAGATATTCCATC	0.423																																					p.D1761Y		Atlas-SNP	.											.	CEP192	340	.	0			c.G5281T						PASS	.						110	110	110					18																	13071144		2203	4300	6503	SO:0001583	missense	55125	exon28			TGCTTAGATATTC	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.3493G>T	chr18.hg19:g.13071144G>T	ENSP00000317156:p.Asp1165Tyr	56.0	0.0	.		61.0	14.0	.	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	hg19		.	.	.	.	.	.	.	.	.	.	G	17.34	3.365339	0.61513	.	.	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	T;T;T	0.47869	0.83;0.83;0.83	5.35	3.54	0.40534	.	0.121003	0.53938	D	0.000055	T	0.64875	0.2638	M	0.73962	2.25	0.58432	D	0.999998	B;D;B	0.89917	0.368;1.0;0.328	B;D;B	0.79108	0.091;0.992;0.104	T	0.67692	-0.5605	10	0.87932	D	0	-11.9129	9.8383	0.40982	0.0725:0.0:0.7869:0.1406	.	1286;1761;363	C9JT09;E9PF99;Q9HCK3	.;.;.	Y	1761;1165;1165;1286	ENSP00000427550:D1761Y;ENSP00000317156:D1165Y;ENSP00000389190:D1286Y	ENSP00000317156:D1165Y	D	+	1	0	CEP192	13061144	1.000000	0.71417	0.650000	0.29550	0.606000	0.37113	3.512000	0.53407	1.230000	0.43646	0.650000	0.86243	GAT	.	.	.	none		0.423	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142		T	13071144	G	T	13071144	3	4	150	1	0	0	0	0	1	0	0	0	3253	942	33	4	5387	4	CEP192	18	13071144	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	2599230	13071144	65006104	67	8969											
ZNF519	162655	hgsc.bcm.edu	37	chr18	14105675	14105675	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttacatttgtaaggtttctcTccagtatgaattttctgatg	9	19	7	6	0	2	2	0	2	2	0	4	2	3	2	1	1	1	3	1	1	4	7			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr18:14105675T>C	ENST00000590202.1	-	3	1016	c.864A>G	c.(862-864)ggA>ggG	p.G288G	RP11-411B10.3_ENST00000592926.1_RNA|ZNF519_ENST00000589203.1_Intron|ZNF519_ENST00000589498.1_Intron	NM_145287.3	NP_660330.2	Q8TB69	ZN519_HUMAN	zinc finger protein 519	288					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						AAGGTTTCTCTCCAGTATGAA	0.363																																					p.G288G		Atlas-SNP	.											.	ZNF519	53	.	0			c.A864G						PASS	.						49	53	52					18																	14105675		2203	4299	6502	SO:0001819	synonymous_variant	162655	exon3			TTTCTCTCCAGTA	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.864A>G	chr18.hg19:g.14105675T>C		78.0	0.0	.		83.0	18.0	.	NM_145287		Silent	SNP	ENST00000590202.1	hg19	CCDS32797.1																																																																																			.	.	.	none		0.363	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287		C	14105675	T	C	14105675	2	2	150	1	0	0	0	0	0	0	0	1	17976	1538	54	3		3	ZNF519	18	14105675	Silent	SNP	T	TCGA-DW-7838-01A-11D-2136-08	1034531	14105675	63971573	68	8970											
LAMA3	3909	hgsc.bcm.edu	37	chr18	21451430	21451430	+	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	gccagcagccgtgccccagtGtctagggaggagctgatgac	8	6	15	12	1	1	2	0	2	1	0	1	4	1	4	4	2	4	2	4	2	1	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr18:21451430G>T	ENST00000313654.9	+	38	5044	c.4803G>T	c.(4801-4803)gtG>gtT	p.V1601V	LAMA3_ENST00000399516.3_Silent_p.V1601V|LAMA3_ENST00000587184.1_5'Flank|LAMA3_ENST00000269217.6_5'Flank	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	1601	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					GTGCCCCAGTGTCTAGGGAGG	0.552																																					p.V1601V		Atlas-SNP	.											.	LAMA3	397	.	0			c.G4803T						PASS	.						66	69	68					18																	21451430		2040	4193	6233	SO:0001819	synonymous_variant	3909	exon38			CCCAGTGTCTAGG	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.4803G>T	chr18.hg19:g.21451430G>T		112.0	0.0	.		85.0	14.0	.	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	hg19	CCDS42419.1																																																																																			.	.	.	none		0.552	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		T	21451430	G	T	21451430	2	4	150	1	0	0	0	0	0	0	0	1	8614	1364	48	4		4	LAMA3	18	21451430	Silent	SNP	G	TCGA-DW-7838-01A-11D-2136-08	7345755	21451430	56625818	69	8971											
ZNF521	25925	hgsc.bcm.edu	37	chr18	22805629	22805629	+	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	ttgcaagatgtgcacctataGactttcttttcgttactgtg	8	17	8	8	1	1	2	0	0	1	2	2	2	1	2	1	0	3	3	1	0	4	7			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr18:22805629G>C	ENST00000361524.3	-	4	2401	c.2253C>G	c.(2251-2253)gtC>gtG	p.V751V	ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000584787.1_Silent_p.V531V|ZNF521_ENST00000538137.2_Silent_p.V751V	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	751					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)					TGCACCTATAGACTTTCTTTT	0.468			T	PAX5	ALL																																p.V751V		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	.	ZNF521	269	.	0			c.C2253G						PASS	.						75	71	72					18																	22805629		2203	4300	6503	SO:0001819	synonymous_variant	25925	exon4			CCTATAGACTTTC	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.2253C>G	chr18.hg19:g.22805629G>C		79.0	0.0	.		83.0	16.0	.	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Silent	SNP	ENST00000361524.3	hg19	CCDS32806.1																																																																																			.	.	.	none		0.468	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		C	22805629	G	C	22805629	2	2	150	1	0	0	0	0	0	0	0	1	17977	929	33	4		4	ZNF521	18	22805629	Silent	SNP	G	TCGA-DW-7838-01A-11D-2136-08	1354199	22805629	55271619	70	8972											
ZNF430	80264	hgsc.bcm.edu	37	chr19	21240780	21240780	+	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	ctttcaaccagtcctcaaacCttattgaacaaagtaattca	15	12	3	11	0	3	1	3	1	0	0	4	1	4	1	3	0	3	1	3	0	6	5			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:21240780C>G	ENST00000261560.5	+	5	1847	c.1666C>G	c.(1666-1668)Ctt>Gtt	p.L556V	AC012627.1_ENST00000578233.1_RNA	NM_001172671.1|NM_025189.3	NP_001166142.1|NP_079465.3	Q9H8G1	ZN430_HUMAN	zinc finger protein 430	556					regulation of transcription, DNA-templated (GO:0006355)|substantia nigra development (GO:0021762)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23						GTCCTCAAACCTTATTGAACA	0.383																																					p.L556V		Atlas-SNP	.											.	ZNF430	59	.	0			c.C1666G						PASS	.						36	41	40					19																	21240780		2182	4285	6467	SO:0001583	missense	80264	exon5			TCAAACCTTATTG	AK023721	CCDS32978.1	19p12	2013-01-08				ENSG00000118620		"Zinc fingers, C2H2-type", "-"	20808	protein-coding gene	gene with protein product							Standard	NM_025189		Approved	FLJ13659	uc002npj.3	Q9H8G1		ENST00000261560.5:c.1666C>G	chr19.hg19:g.21240780C>G	ENSP00000261560:p.Leu556Val	49.0	0.0	.		39.0	10.0	.	NM_025189	Q86V70	Missense_Mutation	SNP	ENST00000261560.5	hg19	CCDS32978.1	.	.	.	.	.	.	.	.	.	.	.	7.976	0.750166	0.15778	.	.	ENSG00000118620	ENST00000261560	T	0.68331	-0.32	1.01	1.01	0.19927	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.81341	0.4802	M	0.88105	2.93	0.09310	N	1	D;P	0.57571	0.98;0.457	D;B	0.68353	0.957;0.329	T	0.68685	-0.5343	9	0.87932	D	0	.	8.8921	0.35441	0.0:1.0:0.0:0.0	.	555;556	Q2NKJ9;Q9H8G1	.;ZN430_HUMAN	V	556	ENSP00000261560:L556V	ENSP00000261560:L556V	L	+	1	0	ZNF430	21032620	0.000000	0.05858	0.014000	0.15608	0.014000	0.08584	-0.502000	0.06390	0.453000	0.26858	0.456000	0.33151	CTT	.	.	.	none		0.383	ZNF430-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463539.1	NM_025189		G	21240780	C	G	21240780	3	3	150	1	0	0	0	0	1	0	0	0	17916	681	24	4	1684	4	ZNF430	19	21240780	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08		21240780	37888203	71	8973											
DPY19L3	147991	hgsc.bcm.edu	37	chr19	32930113	32930113	+	Missense_Mutation	SNP	T	T	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	agcagcaattacatatttccTgagaccaaacttacagcctc	14	10	5	12	0	0	1	0	1	0	1	2	2	1	1	3	0	6	2	3	0	5	4			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:32930113T>G	ENST00000342179.5	+	7	907	c.692T>G	c.(691-693)cTg>cGg	p.L231R	DPY19L3_ENST00000392250.2_Missense_Mutation_p.L231R|DPY19L3_ENST00000586987.1_Missense_Mutation_p.L231R	NM_207325.2	NP_997208.2	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3 (C. elegans)	231						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)					ACATATTTCCTGAGACCAAAC	0.363																																					p.L231R		Atlas-SNP	.											.	DPY19L3	70	.	0			c.T692G						PASS	.						133	131	132					19																	32930113		2203	4300	6503	SO:0001583	missense	147991	exon7			ATTTCCTGAGACC		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.692T>G	chr19.hg19:g.32930113T>G	ENSP00000344937:p.Leu231Arg	124.0	0.0	.		80.0	15.0	.	NM_001172774	Q68DC7|Q6ZTB7|Q6ZTS2	Missense_Mutation	SNP	ENST00000342179.5	hg19	CCDS12422.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.333525	0.81801	.	.	ENSG00000178904	ENST00000392250;ENST00000319326;ENST00000342179	T;T	0.65549	-0.16;-0.16	5.66	5.66	0.87406	.	0.075638	0.53938	D	0.000041	T	0.81331	0.4800	M	0.84683	2.71	0.53005	D	0.99996	D	0.76494	0.999	D	0.76575	0.988	D	0.84659	0.0705	10	0.87932	D	0	-8.1242	15.8965	0.79338	0.0:0.0:0.0:1.0	.	231	Q6ZPD9	D19L3_HUMAN	R	231	ENSP00000376081:L231R;ENSP00000344937:L231R	ENSP00000315672:L231R	L	+	2	0	DPY19L3	37621953	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.816000	0.86201	2.163000	0.67991	0.460000	0.39030	CTG	.	.	.	none		0.363	DPY19L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450311.1	NM_207325		G	32930113	T	G	32930113	3	3	150	1	0	0	0	0	1	0	0	0	4744	1580	55	5	714	5	DPY19L3	19	32930113	Missense_Mutation	SNP	T	TCGA-DW-7838-01A-11D-2136-08	11689333	32930113	26198870	72	8974											
ATP1A3	478	hgsc.bcm.edu	37	chr19	42485703	42485703	+	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	tctcagccactttcttgttgCgttcacgcatcagcttcacg	6	14	7	14	3	5	0	4	0	2	0	6	0	5	0	1	0	3	4	1	0	0	5			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:42485703C>A	ENST00000302102.5	-	11	1538	c.1388G>T	c.(1387-1389)cGc>cTc	p.R463L	ATP1A3_ENST00000545399.1_Missense_Mutation_p.R476L|ATP1A3_ENST00000602133.1_Missense_Mutation_p.R433L|ATP1A3_ENST00000543770.1_Missense_Mutation_p.R474L	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						TTTCTTGTTGCGTTCACGCAT	0.552																																					p.R476L		Atlas-SNP	.											.	ATP1A3	117	.	0			c.G1427T						PASS	.						111	95	100					19																	42485703		2203	4300	6503	SO:0001583	missense	478	exon11			TTGTTGCGTTCAC		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.1388G>T	chr19.hg19:g.42485703C>A	ENSP00000302397:p.Arg463Leu	111.0	0.0	.		76.0	4.0	.	NM_001256214	B7Z2T0|B7Z401|F5H6J6|Q16732|Q16735|Q969K5	Missense_Mutation	SNP	ENST00000302102.5	hg19	CCDS12594.1	.	.	.	.	.	.	.	.	.	.	C	15.60	2.882720	0.51908	.	.	ENSG00000105409	ENST00000302102;ENST00000441343;ENST00000545399;ENST00000368080;ENST00000535899;ENST00000543770	D;D;D;D	0.95377	-3.69;-3.69;-3.69;-3.69	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	0.89760	0.6808	N	0.20483	0.58	0.45108	D	0.998124	B;B;B;B	0.29136	0.004;0.002;0.234;0.003	B;B;B;B	0.31869	0.025;0.022;0.137;0.038	D	0.87571	0.2478	10	0.72032	D	0.01	.	7.5742	0.27926	0.0:0.8868:0.0:0.1132	.	476;474;463;463	B7Z2T0;F5H6J6;E9PC51;P13637	.;.;.;AT1A3_HUMAN	L	463;463;476;433;207;474	ENSP00000302397:R463L;ENSP00000411503:R463L;ENSP00000444688:R476L;ENSP00000437577:R474L	ENSP00000302397:R463L	R	-	2	0	ATP1A3	47177543	0.261000	0.24063	0.961000	0.40146	0.992000	0.81027	1.374000	0.34283	2.449000	0.82847	0.561000	0.74099	CGC	.	.	.	none		0.552	ATP1A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268107.1	NM_152296		A	42485703	C	A	42485703	3	1	150	1	0	0	0	0	1	0	0	0	1130	768	27	4	1705	4	ATP1A3	19	42485703	Missense_Mutation	SNP	C	TCGA-DW-7838-01A-11D-2136-08	9555590	42485703	16643280	73	8975											
ZNF473	25888	hgsc.bcm.edu	37	chr19	50550199	50550199	+	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	gcccatctcaaccagcacctGagagttcacacccaggagac	12	5	8	16	0	2	2	2	1	1	2	3	4	2	2	4	1	2	2	4	1	1	1			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:50550199G>T	ENST00000595661.1	+	6	2994	c.2499G>T	c.(2497-2499)ctG>ctT	p.L833L	ZNF473_ENST00000445728.3_Silent_p.L821L|CTD-2126E3.3_ENST00000599914.1_RNA|ZNF473_ENST00000270617.3_Silent_p.L833L|ZNF473_ENST00000391821.2_Silent_p.L833L|CTD-2126E3.3_ENST00000599410.1_RNA|ZNF473_ENST00000601364.1_Intron			Q8WTR7	ZN473_HUMAN	zinc finger protein 473	833					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37		all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.00111)|OV - Ovarian serous cystadenocarcinoma(262;0.0058)		ACCAGCACCTGAGAGTTCACA	0.517											OREG0025632	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L833L		Atlas-SNP	.											.	ZNF473	86	.	0			c.G2499T						PASS	.						68	71	70					19																	50550199		2203	4300	6503	SO:0001819	synonymous_variant	25888	exon5			GCACCTGAGAGTT	AB032967	CCDS33077.1	19q13.33	2013-01-08						"Zinc fingers, C2H2-type", "-"	23239	protein-coding gene	gene with protein product						11782445	Standard	NM_015428		Approved	KIAA1141, DKFZP434N043, HZFP100	uc002prn.3	Q8WTR7		ENST00000595661.1:c.2499G>T	chr19.hg19:g.50550199G>T		77.0	0.0	.	970	79.0	18.0	.	NM_015428	A8K8T7|Q9ULS9|Q9Y4Q7	Silent	SNP	ENST00000595661.1	hg19	CCDS33077.1																																																																																			.	.	.	none		0.517	ZNF473-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464833.1	XM_046390		T	50550199	G	T	50550199	2	4	150	1	0	0	0	0	0	0	0	1	17943	1277	45	4		4	ZNF473	19	50550199	Silent	SNP	G	TCGA-DW-7838-01A-11D-2136-08	8064496	50550199	8578784	74	8976											
ZNF28	7576	hgsc.bcm.edu	37	chr19	53303801	53303801	+	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	gtaaggcttctctccagtgtGaattatactatgttttgcca	9	16	8	8	0	1	1	0	1	1	0	3	1	2	1	2	1	2	3	2	1	5	7			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:53303801G>C	ENST00000457749.2	-	4	1416	c.1297C>G	c.(1297-1299)Cac>Gac	p.H433D	ZNF28_ENST00000360272.4_Missense_Mutation_p.H380D|ZNF28_ENST00000414252.2_Missense_Mutation_p.H380D|ZNF28_ENST00000438150.2_Missense_Mutation_p.H380D	NM_006969.3	NP_008900.3	P17035	ZNF28_HUMAN	zinc finger protein 28	433					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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.H380Y(2)|p.H433Y(1)		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)		TCTCCAGTGTGAATTATACTA	0.373																																					p.H433D		Atlas-SNP	.											ZNF28_ENST00000457749,NS,carcinoma,0,3	ZNF28	191	.	3	Substitution - Missense(3)	breast(3)	c.C1297G						PASS	.						113	120	118					19																	53303801		2203	4300	6503	SO:0001583	missense	7576	exon4			CAGTGTGAATTAT	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.1297C>G	chr19.hg19:g.53303801G>C	ENSP00000397693:p.His433Asp	289.0	0.0	.		200.0	30.0	.	NM_006969	A8KAK9|B4E3G0|B9EIK7|Q5H9V1|Q5HYM9|Q6ZML9|Q6ZN56	Missense_Mutation	SNP	ENST00000457749.2	hg19	CCDS33093.2	.	.	.	.	.	.	.	.	.	.	-	14.52	2.559448	0.45590	.	.	ENSG00000198538	ENST00000438150;ENST00000457749;ENST00000360272;ENST00000414252;ENST00000391783	T;T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28;-0.28	1.74	0.624	0.17659	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.84433	0.5471	H	0.96460	3.825	0.27520	N	0.951416	D	0.63880	0.993	D	0.79784	0.993	T	0.73257	-0.4040	9	0.87932	D	0	.	6.9561	0.24572	0.1616:0.0:0.8384:0.0	.	433	P17035	ZNF28_HUMAN	D	380;433;380;380;380	ENSP00000412143:H380D;ENSP00000397693:H433D;ENSP00000353410:H380D;ENSP00000444965:H380D;ENSP00000375661:H380D	ENSP00000353410:H380D	H	-	1	0	ZNF28	57995613	1.000000	0.71417	0.003000	0.11579	0.128000	0.20619	4.471000	0.60182	0.072000	0.16694	0.186000	0.17326	CAC	.	.	.	none		0.373	ZNF28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336038.2	NM_006969		C	53303801	G	C	53303801	3	2	150	1	0	0	0	0	1	0	0	0	17825	1290	45	4	863	4	ZNF28	19	53303801	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08	2753602	53303801	5825182	75	8977											
FCAR	2204	hgsc.bcm.edu	37	chr19	55401195	55401196	+	Missense_Mutation	DNP	TG	TG	GT																															acagatgtgtcagccaggatTgacctttgcacgaacaccaa																										TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:55401195_55401196TG>GT	ENST00000355524.3	+	5	840_841	c.830_831TG>GT	c.(829-831)tTG>tGT	p.L277C	FCAR_ENST00000353758.4_Missense_Mutation_p.L168C|FCAR_ENST00000391723.3_3'UTR|FCAR_ENST00000345937.4_Missense_Mutation_p.L181C|FCAR_ENST00000391725.3_Missense_Mutation_p.L255C|FCAR_ENST00000482092.2_3'UTR|FCAR_ENST00000391724.3_Missense_Mutation_p.L243C|CTB-61M7.2_ENST00000594721.1_lincRNA|FCAR_ENST00000359272.4_Missense_Mutation_p.L265C|FCAR_ENST00000391726.3_Missense_Mutation_p.L169C	NM_002000.2	NP_001991.1	P24071	FCAR_HUMAN	Fc fragment of IgA, receptor for	277					immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(2)	24				GBM - Glioblastoma multiforme(193;0.0443)		CAGCCAGGATTGACCTTTGCAC	0.525																																					p.L277W|p.L277F		Atlas-SNP	.											.|FCAR,NS,malignant_melanoma,0,2	FCAR	110	.	0			c.T830G|c.G831T						PASS	.																																			SO:0001583	missense	2204	exon5			CAGGATTGACCTT|AGGATTGACCTTT	X54150	CCDS12907.1, CCDS12908.1, CCDS12909.1, CCDS12910.1, CCDS42622.1, CCDS42623.1, CCDS42624.1, CCDS42625.1, CCDS46180.1	19q13.42	2013-01-29			ENSG00000186431	ENSG00000186431		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3608	protein-coding gene	gene with protein product		147045				1577457	Standard	NM_133269		Approved	CD89	uc002qhr.1	P24071	OTTHUMG00000065936	Exception_encountered	chr19.hg19:g.55401195_55401196delinsGT	ENSP00000347714:p.Leu277Cys	209.0|207.0	0.0	.		233.0|228.0	36.0	.	NM_002000	Q13603|Q13604|Q15727|Q15728|Q1AJL7|Q1AJL8|Q1AJL9|Q53X38|Q53X39|Q92587|Q92588|Q92590|Q92592|Q92593|Q9UEK0	Missense_Mutation	SNP	ENST00000355524.3	hg19	CCDS12907.1																																																																																			.	.	.	none		0.525	FCAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000141243.1	NM_002000		GT	55401196	TG	GT	55401195	3	3	150	1	0	0	0	0	1	0	0	0	5780	1821	63	5	919	5	FCAR	19	55401195	Missense_Mutation	DNP	TG	TCGA-DW-7838-01A-11D-2136-08	2097394	55401195	3727788	76	8978											
HIRA	7290	hgsc.bcm.edu	37	chr22	19393327	19393327	+	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	accgcctgaatgattccggaGgatagagacacaccgccact	12	6	10	13	3	0	3	0	2	0	1	1	6	1	5	5	2	0	0	5	2	2	2			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr22:19393327G>T	ENST00000263208.5	-	5	635	c.379C>A	c.(379-381)Ctc>Atc	p.L127I	HIRA_ENST00000546308.1_Missense_Mutation_p.L83I|HIRA_ENST00000340170.4_Missense_Mutation_p.L127I|HIRA_ENST00000464189.1_5'UTR|HIRA_ENST00000541063.1_Missense_Mutation_p.L83I	NM_003325.3	NP_003316.3	P54198	HIRA_HUMAN	histone cell cycle regulator	127					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)					TGATTCCGGAGGATAGAGACA	0.612																																					p.L127I		Atlas-SNP	.											.	HIRA	100	.	0			c.C379A						PASS	.						86	70	76					22																	19393327		2203	4300	6503	SO:0001583	missense	7290	exon5			TCCGGAGGATAGA	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.379C>A	chr22.hg19:g.19393327G>T	ENSP00000263208:p.Leu127Ile	63.0	0.0	.		97.0	4.0	.	NM_003325	Q05BU9|Q8IXN2	Missense_Mutation	SNP	ENST00000263208.5	hg19	CCDS13759.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.907418	0.92107	.	.	ENSG00000100084	ENST00000340170;ENST00000263208;ENST00000541063;ENST00000546308	T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26	4.86	4.86	0.63082	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	0.80502	0.4635	M	0.63843	1.955	0.80722	D	1	D;D	0.89917	0.996;1.0	D;D	0.97110	0.986;1.0	T	0.82592	-0.0381	10	0.87932	D	0	-14.4293	18.1731	0.89753	0.0:0.0:1.0:0.0	.	127;127	P54198-2;P54198	.;HIRA_HUMAN	I	127;127;83;83	ENSP00000345350:L127I;ENSP00000263208:L127I;ENSP00000446073:L83I;ENSP00000441870:L83I	ENSP00000263208:L127I	L	-	1	0	HIRA	17773327	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.187000	0.77730	2.519000	0.84933	0.563000	0.77884	CTC	.	.	.	none		0.612	HIRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316488.2	NM_003325		T	19393327	G	T	19393327	3	4	150	1	0	0	0	0	1	0	0	0	7127	1000	35	4	2758	4	HIRA	22	19393327	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08		19393327	31911239	77	8979											
PAK3	5063	hgsc.bcm.edu	37	chrX	110366494	110366494	+	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	ttcgctctatcttcccaggaGgaggggataaaagtaaagta	13	10	11	7	1	2	0	0	0	2	0	4	3	3	3	1	4	0	3	1	4	6	6			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chrX:110366494G>A	ENST00000372010.1	+	5	605	c.163G>A	c.(163-165)Gga>Aga	p.G55R	PAK3_ENST00000262836.4_Missense_Mutation_p.G55R|PAK3_ENST00000518291.1_Missense_Mutation_p.G55R|PAK3_ENST00000446737.1_Missense_Mutation_p.G55R|PAK3_ENST00000417227.1_Missense_Mutation_p.G55R|PAK3_ENST00000360648.4_Missense_Mutation_p.G55R|PAK3_ENST00000425146.1_Missense_Mutation_p.G55R|PAK3_ENST00000519681.1_Missense_Mutation_p.G55R|PAK3_ENST00000372007.5_Missense_Mutation_p.G55R			O75914	PAK3_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 3	55					activation of MAPK activity (GO:0000187)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|dendritic spine morphogenesis (GO:0060997)|MAPK cascade (GO:0000165)|regulation of actin filament polymerization (GO:0030833)|synapse organization (GO:0050808)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(15)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	41						CTTCCCAGGAGGAGGGGATAA	0.448										TSP Lung(19;0.15)																											p.G55R		Atlas-SNP	.											.	PAK3	179	.	0			c.G163A						PASS	.						70	69	70					X																	110366494		2203	4300	6503	SO:0001583	missense	5063	exon3			CCAGGAGGAGGGG	AF068864	CCDS14554.1, CCDS48151.1, CCDS48152.1, CCDS48153.1	Xq22.3	2008-06-17	2008-06-17		ENSG00000077264	ENSG00000077264			8592	protein-coding gene	gene with protein product		300142	"mental retardation, X-linked 47", "p21 (CDKN1A)-activated kinase 3"	MRX30, MRX47		8826460, 9731525	Standard	NM_002578		Approved	hPAK3, bPAK	uc010npv.1	O75914	OTTHUMG00000022202	ENST00000372010.1:c.163G>A	chrX.hg19:g.110366494G>A	ENSP00000361080:p.Gly55Arg	50.0	0.0	.		47.0	15.0	.	NM_001128166	A8K389|B1GX77|B1GX78|B1GX79|Q5JWX1|Q5JWX2|Q7Z2D6|Q7Z2E4|Q7Z3Z8|Q8WWK5|Q8WX23|Q9P0J8	Missense_Mutation	SNP	ENST00000372010.1	hg19	CCDS48153.1	.	.	.	.	.	.	.	.	.	.	G	16.93	3.257186	0.59321	.	.	ENSG00000077264	ENST00000446737;ENST00000425146;ENST00000372010;ENST00000519681;ENST00000372007;ENST00000518291;ENST00000429193;ENST00000360648;ENST00000417227;ENST00000262836	T;T;T;T;T;T;T;T;T	0.71461	-0.55;-0.55;-0.57;-0.56;-0.55;-0.54;-0.54;-0.56;-0.57	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.68284	0.2984	L	0.29908	0.895	0.80722	D	1	P;P;B;B	0.43607	0.801;0.812;0.399;0.037	P;P;B;B	0.48454	0.578;0.578;0.194;0.049	T	0.64322	-0.6435	10	0.22706	T	0.39	.	18.4314	0.90627	0.0:0.0:1.0:0.0	.	55;55;55;55	O75914-4;O75914-3;O75914;O75914-2	.;.;PAK3_HUMAN;.	R	55	ENSP00000410853:G55R;ENSP00000401982:G55R;ENSP00000361080:G55R;ENSP00000429113:G55R;ENSP00000361077:G55R;ENSP00000428921:G55R;ENSP00000353864:G55R;ENSP00000389172:G55R;ENSP00000262836:G55R	ENSP00000262836:G55R	G	+	1	0	PAK3	110253150	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.143000	0.94623	2.380000	0.81148	0.600000	0.82982	GGA	.	.	.	none		0.448	PAK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057918.1	NM_002578		A	110366494	G	A	110366494	3	1	150	1	0	0	0	0	1	0	0	0	11409	1001	35	2	165	2	PAK3	23	110366494	Missense_Mutation	SNP	G	TCGA-DW-7838-01A-11D-2136-08		110366494	44904066	78	8980											
COL11A1	1301	hgsc.bcm.edu	37	chr1	103400626	103400626	+	Frame_Shift_Del	DEL	G	G	-																															gaatactcacagcaattccaGgggcaccaactggtccttga																										TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr1:103400626delG	ENST00000370096.3	-	45	3794	c.3482delC	c.(3481-3483)cctfs	p.P1161fs	COL11A1_ENST00000358392.2_Frame_Shift_Del_p.P1173fs|COL11A1_ENST00000512756.1_Frame_Shift_Del_p.P1045fs|COL11A1_ENST00000353414.4_Frame_Shift_Del_p.P1122fs	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	1161	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)		AGCAATTCCAGGGGCACCAAC	0.448																																					p.P1173fs		Atlas-INDEL	.											.	COL11A1	972	.	0			c.3519delT						PASS	.						37	39	38					1																	103400626		2203	4300	6503	SO:0001589	frameshift_variant	1301	exon45			.	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.3482delC	chr1.hg19:g.103400626delG	ENSP00000359114:p.Pro1161fs	43.0	0.0	0		48.0	18.0	0.375	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Frame_Shift_Del	DEL	ENST00000370096.3	hg19	CCDS778.1																																																																																			.	.	.	none		0.448	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		-	103400626	G	-	103400626	7	5	151	1	0	1	0	1	0	0	0	0	3669	1000	35	0	2030	0	COL11A1	1	103400626	Frame_Shift_Del	DEL	G	TCGA-DW-7839-01A-11D-2136-08		103400626	145849995	1	8981											
CR1L	1379	hgsc.bcm.edu	37	chr1	207818592	207818592	+	Missense_Mutation	SNP	T	T	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	gccgctcatggcgcctcccgTccgtctcgagcgtccctttc	2	10	10	19	6	2	0	1	0	1	0	7	1	5	0	5	1	1	1	5	1	0	1			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr1:207818592T>G	ENST00000508064.2	+	1	74	c.14T>G	c.(13-15)gTc>gGc	p.V5G		NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	5						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						GCGCCTCCCGTCCGTCTCGAG	0.657																																					p.V5G		Atlas-SNP	.											.	CR1L	97	.	0			c.T14G						PASS	.						62	68	66					1																	207818592		2203	4300	6503	SO:0001583	missense	1379	exon1			CTCCCGTCCGTCT	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.14T>G	chr1.hg19:g.207818592T>G	ENSP00000421736:p.Val5Gly	172.0	0.0	.		117.0	59.0	.	NM_175710	Q32MC9|Q8NEU7	Missense_Mutation	SNP	ENST00000508064.2	hg19	CCDS44310.1	.	.	.	.	.	.	.	.	.	.	T	10.27	1.304420	0.23736	.	.	ENSG00000197721	ENST00000444269;ENST00000508064	T	0.32023	1.47	2.95	-5.9	0.02275	.	.	.	.	.	T	0.04952	0.0133	N	0.00436	-1.5	0.09310	N	1	P	0.41475	0.751	B	0.36989	0.238	T	0.23404	-1.0189	9	0.16420	T	0.52	.	0.9185	0.01310	0.2027:0.1365:0.2268:0.434	.	5	Q2VPA4	CR1L_HUMAN	G	5	ENSP00000421736:V5G	ENSP00000437875:V5G	V	+	2	0	CR1L	205885215	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-2.381000	0.01065	-1.286000	0.02384	-1.304000	0.01323	GTC	.	.	.	none		0.657	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735		G	207818592	T	G	207818592	3	3	151	1	0	0	0	0	1	0	0	0	3843	1667	58	5	16	5	CR1L	1	207818592	Missense_Mutation	SNP	T	TCGA-DW-7839-01A-11D-2136-08	104417966	207818592	41432029	2	8982											
C1orf35	79169	hgsc.bcm.edu	37	chr1	228290925	228290925	+	Missense_Mutation	SNP	A	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	gcctccacgactggagccgaAcatggcgccgggaaggcagt	9	4	15	13	4	0	0	0	0	0	0	1	4	1	2	4	4	2	1	4	4	2	0			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr1:228290925A>C	ENST00000272139.4	-	1	238	c.4T>G	c.(4-6)Ttc>Gtc	p.F2V	C1orf35_ENST00000472617.1_5'UTR	NM_024319.2	NP_077295.1	Q9BU76	MMTA2_HUMAN	chromosome 1 open reading frame 35	2							poly(A) RNA binding (GO:0044822)			large_intestine(1)|lung(1)|skin(1)	3		Prostate(94;0.0488)				CTGGAGCCGAACATGGCGCCG	0.682																																					p.F2V		Atlas-SNP	.											.	C1orf35	17	.	0			c.T4G						PASS	.						30	31	31					1																	228290925		2201	4299	6500	SO:0001583	missense	79169	exon1			AGCCGAACATGGC	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.4T>G	chr1.hg19:g.228290925A>C	ENSP00000272139:p.Phe2Val	62.0	0.0	.		48.0	28.0	.	NM_024319	Q6P5Y0|Q6ZTZ6|Q6ZWA6|Q8IZH3	Missense_Mutation	SNP	ENST00000272139.4	hg19	CCDS1566.1	.	.	.	.	.	.	.	.	.	.	A	17.93	3.510193	0.64522	.	.	ENSG00000143793	ENST00000272139	.	.	.	3.88	2.74	0.32292	.	0.000000	0.85682	D	0.000000	T	0.61009	0.2313	M	0.62723	1.935	0.53005	D	0.999965	D	0.58268	0.982	P	0.52554	0.702	T	0.61207	-0.7109	9	0.66056	D	0.02	-15.7163	8.1877	0.31348	0.8997:0.0:0.1003:0.0	.	2	Q9BU76	MMTA2_HUMAN	V	2	.	ENSP00000272139:F2V	F	-	1	0	C1orf35	226357548	1.000000	0.71417	0.996000	0.52242	0.219000	0.24729	6.640000	0.74319	0.548000	0.28955	0.254000	0.18369	TTC	.	.	.	none		0.682	C1orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092245.1	NM_024319		C	228290925	A	C	228290925	3	2	151	1	0	0	0	0	1	0	0	0	2040	43	2	5	819	5	C1orf35	1	228290925	Missense_Mutation	SNP	A	TCGA-DW-7839-01A-11D-2136-08	20472333	228290925	20959696	3	8983											
ALMS1	7840	hgsc.bcm.edu	37	chr2	73827935	73827935	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttggtcagaagaaaaacgTgaagagaaaatgctctttac	16	10	9	6	1	3	4	1	1	2	3	3	5	3	4	0	1	3	1	0	1	7	3			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr2:73827935T>C	ENST00000264448.6	+	18	11907	c.11796T>C	c.(11794-11796)cgT>cgC	p.R3932R	ALMS1_ENST00000409009.1_Silent_p.R3890R	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	3932					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						AAGAAAAACGTGAAGAGAAAA	0.408																																					p.R3932R		Atlas-SNP	.											.	ALMS1	384	.	0			c.T11796C						PASS	.						91	92	91					2																	73827935		2203	4300	6503	SO:0001819	synonymous_variant	7840	exon18			AAAACGTGAAGAG	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.11796T>C	chr2.hg19:g.73827935T>C		76.0	0.0	.		51.0	28.0	.	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.	.	none		0.408	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		C	73827935	T	C	73827935	2	2	151	1	0	0	0	0	0	0	0	1	535	1683	59	3		3	ALMS1	2	73827935	Silent	SNP	T	TCGA-DW-7839-01A-11D-2136-08		73827935	169371438	4	8984											
SPAG16	79582	hgsc.bcm.edu	37	chr2	214161997	214161997	+	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	gtgatctagataccagatgaCaattttagcatcccagaagg	14	10	9	8	0	1	5	0	2	1	3	2	5	2	5	2	1	2	1	2	1	5	4			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr2:214161997C>G	ENST00000331683.5	+	3	290	c.195C>G	c.(193-195)gaC>gaG	p.D65E	SPAG16_ENST00000414961.2_3'UTR|SPAG16_ENST00000432529.2_Missense_Mutation_p.D65E|SPAG16_ENST00000447990.1_Missense_Mutation_p.D65E|SPAG16_ENST00000413312.1_Missense_Mutation_p.D34E|SPAG16_ENST00000272898.7_Missense_Mutation_p.D65E|SPAG16_ENST00000374309.3_Missense_Mutation_p.T11R	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	65					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)		TACCAGATGACAATTTTAGCA	0.358																																					p.D65E		Atlas-SNP	.											.	SPAG16	134	.	0			c.C195G						PASS	.						79	82	81					2																	214161997		2203	4300	6503	SO:0001583	missense	79582	exon3			AGATGACAATTTT	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.195C>G	chr2.hg19:g.214161997C>G	ENSP00000332592:p.Asp65Glu	61.0	0.0	.		99.0	36.0	.	NM_024532	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Missense_Mutation	SNP	ENST00000331683.5	hg19	CCDS2396.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.42|12.42	1.932017|1.932017	0.34096|0.34096	.|.	.|.	ENSG00000144451|ENSG00000144451	ENST00000331683;ENST00000432529;ENST00000413312;ENST00000272898;ENST00000447990|ENST00000374309	T|T	0.57752|0.58210	0.38|0.35	5.7|5.7	1.2|1.2	0.21068|0.21068	.|.	0.071260|.	0.51477|.	D|.	0.000088|.	T|T	0.40322|0.40322	0.1112|0.1112	L|L	0.41632|0.41632	1.29|1.29	0.23309|0.23309	N|N	0.997933|0.997933	P;P;B;P;B|B;B	0.43287|0.12013	0.75;0.802;0.036;0.734;0.06|0.001;0.005	B;B;B;B;B|B;B	0.43478|0.17433	0.168;0.137;0.014;0.421;0.082|0.002;0.018	T|T	0.37709|0.37709	-0.9694|-0.9694	10|9	0.52906|0.87932	T|D	0.07|0	.|.	5.0287|5.0287	0.14398|0.14398	0.0:0.4882:0.1541:0.3577|0.0:0.4882:0.1541:0.3577	.|.	34;5;65;65;65|11;2	Q8N0X2-3;Q4G1A2;Q8N0X2;E7EWV3;Q8N0X2-4|B4DYB5;Q8N0X2-2	.;.;SPG16_HUMAN;.;.|.;.	E|R	65;65;34;65;65|11	ENSP00000332592:D65E|ENSP00000363428:T11R	ENSP00000272898:D65E|ENSP00000363428:T11R	D|T	+|+	3|2	2|0	SPAG16|SPAG16	213870242|213870242	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.625000|0.625000	0.37756|0.37756	0.625000|0.625000	0.24477|0.24477	0.022000|0.022000	0.15160|0.15160	-1.151000|-1.151000	0.01829|0.01829	GAC|ACA	.	.	.	none		0.358	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532		G	214161997	C	G	214161997	3	3	151	1	0	0	0	0	1	0	0	0	14991	477	17	4	205	4	SPAG16	2	214161997	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08	140334062	214161997	29037376	5	8985											
XRN1	54464	hgsc.bcm.edu	37	chr3	142141567	142141567	+	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	aatcatctattatcctttcaAtatcatatttaaatgtgatc	14	18	2	7	0	4	1	3	1	1	0	6	1	5	1	1	0	0	0	1	0	8	7			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr3:142141567A>T	ENST00000264951.4	-	8	941	c.824T>A	c.(823-825)aTt>aAt	p.I275N	RNU1-100P_ENST00000365255.1_RNA|XRN1_ENST00000544157.1_Missense_Mutation_p.I65N|XRN1_ENST00000392981.2_Missense_Mutation_p.I275N|XRN1_ENST00000463916.1_Missense_Mutation_p.I275N	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	275					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						TATCCTTTCAATATCATATTT	0.323																																					p.I275N		Atlas-SNP	.											.	XRN1	138	.	0			c.T824A						PASS	.						70	77	75					3																	142141567		2202	4299	6501	SO:0001583	missense	54464	exon8			CTTTCAATATCAT	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.824T>A	chr3.hg19:g.142141567A>T	ENSP00000264951:p.Ile275Asn	88.0	0.0	.		66.0	28.0	.	NM_001042604	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Missense_Mutation	SNP	ENST00000264951.4	hg19	CCDS3123.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.466391	0.84425	.	.	ENSG00000114127	ENST00000264951;ENST00000392981;ENST00000463916;ENST00000544157;ENST00000477237	T;T	0.34472	1.36;1.36	5.69	5.69	0.88448	.	0.163395	0.56097	D	0.000029	T	0.60301	0.2258	M	0.77103	2.36	0.54753	D	0.999985	D;P;D;D;P	0.56968	0.978;0.879;0.963;0.96;0.932	D;P;P;P;P	0.65323	0.934;0.754;0.615;0.782;0.492	T	0.63033	-0.6727	10	0.51188	T	0.08	-19.9739	15.9662	0.79974	1.0:0.0:0.0:0.0	.	65;275;136;275;275	B4E2K3;Q8IZH2-3;B3KW17;Q8IZH2-2;Q8IZH2	.;.;.;.;XRN1_HUMAN	N	275;275;275;65;136	ENSP00000264951:I275N;ENSP00000376707:I275N	ENSP00000264951:I275N	I	-	2	0	XRN1	143624257	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.930000	0.92872	2.171000	0.68590	0.528000	0.53228	ATT	.	.	.	none		0.323	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001		T	142141567	A	T	142141567	3	4	151	1	0	0	0	0	1	0	0	0	17471	101	4	5	4436	5	XRN1	3	142141567	Missense_Mutation	SNP	A	TCGA-DW-7839-01A-11D-2136-08		142141567	55880863	6	8986											
SLBP	7884	hgsc.bcm.edu	37	chr4	1701385	1701385	+	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	taggacactttcatctgtctCaaagtcagccggcacagtag	11	10	9	11	1	4	0	3	0	2	0	5	1	4	1	1	2	1	2	1	2	3	3			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr4:1701385C>G	ENST00000489418.1	-	5	751	c.385G>C	c.(385-387)Gag>Cag	p.E129Q	SLBP_ENST00000318386.4_Missense_Mutation_p.E136Q|SLBP_ENST00000488267.1_Missense_Mutation_p.E94Q|SLBP_ENST00000429429.2_Missense_Mutation_p.E90Q	NM_006527.2	NP_006518.1	Q14493	SLBP_HUMAN	stem-loop binding protein	129	RNA-binding.				gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA transport (GO:0051028)|nuclear cell cycle DNA replication (GO:0033260)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone pre-mRNA 3'end processing complex (GO:0071204)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	histone pre-mRNA DCP binding (GO:0071208)|histone pre-mRNA stem-loop binding (GO:0071207)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(2)|lung(2)	5		Breast(71;0.212)|all_epithelial(65;0.241)	OV - Ovarian serous cystadenocarcinoma(23;0.0055)			TCATCTGTCTCAAAGTCAGCC	0.398																																					p.E129Q		Atlas-SNP	.											.	SLBP	12	.	0			c.G385C						PASS	.						126	117	120					4																	1701385		2203	4300	6503	SO:0001583	missense	7884	exon5			CTGTCTCAAAGTC	Z71188	CCDS3350.1	4p16.3	2008-02-11	2008-02-11		ENSG00000163950	ENSG00000163950			10904	protein-coding gene	gene with protein product	"histone binding protein"	602422	"stem-loop (histone) binding protein"			9049306, 1338771	Standard	NM_006527		Approved	HBP	uc003gdi.1	Q14493	OTTHUMG00000089349	ENST00000489418.1:c.385G>C	chr4.hg19:g.1701385C>G	ENSP00000417686:p.Glu129Gln	138.0	0.0	.		114.0	56.0	.	NM_006527	B3KRJ5	Missense_Mutation	SNP	ENST00000489418.1	hg19	CCDS3350.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	29.7|29.7|29.7	5.030846|5.030846|5.030846	0.93575|0.93575|0.93575	.|.|.	.|.|.	ENSG00000163950|ENSG00000163950|ENSG00000163950	ENST00000429429;ENST00000489418;ENST00000460392;ENST00000318386;ENST00000488267|ENST00000483348|ENST00000480936	.|.|.	.|.|.	.|.|.	5.08|5.08|5.08	5.08|5.08|5.08	0.68730|0.68730|0.68730	.|.|.	0.103824|.|.	0.64402|.|.	D|.|.	0.000005|.|.	D|D|.	0.84781|0.84781|.	0.5548|0.5548|.	M|M|M	0.89534|0.89534|0.89534	3.04|3.04|3.04	0.80722|0.80722|0.80722	D|D|D	1|1|1	D;P;D;D;D|.|.	0.89917|.|.	1.0;0.915;0.985;0.985;0.985|.|.	D;P;P;P;P|.|.	0.91635|.|.	0.999;0.653;0.804;0.804;0.804|.|.	D|D|.	0.87783|0.87783|.	0.2613|0.2613|.	9|5|.	0.72032|.|.	D|.|.	0.01|.|.	-9.2509|-9.2509|-9.2509	18.53|18.53|18.53	0.90987|0.90987|0.90987	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	94;136;90;109;129|.|.	E7EUV9;F8W8D3;B3KRJ5;C9IY53;Q14493|.|.	.;.;.;.;SLBP_HUMAN|.|.	Q|F|S	90;129;109;136;94|83|136	.|.|.	ENSP00000316490:E136Q|.|.	E|L|X	-|-|-	1|3|2	0|2|2	SLBP|SLBP|SLBP	1671183|1671183|1671183	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.949000|0.949000|0.949000	0.38748|0.38748|0.38748	0.969000|0.969000|0.969000	0.65631|0.65631|0.65631	7.142000|7.142000|7.142000	0.77339|0.77339|0.77339	2.382000|2.382000|2.382000	0.81193|0.81193|0.81193	0.644000|0.644000|0.644000	0.83932|0.83932|0.83932	GAG|TTG|TGA	.	.	.	none		0.398	SLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203176.1	NM_006527		G	1701385	C	G	1701385	3	3	151	1	0	0	0	0	1	0	0	0	14385	835	29	4	443	4	SLBP	4	1701385	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08		1701385	189452891	7	8987											
BOD1L	259282	hgsc.bcm.edu	37	chr4	13604361	13604361	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caatcacgcccgttaacttaCttccaagaggcatgattacc	12	10	6	13	2	1	2	1	1	0	1	2	2	2	2	3	1	3	2	3	1	5	4			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr4:13604361C>T	ENST00000040738.5	-	10	4298	c.4163G>A	c.(4162-4164)aGt>aAt	p.S1388N		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1388						nucleus (GO:0005634)	DNA binding (GO:0003677)										CGTTAACTTACTTCCAAGAGG	0.418																																					p.S1388N		Atlas-SNP	.											.	.	.	.	0			c.G4163A						PASS	.						139	134	135					4																	13604361		2203	4300	6503	SO:0001583	missense	259282	exon10			AACTTACTTCCAA	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.4163G>A	chr4.hg19:g.13604361C>T	ENSP00000040738:p.Ser1388Asn	127.0	0.0	.		125.0	63.0	.	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	hg19	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	C	8.574	0.880637	0.17467	.	.	ENSG00000038219	ENST00000040738	T	0.06768	3.26	5.02	0.266	0.15617	.	0.228445	0.31577	N	0.007419	T	0.04952	0.0133	N	0.24115	0.695	0.09310	N	1	B	0.14438	0.01	B	0.10450	0.005	T	0.34775	-0.9815	10	0.38643	T	0.18	0.0109	6.4855	0.22087	0.0:0.5089:0.1283:0.3629	.	1388	Q8NFC6	BOD1L_HUMAN	N	1388	ENSP00000040738:S1388N	ENSP00000040738:S1388N	S	-	2	0	BOD1L	13213459	0.008000	0.16893	0.000000	0.03702	0.002000	0.02628	0.472000	0.22116	0.111000	0.17947	-0.136000	0.14681	AGT	.	.	.	none		0.418	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		T	13604361	C	T	13604361	3	4	151	1	0	0	0	0	1	0	0	0	1483	565	20	2	5060	2	BOD1L	4	13604361	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08	11902976	13604361	177549915	8	8988											
GRIA1	2890	hgsc.bcm.edu	37	chr5	153078528	153078528	+	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	gcggcagagattgccaagcaCgtgggctactcctaccgtct	8	8	12	13	3	1	1	0	0	1	1	2	2	2	1	3	2	4	3	3	2	3	3			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr5:153078528C>G	ENST00000285900.5	+	10	1690	c.1347C>G	c.(1345-1347)caC>caG	p.H449Q	GRIA1_ENST00000521843.2_Missense_Mutation_p.H380Q|GRIA1_ENST00000448073.4_Missense_Mutation_p.H459Q|GRIA1_ENST00000518142.1_Missense_Mutation_p.H369Q|GRIA1_ENST00000518783.1_Missense_Mutation_p.H459Q|GRIA1_ENST00000340592.5_Missense_Mutation_p.H449Q	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	449					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)	TTGCCAAGCACGTGGGCTACT	0.537																																					p.H459Q		Atlas-SNP	.											.	GRIA1	321	.	0			c.C1377G						PASS	.						110	98	102					5																	153078528		2203	4300	6503	SO:0001583	missense	2890	exon10			CAAGCACGTGGGC		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.1347C>G	chr5.hg19:g.153078528C>G	ENSP00000285900:p.His449Gln	104.0	0.0	.		74.0	33.0	.	NM_001258021	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Missense_Mutation	SNP	ENST00000285900.5	hg19	CCDS4322.1	.	.	.	.	.	.	.	.	.	.	C	15.85	2.955998	0.53293	.	.	ENSG00000155511	ENST00000285900;ENST00000544403;ENST00000518142;ENST00000537037;ENST00000340592;ENST00000521843;ENST00000544794;ENST00000518783;ENST00000448073	T;T;T;T;T;T;T	0.37584	1.8;1.8;1.19;1.8;1.8;1.8;1.19	5.44	-4.24	0.03777	Glutamate receptor, L-glutamate/glycine-binding (2);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	T	0.44891	0.1315	L	0.55103	1.725	0.58432	D	0.999994	D;D;B;D;D;D	0.56521	0.976;0.976;0.012;0.976;0.971;0.962	P;P;B;P;P;P	0.59761	0.82;0.863;0.018;0.82;0.726;0.849	T	0.44997	-0.9291	10	0.44086	T	0.13	.	15.008	0.71527	0.0:0.6256:0.0:0.3744	.	459;459;369;459;449;449	E7ESV8;B7Z9G9;B7Z3F6;B7Z2W8;P42261-2;P42261	.;.;.;.;.;GRIA1_HUMAN	Q	449;449;369;403;449;380;380;459;459	ENSP00000285900:H449Q;ENSP00000427920:H369Q;ENSP00000339343:H449Q;ENSP00000427864:H380Q;ENSP00000442108:H380Q;ENSP00000428994:H459Q;ENSP00000415569:H459Q	ENSP00000285900:H449Q	H	+	3	2	GRIA1	153058721	0.000000	0.05858	0.981000	0.43875	0.975000	0.68041	-1.954000	0.01525	-0.842000	0.04195	-0.794000	0.03295	CAC	.	.	.	none		0.537	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3			G	153078528	C	G	153078528	3	3	151	1	0	0	0	0	1	0	0	0	6774	535	19	4	1385	4	GRIA1	5	153078528	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08		153078528	27836732	9	8989											
PTK7	5754	hgsc.bcm.edu	37	chr6	43044271	43044271	+	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	gccagaccccgccggttgccTctgctcagcgtcctgctgct	3	9	11	18	3	2	1	1	0	1	1	3	1	3	1	6	1	5	4	6	1	0	1			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr6:43044271T>G	ENST00000230419.4	+	1	266	c.45T>G	c.(43-45)ccT>ccG	p.P15P	PTK7_ENST00000349241.2_Silent_p.P15P|PTK7_ENST00000481273.1_5'Flank|PTK7_ENST00000352931.2_Silent_p.P15P|PTK7_ENST00000471863.1_Silent_p.P15P|PTK7_ENST00000345201.2_Silent_p.P15P|RP11-387M24.5_ENST00000606123.1_RNA|PTK7_ENST00000476760.1_Silent_p.P15P	NM_002821.4	NP_002812.2	Q13308	PTK7_HUMAN	protein tyrosine kinase 7	15					actin cytoskeleton reorganization (GO:0031532)|axis elongation (GO:0003401)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|establishment of epithelial cell apical/basal polarity (GO:0045198)|establishment of planar polarity (GO:0001736)|lung-associated mesenchyme development (GO:0060484)|neural tube closure (GO:0001843)|peptidyl-tyrosine phosphorylation (GO:0018108)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of neuron projection development (GO:0010976)|signal transduction (GO:0007165)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(12)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			GCCGGTTGCCTCTGCTCAGCG	0.716																																					p.P15P		Atlas-SNP	.											.	PTK7	101	.	0			c.T45G						PASS	.						7	10	9					6																	43044271		2101	4167	6268	SO:0001819	synonymous_variant	5754	exon1			GTTGCCTCTGCTC	AF447176	CCDS4884.1, CCDS4885.1, CCDS4886.1, CCDS4887.1, CCDS59021.1	6p21.1-p12.2	2013-02-18	2013-02-18		ENSG00000112655	ENSG00000112655	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9618	protein-coding gene	gene with protein product		601890	"PTK7 protein tyrosine kinase 7"			7478540	Standard	NM_002821		Approved	CCK4	uc011dve.2	Q13308	OTTHUMG00000014721	ENST00000230419.4:c.45T>G	chr6.hg19:g.43044271T>G		34.0	0.0	.		25.0	18.0	.	NM_152882	A8K974|B7Z477|E9PFZ5|Q13417|Q5T650|Q6IQ54|Q8NFA5|Q8NFA6|Q8NFA7|Q8NFA8	Silent	SNP	ENST00000230419.4	hg19	CCDS4884.1																																																																																			.	.	.	none		0.716	PTK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040580.2			G	43044271	T	G	43044271	2	3	151	1	0	0	0	0	0	0	0	1	12776	1538	54	5		5	PTK7	6	43044271	Silent	SNP	T	TCGA-DW-7839-01A-11D-2136-08		43044271	128070796	10	8990											
SP8	221833	hgsc.bcm.edu	37	chr7	20824956	20824956	+	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	gaggagccgccgccgccgccCccgccgccgccgccgctgcc	2	1	14	24	9	0	0	0	0	0	0	0	2	0	1	11	1	2	1	11	1	0	0	rs201180283		TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	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	chr7.hg19:g.20824956C>G		9.0	0.0	.		12.0	4.0	.	NM_182700	Q7Z615|Q7Z616|Q96MJ1	Silent	SNP	ENST00000361443.4	hg19	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	151	1	0	0	0	0	0	0	0	1	14983	610	22	4		4	SP8	7	20824956	Silent	SNP	C	TCGA-DW-7839-01A-11D-2136-08		20824956	138313707	11	8991											
HNRNPA2B1	3181	hgsc.bcm.edu	37	chr7	26235509	26235509	+	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	attatagccatccccaaatcCacgtccactgccatatccat	12	10	3	16	1	0	0	0	0	0	0	4	0	4	0	7	0	2	0	7	0	4	3			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr7:26235509C>T	ENST00000354667.4	-	8	883	c.715G>A	c.(715-717)Gga>Aga	p.G239R	HNRNPA2B1_ENST00000356674.7_Missense_Mutation_p.G227R	NM_031243.2	NP_112533.1	P22626	ROA2_HUMAN	heterogeneous nuclear ribonucleoprotein A2/B1	239	Gly-rich.				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						TCCCCAAATCCACGTCCACTG	0.378			T	ETV1	prostate																																p.G239R		Atlas-SNP	.		Dom	yes		7	7p15	3181	heterogeneous nuclear ribonucleoprotein A2/B1		E	.	HNRNPA2B1	70	.	0			c.G715A						PASS	.						110	94	100					7																	26235509		2203	4300	6503	SO:0001583	missense	3181	exon8			CAAATCCACGTCC	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.715G>A	chr7.hg19:g.26235509C>T	ENSP00000346694:p.Gly239Arg	99.0	0.0	.		74.0	33.0	.	NM_031243	A8K064|P22627|Q9UC98|Q9UDJ2	Missense_Mutation	SNP	ENST00000354667.4	hg19	CCDS43557.1	.	.	.	.	.	.	.	.	.	.	C	17.40	3.379588	0.61845	.	.	ENSG00000122566	ENST00000354667;ENST00000356674	D;D	0.86627	-2.15;-2.15	5.92	5.92	0.95590	.	0.000000	0.64402	D	0.000002	D	0.89015	0.6595	M	0.65677	2.01	0.40149	D	0.976921	D;D	0.56968	0.978;0.963	P;B	0.48524	0.58;0.376	D	0.86218	0.1629	10	0.20046	T	0.44	.	20.327	0.98704	0.0:1.0:0.0:0.0	.	227;239	P22626-2;P22626	.;ROA2_HUMAN	R	239;227	ENSP00000346694:G239R;ENSP00000349101:G227R	ENSP00000346694:G239R	G	-	1	0	HNRNPA2B1	26202034	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.505000	0.60421	2.794000	0.96219	0.650000	0.86243	GGA	.	.	.	none		0.378	HNRNPA2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214109.1	NM_002137		T	26235509	C	T	26235509	3	4	151	1	0	0	0	0	1	0	0	0	7266	603	21	2	362	2	HNRNPA2B1	7	26235509	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08	5410553	26235509	132903154	12	8992											
SAMD9	54809	hgsc.bcm.edu	37	chr7	92734994	92734994	+	Frame_Shift_Del	DEL	T	T	-																															ttatcttctatgagctcaacTtttagtgacttagaaccttt																										TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr7:92734994delT	ENST00000379958.2	-	3	686	c.417delA	c.(415-417)aaafs	p.K139fs		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	139						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)			TGAGCTCAACTTTTAGTGACT	0.358																																					p.V140fs		Atlas-INDEL	.											.	SAMD9	239	.	0			c.418delG						PASS	.						124	134	130					7																	92734994		2203	4300	6503	SO:0001589	frameshift_variant	54809	exon2			.	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.417delA	chr7.hg19:g.92734994delT	ENSP00000369292:p.Lys139fs	102.0	0.0	0		113.0	50.0	0.442478	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Frame_Shift_Del	DEL	ENST00000379958.2	hg19	CCDS34680.1																																																																																			.	.	.	none		0.358	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		-	92734994	T	-	92734994	7	5	151	1	0	1	0	1	0	0	0	0	13839	1606	56	0	4356	0	SAMD9	7	92734994	Frame_Shift_Del	DEL	T	TCGA-DW-7839-01A-11D-2136-08	66499485	92734994	66403669	13	8993											
MGAM	8972	hgsc.bcm.edu	37	chr7	141731533	141731533	+	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	accaatcccaactgtgctgtTtggtggacaaaggaatttga	12	11	10	8	0	0	1	0	1	0	0	1	3	1	3	2	3	2	2	2	3	4	2			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr7:141731533T>G	ENST00000549489.2	+	13	1619	c.1524T>G	c.(1522-1524)gtT>gtG	p.V508V	MGAM_ENST00000475668.2_Silent_p.V508V	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	508	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)	ACTGTGCTGTTTGGTGGACAA	0.363																																					p.V508V		Atlas-SNP	.											.	MGAM	767	.	0			c.T1524G						PASS	.						169	157	161					7																	141731533		1835	4091	5926	SO:0001819	synonymous_variant	8972	exon13			TGCTGTTTGGTGG	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.1524T>G	chr7.hg19:g.141731533T>G		109.0	0.0	.		149.0	70.0	.	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	hg19	CCDS47727.1																																																																																			.	.	.	none		0.363	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			G	141731533	T	G	141731533	2	3	151	1	0	0	0	0	0	0	0	1	9548	1828	64	5		5	MGAM	7	141731533	Silent	SNP	T	TCGA-DW-7839-01A-11D-2136-08	48996539	141731533	17407130	14	8994											
TAS2R41	259287	hgsc.bcm.edu	37	chr7	143175477	143175477	+	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	ttctgggaacatgacctacaAgtggaatacaaggatagaaa	17	8	10	6	0	1	2	0	1	1	1	1	5	1	5	1	3	3	0	1	3	8	4			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr7:143175477A>T	ENST00000408916.1	+	1	512	c.512A>T	c.(511-513)aAg>aTg	p.K171M	EPHA1-AS1_ENST00000429289.1_RNA	NM_176883.2	NP_795364.2	P59536	T2R41_HUMAN	taste receptor, type 2, member 41	171					sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(2)|lung(10)|pancreas(1)|prostate(2)|skin(1)	18	Melanoma(164;0.15)					ATGACCTACAAGTGGAATACA	0.358																																					p.K171M		Atlas-SNP	.											.	TAS2R41	43	.	0			c.A512T						PASS	.						65	63	63					7																	143175477		1827	4093	5920	SO:0001583	missense	259287	exon1			CCTACAAGTGGAA	AF494232	CCDS43663.1	7q34	2012-08-22			ENSG00000221855	ENSG00000221855		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18883	protein-coding gene	gene with protein product		613965				12379855	Standard	NM_176883		Approved	T2R59	uc003wdc.1	P59536	OTTHUMG00000155892	ENST00000408916.1:c.512A>T	chr7.hg19:g.143175477A>T	ENSP00000386201:p.Lys171Met	76.0	0.0	.		50.0	20.0	.	NM_176883	P59550|Q495I2|Q50KJ5|Q50KJ6|Q50KJ7|Q645W7	Missense_Mutation	SNP	ENST00000408916.1	hg19	CCDS43663.1	.	.	.	.	.	.	.	.	.	.	A	2.606	-0.291927	0.05568	.	.	ENSG00000221855	ENST00000408916	T	0.00824	5.65	5.79	3.37	0.38596	.	2.257240	0.02520	U	0.092493	T	0.01454	0.0047	L	0.49571	1.57	0.09310	N	1	B	0.32573	0.376	B	0.26202	0.067	T	0.48115	-0.9063	10	0.41790	T	0.15	.	6.5138	0.22236	0.6261:0.2953:0.0786:0.0	.	171	P59536	T2R41_HUMAN	M	171	ENSP00000386201:K171M	ENSP00000386201:K171M	K	+	2	0	TAS2R41	142885599	0.000000	0.05858	0.119000	0.21687	0.009000	0.06853	0.535000	0.23114	1.000000	0.39049	0.533000	0.62120	AAG	.	.	.	none		0.358	TAS2R41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342149.1			T	143175477	A	T	143175477	3	4	151	1	0	0	0	0	1	0	0	0	15591	72	3	5	514	5	TAS2R41	7	143175477	Missense_Mutation	SNP	A	TCGA-DW-7839-01A-11D-2136-08	1443944	143175477	15963186	15	8995											
LRRC14	9684	hgsc.bcm.edu	37	chr8	145746824	145746825	+	Frame_Shift_Del	DEL	AT	AT	-																															atgtgctctggaccacggacAtctacgggcgactggctgcg																								rs571447719		TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr8:145746824_145746825delAT	ENST00000292524.1	+	4	1590_1591	c.1444_1445delAT	c.(1444-1446)atcfs	p.I482fs	LRRC14_ENST00000529022.1_Frame_Shift_Del_p.I482fs	NM_001272036.1|NM_014665.2	NP_001258965.1|NP_055480.1	Q15048	LRC14_HUMAN	leucine rich repeat containing 14	482										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)			GACCACGGACATCTACGGGCGA	0.589																																					p.481_482del		Atlas-INDEL	.											.	LRRC14	25	.	0			c.1443_1444del						PASS	.																																			SO:0001589	frameshift_variant	9684	exon5			.	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.1444_1445delAT	chr8.hg19:g.145746824_145746825delAT	ENSP00000292524:p.Ile482fs	88.0	0.0	0		47.0	23.0	0.489362	NM_001272036	A8K0A8|D3DWM8	Frame_Shift_Del	DEL	ENST00000292524.1	hg19	CCDS6432.1																																																																																			.	.	.	none		0.589	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665		-	145746825	AT	-	145746824	7	5	151	1	0	1	0	1	0	0	0	0	8975	217	8	0	1454	0	LRRC14	8	145746824	Frame_Shift_Del	DEL	AT	TCGA-DW-7839-01A-11D-2136-08		145746824	617198	16	8996											
DENND4C	55667	hgsc.bcm.edu	37	chr9	19316719	19316719	+	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	cagcttgagatggaaattcaAgaggcatttttgcgctttat	11	14	10	6	1	1	2	1	1	0	2	1	4	1	3	0	2	2	3	0	2	3	6			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr9:19316719A>T	ENST00000380432.2	+	8	1014	c.981A>T	c.(979-981)caA>caT	p.Q327H	DENND4C_ENST00000602925.1_Missense_Mutation_p.Q563H|DENND4C_ENST00000434457.2_Missense_Mutation_p.Q563H			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	327	dDENN. {ECO:0000255|PROSITE- ProRule:PRU00306}.				cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						TGGAAATTCAAGAGGCATTTT	0.403																																					p.Q563H		Atlas-SNP	.											.	DENND4C	120	.	0			c.A1689T						PASS	.						121	135	130					9																	19316719		2203	4300	6503	SO:0001583	missense	55667	exon12			AATTCAAGAGGCA	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.981A>T	chr9.hg19:g.19316719A>T	ENSP00000369797:p.Gln327His	237.0	0.0	.		212.0	95.0	.	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	hg19		.	.	.	.	.	.	.	.	.	.	A	16.63	3.176330	0.57692	.	.	ENSG00000137145	ENST00000380437	.	.	.	4.98	-1.92	0.07618	dDENN (3);	0.051808	0.85682	D	0.000000	T	0.75547	0.3864	M	0.79805	2.47	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.75616	-0.3256	9	0.87932	D	0	-12.7766	11.8182	0.52224	0.5022:0.0:0.4978:0.0	.	327	Q5VZ89	DEN4C_HUMAN	H	327	.	ENSP00000369802:Q327H	Q	+	3	2	DENND4C	19306719	0.437000	0.25593	0.989000	0.46669	0.789000	0.44602	-0.194000	0.09559	-0.503000	0.06586	-0.561000	0.04177	CAA	.	.	.	none		0.403	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925		T	19316719	A	T	19316719	3	4	151	1	0	0	0	0	1	0	0	0	4437	69	3	5	1011	5	DENND4C	9	19316719	Missense_Mutation	SNP	A	TCGA-DW-7839-01A-11D-2136-08		19316719	121896712	17	8997											
DENND1A	57706	hgsc.bcm.edu	37	chr9	126214605	126214605	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctttggtctttacagtatTcagaattgctccacttcctt	7	18	6	10	0	2	1	1	0	1	1	4	1	4	1	2	1	3	3	2	1	3	8			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr9:126214605T>C	ENST00000373624.2	-	17	1450	c.1249A>G	c.(1249-1251)Aat>Gat	p.N417D	DENND1A_ENST00000394215.2_Missense_Mutation_p.N387D|DENND1A_ENST00000394219.3_Missense_Mutation_p.N385D|DENND1A_ENST00000542603.1_Missense_Mutation_p.N159D|DENND1A_ENST00000473039.1_5'UTR|DENND1A_ENST00000373620.3_Missense_Mutation_p.N417D|DENND1A_ENST00000373618.1_Missense_Mutation_p.N385D	NM_020946.1	NP_065997.1	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A	417					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						TTTACAGTATTCAGAATTGCT	0.413																																					p.N417D		Atlas-SNP	.											.	DENND1A	112	.	0			c.A1249G						PASS	.						173	152	159					9																	126214605		2203	4300	6503	SO:0001583	missense	57706	exon17			CAGTATTCAGAAT	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.1249A>G	chr9.hg19:g.126214605T>C	ENSP00000362727:p.Asn417Asp	112.0	0.0	.		79.0	5.0	.	NM_024820	A8MZA3|B1AM80|B7Z3C8|B7Z669|D3PFD3|Q05C88|Q5VWF0|Q6PJZ5|Q8IVD6|Q9H796	Missense_Mutation	SNP	ENST00000373624.2	hg19	CCDS35133.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.369121	0.82463	.	.	ENSG00000119522	ENST00000373624;ENST00000542603;ENST00000394219;ENST00000373620;ENST00000394215;ENST00000373618	T;T;T;T;T;T	0.25085	3.28;1.82;3.18;3.32;3.17;3.19	5.47	5.47	0.80525	.	0.093202	0.64402	D	0.000001	T	0.54775	0.1879	M	0.83012	2.62	0.54753	D	0.99998	D;D;D;D;D;D;D	0.76494	0.975;0.975;0.984;0.999;0.984;0.958;0.996	P;P;P;D;P;P;P	0.77557	0.883;0.883;0.84;0.99;0.879;0.767;0.877	T	0.60722	-0.7207	10	0.59425	D	0.04	-17.7065	15.5608	0.76244	0.0:0.0:0.0:1.0	.	385;375;385;387;417;417;237	Q8TEH3-6;Q8TEH3-7;Q8TEH3-4;Q8TEH3-5;Q8TEH3-2;Q8TEH3;Q9HCG4	.;.;.;.;.;DEN1A_HUMAN;.	D	417;159;385;417;387;385	ENSP00000362727:N417D;ENSP00000437457:N159D;ENSP00000377766:N385D;ENSP00000362722:N417D;ENSP00000377763:N387D;ENSP00000362720:N385D	ENSP00000362720:N385D	N	-	1	0	DENND1A	125254426	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.570000	0.67398	2.076000	0.62316	0.459000	0.35465	AAT	.	.	.	none		0.413	DENND1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053997.1	NM_024820		C	126214605	T	C	126214605	3	2	151	1	0	0	0	0	1	0	0	0	4428	1783	62	3	1911	3	DENND1A	9	126214605	Missense_Mutation	SNP	T	TCGA-DW-7839-01A-11D-2136-08	106897886	126214605	14998826	18	8998											
CUBN	8029	hgsc.bcm.edu	37	chr10	16943441	16943441	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatcactccactgtcacctaTctgtattccgccacaatctg	9	12	5	15	1	4	0	2	0	2	0	6	1	6	0	4	0	0	1	4	0	3	3			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr10:16943441T>C	ENST00000377833.4	-	52	8145	c.8080A>G	c.(8080-8082)Ata>Gta	p.I2694V		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2694	CUB 20. {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)	CTGTCACCTATCTGTATTCCG	0.443																																					p.I2694V		Atlas-SNP	.											.	CUBN	515	.	0			c.A8080G						PASS	.						130	105	114					10																	16943441		2203	4300	6503	SO:0001583	missense	8029	exon52			CACCTATCTGTAT	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.8080A>G	chr10.hg19:g.16943441T>C	ENSP00000367064:p.Ile2694Val	88.0	0.0	.		92.0	53.0	.	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	T	6.883	0.532398	0.13127	.	.	ENSG00000107611	ENST00000377833	T	0.17528	2.27	5.63	0.664	0.17890	CUB (5);	0.936616	0.08810	N	0.890473	T	0.08313	0.0207	N	0.17594	0.5	0.32205	N	0.577314	B	0.18310	0.027	B	0.21708	0.036	T	0.42085	-0.9472	10	0.22109	T	0.4	.	0.1187	0.00063	0.2416:0.2042:0.2266:0.3276	.	2694	O60494	CUBN_HUMAN	V	2694	ENSP00000367064:I2694V	ENSP00000367064:I2694V	I	-	1	0	CUBN	16983447	0.835000	0.29415	0.056000	0.19401	0.756000	0.42949	1.368000	0.34216	-0.064000	0.13043	0.477000	0.44152	ATA	.	.	.	none		0.443	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		C	16943441	T	C	16943441	3	2	151	1	0	0	0	0	1	0	0	0	4053	1435	50	3	2855	3	CUBN	10	16943441	Missense_Mutation	SNP	T	TCGA-DW-7839-01A-11D-2136-08		16943441	118591306	19	8999											
NRG3	10718	hgsc.bcm.edu	37	chr10	83635770	83635770	+	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	ccaggcaatgccctcctggcCtactgcggcatacgctacct	7	8	9	17	2	0	0	0	0	0	0	1	0	1	0	5	3	5	3	5	3	4	3			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr10:83635770C>A	ENST00000404547.1	+	1	674	c.674C>A	c.(673-675)cCt>cAt	p.P225H	NRG3_ENST00000372142.2_5'Flank|NRG3_ENST00000556918.1_5'Flank|NRG3_ENST00000372141.2_Missense_Mutation_p.P225H|NRG3_ENST00000404576.2_5'Flank			P56975	NRG3_HUMAN	neuregulin 3	225	Ser/Thr-rich.				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)		CCCTCCTGGCCTACTGCGGCA	0.617																																					p.P225H		Atlas-SNP	.											.	NRG3	301	.	0			c.C674A						PASS	.						101	80	87					10																	83635770		2203	4300	6503	SO:0001583	missense	10718	exon1			CCTGGCCTACTGC	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.674C>A	chr10.hg19:g.83635770C>A	ENSP00000384796:p.Pro225His	77.0	0.0	.		58.0	28.0	.	NM_001165972	A4D7U1|Q0PEH2|Q5VYH3	Missense_Mutation	SNP	ENST00000404547.1	hg19	CCDS31233.1	.	.	.	.	.	.	.	.	.	.	C	16.99	3.273875	0.59649	.	.	ENSG00000185737	ENST00000372141;ENST00000404547;ENST00000537287	T;T	0.33438	1.41;1.43	3.89	3.89	0.44902	.	0.000000	0.45361	D	0.000364	T	0.44074	0.1276	L	0.40543	1.245	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.66847	0.947;0.947	T	0.44050	-0.9353	10	0.87932	D	0	-21.024	13.7841	0.63099	0.0:1.0:0.0:0.0	.	225;225	B9EGV5;P56975-4	.;.	H	225	ENSP00000361214:P225H;ENSP00000384796:P225H	ENSP00000361214:P225H	P	+	2	0	NRG3	83625750	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.474000	0.66781	2.186000	0.69663	0.549000	0.68633	CCT	.	.	.	none		0.617	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086		A	83635770	C	A	83635770	3	1	151	1	0	0	0	0	1	0	0	0	10656	681	24	4	676	4	NRG3	10	83635770	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08	66692329	83635770	51898977	20	9000											
EPS8L2	64787	hgsc.bcm.edu	37	chr11	723296	723296	+	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	ccagaagcacagccccacttCagagcccacccccccggggg	9	2	10	20	1	1	2	1	0	0	2	1	2	1	2	7	2	3	1	7	2	1	1	rs142895363		TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr11:723296C>A	ENST00000533256.1	+	16	1772	c.1397C>A	c.(1396-1398)tCa>tAa	p.S466*	EPS8L2_ENST00000526198.1_Nonsense_Mutation_p.S482*|EPS8L2_ENST00000318562.8_Nonsense_Mutation_p.S466*|EPS8L2_ENST00000530636.1_Nonsense_Mutation_p.S466*|AP006621.9_ENST00000527021.2_RNA			Q9H6S3	ES8L2_HUMAN	EPS8-like 2	466					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)		AGCCCCACTTCAGAGCCCACC	0.602											OREG0020659	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S466X		Atlas-SNP	.											.	EPS8L2	42	.	0			c.C1397A						PASS	.						85	84	85					11																	723296		2203	4300	6503	SO:0001587	stop_gained	64787	exon15			CCACTTCAGAGCC	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.1397C>A	chr11.hg19:g.723296C>A	ENSP00000435585:p.Ser466*	184.0	0.0	.	590	134.0	59.0	.	NM_022772	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Nonsense_Mutation	SNP	ENST00000533256.1	hg19	CCDS31328.1	.	.	.	.	.	.	.	.	.	.	c	34	5.392509	0.96009	.	.	ENSG00000177106	ENST00000318562;ENST00000533256;ENST00000530636;ENST00000526198	.	.	.	2.79	1.87	0.25490	.	3.938280	0.01227	U	0.008254	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	2.7601	7.8157	0.29258	0.0:0.868:0.0:0.132	.	.	.	.	X	466;466;466;482	.	ENSP00000320828:S466X	S	+	2	0	EPS8L2	713296	0.002000	0.14202	0.005000	0.12908	0.020000	0.10135	0.499000	0.22546	0.538000	0.28769	-0.642000	0.03964	TCA	.	C|0.999;T|0.001	.	alt		0.602	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772		A	723296	C	A	723296	4	1	151	1	0	0	0	0	0	1	0	0	5198	838	29	4	1451	4	EPS8L2	11	723296	Nonsense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08		723296	134283220	21	9001											
SPRYD5	84767	hgsc.bcm.edu	37	chr11	55658774	55658774	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttcacatctggcaaatattAttgggaggttcatatggggg	10	14	12	5	0	3	0	2	0	1	0	3	1	3	1	0	5	0	2	0	5	4	6			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr11:55658774A>G	ENST00000449290.2	+	7	1117	c.1025A>G	c.(1024-1026)tAt>tGt	p.Y342C	TRIM51_ENST00000244891.3_Missense_Mutation_p.Y199C	NM_032681.3	NP_116070.2	Q9BSJ1	TRI51_HUMAN	tripartite motif-containing 51	342	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)										GGCAAATATTATTGGGAGGTT	0.423																																					p.Y342C		Atlas-SNP	.											.	.	.	.	0			c.A1025G						PASS	.						82	88	86					11																	55658774		2101	4042	6143	SO:0001583	missense	84767	exon7			AATATTATTGGGA	BC005014		11p11	2013-01-09	2012-05-18	2012-05-18	ENSG00000124900	ENSG00000124900		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19023	protein-coding gene	gene with protein product			"SPRY domain containing 5"	SPRYD5			Standard	NM_032681		Approved	TRIM51A	uc010rip.2	Q9BSJ1	OTTHUMG00000156437	ENST00000449290.2:c.1025A>G	chr11.hg19:g.55658774A>G	ENSP00000395086:p.Tyr342Cys	80.0	0.0	.		125.0	56.0	.	NM_032681	A6NMG2	Missense_Mutation	SNP	ENST00000449290.2	hg19		.	.	.	.	.	.	.	.	.	.	.	14.48	2.548928	0.45383	.	.	ENSG00000124900	ENST00000449290;ENST00000244891	T;T	0.74947	-0.89;-0.89	1.36	1.36	0.22044	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	D	0.85561	0.5725	M	0.89715	3.055	0.27185	N	0.960562	D	0.89917	1.0	D	0.97110	1.0	T	0.73235	-0.4047	9	0.87932	D	0	.	5.1325	0.14917	1.0:0.0:0.0:0.0	.	342	Q9BSJ1	SPRY5_HUMAN	C	342;199	ENSP00000395086:Y342C;ENSP00000244891:Y199C	ENSP00000244891:Y199C	Y	+	2	0	SPRYD5	55415350	1.000000	0.71417	0.075000	0.20258	0.398000	0.30690	3.446000	0.52928	0.540000	0.28808	0.136000	0.15936	TAT	.	.	.	none		0.423	TRIM51-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000391522.1	NM_032681		G	55658774	A	G	55658774	3	3	151	1	0	0	0	0	1	0	0	0	15123	449	16	3	1047	3	SPRYD5	11	55658774	Missense_Mutation	SNP	A	TCGA-DW-7839-01A-11D-2136-08	54935478	55658774	79347742	22	9002											
B3GNT1	11041	hgsc.bcm.edu	37	chr11	66114291	66114291	+	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	tggttgctctgatccagcatTtcccgcaggcctctccacag	6	11	9	15	1	2	1	0	1	2	0	5	1	4	1	4	2	2	4	4	2	0	2			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr11:66114291T>A	ENST00000311181.4	-	1	872	c.726A>T	c.(724-726)gaA>gaT	p.E242D	BRMS1_ENST00000425825.2_5'Flank|BRMS1_ENST00000359957.3_5'Flank|RP11-867G23.8_ENST00000531602.1_5'Flank	NM_006876.2	NP_006867.1	O43505	B3GN1_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 1	242					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						GATCCAGCATTTCCCGCAGGC	0.612																																					p.E242D		Atlas-SNP	.											.	B3GNT1	28	.	0			c.A726T						PASS	.						75	79	78					11																	66114291		2200	4295	6495	SO:0001583	missense	11041	exon1			CAGCATTTCCCGC	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.726A>T	chr11.hg19:g.66114291T>A	ENSP00000309096:p.Glu242Asp	240.0	0.0	.		169.0	82.0	.	NM_006876	Q4TTN0	Missense_Mutation	SNP	ENST00000311181.4	hg19	CCDS8136.1	.	.	.	.	.	.	.	.	.	.	T	10.34	1.322423	0.23994	.	.	ENSG00000174684	ENST00000311181;ENST00000538757	T	0.22539	1.95	5.29	0.868	0.19090	.	0.396932	0.27876	N	0.017483	T	0.08044	0.0201	N	0.10837	0.055	0.28440	N	0.916866	B	0.13145	0.007	B	0.15052	0.012	T	0.31420	-0.9944	10	0.15066	T	0.55	-16.142	4.6684	0.12676	0.0:0.3853:0.1676:0.4471	.	242	O43505	B3GN1_HUMAN	D	242;13	ENSP00000309096:E242D	ENSP00000309096:E242D	E	-	3	2	B3GNT1	65870867	0.994000	0.37717	1.000000	0.80357	0.997000	0.91878	0.024000	0.13555	0.256000	0.21614	0.379000	0.24179	GAA	.	.	.	none		0.612	B3GNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392959.1	NM_006876		A	66114291	T	A	66114291	3	1	151	1	0	0	0	0	1	0	0	0	1256	1838	64	5	529	5	B3GNT1	11	66114291	Missense_Mutation	SNP	T	TCGA-DW-7839-01A-11D-2136-08	10455517	66114291	68892225	23	9003											
PICALM	8301	hgsc.bcm.edu	37	chr11	85722090	85722090	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tacctctgcaactttgaggaActctgagattcttgtcatcc	9	14	7	11	0	4	2	1	2	3	1	5	4	5	3	2	1	4	1	2	1	3	4			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr11:85722090A>G	ENST00000393346.3	-	7	896	c.748T>C	c.(748-750)Ttc>Ctc	p.F250L	PICALM_ENST00000526033.1_Missense_Mutation_p.F250L|PICALM_ENST00000532317.1_Missense_Mutation_p.F250L|PICALM_ENST00000356360.5_Missense_Mutation_p.F250L|PICALM_ENST00000528398.1_Missense_Mutation_p.F199L			Q13492	PICAL_HUMAN	phosphatidylinositol binding clathrin assembly protein	250	Interaction with FAM64A.				axonogenesis (GO:0007409)|cargo loading into vesicle (GO:0035459)|cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|hemopoiesis (GO:0030097)|iron ion homeostasis (GO:0055072)|iron ion import into cell (GO:0097459)|negative regulation of gene expression (GO:0010629)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of receptor-mediated endocytosis (GO:0048261)|positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902961)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902959)|regulation of endocytosis (GO:0030100)|regulation of protein localization (GO:0032880)|synaptic vesicle maturation (GO:0016188)|vesicle-mediated transport (GO:0016192)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neurofibrillary tangle (GO:0097418)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|vesicle (GO:0031982)	1-phosphatidylinositol binding (GO:0005545)|clathrin adaptor activity (GO:0035615)|clathrin binding (GO:0030276)|clathrin heavy chain binding (GO:0032050)			endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)				ACTTTGAGGAACTCTGAGATT	0.343			T	"MLLT10, MLL"	"TALL, AML, "																																p.F250L		Atlas-SNP	.		Dom	yes		11	11q14	8301	phosphatidylinositol binding clathrin assembly protein (CALM)		L	.	PICALM	82	.	0			c.T748C						PASS	.						128	112	118					11																	85722090		2202	4298	6500	SO:0001583	missense	8301	exon7			TGAGGAACTCTGA	BC048259	CCDS8272.1, CCDS31653.1, CCDS55783.1, CCDS55784.1	11q14	2008-02-01			ENSG00000073921	ENSG00000073921			15514	protein-coding gene	gene with protein product		603025				8643484	Standard	NM_001206947		Approved	CALM, CLTH	uc001pbm.3	Q13492	OTTHUMG00000166981	ENST00000393346.3:c.748T>C	chr11.hg19:g.85722090A>G	ENSP00000377015:p.Phe250Leu	18.0	0.0	.		30.0	18.0	.	NM_007166	B4DTM3|E9PN05|F8VPG7|O60700|Q4LE54|Q6GMQ6|Q86XZ9	Missense_Mutation	SNP	ENST00000393346.3	hg19	CCDS8272.1	.	.	.	.	.	.	.	.	.	.	A	34	5.324333	0.95708	.	.	ENSG00000073921	ENST00000532317;ENST00000526033;ENST00000447890;ENST00000393346;ENST00000528398;ENST00000356360	T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6	5.48	5.48	0.80851	ANTH (1);Clathrin adaptor, phosphoinositide-binding, GAT-like (1);	0.000000	0.85682	D	0.000000	T	0.76248	0.3961	M	0.87617	2.895	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.991;1.0	D;D;D;D	0.97110	0.994;1.0;0.981;1.0	T	0.80236	-0.1466	9	.	.	.	-19.6257	15.8605	0.79017	1.0:0.0:0.0:0.0	.	199;250;250;250	E9PN05;F8VPG7;Q13492;Q13492-3	.;.;PICAL_HUMAN;.	L	250;250;250;250;199;250	ENSP00000436958:F250L;ENSP00000433846:F250L;ENSP00000377015:F250L;ENSP00000434884:F199L;ENSP00000348718:F250L	.	F	-	1	0	PICALM	85399738	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.339000	0.96797	2.197000	0.70478	0.533000	0.62120	TTC	.	.	.	none		0.343	PICALM-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392224.1	NM_007166		G	85722090	A	G	85722090	3	3	151	1	0	0	0	0	1	0	0	0	11887	43	2	3	1294	3	PICALM	11	85722090	Missense_Mutation	SNP	A	TCGA-DW-7839-01A-11D-2136-08	19607799	85722090	49284426	24	9004											
FAT3	120114	hgsc.bcm.edu	37	chr11	92590392	92590392	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcacaggaggactgtgtcCggggtccaacgatccttgtg	7	10	14	10	2	1	0	1	0	0	0	4	3	4	2	3	4	1	0	3	4	1	1	rs368909373		TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr11:92590392C>T	ENST00000298047.6	+	19	11395	c.11378C>T	c.(11377-11379)cCg>cTg	p.P3793L	FAT3_ENST00000409404.2_Missense_Mutation_p.P3793L|FAT3_ENST00000525166.1_Missense_Mutation_p.P3643L|FAT3_ENST00000533797.1_Missense_Mutation_p.P128L			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3793					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)				GGACTGTGTCCGGGGTCCAAC	0.527										TCGA Ovarian(4;0.039)																											p.P3793L		Atlas-SNP	.											.	FAT3	1822	.	0			c.C11378T						PASS	.	C	LEU/PRO	2,4000		0,2,1999	103	106	105		11378	5.9	0.9	11		105	0,8334		0,0,4167	no	missense	FAT3	NM_001008781.2	98	0,2,6166	TT,TC,CC		0.0,0.05,0.0162	benign	3793/4558	92590392	2,12334	2001	4167	6168	SO:0001583	missense	120114	exon19			TGTGTCCGGGGTC	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.11378C>T	chr11.hg19:g.92590392C>T	ENSP00000298047:p.Pro3793Leu	168.0	0.0	.		113.0	51.0	.	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	C	20.7	4.040675	0.75732	5.0E-4	0.0	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166;ENST00000533797	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	5.95	5.95	0.96441	.	.	.	.	.	T	0.34832	0.0911	L	0.53249	1.67	0.80722	D	1	D;B	0.59357	0.985;0.399	B;B	0.41271	0.352;0.04	T	0.13045	-1.0524	9	0.51188	T	0.08	.	20.3932	0.98965	0.0:1.0:0.0:0.0	.	3793;3793	Q8TDW7-3;Q8TDW7	.;FAT3_HUMAN	L	3793;3793;3643;128	ENSP00000298047:P3793L;ENSP00000387040:P3793L;ENSP00000432586:P3643L;ENSP00000436399:P128L	ENSP00000298047:P3793L	P	+	2	0	FAT3	92230040	0.995000	0.38212	0.922000	0.36590	0.908000	0.53690	6.655000	0.74392	2.824000	0.97209	0.655000	0.94253	CCG	.	.	.	weak		0.527	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92590392	C	T	92590392	3	4	151	1	0	0	0	0	1	0	0	0	5698	652	23	1	11452	1	FAT3	11	92590392	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08	6868302	92590392	42416124	25	9005											
PPFIBP1	8496	hgsc.bcm.edu	37	chr12	27787953	27787953	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggaagacctgcgtggattgTtagagatgatggaaacagat	13	10	14	4	1	0	4	0	1	0	3	0	8	0	7	1	3	2	1	1	3	3	2			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr12:27787953T>C	ENST00000318304.8	+	4	458	c.175T>C	c.(175-177)Tta>Cta	p.L59L	PPFIBP1_ENST00000545334.1_Silent_p.L59L|PPFIBP1_ENST00000228425.6_Silent_p.L59L|PPFIBP1_ENST00000542629.1_Silent_p.L59L|PPFIBP1_ENST00000537927.1_Intron|PPFIBP1_ENST00000535047.1_Silent_p.L59L	NM_001198916.1|NM_177444.2	NP_001185845.1|NP_803193	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)	59					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)					GCGTGGATTGTTAGAGATGAT	0.458																																					p.L59L		Atlas-SNP	.											.	PPFIBP1	153	.	0			c.T175C						PASS	.						108	110	110					12																	27787953		2203	4300	6503	SO:0001819	synonymous_variant	8496	exon4			GGATTGTTAGAGA	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.175T>C	chr12.hg19:g.27787953T>C		112.0	0.0	.		103.0	46.0	.	NM_003622	O75336|Q86X70|Q9NY03|Q9ULJ0	Silent	SNP	ENST00000318304.8	hg19	CCDS55812.1																																																																																			.	.	.	none		0.458	PPFIBP1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402877.1	NM_003622		C	27787953	T	C	27787953	2	2	151	1	0	0	0	0	0	0	0	1	12320	1722	60	3		3	PPFIBP1	12	27787953	Silent	SNP	T	TCGA-DW-7839-01A-11D-2136-08		27787953	106063942	26	9006											
ARF3	377	hgsc.bcm.edu	37	chr12	49333834	49333834	+	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	tcgaatcttgtcctggccacCcacatcccacactgtaaagc	10	9	6	16	1	1	0	0	0	1	0	4	1	3	0	4	1	1	1	4	1	3	2			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr12:49333834C>G	ENST00000256682.4	-	3	539	c.205G>C	c.(205-207)Ggt>Cgt	p.G69R	ARF3_ENST00000541959.1_Missense_Mutation_p.G69R|AC073610.5_ENST00000537495.1_5'Flank|ARF3_ENST00000541967.1_5'Flank|RP11-302B13.5_ENST00000398092.4_Missense_Mutation_p.G69R|ARF3_ENST00000447318.2_Intron	NM_001659.2	NP_001650.1	P61204	ARF3_HUMAN	ADP-ribosylation factor 3	69					GTP catabolic process (GO:0006184)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|lung(2)|skin(1)	4						TCCTGGCCACCCACATCCCAC	0.502																																					p.G69R	Pancreas(189;1862 2134 4419 30933 49364)	Atlas-SNP	.											.	ARF3	11	.	0			c.G205C						PASS	.						198	158	171					12																	49333834		2203	4300	6503	SO:0001583	missense	377	exon3			GGCCACCCACATC	M74491	CCDS8774.1	12q13.12	2013-01-22			ENSG00000134287	ENSG00000134287		"ADP-ribosylation factors"	654	protein-coding gene	gene with protein product	"small GTP binding protein"	103190				8661066	Standard	NM_001659		Approved		uc001rsr.2	P61204	OTTHUMG00000168080	ENST00000256682.4:c.205G>C	chr12.hg19:g.49333834C>G	ENSP00000256682:p.Gly69Arg	182.0	0.0	.		101.0	41.0	.	NM_001659	A8K6G8|B7ZB63|P16587	Missense_Mutation	SNP	ENST00000256682.4	hg19	CCDS8774.1	.	.	.	.	.	.	.	.	.	.	C	16.88	3.243385	0.58995	.	.	ENSG00000134287	ENST00000398092;ENST00000256682;ENST00000541959;ENST00000541236	D;D;D;D	0.84223	-1.82;-1.82;-1.82;-1.82	4.72	3.82	0.43975	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.96030	0.8707	H	0.99887	4.895	0.80722	D	1	D	0.67145	0.996	D	0.70716	0.97	D	0.97028	0.9748	10	0.87932	D	0	.	13.5059	0.61483	0.1577:0.8423:0.0:0.0	.	69	P61204	ARF3_HUMAN	R	69	ENSP00000438507:G69R;ENSP00000256682:G69R;ENSP00000438510:G69R;ENSP00000438063:G69R	ENSP00000256682:G69R	G	-	1	0	ARF3	47620101	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.814000	0.86154	1.096000	0.41439	0.462000	0.41574	GGT	.	.	.	none		0.502	ARF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258242.2	NM_001659		G	49333834	C	G	49333834	3	3	151	1	0	0	0	0	1	0	0	0	845	623	22	4	352	4	ARF3	12	49333834	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08	21545881	49333834	84518061	27	9007											
MBD6	114785	hgsc.bcm.edu	37	chr12	57920964	57920964	+	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	cctcatagctttaaattctgCgctgctggctgccaccctgg	6	12	9	14	1	2	0	1	0	1	0	2	0	2	0	3	2	4	4	3	2	3	4			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr12:57920964C>T	ENST00000355673.3	+	7	2392	c.2036C>T	c.(2035-2037)gCg>gTg	p.A679V	MBD6_ENST00000431731.2_Missense_Mutation_p.A679V	NM_052897.3	NP_443129.3	Q96DN6	MBD6_HUMAN	methyl-CpG binding domain protein 6	679	Pro-rich.					chromocenter (GO:0010369)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|urinary_tract(1)	31						TTAAATTCTGCGCTGCTGGCT	0.597																																					p.A679V		Atlas-SNP	.											.	MBD6	99	.	0			c.C2036T						PASS	.						11	12	12					12																	57920964		2195	4290	6485	SO:0001583	missense	114785	exon7			ATTCTGCGCTGCT	AB067474	CCDS8944.1	12q13.2	2008-02-05				ENSG00000166987			20445	protein-coding gene	gene with protein product						12529184	Standard	NM_052897		Approved	KIAA1887	uc001soj.1	Q96DN6		ENST00000355673.3:c.2036C>T	chr12.hg19:g.57920964C>T	ENSP00000347896:p.Ala679Val	35.0	0.0	.		18.0	13.0	.	NM_052897	Q8N3M0|Q8NA81|Q96Q00	Missense_Mutation	SNP	ENST00000355673.3	hg19	CCDS8944.1	.	.	.	.	.	.	.	.	.	.	C	15.12	2.737980	0.49045	.	.	ENSG00000166987	ENST00000355673;ENST00000431731;ENST00000300263	.	.	.	5.2	4.32	0.51571	.	0.738053	0.11966	N	0.512271	T	0.26011	0.0634	N	0.08118	0	0.41634	D	0.989031	P;P	0.45428	0.858;0.675	B;B	0.32928	0.109;0.155	T	0.14643	-1.0465	9	0.66056	D	0.02	-3.2719	12.8722	0.57970	0.0:0.9201:0.0:0.0799	.	679;679	Q6P0P0;Q96DN6	.;MBD6_HUMAN	V	679;679;143	.	ENSP00000300263:A143V	A	+	2	0	MBD6	56207231	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.754000	0.47532	1.350000	0.45770	0.561000	0.74099	GCG	.	.	.	none		0.597	MBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407250.1			T	57920964	C	T	57920964	3	4	151	1	0	0	0	0	1	0	0	0	9355	768	27	1	2054	1	MBD6	12	57920964	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08	8587130	57920964	75930931	28	9008											
MED13L	23389	hgsc.bcm.edu	37	chr12	116429670	116429670	+	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	ctcctgccccactattgctgGctggggcagcgctgttcaac	5	10	11	15	1	1	0	1	0	0	0	2	0	2	0	3	3	4	5	3	3	2	3			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr12:116429670G>C	ENST00000281928.3	-	17	3295	c.3089C>G	c.(3088-3090)gCc>gGc	p.A1030G		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1030						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)		ACTATTGCTGGCTGGGGCAGC	0.572																																					p.A1030G		Atlas-SNP	.											.	MED13L	193	.	0			c.C3089G						PASS	.						63	55	58					12																	116429670		2203	4300	6503	SO:0001583	missense	23389	exon17			TTGCTGGCTGGGG	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.3089C>G	chr12.hg19:g.116429670G>C	ENSP00000281928:p.Ala1030Gly	79.0	0.0	.		77.0	35.0	.	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Missense_Mutation	SNP	ENST00000281928.3	hg19	CCDS9177.1	.	.	.	.	.	.	.	.	.	.	G	14.60	2.582626	0.46006	.	.	ENSG00000123066	ENST00000281928	T	0.75260	-0.92	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.75019	0.3793	L	0.36672	1.1	0.49915	D	0.999835	D	0.58268	0.982	P	0.49999	0.628	T	0.75639	-0.3248	10	0.51188	T	0.08	.	19.6873	0.95984	0.0:0.0:1.0:0.0	.	1030	Q71F56	MD13L_HUMAN	G	1030	ENSP00000281928:A1030G	ENSP00000281928:A1030G	A	-	2	0	MED13L	114914053	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	5.549000	0.67261	2.890000	0.99128	0.585000	0.79938	GCC	.	.	.	none		0.572	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3			C	116429670	G	C	116429670	3	2	151	1	0	0	0	0	1	0	0	0	9438	1203	42	4	3603	4	MED13L	12	116429670	Missense_Mutation	SNP	G	TCGA-DW-7839-01A-11D-2136-08	58508706	116429670	17422225	29	9009											
STARD13	90627	hgsc.bcm.edu	37	chr13	33700266	33700266	+	Missense_Mutation	SNP	T	T	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	ctcagtgcttgctgaatactTtgaggcaggggctgtcccgt	6	12	13	10	1	1	2	1	2	0	0	2	2	2	2	1	3	3	4	1	3	2	3	rs143789881		TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr13:33700266T>G	ENST00000336934.5	-	7	2150	c.2034A>C	c.(2032-2034)caA>caC	p.Q678H	STARD13_ENST00000255486.4_Missense_Mutation_p.Q670H|STARD13_ENST00000399365.3_Missense_Mutation_p.Q560H	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	678	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)|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)		GCTGAATACTTTGAGGCAGGG	0.542																																					p.Q678H		Atlas-SNP	.											.	STARD13	100	.	0			c.A2034C						PASS	.						174	146	156					13																	33700266		2203	4300	6503	SO:0001583	missense	90627	exon7			AATACTTTGAGGC	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.2034A>C	chr13.hg19:g.33700266T>G	ENSP00000338785:p.Gln678His	210.0	0.0	.		185.0	91.0	.	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Missense_Mutation	SNP	ENST00000336934.5	hg19	CCDS9348.1	.	.	.	.	.	.	.	.	.	.	T	13.98	2.399557	0.42512	.	.	ENSG00000133121	ENST00000399365;ENST00000255486;ENST00000336934;ENST00000399364	T;T;T	0.18502	2.21;2.21;2.21	6.17	2.43	0.29744	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.120228	0.64402	D	0.000011	T	0.25827	0.0629	L	0.51914	1.62	0.80722	D	1	D;B;B	0.53745	0.962;0.048;0.129	P;B;B	0.58928	0.848;0.193;0.084	T	0.00970	-1.1496	10	0.40728	T	0.16	.	7.0057	0.24836	0.112:0.6413:0.0:0.2467	.	643;678;670	Q9Y3M8-4;Q9Y3M8;Q9Y3M8-2	.;STA13_HUMAN;.	H	560;670;678;670	ENSP00000382300:Q560H;ENSP00000255486:Q670H;ENSP00000338785:Q678H	ENSP00000255486:Q670H	Q	-	3	2	STARD13	32598266	0.993000	0.37304	0.981000	0.43875	0.797000	0.45037	0.424000	0.21330	0.174000	0.19809	-1.082000	0.02213	CAA	.	T|1.000;C|0.000	.	alt		0.542	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466		G	33700266	T	G	33700266	3	3	151	1	0	0	0	0	1	0	0	0	15268	1838	64	5	1339	5	STARD13	13	33700266	Missense_Mutation	SNP	T	TCGA-DW-7839-01A-11D-2136-08		33700266	81469612	30	9010											
SLC38A6	145389	hgsc.bcm.edu	37	chr14	61449295	61449295	+	Missense_Mutation	SNP	A	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	ttaatttgatgaatgccatcAtgggaagtggcatccttggc	10	13	11	7	0	1	2	1	2	0	0	2	3	2	3	2	3	1	1	2	3	3	3			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr14:61449295A>C	ENST00000267488.4	+	2	291	c.175A>C	c.(175-177)Atg>Ctg	p.M59L	SLC38A6_ENST00000456840.2_Missense_Mutation_p.M36L|SLC38A6_ENST00000554304.1_3'UTR|SLC38A6_ENST00000354886.2_Missense_Mutation_p.M59L|TRMT5_ENST00000261249.6_5'Flank|RP11-193F5.1_ENST00000553946.1_RNA	NM_153811.2	NP_722518.2	Q8IZM9	S38A6_HUMAN	solute carrier family 38, member 6	59					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)		GAATGCCATCATGGGAAGTGG	0.368																																					p.M59L		Atlas-SNP	.											.	SLC38A6	87	.	0			c.A175C						PASS	.						209	187	195					14																	61449295		2203	4300	6503	SO:0001583	missense	145389	exon2			GCCATCATGGGAA	AF070578	CCDS9751.1, CCDS53900.1	14q23.1	2013-05-22			ENSG00000139974	ENSG00000139974		"Solute carriers"	19863	protein-coding gene	gene with protein product							Standard	NM_153811		Approved	NAT-1	uc001xfh.2	Q8IZM9	OTTHUMG00000140335	ENST00000267488.4:c.175A>C	chr14.hg19:g.61449295A>C	ENSP00000267488:p.Met59Leu	110.0	0.0	.		102.0	48.0	.	NM_153811	C9JWA6|Q86SY5	Missense_Mutation	SNP	ENST00000267488.4	hg19	CCDS9751.1	.	.	.	.	.	.	.	.	.	.	A	18.58	3.655540	0.67586	.	.	ENSG00000139974	ENST00000354886;ENST00000267488;ENST00000451406;ENST00000456840;ENST00000526105	T;T;T;T;T	0.02121	4.44;4.44;4.44;4.44;4.44	5.63	5.63	0.86233	.	0.149549	0.85682	D	0.000000	T	0.02929	0.0087	L	0.35542	1.07	0.54753	D	0.999988	B;B;B	0.14012	0.009;0.004;0.006	B;B;B	0.15052	0.005;0.01;0.012	T	0.55398	-0.8147	10	0.35671	T	0.21	.	16.1307	0.81436	1.0:0.0:0.0:0.0	.	36;59;59	E7ETF2;Q8IZM9-2;Q8IZM9	.;.;S38A6_HUMAN	L	59;59;54;36;5	ENSP00000346959:M59L;ENSP00000267488:M59L;ENSP00000395851:M54L;ENSP00000413863:M36L;ENSP00000451244:M5L	ENSP00000267488:M59L	M	+	1	0	SLC38A6	60519048	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.794000	0.75135	2.263000	0.75096	0.533000	0.62120	ATG	.	.	.	none		0.368	SLC38A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276957.1			C	61449295	A	C	61449295	3	2	151	1	0	0	0	0	1	0	0	0	14621	217	8	5	181	5	SLC38A6	14	61449295	Missense_Mutation	SNP	A	TCGA-DW-7839-01A-11D-2136-08		61449295	45900245	31	9011											
HOMER2	9455	hgsc.bcm.edu	37	chr15	83518619	83518620	+	Frame_Shift_Ins	INS	-	-	T																															tctgtctttaaggaacgcacINStttgtcttccaggttttgat																										TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr15:83518619_83518620insT	ENST00000304231.8	-	9	1104_1105	c.912_913insA	c.(910-915)aaagtgfs	p.V305fs	HOMER2_ENST00000399166.2_Frame_Shift_Ins_p.V239fs|HOMER2_ENST00000426485.1_Frame_Shift_Ins_p.V250fs|HOMER2_ENST00000450735.2_Frame_Shift_Ins_p.V294fs	NM_199330.2	NP_955362.1	Q9NSB8	HOME2_HUMAN	homer homolog 2 (Drosophila)	305					behavioral response to cocaine (GO:0048148)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|chemical homeostasis within a tissue (GO:0048875)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)				cervix(1)|endometrium(2)|lung(6)	9						AAGGAACGCACTTTGTCTTCCA	0.505											OREG0023389	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V305fs		Atlas-INDEL	.											.	HOMER2	63	.	0			c.913_914insA						PASS	.																																			SO:0001589	frameshift_variant	9455	exon9			.	AF093264	CCDS45334.1, CCDS45336.1	15q24.3	2008-02-05				ENSG00000103942			17513	protein-coding gene	gene with protein product		604799				9808459, 9808458	Standard	NM_199330		Approved	CPD, Cupidin, Vesl-2, HOMER-2B, HOMER-2, HOMER-2A	uc002bjg.3	Q9NSB8		ENST00000304231.8:c.913dupA	chr15.hg19:g.83518622_83518622dupT	ENSP00000305632:p.Val305fs	152.0	0.0	0	1222	112.0	53.0	0.473214	NM_199330	O95269|O95349|Q9NSB6|Q9NSB7|Q9UNT7	Frame_Shift_Ins	INS	ENST00000304231.8	hg19	CCDS45334.1																																																																																			.	.	.	none		0.505	HOMER2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418689.1			T	83518620	-	T	83518619	7	5	151	1	0	1	1	0	0	0	0	0	7286	565	20	0	155	0	HOMER2	15	83518619	Frame_Shift_Ins	INS	-	TCGA-DW-7839-01A-11D-2136-08		83518619	19012773	32	9012											
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24802526	24802526	+	Frame_Shift_Del	DEL	G	G	-																															ggtggtctgtttctgccagtGataactggggagaaacttca																										TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr16:24802526delG	ENST00000395799.3	+	6	2692	c.2563delG	c.(2563-2565)gatfs	p.D855fs	TNRC6A_ENST00000315183.7_Frame_Shift_Del_p.D855fs	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	855	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)		TTCTGCCAGTGATAACTGGGG	0.478																																					p.S854fs		Atlas-INDEL	.											.	TNRC6A	171	.	0			c.2562delT						PASS	.						80	79	79					16																	24802526		2197	4300	6497	SO:0001589	frameshift_variant	27327	exon6			.	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.2563delG	chr16.hg19:g.24802526delG	ENSP00000379144:p.Asp855fs	73.0	0.0	0		67.0	28.0	0.41791	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Frame_Shift_Del	DEL	ENST00000395799.3	hg19	CCDS10624.2																																																																																			.	.	.	none		0.478	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		-	24802526	G	-	24802526	7	5	151	1	0	1	0	1	0	0	0	0	16352	1290	45	0	2585	0	TNRC6A	16	24802526	Frame_Shift_Del	DEL	G	TCGA-DW-7839-01A-11D-2136-08		24802526	65552227	33	9013											
ADAD2	161931	hgsc.bcm.edu	37	chr16	84228944	84228944	+	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	cgtgaaggagatctacaagcTggtggctctgggcaccggca	9	7	15	10	2	2	2	0	1	2	1	2	3	2	2	1	5	2	4	1	5	3	1			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr16:84228944T>A	ENST00000315906.5	+	5	828	c.776T>A	c.(775-777)cTg>cAg	p.L259Q	RP11-486L19.2_ENST00000536986.1_RNA|RP11-486L19.2_ENST00000561900.1_RNA|RP11-486L19.2_ENST00000565643.1_RNA|ADAD2_ENST00000268624.3_Missense_Mutation_p.L341Q|RP11-486L19.2_ENST00000569834.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	259					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						ATCTACAAGCTGGTGGCTCTG	0.677																																					p.L341Q		Atlas-SNP	.											.	ADAD2	46	.	0			c.T1022A						PASS	.						13	15	15					16																	84228944		2167	4266	6433	SO:0001583	missense	161931	exon6			ACAAGCTGGTGGC	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.776T>A	chr16.hg19:g.84228944T>A	ENSP00000325153:p.Leu259Gln	59.0	0.0	.		28.0	11.0	.	NM_139174	B2RCL6|Q8NA94	Missense_Mutation	SNP	ENST00000315906.5	hg19	CCDS45536.1	.	.	.	.	.	.	.	.	.	.	T	15.79	2.937894	0.52972	.	.	ENSG00000140955	ENST00000315906;ENST00000268624	T;T	0.19938	2.11;2.12	5.22	5.22	0.72569	.	0.300709	0.27618	N	0.018561	T	0.39462	0.1079	L	0.49126	1.545	0.38021	D	0.934833	D;D	0.89917	1.0;1.0	D;D	0.85130	0.995;0.997	T	0.40059	-0.9583	10	0.87932	D	0	-12.5673	11.7794	0.52003	0.0:0.0:0.0:1.0	.	259;341	Q8NCV1;Q8NCV1-2	ADAD2_HUMAN;.	Q	259;341	ENSP00000325153:L259Q;ENSP00000268624:L341Q	ENSP00000268624:L341Q	L	+	2	0	ADAD2	82786445	1.000000	0.71417	0.881000	0.34555	0.081000	0.17604	5.029000	0.64121	2.088000	0.63022	0.528000	0.53228	CTG	.	.	.	none		0.677	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174		A	84228944	T	A	84228944	3	1	151	1	0	0	0	0	1	0	0	0	232	1580	55	5	1044	5	ADAD2	16	84228944	Missense_Mutation	SNP	T	TCGA-DW-7839-01A-11D-2136-08	59426418	84228944	6125809	34	9014											
SREBF1	6720	hgsc.bcm.edu	37	chr17	17721579	17721579	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaagccaggactcactgcttTtgtggacagcagtgcgcaga	11	8	12	10	1	1	1	1	0	0	1	1	3	1	3	1	2	4	3	1	2	1	2			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr17:17721579T>C	ENST00000261646.5	-	6	1362	c.1178A>G	c.(1177-1179)aAa>aGa	p.K393R	SREBF1_ENST00000355815.4_Missense_Mutation_p.K423R|SREBF1_ENST00000395757.1_Missense_Mutation_p.K139R|SREBF1_ENST00000583732.1_5'Flank|SREBF1_ENST00000435530.2_Missense_Mutation_p.K393R|SREBF1_ENST00000338854.5_Missense_Mutation_p.K393R	NM_004176.4	NP_004167.3	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription factor 1	393	Interaction with LMNA. {ECO:0000250}.|Leucine-zipper.				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						CTCACTGCTTTTGTGGACAGC	0.567																																					p.K423R		Atlas-SNP	.											.	SREBF1	47	.	0			c.A1268G						PASS	.						126	105	112					17																	17721579		2203	4300	6503	SO:0001583	missense	6720	exon7			CTGCTTTTGTGGA	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.1178A>G	chr17.hg19:g.17721579T>C	ENSP00000261646:p.Lys393Arg	124.0	0.0	.		102.0	27.0	.	NM_001005291	B0I4X3|B0I4X4|D3DXC4|Q16062|Q59F52|Q6P4R7|Q6PFW7|Q6PJ36|Q8TAK9	Missense_Mutation	SNP	ENST00000261646.5	hg19	CCDS11189.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.472206	0.84533	.	.	ENSG00000072310	ENST00000338854;ENST00000355815;ENST00000261646;ENST00000395757;ENST00000418712;ENST00000423161;ENST00000435530	T;T;T;T;T	0.80738	0.37;0.4;0.4;0.88;-1.41	5.13	2.6	0.31112	Helix-loop-helix DNA-binding (2);	0.049203	0.85682	N	0.000000	D	0.83496	0.5267	L	0.50333	1.59	0.58432	D	0.999998	D;B;D;D	0.89917	0.998;0.402;1.0;1.0	D;B;D;D	0.91635	0.993;0.235;0.997;0.999	T	0.79674	-0.1705	10	0.51188	T	0.08	-4.0837	6.0908	0.19993	0.0:0.1068:0.1545:0.7388	.	393;369;393;423	B0I4X3;B0I4X4;P36956;P36956-4	.;.;SRBP1_HUMAN;.	R	393;423;393;139;230;319;393	ENSP00000345822:K393R;ENSP00000348069:K423R;ENSP00000261646:K393R;ENSP00000379106:K139R;ENSP00000413389:K393R	ENSP00000261646:K393R	K	-	2	0	SREBF1	17662304	0.997000	0.39634	0.970000	0.41538	0.899000	0.52679	2.228000	0.42981	0.187000	0.20147	0.459000	0.35465	AAA	.	.	.	none		0.567	SREBF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131771.1	NM_004176		C	17721579	T	C	17721579	3	2	151	1	0	0	0	0	1	0	0	0	15153	1841	64	3	2321	3	SREBF1	17	17721579	Missense_Mutation	SNP	T	TCGA-DW-7839-01A-11D-2136-08		17721579	63473631	35	9015											
ERBB2	2064	hgsc.bcm.edu	37	chr17	37880219	37880220	+	Missense_Mutation	DNP	TT	TT	CC																															ttccagtggccatcaaagtgTtgagggaaaacacatccccc																								rs121913470|rs121913469		TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr17:37880219_37880220TT>CC	ENST00000269571.5	+	19	2422_2423	c.2263_2264TT>CC	c.(2263-2265)TTg>CCg	p.L755P	ERBB2_ENST00000541774.1_Missense_Mutation_p.L740P|ERBB2_ENST00000445658.2_Missense_Mutation_p.L479P|ERBB2_ENST00000584601.1_Missense_Mutation_p.L725P|ERBB2_ENST00000406381.2_Missense_Mutation_p.L725P|MIR4728_ENST00000580969.1_RNA|ERBB2_ENST00000540147.1_Missense_Mutation_p.L725P|ERBB2_ENST00000584450.1_Missense_Mutation_p.L755P			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	755	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		L -> P (in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:15457249}.		axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)	p.L755S(10)|p.L755P(2)|p.L755_S760>A(1)		NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	CATCAAAGTGTTGAGGGAAAAC	0.53	L755S(LN229_CENTRAL_NERVOUS_SYSTEM)	1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)																											p.L755L|p.L755S		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,NS,carcinoma,-1,1|ERBB2,NS,carcinoma,0,20	ERBB2	429	.	13	Substitution - Missense(12)|Complex - insertion inframe(1)	breast(7)|lung(3)|stomach(2)|large_intestine(1)	c.T2263C|c.T2264C						PASS	.																																			SO:0001583	missense	2064	exon19			AAAGTGTTGAGGG|AAGTGTTGAGGGA	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		Exception_encountered	chr17.hg19:g.37880219_37880220delinsCC	ENSP00000269571:p.Leu755Pro	89.0|88.0	0.0	.		74.0|71.0	48.0|45.0	.	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Silent|Missense_Mutation	SNP	ENST00000269571.5	hg19	CCDS32642.1																																																																																			.	.	.	alt|weak		0.53	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			CC	37880220	TT	CC	37880219	3	2	151	1	0	0	0	0	1	0	0	0	5208	1722	60	3	2337	3	ERBB2	17	37880219	Missense_Mutation	DNP	TT	TCGA-DW-7839-01A-11D-2136-08	20158640	37880219	43314991	36	9016											
MUC16	94025	hgsc.bcm.edu	37	chr19	9075468	9075468	+	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	gccatgtggttgttgacataGaaactattgcttgttccctg	8	15	10	8	0	0	2	0	1	0	1	1	2	1	2	2	1	2	4	2	1	3	7			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr19:9075468G>C	ENST00000397910.4	-	3	12181	c.11978C>G	c.(11977-11979)tCt>tGt	p.S3993C		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3995	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						TGTTGACATAGAAACTATTGC	0.488																																					p.S3993C		Atlas-SNP	.											MUC16_ENST00000397910,colon,carcinoma,0,2	MUC16	4315	.	0			c.C11978G						PASS	.						85	82	83					19																	9075468		2075	4186	6261	SO:0001583	missense	94025	exon3			GACATAGAAACTA	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.11978C>G	chr19.hg19:g.9075468G>C	ENSP00000381008:p.Ser3993Cys	43.0	0.0	.		46.0	2.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	2.284	-0.363940	0.05103	.	.	ENSG00000181143	ENST00000397910	T	0.39592	1.07	2.18	-1.2	0.09554	.	.	.	.	.	T	0.50257	0.1605	L	0.50333	1.59	.	.	.	D	0.89917	1.0	D	0.79108	0.992	T	0.55412	-0.8145	8	0.87932	D	0	.	4.9481	0.14000	0.5113:0.0:0.4887:0.0	.	3993	B5ME49	.	C	3993	ENSP00000381008:S3993C	ENSP00000381008:S3993C	S	-	2	0	MUC16	8936468	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.113000	0.10774	-0.220000	0.09988	0.313000	0.20887	TCT	.	.	.	none		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9075468	G	C	9075468	3	2	151	1	0	0	0	0	1	0	0	0	9980	942	33	4	31873	4	MUC16	19	9075468	Missense_Mutation	SNP	G	TCGA-DW-7839-01A-11D-2136-08		9075468	50053515	37	9017											
DMPK	1760	hgsc.bcm.edu	37	chr19	46281110	46281110	+	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	ggacaggtagtctggggtgcCcacagccaccagcgaccgca	9	4	14	14	2	1	0	0	0	1	0	1	2	1	1	4	4	3	2	4	4	1	1			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr19:46281110C>T	ENST00000291270.4	-	7	822	c.697G>A	c.(697-699)Ggc>Agc	p.G233S	DMPK_ENST00000354227.5_Missense_Mutation_p.G233S|DMPK_ENST00000458663.2_Missense_Mutation_p.G233S|DMPK_ENST00000447742.2_Missense_Mutation_p.G233S|DMPK_ENST00000595361.1_5'Flank|DMPK_ENST00000343373.4_Missense_Mutation_p.G243S|DMPK_ENST00000600757.1_Missense_Mutation_p.G243S	NM_004409.3	NP_004400.4	Q09013	DMPK_HUMAN	dystrophia myotonica-protein kinase	233	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		TCTGGGGTGCCCACAGCCACC	0.692																																					p.G243S	Esophageal Squamous(35;307 869 9153 24033 28903)	Atlas-SNP	.											.	DMPK	74	.	0			c.G727A						PASS	.						34	38	37					19																	46281110		2200	4292	6492	SO:0001583	missense	1760	exon6			GGGTGCCCACAGC	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.697G>A	chr19.hg19:g.46281110C>T	ENSP00000291270:p.Gly233Ser	166.0	0.0	.		98.0	43.0	.	NM_001081563	E5KR08|Q16205|Q6P5Z6	Missense_Mutation	SNP	ENST00000291270.4	hg19	CCDS12674.1	.	.	.	.	.	.	.	.	.	.	c	35	5.523740	0.96431	.	.	ENSG00000104936	ENST00000458663;ENST00000342805;ENST00000291270;ENST00000447742;ENST00000377750;ENST00000343373;ENST00000348168;ENST00000354227	T;T;T;T;T	0.58210	0.35;0.35;0.35;0.35;0.35	4.77	4.77	0.60923	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	0.43747	D	0.000533	T	0.80929	0.4718	H	0.95982	3.75	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;0.999;0.999;1.0;1.0;1.0;1.0;1.0	D	0.87078	0.2164	10	0.87932	D	0	.	15.3285	0.74186	0.0:1.0:0.0:0.0	.	233;233;259;233;233;233;280;243	Q09013-12;Q09013-16;G5E982;E5KR07;E5KR05;Q09013;Q59FU6;E5KR08	.;.;.;.;.;DMPK_HUMAN;.;.	S	233;259;233;233;233;243;243;233	ENSP00000401753:G233S;ENSP00000291270:G233S;ENSP00000413417:G233S;ENSP00000345997:G243S;ENSP00000346168:G233S	ENSP00000291270:G233S	G	-	1	0	DMPK	50972950	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.606000	0.82863	2.455000	0.83008	0.655000	0.94253	GGC	.	.	.	none		0.692	DMPK-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460572.1	NM_004409		T	46281110	C	T	46281110	3	4	151	1	0	0	0	0	1	0	0	0	4586	623	22	2	1235	2	DMPK	19	46281110	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08	37205642	46281110	12847873	38	9018											
NLRP2	55655	hgsc.bcm.edu	37	chr19	55494859	55494859	+	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	ttgtaagggtggacattcaaCggtgacagacctgcaggagc	11	8	14	8	1	1	2	1	1	0	1	1	4	1	4	1	4	3	2	1	4	2	3			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr19:55494859C>T	ENST00000543010.1	+	6	1936	c.1793C>T	c.(1792-1794)aCg>aTg	p.T598M	NLRP2_ENST00000448584.2_Missense_Mutation_p.T598M|NLRP2_ENST00000538819.1_Missense_Mutation_p.T574M|NLRP2_ENST00000263437.6_Missense_Mutation_p.T595M|NLRP2_ENST00000537859.1_Missense_Mutation_p.T576M|NLRP2_ENST00000427260.2_Missense_Mutation_p.T575M|NLRP2_ENST00000391721.4_Missense_Mutation_p.T574M|NLRP2_ENST00000339757.7_Missense_Mutation_p.T576M	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	598					positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		GGACATTCAACGGTGACAGAC	0.537																																					p.T598M		Atlas-SNP	.											.	NLRP2	161	.	0			c.C1793T						PASS	.						107	92	97					19																	55494859		2203	4300	6503	SO:0001583	missense	55655	exon6			ATTCAACGGTGAC	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"Nucleotide-binding domain and leucine rich repeat containing"	22948	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"	609364	"NACHT, leucine rich repeat and PYD containing 2"	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.1793C>T	chr19.hg19:g.55494859C>T	ENSP00000445135:p.Thr598Met	95.0	0.0	.		84.0	39.0	.	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Missense_Mutation	SNP	ENST00000543010.1	hg19	CCDS12913.1	.	.	.	.	.	.	.	.	.	.	C	12.81	2.048824	0.36181	.	.	ENSG00000022556	ENST00000543010;ENST00000391721;ENST00000339757;ENST00000448584;ENST00000537859;ENST00000427260;ENST00000538819;ENST00000263437	T;T;T;T;T;T;T;T	0.74842	-0.87;-0.78;-0.8;-0.87;-0.8;-0.88;-0.78;-0.87	1.94	-0.27	0.12926	.	.	.	.	.	T	0.72095	0.3418	L	0.40543	1.245	0.09310	N	1	D;D;D;D;D	0.63880	0.993;0.993;0.988;0.993;0.988	P;P;P;P;P	0.58391	0.749;0.838;0.693;0.838;0.693	T	0.59894	-0.7368	9	0.48119	T	0.1	.	4.2569	0.10721	0.0:0.6265:0.0:0.3735	.	575;576;595;574;598	B4DZL7;Q9NX02-2;A8K9G6;Q9NX02-4;Q9NX02	.;.;.;.;NALP2_HUMAN	M	598;574;576;598;576;575;574;595	ENSP00000445135:T598M;ENSP00000375601:T574M;ENSP00000344074:T576M;ENSP00000409370:T598M;ENSP00000440601:T576M;ENSP00000402474:T575M;ENSP00000441133:T574M;ENSP00000263437:T595M	ENSP00000263437:T595M	T	+	2	0	NLRP2	60186671	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.276000	0.08514	-0.000000	0.14550	0.561000	0.74099	ACG	.	.	.	none		0.537	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852		T	55494859	C	T	55494859	3	4	151	1	0	0	0	0	1	0	0	0	10484	536	19	1	1811	1	NLRP2	19	55494859	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08	9213749	55494859	3634124	39	9019											
SNX5	27131	hgsc.bcm.edu	37	chr20	17933351	17933351	+	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	ttcttaaacacagcgagataCtcactgaaaagagatgtgca	16	9	8	8	1	2	3	1	1	1	2	2	5	2	3	0	0	4	1	0	0	5	3			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr20:17933351C>G	ENST00000377768.3	-	6	705	c.393G>C	c.(391-393)gaG>gaC	p.E131D	SNX5_ENST00000377759.4_Missense_Mutation_p.E131D|SNX5_ENST00000483485.1_5'UTR	NM_152227.1	NP_689413.1	Q9Y5X3	SNX5_HUMAN	sorting nexin 5	131	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						CAGCGAGATACTCACTGAAAA	0.453																																					p.E131D		Atlas-SNP	.											.	SNX5	38	.	0			c.G393C						PASS	.						53	47	49					20																	17933351		2203	4300	6503	SO:0001583	missense	27131	exon5			GAGATACTCACTG	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.393G>C	chr20.hg19:g.17933351C>G	ENSP00000366998:p.Glu131Asp	37.0	0.0	.		33.0	15.0	.	NM_014426	B7ZKN3|D3DW26|Q52LC4|Q7KZN0|Q9BWP0	Missense_Mutation	SNP	ENST00000377768.3	hg19	CCDS13130.1	.	.	.	.	.	.	.	.	.	.	C	15.20	2.763778	0.49574	.	.	ENSG00000089006	ENST00000377768;ENST00000377759;ENST00000431277;ENST00000419004	T;T;T;T	0.39997	1.05;1.05;1.05;1.05	5.66	-7.72	0.01250	Phox homologous domain (5);	0.000000	0.85682	D	0.000000	T	0.43656	0.1257	M	0.68593	2.085	0.52099	D	0.999949	B;P	0.44006	0.435;0.824	B;P	0.48141	0.366;0.568	T	0.60311	-0.7288	10	0.38643	T	0.18	.	16.5172	0.84304	0.0:0.2582:0.0:0.7418	.	152;131	B7Z476;Q9Y5X3	.;SNX5_HUMAN	D	131;131;94;96	ENSP00000366998:E131D;ENSP00000366988:E131D;ENSP00000404448:E94D;ENSP00000406731:E96D	ENSP00000366988:E131D	E	-	3	2	SNX5	17881351	0.985000	0.35326	0.546000	0.28166	0.781000	0.44180	0.195000	0.17155	-1.620000	0.01564	-1.124000	0.02001	GAG	.	.	.	none		0.453	SNX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078137.4			G	17933351	C	G	17933351	3	3	151	1	0	0	0	0	1	0	0	0	14918	564	20	4	857	4	SNX5	20	17933351	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08		17933351	45092169	40	9020											
WFDC10A	140832	hgsc.bcm.edu	37	chr20	44258534	44258534	+	Frame_Shift_Del	DEL	A	A	-																															gaggataccgtgacaagaagAggatgcagagtaggtgatgg																										TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chr20:44258534delA	ENST00000372643.3	+	1	370	c.82delA	c.(82-84)aggfs	p.R28fs	WFDC9_ENST00000326000.1_Intron	NM_080753.2	NP_542791.1	Q9H1F0	WF10A_HUMAN	WAP four-disulfide core domain 10A	28						extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			large_intestine(2)	2		Myeloproliferative disorder(115;0.0122)				TGACAAGAAGAGGATGCAGAG	0.577											OREG0025983	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K27fs		Atlas-INDEL	.											.	WFDC10A	7	.	0			c.81delG						PASS	.						165	130	142					20																	44258534		2203	4300	6503	SO:0001589	frameshift_variant	140832	exon1			.	AL031671	CCDS13363.1	20q13.11	2013-01-21	2003-02-21	2003-02-21	ENSG00000180305	ENSG00000180305		"WAP four-disulfide core domain containing"	16139	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 146"	C20orf146		12206714	Standard	NM_080753		Approved	dJ688G8.3, WAP10	uc002xoz.3	Q9H1F0	OTTHUMG00000046331	ENST00000372643.3:c.82delA	chr20.hg19:g.44258534delA	ENSP00000361726:p.Arg28fs	53.0	0.0	0	922	49.0	20.0	0.408163	NM_080753	A2RRE9|Q5TGZ7	Frame_Shift_Del	DEL	ENST00000372643.3	hg19	CCDS13363.1																																																																																			.	.	.	none		0.577	WFDC10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106944.2			-	44258534	A	-	44258534	7	5	151	1	0	1	0	1	0	0	0	0	17359	295	11	0	84	0	WFDC10A	20	44258534	Frame_Shift_Del	DEL	A	TCGA-DW-7839-01A-11D-2136-08	26325183	44258534	18766986	41	9021											
NUDT10	170685	hgsc.bcm.edu	37	chrX	51075840	51075840	+	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	gaagtgcaaacccaaccagaCacggacctacgaccccgagg	14	2	10	15	3	0	1	0	0	0	1	0	5	0	2	5	2	4	1	5	2	4	1			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chrX:51075840C>T	ENST00000376006.3	+	2	243	c.23C>T	c.(22-24)aCa>aTa	p.T8I	NUDT10_ENST00000356450.2_Missense_Mutation_p.T8I	NM_153183.2	NP_694853.1	Q9BW91	NUDT9_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 10	0					ADP catabolic process (GO:0046032)|IDP catabolic process (GO:0046709)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|mitochondrial matrix (GO:0005759)	adenosine-diphosphatase activity (GO:0043262)|ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)			cervix(1)|endometrium(8)|kidney(1)|large_intestine(1)|lung(1)|prostate(3)|upper_aerodigestive_tract(1)	16	Ovarian(276;0.236)					CCCAACCAGACACGGACCTAC	0.677																																					p.T8I	NSCLC(90;1817 2035 37909 38249)	Atlas-SNP	.											.	NUDT10	28	.	0			c.C23T						PASS	.						48	36	40					X																	51075840		2203	4300	6503	SO:0001583	missense	170685	exon2			ACCAGACACGGAC	AF469196	CCDS35278.1	Xp11.22-p11.1	2014-05-20			ENSG00000122824	ENSG00000122824		"Nudix motif containing"	17621	protein-coding gene	gene with protein product		300527				12105228	Standard	NM_153183		Approved	DIPP3a, hDIPP3alpha	uc004dph.3	Q8NFP7	OTTHUMG00000021530	ENST00000376006.3:c.23C>T	chrX.hg19:g.51075840C>T	ENSP00000365174:p.Thr8Ile	94.0	0.0	.		68.0	12.0	.	NM_153183	Q8NBN1|Q8NCB9|Q8NG25	Missense_Mutation	SNP	ENST00000376006.3	hg19	CCDS35278.1	.	.	.	.	.	.	.	.	.	.	C	14.72	2.619529	0.46736	.	.	ENSG00000122824	ENST00000376006;ENST00000356450	T;T	0.41758	0.99;0.99	2.61	2.61	0.31194	NUDIX hydrolase domain-like (1);	0.000000	0.85682	D	0.000000	T	0.31263	0.0791	L	0.40543	1.245	0.38831	D	0.955848	B	0.06786	0.001	B	0.08055	0.003	T	0.39440	-0.9614	9	0.33141	T	0.24	-26.7854	10.5501	0.45083	0.0:1.0:0.0:0.0	.	8	Q8NFP7	NUD10_HUMAN	I	8	ENSP00000365174:T8I;ENSP00000348831:T8I	ENSP00000348831:T8I	T	+	2	0	NUDT10	51092580	1.000000	0.71417	1.000000	0.80357	0.813000	0.45954	4.938000	0.63519	1.602000	0.50124	0.429000	0.28392	ACA	.	.	.	none		0.677	NUDT10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056578.1	NM_153183		T	51075840	C	T	51075840	3	4	151	1	0	0	0	0	1	0	0	0	10733	478	17	2	25	2	NUDT10	23	51075840	Missense_Mutation	SNP	C	TCGA-DW-7839-01A-11D-2136-08		51075840	104194720	42	9022											
NUDT11	55190	hgsc.bcm.edu	37	chrX	51239274	51239274	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcggggtcgtaggtccgcGtctggttgggtttgcacttc	2	13	15	11	4	1	0	0	0	1	0	5	0	2	0	2	5	1	4	2	5	1	4			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chrX:51239274G>A	ENST00000375992.3	-	1	174	c.23C>T	c.(22-24)aCg>aTg	p.T8M		NM_018159.3	NP_060629.2	Q96G61	NUD11_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 11	8					inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular (GO:0005622)	diphosphoinositol-polyphosphate diphosphatase activity (GO:0008486)|inositol diphosphate tetrakisphosphate diphosphatase activity (GO:0052840)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity (GO:0052846)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052847)|inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity (GO:0052843)|inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052848)|inositol-3-diphosphate-1,2,4,5,6-pentakisphosphate diphosphatase activity (GO:0052844)|inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity (GO:0052845)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(2)	9	Ovarian(276;0.236)					GTAGGTCCGCGTCTGGTTGGG	0.682										HNSCC(48;0.14)																											p.T8M	GBM(38;198 791 1498 11752 13599)	Atlas-SNP	.											.	NUDT11	22	.	0			c.C23T						PASS	.						20	17	18					X																	51239274		2199	4298	6497	SO:0001583	missense	55190	exon1			GTCCGCGTCTGGT	AK001490	CCDS43952.1	Xp11.22-p11.1	2014-05-20			ENSG00000196368	ENSG00000196368		"Nudix motif containing"	18011	protein-coding gene	gene with protein product						12105228	Standard	NM_018159		Approved	DIPP3b, FLJ10628, hDIPP3beta	uc010njt.3	Q96G61	OTTHUMG00000021531	ENST00000375992.3:c.23C>T	chrX.hg19:g.51239274G>A	ENSP00000365160:p.Thr8Met	41.0	0.0	.		26.0	12.0	.	NM_018159	Q9NVN0	Missense_Mutation	SNP	ENST00000375992.3	hg19	CCDS43952.1	.	.	.	.	.	.	.	.	.	.	G	16.48	3.134884	0.56828	.	.	ENSG00000196368	ENST00000375992	T	0.40756	1.02	3.0	2.01	0.26516	NUDIX hydrolase domain-like (1);	0.000000	0.85682	D	0.000000	T	0.36635	0.0974	M	0.70275	2.135	0.36766	D	0.883520	P	0.43750	0.816	B	0.37692	0.256	T	0.55270	-0.8167	9	0.48119	T	0.1	-26.7854	8.2508	0.31717	0.0:0.0:0.7647:0.2353	.	8	Q96G61	NUD11_HUMAN	M	8	ENSP00000365160:T8M	ENSP00000365160:T8M	T	-	2	0	NUDT11	51256014	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	8.357000	0.90088	1.514000	0.48869	0.544000	0.68410	ACG	.	.	.	none		0.682	NUDT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056579.1			A	51239274	G	A	51239274	3	1	151	1	0	0	0	0	1	0	0	0	10734	1145	40	1	479	1	NUDT11	23	51239274	Missense_Mutation	SNP	G	TCGA-DW-7839-01A-11D-2136-08	163434	51239274	104031286	43	9023											
RGAG4	340526	hgsc.bcm.edu	37	chrX	71351213	71351213	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccgcaaggacgggcactaTgggtactggccagcggatgt	8	7	15	11	3	0	0	0	0	0	0	1	2	1	2	2	5	2	3	2	5	3	2			TCGA-DW-7839-01A-11D-2136-08	TCGA-DW-7839-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d305b7d5-cbb1-41bf-8b2b-1cc2ba653c20	59a27c03-2a9d-4978-81e0-94d09e0e5d43	g.chrX:71351213T>C	ENST00000545866.1	-	1	545	c.178A>G	c.(178-180)Ata>Gta	p.I60V	RGAG4_ENST00000609883.1_Missense_Mutation_p.I60V|NHSL2_ENST00000540800.1_Intron|NHSL2_ENST00000510661.1_5'Flank|NHSL2_ENST00000373677.1_5'Flank|NHSL2_ENST00000535692.1_5'Flank	NM_001024455.3	NP_001019626.1	Q5HYW3	RGAG4_HUMAN	retrotransposon gag domain containing 4	60										cervix(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|skin(1)	24	Renal(35;0.156)					ACGGGCACTATGGGTACTGGC	0.617													T|||	3	0.000794702	0	0.0043	3775	,	,		8298	0		0	False		,,,				2504	0				p.I60V		Atlas-SNP	.											.	RGAG4	63	.	0			c.A178G						PASS	.						49	52	52					X																	71351213		1948	4125	6073	SO:0001583	missense	340526	exon1			GCACTATGGGTAC	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.178A>G	chrX.hg19:g.71351213T>C	ENSP00000441366:p.Ile60Val	190.0	0.0	.		118.0	53.0	.	NM_001024455	A7E2W7|Q8NCM4|Q9NPX1	Missense_Mutation	SNP	ENST00000545866.1	hg19	CCDS55446.1	.	.	.	.	.	.	.	.	.	.	T	0.155	-1.087731	0.01873	.	.	ENSG00000242732	ENST00000545866;ENST00000479991	T;T	0.12774	2.65;2.65	3.58	-1.73	0.08081	.	.	.	.	.	T	0.05181	0.0138	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43130	-0.9410	8	.	.	.	.	4.2089	0.10502	0.2097:0.5432:0.0:0.2471	.	60	Q5HYW3	RGAG4_HUMAN	V	60	ENSP00000441366:I60V;ENSP00000418667:I60V	.	I	-	1	0	RGAG4	71267938	0.096000	0.21769	0.004000	0.12327	0.666000	0.39218	-0.475000	0.06599	-0.475000	0.06852	-0.438000	0.05819	ATA	.	.	.	none		0.617	RGAG4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057171.1	NM_001024455		C	71351213	T	C	71351213	3	2	151	1	0	0	0	0	1	0	0	0	13288	1464	51	3	1535	3	RGAG4	23	71351213	Missense_Mutation	SNP	T	TCGA-DW-7839-01A-11D-2136-08	20111939	71351213	83919347	44	9024											
KIAA1751	85452	hgsc.bcm.edu	37	chr1	1887063	1887063	+	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	ctcccctgggcccctcagccCcctggaatgctgccctgagg	4	7	11	19	0	1	1	1	1	0	0	2	2	2	2	7	3	3	1	7	3	1	0			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:1887063C>T								TMEM52 (36351 upstream) : C1orf222 (32499 downstream)																							CCCCTCAGCCCCCTGGAATGC	0.597																																					p.G748E		Atlas-SNP	.											KIAA1751,NS,carcinoma,0,1	KIAA1751	92	.	0			c.G2243A						PASS	.						61	67	65					1																	1887063		1913	4097	6010	SO:0001628	intergenic_variant	85452	exon18			TCAGCCCCCTGGA																													chr1.hg19:g.1887063C>T		149.0	0.0	.		149.0	38.0	.	NM_001080484		Missense_Mutation	SNP		hg19		.	.	.	.	.	.	.	.	.	.	C	11.65	1.701128	0.30142	.	.	ENSG00000142609	ENST00000270720	.	.	.	1.45	-0.582	0.11709	.	0.105878	0.36665	N	0.002476	T	0.14657	0.0354	N	0.08118	0	0.09310	N	1	B	0.19817	0.039	B	0.11329	0.006	T	0.11494	-1.0585	9	0.87932	D	0	.	3.7893	0.08713	0.0:0.5066:0.0:0.4934	.	748	Q9C0B2	K1751_HUMAN	E	748	.	ENSP00000270720:G748E	G	-	2	0	C1orf222	1876923	0.000000	0.05858	0.001000	0.08648	0.193000	0.23685	0.050000	0.14120	-0.199000	0.10317	0.462000	0.41574	GGG	.	.	.	none	0	0.597									T	1887063	C	T	1887063	1	4	152	0	1	0	0	0	0	0	0	0	8263	623	22	2		2	KIAA1751	1	1887063	IGR	SNP	C	TCGA-DW-7840-01A-11D-2136-08		1887063	247363558	1	9025											
CAMTA1	23261	hgsc.bcm.edu	37	chr1	7721912	7721912	+	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	gcggacccacaactgcctctGcaccggcagcctgggtgagc	7	5	13	16	2	1	1	0	1	1	0	1	2	1	2	4	3	5	2	4	3	1	0			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:7721912G>C	ENST00000303635.7	+	8	998	c.791G>C	c.(790-792)tGc>tCc	p.C264S	CAMTA1_ENST00000439411.2_Missense_Mutation_p.C264S	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	264					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)		AACTGCCTCTGCACCGGCAGC	0.687			T	WWTR1	epitheliod hemangioendothelioma																																p.C264S		Atlas-SNP	.		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	.	CAMTA1	226	.	0			c.G791C						PASS	.						26	25	26					1																	7721912		2199	4298	6497	SO:0001583	missense	23261	exon8			GCCTCTGCACCGG	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.791G>C	chr1.hg19:g.7721912G>C	ENSP00000306522:p.Cys264Ser	34.0	0.0	.		23.0	9.0	.	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Missense_Mutation	SNP	ENST00000303635.7	hg19	CCDS30576.1	.	.	.	.	.	.	.	.	.	.	g	18.00	3.526318	0.64860	.	.	ENSG00000171735	ENST00000303635;ENST00000439411	T;T	0.52526	0.66;0.66	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.42539	0.1207	L	0.58101	1.795	0.80722	D	1	B	0.32573	0.376	B	0.27380	0.079	T	0.38112	-0.9676	10	0.10902	T	0.67	-19.7455	18.2029	0.89844	0.0:0.0:1.0:0.0	.	264	Q9Y6Y1	CMTA1_HUMAN	S	264	ENSP00000306522:C264S;ENSP00000402561:C264S	ENSP00000306522:C264S	C	+	2	0	CAMTA1	7644499	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.654000	0.98509	2.382000	0.81193	0.543000	0.68304	TGC	.	.	.	none		0.687	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215		C	7721912	G	C	7721912	3	2	152	1	0	0	0	0	1	0	0	0	2615	1319	46	4	821	4	CAMTA1	1	7721912	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	5834849	7721912	241528709	2	9026											
RERE	473	hgsc.bcm.edu	37	chr1	8424145	8424145	+	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	actccgccgtgtcctcatgcTatgcttcccactgagcccat	6	11	7	17	2	1	1	1	1	0	0	4	1	4	1	5	0	3	2	5	0	1	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:8424145T>A	ENST00000337907.3	-	16	2345	c.1711A>T	c.(1711-1713)Agc>Tgc	p.S571C	RERE_ENST00000377464.1_Missense_Mutation_p.S303C|RERE_ENST00000476556.1_Missense_Mutation_p.S17C|RERE_ENST00000400907.2_Intron|RERE_ENST00000400908.2_Missense_Mutation_p.S571C|RERE_ENST00000460659.1_5'Flank	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	571					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)		GTCCTCATGCTATGCTTCCCA	0.602																																					p.S571C		Atlas-SNP	.											.	RERE	129	.	0			c.A1711T						PASS	.						76	65	69					1																	8424145		2203	4300	6503	SO:0001583	missense	473	exon16			TCATGCTATGCTT	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.1711A>T	chr1.hg19:g.8424145T>A	ENSP00000338629:p.Ser571Cys	84.0	0.0	.		100.0	42.0	.	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Missense_Mutation	SNP	ENST00000337907.3	hg19	CCDS95.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.182080	0.78677	.	.	ENSG00000142599	ENST00000337907;ENST00000377464;ENST00000476556;ENST00000400908	T;T;T	0.06768	3.26;3.26;3.26	5.17	5.17	0.71159	.	.	.	.	.	T	0.26122	0.0637	M	0.63428	1.95	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.995	T	0.00498	-1.1704	9	0.59425	D	0.04	-23.1488	14.3401	0.66619	0.0:0.0:0.0:1.0	.	303;571	B1AKN3;Q9P2R6	.;RERE_HUMAN	C	571;303;17;571	ENSP00000338629:S571C;ENSP00000366684:S303C;ENSP00000383700:S571C	ENSP00000338629:S571C	S	-	1	0	RERE	8346732	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.520000	0.81821	2.171000	0.68590	0.459000	0.35465	AGC	.	.	.	none		0.602	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1			A	8424145	T	A	8424145	3	1	152	1	0	0	0	0	1	0	0	0	13244	1522	53	5	3025	5	RERE	1	8424145	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	702233	8424145	240826476	3	9027											
HMGCL	3155	hgsc.bcm.edu	37	chr1	24147039	24147039	+	Missense_Mutation	SNP	A	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	tctcggggaccaacttccacAattttcacccgctttggtaa	9	12	7	13	2	2	0	1	0	1	0	4	1	3	1	3	3	1	2	3	3	3	5			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:24147039A>C	ENST00000374490.3	-	2	148	c.105T>G	c.(103-105)atT>atG	p.I35M	HMGCL_ENST00000509389.1_5'UTR|HMGCL_ENST00000436439.2_Missense_Mutation_p.I35M|HMGCL_ENST00000374483.4_Missense_Mutation_p.I10M	NM_000191.2	NP_000182.2	P35914	HMGCL_HUMAN	3-hydroxymethyl-3-methylglutaryl-CoA lyase	35					acyl-CoA metabolic process (GO:0006637)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|ketone body biosynthetic process (GO:0046951)|leucine catabolic process (GO:0006552)|liver development (GO:0001889)|mitochondrion organization (GO:0007005)|protein tetramerization (GO:0051262)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	carboxylic acid binding (GO:0031406)|fatty-acyl-CoA binding (GO:0000062)|hydroxymethylglutaryl-CoA lyase activity (GO:0004419)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	12		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;0.0044)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.38e-24)|Colorectal(126;5.58e-08)|COAD - Colon adenocarcinoma(152;3.12e-06)|GBM - Glioblastoma multiforme(114;4.9e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000982)|KIRC - Kidney renal clear cell carcinoma(1967;0.0034)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0856)|LUSC - Lung squamous cell carcinoma(448;0.188)		CAACTTCCACAATTTTCACCC	0.403																																					p.I35M		Atlas-SNP	.											.	HMGCL	22	.	0			c.T105G						PASS	.						159	141	147					1																	24147039		2203	4300	6503	SO:0001583	missense	3155	exon2			TTCCACAATTTTC	BC010570	CCDS243.1, CCDS53279.1	1p36.1-p35	2010-04-30	2010-04-30		ENSG00000117305	ENSG00000117305	4.1.3.4		5005	protein-coding gene	gene with protein product	"hydroxymethylglutaricaciduria"	613898	"3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase"			8102917, 8978493	Standard	NM_001166059		Approved	HL	uc001bib.3	P35914	OTTHUMG00000002963	ENST00000374490.3:c.105T>G	chr1.hg19:g.24147039A>C	ENSP00000363614:p.Ile35Met	133.0	0.0	.		149.0	53.0	.	NM_000191	B4DUP4|B7UCC6|D3Y5K7|Q6IBC0|Q96FP8	Missense_Mutation	SNP	ENST00000374490.3	hg19	CCDS243.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.82|14.82	2.650811|2.650811	0.47362|0.47362	.|.	.|.	ENSG00000117305|ENSG00000117305	ENST00000374490;ENST00000436439;ENST00000374483;ENST00000543166|ENST00000235958	D;D;D|.	0.98862|.	-5.19;-5.1;-5.19|.	5.27|5.27	0.302|0.302	0.15786|0.15786	Aldolase-type TIM barrel (1);Pyruvate carboxyltransferase (1);|.	0.147080|.	0.64402|.	D|.	0.000011|.	T|T	0.30448|0.30448	0.0765|0.0765	N|N	0.08118|0.08118	0|0	0.41038|0.41038	D|D	0.985205|0.985205	P;B;B;B|.	0.37141|.	0.584;0.08;0.08;0.08|.	B;B;B;B|.	0.40741|.	0.338;0.339;0.232;0.339|.	T|T	0.04440|0.04440	-1.0951|-1.0951	10|5	0.66056|.	D|.	0.02|.	-0.2207|-0.2207	8.6087|8.6087	0.33789|0.33789	0.566:0.0:0.434:0.0|0.566:0.0:0.434:0.0	.|.	35;35;10;35|.	B4DUP4;Q6IBC0;B1AK13;P35914|.	.;.;.;HMGCL_HUMAN|.	M|W	35;35;10;10|31	ENSP00000363614:I35M;ENSP00000389281:I35M;ENSP00000363607:I10M|.	ENSP00000363607:I10M|.	I|L	-|-	3|2	3|0	HMGCL|HMGCL	24019626|24019626	0.519000|0.519000	0.26242|0.26242	1.000000|1.000000	0.80357|0.80357	0.931000|0.931000	0.56810|0.56810	-0.299000|-0.299000	0.08254|0.08254	0.132000|0.132000	0.18615|0.18615	-0.385000|-0.385000	0.06624|0.06624	ATT|TTG	.	.	.	none		0.403	HMGCL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008253.2	NM_000191		C	24147039	A	C	24147039	3	2	152	1	0	0	0	0	1	0	0	0	7236	126	5	5	904	5	HMGCL	1	24147039	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08	15722894	24147039	225103582	4	9028											
PHACTR4	65979	hgsc.bcm.edu	37	chr1	28785697	28785697	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaagagcaagttctcaggcTttggcaagatcttcaagccc	11	9	11	10	0	3	2	2	0	2	2	4	3	3	3	1	3	2	4	1	3	4	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:28785697T>C	ENST00000373839.3	+	3	379	c.118T>C	c.(118-120)Ttt>Ctt	p.F40L	PHACTR4_ENST00000373836.3_Missense_Mutation_p.F50L|PHACTR4_ENST00000493669.1_3'UTR	NM_001048183.1	NP_001041648.1	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	40					actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		GTTCTCAGGCTTTGGCAAGAT	0.448																																					p.F50L		Atlas-SNP	.											.	PHACTR4	64	.	0			c.T148C						PASS	.						87	84	85					1																	28785697		1904	4119	6023	SO:0001583	missense	65979	exon2			TCAGGCTTTGGCA	AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138		"Phosphatase and actin regulators"	25793	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 124"	608726				11483580, 15107502	Standard	NM_023923		Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373839.3:c.118T>C	chr1.hg19:g.28785697T>C	ENSP00000362945:p.Phe40Leu	93.0	0.0	.		84.0	28.0	.	NM_023923	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	Missense_Mutation	SNP	ENST00000373839.3	hg19	CCDS41293.1	.	.	.	.	.	.	.	.	.	.	T	15.01	2.706660	0.48412	.	.	ENSG00000204138	ENST00000373839;ENST00000373836;ENST00000373838	T;T	0.12465	2.68;2.69	5.28	5.28	0.74379	.	0.185233	0.48767	N	0.000178	T	0.06234	0.0161	N	0.04132	-0.27	0.36529	D	0.870593	B;B;B	0.14012	0.005;0.003;0.009	B;B;B	0.16722	0.009;0.004;0.016	T	0.13469	-1.0508	10	0.02654	T	1	-1.0711	14.6855	0.69047	0.0:0.0:0.0:1.0	.	50;40;24	Q8IZ21-2;Q8IZ21;Q8IZ21-3	.;PHAR4_HUMAN;.	L	40;50;39	ENSP00000362945:F40L;ENSP00000362942:F50L	ENSP00000362942:F50L	F	+	1	0	PHACTR4	28658284	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.667000	0.37471	2.128000	0.65567	0.528000	0.53228	TTT	.	.	.	none		0.448	PHACTR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009868.4	NM_023923		C	28785697	T	C	28785697	3	2	152	1	0	0	0	0	1	0	0	0	11819	1609	56	3	174	3	PHACTR4	1	28785697	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	4638658	28785697	220464924	5	9029											
PUM1	9698	hgsc.bcm.edu	37	chr1	31406096	31406096	+	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	ggggccacagatgggccctaAgtcaacaccgttcttcatgt	9	9	11	12	1	3	1	2	0	1	1	3	1	3	1	3	3	1	1	3	3	2	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:31406096A>T	ENST00000257075.5	-	22	3616	c.3523T>A	c.(3523-3525)Tta>Ata	p.L1175I	PUM1_ENST00000373747.3_Missense_Mutation_p.L1178I|PUM1_ENST00000440538.2_Missense_Mutation_p.L1151I|PUM1_ENST00000423018.2_Missense_Mutation_p.L1033I|PUM1_ENST00000424085.2_Missense_Mutation_p.L933I|PUM1_ENST00000373742.2_Missense_Mutation_p.L1116I|PUM1_ENST00000426105.2_Missense_Mutation_p.L1177I|SNORD103A_ENST00000363284.1_RNA|PUM1_ENST00000373741.4_Missense_Mutation_p.L1213I	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	1175					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)		ATGGGCCCTAAGTCAACACCG	0.552																																					p.L1177I		Atlas-SNP	.											.	PUM1	107	.	0			c.T3529A						PASS	.						187	165	173					1																	31406096		2203	4300	6503	SO:0001583	missense	9698	exon22			GCCCTAAGTCAAC	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.3523T>A	chr1.hg19:g.31406096A>T	ENSP00000257075:p.Leu1175Ile	178.0	0.0	.		162.0	63.0	.	NM_001020658	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Missense_Mutation	SNP	ENST00000257075.5	hg19	CCDS338.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.95|17.95	3.512828|3.512828	0.64522|0.64522	.|.	.|.	ENSG00000134644|ENSG00000134644	ENST00000525843;ENST00000498419|ENST00000424085;ENST00000257075;ENST00000373747;ENST00000373749;ENST00000426105;ENST00000440538;ENST00000373741;ENST00000423018;ENST00000373742	.|T;T;T;T;T;T;T;T	.|0.20332	.|2.14;2.08;2.34;2.34;2.42;2.33;2.44;2.1	4.96|4.96	4.96|4.96	0.65561|0.65561	.|.	0.000000|0.000000	0.64402|0.64402	D|D	0.000002|0.000002	T|T	0.34658|0.34658	0.0905|0.0905	L|L	0.56396|0.56396	1.775|1.775	0.80722|0.80722	D|D	1|1	.|D;B;B;B;B;P;B;D	.|0.67145	.|0.991;0.125;0.259;0.33;0.374;0.58;0.374;0.996	.|D;B;B;B;B;B;B;D	.|0.65773	.|0.938;0.076;0.076;0.159;0.168;0.183;0.168;0.913	T|T	0.14172|0.14172	-1.0482|-1.0482	6|10	.|0.51188	.|T	.|0.08	-3.3845|-3.3845	5.2679|5.2679	0.15609|0.15609	0.7814:0.0:0.2186:0.0|0.7814:0.0:0.2186:0.0	.|.	.|1116;1033;1213;1151;1175;1177;1178;1177	.|B4DG92;E7EWT3;Q5T1Z8;Q14671-2;Q14671;E9PCJ0;Q5T1Z4;Q53HH5	.|.;.;.;.;PUM1_HUMAN;.;.;.	H|I	1113;888|933;1175;1178;915;1177;1151;1213;1033;1116	.|ENSP00000400141:L933I;ENSP00000257075:L1175I;ENSP00000362852:L1178I;ENSP00000391723:L1177I;ENSP00000401777:L1151I;ENSP00000362846:L1213I;ENSP00000399440:L1033I;ENSP00000362847:L1116I	.|ENSP00000257075:L1175I	L|L	-|-	2|1	0|2	PUM1|PUM1	31178683|31178683	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	1.430000|1.430000	0.34914|0.34914	2.095000|2.095000	0.63458|0.63458	0.454000|0.454000	0.30748|0.30748	CTT|TTA	.	.	.	none		0.552	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1			T	31406096	A	T	31406096	3	4	152	1	0	0	0	0	1	0	0	0	12838	69	3	5	41	5	PUM1	1	31406096	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08	2620399	31406096	217844525	6	9030											
RBM15	64783	hgsc.bcm.edu	37	chr1	110883658	110883658	+	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	tctgcagcctctgcccttgaCtcattatgagctggtgacag	7	12	10	12	0	3	3	1	3	2	0	3	3	3	3	2	1	4	2	2	1	1	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:110883658C>G	ENST00000369784.3	+	1	2531	c.1631C>G	c.(1630-1632)aCt>aGt	p.T544S	RBM15_ENST00000602849.1_Missense_Mutation_p.T544S|RP5-1074L1.1_ENST00000449169.1_RNA|RBM15_ENST00000487146.2_Missense_Mutation_p.T544S	NM_022768.4	NP_073605.4	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	544					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)		CTGCCCTTGACTCATTATGAG	0.547			T	MKL1	acute megakaryocytic leukemia																																p.T544S		Atlas-SNP	.		Dom	yes		1	1p13	64783	RNA binding motif protein 15		L	.	RBM15	93	.	0			c.C1631G						PASS	.						74	71	72					1																	110883658		2203	4300	6503	SO:0001583	missense	64783	exon1			CCTTGACTCATTA	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.1631C>G	chr1.hg19:g.110883658C>G	ENSP00000358799:p.Thr544Ser	107.0	0.0	.		143.0	57.0	.	NM_022768	A1A693|Q3ZB86|Q4V760|Q5D058|Q5T613|Q86VW9|Q96PE4|Q96SC5|Q96SC6|Q96SC9|Q96SD0|Q96T38|Q9BRA5|Q9H6R8|Q9H9Y0	Missense_Mutation	SNP	ENST00000369784.3	hg19	CCDS822.1	.	.	.	.	.	.	.	.	.	.	C	6.069	0.381059	0.11466	.	.	ENSG00000162775	ENST00000369784	T	0.15952	2.38	4.44	4.44	0.53790	.	0.000000	0.44688	D	0.000431	T	0.03915	0.0110	N	0.22421	0.69	0.27060	N	0.963566	B;B	0.24426	0.103;0.063	B;B	0.22386	0.039;0.017	T	0.31251	-0.9950	10	0.10636	T	0.68	-8.2962	13.8608	0.63559	0.0:0.8463:0.1537:0.0	.	544;544	Q96T37-3;Q96T37	.;RBM15_HUMAN	S	544	ENSP00000358799:T544S	ENSP00000358799:T544S	T	+	2	0	RBM15	110685181	0.985000	0.35326	1.000000	0.80357	0.993000	0.82548	2.270000	0.43355	2.306000	0.77630	0.655000	0.94253	ACT	.	.	.	none		0.547	RBM15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000031114.2	NM_022768		G	110883658	C	G	110883658	3	3	152	1	0	0	0	0	1	0	0	0	13129	565	20	4	1633	4	RBM15	1	110883658	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	79477562	110883658	138366963	7	9031											
ADCY10	55811	hgsc.bcm.edu	37	chr1	167870956	167870956	+	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	cctgggtctcaaacaatccaTggatctccaggctacattta	11	11	7	12	0	2	0	1	0	2	0	5	1	3	1	3	3	2	1	3	3	4	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:167870956T>A	ENST00000367851.4	-	5	564	c.380A>T	c.(379-381)cAt>cTt	p.H127L	ADCY10_ENST00000545172.1_Intron|ADCY10_ENST00000367848.1_Missense_Mutation_p.H35L	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	127	Guanylate cyclase 1. {ECO:0000255|PROSITE-ProRule:PRU00099}.				cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						AAACAATCCATGGATCTCCAG	0.478																																					p.H127L		Atlas-SNP	.											.	ADCY10	175	.	0			c.A380T						PASS	.						170	167	168					1																	167870956		2203	4300	6503	SO:0001583	missense	55811	exon5			AATCCATGGATCT	AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	4.6.1.1	"Adenylate cyclases"	21285	protein-coding gene	gene with protein product	"soluble adenylyl cyclase", "Hypercalciuria, absorptive, 2"	605205					Standard	XM_006711449		Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.380A>T	chr1.hg19:g.167870956T>A	ENSP00000356825:p.His127Leu	198.0	0.0	.		237.0	83.0	.	NM_018417	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Missense_Mutation	SNP	ENST00000367851.4	hg19	CCDS1265.1	.	.	.	.	.	.	.	.	.	.	T	19.61	3.859754	0.71834	.	.	ENSG00000143199	ENST00000367851;ENST00000367848	T;T	0.78003	-1.14;1.49	5.76	5.76	0.90799	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.177315	0.39985	N	0.001214	T	0.67468	0.2896	L	0.27053	0.805	0.35716	D	0.816771	D;D	0.61697	0.988;0.99	P;P	0.62491	0.844;0.903	T	0.66666	-0.5866	9	0.11794	T	0.64	-17.7472	12.4728	0.55797	0.0:0.0:0.0:1.0	.	35;127	Q96PN6-2;Q96PN6	.;ADCYA_HUMAN	L	127;35	ENSP00000356825:H127L;ENSP00000356822:H35L	ENSP00000356822:H35L	H	-	2	0	ADCY10	166137580	1.000000	0.71417	0.922000	0.36590	0.701000	0.40568	4.710000	0.61873	2.193000	0.70182	0.450000	0.29827	CAT	.	.	.	none		0.478	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417		A	167870956	T	A	167870956	3	1	152	1	0	0	0	0	1	0	0	0	293	1464	51	5	4568	5	ADCY10	1	167870956	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	56987298	167870956	81379665	8	9032											
IKBKE	9641	hgsc.bcm.edu	37	chr1	206651658	206651658	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcccaggcagtcctgcaccAcatctatatccatgcccaca	10	8	6	17	0	1	0	0	0	1	0	4	0	4	0	5	1	2	2	5	1	2	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:206651658A>G	ENST00000367120.3	+	9	1341	c.968A>G	c.(967-969)cAc>cGc	p.H323R	IKBKE_ENST00000537984.1_Missense_Mutation_p.H238R	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	323					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)					GTCCTGCACCACATCTATATC	0.572																																					p.H323R		Atlas-SNP	.											.	IKBKE	77	.	0			c.A968G						PASS	.						201	170	181					1																	206651658		2203	4300	6503	SO:0001583	missense	9641	exon9			TGCACCACATCTA	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.968A>G	chr1.hg19:g.206651658A>G	ENSP00000356087:p.His323Arg	247.0	0.0	.		241.0	66.0	.	NM_001193322	D3DT78|Q3B754|Q3KR43|Q5JTS6	Missense_Mutation	SNP	ENST00000367120.3	hg19	CCDS30996.1	.	.	.	.	.	.	.	.	.	.	a	6.092	0.385235	0.11524	.	.	ENSG00000143466	ENST00000367120;ENST00000537984	T;T	0.62105	0.05;0.2	5.31	2.99	0.34606	.	0.288882	0.40818	N	0.001016	T	0.39226	0.1070	N	0.17474	0.49	0.23351	N	0.997852	B;B	0.06786	0.001;0.0	B;B	0.06405	0.001;0.002	T	0.18871	-1.0323	10	0.11182	T	0.66	-5.285	8.6511	0.34035	0.7589:0.0:0.2411:0.0	.	238;323	Q3B754;Q14164	.;IKKE_HUMAN	R	323;238	ENSP00000356087:H323R;ENSP00000444529:H238R	ENSP00000356087:H323R	H	+	2	0	IKBKE	204718281	0.715000	0.27946	0.538000	0.28064	0.720000	0.41350	1.322000	0.33689	0.345000	0.23873	0.454000	0.30748	CAC	.	.	.	none		0.572	IKBKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088484.1			G	206651658	A	G	206651658	3	3	152	1	0	0	0	0	1	0	0	0	7619	159	6	3	994	3	IKBKE	1	206651658	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08	38780702	206651658	42598963	9	9033											
SYT14	255928	hgsc.bcm.edu	37	chr1	210267875	210267875	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acaggtcatgaaatagaaagTtttcataataaaggatatga	19	11	8	3	0	2	3	2	2	0	1	2	4	2	4	0	2	0	1	0	2	7	6			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr1:210267875T>C	ENST00000472886.1	+	5	665	c.651T>C	c.(649-651)agT>agC	p.S217S	SYT14_ENST00000534859.1_Silent_p.S217S|SYT14_ENST00000271745.7_3'UTR|SYT14_ENST00000367019.1_Silent_p.S217S|SYT14_ENST00000367015.1_Silent_p.S179S|SYT14_ENST00000399639.2_Silent_p.S217S|SYT14_ENST00000537238.1_Silent_p.S179S|SYT14_ENST00000422431.1_Silent_p.S262S			Q8NB59	SYT14_HUMAN	synaptotagmin XIV	217					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)		AAATAGAAAGTTTTCATAATA	0.393																																					p.S262S		Atlas-SNP	.											.	SYT14	89	.	0			c.T786C						PASS	.						82	81	81					1																	210267875		2203	4300	6503	SO:0001819	synonymous_variant	255928	exon6			AGAAAGTTTTCAT	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.651T>C	chr1.hg19:g.210267875T>C		71.0	0.0	.		66.0	26.0	.	NM_001146264	B1AJU0|B1AJU1|F5H426|Q5THX7|Q707N3|Q707N4|Q707N5|Q707N6|Q707N7	Silent	SNP	ENST00000472886.1	hg19	CCDS31014.1																																																																																			.	.	.	none		0.393	SYT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089124.1	NM_153262		C	210267875	T	C	210267875	2	2	152	1	0	0	0	0	0	0	0	1	15482	1722	60	3		3	SYT14	1	210267875	Silent	SNP	T	TCGA-DW-7840-01A-11D-2136-08	3616217	210267875	38982746	10	9034											
SLC30A6	55676	hgsc.bcm.edu	37	chr2	32422810	32422810	+	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	ttccgggacttagcagtatcTtccttccccgaatgaatcca	9	12	7	13	2	1	1	0	1	1	0	5	3	5	2	5	1	1	2	5	1	4	5			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr2:32422810T>A	ENST00000282587.5	+	10	617	c.580T>A	c.(580-582)Ttc>Atc	p.F194I	SLC30A6_ENST00000406369.1_Missense_Mutation_p.F120I|SLC30A6_ENST00000538303.1_Missense_Mutation_p.F165I|SLC30A6_ENST00000357055.3_5'UTR|SLC30A6_ENST00000379343.2_Missense_Mutation_p.F234I|SLC30A6_ENST00000435660.1_Missense_Mutation_p.F194I	NM_017964.3	NP_060434.2	Q6NXT4	ZNT6_HUMAN	solute carrier family 30 (zinc transporter), member 6	194					cellular protein metabolic process (GO:0044267)|Golgi to endosome transport (GO:0006895)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(4)|lung(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					TAGCAGTATCTTCCTTCCCCG	0.348																																					p.F234I		Atlas-SNP	.											.	SLC30A6	37	.	0			c.T700A						PASS	.						195	185	188					2																	32422810		2203	4300	6503	SO:0001583	missense	55676	exon11			AGTATCTTCCTTC	AK055663	CCDS1780.1, CCDS54341.1, CCDS54342.1, CCDS54343.1	2p22.3	2013-05-22			ENSG00000152683	ENSG00000152683		"Solute carriers"	19305	protein-coding gene	gene with protein product		611148					Standard	NM_017964		Approved	FLJ31101, ZNT6	uc002rof.2	Q6NXT4	OTTHUMG00000128456	ENST00000282587.5:c.580T>A	chr2.hg19:g.32422810T>A	ENSP00000282587:p.Phe194Ile	144.0	0.0	.		151.0	58.0	.	NM_001193513	A5YM45|B7Z901|Q8N5C9|Q96NC3	Missense_Mutation	SNP	ENST00000282587.5	hg19	CCDS1780.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.093791	0.76870	.	.	ENSG00000152683	ENST00000379343;ENST00000440718;ENST00000282587;ENST00000435660;ENST00000538303;ENST00000406369	T;T;T;T;T;T	0.62105	0.07;0.05;0.07;0.07;0.07;0.07	6.07	6.07	0.98685	.	0.101567	0.64402	D	0.000002	T	0.57051	0.2027	L	0.34521	1.04	0.80722	D	1	B;B;B;B	0.34399	0.367;0.452;0.202;0.31	B;B;B;B	0.40702	0.338;0.164;0.205;0.113	T	0.53457	-0.8436	10	0.23302	T	0.38	-14.6144	15.6102	0.76710	0.0:0.0:0.0:1.0	.	165;194;234;194	B7Z901;Q6NXT4-3;Q6NXT4-2;Q6NXT4	.;.;.;ZNT6_HUMAN	I	234;165;194;194;165;120	ENSP00000368648:F234I;ENSP00000393946:F165I;ENSP00000282587:F194I;ENSP00000399005:F194I;ENSP00000440678:F165I;ENSP00000384041:F120I	ENSP00000282587:F194I	F	+	1	0	SLC30A6	32276314	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.462000	0.66707	2.330000	0.79161	0.528000	0.53228	TTC	.	.	.	none		0.348	SLC30A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250254.2			A	32422810	T	A	32422810	3	1	152	1	0	0	0	0	1	0	0	0	14572	1609	56	5	618	5	SLC30A6	2	32422810	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08		32422810	210776563	11	9035											
MTIF2	4528	hgsc.bcm.edu	37	chr2	55470636	55470636	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgttcttttctttctaaaaAccgtagaattgatctcttct	9	20	4	8	1	5	2	0	1	5	1	6	2	5	2	1	0	1	2	1	0	5	9			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr2:55470636A>G	ENST00000263629.4	-	12	1795	c.1480T>C	c.(1480-1482)Ttt>Ctt	p.F494L	MTIF2_ENST00000394600.3_Missense_Mutation_p.F494L|MTIF2_ENST00000403721.1_Missense_Mutation_p.F494L	NM_002453.2	NP_002444.2	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2	494					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						CTTTCTAAAAACCGTAGAATT	0.338																																					p.F494L		Atlas-SNP	.											.	MTIF2	64	.	0			c.T1480C						PASS	.						146	146	146					2																	55470636		2203	4300	6503	SO:0001583	missense	4528	exon12			CTAAAAACCGTAG	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.1480T>C	chr2.hg19:g.55470636A>G	ENSP00000263629:p.Phe494Leu	145.0	0.0	.		145.0	48.0	.	NM_002453	D6W5D0	Missense_Mutation	SNP	ENST00000263629.4	hg19	CCDS1853.1	.	.	.	.	.	.	.	.	.	.	A	11.25	1.584682	0.28268	.	.	ENSG00000085760	ENST00000403721;ENST00000263629;ENST00000394600;ENST00000418823	T;T;T;T	0.56275	0.47;0.47;0.47;1.05	5.6	5.6	0.85130	Translation initiation factor IF- 2, domain 3 (1);	0.270733	0.37577	N	0.002040	T	0.41766	0.1173	L	0.38175	1.15	0.42010	D	0.990935	B	0.02656	0.0	B	0.01281	0.0	T	0.33394	-0.9870	10	0.09084	T	0.74	-2.2567	15.7861	0.78304	1.0:0.0:0.0:0.0	.	494	P46199	IF2M_HUMAN	L	494;494;494;172	ENSP00000384481:F494L;ENSP00000263629:F494L;ENSP00000378099:F494L;ENSP00000403492:F172L	ENSP00000263629:F494L	F	-	1	0	MTIF2	55324140	1.000000	0.71417	0.207000	0.23584	0.007000	0.05969	6.152000	0.71812	2.136000	0.66102	0.533000	0.62120	TTT	.	.	.	none		0.338	MTIF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251486.4	NM_002453		G	55470636	A	G	55470636	3	3	152	1	0	0	0	0	1	0	0	0	9941	43	2	3	723	3	MTIF2	2	55470636	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08	23047826	55470636	187728737	12	9036											
USP34	9736	hgsc.bcm.edu	37	chr2	61493234	61493234	+	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	cttgaagaatgtgatttgcaCtttggctgttgtcggtcctt	6	17	11	7	1	0	3	0	2	0	1	2	3	1	3	1	2	1	3	1	2	2	5			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr2:61493234C>T	ENST00000398571.2	-	42	5578	c.5502G>A	c.(5500-5502)aaG>aaA	p.K1834K		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	1834					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)			GTGATTTGCACTTTGGCTGTT	0.408																																					p.K1834K		Atlas-SNP	.											.	USP34	334	.	0			c.G5502A						PASS	.						123	111	115					2																	61493234		1848	4096	5944	SO:0001819	synonymous_variant	9736	exon42			TTTGCACTTTGGC	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.5502G>A	chr2.hg19:g.61493234C>T		67.0	0.0	.		82.0	33.0	.	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Silent	SNP	ENST00000398571.2	hg19	CCDS42686.1																																																																																			.	.	.	none		0.408	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			T	61493234	C	T	61493234	2	4	152	1	0	0	0	0	0	0	0	1	17077	564	20	2		2	USP34	2	61493234	Silent	SNP	C	TCGA-DW-7840-01A-11D-2136-08	6022598	61493234	181706139	13	9037											
IL1F5	26525	hgsc.bcm.edu	37	chr2	113820191	113820191	+	Frame_Shift_Del	DEL	G	G	-																															cagcctgtcagactcacccaGcttcccgagaatggtggctg																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr2:113820191delG	ENST00000393200.2	+	5	566	c.405delG	c.(403-405)cagfs	p.Q135fs	IL36RN_ENST00000346807.3_Frame_Shift_Del_p.Q135fs	NM_012275.2	NP_036407.1	Q9UBH0	I36RA_HUMAN	interleukin 36 receptor antagonist	135					antifungal humoral response (GO:0019732)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of interferon-gamma secretion (GO:1902714)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-6 production (GO:0032715)	extracellular space (GO:0005615)	interleukin-1 receptor antagonist activity (GO:0005152)			large_intestine(3)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	11						GACTCACCCAGCTTCCCGAGA	0.632																																					p.Q135fs		Atlas-INDEL	.											.	IL36RN	15	.	0			c.404delA						PASS	.						50	48	49					2																	113820191		2203	4300	6503	SO:0001589	frameshift_variant	26525	exon5			.	AF201830	CCDS2111.1	2q14	2014-09-17	2011-06-06	2011-06-06	ENSG00000136695	ENSG00000136695		"Interleukins and interleukin receptors"	15561	protein-coding gene	gene with protein product	"family of interleukin 1-delta", "interleukin-1 receptor antagonist homolog 1", "interleukin-1 HY1", "IL-1 related protein 3"	605507	"interleukin 1 family, member 5 (delta)"	IL1F5		10625660, 10512743, 11574262	Standard	NM_012275		Approved	FIL1, FIL1(DELTA), FIL1D, IL1HY1, IL1RP3, IL1L1, IL-1F5, IL36RA, MGC29840	uc002tit.3	Q9UBH0	OTTHUMG00000131337	ENST00000393200.2:c.405delG	chr2.hg19:g.113820191delG	ENSP00000376896:p.Gln135fs	101.0	0.0	0		71.0	18.0	0.253521	NM_173170	A8K2I4|Q56AT9|Q7RTZ6	Frame_Shift_Del	DEL	ENST00000393200.2	hg19	CCDS2111.1																																																																																			.	.	.	none		0.632	IL36RN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330729.1	NM_173170		-	113820191	G	-	113820191	7	5	152	1	0	1	0	1	0	0	0	0	7660	962	34	0	419	0	IL1F5	2	113820191	Frame_Shift_Del	DEL	G	TCGA-DW-7840-01A-11D-2136-08	52326957	113820191	129379182	14	9038											
RAB3GAP1	22930	hgsc.bcm.edu	37	chr2	135891507	135891507	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttgtgtctctgtatgatcaAtttttaccatggagggttga	8	18	10	5	0	2	2	1	2	1	0	3	3	2	3	1	2	1	2	1	2	3	6	rs578182809		TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr2:135891507A>G	ENST00000264158.8	+	15	1446	c.1403A>G	c.(1402-1404)aAt>aGt	p.N468S	SNORA40_ENST00000385573.1_RNA|RAB3GAP1_ENST00000442034.1_Missense_Mutation_p.N468S|RAB3GAP1_ENST00000487003.1_3'UTR|ZRANB3_ENST00000412849.1_5'Flank|RAB3GAP1_ENST00000539493.1_Missense_Mutation_p.N424S	NM_012233.2	NP_036365.1	Q15042	RB3GP_HUMAN	RAB3 GTPase activating protein subunit 1 (catalytic)	468					brain development (GO:0007420)|camera-type eye development (GO:0043010)|establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|face morphogenesis (GO:0060325)|hypothalamus development (GO:0021854)|lipid particle organization (GO:0034389)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of calcium ion-dependent exocytosis of neurotransmitter (GO:1903233)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of GTPase activity (GO:0043087)|regulation of short-term neuronal synaptic plasticity (GO:0048172)	cytoplasm (GO:0005737)|endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(10)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32				BRCA - Breast invasive adenocarcinoma(221;0.117)		TGTATGATCAATTTTTACCAT	0.383													A|||	1	0.000199681	8e-04	0	5008	,	,		16221	0		0	False		,,,				2504	0				p.N468S		Atlas-SNP	.											RAB3GAP1,NS,carcinoma,0,1	RAB3GAP1	87	.	0			c.A1403G						PASS	.						134	133	133					2																	135891507		2203	4300	6503	SO:0001583	missense	22930	exon15			TGATCAATTTTTA	D31886	CCDS33294.1, CCDS54402.1	2q21.3	2013-07-09			ENSG00000115839	ENSG00000115839			17063	protein-coding gene	gene with protein product		602536				9030515, 15696165	Standard	NM_012233		Approved	RAB3GAP, KIAA0066, RAB3GAP130, WARBM1	uc010fnf.3	Q15042	OTTHUMG00000154889	ENST00000264158.8:c.1403A>G	chr2.hg19:g.135891507A>G	ENSP00000264158:p.Asn468Ser	157.0	0.0	.		128.0	46.0	.	NM_001172435	A6H8Z3|C9J837|Q659F5|Q8TBB4	Missense_Mutation	SNP	ENST00000264158.8	hg19	CCDS33294.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.421038	0.83559	.	.	ENSG00000115839	ENST00000264158;ENST00000539493;ENST00000442034	T;T;T	0.48522	0.81;0.81;0.81	4.95	4.95	0.65309	.	0.043485	0.85682	D	0.000000	T	0.58337	0.2115	L	0.50333	1.59	0.58432	D	0.999995	D;D	0.76494	0.999;0.999	D;P	0.63283	0.913;0.883	T	0.53570	-0.8420	10	0.22109	T	0.4	-20.1443	14.9142	0.70781	1.0:0.0:0.0:0.0	.	468;468	C9J837;Q15042	.;RB3GP_HUMAN	S	468;424;468	ENSP00000264158:N468S;ENSP00000444306:N424S;ENSP00000411418:N468S	ENSP00000264158:N468S	N	+	2	0	RAB3GAP1	135607977	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.127000	0.94417	1.992000	0.58205	0.482000	0.46254	AAT	.	.	.	none		0.383	RAB3GAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337514.2	NM_012233		G	135891507	A	G	135891507	3	3	152	1	0	0	0	0	1	0	0	0	12948	101	4	3	1461	3	RAB3GAP1	2	135891507	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08	22071316	135891507	107307866	15	9039											
ABTB1	80325	hgsc.bcm.edu	37	chr3	127396051	127396051	+	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	tgtgtgaaggtgctgaccatCgagcccccacctgcagaccc	8	7	11	15	1	0	3	0	2	0	1	1	4	0	3	5	1	3	2	5	1	1	0	rs368024563		TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr3:127396051C>A	ENST00000232744.8	+	8	770	c.684C>A	c.(682-684)atC>atA	p.I228I	ABTB1_ENST00000468137.1_Silent_p.I86I|ABTB1_ENST00000453791.2_Silent_p.I86I|ABTB1_ENST00000393363.3_Silent_p.I86I					ankyrin repeat and BTB (POZ) domain containing 1											central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	10						TGCTGACCATCGAGCCCCCAC	0.682																																					p.I228I		Atlas-SNP	.											.	ABTB1	36	.	0			c.C684A						PASS	.						36	32	33					3																	127396051		2201	4297	6498	SO:0001819	synonymous_variant	80325	exon8			GACCATCGAGCCC	AB053324	CCDS3045.1, CCDS46901.1	3q21	2013-01-10			ENSG00000114626	ENSG00000114626		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	18275	protein-coding gene	gene with protein product		608308				10891360, 11494141	Standard	NM_172027		Approved	BPOZ, EF1ABP, Btb3, BTBD21	uc003ejt.3	Q969K4	OTTHUMG00000159636	ENST00000232744.8:c.684C>A	chr3.hg19:g.127396051C>A		23.0	0.0	.		19.0	8.0	.	NM_172027		Silent	SNP	ENST00000232744.8	hg19	CCDS3045.1																																																																																			.	.	.	alt		0.682	ABTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356595.1	NM_172027		A	127396051	C	A	127396051	2	1	152	1	0	0	0	0	0	0	0	1	102	874	31	4		4	ABTB1	3	127396051	Silent	SNP	C	TCGA-DW-7840-01A-11D-2136-08		127396051	70626379	16	9040											
LSG1	55341	hgsc.bcm.edu	37	chr3	194379786	194379786	+	Missense_Mutation	SNP	T	T	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	tggcccaggcactccgctgcTcagcagtcagcaagtctgcc	7	7	11	16	1	3	0	2	0	1	0	4	0	4	0	3	2	4	5	3	2	1	0			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr3:194379786T>G	ENST00000265245.5	-	7	973	c.659A>C	c.(658-660)gAg>gCg	p.E220A		NM_018385.2	NP_060855.2	Q9H089	LSG1_HUMAN	large 60S subunit nuclear export GTPase 1	220	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)		ACTCCGCTGCTCAGCAGTCAG	0.458																																					p.E220A		Atlas-SNP	.											.	LSG1	38	.	0			c.A659C						PASS	.						160	168	165					3																	194379786		2203	4300	6503	SO:0001583	missense	55341	exon7			CGCTGCTCAGCAG		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.659A>C	chr3.hg19:g.194379786T>G	ENSP00000265245:p.Glu220Ala	263.0	0.0	.		265.0	96.0	.	NM_018385	A0JLT4|A0PJK3|A6NI18|Q7L9H8|Q9NUK8	Missense_Mutation	SNP	ENST00000265245.5	hg19	CCDS33922.1	.	.	.	.	.	.	.	.	.	.	T	18.27	3.586546	0.66105	.	.	ENSG00000041802	ENST00000265245	D	0.91631	-2.88	6.17	2.65	0.31530	.	0.224693	0.45867	D	0.000326	D	0.88028	0.6327	L	0.35288	1.05	0.58432	D	0.999998	P	0.41498	0.752	P	0.46208	0.507	D	0.83890	0.0284	10	0.26408	T	0.33	.	9.937	0.41556	0.0:0.1846:0.0:0.8154	.	220	Q9H089	LSG1_HUMAN	A	220	ENSP00000265245:E220A	ENSP00000265245:E220A	E	-	2	0	LSG1	195861075	1.000000	0.71417	0.999000	0.59377	0.913000	0.54294	3.985000	0.56930	1.160000	0.42584	0.533000	0.62120	GAG	.	.	.	none		0.458	LSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342740.1	NM_018385		G	194379786	T	G	194379786	3	3	152	1	0	0	0	0	1	0	0	0	9056	1551	54	5	1349	5	LSG1	3	194379786	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	66983735	194379786	3642644	17	9041											
TFRC	7037	hgsc.bcm.edu	37	chr3	195782165	195782166	+	Missense_Mutation	DNP	TC	TC	AG																															tggtacccaaataaggataaTctgtgtcctgcaagacaacg																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr3:195782165_195782166TC>AG	ENST00000360110.4	-	17	1853_1854	c.1684_1685GA>CT	c.(1684-1686)GAt>CTt	p.D562L	TFRC_ENST00000535031.1_Missense_Mutation_p.D280L|TFRC_ENST00000420415.1_Missense_Mutation_p.D481L|TFRC_ENST00000465288.1_5'Flank|TFRC_ENST00000540528.1_3'UTR|TFRC_ENST00000392396.3_Missense_Mutation_p.D562L	NM_001128148.1	NP_001121620.1	P02786	TFR1_HUMAN	transferrin receptor	562					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)	ATAAGGATAATCTGTGTCCTGC	0.5			T	BCL6	NHL																																p.D562V|p.D562H		Atlas-SNP	.		Dom	yes		3	3q29	7037	"transferrin receptor (p90, CD71)"		L	.	TFRC	54	.	0			c.A1685T|c.G1684C						PASS	.																																			SO:0001583	missense	7037	exon17			GGATAATCTGTGT|GATAATCTGTGTC	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.1684_1685delinsAG	chr3.hg19:g.195782165_195782166delinsAG	ENSP00000353224:p.Asp562Leu	77.0|76.0	0.0	.		68.0|67.0	26.0|25.0	.	NM_001128148	D3DXB0|Q1HE24|Q59G55|Q9UCN0|Q9UCU5|Q9UDF9|Q9UK21	Missense_Mutation	SNP	ENST00000360110.4	hg19	CCDS3312.1																																																																																			.	.	.	none		0.5	TFRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341346.1			AG	195782166	TC	AG	195782165	3	1	152	1	0	0	0	0	1	0	0	0	15824	1435	50	5	609	5	TFRC	3	195782165	Missense_Mutation	DNP	TC	TCGA-DW-7840-01A-11D-2136-08	1402379	195782165	2240265	18	9042											
CEP135	9662	hgsc.bcm.edu	37	chr4	56874494	56874494	+	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	atttttgtaatttctataggAaaaagctgttgctcaaatga	14	16	7	4	0	2	1	1	1	1	0	2	2	2	2	0	1	2	4	0	1	6	7			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr4:56874494A>G	ENST00000257287.4	+	18	2406	c.2282A>G	c.(2281-2283)gAa>gGa	p.E761G		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	761					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)					TTTCTATAGGAAAAAGCTGTT	0.289																																					p.E761G		Atlas-SNP	.											.	CEP135	115	.	0			c.A2282G						PASS	.						60	64	63					4																	56874494		2201	4299	6500	SO:0001630	splice_region_variant	9662	exon18			TATAGGAAAAAGC	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.2281-1A>G	chr4.hg19:g.56874494A>G		91.0	0.0	.		84.0	5.0	.	NM_025009	B2RMY0|O75130|Q58F25|Q9H8H7	Missense_Mutation	SNP	ENST00000257287.4	hg19	CCDS33986.1	.	.	.	.	.	.	.	.	.	.	A	14.20	2.463771	0.43736	.	.	ENSG00000174799	ENST00000257287	T	0.35048	1.33	5.48	5.48	0.80851	.	0.043970	0.85682	D	0.000000	T	0.50137	0.1598	M	0.78049	2.395	0.54753	D	0.999988	D	0.56287	0.975	P	0.51385	0.668	T	0.55341	-0.8156	10	0.54805	T	0.06	.	12.2418	0.54546	1.0:0.0:0.0:0.0	.	761	Q66GS9	CP135_HUMAN	G	761	ENSP00000257287:E761G	ENSP00000257287:E761G	E	+	2	0	CEP135	56569251	1.000000	0.71417	1.000000	0.80357	0.043000	0.13939	5.412000	0.66392	2.182000	0.69389	0.528000	0.53228	GAA	.	.	.	none		0.289	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009	Missense_Mutation	G	56874494	A	G	56874494	5	3	152	1	0	0	0	0	0	0	1	0	3249	260	9	3	2348	3	CEP135	4	56874494	Splice_Site	SNP	A	TCGA-DW-7840-01A-11D-2136-08		56874494	134279782	19	9043											
RCHY1	25898	hgsc.bcm.edu	37	chr4	76415883	76415883	+	Missense_Mutation	SNP	A	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	cctggtcatatctaaagcagAgtgcatacataatggacatc	14	10	8	9	0	2	1	1	0	1	1	3	2	2	2	1	2	3	2	1	2	5	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr4:76415883A>C	ENST00000324439.5	-	8	963	c.565T>G	c.(565-567)Tct>Gct	p.S189A	RCHY1_ENST00000380840.2_Missense_Mutation_p.S149A|RCHY1_ENST00000514021.1_5'Flank|RCHY1_ENST00000512706.1_Missense_Mutation_p.S167A|RCHY1_ENST00000513257.1_Missense_Mutation_p.S180A|RCHY1_ENST00000451788.1_Missense_Mutation_p.L188R	NM_001278536.1|NM_001278538.1|NM_001278539.1	NP_001265465.1|NP_001265467.1|NP_001265468.1	Q96PM5	ZN363_HUMAN	ring finger and CHY zinc finger domain containing 1, E3 ubiquitin protein ligase	189					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(2)|pancreas(1)	3			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			TCTAAAGCAGAGTGCATACAT	0.373																																					p.S189A		Atlas-SNP	.											.	RCHY1	17	.	0			c.T565G						PASS	.						133	113	120					4																	76415883		2203	4300	6503	SO:0001583	missense	25898	exon8			AAGCAGAGTGCAT	AF255666	CCDS3567.1, CCDS34012.1, CCDS63990.1, CCDS63991.1, CCDS63992.1	4q21.1-q21.3	2014-02-17	2012-02-23	2004-03-30	ENSG00000163743	ENSG00000163743		"RING-type (C3HC4) zinc fingers"	17479	protein-coding gene	gene with protein product	"androgen-receptor N-terminal-interacting protein", "p53-induced protein with a RING-H2 domain", "zinc finger, CHY-type"	607680	"zinc finger protein 363", "ring finger and CHY zinc finger domain containing 1"	ZNF363		12654245	Standard	NM_015436		Approved	CHIMP, DKFZp586C1620, PRO1996, RNF199, ARNIP, PIRH2, ZCHY	uc003hik.3	Q96PM5	OTTHUMG00000130105	ENST00000324439.5:c.565T>G	chr4.hg19:g.76415883A>C	ENSP00000321239:p.Ser189Ala	62.0	0.0	.		80.0	26.0	.	NM_015436	B3KRG3|C7E541|C7E542|C7E543|D3YRV2|E7EMC8|E7ETW5|J3KPI0|Q2KN33|Q59GN7|Q86X26|Q96PR5	Missense_Mutation	SNP	ENST00000324439.5	hg19	CCDS3567.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.67|14.67	2.604259|2.604259	0.46423|0.46423	.|.	.|.	ENSG00000163743|ENSG00000163743	ENST00000451788|ENST00000324439;ENST00000380840;ENST00000512706;ENST00000513257;ENST00000507014	.|T;T;T	.|0.35048	.|1.38;1.33;1.38	5.87|5.87	5.87|5.87	0.94306|0.94306	.|Zinc finger, RING/FYVE/PHD-type (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.60235|0.60235	0.2253|0.2253	.|.	.|.	.|.	0.32406|0.32406	N|N	0.551239|0.551239	.|D;D;D;D	.|0.89917	.|0.996;0.997;0.996;1.0	.|D;D;D;D	.|0.79108	.|0.987;0.992;0.987;0.987	T|T	0.71721|0.71721	-0.4507|-0.4507	5|9	0.22706|0.66056	T|D	0.39|0.02	-9.2258|-9.2258	14.2238|14.2238	0.65845|0.65845	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|140;167;180;189	.|E7EMC8;E7ETW5;Q96PM5-2;Q96PM5	.|.;.;.;ZN363_HUMAN	R|A	188|189;149;167;180;140	.|ENSP00000321239:S189A;ENSP00000370220:S149A;ENSP00000423976:S167A	ENSP00000401041:L188R|ENSP00000321239:S189A	L|S	-|-	2|1	0|0	RCHY1|RCHY1	76634907|76634907	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.962000|0.962000	0.63368|0.63368	7.352000|7.352000	0.79404|0.79404	2.239000|2.239000	0.73571|0.73571	0.528000|0.528000	0.53228|0.53228	CTC|TCT	.	.	.	none		0.373	RCHY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252411.2	NM_015436		C	76415883	A	C	76415883	3	2	152	1	0	0	0	0	1	0	0	0	13190	304	11	5	228	5	RCHY1	4	76415883	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08	19541389	76415883	114738393	20	9044											
BMP2K	55589	hgsc.bcm.edu	37	chr4	79786783	79786783	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccaaaggccaactctgctacTactgccactcccagtgtgct	9	9	7	16	0	1	0	0	0	1	0	2	0	2	0	4	1	6	2	4	1	4	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr4:79786783T>C	ENST00000335016.5	+	10	1306	c.1140T>C	c.(1138-1140)acT>acC	p.T380T	BMP2K_ENST00000502871.1_Silent_p.T380T	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	380					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						ACTCTGCTACTACTGCCACTC	0.418																																					p.T380T		Atlas-SNP	.											.	BMP2K	169	.	0			c.T1140C						PASS	.						122	110	114					4																	79786783		2203	4300	6503	SO:0001819	synonymous_variant	55589	exon10			TGCTACTACTGCC	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.1140T>C	chr4.hg19:g.79786783T>C		104.0	0.0	.		104.0	44.0	.	NM_017593	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Silent	SNP	ENST00000335016.5	hg19	CCDS47083.1	.	.	.	.	.	.	.	.	.	.	T	7.526	0.657778	0.14645	.	.	ENSG00000138756	ENST00000502613	.	.	.	5.26	-0.259	0.12971	.	.	.	.	.	T	0.56156	0.1966	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50800	-0.8785	4	.	.	.	-3.7779	9.9454	0.41604	0.0:0.4316:0.0:0.5684	.	.	.	.	H	73	.	.	Y	+	1	0	BMP2K	80005807	0.986000	0.35501	0.891000	0.34965	0.665000	0.39181	0.684000	0.25364	0.047000	0.15862	-0.290000	0.09829	TAC	.	.	.	none		0.418	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593		C	79786783	T	C	79786783	2	2	152	1	0	0	0	0	0	0	0	1	1460	1509	53	3		3	BMP2K	4	79786783	Silent	SNP	T	TCGA-DW-7840-01A-11D-2136-08	3370900	79786783	111367493	21	9045											
CENPE	1062	hgsc.bcm.edu	37	chr4	104081805	104081805	+	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	tttcctcagcctttctacttCagaaggtaaagatttcaatt	11	16	5	9	0	4	2	3	0	1	2	5	2	5	2	2	1	2	1	2	1	5	7			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr4:104081805C>T	ENST00000265148.3	-	21	2352	c.2263G>A	c.(2263-2265)Gaa>Aaa	p.E755K	CENPE_ENST00000380026.3_Missense_Mutation_p.E730K	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	755					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)		CTTTCTACTTCAGAAGGTAAA	0.318																																					p.E755K		Atlas-SNP	.											.	CENPE	253	.	0			c.G2263A						PASS	.						65	69	67					4																	104081805		2201	4291	6492	SO:0001583	missense	1062	exon21			CTACTTCAGAAGG	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.2263G>A	chr4.hg19:g.104081805C>T	ENSP00000265148:p.Glu755Lys	90.0	0.0	.		85.0	39.0	.	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	hg19	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	C	15.20	2.761920	0.49468	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026;ENST00000503705	T;T;T	0.71817	3.8;-0.6;3.8	4.58	4.58	0.56647	.	.	.	.	.	T	0.77631	0.4159	L	0.54323	1.7	0.51767	D	0.999931	D;D	0.76494	0.974;0.999	P;D	0.65987	0.726;0.94	T	0.78155	-0.2314	9	0.54805	T	0.06	.	10.406	0.44256	0.0:0.8981:0.0:0.1019	.	730;755	Q02224-3;Q02224	.;CENPE_HUMAN	K	755;755;730;755	ENSP00000265148:E755K;ENSP00000369365:E730K;ENSP00000423981:E755K	ENSP00000265148:E755K	E	-	1	0	CENPE	104301254	0.998000	0.40836	0.762000	0.31397	0.169000	0.22640	2.456000	0.44997	2.254000	0.74563	0.650000	0.86243	GAA	.	.	.	none		0.318	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	104081805	C	T	104081805	3	4	152	1	0	0	0	0	1	0	0	0	3232	835	29	2	5958	2	CENPE	4	104081805	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	24295022	104081805	87072471	22	9046											
LRBA	987	hgsc.bcm.edu	37	chr4	151821345	151821345	+	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	accaatgaattccgtggacaGataagtatagagcatcagtt	15	10	9	7	1	1	3	1	1	0	2	2	4	2	4	2	1	1	3	2	1	5	5			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr4:151821345G>T	ENST00000357115.3	-	14	2023	c.1780C>A	c.(1780-1782)Ctg>Atg	p.L594M	LRBA_ENST00000535741.1_Missense_Mutation_p.L594M|LRBA_ENST00000507224.1_Missense_Mutation_p.L594M|LRBA_ENST00000510413.1_Missense_Mutation_p.L594M	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	594						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)					TCCGTGGACAGATAAGTATAG	0.413																																					p.L594M		Atlas-SNP	.											.	LRBA	253	.	0			c.C1780A						PASS	.						108	100	103					4																	151821345		2203	4300	6503	SO:0001583	missense	987	exon14			TGGACAGATAAGT	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.1780C>A	chr4.hg19:g.151821345G>T	ENSP00000349629:p.Leu594Met	77.0	0.0	.		68.0	24.0	.	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Missense_Mutation	SNP	ENST00000357115.3	hg19	CCDS3773.1	.	.	.	.	.	.	.	.	.	.	G	16.92	3.255995	0.59321	.	.	ENSG00000198589	ENST00000535741;ENST00000510413;ENST00000357115;ENST00000507224	T;T;T;T	0.23754	1.89;1.89;1.89;1.89	5.59	2.91	0.33838	Armadillo-type fold (1);	0.000000	0.52532	D	0.000071	T	0.22589	0.0545	L	0.58669	1.825	0.44380	D	0.997282	P;P;P	0.46277	0.802;0.776;0.875	B;B;B	0.40825	0.122;0.282;0.341	T	0.02352	-1.1172	10	0.54805	T	0.06	.	5.799	0.18403	0.3233:0.0:0.5523:0.1244	.	594;594;594	E9PEM5;P50851;P50851-2	.;LRBA_HUMAN;.	M	594	ENSP00000446299:L594M;ENSP00000421552:L594M;ENSP00000349629:L594M;ENSP00000422180:L594M	ENSP00000349629:L594M	L	-	1	2	LRBA	152040795	1.000000	0.71417	0.984000	0.44739	0.998000	0.95712	1.337000	0.33862	0.714000	0.32081	0.655000	0.94253	CTG	.	.	.	none		0.413	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			T	151821345	G	T	151821345	3	4	152	1	0	0	0	0	1	0	0	0	8938	933	33	4	6991	4	LRBA	4	151821345	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	47739540	151821345	39332931	23	9047											
WWC2	80014	hgsc.bcm.edu	37	chr4	184182067	184182067	+	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	gctttttgtctttcagcctcTctgccagcaccctgtccatg	4	15	7	15	0	3	0	1	0	2	0	5	0	4	0	4	0	3	2	4	0	0	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr4:184182067T>A	ENST00000403733.3	+	11	1490	c.1291T>A	c.(1291-1293)Tct>Act	p.S431T	WWC2_ENST00000504005.1_Missense_Mutation_p.S113T|WWC2_ENST00000513834.1_Missense_Mutation_p.S431T|WWC2_ENST00000448232.2_Missense_Mutation_p.S431T|WWC2_ENST00000378925.3_Missense_Mutation_p.S333T	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	431	Ser-rich.				negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		TTTCAGCCTCTCTGCCAGCAC	0.507																																					p.S431T		Atlas-SNP	.											.	WWC2	78	.	0			c.T1291A						PASS	.						29	29	29					4																	184182067		2203	4300	6503	SO:0001583	missense	80014	exon11			AGCCTCTCTGCCA	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.1291T>A	chr4.hg19:g.184182067T>A	ENSP00000384222:p.Ser431Thr	27.0	0.0	.		36.0	18.0	.	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Missense_Mutation	SNP	ENST00000403733.3	hg19	CCDS34109.2	.	.	.	.	.	.	.	.	.	.	T	24.6	4.551586	0.86127	.	.	ENSG00000151718	ENST00000403733;ENST00000378925;ENST00000513834;ENST00000448232;ENST00000504005	T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9	4.86	4.86	0.63082	.	0.000000	0.64402	D	0.000002	T	0.65207	0.2669	M	0.80183	2.485	0.58432	D	0.999996	D	0.69078	0.997	D	0.75020	0.985	T	0.68864	-0.5296	10	0.49607	T	0.09	-16.2476	14.628	0.68635	0.0:0.0:0.0:1.0	.	431	Q6AWC2	WWC2_HUMAN	T	431;333;431;431;113	ENSP00000384222:S431T;ENSP00000368205:S333T;ENSP00000425054:S431T;ENSP00000398577:S431T;ENSP00000427569:S113T	ENSP00000368205:S333T	S	+	1	0	WWC2	184419061	1.000000	0.71417	0.993000	0.49108	0.935000	0.57460	7.833000	0.86765	2.046000	0.60703	0.528000	0.53228	TCT	.	.	.	none		0.507	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949		A	184182067	T	A	184182067	3	1	152	1	0	0	0	0	1	0	0	0	17424	1551	54	5	1333	5	WWC2	4	184182067	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	32360722	184182067	6972209	24	9048											
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5461992	5461992	+	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	acaatcctgtagaattcaagAccactgcatcggtgttgcct	11	11	8	11	1	1	2	1	0	0	2	3	2	2	2	3	1	2	3	3	1	4	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr5:5461992A>T	ENST00000296564.7	+	13	2767	c.2545A>T	c.(2545-2547)Acc>Tcc	p.T849S		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		849					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						AGAATTCAAGACCACTGCATC	0.413																																					p.T849S		Atlas-SNP	.											.	KIAA0947	301	.	0			c.A2545T						PASS	.						92	87	89					5																	5461992		1888	4110	5998	SO:0001583	missense	23379	exon13			TTCAAGACCACTG																												ENST00000296564.7:c.2545A>T	chr5.hg19:g.5461992A>T	ENSP00000296564:p.Thr849Ser	109.0	0.0	.		96.0	41.0	.	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	hg19	CCDS47187.1	.	.	.	.	.	.	.	.	.	.	a	5.614	0.297970	0.10622	.	.	ENSG00000164151	ENST00000296564	T	0.09445	2.98	4.94	0.61	0.17580	.	0.400941	0.21055	N	0.080924	T	0.04407	0.0121	N	0.08118	0	0.09310	N	1	B	0.20780	0.048	B	0.14023	0.01	T	0.43750	-0.9372	10	0.20046	T	0.44	-7.0261	7.5819	0.27970	0.1086:0.5191:0.3723:0.0	.	849	Q9Y2F5	K0947_HUMAN	S	849	ENSP00000296564:T849S	ENSP00000296564:T849S	T	+	1	0	KIAA0947	5514992	0.000000	0.05858	0.000000	0.03702	0.233000	0.25261	0.042000	0.13949	-0.216000	0.10048	0.378000	0.23410	ACC	.	.	.	none		0.413	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			T	5461992	A	T	5461992	3	4	152	1	0	0	0	0	1	0	0	0	8209	275	10	5	2595	5	KIAA0947	5	5461992	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08		5461992	175453268	25	9049											
ITGA1	3672	hgsc.bcm.edu	37	chr5	52211309	52211309	+	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	cacagcgtattccatcaggtGgggatggtaagacactgaaa	13	8	12	8	1	1	2	1	1	0	1	2	3	2	3	1	4	1	2	1	4	3	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr5:52211309G>T	ENST00000282588.6	+	15	2331	c.1873G>T	c.(1873-1875)Ggg>Tgg	p.G625W		NM_181501.1	NP_852478.1	P56199	ITA1_HUMAN	integrin, alpha 1	625					activation of MAPK activity (GO:0000187)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular extravasation (GO:0045123)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neutrophil chemotaxis (GO:0030593)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|vasodilation (GO:0042311)	acrosomal vesicle (GO:0001669)|basal part of cell (GO:0045178)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha1-beta1 complex (GO:0034665)|integrin complex (GO:0008305)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|protein phosphatase binding (GO:0019903)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(19)|ovary(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				TCCATCAGGTGGGGATGGTAA	0.388																																					p.G625W		Atlas-SNP	.											.	ITGA1	112	.	0			c.G1873T						PASS	.						146	147	147					5																	52211309		2203	4300	6503	SO:0001583	missense	3672	exon15			TCAGGTGGGGATG	X68742	CCDS3955.1	5q11.1	2010-03-23			ENSG00000213949	ENSG00000213949		"CD molecules", "Integrins"	6134	protein-coding gene	gene with protein product		192968				8428973, 11937138	Standard	NM_181501		Approved	VLA1, CD49a	uc003jou.3	P56199	OTTHUMG00000131163	ENST00000282588.6:c.1873G>T	chr5.hg19:g.52211309G>T	ENSP00000282588:p.Gly625Trp	171.0	0.0	.		157.0	62.0	.	NM_181501	B2RNU0	Missense_Mutation	SNP	ENST00000282588.6	hg19	CCDS3955.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.672050	0.88348	.	.	ENSG00000213949	ENST00000282588	T	0.56103	0.48	5.53	5.53	0.82687	.	0.053424	0.85682	D	0.000000	T	0.69557	0.3124	L	0.56769	1.78	0.80722	D	1	D	0.71674	0.998	D	0.68192	0.956	T	0.65693	-0.6106	10	0.38643	T	0.18	.	19.8228	0.96604	0.0:0.0:1.0:0.0	.	625	P56199	ITA1_HUMAN	W	625	ENSP00000282588:G625W	ENSP00000282588:G625W	G	+	1	0	ITGA1	52247066	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.066000	0.93949	2.759000	0.94783	0.650000	0.86243	GGG	.	.	.	none		0.388	ITGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253855.3	NM_181501		T	52211309	G	T	52211309	3	4	152	1	0	0	0	0	1	0	0	0	7879	1348	47	4	1931	4	ITGA1	5	52211309	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	46749317	52211309	128703951	26	9050											
LHFPL2	10184	hgsc.bcm.edu	37	chr5	77784725	77784725	+	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	attgtctcttccaaactaaaGgaggcagatcagatttttcc	12	13	7	9	0	2	2	1	0	1	2	5	3	4	3	2	2	1	1	2	2	3	5			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr5:77784725G>A	ENST00000515007.2	-	3	992	c.682C>T	c.(682-684)Ctt>Ttt	p.L228F	LHFPL2_ENST00000380345.2_Missense_Mutation_p.L228F			Q6ZUX7	LHPL2_HUMAN	lipoma HMGIC fusion partner-like 2	228						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)		CCAAACTAAAGGAGGCAGATC	0.408																																					p.L228F		Atlas-SNP	.											.	LHFPL2	9	.	0			c.C682T						PASS	.						128	127	127					5																	77784725		2203	4300	6503	SO:0001583	missense	10184	exon5			ACTAAAGGAGGCA	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.682C>T	chr5.hg19:g.77784725G>A	ENSP00000425906:p.Leu228Phe	135.0	0.0	.		124.0	52.0	.	NM_005779	B2RMQ6|Q7Z5P0|Q92605	Missense_Mutation	SNP	ENST00000515007.2	hg19	CCDS4042.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.026712	0.93518	.	.	ENSG00000145685	ENST00000380345;ENST00000515007	T;T	0.78924	-1.22;-1.22	5.94	5.94	0.96194	.	0.055945	0.64402	D	0.000001	D	0.84115	0.5401	M	0.72118	2.19	0.80722	D	1	P	0.50272	0.933	P	0.51193	0.662	D	0.85187	0.1007	10	0.72032	D	0.01	.	19.3618	0.94442	0.0:0.0:1.0:0.0	.	228	Q6ZUX7	LHPL2_HUMAN	F	228	ENSP00000369702:L228F;ENSP00000425906:L228F	ENSP00000369702:L228F	L	-	1	0	LHFPL2	77820481	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	9.476000	0.97823	2.820000	0.97059	0.650000	0.86243	CTT	.	.	.	none		0.408	LHFPL2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369098.2	NM_005779		A	77784725	G	A	77784725	3	1	152	1	0	0	0	0	1	0	0	0	8772	1000	35	2	8	2	LHFPL2	5	77784725	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	25573416	77784725	103130535	27	9051											
PCDHB14	56122	hgsc.bcm.edu	37	chr5	140605207	140605207	+	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	tcggtgctcctgttcgtggcGgtgcggctgtgcaggaggag	3	10	19	9	4	0	0	0	0	0	0	3	2	1	2	1	6	3	4	1	6	0	1			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr5:140605207G>C	ENST00000239449.4	+	1	2130	c.2130G>C	c.(2128-2130)gcG>gcC	p.A710A	PCDHB14_ENST00000515856.2_Silent_p.A557A	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	710					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			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)			TGTTCGTGGCGGTGCGGCTGT	0.701																																					p.A710A	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.G2130C						PASS	.						68	84	79					5																	140605207		2184	4245	6429	SO:0001819	synonymous_variant	56122	exon1			CGTGGCGGTGCGG	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.2130G>C	chr5.hg19:g.140605207G>C		391.0	0.0	.		333.0	109.0	.	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Silent	SNP	ENST00000239449.4	hg19	CCDS4256.1																																																																																			.	.	.	none		0.701	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934		C	140605207	G	C	140605207	2	2	152	1	0	0	0	0	0	0	0	1	11546	1103	39	4		4	PCDHB14	5	140605207	Silent	SNP	G	TCGA-DW-7840-01A-11D-2136-08	62820482	140605207	40310053	28	9052											
C6orf105	84830	hgsc.bcm.edu	37	chr6	11723657	11723657	+	Frame_Shift_Del	DEL	C	C	-																															gtagctgagagagaagaaagCtgctagacccaagaggctga																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr6:11723657delC	ENST00000414691.3	-	5	993	c.583delG	c.(583-585)gctfs	p.A195fs	ADTRP_ENST00000514824.1_5'UTR|ADTRP_ENST00000379413.2_Frame_Shift_Del_p.A195fs|ADTRP_ENST00000229583.5_Frame_Shift_Del_p.A213fs	NM_032744.3	NP_116133.1	Q96IZ2	ADTRP_HUMAN	androgen-dependent TFPI-regulating protein	195						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											GAGAAGAAAGCTGCTAGACCC	0.483																																					p.A213fs		Atlas-INDEL	.											.,1	ADTRP	3	.	0			c.638delC						PASS	.						209	208	209					6																	11723657		2203	4300	6503	SO:0001589	frameshift_variant	84830	exon6			.	AJ420520	CCDS4521.1, CCDS47374.1	6p24.1	2012-01-30	2012-01-27	2012-01-27	ENSG00000111863	ENSG00000111863			21214	protein-coding gene	gene with protein product	"androgen-induced 1-like"	614348	"chromosome 6 open reading frame 105"	C6orf105		21868574	Standard	NM_032744		Approved	dJ413H6.1, AIG1L	uc011dip.2	Q96IZ2	OTTHUMG00000014260	ENST00000414691.3:c.583delG	chr6.hg19:g.11723657delC	ENSP00000404416:p.Ala195fs	246.0	0.0	0		259.0	92.0	0.355212	NM_001143948	B2R7T9|B4DV39|Q5THW1	Frame_Shift_Del	DEL	ENST00000414691.3	hg19	CCDS4521.1																																																																																			.	.	.	none		0.483	ADTRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039864.3	NM_032744		-	11723657	C	-	11723657	7	5	152	1	0	1	0	1	0	0	0	0	2320	797	28	0	117	0	C6orf105	6	11723657	Frame_Shift_Del	DEL	C	TCGA-DW-7840-01A-11D-2136-08		11723657	159391410	29	9053											
SLC22A7	10864	hgsc.bcm.edu	37	chr6	43267444	43267444	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catctgcagcctccgtcagcTatgtaatgtttgccatcacc	8	12	7	14	1	3	0	2	0	1	0	4	0	4	0	4	0	4	4	4	0	2	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr6:43267444T>C	ENST00000372585.5	+	4	678	c.583T>C	c.(583-585)Tat>Cat	p.Y195H	SLC22A7_ENST00000372589.3_Missense_Mutation_p.Y193H|SLC22A7_ENST00000372574.3_Missense_Mutation_p.Y193H|SLC22A7_ENST00000487175.1_3'UTR	NM_153320.2	NP_696961.2	Q9Y694	S22A7_HUMAN	solute carrier family 22 (organic anion transporter), member 7	195					organic anion transport (GO:0015711)|response to stilbenoid (GO:0035634)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			NS(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(3)	26			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)		Acetylsalicylic acid(DB00945)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Cimetidine(DB00501)|Clarithromycin(DB01211)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Docetaxel(DB01248)|Enalapril(DB00584)|Erythromycin(DB00199)|Fluorouracil(DB00544)|Ganciclovir(DB01004)|Glyburide(DB01016)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Oxtriphylline(DB01303)|Oxytetracycline(DB00595)|Pravastatin(DB00175)|Probenecid(DB01032)|Rifampicin(DB01045)|Salicylic acid(DB00936)|Testosterone(DB00624)|Tetracycline(DB00759)|Theophylline(DB00277)|Valproic Acid(DB00313)|Zalcitabine(DB00943)|Zidovudine(DB00495)	CTCCGTCAGCTATGTAATGTT	0.602																																					p.Y195H		Atlas-SNP	.											.	SLC22A7	69	.	0			c.T583C						PASS	.						91	89	89					6																	43267444		2203	4300	6503	SO:0001583	missense	10864	exon3			GTCAGCTATGTAA	AF097518	CCDS4892.1, CCDS4893.2	6p21.1	2013-05-22			ENSG00000137204	ENSG00000137204		"Solute carriers"	10971	protein-coding gene	gene with protein product		604995				9650585, 10773670	Standard	XM_006714970		Approved	NLT, OAT2	uc003out.3	Q9Y694	OTTHUMG00000014726	ENST00000372585.5:c.583T>C	chr6.hg19:g.43267444T>C	ENSP00000361666:p.Tyr195His	166.0	0.0	.		178.0	68.0	.	NM_153320	B2CZX6|Q5T046|Q5T048|Q5T050|Q9H2W5	Missense_Mutation	SNP	ENST00000372585.5	hg19	CCDS4893.2	.	.	.	.	.	.	.	.	.	.	T	26.8	4.776980	0.90195	.	.	ENSG00000137204	ENST00000451757;ENST00000449231;ENST00000372589;ENST00000372585;ENST00000372574	T;T;T;T;T	0.58210	0.35;0.35;0.35;0.35;0.35	5.56	5.56	0.83823	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.068530	0.64402	D	0.000011	T	0.73273	0.3566	M	0.92077	3.27	0.45295	D	0.998297	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.994;0.99;0.986	T	0.80795	-0.1223	10	0.72032	D	0.01	.	13.2267	0.59919	0.0:0.0:0.0:1.0	.	195;193;193	Q9Y694;Q9Y694-2;Q9Y694-3	S22A7_HUMAN;.;.	H	64;254;193;195;193	ENSP00000416052:Y64H;ENSP00000411818:Y254H;ENSP00000361670:Y193H;ENSP00000361666:Y195H;ENSP00000361655:Y193H	ENSP00000361655:Y193H	Y	+	1	0	SLC22A7	43375422	1.000000	0.71417	0.993000	0.49108	0.986000	0.74619	4.783000	0.62403	2.109000	0.64355	0.379000	0.24179	TAT	.	.	.	none		0.602	SLC22A7-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040588.1			C	43267444	T	C	43267444	3	2	152	1	0	0	0	0	1	0	0	0	14472	1522	53	3	593	3	SLC22A7	6	43267444	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	31543787	43267444	127847623	30	9054											
EPHA7	2045	hgsc.bcm.edu	37	chr6	93969151	93969151	+	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	tggacagctctatttgggtcCtcataggtttcagggtcaat	8	14	11	8	0	4	0	3	0	1	0	5	1	5	1	1	4	1	2	1	4	3	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr6:93969151C>A	ENST00000369303.4	-	10	2029	c.1845G>T	c.(1843-1845)gaG>gaT	p.E615D		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	615					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)		TATTTGGGTCCTCATAGGTTT	0.428																																					p.E615D		Atlas-SNP	.											.	EPHA7	251	.	0			c.G1845T						PASS	.						221	199	206					6																	93969151		2203	4300	6503	SO:0001583	missense	2045	exon10			TGGGTCCTCATAG	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.1845G>T	chr6.hg19:g.93969151C>A	ENSP00000358309:p.Glu615Asp	172.0	0.0	.		168.0	72.0	.	NM_004440	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Missense_Mutation	SNP	ENST00000369303.4	hg19	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	C	11.38	1.622257	0.28889	.	.	ENSG00000135333	ENST00000369303	T	0.22336	1.96	5.9	5.9	0.94986	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.37320	0.0999	M	0.91972	3.26	0.80722	D	1	B;B;B	0.33755	0.424;0.002;0.001	P;B;B	0.46419	0.516;0.002;0.001	T	0.26538	-1.0100	10	0.59425	D	0.04	.	14.4356	0.67279	0.0:0.93:0.0:0.07	.	611;610;615	Q15375-4;Q15375-2;Q15375	.;.;EPHA7_HUMAN	D	615	ENSP00000358309:E615D	ENSP00000358309:E615D	E	-	3	2	EPHA7	94025872	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.753000	0.38359	2.786000	0.95864	0.563000	0.77884	GAG	.	.	.	none		0.428	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1			A	93969151	C	A	93969151	3	1	152	1	0	0	0	0	1	0	0	0	5174	680	24	4	1183	4	EPHA7	6	93969151	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	50701707	93969151	77145916	31	9055											
AIM1	202	hgsc.bcm.edu	37	chr6	106967843	106967843	+	Frame_Shift_Del	DEL	T	T	-																															cctgtgtctcgtcagaacaaTgagaaaatgccacttttaga																								rs551716379		TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr6:106967843delT	ENST00000369066.3	+	2	2023	c.1536delT	c.(1534-1536)aatfs	p.N512fs		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)		GTCAGAACAATGAGAAAATGC	0.453																																					p.N512fs		Atlas-INDEL	.											.	AIM1	161	.	0			c.1535delA						PASS	.						82	90	87					6																	106967843		2203	4300	6503	SO:0001589	frameshift_variant	202	exon2			.	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.1536delT	chr6.hg19:g.106967843delT	ENSP00000358062:p.Asn512fs	120.0	0.0	0		150.0	60.0	0.4	NM_001624	Q6P2P0|Q9BTM3	Frame_Shift_Del	DEL	ENST00000369066.3	hg19	CCDS34506.1																																																																																			.	.	.	none		0.453	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			-	106967843	T	-	106967843	7	5	152	1	0	1	0	1	0	0	0	0	430	1461	51	0	1542	0	AIM1	6	106967843	Frame_Shift_Del	DEL	T	TCGA-DW-7840-01A-11D-2136-08	12998692	106967843	64147224	32	9056											
SOBP	55084	hgsc.bcm.edu	37	chr6	107827597	107827597	+	Frame_Shift_Del	DEL	T	T	-																															agtgtgcccattattgtaccTttaattccaccacctttcat																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr6:107827597delT	ENST00000317357.5	+	3	1046	c.387delT	c.(385-387)cctfs	p.P129fs		NM_018013.3	NP_060483.3			sine oculis binding protein homolog (Drosophila)											endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	26		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)		TTATTGTACCTTTAATTCCAC	0.423																																					p.P129fs		Atlas-INDEL	.											.	SOBP	53	.	0			c.386delC						PASS	.						204	194	197					6																	107827597		1912	4142	6054	SO:0001589	frameshift_variant	55084	exon3			.	AK001021	CCDS43488.1	6q21	2007-03-15			ENSG00000112320	ENSG00000112320			29256	protein-coding gene	gene with protein product		613667					Standard	NM_018013		Approved	FLJ10159	uc003prx.3	A7XYQ1	OTTHUMG00000015312	ENST00000317357.5:c.387delT	chr6.hg19:g.107827597delT	ENSP00000318900:p.Pro129fs	256.0	0.0	0		300.0	100.0	0.333333	NM_018013		Frame_Shift_Del	DEL	ENST00000317357.5	hg19	CCDS43488.1																																																																																			.	.	.	none		0.423	SOBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041693.2	NM_018013		-	107827597	T	-	107827597	7	5	152	1	0	1	0	1	0	0	0	0	14925	1596	56	0	397	0	SOBP	6	107827597	Frame_Shift_Del	DEL	T	TCGA-DW-7840-01A-11D-2136-08	859754	107827597	63287470	33	9057											
OSTM1	28962	hgsc.bcm.edu	37	chr6	108395713	108395713	+	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	cctccagcaactgctgctccGacaggaggtcgtggaagacc	9	6	12	14	2	0	1	0	0	0	1	3	4	2	3	4	3	4	3	4	3	2	0	rs201176284	byFrequency	TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr6:108395713G>C	ENST00000193322.3	-	1	228	c.143C>G	c.(142-144)tCg>tGg	p.S48W		NM_014028.3	NP_054747.2	Q86WC4	OSTM1_HUMAN	osteopetrosis associated transmembrane protein 1	48					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)		CTGCTGCTCCGACAGGAGGTC	0.711													G|||	5	0.000998403	0.0038	0	5008	,	,		12709	0		0	False		,,,				2504	0				p.S48W	Melanoma(162;1427 1909 3096 17430 21396)	Atlas-SNP	.											.	OSTM1	22	.	0			c.C143G						PASS	.	G	TRP/SER	12,4304		0,12,2146	7	7	7		143	4.1	1	6		7	0,8426		0,0,4213	yes	missense	OSTM1	NM_014028.3	177	0,12,6359	CC,CG,GG		0.0,0.278,0.0942	probably-damaging	48/335	108395713	12,12730	2158	4213	6371	SO:0001583	missense	28962	exon1			TGCTCCGACAGGA	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.143C>G	chr6.hg19:g.108395713G>C	ENSP00000193322:p.Ser48Trp	3.0	0.0	.		12.0	4.0	.	NM_014028	E1P5E3|Q5R391|Q6PCA7|Q7RTW6|Q8NC29|Q8TC82|Q9Y2S9	Missense_Mutation	SNP	ENST00000193322.3	hg19	CCDS5062.1	.	.	.	.	.	.	.	.	.	.	G	19.44	3.828523	0.71258	0.00278	0.0	ENSG00000081087	ENST00000193322	T	0.55234	0.53	4.96	4.08	0.47627	.	0.095194	0.43110	D	0.000605	T	0.37865	0.1019	M	0.70595	2.14	0.44627	D	0.9976	B	0.16166	0.016	B	0.14023	0.01	T	0.48281	-0.9049	10	0.87932	D	0	-17.7201	12.5335	0.56128	0.0:0.1806:0.8194:0.0	.	48	Q86WC4	OSTM1_HUMAN	W	48	ENSP00000193322:S48W	ENSP00000193322:S48W	S	-	2	0	OSTM1	108502406	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	5.376000	0.66178	1.199000	0.43173	0.655000	0.94253	TCG	.	.	.	weak		0.711	OSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041709.3	NM_014028		C	108395713	G	C	108395713	3	2	152	1	0	0	0	0	1	0	0	0	11305	1059	37	4	885	4	OSTM1	6	108395713	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	568116	108395713	62719354	34	9058											
MAP3K4	4216	hgsc.bcm.edu	37	chr6	161470014	161470014	+	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	acttttgctaaagcttacctCagtctcaaagaaaaaagaca	17	10	5	9	0	2	2	2	0	1	2	3	2	2	2	1	0	3	2	1	0	7	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr6:161470014C>A	ENST00000392142.4	+	3	858	c.710C>A	c.(709-711)tCa>tAa	p.S237*	MAP3K4_ENST00000366920.2_Nonsense_Mutation_p.S237*|MAP3K4_ENST00000348824.7_Nonsense_Mutation_p.S237*|MAP3K4_ENST00000366919.2_Nonsense_Mutation_p.S237*	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	237					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)	p.S237L(2)		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)		AAGCTTACCTCAGTCTCAAAG	0.433																																					p.S237X		Atlas-SNP	.											MAP3K4_ENST00000392142,NS,carcinoma,0,2	MAP3K4	364	.	2	Substitution - Missense(2)	cervix(2)	c.C710A						PASS	.						41	41	41					6																	161470014		2203	4300	6503	SO:0001587	stop_gained	4216	exon3			TTACCTCAGTCTC	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.710C>A	chr6.hg19:g.161470014C>A	ENSP00000375986:p.Ser237*	49.0	0.0	.		54.0	23.0	.	NM_006724	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Nonsense_Mutation	SNP	ENST00000392142.4	hg19	CCDS34565.1	.	.	.	.	.	.	.	.	.	.	C	38	6.894608	0.97916	.	.	ENSG00000085511	ENST00000366919;ENST00000392142;ENST00000540111;ENST00000366920;ENST00000348824	.	.	.	6.14	6.14	0.99180	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-19.6238	20.819	0.99723	0.0:1.0:0.0:0.0	.	.	.	.	X	237	.	ENSP00000297332:S237X	S	+	2	0	MAP3K4	161390004	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.454000	0.80714	2.927000	0.99377	0.637000	0.83480	TCA	.	.	.	none		0.433	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			A	161470014	C	A	161470014	4	1	152	1	0	0	0	0	0	1	0	0	9259	838	29	4	720	4	MAP3K4	6	161470014	Nonsense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	53074301	161470014	9645053	35	9059											
HEATR2	54919	hgsc.bcm.edu	37	chr7	803456	803456	+	Missense_Mutation	SNP	T	T	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	cctccaggcacaggagacgaTggactcactggccatggtgg	9	6	14	12	1	1	1	1	0	0	1	2	4	2	2	3	6	0	1	3	6	0	0			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr7:803456T>G	ENST00000297440.6	+	8	1648	c.1628T>G	c.(1627-1629)aTg>aGg	p.M543R	HEATR2_ENST00000313147.5_Missense_Mutation_p.M543R	NM_017802.3	NP_060272.3	Q86Y56	HEAT2_HUMAN	HEAT repeat containing 2	543						cytoplasm (GO:0005737)				breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|prostate(4)|skin(1)	22		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0182)|Epithelial(4;5.48e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.95e-16)|all cancers(6;2.98e-14)		CAGGAGACGATGGACTCACTG	0.607																																					p.M543R		Atlas-SNP	.											.	HEATR2	62	.	0			c.T1628G						PASS	.						132	110	117					7																	803456		2202	4300	6502	SO:0001583	missense	54919	exon8			AGACGATGGACTC	AL832914, AK000404, NM_017802, AK056233	CCDS34580.1	7p22.3	2014-05-06	2006-05-19		ENSG00000164818	ENSG00000164818			26013	protein-coding gene	gene with protein product		614864				23040496	Standard	NM_017802		Approved	FLJ20397, FLJ31671, FLJ39381, FLJ25564, CILD18	uc010krz.1	Q86Y56	OTTHUMG00000151416	ENST00000297440.6:c.1628T>G	chr7.hg19:g.803456T>G	ENSP00000297440:p.Met543Arg	137.0	0.0	.		261.0	44.0	.	NM_017802	Q69YL1|Q96FI9|Q9NX75	Missense_Mutation	SNP	ENST00000297440.6	hg19	CCDS34580.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.28|14.28	2.488084|2.488084	0.44249|0.44249	.|.	.|.	ENSG00000164818|ENSG00000164818	ENST00000440747|ENST00000297440;ENST00000313147;ENST00000537862	.|T;T	.|0.67523	.|-0.27;-0.27	5.03|5.03	5.03|5.03	0.67393|0.67393	.|Armadillo-like helical (1);Armadillo-type fold (1);	.|0.303789	.|0.36893	.|N	.|0.002346	T|T	0.70055|0.70055	0.3180|0.3180	M|M	0.68317|0.68317	2.08|2.08	0.09310|0.09310	N|N	0.999993|0.999993	.|P;P	.|0.45715	.|0.788;0.865	.|B;P	.|0.45610	.|0.272;0.487	T|T	0.68070|0.68070	-0.5506|-0.5506	5|10	.|0.72032	.|D	.|0.01	-30.0578|-30.0578	15.0356|15.0356	0.71744|0.71744	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|543;289	.|Q86Y56;F5H8D4	.|HEAT2_HUMAN;.	E|R	344|543;543;289	.|ENSP00000297440:M543R;ENSP00000321451:M543R	.|ENSP00000297440:M543R	D|M	+|+	3|2	2|0	HEATR2|HEATR2	769982|769982	0.998000|0.998000	0.40836|0.40836	0.021000|0.021000	0.16686|0.16686	0.005000|0.005000	0.04900|0.04900	2.733000|2.733000	0.47360|0.47360	2.008000|2.008000	0.58898|0.58898	0.459000|0.459000	0.35465|0.35465	GAT|ATG	.	.	.	none		0.607	HEATR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322542.1	NM_017802		G	803456	T	G	803456	3	3	152	1	0	0	0	0	1	0	0	0	7035	1464	51	5	1658	5	HEATR2	7	803456	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08		803456	158335207	36	9060											
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47870900	47870900	+	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	tgcagagctccaccaaggctGaagggcccttgaccactggg	9	6	13	13	0	0	3	0	2	0	1	1	3	1	3	4	3	2	3	4	3	2	1			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr7:47870900G>C	ENST00000289672.2	-	42	6438	c.6388C>G	c.(6388-6390)Cag>Gag	p.Q2130E		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2130					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						CACCAAGGCTGAAGGGCCCTT	0.562																																					p.Q2130E		Atlas-SNP	.											.	PKD1L1	328	.	0			c.C6388G						PASS	.						93	83	86					7																	47870900		2203	4300	6503	SO:0001583	missense	168507	exon42			AAGGCTGAAGGGC	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.6388C>G	chr7.hg19:g.47870900G>C	ENSP00000289672:p.Gln2130Glu	105.0	0.0	.		211.0	48.0	.	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	hg19	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	G	8.099	0.776205	0.16051	.	.	ENSG00000158683	ENST00000289672	T	0.18960	2.18	5.1	2.25	0.28309	.	1.969070	0.02438	N	0.084314	T	0.13157	0.0319	N	0.22421	0.69	0.09310	N	1	B	0.13145	0.007	B	0.14578	0.011	T	0.23655	-1.0182	10	0.06625	T	0.88	1.9044	4.372	0.11253	0.1915:0.0:0.629:0.1795	.	2130	Q8TDX9	PK1L1_HUMAN	E	2130	ENSP00000289672:Q2130E	ENSP00000289672:Q2130E	Q	-	1	0	PKD1L1	47837425	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	0.141000	0.16076	0.166000	0.19597	0.563000	0.77884	CAG	.	.	.	none		0.562	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		C	47870900	G	C	47870900	3	2	152	1	0	0	0	0	1	0	0	0	11971	1299	45	4	2225	4	PKD1L1	7	47870900	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	47067444	47870900	111267763	37	9061											
COL1A2	1278	hgsc.bcm.edu	37	chr7	94057039	94057039	+	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	ctacagggctgaccagcctcGctcagcaccttctctcagac	8	8	8	17	1	3	2	2	1	1	1	5	2	3	2	3	1	3	3	3	1	1	2	rs145541630		TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr7:94057039G>T	ENST00000297268.6	+	49	3839	c.3368G>T	c.(3367-3369)cGc>cTc	p.R1123L		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	1123				Missing (in Ref. 17; CAA23761). {ECO:0000305}.	blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	GACCAGCCTCGCTCAGCACCT	0.547										HNSCC(75;0.22)																											p.R1123L		Atlas-SNP	.											.	COL1A2	240	.	0			c.G3368T						PASS	.						98	97	98					7																	94057039		2203	4300	6503	SO:0001583	missense	1278	exon49			AGCCTCGCTCAGC	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.3368G>T	chr7.hg19:g.94057039G>T	ENSP00000297268:p.Arg1123Leu	113.0	0.0	.		261.0	53.0	.	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	hg19	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	G	17.49	3.401592	0.62288	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.89552	-2.53	5.71	5.71	0.89125	.	0.000000	0.56097	D	0.000040	D	0.88757	0.6523	N	0.14661	0.345	0.34308	D	0.68511	D	0.60160	0.987	D	0.67725	0.953	D	0.90766	0.4668	10	0.41790	T	0.15	.	15.7376	0.77859	0.0:0.0:1.0:0.0	.	1123	P08123	CO1A2_HUMAN	L	1123;1124	ENSP00000297268:R1123L	ENSP00000297268:R1123L	R	+	2	0	COL1A2	93894975	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.489000	0.60309	2.873000	0.98535	0.561000	0.74099	CGC	.	G|1.000;A|0.000	.	alt		0.547	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		T	94057039	G	T	94057039	3	4	152	1	0	0	0	0	1	0	0	0	3680	1087	38	4	3562	4	COL1A2	7	94057039	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	46186139	94057039	65081624	38	9062											
SRRT	51593	hgsc.bcm.edu	37	chr7	100485469	100485473	+	Frame_Shift_Del	DEL	GCCCC	GCCCC	-																															caagccagcccagccacctgGccccgcccagagtaagatac																								rs568329863		TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	GCCCC	GCCCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr7:100485469_100485473delGCCCC	ENST00000347433.4	+	17	2473_2477	c.2315_2319delGCCCC	c.(2314-2319)ggccccfs	p.GP772fs	SRRT_ENST00000457580.2_Frame_Shift_Del_p.GP772fs|SRRT_ENST00000388793.4_Frame_Shift_Del_p.GP771fs|SRRT_ENST00000432932.1_Frame_Shift_Del_p.GP771fs			Q9BXP5	SRRT_HUMAN	serrate, RNA effector molecule	772	Pro-rich.				cell proliferation (GO:0008283)|neuronal stem cell maintenance (GO:0097150)|primary miRNA processing (GO:0031053)|regulation of transcription, DNA-templated (GO:0006355)|response to arsenic-containing substance (GO:0046685)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						CAGCCACCTGGCCCCGCCCAGAGTA	0.512																																					p.772_773del		Atlas-INDEL	.											.	SRRT	108	.	0			c.2314_2318del						PASS	.																																			SO:0001589	frameshift_variant	51593	exon17			.		CCDS34709.1, CCDS47665.1, CCDS47666.1, CCDS47667.1	7q21	2014-04-14	2014-04-14		ENSG00000087087	ENSG00000087087			24101	protein-coding gene	gene with protein product	"arsenite resistance protein"	614469	"serrate RNA effector molecule homolog (Arabidopsis)"			11239002, 11230166	Standard	NM_015908		Approved	Asr2, serrate, ARS2	uc003uwy.2	Q9BXP5	OTTHUMG00000157031	ENST00000347433.4:c.2315_2319delGCCCC	chr7.hg19:g.100485469_100485473delGCCCC	ENSP00000314491:p.Gly772fs	107.0	0.0	0		224.0	18.0	0.0803571	NM_001128853	A4D2E5|A4D2E6|A6NK22|B4DJL4|B4DZA6|O95808|Q32MI4|Q6NT74|Q8TDQ5|Q9BWP6|Q9BXP4|Q9Y4S4	Frame_Shift_Del	DEL	ENST00000347433.4	hg19	CCDS34709.1																																																																																			.	.	.	none		0.512	SRRT-004	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347168.1	NM_015908		-	100485473	GCCCC	-	100485469	7	5	152	1	0	1	0	1	0	0	0	0	15184	1203	42	0	2377	0	SRRT	7	100485469	Frame_Shift_Del	DEL	GCCCC	TCGA-DW-7840-01A-11D-2136-08	6428430	100485469	58653194	39	9063											
GPR37	2861	hgsc.bcm.edu	37	chr7	124404923	124404923	+	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	ctctcccccagacaagtttcGtttctggacgcaggggcgac	7	9	11	14	3	2	1	0	0	2	1	4	3	2	2	2	3	0	3	2	3	1	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr7:124404923G>C	ENST00000303921.2	-	1	758	c.108C>G	c.(106-108)aaC>aaG	p.N36K		NM_005302.3	NP_005293.1	O15354	GPR37_HUMAN	G protein-coupled receptor 37 (endothelin receptor type B-like)	36					dopamine biosynthetic process (GO:0042416)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotion involved in locomotory behavior (GO:0031987)|positive regulation of dopamine metabolic process (GO:0045964)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ubiquitin ligase complex (GO:0000151)	G-protein coupled receptor activity (GO:0004930)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						GACAAGTTTCGTTTCTGGACG	0.652																																					p.N36K		Atlas-SNP	.											.	GPR37	89	.	0			c.C108G						PASS	.						23	24	24					7																	124404923		2203	4300	6503	SO:0001583	missense	2861	exon1			AGTTTCGTTTCTG		CCDS5792.1	7q31	2012-08-21			ENSG00000170775	ENSG00000170775		"GPCR / Class A : Orphans"	4494	protein-coding gene	gene with protein product		602583				9339362	Standard	NM_005302		Approved	EDNRBL, hET(B)R-LP, PAELR	uc003vli.4	O15354	OTTHUMG00000157197	ENST00000303921.2:c.108C>G	chr7.hg19:g.124404923G>C	ENSP00000306449:p.Asn36Lys	46.0	0.0	.		86.0	61.0	.	NM_005302	A4D0Y6|O00348|O14768|Q8TD39	Missense_Mutation	SNP	ENST00000303921.2	hg19	CCDS5792.1	.	.	.	.	.	.	.	.	.	.	G	6.209	0.406650	0.11754	.	.	ENSG00000170775	ENST00000303921	T	0.08896	3.04	5.31	-0.565	0.11771	.	0.220305	0.48286	N	0.000186	T	0.04861	0.0131	L	0.27053	0.805	0.09310	N	0.999998	B	0.09022	0.002	B	0.06405	0.002	T	0.30001	-0.9993	10	0.49607	T	0.09	-16.1704	4.5608	0.12160	0.2984:0.3038:0.3978:0.0	.	36	O15354	GPR37_HUMAN	K	36	ENSP00000306449:N36K	ENSP00000306449:N36K	N	-	3	2	GPR37	124192159	0.000000	0.05858	0.005000	0.12908	0.024000	0.10985	0.501000	0.22578	-0.292000	0.08999	0.655000	0.94253	AAC	.	.	.	none		0.652	GPR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347873.1	NM_005302		C	124404923	G	C	124404923	3	2	152	1	0	0	0	0	1	0	0	0	6698	1136	40	4	1741	4	GPR37	7	124404923	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	23919454	124404923	34733740	40	9064											
MLL3	58508	hgsc.bcm.edu	37	chr7	151962168	151962168	+	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	caggacattgccaacctgcaCgttttaatggagtaaccgct	11	10	9	11	2	0	0	0	0	0	0	0	2	0	2	3	2	4	4	3	2	3	4	rs138908625	byFrequency	TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr7:151962168C>G	ENST00000262189.6	-	8	1357	c.1139G>C	c.(1138-1140)cGt>cCt	p.R380P	KMT2C_ENST00000355193.2_Missense_Mutation_p.R380P	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	380					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.R380L(4)									CCAACCTGCACGTTTTAATGG	0.443																																					p.R380P		Atlas-SNP	.											MLL3_ENST00000355193,extremity,malignant_melanoma,0,4	MLL3	1564	.	4	Substitution - Missense(4)	skin(4)	c.G1139C						PASS	.						410	369	383					7																	151962168		2203	4300	6503	SO:0001583	missense	58508	exon8			CCTGCACGTTTTA	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.1139G>C	chr7.hg19:g.151962168C>G	ENSP00000262189:p.Arg380Pro	771.0	0.0	.		901.0	146.0	.	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	13.77	2.337586	0.41398	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.98849	-5.18;-5.18	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);	0.000000	0.38548	U	0.001645	D	0.98701	0.9564	L	0.52759	1.655	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	D	0.99905	1.1175	10	0.66056	D	0.02	.	17.9157	0.88950	0.0:1.0:0.0:0.0	.	380	Q8NEZ4	MLL3_HUMAN	P	380	ENSP00000262189:R380P;ENSP00000347325:R380P	ENSP00000262189:R380P	R	-	2	0	MLL3	151593101	1.000000	0.71417	1.000000	0.80357	0.560000	0.35617	6.039000	0.70972	2.271000	0.75665	0.557000	0.71058	CGT	.	C|0.500;A|0.500	.	alt		0.443	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			G	151962168	C	G	151962168	3	3	152	1	0	0	0	0	1	0	0	0	9629	536	19	4	13804	4	MLL3	7	151962168	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	27557245	151962168	7176495	41	9065											
SETX	23064	hgsc.bcm.edu	37	chr9	135156906	135156906	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatctcctactaggatgagcTtattgcagcgatggatgagt	10	12	12	7	1	1	2	0	2	1	0	2	6	1	4	1	2	4	2	1	2	3	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr9:135156906T>C	ENST00000224140.5	-	20	6784	c.6602A>G	c.(6601-6603)aAg>aGg	p.K2201R	SETX_ENST00000393220.1_Missense_Mutation_p.K2201R|SETX_ENST00000372169.2_Missense_Mutation_p.K2201R	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	2201					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)		TAGGATGAGCTTATTGCAGCG	0.418																																					p.K2201R		Atlas-SNP	.											.	SETX	234	.	0			c.A6602G						PASS	.						127	117	121					9																	135156906		2203	4300	6503	SO:0001583	missense	23064	exon20			ATGAGCTTATTGC	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.6602A>G	chr9.hg19:g.135156906T>C	ENSP00000224140:p.Lys2201Arg	130.0	0.0	.		118.0	53.0	.	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	hg19	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	T	16.95	3.263460	0.59431	.	.	ENSG00000107290	ENST00000224140;ENST00000436441;ENST00000372169;ENST00000393220	D;D;D;D	0.82081	-1.57;-1.57;-1.57;-1.57	5.56	5.56	0.83823	.	0.148494	0.47455	D	0.000240	D	0.85141	0.5629	N	0.25825	0.765	0.37682	D	0.923524	B;D;D	0.69078	0.123;0.99;0.997	B;D;D	0.77557	0.42;0.956;0.99	D	0.86395	0.1738	10	0.36615	T	0.2	.	14.907	0.70727	0.0:0.0:0.0:1.0	.	2201;2201;2201	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	R	2201;443;2201;2201	ENSP00000224140:K2201R;ENSP00000409143:K443R;ENSP00000361242:K2201R;ENSP00000376913:K2201R	ENSP00000224140:K2201R	K	-	2	0	SETX	134146727	1.000000	0.71417	1.000000	0.80357	0.457000	0.32468	3.550000	0.53691	2.123000	0.65237	0.528000	0.53228	AAG	.	.	.	none		0.418	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		C	135156906	T	C	135156906	3	2	152	1	0	0	0	0	1	0	0	0	14154	1609	56	3	1459	3	SETX	9	135156906	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08		135156906	6056525	42	9066											
SUV39H2	79723	hgsc.bcm.edu	37	chr10	14939337	14939338	+	Missense_Mutation	DNP	AC	AC	TT																															aaattaaaatcccacctggtActcccatctatgaatgcaac																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr10:14939337_14939338AC>TT	ENST00000354919.6	+	3	670_671	c.670_671AC>TT	c.(670-672)ACt>TTt	p.T224F	SUV39H2_ENST00000313519.5_Missense_Mutation_p.T164F|SUV39H2_ENST00000378325.3_Intron	NM_001193424.1	NP_001180353.1	Q9H5I1	SUV92_HUMAN	suppressor of variegation 3-9 homolog 2 (Drosophila)	224	Pre-SET. {ECO:0000255|PROSITE- ProRule:PRU00157}.				cell differentiation (GO:0030154)|chromatin assembly or disassembly (GO:0006333)|chromatin remodeling (GO:0006338)|histone H3-K9 dimethylation (GO:0036123)|histone H3-K9 trimethylation (GO:0036124)|male meiosis (GO:0007140)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|chromosome, centromeric region (GO:0000775)|nuclear heterochromatin (GO:0005720)	chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)	19						CCCACCTGGTACTCCCATCTAT	0.396																																					p.T224S|p.T224I		Atlas-SNP	.											.	SUV39H2	72	.	0			c.A670T|c.C671T						PASS	.																																			SO:0001583	missense	79723	exon3			CCTGGTACTCCCA|CTGGTACTCCCAT	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	Exception_encountered	chr10.hg19:g.14939337_14939338delinsTT	ENSP00000346997:p.Thr224Phe	138.0	0.0	.		132.0|131.0	47.0|49.0	.	NM_001193424	D3DRT4|Q5JSS4|Q5JSS5|Q6I9Y3|Q8ND06	Missense_Mutation	SNP	ENST00000354919.6	hg19	CCDS53494.1																																																																																			.	.	.	none		0.396	SUV39H2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046947.2	NM_024670		TT	14939338	AC	TT	14939337	3	4	152	1	0	0	0	0	1	0	0	0	15425	391	14	5	492	5	SUV39H2	10	14939337	Missense_Mutation	DNP	AC	TCGA-DW-7840-01A-11D-2136-08		14939337	120595410	43	9067											
KIAA1217	56243	hgsc.bcm.edu	37	chr10	24835172	24835172	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagggcaccaggaccatccaTactcccagcctcaccagcta	12	5	7	17	0	1	0	1	0	0	0	3	1	3	1	6	2	3	2	6	2	3	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr10:24835172T>C	ENST00000376454.3	+	21	5781	c.5751T>C	c.(5749-5751)caT>caC	p.H1917H	KIAA1217_ENST00000376451.2_3'UTR|KIAA1217_ENST00000376452.3_Silent_p.H1348H|KIAA1217_ENST00000376462.1_Silent_p.H1238H|KIAA1217_ENST00000458595.1_Silent_p.H1323H|KIAA1217_ENST00000396445.1_3'UTR	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1917					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						GGACCATCCATACTCCCAGCC	0.532																																					p.H1917H		Atlas-SNP	.											.	KIAA1217	235	.	0			c.T5751C						PASS	.						76	70	72					10																	24835172		2203	4300	6503	SO:0001819	synonymous_variant	56243	exon21			CATCCATACTCCC	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.5751T>C	chr10.hg19:g.24835172T>C		111.0	0.0	.		99.0	51.0	.	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Silent	SNP	ENST00000376454.3	hg19	CCDS31165.1																																																																																			.	.	.	none		0.532	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		C	24835172	T	C	24835172	2	2	152	1	0	0	0	0	0	0	0	1	8223	1403	49	3		3	KIAA1217	10	24835172	Silent	SNP	T	TCGA-DW-7840-01A-11D-2136-08	9895835	24835172	110699575	44	9068											
ARMC4	55130	hgsc.bcm.edu	37	chr10	28270470	28270470	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggtttttataaattgaaccTtttctctcataattaacgtc	12	18	4	7	1	2	1	1	1	1	0	4	1	2	1	1	1	2	1	1	1	6	9			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr10:28270470T>C	ENST00000305242.5	-	7	953	c.861A>G	c.(859-861)aaA>aaG	p.K287K	ARMC4_ENST00000239715.3_Silent_p.K144K|ARMC4_ENST00000480504.1_5'UTR|ARMC4_ENST00000545014.1_5'UTR|ARMC4_ENST00000537576.1_5'UTR	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	287					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						AAATTGAACCTTTTCTCTCAT	0.294																																					p.K287K		Atlas-SNP	.											.	ARMC4	177	.	0			c.A861G						PASS	.						99	104	102					10																	28270470		2202	4296	6498	SO:0001819	synonymous_variant	55130	exon7			TGAACCTTTTCTC	AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"Armadillo repeat containing"	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.861A>G	chr10.hg19:g.28270470T>C		170.0	0.0	.		127.0	8.0	.	NM_018076	A8K906|B7Z7I1|Q9H0C0	Silent	SNP	ENST00000305242.5	hg19	CCDS7157.1																																																																																			.	.	.	none		0.294	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1	NM_018076		C	28270470	T	C	28270470	2	2	152	1	0	0	0	0	0	0	0	1	953	1606	56	3		3	ARMC4	10	28270470	Silent	SNP	T	TCGA-DW-7840-01A-11D-2136-08	3435298	28270470	107264277	45	9069											
CUL2	8453	hgsc.bcm.edu	37	chr10	35324145	35324145	+	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	gctcgaaggccctcatcatgGatgtggttttgcagctcctg	6	12	12	11	1	2	0	2	0	0	0	4	2	3	1	2	3	2	4	2	3	1	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr10:35324145G>T	ENST00000374748.1	-	11	1270	c.957C>A	c.(955-957)atC>atA	p.I319I	CUL2_ENST00000374751.3_Silent_p.I319I|CUL2_ENST00000602371.1_Silent_p.I262I|CUL2_ENST00000374749.3_Silent_p.I319I|CUL2_ENST00000537177.1_Silent_p.I338I|CUL2_ENST00000374746.1_Silent_p.I319I|CUL2_ENST00000374742.1_Silent_p.I319I			Q13617	CUL2_HUMAN	cullin 2	319					cell cycle arrest (GO:0007050)|cellular response to hypoxia (GO:0071456)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	Cul2-RING ubiquitin ligase complex (GO:0031462)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|VCB complex (GO:0030891)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|prostate(2)|skin(1)|urinary_tract(2)	31						CCTCATCATGGATGTGGTTTT	0.473																																					p.I338I		Atlas-SNP	.											.	CUL2	63	.	0			c.C1014A						PASS	.						155	126	136					10																	35324145		2203	4300	6503	SO:0001819	synonymous_variant	8453	exon10			ATCATGGATGTGG	U83410	CCDS7179.1, CCDS73086.1	10p11.2	2011-05-24			ENSG00000108094	ENSG00000108094			2552	protein-coding gene	gene with protein product		603135				8681378	Standard	NM_003591		Approved		uc021ppa.1	Q13617	OTTHUMG00000017950	ENST00000374748.1:c.957C>A	chr10.hg19:g.35324145G>T		59.0	0.0	.		63.0	21.0	.	NM_001198778	B3KT95|B7Z6K8|D3DRY6|G3V1S2|O00200|Q5T2B6|Q9UNF9	Silent	SNP	ENST00000374748.1	hg19	CCDS7179.1																																																																																			.	.	.	none		0.473	CUL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047538.1	NM_003591		T	35324145	G	T	35324145	2	4	152	1	0	0	0	0	0	0	0	1	4057	1164	41	4		4	CUL2	10	35324145	Silent	SNP	G	TCGA-DW-7840-01A-11D-2136-08	7053675	35324145	100210602	46	9070											
ALOX5	240	hgsc.bcm.edu	37	chr10	45869784	45869784	+	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	cagtggttcgccggcactgaCgactacatctacctcagcct	8	9	9	15	3	2	1	1	1	1	0	3	2	2	1	3	2	3	2	3	2	2	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr10:45869784C>A	ENST00000374391.2	+	1	110	c.57C>A	c.(55-57)gaC>gaA	p.D19E	ALOX5_ENST00000542434.1_Missense_Mutation_p.D19E	NM_000698.3|NM_001256153.1	NP_000689.1|NP_001243082.1	P09917	LOX5_HUMAN	arachidonate 5-lipoxygenase	19	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				arachidonic acid metabolic process (GO:0019369)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|leukotriene production involved in inflammatory response (GO:0002540)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular space (GO:0005615)|nuclear envelope (GO:0005635)|nuclear envelope lumen (GO:0005641)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)	arachidonate 5-lipoxygenase activity (GO:0004051)|iron ion binding (GO:0005506)			breast(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Lung SC(717;0.0257)			Aminosalicylic Acid(DB00233)|Balsalazide(DB01014)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Masoprocol(DB00179)|Meclofenamic acid(DB00939)|Mesalazine(DB00244)|Minocycline(DB01017)|Montelukast(DB00471)|Sulfasalazine(DB00795)|Vitamin E(DB00163)|Zileuton(DB00744)	CCGGCACTGACGACTACATCT	0.701																																					p.D19E		Atlas-SNP	.											.	ALOX5	88	.	0			c.C57A						PASS	.						28	19	22					10																	45869784		2161	4260	6421	SO:0001583	missense	240	exon1			CACTGACGACTAC	J03571	CCDS7212.1, CCDS58078.1	10q11.2	2008-03-18			ENSG00000012779	ENSG00000012779	1.13.11.34	"Arachidonate lipoxygenases"	435	protein-coding gene	gene with protein product		152390				2565035	Standard	NM_001256153		Approved	5-LOX	uc001jce.4	P09917	OTTHUMG00000018081	ENST00000374391.2:c.57C>A	chr10.hg19:g.45869784C>A	ENSP00000363512:p.Asp19Glu	10.0	0.0	.		12.0	6.0	.	NM_000698	B7ZLS0|E5FPY5|E5FPY7|E5FPY8|Q5JQ14	Missense_Mutation	SNP	ENST00000374391.2	hg19	CCDS7212.1	.	.	.	.	.	.	.	.	.	.	c	13.35	2.210677	0.39102	.	.	ENSG00000012779	ENST00000542434;ENST00000374391	T;T	0.66280	-0.2;-0.2	4.82	1.81	0.25067	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	0.051214	0.85682	D	0.000000	T	0.75042	0.3796	M	0.88310	2.945	0.49798	D	0.999823	D;D;D	0.76494	0.998;0.999;0.985	P;D;P	0.69142	0.757;0.962;0.554	T	0.70651	-0.4813	10	0.30854	T	0.27	-37.9305	4.7968	0.13276	0.0:0.5691:0.1591:0.2717	.	19;19;19	B7ZLS0;E5FPY8;P09917	.;.;LOX5_HUMAN	E	19	ENSP00000437634:D19E;ENSP00000363512:D19E	ENSP00000363512:D19E	D	+	3	2	ALOX5	45189790	1.000000	0.71417	1.000000	0.80357	0.016000	0.09150	1.011000	0.29911	0.420000	0.25954	-0.533000	0.04299	GAC	.	.	.	none		0.701	ALOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047780.1			A	45869784	C	A	45869784	3	1	152	1	0	0	0	0	1	0	0	0	540	535	19	4	59	4	ALOX5	10	45869784	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	10545639	45869784	89664963	47	9071											
GRID1	2894	hgsc.bcm.edu	37	chr10	87407050	87407050	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcagcaaacgtgctgtccTgctccagggggttggtgccc	5	10	14	12	1	1	0	1	0	0	0	3	0	3	0	3	3	5	5	3	3	1	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr10:87407050T>C	ENST00000327946.7	-	13	2187	c.2102A>G	c.(2101-2103)cAg>cGg	p.Q701R	RN7SKP238_ENST00000516483.1_RNA|RP11-93H12.4_ENST00000474115.2_RNA|GRID1_ENST00000536331.1_Missense_Mutation_p.Q272R	NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	701					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						CGTGCTGTCCTGCTCCAGGGG	0.552										Multiple Myeloma(13;0.14)																											p.Q701R		Atlas-SNP	.											.	GRID1	204	.	0			c.A2102G						PASS	.						271	252	259					10																	87407050		2203	4300	6503	SO:0001583	missense	2894	exon13			CTGTCCTGCTCCA	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.2102A>G	chr10.hg19:g.87407050T>C	ENSP00000330148:p.Gln701Arg	418.0	0.0	.		427.0	157.0	.	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Missense_Mutation	SNP	ENST00000327946.7	hg19	CCDS31236.1	.	.	.	.	.	.	.	.	.	.	T	13.52	2.261225	0.39995	.	.	ENSG00000182771	ENST00000327946;ENST00000536331	T;T	0.27402	1.67;1.67	5.7	5.7	0.88788	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.000000	0.85682	D	0.000000	T	0.35248	0.0925	N	0.11106	0.095	0.80722	D	1	D	0.59357	0.985	D	0.74023	0.982	T	0.28650	-1.0037	10	0.26408	T	0.33	.	15.1462	0.72653	0.0:0.0:0.0:1.0	.	701	Q9ULK0	GRID1_HUMAN	R	701;272	ENSP00000330148:Q701R;ENSP00000444455:Q272R	ENSP00000330148:Q701R	Q	-	2	0	GRID1	87397030	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.698000	0.84413	2.175000	0.68902	0.528000	0.53228	CAG	.	.	.	none		0.552	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613		C	87407050	T	C	87407050	3	2	152	1	0	0	0	0	1	0	0	0	6778	1580	55	3	943	3	GRID1	10	87407050	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	41537266	87407050	48127697	48	9072											
NRAP	4892	hgsc.bcm.edu	37	chr10	115411657	115411657	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcgttcatcatgccctctctTatactccacctgatgagaag	9	12	7	13	1	3	2	2	2	1	1	5	3	4	2	3	0	2	1	3	0	3	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr10:115411657T>C	ENST00000359988.3	-	7	824	c.580A>G	c.(580-582)Aag>Gag	p.K194E	NRAP_ENST00000360478.3_Missense_Mutation_p.K194E|NRAP_ENST00000369360.3_Missense_Mutation_p.K194E|NRAP_ENST00000369358.4_Missense_Mutation_p.K194E	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)		TGCCCTCTCTTATACTCCACC	0.547																																					p.K194E		Atlas-SNP	.											.	NRAP	208	.	0			c.A580G						PASS	.						108	88	94					10																	115411657		2203	4300	6503	SO:0001583	missense	4892	exon7			CTCTCTTATACTC		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.580A>G	chr10.hg19:g.115411657T>C	ENSP00000353078:p.Lys194Glu	66.0	0.0	.		71.0	21.0	.	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	hg19	CCDS7579.1	.	.	.	.	.	.	.	.	.	.	T	18.89	3.719870	0.68844	.	.	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	T;T;T;T	0.69040	-0.37;-0.37;-0.37;-0.37	6.03	6.03	0.97812	.	0.044427	0.85682	D	0.000000	D	0.82393	0.5027	M	0.87827	2.91	0.43988	D	0.996689	D;D;D	0.59357	0.985;0.982;0.985	P;P;D	0.64506	0.868;0.879;0.926	D	0.85146	0.0983	10	0.66056	D	0.02	.	12.952	0.58407	0.0:0.0:0.0:1.0	.	194;194;194	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	E	194	ENSP00000358365:K194E;ENSP00000358367:K194E;ENSP00000353078:K194E;ENSP00000353666:K194E	ENSP00000353078:K194E	K	-	1	0	NRAP	115401647	1.000000	0.71417	1.000000	0.80357	0.214000	0.24535	6.117000	0.71577	2.313000	0.78055	0.454000	0.30748	AAG	.	.	.	none		0.547	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175		C	115411657	T	C	115411657	3	2	152	1	0	0	0	0	1	0	0	0	10645	1763	61	3	4756	3	NRAP	10	115411657	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	28004607	115411657	20123090	49	9073											
IFITM1	8519	hgsc.bcm.edu	37	chr11	315058	315058	+	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	cctgttactggtattcggctCtgtgacagtctaccatatta	8	15	8	10	1	2	1	0	1	2	0	3	1	2	1	2	2	2	3	2	2	5	6			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr11:315058C>G	ENST00000408968.3	+	2	641	c.323C>G	c.(322-324)tCt>tGt	p.S108C	IFITM1_ENST00000528780.1_Missense_Mutation_p.S108C|IFITM1_ENST00000328221.5_Missense_Mutation_p.S108C	NM_003641.3	NP_003632	P13164	IFM1_HUMAN	interferon induced transmembrane protein 1	108	Interaction with CAV1.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|intracellular signal transduction (GO:0035556)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|ossification (GO:0001503)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of immune response (GO:0050776)|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)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor signaling protein activity (GO:0005057)			large_intestine(1)|lung(3)	4		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)		GTATTCGGCTCTGTGACAGTC	0.507																																					p.S108C		Atlas-SNP	.											IFITM1,NS,carcinoma,0,1	IFITM1	15	.	0			c.C323G						PASS	.						129	129	129					11																	315058		1942	4128	6070	SO:0001583	missense	8519	exon2			TCGGCTCTGTGAC	J04164	CCDS41584.1	11p15.5	2012-03-15	2012-03-13		ENSG00000185885	ENSG00000185885		"CD molecules"	5412	protein-coding gene	gene with protein product	"interferon-induced transmembrane protein 1"	604456	"interferon induced transmembrane protein 1 (9-27)"	IFI17		7559564	Standard	NM_003641		Approved	9-27, CD225	uc001loy.4	P13164		ENST00000408968.3:c.323C>G	chr11.hg19:g.315058C>G	ENSP00000386187:p.Ser108Cys	114.0	0.0	.		122.0	35.0	.	NM_003641	Q15322|Q53XZ0	Missense_Mutation	SNP	ENST00000408968.3	hg19	CCDS41584.1	.	.	.	.	.	.	.	.	.	.	C	13.15	2.150346	0.37923	.	.	ENSG00000185885	ENST00000528780;ENST00000328221;ENST00000408968	T;T;T	0.80304	-1.36;-1.36;-1.36	3.73	-0.746	0.11095	.	.	.	.	.	T	0.61578	0.2358	N	0.24115	0.695	0.09310	N	1	B	0.14012	0.009	B	0.15870	0.014	T	0.45571	-0.9252	9	0.38643	T	0.18	.	0.8934	0.01259	0.1942:0.4108:0.1719:0.2231	.	108	P13164	IFM1_HUMAN	C	108	ENSP00000437057:S108C;ENSP00000330825:S108C;ENSP00000386187:S108C	ENSP00000330825:S108C	S	+	2	0	IFITM1	305058	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-1.419000	0.02460	-0.422000	0.07405	0.313000	0.20887	TCT	.	.	.	none		0.507	IFITM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383595.1	NM_003641		G	315058	C	G	315058	3	3	152	1	0	0	0	0	1	0	0	0	7533	913	32	4	329	4	IFITM1	11	315058	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08		315058	134691458	50	9074											
SIGIRR	59307	hgsc.bcm.edu	37	chr11	407548	407548	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcagtcgctgtaggagacgtAggcgtcgtagagcttcccgt	7	9	15	10	5	0	2	0	0	0	2	3	3	1	2	1	2	1	6	1	2	3	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr11:407548A>G	ENST00000431843.2	-	6	808	c.502T>C	c.(502-504)Tac>Cac	p.Y168H	SIGIRR_ENST00000332725.3_Missense_Mutation_p.Y168H|SIGIRR_ENST00000529486.1_5'UTR|SIGIRR_ENST00000531205.1_Missense_Mutation_p.Y168H|SIGIRR_ENST00000397632.3_Missense_Mutation_p.Y168H|SIGIRR_ENST00000382520.2_Missense_Mutation_p.Y168H	NM_001135054.1	NP_001128526.1	Q6IA17	SIGIR_HUMAN	single immunoglobulin and toll-interleukin 1 receptor (TIR) domain	168	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				acute-phase response (GO:0006953)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				cervix(2)|endometrium(1)|liver(1)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	13		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)		TAGGAGACGTAGGCGTCGTAG	0.647																																					p.Y168H		Atlas-SNP	.											.	SIGIRR	22	.	0			c.T502C						PASS	.						26	27	27					11																	407548		2189	4291	6480	SO:0001583	missense	59307	exon6			AGACGTAGGCGTC		CCDS31325.1	11p15.5	2013-01-11	2005-10-10					"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	30575	protein-coding gene	gene with protein product	"single immunoglobulin domain IL1R1 related"	605478				10346978	Standard	NM_021805		Approved	TIR8	uc001lpe.1	Q6IA17		ENST00000431843.2:c.502T>C	chr11.hg19:g.407548A>G	ENSP00000403104:p.Tyr168His	21.0	0.0	.		40.0	10.0	.	NM_001135053	Q3KQY2|Q6UXI3|Q9H733	Missense_Mutation	SNP	ENST00000431843.2	hg19	CCDS31325.1	.	.	.	.	.	.	.	.	.	.	a	17.94	3.510696	0.64522	.	.	ENSG00000185187	ENST00000431843;ENST00000397632;ENST00000332725;ENST00000531205;ENST00000382520;ENST00000528209	T;T;T;T;T;T	0.12147	2.71;2.71;2.71;2.71;2.71;2.71	2.75	2.75	0.32379	Toll/interleukin-1 receptor homology (TIR) domain (3);	0.240626	0.36303	N	0.002663	T	0.36082	0.0954	M	0.83118	2.625	0.58432	D	0.999999	D;D	0.76494	0.999;0.987	D;D	0.72625	0.978;0.944	T	0.30001	-0.9993	10	0.87932	D	0	.	10.2759	0.43510	1.0:0.0:0.0:0.0	.	168;168	C9JFX4;Q6IA17	.;SIGIR_HUMAN	H	168;168;168;168;168;64	ENSP00000403104:Y168H;ENSP00000380756:Y168H;ENSP00000333656:Y168H;ENSP00000433022:Y168H;ENSP00000371960:Y168H;ENSP00000435135:Y64H	ENSP00000333656:Y168H	Y	-	1	0	SIGIRR	397548	1.000000	0.71417	1.000000	0.80357	0.238000	0.25445	4.453000	0.60061	1.525000	0.49052	0.240000	0.17902	TAC	.	.	.	none		0.647	SIGIRR-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383884.3	NM_021805		G	407548	A	G	407548	3	3	152	1	0	0	0	0	1	0	0	0	14317	420	15	3	750	3	SIGIRR	11	407548	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08	92490	407548	134598968	51	9075											
ALKBH3	221120	hgsc.bcm.edu	37	chr11	43905565	43905565	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcctgagccacgagtgatTgagtaagtaatttgctgtct	9	13	11	8	1	1	3	0	3	1	0	2	4	2	3	2	0	2	4	2	0	2	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr11:43905565T>C	ENST00000302708.4	+	4	627	c.216T>C	c.(214-216)atT>atC	p.I72I	ALKBH3_ENST00000532410.1_3'UTR|ALKBH3_ENST00000378840.4_Silent_p.I72I	NM_139178.3	NP_631917.1	Q96Q83	ALKB3_HUMAN	alkB, alkylation repair homolog 3 (E. coli)	72					cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA repair (GO:0006281)|oxidative single-stranded DNA demethylation (GO:0035552)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)|L-ascorbic acid binding (GO:0031418)			endometrium(2)|kidney(1)|lung(4)|prostate(1)	8					Vitamin C(DB00126)	CACGAGTGATTGAGTAAGTAA	0.433								Direct reversal of damage																													p.I72I		Atlas-SNP	.											.	ALKBH3	33	.	0			c.T216C						PASS	.						256	225	236					11																	43905565		2203	4300	6503	SO:0001819	synonymous_variant	221120	exon4			AGTGATTGAGTAA	AB042029	CCDS7906.1	11p11.2	2013-10-11			ENSG00000166199	ENSG00000166199		"Alkylation repair homologs"	30141	protein-coding gene	gene with protein product		610603				22055184	Standard	NM_139178		Approved	DEPC-1	uc001mxs.2	Q96Q83	OTTHUMG00000166417	ENST00000302708.4:c.216T>C	chr11.hg19:g.43905565T>C		233.0	0.0	.		214.0	83.0	.	NM_139178	A6NDJ1|Q3SYI0|Q6NX57|Q96BU8	Silent	SNP	ENST00000302708.4	hg19	CCDS7906.1																																																																																			.	.	.	none		0.433	ALKBH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389693.1	NM_139178		C	43905565	T	C	43905565	2	2	152	1	0	0	0	0	0	0	0	1	528	1800	63	3		3	ALKBH3	11	43905565	Silent	SNP	T	TCGA-DW-7840-01A-11D-2136-08	43498017	43905565	91100951	52	9076											
PC	5091	hgsc.bcm.edu	37	chr11	66617140	66617141	+	Frame_Shift_Ins	INS	-	-	G																															gcgagtattcaggctatccaINSgggggccaaaggtggcagtg																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr11:66617140_66617141insG	ENST00000393958.2	-	20	3181_3182	c.3088_3089insC	c.(3088-3090)ctgfs	p.L1030fs	PC_ENST00000528224.1_5'UTR|PC_ENST00000529047.1_Frame_Shift_Ins_p.L150fs|PC_ENST00000393960.1_Frame_Shift_Ins_p.L1030fs|PC_ENST00000393955.2_Frame_Shift_Ins_p.L1030fs	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	1030					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)	CAGGCTATCCAGGGGGCCAAAG	0.604																																					p.L1030fs		Atlas-INDEL	.											.	PC	116	.	0			c.3089_3090insC						PASS	.																																			SO:0001589	frameshift_variant	5091	exon20			.	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.3089dupC	chr11.hg19:g.66617145_66617145dupG	ENSP00000377530:p.Leu1030fs	77.0	0.0	0		77.0	18.0	0.233766	NM_000920	B4DN00|Q16705	Frame_Shift_Ins	INS	ENST00000393958.2	hg19	CCDS8152.1																																																																																			.	.	.	none		0.604	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716		G	66617141	-	G	66617140	7	5	152	1	0	1	1	0	0	0	0	0	11504	188	7	0	459	0	PC	11	66617140	Frame_Shift_Ins	INS	-	TCGA-DW-7840-01A-11D-2136-08	22711575	66617140	68389376	53	9077											
PC	5091	hgsc.bcm.edu	37	chr11	66620716	66620716	+	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	gtctcgggccagaccgaggtAgtgcaacagcttttgggccc	7	8	14	12	2	1	1	0	0	1	1	2	2	1	1	3	3	3	3	3	3	2	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr11:66620716A>T	ENST00000393958.2	-	12	1600	c.1507T>A	c.(1507-1509)Tac>Aac	p.Y503N	PC_ENST00000529047.1_5'Flank|PC_ENST00000393960.1_Missense_Mutation_p.Y503N|PC_ENST00000393955.2_Missense_Mutation_p.Y503N	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	503					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)	AGACCGAGGTAGTGCAACAGC	0.622																																					p.Y503N		Atlas-SNP	.											.	PC	116	.	0			c.T1507A						PASS	.						122	92	102					11																	66620716		2200	4295	6495	SO:0001583	missense	5091	exon12			CGAGGTAGTGCAA	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.1507T>A	chr11.hg19:g.66620716A>T	ENSP00000377530:p.Tyr503Asn	104.0	0.0	.		88.0	28.0	.	NM_000920	B4DN00|Q16705	Missense_Mutation	SNP	ENST00000393958.2	hg19	CCDS8152.1	.	.	.	.	.	.	.	.	.	.	A	17.36	3.370348	0.61624	.	.	ENSG00000173599	ENST00000393955;ENST00000393958;ENST00000393960	D;D;D	0.96745	-4.11;-4.11;-4.11	4.15	4.15	0.48705	.	0.000000	0.85682	D	0.000000	D	0.98435	0.9479	H	0.95780	3.72	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	D	0.98985	1.0806	10	0.87932	D	0	-24.4033	11.2003	0.48736	1.0:0.0:0.0:0.0	.	503	P11498	PYC_HUMAN	N	503	ENSP00000377527:Y503N;ENSP00000377530:Y503N;ENSP00000377532:Y503N	ENSP00000377527:Y503N	Y	-	1	0	PC	66377292	1.000000	0.71417	1.000000	0.80357	0.264000	0.26372	8.288000	0.89921	1.744000	0.51775	0.379000	0.24179	TAC	.	.	.	none		0.622	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716		T	66620716	A	T	66620716	3	4	152	1	0	0	0	0	1	0	0	0	11504	420	15	5	2073	5	PC	11	66620716	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08	3576	66620716	68385800	54	9078											
PHLDB1	23187	hgsc.bcm.edu	37	chr11	118513026	118513026	+	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	agcagtggtaccaggagctgAtggccgggctggggactggc	7	6	19	9	1	0	1	0	1	0	0	0	3	0	3	2	7	3	4	2	7	1	1			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr11:118513026A>T	ENST00000361417.2	+	14	3202	c.2791A>T	c.(2791-2793)Atg>Ttg	p.M931L	PHLDB1_ENST00000527898.1_Intron|PHLDB1_ENST00000534672.1_Intron|PHLDB1_ENST00000524713.1_Missense_Mutation_p.M74L|PHLDB1_ENST00000356063.5_Intron	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	931										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)		CCAGGAGCTGATGGCCGGGCT	0.642																																					p.M931L		Atlas-SNP	.											.	PHLDB1	103	.	0			c.A2791T						PASS	.						76	79	78					11																	118513026		2200	4295	6495	SO:0001583	missense	23187	exon13			GAGCTGATGGCCG		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.2791A>T	chr11.hg19:g.118513026A>T	ENSP00000354498:p.Met931Leu	151.0	0.0	.		155.0	53.0	.	NM_001144758	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Missense_Mutation	SNP	ENST00000361417.2	hg19	CCDS8401.1	.	.	.	.	.	.	.	.	.	.	A	15.56	2.870388	0.51588	.	.	ENSG00000019144	ENST00000361417;ENST00000361465;ENST00000358191;ENST00000524713	T;T	0.50813	1.52;0.73	5.14	5.14	0.70334	.	0.543120	0.21674	N	0.070828	T	0.34832	0.0911	L	0.40543	1.245	0.26911	N	0.966889	B;B;B	0.24576	0.106;0.039;0.01	B;B;B	0.25614	0.062;0.019;0.011	T	0.27706	-1.0066	10	0.02654	T	1	-9.3743	12.3456	0.55119	1.0:0.0:0.0:0.0	.	69;74;931	B7Z2B9;B4DK17;Q86UU1	.;.;PHLB1_HUMAN	L	931;690;295;74	ENSP00000354498:M931L;ENSP00000434905:M74L	ENSP00000350921:M295L	M	+	1	0	PHLDB1	118018236	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.723000	0.54955	1.925000	0.55765	0.379000	0.24179	ATG	.	.	.	none		0.642	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157		T	118513026	A	T	118513026	3	4	152	1	0	0	0	0	1	0	0	0	11858	333	12	5	2837	5	PHLDB1	11	118513026	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08	51892310	118513026	16493490	55	9079											
LRP6	4040	hgsc.bcm.edu	37	chr12	12334248	12334248	+	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	gatgtagccttccacaggatCgtaatctatggcaatggcat	11	11	10	9	1	1	0	0	0	1	0	3	2	2	1	2	3	1	4	2	3	4	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr12:12334248C>T	ENST00000261349.4	-	6	1178	c.1102G>A	c.(1102-1104)Gat>Aat	p.D368N	LRP6_ENST00000543091.1_Missense_Mutation_p.D368N	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	368	Beta-propeller 2.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				TCCACAGGATCGTAATCTATG	0.453																																					p.D368N		Atlas-SNP	.											.	LRP6	170	.	0			c.G1102A						PASS	.						199	170	180					12																	12334248		2203	4300	6503	SO:0001583	missense	4040	exon6			CAGGATCGTAATC	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.1102G>A	chr12.hg19:g.12334248C>T	ENSP00000261349:p.Asp368Asn	171.0	0.0	.		295.0	162.0	.	NM_002336	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	hg19	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.848081	0.91277	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.92545	-3.06;-3.06	5.82	5.82	0.92795	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000006	D	0.96396	0.8824	M	0.89534	3.04	0.80722	D	1	D;D	0.67145	0.994;0.996	P;P	0.57960	0.79;0.83	D	0.96559	0.9414	10	0.72032	D	0.01	.	20.0991	0.97865	0.0:1.0:0.0:0.0	.	368;368	F5H7J9;O75581	.;LRP6_HUMAN	N	368	ENSP00000261349:D368N;ENSP00000442472:D368N	ENSP00000261349:D368N	D	-	1	0	LRP6	12225515	1.000000	0.71417	0.999000	0.59377	0.942000	0.58702	5.999000	0.70665	2.752000	0.94435	0.655000	0.94253	GAT	.	.	.	none		0.453	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			T	12334248	C	T	12334248	3	4	152	1	0	0	0	0	1	0	0	0	8969	884	31	1	3811	1	LRP6	12	12334248	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08		12334248	121517647	56	9080											
PPFIA2	8499	hgsc.bcm.edu	37	chr12	81671123	81671123	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcatgttggcttgcttcccGtcttctttctagttcttttc	2	22	6	11	1	5	0	1	0	4	0	7	0	6	0	1	1	1	4	1	1	1	10			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr12:81671123G>A	ENST00000549396.1	-	28	3443	c.3283C>T	c.(3283-3285)Cgg>Tgg	p.R1095W	PPFIA2_ENST00000407050.4_Missense_Mutation_p.R994W|PPFIA2_ENST00000548586.1_Missense_Mutation_p.R1089W|PPFIA2_ENST00000541017.1_Missense_Mutation_p.R281W|PPFIA2_ENST00000333447.7_Missense_Mutation_p.R1083W|PPFIA2_ENST00000541570.2_Missense_Mutation_p.R631W|PPFIA2_ENST00000549325.1_Missense_Mutation_p.R1080W|PPFIA2_ENST00000550359.2_Missense_Mutation_p.R942W|PPFIA2_ENST00000443686.3_Missense_Mutation_p.R990W|PPFIA2_ENST00000550584.2_Missense_Mutation_p.R1095W|PPFIA2_ENST00000552948.1_Missense_Mutation_p.R1074W|PPFIA2_ENST00000545296.2_Intron|RP11-121G22.3_ENST00000549161.1_lincRNA	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	1095					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						CTTGCTTCCCGTCTTCTTTCT	0.274																																					p.R1095W		Atlas-SNP	.											.	PPFIA2	207	.	0			c.C3283T						PASS	.						130	117	121					12																	81671123		1797	4055	5852	SO:0001583	missense	8499	exon27			CTTCCCGTCTTCT	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.3283C>T	chr12.hg19:g.81671123G>A	ENSP00000450337:p.Arg1095Trp	15.0	0.0	.		20.0	12.0	.	NM_001220473	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Missense_Mutation	SNP	ENST00000549396.1	hg19	CCDS55857.1	.	.	.	.	.	.	.	.	.	.	G	18.73	3.686642	0.68157	.	.	ENSG00000139220	ENST00000549396;ENST00000549325;ENST00000541570;ENST00000541017;ENST00000407050;ENST00000541501;ENST00000333447;ENST00000548586;ENST00000443686;ENST00000552948	T;T;T;T;T;T;T;T;T	0.38240	1.92;1.93;1.55;1.15;1.5;1.92;1.92;1.6;1.85	5.71	3.83	0.44106	Sterile alpha motif/pointed domain (1);	0.131846	0.49916	D	0.000132	T	0.69178	0.3082	H	0.94847	3.59	0.58432	D	0.999996	D	0.89917	1.0	D	0.83275	0.996	T	0.77705	-0.2488	10	0.87932	D	0	-12.2793	13.6442	0.62270	0.0:0.0:0.4348:0.5652	.	1095	O75334	LIPA2_HUMAN	W	1095;1080;631;281;994;1106;1083;1089;990;1074	ENSP00000450337:R1095W;ENSP00000450298:R1080W;ENSP00000438337:R631W;ENSP00000445532:R281W;ENSP00000385093:R994W;ENSP00000327416:R1083W;ENSP00000449338:R1089W;ENSP00000388373:R990W;ENSP00000447868:R1074W	ENSP00000327416:R1083W	R	-	1	2	PPFIA2	80195254	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.119000	0.50422	0.721000	0.32231	-0.181000	0.13052	CGG	.	.	.	none		0.274	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1			A	81671123	G	A	81671123	3	1	152	1	0	0	0	0	1	0	0	0	12317	1144	40	1	510	1	PPFIA2	12	81671123	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	69336875	81671123	52180772	57	9081											
RASSF9	9182	hgsc.bcm.edu	37	chr12	86199543	86199543	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccctttcggagcctctccacTtctctatgatgcagtaatca	8	13	6	14	1	3	1	1	1	2	0	6	2	3	2	3	1	2	2	3	1	2	4	rs367564230		TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr12:86199543T>C	ENST00000361228.3	-	2	613	c.245A>G	c.(244-246)aAg>aGg	p.K82R		NM_005447.3	NP_005438.2	O75901	RASF9_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	82	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				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						GCCTCTCCACTTCTCTATGAT	0.473																																					p.K82R		Atlas-SNP	.											.	RASSF9	100	.	0			c.A245G						PASS	.						95	95	95					12																	86199543		1885	4121	6006	SO:0001583	missense	9182	exon2			CTCCACTTCTCTA		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.245A>G	chr12.hg19:g.86199543T>C	ENSP00000354884:p.Lys82Arg	137.0	0.0	.		216.0	53.0	.	NM_005447	B3KMQ4|Q8N5U8	Missense_Mutation	SNP	ENST00000361228.3	hg19	CCDS44950.1	.	.	.	.	.	.	.	.	.	.	T	16.30	3.084459	0.55861	.	.	ENSG00000198774	ENST00000361228	T	0.46451	0.87	4.82	4.82	0.62117	Ras-association (2);	0.139782	0.47852	D	0.000216	T	0.30479	0.0766	L	0.33485	1.01	0.37061	D	0.898052	P	0.46784	0.884	B	0.39152	0.292	T	0.22487	-1.0215	10	0.16420	T	0.52	-5.5864	14.68	0.69009	0.0:0.0:0.0:1.0	.	82	O75901	RASF9_HUMAN	R	82	ENSP00000354884:K82R	ENSP00000354884:K82R	K	-	2	0	RASSF9	84723674	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.997000	0.40786	1.941000	0.56285	0.421000	0.28195	AAG	.	.	.	alt		0.473	RASSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406109.1			C	86199543	T	C	86199543	3	2	152	1	0	0	0	0	1	0	0	0	13106	1609	56	3	1066	3	RASSF9	12	86199543	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	4528420	86199543	47652352	58	9082											
ATP2A2	488	hgsc.bcm.edu	37	chr12	110765478	110765478	+	Frame_Shift_Del	DEL	C	C	-																															aggagagaacaccccttcagCaaaaactagatgaatttggg																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr12:110765478delC	ENST00000539276.2	+	8	860	c.751delC	c.(751-753)caafs	p.Q251fs	ATP2A2_ENST00000308664.6_Frame_Shift_Del_p.Q251fs|ATP2A2_ENST00000395494.2_Frame_Shift_Del_p.Q224fs			P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	251					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						ACCCCTTCAGCAAAAACTAGA	0.453																																					p.Q250fs		Atlas-INDEL	.											.	ATP2A2	78	.	0			c.750delG						PASS	.						166	166	166					12																	110765478		2203	4300	6503	SO:0001589	frameshift_variant	488	exon8			.		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.751delC	chr12.hg19:g.110765478delC	ENSP00000440045:p.Gln251fs	237.0	0.0	0		346.0	90.0	0.260116	NM_170665	A6NDN7|B4DF05|P16614|Q86VJ2	Frame_Shift_Del	DEL	ENST00000539276.2	hg19	CCDS9144.1																																																																																			.	.	.	none		0.453	ATP2A2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403539.1	NM_001681		-	110765478	C	-	110765478	7	5	152	1	0	1	0	1	0	0	0	0	1137	711	25	0	781	0	ATP2A2	12	110765478	Frame_Shift_Del	DEL	C	TCGA-DW-7840-01A-11D-2136-08	24565935	110765478	23086417	59	9083											
TECPR2	9895	hgsc.bcm.edu	37	chr14	102906785	102906786	+	Missense_Mutation	DNP	GG	GG	TT																															ttccataggagcccttctctGgaagattgaacagaaatcta																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr14:102906785_102906786GG>TT	ENST00000359520.7	+	11	2817_2818	c.2591_2592GG>TT	c.(2590-2592)tGG>tTT	p.W864F	TECPR2_ENST00000558678.1_Missense_Mutation_p.W864F	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	864					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						GCCCTTCTCTGGAAGATTGAAC	0.446																																					p.W864L|p.W864C		Atlas-SNP	.											.	TECPR2	114	.	0			c.G2591T|c.G2592T						PASS	.																																			SO:0001583	missense	9895	exon11			TTCTCTGGAAGAT|TCTCTGGAAGATT	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		Exception_encountered	chr14.hg19:g.102906785_102906786delinsTT	ENSP00000352510:p.Trp864Phe	179.0|177.0	0.0	.		187.0|183.0	64.0|63.0	.	NM_001172631	A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	Missense_Mutation	SNP	ENST00000359520.7	hg19	CCDS32162.1																																																																																			.	.	.	none		0.446	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415056.2	NM_014844		TT	102906786	GG	TT	102906785	3	4	152	1	0	0	0	0	1	0	0	0	15756	1357	47	4	2629	4	TECPR2	14	102906785	Missense_Mutation	DNP	GG	TCGA-DW-7840-01A-11D-2136-08		102906785	4442755	60	9084											
TRPM1	4308	hgsc.bcm.edu	37	chr15	31362391	31362391	+	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	tgggtgttgcacttggcagaGgggggatatgctggttggtg	5	12	20	4	0	0	1	0	0	0	1	0	2	0	2	0	7	2	5	0	7	1	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr15:31362391G>T	ENST00000256552.6	-	4	269	c.122C>A	c.(121-123)cCt>cAt	p.P41H	TRPM1_ENST00000397795.2_Missense_Mutation_p.P19H|TRPM1_ENST00000542188.1_Missense_Mutation_p.P58H|TRPM1_ENST00000559179.1_Missense_Mutation_p.P19H	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)		ACTTGGCAGAGGGGGGATATG	0.507																																					p.P58H		Atlas-SNP	.											.	TRPM1	183	.	0			c.C173A						PASS	.						243	229	234					15																	31362391		1976	4162	6138	SO:0001583	missense	4308	exon3			GGCAGAGGGGGGA	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.122C>A	chr15.hg19:g.31362391G>T	ENSP00000256552:p.Pro41His	370.0	1.0	.		382.0	147.0	.	NM_001252020		Missense_Mutation	SNP	ENST00000256552.6	hg19	CCDS58346.1	.	.	.	.	.	.	.	.	.	.	G	10.39	1.336399	0.24253	.	.	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	T;T;T	0.55760	0.5;0.5;0.5	6.03	5.12	0.69794	.	0.408600	0.22654	U	0.057296	T	0.60340	0.2261	L	0.36672	1.1	0.33691	D	0.613333	D;D	0.71674	0.998;0.983	D;P	0.73708	0.981;0.827	T	0.71192	-0.4665	10	0.72032	D	0.01	-15.4292	9.4507	0.38725	0.2106:0.0:0.7894:0.0	.	19;19	Q6PE48;Q7Z4N2	.;TRPM1_HUMAN	H	19;58;41;19	ENSP00000380897:P19H;ENSP00000437849:P58H;ENSP00000256552:P41H	ENSP00000256552:P41H	P	-	2	0	TRPM1	29149683	1.000000	0.71417	0.918000	0.36340	0.307000	0.27823	3.722000	0.54948	1.541000	0.49316	0.655000	0.94253	CCT	.	.	.	none		0.507	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420		T	31362391	G	T	31362391	3	4	152	1	0	0	0	0	1	0	0	0	16597	1000	35	4	4855	4	TRPM1	15	31362391	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08		31362391	71169001	61	9085											
ANKDD1A	348094	hgsc.bcm.edu	37	chr15	65223120	65223120	+	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	cctggaggagcagaatgcggTgagtcaccgcctggggatgg	8	6	18	9	2	1	2	1	1	0	1	1	5	1	5	3	6	2	1	3	6	1	0			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr15:65223120T>G	ENST00000380230.3	+	7	698		c.e7+2		ANKDD1A_ENST00000491145.1_Splice_Site|ANKDD1A_ENST00000496660.1_Splice_Site|ANKDD1A_ENST00000395720.1_Splice_Site|ANKDD1A_ENST00000357698.3_Splice_Site|ANKDD1A_ENST00000395723.1_Splice_Site|ANKDD1A_ENST00000319580.8_Splice_Site	NM_182703.3	NP_874362.3	Q495B1	AKD1A_HUMAN	ankyrin repeat and death domain containing 1A						signal transduction (GO:0007165)					NS(1)|endometrium(1)|large_intestine(10)|liver(2)|lung(4)|ovary(1)|prostate(2)	21						CAGAATGCGGTGAGTCACCGC	0.607																																					.		Atlas-SNP	.											.	ANKDD1A	47	.	0			c.669+2T>G						PASS	.						68	54	59					15																	65223120		2202	4299	6501	SO:0001630	splice_region_variant	348094	exon7			ATGCGGTGAGTCA		CCDS10197.2	15q22.31	2013-01-10	2006-02-16		ENSG00000166839	ENSG00000166839		"Ankyrin repeat domain containing"	28002	protein-coding gene	gene with protein product						12477932	Standard	NM_182703		Approved	FLJ25870	uc002aoa.3	Q495B1	OTTHUMG00000133051	ENST00000380230.3:c.669+2T>G	chr15.hg19:g.65223120T>G		24.0	0.0	.		33.0	14.0	.	NM_182703	Q495B2|Q495B3|Q8N7A0|Q8NBS5	Splice_Site	SNP	ENST00000380230.3	hg19	CCDS10197.2	.	.	.	.	.	.	.	.	.	.	T	17.32	3.360134	0.61403	.	.	ENSG00000166839	ENST00000380230;ENST00000357698;ENST00000395720;ENST00000319597;ENST00000496660;ENST00000483400;ENST00000395723	.	.	.	4.01	4.01	0.46588	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.27	0.37666	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ANKDD1A	63010173	1.000000	0.71417	0.940000	0.37924	0.376000	0.30014	5.235000	0.65348	1.699000	0.51192	0.459000	0.35465	.	.	.	.	none		0.607	ANKDD1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256705.2	NM_182703	Intron	G	65223120	T	G	65223120	5	3	152	1	0	0	0	0	0	0	1	0	624	1710	59	5	697	5	ANKDD1A	15	65223120	Splice_Site	SNP	T	TCGA-DW-7840-01A-11D-2136-08	33860729	65223120	37308272	62	9086											
IGDCC4	57722	hgsc.bcm.edu	37	chr15	65684505	65684505	+	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	ctcatactgcttcactttctTcttgagccggacaggcccca	7	12	7	15	1	4	1	2	1	2	0	4	2	4	2	3	2	3	1	3	2	1	5			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr15:65684505T>A	ENST00000352385.2	-	11	2298	c.2089A>T	c.(2089-2091)Aag>Tag	p.K697*		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	697	Fibronectin type-III 3. {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						TTCACTTTCTTCTTGAGCCGG	0.632																																					p.K697X		Atlas-SNP	.											.	IGDCC4	95	.	0			c.A2089T						PASS	.						32	39	37					15																	65684505		2184	4286	6470	SO:0001587	stop_gained	57722	exon11			CTTTCTTCTTGAG		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.2089A>T	chr15.hg19:g.65684505T>A	ENSP00000319623:p.Lys697*	91.0	0.0	.		112.0	44.0	.	NM_020962	Q9HCE4	Nonsense_Mutation	SNP	ENST00000352385.2	hg19	CCDS10206.1	.	.	.	.	.	.	.	.	.	.	T	41	8.769097	0.98948	.	.	ENSG00000103742	ENST00000352385;ENST00000356152	.	.	.	5.49	4.38	0.52667	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	-23.8407	10.907	0.47086	0.0:0.0731:0.0:0.9269	.	.	.	.	X	697;426	.	ENSP00000319623:K697X	K	-	1	0	IGDCC4	63471558	1.000000	0.71417	1.000000	0.80357	0.672000	0.39443	5.434000	0.66526	0.947000	0.37659	0.533000	0.62120	AAG	.	.	.	none		0.632	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962		A	65684505	T	A	65684505	4	1	152	1	0	0	0	0	0	1	0	0	7576	1792	62	5	1703	5	IGDCC4	15	65684505	Nonsense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	461385	65684505	36846887	63	9087											
MAP2K5	5607	hgsc.bcm.edu	37	chr15	67985904	67985904	+	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	ttggaacaaatgcttatatgGcggtaagtaaacttatgcaa	15	12	9	5	1	0	0	0	0	0	0	0	1	0	1	0	3	4	4	0	3	9	6			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr15:67985904G>T	ENST00000178640.5	+	15	1597	c.970G>T	c.(970-972)Gcg>Tcg	p.A324S	MAP2K5_ENST00000395476.2_Missense_Mutation_p.A324S|MAP2K5_ENST00000354498.5_Missense_Mutation_p.A288S|MAP2K5_ENST00000340972.4_Missense_Mutation_p.A134S	NM_145160.2	NP_660143.1	Q13163	MP2K5_HUMAN	mitogen-activated protein kinase kinase 5	324	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cellular response to growth factor stimulus (GO:0071363)|cellular response to laminar fluid shear stress (GO:0071499)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|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 extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of response to cytokine stimulus (GO:0060761)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleus (GO:0005634)|spindle (GO:0005819)	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)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|skin(1)	16						TGCTTATATGGCGGTAAGTAA	0.303																																					p.A324S		Atlas-SNP	.											.	MAP2K5	70	.	0			c.G970T						PASS	.						132	126	128					15																	67985904		2200	4297	6497	SO:0001583	missense	5607	exon15			TATATGGCGGTAA	U25265	CCDS10224.1, CCDS42051.1, CCDS55970.1	15q22.31	2011-06-09			ENSG00000137764	ENSG00000137764		"Mitogen-activated protein kinase cascade / Kinase kinases"	6845	protein-coding gene	gene with protein product		602520		PRKMK5		7759517	Standard	NM_002757		Approved	MEK5, MAPKK5, HsT17454	uc002aqu.3	Q13163	OTTHUMG00000133264	ENST00000178640.5:c.970G>T	chr15.hg19:g.67985904G>T	ENSP00000178640:p.Ala324Ser	86.0	0.0	.		95.0	30.0	.	NM_145160	B4DE43|Q92961|Q92962	Missense_Mutation	SNP	ENST00000178640.5	hg19	CCDS10224.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.107121	0.37145	.	.	ENSG00000137764	ENST00000541298;ENST00000395476;ENST00000178640;ENST00000354498;ENST00000340972	T;T;T;T	0.19394	2.15;2.15;2.15;2.15	5.58	5.58	0.84498	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	0.36358	0.0964	L	0.31752	0.955	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	0.02728	-1.1118	10	0.28530	T	0.3	-16.1519	19.5552	0.95342	0.0:0.0:1.0:0.0	.	134;324;324	A6NK28;Q13163-2;Q13163	.;.;MP2K5_HUMAN	S	324;324;324;288;134	ENSP00000378859:A324S;ENSP00000178640:A324S;ENSP00000346493:A288S;ENSP00000342101:A134S	ENSP00000178640:A324S	A	+	1	0	MAP2K5	65772958	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.968000	0.93407	2.630000	0.89119	0.585000	0.79938	GCG	.	.	.	none		0.303	MAP2K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257041.1	NM_145162		T	67985904	G	T	67985904	3	4	152	1	0	0	0	0	1	0	0	0	9247	1203	42	4	1028	4	MAP2K5	15	67985904	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	2301399	67985904	34545488	64	9088											
RASGRF1	5923	hgsc.bcm.edu	37	chr15	79254568	79254568	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caaaagattggtccagtaaaTattgcgttacctgagaaaag	16	10	9	6	1	0	2	0	1	0	2	1	3	1	2	2	1	2	2	2	1	8	5			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr15:79254568T>C	ENST00000419573.3	-	28	4014	c.3740A>G	c.(3739-3741)tAt>tGt	p.Y1247C	RASGRF1_ENST00000394745.3_Missense_Mutation_p.Y463C|RASGRF1_ENST00000558480.2_Missense_Mutation_p.Y1231C	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	1247	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						GTCCAGTAAATATTGCGTTAC	0.468																																					p.Y1247C		Atlas-SNP	.											.	RASGRF1	168	.	0			c.A3740G						PASS	.						58	56	56					15																	79254568		2196	4290	6486	SO:0001583	missense	5923	exon28			AGTAAATATTGCG	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.3740A>G	chr15.hg19:g.79254568T>C	ENSP00000405963:p.Tyr1247Cys	11.0	0.0	.		13.0	5.0	.	NM_002891	F8VPA5|H0YKF2|J3KQP9|Q16027	Missense_Mutation	SNP	ENST00000419573.3	hg19	CCDS10309.1	.	.	.	.	.	.	.	.	.	.	T	16.60	3.169141	0.57584	.	.	ENSG00000058335	ENST00000419573;ENST00000394741;ENST00000394745	T;T	0.34472	1.36;1.36	3.96	3.96	0.45880	Guanine-nucleotide dissociation stimulator CDC25 (3);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.64402	D	0.000003	T	0.56381	0.1981	M	0.78801	2.425	0.80722	D	1	D;D	0.76494	0.998;0.999	P;D	0.68483	0.867;0.958	T	0.60826	-0.7186	10	0.87932	D	0	.	9.5252	0.39160	0.0:0.0:0.0:1.0	.	1249;1231	Q13972;F8VPA5	RGRF1_HUMAN;.	C	1247;1231;463	ENSP00000405963:Y1247C;ENSP00000378228:Y463C	ENSP00000378224:Y1231C	Y	-	2	0	RASGRF1	77041623	1.000000	0.71417	0.170000	0.22879	0.948000	0.59901	6.883000	0.75595	1.545000	0.49373	0.402000	0.26972	TAT	.	.	.	none		0.468	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891		C	79254568	T	C	79254568	3	2	152	1	0	0	0	0	1	0	0	0	13085	1406	49	3	85	3	RASGRF1	15	79254568	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	11268664	79254568	23276824	65	9089											
MYH8	4626	hgsc.bcm.edu	37	chr17	10312636	10312636	+	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	gtggaaaagagactggctagAgtcttcattgcagacttctg	11	11	12	7	0	3	3	1	0	2	3	3	5	3	4	0	2	1	2	0	2	3	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr17:10312636A>T	ENST00000403437.2	-	16	1951	c.1857T>A	c.(1855-1857)acT>acA	p.T619T	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	619	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						GACTGGCTAGAGTCTTCATTG	0.423									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																												p.T619T		Atlas-SNP	.											.	MYH8	346	.	0			c.T1857A						PASS	.						67	69	68					17																	10312636		2203	4300	6503	SO:0001819	synonymous_variant	4626	exon16	Familial Cancer Database	Carney Complex Variant	GGCTAGAGTCTTC		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.1857T>A	chr17.hg19:g.10312636A>T		124.0	0.0	.		147.0	77.0	.	NM_002472	Q14910	Silent	SNP	ENST00000403437.2	hg19	CCDS11153.1																																																																																			.	.	.	none		0.423	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		T	10312636	A	T	10312636	2	4	152	1	0	0	0	0	0	0	0	1	10048	291	11	5		5	MYH8	17	10312636	Silent	SNP	A	TCGA-DW-7840-01A-11D-2136-08		10312636	70882574	66	9090											
C19orf21	126353	hgsc.bcm.edu	37	chr19	758211	758211	+	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	gaaggtgaaccgcatcccacCtgatgcctaccagccgtacc	10	6	9	16	2	0	2	0	2	0	0	1	3	1	2	7	1	5	2	7	1	4	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr19:758211C>A	ENST00000215582.6	+	2	1368	c.1265C>A	c.(1264-1266)cCt>cAt	p.P422H		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	422					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											CGCATCCCACCTGATGCCTAC	0.652																																					p.P422H		Atlas-SNP	.											.	C19orf21	56	.	0			c.C1265A						PASS	.						25	20	22					19																	758211		2201	4298	6499	SO:0001583	missense	126353	exon2			TCCCACCTGATGC	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.1265C>A	chr19.hg19:g.758211C>A	ENSP00000215582:p.Pro422His	32.0	0.0	.		47.0	25.0	.	NM_173481		Missense_Mutation	SNP	ENST00000215582.6	hg19	CCDS12042.1	.	.	.	.	.	.	.	.	.	.	C	15.39	2.819234	0.50633	.	.	ENSG00000099812	ENST00000215582	T	0.35421	1.31	4.11	-1.68	0.08212	.	2.124670	0.02785	N	0.121388	T	0.47173	0.1431	L	0.54323	1.7	0.09310	N	1	D	0.69078	0.997	P	0.57548	0.823	T	0.41875	-0.9484	10	0.59425	D	0.04	-0.009	5.8678	0.18786	0.0:0.4423:0.1475:0.4102	.	422	Q8IVT2	CS021_HUMAN	H	422	ENSP00000215582:P422H	ENSP00000215582:P422H	P	+	2	0	C19orf21	709211	0.000000	0.05858	0.001000	0.08648	0.398000	0.30690	-0.883000	0.04170	-0.165000	0.10908	0.491000	0.48974	CCT	.	.	.	none		0.652	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481		A	758211	C	A	758211	3	1	152	1	0	0	0	0	1	0	0	0	1915	681	24	4	1267	4	C19orf21	19	758211	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08		758211	58370772	67	9091											
TUBB4	10382	hgsc.bcm.edu	37	chr19	6501326	6501326	+	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	aagttgtccggccgaaagatCtgaccgaaggggccagaacg	12	5	14	10	4	1	3	0	1	1	2	2	5	2	3	4	3	1	1	4	3	4	1			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr19:6501326C>A	ENST00000264071.2	-	3	620	c.249G>T	c.(247-249)caG>caT	p.Q83H	TUBB4A_ENST00000598006.1_Missense_Mutation_p.R69I|TUBB4A_ENST00000601152.1_Missense_Mutation_p.R58I|TUBB4A_ENST00000540257.1_Missense_Mutation_p.Q83H|TUBB4A_ENST00000596926.1_Missense_Mutation_p.Q83H			P04350	TBB4A_HUMAN	tubulin, beta 4A class IVa	83					'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)										GCCGAAAGATCTGACCGAAGG	0.577																																					p.Q83H		Atlas-SNP	.											.	.	.	.	0			c.G249T						PASS	.						49	44	46					19																	6501326		2203	4300	6503	SO:0001583	missense	10382	exon3			AAAGATCTGACCG	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.249G>T	chr19.hg19:g.6501326C>A	ENSP00000264071:p.Gln83His	65.0	0.0	.		53.0	27.0	.	NM_006087	B3KQP4|Q969E5	Missense_Mutation	SNP	ENST00000264071.2	hg19	CCDS12168.1	.	.	.	.	.	.	.	.	.	.	C	5.184	0.219490	0.09863	.	.	ENSG00000104833	ENST00000264071;ENST00000540257;ENST00000412858	T;T	0.70164	-0.46;-0.46	3.83	1.13	0.20643	.	0.000000	0.64402	D	0.000003	T	0.65491	0.2696	M	0.82923	2.615	0.40614	D	0.981708	B	0.10296	0.003	B	0.08055	0.003	T	0.67039	-0.5771	10	0.87932	D	0	.	9.7907	0.40704	0.0:0.7717:0.0:0.2283	.	83	P04350	TBB4A_HUMAN	H	83	ENSP00000264071:Q83H;ENSP00000443590:Q83H	ENSP00000264071:Q83H	Q	-	3	2	TUBB4	6452326	1.000000	0.71417	1.000000	0.80357	0.432000	0.31715	2.026000	0.41069	0.592000	0.29728	0.313000	0.20887	CAG	.	.	.	none		0.577	TUBB4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457841.1	NM_006087		A	6501326	C	A	6501326	3	1	152	1	0	0	0	0	1	0	0	0	16770	912	32	4	1093	4	TUBB4	19	6501326	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	5743115	6501326	52627657	68	9092											
ZNF557	79230	hgsc.bcm.edu	37	chr19	7083599	7083599	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagaaatcctatgagtgcagTgattgtggaaaatcctttaa	14	12	10	5	0	0	3	0	2	0	1	2	5	2	4	2	1	1	1	2	1	5	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr19:7083599T>C	ENST00000439035.2	+	8	1356	c.1116T>C	c.(1114-1116)agT>agC	p.S372S	ZNF557_ENST00000414706.1_Silent_p.S379S|ZNF557_ENST00000252840.6_Silent_p.S379S			Q8N988	ZN557_HUMAN	zinc finger protein 557	372					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(6)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17				Lung(535;0.179)		ATGAGTGCAGTGATTGTGGAA	0.368																																					p.S379S		Atlas-SNP	.											.	ZNF557	40	.	0			c.T1137C						PASS	.						64	68	67					19																	7083599		2125	4254	6379	SO:0001819	synonymous_variant	79230	exon8			GTGCAGTGATTGT	AK095524	CCDS42485.1, CCDS45945.1	19p13.2	2013-09-20			ENSG00000130544	ENSG00000130544		"Zinc fingers, C2H2-type", "-"	28632	protein-coding gene	gene with protein product						12477932	Standard	NM_024341		Approved	MGC4054	uc002mgc.3	Q8N988	OTTHUMG00000181977	ENST00000439035.2:c.1116T>C	chr19.hg19:g.7083599T>C		76.0	0.0	.		65.0	16.0	.	NM_001044387	Q6PEJ3|Q9BTZ1	Silent	SNP	ENST00000439035.2	hg19	CCDS45945.1																																																																																			.	.	.	none		0.368	ZNF557-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458502.1	NM_024341		C	7083599	T	C	7083599	2	2	152	1	0	0	0	0	0	0	0	1	18000	1693	59	3		3	ZNF557	19	7083599	Silent	SNP	T	TCGA-DW-7840-01A-11D-2136-08	582273	7083599	52045384	69	9093											
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11135092	11135092	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagggcgtgctgctgactgAtggctccgagaaggacaaga	11	6	15	9	2	0	4	0	2	0	2	1	6	1	5	1	3	2	3	1	3	3	0			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr19:11135092A>G	ENST00000429416.3	+	22	3340	c.3059A>G	c.(3058-3060)gAt>gGt	p.D1020G	SMARCA4_ENST00000413806.3_Missense_Mutation_p.D1020G|SMARCA4_ENST00000589677.1_Missense_Mutation_p.D1020G|SMARCA4_ENST00000358026.2_Missense_Mutation_p.D1020G|SMARCA4_ENST00000344626.4_Missense_Mutation_p.D1020G|SMARCA4_ENST00000590574.1_Missense_Mutation_p.D1020G|SMARCA4_ENST00000541122.2_Missense_Mutation_p.D1020G|SMARCA4_ENST00000450717.3_Missense_Mutation_p.D1020G|SMARCA4_ENST00000444061.3_Missense_Mutation_p.D1020G	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1020					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)				CTGCTGACTGATGGCTCCGAG	0.632			"F, N, Mis"		NSCLC																																p.D1020G		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.A3059G						PASS	.						73	58	63					19																	11135092		2203	4300	6503	SO:0001583	missense	6597	exon21			TGACTGATGGCTC	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.3059A>G	chr19.hg19:g.11135092A>G	ENSP00000395654:p.Asp1020Gly	77.0	0.0	.		66.0	21.0	.	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	A	16.59	3.166378	0.57476	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	T;T;T;T;T;T;T	0.81247	-1.47;-1.47;-1.47;-1.47;-1.47;-1.47;-1.47	4.76	4.76	0.60689	SNF2-related (1);	0.000000	0.85682	D	0.000000	T	0.82130	0.4970	L	0.37897	1.145	0.58432	D	0.999994	D;B;P;B;D;B;P;P	0.56287	0.975;0.418;0.78;0.002;0.975;0.0;0.78;0.78	P;B;B;B;P;B;P;P	0.57720	0.826;0.304;0.377;0.007;0.826;0.014;0.531;0.531	D	0.84375	0.0546	10	0.87932	D	0	-36.5944	13.3812	0.60768	1.0:0.0:0.0:0.0	.	1020;1020;1020;1020;1020;240;1020;1020	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;A7E2E1;P51532	.;.;.;.;.;.;.;SMCA4_HUMAN	G	1020;1020;1084;1020;1020;1020;1020;1020	ENSP00000395654:D1020G;ENSP00000350720:D1020G;ENSP00000343896:D1020G;ENSP00000445036:D1020G;ENSP00000392837:D1020G;ENSP00000397783:D1020G;ENSP00000414727:D1020G	ENSP00000343896:D1020G	D	+	2	0	SMARCA4	10996092	1.000000	0.71417	0.922000	0.36590	0.498000	0.33706	8.908000	0.92640	1.997000	0.58415	0.533000	0.62120	GAT	.	.	.	none		0.632	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		G	11135092	A	G	11135092	3	3	152	1	0	0	0	0	1	0	0	0	14783	333	12	3	3137	3	SMARCA4	19	11135092	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08	4051493	11135092	47993891	70	9094											
ZNF443	10224	hgsc.bcm.edu	37	chr19	12541116	12541116	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggaactgagagaagcaaatgCtttcccacattccttacatt	13	11	7	10	0	0	2	0	1	0	1	2	4	2	3	2	1	4	2	2	1	4	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr19:12541116C>T	ENST00000301547.5	-	4	2067	c.1870G>A	c.(1870-1872)Gca>Aca	p.A624T	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	624					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						GAAGCAAATGCTTTCCCACAT	0.408																																					p.A624T		Atlas-SNP	.											.	ZNF443	63	.	0			c.G1870A						PASS	.						62	68	66					19																	12541116		2200	4292	6492	SO:0001583	missense	10224	exon4			CAAATGCTTTCCC	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.1870G>A	chr19.hg19:g.12541116C>T	ENSP00000301547:p.Ala624Thr	183.0	0.0	.		218.0	64.0	.	NM_005815		Missense_Mutation	SNP	ENST00000301547.5	hg19	CCDS32918.1	.	.	.	.	.	.	.	.	.	.	C	10.87	1.473549	0.26423	.	.	ENSG00000180855	ENST00000301547;ENST00000411622	T	0.13778	2.56	1.36	-0.965	0.10323	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09686	0.0238	L	0.28504	0.86	0.09310	N	1	B	0.30664	0.289	B	0.37888	0.26	T	0.39231	-0.9624	9	0.38643	T	0.18	.	1.9484	0.03361	0.2638:0.3516:0.0:0.3846	.	624	Q9Y2A4	ZN443_HUMAN	T	624;596	ENSP00000301547:A624T	ENSP00000301547:A624T	A	-	1	0	ZNF443	12402116	0.000000	0.05858	0.001000	0.08648	0.586000	0.36452	-1.775000	0.01783	-0.214000	0.10078	0.454000	0.30748	GCA	.	.	.	none		0.408	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815		T	12541116	C	T	12541116	3	4	152	1	0	0	0	0	1	0	0	0	17928	797	28	2	149	2	ZNF443	19	12541116	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	1406024	12541116	46587867	71	9095											
RHPN2	85415	hgsc.bcm.edu	37	chr19	33493859	33493859	+	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	gagcatggcagggctcatgtCgtaacttggagtatgggtaa	10	10	15	6	1	1	0	1	0	0	0	2	2	1	1	0	4	2	6	0	4	3	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr19:33493859C>T	ENST00000254260.3	-	8	843	c.808G>A	c.(808-810)Gac>Aac	p.D270N	RHPN2_ENST00000400226.4_Missense_Mutation_p.D119N	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	270	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)		p.D270N(1)		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)					GGGCTCATGTCGTAACTTGGA	0.433																																					p.D270N		Atlas-SNP	.											RHPN2,colon,carcinoma,0,1	RHPN2	107	.	1	Substitution - Missense(1)	large_intestine(1)	c.G808A						PASS	.						51	46	48					19																	33493859		2203	4300	6503	SO:0001583	missense	85415	exon8			TCATGTCGTAACT	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.808G>A	chr19.hg19:g.33493859C>T	ENSP00000254260:p.Asp270Asn	62.0	0.0	.		83.0	4.0	.	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	hg19	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	C	31	5.102511	0.94245	.	.	ENSG00000131941	ENST00000254260;ENST00000400226	T;T	0.55760	0.5;0.5	4.7	4.7	0.59300	BRO1 domain (3);	0.000000	0.85682	D	0.000000	T	0.79221	0.4409	H	0.95187	3.635	0.80722	D	1	D	0.71674	0.998	P	0.60789	0.879	D	0.86783	0.1980	10	0.87932	D	0	0.141	18.0539	0.89358	0.0:1.0:0.0:0.0	.	270	Q8IUC4	RHPN2_HUMAN	N	270;119	ENSP00000254260:D270N;ENSP00000402244:D119N	ENSP00000254260:D270N	D	-	1	0	RHPN2	38185699	1.000000	0.71417	0.996000	0.52242	0.938000	0.57974	7.752000	0.85141	2.325000	0.78763	0.478000	0.44815	GAC	.	.	.	none		0.433	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103		T	33493859	C	T	33493859	3	4	152	1	0	0	0	0	1	0	0	0	13364	884	31	1	1284	1	RHPN2	19	33493859	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	20952743	33493859	25635124	72	9096											
SIGLEC11	114132	hgsc.bcm.edu	37	chr19	50463980	50463980	+	Frame_Shift_Del	DEL	T	T	-																															gaatcggtcccgggtgctcaTttccacctctcgactctggt																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr19:50463980delT	ENST00000447370.2	-	2	379	c.289delA	c.(289-291)atgfs	p.M97fs	CTC-326K19.6_ENST00000451973.1_5'Flank|SIGLEC11_ENST00000426971.2_Frame_Shift_Del_p.M97fs	NM_052884.2	NP_443116.2	Q96RL6	SIG11_HUMAN	sialic acid binding Ig-like lectin 11	97	Ig-like V-type.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(6)|pancreas(1)|prostate(1)|skin(1)	32		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00107)|OV - Ovarian serous cystadenocarcinoma(262;0.00517)		CGGGTGCTCATTTCCACCTCT	0.582																																					p.M97fs		Atlas-INDEL	.											.	SIGLEC11	70	.	0			c.290delT						PASS	.						19	23	22					19																	50463980		2107	4293	6400	SO:0001589	frameshift_variant	114132	exon2			.	AF337818	CCDS12790.2, CCDS46150.1	19q13.3	2013-01-29			ENSG00000161640	ENSG00000161640		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15622	protein-coding gene	gene with protein product		607157				11986327	Standard	NM_052884		Approved		uc010ybi.2	Q96RL6	OTTHUMG00000157077	ENST00000447370.2:c.289delA	chr19.hg19:g.50463980delT	ENSP00000412361:p.Met97fs	116.0	0.0	0		124.0	11.0	0.0887097	NM_001135163		Frame_Shift_Del	DEL	ENST00000447370.2	hg19	CCDS12790.2																																																																																			.	.	.	none		0.582	SIGLEC11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347382.1	NM_052884		-	50463980	T	-	50463980	7	5	152	1	0	1	0	1	0	0	0	0	14320	1493	52	0	1847	0	SIGLEC11	19	50463980	Frame_Shift_Del	DEL	T	TCGA-DW-7840-01A-11D-2136-08	16970121	50463980	8665003	73	9097											
ZNF814	730051	hgsc.bcm.edu	37	chr19	58386399	58386399	+	Frame_Shift_Del	DEL	T	T	-																															tcccccaggcctcacacctgTgcagtttctgcttgtgatgt																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr19:58386399delT	ENST00000435989.2	-	3	593	c.359delA	c.(358-360)cacfs	p.H120fs	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597832.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	120					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						CTCACACCTGTGCAGTTTCTG	0.502																																					p.H120fs		Atlas-INDEL	.											.	ZNF814	93	.	0			c.360delC						PASS	.						18	14	15					19																	58386399		692	1568	2260	SO:0001589	frameshift_variant	730051	exon3			.		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.359delA	chr19.hg19:g.58386399delT	ENSP00000410545:p.His120fs	109.0	0.0	0		118.0	16.0	0.135593	NM_001144989	A6NF35	Frame_Shift_Del	DEL	ENST00000435989.2	hg19	CCDS46212.1																																																																																			.	.	.	none		0.502	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		-	58386399	T	-	58386399	7	5	152	1	0	1	0	1	0	0	0	0	18188	1696	59	0	2212	0	ZNF814	19	58386399	Frame_Shift_Del	DEL	T	TCGA-DW-7840-01A-11D-2136-08	7922419	58386399	742584	74	9098											
DNMT3B	1789	hgsc.bcm.edu	37	chr20	31374365	31374365	+	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	agaggcacaggccttccccaCgttccacccgaggccggcag	8	4	12	17	3	0	1	0	0	0	1	2	2	2	1	6	4	0	3	6	4	0	2			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr20:31374365C>G	ENST00000328111.2	+	5	685	c.364C>G	c.(364-366)Cgt>Ggt	p.R122G	DNMT3B_ENST00000443239.3_Intron|DNMT3B_ENST00000456297.2_Intron|DNMT3B_ENST00000353855.2_Missense_Mutation_p.R122G|DNMT3B_ENST00000348286.2_Missense_Mutation_p.R122G|DNMT3B_ENST00000201963.3_Missense_Mutation_p.R134G|DNMT3B_ENST00000344505.4_Missense_Mutation_p.R122G|DNMT3B_ENST00000375623.4_Intron	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta	122	Interaction with DNMT1 and DNMT3A.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)	p.R134C(1)|p.R122C(1)		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						GCCTTCCCCACGTTCCACCCG	0.632																																					p.R134G		Atlas-SNP	.											DNMT3B_ENST00000201963,NS,carcinoma,0,2	DNMT3B	196	.	2	Substitution - Missense(2)	lung(2)	c.C400G						PASS	.						68	66	66					20																	31374365		2203	4300	6503	SO:0001583	missense	1789	exon5			TCCCCACGTTCCA		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.364C>G	chr20.hg19:g.31374365C>G	ENSP00000328547:p.Arg122Gly	114.0	0.0	.		123.0	54.0	.	NM_175850	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Missense_Mutation	SNP	ENST00000328111.2	hg19	CCDS13205.1	.	.	.	.	.	.	.	.	.	.	C	10.84	1.465264	0.26335	.	.	ENSG00000088305	ENST00000328111;ENST00000537219;ENST00000353855;ENST00000348286;ENST00000344505;ENST00000201963	D;D;D;D;D	0.98400	-4.67;-4.89;-4.82;-4.77;-4.91	4.84	3.86	0.44501	.	0.246993	0.38326	N	0.001738	D	0.97219	0.9091	L	0.27053	0.805	0.23070	N	0.998346	D;P;P;P	0.71674	0.998;0.811;0.804;0.752	D;B;B;B	0.80764	0.994;0.309;0.28;0.191	D	0.92382	0.5914	10	0.26408	T	0.33	-6.5354	9.8664	0.41145	0.2125:0.7875:0.0:0.0	.	134;122;122;122	Q9UBC3-6;Q9UBC3-3;Q9UBC3-2;Q9UBC3	.;.;.;DNM3B_HUMAN	G	122;208;122;122;122;134	ENSP00000328547:R122G;ENSP00000313397:R122G;ENSP00000337764:R122G;ENSP00000345105:R122G;ENSP00000201963:R134G	ENSP00000201963:R134G	R	+	1	0	DNMT3B	30838026	0.456000	0.25744	0.018000	0.16275	0.031000	0.12232	1.919000	0.40015	1.211000	0.43351	0.561000	0.74099	CGT	.	.	.	none		0.632	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892		G	31374365	C	G	31374365	3	3	152	1	0	0	0	0	1	0	0	0	4679	536	19	4	418	4	DNMT3B	20	31374365	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08		31374365	31651155	75	9099											
MMP24	10893	hgsc.bcm.edu	37	chr20	33851627	33851627	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggtggctgtgcatgagcTgggccacgcgctgggactgg	4	8	18	11	2	0	1	0	1	0	0	0	2	0	2	2	5	2	4	2	5	0	0			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr20:33851627T>C	ENST00000246186.6	+	5	936	c.851T>C	c.(850-852)cTg>cCg	p.L284P	MMP24-AS1_ENST00000433764.1_RNA|MMP24-AS1_ENST00000566203.2_RNA|MMP24-AS1_ENST00000453892.1_RNA|MMP24-AS1_ENST00000438751.1_RNA|EDEM2_ENST00000540582.1_Intron|MMP24-AS1_ENST00000454184.1_RNA|MMP24-AS1_ENST00000456350.1_RNA	NM_006690.3	NP_006681.1	Q9Y5R2	MMP24_HUMAN	matrix metallopeptidase 24 (membrane-inserted)	284					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)	GTGCATGAGCTGGGCCACGCG	0.622																																					p.L284P		Atlas-SNP	.											.	MMP24	35	.	0			c.T851C						PASS	.						24	24	24					20																	33851627		2203	4300	6503	SO:0001583	missense	10893	exon5			ATGAGCTGGGCCA	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.851T>C	chr20.hg19:g.33851627T>C	ENSP00000246186:p.Leu284Pro	16.0	0.0	.		23.0	10.0	.	NM_006690	B7ZBG8|Q9H440	Missense_Mutation	SNP	ENST00000246186.6	hg19	CCDS46593.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.546808	0.86022	.	.	ENSG00000125966	ENST00000246186;ENST00000540655	T	0.35605	1.3	5.05	5.05	0.67936	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.000000	0.64402	D	0.000004	T	0.72145	0.3424	H	0.96916	3.905	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82337	-0.0507	10	0.87932	D	0	.	14.1037	0.65075	0.0:0.0:0.0:1.0	.	284	Q9Y5R2	MMP24_HUMAN	P	284;232	ENSP00000246186:L284P	ENSP00000246186:L284P	L	+	2	0	MMP24	33315043	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.819000	0.86621	2.105000	0.64084	0.533000	0.62120	CTG	.	.	.	none		0.622	MMP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078851.4	NM_006690		C	33851627	T	C	33851627	3	2	152	1	0	0	0	0	1	0	0	0	9668	1580	55	3	619	3	MMP24	20	33851627	Missense_Mutation	SNP	T	TCGA-DW-7840-01A-11D-2136-08	2477262	33851627	29173893	76	9100											
SGK2	10110	hgsc.bcm.edu	37	chr20	42203603	42203603	+	Frame_Shift_Del	DEL	T	T	-																															atgatcgagcagtggactggTggtgcttgggggcagtcctc																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr20:42203603delT	ENST00000341458.4	+	9	1051	c.832delT	c.(832-834)tggfs	p.W278fs	SGK2_ENST00000423407.3_Frame_Shift_Del_p.W218fs|SGK2_ENST00000426287.1_Frame_Shift_Del_p.W244fs|SGK2_ENST00000373100.1_Frame_Shift_Del_p.W218fs|SGK2_ENST00000373092.3_Frame_Shift_Del_p.W218fs|SGK2_ENST00000373077.1_Frame_Shift_Del_p.W217fs	NM_016276.3	NP_057360.2	Q9HBY8	SGK2_HUMAN	serum/glucocorticoid regulated kinase 2	278	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)			AGTGGACTGGTGGTGCTTGGG	0.512																																					p.W277fs		Atlas-INDEL	.											.	SGK2	50	.	0			c.831delG						PASS	.						114	103	107					20																	42203603		2203	4300	6503	SO:0001589	frameshift_variant	10110	exon9			.	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.832delT	chr20.hg19:g.42203603delT	ENSP00000340608:p.Trp278fs	52.0	0.0	0		48.0	21.0	0.4375	NM_016276	Q52PK5|Q5H8Y6|Q5H8Z1|Q5TZR3|Q9UKG6	Frame_Shift_Del	DEL	ENST00000341458.4	hg19	CCDS13320.1																																																																																			.	.	.	none		0.512	SGK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080383.1			-	42203603	T	-	42203603	7	5	152	1	0	1	0	1	0	0	0	0	14222	1696	59	0	866	0	SGK2	20	42203603	Frame_Shift_Del	DEL	T	TCGA-DW-7840-01A-11D-2136-08	8351976	42203603	20821917	77	9101											
C20orf177	63939	hgsc.bcm.edu	37	chr20	58519969	58519969	+	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	ggaaaccagcggtcacattcGagttcccaaacaggcagctg	12	6	11	12	2	1	0	1	0	0	0	3	2	2	1	2	3	4	3	2	3	2	2	rs377074437		TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr20:58519969G>C	ENST00000358293.3	+	5	1386	c.971G>C	c.(970-972)cGa>cCa	p.R324P	FAM217B_ENST00000360816.3_Missense_Mutation_p.R324P|FAM217B_ENST00000469084.1_3'UTR	NM_001190826.1	NP_001177755.1	Q9NTX9	F217B_HUMAN	family with sequence similarity 217, member B	324																	GGTCACATTCGAGTTCCCAAA	0.493																																					p.R324P		Atlas-SNP	.											.	.	.	.	0			c.G971C						PASS	.						65	68	67					20																	58519969		2203	4300	6503	SO:0001583	missense	63939	exon4			ACATTCGAGTTCC	AL109928	CCDS13484.1	20q13.33	2012-02-07	2012-02-07	2012-02-07	ENSG00000196227	ENSG00000196227			16170	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 177"	C20orf177			Standard	NM_022106		Approved	dJ551D2.5	uc002ybc.3	Q9NTX9	OTTHUMG00000032873	ENST00000358293.3:c.971G>C	chr20.hg19:g.58519969G>C	ENSP00000351040:p.Arg324Pro	76.0	0.0	.		98.0	4.0	.	NM_022106	B3KWH1|Q9NTA3	Missense_Mutation	SNP	ENST00000358293.3	hg19	CCDS13484.1	.	.	.	.	.	.	.	.	.	.	G	19.36	3.813583	0.70912	.	.	ENSG00000196227	ENST00000358293;ENST00000360816	T;T	0.26660	1.72;1.72	5.35	4.4	0.53042	.	0.512737	0.15763	N	0.245848	T	0.38268	0.1034	L	0.29908	0.895	0.19300	N	0.999975	D	0.89917	1.0	D	0.83275	0.996	T	0.11817	-1.0572	10	0.48119	T	0.1	-14.475	13.4353	0.61079	0.0753:0.0:0.9247:0.0	.	324	Q9NTX9	CT177_HUMAN	P	324	ENSP00000351040:R324P;ENSP00000354056:R324P	ENSP00000351040:R324P	R	+	2	0	C20orf177	57953364	0.341000	0.24801	0.133000	0.22050	0.030000	0.12068	3.151000	0.50670	2.497000	0.84241	0.591000	0.81541	CGA	.	.	.	alt		0.493	FAM217B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268139.1	NM_022106		C	58519969	G	C	58519969	3	2	152	1	0	0	0	0	1	0	0	0	2098	1058	37	4	973	4	C20orf177	20	58519969	Missense_Mutation	SNP	G	TCGA-DW-7840-01A-11D-2136-08	16316366	58519969	4505551	78	9102											
KRTAP10-12	386685	hgsc.bcm.edu	37	chr21	46117131	46117131	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaccatgtccgtctgctcCagcgacctgagctatggcag	7	9	10	15	2	1	1	0	1	1	0	4	2	4	1	5	1	3	3	5	1	1	1	rs554572469|rs372249758	byFrequency	TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr21:46117131C>T	ENST00000400365.3	+	1	45	c.15C>T	c.(13-15)tcC>tcT	p.S5S	TSPEAR_ENST00000323084.4_Intron	NM_198699.1	NP_941972.1	P60413	KR10C_HUMAN	keratin associated protein 10-12	5						keratin filament (GO:0045095)				large_intestine(1)|lung(8)	9						CCGTCTGCTCCAGCGACCTGA	0.632																																					p.S5S		Atlas-SNP	.											.	KRTAP10-12	21	.	0			c.C15T						PASS	.	C	,	0,4330		0,0,2165	83	95	91		,15	2.2	1	21		91	1,8545		0,1,4272	no	intron,coding-synonymous	TSPEAR,KRTAP10-12	NM_144991.2,NM_198699.1	,	0,1,6437	TT,TC,CC		0.0117,0.0,0.0078	,	,5/246	46117131	1,12875	2165	4273	6438	SO:0001819	synonymous_variant	386685	exon1			CTGCTCCAGCGAC	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.15C>T	chr21.hg19:g.46117131C>T		217.0	0.0	.		188.0	70.0	.	NM_198699	B2RPA3	Silent	SNP	ENST00000400365.3	hg19	CCDS42967.1																																																																																			.	.	.	weak		0.632	KRTAP10-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128032.1	NM_198699		T	46117131	C	T	46117131	2	4	152	1	0	0	0	0	0	0	0	1	8515	581	21	2		2	KRTAP10-12	21	46117131	Silent	SNP	C	TCGA-DW-7840-01A-11D-2136-08		46117131	2012764	79	9103											
C21orf58	54058	hgsc.bcm.edu	37	chr21	47731374	47731374	+	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	aatatggaacacttaccttcCttaatacttcctgaccgttg	11	14	5	11	1	0	1	0	1	0	0	2	2	2	2	4	1	3	1	4	1	6	7			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr21:47731374C>A	ENST00000291691.7	-	6	1853	c.717G>T	c.(715-717)aaG>aaT	p.K239N	C21orf58_ENST00000472607.1_5'UTR|C21orf58_ENST00000397683.1_Missense_Mutation_p.K133N|C21orf58_ENST00000397679.1_Missense_Mutation_p.K133N|C21orf58_ENST00000397682.3_Missense_Mutation_p.K133N|C21orf58_ENST00000397680.1_Missense_Mutation_p.K133N	NM_058180.3	NP_478060.2	P58505	CU058_HUMAN	chromosome 21 open reading frame 58	239										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(1)|pancreas(1)	9	Breast(49;0.112)			Colorectal(79;0.239)		ACTTACCTTCCTTAATACTTC	0.488																																					p.K239N		Atlas-SNP	.											.	C21orf58	25	.	0			c.G717T						PASS	.						109	90	97					21																	47731374		2202	4299	6501	SO:0001583	missense	54058	exon6			ACCTTCCTTAATA		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.717G>T	chr21.hg19:g.47731374C>A	ENSP00000291691:p.Lys239Asn	22.0	0.0	.		19.0	9.0	.	NM_058180	B3KPI1	Missense_Mutation	SNP	ENST00000291691.7	hg19	CCDS13735.1	.	.	.	.	.	.	.	.	.	.	C	14.90	2.674609	0.47781	.	.	ENSG00000160298	ENST00000397683;ENST00000417060;ENST00000397682;ENST00000291691;ENST00000397679;ENST00000397680	T;T;T;T;T;T	0.68903	0.21;-0.34;0.21;-0.36;0.21;0.21	5.46	1.62	0.23740	.	0.148272	0.42548	D	0.000695	T	0.69806	0.3152	L	0.39898	1.24	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.79784	0.993;0.993;0.985	T	0.68911	-0.5284	10	0.87932	D	0	-21.1468	7.2122	0.25939	0.0:0.6518:0.0:0.3482	.	239;133;239	P58505;Q8N7N9;P58505-2	CU058_HUMAN;.;.	N	133;201;133;239;133;133	ENSP00000380799:K133N;ENSP00000402356:K201N;ENSP00000380798:K133N;ENSP00000291691:K239N;ENSP00000380796:K133N;ENSP00000380797:K133N	ENSP00000291691:K239N	K	-	3	2	C21orf58	46555802	0.998000	0.40836	1.000000	0.80357	0.392000	0.30506	0.249000	0.18216	0.711000	0.32018	-0.199000	0.12753	AAG	.	.	.	none		0.488	C21orf58-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207283.1	NM_058180		A	47731374	C	A	47731374	3	1	152	1	0	0	0	0	1	0	0	0	2131	680	24	4	263	4	C21orf58	21	47731374	Missense_Mutation	SNP	C	TCGA-DW-7840-01A-11D-2136-08	1614243	47731374	398521	80	9104											
ZNRF3	84133	hgsc.bcm.edu	37	chr22	29445939	29445939	+	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	tccaccttccgcagctccctCagcagcgactatgacccctt	7	9	6	19	2	1	1	1	1	0	0	4	2	4	1	6	0	3	3	6	0	1	3			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr22:29445939C>G	ENST00000544604.2	+	8	1945	c.1770C>G	c.(1768-1770)ctC>ctG	p.L590L	ZNRF3_ENST00000402174.1_Silent_p.L490L|ZNRF3_ENST00000332811.4_Silent_p.L490L|ZNRF3_ENST00000406323.3_Silent_p.L490L	NM_001206998.1	NP_001193927.1	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	590					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						GCAGCTCCCTCAGCAGCGACT	0.672																																					p.L590L		Atlas-SNP	.											.	ZNRF3	75	.	0			c.C1770G						PASS	.						54	62	59					22																	29445939		2076	4222	6298	SO:0001819	synonymous_variant	84133	exon8			CTCCCTCAGCAGC	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.1770C>G	chr22.hg19:g.29445939C>G		220.0	0.0	.		235.0	81.0	.	NM_001206998	B3KU18|Q6ICH1|Q6NTF8|Q8WU18	Silent	SNP	ENST00000544604.2	hg19	CCDS56225.1																																																																																			.	.	.	none		0.672	ZNRF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320943.2	XM_290972		G	29445939	C	G	29445939	2	3	152	1	0	0	0	0	0	0	0	1	18225	813	29	4		4	ZNRF3	22	29445939	Silent	SNP	C	TCGA-DW-7840-01A-11D-2136-08		29445939	21858627	81	9105											
RFPL3	10738	hgsc.bcm.edu	37	chr22	32754385	32754386	+	Frame_Shift_Del	DEL	GC	GC	-																															atcaaggaactggagcccaaGctgaagaagattctacagat																								rs9621427	byFrequency	TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr22:32754385_32754386delGC	ENST00000249007.4	+	1	532_533	c.327_328delGC	c.(325-330)aagctgfs	p.KL109fs	RFPL3S_ENST00000461833.1_5'Flank|RFPL3_ENST00000397468.1_Frame_Shift_Del_p.KL80fs|RFPL3_ENST00000382088.3_Frame_Shift_Del_p.KL80fs	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	109	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.						zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						TGGAGCCCAAGCTGAAGAAGAT	0.5																																					p.109_109del		Atlas-INDEL	.											.	RFPL3	91	.	0			c.326_327del						PASS	.																																			SO:0001589	frameshift_variant	10738	exon1			.	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.327_328delGC	chr22.hg19:g.32754385_32754386delGC	ENSP00000249007:p.Lys109fs	174.0	0.0	0		184.0	72.0	0.391304	NM_001098535	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Frame_Shift_Del	DEL	ENST00000249007.4	hg19	CCDS43011.1																																																																																			.	.	.	none		0.5	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604		-	32754386	GC	-	32754385	7	5	152	1	0	1	0	1	0	0	0	0	13268	962	34	0	329	0	RFPL3	22	32754385	Frame_Shift_Del	DEL	GC	TCGA-DW-7840-01A-11D-2136-08	3308446	32754385	18550181	82	9106											
EP300	2033	hgsc.bcm.edu	37	chr22	41574164	41574176	+	Frame_Shift_Del	DEL	CACAGCAGCAACT	CACAGCAGCAACT	-																															tggcctgccccagcagcaacCacagcagcaactccagccac																										TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	CACAGCAGCAACT	CACAGCAGCAACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chr22:41574164_41574176delCACAGCAGCAACT	ENST00000263253.7	+	31	7668_7680	c.6449_6461delCACAGCAGCAACT	c.(6448-6462)ccacagcagcaactcfs	p.PQQQL2150fs	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	2150	Interaction with HTLV-1 Tax.|Interaction with NCOA2.				apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						CAGCAGCAACCACAGCAGCAACTCCAGCCACCC	0.582			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.2150_2154del		Atlas-INDEL	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300	367	.	0			c.6448_6460del						PASS	.																																			SO:0001589	frameshift_variant	2033	exon31	Familial Cancer Database	Broad Thumb-Hallux syndrome	.	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.6449_6461delCACAGCAGCAACT	chr22.hg19:g.41574164_41574176delCACAGCAGCAACT	ENSP00000263253:p.Pro2150fs	120.0	0.0	0		106.0	42.0	0.396226	NM_001429	B1AKC2	Frame_Shift_Del	DEL	ENST00000263253.7	hg19	CCDS14010.1																																																																																			.	.	.	none		0.582	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		-	41574176	CACAGCAGCAACT	-	41574164	7	5	152	1	0	1	0	1	0	0	0	0	5150	594	21	0	6571	0	EP300	22	41574164	Frame_Shift_Del	DEL	CACAGCAGCAACT	TCGA-DW-7840-01A-11D-2136-08	8819779	41574164	9730402	83	9107											
SH3KBP1	30011	hgsc.bcm.edu	37	chrX	19626146	19626146	+	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	ttcagctctccttcccaccaGcctacgtcgatgcagtccta	7	11	6	17	2	2	0	1	0	1	0	6	1	4	0	5	0	4	2	5	0	2	4			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chrX:19626146G>T	ENST00000397821.3	-	9	1205	c.915C>A	c.(913-915)ggC>ggA	p.G305G	SH3KBP1_ENST00000379716.1_Silent_p.G67G|SH3KBP1_ENST00000379698.4_Silent_p.G268G|SH3KBP1_ENST00000379697.3_Silent_p.G349G|SH3KBP1_ENST00000477102.1_5'UTR|SH3KBP1_ENST00000541422.1_Silent_p.G44G	NM_031892.2	NP_114098.1	Q96B97	SH3K1_HUMAN	SH3-domain kinase binding protein 1	305	SH3 3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apoptotic process (GO:0006915)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|regulation of cell shape (GO:0008360)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(4)	29						CTTCCCACCAGCCTACGTCGA	0.537																																					p.G305G		Atlas-SNP	.											.	SH3KBP1	96	.	0			c.C915A						PASS	.						82	64	70					X																	19626146		2203	4300	6503	SO:0001819	synonymous_variant	30011	exon9			CCACCAGCCTACG	AF230904	CCDS14193.1, CCDS35213.1, CCDS55383.1	Xp22.1-p21.3	2008-02-05			ENSG00000147010	ENSG00000147010			13867	protein-coding gene	gene with protein product		300374				8889549, 7566098	Standard	NM_031892		Approved	CIN85	uc004czm.3	Q96B97	OTTHUMG00000021227	ENST00000397821.3:c.915C>A	chrX.hg19:g.19626146G>T		38.0	0.0	.		50.0	40.0	.	NM_031892	B7Z1D5|Q5JPT4|Q5JPT5|Q8IWX6|Q8IX98|Q96RN4|Q9NYR0	Silent	SNP	ENST00000397821.3	hg19	CCDS14193.1																																																																																			.	.	.	none		0.537	SH3KBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055992.1	NM_031892		T	19626146	G	T	19626146	2	4	152	1	0	0	0	0	0	0	0	1	14268	958	34	4		4	SH3KBP1	23	19626146	Silent	SNP	G	TCGA-DW-7840-01A-11D-2136-08		19626146	135644414	84	9108											
DCAF12L1	139170	hgsc.bcm.edu	37	chrX	125685498	125685498	+	Missense_Mutation	SNP	A	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	gggagccctgaccggtgcccAcagtgatgatgtggcggtag	7	7	17	10	2	0	3	0	3	0	0	0	4	0	4	3	4	2	1	3	4	1	1			TCGA-DW-7840-01A-11D-2136-08	TCGA-DW-7840-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9967ba89-7c82-4192-b2fa-ff7dfd8e1d38	0f3c3813-e814-4e7f-9a99-c3c2abc1d0bd	g.chrX:125685498A>C	ENST00000371126.1	-	1	1336	c.1094T>G	c.(1093-1095)gTg>gGg	p.V365G		NM_178470.4	NP_848565.2	Q5VU92	DC121_HUMAN	DDB1 and CUL4 associated factor 12-like 1	365										breast(1)|central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(39)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68						ACCGGTGCCCACAGTGATGAT	0.632																																					p.V365G		Atlas-SNP	.											.	DCAF12L1	135	.	0			c.T1094G						PASS	.						35	38	37					X																	125685498		2203	4299	6502	SO:0001583	missense	139170	exon1			GTGCCCACAGTGA	BC035674	CCDS14610.1	Xq25	2013-01-09	2009-07-17	2009-07-17	ENSG00000198889	ENSG00000198889		"WD repeat domain containing"	29395	protein-coding gene	gene with protein product			"WD repeat domain 40B"	WDR40B		12477932	Standard	NM_178470		Approved	KIAA1892L	uc004eul.3	Q5VU92	OTTHUMG00000022353	ENST00000371126.1:c.1094T>G	chrX.hg19:g.125685498A>C	ENSP00000360167:p.Val365Gly	48.0	0.0	.		66.0	55.0	.	NM_178470	Q8IYK3	Missense_Mutation	SNP	ENST00000371126.1	hg19	CCDS14610.1	.	.	.	.	.	.	.	.	.	.	A	14.03	2.414963	0.42817	.	.	ENSG00000198889	ENST00000371126	T	0.66099	-0.19	3.64	3.64	0.41730	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.343553	0.17248	N	0.181261	T	0.65491	0.2696	M	0.73962	2.25	0.58432	D	0.999996	D	0.54397	0.966	P	0.47299	0.543	T	0.70691	-0.4802	10	0.87932	D	0	.	9.8475	0.41037	1.0:0.0:0.0:0.0	.	365	Q5VU92	DC121_HUMAN	G	365	ENSP00000360167:V365G	ENSP00000360167:V365G	V	-	2	0	DCAF12L1	125513179	1.000000	0.71417	0.124000	0.21820	0.171000	0.22731	5.855000	0.69510	1.683000	0.51011	0.350000	0.21858	GTG	.	.	.	none		0.632	DCAF12L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058186.1	NM_178470		C	125685498	A	C	125685498	3	2	152	1	0	0	0	0	1	0	0	0	4266	159	6	5	301	5	DCAF12L1	23	125685498	Missense_Mutation	SNP	A	TCGA-DW-7840-01A-11D-2136-08	106059352	125685498	29585062	85	9109											
ERRFI1	54206	hgsc.bcm.edu	37	chr1	8075366	8075383	+	Splice_Site	DEL	AGAATACATACCAAGTGG	AGAATACATACCAAGTGG	-																															atcagattttcagaatacatAccaagtggtattaggcgctc																								rs147802351	byFrequency	TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	AGAATACATACCAAGTGG	AGAATACATACCAAGTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr1:8075366_8075383delAGAATACATACCAAGTGG	ENST00000377482.5	-	3	410_426	c.187_203delCCACTTGGTATGTATTCT	c.(187-204)ccacttggtatgtattct>t	p.PLGMYS63del	ERRFI1_ENST00000467067.1_In_Frame_Del_p.PLGMYS63del|ERRFI1_ENST00000469499.1_Intron|ERRFI1_ENST00000474874.1_Intron	NM_018948.3	NP_061821.1	Q9UJM3	ERRFI_HUMAN	ERBB receptor feedback inhibitor 1	63					lung alveolus development (GO:0048286)|lung epithelium development (GO:0060428)|lung vasculature development (GO:0060426)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of protein autophosphorylation (GO:0031953)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of keratinocyte differentiation (GO:0045616)|response to stress (GO:0006950)|skin morphogenesis (GO:0043589)	cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|Rho GTPase activator activity (GO:0005100)			breast(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(3)|ovary(1)|prostate(1)|skin(2)	16	Ovarian(185;0.06)|all_lung(157;0.151)	all_epithelial(116;1.76e-16)|all_lung(118;3.66e-05)|Lung NSC(185;0.000163)|Renal(390;0.000469)|Colorectal(325;0.0033)|Breast(348;0.0044)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.33e-70)|GBM - Glioblastoma multiforme(8;8.05e-37)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;6.9e-06)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.000985)|READ - Rectum adenocarcinoma(331;0.0642)		CAGAATACATACCAAGTGGTATTAGGCGCTCCTGAGCA	0.413																																					p.66_68del		Atlas-INDEL	.											.	ERRFI1	42	.	0			c.197_202del						PASS	.																																			SO:0001630	splice_region_variant	54206	exon3			.	BC025337	CCDS94.1	1p36.23	2008-02-05			ENSG00000116285	ENSG00000116285			18185	protein-coding gene	gene with protein product		608069				10749885, 2780291, 12226756, 11003669	Standard	NM_018948		Approved	MIG-6, GENE-33, RALT	uc001aoz.3	Q9UJM3	OTTHUMG00000001221	ENST00000377482.5:c.202+1CCACTTGGTATGTATTCT>-	chr1.hg19:g.8075366_8075383delAGAATACATACCAAGTGG		89.0	0.0	0		80.0	12.0	0.15	NM_018948	B2RDX9|Q9NTG9|Q9UD05	In_Frame_Del	DEL	ENST00000377482.5	hg19	CCDS94.1																																																																																			.	.	.	none		0.413	ERRFI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003617.1	NM_018948	In_Frame_Del	-	8075383	AGAATACATACCAAGTGG	-	8075366	8	5	153	1	0	1	0	1	0	0	1	0	5246	405	14	0	1192	0	ERRFI1	1	8075366	Splice_Site	DEL	AGAATACATACCAAGTGG	TCGA-DW-7841-01A-11D-2136-08		8075366	241175255	1	9110											
SYDE2	84144	hgsc.bcm.edu	37	chr1	85648788	85648788	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttatctggcaatgaccaatTaattgaactgccttttttca	11	17	5	8	0	2	2	1	2	1	0	2	2	2	2	2	1	2	1	2	1	5	7			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr1:85648788T>C	ENST00000341460.5	-	3	1586	c.1537A>G	c.(1537-1539)Aat>Gat	p.N513D		NM_032184.1	NP_115560.1	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	513					activation of Rho GTPase activity (GO:0032862)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	20				all cancers(265;0.0126)|Epithelial(280;0.0336)		AATGACCAATTAATTGAACTG	0.383																																					p.N513D		Atlas-SNP	.											.	SYDE2	135	.	0			c.A1537G						PASS	.						118	120	119					1																	85648788		1831	4083	5914	SO:0001583	missense	84144	exon3			ACCAATTAATTGA	AL834286	CCDS44169.1	1p22.3	2008-02-05		2005-08-09	ENSG00000097096	ENSG00000097096			25841	protein-coding gene	gene with protein product							Standard	NM_032184		Approved	FLJ13815	uc009wcm.3	Q5VT97	OTTHUMG00000009956	ENST00000341460.5:c.1537A>G	chr1.hg19:g.85648788T>C	ENSP00000340594:p.Asn513Asp	154.0	0.0	.		156.0	9.0	.	NM_032184	Q5VT96|Q8NDB8|Q9H8A6	Missense_Mutation	SNP	ENST00000341460.5	hg19	CCDS44169.1	.	.	.	.	.	.	.	.	.	.	T	16.85	3.237512	0.58886	.	.	ENSG00000097096	ENST00000341460	T	0.09073	3.02	5.41	3.06	0.35304	.	0.205916	0.48767	D	0.000174	T	0.04770	0.0129	M	0.68952	2.095	0.28339	N	0.921432	D;P	0.52996	0.957;0.787	B;B	0.44278	0.445;0.295	T	0.20207	-1.0282	10	0.56958	D	0.05	.	8.1975	0.31405	0.0:0.0701:0.1349:0.795	.	513;513	Q5VT97;Q5VT97-2	SYDE2_HUMAN;.	D	513	ENSP00000340594:N513D	ENSP00000340594:N513D	N	-	1	0	SYDE2	85421376	1.000000	0.71417	0.992000	0.48379	0.998000	0.95712	3.969000	0.56816	0.359000	0.24239	0.528000	0.53228	AAT	.	.	.	none		0.383	SYDE2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127989.2			C	85648788	T	C	85648788	3	2	153	1	0	0	0	0	1	0	0	0	15448	1754	61	3	2067	3	SYDE2	1	85648788	Missense_Mutation	SNP	T	TCGA-DW-7841-01A-11D-2136-08	77573422	85648788	163601833	2	9111											
LAMB3	3914	hgsc.bcm.edu	37	chr1	209800244	209800244	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggccacgtctccataggtcCggtctggacactggcggatg	6	9	14	12	3	2	0	0	0	2	0	4	2	3	2	3	6	0	0	3	6	1	1	rs144249951		TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr1:209800244C>T	ENST00000356082.4	-	13	1699	c.1565G>A	c.(1564-1566)cGg>cAg	p.R522Q	LAMB3_ENST00000391911.1_Missense_Mutation_p.R522Q|LAMB3_ENST00000367030.3_Missense_Mutation_p.R522Q	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	522	Laminin EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00460}.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		TCCATAGGTCCGGTCTGGACA	0.672													C|||	1	0.000199681	0	0	5008	,	,		20065	0		0.001	False		,,,				2504	0				p.R522Q		Atlas-SNP	.											.	LAMB3	136	.	0			c.G1565A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	54	45	48		1565,1565,1565	-0.5	0.1	1	dbSNP_134	48	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	LAMB3	NM_000228.2,NM_001017402.1,NM_001127641.1	43,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	522/1173,522/1173,522/1173	209800244	1,13005	2203	4300	6503	SO:0001583	missense	3914	exon13			TAGGTCCGGTCTG	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.1565G>A	chr1.hg19:g.209800244C>T	ENSP00000348384:p.Arg522Gln	68.0	0.0	.		73.0	15.0	.	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Missense_Mutation	SNP	ENST00000356082.4	hg19	CCDS1487.1	.	.	.	.	.	.	.	.	.	.	C	10.87	1.471943	0.26423	0.0	1.16E-4	ENSG00000196878	ENST00000391911;ENST00000356082;ENST00000367030	T;T;T	0.61158	0.13;0.13;0.13	5.7	-0.461	0.12172	EGF-like, laminin (3);	0.489478	0.22676	N	0.057015	T	0.41305	0.1153	L	0.35854	1.095	0.09310	N	1	B	0.28082	0.2	B	0.27076	0.076	T	0.24548	-1.0157	10	0.21540	T	0.41	.	10.3743	0.44073	0.0:0.6147:0.0:0.3853	.	522	Q13751	LAMB3_HUMAN	Q	522	ENSP00000375778:R522Q;ENSP00000348384:R522Q;ENSP00000355997:R522Q	ENSP00000348384:R522Q	R	-	2	0	LAMB3	207866867	0.000000	0.05858	0.055000	0.19348	0.114000	0.19823	0.138000	0.16016	-0.213000	0.10094	0.650000	0.86243	CGG	.	C|1.000;T|0.000	0.000	weak		0.672	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228		T	209800244	C	T	209800244	3	4	153	1	0	0	0	0	1	0	0	0	8619	652	23	1	1997	1	LAMB3	1	209800244	Missense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08	124151456	209800244	39450377	3	9112											
LRPPRC	10128	hgsc.bcm.edu	37	chr2	44207047	44207047	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcaggcaagagagaaccacaActacgtagtagaagcaaggc	17	4	11	9	1	1	3	1	0	0	3	1	4	1	3	1	2	4	4	1	2	8	3			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr2:44207047A>G	ENST00000260665.7	-	3	444	c.387T>C	c.(385-387)agT>agC	p.S129S	LRPPRC_ENST00000409946.1_Silent_p.S129S|LRPPRC_ENST00000409659.1_Silent_p.S129S	NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	129					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)				GAGAACCACAACTACGTAGTA	0.368																																					p.S129S		Atlas-SNP	.											.	LRPPRC	105	.	0			c.T387C						PASS	.						86	79	82					2																	44207047		2203	4300	6503	SO:0001819	synonymous_variant	10128	exon3			ACCACAACTACGT	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.387T>C	chr2.hg19:g.44207047A>G		50.0	0.0	.		75.0	23.0	.	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Silent	SNP	ENST00000260665.7	hg19	CCDS33189.1																																																																																			.	.	.	none		0.368	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259		G	44207047	A	G	44207047	2	3	153	1	0	0	0	0	0	0	0	1	8972	40	2	3		3	LRPPRC	2	44207047	Silent	SNP	A	TCGA-DW-7841-01A-11D-2136-08		44207047	198992326	4	9113											
ACVR2A	92	hgsc.bcm.edu	37	chr2	148684830	148684834	+	Frame_Shift_Del	DEL	AATCT	AATCT	-																															tgttgactttcctcccaaagAatctagtctatgatggttgc																										TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	AATCT	AATCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr2:148684830_148684834delAATCT	ENST00000241416.7	+	11	2165_2169	c.1529_1533delAATCT	c.(1528-1533)gaatctfs	p.ES510fs	ACVR2A_ENST00000404590.1_Frame_Shift_Del_p.ES510fs|ACVR2A_ENST00000495775.1_3'UTR|ACVR2A_ENST00000535787.1_Frame_Shift_Del_p.ES402fs	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	510					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		CCTCCCAAAGAATCTAGTCTATGAT	0.395																																					p.510_511del		Atlas-INDEL	.											ACVR2A,NS,carcinoma,0,2	ACVR2A	125	.	0			c.1528_1532del						PASS	.																																			SO:0001589	frameshift_variant	92	exon11			.		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.1529_1533delAATCT	chr2.hg19:g.148684830_148684834delAATCT	ENSP00000241416:p.Glu510fs	49.0	0.0	0		80.0	17.0	0.2125	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Frame_Shift_Del	DEL	ENST00000241416.7	hg19	CCDS33301.1																																																																																			.	.	.	none		0.395	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616		-	148684834	AATCT	-	148684830	7	5	153	1	0	1	0	1	0	0	0	0	223	246	9	0	1571	0	ACVR2A	2	148684830	Frame_Shift_Del	DEL	AATCT	TCGA-DW-7841-01A-11D-2136-08	104477783	148684830	94514543	5	9114											
SCN7A	6332	hgsc.bcm.edu	37	chr2	167284362	167284362	+	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	taaaccaattgttctctacaAtcttgcagcaggttttcctg	10	15	6	10	0	2	0	0	0	2	0	4	0	3	0	2	1	4	4	2	1	5	7			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr2:167284362A>T	ENST00000409855.1	-	17	2915	c.2789T>A	c.(2788-2790)aTt>aAt	p.I930N		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	930					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)	GTTCTCTACAATCTTGCAGCA	0.458																																					p.I930N		Atlas-SNP	.											.	SCN7A	410	.	0			c.T2789A						PASS	.						134	128	130					2																	167284362		1885	4118	6003	SO:0001583	missense	6332	exon17			TCTACAATCTTGC	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.2789T>A	chr2.hg19:g.167284362A>T	ENSP00000386796:p.Ile930Asn	30.0	0.0	.		46.0	15.0	.	NM_002976		Missense_Mutation	SNP	ENST00000409855.1	hg19	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.242192	0.79912	.	.	ENSG00000136546	ENST00000409855;ENST00000259060	D	0.89617	-2.54	5.02	5.02	0.67125	Sodium ion transport-associated (1);	0.000000	0.64402	D	0.000008	D	0.94932	0.8361	M	0.89904	3.07	0.52501	D	0.99995	D	0.76494	0.999	D	0.72338	0.977	D	0.95644	0.8701	10	0.87932	D	0	.	12.9965	0.58650	1.0:0.0:0.0:0.0	.	930	Q01118	SCN7A_HUMAN	N	930	ENSP00000386796:I930N	ENSP00000259060:I930N	I	-	2	0	SCN7A	166992608	1.000000	0.71417	0.999000	0.59377	0.861000	0.49209	7.324000	0.79115	2.228000	0.72767	0.482000	0.46254	ATT	.	.	.	none		0.458	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1			T	167284362	A	T	167284362	3	4	153	1	0	0	0	0	1	0	0	0	13936	101	4	5	2295	5	SCN7A	2	167284362	Missense_Mutation	SNP	A	TCGA-DW-7841-01A-11D-2136-08	18599532	167284362	75915011	6	9115											
SHISA5	51246	hgsc.bcm.edu	37	chr3	48510782	48510782	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagggtctcgtggtaggcCggtgggcccatgggctgggc	3	7	20	11	2	1	0	0	0	1	0	2	0	1	0	3	7	0	2	3	7	1	1			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr3:48510782C>T	ENST00000296444.2	-	5	957	c.621G>A	c.(619-621)ccG>ccA	p.P207P	SHISA5_ENST00000465449.1_5'UTR|SHISA5_ENST00000443308.2_Silent_p.P200P|SHISA5_ENST00000444115.1_Silent_p.P176P|SHISA5_ENST00000426002.1_Silent_p.P104P|SHISA5_ENST00000442747.1_Silent_p.P176P	NM_001272065.1|NM_016479.3	NP_001258994.1|NP_057563.3	Q8N114	SHSA5_HUMAN	shisa family member 5	207	Pro-rich.				intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)	signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			large_intestine(1)|lung(1)	2						CGTGGTAGGCCGGTGGGCCCA	0.657																																					p.P207P		Atlas-SNP	.											.	SHISA5	10	.	0			c.G621A						PASS	.						97	95	96					3																	48510782		2203	4300	6503	SO:0001819	synonymous_variant	51246	exon5			GTAGGCCGGTGGG	AF520698	CCDS2770.1, CCDS63621.1, CCDS63622.1, CCDS63623.1	3p21.31	2013-07-31	2013-07-31		ENSG00000164054	ENSG00000164054		"Shisa homologs"	30376	protein-coding gene	gene with protein product		607290	"shisa homolog 5 (Xenopus laevis)"			11042152, 12135983	Standard	NM_016479		Approved	SCOTIN, hShisa5	uc011bbk.1	Q8N114	OTTHUMG00000133529	ENST00000296444.2:c.621G>A	chr3.hg19:g.48510782C>T		148.0	0.0	.		135.0	30.0	.	NM_016479	B3KW99|F8W9N8|Q69YY9|Q7Z433|Q8NHL9|Q96MW8|Q9BV58	Silent	SNP	ENST00000296444.2	hg19	CCDS2770.1	.	.	.	.	.	.	.	.	.	.	C	3.542	-0.093509	0.07053	.	.	ENSG00000164054	ENST00000536074	.	.	.	5.05	-10.1	0.00402	.	.	.	.	.	T	0.47563	0.1452	.	.	.	0.42593	D	0.993257	.	.	.	.	.	.	T	0.60895	-0.7172	5	0.87932	D	0	-31.2522	1.378	0.02225	0.2716:0.1192:0.152:0.4572	.	.	.	.	Q	28	.	ENSP00000445956:R28Q	R	-	2	0	SHISA5	48485786	0.000000	0.05858	0.031000	0.17742	0.469000	0.32828	-4.182000	0.00278	-2.526000	0.00494	-0.251000	0.11542	CGG	.	.	.	none		0.657	SHISA5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257504.3	NM_016479		T	48510782	C	T	48510782	2	4	153	1	0	0	0	0	0	0	0	1	14296	639	23	1		1	SHISA5	3	48510782	Silent	SNP	C	TCGA-DW-7841-01A-11D-2136-08		48510782	149511648	7	9116											
SLC35A5	55032	hgsc.bcm.edu	37	chr3	112282282	112282290	+	In_Frame_Del	DEL	TATGCTCCT	TATGCTCCT	-																															gtgctgtagtcatcctgtaaTatgctccttgtcaacaatgt																								rs201886373|rs377335674|rs369182750		TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	TATGCTCCT	TATGCTCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr3:112282282_112282290delTATGCTCCT	ENST00000492406.1	+	2	315_323	c.32_40delTATGCTCCT	c.(31-42)atatgctccttg>atg	p.11_14ICSL>M	ATG3_ENST00000402314.2_5'Flank|ATG3_ENST00000283290.5_5'Flank|ATG3_ENST00000495756.1_5'Flank	NM_017945.2	NP_060415.1	Q9BS91	S35A5_HUMAN	solute carrier family 35, member A5	11					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						CATCCTGTAATATGCTCCTTGTCAACAAT	0.378																																					p.11_13del		Atlas-INDEL	.											.	SLC35A5	40	.	0			c.31_39del						PASS	.																																			SO:0001651	inframe_deletion	55032	exon2			.	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.32_40delTATGCTCCT	chr3.hg19:g.112282282_112282290delTATGCTCCT	ENSP00000417654:p.Ile11_Leu14delinsMet	98.0	0.0	0		89.0	19.0	0.213483	NM_017945	D3DN66|Q69YY6|Q6ZMD6|Q9NWM9	In_Frame_Del	DEL	ENST00000492406.1	hg19	CCDS2967.1																																																																																			.	.	.	none		0.378	SLC35A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354184.1	NM_017945		-	112282290	TATGCTCCT	-	112282282	7	5	153	1	0	1	0	1	0	0	0	0	14587	1406	49	0	34	0	SLC35A5	3	112282282	In_Frame_Del	DEL	TATGCTCCT	TCGA-DW-7841-01A-11D-2136-08	63771500	112282282	85740148	8	9117											
KPNA4	3840	hgsc.bcm.edu	37	chr3	160249310	160249310	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccagattttattaagtcaTcaattggtggatttcgatca	11	17	7	6	1	3	1	3	0	0	1	5	3	4	2	1	2	0	0	1	2	3	6			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr3:160249310T>C	ENST00000334256.4	-	6	628	c.323A>G	c.(322-324)gAt>gGt	p.D108G		NM_002268.4	NP_002259.1	O00629	IMA3_HUMAN	karyopherin alpha 4 (importin alpha 3)	108					cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	protein transporter activity (GO:0008565)			breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)	22			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)			TATTAAGTCATCAATTGGTGG	0.269																																					p.D108G		Atlas-SNP	.											.	KPNA4	50	.	0			c.A323G						PASS	.						86	97	93					3																	160249310		2203	4293	6496	SO:0001583	missense	3840	exon6			AAGTCATCAATTG	AB002533	CCDS3191.1	3q25.33	2013-02-14			ENSG00000186432	ENSG00000186432		"Importins", "Armadillo repeat containing"	6397	protein-coding gene	gene with protein product		602970				9168958, 9395085	Standard	NM_002268		Approved	QIP1, SRP3, IPOA3, MGC12217, MGC26703	uc003fdn.3	O00629	OTTHUMG00000159033	ENST00000334256.4:c.323A>G	chr3.hg19:g.160249310T>C	ENSP00000334373:p.Asp108Gly	153.0	0.0	.		139.0	31.0	.	NM_002268	A8K4S6|D3DNM2|O00190	Missense_Mutation	SNP	ENST00000334256.4	hg19	CCDS3191.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.773313	0.90108	.	.	ENSG00000186432	ENST00000334256	T	0.32272	1.46	5.44	5.44	0.79542	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.65688	0.2715	M	0.93328	3.405	0.80722	D	1	D	0.67145	0.996	D	0.72075	0.976	T	0.75769	-0.3201	10	0.72032	D	0.01	.	15.6624	0.77197	0.0:0.0:0.0:1.0	.	108	O00629	IMA4_HUMAN	G	108	ENSP00000334373:D108G	ENSP00000334373:D108G	D	-	2	0	KPNA4	161732004	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.797000	0.85911	2.284000	0.76573	0.528000	0.53228	GAT	.	.	.	none		0.269	KPNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352960.1	NM_002268		C	160249310	T	C	160249310	3	2	153	1	0	0	0	0	1	0	0	0	8439	1435	50	3	1290	3	KPNA4	3	160249310	Missense_Mutation	SNP	T	TCGA-DW-7841-01A-11D-2136-08	47967028	160249310	37773120	9	9118											
SLC30A9	10463	hgsc.bcm.edu	37	chr4	42037333	42037333	+	Missense_Mutation	SNP	T	T	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	tattaagagaatacagagatTtcttgggaaataccaaggta	17	11	9	4	0	1	2	0	0	1	2	1	5	1	3	1	2	2	1	1	2	8	7			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr4:42037333T>G	ENST00000264451.7	+	7	832	c.652T>G	c.(652-654)Ttc>Gtc	p.F218V		NM_006345.3	NP_006336.3	Q6PML9	ZNT9_HUMAN	solute carrier family 30 (zinc transporter), member 9	218					nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|zinc ion transport (GO:0006829)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cation transmembrane transporter activity (GO:0008324)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F218V(1)		central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						ATACAGAGATTTCTTGGGAAA	0.299																																					p.F218V		Atlas-SNP	.											SLC30A9,NS,carcinoma,0,1	SLC30A9	58	.	1	Substitution - Missense(1)	kidney(1)	c.T652G						PASS	.						56	62	60					4																	42037333		2200	4282	6482	SO:0001583	missense	10463	exon7			AGAGATTTCTTGG	AF006621	CCDS3465.1	4p13	2013-05-22	2003-09-09	2003-09-10	ENSG00000014824	ENSG00000014824		"Solute carriers"	1329	protein-coding gene	gene with protein product	"GRIP1-dependent nuclear receptor coactivator"	604604	"chromosome 4 open reading frame 1"	C4orf1		10409434, 11906820	Standard	NM_006345		Approved	HUEL, ZNT9, GAC63	uc003gwl.3	Q6PML9	OTTHUMG00000099387	ENST00000264451.7:c.652T>G	chr4.hg19:g.42037333T>G	ENSP00000264451:p.Phe218Val	123.0	0.0	.		139.0	33.0	.	NM_006345	Q4W5B6|Q7Z5I7|Q8TBB2|Q9Y6R2	Missense_Mutation	SNP	ENST00000264451.7	hg19	CCDS3465.1	.	.	.	.	.	.	.	.	.	.	T	9.461	1.093124	0.20471	.	.	ENSG00000014824	ENST00000264451;ENST00000536881	T	0.54866	0.55	4.48	4.48	0.54585	.	0.000000	0.85682	D	0.000000	T	0.37732	0.1014	L	0.34521	1.04	0.58432	D	0.999996	P	0.43352	0.804	B	0.38842	0.283	T	0.13872	-1.0493	10	0.16420	T	0.52	-12.6044	11.5359	0.50636	0.0:0.0:0.0:1.0	.	218	Q6PML9	ZNT9_HUMAN	V	218;46	ENSP00000264451:F218V	ENSP00000264451:F218V	F	+	1	0	SLC30A9	41732090	1.000000	0.71417	0.997000	0.53966	0.962000	0.63368	4.876000	0.63079	2.003000	0.58678	0.397000	0.26171	TTC	.	.	.	none		0.299	SLC30A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216842.3			G	42037333	T	G	42037333	3	3	153	1	0	0	0	0	1	0	0	0	14575	1841	64	5	678	5	SLC30A9	4	42037333	Missense_Mutation	SNP	T	TCGA-DW-7841-01A-11D-2136-08		42037333	149116943	10	9119											
ZCCHC9	84240	hgsc.bcm.edu	37	chr5	80600585	80600585	+	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	actgatgaaattatgaccagGtgggcccgagttagtaccac	12	9	11	9	1	0	3	0	3	0	0	0	4	0	3	3	2	1	2	3	2	4	3			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr5:80600585G>A	ENST00000254037.2	+	1	3164	c.9G>A	c.(7-9)agG>agA	p.R3R	ZCCHC9_ENST00000506458.1_Intron|ZCCHC9_ENST00000407610.3_Silent_p.R3R|ZCCHC9_ENST00000438268.2_Silent_p.R3R|ZCCHC9_ENST00000380199.5_Silent_p.R3R			Q8N567	ZCHC9_HUMAN	zinc finger, CCHC domain containing 9	3					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)		TTATGACCAGGTGGGCCCGAG	0.423																																					p.R3R		Atlas-SNP	.											ZCCHC9,NS,carcinoma,0,1	ZCCHC9	26	.	0			c.G9A						PASS	.						81	76	77					5																	80600585		2203	4300	6503	SO:0001819	synonymous_variant	84240	exon2			GACCAGGTGGGCC	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.9G>A	chr5.hg19:g.80600585G>A		83.0	0.0	.		124.0	34.0	.	NM_001131036	B2RAE7|Q9H027	Silent	SNP	ENST00000254037.2	hg19	CCDS4054.1																																																																																			.	.	.	none		0.423	ZCCHC9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239213.1	NM_032280		A	80600585	G	A	80600585	2	1	153	1	0	0	0	0	0	0	0	1	17607	1252	44	2		2	ZCCHC9	5	80600585	Silent	SNP	G	TCGA-DW-7841-01A-11D-2136-08		80600585	100314675	11	9120											
PCDHGA6	56109	hgsc.bcm.edu	37	chr5	140753888	140753888	+	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	agcttttctctctgaatccgCgaaacggcagcttggtcacc	8	11	9	13	3	3	1	1	1	2	0	5	2	4	1	2	2	3	3	2	2	2	3			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr5:140753888C>T	ENST00000517434.1	+	1	238	c.238C>T	c.(238-240)Cga>Tga	p.R80*	PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA5_ENST00000518069.1_Intron	NM_018919.2|NM_032086.1	NP_061742.1|NP_114475.1	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6	80	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|large_intestine(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTGAATCCGCGAAACGGCAG	0.577																																					p.R80X		Atlas-SNP	.											.	PCDHGA6	219	.	0			c.C238T						PASS	.						51	58	55					5																	140753888		2200	4300	6500	SO:0001587	stop_gained	56109	exon1			AATCCGCGAAACG	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.238C>T	chr5.hg19:g.140753888C>T	ENSP00000429601:p.Arg80*	84.0	0.0	.		103.0	36.0	.	NM_018919	A6H8K7|B2RN55|Q9Y5D1	Nonsense_Mutation	SNP	ENST00000517434.1	hg19	CCDS54926.1	.	.	.	.	.	.	.	.	.	.	.	12.46	1.943892	0.34283	.	.	ENSG00000253731	ENST00000517434	.	.	.	5.09	-0.279	0.12890	.	0.000000	0.29253	U	0.012681	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	1.6064	0.02684	0.3336:0.2219:0.2969:0.1477	.	.	.	.	X	80	.	ENSP00000429601:R80X	R	+	1	2	PCDHGA6	140734072	0.000000	0.05858	0.001000	0.08648	0.189000	0.23516	-0.696000	0.05104	0.091000	0.17302	0.650000	0.86243	CGA	.	.	.	none		0.577	PCDHGA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374743.1	NM_018919		T	140753888	C	T	140753888	4	4	153	1	0	0	0	0	0	1	0	0	11565	760	27	1	240	1	PCDHGA6	5	140753888	Nonsense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08	60153303	140753888	40161372	12	9121											
PWWP2A	114825	hgsc.bcm.edu	37	chr5	159520919	159520919	+	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	aagctcagctcgggatgcggGacaggagaagggtcatcggg	10	5	18	8	3	2	1	2	0	0	1	4	4	2	3	0	5	3	2	0	5	2	0			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr5:159520919G>A	ENST00000307063.7	-	2	772	c.738C>T	c.(736-738)gtC>gtT	p.V246V	PWWP2A_ENST00000523662.1_Silent_p.V246V|PWWP2A_ENST00000456329.3_Silent_p.V246V	NM_001130864.1	NP_001124336.1	Q96N64	PWP2A_HUMAN	PWWP domain containing 2A	246	Pro-rich.									kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CGGGATGCGGGACAGGAGAAG	0.512																																					p.V246V		Atlas-SNP	.											.	PWWP2A	64	.	0			c.C738T						PASS	.						115	114	114					5																	159520919		1983	4144	6127	SO:0001819	synonymous_variant	114825	exon2			ATGCGGGACAGGA		CCDS47331.1, CCDS47332.1, CCDS58990.1	5q33.3	2011-03-23			ENSG00000170234	ENSG00000170234			29406	protein-coding gene	gene with protein product							Standard	NM_052927		Approved	KIAA1935	uc011ded.2	Q96N64	OTTHUMG00000163546	ENST00000307063.7:c.738C>T	chr5.hg19:g.159520919G>A		111.0	0.0	.		116.0	33.0	.	NM_052927	G5EA07|Q2HJJ2|Q8IYR3|Q96PV3	Silent	SNP	ENST00000307063.7	hg19	CCDS47332.1																																																																																			.	.	.	none		0.512	PWWP2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374092.1			A	159520919	G	A	159520919	2	1	153	1	0	0	0	0	0	0	0	1	12858	1161	41	2		2	PWWP2A	5	159520919	Silent	SNP	G	TCGA-DW-7841-01A-11D-2136-08	18767031	159520919	21394341	13	9122											
ANKS1A	23294	hgsc.bcm.edu	37	chr6	35047314	35047314	+	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	tgaaggctctgggttatgacGggaacagcccccctagcgtg	8	8	14	11	2	1	2	0	2	1	0	1	3	1	3	3	3	3	2	3	3	4	2	rs370130506		TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr6:35047314G>T	ENST00000360359.3	+	15	2443	c.2305G>T	c.(2305-2307)Ggg>Tgg	p.G769W	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	769					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						GGGTTATGACGGGAACAGCCC	0.597																																					p.G769W		Atlas-SNP	.											.	ANKS1A	123	.	0			c.G2305T						PASS	.						92	79	83					6																	35047314		2203	4300	6503	SO:0001583	missense	23294	exon15			TATGACGGGAACA	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.2305G>T	chr6.hg19:g.35047314G>T	ENSP00000353518:p.Gly769Trp	92.0	0.0	.		93.0	4.0	.	NM_015245	A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7	Missense_Mutation	SNP	ENST00000360359.3	hg19	CCDS4798.1	.	.	.	.	.	.	.	.	.	.	G	18.38	3.610918	0.66558	.	.	ENSG00000064999	ENST00000360359;ENST00000373990	T	0.51817	0.69	5.11	5.11	0.69529	Sterile alpha motif domain (1);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.000000	0.50627	D	0.000119	T	0.60958	0.2309	M	0.62723	1.935	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.97110	0.997;0.999;1.0	T	0.64647	-0.6358	10	0.87932	D	0	-24.9218	17.075	0.86584	0.0:0.0:1.0:0.0	.	95;95;769	Q49AR9;E7EM84;Q92625	.;.;ANS1A_HUMAN	W	769;95	ENSP00000353518:G769W	ENSP00000353518:G769W	G	+	1	0	ANKS1A	35155292	1.000000	0.71417	0.560000	0.28344	0.348000	0.29142	8.954000	0.93051	2.519000	0.84933	0.561000	0.74099	GGG	.	.	.	alt		0.597	ANKS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040262.1	XM_166478		T	35047314	G	T	35047314	3	4	153	1	0	0	0	0	1	0	0	0	688	1116	39	4	2363	4	ANKS1A	6	35047314	Missense_Mutation	SNP	G	TCGA-DW-7841-01A-11D-2136-08		35047314	136067753	14	9123											
TNFAIP3	7128	hgsc.bcm.edu	37	chr6	138200108	138200108	+	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	gcaacttcacgccagccacgCcccagaccacacaaggcact	12	3	7	19	2	1	1	1	0	0	1	1	1	1	1	5	1	2	2	5	1	2	1			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr6:138200108C>T	ENST00000237289.4	+	7	1592	c.1526C>T	c.(1525-1527)gCc>gTc	p.A509V		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	509	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)|p.A506fs*21(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)		GCCAGCCACGCCCCAGACCAC	0.562			"D, N, F"		"marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"																																p.A509V	GBM(130;153 1739 22295 28918 47987)	Atlas-SNP	.		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.C1526T						PASS	.						53	57	56					6																	138200108		2203	4300	6503	SO:0001583	missense	7128	exon7			GCCACGCCCCAGA	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.1526C>T	chr6.hg19:g.138200108C>T	ENSP00000237289:p.Ala509Val	74.0	0.0	.		73.0	17.0	.	NM_001270507	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Missense_Mutation	SNP	ENST00000237289.4	hg19	CCDS5187.1	.	.	.	.	.	.	.	.	.	.	C	8.783	0.928799	0.18131	.	.	ENSG00000118503	ENST00000237289;ENST00000535574;ENST00000544646	T	0.23950	1.88	5.88	0.17	0.15021	.	2.360930	0.01293	N	0.010090	T	0.06005	0.0156	L	0.29908	0.895	0.09310	N	1	B	0.20671	0.047	B	0.19148	0.024	T	0.21690	-1.0238	10	0.31617	T	0.26	-3.2172	3.4733	0.07575	0.336:0.2854:0.3007:0.078	.	509	P21580	TNAP3_HUMAN	V	509	ENSP00000237289:A509V	ENSP00000237289:A509V	A	+	2	0	TNFAIP3	138241801	0.000000	0.05858	0.001000	0.08648	0.055000	0.15305	0.071000	0.14594	0.072000	0.16694	0.655000	0.94253	GCC	.	.	.	none		0.562	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1			T	138200108	C	T	138200108	3	4	153	1	0	0	0	0	1	0	0	0	16286	739	26	2	1548	2	TNFAIP3	6	138200108	Missense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08	103152794	138200108	32914959	15	9124											
CBX3	11335	hgsc.bcm.edu	37	chr7	26251700	26251700	+	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	atttttctttttcttaaaacAggaaagattcagatgaggca	14	15	7	5	0	3	3	1	1	2	2	3	4	3	4	0	2	1	1	0	2	3	6			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr7:26251700A>T	ENST00000337620.4	+	6	853		c.e6-1		CBX3_ENST00000409747.1_Splice_Site|CBX3_ENST00000396386.2_Splice_Site	NM_007276.4	NP_009207.2	Q13185	CBX3_HUMAN	chromobox homolog 3						chromatin remodeling (GO:0006338)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome, centromeric region (GO:0000779)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nuclear pericentric heterochromatin (GO:0031618)|nucleus (GO:0005634)|spindle (GO:0005819)	enzyme binding (GO:0019899)|histone methyltransferase binding (GO:1990226)|identical protein binding (GO:0042802)|protein domain specific binding (GO:0019904)			endometrium(4)|large_intestine(2)|lung(2)|ovary(1)	9						TTCTTAAAACAGGAAAGATTC	0.358																																					.		Atlas-SNP	.											.	CBX3	25	.	0			c.426-2A>T						PASS	.						49	50	50					7																	26251700		2203	4300	6503	SO:0001630	splice_region_variant	11335	exon6			TAAAACAGGAAAG	U26312	CCDS5398.1	7p15.2	2010-07-06	2010-06-24		ENSG00000122565	ENSG00000122565			1553	protein-coding gene	gene with protein product	"HP1 gamma homolog (Drosophila)"	604477	"chromobox homolog 3 (Drosophila HP1 gamma)"			8663349	Standard	NM_016587		Approved	HP1Hs-gamma	uc003sxu.3	Q13185	OTTHUMG00000022911	ENST00000337620.4:c.426-1A>T	chr7.hg19:g.26251700A>T		58.0	0.0	.		68.0	5.0	.	NM_007276	Q96CD7|Q99409|Q9BVS3|Q9P0Z6	Splice_Site	SNP	ENST00000337620.4	hg19	CCDS5398.1	.	.	.	.	.	.	.	.	.	.	A	17.47	3.397838	0.62177	.	.	ENSG00000122565	ENST00000337620;ENST00000396386	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9596	0.79918	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CBX3	26218225	1.000000	0.71417	0.985000	0.45067	0.622000	0.37654	9.240000	0.95396	2.231000	0.72958	0.533000	0.62120	.	.	.	.	none		0.358	CBX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214117.1	NM_007276	Intron	T	26251700	A	T	26251700	5	4	153	1	0	0	0	0	0	0	1	0	2721	202	7	5	442	5	CBX3	7	26251700	Splice_Site	SNP	A	TCGA-DW-7841-01A-11D-2136-08		26251700	132886963	16	9125											
ADAM9	8754	hgsc.bcm.edu	37	chr8	38880710	38880711	+	Frame_Shift_Ins	INS	-	-	GG																															atattcgaattgtgctagttINSggactggagatttggaccaa																										TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr8:38880710_38880711insGG	ENST00000487273.2	+	9	858_859	c.780_781insGG	c.(781-783)ggafs	p.G261fs		NM_003816.2	NP_003807.1	Q13443	ADAM9_HUMAN	ADAM metallopeptidase domain 9	261	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				activation of MAPKK activity (GO:0000186)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to lipopolysaccharide (GO:0071222)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein secretion (GO:0050714)|response to calcium ion (GO:0051592)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to laminar fluid shear stress (GO:0034616)|response to manganese ion (GO:0010042)|response to tumor necrosis factor (GO:0034612)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)	collagen binding (GO:0005518)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein kinase C binding (GO:0005080)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)			TTGTGCTAGTTGGACTGGAGAT	0.376																																					p.V260fs		Atlas-INDEL	.											.	ADAM9	66	.	0			c.780_781insGG						PASS	.																																			SO:0001589	frameshift_variant	8754	exon9			.	U41766	CCDS6112.1	8p11.23	2011-03-18	2010-06-24		ENSG00000168615	ENSG00000168615		"ADAM metallopeptidase domain containing"	216	protein-coding gene	gene with protein product	"meltrin gamma"	602713	"a disintegrin and metalloproteinase domain 9 (meltrin gamma)", "cone rod dystrophy 9"	CORD9		8647900, 11581183, 19409519	Standard	NR_027638		Approved	MDC9, KIAA0021, MCMP, Mltng	uc003xmr.3	Q13443	OTTHUMG00000159783	ENST00000487273.2:c.781_782dupGG	chr8.hg19:g.38880711_38880712dupGG	ENSP00000419446:p.Gly261fs	84.0	0.0	0		80.0	26.0	0.325	NM_003816	B7ZLN7|Q10718|Q8NFM6	Frame_Shift_Ins	INS	ENST00000487273.2	hg19	CCDS6112.1																																																																																			.	.	.	none		0.376	ADAM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357291.2			GG	38880711	-	GG	38880710	7	5	153	1	0	1	1	0	0	0	0	0	253	1799	63	0	814	0	ADAM9	8	38880710	Frame_Shift_Ins	INS	-	TCGA-DW-7841-01A-11D-2136-08		38880710	107483312	17	9126											
FAM91A1	157769	hgsc.bcm.edu	37	chr8	124787418	124787418	+	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	aagaaagatgaacgcagataCtatgaggaactgctaaagta	19	7	10	5	1	0	5	0	2	0	3	0	6	0	6	0	1	4	3	0	1	9	4			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr8:124787418C>A	ENST00000334705.7	+	3	435	c.189C>A	c.(187-189)taC>taA	p.Y63*	FAM91A1_ENST00000521166.1_Nonsense_Mutation_p.Y63*	NM_144963.2	NP_659400	Q658Y4	F91A1_HUMAN	family with sequence similarity 91, member A1	63										breast(4)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28	Lung NSC(37;8.76e-13)|Ovarian(258;0.00744)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00192)			AACGCAGATACTATGAGGAAC	0.363																																					p.Y63X		Atlas-SNP	.											.	FAM91A1	77	.	0			c.C189A						PASS	.						91	80	84					8																	124787418		1882	4109	5991	SO:0001587	stop_gained	157769	exon3			CAGATACTATGAG	AK074370	CCDS6346.2	8q24.13	2005-10-04			ENSG00000176853	ENSG00000176853			26306	protein-coding gene	gene with protein product						12477932	Standard	XM_005250806		Approved	FLJ23790	uc003yqv.3	Q658Y4	OTTHUMG00000133021	ENST00000334705.7:c.189C>A	chr8.hg19:g.124787418C>A	ENSP00000335082:p.Tyr63*	56.0	0.0	.		74.0	33.0	.	NM_144963	B6YY23|Q658T5|Q8TE89	Nonsense_Mutation	SNP	ENST00000334705.7	hg19	CCDS6346.2	.	.	.	.	.	.	.	.	.	.	C	28.1	4.892276	0.91889	.	.	ENSG00000176853	ENST00000521166;ENST00000334705;ENST00000395537	.	.	.	5.33	3.52	0.40303	.	0.000000	0.64402	U	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.0665	0.42306	0.0:0.7624:0.0:0.2376	.	.	.	.	X	63	.	ENSP00000335082:Y63X	Y	+	3	2	FAM91A1	124856599	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	1.080000	0.30779	0.619000	0.30197	0.655000	0.94253	TAC	.	.	.	none		0.363	FAM91A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256607.1	NM_144963		A	124787418	C	A	124787418	4	1	153	1	0	0	0	0	0	1	0	0	5658	576	20	4	199	4	FAM91A1	8	124787418	Nonsense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08	85906708	124787418	21576604	18	9127											
SUSD1	64420	hgsc.bcm.edu	37	chr9	114820886	114820886	+	Frame_Shift_Del	DEL	C	C	-																															catcagcatcagaggcgttgCtaaagaaggaggaagcgcct																										TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr9:114820886delC	ENST00000374270.3	-	14	2103	c.1931delG	c.(1930-1932)agcfs	p.S644fs	SUSD1_ENST00000374264.2_Frame_Shift_Del_p.S644fs|SUSD1_ENST00000374263.3_Frame_Shift_Del_p.S644fs	NM_022486.3	NP_071931.2	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1	644						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)		SUSD1/ROD1(2)	central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						AGAGGCGTTGCTAAAGAAGGA	0.473																																					p.S644fs		Atlas-INDEL	.											.	SUSD1	51	.	0			c.1932delC						PASS	.						114	111	112					9																	114820886		2203	4300	6503	SO:0001589	frameshift_variant	64420	exon14			.	AL137432	CCDS6783.1, CCDS65105.1, CCDS65106.1	9q31.3-q33.1	2008-02-05			ENSG00000106868	ENSG00000106868			25413	protein-coding gene	gene with protein product						12975309	Standard	NM_022486		Approved	DKFZP761E1824	uc004bfu.3	Q6UWL2	OTTHUMG00000020499	ENST00000374270.3:c.1931delG	chr9.hg19:g.114820886delC	ENSP00000363388:p.Ser644fs	135.0	0.0	0		144.0	34.0	0.236111	NM_022486	A1A4C5|A8KA03|Q5T8V6|Q5T8V7|Q6P9G7|Q8WU83|Q96DM9|Q9H6V2|Q9NTA7	Frame_Shift_Del	DEL	ENST00000374270.3	hg19	CCDS6783.1																																																																																			.	.	.	none		0.473	SUSD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053668.3	NM_022486		-	114820886	C	-	114820886	7	5	153	1	0	1	0	1	0	0	0	0	15419	797	28	0	328	0	SUSD1	9	114820886	Frame_Shift_Del	DEL	C	TCGA-DW-7841-01A-11D-2136-08		114820886	26392545	19	9128	92	2									
SUSD1	64420	hgsc.bcm.edu	37	chr9	114820888	114820888	+	Missense_Mutation	SNP	A	A	T																															tcagcatcagaggcgttgctAaagaaggaggaagcgccttc																										TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr9:114820888A>T	ENST00000374270.3	-	14	2101	c.1929T>A	c.(1927-1929)ttT>ttA	p.F643L	SUSD1_ENST00000374264.2_Missense_Mutation_p.F643L|SUSD1_ENST00000374263.3_Missense_Mutation_p.F643L	NM_022486.3	NP_071931.2	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1	643						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)		SUSD1/ROD1(2)	central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						AGGCGTTGCTAAAGAAGGAGG	0.478																																					p.F643L		Atlas-SNP	.											.	SUSD1	51	.	0			c.T1929A						PASS	.						113	110	111					9																	114820888		2203	4300	6503	SO:0001583	missense	64420	exon14			GTTGCTAAAGAAG	AL137432	CCDS6783.1, CCDS65105.1, CCDS65106.1	9q31.3-q33.1	2008-02-05			ENSG00000106868	ENSG00000106868			25413	protein-coding gene	gene with protein product						12975309	Standard	NM_022486		Approved	DKFZP761E1824	uc004bfu.3	Q6UWL2	OTTHUMG00000020499	ENST00000374270.3:c.1929T>A	chr9.hg19:g.114820888A>T	ENSP00000363388:p.Phe643Leu	134.0	0.0	.		146.0	36.0	.	NM_022486	A1A4C5|A8KA03|Q5T8V6|Q5T8V7|Q6P9G7|Q8WU83|Q96DM9|Q9H6V2|Q9NTA7	Missense_Mutation	SNP	ENST00000374270.3	hg19	CCDS6783.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.65|17.65	3.441634|3.441634	0.63067|0.63067	.|.	.|.	ENSG00000106868|ENSG00000106868	ENST00000374270;ENST00000374263;ENST00000374264|ENST00000355396	T;T;T|.	0.51817|.	0.69;0.69;0.69|.	5.44|5.44	1.84|1.84	0.25277|0.25277	.|.	0.000000|.	0.49305|.	D|.	0.000147|.	T|.	0.55369|.	0.1916|.	M|M	0.64630|0.64630	1.985|1.985	0.31889|0.31889	N|N	0.617461|0.617461	D;D;D|.	0.71674|.	0.998;0.998;0.997|.	D;D;D|.	0.80764|.	0.987;0.994;0.985|.	T|.	0.58918|.	-0.7551|.	10|.	0.62326|.	D|.	0.03|.	-9.2496|-9.2496	9.0743|9.0743	0.36511|0.36511	0.7896:0.0:0.2104:0.0|0.7896:0.0:0.2104:0.0	.|.	643;643;643|.	F8WAQ1;Q6UWL2-2;Q6UWL2|.	.;.;SUSD1_HUMAN|.	L|K	643|627	ENSP00000363388:F643L;ENSP00000363381:F643L;ENSP00000363382:F643L|.	ENSP00000363381:F643L|.	F|X	-|-	3|1	2|0	SUSD1|SUSD1	113860709|113860709	1.000000|1.000000	0.71417|0.71417	0.911000|0.911000	0.35937|0.35937	0.551000|0.551000	0.35334|0.35334	1.139000|1.139000	0.31504|0.31504	0.066000|0.066000	0.16515|0.16515	-0.411000|-0.411000	0.06167|0.06167	TTT|TAG	.	.	.	none		0.478	SUSD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053668.3	NM_022486		T	114820888	A	T	114820888	3	4	153	1	0	0	0	0	1	0	0	0	15419	359	13	5	330	5	SUSD1	9	114820888	Missense_Mutation	SNP	A	TCGA-DW-7841-01A-11D-2136-08	2	114820888	26392543	20	9129	92	2									
COL17A1	1308	hgsc.bcm.edu	37	chr10	105793785	105793785	+	Frame_Shift_Del	DEL	G	G	-																															gctcccaatagtccgccattGccagcatacatgccgccttc																										TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr10:105793785delG	ENST00000353479.5	-	52	4364	c.4074delC	c.(4072-4074)ggcfs	p.G1358fs	COL17A1_ENST00000369733.3_Frame_Shift_Del_p.G1276fs	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	1358	Triple-helical region.				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|hemidesmosome (GO:0030056)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				NS(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|liver(1)|lung(22)|ovary(5)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	62		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		GTCCGCCATTGCCAGCATACA	0.572																																					p.N1359fs		Atlas-INDEL	.											.	COL17A1	149	.	0			c.4075delA						PASS	.						98	95	96					10																	105793785		2203	4300	6503	SO:0001589	frameshift_variant	1308	exon52			.	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.4074delC	chr10.hg19:g.105793785delG	ENSP00000340937:p.Gly1358fs	104.0	0.0	0		99.0	17.0	0.171717	NM_000494	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Frame_Shift_Del	DEL	ENST00000353479.5	hg19	CCDS7554.1																																																																																			.	.	.	none		0.572	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494		-	105793785	G	-	105793785	7	5	153	1	0	1	0	1	0	0	0	0	3676	1306	46	0	439	0	COL17A1	10	105793785	Frame_Shift_Del	DEL	G	TCGA-DW-7841-01A-11D-2136-08		105793785	29740962	21	9130											
SBF2	81846	hgsc.bcm.edu	37	chr11	10011061	10011061	+	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	tacatttttgaatagttgctCagcaagttccctgacatgct	10	15	7	9	0	1	2	1	2	0	0	2	2	2	2	1	0	4	5	1	0	4	6			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr11:10011061C>T	ENST00000256190.8	-	13	1515	c.1378G>A	c.(1378-1380)Gag>Aag	p.E460K		NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN	SET binding factor 2	460					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)		AATAGTTGCTCAGCAAGTTCC	0.303																																					p.E460K		Atlas-SNP	.											.	SBF2	146	.	0			c.G1378A						PASS	.						99	101	100					11																	10011061		2200	4292	6492	SO:0001583	missense	81846	exon13			GTTGCTCAGCAAG	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.1378G>A	chr11.hg19:g.10011061C>T	ENSP00000256190:p.Glu460Lys	56.0	0.0	.		61.0	15.0	.	NM_030962	Q3MJF0|Q68DQ3|Q6P459|Q6PJD1|Q7Z325|Q7Z621|Q86VE2|Q96FE2|Q9C097	Missense_Mutation	SNP	ENST00000256190.8	hg19	CCDS31427.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.489124	0.84962	.	.	ENSG00000133812	ENST00000256190	D	0.85629	-2.01	6.04	6.04	0.98038	.	0.230274	0.43416	D	0.000562	D	0.90539	0.7035	L	0.48986	1.54	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86724	0.1944	10	0.25106	T	0.35	.	20.5948	0.99439	0.0:1.0:0.0:0.0	.	460	Q86WG5	MTMRD_HUMAN	K	460	ENSP00000256190:E460K	ENSP00000256190:E460K	E	-	1	0	SBF2	9967637	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.324000	0.65863	2.873000	0.98535	0.563000	0.77884	GAG	.	.	.	none		0.303	SBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386911.2	NM_030962		T	10011061	C	T	10011061	3	4	153	1	0	0	0	0	1	0	0	0	13872	835	29	2	4283	2	SBF2	11	10011061	Missense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08		10011061	124995455	22	9131											
SLCO2B1	11309	hgsc.bcm.edu	37	chr11	74880776	74880776	+	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	ggctgggcagcctcatgctgCgcctttatgtggacattaac	7	11	12	11	1	1	0	1	0	0	0	1	1	1	1	2	3	4	3	2	3	2	3			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr11:74880776C>A	ENST00000289575.5	+	6	1143	c.748C>A	c.(748-750)Cgc>Agc	p.R250S	SLCO2B1_ENST00000526660.1_Intron|SLCO2B1_ENST00000532236.1_Missense_Mutation_p.R134S|SLCO2B1_ENST00000428359.2_Missense_Mutation_p.R228S|SLCO2B1_ENST00000341411.4_Intron|SLCO2B1_ENST00000531756.1_Intron|SLCO2B1_ENST00000525650.1_Missense_Mutation_p.R106S|SLCO2B1_ENST00000454962.2_Intron	NM_007256.4	NP_009187	O94956	SO2B1_HUMAN	solute carrier organic anion transporter family, member 2B1	250					liver development (GO:0001889)|sodium-independent icosanoid transport (GO:0071718)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid transmembrane transporter activity (GO:0015125)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)	p.R250C(1)		breast(2)|endometrium(1)|large_intestine(7)|lung(20)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	39					Acetic acid(DB03166)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Digoxin(DB00390)|Dinoprostone(DB00917)|Ergoloid mesylate(DB01049)|Estradiol(DB00783)|Estrone(DB00655)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Glyburide(DB01016)|Ibuprofen(DB01050)|Iloprost(DB01088)|Latanoprost(DB00654)|Montelukast(DB00471)|Niacin(DB00627)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Tolbutamide(DB01124)	CCTCATGCTGCGCCTTTATGT	0.542																																					p.R250S		Atlas-SNP	.											SLCO2B1,rectum,carcinoma,0,1	SLCO2B1	84	.	1	Substitution - Missense(1)	large_intestine(1)	c.C748A						PASS	.						128	120	123					11																	74880776		2200	4293	6493	SO:0001583	missense	11309	exon6			ATGCTGCGCCTTT	AB026256	CCDS8235.1, CCDS44683.1, CCDS53679.1	11q13	2013-05-22	2003-11-25	2003-11-26				"Solute carriers"	10962	protein-coding gene	gene with protein product		604988	"solute carrier family 21 (organic anion transporter), member 9"	SLC21A9			Standard	NM_007256		Approved	OATP-B, OATP2B1	uc001owb.3	O94956		ENST00000289575.5:c.748C>A	chr11.hg19:g.74880776C>A	ENSP00000289575:p.Arg250Ser	158.0	0.0	.		155.0	43.0	.	NM_007256	A8K2G9|B4DGA9|B4DTB0|E7ERN5|E9PPU8|Q9H2Z0|Q9UFU1	Missense_Mutation	SNP	ENST00000289575.5	hg19	CCDS8235.1	.	.	.	.	.	.	.	.	.	.	C	16.04	3.010553	0.54361	.	.	ENSG00000137491	ENST00000289575;ENST00000532236;ENST00000525650;ENST00000428359;ENST00000526839	T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98	4.83	2.77	0.32553	Major facilitator superfamily domain, general substrate transporter (1);	0.060626	0.64402	N	0.000004	T	0.41558	0.1164	L	0.39566	1.225	0.80722	D	1	P;P	0.49358	0.812;0.923	B;P	0.51170	0.425;0.661	T	0.15838	-1.0423	10	0.29301	T	0.29	.	11.6849	0.51481	0.326:0.674:0.0:0.0	.	106;250	E9PPU8;O94956	.;SO2B1_HUMAN	S	250;134;106;228;126	ENSP00000289575:R250S;ENSP00000434112:R134S;ENSP00000436324:R106S;ENSP00000388912:R228S;ENSP00000434742:R126S	ENSP00000289575:R250S	R	+	1	0	SLCO2B1	74558424	0.932000	0.31603	0.996000	0.52242	0.937000	0.57800	1.528000	0.35985	1.218000	0.43458	0.650000	0.86243	CGC	.	.	.	none		0.542	SLCO2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383933.1	NM_007256		A	74880776	C	A	74880776	3	1	153	1	0	0	0	0	1	0	0	0	14740	768	27	4	770	4	SLCO2B1	11	74880776	Missense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08	64869715	74880776	60125740	23	9132											
BAZ2A	11176	hgsc.bcm.edu	37	chr12	57005874	57005874	+	Missense_Mutation	SNP	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	ctagggagactgctggggagGttgttggcgagactgctggt	6	10	19	6	1	0	2	0	0	0	2	0	5	0	3	0	6	2	4	0	6	1	3			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr12:57005874G>A	ENST00000551812.1	-	6	1491	c.1298C>T	c.(1297-1299)aCc>aTc	p.T433I	BAZ2A_ENST00000179765.5_Missense_Mutation_p.T401I|BAZ2A_ENST00000549884.1_Missense_Mutation_p.T431I|BAZ2A_ENST00000379441.3_Missense_Mutation_p.T403I	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	433					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						TGCTGGGGAGGTTGTTGGCGA	0.542																																					p.T433I		Atlas-SNP	.											.	BAZ2A	263	.	0			c.C1298T						PASS	.						101	115	110					12																	57005874		2101	4218	6319	SO:0001583	missense	11176	exon6			GGGGAGGTTGTTG	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.1298C>T	chr12.hg19:g.57005874G>A	ENSP00000446880:p.Thr433Ile	37.0	0.0	.		73.0	55.0	.	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Missense_Mutation	SNP	ENST00000551812.1	hg19	CCDS44924.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.854|6.854	0.526813|0.526813	0.13066|0.13066	.|.	.|.	ENSG00000076108|ENSG00000076108	ENST00000551996|ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549884	.|T;T;T;T	.|0.58210	.|0.35;0.35;0.35;0.35	5.45|5.45	-0.694|-0.694	0.11294|0.11294	.|.	.|1.012260	.|0.07909	.|N	.|0.973899	T|T	0.29355|0.29355	0.0731|0.0731	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	0.999997|0.999997	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.23048|0.23048	-1.0199|-1.0199	5|10	.|0.72032	.|D	.|0.01	.|.	5.0786|5.0786	0.14644|0.14644	0.2123:0.0:0.5335:0.2543|0.2123:0.0:0.5335:0.2543	.|.	.|431;433	.|F8VU39;Q9UIF9	.|.;BAZ2A_HUMAN	S|I	81|403;401;433;431	.|ENSP00000368754:T403I;ENSP00000179765:T401I;ENSP00000446880:T433I;ENSP00000447941:T431I	.|ENSP00000179765:T401I	P|T	-|-	1|2	0|0	BAZ2A|BAZ2A	55292141|55292141	0.835000|0.835000	0.29415|0.29415	0.009000|0.009000	0.14445|0.14445	0.194000|0.194000	0.23727|0.23727	0.260000|0.260000	0.18424|0.18424	-0.209000|-0.209000	0.10156|0.10156	-0.182000|-0.182000	0.12963|0.12963	CCT|ACC	.	.	.	none		0.542	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449		A	57005874	G	A	57005874	3	1	153	1	0	0	0	0	1	0	0	0	1331	1261	44	2	4515	2	BAZ2A	12	57005874	Missense_Mutation	SNP	G	TCGA-DW-7841-01A-11D-2136-08		57005874	76846021	24	9133											
MLXIP	22877	hgsc.bcm.edu	37	chr12	122618012	122618012	+	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	agggctgtgaacacacctccCggactgaggacccgtttatc	9	8	11	13	2	0	2	0	2	0	0	2	4	1	4	3	3	1	2	3	3	2	2			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr12:122618012C>A	ENST00000319080.7	+	9	1342	c.1210C>A	c.(1210-1212)Cgg>Agg	p.R404R	MLXIP_ENST00000377037.2_Silent_p.R11R|MLXIP_ENST00000538698.1_Silent_p.R11R					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)		ACACACCTCCCGGACTGAGGA	0.647																																					p.R404R	Esophageal Squamous(105;787 1493 16200 18566 52466)	Atlas-SNP	.											.	MLXIP	46	.	0			c.C1210A						PASS	.						24	28	27					12																	122618012		2043	4171	6214	SO:0001819	synonymous_variant	22877	exon9			ACCTCCCGGACTG	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.1210C>A	chr12.hg19:g.122618012C>A		39.0	0.0	.		77.0	4.0	.	NM_014938		Silent	SNP	ENST00000319080.7	hg19																																																																																				.	.	.	none		0.647	MLXIP-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401718.2	NM_014938		A	122618012	C	A	122618012	2	1	153	1	0	0	0	0	0	0	0	1	9643	643	23	4		4	MLXIP	12	122618012	Silent	SNP	C	TCGA-DW-7841-01A-11D-2136-08	65612138	122618012	11233883	25	9134											
KBTBD7	84078	hgsc.bcm.edu	37	chr13	41767953	41767953	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccagctgtagcatgtcggaGgccgcgtacaggcgctgcac	7	7	14	13	4	0	0	0	0	0	0	2	1	1	1	2	3	4	6	2	3	2	2			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr13:41767953G>A	ENST00000379483.3	-	1	749	c.441C>T	c.(439-441)gcC>gcT	p.A147A		NM_032138.4	NP_115514.2	Q8WVZ9	KBTB7_HUMAN	kelch repeat and BTB (POZ) domain containing 7	147										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(4)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Lung NSC(96;0.000105)|Breast(139;0.00715)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.21e-09)|Epithelial(112;6.99e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000196)|GBM - Glioblastoma multiforme(144;0.000857)|BRCA - Breast invasive adenocarcinoma(63;0.0669)		GCATGTCGGAGGCCGCGTACA	0.587																																					p.A147A		Atlas-SNP	.											.	KBTBD7	60	.	0			c.C441T						PASS	.						109	91	97					13																	41767953		2203	4300	6503	SO:0001819	synonymous_variant	84078	exon1			GTCGGAGGCCGCG	AL136782	CCDS9377.1	13q13.3	2013-01-08			ENSG00000120696	ENSG00000120696		"BTB/POZ domain containing"	25266	protein-coding gene	gene with protein product						11230166	Standard	NM_032138		Approved	DKFZP434E2318	uc001uxw.1	Q8WVZ9	OTTHUMG00000016789	ENST00000379483.3:c.441C>T	chr13.hg19:g.41767953G>A		115.0	0.0	.		105.0	31.0	.	NM_032138	B5TZ86|Q5T6Y7|Q8NB99|Q9H0I6	Silent	SNP	ENST00000379483.3	hg19	CCDS9377.1																																																																																			.	.	.	none		0.587	KBTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044660.1	NM_032138		A	41767953	G	A	41767953	2	1	153	1	0	0	0	0	0	0	0	1	8005	987	35	2		2	KBTBD7	13	41767953	Silent	SNP	G	TCGA-DW-7841-01A-11D-2136-08		41767953	73401925	26	9135											
TDRD3	81550	hgsc.bcm.edu	37	chr13	61103190	61103190	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agccagcaggacctgtcacaGctgtaccctgtgatgataaa	12	8	10	11	0	1	2	1	2	0	0	1	3	1	3	3	1	4	3	3	1	3	2			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr13:61103190G>A	ENST00000196169.3	+	11	2340	c.1552G>A	c.(1552-1554)Gct>Act	p.A518T	TDRD3_ENST00000377894.2_Missense_Mutation_p.A518T|TDRD3_ENST00000535286.1_Missense_Mutation_p.A611T|TDRD3_ENST00000377881.2_Missense_Mutation_p.A518T	NM_001146071.1|NM_030794.2	NP_001139543.1|NP_110421.1	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3	518					chromatin modification (GO:0016568)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	40		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)		ACCTGTCACAGCTGTACCCTG	0.398																																					p.A611T	Colon(36;164 906 35820 50723)	Atlas-SNP	.											.	TDRD3	123	.	0			c.G1831A						PASS	.						54	54	54					13																	61103190		2203	4300	6503	SO:0001583	missense	81550	exon11			GTCACAGCTGTAC	AK023578	CCDS9441.1, CCDS53872.1	13q14.3	2013-01-23			ENSG00000083544	ENSG00000083544		"Tudor domain containing"	20612	protein-coding gene	gene with protein product		614392					Standard	NM_030794		Approved	FLJ21007	uc010aeg.3	Q9H7E2	OTTHUMG00000017007	ENST00000196169.3:c.1552G>A	chr13.hg19:g.61103190G>A	ENSP00000196169:p.Ala518Thr	57.0	0.0	.		84.0	32.0	.	NM_001146070	B2MWP9|Q53XA6|Q6P992	Missense_Mutation	SNP	ENST00000196169.3	hg19	CCDS9441.1	.	.	.	.	.	.	.	.	.	.	G	0.227	-1.023813	0.02061	.	.	ENSG00000083544	ENST00000196169;ENST00000377881;ENST00000377894;ENST00000535286	D;D;D;D	0.93763	-3.28;-3.28;-3.28;-3.26	5.84	-1.01	0.10169	.	0.741305	0.14224	N	0.333183	D	0.85974	0.5822	L	0.47716	1.5	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	0.68911	-0.5284	10	0.12103	T	0.63	-1.2106	3.7879	0.08707	0.4174:0.0981:0.3852:0.0994	.	611;517;518	Q9H7E2-3;Q9H7E2-2;Q9H7E2	.;.;TDRD3_HUMAN	T	518;518;518;611	ENSP00000196169:A518T;ENSP00000367113:A518T;ENSP00000367126:A518T;ENSP00000440190:A611T	ENSP00000196169:A518T	A	+	1	0	TDRD3	60001191	0.000000	0.05858	0.000000	0.03702	0.389000	0.30415	0.087000	0.14958	-0.343000	0.08351	-0.813000	0.03139	GCT	.	.	.	none		0.398	TDRD3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045175.2	NM_030794		A	61103190	G	A	61103190	3	1	153	1	0	0	0	0	1	0	0	0	15744	971	34	2	1873	2	TDRD3	13	61103190	Missense_Mutation	SNP	G	TCGA-DW-7841-01A-11D-2136-08	19335237	61103190	54066688	27	9136											
FANCM	57697	hgsc.bcm.edu	37	chr14	45650876	45650876	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aagttgattctccacttcatGctgtcaaaaagcgcagattt	12	13	7	9	1	3	2	2	1	1	1	4	2	3	2	1	0	2	3	1	0	3	4			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr14:45650876G>A	ENST00000267430.5	+	16	4439	c.4354G>A	c.(4354-4356)Gct>Act	p.A1452T	FANCM_ENST00000555013.1_3'UTR|FANCM_ENST00000542564.2_Missense_Mutation_p.A1426T	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1452					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						TCCACTTCATGCTGTCAAAAA	0.318								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.A1452T		Atlas-SNP	.											.	FANCM	225	.	0			c.G4354A						PASS	.						59	60	60					14																	45650876		2203	4296	6499	SO:0001583	missense	57697	exon16	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CTTCATGCTGTCA	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.4354G>A	chr14.hg19:g.45650876G>A	ENSP00000267430:p.Ala1452Thr	48.0	0.0	.		50.0	13.0	.	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	hg19	CCDS32070.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.81|19.81	3.897408|3.897408	0.72639|0.72639	.|.	.|.	ENSG00000187790|ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250|ENST00000554809	T;T;T|.	0.20069|.	2.7;2.7;2.1|.	5.25|5.25	4.36|4.36	0.52297|0.52297	.|.	0.807093|.	0.11373|.	N|.	0.570657|.	T|T	0.39600|0.39600	0.1084|0.1084	L|L	0.43152|0.43152	1.355|1.355	0.29859|0.29859	N|N	0.827775|0.827775	D;P|.	0.65815|.	0.995;0.953|.	P;P|.	0.53760|.	0.734;0.631|.	T|T	0.35051|0.35051	-0.9804|-0.9804	10|5	0.14656|.	T|.	0.56|.	.|.	8.1721|8.1721	0.31260|0.31260	0.1826:0.0:0.8174:0.0|0.1826:0.0:0.8174:0.0	.|.	1426;1452|.	B2RTQ9;Q8IYD8|.	.;FANCM_HUMAN|.	T|Y	1452;1426;968|384	ENSP00000267430:A1452T;ENSP00000442493:A1426T;ENSP00000452033:A968T|.	ENSP00000267430:A1452T|.	A|C	+|+	1|2	0|0	FANCM|FANCM	44720626|44720626	0.997000|0.997000	0.39634|0.39634	0.995000|0.995000	0.50966|0.50966	0.985000|0.985000	0.73830|0.73830	3.470000|3.470000	0.53100|0.53100	1.348000|1.348000	0.45733|0.45733	0.467000|0.467000	0.42956|0.42956	GCT|TGC	.	.	.	none		0.318	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		A	45650876	G	A	45650876	3	1	153	1	0	0	0	0	1	0	0	0	5678	1319	46	2	4416	2	FANCM	14	45650876	Missense_Mutation	SNP	G	TCGA-DW-7841-01A-11D-2136-08		45650876	61698664	28	9137											
TBPL2	387332	hgsc.bcm.edu	37	chr14	55890942	55890942	+	Missense_Mutation	SNP	A	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	gtggttttaccattctataaAtaagaccaggaaacagttca	15	12	7	7	0	2	1	1	0	1	1	2	2	2	2	2	2	2	2	2	2	6	7			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr14:55890942A>C	ENST00000247219.5	-	6	1056	c.986T>G	c.(985-987)aTt>aGt	p.I329S		NM_199047.2	NP_950248.1			TATA box binding protein like 2											endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	8						CATTCTATAAATAAGACCAGG	0.348																																					p.I329S		Atlas-SNP	.											.	TBPL2	27	.	0			c.T986G						PASS	.						110	102	105					14																	55890942		2203	4298	6501	SO:0001583	missense	387332	exon6			CTATAAATAAGAC	AY457923	CCDS9724.1	14q22.2	2004-06-03			ENSG00000182521	ENSG00000182521			19841	protein-coding gene	gene with protein product		608964				14634207	Standard	NM_199047		Approved	TRF3, TBP2	uc001xby.3	Q6SJ96	OTTHUMG00000140313	ENST00000247219.5:c.986T>G	chr14.hg19:g.55890942A>C	ENSP00000247219:p.Ile329Ser	151.0	0.0	.		142.0	40.0	.	NM_199047		Missense_Mutation	SNP	ENST00000247219.5	hg19	CCDS9724.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.464312	0.84425	.	.	ENSG00000182521	ENST00000247219	T	0.57273	0.41	5.41	5.41	0.78517	Transcription factor TFIID, C-terminal/DNA glycosylase, N-terminal (1);Beta2-adaptin/TATA-box binding, C-terminal (1);	0.054773	0.64402	D	0.000001	T	0.75889	0.3911	M	0.93939	3.475	0.80722	D	1	D	0.63880	0.993	P	0.57776	0.827	T	0.83328	-0.0014	10	0.87932	D	0	-12.6468	14.6315	0.68660	1.0:0.0:0.0:0.0	.	329	Q6SJ96	TBPL2_HUMAN	S	329	ENSP00000247219:I329S	ENSP00000247219:I329S	I	-	2	0	TBPL2	54960695	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.138000	0.94501	2.050000	0.60909	0.528000	0.53228	ATT	.	.	.	none		0.348	TBPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276916.1	NM_199047		C	55890942	A	C	55890942	3	2	153	1	0	0	0	0	1	0	0	0	15658	101	4	5	149	5	TBPL2	14	55890942	Missense_Mutation	SNP	A	TCGA-DW-7841-01A-11D-2136-08	10240066	55890942	51458598	29	9138											
KCNH5	27133	hgsc.bcm.edu	37	chr14	63447722	63447722	+	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	acctctccaccgggccccacGaaagtcgtgtgaaaatttaa	12	8	8	13	3	1	1	0	1	1	0	3	2	1	1	5	1	0	0	5	1	4	2	rs376391048		TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr14:63447722G>T	ENST00000322893.7	-	6	1078	c.810C>A	c.(808-810)ttC>ttA	p.F270L	KCNH5_ENST00000420622.2_Missense_Mutation_p.F270L|KCNH5_ENST00000394964.2_Missense_Mutation_p.F212L|KCNH5_ENST00000394968.1_Missense_Mutation_p.F212L	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	270					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)		CGGGCCCCACGAAAGTCGTGT	0.433																																					p.F270L		Atlas-SNP	.											.	KCNH5	320	.	0			c.C810A						PASS	.						61	63	62					14																	63447722		2203	4300	6503	SO:0001583	missense	27133	exon6			CCCCACGAAAGTC	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.810C>A	chr14.hg19:g.63447722G>T	ENSP00000321427:p.Phe270Leu	62.0	0.0	.		81.0	35.0	.	NM_172375	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	hg19	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	G	17.91	3.505267	0.64410	.	.	ENSG00000140015	ENST00000322893;ENST00000420622;ENST00000394968;ENST00000394964	D;D;D;D	0.95171	-3.63;-3.63;-3.63;-3.63	5.54	1.95	0.26073	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.95401	0.8507	M	0.64404	1.975	0.80722	D	1	P;P;D;D	0.61080	0.893;0.899;0.963;0.989	P;P;P;D	0.66084	0.602;0.603;0.603;0.941	D	0.93621	0.6948	10	0.87932	D	0	.	8.8508	0.35199	0.7805:0.0:0.2195:0.0	.	212;212;270;270	Q86XI1;Q8NCM2-3;Q8NCM2-2;Q8NCM2	.;.;.;KCNH5_HUMAN	L	270;270;212;212	ENSP00000321427:F270L;ENSP00000395439:F270L;ENSP00000378419:F212L;ENSP00000378415:F212L	ENSP00000321427:F270L	F	-	3	2	KCNH5	62517475	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	1.301000	0.33447	0.086000	0.17137	-0.482000	0.04802	TTC	.	.	.	alt		0.433	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		T	63447722	G	T	63447722	3	4	153	1	0	0	0	0	1	0	0	0	8042	1049	37	4	2214	4	KCNH5	14	63447722	Missense_Mutation	SNP	G	TCGA-DW-7841-01A-11D-2136-08	7556780	63447722	43901818	30	9139											
RYR3	6263	hgsc.bcm.edu	37	chr15	33603296	33603296	+	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	cgagatccagtttctgaggaCtgtgagtctccgcggcgggg	6	9	16	10	4	2	3	0	2	2	1	4	5	3	4	2	4	0	1	2	4	0	1			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr15:33603296C>T	ENST00000389232.4	+	1	120	c.50C>T	c.(49-51)aCt>aTt	p.T17I	RP11-489D6.2_ENST00000559457.1_RNA|RYR3_ENST00000415757.3_Splice_Site_p.T17I|RP11-489D6.2_ENST00000561458.1_RNA	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	17					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)		TTTCTGAGGACTGTGAGTCTC	0.756																																					p.T17I		Atlas-SNP	.											.	RYR3	760	.	0			c.C50T						PASS	.						25	32	30					15																	33603296		1919	4113	6032	SO:0001630	splice_region_variant	6263	exon1			TGAGGACTGTGAG		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.51+1C>T	chr15.hg19:g.33603296C>T		48.0	0.0	.		47.0	16.0	.	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	C	16.27	3.077125	0.55753	.	.	ENSG00000198838	ENST00000389232;ENST00000415757	D;D	0.98090	-4.71;-4.71	4.63	3.7	0.42460	Inositol 1,4,5-trisphosphate/ryanodine receptor (1);	1.170300	0.06443	U	0.726384	D	0.96987	0.9016	L	0.49126	1.545	0.38096	D	0.937129	B;B	0.29253	0.144;0.239	B;B	0.38264	0.126;0.269	D	0.90850	0.4730	10	0.54805	T	0.06	.	12.9534	0.58413	0.1639:0.8361:0.0:0.0	.	17;17	Q15413-2;Q15413	.;RYR3_HUMAN	I	17	ENSP00000373884:T17I;ENSP00000399610:T17I	ENSP00000373884:T17I	T	+	2	0	RYR3	31390588	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.045000	0.64220	1.130000	0.42092	0.462000	0.41574	ACT	.	.	.	none		0.756	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		Missense_Mutation	T	33603296	C	T	33603296	5	4	153	1	0	0	0	0	0	0	1	0	13783	579	20	2	52	2	RYR3	15	33603296	Splice_Site	SNP	C	TCGA-DW-7841-01A-11D-2136-08		33603296	68928096	31	9140											
TLN2	83660	hgsc.bcm.edu	37	chr15	63097949	63097949	+	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	ttgctactgccaacctgagcCggaaagccgtgtcagatatg	10	9	11	11	2	1	2	1	1	0	1	1	3	1	3	4	1	6	1	4	1	4	3			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr15:63097949C>A	ENST00000561311.1	+	50	6858	c.6628C>A	c.(6628-6630)Cgg>Agg	p.R2210R	TLN2_ENST00000306829.6_Silent_p.R2210R			Q9Y4G6	TLN2_HUMAN	talin 2	2210					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						CAACCTGAGCCGGAAAGCCGT	0.517																																					p.R2210R		Atlas-SNP	.											.	TLN2	253	.	0			c.C6628A						PASS	.						84	72	76					15																	63097949		2203	4300	6503	SO:0001819	synonymous_variant	83660	exon48			CTGAGCCGGAAAG	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.6628C>A	chr15.hg19:g.63097949C>A		87.0	0.0	.		83.0	4.0	.	NM_015059	A6NLB8	Silent	SNP	ENST00000561311.1	hg19	CCDS32261.1																																																																																			.	.	.	none		0.517	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			A	63097949	C	A	63097949	2	1	153	1	0	0	0	0	0	0	0	1	15960	643	23	4		4	TLN2	15	63097949	Silent	SNP	C	TCGA-DW-7841-01A-11D-2136-08	29494653	63097949	39433443	32	9141											
ADPGK	83440	hgsc.bcm.edu	37	chr15	73045222	73045222	+	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	ttcagcccaagggaagtcacCgcgggaaagacctgctaaca	13	5	11	12	2	2	1	2	0	0	1	2	3	2	3	3	2	3	1	3	2	4	2			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr15:73045222C>A	ENST00000311669.8	-	7	1044	c.951G>T	c.(949-951)gcG>gcT	p.A317A	ADPGK_ENST00000567733.1_5'Flank|ADPGK_ENST00000456471.2_Silent_p.A43A	NM_031284.4	NP_112574.3	Q9BRR6	ADPGK_HUMAN	ADP-dependent glucokinase	318	ADPK. {ECO:0000255|PROSITE- ProRule:PRU00584}.				glycolytic process (GO:0006096)	extracellular region (GO:0005576)|membrane (GO:0016020)	ADP-specific glucokinase activity (GO:0043843)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|skin(1)	7						GGGAAGTCACCGCGGGAAAGA	0.478																																					p.A317A		Atlas-SNP	.											.	ADPGK	19	.	0			c.G951T						PASS	.						36	36	36					15																	73045222		1925	4115	6040	SO:0001819	synonymous_variant	83440	exon7			AGTCACCGCGGGA	AL136873	CCDS42057.1	15q24.1	2012-07-02			ENSG00000159322	ENSG00000159322			25250	protein-coding gene	gene with protein product		611861				11230166	Standard	NM_031284		Approved	DKFZp434B195, ADP-GK	uc002avf.4	Q9BRR6	OTTHUMG00000172777	ENST00000311669.8:c.951G>T	chr15.hg19:g.73045222C>A		66.0	0.0	.		71.0	4.0	.	NM_031284	Q49AU7|Q8NBI1|Q8WZ90|Q96NF8|Q9H0A7	Silent	SNP	ENST00000311669.8	hg19	CCDS42057.1																																																																																			.	.	.	none		0.478	ADPGK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420434.1	NM_031284		A	73045222	C	A	73045222	2	1	153	1	0	0	0	0	0	0	0	1	330	639	23	4		4	ADPGK	15	73045222	Silent	SNP	C	TCGA-DW-7841-01A-11D-2136-08	9947273	73045222	29486170	33	9142											
WDR90	197335	hgsc.bcm.edu	37	chr16	716291	716291	+	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	cctgcacagggacaaccttcCgtgtgctgagtgaccaccag	9	7	11	14	1	0	2	0	2	0	0	1	3	1	3	5	1	3	2	5	1	1	1	rs143767432	byFrequency	TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr16:716291C>A	ENST00000293879.4	+	37	4681	c.4681C>A	c.(4681-4683)Cgt>Agt	p.R1561S	WDR90_ENST00000547543.1_3'UTR|WDR90_ENST00000549091.1_Missense_Mutation_p.R1563S|WDR90_ENST00000315764.4_Missense_Mutation_p.R160S|RHOT2_ENST00000315082.4_5'Flank|WDR90_ENST00000547944.1_Missense_Mutation_p.R160S			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1561										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				GACAACCTTCCGTGTGCTGAG	0.627																																					p.R1561S		Atlas-SNP	.											WDR90,NS,carcinoma,0,2	WDR90	107	.	0			c.C4681A						PASS	.						46	55	52					16																	716291		2025	4175	6200	SO:0001583	missense	197335	exon37			ACCTTCCGTGTGC	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.4681C>A	chr16.hg19:g.716291C>A	ENSP00000293879:p.Arg1561Ser	105.0	0.0	.		98.0	27.0	.	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	hg19	CCDS42092.1	.	.	.	.	.	.	.	.	.	.	C	18.03	3.532400	0.64972	.	.	ENSG00000161996	ENST00000549091;ENST00000293879;ENST00000547944;ENST00000315764	T;T;T;T	0.66099	3.39;1.54;-0.19;1.59	3.96	3.0	0.34707	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.649291	0.16302	N	0.220408	T	0.74898	0.3777	M	0.84433	2.695	0.49051	D	0.999749	D;D;D;D	0.89917	0.999;1.0;0.98;0.998	D;D;P;P	0.71184	0.972;0.968;0.671;0.892	T	0.73981	-0.3811	10	0.08837	T	0.75	.	9.2755	0.37696	0.0:0.8986:0.0:0.1014	.	160;160;160;1561	Q96KV7-10;Q96KV7-7;G3V201;Q96KV7	.;.;.;WDR90_HUMAN	S	1563;1561;160;160	ENSP00000448122:R1563S;ENSP00000293879:R1561S;ENSP00000449576:R160S;ENSP00000322808:R160S	ENSP00000293879:R1561S	R	+	1	0	WDR90	656292	0.083000	0.21467	0.303000	0.25071	0.729000	0.41735	1.907000	0.39897	0.877000	0.35895	0.561000	0.74099	CGT	.	C|0.996;T|0.004	.	alt		0.627	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294		A	716291	C	A	716291	3	1	153	1	0	0	0	0	1	0	0	0	17349	652	23	4	4827	4	WDR90	16	716291	Missense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08		716291	89638462	34	9143											
TMC5	79838	hgsc.bcm.edu	37	chr16	19498618	19498618	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcccatccttcaccggggTcttgtgcaccctggccatca	5	12	8	16	1	3	0	2	0	1	0	5	0	5	0	5	3	1	1	5	3	0	3			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr16:19498618T>C	ENST00000396229.2	+	17	3292	c.2543T>C	c.(2542-2544)gTc>gCc	p.V848A	TMC5_ENST00000561503.1_Missense_Mutation_p.V489A|TMC5_ENST00000541464.1_Missense_Mutation_p.V796A|TMC5_ENST00000564959.1_Missense_Mutation_p.V531A|TMC5_ENST00000381414.4_Missense_Mutation_p.V848A|CTA-363E6.6_ENST00000561762.1_RNA|TMC5_ENST00000542583.2_Missense_Mutation_p.V848A|TMC5_ENST00000219821.5_Missense_Mutation_p.V602A	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	848					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						TTCACCGGGGTCTTGTGCACC	0.522																																					p.V848A		Atlas-SNP	.											.	TMC5	169	.	0			c.T2543C						PASS	.						67	58	61					16																	19498618		2197	4300	6497	SO:0001583	missense	79838	exon17			CCGGGGTCTTGTG	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.2543T>C	chr16.hg19:g.19498618T>C	ENSP00000379531:p.Val848Ala	63.0	0.0	.		77.0	4.0	.	NM_001105249	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Missense_Mutation	SNP	ENST00000396229.2	hg19	CCDS45431.1	.	.	.	.	.	.	.	.	.	.	T	16.51	3.144011	0.57044	.	.	ENSG00000103534	ENST00000541464;ENST00000381414;ENST00000396229;ENST00000542583;ENST00000219821;ENST00000440743	T;T;T;T;T	0.67523	-0.11;-0.09;-0.13;-0.13;-0.27	5.72	3.48	0.39840	.	0.235749	0.43110	N	0.000604	T	0.43010	0.1228	N	0.13299	0.325	0.37439	D	0.914337	B;B;B;B;B;B	0.26120	0.142;0.001;0.025;0.014;0.019;0.018	B;B;B;B;B;B	0.24006	0.05;0.003;0.05;0.022;0.022;0.034	T	0.28073	-1.0055	10	0.08837	T	0.75	-19.7366	9.3727	0.38264	0.0:0.148:0.0:0.852	.	796;531;602;602;848;848	F5GYU8;E7EU57;Q6UXY8-3;B3KUQ8;Q6UXY8;Q6UXY8-2	.;.;.;.;TMC5_HUMAN;.	A	796;848;848;848;602;531	ENSP00000441227:V796A;ENSP00000370822:V848A;ENSP00000379531:V848A;ENSP00000446274:V848A;ENSP00000219821:V602A	ENSP00000219821:V602A	V	+	2	0	TMC5	19406119	1.000000	0.71417	0.948000	0.38648	0.985000	0.73830	3.080000	0.50112	0.443000	0.26582	0.533000	0.62120	GTC	.	.	.	none		0.522	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780		C	19498618	T	C	19498618	3	2	153	1	0	0	0	0	1	0	0	0	16000	1667	58	3	2915	3	TMC5	16	19498618	Missense_Mutation	SNP	T	TCGA-DW-7841-01A-11D-2136-08	18782327	19498618	70856135	35	9144											
GTF3C1	2975	hgsc.bcm.edu	37	chr16	27519910	27519910	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcacagcattcttgcttctAgttttcccacattcatagcc	8	14	6	13	0	3	0	1	0	2	0	4	0	4	0	2	1	3	4	2	1	2	8			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr16:27519910A>G	ENST00000356183.4	-	8	1208	c.1193T>C	c.(1192-1194)cTa>cCa	p.L398P	GTF3C1_ENST00000561623.1_Missense_Mutation_p.L398P	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	398					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						TCTTGCTTCTAGTTTTCCCAC	0.468																																					p.L398P		Atlas-SNP	.											.	GTF3C1	210	.	0			c.T1193C						PASS	.						195	159	171					16																	27519910		2197	4300	6497	SO:0001583	missense	2975	exon8			GCTTCTAGTTTTC	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.1193T>C	chr16.hg19:g.27519910A>G	ENSP00000348510:p.Leu398Pro	91.0	0.0	.		118.0	36.0	.	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	hg19	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.353988	0.82243	.	.	ENSG00000077235	ENST00000356183;ENST00000388971	T	0.32272	1.46	5.41	5.41	0.78517	.	0.000000	0.64402	D	0.000002	T	0.45597	0.1350	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.45190	-0.9278	10	0.72032	D	0.01	-4.7197	15.1534	0.72720	1.0:0.0:0.0:0.0	.	398;398	Q12789;Q12789-3	TF3C1_HUMAN;.	P	398;396	ENSP00000348510:L398P	ENSP00000348510:L398P	L	-	2	0	GTF3C1	27427411	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.677000	0.91203	2.054000	0.61138	0.528000	0.53228	CTA	.	.	.	none		0.468	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520		G	27519910	A	G	27519910	3	3	153	1	0	0	0	0	1	0	0	0	6879	420	15	3	5256	3	GTF3C1	16	27519910	Missense_Mutation	SNP	A	TCGA-DW-7841-01A-11D-2136-08	8021292	27519910	62834843	36	9145											
PELP1	27043	hgsc.bcm.edu	37	chr17	4575082	4575082	+	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	ttgtcactcccatcctcagtCtcctcttccaacagggttgg	6	13	7	15	0	4	0	2	0	2	0	8	0	7	0	4	2	1	1	4	2	1	3			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr17:4575082C>T	ENST00000574876.1	-	16	3221	c.3204G>A	c.(3202-3204)gaG>gaA	p.E1068E	PELP1_ENST00000436683.2_Silent_p.E844E|PELP1_ENST00000572293.1_Silent_p.E1118E|PELP1_ENST00000301396.4_Silent_p.E1212E|PELP1_ENST00000269230.7_Silent_p.E978E			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	1068	Glu-rich.|Pro-rich.				cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						CATCCTCAGTCTCCTCTTCCA	0.602																																					p.E1068E		Atlas-SNP	.											.	PELP1	102	.	0			c.G3204A						PASS	.						27	28	27					17																	4575082		1913	4111	6024	SO:0001819	synonymous_variant	27043	exon16			CTCAGTCTCCTCT		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.3204G>A	chr17.hg19:g.4575082C>T		49.0	0.0	.		67.0	12.0	.	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Silent	SNP	ENST00000574876.1	hg19	CCDS58503.1																																																																																			.	.	.	none		0.602	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389		T	4575082	C	T	4575082	2	4	153	1	0	0	0	0	0	0	0	1	11732	912	32	2		2	PELP1	17	4575082	Silent	SNP	C	TCGA-DW-7841-01A-11D-2136-08		4575082	76620128	37	9146											
SOX15	6665	hgsc.bcm.edu	37	chr17	7492754	7492754	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccactgcgcgcccaggcgctTggagatctcggagttgtgca	6	8	14	13	4	1	1	0	0	1	1	2	3	1	2	2	3	2	3	2	3	0	2			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr17:7492754T>C	ENST00000250055.2	-	1	734	c.241A>G	c.(241-243)Aag>Gag	p.K81E	SOX15_ENST00000570788.1_Missense_Mutation_p.K81E|MPDU1_ENST00000423172.2_Intron|FXR2_ENST00000573057.1_5'Flank|SOX15_ENST00000538513.2_Missense_Mutation_p.K81E	NM_006942.1	NP_008873.1	O60248	SOX15_HUMAN	SRY (sex determining region Y)-box 15	81					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						CCCAGGCGCTTGGAGATCTCG	0.667											OREG0024139	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K81E		Atlas-SNP	.											.	SOX15	10	.	0			c.A241G						PASS	.						31	34	33					17																	7492754		2203	4300	6503	SO:0001583	missense	6665	exon1			GGCGCTTGGAGAT	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.241A>G	chr17.hg19:g.7492754T>C	ENSP00000355354:p.Lys81Glu	52.0	0.0	.	642	58.0	22.0	.	NM_006942	B4DWU7|D3DTQ0|P35717|Q9Y6W7	Missense_Mutation	SNP	ENST00000250055.2	hg19	CCDS32549.1	.	.	.	.	.	.	.	.	.	.	T	35	5.577422	0.96565	.	.	ENSG00000129194	ENST00000250055;ENST00000538513	D;D	0.98717	-5.09;-5.09	5.38	5.38	0.77491	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.111127	0.41097	D	0.000944	D	0.99414	0.9793	H	0.96633	3.855	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98487	1.0608	10	0.87932	D	0	.	13.4332	0.61068	0.0:0.0:0.0:1.0	.	81	O60248	SOX15_HUMAN	E	81	ENSP00000355354:K81E;ENSP00000439311:K81E	ENSP00000355354:K81E	K	-	1	0	SOX15	7433478	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.098000	0.71458	2.276000	0.75962	0.454000	0.30748	AAG	.	.	.	none		0.667	SOX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440757.1	NM_006942		C	7492754	T	C	7492754	3	2	153	1	0	0	0	0	1	0	0	0	14959	1821	63	3	468	3	SOX15	17	7492754	Missense_Mutation	SNP	T	TCGA-DW-7841-01A-11D-2136-08	2917672	7492754	73702456	38	9147											
TLCD1	116238	hgsc.bcm.edu	37	chr17	27052951	27052951	+	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	gcccagatccccgacacaatGgagtgagcgaaggagacgag	13	3	14	11	3	0	3	0	1	0	2	1	8	1	4	3	2	1	0	3	2	2	0			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr17:27052951G>T	ENST00000292090.3	-	1	275	c.165C>A	c.(163-165)tcC>tcA	p.S55S	SNORD42A_ENST00000459584.1_RNA|AC010761.14_ENST00000587898.1_RNA|NEK8_ENST00000268766.6_5'Flank|SNORD4B_ENST00000459083.1_RNA|TLCD1_ENST00000394933.3_Intron	NM_138463.3	NP_612472.1	Q96CP7	TLCD1_HUMAN	TLC domain containing 1	55	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)					CCGACACAATGGAGTGAGCGA	0.682																																					p.S55S		Atlas-SNP	.											.	TLCD1	15	.	0			c.C165A						PASS	.						25	24	24					17																	27052951		2203	4300	6503	SO:0001819	synonymous_variant	116238	exon1			CACAATGGAGTGA	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.165C>A	chr17.hg19:g.27052951G>T		63.0	0.0	.		82.0	31.0	.	NM_138463	A8MYP9	Silent	SNP	ENST00000292090.3	hg19	CCDS11242.1																																																																																			.	.	.	none		0.682	TLCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255973.1	NM_138463		T	27052951	G	T	27052951	2	4	153	1	0	0	0	0	0	0	0	1	15949	1335	47	4		4	TLCD1	17	27052951	Silent	SNP	G	TCGA-DW-7841-01A-11D-2136-08	19560197	27052951	54142259	39	9148											
PIPOX	51268	hgsc.bcm.edu	37	chr17	27380072	27380083	+	In_Frame_Del	DEL	GGTTGCCCAGGG	GGTTGCCCAGGG	-																															gcaacgtttcccaaatattcGgttgcccaggggagaagtgg																								rs148024165	byFrequency	TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	GGTTGCCCAGGG	GGTTGCCCAGGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr17:27380072_27380083delGGTTGCCCAGGG	ENST00000323372.4	+	3	724_735	c.398_409delGGTTGCCCAGGG	c.(397-411)cggttgcccagggga>cga	p.LPRG134del	PIPOX_ENST00000583215.1_3'UTR	NM_016518.2	NP_057602.2	Q9P0Z9	SOX_HUMAN	pipecolic acid oxidase	134					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)	CCAAATATTCGGTTGCCCAGGGGAGAAGTGGG	0.495																																					p.133_136del		Atlas-INDEL	.											.	PIPOX	42	.	0			c.397_408del						PASS	.																																			SO:0001651	inframe_deletion	51268	exon3			.	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.398_409delGGTTGCCCAGGG	chr17.hg19:g.27380072_27380083delGGTTGCCCAGGG	ENSP00000317721:p.Leu134_Gly137del	148.0	0.0	0		126.0	27.0	0.214286	NM_016518	B3KNH0|Q96H28|Q9C070	In_Frame_Del	DEL	ENST00000323372.4	hg19	CCDS11248.1																																																																																			.	.	.	none		0.495	PIPOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255954.1	NM_016518		-	27380083	GGTTGCCCAGGG	-	27380072	7	5	153	1	0	1	0	1	0	0	0	0	11950	1116	39	0	408	0	PIPOX	17	27380072	In_Frame_Del	DEL	GGTTGCCCAGGG	TCGA-DW-7841-01A-11D-2136-08	327121	27380072	53815138	40	9149											
DDX52	11056	hgsc.bcm.edu	37	chr17	36003445	36003445	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgaaagagatcgtggacgTccatctttacccagaaagcg	12	7	12	10	4	1	2	0	0	1	2	3	5	2	3	2	2	2	0	2	2	3	2			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr17:36003445T>C	ENST00000349699.2	-	1	48	c.5A>G	c.(4-6)gAc>gGc	p.D2G	DDX52_ENST00000394367.3_5'UTR|RP11-697E22.2_ENST00000586950.1_RNA|RP11-697E22.2_ENST00000586163.1_RNA	NM_007010.3	NP_008941.2	Q9Y2R4	DDX52_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	2						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)				ATCGTGGACGTCCATCTTTAC	0.622																																					p.D2G		Atlas-SNP	.											.	DDX52	40	.	0			c.A5G						PASS	.						43	43	43					17																	36003445		2203	4300	6503	SO:0001583	missense	11056	exon1			TGGACGTCCATCT	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.5A>G	chr17.hg19:g.36003445T>C	ENSP00000268854:p.Asp2Gly	77.0	0.0	.		85.0	17.0	.	NM_007010	Q86YG1|Q8N213|Q9NVE0|Q9Y482	Missense_Mutation	SNP	ENST00000349699.2	hg19	CCDS11323.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.847823	0.91277	.	.	ENSG00000141141	ENST00000349699	T	0.18960	2.18	5.26	5.26	0.73747	.	37.662000	0.00397	N	0.000053	T	0.40196	0.1107	L	0.54323	1.7	0.80722	D	1	D	0.61697	0.99	P	0.54140	0.743	T	0.03545	-1.1026	10	0.87932	D	0	.	11.4972	0.50415	0.0:0.0:0.0:1.0	.	2	Q9Y2R4	DDX52_HUMAN	G	2	ENSP00000268854:D2G	ENSP00000268854:D2G	D	-	2	0	DDX52	33077558	0.996000	0.38824	0.931000	0.37212	0.923000	0.55619	3.812000	0.55628	2.218000	0.71995	0.533000	0.62120	GAC	.	.	.	none		0.622	DDX52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256795.1	NM_152300		C	36003445	T	C	36003445	3	2	153	1	0	0	0	0	1	0	0	0	4372	1667	58	3	1854	3	DDX52	17	36003445	Missense_Mutation	SNP	T	TCGA-DW-7841-01A-11D-2136-08	8623373	36003445	45191765	41	9150											
KRT27	342574	hgsc.bcm.edu	37	chr17	38933310	38933310	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtggatttctcttccacagTgtgaactctggatgagagaa	10	12	12	7	0	2	3	0	2	2	1	4	6	3	5	1	3	1	0	1	3	2	2			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr17:38933310T>C	ENST00000301656.3	-	8	1361	c.1321A>G	c.(1321-1323)Act>Gct	p.T441A	KRT27_ENST00000540723.1_5'UTR	NM_181537.3	NP_853515.2			keratin 27											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				TCTTCCACAGTGTGAACTCTG	0.413																																					p.T441A		Atlas-SNP	.											.	KRT27	41	.	0			c.A1321G						PASS	.						118	121	120					17																	38933310		2203	4300	6503	SO:0001583	missense	342574	exon8			CCACAGTGTGAAC	AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"-", "Intermediate filaments type I, keratins (acidic)"	30841	protein-coding gene	gene with protein product			"keratin 25C"	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.1321A>G	chr17.hg19:g.38933310T>C	ENSP00000301656:p.Thr441Ala	120.0	0.0	.		133.0	28.0	.	NM_181537		Missense_Mutation	SNP	ENST00000301656.3	hg19	CCDS11375.1	.	.	.	.	.	.	.	.	.	.	T	12.82	2.053696	0.36277	.	.	ENSG00000171446	ENST00000301656	D	0.82081	-1.57	5.66	1.64	0.23874	.	0.290739	0.30260	N	0.010040	T	0.63534	0.2519	N	0.19112	0.55	0.19945	N	0.999941	B	0.02656	0.0	B	0.01281	0.0	T	0.47849	-0.9085	10	0.36615	T	0.2	.	0.5754	0.00702	0.2019:0.1756:0.1465:0.4761	.	441	Q7Z3Y8	K1C27_HUMAN	A	441	ENSP00000301656:T441A	ENSP00000301656:T441A	T	-	1	0	KRT27	36186836	0.000000	0.05858	0.645000	0.29479	0.941000	0.58515	-0.027000	0.12371	0.471000	0.27319	0.528000	0.53228	ACT	.	.	.	none		0.413	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537		C	38933310	T	C	38933310	3	2	153	1	0	0	0	0	1	0	0	0	8471	1696	59	3	62	3	KRT27	17	38933310	Missense_Mutation	SNP	T	TCGA-DW-7841-01A-11D-2136-08	2929865	38933310	42261900	42	9151											
FOXJ1	2302	hgsc.bcm.edu	37	chr17	74134123	74134123	+	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	ggggtcaatgcgccagaagcCccccttgcctggttcgtcct	5	9	12	15	2	1	1	1	0	0	1	3	1	2	1	6	3	3	1	6	3	2	2			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr17:74134123C>A	ENST00000322957.6	-	3	931	c.577G>T	c.(577-579)Ggc>Tgc	p.G193C	RNF157-AS1_ENST00000585542.1_RNA|RNF157-AS1_ENST00000590137.1_RNA	NM_001454.3	NP_001445.2	Q92949	FOXJ1_HUMAN	forkhead box J1	193					actin cytoskeleton organization (GO:0030036)|activation of Rho GTPase activity (GO:0032862)|brain development (GO:0007420)|central tolerance induction (GO:0002508)|cilium assembly (GO:0042384)|epithelium development (GO:0060429)|establishment of apical/basal cell polarity (GO:0035089)|glomerular parietal epithelial cell development (GO:0072016)|humoral immune response (GO:0006959)|left/right pattern formation (GO:0060972)|leukocyte migration (GO:0050900)|lung epithelium development (GO:0060428)|metanephric part of ureteric bud development (GO:0035502)|negative regulation of B cell activation (GO:0050869)|negative regulation of germinal center formation (GO:0002635)|negative regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002924)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell differentiation in thymus (GO:0033085)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pattern specification process (GO:0007389)|positive regulation of central B cell tolerance induction (GO:0002897)|positive regulation of lung ciliated cell differentiation (GO:1901248)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			large_intestine(1)|liver(1)|pancreas(1)|skin(1)	4			LUSC - Lung squamous cell carcinoma(166;0.187)			CGCCAGAAGCCCCCCTTGCCT	0.607																																					p.G193C		Atlas-SNP	.											.	FOXJ1	11	.	0			c.G577T						PASS	.						39	43	41					17																	74134123		2203	4300	6503	SO:0001583	missense	2302	exon3			AGAAGCCCCCCTT	X99349	CCDS32739.1	17q25.1	2008-05-14				ENSG00000129654		"Forkhead boxes"	3816	protein-coding gene	gene with protein product		602291		FKHL13		9073514, 16518568	Standard	NM_001454		Approved	HFH-4, HFH4	uc002jqx.3	Q92949		ENST00000322957.6:c.577G>T	chr17.hg19:g.74134123C>A	ENSP00000323880:p.Gly193Cys	70.0	0.0	.		58.0	19.0	.	NM_001454	O00630	Missense_Mutation	SNP	ENST00000322957.6	hg19	CCDS32739.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.986309	0.74589	.	.	ENSG00000129654	ENST00000322957	D	0.95482	-3.72	4.68	4.68	0.58851	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.85682	D	0.000000	D	0.96580	0.8884	L	0.42581	1.335	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97558	1.0096	10	0.87932	D	0	.	17.5787	0.87958	0.0:1.0:0.0:0.0	.	193	Q92949	FOXJ1_HUMAN	C	193	ENSP00000323880:G193C	ENSP00000323880:G193C	G	-	1	0	FOXJ1	71645718	1.000000	0.71417	0.999000	0.59377	0.602000	0.36980	5.893000	0.69798	2.153000	0.67306	0.561000	0.74099	GGC	.	.	.	none		0.607	FOXJ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449856.1	NM_001454		A	74134123	C	A	74134123	3	1	153	1	0	0	0	0	1	0	0	0	6018	623	22	4	692	4	FOXJ1	17	74134123	Missense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08	35200813	74134123	7061087	43	9152											
C17orf70	80233	hgsc.bcm.edu	37	chr17	79514289	79514299	+	Frame_Shift_Del	DEL	TGAGACTGTAG	TGAGACTGTAG	-																															ggccccgcccaccacctcccTgagactgtagaacagcgtgc																										TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	TGAGACTGTAG	TGAGACTGTAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr17:79514289_79514299delTGAGACTGTAG	ENST00000327787.8	-	5	1855_1865	c.1809_1819delCTACAGTCTCA	c.(1807-1821)ttctacagtctcaggfs	p.FYSLR603fs	C17orf70_ENST00000537152.1_Frame_Shift_Del_p.FYSLR452fs|C17orf70_ENST00000425898.2_Frame_Shift_Del_p.FYSLR252fs			Q0VG06	FP100_HUMAN	chromosome 17 open reading frame 70	603					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)			ACCACCTCCCTGAGACTGTAGAACAGCGTGC	0.682																																					p.604_607del		Atlas-INDEL	.											.	C17orf70	79	.	0			c.1810_1820del						PASS	.																																			SO:0001589	frameshift_variant	80233	exon5			.	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.1809_1819delCTACAGTCTCA	chr17.hg19:g.79514289_79514299delTGAGACTGTAG	ENSP00000333283:p.Phe603fs	90.0	0.0	0		92.0	30.0	0.326087	NM_025161	A6NNM1|Q8N3F7|Q9BV13|Q9H6K7|Q9H7E8	Frame_Shift_Del	DEL	ENST00000327787.8	hg19	CCDS32765.2																																																																																			.	.	.	none		0.682	C17orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396170.1	NM_025161		-	79514299	TGAGACTGTAG	-	79514289	7	5	153	1	0	1	0	1	0	0	0	0	1879	1579	55	0	846	0	C17orf70	17	79514289	Frame_Shift_Del	DEL	TGAGACTGTAG	TCGA-DW-7841-01A-11D-2136-08	5380166	79514289	1680921	44	9153											
ARID3A	1820	hgsc.bcm.edu	37	chr19	971936	971936	+	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	tctgctcccaacaaaggaggCggcggcggcggcggcagcag	8	3	17	13	5	1	0	0	0	1	0	2	1	2	1	1	7	3	3	1	7	2	0	rs138086881	byFrequency	TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr19:971936C>G	ENST00000263620.3	+	9	1980	c.1653C>G	c.(1651-1653)ggC>ggG	p.G551G		NM_005224.2	NP_005215.1	Q99856	ARI3A_HUMAN	AT rich interactive domain 3A (BRIGHT-like)	551	Gly-rich.|Important for cytoplasmic localization. {ECO:0000250}.					cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACAAAGGAggcggcggcggcg	0.657																																					p.G551G	Pancreas(29;54 1022 32760 50921)	Atlas-SNP	.											ARID3A,NS,carcinoma,0,1	ARID3A	35	.	0			c.C1653G						PASS	.						25	33	30					19																	971936		2196	4289	6485	SO:0001819	synonymous_variant	1820	exon9			AGGAGGCGGCGGC	U88047	CCDS12050.1	19p13.3	2013-02-07	2006-11-08	2004-01-30		ENSG00000116017		"-"	3031	protein-coding gene	gene with protein product		603265	"dead ringer-like 1 (Drosophila)", "AT rich interactive domain 3A (BRIGHT- like)"	DRIL1		9722953	Standard	NM_005224		Approved	BRIGHT	uc002lql.3	Q99856		ENST00000263620.3:c.1653C>G	chr19.hg19:g.971936C>G		67.0	0.0	.		89.0	5.0	.	NM_005224	Q5I858|Q6P9C6|Q8IZA7|Q8N4Z3	Silent	SNP	ENST00000263620.3	hg19	CCDS12050.1																																																																																			.	C|0.999;T|0.001	.	alt		0.657	ARID3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458219.1	NM_005224		G	971936	C	G	971936	2	3	153	1	0	0	0	0	0	0	0	1	916	755	27	4		4	ARID3A	19	971936	Silent	SNP	C	TCGA-DW-7841-01A-11D-2136-08		971936	58157047	45	9154											
CACNG7	59284	hgsc.bcm.edu	37	chr19	54418709	54418709	+	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	caacatcggccacatccgccCgcagaggaccattctggctt	9	7	9	16	3	1	1	0	0	1	1	3	2	2	2	4	3	1	2	4	3	1	2			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr19:54418709C>A	ENST00000391767.1	+	4	586	c.374C>A	c.(373-375)cCg>cAg	p.P125Q	CACNG7_ENST00000468076.1_3'UTR|CACNG7_ENST00000391766.1_Missense_Mutation_p.P125Q|CACNG7_ENST00000222212.2_Missense_Mutation_p.P125Q			P62955	CCG7_HUMAN	calcium channel, voltage-dependent, gamma subunit 7	125					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)	p.P125L(1)		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)		CACATCCGCCCGCAGAGGACC	0.597																																					p.P125Q		Atlas-SNP	.											CACNG7,colon,carcinoma,0,1	CACNG7	58	.	1	Substitution - Missense(1)	large_intestine(1)	c.C374A						PASS	.						115	101	105					19																	54418709		2203	4300	6503	SO:0001583	missense	59284	exon3			TCCGCCCGCAGAG	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.374C>A	chr19.hg19:g.54418709C>A	ENSP00000375647:p.Pro125Gln	98.0	1.0	.		103.0	5.0	.	NM_031896	Q52LL8|Q8VBX3|Q8WXS6|Q9BXT1	Missense_Mutation	SNP	ENST00000391767.1	hg19	CCDS12868.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.110454	0.77210	.	.	ENSG00000105605	ENST00000391767;ENST00000222212;ENST00000391766	D;D;D	0.88509	-2.39;-2.39;-2.39	3.91	3.91	0.45181	.	0.000000	0.85682	D	0.000000	D	0.92368	0.7578	M	0.68952	2.095	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	D	0.89898	0.4042	10	0.22109	T	0.4	-9.9231	14.2221	0.65833	0.0:1.0:0.0:0.0	.	125	P62955	CCG7_HUMAN	Q	125	ENSP00000375647:P125Q;ENSP00000222212:P125Q;ENSP00000375646:P125Q	ENSP00000222212:P125Q	P	+	2	0	CACNG7	59110521	1.000000	0.71417	0.963000	0.40424	0.979000	0.70002	7.180000	0.77674	2.469000	0.83416	0.563000	0.77884	CCG	.	.	.	none		0.597	CACNG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139240.2			A	54418709	C	A	54418709	3	1	153	1	0	0	0	0	1	0	0	0	2564	652	23	4	384	4	CACNG7	19	54418709	Missense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08	53446773	54418709	4710274	46	9155											
ZNF497	162968	hgsc.bcm.edu	37	chr19	58867603	58867603	+	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	gccgcaagcgtagggcctctCgcccgtgtgcgtgcgccggt	3	7	16	15	7	1	0	0	0	1	0	2	0	1	0	4	2	3	2	4	2	2	1			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr19:58867603C>A	ENST00000311044.3	-	3	1587	c.1399G>T	c.(1399-1401)Gag>Tag	p.E467*	A1BG_ENST00000263100.3_5'Flank|CTD-2619J13.9_ENST00000599952.1_RNA|A1BG-AS1_ENST00000593374.1_RNA|A1BG-AS1_ENST00000600379.1_RNA|A1BG-AS1_ENST00000593960.1_RNA|A1BG-AS1_ENST00000594950.1_RNA|A1BG-AS1_ENST00000599728.1_RNA|A1BG-AS1_ENST00000600686.1_RNA|ZNF497_ENST00000425453.3_Nonsense_Mutation_p.E467*|CTD-2619J13.8_ENST00000599109.1_RNA|A1BG-AS1_ENST00000595302.1_RNA	NM_198458.2	NP_940860.2	Q6ZNH5	ZN497_HUMAN	zinc finger protein 497	467					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|lung(3)|skin(2)	7		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;0.0278)		TAGGGCCTCTCGCCCGTGTGC	0.692																																					p.E467X		Atlas-SNP	.											.	ZNF497	22	.	0			c.G1399T						PASS	.						15	17	16					19																	58867603		2194	4293	6487	SO:0001587	stop_gained	162968	exon2			GCCTCTCGCCCGT	AK126727	CCDS12977.1	19q13.43	2013-01-08			ENSG00000174586	ENSG00000174586		"Zinc fingers, C2H2-type"	23714	protein-coding gene	gene with protein product							Standard	NM_198458		Approved	FLJ44773	uc002qsi.2	Q6ZNH5		ENST00000311044.3:c.1399G>T	chr19.hg19:g.58867603C>A	ENSP00000311183:p.Glu467*	17.0	0.0	.		30.0	9.0	.	NM_001207009	Q05AG8|Q0VF48|Q6ZTD2|Q9UIA8	Nonsense_Mutation	SNP	ENST00000311044.3	hg19	CCDS12977.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.257589	0.80246	.	.	ENSG00000174586	ENST00000311044;ENST00000425453	.	.	.	1.24	0.059	0.14330	.	.	.	.	.	.	.	.	.	.	.	0.53005	D	0.999969	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	8.3137	0.32086	0.0:0.7513:0.2487:0.0	.	.	.	.	X	467	.	ENSP00000311183:E467X	E	-	1	0	ZNF497	63559415	0.568000	0.26635	0.001000	0.08648	0.280000	0.26924	2.887000	0.48586	0.066000	0.16515	0.195000	0.17529	GAG	.	.	.	none		0.692	ZNF497-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466942.2	NM_198458		A	58867603	C	A	58867603	4	1	153	1	0	0	0	0	0	1	0	0	17958	893	31	4	101	4	ZNF497	19	58867603	Nonsense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08	4448894	58867603	261380	47	9156											
CTCFL	140690	hgsc.bcm.edu	37	chr20	56090837	56090837	+	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	gcatagctgcactggcaacaCtgaaaggggcgctccccagt	10	6	12	13	1	0	1	0	1	0	0	1	1	1	1	2	3	3	5	2	3	3	1			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr20:56090837C>G	ENST00000608263.1	-	5	1774	c.1113G>C	c.(1111-1113)caG>caC	p.Q371H	CTCFL_ENST00000423479.3_Missense_Mutation_p.Q371H|CTCFL_ENST00000371196.2_Missense_Mutation_p.Q371H|CTCFL_ENST00000539382.1_Missense_Mutation_p.Q166H|CTCFL_ENST00000432255.2_Intron|CTCFL_ENST00000608903.1_Missense_Mutation_p.Q109H|CTCFL_ENST00000429804.3_Missense_Mutation_p.Q371H|CTCFL_ENST00000608858.1_5'UTR|CTCFL_ENST00000422869.2_Missense_Mutation_p.Q371H|CTCFL_ENST00000609232.1_Missense_Mutation_p.Q371H|CTCFL_ENST00000433949.3_Missense_Mutation_p.Q166H|CTCFL_ENST00000608440.1_Missense_Mutation_p.Q371H|CTCFL_ENST00000502686.2_Missense_Mutation_p.Q109H|CTCFL_ENST00000608425.1_Missense_Mutation_p.Q371H|CTCFL_ENST00000243914.3_Missense_Mutation_p.Q371H	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	371					cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			ACTGGCAACACTGAAAGGGGC	0.473																																					p.Q371H		Atlas-SNP	.											.	CTCFL	97	.	0			c.G1113C						PASS	.						173	164	167					20																	56090837		2203	4300	6503	SO:0001583	missense	140690	exon5			GCAACACTGAAAG		CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"Zinc fingers, C2H2-type"	16234	protein-coding gene	gene with protein product	"cancer/testis antigen 27"	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.1113G>C	chr20.hg19:g.56090837C>G	ENSP00000476783:p.Gln371His	247.0	0.0	.		296.0	139.0	.	NM_001269044	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Missense_Mutation	SNP	ENST00000608263.1	hg19	CCDS13459.1	.	.	.	.	.	.	.	.	.	.	C	12.79	2.042881	0.36085	.	.	ENSG00000124092	ENST00000423479;ENST00000243914;ENST00000371196;ENST00000429804;ENST00000433949;ENST00000502686;ENST00000422109;ENST00000426658;ENST00000539382;ENST00000422869	T;T;T;T;T;T;T;T;T;T	0.19394	2.15;2.15;2.15;2.15;2.15;2.15;2.15;2.15;2.15;2.15	5.24	3.07	0.35406	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.342601	0.21292	N	0.076960	T	0.15869	0.0382	L	0.37466	1.105	0.39176	D	0.962686	B;B;B;B;B	0.25390	0.025;0.077;0.03;0.077;0.125	B;B;B;B;B	0.28011	0.05;0.045;0.082;0.045;0.085	T	0.09271	-1.0682	10	0.72032	D	0.01	-35.7918	5.7172	0.17966	0.0:0.5692:0.2418:0.1889	.	371;371;371;371;371	A6XGM9;A6XGM2;E7EUE3;A6XGL8;Q8NI51	.;.;.;.;CTCFL_HUMAN	H	371;371;371;371;371;109;371;371;166;371	ENSP00000415579:Q371H;ENSP00000243914:Q371H;ENSP00000360239:Q371H;ENSP00000415329:Q371H;ENSP00000392034:Q371H;ENSP00000437999:Q109H;ENSP00000413713:Q371H;ENSP00000403369:Q371H;ENSP00000439998:Q166H;ENSP00000399061:Q371H	ENSP00000243914:Q371H	Q	-	3	2	CTCFL	55524243	1.000000	0.71417	0.998000	0.56505	0.813000	0.45954	1.660000	0.37397	1.327000	0.45338	0.650000	0.86243	CAG	.	.	.	none		0.473	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618		G	56090837	C	G	56090837	3	3	153	1	0	0	0	0	1	0	0	0	4003	564	20	4	902	4	CTCFL	20	56090837	Missense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08		56090837	6934683	48	9157											
PDE9A	5152	hgsc.bcm.edu	37	chr21	44185564	44185565	+	Frame_Shift_Ins	INS	-	-	G																															gattctttcaaagagaaaatINSggagaattttgactacagca																										TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr21:44185564_44185565insG	ENST00000291539.6	+	15	1376_1377	c.1316_1317insG	c.(1315-1320)atggagfs	p.E440fs	PDE9A_ENST00000335440.6_Frame_Shift_Ins_p.E338fs|PDE9A_ENST00000398236.3_Frame_Shift_Ins_p.E354fs|PDE9A_ENST00000398229.3_Frame_Shift_Ins_p.E306fs|PDE9A_ENST00000328862.6_Frame_Shift_Ins_p.E414fs|PDE9A_ENST00000380328.2_Frame_Shift_Ins_p.E387fs|PDE9A_ENST00000349112.3_Frame_Shift_Ins_p.E312fs|PDE9A_ENST00000398232.3_Frame_Shift_Ins_p.E373fs|PDE9A_ENST00000470987.1_3'UTR|PDE9A_ENST00000398234.3_Frame_Shift_Ins_p.E339fs|PDE9A_ENST00000335512.4_Frame_Shift_Ins_p.E380fs|PDE9A_ENST00000398225.3_Frame_Shift_Ins_p.E399fs|PDE9A_ENST00000398227.3_Frame_Shift_Ins_p.E280fs|PDE9A_ENST00000539837.1_Frame_Shift_Ins_p.E312fs|PDE9A_ENST00000398224.3_Frame_Shift_Ins_p.E313fs	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	440	Catalytic. {ECO:0000250}.				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)	AAAGAGAAAATGGAGAATTTTG	0.48																																					p.M439fs		Atlas-INDEL	.											.	PDE9A	69	.	0			c.1316_1317insG						PASS	.																																			SO:0001589	frameshift_variant	5152	exon15			.	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.1318dupG	chr21.hg19:g.44185566_44185566dupG	ENSP00000291539:p.Glu440fs	53.0	0.0	0		41.0	16.0	0.390244	NM_002606	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	Frame_Shift_Ins	INS	ENST00000291539.6	hg19	CCDS13690.1																																																																																			.	.	.	none		0.48	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1			G	44185565	-	G	44185564	7	5	153	1	0	1	1	0	0	0	0	0	11662	1464	51	0	1454	0	PDE9A	21	44185564	Frame_Shift_Ins	INS	-	TCGA-DW-7841-01A-11D-2136-08		44185564	3944331	49	9158											
MICAL3	57553	hgsc.bcm.edu	37	chr22	18293564	18293564	+	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	cttggcattcagttcctcctCcgtgtaggttcttggctgga	4	15	11	11	1	2	0	1	0	1	0	5	1	5	1	3	4	0	5	3	4	1	6			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr22:18293564C>T	ENST00000441493.2	-	28	5813	c.5461G>A	c.(5461-5463)Gag>Aag	p.E1821K	XXbac-B461K10.4_ENST00000476405.1_RNA|MICAL3_ENST00000580469.1_5'UTR	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	1821					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)		AGTTCCTCCTCCGTGTAGGTT	0.602																																					p.E1821K		Atlas-SNP	.											.	MICAL3	53	.	0			c.G5461A						PASS	.						78	81	80					22																	18293564		2181	4279	6460	SO:0001583	missense	57553	exon28			CCTCCTCCGTGTA	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.5461G>A	chr22.hg19:g.18293564C>T	ENSP00000416015:p.Glu1821Lys	91.0	0.0	.		93.0	21.0	.	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Missense_Mutation	SNP	ENST00000441493.2	hg19	CCDS46659.1	.	.	.	.	.	.	.	.	.	.	C	17.11	3.305044	0.60305	.	.	ENSG00000093100	ENST00000441493	T	0.65178	-0.14	4.81	4.81	0.61882	.	0.182495	0.46442	D	0.000288	T	0.66519	0.2797	L	0.34521	1.04	0.80722	D	1	D	0.67145	0.996	P	0.60415	0.874	T	0.62407	-0.6861	10	0.21540	T	0.41	.	17.8904	0.88870	0.0:1.0:0.0:0.0	.	1821	Q7RTP6	MICA3_HUMAN	K	1821	ENSP00000416015:E1821K	ENSP00000416015:E1821K	E	-	1	0	XXbac-B461K10.4	16673564	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	7.818000	0.86416	2.215000	0.71742	0.462000	0.41574	GAG	.	.	.	none		0.602	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			T	18293564	C	T	18293564	3	4	153	1	0	0	0	0	1	0	0	0	9578	864	30	2	567	2	MICAL3	22	18293564	Missense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08		18293564	33011002	50	9159											
SEC14L2	23541	hgsc.bcm.edu	37	chr22	30805476	30805477	+	Splice_Site	INS	-	-	T																															cgtctttttgttgttaaaggINStaagttgggaatttcttgtg																										TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr22:30805476_30805477insT	ENST00000312932.9	+	7	840		c.e7+1		RP4-539M6.19_ENST00000439838.1_Splice_Site|SEC14L2_ENST00000402592.3_Splice_Site|SEC14L2_ENST00000405717.3_Splice_Site|SEC14L2_ENST00000403484.1_Splice_Site	NM_012429.3	NP_036561.1	O76054	S14L2_HUMAN	SEC14-like 2 (S. cerevisiae)						positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cholesterol biosynthetic process (GO:0045540)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	phospholipid binding (GO:0005543)|transporter activity (GO:0005215)|vitamin E binding (GO:0008431)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|urinary_tract(1)	10					Vitamin E(DB00163)	GTTGTTAAAGGTAAGTTGGGAA	0.436																																					.		Atlas-INDEL	.											.	SEC14L2	24	.	0			c.580+1->T						PASS	.																																			SO:0001630	splice_region_variant	23541	exon7			.	AL096881	CCDS13876.1, CCDS46685.1, CCDS56228.1	22q12.2	2010-08-19	2001-11-28		ENSG00000100003	ENSG00000100003			10699	protein-coding gene	gene with protein product	"supernatant protein factor"	607558	"SEC14 (S. cerevisiae)-like 2"	C22orf6		10591208	Standard	NM_033382		Approved	TAP, SPF, KIAA1186, KIAA1658	uc003ahr.3	O76054	OTTHUMG00000151024	ENST00000312932.9:c.580+1->T	chr22.hg19:g.30805477_30805477dupT		136.0	0.0	0		122.0	33.0	0.270492	NM_033382	B7Z8Q1|F5H3U4|Q53EQ2|Q6PD61|Q9ULN4	Splice_Site	INS	ENST00000312932.9	hg19	CCDS13876.1																																																																																			.	.	.	none		0.436	SEC14L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321018.4	NM_012429	Intron	T	30805477	-	T	30805476	8	5	153	1	0	1	1	0	0	0	1	0	13995	1275	44	0	607	0	SEC14L2	22	30805476	Splice_Site	INS	-	TCGA-DW-7841-01A-11D-2136-08	12511912	30805476	20499090	51	9160											
MEI1	150365	hgsc.bcm.edu	37	chr22	42154472	42154472	+	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	gatcgccagtacatggagggAgctgctcgccagagacagta	11	6	14	10	2	0	1	0	0	0	1	2	5	0	3	2	2	3	4	2	2	2	2			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr22:42154472A>C	ENST00000401548.3	+	18	2095	c.2055A>C	c.(2053-2055)ggA>ggC	p.G685G	MEI1_ENST00000300398.4_5'UTR|MEI1_ENST00000400107.1_Silent_p.G53G|MEI1_ENST00000540833.1_Silent_p.G425G|MEI1_ENST00000540880.1_Silent_p.G3G	NM_152513.3	NP_689726.3			meiosis inhibitor 1											breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						ACATGGAGGGAGCTGCTCGCC	0.582																																					p.G685G		Atlas-SNP	.											.	MEI1	87	.	0			c.A2055C						PASS	.						56	58	57					22																	42154472		2038	4190	6228	SO:0001819	synonymous_variant	150365	exon18			GGAGGGAGCTGCT	AK092934	CCDS46718.1	22q13.2	2013-10-11			ENSG00000167077	ENSG00000167077			28613	protein-coding gene	gene with protein product	"spermatogenesis associated 38"	608797				16683055	Standard	XM_006724154		Approved	MGC40042, SPATA38	uc003baz.1	Q5TIA1	OTTHUMG00000030083	ENST00000401548.3:c.2055A>C	chr22.hg19:g.42154472A>C		36.0	0.0	.		36.0	12.0	.	NM_152513		Silent	SNP	ENST00000401548.3	hg19	CCDS46718.1																																																																																			.	.	.	none		0.582	MEI1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000074937.3	NM_152513		C	42154472	A	C	42154472	2	2	153	1	0	0	0	0	0	0	0	1	9472	291	11	5		5	MEI1	22	42154472	Silent	SNP	A	TCGA-DW-7841-01A-11D-2136-08	11348996	42154472	9150094	52	9161											
POLDIP3	84271	hgsc.bcm.edu	37	chr22	43010826	43010826	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcctttcgccgccgccccgCgcttcctgatgagttcgtcc	2	11	10	18	6	0	2	0	2	0	0	5	2	3	2	7	0	0	2	7	0	0	3			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr22:43010826C>T	ENST00000252115.5	-	1	142	c.38G>A	c.(37-39)cGc>cAc	p.R13H	POLDIP3_ENST00000339677.6_Missense_Mutation_p.R13H|RNU12_ENST00000362512.1_lincRNA|POLDIP3_ENST00000348657.2_Missense_Mutation_p.R13H	NM_032311.3	NP_115687.2	Q9BY77	PDIP3_HUMAN	polymerase (DNA-directed), delta interacting protein 3	13					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						CGCCGCCCCGCGCTTCCTGAT	0.667																																					p.R13H	Ovarian(52;967 1128 5875 19997 42537)	Atlas-SNP	.											.	POLDIP3	58	.	0			c.G38A						PASS	.						45	50	48					22																	43010826		2203	4300	6503	SO:0001583	missense	84271	exon1			GCCCCGCGCTTCC		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.38G>A	chr22.hg19:g.43010826C>T	ENSP00000252115:p.Arg13His	125.0	0.0	.		110.0	26.0	.	NM_178136	A8K6F8|A8K6V9|Q009A7|Q5H972|Q6PGN6|Q7Z6Z0|Q9NSP5|Q9NSP6	Missense_Mutation	SNP	ENST00000252115.5	hg19	CCDS14038.1	.	.	.	.	.	.	.	.	.	.	C	34	5.316914	0.95682	.	.	ENSG00000100227	ENST00000348657;ENST00000252115;ENST00000415122;ENST00000339677;ENST00000452567	.	.	.	4.4	4.4	0.53042	.	0.000000	0.85682	D	0.000000	T	0.76506	0.3997	L	0.59436	1.845	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.974;0.998;0.992;0.965	T	0.79654	-0.1713	9	0.87932	D	0	-17.6392	17.5459	0.87861	0.0:1.0:0.0:0.0	.	13;13;13;13	B4E0L0;Q6R954;Q9BY77-2;Q9BY77	.;.;.;PDIP3_HUMAN	H	13	.	ENSP00000252115:R13H	R	-	2	0	POLDIP3	41340770	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	5.800000	0.69108	2.439000	0.82584	0.557000	0.71058	CGC	.	.	.	none		0.667	POLDIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320433.1	NM_032311		T	43010826	C	T	43010826	3	4	153	1	0	0	0	0	1	0	0	0	12202	768	27	1	1263	1	POLDIP3	22	43010826	Missense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08	856354	43010826	8293740	53	9162											
MCAT	27349	hgsc.bcm.edu	37	chr22	43533107	43533107	+	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	ctcttggtgtcctgaaatcaCcctgcaatctggaaagaggt	10	11	10	10	0	3	2	1	1	2	1	4	3	4	3	2	3	1	1	2	3	3	1			TCGA-DW-7841-01A-11D-2136-08	TCGA-DW-7841-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa4db950-5986-4268-9554-23eeace63f53	77e5cfbb-e4ce-45f5-98d2-46ee8a5598ea	g.chr22:43533107C>T	ENST00000290429.6	-	3	754	c.709G>A	c.(709-711)Gtg>Atg	p.V237M	MCAT_ENST00000327555.5_Intron	NM_173467.4	NP_775738.3	Q8IVS2	FABD_HUMAN	malonyl CoA:ACP acyltransferase (mitochondrial)	237					fatty acid biosynthetic process (GO:0006633)|metabolic process (GO:0008152)	mitochondrion (GO:0005739)	[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|poly(A) RNA binding (GO:0044822)|transferase activity (GO:0016740)			breast(1)|endometrium(3)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(1)	11		Ovarian(80;0.0694)				CCTGAAATCACCCTGCAATCT	0.532											OREG0026613	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V237M		Atlas-SNP	.											.	MCAT	26	.	0			c.G709A						PASS	.						194	185	188					22																	43533107		2203	4300	6503	SO:0001583	missense	27349	exon3			AAATCACCCTGCA	AL359401	CCDS14045.1, CCDS33660.1	22q13.2	2010-04-27			ENSG00000100294	ENSG00000100294	2.3.1.39		29622	protein-coding gene	gene with protein product		614479				12882974	Standard	NM_173467		Approved	MT, MCT, fabD, FASN2C, NET62	uc003bdl.1	Q8IVS2	OTTHUMG00000150704	ENST00000290429.6:c.709G>A	chr22.hg19:g.43533107C>T	ENSP00000290429:p.Val237Met	211.0	0.0	.	917	245.0	62.0	.	NM_173467	B0QY72|O95510|O95511	Missense_Mutation	SNP	ENST00000290429.6	hg19	CCDS33660.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.667793	0.88348	.	.	ENSG00000100294	ENST00000290429	T	0.52295	0.67	5.13	5.13	0.70059	Acyl transferase/acyl hydrolase/lysophospholipase (1);Malonyl-CoA ACP transacylase, ACP-binding (1);Acyl transferase (1);	0.000000	0.85682	D	0.000000	T	0.80859	0.4704	H	0.97365	3.99	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88241	0.2910	10	0.87932	D	0	-25.5062	18.5829	0.91178	0.0:1.0:0.0:0.0	.	237	Q8IVS2	FABD_HUMAN	M	237	ENSP00000290429:V237M	ENSP00000290429:V237M	V	-	1	0	MCAT	41863051	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.277000	0.78572	2.387000	0.81309	0.591000	0.81541	GTG	.	.	.	none		0.532	MCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319677.2	NM_173467		T	43533107	C	T	43533107	3	4	153	1	0	0	0	0	1	0	0	0	9379	507	18	2	471	2	MCAT	22	43533107	Missense_Mutation	SNP	C	TCGA-DW-7841-01A-11D-2136-08	522281	43533107	7771459	54	9163											
FOXE3	2301	hgsc.bcm.edu	37	chr1	47882415	47882415	+	Missense_Mutation	SNP	A	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	gggcaacccgggcaagggcaActactggacgctggaccccg	9	3	15	14	3	0	0	0	0	0	0	0	2	0	2	3	5	3	4	3	5	4	1			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr1:47882415A>C	ENST00000335071.2	+	1	672	c.428A>C	c.(427-429)aAc>aCc	p.N143T		NM_012186.2	NP_036318.1	Q13461	FOXE3_HUMAN	forkhead box E3	143					camera-type eye development (GO:0043010)|cell development (GO:0048468)|positive regulation of epithelial cell proliferation (GO:0050679)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(3)|prostate(1)|upper_aerodigestive_tract(1)	5				READ - Rectum adenocarcinoma(2;0.0908)		GGCAAGGGCAACTACTGGACG	0.687																																					p.N143T		Atlas-SNP	.											.	FOXE3	8	.	0			c.A428C						PASS	.						41	43	43					1																	47882415		2203	4299	6502	SO:0001583	missense	2301	exon1			AGGGCAACTACTG	AF275722	CCDS550.1	1p32	2008-02-05			ENSG00000186790	ENSG00000186790		"Forkhead boxes"	3808	protein-coding gene	gene with protein product		601094		FKHL12		8825632	Standard	NM_012186		Approved	FREAC8	uc001crk.3	Q13461	OTTHUMG00000007954	ENST00000335071.2:c.428A>C	chr1.hg19:g.47882415A>C	ENSP00000334472:p.Asn143Thr	101.0	0.0	.		103.0	30.0	.	NM_012186	Q5SVY9|Q9NQV9	Missense_Mutation	SNP	ENST00000335071.2	hg19	CCDS550.1	.	.	.	.	.	.	.	.	.	.	a	20.1	3.934136	0.73442	.	.	ENSG00000186790	ENST00000335071	D	0.95518	-3.73	3.45	3.45	0.39498	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.41097	U	0.000952	D	0.97467	0.9171	M	0.87328	2.875	0.54753	D	0.999982	D	0.71674	0.998	D	0.70487	0.969	D	0.97641	1.0148	10	0.62326	D	0.03	.	12.082	0.53675	1.0:0.0:0.0:0.0	.	143	Q13461	FOXE3_HUMAN	T	143	ENSP00000334472:N143T	ENSP00000334472:N143T	N	+	2	0	FOXE3	47655002	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	3.748000	0.55142	1.427000	0.47276	0.373000	0.22412	AAC	.	.	.	none		0.687	FOXE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021836.1	NM_012186		C	47882415	A	C	47882415	3	2	154	1	0	0	0	0	1	0	0	0	6011	43	2	5	430	5	FOXE3	1	47882415	Missense_Mutation	SNP	A	TCGA-DW-7842-01A-11D-2136-08		47882415	201368206	1	9164											
PEA15	8682	hgsc.bcm.edu	37	chr1	160181403	160181403	+	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	cttgaagatctagaacagctCaagtcggcctgcaaggaaga	14	7	11	9	1	2	4	1	1	1	3	3	5	2	5	1	2	3	2	1	2	6	2			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr1:160181403C>A	ENST00000360472.4	+	2	257	c.69C>A	c.(67-69)ctC>ctA	p.L23L	RP11-536C5.7_ENST00000418602.1_RNA|PEA15_ENST00000368077.1_Silent_p.L23L|PEA15_ENST00000488858.1_3'UTR|PEA15_ENST00000368076.1_Silent_p.L44L	NM_003768.3	NP_003759.1	Q15121	PEA15_HUMAN	phosphoprotein enriched in astrocytes 15	23	DED. {ECO:0000255|PROSITE- ProRule:PRU00065}.				apoptotic process (GO:0006915)|carbohydrate transport (GO:0008643)|DNA damage checkpoint (GO:0000077)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of glucose import (GO:0046325)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|response to morphine (GO:0043278)|transport (GO:0006810)	cytoplasm (GO:0005737)|microtubule associated complex (GO:0005875)				large_intestine(1)|lung(4)	5	all_cancers(52;3.11e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TAGAACAGCTCAAGTCGGCCT	0.542																																					p.L23L		Atlas-SNP	.											.	PEA15	7	.	0			c.C69A						PASS	.						135	112	120					1																	160181403		2203	4300	6503	SO:0001819	synonymous_variant	8682	exon2			ACAGCTCAAGTCG	Y13736	CCDS1199.1, CCDS72954.1	1q21.1	2008-07-18			ENSG00000162734	ENSG00000162734			8822	protein-coding gene	gene with protein product	"Phosphoprotein enriched in astrocytes, 15kD", "homolog of mouse MAT-1 oncogene"	603434				9205133	Standard	XM_005245564		Approved	HMAT1, MAT1, PED, PEA-15, MAT1H, HUMMAT1H	uc001fvk.3	Q15121	OTTHUMG00000031605	ENST00000360472.4:c.69C>A	chr1.hg19:g.160181403C>A		131.0	0.0	.		100.0	16.0	.	NM_003768	B1AKZ3|O00511	Silent	SNP	ENST00000360472.4	hg19	CCDS1199.1																																																																																			.	.	.	none		0.542	PEA15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077407.1	NM_003768		A	160181403	C	A	160181403	2	1	154	1	0	0	0	0	0	0	0	1	11718	813	29	4		4	PEA15	1	160181403	Silent	SNP	C	TCGA-DW-7842-01A-11D-2136-08	112298988	160181403	89069218	2	9165											
PROM2	150696	hgsc.bcm.edu	37	chr2	95941238	95941238	+	Missense_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	aggccctactgaatgagctgGcctccgtgaaggtgaatgag	10	8	14	9	1	0	5	0	5	0	0	1	5	1	5	3	3	2	1	3	3	4	1			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr2:95941238G>A	ENST00000317620.9	+	2	407	c.274G>A	c.(274-276)Gcc>Acc	p.A92T	PROM2_ENST00000317668.4_Missense_Mutation_p.A92T|PROM2_ENST00000403131.2_Missense_Mutation_p.A92T|PROM2_ENST00000463580.1_3'UTR|PROM2_ENST00000542147.1_Missense_Mutation_p.A92T	NM_001165978.1	NP_001159450.1	Q8N271	PROM2_HUMAN	prominin 2	92					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						GAATGAGCTGGCCTCCGTGAA	0.602																																					p.A92T		Atlas-SNP	.											.	PROM2	78	.	0			c.G274A						PASS	.						99	87	91					2																	95941238		2203	4300	6503	SO:0001583	missense	150696	exon2			GAGCTGGCCTCCG	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.274G>A	chr2.hg19:g.95941238G>A	ENSP00000318270:p.Ala92Thr	88.0	0.0	.		82.0	27.0	.	NM_001165977	A8K2V1|Q2HIX6|Q8NB84|Q8TAE2	Missense_Mutation	SNP	ENST00000317620.9	hg19	CCDS2012.1	.	.	.	.	.	.	.	.	.	.	G	13.29	2.194115	0.38707	.	.	ENSG00000155066	ENST00000403131;ENST00000317668;ENST00000317620;ENST00000542147	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	4.57	-4.2	0.03823	.	1.178410	0.06360	N	0.711489	T	0.34077	0.0885	L	0.44542	1.39	0.09310	N	1	P	0.43578	0.811	B	0.40602	0.334	T	0.37079	-0.9721	10	0.14252	T	0.57	-1.8729	15.0393	0.71777	0.0:0.0:0.1886:0.8114	.	92	Q8N271	PROM2_HUMAN	T	92	ENSP00000385716:A92T;ENSP00000318520:A92T;ENSP00000318270:A92T;ENSP00000442542:A92T	ENSP00000318270:A92T	A	+	1	0	PROM2	95304965	0.000000	0.05858	0.001000	0.08648	0.580000	0.36256	-2.235000	0.01202	-0.468000	0.06922	0.462000	0.41574	GCC	.	.	.	none		0.602	PROM2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252771.1	NM_144707		A	95941238	G	A	95941238	3	1	154	1	0	0	0	0	1	0	0	0	12566	1203	42	2	280	2	PROM2	2	95941238	Missense_Mutation	SNP	G	TCGA-DW-7842-01A-11D-2136-08		95941238	147258135	3	9166											
ATG16L1	55054	hgsc.bcm.edu	37	chr2	234173559	234173559	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attgcagaatgtttgcagacTatctctgacctggagacgga	11	11	11	8	1	1	4	0	1	1	3	2	6	1	5	1	2	2	3	1	2	2	3			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr2:234173559T>C	ENST00000392017.4	+	5	668	c.411T>C	c.(409-411)acT>acC	p.T137T	ATG16L1_ENST00000392020.4_Silent_p.T137T|ATG16L1_ENST00000373525.5_Intron|ATG16L1_ENST00000392018.1_Silent_p.T137T|ATG16L1_ENST00000347464.5_Intron	NM_001190266.1|NM_001190267.1|NM_030803.6	NP_001177195.1|NP_001177196.1|NP_110430.5	Q676U5	A16L1_HUMAN	autophagy related 16-like 1 (S. cerevisiae)	137					autophagic vacuole assembly (GO:0000045)|negative stranded viral RNA replication (GO:0039689)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|autophagic vacuole membrane (GO:0000421)|axoneme (GO:0005930)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(7)|prostate(3)|skin(1)	25		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0539)		Epithelial(121;1.53e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000379)|LUSC - Lung squamous cell carcinoma(224;0.00619)|Lung(119;0.00732)|GBM - Glioblastoma multiforme(43;0.11)		GTTTGCAGACTATCTCTGACC	0.527																																					p.T137T		Atlas-SNP	.											.	ATG16L1	83	.	0			c.T411C						PASS	.						109	97	101					2																	234173559		2203	4300	6503	SO:0001819	synonymous_variant	55054	exon5			GCAGACTATCTCT	AK000897	CCDS2502.2, CCDS2503.2, CCDS54438.1	2q37.1	2014-02-12	2012-06-06	2005-09-13	ENSG00000085978	ENSG00000085978		"WD repeat domain containing"	21498	protein-coding gene	gene with protein product		610767	"APG16 autophagy 16-like (S. cerevisiae)", "ATG16 autophagy related 16-like (S. cerevisiae)", "ATG16 autophagy related 16-like 1 (S. cerevisiae)"	APG16L, ATG16L			Standard	NM_017974		Approved	WDR30, FLJ10035, ATG16A	uc002vty.3	Q676U5	OTTHUMG00000133619	ENST00000392017.4:c.411T>C	chr2.hg19:g.234173559T>C		129.0	0.0	.		114.0	38.0	.	NM_017974	A3EXK9|A3EXL0|B6ZDH0|Q6IPN1|Q6UXW4|Q6ZVZ5|Q8NCY2|Q96JV5|Q9H619	Silent	SNP	ENST00000392017.4	hg19	CCDS2503.2																																																																																			.	.	.	none		0.527	ATG16L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257069.2	NM_017974		C	234173559	T	C	234173559	2	2	154	1	0	0	0	0	0	0	0	1	1091	1509	53	3		3	ATG16L1	2	234173559	Silent	SNP	T	TCGA-DW-7842-01A-11D-2136-08	138232321	234173559	9025814	4	9167											
SCRN1	9805	hgsc.bcm.edu	37	chr7	29994945	29994945	+	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	ttatcattatggcataggtcCttggaacttggtcgattgaa	10	15	10	6	1	1	1	1	1	0	0	3	3	2	2	1	4	1	1	1	4	5	6	rs75604334	byFrequency	TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr7:29994945C>T	ENST00000426154.1	-	3	367	c.191G>A	c.(190-192)aGg>aAg	p.R64K	SCRN1_ENST00000494620.1_5'UTR|SCRN1_ENST00000434476.2_Missense_Mutation_p.R84K|SCRN1_ENST00000242059.5_Missense_Mutation_p.R64K|SCRN1_ENST00000416113.2_5'Flank|SCRN1_ENST00000425819.2_5'UTR|SCRN1_ENST00000409497.1_Missense_Mutation_p.R64K|SCRN1_ENST00000409570.1_Missense_Mutation_p.R64K	NM_001145513.1	NP_001138985.1	Q12765	SCRN1_HUMAN	secernin 1	64					exocytosis (GO:0006887)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	dipeptidase activity (GO:0016805)			breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(12)|ovary(2)|prostate(2)|skin(2)	25						GGCATAGGTCCTTGGAACTTG	0.488																																					p.R84K		Atlas-SNP	.											.	SCRN1	85	.	0			c.G251A						PASS	.						109	105	107					7																	29994945		2203	4300	6503	SO:0001583	missense	9805	exon3			TAGGTCCTTGGAA	D83777	CCDS5422.1, CCDS47567.1, CCDS47568.1	7p14.3-p14.1	2006-09-06			ENSG00000136193	ENSG00000136193			22192	protein-coding gene	gene with protein product		614965				12221138	Standard	NM_014766		Approved	KIAA0193	uc011kaa.2	Q12765	OTTHUMG00000097093	ENST00000426154.1:c.191G>A	chr7.hg19:g.29994945C>T	ENSP00000409068:p.Arg64Lys	124.0	0.0	.		164.0	53.0	.	NM_001145514	A8K0E9|B4DHM0|B4DIP5|C9JPG0|Q25QX7|Q8IWD1	Missense_Mutation	SNP	ENST00000426154.1	hg19	CCDS5422.1	.	.	.	.	.	.	.	.	.	.	C	5.644	0.303441	0.10678	.	.	ENSG00000136193	ENST00000242059;ENST00000426154;ENST00000409497;ENST00000434476;ENST00000421434;ENST00000438497;ENST00000409570	T;T;T;T;T;T;T	0.28666	3.37;3.37;3.37;3.35;2.36;1.63;1.6	5.7	3.89	0.44902	.	0.133460	0.52532	N	0.000069	T	0.14184	0.0343	N	0.11789	0.175	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.002	T	0.09487	-1.0672	9	.	.	.	-20.2169	6.2825	0.21015	0.0:0.6834:0.0:0.3166	.	84;64	C9JPG0;Q12765	.;SCRN1_HUMAN	K	64;64;64;84;64;64;64	ENSP00000242059:R64K;ENSP00000409068:R64K;ENSP00000386872:R64K;ENSP00000388942:R84K;ENSP00000413184:R64K;ENSP00000406289:R64K;ENSP00000387052:R64K	.	R	-	2	0	SCRN1	29961470	1.000000	0.71417	0.996000	0.52242	0.879000	0.50718	1.824000	0.39072	1.426000	0.47256	0.557000	0.71058	AGG	.	C|0.982;G|0.018	.	alt		0.488	SCRN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214231.2	NM_014766		T	29994945	C	T	29994945	3	4	154	1	0	0	0	0	1	0	0	0	13951	681	24	2	1077	2	SCRN1	7	29994945	Missense_Mutation	SNP	C	TCGA-DW-7842-01A-11D-2136-08		29994945	129143718	5	9168											
DOCK4	9732	hgsc.bcm.edu	37	chr7	111368503	111368503	+	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	tagcgggacggggcgccgcaGagtccgctcgtagacgctgt	6	6	17	12	7	0	2	0	0	0	2	2	3	1	3	2	3	1	4	2	3	2	2			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr7:111368503G>C	ENST00000437633.1	-	52	5984	c.5728C>G	c.(5728-5730)Ctg>Gtg	p.L1910V	DOCK4_ENST00000494651.2_Missense_Mutation_p.L793V|DOCK4_ENST00000428084.1_Missense_Mutation_p.L1919V	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1910	Pro-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)				GGGCGCCGCAGAGTCCGCTCG	0.726																																					p.L1910V		Atlas-SNP	.											.	DOCK4	365	.	0			c.C5728G						PASS	.						22	29	27					7																	111368503		2060	4183	6243	SO:0001583	missense	9732	exon52			GCCGCAGAGTCCG		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.5728C>G	chr7.hg19:g.111368503G>C	ENSP00000404179:p.Leu1910Val	98.0	0.0	.		113.0	6.0	.	NM_014705	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	hg19	CCDS47688.1	.	.	.	.	.	.	.	.	.	.	G	12.75	2.033027	0.35893	.	.	ENSG00000128512	ENST00000352877;ENST00000428084;ENST00000494651;ENST00000437633;ENST00000342288	T;T;T	0.32023	1.47;1.47;1.47	5.59	3.43	0.39272	.	0.139401	0.49305	N	0.000144	T	0.15392	0.0371	N	0.19112	0.55	0.29489	N	0.855803	B;B;B;B;B;P	0.39181	0.0;0.045;0.046;0.001;0.036;0.663	B;B;B;B;B;B	0.33196	0.002;0.045;0.019;0.002;0.009;0.159	T	0.07635	-1.0762	10	0.34782	T	0.22	.	7.1126	0.25399	0.1735:0.1686:0.6579:0.0	.	779;793;1955;1910;1881;223	B7Z2K9;F5GXW1;Q149N5;Q8N1I0;Q8N1I0-2;Q8N1I0-4	.;.;.;DOCK4_HUMAN;.;.	V	1898;1919;793;1910;1869	ENSP00000410746:L1919V;ENSP00000440944:L793V;ENSP00000404179:L1910V	ENSP00000345432:L1869V	L	-	1	2	DOCK4	111155739	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.165000	0.31822	1.340000	0.45581	0.655000	0.94253	CTG	.	.	.	none		0.726	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705		C	111368503	G	C	111368503	3	2	154	1	0	0	0	0	1	0	0	0	4691	933	33	4	176	4	DOCK4	7	111368503	Missense_Mutation	SNP	G	TCGA-DW-7842-01A-11D-2136-08	81373558	111368503	47770160	6	9169											
GALNT11	63917	hgsc.bcm.edu	37	chr7	151805279	151805279	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctacagctcgtcccctgtcgTccgcggagggttcaactggg	5	9	13	14	4	1	0	1	0	0	0	5	1	3	1	3	3	3	2	3	3	2	2			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr7:151805279T>C	ENST00000434507.1	+	8	1306	c.869T>C	c.(868-870)gTc>gCc	p.V290A	GALNT11_ENST00000452146.2_Missense_Mutation_p.V209A|GALNT11_ENST00000320311.2_Missense_Mutation_p.V290A|GALNT11_ENST00000430044.2_Missense_Mutation_p.V290A|GALNT11_ENST00000422997.2_3'UTR			Q8NCW6	GLT11_HUMAN	polypeptide N-acetylgalactosaminyltransferase 11	290					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)		TCCCCTGTCGTCCGCGGAGGG	0.602																																					p.V290A		Atlas-SNP	.											.	GALNT11	59	.	0			c.T869C						PASS	.						70	69	69					7																	151805279		2203	4300	6503	SO:0001583	missense	63917	exon6			CTGTCGTCCGCGG	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.869T>C	chr7.hg19:g.151805279T>C	ENSP00000416787:p.Val290Ala	90.0	0.0	.		143.0	106.0	.	NM_022087	B3KWF4|Q6PCD1|Q9H6C2|Q9H6Z5|Q9UDR8	Missense_Mutation	SNP	ENST00000434507.1	hg19	CCDS5930.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.690916	0.88735	.	.	ENSG00000178234	ENST00000430044;ENST00000452146;ENST00000443352;ENST00000434507;ENST00000320311	T;T;T;T	0.59083	0.29;0.29;0.29;0.29	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.59432	0.2193	N	0.13235	0.315	0.80722	D	1	D;D;D	0.89917	0.988;1.0;0.998	D;D;D	0.91635	0.934;0.999;0.971	T	0.58301	-0.7660	10	0.22109	T	0.4	.	15.2076	0.73192	0.0:0.0:0.0:1.0	.	209;290;290	B7Z5G5;B3KWF4;Q8NCW6	.;.;GLT11_HUMAN	A	290;209;290;290;290	ENSP00000395122:V290A;ENSP00000393399:V209A;ENSP00000416787:V290A;ENSP00000315835:V290A	ENSP00000315835:V290A	V	+	2	0	GALNT11	151436212	1.000000	0.71417	0.696000	0.30242	0.671000	0.39405	6.290000	0.72712	1.980000	0.57719	0.528000	0.53228	GTC	.	.	.	none		0.602	GALNT11-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348184.1	NM_022087		C	151805279	T	C	151805279	3	2	154	1	0	0	0	0	1	0	0	0	6216	1667	58	3	887	3	GALNT11	7	151805279	Missense_Mutation	SNP	T	TCGA-DW-7842-01A-11D-2136-08	40436776	151805279	7333384	7	9170											
MYOM2	9172	hgsc.bcm.edu	37	chr8	2063780	2063780	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aattaaatgtgacaaagctaCtggcattattgagatggtga	15	12	10	4	0	0	3	0	3	0	1	0	4	0	3	0	2	2	2	0	2	6	4			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr8:2063780C>T	ENST00000262113.4	+	26	3350	c.3209C>T	c.(3208-3210)aCt>aTt	p.T1070I	MYOM2_ENST00000523438.1_Missense_Mutation_p.T495I	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	1070					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)		GACAAAGCTACTGGCATTATT	0.383																																					p.T1070I		Atlas-SNP	.											.	MYOM2	251	.	0			c.C3209T						PASS	.						180	173	175					8																	2063780		2203	4300	6503	SO:0001583	missense	9172	exon26			AAGCTACTGGCAT		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.3209C>T	chr8.hg19:g.2063780C>T	ENSP00000262113:p.Thr1070Ile	128.0	0.0	.		79.0	36.0	.	NM_003970	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	hg19	CCDS5957.1	.	.	.	.	.	.	.	.	.	.	C	13.00	2.106096	0.37145	.	.	ENSG00000036448	ENST00000262113;ENST00000523438	T;T	0.43688	0.94;0.94	5.32	5.32	0.75619	.	0.155634	0.56097	D	0.000032	T	0.50292	0.1607	M	0.72118	2.19	0.09310	N	1	P	0.43542	0.81	P	0.47118	0.538	T	0.53627	-0.8412	10	0.72032	D	0.01	.	11.9689	0.53051	0.1347:0.7352:0.13:0.0	.	1070	P54296	MYOM2_HUMAN	I	1070;495	ENSP00000262113:T1070I;ENSP00000428396:T495I	ENSP00000262113:T1070I	T	+	2	0	MYOM2	2051187	0.950000	0.32346	0.017000	0.16124	0.264000	0.26372	3.170000	0.50816	2.495000	0.84180	0.655000	0.94253	ACT	.	.	.	none		0.383	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970		T	2063780	C	T	2063780	3	4	154	1	0	0	0	0	1	0	0	0	10099	565	20	2	3307	2	MYOM2	8	2063780	Missense_Mutation	SNP	C	TCGA-DW-7842-01A-11D-2136-08		2063780	144300242	8	9171											
MTUS1	57509	hgsc.bcm.edu	37	chr8	17513393	17513393	+	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	tgctcttgcaattgcattttGtacttctctgcttcttcaat	6	20	5	10	0	4	0	1	0	3	0	5	0	4	0	0	0	5	5	0	0	3	8			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr8:17513393G>T	ENST00000262102.6	-	9	3311	c.3087C>A	c.(3085-3087)taC>taA	p.Y1029*	MTUS1_ENST00000381861.3_Nonsense_Mutation_p.Y276*|MTUS1_ENST00000297488.6_Nonsense_Mutation_p.Y195*|MTUS1_ENST00000519263.1_Nonsense_Mutation_p.Y975*|MTUS1_ENST00000381869.3_Nonsense_Mutation_p.Y975*|MTUS1_ENST00000544260.1_Nonsense_Mutation_p.Y174*|MTUS1_ENST00000518713.1_5'UTR|MTUS1_ENST00000400046.1_Nonsense_Mutation_p.Y101*	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	1029					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)		ATTGCATTTTGTACTTCTCTG	0.448																																					p.Y1029X		Atlas-SNP	.											.	MTUS1	144	.	0			c.C3087A						PASS	.						153	141	145					8																	17513393		1890	4122	6012	SO:0001587	stop_gained	57509	exon9			CATTTTGTACTTC	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.3087C>A	chr8.hg19:g.17513393G>T	ENSP00000262102:p.Tyr1029*	141.0	0.0	.		115.0	5.0	.	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Nonsense_Mutation	SNP	ENST00000262102.6	hg19	CCDS43717.1	.	.	.	.	.	.	.	.	.	.	G	42	9.591954	0.99214	.	.	ENSG00000129422	ENST00000381869;ENST00000544260;ENST00000400046;ENST00000297488;ENST00000381861;ENST00000262102;ENST00000519263	.	.	.	5.25	-7.98	0.01135	.	0.172675	0.53938	D	0.000060	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.084	17.0702	0.86571	0.2982:0.0:0.7018:0.0	.	.	.	.	X	975;174;101;195;276;1029;975	.	ENSP00000262102:Y1029X	Y	-	3	2	MTUS1	17557673	0.970000	0.33590	0.144000	0.22314	0.384000	0.30261	0.123000	0.15708	-1.650000	0.01506	-0.218000	0.12543	TAC	.	.	.	none		0.448	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		T	17513393	G	T	17513393	4	4	154	1	0	0	0	0	0	1	0	0	9972	1372	48	4	753	4	MTUS1	8	17513393	Nonsense_Mutation	SNP	G	TCGA-DW-7842-01A-11D-2136-08	15449613	17513393	128850629	9	9172											
KIAA1529	100499483	hgsc.bcm.edu	37	chr9	100117239	100117239	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctgtggaccttattttcatAgagaaaatccagcggttgct	10	14	9	8	1	2	1	1	0	1	1	3	3	3	2	2	2	2	2	2	2	4	5			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr9:100117239A>G	ENST00000357054.1	+	35	4193	c.3258A>G	c.(3256-3258)atA>atG	p.I1086M	CCDC180_ENST00000375202.2_Missense_Mutation_p.I1115M|CCDC180_ENST00000395220.1_3'UTR|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000529487.1_Missense_Mutation_p.I1115M			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	1086						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											TTATTTTCATAGAGAAAATCC	0.418																																					p.I1115M		Atlas-SNP	.											.	.	.	.	0			c.A3345G						PASS	.						74	75	75					9																	100117239		2203	4300	6503	SO:0001583	missense	0	exon24			TTTCATAGAGAAA	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.3258A>G	chr9.hg19:g.100117239A>G	ENSP00000349562:p.Ile1086Met	112.0	0.0	.		108.0	48.0	.	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Missense_Mutation	SNP	ENST00000357054.1	hg19		.	.	.	.	.	.	.	.	.	.	A	14.21	2.467293	0.43839	.	.	ENSG00000197816	ENST00000357054;ENST00000375202;ENST00000529487	T;T;T	0.10099	3.17;2.91;2.91	5.16	-0.113	0.13568	.	0.642133	0.16850	N	0.196982	T	0.04952	0.0133	N	0.16478	0.41	0.80722	D	1	B;P	0.37370	0.083;0.592	B;B	0.35240	0.044;0.198	T	0.49707	-0.8911	10	0.27785	T	0.31	-2.8056	4.2902	0.10874	0.6091:0.0:0.2494:0.1415	.	1254;1086	B7ZMG3;Q9P1Z9	.;CI174_HUMAN	M	1086;1115;1115	ENSP00000349562:I1086M;ENSP00000364348:I1115M;ENSP00000434727:I1115M	ENSP00000349562:I1086M	I	+	3	3	C9orf174	99157060	0.990000	0.36364	0.986000	0.45419	0.999000	0.98932	0.166000	0.16583	0.022000	0.15160	0.533000	0.62120	ATA	.	.	.	none		0.418	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893		G	100117239	A	G	100117239	3	3	154	1	0	0	0	0	1	0	0	0	8247	410	15	3	3352	3	KIAA1529	9	100117239	Missense_Mutation	SNP	A	TCGA-DW-7842-01A-11D-2136-08		100117239	41096192	10	9173											
DNAJC25-GNG10	2790	hgsc.bcm.edu	37	chr9	114429094	114429094	+	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	gttgctgtccctttgtttcaGgtctctcaggcagctgcaga	5	14	11	11	0	3	1	2	0	1	1	5	1	4	1	1	2	3	6	1	2	0	3			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr9:114429094G>A	ENST00000374293.4	+	2	381		c.e2-1		DNAJC25_ENST00000556107.1_Splice_Site|DNAJC25-GNG10_ENST00000374294.3_Splice_Site	NM_001017998.3|NM_001198664.1	NP_001017998.1|NP_001185593.1	P50151	GBG10_HUMAN	guanine nucleotide binding protein (G protein), gamma 10						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)|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)	GTPase activity (GO:0003924)|signal transducer activity (GO:0004871)			kidney(1)	1						CTTTGTTTCAGGTCTCTCAGG	0.522																																					.		Atlas-SNP	.											.	DNAJC25-GNG10	7	.	0			c.337-1G>A						PASS	.						80	67	71					9																	114429094		2203	4300	6503	SO:0001630	splice_region_variant	552891	exon2			GTTTCAGGTCTCT		CCDS35107.1	9q31.3	2010-08-17			ENSG00000242616	ENSG00000242616			4402	protein-coding gene	gene with protein product		604389				7665596	Standard	NM_001017998		Approved			P50151	OTTHUMG00000157193	ENST00000374293.4:c.82-1G>A	chr9.hg19:g.114429094G>A		56.0	0.0	.		43.0	14.0	.	NM_004125	Q3B7K2|Q4VC27	Splice_Site	SNP	ENST00000374293.4	hg19	CCDS35107.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.486423	0.84854	.	.	ENSG00000059769;ENSG00000244115;ENSG00000242616	ENST00000556107;ENST00000374294;ENST00000374293	.	.	.	5.41	5.41	0.78517	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.1488	0.93479	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DNAJC25-GNG10;GNG10;DNAJC25	113468915	1.000000	0.71417	0.997000	0.53966	0.892000	0.51952	9.460000	0.97641	2.688000	0.91661	0.655000	0.94253	.	.	.	.	none		0.522	GNG10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053644.2		Intron	A	114429094	G	A	114429094	5	1	154	1	0	0	0	0	0	0	1	0	4646	1014	35	2	342	2	DNAJC25-GNG10	9	114429094	Splice_Site	SNP	G	TCGA-DW-7842-01A-11D-2136-08	14311855	114429094	26784337	11	9174											
ZER1	10444	hgsc.bcm.edu	37	chr9	131513498	131513498	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctcaggccggtgctccgtgTaggcctcgatggcattcagc	5	10	13	13	3	2	0	2	0	1	0	5	1	3	0	3	4	2	3	3	4	1	2			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr9:131513498T>C	ENST00000291900.2	-	7	1494	c.1088A>G	c.(1087-1089)tAc>tGc	p.Y363C	snoU13_ENST00000459043.1_RNA|ZER1_ENST00000494461.1_5'Flank	NM_006336.2	NP_006327.2	Q7Z7L7	ZER1_HUMAN	zyg-11 related, cell cycle regulator	363					protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein transferase activity (GO:0051438)	Cul2-RING ubiquitin ligase complex (GO:0031462)	ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	15						GTGCTCCGTGTAGGCCTCGAT	0.602																																					p.Y363C		Atlas-SNP	.											ZER1,NS,carcinoma,0,1	ZER1	49	.	0			c.A1088G						PASS	.						93	76	82					9																	131513498		2203	4300	6503	SO:0001583	missense	10444	exon7			TCCGTGTAGGCCT	X99802	CCDS6910.1	9q33.3	2013-01-17	2012-12-10	2007-01-04	ENSG00000160445	ENSG00000160445		"ZYG11 cell cycle regulator family"	30960	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 60", "zyg-11 homolog B (C. elegans)-like", "zer-1 homolog (C. elegans)"	C9orf60, ZYG11BL		11719588	Standard	NM_006336		Approved	ZYG, Hzyg	uc004bwa.2	Q7Z7L7	OTTHUMG00000020759	ENST00000291900.2:c.1088A>G	chr9.hg19:g.131513498T>C	ENSP00000291900:p.Tyr363Cys	32.0	0.0	.		34.0	3.0	.	NM_006336	O00156|Q5T272|Q5T273	Missense_Mutation	SNP	ENST00000291900.2	hg19	CCDS6910.1	.	.	.	.	.	.	.	.	.	.	T	19.22	3.785754	0.70337	.	.	ENSG00000160445	ENST00000291900	T	0.07688	3.17	5.24	5.24	0.73138	Armadillo-type fold (1);	0.060055	0.64402	D	0.000002	T	0.22781	0.0550	L	0.51914	1.62	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.00425	-1.1747	10	0.44086	T	0.13	-35.0868	14.3759	0.66874	0.0:0.0:0.0:1.0	.	363	Q7Z7L7	ZER1_HUMAN	C	363	ENSP00000291900:Y363C	ENSP00000291900:Y363C	Y	-	2	0	ZER1	130553319	1.000000	0.71417	1.000000	0.80357	0.799000	0.45148	7.499000	0.81566	2.011000	0.59026	0.254000	0.18369	TAC	.	.	.	none		0.602	ZER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054491.1	NM_006336		C	131513498	T	C	131513498	3	2	154	1	0	0	0	0	1	0	0	0	17637	1638	57	3	1252	3	ZER1	9	131513498	Missense_Mutation	SNP	T	TCGA-DW-7842-01A-11D-2136-08	17084404	131513498	9699933	12	9175											
VIM	7431	hgsc.bcm.edu	37	chr10	17276732	17276732	+	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	tgccaaccggaacaatgacgCcctgcgccaggcaaagcagg	12	3	12	14	3	0	1	0	1	0	0	0	2	0	2	4	3	5	2	4	3	4	0			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr10:17276732C>G	ENST00000224237.5	+	5	1068	c.923C>G	c.(922-924)gCc>gGc	p.A308G	RP11-124N14.3_ENST00000456355.1_RNA|VIM_ENST00000544301.1_Missense_Mutation_p.A308G			P08670	VIME_HUMAN	vimentin	308	Coil 2.|Rod.				apoptotic process (GO:0006915)|astrocyte development (GO:0014002)|Bergmann glial cell differentiation (GO:0060020)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular component movement (GO:0006928)|intermediate filament organization (GO:0045109)|lens fiber cell development (GO:0070307)|muscle filament sliding (GO:0030049)|negative regulation of neuron projection development (GO:0010977)|positive regulation of gene expression (GO:0010628)|viral process (GO:0016032)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|neuron projection (GO:0043005)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	double-stranded RNA binding (GO:0003725)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						AACAATGACGCCCTGCGCCAG	0.512																																					p.A308G		Atlas-SNP	.											.	VIM	71	.	0			c.C923G						PASS	.						94	89	91					10																	17276732		2203	4300	6503	SO:0001583	missense	7431	exon6			ATGACGCCCTGCG	M14144	CCDS7120.1	10p13	2013-01-16			ENSG00000026025	ENSG00000026025		"Intermediate filaments type III"	12692	protein-coding gene	gene with protein product		193060					Standard	NM_003380		Approved		uc001iou.2	P08670	OTTHUMG00000017744	ENST00000224237.5:c.923C>G	chr10.hg19:g.17276732C>G	ENSP00000224237:p.Ala308Gly	134.0	0.0	.		116.0	17.0	.	NM_003380	B0YJC2|D3DRU4|Q15867|Q15868|Q15869|Q548L2|Q6LER9|Q8N850|Q96ML2|Q9NTM3	Missense_Mutation	SNP	ENST00000224237.5	hg19	CCDS7120.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.627666	0.87560	.	.	ENSG00000026025	ENST00000544301;ENST00000224237;ENST00000545533;ENST00000421459	D;D;D	0.89681	-2.55;-2.55;-2.55	6.05	6.05	0.98169	Filament (1);	0.000000	0.46442	D	0.000298	D	0.95439	0.8519	M	0.91090	3.175	0.80722	D	1	D;D;D;D	0.69078	0.989;0.985;0.995;0.997	P;P;D;D	0.69479	0.897;0.902;0.941;0.964	D	0.92981	0.6406	10	0.18710	T	0.47	.	20.6031	0.99464	0.0:1.0:0.0:0.0	.	295;295;308;308	F5H288;B3KRK8;B0YJC4;P08670	.;.;.;VIME_HUMAN	G	308;308;295;134	ENSP00000446007:A308G;ENSP00000224237:A308G;ENSP00000391842:A134G	ENSP00000224237:A308G	A	+	2	0	VIM	17316738	1.000000	0.71417	1.000000	0.80357	0.369000	0.29798	7.811000	0.86092	2.881000	0.98747	0.637000	0.83480	GCC	.	.	.	none		0.512	VIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047015.1	NM_003380		G	17276732	C	G	17276732	3	3	154	1	0	0	0	0	1	0	0	0	17178	739	26	4	941	4	VIM	10	17276732	Missense_Mutation	SNP	C	TCGA-DW-7842-01A-11D-2136-08		17276732	118258015	13	9176											
ARHGAP21	57584	hgsc.bcm.edu	37	chr10	24885703	24885704	+	Frame_Shift_Ins	INS	-	-	G																															tggtgggcagtcatctagtcINSggacgccgaaagttcctgta																										TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr10:24885703_24885704insG	ENST00000396432.2	-	17	3928_3929	c.3442_3443insC	c.(3442-3444)cgafs	p.R1148fs	ARHGAP21_ENST00000320481.6_Frame_Shift_Ins_p.R935fs|ARHGAP21_ENST00000493154.1_5'Flank	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	1147	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						GTCATCTAGTCGGACGCCGAAA	0.455																																					p.R1148fs		Atlas-INDEL	.											.	ARHGAP21	185	.	0			c.3443_3444insC						PASS	.																																			SO:0001589	frameshift_variant	57584	exon17			.	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.3443dupC	chr10.hg19:g.24885705_24885705dupG	ENSP00000379709:p.Arg1148fs	119.0	0.0	0		99.0	42.0	0.424242	NM_020824	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Frame_Shift_Ins	INS	ENST00000396432.2	hg19	CCDS7144.2																																																																																			.	.	.	none		0.455	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824		G	24885704	-	G	24885703	7	5	154	1	0	1	1	0	0	0	0	0	871	884	31	0	2473	0	ARHGAP21	10	24885703	Frame_Shift_Ins	INS	-	TCGA-DW-7842-01A-11D-2136-08	7608971	24885703	110649044	14	9177											
PPA1	5464	hgsc.bcm.edu	37	chr10	71969322	71969322	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgacatattaccttatcttTaaattctgcattaaacgcaa	15	15	3	8	1	2	1	0	1	2	0	2	1	2	1	1	0	3	2	1	0	8	7	rs80155016		TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr10:71969322T>C	ENST00000373232.3	-	7	730	c.631A>G	c.(631-633)Aaa>Gaa	p.K211E		NM_021129.3	NP_066952.1	Q15181	IPYR_HUMAN	pyrophosphatase (inorganic) 1	211					diphosphate metabolic process (GO:0071344)|gene expression (GO:0010467)|phosphate-containing compound metabolic process (GO:0006796)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)			breast(2)|endometrium(1)|large_intestine(2)|lung(3)|skin(2)	10						ACCTTATCTTTAAATTCTGCA	0.348																																					p.K211E		Atlas-SNP	.											.	PPA1	24	.	0			c.A631G						PASS	.						98	94	95					10																	71969322		2203	4300	6503	SO:0001583	missense	5464	exon7			TATCTTTAAATTC	AF154065	CCDS7299.1	10q11.1-q24	2012-10-02	2005-10-07	2005-10-07	ENSG00000180817	ENSG00000180817	3.6.1.1		9226	protein-coding gene	gene with protein product	"cytosolic inorganic pyrophosphatase", "inorganic pyrophosphatase 1", "pyrophosphate phospho-hydrolase"	179030	"pyrophosphatase (inorganic)"	PP		10542310, 975879	Standard	NM_021129		Approved	SID6-8061, Ppase, IOPPP, PP1	uc001jqv.1	Q15181	OTTHUMG00000018399	ENST00000373232.3:c.631A>G	chr10.hg19:g.71969322T>C	ENSP00000362329:p.Lys211Glu	85.0	0.0	.		81.0	6.0	.	NM_021129	Q2M348|Q5SQT7|Q6P7P4|Q9UQJ5|Q9Y5B1	Missense_Mutation	SNP	ENST00000373232.3	hg19	CCDS7299.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.843400	0.91197	.	.	ENSG00000180817	ENST00000373232	T	0.44083	0.93	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.66197	0.2765	M	0.83312	2.635	0.80722	D	1	D	0.67145	0.996	D	0.68192	0.956	T	0.71902	-0.4452	10	0.72032	D	0.01	-6.013	14.3548	0.66730	0.0:0.0:0.0:1.0	.	211	Q15181	IPYR_HUMAN	E	211	ENSP00000362329:K211E	ENSP00000362329:K211E	K	-	1	0	PPA1	71639328	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	7.796000	0.85898	2.078000	0.62432	0.460000	0.39030	AAA	.	.	.	weak		0.348	PPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048490.2	NM_021129		C	71969322	T	C	71969322	3	2	154	1	0	0	0	0	1	0	0	0	12293	1763	61	3	258	3	PPA1	10	71969322	Missense_Mutation	SNP	T	TCGA-DW-7842-01A-11D-2136-08	47083619	71969322	63565425	15	9178											
C11orf49	79096	hgsc.bcm.edu	37	chr11	47074069	47074069	+	Splice_Site	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	gaactgtgggcaaaaatggcGgtaagtcttcccaaattctt	12	11	10	8	1	2	0	0	0	2	0	3	1	3	0	1	3	1	2	1	3	5	4			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr11:47074069G>T	ENST00000278460.7	+	3	339	c.280G>T	c.(280-282)Gat>Tat	p.D94Y	C11orf49_ENST00000378618.2_Splice_Site_p.D94Y|C11orf49_ENST00000527268.1_3'UTR|C11orf49_ENST00000536126.1_5'UTR|C11orf49_ENST00000395460.2_Splice_Site_p.D94Y|C11orf49_ENST00000378615.3_Splice_Site_p.D94Y|C11orf49_ENST00000543718.1_Intron	NM_001003677.1|NM_024113.3	NP_001003677.1|NP_077018.1	Q9H6J7	CK049_HUMAN	chromosome 11 open reading frame 49	94						nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(1)	11						CAAAAATGGCGGTAAGTCTTC	0.463																																					p.D94Y		Atlas-SNP	.											.	C11orf49	41	.	0			c.G280T						PASS	.						101	102	102					11																	47074069		2201	4299	6500	SO:0001630	splice_region_variant	79096	exon3			AATGGCGGTAAGT	AL136575	CCDS7925.1, CCDS31479.1, CCDS31480.1, CCDS41641.1	11p11.2	2006-02-02			ENSG00000149179	ENSG00000149179			28720	protein-coding gene	gene with protein product							Standard	NM_001003677		Approved	FLJ22210, MGC4707	uc001ndr.4	Q9H6J7	OTTHUMG00000166725	ENST00000278460.7:c.280+1G>T	chr11.hg19:g.47074069G>T		82.0	0.0	.		102.0	47.0	.	NM_001003677	D3DQQ8|E9PAX7|Q7L077|Q96CS8|Q9BQH4|Q9BUW5	Missense_Mutation	SNP	ENST00000278460.7	hg19	CCDS7925.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.879678	0.91740	.	.	ENSG00000149179	ENST00000278460;ENST00000378618;ENST00000395460;ENST00000378615;ENST00000526827	T;T;T;T;T	0.23552	1.9;1.9;1.9;1.9;1.9	6.03	6.03	0.97812	.	0.097269	0.64402	D	0.000002	T	0.55289	0.1911	M	0.74881	2.28	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.79784	0.993;0.977;0.977	T	0.54351	-0.8307	10	0.87932	D	0	-17.2898	20.5568	0.99304	0.0:0.0:1.0:0.0	.	94;94;94	E9PAX7;Q9H6J7-2;Q9H6J7	.;.;CK049_HUMAN	Y	94;94;94;94;20	ENSP00000278460:D94Y;ENSP00000367881:D94Y;ENSP00000378844:D94Y;ENSP00000367878:D94Y;ENSP00000433707:D20Y	ENSP00000278460:D94Y	D	+	1	0	C11orf49	47030645	1.000000	0.71417	0.986000	0.45419	0.971000	0.66376	8.948000	0.93006	2.861000	0.98227	0.655000	0.94253	GAT	.	.	.	none		0.463	C11orf49-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391218.1	NM_024113	Missense_Mutation	T	47074069	G	T	47074069	5	4	154	1	0	0	0	0	0	0	1	0	1647	1130	39	4	290	4	C11orf49	11	47074069	Splice_Site	SNP	G	TCGA-DW-7842-01A-11D-2136-08		47074069	87932447	16	9179											
ANKRD13D	338692	hgsc.bcm.edu	37	chr11	67059495	67059495	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgatggaagtggaccatgAccggcaggtggtgcatgtgg	8	8	19	6	1	0	2	0	2	0	0	0	4	0	4	2	7	1	2	2	7	1	0			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr11:67059495A>G	ENST00000447274.2	+	6	1489	c.314A>G	c.(313-315)gAc>gGc	p.D105G	ANKRD13D_ENST00000511455.2_Missense_Mutation_p.D192G|ANKRD13D_ENST00000514166.1_Missense_Mutation_p.D105G|ANKRD13D_ENST00000308440.6_Missense_Mutation_p.D105G			Q6ZTN6	AN13D_HUMAN	ankyrin repeat domain 13 family, member D	105						endosome (GO:0005768)|plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			GTGGACCATGACCGGCAGGTG	0.672																																					p.D192G		Atlas-SNP	.											.	ANKRD13D	71	.	0			c.A575G						PASS	.						36	38	37					11																	67059495		2200	4294	6494	SO:0001583	missense	338692	exon6			ACCATGACCGGCA	AK027313	CCDS31616.1, CCDS31616.2	11q13.2	2013-01-11		2005-08-09	ENSG00000172932	ENSG00000172932		"Ankyrin repeat domain containing"	27880	protein-coding gene	gene with protein product		615126					Standard	NM_207354		Approved		uc001okd.2	Q6ZTN6	OTTHUMG00000162929	ENST00000447274.2:c.314A>G	chr11.hg19:g.67059495A>G	ENSP00000402616:p.Asp105Gly	101.0	0.0	.		57.0	4.0	.	NM_207354	D6RCN6|Q0VAK0|Q0VGC3|Q6ZVD0|Q86SU1	Missense_Mutation	SNP	ENST00000447274.2	hg19		.	.	.	.	.	.	.	.	.	.	A	24.6	4.554741	0.86231	.	.	ENSG00000172932	ENST00000447274;ENST00000511455;ENST00000308440;ENST00000514166	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	3.9	3.9	0.45041	.	0.074445	0.52532	D	0.000070	T	0.63462	0.2513	M	0.80183	2.485	0.58432	D	0.999999	D;P	0.89917	1.0;0.624	D;P	0.75484	0.986;0.525	T	0.66736	-0.5848	10	0.48119	T	0.1	-35.5096	12.1809	0.54211	1.0:0.0:0.0:0.0	.	192;105	Q6ZTN6-3;Q6ZTN6	.;AN13D_HUMAN	G	105;192;105;105	ENSP00000402616:D105G;ENSP00000427130:D192G;ENSP00000310874:D105G;ENSP00000444404:D105G	ENSP00000310874:D105G	D	+	2	0	ANKRD13D	66816071	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.912000	0.92726	1.785000	0.52413	0.459000	0.35465	GAC	.	.	.	none		0.672	ANKRD13D-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000371067.2	NM_207354		G	67059495	A	G	67059495	3	3	154	1	0	0	0	0	1	0	0	0	644	275	10	3	597	3	ANKRD13D	11	67059495	Missense_Mutation	SNP	A	TCGA-DW-7842-01A-11D-2136-08	19985426	67059495	67947021	17	9180											
ARHGEF17	9828	hgsc.bcm.edu	37	chr11	73020470	73020470	+	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	agggcccgccgcagctgcctGgagcccagagtccggcctac	6	4	14	17	3	0	1	0	0	0	1	1	2	1	2	6	3	4	2	6	3	1	1			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr11:73020470G>A	ENST00000263674.3	+	1	1137	c.787G>A	c.(787-789)Gga>Aga	p.G263R	RP11-800A3.7_ENST00000546324.1_RNA	NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	263					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						GCAGCTGCCTGGAGCCCAGAG	0.721																																					p.G263R		Atlas-SNP	.											.	ARHGEF17	117	.	0			c.G787A						PASS	.						10	14	13					11																	73020470		2079	4096	6175	SO:0001583	missense	9828	exon1			CTGCCTGGAGCCC	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.787G>A	chr11.hg19:g.73020470G>A	ENSP00000263674:p.Gly263Arg	47.0	0.0	.		44.0	23.0	.	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Missense_Mutation	SNP	ENST00000263674.3	hg19	CCDS8221.1	.	.	.	.	.	.	.	.	.	.	G	11.49	1.654144	0.29425	.	.	ENSG00000110237	ENST00000263674	T	0.64260	-0.09	4.85	0.091	0.14466	.	0.445825	0.16707	N	0.202865	T	0.43656	0.1257	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.39251	-0.9623	10	0.87932	D	0	-19.5376	8.2312	0.31599	0.1586:0.385:0.4564:0.0	.	263	Q96PE2	ARHGH_HUMAN	R	263	ENSP00000263674:G263R	ENSP00000263674:G263R	G	+	1	0	ARHGEF17	72698118	0.001000	0.12720	0.001000	0.08648	0.237000	0.25408	0.062000	0.14389	0.096000	0.17463	-0.502000	0.04539	GGA	.	.	.	none		0.721	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		A	73020470	G	A	73020470	3	1	154	1	0	0	0	0	1	0	0	0	900	1349	47	2	789	2	ARHGEF17	11	73020470	Missense_Mutation	SNP	G	TCGA-DW-7842-01A-11D-2136-08	5960975	73020470	61986046	18	9181											
MED17	9440	hgsc.bcm.edu	37	chr11	93542943	93542943	+	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	aggttatgggctggcaagtaCtgagcttcagtaatcatgtg	10	12	13	6	0	2	1	2	1	0	0	2	1	2	1	0	3	2	6	0	3	4	4			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr11:93542943C>A	ENST00000251871.3	+	11	1932	c.1645C>A	c.(1645-1647)Ctg>Atg	p.L549M	MED17_ENST00000533367.1_3'UTR	NM_004268.4	NP_004259.3	Q9NVC6	MED17_HUMAN	mediator complex subunit 17	549					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)				CTGGCAAGTACTGAGCTTCAG	0.493																																					p.L549M		Atlas-SNP	.											.	MED17	37	.	0			c.C1645A						PASS	.						233	193	206					11																	93542943		2201	4298	6499	SO:0001583	missense	9440	exon11			CAAGTACTGAGCT	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.1645C>A	chr11.hg19:g.93542943C>A	ENSP00000251871:p.Leu549Met	189.0	0.0	.		163.0	71.0	.	NM_004268	B3KN07|Q9HA81|Q9UNP7|Q9Y2W0|Q9Y660	Missense_Mutation	SNP	ENST00000251871.3	hg19	CCDS8295.1	.	.	.	.	.	.	.	.	.	.	C	31	5.067027	0.93898	.	.	ENSG00000042429	ENST00000251871;ENST00000427225	T	0.64991	-0.13	5.65	5.65	0.86999	.	0.063209	0.64402	D	0.000003	T	0.79040	0.4379	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	T	0.79424	-0.1809	10	0.72032	D	0.01	-15.3186	20.0822	0.97779	0.0:1.0:0.0:0.0	.	549	Q9NVC6	MED17_HUMAN	M	549;519	ENSP00000251871:L549M	ENSP00000251871:L549M	L	+	1	2	MED17	93182591	1.000000	0.71417	0.719000	0.30619	0.979000	0.70002	4.846000	0.62860	2.826000	0.97356	0.563000	0.77884	CTG	.	.	.	none		0.493	MED17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394800.2	NM_004268		A	93542943	C	A	93542943	3	1	154	1	0	0	0	0	1	0	0	0	9442	564	20	4	1687	4	MED17	11	93542943	Missense_Mutation	SNP	C	TCGA-DW-7842-01A-11D-2136-08	20522473	93542943	41463573	19	9182											
VPS26B	112936	hgsc.bcm.edu	37	chr11	134115448	134115448	+	Silent	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	tccctgggtgaggtgcggacCcccagccagctgtctgacaa	7	7	13	14	1	1	2	0	2	1	0	2	3	2	3	4	3	3	1	4	3	1	0			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr11:134115448C>T	ENST00000281187.5	+	6	1453	c.975C>T	c.(973-975)acC>acT	p.T325T	VPS26B_ENST00000525095.2_Silent_p.T325T	NM_052875.3	NP_443107.1	Q4G0F5	VP26B_HUMAN	vacuolar protein sorting 26 homolog B (S. pombe)	325					protein transport (GO:0015031)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)				breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)	14	all_hematologic(175;0.127)	all_cancers(12;1.1e-21)|all_epithelial(12;3.77e-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;2.43e-10)|all cancers(11;2.94e-09)|BRCA - Breast invasive adenocarcinoma(10;9.57e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00164)|Lung(977;0.216)		AGGTGCGGACCCCCAGCCAGC	0.652																																					p.T325T	Colon(171;1263 1952 15904 45703 47982)	Atlas-SNP	.											.	VPS26B	30	.	0			c.C975T						PASS	.						44	37	39					11																	134115448		2201	4297	6498	SO:0001819	synonymous_variant	112936	exon6			GCGGACCCCCAGC		CCDS8495.1	11q25	2008-02-05	2007-01-12		ENSG00000151502	ENSG00000151502			28119	protein-coding gene	gene with protein product		610027	"vacuolar protein sorting 26 homolog B (yeast)"			16190980	Standard	NM_052875		Approved	MGC10485, Pep8b	uc001qhe.3	Q4G0F5	OTTHUMG00000167175	ENST00000281187.5:c.975C>T	chr11.hg19:g.134115448C>T		37.0	0.0	.		32.0	18.0	.	NM_052875	Q96A55	Silent	SNP	ENST00000281187.5	hg19	CCDS8495.1																																																																																			.	.	.	none		0.652	VPS26B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393591.1	NM_052875		T	134115448	C	T	134115448	2	4	154	1	0	0	0	0	0	0	0	1	17210	610	22	2		2	VPS26B	11	134115448	Silent	SNP	C	TCGA-DW-7842-01A-11D-2136-08	40572505	134115448	891068	20	9183											
PTGDR	5729	hgsc.bcm.edu	37	chr14	52734893	52734894	+	Missense_Mutation	DNP	CT	CT	AG																															tctttgggctctcctcgacaCtgcaactcctggccatggca																										TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr14:52734893_52734894CT>AG	ENST00000306051.2	+	1	463_464	c.361_362CT>AG	c.(361-363)CTg>AGg	p.L121R	PTGDR_ENST00000553372.1_Missense_Mutation_p.L121R	NM_000953.2	NP_000944.1	Q13258	PD2R_HUMAN	prostaglandin D2 receptor (DP)	121					adenosine metabolic process (GO:0046085)|cellular response to prostaglandin D stimulus (GO:0071799)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|male sex determination (GO:0030238)|sleep (GO:0030431)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	prostaglandin D receptor activity (GO:0004956)|prostaglandin J receptor activity (GO:0001785)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Breast(41;0.0639)|all_epithelial(31;0.0887)				Nedocromil(DB00716)	CTCCTCGACACTGCAACTCCTG	0.629																																					p.L121M|p.L121R		Atlas-SNP	.											.	PTGDR	58	.	0			c.C361A|c.T362G						PASS	.																																			SO:0001583	missense	5729	exon1			TCGACACTGCAAC|CGACACTGCAACT	U31332	CCDS9707.1, CCDS61454.1	14q22.1	2012-08-08			ENSG00000168229	ENSG00000168229		"GPCR / Class A : Prostanoid receptors"	9591	protein-coding gene	gene with protein product		604687				7642548	Standard	NM_000953		Approved	DP, DP1, PTGDR1	uc001wzq.3	Q13258	OTTHUMG00000140299	Exception_encountered	chr14.hg19:g.52734893_52734894delinsAG	ENSP00000303424:p.Leu121Arg	306.0|309.0	0.0	.		229.0|231.0	82.0|81.0	.	NM_000953	G3V5L3|Q13250|Q13251|Q1ZZ52	Missense_Mutation	SNP	ENST00000306051.2	hg19	CCDS9707.1																																																																																			.	.	.	none		0.629	PTGDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276889.1	NM_000953		AG	52734894	CT	AG	52734893	3	1	154	1	0	0	0	0	1	0	0	0	12751	564	20	4	363	4	PTGDR	14	52734893	Missense_Mutation	DNP	CT	TCGA-DW-7842-01A-11D-2136-08		52734893	54614647	21	9184											
PLA2G4F	255189	hgsc.bcm.edu	37	chr15	42442584	42442584	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccttacctcccccagggccAcagaacactgttcctcctgg	7	8	8	18	0	0	1	0	0	0	1	3	1	3	1	7	2	2	1	7	2	2	2			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr15:42442584A>G	ENST00000382396.4	-	9	958	c.872T>C	c.(871-873)gTg>gCg	p.V291A	PLA2G4F_ENST00000397272.3_Missense_Mutation_p.V291A			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	291					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)		CCCCAGGGCCACAGAACACTG	0.652																																					p.V291A		Atlas-SNP	.											.	PLA2G4F	75	.	0			c.T872C						PASS	.						22	23	22					15																	42442584		2203	4299	6502	SO:0001583	missense	255189	exon9			AGGGCCACAGAAC		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.872T>C	chr15.hg19:g.42442584A>G	ENSP00000371833:p.Val291Ala	31.0	0.0	.		29.0	15.0	.	NM_213600	Q6ZMC8	Missense_Mutation	SNP	ENST00000382396.4	hg19	CCDS32204.1	.	.	.	.	.	.	.	.	.	.	A	11.42	1.632244	0.29068	.	.	ENSG00000168907	ENST00000290497;ENST00000397272;ENST00000382396;ENST00000357924;ENST00000443825	T;T	0.01560	4.77;4.82	4.88	4.88	0.63580	Lysophospholipase, catalytic domain (1);	0.320592	0.21644	N	0.071298	T	0.02848	0.0085	M	0.64404	1.975	0.31744	N	0.635362	P;P	0.46395	0.877;0.877	B;B	0.38106	0.265;0.197	T	0.12142	-1.0559	10	0.72032	D	0.01	-9.9511	11.1909	0.48685	1.0:0.0:0.0:0.0	.	78;291	A2RRC4;Q68DD2	.;PA24F_HUMAN	A	287;291;291;291;291	ENSP00000380442:V291A;ENSP00000371833:V291A	ENSP00000290497:V287A	V	-	2	0	PLA2G4F	40229876	0.055000	0.20627	0.840000	0.33206	0.044000	0.14063	4.335000	0.59298	1.982000	0.57802	0.533000	0.62120	GTG	.	.	.	none		0.652	PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600		G	42442584	A	G	42442584	3	3	154	1	0	0	0	0	1	0	0	0	12013	159	6	3	1725	3	PLA2G4F	15	42442584	Missense_Mutation	SNP	A	TCGA-DW-7842-01A-11D-2136-08		42442584	60088808	22	9185											
C15orf42	90381	hgsc.bcm.edu	37	chr15	90129030	90129030	+	Missense_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	tatgatcctcactgtgtgccGcaccaaggaggctgaatttc	9	11	10	11	1	1	2	1	2	0	0	3	3	2	3	3	2	1	2	3	2	3	2			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr15:90129030G>A	ENST00000268138.7	+	4	1373	c.1268G>A	c.(1267-1269)cGc>cAc	p.R423H	TICRR_ENST00000560985.1_Missense_Mutation_p.R422H|RP11-429B14.1_ENST00000559041.1_RNA			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	423					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)										ACTGTGTGCCGCACCAAGGAG	0.542																																					p.R423H		Atlas-SNP	.											.	.	.	.	0			c.G1268A						PASS	.						86	88	87					15																	90129030		1978	4151	6129	SO:0001583	missense	90381	exon4			TGTGCCGCACCAA	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.1268G>A	chr15.hg19:g.90129030G>A	ENSP00000268138:p.Arg423His	90.0	0.0	.		68.0	6.0	.	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Missense_Mutation	SNP	ENST00000268138.7	hg19	CCDS10352.2	.	.	.	.	.	.	.	.	.	.	g	3.132	-0.178303	0.06380	.	.	ENSG00000140534	ENST00000268138	T	0.13901	2.55	5.24	-2.38	0.06622	.	0.846013	0.11198	N	0.589141	T	0.08447	0.0210	L	0.27053	0.805	0.09310	N	1	B	0.14438	0.01	B	0.08055	0.003	T	0.28964	-1.0027	10	0.46703	T	0.11	0.7395	7.3452	0.26660	0.4494:0.1087:0.4419:0.0	.	423	Q7Z2Z1	TICRR_HUMAN	H	423	ENSP00000268138:R423H	ENSP00000268138:R423H	R	+	2	0	C15orf42	87930034	0.000000	0.05858	0.005000	0.12908	0.010000	0.07245	-0.060000	0.11712	-0.695000	0.05105	-0.150000	0.13652	CGC	.	.	.	none		0.542	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259		A	90129030	G	A	90129030	3	1	154	1	0	0	0	0	1	0	0	0	1798	1087	38	1	1282	1	C15orf42	15	90129030	Missense_Mutation	SNP	G	TCGA-DW-7842-01A-11D-2136-08	47686446	90129030	12402362	23	9186											
DSG4	147409	hgsc.bcm.edu	37	chr18	28980927	28980927	+	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	attttctagagaatttgataAgaagtcaaaatatattatca	18	15	5	3	0	3	3	2	1	1	2	3	4	3	3	0	0	0	0	0	0	9	8			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr18:28980927A>T	ENST00000308128.4	+	10	1496	c.1361A>T	c.(1360-1362)aAg>aTg	p.K454M	DSG4_ENST00000359747.4_Missense_Mutation_p.K454M|RP11-534N16.1_ENST00000578477.1_RNA|RP11-534N16.1_ENST00000581452.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	454	Cadherin 4. {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)			GAATTTGATAAGAAGTCAAAA	0.289																																					p.K454M		Atlas-SNP	.											.	DSG4	343	.	0			c.A1361T						PASS	.						43	48	47					18																	28980927		2199	4283	6482	SO:0001583	missense	147409	exon10			TTGATAAGAAGTC	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.1361A>T	chr18.hg19:g.28980927A>T	ENSP00000311859:p.Lys454Met	77.0	0.0	.		78.0	37.0	.	NM_001134453	A2RUI1|Q6Y9L9|Q8IXV4	Missense_Mutation	SNP	ENST00000308128.4	hg19	CCDS11897.1	.	.	.	.	.	.	.	.	.	.	A	11.68	1.710083	0.30322	.	.	ENSG00000175065	ENST00000308128;ENST00000359747	T;T	0.52754	0.65;0.65	5.24	-7.62	0.01294	Cadherin (4);Cadherin-like (1);	1.092760	0.07279	N	0.870439	T	0.14657	0.0354	N	0.01188	-0.97	0.21740	N	0.999565	B;B	0.18013	0.025;0.003	B;B	0.19666	0.025;0.026	T	0.23226	-1.0194	10	0.62326	D	0.03	.	2.8038	0.05422	0.1395:0.4432:0.1978:0.2195	.	454;454	Q86SJ6-2;Q86SJ6	.;DSG4_HUMAN	M	454	ENSP00000311859:K454M;ENSP00000352785:K454M	ENSP00000311859:K454M	K	+	2	0	DSG4	27234925	0.528000	0.26314	0.657000	0.29651	0.818000	0.46254	0.238000	0.18004	-1.023000	0.03342	-2.955000	0.00083	AAG	.	.	.	none		0.289	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986		T	28980927	A	T	28980927	3	4	154	1	0	0	0	0	1	0	0	0	4781	72	3	5	1399	5	DSG4	18	28980927	Missense_Mutation	SNP	A	TCGA-DW-7842-01A-11D-2136-08		28980927	49096321	24	9187											
WDR18	57418	hgsc.bcm.edu	37	chr19	992048	992048	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgccccacttcaacaagcAcctgctgggcgccgagcacg	8	5	11	17	3	1	0	1	0	0	0	1	1	1	0	4	1	5	4	4	1	2	1			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr19:992048A>G	ENST00000251289.5	+	8	1048	c.1025A>G	c.(1024-1026)cAc>cGc	p.H342R	WDR18_ENST00000587001.2_Missense_Mutation_p.H342R	NM_024100.3	NP_077005.2	Q9BV38	WDR18_HUMAN	WD repeat domain 18	342					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|lung(2)|skin(2)	7		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TTCAACAAGCACCTGCTGGGC	0.716																																					p.H342R		Atlas-SNP	.											.	WDR18	20	.	0			c.A1025G						PASS	.						9	10	9					19																	992048		2129	4155	6284	SO:0001583	missense	57418	exon8			ACAAGCACCTGCT		CCDS12051.1	19p13.3	2013-01-09				ENSG00000065268		"WD repeat domain containing"	17956	protein-coding gene	gene with protein product	"Involved in Processing ITS2 3 homolog (S. cerevisiae)"					22190735	Standard	NM_024100		Approved	Ipi3	uc002lqm.1	Q9BV38		ENST00000251289.5:c.1025A>G	chr19.hg19:g.992048A>G	ENSP00000251289:p.His342Arg	9.0	0.0	.		27.0	16.0	.	NM_024100	O60390|Q9BWR2	Missense_Mutation	SNP	ENST00000251289.5	hg19	CCDS12051.1	.	.	.	.	.	.	.	.	.	.	A	11.62	1.692269	0.30052	.	.	ENSG00000065268	ENST00000251289	T	0.69435	-0.4	4.28	4.28	0.50868	.	0.056115	0.64402	D	0.000001	T	0.60843	0.2300	M	0.63843	1.955	0.44798	D	0.997803	P	0.50272	0.933	B	0.44108	0.441	T	0.62020	-0.6942	10	0.06757	T	0.87	.	12.3826	0.55315	1.0:0.0:0.0:0.0	.	342	Q9BV38	WDR18_HUMAN	R	342	ENSP00000251289:H342R	ENSP00000251289:H342R	H	+	2	0	WDR18	943048	1.000000	0.71417	1.000000	0.80357	0.541000	0.35023	5.202000	0.65169	1.806000	0.52798	0.402000	0.26972	CAC	.	.	.	none		0.716	WDR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458225.2			G	992048	A	G	992048	3	3	154	1	0	0	0	0	1	0	0	0	17290	159	6	3	1055	3	WDR18	19	992048	Missense_Mutation	SNP	A	TCGA-DW-7842-01A-11D-2136-08		992048	58136935	25	9188											
NLRP5	126206	hgsc.bcm.edu	37	chr19	56511120	56511120	+	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	tgcaggaggacttgaacttgGagctgctgctctgctctcag	7	11	13	10	0	2	1	1	1	2	0	3	4	2	4	0	3	6	5	0	3	1	2			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr19:56511120G>A	ENST00000390649.3	+	1	29	c.29G>A	c.(28-30)gGa>gAa	p.G10E		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	10					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)		cttgaacttggagctgcTGCT	0.517																																					p.G10E		Atlas-SNP	.											.	NLRP5	217	.	0			c.G29A						PASS	.						208	212	210					19																	56511120		2101	4218	6319	SO:0001583	missense	126206	exon1			AACTTGGAGCTGC	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.29G>A	chr19.hg19:g.56511120G>A	ENSP00000375063:p.Gly10Glu	241.0	0.0	.		234.0	35.0	.	NM_153447	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	hg19	CCDS12938.1	.	.	.	.	.	.	.	.	.	.	G	7.564	0.665223	0.14710	.	.	ENSG00000171487	ENST00000390649	T	0.74106	-0.81	0.492	0.492	0.16872	.	.	.	.	.	T	0.68860	0.3047	N	0.08118	0	0.09310	N	1	D	0.76494	0.999	D	0.71184	0.972	T	0.59215	-0.7496	8	0.87932	D	0	.	.	.	.	.	10	P59047	NALP5_HUMAN	E	10	ENSP00000375063:G10E	ENSP00000375063:G10E	G	+	2	0	NLRP5	61202932	0.005000	0.15991	0.037000	0.18230	0.032000	0.12392	-0.354000	0.07681	0.528000	0.28580	0.298000	0.19748	GGA	.	.	.	none		0.517	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447		A	56511120	G	A	56511120	3	1	154	1	0	0	0	0	1	0	0	0	10487	1174	41	2	31	2	NLRP5	19	56511120	Missense_Mutation	SNP	G	TCGA-DW-7842-01A-11D-2136-08	55519072	56511120	2617863	26	9189											
SLC19A1	6573	hgsc.bcm.edu	37	chr21	46935688	46935688	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctgcagcctcagggcctgAggcttgggcggagcacagag	8	6	16	11	1	2	2	1	1	1	1	2	3	2	3	2	4	3	3	2	4	0	1			TCGA-DW-7842-01A-11D-2136-08	TCGA-DW-7842-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fe91ee01-61e4-4310-b1e9-387033d215a6	bbdb56a6-a63a-419c-91dc-54bd9502aa64	g.chr21:46935688A>G	ENST00000311124.4	-	6	1812	c.1660T>C	c.(1660-1662)Tca>Cca	p.S554P	SLC19A1_ENST00000567670.1_Intron|SLC19A1_ENST00000380010.4_Intron|SLC19A1_ENST00000468508.1_5'Flank|SLC19A1_ENST00000485649.2_Missense_Mutation_p.S514P	NM_194255.2	NP_919231.1	P41440	S19A1_HUMAN	solute carrier family 19 (folate transporter), member 1	554					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)	TCAGGGCCTGAGGCTTGGGCG	0.637																																					p.S554P		Atlas-SNP	.											.	SLC19A1	53	.	0			c.T1660C						PASS	.						44	44	44					21																	46935688		2203	4300	6503	SO:0001583	missense	6573	exon6			GGCCTGAGGCTTG	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.1660T>C	chr21.hg19:g.46935688A>G	ENSP00000308895:p.Ser554Pro	65.0	0.0	.		57.0	4.0	.	NM_194255	B2R7U8|B7Z8C3|E9PFY4|O00553|O60227|Q13026|Q9BTX8	Missense_Mutation	SNP	ENST00000311124.4	hg19	CCDS13725.1	.	.	.	.	.	.	.	.	.	.	A	14.08	2.430071	0.43122	.	.	ENSG00000173638	ENST00000311124;ENST00000485649	D;D	0.84944	-1.91;-1.92	2.86	-2.08	0.07254	.	.	.	.	.	T	0.64713	0.2623	N	0.19112	0.55	0.09310	N	1	P;P	0.42078	0.77;0.77	B;B	0.32090	0.14;0.14	T	0.59700	-0.7405	9	0.87932	D	0	.	0.6492	0.00823	0.4614:0.2055:0.1326:0.2004	.	514;554	B7Z8C3;P41440	.;S19A1_HUMAN	P	554;514	ENSP00000308895:S554P;ENSP00000441772:S514P	ENSP00000308895:S554P	S	-	1	0	SLC19A1	45760116	0.002000	0.14202	0.000000	0.03702	0.004000	0.04260	-0.670000	0.05256	-0.524000	0.06400	-0.456000	0.05471	TCA	.	.	.	none		0.637	SLC19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206796.1			G	46935688	A	G	46935688	3	3	154	1	0	0	0	0	1	0	0	0	14441	304	11	3	119	3	SLC19A1	21	46935688	Missense_Mutation	SNP	A	TCGA-DW-7842-01A-11D-2136-08		46935688	1194207	27	9190											
TMEM52	339456	hgsc.bcm.edu	37	chr1	1850654	1850654	+	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	aggagcggcaggagcggcagGagcggcagcagcagccgcag	10	0	20	11	4	0	0	0	0	0	0	0	3	0	3	1	6	6	6	1	6	0	0			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr1:1850654G>C	ENST00000310991.3	-	1	58	c.51C>G	c.(49-51)ctC>ctG	p.L17L	TMEM52_ENST00000378602.3_5'Flank	NM_178545.3	NP_848640.1	Q8NDY8	TMM52_HUMAN	transmembrane protein 52	17						integral component of membrane (GO:0016021)				NS(1)|prostate(1)|stomach(1)	3	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)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.82e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.75e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		ggagcggcaggagcggcagca	0.771																																					p.L17L		Atlas-SNP	.											TMEM52,NS,carcinoma,0,1	TMEM52	21	.	0			c.C51G						PASS	.						1	2	1					1																	1850654		671	1684	2355	SO:0001819	synonymous_variant	339456	exon1			CGGCAGGAGCGGC	AJ278736	CCDS35.1	1p36.33	2008-02-05			ENSG00000178821	ENSG00000178821			27916	protein-coding gene	gene with protein product							Standard	NM_178545		Approved		uc001aij.2	Q8NDY8	OTTHUMG00000000944	ENST00000310991.3:c.51C>G	chr1.hg19:g.1850654G>C		0.0	0.0	.		7.0	2.0	.	NM_178545	Q4VXS6|Q6UX25	Silent	SNP	ENST00000310991.3	hg19	CCDS35.1	.	.	.	.	.	.	.	.	.	.	.	4.530	0.098402	0.08681	.	.	ENSG00000178821	ENST00000378598	.	.	.	0.149	0.149	0.14863	.	.	.	.	.	T	0.39489	0.1080	.	.	.	0.22446	N	0.999091	.	.	.	.	.	.	T	0.39035	-0.9633	4	0.87932	D	0	.	.	.	.	.	.	.	.	C	15	.	ENSP00000367861:S15C	S	-	2	0	TMEM52	1840514	0.001000	0.12720	0.009000	0.14445	0.010000	0.07245	0.286000	0.18902	0.192000	0.20272	0.195000	0.17529	TCC	.	.	.	none		0.771	TMEM52-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000002781.1	NM_178545		C	1850654	G	C	1850654	2	2	155	1	0	0	0	0	0	0	0	1	16190	1161	41	4		4	TMEM52	1	1850654	Silent	SNP	G	TCGA-DW-7963-01B-11D-A28G-10		1850654	247399967	1	9191											
KIAA2013	90231	hgsc.bcm.edu	37	chr1	11986231	11986231	+	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	gaggccaagcaggcagaggaGgcggcgggcccagctgctcg	8	2	19	12	3	0	1	0	0	0	1	1	3	0	2	2	6	3	4	2	6	1	0	rs552116013	byFrequency	TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr1:11986231G>A	ENST00000376572.3	-	1	249	c.64C>T	c.(64-66)Ctc>Ttc	p.L22F	KIAA2013_ENST00000376576.3_Missense_Mutation_p.L22F	NM_138346.2	NP_612355.1	Q8IYS2	K2013_HUMAN	KIAA2013	22						integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	7	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00149)|all_lung(284;0.00189)|Breast(348;0.00586)|Colorectal(325;0.0062)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0556)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AGGCAGAGGAGGCGGCGGGCC	0.771													G|||	26	0.00519169	0.0166	0.0043	5008	,	,		4617	0		0.001	False		,,,				2504	0				p.L22F		Atlas-SNP	.											.	KIAA2013	25	.	0			c.C64T						PASS	.						1	1	1					1																	11986231		852	2025	2877	SO:0001583	missense	90231	exon1			AGAGGAGGCGGCG	AB095933	CCDS141.1	1p36.22	2011-02-09			ENSG00000116685	ENSG00000116685			28513	protein-coding gene	gene with protein product						12477932	Standard	NM_138346		Approved	MGC33867, RP5-1077B9.1	uc001atk.3	Q8IYS2	OTTHUMG00000002391	ENST00000376572.3:c.64C>T	chr1.hg19:g.11986231G>A	ENSP00000365756:p.Leu22Phe	0.0	0.0	.		4.0	4.0	.	NM_138346	Q5JXC1|Q8IVF8|Q8NDI7|Q9BSY1	Missense_Mutation	SNP	ENST00000376572.3	hg19	CCDS141.1	.	.	.	.	.	.	.	.	.	.	G	18.76	3.691701	0.68271	.	.	ENSG00000116685	ENST00000376572;ENST00000376576	.	.	.	2.55	1.47	0.22746	.	0.221922	0.29040	U	0.013323	T	0.31638	0.0803	N	0.14661	0.345	0.29766	N	0.835158	D;P	0.61080	0.989;0.954	P;P	0.59487	0.858;0.812	T	0.08659	-1.0711	9	0.46703	T	0.11	-19.9466	7.5843	0.27982	0.0:0.4455:0.5544:0.0	.	22;22	Q8IYS2-2;Q8IYS2	.;K2013_HUMAN	F	22	.	ENSP00000365756:L22F	L	-	1	0	KIAA2013	11908818	0.998000	0.40836	0.999000	0.59377	0.991000	0.79684	0.719000	0.25881	1.409000	0.46915	0.563000	0.77884	CTC	.	.	.	none		0.771	KIAA2013-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006858.1	NM_138346		A	11986231	G	A	11986231	3	1	155	1	0	0	0	0	1	0	0	0	8274	1000	35	2	1852	2	KIAA2013	1	11986231	Missense_Mutation	SNP	G	TCGA-DW-7963-01B-11D-A28G-10	10135577	11986231	237264390	2	9192											
UBXN11	91544	hgsc.bcm.edu	37	chr1	26608865	26608865	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggactggggccgggaccgggAccgggactggggccgggacc	5	2	22	12	4	0	0	0	0	0	0	0	5	0	5	5	9	0	0	5	9	0	0			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr1:26608865A>G	ENST00000374222.1	-	16	1952	c.1488T>C	c.(1486-1488)ggT>ggC	p.G496G	UBXN11_ENST00000374223.1_Silent_p.G253G|UBXN11_ENST00000314675.7_Silent_p.G376G|UBXN11_ENST00000357089.4_Silent_p.G463G|UBXN11_ENST00000374221.3_Silent_p.G496G|UBXN11_ENST00000374217.2_Silent_p.G463G			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						cgggaccgggaccgggactgg	0.721																																					p.G496G		Atlas-SNP	.											.	UBXN11	54	.	1	Deletion - In frame(1)	ovary(1)	c.T1488C						PASS	.						25	29	28					1																	26608865		1768	4016	5784	SO:0001819	synonymous_variant	91544	exon16			ACCGGGACCGGGA	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.1488T>C	chr1.hg19:g.26608865A>G		21.0	0.0	.		32.0	18.0	.	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Silent	SNP	ENST00000374222.1	hg19	CCDS41288.1																																																																																			.	.	.	none		0.721	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345		G	26608865	A	G	26608865	2	3	155	1	0	0	0	0	0	0	0	1	16925	262	10	3		3	UBXN11	1	26608865	Silent	SNP	A	TCGA-DW-7963-01B-11D-A28G-10	14622634	26608865	222641756	3	9193											
ECHDC2	55268	hgsc.bcm.edu	37	chr1	53362195	53362195	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaaggttaaaatgggggtcaTttgccaacaaatttgggagt	13	11	13	4	0	1	0	1	0	0	0	1	2	1	1	1	4	2	1	1	4	5	3			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr1:53362195T>C	ENST00000371522.4	-	10	969	c.876A>G	c.(874-876)aaA>aaG	p.K292K	ECHDC2_ENST00000536120.1_Silent_p.K246K|ECHDC2_ENST00000358358.5_Silent_p.K261K	NM_001198961.1	NP_001185890.1	Q86YB7	ECHD2_HUMAN	enoyl CoA hydratase domain containing 2	292					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	lyase activity (GO:0016829)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|urinary_tract(1)	12						ATGGGGGTCATTTGCCAACAA	0.488																																					p.K292K		Atlas-SNP	.											.	ECHDC2	37	.	0			c.A876G						PASS	.						71	73	72					1																	53362195		2203	4300	6503	SO:0001819	synonymous_variant	55268	exon10			GGGTCATTTGCCA	AF258590	CCDS571.1, CCDS55600.1, CCDS72794.1	1p32.3	2010-04-30	2010-04-30		ENSG00000121310	ENSG00000121310			23408	protein-coding gene	gene with protein product			"enoyl Coenzyme A hydratase domain containing 2"				Standard	NM_018281		Approved	FLJ10948	uc001cup.4	Q86YB7	OTTHUMG00000008927	ENST00000371522.4:c.876A>G	chr1.hg19:g.53362195T>C		75.0	0.0	.		49.0	13.0	.	NM_001198961	D3DQ36|Q9NV38	Silent	SNP	ENST00000371522.4	hg19	CCDS55600.1																																																																																			.	.	.	none		0.488	ECHDC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024712.3	NM_018281		C	53362195	T	C	53362195	2	2	155	1	0	0	0	0	0	0	0	1	4896	1490	52	3		3	ECHDC2	1	53362195	Silent	SNP	T	TCGA-DW-7963-01B-11D-A28G-10	26753330	53362195	195888426	4	9194											
USH2A	7399	hgsc.bcm.edu	37	chr1	216262462	216262462	+	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	tgccatgatcattagttgtaGttacttccactggtgacccc	8	14	8	11	0	1	2	1	2	0	0	2	2	2	2	4	1	2	3	4	1	3	5			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr1:216262462G>T	ENST00000307340.3	-	23	5164	c.4778C>A	c.(4777-4779)aCt>aAt	p.T1593N	RP11-22M7.2_ENST00000446411.1_RNA|RP11-22M7.2_ENST00000430890.1_RNA|RP11-22M7.2_ENST00000442606.1_RNA|RP11-22M7.2_ENST00000445619.1_RNA|USH2A_ENST00000366943.2_Missense_Mutation_p.T1593N	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1593	Laminin G-like 1. {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)		ATTAGTTGTAGTTACTTCCAC	0.333										HNSCC(13;0.011)																											p.T1593N		Atlas-SNP	.											.	USH2A	1168	.	0			c.C4778A						PASS	.						184	168	173					1																	216262462		2203	4300	6503	SO:0001583	missense	7399	exon23			GTTGTAGTTACTT	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.4778C>A	chr1.hg19:g.216262462G>T	ENSP00000305941:p.Thr1593Asn	74.0	0.0	.		52.0	18.0	.	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	17.23	3.336688	0.60963	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.80304	-1.36;-1.36	5.8	4.88	0.63580	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);	0.000000	0.45361	D	0.000370	D	0.87006	0.6070	M	0.73962	2.25	0.38859	D	0.95643	D	0.61080	0.989	P	0.58780	0.845	D	0.87966	0.2733	10	0.41790	T	0.15	.	15.1749	0.72903	0.0:0.2669:0.7331:0.0	.	1593	O75445	USH2A_HUMAN	N	1593	ENSP00000305941:T1593N;ENSP00000355910:T1593N	ENSP00000305941:T1593N	T	-	2	0	USH2A	214329085	1.000000	0.71417	0.699000	0.30290	0.787000	0.44495	5.826000	0.69293	1.417000	0.47077	0.655000	0.94253	ACT	.	.	.	none		0.333	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216262462	G	T	216262462	3	4	155	1	0	0	0	0	1	0	0	0	17048	1029	36	4	11030	4	USH2A	1	216262462	Missense_Mutation	SNP	G	TCGA-DW-7963-01B-11D-A28G-10	162900267	216262462	32988159	5	9195											
RYR2	6262	hgsc.bcm.edu	37	chr1	237730023	237730023	+	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	gagtcgtcctggttgtcaacCggatcaggagcttggctcag	7	10	14	10	2	3	0	3	0	0	0	5	3	4	2	2	4	2	3	2	4	1	2			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr1:237730023C>G	ENST00000366574.2	+	28	3688	c.3371C>G	c.(3370-3372)cCg>cGg	p.P1124R	RYR2_ENST00000542537.1_Missense_Mutation_p.P1108R|RYR2_ENST00000360064.6_Missense_Mutation_p.P1122R	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1124	4 X approximate repeats.|B30.2/SPRY 2. {ECO:0000255|PROSITE- ProRule:PRU00548}.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GGTTGTCAACCGGATCAGGAG	0.532																																					p.P1124R		Atlas-SNP	.											RYR2,colon,carcinoma,0,1	RYR2	1273	.	0			c.C3371G						PASS	.						218	216	217					1																	237730023		2066	4209	6275	SO:0001583	missense	6262	exon28			GTCAACCGGATCA	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.3371C>G	chr1.hg19:g.237730023C>G	ENSP00000355533:p.Pro1124Arg	152.0	0.0	.		185.0	48.0	.	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.966699	0.74131	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	T;T;T	0.55588	0.51;0.51;0.51	5.29	5.29	0.74685	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.64402	D	0.000008	T	0.72558	0.3475	M	0.72894	2.215	0.80722	D	1	D	0.71674	0.998	D	0.69824	0.966	T	0.75814	-0.3185	10	0.87932	D	0	.	18.9442	0.92615	0.0:1.0:0.0:0.0	.	1124	Q92736	RYR2_HUMAN	R	1124;1122;1108	ENSP00000355533:P1124R;ENSP00000353174:P1122R;ENSP00000443798:P1108R	ENSP00000353174:P1122R	P	+	2	0	RYR2	235796646	1.000000	0.71417	0.114000	0.21550	0.563000	0.35712	7.814000	0.86154	2.465000	0.83290	0.655000	0.94253	CCG	.	.	.	none		0.532	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		G	237730023	C	G	237730023	3	3	155	1	0	0	0	0	1	0	0	0	13782	652	23	4	3481	4	RYR2	1	237730023	Missense_Mutation	SNP	C	TCGA-DW-7963-01B-11D-A28G-10	21467561	237730023	11520598	6	9196											
OXER1	165140	hgsc.bcm.edu	37	chr2	42990999	42990999	+	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	agggccaaactgttccccacCaggcccaggacaaactccag	12	4	9	16	0	0	0	0	0	0	0	2	1	2	1	6	3	2	1	6	3	2	1			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr2:42990999C>A	ENST00000378661.2	-	1	402	c.321G>T	c.(319-321)ctG>ctT	p.L107L		NM_148962.4	NP_683765.1	Q8TDS5	OXER1_HUMAN	oxoeicosanoid (OXE) receptor 1	107					G-protein coupled receptor signaling pathway (GO:0007186)|regulation of cAMP biosynthetic process (GO:0030817)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	5(S)-hydroxyperoxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050648)|5-hydroxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050647)|5-oxo-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050646)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	10						TGTTCCCCACCAGGCCCAGGA	0.647																																					p.L107L		Atlas-SNP	.											.	OXER1	33	.	0			c.G321T						PASS	.						43	47	45					2																	42990999		2203	4300	6503	SO:0001819	synonymous_variant	165140	exon1			CCCCACCAGGCCC	AB083055	CCDS1810.1	2p22.1	2012-08-10			ENSG00000162881	ENSG00000162881		"GPCR / Class A : Leukotriene receptors"	24884	protein-coding gene	gene with protein product	"5-oxo-ETE acid G-protein-coupled receptor 1"					12065583, 15001665	Standard	NM_148962		Approved	GPCR, TG1019, GPR170	uc002rss.3	Q8TDS5	OTTHUMG00000128643	ENST00000378661.2:c.321G>T	chr2.hg19:g.42990999C>A		100.0	0.0	.		100.0	34.0	.	NM_148962	Q86WP7|Q8NGW4	Silent	SNP	ENST00000378661.2	hg19	CCDS1810.1																																																																																			.	.	.	none		0.647	OXER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250514.1	NM_148962		A	42990999	C	A	42990999	2	1	155	1	0	0	0	0	0	0	0	1	11338	581	21	4		4	OXER1	2	42990999	Silent	SNP	C	TCGA-DW-7963-01B-11D-A28G-10		42990999	200208374	7	9197											
OSBPL11	114885	hgsc.bcm.edu	37	chr3	125298795	125298795	+	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	gtgatattacagctcctgcaAgctgcaaagttcctctaggt	10	12	9	10	0	1	1	0	1	1	0	3	1	3	1	2	1	5	5	2	1	5	4			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr3:125298795A>T	ENST00000296220.5	-	3	612	c.323T>A	c.(322-324)cTt>cAt	p.L108H		NM_022776.4	NP_073613.2	Q9BXB4	OSB11_HUMAN	oxysterol binding protein-like 11	108	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|positive regulation of sequestering of triglyceride (GO:0010890)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)			NS(1)|breast(1)|cervix(1)|kidney(2)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	27						AGCTCCTGCAAGCTGCAAAGT	0.403																																					p.L108H		Atlas-SNP	.											.	OSBPL11	64	.	0			c.T323A						PASS	.						118	121	120					3																	125298795		2203	4300	6503	SO:0001583	missense	114885	exon3			CCTGCAAGCTGCA	AF392454	CCDS3033.1	3q21	2013-01-10			ENSG00000144909	ENSG00000144909		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16397	protein-coding gene	gene with protein product		606739					Standard	NM_022776		Approved	ORP-11, ORP11, FLJ13012, FLJ13164	uc003eic.3	Q9BXB4	OTTHUMG00000159571	ENST00000296220.5:c.323T>A	chr3.hg19:g.125298795A>T	ENSP00000296220:p.Leu108His	101.0	0.0	.		130.0	25.0	.	NM_022776	A8K9I7	Missense_Mutation	SNP	ENST00000296220.5	hg19	CCDS3033.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.595561	0.86953	.	.	ENSG00000144909	ENST00000296220	D	0.84223	-1.82	5.07	5.07	0.68467	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.071226	0.56097	D	0.000021	D	0.94739	0.8302	H	0.96301	3.8	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96314	0.9231	10	0.87932	D	0	0.5235	14.9917	0.71393	1.0:0.0:0.0:0.0	.	108	Q9BXB4	OSB11_HUMAN	H	108	ENSP00000296220:L108H	ENSP00000296220:L108H	L	-	2	0	OSBPL11	126781485	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.073000	0.93992	2.124000	0.65301	0.533000	0.62120	CTT	.	.	.	none		0.403	OSBPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356295.1	NM_022776		T	125298795	A	T	125298795	3	4	155	1	0	0	0	0	1	0	0	0	11283	72	3	5	1964	5	OSBPL11	3	125298795	Missense_Mutation	SNP	A	TCGA-DW-7963-01B-11D-A28G-10		125298795	72723635	8	9198											
NPHP3	27031	hgsc.bcm.edu	37	chr3	132418235	132418235	+	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	gtttctacattcacagaaacAattactcttacattcactgg	13	14	4	10	0	4	1	2	0	2	1	4	1	4	1	0	1	4	1	0	1	5	6			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr3:132418235A>T	ENST00000337331.5	-	13	2033	c.1947T>A	c.(1945-1947)atT>atA	p.I649I	NPHP3_ENST00000326682.8_Silent_p.I649I	NM_153240.4	NP_694972.3	Q7Z494	NPHP3_HUMAN	nephronophthisis 3 (adolescent)	649					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						TCACAGAAACAATTACTCTTA	0.328																																					p.I649I		Atlas-SNP	.											.	NPHP3	110	.	0			c.T1947A						PASS	.						122	107	112					3																	132418235		2203	4300	6503	SO:0001819	synonymous_variant	27031	exon13			AGAAACAATTACT	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.1947T>A	chr3.hg19:g.132418235A>T		48.0	0.0	.		61.0	22.0	.	NM_153240	Q5JPE3|Q5JPE6|Q68D99|Q6NVH3|Q7Z492|Q7Z493|Q8N9R2|Q8NCM5|Q96N70|Q96NK2	Silent	SNP	ENST00000337331.5	hg19	CCDS3078.1																																																																																			.	.	.	none		0.328	NPHP3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357020.2	NM_153240		T	132418235	A	T	132418235	2	4	155	1	0	0	0	0	0	0	0	1	10587	126	5	5		5	NPHP3	3	132418235	Silent	SNP	A	TCGA-DW-7963-01B-11D-A28G-10	7119440	132418235	65604195	9	9199											
F12	2161	hgsc.bcm.edu	37	chr5	176833055	176833058	+	Frame_Shift_Del	DEL	AGTG	AGTG	-																															tggcagggctccccggtgacAgtgagaactgcagggacaac																								rs149368999	byFrequency	TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	AGTG	AGTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr5:176833055_176833058delAGTG	ENST00000253496.3	-	3	168_171	c.120_123delCACT	c.(118-123)ctcactfs	p.LT40fs	F12_ENST00000514943.1_5'Flank	NM_000505.3	NP_000496.2	P00748	FA12_HUMAN	coagulation factor XII (Hageman factor)	40					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)	CCCCGGTGACAGTGAGAACTGCAG	0.588									Hereditary Angioedema																												p.41_42del		Atlas-Indel,Pindel	.											.	F12	35	.	0			c.121_124del						PASS	.																																			SO:0001589	frameshift_variant	2161	exon3	Familial Cancer Database	HAE, type I-III, Hereditary Angioneurotic Edema, HANE,	.	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.120_123delCACT	chr5.hg19:g.176833055_176833058delAGTG	ENSP00000253496:p.Leu40fs	63.0	0.0	0		71.0	23.0	0.323944	NM_000505	P78339	Frame_Shift_Del	DEL	ENST00000253496.3	hg19	CCDS34302.1																																																																																			.	.	.	none		0.588	F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373217.1			-	176833058	AGTG	-	176833055	7	5	155	1	0	1	0	1	0	0	0	0	5341	175	7	0	1772	0	F12	5	176833055	Frame_Shift_Del	DEL	AGTG	TCGA-DW-7963-01B-11D-A28G-10		176833055	4082205	10	9200											
SLC22A3	6581	hgsc.bcm.edu	37	chr6	160769796	160769796	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgcgcggacccactcgcCgccttccccaaccgctcggc	5	5	10	21	6	0	0	0	0	0	0	3	1	1	1	6	2	3	2	6	2	1	1			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr6:160769796C>T	ENST00000275300.2	+	1	497	c.345C>T	c.(343-345)gcC>gcT	p.A115A	SLC22A3_ENST00000392145.1_Silent_p.A115A	NM_021977.3	NP_068812.1	O75751	S22A3_HUMAN	solute carrier family 22 (organic cation transporter), member 3	115					dopamine transport (GO:0015872)|drug transmembrane transport (GO:0006855)|histamine uptake (GO:0051615)|organic cation transport (GO:0015695)|quaternary ammonium group transport (GO:0015697)|regulation of appetite (GO:0032098)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dopamine transmembrane transporter activity (GO:0005329)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|toxin transporter activity (GO:0019534)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		Breast(66;0.00028)|Ovarian(120;0.0308)|Prostate(117;0.218)		OV - Ovarian serous cystadenocarcinoma(65;9.47e-17)|BRCA - Breast invasive adenocarcinoma(81;9.75e-06)	Adefovir Dipivoxil(DB00718)|Amphetamine(DB00182)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Colchicine(DB01394)|Desipramine(DB01151)|Dopamine(DB00988)|Estradiol(DB00783)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imipramine(DB00458)|Irinotecan(DB00762)|Lamivudine(DB00709)|Melphalan(DB01042)|Metformin(DB00331)|Methamphetamine(DB01577)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Phenoxybenzamine(DB00925)|Prazosin(DB00457)|Procainamide(DB01035)|Progesterone(DB00396)|Testosterone(DB00624)|Vincristine(DB00541)	ACCCACTCGCCGCCTTCCCCA	0.756																																					p.A115A		Atlas-SNP	.											.	SLC22A3	58	.	0			c.C345T						PASS	.						3	3	3					6																	160769796		1659	3388	5047	SO:0001819	synonymous_variant	6581	exon1			ACTCGCCGCCTTC	AF078749	CCDS5277.1	6q25.3	2013-07-18	2013-07-18		ENSG00000146477	ENSG00000146477		"Solute carriers"	10967	protein-coding gene	gene with protein product		604842	"solute carrier family 22 (extraneuronal monoamine transporter), member 3"			9632645, 9933568	Standard	NM_021977		Approved	OCT3, EMT	uc003qti.4	O75751	OTTHUMG00000015953	ENST00000275300.2:c.345C>T	chr6.hg19:g.160769796C>T		0.0	0.0	.		23.0	11.0	.	NM_021977	Q5SYN6|Q9UP02	Silent	SNP	ENST00000275300.2	hg19	CCDS5277.1																																																																																			.	.	.	none		0.756	SLC22A3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042953.1	NM_021977		T	160769796	C	T	160769796	2	4	155	1	0	0	0	0	0	0	0	1	14468	639	23	1		1	SLC22A3	6	160769796	Silent	SNP	C	TCGA-DW-7963-01B-11D-A28G-10		160769796	10345271	11	9201											
TBP	6908	hgsc.bcm.edu	37	chr6	170871004	170871004	+	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	gagcaacaaaggcagcagcaGcaacaacaacagcagcagca	19	0	10	12	0	0	0	0	0	0	0	0	1	0	0	0	1	11	8	0	1	5	0			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr6:170871004G>A	ENST00000392092.2	+	3	459	c.180G>A	c.(178-180)caG>caA	p.Q60Q	TBP_ENST00000540980.1_Silent_p.Q40Q|TBP_ENST00000230354.6_Silent_p.Q60Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	60	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		Ggcagcagcagcaacaacaac	0.542																																					p.Q60Q		Atlas-SNP	.											.	TBP	58	.	0			c.G180A						PASS	.						43	45	44					6																	170871004		2203	4300	6503	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAACAA	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"General transcription factors"	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.180G>A	chr6.hg19:g.170871004G>A		58.0	0.0	.		75.0	10.0	.	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	hg19	CCDS5315.1																																																																																			.	.	.	none		0.542	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		A	170871004	G	A	170871004	2	1	155	1	0	0	0	0	0	0	0	1	15656	962	34	2		2	TBP	6	170871004	Silent	SNP	G	TCGA-DW-7963-01B-11D-A28G-10	10101208	170871004	244063	12	9202											
TNRC18	84629	hgsc.bcm.edu	37	chr7	5352626	5352626	+	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	gaggaagaggaggaggaggaAgaggaggatgaggaggagga	16	1	24	0	0	0	3	0	1	0	2	0	14	0	13	0	10	0	0	0	10	2	0	rs180704395		TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr7:5352626A>T	ENST00000430969.1	-	27	8244	c.7896T>A	c.(7894-7896)tcT>tcA	p.S2632S	TNRC18_ENST00000399537.4_Silent_p.S2632S	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2632	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)		aggaggaggaagaggaggatg	0.627																																					p.S2632S		Atlas-SNP	.											TNRC18_ENST00000430969,NS,malignant_melanoma,0,3	TNRC18	311	.	0			c.T7896A						PASS	.						6	7	7					7																	5352626		1437	3278	4715	SO:0001819	synonymous_variant	84629	exon27			GGAGGAAGAGGAG	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.7896T>A	chr7.hg19:g.5352626A>T		3.0	0.0	.		16.0	3.0	.	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	hg19	CCDS47534.1	.	.	.	.	.	.	.	.	.	.	N	0.241	-1.013754	0.02095	.	.	ENSG00000182095	ENST00000399544	.	.	.	4.15	0.579	0.17397	.	0.267986	0.19999	N	0.101365	T	0.62829	0.2460	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61426	-0.7065	6	0.87932	D	0	.	8.5864	0.33660	0.458:0.0:0.542:0.0	.	.	.	.	H	1145	.	ENSP00000382459:L1145H	L	-	2	0	TNRC18	5319152	0.991000	0.36638	0.765000	0.31456	0.005000	0.04900	0.298000	0.19120	-0.159000	0.11021	-1.232000	0.01568	CTT	.	A|0.966;G|0.034	.	alt		0.627	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	5352626	A	T	5352626	2	4	155	1	0	0	0	0	0	0	0	1	16351	59	3	5		5	TNRC18	7	5352626	Silent	SNP	A	TCGA-DW-7963-01B-11D-A28G-10		5352626	153786037	13	9203											
TAF6	6878	hgsc.bcm.edu	37	chr7	99707631	99707631	+	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	atgttgctcagcacagggccGtccagcacactgcggatccg	8	7	12	14	3	1	0	1	0	0	0	3	1	3	1	3	2	4	4	3	2	0	1	rs148894017		TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr7:99707631G>A	ENST00000344095.4	-	12	1749	c.1224C>T	c.(1222-1224)gaC>gaT	p.D408D	TAF6_ENST00000452041.1_Silent_p.D408D|TAF6_ENST00000453269.2_Silent_p.D408D|AP4M1_ENST00000421755.1_Intron|TAF6_ENST00000418432.2_Silent_p.D332D|TAF6_ENST00000437822.2_Silent_p.D445D|TAF6_ENST00000472509.1_Silent_p.D465D	NM_005641.3	NP_005632.1	P49848	TAF6_HUMAN	TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80kDa	408					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)					GCACAGGGCCGTCCAGCACAC	0.587																																					p.D445D		Atlas-SNP	.											.	TAF6	55	.	0			c.C1335T						PASS	.	G	,,	0,4406		0,0,2203	110	97	101		1335,1224,1224	-6.5	0.9	7	dbSNP_134	101	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	TAF6	NM_001190415.1,NM_005641.3,NM_139315.2	,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,	445/715,408/678,408/678	99707631	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	6878	exon12			AGGGCCGTCCAGC		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.1224C>T	chr7.hg19:g.99707631G>A		124.0	0.0	.		155.0	37.0	.	NM_001190415	A4D2B2|A4D2B3|B4DT11|D6W5U2|Q6AI29	Silent	SNP	ENST00000344095.4	hg19	CCDS5686.1																																																																																			.	G|1.000;A|0.000	0.000	weak		0.587	TAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337024.2	NM_005641		A	99707631	G	A	99707631	2	1	155	1	0	0	0	0	0	0	0	1	15542	1136	40	1		1	TAF6	7	99707631	Silent	SNP	G	TCGA-DW-7963-01B-11D-A28G-10	94355005	99707631	59431032	14	9204											
AKNA	80709	hgsc.bcm.edu	37	chr9	117143567	117143567	+	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	gccgccgctgggggcccttcCccaggccaggctcagcccag	4	4	14	19	2	1	0	1	0	0	0	2	0	2	0	7	4	1	2	7	4	0	1			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr9:117143567C>A	ENST00000307564.4	-	2	208	c.47G>T	c.(46-48)gGg>gTg	p.G16V	AKNA_ENST00000312033.3_Missense_Mutation_p.G16V|AKNA_ENST00000374088.3_Missense_Mutation_p.G16V	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	16					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						GGGGCCCTTCCCCAGGCCAGG	0.622																																					p.G16V		Atlas-SNP	.											.	AKNA	119	.	0			c.G47T						PASS	.						35	28	31					9																	117143567		2201	4299	6500	SO:0001583	missense	80709	exon2			CCCTTCCCCAGGC	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.47G>T	chr9.hg19:g.117143567C>A	ENSP00000303769:p.Gly16Val	38.0	0.0	.		83.0	25.0	.	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	hg19	CCDS6805.1	.	.	.	.	.	.	.	.	.	.	C	13.20	2.167000	0.38217	.	.	ENSG00000106948	ENST00000307564;ENST00000374088;ENST00000312033;ENST00000394574	T;T;T	0.58940	1.58;1.58;0.3	3.83	3.83	0.44106	.	0.000000	0.43919	D	0.000520	T	0.64023	0.2561	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.66614	-0.5879	10	0.87932	D	0	-30.4003	11.5452	0.50690	0.0:1.0:0.0:0.0	.	16;16	Q7Z591-6;Q7Z591	.;AKNA_HUMAN	V	16	ENSP00000303769:G16V;ENSP00000363201:G16V;ENSP00000309222:G16V	ENSP00000303769:G16V	G	-	2	0	AKNA	116183388	0.873000	0.30073	0.977000	0.42913	0.053000	0.15095	1.457000	0.35212	2.460000	0.83146	0.561000	0.74099	GGG	.	.	.	none		0.622	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767		A	117143567	C	A	117143567	3	1	155	1	0	0	0	0	1	0	0	0	463	623	22	4	4356	4	AKNA	9	117143567	Missense_Mutation	SNP	C	TCGA-DW-7963-01B-11D-A28G-10		117143567	24069864	15	9205											
GAD2	2572	hgsc.bcm.edu	37	chr10	26506915	26506915	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caactacgcgtttctccatgCaacaggtaaagactcagcgg	12	8	9	12	3	2	1	1	0	1	1	3	1	2	1	1	2	5	3	1	2	5	3			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr10:26506915C>T	ENST00000376261.3	+	3	784	c.281C>T	c.(280-282)gCa>gTa	p.A94V	GAD2_ENST00000376248.1_5'Flank|GAD2_ENST00000259271.3_Missense_Mutation_p.A94V	NM_001134366.1	NP_001127838.1	Q05329	DCE2_HUMAN	glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa)	94					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						TTTCTCCATGCAACAGGTAAA	0.721																																					p.A94V		Atlas-SNP	.											.	GAD2	116	.	0			c.C281T						PASS	.						27	36	33					10																	26506915		2200	4295	6495	SO:0001583	missense	2572	exon3			TCCATGCAACAGG	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.281C>T	chr10.hg19:g.26506915C>T	ENSP00000365437:p.Ala94Val	77.0	0.0	.		195.0	54.0	.	NM_000818	Q9UD87	Missense_Mutation	SNP	ENST00000376261.3	hg19	CCDS7149.1	.	.	.	.	.	.	.	.	.	.	C	15.99	2.996975	0.54147	.	.	ENSG00000136750	ENST00000376261;ENST00000259271;ENST00000428517	T;T;T	0.59638	0.25;0.25;0.25	5.84	4.88	0.63580	.	0.414814	0.27068	N	0.021100	T	0.51398	0.1672	L	0.54323	1.7	0.80722	D	1	P;B	0.39480	0.675;0.048	B;B	0.32864	0.154;0.016	T	0.59289	-0.7482	10	0.56958	D	0.05	-3.897	16.0867	0.81060	0.0:0.866:0.134:0.0	.	94;94	Q4G154;Q05329	.;DCE2_HUMAN	V	94	ENSP00000365437:A94V;ENSP00000259271:A94V;ENSP00000390434:A94V	ENSP00000259271:A94V	A	+	2	0	GAD2	26546921	1.000000	0.71417	1.000000	0.80357	0.014000	0.08584	4.858000	0.62947	2.768000	0.95171	0.561000	0.74099	GCA	.	.	.	none		0.721	GAD2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047255.1	NM_000818		T	26506915	C	T	26506915	3	4	155	1	0	0	0	0	1	0	0	0	6187	710	25	2	291	2	GAD2	10	26506915	Missense_Mutation	SNP	C	TCGA-DW-7963-01B-11D-A28G-10		26506915	109027832	16	9206											
KIF5B	3799	hgsc.bcm.edu	37	chr10	32326205	32326205	+	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	ttcactaccagctaaatcaaCcagataaagttttccactca	15	11	3	12	0	3	1	3	0	0	1	4	1	4	1	3	0	3	2	3	0	6	6			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr10:32326205C>A	ENST00000302418.4	-	8	1145	c.688G>T	c.(688-690)Gtt>Ttt	p.V230F		NM_004521.2	NP_004512.1	P33176	KINH_HUMAN	kinesin family member 5B	230	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				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)				GCTAAATCAACCAGATAAAGT	0.338			T	"RET, ALK"	NSCLC																																p.V230F		Atlas-SNP	.		Dom	yes		10	10p11.22	3799	kinesin family member 5B		E	.	KIF5B	81	.	0			c.G688T						PASS	.						127	110	116					10																	32326205		2202	4298	6500	SO:0001583	missense	3799	exon8			AATCAACCAGATA	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.688G>T	chr10.hg19:g.32326205C>A	ENSP00000307078:p.Val230Phe	89.0	0.0	.		77.0	10.0	.	NM_004521	A0AVB2|Q5VZ85	Missense_Mutation	SNP	ENST00000302418.4	hg19	CCDS7171.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.891963	0.91889	.	.	ENSG00000170759	ENST00000302418	D	0.83335	-1.71	5.0	5.0	0.66597	Kinesin, motor domain (5);Kinesin, motor region, conserved site (1);	0.062994	0.64402	D	0.000007	D	0.95404	0.8508	H	0.99299	4.505	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.97679	1.0171	10	0.87932	D	0	.	18.6607	0.91471	0.0:1.0:0.0:0.0	.	230	P33176	KINH_HUMAN	F	230	ENSP00000307078:V230F	ENSP00000307078:V230F	V	-	1	0	KIF5B	32366211	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.811000	0.86092	2.449000	0.82847	0.557000	0.71058	GTT	.	.	.	none		0.338	KIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047467.1	NM_004521		A	32326205	C	A	32326205	3	1	155	1	0	0	0	0	1	0	0	0	8313	507	18	4	2275	4	KIF5B	10	32326205	Missense_Mutation	SNP	C	TCGA-DW-7963-01B-11D-A28G-10	5819290	32326205	103208542	17	9207											
MUC2	4583	hgsc.bcm.edu	37	chr11	1093204	1093204	+	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	ccggcacacagtccccaaccCcaacagccatcaccaccacc	12	2	4	23	1	1	0	1	0	0	0	2	0	2	0	9	1	3	1	9	1	2	0	rs56299570		TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr11:1093204C>A	ENST00000441003.2	+	30	5050	c.5023C>A	c.(5023-5025)Cca>Aca	p.P1675T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.P1642T|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)		p.P1675T(1)|p.P1642T(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)	gtccccaaccccaacagccat	0.627																																					p.P1675T		Atlas-SNP	.											MUC2_ENST00000441003,caecum,carcinoma,0,4	MUC2	614	.	2	Substitution - Missense(2)	kidney(2)	c.C5023A						PASS	.																																			SO:0001583	missense	4583	exon30			CCAACCCCAACAG	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.5023C>A	chr11.hg19:g.1093204C>A	ENSP00000415183:p.Pro1675Thr	70.0	1.0	.		55.0	5.0	.	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	C	0.954	-0.705464	0.03255	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.09073	3.02;3.53	1.75	-3.49	0.04724	.	0.575351	0.10542	U	0.662513	T	0.04092	0.0114	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45381	-0.9265	9	0.16896	T	0.51	.	6.9769	0.24681	0.6778:0.3222:0.0:0.0	rs56299570	1675	E7EUV1	.	T	1675;1642	ENSP00000415183:P1675T;ENSP00000351956:P1642T	ENSP00000351956:P1642T	P	+	1	0	MUC2	1083204	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-3.268000	0.00533	-1.450000	0.01936	0.184000	0.17185	CCA	.	.	.	weak		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1093204	C	A	1093204	3	1	155	1	0	0	0	0	1	0	0	0	9982	623	22	4	5141	4	MUC2	11	1093204	Missense_Mutation	SNP	C	TCGA-DW-7963-01B-11D-A28G-10		1093204	133913312	18	9208											
STIM1	6786	hgsc.bcm.edu	37	chr11	4104179	4104179	+	Missense_Mutation	SNP	T	T	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	cgtggcccacagctcttcccTggatgatgtagatcataaaa	11	10	9	11	1	2	2	1	1	1	1	3	3	3	3	2	2	1	2	2	2	3	3			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr11:4104179T>G	ENST00000300737.4	+	9	1774	c.1205T>G	c.(1204-1206)cTg>cGg	p.L402R	STIM1_ENST00000527651.1_Missense_Mutation_p.L402R|STIM1_ENST00000533977.1_Missense_Mutation_p.L229R	NM_003156.3	NP_003147.2	Q13586	STIM1_HUMAN	stromal interaction molecule 1	402	SOAR/CAD.				activation of store-operated calcium channel activity (GO:0032237)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|regulation of calcium ion transport (GO:0051924)|regulation of store-operated calcium entry (GO:2001256)|store-operated calcium entry (GO:0002115)	cortical endoplasmic reticulum (GO:0032541)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|growth cone (GO:0030426)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of plasma membrane (GO:0005887)|microtubule (GO:0005874)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|microtubule plus-end binding (GO:0051010)|store-operated calcium channel activity (GO:0015279)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|liver(1)|lung(14)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)		AGCTCTTCCCTGGATGATGTA	0.448																																					p.L402R		Atlas-SNP	.											.	STIM1	55	.	0			c.T1205G						PASS	.						104	93	97					11																	4104179		2201	4298	6499	SO:0001583	missense	6786	exon9			CTTCCCTGGATGA	BC021300, U52426	CCDS7749.1, CCDS60706.1, CCDS73247.1	11p15.5	2014-09-17			ENSG00000167323	ENSG00000167323		"Sterile alpha motif (SAM) domain containing"	11386	protein-coding gene	gene with protein product		605921				8921403, 11463338, 11983428	Standard	NM_003156		Approved	GOK, D11S4896E	uc021qco.1	Q13586	OTTHUMG00000133360	ENST00000300737.4:c.1205T>G	chr11.hg19:g.4104179T>G	ENSP00000300737:p.Leu402Arg	365.0	0.0	.		324.0	102.0	.	NM_003156	E9PQJ4|Q8N382	Missense_Mutation	SNP	ENST00000300737.4	hg19	CCDS7749.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.99|19.99	3.928765|3.928765	0.73327|0.73327	.|.	.|.	ENSG00000167323|ENSG00000167323	ENST00000300737;ENST00000527651;ENST00000533977|ENST00000526596	T;T;T|.	0.81330|.	-0.52;-1.48;-0.51|.	5.31|5.31	5.31|5.31	0.75309|0.75309	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.73009|0.73009	0.3532|0.3532	M|M	0.72118|0.72118	2.19|2.19	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	0.999;1.0|.	D;D|.	0.69307|.	0.946;0.963|.	T|T	0.73528|0.73528	-0.3954|-0.3954	10|5	0.87932|.	D|.	0|.	-15.7324|-15.7324	14.4442|14.4442	0.67338|0.67338	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	402;402|.	E9PQJ4;Q13586|.	.;STIM1_HUMAN|.	R|G	402;402;229|133	ENSP00000300737:L402R;ENSP00000436208:L402R;ENSP00000434767:L229R|.	ENSP00000300737:L402R|.	L|W	+|+	2|1	0|0	STIM1|STIM1	4060755|4060755	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	7.687000|7.687000	0.84139|0.84139	2.007000|2.007000	0.58848|0.58848	0.374000|0.374000	0.22700|0.22700	CTG|TGG	.	.	.	none		0.448	STIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257196.1	NM_003156		G	4104179	T	G	4104179	3	3	155	1	0	0	0	0	1	0	0	0	15295	1580	55	5	1239	5	STIM1	11	4104179	Missense_Mutation	SNP	T	TCGA-DW-7963-01B-11D-A28G-10	3010975	4104179	130902337	19	9209											
ALX1	8092	hgsc.bcm.edu	37	chr12	85674223	85674223	+	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	ccctgccccgcgccgagcatCacgtgcgcttggagaggacc	6	5	13	17	5	1	1	1	0	0	1	1	4	1	2	5	2	3	2	5	2	0	1			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr12:85674223C>T	ENST00000316824.3	+	1	339	c.184C>T	c.(184-186)Cac>Tac	p.H62Y		NM_006982.2	NP_008913.2	Q15699	ALX1_HUMAN	ALX homeobox 1	62					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)		CGCCGAGCATCACGTGCGCTT	0.637																																					p.H62Y		Atlas-SNP	.											.	ALX1	61	.	0			c.C184T						PASS	.						34	35	35					12																	85674223		2203	4300	6503	SO:0001583	missense	8092	exon1			GAGCATCACGTGC	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.184C>T	chr12.hg19:g.85674223C>T	ENSP00000315417:p.His62Tyr	76.0	0.0	.		120.0	5.0	.	NM_006982	Q546C8|Q96FH4	Missense_Mutation	SNP	ENST00000316824.3	hg19	CCDS9028.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.496984	0.85069	.	.	ENSG00000180318	ENST00000316824	D	0.92149	-2.98	5.47	5.47	0.80525	.	0.115168	0.64402	D	0.000015	D	0.88633	0.6489	N	0.19112	0.55	0.80722	D	1	P	0.39094	0.659	B	0.42959	0.403	D	0.87426	0.2385	10	0.32370	T	0.25	.	19.3325	0.94297	0.0:1.0:0.0:0.0	.	62	Q15699	ALX1_HUMAN	Y	62	ENSP00000315417:H62Y	ENSP00000315417:H62Y	H	+	1	0	ALX1	84198354	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.483000	0.60264	2.558000	0.86282	0.650000	0.86243	CAC	.	.	.	none		0.637	ALX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406072.1	NM_006982		T	85674223	C	T	85674223	3	4	155	1	0	0	0	0	1	0	0	0	556	826	29	2	186	2	ALX1	12	85674223	Missense_Mutation	SNP	C	TCGA-DW-7963-01B-11D-A28G-10		85674223	48177672	20	9210											
HECTD1	25831	hgsc.bcm.edu	37	chr14	31576342	31576342	+	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	caagaaaattccaaggaaatGaaacagtttcgtgatccttt	16	11	7	7	1	0	3	0	2	0	1	3	4	2	4	2	1	1	1	2	1	6	3			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr14:31576342G>A	ENST00000399332.1	-	38	7224	c.6736C>T	c.(6736-6738)Cat>Tat	p.H2246Y	HECTD1_ENST00000553700.1_Missense_Mutation_p.H2246Y	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	2246	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		CCAAGGAAATGAAACAGTTTC	0.383																																					p.H2246Y		Atlas-SNP	.											.	HECTD1	159	.	0			c.C6736T						PASS	.						113	108	110					14																	31576342		1901	4112	6013	SO:0001583	missense	25831	exon38			GGAAATGAAACAG	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.6736C>T	chr14.hg19:g.31576342G>A	ENSP00000382269:p.His2246Tyr	191.0	0.0	.		161.0	36.0	.	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	hg19	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	G	3.742	-0.053467	0.07362	.	.	ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332	T;T	0.56941	0.43;0.43	6.06	6.06	0.98353	HECT (4);	0.256570	0.26903	U	0.021909	T	0.31949	0.0813	N	0.11201	0.11	0.46298	D	0.99897	P	0.35208	0.49	B	0.32762	0.152	T	0.28138	-1.0053	10	0.02654	T	1	-11.499	18.8088	0.92050	0.0:0.0:1.0:0.0	.	2246	Q9ULT8	HECD1_HUMAN	Y	2246;2248;2246	ENSP00000450697:H2246Y;ENSP00000382269:H2246Y	ENSP00000261312:H2248Y	H	-	1	0	HECTD1	30646093	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.391000	0.73208	2.871000	0.98454	0.655000	0.94253	CAT	.	.	.	none		0.383	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			A	31576342	G	A	31576342	3	1	155	1	0	0	0	0	1	0	0	0	7046	1290	45	2	1120	2	HECTD1	14	31576342	Missense_Mutation	SNP	G	TCGA-DW-7963-01B-11D-A28G-10		31576342	75773198	21	9211											
KIF7	374654	hgsc.bcm.edu	37	chr15	90174782	90174782	+	Missense_Mutation	SNP	T	T	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	gtcgatctccaggcgctgctTgagcagcgagtccttctcct	5	11	11	14	3	2	1	0	1	2	0	6	3	3	1	3	1	3	3	3	1	0	2			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr15:90174782T>G	ENST00000394412.3	-	15	3131	c.3055A>C	c.(3055-3057)Aag>Cag	p.K1019Q	KIF7_ENST00000558928.1_5'Flank	NM_198525.2	NP_940927.2	Q2M1P5	KIF7_HUMAN	kinesin family member 7	1019					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)			AGGCGCTGCTTGAGCAGCGAG	0.677																																					p.K1019Q		Atlas-SNP	.											.	KIF7	130	.	0			c.A3055C						PASS	.						29	27	27					15																	90174782		2199	4292	6491	SO:0001583	missense	374654	exon15			GCTGCTTGAGCAG	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.3055A>C	chr15.hg19:g.90174782T>G	ENSP00000377934:p.Lys1019Gln	69.0	0.0	.		100.0	32.0	.	NM_198525	Q3SXY0|Q6UXE9|Q8IW72	Missense_Mutation	SNP	ENST00000394412.3	hg19	CCDS32325.2	.	.	.	.	.	.	.	.	.	.	T	28.0	4.877591	0.91664	.	.	ENSG00000166813	ENST00000394412	T	0.48836	0.8	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.66577	0.2803	M	0.70275	2.135	0.54753	D	0.999983	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.994	T	0.67321	-0.5700	10	0.40728	T	0.16	.	14.4086	0.67101	0.0:0.0:0.0:1.0	.	505;1019	B7ZKY4;Q2M1P5	.;KIF7_HUMAN	Q	1019	ENSP00000377934:K1019Q	ENSP00000377934:K1019Q	K	-	1	0	KIF7	87975786	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.570000	0.82390	1.802000	0.52723	0.379000	0.24179	AAG	.	.	.	none		0.677	KIF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347782.1	NM_198525		G	90174782	T	G	90174782	3	3	155	1	0	0	0	0	1	0	0	0	8316	1821	63	5	996	5	KIF7	15	90174782	Missense_Mutation	SNP	T	TCGA-DW-7963-01B-11D-A28G-10		90174782	12356610	22	9212											
TRIM72	260434	hgsc.bcm.edu	37	chr16	31226442	31226442	+	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	tgccgccgaggcccacgcacGcctcaaggtgcgggatccgc	6	4	14	17	6	1	0	1	0	0	0	2	2	2	1	5	3	2	1	5	3	1	0			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr16:31226442G>A	ENST00000302964.3	-	0	813				TRIM72_ENST00000322122.3_Missense_Mutation_p.R128H|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						GCCCACGCACGCCTCAAGGTG	0.687																																					p.R128H		Atlas-SNP	.											.	TRIM72	32	.	0			c.G383A						PASS	.						9	9	9					16																	31226442		1778	3412	5190	SO:0001628	intergenic_variant	493829	exon2			ACGCACGCCTCAA		CCDS10710.1	16p11.2	2008-02-05	2005-12-02		ENSG00000169900	ENSG00000169900			30261	protein-coding gene	gene with protein product		615700	"pyrin domain containing 1"			11786556, 16905547	Standard	NM_152901		Approved	ASC2, POP1	uc002ebo.3	Q8WXC3	OTTHUMG00000132407		chr16.hg19:g.31226442G>A		0.0	0.0	.		31.0	19.0	.	NM_001008274	B2R8L4|Q8NFP8	Missense_Mutation	SNP	ENST00000302964.3	hg19	CCDS10710.1	.	.	.	.	.	.	.	.	.	.	G	19.37	3.815564	0.70912	.	.	ENSG00000177238	ENST00000322122	T	0.57436	0.4	4.93	4.93	0.64822	.	0.080103	0.48767	D	0.000171	T	0.62441	0.2428	L	0.58101	1.795	0.34316	D	0.686018	D	0.89917	1.0	D	0.67725	0.953	T	0.65340	-0.6192	10	0.16420	T	0.52	.	10.896	0.47023	0.0887:0.0:0.9113:0.0	.	128	Q6ZMU5	TRI72_HUMAN	H	128	ENSP00000312675:R128H	ENSP00000312675:R128H	R	+	2	0	TRIM72	31133943	0.998000	0.40836	0.997000	0.53966	0.042000	0.13812	3.403000	0.52615	2.454000	0.82982	0.655000	0.94253	CGC	.	.	.	none		0.687	PYDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255543.2	NM_152901		A	31226442	G	A	31226442	1	1	155	0	1	0	0	0	0	0	0	0	16557	1087	38	1		1	TRIM72	16	31226442	IGR	SNP	G	TCGA-DW-7963-01B-11D-A28G-10		31226442	59128311	23	9213											
ZDHHC7	55625	hgsc.bcm.edu	37	chr16	85010785	85010785	+	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	agaagaccctcaaggcacagGaagatcaacaggattacagt	17	5	10	9	0	2	3	2	0	0	3	2	5	2	5	1	3	2	1	1	3	5	1			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr16:85010785G>A	ENST00000313732.4	-	7	1018	c.666C>T	c.(664-666)ttC>ttT	p.F222F	ZDHHC7_ENST00000564466.1_Silent_p.F259F|ZDHHC7_ENST00000569488.1_5'UTR	NM_017740.2	NP_060210.2	Q9NXF8	ZDHC7_HUMAN	zinc finger, DHHC-type containing 7	222					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						CAAGGCACAGGAAGATCAACA	0.463																																					p.F259F		Atlas-SNP	.											.	ZDHHC7	55	.	0			c.C777T						PASS	.						155	139	144					16																	85010785		2199	4300	6499	SO:0001819	synonymous_variant	55625	exon8			GCACAGGAAGATC	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.666C>T	chr16.hg19:g.85010785G>A		165.0	0.0	.		209.0	45.0	.	NM_001145548	D3DUM1|Q8WV42|Q9NVD8	Silent	SNP	ENST00000313732.4	hg19	CCDS10950.1																																																																																			.	.	.	none		0.463	ZDHHC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269087.1	NM_017740		A	85010785	G	A	85010785	2	1	155	1	0	0	0	0	0	0	0	1	17632	1165	41	2		2	ZDHHC7	16	85010785	Silent	SNP	G	TCGA-DW-7963-01B-11D-A28G-10	53784343	85010785	5343968	24	9214											
ZNF429	353088	hgsc.bcm.edu	37	chr19	21720704	21720704	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aacataagaaaattcatactAgagagaaaccttacaaatgt	21	9	5	6	0	1	3	1	0	0	3	1	4	1	3	1	0	4	0	1	0	9	5			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr19:21720704A>G	ENST00000358491.4	+	4	2057	c.1849A>G	c.(1849-1851)Aga>Gga	p.R617G	ZNF429_ENST00000597078.1_Intron	NM_001001415.2	NP_001001415.2	Q86V71	ZN429_HUMAN	zinc finger protein 429	617					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						AATTCATACTAGAGAGAAACC	0.373																																					p.R617G		Atlas-SNP	.											ZNF429,NS,malignant_melanoma,0,1	ZNF429	338	.	0			c.A1849G						PASS	.						59	65	63					19																	21720704		2081	4245	6326	SO:0001583	missense	353088	exon4			CATACTAGAGAGA	AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013		"Zinc fingers, C2H2-type", "-"	20817	protein-coding gene	gene with protein product							Standard	NM_001001415		Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000358491.4:c.1849A>G	chr19.hg19:g.21720704A>G	ENSP00000351280:p.Arg617Gly	59.0	0.0	.		63.0	3.0	.	NM_001001415	A6NLV7|Q9BZE6	Missense_Mutation	SNP	ENST00000358491.4	hg19	CCDS42537.1	.	.	.	.	.	.	.	.	.	.	.	0.007	-1.970090	0.00457	.	.	ENSG00000197013	ENST00000358491	T	0.11495	2.77	1.25	-2.5	0.06384	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01489	0.0048	N	0.00094	-2.165	0.27992	N	0.935624	B	0.02656	0.0	B	0.01281	0.0	T	0.42666	-0.9438	9	0.02654	T	1	.	7.448	0.27221	0.2389:0.0:0.7611:0.0	.	617	Q86V71	ZN429_HUMAN	G	617	ENSP00000351280:R617G	ENSP00000351280:R617G	R	+	1	2	ZNF429	21512544	0.360000	0.24964	0.000000	0.03702	0.008000	0.06430	0.999000	0.29757	-0.893000	0.03930	-0.627000	0.03993	AGA	.	.	.	none		0.373	ZNF429-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463981.1	NM_001001415		G	21720704	A	G	21720704	3	3	155	1	0	0	0	0	1	0	0	0	17914	412	15	3	1863	3	ZNF429	19	21720704	Missense_Mutation	SNP	A	TCGA-DW-7963-01B-11D-A28G-10		21720704	37408279	25	9215											
DNMT3B	1789	hgsc.bcm.edu	37	chr20	31389169	31389169	+	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	gatgaccggccgttcttctgGatgtttgagaatgttgtagc	7	14	13	7	2	2	2	0	2	2	1	2	5	2	3	2	2	1	4	2	2	2	5			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr20:31389169G>C	ENST00000328111.2	+	19	2403	c.2082G>C	c.(2080-2082)tgG>tgC	p.W694C	DNMT3B_ENST00000443239.3_Missense_Mutation_p.W632C|DNMT3B_ENST00000201963.3_Missense_Mutation_p.W686C|DNMT3B_ENST00000348286.2_Missense_Mutation_p.W674C|DNMT3B_ENST00000353855.2_Missense_Mutation_p.W674C|DNMT3B_ENST00000456297.2_Missense_Mutation_p.W598C|DNMT3B_ENST00000344505.4_Missense_Mutation_p.W674C	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta	694	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						CGTTCTTCTGGATGTTTGAGA	0.532																																					p.W694C		Atlas-SNP	.											.	DNMT3B	196	.	0			c.G2082C						PASS	.						105	95	98					20																	31389169		2203	4300	6503	SO:0001583	missense	1789	exon19			CTTCTGGATGTTT		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.2082G>C	chr20.hg19:g.31389169G>C	ENSP00000328547:p.Trp694Cys	216.0	0.0	.		264.0	77.0	.	NM_006892	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Missense_Mutation	SNP	ENST00000328111.2	hg19	CCDS13205.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.875757	0.91664	.	.	ENSG00000088305	ENST00000328111;ENST00000353855;ENST00000348286;ENST00000443239;ENST00000456297;ENST00000344505;ENST00000201963	D;D;D;D;D;D;D	0.84070	-1.8;-1.8;-1.8;-1.8;-1.8;-1.8;-1.8	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	D	0.91858	0.7423	M	0.80508	2.5	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.992;0.998;0.999;0.999;0.987;0.999;0.999	D	0.92078	0.5670	10	0.87932	D	0	-23.2234	19.2924	0.94105	0.0:0.0:1.0:0.0	.	598;632;393;686;674;674;694	E9PBF2;E7EN63;B3KM53;Q9UBC3-6;Q9UBC3-3;Q9UBC3-2;Q9UBC3	.;.;.;.;.;.;DNM3B_HUMAN	C	694;674;674;632;598;674;686	ENSP00000328547:W694C;ENSP00000313397:W674C;ENSP00000337764:W674C;ENSP00000403169:W632C;ENSP00000412305:W598C;ENSP00000345105:W674C;ENSP00000201963:W686C	ENSP00000201963:W686C	W	+	3	0	DNMT3B	30852830	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.835000	0.99442	2.878000	0.98634	0.650000	0.86243	TGG	.	.	.	none		0.532	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892		C	31389169	G	C	31389169	3	2	155	1	0	0	0	0	1	0	0	0	4679	1183	41	4	2192	4	DNMT3B	20	31389169	Missense_Mutation	SNP	G	TCGA-DW-7963-01B-11D-A28G-10		31389169	31636351	26	9216											
L3MBTL	26013	hgsc.bcm.edu	37	chr20	42162966	42162966	+	Missense_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	tcaatatgaagctggaggctGtggaccgcaggaacccagcc	11	6	13	11	1	1	1	1	1	0	0	1	4	1	4	3	4	3	3	3	4	4	1			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr20:42162966G>A	ENST00000427442.2	+	15	1735	c.1576G>A	c.(1576-1578)Gtg>Atg	p.V526M	L3MBTL1_ENST00000444063.1_Missense_Mutation_p.V458M|L3MBTL1_ENST00000418998.1_Missense_Mutation_p.V526M|L3MBTL1_ENST00000373135.3_Missense_Mutation_p.V458M|L3MBTL1_ENST00000373134.1_Missense_Mutation_p.V458M			Q9Y468	LMBL1_HUMAN	l(3)mbt-like 1 (Drosophila)	458					chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of mitosis (GO:0007088)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|nucleosome binding (GO:0031491)|SAM domain binding (GO:0032093)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(3)|ovary(1)|skin(2)	7						GCTGGAGGCTGTGGACCGCAG	0.632																																					p.V526M		Atlas-SNP	.											.	L3MBTL1	105	.	0			c.G1576A						PASS	.						45	47	46					20																	42162966		2203	4300	6503	SO:0001583	missense	26013	exon15			GAGGCTGTGGACC	U89358	CCDS13319.1, CCDS46602.1, CCDS46602.2	20q13.12	2013-01-10	2010-09-03	2010-09-03	ENSG00000185513	ENSG00000185513		"Zinc fingers, C2HC-type containing", "Sterile alpha motif (SAM) domain containing"	15905	protein-coding gene	gene with protein product	"lethal (3) malignant brain tumor l(3)"	608802	"l(3)mbt (Drosophila)-like", "l(3)mbt-like (Drosophila)"	L3MBTL		10445843, 17540172	Standard	NM_032107		Approved	ZC2HC3, dJ138B7.3, DKFZp586P1522, KIAA0681	uc010zwh.2	Q9Y468	OTTHUMG00000032503	ENST00000427442.2:c.1576G>A	chr20.hg19:g.42162966G>A	ENSP00000402107:p.Val526Met	79.0	0.0	.		101.0	25.0	.	NM_032107	B4DRC9|E1P5W7|Q5H8Y8|Q5H8Y9|Q8IUV7|Q9H1E6|Q9H1G5|Q9UG06|Q9UJB9|Q9Y4C9	Missense_Mutation	SNP	ENST00000427442.2	hg19	CCDS46602.2	.	.	.	.	.	.	.	.	.	.	G	31	5.080728	0.94050	.	.	ENSG00000185513	ENST00000427442;ENST00000418998;ENST00000373135;ENST00000444063;ENST00000373134;ENST00000422861;ENST00000373133	T;T;T;T;T;T	0.37584	1.19;1.19;1.19;1.19;1.19;1.19	5.39	5.39	0.77823	.	0.115236	0.64402	D	0.000019	T	0.69324	0.3098	M	0.91459	3.21	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.997;0.997;1.0;0.996	T	0.76170	-0.3057	10	0.87932	D	0	.	18.0965	0.89492	0.0:0.0:1.0:0.0	.	526;110;458;458	Q9Y468-5;Q9Y468-3;Q9Y468-2;Q9Y468-1	.;.;.;.	M	526;526;458;458;458;244;110	ENSP00000402107:V526M;ENSP00000398516:V526M;ENSP00000362227:V458M;ENSP00000403316:V458M;ENSP00000362226:V458M;ENSP00000410139:V244M	ENSP00000362225:V110M	V	+	1	0	L3MBTL1	41596380	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.598000	0.98277	2.804000	0.96469	0.655000	0.94253	GTG	.	.	.	none		0.632	L3MBTL1-007	KNOWN	upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079300.3	NM_032107		A	42162966	G	A	42162966	3	1	155	1	0	0	0	0	1	0	0	0	8598	1377	48	2	1418	2	L3MBTL	20	42162966	Missense_Mutation	SNP	G	TCGA-DW-7963-01B-11D-A28G-10	10773797	42162966	20862554	27	9217											
DOPEY2	9980	hgsc.bcm.edu	37	chr21	37642372	37642372	+	Missense_Mutation	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	cggctcttccttggagcaaaCcagctggctaagcagaaacc	11	7	10	13	1	1	1	0	0	1	1	2	2	2	2	3	3	5	5	3	3	3	3			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr21:37642372C>T	ENST00000399151.3	+	27	5634	c.5549C>T	c.(5548-5550)aCc>aTc	p.T1850I		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	1850					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						TTGGAGCAAACCAGCTGGCTA	0.493																																					p.T1850I		Atlas-SNP	.											.	DOPEY2	184	.	0			c.C5549T						PASS	.						104	109	108					21																	37642372		2203	4300	6503	SO:0001583	missense	9980	exon27			AGCAAACCAGCTG	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.5549C>T	chr21.hg19:g.37642372C>T	ENSP00000382104:p.Thr1850Ile	79.0	0.0	.		82.0	25.0	.	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Missense_Mutation	SNP	ENST00000399151.3	hg19	CCDS13643.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.422737	0.83559	.	.	ENSG00000142197	ENST00000399151	T	0.14516	2.5	5.47	4.59	0.56863	.	0.049713	0.85682	N	0.000000	T	0.41119	0.1145	M	0.85542	2.76	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.41998	-0.9477	10	0.51188	T	0.08	-3.5123	13.7957	0.63168	0.0:0.9267:0.0:0.0733	.	1850;1850	Q9Y3R5-2;Q9Y3R5	.;DOP2_HUMAN	I	1850	ENSP00000382104:T1850I	ENSP00000382104:T1850I	T	+	2	0	DOPEY2	36564242	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.300000	0.78841	1.311000	0.45024	0.650000	0.86243	ACC	.	.	.	none		0.493	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128		T	37642372	C	T	37642372	3	4	155	1	0	0	0	0	1	0	0	0	4710	507	18	2	5651	2	DOPEY2	21	37642372	Missense_Mutation	SNP	C	TCGA-DW-7963-01B-11D-A28G-10		37642372	10487523	28	9218											
ZBED4	9889	hgsc.bcm.edu	37	chr22	50279802	50279802	+	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	cgtgcagtgcttcagccataCggtgaacctgatcgtcagcg	8	9	12	12	4	2	2	2	2	0	0	3	2	2	2	2	1	6	2	2	1	2	2			TCGA-DW-7963-01B-11D-A28G-10	TCGA-DW-7963-10C-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	15b3020f-71db-4d0e-8f6a-edf5552e3064	a522a63d-1b4f-46ea-bcfc-5dbbc855a5bb	g.chr22:50279802C>T	ENST00000216268.5	+	2	2969	c.2492C>T	c.(2491-2493)aCg>aTg	p.T831M		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	831						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)		TTCAGCCATACGGTGAACCTG	0.642																																					p.T831M		Atlas-SNP	.											ZBED4,NS,adenocarcinoma,0,1	ZBED4	102	.	0			c.C2492T						PASS	.						35	35	35					22																	50279802		2202	4300	6502	SO:0001583	missense	9889	exon2			GCCATACGGTGAA	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.2492C>T	chr22.hg19:g.50279802C>T	ENSP00000216268:p.Thr831Met	114.0	1.0	.		159.0	49.0	.	NM_014838	B2RZH1|Q1ECU0|Q9UGG8	Missense_Mutation	SNP	ENST00000216268.5	hg19	CCDS33677.1	.	.	.	.	.	.	.	.	.	.	C	14.16	2.451158	0.43531	.	.	ENSG00000100426	ENST00000216268	T	0.23348	1.91	5.57	3.46	0.39613	Ribonuclease H-like (1);	0.113857	0.64402	N	0.000019	T	0.47911	0.1471	M	0.77820	2.39	0.49483	D	0.999791	D	0.89917	1.0	D	0.71656	0.974	T	0.44757	-0.9307	10	0.54805	T	0.06	-22.2447	10.3753	0.44079	0.1354:0.7951:0.0:0.0695	.	831	O75132	ZBED4_HUMAN	M	831	ENSP00000216268:T831M	ENSP00000216268:T831M	T	+	2	0	ZBED4	48665806	0.999000	0.42202	0.659000	0.29680	0.301000	0.27625	4.300000	0.59079	0.688000	0.31529	0.655000	0.94253	ACG	.	.	.	none		0.642	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838		T	50279802	C	T	50279802	3	4	155	1	0	0	0	0	1	0	0	0	17532	536	19	1	2494	1	ZBED4	22	50279802	Missense_Mutation	SNP	C	TCGA-DW-7963-01B-11D-A28G-10		50279802	1024764	29	9219											
ZCCHC17	51538	hgsc.bcm.edu	37	chr1	31836979	31836979	+	Missense_Mutation	SNP	A	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	ggcaaggcacacatcaaaagAcagcaaggcagcaaagaaga	20	1	11	9	0	1	3	1	0	0	3	1	3	1	3	0	3	2	5	0	3	6	0	rs111803813		TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr1:31836979A>C	ENST00000373714.1	+	8	926	c.665A>C	c.(664-666)gAc>gCc	p.D222A	ZCCHC17_ENST00000546109.1_Missense_Mutation_p.D214A|ZCCHC17_ENST00000344147.5_Missense_Mutation_p.D222A|FABP3_ENST00000497275.1_5'Flank|ZCCHC17_ENST00000422613.2_Missense_Mutation_p.D224A	NM_001282568.1|NM_001282570.1	NP_001269497.1|NP_001269499.1	Q9NP64	NO40_HUMAN	zinc finger, CCHC domain containing 17	222	Lys-rich.					cytosolic large ribosomal subunit (GO:0022625)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(2)|ovary(1)|skin(1)	6		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)|all_neural(195;0.146)|Medulloblastoma(700;0.151)|Breast(348;0.222)		STAD - Stomach adenocarcinoma(196;0.0215)|READ - Rectum adenocarcinoma(331;0.168)		ACATCAAAAGACAGCAAGGCA	0.433																																					p.D222A		Atlas-SNP	.											.	ZCCHC17	30	.	0			c.A665C						PASS	.						82	86	85					1																	31836979		2203	4300	6503	SO:0001583	missense	51538	exon8			CAAAAGACAGCAA	AF151085	CCDS341.1, CCDS60061.1, CCDS72741.1, CCDS72742.1, CCDS72743.1, CCDS72744.1	1p35.2	2008-05-02			ENSG00000121766	ENSG00000121766		"Zinc fingers, CCHC domain containing"	30246	protein-coding gene	gene with protein product						12202495, 12893261	Standard	NM_001282572		Approved	PS1D, HSPC251, pNO40	uc001bsp.1	Q9NP64	OTTHUMG00000003791	ENST00000373714.1:c.665A>C	chr1.hg19:g.31836979A>C	ENSP00000362819:p.Asp222Ala	99.0	0.0	.		133.0	23.0	.	NM_016505	B4DY38|D3DPN4|Q6PKH4|Q9NYG4|Q9P0M8	Missense_Mutation	SNP	ENST00000373714.1	hg19	CCDS341.1	.	.	.	.	.	.	.	.	.	.	A	16.09	3.025038	0.54683	.	.	ENSG00000121766	ENST00000344147;ENST00000373714;ENST00000546109;ENST00000422613	.	.	.	5.08	5.08	0.68730	.	0.376195	0.32055	N	0.006643	T	0.41488	0.1161	N	0.19112	0.55	0.25685	N	0.98575	D;B;B	0.69078	0.997;0.023;0.008	D;B;B	0.75484	0.986;0.007;0.001	T	0.23904	-1.0175	9	0.66056	D	0.02	.	9.0275	0.36239	0.814:0.186:0.0:0.0	.	224;214;222	E7EPF0;B4DY38;Q9NP64	.;.;NO40_HUMAN	A	222;222;214;224	.	ENSP00000343557:D222A	D	+	2	0	ZCCHC17	31609566	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.513000	0.45494	2.135000	0.66039	0.528000	0.53228	GAC	.	G|1.000;|0.000	.	alt		0.433	ZCCHC17-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010665.1	NM_016505		C	31836979	A	C	31836979	3	2	156	1	0	0	0	0	1	0	0	0	17597	275	10	5	691	5	ZCCHC17	1	31836979	Missense_Mutation	SNP	A	TCGA-DZ-6131-01A-11D-1961-08		31836979	217413642	1	9220											
ADAM30	11085	hgsc.bcm.edu	37	chr1	120436921	120436921	+	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	aaattgacgagggaatcgccCctctgagcagtcctggaggc	10	7	13	11	2	1	2	0	2	1	0	3	5	2	4	3	3	1	1	3	3	2	1			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr1:120436921C>T	ENST00000369400.1	-	1	2197	c.2039G>A	c.(2038-2040)gGg>gAg	p.G680E		NM_021794.3	NP_068566.2	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30	680					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(16)|ovary(2)|skin(2)	38	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;1.55e-06)|Lung NSC(69;1.04e-05)|all_epithelial(167;0.00138)		Lung(183;0.0204)|LUSC - Lung squamous cell carcinoma(189;0.117)		GGGAATCGCCCCTCTGAGCAG	0.473																																					p.G680E		Atlas-SNP	.											.	ADAM30	88	.	0			c.G2039A						PASS	.						65	64	64					1																	120436921		2203	4300	6503	SO:0001583	missense	11085	exon1			ATCGCCCCTCTGA	AF171932	CCDS907.1	1p12	2012-05-16	2005-08-18		ENSG00000134249	ENSG00000134249		"ADAM metallopeptidase domain containing"	208	protein-coding gene	gene with protein product		604779	"a disintegrin and metalloproteinase domain 30"				Standard	NM_021794		Approved	svph4	uc001eij.3	Q9UKF2	OTTHUMG00000012176	ENST00000369400.1:c.2039G>A	chr1.hg19:g.120436921C>T	ENSP00000358407:p.Gly680Glu	65.0	0.0	.		95.0	31.0	.	NM_021794	A8K8W8|Q5T3X6|Q9UKF1	Missense_Mutation	SNP	ENST00000369400.1	hg19	CCDS907.1	.	.	.	.	.	.	.	.	.	.	C	0.006	-2.021307	0.00414	.	.	ENSG00000134249	ENST00000369400;ENST00000543066	T	0.01126	5.3	5.05	-10.1	0.00402	.	3.564080	0.01402	N	0.013659	T	0.00109	0.0003	N	0.05031	-0.125	0.09310	N	1	B	0.13145	0.007	B	0.13407	0.009	T	0.47394	-0.9121	10	0.02654	T	1	.	1.9545	0.03373	0.4755:0.1902:0.2118:0.1224	.	680	Q9UKF2	ADA30_HUMAN	E	680	ENSP00000358407:G680E	ENSP00000358407:G680E	G	-	2	0	ADAM30	120238444	.	.	0.000000	0.03702	0.002000	0.02628	.	.	-4.800000	0.00031	-1.047000	0.02352	GGG	.	.	.	none		0.473	ADAM30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033678.1	NM_021794		T	120436921	C	T	120436921	3	4	156	1	0	0	0	0	1	0	0	0	248	623	22	2	337	2	ADAM30	1	120436921	Missense_Mutation	SNP	C	TCGA-DZ-6131-01A-11D-1961-08	88599942	120436921	128813700	2	9221											
AIM2	9447	hgsc.bcm.edu	37	chr1	159033450	159033450	+	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	aggtcaaataatatgtttttCttcttttctgttacctataa	11	20	4	6	0	4	0	1	0	3	0	4	0	4	0	1	1	1	2	1	1	6	10			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr1:159033450C>G	ENST00000368130.4	-	5	1119	c.831G>C	c.(829-831)aaG>aaC	p.K277N	AIM2_ENST00000411768.1_5'Flank	NM_004833.1	NP_004824.1	O14862	AIM2_HUMAN	absent in melanoma 2	277	HIN-200. {ECO:0000255|PROSITE- ProRule:PRU00106}.				activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to drug (GO:0035690)|cellular response to interferon-beta (GO:0035458)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein oligomerization (GO:0032461)|pyroptosis (GO:0070269)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)			breast(1)|large_intestine(1)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(1)	16	all_hematologic(112;0.0429)					ATATGTTTTTCTTCTTTTCTG	0.398																																					p.K277N		Atlas-SNP	.											.	AIM2	70	.	0			c.G831C						PASS	.						117	121	120					1																	159033450		2203	4300	6503	SO:0001583	missense	9447	exon5			GTTTTTCTTCTTT	AF024714	CCDS1181.1	1q22	2008-07-18			ENSG00000163568	ENSG00000163568			357	protein-coding gene	gene with protein product		604578				9242382	Standard	NM_004833		Approved	PYHIN4	uc001ftj.1	O14862	OTTHUMG00000037183	ENST00000368130.4:c.831G>C	chr1.hg19:g.159033450C>G	ENSP00000357112:p.Lys277Asn	167.0	0.0	.		199.0	60.0	.	NM_004833	A8K7M7|Q5T3V9|Q96FG9	Missense_Mutation	SNP	ENST00000368130.4	hg19	CCDS1181.1	.	.	.	.	.	.	.	.	.	.	C	2.160	-0.392489	0.04899	.	.	ENSG00000163568	ENST00000368130;ENST00000368129	T;T	0.14266	2.52;2.52	3.92	-4.82	0.03171	HIN-200/IF120x (2);Nucleic acid-binding, OB-fold (1);	1.433050	0.05063	N	0.480252	T	0.01558	0.0050	N	0.17723	0.515	0.09310	N	1	B	0.21606	0.058	B	0.19391	0.025	T	0.42816	-0.9429	10	0.14252	T	0.57	-0.6466	1.0125	0.01500	0.1428:0.2093:0.2823:0.3657	.	277	O14862	AIM2_HUMAN	N	277;140	ENSP00000357112:K277N;ENSP00000357111:K140N	ENSP00000357111:K140N	K	-	3	2	AIM2	157300074	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.991000	0.03728	-0.739000	0.04809	-1.099000	0.02127	AAG	.	.	.	none		0.398	AIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090341.1	NM_004833		G	159033450	C	G	159033450	3	3	156	1	0	0	0	0	1	0	0	0	432	912	32	4	208	4	AIM2	1	159033450	Missense_Mutation	SNP	C	TCGA-DZ-6131-01A-11D-1961-08	38596529	159033450	90217171	3	9222											
GLUL	2752	hgsc.bcm.edu	37	chr1	182356292	182356292	+	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	gccttcgattgtacttgaaaActtcacataacaccagcttg	12	12	6	11	1	1	1	1	1	0	0	2	2	1	1	2	0	4	2	2	0	4	7			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr1:182356292A>T	ENST00000331872.6	-	3	842	c.302T>A	c.(301-303)gTt>gAt	p.V101D	GLUL_ENST00000311223.5_Missense_Mutation_p.V101D|GLUL_ENST00000417584.2_Missense_Mutation_p.V101D|GLUL_ENST00000491322.1_5'UTR|GLUL_ENST00000339526.4_Missense_Mutation_p.V101D	NM_001033044.2	NP_001028216.1	P15104	GLNA_HUMAN	glutamate-ammonia ligase	101					cell proliferation (GO:0008283)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to starvation (GO:0009267)|glutamate catabolic process (GO:0006538)|glutamine biosynthetic process (GO:0006542)|neurotransmitter uptake (GO:0001504)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of insulin secretion (GO:0032024)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein homooligomerization (GO:0051260)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glial cell projection (GO:0097386)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perikaryon (GO:0043204)|protein complex (GO:0043234)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|glutamate-ammonia ligase activity (GO:0004356)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			endometrium(2)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(1)	16					Ceftriaxone(DB01212)|Diazoxide(DB01119)|L-Glutamine(DB00130)|L-Methionine(DB00134)|Pegvisomant(DB00082)	GTACTTGAAAACTTCACATAA	0.493																																					p.V101D		Atlas-SNP	.											.	GLUL	38	.	0			c.T302A						PASS	.						112	101	105					1																	182356292		2203	4300	6503	SO:0001583	missense	2752	exon3			TTGAAAACTTCAC	AL161952	CCDS1344.1	1q31	2010-05-04	2010-05-04		ENSG00000135821	ENSG00000135821	6.3.1.2		4341	protein-coding gene	gene with protein product	"glutamine synthetase"	138290	"glutamate-ammonia ligase (glutamine synthase)"	GLNS		1681907, 2888076	Standard	NM_002065		Approved		uc001gpa.2	P15104	OTTHUMG00000037407	ENST00000331872.6:c.302T>A	chr1.hg19:g.182356292A>T	ENSP00000356537:p.Val101Asp	109.0	0.0	.		106.0	10.0	.	NM_001033056	Q499Y9|Q5T9Z1|Q7Z3W4|Q8IZ17	Missense_Mutation	SNP	ENST00000331872.6	hg19	CCDS1344.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.704904	0.88924	.	.	ENSG00000135821	ENST00000331872;ENST00000311223;ENST00000417584;ENST00000339526;ENST00000435013	T;T;T;T	0.57107	0.42;0.42;0.42;0.42	4.79	4.79	0.61399	Glutamine synthetase, beta-Grasp (3);	0.057690	0.64402	D	0.000002	T	0.78534	0.4298	M	0.93678	3.445	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.84301	0.0505	10	0.72032	D	0.01	-23.933	13.4137	0.60956	1.0:0.0:0.0:0.0	.	101	P15104	GLNA_HUMAN	D	101	ENSP00000356537:V101D;ENSP00000307900:V101D;ENSP00000398320:V101D;ENSP00000344958:V101D	ENSP00000307900:V101D	V	-	2	0	GLUL	180622915	1.000000	0.71417	0.998000	0.56505	0.884000	0.51177	8.881000	0.92415	1.897000	0.54924	0.533000	0.62120	GTT	.	.	.	none		0.493	GLUL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091043.1	NM_002065		T	182356292	A	T	182356292	3	4	156	1	0	0	0	0	1	0	0	0	6485	43	2	5	839	5	GLUL	1	182356292	Missense_Mutation	SNP	A	TCGA-DZ-6131-01A-11D-1961-08	23322842	182356292	66894329	4	9223											
PTGS2	5743	hgsc.bcm.edu	37	chr1	186645691	186645691	+	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	cgcatactctgttgtgttccCgcagccagattgtggcatac	7	12	10	12	2	1	1	0	0	1	1	2	1	2	1	2	1	3	5	2	1	2	5	rs148160346		TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr1:186645691C>A	ENST00000367468.5	-	7	1014	c.878G>T	c.(877-879)cGg>cTg	p.R293L	PTGS2_ENST00000490885.2_5'UTR	NM_000963.2	NP_000954.1	P35354	PGH2_HUMAN	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	293					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)	p.R293L(2)		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)	GTTGTGTTCCCGCAGCCAGAT	0.502																																					p.R293L		Atlas-SNP	.											PTGS2_ENST00000367468,NS,carcinoma,-1,2	PTGS2	144	.	2	Substitution - Missense(2)	lung(2)	c.G878T						PASS	.						144	132	136					1																	186645691		2203	4300	6503	SO:0001583	missense	5743	exon7			TGTTCCCGCAGCC	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.878G>T	chr1.hg19:g.186645691C>A	ENSP00000356438:p.Arg293Leu	114.0	0.0	.		152.0	7.0	.	NM_000963	A8K802|Q16876	Missense_Mutation	SNP	ENST00000367468.5	hg19	CCDS1371.1	.	.	.	.	.	.	.	.	.	.	C	33	5.214936	0.95104	.	.	ENSG00000073756	ENST00000367468	T	0.81163	-1.46	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.93690	0.7984	H	0.96720	3.87	0.80722	D	1	D;D	0.89917	0.996;1.0	D;D	0.97110	0.968;1.0	D	0.95450	0.8533	10	0.87932	D	0	-21.2931	19.4407	0.94820	0.0:1.0:0.0:0.0	.	293;293	Q8IZA9;P35354	.;PGH2_HUMAN	L	293	ENSP00000356438:R293L	ENSP00000356438:R293L	R	-	2	0	PTGS2	184912314	0.997000	0.39634	0.982000	0.44146	0.787000	0.44495	7.627000	0.83176	2.586000	0.87340	0.650000	0.86243	CGG	.	C|1.000;T|0.000	.	alt		0.502	PTGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086157.2	NM_000963		A	186645691	C	A	186645691	3	1	156	1	0	0	0	0	1	0	0	0	12767	652	23	4	952	4	PTGS2	1	186645691	Missense_Mutation	SNP	C	TCGA-DZ-6131-01A-11D-1961-08	4289399	186645691	62604930	5	9224											
APOB	338	hgsc.bcm.edu	37	chr2	21229220	21229220	+	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	caatagttcctgaatattccCgagaaagaaccgaacccttg	14	9	7	11	2	0	3	0	1	0	2	2	5	2	3	4	0	2	1	4	0	7	5	rs201156840		TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr2:21229220C>A	ENST00000233242.1	-	26	10647	c.10520G>T	c.(10519-10521)cGg>cTg	p.R3507L		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3507	Heparin-binding.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.R3507L(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGAATATTCCCGAGAAAGAAC	0.448																																					p.R3507L		Atlas-SNP	.											.	APOB	761	.	1	Substitution - Missense(1)	lung(1)	c.G10520T	GRCh37	CM952192	APOB	M		PASS	.						109	110	110					2																	21229220		2203	4300	6503	SO:0001583	missense	338	exon26			TATTCCCGAGAAA	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.10520G>T	chr2.hg19:g.21229220C>A	ENSP00000233242:p.Arg3507Leu	133.0	0.0	.		169.0	8.0	.	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	C	10.89	1.478915	0.26511	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.79653	-1.29	5.67	-3.39	0.04868	.	0.839091	0.10443	N	0.674080	T	0.72334	0.3447	L	0.57536	1.79	0.19775	N	0.999952	B	0.26744	0.158	B	0.23150	0.044	T	0.60193	-0.7311	10	0.46703	T	0.11	.	8.7607	0.34672	0.1204:0.2037:0.0:0.6758	.	3507	P04114	APOB_HUMAN	L	3507	ENSP00000233242:R3507L	ENSP00000233242:R3507L	R	-	2	0	APOB	21082725	0.000000	0.05858	0.411000	0.26484	0.262000	0.26303	-2.376000	0.01070	-0.552000	0.06167	-0.136000	0.14681	CGG	.	.	.	weak		0.448	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21229220	C	A	21229220	3	1	156	1	0	0	0	0	1	0	0	0	785	652	23	4	3187	4	APOB	2	21229220	Missense_Mutation	SNP	C	TCGA-DZ-6131-01A-11D-1961-08		21229220	221970153	6	9225											
ZDBF2	57683	hgsc.bcm.edu	37	chr2	207171574	207171574	+	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	gatgctgaaggaaaagaacgGcacattgacctggaagatga	16	6	13	6	1	0	5	0	3	0	2	0	8	0	7	1	3	2	2	1	3	5	1			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr2:207171574G>A	ENST00000374423.3	+	5	2708	c.2322G>A	c.(2320-2322)cgG>cgA	p.R774R		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	774							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						GAAAAGAACGGCACATTGACC	0.428																																					p.R774R		Atlas-SNP	.											ZDBF2_ENST00000374423,caecum,carcinoma,0,2	ZDBF2	531	.	0			c.G2322A						PASS	.						174	175	175					2																	207171574		1927	4125	6052	SO:0001819	synonymous_variant	57683	exon5			AGAACGGCACATT	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.2322G>A	chr2.hg19:g.207171574G>A		263.0	0.0	.		340.0	54.0	.	NM_020923	Q6ZNP7|Q6ZSN8	Silent	SNP	ENST00000374423.3	hg19	CCDS46501.1																																																																																			.	.	.	none		0.428	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		A	207171574	G	A	207171574	2	1	156	1	0	0	0	0	0	0	0	1	17611	1190	42	2		2	ZDBF2	2	207171574	Silent	SNP	G	TCGA-DZ-6131-01A-11D-1961-08	185942354	207171574	36027799	7	9226											
ABCA12	26154	hgsc.bcm.edu	37	chr2	215865517	215865517	+	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	agtttgcaattcaatgattgCtctttcaatactatcctgta	11	17	5	8	0	3	1	2	1	1	0	4	1	4	1	1	0	3	4	1	0	6	7			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr2:215865517C>G	ENST00000272895.7	-	22	3310	c.3091G>C	c.(3091-3093)Gca>Cca	p.A1031P	ABCA12_ENST00000389661.4_Missense_Mutation_p.A713P	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1031					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)		TCAATGATTGCTCTTTCAATA	0.428																																					p.A1031P	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											ABCA12,NS,carcinoma,0,1	ABCA12	368	.	0			c.G3091C						PASS	.						125	131	129					2																	215865517		2203	4300	6503	SO:0001583	missense	26154	exon22			TGATTGCTCTTTC	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.3091G>C	chr2.hg19:g.215865517C>G	ENSP00000272895:p.Ala1031Pro	191.0	0.0	.		226.0	78.0	.	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	hg19	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.864070	0.91511	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.88046	-2.33;-2.33	5.73	5.73	0.89815	.	0.000000	0.64402	D	0.000001	D	0.94896	0.8350	M	0.88906	2.99	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95165	0.8285	10	0.87932	D	0	.	19.9082	0.97015	0.0:1.0:0.0:0.0	.	1031;713	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	P	1031;713	ENSP00000272895:A1031P;ENSP00000374312:A713P	ENSP00000272895:A1031P	A	-	1	0	ABCA12	215573762	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	7.594000	0.82698	2.705000	0.92388	0.555000	0.69702	GCA	.	.	.	none		0.428	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		G	215865517	C	G	215865517	3	3	156	1	0	0	0	0	1	0	0	0	30	797	28	4	4824	4	ABCA12	2	215865517	Missense_Mutation	SNP	C	TCGA-DZ-6131-01A-11D-1961-08	8693943	215865517	27333856	8	9227											
DAPP1	27071	hgsc.bcm.edu	37	chr4	100787246	100787246	+	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	caaagaccggagtagaagctGatgagtggatcaagatatta	16	8	12	5	1	1	5	1	2	0	3	1	7	1	7	1	2	1	2	1	2	6	3			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr4:100787246G>C	ENST00000512369.1	+	8	810	c.742G>C	c.(742-744)Gat>Cat	p.D248H	DAPP1_ENST00000296414.7_Missense_Mutation_p.D248H	NM_014395.2	NP_055210.2	Q9UN19	DAPP1_HUMAN	dual adaptor of phosphotyrosine and 3-phosphoinositides	248	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|lung(4)	6				OV - Ovarian serous cystadenocarcinoma(123;7.04e-09)		AGTAGAAGCTGATGAGTGGAT	0.343																																					p.D248H		Atlas-SNP	.											.	DAPP1	47	.	0			c.G742C						PASS	.						91	83	86					4																	100787246		1863	4100	5963	SO:0001583	missense	27071	exon8			GAAGCTGATGAGT	AF186022	CCDS47112.1	4q25-q27	2013-02-14			ENSG00000070190	ENSG00000070190		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	16500	protein-coding gene	gene with protein product		605768				10432293	Standard	NM_014395		Approved	BAM32	uc003hvf.4	Q9UN19	OTTHUMG00000160974	ENST00000512369.1:c.742G>C	chr4.hg19:g.100787246G>C	ENSP00000423602:p.Asp248His	52.0	0.0	.		63.0	13.0	.	NM_014395	Q8TCK5|Q9UHF2	Missense_Mutation	SNP	ENST00000512369.1	hg19	CCDS47112.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.773356	0.90108	.	.	ENSG00000070190	ENST00000296414;ENST00000512369	T;T	0.75589	-0.95;-0.95	6.07	6.07	0.98685	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	D	0.83362	0.5238	L	0.55834	1.745	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.68943	0.956;0.961	T	0.79329	-0.1848	10	0.31617	T	0.26	-8.6315	19.4308	0.94765	0.0:0.0:1.0:0.0	.	248;248	Q9UN19-2;Q9UN19	.;DAPP1_HUMAN	H	248	ENSP00000296414:D248H;ENSP00000423602:D248H	ENSP00000296414:D248H	D	+	1	0	DAPP1	101006269	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.197000	0.89727	2.885000	0.99019	0.655000	0.94253	GAT	.	.	.	none		0.343	DAPP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363215.1			C	100787246	G	C	100787246	3	2	156	1	0	0	0	0	1	0	0	0	4241	1290	45	4	772	4	DAPP1	4	100787246	Missense_Mutation	SNP	G	TCGA-DZ-6131-01A-11D-1961-08		100787246	90367030	9	9228											
GALNT7	51809	hgsc.bcm.edu	37	chr4	174225146	174225146	+	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	caacgtgtttttccttcataGatatggcagtgtggtggcaa	9	14	11	7	1	1	1	1	0	0	1	2	1	2	1	1	3	1	3	1	3	4	5			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr4:174225146G>A	ENST00000265000.4	+	8	1349		c.e8-1			NM_017423.2	NP_059119.2	Q86SF2	GALT7_HUMAN	polypeptide N-acetylgalactosaminyltransferase 7						carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			central_nervous_system(1)|kidney(3)|large_intestine(5)|liver(1)|lung(9)	19		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;1.87e-18)|Epithelial(43;3.44e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-09)|STAD - Stomach adenocarcinoma(60;0.0019)|GBM - Glioblastoma multiforme(59;0.0119)|LUSC - Lung squamous cell carcinoma(193;0.0199)		TTCCTTCATAGATATGGCAGT	0.343																																					.		Atlas-SNP	.											.	GALNT7	61	.	0			c.1267-1G>A						PASS	.						137	126	130					4																	174225146		2203	4300	6503	SO:0001630	splice_region_variant	51809	exon8			TTCATAGATATGG	AJ002744	CCDS3815.1	4q31.1	2014-03-13	2014-03-13		ENSG00000109586	ENSG00000109586		"Glycosyltransferase family 2 domain containing"	4129	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 7"	605005	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7)"			10544240	Standard	NM_017423		Approved	GALNAC-T7	uc003isz.4	Q86SF2	OTTHUMG00000160817	ENST00000265000.4:c.1267-1G>A	chr4.hg19:g.174225146G>A		135.0	0.0	.		178.0	57.0	.	NM_017423	B3KQU3|Q7Z5W7|Q9UJ28	Splice_Site	SNP	ENST00000265000.4	hg19	CCDS3815.1	.	.	.	.	.	.	.	.	.	.	G	17.14	3.313963	0.60414	.	.	ENSG00000109586	ENST00000265000;ENST00000505308;ENST00000458613	.	.	.	5.75	5.75	0.90469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.9439	0.97175	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GALNT7	174461721	1.000000	0.71417	0.997000	0.53966	0.593000	0.36681	9.476000	0.97823	2.706000	0.92434	0.561000	0.74099	.	.	.	.	none		0.343	GALNT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362456.2	NM_017423	Intron	A	174225146	G	A	174225146	5	1	156	1	0	0	0	0	0	0	1	0	6225	956	33	2	1296	2	GALNT7	4	174225146	Splice_Site	SNP	G	TCGA-DZ-6131-01A-11D-1961-08	73437900	174225146	16929130	10	9229											
ARSK	153642	hgsc.bcm.edu	37	chr5	94922371	94922371	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actgcactggaagatttacaAaaaaagaaattaagaatatt	21	10	6	4	0	0	3	0	0	0	3	0	4	0	4	0	1	2	1	0	1	9	5	rs201849642		TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr5:94922371A>G	ENST00000380009.4	+	5	1010	c.805A>G	c.(805-807)Aaa>Gaa	p.K269E		NM_198150.2	NP_937793.1	Q6UWY0	ARSK_HUMAN	arylsulfatase family, member K	269					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)		AAGATTTACAAAAAAAGAAAT	0.338																																					p.K269E		Atlas-SNP	.											.	ARSK	29	.	0			c.A805G						PASS	.						61	65	64					5																	94922371		2201	4297	6498	SO:0001583	missense	153642	exon5			TTTACAAAAAAAG		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.805A>G	chr5.hg19:g.94922371A>G	ENSP00000369346:p.Lys269Glu	53.0	0.0	.		86.0	20.0	.	NM_198150	A2BDE3|B4E1I4|Q3ZCW3|Q8N3Q8	Missense_Mutation	SNP	ENST00000380009.4	hg19	CCDS4073.1	.	.	.	.	.	.	.	.	.	.	A	3.355	-0.131627	0.06753	.	.	ENSG00000164291	ENST00000380009	D	0.99891	-7.56	5.93	-1.94	0.07571	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.568944	0.20517	N	0.090774	D	0.97851	0.9294	N	0.03016	-0.435	0.30818	N	0.738095	B	0.06786	0.001	B	0.06405	0.002	D	0.99988	1.3720	10	0.02654	T	1	-0.6336	8.1825	0.31319	0.5545:0.1084:0.3371:0.0	.	269	Q6UWY0	ARSK_HUMAN	E	269	ENSP00000369346:K269E	ENSP00000369346:K269E	K	+	1	0	ARSK	94948127	0.982000	0.34865	0.741000	0.31004	0.871000	0.50021	0.596000	0.24044	-0.248000	0.09583	-0.132000	0.14878	AAA	.	A|0.999;G|0.001	0.001	weak		0.338	ARSK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241652.2	NM_198150		G	94922371	A	G	94922371	3	3	156	1	0	0	0	0	1	0	0	0	996	15	1	3	823	3	ARSK	5	94922371	Missense_Mutation	SNP	A	TCGA-DZ-6131-01A-11D-1961-08		94922371	85992889	11	9230											
TEX15	56154	hgsc.bcm.edu	37	chr8	30694449	30694449	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttagaagcaggtatttgagaTtgaaaatacccattcactgg	14	12	9	6	0	1	3	1	2	0	2	1	4	1	3	1	2	2	2	1	2	6	6			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr8:30694449T>C	ENST00000256246.2	-	3	8276	c.8202A>G	c.(8200-8202)caA>caG	p.Q2734Q		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	2734					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)		GTATTTGAGATTGAAAATACC	0.408																																					p.Q2734Q		Atlas-SNP	.											.	TEX15	350	.	0			c.A8202G						PASS	.						97	100	99					8																	30694449		2203	4300	6503	SO:0001819	synonymous_variant	56154	exon3			TTGAGATTGAAAA	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.8202A>G	chr8.hg19:g.30694449T>C		67.0	0.0	.		104.0	43.0	.	NM_031271		Silent	SNP	ENST00000256246.2	hg19	CCDS6080.1																																																																																			.	.	.	none		0.408	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			C	30694449	T	C	30694449	2	2	156	1	0	0	0	0	0	0	0	1	15791	1490	52	3		3	TEX15	8	30694449	Silent	SNP	T	TCGA-DZ-6131-01A-11D-1961-08		30694449	115669573	12	9231											
C9orf84	158401	hgsc.bcm.edu	37	chr9	114454268	114454270	+	In_Frame_Del	DEL	CTC	CTC	-																															aaccttttgcttcatgtgttCtccttttctgagaatttata																										TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr9:114454268_114454270delCTC	ENST00000318737.4	-	25	3923_3925	c.3795_3797delGAG	c.(3793-3798)aggaga>aga	p.1265_1266RR>R	C9orf84_ENST00000394777.4_In_Frame_Del_p.1191_1192RR>R|C9orf84_ENST00000374287.3_In_Frame_Del_p.1265_1266RR>R|C9orf84_ENST00000394779.3_In_Frame_Del_p.1226_1227RR>R	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	1265										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						TTCATGTGTTCTCCTTTTCTGAG	0.369																																					p.1266_1266del		Atlas-INDEL	.											.	C9orf84	207	.	0			c.3796_3798del						PASS	.																																			SO:0001651	inframe_deletion	158401	exon25			.	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.3795_3797delGAG	chr9.hg19:g.114454268_114454270delCTC	ENSP00000322108:p.Arg1266del	45.0	0.0	0		56.0	10.0	0.178571	NM_173521	A2A2V3|Q2M1H8|Q96M73	In_Frame_Del	DEL	ENST00000318737.4	hg19	CCDS6781.3																																																																																			.	.	.	none		0.369	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521		-	114454270	CTC	-	114454268	7	5	156	1	0	1	0	1	0	0	0	0	2502	913	32	0	545	0	C9orf84	9	114454268	In_Frame_Del	DEL	CTC	TCGA-DZ-6131-01A-11D-1961-08		114454268	26759163	13	9232											
MUC2	4583	hgsc.bcm.edu	37	chr11	1099777	1099777	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcctaggctgtgtgggaccTgacaatgtgcccagagaggt	8	10	14	9	0	0	2	0	1	0	1	1	4	1	3	3	3	1	1	3	3	2	2			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr11:1099777T>C	ENST00000441003.2	+	40	7401	c.7374T>C	c.(7372-7374)ccT>ccC	p.P2458P		NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4820					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)	GTGTGGGACCTGACAATGTGC	0.572																																					p.P2454P		Atlas-SNP	.											.	MUC2	614	.	0			c.T7362C						PASS	.						140	152	148					11																	1099777		2080	4206	6286	SO:0001819	synonymous_variant	4583	exon41			GGGACCTGACAAT	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.7374T>C	chr11.hg19:g.1099777T>C		174.0	0.0	.		137.0	54.0	.	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	hg19																																																																																				.	.	.	none		0.572	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		C	1099777	T	C	1099777	2	2	156	1	0	0	0	0	0	0	0	1	9982	1567	55	3		3	MUC2	11	1099777	Silent	SNP	T	TCGA-DZ-6131-01A-11D-1961-08		1099777	133906739	14	9233											
FZD4	8322	hgsc.bcm.edu	37	chr11	86663408	86663408	+	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	aatccaaattccttcaggacGggttcacagcgtctcttgac	10	11	8	12	2	3	1	2	1	1	0	6	2	5	2	2	2	1	1	2	2	2	4			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr11:86663408G>T	ENST00000531380.1	-	2	695	c.390C>A	c.(388-390)ccC>ccA	p.P130P	PRSS23_ENST00000533902.2_3'UTR	NM_012193.3	NP_036325.2	Q9ULV1	FZD4_HUMAN	frizzled class receptor 4	130	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|cerebellum vasculature morphogenesis (GO:0061301)|extracellular matrix-cell signaling (GO:0035426)|locomotion involved in locomotory behavior (GO:0031987)|negative regulation of cell-substrate adhesion (GO:0010812)|neuron differentiation (GO:0030182)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal blood vessel morphogenesis (GO:0061304)|sensory perception of sound (GO:0007605)|substrate adhesion-dependent cell spreading (GO:0034446)|vasculogenesis (GO:0001570)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.P130P(1)		breast(1)|kidney(1)|large_intestine(3)|lung(9)|prostate(6)|skin(1)	21		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CCTTCAGGACGGGTTCACAGC	0.517																																					p.P130P		Atlas-SNP	.											FZD4,NS,carcinoma,0,1	FZD4	52	.	1	Substitution - coding silent(1)	lung(1)	c.C390A						PASS	.						99	105	103					11																	86663408		2201	4299	6500	SO:0001819	synonymous_variant	8322	exon2			CAGGACGGGTTCA	AB032417	CCDS8279.1	11q14-q21	2014-01-29	2014-01-29			ENSG00000174804		"GPCR / Class F : Frizzled receptors", "CD molecules"	4042	protein-coding gene	gene with protein product		604579	"frizzled (Drosophila) homolog 4", "exudative vitreoretinopathy 1", "frizzled homolog 4 (Drosophila)", "frizzled 4, seven transmembrane spanning receptor", "frizzled family receptor 4"	EVR1		10544037, 15024691	Standard	NM_012193		Approved	CD344	uc001pce.3	Q9ULV1		ENST00000531380.1:c.390C>A	chr11.hg19:g.86663408G>T		217.0	1.0	.		212.0	12.0	.	NM_012193	A8K9Q3|Q14C97|Q6S9E4	Silent	SNP	ENST00000531380.1	hg19	CCDS8279.1																																																																																			.	.	.	none		0.517	FZD4-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393818.2	NM_012193		T	86663408	G	T	86663408	2	4	156	1	0	0	0	0	0	0	0	1	6139	1103	39	4		4	FZD4	11	86663408	Silent	SNP	G	TCGA-DZ-6131-01A-11D-1961-08	85563631	86663408	48343108	15	9234											
A2ML1	144568	hgsc.bcm.edu	37	chr12	9000291	9000291	+	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	gacagagagctgagcaaccgCtctgtgagtaactgtctgct	10	9	12	10	1	2	3	0	2	2	1	2	5	2	3	1	0	5	5	1	0	2	1			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr12:9000291C>T	ENST00000299698.7	+	15	2010	c.1830C>T	c.(1828-1830)cgC>cgT	p.R610R	A2ML1_ENST00000540049.1_3'UTR|A2ML1_ENST00000539547.1_Silent_p.R119R	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						TGAGCAACCGCTCTGTGAGTA	0.557																																					p.R610R		Atlas-SNP	.											.	A2ML1	199	.	0			c.C1830T						PASS	.						78	77	78					12																	9000291		1955	4145	6100	SO:0001819	synonymous_variant	144568	exon15			CAACCGCTCTGTG	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.1830C>T	chr12.hg19:g.9000291C>T		173.0	0.0	.		199.0	15.0	.	NM_144670		Silent	SNP	ENST00000299698.7	hg19	CCDS8596.2																																																																																			.	.	.	none		0.557	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670		T	9000291	C	T	9000291	2	4	156	1	0	0	0	0	0	0	0	1	5	784	28	2		2	A2ML1	12	9000291	Silent	SNP	C	TCGA-DZ-6131-01A-11D-1961-08		9000291	124851604	16	9235											
TMEM5	10329	hgsc.bcm.edu	37	chr12	64174892	64174892	+	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	taaaactagccttcaaatatTagataaatccacgaaaggaa	20	9	5	7	1	1	1	1	0	0	1	2	3	2	2	2	1	2	0	2	1	10	6			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr12:64174892T>G	ENST00000261234.6	+	2	421	c.263T>G	c.(262-264)tTa>tGa	p.L88*	TMEM5_ENST00000537373.1_5'UTR|TMEM5_ENST00000537982.1_3'UTR|RP11-415I12.3_ENST00000509615.2_RNA	NM_014254.1	NP_055069.1	Q9Y2B1	TMEM5_HUMAN	transmembrane protein 5	88						integral component of plasma membrane (GO:0005887)				breast(1)|large_intestine(3)|liver(2)|lung(7)|prostate(1)|skin(1)	15		Myeloproliferative disorder(1001;0.0255)	BRCA - Breast invasive adenocarcinoma(9;0.0985)	GBM - Glioblastoma multiforme(28;9e-08)|BRCA - Breast invasive adenocarcinoma(357;0.000175)		CTTCAAATATTAGATAAATCC	0.363																																					p.L88X		Atlas-SNP	.											.	TMEM5	35	.	0			c.T263G						PASS	.						82	89	86					12																	64174892		2203	4300	6503	SO:0001587	stop_gained	10329	exon2			AAATATTAGATAA	AB015633	CCDS8966.1, CCDS61179.1	12q14.1	2013-05-07			ENSG00000118600	ENSG00000118600			13530	protein-coding gene	gene with protein product		605862				10072769, 23217329	Standard	NM_014254		Approved	HP10481	uc001srq.2	Q9Y2B1	OTTHUMG00000168730	ENST00000261234.6:c.263T>G	chr12.hg19:g.64174892T>G	ENSP00000261234:p.Leu88*	163.0	0.0	.		247.0	85.0	.	NM_014254	A8K017|Q6PKD6	Nonsense_Mutation	SNP	ENST00000261234.6	hg19	CCDS8966.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.051948	0.75960	.	.	ENSG00000118600	ENST00000261234	.	.	.	4.34	4.34	0.51931	.	0.447903	0.20965	N	0.082490	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.428	10.4561	0.44550	0.0:0.0:0.0:1.0	.	.	.	.	X	88	.	.	L	+	2	0	TMEM5	62461159	0.996000	0.38824	0.945000	0.38365	0.457000	0.32468	4.615000	0.61190	1.897000	0.54924	0.402000	0.26972	TTA	.	.	.	none		0.363	TMEM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400821.1	NM_014254		G	64174892	T	G	64174892	4	3	156	1	0	0	0	0	0	1	0	0	16186	1764	61	5	269	5	TMEM5	12	64174892	Nonsense_Mutation	SNP	T	TCGA-DZ-6131-01A-11D-1961-08	55174601	64174892	69677003	17	9236											
PPP1R12A	4659	hgsc.bcm.edu	37	chr12	80203769	80203769	+	Missense_Mutation	SNP	T	T	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	ctcttcttctttgggagaaaTttttgtagctgtggttggaa	7	18	11	5	0	3	1	0	0	3	1	3	3	3	2	0	3	1	3	0	3	3	7			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr12:80203769T>G	ENST00000450142.2	-	10	1527	c.1261A>C	c.(1261-1263)Att>Ctt	p.I421L	PPP1R12A_ENST00000437004.2_Missense_Mutation_p.I421L|PPP1R12A_ENST00000546369.1_Missense_Mutation_p.I334L|PPP1R12A_ENST00000261207.5_Missense_Mutation_p.I421L|PPP1R12A_ENST00000550107.1_Missense_Mutation_p.I421L	NM_002480.2	NP_002471.1	O14974	MYPT1_HUMAN	protein phosphatase 1, regulatory subunit 12A	421					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						TTGGGAGAAATTTTTGTAGCT	0.363																																					p.I421L		Atlas-SNP	.											.	PPP1R12A	76	.	0			c.A1261C						PASS	.						86	76	79					12																	80203769		1802	4069	5871	SO:0001583	missense	4659	exon10			GAGAAATTTTTGT	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.1261A>C	chr12.hg19:g.80203769T>G	ENSP00000389168:p.Ile421Leu	45.0	0.0	.		70.0	21.0	.	NM_002480	B4DZ09|F8VWB4|Q2NKL4|Q569H0|Q86WU3|Q8NFR6|Q9BYH0	Missense_Mutation	SNP	ENST00000450142.2	hg19	CCDS44947.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	2.128|2.128	-0.399892|-0.399892	0.04865|0.04865	.|.	.|.	ENSG00000058272|ENSG00000058272	ENST00000261207;ENST00000546189;ENST00000360825;ENST00000341878;ENST00000312727;ENST00000450142;ENST00000437004;ENST00000546369;ENST00000550107;ENST00000547330;ENST00000547131|ENST00000553081	T;T;T;T;T;T;T|T	0.39997|0.34667	1.43;1.43;1.45;1.49;1.44;1.44;1.05|1.35	5.86|5.86	0.0418|0.0418	0.14214|0.14214	.|.	0.725412|.	0.14249|.	N|.	0.331574|.	T|T	0.18045|0.18045	0.0433|0.0433	N|N	0.03608|0.03608	-0.345|-0.345	0.26994|0.26994	N|N	0.965072|0.965072	B;B;B;B|.	0.24823|.	0.112;0.002;0.0;0.0|.	B;B;B;B|.	0.20384|.	0.029;0.001;0.0;0.0|.	T|T	0.26224|0.26224	-1.0109|-1.0109	10|7	0.08381|0.54805	T|T	0.77|0.06	.|.	9.6186|9.6186	0.39708|0.39708	0.0:0.558:0.0:0.442|0.0:0.558:0.0:0.442	.|.	421;421;421;421|.	F8W8Q6;O14974-2;O14974-3;O14974|.	.;.;.;MYPT1_HUMAN|.	L|N	421;421;421;421;421;421;421;334;421;421;116|24	ENSP00000261207:I421L;ENSP00000389168:I421L;ENSP00000416769:I421L;ENSP00000449514:I334L;ENSP00000446855:I421L;ENSP00000446816:I421L;ENSP00000450061:I116L|ENSP00000447144:K24N	ENSP00000261207:I421L|ENSP00000447144:K24N	I|K	-|-	1|3	0|2	PPP1R12A|PPP1R12A	78727900|78727900	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.852000|0.852000	0.48524|0.48524	0.848000|0.848000	0.27710|0.27710	0.016000|0.016000	0.14998|0.14998	0.467000|0.467000	0.42956|0.42956	ATT|AAA	.	.	.	none		0.363	PPP1R12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407254.2	NM_002480		G	80203769	T	G	80203769	3	3	156	1	0	0	0	0	1	0	0	0	12364	1493	52	5	1895	5	PPP1R12A	12	80203769	Missense_Mutation	SNP	T	TCGA-DZ-6131-01A-11D-1961-08	16028877	80203769	53648126	18	9237											
P2RX7	5027	hgsc.bcm.edu	37	chr12	121622232	121622232	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgactcctagatccagggAtagccccgtctggtgccagt	7	8	13	13	2	1	1	0	0	1	1	3	3	3	2	5	3	2	0	5	3	2	2			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr12:121622232A>G	ENST00000546057.1	+	13	1558	c.1415A>G	c.(1414-1416)gAt>gGt	p.D472G	P2RX7_ENST00000535250.1_Missense_Mutation_p.D382G|P2RX7_ENST00000328963.5_Missense_Mutation_p.D302G|P2RX7_ENST00000443520.3_3'UTR|P2RX7_ENST00000541446.1_Missense_Mutation_p.D183G	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	472					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)					AGATCCAGGGATAGCCCCGTC	0.617																																					p.D472G		Atlas-SNP	.											.	P2RX7	53	.	0			c.A1415G						PASS	.						67	63	64					12																	121622232		2203	4300	6503	SO:0001583	missense	5027	exon13			CCAGGGATAGCCC	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.1415A>G	chr12.hg19:g.121622232A>G	ENSP00000442349:p.Asp472Gly	77.0	0.0	.		68.0	4.0	.	NM_002562	A8K2Z0|E7EMK6|F5H6P2|F5H7E8|F8W951|O14991|Q4VKH8|Q4VKH9|Q4VKI0|Q4VKI1|Q4VKI2|Q4VKI3|Q4VKI4|Q7Z771|Q96EV7	Missense_Mutation	SNP	ENST00000546057.1	hg19	CCDS9213.1	.	.	.	.	.	.	.	.	.	.	A	15.06	2.721694	0.48728	.	.	ENSG00000089041	ENST00000546057;ENST00000328963;ENST00000535250;ENST00000541446	T;T;T;T	0.05081	4.39;4.01;4.18;3.5	5.21	-0.0551	0.13811	.	1.055260	0.07477	N	0.903142	T	0.06188	0.0160	L	0.44542	1.39	0.09310	N	1	B;B;B;B	0.06786	0.001;0.001;0.001;0.0	B;B;B;B	0.08055	0.003;0.002;0.003;0.002	T	0.41980	-0.9478	10	0.38643	T	0.18	.	5.215	0.15338	0.6048:0.1445:0.2507:0.0	.	302;183;382;472	F8W951;F5H6P2;F5H7E8;Q99572	.;.;.;P2RX7_HUMAN	G	472;302;382;183	ENSP00000442349:D472G;ENSP00000330696:D302G;ENSP00000442572:D382G;ENSP00000437471:D183G	ENSP00000330696:D302G	D	+	2	0	P2RX7	120106615	0.000000	0.05858	0.091000	0.20842	0.830000	0.47004	-0.143000	0.10296	0.321000	0.23259	0.482000	0.46254	GAT	.	.	.	none		0.617	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562		G	121622232	A	G	121622232	3	3	156	1	0	0	0	0	1	0	0	0	11352	333	12	3	1465	3	P2RX7	12	121622232	Missense_Mutation	SNP	A	TCGA-DZ-6131-01A-11D-1961-08	41418463	121622232	12229663	19	9238											
PCDH8	5100	hgsc.bcm.edu	37	chr13	53422307	53422307	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagccgctcgcggtccaggcCggcgtccccgacggtcagct	4	5	14	18	7	1	0	1	0	0	0	4	1	3	0	5	4	2	2	5	4	0	0	rs570624635	byFrequency	TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr13:53422307C>T	ENST00000377942.3	-	1	468	c.265G>A	c.(265-267)Ggc>Agc	p.G89S	PCDH8_ENST00000338862.4_Missense_Mutation_p.G89S	NM_002590.3	NP_002581.2	O95206	PCDH8_HUMAN	protocadherin 8	89	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|morphogenesis of embryonic epithelium (GO:0016331)|somitogenesis (GO:0001756)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(23)|ovary(1)|skin(1)|urinary_tract(1)	36		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.19e-08)		CGGTCCAGGCCGGCGTCCCCG	0.657																																					p.G89S	GBM(36;25 841 9273 49207)	Atlas-SNP	.											PCDH8,NS,carcinoma,0,1	PCDH8	95	.	0			c.G265A						PASS	.						35	38	37					13																	53422307		2201	4296	6497	SO:0001583	missense	5100	exon1			CCAGGCCGGCGTC	AF061573	CCDS9438.1, CCDS9439.1	13q21.1	2010-02-22			ENSG00000136099	ENSG00000136099		"Cadherins / Protocadherins : Non-clustered"	8660	protein-coding gene	gene with protein product		603580				9787079, 9315676	Standard	NM_002590		Approved	PAPC, ARCADLIN	uc001vhi.3	O95206	OTTHUMG00000016979	ENST00000377942.3:c.265G>A	chr13.hg19:g.53422307C>T	ENSP00000367177:p.Gly89Ser	91.0	0.0	.		96.0	35.0	.	NM_032949	B4DMV7|Q5TAN1|Q5TAN2|Q8IYE9|Q96SF1	Missense_Mutation	SNP	ENST00000377942.3	hg19	CCDS9438.1	.	.	.	.	.	.	.	.	.	.	C	18.92	3.724665	0.68959	.	.	ENSG00000136099	ENST00000377942;ENST00000338862;ENST00000418407;ENST00000448969	T;T	0.26373	1.74;1.74	4.99	4.99	0.66335	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.000000	0.41605	D	0.000846	T	0.33702	0.0872	N	0.20530	0.585	0.32118	N	0.588379	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	T	0.28650	-1.0037	10	0.32370	T	0.25	.	13.1397	0.59428	0.0:0.84:0.1599:0.0	.	89;89	O95206-2;O95206	.;PCDH8_HUMAN	S	89	ENSP00000367177:G89S;ENSP00000341350:G89S	ENSP00000341350:G89S	G	-	1	0	PCDH8	52320308	0.981000	0.34729	0.997000	0.53966	0.948000	0.59901	2.542000	0.45744	2.337000	0.79520	0.561000	0.74099	GGC	.	.	.	none		0.657	PCDH8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045108.2	NM_002590		T	53422307	C	T	53422307	3	4	156	1	0	0	0	0	1	0	0	0	11524	652	23	1	2959	1	PCDH8	13	53422307	Missense_Mutation	SNP	C	TCGA-DZ-6131-01A-11D-1961-08		53422307	61747571	20	9239											
MAGEL2	54551	hgsc.bcm.edu	37	chr15	23890238	23890238	+	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	tgcttcttcttccgggtggcCttgccggagcggcgtggcgg	1	11	17	12	5	2	0	0	0	2	0	3	1	3	1	3	6	3	1	3	6	0	4			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr15:23890238C>G	ENST00000532292.1	-	1	937	c.843G>C	c.(841-843)aaG>aaC	p.K281N		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2	164					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)		TCCGGGTGGCCTTGCCGGAGC	0.637																																					p.K884N		Atlas-SNP	.											.	MAGEL2	108	.	0			c.G2652C						PASS	.						42	49	47					15																	23890238		2189	4294	6483	SO:0001583	missense	54551	exon1			GGTGGCCTTGCCG	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.843G>C	chr15.hg19:g.23890238C>G	ENSP00000433433:p.Lys281Asn	107.0	0.0	.		111.0	13.0	.	NM_019066		Missense_Mutation	SNP	ENST00000532292.1	hg19		.	.	.	.	.	.	.	.	.	.	C	15.19	2.758766	0.49468	.	.	ENSG00000254585	ENST00000532292	.	.	.	4.22	0.668	0.17912	.	.	.	.	.	T	0.23688	0.0573	N	0.24115	0.695	0.24891	N	0.99217	.	.	.	.	.	.	T	0.26916	-1.0089	5	.	.	.	.	7.2244	0.26007	0.0:0.461:0.0:0.539	.	.	.	.	T	313	.	.	R	-	2	0	MAGEL2	21441331	0.347000	0.24853	0.771000	0.31576	0.872000	0.50106	-0.733000	0.04898	0.092000	0.17331	-0.302000	0.09304	AGG	.	.	.	none		0.637	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395182.2	NM_019066		G	23890238	C	G	23890238	3	3	156	1	0	0	0	0	1	0	0	0	9196	680	24	4	1101	4	MAGEL2	15	23890238	Missense_Mutation	SNP	C	TCGA-DZ-6131-01A-11D-1961-08		23890238	78641154	21	9240											
MGRN1	23295	hgsc.bcm.edu	37	chr16	4700468	4700468	+	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	catggatctgaacttcctggGcagccgcccggtccaggtgg	6	8	14	13	2	1	1	0	1	1	0	3	2	3	2	4	5	2	1	4	5	1	1			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr16:4700468G>T	ENST00000399577.5	+	2	284	c.191G>T	c.(190-192)gGc>gTc	p.G64V	MGRN1_ENST00000415496.1_Missense_Mutation_p.G64V|MGRN1_ENST00000588994.1_Missense_Mutation_p.G64V|MGRN1_ENST00000262370.7_Missense_Mutation_p.G64V|MGRN1_ENST00000586183.1_Missense_Mutation_p.G64V	NM_001142290.2	NP_001135762.1	O60291	MGRN1_HUMAN	mahogunin ring finger 1, E3 ubiquitin protein ligase	64					endosome to lysosome transport (GO:0008333)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18						AACTTCCTGGGCAGCCGCCCG	0.597																																					p.G64V		Atlas-SNP	.											.	MGRN1	66	.	0			c.G191T						PASS	.						76	81	80					16																	4700468		1892	4125	6017	SO:0001583	missense	23295	exon2			TCCTGGGCAGCCG	AB011116	CCDS42115.1, CCDS45401.1, CCDS45402.1, CCDS45401.2, CCDS59256.1	16p13	2012-02-23	2012-02-23					"RING-type (C3HC4) zinc fingers"	20254	protein-coding gene	gene with protein product		607559	"mahogunin, ring finger 1"			9628581	Standard	NM_015246		Approved	KIAA0544, RNF156	uc002cxa.3	O60291		ENST00000399577.5:c.191G>T	chr16.hg19:g.4700468G>T	ENSP00000382487:p.Gly64Val	182.0	0.0	.		140.0	46.0	.	NM_001142291	A4URL3|A4URL4|Q86W76	Missense_Mutation	SNP	ENST00000399577.5	hg19	CCDS45402.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.518548	0.85495	.	.	ENSG00000102858	ENST00000262370;ENST00000399577;ENST00000415496;ENST00000536343	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	5.4	5.4	0.78164	.	0.099811	0.64402	D	0.000001	T	0.62183	0.2407	M	0.86864	2.845	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;0.998;0.979;0.996;0.991;1.0	T	0.68907	-0.5285	10	0.87932	D	0	-46.144	16.6736	0.85273	0.0:0.0:1.0:0.0	.	64;64;64;64;64;64	O60291-4;O60291-3;B4DR12;E9PB19;O60291-2;O60291	.;.;.;.;.;MGRN1_HUMAN	V	64	ENSP00000262370:G64V;ENSP00000382487:G64V;ENSP00000393311:G64V;ENSP00000443810:G64V	ENSP00000262370:G64V	G	+	2	0	MGRN1	4640469	1.000000	0.71417	1.000000	0.80357	0.765000	0.43378	9.785000	0.99042	2.537000	0.85549	0.561000	0.74099	GGC	.	.	.	none		0.597	MGRN1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000432060.2			T	4700468	G	T	4700468	3	4	156	1	0	0	0	0	1	0	0	0	9566	1203	42	4	197	4	MGRN1	16	4700468	Missense_Mutation	SNP	G	TCGA-DZ-6131-01A-11D-1961-08		4700468	85654285	22	9241											
CMTM1	113540	hgsc.bcm.edu	37	chr16	66612903	66612903	+	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	cgccccgcagaggcccgcctGaagccagcccggcgccctag	6	2	13	20	5	0	2	0	1	0	1	0	2	0	2	7	2	2	1	7	2	2	1			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr16:66612903G>A	ENST00000457188.2	+	4	630	c.509G>A	c.(508-510)tGa>tAa	p.*170*	CMTM1_ENST00000533666.1_3'UTR|CMTM1_ENST00000529506.1_Silent_p.*71*|CMTM1_ENST00000528324.1_3'UTR|CMTM2_ENST00000379486.2_5'Flank|CMTM1_ENST00000332695.7_Silent_p.*123*|CMTM1_ENST00000328020.6_3'UTR|CMTM1_ENST00000531885.1_3'UTR|CMTM1_ENST00000336328.6_Silent_p.*117*|CMTM2_ENST00000268595.2_5'Flank|CMTM1_ENST00000533953.1_Silent_p.*239*|RP11-403P17.2_ENST00000568430.1_RNA|CMTM1_ENST00000379500.2_Silent_p.*287*|CKLF-CMTM1_ENST00000527729.1_Silent_p.*116*	NM_181269.2	NP_851786.1	Q8IZ96	CKLF1_HUMAN	CKLF-like MARVEL transmembrane domain containing 1	0					chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)	7		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0702)|Epithelial(162;0.222)		AGGCCCGCCTGAAGCCAGCCC	0.627																																					p.X287X		Atlas-SNP	.											.	CMTM1	34	.	0			c.G860A						PASS	.						34	41	38					16																	66612903		2201	4299	6500	SO:0001819	synonymous_variant	113540	exon4			CCGCCTGAAGCCA	AF278577	CCDS10810.1, CCDS10811.1, CCDS10812.2, CCDS45503.1, CCDS45504.1, CCDS54019.1, CCDS54020.1, CCDS54021.1	16q22.1	2009-10-06	2005-11-08	2005-11-08	ENSG00000089505	ENSG00000089505			19172	protein-coding gene	gene with protein product		607884	"chemokine-like factor super family 1", "chemokine-like factor superfamily 1"	CKLFSF1		12782130	Standard	NM_181268		Approved	CKLFH1a, CKLFH	uc002epr.4	Q8IZ96	OTTHUMG00000137502	ENST00000457188.2:c.509G>A	chr16.hg19:g.66612903G>A		95.0	0.0	.		101.0	38.0	.	NM_052999	Q2PPY5|Q6PEV5|Q8IU76|Q8IU83|Q8IU86|Q8IU93|Q8IZ87|Q8IZ88|Q8IZ89|Q8IZ90|Q8IZ91|Q8IZ92|Q8IZ93|Q8IZ94|Q8IZ95|Q96JC2|Q96JC3	Silent	SNP	ENST00000457188.2	hg19	CCDS45503.1																																																																																			.	.	.	none		0.627	CMTM1-015	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390261.2	NM_052999		A	66612903	G	A	66612903	2	1	156	1	0	0	0	0	0	0	0	1	3584	1285	45	2		2	CMTM1	16	66612903	Silent	SNP	G	TCGA-DZ-6131-01A-11D-1961-08	61912435	66612903	23741850	23	9242											
TMEM49	81671	hgsc.bcm.edu	37	chr17	57812735	57812735	+	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	tgaaaagaagaggagggagcGggaagaaaggcagaatattg	18	4	17	2	1	0	5	0	1	0	4	0	8	0	8	0	4	1	1	0	4	7	2			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr17:57812735G>T	ENST00000262291.4	+	3	423	c.113G>T	c.(112-114)cGg>cTg	p.R38L	VMP1_ENST00000539763.1_Intron|VMP1_ENST00000536180.1_5'UTR|VMP1_ENST00000537567.1_5'UTR|VMP1_ENST00000545362.1_Missense_Mutation_p.R38L	NM_030938.3	NP_112200.2	Q96GC9	VMP1_HUMAN	vacuole membrane protein 1	38					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						AGGAGGGAGCGGGAAGAAAGG	0.398																																					p.R38L		Atlas-SNP	.											.	VMP1	49	.	0			c.G113T						PASS	.						95	85	89					17																	57812735		2203	4300	6503	SO:0001583	missense	81671	exon3			GGGAGCGGGAAGA		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.113G>T	chr17.hg19:g.57812735G>T	ENSP00000262291:p.Arg38Leu	49.0	0.0	.		74.0	7.0	.	NM_030938	B4DVV9|Q9H0P4|Q9P089	Missense_Mutation	SNP	ENST00000262291.4	hg19	CCDS11619.1	.	.	.	.	.	.	.	.	.	.	G	17.55	3.418001	0.62622	.	.	ENSG00000062716	ENST00000262291;ENST00000545362	.	.	.	5.46	5.46	0.80206	.	0.056181	0.64402	D	0.000001	T	0.70430	0.3223	M	0.71581	2.175	0.80722	D	1	P;P	0.47191	0.891;0.785	P;B	0.47044	0.535;0.43	T	0.74390	-0.3681	9	0.62326	D	0.03	-13.682	19.321	0.94240	0.0:0.0:1.0:0.0	.	38;38	F5H2J3;Q96GC9	.;VMP1_HUMAN	L	38	.	ENSP00000262291:R38L	R	+	2	0	VMP1	55167517	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.973000	0.49264	2.548000	0.85928	0.591000	0.81541	CGG	.	.	.	none		0.398	VMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448793.1	NM_030938		T	57812735	G	T	57812735	3	4	156	1	0	0	0	0	1	0	0	0	16185	1116	39	4	119	4	TMEM49	17	57812735	Missense_Mutation	SNP	G	TCGA-DZ-6131-01A-11D-1961-08		57812735	23382475	24	9243											
ZNF337	26152	hgsc.bcm.edu	37	chr20	25656223	25656223	+	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	caattaaatggcctttccccCgagtgtgtccactgatgtct	8	13	8	12	1	1	1	0	1	1	0	3	2	3	1	4	1	0	0	4	1	3	2	rs370580651		TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr20:25656223C>A	ENST00000376436.1	-	4	2240	c.1701G>T	c.(1699-1701)tcG>tcT	p.S567S	RP4-694B14.5_ENST00000428254.1_RNA|RP4-694B14.5_ENST00000421829.1_RNA|ZNF337_ENST00000481610.1_5'Flank|ZNF337_ENST00000538750.1_Silent_p.S535S|RP4-694B14.5_ENST00000439498.1_RNA|RP4-694B14.5_ENST00000414393.1_RNA|ZNF337_ENST00000252979.5_Silent_p.S567S|RP4-694B14.5_ENST00000455791.1_RNA			Q9Y3M9	ZN337_HUMAN	zinc finger protein 337	567					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.S567S(1)		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						GCCTTTCCCCCGAGTGTGTCC	0.473																																					p.S567S		Atlas-SNP	.											.	ZNF337	65	.	1	Substitution - coding silent(1)	lung(1)	c.G1701T						PASS	.						89	82	84					20																	25656223		2203	4300	6503	SO:0001819	synonymous_variant	26152	exon5			TTCCCCCGAGTGT		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.1701G>T	chr20.hg19:g.25656223C>A		143.0	0.0	.		156.0	7.0	.	NM_015655	B4DSM2|Q9Y3Y5	Silent	SNP	ENST00000376436.1	hg19	CCDS13174.1																																																																																			.	.	.	alt		0.473	ZNF337-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078454.1			A	25656223	C	A	25656223	2	1	156	1	0	0	0	0	0	0	0	1	17865	639	23	4		4	ZNF337	20	25656223	Silent	SNP	C	TCGA-DZ-6131-01A-11D-1961-08		25656223	37369297	25	9244											
ZNF295	49854	hgsc.bcm.edu	37	chr21	43413770	43413770	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caaacaatgacacttctcttTtgagaactgttttcatcatc	12	15	4	10	0	3	2	2	2	1	1	5	3	3	2	0	0	2	1	0	0	3	5			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr21:43413770T>C	ENST00000310826.5	-	3	618	c.435A>G	c.(433-435)caA>caG	p.Q145Q	ZBTB21_ENST00000398505.3_Silent_p.Q145Q|ZBTB21_ENST00000465968.1_Intron|ZBTB21_ENST00000398499.1_Silent_p.Q145Q|ZBTB21_ENST00000398511.3_Silent_p.Q145Q	NM_001098402.1	NP_001091872.1	Q9ULJ3	ZBT21_HUMAN	zinc finger and BTB domain containing 21	145					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)										CACTTCTCTTTTGAGAACTGT	0.403																																					p.Q145Q		Atlas-SNP	.											.	.	.	.	0			c.A435G						PASS	.						98	88	91					21																	43413770		2203	4300	6503	SO:0001819	synonymous_variant	49854	exon3			TCTCTTTTGAGAA	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.435A>G	chr21.hg19:g.43413770T>C		112.0	0.0	.		130.0	56.0	.	NM_001098402	Q5R2W1|Q5R2W2|Q6P4R0	Silent	SNP	ENST00000310826.5	hg19	CCDS13678.1																																																																																			.	.	.	none		0.403	ZBTB21-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195308.1	NM_020727		C	43413770	T	C	43413770	2	2	156	1	0	0	0	0	0	0	0	1	17839	1838	64	3		3	ZNF295	21	43413770	Silent	SNP	T	TCGA-DZ-6131-01A-11D-1961-08		43413770	4716125	26	9245											
KRTAP10-10	353333	hgsc.bcm.edu	37	chr21	46057373	46057373	+	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	tccatctgctccagcgcctgCactgactcttggcgggtagt	5	11	11	14	2	2	1	0	1	2	0	4	1	4	1	3	2	3	3	3	2	1	2			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chr21:46057373C>T	ENST00000380095.1	+	1	101	c.39C>T	c.(37-39)tgC>tgT	p.C13C	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	13						keratin filament (GO:0045095)		p.C13C(1)		NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						CCAGCGCCTGCACTGACTCTT	0.652																																					p.C13C		Atlas-SNP	.											KRTAP10-10,NS,carcinoma,0,1	KRTAP10-10	37	.	1	Substitution - coding silent(1)	endometrium(1)	c.C39T						PASS	.						104	109	108					21																	46057373		2203	4300	6503	SO:0001819	synonymous_variant	353333	exon1			CGCCTGCACTGAC	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.39C>T	chr21.hg19:g.46057373C>T		219.0	0.0	.		201.0	37.0	.	NM_181688		Silent	SNP	ENST00000380095.1	hg19	CCDS33585.1																																																																																			.	.	.	none		0.652	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688		T	46057373	C	T	46057373	2	4	156	1	0	0	0	0	0	0	0	1	8513	718	25	2		2	KRTAP10-10	21	46057373	Silent	SNP	C	TCGA-DZ-6131-01A-11D-1961-08	2643603	46057373	2072522	27	9246											
FAM47B	170062	hgsc.bcm.edu	37	chrX	34961454	34961454	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttgggctcgttgtgaggcccGggagaagacaaccgaggtac	9	7	16	9	3	0	3	0	1	0	2	1	5	0	3	2	4	2	3	2	4	3	3			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chrX:34961454G>A	ENST00000329357.5	+	1	542	c.506G>A	c.(505-507)cGg>cAg	p.R169Q		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	169										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						TGTGAGGCCCGGGAGAAGACA	0.592																																					p.R169Q		Atlas-SNP	.											.	FAM47B	209	.	0			c.G506A						PASS	.						36	35	35					X																	34961454		2202	4300	6502	SO:0001583	missense	170062	exon1			AGGCCCGGGAGAA	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.506G>A	chrX.hg19:g.34961454G>A	ENSP00000328307:p.Arg169Gln	34.0	0.0	.		36.0	30.0	.	NM_152631	Q5JQN5|Q6PIG3	Missense_Mutation	SNP	ENST00000329357.5	hg19	CCDS14236.1	.	.	.	.	.	.	.	.	.	.	G	1.355	-0.590410	0.03799	.	.	ENSG00000189132	ENST00000329357	T	0.14266	2.52	0.843	-0.104	0.13605	.	.	.	.	.	T	0.04952	0.0133	N	0.05259	-0.085	0.09310	N	1	B	0.19073	0.033	B	0.08055	0.003	T	0.45175	-0.9279	8	0.13108	T	0.6	.	.	.	.	.	169	Q8NA70	FA47B_HUMAN	Q	169	ENSP00000328307:R169Q	ENSP00000328307:R169Q	R	+	2	0	FAM47B	34871375	0.070000	0.21116	0.001000	0.08648	0.009000	0.06853	-2.406000	0.01044	-0.099000	0.12263	-0.780000	0.03373	CGG	.	.	.	none		0.592	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631		A	34961454	G	A	34961454	3	1	156	1	0	0	0	0	1	0	0	0	5577	1116	39	1	508	1	FAM47B	23	34961454	Missense_Mutation	SNP	G	TCGA-DZ-6131-01A-11D-1961-08		34961454	120309106	28	9247											
IQSEC2	23096	hgsc.bcm.edu	37	chrX	53268433	53268433	+	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	gggggaaagactgacggaaaCtgtacgtcaccaagatcttc	13	7	12	9	2	2	3	1	1	1	2	3	5	2	5	1	3	2	1	1	3	4	2			TCGA-DZ-6131-01A-11D-1961-08	TCGA-DZ-6131-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	29368ff9-9921-468b-89e7-f004ec2ddb39	3e6c0c90-5ee6-4ec6-ba68-59aae72c362c	g.chrX:53268433C>G	ENST00000375368.5	-	10	3229	c.3029G>C	c.(3028-3030)aGt>aCt	p.S1010T	IQSEC2_ENST00000396435.3_Missense_Mutation_p.S1020T|IQSEC2_ENST00000375365.2_Missense_Mutation_p.S815T			Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2	1010	PH.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|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						CTGACGGAAACTGTACGTCAC	0.502											OREG0019800	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S1020T		Atlas-SNP	.											.	IQSEC2	195	.	0			c.G3059C						PASS	.						114	103	107					X																	53268433		2203	4300	6503	SO:0001583	missense	23096	exon11			CGGAAACTGTACG	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.3029G>C	chrX.hg19:g.53268433C>G	ENSP00000364517:p.Ser1010Thr	58.0	0.0	.	991	42.0	33.0	.	NM_001111125	B3KT97|C7SDG1|O60275|Q5JUX1	Missense_Mutation	SNP	ENST00000375368.5	hg19		.	.	.	.	.	.	.	.	.	.	C	14.06	2.422471	0.43020	.	.	ENSG00000124313	ENST00000396435;ENST00000375368;ENST00000375365	T;T;T	0.54071	0.59;0.59;0.59	5.61	5.61	0.85477	.	.	.	.	.	T	0.52240	0.1722	N	0.19112	0.55	0.80722	D	1	B;P	0.39903	0.039;0.694	B;P	0.56434	0.105;0.798	T	0.40001	-0.9586	9	0.02654	T	1	.	17.3443	0.87306	0.0:1.0:0.0:0.0	.	1020;815	Q5JU85-2;Q5JU85-3	.;.	T	1020;1010;815	ENSP00000379712:S1020T;ENSP00000364517:S1010T;ENSP00000364514:S815T	ENSP00000364514:S815T	S	-	2	0	IQSEC2	53285158	0.998000	0.40836	1.000000	0.80357	0.962000	0.63368	2.668000	0.46816	2.363000	0.80096	0.511000	0.50034	AGT	.	.	.	none		0.502	IQSEC2-201	KNOWN	basic	protein_coding	protein_coding		XM_291345		G	53268433	C	G	53268433	3	3	156	1	0	0	0	0	1	0	0	0	7825	565	20	4	1427	4	IQSEC2	23	53268433	Missense_Mutation	SNP	C	TCGA-DZ-6131-01A-11D-1961-08	18306979	53268433	102002127	29	9248											
SLC2A5	6518	hgsc.bcm.edu	37	chr1	9097752	9097752	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggttgatctctatgaacgTcttggccttggtctccggga	5	14	12	10	2	3	2	0	2	3	0	5	3	3	3	2	4	1	1	2	4	2	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:9097752T>C	ENST00000377424.4	-	12	1578	c.1399A>G	c.(1399-1401)Acg>Gcg	p.T467A	SLC2A5_ENST00000536305.1_Missense_Mutation_p.T408A|SLC2A5_ENST00000535586.1_Missense_Mutation_p.T352A	NM_003039.2	NP_003030.1	P22732	GTR5_HUMAN	solute carrier family 2 (facilitated glucose/fructose transporter), member 5	467					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)		TCTATGAACGTCTTGGCCTTG	0.512																																					p.T467A		Atlas-SNP	.											.	SLC2A5	77	.	0			c.A1399G						PASS	.						127	131	130					1																	9097752		2203	4300	6503	SO:0001583	missense	6518	exon12			TGAACGTCTTGGC	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.1399A>G	chr1.hg19:g.9097752T>C	ENSP00000366641:p.Thr467Ala	209.0	0.0	.		181.0	30.0	.	NM_003039	Q14770|Q5T977|Q8IVB3	Missense_Mutation	SNP	ENST00000377424.4	hg19	CCDS99.1	.	.	.	.	.	.	.	.	.	.	T	18.61	3.661340	0.67700	.	.	ENSG00000142583	ENST00000377424;ENST00000456780;ENST00000536305;ENST00000535586	T;T;T	0.76448	-1.02;-1.02;-1.02	5.53	5.53	0.82687	Major facilitator superfamily domain, general substrate transporter (1);	0.047424	0.85682	D	0.000000	D	0.89842	0.6832	M	0.93197	3.39	0.53005	D	0.999969	D;D;D	0.61080	0.971;0.971;0.989	P;P;D	0.64042	0.872;0.872;0.921	D	0.92195	0.5763	10	0.87932	D	0	.	13.3288	0.60475	0.0:0.0:0.0:1.0	.	423;408;467	B4DG19;B4DU31;P22732	.;.;GTR5_HUMAN	A	467;450;408;352	ENSP00000366641:T467A;ENSP00000440688:T408A;ENSP00000442744:T352A	ENSP00000366641:T467A	T	-	1	0	SLC2A5	9020339	1.000000	0.71417	0.853000	0.33588	0.611000	0.37282	3.992000	0.56980	2.220000	0.72140	0.533000	0.62120	ACG	.	.	.	none		0.512	SLC2A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004932.1	NM_003039		C	9097752	T	C	9097752	3	2	157	1	0	0	0	0	1	0	0	0	14561	1667	58	3	110	3	SLC2A5	1	9097752	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08		9097752	240152869	1	9249											
ALPL	249	hgsc.bcm.edu	37	chr1	21902288	21902288	+	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	aggccctgcatgaggcggtgGagatggaccgggccatcggg	7	5	19	10	3	0	2	0	1	0	1	1	4	0	3	3	7	1	1	3	7	0	0			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:21902288G>A	ENST00000374840.3	+	10	1310	c.1060G>A	c.(1060-1062)Gag>Aag	p.E354K	ALPL_ENST00000374832.1_Missense_Mutation_p.E354K|ALPL_ENST00000539907.1_Missense_Mutation_p.E277K|ALPL_ENST00000374829.1_5'UTR|ALPL_ENST00000425315.2_Missense_Mutation_p.E354K|ALPL_ENST00000540617.1_Missense_Mutation_p.E299K|ALPL_ENST00000374830.1_5'UTR	NM_000478.4	NP_000469.3	P05186	PPBT_HUMAN	alkaline phosphatase, liver/bone/kidney	354			E -> D (in HOPS).		cellular response to organic cyclic compound (GO:0071407)|cementum mineralization (GO:0071529)|developmental process involved in reproduction (GO:0003006)|endochondral ossification (GO:0001958)|osteoblast differentiation (GO:0001649)|response to antibiotic (GO:0046677)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to vitamin D (GO:0033280)|skeletal system development (GO:0001501)	anchored component of membrane (GO:0031225)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	26		all_lung(284;2.19e-05)|Lung NSC(340;2.22e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;8.7e-28)|COAD - Colon adenocarcinoma(152;1.57e-05)|GBM - Glioblastoma multiforme(114;2.66e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000177)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00856)|READ - Rectum adenocarcinoma(331;0.0623)|Lung(427;0.146)	Amifostine(DB01143)|Fospropofol(DB06716)	TGAGGCGGTGGAGATGGACCG	0.612																																					p.E354K		Atlas-SNP	.											.	ALPL	50	.	0			c.G1060A						PASS	.						142	136	138					1																	21902288		2203	4300	6503	SO:0001583	missense	249	exon10			GCGGTGGAGATGG	BC021289	CCDS217.1, CCDS53274.1, CCDS53275.1	1p36.12	2008-02-05			ENSG00000162551	ENSG00000162551	3.1.3.1		438	protein-coding gene	gene with protein product		171760		HOPS		3532105, 3446011	Standard	NM_001127501		Approved	TNSALP	uc001bet.3	P05186	OTTHUMG00000002949	ENST00000374840.3:c.1060G>A	chr1.hg19:g.21902288G>A	ENSP00000363973:p.Glu354Lys	278.0	0.0	.		186.0	25.0	.	NM_000478	A1A4E7|B2RMP8|B7Z387|B7Z4Y6|O75090|Q2TAI7|Q59EJ7|Q5BKZ5|Q5VTG5|Q6NZI8|Q8WU32|Q9UBK0	Missense_Mutation	SNP	ENST00000374840.3	hg19	CCDS217.1	.	.	.	.	.	.	.	.	.	.	G	13.89	2.371272	0.42003	.	.	ENSG00000162551	ENST00000539907;ENST00000540617;ENST00000374840;ENST00000374832;ENST00000425315	D;D;D;D;D	0.96716	-4.1;-4.1;-4.1;-4.1;-4.1	4.91	3.99	0.46301	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.056236	0.64402	D	0.000001	D	0.96796	0.8954	M	0.83852	2.665	0.51233	D	0.999917	B;P	0.52692	0.407;0.955	P;P	0.54544	0.507;0.755	D	0.95649	0.8705	10	0.52906	T	0.07	-8.6255	7.1413	0.25558	0.0934:0.1721:0.7345:0.0	.	277;354	B7Z387;P05186	.;PPBT_HUMAN	K	277;299;354;354;354	ENSP00000437674:E277K;ENSP00000442672:E299K;ENSP00000363973:E354K;ENSP00000363965:E354K;ENSP00000394765:E354K	ENSP00000363965:E354K	E	+	1	0	ALPL	21774875	1.000000	0.71417	0.892000	0.35008	0.007000	0.05969	5.646000	0.67916	1.071000	0.40834	-0.291000	0.09656	GAG	.	.	.	none		0.612	ALPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000008202.1	NM_000478		A	21902288	G	A	21902288	3	1	157	1	0	0	0	0	1	0	0	0	547	1175	41	2	1094	2	ALPL	1	21902288	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	12804536	21902288	227348333	2	9250											
WASF2	10163	hgsc.bcm.edu	37	chr1	27739179	27739179	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgcatccacgttttcaacAcagccaatgctgccattctg	9	12	6	14	1	2	0	1	0	1	0	3	0	3	0	3	0	5	3	3	0	2	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:27739179A>G	ENST00000430629.2	-	7	926	c.711T>C	c.(709-711)tgT>tgC	p.C237C	WASF2_ENST00000536657.1_Silent_p.C237C	NM_001201404.1|NM_006990.3	NP_001188333.1|NP_008921.1	Q9Y6W5	WASF2_HUMAN	WAS protein family, member 2	237					actin cytoskeleton organization (GO:0030036)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of lamellipodium assembly (GO:0010592)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|SCAR complex (GO:0031209)	actin binding (GO:0003779)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	18		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0446)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.7e-08)|COAD - Colon adenocarcinoma(152;2e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00139)|KIRC - Kidney renal clear cell carcinoma(1967;0.00204)|STAD - Stomach adenocarcinoma(196;0.00325)|READ - Rectum adenocarcinoma(331;0.0481)		CGTTTTCAACACAGCCAATGC	0.488																																					p.C237C		Atlas-SNP	.											.	WASF2	41	.	0			c.T711C						PASS	.						153	137	142					1																	27739179		2203	4300	6503	SO:0001819	synonymous_variant	10163	exon7			TTCAACACAGCCA	AB026542	CCDS304.1, CCDS55582.1	1p36.11	2011-05-10			ENSG00000158195	ENSG00000158195			12733	protein-coding gene	gene with protein product		605875				10381382	Standard	NM_006990		Approved	WAVE2, SCAR2	uc001bof.2	Q9Y6W5	OTTHUMG00000003393	ENST00000430629.2:c.711T>C	chr1.hg19:g.27739179A>G		147.0	0.0	.		128.0	22.0	.	NM_006990	B4DZN0|O60794|Q9UDY7	Silent	SNP	ENST00000430629.2	hg19	CCDS304.1																																																																																			.	.	.	none		0.488	WASF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009516.1	NM_006990		G	27739179	A	G	27739179	2	3	157	1	0	0	0	0	0	0	0	1	17265	157	6	3		3	WASF2	1	27739179	Silent	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	5836891	27739179	221511442	3	9251											
TESK2	10420	hgsc.bcm.edu	37	chr1	45813333	45813333	+	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	caggtgccatccagaatgggGaacccaccacggccagcttc	10	5	11	15	1	0	1	0	0	0	1	2	2	1	2	5	4	3	1	5	4	2	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:45813333G>A	ENST00000372086.3	-	7	1056	c.656C>T	c.(655-657)tCc>tTc	p.S219F	TESK2_ENST00000486676.1_5'UTR|TESK2_ENST00000372084.1_Missense_Mutation_p.S219F|TESK2_ENST00000538496.1_Missense_Mutation_p.S136F|TESK2_ENST00000341771.6_Missense_Mutation_p.S219F	NM_007170.2	NP_009101.2	Q96S53	TESK2_HUMAN	testis-specific kinase 2	219	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|focal adhesion assembly (GO:0048041)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	32	Acute lymphoblastic leukemia(166;0.155)					CCAGAATGGGGAACCCACCAC	0.473																																					p.S219F		Atlas-SNP	.											.	TESK2	60	.	0			c.C656T						PASS	.						112	113	113					1																	45813333		1904	4153	6057	SO:0001583	missense	10420	exon7			AATGGGGAACCCA	AJ132545	CCDS41323.1	1p32	2010-04-27			ENSG00000070759	ENSG00000070759	2.7.12.1		11732	protein-coding gene	gene with protein product		604746				10512679	Standard	NM_007170		Approved		uc001cns.1	Q96S53	OTTHUMG00000007680	ENST00000372086.3:c.656C>T	chr1.hg19:g.45813333G>A	ENSP00000361158:p.Ser219Phe	217.0	0.0	.		175.0	38.0	.	NM_007170	Q5T422|Q5T423|Q8N520|Q9Y3Q6	Missense_Mutation	SNP	ENST00000372086.3	hg19	CCDS41323.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.874832	0.91664	.	.	ENSG00000070759	ENST00000372084;ENST00000372086;ENST00000372083;ENST00000341771;ENST00000538496	T;T;T;T	0.69926	-0.44;-0.12;-0.44;-0.12	5.98	5.98	0.97165	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.104533	0.43110	N	0.000604	D	0.84933	0.5582	M	0.87900	2.915	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.86499	0.1802	10	0.87932	D	0	-17.2903	18.6171	0.91306	0.0:0.0:1.0:0.0	.	219;219	Q96S53-3;Q96S53	.;TESK2_HUMAN	F	219;219;203;219;136	ENSP00000361156:S219F;ENSP00000361158:S219F;ENSP00000343940:S219F;ENSP00000441746:S136F	ENSP00000343940:S219F	S	-	2	0	TESK2	45585920	1.000000	0.71417	1.000000	0.80357	0.718000	0.41266	7.907000	0.87430	2.843000	0.97960	0.585000	0.79938	TCC	.	.	.	none		0.473	TESK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020523.1	NM_007170		A	45813333	G	A	45813333	3	1	157	1	0	0	0	0	1	0	0	0	15780	1174	41	2	1079	2	TESK2	1	45813333	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	18074154	45813333	203437288	4	9252											
TMEM69	51249	hgsc.bcm.edu	37	chr1	46159260	46159260	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctatctttcttgggtgggAtcagatggggttttgctcta	5	17	12	7	0	4	1	1	0	3	1	5	2	5	2	1	4	1	2	1	4	2	6			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:46159260A>G	ENST00000372025.4	+	3	1584	c.427A>G	c.(427-429)Atc>Gtc	p.I143V	RP11-767N6.7_ENST00000430643.1_RNA|TMEM69_ENST00000496366.1_3'UTR	NM_016486.3	NP_057570.2	Q5SWH9	TMM69_HUMAN	transmembrane protein 69	143						integral component of membrane (GO:0016021)				kidney(3)|lung(4)|ovary(1)	8	Acute lymphoblastic leukemia(166;0.155)					CTTGGGTGGGATCAGATGGGG	0.438																																					p.I143V		Atlas-SNP	.											.	TMEM69	20	.	0			c.A427G						PASS	.						89	87	88					1																	46159260		1859	4090	5949	SO:0001583	missense	51249	exon3			GGTGGGATCAGAT	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.427A>G	chr1.hg19:g.46159260A>G	ENSP00000361095:p.Ile143Val	196.0	0.0	.		176.0	31.0	.	NM_016486	Q3SWW5|Q7Z2G0|Q9P0P9	Missense_Mutation	SNP	ENST00000372025.4	hg19	CCDS41325.1	.	.	.	.	.	.	.	.	.	.	A	4.400	0.073919	0.08485	.	.	ENSG00000159596	ENST00000372025	.	.	.	5.83	-1.16	0.09678	.	0.588234	0.19061	N	0.123779	T	0.23330	0.0564	N	0.20357	0.565	0.19575	N	0.999966	B	0.10296	0.003	B	0.10450	0.005	T	0.25745	-1.0123	9	0.11794	T	0.64	-0.7606	12.6228	0.56614	0.7619:0.0:0.2381:0.0	.	143	Q5SWH9	TMM69_HUMAN	V	143	.	ENSP00000361095:I143V	I	+	1	0	TMEM69	45931847	0.218000	0.23608	0.138000	0.22173	0.907000	0.53573	0.632000	0.24583	-0.248000	0.09583	-0.415000	0.06103	ATC	.	.	.	none		0.438	TMEM69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098390.1	NM_016486		G	46159260	A	G	46159260	3	3	157	1	0	0	0	0	1	0	0	0	16210	333	12	3	433	3	TMEM69	1	46159260	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	345927	46159260	203091361	5	9253											
ZFYVE9	9372	hgsc.bcm.edu	37	chr1	52704507	52704507	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agacacaccagcagcaaattAtctatctaatggttgtgatt	14	12	7	8	0	2	2	0	1	2	1	2	2	2	2	1	1	2	3	1	1	4	5			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:52704507A>G	ENST00000371591.1	+	3	1549	c.1418A>G	c.(1417-1419)tAt>tGt	p.Y473C	ZFYVE9_ENST00000357206.2_Missense_Mutation_p.Y473C|ZFYVE9_ENST00000287727.3_Missense_Mutation_p.Y473C	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	473					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						GCAGCAAATTATCTATCTAAT	0.378																																					p.Y473C		Atlas-SNP	.											.	ZFYVE9	131	.	0			c.A1418G						PASS	.						95	101	99					1																	52704507		2203	4299	6502	SO:0001583	missense	9372	exon4			CAAATTATCTATC	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.1418A>G	chr1.hg19:g.52704507A>G	ENSP00000360647:p.Tyr473Cys	173.0	0.0	.		176.0	32.0	.	NM_007323	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Missense_Mutation	SNP	ENST00000371591.1	hg19	CCDS563.1	.	.	.	.	.	.	.	.	.	.	A	7.890	0.732073	0.15507	.	.	ENSG00000157077	ENST00000357206;ENST00000361625;ENST00000287727;ENST00000371591	T;T;T;T	0.51574	1.19;0.7;1.19;1.19	5.69	4.78	0.61160	.	0.445610	0.20824	N	0.085019	T	0.25005	0.0607	N	0.08118	0	0.20764	N	0.99985	B;B;B	0.33512	0.415;0.01;0.0	B;B;B	0.33392	0.163;0.002;0.0	T	0.09662	-1.0664	10	0.38643	T	0.18	.	6.1713	0.20418	0.1413:0.6538:0.1348:0.0701	.	473;473;473	O95405-2;O95405;O95405-3	.;ZFYV9_HUMAN;.	C	473	ENSP00000349737:Y473C;ENSP00000355358:Y473C;ENSP00000287727:Y473C;ENSP00000360647:Y473C	ENSP00000287727:Y473C	Y	+	2	0	ZFYVE9	52477095	1.000000	0.71417	0.843000	0.33291	0.920000	0.55202	1.818000	0.39012	1.420000	0.47138	-0.132000	0.14878	TAT	.	.	.	none		0.378	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324		G	52704507	A	G	52704507	3	3	157	1	0	0	0	0	1	0	0	0	17683	449	16	3	1424	3	ZFYVE9	1	52704507	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	6545247	52704507	196546114	6	9254											
ZYG11B	79699	hgsc.bcm.edu	37	chr1	53262039	53262039	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgcaaaggatggcagttgcTatcatttctatcctggctgc	9	13	10	9	0	2	0	1	0	1	0	3	1	3	1	1	3	3	5	1	3	3	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:53262039T>C	ENST00000294353.6	+	7	1555	c.1410T>C	c.(1408-1410)gcT>gcC	p.A470A	ZYG11B_ENST00000443756.2_Silent_p.A470A|ZYG11B_ENST00000545132.1_Silent_p.A470A	NM_024646.2	NP_078922.1	Q9C0D3	ZY11B_HUMAN	zyg-11 family member B, cell cycle regulator	470										breast(1)|endometrium(1)|kidney(6)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	30						TGGCAGTTGCTATCATTTCTA	0.433																																					p.A470A		Atlas-SNP	.											.	ZYG11B	61	.	0			c.T1410C						PASS	.						82	76	78					1																	53262039		2203	4300	6503	SO:0001819	synonymous_variant	79699	exon7			AGTTGCTATCATT	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.1410T>C	chr1.hg19:g.53262039T>C		69.0	0.0	.		71.0	10.0	.	NM_024646	Q8N2X3|Q9H8L8	Silent	SNP	ENST00000294353.6	hg19	CCDS30717.1																																																																																			.	.	.	none		0.433	ZYG11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024749.1	NM_024646		C	53262039	T	C	53262039	2	2	157	1	0	0	0	0	0	0	0	1	18265	1509	53	3		3	ZYG11B	1	53262039	Silent	SNP	T	TCGA-DZ-6132-01A-11D-1961-08	557532	53262039	195988582	7	9255											
ODF2L	57489	hgsc.bcm.edu	37	chr1	86851227	86851227	+	Missense_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	taccaactccgcttccttaaGtgttgcttccaattcagtct	8	15	5	13	1	2	0	1	0	1	0	5	0	5	0	4	0	3	3	4	0	4	6			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:86851227G>A	ENST00000359242.3	-	3	441	c.160C>T	c.(160-162)Ctt>Ttt	p.L54F	ODF2L_ENST00000370566.3_Missense_Mutation_p.L54F|ODF2L_ENST00000317336.7_Missense_Mutation_p.L54F|ODF2L_ENST00000394731.1_Intron|ODF2L_ENST00000294678.2_Missense_Mutation_p.L54F|ODF2L_ENST00000370567.1_Missense_Mutation_p.L54F	NM_001007022.2	NP_001007023.2	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like	54						centrosome (GO:0005813)				endometrium(2)|kidney(2)|large_intestine(10)|lung(6)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	24				all cancers(265;0.0313)|Epithelial(280;0.0611)		GCTTCCTTAAGTGTTGCTTCC	0.323																																					p.L54F		Atlas-SNP	.											.	ODF2L	53	.	0			c.C160T						PASS	.						87	84	85					1																	86851227		2203	4298	6501	SO:0001583	missense	57489	exon3			CCTTAAGTGTTGC		CCDS30763.1, CCDS41354.1, CCDS30763.2, CCDS41354.2, CCDS53339.1	1p22.3	2008-02-05			ENSG00000122417	ENSG00000122417			29225	protein-coding gene	gene with protein product						10574462	Standard	NM_020729		Approved	KIAA1229	uc001dll.2	Q9ULJ1	OTTHUMG00000010080	ENST00000359242.3:c.160C>T	chr1.hg19:g.86851227G>A	ENSP00000359600:p.Leu54Phe	43.0	0.0	.		53.0	12.0	.	NM_001184766	A8MU56|B4E037|Q05C40|Q5BJG5|Q5TBX3|Q5TBX4|Q86X31	Missense_Mutation	SNP	ENST00000359242.3	hg19	CCDS41354.2	.	.	.	.	.	.	.	.	.	.	G	11.71	1.718586	0.30503	.	.	ENSG00000122417	ENST00000441121;ENST00000370566;ENST00000359242;ENST00000317336;ENST00000370567;ENST00000294678;ENST00000465959	T;T;T;T;T	0.39056	1.1;1.1;1.15;1.15;1.12	5.4	0.554	0.17241	.	0.523188	0.20488	N	0.091342	T	0.06280	0.0162	N	0.04768	-0.165	0.44417	D	0.997339	B;B;B;B;B	0.24043	0.001;0.027;0.008;0.011;0.096	B;B;B;B;B	0.21360	0.004;0.013;0.012;0.009;0.034	T	0.15752	-1.0426	10	0.38643	T	0.18	0.4325	1.1465	0.01776	0.2214:0.1715:0.4328:0.1743	.	54;54;54;54;54	B4E037;Q9ULJ1-2;Q9ULJ1-4;Q9ULJ1-3;Q9ULJ1	.;.;.;.;ODF2L_HUMAN	F	54	ENSP00000359597:L54F;ENSP00000359600:L54F;ENSP00000320165:L54F;ENSP00000359598:L54F;ENSP00000294678:L54F	ENSP00000294678:L54F	L	-	1	0	ODF2L	86623815	0.325000	0.24660	0.872000	0.34217	0.966000	0.64601	0.460000	0.21924	0.196000	0.20367	0.650000	0.86243	CTT	.	.	.	none		0.323	ODF2L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027873.2			A	86851227	G	A	86851227	3	1	157	1	0	0	0	0	1	0	0	0	10835	1029	36	2	1990	2	ODF2L	1	86851227	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	33589188	86851227	162399394	8	9256											
ARHGAP29	9411	hgsc.bcm.edu	37	chr1	94639942	94639942	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcattgtagtcttggcagttAggctgttttgttcatactgt	6	19	10	6	0	3	0	2	0	1	0	3	0	3	0	0	2	1	6	0	2	3	8			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:94639942A>G	ENST00000260526.6	-	23	3451	c.3269T>C	c.(3268-3270)cTa>cCa	p.L1090P	ARHGAP29_ENST00000482481.1_5'Flank	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	1090					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)		CTTGGCAGTTAGGCTGTTTTG	0.418																																					p.L1090P		Atlas-SNP	.											.	ARHGAP29	132	.	0			c.T3269C						PASS	.						228	214	218					1																	94639942		2203	4300	6503	SO:0001583	missense	9411	exon23			GCAGTTAGGCTGT		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.3269T>C	chr1.hg19:g.94639942A>G	ENSP00000260526:p.Leu1090Pro	428.0	0.0	.		341.0	56.0	.	NM_004815	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Missense_Mutation	SNP	ENST00000260526.6	hg19	CCDS748.1	.	.	.	.	.	.	.	.	.	.	A	14.86	2.660169	0.47572	.	.	ENSG00000137962	ENST00000260526	T	0.24723	1.84	5.73	-1.98	0.07480	.	1.632400	0.04169	N	0.324470	T	0.04497	0.0123	L	0.29908	0.895	0.09310	N	1	P	0.50710	0.938	B	0.33799	0.17	T	0.21827	-1.0234	10	0.48119	T	0.1	3.2259	2.7638	0.05314	0.5497:0.1174:0.2307:0.1023	.	1090	Q52LW3	RHG29_HUMAN	P	1090	ENSP00000260526:L1090P	ENSP00000260526:L1090P	L	-	2	0	ARHGAP29	94412530	0.041000	0.20044	0.000000	0.03702	0.391000	0.30476	0.816000	0.27267	-0.171000	0.10797	0.482000	0.46254	CTA	.	.	.	none		0.418	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815		G	94639942	A	G	94639942	3	3	157	1	0	0	0	0	1	0	0	0	878	420	15	3	520	3	ARHGAP29	1	94639942	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	7788715	94639942	154610679	9	9257											
GSTM1	2944	hgsc.bcm.edu	37	chr1	110233169	110233169	+	Missense_Mutation	SNP	T	T	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	ccttcccaaatctgaaggacTtcatctcccgctttgaggtg	8	12	8	13	1	3	2	1	2	2	0	5	3	4	3	3	2	0	1	3	2	2	3			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:110233169T>G	ENST00000309851.5	+	7	604	c.550T>G	c.(550-552)Ttc>Gtc	p.F184V	GSTM1_ENST00000369819.2_Intron|GSTM2_ENST00000460717.3_Intron|GSTM1_ENST00000483399.2_Intron|GSTM1_ENST00000349334.3_Intron|AC000032.2_ENST00000562538.1_RNA|GSTM2_ENST00000369831.2_Intron|GSTM1_ENST00000490021.2_Intron|GSTM1_ENST00000369823.2_Missense_Mutation_p.F203V	NM_000561.3	NP_000552.2	P09488	GSTM1_HUMAN	glutathione S-transferase mu 1	184	GST C-terminal.				cellular detoxification of nitrogen compound (GO:0070458)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|nitrobenzene metabolic process (GO:0018916)|small molecule metabolic process (GO:0044281)|xenobiotic catabolic process (GO:0042178)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	enzyme binding (GO:0019899)|glutathione binding (GO:0043295)|glutathione transferase activity (GO:0004364)|protein homodimerization activity (GO:0042803)			endometrium(1)|lung(1)|ovary(1)	3		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		all cancers(265;0.0122)|Colorectal(144;0.0129)|Epithelial(280;0.0146)|Lung(183;0.0422)|COAD - Colon adenocarcinoma(174;0.047)|LUSC - Lung squamous cell carcinoma(189;0.227)	Azathioprine(DB00993)|Busulfan(DB01008)|Carboplatin(DB00958)|Cisplatin(DB00515)|Glutathione(DB00143)|Oxaliplatin(DB00526)	TCTGAAGGACTTCATCTCCCG	0.488									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia																												p.F184V		Atlas-SNP	.											.	GSTM1	13	.	0			c.T550G						PASS	.						209	116	148					1																	110233169		2158	4209	6367	SO:0001583	missense	2944	exon7	Familial Cancer Database	incl.: Familial Head and Neck Cancer; ;AIMAH, Cushing disease, Adrenal, Familial	AAGGACTTCATCT	BC036805	CCDS809.1, CCDS810.1	1p13.3	2012-06-21	2008-11-26		ENSG00000134184	ENSG00000134184	2.5.1.18	"Glutathione S-transferases / Soluble"	4632	protein-coding gene	gene with protein product		138350	"glutathione S-transferase M1"	GST1			Standard	NM_000561		Approved	MU, H-B	uc001dyk.3	P09488	OTTHUMG00000011635	ENST00000309851.5:c.550T>G	chr1.hg19:g.110233169T>G	ENSP00000311469:p.Phe184Val	317.0	0.0	.		240.0	72.0	.	NM_000561	Q5GHG0|Q6FH88|Q8TC98|Q9UC96	Missense_Mutation	SNP	ENST00000309851.5	hg19	CCDS809.1	.	.	.	.	.	.	.	.	.	.	T	12.77	2.037761	0.35989	.	.	ENSG00000134184	ENST00000369823;ENST00000309851	T;T	0.02345	4.33;4.33	3.53	3.53	0.40419	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.149445	0.43416	U	0.000564	T	0.14056	0.0340	H	0.96269	3.795	0.80722	D	1	D	0.71674	0.998	D	0.87578	0.998	T	0.01810	-1.1269	10	0.87932	D	0	.	9.98	0.41809	0.0:0.0:0.0:1.0	.	184	P09488	GSTM1_HUMAN	V	203;184	ENSP00000358838:F203V;ENSP00000311469:F184V	ENSP00000311469:F184V	F	+	1	0	GSTM1	110034692	1.000000	0.71417	0.979000	0.43373	0.246000	0.25737	3.033000	0.49743	1.594000	0.50039	0.459000	0.35465	TTC	.	.	.	none		0.488	GSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032151.2	NM_000561		G	110233169	T	G	110233169	3	3	157	1	0	0	0	0	1	0	0	0	6844	1609	56	5	576	5	GSTM1	1	110233169	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08	15593227	110233169	139017452	10	9258											
ATP1A2	477	hgsc.bcm.edu	37	chr1	160105252	160105252	+	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	tgtggccgtgacgggtgacgGggtgaacgactcccctgcat	6	8	16	11	4	0	3	0	3	0	0	1	4	1	3	3	4	2	1	3	4	1	0			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:160105252G>A	ENST00000361216.3	+	16	2233	c.2144G>A	c.(2143-2145)gGg>gAg	p.G715E	ATP1A2_ENST00000392233.3_Missense_Mutation_p.G715E	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	715			G -> R (in FHM2; de novo mutation in a sporadic case). {ECO:0000269|PubMed:21352219}.		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)			ACGGGTGACGGGGTGAACGAC	0.602																																					p.G715E		Atlas-SNP	.											.	ATP1A2	167	.	0			c.G2144A						PASS	.						170	123	139					1																	160105252		2203	4300	6503	SO:0001583	missense	477	exon16			GTGACGGGGTGAA	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.2144G>A	chr1.hg19:g.160105252G>A	ENSP00000354490:p.Gly715Glu	110.0	0.0	.		73.0	12.0	.	NM_000702	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Missense_Mutation	SNP	ENST00000361216.3	hg19	CCDS1196.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.5|25.5	4.642964|4.642964	0.87859|0.87859	.|.	.|.	ENSG00000018625|ENSG00000018625	ENST00000361216;ENST00000392233;ENST00000435866|ENST00000447527	D;D|D	0.99483|0.99499	-5.99;-5.99|-6.02	4.31|4.31	4.31|4.31	0.51392|0.51392	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type,  transmembrane domain (1);|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	D|D	0.99806|0.99806	0.9916|0.9916	H|H	0.99182|0.99182	4.46|4.46	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	0.96615|0.96615	0.9455|0.9455	10|8	0.87932|0.87932	D|D	0|0	.|.	16.0832|16.0832	0.81020|0.81020	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	615;715|.	F5GXJ7;P50993|.	.;AT1A2_HUMAN|.	E|R	715;715;418|426	ENSP00000354490:G715E;ENSP00000376066:G715E|ENSP00000411705:G426R	ENSP00000354490:G715E|ENSP00000411705:G426R	G|G	+|+	2|1	0|0	ATP1A2|ATP1A2	158371876|158371876	1.000000|1.000000	0.71417|0.71417	0.897000|0.897000	0.35233|0.35233	0.889000|0.889000	0.51656|0.51656	9.593000|9.593000	0.98250|0.98250	2.383000|2.383000	0.81215|0.81215	0.561000|0.561000	0.74099|0.74099	GGG|GGG	.	.	.	none		0.602	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702		A	160105252	G	A	160105252	3	1	157	1	0	0	0	0	1	0	0	0	1129	1232	43	2	2206	2	ATP1A2	1	160105252	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	49872083	160105252	89145369	11	9259											
NME7	29922	hgsc.bcm.edu	37	chr1	169102046	169102046	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attatccaagatcttgaagaAgtattgaacctgaaacggag	16	10	9	6	1	1	5	0	3	1	2	2	6	2	6	2	1	2	1	2	1	7	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:169102046A>G	ENST00000367811.3	-	12	1364	c.1108T>C	c.(1108-1110)Ttc>Ctc	p.F370L	NME7_ENST00000472647.1_Missense_Mutation_p.F334L	NM_013330.3	NP_037462.1	Q9Y5B8	NDK7_HUMAN	NME/NM23 family member 7	370					brain development (GO:0007420)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|CTP biosynthetic process (GO:0006241)|determination of left/right symmetry (GO:0007368)|epithelial cilium movement (GO:0003351)|GTP biosynthetic process (GO:0006183)|intraciliary transport (GO:0042073)|left/right pattern formation (GO:0060972)|UTP biosynthetic process (GO:0006228)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside diphosphate kinase activity (GO:0004550)			central_nervous_system(1)|kidney(1)|large_intestine(5)|lung(8)|skin(1)	16	all_hematologic(923;0.208)					ATCTTGAAGAAGTATTGAACC	0.388																																					p.F370L		Atlas-SNP	.											.	NME7	34	.	0			c.T1108C						PASS	.						122	110	114					1																	169102046		2203	4300	6503	SO:0001583	missense	29922	exon12			TGAAGAAGTATTG	AF153191	CCDS1277.1, CCDS44274.1	1q24.2	2014-07-31	2012-05-18		ENSG00000143156	ENSG00000143156			20461	protein-coding gene	gene with protein product	"cilia and flagella associated protein 67"	613465	"non-metastatic cells 7, protein expressed in (nucleoside-diphosphate kinase)"			19852809	Standard	NM_197972		Approved	FLJ37194, NM23-H7, CFAP67	uc001gfu.3	Q9Y5B8	OTTHUMG00000034586	ENST00000367811.3:c.1108T>C	chr1.hg19:g.169102046A>G	ENSP00000356785:p.Phe370Leu	71.0	0.0	.		66.0	7.0	.	NM_013330	A8K3T6|A8MY09|B3KSW9|Q5TGZ4	Missense_Mutation	SNP	ENST00000367811.3	hg19	CCDS1277.1	.	.	.	.	.	.	.	.	.	.	A	15.81	2.943147	0.53079	.	.	ENSG00000143156	ENST00000472647;ENST00000367811	T;T	0.55234	0.53;0.53	6.17	6.17	0.99709	.	0.557913	0.21023	N	0.081462	T	0.50837	0.1639	M	0.84683	2.71	0.45995	D	0.998806	B	0.20988	0.05	B	0.31686	0.134	T	0.54132	-0.8339	9	0.34782	T	0.22	-13.3948	16.8222	0.85835	1.0:0.0:0.0:0.0	.	370	Q9Y5B8	NDK7_HUMAN	L	334;370	ENSP00000433341:F334L;ENSP00000356785:F370L	ENSP00000356785:F370L	F	-	1	0	NME7	167368670	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.416000	0.90244	2.371000	0.80710	0.533000	0.62120	TTC	.	.	.	none		0.388	NME7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083688.1	NM_013330		G	169102046	A	G	169102046	3	3	157	1	0	0	0	0	1	0	0	0	10503	72	3	3	26	3	NME7	1	169102046	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	8996794	169102046	80148575	12	9260											
PPFIA4	8497	hgsc.bcm.edu	37	chr1	203036824	203036824	+	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	gggggctgtgtgcctgcagaAccagtcttcagtatggcatc	7	10	14	10	0	2	1	1	0	1	1	3	1	2	1	2	3	3	4	2	3	2	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:203036824A>G	ENST00000447715.2	+	31	3427	c.2986A>G	c.(2986-2988)Acc>Gcc	p.T996A	PPFIA4_ENST00000295706.4_Splice_Site_p.T503A|PPFIA4_ENST00000414050.2_Splice_Site_p.T725A|PPFIA4_ENST00000599966.1_Splice_Site_p.T503A|PPFIA4_ENST00000367240.2_Splice_Site_p.T997A|PPFIA4_ENST00000272198.6_Splice_Site_p.T512A			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	996	SAM 2. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(20)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	50						TGCCTGCAGAACCAGTCTTCA	0.552																																					p.T512A		Atlas-SNP	.											.	PPFIA4	139	.	0			c.A1534G						PASS	.						78	84	82					1																	203036824		2156	4266	6422	SO:0001630	splice_region_variant	8497	exon13			TGCAGAACCAGTC	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.2985-1A>G	chr1.hg19:g.203036824A>G		94.0	0.0	.		67.0	8.0	.	NM_015053	A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Missense_Mutation	SNP	ENST00000447715.2	hg19		.	.	.	.	.	.	.	.	.	.	A	10.88	1.474689	0.26511	.	.	ENSG00000143847	ENST00000367240;ENST00000447715;ENST00000295706;ENST00000414050;ENST00000272198	T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83	3.89	2.72	0.32119	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.349867	0.20011	U	0.101127	T	0.27933	0.0688	N	0.11892	0.195	0.80722	D	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.001;0.0;0.0;0.001	T	0.04930	-1.0917	10	0.44086	T	0.13	-16.0337	9.5608	0.39369	0.9138:0.0:0.0862:0.0	.	725;996;198;503;512	B4DIS5;B1N949;B3KN22;O75335-2;O75335	.;.;.;.;LIPA4_HUMAN	A	997;996;503;725;512	ENSP00000356209:T997A;ENSP00000402576:T996A;ENSP00000295706:T503A;ENSP00000400379:T725A;ENSP00000272198:T512A	ENSP00000272198:T512A	T	+	1	0	PPFIA4	201303447	0.971000	0.33674	1.000000	0.80357	0.968000	0.65278	2.234000	0.43035	0.618000	0.30179	0.397000	0.26171	ACC	.	.	.	none		0.552	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053	Missense_Mutation	G	203036824	A	G	203036824	5	3	157	1	0	0	0	0	0	0	1	0	12319	57	2	3	1584	3	PPFIA4	1	203036824	Splice_Site	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	33934778	203036824	46213797	13	9261											
C1orf55	163859	hgsc.bcm.edu	37	chr1	226175877	226175877	+	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	gcctcccagagtcagtcaccGggatctgcagttgttctggt	6	11	12	12	1	4	1	2	0	2	1	5	2	5	2	3	2	1	3	3	2	0	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr1:226175877G>T	ENST00000272091.7	-	6	872	c.854C>A	c.(853-855)cCg>cAg	p.P285Q		NM_152608.3	NP_689821.3	Q6IQ49	SDE2_HUMAN	SDE2 telomere maintenance homolog (S. pombe)	285																	GTCAGTCACCGGGATCTGCAG	0.502																																					p.P285Q		Atlas-SNP	.											.	.	.	.	0			c.C854A						PASS	.						175	164	168					1																	226175877		1943	4144	6087	SO:0001583	missense	163859	exon6			GTCACCGGGATCT	BC071563	CCDS41473.1	1q42.12	2012-06-26	2012-06-26	2012-06-26	ENSG00000143751	ENSG00000143751			26643	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 55"	C1orf55		21333630	Standard	NM_152608		Approved	FLJ35382	uc001hpu.4	Q6IQ49	OTTHUMG00000037504	ENST00000272091.7:c.854C>A	chr1.hg19:g.226175877G>T	ENSP00000272091:p.Pro285Gln	311.0	0.0	.		236.0	10.0	.	NM_152608	A8K4P3|Q5TD36|Q6ZS26|Q8NAG7	Missense_Mutation	SNP	ENST00000272091.7	hg19	CCDS41473.1	.	.	.	.	.	.	.	.	.	.	G	14.83	2.653524	0.47362	.	.	ENSG00000143751	ENST00000272091;ENST00000366818;ENST00000366817	T;T	0.53206	0.78;0.63	6.05	0.9	0.19278	.	0.513077	0.23622	N	0.046231	T	0.34135	0.0887	L	0.59436	1.845	0.09310	N	1	B;B	0.23591	0.088;0.021	B;B	0.25614	0.062;0.017	T	0.18085	-1.0348	10	0.21540	T	0.41	-0.685	1.397	0.02263	0.2086:0.1076:0.3867:0.2972	.	273;285	Q6IQ49-2;Q6IQ49	.;CA055_HUMAN	Q	285;273;190	ENSP00000272091:P285Q;ENSP00000355782:P190Q	ENSP00000272091:P285Q	P	-	2	0	C1orf55	224242500	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.191000	0.17076	-0.069000	0.12931	0.650000	0.86243	CCG	.	.	.	none		0.502	SDE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091310.1	NM_152608		T	226175877	G	T	226175877	3	4	157	1	0	0	0	0	1	0	0	0	2049	1116	39	4	509	4	C1orf55	1	226175877	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	23139053	226175877	23074744	14	9262											
GMPPA	29926	hgsc.bcm.edu	37	chr2	220370077	220370077	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtatctggagtcagatcaagTccgcagggtatggaaggctg	10	9	15	7	1	3	1	2	0	1	1	4	3	4	3	1	4	0	4	1	4	4	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr2:220370077T>C	ENST00000358215.3	+	8	1117	c.748T>C	c.(748-750)Tcc>Ccc	p.S250P	GMPPA_ENST00000313597.5_Missense_Mutation_p.S250P|AC053503.11_ENST00000429882.1_RNA|GMPPA_ENST00000373908.1_Missense_Mutation_p.S250P|GMPPA_ENST00000373917.3_Missense_Mutation_p.S250P|GMPPA_ENST00000341142.3_Missense_Mutation_p.S250P	NM_205847.2	NP_995319.1	Q96IJ6	GMPPA_HUMAN	GDP-mannose pyrophosphorylase A	250					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)		TCAGATCAAGTCCGCAGGGTA	0.607																																					p.S250P		Atlas-SNP	.											.	GMPPA	50	.	0			c.T748C						PASS	.						64	65	65					2																	220370077		2203	4300	6503	SO:0001583	missense	29926	exon8			ATCAAGTCCGCAG	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.748T>C	chr2.hg19:g.220370077T>C	ENSP00000350949:p.Ser250Pro	142.0	0.0	.		120.0	22.0	.	NM_205847	A6NJ74|A8K3Q6|B3KMT4|Q53GI0|Q9NWC3|Q9Y5P5	Missense_Mutation	SNP	ENST00000358215.3	hg19	CCDS2441.1	.	.	.	.	.	.	.	.	.	.	t	25.4	4.632235	0.87660	.	.	ENSG00000144591	ENST00000313597;ENST00000373917;ENST00000358215;ENST00000373908;ENST00000435316;ENST00000341142	D;D;D;D;T;D	0.94650	-3.48;-3.48;-3.48;-3.48;1.84;-3.48	4.9	4.9	0.64082	.	0.271361	0.37530	N	0.002048	D	0.96592	0.8888	M	0.73962	2.25	0.80722	D	1	D;D	0.71674	0.998;0.97	D;P	0.66847	0.947;0.737	D	0.96980	0.9714	10	0.66056	D	0.02	-23.7265	14.211	0.65764	0.0:0.0:0.0:1.0	.	250;250	Q96IJ6-2;Q96IJ6	.;GMPPA_HUMAN	P	250;250;250;250;215;250	ENSP00000315925:S250P;ENSP00000363027:S250P;ENSP00000350949:S250P;ENSP00000363016:S250P;ENSP00000411060:S215P;ENSP00000340760:S250P	ENSP00000315925:S250P	S	+	1	0	GMPPA	220078321	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	7.745000	0.85046	1.828000	0.53243	0.529000	0.55759	TCC	.	.	.	none		0.607	GMPPA-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130230.1	NM_013335		C	220370077	T	C	220370077	3	2	157	1	0	0	0	0	1	0	0	0	6501	1667	58	3	774	3	GMPPA	2	220370077	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08		220370077	22829296	15	9263											
CAMK1	8536	hgsc.bcm.edu	37	chr3	9801228	9801228	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcactcaccgactggtggaTattcttatctagagctgtat	9	14	8	10	1	4	1	2	0	2	1	4	3	4	2	1	2	1	2	1	2	4	5			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr3:9801228T>C	ENST00000256460.3	-	10	1033	c.856A>G	c.(856-858)Atc>Gtc	p.I286V	OGG1_ENST00000449570.2_Intron|OGG1_ENST00000302036.7_Intron|OGG1_ENST00000383826.5_Intron|OGG1_ENST00000302008.8_Intron|OGG1_ENST00000349503.5_Intron	NM_003656.4	NP_003647.1	Q14012	KCC1A_HUMAN	calcium/calmodulin-dependent protein kinase I	286	Autoinhibitory domain.				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)		GACTGGTGGATATTCTTATCT	0.537																																					p.I286V		Atlas-SNP	.											.	CAMK1	32	.	0			c.A856G						PASS	.						179	171	174					3																	9801228		2203	4300	6503	SO:0001583	missense	8536	exon10			GGTGGATATTCTT	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.856A>G	chr3.hg19:g.9801228T>C	ENSP00000256460:p.Ile286Val	250.0	0.0	.		204.0	42.0	.	NM_003656	Q3KPF6	Missense_Mutation	SNP	ENST00000256460.3	hg19	CCDS2582.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.4|23.4	4.415377|4.415377	0.83449|0.83449	.|.	.|.	ENSG00000134072|ENSG00000134072	ENST00000256460|ENST00000421120	T|.	0.39056|.	1.1|.	5.95|5.95	5.95|5.95	0.96441|0.96441	Protein kinase-like domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.80407|0.80407	0.4617|0.4617	M|M	0.87038|0.87038	2.855|2.855	0.80722|0.80722	D|D	1|1	P;P|.	0.48162|.	0.906;0.906|.	P;P|.	0.45099|.	0.469;0.469|.	T|T	0.83025|0.83025	-0.0165|-0.0165	10|5	0.59425|.	D|.	0.04|.	-11.1309|-11.1309	16.0971|16.0971	0.81132|0.81132	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	286;286|.	Q14012;B0YIY3|.	KCC1A_HUMAN;.|.	V|C	286|132	ENSP00000256460:I286V|.	ENSP00000256460:I286V|.	I|Y	-|-	1|2	0|0	CAMK1|CAMK1	9776228|9776228	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.589000|7.589000	0.82641|0.82641	2.279000|2.279000	0.76181|0.76181	0.533000|0.533000	0.62120|0.62120	ATC|TAT	.	.	.	none		0.537	CAMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250206.1	NM_003656		C	9801228	T	C	9801228	3	2	157	1	0	0	0	0	1	0	0	0	2598	1406	49	3	268	3	CAMK1	3	9801228	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08		9801228	188221202	16	9264											
GPD1L	23171	hgsc.bcm.edu	37	chr3	32169609	32169609	+	Missense_Mutation	SNP	A	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	aattggtaataatgtcaagaAacttcagaaatttgcctcca	16	12	6	7	0	2	2	2	0	0	2	3	2	3	2	2	1	2	1	2	1	6	5			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr3:32169609A>C	ENST00000282541.5	+	2	290	c.89A>C	c.(88-90)aAa>aCa	p.K30T		NM_015141.3	NP_055956.1	Q8N335	GPD1L_HUMAN	glycerol-3-phosphate dehydrogenase 1-like	30					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						AATGTCAAGAAACTTCAGAAA	0.368																																					p.K30T		Atlas-SNP	.											.	GPD1L	25	.	0			c.A89C						PASS	.						59	59	59					3																	32169609		2203	4300	6503	SO:0001583	missense	23171	exon2			TCAAGAAACTTCA	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.89A>C	chr3.hg19:g.32169609A>C	ENSP00000282541:p.Lys30Thr	50.0	0.0	.		49.0	9.0	.	NM_015141	A8K9U3|Q14702|Q9BRM5	Missense_Mutation	SNP	ENST00000282541.5	hg19	CCDS33729.1	.	.	.	.	.	.	.	.	.	.	A	12.00	1.807729	0.31961	.	.	ENSG00000152642	ENST00000282541;ENST00000425459	T;T	0.58652	0.32;1.2	4.8	3.62	0.41486	Glycerol-3-phosphate dehydrogenase, NAD-dependent, N-terminal (1);NAD(P)-binding domain (1);	0.435694	0.28257	N	0.016007	T	0.52917	0.1764	M	0.70595	2.14	0.29089	N	0.882201	B	0.06786	0.001	B	0.20184	0.028	T	0.52697	-0.8541	10	0.46703	T	0.11	-9.553	6.5277	0.22310	0.6226:0.3005:0.0769:0.0	.	30	Q8N335	GPD1L_HUMAN	T	30	ENSP00000282541:K30T;ENSP00000408770:K30T	ENSP00000282541:K30T	K	+	2	0	GPD1L	32144613	0.036000	0.19791	0.834000	0.33040	0.984000	0.73092	2.830000	0.48136	0.938000	0.37419	0.459000	0.35465	AAA	.	.	.	none		0.368	GPD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341975.2	NM_015141		C	32169609	A	C	32169609	3	2	157	1	0	0	0	0	1	0	0	0	6612	14	1	5	95	5	GPD1L	3	32169609	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	22368381	32169609	165852821	17	9265											
RPL24	6152	hgsc.bcm.edu	37	chr3	101401697	101401698	+	Frame_Shift_Ins	INS	-	-	A																															tcagcaagagatgcaccagtINSaatggccctctggaatttga																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr3:101401697_101401698insA	ENST00000394077.3	-	4	351_352	c.246_247insT	c.(244-249)attactfs	p.T83fs	RPL24_ENST00000469605.1_Frame_Shift_Ins_p.T83fs|RPL24_ENST00000495401.1_Frame_Shift_Ins_p.T83fs	NM_000986.3	NP_000977.1	P83731	RL24_HUMAN	ribosomal protein L24	83					cellular protein metabolic process (GO:0044267)|exit from mitosis (GO:0010458)|gene expression (GO:0010467)|mitotic cell cycle checkpoint (GO:0007093)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|optic nerve development (GO:0021554)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|ribosomal large subunit assembly (GO:0000027)|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)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			large_intestine(1)|lung(2)|urinary_tract(1)	4						GATGCACCAGTAATGGCCCTCT	0.436																																					p.T83fs		Atlas-INDEL	.											.	RPL24	8	.	0			c.247_248insT						PASS	.																																			SO:0001589	frameshift_variant	6152	exon4			.	AB007177	CCDS33809.1	3q12	2011-04-06			ENSG00000114391	ENSG00000114391		"L ribosomal proteins"	10325	protein-coding gene	gene with protein product		604180				9582194	Standard	NM_000986		Approved	L24	uc003dvh.1	P83731	OTTHUMG00000159146	ENST00000394077.3:c.247dupT	chr3.hg19:g.101401699_101401699dupA	ENSP00000377640:p.Thr83fs	96.0	0.0	0		98.0	23.0	0.234694	NM_000986	B2R4Y3|P38663|Q6IBS3	Frame_Shift_Ins	INS	ENST00000394077.3	hg19	CCDS33809.1																																																																																			.	.	.	none		0.436	RPL24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353487.1	NM_000986		A	101401698	-	A	101401697	7	5	157	1	0	1	1	0	0	0	0	0	13585	1638	57	0	238	0	RPL24	3	101401697	Frame_Shift_Ins	INS	-	TCGA-DZ-6132-01A-11D-1961-08	69232088	101401697	96620733	18	9266											
FAM55C	91775	hgsc.bcm.edu	37	chr3	101540473	101540473	+	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	gtctcacttcagcaccttccCtttggaagtgtacatccggc	7	12	8	14	1	2	0	2	0	1	0	5	1	4	1	3	2	2	2	3	2	2	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr3:101540473C>G	ENST00000491511.2	+	8	2311	c.1355C>G	c.(1354-1356)cCt>cGt	p.P452R	NXPE3_ENST00000422132.1_Missense_Mutation_p.P452R|NXPE3_ENST00000273347.5_Missense_Mutation_p.P452R|RP11-49I4.3_ENST00000490324.2_RNA|NXPE3_ENST00000477909.1_Missense_Mutation_p.P452R	NM_001134456.1	NP_001127928.1	Q969Y0	NXPE3_HUMAN	neurexophilin and PC-esterase domain family, member 3	452						extracellular region (GO:0005576)											AGCACCTTCCCTTTGGAAGTG	0.552																																					p.P452R		Atlas-SNP	.											.	.	.	.	0			c.C1355G						PASS	.						113	99	104					3																	101540473		2203	4300	6503	SO:0001583	missense	91775	exon8			CCTTCCCTTTGGA	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.1355C>G	chr3.hg19:g.101540473C>G	ENSP00000417485:p.Pro452Arg	85.0	0.0	.		64.0	11.0	.	NM_145037	A8K0X4|D3DN53|Q7Z2S8	Missense_Mutation	SNP	ENST00000491511.2	hg19	CCDS2945.1	.	.	.	.	.	.	.	.	.	.	C	31	5.070163	0.93950	.	.	ENSG00000144815	ENST00000273347;ENST00000491511;ENST00000477909;ENST00000422132	T;T;T;T	0.27557	1.66;1.66;1.66;1.66	6.03	6.03	0.97812	.	0.044822	0.85682	D	0.000000	T	0.67325	0.2881	M	0.91717	3.235	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73017	-0.4115	10	0.87932	D	0	-17.0676	20.5568	0.99304	0.0:1.0:0.0:0.0	.	452	Q969Y0	FA55C_HUMAN	R	452	ENSP00000273347:P452R;ENSP00000417485:P452R;ENSP00000418369:P452R;ENSP00000396421:P452R	ENSP00000273347:P452R	P	+	2	0	FAM55C	103023163	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.747000	0.85070	2.861000	0.98227	0.655000	0.94253	CCT	.	.	.	none		0.552	NXPE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353711.2	NM_145037		G	101540473	C	G	101540473	3	3	157	1	0	0	0	0	1	0	0	0	5593	681	24	4	1373	4	FAM55C	3	101540473	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	138776	101540473	96481957	19	9267											
MYH15	22989	hgsc.bcm.edu	37	chr3	108107907	108107918	+	In_Frame_Del	DEL	TTCCAGTTCACG	TTCCAGTTCACG	-																															atttcaccctccagttcaccTtccagttcacgaacctgcaa																								rs143417195	byFrequency	TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	TTCCAGTTCACG	TTCCAGTTCACG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr3:108107907_108107918delTTCCAGTTCACG	ENST00000273353.3	-	39	5550_5561	c.5494_5505delCGTGAACTGGAA	c.(5494-5505)cgtgaactggaadel	p.RELE1832del		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1832						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.R1832S(1)		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						CCAGTTCACCTTCCAGTTCACGAACCTGCAAC	0.524																																					p.1832_1836del		Atlas-INDEL	.											.	MYH15	223	.	1	Substitution - Missense(1)	lung(1)	c.5495_5506del						PASS	.																																			SO:0001651	inframe_deletion	22989	exon39			.	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.5494_5505delCGTGAACTGGAA	chr3.hg19:g.108107907_108107918delTTCCAGTTCACG	ENSP00000273353:p.Arg1832_Glu1835del	242.0	0.0	0		136.0	21.0	0.154412	NM_014981		In_Frame_Del	DEL	ENST00000273353.3	hg19	CCDS43127.1																																																																																			.	.	.	none		0.524	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		-	108107918	TTCCAGTTCACG	-	108107907	7	5	157	1	0	1	0	1	0	0	0	0	10041	1606	56	0	351	0	MYH15	3	108107907	In_Frame_Del	DEL	TTCCAGTTCACG	TCGA-DZ-6132-01A-11D-1961-08	6567434	108107907	89914523	20	9268											
POLQ	10721	hgsc.bcm.edu	37	chr3	121260288	121260288	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caaaacccgcttcaaaataaGtaattctgccacaagagtct	16	9	5	11	1	3	1	1	0	2	1	3	1	3	1	2	0	2	2	2	0	7	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr3:121260288G>A	ENST00000264233.5	-	3	510	c.382C>T	c.(382-384)Ctt>Ttt	p.L128F		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	128	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)		TTCAAAATAAGTAATTCTGCC	0.348								DNA polymerases (catalytic subunits)																													p.L128F	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.C382T						PASS	.						145	164	157					3																	121260288		2203	4300	6503	SO:0001583	missense	10721	exon3			AAATAAGTAATTC	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.382C>T	chr3.hg19:g.121260288G>A	ENSP00000264233:p.Leu128Phe	380.0	0.0	.		448.0	78.0	.	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	hg19	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.569858	0.86542	.	.	ENSG00000051341	ENST00000264233;ENST00000393672	T	0.60672	0.17	5.74	5.74	0.90152	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.275715	0.37261	N	0.002169	T	0.79787	0.4506	M	0.83603	2.65	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81741	-0.0794	10	0.87932	D	0	.	19.9346	0.97133	0.0:0.0:1.0:0.0	.	128	O75417	DPOLQ_HUMAN	F	128;263	ENSP00000264233:L128F	ENSP00000264233:L128F	L	-	1	0	POLQ	122742978	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.652000	0.54439	2.712000	0.92718	0.563000	0.77884	CTT	.	.	.	none		0.348	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		A	121260288	G	A	121260288	3	1	157	1	0	0	0	0	1	0	0	0	12215	1029	36	2	7502	2	POLQ	3	121260288	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	13152381	121260288	76762142	21	9269											
ATR	545	hgsc.bcm.edu	37	chr3	142284995	142284995	+	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	ctttggcctcatggcttccaCtcacatttacaaacataagt	11	13	5	12	0	2	0	2	0	0	0	3	0	3	0	2	2	2	1	2	2	3	5	rs200407265		TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr3:142284995C>T	ENST00000350721.4	-	3	381	c.260G>A	c.(259-261)aGt>aAt	p.S87N	ATR_ENST00000383101.3_Missense_Mutation_p.S87N	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	87					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						ATGGCTTCCACTCACATTTAC	0.413								Other conserved DNA damage response genes																													p.S87N		Atlas-SNP	.											.	ATR	285	.	0			c.G260A						PASS	.						107	101	103					3																	142284995		2203	4300	6503	SO:0001583	missense	545	exon3			CTTCCACTCACAT	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.260G>A	chr3.hg19:g.142284995C>T	ENSP00000343741:p.Ser87Asn	98.0	0.0	.		111.0	23.0	.	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	hg19	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	C	2.407	-0.336336	0.05278	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.30448	1.53;1.53	5.53	0.0727	0.14388	.	1.113090	0.06757	N	0.781079	T	0.07548	0.0190	N	0.00926	-1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36553	-0.9743	10	0.02654	T	1	-9.1875	2.5644	0.04779	0.1129:0.2236:0.1159:0.5476	.	87	Q13535	ATR_HUMAN	N	87	ENSP00000343741:S87N;ENSP00000372581:S87N	ENSP00000343741:S87N	S	-	2	0	ATR	143767685	0.931000	0.31567	1.000000	0.80357	0.976000	0.68499	0.080000	0.14802	0.369000	0.24510	-0.414000	0.06135	AGT	.	C|1.000;A|0.000	.	alt		0.413	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		T	142284995	C	T	142284995	3	4	157	1	0	0	0	0	1	0	0	0	1204	565	20	2	7854	2	ATR	3	142284995	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	21024707	142284995	55737435	22	9270											
SLC7A14	57709	hgsc.bcm.edu	37	chr3	170201153	170201154	+	Frame_Shift_Ins	INS	-	-	A																															aaatgaccctcggcatcgggINSaagagggaccccagcaagct																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr3:170201153_170201154insA	ENST00000231706.5	-	6	1379_1380	c.1064_1065insT	c.(1063-1065)ttcfs	p.F355fs	CLDN11_ENST00000486975.1_Intron|CLDN11_ENST00000451576.1_Intron	NM_020949.2	NP_066000.2	Q8TBB6	S7A14_HUMAN	solute carrier family 7, member 14	355					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)			TCGGCATCGGGAAGAGGGACCC	0.54											OREG0015917	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F355fs		Atlas-INDEL	.											.	SLC7A14	110	.	0			c.1065_1066insT						PASS	.																																			SO:0001589	frameshift_variant	57709	exon6			.	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.1065dupT	chr3.hg19:g.170201155_170201155dupA	ENSP00000231706:p.Phe355fs	166.0	0.0	0	1883	117.0	14.0	0.119658	NM_020949	B3KV33|Q9HCF9	Frame_Shift_Ins	INS	ENST00000231706.5	hg19	CCDS33892.1																																																																																			.	.	.	none		0.54	SLC7A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352598.2	NM_020949		A	170201154	-	A	170201153	7	5	157	1	0	1	1	0	0	0	0	0	14709	1165	41	0	1262	0	SLC7A14	3	170201153	Frame_Shift_Ins	INS	-	TCGA-DZ-6132-01A-11D-1961-08	27916158	170201153	27821277	23	9271											
LAMP3	27074	hgsc.bcm.edu	37	chr3	182870222	182870222	+	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	caacagaaggttggattttcGggtgccacagttcccagagg	10	9	13	9	1	0	2	0	0	0	2	2	3	1	3	2	4	2	2	2	4	2	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr3:182870222G>T	ENST00000265598.3	-	3	1084	c.829C>A	c.(829-831)Cga>Aga	p.R277R	LAMP3_ENST00000466939.1_Silent_p.R253R	NM_014398.3	NP_055213.2	Q9UQV4	LAMP3_HUMAN	lysosomal-associated membrane protein 3	277					cell proliferation (GO:0008283)|immune system process (GO:0002376)	alveolar lamellar body membrane (GO:0097233)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)		p.R277R(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(9)|ovary(2)|prostate(2)	28	all_cancers(143;9.14e-14)|Ovarian(172;0.0355)		all cancers(12;2.91e-44)|Epithelial(37;5.52e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;4.16e-21)			TTGGATTTTCGGGTGCCACAG	0.458																																					p.R277R		Atlas-SNP	.											.	LAMP3	48	.	1	Substitution - coding silent(1)	lung(1)	c.C829A						PASS	.						174	186	182					3																	182870222		2203	4300	6503	SO:0001819	synonymous_variant	27074	exon3			ATTTTCGGGTGCC	AB013924	CCDS3242.1	3q26.3-q27	2011-11-24			ENSG00000078081	ENSG00000078081		"CD molecules"	14582	protein-coding gene	gene with protein product		605883				9721848	Standard	NM_014398		Approved	LAMP, TSC403, DC-LAMP, DCLAMP, CD208	uc003flh.4	Q9UQV4	OTTHUMG00000158387	ENST00000265598.3:c.829C>A	chr3.hg19:g.182870222G>T		384.0	0.0	.		415.0	17.0	.	NM_014398	D3DNS4|O94781|Q8NEC8	Silent	SNP	ENST00000265598.3	hg19	CCDS3242.1																																																																																			.	.	.	none		0.458	LAMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350863.1			T	182870222	G	T	182870222	2	4	157	1	0	0	0	0	0	0	0	1	8626	1124	39	4		4	LAMP3	3	182870222	Silent	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	12669069	182870222	15152208	24	9272											
N4BP2	55728	hgsc.bcm.edu	37	chr4	40122682	40122682	+	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	tacttttaccaatagtgcacCaactgtttctggagtagtag	11	14	8	8	0	1	0	0	0	1	0	1	1	1	1	2	1	4	4	2	1	7	7			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr4:40122682C>G	ENST00000261435.6	+	9	3367	c.2951C>G	c.(2950-2952)cCa>cGa	p.P984R		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	984					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						AATAGTGCACCAACTGTTTCT	0.443																																					p.P984R		Atlas-SNP	.											.	N4BP2	166	.	0			c.C2951G						PASS	.						84	80	82					4																	40122682		2203	4300	6503	SO:0001583	missense	55728	exon9			GTGCACCAACTGT	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.2951C>G	chr4.hg19:g.40122682C>G	ENSP00000261435:p.Pro984Arg	70.0	0.0	.		58.0	9.0	.	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	hg19	CCDS3457.1	.	.	.	.	.	.	.	.	.	.	C	3.483	-0.105433	0.06967	.	.	ENSG00000078177	ENST00000261435;ENST00000381804	T	0.21543	2.0	5.1	4.25	0.50352	.	0.600314	0.17354	N	0.177287	T	0.22898	0.0553	L	0.54323	1.7	0.09310	N	1	D;P	0.53151	0.958;0.93	P;B	0.45506	0.483;0.289	T	0.11421	-1.0588	10	0.48119	T	0.1	0.0045	8.0754	0.30714	0.0:0.8201:0.0:0.1799	.	984;984	Q86UW6-2;Q86UW6	.;N4BP2_HUMAN	R	984;904	ENSP00000261435:P984R	ENSP00000261435:P984R	P	+	2	0	N4BP2	39799077	0.020000	0.18652	0.005000	0.12908	0.002000	0.02628	2.644000	0.46613	1.513000	0.48852	0.655000	0.94253	CCA	.	.	.	none		0.443	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177		G	40122682	C	G	40122682	3	3	157	1	0	0	0	0	1	0	0	0	10117	594	21	4	2977	4	N4BP2	4	40122682	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08		40122682	151031594	25	9273											
SCD5	79966	hgsc.bcm.edu	37	chr4	83557889	83557889	+	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	agaatagaggccaagaagtaGgaattccacagactctctcc	15	7	9	10	0	1	4	0	0	1	4	4	5	3	5	3	2	0	1	3	2	6	3			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr4:83557889G>C	ENST00000319540.4	-	4	976	c.657C>G	c.(655-657)tcC>tcG	p.S219S		NM_001037582.2	NP_001032671.2	Q86SK9	SCD5_HUMAN	stearoyl-CoA desaturase 5	219					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)			endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	13		Colorectal(4;0.0323)|Hepatocellular(203;0.115)				CCAAGAAGTAGGAATTCCACA	0.537																																					p.S219S		Atlas-SNP	.											.	SCD5	58	.	0			c.C657G						PASS	.						108	95	100					4																	83557889		2203	4300	6503	SO:0001819	synonymous_variant	79966	exon4			GAAGTAGGAATTC	AF389338	CCDS3595.1, CCDS34024.1	4q21.3	2013-01-25	2005-06-09	2005-06-09	ENSG00000145284	ENSG00000145284		"Fatty acid desaturases"	21088	protein-coding gene	gene with protein product		608370	"stearoyl-CoA desaturase 4"	SCD4		12477932	Standard	NM_024906		Approved	ACOD4, FLJ21032, FADS4, HSCD5	uc003hna.2	Q86SK9	OTTHUMG00000130293	ENST00000319540.4:c.657C>G	chr4.hg19:g.83557889G>C		85.0	0.0	.		45.0	9.0	.	NM_001037582	B2RPG0|Q4W5Q5|Q8NDS0|Q9H7D1	Silent	SNP	ENST00000319540.4	hg19	CCDS34024.1																																																																																			.	.	.	none		0.537	SCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252635.1	NM_024906		C	83557889	G	C	83557889	2	2	157	1	0	0	0	0	0	0	0	1	13900	987	35	4		4	SCD5	4	83557889	Silent	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	43435207	83557889	107596387	26	9274											
ANK2	287	hgsc.bcm.edu	37	chr4	114195785	114195785	+	Frame_Shift_Del	DEL	G	G	-																															tcctattggaagcaggagcaGcccactccttagctaccaag																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr4:114195785delG	ENST00000357077.4	+	15	1716	c.1663delG	c.(1663-1665)gccfs	p.A555fs	ANK2_ENST00000264366.6_Frame_Shift_Del_p.A555fs|ANK2_ENST00000506722.1_Frame_Shift_Del_p.A534fs|ANK2_ENST00000394537.3_Frame_Shift_Del_p.A555fs	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	555					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)		AGCAGGAGCAGCCCACTCCTT	0.517																																					p.A554fs		Atlas-INDEL	.											.	ANK2	576	.	0			c.1662delA						PASS	.						80	78	79					4																	114195785		2203	4300	6503	SO:0001589	frameshift_variant	287	exon15			.	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.1663delG	chr4.hg19:g.114195785delG	ENSP00000349588:p.Ala555fs	85.0	0.0	0		69.0	12.0	0.173913	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Frame_Shift_Del	DEL	ENST00000357077.4	hg19	CCDS3702.1																																																																																			.	.	.	none		0.517	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		-	114195785	G	-	114195785	7	5	157	1	0	1	0	1	0	0	0	0	621	971	34	0	1746	0	ANK2	4	114195785	Frame_Shift_Del	DEL	G	TCGA-DZ-6132-01A-11D-1961-08	30637896	114195785	76958491	27	9275											
KIAA0922	23240	hgsc.bcm.edu	37	chr4	154557454	154557454	+	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	ttcctcatttatacttcagcCctacctcacaagcacccgaa	11	11	3	16	1	3	0	3	0	0	0	4	1	4	0	4	0	4	1	4	0	5	6			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr4:154557454C>T	ENST00000409663.3	+	35	4608	c.4556C>T	c.(4555-4557)cCc>cTc	p.P1519L	KIAA0922_ENST00000440693.1_Splice_Site_p.P1436L|KIAA0922_ENST00000409959.3_Splice_Site_p.P1520L	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	1519						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)				ATACTTCAGCCCTACCTCACA	0.413																																					p.P1520L		Atlas-SNP	.											.	KIAA0922	214	.	0			c.C4559T						PASS	.						76	85	82					4																	154557454		2203	4300	6503	SO:0001630	splice_region_variant	23240	exon35			TTCAGCCCTACCT	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.4555-1C>T	chr4.hg19:g.154557454C>T		230.0	0.0	.		208.0	24.0	.	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	hg19	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	C	22.5	4.298160	0.81025	.	.	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	T;T;T;T	0.31510	1.76;1.49;1.75;1.51	5.93	5.07	0.68467	.	0.056199	0.64402	D	0.000001	T	0.50034	0.1592	L	0.52573	1.65	0.80722	D	1	D;D;D	0.71674	0.998;0.997;0.995	D;D;P	0.68621	0.959;0.934;0.86	T	0.53129	-0.8482	10	0.87932	D	0	-12.4672	16.3753	0.83383	0.133:0.867:0.0:0.0	.	1436;1520;1519	A2VDJ0-3;A2VDJ0-5;A2VDJ0	.;.;T131L_HUMAN	L	1519;1436;1520;1297	ENSP00000386574:P1519L;ENSP00000409663:P1436L;ENSP00000386787:P1520L;ENSP00000240487:P1297L	ENSP00000240487:P1297L	P	+	2	0	KIAA0922	154776904	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.205000	0.77881	1.466000	0.48025	0.655000	0.94253	CCC	.	.	.	none		0.413	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	Missense_Mutation	T	154557454	C	T	154557454	5	4	157	1	0	0	0	0	0	0	1	0	8208	637	22	2	4697	2	KIAA0922	4	154557454	Splice_Site	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	40361669	154557454	36596822	28	9276											
FNIP2	57600	hgsc.bcm.edu	37	chr4	159756556	159756556	+	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	tttcttgttcctttatcttaGcacacagcacaccagttgat	9	16	5	11	0	2	1	0	1	2	0	3	1	3	1	2	0	2	4	2	0	2	7			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr4:159756556G>A	ENST00000264433.6	+	7	730		c.e7-1		FNIP2_ENST00000379346.3_Splice_Site	NM_020840.1	NP_065891.1	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2						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)		CTTTATCTTAGCACACAGCAC	0.383																																					.		Atlas-SNP	.											.	FNIP2	90	.	0			c.656-1G>A						PASS	.						258	258	258					4																	159756556		1966	4155	6121	SO:0001630	splice_region_variant	57600	exon7			ATCTTAGCACACA	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.656-1G>A	chr4.hg19:g.159756556G>A		305.0	0.0	.		298.0	56.0	.	NM_020840	Q05DC3|Q96I31|Q9H994	Splice_Site	SNP	ENST00000264433.6	hg19	CCDS47155.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.225241	0.79576	.	.	ENSG00000052795	ENST00000264433;ENST00000512986;ENST00000379346;ENST00000504715	.	.	.	5.91	5.91	0.95273	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.2857	0.98533	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FNIP2	159976006	1.000000	0.71417	0.995000	0.50966	0.794000	0.44872	9.224000	0.95209	2.803000	0.96430	0.650000	0.86243	.	.	.	.	none		0.383	FNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366602.1	NM_020840	Intron	A	159756556	G	A	159756556	5	1	157	1	0	0	0	0	0	0	1	0	5983	985	34	2	681	2	FNIP2	4	159756556	Splice_Site	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	5199102	159756556	31397720	29	9277											
LIFR	3977	hgsc.bcm.edu	37	chr5	38489203	38489203	+	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	attctaaaaccctcatcttaGatgtgtctctttctcctttt	8	19	3	11	0	5	1	1	0	4	1	7	1	5	1	2	0	1	0	2	0	3	6			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr5:38489203G>A	ENST00000263409.4	-	16	2474	c.2312C>T	c.(2311-2313)tCt>tTt	p.S771F	LIFR_ENST00000503088.1_5'Flank|LIFR_ENST00000453190.2_Missense_Mutation_p.S771F	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	771	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)					CCTCATCTTAGATGTGTCTCT	0.343			T	PLAG1	salivary adenoma																																p.S771F	Melanoma(13;4 730 6426 9861 34751)	Atlas-SNP	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	.	LIFR	348	.	0			c.C2312T						PASS	.						80	84	83					5																	38489203		2203	4300	6503	SO:0001583	missense	3977	exon16			ATCTTAGATGTGT	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.2312C>T	chr5.hg19:g.38489203G>A	ENSP00000263409:p.Ser771Phe	96.0	0.0	.		109.0	26.0	.	NM_002310	Q6LCD9	Missense_Mutation	SNP	ENST00000263409.4	hg19	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	G	12.77	2.037720	0.35989	.	.	ENSG00000113594	ENST00000263409;ENST00000453190	T;T	0.53423	0.62;0.62	5.78	4.92	0.64577	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.715180	0.14869	N	0.293661	T	0.46367	0.1389	M	0.76838	2.35	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.46624	-0.9178	10	0.09084	T	0.74	-6.9518	11.4001	0.49864	0.1549:0.0:0.8451:0.0	.	771	P42702	LIFR_HUMAN	F	771	ENSP00000263409:S771F;ENSP00000398368:S771F	ENSP00000263409:S771F	S	-	2	0	LIFR	38524960	0.985000	0.35326	0.823000	0.32752	0.952000	0.60782	2.593000	0.46180	1.456000	0.47831	0.650000	0.86243	TCT	.	.	.	none		0.343	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310		A	38489203	G	A	38489203	3	1	157	1	0	0	0	0	1	0	0	0	8787	942	33	2	1001	2	LIFR	5	38489203	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08		38489203	142426057	30	9278											
PCDHGC4	56098	hgsc.bcm.edu	37	chr5	140864817	140864817	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctcttttaccacctgggttAcgtttgtgggcagatccgct	5	14	10	12	2	1	1	0	0	1	1	2	1	2	1	4	2	2	4	4	2	2	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr5:140864817A>G	ENST00000306593.1	+	1	77	c.77A>G	c.(76-78)tAc>tGc	p.Y26C	PCDHGA12_ENST00000252085.3_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron	NM_018928.2|NM_032406.1	NP_061751.1|NP_115782.1	Q9Y5F7	PCDGL_HUMAN	protocadherin gamma subfamily C, 4	26					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(13)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	42			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CACCTGGGTTACGTTTGTGGG	0.542																																					p.Y26C		Atlas-SNP	.											.	PCDHGC4	91	.	0			c.A77G						PASS	.						61	64	63					5																	140864817		2203	4300	6503	SO:0001583	missense	56098	exon1			TGGGTTACGTTTG	AF152525	CCDS4262.1, CCDS75349.1	5q31	2010-01-26			ENSG00000242419	ENSG00000242419		"Cadherins / Protocadherins : Clustered"	8717	other	protocadherin		606305				10380929	Standard	NM_018928		Approved	PCDH-GAMMA-C4		Q9Y5F7	OTTHUMG00000129625	ENST00000306593.1:c.77A>G	chr5.hg19:g.140864817A>G	ENSP00000306918:p.Tyr26Cys	117.0	0.0	.		86.0	15.0	.	NM_018928	Q495T2|Q9Y5C3	Missense_Mutation	SNP	ENST00000306593.1	hg19	CCDS4262.1	.	.	.	.	.	.	.	.	.	.	A	8.646	0.897050	0.17686	.	.	ENSG00000242419	ENST00000306593	T	0.46819	0.86	4.81	4.81	0.61882	.	.	.	.	.	T	0.26557	0.0649	N	0.08118	0	0.09310	N	1	B;B	0.16396	0.017;0.001	B;B	0.16722	0.016;0.004	T	0.07888	-1.0749	9	0.38643	T	0.18	.	6.6967	0.23203	0.6868:0.231:0.0822:0.0	.	26;26	Q9Y5F7-2;Q9Y5F7	.;PCDGL_HUMAN	C	26	ENSP00000306918:Y26C	ENSP00000306918:Y26C	Y	+	2	0	PCDHGC4	140845001	0.831000	0.29352	0.975000	0.42487	0.979000	0.70002	2.204000	0.42761	2.012000	0.59069	0.459000	0.35465	TAC	.	.	.	none		0.542	PCDHGC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251820.1	NM_018928		G	140864817	A	G	140864817	3	3	157	1	0	0	0	0	1	0	0	0	11577	391	14	3	79	3	PCDHGC4	5	140864817	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	102375614	140864817	40050443	31	9279											
SYNPO	11346	hgsc.bcm.edu	37	chr5	150027927	150027927	+	Frame_Shift_Del	DEL	A	A	-																															gtaccactggtggtttatctAaaggagaatgcagcactgct																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr5:150027927delA	ENST00000394243.1	+	3	1196	c.822delA	c.(820-822)ctafs	p.L274fs	SYNPO_ENST00000519664.1_Frame_Shift_Del_p.L30fs|SYNPO_ENST00000307662.4_Frame_Shift_Del_p.L30fs|SYNPO_ENST00000518872.1_Intron|SYNPO_ENST00000522122.1_Frame_Shift_Del_p.L274fs	NM_001166208.1	NP_001159680.1	Q8N3V7	SYNPO_HUMAN	synaptopodin	274					positive regulation of actin filament bundle assembly (GO:0032233)|regulation of stress fiber assembly (GO:0051492)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic membrane (GO:0045211)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin binding (GO:0003779)			NS(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(4)|prostate(1)|urinary_tract(2)	18		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGGTTTATCTAAAGGAGAATG	0.602																																					p.L274fs		Atlas-INDEL	.											.	SYNPO	147	.	0			c.821delT						PASS	.						82	91	88					5																	150027927		2203	4300	6503	SO:0001589	frameshift_variant	11346	exon3			.	AF499137	CCDS4308.1, CCDS54937.1, CCDS54938.1	5q33.1	2008-02-05			ENSG00000171992	ENSG00000171992			30672	protein-coding gene	gene with protein product		608155				9314539, 10470851	Standard	NM_007286		Approved	KIAA1029	uc003lsn.3	Q8N3V7	OTTHUMG00000130078	ENST00000394243.1:c.822delA	chr5.hg19:g.150027927delA	ENSP00000377789:p.Leu274fs	135.0	0.0	0		92.0	24.0	0.26087	NM_001166209	A5PKZ8|D3DQG8|O15271|Q9UPX1	Frame_Shift_Del	DEL	ENST00000394243.1	hg19	CCDS54937.1																																																																																			.	.	.	none		0.602	SYNPO-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252371.1	NM_007286		-	150027927	A	-	150027927	7	5	157	1	0	1	0	1	0	0	0	0	15468	349	13	0	828	0	SYNPO	5	150027927	Frame_Shift_Del	DEL	A	TCGA-DZ-6132-01A-11D-1961-08	9163110	150027927	30887333	32	9280											
OR2J3	442186	hgsc.bcm.edu	37	chr6	29079815	29079815	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taggaaacctgttcatcatcAtcctgtcatacctggactcc	10	12	6	13	0	4	0	4	0	0	0	6	2	6	2	4	2	2	1	4	2	3	3			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr6:29079815A>G	ENST00000377169.1	+	1	148	c.148A>G	c.(148-150)Atc>Gtc	p.I50V		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	50						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						GTTCATCATCATCCTGTCATA	0.423																																					p.I50V		Atlas-SNP	.											.	OR2J3	53	.	0			c.A148G						PASS	.						291	305	300					6																	29079815		1349	2628	3977	SO:0001583	missense	442186	exon1			ATCATCATCCTGT		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.148A>G	chr6.hg19:g.29079815A>G	ENSP00000366374:p.Ile50Val	337.0	0.0	.		269.0	53.0	.	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Missense_Mutation	SNP	ENST00000377169.1	hg19	CCDS43433.1	.	.	.	.	.	.	.	.	.	.	A	2.071	-0.413113	0.04799	.	.	ENSG00000204701	ENST00000377169	T	0.03889	3.77	2.78	1.58	0.23477	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00784	0.0026	N	0.05414	-0.055	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.48080	-0.9066	9	0.48119	T	0.1	.	4.2981	0.10911	0.682:0.2023:0.1157:0.0	.	50	O76001	OR2J3_HUMAN	V	50	ENSP00000366374:I50V	ENSP00000366374:I50V	I	+	1	0	OR2J3	29187794	0.000000	0.05858	0.992000	0.48379	0.314000	0.28054	-0.814000	0.04486	0.295000	0.22570	0.358000	0.22013	ATC	.	.	.	none		0.423	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2			G	29079815	A	G	29079815	3	3	157	1	0	0	0	0	1	0	0	0	11011	217	8	3	150	3	OR2J3	6	29079815	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08		29079815	142035252	33	9281											
ZBTB22	9278	hgsc.bcm.edu	37	chr6	33284668	33284668	+	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	gcaggggaagtgctgccccaCtgggagacagaggagatggc	10	4	18	9	0	0	3	0	0	0	3	0	6	0	4	2	5	2	2	2	5	1	0			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr6:33284668C>T	ENST00000431845.2	-	2	177	c.26G>A	c.(25-27)aGt>aAt	p.S9N	TAPBP_ENST00000489157.1_5'Flank|DAXX_ENST00000477162.1_5'Flank|ZBTB22_ENST00000418724.1_Missense_Mutation_p.S9N|TAPBP_ENST00000456592.2_5'Flank|TAPBP_ENST00000426633.2_5'Flank|TAPBP_ENST00000434618.2_5'Flank|TAPBP_ENST00000475304.1_5'Flank	NM_005453.4	NP_005444.4	O15209	ZBT22_HUMAN	zinc finger and BTB domain containing 22	9					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						TGCTGCCCCACTGGGAGACAG	0.657																																					p.S9N		Atlas-SNP	.											.	ZBTB22	48	.	0			c.G26A						PASS	.						18	22	21					6																	33284668		2202	4295	6497	SO:0001583	missense	9278	exon2			GCCCCACTGGGAG	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.26G>A	chr6.hg19:g.33284668C>T	ENSP00000407545:p.Ser9Asn	82.0	0.0	.		47.0	10.0	.	NM_001145338	B0V007|Q5HYV4|Q5STL0|Q5STR7|Q8WV82	Missense_Mutation	SNP	ENST00000431845.2	hg19	CCDS4775.1	.	.	.	.	.	.	.	.	.	.	C	12.63	1.996665	0.35226	.	.	ENSG00000236104	ENST00000418724;ENST00000431845;ENST00000441117	T;T;T	0.64803	3.38;3.38;-0.12	4.68	2.67	0.31697	.	.	.	.	.	T	0.17831	0.0428	N	0.08118	0	0.26387	N	0.976649	B	0.16166	0.016	B	0.14578	0.011	T	0.11567	-1.0582	9	0.38643	T	0.18	.	4.8891	0.13717	0.0:0.6566:0.2229:0.1205	.	9	O15209	ZBT22_HUMAN	N	9	ENSP00000404403:S9N;ENSP00000407545:S9N;ENSP00000413172:S9N	ENSP00000404403:S9N	S	-	2	0	ZBTB22	33392646	0.013000	0.17824	1.000000	0.80357	0.995000	0.86356	1.367000	0.34204	1.172000	0.42781	0.638000	0.83543	AGT	.	.	.	none		0.657	ZBTB22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076183.2			T	33284668	C	T	33284668	3	4	157	1	0	0	0	0	1	0	0	0	17542	565	20	2	1882	2	ZBTB22	6	33284668	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	4204853	33284668	137830399	34	9282											
UBR2	23304	hgsc.bcm.edu	37	chr6	42559909	42559909	+	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	agactgtgcagttgatccaaCttgtgttttgtgcatggagt	8	15	12	6	0	0	2	0	1	0	1	1	3	1	3	1	1	3	4	1	1	1	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr6:42559909C>G	ENST00000372899.1	+	3	617	c.359C>G	c.(358-360)aCt>aGt	p.T120S	UBR2_ENST00000372901.1_Missense_Mutation_p.T120S|UBR2_ENST00000372903.2_Missense_Mutation_p.T120S	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	120					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)			GTTGATCCAACTTGTGTTTTG	0.323																																					p.T120S		Atlas-SNP	.											.	UBR2	134	.	0			c.C359G						PASS	.						112	101	105					6																	42559909		2203	4300	6503	SO:0001583	missense	23304	exon3			ATCCAACTTGTGT	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.359C>G	chr6.hg19:g.42559909C>G	ENSP00000361990:p.Thr120Ser	89.0	0.0	.		78.0	11.0	.	NM_001184801	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	hg19	CCDS4870.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.730359	0.89390	.	.	ENSG00000024048	ENST00000372903;ENST00000372899;ENST00000372901	D;D;D	0.82255	-1.59;-1.59;-1.59	5.24	5.24	0.73138	Zinc finger, N-recognin, metazoa (1);Zinc finger, N-recognin (2);	0.000000	0.85682	D	0.000000	D	0.88887	0.6559	M	0.73319	2.225	0.80722	D	1	D;D	0.76494	0.999;0.992	D;P	0.81914	0.995;0.894	D	0.87768	0.2603	10	0.41790	T	0.15	-11.9828	18.4238	0.90602	0.0:1.0:0.0:0.0	.	120;120	Q8IWV8;Q8IWV8-2	UBR2_HUMAN;.	S	120	ENSP00000361994:T120S;ENSP00000361990:T120S;ENSP00000361992:T120S	ENSP00000361990:T120S	T	+	2	0	UBR2	42667887	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.756000	0.74919	2.459000	0.83118	0.655000	0.94253	ACT	.	.	.	none		0.323	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255		G	42559909	C	G	42559909	3	3	157	1	0	0	0	0	1	0	0	0	16914	565	20	4	369	4	UBR2	6	42559909	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	9275241	42559909	128555158	35	9283											
SLC35B2	347734	hgsc.bcm.edu	37	chr6	44222677	44222677	+	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	aactgcccaatggtgtaaaaGatgaagagctggccacatgc	14	7	11	9	0	0	3	0	1	0	2	0	3	0	3	2	2	4	2	2	2	5	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr6:44222677G>C	ENST00000393812.3	-	4	1208	c.1065C>G	c.(1063-1065)atC>atG	p.I355M	SLC35B2_ENST00000495706.1_5'UTR|MIR4647_ENST00000583964.1_RNA|SLC35B2_ENST00000393810.1_3'UTR|SLC35B2_ENST00000538577.1_Missense_Mutation_p.I262M|SLC35B2_ENST00000537814.1_Missense_Mutation_p.I222M	NM_178148.2	NP_835361.1	Q8TB61	S35B2_HUMAN	solute carrier family 35 (adenosine 3'-phospho 5'-phosphosulfate transporter), member B2	355					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)			TGGTGTAAAAGATGAAGAGCT	0.577																																					p.I355M		Atlas-SNP	.											.	SLC35B2	40	.	0			c.C1065G						PASS	.						59	52	54					6																	44222677		2203	4300	6503	SO:0001583	missense	347734	exon4			GTAAAAGATGAAG	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.1065C>G	chr6.hg19:g.44222677G>C	ENSP00000377401:p.Ile355Met	47.0	0.0	.		29.0	6.0	.	NM_178148	B4DDU9|F5H7Y9|Q2VY06|Q53GA3|Q5T9W1|Q5T9W2|Q7Z2G3|Q8NBK6|Q96AR6	Missense_Mutation	SNP	ENST00000393812.3	hg19	CCDS34462.1	.	.	.	.	.	.	.	.	.	.	g	16.92	3.256373	0.59321	.	.	ENSG00000157593	ENST00000393812;ENST00000537814;ENST00000538577;ENST00000341553	T;T;T	0.40476	1.03;1.03;1.03	5.0	2.85	0.33270	.	0.000000	0.85682	D	0.000000	T	0.67031	0.2850	H	0.96460	3.825	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	T	0.77838	-0.2439	10	0.87932	D	0	-30.6983	12.2066	0.54355	0.1659:0.0:0.8341:0.0	.	262;355	F5H7Y9;Q8TB61	.;S35B2_HUMAN	M	355;222;262;315	ENSP00000377401:I355M;ENSP00000440340:I222M;ENSP00000443845:I262M	ENSP00000342455:I315M	I	-	3	3	SLC35B2	44330655	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	2.845000	0.48254	1.121000	0.41925	0.540000	0.68198	ATC	.	.	.	none		0.577	SLC35B2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040724.2			C	44222677	G	C	44222677	3	2	157	1	0	0	0	0	1	0	0	0	14589	932	33	4	237	4	SLC35B2	6	44222677	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	1662768	44222677	126892390	36	9284											
TPST1	8460	hgsc.bcm.edu	37	chr7	65705725	65705725	+	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	gagaggaaaccagggtcattCcccgaatcctggccctgaag	11	6	12	12	1	1	2	1	1	0	1	3	5	3	3	5	3	1	0	5	3	3	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr7:65705725C>A	ENST00000304842.5	+	2	738	c.313C>A	c.(313-315)Ccc>Acc	p.P105T	TPST1_ENST00000480281.1_Intron	NM_003596.3	NP_003587.1	O60507	TPST1_HUMAN	tyrosylprotein sulfotransferase 1	105					inflammatory response (GO:0006954)|peptidyl-tyrosine sulfation (GO:0006478)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein-tyrosine sulfotransferase activity (GO:0008476)			NS(1)|biliary_tract(1)|breast(1)|kidney(3)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	11						CAGGGTCATTCCCCGAATCCT	0.527																																					p.P105T		Atlas-SNP	.											.	TPST1	25	.	0			c.C313A						PASS	.						96	93	94					7																	65705725		2203	4300	6503	SO:0001583	missense	8460	exon2			GTCATTCCCCGAA	AF038009	CCDS5533.1	7q11.21	2012-12-13			ENSG00000169902	ENSG00000169902	2.8.2.20	"Sulfotransferases, membrane-bound"	12020	protein-coding gene	gene with protein product	"transport and golgi organization 13 homolog A (Drosophila)"	603125				9501187	Standard	NM_003596		Approved	TANGO13A	uc003tuw.3	O60507	OTTHUMG00000023871	ENST00000304842.5:c.313C>A	chr7.hg19:g.65705725C>A	ENSP00000302413:p.Pro105Thr	74.0	0.0	.		96.0	39.0	.	NM_003596	A4D2M0|Q6FGM7	Missense_Mutation	SNP	ENST00000304842.5	hg19	CCDS5533.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.574392	0.86542	.	.	ENSG00000169902	ENST00000304842;ENST00000544114;ENST00000451388	T;T	0.41065	1.01;1.01	5.78	5.78	0.91487	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	T	0.72334	0.3447	M	0.89658	3.05	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.80764	0.986;0.994	T	0.76498	-0.2937	10	0.56958	D	0.05	-14.1045	19.0054	0.92848	0.0:1.0:0.0:0.0	.	105;105	F5H7U7;O60507	.;TPST1_HUMAN	T	105	ENSP00000302413:P105T;ENSP00000391338:P105T	ENSP00000302413:P105T	P	+	1	0	TPST1	65343160	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.950000	0.75977	2.723000	0.93209	0.585000	0.79938	CCC	.	.	.	none		0.527	TPST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251705.2	NM_003596		A	65705725	C	A	65705725	3	1	157	1	0	0	0	0	1	0	0	0	16439	855	30	4	315	4	TPST1	7	65705725	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08		65705725	93432938	37	9285											
ELN	2006	hgsc.bcm.edu	37	chr7	73474279	73474279	+	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	tcctggtgtcggtgtggctcCtggagttggcttggctcctg	1	14	16	10	1	0	0	0	0	0	0	4	1	3	1	3	6	0	4	3	6	0	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr7:73474279C>T	ENST00000252034.7	+	23	1877	c.1478C>T	c.(1477-1479)cCt>cTt	p.P493L	ELN_ENST00000357036.5_Missense_Mutation_p.P498L|ELN_ENST00000380553.4_Missense_Mutation_p.P357L|ELN_ENST00000414324.1_Missense_Mutation_p.P469L|ELN_ENST00000380584.4_Missense_Mutation_p.P460L|ELN_ENST00000380575.4_Missense_Mutation_p.P464L|ELN_ENST00000380562.4_Missense_Mutation_p.P499L|ELN_ENST00000429192.1_Missense_Mutation_p.P479L|CTB-51J22.1_ENST00000435932.1_RNA|ELN_ENST00000445912.1_Missense_Mutation_p.P493L|ELN_ENST00000320492.7_Missense_Mutation_p.P412L|ELN_ENST00000358929.4_Missense_Mutation_p.P528L|ELN_ENST00000380576.5_Missense_Mutation_p.P474L|ELN_ENST00000320399.6_Missense_Mutation_p.P493L|ELN_ENST00000458204.1_Missense_Mutation_p.P483L	NM_000501.2|NM_001278915.1	NP_000492.2|NP_001265844.1	P15502	ELN_HUMAN	elastin	0	Ala-rich.				blood circulation (GO:0008015)|blood vessel remodeling (GO:0001974)|cell proliferation (GO:0008283)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|organ morphogenesis (GO:0009887)|regulation of actin filament polymerization (GO:0030833)|respiratory gaseous exchange (GO:0007585)|skeletal muscle tissue development (GO:0007519)|stress fiber assembly (GO:0043149)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(4)|pancreas(2)|prostate(1)|skin(2)|stomach(1)	32		Lung NSC(55;0.159)				GGTGTGGCTCCTGGAGTTGGC	0.612			T	PAX5	B-ALL		"Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome"																														p.P498L		Atlas-SNP	.		Dom	yes		7	7q11.23	2006	elastin	yes	L	.	ELN	81	.	0			c.C1493T						PASS	.						205	192	196					7																	73474279		2203	4300	6503	SO:0001583	missense	2006	exon23			TGGCTCCTGGAGT		CCDS5562.2, CCDS43598.1, CCDS43599.1, CCDS47611.1, CCDS47612.1, CCDS64673.1, CCDS64674.1, CCDS64675.1, CCDS64676.1, CCDS64677.1, CCDS64678.1, CCDS75616.1, CCDS75617.1	7q11.1-q21.1	2008-08-01	2008-08-01		ENSG00000049540	ENSG00000049540			3327	protein-coding gene	gene with protein product	"tropoelastin", "supravalvular aortic stenosis", "Williams-Beuren syndrome"	130160				8096434	Standard	NM_001278939		Approved	WBS, WS, SVAS	uc003tzn.3	P15502	OTTHUMG00000150229	ENST00000252034.7:c.1478C>T	chr7.hg19:g.73474279C>T	ENSP00000252034:p.Pro493Leu	408.0	1.0	.		376.0	128.0	.	NM_001081754	B3KTS6|O15336|O15337|Q14233|Q14234|Q14235|Q14238|Q6P0L4|Q6ZWJ6|Q75MU5|Q7Z316|Q7Z3F5|Q9UMF5	Missense_Mutation	SNP	ENST00000252034.7	hg19	CCDS5562.2	.	.	.	.	.	.	.	.	.	.	C	14.98	2.695839	0.48202	.	.	ENSG00000049540	ENST00000445912;ENST00000252034;ENST00000358929;ENST00000320492;ENST00000414324;ENST00000380562;ENST00000380575;ENST00000380584;ENST00000458204;ENST00000357036;ENST00000429192;ENST00000380553;ENST00000380576;ENST00000320399	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.44482	1.42;1.35;1.26;1.39;0.95;1.27;0.92;1.18;1.41;1.4;0.95;1.07;1.0;1.38	2.86	2.86	0.33363	.	.	.	.	.	T	0.41119	0.1145	.	.	.	0.80722	D	1	P;P;P;P;P;P;P;P;P;P;P;P;P	0.51351	0.573;0.573;0.573;0.573;0.573;0.573;0.573;0.573;0.573;0.944;0.573;0.573;0.573	B;B;B;B;B;B;B;B;B;P;B;B;B	0.44811	0.199;0.199;0.199;0.199;0.199;0.199;0.199;0.199;0.199;0.461;0.199;0.199;0.199	T	0.47302	-0.9128	8	0.62326	D	0.03	.	11.5518	0.50725	0.0:1.0:0.0:0.0	.	493;412;469;483;499;464;479;498;474;357;404;460;493	E7ENM0;G5E950;G3V0G6;E7EN65;P15502-1;P15502-7;P15502-12;P15502-5;P15502-13;P15502-11;B3KRT8;P15502-8;P15502-2	.;.;.;.;.;.;.;.;.;.;.;.;.	L	493;493;528;412;469;499;464;460;483;498;479;357;474;493	ENSP00000389857:P493L;ENSP00000252034:P493L;ENSP00000351807:P528L;ENSP00000315607:P412L;ENSP00000392575:P469L;ENSP00000369936:P499L;ENSP00000369949:P464L;ENSP00000369958:P460L;ENSP00000403162:P483L;ENSP00000349540:P498L;ENSP00000391129:P479L;ENSP00000369926:P357L;ENSP00000369950:P474L;ENSP00000313565:P493L	ENSP00000252034:P493L	P	+	2	0	ELN	73112215	0.159000	0.22864	0.014000	0.15608	0.005000	0.04900	3.649000	0.54417	1.625000	0.50366	0.555000	0.69702	CCT	.	.	.	none		0.612	ELN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316913.1	NM_000501		T	73474279	C	T	73474279	3	4	157	1	0	0	0	0	1	0	0	0	5073	681	24	2	1583	2	ELN	7	73474279	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	7768554	73474279	85664384	38	9286											
DLD	1738	hgsc.bcm.edu	37	chr7	107542828	107542828	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgcttgaatgttggttgtaTtccttctaaggtgagcatgt	8	17	11	5	0	1	2	0	2	1	0	2	2	2	2	1	2	2	5	1	2	3	7			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr7:107542828T>C	ENST00000205402.5	+	4	538	c.257T>C	c.(256-258)aTt>aCt	p.I86T	DLD_ENST00000494441.1_3'UTR|DLD_ENST00000537148.1_Intron|DLD_ENST00000440410.1_Intron|DLD_ENST00000437604.2_Missense_Mutation_p.I86T	NM_000108.3	NP_000099.2	P09622	DLDH_HUMAN	dihydrolipoamide dehydrogenase	86					branched-chain amino acid catabolic process (GO:0009083)|cell redox homeostasis (GO:0045454)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|gastrulation (GO:0007369)|lysine catabolic process (GO:0006554)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|proteolysis (GO:0006508)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of membrane potential (GO:0042391)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|tricarboxylic acid cycle (GO:0006099)	acrosomal matrix (GO:0043159)|cilium (GO:0005929)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dihydrolipoyl dehydrogenase activity (GO:0004148)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(1)|lung(10)|prostate(1)	20					Flavin adenine dinucleotide(DB03147)	GTTGGTTGTATTCCTTCTAAG	0.368																																					p.I86T		Atlas-SNP	.											.	DLD	72	.	0			c.T257C						PASS	.						295	259	271					7																	107542828		2203	4300	6503	SO:0001583	missense	1738	exon4			GTTGTATTCCTTC	AB209703	CCDS5749.1	7q31-q32	2006-05-22	2006-05-22		ENSG00000091140	ENSG00000091140	1.8.1.4		2898	protein-coding gene	gene with protein product	"E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex"	238331	"dihydrolipoamide dehydrogenase (E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex)"	LAD, GCSL			Standard	NM_000108		Approved	DLDH	uc003vet.3	P09622	OTTHUMG00000154813	ENST00000205402.5:c.257T>C	chr7.hg19:g.107542828T>C	ENSP00000205402:p.Ile86Thr	75.0	0.0	.		97.0	31.0	.	NM_000108	B2R5X0|B4DHG0|B4DT69|Q14131|Q14167|Q59EV8|Q8WTS4	Missense_Mutation	SNP	ENST00000205402.5	hg19	CCDS5749.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.430417	0.83776	.	.	ENSG00000091140	ENST00000205402;ENST00000417551;ENST00000437604;ENST00000539590	T;T;T	0.56103	0.48;0.48;0.48	6.17	6.17	0.99709	Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.82365	0.5021	H	0.96691	3.865	0.80722	D	1	P;D	0.54397	0.945;0.966	D;D	0.83275	0.955;0.996	D	0.87980	0.2742	10	0.87932	D	0	-11.8281	16.0034	0.80327	0.0:0.0:0.0:1.0	.	86;86	B4DT69;P09622	.;DLDH_HUMAN	T	86;86;86;36	ENSP00000205402:I86T;ENSP00000390667:I86T;ENSP00000387542:I86T	ENSP00000205402:I86T	I	+	2	0	DLD	107330064	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.900000	0.75687	2.371000	0.80710	0.533000	0.62120	ATT	.	.	.	none		0.368	DLD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337194.3	NM_000108		C	107542828	T	C	107542828	3	2	157	1	0	0	0	0	1	0	0	0	4553	1493	52	3	271	3	DLD	7	107542828	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08	34068549	107542828	51595835	39	9287											
MET	4233	hgsc.bcm.edu	37	chr7	116417457	116417457	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcacagggcattttggttgtGtatatcatgggactttgttg	7	16	13	5	0	1	0	1	0	0	0	1	1	1	1	0	3	0	5	0	3	2	7			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr7:116417457G>A	ENST00000318493.6	+	16	3515	c.3328G>A	c.(3328-3330)Gta>Ata	p.V1110I	MET_ENST00000397752.3_Missense_Mutation_p.V1092I|MET_ENST00000539704.1_5'UTR			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)			TTTTGGTTGTGTATATCATGG	0.338			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.V1110I		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.G3328A	GRCh37	CM990852	MET	M		PASS	.						191	176	180					7																	116417457		1827	4084	5911	SO:0001583	missense	4233	exon16	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	GGTTGTGTATATC	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.3328G>A	chr7.hg19:g.116417457G>A	ENSP00000317272:p.Val1110Ile	158.0	0.0	.		223.0	26.0	.	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.834124	0.91036	.	.	ENSG00000105976	ENST00000397752;ENST00000318493	T;T	0.64991	-0.13;-0.13	5.16	5.16	0.70880	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.81178	0.4768	M	0.80422	2.495	0.80722	D	1	D;D	0.76494	0.999;0.99	D;D	0.85130	0.997;0.99	D	0.83726	0.0195	10	0.87932	D	0	.	19.0107	0.92871	0.0:0.0:1.0:0.0	.	1110;1092	P08581-2;P08581	.;MET_HUMAN	I	1092;1110	ENSP00000380860:V1092I;ENSP00000317272:V1110I	ENSP00000317272:V1110I	V	+	1	0	MET	116204693	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	9.813000	0.99286	2.560000	0.86352	0.563000	0.77884	GTA	.	.	.	none		0.338	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			A	116417457	G	A	116417457	3	1	157	1	0	0	0	0	1	0	0	0	9492	1377	48	2	3386	2	MET	7	116417457	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	8874629	116417457	42721206	40	9288											
FAM40B	57464	hgsc.bcm.edu	37	chr7	129120722	129120722	+	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	tgaccaaatggaaacattccCggaccatggtgagtgtggtt	11	10	12	8	1	0	2	0	2	0	0	1	4	1	4	3	4	1	1	3	4	2	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr7:129120722C>A	ENST00000249344.2	+	19	2081	c.2041C>A	c.(2041-2043)Cgg>Agg	p.R681R	STRIP2_ENST00000435494.2_Silent_p.R681R	NM_020704.2	NP_065755.1	Q9ULQ0	STRP2_HUMAN	striatin interacting protein 2	681					cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)		p.R681R(1)|p.R681W(1)									GAAACATTCCCGGACCATGGT	0.428																																					p.R681R		Atlas-SNP	.											FAM40B,NS,carcinoma,0,1	.	.	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	lung(2)	c.C2041A						PASS	.						141	122	128					7																	129120722		2203	4300	6503	SO:0001819	synonymous_variant	57464	exon19			CATTCCCGGACCA	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.2041C>A	chr7.hg19:g.129120722C>A		118.0	0.0	.		102.0	6.0	.	NM_020704	Q8WUZ4	Silent	SNP	ENST00000249344.2	hg19	CCDS34752.1																																																																																			.	.	.	none		0.428	STRIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349418.1	NM_001134336		A	129120722	C	A	129120722	2	1	157	1	0	0	0	0	0	0	0	1	5568	643	23	4		4	FAM40B	7	129120722	Silent	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	12703265	129120722	30017941	41	9289											
MCPH1	79648	hgsc.bcm.edu	37	chr8	6302563	6302563	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctgccatcaagccctgcTcagttgagctgcagaagtct	9	9	10	13	0	3	2	2	1	1	1	3	2	3	2	2	0	6	5	2	0	2	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr8:6302563T>C	ENST00000344683.5	+	8	1396	c.1320T>C	c.(1318-1320)gcT>gcC	p.A440A	MCPH1_ENST00000522905.1_Silent_p.A392A|MCPH1_ENST00000519480.1_Silent_p.A440A	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	440					cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)		AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		CAAGCCCTGCTCAGTTGAGCT	0.403																																					p.A440A	Colon(95;1448 1467 8277 34473 35819)	Atlas-SNP	.											.	MCPH1	65	.	0			c.T1320C						PASS	.						90	88	89					8																	6302563		1903	4122	6025	SO:0001819	synonymous_variant	79648	exon8			CCCTGCTCAGTTG	AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"BRCT-repeat inhibitor of TERT expression 1"	607117	"microcephaly, primary autosomal recessive 1"			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.1320T>C	chr8.hg19:g.6302563T>C		117.0	0.0	.		120.0	18.0	.	NM_001172574	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Silent	SNP	ENST00000344683.5	hg19	CCDS43689.1																																																																																			.	.	.	none		0.403	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596		C	6302563	T	C	6302563	2	2	157	1	0	0	0	0	0	0	0	1	9405	1538	54	3		3	MCPH1	8	6302563	Silent	SNP	T	TCGA-DZ-6132-01A-11D-1961-08		6302563	140061459	42	9290											
ST18	9705	hgsc.bcm.edu	37	chr8	53092686	53092686	+	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	ctctcctccttgctacctgcGgtagagtgaccatgtgtttc	5	14	9	13	1	1	2	0	1	1	1	4	2	2	2	4	1	3	3	4	1	2	4	rs137908806		TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr8:53092686G>T	ENST00000276480.7	-	9	956	c.273C>A	c.(271-273)acC>acA	p.T91T		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	91					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				TGCTACCTGCGGTAGAGTGAC	0.517																																					p.T91T		Atlas-SNP	.											ST18,NS,carcinoma,0,1	ST18	212	.	0			c.C273A						PASS	.						258	210	226					8																	53092686		2203	4300	6503	SO:0001819	synonymous_variant	9705	exon9			ACCTGCGGTAGAG	AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"Zinc fingers, C2HC-type containing"	18695	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 3"		"zinc finger protein 387", "suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.273C>A	chr8.hg19:g.53092686G>T		268.0	0.0	.		248.0	13.0	.	NM_014682	Q17RY1	Silent	SNP	ENST00000276480.7	hg19	CCDS6149.1																																																																																			.	G|1.000;A|0.000	.	alt		0.517	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1			T	53092686	G	T	53092686	2	4	157	1	0	0	0	0	0	0	0	1	15224	1103	39	4		4	ST18	8	53092686	Silent	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	46790123	53092686	93271336	43	9291											
ADCY8	114	hgsc.bcm.edu	37	chr8	131921969	131921969	+	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	cttacccagggattcctccaGattcgagtttgtttgcaata	9	14	8	10	1	0	1	0	0	0	1	3	3	2	2	3	1	2	3	3	1	3	6	rs368729916		TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr8:131921969G>C	ENST00000286355.5	-	6	3717	c.1625C>G	c.(1624-1626)tCt>tGt	p.S542C	ADCY8_ENST00000377928.3_Missense_Mutation_p.S542C	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	542					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			GATTCCTCCAGATTCGAGTTT	0.463										HNSCC(32;0.087)																											p.S542C		Atlas-SNP	.											.	ADCY8	291	.	0			c.C1625G						PASS	.	G	CYS/SER	1,4405	2.1+/-5.4	0,1,2202	242	216	225		1625	5.9	1	8		225	0,8600		0,0,4300	no	missense	ADCY8	NM_001115.2	112	0,1,6502	CC,CG,GG		0.0,0.0227,0.0077	probably-damaging	542/1252	131921969	1,13005	2203	4300	6503	SO:0001583	missense	114	exon6			CCTCCAGATTCGA	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.1625C>G	chr8.hg19:g.131921969G>C	ENSP00000286355:p.Ser542Cys	372.0	0.0	.		337.0	67.0	.	NM_001115		Missense_Mutation	SNP	ENST00000286355.5	hg19	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	G	31	5.072076	0.93950	2.27E-4	0.0	ENSG00000155897	ENST00000286355;ENST00000377928;ENST00000522949	D;D;D	0.87029	-2.2;-2.2;-2.2	5.93	5.93	0.95920	Adenylyl cyclase class-3/4/guanylyl cyclase (4);	0.052374	0.85682	D	0.000000	D	0.96423	0.8833	H	0.98276	4.19	0.49483	D	0.999792	D;D	0.69078	0.995;0.997	D;D	0.68353	0.957;0.953	D	0.97510	1.0066	10	0.87932	D	0	.	19.3421	0.94347	0.0:0.0:1.0:0.0	.	542;542	E7EVL1;P40145	.;ADCY8_HUMAN	C	542;542;157	ENSP00000286355:S542C;ENSP00000367161:S542C;ENSP00000428010:S157C	ENSP00000286355:S542C	S	-	2	0	ADCY8	131991151	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.826000	0.97356	0.655000	0.94253	TCT	.	.	.	weak		0.463	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			C	131921969	G	C	131921969	3	2	157	1	0	0	0	0	1	0	0	0	300	942	33	4	2182	4	ADCY8	8	131921969	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	78829283	131921969	14442053	44	9292											
TEK	7010	hgsc.bcm.edu	37	chr9	27197591	27197591	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atctcactgcttggacccttAgtgacagtaagtaattcatg	11	13	8	9	0	2	1	2	1	1	0	3	2	2	2	1	1	1	3	1	1	3	5			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr9:27197591A>G	ENST00000380036.4	+	12	2345	c.1903A>G	c.(1903-1905)Agt>Ggt	p.S635G	TEK_ENST00000519097.1_Missense_Mutation_p.S488G|TEK_ENST00000406359.4_Missense_Mutation_p.S592G|RNA5SP280_ENST00000411230.1_RNA	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	635	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	TTGGACCCTTAGTGACAGTAA	0.493																																					p.S635G		Atlas-SNP	.											.	TEK	250	.	0			c.A1903G						PASS	.						39	40	40					9																	27197591		2203	4300	6503	SO:0001583	missense	7010	exon12			ACCCTTAGTGACA	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.1903A>G	chr9.hg19:g.27197591A>G	ENSP00000369375:p.Ser635Gly	44.0	0.0	.		38.0	8.0	.	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Missense_Mutation	SNP	ENST00000380036.4	hg19	CCDS6519.1	.	.	.	.	.	.	.	.	.	.	A	9.271	1.045584	0.19748	.	.	ENSG00000120156	ENST00000519097;ENST00000380036;ENST00000406359;ENST00000519080	T;T;T;T	0.53206	0.63;0.63;0.63;0.63	5.54	5.54	0.83059	Fibronectin, type III (1);	0.000000	0.64402	D	0.000010	T	0.62816	0.2459	L	0.56769	1.78	0.51233	D	0.999913	B;P;D;B	0.63880	0.281;0.462;0.993;0.361	B;B;D;B	0.68192	0.056;0.141;0.956;0.081	T	0.58457	-0.7633	10	0.23302	T	0.38	.	15.6853	0.77405	1.0:0.0:0.0:0.0	.	488;668;592;635	E7EWI2;Q59HG2;B4DHD3;Q02763	.;.;.;TIE2_HUMAN	G	488;635;592;445	ENSP00000430686:S488G;ENSP00000369375:S635G;ENSP00000383977:S592G;ENSP00000428337:S445G	ENSP00000369375:S635G	S	+	1	0	TEK	27187591	0.999000	0.42202	0.744000	0.31058	0.104000	0.19210	4.662000	0.61525	2.117000	0.64856	0.533000	0.62120	AGT	.	.	.	none		0.493	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3			G	27197591	A	G	27197591	3	3	157	1	0	0	0	0	1	0	0	0	15763	420	15	3	1949	3	TEK	9	27197591	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08		27197591	114015840	45	9293											
ZCCHC6	79670	hgsc.bcm.edu	37	chr9	88943326	88943326	+	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	tgtgtcccctgcagcactgtCagtatgttcccagatcacaa	9	11	8	13	0	2	1	2	0	0	1	4	1	4	1	3	0	2	4	3	0	2	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr9:88943326C>G	ENST00000375963.3	-	11	1709	c.1537G>C	c.(1537-1539)Gac>Cac	p.D513H	ZCCHC6_ENST00000375961.2_Missense_Mutation_p.D513H|ZCCHC6_ENST00000375960.2_Missense_Mutation_p.D390H|ZCCHC6_ENST00000277141.6_5'UTR	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	513					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						GCAGCACTGTCAGTATGTTCC	0.408																																					p.D513H		Atlas-SNP	.											.	ZCCHC6	105	.	0			c.G1537C						PASS	.						246	214	225					9																	88943326		2203	4300	6503	SO:0001583	missense	79670	exon11			CACTGTCAGTATG	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.1537G>C	chr9.hg19:g.88943326C>G	ENSP00000365130:p.Asp513His	253.0	0.0	.		232.0	48.0	.	NM_024617	Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	Missense_Mutation	SNP	ENST00000375963.3	hg19	CCDS35057.1	.	.	.	.	.	.	.	.	.	.	C	14.86	2.662242	0.47572	.	.	ENSG00000083223	ENST00000375960;ENST00000375961;ENST00000375963	T;T;T	0.46819	0.86;1.06;1.06	4.35	4.35	0.52113	.	0.478121	0.23602	N	0.046437	T	0.55162	0.1903	L	0.36672	1.1	0.19945	N	0.999947	D;D	0.69078	0.997;0.991	P;P	0.61132	0.884;0.769	T	0.49551	-0.8928	10	0.66056	D	0.02	-18.5595	15.1952	0.73081	0.0:1.0:0.0:0.0	.	390;513	Q5VYS8-4;Q5VYS8	.;TUT7_HUMAN	H	390;513;513	ENSP00000365127:D390H;ENSP00000365128:D513H;ENSP00000365130:D513H	ENSP00000365127:D390H	D	-	1	0	ZCCHC6	88133146	0.448000	0.25681	0.092000	0.20876	0.015000	0.08874	1.298000	0.33412	2.699000	0.92147	0.462000	0.41574	GAC	.	.	.	none		0.408	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1	NM_024617		G	88943326	C	G	88943326	3	3	157	1	0	0	0	0	1	0	0	0	17604	826	29	4	3018	4	ZCCHC6	9	88943326	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	61745735	88943326	52270105	46	9294											
ZFP37	7539	hgsc.bcm.edu	37	chr9	115806495	115806495	+	Frame_Shift_Del	DEL	G	G	-																															gactgcaacttccctgaggaGtttgttttgagatttctgga																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr9:115806495delG	ENST00000374227.3	-	4	430	c.403delC	c.(403-405)ctcfs	p.L136fs	ZFP37_ENST00000553380.1_Frame_Shift_Del_p.L151fs|ZFP37_ENST00000555206.1_Frame_Shift_Del_p.L137fs	NM_001282515.1|NM_001282518.1	NP_001269444.1|NP_001269447.1	Q9Y6Q3	ZFP37_HUMAN	ZFP37 zinc finger protein	136					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						TCCCTGAGGAGTTTGTTTTGA	0.353																																					p.L135fs		Atlas-INDEL	.											.	ZFP37	93	.	0			c.404delT						PASS	.						85	91	89					9																	115806495		2171	4194	6365	SO:0001589	frameshift_variant	7539	exon4			.	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.403delC	chr9.hg19:g.115806495delG	ENSP00000363344:p.Leu136fs	165.0	0.0	0		196.0	29.0	0.147959	NM_003408	A0AVJ9|B4DVX4|G3V3L7|Q5T7Q4	Frame_Shift_Del	DEL	ENST00000374227.3	hg19	CCDS6787.1																																																																																			.	.	.	none		0.353	ZFP37-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055439.1	NM_003408		-	115806495	G	-	115806495	7	5	157	1	0	1	0	1	0	0	0	0	17660	1029	36	0	1493	0	ZFP37	9	115806495	Frame_Shift_Del	DEL	G	TCGA-DZ-6132-01A-11D-1961-08	26863169	115806495	25406936	47	9295											
CRAT	1384	hgsc.bcm.edu	37	chr9	131864688	131864688	+	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	gggccacccacctggtagttGtgtaccacggtgatgtgcgt	6	10	14	11	2	0	1	0	1	0	0	0	1	0	1	4	3	2	3	4	3	2	3			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr9:131864688G>T	ENST00000318080.2	-	5	915	c.621C>A	c.(619-621)caC>caA	p.H207Q	CRAT_ENST00000464290.1_5'UTR|RP11-247A12.1_ENST00000434250.1_RNA	NM_000755.3|NM_001257363.1	NP_000746|NP_001244292.1	P43155	CACP_HUMAN	carnitine O-acetyltransferase	207					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)	CCTGGTAGTTGTGTACCACGG	0.642																																					p.H207Q		Atlas-SNP	.											.	CRAT	43	.	0			c.C621A						PASS	.						147	128	135					9																	131864688		2203	4300	6503	SO:0001583	missense	1384	exon5			GTAGTTGTGTACC	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.621C>A	chr9.hg19:g.131864688G>T	ENSP00000315013:p.His207Gln	232.0	0.0	.		162.0	42.0	.	NM_000755	Q5T952|Q9BW16	Missense_Mutation	SNP	ENST00000318080.2	hg19	CCDS6919.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.223146	0.79464	.	.	ENSG00000095321	ENST00000351352;ENST00000318080	D	0.89343	-2.5	5.37	4.23	0.50019	.	0.000000	0.85682	D	0.000000	D	0.92528	0.7627	M	0.76170	2.325	0.80722	D	1	D	0.62365	0.991	D	0.68039	0.955	D	0.90458	0.4444	10	0.31617	T	0.26	-47.0361	10.6033	0.45379	0.12:0.0:0.88:0.0	.	207	P43155	CACP_HUMAN	Q	207	ENSP00000315013:H207Q	ENSP00000315013:H207Q	H	-	3	2	CRAT	130904509	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.076000	0.57591	0.913000	0.36797	0.561000	0.74099	CAC	.	.	.	none		0.642	CRAT-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253700.1			T	131864688	G	T	131864688	3	4	157	1	0	0	0	0	1	0	0	0	3849	1368	48	4	1299	4	CRAT	9	131864688	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	16058193	131864688	9348743	48	9296											
ARHGAP21	57584	hgsc.bcm.edu	37	chr10	24908604	24908604	+	Frame_Shift_Del	DEL	T	T	-																															gtctggcgtccagatggaggTttttcccttaggatgacagc																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr10:24908604delT	ENST00000396432.2	-	9	2706	c.2220delA	c.(2218-2220)aaafs	p.K740fs	ARHGAP21_ENST00000320481.6_Frame_Shift_Del_p.K527fs	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	739					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						CAGATGGAGGTTTTTCCCTTA	0.453																																					p.P741fs		Atlas-INDEL	.											.	ARHGAP21	185	.	0			c.2221delC						PASS	.						102	96	98					10																	24908604		2203	4300	6503	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.2220delA	chr10.hg19:g.24908604delT	ENSP00000379709:p.Lys740fs	177.0	0.0	0		156.0	25.0	0.160256	NM_020824	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Frame_Shift_Del	DEL	ENST00000396432.2	hg19	CCDS7144.2																																																																																			.	.	.	none		0.453	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824		-	24908604	T	-	24908604	7	5	157	1	0	1	0	1	0	0	0	0	871	1722	60	0	3728	0	ARHGAP21	10	24908604	Frame_Shift_Del	DEL	T	TCGA-DZ-6132-01A-11D-1961-08		24908604	110626143	49	9297											
STOX1	219736	hgsc.bcm.edu	37	chr10	70645179	70645179	+	Frame_Shift_Del	DEL	T	T	-																															ccttggattcctcaagaatcTttgatggtaaagccaaagag																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr10:70645179delT	ENST00000298596.6	+	3	1710	c.1627delT	c.(1627-1629)tttfs	p.F543fs	STOX1_ENST00000399165.4_Intron|STOX1_ENST00000421961.2_Frame_Shift_Del_p.F433fs|STOX1_ENST00000399162.2_Intron|STOX1_ENST00000399169.4_Frame_Shift_Del_p.F543fs	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	543						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						CTCAAGAATCTTTGATGGTAA	0.418																																					p.I542fs		Atlas-INDEL	.											STOX1,NS,carcinoma,0,1	STOX1	75	.	0			c.1626delC						PASS	.						66	60	62					10																	70645179		1853	4096	5949	SO:0001589	frameshift_variant	219736	exon3			.	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.1627delT	chr10.hg19:g.70645179delT	ENSP00000298596:p.Phe543fs	63.0	0.0	0		53.0	12.0	0.226415	NM_152709	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Frame_Shift_Del	DEL	ENST00000298596.6	hg19	CCDS41535.1																																																																																			.	.	.	none		0.418	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709		-	70645179	T	-	70645179	7	5	157	1	0	1	0	1	0	0	0	0	15331	1609	56	0	1637	0	STOX1	10	70645179	Frame_Shift_Del	DEL	T	TCGA-DZ-6132-01A-11D-1961-08	45736575	70645179	64889568	50	9298											
IKZF5	64376	hgsc.bcm.edu	37	chr10	124755609	124755609	+	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	atcaaaggtcctttcaaaccCgtctactaacattcctgagt	12	12	5	12	1	3	1	2	1	1	0	5	1	5	1	3	1	3	0	3	1	4	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr10:124755609C>A	ENST00000368886.5	-	4	537	c.217G>T	c.(217-219)Ggg>Tgg	p.G73W	IKZF5_ENST00000479103.1_5'Flank|PSTK_ENST00000497219.1_Intron	NM_001271840.1	NP_001258769.1	Q9H5V7	IKZF5_HUMAN	IKAROS family zinc finger 5 (Pegasus)	73					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|lung(3)|prostate(1)	6		all_neural(114;0.169)|Colorectal(57;0.178)|Glioma(114;0.222)		Colorectal(40;0.0701)|COAD - Colon adenocarcinoma(40;0.0754)		CTTTCAAACCCGTCTACTAAC	0.443																																					p.G73W		Atlas-SNP	.											.	IKZF5	26	.	0			c.G217T						PASS	.						128	125	126					10																	124755609		1880	4108	5988	SO:0001583	missense	64376	exon4			CAAACCCGTCTAC	AF230808	CCDS41574.1	10q26	2011-05-31	2006-08-25	2006-08-25	ENSG00000095574	ENSG00000095574		"Zinc fingers, C2H2-type", "IKAROS zinc fingers"	14283	protein-coding gene	gene with protein product		606238	"zinc finger protein, subfamily 1A, 5", "zinc finger protein, subfamily 1A, 5 (Pegasus)"	ZNFN1A5		10978333	Standard	NM_001271840		Approved	Pegasus, FLJ22973	uc021qaj.2	Q9H5V7	OTTHUMG00000019192	ENST00000368886.5:c.217G>T	chr10.hg19:g.124755609C>A	ENSP00000357881:p.Gly73Trp	157.0	0.0	.		136.0	8.0	.	NM_001271840	B3KVH7|D3DRE7|Q9H2T0	Missense_Mutation	SNP	ENST00000368886.5	hg19	CCDS41574.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.862844	0.91511	.	.	ENSG00000095574	ENST00000368886	T	0.07327	3.2	6.17	5.25	0.73442	.	0.046543	0.85682	N	0.000000	T	0.18257	0.0438	N	0.24115	0.695	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.03641	-1.1017	10	0.66056	D	0.02	-6.9707	16.7418	0.85461	0.1302:0.8698:0.0:0.0	.	73	Q9H5V7	IKZF5_HUMAN	W	73	ENSP00000357881:G73W	ENSP00000357881:G73W	G	-	1	0	IKZF5	124745599	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.487000	0.81328	1.561000	0.49584	0.655000	0.94253	GGG	.	.	.	none		0.443	IKZF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050820.2	NM_022466		A	124755609	C	A	124755609	3	1	157	1	0	0	0	0	1	0	0	0	7625	652	23	4	1050	4	IKZF5	10	124755609	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	54110430	124755609	10779138	51	9299											
MKI67	4288	hgsc.bcm.edu	37	chr10	129902189	129902189	+	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	tactttgatgccctcatcacCgcttgctggttctttgtgtg	4	17	9	11	1	3	1	2	1	1	0	3	1	3	1	2	1	3	3	2	1	1	5	rs537885553	byFrequency	TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr10:129902189C>A	ENST00000368654.3	-	13	8290	c.7915G>T	c.(7915-7917)Ggt>Tgt	p.G2639C	MKI67_ENST00000368653.3_Missense_Mutation_p.G2279C	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2639	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)				CCCTCATCACCGCTTGCTGGT	0.493																																					p.G2639C		Atlas-SNP	.											.	MKI67	363	.	0			c.G7915T						PASS	.						163	155	158					10																	129902189		2203	4300	6503	SO:0001583	missense	4288	exon13			CATCACCGCTTGC	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.7915G>T	chr10.hg19:g.129902189C>A	ENSP00000357643:p.Gly2639Cys	212.0	0.0	.		161.0	8.0	.	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	hg19	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	C	12.39	1.922972	0.33908	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02323	4.34;4.34	2.66	-2.89	0.05665	.	2.905960	0.01493	N	0.017166	T	0.05456	0.0144	L	0.27053	0.805	0.09310	N	1	D;P;P	0.63880	0.993;0.91;0.9	P;P;P	0.55112	0.769;0.473;0.673	T	0.31024	-0.9958	10	0.56958	D	0.05	.	7.7285	0.28773	0.0:0.3498:0.0:0.6502	.	2638;2279;2639	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	C	2639;2279;2638	ENSP00000357643:G2639C;ENSP00000357642:G2279C	ENSP00000357642:G2279C	G	-	1	0	MKI67	129792179	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.539000	0.06113	-0.797000	0.04450	-0.261000	0.10672	GGT	.	.	.	none		0.493	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		A	129902189	C	A	129902189	3	1	157	1	0	0	0	0	1	0	0	0	9605	652	23	4	1867	4	MKI67	10	129902189	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	5146580	129902189	5632558	52	9300											
ZNF143	7702	hgsc.bcm.edu	37	chr11	9519250	9519250	+	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	ttaaaaagtcacgtcagaacTcatacaggagaaaagccata	19	7	7	8	1	3	2	3	0	0	2	3	3	3	2	1	1	3	0	1	1	8	3	rs373920789		TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr11:9519250T>G	ENST00000396602.2	+	10	989	c.870T>G	c.(868-870)acT>acG	p.T290T	ZNF143_ENST00000396597.3_Silent_p.T259T|ZNF143_ENST00000396604.1_Silent_p.T289T|ZNF143_ENST00000530463.1_Silent_p.T289T|ZNF143_ENST00000299606.2_Silent_p.T262T	NM_001282656.1|NM_001282657.1|NM_003442.5	NP_001269585.1|NP_001269586.1|NP_003433.3	P52747	ZN143_HUMAN	zinc finger protein 143	290					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	13				all cancers(16;4.12e-09)|Epithelial(150;2.29e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0212)		ACGTCAGAACTCATACAGGAG	0.328																																					p.T290T		Atlas-SNP	.											.	ZNF143	38	.	0			c.T870G						PASS	.	T		3,4399	6.2+/-15.9	0,3,2198	65	66	66		870	2.7	1	11		66	0,8588		0,0,4294	no	coding-synonymous	ZNF143	NM_003442.5		0,3,6492	GG,GT,TT		0.0,0.0682,0.0231		290/639	9519250	3,12987	2201	4294	6495	SO:0001819	synonymous_variant	7702	exon10			CAGAACTCATACA	U09850	CCDS7799.2, CCDS60720.1, CCDS60721.1	11p15.4	2013-01-08	2006-06-13		ENSG00000166478	ENSG00000166478		"Zinc fingers, C2H2-type"	12928	protein-coding gene	gene with protein product		603433	"zinc finger protein 143 (clone pHZ-1)"				Standard	NM_003442		Approved	SBF, pHZ-1, STAF	uc001mhr.3	P52747	OTTHUMG00000149922	ENST00000396602.2:c.870T>G	chr11.hg19:g.9519250T>G		69.0	0.0	.		56.0	8.0	.	NM_003442	A8K518|B4DLY5|E7ER34|O75559|Q8WUK9	Silent	SNP	ENST00000396602.2	hg19	CCDS7799.2																																																																																			.	.	.	weak		0.328	ZNF143-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313921.2	NM_003442		G	9519250	T	G	9519250	2	3	157	1	0	0	0	0	0	0	0	1	17744	1538	54	5		5	ZNF143	11	9519250	Silent	SNP	T	TCGA-DZ-6132-01A-11D-1961-08		9519250	125487266	53	9301											
GIF	2694	hgsc.bcm.edu	37	chr11	59610049	59610049	+	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	tagaaggctgatgcttcagcGttggggcctccgaaggggat	8	9	16	8	2	1	2	1	1	0	1	2	4	2	3	2	5	2	3	2	5	3	3			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr11:59610049G>C	ENST00000257248.2	-	4	425	c.378C>G	c.(376-378)aaC>aaG	p.N126K	GIF_ENST00000541311.1_Missense_Mutation_p.N101K	NM_005142.2	NP_005133.2	P27352	IF_HUMAN	gastric intrinsic factor (vitamin B synthesis)	126					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)	apical plasma membrane (GO:0016324)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|lysosomal lumen (GO:0043202)|microvillus (GO:0005902)	cobalamin binding (GO:0031419)			large_intestine(4)|liver(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	17					Cyanocobalamin(DB00115)	ATGCTTCAGCGTTGGGGCCTC	0.522																																					p.N126K	NSCLC(53;1139 1245 16872 38474 42853)	Atlas-SNP	.											GIF,NS,adenocarcinoma,0,1	GIF	43	.	0			c.C378G						PASS	.						68	61	63					11																	59610049		2201	4295	6496	SO:0001583	missense	2694	exon4			TTCAGCGTTGGGG	X76562	CCDS7977.1	11q12.1	2013-09-20			ENSG00000134812	ENSG00000134812			4268	protein-coding gene	gene with protein product		609342				2071148	Standard	NM_005142		Approved	TCN3, IF, IFMH, INF	uc001noi.3	P27352	OTTHUMG00000167399	ENST00000257248.2:c.378C>G	chr11.hg19:g.59610049G>C	ENSP00000257248:p.Asn126Lys	81.0	1.0	.		58.0	9.0	.	NM_005142	B2RAN8|B4DVZ1	Missense_Mutation	SNP	ENST00000257248.2	hg19	CCDS7977.1	.	.	.	.	.	.	.	.	.	.	G	10.68	1.417564	0.25552	.	.	ENSG00000134812	ENST00000257248;ENST00000541311	T;T	0.35973	1.28;1.28	5.63	-11.3	0.00108	.	1.313500	0.04767	N	0.427342	T	0.21590	0.0520	L	0.29908	0.895	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.22208	-1.0223	10	0.48119	T	0.1	1.5143	8.9085	0.35539	0.1072:0.0807:0.5605:0.2515	.	126	P27352	IF_HUMAN	K	126;101	ENSP00000257248:N126K;ENSP00000440427:N101K	ENSP00000257248:N126K	N	-	3	2	GIF	59366625	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-3.689000	0.00392	-2.813000	0.00347	-2.048000	0.00412	AAC	.	.	.	none		0.522	GIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394497.1	NM_005142		C	59610049	G	C	59610049	3	2	157	1	0	0	0	0	1	0	0	0	6383	1136	40	4	899	4	GIF	11	59610049	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	50090799	59610049	75396467	54	9302											
FADS1	3992	hgsc.bcm.edu	37	chr11	61578255	61578255	+	Missense_Mutation	SNP	A	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	gatcttccccaaggcaaagaAgaagggatgcatgttgatgt	13	9	12	7	0	1	3	0	1	1	2	2	5	2	4	2	2	1	3	2	2	4	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr11:61578255A>C	ENST00000350997.7	-	5	1115	c.883T>G	c.(883-885)Ttc>Gtc	p.F295V	FADS1_ENST00000433932.1_Missense_Mutation_p.F154V|FADS2_ENST00000574708.1_Intron|FADS1_ENST00000542506.1_Missense_Mutation_p.F154V	NM_013402.4	NP_037534.3	O60427	FADS1_HUMAN	fatty acid desaturase 1	238					alpha-linolenic acid metabolic process (GO:0036109)|cell-cell signaling (GO:0007267)|cellular lipid metabolic process (GO:0044255)|cellular response to starvation (GO:0009267)|icosanoid biosynthetic process (GO:0046456)|linoleic acid metabolic process (GO:0043651)|phospholipid biosynthetic process (GO:0008654)|regulation of cell differentiation (GO:0045595)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid biosynthetic process (GO:0006636)|unsaturated fatty acid metabolic process (GO:0033559)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	C-5 sterol desaturase activity (GO:0000248)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)			central_nervous_system(1)|endometrium(1)|lung(1)|urinary_tract(1)	4					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	AAGGCAAAGAAGAAGGGATGC	0.567																																					p.F295V		Atlas-SNP	.											.	FADS1	19	.	0			c.T883G						PASS	.						137	150	145					11																	61578255		2112	4243	6355	SO:0001583	missense	3992	exon5			CAAAGAAGAAGGG		CCDS8011.2	11q12-q13.1	2013-01-25			ENSG00000149485	ENSG00000149485	1.14.19.3	"Fatty acid desaturases"	3574	protein-coding gene	gene with protein product	"delta-5 desaturase"	606148		LLCDL1			Standard	NM_013402		Approved	D5D, FADSD5, TU12, FADS6	uc010rlm.2	O60427	OTTHUMG00000157155	ENST00000350997.7:c.883T>G	chr11.hg19:g.61578255A>C	ENSP00000322229:p.Phe295Val	218.0	0.0	.		146.0	26.0	.	NM_013402	A8K0I7|B2RAI0|Q53GM5|Q8N3A6|Q8NCC7|Q8NCG0|Q96I39|Q96SV3|Q96T10|Q9NRP8|Q9NYX1	Missense_Mutation	SNP	ENST00000350997.7	hg19	CCDS8011.2	.	.	.	.	.	.	.	.	.	.	A	10.51	1.369315	0.24771	.	.	ENSG00000149485	ENST00000543488;ENST00000350997;ENST00000412725;ENST00000433932;ENST00000542506;ENST00000539999;ENST00000540767;ENST00000545245	T;T;T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39;-0.39;-0.39	5.06	2.75	0.32379	Fatty acid desaturase, type 1 (1);	0.000000	0.50627	U	0.000109	T	0.35248	0.0925	N	0.02973	-0.45	0.42328	D	0.992286	B	0.27192	0.171	B	0.27500	0.08	T	0.06770	-1.0808	10	0.25106	T	0.35	-29.7375	4.9109	0.13821	0.7052:0.0:0.1563:0.1385	.	238	O60427	FADS1_HUMAN	V	171;295;154;154;154;24;154;154	ENSP00000322229:F295V;ENSP00000405087:F154V;ENSP00000441403:F154V;ENSP00000443587:F24V;ENSP00000441871:F154V;ENSP00000442170:F154V	ENSP00000322229:F295V	F	-	1	0	FADS1	61334831	0.998000	0.40836	1.000000	0.80357	0.986000	0.74619	3.525000	0.53502	0.893000	0.36288	-0.250000	0.11733	TTC	.	.	.	none		0.567	FADS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347648.2	NM_013402		C	61578255	A	C	61578255	3	2	157	1	0	0	0	0	1	0	0	0	5369	72	3	5	654	5	FADS1	11	61578255	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	1968206	61578255	73428261	55	9303											
SLC22A8	9376	hgsc.bcm.edu	37	chr11	62760990	62760990	+	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	cccgaggagggcggtgatccCgtagatgatattggggatga	9	8	17	7	3	0	4	0	3	0	1	1	7	1	6	2	5	0	1	2	5	2	3	rs374075913		TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr11:62760990C>A	ENST00000336232.2	-	10	1570	c.1435G>T	c.(1435-1437)Ggg>Tgg	p.G479W	SLC22A8_ENST00000545207.1_Missense_Mutation_p.G388W|SLC22A8_ENST00000535878.1_Missense_Mutation_p.G356W|SLC22A8_ENST00000542795.1_5'Flank|SLC22A8_ENST00000430500.2_Missense_Mutation_p.G479W|SLC22A8_ENST00000311438.8_Missense_Mutation_p.G479W	NM_001184732.1|NM_001184736.1|NM_004254.3	NP_001171661.1|NP_001171665.1|NP_004245.2	Q8TCC7	S22A8_HUMAN	solute carrier family 22 (organic anion transporter), member 8	479				YGI -> FTGS (in Ref. 1; AAD19357). {ECO:0000305}.	glutathione transport (GO:0034635)|response to methotrexate (GO:0031427)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|quaternary ammonium group transmembrane transporter activity (GO:0015651)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	28					Aciclovir(DB00787)|Adefovir Dipivoxil(DB00718)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Aspartame(DB00168)|Baclofen(DB00181)|Benzylpenicillin(DB01053)|Bumetanide(DB00887)|Cefacetrile(DB01414)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Ceftriaxone(DB01212)|Cephalexin(DB00567)|Cilastatin(DB01597)|Cimetidine(DB00501)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Enalapril(DB00584)|Estradiol(DB00783)|Famotidine(DB00927)|Furosemide(DB00695)|Ganciclovir(DB01004)|Guanidine(DB00536)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|L-Carnitine(DB00583)|Liothyronine(DB00279)|Liotrix(DB01583)|Melatonin(DB01065)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Methyltestosterone(DB06710)|Minocycline(DB01017)|Novobiocin(DB01051)|Oseltamivir(DB00198)|Ouabain(DB01092)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Ranitidine(DB00863)|Salicylic acid(DB00936)|Saxagliptin(DB06335)|Succinic acid(DB00139)|Tenofovir(DB00300)|Tenoxicam(DB00469)|Testosterone(DB00624)|Tetracycline(DB00759)|Valaciclovir(DB00577)|Valproic Acid(DB00313)|Zidovudine(DB00495)	GCGGTGATCCCGTAGATGATA	0.577																																					p.G479W		Atlas-SNP	.											.	SLC22A8	60	.	0			c.G1435T						PASS	.						98	94	96					11																	62760990		2201	4298	6499	SO:0001583	missense	9376	exon10			TGATCCCGTAGAT	AF097491, BC022387	CCDS8042.1, CCDS53643.1, CCDS53644.1	11q12.3	2013-05-22			ENSG00000149452	ENSG00000149452		"Solute carriers"	10972	protein-coding gene	gene with protein product		607581				10049739	Standard	NM_004254		Approved	OAT3	uc001nwo.3	Q8TCC7	OTTHUMG00000167768	ENST00000336232.2:c.1435G>T	chr11.hg19:g.62760990C>A	ENSP00000337335:p.Gly479Trp	137.0	0.0	.		130.0	8.0	.	NM_001184732	B4DPH7|F5GWA8|F5H5J1|O95820|Q59EW9|Q96TC1	Missense_Mutation	SNP	ENST00000336232.2	hg19	CCDS8042.1	.	.	.	.	.	.	.	.	.	.	C	18.33	3.600516	0.66332	.	.	ENSG00000149452	ENST00000336232;ENST00000540631;ENST00000545207;ENST00000535878;ENST00000311438;ENST00000430500	T;T;T;T;T	0.61392	0.11;0.11;0.11;0.11;0.11	5.9	4.99	0.66335	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.110148	0.64402	D	0.000009	D	0.82572	0.5066	H	0.96111	3.77	0.45452	D	0.998421	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.87435	0.2391	10	0.87932	D	0	.	12.596	0.56470	0.0:0.9204:0.0:0.0796	.	479;479	Q8TCC7-2;Q8TCC7	.;S22A8_HUMAN	W	479;465;388;356;479;479	ENSP00000337335:G479W;ENSP00000441658:G388W;ENSP00000443368:G356W;ENSP00000311463:G479W;ENSP00000398548:G479W	ENSP00000311463:G479W	G	-	1	0	SLC22A8	62517566	0.996000	0.38824	0.079000	0.20413	0.703000	0.40648	4.811000	0.62606	1.503000	0.48686	0.591000	0.81541	GGG	.	.	.	alt		0.577	SLC22A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396191.1	NM_004254		A	62760990	C	A	62760990	3	1	157	1	0	0	0	0	1	0	0	0	14473	652	23	4	201	4	SLC22A8	11	62760990	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	1182735	62760990	72245526	56	9304											
STYK1	55359	hgsc.bcm.edu	37	chr12	10780290	10780290	+	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	atatacttgtttttctgtgaGatcatagagaagaccatcca	13	14	7	7	0	2	3	1	1	1	3	3	5	3	3	2	0	1	1	2	0	4	6			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr12:10780290G>C	ENST00000075503.3	-	7	1187	c.667C>G	c.(667-669)Ctc>Gtc	p.L223V		NM_018423.2	NP_060893.2	Q6J9G0	STYK1_HUMAN	serine/threonine/tyrosine kinase 1	223	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	26						TTTTCTGTGAGATCATAGAGA	0.398										HNSCC(73;0.22)																											p.L223V		Atlas-SNP	.											.	STYK1	55	.	0			c.C667G						PASS	.						209	145	167					12																	10780290		2203	4300	6503	SO:0001583	missense	55359	exon7			CTGTGAGATCATA	AF251059	CCDS8629.1	12p13.2	2005-01-21							18889	protein-coding gene	gene with protein product		611433				12841579	Standard	NM_018423		Approved	SuRTK106, DKFZp761P1010, NOK	uc001qys.2	Q6J9G0		ENST00000075503.3:c.667C>G	chr12.hg19:g.10780290G>C	ENSP00000075503:p.Leu223Val	57.0	0.0	.		77.0	24.0	.	NM_018423	B2R9T2|Q52LR3|Q9BXY2|Q9NSH1	Missense_Mutation	SNP	ENST00000075503.3	hg19	CCDS8629.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.34|13.34	2.207320|2.207320	0.39003|0.39003	.|.	.|.	ENSG00000060140|ENSG00000060140	ENST00000542924|ENST00000075503	.|T	.|0.74106	.|-0.81	5.11|5.11	3.25|3.25	0.37280|0.37280	.|Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|0.092391	.|0.47093	.|D	.|0.000250	T|T	0.73305|0.73305	0.3570|0.3570	L|L	0.56340|0.56340	1.77|1.77	0.40939|0.40939	D|D	0.984457|0.984457	.|B	.|0.22080	.|0.064	.|B	.|0.35727	.|0.209	T|T	0.72640|0.72640	-0.4232|-0.4232	5|10	.|0.87932	.|D	.|0	-6.5489|-6.5489	12.1571|12.1571	0.54083|0.54083	0.0:0.0:0.6901:0.3098|0.0:0.0:0.6901:0.3098	.|.	.|223	.|Q6J9G0	.|STYK1_HUMAN	M|V	66|223	.|ENSP00000075503:L223V	.|ENSP00000075503:L223V	I|L	-|-	3|1	3|0	STYK1|STYK1	10671557|10671557	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	2.014000|2.014000	0.40951|0.40951	0.706000|0.706000	0.31912|0.31912	-0.181000|-0.181000	0.13052|0.13052	ATC|CTC	.	.	.	none		0.398	STYK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399622.1	NM_018423		C	10780290	G	C	10780290	3	2	157	1	0	0	0	0	1	0	0	0	15371	942	33	4	621	4	STYK1	12	10780290	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08		10780290	123071605	57	9305											
PLEKHA5	54477	hgsc.bcm.edu	37	chr12	19506893	19506893	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atcttcgacaatagcttcctAtgtaaccttgaggaaaacta	14	12	6	9	1	1	1	0	1	1	0	3	3	2	2	2	1	3	2	2	1	7	7			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr12:19506893A>G	ENST00000299275.6	+	20	2603	c.2597A>G	c.(2596-2598)tAt>tGt	p.Y866C	PLEKHA5_ENST00000355397.3_Missense_Mutation_p.Y924C|PLEKHA5_ENST00000538714.1_Missense_Mutation_p.Y924C|PLEKHA5_ENST00000539256.1_Missense_Mutation_p.Y624C|PLEKHA5_ENST00000424268.1_Missense_Mutation_p.Y855C|PLEKHA5_ENST00000317589.4_Missense_Mutation_p.Y929C|PLEKHA5_ENST00000429027.2_Missense_Mutation_p.Y1032C|PLEKHA5_ENST00000359180.3_Missense_Mutation_p.Y810C|PLEKHA5_ENST00000543806.1_Missense_Mutation_p.Y848C	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	866					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)					ATAGCTTCCTATGTAACCTTG	0.368																																					p.Y1032C	Pancreas(196;329 2193 11246 14234 19524)	Atlas-SNP	.											.	PLEKHA5	198	.	0			c.A3095G						PASS	.						125	119	121					12																	19506893		2203	4300	6503	SO:0001583	missense	54477	exon26			CTTCCTATGTAAC	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.2597A>G	chr12.hg19:g.19506893A>G	ENSP00000299275:p.Tyr866Cys	87.0	0.0	.		112.0	25.0	.	NM_001256470	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Missense_Mutation	SNP	ENST00000299275.6	hg19	CCDS8682.1	.	.	.	.	.	.	.	.	.	.	A	19.53	3.845797	0.71603	.	.	ENSG00000052126	ENST00000317589;ENST00000355397;ENST00000359180;ENST00000542828;ENST00000429027;ENST00000299275;ENST00000539256;ENST00000538714;ENST00000424268;ENST00000543806;ENST00000536974;ENST00000538972	T;T;T;T;T;T;T;T;T;T;T	0.31247	2.93;2.93;1.5;2.93;2.93;2.93;2.93;2.93;2.93;2.93;1.5	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.57227	0.2039	M	0.80746	2.51	0.50813	D	0.999898	D;D;D;D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.91635	0.992;0.998;0.996;0.997;0.999;0.994;0.959;0.982	T	0.60105	-0.7328	10	0.41790	T	0.15	-12.8632	14.8567	0.70344	1.0:0.0:0.0:0.0	.	929;848;855;1027;810;1032;866;924	Q9HAU0-4;F5H0I0;E7EME8;B4DHK5;Q9HAU0-5;E9PHQ3;Q9HAU0;Q9HAU0-2	.;.;.;.;.;.;PKHA5_HUMAN;.	C	929;924;810;1028;1032;866;624;924;855;848;821;147	ENSP00000325155:Y929C;ENSP00000347560:Y924C;ENSP00000352104:Y810C;ENSP00000404296:Y1032C;ENSP00000299275:Y866C;ENSP00000440611:Y624C;ENSP00000439673:Y924C;ENSP00000400411:Y855C;ENSP00000439837:Y848C;ENSP00000440371:Y821C;ENSP00000443553:Y147C	ENSP00000299275:Y866C	Y	+	2	0	PLEKHA5	19398160	1.000000	0.71417	0.690000	0.30148	0.968000	0.65278	6.016000	0.70798	1.890000	0.54733	0.372000	0.22366	TAT	.	.	.	none		0.368	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012		G	19506893	A	G	19506893	3	3	157	1	0	0	0	0	1	0	0	0	12066	449	16	3	2993	3	PLEKHA5	12	19506893	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	8726603	19506893	114345002	58	9306											
SLC38A4	55089	hgsc.bcm.edu	37	chr12	47178364	47178364	+	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	aatggaaacaaaagctccaaTttttcccggccatccaaatg	15	9	6	11	1	0	0	0	0	0	0	3	1	3	1	4	2	2	1	4	2	6	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr12:47178364T>A	ENST00000447411.1	-	6	660	c.454A>T	c.(454-456)Att>Ttt	p.I152F	SLC38A4_ENST00000266579.4_Missense_Mutation_p.I152F	NM_001143824.1	NP_001137296.1	Q969I6	S38A4_HUMAN	solute carrier family 38, member 4	152					amino acid transport (GO:0006865)|ion transport (GO:0006811)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|symporter activity (GO:0015293)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|skin(1)	21	Lung SC(27;0.192)|Renal(347;0.236)					AAAGCTCCAATTTTTCCCGGC	0.333																																					p.I152F		Atlas-SNP	.											.	SLC38A4	58	.	0			c.A454T						PASS	.						109	107	107					12																	47178364		2203	4300	6503	SO:0001583	missense	55089	exon6			CTCCAATTTTTCC	AF193836	CCDS8750.1	12q13	2013-05-22				ENSG00000139209		"Solute carriers"	14679	protein-coding gene	gene with protein product		608065				11414754	Standard	NM_018018		Approved	PAAT, NAT3, ATA3	uc001rpj.2	Q969I6		ENST00000447411.1:c.454A>T	chr12.hg19:g.47178364T>A	ENSP00000389843:p.Ile152Phe	169.0	0.0	.		175.0	26.0	.	NM_001143824	A8K553	Missense_Mutation	SNP	ENST00000447411.1	hg19	CCDS8750.1	.	.	.	.	.	.	.	.	.	.	T	13.45	2.242201	0.39598	.	.	ENSG00000139209	ENST00000395426;ENST00000447411;ENST00000266579;ENST00000547477;ENST00000546940	T;T;T;T	0.02421	4.3;4.3;4.3;4.3	6.07	4.9	0.64082	.	0.311957	0.37906	N	0.001896	T	0.03053	0.0090	L	0.33624	1.015	0.50813	D	0.999895	B	0.09022	0.002	B	0.15870	0.014	T	0.50898	-0.8773	10	0.27785	T	0.31	-8.8755	11.1795	0.48620	0.2577:0.0:0.0:0.7423	.	152	Q969I6	S38A4_HUMAN	F	152	ENSP00000389843:I152F;ENSP00000266579:I152F;ENSP00000450071:I152F;ENSP00000448543:I152F	ENSP00000266579:I152F	I	-	1	0	SLC38A4	45464631	1.000000	0.71417	0.996000	0.52242	0.736000	0.42039	3.555000	0.53727	1.067000	0.40740	0.533000	0.62120	ATT	.	.	.	none		0.333	SLC38A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404574.1			A	47178364	T	A	47178364	3	1	157	1	0	0	0	0	1	0	0	0	14619	1493	52	5	1233	5	SLC38A4	12	47178364	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08	27671471	47178364	86673531	59	9307											
EIF4B	1975	hgsc.bcm.edu	37	chr12	53416313	53416313	+	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	ttttggccgtgatagaaatcGggattctgacaaaacagata	14	11	10	6	2	1	4	0	2	1	2	2	5	1	5	1	2	1	0	1	2	5	5			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr12:53416313G>C	ENST00000262056.9	+	6	895	c.569G>C	c.(568-570)cGg>cCg	p.R190P	EIF4B_ENST00000420463.3_Missense_Mutation_p.R190P|EIF4B_ENST00000416762.3_Missense_Mutation_p.R151P|RP11-983P16.4_ENST00000552905.1_RNA	NM_001417.4	NP_001408.2	P23588	IF4B_HUMAN	eukaryotic translation initiation factor 4B	190	Arg-rich.|Asp-rich.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation initiation factor activity (GO:0003743)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)	22						GATAGAAATCGGGATTCTGAC	0.418																																					p.R190P		Atlas-SNP	.											.	EIF4B	38	.	0			c.G569C						PASS	.						133	112	119					12																	53416313		1863	4102	5965	SO:0001583	missense	1975	exon6			GAAATCGGGATTC	X55733	CCDS41788.1, CCDS73474.1	12q13.13	2013-02-12			ENSG00000063046	ENSG00000063046		"RNA binding motif (RRM) containing"	3285	protein-coding gene	gene with protein product		603928					Standard	XM_005268709		Approved		uc001sbh.4	P23588	OTTHUMG00000169570	ENST00000262056.9:c.569G>C	chr12.hg19:g.53416313G>C	ENSP00000262056:p.Arg190Pro	105.0	0.0	.		114.0	16.0	.	NM_001417	Q4G0E3|Q53HQ2|Q6GPH5|Q6IB46|Q8WYK5	Missense_Mutation	SNP	ENST00000262056.9	hg19	CCDS41788.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.124924	0.56613	.	.	ENSG00000063046	ENST00000262056;ENST00000551002;ENST00000420463;ENST00000430205;ENST00000416762;ENST00000552490	T;D;D;D;D	0.94232	0.54;-3.36;-3.36;-3.38;-3.36	3.59	2.7	0.31948	.	0.065726	0.53938	D	0.000044	D	0.87993	0.6318	L	0.27053	0.805	0.58432	D	0.999999	B;B;B	0.33807	0.426;0.301;0.301	B;B;B	0.36504	0.226;0.113;0.113	D	0.86321	0.1692	10	0.56958	D	0.05	.	10.7402	0.46149	0.0982:0.0:0.9018:0.0	.	151;190;190	B4DS13;E7EX17;P23588	.;.;IF4B_HUMAN	P	190;144;190;190;151;190	ENSP00000262056:R190P;ENSP00000447192:R144P;ENSP00000388806:R190P;ENSP00000412530:R151P;ENSP00000450324:R190P	ENSP00000262056:R190P	R	+	2	0	EIF4B	51702580	1.000000	0.71417	0.979000	0.43373	0.935000	0.57460	6.380000	0.73158	1.077000	0.40990	0.650000	0.86243	CGG	.	.	.	none		0.418	EIF4B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404852.2	NM_001417		C	53416313	G	C	53416313	3	2	157	1	0	0	0	0	1	0	0	0	5029	1116	39	4	591	4	EIF4B	12	53416313	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	6237949	53416313	80435582	60	9308											
RAB5B	5869	hgsc.bcm.edu	37	chr12	56385887	56385887	+	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	ctttttatctctagctaagaAgttgccaaagagtgaacccc	12	12	7	10	0	1	3	0	1	1	2	2	3	1	3	3	0	3	2	3	0	6	6			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr12:56385887A>T	ENST00000360299.5	+	6	760	c.539A>T	c.(538-540)aAg>aTg	p.K180M	RAB5B_ENST00000448789.2_Missense_Mutation_p.K139M|RAB5B_ENST00000553116.1_Missense_Mutation_p.K180M	NM_002868.3	NP_002859.1	P61020	RAB5B_HUMAN	RAB5B, member RAS oncogene family	180					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)			CTAGCTAAGAAGTTGCCAAAG	0.507																																					p.K180M		Atlas-SNP	.											.	RAB5B	22	.	0			c.A539T						PASS	.						59	60	60					12																	56385887		2203	4300	6503	SO:0001583	missense	5869	exon6			CTAAGAAGTTGCC		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.539A>T	chr12.hg19:g.56385887A>T	ENSP00000353444:p.Lys180Met	86.0	0.0	.		105.0	35.0	.	NM_002868	A8K982|B4DKD7|P35239|P35277|Q6PIK9|Q86TH0|Q8IXL2	Missense_Mutation	SNP	ENST00000360299.5	hg19	CCDS8900.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.65|16.65	3.183016|3.183016	0.57800|0.57800	.|.	.|.	ENSG00000111540|ENSG00000111540	ENST00000549218|ENST00000553116;ENST00000360299;ENST00000448789	.|T;T;T	.|0.80033	.|-1.17;-1.17;-1.33	4.97|4.97	4.97|4.97	0.65823|0.65823	.|.	.|0.080850	.|0.49916	.|D	.|0.000138	D|D	0.84710|0.84710	0.5532|0.5532	L|L	0.54863|0.54863	1.705|1.705	0.58432|0.58432	D|D	0.999999|0.999999	.|D;P;P	.|0.53619	.|0.961;0.55;0.911	.|P;P;P	.|0.57548	.|0.823;0.575;0.69	D|D	0.86486|0.86486	0.1794|0.1794	5|10	.|0.87932	.|D	.|0	-7.6032|-7.6032	14.1258|14.1258	0.65219|0.65219	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|139;180;180	.|B4DKD7;Q6FI54;P61020	.|.;.;RAB5B_HUMAN	D|M	99|180;180;139	.|ENSP00000450168:K180M;ENSP00000353444:K180M;ENSP00000391319:K139M	.|ENSP00000353444:K180M	E|K	+|+	3|2	2|0	RAB5B|RAB5B	54672154|54672154	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.605000|5.605000	0.67634|0.67634	2.236000|2.236000	0.73375|0.73375	0.529000|0.529000	0.55759|0.55759	GAA|AAG	.	.	.	none		0.507	RAB5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405396.1			T	56385887	A	T	56385887	3	4	157	1	0	0	0	0	1	0	0	0	12962	72	3	5	557	5	RAB5B	12	56385887	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	2969574	56385887	77466008	61	9309											
GRIP1	23426	hgsc.bcm.edu	37	chr12	66765625	66765625	+	Frame_Shift_Del	DEL	A	A	-																															gcgagctgctgcgctcctggAagctggcctgtcgccccagc																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr12:66765625delA	ENST00000398016.3	-	22	2773	c.2705delT	c.(2704-2706)ttcfs	p.F902fs	GRIP1_ENST00000286445.7_Frame_Shift_Del_p.F939fs|GRIP1_ENST00000359742.4_Frame_Shift_Del_p.F954fs	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)		GCGCTCCTGGAAGCTGGCCTG	0.552																																					p.F902fs		Atlas-INDEL	.											.	GRIP1	106	.	0			c.2706delC						PASS	.						86	94	91					12																	66765625		2074	4214	6288	SO:0001589	frameshift_variant	23426	exon22			.	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.2705delT	chr12.hg19:g.66765625delA	ENSP00000381098:p.Phe902fs	219.0	0.0	0		202.0	34.0	0.168317	NM_021150	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Frame_Shift_Del	DEL	ENST00000398016.3	hg19	CCDS41807.1																																																																																			.	.	.	none		0.552	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2			-	66765625	A	-	66765625	7	5	157	1	0	1	0	1	0	0	0	0	6794	246	9	0	537	0	GRIP1	12	66765625	Frame_Shift_Del	DEL	A	TCGA-DZ-6132-01A-11D-1961-08	10379738	66765625	67086270	62	9310											
RCBTB1	55213	hgsc.bcm.edu	37	chr13	50115836	50115836	+	Frame_Shift_Del	DEL	C	C	-																															agcatcttctggcggcaggtCgactgtgtctgtgtagaggt																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr13:50115836delC	ENST00000378302.2	-	11	1560	c.1300delG	c.(1300-1302)gacfs	p.D434fs	RCBTB1_ENST00000471984.1_5'Flank|RCBTB1_ENST00000258646.3_Frame_Shift_Del_p.D434fs	NM_018191.3	NP_060661.3	Q8NDN9	RCBT1_HUMAN	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1	434	BTB 1. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cell cycle (GO:0007049)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(1)	16		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;4.7e-09)		GGCGGCAGGTCGACTGTGTCT	0.458																																					p.D434fs		Atlas-INDEL	.											.	RCBTB1	34	.	0			c.1301delA						PASS	.						156	116	130					13																	50115836		2203	4300	6503	SO:0001589	frameshift_variant	55213	exon11			.	AF334406	CCDS9418.1	13q14	2013-01-08			ENSG00000136144	ENSG00000136144		"BTB/POZ domain containing"	18243	protein-coding gene	gene with protein product		607867				11306461	Standard	XM_005266441		Approved	FLJ10716, CLLD7, CLLL7	uc001vde.1	Q8NDN9	OTTHUMG00000016915	ENST00000378302.2:c.1300delG	chr13.hg19:g.50115836delC	ENSP00000367552:p.Asp434fs	95.0	0.0	0		86.0	15.0	0.174419	NM_018191	Q8IY29|Q969U9	Frame_Shift_Del	DEL	ENST00000378302.2	hg19	CCDS9418.1																																																																																			.	.	.	none		0.458	RCBTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044912.2	NM_018191		-	50115836	C	-	50115836	7	5	157	1	0	1	0	1	0	0	0	0	13184	884	31	0	307	0	RCBTB1	13	50115836	Frame_Shift_Del	DEL	C	TCGA-DZ-6132-01A-11D-1961-08		50115836	65054042	63	9311											
BIVM	54841	hgsc.bcm.edu	37	chr13	103492131	103492131	+	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	agtgctagtttccatcaggaCtcggcatggaaaaagatgtc	12	10	11	8	1	1	1	1	0	0	1	4	3	2	3	1	3	1	3	1	3	3	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr13:103492131C>G	ENST00000257336.1	+	11	2107	c.1428C>G	c.(1426-1428)gaC>gaG	p.D476E	BIVM_ENST00000419638.1_3'UTR|BIVM_ENST00000448849.2_Missense_Mutation_p.D254E|BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.L448V	NM_017693.3	NP_060163.2	Q86UB2	BIVM_HUMAN	basic, immunoglobulin-like variable motif containing	476						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)					TCCATCAGGACTCGGCATGGA	0.468																																					p.D476E		Atlas-SNP	.											.	.	.	.	0			c.C1428G						PASS	.						154	144	147					13																	103492131		2203	4300	6503	SO:0001583	missense	0	exon9			TCAGGACTCGGCA	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.1428C>G	chr13.hg19:g.103492131C>G	ENSP00000257336:p.Asp476Glu	153.0	0.0	.		164.0	30.0	.	NM_001204425	Q2M1J2|Q9NXM4	Missense_Mutation	SNP	ENST00000257336.1	hg19	CCDS9505.1	.	.	.	.	.	.	.	.	.	.	C	0.020	-1.437445	0.01098	.	.	ENSG00000134897;ENSG00000134897;ENSG00000134899	ENST00000257336;ENST00000448849;ENST00000418659	.	.	.	5.4	-0.762	0.11034	.	0.188352	0.45606	D	0.000360	T	0.03651	0.0104	N	0.00347	-1.61	0.19300	N	0.999976	B;B;B	0.21606	0.0;0.058;0.005	B;B;B	0.17098	0.001;0.017;0.004	T	0.35624	-0.9781	9	0.02654	T	1	-13.3799	2.8027	0.05419	0.0935:0.3232:0.301:0.2823	.	254;447;476	Q86UB2-2;Q59FZ7;Q86UB2	.;.;BIVM_HUMAN	E	476;254;447	.	ENSP00000257336:D476E	D	+	3	2	ERCC5;BIVM	102290132	0.097000	0.21791	0.768000	0.31515	0.791000	0.44710	-0.250000	0.08830	-0.183000	0.10585	-1.255000	0.01485	GAC	.	.	.	none		0.468	BIVM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045704.2			G	103492131	C	G	103492131	3	3	157	1	0	0	0	0	1	0	0	0	1441	564	20	4	1483	4	BIVM	13	103492131	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	53376295	103492131	11677747	64	9312											
ANPEP	290	hgsc.bcm.edu	37	chr15	90349567	90349567	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagcgtcacccggtaggaaTcgggtttcagcgtgttgggg	6	10	16	9	4	3	0	3	0	0	0	4	1	3	1	1	5	2	3	1	5	2	3			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr15:90349567T>C	ENST00000300060.6	-	2	561	c.248A>G	c.(247-249)gAt>gGt	p.D83G		NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	83	Metalloprotease.				angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	CCGGTAGGAATCGGGTTTCAG	0.617																																					p.D83G	NSCLC(30;827 977 2459 19669 26125)	Atlas-SNP	.											.	ANPEP	124	.	0			c.A248G						PASS	.						126	102	110					15																	90349567		2200	4299	6499	SO:0001583	missense	290	exon2			TAGGAATCGGGTT	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"CD molecules"	500	protein-coding gene	gene with protein product	"aminopeptidase N", "aminopeptidase M", "microsomal aminopeptidase"	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.248A>G	chr15.hg19:g.90349567T>C	ENSP00000300060:p.Asp83Gly	137.0	0.0	.		85.0	18.0	.	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Missense_Mutation	SNP	ENST00000300060.6	hg19	CCDS10356.1	.	.	.	.	.	.	.	.	.	.	T	6.216	0.408075	0.11754	.	.	ENSG00000166825	ENST00000300060	T	0.02631	4.22	4.74	0.264	0.15607	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	2.111890	0.01982	N	0.044922	T	0.06096	0.0158	M	0.73962	2.25	0.09310	N	1	B	0.26672	0.156	B	0.33121	0.158	T	0.46359	-0.9197	10	0.23891	T	0.37	.	4.6468	0.12575	0.3933:0.0958:0.0:0.5109	.	83	P15144	AMPN_HUMAN	G	83	ENSP00000300060:D83G	ENSP00000300060:D83G	D	-	2	0	ANPEP	88150571	0.000000	0.05858	0.011000	0.14972	0.152000	0.21847	0.560000	0.23500	0.163000	0.19507	0.383000	0.25322	GAT	.	.	.	none		0.617	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1			C	90349567	T	C	90349567	3	2	157	1	0	0	0	0	1	0	0	0	710	1435	50	3	2735	3	ANPEP	15	90349567	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08		90349567	12181825	65	9313											
SV2B	9899	hgsc.bcm.edu	37	chr15	91769497	91769497	+	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	agtcgcagaaccaaggaatgGatgactacaagtatcaggac	16	6	11	8	1	1	2	1	1	0	1	2	5	1	5	1	3	2	2	1	3	6	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr15:91769497G>C	ENST00000394232.1	+	2	474	c.4G>C	c.(4-6)Gat>Cat	p.D2H	SV2B_ENST00000557291.1_Intron|SV2B_ENST00000545111.2_Intron|SV2B_ENST00000330276.4_Missense_Mutation_p.D2H	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	2					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)			CCAAGGAATGGATGACTACAA	0.478																																					p.D2H		Atlas-SNP	.											.	SV2B	98	.	0			c.G4C						PASS	.						72	58	63					15																	91769497		2198	4298	6496	SO:0001583	missense	9899	exon3			GGAATGGATGACT	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.4G>C	chr15.hg19:g.91769497G>C	ENSP00000377779:p.Asp2His	47.0	0.0	.		44.0	12.0	.	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Missense_Mutation	SNP	ENST00000394232.1	hg19	CCDS10370.1	.	.	.	.	.	.	.	.	.	.	G	17.76	3.469419	0.63625	.	.	ENSG00000185518	ENST00000394232;ENST00000330276	T;T	0.64803	-0.12;-0.12	5.71	4.79	0.61399	.	0.237482	0.42821	D	0.000651	T	0.65249	0.2673	M	0.68317	2.08	0.48830	D	0.999714	P	0.37015	0.578	B	0.41988	0.372	T	0.69007	-0.5259	10	0.72032	D	0.01	-15.0004	13.3113	0.60382	0.077:0.0:0.923:0.0	.	2	Q7L1I2	SV2B_HUMAN	H	2	ENSP00000377779:D2H;ENSP00000332818:D2H	ENSP00000332818:D2H	D	+	1	0	SV2B	89570501	1.000000	0.71417	0.999000	0.59377	0.874000	0.50279	7.523000	0.81856	1.411000	0.46957	0.563000	0.77884	GAT	.	.	.	none		0.478	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848		C	91769497	G	C	91769497	3	2	157	1	0	0	0	0	1	0	0	0	15430	1174	41	4	6	4	SV2B	15	91769497	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	1419930	91769497	10761895	66	9314											
RBBP6	5930	hgsc.bcm.edu	37	chr16	24582943	24582943	+	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	aaataaaccaagggaagagaGagatttgcctaaaaaaggaa	22	5	10	4	0	0	2	0	0	0	2	0	6	0	4	2	2	2	0	2	2	9	3			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr16:24582943G>C	ENST00000319715.4	+	18	4988	c.4556G>C	c.(4555-4557)aGa>aCa	p.R1519T	RBBP6_ENST00000381039.3_Missense_Mutation_p.R679T|RBBP6_ENST00000348022.2_Missense_Mutation_p.R1485T	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1519	Interaction with p53. {ECO:0000250}.				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)		AGGGAAGAGAGAGATTTGCCT	0.358																																					p.R1519T		Atlas-SNP	.											.	RBBP6	158	.	0			c.G4556C						PASS	.						40	39	39					16																	24582943		2197	4298	6495	SO:0001583	missense	5930	exon18			AAGAGAGAGATTT		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.4556G>C	chr16.hg19:g.24582943G>C	ENSP00000317872:p.Arg1519Thr	42.0	0.0	.		45.0	8.0	.	NM_006910	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Missense_Mutation	SNP	ENST00000319715.4	hg19	CCDS10621.1	.	.	.	.	.	.	.	.	.	.	G	15.34	2.805084	0.50315	.	.	ENSG00000122257	ENST00000381039;ENST00000319715;ENST00000348022	T;T;T	0.19105	2.17;2.4;2.41	6.03	1.9	0.25705	.	0.190657	0.41396	D	0.000897	T	0.12475	0.0303	L	0.27053	0.805	0.27887	N	0.939455	P;B;B	0.39480	0.675;0.241;0.155	B;B;B	0.35550	0.205;0.148;0.071	T	0.12502	-1.0545	10	0.30078	T	0.28	-17.338	10.6299	0.45530	0.2533:0.0:0.7467:0.0	.	679;1485;1519	Q7Z6E9-4;Q7Z6E9-2;Q7Z6E9	.;.;RBBP6_HUMAN	T	679;1519;1485	ENSP00000370427:R679T;ENSP00000317872:R1519T;ENSP00000316291:R1485T	ENSP00000317872:R1519T	R	+	2	0	RBBP6	24490444	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	3.017000	0.49615	0.428000	0.26173	0.557000	0.71058	AGA	.	.	.	none		0.358	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910		C	24582943	G	C	24582943	3	2	157	1	0	0	0	0	1	0	0	0	13116	942	33	4	4680	4	RBBP6	16	24582943	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08		24582943	65771810	67	9315											
RPGRIP1L	23322	hgsc.bcm.edu	37	chr16	53691402	53691402	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttgtgttgcataattagcAtgtttcttgtcttttccagc	6	21	7	7	0	2	0	0	0	2	0	3	0	3	0	1	0	3	4	1	0	2	9			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr16:53691402A>G	ENST00000379925.3	-	13	1594	c.1544T>C	c.(1543-1545)aTg>aCg	p.M515T	RPGRIP1L_ENST00000564374.1_Missense_Mutation_p.M515T|RPGRIP1L_ENST00000563746.1_Missense_Mutation_p.M515T|RPGRIP1L_ENST00000262135.4_Missense_Mutation_p.M515T	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	515					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)				CATAATTAGCATGTTTCTTGT	0.313																																					p.M515T		Atlas-SNP	.											.	RPGRIP1L	118	.	0			c.T1544C						PASS	.						88	81	83					16																	53691402		2196	4300	6496	SO:0001583	missense	23322	exon13			ATTAGCATGTTTC		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.1544T>C	chr16.hg19:g.53691402A>G	ENSP00000369257:p.Met515Thr	57.0	0.0	.		89.0	17.0	.	NM_001127897	A0PJ88|Q9Y2K8	Missense_Mutation	SNP	ENST00000379925.3	hg19	CCDS32447.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.138906	0.77775	.	.	ENSG00000103494	ENST00000379925;ENST00000262135	T;D	0.81579	-0.02;-1.51	6.04	6.04	0.98038	.	0.099515	0.64402	D	0.000001	D	0.87834	0.6277	M	0.72118	2.19	0.80722	D	1	D;D;D;D	0.76494	0.972;0.972;0.972;0.999	P;P;P;D	0.68765	0.632;0.706;0.706;0.96	D	0.86184	0.1608	10	0.30078	T	0.28	-18.3503	14.8183	0.70052	1.0:0.0:0.0:0.0	.	515;515;515;515	B4E3M8;B7ZKJ9;Q68CZ1;Q68CZ1-2	.;.;FTM_HUMAN;.	T	515	ENSP00000369257:M515T;ENSP00000262135:M515T	ENSP00000262135:M515T	M	-	2	0	RPGRIP1L	52248903	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.353000	0.90077	2.317000	0.78254	0.460000	0.39030	ATG	.	.	.	none		0.313	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272		G	53691402	A	G	53691402	3	3	157	1	0	0	0	0	1	0	0	0	13563	217	8	3	2463	3	RPGRIP1L	16	53691402	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	29108459	53691402	36663351	68	9316											
ADAP2	55803	hgsc.bcm.edu	37	chr17	29261211	29261211	+	Frame_Shift_Del	DEL	G	G	-																															ttgctgcttaaggtaaccgaGaaggattcctgtggaagcga																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr17:29261211delG	ENST00000330889.3	+	5	741	c.406delG	c.(406-408)gaafs	p.E136fs	ADAP2_ENST00000580525.1_Frame_Shift_Del_p.E142fs	NM_018404.2	NP_060874.1	Q9NPF8	ADAP2_HUMAN	ArfGAP with dual PH domains 2	136	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				heart development (GO:0007507)|regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|mitochondrial envelope (GO:0005740)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein binding, bridging (GO:0030674)|zinc ion binding (GO:0008270)	p.?(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	13						AGGTAACCGAGAAGGATTCCT	0.478																																					p.R135fs		Atlas-INDEL	.											.	ADAP2	36	.	1	Unknown(1)	central_nervous_system(1)	c.405delA						PASS	.						96	80	85					17																	29261211		2203	4300	6503	SO:0001589	frameshift_variant	55803	exon5			.	AJ238994	CCDS11261.1	17q11.2	2013-01-10	2008-09-22	2008-09-22	ENSG00000184060	ENSG00000184060		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	16487	protein-coding gene	gene with protein product		608635	"centaurin, alpha 2"	CENTA2			Standard	XM_005258008		Approved		uc002hfx.3	Q9NPF8	OTTHUMG00000132868	ENST00000330889.3:c.406delG	chr17.hg19:g.29261211delG	ENSP00000329468:p.Glu136fs	51.0	0.0	0		59.0	10.0	0.169492	NM_018404	Q8N4Q6|Q96SD5	Frame_Shift_Del	DEL	ENST00000330889.3	hg19	CCDS11261.1																																																																																			.	.	.	none		0.478	ADAP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256346.1	NM_018404		-	29261211	G	-	29261211	7	5	157	1	0	1	0	1	0	0	0	0	280	943	33	0	424	0	ADAP2	17	29261211	Frame_Shift_Del	DEL	G	TCGA-DZ-6132-01A-11D-1961-08		29261211	51933999	69	9317											
CBX1	10951	hgsc.bcm.edu	37	chr17	46152378	46152378	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccgactcaccatttcatcaGgaacatgagctctccactgg	10	9	8	14	1	4	1	3	1	1	0	5	3	4	2	3	2	2	1	3	2	1	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr17:46152378G>A	ENST00000393408.3	-	4	883	c.403C>T	c.(403-405)Ctg>Ttg	p.L135L	CBX1_ENST00000225603.4_Silent_p.L135L|CBX1_ENST00000495350.1_Silent_p.L135L	NM_006807.4	NP_006798.1	P83916	CBX1_HUMAN	chromobox homolog 1	135	Chromo 2; shadow subtype. {ECO:0000255|PROSITE-ProRule:PRU00053}.				negative regulation of transcription, DNA-templated (GO:0045892)	chromatin (GO:0000785)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear heterochromatin (GO:0005720)|nucleoplasm (GO:0005654)|pericentric heterochromatin (GO:0005721)|spindle (GO:0005819)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone methyltransferase binding (GO:1990226)			breast(1)|central_nervous_system(1)|kidney(1)|prostate(1)	4						CATTTCATCAGGAACATGAGC	0.483																																					p.L135L	NSCLC(136;694 2497 38792 39034)	Atlas-SNP	.											.	CBX1	18	.	0			c.C403T						PASS	.						137	138	138					17																	46152378		2203	4300	6503	SO:0001819	synonymous_variant	10951	exon4			TCATCAGGAACAT	U35451	CCDS11525.1	17q21.32	2010-07-06	2010-06-24		ENSG00000108468	ENSG00000108468			1551	protein-coding gene	gene with protein product	"HP1 beta homolog (Drosophila )"	604511	"chromobox homolog 1 (Drosophila HP1 beta)"			9169582	Standard	NM_001127228		Approved	HP1Hs-beta, M31, MOD1, CBX, HP1-BETA	uc002ind.4	P83916	OTTHUMG00000150417	ENST00000393408.3:c.403C>T	chr17.hg19:g.46152378G>A		273.0	0.0	.		268.0	62.0	.	NM_006807	P23197	Silent	SNP	ENST00000393408.3	hg19	CCDS11525.1																																																																																			.	.	.	none		0.483	CBX1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318016.1	NM_006807		A	46152378	G	A	46152378	2	1	157	1	0	0	0	0	0	0	0	1	2719	991	35	2		2	CBX1	17	46152378	Silent	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	16891167	46152378	35042832	70	9318											
MTMR4	9110	hgsc.bcm.edu	37	chr17	56572475	56572475	+	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	aaaggggagtccatcatcatCcaaatacagaggaggcactg	15	6	11	9	0	2	1	2	0	0	1	4	3	4	3	2	4	1	1	2	4	3	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr17:56572475C>T	ENST00000323456.5	-	16	3152	c.3028G>A	c.(3028-3030)Gat>Aat	p.D1010N	MTMR4_ENST00000579925.1_Missense_Mutation_p.D953N	NM_004687.4	NP_004678.3	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	1010					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)					CCATCATCATCCAAATACAGA	0.512																																					p.D1010N		Atlas-SNP	.											.	MTMR4	91	.	0			c.G3028A						PASS	.						204	179	187					17																	56572475		2203	4300	6503	SO:0001583	missense	9110	exon16			CATCATCCAAATA	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.3028G>A	chr17.hg19:g.56572475C>T	ENSP00000325285:p.Asp1010Asn	205.0	0.0	.		214.0	58.0	.	NM_004687	D3DTZ6|Q8IV27|Q9Y4D5	Missense_Mutation	SNP	ENST00000323456.5	hg19	CCDS11608.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.689025	0.88735	.	.	ENSG00000108389	ENST00000323456	D	0.96885	-4.16	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.97626	0.9222	L	0.58101	1.795	0.48452	D	0.999659	D	0.89917	1.0	D	0.85130	0.997	D	0.98181	1.0457	10	0.66056	D	0.02	.	18.5538	0.91075	0.0:1.0:0.0:0.0	.	1010	Q9NYA4	MTMR4_HUMAN	N	1010	ENSP00000325285:D1010N	ENSP00000325285:D1010N	D	-	1	0	MTMR4	53927474	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.104000	0.77024	2.627000	0.88993	0.555000	0.69702	GAT	.	.	.	none		0.512	MTMR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444721.1	NM_004687		T	56572475	C	T	56572475	3	4	157	1	0	0	0	0	1	0	0	0	9953	855	30	2	575	2	MTMR4	17	56572475	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	10420097	56572475	24622735	71	9319											
CLTC	1213	hgsc.bcm.edu	37	chr17	57771125	57771125	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctgacagcaggacccagtgTtgccgtccctccccaggcac	7	6	11	17	1	0	1	0	1	0	0	2	2	2	2	5	2	2	4	5	2	0	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr17:57771125T>C	ENST00000269122.3	+	32	5214	c.4940T>C	c.(4939-4941)gTt>gCt	p.V1647A	CLTC_ENST00000579456.1_Missense_Mutation_p.V584A	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	1647	Heavy chain arm.|Proximal segment.|Trimerization. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					GGACCCAGTGTTGCCGTCCCT	0.557			T	"ALK, TFE3"	"ALCL, renal "																																p.V1647A		Atlas-SNP	.		Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	.	CLTC	124	.	0			c.T4940C						PASS	.						144	116	125					17																	57771125		2203	4300	6503	SO:0001583	missense	1213	exon32			CCAGTGTTGCCGT	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.4940T>C	chr17.hg19:g.57771125T>C	ENSP00000269122:p.Val1647Ala	151.0	0.0	.		144.0	55.0	.	NM_004859	D3DU00|Q6N0A0|Q86TF2	Missense_Mutation	SNP	ENST00000269122.3	hg19	CCDS32696.1	.	.	.	.	.	.	.	.	.	.	T	12.39	1.923961	0.34002	.	.	ENSG00000141367	ENST00000269122	T	0.10668	2.85	6.08	6.08	0.98989	.	0.052581	0.85682	D	0.000000	T	0.07728	0.0194	N	0.14661	0.345	0.80722	D	1	B	0.13145	0.007	B	0.12156	0.007	T	0.36212	-0.9757	10	0.14252	T	0.57	.	16.6438	0.85155	0.0:0.0:0.0:1.0	.	1647	Q00610	CLH1_HUMAN	A	1647	ENSP00000269122:V1647A	ENSP00000269122:V1647A	V	+	2	0	CLTC	55125907	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.162000	0.71874	2.333000	0.79357	0.533000	0.62120	GTT	.	.	.	none		0.557	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859		C	57771125	T	C	57771125	3	2	157	1	0	0	0	0	1	0	0	0	3568	1725	60	3	5066	3	CLTC	17	57771125	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08	1198650	57771125	23424085	72	9320											
INTS2	57508	hgsc.bcm.edu	37	chr17	59945081	59945082	+	In_Frame_Ins	INS	-	-	GAA																															tggtttctcctttatttgttINSgaagacctacaacataaggg																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr17:59945081_59945082insGAA	ENST00000444766.3	-	25	3526_3527	c.3451_3452insTTC	c.(3451-3453)caa>cTTCaa	p.1150_1151insL	INTS2_ENST00000251334.6_In_Frame_Ins_p.1142_1143insL	NM_020748.2	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	1150					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020)				NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	38						CTTTATTTGTTGAAGACCTACA	0.351																																					p.Q1151delinsLQ		Atlas-INDEL	.											.	INTS2	89	.	0			c.3452_3453insTTC						PASS	.																																			SO:0001652	inframe_insertion	57508	exon25			.	AB033113	CCDS45750.1	17q23.2	2006-04-26	2006-03-15	2006-03-15		ENSG00000108506			29241	protein-coding gene	gene with protein product		611346	"KIAA1287"	KIAA1287		16239144	Standard	NR_026641		Approved	INT2	uc002izn.3	Q9H0H0		ENST00000444766.3:c.3449_3451dupTTC	chr17.hg19:g.59945082_59945084dupGAA	ENSP00000414237:p.Leu1150_Leu1150dup	100.0	0.0	0		132.0	27.0	0.204545	NM_020748	Q9ULD3	In_Frame_Ins	INS	ENST00000444766.3	hg19	CCDS45750.1																																																																																			.	.	.	none		0.351	INTS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000445368.1	NM_020748		GAA	59945082	-	GAA	59945081	7	5	157	1	0	1	1	0	0	0	0	0	7785	1812	63	0	166	0	INTS2	17	59945081	In_Frame_Ins	INS	-	TCGA-DZ-6132-01A-11D-1961-08	2173956	59945081	21250129	73	9321											
ACE	1636	hgsc.bcm.edu	37	chr17	61570904	61570904	+	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	agacttacctgtggccttgaGggagggtgccaaccccggct	7	8	14	12	1	0	2	0	1	0	1	0	3	0	3	5	4	3	1	5	4	2	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr17:61570904G>T	ENST00000290866.4	+	20	3044	c.3020G>T	c.(3019-3021)aGg>aTg	p.R1007M	ACE_ENST00000428043.1_Missense_Mutation_p.R1007M|ACE_ENST00000413513.3_Missense_Mutation_p.R433M|ACE_ENST00000290863.6_Missense_Mutation_p.R433M|ACE_ENST00000421982.2_Missense_Mutation_p.R253M|ACE_ENST00000577647.1_Missense_Mutation_p.R433M|ACE_ENST00000490216.2_Missense_Mutation_p.R433M	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	1007	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)	GTGGCCTTGAGGGAGGGTGCC	0.582																																					p.R1007M		Atlas-SNP	.											.	ACE	187	.	0			c.G3020T						PASS	.						80	74	76					17																	61570904		2203	4300	6503	SO:0001583	missense	1636	exon20			CCTTGAGGGAGGG	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.3020G>T	chr17.hg19:g.61570904G>T	ENSP00000290866:p.Arg1007Met	86.0	0.0	.		87.0	18.0	.	NM_000789	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Missense_Mutation	SNP	ENST00000290866.4	hg19	CCDS11637.1	.	.	.	.	.	.	.	.	.	.	G	14.72	2.618950	0.46736	.	.	ENSG00000159640	ENST00000290866;ENST00000428043;ENST00000290863;ENST00000413513;ENST00000421982	T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.80628	0.4659	H	0.97340	3.985	0.80722	D	1	D;D;D;D	0.89917	1.0;0.996;0.999;1.0	D;D;D;D	0.97110	0.992;0.976;0.986;1.0	D	0.88380	0.3001	10	0.87932	D	0	-34.8796	18.0898	0.89471	0.0:0.0:1.0:0.0	.	253;433;433;1007	F6X3S4;B4DXI3;P12821-3;P12821	.;.;.;ACE_HUMAN	M	1007;1007;433;433;253	ENSP00000290866:R1007M;ENSP00000397593:R1007M;ENSP00000290863:R433M;ENSP00000392247:R433M;ENSP00000387760:R253M	ENSP00000290863:R433M	R	+	2	0	ACE	58924636	1.000000	0.71417	0.966000	0.40874	0.792000	0.44763	7.975000	0.88055	2.262000	0.75019	0.561000	0.74099	AGG	.	.	.	none		0.582	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2			T	61570904	G	T	61570904	3	4	157	1	0	0	0	0	1	0	0	0	136	1000	35	4	3301	4	ACE	17	61570904	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	1625823	61570904	19624306	74	9322											
GRB2	2885	hgsc.bcm.edu	37	chr17	73316567	73316567	+	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	tgacatggataaaatctcccCggcggaagcccagctctcca	11	7	9	14	2	2	1	0	1	2	0	4	3	2	3	4	3	2	1	4	3	3	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr17:73316567C>A	ENST00000392562.1	-	6	1318	c.536G>T	c.(535-537)cGg>cTg	p.R179L	GRB2_ENST00000316615.5_Missense_Mutation_p.R138L|GRB2_ENST00000392564.1_Missense_Mutation_p.R179L|GRB2_ENST00000578961.1_Missense_Mutation_p.G123W|GRB2_ENST00000316804.5_Missense_Mutation_p.R179L|GRB2_ENST00000462266.1_5'UTR|GRB2_ENST00000392563.1_Missense_Mutation_p.R138L			P62993	GRB2_HUMAN	growth factor receptor-bound protein 2	179	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.				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)	p.R179L(1)		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)	AAAATCTCCCCGGCGGAAGCC	0.557																																					p.R179L		Atlas-SNP	.											.	GRB2	33	.	1	Substitution - Missense(1)	lung(1)	c.G536T						PASS	.						84	92	89					17																	73316567		2203	4300	6503	SO:0001583	missense	2885	exon6			TCTCCCCGGCGGA		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.536G>T	chr17.hg19:g.73316567C>A	ENSP00000376345:p.Arg179Leu	266.0	0.0	.		223.0	10.0	.	NM_002086	P29354|Q14450|Q63057|Q63059	Missense_Mutation	SNP	ENST00000392562.1	hg19	CCDS11721.1	.	.	.	.	.	.	.	.	.	.	C	35	5.427609	0.96131	.	.	ENSG00000177885	ENST00000316804;ENST00000392562;ENST00000392564;ENST00000392563;ENST00000316615	T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76	5.45	5.45	0.79879	Src homology-3 domain (4);	0.000000	0.85682	D	0.000000	T	0.71879	0.3392	M	0.83953	2.67	0.80722	D	1	D;D	0.76494	0.999;0.964	D;P	0.69307	0.963;0.895	T	0.73357	-0.4008	10	0.52906	T	0.07	-32.5557	19.4688	0.94954	0.0:1.0:0.0:0.0	.	138;179	P62993-2;P62993	.;GRB2_HUMAN	L	179;179;179;138;138	ENSP00000339007:R179L;ENSP00000376345:R179L;ENSP00000376347:R179L;ENSP00000376346:R138L;ENSP00000317360:R138L	ENSP00000317360:R138L	R	-	2	0	GRB2	70828162	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.921000	0.70028	2.838000	0.97847	0.561000	0.74099	CGG	.	.	.	none		0.557	GRB2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259476.1			A	73316567	C	A	73316567	3	1	157	1	0	0	0	0	1	0	0	0	6765	652	23	4	121	4	GRB2	17	73316567	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	11745663	73316567	7878643	75	9323											
BAIAP2	10458	hgsc.bcm.edu	37	chr17	79082274	79082274	+	Splice_Site	DEL	G	G	-																															tgtttctgcctctgcccccaGggcctggatgactatggagc																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr17:79082274delG	ENST00000321300.6	+	13	1593		c.e13-1		BAIAP2_ENST00000575712.1_Splice_Site|BAIAP2_ENST00000435091.3_Splice_Site|BAIAP2_ENST00000428708.2_Splice_Site|BAIAP2_ENST00000321280.7_Splice_Site|BAIAP2_ENST00000392411.3_Splice_Site|BAIAP2_ENST00000416299.2_Splice_Site|BAIAP2_ENST00000575245.1_Splice_Site	NM_001144888.1|NM_017451.2	NP_001138360.1|NP_059345.1	Q9UQB8	BAIP2_HUMAN	BAI1-associated protein 2						actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|filopodium assembly (GO:0046847)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of synaptic plasticity (GO:0048167)|response to bacterium (GO:0009617)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	cytoskeletal adaptor activity (GO:0008093)|identical protein binding (GO:0042802)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)	18	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			TCTGCCCCCAGGGCCTGGATG	0.637																																					.		Atlas-INDEL	.											.	BAIAP2	74	.	0			c.1501-2G>-						PASS	.						72	70	71					17																	79082274		2203	4300	6503	SO:0001630	splice_region_variant	10458	exon13			.	AB015019	CCDS11775.1, CCDS11776.1, CCDS11777.1, CCDS45806.1	17q25.3	2014-09-11			ENSG00000175866				947	protein-coding gene	gene with protein product		605475				10343108	Standard	NM_017451		Approved	BAP2	uc002jzg.2	Q9UQB8	OTTHUMG00000177698	ENST00000321300.6:c.1501-1G>-	chr17.hg19:g.79082274delG		70.0	0.0	0		55.0	12.0	0.218182	NM_001144888	O43858|Q53HB1|Q86WC1|Q8N5C0|Q96CR7|Q9UBR3|Q9UQ43	Splice_Site	DEL	ENST00000321300.6	hg19	CCDS11775.1																																																																																			.	.	.	none		0.637	BAIAP2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438553.1		Intron	-	79082274	G	-	79082274	8	5	157	1	0	1	0	1	0	0	1	0	1301	1014	35	0	1550	0	BAIAP2	17	79082274	Splice_Site	DEL	G	TCGA-DZ-6132-01A-11D-1961-08	5765707	79082274	2112936	76	9324											
DYM	54808	hgsc.bcm.edu	37	chr18	46956680	46956680	+	Missense_Mutation	SNP	T	T	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	ctgattccagaacgggtcatTctcagagatagattccgtgc	10	11	10	10	2	2	4	2	1	1	3	5	5	4	4	2	1	2	0	2	1	2	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr18:46956680T>G	ENST00000269445.6	-	2	542	c.85A>C	c.(85-87)Aat>Cat	p.N29H	DYM_ENST00000442713.2_Missense_Mutation_p.N29H|DYM_ENST00000584977.1_5'UTR|RP11-110H1.9_ENST00000583579.1_RNA	NM_017653.3	NP_060123.3	Q7RTS9	DYM_HUMAN	dymeclin	29					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						AACGGGTCATTCTCAGAGATA	0.423																																					p.N29H		Atlas-SNP	.											.	DYM	52	.	0			c.A85C						PASS	.						147	146	146					18																	46956680		2203	4300	6503	SO:0001583	missense	54808	exon2			GGTCATTCTCAGA	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.85A>C	chr18.hg19:g.46956680T>G	ENSP00000269445:p.Asn29His	169.0	0.0	.		171.0	29.0	.	NM_017653	A8K5I8|B2RCF9|B4DKI7|Q3ZTS8|Q6P2P5|Q8N2M0|Q9BVE9|Q9NPU7	Missense_Mutation	SNP	ENST00000269445.6	hg19	CCDS11937.1	.	.	.	.	.	.	.	.	.	.	T	14.56	2.571437	0.45798	.	.	ENSG00000141627	ENST00000442713;ENST00000269445	D;D	0.82893	-1.66;-1.66	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	D	0.90841	0.7123	M	0.78801	2.425	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.78314	0.991;0.983	D	0.91823	0.5469	10	0.87932	D	0	-23.1803	15.1469	0.72662	0.0:0.0:0.0:1.0	.	29;29	Q7RTS9-2;Q7RTS9	.;DYM_HUMAN	H	29	ENSP00000395942:N29H;ENSP00000269445:N29H	ENSP00000269445:N29H	N	-	1	0	DYM	45210678	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.007000	0.76335	2.371000	0.80710	0.533000	0.62120	AAT	.	.	.	none		0.423	DYM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255912.3	NM_017653		G	46956680	T	G	46956680	3	3	157	1	0	0	0	0	1	0	0	0	4842	1783	62	5	1988	5	DYM	18	46956680	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08		46956680	31120568	77	9325											
SOCS6	9306	hgsc.bcm.edu	37	chr18	67992496	67992496	+	Frame_Shift_Del	DEL	A	A	-																															tgaagagctcggcttctcatAatggagacctgcatcttcac																										TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr18:67992496delA	ENST00000397942.3	+	2	908	c.592delA	c.(592-594)aatfs	p.N198fs	SOCS6_ENST00000582322.1_Frame_Shift_Del_p.N198fs	NM_004232.3	NP_004223.2	O14544	SOCS6_HUMAN	suppressor of cytokine signaling 6	198					defense response (GO:0006952)|JAK-STAT cascade (GO:0007259)|negative regulation of signal transduction (GO:0009968)|negative regulation of T cell activation (GO:0050868)|proteasomal protein catabolic process (GO:0010498)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|immunological synapse (GO:0001772)				NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)	22		Esophageal squamous(42;0.129)|Colorectal(73;0.152)				GGCTTCTCATAATGGAGACCT	0.512																																					p.H197fs	Melanoma(84;1024 1361 24382 36583 42651)	Atlas-INDEL	.											.	SOCS6	54	.	0			c.591delT						PASS	.						108	94	99					18																	67992496		2203	4300	6503	SO:0001589	frameshift_variant	9306	exon2			.	AB006968	CCDS11998.1	18q22	2013-02-14	2004-02-25	2004-02-27	ENSG00000170677	ENSG00000170677		"Suppressors of cytokine signaling", "SH2 domain containing"	16833	protein-coding gene	gene with protein product		605118	"suppressor of cytokine signaling 4"	SOCS4		9344848, 11042152	Standard	NM_004232		Approved	CIS4, SSI4, HSPC060, STATI4, STAI4, Cish4	uc002lkr.1	O14544	OTTHUMG00000132816	ENST00000397942.3:c.592delA	chr18.hg19:g.67992496delA	ENSP00000381034:p.Asn198fs	146.0	0.0	0		129.0	28.0	0.217054	NM_004232	Q8WUM3	Frame_Shift_Del	DEL	ENST00000397942.3	hg19	CCDS11998.1																																																																																			.	.	.	none		0.512	SOCS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256270.2			-	67992496	A	-	67992496	7	5	157	1	0	1	0	1	0	0	0	0	14931	362	13	0	594	0	SOCS6	18	67992496	Frame_Shift_Del	DEL	A	TCGA-DZ-6132-01A-11D-1961-08	21035816	67992496	10084752	78	9326											
MYO1F	4542	hgsc.bcm.edu	37	chr19	8616967	8616967	+	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	ttcattttgcatgaccacgcGggacttctccagcaagaagt	10	11	9	11	2	2	2	1	1	1	1	3	3	2	3	2	1	2	2	2	1	2	4			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:8616967G>T	ENST00000338257.8	-	7	853	c.586C>A	c.(586-588)Cgc>Agc	p.R196S	AC092316.1_ENST00000598703.1_RNA	NM_012335.3	NP_036467.2	O00160	MYO1F_HUMAN	myosin IF	196	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)	p.R196S(1)		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						ATGACCACGCGGGACTTCTCC	0.572																																					p.R196S		Atlas-SNP	.											MYO1F,colon,carcinoma,0,1	MYO1F	128	.	1	Substitution - Missense(1)	kidney(1)	c.C586A						PASS	.						92	93	93					19																	8616967		1977	4198	6175	SO:0001583	missense	4542	exon7			CCACGCGGGACTT	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.586C>A	chr19.hg19:g.8616967G>T	ENSP00000344871:p.Arg196Ser	188.0	0.0	.		125.0	7.0	.	NM_012335	Q8WWN7	Missense_Mutation	SNP	ENST00000338257.8	hg19	CCDS42494.1	.	.	.	.	.	.	.	.	.	.	G	17.73	3.461130	0.63513	.	.	ENSG00000142347	ENST00000305795;ENST00000338257	D	0.96885	-4.16	3.93	2.82	0.32997	Myosin head, motor domain (2);	0.000000	0.64402	D	0.000001	D	0.98865	0.9616	H	0.99336	4.52	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.993;0.993	D	0.98183	1.0458	10	0.87932	D	0	.	12.9806	0.58562	0.0:0.0:0.827:0.173	.	196;196;196	B4DVP3;B0I1T1;O00160	.;.;MYO1F_HUMAN	S	241;196	ENSP00000344871:R196S	ENSP00000304899:R241S	R	-	1	0	MYO1F	8522967	0.996000	0.38824	0.995000	0.50966	0.987000	0.75469	2.332000	0.43903	2.048000	0.60808	0.460000	0.39030	CGC	.	.	.	none		0.572	MYO1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342716.2			T	8616967	G	T	8616967	3	4	157	1	0	0	0	0	1	0	0	0	10080	1116	39	4	2798	4	MYO1F	19	8616967	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08		8616967	50512016	79	9327											
ZNF699	374879	hgsc.bcm.edu	37	chr19	9406673	9406673	+	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	tcatactgtatctttccagtGtgatctctcacatgtgctct	7	17	6	11	0	5	1	2	1	3	0	7	1	6	1	1	0	2	2	1	0	2	3			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:9406673G>C	ENST00000591998.1	-	6	1635	c.1407C>G	c.(1405-1407)caC>caG	p.H469Q	ZNF699_ENST00000308650.3_Missense_Mutation_p.H469Q|CTC-325H20.4_ENST00000591336.1_RNA			Q32M78	ZN699_HUMAN	zinc finger protein 699	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(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						TCTTTCCAGTGTGATCTCTCA	0.458																																					p.H469Q		Atlas-SNP	.											.	ZNF699	67	.	0			c.C1407G						PASS	.						60	64	63					19																	9406673		2200	4296	6496	SO:0001583	missense	374879	exon5			TCCAGTGTGATCT	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.1407C>G	chr19.hg19:g.9406673G>C	ENSP00000467723:p.His469Gln	57.0	0.0	.		55.0	8.0	.	NM_198535	Q8N9A1	Missense_Mutation	SNP	ENST00000591998.1	hg19	CCDS42495.1	.	.	.	.	.	.	.	.	.	.	g	13.65	2.301105	0.40694	.	.	ENSG00000196110	ENST00000308650	T	0.66995	-0.24	3.28	-0.0525	0.13822	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.39407	N	0.001377	T	0.80008	0.4545	M	0.90425	3.115	0.24473	N	0.994389	D	0.71674	0.998	D	0.75484	0.986	T	0.68796	-0.5314	10	0.87932	D	0	.	5.9659	0.19325	0.4949:0.0:0.5051:0.0	.	469	Q32M78	ZN699_HUMAN	Q	469	ENSP00000311596:H469Q	ENSP00000311596:H469Q	H	-	3	2	ZNF699	9267673	0.909000	0.30893	0.019000	0.16419	0.771000	0.43674	0.275000	0.18698	0.085000	0.17107	0.550000	0.68814	CAC	.	.	.	none		0.458	ZNF699-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449010.1	NM_198535		C	9406673	G	C	9406673	3	2	157	1	0	0	0	0	1	0	0	0	18113	1368	48	4	525	4	ZNF699	19	9406673	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	789706	9406673	49722310	80	9328											
ATG4D	84971	hgsc.bcm.edu	37	chr19	10655668	10655668	+	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	tccagcgggactttgtgtccCgcctgtggctcacataccgc	5	10	11	15	3	1	0	1	0	0	0	3	1	3	1	4	2	2	1	4	2	1	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:10655668C>A	ENST00000309469.4	+	3	528	c.355C>A	c.(355-357)Cgc>Agc	p.R119S	ATG4D_ENST00000540862.1_5'Flank	NM_032885.4	NP_116274.3	Q86TL0	ATG4D_HUMAN	autophagy related 4D, cysteine peptidase	119					apoptotic process (GO:0006915)|autophagy (GO:0006914)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activity (GO:0004197)			NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	19			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)			CTTTGTGTCCCGCCTGTGGCT	0.657																																					p.R119S		Atlas-SNP	.											.	ATG4D	47	.	0			c.C355A						PASS	.						87	97	94					19																	10655668		2203	4300	6503	SO:0001583	missense	84971	exon3			GTGTCCCGCCTGT	AJ312332	CCDS12241.1	19p13.2	2014-02-12	2012-06-06	2005-09-11	ENSG00000130734	ENSG00000130734			20789	protein-coding gene	gene with protein product		611340	"AUT-like 4, cysteine endopeptidase (S. cerevisiae)", "APG4 autophagy 4 homolog D (S. cerevisiae)", "ATG4 autophagy related 4 homolog D (S. cerevisiae)"	AUTL4, APG4D		12446702	Standard	NM_032885		Approved	APG4-D	uc002mov.3	Q86TL0	OTTHUMG00000180582	ENST00000309469.4:c.355C>A	chr19.hg19:g.10655668C>A	ENSP00000311318:p.Arg119Ser	290.0	0.0	.		177.0	9.0	.	NM_032885	Q969K0	Missense_Mutation	SNP	ENST00000309469.4	hg19	CCDS12241.1	.	.	.	.	.	.	.	.	.	.	C	14.94	2.686824	0.48097	.	.	ENSG00000130734	ENST00000309469	T	0.48201	0.82	5.06	2.88	0.33553	.	0.292459	0.30538	N	0.009414	T	0.70561	0.3238	M	0.92077	3.27	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.77557	0.988;0.974;0.99	T	0.70676	-0.4806	10	0.72032	D	0.01	7.4899	6.9005	0.24281	0.3089:0.6081:0.0:0.0831	.	56;142;119	B4DGM8;B7ZAY9;Q86TL0	.;.;ATG4D_HUMAN	S	119	ENSP00000311318:R119S	ENSP00000311318:R119S	R	+	1	0	ATG4D	10516668	0.661000	0.27430	0.758000	0.31321	0.002000	0.02628	1.319000	0.33655	0.503000	0.28060	-0.196000	0.12772	CGC	.	.	.	none		0.657	ATG4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452022.1	NM_032885		A	10655668	C	A	10655668	3	1	157	1	0	0	0	0	1	0	0	0	1099	652	23	4	365	4	ATG4D	19	10655668	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	1248995	10655668	48473315	81	9329											
UNC13A	23025	hgsc.bcm.edu	37	chr19	17763482	17763482	+	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	tagacatctctccttctcccCgggcctgcaggacagacaga	9	8	9	15	1	2	3	0	0	2	3	5	4	3	4	4	2	1	1	4	2	1	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:17763482C>A	ENST00000519716.2	-	12	1396	c.1397G>T	c.(1396-1398)cGg>cTg	p.R466L	UNC13A_ENST00000551649.1_Missense_Mutation_p.R466L|UNC13A_ENST00000428389.2_Missense_Mutation_p.R554L|UNC13A_ENST00000252773.7_Missense_Mutation_p.R466L|UNC13A_ENST00000550896.1_Missense_Mutation_p.R466L|UNC13A_ENST00000552293.1_Missense_Mutation_p.R466L	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	466					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						TCCTTCTCCCCGGGCCTGCAG	0.572																																					p.R466L		Atlas-SNP	.											.	UNC13A	299	.	0			c.G1397T						PASS	.						220	223	222					19																	17763482		1949	4140	6089	SO:0001583	missense	23025	exon12			TCTCCCCGGGCCT	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.1397G>T	chr19.hg19:g.17763482C>A	ENSP00000429562:p.Arg466Leu	473.0	0.0	.		363.0	16.0	.	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	hg19	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	C	10.57	1.385968	0.25031	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	T;T;T;T;T;T	0.80994	-1.43;-1.44;-1.43;-1.29;-1.3;-1.43	4.06	4.06	0.47325	.	0.640937	0.11863	U	0.522146	T	0.69682	0.3138	N	0.24115	0.695	0.35688	D	0.814642	B	0.09022	0.002	B	0.09377	0.004	T	0.67213	-0.5727	10	0.27082	T	0.32	-3.9885	13.7484	0.62890	0.0:1.0:0.0:0.0	.	466	Q9UPW8	UN13A_HUMAN	L	466;554;466;466;466;466	ENSP00000429562:R466L;ENSP00000400409:R554L;ENSP00000252773:R466L;ENSP00000447236:R466L;ENSP00000447572:R466L;ENSP00000446831:R466L	ENSP00000252773:R466L	R	-	2	0	UNC13A	17624482	1.000000	0.71417	1.000000	0.80357	0.697000	0.40408	2.345000	0.44018	2.103000	0.63969	0.491000	0.48974	CGG	.	.	.	none		0.572	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		A	17763482	C	A	17763482	3	1	157	1	0	0	0	0	1	0	0	0	16996	652	23	4	3838	4	UNC13A	19	17763482	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	7107814	17763482	41365501	82	9330											
PIK3R2	5296	hgsc.bcm.edu	37	chr19	18274091	18274091	+	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	aggaccagattgtcaaggagGacagcgtggaggcagtgggc	11	5	18	7	1	1	1	1	0	0	1	1	5	1	5	1	6	1	1	1	6	1	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:18274091G>A	ENST00000593731.1	+	11	1869	c.1309G>A	c.(1309-1311)Gac>Aac	p.D437N	PIK3R2_ENST00000222254.8_Missense_Mutation_p.D437N			O00459	P85B_HUMAN	phosphoinositide-3-kinase, regulatory subunit 2 (beta)	437					blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	phosphatidylinositol 3-kinase regulator activity (GO:0035014)|receptor tyrosine kinase binding (GO:0030971)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(3)|pancreas(1)|stomach(1)	24					Isoprenaline(DB01064)	TGTCAAGGAGGACAGCGTGGA	0.577																																					p.D437N		Atlas-SNP	.											.	PIK3R2	48	.	0			c.G1309A						PASS	.						125	107	113					19																	18274091		2203	4300	6503	SO:0001583	missense	5296	exon11			AAGGAGGACAGCG		CCDS12371.1	19p13.11	2013-03-28	2008-02-04		ENSG00000105647	ENSG00000105647		"SH2 domain containing"	8980	protein-coding gene	gene with protein product		603157				1314371	Standard	NM_005027		Approved	P85B, p85	uc002nia.2	O00459	OTTHUMG00000183383	ENST00000593731.1:c.1309G>A	chr19.hg19:g.18274091G>A	ENSP00000471914:p.Asp437Asn	135.0	0.0	.		75.0	13.0	.	NM_005027	Q5EAT5|Q9UPH9	Missense_Mutation	SNP	ENST00000593731.1	hg19	CCDS12371.1	.	.	.	.	.	.	.	.	.	.	G	15.05	2.719551	0.48728	.	.	ENSG00000105647	ENST00000222254	T	0.47869	0.83	4.08	4.08	0.47627	.	0.102115	0.64402	D	0.000002	T	0.40171	0.1106	L	0.43152	1.355	0.42153	D	0.991565	B	0.19583	0.037	B	0.15052	0.012	T	0.38950	-0.9637	10	0.52906	T	0.07	-47.255	12.9549	0.58421	0.0:0.0:0.8377:0.1623	.	437	O00459	P85B_HUMAN	N	437	ENSP00000222254:D437N	ENSP00000222254:D437N	D	+	1	0	PIK3R2	18135091	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.262000	0.65501	2.216000	0.71823	0.561000	0.74099	GAC	.	.	.	none		0.577	PIK3R2-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000466386.2	NM_005027		A	18274091	G	A	18274091	3	1	157	1	0	0	0	0	1	0	0	0	11926	1174	41	2	1347	2	PIK3R2	19	18274091	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	510609	18274091	40854892	83	9331											
ZNF85	7639	hgsc.bcm.edu	37	chr19	21132138	21132138	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttaaccgattctcaactcTtactacccataagataattc	13	15	2	11	1	2	1	1	0	2	1	4	2	2	1	2	0	4	0	2	0	6	8			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:21132138T>C	ENST00000328178.8	+	4	931	c.818T>C	c.(817-819)cTt>cCt	p.L273P	ZNF85_ENST00000345030.6_Missense_Mutation_p.L240P|ZNF85_ENST00000601023.1_Missense_Mutation_p.L214P	NM_001256173.1|NM_003429.4	NP_001243102.1|NP_003420.2	Q03923	ZNF85_HUMAN	zinc finger protein 85	273					transcription, DNA-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						TTCTCAACTCTTACTACCCAT	0.348																																					p.L303P		Atlas-SNP	.											.	ZNF85	72	.	0			c.T908C						PASS	.						26	29	28					19																	21132138		2193	4286	6479	SO:0001583	missense	7639	exon5			CAACTCTTACTAC	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.818T>C	chr19.hg19:g.21132138T>C	ENSP00000329793:p.Leu273Pro	59.0	0.0	.		32.0	4.0	.	NM_001256171	B9ZVP4|Q6NVI0	Missense_Mutation	SNP	ENST00000328178.8	hg19	CCDS32977.1	.	.	.	.	.	.	.	.	.	.	.	11.50	1.657272	0.29425	.	.	ENSG00000105750	ENST00000328178;ENST00000345030;ENST00000421385	T;T	0.53857	0.6;0.6	1.35	1.35	0.21983	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.76263	0.3963	H	0.94620	3.56	0.25920	N	0.983126	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.63350	-0.6657	9	0.87932	D	0	.	7.5498	0.27790	0.0:0.0:0.0:1.0	.	240;214;273	Q03923-2;Q49A12;Q03923	.;.;ZNF85_HUMAN	P	273;240;148	ENSP00000329793:L273P;ENSP00000342340:L240P	ENSP00000329793:L273P	L	+	2	0	ZNF85	20923978	0.117000	0.22190	0.004000	0.12327	0.013000	0.08279	2.803000	0.47924	0.569000	0.29329	0.379000	0.24179	CTT	.	.	.	none		0.348	ZNF85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463430.1	NM_003429		C	21132138	T	C	21132138	3	2	157	1	0	0	0	0	1	0	0	0	18205	1609	56	3	832	3	ZNF85	19	21132138	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08	2858047	21132138	37996845	84	9332											
SUPT5H	6829	hgsc.bcm.edu	37	chr19	39964723	39964723	+	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	ccctcgtccccacaggtcaaCccacaatacaacccgcagac	12	4	5	20	2	1	1	1	0	0	1	3	1	2	1	5	1	3	1	5	1	4	1			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:39964723C>A	ENST00000599117.1	+	27	2980	c.2613C>A	c.(2611-2613)aaC>aaA	p.N871K	SUPT5H_ENST00000359191.6_Missense_Mutation_p.N867K|SUPT5H_ENST00000402194.2_Missense_Mutation_p.N867K|SUPT5H_ENST00000432763.2_Missense_Mutation_p.N871K|SUPT5H_ENST00000598725.1_Missense_Mutation_p.N871K			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	871	10 X 8 AA approximate tandem repeats of P-[TS]-P-S-P-[QA]-[SG]-Y, motif CTR2.|Pro-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)			CACAGGTCAACCCACAATACA	0.647											OREG0025462	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N871K		Atlas-SNP	.											.	SUPT5H	119	.	0			c.C2613A						PASS	.						84	89	87					19																	39964723		2203	4300	6503	SO:0001583	missense	6829	exon25			GGTCAACCCACAA	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.2613C>A	chr19.hg19:g.39964723C>A	ENSP00000470252:p.Asn871Lys	121.0	0.0	.	889	66.0	11.0	.	NM_003169	O43279|Q59G52|Q99639	Missense_Mutation	SNP	ENST00000599117.1	hg19	CCDS12536.1	.	.	.	.	.	.	.	.	.	.	C	15.70	2.910409	0.52439	.	.	ENSG00000196235	ENST00000432763;ENST00000402194;ENST00000378524;ENST00000359191	.	.	.	5.36	3.19	0.36642	.	0.043680	0.85682	D	0.000000	T	0.51652	0.1687	L	0.53249	1.67	0.58432	D	0.999995	B;B;B	0.34200	0.367;0.387;0.441	B;B;B	0.37550	0.253;0.131;0.206	T	0.48736	-0.9009	8	.	.	.	-34.0435	10.5839	0.45271	0.0:0.8333:0.0:0.1667	.	663;867;871	B4DJK4;O00267-2;O00267	.;.;SPT5H_HUMAN	K	871;867;849;871	.	.	N	+	3	2	SUPT5H	44656563	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	2.352000	0.44080	1.235000	0.43724	0.462000	0.41574	AAC	.	.	.	none		0.647	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1	NM_003169		A	39964723	C	A	39964723	3	1	157	1	0	0	0	0	1	0	0	0	15411	506	18	4	2711	4	SUPT5H	19	39964723	Missense_Mutation	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	18832585	39964723	19164260	85	9333											
ZNF223	7766	hgsc.bcm.edu	37	chr19	44570872	44570872	+	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	gagatatgtagtgtgagcttCcgtcttaggtcaagtcttaa	10	14	11	6	1	3	2	1	1	2	1	4	3	4	2	1	1	1	2	1	1	5	5			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:44570872C>T	ENST00000434772.3	+	5	1146	c.891C>T	c.(889-891)ttC>ttT	p.F297F	ZNF223_ENST00000591793.1_Silent_p.F407F	NM_013361.4	NP_037493.3	Q9UK11	ZN223_HUMAN	zinc finger protein 223	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(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18		Prostate(69;0.0352)				GTGTGAGCTTCCGTCTTAGGT	0.448																																					p.F297F		Atlas-SNP	.											.	ZNF223	61	.	0			c.C891T						PASS	.						131	126	128					19																	44570872		2203	4300	6503	SO:0001819	synonymous_variant	7766	exon5			GAGCTTCCGTCTT	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.891C>T	chr19.hg19:g.44570872C>T		148.0	0.0	.		107.0	15.0	.	NM_013361	Q15736|Q8TBJ3|Q9HCA9	Silent	SNP	ENST00000434772.3	hg19	CCDS12635.1																																																																																			.	.	.	none		0.448	ZNF223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460469.2			T	44570872	C	T	44570872	2	4	157	1	0	0	0	0	0	0	0	1	17789	854	30	2		2	ZNF223	19	44570872	Silent	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	4606149	44570872	14558111	86	9334											
FCGRT	2217	hgsc.bcm.edu	37	chr19	50017313	50017313	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggaaaaccaggtgtcctggtAttgggagaaagagaccacag	14	6	14	7	0	0	2	0	0	0	2	1	5	1	3	3	4	1	1	3	4	4	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:50017313A>G	ENST00000221466.5	+	3	734	c.248A>G	c.(247-249)tAt>tGt	p.Y83C	FCGRT_ENST00000596975.1_Missense_Mutation_p.Y83C|FCGRT_ENST00000426395.3_Missense_Mutation_p.Y83C|FCGRT_ENST00000599988.1_Intron|FCGRT_ENST00000594823.1_3'UTR	NM_001136019.2	NP_001129491.1	P55899	FCGRN_HUMAN	Fc fragment of IgG, receptor, transporter, alpha	83	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)		GTGTCCTGGTATTGGGAGAAA	0.582																																					p.Y83C		Atlas-SNP	.											.	FCGRT	23	.	0			c.A248G						PASS	.						41	47	45					19																	50017313		2203	4300	6503	SO:0001583	missense	2217	exon3			CCTGGTATTGGGA	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.248A>G	chr19.hg19:g.50017313A>G	ENSP00000221466:p.Tyr83Cys	63.0	0.0	.		49.0	19.0	.	NM_001136019	Q5HYM5|Q9HBV7|Q9NZ19	Missense_Mutation	SNP	ENST00000221466.5	hg19	CCDS12770.1	.	.	.	.	.	.	.	.	.	.	A	16.54	3.150611	0.57151	.	.	ENSG00000104870	ENST00000221466;ENST00000426395;ENST00000415900;ENST00000452439	T;T	0.01185	5.21;5.21	4.83	2.61	0.31194	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.374848	0.19651	N	0.109214	T	0.07369	0.0186	M	0.93197	3.39	0.41878	D	0.990305	D	0.89917	1.0	D	0.83275	0.996	T	0.00662	-1.1621	10	0.87932	D	0	.	3.4456	0.07480	0.6789:0.0:0.1082:0.2129	.	83	P55899	FCGRN_HUMAN	C	83	ENSP00000221466:Y83C;ENSP00000410798:Y83C	ENSP00000221466:Y83C	Y	+	2	0	FCGRT	54709125	0.976000	0.34144	0.999000	0.59377	0.876000	0.50452	2.603000	0.46266	0.868000	0.35678	0.459000	0.35465	TAT	.	.	.	none		0.582	FCGRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465267.1			G	50017313	A	G	50017313	3	3	157	1	0	0	0	0	1	0	0	0	5793	449	16	3	254	3	FCGRT	19	50017313	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	5446441	50017313	9111670	87	9335											
ZNF473	25888	hgsc.bcm.edu	37	chr19	50549983	50549983	+	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	gaaaagccttatgtttgtcaGgaatgcgggaaagccttcac	12	10	11	8	1	2	0	2	0	0	0	2	3	2	2	2	2	3	1	2	2	5	3			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:50549983G>C	ENST00000595661.1	+	6	2778	c.2283G>C	c.(2281-2283)caG>caC	p.Q761H	ZNF473_ENST00000391821.2_Missense_Mutation_p.Q761H|ZNF473_ENST00000445728.3_Missense_Mutation_p.Q749H|ZNF473_ENST00000270617.3_Missense_Mutation_p.Q761H|CTD-2126E3.3_ENST00000599914.1_RNA|ZNF473_ENST00000601364.1_Intron|CTD-2126E3.3_ENST00000599410.1_RNA			Q8WTR7	ZN473_HUMAN	zinc finger protein 473	761					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37		all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.00111)|OV - Ovarian serous cystadenocarcinoma(262;0.0058)		ATGTTTGTCAGGAATGCGGGA	0.522											OREG0025632	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q761H		Atlas-SNP	.											.	ZNF473	86	.	0			c.G2283C						PASS	.						80	80	80					19																	50549983		2203	4300	6503	SO:0001583	missense	25888	exon5			TTGTCAGGAATGC	AB032967	CCDS33077.1	19q13.33	2013-01-08						"Zinc fingers, C2H2-type", "-"	23239	protein-coding gene	gene with protein product						11782445	Standard	NM_015428		Approved	KIAA1141, DKFZP434N043, HZFP100	uc002prn.3	Q8WTR7		ENST00000595661.1:c.2283G>C	chr19.hg19:g.50549983G>C	ENSP00000472808:p.Gln761His	136.0	0.0	.	970	111.0	26.0	.	NM_015428	A8K8T7|Q9ULS9|Q9Y4Q7	Missense_Mutation	SNP	ENST00000595661.1	hg19	CCDS33077.1	.	.	.	.	.	.	.	.	.	.	G	13.47	2.247320	0.39697	.	.	ENSG00000142528	ENST00000270617;ENST00000391821;ENST00000445728	T;T;T	0.07800	3.16;3.16;3.16	3.84	1.72	0.24424	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.611213	0.13601	N	0.375867	T	0.07007	0.0178	N	0.02916	-0.46	0.25928	N	0.983026	D	0.61080	0.989	P	0.60173	0.87	T	0.30446	-0.9978	10	0.44086	T	0.13	-0.3948	5.7557	0.18172	0.3335:0.0:0.6665:0.0	.	761	Q8WTR7	ZN473_HUMAN	H	761;761;749	ENSP00000270617:Q761H;ENSP00000375697:Q761H;ENSP00000388961:Q749H	ENSP00000270617:Q761H	Q	+	3	2	ZNF473	55241795	0.000000	0.05858	0.978000	0.43139	0.764000	0.43329	-1.663000	0.01968	0.603000	0.29913	0.650000	0.86243	CAG	.	.	.	none		0.522	ZNF473-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464833.1	XM_046390		C	50549983	G	C	50549983	3	2	157	1	0	0	0	0	1	0	0	0	17943	991	35	4	2297	4	ZNF473	19	50549983	Missense_Mutation	SNP	G	TCGA-DZ-6132-01A-11D-1961-08	532670	50549983	8579000	88	9336											
TTYH1	57348	hgsc.bcm.edu	37	chr19	54937848	54937848	+	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	gccctaccctctcccctcccAggtggctggcctacgtcctc	3	9	8	21	1	1	0	0	0	1	0	5	0	3	0	7	3	2	1	7	3	2	2			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:54937848A>G	ENST00000376530.3	+	5	741		c.e5-1		TTYH1_ENST00000391739.3_Splice_Site|TTYH1_ENST00000301194.4_Splice_Site|TTYH1_ENST00000489425.1_Splice_Site|TTYH1_ENST00000376531.3_Splice_Site	NM_001201461.1|NM_020659.3	NP_001188390.1|NP_065710.1	Q9H313	TTYH1_HUMAN	tweety family member 1						cell-substrate adhesion (GO:0031589)|chloride transport (GO:0006821)|filopodium assembly (GO:0046847)|ion transmembrane transport (GO:0034220)|iron ion transmembrane transport (GO:0034755)|iron ion transport (GO:0006826)|mitotic nuclear division (GO:0007067)|regulation of anion transport (GO:0044070)|single organismal cell-cell adhesion (GO:0016337)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|filopodium membrane (GO:0031527)|filopodium tip (GO:0032433)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum membrane (GO:0030868)	calcium ion binding (GO:0005509)|iron ion transmembrane transporter activity (GO:0005381)|volume-sensitive chloride channel activity (GO:0072320)	p.?(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0767)		CTCCCCTCCCAGGTGGCTGGC	0.652																																					.		Atlas-SNP	.											TTYH1,larynx,carcinoma,0,1	TTYH1	78	.	1	Unknown(1)	upper_aerodigestive_tract(1)	c.639-2A>G						PASS	.						96	79	85					19																	54937848		2203	4300	6503	SO:0001630	splice_region_variant	57348	exon5			CCTCCCAGGTGGC	AF177909	CCDS12893.1, CCDS33106.1, CCDS56102.1	19q13.4	2013-09-02	2013-09-02		ENSG00000167614	ENSG00000167614			13476	protein-coding gene	gene with protein product		605784	"tweety (Drosophila) homolog 1", "tweety homolog 1 (Drosophila)"			10950931	Standard	NM_020659		Approved		uc002qfr.3	Q9H313	OTTHUMG00000065544	ENST00000376530.3:c.639-1A>G	chr19.hg19:g.54937848A>G		162.0	1.0	.		116.0	21.0	.	NM_001005367	B0VJY3|B0VJY4|B0VJY5|B2VAL9|Q5U682|Q68A17|Q6L750|Q6ZTE5|Q8WUU2	Splice_Site	SNP	ENST00000376530.3	hg19	CCDS12893.1	.	.	.	.	.	.	.	.	.	.	A	17.80	3.478123	0.63849	.	.	ENSG00000167614	ENST00000301194;ENST00000376530;ENST00000445095;ENST00000391739;ENST00000376531	.	.	.	4.58	4.58	0.56647	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2014	0.54328	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TTYH1	59629660	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	4.433000	0.59929	1.836000	0.53414	0.459000	0.35465	.	.	.	.	none		0.652	TTYH1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140498.1		Intron	G	54937848	A	G	54937848	5	3	157	1	0	0	0	0	0	0	1	0	16751	202	7	3	655	3	TTYH1	19	54937848	Splice_Site	SNP	A	TCGA-DZ-6132-01A-11D-1961-08	4387865	54937848	4191135	89	9337											
KIR2DL4	3811	hgsc.bcm.edu	37	chr19	55324637	55324637	+	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	1	0	0	0	0	0	0	0	0	0	agtggccatcatcctctttaCcatccttcccttctttctcc	5	16	3	17	0	4	0	1	0	3	0	8	0	7	0	6	1	1	0	6	1	1	5			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr19:55324637C>T	ENST00000538269.1	+	2	61				KIR2DL4_ENST00000396293.1_Intron|KIR2DL4_ENST00000463062.1_3'UTR|KIR2DL4_ENST00000345540.5_Intron|KIR3DL1_ENST00000402254.2_Intron|KIR2DL4_ENST00000396284.2_Missense_Mutation_p.T253I|KIR2DL4_ENST00000357494.4_Intron|KIR2DL4_ENST00000346587.4_Intron|KIR3DL1_ENST00000541392.1_Intron|KIR2DL4_ENST00000359085.4_Missense_Mutation_p.T255I			P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 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)		ATCCTCTTTACCATCCTTCCC	0.502																																					p.T255I		Atlas-SNP	.											.	KIR2DL4	62	.	0			c.C764T						PASS	.						120	185	164					19																	55324637		2009	4160	6169	SO:0001627	intron_variant	3805	exon6			TCTTTACCATCCT	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	ENST00000538269.1:c.35-4352C>T	chr19.hg19:g.55324637C>T		57.0	0.0	.		63.0	25.0	.	NM_001080772	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000538269.1	hg19		.	.	.	.	.	.	.	.	.	.	c	0	-2.781565	0.00079	.	.	ENSG00000189013	ENST00000396284;ENST00000359085;ENST00000396289	T;T;T	0.00454	7.39;7.32;7.4	0.569	-1.14	0.09741	.	6.239890	0.01410	N	0.013962	T	0.00271	0.0008	N	0.25060	0.705	0.09310	N	1	B;B;B	0.16802	0.019;0.0;0.001	B;B;B	0.23852	0.049;0.002;0.016	T	0.46596	-0.9180	9	0.28530	T	0.3	.	.	.	.	.	255;253;238	Q99706;E7EST5;Q99706-2	KI2L4_HUMAN;.;.	I	253;255;253	ENSP00000379580:T253I;ENSP00000351988:T255I;ENSP00000379584:T253I	ENSP00000351988:T255I	T	+	2	0	KIR2DL4	60016449	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.795000	0.00764	-1.106000	0.03008	-1.140000	0.01884	ACC	.	.	.	none		0.502	KIR3DL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_013289		T	55324637	C	T	55324637	1	4	157	0	1	0	0	0	0	0	0	0	8325	507	18	2		2	KIR2DL4	19	55324637	Intron	SNP	C	TCGA-DZ-6132-01A-11D-1961-08	386789	55324637	3804346	90	9338											
STAU1	6780	hgsc.bcm.edu	37	chr20	47741019	47741019	+	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	aacagctatggcggcattttTctttgaaatcttcttgcttt	8	18	7	8	1	3	1	0	1	3	0	3	1	3	1	0	2	3	3	0	2	3	7			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr20:47741019T>A	ENST00000371856.2	-	7	1125	c.715A>T	c.(715-717)Aaa>Taa	p.K239*	STAU1_ENST00000347458.5_Nonsense_Mutation_p.K158*|STAU1_ENST00000371792.1_Nonsense_Mutation_p.K158*|STAU1_ENST00000371802.1_Nonsense_Mutation_p.K164*|STAU1_ENST00000360426.4_Nonsense_Mutation_p.K158*|STAU1_ENST00000340954.7_Nonsense_Mutation_p.K158*|STAU1_ENST00000371828.3_Nonsense_Mutation_p.K164*	NM_017453.2	NP_059347.2	O95793	STAU1_HUMAN	staufen double-stranded RNA binding protein 1	239	DRBM 2. {ECO:0000255|PROSITE- ProRule:PRU00266}.				intracellular mRNA localization (GO:0008298)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|rough endoplasmic reticulum (GO:0005791)	double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|liver(1)|lung(6)|ovary(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	23			BRCA - Breast invasive adenocarcinoma(12;0.000644)|Colorectal(8;0.198)			GCGGCATTTTTCTTTGAAATC	0.483																																					p.K239X		Atlas-SNP	.											.	STAU1	54	.	0			c.A715T						PASS	.						150	167	161					20																	47741019		2203	4300	6503	SO:0001587	stop_gained	6780	exon7			CATTTTTCTTTGA		CCDS13414.1, CCDS13415.1, CCDS33481.1	20q13.1	2014-06-13	2013-06-05	2005-11-04	ENSG00000124214	ENSG00000124214			11370	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 150"	601716	"staufen (Drosophila, RNA-binding protein)", "staufen, RNA binding protein (Drosophila)", "staufen, RNA binding protein, homolog 1 (Drosophila)"	STAU		8884277, 15680326	Standard	XM_005260524		Approved	PPP1R150	uc002xud.3	O95793	OTTHUMG00000032691	ENST00000371856.2:c.715A>T	chr20.hg19:g.47741019T>A	ENSP00000360922:p.Lys239*	248.0	0.0	.		268.0	78.0	.	NM_017453	A8K9Z4|E1P5Y1|E1P608|Q5JW29|Q6GTM4|Q9H5B4|Q9H5B5|Q9Y3Q2	Nonsense_Mutation	SNP	ENST00000371856.2	hg19	CCDS13414.1	.	.	.	.	.	.	.	.	.	.	T	39	7.406203	0.98265	.	.	ENSG00000124214	ENST00000371828;ENST00000340954;ENST00000371856;ENST00000360426;ENST00000347458;ENST00000371805;ENST00000371802;ENST00000371792;ENST00000437404	.	.	.	5.33	5.33	0.75918	.	0.087311	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.3231	15.3236	0.74141	0.0:0.0:0.0:1.0	.	.	.	.	X	164;158;239;158;158;158;164;158;164	.	ENSP00000345425:K158X	K	-	1	0	STAU1	47174426	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	8.036000	0.88901	2.017000	0.59298	0.528000	0.53228	AAA	.	.	.	none		0.483	STAU1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079633.1	NM_017453		A	47741019	T	A	47741019	4	1	157	1	0	0	0	0	0	1	0	0	15284	1792	62	5	1050	5	STAU1	20	47741019	Nonsense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08		47741019	15284501	91	9339											
DSCAM	1826	hgsc.bcm.edu	37	chr21	41496202	41496202	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agggggaagccaggacacaaAgaccatggaggctgaggccg	13	2	17	9	1	0	2	0	1	0	1	0	5	0	5	3	6	1	1	3	6	2	0			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chr21:41496202A>G	ENST00000400454.1	-	20	4093	c.3616T>C	c.(3616-3618)Ttt>Ctt	p.F1206L		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1206	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				CAGGACACAAAGACCATGGAG	0.562																																					p.F1206L	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.T3616C						PASS	.						103	116	112					21																	41496202		2044	4179	6223	SO:0001583	missense	1826	exon20			ACACAAAGACCAT	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.3616T>C	chr21.hg19:g.41496202A>G	ENSP00000383303:p.Phe1206Leu	207.0	0.0	.		163.0	26.0	.	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	hg19	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	A	9.620	1.133520	0.21041	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.55413	0.52;0.52	5.2	4.05	0.47172	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.054089	0.85682	D	0.000000	T	0.26085	0.0636	N	0.02830	-0.485	0.37429	D	0.913953	P	0.35192	0.489	B	0.39379	0.298	T	0.32322	-0.9911	10	0.02654	T	1	.	10.7978	0.46470	0.9249:0.0:0.0751:0.0	.	1206	O60469	DSCAM_HUMAN	L	1206;958	ENSP00000383303:F1206L;ENSP00000385342:F958L	ENSP00000383303:F1206L	F	-	1	0	DSCAM	40418072	1.000000	0.71417	0.998000	0.56505	0.602000	0.36980	5.892000	0.69790	0.805000	0.34159	-0.371000	0.07208	TTT	.	.	.	none		0.562	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		G	41496202	A	G	41496202	3	3	157	1	0	0	0	0	1	0	0	0	4770	72	3	3	2478	3	DSCAM	21	41496202	Missense_Mutation	SNP	A	TCGA-DZ-6132-01A-11D-1961-08		41496202	6633693	92	9340											
HDHD1A	8226	hgsc.bcm.edu	37	chrX	7023838	7023838	+	Missense_Mutation	SNP	T	T	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	gtatttcttgtcatagcgatTacatatttcttgaaacacca	12	16	5	8	1	3	1	1	1	2	0	3	2	3	1	1	0	3	1	1	0	5	8			TCGA-DZ-6132-01A-11D-1961-08	TCGA-DZ-6132-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be6d6e8a-236f-4a34-a19c-c7d6290d97f0	499ed479-d046-4343-9bd4-14b7201bdc55	g.chrX:7023838T>G	ENST00000381077.5	-	2	179	c.103A>C	c.(103-105)Aat>Cat	p.N35H	HDHD1_ENST00000498474.2_5'UTR|HDHD1_ENST00000424830.2_Missense_Mutation_p.N58H|HDHD1_ENST00000412827.2_Missense_Mutation_p.N35H|HDHD1_ENST00000540122.1_Missense_Mutation_p.N35H	NM_001178136.1|NM_012080.4	NP_001171607.1|NP_036212.3	Q08623	HDHD1_HUMAN	haloacid dehalogenase-like hydrolase domain containing 1	35					nucleotide metabolic process (GO:0009117)	extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)			breast(2)|large_intestine(1)|lung(3)	6						TCATAGCGATTACATATTTCT	0.393																																					p.N58H		Atlas-SNP	.											.	HDHD1	21	.	0			c.A172C						PASS	.						55	46	49					X																	7023838		1847	4082	5929	SO:0001583	missense	8226	exon3			AGCGATTACATAT	M86934	CCDS48075.1, CCDS48076.1, CCDS55366.1, CCDS55367.1	Xp22.32	2010-07-21	2010-07-21	2010-07-21	ENSG00000130021	ENSG00000130021			16818	protein-coding gene	gene with protein product		306480	"family with sequence similarity 16, member A, X-linked", "haloacid dehalogenase-like hydrolase domain containing 1A"	FAM16AX, HDHD1A		1734713, 1284467	Standard	NM_012080		Approved	DXF68S1E, GS1	uc011mhm.1	Q08623	OTTHUMG00000021101	ENST00000381077.5:c.103A>C	chrX.hg19:g.7023838T>G	ENSP00000370467:p.Asn35His	34.0	0.0	.		33.0	12.0	.	NM_001135565	B2R7X6|B4DV93|B7Z6Q3|E9PAV8|F5GWZ2|Q53F84|Q96EB8	Missense_Mutation	SNP	ENST00000381077.5	hg19	CCDS48075.1	.	.	.	.	.	.	.	.	.	.	c	7.623	0.677318	0.14841	.	.	ENSG00000130021	ENST00000381077;ENST00000544385;ENST00000412827;ENST00000424830;ENST00000540122;ENST00000486446	T;T;T;T;T	0.30714	3.42;1.52;3.42;3.42;3.42	4.01	4.01	0.46588	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);	0.660693	0.15594	N	0.254263	T	0.23766	0.0575	N	0.21282	0.65	0.09310	N	1	D;B;P;B;B	0.53745	0.962;0.346;0.711;0.045;0.136	B;B;P;B;B	0.46419	0.4;0.382;0.516;0.057;0.201	T	0.05500	-1.0881	10	0.45353	T	0.12	-18.7046	7.1959	0.25853	0.0:0.7837:0.0:0.2163	.	35;35;58;35;35	Q08623-3;Q08623-2;E9PAV8;E7EVH9;Q08623	.;.;.;.;HDHD1_HUMAN	H	35;51;35;58;35;35	ENSP00000370467:N35H;ENSP00000406260:N35H;ENSP00000396452:N58H;ENSP00000441208:N35H;ENSP00000430995:N35H	ENSP00000370467:N35H	N	-	1	0	HDHD1	7033838	0.177000	0.23109	0.002000	0.10522	0.370000	0.29829	0.823000	0.27366	0.559000	0.29153	-0.177000	0.13119	AAT	.	.	.	none		0.393	HDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055683.2	NM_012080		G	7023838	T	G	7023838	3	3	157	1	0	0	0	0	1	0	0	0	7029	1754	61	5	716	5	HDHD1A	23	7023838	Missense_Mutation	SNP	T	TCGA-DZ-6132-01A-11D-1961-08		7023838	148246722	93	9341											
UBR4	23352	hgsc.bcm.edu	37	chr1	19448476	19448477	+	Frame_Shift_Ins	INS	-	-	A																															ttgatggttcgctgggcggcINSaatctctgcacaggctttca																										TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr1:19448476_19448477insA	ENST00000375254.3	-	67	9873_9874	c.9846_9847insT	c.(9844-9849)attgccfs	p.A3283fs	UBR4_ENST00000375226.2_Frame_Shift_Ins_p.A3259fs|UBR4_ENST00000375267.2_Frame_Shift_Ins_p.A3283fs|UBR4_ENST00000375217.2_Frame_Shift_Ins_p.A3276fs	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	3283					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)		CGCTGGGCGGCAATCTCTGCAC	0.485																																					p.A3283fs		Atlas-INDEL	.											.	UBR4	415	.	0			c.9847_9848insT						PASS	.																																			SO:0001589	frameshift_variant	23352	exon67			.	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.9847dupT	chr1.hg19:g.19448478_19448478dupA	ENSP00000364403:p.Ala3283fs	105.0	0.0	0		75.0	30.0	0.4	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Frame_Shift_Ins	INS	ENST00000375254.3	hg19	CCDS189.1																																																																																			.	.	.	none		0.485	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		A	19448477	-	A	19448476	7	5	158	1	0	1	1	0	0	0	0	0	16916	710	25	0	5864	0	UBR4	1	19448476	Frame_Shift_Ins	INS	-	TCGA-DZ-6133-01A-11D-1961-08		19448476	229802145	1	9342											
ZNF436	80818	hgsc.bcm.edu	37	chr1	23688888	23688888	+	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	cagtggtatggcttctctccCgtgtgggctctgcgatgacg	4	12	14	11	3	2	1	0	1	2	0	4	2	3	1	1	3	1	3	1	3	1	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr1:23688888C>A	ENST00000314011.4	-	4	1123	c.987G>T	c.(985-987)acG>acT	p.T329T	ZNF436_ENST00000374608.3_Silent_p.T329T	NM_001077195.1	NP_001070663.1	Q9C0F3	ZN436_HUMAN	zinc finger protein 436	329					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)		GCTTCTCTCCCGTGTGGGCTC	0.517																																					p.T329T		Atlas-SNP	.											.	ZNF436	49	.	0			c.G987T						PASS	.						118	113	114					1																	23688888		2203	4300	6503	SO:0001819	synonymous_variant	80818	exon4			CTCTCCCGTGTGG	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.987G>T	chr1.hg19:g.23688888C>A		226.0	0.0	.		150.0	9.0	.	NM_001077195	Q658I9	Silent	SNP	ENST00000314011.4	hg19	CCDS233.1																																																																																			.	.	.	none		0.517	ZNF436-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008908.1	NM_030634		A	23688888	C	A	23688888	2	1	158	1	0	0	0	0	0	0	0	1	17921	639	23	4		4	ZNF436	1	23688888	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	4240412	23688888	225561733	2	9343											
PSMB4	5692	hgsc.bcm.edu	37	chr1	151372078	151372078	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	actaagatggaagcgtttttGgggtcgcggtccggactttg	7	12	15	7	4	0	1	0	0	0	1	2	3	1	3	1	5	1	1	1	5	2	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr1:151372078G>A	ENST00000290541.6	+	1	69	c.15G>A	c.(13-15)ttG>ttA	p.L5L		NM_002796.2	NP_002787.2	P28070	PSB4_HUMAN	proteasome (prosome, macropain) subunit, beta type, 4	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 inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	lipopolysaccharide binding (GO:0001530)|threonine-type endopeptidase activity (GO:0004298)			endometrium(1)|lung(9)|ovary(2)|prostate(1)|skin(1)	14	Lung SC(34;0.00471)|Ovarian(49;0.00871)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			AAGCGTTTTTGGGGTCGCGGT	0.542																																					p.L5L		Atlas-SNP	.											.	PSMB4	18	.	0			c.G15A						PASS	.						56	61	59					1																	151372078		2202	4297	6499	SO:0001819	synonymous_variant	5692	exon1			GTTTTTGGGGTCG	D26600	CCDS996.1	1q21	2008-02-05			ENSG00000159377	ENSG00000159377		"Proteasome (prosome, macropain) subunits"	9541	protein-coding gene	gene with protein product		602177				7918633	Standard	NM_002796		Approved	HN3, PROS26	uc001eyc.1	P28070	OTTHUMG00000012494	ENST00000290541.6:c.15G>A	chr1.hg19:g.151372078G>A		274.0	1.0	.		135.0	55.0	.	NM_002796	B2R9L3|P31148|Q5SZS5|Q6IBI4|Q969L6	Silent	SNP	ENST00000290541.6	hg19	CCDS996.1																																																																																			.	.	.	none		0.542	PSMB4-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034885.1	NM_002796		A	151372078	G	A	151372078	2	1	158	1	0	0	0	0	0	0	0	1	12689	1339	47	2		2	PSMB4	1	151372078	Silent	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	127683190	151372078	97878543	3	9344											
RIT1	6016	hgsc.bcm.edu	37	chr1	155870300	155870300	+	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	tttctttcctacgtatctccCgtacaagggcatggaaaaca	11	12	7	11	2	2	0	0	0	2	0	4	1	3	1	2	2	3	3	2	2	6	5			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr1:155870300C>A	ENST00000368323.3	-	6	743	c.539G>T	c.(538-540)cGg>cTg	p.R180L	RIT1_ENST00000539040.1_Missense_Mutation_p.R144L|RIT1_ENST00000368322.3_Missense_Mutation_p.R197L	NM_006912.5	NP_008843.1	Q92963	RIT1_HUMAN	Ras-like without CAAX 1	180					GTP catabolic process (GO:0006184)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|GTP binding (GO:0005525)	p.R180L(2)		breast(1)|kidney(1)|large_intestine(3)|lung(12)|skin(1)|urinary_tract(1)	19	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;1.79e-05)			ACGTATCTCCCGTACAAGGGC	0.453																																					p.R197L		Atlas-SNP	.											.	RIT1	34	.	2	Substitution - Missense(2)	lung(1)|kidney(1)	c.G590T						PASS	.						243	242	242					1																	155870300		2203	4300	6503	SO:0001583	missense	6016	exon6			ATCTCCCGTACAA	AF084462	CCDS1123.1, CCDS58037.1, CCDS58036.1	1q21.2	2014-05-09	2002-09-11	2002-09-13	ENSG00000143622	ENSG00000143622			10023	protein-coding gene	gene with protein product	"Ric-like, expressed in many tissues", "GTP-binding protein Roc1"	609591	"Ric (Drosophila)-like, expressed in many tissues"	RIT		8824319, 8918462	Standard	NM_006912		Approved	RIBB, ROC1, MGC125864, MGC125865	uc031pqc.1	Q92963	OTTHUMG00000014104	ENST00000368323.3:c.539G>T	chr1.hg19:g.155870300C>A	ENSP00000357306:p.Arg180Leu	381.0	0.0	.		282.0	14.0	.	NM_001256821	B4DQE8|O00646|O00720|Q5VY89|Q5VY90	Missense_Mutation	SNP	ENST00000368323.3	hg19	CCDS1123.1	.	.	.	.	.	.	.	.	.	.	C	34	5.326793	0.95708	.	.	ENSG00000143622	ENST00000368323;ENST00000539040;ENST00000368322	T;T;T	0.79033	-1.23;-1.23;-1.23	5.8	5.8	0.92144	.	0.000000	0.64402	D	0.000003	D	0.88024	0.6326	M	0.84082	2.675	0.80722	D	1	D	0.76494	0.999	D	0.71184	0.972	D	0.88703	0.3217	10	0.87932	D	0	.	19.6495	0.95795	0.0:1.0:0.0:0.0	.	180	Q92963	RIT1_HUMAN	L	180;144;197	ENSP00000357306:R180L;ENSP00000441950:R144L;ENSP00000357305:R197L	ENSP00000357305:R197L	R	-	2	0	RIT1	154136924	1.000000	0.71417	0.993000	0.49108	0.967000	0.64934	6.557000	0.73937	2.746000	0.94184	0.591000	0.81541	CGG	.	.	.	none		0.453	RIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039593.1	NM_006912		A	155870300	C	A	155870300	3	1	158	1	0	0	0	0	1	0	0	0	13399	652	23	4	124	4	RIT1	1	155870300	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	4498222	155870300	93380321	4	9345											
SPATA17	128153	hgsc.bcm.edu	37	chr1	217975148	217975148	+	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	atggtcctatttcttacaaaGaacaattccgaagtgaaaat	16	12	6	7	1	1	2	0	1	1	1	3	3	3	2	2	1	2	0	2	1	8	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr1:217975148G>T	ENST00000366933.4	+	9	1016	c.961G>T	c.(961-963)Gaa>Taa	p.E321*	SPATA17_ENST00000471021.1_3'UTR	NM_138796.2	NP_620151.1	Q96L03	SPT17_HUMAN	spermatogenesis associated 17	321						cytoplasm (GO:0005737)		p.E321Q(1)		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)		TTCTTACAAAGAACAATTCCG	0.294																																					p.E321X		Atlas-SNP	.											SPATA17,NS,malignant_melanoma,0,3	SPATA17	59	.	1	Substitution - Missense(1)	urinary_tract(1)	c.G961T						PASS	.						50	51	51					1																	217975148		2200	4289	6489	SO:0001587	stop_gained	128153	exon9			TACAAAGAACAAT	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.961G>T	chr1.hg19:g.217975148G>T	ENSP00000355900:p.Glu321*	48.0	0.0	.		62.0	28.0	.	NM_138796	A5D6N2	Nonsense_Mutation	SNP	ENST00000366933.4	hg19	CCDS1519.1	.	.	.	.	.	.	.	.	.	.	G	14.64	2.596073	0.46318	.	.	ENSG00000162814	ENST00000366933	.	.	.	4.9	-9.8	0.00490	.	0.673920	0.13287	N	0.399280	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	5.0379	3.3861	0.07272	0.4661:0.3189:0.0955:0.1195	.	.	.	.	X	321	.	ENSP00000355900:E321X	E	+	1	0	SPATA17	216041771	0.011000	0.17503	0.000000	0.03702	0.106000	0.19336	0.664000	0.25068	-2.528000	0.00493	-0.253000	0.11424	GAA	.	.	.	none		0.294	SPATA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092433.2	NM_138796		T	217975148	G	T	217975148	4	4	158	1	0	0	0	0	0	1	0	0	15014	943	33	4	995	4	SPATA17	1	217975148	Nonsense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	62104848	217975148	31275473	5	9346											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228494234	228494234	+	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	gccgggagccacggcttcagGgctgcaccgcggagctggtg	5	5	18	13	4	1	0	1	0	0	0	1	2	1	2	3	5	3	4	3	5	0	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr1:228494234G>A	ENST00000422127.1	+	44	11865	c.11821G>A	c.(11821-11823)Ggc>Agc	p.G3941S	OBSCN_ENST00000366707.4_Missense_Mutation_p.G1575S|OBSCN_ENST00000570156.2_Missense_Mutation_p.G4898S|OBSCN_ENST00000284548.11_Missense_Mutation_p.G3941S|OBSCN_ENST00000366709.4_Missense_Mutation_p.G1060S	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3941	Ig-like 40.				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)				ACGGCTTCAGGGCTGCACCGC	0.632																																					p.G4898S		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G14692A						PASS	.						31	35	34					1																	228494234		1988	4166	6154	SO:0001583	missense	84033	exon55			CTTCAGGGCTGCA	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.11821G>A	chr1.hg19:g.228494234G>A	ENSP00000409493:p.Gly3941Ser	99.0	0.0	.		61.0	30.0	.	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	18.45	3.626354	0.66901	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28	5.28	5.28	0.74379	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.071555	0.53938	D	0.000043	D	0.85452	0.5700	M	0.89968	3.075	0.32886	D	0.511166	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.992	D	0.89300	0.3625	10	0.48119	T	0.1	.	18.9154	0.92503	0.0:0.0:1.0:0.0	.	3941;3941	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	S	3941;3941;1575;1060	ENSP00000284548:G3941S;ENSP00000409493:G3941S;ENSP00000355668:G1575S;ENSP00000355670:G1060S	ENSP00000284548:G3941S	G	+	1	0	OBSCN	226560857	1.000000	0.71417	0.595000	0.28798	0.119000	0.20118	7.341000	0.79300	2.488000	0.83962	0.462000	0.41574	GGC	.	.	.	none		0.632	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228494234	G	A	228494234	3	1	158	1	0	0	0	0	1	0	0	0	10819	1232	43	2	11991	2	OBSCN	1	228494234	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	10519086	228494234	20756387	6	9347											
ACTR1B	10120	hgsc.bcm.edu	37	chr2	98277105	98277105	+	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	ccgcatgtgcttcggccgccCgacactgttaggacggataa	8	8	12	13	5	0	0	0	0	0	0	1	3	0	2	3	3	1	3	3	3	2	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr2:98277105C>A	ENST00000289228.5	-	3	334	c.118G>T	c.(118-120)Ggg>Tgg	p.G40W		NM_005735.3	NP_005726.1	P42025	ACTY_HUMAN	ARP1 actin-related protein 1 homolog B, centractin beta (yeast)	40					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)			endometrium(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	15						TTCGGCCGCCCGACACTGTTA	0.592																																					p.G40W		Atlas-SNP	.											.	ACTR1B	34	.	0			c.G118T						PASS	.						87	87	87					2																	98277105		2203	4300	6503	SO:0001583	missense	10120	exon3			GCCGCCCGACACT	X82207	CCDS2033.1	2q11.1-q11.2	2008-05-20	2001-11-28		ENSG00000115073	ENSG00000115073			168	protein-coding gene	gene with protein product		605144	"ARP1 (actin-related protein 1, yeast) homolog B (centractin beta)"	CTRN2		7696711, 10343100	Standard	NM_005735		Approved		uc002syb.2	P42025	OTTHUMG00000130549	ENST00000289228.5:c.118G>T	chr2.hg19:g.98277105C>A	ENSP00000289228:p.Gly40Trp	134.0	0.0	.		124.0	8.0	.	NM_005735	D3DVH2|Q53SK5|Q9BRB7	Missense_Mutation	SNP	ENST00000289228.5	hg19	CCDS2033.1	.	.	.	.	.	.	.	.	.	.	.	20.3	3.966488	0.74131	.	.	ENSG00000115073	ENST00000289228	D	0.96619	-4.07	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	D	0.99013	0.9663	H	0.98754	4.32	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99191	1.0870	10	0.87932	D	0	.	16.8234	0.85924	0.0:1.0:0.0:0.0	.	40	P42025	ACTY_HUMAN	W	40	ENSP00000289228:G40W	ENSP00000289228:G40W	G	-	1	0	ACTR1B	97643537	1.000000	0.71417	0.989000	0.46669	0.390000	0.30446	7.795000	0.85887	2.591000	0.87537	0.561000	0.74099	GGG	.	.	.	none		0.592	ACTR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252973.1	NM_005735		A	98277105	C	A	98277105	3	1	158	1	0	0	0	0	1	0	0	0	210	652	23	4	1048	4	ACTR1B	2	98277105	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08		98277105	144922268	7	9348											
MAP4K4	9448	hgsc.bcm.edu	37	chr2	102493544	102493544	+	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	gggaaggtctatcctcttatCaaccgaagacgatttcaaca	13	10	8	10	2	4	1	2	0	2	1	5	4	5	2	2	2	2	0	2	2	6	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr2:102493544C>A	ENST00000347699.4	+	24	2886	c.2886C>A	c.(2884-2886)atC>atA	p.I962I	MAP4K4_ENST00000456652.1_Silent_p.I761I|MAP4K4_ENST00000413150.2_Silent_p.I877I|MAP4K4_ENST00000425019.1_Silent_p.I995I|MAP4K4_ENST00000324219.4_Silent_p.I1043I|MAP4K4_ENST00000350198.4_Silent_p.I881I|MAP4K4_ENST00000350878.4_Silent_p.I1002I|MAP4K4_ENST00000302217.5_Silent_p.I765I	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4	962	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.|Mediates interaction with RAP2A.				intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of JNK cascade (GO:0046328)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						ATCCTCTTATCAACCGAAGAC	0.453																																					p.I996I		Atlas-SNP	.											.	MAP4K4	111	.	0			c.C2988A						PASS	.						180	175	177					2																	102493544		2019	4184	6203	SO:0001819	synonymous_variant	9448	exon25			TCTTATCAACCGA	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.2886C>A	chr2.hg19:g.102493544C>A		54.0	0.0	.		94.0	54.0	.	NM_145686	O75172|Q9NST7	Silent	SNP	ENST00000347699.4	hg19	CCDS56130.1	.	.	.	.	.	.	.	.	.	.	C	9.992	1.230967	0.22542	.	.	ENSG00000071054	ENST00000421882	.	.	.	5.48	5.48	0.80851	.	.	.	.	.	T	0.60314	0.2259	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57974	-0.7718	4	.	.	.	.	8.8578	0.35238	0.15:0.7754:0.0:0.0745	.	.	.	.	K	779	.	.	Q	+	1	0	MAP4K4	101859976	0.991000	0.36638	1.000000	0.80357	0.976000	0.68499	0.386000	0.20702	2.717000	0.92951	0.655000	0.94253	CAA	.	.	.	none		0.453	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834		A	102493544	C	A	102493544	2	1	158	1	0	0	0	0	0	0	0	1	9269	816	29	4		4	MAP4K4	2	102493544	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	4216439	102493544	140705829	8	9349											
UPP2	151531	hgsc.bcm.edu	37	chr2	158971732	158971732	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctgtgctgggacagacagAtactgtatgtacaaaaccgg	13	9	11	8	1	1	2	0	0	1	2	1	3	1	3	1	2	4	3	1	2	5	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr2:158971732A>G	ENST00000005756.4	+	3	494	c.300A>G	c.(298-300)agA>agG	p.R100R	UPP2_ENST00000605860.1_Silent_p.R157R|UPP2_ENST00000460456.1_Intron|UPP2_ENST00000409859.4_Silent_p.R157R	NM_173355.3	NP_775491.1	O95045	UPP2_HUMAN	uridine phosphorylase 2	100					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)	GGACAGACAGATACTGTATGT	0.458																																					p.R157R		Atlas-SNP	.											.	UPP2	60	.	0			c.A471G						PASS	.						105	104	104					2																	158971732		2203	4300	6503	SO:0001819	synonymous_variant	151531	exon5			AGACAGATACTGT	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.300A>G	chr2.hg19:g.158971732A>G		140.0	0.0	.		131.0	39.0	.	NM_001135098	B3KV87	Silent	SNP	ENST00000005756.4	hg19	CCDS2207.1																																																																																			.	.	.	none		0.458	UPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254929.2	NM_173355		G	158971732	A	G	158971732	2	3	158	1	0	0	0	0	0	0	0	1	17025	330	12	3		3	UPP2	2	158971732	Silent	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	56478188	158971732	84227641	9	9350											
TTN	7273	hgsc.bcm.edu	37	chr2	179430006	179430006	+	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	gcactatttgttgccgttacGgtgtattttccaaagtcatc	8	16	8	9	2	1	0	1	0	0	0	3	0	2	0	2	1	2	4	2	1	4	7			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr2:179430006G>T	ENST00000591111.1	-	276	76154	c.75930C>A	c.(75928-75930)acC>acA	p.T25310T	TTN_ENST00000460472.2_Silent_p.T17886T|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.T18078T|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Silent_p.T26951T|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000359218.5_Silent_p.T18011T|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Silent_p.T24383T|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000438095.1_RNA			Q8WZ42	TITIN_HUMAN	titin	25310	Ig-like 124.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.T24381T(1)|p.T17886T(1)|p.T18078T(1)|p.T18011T(1)|p.T24383T(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTGCCGTTACGGTGTATTTTC	0.413																																					p.T26951T		Atlas-SNP	.											.	TTN	18412	.	5	Substitution - coding silent(5)	lung(5)	c.C80853A						PASS	.						131	125	127					2																	179430006		1882	4116	5998	SO:0001819	synonymous_variant	7273	exon326			CGTTACGGTGTAT	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.75930C>A	chr2.hg19:g.179430006G>T		211.0	0.0	.		271.0	11.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.	.	none		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179430006	G	T	179430006	2	4	158	1	0	0	0	0	0	0	0	1	16747	1103	39	4		4	TTN	2	179430006	Silent	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	20458274	179430006	63769367	10	9351											
TTN	7273	hgsc.bcm.edu	37	chr2	179468605	179468605	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaacggaagcatacttacatAtgggatctcctgcaacctct	13	10	7	11	1	2	0	0	0	2	0	3	2	2	2	2	2	6	2	2	2	6	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr2:179468605A>G	ENST00000591111.1	-	232	50110	c.49886T>C	c.(49885-49887)aTa>aCa	p.I16629T	TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I9205T|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I9397T|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.I18270T|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.I9330T|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.I15702T|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	16629			I -> M. {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)			ATACTTACATATGGGATCTCC	0.398																																					p.I18270T		Atlas-SNP	.											.	TTN	18412	.	0			c.T54809C						PASS	.						65	62	63					2																	179468605		1886	4096	5982	SO:0001583	missense	7273	exon282			TTACATATGGGAT	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.49886T>C	chr2.hg19:g.179468605A>G	ENSP00000465570:p.Ile16629Thr	105.0	0.0	.		78.0	28.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	10.22	1.289353	0.23478	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	6.06	4.85	0.62838	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.36276	0.0961	L	0.52759	1.655	0.33898	D	0.638219	B;B;B;B	0.32245	0.361;0.361;0.361;0.361	B;B;B;B	0.24155	0.051;0.051;0.051;0.051	T	0.55490	-0.8133	9	0.87932	D	0	.	12.2928	0.54827	0.8732:0.0:0.0:0.1268	.	9205;9330;9397;16629	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	15702;9205;9397;9330;9205	ENSP00000343764:I15702T;ENSP00000434586:I9205T;ENSP00000340554:I9397T;ENSP00000352154:I9330T	ENSP00000340554:I9397T	I	-	2	0	TTN	179176850	1.000000	0.71417	0.999000	0.59377	0.935000	0.57460	1.934000	0.40163	2.323000	0.78572	0.528000	0.53228	ATA	.	.	.	none		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179468605	A	G	179468605	3	3	158	1	0	0	0	0	1	0	0	0	16747	449	16	3	53208	3	TTN	2	179468605	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	38599	179468605	63730768	11	9352											
RPL37A	6168	hgsc.bcm.edu	37	chr2	217364692	217364692	+	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	accaagatgaagagacgagcTgtggggatctggcactgtgg	11	7	16	7	1	1	3	0	1	1	2	1	6	1	4	1	4	1	2	1	4	2	0			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr2:217364692T>A	ENST00000491306.1	+	3	839	c.153T>A	c.(151-153)gcT>gcA	p.A51A	RPL37A_ENST00000456586.1_Silent_p.A27A|AC098820.3_ENST00000453157.1_RNA|RPL37A_ENST00000446558.1_Silent_p.A51A|RPL37A_ENST00000598925.1_Silent_p.A27A|RPL37A_ENST00000600880.1_Silent_p.A51A|RPL37A_ENST00000441179.2_Silent_p.A27A|AC098820.3_ENST00000438978.1_RNA|RPL37A_ENST00000427280.2_Silent_p.A27A	NM_000998.4	NP_000989.1	P61513	RL37A_HUMAN	ribosomal protein L37a	51					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)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			NS(1)|ovary(1)	2		Renal(323;0.0458)		Epithelial(149;3.51e-06)|all cancers(144;0.000249)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGAGACGAGCTGTGGGGATCT	0.443																																					p.A51A		Atlas-SNP	.											.	RPL37A	9	.	0			c.T153A						PASS	.						129	125	126					2																	217364692		2203	4300	6503	SO:0001819	synonymous_variant	6168	exon3			ACGAGCTGTGGGG		CCDS2404.1	2q35	2011-04-06			ENSG00000197756	ENSG00000197756		"L ribosomal proteins"	10348	protein-coding gene	gene with protein product		613314				1437567	Standard	NM_000998		Approved	L37A	uc002vgf.3	P61513	OTTHUMG00000133052	ENST00000491306.1:c.153T>A	chr2.hg19:g.217364692T>A		159.0	0.0	.		177.0	92.0	.	NM_000998	P12751|Q6FGF5	Silent	SNP	ENST00000491306.1	hg19	CCDS2404.1																																																																																			.	.	.	none		0.443	RPL37A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256665.2	NM_000998		A	217364692	T	A	217364692	2	1	158	1	0	0	0	0	0	0	0	1	13603	1567	55	5		5	RPL37A	2	217364692	Silent	SNP	T	TCGA-DZ-6133-01A-11D-1961-08	37896087	217364692	25834681	12	9353											
NBEAL2	23218	hgsc.bcm.edu	37	chr3	47049869	47049869	+	Missense_Mutation	SNP	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	ctggacctattttccacctgGcattggggtccgaaggccag	7	10	12	12	1	0	0	0	0	0	0	2	2	2	1	5	5	0	1	5	5	2	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr3:47049869G>A	ENST00000450053.3	+	51	7995	c.7816G>A	c.(7816-7818)Gca>Aca	p.A2606T	NBEAL2_ENST00000292309.5_Missense_Mutation_p.A2422T|NBEAL2_ENST00000383740.2_Missense_Mutation_p.A855T	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	2606					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)		TTTCCACCTGGCATTGGGGTC	0.597																																					p.A2606T		Atlas-SNP	.											.	NBEAL2	267	.	0			c.G7816A						PASS	.						49	48	48					3																	47049869		2037	4171	6208	SO:0001583	missense	23218	exon51			CACCTGGCATTGG	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.7816G>A	chr3.hg19:g.47049869G>A	ENSP00000415034:p.Ala2606Thr	33.0	0.0	.		43.0	25.0	.	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Missense_Mutation	SNP	ENST00000450053.3	hg19	CCDS46817.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	16.62|16.62|16.62	3.173416|3.173416|3.173416	0.57584|0.57584|0.57584	.|.|.	.|.|.	ENSG00000160796|ENSG00000160796|ENSG00000160796	ENST00000292309;ENST00000383740;ENST00000450053;ENST00000445550|ENST00000443829|ENST00000416683	T;T;T|.|.	0.20069|.|.	2.1;2.1;2.1|.|.	5.15|5.15|5.15	5.15|5.15|5.15	0.70609|0.70609|0.70609	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);|.|.	0.716976|.|.	0.13800|.|.	N|.|.	0.361890|.|.	T|T|.	0.71558|0.71558|.	0.3354|0.3354|.	M|M|M	0.61703|0.61703|0.61703	1.905|1.905|1.905	0.38807|0.38807|0.38807	D|D|D	0.955327|0.955327|0.955327	B;B|.|.	0.26845|.|.	0.161;0.007|.|.	B;B|.|.	0.23852|.|.	0.049;0.01|.|.	T|T|.	0.71686|0.71686|.	-0.4518|-0.4518|.	10|5|.	0.33141|.|.	T|.|.	0.24|.|.	.|.|.	16.1634|16.1634|16.1634	0.81734|0.81734|0.81734	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	2422;2606|.|.	Q6ZNJ1-2;Q6ZNJ1|.|.	.;NBEL2_HUMAN|.|.	T|D|X	2422;855;2606;549|944|1893	ENSP00000292309:A2422T;ENSP00000373246:A855T;ENSP00000415034:A2606T|.|.	ENSP00000292309:A2422T|.|.	A|G|W	+|+|+	1|2|3	0|0|0	NBEAL2|NBEAL2|NBEAL2	47024873|47024873|47024873	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.988000|0.988000|0.988000	0.46212|0.46212|0.46212	0.695000|0.695000|0.695000	0.40330|0.40330|0.40330	4.551000|4.551000|4.551000	0.60740|0.60740|0.60740	2.669000|2.669000|2.669000	0.90835|0.90835|0.90835	0.561000|0.561000|0.561000	0.74099|0.74099|0.74099	GCA|GGC|TGG	.	.	.	none		0.597	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		A	47049869	G	A	47049869	3	1	158	1	0	0	0	0	1	0	0	0	10196	1203	42	2	8018	2	NBEAL2	3	47049869	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08		47049869	150972561	13	9354											
NICN1	84276	hgsc.bcm.edu	37	chr3	49463424	49463424	+	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	gatattctagccatgtcacaCagcatctgacacacacacac	14	8	5	14	0	3	1	1	1	2	0	3	2	3	1	1	0	2	1	1	0	2	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr3:49463424C>G	ENST00000273598.3	-	3	401	c.315G>C	c.(313-315)ctG>ctC	p.L105L	NICN1-AS1_ENST00000424915.1_RNA|NICN1_ENST00000422593.1_5'UTR|NICN1_ENST00000436744.2_Intron	NM_032316.3	NP_115692.1	Q9BSH3	NICN1_HUMAN	nicolin 1	105						microtubule (GO:0005874)|nucleus (GO:0005634)				kidney(1)|large_intestine(3)|lung(1)	5				BRCA - Breast invasive adenocarcinoma(193;4.52e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CCATGTCACACAGCATCTGAC	0.567																																					p.L105L		Atlas-SNP	.											.	NICN1	15	.	0			c.G315C						PASS	.						87	65	72					3																	49463424		2203	4300	6503	SO:0001819	synonymous_variant	84276	exon3			GTCACACAGCATC	AJ299740	CCDS2798.1	3p21.31	2008-07-18			ENSG00000145029	ENSG00000145029			18317	protein-coding gene	gene with protein product		611516				12392556	Standard	NM_032316		Approved	MGC12936	uc003cwz.1	Q9BSH3	OTTHUMG00000156848	ENST00000273598.3:c.315G>C	chr3.hg19:g.49463424C>G		54.0	0.0	.		41.0	13.0	.	NM_032316	Q8IZQ2	Silent	SNP	ENST00000273598.3	hg19	CCDS2798.1																																																																																			.	.	.	none		0.567	NICN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346224.3	NM_032316		G	49463424	C	G	49463424	2	3	158	1	0	0	0	0	0	0	0	1	10420	465	17	4		4	NICN1	3	49463424	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	2413555	49463424	148559006	14	9355											
PCBP4	57060	hgsc.bcm.edu	37	chr3	51995031	51995031	+	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	gagctaggcacctaccttccCgatgatgctgcccacttcct	7	10	8	16	1	0	1	0	1	0	0	2	3	2	1	5	1	4	3	5	1	2	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr3:51995031C>A	ENST00000461554.1	-	4	431	c.100G>T	c.(100-102)Ggg>Tgg	p.G34W	RP11-155D18.14_ENST00000489595.2_Missense_Mutation_p.G34W|PCBP4_ENST00000395013.3_5'UTR|RP11-155D18.12_ENST00000488257.1_RNA|PCBP4_ENST00000428823.2_Missense_Mutation_p.G34W|PCBP4_ENST00000395014.2_5'Flank|PCBP4_ENST00000471622.1_Missense_Mutation_p.G34W|PCBP4_ENST00000355852.2_Missense_Mutation_p.G34W|PCBP4_ENST00000322099.7_Missense_Mutation_p.G34W|PCBP4_ENST00000484633.1_Missense_Mutation_p.G34W	NM_001174100.1	NP_001167571.1	P57723	PCBP4_HUMAN	poly(rC) binding protein 4	34	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)	p.G34W(1)		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)		CCTACCTTCCCGATGATGCTG	0.587																																					p.G34W		Atlas-SNP	.											.	PCBP4	35	.	1	Substitution - Missense(1)	lung(1)	c.G100T						PASS	.						127	128	127					3																	51995031		2203	4300	6503	SO:0001583	missense	57060	exon3			CCTTCCCGATGAT	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.100G>T	chr3.hg19:g.51995031C>A	ENSP00000417196:p.Gly34Trp	207.0	0.0	.		180.0	13.0	.	NM_033008	Q96AH7	Missense_Mutation	SNP	ENST00000461554.1	hg19	CCDS2839.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.803867	0.90623	.	.	ENSG00000090097	ENST00000355852;ENST00000322099;ENST00000461554;ENST00000484633;ENST00000428823;ENST00000471622;ENST00000294192;ENST00000468324;ENST00000466412;ENST00000497653;ENST00000489595;ENST00000490063;ENST00000483411;ENST00000461544	D;D;D;D;D;D;D;D;D;D;D;D;D	0.88741	-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42;-2.42	4.92	4.92	0.64577	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	.	.	.	.	D	0.97288	0.9113	H	0.99404	4.55	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	0.99478	1.0947	9	0.87932	D	0	.	18.0881	0.89464	0.0:1.0:0.0:0.0	.	34;34;34;34	C9J0A4;P57723-2;E7EST1;P57723	.;.;.;PCBP4_HUMAN	W	34	ENSP00000348111:G34W;ENSP00000322341:G34W;ENSP00000417196:G34W;ENSP00000417100:G34W;ENSP00000395030:G34W;ENSP00000418925:G34W;ENSP00000419694:G34W;ENSP00000419557:G34W;ENSP00000417916:G34W;ENSP00000420008:G34W;ENSP00000418312:G34W;ENSP00000418997:G34W;ENSP00000419672:G34W	ENSP00000294192:G34W	G	-	1	0	PCBP4	51970071	1.000000	0.71417	0.989000	0.46669	0.807000	0.45602	5.997000	0.70646	2.431000	0.82371	0.561000	0.74099	GGG	.	.	.	none		0.587	PCBP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348597.1	NM_020418		A	51995031	C	A	51995031	3	1	158	1	0	0	0	0	1	0	0	0	11510	652	23	4	1155	4	PCBP4	3	51995031	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	2531607	51995031	146027399	15	9356											
POC1A	25886	hgsc.bcm.edu	37	chr3	52109979	52109979	+	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	tgtcttctgtcagtgtcaacCgctgctccagaatggagact	8	12	10	11	1	4	2	2	0	2	2	5	3	5	2	2	1	2	2	2	1	2	1	rs375422052		TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr3:52109979C>A	ENST00000296484.2	-	11	1187	c.1148G>T	c.(1147-1149)cGg>cTg	p.R383L	POC1A_ENST00000474012.1_Missense_Mutation_p.R345L|POC1A_ENST00000394970.2_Missense_Mutation_p.R335L	NM_015426.4	NP_056241.3	Q8NBT0	POC1A_HUMAN	POC1 centriolar protein A	383					cell projection organization (GO:0030030)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|spindle pole (GO:0000922)				endometrium(1)|large_intestine(4)|liver(1)|lung(4)|prostate(3)|skin(1)	14						CAGTGTCAACCGCTGCTCCAG	0.547																																					p.R383L		Atlas-SNP	.											.	POC1A	32	.	0			c.G1148T						PASS	.						136	119	124					3																	52109979		2203	4300	6503	SO:0001583	missense	25886	exon11			GTCAACCGCTGCT	AL117629	CCDS2846.1, CCDS54591.1, CCDS54592.1	3p21.2	2014-05-02	2013-08-21	2010-03-26	ENSG00000164087	ENSG00000164087		"WD repeat domain containing"	24488	protein-coding gene	gene with protein product		614783	"WD repeat domain 51A", "POC1 centriolar protein homolog A (Chlamydomonas)"	WDR51A		19109428, 22840364	Standard	NM_015426		Approved	DKFZP434C245	uc003dcu.3	Q8NBT0	OTTHUMG00000157817	ENST00000296484.2:c.1148G>T	chr3.hg19:g.52109979C>A	ENSP00000296484:p.Arg383Leu	196.0	0.0	.		214.0	10.0	.	NM_015426	A4FUW4|E9PFC6|Q0VDF8|Q2TAK6|Q96IK6|Q9UFJ8	Missense_Mutation	SNP	ENST00000296484.2	hg19	CCDS2846.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.901179	0.92035	.	.	ENSG00000164087	ENST00000296484;ENST00000394970;ENST00000474012	T;T;T	0.71461	-0.57;-0.57;-0.57	5.35	5.35	0.76521	.	0.063133	0.64402	D	0.000011	D	0.84593	0.5506	M	0.82323	2.585	0.43338	D	0.995389	D;D	0.89917	0.994;1.0	P;D	0.85130	0.879;0.997	D	0.85983	0.1484	10	0.66056	D	0.02	.	14.4269	0.67222	0.0:1.0:0.0:0.0	.	335;383	Q8NBT0-2;Q8NBT0	.;POC1A_HUMAN	L	383;335;345	ENSP00000296484:R383L;ENSP00000378421:R335L;ENSP00000418968:R345L	ENSP00000296484:R383L	R	-	2	0	POC1A	52085019	1.000000	0.71417	0.977000	0.42913	0.993000	0.82548	5.066000	0.64351	2.786000	0.95864	0.655000	0.94253	CGG	.	.	.	alt		0.547	POC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349685.1	NM_015426		A	52109979	C	A	52109979	3	1	158	1	0	0	0	0	1	0	0	0	12182	652	23	4	79	4	POC1A	3	52109979	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	114948	52109979	145912451	16	9357											
SFMBT1	51460	hgsc.bcm.edu	37	chr3	52988412	52988412	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcttaattctacctcttccAtaccagagccggcatctaga	11	11	6	13	1	3	2	0	0	3	2	4	2	4	2	4	1	4	2	4	1	4	6			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr3:52988412A>G	ENST00000394752.3	-	3	426	c.44T>C	c.(43-45)aTg>aCg	p.M15T	SFMBT1_ENST00000470575.1_5'UTR|SFMBT1_ENST00000394750.1_Missense_Mutation_p.M15T|SFMBT1_ENST00000358080.2_Missense_Mutation_p.M15T|SFMBT1_ENST00000296295.6_Missense_Mutation_p.M15T	NM_016329.3	NP_057413.2	Q9UHJ3	SMBT1_HUMAN	Scm-like with four mbt domains 1	15					cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|negative regulation of muscle organ development (GO:0048635)|negative regulation of transcription, DNA-templated (GO:0045892)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)			breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	24				BRCA - Breast invasive adenocarcinoma(193;9.91e-05)|Kidney(197;0.000644)|KIRC - Kidney renal clear cell carcinoma(197;0.000792)|OV - Ovarian serous cystadenocarcinoma(275;0.113)		TACCTCTTCCATACCAGAGCC	0.333																																					p.M15T		Atlas-SNP	.											.	SFMBT1	53	.	0			c.T44C						PASS	.						111	116	114					3																	52988412		2203	4300	6503	SO:0001583	missense	51460	exon3			TCTTCCATACCAG	AF168132	CCDS2867.1	3p21.31	2013-01-10			ENSG00000163935	ENSG00000163935		"Sterile alpha motif (SAM) domain containing"	20255	protein-coding gene	gene with protein product		607319				10661410	Standard	NM_016329		Approved	RU1, DKFZp434L243, SFMBT	uc003dgh.3	Q9UHJ3	OTTHUMG00000159052	ENST00000394752.3:c.44T>C	chr3.hg19:g.52988412A>G	ENSP00000378235:p.Met15Thr	223.0	0.0	.		226.0	135.0	.	NM_016329	Q402F7|Q96C73|Q9Y4Q9	Missense_Mutation	SNP	ENST00000394752.3	hg19	CCDS2867.1	.	.	.	.	.	.	.	.	.	.	A	11.09	1.536575	0.27475	.	.	ENSG00000163935	ENST00000394752;ENST00000358080;ENST00000296295;ENST00000394750;ENST00000482396;ENST00000483069;ENST00000497586	T;T;T;T;T;T	0.40756	2.62;2.62;2.62;2.62;2.03;1.02	5.7	5.7	0.88788	.	0.544403	0.20072	N	0.099858	T	0.31827	0.0809	N	0.24115	0.695	0.28463	N	0.915804	B	0.02656	0.0	B	0.17722	0.019	T	0.13335	-1.0513	10	0.24483	T	0.36	.	15.6127	0.76740	1.0:0.0:0.0:0.0	.	15	Q9UHJ3	SMBT1_HUMAN	T	15	ENSP00000378235:M15T;ENSP00000350789:M15T;ENSP00000296295:M15T;ENSP00000378233:M15T;ENSP00000418860:M15T;ENSP00000418950:M15T	ENSP00000296295:M15T	M	-	2	0	SFMBT1	52963452	1.000000	0.71417	0.990000	0.47175	0.489000	0.33432	5.542000	0.67218	2.164000	0.68074	0.477000	0.44152	ATG	.	.	.	none		0.333	SFMBT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353040.3	NM_016329		G	52988412	A	G	52988412	3	3	158	1	0	0	0	0	1	0	0	0	14170	217	8	3	2632	3	SFMBT1	3	52988412	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	878433	52988412	145034018	17	9358											
FAM3D	131177	hgsc.bcm.edu	37	chr3	58625897	58625897	+	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	ttctgtcccagcacagctccCgtggttcctaggggttaaga	7	11	11	12	1	1	1	0	0	1	1	4	1	4	1	3	3	2	4	3	3	2	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr3:58625897C>A	ENST00000358781.2	-	7	640	c.330G>T	c.(328-330)acG>acT	p.T110T		NM_138805.2	NP_620160.1	Q96BQ1	FAM3D_HUMAN	family with sequence similarity 3, member D	110					negative regulation of insulin secretion (GO:0046676)	extracellular region (GO:0005576)	cytokine activity (GO:0005125)	p.T110T(1)		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)		GCACAGCTCCCGTGGTTCCTA	0.522																																					p.T110T		Atlas-SNP	.											.	FAM3D	29	.	1	Substitution - coding silent(1)	lung(1)	c.G330T						PASS	.						227	192	204					3																	58625897		2203	4300	6503	SO:0001819	synonymous_variant	131177	exon7			AGCTCCCGTGGTT	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.330G>T	chr3.hg19:g.58625897C>A		218.0	0.0	.		192.0	10.0	.	NM_138805	Q547G2	Silent	SNP	ENST00000358781.2	hg19	CCDS2893.1																																																																																			.	.	.	none		0.522	FAM3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353494.1	NM_138805		A	58625897	C	A	58625897	2	1	158	1	0	0	0	0	0	0	0	1	5566	639	23	4		4	FAM3D	3	58625897	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	5637485	58625897	139396533	18	9359											
ZBTB11	27107	hgsc.bcm.edu	37	chr3	101390027	101390027	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagctcctttctcaataaaaAgatctcgaaaatactcgcta	15	11	4	11	2	2	1	1	0	2	1	6	2	3	1	1	0	2	2	1	0	8	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr3:101390027A>G	ENST00000312938.4	-	3	1305	c.725T>C	c.(724-726)cTt>cCt	p.L242P	ZBTB11_ENST00000461821.1_3'UTR	NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	242	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						CTCAATAAAAAGATCTCGAAA	0.363																																					p.L242P		Atlas-SNP	.											.	ZBTB11	77	.	0			c.T725C						PASS	.						73	73	73					3																	101390027		2203	4300	6503	SO:0001583	missense	27107	exon3			ATAAAAAGATCTC	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.725T>C	chr3.hg19:g.101390027A>G	ENSP00000326200:p.Leu242Pro	82.0	0.0	.		101.0	29.0	.	NM_014415	Q2NKP9	Missense_Mutation	SNP	ENST00000312938.4	hg19	CCDS2943.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.495399	0.85069	.	.	ENSG00000066422	ENST00000312938	T	0.73681	-0.77	5.48	5.48	0.80851	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.88948	0.6576	M	0.91872	3.25	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91470	0.5196	10	0.87932	D	0	-12.2938	15.5729	0.76354	1.0:0.0:0.0:0.0	.	242	O95625	ZBT11_HUMAN	P	242	ENSP00000326200:L242P	ENSP00000326200:L242P	L	-	2	0	ZBTB11	102872717	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.092000	0.63282	0.533000	0.62120	CTT	.	.	.	none		0.363	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415		G	101390027	A	G	101390027	3	3	158	1	0	0	0	0	1	0	0	0	17536	72	3	3	2472	3	ZBTB11	3	101390027	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	42764130	101390027	96632403	19	9360											
ALDH1L1	10840	hgsc.bcm.edu	37	chr3	125850317	125850317	+	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	gccagcgtgtagacggcaccCgcatccagggcctcaatggt	8	6	13	14	3	1	1	1	0	0	1	2	1	2	1	4	3	1	3	4	3	2	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr3:125850317C>A	ENST00000393434.2	-	13	1882	c.1533G>T	c.(1531-1533)gcG>gcT	p.A511A	ALDH1L1_ENST00000452905.2_Silent_p.A410A|ALDH1L1_ENST00000273450.3_Silent_p.A521A|ALDH1L1_ENST00000472186.1_Silent_p.A511A|ALDH1L1_ENST00000393431.2_Intron	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	511	Aldehyde dehydrogenase.		A -> V (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		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)	p.A511A(1)		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)	AGACGGCACCCGCATCCAGGG	0.637																																					p.A521A		Atlas-SNP	.											ALDH1L1,caecum,carcinoma,0,1	ALDH1L1	138	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1563T						PASS	.						90	79	83					3																	125850317		2203	4300	6503	SO:0001819	synonymous_variant	10840	exon13			GGCACCCGCATCC	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.1533G>T	chr3.hg19:g.125850317C>A		110.0	0.0	.		101.0	9.0	.	NM_001270364	B4DG36|E9PBX3|Q68CS1	Silent	SNP	ENST00000393434.2	hg19	CCDS3034.1																																																																																			.	.	.	none		0.637	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190		A	125850317	C	A	125850317	2	1	158	1	0	0	0	0	0	0	0	1	494	639	23	4		4	ALDH1L1	3	125850317	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	24460290	125850317	72172113	20	9361											
SLCO2A1	6578	hgsc.bcm.edu	37	chr3	133692538	133692538	+	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	aaggtgtactggtagggctcGgagaggaagtgtgggagggt	9	8	21	3	1	0	1	0	0	0	1	1	4	0	3	0	7	1	3	0	7	4	2	rs150677069		TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr3:133692538G>C	ENST00000310926.4	-	3	639	c.366C>G	c.(364-366)tcC>tcG	p.S122S	SLCO2A1_ENST00000493729.1_Silent_p.S122S|SLCO2A1_ENST00000478651.1_5'UTR	NM_005630.2	NP_005621.2	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family, member 2A1	122					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)	GGTAGGGCTCGGAGAGGAAGT	0.582																																					p.S122S		Atlas-SNP	.											.	SLCO2A1	72	.	0			c.C366G						PASS	.						87	73	78					3																	133692538		2203	4300	6503	SO:0001819	synonymous_variant	6578	exon3			GGGCTCGGAGAGG		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.366C>G	chr3.hg19:g.133692538G>C		43.0	0.0	.		34.0	9.0	.	NM_005630	Q86V98|Q8IUN2	Silent	SNP	ENST00000310926.4	hg19	CCDS3084.1																																																																																			.	G|1.000;A|0.000	.	alt		0.582	SLCO2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357131.1	NM_005630		C	133692538	G	C	133692538	2	2	158	1	0	0	0	0	0	0	0	1	14739	1103	39	4		4	SLCO2A1	3	133692538	Silent	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	7842221	133692538	64329892	21	9362											
PSMD2	5708	hgsc.bcm.edu	37	chr3	184026587	184026587	+	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	gttgttggcccacggggaacGggcagaattggccactgagg	8	7	17	9	2	0	2	0	1	0	1	0	3	0	3	2	6	1	3	2	6	2	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr3:184026587G>T	ENST00000310118.4	+	21	3194	c.2636G>T	c.(2635-2637)cGg>cTg	p.R879L	EIF2B5_ENST00000444495.1_Intron|PSMD2_ENST00000439383.1_Missense_Mutation_p.R749L|PSMD2_ENST00000435761.1_Missense_Mutation_p.R720L	NM_002808.3	NP_002799.3	Q13200	PSMD2_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 2	879					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)	CACGGGGAACGGGCAGAATTG	0.537											OREG0015948	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R879L	Colon(24;313 636 6917 9932 15554)	Atlas-SNP	.											.	PSMD2	56	.	0			c.G2636T						PASS	.						110	113	112					3																	184026587		2203	4300	6503	SO:0001583	missense	5708	exon21			GGGAACGGGCAGA	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.2636G>T	chr3.hg19:g.184026587G>T	ENSP00000310129:p.Arg879Leu	262.0	0.0	.	1989	246.0	11.0	.	NM_002808	B4DX07|B4DXY1|E7EW34|E9PCS3|Q12932|Q15321|Q53XQ4|Q96I12	Missense_Mutation	SNP	ENST00000310118.4	hg19	CCDS3258.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.493660	0.84962	.	.	ENSG00000175166	ENST00000310118;ENST00000358216;ENST00000538096;ENST00000435761;ENST00000439383	T;T;T	0.49720	0.77;0.77;0.77	5.72	4.85	0.62838	.	0.119862	0.56097	D	0.000039	T	0.74566	0.3733	M	0.89658	3.05	0.51482	D	0.999922	D;D	0.76494	0.999;0.987	D;D	0.77557	0.99;0.953	T	0.81300	-0.0995	10	0.66056	D	0.02	-8.4473	16.6435	0.85138	0.0:0.1301:0.8699:0.0	.	720;879	E9PCS3;Q13200	.;PSMD2_HUMAN	L	879;551;871;720;749	ENSP00000310129:R879L;ENSP00000402618:R720L;ENSP00000416028:R749L	ENSP00000310129:R879L	R	+	2	0	PSMD2	185509281	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.380000	0.97202	1.429000	0.47314	-0.122000	0.15005	CGG	.	.	.	none		0.537	PSMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345843.1	NM_002808		T	184026587	G	T	184026587	3	4	158	1	0	0	0	0	1	0	0	0	12708	1116	39	4	2718	4	PSMD2	3	184026587	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	50334049	184026587	13995843	22	9363											
ATP13A3	79572	hgsc.bcm.edu	37	chr3	194146121	194146121	+	Missense_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	ttccttttgaaaaggcaattGccactatgaggtactgaaaa	14	12	8	7	0	0	3	0	3	0	0	1	3	1	3	2	2	2	2	2	2	7	6			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr3:194146121G>A	ENST00000439040.1	-	30	4054	c.3263C>T	c.(3262-3264)gCa>gTa	p.A1088V	ATP13A3_ENST00000256031.4_Missense_Mutation_p.A1088V			Q9H7F0	AT133_HUMAN	ATPase type 13A3	1088						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)		AAAGGCAATTGCCACTATGAG	0.353																																					p.A1088V		Atlas-SNP	.											.	ATP13A3	94	.	0			c.C3263T						PASS	.						97	90	93					3																	194146121		1821	4076	5897	SO:0001583	missense	79572	exon29			GCAATTGCCACTA	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.3263C>T	chr3.hg19:g.194146121G>A	ENSP00000416508:p.Ala1088Val	69.0	0.0	.		101.0	54.0	.	NM_024524	Q8NC11|Q96KS1	Missense_Mutation	SNP	ENST00000439040.1	hg19	CCDS43187.1	.	.	.	.	.	.	.	.	.	.	G	33	5.207024	0.95033	.	.	ENSG00000133657	ENST00000439040;ENST00000256031	T;T	0.74947	-0.89;-0.89	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.87204	0.6119	M	0.82630	2.6	0.80722	D	1	D	0.65815	0.995	D	0.66847	0.947	D	0.87360	0.2343	10	0.49607	T	0.09	-22.6896	19.4395	0.94813	0.0:0.0:1.0:0.0	.	1088	Q9H7F0	AT133_HUMAN	V	1088	ENSP00000416508:A1088V;ENSP00000256031:A1088V	ENSP00000256031:A1088V	A	-	2	0	ATP13A3	195627410	1.000000	0.71417	0.989000	0.46669	0.980000	0.70556	9.476000	0.97823	2.591000	0.87537	0.591000	0.81541	GCA	.	.	.	none		0.353	ATP13A3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342799.2	NM_024524		A	194146121	G	A	194146121	3	1	158	1	0	0	0	0	1	0	0	0	1125	1319	46	2	433	2	ATP13A3	3	194146121	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	10119534	194146121	3876309	23	9364											
ZBTB49	166793	hgsc.bcm.edu	37	chr4	4322599	4322599	+	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	cagagctcagactctttctcCcaagacacgtctgtgacgct	9	10	8	14	2	4	4	1	1	3	3	5	4	4	4	1	0	1	2	1	0	1	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr4:4322599C>A	ENST00000337872.4	+	8	1975	c.1854C>A	c.(1852-1854)tcC>tcA	p.S618S	ZBTB49_ENST00000355834.3_Silent_p.S496S|RP11-265O12.1_ENST00000509015.1_lincRNA|ZBTB49_ENST00000538529.1_Silent_p.S101S	NM_145291.3	NP_660334.3	Q6ZSB9	ZBT49_HUMAN	zinc finger and BTB domain containing 49	618					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						ACTCTTTCTCCCAAGACACGT	0.547																																					p.S618S		Atlas-SNP	.											.	ZBTB49	63	.	0			c.C1854A						PASS	.						54	51	52					4																	4322599		2203	4300	6503	SO:0001819	synonymous_variant	166793	exon8			TTTCTCCCAAGAC	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.1854C>A	chr4.hg19:g.4322599C>A		62.0	0.0	.		39.0	21.0	.	NM_145291	Q59FJ4|Q5EBN0|Q8TB80	Silent	SNP	ENST00000337872.4	hg19	CCDS3375.1																																																																																			.	.	.	none		0.547	ZBTB49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206688.3	NM_145291		A	4322599	C	A	4322599	2	1	158	1	0	0	0	0	0	0	0	1	17562	610	22	4		4	ZBTB49	4	4322599	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08		4322599	186831677	24	9365											
CCKAR	886	hgsc.bcm.edu	37	chr4	26483517	26483517	+	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	ggttcctgagaggcggcgctCtgcggaggcggtgtcgtagg	4	8	20	9	5	1	1	0	1	1	1	3	3	2	2	1	7	1	3	1	7	1	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr4:26483517C>T	ENST00000295589.3	-	5	1224	c.1030G>A	c.(1030-1032)Gag>Aag	p.E344K		NM_000730.2	NP_000721.1	P32238	CCKAR_HUMAN	cholecystokinin A receptor	344					axonogenesis (GO:0007409)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|feeding behavior (GO:0007631)|forebrain development (GO:0030900)|neuron migration (GO:0001764)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|response to nutrient (GO:0007584)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cholecystokinin receptor activity (GO:0004951)			NS(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(14)|pancreas(1)|skin(1)	29		Breast(46;0.0503)			Ceruletide(DB00403)	AGGCGGCGCTCTGCGGAGGCG	0.592																																					p.E344K		Atlas-SNP	.											.	CCKAR	74	.	0			c.G1030A						PASS	.						103	95	98					4																	26483517		2203	4300	6503	SO:0001583	missense	886	exon5			GGCGCTCTGCGGA	L19315	CCDS3438.1	4p15.2	2013-09-20			ENSG00000163394	ENSG00000163394		"GPCR / Class A : Cholecystokinin receptors"	1570	protein-coding gene	gene with protein product		118444					Standard	NM_000730		Approved		uc003gse.1	P32238	OTTHUMG00000128567	ENST00000295589.3:c.1030G>A	chr4.hg19:g.26483517C>T	ENSP00000295589:p.Glu344Lys	120.0	0.0	.		77.0	34.0	.	NM_000730	B2R9Z5	Missense_Mutation	SNP	ENST00000295589.3	hg19	CCDS3438.1	.	.	.	.	.	.	.	.	.	.	C	6.038	0.375400	0.11409	.	.	ENSG00000163394	ENST00000295589	T	0.72051	-0.62	5.29	3.53	0.40419	GPCR, rhodopsin-like superfamily (1);	0.163417	0.52532	D	0.000076	T	0.49029	0.1533	N	0.11698	0.16	0.28765	N	0.900671	B	0.14012	0.009	B	0.17098	0.017	T	0.37731	-0.9693	10	0.23302	T	0.38	.	9.6172	0.39698	0.0:0.6564:0.2699:0.0737	.	344	P32238	CCKAR_HUMAN	K	344	ENSP00000295589:E344K	ENSP00000295589:E344K	E	-	1	0	CCKAR	26092615	0.886000	0.30341	0.983000	0.44433	0.058000	0.15608	1.765000	0.38481	1.205000	0.43262	0.563000	0.77884	GAG	.	.	.	none		0.592	CCKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250418.2			T	26483517	C	T	26483517	3	4	158	1	0	0	0	0	1	0	0	0	2882	922	32	2	260	2	CCKAR	4	26483517	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	22160918	26483517	164670759	25	9366											
ANXA3	306	hgsc.bcm.edu	37	chr4	79516549	79516549	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtttagggcagaagagatgaAagtctgaaagtggatgagca	15	8	15	3	0	1	5	0	3	1	2	1	7	1	6	0	2	1	3	0	2	4	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr4:79516549A>G	ENST00000264908.6	+	8	877	c.498A>G	c.(496-498)gaA>gaG	p.E166E	ANXA3_ENST00000503570.2_Silent_p.E127E|ANXA3_ENST00000512884.1_Silent_p.E127E	NM_005139.2	NP_005130.1	P12429	ANXA3_HUMAN	annexin A3	166					defense response to bacterium (GO:0042742)|neutrophil degranulation (GO:0043312)|phagocytosis (GO:0006909)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|specific granule (GO:0042581)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|phospholipase A2 inhibitor activity (GO:0019834)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15						GAAGAGATGAAAGTCTGAAAG	0.443																																					p.E166E	GBM(2;126 157 27790 28920 42492)	Atlas-SNP	.											.	ANXA3	35	.	0			c.A498G						PASS	.						184	186	186					4																	79516549		2203	4300	6503	SO:0001819	synonymous_variant	306	exon8			AGATGAAAGTCTG	M63310	CCDS3584.1	4q21.21	2009-07-10			ENSG00000138772	ENSG00000138772	3.1.4.43	"Annexins"	541	protein-coding gene	gene with protein product		106490		ANX3		1830024	Standard	XM_005262973		Approved		uc003hld.3	P12429	OTTHUMG00000130198	ENST00000264908.6:c.498A>G	chr4.hg19:g.79516549A>G		265.0	0.0	.		259.0	95.0	.	NM_005139	B2R9W6|Q6LET2	Silent	SNP	ENST00000264908.6	hg19	CCDS3584.1																																																																																			.	.	.	none		0.443	ANXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252516.3	NM_005139		G	79516549	A	G	79516549	2	3	158	1	0	0	0	0	0	0	0	1	719	11	1	3		3	ANXA3	4	79516549	Silent	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	53033032	79516549	111637727	26	9367											
PLRG1	5356	hgsc.bcm.edu	37	chr4	155470082	155470082	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgtgtacagaatgtttctgTacctcctaaaaaaaaagaat	16	12	7	6	0	1	2	0	0	1	2	2	2	2	2	2	0	2	3	2	0	9	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr4:155470082T>C	ENST00000499023.2	-	2	141	c.15A>G	c.(13-15)gtA>gtG	p.V5V	PLRG1_ENST00000393905.2_Silent_p.V5V|PLRG1_ENST00000302078.5_Silent_p.V5V	NM_001201564.1|NM_002669.3	NP_001188493.1|NP_002660.1	O43660	PLRG1_HUMAN	pleiotropic regulator 1	5					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|protein localization to nucleus (GO:0034504)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|skin(1)|urinary_tract(1)	22	all_hematologic(180;0.215)	Renal(120;0.0854)				AATGTTTCTGTACCTCCTAAA	0.353																																					p.V5V		Atlas-SNP	.											.	PLRG1	43	.	0			c.A15G						PASS	.						76	71	73					4																	155470082		2203	4300	6503	SO:0001819	synonymous_variant	5356	exon2			TTTCTGTACCTCC	AF044333	CCDS34083.1, CCDS56341.1	4q31.2-q32.1	2013-01-10	2011-05-19		ENSG00000171566	ENSG00000171566		"WD repeat domain containing"	9089	protein-coding gene	gene with protein product	"transport and golgi organization 4 homolog (Drosophila)"	605961	"pleiotropic regulator 1 (PRL1, Arabidopsis homolog)", "pleiotropic regulator 1 (PRL1 homolog, Arabidopsis)"				Standard	NM_002669		Approved	PRL1, Prp46, PRPF46, Cwc1, TANGO4	uc003iny.3	O43660	OTTHUMG00000161411	ENST00000499023.2:c.15A>G	chr4.hg19:g.155470082T>C		31.0	0.0	.		29.0	11.0	.	NM_002669	B3KMK4|Q3KQY5|Q8WUD8	Silent	SNP	ENST00000499023.2	hg19	CCDS34083.1																																																																																			.	.	.	none		0.353	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364824.1	NM_002669		C	155470082	T	C	155470082	2	2	158	1	0	0	0	0	0	0	0	1	12113	1625	57	3		3	PLRG1	4	155470082	Silent	SNP	T	TCGA-DZ-6133-01A-11D-1961-08	75953533	155470082	35684194	27	9368											
PCSK1	5122	hgsc.bcm.edu	37	chr5	95728748	95728748	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaccagagcttgaagcagcCggtcgtctctgtgcttgtaa	8	10	11	12	2	1	2	0	1	1	1	3	2	1	2	3	1	4	4	3	1	2	3	rs140941383		TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr5:95728748C>T	ENST00000311106.3	-	14	2456	c.2219G>A	c.(2218-2220)cGg>cAg	p.R740Q	PCSK1_ENST00000513085.1_5'UTR|CTD-2337A12.1_ENST00000502645.2_RNA|PCSK1_ENST00000508626.1_Missense_Mutation_p.R693Q	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	740					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)"	TTGAAGCAGCCGGTCGTCTCT	0.398																																					p.R740Q		Atlas-SNP	.											.	PCSK1	93	.	0			c.G2219A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	163	170	168		2219,2078,1289	5.1	1	5	dbSNP_134	168	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	PCSK1	NM_000439.4,NM_001177875.1,NM_001177876.1	43,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	740/754,693/707,430/444	95728748	1,13005	2203	4300	6503	SO:0001583	missense	5122	exon14			AGCAGCCGGTCGT		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.2219G>A	chr5.hg19:g.95728748C>T	ENSP00000308024:p.Arg740Gln	306.0	1.0	.		255.0	109.0	.	NM_000439	B7Z8T7|E9PHA1|P78478|Q92532	Missense_Mutation	SNP	ENST00000311106.3	hg19	CCDS4081.1	.	.	.	.	.	.	.	.	.	.	C	34	5.313465	0.95655	0.0	1.16E-4	ENSG00000175426	ENST00000311106;ENST00000508626	T;T	0.71341	-0.41;-0.56	6.03	5.11	0.69529	Prohormone convertase enzyme (1);	0.058685	0.64402	D	0.000001	T	0.74222	0.3688	L	0.34521	1.04	0.49130	D	0.999758	D;D	0.71674	0.997;0.998	P;P	0.59825	0.864;0.834	T	0.76364	-0.2986	10	0.72032	D	0.01	-22.6652	15.7754	0.78209	0.1369:0.8631:0.0:0.0	.	693;740	E9PHA1;P29120	.;NEC1_HUMAN	Q	740;693	ENSP00000308024:R740Q;ENSP00000421600:R693Q	ENSP00000308024:R740Q	R	-	2	0	PCSK1	95754504	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.354000	0.59417	2.861000	0.98227	0.655000	0.94253	CGG	.	C|1.000;T|0.000	0.000	weak		0.398	PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1	NM_000439		T	95728748	C	T	95728748	3	4	158	1	0	0	0	0	1	0	0	0	11607	652	23	1	46	1	PCSK1	5	95728748	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08		95728748	85186512	28	9369											
CHD1	1105	hgsc.bcm.edu	37	chr5	98236974	98236974	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aactgcttttctctctctctTcttcagattctgaatctgaa	8	18	4	11	0	7	3	1	2	6	1	9	3	7	3	0	0	2	1	0	0	3	5	rs370850474		TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr5:98236974T>C	ENST00000284049.3	-	5	652	c.503A>G	c.(502-504)gAa>gGa	p.E168G		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	168					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)	CTCTCTCTCTTCTTCAGATTC	0.358																																					p.E168G		Atlas-SNP	.											.	CHD1	137	.	0			c.A503G						PASS	.	T	GLY/GLU	0,4406		0,0,2203	137	133	134		503	5.6	1	5		134	4,8596	3.7+/-12.6	0,4,4296	no	missense	CHD1	NM_001270.2	98	0,4,6499	CC,CT,TT		0.0465,0.0,0.0308	benign	168/1711	98236974	4,13002	2203	4300	6503	SO:0001583	missense	1105	exon5			CTCTCTTCTTCAG	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.503A>G	chr5.hg19:g.98236974T>C	ENSP00000284049:p.Glu168Gly	149.0	0.0	.		144.0	63.0	.	NM_001270	Q17RZ3	Missense_Mutation	SNP	ENST00000284049.3	hg19	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	T	13.94	2.388330	0.42308	0.0	4.65E-4	ENSG00000153922	ENST00000284049;ENST00000540681	D	0.90385	-2.66	5.62	5.62	0.85841	.	0.000000	0.34507	U	0.003918	D	0.82986	0.5156	N	0.14661	0.345	0.51012	D	0.999905	B	0.16603	0.018	B	0.16722	0.016	T	0.78352	-0.2237	10	0.34782	T	0.22	.	14.6925	0.69096	0.0:0.0:0.0:1.0	.	168	O14646	CHD1_HUMAN	G	168	ENSP00000284049:E168G	ENSP00000284049:E168G	E	-	2	0	CHD1	98264874	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	2.936000	0.48971	2.254000	0.74563	0.528000	0.53228	GAA	.	.	.	weak		0.358	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270		C	98236974	T	C	98236974	3	2	158	1	0	0	0	0	1	0	0	0	3325	1783	62	3	4753	3	CHD1	5	98236974	Missense_Mutation	SNP	T	TCGA-DZ-6133-01A-11D-1961-08	2508226	98236974	82678286	29	9370											
GTF2H4	2968	hgsc.bcm.edu	37	chr6	30877829	30877829	+	Silent	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	cgccagaacctccgcattgcCcttctgggtgggtatgtcac	6	10	11	14	2	2	1	1	0	1	1	3	1	3	1	4	2	2	2	4	2	2	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr6:30877829C>T	ENST00000259895.4	+	4	586	c.363C>T	c.(361-363)gcC>gcT	p.A121A	GTF2H4_ENST00000376316.2_Silent_p.A121A|GTF2H4_ENST00000539324.1_Silent_p.A65A|RN7SL175P_ENST00000580375.1_RNA	NM_001517.4	NP_001508.1	Q92759	TF2H4_HUMAN	general transcription factor IIH, polypeptide 4, 52kDa	121					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						TCCGCATTGCCCTTCTGGGTG	0.582								Nucleotide excision repair (NER)																													p.A121A		Atlas-SNP	.											.	GTF2H4	38	.	0			c.C363T						PASS	.						114	130	124					6																	30877829		1510	2708	4218	SO:0001819	synonymous_variant	2968	exon4			CATTGCCCTTCTG	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.363C>T	chr6.hg19:g.30877829C>T		243.0	1.0	.		133.0	57.0	.	NM_001517	B4DTJ5|Q76KU4	Silent	SNP	ENST00000259895.4	hg19	CCDS34386.1																																																																																			.	.	.	none		0.582	GTF2H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076044.3	NM_001517		T	30877829	C	T	30877829	2	4	158	1	0	0	0	0	0	0	0	1	6872	610	22	2		2	GTF2H4	6	30877829	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08		30877829	140237238	30	9371											
HLA-DQA2	3118	hgsc.bcm.edu	37	chr6	32714066	32714066	+	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	ctcacagagactttggtctgCgccctggggttgtctgtggg	4	12	15	10	1	3	1	1	0	2	1	3	2	3	1	1	4	1	1	1	4	0	2	rs572758897		TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr6:32714066C>T	ENST00000374940.3	+	4	765	c.663C>T	c.(661-663)tgC>tgT	p.C221C		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	221					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|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)|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)			endometrium(2)|large_intestine(3)|lung(7)|skin(1)	13					"""Insulin(DB00071)"	CTTTGGTCTGCGCCCTGGGGT	0.552													.|||	1	0.000199681	0	0	5008	,	,		21667	0		0	False		,,,				2504	0.001				p.C221C		Atlas-SNP	.											.	HLA-DQA2	27	.	0			c.C663T						PASS	.						163	160	161					6																	32714066		1511	2709	4220	SO:0001819	synonymous_variant	3118	exon4			GGTCTGCGCCCTG		CCDS4753.1	6p21.3	2013-01-11			ENSG00000237541	ENSG00000237541		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4943	protein-coding gene	gene with protein product		613503		HLA-DXA			Standard	NM_020056		Approved		uc003obx.3	P01906	OTTHUMG00000031108	ENST00000374940.3:c.663C>T	chr6.hg19:g.32714066C>T		217.0	1.0	.		154.0	73.0	.	NM_020056	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	Silent	SNP	ENST00000374940.3	hg19	CCDS4753.1																																																																																			.	.	.	none		0.552	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076179.2	NM_020056		T	32714066	C	T	32714066	2	4	158	1	0	0	0	0	0	0	0	1	7212	776	27	1		1	HLA-DQA2	6	32714066	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	1836237	32714066	138401001	31	9372											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152671451	152671451	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catggtctttgactttcgccTccagactgaagacatgctcc	8	12	8	13	1	1	4	0	2	1	2	4	4	3	4	3	1	1	1	3	1	1	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr6:152671451T>C	ENST00000367255.5	-	72	12354	c.11753A>G	c.(11752-11754)gAg>gGg	p.E3918G	SYNE1_ENST00000265368.4_Missense_Mutation_p.E3918G|SYNE1_ENST00000448038.1_Intron|SYNE1_ENST00000423061.1_Intron|SYNE1_ENST00000341594.5_Missense_Mutation_p.E3842G	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3918					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)		GACTTTCGCCTCCAGACTGAA	0.473										HNSCC(10;0.0054)																											p.E3918G		Atlas-SNP	.											SYNE1_ENST00000265368,NS,carcinoma,0,2	SYNE1	3227	.	0			c.A11753G						PASS	.						102	93	96					6																	152671451		2203	4300	6503	SO:0001583	missense	23345	exon72			TTCGCCTCCAGAC	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.11753A>G	chr6.hg19:g.152671451T>C	ENSP00000356224:p.Glu3918Gly	155.0	0.0	.		85.0	23.0	.	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	T	14.89	2.671137	0.47781	.	.	ENSG00000131018	ENST00000367255;ENST00000265368;ENST00000341594	T;T;T	0.41400	1.0;1.0;1.0	5.93	5.93	0.95920	.	0.000000	0.64402	D	0.000009	T	0.51041	0.1651	L	0.55481	1.735	0.80722	D	1	D;D;D	0.63046	0.992;0.992;0.992	D;D;D	0.64687	0.928;0.928;0.928	T	0.54879	-0.8227	10	0.72032	D	0.01	.	16.3943	0.83563	0.0:0.0:0.0:1.0	.	3918;3918;3918	B7ZBC3;Q8NF91;E7EQI5	.;SYNE1_HUMAN;.	G	3918;3918;3842	ENSP00000356224:E3918G;ENSP00000265368:E3918G;ENSP00000341887:E3842G	ENSP00000265368:E3918G	E	-	2	0	SYNE1	152713144	0.857000	0.29778	0.800000	0.32199	0.939000	0.58152	2.153000	0.42282	2.281000	0.76405	0.533000	0.62120	GAG	.	.	.	none		0.473	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		C	152671451	T	C	152671451	3	2	158	1	0	0	0	0	1	0	0	0	15457	1551	54	3	15013	3	SYNE1	6	152671451	Missense_Mutation	SNP	T	TCGA-DZ-6133-01A-11D-1961-08	119957385	152671451	18443616	32	9373											
ARID1B	57492	hgsc.bcm.edu	37	chr6	157527600	157527600	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gacgccgctgcagacccaaaGgagaagcccaagcaagccag	14	1	12	14	2	0	2	0	0	0	2	0	4	0	2	4	1	4	3	4	1	4	0			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr6:157527600G>A	ENST00000350026.5	+	19	5287	c.5286G>A	c.(5284-5286)aaG>aaA	p.K1762K	ARID1B_ENST00000275248.4_Silent_p.K1757K|ARID1B_ENST00000367148.1_Silent_p.K1815K|ARID1B_ENST00000346085.5_Silent_p.K1775K	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1762					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)		CAGACCCAAAGGAGAAGCCCA	0.517																																					p.K1775K		Atlas-SNP	.											.	ARID1B	320	.	0			c.G5325A						PASS	.						60	61	61					6																	157527600		2203	4296	6499	SO:0001819	synonymous_variant	57492	exon20			CCCAAAGGAGAAG	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.5286G>A	chr6.hg19:g.157527600G>A		133.0	0.0	.		114.0	43.0	.	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Silent	SNP	ENST00000350026.5	hg19	CCDS5251.2																																																																																			.	.	.	none		0.517	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		A	157527600	G	A	157527600	2	1	158	1	0	0	0	0	0	0	0	1	914	991	35	2		2	ARID1B	6	157527600	Silent	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	4856149	157527600	13587467	33	9374											
CDK13	8621	hgsc.bcm.edu	37	chr7	40117701	40117701	+	Frame_Shift_Del	DEL	T	T	-																															agaagcaatatcgtcgaaagTtaagagaagaatttgttttg																										TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr7:40117701delT	ENST00000181839.4	+	10	3483	c.2878delT	c.(2878-2880)ttafs	p.L960fs	CDK13_ENST00000340829.5_Frame_Shift_Del_p.L960fs	NM_003718.4|NM_031267.3	NP_003709.3|NP_112557.2	Q14004	CDK13_HUMAN	cyclin-dependent kinase 13	960	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				alternative mRNA splicing, via spliceosome (GO:0000380)|hemopoiesis (GO:0030097)|multicellular organismal development (GO:0007275)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|positive regulation of cell proliferation (GO:0008284)|regulation of mitosis (GO:0007088)|viral process (GO:0016032)	cyclin K-CDK13 complex (GO:0002945)|extracellular space (GO:0005615)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(2)|prostate(2)|skin(5)|stomach(2)|urinary_tract(1)	49						TCGTCGAAAGTTAAGAGAAGA	0.348																																					p.K959fs		Atlas-INDEL	.											.	CDK13	114	.	0			c.2877delG						PASS	.						152	143	146					7																	40117701		2203	4300	6503	SO:0001589	frameshift_variant	8621	exon10			.	M80629	CCDS5461.1, CCDS5462.1	7p14.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000065883	ENSG00000065883		"Cyclin-dependent kinases"	1733	protein-coding gene	gene with protein product	"cholinesterase-related cell division controller"	603309	"cell division cycle 2-like 5 (cholinesterase-related cell division controller)"	CDC2L5		1731328, 19884882	Standard	NM_003718		Approved	CHED, CDC2L, KIAA1791	uc003thh.4	Q14004	OTTHUMG00000023726	ENST00000181839.4:c.2878delT	chr7.hg19:g.40117701delT	ENSP00000181839:p.Leu960fs	78.0	0.0	0		139.0	64.0	0.460432	NM_003718	Q53G78|Q6DKQ9|Q75MH4|Q75MH5|Q96JN4|Q9H4A0|Q9H4A1|Q9UDR4	Frame_Shift_Del	DEL	ENST00000181839.4	hg19	CCDS5461.1																																																																																			.	.	.	none		0.348	CDK13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250726.2	NM_003718		-	40117701	T	-	40117701	7	5	158	1	0	1	0	1	0	0	0	0	3131	1722	60	0	2916	0	CDK13	7	40117701	Frame_Shift_Del	DEL	T	TCGA-DZ-6133-01A-11D-1961-08		40117701	119020962	34	9375											
ABCB1	5243	hgsc.bcm.edu	37	chr7	87179321	87179321	+	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	tcaccacaccaatgatttccCgtagaaaccttacatttatg	13	12	4	12	1	1	2	1	1	0	1	2	2	2	2	4	0	2	1	4	0	5	5			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr7:87179321C>A	ENST00000265724.3	-	14	1817	c.1400G>T	c.(1399-1401)cGg>cTg	p.R467L	ABCB1_ENST00000543898.1_Missense_Mutation_p.R403L	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	467	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)	p.R467L(2)		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)	AATGATTTCCCGTAGAAACCT	0.403																																					p.R467L		Atlas-SNP	.											.	ABCB1	263	.	2	Substitution - Missense(2)	lung(2)	c.G1400T						PASS	.						147	134	139					7																	87179321		2203	4300	6503	SO:0001583	missense	5243	exon14			ATTTCCCGTAGAA	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.1400G>T	chr7.hg19:g.87179321C>A	ENSP00000265724:p.Arg467Leu	171.0	0.0	.		243.0	12.0	.	NM_000927	A8K294|B5AK60|Q12755|Q14812	Missense_Mutation	SNP	ENST00000265724.3	hg19	CCDS5608.1	.	.	.	.	.	.	.	.	.	.	C	33	5.256424	0.95336	.	.	ENSG00000085563	ENST00000543174;ENST00000265724;ENST00000543898	D;D	0.94793	-3.52;-3.52	6.16	6.16	0.99307	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.97717	0.9251	M	0.84511	2.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.97561	1.0098	10	0.87932	D	0	-21.7962	20.8598	0.99761	0.0:1.0:0.0:0.0	.	403;467	B5AK60;P08183	.;MDR1_HUMAN	L	248;467;403	ENSP00000265724:R467L;ENSP00000444095:R403L	ENSP00000265724:R467L	R	-	2	0	ABCB1	87017257	0.984000	0.35163	1.000000	0.80357	0.959000	0.62525	7.818000	0.86416	2.937000	0.99478	0.650000	0.86243	CGG	.	.	.	none		0.403	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927		A	87179321	C	A	87179321	3	1	158	1	0	0	0	0	1	0	0	0	40	652	23	4	2506	4	ABCB1	7	87179321	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	47061620	87179321	71959342	35	9376											
ANGPT2	285	hgsc.bcm.edu	37	chr8	6360731	6360731	+	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	tatttgtgttctgcctctgtGgatagtacattccgttcaag	7	17	9	8	1	3	0	1	0	2	0	4	1	4	1	2	1	2	3	2	1	4	7			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr8:6360731G>T	ENST00000325203.5	-	9	1856	c.1382C>A	c.(1381-1383)cCa>cAa	p.P461Q	ANGPT2_ENST00000415216.1_Missense_Mutation_p.P460Q|MCPH1_ENST00000344683.5_Intron|ANGPT2_ENST00000338312.6_Missense_Mutation_p.P409Q			O15123	ANGP2_HUMAN	angiopoietin 2	461	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to growth factor stimulus (GO:0071363)|germ cell development (GO:0007281)|glomerulus vasculature development (GO:0072012)|leukocyte migration (GO:0050900)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of positive chemotaxis (GO:0050928)|organ regeneration (GO:0031100)|positive regulation of angiogenesis (GO:0045766)|response to activity (GO:0014823)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to radiation (GO:0009314)|signal transduction (GO:0007165)|Tie signaling pathway (GO:0048014)	cell projection (GO:0042995)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17		Hepatocellular(245;0.0663)		Colorectal(4;0.0142)|READ - Rectum adenocarcinoma(4;0.19)|COAD - Colon adenocarcinoma(4;0.226)		CTGCCTCTGTGGATAGTACAT	0.463																																					p.P461Q		Atlas-SNP	.											.	ANGPT2	126	.	0			c.C1382A						PASS	.						235	190	205					8																	6360731		2203	4300	6503	SO:0001583	missense	285	exon9			CTCTGTGGATAGT	AF004327	CCDS5958.1, CCDS47761.1	8p23	2013-02-06			ENSG00000091879	ENSG00000091879		"Fibrinogen C domain containing"	485	protein-coding gene	gene with protein product		601922				9545648	Standard	NM_001147		Approved	Ang2	uc003wqj.4	O15123	OTTHUMG00000090365	ENST00000325203.5:c.1382C>A	chr8.hg19:g.6360731G>T	ENSP00000314897:p.Pro461Gln	88.0	0.0	.		66.0	24.0	.	NM_001147	A0AV38|A8K205|B7ZLM7|Q9NRR7|Q9P2Y7	Missense_Mutation	SNP	ENST00000325203.5	hg19	CCDS5958.1	.	.	.	.	.	.	.	.	.	.	G	14.06	2.422644	0.43020	.	.	ENSG00000091879	ENST00000325203;ENST00000415216;ENST00000338312	T;T;T	0.75050	-0.9;-0.9;-0.9	6.17	6.17	0.99709	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1);	0.112483	0.64402	D	0.000006	T	0.57621	0.2066	N	0.10685	0.025	0.42845	D	0.994062	B;B;B	0.27229	0.069;0.069;0.172	B;B;B	0.25506	0.015;0.015;0.061	T	0.54761	-0.8245	10	0.22109	T	0.4	.	18.3732	0.90420	0.0:0.0:1.0:0.0	.	409;460;461	O15123-2;O15123-3;O15123	.;.;ANGP2_HUMAN	Q	461;460;409	ENSP00000314897:P461Q;ENSP00000400782:P460Q;ENSP00000343517:P409Q	ENSP00000314897:P461Q	P	-	2	0	ANGPT2	6348139	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.047000	0.57383	2.941000	0.99782	0.655000	0.94253	CCA	.	.	.	none		0.463	ANGPT2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206737.1	NM_001147		T	6360731	G	T	6360731	3	4	158	1	0	0	0	0	1	0	0	0	611	1348	47	4	112	4	ANGPT2	8	6360731	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08		6360731	140003291	36	9377											
BIN3	55909	hgsc.bcm.edu	37	chr8	22488017	22488017	+	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	cagggccgtcaccatgttcaGaaggtcctggtcttgctcac	7	10	11	13	1	4	1	3	0	1	1	5	1	5	1	3	3	1	2	3	3	1	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr8:22488017G>A	ENST00000276416.6	-	5	303	c.235C>T	c.(235-237)Ctg>Ttg	p.L79L	BIN3_ENST00000399977.4_Silent_p.L31L|BIN3_ENST00000519335.1_5'UTR|BIN3_ENST00000519513.1_Silent_p.L25L|BIN3_ENST00000520292.1_Silent_p.L79L	NM_018688.4	NP_061158.1	Q9NQY0	BIN3_HUMAN	bridging integrator 3	79	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				actin filament organization (GO:0007015)|barrier septum assembly (GO:0000917)|cytokinesis (GO:0000910)|myoblast migration involved in skeletal muscle regeneration (GO:0014839)|protein localization (GO:0008104)|regulation of lamellipodium assembly (GO:0010591)|skeletal muscle fiber development (GO:0048741)|unidimensional cell growth (GO:0009826)	actin filament (GO:0005884)|cytoplasm (GO:0005737)	cytoskeletal adaptor activity (GO:0008093)			kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	9		Prostate(55;0.0424)|Breast(100;0.102)|all_epithelial(46;0.143)		BRCA - Breast invasive adenocarcinoma(99;0.00664)|Colorectal(74;0.0189)|COAD - Colon adenocarcinoma(73;0.0727)		ACCATGTTCAGAAGGTCCTGG	0.532																																					p.L79L		Atlas-SNP	.											.	BIN3	16	.	0			c.C235T						PASS	.						176	176	176					8																	22488017		2001	4169	6170	SO:0001819	synonymous_variant	55909	exon5			TGTTCAGAAGGTC		CCDS47825.1	8p21.2	2008-07-04			ENSG00000147439	ENSG00000147439			1054	protein-coding gene	gene with protein product		606396				16524918	Standard	NM_018688		Approved		uc003xcl.3	Q9NQY0	OTTHUMG00000163844	ENST00000276416.6:c.235C>T	chr8.hg19:g.22488017G>A		289.0	0.0	.		165.0	65.0	.	NM_018688	Q9BVG2|Q9NVY9	Silent	SNP	ENST00000276416.6	hg19	CCDS47825.1																																																																																			.	.	.	none		0.532	BIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375895.1			A	22488017	G	A	22488017	2	1	158	1	0	0	0	0	0	0	0	1	1434	933	33	2		2	BIN3	8	22488017	Silent	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	16127286	22488017	123876005	37	9378											
RAB11FIP1	80223	hgsc.bcm.edu	37	chr8	37732715	37732715	+	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	attgatgcagacattagagcGggaaaggacatcattcttag	14	10	11	6	1	2	3	1	1	1	2	2	5	2	5	0	2	2	1	0	2	3	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr8:37732715G>T	ENST00000330843.4	-	3	952	c.940C>A	c.(940-942)Cgc>Agc	p.R314S	RAB11FIP1_ENST00000287263.4_Missense_Mutation_p.R314S|RAB11FIP1_ENST00000524118.1_Missense_Mutation_p.R166S|RAB11FIP1_ENST00000522727.1_Missense_Mutation_p.R166S|RAB11FIP1_ENST00000523182.1_5'Flank	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	314					protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)		p.R314C(1)|p.R314S(1)		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)			ACATTAGAGCGGGAAAGGACA	0.507																																					p.R314S		Atlas-SNP	.											RAB11FIP1,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	RAB11FIP1	105	.	2	Substitution - Missense(2)	lung(1)|central_nervous_system(1)	c.C940A						PASS	.						260	251	254					8																	37732715		2203	4300	6503	SO:0001583	missense	80223	exon3			TAGAGCGGGAAAG	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.940C>A	chr8.hg19:g.37732715G>T	ENSP00000331342:p.Arg314Ser	473.0	1.0	.		302.0	13.0	.	NM_025151	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Missense_Mutation	SNP	ENST00000330843.4	hg19	CCDS34882.1	.	.	.	.	.	.	.	.	.	.	G	17.57	3.422554	0.62622	.	.	ENSG00000156675	ENST00000287263;ENST00000330843;ENST00000522727;ENST00000524118	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	5.24	5.24	0.73138	.	0.222920	0.31922	N	0.006857	T	0.55800	0.1943	M	0.78049	2.395	0.33156	D	0.546361	D;D;D;D	0.89917	0.983;0.991;1.0;0.994	P;P;D;P	0.87578	0.799;0.873;0.998;0.84	T	0.69716	-0.5070	10	0.72032	D	0.01	-11.1297	12.9824	0.58572	0.0:0.0:0.728:0.272	.	166;166;314;314	E7EX40;Q6WKZ4-2;Q6WKZ4-3;Q6WKZ4	.;.;.;RFIP1_HUMAN	S	314;314;166;166	ENSP00000287263:R314S;ENSP00000331342:R314S;ENSP00000430009:R166S;ENSP00000430680:R166S	ENSP00000287263:R314S	R	-	1	0	RAB11FIP1	37851873	1.000000	0.71417	0.999000	0.59377	0.802000	0.45316	2.192000	0.42649	2.445000	0.82738	0.655000	0.94253	CGC	.	.	.	none		0.507	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151		T	37732715	G	T	37732715	3	4	158	1	0	0	0	0	1	0	0	0	12906	1116	39	4	2927	4	RAB11FIP1	8	37732715	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	15244698	37732715	108631307	38	9379											
PTPRD	5789	hgsc.bcm.edu	37	chr9	8471073	8471073	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcttcaaaggcacaattatTatgtagtaacctctgcacaa	14	13	5	9	0	3	0	1	0	2	0	3	0	3	0	1	1	2	4	1	1	7	6			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr9:8471073T>C	ENST00000381196.4	-	28	3969	c.3426A>G	c.(3424-3426)atA>atG	p.I1142M	PTPRD_ENST00000360074.4_Missense_Mutation_p.I1129M|PTPRD_ENST00000358503.5_Missense_Mutation_p.I1120M|PTPRD_ENST00000355233.5_Missense_Mutation_p.I731M|PTPRD_ENST00000486161.1_Missense_Mutation_p.I731M|PTPRD_ENST00000397617.3_Missense_Mutation_p.I721M|PTPRD_ENST00000540109.1_Missense_Mutation_p.I1142M|PTPRD_ENST00000356435.5_Missense_Mutation_p.I1142M|PTPRD_ENST00000397606.3_Missense_Mutation_p.I721M|PTPRD_ENST00000397611.3_Missense_Mutation_p.I728M|PTPRD_ENST00000537002.1_Missense_Mutation_p.I728M	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1142					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)		GCACAATTATTATGTAGTAAC	0.393										TSP Lung(15;0.13)																											p.I1142M		Atlas-SNP	.											.	PTPRD	1348	.	0			c.A3426G						PASS	.						115	113	114					9																	8471073		2203	4300	6503	SO:0001583	missense	5789	exon31			AATTATTATGTAG	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.3426A>G	chr9.hg19:g.8471073T>C	ENSP00000370593:p.Ile1142Met	106.0	0.0	.		122.0	56.0	.	NM_002839	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	hg19	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	T	18.88	3.717523	0.68844	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606	T;T;T;T;T;T;T;T;T;T;T	0.60672	0.17;0.17;0.17;0.17;0.17;0.17;0.17;0.17;0.17;0.17;0.17	5.72	4.56	0.56223	.	0.093861	0.64402	D	0.000001	T	0.70919	0.3279	M	0.69358	2.11	0.48762	D	0.999701	P;P;B;P;D;D;B;P;B	0.59357	0.835;0.868;0.435;0.855;0.985;0.973;0.035;0.736;0.097	P;P;B;B;D;P;B;B;B	0.77557	0.707;0.501;0.221;0.359;0.99;0.807;0.026;0.372;0.016	T	0.69924	-0.5013	9	.	.	.	.	9.7155	0.40272	0.286:0.0:0.0:0.714	.	721;726;731;731;728;728;1129;1142;1142	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	M	1142;1142;1129;1120;731;721;728;728;613;1142;731;721	ENSP00000370593:I1142M;ENSP00000348812:I1142M;ENSP00000353187:I1129M;ENSP00000351293:I1120M;ENSP00000347373:I731M;ENSP00000380741:I721M;ENSP00000380735:I728M;ENSP00000440515:I728M;ENSP00000438164:I1142M;ENSP00000417093:I731M;ENSP00000380731:I721M	.	I	-	3	3	PTPRD	8461073	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.376000	0.44292	0.960000	0.38005	0.533000	0.62120	ATA	.	.	.	none		0.393	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			C	8471073	T	C	8471073	3	2	158	1	0	0	0	0	1	0	0	0	12812	1744	61	3	2441	3	PTPRD	9	8471073	Missense_Mutation	SNP	T	TCGA-DZ-6133-01A-11D-1961-08		8471073	132742358	39	9380											
TOPORS	10210	hgsc.bcm.edu	37	chr9	32541815	32541815	+	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	tggtaattacaactggggaaCgtgaagcattatctccatgg	12	11	11	7	1	1	1	0	1	1	0	2	2	1	2	1	4	4	2	1	4	6	3	rs371709773		TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr9:32541815C>G	ENST00000360538.2	-	3	2824	c.2708G>C	c.(2707-2709)cGt>cCt	p.R903P	TOPORS_ENST00000379858.1_Missense_Mutation_p.R838P	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	903	Interaction with UBE2I.				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)		AACTGGGGAACGTGAAGCATT	0.368																																					p.R903P		Atlas-SNP	.											.	TOPORS	127	.	0			c.G2708C						PASS	.						195	186	189					9																	32541815		2203	4300	6503	SO:0001583	missense	10210	exon3			GGGGAACGTGAAG	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.2708G>C	chr9.hg19:g.32541815C>G	ENSP00000353735:p.Arg903Pro	240.0	0.0	.		184.0	71.0	.	NM_005802	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	hg19	CCDS6527.1	.	.	.	.	.	.	.	.	.	.	C	10.82	1.457297	0.26161	.	.	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.15017	2.46;2.47	5.81	0.86	0.19042	.	0.565792	0.16222	N	0.224014	T	0.07999	0.0200	N	0.14661	0.345	0.18873	N	0.999987	B	0.31730	0.337	B	0.26614	0.071	T	0.24621	-1.0155	10	0.52906	T	0.07	-1.0409	5.7492	0.18138	0.0:0.4435:0.1994:0.3571	.	903	Q9NS56	TOPRS_HUMAN	P	903;838	ENSP00000353735:R903P;ENSP00000369187:R838P	ENSP00000353735:R903P	R	-	2	0	TOPORS	32531815	0.000000	0.05858	0.985000	0.45067	0.702000	0.40608	-0.615000	0.05597	0.113000	0.18004	-0.133000	0.14855	CGT	.	.	.	alt		0.368	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		G	32541815	C	G	32541815	3	3	158	1	0	0	0	0	1	0	0	0	16382	536	19	4	433	4	TOPORS	9	32541815	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	24070742	32541815	108671616	40	9381											
VCP	7415	hgsc.bcm.edu	37	chr9	35061057	35061057	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagagttcatgacctcggcAtcaatggtctcatcctctag	10	11	9	11	1	4	2	3	1	2	1	7	3	5	2	2	2	0	2	2	2	2	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr9:35061057A>G	ENST00000358901.6	-	11	2209	c.1314T>C	c.(1312-1314)gaT>gaC	p.D438D		NM_007126.3	NP_009057.1	P55072	TERA_HUMAN	valosin containing protein	438					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|aggresome assembly (GO:0070842)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|establishment of protein localization (GO:0045184)|positive regulation of Lys63-specific deubiquitinase activity (GO:1903007)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein K63-linked deubiquitination (GO:1903006)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|retrograde protein transport, ER to cytosol (GO:0030970)|translesion synthesis (GO:0019985)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Hrd1p ubiquitin ligase complex (GO:0000836)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|site of double-strand break (GO:0035861)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|deubiquitinase activator activity (GO:0035800)|lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|protein domain specific binding (GO:0019904)|protein phosphatase binding (GO:0019903)|ubiquitin-specific protease binding (GO:1990381)			breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			TGACCTCGGCATCAATGGTCT	0.537																																					p.D438D		Atlas-SNP	.											.	VCP	64	.	0			c.T1314C						PASS	.						229	212	218					9																	35061057		2203	4300	6503	SO:0001819	synonymous_variant	7415	exon11			CTCGGCATCAATG	AC004472	CCDS6573.1	9p13.3	2014-09-17	2011-01-25		ENSG00000165280	ENSG00000165280		"ATPases / AAA-type"	12666	protein-coding gene	gene with protein product		601023	"valosin-containing protein"			8595912, 7553851	Standard	NM_007126		Approved	IBMPFD, p97	uc003zvy.2	P55072	OTTHUMG00000019855	ENST00000358901.6:c.1314T>C	chr9.hg19:g.35061057A>G		409.0	1.0	.		252.0	122.0	.	NM_007126	B2R5T8|Q0V924|Q2TAI5|Q969G7|Q9UCD5	Silent	SNP	ENST00000358901.6	hg19	CCDS6573.1																																																																																			.	.	.	none		0.537	VCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052290.1	NM_007126		G	35061057	A	G	35061057	2	3	158	1	0	0	0	0	0	0	0	1	17152	214	8	3		3	VCP	9	35061057	Silent	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	2519242	35061057	106152374	41	9382											
TMEM2	23670	hgsc.bcm.edu	37	chr9	74313090	74313090	+	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	taactgtggccatgcctgtgGcttttggctttgagatacaa	8	14	11	8	0	0	1	0	1	0	1	0	2	0	1	2	3	3	2	2	3	3	5			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr9:74313090G>T	ENST00000377044.4	-	20	3947	c.3408C>A	c.(3406-3408)agC>agA	p.S1136R	TMEM2_ENST00000377066.5_Missense_Mutation_p.S1073R|TMEM2_ENST00000396272.3_Missense_Mutation_p.S129R	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	1136					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)		CATGCCTGTGGCTTTTGGCTT	0.413																																					p.S1136R		Atlas-SNP	.											.	TMEM2	112	.	0			c.C3408A						PASS	.						155	125	135					9																	74313090		2203	4300	6503	SO:0001583	missense	23670	exon20			CCTGTGGCTTTTG		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.3408C>A	chr9.hg19:g.74313090G>T	ENSP00000366243:p.Ser1136Arg	156.0	0.0	.		146.0	54.0	.	NM_013390	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Missense_Mutation	SNP	ENST00000377044.4	hg19	CCDS6638.1	.	.	.	.	.	.	.	.	.	.	G	13.04	2.118919	0.37436	.	.	ENSG00000135048	ENST00000377044;ENST00000377066;ENST00000396272	T;T;T	0.42900	0.96;0.96;0.96	5.8	3.79	0.43588	.	0.343603	0.37053	N	0.002263	T	0.24160	0.0585	N	0.14661	0.345	0.27366	N	0.95581	B;B	0.12630	0.004;0.006	B;B	0.16722	0.007;0.016	T	0.17077	-1.0381	10	0.16420	T	0.52	.	10.9787	0.47482	0.2588:0.0:0.7412:0.0	.	1136;1073	Q9UHN6;Q9UHN6-2	TMEM2_HUMAN;.	R	1136;1073;129	ENSP00000366243:S1136R;ENSP00000366266:S1073R;ENSP00000379569:S129R	ENSP00000366243:S1136R	S	-	3	2	TMEM2	73502910	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	0.723000	0.25939	0.658000	0.30925	0.563000	0.77884	AGC	.	.	.	none		0.413	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390		T	74313090	G	T	74313090	3	4	158	1	0	0	0	0	1	0	0	0	16133	1194	42	4	763	4	TMEM2	9	74313090	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	39252033	74313090	66900341	42	9383											
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84609482	84609482	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtggtttaataaacccagcaTatcatatgaagaacaagaaa	19	9	7	6	0	1	3	1	1	0	2	1	3	1	3	1	1	3	2	1	1	9	5			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr9:84609482T>C	ENST00000344803.2	+	4	4144	c.4097T>C	c.(4096-4098)aTa>aCa	p.I1366T		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	1366					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											AAACCCAGCATATCATATGAA	0.433																																					p.I1366T		Atlas-SNP	.											.	.	.	.	0			c.T4097C						PASS	.						28	25	26					9																	84609482		1844	4078	5922	SO:0001583	missense	389763	exon4			CCAGCATATCATA		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.4097T>C	chr9.hg19:g.84609482T>C	ENSP00000341988:p.Ile1366Thr	40.0	0.0	.		25.0	12.0	.	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	hg19	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	T	1.389	-0.581436	0.03854	.	.	ENSG00000214929	ENST00000344803	T	0.04706	3.57	3.23	-6.46	0.01908	.	.	.	.	.	T	0.01765	0.0056	N	0.12182	0.205	0.09310	N	1	B	0.20988	0.05	B	0.17722	0.019	T	0.45145	-0.9281	9	0.09084	T	0.74	5.4727	0.8658	0.01203	0.3696:0.2351:0.248:0.1473	.	1366	Q6ZQQ2	F75D1_HUMAN	T	1366	ENSP00000341988:I1366T	ENSP00000341988:I1366T	I	+	2	0	FAM75D1	83799302	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.596000	0.02091	-2.589000	0.00457	-0.313000	0.08912	ATA	.	.	.	none		0.433	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		C	84609482	T	C	84609482	3	2	158	1	0	0	0	0	1	0	0	0	5939	1406	49	3	4111	3	FLJ46321	9	84609482	Missense_Mutation	SNP	T	TCGA-DZ-6133-01A-11D-1961-08	10296392	84609482	56603949	43	9384											
PAPPA	5069	hgsc.bcm.edu	37	chr9	118949550	118949550	+	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	tttctccttgaagacagaccGagcccggcaagtgaccacca	11	7	9	14	2	1	4	0	2	1	2	2	5	1	4	5	1	1	1	5	1	2	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr9:118949550G>T	ENST00000328252.3	+	2	902	c.533G>T	c.(532-534)cGa>cTa	p.R178L	PAPPA_ENST00000534838.1_5'Flank	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	178					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						AAGACAGACCGAGCCCGGCAA	0.532																																					p.R178L		Atlas-SNP	.											.	PAPPA	243	.	0			c.G533T						PASS	.						84	79	81					9																	118949550		2203	4300	6503	SO:0001583	missense	5069	exon2			CAGACCGAGCCCG		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.533G>T	chr9.hg19:g.118949550G>T	ENSP00000330658:p.Arg178Leu	132.0	0.0	.		76.0	29.0	.	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Missense_Mutation	SNP	ENST00000328252.3	hg19	CCDS6813.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.948966	0.92660	.	.	ENSG00000182752	ENST00000328252	T	0.73681	-0.77	6.07	6.07	0.98685	Concanavalin A-like lectin/glucanase (1);LamG-like jellyroll fold (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.85682	D	0.000000	D	0.88709	0.6510	M	0.84433	2.695	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88974	0.3403	10	0.87932	D	0	-25.065	20.6439	0.99570	0.0:0.0:1.0:0.0	.	178	Q13219	PAPP1_HUMAN	L	178	ENSP00000330658:R178L	ENSP00000330658:R178L	R	+	2	0	PAPPA	117989371	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.827000	0.99397	2.884000	0.98904	0.655000	0.94253	CGA	.	.	.	none		0.532	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		T	118949550	G	T	118949550	3	4	158	1	0	0	0	0	1	0	0	0	11439	1058	37	4	539	4	PAPPA	9	118949550	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	34340068	118949550	22263881	44	9385											
SPTAN1	6709	hgsc.bcm.edu	37	chr9	131370474	131370474	+	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	cgggaggccttcttgaatacCgaagacaaaggagactcact	13	7	11	10	2	2	3	1	1	1	2	2	6	2	4	2	3	1	0	2	3	4	3	rs2228951	byFrequency	TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr9:131370474C>A	ENST00000372731.4	+	34	4520	c.4410C>A	c.(4408-4410)acC>acA	p.T1470T	SPTAN1_ENST00000358161.5_Silent_p.T1470T|SPTAN1_ENST00000372739.3_Silent_p.T1470T	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1470					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)	p.T1470T(1)		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						TCTTGAATACCGAAGACAAAG	0.517																																					p.T1470T	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	1	Substitution - coding silent(1)	lung(1)	c.C4410A						PASS	.						162	166	165					9																	131370474		2203	4300	6503	SO:0001819	synonymous_variant	6709	exon34			GAATACCGAAGAC	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.4410C>A	chr9.hg19:g.131370474C>A		323.0	0.0	.		212.0	11.0	.	NM_003127	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Silent	SNP	ENST00000372731.4	hg19	CCDS6905.1																																																																																			.	C|0.996;T|0.004	.	alt		0.517	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		A	131370474	C	A	131370474	2	1	158	1	0	0	0	0	0	0	0	1	15129	639	23	4		4	SPTAN1	9	131370474	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	12420924	131370474	9842957	45	9386											
CPEB3	22849	hgsc.bcm.edu	37	chr10	93812079	93812079	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcgcccagcagtattcacAgtaatactgcagacaggtga	12	8	10	11	1	1	2	1	1	0	1	2	2	1	2	1	1	3	5	1	1	3	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr10:93812079A>G	ENST00000265997.4	-	10	2159	c.1987T>C	c.(1987-1989)Tgt>Cgt	p.C663R	CPEB3_ENST00000412050.4_Missense_Mutation_p.C649R	NM_014912.4	NP_055727.3	Q8NE35	CPEB3_HUMAN	cytoplasmic polyadenylation element binding protein 3	663					3'-UTR-mediated mRNA destabilization (GO:0061158)|cellular response to amino acid stimulus (GO:0071230)|long-term memory (GO:0007616)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation (GO:0017148)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of mRNA polyadenylation (GO:1900365)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|regulation of dendritic spine development (GO:0060998)|regulation of synaptic plasticity (GO:0048167)|translation (GO:0006412)	apical dendrite (GO:0097440)|CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuron projection (GO:0043005)|nucleus (GO:0005634)|synapse (GO:0045202)	mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|translation factor activity, nucleic acid binding (GO:0008135)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0869)				CAGTATTCACAGTAATACTGC	0.592																																					p.C663R		Atlas-SNP	.											.	CPEB3	43	.	0			c.T1987C						PASS	.						101	86	91					10																	93812079		2203	4300	6503	SO:0001583	missense	22849	exon10			ATTCACAGTAATA	AB023157	CCDS31246.1, CCDS53553.1	10q23.33	2013-02-12			ENSG00000107864	ENSG00000107864		"RNA binding motif (RRM) containing"	21746	protein-coding gene	gene with protein product		610606				10231032, 12672660	Standard	NM_014912		Approved	KIAA0940	uc001khw.2	Q8NE35	OTTHUMG00000018756	ENST00000265997.4:c.1987T>C	chr10.hg19:g.93812079A>G	ENSP00000265997:p.Cys663Arg	86.0	0.0	.		45.0	19.0	.	NM_014912	Q5T389|Q9NQJ7|Q9Y2E9	Missense_Mutation	SNP	ENST00000265997.4	hg19	CCDS31246.1	.	.	.	.	.	.	.	.	.	.	A	16.70	3.195744	0.58126	.	.	ENSG00000107864	ENST00000394210;ENST00000412050;ENST00000265997	T;T	0.25414	1.8;1.8	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.58424	0.2121	M	0.89214	3.015	0.80722	D	1	D;D;D	0.89917	1.0;0.995;0.997	D;D;D	0.91635	0.999;0.986;0.994	T	0.67469	-0.5663	10	0.87932	D	0	-10.7449	15.5925	0.76543	1.0:0.0:0.0:0.0	.	663;649;649	Q8NE35;Q5QP71;Q8NE35-2	CPEB3_HUMAN;.;.	R	649;649;663	ENSP00000398310:C649R;ENSP00000265997:C663R	ENSP00000265997:C663R	C	-	1	0	CPEB3	93802059	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.339000	0.96797	2.094000	0.63399	0.482000	0.46254	TGT	.	.	.	none		0.592	CPEB3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049387.2	NM_014912		G	93812079	A	G	93812079	3	3	158	1	0	0	0	0	1	0	0	0	3804	188	7	3	113	3	CPEB3	10	93812079	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08		93812079	41722668	46	9387											
RRP12	23223	hgsc.bcm.edu	37	chr10	99120314	99120314	+	Frame_Shift_Del	DEL	G	G	-																															aagcctcaccttggtactgaGggggtatctccagctcctcc																										TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr10:99120314delG	ENST00000370992.4	-	31	3740	c.3629delC	c.(3628-3630)cctfs	p.P1210fs	RRP12_ENST00000315563.6_Frame_Shift_Del_p.P1110fs|RRP12_ENST00000536831.1_Frame_Shift_Del_p.P928fs|RRP12_ENST00000414986.1_Frame_Shift_Del_p.P1149fs|RRP12_ENST00000479481.1_5'UTR	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	1210						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)		TTGGTACTGAGGGGGTATCTC	0.557																																					p.P1210fs		Atlas-INDEL	.											.	RRP12	97	.	0			c.3630delT						PASS	.						170	143	152					10																	99120314		2203	4300	6503	SO:0001589	frameshift_variant	23223	exon31			.		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.3629delC	chr10.hg19:g.99120314delG	ENSP00000360031:p.Pro1210fs	133.0	0.0	0		81.0	39.0	0.481481	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Frame_Shift_Del	DEL	ENST00000370992.4	hg19	CCDS7457.1																																																																																			.	.	.	none		0.557	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179		-	99120314	G	-	99120314	7	5	158	1	0	1	0	1	0	0	0	0	13699	1000	35	0	280	0	RRP12	10	99120314	Frame_Shift_Del	DEL	G	TCGA-DZ-6133-01A-11D-1961-08	5308235	99120314	36414433	47	9388											
HARBI1	283254	hgsc.bcm.edu	37	chr11	46637368	46637368	+	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	acccccatcacccctggcatCcctgccaacccatagaattc	10	7	4	20	0	1	1	1	0	0	1	3	1	2	1	7	1	2	1	7	1	3	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr11:46637368C>A	ENST00000326737.3	-	2	667	c.420G>T	c.(418-420)ggG>ggT	p.G140G	ATG13_ENST00000528494.1_5'Flank|ATG13_ENST00000359513.4_5'Flank|ATG13_ENST00000529655.1_5'Flank|ATG13_ENST00000434074.1_5'Flank|ATG13_ENST00000526508.1_5'Flank|ATG13_ENST00000312040.4_5'Flank|ATG13_ENST00000530500.1_5'Flank|ATG13_ENST00000451945.1_5'Flank|ATG13_ENST00000524625.1_5'Flank	NM_173811.3	NP_776172.1	Q96MB7	HARB1_HUMAN	harbinger transposase derived 1	140						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						CCCCTGGCATCCCTGCCAACC	0.512																																					p.G140G		Atlas-SNP	.											.	HARBI1	19	.	0			c.G420T						PASS	.						201	196	198					11																	46637368		2201	4299	6500	SO:0001819	synonymous_variant	283254	exon2			TGGCATCCCTGCC	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.420G>T	chr11.hg19:g.46637368C>A		417.0	0.0	.		226.0	84.0	.	NM_173811	D3DQP9	Silent	SNP	ENST00000326737.3	hg19	CCDS7920.1																																																																																			.	.	.	none		0.512	HARBI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390291.1	NM_173811		A	46637368	C	A	46637368	2	1	158	1	0	0	0	0	0	0	0	1	6965	842	30	4		4	HARBI1	11	46637368	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08		46637368	88369148	48	9389											
SAPS3	55291	hgsc.bcm.edu	37	chr11	68377390	68377390	+	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	agtgaggaagggaaactgtcTacctctcaagatgctgcttg	11	10	12	8	0	2	2	1	1	2	1	3	4	2	4	1	2	4	2	1	2	4	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr11:68377390T>A	ENST00000393800.2	+	23	2723	c.2469T>A	c.(2467-2469)tcT>tcA	p.S823S	PPP6R3_ENST00000393801.3_Silent_p.S829S|PPP6R3_ENST00000524845.1_Silent_p.S794S|PPP6R3_ENST00000534534.1_Silent_p.S591S|PPP6R3_ENST00000524904.1_Silent_p.S817S|PPP6R3_ENST00000529710.1_Silent_p.S743S|PPP6R3_ENST00000393799.2_Silent_p.S829S|PPP6R3_ENST00000265636.5_Silent_p.S743S|PPP6R3_ENST00000265637.4_Silent_p.S777S|PPP6R3_ENST00000527403.2_Silent_p.S788S	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	823					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						GGAAACTGTCTACCTCTCAAG	0.577																																					p.S829S		Atlas-SNP	.											.	PPP6R3	159	.	0			c.T2487A						PASS	.						174	149	157					11																	68377390		2200	4294	6494	SO:0001819	synonymous_variant	55291	exon24			ACTGTCTACCTCT	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.2469T>A	chr11.hg19:g.68377390T>A		205.0	0.0	.		124.0	54.0	.	NM_001164160	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Silent	SNP	ENST00000393800.2	hg19	CCDS53672.1																																																																																			.	.	.	none		0.577	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1	NM_018312		A	68377390	T	A	68377390	2	1	158	1	0	0	0	0	0	0	0	1	13851	1509	53	5		5	SAPS3	11	68377390	Silent	SNP	T	TCGA-DZ-6133-01A-11D-1961-08	21740022	68377390	66629126	49	9390											
CACNA1C	775	hgsc.bcm.edu	37	chr12	2566788	2566788	+	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	cagatggggcaaacgctctcGgagggaaaggggccggattt	10	6	17	8	3	1	1	0	0	1	1	2	4	1	4	1	7	1	2	1	7	2	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr12:2566788G>T	ENST00000347598.4	+	5	673	c.673G>T	c.(673-675)Gga>Tga	p.G225*	CACNA1C_ENST00000399641.1_Nonsense_Mutation_p.G225*|CACNA1C_ENST00000399655.1_Nonsense_Mutation_p.G225*|CACNA1C_ENST00000399595.1_Nonsense_Mutation_p.G225*|CACNA1C_ENST00000399644.1_Nonsense_Mutation_p.G225*|CACNA1C_ENST00000335762.5_Nonsense_Mutation_p.G225*|CACNA1C_ENST00000480911.1_Nonsense_Mutation_p.G225*|CACNA1C_ENST00000399638.1_Nonsense_Mutation_p.G225*|CACNA1C_ENST00000399603.1_Nonsense_Mutation_p.G225*|CACNA1C_ENST00000399649.1_Nonsense_Mutation_p.G225*|CACNA1C_ENST00000344100.3_Nonsense_Mutation_p.G225*|CACNA1C_ENST00000399629.1_Nonsense_Mutation_p.G225*|CACNA1C_ENST00000399597.1_Nonsense_Mutation_p.G225*|CACNA1C_ENST00000399591.1_Nonsense_Mutation_p.G225*|CACNA1C_ENST00000399617.1_Nonsense_Mutation_p.G225*|CACNA1C_ENST00000406454.3_Nonsense_Mutation_p.G225*|CACNA1C_ENST00000399637.1_Nonsense_Mutation_p.G225*|CACNA1C_ENST00000399606.1_Nonsense_Mutation_p.G225*|CACNA1C_ENST00000402845.3_Nonsense_Mutation_p.G225*|CACNA1C_ENST00000399621.1_Nonsense_Mutation_p.G225*|CACNA1C_ENST00000327702.7_Nonsense_Mutation_p.G225*|CACNA1C_ENST00000399601.1_Nonsense_Mutation_p.G225*|CACNA1C_ENST00000399634.1_Nonsense_Mutation_p.G225*	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	225					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)	p.G225R(3)|p.G255R(1)		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)	AAACGCTCTCGGAGGGAAAGG	0.552																																					p.G225X		Atlas-SNP	.											CACNA1C_ENST00000344100,NS,carcinoma,0,2	CACNA1C	1023	.	4	Substitution - Missense(4)	lung(4)	c.G673T						PASS	.						121	135	131					12																	2566788		2035	4188	6223	SO:0001587	stop_gained	775	exon5			GCTCTCGGAGGGA	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.673G>T	chr12.hg19:g.2566788G>T	ENSP00000266376:p.Gly225*	340.0	0.0	.		246.0	10.0	.	NM_001129831	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Nonsense_Mutation	SNP	ENST00000347598.4	hg19	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	G	34	5.375230	0.95923	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000480911;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	.	.	.	4.15	4.15	0.48705	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.6608	0.85240	0.0:0.0:1.0:0.0	.	.	.	.	X	225;225;225;225;225;225;225;225;225;225;225;225;225;225;225;225;225;225;225;225;225;225;225;66	.	ENSP00000323129:G66X	G	+	1	0	CACNA1C	2437049	1.000000	0.71417	0.907000	0.35723	0.604000	0.37047	9.542000	0.98086	2.139000	0.66308	0.563000	0.77884	GGA	.	.	.	none		0.552	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		T	2566788	G	T	2566788	4	4	158	1	0	0	0	0	0	1	0	0	2542	1117	39	4	691	4	CACNA1C	12	2566788	Nonsense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08		2566788	131285107	50	9391											
PEX5	5830	hgsc.bcm.edu	37	chr12	7343122	7343122	+	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	agccccggcctctgaggcagTgagtgttcttgaggtggaaa	8	9	15	9	1	2	3	0	3	2	0	2	4	2	4	3	4	1	2	3	4	1	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr12:7343122T>C	ENST00000455147.2	+	3	727		c.e3+2		PEX5_ENST00000412720.2_Splice_Site|PEX5_ENST00000266563.5_Splice_Site|PEX5_ENST00000434354.2_Missense_Mutation_p.V50A|RP11-273B20.3_ENST00000543061.1_RNA|PEX5_ENST00000420616.2_Splice_Site|RP11-273B20.3_ENST00000545794.1_RNA|PEX5_ENST00000545220.1_Intron|PEX5_ENST00000266564.3_Splice_Site	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						TCTGAGGCAGTGAGTGTTCTT	0.632																																					p.V50A		Atlas-SNP	.											.	PEX5	63	.	0			c.T149C						PASS	.						24	27	26					12																	7343122		2200	4294	6494	SO:0001630	splice_region_variant	5830	exon2			AGGCAGTGAGTGT	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+2T>C	chr12.hg19:g.7343122T>C		22.0	0.0	.		21.0	11.0	.	NM_001131023	A8K891|B4DZ45|B7ZAD5|D3DUT8|Q15115|Q15266|Q96FN7	Missense_Mutation	SNP	ENST00000455147.2	hg19	CCDS44823.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.99|17.99	3.522704|3.522704	0.64747|0.64747	.|.	.|.	ENSG00000139197|ENSG00000139197	ENST00000542539;ENST00000455147;ENST00000540398;ENST00000266563;ENST00000544456;ENST00000545574;ENST00000420616;ENST00000412720;ENST00000536841;ENST00000537873;ENST00000266564|ENST00000434354;ENST00000396637	.|D;D	.|0.88046	.|-2.33;-2.09	3.59|3.59	3.59|3.59	0.41128|0.41128	.|.	.|.	.|.	.|.	.|.	.|D	.|0.90950	.|0.7155	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|P	.|0.43392	.|0.805	.|P	.|0.59424	.|0.857	.|D	.|0.89996	.|0.4111	.|7	.|.	.|.	.|.	.|.	10.9229|10.9229	0.47176|0.47176	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|50	.|B4DZ45	.|.	.|A	-1|50	.|ENSP00000407401:V50A;ENSP00000379877:V50A	.|.	.|V	+|+	.|2	.|0	PEX5|PEX5	7234389|7234389	1.000000|1.000000	0.71417|0.71417	0.983000|0.983000	0.44433|0.44433	0.526000|0.526000	0.34562|0.34562	2.840000|2.840000	0.48215|0.48215	1.654000|1.654000	0.50703|0.50703	0.342000|0.342000	0.21767|0.21767	.|GTG	.	.	.	none		0.632	PEX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398611.1	NM_000319	Intron	C	7343122	T	C	7343122	5	2	158	1	0	0	0	0	0	0	1	0	11755	1710	59	3	151	3	PEX5	12	7343122	Splice_Site	SNP	T	TCGA-DZ-6133-01A-11D-1961-08	4776334	7343122	126508773	51	9392											
ITPR2	3709	hgsc.bcm.edu	37	chr12	26749865	26749865	+	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	ccctcactatgtcgtccagcGggagaagggaattacacttg	10	9	11	11	2	1	1	1	0	0	1	3	3	2	2	2	2	2	0	2	2	4	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr12:26749865G>T	ENST00000381340.3	-	31	4621	c.4205C>A	c.(4204-4206)cCg>cAg	p.P1402Q		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1402					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)	GTCGTCCAGCGGGAGAAGGGA	0.488																																					p.P1402Q		Atlas-SNP	.											.	ITPR2	270	.	0			c.C4205A						PASS	.						93	94	94					12																	26749865		2067	4214	6281	SO:0001583	missense	3709	exon31			TCCAGCGGGAGAA	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.4205C>A	chr12.hg19:g.26749865G>T	ENSP00000370744:p.Pro1402Gln	97.0	0.0	.		126.0	9.0	.	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	hg19	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.546239	0.86022	.	.	ENSG00000123104	ENST00000381340	D	0.92647	-3.08	4.44	4.44	0.53790	.	0.111229	0.64402	D	0.000006	D	0.96219	0.8767	M	0.83953	2.67	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96883	0.9647	10	0.87932	D	0	.	17.6058	0.88037	0.0:0.0:1.0:0.0	.	1402	Q14571	ITPR2_HUMAN	Q	1402	ENSP00000370744:P1402Q	ENSP00000370744:P1402Q	P	-	2	0	ITPR2	26641132	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	9.584000	0.98220	2.440000	0.82611	0.650000	0.86243	CCG	.	.	.	none		0.488	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		T	26749865	G	T	26749865	3	4	158	1	0	0	0	0	1	0	0	0	7928	1116	39	4	4008	4	ITPR2	12	26749865	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	19406743	26749865	107102030	52	9393											
IPO8	10526	hgsc.bcm.edu	37	chr12	30790088	30790088	+	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	tgcaattccaaaaggatactCagtcctattatacacatctt	14	13	4	10	0	2	0	1	0	1	0	4	1	4	1	2	1	3	1	2	1	7	6			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr12:30790088C>G	ENST00000256079.4	-	22	2861	c.2523G>C	c.(2521-2523)ctG>ctC	p.L841L	IPO8_ENST00000544829.1_Silent_p.L636L	NM_006390.3	NP_006381.2	O15397	IPO8_HUMAN	importin 8	841					intracellular protein transport (GO:0006886)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	Ran GTPase binding (GO:0008536)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(16)|liver(1)|lung(22)|prostate(2)|skin(2)|urinary_tract(2)	52	all_lung(12;6.66e-10)|Lung NSC(12;4.84e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					AAAGGATACTCAGTCCTATTA	0.393																																					p.L841L		Atlas-SNP	.											.	IPO8	105	.	0			c.G2523C						PASS	.						133	120	124					12																	30790088		2203	4300	6503	SO:0001819	synonymous_variant	10526	exon22			GATACTCAGTCCT	U77494	CCDS8719.1, CCDS53773.1	12p11.21	2011-05-23	2003-03-11	2003-03-14	ENSG00000133704	ENSG00000133704		"Importins"	9853	protein-coding gene	gene with protein product		605600	"RAN binding protein 8"	RANBP8		9214382	Standard	NM_006390		Approved	IMP8	uc001rjd.3	O15397	OTTHUMG00000169172	ENST00000256079.4:c.2523G>C	chr12.hg19:g.30790088C>G		93.0	0.0	.		126.0	78.0	.	NM_006390	B7Z7M3	Silent	SNP	ENST00000256079.4	hg19	CCDS8719.1																																																																																			.	.	.	none		0.393	IPO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402700.2	NM_006390		G	30790088	C	G	30790088	2	3	158	1	0	0	0	0	0	0	0	1	7805	813	29	4		4	IPO8	12	30790088	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	4040223	30790088	103061807	53	9394											
FAM60A	58516	hgsc.bcm.edu	37	chr12	31435663	31435663	+	Missense_Mutation	SNP	A	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	cagtcaccactcctgagtggAgatgggcagaggctctggcc	8	7	14	12	0	2	3	1	1	1	2	3	4	3	3	3	4	0	2	3	4	0	0			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr12:31435663A>C	ENST00000337682.4	-	6	1017	c.649T>G	c.(649-651)Tcc>Gcc	p.S217A	FAM60A_ENST00000539409.1_Missense_Mutation_p.S69A|FAM60A_ENST00000395766.1_Missense_Mutation_p.S69A|FAM60A_ENST00000542983.1_Missense_Mutation_p.S69A|FAM60A_ENST00000454658.2_Missense_Mutation_p.S217A	NM_001135812.1	NP_001129284.1	Q9NP50	FA60A_HUMAN	family with sequence similarity 60, member A	217					negative regulation of cell migration (GO:0030336)	Sin3 complex (GO:0016580)				large_intestine(1)|lung(2)	3	all_cancers(9;5.22e-13)|all_epithelial(9;4e-13)|all_lung(12;1.2e-11)|Lung NSC(12;2.17e-09)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0207)|Lung SC(12;0.0592)|Esophageal squamous(101;0.162)					TCCTGAGTGGAGATGGGCAGA	0.453																																					p.S217A		Atlas-SNP	.											.	FAM60A	16	.	0			c.T649G						PASS	.						38	40	39					12																	31435663		2203	4297	6500	SO:0001583	missense	58516	exon7			GAGTGGAGATGGG	AF212220	CCDS8723.1	12p11.21	2012-11-30	2005-04-07	2005-04-07	ENSG00000139146	ENSG00000139146			30702	protein-coding gene	gene with protein product		615027	"chromosome 12 open reading frame 14"	C12orf14		11042152, 22984288, 22865885	Standard	NM_021238		Approved	TERA	uc001rke.3	Q9NP50	OTTHUMG00000168586	ENST00000337682.4:c.649T>G	chr12.hg19:g.31435663A>C	ENSP00000337477:p.Ser217Ala	112.0	0.0	.		94.0	51.0	.	NM_021238	D3DUV8|Q9BSZ8	Missense_Mutation	SNP	ENST00000337682.4	hg19	CCDS8723.1	.	.	.	.	.	.	.	.	.	.	A	10.12	1.262656	0.23051	.	.	ENSG00000139146	ENST00000539409;ENST00000337682;ENST00000454658;ENST00000398170;ENST00000395766;ENST00000542983	T;T	0.41758	0.99;0.99	4.26	0.167	0.15006	.	0.592620	0.16969	N	0.192195	T	0.17704	0.0425	N	0.08118	0	0.29822	N	0.830762	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.18272	-1.0342	10	0.20519	T	0.43	-15.4818	5.7799	0.18299	0.5453:0.3628:0.0919:0.0	.	217;258	Q9NP50;B7Z287	FA60A_HUMAN;.	A	69;217;217;258;69;69	ENSP00000337477:S217A;ENSP00000393279:S217A	ENSP00000337477:S217A	S	-	1	0	FAM60A	31326930	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	0.828000	0.27435	0.078000	0.16900	0.482000	0.46254	TCC	.	.	.	none		0.453	FAM60A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400347.1	NM_021238		C	31435663	A	C	31435663	3	2	158	1	0	0	0	0	1	0	0	0	5602	304	11	5	20	5	FAM60A	12	31435663	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	645575	31435663	102416232	54	9395											
SCN8A	6334	hgsc.bcm.edu	37	chr12	52145329	52145329	+	Frame_Shift_Del	DEL	C	C	-																															ctgtttatggcaatggagcaCcatcctatgacaccacaatt																										TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr12:52145329delC	ENST00000354534.6	+	14	2500	c.2322delC	c.(2320-2322)cacfs	p.H775fs	SCN8A_ENST00000545061.1_Frame_Shift_Del_p.H775fs|SCN8A_ENST00000550891.1_Frame_Shift_Del_p.H775fs	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit	775					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)	CAATGGAGCACCATCCTATGA	0.418																																					p.H774fs		Atlas-INDEL	.											.	SCN8A	331	.	0			c.2321delA						PASS	.						147	140	142					12																	52145329		2052	4218	6270	SO:0001589	frameshift_variant	6334	exon14			.	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.2322delC	chr12.hg19:g.52145329delC	ENSP00000346534:p.His775fs	108.0	0.0	0		109.0	36.0	0.330275	NM_001177984	B9VWG8|O95788|Q9NYX2|Q9UPB2	Frame_Shift_Del	DEL	ENST00000354534.6	hg19	CCDS44891.1																																																																																			.	.	.	none		0.418	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404372.3	NM_014191		-	52145329	C	-	52145329	7	5	158	1	0	1	0	1	0	0	0	0	13937	506	18	0	2372	0	SCN8A	12	52145329	Frame_Shift_Del	DEL	C	TCGA-DZ-6133-01A-11D-1961-08	20709666	52145329	81706566	55	9396											
TMPO	7112	hgsc.bcm.edu	37	chr12	98941479	98941479	+	Frame_Shift_Del	DEL	A	A	-																															cttggcagatgtcaagtcagAaaagacaaaaaagggacgct																										TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr12:98941479delA	ENST00000556029.1	+	9	1564	c.1208delA	c.(1207-1209)gaafs	p.E403fs	TMPO_ENST00000393053.2_Frame_Shift_Del_p.E294fs|TMPO_ENST00000548223.1_3'UTR|TMPO_ENST00000343315.5_Frame_Shift_Del_p.E363fs	NM_001032283.2	NP_001027454.1	P42167	LAP2B_HUMAN	thymopoietin	403	Nucleoplasmic. {ECO:0000255}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)|lamin binding (GO:0005521)			breast(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						GTCAAGTCAGAAAAGACAAAA	0.408																																					p.E403fs		Atlas-INDEL	.											.	TMPO	111	.	0			c.1207delG						PASS	.						107	107	107					12																	98941479		2203	4300	6503	SO:0001589	frameshift_variant	7112	exon9			.		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.1208delA	chr12.hg19:g.98941479delA	ENSP00000450627:p.Glu403fs	95.0	0.0	0		109.0	47.0	0.431193	NM_001032283	A2T926|Q14861	Frame_Shift_Del	DEL	ENST00000556029.1	hg19	CCDS31879.1																																																																																			.	.	.	none		0.408	TMPO-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407973.2	NM_003276		-	98941479	A	-	98941479	7	5	158	1	0	1	0	1	0	0	0	0	16249	246	9	0	2766	0	TMPO	12	98941479	Frame_Shift_Del	DEL	A	TCGA-DZ-6133-01A-11D-1961-08	46796150	98941479	34910416	56	9397											
HSP90B1	7184	hgsc.bcm.edu	37	chr12	104336447	104336447	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccactcgaatcgaacacgtcTtgctaaacttcttaggttcc	10	12	6	13	3	2	0	0	0	2	0	5	2	3	0	2	1	3	2	2	1	5	5			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr12:104336447T>C	ENST00000299767.5	+	12	1699	c.1517T>C	c.(1516-1518)cTt>cCt	p.L506P		NM_003299.2	NP_003290.1	P14625	ENPL_HUMAN	heat shock protein 90kDa beta (Grp94), member 1	506					actin rod assembly (GO:0031247)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular response to ATP (GO:0071318)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|protein folding (GO:0006457)|protein transport (GO:0015031)|regulation of phosphoprotein phosphatase activity (GO:0043666)|response to hypoxia (GO:0001666)|sequestering of calcium ion (GO:0051208)|toll-like receptor signaling pathway (GO:0002224)	cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|low-density lipoprotein particle receptor binding (GO:0050750)|protein phosphatase binding (GO:0019903)|RNA binding (GO:0003723)|virion binding (GO:0046790)			central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(4)	29					Rifabutin(DB00615)	CGAACACGTCTTGCTAAACTT	0.373																																					p.L506P		Atlas-SNP	.											.	HSP90B1	72	.	0			c.T1517C						PASS	.						116	113	114					12																	104336447		2203	4300	6503	SO:0001583	missense	7184	exon12			CACGTCTTGCTAA	AY040226	CCDS9094.1	12q24.2-q24.3	2011-09-02	2006-02-24	2006-02-24		ENSG00000166598		"Heat shock proteins / HSPC"	12028	protein-coding gene	gene with protein product		191175	"tumor rejection antigen (gp96) 1"	TRA1		16269234	Standard	NM_003299		Approved	GP96, GRP94	uc001tkb.2	P14625	OTTHUMG00000170118	ENST00000299767.5:c.1517T>C	chr12.hg19:g.104336447T>C	ENSP00000299767:p.Leu506Pro	115.0	0.0	.		159.0	94.0	.	NM_003299	Q96A97	Missense_Mutation	SNP	ENST00000299767.5	hg19	CCDS9094.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.696033	0.88830	.	.	ENSG00000166598	ENST00000299767;ENST00000421266	T	0.18016	2.24	6.16	6.16	0.99307	Ribosomal protein S5 domain 2-type fold (1);	0.000000	0.85682	D	0.000000	T	0.62514	0.2434	H	0.98701	4.305	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79080	-0.1950	10	0.87932	D	0	.	16.8061	0.85666	0.0:0.0:0.0:1.0	.	506	P14625	ENPL_HUMAN	P	506;256	ENSP00000299767:L506P	ENSP00000299767:L506P	L	+	2	0	HSP90B1	102860577	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.367000	0.80283	0.528000	0.53228	CTT	.	.	.	none		0.373	HSP90B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407349.1	NM_003299		C	104336447	T	C	104336447	3	2	158	1	0	0	0	0	1	0	0	0	7410	1609	56	3	1563	3	HSP90B1	12	104336447	Missense_Mutation	SNP	T	TCGA-DZ-6133-01A-11D-1961-08	5394968	104336447	29515448	57	9398											
MYO1H	283446	hgsc.bcm.edu	37	chr12	109834250	109834250	+	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	aactaaataaccatttcatcCtcatttctggagagagtggg	13	12	8	8	0	3	1	2	0	1	1	4	3	4	2	2	2	2	0	2	2	4	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr12:109834250C>T	ENST00000431443.2	+	3	304	c.304C>T	c.(304-306)Ctc>Ttc	p.L102F	MYO1H_ENST00000310903.5_Missense_Mutation_p.L102F	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	102	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						CCATTTCATCCTCATTTCTGG	0.458																																					p.L102F		Atlas-SNP	.											MYO1H,NS,carcinoma,0,1	MYO1H	98	.	0			c.C304T						PASS	.						68	68	68					12																	109834250		1957	4152	6109	SO:0001583	missense	283446	exon3			TTCATCCTCATTT		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.304C>T	chr12.hg19:g.109834250C>T	ENSP00000444076:p.Leu102Phe	61.0	0.0	.		88.0	46.0	.	NM_001101421	F5H3C6	Missense_Mutation	SNP	ENST00000431443.2	hg19		.	.	.	.	.	.	.	.	.	.	C	23.2	4.392377	0.83011	.	.	ENSG00000174527	ENST00000310903;ENST00000431443	D;D	0.89875	-2.58;-2.58	4.8	4.8	0.61643	.	.	.	.	.	D	0.96914	0.8992	H	0.98370	4.215	0.46981	D	0.999273	D	0.89917	1.0	D	0.91635	0.999	D	0.98431	1.0582	9	0.87932	D	0	.	17.7816	0.88526	0.0:1.0:0.0:0.0	.	102	F5H3C6	.	F	102	ENSP00000439182:L102F;ENSP00000444076:L102F	ENSP00000439182:L102F	L	+	1	0	MYO1H	108318633	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.258000	0.51507	2.615000	0.88500	0.644000	0.83932	CTC	.	.	.	none		0.458	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597		T	109834250	C	T	109834250	3	4	158	1	0	0	0	0	1	0	0	0	10082	681	24	2	314	2	MYO1H	12	109834250	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	5497803	109834250	24017645	58	9399											
NCOR2	9612	hgsc.bcm.edu	37	chr12	124848291	124848291	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtggcttctggggtgaggcAttggcccgggggtcgccagt	4	9	19	9	2	1	1	0	1	1	0	2	1	1	1	2	7	0	2	2	7	0	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr12:124848291A>G	ENST00000405201.1	-	21	2862	c.2862T>C	c.(2860-2862)aaT>aaC	p.N954N	NCOR2_ENST00000404621.1_Silent_p.N936N|NCOR2_ENST00000356219.3_Silent_p.N954N|NCOR2_ENST00000404121.2_Silent_p.N507N|NCOR2_ENST00000397355.1_Silent_p.N937N|NCOR2_ENST00000429285.2_Silent_p.N936N			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	954					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)		GGGGTGAGGCATTGGCCCGGG	0.697																																					p.N954N		Atlas-SNP	.											.	NCOR2	475	.	0			c.T2862C						PASS	.						39	56	51					12																	124848291		2023	4151	6174	SO:0001819	synonymous_variant	9612	exon23			TGAGGCATTGGCC	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.2862T>C	chr12.hg19:g.124848291A>G		190.0	0.0	.		145.0	77.0	.	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	hg19	CCDS41858.2																																																																																			.	.	.	none		0.697	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		G	124848291	A	G	124848291	2	3	158	1	0	0	0	0	0	0	0	1	10243	214	8	3		3	NCOR2	12	124848291	Silent	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	15014041	124848291	9003604	59	9400											
EP400	57634	hgsc.bcm.edu	37	chr12	132522561	132522562	+	Missense_Mutation	DNP	GC	GC	AT																															atgctggcttcccggtcaaaGctgaggagtttgtggtgctt																										TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr12:132522561_132522562GC>AT	ENST00000333577.4	+	33	6344_6345	c.6235_6236GC>AT	c.(6235-6237)GCt>ATt	p.A2079I	EP400_ENST00000389562.2_Missense_Mutation_p.A2042I|EP400_ENST00000332482.4_Missense_Mutation_p.A2006I|EP400_ENST00000389561.2_Missense_Mutation_p.A2043I|EP400_ENST00000330386.6_Missense_Mutation_p.A1962I			Q96L91	EP400_HUMAN	E1A binding protein p400	2079					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)		CCCGGTCAAAGCTGAGGAGTTT	0.465																																					p.A2043T|p.A2043V		Atlas-SNP	.											.	EP400	370	.	0			c.G6127A|c.C6128T						PASS	.																																			SO:0001583	missense	57634	exon32			GTCAAAGCTGAGG|TCAAAGCTGAGGA	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		Exception_encountered	chr12.hg19:g.132522561_132522562delinsAT	ENSP00000333602:p.Ala2079Ile	230.0|231.0	0.0	.		230.0|229.0	61.0|60.0	.	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	hg19																																																																																				.	.	.	none		0.465	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		AT	132522562	GC	AT	132522561	3	1	158	1	0	0	0	0	1	0	0	0	5151	971	34	2	6246	2	EP400	12	132522561	Missense_Mutation	DNP	GC	TCGA-DZ-6133-01A-11D-1961-08	7674270	132522561	1329334	60	9401											
KBTBD6	89890	hgsc.bcm.edu	37	chr13	41704906	41704906	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attcatacacagtcacccggTtctttttccactgtggggtg	7	14	9	11	1	3	0	2	0	1	0	4	0	4	0	2	3	1	1	2	3	1	5			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr13:41704906T>C	ENST00000379485.1	-	1	1976	c.1742A>G	c.(1741-1743)aAc>aGc	p.N581S	KBTBD6_ENST00000499385.2_Missense_Mutation_p.N515S	NM_152903.4	NP_690867.3	Q86V97	KBTB6_HUMAN	kelch repeat and BTB (POZ) domain containing 6	581										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)		AGTCACCCGGTTCTTTTTCCA	0.408																																					p.N581S		Atlas-SNP	.											.	KBTBD6	83	.	0			c.A1742G						PASS	.						179	179	179					13																	41704906		2203	4300	6503	SO:0001583	missense	89890	exon1			ACCCGGTTCTTTT	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.1742A>G	chr13.hg19:g.41704906T>C	ENSP00000368799:p.Asn581Ser	230.0	0.0	.		257.0	154.0	.	NM_152903	Q5T6Y8|Q8N8L0|Q8NDM5|Q96MP6	Missense_Mutation	SNP	ENST00000379485.1	hg19	CCDS9376.1	.	.	.	.	.	.	.	.	.	.	t	14.19	2.460466	0.43736	.	.	ENSG00000165572	ENST00000379485;ENST00000499385	T;T	0.66995	-0.24;-0.24	3.8	2.62	0.31277	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.67804	0.2932	L	0.32530	0.975	0.31105	N	0.710602	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.994	T	0.65092	-0.6252	10	0.36615	T	0.2	.	6.7322	0.23388	0.0:0.1222:0.0:0.8778	.	515;581	F5GZN7;Q86V97	.;KBTB6_HUMAN	S	581;515	ENSP00000368799:N581S;ENSP00000444326:N515S	ENSP00000368799:N581S	N	-	2	0	KBTBD6	40602906	1.000000	0.71417	0.500000	0.27589	0.968000	0.65278	3.578000	0.53892	0.649000	0.30751	0.379000	0.24179	AAC	.	.	.	none		0.408	KBTBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044657.1	NM_152903		C	41704906	T	C	41704906	3	2	158	1	0	0	0	0	1	0	0	0	8004	1725	60	3	286	3	KBTBD6	13	41704906	Missense_Mutation	SNP	T	TCGA-DZ-6133-01A-11D-1961-08		41704906	73464972	61	9402											
NALCN	259232	hgsc.bcm.edu	37	chr13	101944368	101944368	+	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	gtggctgttgaggtagtgctGcttctcgatccccacatttg	5	14	12	10	1	1	1	0	1	1	0	3	2	2	1	2	2	2	5	2	2	1	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr13:101944368G>T	ENST00000251127.6	-	9	1101	c.1020C>A	c.(1018-1020)agC>agA	p.S340R	NALCN_ENST00000376196.3_Missense_Mutation_p.S340R|NALCN_ENST00000470333.1_5'UTR	NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	340					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					AGGTAGTGCTGCTTCTCGATC	0.438																																					p.S340R		Atlas-SNP	.											.	NALCN	431	.	0			c.C1020A						PASS	.						317	247	271					13																	101944368		2203	4300	6503	SO:0001583	missense	259232	exon9			AGTGCTGCTTCTC	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.1020C>A	chr13.hg19:g.101944368G>T	ENSP00000251127:p.Ser340Arg	69.0	0.0	.		52.0	33.0	.	NM_052867	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	hg19	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	G	12.43	1.936423	0.34189	.	.	ENSG00000102452	ENST00000251127;ENST00000376196	D;D	0.98362	-4.55;-4.89	6.16	4.42	0.53409	.	0.000000	0.85682	D	0.000000	D	0.92808	0.7713	N	0.08118	0	0.80722	D	1	B;B;B	0.22851	0.008;0.076;0.008	B;B;B	0.15870	0.006;0.014;0.006	D	0.89936	0.4069	10	0.23891	T	0.37	.	10.2255	0.43222	0.2563:0.0:0.7437:0.0	.	340;340;340	F2Z323;B3KSZ6;Q8IZF0	.;.;NALCN_HUMAN	R	340	ENSP00000251127:S340R;ENSP00000365367:S340R	ENSP00000251127:S340R	S	-	3	2	NALCN	100742369	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	3.963000	0.56773	1.616000	0.50265	0.650000	0.86243	AGC	.	.	.	none		0.438	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		T	101944368	G	T	101944368	3	4	158	1	0	0	0	0	1	0	0	0	10155	1310	46	4	4340	4	NALCN	13	101944368	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	60239462	101944368	13225510	62	9403											
SIPA1L1	26037	hgsc.bcm.edu	37	chr14	72055716	72055716	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atccttggtctctggacctcTgtctcattcagccagtttta	6	16	7	12	0	4	0	2	0	3	0	7	1	5	1	3	2	1	1	3	2	1	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr14:72055716T>C	ENST00000555818.1	+	2	1475	c.1127T>C	c.(1126-1128)cTg>cCg	p.L376P	SIPA1L1_ENST00000358550.2_Missense_Mutation_p.L376P|SIPA1L1_ENST00000381232.3_Missense_Mutation_p.L376P	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	376					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)		TCTGGACCTCTGTCTCATTCA	0.498																																					p.L376P		Atlas-SNP	.											.	SIPA1L1	219	.	0			c.T1127C						PASS	.						59	61	60					14																	72055716		2203	4300	6503	SO:0001583	missense	26037	exon2			GACCTCTGTCTCA	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.1127T>C	chr14.hg19:g.72055716T>C	ENSP00000450832:p.Leu376Pro	111.0	0.0	.		68.0	25.0	.	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	hg19	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	T	7.254	0.603889	0.14002	.	.	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550	T;T;T	0.78003	-1.14;-1.13;-1.14	6.07	4.94	0.65067	.	0.129948	0.56097	D	0.000037	T	0.55033	0.1895	N	0.03608	-0.345	0.80722	D	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.001;0.003;0.001	T	0.53287	-0.8460	10	0.30078	T	0.28	-17.1009	11.6847	0.51479	0.0:0.0683:0.0:0.9317	.	376;376;376	A6H8W6;O43166-2;O43166	.;.;SI1L1_HUMAN	P	376	ENSP00000370630:L376P;ENSP00000450832:L376P;ENSP00000351352:L376P	ENSP00000351352:L376P	L	+	2	0	SIPA1L1	71125469	1.000000	0.71417	0.996000	0.52242	0.343000	0.28985	4.668000	0.61568	2.326000	0.78906	0.533000	0.62120	CTG	.	.	.	none		0.498	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		C	72055716	T	C	72055716	3	2	158	1	0	0	0	0	1	0	0	0	14342	1580	55	3	1129	3	SIPA1L1	14	72055716	Missense_Mutation	SNP	T	TCGA-DZ-6133-01A-11D-1961-08		72055716	35293824	63	9404											
THBS1	7057	hgsc.bcm.edu	37	chr15	39885267	39885267	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgccagacatcgatgacaTctgtcctgagaatgttgaca	11	11	10	9	1	1	4	0	3	1	2	3	6	2	4	2	0	1	1	2	0	1	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr15:39885267T>C	ENST00000260356.5	+	18	2999	c.2834T>C	c.(2833-2835)aTc>aCc	p.I945T	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	945					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)		ATCGATGACATCTGTCCTGAG	0.478																																					p.I945T		Atlas-SNP	.											.	THBS1	106	.	0			c.T2834C						PASS	.						78	68	71					15																	39885267		2200	4297	6497	SO:0001583	missense	7057	exon18			ATGACATCTGTCC		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.2834T>C	chr15.hg19:g.39885267T>C	ENSP00000260356:p.Ile945Thr	104.0	0.0	.		73.0	33.0	.	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	hg19	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	T	19.57	3.852666	0.71719	.	.	ENSG00000137801	ENST00000260356	D	0.98164	-4.76	5.68	5.68	0.88126	.	0.000000	0.36778	N	0.002417	D	0.94598	0.8259	N	0.04880	-0.145	0.49798	D	0.999827	P;P	0.47762	0.725;0.9	B;B	0.43990	0.438;0.387	D	0.95190	0.8307	10	0.39692	T	0.17	-26.1702	15.8963	0.79336	0.0:0.0:0.0:1.0	.	860;945	B4E3J7;P07996	.;TSP1_HUMAN	T	945	ENSP00000260356:I945T	ENSP00000260356:I945T	I	+	2	0	THBS1	37672559	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.036000	0.88901	2.153000	0.67306	0.533000	0.62120	ATC	.	.	.	none		0.478	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		C	39885267	T	C	39885267	3	2	158	1	0	0	0	0	1	0	0	0	15865	1435	50	3	2900	3	THBS1	15	39885267	Missense_Mutation	SNP	T	TCGA-DZ-6133-01A-11D-1961-08		39885267	62646125	64	9405											
ZFP106	64397	hgsc.bcm.edu	37	chr15	42742117	42742117	+	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	tgtctcactctttcggtgacCgctaatattgcgaatgcggc	7	13	10	11	4	2	1	1	1	2	0	4	2	2	1	1	2	2	1	1	2	3	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr15:42742117C>A	ENST00000263805.4	-	2	2610	c.2284G>T	c.(2284-2286)Ggt>Tgt	p.G762C	ZNF106_ENST00000565380.1_Intron|ZNF106_ENST00000565611.1_Intron	NM_001284306.1|NM_001284307.1|NM_022473.1	NP_001271235.1|NP_001271236.1|NP_071918.1	Q9H2Y7	ZN106_HUMAN	zinc finger protein 106	762					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)										TTTCGGTGACCGCTAATATTG	0.498																																					p.G762C		Atlas-SNP	.											.	ZFP106	117	.	0			c.G2284T						PASS	.						169	166	167					15																	42742117		2203	4299	6502	SO:0001583	missense	64397	exon2			GGTGACCGCTAAT	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.2284G>T	chr15.hg19:g.42742117C>A	ENSP00000263805:p.Gly762Cys	252.0	0.0	.		163.0	9.0	.	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Missense_Mutation	SNP	ENST00000263805.4	hg19	CCDS32208.1	.	.	.	.	.	.	.	.	.	.	C	19.95	3.922319	0.73213	.	.	ENSG00000103994	ENST00000263805	T	0.50813	0.73	5.93	5.93	0.95920	.	0.118074	0.64402	D	0.000020	T	0.58018	0.2093	M	0.61703	1.905	0.80722	D	1	P;P	0.52316	0.952;0.921	P;B	0.51516	0.672;0.395	T	0.57631	-0.7778	10	0.51188	T	0.08	-20.8928	16.562	0.84569	0.131:0.869:0.0:0.0	.	545;762	B4DGC7;Q9H2Y7	.;ZF106_HUMAN	C	762	ENSP00000263805:G762C	ENSP00000263805:G762C	G	-	1	0	ZFP106	40529409	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	5.703000	0.68340	2.805000	0.96524	0.650000	0.86243	GGT	.	.	.	none		0.498	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473		A	42742117	C	A	42742117	3	1	158	1	0	0	0	0	1	0	0	0	17649	652	23	4	3439	4	ZFP106	15	42742117	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	2856850	42742117	59789275	65	9406											
EPB42	2038	hgsc.bcm.edu	37	chr15	43508525	43508525	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaatgcacggactggagcgCggaagtacaggatgatggtg	12	6	17	6	3	0	1	0	1	0	0	0	6	0	5	0	5	3	2	0	5	3	1	rs202154600		TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr15:43508525C>T	ENST00000441366.2	-	2	362	c.137G>A	c.(136-138)cGc>cAc	p.R46H	EPB42_ENST00000300215.3_Missense_Mutation_p.R76H|EPB42_ENST00000540029.1_Missense_Mutation_p.R46H	NM_000119.2|NM_001114134.1	NP_000110.2|NP_001107606.1	P16452	EPB42_HUMAN	erythrocyte membrane protein band 4.2	46					cell morphogenesis (GO:0000902)|erythrocyte maturation (GO:0043249)|hemoglobin metabolic process (GO:0020027)|iron ion homeostasis (GO:0055072)|peptide cross-linking (GO:0018149)|regulation of cell shape (GO:0008360)|spleen development (GO:0048536)	cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)|structural constituent of cytoskeleton (GO:0005200)			endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20		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;0.215)		GBM - Glioblastoma multiforme(94;8.7e-07)		GACTGGAGCGCGGAAGTACAG	0.597																																					p.R76H		Atlas-SNP	.											EPB42,caecum,carcinoma,0,1	EPB42	53	.	0			c.G227A						PASS	.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	102	90	94		227,137	-5	0	15		94	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense	EPB42	NM_000119.2,NM_001114134.1	29,29	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	76/722,46/692	43508525	1,13003	2203	4299	6502	SO:0001583	missense	2038	exon2			GGAGCGCGGAAGT	M60298	CCDS10093.1, CCDS45249.1	15q15-q21	2013-05-02			ENSG00000166947	ENSG00000166947		"Transglutaminases"	3381	protein-coding gene	gene with protein product	"Erythrocyte surface protein band 4.2"	177070				1284644	Standard	NM_000119		Approved	PA, MGC116735, MGC116737	uc001zrb.4	P16452	OTTHUMG00000130701	ENST00000441366.2:c.137G>A	chr15.hg19:g.43508525C>T	ENSP00000396616:p.Arg46His	121.0	1.0	.		72.0	33.0	.	NM_000119	Q4KKX0|Q4VB97	Missense_Mutation	SNP	ENST00000441366.2	hg19	CCDS45249.1	.	.	.	.	.	.	.	.	.	.	C	11.20	1.569261	0.28003	0.0	1.16E-4	ENSG00000166947	ENST00000300215;ENST00000540029;ENST00000441366;ENST00000397027	D;D;D	0.84873	-1.91;-1.91;-1.91	5.02	-5.0	0.03001	Immunoglobulin E-set (1);Transglutaminase, N-terminal (1);Immunoglobulin-like fold (1);	1.112950	0.06532	N	0.741688	T	0.73860	0.3641	N	0.13235	0.315	0.09310	N	1	P;B;B	0.35774	0.519;0.009;0.003	B;B;B	0.40940	0.344;0.002;0.002	T	0.66040	-0.6022	10	0.46703	T	0.11	-0.001	8.754	0.34635	0.0:0.2841:0.1106:0.6053	.	46;76;46	F5H563;P16452-2;P16452	.;.;EPB42_HUMAN	H	76;46;46;46	ENSP00000300215:R76H;ENSP00000444699:R46H;ENSP00000396616:R46H	ENSP00000300215:R76H	R	-	2	0	EPB42	41295817	0.000000	0.05858	0.000000	0.03702	0.082000	0.17680	-0.989000	0.03736	-0.915000	0.03823	-0.140000	0.14226	CGC	.	C|0.999;T|0.001	0.001	weak		0.597	EPB42-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432219.1	NM_000119		T	43508525	C	T	43508525	3	4	158	1	0	0	0	0	1	0	0	0	5160	768	27	1	1986	1	EPB42	15	43508525	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	766408	43508525	59022867	66	9407											
HMG20A	10363	hgsc.bcm.edu	37	chr15	77756662	77756662	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttgtggaggatctctctcAaggtcagttgcttcagagtg	8	14	12	7	0	4	1	3	0	2	1	6	3	4	3	0	3	1	2	0	3	1	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr15:77756662A>G	ENST00000381714.3	+	4	598	c.170A>G	c.(169-171)cAa>cGa	p.Q57R	HMG20A_ENST00000336216.4_Missense_Mutation_p.Q57R	NM_018200.2	NP_060670.1	Q9NP66	HM20A_HUMAN	high mobility group 20A	57					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						GATCTCTCTCAAGGTCAGTTG	0.448																																					p.Q57R		Atlas-SNP	.											.	HMG20A	48	.	0			c.A170G						PASS	.						130	110	117					15																	77756662		2196	4294	6490	SO:0001583	missense	10363	exon4			TCTCTCAAGGTCA	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.170A>G	chr15.hg19:g.77756662A>G	ENSP00000371133:p.Gln57Arg	101.0	0.0	.		93.0	38.0	.	NM_018200	A6NHY3|D3DW78|Q53G31|Q9NSF6	Missense_Mutation	SNP	ENST00000381714.3	hg19	CCDS10295.1	.	.	.	.	.	.	.	.	.	.	A	16.35	3.099511	0.56183	.	.	ENSG00000140382	ENST00000336216;ENST00000381714	T;T	0.69926	-0.44;-0.44	5.71	4.59	0.56863	.	0.387563	0.28431	N	0.015378	T	0.67211	0.2869	L	0.27053	0.805	0.36537	D	0.871089	P;B	0.39094	0.659;0.003	P;B	0.55391	0.775;0.007	T	0.72184	-0.4367	10	0.52906	T	0.07	-14.0293	9.4942	0.38978	0.9188:0.0:0.0812:0.0	.	57;57	Q9NP66;Q9NP66-2	HM20A_HUMAN;.	R	57	ENSP00000336856:Q57R;ENSP00000371133:Q57R	ENSP00000336856:Q57R	Q	+	2	0	HMG20A	75543717	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.285000	0.51716	0.993000	0.38866	0.533000	0.62120	CAA	.	.	.	none		0.448	HMG20A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419512.2	NM_018200		G	77756662	A	G	77756662	3	3	158	1	0	0	0	0	1	0	0	0	7228	130	5	3	176	3	HMG20A	15	77756662	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	34248137	77756662	24774730	67	9408											
TSC2	7249	hgsc.bcm.edu	37	chr16	2130345	2130345	+	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	atgtgcccctgctgacccagGgctgggcggagatcctggtc	5	8	15	13	1	0	2	0	1	0	1	2	3	1	2	4	4	2	2	4	4	0	0			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr16:2130345G>A	ENST00000219476.3	+	30	4207	c.3577G>A	c.(3577-3579)Ggc>Agc	p.G1193S	TSC2_ENST00000350773.4_Missense_Mutation_p.G1193S|TSC2_ENST00000439673.2_Missense_Mutation_p.G1113S|TSC2_ENST00000382538.6_Missense_Mutation_p.G1101S|TSC2_ENST00000353929.4_Missense_Mutation_p.G1150S|TSC2_ENST00000401874.2_Missense_Mutation_p.G1149S|TSC2_ENST00000568454.1_Missense_Mutation_p.G1160S	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	1193					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)				GCTGACCCAGGGCTGGGCGGA	0.662			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.G1193S		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	.	TSC2	364	.	0			c.G3577A						PASS	.						41	46	45					16																	2130345		2198	4296	6494	SO:0001583	missense	7249	exon30	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	ACCCAGGGCTGGG	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.3577G>A	chr16.hg19:g.2130345G>A	ENSP00000219476:p.Gly1193Ser	118.0	0.0	.		98.0	25.0	.	NM_001114382	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Missense_Mutation	SNP	ENST00000219476.3	hg19	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	G	34	5.377719	0.95945	.	.	ENSG00000103197	ENST00000219476;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000382538;ENST00000350773	D;D;D;D;D	0.94046	-3.28;-3.29;-3.34;-3.34;-3.24	4.74	4.74	0.60224	.	0.000000	0.85682	D	0.000000	D	0.96005	0.8699	M	0.66939	2.045	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;0.997;0.968;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;0.99;0.91;1.0;0.999;0.994	D	0.95223	0.8335	10	0.34782	T	0.22	-36.9837	17.7425	0.88411	0.0:0.0:1.0:0.0	.	1101;1113;1193;1149;1149;1193	B4DIL8;P49815-6;P49815-4;P49815-3;P49815-5;P49815	.;.;.;.;.;TSC2_HUMAN	S	1193;1150;1150;1113;1101;1193	ENSP00000219476:G1193S;ENSP00000248099:G1150S;ENSP00000399232:G1113S;ENSP00000371978:G1101S;ENSP00000344383:G1193S	ENSP00000219476:G1193S	G	+	1	0	TSC2	2070346	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.929000	0.92859	2.196000	0.70406	0.561000	0.74099	GGC	.	.	.	none		0.662	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		A	2130345	G	A	2130345	3	1	158	1	0	0	0	0	1	0	0	0	16618	1232	43	2	3691	2	TSC2	16	2130345	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08		2130345	88224408	68	9409											
LOC81691	81691	hgsc.bcm.edu	37	chr16	20851091	20851091	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctacaggttcttgagcaggcCagagtggaaatccccctgtt	9	10	11	11	0	1	2	0	1	1	1	2	3	2	3	3	3	2	3	3	3	2	4			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr16:20851091C>T	ENST00000261377.6	+	14	1607	c.1398C>T	c.(1396-1398)gcC>gcT	p.A466A	AC004381.6_ENST00000564274.1_Silent_p.A466A|ERI2_ENST00000564349.1_Intron|AC004381.6_ENST00000348433.6_Silent_p.A466A	NM_001199053.1|NM_030941.2	NP_001185982.1|NP_112203.2																					TTGAGCAGGCCAGAGTGGAAA	0.448																																					p.A466A		Atlas-SNP	.											.	LOC81691	41	.	0			c.C1398T						PASS	.						288	274	279					16																	20851091		2201	4300	6501	SO:0001819	synonymous_variant	0	exon14			GCAGGCCAGAGTG																												ENST00000261377.6:c.1398C>T	chr16.hg19:g.20851091C>T		517.0	1.0	.		503.0	316.0	.	NM_030941		Silent	SNP	ENST00000261377.6	hg19	CCDS10591.1																																																																																			.	.	.	none		0.448	AC004381.6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254418.2			T	20851091	C	T	20851091	2	4	158	1	0	0	0	0	0	0	0	1	8897	581	21	2		2	LOC81691	16	20851091	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	18720746	20851091	69503662	69	9410											
DULLARD	23399	hgsc.bcm.edu	37	chr17	7149598	7149598	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtaatatctcctcttaagaAtgcttctgctattgtccagt	9	17	6	9	0	3	1	0	0	3	1	5	1	4	1	2	0	2	3	2	0	5	6			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr17:7149598A>G	ENST00000573600.1	-	6	873	c.452T>C	c.(451-453)aTt>aCt	p.I151T	CTDNEP1_ENST00000572043.1_Missense_Mutation_p.I18T|CTD-2545G14.7_ENST00000570760.2_5'Flank|CTDNEP1_ENST00000318988.6_Missense_Mutation_p.I151T|CTDNEP1_ENST00000574322.1_Missense_Mutation_p.I151T			O95476	CNEP1_HUMAN	CTD nuclear envelope phosphatase 1	151	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.				gamete generation (GO:0007276)|mesoderm development (GO:0007498)|nuclear envelope organization (GO:0006998)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of triglyceride biosynthetic process (GO:0010867)|protein dephosphorylation (GO:0006470)|protein localization to nucleus (GO:0034504)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|Nem1-Spo7 phosphatase complex (GO:0071595)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)	protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(9)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	15						CCTCTTAAGAATGCTTCTGCT	0.498																																					p.I151T		Atlas-SNP	.											.	CTDNEP1	26	.	0			c.T452C						PASS	.						117	108	111					17																	7149598		2203	4300	6503	SO:0001583	missense	23399	exon5			TTAAGAATGCTTC	AJ011916	CCDS11093.1	17p13	2012-11-27	2010-10-27	2010-10-27	ENSG00000175826	ENSG00000175826		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	19085	protein-coding gene	gene with protein product	"C-terminal domain nuclear envelope phosphatase 1"	610684	"dullard homolog (Xenopus laevis)"	DULLARD		12083771, 17141153	Standard	NM_015343		Approved	HSA011916, NET56	uc002gfd.2	O95476	OTTHUMG00000102180	ENST00000573600.1:c.452T>C	chr17.hg19:g.7149598A>G	ENSP00000461749:p.Ile151Thr	155.0	0.0	.		154.0	42.0	.	NM_001143775	D3DTN7|Q96GQ9	Missense_Mutation	SNP	ENST00000573600.1	hg19	CCDS11093.1	.	.	.	.	.	.	.	.	.	.	A	14.87	2.663502	0.47572	.	.	ENSG00000175826	ENST00000318988	T	0.17691	2.26	4.92	4.92	0.64577	NLI interacting factor (3);Dullard phosphatase domain, eukaryotic (1);HAD-like domain (2);	0.057069	0.64402	D	0.000001	T	0.27900	0.0687	M	0.78223	2.4	0.58432	D	0.999998	B	0.21309	0.054	B	0.34038	0.174	T	0.09079	-1.0691	10	0.59425	D	0.04	-8.3255	12.5573	0.56261	1.0:0.0:0.0:0.0	.	151	O95476	CNEP1_HUMAN	T	151	ENSP00000321732:I151T	ENSP00000321732:I151T	I	-	2	0	CTDNEP1	7090322	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.729000	0.84864	2.062000	0.61559	0.482000	0.46254	ATT	.	.	.	none		0.498	CTDNEP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440215.1	NM_015343		G	7149598	A	G	7149598	3	3	158	1	0	0	0	0	1	0	0	0	4801	101	4	3	298	3	DULLARD	17	7149598	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08		7149598	74045612	70	9411											
NCOR1	9611	hgsc.bcm.edu	37	chr17	16089949	16089949	+	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	gctgttgctgcaaaagctgtGatgcctgactcacttcaaga	10	11	10	10	0	2	3	2	2	0	1	2	3	2	3	1	0	4	5	1	0	3	2			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr17:16089949G>C	ENST00000268712.3	-	3	418	c.161C>G	c.(160-162)tCa>tGa	p.S54*	NCOR1_ENST00000395848.1_Intron|NCOR1_ENST00000395851.1_Nonsense_Mutation_p.S54*	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	54	Interaction with ZBTB33 and HEXIM1.				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)		CAAAAGCTGTGATGCCTGACT	0.403																																					p.S54X		Atlas-SNP	.											.	NCOR1	240	.	0			c.C161G						PASS	.						91	81	84					17																	16089949		2203	4300	6503	SO:0001587	stop_gained	9611	exon2			AGCTGTGATGCCT	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.161C>G	chr17.hg19:g.16089949G>C	ENSP00000268712:p.Ser54*	70.0	0.0	.		98.0	29.0	.	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Nonsense_Mutation	SNP	ENST00000268712.3	hg19	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	G	38	6.755855	0.97813	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000458113;ENST00000411510;ENST00000436828;ENST00000430577	.	.	.	5.78	5.78	0.91487	.	0.177313	0.39407	N	0.001372	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-9.9916	19.0021	0.92838	0.0:0.0:1.0:0.0	.	.	.	.	X	54	.	ENSP00000268712:S54X	S	-	2	0	NCOR1	16030674	1.000000	0.71417	0.991000	0.47740	0.976000	0.68499	6.537000	0.73847	2.724000	0.93272	0.563000	0.77884	TCA	.	.	.	none		0.403	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		C	16089949	G	C	16089949	4	2	158	1	0	0	0	0	0	1	0	0	10242	1294	45	4	7337	4	NCOR1	17	16089949	Nonsense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	8940351	16089949	65105261	71	9412											
SRCIN1	80725	hgsc.bcm.edu	37	chr17	36708962	36708962	+	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	tcgcaggccccagacccaccCttgagctctgtcagcgtctc	6	8	9	18	2	3	2	1	1	2	1	5	2	3	2	4	1	2	2	4	1	0	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr17:36708962C>G	ENST00000264659.7	-	12	2555	c.2331G>C	c.(2329-2331)aaG>aaC	p.K777N	SRCIN1_ENST00000578925.1_Splice_Site_p.K811N|SRCIN1_ENST00000398579.4_5'UTR	NM_025248.2	NP_079524.2	Q9C0H9	SRCN1_HUMAN	SRC kinase signaling inhibitor 1	649					exocytosis (GO:0006887)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell migration (GO:0030334)|regulation of dendritic spine morphogenesis (GO:0061001)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	protein kinase binding (GO:0019901)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	19						CAGACCCACCCTTGAGCTCTG	0.632																																					p.K777N		Atlas-SNP	.											.	SRCIN1	66	.	0			c.G2331C						PASS	.						54	63	60					17																	36708962		2142	4265	6407	SO:0001630	splice_region_variant	80725	exon12			CCCACCCTTGAGC		CCDS45660.1	17q12	2009-12-14			ENSG00000017373	ENSG00000277363			29506	protein-coding gene	gene with protein product	"p130Cas-associated protein", "SNAP-25-interacting protein"	610786				11214970	Standard	NM_025248		Approved	SNIP, p140Cap, KIAA1684	uc002hqd.3	Q9C0H9		ENST00000264659.7:c.2332+1G>C	chr17.hg19:g.36708962C>G		121.0	0.0	.		99.0	32.0	.	NM_025248	Q75T46|Q8N4W8	Missense_Mutation	SNP	ENST00000264659.7	hg19	CCDS45660.1	.	.	.	.	.	.	.	.	.	.	C	18.16	3.563310	0.65538	.	.	ENSG00000017373	ENST00000264659;ENST00000542707;ENST00000398579	T	0.54071	0.59	4.73	3.75	0.43078	.	0.000000	0.85682	D	0.000000	T	0.67107	0.2858	M	0.75085	2.285	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	0.998;0.999;0.999;0.999	T	0.68047	-0.5512	10	0.62326	D	0.03	-8.7012	6.4948	0.22136	0.0:0.7228:0.0:0.2772	.	83;649;649;777	Q9C0H9-4;Q9C0H9-2;Q9C0H9;Q9C0H9-5	.;.;SRCN1_HUMAN;.	N	777;558;631	ENSP00000264659:K777N	ENSP00000264659:K777N	K	-	3	2	SRCIN1	33962488	0.960000	0.32886	1.000000	0.80357	0.960000	0.62799	0.115000	0.15540	1.341000	0.45600	0.555000	0.69702	AAG	.	.	.	none		0.632	SRCIN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441878.4	NM_025248	Missense_Mutation	G	36708962	C	G	36708962	5	3	158	1	0	0	0	0	0	0	1	0	15148	695	24	4	1252	4	SRCIN1	17	36708962	Splice_Site	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	20619013	36708962	44486248	72	9413											
CASC3	22794	hgsc.bcm.edu	37	chr17	38319005	38319005	+	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	gggcgtcagcgaaagctatgGaaggatgagggtcgctggga	10	6	19	6	3	1	1	1	1	0	0	2	5	1	4	0	5	2	2	0	5	3	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr17:38319005G>A	ENST00000264645.7	+	6	862	c.636G>A	c.(634-636)tgG>tgA	p.W212*		NM_007359.4	NP_031385.2	O15234	CASC3_HUMAN	cancer susceptibility candidate 3	212	Necessary for RNA-binding, interaction with MAGOH and localization in nucleus speckles.|Sufficient to form the EJC.				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						GAAAGCTATGGAAGGATGAGG	0.493																																					p.W212X		Atlas-SNP	.											.	CASC3	39	.	0			c.G636A						PASS	.						72	66	68					17																	38319005		2203	4300	6503	SO:0001587	stop_gained	22794	exon6			GCTATGGAAGGAT	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.636G>A	chr17.hg19:g.38319005G>A	ENSP00000264645:p.Trp212*	67.0	0.0	.		59.0	15.0	.	NM_007359	A8K8R0	Nonsense_Mutation	SNP	ENST00000264645.7	hg19	CCDS11362.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.388249	0.82902	.	.	ENSG00000108349	ENST00000264645;ENST00000418132;ENST00000394114	.	.	.	4.63	4.63	0.57726	.	0.114993	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.2823	17.6407	0.88135	0.0:0.0:1.0:0.0	.	.	.	.	X	212	.	ENSP00000264645:W212X	W	+	3	0	CASC3	35572531	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.390000	0.97246	2.565000	0.86533	0.561000	0.74099	TGG	.	.	.	none		0.493	CASC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257127.3	NM_007359		A	38319005	G	A	38319005	4	1	158	1	0	0	0	0	0	1	0	0	2663	1183	41	2	658	2	CASC3	17	38319005	Nonsense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	1610043	38319005	42876205	73	9414											
COIL	8161	hgsc.bcm.edu	37	chr17	55028268	55028268	+	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	cctcctctaactgaaatgccCgcttctttgcttttctaaga	8	15	5	13	1	3	2	0	1	3	1	4	2	4	2	3	0	3	2	3	0	3	6	rs373166690		TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr17:55028268C>A	ENST00000240316.4	-	2	369	c.335G>T	c.(334-336)cGg>cTg	p.R112L		NM_004645.2	NP_004636.1	P38432	COIL_HUMAN	coilin	112						Cajal body (GO:0015030)|cytoplasm (GO:0005737)|female germ cell nucleus (GO:0001674)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	disulfide oxidoreductase activity (GO:0015036)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			NS(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|urinary_tract(1)	15	Breast(9;6.15e-08)					CTGAAATGCCCGCTTCTTTGC	0.368																																					p.R112L		Atlas-SNP	.											.	COIL	49	.	0			c.G335T						PASS	.						94	98	97					17																	55028268		2202	4300	6502	SO:0001583	missense	8161	exon2			AATGCCCGCTTCT	U06632	CCDS11592.1	17q22	2012-10-02			ENSG00000121058	ENSG00000121058			2184	protein-coding gene	gene with protein product		600272				7971277	Standard	NM_004645		Approved	CLN80, p80-coilin	uc002iuu.3	P38432	OTTHUMG00000178126	ENST00000240316.4:c.335G>T	chr17.hg19:g.55028268C>A	ENSP00000240316:p.Arg112Leu	143.0	0.0	.		236.0	10.0	.	NM_004645	B2R931	Missense_Mutation	SNP	ENST00000240316.4	hg19	CCDS11592.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.334670	0.81801	.	.	ENSG00000121058	ENST00000240316	.	.	.	5.84	5.84	0.93424	.	0.238035	0.41194	D	0.000936	T	0.58722	0.2142	L	0.32530	0.975	0.34176	D	0.670392	D	0.89917	1.0	D	0.72982	0.979	T	0.69390	-0.5158	9	0.72032	D	0.01	-17.0434	8.6284	0.33904	0.0:0.7665:0.154:0.0795	.	112	P38432	COIL_HUMAN	L	112	.	ENSP00000240316:R112L	R	-	2	0	COIL	52383267	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.790000	0.47821	2.748000	0.94277	0.650000	0.86243	CGG	.	.	.	alt		0.368	COIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440618.1			A	55028268	C	A	55028268	3	1	158	1	0	0	0	0	1	0	0	0	3667	652	23	4	1419	4	COIL	17	55028268	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	16709263	55028268	26166942	74	9415											
MPO	4353	hgsc.bcm.edu	37	chr17	56348163	56348163	+	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	gcagatgatccggggcaatgAgatctgggccagggcctgtc	8	7	16	10	1	1	3	0	2	1	2	3	4	2	3	3	4	0	2	3	4	1	0			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr17:56348163A>T	ENST00000225275.3	-	12	2268	c.2092T>A	c.(2092-2094)Tca>Aca	p.S698T	MPO_ENST00000340482.3_Missense_Mutation_p.S730T	NM_000250.1	NP_000241.1	P05164	PERM_HUMAN	myeloperoxidase	698					aging (GO:0007568)|defense response (GO:0006952)|defense response to fungus (GO:0050832)|hydrogen peroxide catabolic process (GO:0042744)|hypochlorous acid biosynthetic process (GO:0002149)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of apoptotic process (GO:0043066)|negative regulation of growth of symbiont in host (GO:0044130)|oxidation-reduction process (GO:0055114)|removal of superoxide radicals (GO:0019430)|respiratory burst involved in defense response (GO:0002679)|response to food (GO:0032094)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|response to yeast (GO:0001878)	azurophil granule (GO:0042582)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|secretory granule (GO:0030141)	chromatin binding (GO:0003682)|heme binding (GO:0020037)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(13)|ovary(2)|pancreas(1)|skin(4)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	46					Aminosalicylic Acid(DB00233)|Bivalirudin(DB00006)|Calcipotriol(DB02300)|Carboplatin(DB00958)|Cefaclor(DB00833)|Cefdinir(DB00535)|Cisplatin(DB00515)|Cysteamine(DB00847)|Dapsone(DB00250)|Enoxaparin(DB01225)|Human Serum Albumin(DB00062)|L-Carnitine(DB00583)|Melatonin(DB01065)|Mesalazine(DB00244)|Nabumetone(DB00461)|Octreotide(DB00104)|Oxaliplatin(DB00526)|Propylthiouracil(DB00550)|Ticlopidine(DB00208)|Tolmetin(DB00500)	CGGGGCAATGAGATCTGGGCC	0.547																																					p.S698T		Atlas-SNP	.											.	MPO	114	.	0			c.T2092A						PASS	.						233	180	198					17																	56348163		2203	4300	6503	SO:0001583	missense	4353	exon12			GCAATGAGATCTG		CCDS11604.1	17q21.3-q23	2014-09-17				ENSG00000005381	1.11.1.7		7218	protein-coding gene	gene with protein product		606989					Standard	NM_000250		Approved		uc002ivu.1	P05164		ENST00000225275.3:c.2092T>A	chr17.hg19:g.56348163A>T	ENSP00000225275:p.Ser698Thr	144.0	0.0	.		93.0	57.0	.	NM_000250	A1L4B8|Q14862|Q4PJH5|Q9UCL7	Missense_Mutation	SNP	ENST00000225275.3	hg19	CCDS11604.1	.	.	.	.	.	.	.	.	.	.	A	15.91	2.973327	0.53614	.	.	ENSG00000005381	ENST00000340482;ENST00000225275	T;T	0.68624	-0.34;-0.34	5.76	3.3	0.37823	.	0.161988	0.56097	N	0.000025	T	0.56601	0.1996	L	0.33792	1.035	0.80722	D	1	B	0.19817	0.039	B	0.29524	0.103	T	0.55237	-0.8172	10	0.51188	T	0.08	-34.2797	11.513	0.50504	0.7489:0.0:0.0:0.2511	.	698	P05164	PERM_HUMAN	T	730;698	ENSP00000344419:S730T;ENSP00000225275:S698T	ENSP00000225275:S698T	S	-	1	0	MPO	53703162	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	2.270000	0.43355	0.973000	0.38340	0.533000	0.62120	TCA	.	.	.	none		0.547	MPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443971.1			T	56348163	A	T	56348163	3	4	158	1	0	0	0	0	1	0	0	0	9739	304	11	5	149	5	MPO	17	56348163	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08	1319895	56348163	24847047	75	9416											
KCNJ16	3773	hgsc.bcm.edu	37	chr17	68129132	68129132	+	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	ctagaagctcctatgttcccCgagaaattctctggggccat	9	11	9	12	1	1	2	0	0	1	2	4	3	3	2	4	2	1	2	4	2	4	4	rs142625269		TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr17:68129132C>A	ENST00000589377.1	+	2	1067	c.904C>A	c.(904-906)Cga>Aga	p.R302R	KCNJ16_ENST00000283936.1_Silent_p.R302R|KCNJ16_ENST00000585558.1_Silent_p.R337R|KCNJ16_ENST00000392671.1_Silent_p.R302R|KCNJ16_ENST00000586462.1_Silent_p.R341R|KCNJ16_ENST00000392670.1_Silent_p.R302R	NM_001270422.1	NP_001257351.1	Q9NPI9	KCJ16_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 16	302					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)					CTATGTTCCCCGAGAAATTCT	0.393																																					p.R302R		Atlas-SNP	.											.	KCNJ16	72	.	0			c.C904A						PASS	.						76	82	80					17																	68129132		2203	4300	6503	SO:0001819	synonymous_variant	3773	exon6			GTTCCCCGAGAAA	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.904C>A	chr17.hg19:g.68129132C>A		127.0	0.0	.		151.0	9.0	.	NM_001270422		Silent	SNP	ENST00000589377.1	hg19	CCDS11687.1																																																																																			.	C|1.000;T|0.000	.	alt		0.393	KCNJ16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450880.1	NM_018658		A	68129132	C	A	68129132	2	1	158	1	0	0	0	0	0	0	0	1	8057	644	23	4		4	KCNJ16	17	68129132	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	11780969	68129132	13066078	76	9417											
RAB37	326624	hgsc.bcm.edu	37	chr17	72736999	72736999	+	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	tccggaaccttcatagccacCgtcggcatagacttcagggt	9	9	10	13	3	2	1	2	0	0	1	4	2	3	2	4	3	2	1	4	3	3	4	rs146770958	byFrequency	TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr17:72736999C>A	ENST00000392613.5	+	2	242	c.186C>A	c.(184-186)acC>acA	p.T62T	RAB37_ENST00000392612.3_Intron|RAB37_ENST00000392610.1_Silent_p.T62T|RAB37_ENST00000392614.4_Silent_p.T67T|RAB37_ENST00000340415.3_Intron|RAB37_ENST00000528438.1_Silent_p.T35T|RAB37_ENST00000402449.4_Intron|RAB37_ENST00000392615.5_Intron	NM_001006638.2	NP_001006639.1	Q96AX2	RAB37_HUMAN	RAB37, member RAS oncogene family	62					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|secretory granule (GO:0030141)	GTP binding (GO:0005525)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	12						TCATAGCCACCGTCGGCATAG	0.597																																					p.T67T		Atlas-SNP	.											.	RAB37	69	.	0			c.C201A						PASS	.						101	99	99					17																	72736999		2203	4300	6503	SO:0001819	synonymous_variant	326624	exon2			AGCCACCGTCGGC	BC040547	CCDS11703.1, CCDS32722.1, CCDS54161.1, CCDS54162.1	17q25.2	2008-02-05			ENSG00000172794	ENSG00000172794		"RAB, member RAS oncogene"	30268	protein-coding gene	gene with protein product		609956				10722846	Standard	NM_175738		Approved		uc002jlk.3	Q96AX2	OTTHUMG00000134282	ENST00000392613.5:c.186C>A	chr17.hg19:g.72736999C>A		214.0	0.0	.		188.0	9.0	.	NM_001163989	A8MXF5|A8MYT0|Q8IWA7	Silent	SNP	ENST00000392613.5	hg19	CCDS32722.1																																																																																			.	C|1.000;T|0.000	.	alt		0.597	RAB37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258872.2	NM_175738		A	72736999	C	A	72736999	2	1	158	1	0	0	0	0	0	0	0	1	12940	639	23	4		4	RAB37	17	72736999	Silent	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	4607867	72736999	8458211	77	9418											
PSMD8	5714	hgsc.bcm.edu	37	chr19	38874011	38874011	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcatcgagtatgcccggcAgctggagatgatcgtctgag	8	9	15	9	3	2	3	1	2	1	1	4	5	2	3	1	3	2	3	1	3	1	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr19:38874011A>G	ENST00000215071.4	+	7	1100	c.1034A>G	c.(1033-1035)cAg>cGg	p.Q345R	AC005789.9_ENST00000585411.1_RNA|GGN_ENST00000591809.1_5'Flank|PSMD8_ENST00000602911.1_Missense_Mutation_p.Q282R	NM_002812.4	NP_002803.2	P48556	PSMD8_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	345					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(1)	6	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			TATGCCCGGCAGCTGGAGATG	0.557																																					p.Q345R		Atlas-SNP	.											.	PSMD8	31	.	0			c.A1034G						PASS	.						49	41	43					19																	38874011		2203	4300	6503	SO:0001583	missense	5714	exon7			CCCGGCAGCTGGA	D38047	CCDS12515.2	19q13.2	2009-05-07			ENSG00000099341	ENSG00000099341		"Proteasome (prosome, macropain) subunits"	9566	protein-coding gene	gene with protein product						7621825	Standard	NM_002812		Approved	S14, Nin1p, p31, HIP6, HYPF, Rpn12	uc002oii.4	P48556	OTTHUMG00000150691	ENST00000215071.4:c.1034A>G	chr19.hg19:g.38874011A>G	ENSP00000215071:p.Gln345Arg	66.0	0.0	.		28.0	9.0	.	NM_002812	B4DX18|Q6P1L7	Missense_Mutation	SNP	ENST00000215071.4	hg19	CCDS12515.2	.	.	.	.	.	.	.	.	.	.	A	23.8	4.459422	0.84317	.	.	ENSG00000099341	ENST00000215071	.	.	.	4.27	4.27	0.50696	.	0.000000	0.85682	D	0.000000	T	0.48660	0.1512	L	0.47190	1.495	0.80722	D	1	D	0.54207	0.965	P	0.45071	0.468	T	0.54234	-0.8324	9	0.62326	D	0.03	-19.6009	11.6721	0.51408	1.0:0.0:0.0:0.0	.	345	P48556	PSMD8_HUMAN	R	345	.	ENSP00000215071:Q345R	Q	+	2	0	PSMD8	43565851	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.193000	0.89719	1.919000	0.55581	0.448000	0.29417	CAG	.	.	.	none		0.557	PSMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319627.1	NM_002812		G	38874011	A	G	38874011	3	3	158	1	0	0	0	0	1	0	0	0	12714	188	7	3	1060	3	PSMD8	19	38874011	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08		38874011	20254972	78	9419											
CEACAM6	4680	hgsc.bcm.edu	37	chr19	42260867	42260867	+	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	ccggacagttccatgtatacCgtgagtatttccacatgacc	10	11	8	12	2	0	2	0	2	0	0	2	3	2	3	5	1	1	3	5	1	3	5			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr19:42260867C>A	ENST00000199764.6	+	2	642	c.424C>A	c.(424-426)Ccg>Acg	p.P142T	CEA_ENST00000598976.1_Intron|AC011513.4_ENST00000601409.1_RNA	NM_002483.4	NP_002474.3	P40199	CEAM6_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 6 (non-specific cross reacting antigen)	142	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)		p.P142S(1)		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)		CCATGTATACCGTGAGTATTT	0.488																																					p.P142T		Atlas-SNP	.											CEACAM6,NS,carcinoma,0,1	CEACAM6	52	.	1	Substitution - Missense(1)	breast(1)	c.C424A						PASS	.						242	241	241					19																	42260867		2203	4300	6503	SO:0001630	splice_region_variant	4680	exon2			GTATACCGTGAGT	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.424+1C>A	chr19.hg19:g.42260867C>A		514.0	0.0	.		299.0	17.0	.	NM_002483	Q13774|Q14920|Q53XP7	Missense_Mutation	SNP	ENST00000199764.6	hg19	CCDS12585.1	.	.	.	.	.	.	.	.	.	.	C	6.485	0.457601	0.12342	.	.	ENSG00000086548	ENST00000199764	T	0.20881	2.04	2.15	-0.876	0.10624	.	.	.	.	.	T	0.13927	0.0337	L	0.48877	1.53	0.09310	N	1	B	0.19817	0.039	B	0.24006	0.05	T	0.41998	-0.9477	9	0.02654	T	1	.	7.1362	0.25529	0.0:0.4392:0.5608:0.0	.	142	P40199	CEAM6_HUMAN	T	142	ENSP00000199764:P142T	ENSP00000199764:P142T	P	+	1	0	CEACAM6	46952707	0.001000	0.12720	0.010000	0.14722	0.046000	0.14306	-1.270000	0.02831	0.164000	0.19529	0.305000	0.20034	CCG	.	.	.	none		0.488	CEACAM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321147.1		Missense_Mutation	A	42260867	C	A	42260867	5	1	158	1	0	0	0	0	0	0	1	0	3198	666	23	4	430	4	CEACAM6	19	42260867	Splice_Site	SNP	C	TCGA-DZ-6133-01A-11D-1961-08	3386856	42260867	16868116	79	9420											
ZNF180	7733	hgsc.bcm.edu	37	chr19	44981073	44981073	+	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	acggtttctctccagtgtgaGttctttgatgtgcaacaagc	8	14	10	9	1	2	2	0	2	2	0	4	2	3	2	1	1	3	3	1	1	2	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr19:44981073G>C	ENST00000221327.4	-	5	1906	c.1625C>G	c.(1624-1626)aCt>aGt	p.T542S	ZNF180_ENST00000592529.1_Missense_Mutation_p.T515S|AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000585514.1_5'Flank|ZNF180_ENST00000391956.4_Missense_Mutation_p.T517S	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	542					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)				TCCAGTGTGAGTTCTTTGATG	0.423																																					p.T542S	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											.	ZNF180	103	.	0			c.C1625G						PASS	.						77	77	77					19																	44981073		2203	4300	6503	SO:0001583	missense	7733	exon5			GTGTGAGTTCTTT	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.1625C>G	chr19.hg19:g.44981073G>C	ENSP00000221327:p.Thr542Ser	96.0	0.0	.		89.0	33.0	.	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	hg19	CCDS12639.1	.	.	.	.	.	.	.	.	.	.	G	15.35	2.808114	0.50421	.	.	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.00662	5.93;5.93	5.23	2.85	0.33270	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.43416	D	0.000561	T	0.01029	0.0034	L	0.38692	1.165	0.80722	D	1	P;P;P	0.45428	0.828;0.858;0.858	B;P;P	0.47981	0.335;0.563;0.563	T	0.68884	-0.5291	10	0.62326	D	0.03	-11.2816	5.453	0.16574	0.1458:0.0:0.6595:0.1947	.	517;541;542	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	S	542;517	ENSP00000221327:T542S;ENSP00000375818:T517S	ENSP00000221327:T542S	T	-	2	0	ZNF180	49672913	0.000000	0.05858	1.000000	0.80357	0.982000	0.71751	0.203000	0.17315	2.437000	0.82529	0.467000	0.42956	ACT	.	.	.	none		0.423	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256		C	44981073	G	C	44981073	3	2	158	1	0	0	0	0	1	0	0	0	17760	1029	36	4	457	4	ZNF180	19	44981073	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	2720206	44981073	14147910	80	9421											
LILRA3	11026	hgsc.bcm.edu	37	chr19	54803120	54803120	+	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	acctgcgacttgggctcacgGggcccacggagaagatggcc	8	5	15	13	3	1	2	1	0	0	2	1	4	1	2	3	5	1	1	3	5	1	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr19:54803120G>T	ENST00000251390.3	-	4	648	c.557C>A	c.(556-558)cCc>cAc	p.P186H	LILRA3_ENST00000391745.1_Missense_Mutation_p.P203H|LILRA3_ENST00000391744.3_Intron	NM_006865.3	NP_006856.3	Q8N6C8	LIRA3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3	186	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)		TGGGCTCACGGGGCCCACGGA	0.587																																					p.P186H		Atlas-SNP	.											.	LILRA3	65	.	0			c.C557A						PASS	.						134	113	120					19																	54803120		2195	4162	6357	SO:0001583	missense	11026	exon4			CTCACGGGGCCCA	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.557C>A	chr19.hg19:g.54803120G>T	ENSP00000251390:p.Pro186His	215.0	0.0	.		98.0	44.0	.	NM_006865	J3KPM2|O15469|O15470|O75016|Q8N151|Q8N154|Q8NHJ1|Q8NHJ2|Q8NHJ3|Q8NHJ4	Missense_Mutation	SNP	ENST00000251390.3	hg19	CCDS12887.1	.	.	.	.	.	.	.	.	.	.	G	12.24	1.877305	0.33162	.	.	ENSG00000170866	ENST00000251390;ENST00000391745	T;T	0.03124	4.04;4.04	2.21	1.09	0.20402	Immunoglobulin-like fold (1);	0.593476	0.14797	N	0.297850	T	0.16214	0.0390	M	0.87269	2.87	0.09310	N	1	D	0.89917	1.0	D	0.85130	0.997	T	0.03534	-1.1027	10	0.87932	D	0	.	5.2465	0.15500	0.1757:0.0:0.8243:0.0	.	186	Q8N6C8	LIRA3_HUMAN	H	186;203	ENSP00000251390:P186H;ENSP00000375625:P203H	ENSP00000251390:P186H	P	-	2	0	LILRA3	59494932	0.002000	0.14202	0.008000	0.14137	0.032000	0.12392	0.663000	0.25053	0.493000	0.27837	0.586000	0.80456	CCC	.	.	.	none		0.587	LILRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140236.1			T	54803120	G	T	54803120	3	4	158	1	0	0	0	0	1	0	0	0	8793	1232	43	4	778	4	LILRA3	19	54803120	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08	9822047	54803120	4325863	81	9422											
ZNF324B	388569	hgsc.bcm.edu	37	chr19	58966903	58966903	+	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	cgcctgagcggcagaagccaTgtgcacaggaggtccctggg	8	5	16	12	2	0	2	0	1	0	1	1	3	1	3	3	4	3	2	3	4	1	0			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr19:58966903T>A	ENST00000336614.4	+	4	699	c.592T>A	c.(592-594)Tgt>Agt	p.C198S	ZNF324B_ENST00000391696.1_Missense_Mutation_p.C188S|ZNF324B_ENST00000545523.1_Missense_Mutation_p.C198S	NM_207395.2	NP_997278.2	Q6AW86	Z324B_HUMAN	zinc finger protein 324B	198					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		GCAGAAGCCATGTGCACAGGA	0.672																																					p.C198S		Atlas-SNP	.											.	ZNF324B	58	.	0			c.T592A						PASS	.						36	40	39					19																	58966903		2203	4300	6503	SO:0001583	missense	388569	exon4			AAGCCATGTGCAC	AK127750	CCDS33138.1	19q13.43	2013-01-08				ENSG00000249471		"Zinc fingers, C2H2-type", "-"	33107	protein-coding gene	gene with protein product							Standard	NM_207395		Approved	FLJ45850	uc002qsv.1	Q6AW86		ENST00000336614.4:c.592T>A	chr19.hg19:g.58966903T>A	ENSP00000337473:p.Cys198Ser	117.0	0.0	.		44.0	17.0	.	NM_207395	B2RTZ6|Q6ZMX8|Q6ZS42	Missense_Mutation	SNP	ENST00000336614.4	hg19	CCDS33138.1	.	.	.	.	.	.	.	.	.	.	T	11.83	1.756192	0.31137	.	.	ENSG00000249471	ENST00000336614;ENST00000545523;ENST00000391696	T;T;T	0.06294	3.49;3.49;3.32	2.7	-1.7	0.08159	.	3.208830	0.01016	N	0.003905	T	0.05364	0.0142	L	0.27053	0.805	0.09310	N	1	B;B	0.23185	0.081;0.003	B;B	0.16289	0.015;0.002	T	0.39078	-0.9631	10	0.62326	D	0.03	.	4.2594	0.10733	0.0:0.2411:0.2439:0.5151	.	198;188	Q6AW86;C9JTQ8	Z324B_HUMAN;.	S	198;198;188	ENSP00000337473:C198S;ENSP00000438930:C198S;ENSP00000375578:C188S	ENSP00000337473:C198S	C	+	1	0	ZNF324B	63658715	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.422000	0.02453	-0.415000	0.07484	0.402000	0.26972	TGT	.	.	.	none		0.672	ZNF324B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467038.1	NM_207395		A	58966903	T	A	58966903	3	1	158	1	0	0	0	0	1	0	0	0	17857	1464	51	5	602	5	ZNF324B	19	58966903	Missense_Mutation	SNP	T	TCGA-DZ-6133-01A-11D-1961-08	4163783	58966903	162080	82	9423											
EPB41L1	2036	hgsc.bcm.edu	37	chr20	34800245	34800245	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctggccattagaaagaagAttgagccggaggccgtactg	11	8	14	8	2	1	4	0	1	1	3	1	5	1	5	3	3	2	1	3	3	4	3			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr20:34800245A>G	ENST00000338074.2	+	16	2292	c.2131A>G	c.(2131-2133)Att>Gtt	p.I711V	EPB41L1_ENST00000373941.1_Missense_Mutation_p.I711V|EPB41L1_ENST00000441639.1_Missense_Mutation_p.I637V|EPB41L1_ENST00000373946.3_Missense_Mutation_p.I531V|EPB41L1_ENST00000479336.1_3'UTR|EPB41L1_ENST00000202028.5_Missense_Mutation_p.I637V|EPB41L1_ENST00000373950.2_Missense_Mutation_p.I602V	NM_001258329.1|NM_012156.2	NP_001245258.1|NP_036288.2	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	711					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)					TAGAAAGAAGATTGAGCCGGA	0.493																																					p.I711V		Atlas-SNP	.											.	EPB41L1	111	.	0			c.A2131G						PASS	.						88	79	82					20																	34800245		2203	4300	6503	SO:0001583	missense	2036	exon17			AAGAAGATTGAGC	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.2131A>G	chr20.hg19:g.34800245A>G	ENSP00000337168:p.Ile711Val	93.0	0.0	.		95.0	33.0	.	NM_001258329	O15046|Q4VXM6|Q4VXM7|Q4VXM8|Q4VXN4|Q6ZT61|Q8IUU7|Q96CV5|Q96L65	Missense_Mutation	SNP	ENST00000338074.2	hg19	CCDS13271.1	.	.	.	.	.	.	.	.	.	.	A	16.18	3.050564	0.55218	.	.	ENSG00000088367	ENST00000202028;ENST00000373950;ENST00000397315;ENST00000373951;ENST00000441639;ENST00000373946;ENST00000338074;ENST00000373941;ENST00000454226	D;D;D;D;D;D	0.83755	-1.76;-1.59;-1.76;-1.66;-1.66;-1.62	5.78	4.61	0.57282	.	.	.	.	.	T	0.71099	0.3300	N	0.24115	0.695	0.23391	N	0.997771	B;B;B;B;B;B	0.22983	0.078;0.01;0.047;0.004;0.007;0.0	B;B;B;B;B;B	0.21917	0.018;0.004;0.037;0.004;0.002;0.001	T	0.56786	-0.7921	9	0.24483	T	0.36	.	9.5214	0.39138	0.8228:0.1772:0.0:0.0	.	711;711;531;602;602;637	B7Z653;Q9H4G0;Q9H4G0-4;Q9H4G0-3;B3KUB6;Q9H4G0-2	.;E41L1_HUMAN;.;.;.;.	V	637;602;711;602;637;531;711;711;72	ENSP00000202028:I637V;ENSP00000363061:I602V;ENSP00000399214:I637V;ENSP00000363057:I531V;ENSP00000337168:I711V;ENSP00000363052:I711V	ENSP00000202028:I637V	I	+	1	0	EPB41L1	34263659	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	1.624000	0.37018	2.333000	0.79357	0.533000	0.62120	ATT	.	.	.	none		0.493	EPB41L1-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078978.3	NM_012156		G	34800245	A	G	34800245	3	3	158	1	0	0	0	0	1	0	0	0	5154	333	12	3	2189	3	EPB41L1	20	34800245	Missense_Mutation	SNP	A	TCGA-DZ-6133-01A-11D-1961-08		34800245	28225275	83	9424											
SETD4	54093	hgsc.bcm.edu	37	chr21	37410517	37410517	+	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	tgggctatgtccaaacttgtCttctcattcgtatctgaaat	9	16	7	9	1	3	1	1	1	3	0	6	1	4	1	1	1	1	2	1	1	4	5			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr21:37410517C>G	ENST00000399215.1	-	9	2491	c.1119G>C	c.(1117-1119)aaG>aaC	p.K373N	SETD4_ENST00000399212.1_Missense_Mutation_p.K349N|SETD4_ENST00000481477.1_5'UTR|AP000688.1_ENST00000600312.1_Intron|SETD4_ENST00000332131.4_Missense_Mutation_p.K373N			Q9NVD3	SETD4_HUMAN	SET domain containing 4	373				EILVKYLPSTDKQMDKKISILKDHGYIENLTFGWDGPSWRL LTALKLLCLEAEKFTCWKKVLLGEVISDTNEKTSLDIAQKI CYYFIEETNAVLQKVSHMKDEKEALINQLTLVESLWTEELK ILRASAETLHSLQTAFT -> GWNQLCS (in Ref. 5; AAH02898). {ECO:0000305}.			methyltransferase activity (GO:0008168)			autonomic_ganglia(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	15						CCAAACTTGTCTTCTCATTCG	0.353																																					p.K373N		Atlas-SNP	.											.	SETD4	37	.	0			c.G1119C						PASS	.						179	173	175					21																	37410517		2202	4300	6502	SO:0001583	missense	54093	exon10			ACTTGTCTTCTCA	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.1119G>C	chr21.hg19:g.37410517C>G	ENSP00000382163:p.Lys373Asn	138.0	0.0	.		133.0	62.0	.	NM_017438	B4DT14|D3DSG2|D3DSG4|Q8NE19|Q9BU46	Missense_Mutation	SNP	ENST00000399215.1	hg19	CCDS13640.1	.	.	.	.	.	.	.	.	.	.	C	17.01	3.278952	0.59758	.	.	ENSG00000185917	ENST00000399215;ENST00000399212;ENST00000332131	T;T;T	0.18174	2.23;2.23;2.23	5.79	3.99	0.46301	Rubisco LS methyltransferase, substrate-binding domain (1);	0.633406	0.17880	N	0.158893	T	0.19046	0.0457	L	0.57536	1.79	0.80722	D	1	P;P	0.39920	0.646;0.695	B;B	0.40134	0.214;0.32	T	0.02307	-1.1179	10	0.18276	T	0.48	-14.3562	12.2959	0.54847	0.0:0.8635:0.0:0.1365	.	349;373	Q9NVD3-3;Q9NVD3	.;SETD4_HUMAN	N	373;349;373	ENSP00000382163:K373N;ENSP00000382161:K349N;ENSP00000329189:K373N	ENSP00000329189:K373N	K	-	3	2	SETD4	36332387	0.996000	0.38824	0.885000	0.34714	0.989000	0.77384	2.608000	0.46308	0.799000	0.34018	0.561000	0.74099	AAG	.	.	.	none		0.353	SETD4-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194456.1	NM_017438		G	37410517	C	G	37410517	3	3	158	1	0	0	0	0	1	0	0	0	14146	912	32	4	211	4	SETD4	21	37410517	Missense_Mutation	SNP	C	TCGA-DZ-6133-01A-11D-1961-08		37410517	10719378	84	9425											
CERK	64781	hgsc.bcm.edu	37	chr22	47108141	47108141	+	Missense_Mutation	SNP	T	T	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	tatatccgcttgccttgtccTtttcctccaaacgggttgat	6	16	7	12	2	0	1	0	1	0	0	4	1	4	1	5	1	2	2	5	1	3	7			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chr22:47108141T>G	ENST00000216264.8	-	4	541	c.429A>C	c.(427-429)aaA>aaC	p.K143N	CERK_ENST00000541677.1_5'UTR	NM_022766.5	NP_073603.2	Q8TCT0	CERK1_HUMAN	ceramide kinase	143	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|lipid phosphorylation (GO:0046834)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ceramide kinase activity (GO:0001729)|diacylglycerol kinase activity (GO:0004143)|magnesium ion binding (GO:0000287)|NAD+ kinase activity (GO:0003951)			cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(2)|skin(2)	20		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)|BRCA - Breast invasive adenocarcinoma(115;0.171)		TGCCTTGTCCTTTTCCTCCAA	0.388																																					p.K143N		Atlas-SNP	.											.	CERK	40	.	0			c.A429C						PASS	.						241	179	200					22																	47108141		2203	4300	6503	SO:0001583	missense	64781	exon4			TTGTCCTTTTCCT	AB079066	CCDS14077.1	22q13.31	2008-06-10			ENSG00000100422	ENSG00000100422			19256	protein-coding gene	gene with protein product		610307				11956206, 11258795	Standard	NM_022766		Approved	hCERK, FLJ23239, dA59H18.3, DKFZp434E0211, FLJ21430, KIAA1646, LK4, dA59H18.2	uc003bia.3	Q8TCT0	OTTHUMG00000150395	ENST00000216264.8:c.429A>C	chr22.hg19:g.47108141T>G	ENSP00000216264:p.Lys143Asn	54.0	0.0	.		66.0	26.0	.	NM_022766	A0JNT4|A8K611|Q6NX59|Q9BYB3|Q9UGE5	Missense_Mutation	SNP	ENST00000216264.8	hg19	CCDS14077.1	.	.	.	.	.	.	.	.	.	.	T	14.94	2.686429	0.47991	.	.	ENSG00000100422	ENST00000216264	T	0.15487	2.42	5.2	-1.83	0.07833	Diacylglycerol kinase, catalytic domain (3);	0.109682	0.64402	D	0.000007	T	0.43366	0.1244	M	0.89785	3.06	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.49409	-0.8943	10	0.72032	D	0.01	-14.0309	12.0935	0.53742	0.0:0.6281:0.0:0.3719	.	143	Q8TCT0	CERK1_HUMAN	N	143	ENSP00000216264:K143N	ENSP00000216264:K143N	K	-	3	2	CERK	45486805	0.957000	0.32711	0.303000	0.25071	0.328000	0.28507	1.095000	0.30964	-0.493000	0.06678	0.460000	0.39030	AAA	.	.	.	none		0.388	CERK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317924.2	NM_022766		G	47108141	T	G	47108141	3	3	158	1	0	0	0	0	1	0	0	0	3269	1606	56	5	1224	5	CERK	22	47108141	Missense_Mutation	SNP	T	TCGA-DZ-6133-01A-11D-1961-08		47108141	4196425	85	9426											
FAM123B	139285	hgsc.bcm.edu	37	chrX	63411696	63411696	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcggggtagacaatccctgcGgacaagccccagggcctcac	9	5	12	15	2	1	1	1	0	0	1	3	2	2	2	4	4	2	1	4	4	3	1			TCGA-DZ-6133-01A-11D-1961-08	TCGA-DZ-6133-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dac1245d-4f00-4d28-bbc0-cdaf6beba2d0	e6107469-78da-4831-a87a-9fc0dbccbd8e	g.chrX:63411696G>A	ENST00000330258.3	-	2	1743	c.1471C>T	c.(1471-1473)Cgc>Tgc	p.R491C	AMER1_ENST00000403336.1_Missense_Mutation_p.R491C|AMER1_ENST00000374869.3_Missense_Mutation_p.R491C	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	491					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)									CAATCCCTGCGGACAAGCCCC	0.522																																					p.R491C		Atlas-SNP	.											.	.	.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.C1471T						PASS	.						61	50	54					X																	63411696		2203	4300	6503	SO:0001583	missense	139285	exon2			CCCTGCGGACAAG	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.1471C>T	chrX.hg19:g.63411696G>A	ENSP00000329117:p.Arg491Cys	77.0	0.0	.		25.0	21.0	.	NM_152424	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	hg19	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	G	7.831	0.719945	0.15372	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	T;T;T	0.19532	2.14;2.14;2.14	5.21	3.3	0.37823	.	1.072280	0.07227	N	0.861857	T	0.17704	0.0425	N	0.24115	0.695	0.09310	N	1	P	0.45531	0.86	B	0.40329	0.326	T	0.25984	-1.0116	10	0.72032	D	0.01	0.0109	11.6933	0.51529	0.0:0.0:0.6193:0.3806	.	491	Q5JTC6	F123B_HUMAN	C	491	ENSP00000364003:R491C;ENSP00000329117:R491C;ENSP00000384722:R491C	ENSP00000329117:R491C	R	-	1	0	FAM123B	63328421	0.008000	0.16893	0.004000	0.12327	0.604000	0.37047	1.430000	0.34914	1.289000	0.44618	0.600000	0.82982	CGC	.	.	.	none		0.522	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		A	63411696	G	A	63411696	3	1	158	1	0	0	0	0	1	0	0	0	5427	1116	39	1	1940	1	FAM123B	23	63411696	Missense_Mutation	SNP	G	TCGA-DZ-6133-01A-11D-1961-08		63411696	91858864	86	9427											
HIVEP3	59269	hgsc.bcm.edu	37	chr1	42048765	42048765	+	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	tggctcagggcttcggagtcGgtgatatggtcatcgaagga	8	10	16	7	3	2	1	2	1	0	0	5	4	2	3	0	6	0	2	0	6	2	2			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr1:42048765G>T	ENST00000372583.1	-	4	2589	c.1704C>A	c.(1702-1704)acC>acA	p.T568T	HIVEP3_ENST00000247584.5_Silent_p.T568T|HIVEP3_ENST00000429157.2_Silent_p.T568T|HIVEP3_ENST00000372584.1_Silent_p.T568T	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	568	No DNA binding activity or transactivation activity, but complete prevention of TRAF-dependent NF-Kappa-B activation; associates with TRAF2 and JUN. {ECO:0000250}.				positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T568T(1)		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)				CTTCGGAGTCGGTGATATGGT	0.587																																					p.T568T		Atlas-SNP	.											HIVEP3,NS,carcinoma,0,1	HIVEP3	235	.	1	Substitution - coding silent(1)	endometrium(1)	c.C1704A						PASS	.						49	52	51					1																	42048765		2203	4300	6503	SO:0001819	synonymous_variant	59269	exon4			GGAGTCGGTGATA	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.1704C>A	chr1.hg19:g.42048765G>T		109.0	1.0	.		94.0	5.0	.	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Silent	SNP	ENST00000372583.1	hg19	CCDS463.1																																																																																			.	.	.	none		0.587	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		T	42048765	G	T	42048765	2	4	159	1	0	0	0	0	0	0	0	1	7195	1103	39	4		4	HIVEP3	1	42048765	Silent	SNP	G	TCGA-DZ-6134-01A-11D-1961-08		42048765	207201856	1	9428											
POGZ	23126	hgsc.bcm.edu	37	chr1	151378756	151378756	+	Missense_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	ctgcgggtgagtgggggttgGtggtggggttgcagttgagg	3	11	24	3	1	0	2	0	2	0	0	0	2	0	2	0	8	2	4	0	8	0	3			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr1:151378756G>A	ENST00000271715.2	-	19	3069	c.2755C>T	c.(2755-2757)Cca>Tca	p.P919S	POGZ_ENST00000392723.1_Missense_Mutation_p.P866S|POGZ_ENST00000368863.2_Missense_Mutation_p.P824S|POGZ_ENST00000409503.1_Missense_Mutation_p.P910S|POGZ_ENST00000361398.3_Missense_Mutation_p.P866S|POGZ_ENST00000491586.1_Missense_Mutation_p.P875S|POGZ_ENST00000540984.1_Missense_Mutation_p.P281S|POGZ_ENST00000531094.1_Missense_Mutation_p.P857S	NM_001194937.1|NM_015100.3	NP_001181866.1|NP_055915.2	Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain	919	Pro-rich.				kinetochore assembly (GO:0051382)|mitotic sister chromatid cohesion (GO:0007064)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(10)|kidney(3)|large_intestine(10)|liver(2)|lung(11)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	47	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			GTGGGGGTTGGTGGTGGGGTT	0.592																																					p.P919S		Atlas-SNP	.											.	POGZ	211	.	0			c.C2755T						PASS	.						73	73	73					1																	151378756		2203	4300	6503	SO:0001583	missense	23126	exon19			GGGTTGGTGGTGG	AB007930	CCDS997.1, CCDS998.1, CCDS44222.1, CCDS44222.2, CCDS53365.1, CCDS53366.1	1q21.1	2013-07-22			ENSG00000143442	ENSG00000143442			18801	protein-coding gene	gene with protein product	"zinc finger protein 280E", "putative protein product of Nbla00003"	614787				10976766	Standard	NM_015100		Approved	KIAA0461, ZNF635m, ZNF280E	uc001eyd.2	Q7Z3K3	OTTHUMG00000012499	ENST00000271715.2:c.2755C>T	chr1.hg19:g.151378756G>A	ENSP00000271715:p.Pro919Ser	114.0	0.0	.		140.0	32.0	.	NM_015100	B4DTP8|B4DYL9|B7ZBY5|E9PM80|O75049|Q3LIC4|Q5SZS1|Q5SZS2|Q5SZS3|Q5SZS4|Q8TDZ7|Q9Y4X7	Missense_Mutation	SNP	ENST00000271715.2	hg19	CCDS997.1	.	.	.	.	.	.	.	.	.	.	G	11.49	1.653454	0.29425	.	.	ENSG00000143442	ENST00000392723;ENST00000271715;ENST00000361398;ENST00000368863;ENST00000409503;ENST00000531094;ENST00000540984;ENST00000491586	T;T;T;T;T;T;T;T	0.23552	5.88;5.91;5.88;5.84;5.89;5.88;1.9;5.37	5.87	3.95	0.45737	.	0.748779	0.12616	N	0.453449	T	0.04861	0.0131	N	0.08118	0	0.09310	N	1	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.04013	0.0;0.0;0.0;0.0;0.001;0.0	T	0.34527	-0.9825	10	0.45353	T	0.12	-1.4299	8.593	0.33699	0.0805:0.2988:0.6207:0.0	.	857;910;824;875;866;919	E9PM80;B7ZBY5;Q7Z3K3-5;Q7Z3K3-3;Q7Z3K3-2;Q7Z3K3	.;.;.;.;.;POGZ_HUMAN	S	866;919;866;824;910;857;281;875	ENSP00000376484:P866S;ENSP00000271715:P919S;ENSP00000354467:P866S;ENSP00000357856:P824S;ENSP00000386836:P910S;ENSP00000431259:P857S;ENSP00000443547:P281S;ENSP00000418408:P875S	ENSP00000271715:P919S	P	-	1	0	POGZ	149645380	0.165000	0.22948	0.788000	0.31933	0.966000	0.64601	0.747000	0.26290	1.446000	0.47643	0.655000	0.94253	CCA	.	.	.	none		0.592	POGZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034915.2	NM_207171		A	151378756	G	A	151378756	3	1	159	1	0	0	0	0	1	0	0	0	12193	1261	44	2	1481	2	POGZ	1	151378756	Missense_Mutation	SNP	G	TCGA-DZ-6134-01A-11D-1961-08	109329991	151378756	97871865	2	9429											
ACTA1	58	hgsc.bcm.edu	37	chr1	229568083	229568083	+	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	gtagtcggtgagatcgcggcCcgccaggtccaggcgcatga	7	6	16	12	5	0	2	0	2	0	1	3	3	1	2	3	4	0	2	3	4	1	1			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr1:229568083C>T	ENST00000366684.3	-	4	652	c.550G>A	c.(550-552)Ggc>Agc	p.G184S	ACTA1_ENST00000366683.2_Intron	NM_001100.3	NP_001091.1	P68133	ACTS_HUMAN	actin, alpha 1, skeletal muscle	184			G -> D (in NEM3; mild). {ECO:0000269|PubMed:10508519, ECO:0000269|PubMed:15236405}.		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)				AGATCGCGGCCCGCCAGGTCC	0.677																																					p.G184S		Atlas-SNP	.											.	ACTA1	65	.	0			c.G550A						PASS	.						38	37	38					1																	229568083		2203	4299	6502	SO:0001583	missense	58	exon4			CGCGGCCCGCCAG	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.550G>A	chr1.hg19:g.229568083C>T	ENSP00000355645:p.Gly184Ser	63.0	0.0	.		76.0	13.0	.	NM_001100	P02568|P99020|Q5T8M9	Missense_Mutation	SNP	ENST00000366684.3	hg19	CCDS1578.1	.	.	.	.	.	.	.	.	.	.	C	17.48	3.399571	0.62177	.	.	ENSG00000143632	ENST00000366684;ENST00000366682	D	0.99586	-6.23	4.58	3.67	0.42095	.	0.000000	0.85682	D	0.000000	D	0.99825	0.9922	H	0.99609	4.655	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	D	0.96775	0.9571	10	0.87932	D	0	.	12.6981	0.57016	0.0:0.9198:0.0:0.0802	.	184	P68133	ACTS_HUMAN	S	184;149	ENSP00000355645:G184S	ENSP00000355643:G149S	G	-	1	0	ACTA1	227634706	1.000000	0.71417	0.846000	0.33378	0.920000	0.55202	7.545000	0.82128	1.143000	0.42306	0.650000	0.86243	GGC	.	.	.	none		0.677	ACTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092781.1	NM_001100		T	229568083	C	T	229568083	3	4	159	1	0	0	0	0	1	0	0	0	191	623	22	2	599	2	ACTA1	1	229568083	Missense_Mutation	SNP	C	TCGA-DZ-6134-01A-11D-1961-08	78189327	229568083	19682538	3	9430											
PDIA6	10130	hgsc.bcm.edu	37	chr2	10927529	10927529	+	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	ccaatccccaacgcggtctcAagttcagactgggctccagc	9	7	9	16	2	2	1	2	0	1	1	5	1	4	1	4	2	2	2	4	2	3	1			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr2:10927529A>T	ENST00000272227.3	-	11	1182	c.1035T>A	c.(1033-1035)ctT>ctA	p.L345L	PDIA6_ENST00000404371.2_Silent_p.L397L|PDIA6_ENST00000404824.2_Silent_p.L393L|PDIA6_ENST00000381611.4_Silent_p.L350L|PDIA6_ENST00000540494.1_Silent_p.L342L	NM_001282707.1|NM_005742.2	NP_001269636.1|NP_005733.1	Q15084	PDIA6_HUMAN	protein disulfide isomerase family A, member 6	345					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)		ACGCGGTCTCAAGTTCAGACT	0.488																																					p.L345L	GBM(73;509 1219 34219 41343 41551)	Atlas-SNP	.											.	PDIA6	31	.	0			c.T1035A						PASS	.						81	83	82					2																	10927529		2203	4300	6503	SO:0001819	synonymous_variant	10130	exon11			GGTCTCAAGTTCA	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.1035T>A	chr2.hg19:g.10927529A>T		79.0	0.0	.		80.0	10.0	.	NM_005742	B3KY95|B5MCQ5|B7Z254|B7Z4M8|F8WA83|Q53RC7|Q6ZSH5|Q99778	Silent	SNP	ENST00000272227.3	hg19	CCDS1675.1																																																																																			.	.	.	none		0.488	PDIA6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206933.1	NM_005742		T	10927529	A	T	10927529	2	4	159	1	0	0	0	0	0	0	0	1	11679	117	5	5		5	PDIA6	2	10927529	Silent	SNP	A	TCGA-DZ-6134-01A-11D-1961-08		10927529	232271844	4	9431											
WNT10A	80326	hgsc.bcm.edu	37	chr2	219754883	219754883	+	Missense_Mutation	SNP	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	actggatgcactgcagcgtgGtaagggcctgagccatgggg	8	7	17	9	1	0	1	0	1	0	0	0	2	0	2	2	5	4	3	2	5	1	1			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr2:219754883G>A	ENST00000258411.3	+	3	1187	c.554G>A	c.(553-555)gGt>gAt	p.G185D		NM_025216.2	NP_079492.2	Q9GZT5	WN10A_HUMAN	wingless-type MMTV integration site family, member 10A	185					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)		CTGCAGCGTGGTAAGGGCCTG	0.672																																					p.G185D		Atlas-SNP	.											.	WNT10A	35	.	0			c.G554A						PASS	.						48	43	45					2																	219754883		2203	4300	6503	SO:0001583	missense	80326	exon3			AGCGTGGTAAGGG	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.554G>A	chr2.hg19:g.219754883G>A	ENSP00000258411:p.Gly185Asp	67.0	0.0	.		67.0	13.0	.	NM_025216	Q53S44|Q96TA7|Q9H7S8	Missense_Mutation	SNP	ENST00000258411.3	hg19	CCDS2426.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.760111	0.89932	.	.	ENSG00000135925	ENST00000258411	T	0.75821	-0.97	4.46	4.46	0.54185	.	0.408178	0.26328	N	0.025007	D	0.84165	0.5412	M	0.71581	2.175	0.80722	D	1	D	0.63880	0.993	D	0.64144	0.922	D	0.86269	0.1660	10	0.72032	D	0.01	.	16.6424	0.85129	0.0:0.0:1.0:0.0	.	185	Q9GZT5	WN10A_HUMAN	D	185	ENSP00000258411:G185D	ENSP00000258411:G185D	G	+	2	0	WNT10A	219463127	1.000000	0.71417	0.795000	0.32087	0.929000	0.56500	9.117000	0.94347	2.478000	0.83669	0.655000	0.94253	GGT	.	.	.	none		0.672	WNT10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256730.2	NM_025216		A	219754883	G	A	219754883	3	1	159	1	0	0	0	0	1	0	0	0	17394	1261	44	2	564	2	WNT10A	2	219754883	Missense_Mutation	SNP	G	TCGA-DZ-6134-01A-11D-1961-08	208827354	219754883	23444490	5	9432											
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-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr3:178936082G>A	ENST00000263967.3	+	10	1781	c.1624G>A	c.(1624-1626)Gaa>Aaa	p.E542K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	542	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> K (in CLOVE, KERSEB, CRC and BC; also found in glioblastoma multiforme and endometrial carcinoma; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N- terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|E -> Q (found in an endometrial carcinoma sample; unknown pathological significance). {ECO:0000269|PubMed:16322209}.|E -> V (in BC; unknown pathological significance). {ECO:0000269|PubMed:16353168}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E542K(545)|p.E542Q(10)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TCCTCTCTCTGAAATCACTGA	0.333	E542K(BT483_BREAST)|E542K(CAL51_BREAST)|E542K(HGC27_STOMACH)|E542K(IM95_STOMACH)|E542K(JHUEM1_ENDOMETRIUM)|E542K(NCIH1341_LUNG)|E542K(SW948_LARGE_INTESTINE)|E542K(T84_LARGE_INTESTINE)|E542K(VMCUB1_URINARY_TRACT)	57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.E542K	Colon(199;1504 1750 3362 26421 31210 32040)	Atlas-SNP	.		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	PIK3CA_ENST00000263967,NS,carcinoma,0,2	PIK3CA	8460	.	555	Substitution - Missense(555)	breast(176)|large_intestine(166)|urinary_tract(45)|endometrium(37)|skin(19)|lung(18)|stomach(16)|ovary(16)|thyroid(14)|upper_aerodigestive_tract(9)|central_nervous_system(7)|cervix(6)|liver(6)|oesophagus(5)|penis(4)|kidney(3)|soft_tissue(2)|haematopoietic_and_lymphoid_tissue(2)|prostate(2)|biliary_tract(1)|pituitary(1)	c.G1624A						PASS	.						56	56	56					3																	178936082		1809	4069	5878	SO:0001583	missense	5290	exon10			CTCTCTGAAATCA		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1624G>A	chr3.hg19:g.178936082G>A	ENSP00000263967:p.Glu542Lys	78.0	0.0	.		87.0	24.0	.	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	hg19	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	34	5.360420	0.95877	.	.	ENSG00000121879	ENST00000263967	T	0.62105	0.05	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69287	0.3094	L	0.41356	1.27	0.80722	D	1	D	0.65815	0.995	D	0.63192	0.912	T	0.60296	-0.7291	10	0.09843	T	0.71	-23.9623	20.0024	0.97423	0.0:0.0:1.0:0.0	.	542	P42336	PK3CA_HUMAN	K	542	ENSP00000263967:E542K	ENSP00000263967:E542K	E	+	1	0	PIK3CA	180418776	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAA	.	.	.	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	159	1	0	0	0	0	1	0	0	0	11920	1291	45	2	1658	2	PIK3CA	3	178936082	Missense_Mutation	SNP	G	TCGA-DZ-6134-01A-11D-1961-08		178936082	19086348	6	9433											
NPNT	255743	hgsc.bcm.edu	37	chr4	106859521	106859521	+	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	tgttgttaaaggacaaatacGgtgccagtgcccatcccctg	10	10	10	11	1	0	0	0	0	0	0	1	1	1	1	4	2	3	2	4	2	4	3			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr4:106859521G>T	ENST00000379987.2	+	5	665	c.449G>T	c.(448-450)cGg>cTg	p.R150L	NPNT_ENST00000427316.2_Missense_Mutation_p.R180L|NPNT_ENST00000305572.8_Missense_Mutation_p.R150L|NPNT_ENST00000506666.1_Missense_Mutation_p.R180L|NPNT_ENST00000514622.1_Missense_Mutation_p.R150L|NPNT_ENST00000453617.2_Missense_Mutation_p.R167L	NM_001033047.2	NP_001028219.1	Q6UXI9	NPNT_HUMAN	nephronectin	150	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)		GGACAAATACGGTGCCAGTGC	0.532																																					p.R180L		Atlas-SNP	.											.	NPNT	69	.	0			c.G539T						PASS	.						90	81	84					4																	106859521		2203	4300	6503	SO:0001583	missense	255743	exon6			AAATACGGTGCCA		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.449G>T	chr4.hg19:g.106859521G>T	ENSP00000369323:p.Arg150Leu	77.0	0.0	.		111.0	5.0	.	NM_001184691	A6NFT9|A8K1W4|B4DIT4|B4DYK3|B4E2H7|B4E3H2|D6RCA1|E9PCK8|E9PCQ1|E9PE64|E9PF04	Missense_Mutation	SNP	ENST00000379987.2	hg19	CCDS34046.1	.	.	.	.	.	.	.	.	.	.	G	17.65	3.443175	0.63067	.	.	ENSG00000168743	ENST00000504304;ENST00000379987;ENST00000453617;ENST00000427316;ENST00000514622;ENST00000305572;ENST00000506666;ENST00000503451	D;D;D;T;D;D;T;T	0.86865	-2.18;-2.18;-2.18;-1.05;-2.18;-2.18;-1.07;-0.22	5.22	4.37	0.52481	Epidermal growth factor-like (1);	0.052801	0.85682	D	0.000000	D	0.91764	0.7395	M	0.66506	2.035	0.58432	D	0.999998	D;D;D;D;D;D;D	0.71674	0.998;0.992;0.996;0.985;0.996;0.965;0.997	D;P;P;P;P;P;D	0.69654	0.954;0.86;0.903;0.86;0.903;0.826;0.965	D	0.91899	0.5530	10	0.52906	T	0.07	.	14.1773	0.65549	0.0729:0.0:0.9271:0.0	.	150;180;180;167;197;150;150	E9PF04;E9PE64;E9PCQ1;E9PCK8;D6RH31;Q6UXI9-2;Q6UXI9	.;.;.;.;.;.;NPNT_HUMAN	L	46;150;167;180;150;150;180;197	ENSP00000426951:R46L;ENSP00000369323:R150L;ENSP00000402884:R167L;ENSP00000389252:R180L;ENSP00000422044:R150L;ENSP00000302557:R150L;ENSP00000422474:R180L;ENSP00000426146:R197L	ENSP00000302557:R150L	R	+	2	0	NPNT	107078970	1.000000	0.71417	0.298000	0.25002	0.165000	0.22458	6.341000	0.72977	1.325000	0.45301	0.655000	0.94253	CGG	.	.	.	none		0.532	NPNT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364083.1	NM_198278		T	106859521	G	T	106859521	3	4	159	1	0	0	0	0	1	0	0	0	10597	1116	39	4	616	4	NPNT	4	106859521	Missense_Mutation	SNP	G	TCGA-DZ-6134-01A-11D-1961-08		106859521	84294755	7	9434											
CRIP3	401262	hgsc.bcm.edu	37	chr6	43275462	43275462	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggattgtacaagtaggagccTacaccaccaatgttcacccc	12	8	8	13	0	1	0	1	0	0	0	1	2	1	2	5	2	3	3	5	2	5	5			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr6:43275462T>C	ENST00000274990.4	-	4	220	c.216A>G	c.(214-216)gtA>gtG	p.V72V	ZNF318_ENST00000607252.1_5'UTR|CRIP3_ENST00000372569.3_Silent_p.V72V			Q6Q6R5	CRIP3_HUMAN	cysteine-rich protein 3	72					T cell proliferation (GO:0042098)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)			AGTAGGAGCCTACACCACCAA	0.627																																					p.V72V		Atlas-SNP	.											.	CRIP3	30	.	0			c.A216G						PASS	.						45	48	47					6																	43275462		2203	4300	6503	SO:0001819	synonymous_variant	401262	exon4			GGAGCCTACACCA	AY555741	CCDS4894.2	6p21	2008-02-05			ENSG00000146215	ENSG00000146215			17751	protein-coding gene	gene with protein product						15380775	Standard	NM_206922		Approved	TLP-A, bA480N24.2, TLP	uc003ouu.1	Q6Q6R5	OTTHUMG00000014727	ENST00000274990.4:c.216A>G	chr6.hg19:g.43275462T>C		90.0	0.0	.		97.0	18.0	.	NM_206922	A2A436|Q5T043|Q6Q6R4|Q6Q6R6|Q6Q6R7	Silent	SNP	ENST00000274990.4	hg19		.	.	.	.	.	.	.	.	.	.	T	7.040	0.562412	0.13498	.	.	ENSG00000146215	ENST00000416431	.	.	.	5.52	3.63	0.41609	.	.	.	.	.	T	0.33323	0.0859	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.30592	-0.9973	4	.	.	.	-35.039	4.1803	0.10372	0.1604:0.5979:0.1554:0.0862	.	.	.	.	G	20	.	.	R	-	1	2	CRIP3	43383440	0.290000	0.24343	1.000000	0.80357	0.744000	0.42396	-0.819000	0.04462	1.470000	0.48102	-0.132000	0.14878	AGG	.	.	.	none		0.627	CRIP3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000313968.1			C	43275462	T	C	43275462	2	2	159	1	0	0	0	0	0	0	0	1	3878	1509	53	3		3	CRIP3	6	43275462	Silent	SNP	T	TCGA-DZ-6134-01A-11D-1961-08		43275462	127839605	8	9435											
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-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr6:136599912G>T	ENST00000531224.1	-	4	359	c.107C>A	c.(106-108)tCt>tAt	p.S36Y	BCLAF1_ENST00000530767.1_Missense_Mutation_p.S36Y|BCLAF1_ENST00000527536.1_Missense_Mutation_p.S36Y|BCLAF1_ENST00000527759.1_Intron|BCLAF1_ENST00000353331.4_Intron|BCLAF1_ENST00000392348.2_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	203	.	0			c.C107A						PASS	.						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	chr6.hg19:g.136599912G>T	ENSP00000435210:p.Ser36Tyr	29.0	0.0	.		47.0	6.0	.	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	hg19	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	159	1	0	0	0	0	1	0	0	0	1383	942	33	4	2695	4	BCLAF1	6	136599912	Missense_Mutation	SNP	G	TCGA-DZ-6134-01A-11D-1961-08	93324450	136599912	34515155	9	9436											
FZD1	8321	hgsc.bcm.edu	37	chr7	90894779	90894779	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccctgtgcgagcgcgcgcGccagggctgcgaggcgctca	4	5	16	16	7	1	0	1	0	0	0	2	2	2	0	2	2	3	2	2	2	0	0			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr7:90894779G>A	ENST00000287934.2	+	1	997	c.584G>A	c.(583-585)cGc>cAc	p.R195H		NM_003505.1	NP_003496.1	Q9UP38	FZD1_HUMAN	frizzled class receptor 1	195	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				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)			GAGCGCGCGCGCCAGGGCTGC	0.672																																					p.R195H		Atlas-SNP	.											.	FZD1	64	.	0			c.G584A						PASS	.						52	58	56					7																	90894779		2199	4299	6498	SO:0001583	missense	8321	exon1			GCGCGCGCCAGGG	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.584G>A	chr7.hg19:g.90894779G>A	ENSP00000287934:p.Arg195His	119.0	0.0	.		169.0	33.0	.	NM_003505	A4D1E8|O94815|Q549T8	Missense_Mutation	SNP	ENST00000287934.2	hg19	CCDS5620.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.936514	0.92458	.	.	ENSG00000157240	ENST00000287934	T	0.76839	-1.05	4.69	4.69	0.59074	Frizzled domain (5);	0.000000	0.64402	D	0.000003	D	0.90407	0.6997	H	0.94542	3.55	0.80722	D	1	D	0.65815	0.995	P	0.61132	0.884	D	0.93351	0.6718	10	0.87932	D	0	.	17.7914	0.88553	0.0:0.0:1.0:0.0	.	195	Q9UP38	FZD1_HUMAN	H	195	ENSP00000287934:R195H	ENSP00000287934:R195H	R	+	2	0	FZD1	90732715	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.543000	0.73874	2.430000	0.82344	0.561000	0.74099	CGC	.	.	.	none		0.672	FZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059367.2	NM_003505		A	90894779	G	A	90894779	3	1	159	1	0	0	0	0	1	0	0	0	6135	1087	38	1	586	1	FZD1	7	90894779	Missense_Mutation	SNP	G	TCGA-DZ-6134-01A-11D-1961-08		90894779	68243884	10	9437											
PTCD1	26024	hgsc.bcm.edu	37	chr7	99022814	99022814	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagaccactgtagggggaacGgccccgggggtcaggaggtt	8	5	19	9	2	1	1	1	0	0	1	1	4	1	3	3	7	1	2	3	7	2	2			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr7:99022814G>A	ENST00000292478.4	-	6	1591	c.1341C>T	c.(1339-1341)gcC>gcT	p.A447A	ATP5J2-PTCD1_ENST00000413834.1_Silent_p.A496A|PTCD1_ENST00000555673.1_Silent_p.A496A	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	447					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)			TAGGGGGAACGGCCCCGGGGG	0.647																																					p.A496A		Atlas-SNP	.											.	.	.	.	0			c.C1488T						PASS	.						58	61	60					7																	99022814		2203	4300	6503	SO:0001819	synonymous_variant	100526740	exon7			GGGAACGGCCCCG	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.1341C>T	chr7.hg19:g.99022814G>A		136.0	0.0	.		149.0	50.0	.	NM_001198879	Q3ZB78|Q66K60|Q9UDV2	Silent	SNP	ENST00000292478.4	hg19	CCDS34691.1																																																																																			.	.	.	none		0.647	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1	NM_015545		A	99022814	G	A	99022814	2	1	159	1	0	0	0	0	0	0	0	1	12737	1103	39	1		1	PTCD1	7	99022814	Silent	SNP	G	TCGA-DZ-6134-01A-11D-1961-08	8128035	99022814	60115849	11	9438											
SERPINE1	5054	hgsc.bcm.edu	37	chr7	100780346	100780346	+	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	gacagacccttcctctttgtGgtccggcacaaccccacagg	8	8	9	16	1	1	1	0	0	1	1	3	2	3	1	5	3	1	1	5	3	1	2			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr7:100780346G>C	ENST00000223095.4	+	8	1309	c.1152G>C	c.(1150-1152)gtG>gtC	p.V384V	SERPINE1_ENST00000445463.2_Silent_p.V369V	NM_000602.4	NP_000593.1	P05121	PAI1_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1	384					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to lipopolysaccharide (GO:0071222)|chronological cell aging (GO:0001300)|defense response to Gram-negative bacterium (GO:0050829)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|gene expression (GO:0010467)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell migration (GO:0030336)|negative regulation of endopeptidase activity (GO:0010951)|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 fibrinolysis (GO:0051918)|negative regulation of plasminogen activation (GO:0010757)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell-matrix adhesion (GO:2000098)|negative regulation of vascular wound healing (GO:0061044)|negative regulation of wound healing (GO:0061045)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of leukotriene production involved in inflammatory response (GO:0035491)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of receptor activity (GO:0010469)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(3)	20	Lung NSC(181;0.136)|all_lung(186;0.182)				Alteplase(DB00009)|Anistreplase(DB00029)|Drotrecogin alfa(DB00055)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)	TCCTCTTTGTGGTCCGGCACA	0.552																																					p.V384V		Atlas-SNP	.											.	SERPINE1	60	.	0			c.G1152C						PASS	.						139	117	125					7																	100780346		2203	4300	6503	SO:0001819	synonymous_variant	5054	exon8			CTTTGTGGTCCGG	M16006	CCDS5711.1	7q22.1	2014-02-18	2005-08-18		ENSG00000106366	ENSG00000106366		"Serine (or cysteine) peptidase inhibitors"	8583	protein-coding gene	gene with protein product	"plasminogen activator inhibitor, type I"	173360	"serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1"	PLANH1, PAI1		3097076, 2891140, 24172014	Standard	NM_000602		Approved	PAI	uc003uxt.4	P05121	OTTHUMG00000157107	ENST00000223095.4:c.1152G>C	chr7.hg19:g.100780346G>C		202.0	0.0	.		203.0	27.0	.	NM_000602	B7Z4S0|F8WD53	Silent	SNP	ENST00000223095.4	hg19	CCDS5711.1																																																																																			.	.	.	none		0.552	SERPINE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347458.1	NM_000602		C	100780346	G	C	100780346	2	2	159	1	0	0	0	0	0	0	0	1	14124	1335	47	4		4	SERPINE1	7	100780346	Silent	SNP	G	TCGA-DZ-6134-01A-11D-1961-08	1757532	100780346	58358317	12	9439											
HSDL2	84263	hgsc.bcm.edu	37	chr9	115181173	115181173	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taagtatggtatgtctatgtAtgtgcttggaatggcagaag	11	14	13	3	0	1	1	0	0	1	1	1	2	1	2	0	3	1	5	0	3	7	6			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr9:115181173A>G	ENST00000398805.3	+	6	760	c.533A>G	c.(532-534)tAt>tGt	p.Y178C	HSDL2_ENST00000398803.1_Missense_Mutation_p.Y105C|HSDL2_ENST00000488101.1_3'UTR|HSDL2_ENST00000262542.7_Missense_Mutation_p.Y58C|HSDL2_ENST00000539114.1_Intron	NM_032303.4	NP_115679.2	Q6YN16	HSDL2_HUMAN	hydroxysteroid dehydrogenase like 2	178						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						ATGTCTATGTATGTGCTTGGA	0.274																																					p.Y178C		Atlas-SNP	.											.	HSDL2	24	.	0			c.A533G						PASS	.						146	133	137					9																	115181173		1844	4082	5926	SO:0001583	missense	84263	exon6			CTATGTATGTGCT	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.533A>G	chr9.hg19:g.115181173A>G	ENSP00000381785:p.Tyr178Cys	70.0	0.0	.		83.0	6.0	.	NM_032303	A8K1L4|A8K8X1|A8MSV3|Q658M8|Q9BT58	Missense_Mutation	SNP	ENST00000398805.3	hg19	CCDS43864.1	.	.	.	.	.	.	.	.	.	.	A	4.417	0.077003	0.08485	.	.	ENSG00000119471	ENST00000398805;ENST00000398803;ENST00000262542	D;D;T	0.89810	-2.23;-2.57;2.17	5.54	4.61	0.57282	Short-chain dehydrogenase/reductase, conserved site (1);NAD(P)-binding domain (1);	0.043003	0.85682	N	0.000000	T	0.66237	0.2769	N	0.00611	-1.325	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.67364	-0.5689	10	0.02654	T	1	.	14.288	0.66258	0.0732:0.0:0.9268:0.0	.	105;178	Q6YN16-2;Q6YN16	.;HSDL2_HUMAN	C	178;105;58	ENSP00000381785:Y178C;ENSP00000381783:Y105C;ENSP00000262542:Y58C	ENSP00000262542:Y58C	Y	+	2	0	HSDL2	114220994	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.348000	0.79366	1.462000	0.47948	-0.321000	0.08615	TAT	.	.	.	none		0.274	HSDL2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053681.1	NM_032303		G	115181173	A	G	115181173	3	3	159	1	0	0	0	0	1	0	0	0	7401	449	16	3	555	3	HSDL2	9	115181173	Missense_Mutation	SNP	A	TCGA-DZ-6134-01A-11D-1961-08		115181173	26032258	13	9440											
ALAD	210	hgsc.bcm.edu	37	chr9	116151742	116151742	+	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	tcctttacctcccgcacgatGtccaggtagggcattcccgg	6	10	10	15	3	0	0	0	0	0	0	4	1	4	0	5	3	1	3	5	3	2	4			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr9:116151742G>A	ENST00000409155.3	-	10	973	c.777C>T	c.(775-777)gaC>gaT	p.D259D	ALAD_ENST00000482001.1_5'Flank|ALAD_ENST00000277315.5_Silent_p.D242D	NM_000031.5	NP_000022.3	P13716	HEM2_HUMAN	aminolevulinate dehydratase	259					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)	CCCGCACGATGTCCAGGTAGG	0.567																																					p.D259D		Atlas-SNP	.											.	ALAD	36	.	0			c.C777T						PASS	.						116	110	112					9																	116151742		2203	4300	6503	SO:0001819	synonymous_variant	210	exon10			CACGATGTCCAGG	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.777C>T	chr9.hg19:g.116151742G>A		168.0	0.0	.		112.0	26.0	.	NM_000031	A8K375|B2R6F2|Q16870|Q16871|Q9BVQ9	Silent	SNP	ENST00000409155.3	hg19	CCDS6794.2																																																																																			.	.	.	none		0.567	ALAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053724.3	NM_001003945		A	116151742	G	A	116151742	2	1	159	1	0	0	0	0	0	0	0	1	483	1368	48	2		2	ALAD	9	116151742	Silent	SNP	G	TCGA-DZ-6134-01A-11D-1961-08	970569	116151742	25061689	14	9441											
CAMK1D	57118	hgsc.bcm.edu	37	chr10	12595265	12595265	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttagctgaagagaaggcaaCtggcaagctctttgctgtga	11	11	12	7	0	1	3	0	2	1	1	1	4	1	3	0	2	4	5	0	2	5	3			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr10:12595265C>T	ENST00000378847.3	+	2	471	c.134C>T	c.(133-135)aCt>aTt	p.T45I	CAMK1D_ENST00000378845.1_Missense_Mutation_p.T45I|CAMK1D_ENST00000487696.1_Intron	NM_153498.2	NP_705718.1	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID	45	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				inflammatory response (GO:0006954)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis (GO:0050766)|positive regulation of respiratory burst (GO:0060267)|regulation of dendrite development (GO:0050773)|regulation of granulocyte chemotaxis (GO:0071622)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)	16				GBM - Glioblastoma multiforme(1;3.16e-05)		GAGAAGGCAACTGGCAAGCTC	0.468																																					p.T45I		Atlas-SNP	.											.	CAMK1D	99	.	0			c.C134T						PASS	.						162	150	154					10																	12595265		2203	4300	6503	SO:0001583	missense	57118	exon2			AGGCAACTGGCAA	AF286366	CCDS7091.1, CCDS7092.1	10p13	2003-11-05			ENSG00000183049	ENSG00000183049			19341	protein-coding gene	gene with protein product		607957				11050006	Standard	XM_006717481		Approved	CKLiK	uc001ilo.3	Q8IU85	OTTHUMG00000017683	ENST00000378847.3:c.134C>T	chr10.hg19:g.12595265C>T	ENSP00000368124:p.Thr45Ile	205.0	0.0	.		189.0	35.0	.	NM_153498	B0YIY0|Q9HD31	Missense_Mutation	SNP	ENST00000378847.3	hg19	CCDS7091.1	.	.	.	.	.	.	.	.	.	.	C	14.34	2.507699	0.44558	.	.	ENSG00000183049	ENST00000378847;ENST00000378845	T;T	0.49139	0.79;0.79	5.14	4.23	0.50019	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.055122	0.64402	D	0.000001	T	0.57888	0.2084	M	0.89785	3.06	0.45648	D	0.99857	B;B	0.19073	0.033;0.011	B;B	0.23716	0.048;0.047	T	0.62586	-0.6823	10	0.87932	D	0	-12.4567	13.7457	0.62874	0.0:0.6876:0.3124:0.0	.	45;45	Q8IU85;Q5SQQ7	KCC1D_HUMAN;.	I	45	ENSP00000368124:T45I;ENSP00000368122:T45I	ENSP00000368122:T45I	T	+	2	0	CAMK1D	12635271	1.000000	0.71417	0.981000	0.43875	0.946000	0.59487	3.132000	0.50523	1.127000	0.42034	0.561000	0.74099	ACT	.	.	.	none		0.468	CAMK1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046820.1	NM_020397		T	12595265	C	T	12595265	3	4	159	1	0	0	0	0	1	0	0	0	2599	565	20	2	140	2	CAMK1D	10	12595265	Missense_Mutation	SNP	C	TCGA-DZ-6134-01A-11D-1961-08		12595265	122939482	15	9442											
SLC43A1	8501	hgsc.bcm.edu	37	chr11	57261478	57261478	+	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	acactcactctcaggaaggtTttctgaggtgccccgaacat	10	10	9	12	1	3	1	2	1	2	0	4	3	3	2	2	3	2	1	2	3	2	2			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr11:57261478T>A	ENST00000278426.3	-	8	1214	c.859A>T	c.(859-861)Aac>Tac	p.N287Y	SLC43A1_ENST00000528450.1_Missense_Mutation_p.N287Y|SLC43A1_ENST00000533515.1_5'UTR	NM_003627.5	NP_003618.1			solute carrier family 43 (amino acid system L transporter), member 1											breast(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	19						TCAGGAAGGTTTTCTGAGGTG	0.567											OREG0020651	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N287Y		Atlas-SNP	.											.	SLC43A1	48	.	0			c.A859T						PASS	.						74	65	68					11																	57261478		2201	4296	6497	SO:0001583	missense	8501	exon8			GAAGGTTTTCTGA	AF045584	CCDS7958.1	11q12.1	2013-07-17	2013-07-17	2003-09-12	ENSG00000149150	ENSG00000149150		"Solute carriers"	9225	protein-coding gene	gene with protein product		603733	"prostate cancer overexpressed gene 1"	POV1		9255310, 9722952	Standard	NM_003627		Approved	R00504, PB39	uc001nkk.3	O75387	OTTHUMG00000167030	ENST00000278426.3:c.859A>T	chr11.hg19:g.57261478T>A	ENSP00000278426:p.Asn287Tyr	74.0	0.0	.	1021	62.0	13.0	.	NM_001198810		Missense_Mutation	SNP	ENST00000278426.3	hg19	CCDS7958.1	.	.	.	.	.	.	.	.	.	.	t	15.67	2.901506	0.52227	.	.	ENSG00000149150	ENST00000278426;ENST00000528450;ENST00000533066	T;T;T	0.58060	0.36;0.36;1.47	5.57	-2.09	0.07232	Major facilitator superfamily domain, general substrate transporter (1);	1.826000	0.01877	N	0.037616	T	0.36524	0.0970	N	0.14661	0.345	0.09310	N	1	P	0.48911	0.917	P	0.46419	0.516	T	0.21965	-1.0230	10	0.35671	T	0.21	0.3003	1.7106	0.02891	0.1305:0.2328:0.1338:0.5029	.	287	O75387	LAT3_HUMAN	Y	287;287;256	ENSP00000278426:N287Y;ENSP00000435673:N287Y;ENSP00000435647:N256Y	ENSP00000278426:N287Y	N	-	1	0	SLC43A1	57018054	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	0.234000	0.17930	-0.008000	0.14320	0.459000	0.35465	AAC	.	.	.	none		0.567	SLC43A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392541.1	NM_003627		A	57261478	T	A	57261478	3	1	159	1	0	0	0	0	1	0	0	0	14645	1841	64	5	852	5	SLC43A1	11	57261478	Missense_Mutation	SNP	T	TCGA-DZ-6134-01A-11D-1961-08		57261478	77745038	16	9443											
USP35	57558	hgsc.bcm.edu	37	chr11	77921303	77921303	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtggagctgagccaagggcCgtgctacctcatcctcacac	8	7	12	14	1	2	1	2	1	0	0	3	2	3	2	4	3	4	2	4	3	2	1			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr11:77921303C>T	ENST00000529308.1	+	10	2663	c.2402C>T	c.(2401-2403)cCg>cTg	p.P801L	USP35_ENST00000530267.1_Missense_Mutation_p.P369L|USP35_ENST00000526425.1_Missense_Mutation_p.P532L|USP35_ENST00000441408.2_Missense_Mutation_p.P387L|USP35_ENST00000530535.1_3'UTR	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	801	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)			AGCCAAGGGCCGTGCTACCTC	0.622																																					p.P801L		Atlas-SNP	.											.	USP35	179	.	0			c.C2402T						PASS	.						86	98	94					11																	77921303		2167	4250	6417	SO:0001583	missense	57558	exon10			AAGGGCCGTGCTA	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.2402C>T	chr11.hg19:g.77921303C>T	ENSP00000431876:p.Pro801Leu	165.0	0.0	.		112.0	8.0	.	NM_020798		Missense_Mutation	SNP	ENST00000529308.1	hg19	CCDS41693.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.572013	0.86542	.	.	ENSG00000118369	ENST00000530267;ENST00000529308;ENST00000441408;ENST00000526425	D;D;D;D	0.88975	-2.45;-2.45;-2.45;-2.45	4.35	4.35	0.52113	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.64402	D	0.000019	D	0.96457	0.8844	H	0.96633	3.855	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.98113	1.0421	10	0.87932	D	0	-41.8622	17.0748	0.86583	0.0:1.0:0.0:0.0	.	801;387	Q9P2H5;E7EWV7	UBP35_HUMAN;.	L	369;801;387;532	ENSP00000435468:P369L;ENSP00000431876:P801L;ENSP00000400825:P387L;ENSP00000434942:P532L	ENSP00000400825:P387L	P	+	2	0	USP35	77598951	1.000000	0.71417	0.993000	0.49108	0.817000	0.46193	7.600000	0.82769	2.257000	0.74773	0.436000	0.28706	CCG	.	.	.	none		0.622	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527		T	77921303	C	T	77921303	3	4	159	1	0	0	0	0	1	0	0	0	17078	652	23	1	2436	1	USP35	11	77921303	Missense_Mutation	SNP	C	TCGA-DZ-6134-01A-11D-1961-08	20659825	77921303	57085213	17	9444											
PCF11	51585	hgsc.bcm.edu	37	chr11	82877713	82877713	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagaaaactggcaaagttccAagtctgccaaaagatggaaa	18	7	9	7	0	1	2	0	0	1	2	2	3	2	3	2	2	2	2	2	2	8	2			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr11:82877713A>G	ENST00000298281.4	+	5	2226	c.1774A>G	c.(1774-1776)Aag>Gag	p.K592E		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	592					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						GCAAAGTTCCAAGTCTGCCAA	0.368																																					p.K592E		Atlas-SNP	.											.	PCF11	220	.	0			c.A1774G						PASS	.						71	71	71					11																	82877713		1781	3947	5728	SO:0001583	missense	51585	exon5			AGTTCCAAGTCTG	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.1774A>G	chr11.hg19:g.82877713A>G	ENSP00000298281:p.Lys592Glu	134.0	0.0	.		156.0	29.0	.	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	hg19	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	A	15.75	2.926781	0.52759	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.49720	1.75;0.79;0.77	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000007	T	0.58293	0.2112	L	0.32530	0.975	0.49687	D	0.999816	D;D	0.69078	0.997;0.993	D;D	0.75020	0.985;0.971	T	0.54801	-0.8239	9	.	.	.	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	592;592	E9PQ01;O94913	.;PCF11_HUMAN	E	592	ENSP00000298281:K592E;ENSP00000434540:K592E;ENSP00000431567:K592E	.	K	+	1	0	PCF11	82555361	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.414000	0.73318	2.326000	0.78906	0.533000	0.62120	AAG	.	.	.	none		0.368	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		G	82877713	A	G	82877713	3	3	159	1	0	0	0	0	1	0	0	0	11580	131	5	3	1792	3	PCF11	11	82877713	Missense_Mutation	SNP	A	TCGA-DZ-6134-01A-11D-1961-08	4956410	82877713	52128803	18	9445											
ATF7	11016	hgsc.bcm.edu	37	chr12	53910964	53910964	+	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	gtggggtcatgattacatgcGattgtatcggcatgctcagt	8	13	13	7	2	2	1	2	1	0	0	3	2	2	1	0	3	3	3	0	3	2	3			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr12:53910964G>A	ENST00000548446.2	-	12	1554	c.1442C>T	c.(1441-1443)tCg>tTg	p.S481L	RP11-793H13.3_ENST00000548347.1_RNA|ATF7_ENST00000456903.4_Missense_Mutation_p.S470L|ATF7_ENST00000420353.2_Missense_Mutation_p.S470L|RP11-793H13.10_ENST00000591834.1_Intron|ATF7_ENST00000415113.1_Missense_Mutation_p.S449L|ATF7_ENST00000546661.1_5'UTR|ATF7_ENST00000328463.7_Missense_Mutation_p.S481L			P17544	ATF7_HUMAN	activating transcription factor 7	481	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)	GATTACATGCGATTGTATCGG	0.587																																					p.S470L		Atlas-SNP	.											.	ATF7	51	.	0			c.C1409T						PASS	.						112	109	110					12																	53910964		2075	4216	6291	SO:0001583	missense	11016	exon12			ACATGCGATTGTA	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.1442C>T	chr12.hg19:g.53910964G>A	ENSP00000449938:p.Ser481Leu	171.0	0.0	.		184.0	36.0	.	NM_006856	A5D6Y4|B2RMP1|B4DQL4|Q13814|Q8IVR8|Q9UD83	Missense_Mutation	SNP	ENST00000548446.2	hg19		.	.	.	.	.	.	.	.	.	.	G	24.4	4.522447	0.85600	.	.	ENSG00000170653	ENST00000548446;ENST00000328463;ENST00000306727;ENST00000415113;ENST00000420353;ENST00000456903	T;T;T;T;T	0.56776	0.47;0.47;0.44;0.49;0.49	4.47	4.47	0.54385	.	0.132552	0.52532	D	0.000064	T	0.43233	0.1238	L	0.53249	1.67	0.54753	D	0.999981	P;P;B	0.46327	0.876;0.804;0.0	B;B;B	0.28553	0.091;0.042;0.001	T	0.58797	-0.7573	10	0.87932	D	0	-16.9898	16.5074	0.84276	0.0:0.0:1.0:0.0	.	449;470;481	P17544-2;B2RMP1;P17544	.;.;ATF7_HUMAN	L	481;481;294;449;470;470	ENSP00000449938:S481L;ENSP00000329212:S481L;ENSP00000404880:S449L;ENSP00000399465:S470L;ENSP00000387406:S470L	ENSP00000304187:S294L	S	-	2	0	ATF7	52197231	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	6.990000	0.76225	2.513000	0.84729	0.456000	0.33151	TCG	.	.	.	none		0.587	ATF7-007	KNOWN	NMD_exception|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000406302.2	NM_001130059		A	53910964	G	A	53910964	3	1	159	1	0	0	0	0	1	0	0	0	1086	1059	37	1	46	1	ATF7	12	53910964	Missense_Mutation	SNP	G	TCGA-DZ-6134-01A-11D-1961-08		53910964	79940931	19	9446											
SMARCC2	6601	hgsc.bcm.edu	37	chr12	56558339	56558339	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcggggaggttaatactgaTggagtcagctagactaccaa	13	8	13	7	1	1	2	1	1	0	1	1	4	1	4	1	4	4	2	1	4	5	4			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr12:56558339T>C	ENST00000267064.4	-	27	3402	c.3316A>G	c.(3316-3318)Atc>Gtc	p.I1106V	SMARCC2_ENST00000347471.4_Intron|SMARCC2_ENST00000550164.1_Missense_Mutation_p.I1137V|SMARCC2_ENST00000394023.3_Intron|RP11-977G19.5_ENST00000553176.1_RNA	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	1106	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)			TTAATACTGATGGAGTCAGCT	0.587																																					p.I1106V		Atlas-SNP	.											.	SMARCC2	212	.	0			c.A3316G						PASS	.						103	89	94					12																	56558339		2203	4300	6503	SO:0001583	missense	6601	exon27			TACTGATGGAGTC	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.3316A>G	chr12.hg19:g.56558339T>C	ENSP00000267064:p.Ile1106Val	92.0	0.0	.		120.0	42.0	.	NM_003075	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Missense_Mutation	SNP	ENST00000267064.4	hg19	CCDS8907.1	.	.	.	.	.	.	.	.	.	.	T	10.26	1.300338	0.23650	.	.	ENSG00000139613	ENST00000550164;ENST00000267064	T;T	0.44881	0.91;0.94	5.28	3.99	0.46301	.	0.593150	0.16689	N	0.203617	T	0.20577	0.0495	N	0.08118	0	0.25483	N	0.987717	B	0.02656	0.0	B	0.01281	0.0	T	0.19811	-1.0294	9	.	.	.	-5.712	7.8812	0.29623	0.0:0.1805:0.0:0.8195	.	1106	Q8TAQ2	SMRC2_HUMAN	V	1137;1106	ENSP00000449396:I1137V;ENSP00000267064:I1106V	.	I	-	1	0	SMARCC2	54844606	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.211000	0.32382	0.832000	0.34804	0.460000	0.39030	ATC	.	.	.	none		0.587	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1			C	56558339	T	C	56558339	3	2	159	1	0	0	0	0	1	0	0	0	14789	1464	51	3	336	3	SMARCC2	12	56558339	Missense_Mutation	SNP	T	TCGA-DZ-6134-01A-11D-1961-08	2647375	56558339	77293556	20	9447											
BTBD6	90135	hgsc.bcm.edu	37	chr14	105716270	105716270	+	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	gatcattgtcactcgggaggCcctcaacaccaaagaggcgg	11	6	12	12	2	3	1	3	0	0	1	4	3	3	2	2	4	1	0	2	4	2	1			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr14:105716270C>T	ENST00000392554.3	+	4	1016	c.719C>T	c.(718-720)gCc>gTc	p.A240V	BRF1_ENST00000546474.1_Intron|BRF1_ENST00000327359.3_Intron|BRF1_ENST00000440513.3_Intron|BTBD6_ENST00000463376.2_Missense_Mutation_p.A165V|BRF1_ENST00000379932.4_5'Flank|BTBD6_ENST00000536364.1_Missense_Mutation_p.A240V|BRF1_ENST00000551787.1_5'Flank|BRF1_ENST00000379937.2_Intron|BRF1_ENST00000392557.4_5'Flank|BTBD6_ENST00000327471.3_Missense_Mutation_p.A165V|BRF1_ENST00000446501.2_5'Flank			Q96KE9	BTBD6_HUMAN	BTB (POZ) domain containing 6	240						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)		ACTCGGGAGGCCCTCAACACC	0.617																																					p.A240V		Atlas-SNP	.											.	BTBD6	24	.	0			c.C719T						PASS	.						30	27	28					14																	105716270		2201	4298	6499	SO:0001583	missense	90135	exon5			GGGAGGCCCTCAA	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.719C>T	chr14.hg19:g.105716270C>T	ENSP00000376337:p.Ala240Val	54.0	0.0	.		44.0	7.0	.	NM_033271	Q8IVQ7|Q9BR94	Missense_Mutation	SNP	ENST00000392554.3	hg19	CCDS10002.2	.	.	.	.	.	.	.	.	.	.	C	15.73	2.920172	0.52653	.	.	ENSG00000184887	ENST00000536364;ENST00000537513;ENST00000392554;ENST00000463376;ENST00000327471	T;T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.38;-0.38	5.07	5.07	0.68467	BTB/Kelch-associated (2);	0.118294	0.64402	D	0.000020	T	0.66218	0.2767	L	0.39898	1.24	0.48511	D	0.999668	B	0.29341	0.242	B	0.39935	0.314	T	0.69011	-0.5258	10	0.87932	D	0	-31.8506	15.9457	0.79792	0.0:1.0:0.0:0.0	.	240	Q96KE9	BTBD6_HUMAN	V	240;240;240;165;165	ENSP00000443091:A240V;ENSP00000446223:A240V;ENSP00000376337:A240V;ENSP00000418150:A165V;ENSP00000329361:A165V	ENSP00000329361:A165V	A	+	2	0	BTBD6	104787315	1.000000	0.71417	1.000000	0.80357	0.093000	0.18481	7.655000	0.83696	2.331000	0.79229	0.563000	0.77884	GCC	.	.	.	none		0.617	BTBD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074556.4			T	105716270	C	T	105716270	3	4	159	1	0	0	0	0	1	0	0	0	1547	739	26	2	733	2	BTBD6	14	105716270	Missense_Mutation	SNP	C	TCGA-DZ-6134-01A-11D-1961-08		105716270	1633270	21	9448											
FAM86A	196483	hgsc.bcm.edu	37	chr16	5140457	5140457	+	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	tagtgaagactgccgggttcTcgatggcccattctgcaagg	8	10	13	10	2	2	2	0	1	2	1	3	3	2	2	2	3	2	2	2	3	3	3			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr16:5140457T>A	ENST00000427587.4	-	5	520	c.452A>T	c.(451-453)gAg>gTg	p.E151V	FAM86A_ENST00000458008.4_Missense_Mutation_p.E117V|FAM86A_ENST00000587133.1_Missense_Mutation_p.E90V	NM_201400.2	NP_958802.1	Q96G04	FA86A_HUMAN	family with sequence similarity 86, member A	151						cytoplasm (GO:0005737)				endometrium(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	12						TGCCGGGTTCTCGATGGCCCA	0.642																																					p.E151V		Atlas-SNP	.											.	FAM86A	32	.	0			c.A452T						PASS	.						86	84	85					16																	5140457		2197	4300	6497	SO:0001583	missense	196483	exon5			GGGTTCTCGATGG	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.452A>T	chr16.hg19:g.5140457T>A	ENSP00000398502:p.Glu151Val	128.0	0.0	.		159.0	16.0	.	NM_201400	D3DUF0|Q96S85	Missense_Mutation	SNP	ENST00000427587.4	hg19	CCDS10529.1	.	.	.	.	.	.	.	.	.	.	t	17.73	3.461895	0.63513	.	.	ENSG00000118894	ENST00000458008;ENST00000427587	T;T	0.20200	2.09;2.09	5.02	5.02	0.67125	.	0.188239	0.45867	D	0.000338	T	0.21761	0.0524	N	0.26042	0.785	0.44337	D	0.997227	P;P	0.40731	0.682;0.728	P;P	0.46850	0.522;0.529	T	0.02042	-1.1224	10	0.51188	T	0.08	.	12.2508	0.54597	0.0:0.0:0.0:1.0	.	117;151	Q96G04-2;Q96G04	.;FA86A_HUMAN	V	117;151	ENSP00000389710:E117V;ENSP00000398502:E151V	ENSP00000398502:E151V	E	-	2	0	FAM86A	5080458	0.999000	0.42202	0.910000	0.35882	0.241000	0.25554	6.872000	0.75536	2.117000	0.64856	0.370000	0.22315	GAG	.	.	.	none		0.642	FAM86A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251713.1	NM_201400		A	5140457	T	A	5140457	3	1	159	1	0	0	0	0	1	0	0	0	5650	1551	54	5	556	5	FAM86A	16	5140457	Missense_Mutation	SNP	T	TCGA-DZ-6134-01A-11D-1961-08		5140457	85214296	22	9449											
TPPP3	51673	hgsc.bcm.edu	37	chr16	67424233	67424233	+	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	gtgtatctgctggtgtccgtCagccggtctacagcaccccc	5	10	11	15	2	3	0	1	0	2	0	4	0	4	0	4	2	4	3	4	2	2	2			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr16:67424233C>G	ENST00000564104.1	-	3	1216	c.375G>C	c.(373-375)ctG>ctC	p.L125L	TPPP3_ENST00000290942.5_Silent_p.L125L|TPPP3_ENST00000393957.2_Silent_p.L125L|TPPP3_ENST00000562206.1_Silent_p.L125L|RNU1-123P_ENST00000458950.1_RNA			Q9BW30	TPPP3_HUMAN	tubulin polymerization-promoting protein family member 3	125					microtubule bundle formation (GO:0001578)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	tubulin binding (GO:0015631)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)|prostate(1)	7		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0336)|Epithelial(162;0.0781)		TGGTGTCCGTCAGCCGGTCTA	0.617																																					p.L125L		Atlas-SNP	.											.	TPPP3	13	.	0			c.G375C						PASS	.						129	119	122					16																	67424233		2198	4300	6498	SO:0001819	synonymous_variant	51673	exon5			GTCCGTCAGCCGG	BC000691	CCDS10835.1	16q22.1	2008-02-05			ENSG00000159713	ENSG00000159713			24162	protein-coding gene	gene with protein product						15590652, 17105200	Standard	XM_005255979		Approved	CGI-38, p25gamma, p20	uc002etb.3	Q9BW30	OTTHUMG00000137516	ENST00000564104.1:c.375G>C	chr16.hg19:g.67424233C>G		281.0	0.0	.		268.0	11.0	.	NM_016140	Q49AH9|Q9Y326|Q9Y6H0	Silent	SNP	ENST00000564104.1	hg19	CCDS10835.1																																																																																			.	.	.	none		0.617	TPPP3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421787.2	NM_015964		G	67424233	C	G	67424233	2	3	159	1	0	0	0	0	0	0	0	1	16427	813	29	4		4	TPPP3	16	67424233	Silent	SNP	C	TCGA-DZ-6134-01A-11D-1961-08	62283776	67424233	22930520	23	9450											
MYH2	4620	hgsc.bcm.edu	37	chr17	10426831	10426831	+	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	accctggcctccagtttctgGatctgcttcttcccaccctt	4	14	6	17	0	3	0	0	0	3	0	5	1	5	1	5	2	1	2	5	2	0	4			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr17:10426831G>A	ENST00000245503.5	-	37	5838	c.5454C>T	c.(5452-5454)atC>atT	p.I1818I	RP11-799N11.1_ENST00000399342.2_RNA|MYH2_ENST00000397183.2_Silent_p.I1818I|MYH2_ENST00000532183.2_Intron|RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	1818					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						CCAGTTTCTGGATCTGCTTCT	0.507																																					p.I1818I		Atlas-SNP	.											.	MYH2	390	.	0			c.C5454T						PASS	.						97	103	101					17																	10426831		2203	4300	6503	SO:0001819	synonymous_variant	4620	exon37			TTTCTGGATCTGC		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.5454C>T	chr17.hg19:g.10426831G>A		190.0	0.0	.		230.0	82.0	.	NM_017534	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Silent	SNP	ENST00000245503.5	hg19	CCDS11156.1																																																																																			.	.	.	none		0.507	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534		A	10426831	G	A	10426831	2	1	159	1	0	0	0	0	0	0	0	1	10042	1164	41	2		2	MYH2	17	10426831	Silent	SNP	G	TCGA-DZ-6134-01A-11D-1961-08		10426831	70768379	24	9451											
RDM1	201299	hgsc.bcm.edu	37	chr17	34257138	34257138	+	Missense_Mutation	SNP	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	atgccttttgggctctgtggGcagcccttgcagaataaaac	9	11	11	10	0	1	1	0	0	1	1	1	1	1	1	2	2	4	3	2	2	3	4			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr17:34257138G>A	ENST00000293273.6	-	2	263	c.218C>T	c.(217-219)gCc>gTc	p.A73V	RDM1_ENST00000591402.1_Missense_Mutation_p.A50V|RDM1_ENST00000425909.3_Missense_Mutation_p.A73V|RDM1_ENST00000394527.1_Missense_Mutation_p.A50V|RDM1_ENST00000394528.3_Missense_Mutation_p.A73V|RDM1_ENST00000431884.2_Missense_Mutation_p.A73V|RDM1_ENST00000419453.2_Missense_Mutation_p.A50V|RDM1_ENST00000430160.2_Missense_Mutation_p.A50V|RDM1_ENST00000394529.3_Missense_Mutation_p.A50V	NM_145654.3	NP_663629.1	Q8NG50	RDM1_HUMAN	RAD52 motif containing 1	73	Necessary for nuclear localization and for nucleolar accumulation in response to heat shock.|RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|kidney(3)|large_intestine(2)|ovary(1)|skin(1)|stomach(1)	9		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		GGCTCTGTGGGCAGCCCTTGC	0.493								Other identified genes with known or suspected DNA repair function																													p.A73V		Atlas-SNP	.											.	RDM1	46	.	0			c.C218T						PASS	.						115	125	122					17																	34257138		2203	4300	6503	SO:0001583	missense	201299	exon2			CTGTGGGCAGCCC	AB080728	CCDS11301.1, CCDS42299.1, CCDS54111.1, CCDS54108.1, CCDS54109.1, CCDS54110.1, CCDS59280.1, CCDS59281.1	17q11.2	2014-04-10	2014-04-10	2005-10-20	ENSG00000187456	ENSG00000278023		"RNA binding motif (RRM) containing"	19950	protein-coding gene	gene with protein product		612896	"RAD52 homolog B (S. cerevisiae)", "RAD52 motif 1"	RAD52B		15611051	Standard	NM_001163120		Approved	MGC33977	uc002hkh.3	Q8NG50	OTTHUMG00000188399	ENST00000293273.6:c.218C>T	chr17.hg19:g.34257138G>A	ENSP00000293273:p.Ala73Val	271.0	0.0	.		361.0	23.0	.	NM_001034836	A0JP55|A8MV46|A8MY68|A8MZ92|A8RCS5|A8RCT0|A8RCT5|A8RCT8|A8RCU3|A8RCU8|A8RCW0|A8RCW5	Missense_Mutation	SNP	ENST00000293273.6	hg19	CCDS11301.1	.	.	.	.	.	.	.	.	.	.	G	15.35	2.807688	0.50421	.	.	ENSG00000187456	ENST00000293273;ENST00000394529;ENST00000431884;ENST00000425909;ENST00000436836;ENST00000430160;ENST00000394528;ENST00000394527	T;T;T;T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58;1.58;1.58;1.58	3.78	3.78	0.43462	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.134512	0.49916	D	0.000140	T	0.52108	0.1714	M	0.79475	2.455	0.35240	D	0.777732	D;D;P;P;P;D;D;D;P	0.54397	0.957;0.957;0.946;0.859;0.946;0.957;0.957;0.966;0.946	P;P;B;B;P;P;P;P;P	0.61874	0.751;0.491;0.41;0.41;0.636;0.491;0.545;0.895;0.636	T	0.67090	-0.5758	10	0.54805	T	0.06	-6.8607	13.5182	0.61553	0.0:0.0:1.0:0.0	.	50;50;73;73;50;50;73;73;50	B4DZ74;Q8NG50-4;Q8NG50-5;Q8NG50-10;Q8NG50-2;Q8NG50-11;A8MY68;Q8NG50;Q8NG50-6	.;.;.;.;.;.;.;RDM1_HUMAN;.	V	73;50;73;73;73;50;73;50	ENSP00000293273:A73V;ENSP00000378037:A50V;ENSP00000391290:A73V;ENSP00000393620:A73V;ENSP00000397431:A73V;ENSP00000413421:A50V;ENSP00000378036:A73V;ENSP00000378035:A50V	ENSP00000293273:A73V	A	-	2	0	RDM1	31281251	1.000000	0.71417	0.014000	0.15608	0.101000	0.19017	4.843000	0.62838	2.141000	0.66446	0.655000	0.94253	GCC	.	.	.	none		0.493	RDM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256588.2	NM_145654		A	34257138	G	A	34257138	3	1	159	1	0	0	0	0	1	0	0	0	13210	1203	42	2	704	2	RDM1	17	34257138	Missense_Mutation	SNP	G	TCGA-DZ-6134-01A-11D-1961-08	23830307	34257138	46938072	25	9452											
MLX	6945	hgsc.bcm.edu	37	chr17	40720856	40720856	+	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	cccccatctctgagcgtagaTgatgaggacagtgattacca	11	9	10	11	1	1	5	0	4	1	1	2	6	1	6	3	1	2	1	3	1	2	2			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr17:40720856T>C	ENST00000246912.4	+	4	386	c.333T>C	c.(331-333)gaT>gaC	p.D111D	MLX_ENST00000346833.4_Splice_Site_p.D27D|MLX_ENST00000435881.2_Splice_Site_p.D57D	NM_170607.2	NP_733752.1	Q9UH92	MLX_HUMAN	MLX, MAX dimerization protein	111					energy reserve metabolic process (GO:0006112)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|positive regulation of cellular metabolic process (GO:0031325)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			kidney(3)|large_intestine(4)|lung(1)|ovary(1)|urinary_tract(1)	10		all_cancers(22;4.26e-05)|Breast(137;0.000153)|all_epithelial(22;0.00148)		BRCA - Breast invasive adenocarcinoma(366;0.129)		TGAGCGTAGATGATGAGGACA	0.607																																					p.D111D	GBM(121;657 1601 4665 24731 34640)	Atlas-SNP	.											.	MLX	17	.	0			c.T333C						PASS	.						30	26	27					17																	40720856		2203	4300	6503	SO:0001630	splice_region_variant	6945	exon4			CGTAGATGATGAG	AF213668	CCDS11430.1, CCDS42341.1, CCDS45687.1	17q21.1	2013-05-21	2012-11-15	2005-02-11		ENSG00000108788		"MAX dimerization proteins", "Basic helix-loop-helix proteins"	11645	protein-coding gene	gene with protein product		602976	"transcription factor-like 4", "MAX-like protein X"	TCFL4		8973301	Standard	NM_170607		Approved	MAD7, MXD7, bHLHd13	uc002iag.3	Q9UH92		ENST00000246912.4:c.332-1T>C	chr17.hg19:g.40720856T>C		21.0	0.0	.		23.0	6.0	.	NM_170607	A8K2J3|B2RAV8|B2RD73|Q53XM6|Q96FL2|Q9H2V0|Q9H2V1|Q9H2V2|Q9NXN3	Silent	SNP	ENST00000246912.4	hg19	CCDS11430.1																																																																																			.	.	.	none		0.607	MLX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450415.1	NM_170607	Silent	C	40720856	T	C	40720856	5	2	159	1	0	0	0	0	0	0	1	0	9642	1478	51	3	347	3	MLX	17	40720856	Splice_Site	SNP	T	TCGA-DZ-6134-01A-11D-1961-08	6463718	40720856	40474354	26	9453											
NR2C2AP	126382	hgsc.bcm.edu	37	chr19	19313644	19313645	+	Frame_Shift_Ins	INS	-	-	T																															tcatcctggtcgaaaagatgINStttttttccaaactgccgag																										TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr19:19313644_19313645insT	ENST00000331552.7	-	2	447_448	c.84_85insA	c.(82-87)aaacatfs	p.H29fs	NR2C2AP_ENST00000420605.3_Frame_Shift_Ins_p.H29fs|NR2C2AP_ENST00000544883.1_Frame_Shift_Ins_p.H29fs|NR2C2AP_ENST00000538165.2_Frame_Shift_Ins_p.H29fs	NM_176880.4	NP_795361.1	Q86WQ0	NR2CA_HUMAN	nuclear receptor 2C2-associated protein	29					cell adhesion (GO:0007155)|gene expression (GO:0010467)|transcription initiation from RNA polymerase II promoter (GO:0006367)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)				breast(1)|cervix(1)|kidney(2)|ovary(1)	5			Epithelial(12;0.00235)			TCGAAAAGATGTTTTTTTCCAA	0.54																																					p.H29fs		Atlas-INDEL	.											.	NR2C2AP	7	.	0			c.85_86insA						PASS	.																																			SO:0001589	frameshift_variant	126382	exon2			.	AY101377	CCDS32967.1, CCDS74316.1	19p13.11	2008-01-10				ENSG00000184162			30763	protein-coding gene	gene with protein product	"TR4 orphan receptor associated protein TRA16"	608719				12486131	Standard	XM_005259740		Approved	TRA16	uc002nlx.3	Q86WQ0		ENST00000331552.7:c.85dupA	chr19.hg19:g.19313651_19313651dupT	ENSP00000332823:p.His29fs	138.0	0.0	0		116.0	20.0	0.172414	NM_176880	A6NGP7|B4DW92	Frame_Shift_Ins	INS	ENST00000331552.7	hg19	CCDS32967.1																																																																																			.	.	.	none		0.54	NR2C2AP-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402936.4	NM_176880		T	19313645	-	T	19313644	7	5	159	1	0	1	1	0	0	0	0	0	10631	1377	48	0	350	0	NR2C2AP	19	19313644	Frame_Shift_Ins	INS	-	TCGA-DZ-6134-01A-11D-1961-08		19313644	39815339	27	9454											
DHDH	27294	hgsc.bcm.edu	37	chr19	49447704	49447704	+	Missense_Mutation	SNP	T	T	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	cagtcccaaaggactgcaatTttgacaacggggcaggcatg	12	7	12	10	1	0	1	0	1	0	0	1	2	1	2	1	4	2	3	1	4	3	2			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr19:49447704T>G	ENST00000221403.2	+	6	875	c.835T>G	c.(835-837)Ttt>Gtt	p.F279V	DHDH_ENST00000522614.1_Intron|DHDH_ENST00000523250.1_Missense_Mutation_p.F140V	NM_014475.3	NP_055290.1	Q9UQ10	DHDH_HUMAN	dihydrodiol dehydrogenase (dimeric)	279					carbohydrate metabolic process (GO:0005975)|D-xylose catabolic process (GO:0042843)		D-xylose 1-dehydrogenase (NADP+) activity (GO:0047837)|electron carrier activity (GO:0009055)|NAD(P)+ transhydrogenase activity (GO:0008746)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			central_nervous_system(1)|large_intestine(3)|lung(3)|ovary(1)|soft_tissue(1)	9		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)		GGACTGCAATTTTGACAACGG	0.622																																					p.F279V		Atlas-SNP	.											.	DHDH	35	.	0			c.T835G						PASS	.						65	63	63					19																	49447704		2203	4300	6503	SO:0001583	missense	27294	exon6			TGCAATTTTGACA	AB021933	CCDS12741.1	19q13.3	2008-02-05			ENSG00000104808	ENSG00000104808	1.3.1.20		17887	protein-coding gene	gene with protein product		606377				10477285	Standard	NM_014475		Approved	HUM2DD	uc002ple.1	Q9UQ10	OTTHUMG00000165029	ENST00000221403.2:c.835T>G	chr19.hg19:g.49447704T>G	ENSP00000221403:p.Phe279Val	147.0	0.0	.		110.0	24.0	.	NM_014475		Missense_Mutation	SNP	ENST00000221403.2	hg19	CCDS12741.1	.	.	.	.	.	.	.	.	.	.	T	17.70	3.453658	0.63290	.	.	ENSG00000104808	ENST00000221403;ENST00000523250	T;T	0.21361	2.01;2.01	4.89	3.87	0.44632	.	0.210406	0.49916	D	0.000136	T	0.23330	0.0564	M	0.77616	2.38	0.80722	D	1	B	0.27117	0.168	B	0.28638	0.092	T	0.05903	-1.0857	10	0.33940	T	0.23	-6.6788	6.733	0.23393	0.0:0.1029:0.0:0.8971	.	279	Q9UQ10	DHDH_HUMAN	V	279;140	ENSP00000221403:F279V;ENSP00000428935:F140V	ENSP00000221403:F279V	F	+	1	0	DHDH	54139516	1.000000	0.71417	0.040000	0.18447	0.014000	0.08584	4.583000	0.60964	2.183000	0.69458	0.402000	0.26972	TTT	.	.	.	none		0.622	DHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381477.1	NM_014475		G	49447704	T	G	49447704	3	3	159	1	0	0	0	0	1	0	0	0	4481	1841	64	5	857	5	DHDH	19	49447704	Missense_Mutation	SNP	T	TCGA-DZ-6134-01A-11D-1961-08	30134060	49447704	9681279	28	9455			1	20		2	2	25	T		2.480849e-05
DHDH	27294	hgsc.bcm.edu	37	chr19	49447728	49447728	+	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	acaacggggcaggcatgagtTatgaggccaagcacgtctgg	11	6	15	9	2	1	2	0	2	1	0	1	2	1	2	1	5	2	4	1	5	3	1			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr19:49447728T>A	ENST00000221403.2	+	6	899	c.859T>A	c.(859-861)Tat>Aat	p.Y287N	DHDH_ENST00000522614.1_Intron|DHDH_ENST00000523250.1_Missense_Mutation_p.Y148N	NM_014475.3	NP_055290.1	Q9UQ10	DHDH_HUMAN	dihydrodiol dehydrogenase (dimeric)	287					carbohydrate metabolic process (GO:0005975)|D-xylose catabolic process (GO:0042843)		D-xylose 1-dehydrogenase (NADP+) activity (GO:0047837)|electron carrier activity (GO:0009055)|NAD(P)+ transhydrogenase activity (GO:0008746)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			central_nervous_system(1)|large_intestine(3)|lung(3)|ovary(1)|soft_tissue(1)	9		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)		AGGCATGAGTTATGAGGCCAA	0.627																																					p.Y287N		Atlas-SNP	.											.	DHDH	35	.	0			c.T859A						PASS	.						70	67	68					19																	49447728		2203	4300	6503	SO:0001583	missense	27294	exon6			ATGAGTTATGAGG	AB021933	CCDS12741.1	19q13.3	2008-02-05			ENSG00000104808	ENSG00000104808	1.3.1.20		17887	protein-coding gene	gene with protein product		606377				10477285	Standard	NM_014475		Approved	HUM2DD	uc002ple.1	Q9UQ10	OTTHUMG00000165029	ENST00000221403.2:c.859T>A	chr19.hg19:g.49447728T>A	ENSP00000221403:p.Tyr287Asn	153.0	0.0	.		116.0	20.0	.	NM_014475		Missense_Mutation	SNP	ENST00000221403.2	hg19	CCDS12741.1	.	.	.	.	.	.	.	.	.	.	T	34	5.369860	0.95900	.	.	ENSG00000104808	ENST00000221403;ENST00000523250	T;T	0.24151	1.87;1.87	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.55784	0.1942	M	0.90483	3.12	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.63301	-0.6668	10	0.59425	D	0.04	-13.1857	11.3361	0.49505	0.0:0.0:0.0:1.0	.	287	Q9UQ10	DHDH_HUMAN	N	287;148	ENSP00000221403:Y287N;ENSP00000428935:Y148N	ENSP00000221403:Y287N	Y	+	1	0	DHDH	54139540	0.999000	0.42202	0.059000	0.19551	0.914000	0.54420	6.248000	0.72418	2.252000	0.74401	0.402000	0.26972	TAT	.	.	.	none		0.627	DHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381477.1	NM_014475		A	49447728	T	A	49447728	3	1	159	1	0	0	0	0	1	0	0	0	4481	1754	61	5	881	5	DHDH	19	49447728	Missense_Mutation	SNP	T	TCGA-DZ-6134-01A-11D-1961-08	24	49447728	9681255	29	9456			1	20		2	2	25	T		2.480849e-05
C20orf141	128653	hgsc.bcm.edu	37	chr20	2796280	2796280	+	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	cagcaggaggctctactcctGcaaatgggtacagtctcagg	10	8	12	11	0	2	0	1	0	2	0	4	1	3	1	1	4	4	4	1	4	3	2			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr20:2796280G>T	ENST00000380589.4	+	2	531	c.357G>T	c.(355-357)ctG>ctT	p.L119L	TMEM239_ENST00000554164.1_Intron|TMEM239_ENST00000361033.1_5'Flank|TMEM239_ENST00000380585.1_5'Flank|TMEM239_ENST00000380593.4_Intron|C20orf141_ENST00000603872.1_Silent_p.L119L	NM_080739.2	NP_542777.1	Q9NUB4	CT141_HUMAN	chromosome 20 open reading frame 141	119	Leu-rich.					integral component of membrane (GO:0016021)				endometrium(4)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	10						CTCTACTCCTGCAAATGGGTA	0.627																																					p.L119L		Atlas-SNP	.											.	C20orf141	21	.	0			c.G357T						PASS	.						57	55	56					20																	2796280		2203	4300	6503	SO:0001819	synonymous_variant	128653	exon2			ACTCCTGCAAATG		CCDS13034.1	20p13	2012-10-30			ENSG00000258713	ENSG00000258713			16134	protein-coding gene	gene with protein product							Standard	NM_001256538		Approved	dJ860F19.4	uc002wgw.3	Q9NUB4	OTTHUMG00000031707	ENST00000380589.4:c.357G>T	chr20.hg19:g.2796280G>T		98.0	0.0	.		89.0	14.0	.	NM_080739		Silent	SNP	ENST00000380589.4	hg19	CCDS13034.1																																																																																			.	.	.	none		0.627	C20orf141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077644.2	NM_080739		T	2796280	G	T	2796280	2	4	159	1	0	0	0	0	0	0	0	1	2091	1306	46	4		4	C20orf141	20	2796280	Silent	SNP	G	TCGA-DZ-6134-01A-11D-1961-08		2796280	60229240	30	9457											
NINL	22981	hgsc.bcm.edu	37	chr20	25469911	25469911	+	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	gctcgtattccttcaggactGctgcgaaccgctcctcctgg	5	11	10	15	3	1	0	1	0	0	0	5	2	4	1	4	2	3	4	4	2	2	3			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr20:25469911G>T	ENST00000278886.6	-	13	1719	c.1646C>A	c.(1645-1647)gCa>gAa	p.A549E	NINL_ENST00000422516.1_Missense_Mutation_p.A549E	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	549					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						CTTCAGGACTGCTGCGAACCG	0.617																																					p.A549E		Atlas-SNP	.											.	NINL	148	.	0			c.C1646A						PASS	.						170	155	160					20																	25469911		2203	4300	6503	SO:0001583	missense	22981	exon13			AGGACTGCTGCGA		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.1646C>A	chr20.hg19:g.25469911G>T	ENSP00000278886:p.Ala549Glu	205.0	0.0	.		170.0	24.0	.	NM_025176	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	ENST00000278886.6	hg19	CCDS33452.1	.	.	.	.	.	.	.	.	.	.	g	0.011	-1.724364	0.00694	.	.	ENSG00000101004	ENST00000278886;ENST00000422516	T;T	0.27402	1.91;1.67	4.58	0.0634	0.14348	.	0.597531	0.16327	N	0.219312	T	0.10508	0.0257	N	0.14661	0.345	0.09310	N	1	B;B	0.16603	0.018;0.012	B;B	0.11329	0.005;0.006	T	0.27673	-1.0067	10	0.02654	T	1	-1.509	0.7711	0.01024	0.2336:0.1117:0.2575:0.3972	.	549;549	Q9Y2I6-2;Q9Y2I6	.;NINL_HUMAN	E	549	ENSP00000278886:A549E;ENSP00000410431:A549E	ENSP00000278886:A549E	A	-	2	0	NINL	25417911	0.001000	0.12720	0.000000	0.03702	0.299000	0.27559	0.333000	0.19768	-0.118000	0.11851	0.651000	0.88453	GCA	.	.	.	none		0.617	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176		T	25469911	G	T	25469911	3	4	159	1	0	0	0	0	1	0	0	0	10427	1319	46	4	2550	4	NINL	20	25469911	Missense_Mutation	SNP	G	TCGA-DZ-6134-01A-11D-1961-08	22673631	25469911	37555609	31	9458											
TP53TG5	27296	hgsc.bcm.edu	37	chr20	44005872	44005872	+	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	ccagaggagatgcggagaatCtttggaacactgagcagtga	13	7	14	7	1	1	5	0	2	1	3	1	8	1	6	1	3	3	1	1	3	2	1			TCGA-DZ-6134-01A-11D-1961-08	TCGA-DZ-6134-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	230ddafa-8d9f-4ddc-b864-ba8eb42a31ab	8e8a3cd2-c9ae-4be6-8682-214badaa00a5	g.chr20:44005872C>G	ENST00000372726.3	-	3	390	c.234G>C	c.(232-234)aaG>aaC	p.K78N	TP53TG5_ENST00000494455.1_5'UTR|SYS1-DBNDD2_ENST00000475242.1_Intron|TP53TG5_ENST00000537995.1_Missense_Mutation_p.K62N|SYS1-DBNDD2_ENST00000452133.1_Intron	NM_014477.2	NP_055292.1	Q9Y2B4	T53G5_HUMAN	TP53 target 5	78					intracellular signal transduction (GO:0035556)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|prostate(2)|upper_aerodigestive_tract(1)	12						TGCGGAGAATCTTTGGAACAC	0.512																																					p.K78N		Atlas-SNP	.											.	TP53TG5	36	.	0			c.G234C						PASS	.						168	155	160					20																	44005872		2203	4300	6503	SO:0001583	missense	27296	exon3			GAGAATCTTTGGA	AB017802	CCDS13352.1	20q13.12	2008-09-18	2008-09-18	2008-09-18	ENSG00000124251	ENSG00000124251			15856	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 10"	C20orf10			Standard	NM_014477		Approved	CLG01, dJ453C12.5	uc002xny.3	Q9Y2B4	OTTHUMG00000032582	ENST00000372726.3:c.234G>C	chr20.hg19:g.44005872C>G	ENSP00000361811:p.Lys78Asn	219.0	0.0	.		185.0	11.0	.	NM_014477		Missense_Mutation	SNP	ENST00000372726.3	hg19	CCDS13352.1	.	.	.	.	.	.	.	.	.	.	C	14.63	2.593647	0.46214	.	.	ENSG00000124251	ENST00000372726;ENST00000537995	T;T	0.18338	2.22;2.22	5.43	5.43	0.79202	.	1.020720	0.07785	N	0.953949	T	0.25195	0.0612	L	0.39898	1.24	0.09310	N	1	P	0.49090	0.919	P	0.48704	0.587	T	0.20438	-1.0275	10	0.66056	D	0.02	-0.733	12.8311	0.57746	0.0:0.8361:0.1639:0.0	.	78	Q9Y2B4	T53G5_HUMAN	N	78;62	ENSP00000361811:K78N;ENSP00000438374:K62N	ENSP00000361811:K78N	K	-	3	2	TP53TG5	43439286	0.039000	0.19947	0.020000	0.16555	0.437000	0.31866	2.319000	0.43788	2.720000	0.93068	0.591000	0.81541	AAG	.	.	.	none		0.512	TP53TG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079460.1	NM_014477		G	44005872	C	G	44005872	3	3	159	1	0	0	0	0	1	0	0	0	16403	912	32	4	650	4	TP53TG5	20	44005872	Missense_Mutation	SNP	C	TCGA-DZ-6134-01A-11D-1961-08	18535961	44005872	19019648	32	9459											
MCOLN3	55283	hgsc.bcm.edu	37	chr1	85491894	85491894	+	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	ctaatcacagatctaatgcaGaggattaatgaaaccaagca	18	8	7	8	0	2	3	1	1	1	2	2	4	2	4	1	1	3	2	1	1	5	3			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr1:85491894G>C	ENST00000370589.2	-	8	958	c.906C>G	c.(904-906)ctC>ctG	p.L302L	WDR63_ENST00000370596.1_Intron|MCOLN3_ENST00000370587.1_Silent_p.L302L|MCOLN3_ENST00000474447.1_5'Flank|MCOLN3_ENST00000341115.4_Silent_p.L246L	NM_018298.10	NP_060768.8	Q8TDD5	MCLN3_HUMAN	mucolipin 3	302					auditory receptor cell differentiation (GO:0042491)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|locomotory behavior (GO:0007626)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(6)|kidney(3)|large_intestine(9)|lung(12)|prostate(3)|skin(1)	34				all cancers(265;0.00957)|Epithelial(280;0.0254)		ATCTAATGCAGAGGATTAATG	0.398																																					p.L302L		Atlas-SNP	.											.	MCOLN3	74	.	0			c.C906G						PASS	.						133	121	125					1																	85491894		2203	4300	6503	SO:0001819	synonymous_variant	55283	exon8			AATGCAGAGGATT	AF475085	CCDS701.1, CCDS58009.1	1p22.3	2011-12-16			ENSG00000055732	ENSG00000055732		"Voltage-gated ion channels / Transient receptor potential cation channels"	13358	protein-coding gene	gene with protein product		607400				16382100	Standard	NM_018298		Approved	TRPML3, FLJ11006, TRP-ML3	uc001dkp.3	Q8TDD5	OTTHUMG00000009955	ENST00000370589.2:c.906C>G	chr1.hg19:g.85491894G>C		132.0	0.0	.		116.0	44.0	.	NM_018298	Q5T4H5|Q5T4H6|Q9NV09	Silent	SNP	ENST00000370589.2	hg19	CCDS701.1																																																																																			.	.	.	none		0.398	MCOLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027569.2	NM_018298		C	85491894	G	C	85491894	2	2	160	1	0	0	0	0	0	0	0	1	9404	929	33	4		4	MCOLN3	1	85491894	Silent	SNP	G	TCGA-DZ-6135-01A-11D-1961-08		85491894	163758727	1	9460											
ARHGAP30	257106	hgsc.bcm.edu	37	chr1	161029441	161029441	+	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	ggaggagacccctgagaggcGgtagatcccatccaccactc	10	5	12	14	1	0	3	0	1	0	3	3	6	2	4	5	4	0	1	5	4	1	1			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr1:161029441G>T	ENST00000368013.3	-	2	483	c.163C>A	c.(163-165)Cgc>Agc	p.R55S	ARHGAP30_ENST00000368015.1_Intron|ARHGAP30_ENST00000368016.3_Missense_Mutation_p.R55S	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	55	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)			CCTGAGAGGCGGTAGATCCCA	0.562																																					p.R55S		Atlas-SNP	.											.	ARHGAP30	105	.	0			c.C163A						PASS	.						106	94	98					1																	161029441		2203	4300	6503	SO:0001583	missense	257106	exon2			AGAGGCGGTAGAT	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.163C>A	chr1.hg19:g.161029441G>T	ENSP00000356992:p.Arg55Ser	138.0	0.0	.		140.0	6.0	.	NM_001025598	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Missense_Mutation	SNP	ENST00000368013.3	hg19	CCDS30918.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.106697	0.77096	.	.	ENSG00000186517	ENST00000368016;ENST00000368013	T;T	0.52295	0.67;0.67	4.91	4.91	0.64330	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.73961	0.3654	H	0.97732	4.065	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.82063	-0.0643	10	0.87932	D	0	.	11.1138	0.48249	0.0:0.0:0.8152:0.1848	.	55;55	Q7Z6I6;Q7Z6I6-2	RHG30_HUMAN;.	S	55	ENSP00000356995:R55S;ENSP00000356992:R55S	ENSP00000356992:R55S	R	-	1	0	ARHGAP30	159296065	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.839000	0.39220	2.419000	0.82065	0.484000	0.47621	CGC	.	.	.	none		0.562	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720		T	161029441	G	T	161029441	3	4	160	1	0	0	0	0	1	0	0	0	879	1116	39	4	3186	4	ARHGAP30	1	161029441	Missense_Mutation	SNP	G	TCGA-DZ-6135-01A-11D-1961-08	75537547	161029441	88221180	2	9461											
STON1	11037	hgsc.bcm.edu	37	chr2	48818889	48818889	+	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	tttgctactgttcagttttcCgtgcctgacacctgtgcctc	4	16	8	13	1	1	1	1	1	0	0	3	1	2	1	4	0	4	3	4	0	1	5			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr2:48818889C>A	ENST00000406226.1	+	4	2223	c.2028C>A	c.(2026-2028)tcC>tcA	p.S676S	STON1-GTF2A1L_ENST00000394751.3_Silent_p.S676S|STON1_ENST00000309835.3_Silent_p.S676S|STON1-GTF2A1L_ENST00000309827.2_Silent_p.S676S|STON1-GTF2A1L_ENST00000402114.2_Silent_p.S676S|STON1-GTF2A1L_ENST00000405008.1_Silent_p.S676S|STON1_ENST00000404752.1_Silent_p.S676S|STON1-GTF2A1L_ENST00000394754.1_Silent_p.S676S	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	676	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TTCAGTTTTCCGTGCCTGACA	0.483																																					p.S676S		Atlas-SNP	.											.	STON1	100	.	0			c.C2028A						PASS	.						155	146	149					2																	48818889		2203	4300	6503	SO:0001819	synonymous_variant	11037	exon4			GTTTTCCGTGCCT	AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"stoned B homolog 1 (Drosophila)"	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.2028C>A	chr2.hg19:g.48818889C>A		138.0	0.0	.		129.0	7.0	.	NM_001198595	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Silent	SNP	ENST00000406226.1	hg19	CCDS1841.1																																																																																			.	.	.	none		0.483	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873		A	48818889	C	A	48818889	2	1	160	1	0	0	0	0	0	0	0	1	15328	639	23	4		4	STON1	2	48818889	Silent	SNP	C	TCGA-DZ-6135-01A-11D-1961-08		48818889	194380484	3	9462											
SPRED2	200734	hgsc.bcm.edu	37	chr2	65561771	65561771	+	Frame_Shift_Del	DEL	C	C	-																															cttcgattgctttccttactCccctgtcaaaggctcgggca																										TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr2:65561771delC	ENST00000356388.4	-	3	530	c.341delG	c.(340-342)ggafs	p.G114fs	SPRED2_ENST00000443619.2_Frame_Shift_Del_p.G111fs|SPRED2_ENST00000474228.1_5'UTR	NM_181784.2	NP_861449.2	Q7Z698	SPRE2_HUMAN	sprouty-related, EVH1 domain containing 2	114	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						TTTCCTTACTCCCCTGTCAAA	0.413																																					p.G114fs		Atlas-INDEL	.											.	SPRED2	70	.	0			c.342delA						PASS	.						157	146	150					2																	65561771		2203	4300	6503	SO:0001589	frameshift_variant	200734	exon3			.	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.341delG	chr2.hg19:g.65561771delC	ENSP00000348753:p.Gly114fs	198.0	0.0	0		192.0	68.0	0.354167	NM_181784	A1L3V4|B7Z5K7|D6W5F7|E9PEP0|Q2NKX6	Frame_Shift_Del	DEL	ENST00000356388.4	hg19	CCDS33211.1																																																																																			.	.	.	none		0.413	SPRED2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327632.1			-	65561771	C	-	65561771	7	5	160	1	0	1	0	1	0	0	0	0	15105	855	30	0	931	0	SPRED2	2	65561771	Frame_Shift_Del	DEL	C	TCGA-DZ-6135-01A-11D-1961-08	16742882	65561771	177637602	4	9463											
SULT1C4	27233	hgsc.bcm.edu	37	chr2	108994906	108994906	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtgacatctgggataagaTctggaacttccaagccaagc	12	9	10	10	0	2	2	0	1	2	1	3	4	3	4	2	2	3	0	2	2	4	2			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr2:108994906T>C	ENST00000272452.2	+	1	439	c.113T>C	c.(112-114)aTc>aCc	p.I38T	SULT1C4_ENST00000409309.3_Missense_Mutation_p.I38T	NM_006588.2	NP_006579.2	O75897	ST1C4_HUMAN	sulfotransferase family, cytosolic, 1C, member 4	38					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	sulfotransferase activity (GO:0008146)			endometrium(1)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	12						TGGGATAAGATCTGGAACTTC	0.473																																					p.I38T		Atlas-SNP	.											.	SULT1C4	41	.	0			c.T113C						PASS	.						171	176	174					2																	108994906		2203	4300	6503	SO:0001583	missense	27233	exon1			ATAAGATCTGGAA	AF055584	CCDS2077.1	2q12.3	2008-09-04	2007-03-16	2007-03-16	ENSG00000198075	ENSG00000198075		"Sulfotransferases, cytosolic"	11457	protein-coding gene	gene with protein product		608357	"sulfotransferase family, cytosolic, 1C, member 2"	SULT1C2		10783263, 9852044	Standard	NM_006588		Approved	SULT1C	uc002tea.1	O75897	OTTHUMG00000130958	ENST00000272452.2:c.113T>C	chr2.hg19:g.108994906T>C	ENSP00000272452:p.Ile38Thr	289.0	0.0	.		315.0	134.0	.	NM_006588	Q069I8|Q08AS5|Q53S63	Missense_Mutation	SNP	ENST00000272452.2	hg19	CCDS2077.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.318519	0.81469	.	.	ENSG00000198075	ENST00000272452;ENST00000409309	T;T	0.01918	4.56;4.56	5.06	5.06	0.68205	.	0.127728	0.35555	N	0.003129	T	0.04452	0.0122	N	0.08118	0	0.31369	N	0.680401	P;D;D	0.63880	0.954;0.993;0.991	P;D;D	0.68765	0.476;0.96;0.918	T	0.35773	-0.9775	10	0.66056	D	0.02	.	14.1553	0.65413	0.0:0.0:0.0:1.0	.	38;38;38	Q08AS5;O75897;Q6PD90	.;ST1C4_HUMAN;.	T	38	ENSP00000272452:I38T;ENSP00000387225:I38T	ENSP00000272452:I38T	I	+	2	0	SULT1C4	108361338	0.999000	0.42202	1.000000	0.80357	0.870000	0.49936	4.416000	0.59815	2.125000	0.65367	0.496000	0.49642	ATC	.	.	.	none		0.473	SULT1C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253561.1	NM_006588		C	108994906	T	C	108994906	3	2	160	1	0	0	0	0	1	0	0	0	15391	1435	50	3	115	3	SULT1C4	2	108994906	Missense_Mutation	SNP	T	TCGA-DZ-6135-01A-11D-1961-08	43433135	108994906	134204467	5	9464											
LRP2	4036	hgsc.bcm.edu	37	chr2	170145584	170145584	+	Frame_Shift_Del	DEL	A	A	-																															gatgatataacctgggggacAaaaacacgctcctccatacg																										TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr2:170145584delA	ENST00000263816.3	-	9	1279	c.994delT	c.(994-996)tgtfs	p.C332fs	LRP2_ENST00000443831.1_Frame_Shift_Del_p.C332fs	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	332	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	CCTGGGGGACAAAAACACGCT	0.483																																					p.C332fs		Atlas-INDEL	.											.	LRP2	751	.	0			c.995delG						PASS	.						107	105	106					2																	170145584		2203	4300	6503	SO:0001589	frameshift_variant	4036	exon9			.		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.994delT	chr2.hg19:g.170145584delA	ENSP00000263816:p.Cys332fs	136.0	0.0	0		142.0	41.0	0.288732	NM_004525	O00711|Q16215	Frame_Shift_Del	DEL	ENST00000263816.3	hg19	CCDS2232.1																																																																																			.	.	.	none		0.483	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		-	170145584	A	-	170145584	7	5	160	1	0	1	0	1	0	0	0	0	8963	130	5	0	13257	0	LRP2	2	170145584	Frame_Shift_Del	DEL	A	TCGA-DZ-6135-01A-11D-1961-08	61150678	170145584	73053789	6	9465											
ROBO1	6091	hgsc.bcm.edu	37	chr3	78683096	78683096	+	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	cttacttaccagatgtactaCtgccccggtctgagctgttg	7	13	9	12	1	1	2	0	1	1	1	1	2	1	2	3	1	6	3	3	1	4	5			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr3:78683096C>A	ENST00000464233.1	-	24	3583	c.3470G>T	c.(3469-3471)aGt>aTt	p.S1157I	ROBO1_ENST00000467549.1_Missense_Mutation_p.S1057I|ROBO1_ENST00000436010.2_Missense_Mutation_p.S1118I|ROBO1_ENST00000495273.1_Missense_Mutation_p.S1112I	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	1157					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)		AGATGTACTACTGCCCCGGTC	0.423																																					p.S1157I		Atlas-SNP	.											.	ROBO1	833	.	0			c.G3470T						PASS	.						224	211	215					3																	78683096		1928	4130	6058	SO:0001583	missense	6091	exon24			GTACTACTGCCCC	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.3470G>T	chr3.hg19:g.78683096C>A	ENSP00000420321:p.Ser1157Ile	128.0	0.0	.		155.0	38.0	.	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	hg19	CCDS54611.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.5|22.5	4.301088|4.301088	0.81136|0.81136	.|.	.|.	ENSG00000169855|ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414|ENST00000472273	D;D;D;D|.	0.91464|.	-2.85;-2.85;-2.85;-2.85|.	5.82|5.82	5.82|5.82	0.92795|0.92795	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74756|0.74756	0.3758|0.3758	M|M	0.61703|0.61703	1.905|1.905	0.80722|0.80722	D|D	1|1	D;B;D;P;P|.	0.76494|.	0.997;0.27;0.999;0.754;0.866|.	D;B;D;B;B|.	0.83275|.	0.994;0.082;0.996;0.293;0.376|.	T|T	0.70912|0.70912	-0.4743|-0.4743	9|5	.|.	.|.	.|.	.|.	20.1001|20.1001	0.97870|0.97870	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1121;1157;1112;1057;1118|.	Q9Y6N7-3;Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4|.	.;ROBO1_HUMAN;.;.;.|.	I|L	1118;1112;1157;1112;1057;1161|84	ENSP00000406043:S1118I;ENSP00000420321:S1157I;ENSP00000420637:S1112I;ENSP00000417992:S1057I|.	.|.	S|V	-|-	2|1	0|0	ROBO1|ROBO1	78765786|78765786	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.595000|0.595000	0.36748|0.36748	7.466000|7.466000	0.80914|0.80914	2.760000|2.760000	0.94817|0.94817	0.655000|0.655000	0.94253|0.94253	AGT|GTA	.	.	.	none		0.423	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		A	78683096	C	A	78683096	3	1	160	1	0	0	0	0	1	0	0	0	13526	565	20	4	1517	4	ROBO1	3	78683096	Missense_Mutation	SNP	C	TCGA-DZ-6135-01A-11D-1961-08		78683096	119339334	7	9466											
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113376148	113376148	+	Missense_Mutation	SNP	T	T	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	ctgctgctgctgctgctgctTtatgtagagatggttactat	6	16	11	8	0	0	1	0	0	0	1	0	2	0	1	0	1	7	8	0	1	4	5			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr3:113376148T>G	ENST00000478658.1	-	5	4398	c.4381A>C	c.(4381-4383)Aag>Cag	p.K1461Q	KIAA2018_ENST00000316407.4_Missense_Mutation_p.K1461Q|KIAA2018_ENST00000491165.1_Intron			Q68DE3	K2018_HUMAN	KIAA2018	1461	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						tgctgctgctTTATGTAGAGA	0.498																																					p.K1461Q		Atlas-SNP	.											.	KIAA2018	180	.	0			c.A4381C						PASS	.						66	71	69					3																	113376148		2179	4278	6457	SO:0001583	missense	205717	exon7			GCTGCTTTATGTA	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.4381A>C	chr3.hg19:g.113376148T>G	ENSP00000420721:p.Lys1461Gln	52.0	0.0	.		105.0	7.0	.	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Missense_Mutation	SNP	ENST00000478658.1	hg19	CCDS43133.1	.	.	.	.	.	.	.	.	.	.	T	15.33	2.802014	0.50315	.	.	ENSG00000176542	ENST00000316407;ENST00000478658	T;T	0.31247	1.5;1.5	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.45296	0.1335	L	0.32530	0.975	0.49213	D	0.999766	D	0.71674	0.998	D	0.78314	0.991	T	0.41822	-0.9487	10	0.62326	D	0.03	-15.6625	15.5299	0.75952	0.0:0.0:0.0:1.0	.	1461	Q68DE3	K2018_HUMAN	Q	1461	ENSP00000320794:K1461Q;ENSP00000420721:K1461Q	ENSP00000320794:K1461Q	K	-	1	0	KIAA2018	114858838	1.000000	0.71417	0.987000	0.45799	0.600000	0.36913	7.182000	0.77689	2.254000	0.74563	0.459000	0.35465	AAG	.	.	.	none		0.498	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		G	113376148	T	G	113376148	3	3	160	1	0	0	0	0	1	0	0	0	8275	1850	64	5	2360	5	KIAA2018	3	113376148	Missense_Mutation	SNP	T	TCGA-DZ-6135-01A-11D-1961-08	34693052	113376148	84646282	8	9467											
ADCY5	111	hgsc.bcm.edu	37	chr3	123047579	123047579	+	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	cttcctgagaccaaggacacCgcagtgtactcgcccgctgt	8	8	10	15	3	0	1	0	1	0	1	2	3	1	2	4	1	1	3	4	1	2	2			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr3:123047579C>A	ENST00000462833.1	-	6	2929	c.1717G>T	c.(1717-1719)Ggt>Tgt	p.G573C	ADCY5_ENST00000491190.1_Missense_Mutation_p.G206C|ADCY5_ENST00000309879.5_Missense_Mutation_p.G223C	NM_183357.2	NP_899200.1	O95622	ADCY5_HUMAN	adenylate cyclase 5	573	Guanylate cyclase 1. {ECO:0000255|PROSITE-ProRule:PRU00099}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(22)|ovary(5)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(114;0.0342)		CCAAGGACACCGCAGTGTACT	0.597											OREG0015742	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G573C		Atlas-SNP	.											.	ADCY5	169	.	0			c.G1717T						PASS	.						179	140	153					3																	123047579		2203	4300	6503	SO:0001583	missense	111	exon6			GGACACCGCAGTG	U65473	CCDS3022.1, CCDS56274.1	3q21.1	2013-02-04			ENSG00000173175	ENSG00000173175	4.6.1.1	"Adenylate cyclases"	236	protein-coding gene	gene with protein product		600293				10481931	Standard	NM_183357		Approved	AC5	uc003egh.2	O95622	OTTHUMG00000159517	ENST00000462833.1:c.1717G>T	chr3.hg19:g.123047579C>A	ENSP00000419361:p.Gly573Cys	151.0	0.0	.	1523	189.0	11.0	.	NM_183357	B7Z8A6|Q7RTV7|Q8NFM3	Missense_Mutation	SNP	ENST00000462833.1	hg19	CCDS3022.1	.	.	.	.	.	.	.	.	.	.	C	34	5.403693	0.96051	.	.	ENSG00000173175	ENST00000462833;ENST00000491190;ENST00000309879;ENST00000466617	D;D;D;D	0.90197	-2.63;-2.63;-2.63;-2.63	5.38	5.38	0.77491	Adenylyl cyclase class-3/4/guanylyl cyclase, conserved site (1);Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.85682	D	0.000000	D	0.97536	0.9193	H	0.98407	4.225	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99063	1.0831	10	0.87932	D	0	.	19.1549	0.93506	0.0:1.0:0.0:0.0	.	573;206	O95622;B3KWA8	ADCY5_HUMAN;.	C	573;206;223;132	ENSP00000419361:G573C;ENSP00000418537:G206C;ENSP00000308685:G223C;ENSP00000420082:G132C	ENSP00000308685:G223C	G	-	1	0	ADCY5	124530269	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.529000	0.85273	0.655000	0.94253	GGT	.	.	.	none		0.597	ADCY5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355889.4	XM_171048		A	123047579	C	A	123047579	3	1	160	1	0	0	0	0	1	0	0	0	297	652	23	4	2132	4	ADCY5	3	123047579	Missense_Mutation	SNP	C	TCGA-DZ-6135-01A-11D-1961-08	9671431	123047579	74974851	9	9468											
SSR3	6747	hgsc.bcm.edu	37	chr3	156266708	156266708	+	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	tcaaacctttcatctttctcCttccgagacatctttctatt	8	18	2	13	1	6	1	2	0	4	1	8	2	7	1	3	0	1	0	3	0	2	6			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr3:156266708C>A	ENST00000265044.2	-	3	439	c.345G>T	c.(343-345)aaG>aaT	p.K115N	SSR3_ENST00000496050.1_Missense_Mutation_p.K63N|SSR3_ENST00000476217.1_Missense_Mutation_p.K115N|SSR3_ENST00000463503.1_Missense_Mutation_p.K63N|SSR3_ENST00000467789.1_Missense_Mutation_p.K115N|SSR3_ENST00000478842.1_5'UTR	NM_007107.3	NP_009038.1	Q9UNL2	SSRG_HUMAN	signal sequence receptor, gamma (translocon-associated protein gamma)	115					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	integral component of endoplasmic reticulum membrane (GO:0030176)|Sec61 translocon complex (GO:0005784)				endometrium(1)|prostate(2)	3			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			CATCTTTCTCCTTCCGAGACA	0.363																																					p.K115N		Atlas-SNP	.											.	SSR3	17	.	0			c.G345T						PASS	.						88	85	86					3																	156266708		2203	4300	6503	SO:0001583	missense	6747	exon3			TTTCTCCTTCCGA	BC017203	CCDS3176.1	3q25.31	2004-02-27			ENSG00000114850	ENSG00000114850			11325	protein-coding gene	gene with protein product		606213					Standard	NM_007107		Approved	TRAPG	uc003fau.3	Q9UNL2	OTTHUMG00000158632	ENST00000265044.2:c.345G>T	chr3.hg19:g.156266708C>A	ENSP00000265044:p.Lys115Asn	77.0	0.0	.		116.0	26.0	.	NM_007107	B2R7D0|B4E2P2|D3DNK5|Q549M4	Missense_Mutation	SNP	ENST00000265044.2	hg19	CCDS3176.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.955265	0.73902	.	.	ENSG00000114850	ENST00000265044;ENST00000467789;ENST00000476217;ENST00000463503;ENST00000496050	.	.	.	5.41	2.62	0.31277	.	0.094589	0.64402	D	0.000001	T	0.79015	0.4375	M	0.87827	2.91	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74674	0.984;0.971	T	0.81282	-0.1003	9	0.87932	D	0	-1.3739	11.1574	0.48495	0.0:0.7892:0.0:0.2108	.	115;115	B4E2P2;Q9UNL2	.;SSRG_HUMAN	N	115;115;115;63;63	.	ENSP00000265044:K115N	K	-	3	2	SSR3	157749402	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.461000	0.35255	0.767000	0.33267	0.650000	0.86243	AAG	.	.	.	none		0.363	SSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351521.1	NM_007107		A	156266708	C	A	156266708	3	1	160	1	0	0	0	0	1	0	0	0	15204	680	24	4	224	4	SSR3	3	156266708	Missense_Mutation	SNP	C	TCGA-DZ-6135-01A-11D-1961-08	33219129	156266708	41755722	10	9469											
HELQ	113510	hgsc.bcm.edu	37	chr4	84342848	84342848	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgagcaaggtataaagaacAaaagacagatatagcctgtt	18	9	9	5	0	0	4	0	1	0	3	0	4	0	4	1	1	3	3	1	1	9	6			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr4:84342848A>G	ENST00000295488.3	-	15	2979	c.2817T>C	c.(2815-2817)ttT>ttC	p.F939F	HELQ_ENST00000510985.1_Silent_p.F872F	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	939					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						TATAAAGAACAAAAGACAGAT	0.343								Other identified genes with known or suspected DNA repair function																													p.F939F		Atlas-SNP	.											.	HELQ	95	.	0			c.T2817C						PASS	.						84	83	84					4																	84342848		2203	4300	6503	SO:0001819	synonymous_variant	113510	exon15			AAGAACAAAAGAC	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.2817T>C	chr4.hg19:g.84342848A>G		58.0	0.0	.		61.0	26.0	.	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Silent	SNP	ENST00000295488.3	hg19	CCDS3603.1																																																																																			.	.	.	none		0.343	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636		G	84342848	A	G	84342848	2	3	160	1	0	0	0	0	0	0	0	1	7054	127	5	3		3	HELQ	4	84342848	Silent	SNP	A	TCGA-DZ-6135-01A-11D-1961-08		84342848	106811428	11	9470											
BHMT	635	hgsc.bcm.edu	37	chr5	78415091	78415091	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cactctcccagttcgccagcTtcatcgagagttcctcagag	8	10	8	15	2	3	2	2	0	1	2	7	3	4	2	3	0	1	3	3	0	0	3			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr5:78415091T>C	ENST00000274353.5	+	3	283	c.176T>C	c.(175-177)cTt>cCt	p.L59P	DMGDH_ENST00000520388.1_Intron|BHMT_ENST00000524080.1_Intron	NM_001713.2	NP_001704.2	Q93088	BHMT1_HUMAN	betaine--homocysteine S-methyltransferase	59	Hcy-binding. {ECO:0000255|PROSITE- ProRule:PRU00333}.				amino-acid betaine catabolic process (GO:0006579)|amino-acid betaine metabolic process (GO:0006577)|cellular nitrogen compound metabolic process (GO:0034641)|L-methionine salvage (GO:0071267)|protein methylation (GO:0006479)|regulation of homocysteine metabolic process (GO:0050666)|response to organonitrogen compound (GO:0010243)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	betaine-homocysteine S-methyltransferase activity (GO:0047150)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)	29		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.88e-45)|Epithelial(54;8.07e-41)|all cancers(79;3.51e-36)	L-Methionine(DB00134)	GTTCGCCAGCTTCATCGAGAG	0.438																																					p.L59P		Atlas-SNP	.											.	BHMT	53	.	0			c.T176C						PASS	.						99	94	95					5																	78415091		2203	4300	6503	SO:0001583	missense	635	exon3			GCCAGCTTCATCG	BC012616	CCDS4046.1	5q14.1	2012-09-20	2010-04-28		ENSG00000145692	ENSG00000145692	2.1.1.5		1047	protein-coding gene	gene with protein product	"betaine homocysteine methyltransferase"	602888				8798461, 9281325	Standard	NM_001713		Approved	BHMT1	uc003kfu.4	Q93088	OTTHUMG00000108157	ENST00000274353.5:c.176T>C	chr5.hg19:g.78415091T>C	ENSP00000274353:p.Leu59Pro	98.0	0.0	.		112.0	42.0	.	NM_001713	Q9UNI9	Missense_Mutation	SNP	ENST00000274353.5	hg19	CCDS4046.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.611557	0.87258	.	.	ENSG00000145692	ENST00000274353	T	0.13089	2.62	5.6	5.6	0.85130	Homocysteine S-methyltransferase (4);	0.000000	0.85682	D	0.000000	T	0.48390	0.1497	M	0.92833	3.35	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.61237	-0.7103	10	0.87932	D	0	-13.4798	16.0786	0.80985	0.0:0.0:0.0:1.0	.	59	Q93088	BHMT1_HUMAN	P	59	ENSP00000274353:L59P	ENSP00000274353:L59P	L	+	2	0	BHMT	78450847	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.669000	0.83911	2.254000	0.74563	0.460000	0.39030	CTT	.	.	.	none		0.438	BHMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226961.1	NM_001713		C	78415091	T	C	78415091	3	2	160	1	0	0	0	0	1	0	0	0	1425	1609	56	3	186	3	BHMT	5	78415091	Missense_Mutation	SNP	T	TCGA-DZ-6135-01A-11D-1961-08		78415091	102500169	12	9471											
PGGT1B	5229	hgsc.bcm.edu	37	chr5	114573574	114573574	+	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	cctcccatcttccagctgaaGggctctcaagcccgctaagc	8	8	8	17	1	2	1	1	1	2	0	5	1	4	1	4	1	3	3	4	1	3	2			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr5:114573574G>A	ENST00000419445.1	-	4	480	c.460C>T	c.(460-462)Ctt>Ttt	p.L154F	PGGT1B_ENST00000379615.3_Missense_Mutation_p.L154F	NM_005023.3	NP_005014.2	P53609	PGTB1_HUMAN	protein geranylgeranyltransferase type I, beta subunit	154					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)		TCCAGCTGAAGGGCTCTCAAG	0.383																																					p.L154F		Atlas-SNP	.											.	PGGT1B	26	.	0			c.C460T						PASS	.						72	78	76					5																	114573574		2201	4300	6501	SO:0001583	missense	5229	exon4			GCTGAAGGGCTCT		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.460C>T	chr5.hg19:g.114573574G>A	ENSP00000404676:p.Leu154Phe	161.0	0.0	.		188.0	79.0	.	NM_005023	Q5MJP9	Missense_Mutation	SNP	ENST00000419445.1	hg19	CCDS4116.1	.	.	.	.	.	.	.	.	.	.	G	16.92	3.254124	0.59212	.	.	ENSG00000164219	ENST00000419445;ENST00000379615	T;T	0.32515	1.45;1.45	5.47	4.6	0.57074	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.113305	0.64402	D	0.000008	T	0.64692	0.2621	M	0.91818	3.245	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.993	T	0.75164	-0.3414	10	0.66056	D	0.02	-11.4224	16.6769	0.85281	0.0:0.1298:0.8702:0.0	.	154;154	P53609-2;P53609	.;PGTB1_HUMAN	F	154	ENSP00000404676:L154F;ENSP00000368935:L154F	ENSP00000368935:L154F	L	-	1	0	PGGT1B	114601473	1.000000	0.71417	0.947000	0.38551	0.329000	0.28539	9.740000	0.98839	1.422000	0.47177	0.655000	0.94253	CTT	.	.	.	none		0.383	PGGT1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250855.2	NM_005023		A	114573574	G	A	114573574	3	1	160	1	0	0	0	0	1	0	0	0	11796	1000	35	2	697	2	PGGT1B	5	114573574	Missense_Mutation	SNP	G	TCGA-DZ-6135-01A-11D-1961-08	36158483	114573574	66341686	13	9472											
WDR55	54853	hgsc.bcm.edu	37	chr5	140049032	140049032	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcctggccagtagtggccaTgaccagcgcctcaagttttg	7	11	11	12	1	1	1	1	1	0	0	2	1	2	1	5	2	1	2	5	2	2	4			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr5:140049032T>C	ENST00000358337.5	+	7	1182	c.945T>C	c.(943-945)caT>caC	p.H315H	WDR55_ENST00000520764.1_3'UTR	NM_017706.4	NP_060176	Q9H6Y2	WDR55_HUMAN	WD repeat domain 55	315					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)			GTAGTGGCCATGACCAGCGCC	0.632																																					p.H315H		Atlas-SNP	.											.	WDR55	27	.	0			c.T945C						PASS	.						27	30	29					5																	140049032		2203	4300	6503	SO:0001819	synonymous_variant	54853	exon7			TGGCCATGACCAG	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.945T>C	chr5.hg19:g.140049032T>C		36.0	0.0	.		45.0	18.0	.	NM_017706	Q9NXK4	Silent	SNP	ENST00000358337.5	hg19	CCDS4235.1																																																																																			.	.	.	none		0.632	WDR55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251680.3	NM_017706		C	140049032	T	C	140049032	2	2	160	1	0	0	0	0	0	0	0	1	17319	1461	51	3		3	WDR55	5	140049032	Silent	SNP	T	TCGA-DZ-6135-01A-11D-1961-08	25475458	140049032	40866228	14	9473											
PCDHGC3	5098	hgsc.bcm.edu	37	chr5	140856169	140856169	+	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	ctcgagagcgcgcacgatccCgatgtgggaagcaactcttt	9	8	12	12	5	1	1	0	0	1	1	3	5	2	2	1	1	3	2	1	1	2	1			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr5:140856169C>A	ENST00000308177.3	+	1	590	c.486C>A	c.(484-486)ccC>ccA	p.P162P	PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGB2_ENST00000522605.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	162	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)			CGCACGATCCCGATGTGGGAA	0.567																																					p.P162P		Atlas-SNP	.											.	PCDHGC3	173	.	0			c.C486A						PASS	.						54	56	56					5																	140856169		2203	4300	6503	SO:0001819	synonymous_variant	5098	exon1			CGATCCCGATGTG	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.486C>A	chr5.hg19:g.140856169C>A		125.0	0.0	.		101.0	7.0	.	NM_032402	O60622|Q08192|Q9Y5C4	Silent	SNP	ENST00000308177.3	hg19	CCDS4261.1																																																																																			.	.	.	none		0.567	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588		A	140856169	C	A	140856169	2	1	160	1	0	0	0	0	0	0	0	1	11576	639	23	4		4	PCDHGC3	5	140856169	Silent	SNP	C	TCGA-DZ-6135-01A-11D-1961-08	807137	140856169	40059091	15	9474											
REV3L	5980	hgsc.bcm.edu	37	chr6	111632330	111632330	+	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	ataagaaaaacttcctctgtAttccttggcaaagataaagt	16	12	6	7	0	1	2	0	0	1	2	3	2	3	2	2	1	1	2	2	1	7	6			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr6:111632330A>T	ENST00000358835.3	-	30	9191	c.8737T>A	c.(8737-8739)Tac>Aac	p.Y2913N	REV3L_ENST00000368805.1_Missense_Mutation_p.Y2913N|REV3L_ENST00000368802.3_Missense_Mutation_p.Y2913N|REV3L_ENST00000435970.1_Missense_Mutation_p.Y2835N|RP5-1112D6.8_ENST00000607434.1_RNA|REV3L_ENST00000462119.1_5'UTR			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2913					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)		CTTCCTCTGTATTCCTTGGCA	0.408								DNA polymerases (catalytic subunits)																													p.Y2913N		Atlas-SNP	.											.	REV3L	386	.	0			c.T8737A						PASS	.						179	179	179					6																	111632330		2203	4300	6503	SO:0001583	missense	5980	exon29			CTCTGTATTCCTT	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.8737T>A	chr6.hg19:g.111632330A>T	ENSP00000351697:p.Tyr2913Asn	258.0	0.0	.		267.0	91.0	.	NM_002912	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	hg19	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	A	27.2	4.809421	0.90707	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	T;T;T;T	0.17213	2.29;2.29;2.29;2.29	5.48	5.48	0.80851	DNA-directed DNA polymerase, family B, multifunctional domain (1);	0.069117	0.64402	D	0.000012	T	0.41026	0.1141	M	0.88310	2.945	0.58432	D	0.999999	D	0.69078	0.997	D	0.81914	0.995	T	0.52601	-0.8554	10	0.87932	D	0	-3.7627	15.5643	0.76277	1.0:0.0:0.0:0.0	.	2913	O60673	DPOLZ_HUMAN	N	2913;2913;2913;2835	ENSP00000357792:Y2913N;ENSP00000357795:Y2913N;ENSP00000351697:Y2913N;ENSP00000402003:Y2835N	ENSP00000351697:Y2913N	Y	-	1	0	REV3L	111739023	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.266000	0.95659	2.085000	0.62840	0.455000	0.32223	TAC	.	.	.	none		0.408	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		T	111632330	A	T	111632330	3	4	160	1	0	0	0	0	1	0	0	0	13253	449	16	5	671	5	REV3L	6	111632330	Missense_Mutation	SNP	A	TCGA-DZ-6135-01A-11D-1961-08		111632330	59482737	16	9475											
NFE2L3	9603	hgsc.bcm.edu	37	chr7	26223344	26223347	+	Frame_Shift_Del	DEL	TTCT	TTCT	-																															catctgaatgggacagatacTtctttctctctggaagactt																								rs370809004|rs534912151	byFrequency	TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	TTCT	TTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr7:26223344_26223347delTTCT	ENST00000056233.3	+	3	1033_1036	c.774_777delTTCT	c.(772-777)acttctfs	p.TS258fs		NM_004289.6	NP_004280.5	Q9Y4A8	NF2L3_HUMAN	nuclear factor, erythroid 2-like 3	258					transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(5)|urinary_tract(7)	29						GGACAGATACTTCTTTCTCTCTGG	0.402																																					p.258_259del		Atlas-INDEL	.											.	NFE2L3	77	.	0			c.773_776del						PASS	.																																			SO:0001589	frameshift_variant	9603	exon3			.	AB010812	CCDS5396.1	7p15.2	2013-08-23	2013-08-23		ENSG00000050344	ENSG00000050344		"basic leucine zipper proteins"	7783	protein-coding gene	gene with protein product		604135	"nuclear factor (erythroid-derived 2)-like 3"			10037736	Standard	NM_004289		Approved	Nrf3	uc003sxq.3	Q9Y4A8	OTTHUMG00000023882	ENST00000056233.3:c.774_777delTTCT	chr7.hg19:g.26223348_26223351delTTCT	ENSP00000056233:p.Thr258fs	110.0	0.0	0		129.0	39.0	0.302326	NM_004289	Q6NUS0|Q7Z498|Q86UJ4|Q86VR5|Q9UQA4	Frame_Shift_Del	DEL	ENST00000056233.3	hg19	CCDS5396.1																																																																																			.	.	.	none		0.402	NFE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214088.1			-	26223347	TTCT	-	26223344	7	5	160	1	0	1	0	1	0	0	0	0	10376	1596	56	0	784	0	NFE2L3	7	26223344	Frame_Shift_Del	DEL	TTCT	TCGA-DZ-6135-01A-11D-1961-08		26223344	132915319	17	9476											
MET	4233	hgsc.bcm.edu	37	chr7	116423474	116423474	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagctgccagtgaagtggaTggctttggaaagtctgcaaa	13	9	13	6	0	1	1	0	1	1	0	1	3	1	3	1	3	3	3	1	3	4	1	rs121913245		TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr7:116423474T>C	ENST00000318493.6	+	19	3990	c.3803T>C	c.(3802-3804)aTg>aCg	p.M1268T	MET_ENST00000397752.3_Missense_Mutation_p.M1250T|MET_ENST00000539704.1_Missense_Mutation_p.M120T			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.M1268T(4)		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)			GTGAAGTGGATGGCTTTGGAA	0.393			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.M1268T		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,rectum,carcinoma,+1,5	MET	412	.	4	Substitution - Missense(4)	kidney(4)	c.T3803C	GRCh37	CM992181	MET	M	rs121913245	PASS	.						93	92	92					7																	116423474		1872	4102	5974	SO:0001583	missense	4233	exon19	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	AGTGGATGGCTTT	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.3803T>C	chr7.hg19:g.116423474T>C	ENSP00000317272:p.Met1268Thr	61.0	0.0	.		61.0	25.0	.	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	T	18.99	3.740165	0.69304	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000539704	T;T;T	0.37752	1.18;1.18;1.18	5.68	5.68	0.88126	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	0.61714	0.2369	M	0.75264	2.295	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;1.0	T	0.65734	-0.6096	10	0.87932	D	0	.	16.2225	0.82267	0.0:0.0:0.0:1.0	.	1268;1250	P08581-2;P08581	.;MET_HUMAN	T	1250;1268;120	ENSP00000380860:M1250T;ENSP00000317272:M1268T;ENSP00000445020:M120T	ENSP00000317272:M1268T	M	+	2	0	MET	116210710	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.997000	0.88414	2.289000	0.77006	0.460000	0.39030	ATG	.	.	.	weak		0.393	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			C	116423474	T	C	116423474	3	2	160	1	0	0	0	0	1	0	0	0	9492	1464	51	3	3873	3	MET	7	116423474	Missense_Mutation	SNP	T	TCGA-DZ-6135-01A-11D-1961-08	90200130	116423474	42715189	18	9477											
PRKAG2	51422	hgsc.bcm.edu	37	chr7	151372604	151372604	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgccctgtgtccgggggggAagacgaggcatagatgcgat	8	7	17	9	3	0	2	0	0	0	2	1	5	1	3	2	4	2	1	2	4	2	1			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr7:151372604A>G	ENST00000287878.4	-	4	1090	c.586T>C	c.(586-588)Tcc>Ccc	p.S196P	PRKAG2_ENST00000392801.2_Missense_Mutation_p.S152P|PRKAG2_ENST00000492843.1_Missense_Mutation_p.S72P|PRKAG2_ENST00000433631.2_Missense_Mutation_p.S72P|PRKAG2_ENST00000461529.1_5'Flank	NM_016203.3	NP_057287.2	Q9UGJ0	AAKG2_HUMAN	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	196					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)	TCCGGGGGGGAAGACGAGGCA	0.587																																					p.S196P		Atlas-SNP	.											.	PRKAG2	86	.	0			c.T586C						PASS	.						107	94	98					7																	151372604		2203	4300	6503	SO:0001583	missense	51422	exon4			GGGGGGAAGACGA	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.586T>C	chr7.hg19:g.151372604A>G	ENSP00000287878:p.Ser196Pro	125.0	0.0	.		123.0	5.0	.	NM_016203	Q53Y07|Q6NUI0|Q75MP4|Q9NUZ9|Q9UDN8|Q9ULX8	Missense_Mutation	SNP	ENST00000287878.4	hg19	CCDS5928.1	.	.	.	.	.	.	.	.	.	.	A	8.526	0.869797	0.17322	.	.	ENSG00000106617	ENST00000287878;ENST00000492843;ENST00000433631;ENST00000392801	D;D;D;D	0.91295	-2.16;-2.82;-2.82;-2.56	5.21	1.48	0.22813	.	0.287492	0.34652	N	0.003782	T	0.82066	0.4956	L	0.27053	0.805	0.20926	N	0.999826	B;B;B	0.14805	0.007;0.011;0.001	B;B;B	0.13407	0.008;0.009;0.0	T	0.70385	-0.4886	10	0.51188	T	0.08	.	8.0661	0.30661	0.7474:0.0:0.2526:0.0	.	72;196;196	B7Z6X8;Q8NCK6;Q9UGJ0	.;.;AAKG2_HUMAN	P	196;72;72;152	ENSP00000287878:S196P;ENSP00000419577:S72P;ENSP00000406544:S72P;ENSP00000376549:S152P	ENSP00000287878:S196P	S	-	1	0	PRKAG2	151003537	1.000000	0.71417	0.019000	0.16419	0.005000	0.04900	2.388000	0.44398	0.019000	0.15079	-0.388000	0.06559	TCC	.	.	.	none		0.587	PRKAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348440.2	NM_016203		G	151372604	A	G	151372604	3	3	160	1	0	0	0	0	1	0	0	0	12511	246	9	3	1175	3	PRKAG2	7	151372604	Missense_Mutation	SNP	A	TCGA-DZ-6135-01A-11D-1961-08	34949130	151372604	7766059	19	9478											
TOPORS	10210	hgsc.bcm.edu	37	chr9	32543270	32543270	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagatggtcctggagtttcaTcatcccatggtgcctgacta	9	12	10	10	0	2	2	2	1	0	1	4	3	4	3	3	3	1	1	3	3	2	2			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr9:32543270T>C	ENST00000360538.2	-	3	1369	c.1253A>G	c.(1252-1254)gAt>gGt	p.D418G	TOPORS_ENST00000379858.1_Missense_Mutation_p.D353G	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	418					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)		TGGAGTTTCATCATCCCATGG	0.423																																					p.D418G		Atlas-SNP	.											.	TOPORS	127	.	0			c.A1253G						PASS	.						126	126	126					9																	32543270		2203	4299	6502	SO:0001583	missense	10210	exon3			GTTTCATCATCCC	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.1253A>G	chr9.hg19:g.32543270T>C	ENSP00000353735:p.Asp418Gly	156.0	0.0	.		140.0	59.0	.	NM_005802	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	hg19	CCDS6527.1	.	.	.	.	.	.	.	.	.	.	T	9.322	1.058402	0.19987	.	.	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.18657	2.2;2.21	5.63	5.63	0.86233	.	0.140255	0.33199	N	0.005175	T	0.20292	0.0488	L	0.34521	1.04	0.52099	D	0.999947	P	0.47191	0.891	B	0.42522	0.39	T	0.01252	-1.1405	10	0.59425	D	0.04	-15.9255	14.84	0.70217	0.0:0.0:0.0:1.0	.	418	Q9NS56	TOPRS_HUMAN	G	418;353	ENSP00000353735:D418G;ENSP00000369187:D353G	ENSP00000353735:D418G	D	-	2	0	TOPORS	32533270	1.000000	0.71417	1.000000	0.80357	0.280000	0.26924	7.698000	0.84413	2.145000	0.66743	0.528000	0.53228	GAT	.	.	.	none		0.423	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		C	32543270	T	C	32543270	3	2	160	1	0	0	0	0	1	0	0	0	16382	1435	50	3	1888	3	TOPORS	9	32543270	Missense_Mutation	SNP	T	TCGA-DZ-6135-01A-11D-1961-08		32543270	108670161	20	9479											
SPTAN1	6709	hgsc.bcm.edu	37	chr9	131361264	131361264	+	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	agtgtatggcatgatgcccaGggtaagtttcgggtgctgtg	7	12	16	6	1	0	1	0	1	0	0	1	1	0	1	1	3	2	5	1	3	2	3			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr9:131361264G>T	ENST00000372731.4	+	26	3652	c.3542G>T	c.(3541-3543)aGg>aTg	p.R1181M	SPTAN1_ENST00000372739.3_Splice_Site_p.R1181M|SPTAN1_ENST00000475367.1_3'UTR|SPTAN1_ENST00000358161.5_Splice_Site_p.R1181M	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1181					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						ATGATGCCCAGGGTAAGTTTC	0.398																																					p.R1181M	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.G3542T						PASS	.						195	177	183					9																	131361264		2203	4300	6503	SO:0001630	splice_region_variant	6709	exon26			TGCCCAGGGTAAG	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.3543+1G>T	chr9.hg19:g.131361264G>T		131.0	0.0	.		129.0	57.0	.	NM_003127	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Missense_Mutation	SNP	ENST00000372731.4	hg19	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.758441	0.49468	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	T;T;T	0.51325	0.71;0.73;0.71	5.93	2.99	0.34606	.	0.237058	0.49916	D	0.000123	T	0.27419	0.0673	N	0.08118	0	0.41841	D	0.990122	B;B;P;P;P	0.37276	0.187;0.22;0.589;0.589;0.454	B;B;B;B;B	0.37047	0.121;0.188;0.24;0.24;0.121	T	0.13045	-1.0524	10	0.72032	D	0.01	.	10.0762	0.42362	0.2288:0.0:0.7712:0.0	.	1181;1161;1161;1181;1181	A6NG51;B4DTV8;Q13813-3;Q13813-2;Q13813	.;.;.;.;SPTA2_HUMAN	M	1181;1181;1181;1161	ENSP00000350882:R1181M;ENSP00000361816:R1181M;ENSP00000361824:R1181M	ENSP00000350882:R1181M	R	+	2	0	SPTAN1	130401085	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	1.468000	0.35332	0.342000	0.23796	0.555000	0.69702	AGG	.	.	.	none		0.398	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127	Missense_Mutation	T	131361264	G	T	131361264	5	4	160	1	0	0	0	0	0	0	1	0	15129	1014	35	4	3640	4	SPTAN1	9	131361264	Splice_Site	SNP	G	TCGA-DZ-6135-01A-11D-1961-08	98817994	131361264	9852167	21	9480											
CHD4	1108	hgsc.bcm.edu	37	chr12	6711561	6711561	+	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	cctcctttttttggcgcttgCtcttagggattttagggtcc	3	18	10	10	1	1	0	0	0	1	0	3	1	3	1	3	3	1	2	3	3	2	7			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr12:6711561C>G	ENST00000357008.2	-	3	366	c.203G>C	c.(202-204)aGc>aCc	p.S68T	CHD4_ENST00000309577.6_Missense_Mutation_p.S68T|CHD4_ENST00000544040.1_Missense_Mutation_p.S68T|CHD4_ENST00000544484.1_Missense_Mutation_p.S65T	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	68					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						TTGGCGCTTGCTCTTAGGGAT	0.478																																					p.S68T	Colon(32;586 792 4568 16848 45314)	Atlas-SNP	.											.	CHD4	539	.	0			c.G203C						PASS	.						238	240	239					12																	6711561		2203	4300	6503	SO:0001583	missense	1108	exon3			CGCTTGCTCTTAG	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.203G>C	chr12.hg19:g.6711561C>G	ENSP00000349508:p.Ser68Thr	520.0	0.0	.		417.0	127.0	.	NM_001273	Q8IXZ5	Missense_Mutation	SNP	ENST00000357008.2	hg19	CCDS8552.1	.	.	.	.	.	.	.	.	.	.	C	11.51	1.660131	0.29515	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464;ENST00000545942;ENST00000545584	D;D;D;D;T	0.90197	-2.63;-2.6;-2.62;-2.63;0.88	5.26	5.26	0.73747	.	0.301114	0.34879	N	0.003602	D	0.84106	0.5399	L	0.36672	1.1	0.38243	D	0.941392	B;B;B	0.31817	0.341;0.231;0.341	B;B;B	0.28011	0.085;0.027;0.059	T	0.81773	-0.0779	10	0.12766	T	0.61	-0.8518	14.1344	0.65276	0.1501:0.8499:0.0:0.0	.	68;68;68	Q14839-2;Q14839;F5GWX5	.;CHD4_HUMAN;.	T	65;68;68;68;49;68;68	ENSP00000440392:S65T;ENSP00000440542:S68T;ENSP00000312419:S68T;ENSP00000349508:S68T;ENSP00000437506:S68T	ENSP00000312419:S68T	S	-	2	0	CHD4	6581822	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.832000	0.55783	2.633000	0.89246	0.555000	0.69702	AGC	.	.	.	none		0.478	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273		G	6711561	C	G	6711561	3	3	160	1	0	0	0	0	1	0	0	0	3329	797	28	4	5687	4	CHD4	12	6711561	Missense_Mutation	SNP	C	TCGA-DZ-6135-01A-11D-1961-08		6711561	127140334	22	9481											
TUBA3C	7278	hgsc.bcm.edu	37	chr13	19751148	19751148	+	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	atggccgcgttgacatctttCgggaccacatcccccctgta	7	10	9	15	3	1	1	0	1	1	0	3	2	2	2	5	2	0	2	5	2	1	3			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr13:19751148C>G	ENST00000400113.3	-	4	1079	c.975G>C	c.(973-975)ccG>ccC	p.P325P		NM_006001.2	NP_005992.1	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	325					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(4)|prostate(7)|skin(7)|urinary_tract(1)	72		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)		TGACATCTTTCGGGACCACAT	0.547																																					p.P325P		Atlas-SNP	.											TUBA3C,NS,carcinoma,0,2	TUBA3C	166	.	0			c.G975C						PASS	.						158	130	139					13																	19751148		2203	4300	6503	SO:0001819	synonymous_variant	7278	exon4			ATCTTTCGGGACC	AF005392	CCDS9284.1	13q12.11	2007-06-20	2007-02-12	2007-02-12	ENSG00000198033	ENSG00000198033		"Tubulins"	12408	protein-coding gene	gene with protein product		602528	"tubulin, alpha 2"	TUBA2		9465305	Standard	NM_006001		Approved	bA408E5.3	uc009zzj.3	Q13748	OTTHUMG00000016481	ENST00000400113.3:c.975G>C	chr13.hg19:g.19751148C>G		180.0	2.0	.		138.0	6.0	.	NM_006001	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Silent	SNP	ENST00000400113.3	hg19	CCDS9284.1																																																																																			.	C|1.000;|0.000	.	weak		0.547	TUBA3C-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044007.2	NM_006001		G	19751148	C	G	19751148	2	3	160	1	0	0	0	0	0	0	0	1	16758	871	31	4		4	TUBA3C	13	19751148	Silent	SNP	C	TCGA-DZ-6135-01A-11D-1961-08		19751148	95418730	23	9482											
LNX2	222484	hgsc.bcm.edu	37	chr13	28143269	28143269	+	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	tgccgctccacaggcactgcGcctgtccccaaacagtctgc	7	7	9	18	2	1	0	0	0	1	0	3	0	3	0	5	1	4	2	5	1	1	0			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr13:28143269G>A	ENST00000316334.3	-	3	681	c.552C>T	c.(550-552)ggC>ggT	p.G184G		NM_153371.3	NP_699202.1	Q8N448	LNX2_HUMAN	ligand of numb-protein X 2	184					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)		CAGGCACTGCGCCTGTCCCCA	0.532																																					p.G184G		Atlas-SNP	.											.	LNX2	70	.	0			c.C552T						PASS	.						241	235	237					13																	28143269		2203	4300	6503	SO:0001819	synonymous_variant	222484	exon3			CACTGCGCCTGTC	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.552C>T	chr13.hg19:g.28143269G>A		339.0	1.0	.		346.0	119.0	.	NM_153371	Q5W0P0|Q6ZMH2|Q96SH4	Silent	SNP	ENST00000316334.3	hg19	CCDS9323.1																																																																																			.	.	.	none		0.532	LNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044302.2			A	28143269	G	A	28143269	2	1	160	1	0	0	0	0	0	0	0	1	8873	1074	38	1		1	LNX2	13	28143269	Silent	SNP	G	TCGA-DZ-6135-01A-11D-1961-08	8392121	28143269	87026609	24	9483											
KLHL1	57626	hgsc.bcm.edu	37	chr13	70549759	70549759	+	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	cagactactgtacctatgtgCaggtatctttcggttcccaa	9	13	8	11	1	1	1	0	0	1	1	3	1	2	1	2	2	3	4	2	2	5	6			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr13:70549759C>G	ENST00000377844.4	-	2	1432	c.673G>C	c.(673-675)Gca>Cca	p.A225P	KLHL1_ENST00000545028.1_Intron	NM_020866.2	NP_065917.1	Q9NR64	KLHL1_HUMAN	kelch-like family member 1	225	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				actin cytoskeleton organization (GO:0030036)|adult walking behavior (GO:0007628)|cerebellar Purkinje cell layer development (GO:0021680)|dendrite development (GO:0016358)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	actin binding (GO:0003779)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(56)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	84		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)		TACCTATGTGCAGGTATCTTT	0.403																																					p.A225P		Atlas-SNP	.											.	KLHL1	164	.	0			c.G673C						PASS	.						148	136	140					13																	70549759		2203	4300	6503	SO:0001583	missense	57626	exon2			TATGTGCAGGTAT	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.673G>C	chr13.hg19:g.70549759C>G	ENSP00000367075:p.Ala225Pro	136.0	0.0	.		157.0	50.0	.	NM_020866	A8K5X0|Q5VZ64|Q9H4X4|Q9NR65|Q9P238	Missense_Mutation	SNP	ENST00000377844.4	hg19	CCDS9445.1	.	.	.	.	.	.	.	.	.	.	C	19.70	3.876217	0.72180	.	.	ENSG00000150361	ENST00000377844	T	0.78003	-1.14	5.82	5.82	0.92795	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.172430	0.41097	D	0.000941	D	0.92795	0.7709	H	0.97023	3.925	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.94480	0.7692	10	0.87932	D	0	.	20.0951	0.97834	0.0:1.0:0.0:0.0	.	225	Q9NR64	KLHL1_HUMAN	P	225	ENSP00000367075:A225P	ENSP00000367075:A225P	A	-	1	0	KLHL1	69447760	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.197000	0.77814	2.753000	0.94483	0.467000	0.42956	GCA	.	.	.	none		0.403	KLHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045231.3	NM_020866		G	70549759	C	G	70549759	3	3	160	1	0	0	0	0	1	0	0	0	8372	710	25	4	1613	4	KLHL1	13	70549759	Missense_Mutation	SNP	C	TCGA-DZ-6135-01A-11D-1961-08	42406490	70549759	44620119	25	9484											
UBE3A	7337	hgsc.bcm.edu	37	chr15	25616649	25616649	+	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	acagacacatcatcagggccTaatttttgcaaattgttgtc	12	13	7	9	0	2	1	2	0	0	1	3	1	2	1	1	1	1	2	1	1	2	5			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr15:25616649T>A	ENST00000397954.2	-	4	680	c.681A>T	c.(679-681)ttA>ttT	p.L227F	UBE3A_ENST00000566215.1_Missense_Mutation_p.L204F|UBE3A_ENST00000428984.2_Missense_Mutation_p.L204F|UBE3A_ENST00000232165.3_Missense_Mutation_p.L224F|UBE3A_ENST00000438097.1_Missense_Mutation_p.L204F|SNHG14_ENST00000554726.1_RNA			Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A	227					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)		CATCAGGGCCTAATTTTTGCA	0.418																																					p.L227F		Atlas-SNP	.											.	UBE3A	109	.	0			c.A681T						PASS	.						179	174	176					15																	25616649		2203	4300	6503	SO:0001583	missense	7337	exon7			AGGGCCTAATTTT	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.681A>T	chr15.hg19:g.25616649T>A	ENSP00000381045:p.Leu227Phe	226.0	0.0	.		231.0	80.0	.	NM_000462	A8K8Z9|P78355|Q93066|Q9UEP4|Q9UEP5|Q9UEP6|Q9UEP7|Q9UEP8|Q9UEP9	Missense_Mutation	SNP	ENST00000397954.2	hg19	CCDS45192.1	.	.	.	.	.	.	.	.	.	.	T	5.048	0.194522	0.09599	.	.	ENSG00000114062	ENST00000232165;ENST00000356465;ENST00000397954;ENST00000438097;ENST00000428984	T;T;T;T	0.18657	2.2;2.2;2.2;2.2	5.84	2.23	0.28157	.	0.385567	0.26421	N	0.024461	T	0.09992	0.0245	N	0.14661	0.345	0.47123	D	0.999328	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.17684	-1.0361	10	0.09590	T	0.72	.	9.4825	0.38908	0.0:0.293:0.0:0.707	.	224;227	Q05086-3;Q05086	.;UBE3A_HUMAN	F	224;224;227;204;204	ENSP00000232165:L224F;ENSP00000381045:L227F;ENSP00000411258:L204F;ENSP00000401265:L204F	ENSP00000232165:L224F	L	-	3	2	UBE3A	23167742	0.789000	0.28775	0.833000	0.33012	0.928000	0.56348	-0.010000	0.12743	0.448000	0.26722	0.482000	0.46254	TTA	.	.	.	none		0.418	UBE3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000434203.1	NM_000462		A	25616649	T	A	25616649	3	1	160	1	0	0	0	0	1	0	0	0	16891	1519	53	5	1978	5	UBE3A	15	25616649	Missense_Mutation	SNP	T	TCGA-DZ-6135-01A-11D-1961-08		25616649	76914743	26	9485											
CCDC78	124093	hgsc.bcm.edu	37	chr16	775528	775528	+	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	ggactgcacagccctggctgGtgccatctcctcgcagctcc	5	8	11	17	1	1	0	0	0	1	0	4	1	2	1	4	3	4	4	4	3	0	0			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr16:775528G>T	ENST00000293889.6	-	4	425	c.320C>A	c.(319-321)aCc>aAc	p.T107N	HAGHL_ENST00000341413.4_5'Flank|HAGHL_ENST00000561546.1_5'Flank|HAGHL_ENST00000564545.1_5'Flank|HAGHL_ENST00000564537.1_5'Flank|HAGHL_ENST00000549114.1_5'Flank|HAGHL_ENST00000389703.3_5'Flank	NM_001031737.2	NP_001026907.2	A2IDD5	CCD78_HUMAN	coiled-coil domain containing 78	107					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)				GCCCTGGCTGGTGCCATCTCC	0.652																																					p.T107N		Atlas-SNP	.											.	CCDC78	26	.	0			c.C320A						PASS	.						55	53	53					16																	775528		2194	4297	6491	SO:0001583	missense	124093	exon4			TGGCTGGTGCCAT	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.320C>A	chr16.hg19:g.775528G>T	ENSP00000293889:p.Thr107Asn	47.0	0.0	.		58.0	20.0	.	NM_001031737	B4DNY4|B4E1U6|Q05BY7|Q05CA0|Q6T2V5|Q6ZR33|Q8IUR3|Q8NAY7|Q96S12	Missense_Mutation	SNP	ENST00000293889.6	hg19	CCDS32353.1	.	.	.	.	.	.	.	.	.	.	G	3.380	-0.126581	0.06795	.	.	ENSG00000162004	ENST00000293889	T	0.42900	0.96	3.03	0.647	0.17796	.	0.915341	0.09100	N	0.848716	T	0.18299	0.0439	N	0.08118	0	0.09310	N	1	P;P;P;B	0.39157	0.662;0.662;0.662;0.016	B;B;B;B	0.32624	0.149;0.106;0.149;0.015	T	0.12426	-1.0548	10	0.59425	D	0.04	-0.2556	3.877	0.09061	0.156:0.2512:0.5928:0.0	.	107;107;181;107	A2IDD5-4;A2IDD5-6;A2IDD5-5;A2IDD5	.;.;.;CCD78_HUMAN	N	107	ENSP00000293889:T107N	ENSP00000293889:T107N	T	-	2	0	CCDC78	715529	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-0.489000	0.06490	0.376000	0.24707	0.436000	0.28706	ACC	.	.	.	none		0.652	CCDC78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241665.3	NM_173476		T	775528	G	T	775528	3	4	160	1	0	0	0	0	1	0	0	0	2854	1261	44	4	1040	4	CCDC78	16	775528	Missense_Mutation	SNP	G	TCGA-DZ-6135-01A-11D-1961-08		775528	89579225	27	9486											
SNX29	92017	hgsc.bcm.edu	37	chr16	12618621	12618621	+	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	tacctgcgcagcgtcatgaaCaaagtcatccagatggtccc	11	8	9	13	2	2	2	2	1	0	1	4	2	4	2	3	1	4	1	3	1	3	1			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr16:12618621C>T	ENST00000566228.1	+	20	2310	c.2241C>T	c.(2239-2241)aaC>aaT	p.N747N	SNX29_ENST00000323433.4_Silent_p.N362N|SNX29_ENST00000306030.3_Silent_p.N362N	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	747	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.					extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						GCGTCATGAACAAAGTCATCC	0.522																																					p.N747N		Atlas-SNP	.											.	SNX29	60	.	0			c.C2241T						PASS	.						94	101	99					16																	12618621		2049	4201	6250	SO:0001819	synonymous_variant	92017	exon20			CATGAACAAAGTC	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.2241C>T	chr16.hg19:g.12618621C>T		128.0	0.0	.		110.0	40.0	.	NM_032167	B5MDW2|Q8N2X2|Q9HA26	Silent	SNP	ENST00000566228.1	hg19	CCDS10553.2																																																																																			.	.	.	none		0.522	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422622.1			T	12618621	C	T	12618621	2	4	160	1	0	0	0	0	0	0	0	1	14911	477	17	2		2	SNX29	16	12618621	Silent	SNP	C	TCGA-DZ-6135-01A-11D-1961-08	11843093	12618621	77736132	28	9487											
FAM83G	644815	hgsc.bcm.edu	37	chr17	18881233	18881233	+	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	gttacgtagtcgtcatcatcTtcttcttccaccccatccag	7	14	5	15	2	5	0	2	0	3	0	8	0	7	0	4	0	1	2	4	0	2	5			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr17:18881233T>A	ENST00000388995.6	-	5	1969	c.1746A>T	c.(1744-1746)gaA>gaT	p.E582D	SLC5A10_ENST00000395643.2_Intron|SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000317977.6_Intron|SLC5A10_ENST00000395647.2_Intron|SLC5A10_ENST00000395645.3_Intron|FAM83G_ENST00000585154.2_Missense_Mutation_p.E582D|SLC5A10_ENST00000417251.2_Intron|FAM83G_ENST00000345041.4_Missense_Mutation_p.E582D			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	582					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						CGTCATCATCTTCTTCTTCCA	0.657																																					p.E582D		Atlas-SNP	.											.	FAM83G	51	.	0			c.A1746T						PASS	.						46	53	51					17																	18881233		2011	4159	6170	SO:0001583	missense	644815	exon5			ATCATCTTCTTCT	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.1746A>T	chr17.hg19:g.18881233T>A	ENSP00000373647:p.Glu582Asp	156.0	0.0	.		131.0	44.0	.	NM_001039999	Q3KQZ4|Q6ZW60	Missense_Mutation	SNP	ENST00000388995.6	hg19	CCDS42276.1	.	.	.	.	.	.	.	.	.	.	T	18.80	3.701515	0.68501	.	.	ENSG00000188522	ENST00000388995;ENST00000345041	T;T	0.14640	2.49;2.49	5.72	-5.84	0.02318	.	0.665977	0.14951	N	0.288895	T	0.08313	0.0207	L	0.53249	1.67	0.21802	N	0.999537	B	0.21606	0.058	B	0.17098	0.017	T	0.35425	-0.9789	10	0.19590	T	0.45	-18.4782	3.4372	0.07450	0.0963:0.4161:0.1946:0.2931	.	582	A6ND36	FA83G_HUMAN	D	582	ENSP00000373647:E582D;ENSP00000343279:E582D	ENSP00000343279:E582D	E	-	3	2	FAM83G	18821958	0.010000	0.17322	0.616000	0.29078	0.890000	0.51754	-1.760000	0.01806	-0.435000	0.07264	0.533000	0.62120	GAA	.	.	.	none		0.657	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4			A	18881233	T	A	18881233	3	1	160	1	0	0	0	0	1	0	0	0	5646	1606	56	5	733	5	FAM83G	17	18881233	Missense_Mutation	SNP	T	TCGA-DZ-6135-01A-11D-1961-08		18881233	62313977	29	9488											
CDK5R1	8851	hgsc.bcm.edu	37	chr17	30815101	30815101	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagtgagctgcttcgctgcCtgggtgagtttctctgccgc	3	12	13	13	2	1	2	0	2	1	0	3	2	1	2	3	1	4	4	3	1	0	2			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr17:30815101C>T	ENST00000313401.3	+	2	1152	c.463C>T	c.(463-465)Ctg>Ttg	p.L155L		NM_003885.2	NP_003876.1	Q15078	CD5R1_HUMAN	cyclin-dependent kinase 5, regulatory subunit 1 (p35)	155					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)			GCTTCGCTGCCTGGGTGAGTT	0.667																																					p.L155L		Atlas-SNP	.											.	CDK5R1	30	.	0			c.C463T						PASS	.						44	45	45					17																	30815101		2203	4300	6503	SO:0001819	synonymous_variant	8851	exon2			CGCTGCCTGGGTG	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.463C>T	chr17.hg19:g.30815101C>T		85.0	0.0	.		68.0	26.0	.	NM_003885	E1P664|Q5U0G3	Silent	SNP	ENST00000313401.3	hg19	CCDS11273.1																																																																																			.	.	.	none		0.667	CDK5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256264.1	NM_003885		T	30815101	C	T	30815101	2	4	160	1	0	0	0	0	0	0	0	1	3145	680	24	2		2	CDK5R1	17	30815101	Silent	SNP	C	TCGA-DZ-6135-01A-11D-1961-08	11933868	30815101	50380109	30	9489											
ZNF700	90592	hgsc.bcm.edu	37	chr19	12060395	12060395	+	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	atgtgagaaaggcttttattCtgccaagtcatttcaaacac	13	13	7	8	0	3	1	2	1	1	1	3	2	3	1	1	1	2	1	1	1	4	4			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr19:12060395C>G	ENST00000254321.5	+	4	1699	c.1556C>G	c.(1555-1557)tCt>tGt	p.S519C	ZNF700_ENST00000482090.1_Missense_Mutation_p.S501C|ZNF763_ENST00000590798.1_Intron|CTD-2006C1.12_ENST00000586394.1_RNA|ZNF763_ENST00000591944.1_Intron|ZNF763_ENST00000538752.1_Intron	NM_001271848.1|NM_144566.1	NP_001258777.1|NP_653167.1	Q9H0M5	ZN700_HUMAN	zinc finger protein 700	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)		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						GGCTTTTATTCTGCCAAGTCA	0.383																																					p.S522C		Atlas-SNP	.											.	ZNF700	81	.	0			c.C1565G						PASS	.						59	63	62					19																	12060395		2203	4300	6503	SO:0001583	missense	90592	exon4			TTTATTCTGCCAA	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.1556C>G	chr19.hg19:g.12060395C>G	ENSP00000254321:p.Ser519Cys	88.0	0.0	.		66.0	33.0	.	NM_001271848	B9EGU4	Missense_Mutation	SNP	ENST00000254321.5	hg19	CCDS32915.1	.	.	.	.	.	.	.	.	.	.	c	3.218	-0.160082	0.06502	.	.	ENSG00000196757	ENST00000254321	T	0.07688	3.17	0.672	-1.34	0.09143	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05181	0.0138	N	0.25647	0.755	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.39333	-0.9619	9	0.36615	T	0.2	.	4.3948	0.11358	0.0:0.3788:0.4495:0.1717	.	519	Q9H0M5	ZN700_HUMAN	C	519	ENSP00000254321:S519C	ENSP00000254321:S519C	S	+	2	0	ZNF700	11921395	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.814000	0.04486	-1.070000	0.03149	-0.705000	0.03659	TCT	.	.	.	none		0.383	ZNF700-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344126.2	NM_144566		G	12060395	C	G	12060395	3	3	160	1	0	0	0	0	1	0	0	0	18116	913	32	4	1570	4	ZNF700	19	12060395	Missense_Mutation	SNP	C	TCGA-DZ-6135-01A-11D-1961-08		12060395	47068588	31	9490											
IL4I1	259307	hgsc.bcm.edu	37	chr19	50393785	50393785	+	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	gccaccacgggcgcgttcaaCagcacaagcccggacagcga	11	2	12	16	5	1	0	1	0	0	0	1	2	1	1	3	2	4	2	3	2	2	1			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr19:50393785C>T	ENST00000391826.2	-	8	988	c.846G>A	c.(844-846)ctG>ctA	p.L282L	MIR4750_ENST00000584564.1_RNA|IL4I1_ENST00000595948.1_Silent_p.L304L|IL4I1_ENST00000341114.3_Silent_p.L304L	NM_152899.1	NP_690863.1	Q96RQ9	OXLA_HUMAN	interleukin 4 induced 1	282						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)	GCGCGTTCAACAGCACAAGCC	0.711											OREG0025629	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L304L		Atlas-SNP	.											.	IL4I1	50	.	0			c.G912A						PASS	.						18	18	18					19																	50393785		2202	4299	6501	SO:0001819	synonymous_variant	259307	exon10			GTTCAACAGCACA	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.846G>A	chr19.hg19:g.50393785C>T		42.0	0.0	.	969	50.0	21.0	.	NM_172374	Q1WMJ3|Q4GZN1|Q4GZN2|Q6P2Q3|Q8TEM5|Q96RQ8	Silent	SNP	ENST00000391826.2	hg19	CCDS12787.1																																																																																			.	.	.	none		0.711	IL4I1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466413.1			T	50393785	C	T	50393785	2	4	160	1	0	0	0	0	0	0	0	1	7704	465	17	2		2	IL4I1	19	50393785	Silent	SNP	C	TCGA-DZ-6135-01A-11D-1961-08	38333390	50393785	8735198	32	9491											
ZNF615	284370	hgsc.bcm.edu	37	chr19	52496292	52496292	+	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	ccgcagtcactgcatttgtaCggtttctctcctgtgtgaat	6	15	9	11	2	2	1	1	1	1	0	4	1	3	1	2	1	2	4	2	1	2	3	rs146634089		TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr19:52496292C>A	ENST00000602063.1	-	6	2386	c.2037G>T	c.(2035-2037)ccG>ccT	p.P679P	ZNF615_ENST00000391795.3_Silent_p.P684P|ZNF615_ENST00000594083.1_Silent_p.P690P|ZNF615_ENST00000598071.1_Silent_p.P690P|ZNF615_ENST00000376716.5_Silent_p.P679P			Q8N8J6	ZN615_HUMAN	zinc finger protein 615	679					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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.P679P(1)|p.P690P(1)		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)		TGCATTTGTACGGTTTCTCTC	0.408																																					p.P690P		Atlas-SNP	.											ZNF615,colon,carcinoma,0,2	ZNF615	111	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G2070T						PASS	.						160	155	157					19																	52496292		2203	4300	6503	SO:0001819	synonymous_variant	284370	exon7			TTTGTACGGTTTC	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.2037G>T	chr19.hg19:g.52496292C>A		205.0	2.0	.		201.0	83.0	.	NM_001199324	B7ZKW9|Q2M2Y6|Q5CZB0|Q6ZMT7|Q6ZRB3	Silent	SNP	ENST00000602063.1	hg19	CCDS12846.1																																																																																			.	C|1.000;T|0.000	.	alt		0.408	ZNF615-009	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462391.1	NM_198480		A	52496292	C	A	52496292	2	1	160	1	0	0	0	0	0	0	0	1	18052	523	19	4		4	ZNF615	19	52496292	Silent	SNP	C	TCGA-DZ-6135-01A-11D-1961-08	2102507	52496292	6632691	33	9492											
TRIM28	10155	hgsc.bcm.edu	37	chr19	59057198	59057198	+	Missense_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	ggagtgctcggagcctctgtGtgagacctgtgtagaggcgc	6	9	17	9	2	1	2	0	1	1	2	2	5	1	4	2	3	2	2	2	3	1	1			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr19:59057198G>A	ENST00000253024.5	+	3	810	c.521G>A	c.(520-522)tGt>tAt	p.C174Y	TRIM28_ENST00000341753.6_Intron|RN7SL525P_ENST00000579267.1_RNA	NM_005762.2	NP_005753.1	Q13263	TIF1B_HUMAN	tripartite motif containing 28	174	RBCC domain.				convergent extension involved in axis elongation (GO:0060028)|DNA repair (GO:0006281)|embryonic placenta morphogenesis (GO:0060669)|epithelial to mesenchymal transition (GO:0001837)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein sumoylation (GO:0016925)|protein ubiquitination (GO:0016567)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|Krueppel-associated box domain binding (GO:0035851)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		GAGCCTCTGTGTGAGACCTGT	0.577																																					p.C174Y		Atlas-SNP	.											.	TRIM28	46	.	0			c.G521A						PASS	.						80	75	77					19																	59057198		2203	4300	6503	SO:0001583	missense	10155	exon3			CTCTGTGTGAGAC		CCDS12985.1	19q13.4	2014-06-13	2011-01-25			ENSG00000130726		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Zinc fingers, PHD-type"	16384	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 157"	601742	"tripartite motif-containing 28"			11331580, 11226167	Standard	NM_005762		Approved	TIF1B, KAP1, TF1B, RNF96, PPP1R157	uc002qtg.1	Q13263		ENST00000253024.5:c.521G>A	chr19.hg19:g.59057198G>A	ENSP00000253024:p.Cys174Tyr	129.0	0.0	.		94.0	37.0	.	NM_005762	O00677|Q7Z632|Q93040|Q96IM1	Missense_Mutation	SNP	ENST00000253024.5	hg19	CCDS12985.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.934831	0.73442	.	.	ENSG00000130726	ENST00000253024	D	0.99080	-5.4	4.89	4.89	0.63831	Zinc finger, B-box (3);	0.000000	0.64402	D	0.000017	D	0.99453	0.9806	M	0.93638	3.44	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.98378	1.0557	10	0.87932	D	0	-16.8595	15.9183	0.79539	0.0:0.0:1.0:0.0	.	174	Q13263	TIF1B_HUMAN	Y	174	ENSP00000253024:C174Y	ENSP00000253024:C174Y	C	+	2	0	TRIM28	63749010	1.000000	0.71417	0.998000	0.56505	0.414000	0.31173	9.337000	0.96545	2.432000	0.82394	0.558000	0.71614	TGT	.	.	.	none		0.577	TRIM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467074.1	NM_005762		A	59057198	G	A	59057198	3	1	160	1	0	0	0	0	1	0	0	0	16514	1377	48	2	531	2	TRIM28	19	59057198	Missense_Mutation	SNP	G	TCGA-DZ-6135-01A-11D-1961-08	6560906	59057198	71785	34	9493											
KRTAP26-1	388818	hgsc.bcm.edu	37	chr21	31692296	31692296	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggaggtgagaggaatatggcGggaggttctgagagatcctg	10	8	19	4	1	1	3	0	2	1	2	2	8	2	6	1	6	0	1	1	6	2	2			TCGA-DZ-6135-01A-11D-1961-08	TCGA-DZ-6135-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	555a55c5-0299-42ea-b192-fd3595ea0aec	0d8c5c0b-123a-491f-a521-4dfea8a0d89d	g.chr21:31692296G>A	ENST00000360542.3	-	1	311	c.58C>T	c.(58-60)Cgc>Tgc	p.R20C		NM_203405.1	NP_981950.1	Q6PEX3	KR261_HUMAN	keratin associated protein 26-1	20						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						GGAATATGGCGGGAGGTTCTG	0.532																																					p.R20C		Atlas-SNP	.											KRTAP26-1,colon,carcinoma,0,1	KRTAP26-1	58	.	0			c.C58T						PASS	.																																			SO:0001583	missense	388818	exon1			TATGGCGGGAGGT	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.58C>T	chr21.hg19:g.31692296G>A	ENSP00000353742:p.Arg20Cys	77.0	1.0	.		63.0	5.0	.	NM_203405	B0RZD3	Missense_Mutation	SNP	ENST00000360542.3	hg19	CCDS13588.1	.	.	.	.	.	.	.	.	.	.	g	0.015	-1.544573	0.00934	.	.	ENSG00000197683	ENST00000360542	T	0.02837	4.14	4.95	3.8	0.43715	.	0.425318	0.22440	N	0.060032	T	0.00815	0.0027	N	0.00413	-1.525	0.28406	N	0.918409	B	0.02656	0.0	B	0.01281	0.0	T	0.43097	-0.9412	10	0.02654	T	1	-2.2098	8.113	0.30926	0.9049:0.0:0.0951:0.0	.	20	Q6PEX3	KR261_HUMAN	C	20	ENSP00000353742:R20C	ENSP00000353742:R20C	R	-	1	0	KRTAP26-1	30614167	0.900000	0.30661	0.326000	0.25389	0.313000	0.28021	0.998000	0.29744	0.963000	0.38082	-0.285000	0.09966	CGC	.	.	.	none		0.532	KRTAP26-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128218.1	NM_203405		A	31692296	G	A	31692296	3	1	160	1	0	0	0	0	1	0	0	0	8550	1116	39	1	578	1	KRTAP26-1	21	31692296	Missense_Mutation	SNP	G	TCGA-DZ-6135-01A-11D-1961-08		31692296	16437599	35	9494											
RNF115	27246	hgsc.bcm.edu	37	chr1	145688091	145688091	+	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	aatatttttctgtttcagcaTgacacatgtcctgtatgtag	10	17	7	7	0	2	1	1	1	1	0	3	1	3	1	1	0	1	4	1	0	4	6			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr1:145688091T>A	ENST00000369291.5	+	9	990	c.786T>A	c.(784-786)caT>caA	p.H262Q		NM_014455.2	NP_055270.1			ring finger protein 115											breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	13						TGTTTCAGCATGACACATGTC	0.418																																					p.H262Q		Atlas-SNP	.											.	RNF115	27	.	0			c.T786A						PASS	.						117	112	114					1																	145688091		2203	4300	6503	SO:0001583	missense	27246	exon9			TCAGCATGACACA	AF419857	CCDS72863.1	1q12	2013-01-09	2008-06-16	2008-06-16	ENSG00000121848	ENSG00000265491		"RING-type (C3HC4) zinc fingers"	18154	protein-coding gene	gene with protein product			"zinc finger protein 364"	ZNF364			Standard	NM_014455		Approved	CL469780	uc001eoj.3	Q9Y4L5	OTTHUMG00000013758	ENST00000369291.5:c.786T>A	chr1.hg19:g.145688091T>A	ENSP00000358297:p.His262Gln	171.0	0.0	.		139.0	48.0	.	NM_014455		Missense_Mutation	SNP	ENST00000369291.5	hg19	CCDS922.1	.	.	.	.	.	.	.	.	.	.	T	18.57	3.651541	0.67472	.	.	ENSG00000121848	ENST00000369291	T	0.41758	0.99	5.65	0.199	0.15175	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, RING-H2-type (1);	0.000000	0.85682	D	0.000000	T	0.35624	0.0938	L	0.38733	1.17	0.54753	D	0.999989	D	0.71674	0.998	D	0.69824	0.966	T	0.27971	-1.0058	10	0.72032	D	0.01	-5.7379	9.6735	0.40026	0.0:0.5176:0.0:0.4824	.	262	Q9Y4L5	RN115_HUMAN	Q	262	ENSP00000358297:H262Q	ENSP00000358297:H262Q	H	+	3	2	RNF115	144399448	0.949000	0.32298	0.997000	0.53966	0.972000	0.66771	-0.007000	0.12810	-0.112000	0.11979	0.533000	0.62120	CAT	.	.	.	none		0.418	RNF115-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038554.2	NM_014455		A	145688091	T	A	145688091	3	1	161	1	0	0	0	0	1	0	0	0	13443	1461	51	5	820	5	RNF115	1	145688091	Missense_Mutation	SNP	T	TCGA-EV-5901-01A-11D-1589-08		145688091	103562530	1	9495											
ARHGAP30	257106	hgsc.bcm.edu	37	chr1	161021130	161021130	+	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	ggccagggccaaggccagggCcagggccagggccagaggca	9	0	19	13	0	0	1	0	0	0	1	0	1	0	1	6	7	0	1	6	7	1	0			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr1:161021130C>A	ENST00000368013.3	-	10	1714	c.1394G>T	c.(1393-1395)gGc>gTc	p.G465V	ARHGAP30_ENST00000368016.3_Missense_Mutation_p.G465V|ARHGAP30_ENST00000368015.1_Missense_Mutation_p.G288V	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	465					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)			aaggccagggccagggccagg	0.612																																					p.G465V		Atlas-SNP	.											.	ARHGAP30	105	.	0			c.G1394T						PASS	.						29	31	30					1																	161021130		2203	4298	6501	SO:0001583	missense	257106	exon10			CCAGGGCCAGGGC	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.1394G>T	chr1.hg19:g.161021130C>A	ENSP00000356992:p.Gly465Val	51.0	0.0	.		57.0	20.0	.	NM_001025598	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Missense_Mutation	SNP	ENST00000368013.3	hg19	CCDS30918.1	.	.	.	.	.	.	.	.	.	.	C	14.77	2.633427	0.47049	.	.	ENSG00000186517	ENST00000368016;ENST00000368013;ENST00000368017;ENST00000368015	T;T;T	0.48201	2.6;2.35;0.82	3.83	3.83	0.44106	.	0.323164	0.22031	N	0.065593	T	0.37461	0.1004	L	0.27053	0.805	0.49389	D	0.999786	B;D	0.61697	0.354;0.99	B;P	0.57152	0.074;0.814	T	0.37407	-0.9707	10	0.72032	D	0.01	.	11.4473	0.50131	0.0:1.0:0.0:0.0	.	465;465	Q7Z6I6;Q7Z6I6-2	RHG30_HUMAN;.	V	465;465;317;288	ENSP00000356995:G465V;ENSP00000356992:G465V;ENSP00000356994:G288V	ENSP00000356992:G465V	G	-	2	0	ARHGAP30	159287754	0.992000	0.36948	0.997000	0.53966	0.998000	0.95712	3.749000	0.55150	2.131000	0.65755	0.555000	0.69702	GGC	.	.	.	none		0.612	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720		A	161021130	C	A	161021130	3	1	161	1	0	0	0	0	1	0	0	0	879	739	26	4	1923	4	ARHGAP30	1	161021130	Missense_Mutation	SNP	C	TCGA-EV-5901-01A-11D-1589-08	15333039	161021130	88229491	2	9496											
VPS54	51542	hgsc.bcm.edu	37	chr2	64199372	64199372	+	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	cttgcatctctcatgaatctTctctctctaataaaaagaca	13	14	3	11	0	5	2	1	1	4	1	8	2	5	2	0	0	1	1	0	0	5	4			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr2:64199372T>A	ENST00000272322.4	-	4	539	c.385A>T	c.(385-387)Aag>Tag	p.K129*	VPS54_ENST00000409558.4_Nonsense_Mutation_p.K117*|VPS54_ENST00000354504.3_Nonsense_Mutation_p.K12*			Q9P1Q0	VPS54_HUMAN	vacuolar protein sorting 54 homolog (S. cerevisiae)	129					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						TCATGAATCTTCTCTCTCTAA	0.303																																					p.K129X		Atlas-SNP	.											.	VPS54	57	.	0			c.A385T						PASS	.						69	67	68					2																	64199372		2202	4292	6494	SO:0001587	stop_gained	51542	exon4			GAATCTTCTCTCT	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.385A>T	chr2.hg19:g.64199372T>A	ENSP00000272322:p.Lys129*	52.0	0.0	.		63.0	22.0	.	NM_016516	Q5VIR5|Q86YF7|Q8N6G3|Q9NPV0|Q9NT07|Q9NUJ0	Nonsense_Mutation	SNP	ENST00000272322.4	hg19	CCDS33208.1	.	.	.	.	.	.	.	.	.	.	T	42	9.754681	0.99256	.	.	ENSG00000143952	ENST00000354504;ENST00000272322;ENST00000409558;ENST00000483277;ENST00000394400	.	.	.	5.66	5.66	0.87406	.	0.089994	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.8882	0.79269	0.0:0.0:0.0:1.0	.	.	.	.	X	12;129;117;117;129	.	ENSP00000272322:K129X	K	-	1	0	VPS54	64052876	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.116000	0.64661	2.166000	0.68216	0.454000	0.30748	AAG	.	.	.	none		0.303	VPS54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327062.2	NM_016516		A	64199372	T	A	64199372	4	1	161	1	0	0	0	0	0	1	0	0	17228	1792	62	5	2628	5	VPS54	2	64199372	Nonsense_Mutation	SNP	T	TCGA-EV-5901-01A-11D-1589-08		64199372	179000001	3	9497											
ARID5A	10865	hgsc.bcm.edu	37	chr2	97216937	97216937	+	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	cagcagggcctggcctctggGtcttctgtgtcctttgtggg	2	13	15	11	0	3	0	0	0	3	0	4	0	4	0	3	4	1	1	3	4	0	2			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr2:97216937G>A	ENST00000357485.3	+	7	750	c.672G>A	c.(670-672)ggG>ggA	p.G224G	ARID5A_ENST00000454558.2_Silent_p.G156G	NM_212481.1	NP_997646.1	Q03989	ARI5A_HUMAN	AT rich interactive domain 5A (MRF1-like)	224					chondrocyte differentiation (GO:0002062)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)|skin(1)|urinary_tract(2)	14						TGGCCTCTGGGTCTTCTGTGT	0.602																																					p.G224G		Atlas-SNP	.											.	ARID5A	31	.	0			c.G672A						PASS	.						56	61	60					2																	97216937		2203	4300	6503	SO:0001819	synonymous_variant	10865	exon7			CTCTGGGTCTTCT	M62324	CCDS33251.1	2p11.1	2013-02-07			ENSG00000196843	ENSG00000196843		"-"	17361	protein-coding gene	gene with protein product	"modulator recognition factor 1"	611583				8649988	Standard	NM_212481		Approved	MRF-1, RP11-363D14	uc002swe.3	Q03989	OTTHUMG00000155229	ENST00000357485.3:c.672G>A	chr2.hg19:g.97216937G>A		131.0	0.0	.		108.0	27.0	.	NM_212481	Q6NX37	Silent	SNP	ENST00000357485.3	hg19	CCDS33251.1																																																																																			.	.	.	none		0.602	ARID5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338888.2	NM_212481		A	97216937	G	A	97216937	2	1	161	1	0	0	0	0	0	0	0	1	921	1248	44	2		2	ARID5A	2	97216937	Silent	SNP	G	TCGA-EV-5901-01A-11D-1589-08	33017565	97216937	145982436	4	9498											
CNNM4	26504	hgsc.bcm.edu	37	chr2	97427340	97427340	+	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	tgtcgggcatattttctggcCtcaacctcgggcttatggcc	5	13	11	12	2	2	0	1	0	1	0	4	0	2	0	3	4	1	2	3	4	3	4			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr2:97427340C>A	ENST00000377075.2	+	1	702	c.604C>A	c.(604-606)Ctc>Atc	p.L202I		NM_020184.3	NP_064569.3	Q6P4Q7	CNNM4_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 4	202	DUF21.				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						ATTTTCTGGCCTCAACCTCGG	0.587																																					p.L202I		Atlas-SNP	.											.	CNNM4	48	.	0			c.C604A						PASS	.						85	92	89					2																	97427340		2203	4300	6503	SO:0001583	missense	26504	exon1			TCTGGCCTCAACC	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.604C>A	chr2.hg19:g.97427340C>A	ENSP00000366275:p.Leu202Ile	157.0	0.0	.		125.0	47.0	.	NM_020184	B7Z1U0|C7SQM3|C7SQM4|C7SQM5|Q53RE5|Q9H9G3|Q9HCI0|Q9NRN1	Missense_Mutation	SNP	ENST00000377075.2	hg19	CCDS2024.2	.	.	.	.	.	.	.	.	.	.	c	20.6	4.021298	0.75275	.	.	ENSG00000158158	ENST00000377075	D	0.89485	-2.52	4.85	4.85	0.62838	Domain of unknown function DUF21 (1);	0.077015	0.50627	D	0.000112	D	0.94925	0.8359	M	0.92122	3.275	0.80722	D	1	D	0.76494	0.999	D	0.71656	0.974	D	0.95382	0.8474	10	0.87932	D	0	-12.6701	10.4274	0.44387	0.0:0.908:0.0:0.092	.	202	Q6P4Q7	CNNM4_HUMAN	I	202	ENSP00000366275:L202I	ENSP00000366275:L202I	L	+	1	0	CNNM4	96791067	0.997000	0.39634	1.000000	0.80357	0.994000	0.84299	3.112000	0.50368	2.234000	0.73211	0.556000	0.70494	CTC	.	.	.	none		0.587	CNNM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252954.1	NM_020184		A	97427340	C	A	97427340	3	1	161	1	0	0	0	0	1	0	0	0	3617	681	24	4	606	4	CNNM4	2	97427340	Missense_Mutation	SNP	C	TCGA-EV-5901-01A-11D-1589-08	210403	97427340	145772033	5	9499											
PRPF40A	55660	hgsc.bcm.edu	37	chr2	153532998	153532998	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgatcctgaatagcaggggTactagtaagttgtgcttgtt	9	15	12	5	0	0	2	0	2	0	0	1	2	1	2	1	2	3	6	1	2	5	8	rs372660010		TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr2:153532998T>C	ENST00000410080.1	-	10	1493	c.952A>G	c.(952-954)Acc>Gcc	p.T318A		NM_017892.3	NP_060362.3	O75400	PR40A_HUMAN	PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae)	345					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						ATAGCAGGGGTACTAGTAAGT	0.378																																					p.T318A		Atlas-SNP	.											PRPF40A_ENST00000410080,NS,carcinoma,0,3	PRPF40A	149	.	0			c.A952G						PASS	.	T	ALA/THR	0,3770		0,0,1885	81	77	78		952	3.6	1	2		78	1,8221		0,1,4110	no	missense	PRPF40A	NM_017892.3	58	0,1,5995	CC,CT,TT		0.0122,0.0,0.0083	possibly-damaging	318/931	153532998	1,11991	1885	4111	5996	SO:0001583	missense	55660	exon10			CAGGGGTACTAGT	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.952A>G	chr2.hg19:g.153532998T>C	ENSP00000386458:p.Thr318Ala	23.0	0.0	.		24.0	2.0	.	NM_017892	O43856|O75404|Q8TBQ1|Q9H782|Q9NWU9|Q9P0Q2|Q9Y5A8	Missense_Mutation	SNP	ENST00000410080.1	hg19	CCDS46430.1	.	.	.	.	.	.	.	.	.	.	T	4.743	0.138086	0.09083	0.0	1.22E-4	ENSG00000196504	ENST00000410080;ENST00000356402;ENST00000440252;ENST00000359961;ENST00000545856;ENST00000493468	T	0.30182	1.54	4.77	3.61	0.41365	.	0.488453	0.23416	N	0.048404	T	0.12732	0.0309	N	0.14661	0.345	0.34226	D	0.676017	B;B;B	0.30193	0.272;0.049;0.028	B;B;B	0.17722	0.019;0.015;0.016	T	0.20472	-1.0274	10	0.07813	T	0.8	-1.5293	7.4308	0.27126	0.0:0.1016:0.0:0.8984	.	345;327;318	O75400;O75400-3;E9PFS0	PR40A_HUMAN;.;.	A	318;327;214;265;345;320	ENSP00000386458:T318A	ENSP00000348770:T327A	T	-	1	0	PRPF40A	153241244	0.998000	0.40836	1.000000	0.80357	0.990000	0.78478	0.937000	0.28951	0.934000	0.37316	0.455000	0.32223	ACC	.	.	.	weak		0.378	PRPF40A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333559.2	XM_371575		C	153532998	T	C	153532998	3	2	161	1	0	0	0	0	1	0	0	0	12581	1638	57	3	1908	3	PRPF40A	2	153532998	Missense_Mutation	SNP	T	TCGA-EV-5901-01A-11D-1589-08	56105658	153532998	89666375	6	9500											
PSMD6	9861	hgsc.bcm.edu	37	chr3	64004274	64004274	+	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	aaatatcaaccctatccttaCctaatgattggaagaaaaca	18	10	4	9	0	1	2	1	1	0	1	2	3	2	3	3	1	3	0	3	1	9	5			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr3:64004274C>A	ENST00000295901.4	-	5	967		c.e5+1		RP11-245J9.4_ENST00000462717.1_RNA|RP11-245J9.6_ENST00000605919.1_RNA|PSMD6_ENST00000492933.1_Splice_Site|PSMD6_ENST00000482510.1_Splice_Site|PSMD6_ENST00000394431.2_Splice_Site	NM_014814.1	NP_055629.1	Q15008	PSMD6_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 6						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATPase activity (GO:0016887)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|pancreas(1)|prostate(1)|skin(1)	13		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000805)|Kidney(15;0.00188)|KIRC - Kidney renal clear cell carcinoma(15;0.00212)		CCTATCCTTACCTAATGATTG	0.388																																					.		Atlas-SNP	.											.	PSMD6	30	.	0			c.985+1G>T						PASS	.						78	71	73					3																	64004274		2203	4300	6503	SO:0001630	splice_region_variant	9861	exon7			TCCTTACCTAATG	AF215935	CCDS2901.1, CCDS63677.1, CCDS63678.1, CCDS63679.1	3p14.1	2008-05-22			ENSG00000163636	ENSG00000163636		"Proteasome (prosome, macropain) subunits"	9564	protein-coding gene	gene with protein product						10723133	Standard	NM_001271779		Approved	S10, p44S10, KIAA0107, Rpn7	uc003dmb.2	Q15008	OTTHUMG00000158765	ENST00000295901.4:c.826+1G>T	chr3.hg19:g.64004274C>A		44.0	0.0	.		34.0	12.0	.	NM_001271779	A8K2E0|E9PHI9|Q6UV22	Splice_Site	SNP	ENST00000295901.4	hg19	CCDS2901.1	.	.	.	.	.	.	.	.	.	.	C	18.23	3.577357	0.65878	.	.	ENSG00000163636	ENST00000295901;ENST00000480205;ENST00000492933;ENST00000394431;ENST00000482510	.	.	.	5.94	5.94	0.96194	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.3633	0.98874	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PSMD6	63979314	1.000000	0.71417	1.000000	0.80357	0.501000	0.33797	6.088000	0.71371	2.826000	0.97356	0.561000	0.74099	.	.	.	.	none		0.388	PSMD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352082.1	NM_014814	Intron	A	64004274	C	A	64004274	5	1	161	1	0	0	0	0	0	0	1	0	12712	521	18	4	358	4	PSMD6	3	64004274	Splice_Site	SNP	C	TCGA-EV-5901-01A-11D-1589-08		64004274	134018156	7	9501											
EPHA6	285220	hgsc.bcm.edu	37	chr3	97202865	97202865	+	Missense_Mutation	SNP	A	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	tgaatttgcaaaggagattgAtccctcaagaattcgtattg	13	13	9	6	1	1	4	1	2	0	2	3	5	2	4	1	1	1	2	1	1	5	5			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr3:97202865A>C	ENST00000514100.1	+	7	580	c.338A>C	c.(337-339)gAt>gCt	p.D113A	EPHA6_ENST00000389672.5_Missense_Mutation_p.D721A|EPHA6_ENST00000502694.1_Missense_Mutation_p.D113A|EPHA6_ENST00000442602.2_Missense_Mutation_p.D87A	NM_001278300.1	NP_001265229.1	Q9UF33	EPHA6_HUMAN	EPH receptor A6	627	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						AAGGAGATTGATCCCTCAAGA	0.383																																					p.D721A		Atlas-SNP	.											.	EPHA6	439	.	0			c.A2162C						PASS	.						99	101	100					3																	97202865		1865	4106	5971	SO:0001583	missense	285220	exon10			AGATTGATCCCTC	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.338A>C	chr3.hg19:g.97202865A>C	ENSP00000421711:p.Asp113Ala	42.0	0.0	.		46.0	26.0	.	NM_001080448	D6RAL5	Missense_Mutation	SNP	ENST00000514100.1	hg19		.	.	.	.	.	.	.	.	.	.	A	22.3	4.273321	0.80580	.	.	ENSG00000080224	ENST00000389672;ENST00000514100;ENST00000502694;ENST00000442602	T;T;T;T	0.21932	1.98;1.98;1.98;1.98	5.32	5.32	0.75619	Protein kinase-like domain (1);	.	.	.	.	T	0.54615	0.1869	M	0.89785	3.06	0.80722	D	1	D;D;D;D	0.89917	0.999;0.962;1.0;1.0	P;P;D;D	0.85130	0.907;0.598;0.997;0.962	T	0.65438	-0.6168	9	0.87932	D	0	.	15.3417	0.74303	1.0:0.0:0.0:0.0	.	87;626;113;113	B4DXQ6;Q9UF33;Q9UF33-2;D6RAL5	.;EPHA6_HUMAN;.;.	A	721;113;113;87	ENSP00000374323:D721A;ENSP00000421711:D113A;ENSP00000423950:D113A;ENSP00000403100:D87A	ENSP00000374323:D721A	D	+	2	0	EPHA6	98685555	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.958000	0.93099	2.026000	0.59711	0.454000	0.30748	GAT	.	.	.	none		0.383	EPHA6-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000359997.1	NM_001080448		C	97202865	A	C	97202865	3	2	161	1	0	0	0	0	1	0	0	0	5173	333	12	5	2268	5	EPHA6	3	97202865	Missense_Mutation	SNP	A	TCGA-EV-5901-01A-11D-1589-08	33198591	97202865	100819565	8	9502											
CD86	942	hgsc.bcm.edu	37	chr3	121825262	121825263	+	Frame_Shift_Del	DEL	AT	AT	-																															tccatcagcttgtctgtttcAttccctgatgttacgagcaa																								rs375108955		TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr3:121825262_121825263delAT	ENST00000330540.2	+	4	734_735	c.618_619delAT	c.(616-621)tcattcfs	p.F207fs	CD86_ENST00000493101.1_Frame_Shift_Del_p.F95fs|CD86_ENST00000469710.1_Frame_Shift_Del_p.F125fs|CD86_ENST00000264468.5_Intron|CD86_ENST00000393627.2_Frame_Shift_Del_p.F201fs	NM_175862.4	NP_787058	P42081	CD86_HUMAN	CD86 molecule	207	Ig-like C2-type.				aging (GO:0007568)|B cell activation (GO:0042113)|cell-cell signaling (GO:0007267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to metal ion (GO:0071248)|defense response to virus (GO:0051607)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|immune response (GO:0006955)|innate immune response (GO:0045087)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of T cell anergy (GO:0002668)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 biosynthetic process (GO:0045404)|positive regulation of lymphotoxin A biosynthetic process (GO:0043017)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|response to interferon-gamma (GO:0034341)|response to yeast (GO:0001878)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell proliferation involved in immune response (GO:0002309)|toll-like receptor signaling pathway (GO:0002224)|viral process (GO:0016032)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)|receptor activity (GO:0004872)			breast(2)|endometrium(1)|kidney(1)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	23				GBM - Glioblastoma multiforme(114;0.156)	Abatacept(DB01281)|Antithymocyte globulin(DB00098)|Belatacept(DB06681)	TGTCTGTTTCATTCCCTGATGT	0.391																																					p.206_206del	GBM(67;1379 1389 36064 39806)	Atlas-INDEL	.											.	CD86	43	.	0			c.617_618del						PASS	.																																			SO:0001589	frameshift_variant	942	exon4			.		CCDS3009.1, CCDS43138.1, CCDS56272.1, CCDS56273.1, CCDS74991.1	3q21	2013-01-29	2006-03-28		ENSG00000114013	ENSG00000114013		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1705	protein-coding gene	gene with protein product	"B-lymphocyte antigen B7-2"	601020	"CD86 antigen (CD28 antigen ligand 2, B7-2 antigen)"	CD28LG2		7513726	Standard	NM_006889		Approved	B7.2, B7-2	uc003eet.3	P42081	OTTHUMG00000159482	ENST00000330540.2:c.618_619delAT	chr3.hg19:g.121825262_121825263delAT	ENSP00000332049:p.Phe207fs	263.0	0.0	0		362.0	177.0	0.48895	NM_175862	A0N0P0|B7Z2F3|B7Z702|E7ETN5|E9PC27|Q13655|Q6FHB1|Q6GTS4|Q7M4L5	Frame_Shift_Del	DEL	ENST00000330540.2	hg19	CCDS3009.1																																																																																			.	.	.	none		0.391	CD86-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000355671.1	NM_006889		-	121825263	AT	-	121825262	7	5	161	1	0	1	0	1	0	0	0	0	3045	204	8	0	632	0	CD86	3	121825262	Frame_Shift_Del	DEL	AT	TCGA-EV-5901-01A-11D-1589-08	24622397	121825262	76197168	9	9503											
CEP63	80254	hgsc.bcm.edu	37	chr3	134250746	134250746	+	Frame_Shift_Del	DEL	G	G	-																															atcaagcaagagatgaccatGgaatataagcaggagttgaa																								rs544307188		TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr3:134250746delG	ENST00000337090.3	+	4	455	c.282delG	c.(280-282)atgfs	p.M94fs	CEP63_ENST00000504013.1_3'UTR|CEP63_ENST00000383229.3_Frame_Shift_Del_p.M94fs|CEP63_ENST00000332047.5_Frame_Shift_Del_p.M94fs|CEP63_ENST00000513612.2_Frame_Shift_Del_p.M94fs|CEP63_ENST00000606977.1_Frame_Shift_Del_p.M94fs|CEP63_ENST00000354446.3_Frame_Shift_Del_p.M94fs			Q96MT8	CEP63_HUMAN	centrosomal protein 63kDa	94					centriole replication (GO:0007099)|DNA damage checkpoint (GO:0000077)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|signal transduction in response to DNA damage (GO:0042770)|spindle assembly (GO:0051225)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|spindle pole (GO:0000922)				kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						AGATGACCATGGAATATAAGC	0.353																																					p.M94fs		Atlas-INDEL	.											.	CEP63	56	.	0			c.281delT						PASS	.						171	168	169					3																	134250746		2203	4300	6503	SO:0001589	frameshift_variant	80254	exon4			.	AK056465	CCDS3086.1, CCDS43152.1, CCDS43153.1, CCDS43154.1	3q22.1	2014-02-20			ENSG00000182923	ENSG00000182923			25815	protein-coding gene	gene with protein product		614724				14654843, 24240477	Standard	NM_001042383		Approved	FLJ13386	uc003eqo.1	Q96MT8	OTTHUMG00000159725	ENST00000337090.3:c.282delG	chr3.hg19:g.134250746delG	ENSP00000336524:p.Met94fs	79.0	0.0	0		80.0	41.0	0.5125	NM_001042383	D3DND8|D3DND9|D3DNE0|Q96CR0|Q9H8F5|Q9H8N0	Frame_Shift_Del	DEL	ENST00000337090.3	hg19	CCDS3086.1																																																																																			.	.	.	none		0.353	CEP63-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000470139.1	NM_025180		-	134250746	G	-	134250746	7	5	161	1	0	1	0	1	0	0	0	0	3259	1348	47	0	292	0	CEP63	3	134250746	Frame_Shift_Del	DEL	G	TCGA-EV-5901-01A-11D-1589-08	12425484	134250746	63771684	10	9504											
PHC3	80012	hgsc.bcm.edu	37	chr3	169847187	169847187	+	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	tacagtgctgggatgggggtGggtcttgagttgaattctga	7	13	17	4	0	2	3	0	3	2	0	2	4	2	4	0	4	2	2	0	4	2	4			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr3:169847187G>A	ENST00000494943.1	-	8	1105	c.1037C>T	c.(1036-1038)cCa>cTa	p.P346L	PHC3_ENST00000467570.1_Missense_Mutation_p.P305L|PHC3_ENST00000495893.2_Missense_Mutation_p.P358L			Q8NDX5	PHC3_HUMAN	polyhomeotic homolog 3 (Drosophila)	346	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)			GGATGGGGGTGGGTCTTGAGT	0.488																																					p.P358L		Atlas-SNP	.											.	PHC3	113	.	0			c.C1073T						PASS	.						205	205	205					3																	169847187		2024	4175	6199	SO:0001583	missense	80012	exon8			GGGGGTGGGTCTT		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.1037C>T	chr3.hg19:g.169847187G>A	ENSP00000420271:p.Pro346Leu	127.0	0.0	.		156.0	45.0	.	NM_024947	A2RRP9|Q5HYF0|Q6NSG2|Q8NFT7|Q8NFZ1|Q8TBM2|Q9H971|Q9H9I4	Missense_Mutation	SNP	ENST00000494943.1	hg19		.	.	.	.	.	.	.	.	.	.	G	12.23	1.875524	0.33162	.	.	ENSG00000173889	ENST00000494943;ENST00000495893;ENST00000467570;ENST00000484931	T;T	0.32515	1.45;1.47	5.35	5.35	0.76521	.	0.000000	0.64402	D	0.000001	T	0.37046	0.0989	L	0.55481	1.735	0.80722	D	1	B;P;B;B	0.47302	0.008;0.893;0.0;0.0	B;P;B;B	0.44811	0.006;0.461;0.0;0.002	T	0.08046	-1.0741	10	0.35671	T	0.21	-10.2153	18.6641	0.91483	0.0:0.0:1.0:0.0	.	305;305;346;358	B4E2T1;E7EX82;Q8NDX5;Q8NDX5-7	.;.;PHC3_HUMAN;.	L	346;358;305;184	ENSP00000420271:P346L;ENSP00000420294:P358L	ENSP00000419089:P305L	P	-	2	0	PHC3	171329881	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.385000	0.66231	2.514000	0.84764	0.561000	0.74099	CCA	.	.	.	none		0.488	PHC3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000352182.3	NM_024947		A	169847187	G	A	169847187	3	1	161	1	0	0	0	0	1	0	0	0	11825	1348	47	2	1946	2	PHC3	3	169847187	Missense_Mutation	SNP	G	TCGA-EV-5901-01A-11D-1589-08	35596441	169847187	28175243	11	9505											
PDGFRA	5156	hgsc.bcm.edu	37	chr4	55139834	55139834	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtggaggagaccatcgccGtgcgatgcctggctaagaat	11	7	14	9	3	0	2	0	0	0	2	1	5	0	3	3	3	2	1	3	3	3	1			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr4:55139834G>A	ENST00000257290.5	+	10	1826	c.1495G>A	c.(1495-1497)Gtg>Atg	p.V499M	FIP1L1_ENST00000507166.1_Intron	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	499	Ig-like C2-type 5.				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.V499M(1)		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)	GACCATCGCCGTGCGATGCCT	0.557			"Mis, O, T"	FIP1L1	"GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											p.V499M	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,0,1	PDGFRA	1583	.	1	Substitution - Missense(1)	breast(1)	c.G1495A						PASS	.						85	83	83					4																	55139834		2203	4300	6503	SO:0001583	missense	5156	exon10	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	ATCGCCGTGCGAT	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.1495G>A	chr4.hg19:g.55139834G>A	ENSP00000257290:p.Val499Met	126.0	0.0	.		79.0	25.0	.	NM_006206	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Missense_Mutation	SNP	ENST00000257290.5	hg19	CCDS3495.1	.	.	.	.	.	.	.	.	.	.	G	15.54	2.863494	0.51482	.	.	ENSG00000134853	ENST00000257290	T	0.77750	-1.12	5.9	5.9	0.94986	Immunoglobulin-like fold (1);	0.000000	0.29529	U	0.011898	D	0.86401	0.5924	M	0.73217	2.22	0.80722	D	1	D;D	0.89917	1.0;0.997	D;P	0.75020	0.985;0.882	D	0.86433	0.1762	10	0.56958	D	0.05	.	13.4661	0.61254	0.0709:0.0:0.9291:0.0	.	499;499	P16234-3;P16234	.;PGFRA_HUMAN	M	499	ENSP00000257290:V499M	ENSP00000257290:V499M	V	+	1	0	PDGFRA	54834591	1.000000	0.71417	0.136000	0.22124	0.003000	0.03518	6.915000	0.75770	2.788000	0.95919	0.650000	0.86243	GTG	.	.	.	none		0.557	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206		A	55139834	G	A	55139834	3	1	161	1	0	0	0	0	1	0	0	0	11668	1145	40	1	1529	1	PDGFRA	4	55139834	Missense_Mutation	SNP	G	TCGA-EV-5901-01A-11D-1589-08		55139834	136014442	12	9506											
LPCAT1	79888	hgsc.bcm.edu	37	chr5	1488543	1488543	+	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	aggcaggtcctgtttgtacaAgttccttctggaaaaatcat	11	13	9	8	0	2	0	1	0	1	0	4	1	4	1	2	3	1	4	2	3	4	4			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr5:1488543A>T	ENST00000283415.3	-	5	762	c.630T>A	c.(628-630)acT>acA	p.T210T		NM_024830.3	NP_079106.3	Q8NF37	PCAT1_HUMAN	lysophosphatidylcholine acyltransferase 1	210					cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|negative regulation of phosphatidylcholine biosynthetic process (GO:2001246)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein catabolic process (GO:0045732)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|surfactant homeostasis (GO:0043129)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkenylglycerophosphocholine O-acyltransferase activity (GO:0047159)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|1-alkylglycerophosphocholine O-acyltransferase activity (GO:0047191)|calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)		TGTTTGTACAAGTTCCTTCTG	0.323																																					p.T210T		Atlas-SNP	.											.	LPCAT1	70	.	0			c.T630A						PASS	.						87	90	89					5																	1488543		2203	4300	6503	SO:0001819	synonymous_variant	79888	exon5			TGTACAAGTTCCT	BC020166	CCDS3864.1	5p15.33	2013-01-10	2007-12-17	2007-12-17	ENSG00000153395	ENSG00000153395		"EF-hand domain containing"	25718	protein-coding gene	gene with protein product		610472	"acyltransferase like 2"	AYTL2		8619474, 16704971	Standard	NM_024830		Approved	FLJ12443	uc003jcm.3	Q8NF37	OTTHUMG00000131017	ENST00000283415.3:c.630T>A	chr5.hg19:g.1488543A>T		152.0	0.0	.		107.0	47.0	.	NM_024830	Q1HAQ1|Q7Z4G6|Q8N3U7|Q8WUL8|Q9GZW6	Silent	SNP	ENST00000283415.3	hg19	CCDS3864.1																																																																																			.	.	.	none		0.323	LPCAT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304032.1	NM_024830		T	1488543	A	T	1488543	2	4	161	1	0	0	0	0	0	0	0	1	8917	59	3	5		5	LPCAT1	5	1488543	Silent	SNP	A	TCGA-EV-5901-01A-11D-1589-08		1488543	179426717	13	9507											
NSUN2	54888	hgsc.bcm.edu	37	chr5	6620280	6620280	+	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	ctctttcctgccgtccacatCtatctggagcctgggtatgc	5	13	9	14	1	3	0	0	0	3	0	5	1	5	1	4	2	3	1	4	2	2	3			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr5:6620280C>T	ENST00000264670.6	-	7	1065	c.754G>A	c.(754-756)Gat>Aat	p.D252N	NSUN2_ENST00000505264.1_5'UTR|NSUN2_ENST00000539938.1_Missense_Mutation_p.D16N|NSUN2_ENST00000506139.1_Missense_Mutation_p.D217N	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	252					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						CCGTCCACATCTATCTGGAGC	0.493																																					p.D252N		Atlas-SNP	.											.	NSUN2	82	.	0			c.G754A						PASS	.						108	105	106					5																	6620280		2203	4300	6503	SO:0001583	missense	54888	exon7			CCACATCTATCTG	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.754G>A	chr5.hg19:g.6620280C>T	ENSP00000264670:p.Asp252Asn	125.0	0.0	.		122.0	40.0	.	NM_017755	A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Missense_Mutation	SNP	ENST00000264670.6	hg19	CCDS3869.1	.	.	.	.	.	.	.	.	.	.	C	10.16	1.273421	0.23221	.	.	ENSG00000037474	ENST00000264670;ENST00000539938;ENST00000506139	T;T;T	0.38560	1.16;2.97;1.13	6.02	6.02	0.97574	.	0.084604	0.85682	D	0.000000	T	0.20740	0.0499	N	0.02985	-0.445	0.51767	D	0.999935	B;B	0.15930	0.015;0.005	B;B	0.20384	0.022;0.029	T	0.18808	-1.0325	10	0.12766	T	0.61	-53.9111	14.6603	0.68865	0.0:0.9312:0.0:0.0688	.	217;252	B4DQW2;Q08J23	.;NSUN2_HUMAN	N	252;16;217	ENSP00000264670:D252N;ENSP00000444338:D16N;ENSP00000420957:D217N	ENSP00000264670:D252N	D	-	1	0	NSUN2	6673280	0.863000	0.29885	0.538000	0.28064	0.018000	0.09664	2.600000	0.46240	2.865000	0.98341	0.655000	0.94253	GAT	.	.	.	none		0.493	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755		T	6620280	C	T	6620280	3	4	161	1	0	0	0	0	1	0	0	0	10685	913	32	2	1601	2	NSUN2	5	6620280	Missense_Mutation	SNP	C	TCGA-EV-5901-01A-11D-1589-08	5131737	6620280	174294980	14	9508											
VCAN	1462	hgsc.bcm.edu	37	chr5	82836813	82836813	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagatagaagccaactagAtcacatgggctttcacttca	14	10	8	9	0	3	4	3	1	0	3	3	4	3	4	1	1	2	1	1	1	5	4			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr5:82836813A>G	ENST00000265077.3	+	8	8556	c.7991A>G	c.(7990-7992)gAt>gGt	p.D2664G	VCAN_ENST00000502527.2_Intron|VCAN_ENST00000513016.1_3'UTR|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000343200.5_Missense_Mutation_p.D1677G|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000512590.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2664	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)	AGCCAACTAGATCACATGGGC	0.453																																					p.D2664G		Atlas-SNP	.											.	VCAN	498	.	0			c.A7991G						PASS	.						126	122	123					5																	82836813		2203	4300	6503	SO:0001583	missense	1462	exon8			AACTAGATCACAT	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.7991A>G	chr5.hg19:g.82836813A>G	ENSP00000265077:p.Asp2664Gly	157.0	0.0	.		153.0	45.0	.	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	hg19	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	A	2.766	-0.256719	0.05829	.	.	ENSG00000038427	ENST00000265077;ENST00000343200	T;T	0.35605	1.3;1.3	6.04	2.03	0.26663	.	0.465278	0.21973	N	0.066435	T	0.30324	0.0761	L	0.53249	1.67	0.09310	N	1	B;B	0.17268	0.021;0.012	B;B	0.15484	0.013;0.006	T	0.19582	-1.0301	10	0.35671	T	0.21	.	9.0589	0.36423	0.7098:0.0:0.2902:0.0	.	1677;2664	P13611-2;P13611	.;CSPG2_HUMAN	G	2664;1677	ENSP00000265077:D2664G;ENSP00000340062:D1677G	ENSP00000265077:D2664G	D	+	2	0	VCAN	82872569	0.001000	0.12720	0.002000	0.10522	0.019000	0.09904	0.608000	0.24223	0.540000	0.28808	-0.375000	0.07067	GAT	.	.	.	none		0.453	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		G	82836813	A	G	82836813	3	3	161	1	0	0	0	0	1	0	0	0	17150	333	12	3	8017	3	VCAN	5	82836813	Missense_Mutation	SNP	A	TCGA-EV-5901-01A-11D-1589-08	76216533	82836813	98078447	15	9509											
SLC22A5	6584	hgsc.bcm.edu	37	chr5	131729504	131729504	+	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	cagatgctaagagtcaaaggGtaagaagacctcctctgtca	14	8	10	9	0	3	4	2	0	1	4	4	4	4	4	2	1	1	2	2	1	4	2	rs386134226		TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr5:131729504G>A	ENST00000245407.3	+	9	1807		c.e9+1		SLC22A5_ENST00000435065.2_Splice_Site	NM_003060.3	NP_003051.1	O76082	S22A5_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 5						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)	GAGTCAAAGGGTAAGAAGACC	0.542																																					.		Atlas-SNP	.											.	SLC22A5	34	.	0			c.1586+1G>A						PASS	.						200	186	191					5																	131729504		2203	4300	6503	SO:0001630	splice_region_variant	6584	exon9			CAAAGGGTAAGAA	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.1586+1G>A	chr5.hg19:g.131729504G>A		211.0	0.0	.		154.0	61.0	.	NM_003060	A2Q0V1|B2R844|D3DQ87|Q6ZQZ8|Q96EH6	Splice_Site	SNP	ENST00000245407.3	hg19	CCDS4154.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.828787	0.90955	.	.	ENSG00000197375	ENST00000245407;ENST00000435065	.	.	.	5.87	5.87	0.94306	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.5827	0.99408	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC22A5	131757403	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	9.442000	0.97566	2.941000	0.99782	0.655000	0.94253	.	.	.	.	none		0.542	SLC22A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132631.1	NM_003060	Intron	A	131729504	G	A	131729504	5	1	161	1	0	0	0	0	0	0	1	0	14470	1275	44	2	1621	2	SLC22A5	5	131729504	Splice_Site	SNP	G	TCGA-EV-5901-01A-11D-1589-08	48892691	131729504	49185756	16	9510											
DPYSL3	1809	hgsc.bcm.edu	37	chr5	146780335	146780335	+	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	ggctgtgaagttgtccttccCaattgctttctgggcagtgc	5	14	12	10	0	1	1	0	1	1	0	3	1	3	1	2	2	2	4	2	2	2	4			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr5:146780335C>A	ENST00000398514.3	-	10	1401	c.1030G>T	c.(1030-1032)Ggg>Tgg	p.G344W	DPYSL3_ENST00000534907.1_Intron|DPYSL3_ENST00000343218.5_Missense_Mutation_p.G458W|CTB-108O6.2_ENST00000607270.1_RNA	NM_001387.2	NP_001378.1	Q14195	DPYL3_HUMAN	dihydropyrimidinase-like 3	344					actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cell migration (GO:0030336)|negative regulation of neuron projection development (GO:0010977)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron projection development (GO:0010976)|protein homooligomerization (GO:0051260)|pyrimidine nucleobase catabolic process (GO:0006208)|response to axon injury (GO:0048678)	cell body (GO:0044297)|cytosol (GO:0005829)|extracellular space (GO:0005615)|filamentous actin (GO:0031941)|growth cone (GO:0030426)|lamellipodium (GO:0030027)	chondroitin sulfate binding (GO:0035374)|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)|SH3 domain binding (GO:0017124)			breast(2)|endometrium(1)|kidney(4)|large_intestine(6)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTGTCCTTCCCAATTGCTTTC	0.557																																					p.G458W		Atlas-SNP	.											.	DPYSL3	58	.	0			c.G1372T						PASS	.						112	118	116					5																	146780335		2201	4300	6501	SO:0001583	missense	1809	exon10			CCTTCCCAATTGC	D78014	CCDS43381.1, CCDS56387.1	5q32	2008-02-05							3015	protein-coding gene	gene with protein product		601168				8973361, 9115293	Standard	NM_001197294		Approved	DRP-3, ULIP, CRMP4	uc003loo.3	Q14195		ENST00000398514.3:c.1030G>T	chr5.hg19:g.146780335C>A	ENSP00000381526:p.Gly344Trp	81.0	0.0	.		76.0	4.0	.	NM_001197294	B3SXQ8|Q93012	Missense_Mutation	SNP	ENST00000398514.3	hg19	CCDS43381.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.7|29.7	5.029428|5.029428	0.93518|0.93518	.|.	.|.	ENSG00000113657|ENSG00000113657	ENST00000398514;ENST00000343218|ENST00000520473	D;D|.	0.91894|.	-2.93;-2.93|.	5.53|5.53	5.53|5.53	0.82687|0.82687	Amidohydrolase 1 (1);Metal-dependent hydrolase, composite domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.88422|0.88422	0.6432|0.6432	H|H	0.96547|0.96547	3.84|3.84	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	0.91456|0.91456	0.5185|0.5185	10|5	0.87932|.	D|.	0|.	-11.5514|-11.5514	19.8184|19.8184	0.96581|0.96581	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	458;344|.	B3SXQ8;Q14195|.	.;DPYL3_HUMAN|.	W|L	344;458|42	ENSP00000381526:G344W;ENSP00000343690:G458W|.	ENSP00000343690:G458W|.	G|W	-|-	1|2	0|0	DPYSL3|DPYSL3	146760528|146760528	1.000000|1.000000	0.71417|0.71417	0.971000|0.971000	0.41717|0.41717	0.967000|0.967000	0.64934|0.64934	7.694000|7.694000	0.84235|0.84235	2.761000|2.761000	0.94854|0.94854	0.650000|0.650000	0.86243|0.86243	GGG|TGG	.	.	.	none		0.557	DPYSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373421.2	NM_001387		A	146780335	C	A	146780335	3	1	161	1	0	0	0	0	1	0	0	0	4750	594	21	4	702	4	DPYSL3	5	146780335	Missense_Mutation	SNP	C	TCGA-EV-5901-01A-11D-1589-08	15050831	146780335	34134925	17	9511											
PPP1R10	5514	hgsc.bcm.edu	37	chr6	30577691	30577691	+	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	gctgtccaggcccttgagaaGttctttggggtctatgggac	6	12	14	9	0	2	1	0	1	2	1	3	3	3	2	2	4	0	2	2	4	2	4			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr6:30577691G>T	ENST00000376511.2	-	3	583	c.31C>A	c.(31-33)Ctt>Att	p.L11I	PPP1R10_ENST00000484449.1_5'Flank	NM_002714.3	NP_002705.2	Q96QC0	PP1RA_HUMAN	protein phosphatase 1, regulatory subunit 10	11	Interaction with TOX4. {ECO:0000250}.				protein import into nucleus (GO:0006606)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|PTW/PP1 phosphatase complex (GO:0072357)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(3)|skin(1)	25						CCCTTGAGAAGTTCTTTGGGG	0.468																																					p.L11I		Atlas-SNP	.											.	PPP1R10	60	.	0			c.C31A						PASS	.						112	107	109					6																	30577691		2203	4300	6503	SO:0001583	missense	5514	exon3			TGAGAAGTTCTTT	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.31C>A	chr6.hg19:g.30577691G>T	ENSP00000365694:p.Leu11Ile	106.0	0.0	.		97.0	33.0	.	NM_002714	O00405	Missense_Mutation	SNP	ENST00000376511.2	hg19	CCDS4681.1	.	.	.	.	.	.	.	.	.	.	G	19.22	3.785297	0.70337	.	.	ENSG00000204569	ENST00000376511;ENST00000537132	T	0.54675	0.56	5.65	5.65	0.86999	.	0.119294	0.64402	D	0.000018	T	0.33876	0.0878	L	0.37850	1.14	0.43399	D	0.995525	B	0.30236	0.274	B	0.26416	0.069	T	0.21008	-1.0258	10	0.52906	T	0.07	-18.5396	18.8591	0.92265	0.0:0.0:1.0:0.0	.	11	Q96QC0	PP1RA_HUMAN	I	11	ENSP00000365694:L11I	ENSP00000365694:L11I	L	-	1	0	PPP1R10	30685670	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.210000	0.65214	2.825000	0.97269	0.655000	0.94253	CTT	.	.	.	none		0.468	PPP1R10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076556.2	NM_002714		T	30577691	G	T	30577691	3	4	161	1	0	0	0	0	1	0	0	0	12362	1029	36	4	2863	4	PPP1R10	6	30577691	Missense_Mutation	SNP	G	TCGA-EV-5901-01A-11D-1589-08		30577691	140537376	18	9512											
CCDC129	223075	hgsc.bcm.edu	37	chr7	31683522	31683527	+	In_Frame_Del	DEL	GACTTT	GACTTT	-																															caggaagcccagttcatgacGactttgaaagcccttcagga																										TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	GACTTT	GACTTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr7:31683522_31683527delGACTTT	ENST00000407970.3	+	11	2576_2581	c.2538_2543delGACTTT	c.(2536-2544)acgactttg>acg	p.TL847del	CCDC129_ENST00000319386.3_In_Frame_Del_p.TL699del|CCDC129_ENST00000409210.1_In_Frame_Del_p.TL755del|CCDC129_ENST00000451887.2_In_Frame_Del_p.TL873del	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	847										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						AGTTCATGACGACTTTGAAAGCCCTT	0.549																																					p.872_874del		Atlas-INDEL	.											.	CCDC129	127	.	0			c.2615_2620del						PASS	.																																			SO:0001651	inframe_deletion	223075	exon11			.	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.2538_2543delGACTTT	chr7.hg19:g.31683522_31683527delGACTTT	ENSP00000384416:p.Thr847_Leu848del	64.0	0.0	0		121.0	26.0	0.214876	NM_001257968	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	In_Frame_Del	DEL	ENST00000407970.3	hg19	CCDS5435.2																																																																																			.	.	.	none		0.549	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300		-	31683527	GACTTT	-	31683522	7	5	161	1	0	1	0	1	0	0	0	0	2766	1045	37	0	2576	0	CCDC129	7	31683522	In_Frame_Del	DEL	GACTTT	TCGA-EV-5901-01A-11D-1589-08		31683522	127455141	19	9513											
URGCP	55665	hgsc.bcm.edu	37	chr7	43918184	43918184	+	Missense_Mutation	SNP	A	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	agttgaggtcccgatgccagAagcagtcccactgcctgtgg	8	8	13	12	1	0	2	0	1	0	1	2	3	2	2	4	2	3	2	4	2	1	1			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr7:43918184A>C	ENST00000453200.1	-	6	1371	c.878T>G	c.(877-879)tTc>tGc	p.F293C	URGCP_ENST00000336086.6_Missense_Mutation_p.F250C|URGCP_ENST00000402306.3_Missense_Mutation_p.F284C|URGCP-MRPS24_ENST00000603700.1_Intron|URGCP_ENST00000497914.1_5'UTR|URGCP_ENST00000223341.7_Missense_Mutation_p.F250C|URGCP_ENST00000443736.1_Missense_Mutation_p.F250C|URGCP_ENST00000447717.3_Missense_Mutation_p.F250C			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	293					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						CCGATGCCAGAAGCAGTCCCA	0.602																																					p.F293C		Atlas-SNP	.											.	URGCP	170	.	0			c.T878G						PASS	.						43	47	45					7																	43918184		1981	4149	6130	SO:0001583	missense	55665	exon6			TGCCAGAAGCAGT		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.878T>G	chr7.hg19:g.43918184A>C	ENSP00000396918:p.Phe293Cys	70.0	0.0	.		75.0	21.0	.	NM_001077663	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Missense_Mutation	SNP	ENST00000453200.1	hg19	CCDS47578.1	.	.	.	.	.	.	.	.	.	.	A	19.91	3.914953	0.72983	.	.	ENSG00000106608	ENST00000223341;ENST00000336086;ENST00000402306;ENST00000443736;ENST00000453200;ENST00000447717	T;T;T;T;T;T	0.43688	1.02;1.02;0.95;1.02;0.94;1.02	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.67720	0.2923	M	0.85945	2.785	0.49483	D	0.999796	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.73665	-0.3911	10	0.87932	D	0	-32.908	13.5869	0.61937	1.0:0.0:0.0:0.0	.	284;293	Q8TCY9-2;Q8TCY9	.;URGCP_HUMAN	C	250;250;284;250;293;250	ENSP00000223341:F250C;ENSP00000336872:F250C;ENSP00000384955:F284C;ENSP00000392136:F250C;ENSP00000396918:F293C;ENSP00000402803:F250C	ENSP00000223341:F250C	F	-	2	0	URGCP	43884709	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.761000	0.91691	2.104000	0.64026	0.402000	0.26972	TTC	.	.	.	none		0.602	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664		C	43918184	A	C	43918184	3	2	161	1	0	0	0	0	1	0	0	0	17038	246	9	5	1921	5	URGCP	7	43918184	Missense_Mutation	SNP	A	TCGA-EV-5901-01A-11D-1589-08	12234662	43918184	115220479	20	9514											
BAZ1B	9031	hgsc.bcm.edu	37	chr7	72907199	72907199	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggagcccatttcctttcTcctttttttaatgaagtagg	8	16	9	8	0	1	1	0	1	1	0	3	3	2	3	3	3	1	1	3	3	3	7			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr7:72907199T>C	ENST00000339594.4	-	5	962	c.624A>G	c.(622-624)ggA>ggG	p.G208G	BAZ1B_ENST00000404251.1_Silent_p.G208G	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	208	Mediates the tyrosine-protein kinase activity.				cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				ATTTCCTTTCTCCTTTTTTTA	0.328																																					p.G208G	Esophageal Squamous(112;1167 1561 21085 43672 48228)	Atlas-SNP	.											.	BAZ1B	147	.	0			c.A624G						PASS	.						129	125	127					7																	72907199		2203	4299	6502	SO:0001819	synonymous_variant	9031	exon5			CCTTTCTCCTTTT	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.624A>G	chr7.hg19:g.72907199T>C		51.0	0.0	.		112.0	26.0	.	NM_032408	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Silent	SNP	ENST00000339594.4	hg19	CCDS5549.1																																																																																			.	.	.	none		0.328	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408		C	72907199	T	C	72907199	2	2	161	1	0	0	0	0	0	0	0	1	1330	1538	54	3		3	BAZ1B	7	72907199	Silent	SNP	T	TCGA-EV-5901-01A-11D-1589-08	28989015	72907199	86231464	21	9515											
DNAJC2	27000	hgsc.bcm.edu	37	chr7	102963052	102963053	+	Nonsense_Mutation	DNP	AT	AT	TA																															cttcttccttgaacttttttAtccttggatcacagctgtat																										TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	A|T	A|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr7:102963052_102963053AT>TA	ENST00000379263.3	-	9	1088_1089	c.838_839AT>TA	c.(838-840)ATa>TAa	p.I280*	DNAJC2_ENST00000249270.7_Nonsense_Mutation_p.I280*|PMPCB_ENST00000420236.2_Intron	NM_014377.1	NP_055192.1	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2	280					'de novo' cotranslational protein folding (GO:0051083)|chromatin modification (GO:0016568)|DNA replication (GO:0006260)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|Hsp70 protein binding (GO:0030544)|poly(A) RNA binding (GO:0044822)|ubiquitin binding (GO:0043130)			endometrium(1)|kidney(9)|large_intestine(6)|lung(4)|ovary(1)	21						GAACTTTTTTATCCTTGGATCA	0.337																																					p.I280K|p.I280L		Atlas-SNP	.											.	DNAJC2	46	.	0			c.T839A|c.A838T						PASS	.																																			SO:0001587	stop_gained	27000	exon9			TTTTTTATCCTTG|TTTTTATCCTTGG	X98260	CCDS43628.1, CCDS47679.1	7q22-q32	2011-09-02	2008-07-01	2008-07-01	ENSG00000105821	ENSG00000105821		"Heat shock proteins / DNAJ (HSP40)"	13192	protein-coding gene	gene with protein product		605502	"zuotin related factor 1"	ZRF1		8885239	Standard	NM_001129887		Approved	MPP11, MPHOSPH11, ZUO1, zuotin	uc003vbo.3	Q99543	OTTHUMG00000157202	ENST00000379263.3:c.838_839delinsTA	chr7.hg19:g.102963052_102963053delinsTA	ENSP00000368565:p.Ile280*	53.0	0.0	.		60.0	33.0	.	NM_001129887	A4VCI0|Q9BVX1	Missense_Mutation	SNP	ENST00000379263.3	hg19	CCDS43628.1																																																																																			.	.	.	none		0.337	DNAJC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347891.1			TA	102963053	AT	TA	102963052	4	4	161	1	0	0	0	0	0	1	0	0	4641	449	16	5	1062	5	DNAJC2	7	102963052	Nonsense_Mutation	DNP	AT	TCGA-EV-5901-01A-11D-1589-08	30055853	102963052	56175611	22	9516											
PLEC	5339	hgsc.bcm.edu	37	chr8	144997708	144997708	+	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	tctctgcagccgcctgtgccTgagcccgggcctgtgcctgc	2	9	13	17	2	1	1	0	1	1	0	2	1	1	1	6	1	6	1	6	1	0	0			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr8:144997708T>A	ENST00000322810.4	-	31	6969	c.6800A>T	c.(6799-6801)cAg>cTg	p.Q2267L	PLEC_ENST00000354589.3_Missense_Mutation_p.Q2130L|PLEC_ENST00000398774.2_Missense_Mutation_p.Q2098L|PLEC_ENST00000357649.2_Missense_Mutation_p.Q2134L|PLEC_ENST00000527096.1_Missense_Mutation_p.Q2153L|PLEC_ENST00000354958.2_Missense_Mutation_p.Q2108L|PLEC_ENST00000436759.2_Missense_Mutation_p.Q2157L|PLEC_ENST00000345136.3_Missense_Mutation_p.Q2130L|PLEC_ENST00000356346.3_Missense_Mutation_p.Q2116L	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2267	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						CGCCTGTGCCTGAGCCCGGGC	0.741																																					p.Q2267L		Atlas-SNP	.											.	PLEC	1144	.	0			c.A6800T						PASS	.						8	10	10					8																	144997708		1949	4030	5979	SO:0001583	missense	5339	exon31			TGTGCCTGAGCCC	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.6800A>T	chr8.hg19:g.144997708T>A	ENSP00000323856:p.Gln2267Leu	27.0	0.0	.		24.0	5.0	.	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	hg19	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	T	4.904	0.167918	0.09339	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.78816	-1.17;-1.17;-1.2;-1.21;-1.14;-1.17;-1.17;-1.14;-1.17	4.98	3.77	0.43336	.	0.288111	0.26875	U	0.022050	T	0.62684	0.2448	N	0.16790	0.44	0.32967	D	0.521856	B;B;B;B;B;B;B;B	0.13594	0.008;0.008;0.008;0.005;0.008;0.008;0.008;0.008	B;B;B;B;B;B;B;B	0.12156	0.007;0.007;0.007;0.003;0.007;0.007;0.007;0.007	T	0.64935	-0.6290	10	0.66056	D	0.02	.	10.4644	0.44598	0.1462:0.0:0.0:0.8538	.	2157;2116;2108;2267;2098;2130;2134;2130	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	L	2130;2134;2130;2098;2267;2108;2116;2157;2153	ENSP00000344848:Q2130L;ENSP00000350277:Q2134L;ENSP00000346602:Q2130L;ENSP00000381756:Q2098L;ENSP00000323856:Q2267L;ENSP00000347044:Q2108L;ENSP00000348702:Q2116L;ENSP00000388180:Q2157L;ENSP00000434583:Q2153L	ENSP00000323856:Q2267L	Q	-	2	0	PLEC	145069696	0.350000	0.24878	0.725000	0.30721	0.062000	0.15995	1.232000	0.32636	0.690000	0.31570	0.368000	0.22195	CAG	.	.	.	none		0.741	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		A	144997708	T	A	144997708	3	1	161	1	0	0	0	0	1	0	0	0	12059	1580	55	5	7262	5	PLEC	8	144997708	Missense_Mutation	SNP	T	TCGA-EV-5901-01A-11D-1589-08		144997708	1366314	23	9517											
ABCA2	20	hgsc.bcm.edu	37	chr9	139908396	139908396	+	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	cgggcgcagtggaagcgtttGaccagcagcccgtggaactg	8	6	16	11	4	0	1	0	1	0	0	0	3	0	3	2	3	4	3	2	3	2	1			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr9:139908396G>C	ENST00000371605.3	-	27	4479	c.4332C>G	c.(4330-4332)gtC>gtG	p.V1444V	ABCA2_ENST00000341511.6_Silent_p.V1445V|ABCA2_ENST00000265662.5_Silent_p.V1445V			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	1444					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)		GGAAGCGTTTGACCAGCAGCC	0.672																																					p.V1475V		Atlas-SNP	.											.	ABCA2	113	.	0			c.C4425G						PASS	.						44	56	52					9																	139908396		2147	4225	6372	SO:0001819	synonymous_variant	20	exon28			GCGTTTGACCAGC	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.4332C>G	chr9.hg19:g.139908396G>C		37.0	0.0	.		33.0	11.0	.	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Silent	SNP	ENST00000371605.3	hg19																																																																																				.	.	.	none		0.672	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606		C	139908396	G	C	139908396	2	2	161	1	0	0	0	0	0	0	0	1	32	1277	45	4		4	ABCA2	9	139908396	Silent	SNP	G	TCGA-EV-5901-01A-11D-1589-08		139908396	1305035	24	9518											
ANK3	288	hgsc.bcm.edu	37	chr10	61836183	61836183	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtaagtggtggggagggatcTtgttgctcctgtactccgtt	5	14	15	7	1	1	0	0	0	1	0	3	2	3	2	2	4	2	5	2	4	2	5			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr10:61836183T>C	ENST00000280772.2	-	37	4647	c.4456A>G	c.(4456-4458)Aga>Gga	p.R1486G	ANK3_ENST00000355288.2_Intron|ANK3_ENST00000373827.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	1486					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						GGGAGGGATCTTGTTGCTCCT	0.418																																					p.R1486G		Atlas-SNP	.											.	ANK3	703	.	0			c.A4456G						PASS	.						86	86	86					10																	61836183		2203	4300	6503	SO:0001583	missense	288	exon37			GGGATCTTGTTGC	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.4456A>G	chr10.hg19:g.61836183T>C	ENSP00000280772:p.Arg1486Gly	55.0	0.0	.		58.0	27.0	.	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	hg19	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	T	17.52	3.410662	0.62399	.	.	ENSG00000151150	ENST00000280772	T	0.70045	-0.45	5.69	5.69	0.88448	.	0.000000	0.46145	D	0.000309	T	0.71484	0.3345	L	0.57536	1.79	0.80722	D	1	D	0.56521	0.976	P	0.50109	0.631	T	0.74763	-0.3555	10	0.59425	D	0.04	.	15.9352	0.79698	0.0:0.0:0.0:1.0	.	1486	Q12955	ANK3_HUMAN	G	1486	ENSP00000280772:R1486G	ENSP00000280772:R1486G	R	-	1	2	ANK3	61506189	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.698000	0.84413	2.167000	0.68274	0.477000	0.44152	AGA	.	.	.	none		0.418	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		C	61836183	T	C	61836183	3	2	161	1	0	0	0	0	1	0	0	0	622	1617	56	3	9018	3	ANK3	10	61836183	Missense_Mutation	SNP	T	TCGA-EV-5901-01A-11D-1589-08		61836183	73698564	25	9519											
ZMYND17	118490	hgsc.bcm.edu	37	chr10	75185676	75185676	+	Missense_Mutation	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	gggcactaagctgaattgtgCcaggttccaggggtgaagtt	9	10	15	7	0	0	2	0	2	0	0	1	2	1	2	2	4	2	4	2	4	3	4	rs143815503	byFrequency	TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr10:75185676C>T	ENST00000372912.1	-	4	964	c.962G>A	c.(961-963)gGc>gAc	p.G321D	MSS51_ENST00000299432.2_Missense_Mutation_p.G321D|AL353731.1_ENST00000584907.1_RNA			Q4VC12	MSS51_HUMAN	MSS51 mitochondrial translational activator	321					social behavior (GO:0035176)		metal ion binding (GO:0046872)										CTGAATTGTGCCAGGTTCCAG	0.547																																					p.G321D		Atlas-SNP	.											.	.	.	.	0			c.G962A						PASS	.						76	70	72					10																	75185676		2203	4300	6503	SO:0001583	missense	118490	exon5			ATTGTGCCAGGTT	AK096884	CCDS31221.1	10q22.3	2013-01-10	2013-01-10	2012-02-24	ENSG00000166343	ENSG00000166343		"Zinc fingers, MYND-type"	21000	protein-coding gene	gene with protein product		614773	"zinc finger, MYND-type containing 17", "MSS51 mitochondrial translational activator homolog (S. cerevisiae)"	ZMYND17		19710419	Standard	NM_001024593		Approved	FLJ39565	uc001jud.3	Q4VC12	OTTHUMG00000018464	ENST00000372912.1:c.962G>A	chr10.hg19:g.75185676C>T	ENSP00000362003:p.Gly321Asp	55.0	0.0	.		56.0	4.0	.	NM_001024593	A6NGH6|Q2VP95|Q5F2H5|Q7Z3M9|Q8N8G0	Missense_Mutation	SNP	ENST00000372912.1	hg19	CCDS31221.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.004490	0.74932	.	.	ENSG00000166343	ENST00000299432;ENST00000372912	T;T	0.47869	0.83;0.83	5.64	3.73	0.42828	.	0.228496	0.46758	D	0.000274	T	0.41858	0.1177	L	0.59436	1.845	0.41812	D	0.989971	B;B	0.27140	0.169;0.027	B;B	0.28553	0.091;0.018	T	0.34601	-0.9822	10	0.32370	T	0.25	-6.4632	9.5419	0.39257	0.0:0.7782:0.143:0.0788	.	100;321	Q4VC12-2;Q4VC12	.;ZMY17_HUMAN	D	321	ENSP00000299432:G321D;ENSP00000362003:G321D	ENSP00000299432:G321D	G	-	2	0	ZMYND17	74855682	1.000000	0.71417	0.995000	0.50966	0.964000	0.63967	2.882000	0.48546	1.627000	0.50400	0.650000	0.86243	GGC	.	C|1.000;A|0.000	.	alt		0.547	MSS51-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048652.3	NM_178451		T	75185676	C	T	75185676	3	4	161	1	0	0	0	0	1	0	0	0	17721	739	26	2	432	2	ZMYND17	10	75185676	Missense_Mutation	SNP	C	TCGA-EV-5901-01A-11D-1589-08	13349493	75185676	60349071	26	9520											
GUCY2C	2984	hgsc.bcm.edu	37	chr12	14796597	14796597	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcagttggtagatttcagaCgaccatggacttctgtctta	9	13	10	9	2	3	2	1	0	2	2	3	4	3	3	1	2	0	3	1	2	2	5			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr12:14796597C>T	ENST00000261170.3	-	17	1977	c.1841G>A	c.(1840-1842)cGt>cAt	p.R614H		NM_004963.3	NP_004954.2	P25092	GUC2C_HUMAN	guanylate cyclase 2C (heat stable enterotoxin receptor)	614	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of cell proliferation (GO:0042127)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|toxic substance binding (GO:0015643)			breast(3)|endometrium(7)|kidney(3)|large_intestine(9)|lung(17)|ovary(4)|skin(7)|urinary_tract(1)	51					Linaclotide(DB08890)	AGATTTCAGACGACCATGGAC	0.398																																					p.R614H		Atlas-SNP	.											.	GUCY2C	126	.	0			c.G1841A						PASS	.						162	153	156					12																	14796597		2203	4300	6503	SO:0001583	missense	2984	exon17			TTCAGACGACCAT		CCDS8664.1	12p12	2008-08-18			ENSG00000070019	ENSG00000070019			4688	protein-coding gene	gene with protein product		601330		GUC2C		8661067	Standard	NM_004963		Approved	STAR	uc001rcd.3	P25092	OTTHUMG00000168732	ENST00000261170.3:c.1841G>A	chr12.hg19:g.14796597C>T	ENSP00000261170:p.Arg614His	247.0	0.0	.		217.0	51.0	.	NM_004963	B2RMY6	Missense_Mutation	SNP	ENST00000261170.3	hg19	CCDS8664.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.110733	0.77210	.	.	ENSG00000070019	ENST00000261170	T	0.61980	0.06	5.47	5.47	0.80525	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.56232	0.1971	L	0.28458	0.855	0.80722	D	1	P	0.38767	0.646	B	0.39562	0.303	T	0.59862	-0.7374	10	0.54805	T	0.06	.	19.3191	0.94231	0.0:1.0:0.0:0.0	.	614	P25092	GUC2C_HUMAN	H	614	ENSP00000261170:R614H	ENSP00000261170:R614H	R	-	2	0	GUCY2C	14687864	1.000000	0.71417	0.800000	0.32199	0.988000	0.76386	4.932000	0.63476	2.549000	0.85964	0.650000	0.86243	CGT	.	.	.	none		0.398	GUCY2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400835.1			T	14796597	C	T	14796597	3	4	161	1	0	0	0	0	1	0	0	0	6903	536	19	1	1424	1	GUCY2C	12	14796597	Missense_Mutation	SNP	C	TCGA-EV-5901-01A-11D-1589-08		14796597	119055298	27	9521											
PRKAG1	5571	hgsc.bcm.edu	37	chr12	49396719	49396719	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacctgtgagcaccagggccTgcaggatgtcagacagtgat	10	7	13	11	0	1	3	1	2	0	1	1	4	1	4	3	2	2	2	3	2	0	0			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr12:49396719T>C	ENST00000548065.1	-	12	1415	c.959A>G	c.(958-960)cAg>cGg	p.Q320R	PRKAG1_ENST00000395170.3_Missense_Mutation_p.Q236R|RP11-386G11.5_ENST00000547866.1_RNA|RP11-386G11.5_ENST00000552284.1_RNA|RP11-386G11.5_ENST00000552933.1_RNA|PRKAG1_ENST00000316299.5_Missense_Mutation_p.Q329R|RP11-386G11.5_ENST00000547395.1_RNA|PRKAG1_ENST00000547306.1_Missense_Mutation_p.Q269R|PRKAG1_ENST00000552212.1_Missense_Mutation_p.Q288R			P54619	AAKG1_HUMAN	protein kinase, AMP-activated, gamma 1 non-catalytic subunit	320	CBS 4. {ECO:0000255|PROSITE- ProRule:PRU00703}.				cell cycle arrest (GO:0007050)|fatty acid biosynthetic process (GO:0006633)|insulin receptor signaling pathway (GO:0008286)|membrane organization (GO:0061024)|positive regulation of gene expression (GO:0010628)|positive regulation of protein kinase activity (GO:0045860)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of glycolytic process (GO:0006110)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	9					Acetylsalicylic acid(DB00945)	CACCAGGGCCTGCAGGATGTC	0.547																																					p.Q329R		Atlas-SNP	.											.	PRKAG1	31	.	0			c.A986G						PASS	.						126	96	106					12																	49396719		2203	4300	6503	SO:0001583	missense	5571	exon12			AGGGCCTGCAGGA	U42412	CCDS8777.1, CCDS55824.1, CCDS55825.1	12q12-q14	1998-07-16				ENSG00000181929			9385	protein-coding gene	gene with protein product		602742				8557660, 8621499	Standard	NM_002733		Approved		uc001rsz.3	P54619	OTTHUMG00000170406	ENST00000548065.1:c.959A>G	chr12.hg19:g.49396719T>C	ENSP00000447433:p.Gln320Arg	98.0	0.0	.		92.0	4.0	.	NM_001206709	B4DDT7|Q8N7V9	Missense_Mutation	SNP	ENST00000548065.1	hg19	CCDS8777.1	.	.	.	.	.	.	.	.	.	.	T	12.50	1.955618	0.34471	.	.	ENSG00000181929	ENST00000395170;ENST00000547306;ENST00000316299;ENST00000548065;ENST00000552212;ENST00000551770	D;D;D;D;D;D	0.90563	-2.69;-2.69;-2.69;-2.69;-2.69;-2.69	5.18	5.18	0.71444	Aldolase-type TIM barrel (1);Cystathionine beta-synthase, core (3);	0.000000	0.85682	D	0.000000	T	0.82056	0.4954	N	0.13371	0.34	0.80722	D	1	B;B	0.11235	0.001;0.004	B;B	0.20577	0.03;0.028	T	0.76602	-0.2899	10	0.16420	T	0.52	-6.3299	14.1483	0.65364	0.0:0.0:0.0:1.0	.	329;320	Q8N7V9;P54619	.;AAKG1_HUMAN	R	236;269;329;320;288;240	ENSP00000378599:Q236R;ENSP00000448873:Q269R;ENSP00000323867:Q329R;ENSP00000447433:Q320R;ENSP00000448972:Q288R;ENSP00000449121:Q240R	ENSP00000323867:Q329R	Q	-	2	0	PRKAG1	47682986	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.789000	0.85783	2.179000	0.69175	0.533000	0.62120	CAG	.	.	.	none		0.547	PRKAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408946.1	NM_002733		C	49396719	T	C	49396719	3	2	161	1	0	0	0	0	1	0	0	0	12510	1580	55	3	40	3	PRKAG1	12	49396719	Missense_Mutation	SNP	T	TCGA-EV-5901-01A-11D-1589-08	34600122	49396719	84455176	28	9522											
KDM2B	84678	hgsc.bcm.edu	37	chr12	121947832	121947832	+	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	aagccgtctatgctgggcttCctcggggcatctgtgggggc	4	10	16	11	2	2	0	0	0	2	0	4	0	3	0	2	5	2	3	2	5	2	2			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr12:121947832C>T	ENST00000377071.4	-	11	1257	c.1185G>A	c.(1183-1185)agG>agA	p.R395R	KDM2B_ENST00000538046.2_Silent_p.R305R|KDM2B_ENST00000377069.4_Silent_p.R364R|KDM2B_ENST00000536437.1_Silent_p.R278R|KDM2B_ENST00000542973.1_5'Flank	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	395					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						TGCTGGGCTTCCTCGGGGCAT	0.577																																					p.R395R		Atlas-SNP	.											.	KDM2B	218	.	0			c.G1185A						PASS	.						34	38	37					12																	121947832		1945	4141	6086	SO:0001819	synonymous_variant	84678	exon11			GGGCTTCCTCGGG	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.1185G>A	chr12.hg19:g.121947832C>T		99.0	0.0	.		70.0	24.0	.	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Silent	SNP	ENST00000377071.4	hg19	CCDS41850.1																																																																																			.	.	.	none		0.577	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590		T	121947832	C	T	121947832	2	4	161	1	0	0	0	0	0	0	0	1	8132	854	30	2		2	KDM2B	12	121947832	Silent	SNP	C	TCGA-EV-5901-01A-11D-1589-08	72551113	121947832	11904063	29	9523											
SACS	26278	hgsc.bcm.edu	37	chr13	23909472	23909472	+	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	cagctactccaccacgtgggAaaagagtaatatcttggttc	12	10	9	10	1	1	1	0	0	1	1	3	2	2	2	2	2	2	3	2	2	5	5			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr13:23909472A>T	ENST00000382292.3	-	9	8816	c.8543T>A	c.(8542-8544)tTc>tAc	p.F2848Y	SACS_ENST00000402364.1_Missense_Mutation_p.F2098Y|SACS_ENST00000382298.3_Missense_Mutation_p.F2848Y			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2848					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)		ACCACGTGGGAAAAGAGTAAT	0.408																																					p.F2848Y		Atlas-SNP	.											.	SACS	871	.	0			c.T8543A						PASS	.						85	83	84					13																	23909472		2203	4299	6502	SO:0001583	missense	26278	exon10			CGTGGGAAAAGAG	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.8543T>A	chr13.hg19:g.23909472A>T	ENSP00000371729:p.Phe2848Tyr	139.0	0.0	.		155.0	57.0	.	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	hg19	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	A	28.1	4.889154	0.91889	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.87491	-2.1;-2.26;-2.1	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	D	0.88819	0.6540	L	0.40543	1.245	0.43588	D	0.995931	D	0.59357	0.985	P	0.59221	0.854	D	0.87733	0.2580	10	0.33940	T	0.23	.	15.58	0.76425	1.0:0.0:0.0:0.0	.	2848	Q9NZJ4	SACS_HUMAN	Y	2848;2098;2848	ENSP00000371729:F2848Y;ENSP00000385844:F2098Y;ENSP00000371735:F2848Y	ENSP00000371729:F2848Y	F	-	2	0	SACS	22807472	1.000000	0.71417	0.920000	0.36463	0.995000	0.86356	8.962000	0.93254	2.084000	0.62774	0.449000	0.29647	TTC	.	.	.	none		0.408	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		T	23909472	A	T	23909472	3	4	161	1	0	0	0	0	1	0	0	0	13817	246	9	5	5200	5	SACS	13	23909472	Missense_Mutation	SNP	A	TCGA-EV-5901-01A-11D-1589-08		23909472	91260406	30	9524											
B3GALTL	145173	hgsc.bcm.edu	37	chr13	31821210	31821210	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggctaaacaagaaggtgcAtggaccatacttccgttgtt	11	11	10	9	1	0	1	0	0	0	1	1	2	1	2	2	3	3	4	2	3	5	5			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr13:31821210A>G	ENST00000343307.4	+	5	470	c.321A>G	c.(319-321)gcA>gcG	p.A107A		NM_194318.3	NP_919299.3	Q6Y288	B3GLT_HUMAN	beta 1,3-galactosyltransferase-like	107					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)		AAGAAGGTGCATGGACCATAC	0.418																																					p.A107A		Atlas-SNP	.											.	B3GALTL	48	.	0			c.A321G						PASS	.						166	132	144					13																	31821210		2203	4300	6503	SO:0001819	synonymous_variant	145173	exon5			AGGTGCATGGACC	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.321A>G	chr13.hg19:g.31821210A>G		73.0	0.0	.		105.0	30.0	.	NM_194318	A8K5F8|Q5W0H2|Q6NUI3	Silent	SNP	ENST00000343307.4	hg19	CCDS9341.1																																																																																			.	.	.	none		0.418	B3GALTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044396.3	NM_194318		G	31821210	A	G	31821210	2	3	161	1	0	0	0	0	0	0	0	1	1252	204	8	3		3	B3GALTL	13	31821210	Silent	SNP	A	TCGA-EV-5901-01A-11D-1589-08	7911738	31821210	83348668	31	9525											
RNASE11	122651	hgsc.bcm.edu	37	chr14	21052161	21052161	+	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	gtttgcctgtagtgaactggCacactgtattttccagttct	7	16	9	9	0	1	1	0	1	1	0	2	1	2	1	2	1	2	5	2	1	3	6			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr14:21052161C>A	ENST00000610205.1	-	3	656	c.473G>T	c.(472-474)tGc>tTc	p.C158F	RNASE11_ENST00000553849.1_Missense_Mutation_p.C158F|RNASE11_ENST00000398008.2_Missense_Mutation_p.C158F|RNASE11_ENST00000398009.2_Missense_Mutation_p.C158F|RNASE11_ENST00000432835.2_Missense_Mutation_p.C158F|RNASE11_ENST00000555841.1_Missense_Mutation_p.C158F	NM_145250.3	NP_660293.1	Q8TAA1	RNS11_HUMAN	ribonuclease, RNase A family, 11 (non-active)	158						extracellular region (GO:0005576)	endonuclease activity (GO:0004519)|nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(6)|lung(7)|ovary(3)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	21	all_cancers(95;0.00238)	all_lung(585;0.235)	Epithelial(56;1.85e-06)|all cancers(55;1.46e-05)	GBM - Glioblastoma multiforme(265;0.0139)		AGTGAACTGGCACACTGTATT	0.488																																					p.C158F		Atlas-SNP	.											.	RNASE11	44	.	0			c.G473T						PASS	.						103	87	92					14																	21052161		2203	4300	6503	SO:0001583	missense	122651	exon3			AACTGGCACACTG	BC025410	CCDS9553.1	14q11.1	2013-08-05	2004-11-18	2004-11-18	ENSG00000173464	ENSG00000173464		"Ribonucleases, RNase A"	19269	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 6"	C14orf6			Standard	NM_145250		Approved		uc001vxs.3	Q8TAA1	OTTHUMG00000170990	ENST00000610205.1:c.473G>T	chr14.hg19:g.21052161C>A	ENSP00000476537:p.Cys158Phe	65.0	0.0	.		64.0	4.0	.	NM_145250		Missense_Mutation	SNP	ENST00000610205.1	hg19	CCDS9553.1	.	.	.	.	.	.	.	.	.	.	C	6.403	0.442547	0.12164	.	.	ENSG00000173464	ENST00000335950;ENST00000553849;ENST00000555841;ENST00000398009;ENST00000398008;ENST00000432835;ENST00000443456;ENST00000557503;ENST00000557105	D;D;D;D;D;D;D;D;D	0.92545	-3.06;-3.06;-3.06;-3.06;-3.06;-3.06;-3.06;-3.06;-3.06	3.7	1.83	0.25207	Ribonuclease A, domain (3);	0.198191	0.43579	N	0.000552	D	0.82999	0.5159	N	0.24115	0.695	0.09310	N	1	B	0.21225	0.053	B	0.22601	0.04	T	0.72887	-0.4156	10	0.56958	D	0.05	-25.0727	4.4612	0.11668	0.2199:0.6634:0.0:0.1167	.	158	Q8TAA1	RNS11_HUMAN	F	158	ENSP00000338288:C158F;ENSP00000451318:C158F;ENSP00000451563:C158F;ENSP00000381093:C158F;ENSP00000381092:C158F;ENSP00000395210:C158F;ENSP00000401398:C158F;ENSP00000451839:C158F;ENSP00000452412:C158F	ENSP00000338288:C158F	C	-	2	0	RNASE11	20122001	0.001000	0.12720	0.011000	0.14972	0.015000	0.08874	-0.122000	0.10627	0.521000	0.28445	0.511000	0.50034	TGC	.	.	.	none		0.488	RNASE11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073662.3	NM_145250		A	21052161	C	A	21052161	3	1	161	1	0	0	0	0	1	0	0	0	13414	710	25	4	130	4	RNASE11	14	21052161	Missense_Mutation	SNP	C	TCGA-EV-5901-01A-11D-1589-08		21052161	86297379	32	9526											
ZFP106	64397	hgsc.bcm.edu	37	chr15	42717056	42717056	+	Missense_Mutation	SNP	A	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	atgcaaagaatggttttgctAtggccctccagagttctgag	10	12	11	8	0	1	3	0	1	1	2	2	3	2	3	2	2	2	4	2	2	3	4			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr15:42717056A>C	ENST00000263805.4	-	13	5423	c.5097T>G	c.(5095-5097)caT>caG	p.H1699Q	ZNF106_ENST00000565660.1_5'Flank|ZNF106_ENST00000565380.1_Missense_Mutation_p.H927Q|RNU6-188P_ENST00000364207.1_RNA|ZNF106_ENST00000565611.1_Missense_Mutation_p.H884Q	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	1699					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)										TGGTTTTGCTATGGCCCTCCA	0.522																																					p.H1699Q		Atlas-SNP	.											.	ZFP106	117	.	0			c.T5097G						PASS	.						75	62	67					15																	42717056		2203	4299	6502	SO:0001583	missense	64397	exon13			TTTGCTATGGCCC	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.5097T>G	chr15.hg19:g.42717056A>C	ENSP00000263805:p.His1699Gln	55.0	0.0	.		31.0	14.0	.	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Missense_Mutation	SNP	ENST00000263805.4	hg19	CCDS32208.1	.	.	.	.	.	.	.	.	.	.	A	19.19	3.779019	0.70107	.	.	ENSG00000103994	ENST00000263805;ENST00000434903	T	0.81415	-1.49	5.44	-5.28	0.02755	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	0.88952	0.6577	M	0.86805	2.84	0.51233	D	0.999915	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.996;0.999;0.999	D	0.89321	0.3640	10	0.87932	D	0	-15.4983	17.6295	0.88103	0.1114:0.0:0.8886:0.0	.	927;1699;927	E9PE29;Q9H2Y7;B4DZ40	.;ZF106_HUMAN;.	Q	1699;927	ENSP00000263805:H1699Q	ENSP00000263805:H1699Q	H	-	3	2	ZFP106	40504348	0.990000	0.36364	0.928000	0.36995	0.984000	0.73092	0.230000	0.17852	-0.844000	0.04184	-1.151000	0.01829	CAT	.	.	.	none		0.522	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473		C	42717056	A	C	42717056	3	2	161	1	0	0	0	0	1	0	0	0	17649	446	16	5	582	5	ZFP106	15	42717056	Missense_Mutation	SNP	A	TCGA-EV-5901-01A-11D-1589-08		42717056	59814336	33	9527											
KIAA1199	57214	hgsc.bcm.edu	37	chr15	81230320	81230320	+	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	ctactgggacgaggactcagGgtgagcaggcgcccacttgg	8	6	16	11	2	1	1	1	1	0	0	1	4	1	3	1	5	2	1	1	5	1	2			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr15:81230320G>A	ENST00000394685.3	+	25	3826	c.3407G>A	c.(3406-3408)gGg>gAg	p.G1136E	KIAA1199_ENST00000356249.5_Splice_Site_p.G1136E|RP11-351M8.2_ENST00000560873.1_RNA|KIAA1199_ENST00000220244.3_Splice_Site_p.G1136E			Q8WUJ3	CEMIP_HUMAN		1136					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						GAGGACTCAGGGTGAGCAGGC	0.547																																					p.G1136E		Atlas-SNP	.											.	KIAA1199	118	.	0			c.G3407A						PASS	.						38	33	35					15																	81230320		2203	4300	6503	SO:0001630	splice_region_variant	57214	exon24			ACTCAGGGTGAGC																												ENST00000394685.3:c.3407+1G>A	chr15.hg19:g.81230320G>A		23.0	0.0	.		28.0	14.0	.	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Missense_Mutation	SNP	ENST00000394685.3	hg19	CCDS10315.1	.	.	.	.	.	.	.	.	.	.	G	33	5.227247	0.95173	.	.	ENSG00000103888	ENST00000220244;ENST00000394685;ENST00000356249	T;T;T	0.50813	0.73;0.73;0.73	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.72463	0.3463	M	0.82193	2.58	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.72934	-0.4141	10	0.41790	T	0.15	-33.8466	19.3153	0.94211	0.0:0.0:1.0:0.0	.	1136	Q8WUJ3	K1199_HUMAN	E	1136	ENSP00000220244:G1136E;ENSP00000378177:G1136E;ENSP00000348583:G1136E	ENSP00000220244:G1136E	G	+	2	0	KIAA1199	79017375	1.000000	0.71417	0.998000	0.56505	0.924000	0.55760	9.063000	0.93927	2.559000	0.86315	0.655000	0.94253	GGG	.	.	.	none		0.547	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1		Missense_Mutation	A	81230320	G	A	81230320	5	1	161	1	0	0	0	0	0	0	1	0	8220	1246	43	2	3497	2	KIAA1199	15	81230320	Splice_Site	SNP	G	TCGA-EV-5901-01A-11D-1589-08	38513264	81230320	21301072	34	9528											
BCMO1	53630	hgsc.bcm.edu	37	chr16	81314514	81314514	+	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	ggcatctacaacagccacggCcctgaaggaagaagatggcc	13	4	12	12	1	1	3	0	1	1	2	1	4	1	4	3	4	3	1	3	4	5	1			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr16:81314514C>G	ENST00000258168.2	+	8	1615	c.1154C>G	c.(1153-1155)gCc>gGc	p.A385G	BCMO1_ENST00000425577.2_Missense_Mutation_p.A316G	NM_017429.2	NP_059125.2												p.A385V(1)		breast(2)|endometrium(1)|large_intestine(4)|lung(9)|prostate(3)|skin(3)|stomach(1)	23						ACAGCCACGGCCCTGAAGGAA	0.403																																					p.A385G		Atlas-SNP	.											BCMO1,head_neck,malignant_melanoma,0,1	BCMO1	53	.	1	Substitution - Missense(1)	skin(1)	c.C1154G						PASS	.						71	69	70					16																	81314514		2202	4300	6502	SO:0001583	missense	53630	exon8			CCACGGCCCTGAA																												ENST00000258168.2:c.1154C>G	chr16.hg19:g.81314514C>G	ENSP00000258168:p.Ala385Gly	51.0	0.0	.		50.0	2.0	.	NM_017429		Missense_Mutation	SNP	ENST00000258168.2	hg19	CCDS10934.1	.	.	.	.	.	.	.	.	.	.	C	17.27	3.346163	0.61073	.	.	ENSG00000135697	ENST00000258168;ENST00000425577	D;D	0.95853	-3.83;-3.48	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	D	0.98432	0.9478	M	0.93550	3.43	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98794	1.0737	10	0.62326	D	0.03	-38.9556	19.5968	0.95544	0.0:1.0:0.0:0.0	.	316;385	E7EM88;Q9HAY6	.;BCDO1_HUMAN	G	385;316	ENSP00000258168:A385G;ENSP00000400586:A316G	ENSP00000258168:A385G	A	+	2	0	BCMO1	79872015	1.000000	0.71417	0.995000	0.50966	0.039000	0.13416	5.343000	0.65976	2.793000	0.96121	0.655000	0.94253	GCC	.	.	.	none		0.403	BCMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269056.1			G	81314514	C	G	81314514	3	3	161	1	0	0	0	0	1	0	0	0	1384	739	26	4	1184	4	BCMO1	16	81314514	Missense_Mutation	SNP	C	TCGA-EV-5901-01A-11D-1589-08		81314514	9040239	35	9529											
RAB3A	5864	hgsc.bcm.edu	37	chr19	18313494	18313494	+	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	agaatcttgaacatgtagtcGaagttctgatccgaggactc	12	11	10	8	2	2	3	0	2	2	1	5	6	3	4	1	1	1	2	1	1	4	3			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr19:18313494G>C	ENST00000222256.4	-	2	235	c.57C>G	c.(55-57)ttC>ttG	p.F19L	AC068499.10_ENST00000594805.3_RNA|RAB3A_ENST00000464076.3_Intron|AC068499.10_ENST00000599416.2_RNA|AC068499.10_ENST00000596473.1_RNA	NM_002866.4	NP_002857.1	P20336	RAB3A_HUMAN	RAB3A, member RAS oncogene family	19					axonogenesis (GO:0007409)|constitutive secretory pathway (GO:0045054)|glutamate secretion (GO:0014047)|GTP catabolic process (GO:0006184)|lung development (GO:0030324)|maintenance of presynaptic active zone structure (GO:0048790)|mitochondrion organization (GO:0007005)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|positive regulation of exocytosis (GO:0045921)|post-embryonic development (GO:0009791)|protein transport (GO:0015031)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|respiratory system process (GO:0003016)|response to electrical stimulus (GO:0051602)|sensory perception of touch (GO:0050975)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|synaptic vesicle maturation (GO:0016188)|synaptic vesicle recycling (GO:0036465)	acrosomal vesicle (GO:0001669)|axon (GO:0030424)|clathrin-sculpted acetylcholine transport vesicle membrane (GO:0060201)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|clathrin-sculpted glutamate transport vesicle membrane (GO:0060203)|clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|vesicle (GO:0031982)	ATPase activator activity (GO:0001671)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			NS(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	8						ACATGTAGTCGAAGTTCTGAT	0.582											OREG0025360	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F19L		Atlas-SNP	.											.	RAB3A	23	.	0			c.C57G						PASS	.						257	217	230					19																	18313494		2203	4300	6503	SO:0001583	missense	5864	exon2			GTAGTCGAAGTTC		CCDS12372.1	19p13.2	2008-07-17			ENSG00000105649	ENSG00000105649		"RAB, member RAS oncogene"	9777	protein-coding gene	gene with protein product	"RAS-associated protein RAB3A"	179490				2687157, 7532276	Standard	NM_002866		Approved		uc002nie.2	P20336	OTTHUMG00000137378	ENST00000222256.4:c.57C>G	chr19.hg19:g.18313494G>C	ENSP00000222256:p.Phe19Leu	246.0	0.0	.	724	195.0	56.0	.	NM_002866	A8K0J4|Q9NYE1	Missense_Mutation	SNP	ENST00000222256.4	hg19	CCDS12372.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.017822	0.75161	.	.	ENSG00000105649	ENST00000222256	T	0.79141	-1.24	4.4	0.678	0.17969	.	0.000000	0.85682	D	0.000000	T	0.72890	0.3517	N	0.25890	0.77	0.80722	D	1	D	0.65815	0.995	P	0.59889	0.865	T	0.70490	-0.4857	10	0.87932	D	0	-19.6435	5.4616	0.16619	0.5735:0.0:0.4265:0.0	.	19	P20336	RAB3A_HUMAN	L	19	ENSP00000222256:F19L	ENSP00000222256:F19L	F	-	3	2	RAB3A	18174494	0.677000	0.27577	1.000000	0.80357	0.984000	0.73092	-0.040000	0.12104	0.318000	0.23185	0.313000	0.20887	TTC	.	.	.	none		0.582	RAB3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268056.2	NM_002866		C	18313494	G	C	18313494	3	2	161	1	0	0	0	0	1	0	0	0	12944	1049	37	4	621	4	RAB3A	19	18313494	Missense_Mutation	SNP	G	TCGA-EV-5901-01A-11D-1589-08		18313494	40815489	36	9530											
CSNK2A1	1457	hgsc.bcm.edu	37	chr20	468205	468205	+	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	tgtggacaaagcgttcccatCgctttcgagagtgtctgcag	8	11	12	10	3	1	1	0	0	1	1	4	3	2	2	1	1	2	3	1	1	1	2			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr20:468205C>T	ENST00000217244.3	-	12	1214	c.839G>A	c.(838-840)cGa>cAa	p.R280Q	CSNK2A1_ENST00000400227.3_Missense_Mutation_p.R280Q|CSNK2A1_ENST00000349736.5_Missense_Mutation_p.R280Q|CSNK2A1_ENST00000400217.2_Missense_Mutation_p.R144Q	NM_177559.2	NP_808227.1	P68400	CSK21_HUMAN	casein kinase 2, alpha 1 polypeptide	280	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)			GCGTTCCCATCGCTTTCGAGA	0.502																																					p.R280Q		Atlas-SNP	.											.	CSNK2A1	36	.	0			c.G839A						PASS	.						85	76	80					20																	468205		2203	4300	6503	SO:0001583	missense	1457	exon11			TCCCATCGCTTTC	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.839G>A	chr20.hg19:g.468205C>T	ENSP00000217244:p.Arg280Gln	69.0	0.0	.		70.0	21.0	.	NM_001895	B4DYS6|D3DVV8|P19138|P20426|Q14013|Q5U065	Missense_Mutation	SNP	ENST00000217244.3	hg19	CCDS13003.1	.	.	.	.	.	.	.	.	.	.	C	33	5.233597	0.95207	.	.	ENSG00000101266	ENST00000400227;ENST00000349736;ENST00000217244;ENST00000381973;ENST00000400217	T;T;T;T	0.43294	3.29;3.29;3.29;0.95	5.24	5.24	0.73138	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	0.48352	0.1495	N	0.17594	0.5	0.80722	D	1	D	0.89917	1.0	D	0.65140	0.932	T	0.51426	-0.8707	10	0.52906	T	0.07	-6.9053	17.9724	0.89117	0.0:1.0:0.0:0.0	.	280	P68400	CSK21_HUMAN	Q	280;280;280;280;144	ENSP00000383086:R280Q;ENSP00000339247:R280Q;ENSP00000217244:R280Q;ENSP00000383076:R144Q	ENSP00000217244:R280Q	R	-	2	0	CSNK2A1	416205	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.601000	0.82783	2.713000	0.92767	0.585000	0.79938	CGA	.	.	.	none		0.502	CSNK2A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077466.1	NM_001895		T	468205	C	T	468205	3	4	161	1	0	0	0	0	1	0	0	0	3959	884	31	1	348	1	CSNK2A1	20	468205	Missense_Mutation	SNP	C	TCGA-EV-5901-01A-11D-1589-08		468205	62557315	37	9531											
HMOX1	3162	hgsc.bcm.edu	37	chr22	35779129	35779129	+	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	gatttgtcagaggccctgaaGgaggccaccaaggaggtgca	11	6	15	9	0	1	2	1	1	0	1	1	5	1	4	3	5	1	1	3	5	2	1			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr22:35779129G>T	ENST00000216117.8	+	2	393	c.54G>T	c.(52-54)aaG>aaT	p.K18N		NM_002133.2	NP_002124.1	P09601	HMOX1_HUMAN	heme oxygenase (decycling) 1	18					angiogenesis (GO:0001525)|cell death (GO:0008219)|cellular iron ion homeostasis (GO:0006879)|cellular response to arsenic-containing substance (GO:0071243)|cellular response to cadmium ion (GO:0071276)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient (GO:0031670)|endothelial cell proliferation (GO:0001935)|erythrocyte homeostasis (GO:0034101)|excretion (GO:0007588)|heme catabolic process (GO:0042167)|heme oxidation (GO:0006788)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|iron ion homeostasis (GO:0055072)|low-density lipoprotein particle clearance (GO:0034383)|negative regulation of DNA binding (GO:0043392)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mast cell cytokine production (GO:0032764)|negative regulation of mast cell degranulation (GO:0043305)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smooth muscle cell proliferation (GO:0048662)|porphyrin-containing compound metabolic process (GO:0006778)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of vasodilation (GO:0045909)|protein homooligomerization (GO:0051260)|regulation of angiogenesis (GO:0045765)|regulation of blood pressure (GO:0008217)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to estrogen (GO:0043627)|response to hydrogen peroxide (GO:0042542)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|smooth muscle hyperplasia (GO:0014806)|transmembrane transport (GO:0055085)|wound healing involved in inflammatory response (GO:0002246)	caveola (GO:0005901)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|heme oxygenase (decyclizing) activity (GO:0004392)|metal ion binding (GO:0046872)|phospholipase D activity (GO:0004630)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	16					Vitamin E(DB00163)	AGGCCCTGAAGGAGGCCACCA	0.577																																					p.K18N		Atlas-SNP	.											.	HMOX1	32	.	0			c.G54T						PASS	.						85	78	80					22																	35779129		2203	4300	6503	SO:0001583	missense	3162	exon2			CCTGAAGGAGGCC		CCDS13914.1	22q12	2003-10-13			ENSG00000100292	ENSG00000100292	1.14.99.3		5013	protein-coding gene	gene with protein product		141250				10591208	Standard	NM_002133		Approved	bK286B10, HO-1	uc003ant.2	P09601	OTTHUMG00000150960	ENST00000216117.8:c.54G>T	chr22.hg19:g.35779129G>T	ENSP00000216117:p.Lys18Asn	156.0	0.0	.		94.0	29.0	.	NM_002133		Missense_Mutation	SNP	ENST00000216117.8	hg19	CCDS13914.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.982022	0.74474	.	.	ENSG00000100292	ENST00000412893;ENST00000216117	T;T	0.26957	1.7;1.7	6.06	2.67	0.31697	Haem oxygenase-like, multi-helical (2);	0.000000	0.85682	D	0.000000	T	0.54515	0.1863	M	0.91300	3.195	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	T	0.60367	-0.7277	10	0.87932	D	0	-50.6157	9.0075	0.36120	0.338:0.0:0.662:0.0	.	18	P09601	HMOX1_HUMAN	N	18	ENSP00000413316:K18N;ENSP00000216117:K18N	ENSP00000216117:K18N	K	+	3	2	HMOX1	34109129	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.625000	0.37029	0.909000	0.36697	0.655000	0.94253	AAG	.	.	.	none		0.577	HMOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320657.1			T	35779129	G	T	35779129	3	4	161	1	0	0	0	0	1	0	0	0	7250	991	35	4	60	4	HMOX1	22	35779129	Missense_Mutation	SNP	G	TCGA-EV-5901-01A-11D-1589-08		35779129	15525437	38	9532											
SUN2	25777	hgsc.bcm.edu	37	chr22	39146253	39146253	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgaagtggccaccatccagAgtaaggagcccgcccgtgag	10	4	14	13	3	0	2	0	1	0	1	1	4	1	3	5	2	1	1	5	2	2	1			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chr22:39146253A>G	ENST00000405510.1	-	6	855	c.497T>C	c.(496-498)cTc>cCc	p.L166P	SUN2_ENST00000406622.1_Missense_Mutation_p.L166P|SUN2_ENST00000411587.2_Missense_Mutation_p.L155P|RP3-508I15.14_ENST00000416406.1_RNA|SUN2_ENST00000216064.4_Missense_Mutation_p.L166P|SUN2_ENST00000405018.1_Missense_Mutation_p.L187P	NM_001199580.1	NP_001186509.1	Q9UH99	SUN2_HUMAN	Sad1 and UNC84 domain containing 2	166					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|mitotic spindle organization (GO:0007052)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)	condensed nuclear chromosome (GO:0000794)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|SUN-KASH complex (GO:0034993)	identical protein binding (GO:0042802)|lamin binding (GO:0005521)|microtubule binding (GO:0008017)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)|stomach(1)	15						CACCATCCAGAGTAAGGAGCC	0.602																																					p.L187P		Atlas-SNP	.											.	SUN2	59	.	0			c.T560C						PASS	.						47	52	50					22																	39146253		2203	4300	6503	SO:0001583	missense	25777	exon5			ATCCAGAGTAAGG	AF202723	CCDS13978.1, CCDS56231.1	22q12-q13	2010-05-18	2010-05-18	2010-01-27	ENSG00000100242	ENSG00000100242			14210	protein-coding gene	gene with protein product		613569	"unc-84 homolog B (C. elegans)"	UNC84B		10508607, 10375507	Standard	NM_015374		Approved		uc010gxq.2	Q9UH99	OTTHUMG00000151031	ENST00000405510.1:c.497T>C	chr22.hg19:g.39146253A>G	ENSP00000385740:p.Leu166Pro	82.0	0.0	.		66.0	22.0	.	NM_001199579	B0QY62|O75156|Q2NKN8|Q2T9F7|Q504T5|Q6B4H1|Q7Z3E3	Missense_Mutation	SNP	ENST00000405510.1	hg19	CCDS13978.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.41|14.41	2.527820|2.527820	0.44969|0.44969	.|.	.|.	ENSG00000100242|ENSG00000100242	ENST00000405510;ENST00000216064;ENST00000405018;ENST00000406622;ENST00000411587;ENST00000438058;ENST00000456894;ENST00000420859|ENST00000430185	T;T;T;T;T;T;T;T|.	0.40756|.	2.3;2.3;2.31;2.3;2.16;1.03;1.23;1.02|.	5.09|5.09	5.09|5.09	0.68999|0.68999	.|.	0.691574|.	0.13508|.	N|.	0.382686|.	T|T	0.49029|0.49029	0.1533|0.1533	N|N	0.19112|0.19112	0.55|0.55	0.41384|0.41384	D|D	0.987572|0.987572	P;D;D;D;D|.	0.57257|.	0.826;0.979;0.963;0.971;0.963|.	B;P;P;P;P|.	0.50617|.	0.347;0.642;0.642;0.646;0.521|.	T|T	0.46762|0.46762	-0.9168|-0.9168	10|5	0.87932|.	D|.	0|.	-3.5021|-3.5021	13.3916|13.3916	0.60827|0.60827	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	155;201;166;187;166|.	B4DIU6;B4E2A6;Q2T9F7;B0QY62;Q9UH99|.	.;.;.;.;SUN2_HUMAN|.	P|P	166;166;187;166;155;120;166;120|23	ENSP00000385740:L166P;ENSP00000216064:L166P;ENSP00000385616:L187P;ENSP00000383992:L166P;ENSP00000395601:L155P;ENSP00000406941:L120P;ENSP00000415588:L166P;ENSP00000408834:L120P|.	ENSP00000216064:L166P|.	L|S	-|-	2|1	0|0	SUN2|SUN2	37476199|37476199	0.307000|0.307000	0.24500|0.24500	0.729000|0.729000	0.30791|0.30791	0.137000|0.137000	0.21094|0.21094	1.454000|1.454000	0.35178|0.35178	2.032000|2.032000	0.59987|0.59987	0.528000|0.528000	0.53228|0.53228	CTC|TCT	.	.	.	none		0.602	SUN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321057.1	XM_039332		G	39146253	A	G	39146253	3	3	161	1	0	0	0	0	1	0	0	0	15404	304	11	3	1712	3	SUN2	22	39146253	Missense_Mutation	SNP	A	TCGA-EV-5901-01A-11D-1589-08	3367124	39146253	12158313	39	9533											
DDX3X	1654	hgsc.bcm.edu	37	chrX	41202004	41202004	+	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	tttgagggaactcttttctgGaggcaacactgggattaatt	10	14	11	6	0	2	1	0	1	2	0	2	4	2	4	0	4	2	1	0	4	3	5			TCGA-EV-5901-01A-11D-1589-08	TCGA-EV-5901-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	846543e9-145b-4332-9043-5817b55e2208	8623db0f-675b-4d34-ba2b-5c12aa3e9b7b	g.chrX:41202004G>A	ENST00000399959.2	+	6	1313	c.458G>A	c.(457-459)gGa>gAa	p.G153E	DDX3X_ENST00000457138.2_Missense_Mutation_p.G137E|DDX3X_ENST00000478993.1_3'UTR|RN7SL15P_ENST00000582825.1_RNA|DDX3X_ENST00000441189.2_Intron|DDX3X_ENST00000542215.1_Missense_Mutation_p.G197E	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	153	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						CTCTTTTCTGGAGGCAACACT	0.363										HNSCC(61;0.18)																											p.G153E		Atlas-SNP	.											.	DDX3X	138	.	0			c.G458A						PASS	.						102	93	96					X																	41202004		2049	4205	6254	SO:0001583	missense	1654	exon6			TTTCTGGAGGCAA	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.458G>A	chrX.hg19:g.41202004G>A	ENSP00000382840:p.Gly153Glu	146.0	0.0	.		145.0	54.0	.	NM_001193416	A8K538|B4E3E8|O15536	Missense_Mutation	SNP	ENST00000399959.2	hg19	CCDS43931.1	.	.	.	.	.	.	.	.	.	.	G	13.34	2.209130	0.39003	.	.	ENSG00000215301	ENST00000399959;ENST00000457138;ENST00000542215	T;T;T	0.42513	2.21;2.18;0.97	5.75	5.75	0.90469	.	0.050157	0.85682	D	0.000000	T	0.38799	0.1054	L	0.45228	1.405	0.80722	D	1	B;B;B;B;B	0.11235	0.004;0.002;0.001;0.004;0.004	B;B;B;B;B	0.10450	0.005;0.005;0.003;0.005;0.005	T	0.15407	-1.0438	10	0.20046	T	0.44	-0.7141	18.9517	0.92643	0.0:0.0:1.0:0.0	.	153;137;153;165;153	B4DLU5;B4E3E8;B5BTY4;Q59GX6;O00571	.;.;.;.;DDX3X_HUMAN	E	153;137;197	ENSP00000382840:G153E;ENSP00000392494:G137E;ENSP00000439799:G197E	ENSP00000382840:G153E	G	+	2	0	DDX3X	41086948	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.723000	0.61965	2.424000	0.82194	0.600000	0.82982	GGA	.	.	.	none		0.363	DDX3X-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056253.1	NM_024005		A	41202004	G	A	41202004	3	1	161	1	0	0	0	0	1	0	0	0	4360	1174	41	2	480	2	DDX3X	23	41202004	Missense_Mutation	SNP	G	TCGA-EV-5901-01A-11D-1589-08		41202004	114068556	40	9534											
AHDC1	27245	hgsc.bcm.edu	37	chr1	27875947	27875947	+	Missense_Mutation	SNP	T	T	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	cactgccactgggctggcctTggctccccggctagggaagg	5	7	15	14	1	0	0	0	0	0	0	1	1	1	1	4	6	1	3	4	6	2	2			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr1:27875947T>G	ENST00000247087.5	-	5	3276	c.2680A>C	c.(2680-2682)Aag>Cag	p.K894Q	AHDC1_ENST00000374011.2_Missense_Mutation_p.K894Q			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	894							DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		GGGCTGGCCTTGGCTCCCCGG	0.716																																					p.K894Q		Atlas-SNP	.											.	AHDC1	98	.	0			c.A2680C						PASS	.						19	23	22					1																	27875947		2196	4287	6483	SO:0001583	missense	27245	exon6			TGGCCTTGGCTCC	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.2680A>C	chr1.hg19:g.27875947T>G	ENSP00000247087:p.Lys894Gln	53.0	0.0	.		55.0	33.0	.	NM_001029882	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Missense_Mutation	SNP	ENST00000247087.5	hg19	CCDS30652.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.943941	0.73672	.	.	ENSG00000126705	ENST00000247087;ENST00000374011	T;T	0.55052	0.54;0.54	5.77	5.77	0.91146	.	0.088674	0.42548	D	0.000697	T	0.57504	0.2058	N	0.14661	0.345	0.46774	D	0.999191	D	0.76494	0.999	D	0.83275	0.996	T	0.64740	-0.6336	10	0.72032	D	0.01	-11.4835	15.0705	0.72034	0.0:0.0:0.0:1.0	.	894	Q5TGY3	AHDC1_HUMAN	Q	894	ENSP00000247087:K894Q;ENSP00000363123:K894Q	ENSP00000247087:K894Q	K	-	1	0	AHDC1	27748534	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.070000	0.76763	2.199000	0.70637	0.533000	0.62120	AAG	.	.	.	none		0.716	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3			G	27875947	T	G	27875947	3	3	162	1	0	0	0	0	1	0	0	0	412	1821	63	5	2135	5	AHDC1	1	27875947	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08		27875947	221374674	1	9535											
RLF	6018	hgsc.bcm.edu	37	chr1	40705390	40705391	+	Frame_Shift_Ins	INS	-	-	T																															tgctctacaggggaactttgINSaaatgtaatcatagttccaa																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr1:40705390_40705391insT	ENST00000372771.4	+	8	5043_5044	c.5016_5017insT	c.(5017-5019)aaafs	p.K1673fs		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	1673					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)			GGGGAACTTTGAAATGTAATCA	0.411																																					p.L1672fs		Atlas-INDEL	.											.	RLF	152	.	0			c.5016_5017insT						PASS	.																																			SO:0001589	frameshift_variant	6018	exon8			.		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	Exception_encountered	chr1.hg19:g.40705390_40705391insT	ENSP00000361857:p.Lys1673fs	130.0	0.0	0		103.0	54.0	0.524272	NM_012421	Q14CQ1|Q9NU60	Frame_Shift_Ins	INS	ENST00000372771.4	hg19	CCDS448.1																																																																																			.	.	.	none		0.411	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421		T	40705391	-	T	40705390	7	5	162	1	0	1	1	0	0	0	0	0	13402	1281	45	0	5046	0	RLF	1	40705390	Frame_Shift_Ins	INS	-	TCGA-EV-5902-01A-11D-1589-08	12829443	40705390	208545231	2	9536											
FLG	2312	hgsc.bcm.edu	37	chr1	152279672	152279672	+	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	gtcctggctaaaactggatcCccagttcctgcttgtcctgg	6	12	10	13	0	0	0	0	0	0	0	4	1	4	1	5	3	2	3	5	3	2	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr1:152279672C>A	ENST00000368799.1	-	3	7725	c.7690G>T	c.(7690-7692)Gga>Tga	p.G2564*	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2564	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)			AAACTGGATCCCCAGTTCCTG	0.582									Ichthyosis																												p.G2564X		Atlas-SNP	.											.	FLG	900	.	0			c.G7690T						PASS	.						187	200	196					1																	152279672		2201	4300	6501	SO:0001587	stop_gained	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGATCCCCAGTT	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.7690G>T	chr1.hg19:g.152279672C>A	ENSP00000357789:p.Gly2564*	424.0	1.0	.		433.0	213.0	.	NM_002016	Q01720|Q5T583|Q9UC71	Nonsense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	46	12.137190	0.99639	.	.	ENSG00000143631	ENST00000368799	.	.	.	3.61	-1.65	0.08291	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	.	7.5003	0.27513	0.0:0.4216:0.4707:0.1077	.	.	.	.	X	2564	.	ENSP00000357789:G2564X	G	-	1	0	FLG	150546296	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	0.888000	0.28268	-0.164000	0.10927	0.306000	0.20318	GGA	.	.	.	none		0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152279672	C	A	152279672	4	1	162	1	0	0	0	0	0	1	0	0	5929	632	22	4	4499	4	FLG	1	152279672	Nonsense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08	111574282	152279672	96970949	3	9537											
MYOC	4653	hgsc.bcm.edu	37	chr1	171605341	171605341	+	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	tttgtctcccaggtttgttcGagttccagattctctgggtt	4	18	10	9	1	2	1	0	0	2	1	6	2	3	1	2	2	0	4	2	2	0	6			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr1:171605341G>C	ENST00000037502.6	-	3	1310	c.1239C>G	c.(1237-1239)ctC>ctG	p.L413L		NM_000261.1	NP_000252.1	Q99972	MYOC_HUMAN	myocilin, trabecular meshwork inducible glucocorticoid response	413	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				bone development (GO:0060348)|clustering of voltage-gated sodium channels (GO:0045162)|ERBB2-ERBB3 signaling pathway (GO:0038133)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neuron projection development (GO:0031175)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|osteoblast differentiation (GO:0001649)|positive regulation of cell migration (GO:0030335)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of MAPK cascade (GO:0043408)|skeletal muscle hypertrophy (GO:0014734)	cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|node of Ranvier (GO:0033268)|proteinaceous extracellular matrix (GO:0005578)	fibronectin binding (GO:0001968)|frizzled binding (GO:0005109)|myosin light chain binding (GO:0032027)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|prostate(1)|urinary_tract(2)	28	all_cancers(6;5.47e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					AGGTTTGTTCGAGTTCCAGAT	0.522																																					p.L413L		Atlas-SNP	.											.	MYOC	69	.	0			c.C1239G						PASS	.						210	193	199					1																	171605341		2203	4300	6503	SO:0001819	synonymous_variant	4653	exon3			TTGTTCGAGTTCC	BC029261	CCDS1297.1	1q23-q24	2008-02-05			ENSG00000034971	ENSG00000034971			7610	protein-coding gene	gene with protein product		601652		GLC1A		9169133, 9005853	Standard	NM_000261		Approved	TIGR, JOAG1	uc001ghu.3	Q99972	OTTHUMG00000034789	ENST00000037502.6:c.1239C>G	chr1.hg19:g.171605341G>C		214.0	0.0	.		155.0	63.0	.	NM_000261	B2RD84|O00620|Q7Z6Q9	Silent	SNP	ENST00000037502.6	hg19	CCDS1297.1																																																																																			.	.	.	none		0.522	MYOC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084178.2	NM_000261		C	171605341	G	C	171605341	2	2	162	1	0	0	0	0	0	0	0	1	10093	1045	37	4		4	MYOC	1	171605341	Silent	SNP	G	TCGA-EV-5902-01A-11D-1589-08	19325669	171605341	77645280	4	9538											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228473855	228473855	+	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	tcggccaccttccgttgccgGatctccccggccaactacga	6	8	9	18	5	1	0	0	0	1	0	4	2	2	1	7	3	3	1	7	3	2	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr1:228473855G>C	ENST00000422127.1	+	34	9125	c.9081G>C	c.(9079-9081)cgG>cgC	p.R3027R	OBSCN_ENST00000284548.11_Silent_p.R3027R|OBSCN_ENST00000570156.2_Silent_p.R3456R|OBSCN_ENST00000366707.4_Silent_p.R146R|OBSCN_ENST00000359599.6_Silent_p.R1874R|OBSCN_ENST00000366709.4_Silent_p.R146R	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3027	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)				TCCGTTGCCGGATCTCCCCGG	0.627																																					p.R3456R		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G10368C						PASS	.						33	43	40					1																	228473855		2117	4218	6335	SO:0001819	synonymous_variant	84033	exon39			TTGCCGGATCTCC	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.9081G>C	chr1.hg19:g.228473855G>C		28.0	0.0	.		19.0	12.0	.	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	hg19	CCDS58065.1																																																																																			.	.	.	none		0.627	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		C	228473855	G	C	228473855	2	2	162	1	0	0	0	0	0	0	0	1	10819	1161	41	4		4	OBSCN	1	228473855	Silent	SNP	G	TCGA-EV-5902-01A-11D-1589-08	56868514	228473855	20776766	5	9539											
BIRC6	57448	hgsc.bcm.edu	37	chr2	32667276	32667276	+	Missense_Mutation	SNP	A	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	ctgttggttagctggagttcAttcaaatggacccggaaggt	9	12	13	7	1	2	0	2	0	0	0	2	3	2	3	1	5	1	4	1	5	3	4			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr2:32667276A>C	ENST00000421745.2	+	18	4222	c.4088A>C	c.(4087-4089)cAt>cCt	p.H1363P		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1363					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)					GCTGGAGTTCATTCAAATGGA	0.383																																					p.H1363P	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.A4088C						PASS	.						62	61	61					2																	32667276		2203	4300	6503	SO:0001583	missense	57448	exon18			GAGTTCATTCAAA	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.4088A>C	chr2.hg19:g.32667276A>C	ENSP00000393596:p.His1363Pro	74.0	0.0	.		69.0	37.0	.	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	A	14.04	2.417748	0.42918	.	.	ENSG00000115760	ENST00000421745	T	0.74209	-0.82	5.4	5.4	0.78164	.	0.220885	0.39083	N	0.001466	T	0.66317	0.2777	L	0.29908	0.895	0.40728	D	0.982722	B	0.22604	0.072	B	0.25291	0.059	T	0.65697	-0.6105	10	0.59425	D	0.04	.	15.4322	0.75108	1.0:0.0:0.0:0.0	.	1363	Q9NR09	BIRC6_HUMAN	P	1363	ENSP00000393596:H1363P	ENSP00000393596:H1363P	H	+	2	0	BIRC6	32520780	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.513000	0.60476	2.039000	0.60335	0.519000	0.50382	CAT	.	.	.	none		0.383	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		C	32667276	A	C	32667276	3	2	162	1	0	0	0	0	1	0	0	0	1438	217	8	5	4158	5	BIRC6	2	32667276	Missense_Mutation	SNP	A	TCGA-EV-5902-01A-11D-1589-08		32667276	210532097	6	9540											
HNRPLL	92906	hgsc.bcm.edu	37	chr2	38791355	38791355	+	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	atgatgtagaaaagcaaagcTtcaatgtatagggattggaa	17	10	11	3	0	1	2	1	1	0	1	1	4	1	4	0	2	2	4	0	2	8	5			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr2:38791355T>A	ENST00000449105.3	-	13	1937	c.1598A>T	c.(1597-1599)aAg>aTg	p.K533M	HNRNPLL_ENST00000409328.1_Missense_Mutation_p.K499M|HNRNPLL_ENST00000378915.3_Missense_Mutation_p.K499M|HNRNPLL_ENST00000608859.1_Missense_Mutation_p.K533M|HNRNPLL_ENST00000409636.1_Missense_Mutation_p.K528M			Q8WVV9	HNRLL_HUMAN	heterogeneous nuclear ribonucleoprotein L-like	533					mRNA processing (GO:0006397)|positive regulation of RNA splicing (GO:0033120)	membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)										AAAGCAAAGCTTCAATGTATA	0.289																																					p.K533M		Atlas-SNP	.											.	HNRPLL	19	.	0			c.A1598T						PASS	.						86	94	91					2																	38791355		2203	4298	6501	SO:0001583	missense	92906	exon13			CAAAGCTTCAATG	BC008217	CCDS46261.1, CCDS1796.2	2p22	2014-02-10		2013-06-12	ENSG00000143889	ENSG00000143889		"RNA binding motif (RRM) containing"	25127	protein-coding gene	gene with protein product		611208		HNRPLL		18669861	Standard	NM_138394		Approved		uc021vgc.1	Q8WVV9	OTTHUMG00000102075	ENST00000449105.3:c.1598A>T	chr2.hg19:g.38791355T>A	ENSP00000390625:p.Lys533Met	164.0	0.0	.		142.0	69.0	.	NM_138394	Q53T80|Q5JB51|Q5JB52|Q659B9|Q8IVH5|Q8IVH6|Q96HR5	Missense_Mutation	SNP	ENST00000449105.3	hg19		.	.	.	.	.	.	.	.	.	.	T	19.35	3.810102	0.70797	.	.	ENSG00000143889	ENST00000449105;ENST00000409636;ENST00000378915;ENST00000409328	.	.	.	5.83	5.83	0.93111	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	T	0.80592	0.4652	M	0.81341	2.54	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.83275	0.994;0.994;0.996	T	0.83330	-0.0013	9	0.87932	D	0	.	16.194	0.82011	0.0:0.0:0.0:1.0	.	528;533;533	C9J9G0;D6W592;Q8WVV9	.;.;HNRLL_HUMAN	M	533;528;499;499	.	ENSP00000368195:K499M	K	-	2	0	HNRPLL	38644859	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.360000	0.79487	2.225000	0.72522	0.460000	0.39030	AAG	.	.	.	none		0.289	HNRNPLL-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000219887.2	NM_138394		A	38791355	T	A	38791355	3	1	162	1	0	0	0	0	1	0	0	0	7284	1609	56	5	34	5	HNRPLL	2	38791355	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08	6124079	38791355	204408018	7	9541											
DHX57	90957	hgsc.bcm.edu	37	chr2	39030017	39030017	+	Frame_Shift_Del	DEL	T	T	-																															atactcgactagtttttatcTtctcgtggtacaacaggtag																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr2:39030017delT	ENST00000295373.6	-	23	3983	c.3857delA	c.(3856-3858)aagfs	p.K1286fs		NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	1286							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)				AGTTTTTATCTTCTCGTGGTA	0.468																																					p.K1286fs	Melanoma(191;1090 2095 4375 23729 47341)	Atlas-INDEL	.											.	DHX57	127	.	0			c.3858delG						PASS	.						165	163	164					2																	39030017		2203	4300	6503	SO:0001589	frameshift_variant	90957	exon23			.	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.3857delA	chr2.hg19:g.39030017delT	ENSP00000295373:p.Lys1286fs	237.0	0.0	0		195.0	83.0	0.425641	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Frame_Shift_Del	DEL	ENST00000295373.6	hg19	CCDS1800.1																																																																																			.	.	.	none		0.468	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646		-	39030017	T	-	39030017	7	5	162	1	0	1	0	1	0	0	0	0	4515	1609	56	0	311	0	DHX57	2	39030017	Frame_Shift_Del	DEL	T	TCGA-EV-5902-01A-11D-1589-08	238662	39030017	204169356	8	9542											
SLC3A1	6519	hgsc.bcm.edu	37	chr2	44508525	44508525	+	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	gaaatgtcttttactcattaGgtttaaaattaatcatcgat	14	17	5	5	1	3	0	2	0	1	0	4	2	3	0	0	1	1	1	0	1	6	6			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr2:44508525G>C	ENST00000260649.6	+	3	686		c.e3-1		SLC3A1_ENST00000409229.3_Splice_Site|SLC3A1_ENST00000409741.1_Splice_Site|SLC3A1_ENST00000410056.3_Splice_Site|SLC3A1_ENST00000409387.1_Splice_Site	NM_000341.3	NP_000332.2	Q07837	SLC31_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 1						amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|basic amino acid transport (GO:0015802)|carbohydrate metabolic process (GO:0005975)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|vacuolar membrane (GO:0005774)	amino acid transmembrane transporter activity (GO:0015171)|basic amino acid transmembrane transporter activity (GO:0015174)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|L-cystine transmembrane transporter activity (GO:0015184)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(3)	26		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			L-Cystine(DB00138)	TTACTCATTAGGTTTAAAATT	0.353																																					.		Atlas-SNP	.											.	SLC3A1	62	.	0			c.611-1G>C						PASS	.						64	63	63					2																	44508525		2203	4300	6503	SO:0001630	splice_region_variant	6519	exon3			TCATTAGGTTTAA		CCDS1819.1	2p16.3	2013-07-19	2013-07-19		ENSG00000138079	ENSG00000138079		"Solute carriers"	11025	protein-coding gene	gene with protein product		104614	"solute carrier family 3 (cystine, dibasic and neutral amino acid transporters, activator of cystine, dibasic and neutral amino acid transport), member 1"			8486766, 9186880	Standard	NM_000341		Approved	CSNU1, D2H, RBAT, ATR1, NBAT	uc002ruc.4	Q07837	OTTHUMG00000128759	ENST00000260649.6:c.611-1G>C	chr2.hg19:g.44508525G>C		90.0	0.0	.		74.0	32.0	.	NM_000341	A8K0S1|O00658|Q15295|Q4J6B4|Q4J6B5|Q4J6B6|Q4J6B7|Q4J6B8|Q4J6B9|Q52M92|Q52M94	Splice_Site	SNP	ENST00000260649.6	hg19	CCDS1819.1	.	.	.	.	.	.	.	.	.	.	G	13.02	2.112058	0.37242	.	.	ENSG00000138079	ENST00000260649;ENST00000409387;ENST00000540334;ENST00000410056;ENST00000409741;ENST00000409229;ENST00000541289	.	.	.	4.19	4.19	0.49359	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.147	0.86768	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC3A1	44362029	1.000000	0.71417	0.999000	0.59377	0.336000	0.28762	9.024000	0.93689	2.323000	0.78572	0.551000	0.68910	.	.	.	.	none		0.353	SLC3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250676.1	NM_000341	Intron	C	44508525	G	C	44508525	5	2	162	1	0	0	0	0	0	0	1	0	14639	1014	35	4	620	4	SLC3A1	2	44508525	Splice_Site	SNP	G	TCGA-EV-5902-01A-11D-1589-08	5478508	44508525	198690848	9	9543											
FSHR	2492	hgsc.bcm.edu	37	chr2	49190328	49190328	+	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	tggatatagcagccacagatGaccacaaaggccaggacatt	15	6	10	10	0	0	2	0	1	0	1	0	4	0	4	3	3	2	1	3	3	3	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr2:49190328G>A	ENST00000406846.2	-	10	1751	c.1632C>T	c.(1630-1632)gtC>gtT	p.V544V	FSHR_ENST00000304421.4_Silent_p.V518V|FSHR_ENST00000541117.1_Silent_p.V280V|FSHR_ENST00000346173.3_Silent_p.V482V	NM_000145.3	NP_000136.2	P23945	FSHR_HUMAN	follicle stimulating hormone receptor	544					female gamete generation (GO:0007292)|female gonad development (GO:0008585)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor signaling pathway (GO:0007186)|gonad development (GO:0008406)|male gonad development (GO:0008584)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	follicle-stimulating hormone receptor activity (GO:0004963)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|liver(1)|lung(45)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	73		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Suramin(DB04786)|Urofollitropin(DB00094)	AGCCACAGATGACCACAAAGG	0.532									Gonadal Dysgenesis, 46 XX																												p.V544V		Atlas-SNP	.											.	FSHR	164	.	0			c.C1632T						PASS	.						141	111	121					2																	49190328		2203	4300	6503	SO:0001819	synonymous_variant	2492	exon10	Familial Cancer Database		ACAGATGACCACA		CCDS1843.1, CCDS1844.1, CCDS1844.2	2p21-p16	2014-09-17			ENSG00000170820	ENSG00000170820		"GPCR / Class A : Gonadotropin and TSH receptors"	3969	protein-coding gene	gene with protein product		136435		ODG1		8230163, 8855829	Standard	NM_000145		Approved	FSHRO, LGR1	uc002rww.3	P23945	OTTHUMG00000129259	ENST00000406846.2:c.1632C>T	chr2.hg19:g.49190328G>A		46.0	0.0	.		38.0	18.0	.	NM_000145	A8K947|G5CBS7|G5E967|J3KQ00|Q05AH0|Q16225|Q4QRJ3|Q4ZFZ2|Q53RW2	Silent	SNP	ENST00000406846.2	hg19	CCDS1843.1																																																																																			.	.	.	none		0.532	FSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251367.2			A	49190328	G	A	49190328	2	1	162	1	0	0	0	0	0	0	0	1	6080	1277	45	2		2	FSHR	2	49190328	Silent	SNP	G	TCGA-EV-5902-01A-11D-1589-08	4681803	49190328	194009045	10	9544											
MRPS5	64969	hgsc.bcm.edu	37	chr2	95753148	95753148	+	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	accacacagagcgcttcattCcctgtgcagtcttcacatct	9	11	6	15	1	4	1	2	0	2	1	5	1	5	1	2	0	2	2	2	0	0	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr2:95753148C>G	ENST00000272418.2	-	12	1455	c.1247G>C	c.(1246-1248)gGa>gCa	p.G416A		NM_031902.3	NP_114108.1	P82675	RT05_HUMAN	mitochondrial ribosomal protein S5	416					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20						GCGCTTCATTCCCTGTGCAGT	0.572																																					p.G416A		Atlas-SNP	.											.	MRPS5	52	.	0			c.G1247C						PASS	.						103	96	99					2																	95753148		2203	4300	6503	SO:0001583	missense	64969	exon12			TTCATTCCCTGTG	AB049940	CCDS2010.1	2p11.2-q11.2	2012-09-13			ENSG00000144029	ENSG00000144029		"Mitochondrial ribosomal proteins / small subunits"	14498	protein-coding gene	gene with protein product	"mitochondrial 28S ribosomal protein S5"	611972					Standard	NM_031902		Approved	MRP-S5, S5mt	uc002sub.3	P82675	OTTHUMG00000130394	ENST00000272418.2:c.1247G>C	chr2.hg19:g.95753148C>G	ENSP00000272418:p.Gly416Ala	100.0	0.0	.		84.0	41.0	.	NM_031902	Q4ZFY5|Q96LJ6|Q9BWI4|Q9BYC4	Missense_Mutation	SNP	ENST00000272418.2	hg19	CCDS2010.1	.	.	.	.	.	.	.	.	.	.	C	17.16	3.318910	0.60524	.	.	ENSG00000144029	ENST00000272418	.	.	.	5.98	5.1	0.69264	.	0.052056	0.85682	D	0.000000	T	0.75781	0.3896	M	0.63843	1.955	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.78175	-0.2306	9	0.72032	D	0.01	-16.5572	13.0098	0.58725	0.0:0.9224:0.0:0.0776	.	416	P82675	RT05_HUMAN	A	416	.	ENSP00000272418:G416A	G	-	2	0	MRPS5	95116875	1.000000	0.71417	0.990000	0.47175	0.070000	0.16714	6.883000	0.75595	1.560000	0.49568	0.650000	0.86243	GGA	.	.	.	none		0.572	MRPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252772.1	NM_031902		G	95753148	C	G	95753148	3	3	162	1	0	0	0	0	1	0	0	0	9853	855	30	4	49	4	MRPS5	2	95753148	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08	46562820	95753148	147446225	11	9545											
IL1RL2	8808	hgsc.bcm.edu	37	chr2	102836361	102836361	+	Missense_Mutation	SNP	A	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	aacccatgtctcttttcgggAacataatttgtacacagtaa	13	13	6	9	1	1	0	0	0	1	0	3	1	1	1	1	1	3	2	1	1	5	6			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr2:102836361A>C	ENST00000264257.2	+	8	1001	c.875A>C	c.(874-876)gAa>gCa	p.E292A	IL1RL2_ENST00000441515.2_Missense_Mutation_p.E174A|IL1RL2_ENST00000481806.1_3'UTR|IL1RL2_ENST00000539491.1_Missense_Mutation_p.E292A	NM_003854.2	NP_003845.2	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2	292	Ig-like C2-type 3.				cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of T cell differentiation (GO:0045582)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)			breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|liver(2)|lung(8)|ovary(2)|prostate(1)	26						TCTTTTCGGGAACATAATTTG	0.358																																					p.E292A		Atlas-SNP	.											.	IL1RL2	118	.	0			c.A875C						PASS	.						103	98	100					2																	102836361		2203	4300	6503	SO:0001583	missense	8808	exon8			TTCGGGAACATAA	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.875A>C	chr2.hg19:g.102836361A>C	ENSP00000264257:p.Glu292Ala	93.0	0.0	.		98.0	40.0	.	NM_003854	A4FU63|Q13525|Q45H74|Q53TU8|Q587I8	Missense_Mutation	SNP	ENST00000264257.2	hg19	CCDS2056.1	.	.	.	.	.	.	.	.	.	.	A	5.529	0.282573	0.10458	.	.	ENSG00000115598	ENST00000264257;ENST00000441515;ENST00000539491	T;T;T	0.13901	2.55;2.55;2.55	5.09	2.7	0.31948	.	1.166780	0.05889	N	0.627921	T	0.11495	0.0280	L	0.36672	1.1	0.09310	N	1	B;B	0.25312	0.057;0.123	B;B	0.22753	0.028;0.041	T	0.41342	-0.9514	10	0.17369	T	0.5	.	6.8812	0.24174	0.8123:0.0:0.1877:0.0	.	174;292	A4FU63;Q9HB29	.;ILRL2_HUMAN	A	292;174;292	ENSP00000264257:E292A;ENSP00000413348:E174A;ENSP00000442184:E292A	ENSP00000264257:E292A	E	+	2	0	IL1RL2	102202793	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	0.965000	0.29319	0.357000	0.24183	-0.256000	0.11100	GAA	.	.	.	none		0.358	IL1RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253290.1	NM_003854		C	102836361	A	C	102836361	3	2	162	1	0	0	0	0	1	0	0	0	7671	246	9	5	901	5	IL1RL2	2	102836361	Missense_Mutation	SNP	A	TCGA-EV-5902-01A-11D-1589-08	7083213	102836361	140363012	12	9546											
XIRP2	129446	hgsc.bcm.edu	37	chr2	168115244	168115247	+	Frame_Shift_Del	DEL	TTTC	TTTC	-																															agaagacatctattttagaaTttcttgatctattacccttg																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	TTTC	TTTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr2:168115244_168115247delTTTC	ENST00000409728.1	+	11	2376_2379	c.2287_2290delTTTC	c.(2287-2292)tttcttfs	p.FL763fs	XIRP2_ENST00000409043.1_Frame_Shift_Del_p.FL730fs|XIRP2_ENST00000409605.1_Frame_Shift_Del_p.FL508fs|XIRP2_ENST00000409273.1_3'UTR|XIRP2_ENST00000420519.1_Frame_Shift_Del_p.FL763fs|XIRP2_ENST00000409195.1_3'UTR|XIRP2_ENST00000295237.9_3'UTR|XIRP2_ENST00000409756.2_Frame_Shift_Del_p.FL730fs	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1281					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						TATTTTAGAATTTCTTGATCTATT	0.299																																					p.762_763del		Atlas-INDEL	.											.	XIRP2	914	.	0			c.2286_2289del						PASS	.																																			SO:0001589	frameshift_variant	129446	exon11			.	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.2287_2290delTTTC	chr2.hg19:g.168115244_168115247delTTTC	ENSP00000386619:p.Phe763fs	110.0	0.0	0		92.0	51.0	0.554348	NM_001199143	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Frame_Shift_Del	DEL	ENST00000409728.1	hg19	CCDS56143.1																																																																																			.	.	.	none		0.299	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381		-	168115247	TTTC	-	168115244	7	5	162	1	0	1	0	1	0	0	0	0	17442	1493	52	0	11605	0	XIRP2	2	168115244	Frame_Shift_Del	DEL	TTTC	TCGA-EV-5902-01A-11D-1589-08	65278883	168115244	75084129	13	9547											
CASP10	843	hgsc.bcm.edu	37	chr2	202073930	202073931	+	Frame_Shift_Del	DEL	TG	TG	-																															acggggactgcttcgtgttcTgtattctgacccatgggaga																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr2:202073930_202073931delTG	ENST00000272879.5	+	9	1244_1245	c.1060_1061delTG	c.(1060-1062)tgtfs	p.C354fs	CASP10_ENST00000313728.7_Frame_Shift_Del_p.C287fs|CASP10_ENST00000448480.1_Frame_Shift_Del_p.C311fs|CASP10_ENST00000360132.3_3'UTR|CASP10_ENST00000492363.1_3'UTR|CASP10_ENST00000346817.5_Frame_Shift_Del_p.C311fs|CASP10_ENST00000286186.6_Frame_Shift_Del_p.C354fs	NM_032974.4	NP_116756.2	Q92851	CASPA_HUMAN	caspase 10, apoptosis-related cysteine peptidase	354					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|innate immune response (GO:0045087)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of apoptotic process (GO:0042981)	CD95 death-inducing signaling complex (GO:0031265)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097199)|death effector domain binding (GO:0035877)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	27						CTTCGTGTTCTGTATTCTGACC	0.515																																					p.353_354del		Atlas-INDEL	.											.	CASP10	95	.	0			c.1059_1060del						PASS	.																																			SO:0001589	frameshift_variant	843	exon9			.	U60519	CCDS2338.1, CCDS2339.1, CCDS2340.1, CCDS56159.1, CCDS56160.1	2q33-q34	2014-09-17	2005-08-17		ENSG00000003400	ENSG00000003400	3.4.22.63	"Caspases"	1500	protein-coding gene	gene with protein product		601762	"caspase 10, apoptosis-related cysteine protease"			8755496	Standard	NM_032974		Approved	MCH4	uc002uxj.1	Q92851	OTTHUMG00000132818	ENST00000272879.5:c.1060_1061delTG	chr2.hg19:g.202073930_202073931delTG	ENSP00000272879:p.Cys354fs	218.0	0.0	0		186.0	90.0	0.483871	NM_032977	Q68HC0|Q6KF62|Q6KF63|Q8IUP5|Q8WYQ8|Q99845|Q9Y2U6|Q9Y2U7	Frame_Shift_Del	DEL	ENST00000272879.5	hg19	CCDS2338.1																																																																																			.	.	.	none		0.515	CASP10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256273.1	NM_032977		-	202073931	TG	-	202073930	7	5	162	1	0	1	0	1	0	0	0	0	2671	1580	55	0	1090	0	CASP10	2	202073930	Frame_Shift_Del	DEL	TG	TCGA-EV-5902-01A-11D-1589-08	33958686	202073930	41125443	14	9548											
WNT10A	80326	hgsc.bcm.edu	37	chr2	219754716	219754716	+	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	ttaaccacaggtttccgagaGagcgcttttgcctacgccat	9	11	9	12	3	0	1	0	0	0	1	1	3	1	1	4	1	4	2	4	1	2	5			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr2:219754716G>C	ENST00000258411.3	+	3	1020	c.387G>C	c.(385-387)gaG>gaC	p.E129D	WNT10A_ENST00000483911.1_3'UTR	NM_025216.2	NP_079492.2	Q9GZT5	WN10A_HUMAN	wingless-type MMTV integration site family, member 10A	129					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)		GTTTCCGAGAGAGCGCTTTTG	0.582																																					p.E129D		Atlas-SNP	.											WNT10A,NS,carcinoma,0,1	WNT10A	35	.	0			c.G387C						PASS	.						96	86	90					2																	219754716		2203	4300	6503	SO:0001583	missense	80326	exon3			CCGAGAGAGCGCT	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.387G>C	chr2.hg19:g.219754716G>C	ENSP00000258411:p.Glu129Asp	115.0	0.0	.		119.0	44.0	.	NM_025216	Q53S44|Q96TA7|Q9H7S8	Missense_Mutation	SNP	ENST00000258411.3	hg19	CCDS2426.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.993868	0.74703	.	.	ENSG00000135925	ENST00000258411	D	0.84944	-1.92	4.7	3.82	0.43975	.	0.000000	0.85682	D	0.000000	D	0.94627	0.8268	H	0.97564	4.03	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.95446	0.8530	10	0.72032	D	0.01	.	12.015	0.53309	0.085:0.0:0.915:0.0	.	129	Q9GZT5	WN10A_HUMAN	D	129	ENSP00000258411:E129D	ENSP00000258411:E129D	E	+	3	2	WNT10A	219462960	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.220000	0.42908	1.338000	0.45544	0.655000	0.94253	GAG	.	.	.	none		0.582	WNT10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256730.2	NM_025216		C	219754716	G	C	219754716	3	2	162	1	0	0	0	0	1	0	0	0	17394	933	33	4	397	4	WNT10A	2	219754716	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08	17680786	219754716	23444657	15	9549											
NR1D2	9975	hgsc.bcm.edu	37	chr3	24003534	24003534	+	Missense_Mutation	SNP	T	T	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	aattgaaatgcaaagtgcaaTgaagaccatgatgaacagcc	18	7	9	7	0	0	5	0	4	0	1	0	5	0	5	2	0	4	2	2	0	6	1			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr3:24003534T>G	ENST00000312521.4	+	5	903	c.584T>G	c.(583-585)aTg>aGg	p.M195R	NR1D2_ENST00000492552.1_3'UTR	NM_001145425.1|NM_005126.4	NP_001138897.1|NP_005117	Q14995	NR1D2_HUMAN	nuclear receptor subfamily 1, group D, member 2	195	Hinge.				gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|lipid homeostasis (GO:0055088)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of inflammatory response (GO:0050727)|regulation of lipid metabolic process (GO:0019216)|regulation of skeletal muscle cell differentiation (GO:2001014)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	22						CAAAGTGCAATGAAGACCATG	0.413																																					p.M195R		Atlas-SNP	.											.	NR1D2	52	.	0			c.T584G						PASS	.						72	63	66					3																	24003534		2203	4300	6503	SO:0001583	missense	9975	exon5			GTGCAATGAAGAC	BC045613	CCDS33718.1	3p24.1	2013-01-16			ENSG00000174738	ENSG00000174738		"Nuclear hormone receptors"	7963	protein-coding gene	gene with protein product		602304				7997240, 10198169	Standard	NM_005126		Approved	BD73, RVR, EAR-1r, HZF2, Hs.37288	uc003ccs.2	Q14995	OTTHUMG00000155659	ENST00000312521.4:c.584T>G	chr3.hg19:g.24003534T>G	ENSP00000310006:p.Met195Arg	70.0	0.0	.		60.0	26.0	.	NM_005126	B2R8Q3|O00402|Q86XD4	Missense_Mutation	SNP	ENST00000312521.4	hg19	CCDS33718.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.347423	0.82022	.	.	ENSG00000174738	ENST00000312521;ENST00000396676	D	0.92647	-3.08	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	D	0.95411	0.8510	M	0.67397	2.05	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.95294	0.8397	10	0.52906	T	0.07	.	16.4614	0.84056	0.0:0.0:0.0:1.0	.	195	Q14995	NR1D2_HUMAN	R	195	ENSP00000310006:M195R	ENSP00000310006:M195R	M	+	2	0	NR1D2	23978538	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.635000	0.83286	2.285000	0.76669	0.533000	0.62120	ATG	.	.	.	none		0.413	NR1D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341017.3			G	24003534	T	G	24003534	3	3	162	1	0	0	0	0	1	0	0	0	10623	1464	51	5	602	5	NR1D2	3	24003534	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08		24003534	174018896	16	9550											
TGM4	7047	hgsc.bcm.edu	37	chr3	44935102	44935102	+	Missense_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	catgcctgatgaggacgagcGcaaagagtacatcctcaatg	13	7	11	10	2	1	3	1	2	0	1	2	5	2	4	2	1	3	2	2	1	3	1	rs147559877		TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr3:44935102G>A	ENST00000296125.4	+	5	532	c.464G>A	c.(463-465)cGc>cAc	p.R155H		NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	155					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)	GAGGACGAGCGCAAAGAGTAC	0.507													G|||	1	0.000199681	8e-04	0	5008	,	,		15581	0		0	False		,,,				2504	0				p.R155H		Atlas-SNP	.											.	TGM4	82	.	0			c.G464A						PASS	.	G	HIS/ARG	2,4404	4.2+/-10.8	0,2,2201	129	115	120		464	-1.3	0	3	dbSNP_134	120	0,8600		0,0,4300	no	missense	TGM4	NM_003241.3	29	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging	155/685	44935102	2,13004	2203	4300	6503	SO:0001583	missense	7047	exon5			ACGAGCGCAAAGA	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.464G>A	chr3.hg19:g.44935102G>A	ENSP00000296125:p.Arg155His	90.0	0.0	.		82.0	36.0	.	NM_003241	Q16707|Q96QN4	Missense_Mutation	SNP	ENST00000296125.4	hg19	CCDS2723.1	.	.	.	.	.	.	.	.	.	.	G	14.17	2.455059	0.43634	4.54E-4	0.0	ENSG00000163810	ENST00000296125	D	0.92099	-2.97	2.32	-1.33	0.09172	.	0.000000	0.40818	U	0.001008	D	0.95056	0.8399	M	0.90870	3.155	0.09310	N	0.999991	D	0.89917	1.0	D	0.79784	0.993	D	0.88191	0.2877	10	0.66056	D	0.02	.	4.1154	0.10079	0.3177:0.0:0.5237:0.1586	.	155	P49221	TGM4_HUMAN	H	155	ENSP00000296125:R155H	ENSP00000296125:R155H	R	+	2	0	TGM4	44910106	0.694000	0.27738	0.000000	0.03702	0.008000	0.06430	1.522000	0.35921	-0.584000	0.05913	-0.518000	0.04402	CGC	.	G|1.000;A|0.000	0.000	weak		0.507	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241		A	44935102	G	A	44935102	3	1	162	1	0	0	0	0	1	0	0	0	15844	1087	38	1	482	1	TGM4	3	44935102	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08	20931568	44935102	153087328	17	9551											
LZTFL1	54585	hgsc.bcm.edu	37	chr3	45874547	45874547	+	Missense_Mutation	SNP	T	T	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	aaataataatattaccttgtTtaggagttctgctgttccac	12	16	6	7	0	1	0	0	0	1	0	2	1	2	1	2	1	2	4	2	1	6	9			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr3:45874547T>G	ENST00000296135.6	-	5	625	c.451A>C	c.(451-453)Aac>Cac	p.N151H	LZTFL1_ENST00000539217.1_Missense_Mutation_p.N147H|LZTFL1_ENST00000536047.1_Missense_Mutation_p.N134H|LZTFL1_ENST00000490463.1_5'UTR	NM_001276378.1|NM_020347.2	NP_001263307.1|NP_065080.1	Q9NQ48	LZTL1_HUMAN	leucine zipper transcription factor-like 1	151	Interaction with BSS9.				establishment of protein localization to organelle (GO:0072594)	BBSome (GO:0034464)|cytoplasm (GO:0005737)	identical protein binding (GO:0042802)			endometrium(1)|large_intestine(2)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	8				BRCA - Breast invasive adenocarcinoma(193;0.00867)|KIRC - Kidney renal clear cell carcinoma(197;0.0177)|Kidney(197;0.0208)		ATTACCTTGTTTAGGAGTTCT	0.393																																					p.N151H		Atlas-SNP	.											.	LZTFL1	37	.	0			c.A451C						PASS	.						100	99	99					3																	45874547		2203	4300	6503	SO:0001583	missense	54585	exon5			CCTTGTTTAGGAG	AJ297351	CCDS2731.1, CCDS63608.1, CCDS63609.1	3p21.3	2014-01-28			ENSG00000163818	ENSG00000163818			6741	protein-coding gene	gene with protein product		606568				11352561, 22510444	Standard	NM_020347		Approved	BBS17	uc003cox.2	Q9NQ48	OTTHUMG00000133452	ENST00000296135.6:c.451A>C	chr3.hg19:g.45874547T>G	ENSP00000296135:p.Asn151His	134.0	0.0	.		98.0	35.0	.	NM_020347	B3KSI9|B4E0K7|Q8TC61|Q9NQ56	Missense_Mutation	SNP	ENST00000296135.6	hg19	CCDS2731.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.78|16.78	3.217504|3.217504	0.58560|0.58560	.|.	.|.	ENSG00000163818|ENSG00000163818	ENST00000440576|ENST00000296135;ENST00000536047;ENST00000539217	.|T;T;T	.|0.24151	.|1.87;1.87;1.87	5.49|5.49	5.49|5.49	0.81192|0.81192	.|.	.|0.131960	.|0.64402	.|D	.|0.000002	T|T	0.28333|0.28333	0.0700|0.0700	L|L	0.58302|0.58302	1.8|1.8	0.54753|0.54753	D|D	0.999989|0.999989	.|B	.|0.12013	.|0.005	.|B	.|0.16289	.|0.015	T|T	0.03166|0.03166	-1.1065|-1.1065	5|10	.|0.38643	.|T	.|0.18	-17.4947|-17.4947	14.7592|14.7592	0.69593|0.69593	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|151	.|Q9NQ48	.|LZTL1_HUMAN	T|H	108|151;134;147	.|ENSP00000296135:N151H;ENSP00000439522:N134H;ENSP00000441784:N147H	.|ENSP00000296135:N151H	K|N	-|-	2|1	0|0	LZTFL1|LZTFL1	45849551|45849551	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.986000|0.986000	0.74619|0.74619	7.333000|7.333000	0.79214|0.79214	2.074000|2.074000	0.62210|0.62210	0.528000|0.528000	0.53228|0.53228	AAA|AAC	.	.	.	none		0.393	LZTFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257326.3	NM_020347		G	45874547	T	G	45874547	3	3	162	1	0	0	0	0	1	0	0	0	9143	1841	64	5	472	5	LZTFL1	3	45874547	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08	939445	45874547	152147883	18	9552											
USP4	7375	hgsc.bcm.edu	37	chr3	49362339	49362339	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctcctacctgaccctggtaTagcccagcatcctggacagt	8	9	8	16	0	0	1	0	1	0	0	2	2	2	2	6	2	3	2	6	2	3	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr3:49362339T>C	ENST00000265560.4	-	5	667	c.621A>G	c.(619-621)ctA>ctG	p.L207L	USP4_ENST00000351842.4_Silent_p.L207L|USP4_ENST00000416417.1_Silent_p.L207L|USP4_ENST00000415188.1_Silent_p.L207L	NM_003363.3	NP_003354.2	Q13107	UBP4_HUMAN	ubiquitin specific peptidase 4 (proto-oncogene)	207	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)		GACCCTGGTATAGCCCAGCAT	0.547																																					p.L207L		Atlas-SNP	.											.	USP4	72	.	0			c.A621G						PASS	.						154	156	155					3																	49362339		2203	4300	6503	SO:0001819	synonymous_variant	7375	exon5			CTGGTATAGCCCA	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.621A>G	chr3.hg19:g.49362339T>C		276.0	0.0	.		204.0	99.0	.	NM_199443	A8K6Y0|C9IY91|O43452|O43453|Q08AK8	Silent	SNP	ENST00000265560.4	hg19	CCDS2793.1																																																																																			.	.	.	none		0.547	USP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346069.1	NM_199443		C	49362339	T	C	49362339	2	2	162	1	0	0	0	0	0	0	0	1	17083	1393	49	3		3	USP4	3	49362339	Silent	SNP	T	TCGA-EV-5902-01A-11D-1589-08	3487792	49362339	148660091	19	9553											
CNTN3	5067	hgsc.bcm.edu	37	chr3	74350871	74350871	+	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	taggatataactgggctatgGttgtctttaccttctttcca	8	17	8	8	0	2	0	0	0	2	0	3	1	3	1	2	3	2	2	2	3	5	9			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr3:74350871G>T	ENST00000263665.6	-	14	1899	c.1872C>A	c.(1870-1872)aaC>aaA	p.N624K		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	624	Fibronectin type-III 1. {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)		CTGGGCTATGGTTGTCTTTAC	0.468																																					p.N624K		Atlas-SNP	.											.	CNTN3	174	.	0			c.C1872A						PASS	.						309	273	285					3																	74350871		2203	4300	6503	SO:0001583	missense	5067	exon14			GCTATGGTTGTCT	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.1872C>A	chr3.hg19:g.74350871G>T	ENSP00000263665:p.Asn624Lys	125.0	0.0	.		103.0	48.0	.	NM_020872	B9EK50|Q9H039	Missense_Mutation	SNP	ENST00000263665.6	hg19	CCDS33790.1	.	.	.	.	.	.	.	.	.	.	G	18.24	3.579172	0.65878	.	.	ENSG00000113805	ENST00000263665	T	0.56611	0.45	5.98	2.16	0.27623	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.091203	0.85682	D	0.000000	T	0.71576	0.3356	M	0.89030	3	0.38345	D	0.944171	P	0.46020	0.871	P	0.61132	0.884	T	0.76044	-0.3103	10	0.87932	D	0	.	10.2822	0.43545	0.4578:0.0:0.5422:0.0	.	624	Q9P232	CNTN3_HUMAN	K	624	ENSP00000263665:N624K	ENSP00000263665:N624K	N	-	3	2	CNTN3	74433561	0.972000	0.33761	0.988000	0.46212	0.988000	0.76386	0.098000	0.15189	0.415000	0.25817	0.591000	0.81541	AAC	.	.	.	none		0.468	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872		T	74350871	G	T	74350871	3	4	162	1	0	0	0	0	1	0	0	0	3644	1252	44	4	1250	4	CNTN3	3	74350871	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08	24988532	74350871	123671559	20	9554											
PIK3CB	5291	hgsc.bcm.edu	37	chr3	138456588	138456588	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgatcaccaaaaacatattcTactctcccgctgacttgcaa	13	11	4	13	1	3	2	1	2	2	0	4	2	3	2	2	0	3	2	2	0	5	4			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr3:138456588T>C	ENST00000477593.1	-	5	835	c.762A>G	c.(760-762)gtA>gtG	p.V254V	PIK3CB_ENST00000289153.2_Silent_p.V254V			P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	254	PI3K-RBD. {ECO:0000255|PROSITE- ProRule:PRU00879}.				activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	AAACATATTCTACTCTCCCGC	0.318																																					p.V254V		Atlas-SNP	.											.	PIK3CB	103	.	0			c.A762G						PASS	.						96	88	91					3																	138456588		2203	4300	6503	SO:0001819	synonymous_variant	5291	exon4			ATATTCTACTCTC		CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	"phosphoinositide-3-kinase, catalytic, beta polypeptide"	PIK3C1		8246984	Standard	NM_006219		Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.762A>G	chr3.hg19:g.138456588T>C		118.0	0.0	.		108.0	56.0	.	NM_006219	D3DNF0|Q24JU2	Silent	SNP	ENST00000477593.1	hg19	CCDS3104.1	.	.	.	.	.	.	.	.	.	.	T	0.792	-0.758451	0.03019	.	.	ENSG00000051382	ENST00000462294	.	.	.	5.82	-3.54	0.04653	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-6.8436	11.0692	0.47993	0.1175:0.6147:0.0:0.2678	.	.	.	.	W	122	.	.	X	-	2	0	PIK3CB	139939278	0.887000	0.30362	0.907000	0.35723	0.002000	0.02628	-0.157000	0.10085	-0.658000	0.05366	-1.216000	0.01612	TAG	.	.	.	none		0.318	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358019.1			C	138456588	T	C	138456588	2	2	162	1	0	0	0	0	0	0	0	1	11921	1509	53	3		3	PIK3CB	3	138456588	Silent	SNP	T	TCGA-EV-5902-01A-11D-1589-08	64105717	138456588	59565842	21	9555											
RNF168	165918	hgsc.bcm.edu	37	chr3	196214405	196214405	+	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	ctctgtatgtattcttcactGgctttgttttcttcttcctc	3	22	5	11	0	5	0	1	0	4	0	7	0	6	0	1	1	0	4	1	1	2	9			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr3:196214405G>T	ENST00000318037.3	-	3	1017	c.423C>A	c.(421-423)gcC>gcA	p.A141A		NM_152617.3	NP_689830.2	Q8IYW5	RN168_HUMAN	ring finger protein 168, E3 ubiquitin protein ligase	141	Glu-rich.				cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone H2A K63-linked ubiquitination (GO:0070535)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K13 ubiquitination (GO:0036351)|histone H2A-K15 ubiquitination (GO:0036352)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|negative regulation of translational elongation (GO:0045900)|positive regulation of DNA repair (GO:0045739)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)	20	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)		ATTCTTCACTGGCTTTGTTTT	0.443																																					p.A141A		Atlas-SNP	.											.	RNF168	49	.	0			c.C423A						PASS	.						223	208	213					3																	196214405		2203	4300	6503	SO:0001819	synonymous_variant	165918	exon3			TTCACTGGCTTTG	AK054732	CCDS3317.1	3q29	2014-09-17	2012-02-23		ENSG00000163961	ENSG00000163961		"RING-type (C3HC4) zinc fingers"	26661	protein-coding gene	gene with protein product		612688	"ring finger protein 168"			12477932	Standard	NM_152617		Approved	FLJ35794	uc003fwq.3	Q8IYW5	OTTHUMG00000155582	ENST00000318037.3:c.423C>A	chr3.hg19:g.196214405G>T		231.0	0.0	.		215.0	105.0	.	NM_152617	Q8NA67|Q96NS4	Silent	SNP	ENST00000318037.3	hg19	CCDS3317.1																																																																																			.	.	.	none		0.443	RNF168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340778.1	NM_152617		T	196214405	G	T	196214405	2	4	162	1	0	0	0	0	0	0	0	1	13472	1335	47	4		4	RNF168	3	196214405	Silent	SNP	G	TCGA-EV-5902-01A-11D-1589-08	57757817	196214405	1808025	22	9556											
TLR6	10333	hgsc.bcm.edu	37	chr4	38830116	38830116	+	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	aatgttcatctcagaaaacaCggtgtacaaagctgtctgtg	13	11	9	8	1	3	1	2	0	2	1	4	1	3	1	0	1	3	3	0	1	5	2	rs3796508	byFrequency	TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr4:38830116C>A	ENST00000381950.1	-	1	1044	c.979G>T	c.(979-981)Gtg>Ttg	p.V327L	TLR6_ENST00000436693.2_Missense_Mutation_p.V327L			Q9Y2C9	TLR6_HUMAN	toll-like receptor 6	327			V -> M (in dbSNP:rs3796508). {ECO:0000269|PubMed:21618349, ECO:0000269|Ref.3}.		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						TCAGAAAACACGGTGTACAAA	0.343																																					p.V327L		Atlas-SNP	.											.	TLR6	67	.	0			c.G979T						PASS	.						68	72	71					4																	38830116		2203	4300	6503	SO:0001583	missense	10333	exon2			AAAACACGGTGTA		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.979G>T	chr4.hg19:g.38830116C>A	ENSP00000371376:p.Val327Leu	80.0	0.0	.		72.0	33.0	.	NM_006068	B3Y640|B6CH35|B6RFS4|B6RFS5|Q2NKL3	Missense_Mutation	SNP	ENST00000381950.1	hg19	CCDS3446.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.699200	0.00725	.	.	ENSG00000174130	ENST00000436693;ENST00000381950;ENST00000508542	T;T	0.07216	3.21;3.21	5.08	0.624	0.17659	.	0.875863	0.09937	N	0.736454	T	0.03959	0.0111	N	0.22421	0.69	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.46400	-0.9194	10	0.07482	T	0.82	.	0.9789	0.01432	0.1458:0.2038:0.2868:0.3636	.	327	Q9Y2C9	TLR6_HUMAN	L	327	ENSP00000389600:V327L;ENSP00000371376:V327L	ENSP00000371376:V327L	V	-	1	0	TLR6	38506511	0.000000	0.05858	0.152000	0.22495	0.301000	0.27625	-0.736000	0.04882	0.168000	0.19655	0.491000	0.48974	GTG	.	C|0.981;T|0.019	.	alt		0.343	TLR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250431.1			A	38830116	C	A	38830116	3	1	162	1	0	0	0	0	1	0	0	0	15967	536	19	4	1415	4	TLR6	4	38830116	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08		38830116	152324160	23	9557											
YTHDC1	91746	hgsc.bcm.edu	37	chr4	69203291	69203291	+	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	ctgcaataatatttactaccTcagaaccatctggcgtagga	13	11	7	10	1	2	1	1	0	1	1	2	2	2	2	2	2	4	2	2	2	7	6			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr4:69203291T>G	ENST00000344157.4	-	3	793	c.458A>C	c.(457-459)gAg>gCg	p.E153A	YTHDC1_ENST00000579690.1_Splice_Site_p.E153A|YTHDC1_ENST00000355665.3_Splice_Site_p.E153A	NM_001031732.2	NP_001026902.1	Q96MU7	YTDC1_HUMAN	YTH domain containing 1	153					mRNA splice site selection (GO:0006376)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	30						ATTTACTACCTCAGAACCATC	0.403																																					p.E153A		Atlas-SNP	.											.	YTHDC1	81	.	0			c.A458C						PASS	.						48	47	47					4																	69203291		2200	4300	6500	SO:0001630	splice_region_variant	91746	exon3			ACTACCTCAGAAC	AK098515	CCDS3522.2, CCDS33992.1	4q13.3	2009-01-14			ENSG00000083896	ENSG00000083896			30626	protein-coding gene	gene with protein product						12368078, 10564280	Standard	XM_005265706		Approved	YT521, KIAA1966, YT521-B	uc003hdx.3	Q96MU7	OTTHUMG00000129306	ENST00000344157.4:c.459+1A>C	chr4.hg19:g.69203291T>G		78.0	0.0	.		75.0	38.0	.	NM_001031732	Q4W5Q3|Q7Z622|Q8TF35	Missense_Mutation	SNP	ENST00000344157.4	hg19	CCDS33992.1	.	.	.	.	.	.	.	.	.	.	T	13.61	2.287484	0.40494	.	.	ENSG00000083896	ENST00000344157;ENST00000355665	T;T	0.30448	1.68;1.53	5.29	5.29	0.74685	.	0.369189	0.29396	N	0.012273	T	0.24084	0.0583	L	0.27053	0.805	0.52099	D	0.999947	B;B	0.32573	0.376;0.0	B;B	0.34722	0.188;0.001	T	0.06826	-1.0805	10	0.49607	T	0.09	.	11.8336	0.52309	0.0:0.0:0.1463:0.8537	.	153;153	Q96MU7-2;Q96MU7	.;YTDC1_HUMAN	A	153	ENSP00000339245:E153A;ENSP00000347888:E153A	ENSP00000339245:E153A	E	-	2	0	YTHDC1	68885886	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.195000	0.58400	1.981000	0.57761	0.477000	0.44152	GAG	.	.	.	none		0.403	YTHDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251437.1	NM_133370	Missense_Mutation	G	69203291	T	G	69203291	5	3	162	1	0	0	0	0	0	0	1	0	17508	1565	54	5	1785	5	YTHDC1	4	69203291	Splice_Site	SNP	T	TCGA-EV-5902-01A-11D-1589-08	30373175	69203291	121950985	24	9558											
ENAM	10117	hgsc.bcm.edu	37	chr4	71510231	71510231	+	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	cacctgatgaaggctccaatCcagaaggcatccaaagtcaa	15	6	8	12	0	1	3	1	2	0	1	4	3	4	3	4	2	0	2	4	2	5	0			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr4:71510231C>T	ENST00000396073.3	+	9	3369	c.3088C>T	c.(3088-3090)Cca>Tca	p.P1030S	ENAM_ENST00000472903.1_Intron	NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	1030					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)			AGGCTCCAATCCAGAAGGCAT	0.433																																					p.P1030S		Atlas-SNP	.											.	ENAM	140	.	0			c.C3088T						PASS	.						119	104	109					4																	71510231		2203	4300	6503	SO:0001583	missense	10117	exon9			TCCAATCCAGAAG	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.3088C>T	chr4.hg19:g.71510231C>T	ENSP00000379383:p.Pro1030Ser	127.0	0.0	.		129.0	59.0	.	NM_031889	Q17RI5|Q9H3D1	Missense_Mutation	SNP	ENST00000396073.3	hg19	CCDS3544.2	.	.	.	.	.	.	.	.	.	.	C	10.67	1.416036	0.25552	.	.	ENSG00000132464	ENST00000396073	T	0.37411	1.2	5.97	5.11	0.69529	.	0.116712	0.39407	N	0.001380	T	0.49660	0.1570	M	0.81802	2.56	0.30657	N	0.754852	P	0.50272	0.933	P	0.49477	0.612	T	0.60596	-0.7232	10	0.62326	D	0.03	-10.6665	12.7104	0.57086	0.1631:0.8369:0.0:0.0	.	1030	Q9NRM1	ENAM_HUMAN	S	1030	ENSP00000379383:P1030S	ENSP00000379383:P1030S	P	+	1	0	ENAM	71729095	0.747000	0.28283	0.848000	0.33437	0.024000	0.10985	1.284000	0.33249	2.836000	0.97738	0.655000	0.94253	CCA	.	.	.	none		0.433	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3	NM_031889		T	71510231	C	T	71510231	3	4	162	1	0	0	0	0	1	0	0	0	5114	855	30	2	3118	2	ENAM	4	71510231	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08	2306940	71510231	119644045	25	9559											
ANXA3	306	hgsc.bcm.edu	37	chr4	79512751	79512751	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgaaacatctggtgacttcCggaaagctctgttgactttg	9	12	10	10	2	2	2	0	2	2	0	3	4	3	3	2	2	2	2	2	2	2	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr4:79512751C>T	ENST00000264908.6	+	7	836	c.457C>T	c.(457-459)Cgg>Tgg	p.R153W	ANXA3_ENST00000503570.2_Missense_Mutation_p.R114W|ANXA3_ENST00000512884.1_Missense_Mutation_p.R114W	NM_005139.2	NP_005130.1	P12429	ANXA3_HUMAN	annexin A3	153					defense response to bacterium (GO:0042742)|neutrophil degranulation (GO:0043312)|phagocytosis (GO:0006909)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|specific granule (GO:0042581)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|phospholipase A2 inhibitor activity (GO:0019834)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15						TGGTGACTTCCGGAAAGCTCT	0.343																																					p.R153W	GBM(2;126 157 27790 28920 42492)	Atlas-SNP	.											.	ANXA3	35	.	0			c.C457T						PASS	.						135	139	138					4																	79512751		2203	4300	6503	SO:0001583	missense	306	exon7			GACTTCCGGAAAG	M63310	CCDS3584.1	4q21.21	2009-07-10			ENSG00000138772	ENSG00000138772	3.1.4.43	"Annexins"	541	protein-coding gene	gene with protein product		106490		ANX3		1830024	Standard	XM_005262973		Approved		uc003hld.3	P12429	OTTHUMG00000130198	ENST00000264908.6:c.457C>T	chr4.hg19:g.79512751C>T	ENSP00000264908:p.Arg153Trp	271.0	0.0	.		287.0	114.0	.	NM_005139	B2R9W6|Q6LET2	Missense_Mutation	SNP	ENST00000264908.6	hg19	CCDS3584.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.142653	0.77888	.	.	ENSG00000138772	ENST00000264908;ENST00000512884;ENST00000503570;ENST00000514171	T;T;T;T	0.03831	3.79;3.79;3.79;3.79	5.21	4.3	0.51218	Annexin repeat, conserved site (1);	0.348448	0.28901	N	0.013775	T	0.23410	0.0566	M	0.90759	3.145	0.46260	D	0.998954	D	0.89917	1.0	D	0.69142	0.962	T	0.00593	-1.1654	10	0.87932	D	0	.	10.6705	0.45755	0.3225:0.6775:0.0:0.0	.	153	P12429	ANXA3_HUMAN	W	153;114;114;153	ENSP00000264908:R153W;ENSP00000423068:R114W;ENSP00000421015:R114W;ENSP00000421512:R153W	ENSP00000264908:R153W	R	+	1	2	ANXA3	79731775	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.345000	0.33953	2.708000	0.92522	0.585000	0.79938	CGG	.	.	.	none		0.343	ANXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252516.3	NM_005139		T	79512751	C	T	79512751	3	4	162	1	0	0	0	0	1	0	0	0	719	643	23	1	479	1	ANXA3	4	79512751	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08	8002520	79512751	111641525	26	9560											
TRIO	7204	hgsc.bcm.edu	37	chr5	14471560	14471560	+	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	ggaagaaaggaaatccagctCtttaaagagaagacagtaag	19	6	11	5	0	1	3	0	0	1	3	2	6	2	5	1	2	1	2	1	2	7	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr5:14471560C>T	ENST00000344204.4	+	38	5921	c.5897C>T	c.(5896-5898)tCt>tTt	p.S1966F	TRIO_ENST00000537187.1_Missense_Mutation_p.S1966F	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	1966					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)					AAATCCAGCTCTTTAAAGAGA	0.438																																					p.S1966F		Atlas-SNP	.											.	TRIO	305	.	0			c.C5897T						PASS	.						73	70	71					5																	14471560		2203	4300	6503	SO:0001583	missense	7204	exon38			CCAGCTCTTTAAA	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.5897C>T	chr5.hg19:g.14471560C>T	ENSP00000339299:p.Ser1966Phe	106.0	0.0	.		124.0	89.0	.	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	hg19	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.936293	0.52972	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000513206;ENST00000541447	T;T	0.68479	-0.33;-0.33	5.39	5.39	0.77823	Dbl homology (DH) domain (2);	0.056462	0.64402	D	0.000001	T	0.48150	0.1484	N	0.03608	-0.345	0.47737	D	0.999501	B;B	0.14805	0.011;0.0	B;B	0.15052	0.012;0.001	T	0.45293	-0.9271	10	0.52906	T	0.07	.	19.2167	0.93781	0.0:1.0:0.0:0.0	.	1966;1966	O75962-5;O75962	.;TRIO_HUMAN	F	1966;1966;1653;46	ENSP00000339299:S1966F;ENSP00000446348:S1966F	ENSP00000339299:S1966F	S	+	2	0	TRIO	14524560	1.000000	0.71417	0.951000	0.38953	0.965000	0.64279	5.667000	0.68067	2.537000	0.85549	0.650000	0.86243	TCT	.	.	.	none		0.438	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		T	14471560	C	T	14471560	3	4	162	1	0	0	0	0	1	0	0	0	16564	913	32	2	6047	2	TRIO	5	14471560	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08		14471560	166443700	27	9561											
RICTOR	253260	hgsc.bcm.edu	37	chr5	38954924	38954924	+	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	ttatggtgtactagttgtccAtaaaggtgtataggcaggta	11	14	12	4	0	0	0	0	0	0	0	1	0	1	0	1	4	1	5	1	4	8	8			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr5:38954924A>C	ENST00000357387.3	-	27	2679	c.2649T>G	c.(2647-2649)taT>taG	p.Y883*	RICTOR_ENST00000296782.5_Nonsense_Mutation_p.Y883*|RICTOR_ENST00000503698.1_5'UTR	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2											NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					CTAGTTGTCCATAAAGGTGTA	0.313																																					p.Y883X		Atlas-SNP	.											.	RICTOR	182	.	0			c.T2649G						PASS	.						121	118	119					5																	38954924		2203	4300	6503	SO:0001587	stop_gained	253260	exon27			TTGTCCATAAAGG		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.2649T>G	chr5.hg19:g.38954924A>C	ENSP00000349959:p.Tyr883*	132.0	0.0	.		255.0	148.0	.	NM_152756		Nonsense_Mutation	SNP	ENST00000357387.3	hg19	CCDS34148.1	.	.	.	.	.	.	.	.	.	.	A	38	7.042770	0.98021	.	.	ENSG00000164327	ENST00000357387;ENST00000296782	.	.	.	5.79	3.38	0.38709	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.3188	9.8756	0.41202	0.8005:0.0:0.1995:0.0	.	.	.	.	X	883	.	ENSP00000296782:Y883X	Y	-	3	2	RICTOR	38990681	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	2.863000	0.48396	0.449000	0.26747	0.477000	0.44152	TAT	.	.	.	none		0.313	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756		C	38954924	A	C	38954924	4	2	162	1	0	0	0	0	0	1	0	0	13371	224	8	5	2525	5	RICTOR	5	38954924	Nonsense_Mutation	SNP	A	TCGA-EV-5902-01A-11D-1589-08	24483364	38954924	141960336	28	9562											
PIK3R1	5295	hgsc.bcm.edu	37	chr5	67588178	67588178	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgctgaatggtactggggAgatatctcgaggtaaggcta	11	10	15	5	1	1	2	0	1	1	1	2	5	1	2	0	5	2	4	0	5	5	4			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr5:67588178A>G	ENST00000521381.1	+	8	1624	c.1008A>G	c.(1006-1008)ggA>ggG	p.G336G	PIK3R1_ENST00000320694.8_Silent_p.G36G|PIK3R1_ENST00000396611.1_Silent_p.G336G|PIK3R1_ENST00000274335.5_Silent_p.G336G|PIK3R1_ENST00000336483.5_Silent_p.G66G|PIK3R1_ENST00000521657.1_Silent_p.G336G|PIK3R1_ENST00000523872.1_5'Flank	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	336	SH2 1. {ECO:0000255|PROSITE- ProRule:PRU00191}.				B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.0?(1)|p.?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	GGTACTGGGGAGATATCTCGA	0.393			"Mis, F, O"		"gliobastoma, ovarian, colorectal"					TCGA GBM(4;<1E-08)																											p.G336G		Atlas-SNP	.		Rec	yes		5	5q13.1	5295	"phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"		"E, O"	.	PIK3R1	869	.	2	Whole gene deletion(1)|Unknown(1)	large_intestine(1)|lung(1)	c.A1008G						PASS	.						153	143	146					5																	67588178		2203	4300	6503	SO:0001819	synonymous_variant	5295	exon8			CTGGGGAGATATC	M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"SH2 domain containing"	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1008A>G	chr5.hg19:g.67588178A>G		177.0	0.0	.		225.0	74.0	.	NM_181523	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Silent	SNP	ENST00000521381.1	hg19	CCDS3993.1																																																																																			.	.	.	none		0.393	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		G	67588178	A	G	67588178	2	3	162	1	0	0	0	0	0	0	0	1	11925	291	11	3		3	PIK3R1	5	67588178	Silent	SNP	A	TCGA-EV-5902-01A-11D-1589-08	28633254	67588178	113327082	29	9563											
PIK3R1	5295	hgsc.bcm.edu	37	chr5	67591286	67591286	+	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	tgttcggcaaaagaagttgaAcgagtggttgggcaatgaaa	14	9	14	4	2	0	3	0	2	0	1	1	4	0	3	0	3	1	5	0	3	6	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr5:67591286A>T	ENST00000521381.1	+	14	2400	c.1784A>T	c.(1783-1785)aAc>aTc	p.N595I	PIK3R1_ENST00000320694.8_Missense_Mutation_p.N295I|PIK3R1_ENST00000396611.1_Missense_Mutation_p.N595I|PIK3R1_ENST00000274335.5_Missense_Mutation_p.N595I|PIK3R1_ENST00000336483.5_Missense_Mutation_p.N325I|PIK3R1_ENST00000521657.1_Missense_Mutation_p.N595I|PIK3R1_ENST00000523872.1_Missense_Mutation_p.N232I	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	595					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.M582_D605>I(4)|p.Y580fs*1(1)|p.0?(1)|p.?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	AAGAAGTTGAACGAGTGGTTG	0.368			"Mis, F, O"		"gliobastoma, ovarian, colorectal"					TCGA GBM(4;<1E-08)																											p.N595I		Atlas-SNP	.		Rec	yes		5	5q13.1	5295	"phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"		"E, O"	.	PIK3R1	869	.	7	Complex - deletion inframe(4)|Whole gene deletion(1)|Deletion - Frameshift(1)|Unknown(1)	large_intestine(4)|lung(1)|ovary(1)|central_nervous_system(1)	c.A1784T						PASS	.						152	156	155					5																	67591286		2203	4300	6503	SO:0001583	missense	5295	exon14			AGTTGAACGAGTG	M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"SH2 domain containing"	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1784A>T	chr5.hg19:g.67591286A>T	ENSP00000428056:p.Asn595Ile	87.0	0.0	.		126.0	39.0	.	NM_181523	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Missense_Mutation	SNP	ENST00000521381.1	hg19	CCDS3993.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.587453	0.86851	.	.	ENSG00000145675	ENST00000521381;ENST00000521657;ENST00000396611;ENST00000274335;ENST00000320694;ENST00000336483;ENST00000523872	T;T;T;T;T;T;T	0.31510	1.49;1.49;1.49;1.49;1.49;1.49;1.49	4.84	4.84	0.62591	.	0.042090	0.85682	D	0.000000	T	0.57257	0.2041	M	0.82923	2.615	0.80722	D	1	D;P;P;D	0.67145	0.991;0.811;0.901;0.996	P;P;P;D	0.67725	0.892;0.844;0.844;0.953	T	0.65084	-0.6254	10	0.87932	D	0	-28.7516	14.6086	0.68498	1.0:0.0:0.0:0.0	.	265;325;295;595	B7Z2N8;P27986-2;P27986-3;P27986	.;.;.;P85A_HUMAN	I	595;595;595;595;295;325;232	ENSP00000428056:N595I;ENSP00000429277:N595I;ENSP00000379855:N595I;ENSP00000274335:N595I;ENSP00000323512:N295I;ENSP00000338554:N325I;ENSP00000430098:N232I	ENSP00000274335:N595I	N	+	2	0	PIK3R1	67627042	1.000000	0.71417	0.997000	0.53966	0.929000	0.56500	9.087000	0.94110	2.036000	0.60181	0.377000	0.23210	AAC	.	.	.	none		0.368	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		T	67591286	A	T	67591286	3	4	162	1	0	0	0	0	1	0	0	0	11925	43	2	5	1964	5	PIK3R1	5	67591286	Missense_Mutation	SNP	A	TCGA-EV-5902-01A-11D-1589-08	3108	67591286	113323974	30	9564											
C5orf36	285600	hgsc.bcm.edu	37	chr5	93856355	93856362	+	Frame_Shift_Del	DEL	AAATTTTT	AAATTTTT	-																															taagcactgctttttcaataAaattttttgctgtgaattgt																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	AAATTTTT	AAATTTTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr5:93856355_93856362delAAATTTTT	ENST00000329378.7	-	5	810_817	c.561_568delAAAAATTT	c.(559-570)caaaaaattttafs	p.QKIL187fs	KIAA0825_ENST00000513200.3_Frame_Shift_Del_p.QKIL187fs|KIAA0825_ENST00000427991.2_Frame_Shift_Del_p.QKIL187fs|KIAA0825_ENST00000312498.7_Frame_Shift_Del_p.QKIL187fs	NM_173665.2	NP_775936.1	Q8IV33	K0825_HUMAN	KIAA0825	187										breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(1)	13						TTTTTCAATAAAATTTTTTGCTGTGAAT	0.322																																					p.188_190del		Atlas-INDEL	.											.	KIAA0825	172	.	0			c.562_569del						PASS	.																																			SO:0001589	frameshift_variant	285600	exon5			.	BX648338	CCDS4070.1	5q15	2011-02-23	2011-02-23	2011-02-23	ENSG00000185261	ENSG00000185261			28532	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 36"	C5orf36		12477932	Standard	NM_173665		Approved	DKFZp686F0372, MGC34713	uc011cuk.2	Q8IV33	OTTHUMG00000131331	ENST00000329378.7:c.561_568delAAAAATTT	chr5.hg19:g.93856355_93856362delAAATTTTT	ENSP00000331385:p.Gln187fs	112.0	0.0	0		170.0	25.0	0.147059	NM_001145678	O94914|Q6ZNN2	Frame_Shift_Del	DEL	ENST00000329378.7	hg19	CCDS4070.1																																																																																			.	.	.	none		0.322	KIAA0825-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371180.2	NM_173665		-	93856362	AAATTTTT	-	93856355	7	5	162	1	0	1	0	1	0	0	0	0	2297	11	1	0	3332	0	C5orf36	5	93856355	Frame_Shift_Del	DEL	AAATTTTT	TCGA-EV-5902-01A-11D-1589-08	26265069	93856355	87058905	31	9565											
ACSL6	23305	hgsc.bcm.edu	37	chr5	131324510	131324510	+	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	gggcttacctgtattgatgaTgtagcggatagccccagggc	8	10	14	9	1	0	2	0	2	0	0	0	3	0	3	3	3	3	3	3	3	4	5			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr5:131324510T>A	ENST00000379240.1	-	6	718	c.565A>T	c.(565-567)Atc>Ttc	p.I189F	ACSL6_ENST00000379255.1_Missense_Mutation_p.I154F|ACSL6_ENST00000379244.1_Missense_Mutation_p.I189F|ACSL6_ENST00000379249.3_Missense_Mutation_p.I189F|ACSL6_ENST00000431707.1_Missense_Mutation_p.I154F|ACSL6_ENST00000543479.1_Missense_Mutation_p.I189F|ACSL6_ENST00000379264.2_Missense_Mutation_p.I214F|ACSL6_ENST00000357096.1_Missense_Mutation_p.I154F|ACSL6_ENST00000379272.2_Missense_Mutation_p.I189F|ACSL6_ENST00000296869.4_Missense_Mutation_p.I214F|ACSL6_ENST00000379246.1_Missense_Mutation_p.I200F|ACSL6_ENST00000544770.1_Missense_Mutation_p.I98F			Q9UKU0	ACSL6_HUMAN	acyl-CoA synthetase long-chain family member 6	189					acyl-CoA metabolic process (GO:0006637)|cellular lipid metabolic process (GO:0044255)|cellular response to insulin stimulus (GO:0032869)|fatty acid transport (GO:0015908)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|neuroblast proliferation (GO:0007405)|neuron development (GO:0048666)|phospholipid biosynthetic process (GO:0008654)|positive regulation of neuron projection development (GO:0010976)|positive regulation of plasma membrane long-chain fatty acid transport (GO:0010747)|positive regulation of triglyceride biosynthetic process (GO:0010867)|response to gravity (GO:0009629)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|long-chain fatty acid-CoA ligase activity (GO:0004467)|protein homodimerization activity (GO:0042803)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	35		all_cancers(142;0.107)|Breast(839;0.198)|Lung NSC(810;0.216)|all_lung(232;0.248)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GTATTGATGATGTAGCGGATA	0.572																																					p.I214F		Atlas-SNP	.											.	ACSL6	169	.	0			c.A640T						PASS	.						114	112	113					5																	131324510		2203	4300	6503	SO:0001583	missense	23305	exon6			TGATGATGTAGCG	AB020644	CCDS34228.1, CCDS34229.1, CCDS56381.1, CCDS56382.1, CCDS56383.1	5q31	2008-02-05	2004-02-19	2004-02-20	ENSG00000164398	ENSG00000164398		"Acyl-CoA synthetase family"	16496	protein-coding gene	gene with protein product		604443	"fatty-acid-Coenzyme A ligase, long-chain 6"	FACL6		10502316, 10548543	Standard	NM_015256		Approved	KIAA0837, ACS2, LACS5, LACS2	uc003kvy.2	Q9UKU0	OTTHUMG00000150692	ENST00000379240.1:c.565A>T	chr5.hg19:g.131324510T>A	ENSP00000368542:p.Ile189Phe	220.0	0.0	.		304.0	104.0	.	NM_001009185	J3KPG3|O94924|O95829|Q108M9|Q108N0|Q4G191|Q86TN7	Missense_Mutation	SNP	ENST00000379240.1	hg19		.	.	.	.	.	.	.	.	.	.	T	20.8	4.053835	0.75960	.	.	ENSG00000164398	ENST00000379249;ENST00000379264;ENST00000379272;ENST00000357096;ENST00000379255;ENST00000296869;ENST00000379246;ENST00000379244;ENST00000544770;ENST00000379240;ENST00000431707;ENST00000543479;ENST00000434099;ENST00000430403	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67	5.79	5.79	0.91817	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.81399	0.4814	H	0.98446	4.235	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.998;1.0;1.0;0.998;1.0;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.993;0.995;0.999;0.996;0.988;0.995;0.995	D	0.88843	0.3314	10	0.87932	D	0	.	16.1224	0.81369	0.0:0.0:0.0:1.0	.	189;189;179;189;154;214;214	Q9UKU0-3;Q9UKU0-6;B4DFW3;Q9UKU0;Q9UKU0-7;Q9UKU0-1;Q9UKU0-8	.;.;.;ACSL6_HUMAN;.;.;.	F	189;214;189;154;154;214;200;189;98;189;154;189;154;189	ENSP00000368551:I189F;ENSP00000368566:I214F;ENSP00000368574:I189F;ENSP00000349608:I154F;ENSP00000368557:I154F;ENSP00000296869:I214F;ENSP00000368548:I200F;ENSP00000368546:I189F;ENSP00000445154:I98F;ENSP00000368542:I189F;ENSP00000413329:I154F;ENSP00000442124:I189F;ENSP00000397507:I154F;ENSP00000398423:I189F	ENSP00000296869:I214F	I	-	1	0	ACSL6	131352409	1.000000	0.71417	1.000000	0.80357	0.248000	0.25809	7.953000	0.87836	2.208000	0.71279	0.533000	0.62120	ATC	.	.	.	none		0.572	ACSL6-004	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000132622.1	NM_015256		A	131324510	T	A	131324510	3	1	162	1	0	0	0	0	1	0	0	0	181	1464	51	5	1674	5	ACSL6	5	131324510	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08	37468155	131324510	49590750	32	9566											
MRPL22	29093	hgsc.bcm.edu	37	chr5	154330411	154330411	+	Frame_Shift_Del	DEL	T	T	-																															caatcatatatccacacaagTgcttctcttgacatttctcg																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr5:154330411delT	ENST00000523037.1	+	3	149	c.108delT	c.(106-108)agtfs	p.S36fs	MRPL22_ENST00000439747.3_Frame_Shift_Del_p.S62fs|MRPL22_ENST00000265229.8_Intron|MRPL22_ENST00000522038.1_Frame_Shift_Del_p.S42fs	NM_014180.3	NP_054899.2	Q9NWU5	RM22_HUMAN	mitochondrial ribosomal protein L22	36					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(2)	10	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TCCACACAAGTGCTTCTCTTG	0.398																																					p.S36fs		Atlas-INDEL	.											.	MRPL22	18	.	0			c.107delG						PASS	.						124	122	123					5																	154330411		2203	4300	6503	SO:0001589	frameshift_variant	29093	exon3			.	AB051622	CCDS4331.1, CCDS43391.1	5q33.2	2012-09-13			ENSG00000082515	ENSG00000082515		"Mitochondrial ribosomal proteins / large subunits"	14480	protein-coding gene	gene with protein product		611835					Standard	NM_014180		Approved	MRP-L25, RPML25, HSPC158	uc003lvy.4	Q9NWU5	OTTHUMG00000130190	ENST00000523037.1:c.108delT	chr5.hg19:g.154330411delT	ENSP00000431040:p.Ser36fs	128.0	0.0	0		184.0	125.0	0.679348	NM_014180	A6NGJ8|Q5H9Q1|Q96Q51|Q9P006	Frame_Shift_Del	DEL	ENST00000523037.1	hg19	CCDS4331.1																																																																																			.	.	.	none		0.398	MRPL22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252508.2			-	154330411	T	-	154330411	7	5	162	1	0	1	0	1	0	0	0	0	9795	1693	59	0	118	0	MRPL22	5	154330411	Frame_Shift_Del	DEL	T	TCGA-EV-5902-01A-11D-1589-08	23005901	154330411	26584849	33	9567											
ATP10B	23120	hgsc.bcm.edu	37	chr5	160113261	160113262	+	Missense_Mutation	DNP	GG	GG	TC																															gttcaaaatcaccaggaacaGgaaatagaggttagcccatc																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr5:160113261_160113262GG>TC	ENST00000327245.5	-	6	1140_1141	c.294_295CC>GA	c.(292-297)ttCCtg>ttGAtg	p.98_99FL>LM	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	98					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)			ACCAGGAACAGGAAATAGAGGT	0.45																																					p.L99M|p.F98L		Atlas-SNP	.											.	ATP10B	201	.	0			c.C295A|c.C294G						PASS	.																																			SO:0001583	missense	23120	exon6			GGAACAGGAAATA|GAACAGGAAATAG	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.294_295delinsTC	chr5.hg19:g.160113261_160113262delinsTC	ENSP00000313600:p.F98_L99delinsLM	38.0	0.0	.		57.0	12.0	.	NM_025153	Q9H725	Missense_Mutation	SNP	ENST00000327245.5	hg19	CCDS43394.1																																																																																			.	.	.	none		0.45	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153		TC	160113262	GG	TC	160113261	3	4	162	1	0	0	0	0	1	0	0	0	1117	991	35	4	4174	4	ATP10B	5	160113261	Missense_Mutation	DNP	GG	TCGA-EV-5902-01A-11D-1589-08	5782850	160113261	20801999	34	9568											
BTNL8	79908	hgsc.bcm.edu	37	chr5	180374575	180374575	+	Missense_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	actgggaatactctgctgtgGcctattttttggcattgttg	6	17	11	7	0	1	0	0	0	1	0	1	1	1	1	1	3	2	3	1	3	3	7	rs371555886		TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr5:180374575G>A	ENST00000340184.4	+	4	943	c.737G>A	c.(736-738)gGc>gAc	p.G246D	BTNL8_ENST00000231229.4_Missense_Mutation_p.G246D|BTNL8_ENST00000511704.1_Missense_Mutation_p.G130D|BTNL8_ENST00000508408.1_Missense_Mutation_p.G246D|BTNL8_ENST00000505126.1_Missense_Mutation_p.G39D|BTNL8_ENST00000400707.3_Missense_Mutation_p.G121D|BTNL8_ENST00000533815.2_Missense_Mutation_p.G62D	NM_001040462.2	NP_001035552.1	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8	246					immune system process (GO:0002376)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	28	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTCTGCTGTGGCCTATTTTTT	0.443																																					p.G246D		Atlas-SNP	.											.	BTNL8	114	.	0			c.G737A						PASS	.	G	ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY	0,4406		0,0,2203	231	240	237		737,389,737,362,185,737	-2.9	0	5		237	1,8591	1.2+/-3.3	0,1,4295	yes	missense,missense,missense,missense,missense,missense	BTNL8	NM_001040462.2,NM_001159707.1,NM_001159708.1,NM_001159709.1,NM_001159710.1,NM_024850.2	94,94,94,94,94,94	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	246/501,130/385,246/341,121/376,62/317,246/348	180374575	1,12997	2203	4296	6499	SO:0001583	missense	79908	exon4			GCTGTGGCCTATT	AK025111	CCDS4459.1, CCDS43413.1, CCDS54956.1, CCDS54957.1, CCDS54958.1, CCDS54959.1	5q35.3	2014-01-14			ENSG00000113303	ENSG00000113303		"Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	26131	protein-coding gene	gene with protein product		615606				12975309	Standard	NM_024850		Approved	FLJ21458, BTN9.2	uc003mmp.3	Q6UX41	OTTHUMG00000130932	ENST00000340184.4:c.737G>A	chr5.hg19:g.180374575G>A	ENSP00000342197:p.Gly246Asp	570.0	0.0	.		755.0	485.0	.	NM_001159708	A4QMZ8|A6NEX6|B7Z409|B7Z5B1|E9PEF6|E9PG07|F2Z2B2|F8W712|Q9H730	Missense_Mutation	SNP	ENST00000340184.4	hg19	CCDS43413.1	.	.	.	.	.	.	.	.	.	.	G	6.384	0.438919	0.12104	0.0	1.16E-4	ENSG00000113303	ENST00000231229;ENST00000340184;ENST00000400707;ENST00000508408;ENST00000511704;ENST00000505126;ENST00000533815	T;T;T;T;T;T;T	0.61274	4.8;1.28;0.63;4.8;0.62;0.12;0.19	1.52	-2.87	0.05700	.	.	.	.	.	T	0.52224	0.1721	L	0.34521	1.04	0.09310	N	1	D;D;P;P;P	0.64830	0.982;0.994;0.808;0.808;0.838	P;P;B;B;B	0.59221	0.769;0.854;0.159;0.159;0.367	T	0.44034	-0.9354	9	0.35671	T	0.21	.	3.793	0.08728	0.0:0.2104:0.2868:0.5028	.	121;130;246;246;246	E9PG07;E9PEF6;F2Z2B2;A6NEX6;Q6UX41	.;.;.;.;BTNL8_HUMAN	D	246;246;121;246;130;39;62	ENSP00000231229:G246D;ENSP00000342197:G246D;ENSP00000383543:G121D;ENSP00000424585:G246D;ENSP00000425207:G130D;ENSP00000427441:G39D;ENSP00000435098:G62D	ENSP00000231229:G246D	G	+	2	0	BTNL8	180307181	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.641000	0.05434	-0.893000	0.03930	0.436000	0.28706	GGC	.	.	.	weak		0.443	BTNL8-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368440.1	NM_024850		A	180374575	G	A	180374575	3	1	162	1	0	0	0	0	1	0	0	0	1569	1203	42	2	777	2	BTNL8	5	180374575	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08	20261314	180374575	540685	35	9569											
MTCH1	23787	hgsc.bcm.edu	37	chr6	36949411	36949411	+	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	ggaccttcctccccagcacaTtggtcccaagggtggggggc	6	7	14	14	0	0	0	0	0	0	0	3	1	3	1	5	6	1	1	5	6	1	2			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr6:36949411T>A	ENST00000373627.5	-	2	483	c.359A>T	c.(358-360)aAt>aTt	p.N120I	MTCH1_ENST00000373616.5_Missense_Mutation_p.N120I|MTCH1_ENST00000538808.1_Intron	NM_001271641.1	NP_001258570.1	Q9NZJ7	MTCH1_HUMAN	mitochondrial carrier 1	120					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|neuronal ion channel clustering (GO:0045161)|positive regulation of apoptotic process (GO:0043065)|regulation of signal transduction (GO:0009966)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	6						CCCCAGCACATTGGTCCCAAG	0.562																																					p.N120I		Atlas-SNP	.											.	MTCH1	24	.	0			c.A359T						PASS	.						59	52	54					6																	36949411		2203	4300	6503	SO:0001583	missense	23787	exon2			AGCACATTGGTCC	AF151822	CCDS4828.1, CCDS64411.1	6p21.2	2013-05-22	2011-05-19		ENSG00000137409	ENSG00000137409		"Solute carriers"	17586	protein-coding gene	gene with protein product	"solute carrier family 25, member 49"	610449	"mitochondrial carrier homolog 1 (C. elegans)"			12377771	Standard	NM_014341		Approved	CGI-64, PSAP, SLC25A49	uc003ond.2	Q9NZJ7	OTTHUMG00000014614	ENST00000373627.5:c.359A>T	chr6.hg19:g.36949411T>A	ENSP00000362730:p.Asn120Ile	71.0	0.0	.		21.0	21.0	.	NM_014341	A8KAX5|B2RCE3|Q6PK60|Q6UX45|Q7L465|Q9BW23|Q9NZR6|Q9UJZ5	Missense_Mutation	SNP	ENST00000373627.5	hg19		.	.	.	.	.	.	.	.	.	.	T	19.24	3.788911	0.70337	.	.	ENSG00000137409	ENST00000373616;ENST00000373627;ENST00000337855;ENST00000373550;ENST00000460219	T;T;T	0.48201	0.82;0.82;0.82	4.87	2.42	0.29668	Mitochondrial carrier domain (2);	0.078934	0.49305	D	0.000154	T	0.43787	0.1263	L	0.49126	1.545	0.80722	D	1	D;D;D	0.69078	0.997;0.991;0.99	D;P;P	0.63597	0.916;0.843;0.891	T	0.45527	-0.9255	10	0.72032	D	0.01	-3.3591	7.5839	0.27980	0.0:0.1805:0.0:0.8195	.	102;120;120	Q8IW90;Q9NZJ7;Q9NZJ7-2	.;MTCH1_HUMAN;.	I	120;120;56;56;104	ENSP00000362718:N120I;ENSP00000362730:N120I;ENSP00000419739:N104I	ENSP00000338712:N56I	N	-	2	0	MTCH1	37057389	1.000000	0.71417	0.997000	0.53966	0.959000	0.62525	4.282000	0.58971	0.713000	0.32060	0.402000	0.26972	AAT	.	.	.	none		0.562	MTCH1-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040396.1	NM_014341		A	36949411	T	A	36949411	3	1	162	1	0	0	0	0	1	0	0	0	9920	1493	52	5	803	5	MTCH1	6	36949411	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08		36949411	134165656	36	9570											
SNX10	29887	hgsc.bcm.edu	37	chr7	26412183	26412200	+	Stop_Codon_Del	DEL	GGAATCCTGAAAAATAAT	GGAATCCTGAAAAATAAT	-																															aaagtaaatacagctccgcaGgaatcctgaaaaataattct																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	GGAATCCTGAAAAATAAT	GGAATCCTGAAAAATAAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr7:26412183_26412200delGGAATCCTGAAAAATAAT	ENST00000338523.4	+	0	784_801				SNX10_ENST00000409838.1_Stop_Codon_Del|SNX10_ENST00000396376.1_Stop_Codon_Del|AC004540.4_ENST00000451368.1_RNA|AC004540.4_ENST00000451264.1_RNA|SNX10_ENST00000409367.1_Stop_Codon_Del|SNX10_ENST00000462993.1_3'UTR|SNX10_ENST00000446848.2_Stop_Codon_Del	NM_001199835.1|NM_013322.2	NP_001186764.1|NP_037454.2	Q9Y5X0	SNX10_HUMAN	sorting nexin 10						cilium assembly (GO:0042384)|endosome organization (GO:0007032)|intracellular protein transport (GO:0006886)|osteoclast differentiation (GO:0030316)|protein localization to centrosome (GO:0071539)|protein localization to cilium (GO:0061512)	cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extrinsic component of endosome membrane (GO:0031313)|nucleus (GO:0005634)	1-phosphatidylinositol binding (GO:0005545)|ATPase binding (GO:0051117)			endometrium(1)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	6						CAGCTCCGCAGGAATCCTGAAAAATAATTCTAATGTTA	0.367																																					p.199_202del		Atlas-INDEL	.											.	SNX10	19	.	0			c.596_821del						PASS	.																																			SO:0001567	stop_retained_variant	29887	exon7			.	AF121860	CCDS5399.1, CCDS56470.1	7p15.2	2008-05-22			ENSG00000086300	ENSG00000086300		"Sorting nexins"	14974	protein-coding gene	gene with protein product		614780				17012226	Standard	NM_013322		Approved		uc010kuu.3	Q9Y5X0	OTTHUMG00000023650	Exception_encountered	chr7.hg19:g.26412183_26412200delGGAATCCTGAAAAATAAT		190.0	0.0	0		154.0	45.0	0.292208	NM_013322	E9PFH5|Q8IYT5	Frame_Shift_Del	DEL	ENST00000338523.4	hg19	CCDS5399.1																																																																																			.	.	.	none		0.367	SNX10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214120.1			-	26412200	GGAATCCTGAAAAATAAT	-	26412183	7	5	162	1	0	1	0	1	0	0	0	0	14894	991	35	0	619	0	SNX10	7	26412183	Stop_Codon_Del	DEL	GGAATCCTGAAAAATAAT	TCGA-EV-5902-01A-11D-1589-08		26412183	132726480	37	9571											
GBAS	2631	hgsc.bcm.edu	37	chr7	56045954	56045955	+	Frame_Shift_Del	DEL	AC	AC	-																															acaagcaatctatacaaattAcagtgtgagtgacaggtttg																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr7:56045954_56045955delAC	ENST00000322090.3	+	2	257_258	c.228_229delAC	c.(226-231)ttacagfs	p.Q77fs	GBAS_ENST00000446778.1_Frame_Shift_Del_p.Q77fs|GBAS_ENST00000487370.1_3'UTR	NM_001483.2	NP_001474.1	O75323	NIPS2_HUMAN	glioblastoma amplified sequence	77					ATP biosynthetic process (GO:0006754)|negative regulation of ATP citrate synthase activity (GO:2000984)|oxidative phosphorylation (GO:0006119)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrion (GO:0005739)				breast(1)|central_nervous_system(1)|large_intestine(1)|lung(2)	5	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			TATACAAATTACAGTGTGAGTG	0.361																																					p.76_76del		Atlas-INDEL	.											.	GBAS	16	.	0			c.227_228del						PASS	.																																			SO:0001589	frameshift_variant	2631	exon2			.	AF029786	CCDS5521.1, CCDS56488.1	7p12	2014-03-11			ENSG00000146729	ENSG00000146729			4179	protein-coding gene	gene with protein product		603004				9615231, 9661659, 20888800	Standard	NM_001483		Approved	NIPSNAP2	uc003tre.2	O75323	OTTHUMG00000022932	ENST00000322090.3:c.228_229delAC	chr7.hg19:g.56045954_56045955delAC	ENSP00000313050:p.Gln77fs	187.0	0.0	0		148.0	80.0	0.540541	NM_001483	C9IYJ3|O43801|Q53X96	Frame_Shift_Del	DEL	ENST00000322090.3	hg19	CCDS5521.1																																																																																			.	.	.	none		0.361	GBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251524.1	NM_001483		-	56045955	AC	-	56045954	7	5	162	1	0	1	0	1	0	0	0	0	6276	388	14	0	234	0	GBAS	7	56045954	Frame_Shift_Del	DEL	AC	TCGA-EV-5902-01A-11D-1589-08	29633771	56045954	103092709	38	9572											
LRRN3	54674	hgsc.bcm.edu	37	chr7	110763780	110763780	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taagaaaaatagaagctactAacaaccctagattgtcttac	18	10	5	8	0	1	3	0	0	1	3	1	3	1	3	1	0	5	1	1	0	10	7			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr7:110763780A>G	ENST00000422987.3	+	2	1783	c.952A>G	c.(952-954)Aac>Gac	p.N318D	LRRN3_ENST00000451085.1_Missense_Mutation_p.N318D|IMMP2L_ENST00000452895.1_Intron|IMMP2L_ENST00000437687.1_Intron|IMMP2L_ENST00000447215.1_Intron|IMMP2L_ENST00000415362.1_Intron|IMMP2L_ENST00000450877.1_Intron|IMMP2L_ENST00000331762.3_Intron|LRRN3_ENST00000308478.5_Missense_Mutation_p.N318D|IMMP2L_ENST00000405709.2_Intron|IMMP2L_ENST00000489381.1_Intron	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	318					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)		AGAAGCTACTAACAACCCTAG	0.418																																					p.N318D		Atlas-SNP	.											.	LRRN3	132	.	0			c.A952G						PASS	.						85	88	87					7																	110763780		2203	4300	6503	SO:0001583	missense	54674	exon2			GCTACTAACAACC	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.952A>G	chr7.hg19:g.110763780A>G	ENSP00000412417:p.Asn318Asp	106.0	0.0	.		107.0	59.0	.	NM_018334	O43377|Q6I9V8|Q8IYQ6	Missense_Mutation	SNP	ENST00000422987.3	hg19	CCDS5754.1	.	.	.	.	.	.	.	.	.	.	A	19.37	3.814302	0.70912	.	.	ENSG00000173114	ENST00000308478;ENST00000451085;ENST00000422987	T;T;T	0.59083	0.29;0.29;0.29	5.96	5.96	0.96718	.	0.000000	0.64402	D	0.000002	T	0.63663	0.2530	N	0.20845	0.615	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.64351	-0.6428	10	0.37606	T	0.19	.	16.4311	0.83844	1.0:0.0:0.0:0.0	.	318	Q9H3W5	LRRN3_HUMAN	D	318	ENSP00000312001:N318D;ENSP00000397312:N318D;ENSP00000412417:N318D	ENSP00000312001:N318D	N	+	1	0	LRRN3	110551016	1.000000	0.71417	0.997000	0.53966	0.967000	0.64934	9.339000	0.96797	2.277000	0.76020	0.528000	0.53228	AAC	.	.	.	none		0.418	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334		G	110763780	A	G	110763780	3	3	162	1	0	0	0	0	1	0	0	0	9043	362	13	3	954	3	LRRN3	7	110763780	Missense_Mutation	SNP	A	TCGA-EV-5902-01A-11D-1589-08	54717826	110763780	48374883	39	9573											
TNPO3	23534	hgsc.bcm.edu	37	chr7	128626935	128626935	+	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	ctgcagcagaagccaggggcTtttcacacaggcctttcatc	9	9	10	13	0	2	1	2	0	0	1	3	1	2	1	2	3	3	3	2	3	1	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr7:128626935T>A	ENST00000265388.5	-	12	1681	c.1538A>T	c.(1537-1539)aAg>aTg	p.K513M	TNPO3_ENST00000471166.1_Missense_Mutation_p.K547M|TNPO3_ENST00000471234.1_Intron|TNPO3_ENST00000482320.1_Missense_Mutation_p.K447M|TNPO3_ENST00000393245.1_Missense_Mutation_p.K547M			Q9Y5L0	TNPO3_HUMAN	transportin 3	513					splicing factor protein import into nucleus (GO:0035048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(3)	22						AGCCAGGGGCTTTTCACACAG	0.453																																					p.K513M	Pancreas(147;583 2585 39696 52331)	Atlas-SNP	.											.	TNPO3	148	.	0			c.A1538T						PASS	.						79	81	80					7																	128626935		2203	4300	6503	SO:0001583	missense	23534	exon12			AGGGGCTTTTCAC	AF145029	CCDS5809.1, CCDS55162.1	7q32.2	2014-02-03			ENSG00000064419	ENSG00000064419		"Importins"	17103	protein-coding gene	gene with protein product	"importin 12"	610032	"limb girdle muscular dystrophy 1F (autosomal dominant)"	LGMD1F		10366588, 10713112, 23543484, 23667635	Standard	NM_012470		Approved	TRN-SR, MTR10A, TRN-SR2, IPO12	uc003vol.2	Q9Y5L0	OTTHUMG00000158409	ENST00000265388.5:c.1538A>T	chr7.hg19:g.128626935T>A	ENSP00000265388:p.Lys513Met	123.0	0.0	.		128.0	77.0	.	NM_012470	A4D1K9|C9IZM0|Q6NUM1|Q96G71|Q96GU9|Q9Y3R2	Missense_Mutation	SNP	ENST00000265388.5	hg19	CCDS5809.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.118999	0.77323	.	.	ENSG00000064419	ENST00000393245;ENST00000265388;ENST00000482320;ENST00000471166	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28	5.95	5.95	0.96441	Armadillo-like helical (1);Armadillo-type fold (1);	0.154879	0.56097	D	0.000021	T	0.67924	0.2945	L	0.36672	1.1	0.48571	D	0.999679	D;P	0.63046	0.992;0.895	P;P	0.55999	0.789;0.497	T	0.70920	-0.4741	10	0.66056	D	0.02	-17.8899	10.4289	0.44395	0.0:0.0:0.1635:0.8365	.	547;513	C9J7E5;Q9Y5L0	.;TNPO3_HUMAN	M	547;513;447;547	ENSP00000376936:K547M;ENSP00000265388:K513M;ENSP00000420089:K447M;ENSP00000418267:K547M	ENSP00000265388:K513M	K	-	2	0	TNPO3	128414171	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.677000	0.61634	2.279000	0.76181	0.533000	0.62120	AAG	.	.	.	none		0.453	TNPO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350929.1	NM_012470		A	128626935	T	A	128626935	3	1	162	1	0	0	0	0	1	0	0	0	16349	1609	56	5	1277	5	TNPO3	7	128626935	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08	17863155	128626935	30511728	40	9574											
STMN4	81551	hgsc.bcm.edu	37	chr8	27097566	27097566	+	Frame_Shift_Del	DEL	T	T	-																															gattccatcttctgggccagTttttccttagccatcttgat																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr8:27097566delT	ENST00000265770.7	-	5	568	c.432delA	c.(430-432)aaafs	p.K144fs	STMN4_ENST00000523048.1_Frame_Shift_Del_p.K171fs|STMN4_ENST00000519997.1_Frame_Shift_Del_p.K135fs|STMN4_ENST00000350889.4_Frame_Shift_Del_p.K171fs|STMN4_ENST00000519614.1_Frame_Shift_Del_p.K144fs|STMN4_ENST00000522908.1_Frame_Shift_Del_p.K171fs			Q9H169	STMN4_HUMAN	stathmin-like 4	144	SLD. {ECO:0000255|PROSITE- ProRule:PRU00998}.				regulation of microtubule polymerization or depolymerization (GO:0031110)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)	11		Ovarian(32;0.00167)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0214)|Epithelial(17;9.82e-10)|Colorectal(74;0.142)	Lomustine(DB01206)	TCTGGGCCAGTTTTTCCTTAG	0.517																																					p.L172fs		Atlas-INDEL	.											.	STMN4	28	.	0			c.514delC						PASS	.						233	213	220					8																	27097566		2203	4300	6503	SO:0001589	frameshift_variant	81551	exon6			.		CCDS6055.1, CCDS64851.1, CCDS64852.1, CCDS64854.1	8p21.2	2006-12-09			ENSG00000015592	ENSG00000015592			16078	protein-coding gene	gene with protein product						11230166	Standard	NM_001283054		Approved	RB3	uc003xfj.3	Q9H169	OTTHUMG00000099461	ENST00000265770.7:c.432delA	chr8.hg19:g.27097566delT	ENSP00000265770:p.Lys144fs	186.0	0.0	0		173.0	76.0	0.439306	NM_030795	B7Z2Z7|B7Z4I9|D3DSS8|D3DSS9|G5EA16|Q2TAB9	Frame_Shift_Del	DEL	ENST00000265770.7	hg19																																																																																				.	.	.	none		0.517	STMN4-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000375941.1	NM_030795		-	27097566	T	-	27097566	7	5	162	1	0	1	0	1	0	0	0	0	15323	1722	60	0	145	0	STMN4	8	27097566	Frame_Shift_Del	DEL	T	TCGA-EV-5902-01A-11D-1589-08		27097566	119266456	41	9575											
GBA2	57704	hgsc.bcm.edu	37	chr9	35739010	35739010	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gacttttacctgggtccccaAtatcatgggggatgacgttc	8	12	11	10	1	1	1	1	1	0	0	3	3	2	2	3	3	1	1	3	3	3	4			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr9:35739010A>G	ENST00000378103.3	-	11	2307	c.1784T>C	c.(1783-1785)aTt>aCt	p.I595T	GBA2_ENST00000378088.1_5'Flank|GBA2_ENST00000467252.1_5'UTR|GBA2_ENST00000378094.4_Missense_Mutation_p.I595T|GBA2_ENST00000545786.1_Missense_Mutation_p.I601T	NM_020944.2	NP_065995.1	Q9HCG7	GBA2_HUMAN	glucosidase, beta (bile acid) 2	595					bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|central nervous system neuron development (GO:0021954)|glucosylceramide catabolic process (GO:0006680)|glycoside catabolic process (GO:0016139)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)	beta-glucosidase activity (GO:0008422)|glucosylceramidase activity (GO:0004348)			NS(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(4)|skin(3)	21	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TGGGTCCCCAATATCATGGGG	0.572																																					p.I595T		Atlas-SNP	.											.	GBA2	77	.	0			c.T1784C						PASS	.						78	76	77					9																	35739010		2203	4300	6503	SO:0001583	missense	57704	exon11			TCCCCAATATCAT	AJ309567	CCDS6589.1	9p13.2	2013-09-11			ENSG00000070610	ENSG00000070610			18986	protein-coding gene	gene with protein product	"bile acid beta-glucosidase", "non-lysosomal glucosylceramidase"	609471	"spastic paraplegia 46 (autosomal recessive)"	SPG46		11489889, 23332916, 23332917	Standard	NM_020944		Approved	KIAA1605, AD035, DKFZp762K054	uc003zxw.3	Q9HCG7	OTTHUMG00000021024	ENST00000378103.3:c.1784T>C	chr9.hg19:g.35739010A>G	ENSP00000367343:p.Ile595Thr	52.0	0.0	.		33.0	18.0	.	NM_020944	D3DRP2|Q5TCV6|Q96A51|Q96LY1|Q96SJ2|Q9H2L8	Missense_Mutation	SNP	ENST00000378103.3	hg19	CCDS6589.1	.	.	.	.	.	.	.	.	.	.	A	16.56	3.156258	0.57259	.	.	ENSG00000070610	ENST00000378103;ENST00000378094;ENST00000545786	.	.	.	5.69	5.69	0.88448	Six-hairpin glycosidase-like (1);Glucosylceramidase (1);	0.259629	0.44285	D	0.000468	T	0.64571	0.2610	L	0.58101	1.795	0.80722	D	1	B;P;P	0.35493	0.449;0.493;0.505	B;B;B	0.41374	0.241;0.079;0.355	T	0.67518	-0.5650	9	0.62326	D	0.03	-8.062	14.5115	0.67791	1.0:0.0:0.0:0.0	.	601;595;595	F5H7P6;Q9HCG7-2;Q9HCG7	.;.;GBA2_HUMAN	T	595;595;601	.	ENSP00000367334:I595T	I	-	2	0	GBA2	35729010	1.000000	0.71417	0.973000	0.42090	0.994000	0.84299	8.924000	0.92827	2.171000	0.68590	0.459000	0.35465	ATT	.	.	.	none		0.572	GBA2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055456.1	NM_020944		G	35739010	A	G	35739010	3	3	162	1	0	0	0	0	1	0	0	0	6274	101	4	3	1027	3	GBA2	9	35739010	Missense_Mutation	SNP	A	TCGA-EV-5902-01A-11D-1589-08		35739010	105474421	42	9576											
ZNF169	169841	hgsc.bcm.edu	37	chr9	97063238	97063238	+	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	tgccctgattgtgggcgtggCtttggtcagaaggtcaccct	5	12	14	10	1	2	2	2	1	0	1	2	2	2	2	2	4	1	1	2	4	1	2			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr9:97063238C>T	ENST00000395395.2	+	5	1488	c.1398C>T	c.(1396-1398)ggC>ggT	p.G466G	ZNF169_ENST00000340911.4_3'UTR	NM_194320.2	NP_919301.2	Q14929	ZN169_HUMAN	zinc finger protein 169	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)			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)				GTGGGCGTGGCTTTGGTCAGA	0.577																																					p.G466G		Atlas-SNP	.											.	ZNF169	60	.	0			c.C1398T						PASS	.						73	66	68					9																	97063238		2203	4300	6503	SO:0001819	synonymous_variant	169841	exon5			GCGTGGCTTTGGT	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.1398C>T	chr9.hg19:g.97063238C>T		87.0	0.0	.		79.0	38.0	.	NM_194320	A2AGP5|A8K127|Q6PI28	Silent	SNP	ENST00000395395.2	hg19	CCDS6709.2																																																																																			.	.	.	none		0.577	ZNF169-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253714.1	NM_194320		T	97063238	C	T	97063238	2	4	162	1	0	0	0	0	0	0	0	1	17754	784	28	2		2	ZNF169	9	97063238	Silent	SNP	C	TCGA-EV-5902-01A-11D-1589-08	61324228	97063238	44150193	43	9577											
C9orf84	158401	hgsc.bcm.edu	37	chr9	114503767	114503767	+	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	aatctttacctgtaagcaaaAatgggttcaaagggcttcta	14	12	8	7	0	3	0	1	0	2	0	3	0	3	0	1	2	2	4	1	2	7	6			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr9:114503767A>T	ENST00000318737.4	-	9	1099	c.971T>A	c.(970-972)tTt>tAt	p.F324Y	C9orf84_ENST00000374283.5_Missense_Mutation_p.F388Y|C9orf84_ENST00000374287.3_Missense_Mutation_p.F324Y|C9orf84_ENST00000394779.3_Missense_Mutation_p.F285Y|C9orf84_ENST00000394777.4_Missense_Mutation_p.F285Y	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	324										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						TGTAAGCAAAAATGGGTTCAA	0.323																																					p.F324Y		Atlas-SNP	.											.	C9orf84	207	.	0			c.T971A						PASS	.						66	65	65					9																	114503767		2202	4299	6501	SO:0001583	missense	158401	exon9			AGCAAAAATGGGT	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.971T>A	chr9.hg19:g.114503767A>T	ENSP00000322108:p.Phe324Tyr	75.0	0.0	.		103.0	53.0	.	NM_173521	A2A2V3|Q2M1H8|Q96M73	Missense_Mutation	SNP	ENST00000318737.4	hg19	CCDS6781.3	.	.	.	.	.	.	.	.	.	.	A	12.21	1.869763	0.33069	.	.	ENSG00000165181	ENST00000394779;ENST00000394777;ENST00000374287;ENST00000318737;ENST00000374283	T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82	4.56	3.41	0.39046	.	1.021630	0.07826	N	0.960679	T	0.46483	0.1395	L	0.32530	0.975	0.09310	N	1	P;P;P;P	0.45827	0.718;0.844;0.867;0.867	P;P;B;P	0.49829	0.447;0.528;0.439;0.623	T	0.32745	-0.9895	10	0.62326	D	0.03	-0.5524	6.8232	0.23868	0.8939:0.0:0.1061:0.0	.	285;388;324;285	A6PVK7;Q5VXU9-2;Q5VXU9;A2A2V3	.;.;CI084_HUMAN;.	Y	285;285;324;324;388	ENSP00000378259:F285Y;ENSP00000378257:F285Y;ENSP00000363405:F324Y;ENSP00000322108:F324Y;ENSP00000363401:F388Y	ENSP00000322108:F324Y	F	-	2	0	C9orf84	113543588	0.140000	0.22579	0.106000	0.21319	0.691000	0.40173	0.554000	0.23407	0.876000	0.35872	0.455000	0.32223	TTT	.	.	.	none		0.323	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521		T	114503767	A	T	114503767	3	4	162	1	0	0	0	0	1	0	0	0	2502	14	1	5	3435	5	C9orf84	9	114503767	Missense_Mutation	SNP	A	TCGA-EV-5902-01A-11D-1589-08	17440529	114503767	26709664	44	9578											
AMBP	259	hgsc.bcm.edu	37	chr9	116837296	116837296	+	Frame_Shift_Del	DEL	G	G	-																															ttttctcataagctccagacGtctcctcacagacacctttc																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr9:116837296delG	ENST00000265132.3	-	3	543	c.281delC	c.(280-282)acgfs	p.T94fs		NM_001633.3	NP_001624.1	P02760	AMBP_HUMAN	alpha-1-microglobulin/bikunin precursor	94					cell adhesion (GO:0007155)|female pregnancy (GO:0007565)|heme catabolic process (GO:0042167)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of JNK cascade (GO:0046329)|protein catabolic process (GO:0030163)|protein-chromophore linkage (GO:0018298)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	calcium channel inhibitor activity (GO:0019855)|calcium oxalate binding (GO:0046904)|heme binding (GO:0020037)|IgA binding (GO:0019862)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase inhibitor activity (GO:0004867)|small molecule binding (GO:0036094)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	11					Human Serum Albumin(DB00062)|Serum albumin iodonated(DB00064)	AGCTCCAGACGTCTCCTCACA	0.453																																					p.T94fs		Atlas-INDEL	.											.	AMBP	33	.	0			c.282delG						PASS	.						143	125	131					9																	116837296		2203	4300	6503	SO:0001589	frameshift_variant	259	exon3			.	X04494	CCDS6800.1	9q32-q33	2014-01-22			ENSG00000106927	ENSG00000106927		"Lipocalins"	453	protein-coding gene	gene with protein product	"growth-inhibiting protein 19", "uristatin", "complex-forming glycoprotein heterogeneous in charge", "bikunin", "inter-alpha-trypsin inhibitor light chain", "protein HC", "uronic-acid-rich protein", "trypstatin"	176870		ITI, ITIL		1708673, 1385302	Standard	NM_001633		Approved	UTI, HCP, EDC1, HI30, IATIL, ITILC	uc004bie.4	P02760	OTTHUMG00000020534	ENST00000265132.3:c.281delC	chr9.hg19:g.116837296delG	ENSP00000265132:p.Thr94fs	98.0	0.0	0		99.0	46.0	0.464646	NM_001633	P00977|P02759|P78491|Q2TU33|Q5TBD7|Q9UC58|Q9UDI8	Frame_Shift_Del	DEL	ENST00000265132.3	hg19	CCDS6800.1																																																																																			.	.	.	none		0.453	AMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053758.2	NM_001633		-	116837296	G	-	116837296	7	5	162	1	0	1	0	1	0	0	0	0	564	1145	40	0	809	0	AMBP	9	116837296	Frame_Shift_Del	DEL	G	TCGA-EV-5902-01A-11D-1589-08	2333529	116837296	24376135	45	9579											
RABGAP1	23637	hgsc.bcm.edu	37	chr9	125772734	125772738	+	Frame_Shift_Del	DEL	TTCAG	TTCAG	-																															aggaaaactacagccagtccTtcagttcgcctgccacagtc																								rs201077208		TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	TTCAG	TTCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr9:125772734_125772738delTTCAG	ENST00000373647.4	+	11	1610_1614	c.1476_1480delTTCAG	c.(1474-1482)ccttcagttfs	p.SV493fs		NM_012197.3	NP_036329.3	Q9Y3P9	RBGP1_HUMAN	RAB GTPase activating protein 1	493					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						CAGCCAGTCCTTCAGTTCGCCTGCC	0.4																																					p.492_493del		Atlas-INDEL	.											.	RABGAP1	164	.	0			c.1475_1479del						PASS	.																																			SO:0001589	frameshift_variant	23637	exon11			.	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.1476_1480delTTCAG	chr9.hg19:g.125772734_125772738delTTCAG	ENSP00000362751:p.Ser493fs	73.0	0.0	0		71.0	25.0	0.352113	NM_012197	B9A6L2|Q05CW2|Q6ZMY1|Q9HA28|Q9P0E2|Q9UG67	Frame_Shift_Del	DEL	ENST00000373647.4	hg19	CCDS6848.2																																																																																			.	.	.	none		0.4	RABGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053976.3	NM_012197		-	125772738	TTCAG	-	125772734	7	5	162	1	0	1	0	1	0	0	0	0	12977	1596	56	0	1514	0	RABGAP1	9	125772734	Frame_Shift_Del	DEL	TTCAG	TCGA-EV-5902-01A-11D-1589-08	8935438	125772734	15440697	46	9580											
ZER1	10444	hgsc.bcm.edu	37	chr9	131515779	131515779	+	Frame_Shift_Del	DEL	A	A	-																															agaaaatgtttgtacagccgAagaggctcaaggacaccagg																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr9:131515779delA	ENST00000291900.2	-	4	816	c.410delT	c.(409-411)ttcfs	p.F137fs	ZER1_ENST00000494461.1_5'UTR	NM_006336.2	NP_006327.2	Q7Z7L7	ZER1_HUMAN	zyg-11 related, cell cycle regulator	137					protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein transferase activity (GO:0051438)	Cul2-RING ubiquitin ligase complex (GO:0031462)	ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	15						TGTACAGCCGAAGAGGCTCAA	0.557																																					p.F137fs		Atlas-INDEL	.											.	ZER1	49	.	0			c.411delC						PASS	.						54	57	56					9																	131515779		2203	4300	6503	SO:0001589	frameshift_variant	10444	exon4			.	X99802	CCDS6910.1	9q33.3	2013-01-17	2012-12-10	2007-01-04	ENSG00000160445	ENSG00000160445		"ZYG11 cell cycle regulator family"	30960	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 60", "zyg-11 homolog B (C. elegans)-like", "zer-1 homolog (C. elegans)"	C9orf60, ZYG11BL		11719588	Standard	NM_006336		Approved	ZYG, Hzyg	uc004bwa.2	Q7Z7L7	OTTHUMG00000020759	ENST00000291900.2:c.410delT	chr9.hg19:g.131515779delA	ENSP00000291900:p.Phe137fs	77.0	0.0	0		57.0	26.0	0.45614	NM_006336	O00156|Q5T272|Q5T273	Frame_Shift_Del	DEL	ENST00000291900.2	hg19	CCDS6910.1																																																																																			.	.	.	none		0.557	ZER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054491.1	NM_006336		-	131515779	A	-	131515779	7	5	162	1	0	1	0	1	0	0	0	0	17637	246	9	0	1942	0	ZER1	9	131515779	Frame_Shift_Del	DEL	A	TCGA-EV-5902-01A-11D-1589-08	5743045	131515779	9697652	47	9581											
TUBB2C	10383	hgsc.bcm.edu	37	chr9	140137389	140137389	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtggggtcaccacctgccTgcgcttcccaggccagctca	6	7	12	16	1	2	0	2	0	0	0	3	1	3	0	5	3	3	2	5	3	0	1			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr9:140137389T>C	ENST00000340384.4	+	4	867	c.719T>C	c.(718-720)cTg>cCg	p.L240P		NM_006088.5	NP_006079.1	P68371	TBB4B_HUMAN	tubulin, beta 4B class IVb	240					'de novo' posttranslational protein folding (GO:0051084)|cellular component movement (GO:0006928)|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)|natural killer cell mediated cytotoxicity (GO:0042267)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|vesicle (GO:0031982)	double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|MHC class I protein binding (GO:0042288)|structural constituent of cytoskeleton (GO:0005200)|unfolded protein binding (GO:0051082)									Albendazole(DB00518)|Mebendazole(DB00643)	ACCACCTGCCTGCGCTTCCCA	0.592																																					p.L240P		Atlas-SNP	.											.	.	.	.	0			c.T719C						PASS	.						30	31	31					9																	140137389		2200	4290	6490	SO:0001583	missense	10383	exon4			CCTGCCTGCGCTT	BC019359	CCDS7039.1	9q34.3	2011-10-10	2011-10-10	2011-10-10	ENSG00000188229	ENSG00000188229		"Tubulins"	20771	protein-coding gene	gene with protein product	"class IVb beta-tubulin"	602660	"tubulin, beta 2C"	TUBB2C		3999141	Standard	NM_006088		Approved	Beta2	uc004cmh.1	P68371	OTTHUMG00000131783	ENST00000340384.4:c.719T>C	chr9.hg19:g.140137389T>C	ENSP00000341289:p.Leu240Pro	42.0	0.0	.		52.0	24.0	.	NM_006088	A2BFA2|P05217	Missense_Mutation	SNP	ENST00000340384.4	hg19	CCDS7039.1	.	.	.	.	.	.	.	.	.	.	T	16.11	3.029097	0.54790	.	.	ENSG00000188229	ENST00000340384	T	0.71934	-0.61	5.57	5.57	0.84162	.	0.000000	0.53938	D	0.000043	D	0.91955	0.7452	H	0.99919	4.95	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.95434	0.8519	10	0.87932	D	0	.	14.5794	0.68274	0.0:0.0:0.0:1.0	.	240	P68371	TBB4B_HUMAN	P	240	ENSP00000341289:L240P	ENSP00000341289:L240P	L	+	2	0	TUBB2C	139257210	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.111000	0.71541	2.122000	0.65172	0.533000	0.62120	CTG	.	.	.	none		0.592	TUBB4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254715.1	NM_006088		C	140137389	T	C	140137389	3	2	162	1	0	0	0	0	1	0	0	0	16768	1580	55	3	733	3	TUBB2C	9	140137389	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08	8621610	140137389	1076042	48	9582											
ABLIM1	3983	hgsc.bcm.edu	37	chr10	116225561	116225561	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctcgtggaccgatggatcAtccgatcccgaacatcctgg	8	8	12	13	4	1	0	1	0	0	0	5	5	4	2	4	4	1	1	4	4	1	0			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr10:116225561A>G	ENST00000277895.5	-	12	1434	c.1337T>C	c.(1336-1338)aTg>aCg	p.M446T	ABLIM1_ENST00000392952.3_Missense_Mutation_p.M158T|ABLIM1_ENST00000369266.3_Missense_Mutation_p.M158T|ABLIM1_ENST00000533213.2_Missense_Mutation_p.M386T|ABLIM1_ENST00000369252.4_Missense_Mutation_p.M386T|ABLIM1_ENST00000369253.2_Missense_Mutation_p.M104T	NM_002313.5	NP_002304.3	O14639	ABLM1_HUMAN	actin binding LIM protein 1	446					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)		CCGATGGATCATCCGATCCCG	0.557																																					p.M446T		Atlas-SNP	.											.	ABLIM1	131	.	0			c.T1337C						PASS	.						215	192	200					10																	116225561		2203	4300	6503	SO:0001583	missense	3983	exon12			TGGATCATCCGAT	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.1337T>C	chr10.hg19:g.116225561A>G	ENSP00000277895:p.Met446Thr	178.0	0.0	.		174.0	88.0	.	NM_002313	A6NI16|A6NJ06|A8MXA9|B3KVH2|Q15039|Q5JVV1|Q5JVV2|Q5T6N2|Q5T6N3|Q5T6N5|Q68CQ9|Q9BUP1	Missense_Mutation	SNP	ENST00000277895.5	hg19	CCDS7590.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.82|10.82	1.459451|1.459451	0.26248|0.26248	.|.	.|.	ENSG00000099204|ENSG00000099204	ENST00000336585;ENST00000369252;ENST00000392952;ENST00000369257;ENST00000369267;ENST00000533213;ENST00000369262;ENST00000369263;ENST00000369266;ENST00000369256;ENST00000369260;ENST00000277895;ENST00000369253;ENST00000440467;ENST00000428430|ENST00000392955	T;T;T;T;T;T|.	0.54866|.	0.55;0.55;0.55;0.55;0.55;0.55|.	5.41|5.41	5.41|5.41	0.78517|0.78517	.|.	0.318695|.	0.42548|.	D|.	0.000696|.	T|.	0.38295|.	0.1035|.	N|N	0.08118|0.08118	0|0	0.36815|0.36815	D|D	0.88611|0.88611	B;B;B;B;B;B;B;B;B|.	0.15930|.	0.0;0.002;0.015;0.0;0.0;0.001;0.001;0.0;0.002|.	B;B;B;B;B;B;B;B;B|.	0.22386|.	0.002;0.005;0.039;0.002;0.001;0.004;0.003;0.001;0.009|.	T|.	0.45745|.	-0.9240|.	10|.	0.15499|.	T|.	0.54|.	.|.	14.3083|14.3083	0.66397|0.66397	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	370;130;386;414;446;158;414;370;104|.	B7Z4H1;B4DQA3;F8W8M4;A6NKJ2;O14639;O14639-5;B3KVH2;C9K0X4;O14639-4|.	.;.;.;.;ABLM1_HUMAN;.;.;.;.|.	T|R	446;386;158;104;414;386;474;370;158;370;370;474;158;111;130|355	ENSP00000358256:M386T;ENSP00000376679:M158T;ENSP00000433629:M386T;ENSP00000358270:M158T;ENSP00000414154:M111T;ENSP00000400934:M130T|.	ENSP00000277895:M474T|.	M|X	-|-	2|1	0|0	ABLIM1|ABLIM1	116215551|116215551	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	6.016000|6.016000	0.70798|0.70798	2.185000|2.185000	0.69588|0.69588	0.528000|0.528000	0.53228|0.53228	ATG|TGA	.	.	.	none		0.557	ABLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050469.3			G	116225561	A	G	116225561	3	3	162	1	0	0	0	0	1	0	0	0	94	217	8	3	1043	3	ABLIM1	10	116225561	Missense_Mutation	SNP	A	TCGA-EV-5902-01A-11D-1589-08		116225561	19309186	49	9583											
TRIM22	10346	hgsc.bcm.edu	37	chr11	5717510	5717510	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagaaggaggtgacctgcccCatctgcctggagctcctgac	8	7	13	13	0	1	3	0	2	1	1	2	6	2	5	5	3	3	1	5	3	1	0			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr11:5717510C>T	ENST00000379965.3	+	2	325	c.48C>T	c.(46-48)ccC>ccT	p.P16P	TRIM5_ENST00000380027.1_Intron	NM_001199573.1|NM_006074.4	NP_001186502.1|NP_006065.2	Q8IYM9	TRI22_HUMAN	tripartite motif containing 22	16					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)		TGACCTGCCCCATCTGCCTGG	0.502																																					p.P16P	GBM(104;491 2336 5222)	Atlas-SNP	.											.	TRIM22	66	.	0			c.C48T						PASS	.						87	92	90					11																	5717510		2201	4297	6498	SO:0001819	synonymous_variant	10346	exon2			CTGCCCCATCTGC	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.48C>T	chr11.hg19:g.5717510C>T		66.0	0.0	.		72.0	40.0	.	NM_001199573	Q05CQ0|Q15521	Silent	SNP	ENST00000379965.3	hg19	CCDS41612.1																																																																																			.	.	.	none		0.502	TRIM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143387.2	NM_006074		T	5717510	C	T	5717510	2	4	162	1	0	0	0	0	0	0	0	1	16508	581	21	2		2	TRIM22	11	5717510	Silent	SNP	C	TCGA-EV-5902-01A-11D-1589-08		5717510	129289006	50	9584											
OR2AT4	341152	hgsc.bcm.edu	37	chr11	74800733	74800733	+	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	agacgggtgagccatccactGattcattacaggctgtggca	10	9	12	10	1	1	3	1	2	0	1	2	3	2	3	2	3	2	2	2	3	1	2			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr11:74800733G>A	ENST00000305159.3	-	1	66	c.26C>T	c.(25-27)tCa>tTa	p.S9L		NM_001005285.1	NP_001005285.1	A6NND4	O2AT4_HUMAN	olfactory receptor, family 2, subfamily AT, member 4	9						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(2)	12						GCCATCCACTGATTCATTACA	0.473																																					p.S9L		Atlas-SNP	.											.	OR2AT4	32	.	0			c.C26T						PASS	.						50	52	51					11																	74800733		2200	4292	6492	SO:0001583	missense	341152	exon1			TCCACTGATTCAT	BK004820	CCDS31639.1	11q13.4	2012-08-09			ENSG00000171561	ENSG00000171561		"GPCR / Class A : Olfactory receptors"	19620	protein-coding gene	gene with protein product							Standard	NM_001005285		Approved		uc010rro.2	A6NND4	OTTHUMG00000165370	ENST00000305159.3:c.26C>T	chr11.hg19:g.74800733G>A	ENSP00000304846:p.Ser9Leu	88.0	0.0	.		89.0	43.0	.	NM_001005285	B9EGZ8	Missense_Mutation	SNP	ENST00000305159.3	hg19	CCDS31639.1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.970843	0.53614	.	.	ENSG00000171561	ENST00000305159	T	0.54675	0.56	4.58	4.58	0.56647	.	0.000000	0.28241	U	0.016072	T	0.31702	0.0805	N	0.08118	0	0.36873	D	0.88902	P	0.49783	0.928	B	0.37601	0.254	T	0.51903	-0.8646	10	0.87932	D	0	.	15.2827	0.73801	0.0:0.0:1.0:0.0	.	9	A6NND4	O2AT4_HUMAN	L	9	ENSP00000304846:S9L	ENSP00000304846:S9L	S	-	2	0	OR2AT4	74478381	0.991000	0.36638	0.999000	0.59377	0.919000	0.55068	2.954000	0.49113	2.533000	0.85409	0.462000	0.41574	TCA	.	.	.	none		0.473	OR2AT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383734.1	NM_001005285		A	74800733	G	A	74800733	3	1	162	1	0	0	0	0	1	0	0	0	10994	1294	45	2	939	2	OR2AT4	11	74800733	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08	69083223	74800733	60205783	51	9585											
MYO7A	4647	hgsc.bcm.edu	37	chr11	76867021	76867021	+	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	tccatctactcgccagagcaCatccgccagtataccaacaa	13	7	5	16	2	1	1	0	0	1	1	4	1	3	1	5	0	4	2	5	0	5	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr11:76867021C>T	ENST00000409709.3	+	5	626	c.354C>T	c.(352-354)caC>caT	p.H118H	MYO7A_ENST00000409893.1_Silent_p.H118H|MYO7A_ENST00000458637.2_Silent_p.H118H|MYO7A_ENST00000409619.2_Silent_p.H107H	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	118	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						CGCCAGAGCACATCCGCCAGT	0.562																																					p.H118H		Atlas-SNP	.											.	MYO7A	164	.	0			c.C354T						PASS	.						35	39	38					11																	76867021		2139	4251	6390	SO:0001819	synonymous_variant	4647	exon5			AGAGCACATCCGC	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.354C>T	chr11.hg19:g.76867021C>T		28.0	0.0	.		13.0	9.0	.	NM_001127179	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Silent	SNP	ENST00000409709.3	hg19	CCDS53683.1																																																																																			.	.	.	none		0.562	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		T	76867021	C	T	76867021	2	4	162	1	0	0	0	0	0	0	0	1	10089	477	17	2		2	MYO7A	11	76867021	Silent	SNP	C	TCGA-EV-5902-01A-11D-1589-08	2066288	76867021	58139495	52	9586											
CEP164	22897	hgsc.bcm.edu	37	chr11	117222658	117222658	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taagaagaagaaaaaaaaaaAggaaaagaaagacaagaagg	29	1	10	1	0	0	6	0	0	0	6	0	7	0	7	0	2	0	0	0	2	13	1			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr11:117222658A>G	ENST00000278935.3	+	5	494	c.347A>G	c.(346-348)aAg>aGg	p.K116R		NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	116	Interaction with ATRIP.|Lys-rich.				cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		aaaaaaaaaaaggaaaagaaa	0.502																																					p.K116R		Atlas-SNP	.											CEP164,caecum,carcinoma,0,1	CEP164	121	.	0			c.A347G						PASS	.						33	34	34					11																	117222658		2201	4296	6497	SO:0001583	missense	22897	exon4			AAAAAAAGGAAAA	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.347A>G	chr11.hg19:g.117222658A>G	ENSP00000278935:p.Lys116Arg	32.0	1.0	.		41.0	2.0	.	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	hg19	CCDS31683.1	.	.	.	.	.	.	.	.	.	.	A	15.14	2.744661	0.49151	.	.	ENSG00000110274	ENST00000533153;ENST00000278935;ENST00000525416;ENST00000545330;ENST00000533570;ENST00000529538	T;T;T;T	0.76060	-0.34;-0.03;-0.29;-0.99	5.95	4.82	0.62117	.	0.243999	0.29172	N	0.012934	T	0.80221	0.4583	M	0.62723	1.935	0.34770	D	0.733632	D;P;B;D	0.56521	0.959;0.482;0.023;0.976	P;B;B;P	0.56960	0.65;0.11;0.01;0.81	D	0.85776	0.1358	10	0.62326	D	0.03	-27.2573	11.2799	0.49188	0.9276:0.0:0.0724:0.0	.	116;70;116;116	E9PI34;B7Z884;Q9UPV0;Q9UPV0-2	.;.;CE164_HUMAN;.	R	70;116;70;70;116;116	ENSP00000436034:K70R;ENSP00000278935:K116R;ENSP00000435759:K70R;ENSP00000431302:K116R	ENSP00000278935:K116R	K	+	2	0	CEP164	116727868	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	8.713000	0.91408	1.068000	0.40764	0.533000	0.62120	AAG	.	.	.	none		0.502	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956		G	117222658	A	G	117222658	3	3	162	1	0	0	0	0	1	0	0	0	3251	72	3	3	357	3	CEP164	11	117222658	Missense_Mutation	SNP	A	TCGA-EV-5902-01A-11D-1589-08	40355637	117222658	17783858	53	9587											
C12orf26	84190	hgsc.bcm.edu	37	chr12	82752495	82752495	+	Missense_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	aatccgtgtgggaggagctgGtcgacttgccaccggagaca	9	7	15	10	3	0	1	0	0	0	1	2	5	1	3	3	4	2	1	3	4	1	1			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr12:82752495G>A	ENST00000248306.3	+	1	220	c.151G>A	c.(151-153)Gtc>Atc	p.V51I	METTL25_ENST00000547357.1_3'UTR|CCDC59_ENST00000548126.1_5'UTR|CCDC59_ENST00000256151.7_5'UTR	NM_032230.2	NP_115606.2	Q8N6Q8	MET25_HUMAN	methyltransferase like 25	51							methyltransferase activity (GO:0008168)										GGAGGAGCTGGTCGACTTGCC	0.602											OREG0022008	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V51I		Atlas-SNP	.											.	.	.	.	0			c.G151A						PASS	.						94	79	84					12																	82752495		2203	4300	6503	SO:0001583	missense	84190	exon1			GAGCTGGTCGACT	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.151G>A	chr12.hg19:g.82752495G>A	ENSP00000248306:p.Val51Ile	83.0	0.0	.	1216	103.0	39.0	.	NM_032230	Q9H5Y3	Missense_Mutation	SNP	ENST00000248306.3	hg19	CCDS9024.1	.	.	.	.	.	.	.	.	.	.	G	14.10	2.434382	0.43224	.	.	ENSG00000127720	ENST00000248306;ENST00000548200	T	0.36340	1.26	5.49	1.42	0.22433	.	0.278728	0.40222	N	0.001147	T	0.25494	0.0620	L	0.44542	1.39	0.26395	N	0.976518	B	0.13145	0.007	B	0.15052	0.012	T	0.15378	-1.0439	10	0.29301	T	0.29	-2.0635	7.0129	0.24873	0.2126:0.1248:0.6626:0.0	.	51	Q8N6Q8	CL026_HUMAN	I	51	ENSP00000248306:V51I	ENSP00000248306:V51I	V	+	1	0	C12orf26	81276626	0.991000	0.36638	0.064000	0.19789	0.869000	0.49853	0.289000	0.18957	0.294000	0.22547	0.650000	0.86243	GTC	.	.	.	none		0.602	METTL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408192.1	NM_032230		A	82752495	G	A	82752495	3	1	162	1	0	0	0	0	1	0	0	0	1681	1261	44	2	153	2	C12orf26	12	82752495	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08		82752495	51099400	54	9588											
C13orf23	80209	hgsc.bcm.edu	37	chr13	39587414	39587414	+	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	gctggagagacctgacaatgCaggattaaggcaagcagata	15	6	13	7	0	0	3	0	1	0	2	0	6	0	5	1	3	2	4	1	3	4	2			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr13:39587414C>A	ENST00000352251.3	-	11	2808	c.1975G>T	c.(1975-1977)Gca>Tca	p.A659S	PROSER1_ENST00000484434.3_Intron|PROSER1_ENST00000350125.3_Missense_Mutation_p.A637S	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	659	Ser-rich.																CCTGACAATGCAGGATTAAGG	0.478																																					p.A659S		Atlas-SNP	.											.	.	.	.	0			c.G1975T						PASS	.						131	122	125					13																	39587414		2203	4300	6503	SO:0001583	missense	80209	exon11			ACAATGCAGGATT	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.1975G>T	chr13.hg19:g.39587414C>A	ENSP00000332034:p.Ala659Ser	151.0	0.0	.		99.0	50.0	.	NM_025138	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Missense_Mutation	SNP	ENST00000352251.3	hg19	CCDS9368.2	.	.	.	.	.	.	.	.	.	.	C	10.07	1.248685	0.22880	.	.	ENSG00000120685	ENST00000352251;ENST00000350125	T;T	0.47528	0.84;0.84	5.27	2.55	0.30701	.	.	.	.	.	T	0.32793	0.0841	L	0.29908	0.895	0.09310	N	1	P;P	0.45531	0.86;0.775	B;B	0.38264	0.269;0.197	T	0.05971	-1.0853	8	.	.	.	-13.5541	10.4949	0.44772	0.0:0.7738:0.0:0.2262	.	637;659	A6NJ97;Q86XN7	.;PRSR1_HUMAN	S	659;637	ENSP00000332034:A659S;ENSP00000339123:A637S	.	A	-	1	0	PROSER1	38485414	0.982000	0.34865	0.377000	0.26055	0.533000	0.34776	2.976000	0.49289	0.711000	0.32018	0.561000	0.74099	GCA	.	.	.	none		0.478	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138		A	39587414	C	A	39587414	3	1	162	1	0	0	0	0	1	0	0	0	1723	710	25	4	871	4	C13orf23	13	39587414	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08		39587414	75582464	55	9589											
ZC3H13	23091	hgsc.bcm.edu	37	chr13	46543501	46543502	+	Frame_Shift_Ins	INS	-	-	T																															tcactgaatgctgtatcttcINSttttttctgggagtcctcta																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr13:46543501_46543502insT	ENST00000242848.4	-	14	3525_3526	c.3177_3178insA	c.(3175-3180)aaagaafs	p.E1060fs	ZC3H13_ENST00000282007.3_Frame_Shift_Ins_p.E1060fs|ZC3H13_ENST00000378921.2_Frame_Shift_Ins_p.E16fs			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	1060							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)		GCTGTATCTTCTTTTTTCTGGG	0.475																																					p.E1060fs	Esophageal Squamous(187;747 2077 11056 31291 44172)	Atlas-INDEL	.											.	ZC3H13	197	.	0			c.3178_3179insA						PASS	.																																			SO:0001589	frameshift_variant	23091	exon14			.	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.3178dupA	chr13.hg19:g.46543507_46543507dupT	ENSP00000242848:p.Glu1060fs	169.0	0.0	0		207.0	22.0	0.10628	NM_015070	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Frame_Shift_Ins	INS	ENST00000242848.4	hg19																																																																																				.	.	.	none		0.475	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070		T	46543502	-	T	46543501	7	5	162	1	0	1	1	0	0	0	0	0	17577	922	32	0	1532	0	ZC3H13	13	46543501	Frame_Shift_Ins	INS	-	TCGA-EV-5902-01A-11D-1589-08	6956087	46543501	68626377	56	9590											
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77799654	77799654	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggagggtatgttgtgatttTgcttgcatccttttcgcctc	4	18	11	8	1	0	1	0	1	0	0	3	2	1	2	2	2	2	4	2	2	1	7			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr13:77799654T>C	ENST00000544440.2	-	19	2676	c.2659A>G	c.(2659-2661)Aaa>Gaa	p.K887E	MYCBP2_ENST00000357337.6_Missense_Mutation_p.K887E|MYCBP2_ENST00000407578.2_Missense_Mutation_p.K925E|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)		GTTGTGATTTTGCTTGCATCC	0.413																																					p.K925E		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.A2773G						PASS	.						215	181	192					13																	77799654		2203	4300	6503	SO:0001583	missense	23077	exon19			TGATTTTGCTTGC	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.2659A>G	chr13.hg19:g.77799654T>C	ENSP00000444596:p.Lys887Glu	152.0	0.0	.		146.0	65.0	.	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	hg19		.	.	.	.	.	.	.	.	.	.	T	21.8	4.197089	0.79015	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	T;T;T	0.28666	1.61;1.6;1.61	5.96	5.96	0.96718	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	D	0.000000	T	0.45034	0.1322	L	0.34521	1.04	0.58432	D	0.999998	P	0.52842	0.956	D	0.65010	0.931	T	0.38156	-0.9674	10	0.66056	D	0.02	.	16.4381	0.83884	0.0:0.0:0.0:1.0	.	887	O75592	MYCB2_HUMAN	E	887;925;887	ENSP00000349892:K887E;ENSP00000384288:K925E;ENSP00000444596:K887E	ENSP00000349892:K887E	K	-	1	0	MYCBP2	76697655	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.679000	0.84048	2.280000	0.76307	0.533000	0.62120	AAA	.	.	.	none		0.413	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		C	77799654	T	C	77799654	3	2	162	1	0	0	0	0	1	0	0	0	10025	1821	63	3	11523	3	MYCBP2	13	77799654	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08	31256153	77799654	37370224	57	9591											
IRF9	10379	hgsc.bcm.edu	37	chr14	24632332	24632332	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagccctacaaggtgtatcAgttgctgccaccaggaatcg	10	9	11	11	1	1	1	1	1	0	0	2	2	1	2	3	2	4	3	3	2	4	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr14:24632332A>G	ENST00000396864.3	+	3	625	c.338A>G	c.(337-339)cAg>cGg	p.Q113R	RP11-468E2.4_ENST00000558468.1_3'UTR|IRF9_ENST00000557894.1_Missense_Mutation_p.Q11R	NM_006084.4	NP_006075.3	Q00978	IRF9_HUMAN	interferon regulatory factor 9	113					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|skin(2)	16				GBM - Glioblastoma multiforme(265;0.00853)		AAGGTGTATCAGTTGCTGCCA	0.547																																					p.Q113R		Atlas-SNP	.											.	IRF9	33	.	0			c.A338G						PASS	.						105	102	103					14																	24632332		2203	4300	6503	SO:0001583	missense	10379	exon3			TGTATCAGTTGCT	M87503	CCDS9615.1	14q11.2	2007-07-06	2007-07-06	2007-07-06	ENSG00000213928	ENSG00000213928			6131	protein-coding gene	gene with protein product		147574	"interferon-stimulated transcription factor 3, gamma (48kD)", "interferon-stimulated transcription factor 3, gamma 48kDa"	ISGF3G		1630447, 10199920	Standard	NM_006084		Approved		uc001wmq.3	Q00978	OTTHUMG00000028799	ENST00000396864.3:c.338A>G	chr14.hg19:g.24632332A>G	ENSP00000380073:p.Gln113Arg	125.0	0.0	.		117.0	5.0	.	NM_006084	D3DS61	Missense_Mutation	SNP	ENST00000396864.3	hg19	CCDS9615.1	.	.	.	.	.	.	.	.	.	.	a	2.120	-0.401642	0.04865	.	.	ENSG00000213928	ENST00000396864;ENST00000324076	D;D	0.97505	-4.32;-4.41	5.17	4.29	0.51040	Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (3);	0.000000	0.64402	N	0.000009	D	0.84442	0.5473	N	0.00358	-1.6	0.36264	D	0.854711	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.82151	-0.0599	10	0.02654	T	1	-15.5634	12.9684	0.58499	0.0804:0.0:0.9196:0.0	.	113;113	B4DI86;Q00978	.;IRF9_HUMAN	R	113;43	ENSP00000380073:Q113R;ENSP00000313529:Q43R	ENSP00000313529:Q43R	Q	+	2	0	IRF9	23702172	1.000000	0.71417	0.991000	0.47740	0.262000	0.26303	3.274000	0.51631	1.184000	0.42957	-0.146000	0.13790	CAG	.	.	.	none		0.547	IRF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071927.2			G	24632332	A	G	24632332	3	3	162	1	0	0	0	0	1	0	0	0	7844	188	7	3	344	3	IRF9	14	24632332	Missense_Mutation	SNP	A	TCGA-EV-5902-01A-11D-1589-08		24632332	82717208	58	9592											
MBIP	51562	hgsc.bcm.edu	37	chr14	36770005	36770006	+	Frame_Shift_Ins	INS	-	-	T																															cttacttgaggtggttgaacINSttttcttctttttccagaaa																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr14:36770005_36770006insT	ENST00000416007.4	-	8	999_1000	c.912_913insA	c.(910-915)aaagttfs	p.V305fs	MBIP_ENST00000318473.7_Frame_Shift_Ins_p.V305fs|MBIP_ENST00000359527.7_Frame_Shift_Ins_p.S272fs	NM_001144891.1|NM_016586.2	NP_001138363.1|NP_057670.2	Q9NS73	MBIP1_HUMAN	MAP3K12 binding inhibitory protein 1	305	Interaction with MAP3K12.				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)		GGTGGTTGAACTTTTCTTCTTT	0.243																																					p.V305fs		Atlas-INDEL	.											.	MBIP	25	.	0			c.913_914insA						PASS	.																																			SO:0001589	frameshift_variant	51562	exon8			.	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.913dupA	chr14.hg19:g.36770009_36770009dupT	ENSP00000399718:p.Val305fs	36.0	0.0	0		21.0	11.0	0.52381	NM_016586	Q86TZ2|Q96AS5|Q9BS93|Q9NZE1	Frame_Shift_Ins	INS	ENST00000416007.4	hg19	CCDS9658.1																																																																																			.	.	.	none		0.243	MBIP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276685.2	NM_016586		T	36770006	-	T	36770005	7	5	162	1	0	1	1	0	0	0	0	0	9356	565	20	0	129	0	MBIP	14	36770005	Frame_Shift_Ins	INS	-	TCGA-EV-5902-01A-11D-1589-08	12137673	36770005	70579535	59	9593											
FERMT2	10979	hgsc.bcm.edu	37	chr14	53360052	53360052	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccctctaattcaagtgccTcatcttcagactggtcatct	8	13	6	14	0	7	1	4	0	3	1	7	1	7	1	3	1	1	0	3	1	2	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr14:53360052T>C	ENST00000395631.2	-	4	701	c.485A>G	c.(484-486)gAg>gGg	p.E162G	FERMT2_ENST00000341590.3_Missense_Mutation_p.E162G|FERMT2_ENST00000553373.1_Missense_Mutation_p.E162G|FERMT2_ENST00000343279.4_Missense_Mutation_p.E162G|FERMT2_ENST00000399304.3_Missense_Mutation_p.E162G			Q96AC1	FERM2_HUMAN	fermitin family member 2	162					cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|focal adhesion assembly (GO:0048041)|integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|protein localization to membrane (GO:0072657)|regulation of cell shape (GO:0008360)|substrate adhesion-dependent cell spreading (GO:0034446)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|stress fiber (GO:0001725)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)		ERO1L/FERMT2(2)	NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	20	Breast(41;0.0342)					TTCAAGTGCCTCATCTTCAGA	0.413																																					p.E162G		Atlas-SNP	.											.	FERMT2	59	.	0			c.A485G						PASS	.						137	135	136					14																	53360052		2203	4300	6503	SO:0001583	missense	10979	exon4			AGTGCCTCATCTT	Z24725	CCDS9713.1, CCDS45107.1, CCDS45108.1	14q22.1	2013-01-10	2010-06-24	2007-12-14	ENSG00000073712	ENSG00000073712		"Fermitins", "Pleckstrin homology (PH) domain containing"	15767	protein-coding gene	gene with protein product	"kindlin-2"	607746	"pleckstrin homology domain containing, family C (with FERM domain) member 1", "fermitin family homolog 2 (Drosophila)"	PLEKHC1		8175911, 12697302	Standard	NM_006832		Approved	mig-2, KIND2, UNC112B	uc001xac.3	Q96AC1	OTTHUMG00000140309	ENST00000395631.2:c.485A>G	chr14.hg19:g.53360052T>C	ENSP00000378993:p.Glu162Gly	192.0	0.0	.		177.0	72.0	.	NM_001135000	B5TJY2|Q14840|Q86TY7	Missense_Mutation	SNP	ENST00000395631.2	hg19	CCDS9713.1	.	.	.	.	.	.	.	.	.	.	T	14.38	2.518696	0.44763	.	.	ENSG00000073712	ENST00000395631;ENST00000341590;ENST00000554152;ENST00000343279;ENST00000553373;ENST00000399304;ENST00000554288;ENST00000555692	T;T;T;T;T;T;T	0.48201	0.82;0.82;0.84;0.82;0.82;0.82;1.41	5.77	5.77	0.91146	FERM, N-terminal (1);Band 4.1 domain (1);	0.051253	0.85682	D	0.000000	T	0.36082	0.0954	N	0.14661	0.345	0.51482	D	0.999927	B;B;B	0.26602	0.043;0.154;0.01	B;B;B	0.34038	0.087;0.174;0.099	T	0.18618	-1.0331	10	0.24483	T	0.36	.	16.0828	0.81017	0.0:0.0:0.0:1.0	.	162;162;162	Q96AC1-2;Q96AC1;B5TJY2	.;FERM2_HUMAN;.	G	162;162;104;162;162;162;57;118	ENSP00000378993:E162G;ENSP00000340391:E162G;ENSP00000450741:E104G;ENSP00000342858:E162G;ENSP00000451084:E162G;ENSP00000382243:E162G;ENSP00000451268:E57G	ENSP00000340391:E162G	E	-	2	0	FERMT2	52429802	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	5.957000	0.70323	2.199000	0.70637	0.528000	0.53228	GAG	.	.	.	none		0.413	FERMT2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276907.2	NM_006832		C	53360052	T	C	53360052	3	2	162	1	0	0	0	0	1	0	0	0	5825	1551	54	3	1642	3	FERMT2	14	53360052	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08	16590047	53360052	53989488	60	9594											
CRAMP1L	57585	hgsc.bcm.edu	37	chr16	1718163	1718163	+	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	acacacattagcgactccatCattgagatcgccatcagctc	12	9	6	14	2	2	1	2	1	0	1	5	3	3	1	2	0	2	1	2	0	1	2			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr16:1718163C>T	ENST00000397412.3	+	18	3402	c.3303C>T	c.(3301-3303)atC>atT	p.I1101I	CRAMP1L_ENST00000436138.3_Silent_p.I1098I|CRAMP1L_ENST00000293925.5_Silent_p.I1101I|CRAMP1L_ENST00000262317.4_Silent_p.I479I|LA16c-431H6.6_ENST00000454337.1_3'UTR			Q96RY5	CRML_HUMAN	Crm, cramped-like (Drosophila)	1101	Ser-rich.					nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(6)|pancreas(1)	22						GCGACTCCATCATTGAGATCG	0.607																																					p.I1101I		Atlas-SNP	.											.	CRAMP1L	60	.	0			c.C3303T						PASS	.						64	65	65					16																	1718163		2165	4268	6433	SO:0001819	synonymous_variant	57585	exon17			CTCCATCATTGAG	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.3303C>T	chr16.hg19:g.1718163C>T		102.0	0.0	.		129.0	36.0	.	NM_020825	A8MZL1|B1AJY1|Q8NDN1|Q9P2C1	Silent	SNP	ENST00000397412.3	hg19	CCDS10440.2																																																																																			.	.	.	none		0.607	CRAMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157297.4			T	1718163	C	T	1718163	2	4	162	1	0	0	0	0	0	0	0	1	3848	816	29	2		2	CRAMP1L	16	1718163	Silent	SNP	C	TCGA-EV-5902-01A-11D-1589-08		1718163	88636590	61	9595											
RPGRIP1L	23322	hgsc.bcm.edu	37	chr16	53636027	53636027	+	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	ctgtattgcttgtagacagaCtggagggcatggagagcttc	9	11	14	7	0	0	3	0	0	0	3	1	5	0	4	0	3	2	5	0	3	2	5			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr16:53636027C>A	ENST00000379925.3	-	27	3959	c.3909G>T	c.(3907-3909)caG>caT	p.Q1303H	RPGRIP1L_ENST00000262135.4_Missense_Mutation_p.Q1223H|RPGRIP1L_ENST00000563746.1_Missense_Mutation_p.Q1269H	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	1303					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)				TGTAGACAGACTGGAGGGCAT	0.468																																					p.Q1303H		Atlas-SNP	.											.	RPGRIP1L	118	.	0			c.G3909T						PASS	.						115	94	101					16																	53636027		2198	4300	6498	SO:0001583	missense	23322	exon27			GACAGACTGGAGG		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.3909G>T	chr16.hg19:g.53636027C>A	ENSP00000369257:p.Gln1303His	89.0	0.0	.		107.0	72.0	.	NM_015272	A0PJ88|Q9Y2K8	Missense_Mutation	SNP	ENST00000379925.3	hg19	CCDS32447.1	.	.	.	.	.	.	.	.	.	.	C	0.956	-0.704864	0.03255	.	.	ENSG00000103494	ENST00000379925;ENST00000262135	T;T	0.63913	-0.07;-0.07	5.86	2.79	0.32731	.	0.807726	0.11522	N	0.555606	T	0.33527	0.0866	N	0.08118	0	0.80722	D	1	B;P;P	0.38250	0.13;0.49;0.624	B;B;B	0.31812	0.136;0.136;0.129	T	0.14671	-1.0464	10	0.46703	T	0.11	-0.5926	2.457	0.04532	0.1189:0.437:0.269:0.175	.	1257;1303;1223	B7ZKJ9;Q68CZ1;Q68CZ1-2	.;FTM_HUMAN;.	H	1303;1223	ENSP00000369257:Q1303H;ENSP00000262135:Q1223H	ENSP00000262135:Q1223H	Q	-	3	2	RPGRIP1L	52193528	0.184000	0.23200	0.813000	0.32504	0.392000	0.30506	0.388000	0.20735	0.840000	0.34995	-0.142000	0.14014	CAG	.	.	.	none		0.468	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272		A	53636027	C	A	53636027	3	1	162	1	0	0	0	0	1	0	0	0	13563	564	20	4	42	4	RPGRIP1L	16	53636027	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08	51917864	53636027	36718726	62	9596											
ELMO3	79767	hgsc.bcm.edu	37	chr16	67236330	67236330	+	Missense_Mutation	SNP	T	T	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	agcccaggacttctcacccaTgttcttcggccaagaccaga	10	8	8	15	1	2	2	1	0	2	2	4	3	2	3	4	2	1	1	4	2	1	3			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr16:67236330T>G	ENST00000360833.1	+	13	1457	c.1400T>G	c.(1399-1401)aTg>aGg	p.M467R	ELMO3_ENST00000393997.2_Missense_Mutation_p.M484R|MIR328_ENST00000385213.1_RNA|ELMO3_ENST00000477898.1_Missense_Mutation_p.M318R			Q96BJ8	ELMO3_HUMAN	engulfment and cell motility 3	431	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				apoptotic process (GO:0006915)|phagocytosis (GO:0006909)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				cervix(2)|kidney(4)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	18		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00067)|Epithelial(162;0.00442)|all cancers(182;0.0417)		TTCTCACCCATGTTCTTCGGC	0.597																																					p.M484R		Atlas-SNP	.											.	ELMO3	41	.	0			c.T1451G						PASS	.						84	86	85					16																	67236330		2198	4300	6498	SO:0001583	missense	79767	exon14			CACCCATGTTCTT		CCDS10833.2	16q22.1	2010-03-18	2006-01-20		ENSG00000102890	ENSG00000102890		"Engulfment and cell motility proteins"	17289	protein-coding gene	gene with protein product		606422	"engulfment and cell motility 3 (ced-12 homolog, C. elegans)"			11595183	Standard	NM_024712		Approved	FLJ13824, CED12, ELMO-3, CED-12	uc002esa.3	Q96BJ8	OTTHUMG00000133570	ENST00000360833.1:c.1400T>G	chr16.hg19:g.67236330T>G	ENSP00000354077:p.Met467Arg	203.0	0.0	.		239.0	22.0	.	NM_024712	B4DV86|Q9H8A5	Missense_Mutation	SNP	ENST00000360833.1	hg19		.	.	.	.	.	.	.	.	.	.	T	17.46	3.395742	0.62177	.	.	ENSG00000102890	ENST00000360833;ENST00000393997	T;T	0.29397	1.57;1.57	5.66	5.66	0.87406	Engulfment/cell motility, ELMO (2);	0.165679	0.64402	D	0.000003	T	0.42131	0.1189	M	0.67397	2.05	0.80722	D	1	P;D;D	0.55172	0.822;0.97;0.97	P;P;P	0.48552	0.577;0.581;0.581	T	0.44174	-0.9345	10	0.87932	D	0	-28.916	14.7211	0.69308	0.0:0.0:0.0:1.0	.	431;467;484	Q96BJ8;F8W9E7;Q96BJ8-3	ELMO3_HUMAN;.;.	R	467;484	ENSP00000354077:M467R;ENSP00000377566:M484R	ENSP00000354077:M467R	M	+	2	0	ELMO3	65793831	1.000000	0.71417	1.000000	0.80357	0.646000	0.38490	8.040000	0.89188	2.160000	0.67779	0.533000	0.62120	ATG	.	.	.	none		0.597	ELMO3-001	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000257667.2	NM_024712		G	67236330	T	G	67236330	3	3	162	1	0	0	0	0	1	0	0	0	5069	1464	51	5	1505	5	ELMO3	16	67236330	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08	13600303	67236330	23118423	63	9597											
CNTNAP4	85445	hgsc.bcm.edu	37	chr16	76587277	76587278	+	Frame_Shift_Ins	INS	-	-	GC																															gccacgtggcccctctgaagINSgcagctctgcaccccagcca																										TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr16:76587277_76587278insGC	ENST00000476707.1	+	21	3688_3689	c.3549_3550insGC	c.(3550-3552)gcafs	p.A1184fs	CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000307431.8_Frame_Shift_Ins_p.A1180fs|CNTNAP4_ENST00000478060.1_Frame_Shift_Ins_p.A1108fs|RP11-58C22.1_ENST00000563764.1_5'Flank|CNTNAP4_ENST00000377504.4_Frame_Shift_Ins_p.A1132fs			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	1181	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)				breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						CCCCTCTGAAGGCAGCTCTGCA	0.604																																					p.K1107fs		Atlas-INDEL	.											.	CNTNAP4	600	.	0			c.3321_3322insGC						PASS	.																																			SO:0001589	frameshift_variant	85445	exon21			.	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.3550_3551dupGC	chr16.hg19:g.76587278_76587279dupGC	ENSP00000417628:p.Ala1184fs	21.0	0.0	0		43.0	25.0	0.581395	NM_138994	E9PFZ6|Q86YZ7	Frame_Shift_Ins	INS	ENST00000476707.1	hg19																																																																																				.	.	.	none		0.604	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401		GC	76587278	-	GC	76587277	7	5	162	1	0	1	1	0	0	0	0	0	3651	991	35	0	3639	0	CNTNAP4	16	76587277	Frame_Shift_Ins	INS	-	TCGA-EV-5902-01A-11D-1589-08	9350947	76587277	13767476	64	9598											
CDK5RAP3	80279	hgsc.bcm.edu	37	chr17	46051766	46051766	+	Splice_Site	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	gtttttctgttcttactcagGattggcaggagattatagct	8	17	10	6	0	3	1	1	0	2	1	3	3	3	2	0	3	2	4	0	3	3	7			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr17:46051766G>A	ENST00000338399.4	+	5	392	c.286G>A	c.(286-288)Gat>Aat	p.D96N	RP11-6N17.9_ENST00000582262.1_RNA|CDK5RAP3_ENST00000536708.2_Splice_Site_p.D121N	NM_176096.1	NP_788276.1	Q96JB5	CK5P3_HUMAN	CDK5 regulatory subunit associated protein 3	96					brain development (GO:0007420)|protein ufmylation (GO:0071569)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of neuron differentiation (GO:0045664)	membrane (GO:0016020)	protein kinase binding (GO:0019901)			NS(1)|central_nervous_system(2)|cervix(3)|endometrium(3)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	18						TCTTACTCAGGATTGGCAGGA	0.493																																					p.D96N		Atlas-SNP	.											.	CDK5RAP3	38	.	0			c.G286A						PASS	.						171	171	171					17																	46051766		1981	4164	6145	SO:0001630	splice_region_variant	80279	exon5			ACTCAGGATTGGC	AF110322	CCDS42356.1, CCDS62232.1	17q21.2	2008-07-18				ENSG00000108465			18673	protein-coding gene	gene with protein product	"ischemic heart CDK5 activator-binding protein C53", "LXXLL/leucine-zipper-containing ARFbinding protein"	608202				10721722	Standard	NM_176096		Approved	MST016, FLJ13660, C53, IC53, HSF-27, OK/SW-cl.114, LZAP	uc010wlc.3	Q96JB5		ENST00000338399.4:c.286-1G>A	chr17.hg19:g.46051766G>A		143.0	0.0	.		144.0	15.0	.	NM_176096	B7Z6N4|D3DTU1|D3DTU2|F5H3I5|Q53FA2|Q9H3F8|Q9H8G0|Q9HBR9	Missense_Mutation	SNP	ENST00000338399.4	hg19	CCDS42356.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.898300	0.91962	.	.	ENSG00000108465	ENST00000536708;ENST00000338399	T;T	0.54866	0.55;0.55	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.66386	0.2784	M	0.90977	3.165	0.80722	D	1	B	0.31241	0.315	B	0.35312	0.2	T	0.68511	-0.5389	9	.	.	.	-8.6694	18.4593	0.90732	0.0:0.0:1.0:0.0	.	96	Q96JB5	CK5P3_HUMAN	N	121;96	ENSP00000438886:D121N;ENSP00000344683:D96N	.	D	+	1	0	CDK5RAP3	43406765	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.231000	0.95317	2.670000	0.90874	0.655000	0.94253	GAT	.	.	.	none		0.493	CDK5RAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442913.1	NM_176096	Missense_Mutation	A	46051766	G	A	46051766	5	1	162	1	0	0	0	0	0	0	1	0	3149	1188	41	2	304	2	CDK5RAP3	17	46051766	Splice_Site	SNP	G	TCGA-EV-5902-01A-11D-1589-08		46051766	35143444	65	9599											
APPBP2	10513	hgsc.bcm.edu	37	chr17	58525181	58525181	+	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	tagtccactgtagccctcacCaaaaagtttcttccctgtaa	11	12	5	13	0	2	0	1	0	1	0	4	0	4	0	4	0	1	3	4	0	5	5			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr17:58525181C>A	ENST00000083182.3	-	13	1806	c.1519G>T	c.(1519-1521)Ggt>Tgt	p.G507C		NM_001282476.1|NM_006380.2	NP_001269405.1|NP_006371.2	Q92624	APBP2_HUMAN	amyloid beta precursor protein (cytoplasmic tail) binding protein 2	507					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)			TAGCCCTCACCAAAAAGTTTC	0.308																																					p.G507C		Atlas-SNP	.											.	APPBP2	48	.	0			c.G1519T						PASS	.						55	57	56					17																	58525181		2203	4300	6503	SO:0001583	missense	10513	exon13			CCTCACCAAAAAG	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.1519G>T	chr17.hg19:g.58525181C>A	ENSP00000083182:p.Gly507Cys	145.0	0.0	.		149.0	62.0	.	NM_006380	A8K862|O95095|Q8WVC9	Missense_Mutation	SNP	ENST00000083182.3	hg19	CCDS32699.1	.	.	.	.	.	.	.	.	.	.	C	18.38	3.611670	0.66558	.	.	ENSG00000062725	ENST00000083182	D	0.90385	-2.66	5.5	5.5	0.81552	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	D	0.95175	0.8436	M	0.71036	2.16	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.95322	0.8421	10	0.87932	D	0	-12.3778	19.4753	0.94985	0.0:1.0:0.0:0.0	.	507	Q92624	APBP2_HUMAN	C	507	ENSP00000083182:G507C	ENSP00000083182:G507C	G	-	1	0	APPBP2	55879963	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.453000	0.80700	2.611000	0.88343	0.650000	0.86243	GGT	.	.	.	none		0.308	APPBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449465.1	NM_006380		A	58525181	C	A	58525181	3	1	162	1	0	0	0	0	1	0	0	0	816	594	21	4	242	4	APPBP2	17	58525181	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08	12473415	58525181	22670029	66	9600											
KIAA1012	22878	hgsc.bcm.edu	37	chr18	29488737	29488737	+	Missense_Mutation	SNP	T	T	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	ctgatcgtttaattgcctaaTtgttttctctatatgtggca	8	19	7	7	1	1	1	0	1	1	0	3	1	1	1	1	1	1	3	1	1	4	9			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr18:29488737T>G	ENST00000283351.4	-	7	1437	c.1102A>C	c.(1102-1104)Att>Ctt	p.I368L	TRAPPC8_ENST00000582539.1_Missense_Mutation_p.I314L|TRAPPC8_ENST00000582513.1_Missense_Mutation_p.I368L	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	368					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						AATTGCCTAATTGTTTTCTCT	0.284																																					p.I368L		Atlas-SNP	.											.	TRAPPC8	126	.	0			c.A1102C						PASS	.						45	43	44					18																	29488737		2203	4297	6500	SO:0001583	missense	22878	exon7			GCCTAATTGTTTT	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.1102A>C	chr18.hg19:g.29488737T>G	ENSP00000283351:p.Ile368Leu	84.0	0.0	.		73.0	31.0	.	NM_014939	A0JP15|B3KME5|Q9H0L2	Missense_Mutation	SNP	ENST00000283351.4	hg19	CCDS11901.1	.	.	.	.	.	.	.	.	.	.	T	13.35	2.211203	0.39102	.	.	ENSG00000153339	ENST00000283351	T	0.19806	2.12	5.7	4.55	0.56014	.	0.000000	0.85682	D	0.000000	T	0.27313	0.0670	L	0.39147	1.195	0.53005	D	0.99996	P;D	0.55605	0.655;0.972	P;P	0.56216	0.557;0.794	T	0.01228	-1.1412	10	0.23302	T	0.38	.	11.1138	0.48249	0.0:0.0717:0.0:0.9283	.	368;368	Q6PCC9;Q9Y2L5	.;TPPC8_HUMAN	L	368	ENSP00000283351:I368L	ENSP00000283351:I368L	I	-	1	0	TRAPPC8	27742735	1.000000	0.71417	0.998000	0.56505	0.710000	0.40934	7.231000	0.78106	2.181000	0.69327	0.459000	0.35465	ATT	.	.	.	none		0.284	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939		G	29488737	T	G	29488737	3	3	162	1	0	0	0	0	1	0	0	0	8211	1493	52	5	3297	5	KIAA1012	18	29488737	Missense_Mutation	SNP	T	TCGA-EV-5902-01A-11D-1589-08		29488737	48588511	67	9601											
CNDP2	55748	hgsc.bcm.edu	37	chr18	72179734	72179734	+	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	gggtgtacgggggctcggtgCatgaggccatgactgatctc	6	9	17	9	2	1	3	0	3	1	0	3	3	1	3	1	5	2	3	1	5	1	1			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr18:72179734C>A	ENST00000324262.4	+	7	1025	c.709C>A	c.(709-711)Cat>Aat	p.H237N	CNDP2_ENST00000324301.8_Missense_Mutation_p.H153N|CNDP2_ENST00000579847.1_Missense_Mutation_p.H237N	NM_018235.2	NP_060705.2	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2 (metallopeptidase M20 family)	237					cellular nitrogen compound metabolic process (GO:0034641)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)			breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(5)|ovary(2)|skin(2)|stomach(3)	24		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)		GGGCTCGGTGCATGAGGCCAT	0.562																																					p.H237N		Atlas-SNP	.											.	CNDP2	55	.	0			c.C709A						PASS	.						255	196	216					18																	72179734		2203	4300	6503	SO:0001583	missense	55748	exon7			TCGGTGCATGAGG	AK001692	CCDS12006.1, CCDS54190.1	18q22.3	2014-07-14	2004-07-12		ENSG00000133313	ENSG00000133313	3.4.13.18		24437	protein-coding gene	gene with protein product	"cytosolic nonspecific dipeptidase"	169800	"peptidase A"	PEPA		12473676	Standard	NM_018235		Approved	FLJ10830, CN2, HsT2298, CPGL	uc002llm.2	Q96KP4	OTTHUMG00000132853	ENST00000324262.4:c.709C>A	chr18.hg19:g.72179734C>A	ENSP00000325548:p.His237Asn	131.0	0.0	.		108.0	39.0	.	NM_018235	B3KUG4|Q8WY59|Q9BQ94|Q9NVB4	Missense_Mutation	SNP	ENST00000324262.4	hg19	CCDS12006.1	.	.	.	.	.	.	.	.	.	.	C	12.98	2.100562	0.37048	.	.	ENSG00000133313	ENST00000324262;ENST00000324301	T;T	0.56776	0.44;0.44	5.14	3.33	0.38152	Peptidase M20, dimerisation (1);	0.047588	0.85682	D	0.000000	T	0.59582	0.2204	M	0.73962	2.25	0.80722	D	1	B;B;B	0.25743	0.133;0.021;0.002	B;B;B	0.40410	0.328;0.267;0.084	T	0.59757	-0.7394	10	0.38643	T	0.18	-19.4529	11.6458	0.51261	0.0:0.8542:0.0:0.1458	.	142;153;237	B4DPF1;Q96KP4-2;Q96KP4	.;.;CNDP2_HUMAN	N	237;153	ENSP00000325548:H237N;ENSP00000325756:H153N	ENSP00000325548:H237N	H	+	1	0	CNDP2	70330714	0.989000	0.36119	0.949000	0.38748	0.779000	0.44077	1.712000	0.37940	1.169000	0.42739	0.655000	0.94253	CAT	.	.	.	none		0.562	CNDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256327.1	NM_018235		A	72179734	C	A	72179734	3	1	162	1	0	0	0	0	1	0	0	0	3596	710	25	4	731	4	CNDP2	18	72179734	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08	42690997	72179734	5897514	68	9602											
ZNF236	7776	hgsc.bcm.edu	37	chr18	74561610	74561610	+	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	aacgccacatgagggatcacGagcgaaatgacaaggtatgt	15	6	12	8	3	1	2	1	2	0	0	1	5	1	3	1	2	2	1	1	2	4	1			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr18:74561610G>A	ENST00000253159.8	+	2	376	c.178G>A	c.(178-180)Gag>Aag	p.E60K	ZNF236_ENST00000320610.9_Missense_Mutation_p.E62K	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	60					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)		GAGGGATCACGAGCGAAATGA	0.358																																					p.E60K		Atlas-SNP	.											.	ZNF236	325	.	0			c.G178A						PASS	.						65	62	63					18																	74561610		1875	4104	5979	SO:0001583	missense	7776	exon2			GATCACGAGCGAA	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.178G>A	chr18.hg19:g.74561610G>A	ENSP00000253159:p.Glu60Lys	94.0	0.0	.		88.0	38.0	.	NM_007345	B2RTX9|Q9UL37	Missense_Mutation	SNP	ENST00000253159.8	hg19	CCDS42447.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.244485	0.79912	.	.	ENSG00000130856	ENST00000253159;ENST00000543926;ENST00000320610	T;T	0.16743	2.32;2.32	5.65	5.65	0.86999	Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	T	0.28499	0.0705	N	0.20483	0.58	0.46725	D	0.999171	D;D	0.89917	1.0;0.998	D;P	0.91635	0.999;0.766	T	0.05305	-1.0893	10	0.20519	T	0.43	.	19.7319	0.96186	0.0:0.0:1.0:0.0	.	60;60	Q9NWI2;Q9UL36	.;ZN236_HUMAN	K	60	ENSP00000253159:E60K;ENSP00000444524:E60K	ENSP00000253159:E60K	E	+	1	0	ZNF236	72690598	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	5.692000	0.68256	2.668000	0.90789	0.655000	0.94253	GAG	.	.	.	none		0.358	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1			A	74561610	G	A	74561610	3	1	162	1	0	0	0	0	1	0	0	0	17801	1059	37	1	184	1	ZNF236	18	74561610	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08	2381876	74561610	3515638	69	9603											
MYO1F	4542	hgsc.bcm.edu	37	chr19	8609279	8609279	+	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	cttctgcagcagtgtctggtCtgctcccccgcccgtggcgt	2	11	12	16	3	3	0	0	0	3	0	4	0	4	0	3	2	3	3	3	2	0	1			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr19:8609279C>A	ENST00000338257.8	-	14	1693	c.1426G>T	c.(1426-1428)Gac>Tac	p.D476Y	AC092316.2_ENST00000581156.1_RNA	NM_012335.3	NP_036467.2	O00160	MYO1F_HUMAN	myosin IF	476	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						AGTGTCTGGTCTGCTCCCCCG	0.677																																					p.D476Y		Atlas-SNP	.											.	MYO1F	128	.	0			c.G1426T						PASS	.						22	31	28					19																	8609279		2096	4212	6308	SO:0001583	missense	4542	exon14			TCTGGTCTGCTCC	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.1426G>T	chr19.hg19:g.8609279C>A	ENSP00000344871:p.Asp476Tyr	55.0	0.0	.		49.0	24.0	.	NM_012335	Q8WWN7	Missense_Mutation	SNP	ENST00000338257.8	hg19	CCDS42494.1	.	.	.	.	.	.	.	.	.	.	c	20.5	4.009105	0.75046	.	.	ENSG00000142347	ENST00000305795;ENST00000338257	D	0.92099	-2.97	3.49	3.49	0.39957	Myosin head, motor domain (2);	0.133964	0.47455	U	0.000236	D	0.97081	0.9046	H	0.96576	3.845	0.80722	D	1	D	0.58620	0.983	D	0.67725	0.953	D	0.98150	1.0441	10	0.87932	D	0	.	13.73	0.62781	0.0:1.0:0.0:0.0	.	476	O00160	MYO1F_HUMAN	Y	521;476	ENSP00000344871:D476Y	ENSP00000304899:D521Y	D	-	1	0	MYO1F	8515279	1.000000	0.71417	0.989000	0.46669	0.860000	0.49131	5.743000	0.68655	1.781000	0.52344	0.290000	0.19541	GAC	.	.	.	none		0.677	MYO1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342716.2			A	8609279	C	A	8609279	3	1	162	1	0	0	0	0	1	0	0	0	10080	913	32	4	1930	4	MYO1F	19	8609279	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08		8609279	50519704	70	9604											
CACNA1A	773	hgsc.bcm.edu	37	chr19	13397703	13397703	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgccaggggtgggtcttggCggcccaggtcctgctggatt	3	10	17	11	1	1	0	0	0	1	0	2	1	2	1	3	7	2	1	3	7	0	2	rs200850308		TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr19:13397703C>T	ENST00000360228.5	-	20	3166	c.3167G>A	c.(3166-3168)cGc>cAc	p.R1056H	CACNA1A_ENST00000573710.2_Missense_Mutation_p.R1057H	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	1057					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)	TGGGTCTTGGCGGCCCAGGTC	0.642																																					p.R1057H		Atlas-SNP	.											.	CACNA1A	715	.	0			c.G3170A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	0,3700		0,0,1850	19	22	21		3179,3170,3167,3170,3179	5.2	1	19		21	1,8013		0,1,4006	yes	missense,missense,missense,missense,missense	CACNA1A	NM_000068.3,NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2	29,29,29,29,29	0,1,5856	TT,TC,CC		0.0125,0.0,0.0085	benign,benign,benign,benign,benign	1060/2267,1057/2262,1056/2507,1057/2264,1060/2513	13397703	1,11713	1850	4007	5857	SO:0001583	missense	773	exon20			TCTTGGCGGCCCA	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.3167G>A	chr19.hg19:g.13397703C>T	ENSP00000353362:p.Arg1056His	69.0	0.0	.		54.0	8.0	.	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	hg19	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	C	15.17	2.754278	0.49362	0.0	1.25E-4	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.96168	-3.93	5.19	5.19	0.71726	.	0.663946	0.14837	N	0.295520	D	0.95108	0.8415	L	0.43152	1.355	0.42961	D	0.9944	B;B;D	0.65815	0.343;0.239;0.995	B;B;P	0.51016	0.021;0.034;0.656	D	0.94508	0.7716	10	0.44086	T	0.13	.	17.4837	0.87682	0.0:1.0:0.0:0.0	.	1057;1060;1056	O00555;E9PD31;Q9NS88	CAC1A_HUMAN;.;.	H	1056;1060;1057;1057	ENSP00000353362:R1056H	ENSP00000317661:R1057H	R	-	2	0	CACNA1A	13258703	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.265000	0.51561	2.427000	0.82271	0.555000	0.69702	CGC	.	.	.	weak		0.642	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		T	13397703	C	T	13397703	3	4	162	1	0	0	0	0	1	0	0	0	2540	768	27	1	4567	1	CACNA1A	19	13397703	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08	4788424	13397703	45731280	71	9605											
ZNF780B	163131	hgsc.bcm.edu	37	chr19	40541550	40541550	+	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	agcatgaatactctggtgttGaataaggtttgaactacgat	13	13	10	5	1	1	3	0	3	1	0	1	4	1	3	0	2	4	3	0	2	6	5			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr19:40541550G>T	ENST00000434248.1	-	5	1281	c.1216C>A	c.(1216-1218)Caa>Aaa	p.Q406K	ZNF780B_ENST00000221355.6_Missense_Mutation_p.Q258K	NM_001005851.2	NP_001005851.1	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	406					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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)					CTCTGGTGTTGAATAAGGTTT	0.358																																					p.Q406K		Atlas-SNP	.											.	ZNF780B	143	.	0			c.C1216A						PASS	.						100	107	105					19																	40541550		2203	4300	6503	SO:0001583	missense	163131	exon5			GGTGTTGAATAAG	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.1216C>A	chr19.hg19:g.40541550G>T	ENSP00000391641:p.Gln406Lys	190.0	0.0	.		176.0	79.0	.	NM_001005851	B9EH00	Missense_Mutation	SNP	ENST00000434248.1	hg19	CCDS46077.1	.	.	.	.	.	.	.	.	.	.	G	1.025	-0.683570	0.03353	.	.	ENSG00000128000	ENST00000434248;ENST00000221355	T;T	0.35048	1.33;1.33	2.29	1.07	0.20283	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.21307	0.0513	N	0.01081	-1.03	0.09310	N	1	D	0.57571	0.98	D	0.69824	0.966	T	0.17930	-1.0353	9	0.05833	T	0.94	.	8.391	0.32528	0.0:0.2421:0.7579:0.0	.	406	Q9Y6R6	Z780B_HUMAN	K	406;258	ENSP00000391641:Q406K;ENSP00000221355:Q258K	ENSP00000221355:Q258K	Q	-	1	0	ZNF780B	45233390	0.000000	0.05858	0.006000	0.13384	0.003000	0.03518	-5.529000	0.00115	1.103000	0.41568	0.313000	0.20887	CAA	.	.	.	none		0.358	ZNF780B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338466.1	NM_001005851		T	40541550	G	T	40541550	3	4	162	1	0	0	0	0	1	0	0	0	18165	1299	45	4	1289	4	ZNF780B	19	40541550	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08	27143847	40541550	18587433	72	9606											
ZNF320	162967	hgsc.bcm.edu	37	chr19	53384942	53384942	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctatgtcttcgcaaatgcAaatgaaatcttgattcaagc	13	13	6	9	1	3	2	1	2	2	0	5	2	4	2	1	0	2	2	1	0	5	4			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr19:53384942A>G	ENST00000595635.1	-	8	938	c.437T>C	c.(436-438)tTg>tCg	p.L146S	ZNF320_ENST00000600930.1_Intron|ZNF320_ENST00000391781.2_Missense_Mutation_p.L146S|ZNF320_ENST00000597909.1_Intron	NM_207333.2	NP_997216.2	A2RRD8	ZN320_HUMAN	zinc finger protein 320	146					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(4)|large_intestine(5)|liver(1)|lung(10)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(134;0.0534)		TCGCAAATGCAAATGAAATCT	0.348																																					p.L146S		Atlas-SNP	.											.	ZNF320	67	.	0			c.T437C						PASS	.						117	113	114					19																	53384942		2203	4300	6503	SO:0001583	missense	162967	exon4			AAATGCAAATGAA	AF086262	CCDS33095.1	19q13.41	2014-09-04			ENSG00000182986	ENSG00000182986		"Zinc fingers, C2H2-type", "-"	13842	protein-coding gene	gene with protein product		606427				11536051	Standard	XM_006723059		Approved	ZFPL, DKFZp686G16228	uc002qag.3	A2RRD8	OTTHUMG00000182797	ENST00000595635.1:c.437T>C	chr19.hg19:g.53384942A>G	ENSP00000473091:p.Leu146Ser	218.0	0.0	.		185.0	80.0	.	NM_207333	Q8NDR6	Missense_Mutation	SNP	ENST00000595635.1	hg19	CCDS33095.1	.	.	.	.	.	.	.	.	.	.	-	0.006	-2.115473	0.00349	.	.	ENSG00000182986	ENST00000391781	T	0.12361	2.69	1.39	0.0569	0.14321	.	.	.	.	.	T	0.04998	0.0134	N	0.11427	0.14	0.09310	N	1	B	0.10296	0.003	B	0.01281	0.0	T	0.43245	-0.9403	9	0.02654	T	1	.	5.4228	0.16409	0.2247:0.0:0.7753:0.0	.	146	A2RRD8	ZN320_HUMAN	S	146	ENSP00000375660:L146S	ENSP00000375660:L146S	L	-	2	0	ZNF320	58076754	0.000000	0.05858	0.001000	0.08648	0.155000	0.21991	-0.162000	0.10012	-0.124000	0.11724	0.163000	0.16589	TTG	.	.	.	none		0.348	ZNF320-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463771.1	NM_207333		G	53384942	A	G	53384942	3	3	162	1	0	0	0	0	1	0	0	0	17851	131	5	3	1096	3	ZNF320	19	53384942	Missense_Mutation	SNP	A	TCGA-EV-5902-01A-11D-1589-08	12843392	53384942	5744041	73	9607											
NCAM2	4685	hgsc.bcm.edu	37	chr21	22656582	22656582	+	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	agataatttcaacacagaggGtagtagtgcaaaaggaaggt	17	8	12	4	0	1	2	1	0	0	2	1	3	1	3	0	3	2	3	0	3	7	4			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr21:22656582G>T	ENST00000400546.1	+	3	448	c.199G>T	c.(199-201)Gta>Tta	p.V67L	NCAM2_ENST00000535285.1_Missense_Mutation_p.V92L|NCAM2_ENST00000486367.1_3'UTR|NCAM2_ENST00000284894.7_Intron	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	67	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)		AACACAGAGGGTAGTAGTGCA	0.398																																					p.V67L		Atlas-SNP	.											.	NCAM2	220	.	0			c.G199T						PASS	.						132	122	125					21																	22656582		1859	4101	5960	SO:0001583	missense	4685	exon3			CAGAGGGTAGTAG		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.199G>T	chr21.hg19:g.22656582G>T	ENSP00000383392:p.Val67Leu	71.0	0.0	.		70.0	24.0	.	NM_004540	A8MQ06|B7Z841|Q7Z7F2	Missense_Mutation	SNP	ENST00000400546.1	hg19	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	G	13.01	2.109633	0.37242	.	.	ENSG00000154654	ENST00000400546;ENST00000535285	T;T	0.67345	-0.26;-0.26	5.58	4.7	0.59300	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.104866	0.64402	D	0.000003	T	0.57562	0.2062	L	0.37630	1.12	0.29058	N	0.884114	P;D	0.56968	0.799;0.978	B;P	0.44447	0.251;0.45	T	0.54510	-0.8283	10	0.09338	T	0.73	-17.3832	16.3191	0.82939	0.0715:0.0:0.9285:0.0	.	92;67	B7Z841;O15394	.;NCAM2_HUMAN	L	67;92	ENSP00000383392:V67L;ENSP00000441887:V92L	ENSP00000383392:V67L	V	+	1	0	NCAM2	21578453	1.000000	0.71417	0.498000	0.27564	0.836000	0.47400	3.223000	0.51231	0.735000	0.32537	-1.094000	0.02160	GTA	.	.	.	none		0.398	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		T	22656582	G	T	22656582	3	4	162	1	0	0	0	0	1	0	0	0	10210	1261	44	4	209	4	NCAM2	21	22656582	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08		22656582	25473313	74	9608											
BCL2L13	23786	hgsc.bcm.edu	37	chr22	18138590	18138590	+	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	gcaagagcaacatctttcctCaccccaaggtattatctttg	11	12	6	12	0	3	1	1	0	2	1	4	1	4	1	3	1	2	3	3	1	5	4			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr22:18138590C>T	ENST00000317582.5	+	2	460	c.113C>T	c.(112-114)tCa>tTa	p.S38L	BCL2L13_ENST00000399782.1_Missense_Mutation_p.S38L|BCL2L13_ENST00000418951.2_Missense_Mutation_p.S38L|BCL2L13_ENST00000538149.1_Missense_Mutation_p.H26Y|BCL2L13_ENST00000493680.1_Missense_Mutation_p.S38L|BCL2L13_ENST00000337612.5_5'UTR|BCL2L13_ENST00000543133.1_5'UTR|BCL2L13_ENST00000355028.3_Missense_Mutation_p.S38L	NM_015367.3	NP_056182.2	Q9BXK5	B2L13_HUMAN	BCL2-like 13 (apoptosis facilitator)	38					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			breast(2)|central_nervous_system(1)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|skin(3)|urinary_tract(2)	15		all_epithelial(15;0.123)		Lung(27;0.199)		CATCTTTCCTCACCCCAAGGT	0.358																																					p.S38L		Atlas-SNP	.											BCL2L13,NS,carcinoma,0,1	BCL2L13	27	.	0			c.C113T						PASS	.						94	83	87					22																	18138590		2203	4300	6503	SO:0001583	missense	23786	exon2			TTTCCTCACCCCA	AF146568	CCDS13746.1, CCDS59447.1, CCDS59448.1, CCDS74810.1, CCDS74811.1, CCDS74812.1, CCDS74813.1, CCDS74814.1	22q11	2014-03-07			ENSG00000099968	ENSG00000099968			17164	protein-coding gene	gene with protein product						11262395, 11381032	Standard	NM_015367		Approved	MIL1, BCL-RAMBO	uc002zmw.4	Q9BXK5	OTTHUMG00000150088	ENST00000317582.5:c.113C>T	chr22.hg19:g.18138590C>T	ENSP00000318883:p.Ser38Leu	82.0	0.0	.		34.0	33.0	.	NM_001270732	B3KPE7|Q96B37|Q96IB7|Q9BY01|Q9HC05|Q9UFE0|Q9UKN3	Missense_Mutation	SNP	ENST00000317582.5	hg19	CCDS13746.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.60|12.60	1.986267|1.986267	0.35036|0.35036	.|.	.|.	ENSG00000099968|ENSG00000099968	ENST00000538149|ENST00000399782;ENST00000317582;ENST00000493680;ENST00000355028;ENST00000418951	T|T;T;T;T;T	0.40756|0.05513	1.02|3.43;3.43;3.43;3.43;3.43	5.68|5.68	2.49|2.49	0.30216|0.30216	.|.	.|0.492205	.|0.20751	.|N	.|0.086347	T|T	0.04952|0.04952	0.0133|0.0133	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	B|B;B;B	0.06786|0.11235	0.001|0.004;0.001;0.001	B|B;B;B	0.12156|0.13407	0.007|0.009;0.003;0.004	T|T	0.39418|0.39418	-0.9615|-0.9615	9|10	0.87932|0.38643	D|T	0|0.18	-0.0021|-0.0021	8.7678|8.7678	0.34713|0.34713	0.0:0.7614:0.0:0.2386|0.0:0.7614:0.0:0.2386	.|.	26|38;38;38	B7Z238|E9PDD6;Q9BXK5;Q9BXK5-2	.|.;B2L13_HUMAN;.	Y|L	26|38	ENSP00000441344:H26Y|ENSP00000382682:S38L;ENSP00000318883:S38L;ENSP00000434764:S38L;ENSP00000347133:S38L;ENSP00000410019:S38L	ENSP00000441344:H26Y|ENSP00000318883:S38L	H|S	+|+	1|2	0|0	BCL2L13|BCL2L13	16518590|16518590	0.012000|0.012000	0.17670|0.17670	0.956000|0.956000	0.39512|0.39512	0.989000|0.989000	0.77384|0.77384	0.630000|0.630000	0.24553|0.24553	0.343000|0.343000	0.23821|0.23821	0.591000|0.591000	0.81541|0.81541	CAC|TCA	.	.	.	none		0.358	BCL2L13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316184.1	NM_015367		T	18138590	C	T	18138590	3	4	162	1	0	0	0	0	1	0	0	0	1371	838	29	2	115	2	BCL2L13	22	18138590	Missense_Mutation	SNP	C	TCGA-EV-5902-01A-11D-1589-08		18138590	33165976	75	9609											
NF2	4771	hgsc.bcm.edu	37	chr22	30067890	30067905	+	Frame_Shift_Del	DEL	AGGCTGCTGCAGATGA	AGGCTGCTGCAGATGA	-																															cgagggatgagttggagaggAggctgctgcagatgaaagaa																								rs74315492|rs74315498		TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	AGGCTGCTGCAGATGA	AGGCTGCTGCAGATGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chr22:30067890_30067905delAGGCTGCTGCAGATGA	ENST00000338641.4	+	11	1516_1531	c.1075_1090delAGGCTGCTGCAGATGA	c.(1075-1092)aggctgctgcagatgaaafs	p.RLLQMK359fs	NF2_ENST00000403999.3_Frame_Shift_Del_p.RLLQMK359fs|NF2_ENST00000361452.4_Frame_Shift_Del_p.RLLQMK318fs|NF2_ENST00000334961.7_Frame_Shift_Del_p.RLLQMK276fs|NF2_ENST00000397789.3_Frame_Shift_Del_p.RLLQMK359fs|NF2_ENST00000403435.1_Splice_Site_p.GC334fs|NF2_ENST00000361676.4_Frame_Shift_Del_p.RLLQMK317fs|NF2_ENST00000347330.5_Intron|NF2_ENST00000413209.2_Intron|NF2_ENST00000353887.4_Frame_Shift_Del_p.RLLQMK276fs|NF2_ENST00000361166.4_Frame_Shift_Del_p.RLLQMK359fs	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	359	Glu-rich.				actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.Q362*(4)|p.?(3)|p.M363fs*12(2)|p.L361fs*6(1)|p.M334fs*4(1)|p.L361fs*3(1)|p.M334_Q362del(1)|p.K364fs*5(1)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						GTTGGAGAGGAGGCTGCTGCAGATGAAAGAAGAAGC	0.565			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																												p.358_363del		Atlas-INDEL	.	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	.	NF2	1312	.	14	Deletion - Frameshift(6)|Substitution - Nonsense(4)|Unknown(3)|Deletion - In frame(1)	meninges(5)|soft_tissue(4)|large_intestine(1)|central_nervous_system(1)|endometrium(1)|skin(1)|stomach(1)	c.1074_1089del	GRCh37	CM066148|CM930517	NF2	M	rs74315492|rs74315498	PASS	.																																			SO:0001589	frameshift_variant	4771	exon11	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	.	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"A-kinase anchor proteins"	7773	protein-coding gene	gene with protein product	"moesin-ezrin-radixin like", "schwannomin"	607379	"neurofibromin 2 (bilateral acoustic neuroma)"			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.1075_1090delAGGCTGCTGCAGATGA	chr22.hg19:g.30067890_30067905delAGGCTGCTGCAGATGA	ENSP00000344666:p.Arg359fs	87.0	0.0	0		38.0	22.0	0.578947	NM_181832	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Frame_Shift_Del	DEL	ENST00000338641.4	hg19	CCDS13861.1																																																																																			.	.	.	none		0.565	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268		-	30067905	AGGCTGCTGCAGATGA	-	30067890	7	5	162	1	0	1	0	1	0	0	0	0	10364	295	11	0	1117	0	NF2	22	30067890	Frame_Shift_Del	DEL	AGGCTGCTGCAGATGA	TCGA-EV-5902-01A-11D-1589-08	11929300	30067890	21236676	76	9610											
ODZ1	10178	hgsc.bcm.edu	37	chrX	123519705	123519705	+	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	cgccctgtccccagatgcagGgtctgtagcaatcggccatc	7	8	11	15	2	1	1	0	0	1	1	4	1	2	1	4	2	2	3	4	2	2	1			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chrX:123519705G>T	ENST00000371130.3	-	28	5940	c.5877C>A	c.(5875-5877)acC>acA	p.T1959T	STAG2_ENST00000469481.1_Intron|TENM1_ENST00000422452.2_Silent_p.T1966T	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1959					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)										CCAGATGCAGGGTCTGTAGCA	0.488																																					p.T1966T		Atlas-SNP	.											.	.	.	.	0			c.C5898A						PASS	.						173	144	154					X																	123519705		2203	4300	6503	SO:0001819	synonymous_variant	10178	exon29			ATGCAGGGTCTGT	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.5877C>A	chrX.hg19:g.123519705G>T		154.0	0.0	.		124.0	21.0	.	NM_001163278	B2RTR5|Q5JZ17	Silent	SNP	ENST00000371130.3	hg19	CCDS14609.1																																																																																			.	.	.	none		0.488	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		T	123519705	G	T	123519705	2	4	162	1	0	0	0	0	0	0	0	1	10841	1219	43	4		4	ODZ1	23	123519705	Silent	SNP	G	TCGA-EV-5902-01A-11D-1589-08		123519705	31750855	77	9611											
ZDHHC9	51114	hgsc.bcm.edu	37	chrX	128963040	128963040	+	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	tgaagctggtcctcaacagtGtagccatggagaaaaggaag	14	7	13	7	0	1	2	1	1	0	1	2	4	2	3	2	3	3	2	2	3	6	1			TCGA-EV-5902-01A-11D-1589-08	TCGA-EV-5902-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	05c0e7bb-5be8-4e8d-9724-8063e99cc058	c49e0138-d7e1-4094-9d2d-b41239dea126	g.chrX:128963040G>T	ENST00000357166.6	-	4	636	c.245C>A	c.(244-246)aCa>aAa	p.T82K	ZDHHC9_ENST00000371064.3_Missense_Mutation_p.T82K	NM_016032.3	NP_057116.2	Q9Y397	ZDHC9_HUMAN	zinc finger, DHHC-type containing 9	82					peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein palmitoylation (GO:0018345)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|palmitoyltransferase complex (GO:0002178)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|Ras palmitoyltransferase activity (GO:0043849)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)	19						CCTCAACAGTGTAGCCATGGA	0.522																																					p.T82K		Atlas-SNP	.											.	ZDHHC9	41	.	0			c.C245A						PASS	.						127	102	110					X																	128963040		2203	4300	6503	SO:0001583	missense	51114	exon3			AACAGTGTAGCCA	AF151847	CCDS35395.1	Xq26.1	2008-02-05			ENSG00000188706	ENSG00000188706		"Zinc fingers, DHHC-type"	18475	protein-coding gene	gene with protein product		300646	"zinc finger, DHHC-type containing 10", "chromosome X open reading frame 11"	ZDHHC10, CXorf11		10810093	Standard	NM_001008222		Approved	ZNF379, CGI-89, ZNF380	uc004euw.3	Q9Y397	OTTHUMG00000022375	ENST00000357166.6:c.245C>A	chrX.hg19:g.128963040G>T	ENSP00000349689:p.Thr82Lys	85.0	0.0	.		84.0	82.0	.	NM_001008222	B4F6G2|D3DTF9|Q59EK4|Q5JSW5|Q8WWS7|Q9BPY4|Q9NSP0|Q9NVL0|Q9NVR6	Missense_Mutation	SNP	ENST00000357166.6	hg19	CCDS35395.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.36|19.36	3.812188|3.812188	0.70797|0.70797	.|.	.|.	ENSG00000188706|ENSG00000188706	ENST00000433917|ENST00000357166;ENST00000371064;ENST00000406492	.|T;T;T	.|0.25085	.|1.82;1.82;1.82	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	.|0.088515	.|0.85682	.|D	.|0.000000	T|T	0.39572|0.39572	0.1083|0.1083	M|M	0.75777|0.75777	2.31|2.31	0.51482|0.51482	D|D	0.999924|0.999924	.|P	.|0.41041	.|0.736	.|P	.|0.44422	.|0.449	T|T	0.16305|0.16305	-1.0407|-1.0407	5|10	.|0.36615	.|T	.|0.2	-7.38|-7.38	18.76|18.76	0.91847|0.91847	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|82	.|Q9Y397	.|ZDHC9_HUMAN	N|K	42|82	.|ENSP00000349689:T82K;ENSP00000360103:T82K;ENSP00000383991:T82K	.|ENSP00000349689:T82K	H|T	-|-	1|2	0|0	ZDHHC9|ZDHHC9	128790721|128790721	1.000000|1.000000	0.71417|0.71417	0.972000|0.972000	0.41901|0.41901	0.891000|0.891000	0.51852|0.51852	4.787000|4.787000	0.62432|0.62432	2.375000|2.375000	0.81037|0.81037	0.594000|0.594000	0.82650|0.82650	CAC|ACA	.	.	.	none		0.522	ZDHHC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058213.1	NM_016032		T	128963040	G	T	128963040	3	4	162	1	0	0	0	0	1	0	0	0	17634	1377	48	4	881	4	ZDHHC9	23	128963040	Missense_Mutation	SNP	G	TCGA-EV-5902-01A-11D-1589-08	5443335	128963040	26307520	78	9612											
VPS13D	55187	hgsc.bcm.edu	37	chr1	12304650	12304650	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcagttaccgcctccgtagtTacaaggattgtggagaatat	11	12	10	8	2	1	1	1	0	0	1	2	3	2	2	3	2	2	3	3	2	6	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr1:12304650T>C	ENST00000358136.3	+	5	553	c.423T>C	c.(421-423)gtT>gtC	p.V141V	VPS13D_ENST00000356315.4_Silent_p.V141V	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)		CCTCCGTAGTTACAAGGATTG	0.413																																					p.V141V		Atlas-SNP	.											.	VPS13D	316	.	0			c.T423C						PASS	.						143	133	137					1																	12304650		2203	4300	6503	SO:0001819	synonymous_variant	55187	exon5			CGTAGTTACAAGG	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.423T>C	chr1.hg19:g.12304650T>C		106.0	0.0	.		100.0	4.0	.	NM_015378		Silent	SNP	ENST00000358136.3	hg19	CCDS30588.1																																																																																			.	.	.	none		0.413	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		C	12304650	T	C	12304650	2	2	163	1	0	0	0	0	0	0	0	1	17204	1741	61	3		3	VPS13D	1	12304650	Silent	SNP	T	TCGA-EV-5903-01A-11D-1589-08		12304650	236945971	1	9613											
FAM40A	85369	hgsc.bcm.edu	37	chr1	110587506	110587507	+	Frame_Shift_Ins	INS	-	-	TA																															gagtccagccgcagcaaattINStataggttacactctaggca																										TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr1:110587506_110587507insTA	ENST00000369795.3	+	11	1353_1354	c.1331_1332insTA	c.(1330-1335)tttatafs	p.FI444fs	STRIP1_ENST00000369796.1_Frame_Shift_Ins_p.FI349fs	NM_033088.3	NP_149079.2	Q5VSL9	STRP1_HUMAN	striatin interacting protein 1	444					cortical actin cytoskeleton organization (GO:0030866)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)											CGCAGCAAATTTATAGGTTACA	0.436																																					p.F444fs		Atlas-INDEL	.											.	STRIP1	1	.	0			c.1331_1332insTA						PASS	.																																			SO:0001589	frameshift_variant	85369	exon11			.	AK027649	CCDS30798.1, CCDS59197.1	1p13.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000143093	ENSG00000143093			25916	protein-coding gene	gene with protein product	"FAR11 factor arrest 11 homolog A (yeast)"		"family with sequence similarity 40, member A"	FAM40A		11214970, 12588993, 22782902, 22298706, 18782753	Standard	NM_033088		Approved	FLJ14743, KIAA1761, FAR11A	uc001dza.2	Q5VSL9	OTTHUMG00000170607	ENST00000369795.3:c.1334_1335dupTA	chr1.hg19:g.110587509_110587510dupTA	ENSP00000358810:p.Phe444fs	127.0	0.0	0		107.0	30.0	0.280374	NM_033088	Q0V925|Q5VSL8|Q658K2|Q6ZV31|Q8N598|Q96SN2|Q9C0A2	Frame_Shift_Ins	INS	ENST00000369795.3	hg19	CCDS30798.1																																																																																			.	.	.	none		0.436	STRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032213.1	NM_033088		TA	110587507	-	TA	110587506	7	5	163	1	0	1	1	0	0	0	0	0	5567	1841	64	0	1373	0	FAM40A	1	110587506	Frame_Shift_Ins	INS	-	TCGA-EV-5903-01A-11D-1589-08	98282856	110587506	138663115	2	9614											
LRRC52	440699	hgsc.bcm.edu	37	chr1	165514059	165514059	+	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	ccttataccacctcactactCtggagaccctgtttctgagt	8	13	6	14	0	3	2	1	1	2	1	3	3	3	2	4	1	2	1	4	1	3	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr1:165514059C>G	ENST00000294818.1	+	1	816	c.526C>G	c.(526-528)Ctg>Gtg	p.L176V	RP11-280O1.2_ENST00000421273.1_RNA|RP11-280O1.2_ENST00000438275.1_RNA|RP11-280O1.2_ENST00000416424.1_RNA	NM_001005214.3	NP_001005214.2	Q8N7C0	LRC52_HUMAN	leucine rich repeat containing 52	176					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)	18	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)					CCTCACTACTCTGGAGACCCT	0.512																																					p.L176V		Atlas-SNP	.											.	LRRC52	50	.	0			c.C526G						PASS	.						148	152	151					1																	165514059		2203	4300	6503	SO:0001583	missense	440699	exon1			ACTACTCTGGAGA	AK098677	CCDS30930.1	1q23.3	2008-02-05			ENSG00000162763	ENSG00000162763			32156	protein-coding gene	gene with protein product		615218					Standard	NM_001005214		Approved	FLJ25811	uc001gde.2	Q8N7C0	OTTHUMG00000034625	ENST00000294818.1:c.526C>G	chr1.hg19:g.165514059C>G	ENSP00000294818:p.Leu176Val	200.0	0.0	.		188.0	52.0	.	NM_001005214	A2RUN7|Q5T9K5	Missense_Mutation	SNP	ENST00000294818.1	hg19	CCDS30930.1	.	.	.	.	.	.	.	.	.	.	C	12.19	1.863665	0.32884	.	.	ENSG00000162763	ENST00000294818	T	0.06449	3.3	5.39	5.39	0.77823	.	0.089285	0.53938	D	0.000042	T	0.17195	0.0413	M	0.74881	2.28	0.34422	D	0.697524	D	0.65815	0.995	D	0.67231	0.95	T	0.00436	-1.1740	9	0.72032	D	0.01	.	16.6547	0.85225	0.0:1.0:0.0:0.0	.	176	Q8N7C0	LRC52_HUMAN	V	176	ENSP00000294818:L176V	ENSP00000294818:L176V	L	+	1	2	LRRC52	163780683	1.000000	0.71417	0.049000	0.19019	0.023000	0.10783	5.468000	0.66743	2.517000	0.84864	0.563000	0.77884	CTG	.	.	.	none		0.512	LRRC52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083793.1	NM_001005214		G	165514059	C	G	165514059	3	3	163	1	0	0	0	0	1	0	0	0	9017	912	32	4	528	4	LRRC52	1	165514059	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08	54926553	165514059	83736562	3	9615											
C1orf107	27042	hgsc.bcm.edu	37	chr1	210015618	210015618	+	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	ttccactcaaagcatttgatGaatcacatgaacctactacc	14	11	4	12	0	2	3	2	3	0	0	3	3	3	3	3	0	4	1	3	0	5	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr1:210015618G>A	ENST00000491415.2	+	9	1551	c.1494G>A	c.(1492-1494)atG>atA	p.M498I		NM_014388.6	NP_055203.4	Q68CQ4	DIEXF_HUMAN	digestive organ expansion factor homolog (zebrafish)	498					multicellular organismal development (GO:0007275)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(15)|large_intestine(7)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(2)	53						AGCATTTGATGAATCACATGA	0.418																																					p.M498I		Atlas-SNP	.											.	DIEXF	97	.	0			c.G1494A						PASS	.						82	74	76					1																	210015618		2203	4300	6503	SO:0001583	missense	27042	exon9			TTTGATGAATCAC	BC022964	CCDS1493.1	1q32.2	2011-08-12	2011-02-16	2011-02-16	ENSG00000117597	ENSG00000117597			28440	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 107"	C1orf107		16322560	Standard	NM_014388		Approved	MGC29875, DEF, UTP25	uc001hhr.2	Q68CQ4	OTTHUMG00000036654	ENST00000491415.2:c.1494G>A	chr1.hg19:g.210015618G>A	ENSP00000419005:p.Met498Ile	60.0	0.0	.		67.0	17.0	.	NM_014388	O75992|Q4VY00|Q63HL9	Missense_Mutation	SNP	ENST00000491415.2	hg19	CCDS1493.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.076476	0.76415	.	.	ENSG00000117597	ENST00000491415	T	0.37411	1.2	6.17	6.17	0.99709	.	0.069797	0.85682	D	0.000000	T	0.36580	0.0972	L	0.45228	1.405	0.58432	D	0.999996	P	0.45044	0.849	B	0.39971	0.315	T	0.03315	-1.1049	10	0.35671	T	0.21	-37.8963	20.8794	0.99867	0.0:0.0:1.0:0.0	.	498	Q68CQ4	DIEXF_HUMAN	I	498	ENSP00000419005:M498I	ENSP00000419005:M498I	M	+	3	0	DIEXF	208082241	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.791000	0.85805	2.941000	0.99782	0.655000	0.94253	ATG	.	.	.	none		0.418	DIEXF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089127.2	NM_014388		A	210015618	G	A	210015618	3	1	163	1	0	0	0	0	1	0	0	0	1983	1290	45	2	1528	2	C1orf107	1	210015618	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	44501559	210015618	39235003	4	9616											
KHK	3795	hgsc.bcm.edu	37	chr2	27322367	27322367	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aattgctccactcggatgctTtcccgccaccccgcgtggtg	5	10	10	16	4	0	0	0	0	0	0	3	1	2	1	5	2	2	2	5	2	1	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr2:27322367T>C	ENST00000260599.6	+	7	1246	c.733T>C	c.(733-735)Ttc>Ctc	p.F245L	KHK_ENST00000490823.1_3'UTR|KHK_ENST00000260598.5_Missense_Mutation_p.F245L|CGREF1_ENST00000452318.2_3'UTR|CGREF1_ENST00000402550.1_3'UTR	NM_000221.2	NP_000212.1	P50053	KHK_HUMAN	ketohexokinase (fructokinase)	245					carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose catabolic process (GO:0006001)|regulation of glycogen metabolic process (GO:0070873)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ketohexokinase activity (GO:0004454)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTCGGATGCTTTCCCGCCACC	0.637																																					p.F245L		Atlas-SNP	.											.	KHK	60	.	0			c.T733C						PASS	.						80	82	82					2																	27322367		2203	4300	6503	SO:0001583	missense	3795	exon7			GATGCTTTCCCGC		CCDS1734.1, CCDS1735.1	2p23.3-p23.2	2008-02-05			ENSG00000138030	ENSG00000138030	2.7.1.3		6315	protein-coding gene	gene with protein product		614058				7833921	Standard	NM_000221		Approved		uc002rim.2	P50053	OTTHUMG00000097077	ENST00000260599.6:c.733T>C	chr2.hg19:g.27322367T>C	ENSP00000260599:p.Phe245Leu	133.0	0.0	.		98.0	27.0	.	NM_006488	Q6IBK2|Q99532|Q9BRJ3|Q9UMN1	Missense_Mutation	SNP	ENST00000260599.6	hg19	CCDS1734.1	.	.	.	.	.	.	.	.	.	.	T	17.98	3.519838	0.64634	.	.	ENSG00000138030	ENST00000260599;ENST00000260598	T;T	0.75477	-0.94;-0.94	5.29	4.11	0.48088	Carbohydrate/purine kinase (1);	0.048848	0.85682	D	0.000000	T	0.71324	0.3326	M	0.66939	2.045	0.80722	D	1	B;P;B;P	0.51791	0.021;0.948;0.08;0.948	B;B;B;B	0.43052	0.022;0.406;0.049;0.406	T	0.69621	-0.5096	10	0.38643	T	0.18	-12.9402	10.6793	0.45804	0.0:0.0:0.1603:0.8397	.	245;245;245;245	Q53G56;Q6IBK2;P50053-2;P50053	.;.;.;KHK_HUMAN	L	245	ENSP00000260599:F245L;ENSP00000260598:F245L	ENSP00000260598:F245L	F	+	1	0	KHK	27175871	1.000000	0.71417	0.979000	0.43373	0.490000	0.33462	4.841000	0.62824	0.811000	0.34303	0.454000	0.30748	TTC	.	.	.	none		0.637	KHK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214196.1			C	27322367	T	C	27322367	3	2	163	1	0	0	0	0	1	0	0	0	8156	1841	64	3	898	3	KHK	2	27322367	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08		27322367	215877006	5	9617											
DNAJC5G	285126	hgsc.bcm.edu	37	chr2	27503082	27503082	+	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	aaatagcgaagatgatttttAagagatgaagaaggatgagg	18	9	13	1	1	0	6	0	3	0	3	0	9	0	7	0	2	1	0	0	2	6	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr2:27503082A>T	ENST00000296097.3	+	6	987	c.569A>T	c.(568-570)tAa>tTa	p.*190L	DNAJC5G_ENST00000404433.1_Nonstop_Mutation_p.*174L|DNAJC5G_ENST00000402462.1_Nonstop_Mutation_p.*190L|DNAJC5G_ENST00000406962.1_Nonsense_Mutation_p.K103*|TRIM54_ENST00000380075.2_5'Flank|TRIM54_ENST00000296098.4_5'Flank	NM_173650.1	NP_775921.1	Q8N7S2	DNJ5G_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 5 gamma	0						membrane (GO:0016020)				cervix(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GATGATTTTTAAGAGATGAAG	0.333											OREG0014517	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.X190L		Atlas-SNP	.											.	DNAJC5G	19	.	0			c.A569T						PASS	.						141	153	149					2																	27503082		2203	4300	6503	SO:0001578	stop_lost	285126	exon6			ATTTTTAAGAGAT	AF368277	CCDS1744.1	2p23	2011-09-02			ENSG00000163793	ENSG00000163793		"Heat shock proteins / DNAJ (HSP40)"	24844	protein-coding gene	gene with protein product		613946					Standard	NM_173650		Approved	FLJ40417, CSP-gamma	uc002rjl.1	Q8N7S2	OTTHUMG00000097079	ENST00000296097.3:c.569A>T	chr2.hg19:g.27503082A>T	ENSP00000296097:p.*190Leuext*11	244.0	0.0	.	794	215.0	64.0	.	NM_173650	B4DY29|Q53SY5|Q8IYQ4|Q96RJ8	Missense_Mutation	SNP	ENST00000296097.3	hg19	CCDS1744.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.13|16.13	3.037320|3.037320	0.54896|0.54896	.|.	.|.	ENSG00000163793|ENSG00000163793	ENST00000406962|ENST00000296097;ENST00000402462;ENST00000404433	.|.	.|.	.|.	3.86|3.86	0.87|0.87	0.19102|0.19102	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	2.2003|2.2003	0.03921|0.03921	0.5749:0.0:0.1962:0.2289|0.5749:0.0:0.1962:0.2289	.|.	.|.	.|.	.|.	X|L	103|190;190;174	.|.	.|.	K|X	+|+	1|2	0|2	DNAJC5G|DNAJC5G	27356586|27356586	0.017000|0.017000	0.18338|0.18338	0.000000|0.000000	0.03702|0.03702	0.353000|0.353000	0.29299|0.29299	0.770000|0.770000	0.26618|0.26618	0.154000|0.154000	0.19237|0.19237	0.379000|0.379000	0.24179|0.24179	AAG|TAA	.	.	.	none		0.333	DNAJC5G-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214200.1	NM_173650		T	27503082	A	T	27503082	4	4	163	1	0	0	0	0	0	0	0	0	4654	369	13	5	583	5	DNAJC5G	2	27503082	Nonstop_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	180715	27503082	215696291	6	9618											
LTBP1	4052	hgsc.bcm.edu	37	chr2	33359941	33359941	+	Missense_Mutation	SNP	A	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	caccaagggcagctgtcagaAcagctgtgagaaggggaaca	14	4	14	9	0	1	2	1	1	0	2	1	4	1	3	1	3	4	3	1	3	4	0			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr2:33359941A>C	ENST00000404816.2	+	5	1468	c.1115A>C	c.(1114-1116)aAc>aCc	p.N372T	LTBP1_ENST00000404525.1_Missense_Mutation_p.N46T|LTBP1_ENST00000390003.4_Missense_Mutation_p.N46T|LTBP1_ENST00000354476.3_Missense_Mutation_p.N372T|LTBP1_ENST00000407925.1_Missense_Mutation_p.N46T|LTBP1_ENST00000418533.2_Missense_Mutation_p.N46T|LTBP1_ENST00000402934.1_Missense_Mutation_p.N46T			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	372					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)				AGCTGTCAGAACAGCTGTGAG	0.562																																					p.N372T		Atlas-SNP	.											.	LTBP1	317	.	0			c.A1115C						PASS	.						101	86	92					2																	33359941		2203	4300	6503	SO:0001583	missense	4052	exon5			GTCAGAACAGCTG		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.1115A>C	chr2.hg19:g.33359941A>C	ENSP00000386043:p.Asn372Thr	63.0	0.0	.		74.0	23.0	.	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	hg19	CCDS33177.2	.	.	.	.	.	.	.	.	.	.	A	22.4	4.287221	0.80803	.	.	ENSG00000049323	ENST00000404816;ENST00000354476;ENST00000432635;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925	D;D;D;D;D;D;D	0.84873	-1.91;-1.91;-1.72;-1.66;-1.75;-1.73;-1.69	5.57	5.57	0.84162	.	.	.	.	.	D	0.91133	0.7208	M	0.62723	1.935	0.80722	D	1	D;D;D;D;D;D	0.89917	0.998;0.999;1.0;0.999;0.999;0.999	D;D;D;D;D;D	0.97110	0.995;0.998;1.0;0.998;0.998;0.998	D	0.92071	0.5664	9	0.87932	D	0	.	15.7244	0.77743	1.0:0.0:0.0:0.0	.	372;46;46;46;46;372	Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4	LTBP1_HUMAN;.;.;.;.;.	T	372;372;61;46;46;46;46;46	ENSP00000386043:N372T;ENSP00000346467:N372T;ENSP00000374653:N46T;ENSP00000393057:N46T;ENSP00000384373:N46T;ENSP00000385359:N46T;ENSP00000384091:N46T	ENSP00000346467:N372T	N	+	2	0	LTBP1	33213445	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.228000	0.95250	2.110000	0.64415	0.379000	0.24179	AAC	.	.	.	none		0.562	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		C	33359941	A	C	33359941	3	2	163	1	0	0	0	0	1	0	0	0	9080	43	2	5	1188	5	LTBP1	2	33359941	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	5856859	33359941	209839432	7	9619											
IMMT	10989	hgsc.bcm.edu	37	chr2	86371396	86371396	+	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	aaatcttcctaaacctcactCtggctgcacctgagtggttc	9	12	7	13	0	3	1	1	1	2	0	5	1	4	1	3	2	2	3	3	2	3	3			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr2:86371396C>G	ENST00000410111.3	-	15	2659	c.2272G>C	c.(2272-2274)Gag>Cag	p.E758Q	IMMT_ENST00000449247.2_Missense_Mutation_p.E747Q|IMMT_ENST00000254636.5_Missense_Mutation_p.E659Q|IMMT_ENST00000442664.2_Missense_Mutation_p.E757Q|IMMT_ENST00000409051.2_Missense_Mutation_p.E711Q	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	758				E -> D (in Ref. 3; CAG33074). {ECO:0000305}.	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)	p.E758Q(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						AAACCTCACTCTGGCTGCACC	0.473																																					p.E758Q		Atlas-SNP	.											IMMT,NS,carcinoma,0,1	IMMT	65	.	1	Substitution - Missense(1)	lung(1)	c.G2272C						PASS	.						59	57	58					2																	86371396		1907	4127	6034	SO:0001583	missense	10989	exon15			CTCACTCTGGCTG	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.2272G>C	chr2.hg19:g.86371396C>G	ENSP00000387262:p.Glu758Gln	58.0	0.0	.		65.0	21.0	.	NM_006839	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Missense_Mutation	SNP	ENST00000410111.3	hg19	CCDS46355.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.72|11.72	1.722342|1.722342	0.30503|0.30503	.|.	.|.	ENSG00000132305|ENSG00000132305	ENST00000254636;ENST00000449247;ENST00000410111;ENST00000442664;ENST00000409051;ENST00000545283;ENST00000377310;ENST00000398211;ENST00000409715|ENST00000419070	T;T;T;T;T|.	0.35236|.	1.32;1.35;1.36;1.35;1.34|.	4.44|4.44	3.55|3.55	0.40652|0.40652	.|.	0.145672|.	0.32041|.	N|.	0.006672|.	T|T	0.13157|0.13157	0.0319|0.0319	N|N	0.02011|0.02011	-0.69|-0.69	0.24917|0.24917	N|N	0.992003|0.992003	D;D;D;D;D|.	0.71674|.	0.994;0.997;0.998;0.998;0.989|.	D;D;D;D;P|.	0.79784|.	0.979;0.985;0.993;0.993;0.742|.	T|T	0.18335|0.18335	-1.0340|-1.0340	10|5	0.49607|.	T|.	0.09|.	-13.9033|-13.9033	8.3828|8.3828	0.32481|0.32481	0.0:0.7575:0.1586:0.0839|0.0:0.7575:0.1586:0.0839	.|.	711;746;747;726;758|.	B9A067;B4DKR1;Q16891-2;Q16891-3;Q16891|.	.;.;.;.;IMMT_HUMAN|.	Q|T	659;747;758;757;711;747;726;372;659|612	ENSP00000254636:E659Q;ENSP00000396899:E747Q;ENSP00000387262:E758Q;ENSP00000407788:E757Q;ENSP00000387227:E711Q|.	ENSP00000254636:E659Q|.	E|R	-|-	1|2	0|0	IMMT|IMMT	86224907|86224907	0.036000|0.036000	0.19791|0.19791	0.972000|0.972000	0.41901|0.41901	0.346000|0.346000	0.29079|0.29079	1.134000|1.134000	0.31442|0.31442	1.467000|1.467000	0.48044|0.48044	0.650000|0.650000	0.86243|0.86243	GAG|AGA	.	.	.	none		0.473	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839		G	86371396	C	G	86371396	3	3	163	1	0	0	0	0	1	0	0	0	7725	922	32	4	8	4	IMMT	2	86371396	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08	53011455	86371396	156827977	8	9620											
CWC22	57703	hgsc.bcm.edu	37	chr2	180810243	180810243	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctgatgtgtactttgttatAggatctctccaatttgaacc	9	17	7	8	0	2	2	0	2	2	0	4	3	3	3	2	1	2	2	2	1	5	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr2:180810243A>G	ENST00000410053.3	-	20	2639	c.2340T>C	c.(2338-2340)ccT>ccC	p.P780P	CWC22_ENST00000295749.6_Silent_p.P780P	NM_020943.2	NP_065994.1	Q9HCG8	CWC22_HUMAN	CWC22 spliceosome-associated protein	780					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						ACTTTGTTATAGGATCTCTCC	0.388																																					p.P780P		Atlas-SNP	.											.	CWC22	62	.	0			c.T2340C						PASS	.						222	206	211					2																	180810243		1860	4108	5968	SO:0001819	synonymous_variant	57703	exon20			TGTTATAGGATCT		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.2340T>C	chr2.hg19:g.180810243A>G		289.0	0.0	.		272.0	71.0	.	NM_020943	Q05DC2|Q4G135|Q52LF0|Q6PEX2|Q7Z6I0|Q9H5L3|Q9H6Q6	Silent	SNP	ENST00000410053.3	hg19	CCDS46465.1																																																																																			.	.	.	none		0.388	CWC22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334537.1	NM_020943		G	180810243	A	G	180810243	2	3	163	1	0	0	0	0	0	0	0	1	4070	407	15	3		3	CWC22	2	180810243	Silent	SNP	A	TCGA-EV-5903-01A-11D-1589-08	94438847	180810243	62389130	9	9621											
ERBB4	2066	hgsc.bcm.edu	37	chr2	212295693	212295693	+	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	tcctccatcagcattgtactCtttttcatctccttccaaga	8	16	3	14	0	4	1	2	0	2	1	8	1	7	1	4	0	2	2	4	0	2	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr2:212295693C>A	ENST00000342788.4	-	21	2930	c.2620G>T	c.(2620-2622)Gag>Tag	p.E874*	ERBB4_ENST00000402597.1_Nonsense_Mutation_p.E864*|ERBB4_ENST00000436443.1_Nonsense_Mutation_p.E874*	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	874	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	GCATTGTACTCTTTTTCATCT	0.373										TSP Lung(8;0.080)																											p.E874X		Atlas-SNP	.											ERBB4,colon,carcinoma,0,1	ERBB4	480	.	0			c.G2620T						PASS	.						147	139	142					2																	212295693		2203	4300	6503	SO:0001587	stop_gained	2066	exon21			TGTACTCTTTTTC	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.2620G>T	chr2.hg19:g.212295693C>A	ENSP00000342235:p.Glu874*	200.0	0.0	.		185.0	54.0	.	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Nonsense_Mutation	SNP	ENST00000342788.4	hg19	CCDS2394.1	.	.	.	.	.	.	.	.	.	.	C	33	5.264878	0.95399	.	.	ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597	.	.	.	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	19.0631	0.93100	0.0:1.0:0.0:0.0	.	.	.	.	X	874;874;864	.	ENSP00000342235:E874X	E	-	1	0	ERBB4	212003938	1.000000	0.71417	1.000000	0.80357	0.028000	0.11728	7.747000	0.85070	2.565000	0.86533	0.563000	0.77884	GAG	.	.	.	none		0.373	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		A	212295693	C	A	212295693	4	1	163	1	0	0	0	0	0	1	0	0	5211	922	32	4	1338	4	ERBB4	2	212295693	Nonsense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08	31485450	212295693	30903680	10	9622											
DNAJB2	3300	hgsc.bcm.edu	37	chr2	220149459	220149459	+	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	ggtccagcagacccctgcctCatgccccttggacagcgacc	7	6	10	18	1	1	1	1	0	0	1	2	3	2	2	7	2	4	1	7	2	0	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr2:220149459C>A	ENST00000336576.5	+	9	1013	c.725C>A	c.(724-726)tCa>tAa	p.S242*	DNAJB2_ENST00000392086.4_Nonsense_Mutation_p.S242*|DNAJB2_ENST00000463463.1_3'UTR	NM_006736.5	NP_006727.2	P25686	DNJB2_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 2	242					cell death (GO:0008219)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of inclusion body assembly (GO:0090084)|negative regulation of protein deubiquitination (GO:0090086)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein folding (GO:0006457)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|inclusion body (GO:0016234)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|polyubiquitin binding (GO:0031593)|proteasome binding (GO:0070628)|unfolded protein binding (GO:0051082)			endometrium(4)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	14		Renal(207;0.0474)		Epithelial(149;1.97e-06)|all cancers(144;0.00028)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ACCCCTGCCTCATGCCCCTTG	0.637																																					p.S242X		Atlas-SNP	.											.	DNAJB2	31	.	0			c.C725A						PASS	.						35	34	34					2																	220149459		2203	4299	6502	SO:0001587	stop_gained	3300	exon9			CTGCCTCATGCCC		CCDS2439.1, CCDS46519.1	2q32-q34	2011-09-02			ENSG00000135924	ENSG00000135924		"Heat shock proteins / DNAJ (HSP40)"	5228	protein-coding gene	gene with protein product		604139		HSJ1		1599432, 10516435	Standard	NM_006736		Approved	HSPF3	uc002vkx.1	P25686	OTTHUMG00000133134	ENST00000336576.5:c.725C>A	chr2.hg19:g.220149459C>A	ENSP00000338019:p.Ser242*	50.0	0.0	.		36.0	5.0	.	NM_006736	A8K9P6|Q8IUK1|Q8IUK2|Q96F52	Nonsense_Mutation	SNP	ENST00000336576.5	hg19	CCDS2439.1	.	.	.	.	.	.	.	.	.	.	C	15.68	2.905268	0.52333	.	.	ENSG00000135924	ENST00000336576;ENST00000392086;ENST00000392087	.	.	.	4.83	3.87	0.44632	.	1937.130000	0.00166	N	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.3425	0.60553	0.0:0.9096:0.0:0.0904	.	.	.	.	X	242;242;211	.	ENSP00000338019:S242X	S	+	2	0	DNAJB2	219857703	0.000000	0.05858	0.009000	0.14445	0.006000	0.05464	-0.017000	0.12590	2.512000	0.84698	0.462000	0.41574	TCA	.	.	.	none		0.637	DNAJB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256823.2			A	220149459	C	A	220149459	4	1	163	1	0	0	0	0	0	1	0	0	4622	838	29	4	755	4	DNAJB2	2	220149459	Nonsense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08	7853766	220149459	23049914	11	9623											
HDAC4	9759	hgsc.bcm.edu	37	chr2	239988463	239988463	+	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	catgcttccgaggcgtcgcaAatggcggtcaggtcgtggcc	6	8	15	12	5	1	0	1	0	0	0	4	1	2	0	2	5	1	2	2	5	1	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr2:239988463A>T	ENST00000345617.3	-	24	3734	c.2943T>A	c.(2941-2943)atT>atA	p.I981I	AC017028.4_ENST00000577359.1_RNA|AC017028.3_ENST00000584260.1_RNA|AC017028.10_ENST00000579161.1_RNA|MIR4440_ENST00000583986.1_RNA|AC017028.2_ENST00000578555.1_RNA|HDAC4_ENST00000543185.1_Silent_p.I565I|AC017028.6_ENST00000577291.1_RNA|AC017028.9_ENST00000581111.1_RNA|AC017028.5_ENST00000582834.1_RNA	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	981	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)		AGGCGTCGCAAATGGCGGTCA	0.632																																					p.I981I		Atlas-SNP	.											.	HDAC4	127	.	0			c.T2943A						PASS	.						78	75	76					2																	239988463		2203	4300	6503	SO:0001819	synonymous_variant	9759	exon24			GTCGCAAATGGCG	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.2943T>A	chr2.hg19:g.239988463A>T		139.0	0.0	.		124.0	31.0	.	NM_006037	Q9UND6	Silent	SNP	ENST00000345617.3	hg19	CCDS2529.1	.	.	.	.	.	.	.	.	.	.	A	11.87	1.768867	0.31320	.	.	ENSG00000068024	ENST00000430200	.	.	.	4.21	-5.54	0.02544	.	.	.	.	.	T	0.62829	0.2460	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.64305	-0.6439	4	.	.	.	.	14.9101	0.70749	0.3468:0.0:0.6532:0.0	.	.	.	.	Y	72	.	.	F	-	2	0	HDAC4	239653400	0.715000	0.27946	0.962000	0.40283	0.971000	0.66376	-0.071000	0.11505	-1.038000	0.03279	-0.376000	0.06991	TTT	.	.	.	none		0.632	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037		T	239988463	A	T	239988463	2	4	163	1	0	0	0	0	0	0	0	1	7016	10	1	5		5	HDAC4	2	239988463	Silent	SNP	A	TCGA-EV-5903-01A-11D-1589-08	19839004	239988463	3210910	12	9624											
FARP2	9855	hgsc.bcm.edu	37	chr2	242433435	242433435	+	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	tcctccaggtggatggaggtGatccagggggccagcagctc	7	7	16	11	0	0	1	0	1	0	0	4	3	3	3	4	6	2	2	4	6	0	0			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr2:242433435G>C	ENST00000264042.3	+	27	3230	c.3060G>C	c.(3058-3060)gtG>gtC	p.V1020V	STK25_ENST00000316586.4_3'UTR|STK25_ENST00000478403.1_5'Flank	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	1020	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)		GGATGGAGGTGATCCAGGGGG	0.637																																					p.V1020V		Atlas-SNP	.											.	FARP2	92	.	0			c.G3060C						PASS	.						51	56	55					2																	242433435		2202	4299	6501	SO:0001819	synonymous_variant	9855	exon27			GGAGGTGATCCAG	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.3060G>C	chr2.hg19:g.242433435G>C		113.0	0.0	.		96.0	22.0	.	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Silent	SNP	ENST00000264042.3	hg19	CCDS33424.1	.	.	.	.	.	.	.	.	.	.	G	10.70	1.424530	0.25639	.	.	ENSG00000006607	ENST00000444371;ENST00000412332	.	.	.	4.94	4.04	0.47022	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5752	0.61870	0.0:0.1619:0.8381:0.0	.	.	.	.	S	163;22	.	.	X	+	2	2	FARP2	242082108	1.000000	0.71417	0.997000	0.53966	0.721000	0.41392	0.714000	0.25808	1.176000	0.42840	0.655000	0.94253	TGA	.	.	.	none		0.637	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1			C	242433435	G	C	242433435	2	2	163	1	0	0	0	0	0	0	0	1	5684	1277	45	4		4	FARP2	2	242433435	Silent	SNP	G	TCGA-EV-5903-01A-11D-1589-08	2444972	242433435	765938	13	9625											
CLASP2	23122	hgsc.bcm.edu	37	chr3	33552091	33552091	+	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	ctctggcaaaagcaggtttaGggtttccttggacactctct	8	13	10	10	0	2	0	0	0	2	0	4	1	3	1	1	4	1	4	1	4	3	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr3:33552091G>T	ENST00000468888.2	-	37	4346	c.4300C>A	c.(4300-4302)Cta>Ata	p.L1434I	CLASP2_ENST00000480013.1_Missense_Mutation_p.L1213I|CLASP2_ENST00000399362.4_Missense_Mutation_p.L1433I|CLASP2_ENST00000359576.5_Missense_Mutation_p.L1425I|CLASP2_ENST00000461133.3_Missense_Mutation_p.L1193I|CLASP2_ENST00000539981.1_3'UTR|CLASP2_ENST00000307312.7_Missense_Mutation_p.L915I			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	1214					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						AGCAGGTTTAGGGTTTCCTTG	0.393																																					p.L1435I		Atlas-SNP	.											.	CLASP2	138	.	0			c.C4303A						PASS	.						195	174	181					3																	33552091		1882	4117	5999	SO:0001583	missense	23122	exon37			GGTTTAGGGTTTC	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.4300C>A	chr3.hg19:g.33552091G>T	ENSP00000419974:p.Leu1434Ile	93.0	0.0	.		74.0	13.0	.	NM_015097	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Missense_Mutation	SNP	ENST00000468888.2	hg19		.	.	.	.	.	.	.	.	.	.	G	28.7	4.942933	0.92526	.	.	ENSG00000163539	ENST00000468888;ENST00000399362;ENST00000359576;ENST00000307312;ENST00000480013;ENST00000461133	T;T;T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22;-0.22;-0.22	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.80210	0.4581	L	0.60845	1.875	0.80722	D	1	D;P	0.71674	0.998;0.725	D;P	0.77557	0.99;0.759	T	0.74633	-0.3600	10	0.31617	T	0.26	-16.2438	20.6634	0.99662	0.0:0.0:1.0:0.0	.	1425;1433	F5H604;E7ERI8	.;.	I	1434;1433;1425;915;1213;1193	ENSP00000419974:L1434I;ENSP00000382297:L1433I;ENSP00000352581:L1425I;ENSP00000304743:L915I;ENSP00000417518:L1213I;ENSP00000419305:L1193I	ENSP00000304743:L915I	L	-	1	2	CLASP2	33527095	1.000000	0.71417	0.998000	0.56505	0.972000	0.66771	7.666000	0.83877	2.894000	0.99253	0.655000	0.94253	CTA	.	.	.	none		0.393	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044		T	33552091	G	T	33552091	3	4	163	1	0	0	0	0	1	0	0	0	3457	991	35	4	256	4	CLASP2	3	33552091	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08		33552091	164470339	14	9626											
LAMB2	3913	hgsc.bcm.edu	37	chr3	49159166	49159166	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cactgcctgccgtttcttctGctgtagaggctgccagacta	6	12	10	13	1	2	2	0	0	2	2	2	2	2	2	3	1	4	4	3	1	2	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr3:49159166G>A	ENST00000418109.1	-	31	5215	c.5051C>T	c.(5050-5052)gCa>gTa	p.A1684V	USP19_ENST00000488993.1_5'Flank|USP19_ENST00000453664.1_5'Flank|USP19_ENST00000434032.2_5'Flank|USP19_ENST00000398898.2_5'Flank|USP19_ENST00000398888.2_5'Flank|USP19_ENST00000417901.1_5'Flank|USP19_ENST00000398892.3_5'Flank|LAMB2_ENST00000305544.4_Missense_Mutation_p.A1684V	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	1684	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)		CGTTTCTTCTGCTGTAGAGGC	0.607																																					p.A1684V		Atlas-SNP	.											.	LAMB2	156	.	0			c.C5051T						PASS	.						75	78	77					3																	49159166		2202	4300	6502	SO:0001583	missense	3913	exon30			TCTTCTGCTGTAG		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.5051C>T	chr3.hg19:g.49159166G>A	ENSP00000388325:p.Ala1684Val	163.0	0.0	.		152.0	43.0	.	NM_002292	Q16321	Missense_Mutation	SNP	ENST00000418109.1	hg19	CCDS2789.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.107341	0.77096	.	.	ENSG00000172037	ENST00000418109;ENST00000305544	T;T	0.38240	1.15;1.15	5.79	4.92	0.64577	.	0.000000	0.85682	D	0.000000	T	0.49677	0.1571	L	0.49350	1.555	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.44574	-0.9319	10	0.07325	T	0.83	.	14.8494	0.70284	0.0689:0.0:0.9311:0.0	.	1684	P55268	LAMB2_HUMAN	V	1684	ENSP00000388325:A1684V;ENSP00000307156:A1684V	ENSP00000307156:A1684V	A	-	2	0	LAMB2	49134170	1.000000	0.71417	0.027000	0.17364	0.970000	0.65996	9.339000	0.96797	1.451000	0.47736	0.655000	0.94253	GCA	.	.	.	none		0.607	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		A	49159166	G	A	49159166	3	1	163	1	0	0	0	0	1	0	0	0	8618	1319	46	2	357	2	LAMB2	3	49159166	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	15607075	49159166	148863264	15	9627											
TMEM22	80723	hgsc.bcm.edu	37	chr3	136573495	136573495	+	Frame_Shift_Del	DEL	G	G	-																															tgagtgaaatgaaaaaaaaaGggagagctttctttggaacc																										TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr3:136573495delG	ENST00000446465.2	+	2	821	c.193delG	c.(193-195)gggfs	p.G65fs	RP11-85F14.5_ENST00000461864.1_RNA|RP11-85F14.5_ENST00000474250.1_RNA|SLC35G2_ENST00000393079.3_Frame_Shift_Del_p.G65fs|RP11-85F14.5_ENST00000470236.1_RNA	NM_025246.2	NP_079522.2			solute carrier family 35, member G2									p.G65R(1)									GAAAAAAAAAGGGAGAGCTTT	0.403																																					p.K64fs		Atlas-INDEL	.											.	.	.	.	1	Substitution - Missense(1)	lung(1)	c.192delA						PASS	.						84	94	91					3																	136573495		2203	4300	6503	SO:0001589	frameshift_variant	80723	exon2			.	BC022557	CCDS3091.1	3q22.3	2013-05-22	2012-03-09	2012-03-09	ENSG00000168917	ENSG00000168917		"Solute carriers"	28480	protein-coding gene	gene with protein product			"transmembrane protein 22"	TMEM22		11230166	Standard	NM_001097600		Approved	MGC3295, DKFZp564K2464	uc003erf.4	Q8TBE7	OTTHUMG00000159787	ENST00000446465.2:c.193delG	chr3.hg19:g.136573495delG	ENSP00000400839:p.Gly65fs	146.0	0.0	0		162.0	36.0	0.222222	NM_001097599		Frame_Shift_Del	DEL	ENST00000446465.2	hg19	CCDS3091.1																																																																																			.	.	.	none		0.403	SLC35G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357317.1	NM_025246		-	136573495	G	-	136573495	7	5	163	1	0	1	0	1	0	0	0	0	16155	1000	35	0	195	0	TMEM22	3	136573495	Frame_Shift_Del	DEL	G	TCGA-EV-5903-01A-11D-1589-08	87414329	136573495	61448935	16	9628											
TNFSF10	8743	hgsc.bcm.edu	37	chr3	172227069	172227069	+	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	tgtgagctgctactctctgaGgacctctttctctcactagg	6	14	9	12	0	4	2	1	2	3	0	6	3	4	3	1	2	3	2	1	2	2	3	rs369143448		TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr3:172227069G>C	ENST00000241261.2	-	4	478	c.356C>G	c.(355-357)cCt>cGt	p.P119R	TNFSF10_ENST00000420541.2_Intron	NM_003810.3	NP_003801.1	P50591	TNF10_HUMAN	tumor necrosis factor (ligand) superfamily, member 10	119					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|immune response (GO:0006955)|male gonad development (GO:0008584)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to insulin (GO:0032868)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)			breast(2)|cervix(1)|large_intestine(1)|lung(6)|ovary(1)|skin(4)	15	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.67e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)			TACTCTCTGAGGACCTCTTTC	0.388																																					p.P119R		Atlas-SNP	.											.	TNFSF10	30	.	0			c.C356G						PASS	.						105	102	103					3																	172227069		2203	4300	6503	SO:0001583	missense	8743	exon4			CTCTGAGGACCTC	U37518	CCDS3219.1, CCDS54680.1	3q26	2006-09-20			ENSG00000121858	ENSG00000121858		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11925	protein-coding gene	gene with protein product		603598				8777713, 8663110	Standard	NM_003810		Approved	TRAIL, Apo-2L, TL2, CD253	uc003fid.3	P50591	OTTHUMG00000156917	ENST00000241261.2:c.356C>G	chr3.hg19:g.172227069G>C	ENSP00000241261:p.Pro119Arg	113.0	0.0	.		109.0	25.0	.	NM_003810	A1Y9B3	Missense_Mutation	SNP	ENST00000241261.2	hg19	CCDS3219.1	.	.	.	.	.	.	.	.	.	.	G	4.858	0.159457	0.09236	.	.	ENSG00000121858	ENST00000241261	D	0.86769	-2.17	4.71	-4.74	0.03249	.	1.516980	0.03189	N	0.173149	T	0.80325	0.4602	L	0.54323	1.7	0.09310	N	1	B	0.28324	0.207	B	0.23574	0.047	T	0.64097	-0.6487	10	0.08837	T	0.75	5.0717	8.19	0.31363	0.659:0.1329:0.208:0.0	.	119	P50591	TNF10_HUMAN	R	119	ENSP00000241261:P119R	ENSP00000241261:P119R	P	-	2	0	TNFSF10	173709763	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.053000	0.03500	-0.976000	0.03542	-1.113000	0.02065	CCT	.	.	.	alt		0.388	TNFSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346601.1			C	172227069	G	C	172227069	3	2	163	1	0	0	0	0	1	0	0	0	16313	1000	35	4	497	4	TNFSF10	3	172227069	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	35653574	172227069	25795361	17	9629											
FGF12	2257	hgsc.bcm.edu	37	chr3	192078247	192078247	+	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	gttttcgtccttggtcccatCaatggtaccatctgggtgca	6	14	10	11	1	2	0	1	0	1	0	5	0	4	0	3	3	2	3	3	3	2	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr3:192078247C>A	ENST00000454309.2	-	2	1105	c.280G>T	c.(280-282)Gat>Tat	p.D94Y	FGF12_ENST00000450716.1_Missense_Mutation_p.D32Y|FGF12_ENST00000445105.2_Missense_Mutation_p.D32Y|FGF12_ENST00000430714.1_Intron|FGF12_ENST00000264730.3_Missense_Mutation_p.D32Y	NM_021032.4	NP_066360.1	P61328	FGF12_HUMAN	fibroblast growth factor 12	94					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)		TTGGTCCCATCAATGGTACCA	0.408																																					p.D94Y		Atlas-SNP	.											.	FGF12	88	.	0			c.G280T						PASS	.						178	150	159					3																	192078247		2203	4300	6503	SO:0001583	missense	2257	exon2			TCCCATCAATGGT	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.280G>T	chr3.hg19:g.192078247C>A	ENSP00000413496:p.Asp94Tyr	82.0	0.0	.		79.0	20.0	.	NM_021032	B2R6B7|B2R976|O35339|P70376|Q8TBG5|Q92912|Q93001	Missense_Mutation	SNP	ENST00000454309.2	hg19	CCDS3301.1	.	.	.	.	.	.	.	.	.	.	C	19.73	3.882126	0.72294	.	.	ENSG00000114279	ENST00000264730;ENST00000392454;ENST00000445105;ENST00000454309;ENST00000450716;ENST00000448795;ENST00000418610	T;T;T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39;-0.39;-0.39	5.53	5.53	0.82687	.	0.192095	0.56097	D	0.000035	D	0.82857	0.5128	M	0.85630	2.765	0.80722	D	1	D;D	0.62365	0.981;0.991	P;P	0.62298	0.838;0.9	D	0.85384	0.1121	10	0.72032	D	0.01	.	18.4573	0.90725	0.0:1.0:0.0:0.0	.	32;94	P61328-2;P61328	.;FGF12_HUMAN	Y	32;32;32;94;32;8;32	ENSP00000264730:D32Y;ENSP00000393686:D32Y;ENSP00000413496:D94Y;ENSP00000397635:D32Y;ENSP00000412904:D8Y;ENSP00000395517:D32Y	ENSP00000264730:D32Y	D	-	1	0	FGF12	193560941	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.390000	0.59646	2.613000	0.88420	0.591000	0.81541	GAT	.	.	.	none		0.408	FGF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343160.1	NM_021032		A	192078247	C	A	192078247	3	1	163	1	0	0	0	0	1	0	0	0	5848	826	29	4	467	4	FGF12	3	192078247	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08	19851178	192078247	5944183	18	9630											
SPON2	10417	hgsc.bcm.edu	37	chr4	1165206	1165206	+	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	ggcctcgccgcgctccgcaaAgtcgcgcagcccgttactga	6	6	12	17	7	0	1	0	1	0	0	3	1	1	1	4	1	2	4	4	1	2	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr4:1165206A>T	ENST00000290902.5	-	3	621	c.289T>A	c.(289-291)Ttt>Att	p.F97I	SPON2_ENST00000431380.1_Missense_Mutation_p.F97I	NM_012445.3	NP_036577	Q9BUD6	SPON2_HUMAN	spondin 2, extracellular matrix protein	97	Spondin. {ECO:0000255|PROSITE- ProRule:PRU00364}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|pancreas(1)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(23;0.00805)	UCEC - Uterine corpus endometrioid carcinoma (64;0.139)|Colorectal(103;0.19)		CGCTCCGCAAAGTCGCGCAGC	0.701																																					p.F97I		Atlas-SNP	.											.	SPON2	22	.	0			c.T289A						PASS	.						26	28	27					4																	1165206		2193	4283	6476	SO:0001583	missense	10417	exon3			CCGCAAAGTCGCG	AB027466	CCDS3347.1	4p16.3	2008-07-29			ENSG00000159674	ENSG00000159674			11253	protein-coding gene	gene with protein product	"Mindin", "M-spondin"	605918				10512675, 15094111	Standard	NM_012445		Approved	DIL1	uc003gco.4	Q9BUD6	OTTHUMG00000089002	ENST00000290902.5:c.289T>A	chr4.hg19:g.1165206A>T	ENSP00000290902:p.Phe97Ile	65.0	0.0	.		52.0	8.0	.	NM_012445	D3DVN9|Q4W5N4|Q9ULW1	Missense_Mutation	SNP	ENST00000290902.5	hg19	CCDS3347.1	.	.	.	.	.	.	.	.	.	.	A	19.08	3.757899	0.69648	.	.	ENSG00000159674	ENST00000290902;ENST00000431380;ENST00000503765	T;T;T	0.44881	0.91;0.91;0.91	4.5	4.5	0.54988	Spondin, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.61236	0.2331	M	0.71296	2.17	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.76071	0.987;0.955;0.967	T	0.61187	-0.7113	10	0.35671	T	0.21	.	13.4453	0.61138	1.0:0.0:0.0:0.0	.	97;97;97	D6RB12;D3DVN9;Q9BUD6	.;.;SPON2_HUMAN	I	97	ENSP00000290902:F97I;ENSP00000394832:F97I;ENSP00000424542:F97I	ENSP00000290902:F97I	F	-	1	0	SPON2	1155206	1.000000	0.71417	0.979000	0.43373	0.095000	0.18619	5.240000	0.65378	1.667000	0.50832	0.418000	0.28097	TTT	.	.	.	none		0.701	SPON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202080.2			T	1165206	A	T	1165206	3	4	163	1	0	0	0	0	1	0	0	0	15095	72	3	5	722	5	SPON2	4	1165206	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08		1165206	189989070	19	9631											
KIAA1530	57654	hgsc.bcm.edu	37	chr4	1347115	1347115	+	Missense_Mutation	SNP	A	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	cacaggtgacccctcagatgAggacgaggacagcgacctcg	11	4	13	13	3	1	3	1	2	0	1	2	7	1	5	3	3	1	0	3	3	0	0			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr4:1347115A>C	ENST00000389851.4	+	5	1295	c.848A>C	c.(847-849)gAg>gCg	p.E283A	UVSSA_ENST00000511216.1_Missense_Mutation_p.E283A|UVSSA_ENST00000507531.1_Missense_Mutation_p.E283A	NM_020894.2	NP_065945.2	Q2YD98	UVSSA_HUMAN	UV-stimulated scaffold protein A	283					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)										CCCTCAGATGAGGACGAGGAC	0.657																																					p.E283A		Atlas-SNP	.											.	.	.	.	0			c.A848C						PASS	.						17	18	18					4																	1347115		2193	4283	6476	SO:0001583	missense	57654	exon5			CAGATGAGGACGA	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.848A>C	chr4.hg19:g.1347115A>C	ENSP00000374501:p.Glu283Ala	25.0	0.0	.		23.0	6.0	.	NM_020894	A8K9E6|B2RU11|Q8WTX4|Q9P1Z8	Missense_Mutation	SNP	ENST00000389851.4	hg19	CCDS33938.1	.	.	.	.	.	.	.	.	.	.	A	6.849	0.525889	0.13066	.	.	ENSG00000163945	ENST00000511216;ENST00000389851;ENST00000507531	T;T;T	0.32988	1.43;1.43;1.43	4.13	2.89	0.33648	.	0.479895	0.23176	N	0.051071	T	0.20007	0.0481	L	0.55481	1.735	0.23204	N	0.998124	B	0.30406	0.278	B	0.24974	0.057	T	0.29058	-1.0024	10	0.05721	T	0.95	.	5.9647	0.19318	0.7766:0.0:0.2234:0.0	.	283	Q2YD98	K1530_HUMAN	A	283	ENSP00000425130:E283A;ENSP00000374501:E283A;ENSP00000421741:E283A	ENSP00000374501:E283A	E	+	2	0	KIAA1530	1337115	0.933000	0.31639	0.289000	0.24876	0.208000	0.24298	3.004000	0.49513	0.438000	0.26450	0.260000	0.18958	GAG	.	.	.	none		0.657	UVSSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359480.1	NM_020894		C	1347115	A	C	1347115	3	2	163	1	0	0	0	0	1	0	0	0	8248	304	11	5	862	5	KIAA1530	4	1347115	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	181909	1347115	189807161	20	9632											
DCHS2	54798	hgsc.bcm.edu	37	chr4	155180741	155180741	+	Frame_Shift_Del	DEL	C	C	-																															ttggctttcagacactgatgCctggtaaatgctttgttcaa																										TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr4:155180741delC	ENST00000357232.4	-	20	5379	c.5380delG	c.(5380-5382)gcafs	p.A1794fs		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1794	Cadherin 16. {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)		GACACTGATGCCTGGTAAATG	0.413																																					p.A1794fs		Atlas-INDEL	.											.	DCHS2	594	.	0			c.5381delC						PASS	.						213	191	199					4																	155180741		2203	4300	6503	SO:0001589	frameshift_variant	54798	exon20			.	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.5380delG	chr4.hg19:g.155180741delC	ENSP00000349768:p.Ala1794fs	185.0	0.0	0		205.0	45.0	0.219512	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Frame_Shift_Del	DEL	ENST00000357232.4	hg19	CCDS3785.1																																																																																			.	.	.	none		0.413	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		-	155180741	C	-	155180741	7	5	163	1	0	1	0	1	0	0	0	0	4290	739	26	0	3394	0	DCHS2	4	155180741	Frame_Shift_Del	DEL	C	TCGA-EV-5903-01A-11D-1589-08	153833626	155180741	35973535	21	9633											
FRG1	2483	hgsc.bcm.edu	37	chr4	190864392	190864392	+	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	caaagataagaaaagaaaaaGagaagaagatgaagaaaccc	26	2	9	4	0	0	8	0	1	0	7	0	9	0	8	1	0	1	0	1	0	10	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr4:190864392G>C	ENST00000226798.4	+	2	320	c.98G>C	c.(97-99)aGa>aCa	p.R33T	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	33					mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.R33K(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		aaaagaaaaagagaagaagat	0.308																																					p.R33T		Atlas-SNP	.											FRG1,NS,carcinoma,0,1	FRG1	76	.	1	Substitution - Missense(1)	breast(1)	c.G98C						PASS	.						42	51	48					4																	190864392		2197	4226	6423	SO:0001583	missense	2483	exon2			GAAAAAGAGAAGA	L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536			3954	protein-coding gene	gene with protein product		601278				8733123	Standard	XM_005262880		Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.98G>C	chr4.hg19:g.190864392G>C	ENSP00000226798:p.Arg33Thr	69.0	0.0	.		62.0	3.0	.	NM_004477	A8K775	Missense_Mutation	SNP	ENST00000226798.4	hg19	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	.	5.613	0.297786	0.10622	.	.	ENSG00000109536	ENST00000226798	T	0.30714	1.52	3.1	2.25	0.28309	.	0.286306	0.34046	N	0.004315	T	0.27594	0.0678	M	0.70595	2.14	0.46701	D	0.999166	P	0.34662	0.462	B	0.36534	0.227	T	0.03306	-1.1050	10	0.14252	T	0.57	1.2394	6.1276	0.20187	0.1417:0.0:0.8583:0.0	.	33	Q14331	FRG1_HUMAN	T	33	ENSP00000226798:R33T	ENSP00000226798:R33T	R	+	2	0	FRG1	191101386	1.000000	0.71417	0.991000	0.47740	0.892000	0.51952	2.970000	0.49240	0.874000	0.35823	0.549000	0.68633	AGA	.	.	.	none		0.308	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477		C	190864392	G	C	190864392	3	2	163	1	0	0	0	0	1	0	0	0	6053	942	33	4	104	4	FRG1	4	190864392	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	35683651	190864392	289884	22	9634											
TMEM161B	153396	hgsc.bcm.edu	37	chr5	87521633	87521633	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgtttctagatgaaggtcaAtatcctttggaatggttaat	11	17	9	4	0	2	2	1	1	1	1	3	3	3	3	1	3	0	2	1	3	6	6			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr5:87521633A>G	ENST00000296595.6	-	4	366	c.242T>C	c.(241-243)aTt>aCt	p.I81T	TMEM161B_ENST00000509387.1_5'UTR|TMEM161B_ENST00000512429.1_Missense_Mutation_p.I70T|TMEM161B_ENST00000514135.1_Missense_Mutation_p.I81T|TMEM161B_ENST00000506536.1_5'UTR	NM_153354.3	NP_699185.1	Q8NDZ6	T161B_HUMAN	transmembrane protein 161B	81						integral component of membrane (GO:0016021)				endometrium(4)|large_intestine(3)|lung(9)|skin(3)|upper_aerodigestive_tract(1)	20		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)		ATGAAGGTCAATATCCTTTGG	0.299																																					p.I81T		Atlas-SNP	.											.	TMEM161B	46	.	0			c.T242C						PASS	.						132	129	130					5																	87521633		2202	4298	6500	SO:0001583	missense	153396	exon4			AGGTCAATATCCT	BC037287	CCDS4065.1, CCDS75269.1, CCDS75270.1	5q14.3	2008-02-05			ENSG00000164180	ENSG00000164180			28483	protein-coding gene	gene with protein product						12477932	Standard	NM_001289008		Approved	MGC33214	uc003kjc.3	Q8NDZ6	OTTHUMG00000131323	ENST00000296595.6:c.242T>C	chr5.hg19:g.87521633A>G	ENSP00000296595:p.Ile81Thr	130.0	0.0	.		150.0	30.0	.	NM_153354	Q5CZH7|Q6UWQ6	Missense_Mutation	SNP	ENST00000296595.6	hg19	CCDS4065.1	.	.	.	.	.	.	.	.	.	.	A	16.80	3.222869	0.58668	.	.	ENSG00000164180	ENST00000514135;ENST00000296595;ENST00000512429;ENST00000443393	.	.	.	5.02	5.02	0.67125	.	0.047070	0.85682	D	0.000000	T	0.55369	0.1916	L	0.44542	1.39	0.80722	D	1	B	0.15719	0.014	B	0.18871	0.023	T	0.52056	-0.8626	9	0.35671	T	0.21	-0.078	15.0267	0.71674	1.0:0.0:0.0:0.0	.	81	Q8NDZ6	T161B_HUMAN	T	81;81;70;81	.	ENSP00000296595:I81T	I	-	2	0	TMEM161B	87557389	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.804000	0.91921	2.025000	0.59659	0.383000	0.25322	ATT	.	.	.	none		0.299	TMEM161B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254094.1	NM_153354		G	87521633	A	G	87521633	3	3	163	1	0	0	0	0	1	0	0	0	16089	101	4	3	1257	3	TMEM161B	5	87521633	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08		87521633	93393627	23	9635											
NSD1	64324	hgsc.bcm.edu	37	chr5	176639042	176639042	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actccttcagcaagcatactTgaggaaccactgacagagca	14	7	8	12	0	1	3	1	2	0	1	2	4	2	4	2	1	5	3	2	1	3	3			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr5:176639042T>C	ENST00000439151.2	+	5	3687	c.3642T>C	c.(3640-3642)ctT>ctC	p.L1214L	NSD1_ENST00000347982.4_Silent_p.L945L|NSD1_ENST00000361032.4_Silent_p.L1111L|NSD1_ENST00000354179.4_Silent_p.L945L	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	1214					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)		CAAGCATACTTGAGGAACCAC	0.483			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.L1214L		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.T3642C						PASS	.						84	82	83					5																	176639042		2203	4300	6503	SO:0001819	synonymous_variant	64324	exon5	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	CATACTTGAGGAA	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.3642T>C	chr5.hg19:g.176639042T>C		58.0	0.0	.		55.0	18.0	.	NM_022455	Q96PD8|Q96RN7	Silent	SNP	ENST00000439151.2	hg19	CCDS4412.1																																																																																			.	.	.	none		0.483	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		C	176639042	T	C	176639042	2	2	163	1	0	0	0	0	0	0	0	1	10676	1799	63	3		3	NSD1	5	176639042	Silent	SNP	T	TCGA-EV-5903-01A-11D-1589-08	89117409	176639042	4276218	24	9636											
NUP153	9972	hgsc.bcm.edu	37	chr6	17688708	17688708	+	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	ctcatcggcatataccagatGgtcctctttattttctggcc	7	15	7	12	1	3	1	1	0	2	1	5	1	4	1	3	3	1	1	3	3	3	6			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr6:17688708G>A	ENST00000262077.2	-	2	252	c.253C>T	c.(253-255)Cat>Tat	p.H85Y	NUP153_ENST00000537253.1_Missense_Mutation_p.H85Y	NM_005124.2	NP_005115.2	P49790	NU153_HUMAN	nucleoporin 153kDa	85					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)			TATACCAGATGGTCCTCTTTA	0.438																																					p.H85Y		Atlas-SNP	.											.	NUP153	116	.	0			c.C253T						PASS	.						130	123	125					6																	17688708		2203	4300	6503	SO:0001583	missense	9972	exon2			CCAGATGGTCCTC	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.253C>T	chr6.hg19:g.17688708G>A	ENSP00000262077:p.His85Tyr	189.0	0.0	.		128.0	39.0	.	NM_005124	B4DIK2|E7EPX5|F6QR24|Q4LE47|Q5T9I7|Q7Z743	Missense_Mutation	SNP	ENST00000262077.2	hg19	CCDS4541.1	.	.	.	.	.	.	.	.	.	.	G	14.97	2.693922	0.48202	.	.	ENSG00000124789	ENST00000262077;ENST00000430136;ENST00000537253	T;T	0.08282	3.13;3.11	5.37	5.37	0.77165	.	0.125530	0.35805	N	0.002971	T	0.06600	0.0169	L	0.29908	0.895	0.42291	D	0.99213	D;B;P	0.65815	0.995;0.021;0.94	P;B;B	0.60609	0.877;0.008;0.439	T	0.06144	-1.0843	10	0.02654	T	1	-2.2032	16.8895	0.86083	0.0:0.0:1.0:0.0	.	85;107;85	F6QR24;Q4LE47;P49790	.;.;NU153_HUMAN	Y	85;107;85	ENSP00000262077:H85Y;ENSP00000444029:H85Y	ENSP00000262077:H85Y	H	-	1	0	NUP153	17796687	0.927000	0.31430	0.892000	0.35008	0.127000	0.20565	4.623000	0.61247	2.494000	0.84150	0.650000	0.86243	CAT	.	.	.	none		0.438	NUP153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039953.1			A	17688708	G	A	17688708	3	1	163	1	0	0	0	0	1	0	0	0	10762	1348	47	2	4258	2	NUP153	6	17688708	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08		17688708	153426359	25	9637											
ZNF184	7738	hgsc.bcm.edu	37	chr6	27420017	27420017	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atcatagggtttctccccagTatgagttttttgatgctgag	8	16	10	7	0	2	3	1	3	1	0	3	3	2	3	2	1	1	4	2	1	2	6			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr6:27420017T>C	ENST00000211936.6	-	6	1605	c.1321A>G	c.(1321-1323)Act>Gct	p.T441A	ZNF184_ENST00000377419.1_Missense_Mutation_p.T441A	NM_007149.2	NP_009080.2	Q99676	ZN184_HUMAN	zinc finger protein 184	441					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|kidney(9)|large_intestine(13)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						TTCTCCCCAGTATGAGTTTTT	0.403																																					p.T441A		Atlas-SNP	.											.	ZNF184	89	.	0			c.A1321G						PASS	.						86	86	86					6																	27420017		2203	4300	6503	SO:0001583	missense	7738	exon6			CCCCAGTATGAGT	U66561	CCDS4624.1	6p21.3	2013-01-08	2006-06-28		ENSG00000096654	ENSG00000096654		"Zinc fingers, C2H2-type", "-"	12975	protein-coding gene	gene with protein product		602277	"zinc finger protein 184 (Kruppel-like)"				Standard	NM_007149		Approved		uc003nji.3	Q99676	OTTHUMG00000014478	ENST00000211936.6:c.1321A>G	chr6.hg19:g.27420017T>C	ENSP00000211936:p.Thr441Ala	192.0	0.0	.		157.0	49.0	.	NM_007149	B2R715|O60792|Q8TBA9	Missense_Mutation	SNP	ENST00000211936.6	hg19	CCDS4624.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.937528	0.73557	.	.	ENSG00000096654	ENST00000211936;ENST00000377419	T;T	0.26518	1.73;1.73	5.27	5.27	0.74061	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.130826	0.35585	N	0.003116	T	0.11367	0.0277	L	0.33624	1.015	0.42611	D	0.993316	P	0.46706	0.883	B	0.38921	0.285	T	0.03139	-1.1068	10	0.87932	D	0	.	13.1686	0.59585	0.0:0.0:0.0:1.0	.	441	Q99676	ZN184_HUMAN	A	441	ENSP00000211936:T441A;ENSP00000366636:T441A	ENSP00000211936:T441A	T	-	1	0	ZNF184	27527996	0.995000	0.38212	0.769000	0.31535	0.998000	0.95712	2.951000	0.49089	2.214000	0.71695	0.533000	0.62120	ACT	.	.	.	none		0.403	ZNF184-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040146.1	NM_007149		C	27420017	T	C	27420017	3	2	163	1	0	0	0	0	1	0	0	0	17763	1638	57	3	938	3	ZNF184	6	27420017	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	9731309	27420017	143695050	26	9638											
RGL2	5863	hgsc.bcm.edu	37	chr6	33260849	33260849	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctccatctggactcggatgaTacggcaatcagaggcccctg	9	8	11	13	2	2	2	1	1	1	1	4	4	3	4	3	4	1	1	3	4	2	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr6:33260849T>C	ENST00000497454.1	-	16	2446	c.1951A>G	c.(1951-1953)Atc>Gtc	p.I651V	RGL2_ENST00000437840.2_5'UTR|PFDN6_ENST00000463584.1_Intron	NM_001243738.1|NM_004761.4	NP_001230667.1|NP_004752.1	O15211	RGL2_HUMAN	ral guanine nucleotide dissociation stimulator-like 2	651	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)	intracellular (GO:0005622)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)			breast(2)|cervix(2)|endometrium(7)|kidney(2)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	34						ACTCGGATGATACGGCAATCA	0.597																																					p.I651V		Atlas-SNP	.											.	RGL2	58	.	0			c.A1951G						PASS	.						202	229	220					6																	33260849		2203	4300	6503	SO:0001583	missense	5863	exon16			GGATGATACGGCA		CCDS4774.1	6p21.3	2010-02-17	2004-06-11	2004-06-16	ENSG00000237441	ENSG00000237441			9769	protein-coding gene	gene with protein product		602306	"RAB2, member RAS oncogene family-like"	RAB2L		8976381	Standard	NM_001243738		Approved	KE1.5, HKE1.5	uc003odv.3	O15211	OTTHUMG00000031072	ENST00000497454.1:c.1951A>G	chr6.hg19:g.33260849T>C	ENSP00000420211:p.Ile651Val	409.0	0.0	.		440.0	148.0	.	NM_004761	B4DG72|Q5STK0|Q9Y3F3	Missense_Mutation	SNP	ENST00000497454.1	hg19	CCDS4774.1	.	.	.	.	.	.	.	.	.	.	T	14.82	2.650468	0.47362	.	.	ENSG00000237441	ENST00000497454;ENST00000421215	T	0.49139	0.79	4.6	4.6	0.57074	Ras-association (3);	0.000000	0.85682	D	0.000000	T	0.46073	0.1374	L	0.40543	1.245	0.80722	D	1	D	0.58620	0.983	D	0.73708	0.981	T	0.45131	-0.9282	10	0.42905	T	0.14	.	10.3298	0.43816	0.0:0.0:0.0:1.0	.	651	O15211	RGL2_HUMAN	V	651;515	ENSP00000420211:I651V	ENSP00000400083:I515V	I	-	1	0	RGL2	33368827	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	5.349000	0.66010	1.937000	0.56155	0.523000	0.50628	ATC	.	.	.	none		0.597	RGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076098.2			C	33260849	T	C	33260849	3	2	163	1	0	0	0	0	1	0	0	0	13290	1406	49	3	394	3	RGL2	6	33260849	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	5840832	33260849	137854218	27	9639											
NUDT3	11165	hgsc.bcm.edu	37	chr6	34309651	34309651	+	Missense_Mutation	SNP	T	T	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	atgcatacctcctcacagacTtcacgaactgctgccacact	11	9	5	16	1	2	1	2	0	0	1	3	2	3	1	3	0	5	2	3	0	2	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr6:34309651T>G	ENST00000607016.1	-	2	509	c.198A>C	c.(196-198)gaA>gaC	p.E66D	RPS10-NUDT3_ENST00000605528.1_Missense_Mutation_p.E185D	NM_006703.3	NP_006694.1	O95989	NUDT3_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 3	66	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				cell-cell signaling (GO:0007267)|diadenosine polyphosphate catabolic process (GO:0015961)|diphosphoinositol polyphosphate catabolic process (GO:0071544)|inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	diphosphoinositol-polyphosphate diphosphatase activity (GO:0008486)|inositol diphosphate tetrakisphosphate diphosphatase activity (GO:0052840)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity (GO:0052846)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052847)|inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity (GO:0052843)|inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052848)|inositol-3-diphosphate-1,2,4,5,6-pentakisphosphate diphosphatase activity (GO:0052844)|inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity (GO:0052845)|magnesium ion binding (GO:0000287)			lung(2)	2						CCTCACAGACTTCACGAACTG	0.532																																					p.E185D	GBM(96;1206 1939 18658 39482)	Atlas-SNP	.											.	.	.	.	0			c.A555C						PASS	.						155	119	131					6																	34309651		2203	4300	6503	SO:0001583	missense	0	exon6			ACAGACTTCACGA	AF062530	CCDS4791.1	6p21.2	2014-07-16			ENSG00000272325	ENSG00000272325		"Nudix motif containing"	8050	protein-coding gene	gene with protein product		609228				9822604	Standard	NM_006703		Approved	DIPP		O95989	OTTHUMG00000014545	ENST00000607016.1:c.198A>C	chr6.hg19:g.34309651T>G	ENSP00000476119:p.Glu66Asp	65.0	0.0	.		56.0	12.0	.	NM_001202470	B2R8N4	Missense_Mutation	SNP	ENST00000607016.1	hg19	CCDS4791.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.725873	0.89298	.	.	ENSG00000112664	ENST00000358797	T	0.29917	1.55	5.66	4.5	0.54988	NUDIX hydrolase domain (3);NUDIX hydrolase, conserved site (1);NUDIX hydrolase domain-like (1);	0.000000	0.85682	D	0.000000	T	0.65428	0.2690	H	0.99415	4.555	0.80722	D	1	P	0.48589	0.912	D	0.75020	0.985	T	0.76889	-0.2792	10	0.87932	D	0	-14.5823	10.5134	0.44874	0.0:0.0772:0.0:0.9228	.	66	O95989	NUDT3_HUMAN	D	66	ENSP00000351650:E66D	ENSP00000351650:E66D	E	-	3	2	NUDT3	34417629	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.537000	0.45702	0.989000	0.38761	0.477000	0.44152	GAA	.	.	.	none		0.532	NUDT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040224.2			G	34309651	T	G	34309651	3	3	163	1	0	0	0	0	1	0	0	0	10747	1606	56	5	336	5	NUDT3	6	34309651	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	1048802	34309651	136805416	28	9640											
ENPP4	22875	hgsc.bcm.edu	37	chr6	46108114	46108114	+	Missense_Mutation	SNP	T	T	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	atactacactcttatagattTgagcccagttgctgcaatac	12	13	6	10	0	1	2	0	1	1	1	1	2	1	2	1	0	6	3	1	0	6	7			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr6:46108114T>G	ENST00000321037.4	+	2	1024	c.794T>G	c.(793-795)tTg>tGg	p.L265W		NM_014936.4	NP_055751.1	Q9Y6X5	ENPP4_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 4 (putative)	265					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						CTTATAGATTTGAGCCCAGTT	0.418																																					p.L265W		Atlas-SNP	.											.	ENPP4	44	.	0			c.T794G						PASS	.						79	78	79					6																	46108114		2203	4300	6503	SO:0001583	missense	22875	exon2			TAGATTTGAGCCC	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.794T>G	chr6.hg19:g.46108114T>G	ENSP00000318066:p.Leu265Trp	87.0	0.0	.		66.0	16.0	.	NM_014936	A8K5G1|Q7L2N1	Missense_Mutation	SNP	ENST00000321037.4	hg19	CCDS34468.1	.	.	.	.	.	.	.	.	.	.	T	9.575	1.121947	0.20877	.	.	ENSG00000001561	ENST00000321037;ENST00000371401	T	0.72394	-0.65	5.67	1.87	0.25490	Alkaline-phosphatase-like, core domain (1);	0.743246	0.13551	N	0.379453	T	0.33411	0.0862	L	0.41710	1.295	0.24368	N	0.994846	B	0.14438	0.01	B	0.21917	0.037	T	0.20240	-1.0281	10	0.37606	T	0.19	-1.2896	0.3197	0.00301	0.2449:0.1895:0.2931:0.2725	.	265	Q9Y6X5	ENPP4_HUMAN	W	265	ENSP00000318066:L265W	ENSP00000318066:L265W	L	+	2	0	ENPP4	46216073	0.000000	0.05858	0.992000	0.48379	0.972000	0.66771	-0.065000	0.11617	0.400000	0.25396	0.533000	0.62120	TTG	.	.	.	none		0.418	ENPP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040777.2			G	46108114	T	G	46108114	3	3	163	1	0	0	0	0	1	0	0	0	5134	1821	63	5	796	5	ENPP4	6	46108114	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	11798463	46108114	125006953	29	9641											
DOPEY1	23033	hgsc.bcm.edu	37	chr6	83862020	83862020	+	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	tttatagatatgttatcaccTgcaatggaaaccgcaaacat	15	12	6	8	1	1	1	1	0	0	1	1	2	1	2	2	1	3	3	2	1	7	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr6:83862020T>A	ENST00000349129.2	+	30	6323	c.6063T>A	c.(6061-6063)ccT>ccA	p.P2021P	DOPEY1_ENST00000237163.5_Intron|DOPEY1_ENST00000484282.1_3'UTR|DOPEY1_ENST00000369739.3_Silent_p.P2012P	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	2021					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)		TGTTATCACCTGCAATGGAAA	0.313																																					p.P2021P		Atlas-SNP	.											DOPEY1,NS,carcinoma,0,1	DOPEY1	190	.	0			c.T6063A						PASS	.						59	59	59					6																	83862020		2203	4292	6495	SO:0001819	synonymous_variant	23033	exon30			ATCACCTGCAATG	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.6063T>A	chr6.hg19:g.83862020T>A		71.0	0.0	.		55.0	17.0	.	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Silent	SNP	ENST00000349129.2	hg19	CCDS4996.1																																																																																			.	.	.	none		0.313	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018		A	83862020	T	A	83862020	2	1	163	1	0	0	0	0	0	0	0	1	4709	1567	55	5		5	DOPEY1	6	83862020	Silent	SNP	T	TCGA-EV-5903-01A-11D-1589-08	37753906	83862020	87253047	30	9642											
CDC40	51362	hgsc.bcm.edu	37	chr6	110528715	110528715	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttttttgctttcaggttatgCattagacccttcattagata	9	19	6	7	0	2	2	2	0	0	2	2	2	2	2	1	1	2	3	1	1	4	9			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr6:110528715C>T	ENST00000368932.1	+	5	514	c.413C>T	c.(412-414)gCa>gTa	p.A138V	CDC40_ENST00000368930.1_Missense_Mutation_p.A138V|CDC40_ENST00000307731.1_Missense_Mutation_p.A138V			O60508	PRP17_HUMAN	cell division cycle 40	138					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)	18		all_cancers(87;6.23e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		Epithelial(106;0.0221)|all cancers(137;0.0314)|OV - Ovarian serous cystadenocarcinoma(136;0.034)		TCAGGTTATGCATTAGACCCT	0.249																																					p.A138V		Atlas-SNP	.											.	CDC40	39	.	0			c.C413T						PASS	.						98	107	104					6																	110528715		2203	4295	6498	SO:0001583	missense	51362	exon4			GTTATGCATTAGA	AF015044	CCDS5081.1	6q22.1	2013-01-17	2013-01-17		ENSG00000168438	ENSG00000168438		"WD repeat domain containing"	17350	protein-coding gene	gene with protein product		605585	"cell division cycle 40 homolog (yeast)", "cell division cycle 40 homolog (S. cerevisiae)"			9769104, 9830021	Standard	NM_015891		Approved	PRP17, EHB3, PRPF17, FLJ10564	uc003pua.3	O60508	OTTHUMG00000015358	ENST00000368932.1:c.413C>T	chr6.hg19:g.110528715C>T	ENSP00000357928:p.Ala138Val	182.0	0.0	.		176.0	50.0	.	NM_015891	B2RBC5|O75471|Q5SRN0|Q9UPG1	Missense_Mutation	SNP	ENST00000368932.1	hg19	CCDS5081.1	.	.	.	.	.	.	.	.	.	.	C	34	5.333199	0.95758	.	.	ENSG00000168438	ENST00000368932;ENST00000368933;ENST00000368930;ENST00000307731;ENST00000439165;ENST00000453107	T;T;T;T	0.67171	-0.09;-0.25;-0.25;-0.09	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.79405	0.4440	M	0.86805	2.84	0.80722	D	1	D	0.67145	0.996	P	0.55965	0.788	T	0.82794	-0.0281	10	0.87932	D	0	-9.413	19.9384	0.97150	0.0:1.0:0.0:0.0	.	138	O60508	PRP17_HUMAN	V	138;138;138;138;138;35	ENSP00000357928:A138V;ENSP00000357929:A138V;ENSP00000357926:A138V;ENSP00000304370:A138V	ENSP00000304370:A138V	A	+	2	0	CDC40	110635408	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.252000	0.78309	2.717000	0.92951	0.585000	0.79938	GCA	.	.	.	none		0.249	CDC40-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041791.1	NM_015891		T	110528715	C	T	110528715	3	4	163	1	0	0	0	0	1	0	0	0	3072	710	25	2	427	2	CDC40	6	110528715	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08	26666695	110528715	60586352	31	9643											
SLC16A10	117247	hgsc.bcm.edu	37	chr6	111409219	111409219	+	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	gggtcggtgttcggcatccaGaacgcttgcggggtgctctt	4	11	16	10	4	1	1	0	0	1	1	4	1	2	1	1	5	3	4	1	5	1	3			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr6:111409219G>T	ENST00000368851.5	+	1	439	c.264G>T	c.(262-264)caG>caT	p.Q88H		NM_018593.4	NP_061063.2	Q8TF71	MOT10_HUMAN	solute carrier family 16 (aromatic amino acid transporter), member 10	88					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)	TCGGCATCCAGAACGCTTGCG	0.662																																					p.Q88H		Atlas-SNP	.											.	SLC16A10	33	.	0			c.G264T						PASS	.						51	41	44					6																	111409219		2203	4299	6502	SO:0001583	missense	117247	exon1			CATCCAGAACGCT	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.264G>T	chr6.hg19:g.111409219G>T	ENSP00000357844:p.Gln88His	48.0	0.0	.		44.0	10.0	.	NM_018593	B3KWY0|Q6ZMG0|Q8WVI5	Missense_Mutation	SNP	ENST00000368851.5	hg19	CCDS5089.1	.	.	.	.	.	.	.	.	.	.	G	19.54	3.846966	0.71603	.	.	ENSG00000112394	ENST00000535637;ENST00000368851	T	0.59364	0.27	3.79	3.79	0.43588	Major facilitator superfamily domain, general substrate transporter (1);	0.071282	0.64402	D	0.000016	T	0.33876	0.0878	N	0.13235	0.315	0.80722	D	1	P;B	0.42375	0.778;0.339	P;B	0.44647	0.456;0.134	T	0.37526	-0.9702	10	0.44086	T	0.13	.	15.8498	0.78921	0.0:0.0:1.0:0.0	.	88;88	Q8TF71;Q05BR4	MOT10_HUMAN;.	H	88	ENSP00000357844:Q88H	ENSP00000357844:Q88H	Q	+	3	2	SLC16A10	111515912	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.303000	0.89955	1.950000	0.56595	0.448000	0.29417	CAG	.	.	.	none		0.662	SLC16A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041822.2			T	111409219	G	T	111409219	3	4	163	1	0	0	0	0	1	0	0	0	14416	933	33	4	266	4	SLC16A10	6	111409219	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	880504	111409219	59705848	32	9644											
MAP7	9053	hgsc.bcm.edu	37	chr6	136693761	136693761	+	Frame_Shift_Del	DEL	A	A	-																															catgatgatggggctgcaagAtgctgaacgaggacaaatgg																										TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr6:136693761delA	ENST00000354570.3	-	8	1164	c.754delT	c.(754-756)tctfs	p.S252fs	MAP7_ENST00000432797.2_Frame_Shift_Del_p.S106fs|MAP7_ENST00000438100.2_Frame_Shift_Del_p.S237fs|MAP7_ENST00000454590.1_Frame_Shift_Del_p.S274fs|MAP7_ENST00000544465.1_Frame_Shift_Del_p.S237fs	NM_001198616.1|NM_001198617.1|NM_001198619.1|NM_003980.4	NP_001185545.1|NP_001185546.1|NP_001185548.1|NP_003971.1	Q14244	MAP7_HUMAN	microtubule-associated protein 7	252					cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|establishment or maintenance of cell polarity (GO:0007163)|fertilization (GO:0009566)|germ cell development (GO:0007281)|glycosphingolipid metabolic process (GO:0006687)|homeostasis of number of cells (GO:0048872)|Leydig cell differentiation (GO:0033327)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|nucleus organization (GO:0006997)|organ growth (GO:0035265)|protein localization to plasma membrane (GO:0072659)|response to osmotic stress (GO:0006970)|response to retinoic acid (GO:0032526)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)|structural molecule activity (GO:0005198)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(11)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00199)|OV - Ovarian serous cystadenocarcinoma(155;0.00643)		GGGCTGCAAGATGCTGAACGA	0.488																																					p.S282fs		Atlas-INDEL	.											.	MAP7	63	.	0			c.845delC						PASS	.						175	153	161					6																	136693761		2203	4300	6503	SO:0001589	frameshift_variant	9053	exon8			.	X73882	CCDS5178.1, CCDS56452.1, CCDS56453.1, CCDS56454.1, CCDS56455.1, CCDS75527.1, CCDS75528.1, CCDS75529.1	6q23.2	2008-07-28			ENSG00000135525	ENSG00000135525			6869	protein-coding gene	gene with protein product		604108				8408219	Standard	NM_003980		Approved	E-MAP-115	uc011edg.2	Q14244	OTTHUMG00000015646	ENST00000354570.3:c.754delT	chr6.hg19:g.136693761delA	ENSP00000346581:p.Ser252fs	93.0	0.0	0		116.0	24.0	0.206897	NM_001198609	B7Z290|B7Z400|B7Z5S7|B7Z9U7|C9JPS0|E9PCP3|F5H1E2|Q7Z6S0|Q8TAU5|Q9NY82|Q9NY83	Frame_Shift_Del	DEL	ENST00000354570.3	hg19	CCDS5178.1																																																																																			.	.	.	none		0.488	MAP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042382.2	NM_003980		-	136693761	A	-	136693761	7	5	163	1	0	1	0	1	0	0	0	0	9273	333	12	0	1539	0	MAP7	6	136693761	Frame_Shift_Del	DEL	A	TCGA-EV-5903-01A-11D-1589-08	25284542	136693761	34421306	33	9645											
SHPRH	257218	hgsc.bcm.edu	37	chr6	146264642	146264642	+	Frame_Shift_Del	DEL	T	T	-																															cagtcctctgtttcatgttcTtggttgaattcagagataca																										TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr6:146264642delT	ENST00000367505.2	-	9	2139	c.1875delA	c.(1873-1875)caafs	p.Q625fs	SHPRH_ENST00000438092.2_Frame_Shift_Del_p.Q625fs|SHPRH_ENST00000367503.3_Frame_Shift_Del_p.Q625fs|SHPRH_ENST00000275233.7_Frame_Shift_Del_p.Q625fs			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	625					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)		TTTCATGTTCTTGGTTGAATT	0.408																																					p.E626fs		Atlas-INDEL	.											.	SHPRH	169	.	0			c.1876delG						PASS	.						196	183	187					6																	146264642		1952	4153	6105	SO:0001589	frameshift_variant	257218	exon9			.	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.1875delA	chr6.hg19:g.146264642delT	ENSP00000356475:p.Gln625fs	206.0	0.0	0		234.0	64.0	0.273504	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Frame_Shift_Del	DEL	ENST00000367505.2	hg19	CCDS43513.2																																																																																			.	.	.	none		0.408	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082		-	146264642	T	-	146264642	7	5	163	1	0	1	0	1	0	0	0	0	14304	1606	56	0	3308	0	SHPRH	6	146264642	Frame_Shift_Del	DEL	T	TCGA-EV-5903-01A-11D-1589-08	9570881	146264642	24850425	34	9646											
C7orf27	221927	hgsc.bcm.edu	37	chr7	2587034	2587034	+	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	agaaggagaggaccccagaaCtcaggtcctggactttcagc	12	6	12	11	0	2	3	2	0	0	3	3	6	3	5	3	4	2	0	3	4	2	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr7:2587034C>G	ENST00000340611.4	-	3	462	c.206G>C	c.(205-207)aGt>aCt	p.S69T		NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	69					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						GACCCCAGAACTCAGGTCCTG	0.622																																					p.S69T		Atlas-SNP	.											.	BRAT1	57	.	0			c.G206C						PASS	.						85	79	81					7																	2587034		2203	4300	6503	SO:0001583	missense	221927	exon3			CCAGAACTCAGGT	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.206G>C	chr7.hg19:g.2587034C>G	ENSP00000339637:p.Ser69Thr	101.0	0.0	.		108.0	49.0	.	NM_152743	A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Missense_Mutation	SNP	ENST00000340611.4	hg19	CCDS5334.1	.	.	.	.	.	.	.	.	.	.	C	9.253	1.041205	0.19669	.	.	ENSG00000106009	ENST00000340611	T	0.71103	-0.54	5.01	4.11	0.48088	Armadillo-type fold (1);	0.211492	0.47093	D	0.000255	T	0.68091	0.2963	M	0.72118	2.19	0.09310	N	1	B;P	0.46987	0.184;0.888	B;B	0.42163	0.208;0.378	T	0.66705	-0.5856	10	0.59425	D	0.04	-13.2539	9.9258	0.41492	0.0:0.8427:0.0:0.1573	.	69;69	Q6PJG6-2;Q6PJG6	.;BRAT1_HUMAN	T	69	ENSP00000339637:S69T	ENSP00000339637:S69T	S	-	2	0	BRAT1	2553560	0.000000	0.05858	0.026000	0.17262	0.004000	0.04260	0.191000	0.17076	2.331000	0.79229	0.650000	0.86243	AGT	.	.	.	none		0.622	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239305.2	NM_152743		G	2587034	C	G	2587034	3	3	163	1	0	0	0	0	1	0	0	0	2384	565	20	4	2307	4	C7orf27	7	2587034	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08		2587034	156551629	35	9647											
SCIN	85477	hgsc.bcm.edu	37	chr7	12679988	12679988	+	Missense_Mutation	SNP	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	tcagatccgagtctcccaagGcaaagagcctgttcacctac	11	8	8	14	1	3	2	2	0	1	2	5	3	4	2	4	1	2	2	4	1	3	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr7:12679988G>A	ENST00000297029.5	+	11	1528	c.1427G>A	c.(1426-1428)gGc>gAc	p.G476D	SCIN_ENST00000445618.2_Missense_Mutation_p.G229D|SCIN_ENST00000519209.1_Missense_Mutation_p.G229D	NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	476	Ca(2+)-dependent actin binding.			G -> D (in Ref. 1; AAK60494). {ECO:0000305}.	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)		GTCTCCCAAGGCAAAGAGCCT	0.428																																					p.G476D		Atlas-SNP	.											.	SCIN	105	.	0			c.G1427A						PASS	.						54	52	53					7																	12679988		1843	4090	5933	SO:0001583	missense	85477	exon11			CCCAAGGCAAAGA	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.1427G>A	chr7.hg19:g.12679988G>A	ENSP00000297029:p.Gly476Asp	35.0	0.0	.		91.0	38.0	.	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Missense_Mutation	SNP	ENST00000297029.5	hg19	CCDS47545.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.435588	0.83885	.	.	ENSG00000006747	ENST00000297029;ENST00000519209;ENST00000445618	T;T;T	0.27256	1.68;1.68;1.68	4.56	4.56	0.56223	Gelsolin domain (1);	0.000000	0.85682	D	0.000000	T	0.58779	0.2146	M	0.88906	2.99	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.69807	-0.5045	10	0.87932	D	0	-12.3981	17.3228	0.87240	0.0:0.0:1.0:0.0	.	476	Q9Y6U3	ADSV_HUMAN	D	476;229;229	ENSP00000297029:G476D;ENSP00000430997:G229D;ENSP00000390189:G229D	ENSP00000297029:G476D	G	+	2	0	SCIN	12646513	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.476000	0.97823	2.069000	0.61940	0.561000	0.74099	GGC	.	.	.	none		0.428	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128		A	12679988	G	A	12679988	3	1	163	1	0	0	0	0	1	0	0	0	13918	1203	42	2	1469	2	SCIN	7	12679988	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	10092954	12679988	146458675	36	9648											
IMMP2L	83943	hgsc.bcm.edu	37	chr7	111127299	111127299	+	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	ttctgagttacttacaccaaTgatacaatgtcaccacggtg	12	12	7	10	1	2	2	1	2	1	0	2	2	2	2	2	1	3	1	2	1	5	4	rs201012120		TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr7:111127299T>A	ENST00000405709.2	-	3	676	c.234A>T	c.(232-234)tcA>tcT	p.S78S	IMMP2L_ENST00000437687.1_Silent_p.S78S|IMMP2L_ENST00000447215.1_Silent_p.S78S|IMMP2L_ENST00000415362.1_Silent_p.S78S|IMMP2L_ENST00000331762.3_Silent_p.S78S|IMMP2L_ENST00000452895.1_Silent_p.S78S	NM_032549.3	NP_115938.1	Q96T52	IMP2L_HUMAN	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	78					ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|protein processing involved in protein targeting to mitochondrion (GO:0006627)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|mitochondrial inner membrane peptidase complex (GO:0042720)	peptidase activity (GO:0008233)|serine-type peptidase activity (GO:0008236)			endometrium(3)|large_intestine(6)|lung(5)	14				UCEC - Uterine corpus endometrioid carcinoma (4;0.053)|Epithelial(3;2.27e-07)|all cancers(3;1.36e-05)|STAD - Stomach adenocarcinoma(3;0.00148)|KIRC - Kidney renal clear cell carcinoma(11;0.0339)|Lung(3;0.0375)|Kidney(11;0.0415)|LUSC - Lung squamous cell carcinoma(290;0.173)		CTTACACCAATGATACAATGT	0.363																																					p.S78S		Atlas-SNP	.											.	IMMP2L	32	.	0			c.A234T						PASS	.						102	99	100					7																	111127299		2203	4300	6503	SO:0001819	synonymous_variant	83943	exon3			CACCAATGATACA	AF359563	CCDS5753.1	7q31	2014-01-06	2005-08-17		ENSG00000184903	ENSG00000184903			14598	protein-coding gene	gene with protein product		605977	"IMP2 inner mitochondrial membrane protease-like (S. cerevisiae)", "IMMP2L intronic transcript 1 (non-protein coding)"	IMMP2L-IT1		11254443	Standard	NM_032549		Approved	IMP2	uc010ljr.2	Q96T52	OTTHUMG00000155023	ENST00000405709.2:c.234A>T	chr7.hg19:g.111127299T>A		121.0	0.0	.		208.0	67.0	.	NM_032549	Q75MF1|Q75MN9|Q75MP0|Q75MS5|Q75MS8|Q96HJ2	Silent	SNP	ENST00000405709.2	hg19	CCDS5753.1																																																																																			.	T|1.000;C|0.000	.	alt		0.363	IMMP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338109.4	NM_032549		A	111127299	T	A	111127299	2	1	163	1	0	0	0	0	0	0	0	1	7724	1451	51	5		5	IMMP2L	7	111127299	Silent	SNP	T	TCGA-EV-5903-01A-11D-1589-08	98447311	111127299	48011364	37	9649											
SSPO	23145	hgsc.bcm.edu	37	chr7	149509420	149509420	+	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	gagctgtgggggaggcctgcGgagccggacccgggcctgtg	4	5	21	11	3	0	0	0	0	0	0	0	4	0	3	4	6	3	1	4	6	0	0			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr7:149509420G>A	ENST00000378016.2	+	0	9818							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)			GGAGGCCTGCGGAGCCGGACC	0.726																																					p.R3273Q		Atlas-SNP	.											.	.	.	.	0			c.G9818A						PASS	.						6	7	7					7																	149509420		1692	3840	5532			23145	exon69			GCCTGCGGAGCCG	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149509420G>A		17.0	0.0	.		21.0	5.0	.	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	hg19																																																																																				.	.	.	none		0.726	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				A	149509420	G	A	149509420	1	1	163	0	1	0	0	0	0	0	0	0	15201	1116	39	1		1	SSPO	7	149509420	RNA	SNP	G	TCGA-EV-5903-01A-11D-1589-08	38382121	149509420	9629243	38	9650											
RRS1	23212	hgsc.bcm.edu	37	chr8	67342373	67342373	+	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	ccagggagggaagaggaaagGgggcttgggaggcaagatga	13	3	21	4	0	0	3	0	1	0	2	0	7	0	7	1	7	0	2	1	7	3	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr8:67342373G>A	ENST00000320270.2	+	1	1111	c.1007G>A	c.(1006-1008)gGg>gAg	p.G336E	ADHFE1_ENST00000396623.3_5'Flank|RP11-346I3.4_ENST00000499642.1_lincRNA|ADHFE1_ENST00000379385.4_5'Flank|ADHFE1_ENST00000415254.1_5'Flank	NM_015169.3	NP_055984.1	Q15050	RRS1_HUMAN	RRS1 ribosome biogenesis regulator homolog (S. cerevisiae)	336	Arg/Gly/Lys-rich.				hematopoietic progenitor cell differentiation (GO:0002244)|mitotic metaphase plate congression (GO:0007080)|ribosome biogenesis (GO:0042254)	condensed nuclear chromosome (GO:0000794)|endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			kidney(2)|lung(2)	4		Lung NSC(129;0.197)	Epithelial(68;0.0391)|all cancers(69;0.0898)|BRCA - Breast invasive adenocarcinoma(89;0.111)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			AAGAGGAAAGGGGGCTTGGGA	0.602																																					p.G336E		Atlas-SNP	.											.	RRS1	13	.	0			c.G1007A						PASS	.						34	44	41					8																	67342373		2192	4287	6479	SO:0001583	missense	23212	exon1			GGAAAGGGGGCTT	BC001811	CCDS6189.1	8q13.1	2013-10-22			ENSG00000179041	ENSG00000179041			17083	protein-coding gene	gene with protein product						7788527, 10688653	Standard	NM_015169		Approved	KIAA0112	uc003xwa.3	Q15050	OTTHUMG00000164765	ENST00000320270.2:c.1007G>A	chr8.hg19:g.67342373G>A	ENSP00000322396:p.Gly336Glu	81.0	0.0	.		103.0	27.0	.	NM_015169	Q9BUX8	Missense_Mutation	SNP	ENST00000320270.2	hg19	CCDS6189.1	.	.	.	.	.	.	.	.	.	.	G	13.22	2.170934	0.38315	.	.	ENSG00000179041	ENST00000320270	D	0.89552	-2.53	5.26	4.38	0.52667	.	0.233360	0.44688	D	0.000435	D	0.87621	0.6223	M	0.77486	2.375	0.52501	D	0.999957	B	0.24043	0.096	B	0.18263	0.021	D	0.85609	0.1257	10	0.62326	D	0.03	-32.1208	10.2291	0.43245	0.1636:0.0:0.8364:0.0	.	336	Q15050	RRS1_HUMAN	E	336	ENSP00000322396:G336E	ENSP00000322396:G336E	G	+	2	0	RRS1	67504927	0.999000	0.42202	0.810000	0.32431	0.561000	0.35649	2.865000	0.48412	1.369000	0.46134	0.537000	0.68136	GGG	.	.	.	none		0.602	RRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380126.1	NM_015169		A	67342373	G	A	67342373	3	1	163	1	0	0	0	0	1	0	0	0	13705	1232	43	2	1009	2	RRS1	8	67342373	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08		67342373	79021649	39	9651											
TTC35	9694	hgsc.bcm.edu	37	chr8	109462688	109462688	+	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	tatgaacaggtgatgattgcAgcactagactatggtcggga	12	10	13	6	1	0	4	0	3	0	1	1	5	0	5	0	3	3	2	0	3	4	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr8:109462688A>T	ENST00000220853.3	+	3	221	c.186A>T	c.(184-186)gcA>gcT	p.A62A		NM_014673.3	NP_055488.1	Q15006	EMC2_HUMAN	ER membrane protein complex subunit 2	62						cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|ER membrane protein complex (GO:0072546)|mitochondrion (GO:0005739)|nucleus (GO:0005634)											TGATGATTGCAGCACTAGACT	0.308																																					p.A62A		Atlas-SNP	.											.	.	.	.	0			c.A186T						PASS	.						206	200	202					8																	109462688		2203	4300	6503	SO:0001819	synonymous_variant	9694	exon3			GATTGCAGCACTA	BC021667	CCDS6309.1	8q23.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000104412	ENSG00000104412			28963	protein-coding gene	gene with protein product		607722	"tetratricopeptide repeat domain 35"	KIAA0103, TTC35		7788527, 22119785	Standard	NM_014673		Approved		uc003ymw.1	Q15006	OTTHUMG00000164873	ENST00000220853.3:c.186A>T	chr8.hg19:g.109462688A>T		171.0	0.0	.		157.0	35.0	.	NM_014673	Q8WUE1	Silent	SNP	ENST00000220853.3	hg19	CCDS6309.1	.	.	.	.	.	.	.	.	.	.	A	8.680	0.904927	0.17760	.	.	ENSG00000104412	ENST00000519642	.	.	.	5.86	-9.77	0.00500	.	.	.	.	.	T	0.43743	0.1261	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52328	-0.8590	4	.	.	.	-10.7326	6.6457	0.22934	0.3445:0.0:0.3347:0.3207	.	.	.	.	L	10	.	.	Q	+	2	0	TTC35	109531864	0.354000	0.24912	0.564000	0.28396	0.612000	0.37316	-0.270000	0.08584	-1.322000	0.02278	-1.132000	0.01976	CAG	.	.	.	none		0.308	EMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380717.1	NM_014673		T	109462688	A	T	109462688	2	4	163	1	0	0	0	0	0	0	0	1	16715	175	7	5		5	TTC35	8	109462688	Silent	SNP	A	TCGA-EV-5903-01A-11D-1589-08	42120315	109462688	36901334	40	9652											
C9orf72	203228	hgsc.bcm.edu	37	chr9	27548367	27548367	+	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	gatcgccctctgctgttaaaTcaaggtctatcttcaggttc	8	14	8	11	1	5	0	2	0	3	0	7	1	5	0	1	2	1	3	1	2	4	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr9:27548367T>A	ENST00000380003.3	-	11	1376	c.1313A>T	c.(1312-1314)gAt>gTt	p.D438V	C9orf72_ENST00000488117.1_5'UTR	NM_001256054.1|NM_018325.3	NP_001242983.1|NP_060795.1	Q96LT7	CI072_HUMAN	chromosome 9 open reading frame 72	438					autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|extracellular space (GO:0005615)|lysosome (GO:0005764)|nucleus (GO:0005634)	Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|ovary(4)|pancreas(1)	23		all_neural(11;7.57e-10)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.00016)		TGCTGTTAAATCAAGGTCTAT	0.348																																					p.D438V		Atlas-SNP	.											.	C9orf72	48	.	0			c.A1313T						PASS	.						99	100	100					9																	27548367		2203	4300	6503	SO:0001583	missense	203228	exon11			GTTAAATCAAGGT	AL832467	CCDS6522.1, CCDS6523.1	9p21.1	2014-09-17			ENSG00000147894	ENSG00000147894			28337	protein-coding gene	gene with protein product		614260				21944778, 24549040	Standard	NM_145005		Approved	MGC23980	uc003zqq.3	Q96LT7	OTTHUMG00000019716	ENST00000380003.3:c.1313A>T	chr9.hg19:g.27548367T>A	ENSP00000369339:p.Asp438Val	107.0	0.0	.		143.0	27.0	.	NM_018325	A8K5W0|D3DRK6|G8I0B6|Q6NUS9	Missense_Mutation	SNP	ENST00000380003.3	hg19	CCDS6522.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.338256	0.81911	.	.	ENSG00000147894	ENST00000380003	T	0.52057	0.68	5.75	5.75	0.90469	.	0.042474	0.85682	D	0.000000	T	0.52789	0.1756	N	0.19112	0.55	0.80722	D	1	D	0.71674	0.998	D	0.68943	0.961	T	0.51513	-0.8696	9	.	.	.	.	16.0488	0.80740	0.0:0.0:0.0:1.0	.	438	Q96LT7	CI072_HUMAN	V	438	ENSP00000369339:D438V	.	D	-	2	0	C9orf72	27538367	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.698000	0.84413	2.199000	0.70637	0.374000	0.22700	GAT	.	.	.	none		0.348	C9orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051969.1	NM_018325		A	27548367	T	A	27548367	3	1	163	1	0	0	0	0	1	0	0	0	2497	1435	50	5	136	5	C9orf72	9	27548367	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08		27548367	113665064	41	9653											
NFX1	4799	hgsc.bcm.edu	37	chr9	33319104	33319106	+	In_Frame_Del	DEL	CCT	CCT	-																															gtggaaaagtgtgcggcaagCctctgccttgtggttcctta																										TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr9:33319104_33319106delCCT	ENST00000379540.3	+	9	1947_1949	c.1885_1887delCCT	c.(1885-1887)cctdel	p.P629del	NFX1_ENST00000318524.6_In_Frame_Del_p.P629del|NFX1_ENST00000379521.4_In_Frame_Del_p.P629del	NM_002504.4	NP_002495.2	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1	629					inflammatory response (GO:0006954)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)		GTGCGGCAAGCCTCTGCCTTGTG	0.438																																					p.628_629del		Atlas-INDEL	.											.	NFX1	85	.	0			c.1884_1886del						PASS	.																																			SO:0001651	inframe_deletion	4799	exon9			.	U19759	CCDS6538.1, CCDS6539.1, CCDS6540.1	9p12	2013-12-13			ENSG00000086102	ENSG00000086102			7803	protein-coding gene	gene with protein product		603255				7964459, 2511169	Standard	NM_002504		Approved	NFX2, MGC20369, Tex42, TEG-42	uc003zsq.3	Q12986	OTTHUMG00000019772	ENST00000379540.3:c.1885_1887delCCT	chr9.hg19:g.33319104_33319106delCCT	ENSP00000368856:p.Pro629del	56.0	0.0	0		61.0	22.0	0.360656	NM_147134	A8K6H8|Q5VXW6|Q96EL5|Q9BXI1	In_Frame_Del	DEL	ENST00000379540.3	hg19	CCDS6538.1																																																																																			.	.	.	none		0.438	NFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052069.1			-	33319106	CCT	-	33319104	7	5	163	1	0	1	0	1	0	0	0	0	10394	739	26	0	1919	0	NFX1	9	33319104	In_Frame_Del	DEL	CCT	TCGA-EV-5903-01A-11D-1589-08	5770737	33319104	107894327	42	9654											
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84605892	84605892	+	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	gcttctgcgactgagtcatcGttcactctggcttccacccc	5	12	8	16	2	4	1	2	1	2	0	6	2	5	1	3	1	1	3	3	1	0	3			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr9:84605892G>A	ENST00000344803.2	+	4	554	c.507G>A	c.(505-507)tcG>tcA	p.S169S		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	169					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CTGAGTCATCGTTCACTCTGG	0.562																																					p.S169S		Atlas-SNP	.											.	.	.	.	0			c.G507A						PASS	.						123	123	123					9																	84605892		2001	4169	6170	SO:0001819	synonymous_variant	389763	exon4			GTCATCGTTCACT		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.507G>A	chr9.hg19:g.84605892G>A		79.0	0.0	.		73.0	18.0	.	NM_001001670		Silent	SNP	ENST00000344803.2	hg19	CCDS47986.1																																																																																			.	.	.	none		0.562	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		A	84605892	G	A	84605892	2	1	163	1	0	0	0	0	0	0	0	1	5939	1132	40	1		1	FLJ46321	9	84605892	Silent	SNP	G	TCGA-EV-5903-01A-11D-1589-08	51286788	84605892	56607539	43	9655											
PHF2	5253	hgsc.bcm.edu	37	chr9	96416716	96416716	+	Missense_Mutation	SNP	A	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	gggagaagaccttctatctcAtcaggccggcctcggccaac	9	7	11	14	2	3	2	2	0	2	2	5	3	3	2	4	4	1	0	4	4	3	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr9:96416716A>C	ENST00000359246.4	+	7	1178	c.811A>C	c.(811-813)Atc>Ctc	p.I271L	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	271	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)		CTTCTATCTCATCAGGCCGGC	0.587																																					p.I271L		Atlas-SNP	.											.	PHF2	113	.	0			c.A811C						PASS	.						59	56	57					9																	96416716		2203	4300	6503	SO:0001583	missense	5253	exon7			TATCTCATCAGGC	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.811A>C	chr9.hg19:g.96416716A>C	ENSP00000352185:p.Ile271Leu	79.0	0.0	.		63.0	17.0	.	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Missense_Mutation	SNP	ENST00000359246.4	hg19	CCDS35069.1	.	.	.	.	.	.	.	.	.	.	A	32	5.129480	0.94473	.	.	ENSG00000197724	ENST00000359246	T	0.74947	-0.89	4.79	4.79	0.61399	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.000000	0.85682	D	0.000000	D	0.87026	0.6075	M	0.86028	2.79	0.80722	D	1	D	0.55385	0.971	D	0.76575	0.988	D	0.89290	0.3618	10	0.87932	D	0	-32.051	14.5008	0.67719	1.0:0.0:0.0:0.0	.	271	O75151	PHF2_HUMAN	L	271	ENSP00000352185:I271L	ENSP00000352185:I271L	I	+	1	0	PHF2	95456537	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.037000	0.93765	2.008000	0.58898	0.477000	0.44152	ATC	.	.	.	none		0.587	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392		C	96416716	A	C	96416716	3	2	163	1	0	0	0	0	1	0	0	0	11837	217	8	5	837	5	PHF2	9	96416716	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	11810824	96416716	44796715	44	9656											
ABCA1	19	hgsc.bcm.edu	37	chr9	107599352	107599352	+	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	cttccagatcatggaacacaGccagttcctggaaggtcttg	10	10	10	11	0	2	1	1	0	1	1	4	3	4	3	3	3	2	1	3	3	2	3			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr9:107599352G>T	ENST00000374736.3	-	11	1614	c.1220C>A	c.(1219-1221)gCt>gAt	p.A407D		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	407					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)	ATGGAACACAGCCAGTTCCTG	0.552																																					p.A407D		Atlas-SNP	.											.	ABCA1	244	.	0			c.C1220A						PASS	.						86	71	76					9																	107599352		2203	4300	6503	SO:0001583	missense	19	exon11			AACACAGCCAGTT	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.1220C>A	chr9.hg19:g.107599352G>T	ENSP00000363868:p.Ala407Asp	69.0	0.0	.		53.0	14.0	.	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	hg19	CCDS6762.1	.	.	.	.	.	.	.	.	.	.	G	15.23	2.773257	0.49786	.	.	ENSG00000165029	ENST00000374736	D	0.85861	-2.04	5.7	4.76	0.60689	.	0.209202	0.49916	D	0.000130	T	0.76807	0.4039	L	0.28192	0.835	0.80722	D	1	B	0.06786	0.001	B	0.13407	0.009	T	0.70454	-0.4867	10	0.27082	T	0.32	.	15.0006	0.71469	0.0:0.2679:0.7321:0.0	.	407	O95477	ABCA1_HUMAN	D	407	ENSP00000363868:A407D	ENSP00000363868:A407D	A	-	2	0	ABCA1	106639173	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	5.271000	0.65553	2.687000	0.91594	0.655000	0.94253	GCT	.	.	.	none		0.552	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		T	107599352	G	T	107599352	3	4	163	1	0	0	0	0	1	0	0	0	28	971	34	4	5725	4	ABCA1	9	107599352	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	11182636	107599352	33614079	45	9657											
NUP188	23511	hgsc.bcm.edu	37	chr9	131755475	131755475	+	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	gtgtgttccggtctccaccaGgtggccccaatgtcagtgta	6	11	12	12	1	2	0	1	0	1	0	4	0	3	0	5	3	0	2	5	3	2	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr9:131755475G>A	ENST00000372577.2	+	26	2661		c.e26-1			NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa						carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						GTCTCCACCAGGTGGCCCCAA	0.537											OREG0019527	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-SNP	.											.	NUP188	140	.	0			c.2641-1G>A						PASS	.						100	99	99					9																	131755475		2203	4300	6503	SO:0001630	splice_region_variant	23511	exon26			CCACCAGGTGGCC	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.2641-1G>A	chr9.hg19:g.131755475G>A		69.0	0.0	.	1590	88.0	22.0	.	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Splice_Site	SNP	ENST00000372577.2	hg19	CCDS35156.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.417591	0.83449	.	.	ENSG00000095319	ENST00000356693;ENST00000372577	.	.	.	6.0	6.0	0.97389	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4831	0.95018	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NUP188	130795296	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.423000	0.80229	2.848000	0.98002	0.655000	0.94253	.	.	.	.	none		0.537	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2		Intron	A	131755475	G	A	131755475	5	1	163	1	0	0	0	0	0	0	1	0	10765	1014	35	2	2742	2	NUP188	9	131755475	Splice_Site	SNP	G	TCGA-EV-5903-01A-11D-1589-08	24156123	131755475	9457956	46	9658											
USP20	10868	hgsc.bcm.edu	37	chr9	132618631	132618631	+	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	ccggaccaaacctatgggccTgtctgcaggtaaaagaccct	11	7	10	13	1	1	1	0	0	1	1	1	2	1	2	5	3	2	2	5	3	4	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr9:132618631T>A	ENST00000315480.4	+	4	285	c.127T>A	c.(127-129)Tgt>Agt	p.C43S	USP20_ENST00000358355.1_Missense_Mutation_p.C43S|USP20_ENST00000372429.3_Missense_Mutation_p.C43S			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	43					endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				CCTATGGGCCTGTCTGCAGGT	0.582																																					p.C43S		Atlas-SNP	.											.	USP20	186	.	0			c.T127A						PASS	.						136	137	137					9																	132618631		1947	4141	6088	SO:0001583	missense	10868	exon4			TGGGCCTGTCTGC	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"Ubiquitin-specific peptidases"	12619	protein-coding gene	gene with protein product		615143	"ubiquitin specific protease 20"			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.127T>A	chr9.hg19:g.132618631T>A	ENSP00000313811:p.Cys43Ser	225.0	0.0	.		215.0	60.0	.	NM_001008563	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Missense_Mutation	SNP	ENST00000315480.4	hg19	CCDS43892.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.816658	0.90790	.	.	ENSG00000136878	ENST00000372429;ENST00000315480;ENST00000358355	T;T;T	0.72282	-0.64;-0.64;-0.64	4.99	4.99	0.66335	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, UBP-type (2);	0.000000	0.85682	D	0.000000	D	0.89273	0.6668	H	0.97611	4.04	0.80722	D	1	D	0.69078	0.997	D	0.83275	0.996	D	0.92667	0.6146	10	0.87932	D	0	.	13.5285	0.61609	0.0:0.0:0.0:1.0	.	43	Q9Y2K6	UBP20_HUMAN	S	43	ENSP00000361506:C43S;ENSP00000313811:C43S;ENSP00000351122:C43S	ENSP00000313811:C43S	C	+	1	0	USP20	131658452	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.432000	0.80349	1.880000	0.54463	0.460000	0.39030	TGT	.	.	.	none		0.582	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2			A	132618631	T	A	132618631	3	1	163	1	0	0	0	0	1	0	0	0	17064	1580	55	5	133	5	USP20	9	132618631	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	863156	132618631	8594800	47	9659											
ABL1	25	hgsc.bcm.edu	37	chr9	133730265	133730265	+	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	ccaaaaatggccaaggctggGtcccaagcaactacatcacg	14	5	9	13	1	1	0	1	0	0	0	2	0	2	0	3	3	3	2	3	3	6	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr9:133730265G>C	ENST00000318560.5	+	3	712	c.331G>C	c.(331-333)Gtc>Ctc	p.V111L		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	111	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				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)	CCAAGGCTGGGTCCCAAGCAA	0.522			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"																																p.V130L		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.G388C						PASS	.						107	89	95					9																	133730265		2203	4300	6503	SO:0001583	missense	25	exon3			GGCTGGGTCCCAA	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.331G>C	chr9.hg19:g.133730265G>C	ENSP00000323315:p.Val111Leu	69.0	0.0	.		72.0	15.0	.	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Missense_Mutation	SNP	ENST00000318560.5	hg19	CCDS35166.1	.	.	.	.	.	.	.	.	.	.	G	36	5.707803	0.96821	.	.	ENSG00000097007	ENST00000372348;ENST00000438426;ENST00000318560	T;T	0.55930	0.49;0.49	5.67	5.67	0.87782	Src homology-3 domain (3);	0.000000	0.85682	D	0.000000	T	0.75057	0.3798	M	0.90977	3.165	0.80722	D	1	P;P	0.39862	0.692;0.692	P;P	0.51016	0.656;0.656	T	0.79553	-0.1756	10	0.87932	D	0	.	18.8246	0.92111	0.0:0.0:1.0:0.0	.	111;148	P00519;Q59FK4	ABL1_HUMAN;.	L	130;157;111	ENSP00000361423:V130L;ENSP00000323315:V111L	ENSP00000323315:V111L	V	+	1	0	ABL1	132720086	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.812000	0.99227	2.677000	0.91161	0.638000	0.83543	GTC	.	.	.	none		0.522	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		C	133730265	G	C	133730265	3	2	163	1	0	0	0	0	1	0	0	0	92	1261	44	4	481	4	ABL1	9	133730265	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	1111634	133730265	7483166	48	9660											
LARP4B	23185	hgsc.bcm.edu	37	chr10	858887	858887	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgaggagacttggggggAgtgctctgctctcggctgag	6	9	17	9	1	2	3	0	2	2	1	3	5	2	4	0	5	2	3	0	5	0	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr10:858887A>G	ENST00000316157.3	-	17	2236	c.2196T>C	c.(2194-2196)acT>acC	p.T732T	LARP4B_ENST00000469487.1_5'Flank	NM_015155.1	NP_055970.1	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B	732					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						ACTTGGGGGGAGTGCTCTGCT	0.662																																					p.T732T		Atlas-SNP	.											.	LARP4B	110	.	0			c.T2196C						PASS	.						36	40	39					10																	858887		2202	4298	6500	SO:0001819	synonymous_variant	23185	exon18			GGGGGGAGTGCTC	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.2196T>C	chr10.hg19:g.858887A>G		113.0	0.0	.		111.0	34.0	.	NM_015155	A7MD20|Q5T3R3|Q5T3R4|Q5T3R5|Q68CY4	Silent	SNP	ENST00000316157.3	hg19	CCDS31131.1	.	.	.	.	.	.	.	.	.	.	A	6.457	0.452392	0.12283	.	.	ENSG00000107929	ENST00000448368	.	.	.	6.07	-5.87	0.02297	.	.	.	.	.	T	0.39036	0.1063	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41270	-0.9518	4	.	.	.	-3.3912	3.9687	0.09443	0.1675:0.3281:0.3845:0.12	.	.	.	.	P	333	.	.	S	-	1	0	LARP4B	848887	0.998000	0.40836	0.905000	0.35620	0.944000	0.59088	0.260000	0.18424	-0.881000	0.03992	-1.236000	0.01555	TCC	.	.	.	none		0.662	LARP4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046395.2	NM_015155		G	858887	A	G	858887	2	3	163	1	0	0	0	0	0	0	0	1	8638	291	11	3		3	LARP4B	10	858887	Silent	SNP	A	TCGA-EV-5903-01A-11D-1589-08		858887	134675860	49	9661											
PITRM1	10531	hgsc.bcm.edu	37	chr10	3191832	3191832	+	Missense_Mutation	SNP	A	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	cttggtgaggacgctgcagaAgaggggcacatagggcctca	10	6	16	9	1	1	3	1	1	0	2	1	4	1	4	1	5	1	3	1	5	2	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr10:3191832A>C	ENST00000224949.4	-	16	1886	c.1852T>G	c.(1852-1854)Ttc>Gtc	p.F618V	PITRM1-AS1_ENST00000601046.1_RNA|PITRM1_ENST00000380989.2_Missense_Mutation_p.F618V|PITRM1_ENST00000451104.2_Missense_Mutation_p.F586V|PITRM1_ENST00000380994.1_Missense_Mutation_p.F176V|PITRM1_ENST00000464395.1_5'Flank|PITRM1-AS1_ENST00000598280.1_RNA			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	618					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						ACGCTGCAGAAGAGGGGCACA	0.517																																					p.F618V		Atlas-SNP	.											.	PITRM1	109	.	0			c.T1852G						PASS	.						183	187	186					10																	3191832		2033	4194	6227	SO:0001583	missense	10531	exon16			TGCAGAAGAGGGG	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.1852T>G	chr10.hg19:g.3191832A>C	ENSP00000224949:p.Phe618Val	338.0	0.0	.		280.0	78.0	.	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	hg19	CCDS59208.1	.	.	.	.	.	.	.	.	.	.	a	22.4	4.280763	0.80692	.	.	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000380994;ENST00000451104	T;T;T;T	0.46063	0.88;0.88;0.88;0.88	5.41	4.28	0.50868	Peptidase M16C associated (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.000000	0.85682	D	0.000000	T	0.68559	0.3014	M	0.90309	3.105	0.58432	D	0.999998	D;D;D;D;D	0.89917	0.97;0.997;1.0;1.0;1.0	P;D;D;D;D	0.85130	0.824;0.994;0.997;0.997;0.997	T	0.73582	-0.3937	10	0.87932	D	0	.	11.2282	0.48897	0.9278:0.0:0.0722:0.0	.	611;586;618;618;611	E9PDX6;E7ES23;C9JSL2;Q5JRX3;B4DH07	.;.;.;PREP_HUMAN;.	V	618;611;618;176;586	ENSP00000224949:F618V;ENSP00000370377:F618V;ENSP00000370382:F176V;ENSP00000401201:F586V	ENSP00000224949:F618V	F	-	1	0	PITRM1	3181832	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	7.161000	0.77505	0.900000	0.36469	0.454000	0.30748	TTC	.	.	.	none		0.517	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2			C	3191832	A	C	3191832	3	2	163	1	0	0	0	0	1	0	0	0	11960	72	3	5	1309	5	PITRM1	10	3191832	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	2332945	3191832	132342915	50	9662											
CSGALNACT2	55454	hgsc.bcm.edu	37	chr10	43651227	43651227	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagggtccccttggagagaaActgatatttaatgaaaatga	15	10	11	5	0	0	4	0	3	0	1	1	7	1	5	2	2	1	0	2	2	5	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr10:43651227A>G	ENST00000374466.3	+	2	965	c.630A>G	c.(628-630)aaA>aaG	p.K210K	CSGALNACT2_ENST00000374464.1_Silent_p.K210K	NM_018590.3	NP_061060.3	Q8N6G5	CGAT2_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 2	210					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050652)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)			endometrium(12)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						TTGGAGAGAAACTGATATTTA	0.363																																					p.K210K		Atlas-SNP	.											.	CSGALNACT2	67	.	0			c.A630G						PASS	.						44	46	46					10																	43651227		2203	4299	6502	SO:0001819	synonymous_variant	55454	exon2			AGAGAAACTGATA	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.630A>G	chr10.hg19:g.43651227A>G		85.0	0.0	.		71.0	17.0	.	NM_018590	B3KWL7|Q6MZJ5|Q6MZP6|Q8TCH4|Q9P1I6	Silent	SNP	ENST00000374466.3	hg19	CCDS7201.1																																																																																			.	.	.	none		0.363	CSGALNACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047693.1	NM_018590		G	43651227	A	G	43651227	2	3	163	1	0	0	0	0	0	0	0	1	3941	40	2	3		3	CSGALNACT2	10	43651227	Silent	SNP	A	TCGA-EV-5903-01A-11D-1589-08	40459395	43651227	91883520	51	9663											
POLR3A	11128	hgsc.bcm.edu	37	chr10	79741971	79741971	+	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	accgtgtgtggccatgactgCccgcaggttatcaccttcca	7	10	10	14	2	1	1	1	1	0	0	2	1	2	1	5	2	1	2	5	2	1	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr10:79741971C>G	ENST00000372371.3	-	28	3837	c.3700G>C	c.(3700-3702)Gca>Cca	p.A1234P		NM_007055.3	NP_008986.2	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa	1234					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)			GCCATGACTGCCCGCAGGTTA	0.567																																					p.A1234P		Atlas-SNP	.											.	POLR3A	104	.	0			c.G3700C						PASS	.						188	151	163					10																	79741971		2203	4300	6503	SO:0001583	missense	11128	exon28			TGACTGCCCGCAG	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.3700G>C	chr10.hg19:g.79741971C>G	ENSP00000361446:p.Ala1234Pro	89.0	0.0	.		115.0	34.0	.	NM_007055	Q8IW34|Q8TCW5	Missense_Mutation	SNP	ENST00000372371.3	hg19	CCDS7354.1	.	.	.	.	.	.	.	.	.	.	C	16.69	3.192613	0.58017	.	.	ENSG00000148606	ENST00000539141;ENST00000372371;ENST00000540842	T	0.78126	-1.15	5.99	5.99	0.97316	RNA polymerase Rpb1, domain 5 (1);	0.051369	0.85682	D	0.000000	D	0.83718	0.5315	M	0.87097	2.86	0.58432	D	0.999998	P	0.35155	0.487	B	0.42112	0.376	T	0.83056	-0.0150	9	.	.	.	-11.4876	15.1985	0.73116	0.1408:0.8591:0.0:0.0	.	1234	O14802	RPC1_HUMAN	P	50;1234;1213	ENSP00000361446:A1234P	.	A	-	1	0	POLR3A	79411977	1.000000	0.71417	0.998000	0.56505	0.938000	0.57974	4.200000	0.58433	2.843000	0.97960	0.655000	0.94253	GCA	.	.	.	none		0.567	POLR3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048923.1	NM_007055		G	79741971	C	G	79741971	3	3	163	1	0	0	0	0	1	0	0	0	12235	739	26	4	488	4	POLR3A	10	79741971	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08	36090744	79741971	55792776	52	9664											
KIAA1598	57698	hgsc.bcm.edu	37	chr10	118689489	118689489	+	Missense_Mutation	SNP	C	C	T																															tttgtggagtgtttcattttCtagttgctcttctaattctt																										TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr10:118689489C>T	ENST00000355371.4	-	10	1380	c.883G>A	c.(883-885)Gaa>Aaa	p.E295K	KIAA1598_ENST00000392901.4_Missense_Mutation_p.E235K|KIAA1598_ENST00000392903.2_Missense_Mutation_p.E295K|KIAA1598_ENST00000260777.10_Missense_Mutation_p.E295K|KIAA1598_ENST00000497044.1_5'UTR	NM_001127211.2|NM_001258298.1|NM_001258299.1	NP_001120683.1|NP_001245227.1|NP_001245228.1	A0MZ66	SHOT1_HUMAN	KIAA1598	295					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)		GTTTCATTTTCTAGTTGCTCT	0.308																																					p.E295K		Atlas-SNP	.											.	KIAA1598	74	.	0			c.G883A						PASS	.						163	152	155					10																	118689489		2201	4298	6499	SO:0001583	missense	57698	exon10			CATTTTCTAGTTG	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.883G>A	chr10.hg19:g.118689489C>T	ENSP00000347532:p.Glu295Lys	148.0	0.0	.		137.0	35.0	.	NM_001258299	A8MYU7|B3KRD3|B3KRH2|B3KTE0|B3KTJ7|B3KTJ8|B4E3U1|B7Z7Z9|Q68DG1|Q6PIM5|Q9HCH4|Q9NUV0	Missense_Mutation	SNP	ENST00000355371.4	hg19	CCDS44482.1	.	.	.	.	.	.	.	.	.	.	C	12.59	1.982973	0.34942	.	.	ENSG00000187164	ENST00000392903;ENST00000260777;ENST00000355371;ENST00000392901	T;T;T;T	0.75260	1.61;1.61;1.61;-0.92	5.35	4.45	0.53987	.	0.493073	0.23371	N	0.048907	T	0.65626	0.2709	L	0.52573	1.65	0.32981	D	0.52363	B;B;B	0.26845	0.069;0.008;0.161	B;B;B	0.24701	0.055;0.022;0.033	T	0.67643	-0.5618	10	0.23891	T	0.37	-14.1816	9.9478	0.41621	0.1475:0.6917:0.1608:0.0	.	295;295;265	A0MZ66;A0MZ66-2;A0MZ66-6	SHOT1_HUMAN;.;.	K	295;295;295;235	ENSP00000376636:E295K;ENSP00000260777:E295K;ENSP00000347532:E295K;ENSP00000376635:E235K	ENSP00000260777:E295K	E	-	1	0	KIAA1598	118679479	0.984000	0.35163	0.971000	0.41717	0.986000	0.74619	2.414000	0.44627	1.404000	0.46819	0.561000	0.74099	GAA	.	.	.	none		0.308	KIAA1598-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018330		T	118689489	C	T	118689489	3	4	163	1	0	0	0	0	1	0	0	0	8253	922	32	2	1044	2	KIAA1598	10	118689489	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08	38947518	118689489	16845258	53	9665	93	2									
KIAA1598	57698	hgsc.bcm.edu	37	chr10	118689491	118689491	+	Missense_Mutation	SNP	A	A	G																															tgtggagtgtttcattttctAgttgctcttctaattctttg																										TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr10:118689491A>G	ENST00000355371.4	-	10	1378	c.881T>C	c.(880-882)cTa>cCa	p.L294P	KIAA1598_ENST00000392901.4_Missense_Mutation_p.L234P|KIAA1598_ENST00000392903.2_Missense_Mutation_p.L294P|KIAA1598_ENST00000260777.10_Missense_Mutation_p.L294P|KIAA1598_ENST00000497044.1_5'UTR	NM_001127211.2|NM_001258298.1|NM_001258299.1	NP_001120683.1|NP_001245227.1|NP_001245228.1	A0MZ66	SHOT1_HUMAN	KIAA1598	294					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)		TTCATTTTCTAGTTGCTCTTC	0.303																																					p.L294P		Atlas-SNP	.											.	KIAA1598	74	.	0			c.T881C						PASS	.						161	150	154					10																	118689491		2201	4298	6499	SO:0001583	missense	57698	exon10			TTTTCTAGTTGCT	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.881T>C	chr10.hg19:g.118689491A>G	ENSP00000347532:p.Leu294Pro	146.0	0.0	.		133.0	34.0	.	NM_001258299	A8MYU7|B3KRD3|B3KRH2|B3KTE0|B3KTJ7|B3KTJ8|B4E3U1|B7Z7Z9|Q68DG1|Q6PIM5|Q9HCH4|Q9NUV0	Missense_Mutation	SNP	ENST00000355371.4	hg19	CCDS44482.1	.	.	.	.	.	.	.	.	.	.	A	18.91	3.723729	0.68959	.	.	ENSG00000187164	ENST00000392903;ENST00000260777;ENST00000355371;ENST00000392901	T;T;T;T	0.24538	2.72;2.72;2.72;1.85	5.35	5.35	0.76521	.	0.239875	0.36268	N	0.002695	T	0.48978	0.1530	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	0.999;0.997;1.0	D;D;D	0.87578	0.998;0.994;0.996	T	0.49273	-0.8957	10	0.59425	D	0.04	-9.5016	13.8675	0.63598	1.0:0.0:0.0:0.0	.	294;294;264	A0MZ66;A0MZ66-2;A0MZ66-6	SHOT1_HUMAN;.;.	P	294;294;294;234	ENSP00000376636:L294P;ENSP00000260777:L294P;ENSP00000347532:L294P;ENSP00000376635:L234P	ENSP00000260777:L294P	L	-	2	0	KIAA1598	118679481	0.999000	0.42202	0.840000	0.33206	0.981000	0.71138	5.819000	0.69243	2.163000	0.67991	0.459000	0.35465	CTA	.	.	.	none		0.303	KIAA1598-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018330		G	118689491	A	G	118689491	3	3	163	1	0	0	0	0	1	0	0	0	8253	420	15	3	1046	3	KIAA1598	10	118689491	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	2	118689491	16845256	54	9666	93	2									
GLRX3	10539	hgsc.bcm.edu	37	chr10	131964822	131964822	+	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	caaacataatattcagtttaGcagttttgatatcttctcag	13	16	5	7	0	3	1	2	1	2	0	4	1	3	1	0	0	2	3	0	0	5	9			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr10:131964822G>T	ENST00000368644.1	+	5	552	c.530G>T	c.(529-531)aGc>aTc	p.S177I	GLRX3_ENST00000331244.5_Missense_Mutation_p.S177I	NM_001199868.1	NP_001186797.1	O76003	GLRX3_HUMAN	glutaredoxin 3	177	Glutaredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00686}.				cell redox homeostasis (GO:0045454)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|regulation of the force of heart contraction (GO:0002026)	extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	electron carrier activity (GO:0009055)|iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein disulfide oxidoreductase activity (GO:0015035)			endometrium(1)|large_intestine(5)|lung(7)	13		all_cancers(35;9.59e-07)|all_epithelial(44;1.48e-06)|Lung NSC(174;0.00566)|all_lung(145;0.00949)|Colorectal(57;0.142)|all_neural(114;0.16)|Breast(234;0.173)|Glioma(114;0.222)		OV - Ovarian serous cystadenocarcinoma(35;0.00218)		ATTCAGTTTAGCAGTTTTGAT	0.393																																					p.S177I		Atlas-SNP	.											.	GLRX3	39	.	0			c.G530T						PASS	.						122	121	122					10																	131964822		2203	4300	6503	SO:0001583	missense	10539	exon5			AGTTTAGCAGTTT	AJ010841	CCDS7661.1	10q26	2009-05-29	2007-08-16	2007-08-16	ENSG00000108010	ENSG00000108010			15987	protein-coding gene	gene with protein product	"glutaredoxin 4"	612754	"thioredoxin-like 2"	TXNL2		10636891, 11124703	Standard	NM_006541		Approved	PICOT, bA500G10.4, GRX3, GLRX4, GRX4	uc001lkm.2	O76003	OTTHUMG00000019267	ENST00000368644.1:c.530G>T	chr10.hg19:g.131964822G>T	ENSP00000357633:p.Ser177Ile	162.0	0.0	.		131.0	31.0	.	NM_006541	B3KMP7|B3KMQ5|D3DRG2|Q5JV01|Q96CE0|Q9P1B0|Q9P1B1	Missense_Mutation	SNP	ENST00000368644.1	hg19	CCDS7661.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.573832	0.86542	.	.	ENSG00000108010	ENST00000331244;ENST00000368644	T;T	0.29917	1.55;1.55	5.0	5.0	0.66597	Glutaredoxin (2);Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	T	0.43523	0.1251	L	0.28649	0.875	0.80722	D	1	D	0.63046	0.992	D	0.70487	0.969	T	0.23440	-1.0188	10	0.35671	T	0.21	-14.9931	17.3131	0.87215	0.0:0.0:1.0:0.0	.	177	O76003	GLRX3_HUMAN	I	177	ENSP00000330836:S177I;ENSP00000357633:S177I	ENSP00000330836:S177I	S	+	2	0	GLRX3	131854812	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.365000	0.97139	2.323000	0.78572	0.655000	0.94253	AGC	.	.	.	none		0.393	GLRX3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051021.1	NM_006541		T	131964822	G	T	131964822	3	4	163	1	0	0	0	0	1	0	0	0	6468	971	34	4	548	4	GLRX3	10	131964822	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	13275331	131964822	3569925	55	9667											
LRRC56	115399	hgsc.bcm.edu	37	chr11	552211	552211	+	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	ggccttggctgggctcagggCctggagggaacatggcgtgc	5	7	19	10	1	1	0	1	0	0	0	1	2	1	2	2	7	2	2	2	7	1	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr11:552211C>T	ENST00000270115.7	+	12	1660	c.1160C>T	c.(1159-1161)gCc>gTc	p.A387V		NM_198075.3	NP_932341.1	Q8IYG6	LRC56_HUMAN	leucine rich repeat containing 56	387										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)		GGGCTCAGGGCCTGGAGGGAA	0.657																																					p.A387V		Atlas-SNP	.											.	LRRC56	23	.	0			c.C1160T						PASS	.						41	44	43					11																	552211		2202	4300	6502	SO:0001583	missense	115399	exon12			TCAGGGCCTGGAG		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.1160C>T	chr11.hg19:g.552211C>T	ENSP00000270115:p.Ala387Val	72.0	0.0	.		78.0	25.0	.	NM_198075	Q8N3Q4	Missense_Mutation	SNP	ENST00000270115.7	hg19	CCDS7700.1	.	.	.	.	.	.	.	.	.	.	C	17.56	3.420638	0.62622	.	.	ENSG00000161328	ENST00000270115	T	0.15952	2.38	4.38	4.38	0.52667	.	0.301734	0.24145	N	0.041134	T	0.14570	0.0352	L	0.27053	0.805	0.35067	D	0.762095	P	0.43287	0.802	B	0.42245	0.381	T	0.15549	-1.0433	10	0.59425	D	0.04	0.5026	12.6067	0.56527	0.0:1.0:0.0:0.0	.	387	Q8IYG6	LRC56_HUMAN	V	387	ENSP00000270115:A387V	ENSP00000270115:A387V	A	+	2	0	LRRC56	542211	0.208000	0.23494	0.120000	0.21714	0.036000	0.12997	2.410000	0.44592	2.441000	0.82636	0.561000	0.74099	GCC	.	.	.	none		0.657	LRRC56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254969.1	NM_198075		T	552211	C	T	552211	3	4	163	1	0	0	0	0	1	0	0	0	9019	739	26	2	1194	2	LRRC56	11	552211	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08		552211	134454305	56	9668											
TPP1	8642	hgsc.bcm.edu	37	chr11	6640045	6640045	+	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	gatccgacacagcctgcaccAgctccgagagtctttccaca	10	7	8	16	2	1	1	0	0	1	1	4	4	4	1	5	0	3	2	5	0	0	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr11:6640045A>C	ENST00000299441.3	-	0	10763				TPP1_ENST00000528657.1_3'UTR|RP11-732A19.9_ENST00000545572.1_RNA|TPP1_ENST00000299427.6_Missense_Mutation_p.L64R|TPP1_ENST00000534644.1_Intron|RP11-732A19.5_ENST00000526456.1_RNA|TPP1_ENST00000533371.1_5'UTR	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1						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)		AGCCTGCACCAGCTCCGAGAG	0.622																																					p.L64R		Atlas-SNP	.											.	TPP1	71	.	0			c.T191G						PASS	.						77	68	71					11																	6640045		2201	4296	6497	SO:0001628	intergenic_variant	1200	exon3			TGCACCAGCTCCG	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		chr11.hg19:g.6640045A>C		112.0	0.0	.		88.0	24.0	.	NM_000391	O15098	Missense_Mutation	SNP	ENST00000299441.3	hg19	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.196515	0.79015	.	.	ENSG00000166340	ENST00000299427;ENST00000453338;ENST00000436873	T;T	0.70516	-0.49;-0.49	5.64	4.45	0.53987	Proteinase inhibitor, propeptide (1);Peptidase S53, propeptide (2);	0.231767	0.37530	N	0.002054	T	0.72407	0.3456	L	0.48260	1.515	0.80722	D	1	D;D	0.61697	0.99;0.972	P;P	0.59288	0.855;0.639	T	0.68633	-0.5357	10	0.25751	T	0.34	-18.2713	9.3741	0.38272	0.8409:0.0:0.0:0.1591	.	64;64	B4DEQ3;O14773	.;TPP1_HUMAN	R	64	ENSP00000299427:L64R;ENSP00000398136:L64R	ENSP00000299427:L64R	L	-	2	0	TPP1	6596621	1.000000	0.71417	0.996000	0.52242	0.992000	0.81027	3.517000	0.53443	2.146000	0.66826	0.379000	0.24179	CTG	.	.	.	none		0.622	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		C	6640045	A	C	6640045	1	2	163	0	1	0	0	0	0	0	0	0	16423	188	7	5		5	TPP1	11	6640045	IGR	SNP	A	TCGA-EV-5903-01A-11D-1589-08	6087834	6640045	128366471	57	9669											
F2	2147	hgsc.bcm.edu	37	chr11	46740795	46740795	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgacacactatggcgcacGtccgaggcttgcagctgcct	7	8	12	14	3	0	1	0	1	0	0	1	2	1	1	2	2	3	5	2	2	1	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr11:46740795G>A	ENST00000311907.5	+	1	66	c.10G>A	c.(10-12)Gtc>Atc	p.V4I	F2_ENST00000530231.1_Missense_Mutation_p.V4I	NM_000506.3	NP_000497.1	P00734	THRB_HUMAN	coagulation factor II (thrombin)	4					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)	TATGGCGCACGTCCGAGGCTT	0.577																																					p.V4I	Esophageal Squamous(147;1147 1808 2148 38609 51144)	Atlas-SNP	.											.	F2	75	.	0			c.G10A						PASS	.						47	40	42					11																	46740795		2201	4299	6500	SO:0001583	missense	2147	exon1			GCGCACGTCCGAG	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.10G>A	chr11.hg19:g.46740795G>A	ENSP00000308541:p.Val4Ile	50.0	0.0	.		45.0	14.0	.	NM_000506	B2R7F7|B4E1A7|Q4QZ40|Q53H04|Q53H06|Q69EZ7|Q7Z7P3|Q9UCA1	Missense_Mutation	SNP	ENST00000311907.5	hg19	CCDS31476.1	.	.	.	.	.	.	.	.	.	.	G	4.679	0.126175	0.08931	.	.	ENSG00000180210	ENST00000311907;ENST00000530231	D;D	0.91295	-2.61;-2.82	5.76	1.65	0.23941	.	1.055420	0.07341	N	0.880761	D	0.84293	0.5440	L	0.34521	1.04	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.71258	-0.4646	10	0.87932	D	0	.	4.8209	0.13390	0.3861:0.1476:0.4664:0.0	.	4	P00734	THRB_HUMAN	I	4	ENSP00000308541:V4I;ENSP00000433907:V4I	ENSP00000308541:V4I	V	+	1	0	F2	46697371	0.575000	0.26692	0.994000	0.49952	0.981000	0.71138	0.307000	0.19296	0.047000	0.15862	-0.140000	0.14226	GTC	.	.	.	none		0.577	F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317706.1			A	46740795	G	A	46740795	3	1	163	1	0	0	0	0	1	0	0	0	5344	1145	40	1	12	1	F2	11	46740795	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	40100750	46740795	88265721	58	9670											
LRFN4	78999	hgsc.bcm.edu	37	chr11	66627368	66627368	+	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	actggtcttcactgtggcctTgctggttcggggccgggggg	2	11	18	10	2	2	0	1	0	1	0	3	0	2	0	2	8	1	2	2	8	0	3			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr11:66627368T>A	ENST00000309602.4	+	2	1853	c.1610T>A	c.(1609-1611)tTg>tAg	p.L537*	PC_ENST00000393960.1_Intron|PC_ENST00000393958.2_Intron|PC_ENST00000393955.2_Intron|LRFN4_ENST00000393952.3_Intron	NM_024036.4	NP_076941.2	Q6PJG9	LRFN4_HUMAN	leucine rich repeat and fibronectin type III domain containing 4	537						integral component of membrane (GO:0016021)				breast(1)|lung(1)|prostate(1)	3						ACTGTGGCCTTGCTGGTTCGG	0.711																																					p.L537X		Atlas-SNP	.											.	LRFN4	25	.	0			c.T1610A						PASS	.						34	28	30					11																	66627368		2188	4284	6472	SO:0001587	stop_gained	78999	exon2			TGGCCTTGCTGGT	BC007718	CCDS8153.1	11q13.1	2013-02-11				ENSG00000173621		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	28456	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 6"	612810				16495444, 16828986	Standard	NM_024036		Approved	MGC3103, SALM3., FIGLER6	uc001ojr.3	Q6PJG9		ENST00000309602.4:c.1610T>A	chr11.hg19:g.66627368T>A	ENSP00000312535:p.Leu537*	32.0	0.0	.		31.0	13.0	.	NM_024036	Q4VBZ3|Q59GV4|Q8N644|Q9BWJ0	Nonsense_Mutation	SNP	ENST00000309602.4	hg19	CCDS8153.1	.	.	.	.	.	.	.	.	.	.	T	39	7.854370	0.98525	.	.	ENSG00000173621	ENST00000309602	.	.	.	4.79	4.79	0.61399	.	0.484734	0.15470	N	0.260642	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.2823	0.54771	0.0:0.0:0.0:1.0	.	.	.	.	X	537	.	ENSP00000312535:L537X	L	+	2	0	LRFN4	66383944	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.178000	0.58284	1.799000	0.52666	0.379000	0.24179	TTG	.	.	.	none		0.711	LRFN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393127.1	NM_024036		A	66627368	T	A	66627368	4	1	163	1	0	0	0	0	0	1	0	0	8947	1821	63	5	1616	5	LRFN4	11	66627368	Nonsense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	19886573	66627368	68379148	59	9671											
PCF11	51585	hgsc.bcm.edu	37	chr11	82877690	82877690	+	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	aggcactgaaccaaaggagaAtgtagaaaactggcaaagtt	18	6	11	6	0	0	3	0	1	0	2	0	4	0	3	1	3	2	4	1	3	7	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr11:82877690A>T	ENST00000298281.4	+	5	2203	c.1751A>T	c.(1750-1752)aAt>aTt	p.N584I		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	584					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						CCAAAGGAGAATGTAGAAAAC	0.393																																					p.N584I		Atlas-SNP	.											PCF11_ENST00000298281,NS,carcinoma,0,4	PCF11	220	.	0			c.A1751T						PASS	.						66	66	66					11																	82877690		1824	4044	5868	SO:0001583	missense	51585	exon5			AGGAGAATGTAGA	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.1751A>T	chr11.hg19:g.82877690A>T	ENSP00000298281:p.Asn584Ile	81.0	0.0	.		83.0	14.0	.	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	hg19	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	A	16.07	3.019444	0.54576	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.53206	1.58;0.64;0.63	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000005	T	0.54775	0.1879	L	0.29908	0.895	0.33890	D	0.637211	D;P	0.71674	0.998;0.915	P;B	0.61940	0.896;0.294	T	0.62798	-0.6778	9	.	.	.	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	584;584	E9PQ01;O94913	.;PCF11_HUMAN	I	584	ENSP00000298281:N584I;ENSP00000434540:N584I;ENSP00000431567:N584I	.	N	+	2	0	PCF11	82555338	1.000000	0.71417	0.991000	0.47740	0.967000	0.64934	3.827000	0.55745	2.326000	0.78906	0.533000	0.62120	AAT	.	.	.	none		0.393	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		T	82877690	A	T	82877690	3	4	163	1	0	0	0	0	1	0	0	0	11580	101	4	5	1769	5	PCF11	11	82877690	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	16250322	82877690	52128826	60	9672											
PCF11	51585	hgsc.bcm.edu	37	chr11	82878314	82878314	+	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	aatcttcagattcctaaagaGttaactcttgcaagcaaaag	16	11	6	8	0	3	2	1	0	2	2	4	2	4	2	1	0	3	3	1	0	7	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr11:82878314G>C	ENST00000298281.4	+	6	2417	c.1965G>C	c.(1963-1965)gaG>gaC	p.E655D		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	655					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						TTCCTAAAGAGTTAACTCTTG	0.368																																					p.E655D		Atlas-SNP	.											.	PCF11	220	.	0			c.G1965C						PASS	.						62	61	61					11																	82878314		1875	4100	5975	SO:0001583	missense	51585	exon6			TAAAGAGTTAACT	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.1965G>C	chr11.hg19:g.82878314G>C	ENSP00000298281:p.Glu655Asp	88.0	0.0	.		80.0	20.0	.	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	hg19	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	G	16.59	3.165064	0.57476	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.48836	1.78;0.82;0.8	5.98	1.48	0.22813	.	0.000000	0.64402	D	0.000015	T	0.42381	0.1200	L	0.29908	0.895	0.26221	N	0.979152	D;D	0.67145	0.996;0.985	P;P	0.54499	0.754;0.541	T	0.25398	-1.0133	9	.	.	.	.	8.1397	0.31076	0.5069:0.0:0.4931:0.0	.	655;655	E9PQ01;O94913	.;PCF11_HUMAN	D	655	ENSP00000298281:E655D;ENSP00000434540:E655D;ENSP00000431567:E655D	.	E	+	3	2	PCF11	82555962	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.998000	0.29744	0.412000	0.25729	0.591000	0.81541	GAG	.	.	.	none		0.368	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		C	82878314	G	C	82878314	3	2	163	1	0	0	0	0	1	0	0	0	11580	1020	36	4	1987	4	PCF11	11	82878314	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	624	82878314	52128202	61	9673											
SLC6A13	6540	hgsc.bcm.edu	37	chr12	346349	346349	+	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	ctgtggacttcacccccttcCagatgcagaagtagcagatg	10	9	10	12	0	1	3	1	0	0	3	2	4	2	4	3	1	2	3	3	1	2	3			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr12:346349C>G	ENST00000343164.4	-	6	723	c.671G>C	c.(670-672)tGg>tCg	p.W224S	SLC6A13_ENST00000445055.2_Missense_Mutation_p.W132S	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	224					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)			CACCCCCTTCCAGATGCAGAA	0.632																																					p.W224S		Atlas-SNP	.											.	SLC6A13	62	.	0			c.G671C						PASS	.						87	83	84					12																	346349		2203	4300	6503	SO:0001583	missense	6540	exon6			CCCTTCCAGATGC	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.671G>C	chr12.hg19:g.346349C>G	ENSP00000339260:p.Trp224Ser	190.0	0.0	.		123.0	30.0	.	NM_016615	B4DJL1|Q8TCC2|Q8WW56	Missense_Mutation	SNP	ENST00000343164.4	hg19	CCDS8502.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.782040	0.90282	.	.	ENSG00000010379	ENST00000445055;ENST00000313154;ENST00000343164;ENST00000546319	T;T;T	0.74842	-0.88;-0.88;-0.88	5.5	5.5	0.81552	.	0.054680	0.85682	D	0.000000	D	0.85013	0.5600	M	0.76170	2.325	0.80722	D	1	D;D;D	0.57257	0.979;0.971;0.971	P;P;P	0.59546	0.859;0.827;0.827	D	0.85988	0.1487	10	0.87932	D	0	.	19.6592	0.95857	0.0:1.0:0.0:0.0	.	132;203;224	B4DJL1;B4DJS3;Q9NSD5	.;.;S6A13_HUMAN	S	132;203;224;132	ENSP00000407104:W132S;ENSP00000339260:W224S;ENSP00000444606:W132S	ENSP00000318097:W203S	W	-	2	0	SLC6A13	216610	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.905000	0.69893	2.880000	0.98712	0.650000	0.86243	TGG	.	.	.	none		0.632	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615		G	346349	C	G	346349	3	3	163	1	0	0	0	0	1	0	0	0	14689	595	21	4	1177	4	SLC6A13	12	346349	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08		346349	133505546	62	9674											
DCP1B	196513	hgsc.bcm.edu	37	chr12	2064679	2064679	+	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	atgagatttggattgtcataGatggcagaggaactggttat	12	13	13	3	0	1	3	1	1	0	3	1	6	1	5	0	4	1	2	0	4	3	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr12:2064679G>C	ENST00000280665.6	-	6	649	c.570C>G	c.(568-570)atC>atG	p.I190M	DCP1B_ENST00000541700.1_Intron|DCP1B_ENST00000540622.1_Missense_Mutation_p.I64M|DCP1B_ENST00000397173.4_Missense_Mutation_p.I88M	NM_152640.3	NP_689853.3	Q8IZD4	DCP1B_HUMAN	decapping mRNA 1B	190					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)			GATTGTCATAGATGGCAGAGG	0.413																																					p.I190M		Atlas-SNP	.											.	DCP1B	63	.	0			c.C570G						PASS	.						239	227	231					12																	2064679		2203	4300	6503	SO:0001583	missense	196513	exon6			GTCATAGATGGCA	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.570C>G	chr12.hg19:g.2064679G>C	ENSP00000280665:p.Ile190Met	256.0	0.0	.		207.0	69.0	.	NM_152640	B4DRD1|Q86XH9|Q96BP8|Q96MZ8	Missense_Mutation	SNP	ENST00000280665.6	hg19	CCDS31727.1	.	.	.	.	.	.	.	.	.	.	G	18.95	3.732160	0.69189	.	.	ENSG00000151065	ENST00000280665;ENST00000397173;ENST00000540622	T;T;T	0.23950	2.1;2.1;1.88	5.73	4.84	0.62591	.	0.054750	0.64402	D	0.000001	T	0.49029	0.1533	M	0.67953	2.075	0.45791	D	0.998674	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.971	T	0.51849	-0.8653	10	0.72032	D	0.01	-25.192	13.8354	0.63406	0.0731:0.0:0.9269:0.0	.	88;190	B4DRD1;Q8IZD4	.;DCP1B_HUMAN	M	190;88;64	ENSP00000280665:I190M;ENSP00000380358:I88M;ENSP00000444374:I64M	ENSP00000280665:I190M	I	-	3	3	DCP1B	1934940	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	1.749000	0.38319	1.426000	0.47256	0.655000	0.94253	ATC	.	.	.	none		0.413	DCP1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398244.1	NM_152640		C	2064679	G	C	2064679	3	2	163	1	0	0	0	0	1	0	0	0	4301	932	33	4	1299	4	DCP1B	12	2064679	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	1718330	2064679	131787216	63	9675											
DDX47	51202	hgsc.bcm.edu	37	chr12	12980185	12980185	+	Missense_Mutation	SNP	A	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	gttttccttcctcaggtatgAtgtggaactcttccagcgca	7	14	9	11	1	2	1	1	1	1	0	5	2	5	2	3	2	2	3	3	2	2	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr12:12980185A>C	ENST00000358007.3	+	11	1134	c.1112A>C	c.(1111-1113)gAt>gCt	p.D371A	DDX47_ENST00000352940.4_Missense_Mutation_p.D322A	NM_016355.3	NP_057439.2	Q9H0S4	DDX47_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47	371	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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)		CTCAGGTATGATGTGGAACTC	0.448																																					p.D371A		Atlas-SNP	.											.	DDX47	37	.	0			c.A1112C						PASS	.						110	109	110					12																	12980185		2203	4300	6503	SO:0001583	missense	51202	exon11			GGTATGATGTGGA	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.1112A>C	chr12.hg19:g.12980185A>C	ENSP00000350698:p.Asp371Ala	133.0	0.0	.		126.0	42.0	.	NM_016355	B3KXP4|G5E955|Q96GM0|Q96NV8|Q9UI98	Missense_Mutation	SNP	ENST00000358007.3	hg19	CCDS8655.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.939470	0.73557	.	.	ENSG00000213782	ENST00000352940;ENST00000358007	T;T	0.52983	0.64;3.36	5.64	5.64	0.86602	Helicase, C-terminal (1);	0.050495	0.85682	D	0.000000	T	0.73560	0.3602	M	0.89287	3.02	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.74023	0.982;0.971	T	0.79650	-0.1715	10	0.87932	D	0	-16.8971	15.8578	0.78994	1.0:0.0:0.0:0.0	.	322;371	G5E955;Q9H0S4	.;DDX47_HUMAN	A	322;371	ENSP00000319578:D322A;ENSP00000350698:D371A	ENSP00000319578:D322A	D	+	2	0	DDX47	12871452	1.000000	0.71417	0.944000	0.38274	0.435000	0.31806	8.932000	0.92897	2.147000	0.66899	0.533000	0.62120	GAT	.	.	.	none		0.448	DDX47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400674.1	NM_016355		C	12980185	A	C	12980185	3	2	163	1	0	0	0	0	1	0	0	0	4367	333	12	5	1154	5	DDX47	12	12980185	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	10915506	12980185	120871710	64	9676											
ITPR2	3709	hgsc.bcm.edu	37	chr12	26810769	26810769	+	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	gccaaacttcttcatcatcaAtgtcatctgaaaggatggag	13	11	8	9	0	6	1	4	1	2	0	6	3	6	3	1	2	1	0	1	2	3	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr12:26810769A>T	ENST00000381340.3	-	18	2479	c.2063T>A	c.(2062-2064)aTt>aAt	p.I688N		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	688					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)	TTCATCATCAATGTCATCTGA	0.423																																					p.I688N		Atlas-SNP	.											.	ITPR2	270	.	0			c.T2063A						PASS	.						117	109	112					12																	26810769		1908	4126	6034	SO:0001583	missense	3709	exon18			TCATCAATGTCAT	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.2063T>A	chr12.hg19:g.26810769A>T	ENSP00000370744:p.Ile688Asn	119.0	0.0	.		108.0	33.0	.	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	hg19	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	A	8.672	0.902956	0.17760	.	.	ENSG00000123104	ENST00000381340	D	0.91894	-2.93	4.4	4.4	0.53042	.	0.556787	0.20935	N	0.083032	D	0.83815	0.5336	N	0.14661	0.345	0.80722	D	1	B	0.06786	0.001	B	0.10450	0.005	T	0.78633	-0.2128	10	0.23891	T	0.37	.	12.6771	0.56901	1.0:0.0:0.0:0.0	.	688	Q14571	ITPR2_HUMAN	N	688	ENSP00000370744:I688N	ENSP00000370744:I688N	I	-	2	0	ITPR2	26702036	0.839000	0.29477	0.973000	0.42090	0.226000	0.24999	3.396000	0.52565	1.983000	0.57843	0.533000	0.62120	ATT	.	.	.	none		0.423	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		T	26810769	A	T	26810769	3	4	163	1	0	0	0	0	1	0	0	0	7928	101	4	5	6202	5	ITPR2	12	26810769	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	13830584	26810769	107041126	65	9677											
SLC2A13	114134	hgsc.bcm.edu	37	chr12	40265609	40265609	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagccacctacctgctaaacTaccaaaggtaagctttctgc	12	9	6	14	0	1	0	0	0	1	0	1	0	1	0	4	1	7	3	4	1	6	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr12:40265609T>C	ENST00000280871.4	-	5	1239	c.1189A>G	c.(1189-1191)Agt>Ggt	p.S397G		NM_052885.3	NP_443117.3	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 13	397					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	29		Lung NSC(34;0.105)|all_lung(34;0.123)				CCTGCTAAACTACCAAAGGTA	0.378										HNSCC(50;0.14)																											p.S397G		Atlas-SNP	.											.	SLC2A13	91	.	0			c.A1189G						PASS	.						55	54	54					12																	40265609		2203	4300	6503	SO:0001583	missense	114134	exon5			CTAAACTACCAAA	AJ315644	CCDS8736.2	12q12	2013-05-22			ENSG00000151229	ENSG00000151229		"Solute carriers"	15956	protein-coding gene	gene with protein product	"H(+)-myo-inositol symporter"	611036				11500374	Standard	NM_052885		Approved	HMIT	uc010skm.2	Q96QE2	OTTHUMG00000059743	ENST00000280871.4:c.1189A>G	chr12.hg19:g.40265609T>C	ENSP00000280871:p.Ser397Gly	83.0	0.0	.		90.0	33.0	.	NM_052885	Q17S07	Missense_Mutation	SNP	ENST00000280871.4	hg19	CCDS8736.2	.	.	.	.	.	.	.	.	.	.	T	25.2	4.609414	0.87258	.	.	ENSG00000151229	ENST00000280871	T	0.58797	0.31	5.48	5.48	0.80851	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);Sugar transporter, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.59487	0.2197	N	0.19112	0.55	0.80722	D	1	D	0.65815	0.995	D	0.67382	0.951	T	0.54556	-0.8276	10	0.14252	T	0.57	-16.2802	15.8683	0.79084	0.0:0.0:0.0:1.0	.	397	Q96QE2	MYCT_HUMAN	G	397	ENSP00000280871:S397G	ENSP00000280871:S397G	S	-	1	0	SLC2A13	38551876	1.000000	0.71417	0.996000	0.52242	0.977000	0.68977	7.745000	0.85046	2.214000	0.71695	0.528000	0.53228	AGT	.	.	.	none		0.378	SLC2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132849.2			C	40265609	T	C	40265609	3	2	163	1	0	0	0	0	1	0	0	0	14555	1522	53	3	781	3	SLC2A13	12	40265609	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	13454840	40265609	93586286	66	9678											
MARS	4141	hgsc.bcm.edu	37	chr12	57891971	57891971	+	Missense_Mutation	SNP	A	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	ctggagaaaggaatgtgctcAtcaccagtgccctcccttac	10	9	9	13	0	2	1	2	0	0	1	3	3	3	2	3	2	3	1	3	2	3	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr12:57891971A>C	ENST00000262027.5	+	8	936	c.802A>C	c.(802-804)Atc>Ctc	p.I268L	MARS_ENST00000447721.2_3'UTR|MARS_ENST00000315473.5_Missense_Mutation_p.I34L	NM_004990.3	NP_004981.2	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	268					gene expression (GO:0010467)|methionyl-tRNA aminoacylation (GO:0006431)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methionine-tRNA ligase activity (GO:0004825)|tRNA binding (GO:0000049)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	33			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)	GAATGTGCTCATCACCAGTGC	0.537																																					p.I268L		Atlas-SNP	.											.	MARS	84	.	0			c.A802C						PASS	.						182	131	148					12																	57891971		2203	4300	6503	SO:0001583	missense	4141	exon8			GTGCTCATCACCA	X94754	CCDS8942.1	12q13.3	2014-05-06	2007-02-26		ENSG00000166986	ENSG00000166986	6.1.1.10	"Aminoacyl tRNA synthetases / Class I"	6898	protein-coding gene	gene with protein product	"methionine tRNA ligase 1, cytoplasmic"	156560				10448063, 24482476	Standard	NM_004990		Approved	MetRS, SPG70	uc001sog.3	P56192	OTTHUMG00000169996	ENST00000262027.5:c.802A>C	chr12.hg19:g.57891971A>C	ENSP00000262027:p.Ile268Leu	128.0	0.0	.		89.0	28.0	.	NM_004990	B3KVK7|Q14895|Q53H14|Q96A15|Q96BZ0|Q9NSE0	Missense_Mutation	SNP	ENST00000262027.5	hg19	CCDS8942.1	.	.	.	.	.	.	.	.	.	.	A	26.7	4.760542	0.89932	.	.	ENSG00000166986	ENST00000262027;ENST00000315473	T;T	0.54675	1.05;0.56	4.7	4.7	0.59300	Aminoacyl-tRNA synthetase, class I (M) (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.070998	0.64402	D	0.000014	T	0.69223	0.3087	M	0.85630	2.765	0.54753	D	0.999982	B;P;P	0.45902	0.338;0.606;0.868	B;P;P	0.55087	0.167;0.46;0.768	T	0.74760	-0.3556	10	0.72032	D	0.01	-16.6576	11.9918	0.53180	1.0:0.0:0.0:0.0	.	34;141;268	A6NC17;B4E0E9;P56192	.;.;SYMC_HUMAN	L	268;34	ENSP00000262027:I268L;ENSP00000314653:I34L	ENSP00000262027:I268L	I	+	1	0	MARS	56178238	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.315000	0.51951	1.884000	0.54569	0.459000	0.35465	ATC	.	.	.	none		0.537	MARS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407014.1	NM_004990		C	57891971	A	C	57891971	3	2	163	1	0	0	0	0	1	0	0	0	9323	217	8	5	832	5	MARS	12	57891971	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	17626362	57891971	75959924	67	9679											
NAV3	89795	hgsc.bcm.edu	37	chr12	78513435	78513436	+	Frame_Shift_Ins	INS	-	-	G																															gtggcattcctggccgaggaINSggccacagatccagtaccag																										TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr12:78513435_78513436insG	ENST00000397909.2	+	15	3632_3633	c.3459_3460insG	c.(3460-3462)ggcfs	p.G1154fs	NAV3_ENST00000536525.2_Frame_Shift_Ins_p.G1154fs|NAV3_ENST00000228327.6_Frame_Shift_Ins_p.G1154fs|NAV3_ENST00000266692.7_Frame_Shift_Ins_p.G1154fs			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1154	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						CTGGCCGAGGAGGCCACAGATC	0.525										HNSCC(70;0.22)																											p.G1153fs		Atlas-INDEL	.											.	NAV3	506	.	0			c.3459_3460insG						PASS	.																																			SO:0001589	frameshift_variant	89795	exon15			.	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.3461dupG	chr12.hg19:g.78513437_78513437dupG	ENSP00000381007:p.Gly1154fs	68.0	0.0	0		73.0	20.0	0.273973	NM_014903	Q8NFW7|Q9Y2E7	Frame_Shift_Ins	INS	ENST00000397909.2	hg19																																																																																				.	.	.	none		0.525	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		G	78513436	-	G	78513435	7	5	163	1	0	1	1	0	0	0	0	0	10192	291	11	0	3517	0	NAV3	12	78513435	Frame_Shift_Ins	INS	-	TCGA-EV-5903-01A-11D-1589-08	20621464	78513435	55338460	68	9680											
PEBP1	5037	hgsc.bcm.edu	37	chr12	118577332	118577332	+	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	cagtcctctccgattatgtgGgctcggggcctcccaagggc	5	9	13	14	2	1	0	0	0	1	0	5	1	3	0	4	4	0	1	4	4	2	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr12:118577332G>T	ENST00000261313.2	+	3	674	c.322G>T	c.(322-324)Ggc>Tgc	p.G108C	PEBP1_ENST00000542939.1_3'UTR	NM_002567.2	NP_002558.1	P30086	PEBP1_HUMAN	phosphatidylethanolamine binding protein 1	108	Interaction with RAF1.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|phosphatidylethanolamine binding (GO:0008429)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|serine-type endopeptidase inhibitor activity (GO:0004867)			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CGATTATGTGGGCTCGGGGCC	0.527																																					p.G108C	NSCLC(44;94 1357 12187 49467)	Atlas-SNP	.											.	PEBP1	13	.	0			c.G322T						PASS	.						125	112	116					12																	118577332		2203	4300	6503	SO:0001583	missense	5037	exon3			TATGTGGGCTCGG	X85033	CCDS9187.1	12q24	2009-06-16	2006-02-16	2006-02-16	ENSG00000089220	ENSG00000089220			8630	protein-coding gene	gene with protein product	"Raf kinase inhibitory protein", "hippocampal cholinergic neurostimulating peptide"	604591	"prostatic binding protein"	PBP		15782137	Standard	NM_002567		Approved	RKIP, HCNP, PEBP	uc001twu.1	P30086	OTTHUMG00000168860	ENST00000261313.2:c.322G>T	chr12.hg19:g.118577332G>T	ENSP00000261313:p.Gly108Cys	98.0	0.0	.		89.0	16.0	.	NM_002567	B2R4S1	Missense_Mutation	SNP	ENST00000261313.2	hg19	CCDS9187.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.595001	0.86953	.	.	ENSG00000089220	ENST00000261313;ENST00000418769	T	0.57595	0.39	5.43	4.54	0.55810	.	0.047800	0.85682	D	0.000000	D	0.82614	0.5075	H	0.98426	4.23	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.88953	0.3388	10	0.87932	D	0	.	13.8987	0.63790	0.0734:0.0:0.9265:0.0	.	108;108	B4DRT4;P30086	.;PEBP1_HUMAN	C	108	ENSP00000261313:G108C	ENSP00000261313:G108C	G	+	1	0	PEBP1	117061715	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	9.447000	0.97595	1.280000	0.44463	0.563000	0.77884	GGC	.	.	.	none		0.527	PEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401405.1	NM_002567		T	118577332	G	T	118577332	3	4	163	1	0	0	0	0	1	0	0	0	11720	1232	43	4	332	4	PEBP1	12	118577332	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	40063897	118577332	15274563	69	9681											
PSPC1	55269	hgsc.bcm.edu	37	chr13	20356720	20356720	+	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	gtcgatagtgaaccccatctCctcgtccgggtggtcctctg	5	11	11	14	3	2	1	0	1	2	0	7	2	4	1	5	2	1	0	5	2	2	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr13:20356720C>T	ENST00000338910.4	-	1	337	c.178G>A	c.(178-180)Gag>Aag	p.E60K		NM_001042414.2	NP_001035879.1	Q8WXF1	PSPC1_HUMAN	paraspeckle component 1	60					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)		AACCCCATCTCCTCGTCCGGG	0.692																																					p.E60K		Atlas-SNP	.											.	PSPC1	61	.	0			c.G178A						PASS	.						35	37	36					13																	20356720		1929	4130	6059	SO:0001583	missense	55269	exon2			CCATCTCCTCGTC	AK001817	CCDS41870.1	13q11	2013-02-12			ENSG00000121390	ENSG00000121390		"RNA binding motif (RRM) containing"	20320	protein-coding gene	gene with protein product		612408				11790299	Standard	NM_001042414		Approved	PSP1, FLJ10955	uc021rgx.1	Q8WXF1	OTTHUMG00000016502	ENST00000338910.4:c.178G>A	chr13.hg19:g.20356720C>T	ENSP00000343966:p.Glu60Lys	39.0	0.0	.		76.0	24.0	.	NM_001042414	Q5JTQ3|Q8NCZ9|Q8WXE8|Q9NV36	Missense_Mutation	SNP	ENST00000338910.4	hg19	CCDS41870.1	.	.	.	.	.	.	.	.	.	.	C	13.65	2.301856	0.40694	.	.	ENSG00000121390	ENST00000338910;ENST00000427943	T;T	0.14640	2.49;2.52	4.8	4.8	0.61643	.	0.347470	0.29396	N	0.012262	T	0.12561	0.0305	L	0.36672	1.1	0.45648	D	0.998577	B	0.21688	0.059	B	0.15870	0.014	T	0.11108	-1.0601	10	0.15499	T	0.54	-5.6938	18.0489	0.89341	0.0:1.0:0.0:0.0	.	60	Q8WXF1	PSPC1_HUMAN	K	60	ENSP00000343966:E60K;ENSP00000393069:E60K	ENSP00000343966:E60K	E	-	1	0	PSPC1	19254720	0.983000	0.35010	0.801000	0.32222	0.460000	0.32559	3.317000	0.51968	2.511000	0.84671	0.313000	0.20887	GAG	.	.	.	none		0.692	PSPC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044037.2			T	20356720	C	T	20356720	3	4	163	1	0	0	0	0	1	0	0	0	12726	864	30	2	1429	2	PSPC1	13	20356720	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08		20356720	94813158	70	9682											
SUPT16H	11198	hgsc.bcm.edu	37	chr14	21821861	21821861	+	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	actttgctctgtaagactaaCctgactcttctgcttctgat	8	16	6	11	0	4	3	0	2	4	1	4	3	4	3	1	0	3	3	1	0	2	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr14:21821861C>T	ENST00000216297.2	-	24	3259		c.e24+1			NM_007192.3	NP_009123.1	Q9Y5B9	SP16H_HUMAN	suppressor of Ty 16 homolog (S. cerevisiae)						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)		GTAAGACTAACCTGACTCTTC	0.378																																					.		Atlas-SNP	.											.	SUPT16H	84	.	0			c.2920+1G>A						PASS	.						178	155	163					14																	21821861		2203	4300	6503	SO:0001630	splice_region_variant	11198	exon25			GACTAACCTGACT	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.2920+1G>A	chr14.hg19:g.21821861C>T		161.0	0.0	.		147.0	36.0	.	NM_007192	Q6GMT8|Q6P2F1|Q6PJM1|Q9NRX0	Splice_Site	SNP	ENST00000216297.2	hg19	CCDS9569.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.254717	0.80135	.	.	ENSG00000092201	ENST00000216297	.	.	.	5.21	5.21	0.72293	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.9497	0.89048	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SUPT16H	20891701	1.000000	0.71417	0.998000	0.56505	0.899000	0.52679	6.568000	0.73987	2.602000	0.87976	0.558000	0.71614	.	.	.	.	none		0.378	SUPT16H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074025.2		Intron	T	21821861	C	T	21821861	5	4	163	1	0	0	0	0	0	0	1	0	15408	521	18	2	234	2	SUPT16H	14	21821861	Splice_Site	SNP	C	TCGA-EV-5903-01A-11D-1589-08		21821861	85527679	71	9683											
AP1G2	8906	hgsc.bcm.edu	37	chr14	24036472	24036472	+	Frame_Shift_Del	DEL	C	C	-																															ctcctgggcctgagtcttggCcccgcgaatctcttcgatga																										TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr14:24036472delC	ENST00000308724.5	-	1	807	c.52delG	c.(52-54)gccfs	p.A18fs	AP1G2_ENST00000556277.1_5'UTR|RP11-66N24.3_ENST00000555968.1_RNA|AP1G2_ENST00000397120.3_Frame_Shift_Del_p.A18fs	NM_003917.2	NP_003908.1	O75843	AP1G2_HUMAN	adaptor-related protein complex 1, gamma 2 subunit	18					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	AP-1 adaptor complex (GO:0030121)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|membrane (GO:0016020)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	28	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00672)		TGAGTCTTGGCCCCGCGAATC	0.637											OREG0022606	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A18fs		Atlas-INDEL	.											AP1G2,colon,carcinoma,0,1	AP1G2	75	.	0			c.53delC						PASS	.						53	43	46					14																	24036472		2203	4300	6503	SO:0001589	frameshift_variant	8906	exon2			.	AB015318	CCDS9602.1	14q11.2	2008-07-03			ENSG00000213983	ENSG00000213983			556	protein-coding gene	gene with protein product		603534				9733768, 9762922	Standard	XM_005268167		Approved	G2AD	uc001wkl.2	O75843	OTTHUMG00000028760	ENST00000308724.5:c.52delG	chr14.hg19:g.24036472delC	ENSP00000312442:p.Ala18fs	63.0	0.0	0	768	70.0	15.0	0.214286	NM_003917	D3DS51|O75504	Frame_Shift_Del	DEL	ENST00000308724.5	hg19	CCDS9602.1																																																																																			.	.	.	none		0.637	AP1G2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071812.4	NM_003917		-	24036472	C	-	24036472	7	5	163	1	0	1	0	1	0	0	0	0	733	739	26	0	2389	0	AP1G2	14	24036472	Frame_Shift_Del	DEL	C	TCGA-EV-5903-01A-11D-1589-08	2214611	24036472	83313068	72	9684											
NIN	51199	hgsc.bcm.edu	37	chr14	51219341	51219341	+	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	tccttctggcatagcatttcTgttagacgttgattaagttc	8	17	8	8	1	2	2	0	1	2	1	4	2	3	2	1	1	1	5	1	1	3	7			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr14:51219341T>A	ENST00000382041.3	-	21	5035	c.4845A>T	c.(4843-4845)acA>acT	p.T1615T	NIN_ENST00000324330.9_Silent_p.T1615T|NIN_ENST00000245441.5_Silent_p.T1615T|NIN_ENST00000530997.2_Silent_p.T1615T|NIN_ENST00000453196.1_Silent_p.T1615T|NIN_ENST00000389868.3_Silent_p.T902T|NIN_ENST00000382043.4_Silent_p.T902T	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	1615					centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					ATAGCATTTCTGTTAGACGTT	0.368			T	PDGFRB	MPD																																p.T1615T		Atlas-SNP	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN	475	.	0			c.A4845T						PASS	.						306	295	299					14																	51219341		2203	4300	6503	SO:0001819	synonymous_variant	51199	exon21			CATTTCTGTTAGA	AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"EF-hand domain containing"	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.4845A>T	chr14.hg19:g.51219341T>A		579.0	0.0	.		540.0	165.0	.	NM_020921	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Silent	SNP	ENST00000382041.3	hg19	CCDS32079.1	.	.	.	.	.	.	.	.	.	.	T	9.123	1.009401	0.19277	.	.	ENSG00000100503	ENST00000530997;ENST00000389869;ENST00000530853	.	.	.	5.74	-2.9	0.05648	.	.	.	.	.	.	.	.	.	.	.	0.38083	D	0.936736	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.4293	2.5367	0.04716	0.1233:0.351:0.1277:0.398	.	.	.	.	X	1106	.	.	R	-	1	2	NIN	50289091	0.799000	0.28903	0.876000	0.34364	0.839000	0.47603	-0.187000	0.09656	-0.385000	0.07833	0.533000	0.62120	AGA	.	.	.	none		0.368	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946		A	51219341	T	A	51219341	2	1	163	1	0	0	0	0	0	0	0	1	10424	1567	55	5		5	NIN	14	51219341	Silent	SNP	T	TCGA-EV-5903-01A-11D-1589-08	27182869	51219341	56130199	73	9685											
MNAT1	4331	hgsc.bcm.edu	37	chr14	61434986	61434986	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcctcaccacaggacctTgctggaggctatacttcttc	7	11	9	14	0	2	0	1	0	1	0	3	2	2	2	3	3	3	3	3	3	2	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr14:61434986T>C	ENST00000261245.4	+	8	950	c.849T>C	c.(847-849)ctT>ctC	p.L283L	RP11-193F5.1_ENST00000553946.1_RNA|MNAT1_ENST00000539616.2_Silent_p.L241L	NM_002431.3	NP_002422.1	P51948	MAT1_HUMAN	MNAT CDK-activating kinase assembly factor 1	283					7-methylguanosine mRNA capping (GO:0006370)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to calcium ion (GO:0051592)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|ventricular system development (GO:0021591)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein N-terminus binding (GO:0047485)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(2)	11				OV - Ovarian serous cystadenocarcinoma(108;0.0174)		CACAGGACCTTGCTGGAGGCT	0.398								Direct reversal of damage;Direct reversal of damage;Nucleotide excision repair (NER)																													p.L283L		Atlas-SNP	.											.	MNAT1	24	.	0			c.T849C						PASS	.						133	119	124					14																	61434986		2203	4300	6503	SO:0001819	synonymous_variant	4331	exon8			GGACCTTGCTGGA	X87843	CCDS9750.1, CCDS53899.1	14q23	2013-07-31	2013-07-31		ENSG00000020426	ENSG00000020426		"RING-type (C3HC4) zinc fingers", "General transcription factor IIH complex subunits"	7181	protein-coding gene	gene with protein product	"CDK-activating kinase assembly factor"	602659	"menage a trois 1 (CAK assembly factor)", "menage a trois homolog 1, cyclin H assembly factor (Xenopus laevis)"			9465303	Standard	NM_002431		Approved	MAT1, RNF66	uc001xfd.3	P51948	OTTHUMG00000152340	ENST00000261245.4:c.849T>C	chr14.hg19:g.61434986T>C		112.0	0.0	.		145.0	51.0	.	NM_002431	G3V1U8|Q15817|Q6ICQ7	Silent	SNP	ENST00000261245.4	hg19	CCDS9750.1																																																																																			.	.	.	none		0.398	MNAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276956.1	NM_002431		C	61434986	T	C	61434986	2	2	163	1	0	0	0	0	0	0	0	1	9681	1799	63	3		3	MNAT1	14	61434986	Silent	SNP	T	TCGA-EV-5903-01A-11D-1589-08	10215645	61434986	45914554	74	9686											
PAPLN	89932	hgsc.bcm.edu	37	chr14	73733497	73733497	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtgatacggccaggctatTgtgtgtggtagcaggagaaa	10	9	17	5	1	0	2	0	1	0	1	0	3	0	2	1	5	2	3	1	5	4	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr14:73733497T>C	ENST00000554301.1	+	24	3621	c.3458T>C	c.(3457-3459)tTg>tCg	p.L1153S	PAPLN_ENST00000427855.1_Missense_Mutation_p.L1153S|PAPLN_ENST00000555445.1_Missense_Mutation_p.L1137S|PAPLN_ENST00000381166.3_Intron|PAPLN_ENST00000340738.5_Missense_Mutation_p.L1126S			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	1153	Ig-like C2-type 3.					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)		GCCAGGCTATTGTGTGTGGTA	0.542																																					p.L1126S		Atlas-SNP	.											.	PAPLN	180	.	0			c.T3377C						PASS	.						211	153	173					14																	73733497		2203	4300	6503	SO:0001583	missense	89932	exon24			GGCTATTGTGTGT	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.3458T>C	chr14.hg19:g.73733497T>C	ENSP00000451803:p.Leu1153Ser	31.0	0.0	.		29.0	8.0	.	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Missense_Mutation	SNP	ENST00000554301.1	hg19		.	.	.	.	.	.	.	.	.	.	T	2.259	-0.369785	0.05069	.	.	ENSG00000100767	ENST00000340738;ENST00000427855;ENST00000554301;ENST00000555445	T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14	5.06	-8.09	0.01090	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.28400	0.0702	N	0.03608	-0.345	0.24632	N	0.993617	P;P;B;P	0.39920	0.646;0.695;0.2;0.622	B;B;B;B	0.43331	0.292;0.416;0.077;0.217	T	0.31392	-0.9945	9	0.08837	T	0.75	.	2.1116	0.03704	0.3364:0.3542:0.1653:0.1441	.	1137;1153;352;1126	O95428-5;O95428;O95428-2;O95428-6	.;PPN_HUMAN;.;.	S	1126;1153;1153;1137	ENSP00000345395:L1126S;ENSP00000403403:L1153S;ENSP00000451803:L1153S;ENSP00000451729:L1137S	ENSP00000345395:L1126S	L	+	2	0	PAPLN	72803250	0.000000	0.05858	0.051000	0.19133	0.088000	0.18126	0.124000	0.15728	-1.220000	0.02594	-0.389000	0.06534	TTG	.	.	.	none		0.542	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462		C	73733497	T	C	73733497	3	2	163	1	0	0	0	0	1	0	0	0	11435	1821	63	3	3467	3	PAPLN	14	73733497	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	12298511	73733497	33616043	75	9687											
SOLH	6650	hgsc.bcm.edu	37	chr16	599030	599030	+	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	ggatgacagcttccctcccgGgcccgagtctgtcggcttcc	4	9	12	16	3	1	1	0	1	1	0	5	3	4	2	4	3	1	2	4	3	0	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr16:599030G>A	ENST00000219611.2	+	5	1850	c.1487G>A	c.(1486-1488)gGg>gAg	p.G496E	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	496	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TTCCCTCCCGGGCCCGAGTCT	0.657																																					p.G496E		Atlas-SNP	.											.	SOLH	47	.	0			c.G1487A						PASS	.						105	94	98					16																	599030		2198	4296	6494	SO:0001583	missense	6650	exon5			CTCCCGGGCCCGA	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.1487G>A	chr16.hg19:g.599030G>A	ENSP00000219611:p.Gly496Glu	166.0	0.0	.		156.0	33.0	.	NM_005632	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Missense_Mutation	SNP	ENST00000219611.2	hg19	CCDS10410.1	.	.	.	.	.	.	.	.	.	.	g	17.87	3.495721	0.64186	.	.	ENSG00000103326	ENST00000219611	T	0.39056	1.1	5.04	5.04	0.67666	Peptidase C2, calpain, catalytic domain (3);	0.097082	0.64402	D	0.000001	T	0.46776	0.1410	N	0.12920	0.275	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.40496	-0.9560	10	0.21014	T	0.42	.	16.9735	0.86306	0.0:0.0:1.0:0.0	.	496	O75808	CAN15_HUMAN	E	496	ENSP00000219611:G496E	ENSP00000219611:G496E	G	+	2	0	SOLH	539031	1.000000	0.71417	0.994000	0.49952	0.379000	0.30106	7.684000	0.84104	2.347000	0.79759	0.556000	0.70494	GGG	.	.	.	none		0.657	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1	NM_005632		A	599030	G	A	599030	3	1	163	1	0	0	0	0	1	0	0	0	14938	1232	43	2	1493	2	SOLH	16	599030	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08		599030	89755723	76	9688											
TMEM186	25880	hgsc.bcm.edu	37	chr16	8890423	8890423	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cacagcttttccccgaaaccTacgcacagctcggagaaggg	11	6	10	14	3	0	1	0	0	0	1	2	3	1	1	3	2	4	3	3	2	3	3			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr16:8890423T>C	ENST00000333050.6	-	2	61	c.28A>G	c.(28-30)Agg>Ggg	p.R10G	PMM2_ENST00000268261.4_5'Flank|TMEM186_ENST00000564869.1_Intron|PMM2_ENST00000566983.1_Intron|PMM2_ENST00000539622.1_5'Flank|PMM2_ENST00000537352.1_5'Flank|PMM2_ENST00000569958.1_5'Flank	NM_015421.3	NP_056236.2	Q96B77	TM186_HUMAN	transmembrane protein 186	10						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	9						CCCCGAAACCTACGCACAGCT	0.547																																					p.R10G		Atlas-SNP	.											.	TMEM186	21	.	0			c.A28G						PASS	.						67	70	69					16																	8890423		2197	4300	6497	SO:0001583	missense	25880	exon2			GAAACCTACGCAC	BC015912	CCDS10535.1	16p13.2	2008-02-05	2007-02-08	2007-02-08	ENSG00000184857	ENSG00000184857			24530	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 51"	C16orf51		11230166	Standard	NM_015421		Approved	DKFZP564K2062	uc002cze.3	Q96B77	OTTHUMG00000129696	ENST00000333050.6:c.28A>G	chr16.hg19:g.8890423T>C	ENSP00000331640:p.Arg10Gly	67.0	0.0	.		94.0	24.0	.	NM_015421	B2RAY0|Q9Y4T4	Missense_Mutation	SNP	ENST00000333050.6	hg19	CCDS10535.1	.	.	.	.	.	.	.	.	.	.	T	12.60	1.985216	0.35036	.	.	ENSG00000184857	ENST00000333050	.	.	.	4.53	2.24	0.28232	.	0.345193	0.20611	N	0.088971	T	0.34193	0.0889	L	0.57536	1.79	0.09310	N	1	P	0.36535	0.557	B	0.33620	0.167	T	0.15983	-1.0418	9	0.36615	T	0.2	-12.3261	8.7598	0.34667	0.0:0.0:0.3002:0.6998	.	10	Q96B77	TM186_HUMAN	G	10	.	ENSP00000331640:R10G	R	-	1	2	TMEM186	8797924	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.134000	0.15932	1.030000	0.39839	0.533000	0.62120	AGG	.	.	.	none		0.547	TMEM186-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251903.1	NM_015421		C	8890423	T	C	8890423	3	2	163	1	0	0	0	0	1	0	0	0	16120	1521	53	3	617	3	TMEM186	16	8890423	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	8291393	8890423	81464330	77	9689											
SPNS1	83985	hgsc.bcm.edu	37	chr16	28989282	28989282	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtttggctacctgggtgacAggtacaatcggaagtatctc	9	12	12	8	1	1	1	0	1	1	0	3	2	1	2	1	4	2	4	1	4	5	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr16:28989282A>G	ENST00000311008.11	+	3	738	c.361A>G	c.(361-363)Agg>Ggg	p.R121G	SPNS1_ENST00000565975.1_Missense_Mutation_p.R166G|RP11-264B17.4_ENST00000567209.1_RNA|SPNS1_ENST00000561868.1_Intron|SPNS1_ENST00000334536.8_Missense_Mutation_p.R121G|SPNS1_ENST00000352260.7_Missense_Mutation_p.R99G|RP11-264B17.3_ENST00000569969.1_RNA|SPNS1_ENST00000323081.8_Missense_Mutation_p.R48G	NM_032038.2	NP_114427.1	Q9H2V7	SPNS1_HUMAN	spinster homolog 1 (Drosophila)	121					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						CCTGGGTGACAGGTACAATCG	0.577											OREG0023711	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R121G		Atlas-SNP	.											.	SPNS1	47	.	0			c.A361G						PASS	.						239	183	202					16																	28989282		2197	4300	6497	SO:0001583	missense	83985	exon3			GGTGACAGGTACA	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.361A>G	chr16.hg19:g.28989282A>G	ENSP00000309945:p.Arg121Gly	166.0	0.0	.	806	175.0	79.0	.	NM_001142451	B5MDM9|Q6P182|Q71RB5|Q7L541|Q86VU7|Q8N953|Q8TCS5|Q9BRN5	Missense_Mutation	SNP	ENST00000311008.11	hg19	CCDS10646.1	.	.	.	.	.	.	.	.	.	.	A	17.88	3.497831	0.64186	.	.	ENSG00000169682	ENST00000311008;ENST00000334536;ENST00000352260;ENST00000323081	T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17	4.68	3.54	0.40534	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.81202	0.4773	M	0.92880	3.355	0.58432	D	0.999996	D;D;D;D;D	0.89917	1.0;1.0;0.996;1.0;1.0	D;D;D;D;D	0.97110	0.998;0.999;0.998;0.999;1.0	T	0.82168	-0.0591	10	0.87932	D	0	.	8.7405	0.34554	0.6228:0.3772:0.0:0.0	.	48;99;121;121;121	Q9H2V7-4;Q9H2V7-3;Q9H2V7;Q9H2V7-2;Q9H2V7-5	.;.;SPNS1_HUMAN;.;.	G	121;121;99;48	ENSP00000309945:R121G;ENSP00000335494:R121G;ENSP00000306050:R99G;ENSP00000318228:R48G	ENSP00000309945:R121G	R	+	1	2	SPNS1	28896783	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.943000	0.56621	0.774000	0.33427	0.402000	0.26972	AGG	.	.	.	none		0.577	SPNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254690.2	NM_032038		G	28989282	A	G	28989282	3	3	163	1	0	0	0	0	1	0	0	0	15086	179	7	3	371	3	SPNS1	16	28989282	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08	20098859	28989282	61365471	78	9690											
PMFBP1	83449	hgsc.bcm.edu	37	chr16	72198700	72198700	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctcctccatgcagagctgaTtgtcctgcaaggtcttcctc	6	12	8	15	0	1	2	0	1	1	1	6	2	5	2	5	1	3	3	5	1	1	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr16:72198700T>C	ENST00000237353.10	-	3	389	c.128A>G	c.(127-129)aAt>aGt	p.N43S	PMFBP1_ENST00000355636.6_5'UTR|PMFBP1_ENST00000543746.1_5'UTR|PMFBP1_ENST00000537465.1_Missense_Mutation_p.N43S	NM_031293.2	NP_112583.2	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	43						cytoplasm (GO:0005737)				NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	45		Ovarian(137;0.179)				GCAGAGCTGATTGTCCTGCAA	0.542																																					p.N43S		Atlas-SNP	.											.	PMFBP1	101	.	0			c.A128G						PASS	.						133	111	119					16																	72198700		2198	4300	6498	SO:0001583	missense	83449	exon3			AGCTGATTGTCCT	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.128A>G	chr16.hg19:g.72198700T>C	ENSP00000237353:p.Asn43Ser	128.0	0.0	.		185.0	81.0	.	NM_031293	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Missense_Mutation	SNP	ENST00000237353.10	hg19	CCDS32483.1	.	.	.	.	.	.	.	.	.	.	T	9.847	1.192729	0.21954	.	.	ENSG00000118557	ENST00000537465;ENST00000237353;ENST00000535461;ENST00000539172;ENST00000536211;ENST00000540440	T;T	0.12774	2.65;2.65	5.85	2.17	0.27698	.	0.117279	0.38959	N	0.001506	T	0.05868	0.0153	N	0.19112	0.55	0.80722	D	1	B;B	0.16396	0.017;0.017	B;B	0.12156	0.007;0.007	T	0.30504	-0.9976	10	0.09590	T	0.72	-14.5061	2.3595	0.04304	0.1534:0.0827:0.1601:0.6038	.	43;43	Q8TBY8-2;G3V1Q7	.;.	S	43	ENSP00000443817:N43S;ENSP00000237353:N43S	ENSP00000237353:N43S	N	-	2	0	PMFBP1	70756201	0.858000	0.29795	0.998000	0.56505	0.204000	0.24138	0.499000	0.22546	0.464000	0.27142	-0.290000	0.09829	AAT	.	.	.	none		0.542	PMFBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396473.2	NM_031293		C	72198700	T	C	72198700	3	2	163	1	0	0	0	0	1	0	0	0	12141	1493	52	3	3031	3	PMFBP1	16	72198700	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	43209418	72198700	18156053	79	9691											
C16orf7	9605	hgsc.bcm.edu	37	chr16	89776218	89776219	+	Frame_Shift_Del	DEL	GA	GA	-																															gcagcagaggccacagcgggGagaaaaagggttcctcaatg																								rs565573769		TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	GA	GA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr16:89776218_89776219delGA	ENST00000389386.3	-	11	1478_1479	c.1354_1355delTC	c.(1354-1356)tccfs	p.S452fs	VPS9D1-AS1_ENST00000562866.1_RNA|VPS9D1_ENST00000561976.1_Frame_Shift_Del_p.S382fs|VPS9D1_ENST00000565452.1_5'Flank	NM_004913.2	NP_004904.2	Q9Y2B5	VP9D1_HUMAN	VPS9 domain containing 1	452					ATP synthesis coupled proton transport (GO:0015986)		GTPase activator activity (GO:0005096)|transporter activity (GO:0005215)										CCACAGCGGGGAGAAAAAGGGT	0.619																																					p.452_452del		Atlas-INDEL	.											.	.	.	.	0			c.1355_1356del						PASS	.																																			SO:0001589	frameshift_variant	9605	exon11			.	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.1354_1355delTC	chr16.hg19:g.89776220_89776221delGA	ENSP00000374037:p.Ser452fs	171.0	0.0	0		183.0	31.0	0.169399	NM_004913		Frame_Shift_Del	DEL	ENST00000389386.3	hg19	CCDS42220.1																																																																																			.	.	.	none		0.619	VPS9D1-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422508.1	NM_004913		-	89776219	GA	-	89776218	7	5	163	1	0	1	0	1	0	0	0	0	1830	1174	41	0	560	0	C16orf7	16	89776218	Frame_Shift_Del	DEL	GA	TCGA-EV-5903-01A-11D-1589-08	17577518	89776218	578535	80	9692											
AIPL1	23746	hgsc.bcm.edu	37	chr17	6328845	6328845	+	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	tggctctgcagggggccctgCggacagctctgcagatggtg	5	8	17	11	1	2	1	0	0	2	1	2	2	2	2	1	5	4	4	1	5	0	0	rs201875142		TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr17:6328845C>T	ENST00000381129.3	-	6	1170	c.1090G>A	c.(1090-1092)Gca>Aca	p.A364T	AIPL1_ENST00000574506.1_Missense_Mutation_p.A352T|AIPL1_ENST00000575265.1_3'UTR|AIPL1_ENST00000250087.5_Missense_Mutation_p.A301T|AIPL1_ENST00000576776.1_Missense_Mutation_p.A340T|AIPL1_ENST00000576307.1_Missense_Mutation_p.A304T|AIPL1_ENST00000570466.1_Missense_Mutation_p.A342T	NM_001033055.1|NM_014336.3	NP_001028227.1|NP_055151.3	Q9NZN9	AIPL1_HUMAN	aryl hydrocarbon receptor interacting protein-like 1	364					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)		gggggccctgcggacagctct	0.701																																					p.A364T		Atlas-SNP	.											.	AIPL1	34	.	0			c.G1090A						PASS	.						47	47	47					17																	6328845		2202	4297	6499	SO:0001583	missense	23746	exon6			GCCCTGCGGACAG	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.1090G>A	chr17.hg19:g.6328845C>T	ENSP00000370521:p.Ala364Thr	115.0	0.0	.		150.0	65.0	.	NM_014336	D3DTM4|Q659W3|Q659W4|Q6ZZB6|Q8N6A0|Q9H873|Q9NS10	Missense_Mutation	SNP	ENST00000381129.3	hg19	CCDS11075.1	.	.	.	.	.	.	.	.	.	.	C	0.009	-1.800010	0.00611	.	.	ENSG00000129221	ENST00000381129;ENST00000381128;ENST00000250087	D;D	0.88354	-2.37;-2.28	2.43	-4.86	0.03132	.	14.175600	0.00357	N	0.000030	T	0.68357	0.2992	N	0.02539	-0.55	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	0.62282	-0.6887	10	0.15066	T	0.55	.	0.3578	0.00359	0.2708:0.2404:0.1332:0.3556	.	340;342;301;304;364	Q659W3;Q659W4;Q9NZN9-3;Q9NZN9-2;Q9NZN9	.;.;.;.;AIPL1_HUMAN	T	364;304;301	ENSP00000370521:A364T;ENSP00000250087:A301T	ENSP00000250087:A301T	A	-	1	0	AIPL1	6269569	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.245000	0.01192	-4.315000	0.00057	-3.419000	0.00038	GCA	.	.	.	alt		0.701	AIPL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219828.3	NM_014336		T	6328845	C	T	6328845	3	4	163	1	0	0	0	0	1	0	0	0	436	768	27	1	68	1	AIPL1	17	6328845	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08		6328845	74866365	81	9693			1	21		2	2	24	N	G_C	7.132283e-05
AIPL1	23746	hgsc.bcm.edu	37	chr17	6328868	6328868	+	Missense_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	acagctctgcagatggtgctGtgggtggctctgcaggtggc	5	10	17	9	0	2	1	0	0	2	1	2	1	2	1	0	5	4	5	0	5	0	0			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr17:6328868G>A	ENST00000381129.3	-	6	1147	c.1067C>T	c.(1066-1068)aCa>aTa	p.T356I	AIPL1_ENST00000574506.1_Missense_Mutation_p.T344I|AIPL1_ENST00000575265.1_3'UTR|AIPL1_ENST00000250087.5_Missense_Mutation_p.T293I|AIPL1_ENST00000576776.1_Missense_Mutation_p.T332I|AIPL1_ENST00000576307.1_Missense_Mutation_p.T296I|AIPL1_ENST00000570466.1_Missense_Mutation_p.T334I	NM_001033055.1|NM_014336.3	NP_001028227.1|NP_055151.3	Q9NZN9	AIPL1_HUMAN	aryl hydrocarbon receptor interacting protein-like 1	356					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)		agatggtgctgtgggtggctc	0.692																																					p.T356I		Atlas-SNP	.											.	AIPL1	34	.	0			c.C1067T						PASS	.						72	65	68					17																	6328868		2203	4298	6501	SO:0001583	missense	23746	exon6			GGTGCTGTGGGTG	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.1067C>T	chr17.hg19:g.6328868G>A	ENSP00000370521:p.Thr356Ile	144.0	0.0	.		171.0	79.0	.	NM_014336	D3DTM4|Q659W3|Q659W4|Q6ZZB6|Q8N6A0|Q9H873|Q9NS10	Missense_Mutation	SNP	ENST00000381129.3	hg19	CCDS11075.1	.	.	.	.	.	.	.	.	.	.	G	9.219	1.032866	0.19590	.	.	ENSG00000129221	ENST00000381129;ENST00000381128;ENST00000250087	D;D	0.88818	-2.43;-2.33	2.56	2.56	0.30785	.	13.968300	0.01841	U	0.035287	T	0.81744	0.4887	N	0.19112	0.55	0.09310	N	0.999999	B;B;B;B;B	0.26775	0.099;0.099;0.159;0.159;0.099	B;B;B;B;B	0.15870	0.005;0.005;0.014;0.011;0.005	T	0.69624	-0.5095	10	0.37606	T	0.19	.	8.5789	0.33617	0.0:0.0:1.0:0.0	.	332;334;293;296;356	Q659W3;Q659W4;Q9NZN9-3;Q9NZN9-2;Q9NZN9	.;.;.;.;AIPL1_HUMAN	I	356;296;293	ENSP00000370521:T356I;ENSP00000250087:T293I	ENSP00000250087:T293I	T	-	2	0	AIPL1	6269592	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-1.481000	0.02323	1.405000	0.46838	0.407000	0.27541	ACA	.	.	.	none		0.692	AIPL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219828.3	NM_014336		A	6328868	G	A	6328868	3	1	163	1	0	0	0	0	1	0	0	0	436	1377	48	2	91	2	AIPL1	17	6328868	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	23	6328868	74866342	82	9694			1	21		2	2	24	N	G_C	7.132283e-05
SKAP1	8631	hgsc.bcm.edu	37	chr17	46266785	46266785	+	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	tctgtgggtctgaccaatacCtttgcttttcttctccaagt	6	17	7	11	0	4	1	0	1	4	0	5	1	4	1	3	1	2	1	3	1	3	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr17:46266785C>T	ENST00000336915.6	-	5	427	c.358G>A	c.(358-360)Gat>Aat	p.D120N	SKAP1_ENST00000584924.1_Splice_Site_p.D120N|RP11-456D7.1_ENST00000582246.1_RNA	NM_001075099.1|NM_003726.3	NP_001068567.1|NP_003717.3	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1	120	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of signal transduction (GO:0009967)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|SH2 domain binding (GO:0042169)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)			large_intestine(1)|lung(10)|prostate(2)|skin(4)|urinary_tract(1)	18						TGACCAATACCTTTGCTTTTC	0.433																																					p.D120N		Atlas-SNP	.											.	SKAP1	41	.	0			c.G358A						PASS	.						183	146	158					17																	46266785		2203	4300	6503	SO:0001630	splice_region_variant	8631	exon5			CAATACCTTTGCT	Y11215	CCDS32674.1	17q21.32	2013-01-10	2006-09-28	2006-09-28		ENSG00000141293		"Pleckstrin homology (PH) domain containing"	15605	protein-coding gene	gene with protein product		604969	"src family associated phosphoprotein 1"	SCAP1		9195899	Standard	NM_003726		Approved	SKAP55	uc002ini.1	Q86WV1		ENST00000336915.6:c.358+1G>A	chr17.hg19:g.46266785C>T		108.0	0.0	.		118.0	24.0	.	NM_003726	D3DTV1|O15268	Missense_Mutation	SNP	ENST00000336915.6	hg19	CCDS32674.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.998944	0.54147	.	.	ENSG00000141293	ENST00000336915	T	0.11821	2.74	5.61	5.61	0.85477	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.35770	0.0943	L	0.60904	1.88	0.58432	D	0.999998	P;D	0.76494	0.536;0.999	P;D	0.79784	0.614;0.993	T	0.00783	-1.1568	9	.	.	.	-29.0873	19.225	0.93815	0.0:1.0:0.0:0.0	.	120;120	Q86WV1-2;Q86WV1	.;SKAP1_HUMAN	N	120	ENSP00000338171:D120N	.	D	-	1	0	SKAP1	43621784	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	6.108000	0.71522	2.640000	0.89533	0.563000	0.77884	GAT	.	.	.	none		0.433	SKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443432.1	NM_003726	Missense_Mutation	T	46266785	C	T	46266785	5	4	163	1	0	0	0	0	0	0	1	0	14368	695	24	2	753	2	SKAP1	17	46266785	Splice_Site	SNP	C	TCGA-EV-5903-01A-11D-1589-08	39937917	46266785	34928425	83	9695											
TMX3	54495	hgsc.bcm.edu	37	chr18	66378637	66378637	+	Missense_Mutation	SNP	A	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	tcatcatttcgattttctttAaacctaaaaaacaagaaaac	18	13	2	8	1	3	1	2	0	1	1	4	2	3	1	1	0	3	0	1	0	8	6			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr18:66378637A>C	ENST00000299608.2	-	3	421	c.105T>G	c.(103-105)ttT>ttG	p.F35L	TMX3_ENST00000443099.2_Missense_Mutation_p.F35L|TMX3_ENST00000562706.1_Missense_Mutation_p.F35L	NM_019022.3	NP_061895.3	Q96JJ7	TMX3_HUMAN	thioredoxin-related transmembrane protein 3	35	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	17						GATTTTCTTTAAACCTAAAAA	0.279																																					p.F35L		Atlas-SNP	.											.	TMX3	44	.	0			c.T105G						PASS	.						84	90	88					18																	66378637		2202	4289	6491	SO:0001583	missense	54495	exon3			TTCTTTAAACCTA	BX647846	CCDS32840.1	18q22	2011-10-19	2009-02-23	2009-02-23		ENSG00000166479		"Protein disulfide isomerases"	24718	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 13"		"thioredoxin domain containing 10"	TXNDC10		15623505	Standard	NM_019022		Approved	FLJ20793, KIAA1830, PDIA13	uc002lkf.3	Q96JJ7		ENST00000299608.2:c.105T>G	chr18.hg19:g.66378637A>C	ENSP00000299608:p.Phe35Leu	124.0	0.0	.		92.0	37.0	.	NM_019022	B3KV75|Q52LT7|Q8N5J0|Q9NWJ9	Missense_Mutation	SNP	ENST00000299608.2	hg19	CCDS32840.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.615363	0.87359	.	.	ENSG00000166479	ENST00000299608;ENST00000544714;ENST00000443099	T;T;T	0.06608	3.28;3.28;3.28	5.36	5.36	0.76844	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.000000	0.85682	D	0.000000	T	0.26955	0.0660	M	0.83384	2.64	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.91635	0.998;0.986;0.999	T	0.01596	-1.1316	10	0.52906	T	0.07	.	13.3017	0.60328	1.0:0.0:0.0:0.0	.	35;35;35	B4DIE3;Q96JJ7-2;Q96JJ7	.;.;TMX3_HUMAN	L	35	ENSP00000299608:F35L;ENSP00000444954:F35L;ENSP00000402605:F35L	ENSP00000299608:F35L	F	-	3	2	TMX3	64529617	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	4.620000	0.61226	2.042000	0.60477	0.528000	0.53228	TTT	.	.	.	none		0.279	TMX3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420155.1	NM_019022		C	66378637	A	C	66378637	3	2	163	1	0	0	0	0	1	0	0	0	16280	359	13	5	1315	5	TMX3	18	66378637	Missense_Mutation	SNP	A	TCGA-EV-5903-01A-11D-1589-08		66378637	11698611	84	9696											
ATP8B3	148229	hgsc.bcm.edu	37	chr19	1785678	1785678	+	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	cccaccacgtacagctccggCttctccaggctctgctctgc	5	9	8	19	2	3	0	0	0	3	0	5	0	4	0	4	2	4	5	4	2	1	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr19:1785678C>A	ENST00000310127.6	-	26	3421	c.3183G>T	c.(3181-3183)aaG>aaT	p.K1061N	ATP8B3_ENST00000539485.1_Missense_Mutation_p.K1071N|ATP8B3_ENST00000525591.1_Missense_Mutation_p.K1024N	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	1061					binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACAGCTCCGGCTTCTCCAGGC	0.602																																					p.K1061N		Atlas-SNP	.											.	ATP8B3	108	.	0			c.G3183T						PASS	.						26	29	28					19																	1785678		2120	4237	6357	SO:0001583	missense	148229	exon26			CTCCGGCTTCTCC	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.3183G>T	chr19.hg19:g.1785678C>A	ENSP00000311336:p.Lys1061Asn	25.0	0.0	.		28.0	7.0	.	NM_138813	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Missense_Mutation	SNP	ENST00000310127.6	hg19	CCDS45901.1	.	.	.	.	.	.	.	.	.	.	C	8.917	0.960236	0.18507	.	.	ENSG00000130270	ENST00000310127;ENST00000539485;ENST00000525591	T;T;T	0.70516	-0.49;-0.49;-0.49	4.48	3.39	0.38822	.	0.558416	0.19418	N	0.114773	T	0.40815	0.1132	N	0.02697	-0.525	0.23855	N	0.996656	B;B	0.30664	0.289;0.086	B;B	0.23275	0.045;0.045	T	0.33420	-0.9869	10	0.66056	D	0.02	.	6.6084	0.22737	0.149:0.5306:0.3204:0.0	.	1061;1024	O60423;Q7Z485	AT8B3_HUMAN;.	N	1061;1071;1024	ENSP00000311336:K1061N;ENSP00000443574:K1071N;ENSP00000437115:K1024N	ENSP00000311336:K1061N	K	-	3	2	ATP8B3	1736678	0.965000	0.33210	0.457000	0.27056	0.051000	0.14879	1.815000	0.38981	2.027000	0.59764	0.655000	0.94253	AAG	.	.	.	none		0.602	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813		A	1785678	C	A	1785678	3	1	163	1	0	0	0	0	1	0	0	0	1196	796	28	4	735	4	ATP8B3	19	1785678	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08		1785678	57343305	85	9697											
SFRS14	10147	hgsc.bcm.edu	37	chr19	19115397	19115397	+	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	gaaacaaattgatggacataGttcaaacactttctttcgat	15	13	6	7	1	2	1	1	1	1	0	3	4	2	2	0	1	2	1	0	1	4	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr19:19115397G>T	ENST00000601879.1	-	7	2806	c.2509C>A	c.(2509-2511)Cta>Ata	p.L837I	SUGP2_ENST00000456085.2_Missense_Mutation_p.L606I|SUGP2_ENST00000337018.6_Missense_Mutation_p.L837I|SUGP2_ENST00000600377.1_Missense_Mutation_p.L851I|SUGP2_ENST00000452918.2_Missense_Mutation_p.L837I			Q8IX01	SUGP2_HUMAN	SURP and G patch domain containing 2	837					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						GATGGACATAGTTCAAACACT	0.463																																					p.L837I		Atlas-SNP	.											.	SUGP2	107	.	0			c.C2509A						PASS	.						74	73	73					19																	19115397		2203	4300	6503	SO:0001583	missense	10147	exon7			GACATAGTTCAAA	AB002363	CCDS12392.1	19p13	2013-01-28	2010-08-10	2010-08-10	ENSG00000064607	ENSG00000064607		"G patch domain containing"	18641	protein-coding gene	gene with protein product		607993	"splicing factor, arginine/serine-rich 14"	SFRS14		12594045	Standard	NM_014884		Approved	KIAA0365	uc002nkx.2	Q8IX01		ENST00000601879.1:c.2509C>A	chr19.hg19:g.19115397G>T	ENSP00000472286:p.Leu837Ile	147.0	0.0	.		153.0	41.0	.	NM_014884	C9JI71|O15071|O60369|Q5JPH7|Q8WUF7	Missense_Mutation	SNP	ENST00000601879.1	hg19	CCDS12392.1	.	.	.	.	.	.	.	.	.	.	G	18.29	3.590575	0.66219	.	.	ENSG00000064607	ENST00000337018;ENST00000330854;ENST00000452918;ENST00000456085	T;T;T;T	0.39592	1.07;1.07;1.07;1.07	5.26	5.26	0.73747	SWAP/Surp (1);	0.000000	0.42294	D	0.000725	T	0.46151	0.1378	N	0.16307	0.4	0.39998	D	0.975121	D;D;D	0.76494	0.999;0.976;0.999	D;D;D	0.87578	0.998;0.914;0.997	T	0.45366	-0.9266	10	0.41790	T	0.15	-13.6122	11.5508	0.50719	0.086:0.0:0.914:0.0	.	606;837;837	E7ETX7;A8K5G0;Q8IX01	.;.;SUGP2_HUMAN	I	837;837;837;606	ENSP00000337926:L837I;ENSP00000332373:L837I;ENSP00000389380:L837I;ENSP00000409603:L606I	ENSP00000332373:L837I	L	-	1	2	SUGP2	18976397	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	1.688000	0.37690	2.459000	0.83118	0.563000	0.77884	CTA	.	.	.	none		0.463	SUGP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464627.1	NM_001017392		T	19115397	G	T	19115397	3	4	163	1	0	0	0	0	1	0	0	0	14183	1020	36	4	755	4	SFRS14	19	19115397	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	17329719	19115397	40013586	86	9698											
RINL	126432	hgsc.bcm.edu	37	chr19	39359912	39359925	+	Frame_Shift_Del	DEL	TGCAGCGTCCGCCT	TGCAGCGTCCGCCT	-																															ctctgggatgatcctttctgTgcagcgtccgcctgcggtgc																										TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	TGCAGCGTCCGCCT	TGCAGCGTCCGCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr19:39359912_39359925delTGCAGCGTCCGCCT	ENST00000591812.1	-	11	1686_1699	c.1600_1613delAGGCGGACGCTGCA	c.(1600-1614)aggcggacgctgcacfs	p.RRTLH534fs	CTC-360G5.6_ENST00000593830.1_RNA|RINL_ENST00000598904.1_Frame_Shift_Del_p.RRTLH420fs|RINL_ENST00000340740.3_Frame_Shift_Del_p.RRTLH420fs|RINL_ENST00000602238.1_5'Flank			Q6ZS11	RINL_HUMAN	Ras and Rab interactor-like	534					endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)	actin cytoskeleton (GO:0015629)|cytoplasmic vesicle (GO:0031410)|ruffle (GO:0001726)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(3)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)|urinary_tract(2)	17						ATCCTTTCTGTGCAGCGTCCGCCTGCGGTGCCAC	0.673																																					p.534_538del		Atlas-INDEL	.											.	RINL	32	.	0			c.1601_1614del						PASS	.																																			SO:0001589	frameshift_variant	126432	exon11			.	AK127808	CCDS12522.1, CCDS59386.1	19q13.2	2010-07-13			ENSG00000187994	ENSG00000187994			24795	protein-coding gene	gene with protein product							Standard	NM_001195833		Approved	FLJ45909	uc010xuo.2	Q6ZS11		ENST00000591812.1:c.1600_1613delAGGCGGACGCTGCA	chr19.hg19:g.39359912_39359925delTGCAGCGTCCGCCT	ENSP00000467107:p.Arg534fs	117.0	0.0	0		101.0	19.0	0.188119	NM_001195833	B4DPG5	Frame_Shift_Del	DEL	ENST00000591812.1	hg19	CCDS59386.1																																																																																			.	.	.	none		0.673	RINL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460433.1	NM_198445		-	39359925	TGCAGCGTCCGCCT	-	39359912	7	5	163	1	0	1	0	1	0	0	0	0	13388	1696	59	0	95	0	RINL	19	39359912	Frame_Shift_Del	DEL	TGCAGCGTCCGCCT	TCGA-EV-5903-01A-11D-1589-08	20244515	39359912	19769071	87	9699											
ALDH16A1	126133	hgsc.bcm.edu	37	chr19	49969107	49969107	+	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	tccatggctacgtggctgagGgtggagccaaggacatccga	9	7	15	10	2	0	1	0	1	0	0	2	4	2	3	3	5	2	2	3	5	2	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr19:49969107G>A	ENST00000293350.4	+	13	1844	c.1681G>A	c.(1681-1683)Ggt>Agt	p.G561S	ALDH16A1_ENST00000540132.1_Missense_Mutation_p.G398S|ALDH16A1_ENST00000455361.2_Missense_Mutation_p.G510S|CTD-3148I10.9_ENST00000599536.1_Intron|ALDH16A1_ENST00000433981.2_Missense_Mutation_p.G396S	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	561						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)		CGTGGCTGAGGGTGGAGCCAA	0.642																																					p.G561S		Atlas-SNP	.											.	ALDH16A1	54	.	0			c.G1681A						PASS	.						39	40	40					19																	49969107		2203	4300	6503	SO:0001583	missense	126133	exon13			GCTGAGGGTGGAG	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.1681G>A	chr19.hg19:g.49969107G>A	ENSP00000293350:p.Gly561Ser	69.0	0.0	.		55.0	13.0	.	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Missense_Mutation	SNP	ENST00000293350.4	hg19	CCDS12766.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.007403	0.75046	.	.	ENSG00000161618	ENST00000293350;ENST00000455361;ENST00000540132;ENST00000433981	T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98	4.77	4.77	0.60923	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.220696	0.37623	N	0.002003	D	0.83751	0.5322	M	0.64567	1.98	0.44254	D	0.997108	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.84182	0.0440	10	0.46703	T	0.11	-20.3157	15.3078	0.74008	0.0:0.0:1.0:0.0	.	398;510;561	F5H4B6;B4DLQ1;Q8IZ83	.;.;A16A1_HUMAN	S	561;510;398;396	ENSP00000293350:G561S;ENSP00000410142:G510S;ENSP00000445088:G398S;ENSP00000398675:G396S	ENSP00000293350:G561S	G	+	1	0	ALDH16A1	54660919	0.985000	0.35326	0.999000	0.59377	0.666000	0.39218	1.078000	0.30754	2.206000	0.71126	0.561000	0.74099	GGT	.	.	.	none		0.642	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329		A	49969107	G	A	49969107	3	1	163	1	0	0	0	0	1	0	0	0	488	1232	43	2	1731	2	ALDH16A1	19	49969107	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	10609195	49969107	9159876	88	9700											
ZNF836	162962	hgsc.bcm.edu	37	chr19	52659397	52659397	+	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	tgaattatcttatgtcgagtGagtaatgagccctgtttaaa	12	15	9	5	1	1	3	0	3	1	0	2	4	1	3	1	0	1	2	1	0	6	5			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr19:52659397G>A	ENST00000322146.8	-	5	2060	c.1539C>T	c.(1537-1539)ctC>ctT	p.L513L	CTC-471J1.8_ENST00000594362.1_RNA|ZNF836_ENST00000597252.1_Silent_p.L513L	NM_001102657.1	NP_001096127.1	Q6ZNA1	ZN836_HUMAN	zinc finger protein 836	513					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|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						TATGTCGAGTGAGTAATGAGC	0.388																																					p.L513L		Atlas-SNP	.											.	ZNF836	158	.	0			c.C1539T						PASS	.						75	84	81					19																	52659397		2186	4294	6480	SO:0001819	synonymous_variant	162962	exon5			TCGAGTGAGTAAT	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.1539C>T	chr19.hg19:g.52659397G>A		131.0	0.0	.		109.0	29.0	.	NM_001102657		Silent	SNP	ENST00000322146.8	hg19	CCDS46162.1																																																																																			.	.	.	none		0.388	ZNF836-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462456.1	NM_001102657		A	52659397	G	A	52659397	2	1	163	1	0	0	0	0	0	0	0	1	18199	1277	45	2		2	ZNF836	19	52659397	Silent	SNP	G	TCGA-EV-5903-01A-11D-1589-08	2690290	52659397	6469586	89	9701											
NLRP11	204801	hgsc.bcm.edu	37	chr19	56329449	56329449	+	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	tgaaatcaagaatcttgcgtGccagatacttcttaaaactc	14	12	6	9	1	3	3	1	1	2	2	4	3	3	3	1	0	4	0	1	0	6	4			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr19:56329449G>T	ENST00000589093.1	-	2	185	c.92C>A	c.(91-93)gCa>gAa	p.A31E	NLRP11_ENST00000592953.1_Intron|NLRP11_ENST00000589824.2_Missense_Mutation_p.A31E|NLRP11_ENST00000360133.3_Missense_Mutation_p.A31E|NLRP11_ENST00000443188.1_Missense_Mutation_p.A31E			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	31	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.						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)		AATCTTGCGTGCCAGATACTT	0.413																																					p.A31E		Atlas-SNP	.											.	NLRP11	139	.	0			c.C92A						PASS	.						135	126	129					19																	56329449		2203	4300	6503	SO:0001583	missense	204801	exon4			TTGCGTGCCAGAT	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.92C>A	chr19.hg19:g.56329449G>T	ENSP00000466285:p.Ala31Glu	129.0	0.0	.		113.0	28.0	.	NM_145007	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Missense_Mutation	SNP	ENST00000589093.1	hg19	CCDS12935.1	.	.	.	.	.	.	.	.	.	.	G	0.719	-0.784370	0.02907	.	.	ENSG00000179873	ENST00000443188;ENST00000360133	T;T	0.48522	0.81;0.81	2.56	-5.13	0.02884	Pyrin (2);DEATH-like (2);	.	.	.	.	T	0.23846	0.0577	N	0.22421	0.69	0.09310	N	1	B	0.18461	0.028	B	0.26094	0.066	T	0.26360	-1.0105	9	0.18710	T	0.47	.	0.3757	0.00387	0.2979:0.2202:0.2836:0.1983	.	31	P59045	NAL11_HUMAN	E	31	ENSP00000409898:A31E;ENSP00000353251:A31E	ENSP00000353251:A31E	A	-	2	0	NLRP11	61021261	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.568000	0.02144	-1.980000	0.00990	-2.070000	0.00385	GCA	.	.	.	none		0.413	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007		T	56329449	G	T	56329449	3	4	163	1	0	0	0	0	1	0	0	0	10480	1319	46	4	3045	4	NLRP11	19	56329449	Missense_Mutation	SNP	G	TCGA-EV-5903-01A-11D-1589-08	3670052	56329449	2799534	90	9702											
BPIL1	80341	hgsc.bcm.edu	37	chr20	31601760	31601760	+	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	aacgagtttgatggcagtaaCaggtgggtgcctggtgaggg	9	9	18	5	1	0	2	0	2	0	0	0	3	0	2	1	5	3	3	1	5	2	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr20:31601760C>G	ENST00000170150.3	+	5	648	c.453C>G	c.(451-453)aaC>aaG	p.N151K		NM_025227.1	NP_079503.1	Q8N4F0	BPIB2_HUMAN	BPI fold containing family B, member 2	151						extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										ATGGCAGTAACAGGTGGGTGC	0.582																																					p.N151K		Atlas-SNP	.											.	.	.	.	0			c.C453G						PASS	.						47	41	43					20																	31601760		2203	4300	6503	SO:0001583	missense	80341	exon5			CAGTAACAGGTGG	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.453C>G	chr20.hg19:g.31601760C>G	ENSP00000170150:p.Asn151Lys	49.0	0.0	.		46.0	16.0	.	NM_025227	Q6UWN3|Q6ZME0|Q8NFQ7	Missense_Mutation	SNP	ENST00000170150.3	hg19	CCDS13210.1	.	.	.	.	.	.	.	.	.	.	C	0.777	-0.763664	0.02996	.	.	ENSG00000078898	ENST00000170150	T	0.05025	3.51	3.37	1.32	0.21799	.	1.051320	0.07484	N	0.904509	T	0.04363	0.0120	L	0.27053	0.805	0.21802	N	0.999535	B	0.09022	0.002	B	0.08055	0.003	T	0.43829	-0.9367	10	0.05833	T	0.94	0.1991	7.9791	0.30172	0.4451:0.5549:0.0:0.0	.	151	Q8N4F0	BPIB2_HUMAN	K	151	ENSP00000170150:N151K	ENSP00000170150:N151K	N	+	3	2	BPIFB2	31065421	0.257000	0.24022	0.587000	0.28692	0.145000	0.21501	0.314000	0.19432	0.396000	0.25283	0.491000	0.48974	AAC	.	.	.	none		0.582	BPIFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078652.2	NM_025227		G	31601760	C	G	31601760	3	3	163	1	0	0	0	0	1	0	0	0	1493	477	17	4	467	4	BPIL1	20	31601760	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08		31601760	31423760	91	9703											
C20orf114	92747	hgsc.bcm.edu	37	chr20	31876601	31876601	+	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	cagcatcctgcagcagctgcCgctgctcagtgccatgcggg	6	7	13	15	2	1	0	1	0	0	0	2	0	2	0	3	1	8	6	3	1	0	0	rs201956427		TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr20:31876601C>A	ENST00000253354.1	+	3	331	c.170C>A	c.(169-171)cCg>cAg	p.P57Q		NM_033197.2	NP_149974.2	Q8TDL5	BPIB1_HUMAN	BPI fold containing family B, member 1	57					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)										CAGCAGCTGCCGCTGCTCAGT	0.627																																					p.P57Q		Atlas-SNP	.											.	.	.	.	0			c.C170A						PASS	.						53	47	49					20																	31876601		2202	4300	6502	SO:0001583	missense	92747	exon3			AGCTGCCGCTGCT	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.170C>A	chr20.hg19:g.31876601C>A	ENSP00000253354:p.Pro57Gln	59.0	0.0	.		91.0	4.0	.	NM_033197	A8K2H8|Q5QP43|Q6UWY1|Q6ZRU7|Q96HK6|Q9BQP8|Q9BWZ6|Q9H4V6	Missense_Mutation	SNP	ENST00000253354.1	hg19	CCDS13218.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.489741	0.64074	.	.	ENSG00000125999	ENST00000423645;ENST00000253354	T;T	0.04758	3.56;3.56	5.45	5.45	0.79879	.	0.000000	0.64402	D	0.000004	T	0.23014	0.0556	M	0.80847	2.515	0.40669	D	0.98219	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.00062	-1.2156	10	0.54805	T	0.06	-37.7205	15.5106	0.75779	0.0:1.0:0.0:0.0	.	57;57	B2R7Z6;Q8TDL5	.;BPIB1_HUMAN	Q	57	ENSP00000390471:P57Q;ENSP00000253354:P57Q	ENSP00000253354:P57Q	P	+	2	0	BPIFB1	31340262	0.985000	0.35326	0.976000	0.42696	0.432000	0.31715	3.446000	0.52928	2.941000	0.99782	0.655000	0.94253	CCG	.	C|0.999;T|0.001	.	alt		0.627	BPIFB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106499.2	NM_033197		A	31876601	C	A	31876601	3	1	163	1	0	0	0	0	1	0	0	0	2084	652	23	4	176	4	C20orf114	20	31876601	Missense_Mutation	SNP	C	TCGA-EV-5903-01A-11D-1589-08	274841	31876601	31148919	92	9704											
ZNF341	84905	hgsc.bcm.edu	37	chr20	32376706	32376706	+	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	tgctcagtgtgcgagtctgcGttcaaccgcaaggacaaact	10	9	11	11	3	3	0	2	0	1	0	3	2	3	1	1	1	5	3	1	1	3	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr20:32376706G>T	ENST00000375200.1	+	13	2255	c.1890G>T	c.(1888-1890)gcG>gcT	p.A630A	RP4-553F4.6_ENST00000443171.1_RNA|RP4-553F4.6_ENST00000423074.1_RNA|ZNF341_ENST00000342427.2_Silent_p.A623A|RP4-553F4.6_ENST00000439444.1_RNA	NM_001282933.1	NP_001269862.1	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	630					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.A623A(1)		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						GCGAGTCTGCGTTCAACCGCA	0.547																																					p.A623A		Atlas-SNP	.											ZNF341,NS,carcinoma,0,1	ZNF341	73	.	1	Substitution - coding silent(1)	endometrium(1)	c.G1869T						PASS	.						122	99	107					20																	32376706		2203	4300	6503	SO:0001819	synonymous_variant	84905	exon13			GTCTGCGTTCAAC	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.1890G>T	chr20.hg19:g.32376706G>T		67.0	0.0	.		57.0	19.0	.	NM_032819	A2RUF4|B2RXE5|B7ZM09|Q5JXM8|Q96ST5	Silent	SNP	ENST00000375200.1	hg19																																																																																				.	.	.	none		0.547	ZNF341-201	KNOWN	basic	protein_coding	protein_coding				T	32376706	G	T	32376706	2	4	163	1	0	0	0	0	0	0	0	1	17869	1132	40	4		4	ZNF341	20	32376706	Silent	SNP	G	TCGA-EV-5903-01A-11D-1589-08	500105	32376706	30648814	93	9705											
C21orf45	54069	hgsc.bcm.edu	37	chr21	33651272	33651272	+	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	catttgcccttgtcgccgcaCtcacagccgccagcgcatcc	6	8	8	19	4	1	0	1	0	0	0	3	0	2	0	5	0	3	2	5	0	0	2			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr21:33651272C>T	ENST00000290130.3	-	1	108	c.54G>A	c.(52-54)gaG>gaA	p.E18E	MIS18A-AS1_ENST00000453549.1_RNA	NM_018944.2	NP_061817.1	Q9NYP9	MS18A_HUMAN	MIS18 kinetochore protein A	18					CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)|regulation of DNA methylation (GO:0044030)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)	7						TGTCGCCGCACTCACAGCCGC	0.607																																					p.E18E		Atlas-SNP	.											.	MIS18A	11	.	0			c.G54A						PASS	.						36	39	38					21																	33651272		2202	4296	6498	SO:0001819	synonymous_variant	54069	exon1			GCCGCACTCACAG	AF231921	CCDS13611.1	21q22.11	2013-10-21	2013-10-21	2011-02-23	ENSG00000159055	ENSG00000159055			1286	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 46", "chromosome 21 open reading frame 45", "MIS18 kinetochore protein homolog A (S. pombe)"	C21orf46, C21orf45		17199038	Standard	NM_018944		Approved	B28, FASP1, hMis18alpha	uc002ypi.3	Q9NYP9	OTTHUMG00000085308	ENST00000290130.3:c.54G>A	chr21.hg19:g.33651272C>T		76.0	0.0	.		69.0	16.0	.	NM_018944	B2R562|Q542Z0	Silent	SNP	ENST00000290130.3	hg19	CCDS13611.1																																																																																			.	.	.	none		0.607	MIS18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000193090.1	NM_018944		T	33651272	C	T	33651272	2	4	163	1	0	0	0	0	0	0	0	1	2128	564	20	2		2	C21orf45	21	33651272	Silent	SNP	C	TCGA-EV-5903-01A-11D-1589-08		33651272	14478623	94	9706											
SON	6651	hgsc.bcm.edu	37	chr21	34922663	34922663	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgttggagctgcaggagtcgTcggtggcctcagcgatggag	6	8	18	9	4	1	0	1	0	0	0	3	4	1	3	1	5	3	3	1	5	0	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chr21:34922663T>C	ENST00000356577.4	+	3	1601	c.1126T>C	c.(1126-1128)Tcg>Ccg	p.S376P	SON_ENST00000300278.4_Missense_Mutation_p.S376P|SON_ENST00000381692.2_Intron|SON_ENST00000381679.4_Missense_Mutation_p.S376P|SON_ENST00000290239.6_Missense_Mutation_p.S376P	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	376					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						GCAGGAGTCGTCGGTGGCCTC	0.627																																					p.S376P		Atlas-SNP	.											.	SON	343	.	0			c.T1126C						PASS	.						78	85	82					21																	34922663		2203	4300	6503	SO:0001583	missense	6651	exon3			GAGTCGTCGGTGG	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.1126T>C	chr21.hg19:g.34922663T>C	ENSP00000348984:p.Ser376Pro	153.0	0.0	.		93.0	26.0	.	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	hg19	CCDS13629.1	.	.	.	.	.	.	.	.	.	.	T	12.36	1.913625	0.33815	.	.	ENSG00000159140	ENST00000356577;ENST00000290239;ENST00000300278;ENST00000381679	T;T;T;T	0.14022	2.71;2.72;2.72;2.54	5.43	1.29	0.21616	.	0.277107	0.26272	N	0.025322	T	0.05593	0.0147	N	0.14661	0.345	0.21802	N	0.999532	B;B;B	0.22080	0.038;0.064;0.015	B;B;B	0.22880	0.019;0.042;0.023	T	0.36335	-0.9752	10	0.15499	T	0.54	.	2.7433	0.05259	0.1873:0.2368:0.0:0.5759	.	376;376;376	P18583;P18583-3;P18583-6	SON_HUMAN;.;.	P	376	ENSP00000348984:S376P;ENSP00000290239:S376P;ENSP00000300278:S376P;ENSP00000371095:S376P	ENSP00000290239:S376P	S	+	1	0	SON	33844533	0.991000	0.36638	1.000000	0.80357	0.997000	0.91878	0.194000	0.17135	0.413000	0.25759	0.459000	0.35465	TCG	.	.	.	none		0.627	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		C	34922663	T	C	34922663	3	2	163	1	0	0	0	0	1	0	0	0	14939	1667	58	3	1136	3	SON	21	34922663	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	1271391	34922663	13207232	95	9707											
HDAC6	10013	hgsc.bcm.edu	37	chrX	48682180	48682180	+	Silent	SNP	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	atgctgatgcagggatctagGggcctcactgatcaggtgag	9	9	15	8	0	3	3	2	3	1	0	3	4	3	4	1	4	2	2	1	4	1	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chrX:48682180G>A	ENST00000334136.5	+	26	3466	c.3288G>A	c.(3286-3288)agG>agA	p.R1096R	HDAC6_ENST00000444343.2_Silent_p.R1110R|HDAC6_ENST00000376619.2_Silent_p.R1096R			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	1096					aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	AGGGATCTAGGGGCCTCACTG	0.547																																					p.R1096R	Pancreas(112;205 1675 2305 8976 15959)	Atlas-SNP	.											.	HDAC6	111	.	0			c.G3288A						PASS	.						83	66	72					X																	48682180		2203	4300	6503	SO:0001819	synonymous_variant	10013	exon26			ATCTAGGGGCCTC	AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 90"	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.3288G>A	chrX.hg19:g.48682180G>A		19.0	0.0	.		17.0	12.0	.	NM_006044	O94975|Q6NT75|Q7L3E5|Q96CY0	Silent	SNP	ENST00000334136.5	hg19	CCDS14306.1	.	.	.	.	.	.	.	.	.	.	G	3.939	-0.014623	0.07681	.	.	ENSG00000094631	ENST00000430858	.	.	.	5.56	0.474	0.16768	.	.	.	.	.	T	0.23410	0.0566	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24333	-1.0163	4	.	.	.	0.2517	3.6925	0.08351	0.2664:0.0:0.4392:0.2944	.	.	.	.	E	57	.	.	G	+	2	0	HDAC6	48567124	0.016000	0.18221	0.000000	0.03702	0.048000	0.14542	0.329000	0.19698	-0.044000	0.13491	0.600000	0.82982	GGG	.	.	.	none		0.547	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044		A	48682180	G	A	48682180	2	1	163	1	0	0	0	0	0	0	0	1	7018	1223	43	2		2	HDAC6	23	48682180	Silent	SNP	G	TCGA-EV-5903-01A-11D-1589-08		48682180	106588380	96	9708											
RGAG1	57529	hgsc.bcm.edu	37	chrX	109695935	109695935	+	Missense_Mutation	SNP	T	T	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	agggatgtccatgccactaaTgagagctcaagacccaggag	13	6	12	10	0	1	2	1	1	0	2	2	5	2	4	3	2	2	1	3	2	2	1			TCGA-EV-5903-01A-11D-1589-08	TCGA-EV-5903-10A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	47cd3f3e-d93f-4343-8212-7656684a197c	f11afb9d-944d-4565-a9df-bdd5c35e0568	g.chrX:109695935T>G	ENST00000465301.2	+	3	2336	c.2090T>G	c.(2089-2091)aTg>aGg	p.M697R	RGAG1_ENST00000540313.1_Missense_Mutation_p.M697R	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	697								p.M697T(1)		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						ATGCCACTAATGAGAGCTCAA	0.517																																					p.M697R		Atlas-SNP	.											.	RGAG1	168	.	1	Substitution - Missense(1)	endometrium(1)	c.T2090G						PASS	.						118	99	105					X																	109695935		2203	4300	6503	SO:0001583	missense	57529	exon3			CACTAATGAGAGC	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.2090T>G	chrX.hg19:g.109695935T>G	ENSP00000419786:p.Met697Arg	40.0	0.0	.		33.0	20.0	.	NM_020769	Q9P2M8	Missense_Mutation	SNP	ENST00000465301.2	hg19	CCDS14552.1	.	.	.	.	.	.	.	.	.	.	T	1.022	-0.684599	0.03353	.	.	ENSG00000243978	ENST00000465301;ENST00000540313	T;T	0.48201	0.82;0.82	3.63	2.48	0.30137	.	0.141438	0.32935	N	0.005468	T	0.30792	0.0776	L	0.39898	1.24	0.09310	N	1	P	0.35982	0.531	B	0.35413	0.202	T	0.10989	-1.0606	9	.	.	.	-0.0102	2.2783	0.04108	0.2497:0.1407:0.0:0.6096	.	697	Q8NET4	RGAG1_HUMAN	R	697	ENSP00000419786:M697R;ENSP00000441452:M697R	.	M	+	2	0	RGAG1	109582591	0.001000	0.12720	0.002000	0.10522	0.031000	0.12232	-0.744000	0.04839	0.596000	0.29794	0.486000	0.48141	ATG	.	.	.	none		0.517	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		G	109695935	T	G	109695935	3	3	163	1	0	0	0	0	1	0	0	0	13287	1464	51	5	2092	5	RGAG1	23	109695935	Missense_Mutation	SNP	T	TCGA-EV-5903-01A-11D-1589-08	61013755	109695935	45574625	97	9709											
CGN	57530	hgsc.bcm.edu	37	chr1	151502428	151502428	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcaacagtgctggggcagcGgcgggccgcagtggagacga	8	3	20	10	4	0	1	0	0	0	1	0	3	0	1	1	6	3	4	1	6	1	0			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr1:151502428G>A	ENST00000271636.7	+	12	2283	c.2150G>A	c.(2149-2151)cGg>cAg	p.R717Q	SNORA44_ENST00000517031.1_RNA	NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	711	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)			CTGGGGCAGCGGCGGGCCGCA	0.652																																					p.R717Q		Atlas-SNP	.											.	CGN	106	.	0			c.G2150A						PASS	.						30	37	34					1																	151502428		2203	4300	6503	SO:0001583	missense	57530	exon12			GGCAGCGGCGGGC	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.2150G>A	chr1.hg19:g.151502428G>A	ENSP00000271636:p.Arg717Gln	186.0	0.0	.		208.0	105.0	.	NM_020770	A6H8L3|A7MD22|Q5T386|Q9NR25	Missense_Mutation	SNP	ENST00000271636.7	hg19	CCDS999.1	.	.	.	.	.	.	.	.	.	.	G	13.54	2.267974	0.40095	.	.	ENSG00000143375	ENST00000271636	T	0.64438	-0.1	5.27	5.27	0.74061	.	0.472495	0.21879	N	0.067773	T	0.62332	0.2419	L	0.50919	1.6	0.29222	N	0.87387	D	0.76494	0.999	P	0.60068	0.868	T	0.58685	-0.7593	10	0.39692	T	0.17	-10.0013	16.3784	0.83418	0.0:0.0:1.0:0.0	.	711	Q9P2M7	CING_HUMAN	Q	717	ENSP00000271636:R717Q	ENSP00000271636:R717Q	R	+	2	0	CGN	149769052	0.901000	0.30685	0.933000	0.37362	0.335000	0.28730	2.924000	0.48876	2.439000	0.82584	0.563000	0.77884	CGG	.	.	.	none		0.652	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770		A	151502428	G	A	151502428	3	1	164	1	0	0	0	0	1	0	0	0	3305	1116	39	1	2192	1	CGN	1	151502428	Missense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10		151502428	97748193	1	9710											
SHE	126669	hgsc.bcm.edu	37	chr1	154471704	154471704	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagggtcagcatagtcttctAaaatgatgacctgaaaaaga	17	9	9	6	0	3	4	1	3	2	1	3	4	3	4	1	1	1	1	1	1	6	3			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr1:154471704A>G	ENST00000304760.2	-	2	688	c.602T>C	c.(601-603)tTa>tCa	p.L201S	TDRD10_ENST00000368482.4_5'Flank	NM_001010846.2	NP_001010846.1	Q5VZ18	SHE_HUMAN	Src homology 2 domain containing E	201										breast(4)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)|pancreas(1)	14	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			ATAGTCTTCTAAAATGATGAC	0.448																																					p.L201S		Atlas-SNP	.											.	SHE	41	.	0			c.T602C						PASS	.						129	108	115					1																	154471704		2203	4300	6503	SO:0001583	missense	126669	exon2			TCTTCTAAAATGA	AK074067	CCDS30877.1	1q21.3	2013-02-14			ENSG00000169291	ENSG00000169291		"SH2 domain containing"	27004	protein-coding gene	gene with protein product		610482				9315092	Standard	NM_001010846		Approved		uc001ffb.3	Q5VZ18	OTTHUMG00000036072	ENST00000304760.2:c.602T>C	chr1.hg19:g.154471704A>G	ENSP00000307369:p.Leu201Ser	128.0	0.0	.		133.0	39.0	.	NM_001010846	Q8TEQ5	Missense_Mutation	SNP	ENST00000304760.2	hg19	CCDS30877.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.353420	0.82243	.	.	ENSG00000169291	ENST00000304760	T	0.31510	1.49	5.02	5.02	0.67125	.	0.102997	0.42821	D	0.000657	T	0.41050	0.1142	M	0.72894	2.215	0.42961	D	0.9944	D	0.89917	1.0	D	0.69307	0.963	T	0.22836	-1.0205	10	0.27082	T	0.32	-29.5539	13.7207	0.62725	1.0:0.0:0.0:0.0	.	201	Q5VZ18	SHE_HUMAN	S	201	ENSP00000307369:L201S	ENSP00000307369:L201S	L	-	2	0	SHE	152738328	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.237000	0.89807	2.099000	0.63709	0.533000	0.62120	TTA	.	.	.	none		0.448	SHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087910.2	NM_001010846		G	154471704	A	G	154471704	3	3	164	1	0	0	0	0	1	0	0	0	14289	372	13	3	905	3	SHE	1	154471704	Missense_Mutation	SNP	A	TCGA-F9-A4JJ-01A-11D-A25F-10	2969276	154471704	94778917	2	9711											
ATP1B1	481	hgsc.bcm.edu	37	chr1	169094224	169094232	+	In_Frame_Del	DEL	AAAAGTACA	AAAAGTACA	-																															gaacatagttaggttcctggAaaagtacaaagattcagccc																										TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	AAAAGTACA	AAAAGTACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr1:169094224_169094232delAAAAGTACA	ENST00000367816.1	+	4	858_866	c.329_337delAAAAGTACA	c.(328-339)gaaaagtacaaa>gaa	p.KYK111del	ATP1B1_ENST00000367813.3_In_Frame_Del_p.KYK103del|ATP1B1_ENST00000367815.4_In_Frame_Del_p.KYK111del|ATP1B1_ENST00000499679.3_In_Frame_Del_p.KYK55del			P05026	AT1B1_HUMAN	ATPase, Na+/K+ transporting, beta 1 polypeptide	111					blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular potassium ion homeostasis (GO:0030007)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|leukocyte migration (GO:0050900)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|positive regulation of ATP catabolic process (GO:1903291)|positive regulation of ATPase activity (GO:0032781)|positive regulation of calcium:sodium antiporter activity (GO:1903281)|positive regulation of potassium ion import (GO:1903288)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of sodium ion export from cell (GO:1903278)|potassium ion import (GO:0010107)|protein localization to plasma membrane (GO:0072659)|protein stabilization (GO:0050821)|protein transport into plasma membrane raft (GO:0044861)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression (GO:0010468)|relaxation of cardiac muscle (GO:0055119)|response to hypoxia (GO:0001666)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|vesicle (GO:0031982)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|MHC class II protein complex binding (GO:0023026)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	14	all_hematologic(923;0.208)					AGGTTCCTGGAAAAGTACAAAGATTCAGC	0.392																																					p.110_112del		Atlas-Indel,Pindel	.											.	ATP1B1	29	.	0			c.328_336del						PASS	.																																			SO:0001651	inframe_deletion	481	exon3			.	U16799	CCDS1276.1	1q24.2	2012-10-22			ENSG00000143153	ENSG00000143153		"ATPases / P-type"	804	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit beta-1", "sodium pump subunit beta-1", "sodium-potassium ATPase subunit beta 1 (non-catalytic)"	182330		ATP1B			Standard	NM_001677		Approved		uc001gfr.1	P05026	OTTHUMG00000034590	ENST00000367816.1:c.329_337delAAAAGTACA	chr1.hg19:g.169094224_169094232delAAAAGTACA	ENSP00000356790:p.Lys111_Lys113del	148.0	0.0	0		133.0	29.0	0.218045	NM_001677	Q5TGZ3	In_Frame_Del	DEL	ENST00000367816.1	hg19	CCDS1276.1																																																																																			.	.	.	none		0.392	ATP1B1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083696.1			-	169094232	AAAAGTACA	-	169094224	7	5	164	1	0	1	0	1	0	0	0	0	1132	246	9	0	339	0	ATP1B1	1	169094224	In_Frame_Del	DEL	AAAAGTACA	TCGA-F9-A4JJ-01A-11D-A25F-10	14622520	169094224	80156397	3	9712											
IGFN1	91156	hgsc.bcm.edu	37	chr1	201166405	201166405	+	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	tgcacagcagtaaatgcgtaCggagaggccgcttgctcagt	10	8	13	10	3	1	1	1	0	0	1	1	2	1	1	1	2	5	6	1	2	3	3	rs370452044		TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr1:201166405C>T	ENST00000335211.4	+	5	457	c.327C>T	c.(325-327)taC>taT	p.Y109Y	IGFN1_ENST00000451870.2_Silent_p.Y109Y|IGFN1_ENST00000295591.8_5'UTR	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	109	Ig-like 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						TAAATGCGTACGGAGAGGCCG	0.557																																					p.Y109Y		Atlas-SNP	.											.	IGFN1	220	.	0			c.C327T						PASS	.	C		1,1383		0,1,691	172	157	162		327	-2.2	0.1	1		162	0,3182		0,0,1591	no	coding-synonymous	IGFN1	NM_001164586.1		0,1,2282	TT,TC,CC		0.0,0.0723,0.0219		109/3709	201166405	1,4565	692	1591	2283	SO:0001819	synonymous_variant	91156	exon5			TGCGTACGGAGAG	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.327C>T	chr1.hg19:g.201166405C>T		88.0	0.0	.		130.0	41.0	.	NM_001164586	F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	hg19	CCDS53455.1																																																																																			.	.	.	none		0.557	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275		T	201166405	C	T	201166405	2	4	164	1	0	0	0	0	0	0	0	1	7597	547	19	1		1	IGFN1	1	201166405	Silent	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10	32072181	201166405	48084216	4	9713											
CR1	1378	hgsc.bcm.edu	37	chr1	207669654	207669654	+	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	agcccggagcctgtcgggccGccggcgcccggtctcccctt	2	6	14	19	6	1	0	0	0	1	0	3	1	1	1	7	4	2	0	7	4	0	1			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr1:207669654G>C	ENST00000367049.4	+	1	42	c.42G>C	c.(40-42)ccG>ccC	p.P14P	CR1_ENST00000400960.2_Silent_p.P14P|CR1_ENST00000367052.1_Silent_p.P14P|CR1_ENST00000367053.1_Silent_p.P14P|CR1_ENST00000367051.1_Silent_p.P14P|CR1_ENST00000367050.4_3'UTR	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	14					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						CTGTCGGGCCGCCGGCGCCCG	0.632																																					p.P14P		Atlas-SNP	.											.	CR1	354	.	0			c.G42C						PASS	.						21	27	25					1																	207669654		1819	4077	5896	SO:0001819	synonymous_variant	1378	exon1			CGGGCCGCCGGCG	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.42G>C	chr1.hg19:g.207669654G>C		39.0	0.0	.		48.0	6.0	.	NM_000573	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Silent	SNP	ENST00000367049.4	hg19	CCDS44308.1																																																																																			.	.	.	none		0.632	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573		C	207669654	G	C	207669654	2	2	164	1	0	0	0	0	0	0	0	1	3842	1074	38	4		4	CR1	1	207669654	Silent	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10	6503249	207669654	41580967	5	9714											
FMN2	56776	hgsc.bcm.edu	37	chr1	240255571	240255571	+	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	cacggcaaggggggagggggCggcggcggcggcggggagtc	5	1	26	9	6	0	0	0	0	0	0	1	2	0	2	0	12	0	1	0	12	1	0	rs71929261|rs140531536	byFrequency	TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr1:240255571C>G	ENST00000319653.9	+	1	392	c.162C>G	c.(160-162)ggC>ggG	p.G54G		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	54					cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.G197delG(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			GGGGAgggggcggcggcggcg	0.662																																					p.G54G		Atlas-SNP	.											.	FMN2	451	.	1	Deletion - In frame(1)	prostate(1)	c.C162G						PASS	.						2	3	3					1																	240255571		1816	3578	5394	SO:0001819	synonymous_variant	56776	exon1			AGGGGGCGGCGGC	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.162C>G	chr1.hg19:g.240255571C>G		5.0	0.0	.		9.0	4.0	.	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	hg19	CCDS31069.2																																																																																			.	.	.	none		0.662	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		G	240255571	C	G	240255571	2	3	164	1	0	0	0	0	0	0	0	1	5957	755	27	4		4	FMN2	1	240255571	Silent	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10	32585917	240255571	8995050	6	9715											
FH	2271	hgsc.bcm.edu	37	chr1	241661272	241661272	+	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	tttgctgccttgtcatacccTgaagaaaaaataaaaagacg	16	10	7	8	1	1	3	1	1	0	2	1	3	1	3	2	0	3	1	2	0	8	4			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr1:241661272T>G	ENST00000366560.3	-	10	1429		c.e10-2			NM_000143.3	NP_000134.2	P07954	FUMH_HUMAN	fumarate hydratase						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)		TGTCATACCCTGAAGAAAAAA	0.378			"Mis, N, F"			"lieomyomatosis, renal"			Hereditary Leiomyomatosis and Renal Cell Cancer																												.	Melanoma(148;1573 2486 7381 46575)	Atlas-SNP	.	yes	Rec		hereditary leiomyomatosis and renal cell cancer	1	1q42.1	2271	fumarate hydratase		"E, M"	.	FH	64	.	0			c.1391-2A>C						PASS	.						101	99	100					1																	241661272		2203	4300	6503	SO:0001630	splice_region_variant	2271	exon11	Familial Cancer Database	HLRCC, Reed syndrome, Hereditary Multiple Leiomyomata of Skin and Uterus	ATACCCTGAAGAA	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.1391-2A>C	chr1.hg19:g.241661272T>G		125.0	0.0	.		121.0	32.0	.	NM_000143	B1ANK7	Splice_Site	SNP	ENST00000366560.3	hg19	CCDS1617.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.987598	0.74589	.	.	ENSG00000091483	ENST00000366560	.	.	.	5.75	5.75	0.90469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0202	0.64550	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	FH	239727895	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	6.531000	0.73820	2.188000	0.69820	0.528000	0.53228	.	.	.	.	none		0.378	FH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095490.1	NM_000143	Intron	G	241661272	T	G	241661272	5	3	164	1	0	0	0	0	0	0	1	0	5882	1594	55	5	147	5	FH	1	241661272	Splice_Site	SNP	T	TCGA-F9-A4JJ-01A-11D-A25F-10	1405701	241661272	7589349	7	9716											
LRRTM4	80059	hgsc.bcm.edu	37	chr2	77746638	77746638	+	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	ttgtgcagataagtaattttGttggagcttagaattaattc	12	17	9	3	0	0	2	0	0	0	2	1	3	0	3	0	1	2	4	0	1	5	9			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr2:77746638G>T	ENST00000409093.1	-	3	693	c.357C>A	c.(355-357)aaC>aaA	p.N119K	LRRTM4_ENST00000409088.3_Missense_Mutation_p.N119K|LRRTM4_ENST00000409884.1_Missense_Mutation_p.N119K|LRRTM4_ENST00000409911.1_Missense_Mutation_p.N120K|LRRTM4_ENST00000409282.1_Missense_Mutation_p.N120K			Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	119					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)		AAGTAATTTTGTTGGAGCTTA	0.373																																					p.N119K		Atlas-SNP	.											.	LRRTM4	334	.	0			c.C357A						PASS	.						158	140	145					2																	77746638		1842	4084	5926	SO:0001583	missense	80059	exon3			AATTTTGTTGGAG	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.357C>A	chr2.hg19:g.77746638G>T	ENSP00000386357:p.Asn119Lys	109.0	0.0	.		100.0	27.0	.	NM_024993	Q4FZ98|Q6UXJ7	Missense_Mutation	SNP	ENST00000409093.1	hg19	CCDS46346.1	.	.	.	.	.	.	.	.	.	.	G	14.41	2.526251	0.44969	.	.	ENSG00000176204	ENST00000409911;ENST00000409884;ENST00000409093;ENST00000409088;ENST00000409282	T;T;T;T;T	0.72835	-0.69;-0.69;-0.69;-0.69;-0.69	5.96	4.91	0.64330	.	0.044427	0.85682	D	0.000000	D	0.87873	0.6287	H	0.96489	3.83	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	0.89990	0.4107	10	0.87932	D	0	.	11.0841	0.48076	0.1556:0.0:0.8444:0.0	.	120;119;119	Q4KMX1;Q86VH4-2;Q86VH4	.;.;LRRT4_HUMAN	K	120;119;119;119;120	ENSP00000387228:N120K;ENSP00000387297:N119K;ENSP00000386357:N119K;ENSP00000386236:N119K;ENSP00000386286:N120K	ENSP00000386236:N119K	N	-	3	2	LRRTM4	77600146	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.981000	0.49329	2.826000	0.97356	0.655000	0.94253	AAC	.	.	.	none		0.373	LRRTM4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328225.1	NM_024993		T	77746638	G	T	77746638	3	4	164	1	0	0	0	0	1	0	0	0	9049	1368	48	4	1429	4	LRRTM4	2	77746638	Missense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10		77746638	165452735	8	9717											
YSK4	80122	hgsc.bcm.edu	37	chr2	135738691	135738691	+	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	cccaggccaaacgcctggcaCagccaaagtcaatcagcttt	12	6	8	15	1	2	0	2	0	0	0	2	0	2	0	4	2	3	2	4	2	3	1			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr2:135738691C>G	ENST00000375845.3	-	9	3650	c.3620G>C	c.(3619-3621)tGt>tCt	p.C1207S	MAP3K19_ENST00000392915.1_3'UTR|MAP3K19_ENST00000392918.3_Missense_Mutation_p.C341S|MAP3K19_ENST00000392917.3_Missense_Mutation_p.C339S|MAP3K19_ENST00000358371.4_Missense_Mutation_p.C1094S|MAP3K19_ENST00000315513.3_Missense_Mutation_p.C68S|MAP3K19_ENST00000375844.3_Missense_Mutation_p.C389S	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	1207	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)										ACGCCTGGCACAGCCAAAGTC	0.458																																					p.C1207S		Atlas-SNP	.											.	.	.	.	0			c.G3620C						PASS	.						113	112	112					2																	135738691		2203	4300	6503	SO:0001583	missense	80122	exon9			CTGGCACAGCCAA	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.3620G>C	chr2.hg19:g.135738691C>G	ENSP00000365005:p.Cys1207Ser	66.0	0.0	.		80.0	24.0	.	NM_025052	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	hg19	CCDS2176.2	.	.	.	.	.	.	.	.	.	.	C	21.6	4.167028	0.78339	.	.	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000375844;ENST00000392918;ENST00000392917;ENST00000437365;ENST00000315513	T;T;T;T;T;T;T	0.22539	1.95;1.95;1.95;1.95;1.95;1.95;1.95	5.88	5.88	0.94601	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.50627	D	0.000113	T	0.27384	0.0672	N	0.05031	-0.125	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.998;0.999;0.999;0.999;1.0	T	0.31613	-0.9937	10	0.25106	T	0.35	.	19.2304	0.93836	0.0:1.0:0.0:0.0	.	339;1094;341;389;1207	B7ZMH9;Q56UN5-3;Q56UN5-4;Q56UN5-5;Q56UN5	.;.;.;.;YSK4_HUMAN	S	1207;1094;389;341;339;597;68	ENSP00000365005:C1207S;ENSP00000351140:C1094S;ENSP00000365004:C389S;ENSP00000376650:C341S;ENSP00000376649:C339S;ENSP00000392827:C597S;ENSP00000321160:C68S	ENSP00000321160:C68S	C	-	2	0	YSK4	135455161	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.616000	0.83018	2.782000	0.95742	0.655000	0.94253	TGT	.	.	.	none		0.458	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052		G	135738691	C	G	135738691	3	3	164	1	0	0	0	0	1	0	0	0	17507	478	17	4	374	4	YSK4	2	135738691	Missense_Mutation	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10	57992053	135738691	107460682	9	9718											
PRR21	643905	hgsc.bcm.edu	37	chr2	240982306	240982307	+	In_Frame_Ins	INS	-	-	AGG																															gggtgaagagccgtggatgaINSgccgtgggggaagagctgtt																										TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr2:240982306_240982307insAGG	ENST00000408934.1	-	1	92_93	c.93_94insCCT	c.(91-96)ggctca>ggcCCTtca	p.31_32GS>GPS		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	31										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						GCCGTGGATGAGCCGTGGGGGA	0.564																																					p.S32delinsPS		Atlas-INDEL	.											.	PRR21	53	.	0			c.94_95insCCT						PASS	.																																			SO:0001652	inframe_insertion	643905	exon1			.	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.93_94insCCT	chr2.hg19:g.240982306_240982307insAGG	ENSP00000386166:p.Gly31_Ser32insPro	104.0	0.0	0		148.0	10.0	0.0675676	NM_001080835		In_Frame_Ins	INS	ENST00000408934.1	hg19	CCDS33417.1																																																																																			.	.	.	none		0.564	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835		AGG	240982307	-	AGG	240982306	7	5	164	1	0	1	1	0	0	0	0	0	12602	304	11	0	1078	0	PRR21	2	240982306	In_Frame_Ins	INS	-	TCGA-F9-A4JJ-01A-11D-A25F-10	105243615	240982306	2217067	10	9719											
TRIO	7204	hgsc.bcm.edu	37	chr5	14497115	14497115	+	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	gggaaggactcagcaacaagGtatctgtgaaggtgtgttcg	11	9	15	6	1	2	1	1	1	1	0	3	3	2	3	0	4	2	3	0	4	5	2			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr5:14497115G>C	ENST00000344204.4	+	50	8032	c.8008G>C	c.(8008-8010)Gta>Cta	p.V2670L	TRIO_ENST00000344135.5_Missense_Mutation_p.V169L|TRIO_ENST00000537187.1_Missense_Mutation_p.V2494L	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	2670					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)					CAGCAACAAGGTATCTGTGAA	0.498																																					p.V2670L		Atlas-SNP	.											.	TRIO	305	.	0			c.G8008C						PASS	.						122	103	109					5																	14497115		2203	4300	6503	SO:0001583	missense	7204	exon50			AACAAGGTATCTG	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.8008G>C	chr5.hg19:g.14497115G>C	ENSP00000339299:p.Val2670Leu	169.0	0.0	.		154.0	43.0	.	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	hg19	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	G	31	5.094039	0.94149	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000513206;ENST00000344135	T;T;T	0.68025	-0.3;-0.21;-0.26	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.77253	0.4103	L	0.52759	1.655	0.32172	N	0.581488	D	0.67145	0.996	D	0.67900	0.954	T	0.81075	-0.1097	10	0.59425	D	0.04	.	17.1098	0.86672	0.0:0.0:1.0:0.0	.	2670	O75962	TRIO_HUMAN	L	2670;2494;2357;169	ENSP00000339299:V2670L;ENSP00000446348:V2494L;ENSP00000339291:V169L	ENSP00000339291:V169L	V	+	1	0	TRIO	14550115	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.441000	0.97557	2.461000	0.83175	0.655000	0.94253	GTA	.	.	.	none		0.498	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		C	14497115	G	C	14497115	3	2	164	1	0	0	0	0	1	0	0	0	16564	1261	44	4	8206	4	TRIO	5	14497115	Missense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10		14497115	166418145	11	9720											
TNXB	7148	hgsc.bcm.edu	37	chr6	32037362	32037362	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggccgagatggggcccacaCgcttgccgtggtgcagcccg	5	5	16	15	5	0	1	0	0	0	1	0	2	0	1	4	4	3	2	4	4	0	1			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr6:32037362C>T	ENST00000375244.3	-	15	5756	c.5555G>A	c.(5554-5556)cGt>cAt	p.R1852H	TNXB_ENST00000375247.2_Missense_Mutation_p.R1852H			P22105	TENX_HUMAN	tenascin XB	1934					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						GGGGCCCACACGCTTGCCGTG	0.672																																					p.R1852H		Atlas-SNP	.											.	TNXB	553	.	0			c.G5555A						PASS	.						27	34	32					6																	32037362		2155	4268	6423	SO:0001583	missense	7148	exon15			CCCACACGCTTGC	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.5555G>A	chr6.hg19:g.32037362C>T	ENSP00000364393:p.Arg1852His	99.0	0.0	.		127.0	8.0	.	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	hg19		.	.	.	.	.	.	.	.	.	.	C	19.43	3.825390	0.71143	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.05025	3.51;3.51	5.5	4.44	0.53790	.	0.000000	0.46758	D	0.000265	T	0.22205	0.0535	M	0.93594	3.435	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.09530	-1.0670	10	0.66056	D	0.02	.	12.1698	0.54152	0.0:0.9037:0.0:0.0963	.	1852	P22105-3	.	H	1852	ENSP00000364393:R1852H;ENSP00000364396:R1852H	ENSP00000364393:R1852H	R	-	2	0	TNXB	32145340	0.757000	0.28394	0.251000	0.24312	0.105000	0.19272	2.166000	0.42406	2.598000	0.87819	0.591000	0.81541	CGT	.	.	.	none		0.672	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		T	32037362	C	T	32037362	3	4	164	1	0	0	0	0	1	0	0	0	16358	536	19	1	9278	1	TNXB	6	32037362	Missense_Mutation	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10		32037362	139077705	12	9721											
EYA4	2070	hgsc.bcm.edu	37	chr6	133849920	133849920	+	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	acctcctggctctccaccaaGcactggaattagagtatttg	10	11	8	12	0	1	1	0	0	1	1	3	2	2	2	4	2	1	3	4	2	4	3			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr6:133849920G>T	ENST00000367895.5	+	20	2361	c.1897G>T	c.(1897-1899)Gca>Tca	p.A633S	EYA4_ENST00000431403.2_Missense_Mutation_p.A633S|EYA4_ENST00000430974.2_Intron|RP3-323P13.2_ENST00000607033.1_RNA|EYA4_ENST00000355167.3_Missense_Mutation_p.A633S|EYA4_ENST00000355286.6_Missense_Mutation_p.A610S|EYA4_ENST00000452339.2_Missense_Mutation_p.A579S|EYA4_ENST00000525849.1_Missense_Mutation_p.A610S|EYA4_ENST00000531901.1_Missense_Mutation_p.A639S	NM_004100.4	NP_004091.3	O95677	EYA4_HUMAN	EYA transcriptional coactivator and phosphatase 4	633					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)		TCTCCACCAAGCACTGGAATT	0.453																																					p.A633S	Melanoma(57;398 1237 3528 4702 7415)	Atlas-SNP	.											.	EYA4	196	.	0			c.G1897T						PASS	.						260	238	245					6																	133849920		2203	4300	6503	SO:0001583	missense	2070	exon20			CACCAAGCACTGG	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.1897G>T	chr6.hg19:g.133849920G>T	ENSP00000356870:p.Ala633Ser	277.0	0.0	.		291.0	15.0	.	NM_172105	B7Z7F7|O95464|O95679|Q8IW39|Q9NTR7	Missense_Mutation	SNP	ENST00000367895.5	hg19	CCDS5165.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.636157	0.87760	.	.	ENSG00000112319	ENST00000452339;ENST00000367895;ENST00000355167;ENST00000355286;ENST00000531901;ENST00000525849;ENST00000431403	D;D;D;D;D;D;D	0.93247	-3.19;-3.19;-3.19;-3.19;-3.19;-3.19;-3.19	6.07	6.07	0.98685	EYA (1);	0.000000	0.85682	D	0.000000	D	0.97021	0.9027	M	0.83483	2.645	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;0.999;1.0;0.999	D;D;D;D;D	0.91635	0.999;0.996;0.996;0.999;0.998	D	0.96683	0.9505	10	0.87932	D	0	-22.8527	20.6593	0.99626	0.0:0.0:1.0:0.0	.	639;579;610;633;633	F2Z2Y1;E7EN58;O95677-2;O95677-4;O95677	.;.;.;.;EYA4_HUMAN	S	579;633;633;610;639;610;633	ENSP00000395916:A579S;ENSP00000356870:A633S;ENSP00000347294:A633S;ENSP00000347434:A610S;ENSP00000432770:A639S;ENSP00000433219:A610S;ENSP00000404558:A633S	ENSP00000347294:A633S	A	+	1	0	EYA4	133891613	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.837000	0.99465	2.885000	0.99019	0.655000	0.94253	GCA	.	.	.	none		0.453	EYA4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042282.2	NM_004100		T	133849920	G	T	133849920	3	4	164	1	0	0	0	0	1	0	0	0	5333	971	34	4	2076	4	EYA4	6	133849920	Missense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10	101812558	133849920	37265147	13	9722											
CCDC132	55610	hgsc.bcm.edu	37	chr7	92932815	92932815	+	Missense_Mutation	SNP	T	T	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	tgttcttagagaatgagactTgggaactttgtcctgttaag	10	15	11	5	0	1	2	0	1	1	2	2	5	2	3	1	1	1	2	1	1	4	5			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr7:92932815T>G	ENST00000305866.5	+	17	1533	c.1405T>G	c.(1405-1407)Tgg>Ggg	p.W469G	CCDC132_ENST00000535481.1_Missense_Mutation_p.W189G|CCDC132_ENST00000317751.6_Missense_Mutation_p.W200G|CCDC132_ENST00000544910.1_Missense_Mutation_p.W439G|CCDC132_ENST00000541136.1_Missense_Mutation_p.W280G	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	469						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)			GAATGAGACTTGGGAACTTTG	0.348																																					p.W469G		Atlas-SNP	.											.	CCDC132	136	.	0			c.T1405G						PASS	.						141	135	137					7																	92932815		1823	4079	5902	SO:0001583	missense	55610	exon17			GAGACTTGGGAAC	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.1405T>G	chr7.hg19:g.92932815T>G	ENSP00000307666:p.Trp469Gly	38.0	0.0	.		42.0	16.0	.	NM_017667	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	hg19	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.084073	0.76642	.	.	ENSG00000004766	ENST00000305866;ENST00000544910;ENST00000541136;ENST00000535481;ENST00000317751	T	0.73681	-0.77	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	D	0.86033	0.5836	M	0.80982	2.52	0.80722	D	1	D;D;D	0.57899	0.967;0.981;0.967	D;D;D	0.70487	0.932;0.969;0.932	D	0.88196	0.2880	10	0.87932	D	0	-0.9767	15.0541	0.71897	0.0:0.0:0.0:1.0	.	189;439;469	B4DS55;F5H5U7;Q96JG6	.;.;CC132_HUMAN	G	469;439;280;189;200	ENSP00000325582:W200G	ENSP00000307666:W469G	W	+	1	0	CCDC132	92770751	1.000000	0.71417	0.989000	0.46669	0.997000	0.91878	7.794000	0.85869	2.200000	0.70718	0.460000	0.39030	TGG	.	.	.	none		0.348	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667		G	92932815	T	G	92932815	3	3	164	1	0	0	0	0	1	0	0	0	2769	1812	63	5	1513	5	CCDC132	7	92932815	Missense_Mutation	SNP	T	TCGA-F9-A4JJ-01A-11D-A25F-10		92932815	66205848	14	9723											
KIF13B	23303	hgsc.bcm.edu	37	chr8	29037680	29037680	+	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	tttgaaaactgcatgggatcGgctactctcctcgttcatgt	8	14	9	10	2	2	1	1	1	1	0	5	2	2	2	1	2	3	3	1	2	3	3			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr8:29037680G>A	ENST00000524189.1	-	8	699	c.661C>T	c.(661-663)Cga>Tga	p.R221*	KIF13B_ENST00000521515.1_Nonsense_Mutation_p.R221*	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	221	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)		GCATGGGATCGGCTACTCTCC	0.438																																					p.R221X		Atlas-SNP	.											.	KIF13B	192	.	0			c.C661T						PASS	.						192	192	192					8																	29037680		1932	4134	6066	SO:0001587	stop_gained	23303	exon8			GGGATCGGCTACT	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.661C>T	chr8.hg19:g.29037680G>A	ENSP00000427900:p.Arg221*	319.0	0.0	.		380.0	150.0	.	NM_015254	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Nonsense_Mutation	SNP	ENST00000524189.1	hg19	CCDS55217.1	.	.	.	.	.	.	.	.	.	.	G	35	5.587513	0.96590	.	.	ENSG00000197892	ENST00000524189;ENST00000521515	.	.	.	4.77	2.84	0.33178	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.45	0.61165	0.0:0.0:0.7156:0.2844	.	.	.	.	X	221	.	ENSP00000429201:R221X	R	-	1	2	KIF13B	29093599	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	1.457000	0.35212	1.203000	0.43233	0.563000	0.77884	CGA	.	.	.	none		0.438	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1			A	29037680	G	A	29037680	4	1	164	1	0	0	0	0	0	1	0	0	8282	1124	39	1	4951	1	KIF13B	8	29037680	Nonsense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10		29037680	117326342	15	9724											
WWP1	11059	hgsc.bcm.edu	37	chr8	87443954	87443954	+	Missense_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	aacaacattcaaagatcctcGcaatgggaagtcatctgtgt	14	10	8	9	1	3	1	2	0	1	1	5	2	4	2	1	1	2	1	1	1	5	1	rs554041348		TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr8:87443954G>A	ENST00000517970.1	+	14	1890	c.1583G>A	c.(1582-1584)cGc>cAc	p.R528H	WWP1_ENST00000349423.2_Missense_Mutation_p.R310H|WWP1_ENST00000341922.2_Missense_Mutation_p.R398H|WWP1_ENST00000265428.4_Missense_Mutation_p.R528H	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	528	WW 4. {ECO:0000255|PROSITE- ProRule:PRU00224}.				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						AAAGATCCTCGCAATGGGAAG	0.388													G|||	1	0.000199681	0	0	5008	,	,		18477	0		0	False		,,,				2504	0.001				p.R528H		Atlas-SNP	.											WWP1,NS,carcinoma,0,1	WWP1	97	.	0			c.G1583A						PASS	.						91	90	90					8																	87443954		2203	4300	6503	SO:0001583	missense	11059	exon14			ATCCTCGCAATGG	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.1583G>A	chr8.hg19:g.87443954G>A	ENSP00000427793:p.Arg528His	166.0	0.0	.		149.0	6.0	.	NM_007013	O00307|Q5YLC1|Q96BP4	Missense_Mutation	SNP	ENST00000517970.1	hg19	CCDS6242.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.986456	0.93044	.	.	ENSG00000123124	ENST00000517970;ENST00000265428;ENST00000341922;ENST00000349423	T;T;T;T	0.61980	0.06;0.06;0.14;0.19	5.35	5.35	0.76521	WW/Rsp5/WWP (4);	0.302657	0.33272	N	0.005098	D	0.85592	0.5732	H	0.97732	4.065	0.80722	D	1	D;D	0.69078	0.997;0.995	P;P	0.60236	0.871;0.747	D	0.90859	0.4737	10	0.72032	D	0.01	.	19.0481	0.93030	0.0:0.0:1.0:0.0	.	310;528	Q9H0M0-6;Q9H0M0	.;WWP1_HUMAN	H	528;528;398;310	ENSP00000427793:R528H;ENSP00000265428:R528H;ENSP00000340564:R398H;ENSP00000342665:R310H	ENSP00000265428:R528H	R	+	2	0	WWP1	87513070	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.744000	0.98853	2.498000	0.84270	0.563000	0.77884	CGC	.	.	.	none		0.388	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013		A	87443954	G	A	87443954	3	1	164	1	0	0	0	0	1	0	0	0	17427	1087	38	1	1629	1	WWP1	8	87443954	Missense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10	58406274	87443954	58920068	16	9725											
PHF20L1	51105	hgsc.bcm.edu	37	chr8	133829702	133829702	+	Missense_Mutation	SNP	T	T	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	tcctcttaccgtaatgaatgTcccagggcagaaaaagagga	14	8	10	9	1	1	3	0	1	1	2	3	4	3	4	3	2	1	2	3	2	5	2			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr8:133829702T>G	ENST00000395386.2	+	12	1790	c.1491T>G	c.(1489-1491)tgT>tgG	p.C497W	PHF20L1_ENST00000220847.7_5'UTR|PHF20L1_ENST00000395390.2_Missense_Mutation_p.C472W	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	497							zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			GTAATGAATGTCCCAGGGCAG	0.478																																					p.C497W		Atlas-SNP	.											.	PHF20L1	129	.	0			c.T1491G						PASS	.						74	67	70					8																	133829702		2203	4300	6503	SO:0001583	missense	51105	exon12			TGAATGTCCCAGG	AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"Tudor domain containing", "Zinc fingers, PHD-type"	24280	protein-coding gene	gene with protein product	"tudor domain containing 20B"					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.1491T>G	chr8.hg19:g.133829702T>G	ENSP00000378784:p.Cys497Trp	45.0	0.0	.		74.0	9.0	.	NM_016018	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Missense_Mutation	SNP	ENST00000395386.2	hg19	CCDS6367.2	.	.	.	.	.	.	.	.	.	.	T	15.88	2.964653	0.53507	.	.	ENSG00000129292	ENST00000395383;ENST00000361997;ENST00000395386;ENST00000315808;ENST00000395382;ENST00000395390	T;T;T;T;T	0.52057	0.73;0.68;1.42;0.7;1.43	5.27	3.01	0.34805	.	.	.	.	.	T	0.36524	0.0970	L	0.29908	0.895	0.80722	D	1	B;P;P	0.41569	0.32;0.602;0.755	B;B;B	0.43950	0.134;0.283;0.437	T	0.05451	-1.0884	9	0.38643	T	0.18	-0.054	6.933	0.24451	0.0:0.4761:0.0:0.5239	.	472;497;497	F8W9L8;A8MW92;A8MW92-4	.;P20L1_HUMAN;.	W	501;472;497;497;367;472	ENSP00000378781:C501W;ENSP00000355301:C472W;ENSP00000378784:C497W;ENSP00000324519:C497W;ENSP00000378788:C472W	ENSP00000324519:C497W	C	+	3	2	PHF20L1	133898884	0.394000	0.25246	0.875000	0.34327	0.928000	0.56348	1.393000	0.34497	0.385000	0.24970	0.477000	0.44152	TGT	.	.	.	none		0.478	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018		G	133829702	T	G	133829702	3	3	164	1	0	0	0	0	1	0	0	0	11839	1673	58	5	1539	5	PHF20L1	8	133829702	Missense_Mutation	SNP	T	TCGA-F9-A4JJ-01A-11D-A25F-10	46385748	133829702	12534320	17	9726											
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84608041	84608041	+	Missense_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	tggtgagtgaggaccactgcGttgatacttcccaggaaatt	10	11	12	8	1	0	3	0	3	0	0	1	5	1	5	2	3	2	1	2	3	2	4			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr9:84608041G>A	ENST00000344803.2	+	4	2703	c.2656G>A	c.(2656-2658)Gtt>Att	p.V886I		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	886					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GGACCACTGCGTTGATACTTC	0.438																																					p.V886I		Atlas-SNP	.											.	.	.	.	0			c.G2656A						PASS	.						100	85	90					9																	84608041		1867	4118	5985	SO:0001583	missense	389763	exon4			CACTGCGTTGATA		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.2656G>A	chr9.hg19:g.84608041G>A	ENSP00000341988:p.Val886Ile	290.0	0.0	.		201.0	96.0	.	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	hg19	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	G	6.075	0.382087	0.11524	.	.	ENSG00000214929	ENST00000344803	T	0.49432	0.78	2.92	-1.61	0.08399	.	1.757670	0.03395	N	0.202455	T	0.37237	0.0996	L	0.50333	1.59	0.09310	N	1	B	0.15141	0.012	B	0.10450	0.005	T	0.06144	-1.0843	10	0.23302	T	0.38	0.4107	2.1957	0.03910	0.1774:0.3151:0.3841:0.1234	.	886	Q6ZQQ2	F75D1_HUMAN	I	886	ENSP00000341988:V886I	ENSP00000341988:V886I	V	+	1	0	FAM75D1	83797861	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.475000	0.00987	-0.318000	0.08665	-0.171000	0.13296	GTT	.	.	.	none		0.438	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		A	84608041	G	A	84608041	3	1	164	1	0	0	0	0	1	0	0	0	5939	1145	40	1	2670	1	FLJ46321	9	84608041	Missense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10		84608041	56605390	18	9727											
ITGA8	8516	hgsc.bcm.edu	37	chr10	15688856	15688856	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaaattaccattgtatccaTcttggttcaggtctcctaag	10	16	6	9	0	3	0	1	0	2	0	5	0	4	0	3	2	1	2	3	2	5	7			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr10:15688856T>C	ENST00000378076.3	-	12	1549	c.1196A>G	c.(1195-1197)gAt>gGt	p.D399G		NM_003638.1	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8	399					brain development (GO:0007420)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|metanephros development (GO:0001656)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|substrate adhesion-dependent cell spreading (GO:0034446)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|dendritic spine membrane (GO:0032591)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integrin alpha8-beta1 complex (GO:0034678)|integrin complex (GO:0008305)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	metal ion binding (GO:0046872)			NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	96						ATTGTATCCATCTTGGTTCAG	0.468																																					p.D399G		Atlas-SNP	.											.	ITGA8	230	.	0			c.A1196G						PASS	.						96	89	92					10																	15688856		2203	4300	6503	SO:0001583	missense	8516	exon12			TATCCATCTTGGT	L36531	CCDS31155.1	10p13	2010-03-23			ENSG00000077943	ENSG00000077943		"Integrins"	6144	protein-coding gene	gene with protein product		604063				7768999	Standard	XM_005252633		Approved		uc001ioc.1	P53708	OTTHUMG00000017733	ENST00000378076.3:c.1196A>G	chr10.hg19:g.15688856T>C	ENSP00000367316:p.Asp399Gly	99.0	0.0	.		101.0	7.0	.	NM_003638	B0YJ31|Q5VX94	Missense_Mutation	SNP	ENST00000378076.3	hg19	CCDS31155.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.698910	0.88830	.	.	ENSG00000077943	ENST00000378076;ENST00000538044	T	0.75589	-0.95	5.09	5.09	0.68999	.	0.093018	0.64402	D	0.000001	D	0.89322	0.6682	H	0.94264	3.515	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.69142	0.962;0.943	D	0.92371	0.5905	10	0.87932	D	0	.	14.8578	0.70355	0.0:0.0:0.0:1.0	.	384;399	F5H818;P53708	.;ITA8_HUMAN	G	399;384	ENSP00000367316:D399G	ENSP00000367316:D399G	D	-	2	0	ITGA8	15728862	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.040000	0.89188	1.897000	0.54924	0.460000	0.39030	GAT	.	.	.	none		0.468	ITGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046987.1	NM_003638		C	15688856	T	C	15688856	3	2	164	1	0	0	0	0	1	0	0	0	7889	1435	50	3	2071	3	ITGA8	10	15688856	Missense_Mutation	SNP	T	TCGA-F9-A4JJ-01A-11D-A25F-10		15688856	119845891	19	9728											
TRPM5	29850	hgsc.bcm.edu	37	chr11	2432685	2432685	+	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	ccgtcatgggggtgcagcagCgcctgggtggtgacaccgta	6	7	17	11	3	1	1	1	1	0	0	1	1	1	1	3	4	3	3	3	4	1	1			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr11:2432685C>T	ENST00000155858.6	-	18	2687	c.2679G>A	c.(2677-2679)gcG>gcA	p.A893A	TRPM5_ENST00000452833.1_Silent_p.A895A|TRPM5_ENST00000528453.1_Silent_p.A893A|TRPM5_ENST00000533060.1_Silent_p.A893A	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)		GGTGCAGCAGCGCCTGGGTGG	0.632																																					p.A893A	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.G2679A						PASS	.						33	37	36					11																	2432685		2202	4295	6497	SO:0001819	synonymous_variant	29850	exon18			CAGCAGCGCCTGG	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.2679G>A	chr11.hg19:g.2432685C>T		70.0	0.0	.		88.0	27.0	.	NM_014555		Silent	SNP	ENST00000155858.6	hg19	CCDS31340.1																																																																																			.	.	.	none		0.632	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555		T	2432685	C	T	2432685	2	4	164	1	0	0	0	0	0	0	0	1	16601	755	27	1		1	TRPM5	11	2432685	Silent	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10		2432685	132573831	20	9729											
ACAD8	27034	hgsc.bcm.edu	37	chr11	134131026	134131026	+	Missense_Mutation	SNP	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	aattgggagcgaggggcaggGcttcctcattgccgtgagag	8	8	17	8	2	1	1	1	1	0	1	2	4	2	2	2	4	2	2	2	4	1	3			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr11:134131026G>A	ENST00000281182.4	+	7	900	c.794G>A	c.(793-795)gGc>gAc	p.G265D	ACAD8_ENST00000537423.1_Missense_Mutation_p.G188D|ACAD8_ENST00000524547.1_3'UTR|ACAD8_ENST00000543332.1_Missense_Mutation_p.G167D|ACAD8_ENST00000374752.4_Missense_Mutation_p.G138D	NM_014384.2	NP_055199.1	Q9UKU7	ACAD8_HUMAN	acyl-CoA dehydrogenase family, member 8	265					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)	GAGGGGCAGGGCTTCCTCATT	0.587																																					p.G265D	GBM(65;238 1125 33403 41853 48889)	Atlas-SNP	.											.	ACAD8	33	.	0			c.G794A						PASS	.						70	66	67					11																	134131026		2201	4297	6498	SO:0001583	missense	27034	exon7			GGCAGGGCTTCCT	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.794G>A	chr11.hg19:g.134131026G>A	ENSP00000281182:p.Gly265Asp	175.0	0.0	.		170.0	74.0	.	NM_014384	B7Z5W4|Q6ZWP6|Q9BUS8	Missense_Mutation	SNP	ENST00000281182.4	hg19	CCDS8498.1	.	.	.	.	.	.	.	.	.	.	G	34	5.343370	0.95783	.	.	ENSG00000151498	ENST00000281182;ENST00000537423;ENST00000543332;ENST00000374752;ENST00000537915	D;D;D;D	0.99961	-9.25;-9.25;-9.25;-9.25	5.44	5.44	0.79542	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);	0.000000	0.85682	D	0.000000	D	0.99971	0.9990	H	0.97874	4.095	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.996	D	0.96958	0.9699	10	0.87932	D	0	.	19.2501	0.93921	0.0:0.0:1.0:0.0	.	188;138;265	B7Z5W4;Q6ZWP6;Q9UKU7	.;.;ACAD8_HUMAN	D	265;188;167;138;227	ENSP00000281182:G265D;ENSP00000443763:G188D;ENSP00000438302:G167D;ENSP00000363884:G138D	ENSP00000281182:G265D	G	+	2	0	ACAD8	133636236	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.793000	0.99091	2.561000	0.86390	0.561000	0.74099	GGC	.	.	.	none		0.587	ACAD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393607.1	NM_014384		A	134131026	G	A	134131026	3	1	164	1	0	0	0	0	1	0	0	0	110	1203	42	2	820	2	ACAD8	11	134131026	Missense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10	131698341	134131026	875490	21	9730											
MYO1A	4640	hgsc.bcm.edu	37	chr12	57440666	57440666	+	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	cagtttgtgatgacaccaccGaggggggatcccttgaagtc	9	9	13	10	1	0	3	0	3	0	0	2	5	1	4	3	3	0	1	3	3	1	2	rs561295735	byFrequency	TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr12:57440666G>A	ENST00000442789.2	-	8	809	c.522C>T	c.(520-522)ctC>ctT	p.L174L	MYO1A_ENST00000300119.3_Silent_p.L174L|MYO1A_ENST00000544473.1_Silent_p.L12L	NM_001256041.1	NP_001242970.1	Q9UBC5	MYO1A_HUMAN	myosin IA	174	Myosin motor.				microvillus assembly (GO:0030033)|sensory perception of sound (GO:0007605)|vesicle localization (GO:0051648)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|brush border (GO:0005903)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(7)|urinary_tract(3)	50						TGACACCACCGAGGGGGGATC	0.498													G|||	6	0.00119808	0	0	5008	,	,		20056	0		0	False		,,,				2504	0.0061				p.L174L		Atlas-SNP	.											.	MYO1A	122	.	0			c.C522T						PASS	.						98	93	94					12																	57440666		2203	4300	6503	SO:0001819	synonymous_variant	4640	exon7			ACCACCGAGGGGG	L29137	CCDS8929.1	12q13-q15	2011-09-27			ENSG00000166866	ENSG00000166866		"Myosins / Myosin superfamily : Class I"	7595	protein-coding gene	gene with protein product		601478		MYHL, DFNA48		8884266, 12736868	Standard	NM_001256041		Approved		uc009zpd.3	Q9UBC5	OTTHUMG00000149899	ENST00000442789.2:c.522C>T	chr12.hg19:g.57440666G>A		168.0	0.0	.		188.0	15.0	.	NM_005379	Q9UQD7	Silent	SNP	ENST00000442789.2	hg19	CCDS8929.1																																																																																			.	.	.	none		0.498	MYO1A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313833.2	NM_005379		A	57440666	G	A	57440666	2	1	164	1	0	0	0	0	0	0	0	1	10075	1045	37	1		1	MYO1A	12	57440666	Silent	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10		57440666	76411229	22	9731											
CFL2	1073	hgsc.bcm.edu	37	chr14	35182529	35182529	+	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	tggcatcgtacaaagcatatCggcaatcattcagaggtagc	13	9	10	9	2	2	1	2	0	0	1	4	1	2	1	0	3	3	5	0	3	5	4			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr14:35182529C>T	ENST00000341223.3	-	2	393	c.242G>A	c.(241-243)cGa>cAa	p.R81Q	CFL2_ENST00000555765.1_Missense_Mutation_p.R64Q|CFL2_ENST00000556161.1_Missense_Mutation_p.R64Q|CFL2_ENST00000298159.6_Missense_Mutation_p.R81Q	NM_001243645.1|NM_021914.7	NP_001230574.1|NP_068733.1	Q9Y281	COF2_HUMAN	cofilin 2 (muscle)	81	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				actin filament depolymerization (GO:0030042)|muscle cell cellular homeostasis (GO:0046716)|positive regulation of actin filament depolymerization (GO:0030836)|regulation of dendritic spine morphogenesis (GO:0061001)|sarcomere organization (GO:0045214)	actin cytoskeleton (GO:0015629)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|nucleus (GO:0005634)				breast(3)|endometrium(2)|lung(3)	8	Breast(36;0.0361)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;6.07e-06)|Lung(238;2.23e-05)|Epithelial(34;0.0387)|all cancers(34;0.0814)	GBM - Glioblastoma multiforme(112;0.0424)		CAAAGCATATCGGCAATCATT	0.378																																					p.R81Q		Atlas-SNP	.											.	CFL2	22	.	0			c.G242A						PASS	.						113	108	109					14																	35182529		2203	4300	6503	SO:0001583	missense	1073	exon2			GCATATCGGCAAT	AF087867	CCDS9649.1, CCDS9650.1, CCDS58311.1	14q13.2	2014-09-17			ENSG00000165410	ENSG00000165410			1875	protein-coding gene	gene with protein product	"nemaline myopathy type 7"	601443				8800436	Standard	NM_138638		Approved	NEM7	uc001wsh.3	Q9Y281	OTTHUMG00000029536	ENST00000341223.3:c.242G>A	chr14.hg19:g.35182529C>T	ENSP00000340635:p.Arg81Gln	131.0	0.0	.		94.0	5.0	.	NM_021914	G3V5P4	Missense_Mutation	SNP	ENST00000341223.3	hg19	CCDS9650.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.521545	0.85600	.	.	ENSG00000165410	ENST00000341223;ENST00000298159;ENST00000555765;ENST00000556161	D;D;D;D	0.84944	-1.92;-1.92;-1.92;-1.92	6.02	6.02	0.97574	Actin-binding, cofilin/tropomyosin type (3);	0.000000	0.85682	D	0.000000	D	0.95351	0.8491	H	0.96805	3.885	0.80722	D	1	D	0.71674	0.998	D	0.66847	0.947	D	0.95938	0.8944	10	0.72032	D	0.01	-0.5517	20.5407	0.99260	0.0:1.0:0.0:0.0	.	81	Q9Y281	COF2_HUMAN	Q	81;81;64;64	ENSP00000340635:R81Q;ENSP00000298159:R81Q;ENSP00000452451:R64Q;ENSP00000452188:R64Q	ENSP00000298159:R81Q	R	-	2	0	CFL2	34252280	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.747000	0.85070	2.865000	0.98341	0.655000	0.94253	CGA	.	.	.	none		0.378	CFL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276639.1	NM_138638		T	35182529	C	T	35182529	3	4	164	1	0	0	0	0	1	0	0	0	3293	884	31	1	270	1	CFL2	14	35182529	Missense_Mutation	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10		35182529	72167011	23	9732											
PRC1	9055	hgsc.bcm.edu	37	chr15	91517424	91517424	+	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	gccgcttgctaggtgttcgaGgagcgctgccatacagcatc	7	9	13	12	3	0	0	0	0	0	0	2	2	0	1	2	2	5	5	2	2	2	4			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr15:91517424G>T	ENST00000361188.5	-	11	2614	c.1403C>A	c.(1402-1404)cCt>cAt	p.P468H	PRC1-AS1_ENST00000556200.1_RNA|PRC1_ENST00000361919.3_Missense_Mutation_p.P468H|PRC1_ENST00000442656.2_Missense_Mutation_p.P427H|PRC1_ENST00000394249.3_Missense_Mutation_p.P468H|PRC1-AS1_ENST00000554388.1_RNA					protein regulator of cytokinesis 1									p.P468R(1)		endometrium(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(3)|prostate(1)|skin(2)	25	Lung NSC(78;0.0987)|all_lung(78;0.175)					AGGTGTTCGAGGAGCGCTGCC	0.498																																					p.P468H		Atlas-SNP	.											PRC1,NS,carcinoma,0,1	PRC1	51	.	1	Substitution - Missense(1)	ovary(1)	c.C1403A						PASS	.						201	170	180					15																	91517424		2198	4298	6496	SO:0001583	missense	9055	exon11			GTTCGAGGAGCGC	AF044588	CCDS32334.1, CCDS45352.1, CCDS45353.1, CCDS45353.2	15q26.1	2013-05-29		2006-07-07	ENSG00000198901	ENSG00000198901			9341	protein-coding gene	gene with protein product	"anaphase spindle elongation 1 homolog (S. cerevisiae)"	603484				9885575	Standard	NM_003981		Approved	ASE1	uc002bqm.4	O43663	OTTHUMG00000171685	ENST00000361188.5:c.1403C>A	chr15.hg19:g.91517424G>T	ENSP00000354679:p.Pro468His	274.0	0.0	.		249.0	21.0	.	NM_199413		Missense_Mutation	SNP	ENST00000361188.5	hg19	CCDS45352.1	.	.	.	.	.	.	.	.	.	.	G	18.91	3.723028	0.68959	.	.	ENSG00000198901	ENST00000394249;ENST00000361919;ENST00000361188;ENST00000555455;ENST00000442656	T;T;T;T	0.37752	1.18;1.18;1.18;1.18	5.37	5.37	0.77165	.	0.293466	0.39146	N	0.001451	T	0.61413	0.2345	M	0.71581	2.175	0.38985	D	0.959022	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.75484	0.976;0.976;0.976;0.986	T	0.63989	-0.6512	10	0.59425	D	0.04	-9.2179	18.9064	0.92464	0.0:0.0:1.0:0.0	.	427;468;438;468	O43663-3;F8W9B5;O43663-2;O43663	.;.;.;PRC1_HUMAN	H	468;468;468;71;427	ENSP00000377793:P468H;ENSP00000354618:P468H;ENSP00000354679:P468H;ENSP00000409549:P427H	ENSP00000354679:P468H	P	-	2	0	PRC1	89318428	1.000000	0.71417	0.781000	0.31783	0.590000	0.36582	6.445000	0.73456	2.788000	0.95919	0.650000	0.86243	CCT	.	.	.	none		0.498	PRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414760.1	NM_003981		T	91517424	G	T	91517424	3	4	164	1	0	0	0	0	1	0	0	0	12456	1000	35	4	479	4	PRC1	15	91517424	Missense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10		91517424	11013968	24	9733											
DCUN1D3	123879	hgsc.bcm.edu	37	chr16	20871250	20871250	+	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	aagccctcaggccctgagctGagtgcacctctcccttcccc	6	8	8	19	0	2	2	1	2	1	0	4	2	3	2	6	1	3	2	6	1	1	1			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr16:20871250G>A	ENST00000324344.4	-	3	1158	c.873C>T	c.(871-873)ctC>ctT	p.L291L	DCUN1D3_ENST00000563934.1_Silent_p.L291L|ERI2_ENST00000564349.1_Intron	NM_173475.2	NP_775746.1	Q8IWE4	DCNL3_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 3	291					negative regulation of cell growth (GO:0030308)|positive regulation of apoptotic process (GO:0043065)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)	perinuclear region of cytoplasm (GO:0048471)				NS(2)|breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(2)	14				GBM - Glioblastoma multiforme(48;0.249)		GCCCTGAGCTGAGTGCACCTC	0.577																																					p.L291L		Atlas-SNP	.											.	DCUN1D3	29	.	0			c.C873T						PASS	.						73	63	66					16																	20871250		2201	4300	6501	SO:0001819	synonymous_variant	123879	exon3			TGAGCTGAGTGCA	BC040442	CCDS10592.1	16p12.3	2013-06-10	2013-06-10		ENSG00000188215	ENSG00000188215			28734	protein-coding gene	gene with protein product			"DCN1, defective in cullin neddylation 1, domain containing 3 (S. cerevisiae)"			15988528	Standard	NM_173475		Approved	MGC48972, FLJ41725, DKFZp686O0290	uc002dhz.3	Q8IWE4	OTTHUMG00000131553	ENST00000324344.4:c.873C>T	chr16.hg19:g.20871250G>A		170.0	0.0	.		212.0	91.0	.	NM_173475	B3KVY4	Silent	SNP	ENST00000324344.4	hg19	CCDS10592.1																																																																																			.	.	.	none		0.577	DCUN1D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254415.2	NM_173475		A	20871250	G	A	20871250	2	1	164	1	0	0	0	0	0	0	0	1	4317	1277	45	2		2	DCUN1D3	16	20871250	Silent	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10		20871250	69483503	25	9734											
CDH8	1006	hgsc.bcm.edu	37	chr16	61687954	61687954	+	Missense_Mutation	SNP	A	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	cgtcttcatcatctttgataAttaatggttcatttttatgc	9	20	5	7	1	5	1	3	1	2	0	5	1	5	1	0	1	1	1	0	1	3	8			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr16:61687954A>C	ENST00000577390.1	-	12	2912	c.1958T>G	c.(1957-1959)aTt>aGt	p.I653S	CDH8_ENST00000299345.6_Missense_Mutation_p.I653S|CDH8_ENST00000577730.1_Missense_Mutation_p.I653S	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	653					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)		ATCTTTGATAATTAATGGTTC	0.388																																					p.I653S		Atlas-SNP	.											.	CDH8	273	.	0			c.T1958G						PASS	.						81	78	79					16																	61687954		2203	4300	6503	SO:0001583	missense	1006	exon12			TTGATAATTAATG	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.1958T>G	chr16.hg19:g.61687954A>C	ENSP00000462701:p.Ile653Ser	145.0	0.0	.		177.0	54.0	.	NM_001796	B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	SNP	ENST00000577390.1	hg19	CCDS10802.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.367372	0.82463	.	.	ENSG00000150394	ENST00000299345	T	0.78246	-1.16	5.7	5.7	0.88788	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	T	0.72558	0.3475	L	0.39566	1.225	0.80722	D	1	B	0.23249	0.082	B	0.29663	0.105	T	0.68573	-0.5373	10	0.38643	T	0.18	.	15.1545	0.72730	1.0:0.0:0.0:0.0	.	653	P55286	CADH8_HUMAN	S	653	ENSP00000299345:I653S	ENSP00000299345:I653S	I	-	2	0	CDH8	60245455	1.000000	0.71417	0.984000	0.44739	0.916000	0.54674	9.251000	0.95483	2.164000	0.68074	0.533000	0.62120	ATT	.	.	.	none		0.388	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		C	61687954	A	C	61687954	3	2	164	1	0	0	0	0	1	0	0	0	3118	101	4	5	445	5	CDH8	16	61687954	Missense_Mutation	SNP	A	TCGA-F9-A4JJ-01A-11D-A25F-10	40816704	61687954	28666799	26	9735											
RPL13	6137	hgsc.bcm.edu	37	chr16	89627425	89627425	+	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	acttccacaaggactggcagCggcgcgtggccacgtggttc	7	7	14	13	4	0	0	0	0	0	0	2	1	1	1	2	5	1	2	2	5	1	2			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr16:89627425C>T	ENST00000393099.3	+	1	307	c.58C>T	c.(58-60)Cgg>Tgg	p.R20W	RPL13_ENST00000452368.3_Missense_Mutation_p.R20W|SNORD68_ENST00000363214.1_RNA|RPL13_ENST00000567815.1_Missense_Mutation_p.R20W|RPL13_ENST00000311528.5_Missense_Mutation_p.R20W	NM_033251.2	NP_150254.1	P26373	RL13_HUMAN	ribosomal protein L13	20					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)		GGACTGGCAGCGGCGCGTGGC	0.711																																					p.R20W		Atlas-SNP	.											.	RPL13	11	.	0			c.C58T						PASS	.						14	15	15					16																	89627425		2144	4198	6342	SO:0001583	missense	6137	exon2			TGGCAGCGGCGCG	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.58C>T	chr16.hg19:g.89627425C>T	ENSP00000376811:p.Arg20Trp	48.0	0.0	.		86.0	41.0	.	NM_001243131	B4DLX3|F5H1S2|Q3KQT8|Q567Q8|Q9BPX0	Missense_Mutation	SNP	ENST00000393099.3	hg19	CCDS10979.1	.	.	.	.	.	.	.	.	.	.	c	31	5.083913	0.94050	.	.	ENSG00000167526	ENST00000311528;ENST00000452368;ENST00000393099	T;T;T	0.32753	1.44;1.44;1.44	4.7	2.4	0.29515	.	0.117520	0.53938	U	0.000041	T	0.54679	0.1873	M	0.90705	3.14	0.48511	D	0.999666	D;D;D	0.61697	0.987;0.99;0.99	D;P;P	0.63793	0.918;0.851;0.851	T	0.60105	-0.7328	10	0.87932	D	0	-9.0218	7.8657	0.29535	0.2806:0.6293:0.0:0.0901	.	20;20;20	F5H1S2;A8K4C8;P26373	.;.;RL13_HUMAN	W	20	ENSP00000307889:R20W;ENSP00000438959:R20W;ENSP00000376811:R20W	ENSP00000307889:R20W	R	+	1	2	RPL13	88154926	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	4.902000	0.63266	1.107000	0.41642	0.563000	0.77884	CGG	.	.	.	none		0.711	RPL13-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258294.2	NM_000977		T	89627425	C	T	89627425	3	4	164	1	0	0	0	0	1	0	0	0	13572	759	27	1	60	1	RPL13	16	89627425	Missense_Mutation	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10	27939471	89627425	727328	27	9736											
GPR172B	55065	hgsc.bcm.edu	37	chr17	4937586	4937586	+	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	ggggccagctgcctccacagGgtcaccaccagcagacccag	9	3	12	17	0	1	1	1	0	0	1	2	1	2	1	6	3	3	2	6	3	0	0			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr17:4937586G>T	ENST00000424747.1	-	3	910	c.198C>A	c.(196-198)acC>acA	p.T66T	SLC52A1_ENST00000512825.2_Silent_p.T66T|SLC52A1_ENST00000254853.5_Silent_p.T66T	NM_001104577.1	NP_001098047.1	Q9NWF4	S52A1_HUMAN	solute carrier family 52 (riboflavin transporter), member 1	66					riboflavin transport (GO:0032218)	integral component of plasma membrane (GO:0005887)	riboflavin transporter activity (GO:0032217)|virus receptor activity (GO:0001618)										GCCTCCACAGGGTCACCACCA	0.642																																					p.T66T		Atlas-SNP	.											.	.	.	.	0			c.C198A						PASS	.						49	50	50					17																	4937586		2203	4300	6503	SO:0001819	synonymous_variant	55065	exon3			CCACAGGGTCACC	AY070775	CCDS11066.1	17p13.3	2013-07-17	2013-07-17	2012-02-29	ENSG00000132517	ENSG00000132517		"Solute carriers"	30225	protein-coding gene	gene with protein product	"riboflavin transporter 1"	607883	"G protein-coupled receptor 172B"	GPR172B		12740431, 18632736	Standard	NM_001104577		Approved	FLJ10060, GPCR42, PAR2, hRFT1, RFVT1	uc002gao.4	Q9NWF4	OTTHUMG00000099448	ENST00000424747.1:c.198C>A	chr17.hg19:g.4937586G>T		36.0	0.0	.		79.0	4.0	.	NM_017986	B5MEV1|B5MEV2|Q6P9E0|Q86UT0	Silent	SNP	ENST00000424747.1	hg19	CCDS11066.1																																																																																			.	.	.	none		0.642	SLC52A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216913.1	NM_017986		T	4937586	G	T	4937586	2	4	164	1	0	0	0	0	0	0	0	1	6677	1219	43	4		4	GPR172B	17	4937586	Silent	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10		4937586	76257624	28	9737											
ITGA3	3675	hgsc.bcm.edu	37	chr17	48148253	48148253	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggagtgggacttatctgagtAtagttacaaggacccagagg	12	9	14	6	0	1	2	0	1	1	1	1	5	1	5	1	4	1	2	1	4	5	4			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr17:48148253A>G	ENST00000320031.8	+	5	1040	c.710A>G	c.(709-711)tAt>tGt	p.Y237C	ITGA3_ENST00000544892.1_Missense_Mutation_p.Y12C|ITGA3_ENST00000007722.7_Missense_Mutation_p.Y237C	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)	237					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						TTATCTGAGTATAGTTACAAG	0.502																																					p.Y237C		Atlas-SNP	.											.	ITGA3	128	.	0			c.A710G						PASS	.						206	211	209					17																	48148253		2203	4300	6503	SO:0001583	missense	3675	exon5			CTGAGTATAGTTA	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.710A>G	chr17.hg19:g.48148253A>G	ENSP00000315190:p.Tyr237Cys	236.0	0.0	.		237.0	94.0	.	NM_005501	A7E246|B7ZM80|B9EGQ1|D3DTX4|D3DTX5	Missense_Mutation	SNP	ENST00000320031.8	hg19	CCDS11558.1	.	.	.	.	.	.	.	.	.	.	A	15.96	2.986557	0.53934	.	.	ENSG00000005884	ENST00000544892;ENST00000007722;ENST00000538917;ENST00000320031	T;T;T	0.57107	0.42;0.42;0.42	5.69	3.33	0.38152	.	0.874333	0.10328	N	0.687966	T	0.52108	0.1714	L	0.54323	1.7	0.27793	N	0.942745	D;P	0.56968	0.978;0.898	P;B	0.48901	0.594;0.379	T	0.43442	-0.9391	10	0.46703	T	0.11	.	5.9462	0.19219	0.6614:0.173:0.0:0.1656	.	237;237	P26006-1;P26006	.;ITA3_HUMAN	C	12;237;223;237	ENSP00000446133:Y12C;ENSP00000007722:Y237C;ENSP00000315190:Y237C	ENSP00000007722:Y237C	Y	+	2	0	ITGA3	45503252	0.979000	0.34478	0.526000	0.27913	0.985000	0.73830	1.665000	0.37449	0.961000	0.38030	0.533000	0.62120	TAT	.	.	.	none		0.502	ITGA3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000366298.1	NM_005501		G	48148253	A	G	48148253	3	3	164	1	0	0	0	0	1	0	0	0	7884	449	16	3	728	3	ITGA3	17	48148253	Missense_Mutation	SNP	A	TCGA-F9-A4JJ-01A-11D-A25F-10	43210667	48148253	33046957	29	9738											
TCEB3B	51224	hgsc.bcm.edu	37	chr18	44560193	44560193	+	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	tttgcctgggaggtcatggaGtcagaatccgaaagcggatc	10	9	14	8	2	2	1	2	0	0	1	4	5	3	4	2	4	2	0	2	4	2	1			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr18:44560193G>A	ENST00000332567.4	-	1	1795	c.1443C>T	c.(1441-1443)gaC>gaT	p.D481D	KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000356157.7_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	481					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						AGGTCATGGAGTCAGAATCCG	0.582																																					p.D481D		Atlas-SNP	.											.	TCEB3B	141	.	0			c.C1443T						PASS	.						60	66	64					18																	44560193		2203	4300	6503	SO:0001819	synonymous_variant	51224	exon1			CATGGAGTCAGAA	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.1443C>T	chr18.hg19:g.44560193G>A		197.0	0.0	.		153.0	63.0	.	NM_016427	Q9P2V9	Silent	SNP	ENST00000332567.4	hg19	CCDS11932.1																																																																																			.	.	.	none		0.582	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427		A	44560193	G	A	44560193	2	1	164	1	0	0	0	0	0	0	0	1	15694	1020	36	2		2	TCEB3B	18	44560193	Silent	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10		44560193	33517055	30	9739											
ZNF709	163051	hgsc.bcm.edu	37	chr19	12574997	12574997	+	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	gtttcactccagtgtgagtcCtttcatgcattcgaacagaa	10	13	8	10	1	2	2	2	1	0	1	5	3	4	2	2	0	2	2	2	0	2	3			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr19:12574997C>T	ENST00000397732.3	-	4	1910	c.1739G>A	c.(1738-1740)aGg>aAg	p.R580K	ZNF709_ENST00000428311.1_Missense_Mutation_p.R580K|CTD-3105H18.18_ENST00000598753.1_Intron	NM_152601.3	NP_689814.1	Q8N972	ZN709_HUMAN	zinc finger protein 709	580					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|upper_aerodigestive_tract(3)	6						AGTGTGAGTCCTTTCATGCAT	0.423																																					p.R580K	GBM(33;565 669 12371 29134 51667)	Atlas-SNP	.											.	ZNF709	80	.	0			c.G1739A						PASS	.						139	147	144					19																	12574997		2202	4300	6502	SO:0001583	missense	163051	exon4			TGAGTCCTTTCAT	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.1739G>A	chr19.hg19:g.12574997C>T	ENSP00000380840:p.Arg580Lys	176.0	0.0	.		199.0	57.0	.	NM_152601	A8K4E6	Missense_Mutation	SNP	ENST00000397732.3	hg19	CCDS42504.1	.	.	.	.	.	.	.	.	.	.	C	18.59	3.656147	0.67586	.	.	ENSG00000242852;ENSG00000196826	ENST00000397732;ENST00000428311	T;T	0.18338	2.22;2.22	2.89	1.85	0.25348	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17577	0.0422	L	0.45581	1.43	0.22127	N	0.99935	B	0.27498	0.18	B	0.33121	0.158	T	0.24190	-1.0167	9	0.48119	T	0.1	.	9.5077	0.39058	0.0:0.8844:0.0:0.1156	.	580	Q8N972	ZN709_HUMAN	K	580	ENSP00000380840:R580K;ENSP00000404127:R580K	ENSP00000404127:R580K	R	-	2	0	ZNF709;CTD-2192J16.17	12435997	0.000000	0.05858	0.050000	0.19076	0.605000	0.37080	-0.136000	0.10405	0.797000	0.33971	0.655000	0.94253	AGG	.	.	.	none		0.423	ZNF709-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344088.1	NM_152601		T	12574997	C	T	12574997	3	4	164	1	0	0	0	0	1	0	0	0	18125	681	24	2	190	2	ZNF709	19	12574997	Missense_Mutation	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10		12574997	46553986	31	9740											
FPR3	2359	hgsc.bcm.edu	37	chr19	52327625	52327625	+	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	ctgatcctccacttcattatTggcttcagcgtgcctatgtc	6	15	7	13	1	2	1	2	1	0	0	5	1	4	1	3	1	2	1	3	1	2	5			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr19:52327625T>A	ENST00000339223.4	+	2	803	c.624T>A	c.(622-624)atT>atA	p.I208I	FPR3_ENST00000595991.1_Silent_p.I208I	NM_002030.3	NP_002021.3	P25089	FPR3_HUMAN	formyl peptide receptor 3	208					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						ACTTCATTATTGGCTTCAGCG	0.458																																					p.I208I		Atlas-SNP	.											.	FPR3	66	.	0			c.T624A						PASS	.						146	118	128					19																	52327625		2203	4300	6503	SO:0001819	synonymous_variant	2359	exon2			CATTATTGGCTTC		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.624T>A	chr19.hg19:g.52327625T>A		242.0	0.0	.		155.0	67.0	.	NM_002030		Silent	SNP	ENST00000339223.4	hg19	CCDS12841.1																																																																																			.	.	.	none		0.458	FPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466914.1	NM_002030		A	52327625	T	A	52327625	2	1	164	1	0	0	0	0	0	0	0	1	6047	1800	63	5		5	FPR3	19	52327625	Silent	SNP	T	TCGA-F9-A4JJ-01A-11D-A25F-10	39752628	52327625	6801358	32	9741											
KIAA1755	85449	hgsc.bcm.edu	37	chr20	36870194	36870194	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgatgcagacagactgctcCtcctggggctccacttggag	8	9	12	12	0	0	3	0	1	0	2	3	4	3	4	3	3	2	3	3	3	0	1			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr20:36870194C>T	ENST00000279024.4	-	3	610	c.339G>A	c.(337-339)gaG>gaA	p.E113E		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	113										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)				CAGACTGCTCCTCCTGGGGCT	0.557																																					p.E113E		Atlas-SNP	.											.	KIAA1755	145	.	0			c.G339A						PASS	.						92	90	90					20																	36870194		2203	4300	6503	SO:0001819	synonymous_variant	85449	exon3			CTGCTCCTCCTGG	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.339G>A	chr20.hg19:g.36870194C>T		129.0	0.0	.		184.0	36.0	.	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	hg19	CCDS33467.1																																																																																			.	.	.	none		0.557	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864		T	36870194	C	T	36870194	2	4	164	1	0	0	0	0	0	0	0	1	8264	680	24	2		2	KIAA1755	20	36870194	Silent	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10		36870194	26155326	33	9742											
RBM11	54033	hgsc.bcm.edu	37	chr21	15599303	15599303	+	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	cctcactgaatcatgttccaGatcttgaggctggacccagc	9	10	9	13	0	3	3	2	2	1	1	4	4	4	4	3	2	1	2	3	2	1	2			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chr21:15599303G>T	ENST00000400577.3	+	5	544	c.535G>T	c.(535-537)Gat>Tat	p.D179Y	RBM11_ENST00000468643.1_3'UTR	NM_144770.3	NP_658983.3	P57052	RBM11_HUMAN	RNA binding motif protein 11	179					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)		TCATGTTCCAGATCTTGAGGC	0.458																																					p.D179Y		Atlas-SNP	.											.	RBM11	41	.	0			c.G535T						PASS	.						199	186	190					21																	15599303		1928	4131	6059	SO:0001583	missense	54033	exon5			GTTCCAGATCTTG	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.535G>T	chr21.hg19:g.15599303G>T	ENSP00000383421:p.Asp179Tyr	371.0	1.0	.		364.0	149.0	.	NM_144770	Q6YNC2|Q8NBA1|Q8NFF6	Missense_Mutation	SNP	ENST00000400577.3	hg19	CCDS46635.1	.	.	.	.	.	.	.	.	.	.	G	8.231	0.804684	0.16467	.	.	ENSG00000185272	ENST00000400577	T	0.08546	3.08	2.74	1.85	0.25348	.	0.523863	0.19918	N	0.103153	T	0.08758	0.0217	L	0.51422	1.61	0.09310	N	1	P	0.40144	0.704	B	0.41571	0.36	T	0.16689	-1.0394	10	0.62326	D	0.03	-7.9775	4.814	0.13358	0.2974:0.0:0.7026:0.0	.	179	P57052	RBM11_HUMAN	Y	179	ENSP00000383421:D179Y	ENSP00000383421:D179Y	D	+	1	0	RBM11	14521174	0.201000	0.23410	0.002000	0.10522	0.803000	0.45373	0.649000	0.24843	0.712000	0.32039	0.430000	0.28490	GAT	.	.	.	none		0.458	RBM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157818.1	NM_144770		T	15599303	G	T	15599303	3	4	164	1	0	0	0	0	1	0	0	0	13125	942	33	4	553	4	RBM11	21	15599303	Missense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10		15599303	32530592	34	9743											
GRIPAP1	56850	hgsc.bcm.edu	37	chrX	48840222	48840222	+	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	taattcctgggtcaactgctCcttctcctgccctatttctt	5	17	5	14	0	3	0	1	0	2	0	6	0	5	0	4	1	3	1	4	1	3	6			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chrX:48840222C>T	ENST00000376441.1	-	15	1271	c.1237G>A	c.(1237-1239)Gag>Aag	p.E413K	GRIPAP1_ENST00000376425.3_Missense_Mutation_p.E382K|GRIPAP1_ENST00000376423.4_Missense_Mutation_p.E360K|GRIPAP1_ENST00000376444.3_Missense_Mutation_p.E368K|GRIPAP1_ENST00000473581.1_5'UTR	NM_020137.3	NP_064522.3	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1	413						blood microparticle (GO:0072562)|endosome (GO:0005768)				breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)	10						GTCAACTGCTCCTTCTCCTGC	0.507																																					p.E413K		Atlas-SNP	.											.	GRIPAP1	128	.	0			c.G1237A						PASS	.						268	196	221					X																	48840222		2203	4300	6503	SO:0001583	missense	56850	exon15			ACTGCTCCTTCTC	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.1237G>A	chrX.hg19:g.48840222C>T	ENSP00000365624:p.Glu413Lys	232.0	0.0	.		245.0	17.0	.	NM_020137	A6NL78|Q3MJ75|Q4V327|Q4V330|Q5HYG1|Q6N046|Q96DH8|Q9NQ43|Q9ULQ3	Missense_Mutation	SNP	ENST00000376441.1	hg19	CCDS35248.1	.	.	.	.	.	.	.	.	.	.	-	17.86	3.491722	0.64074	.	.	ENSG00000068400	ENST00000376425;ENST00000376444;ENST00000376441;ENST00000537291;ENST00000376423	T;T;T;T	0.24151	1.87;1.87;1.87;1.87	4.34	4.34	0.51931	.	0.072191	0.53938	D	0.000057	T	0.40670	0.1126	L	0.50333	1.59	0.40778	D	0.983142	D;D;P	0.65815	0.995;0.982;0.873	P;P;B	0.59487	0.858;0.831;0.385	T	0.30909	-0.9962	10	0.46703	T	0.11	-19.9581	15.2526	0.73559	0.0:1.0:0.0:0.0	.	360;303;413	Q4V328-2;Q4V328-3;Q4V328	.;.;GRAP1_HUMAN	K	382;368;413;382;360	ENSP00000365608:E382K;ENSP00000365627:E368K;ENSP00000365624:E413K;ENSP00000365606:E360K	ENSP00000365606:E360K	E	-	1	0	GRIPAP1	48725166	1.000000	0.71417	0.996000	0.52242	0.011000	0.07611	5.495000	0.66912	1.925000	0.55765	0.522000	0.50473	GAG	.	.	.	none		0.507	GRIPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080970.2	NM_207672		T	48840222	C	T	48840222	3	4	164	1	0	0	0	0	1	0	0	0	6796	864	30	2	1390	2	GRIPAP1	23	48840222	Missense_Mutation	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10		48840222	106430338	35	9744											
PCDH11X	27328	hgsc.bcm.edu	37	chrX	91133625	91133625	+	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	gcactgaagcaccagtgaccCcaaatactgagatagctgat	14	7	9	11	0	0	4	0	4	0	1	0	5	0	4	3	0	3	3	3	0	4	2			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chrX:91133625C>A	ENST00000373094.1	+	2	3231	c.2386C>A	c.(2386-2388)Cca>Aca	p.P796T	PCDH11X_ENST00000361724.1_Missense_Mutation_p.P796T|PCDH11X_ENST00000373097.1_Missense_Mutation_p.P796T|PCDH11X_ENST00000298274.8_Missense_Mutation_p.P796T|PCDH11X_ENST00000373088.1_Missense_Mutation_p.P796T|PCDH11X_ENST00000504220.2_Missense_Mutation_p.P796T|PCDH11X_ENST00000361655.2_Missense_Mutation_p.P796T|PCDH11X_ENST00000395337.2_Missense_Mutation_p.P796T|PCDH11X_ENST00000406881.1_Missense_Mutation_p.P796T	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	796					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						ACCAGTGACCCCAAATACTGA	0.438																																					p.P796T	NSCLC(38;925 1092 2571 38200 45895)	Atlas-SNP	.											.	PCDH11X	714	.	0			c.C2386A						PASS	.						145	118	127					X																	91133625		2203	4300	6503	SO:0001583	missense	27328	exon2			GTGACCCCAAATA	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.2386C>A	chrX.hg19:g.91133625C>A	ENSP00000362186:p.Pro796Thr	691.0	1.0	.		497.0	213.0	.	NM_001168363	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Missense_Mutation	SNP	ENST00000373094.1	hg19	CCDS14461.1	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.399277	0.00198	.	.	ENSG00000102290	ENST00000395337;ENST00000373094;ENST00000373097;ENST00000361724;ENST00000373088;ENST00000504220;ENST00000361655;ENST00000406881;ENST00000356934;ENST00000298274	T;T;T;T;T;T;T;T;T	0.27890	1.64;1.64;1.64;1.64;1.64;1.64;1.64;1.64;1.64	5.15	2.3	0.28687	Protocadherin (1);	0.414782	0.27245	N	0.020252	T	0.25382	0.0617	L	0.36672	1.1	0.09310	N	1	B;B;B;B;B;B;B;B	0.22909	0.077;0.017;0.035;0.035;0.035;0.044;0.077;0.032	B;B;B;B;B;B;B;B	0.25987	0.062;0.026;0.039;0.039;0.039;0.065;0.062;0.062	T	0.14559	-1.0468	10	0.22109	T	0.4	.	15.2794	0.73770	0.0:0.4515:0.5485:0.0	.	796;796;796;796;796;796;796;796	Q9BZA7-6;Q9BZA7-5;Q9BZA7-4;Q9BZA7-8;Q9BZA7-3;Q9BZA7;Q9BZA7-7;Q9BZA7-2	.;.;.;.;.;PC11X_HUMAN;.;.	T	796	ENSP00000378746:P796T;ENSP00000362186:P796T;ENSP00000362189:P796T;ENSP00000355040:P796T;ENSP00000362180:P796T;ENSP00000423762:P796T;ENSP00000355105:P796T;ENSP00000384758:P796T;ENSP00000298274:P796T	ENSP00000298274:P796T	P	+	1	0	PCDH11X	91020281	0.999000	0.42202	0.001000	0.08648	0.003000	0.03518	1.394000	0.34509	0.053000	0.16036	-0.226000	0.12346	CCA	.	.	.	none		0.438	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969		A	91133625	C	A	91133625	3	1	164	1	0	0	0	0	1	0	0	0	11515	623	22	4	2392	4	PCDH11X	23	91133625	Missense_Mutation	SNP	C	TCGA-F9-A4JJ-01A-11D-A25F-10	42293403	91133625	64136935	36	9745											
LAMP2	3920	hgsc.bcm.edu	37	chrX	119581842	119581842	+	Missense_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	cacagtggtgtgtatggtggGtgccactgttgaagttttgt	6	15	15	5	0	0	1	0	1	0	0	0	1	0	1	1	3	1	3	1	3	2	4			TCGA-F9-A4JJ-01A-11D-A25F-10	TCGA-F9-A4JJ-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e4d764c-5196-4566-ae92-e291608bcd73	05c628cd-15ec-47b2-851d-fdcd131c5172	g.chrX:119581842G>A	ENST00000200639.4	-	5	731	c.595C>T	c.(595-597)Ccc>Tcc	p.P199S	LAMP2_ENST00000434600.2_Missense_Mutation_p.P199S|LAMP2_ENST00000538785.1_Missense_Mutation_p.P88S|LAMP2_ENST00000540603.1_Missense_Mutation_p.P152S|LAMP2_ENST00000371335.4_Missense_Mutation_p.P199S			P13473	LAMP2_HUMAN	lysosomal-associated membrane protein 2	199	Hinge.				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						TGTATGGTGGGTGCCACTGTT	0.408																																					p.P199S		Atlas-SNP	.											.	LAMP2	101	.	0			c.C595T						PASS	.						229	204	212					X																	119581842		2203	4300	6503	SO:0001583	missense	3920	exon5			TGGTGGGTGCCAC	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.595C>T	chrX.hg19:g.119581842G>A	ENSP00000200639:p.Pro199Ser	132.0	0.0	.		125.0	9.0	.	NM_013995	A8K4X5|D3DTF0|Q16641|Q6Q3G8|Q96J30|Q99534|Q9UD93	Missense_Mutation	SNP	ENST00000200639.4	hg19	CCDS14599.1	.	.	.	.	.	.	.	.	.	.	G	14.73	2.623881	0.46840	.	.	ENSG00000005893	ENST00000434600;ENST00000538785;ENST00000200639;ENST00000371335;ENST00000540603	T;T;T;T;T	0.66995	-0.15;0.23;-0.24;-0.13;-0.13	5.98	3.11	0.35812	.	0.053375	0.85682	D	0.000000	T	0.81823	0.4904	M	0.88704	2.975	0.19775	N	0.99996	D;D;D;D;D	0.76494	0.997;0.995;0.996;0.999;0.995	D;D;D;D;D	0.73708	0.965;0.965;0.941;0.981;0.965	T	0.72802	-0.4183	10	0.72032	D	0.01	-7.1395	10.4302	0.44403	0.0:0.1116:0.5665:0.3219	.	152;88;199;199;199	B4E2S7;B7Z2R9;P13473-2;P13473;Q6Q3G8	.;.;.;LAMP2_HUMAN;.	S	199;88;199;199;152	ENSP00000408411:P199S;ENSP00000440506:P88S;ENSP00000200639:P199S;ENSP00000360386:P199S;ENSP00000440479:P152S	ENSP00000200639:P199S	P	-	1	0	LAMP2	119465870	0.975000	0.34042	0.079000	0.20413	0.014000	0.08584	1.620000	0.36976	1.244000	0.43870	0.600000	0.82982	CCC	.	.	.	none		0.408	LAMP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058099.1			A	119581842	G	A	119581842	3	1	164	1	0	0	0	0	1	0	0	0	8625	1261	44	2	948	2	LAMP2	23	119581842	Missense_Mutation	SNP	G	TCGA-F9-A4JJ-01A-11D-A25F-10	28448217	119581842	35688718	37	9746											
TTN	7273	hgsc.bcm.edu	37	chr2	179612896	179612896	+	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	tctcagaaagatcagtttctTctatatctgcagatgaggtt	11	15	8	7	0	5	4	2	1	4	3	6	4	5	4	0	1	1	3	0	1	3	5			TCGA-F9-A7Q0-01A-11D-A35Z-10	TCGA-F9-A7Q0-10B-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8a7f344-08bd-4b20-bbdd-94915425f00f	dfc4913f-381a-4897-828e-6f8666d652ef	g.chr2:179612896T>C	ENST00000591111.1	-	45	10585				TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000360870.5_Missense_Mutation_p.E4744G|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000589042.1_Intron|TTN_ENST00000342175.6_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)			ATCAGTTTCTTCTATATCTGC	0.363																																					p.E4744G		Atlas-SNP	.											.	TTN	18412	.	0			c.A14231G						PASS	.						65	66	66					2																	179612896		2201	4297	6498	SO:0001627	intron_variant	7273	exon46			GTTTCTTCTATAT	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+4954A>G	chr2.hg19:g.179612896T>C		141.0	0.0	.		98.0	39.0	.	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	10.89	1.478131	0.26511	.	.	ENSG00000155657	ENST00000360870;ENST00000306136	T	0.57107	0.42	5.54	-2.93	0.05598	.	.	.	.	.	T	0.23171	0.0560	N	0.00926	-1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22765	-1.0207	9	0.66056	D	0.02	.	13.0978	0.59202	0.0:0.2102:0.0:0.7898	.	4744	Q8WZ42-6	.	G	4744;58	ENSP00000354117:E4744G	ENSP00000304714:E58G	E	-	2	0	TTN	179321141	0.004000	0.15560	0.000000	0.03702	0.008000	0.06430	0.313000	0.19415	-0.565000	0.06061	-0.248000	0.11899	GAA	.	.	.	none		0.363	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179612896	T	C	179612896	1	2	165	0	1	0	0	0	0	0	0	0	16747	1783	62	3		3	TTN	2	179612896	Intron	SNP	T	TCGA-F9-A7Q0-01A-11D-A35Z-10		179612896	63586477	1	9747											
QARS	5859	hgsc.bcm.edu	37	chr3	49137278	49137278	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgtgtagtcgtaggtgggaTagatgcacctgtggggcata	8	11	17	5	1	0	1	0	0	0	1	1	2	0	2	1	4	1	4	1	4	4	4	rs143462532		TCGA-F9-A7Q0-01A-11D-A35Z-10	TCGA-F9-A7Q0-10B-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8a7f344-08bd-4b20-bbdd-94915425f00f	dfc4913f-381a-4897-828e-6f8666d652ef	g.chr3:49137278T>C	ENST00000306125.6	-	15	1641	c.1304A>G	c.(1303-1305)tAt>tGt	p.Y435C	QARS_ENST00000414533.1_Missense_Mutation_p.Y424C|QARS_ENST00000470225.1_5'Flank			P47897	SYQ_HUMAN	glutaminyl-tRNA synthetase	435					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)	GTAGGTGGGATAGATGCACCT	0.627																																					p.Y435C		Atlas-SNP	.											.	QARS	55	.	0			c.A1304G						PASS	.	T	CYS/TYR	0,4406		0,0,2203	174	160	165		1304	5.2	1	3	dbSNP_134	165	1,8599	1.2+/-3.3	0,1,4299	no	missense	QARS	NM_005051.1	194	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	probably-damaging	435/776	49137278	1,13005	2203	4300	6503	SO:0001583	missense	5859	exon15			GTGGGATAGATGC	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.1304A>G	chr3.hg19:g.49137278T>C	ENSP00000307567:p.Tyr435Cys	77.0	0.0	.		63.0	22.0	.	NM_005051	B4DWJ2	Missense_Mutation	SNP	ENST00000306125.6	hg19	CCDS2788.1	.	.	.	.	.	.	.	.	.	.	T	18.65	3.669713	0.67814	0.0	1.16E-4	ENSG00000172053	ENST00000306125;ENST00000414533	T;T	0.26067	1.76;1.76	5.17	5.17	0.71159	Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.70395	0.3219	H	0.99565	4.63	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.84542	0.0639	10	0.87932	D	0	-16.4213	15.0382	0.71767	0.0:0.0:0.0:1.0	.	424;435	B4DWJ2;P47897	.;SYQ_HUMAN	C	435;424	ENSP00000307567:Y435C;ENSP00000390015:Y424C	ENSP00000307567:Y435C	Y	-	2	0	QARS	49112282	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.593000	0.82686	1.948000	0.56530	0.533000	0.62120	TAT	.	T|1.000;C|0.000	0.000	weak		0.627	QARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345689.2	NM_005051		C	49137278	T	C	49137278	3	2	165	1	0	0	0	0	1	0	0	0	12884	1406	49	3	1063	3	QARS	3	49137278	Missense_Mutation	SNP	T	TCGA-F9-A7Q0-01A-11D-A35Z-10		49137278	148885152	2	9748											
CLDN11	5010	hgsc.bcm.edu	37	chr3	170150353	170150353	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatctggttccctgtgtgcGcccaccgtgagaccaccatc	6	9	9	17	2	1	1	0	1	1	1	3	2	2	1	6	1	1	1	6	1	0	1	rs549752354		TCGA-F9-A7Q0-01A-11D-A35Z-10	TCGA-F9-A7Q0-10B-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8a7f344-08bd-4b20-bbdd-94915425f00f	dfc4913f-381a-4897-828e-6f8666d652ef	g.chr3:170150353G>A	ENST00000064724.3	+	3	635	c.433G>A	c.(433-435)Gcc>Acc	p.A145T	CLDN11_ENST00000489485.1_3'UTR|CLDN11_ENST00000486975.1_Intron|CLDN11_ENST00000451576.1_Intron	NM_005602.5	NP_005593.2	O75508	CLD11_HUMAN	claudin 11	145					axon ensheathment (GO:0008366)|calcium-independent cell-cell adhesion (GO:0016338)|spermatogenesis (GO:0007283)	basal part of cell (GO:0045178)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)	p.A145T(1)		central_nervous_system(2)|endometrium(2)|large_intestine(1)|liver(2)|lung(3)|ovary(2)	12	all_cancers(22;5.62e-23)|all_epithelial(15;7.54e-28)|all_lung(20;2.51e-17)|Lung NSC(18;1.02e-16)|Ovarian(172;0.000567)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			CCCTGTGTGCGCCCACCGTGA	0.607													G|||	1	0.000199681	8e-04	0	5008	,	,		17627	0		0	False		,,,				2504	0				p.A145T		Atlas-SNP	.											CLDN11,NS,carcinoma,0,1	CLDN11	28	.	1	Substitution - Missense(1)	lung(1)	c.G433A						PASS	.						164	147	153					3																	170150353		2203	4300	6503	SO:0001583	missense	5010	exon3			GTGTGCGCCCACC	AF068863	CCDS3213.1	3q26.2-q26.3	2008-08-01	2008-08-01		ENSG00000013297	ENSG00000013297		"Claudins"	8514	protein-coding gene	gene with protein product		601326	"oligodendrocyte transmembrane protein"	OTM		8661061, 8797478	Standard	NM_005602		Approved	OSP	uc003fgx.3	O75508	OTTHUMG00000158940	ENST00000064724.3:c.433G>A	chr3.hg19:g.170150353G>A	ENSP00000064724:p.Ala145Thr	106.0	0.0	.		88.0	36.0	.	NM_005602	B2R7C1|D3DNQ5|Q5U0P3	Missense_Mutation	SNP	ENST00000064724.3	hg19	CCDS3213.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.146380	0.77888	.	.	ENSG00000013297	ENST00000064724	D	0.88586	-2.4	5.74	5.74	0.90152	.	0.051247	0.85682	D	0.000000	T	0.80210	0.4581	L	0.31157	0.91	0.80722	D	1	P	0.41214	0.742	B	0.31191	0.125	T	0.80852	-0.1197	10	0.39692	T	0.17	.	13.1577	0.59527	0.0728:0.0:0.9272:0.0	.	145	O75508	CLD11_HUMAN	T	145	ENSP00000064724:A145T	ENSP00000064724:A145T	A	+	1	0	CLDN11	171633047	1.000000	0.71417	0.998000	0.56505	0.942000	0.58702	5.137000	0.64789	2.723000	0.93209	0.655000	0.94253	GCC	.	.	.	none		0.607	CLDN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352403.1	NM_005602		A	170150353	G	A	170150353	3	1	165	1	0	0	0	0	1	0	0	0	3475	1087	38	1	443	1	CLDN11	3	170150353	Missense_Mutation	SNP	G	TCGA-F9-A7Q0-01A-11D-A35Z-10	121013075	170150353	27872077	3	9749											
PCDHB2	56133	hgsc.bcm.edu	37	chr5	140476411	140476411	+	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	ctgctgctcccggaggcggcAccggcccaggcccaggccga	5	3	15	18	4	0	0	0	0	0	0	1	2	1	1	5	6	2	3	5	6	0	0			TCGA-F9-A7Q0-01A-11D-A35Z-10	TCGA-F9-A7Q0-10B-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8a7f344-08bd-4b20-bbdd-94915425f00f	dfc4913f-381a-4897-828e-6f8666d652ef	g.chr5:140476411A>C	ENST00000194155.4	+	1	2185	c.2037A>C	c.(2035-2037)gcA>gcC	p.A679A		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	679					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A679A(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(22)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGGAGGCGGCACCGGCCCAGG	0.687																																					p.A679A		Atlas-SNP	.											PCDHB2,NS,carcinoma,0,1	PCDHB2	163	.	1	Substitution - coding silent(1)	lung(1)	c.A2037C						PASS	.						65	67	66					5																	140476411		2178	4247	6425	SO:0001819	synonymous_variant	56133	exon1			GGCGGCACCGGCC	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.2037A>C	chr5.hg19:g.140476411A>C		123.0	2.0	.		131.0	7.0	.	NM_018936	Q4KMU1	Silent	SNP	ENST00000194155.4	hg19	CCDS4244.1																																																																																			.	.	.	none		0.687	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936		C	140476411	A	C	140476411	2	2	165	1	0	0	0	0	0	0	0	1	11549	146	6	5		5	PCDHB2	5	140476411	Silent	SNP	A	TCGA-F9-A7Q0-01A-11D-A35Z-10		140476411	40438849	4	9750											
KIF4B	285643	hgsc.bcm.edu	37	chr5	154395607	154395607	+	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	aggtcacagataagcggaaaGagactcagagccatggaaag	17	4	13	7	1	2	3	2	0	0	3	2	6	2	5	1	3	2	0	1	3	3	1	rs267600506		TCGA-F9-A7Q0-01A-11D-A35Z-10	TCGA-F9-A7Q0-10B-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8a7f344-08bd-4b20-bbdd-94915425f00f	dfc4913f-381a-4897-828e-6f8666d652ef	g.chr5:154395607G>T	ENST00000435029.4	+	1	2348	c.2188G>T	c.(2188-2190)Gag>Tag	p.E730*		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	730	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)			TAAGCGGAAAGAGACTCAGAG	0.493																																					p.E730X		Atlas-SNP	.											.	KIF4B	307	.	0			c.G2188T						PASS	.						96	95	95					5																	154395607		2203	4300	6503	SO:0001587	stop_gained	285643	exon1			CGGAAAGAGACTC	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.2188G>T	chr5.hg19:g.154395607G>T	ENSP00000387875:p.Glu730*	628.0	0.0	.		531.0	104.0	.	NM_001099293		Nonsense_Mutation	SNP	ENST00000435029.4	hg19	CCDS47324.1	.	.	.	.	.	.	.	.	.	.	g	21.2	4.119569	0.77323	.	.	ENSG00000226650	ENST00000435029	.	.	.	2.54	1.63	0.23807	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	.	9.0371	0.36293	0.0:0.2298:0.7702:0.0	.	.	.	.	X	730	.	ENSP00000387875:E730X	E	+	1	0	KIF4B	154375800	1.000000	0.71417	0.092000	0.20876	0.077000	0.17291	2.376000	0.44292	0.185000	0.20105	-0.257000	0.10917	GAG	.	.	.	none		0.493	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1			T	154395607	G	T	154395607	4	4	165	1	0	0	0	0	0	1	0	0	8311	943	33	4	2190	4	KIF4B	5	154395607	Nonsense_Mutation	SNP	G	TCGA-F9-A7Q0-01A-11D-A35Z-10	13919196	154395607	26519653	5	9751											
WNT2	7472	hgsc.bcm.edu	37	chr7	116937828	116937828	+	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	cttcctccagagataatcgcCcgttttcctgaagtcggcca	8	11	8	14	3	0	2	0	1	0	1	5	3	3	2	5	1	0	1	5	1	2	4			TCGA-F9-A7Q0-01A-11D-A35Z-10	TCGA-F9-A7Q0-10B-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8a7f344-08bd-4b20-bbdd-94915425f00f	dfc4913f-381a-4897-828e-6f8666d652ef	g.chr7:116937828C>T	ENST00000265441.3	-	4	990	c.691G>A	c.(691-693)Ggc>Agc	p.G231S		NM_003391.2	NP_003382.1	P09544	WNT2_HUMAN	wingless-type MMTV integration site family member 2	231					atrial cardiac muscle tissue morphogenesis (GO:0055009)|canonical Wnt signaling pathway (GO:0060070)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|iris morphogenesis (GO:0061072)|labyrinthine layer blood vessel development (GO:0060716)|lens development in camera-type eye (GO:0002088)|lung development (GO:0030324)|lung induction (GO:0060492)|mammary gland epithelium development (GO:0061180)|neuron differentiation (GO:0030182)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)			breast(2)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|ovary(3)|prostate(1)|skin(2)	31	all_epithelial(6;2.24e-06)|Lung NSC(10;0.000936)|all_lung(10;0.00109)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		AGATAATCGCCCGTTTTCCTG	0.532																																					p.G231S		Atlas-SNP	.											.	WNT2	56	.	0			c.G691A						PASS	.						107	98	101					7																	116937828		2203	4300	6503	SO:0001583	missense	7472	exon4			AATCGCCCGTTTT	X07876	CCDS5771.1	7q31	2013-02-28			ENSG00000105989	ENSG00000105989		"Wingless-type MMTV integration sites", "Endogenous ligands"	12780	protein-coding gene	gene with protein product	"secreted growth factor"	147870		INT1L1		2971536	Standard	NM_003391		Approved	IRP	uc003viz.3	P09544	OTTHUMG00000023428	ENST00000265441.3:c.691G>A	chr7.hg19:g.116937828C>T	ENSP00000265441:p.Gly231Ser	98.0	0.0	.		86.0	41.0	.	NM_003391	A4D0V1|Q75N05|Q9UDP9	Missense_Mutation	SNP	ENST00000265441.3	hg19	CCDS5771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.00|15.00	2.704256|2.704256	0.48412|0.48412	.|.	.|.	ENSG00000105989|ENSG00000105989	ENST00000491214|ENST00000265441	T|T	0.64618|0.80824	-0.11|-1.42	5.58|5.58	4.7|4.7	0.59300|0.59300	.|.	0.048024|0.048024	0.85682|0.85682	D|D	0.000000|0.000000	D|D	0.90700|0.90700	0.7082|0.7082	M|M	0.86651|0.86651	2.83|2.83	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D	.|0.65815	.|0.995;0.995	.|D;D	.|0.76575	.|0.988;0.988	D|D	0.92513|0.92513	0.6018|0.6018	8|10	0.87932|0.87932	D|D	0|0	.|.	15.8497|15.8497	0.78921|0.78921	0.0:0.864:0.136:0.0|0.0:0.864:0.136:0.0	.|.	.|231;231	.|A4D0V1;P09544	.|.;WNT2_HUMAN	E|S	138|231	ENSP00000419466:G138E|ENSP00000265441:G231S	ENSP00000419466:G138E|ENSP00000265441:G231S	G|G	-|-	2|1	0|0	WNT2|WNT2	116725064|116725064	1.000000|1.000000	0.71417|0.71417	0.911000|0.911000	0.35937|0.35937	0.478000|0.478000	0.33099|0.33099	7.776000|7.776000	0.85560|0.85560	1.479000|1.479000	0.48272|0.48272	0.561000|0.561000	0.74099|0.74099	GGG|GGC	.	.	.	none		0.532	WNT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059749.3	NM_003391		T	116937828	C	T	116937828	3	4	165	1	0	0	0	0	1	0	0	0	17398	623	22	2	399	2	WNT2	7	116937828	Missense_Mutation	SNP	C	TCGA-F9-A7Q0-01A-11D-A35Z-10		116937828	42200835	6	9752											
INCENP	3619	hgsc.bcm.edu	37	chr11	61914249	61914249	+	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	cagcgggagcaggagcggcgGgagcaggagcggcgcgagca	9	0	22	10	6	0	0	0	0	0	0	0	5	0	4	0	6	6	3	0	6	0	0	rs113959967	byFrequency	TCGA-F9-A7Q0-01A-11D-A35Z-10	TCGA-F9-A7Q0-10B-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8a7f344-08bd-4b20-bbdd-94915425f00f	dfc4913f-381a-4897-828e-6f8666d652ef	g.chr11:61914249G>C	ENST00000394818.3	+	15	2281	c.2079G>C	c.(2077-2079)cgG>cgC	p.R693R	INCENP_ENST00000278849.4_Silent_p.R689R	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	693					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						aggagcggcgggagcaggagc	0.721													G|||	23	0.00459265	0.0045	0	5008	,	,		11611	0.004		0.005	False		,,,				2504	0.0082				p.R693R		Atlas-SNP	.											.	INCENP	122	.	0			c.G2079C						PASS	.																																			SO:0001819	synonymous_variant	3619	exon15			GCGGCGGGAGCAG	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.2079G>C	chr11.hg19:g.61914249G>C		132.0	0.0	.		119.0	44.0	.	NM_001040694	A8MQD2|Q5Y192	Silent	SNP	ENST00000394818.3	hg19	CCDS44624.1																																																																																			.	G|0.500;C|0.500	0.500	weak		0.721	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238		C	61914249	G	C	61914249	2	2	165	1	0	0	0	0	0	0	0	1	7740	1219	43	4		4	INCENP	11	61914249	Silent	SNP	G	TCGA-F9-A7Q0-01A-11D-A35Z-10		61914249	73092267	7	9753			1	22		2	2	31	N	G_C	1.550538e-05
INCENP	3619	hgsc.bcm.edu	37	chr11	61914279	61914279	+	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	cggcgcgagcaggagcggcgCgagcaggagcggcgggagca	8	0	22	11	8	0	0	0	0	0	0	0	5	0	3	0	6	5	3	0	6	0	0	rs371735595	byFrequency	TCGA-F9-A7Q0-01A-11D-A35Z-10	TCGA-F9-A7Q0-10B-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8a7f344-08bd-4b20-bbdd-94915425f00f	dfc4913f-381a-4897-828e-6f8666d652ef	g.chr11:61914279C>G	ENST00000394818.3	+	15	2311	c.2109C>G	c.(2107-2109)cgC>cgG	p.R703R	INCENP_ENST00000278849.4_Silent_p.R699R	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	703					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						aggagcggcgcgagcaggagc	0.751																																					p.R703R		Atlas-SNP	.											.	INCENP	122	.	0			c.C2109G						PASS	.						3	5	4					11																	61914279		1777	3550	5327	SO:0001819	synonymous_variant	3619	exon15			GCGGCGCGAGCAG	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.2109C>G	chr11.hg19:g.61914279C>G		118.0	0.0	.		84.0	19.0	.	NM_001040694	A8MQD2|Q5Y192	Silent	SNP	ENST00000394818.3	hg19	CCDS44624.1																																																																																			.	.	.	alt		0.751	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238		G	61914279	C	G	61914279	2	3	165	1	0	0	0	0	0	0	0	1	7740	755	27	4		4	INCENP	11	61914279	Silent	SNP	C	TCGA-F9-A7Q0-01A-11D-A35Z-10	30	61914279	73092237	8	9754			1	22		2	2	31	N	G_C	1.550538e-05
SAV1	60485	hgsc.bcm.edu	37	chr14	51101991	51101991	+	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	agggcttgtctgtatgcttcAtacattttaacaatctgctc	9	16	7	9	0	3	0	1	0	2	0	4	0	3	0	0	1	4	4	0	1	4	6			TCGA-F9-A7Q0-01A-11D-A35Z-10	TCGA-F9-A7Q0-10B-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8a7f344-08bd-4b20-bbdd-94915425f00f	dfc4913f-381a-4897-828e-6f8666d652ef	g.chr14:51101991A>T	ENST00000324679.4	-	5	1425	c.1062T>A	c.(1060-1062)taT>taA	p.Y354*	RN7SL452P_ENST00000482923.2_RNA	NM_021818.3	NP_068590.1	Q9H4B6	SAV1_HUMAN	salvador family WW domain containing protein 1	354	SARAH. {ECO:0000255|PROSITE- ProRule:PRU00310}.				hair follicle development (GO:0001942)|hippo signaling (GO:0035329)|intestinal epithelial cell differentiation (GO:0060575)|keratinocyte differentiation (GO:0030216)|lung epithelial cell differentiation (GO:0060487)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of epithelial cell proliferation (GO:0050680)|positive regulation of apoptotic process (GO:0043065)|regulation of stem cell maintenance (GO:2000036)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)				breast(1)|kidney(2)|lung(2)|prostate(1)	6	all_epithelial(31;0.000611)|Breast(41;0.0333)					TGTATGCTTCATACATTTTAA	0.413																																					p.Y354X		Atlas-SNP	.											.	SAV1	18	.	0			c.T1062A						PASS	.						126	119	122					14																	51101991		2203	4300	6503	SO:0001587	stop_gained	60485	exon5			TGCTTCATACATT	AK023071	CCDS9701.1	14q13-q23	2014-04-14	2014-04-14		ENSG00000151748	ENSG00000151748			17795	protein-coding gene	gene with protein product	"WW domain-containing adaptor 45"	607203	"salvador homolog 1 (Drosophila)"			12202036, 11027580	Standard	NM_021818		Approved	WW45, WWP4, salvador	uc001wyh.2	Q9H4B6	OTTHUMG00000140293	ENST00000324679.4:c.1062T>A	chr14.hg19:g.51101991A>T	ENSP00000324729:p.Tyr354*	129.0	0.0	.		78.0	56.0	.	NM_021818	A8K4B8|D3DSB6|Q6IA58|Q9H949|Q9HAK9	Nonsense_Mutation	SNP	ENST00000324679.4	hg19	CCDS9701.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.47|15.47	2.841904|2.841904	0.51057|0.51057	.|.	.|.	ENSG00000151748|ENSG00000151748	ENST00000557458|ENST00000555720;ENST00000324679;ENST00000535862	.|.	.|.	.|.	5.77|5.77	3.38|3.38	0.38709|0.38709	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|0.02654	.|T	.|1	-11.6598|-11.6598	7.6945|7.6945	0.28587|0.28587	0.7701:0.0:0.2299:0.0|0.7701:0.0:0.2299:0.0	.|.	.|.	.|.	.|.	R|X	60|286;354;321	.|.	.|ENSP00000324729:Y354X	X|Y	-|-	1|3	0|2	SAV1|SAV1	50171741|50171741	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.493000|0.493000	0.33554|0.33554	0.704000|0.704000	0.25661|0.25661	0.966000|0.966000	0.38159|0.38159	0.533000|0.533000	0.62120|0.62120	TGA|TAT	.	.	.	none		0.413	SAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276879.1			T	51101991	A	T	51101991	4	4	165	1	0	0	0	0	0	1	0	0	13869	224	8	5	93	5	SAV1	14	51101991	Nonsense_Mutation	SNP	A	TCGA-F9-A7Q0-01A-11D-A35Z-10		51101991	56247549	9	9755											
ZNF19	7567	hgsc.bcm.edu	37	chr16	71509777	71509777	+	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	atttgcattatcattaaaggCtcgcccacactcctcacact	11	12	4	14	1	2	0	2	0	0	0	4	0	3	0	2	1	1	2	2	1	3	3			TCGA-F9-A7Q0-01A-11D-A35Z-10	TCGA-F9-A7Q0-10B-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8a7f344-08bd-4b20-bbdd-94915425f00f	dfc4913f-381a-4897-828e-6f8666d652ef	g.chr16:71509777C>T	ENST00000288177.5	-	6	928	c.673G>A	c.(673-675)Gcc>Acc	p.A225T	ZNF19_ENST00000565637.1_Missense_Mutation_p.A183T|ZNF19_ENST00000565100.2_Missense_Mutation_p.A155T|ZNF19_ENST00000564230.1_Missense_Mutation_p.A225T|AC010547.9_ENST00000561908.1_Intron|ZNF19_ENST00000567225.1_Intron	NM_006961.3	NP_008892.2	P17023	ZNF19_HUMAN	zinc finger protein 19	225					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|prostate(1)|stomach(1)	22		Ovarian(137;0.00965)		BRCA - Breast invasive adenocarcinoma(221;0.0161)|Kidney(780;0.0598)		TCATTAAAGGCTCGCCCACAC	0.453																																					p.A225T		Atlas-SNP	.											.	ZNF19	46	.	0			c.G673A						PASS	.						69	77	75					16																	71509777		2198	4300	6498	SO:0001583	missense	7567	exon6			TAAAGGCTCGCCC	X52343	CCDS10901.1	16q22	2013-01-08	2006-05-10		ENSG00000157429	ENSG00000157429		"Zinc fingers, C2H2-type", "-"	12981	protein-coding gene	gene with protein product		194525	"zinc finger protein 19 (KOX 12)"			1505991, 1946370	Standard	NM_006961		Approved	KOX12, MGC51021	uc002fam.1	P17023	OTTHUMG00000137593	ENST00000288177.5:c.673G>A	chr16.hg19:g.71509777C>T	ENSP00000288177:p.Ala225Thr	154.0	0.0	.		137.0	45.0	.	NM_006961	A8K895|Q86Y66|Q8NDE2|Q96M79|Q96NE5	Missense_Mutation	SNP	ENST00000288177.5	hg19	CCDS10901.1	.	.	.	.	.	.	.	.	.	.	C	17.28	3.350126	0.61183	.	.	ENSG00000157429	ENST00000288177	T	0.16897	2.31	3.4	3.4	0.38934	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35495	N	0.003161	T	0.07683	0.0193	N	0.04880	-0.145	0.27067	N	0.963422	B	0.25351	0.124	B	0.28385	0.089	T	0.19745	-1.0296	10	0.33141	T	0.24	.	6.7551	0.23510	0.0:0.8751:0.0:0.1248	.	225	P17023	ZNF19_HUMAN	T	225	ENSP00000288177:A225T	ENSP00000288177:A225T	A	-	1	0	ZNF19	70067278	0.000000	0.05858	0.946000	0.38457	0.873000	0.50193	0.356000	0.20181	2.202000	0.70862	0.655000	0.94253	GCC	.	.	.	none		0.453	ZNF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268993.2	NM_006961		T	71509777	C	T	71509777	3	4	165	1	0	0	0	0	1	0	0	0	17767	797	28	2	707	2	ZNF19	16	71509777	Missense_Mutation	SNP	C	TCGA-F9-A7Q0-01A-11D-A35Z-10		71509777	18844976	10	9756											
RFFL	117584	hgsc.bcm.edu	37	chr17	33348798	33348798	+	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	ttcttacagtccaagcaggtCtgctgcttagagcaaaagac	12	10	9	10	0	2	2	0	0	2	2	3	2	3	2	1	1	5	4	1	1	5	3			TCGA-F9-A7Q0-01A-11D-A35Z-10	TCGA-F9-A7Q0-10B-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8a7f344-08bd-4b20-bbdd-94915425f00f	dfc4913f-381a-4897-828e-6f8666d652ef	g.chr17:33348798C>T	ENST00000315249.7	-	3	405	c.183G>A	c.(181-183)caG>caA	p.Q61Q	RFFL_ENST00000584655.1_Silent_p.Q61Q|RFFL_ENST00000378516.2_Silent_p.Q61Q|RFFL_ENST00000447669.2_Silent_p.Q61Q|RAD51L3-RFFL_ENST00000593039.1_Intron|RFFL_ENST00000268850.7_Silent_p.Q61Q|RFFL_ENST00000413582.2_Silent_p.Q61Q|RFFL_ENST00000415395.2_Silent_p.Q61Q|RFFL_ENST00000394597.2_Silent_p.Q61Q					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)		CCAAGCAGGTCTGCTGCTTAG	0.517																																					p.Q61Q		Atlas-SNP	.											.	RFFL	27	.	0			c.G183A						PASS	.						52	52	52					17																	33348798		2203	4299	6502	SO:0001819	synonymous_variant	117584	exon3			GCAGGTCTGCTGC	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.183G>A	chr17.hg19:g.33348798C>T		167.0	0.0	.		122.0	50.0	.	NM_001017368		Silent	SNP	ENST00000315249.7	hg19	CCDS11286.1																																																																																			.	.	.	none		0.517	RFFL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256460.2	NM_057178		T	33348798	C	T	33348798	2	4	165	1	0	0	0	0	0	0	0	1	13263	912	32	2		2	RFFL	17	33348798	Silent	SNP	C	TCGA-F9-A7Q0-01A-11D-A35Z-10		33348798	47846412	11	9757											
MUC16	94025	hgsc.bcm.edu	37	chr19	9008207	9008207	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgttccggtccagggtgtaGgggcccagctctttgatgcc	4	11	14	12	1	1	1	0	1	1	0	3	1	3	1	4	4	2	3	4	4	1	3			TCGA-F9-A7Q0-01A-11D-A35Z-10	TCGA-F9-A7Q0-10B-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8a7f344-08bd-4b20-bbdd-94915425f00f	dfc4913f-381a-4897-828e-6f8666d652ef	g.chr19:9008207G>A	ENST00000397910.4	-	41	39548	c.39345C>T	c.(39343-39345)ccC>ccT	p.P13115P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13117	SEA 7. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CCAGGGTGTAGGGGCCCAGCT	0.547																																					p.P13115P		Atlas-SNP	.											.	MUC16	4315	.	0			c.C39345T						PASS	.						210	191	197					19																	9008207		2018	4185	6203	SO:0001819	synonymous_variant	94025	exon41			GGTGTAGGGGCCC	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.39345C>T	chr19.hg19:g.9008207G>A		133.0	0.0	.		122.0	9.0	.	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.	.	none		0.547	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9008207	G	A	9008207	2	1	165	1	0	0	0	0	0	0	0	1	9980	987	35	2		2	MUC16	19	9008207	Silent	SNP	G	TCGA-F9-A7Q0-01A-11D-A35Z-10		9008207	50120776	12	9758											
DNM2	1785	hgsc.bcm.edu	37	chr19	10886526	10886526	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctggctgtcacgcccgccaAcatggacctggccaactccg	7	7	10	17	3	2	0	1	0	1	0	3	1	3	1	5	3	2	1	5	3	2	0			TCGA-F9-A7Q0-01A-11D-A35Z-10	TCGA-F9-A7Q0-10B-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8a7f344-08bd-4b20-bbdd-94915425f00f	dfc4913f-381a-4897-828e-6f8666d652ef	g.chr19:10886526A>G	ENST00000355667.6	+	4	613	c.533A>G	c.(532-534)aAc>aGc	p.N178S	DNM2_ENST00000591819.1_3'UTR|DNM2_ENST00000408974.4_Missense_Mutation_p.N178S|DNM2_ENST00000314646.5_Missense_Mutation_p.N178S|DNM2_ENST00000359692.6_Missense_Mutation_p.N178S|DNM2_ENST00000585892.1_Missense_Mutation_p.N178S|DNM2_ENST00000389253.4_Missense_Mutation_p.N178S	NM_001005360.2|NM_001190716.1	NP_001005360.1|NP_001177645.1	P50570	DYN2_HUMAN	dynamin 2	178	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)			ACGCCCGCCAACATGGACCTG	0.607			"F, N, Splice, Mis, O"		ETP ALL																																p.N178S		Atlas-SNP	.		Rec	yes		19	19p13.2	1785	dynamin 2		L	.	DNM2	175	.	0			c.A533G						PASS	.						74	68	70					19																	10886526		2203	4300	6503	SO:0001583	missense	1785	exon4			CCGCCAACATGGA		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.533A>G	chr19.hg19:g.10886526A>G	ENSP00000347890:p.Asn178Ser	87.0	0.0	.		77.0	37.0	.	NM_001005361	A8K1B6|E7EV30|E9PEQ4|K7ESI9|Q5I0Y0|Q7Z5S3|Q9UPH4	Missense_Mutation	SNP	ENST00000355667.6	hg19	CCDS45968.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.224596	0.79576	.	.	ENSG00000079805	ENST00000389252;ENST00000408974;ENST00000355667;ENST00000359692;ENST00000389253;ENST00000314646	D;D;D;D;D	0.97378	-4.36;-4.36;-4.36;-4.36;-4.36	5.38	5.38	0.77491	Dynamin, GTPase domain (2);	0.000000	0.85682	D	0.000000	D	0.98298	0.9436	M	0.83852	2.665	0.80722	D	1	D;D;D;D	0.89917	1.0;0.992;1.0;0.988	D;P;D;P	0.71656	0.974;0.693;0.974;0.678	D	0.99334	1.0910	10	0.87932	D	0	.	14.3763	0.66879	1.0:0.0:0.0:0.0	.	178;178;178;178	A8K1B6;P50570-2;P50570;E9PEQ4	.;.;DYN2_HUMAN;.	S	167;178;178;178;178;178	ENSP00000386192:N178S;ENSP00000347890:N178S;ENSP00000352721:N178S;ENSP00000373905:N178S;ENSP00000313164:N178S	ENSP00000313164:N178S	N	+	2	0	DNM2	10747526	1.000000	0.71417	1.000000	0.80357	0.595000	0.36748	9.339000	0.96797	2.046000	0.60703	0.459000	0.35465	AAC	.	.	.	none		0.607	DNM2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452592.1	NM_004945		G	10886526	A	G	10886526	3	3	165	1	0	0	0	0	1	0	0	0	4674	43	2	3	547	3	DNM2	19	10886526	Missense_Mutation	SNP	A	TCGA-F9-A7Q0-01A-11D-A35Z-10	1878319	10886526	48242457	13	9759											
CYP2A7	1549	hgsc.bcm.edu	37	chr19	41386516	41386516	+	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	gagctgcttggcgcgctcccCgttgctgaacgccacgcctg	4	8	13	16	5	0	1	0	1	0	0	1	2	1	1	4	1	4	5	4	1	1	2	rs376282662		TCGA-F9-A7Q0-01A-11D-A35Z-10	TCGA-F9-A7Q0-10B-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8a7f344-08bd-4b20-bbdd-94915425f00f	dfc4913f-381a-4897-828e-6f8666d652ef	g.chr19:41386516C>A	ENST00000301146.4	-	3	902	c.361G>T	c.(361-363)Ggg>Tgg	p.G121W	CTC-490E21.12_ENST00000601627.1_Intron|CYP2A7_ENST00000291764.3_Missense_Mutation_p.G70W	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	121						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)			GCGCGCTCCCCGTTGCTGAAC	0.701																																					p.G121W		Atlas-SNP	.											.	CYP2A7	71	.	0			c.G361T						PASS	.						17	16	16					19																	41386516		2159	4179	6338	SO:0001583	missense	1549	exon3			GCTCCCCGTTGCT	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.361G>T	chr19.hg19:g.41386516C>A	ENSP00000301146:p.Gly121Trp	147.0	0.0	.		144.0	8.0	.	NM_000764	Q13121	Missense_Mutation	SNP	ENST00000301146.4	hg19	CCDS12569.1	.	.	.	.	.	.	.	.	.	.	c	13.70	2.314842	0.40996	.	.	ENSG00000198077	ENST00000301146;ENST00000291764	T;T	0.20200	4.45;2.09	2.16	2.16	0.27623	.	0.059304	0.64402	N	0.000003	T	0.45296	0.1335	H	0.94385	3.53	0.40331	D	0.978924	D;D;P	0.56521	0.976;0.965;0.772	P;P;B	0.52386	0.697;0.674;0.286	T	0.63800	-0.6555	10	0.72032	D	0.01	.	11.4345	0.50060	0.0:1.0:0.0:0.0	.	121;70;121	B7ZKR0;F8W816;P20853	.;.;CP2A7_HUMAN	W	121;70	ENSP00000301146:G121W;ENSP00000291764:G70W	ENSP00000291764:G70W	G	-	1	0	CYP2A7	46078356	0.463000	0.25799	0.369000	0.25952	0.023000	0.10783	1.564000	0.36375	1.211000	0.43351	0.175000	0.17021	GGG	.	.	.	alt		0.701	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589		A	41386516	C	A	41386516	3	1	165	1	0	0	0	0	1	0	0	0	4165	652	23	4	1151	4	CYP2A7	19	41386516	Missense_Mutation	SNP	C	TCGA-F9-A7Q0-01A-11D-A35Z-10	30499990	41386516	17742467	14	9760											
BPIL1	80341	hgsc.bcm.edu	37	chr20	31608183	31608183	+	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	gtccaaggtgaagcttcaggGgaccacgtctgtgctggggt	7	9	16	9	1	2	1	1	1	1	0	3	2	3	2	2	5	2	2	2	5	2	1			TCGA-F9-A7Q0-01A-11D-A35Z-10	TCGA-F9-A7Q0-10B-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8a7f344-08bd-4b20-bbdd-94915425f00f	dfc4913f-381a-4897-828e-6f8666d652ef	g.chr20:31608183G>A	ENST00000170150.3	+	12	1325	c.1130G>A	c.(1129-1131)gGg>gAg	p.G377E		NM_025227.1	NP_079503.1	Q8N4F0	BPIB2_HUMAN	BPI fold containing family B, member 2	377						extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										AAGCTTCAGGGGACCACGTCT	0.602																																					p.G377E		Atlas-SNP	.											.	.	.	.	0			c.G1130A						PASS	.						115	100	105					20																	31608183		2203	4300	6503	SO:0001583	missense	80341	exon12			TTCAGGGGACCAC	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.1130G>A	chr20.hg19:g.31608183G>A	ENSP00000170150:p.Gly377Glu	102.0	0.0	.		115.0	53.0	.	NM_025227	Q6UWN3|Q6ZME0|Q8NFQ7	Missense_Mutation	SNP	ENST00000170150.3	hg19	CCDS13210.1	.	.	.	.	.	.	.	.	.	.	G	15.68	2.904186	0.52333	.	.	ENSG00000078898	ENST00000170150	T	0.16897	2.31	4.24	2.23	0.28157	.	0.263443	0.27039	N	0.021235	T	0.25865	0.0630	M	0.66939	2.045	0.40553	D	0.981136	P	0.45634	0.863	P	0.48738	0.588	T	0.06679	-1.0813	10	0.66056	D	0.02	-12.3476	10.618	0.45462	0.0:0.3805:0.6195:0.0	.	377	Q8N4F0	BPIB2_HUMAN	E	377	ENSP00000170150:G377E	ENSP00000170150:G377E	G	+	2	0	BPIFB2	31071844	0.925000	0.31364	0.836000	0.33094	0.727000	0.41649	1.133000	0.31430	0.703000	0.31848	0.561000	0.74099	GGG	.	.	.	none		0.602	BPIFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078652.2	NM_025227		A	31608183	G	A	31608183	3	1	165	1	0	0	0	0	1	0	0	0	1493	1232	43	2	1172	2	BPIL1	20	31608183	Missense_Mutation	SNP	G	TCGA-F9-A7Q0-01A-11D-A35Z-10		31608183	31417337	15	9761											
AURKA	6790	hgsc.bcm.edu	37	chr20	54963211	54963211	+	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	attacagattattcaatttaCcttaacaggtcctgaaatgc	14	14	5	8	0	1	2	1	1	0	1	2	2	2	2	2	1	4	0	2	1	6	6			TCGA-F9-A7Q0-01A-11D-A35Z-10	TCGA-F9-A7Q0-10B-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a8a7f344-08bd-4b20-bbdd-94915425f00f	dfc4913f-381a-4897-828e-6f8666d652ef	g.chr20:54963211C>G	ENST00000347343.2	-	2	310		c.e2+1		AURKA_ENST00000395909.4_Splice_Site|AURKA_ENST00000395915.3_Splice_Site|AURKA_ENST00000395913.3_Splice_Site|AURKA_ENST00000371356.2_Splice_Site|AURKA_ENST00000395911.1_Splice_Site|AURKA_ENST00000395914.1_Splice_Site|AURKA_ENST00000395907.1_Splice_Site|AURKA_ENST00000312783.6_Splice_Site	NM_003600.2	NP_003591.2	O14965	AURKA_HUMAN	aurora kinase A						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|anterior/posterior axis specification (GO:0009948)|centrosome localization (GO:0051642)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic centrosome separation (GO:0007100)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein binding (GO:0032091)|negative regulation of spindle checkpoint (GO:0090233)|neuron projection extension (GO:1990138)|positive regulation of mitosis (GO:0045840)|positive regulation of oocyte maturation (GO:1900195)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein autophosphorylation (GO:0046777)|protein localization to centrosome (GO:0071539)|protein phosphorylation (GO:0006468)|regulation of centrosome cycle (GO:0046605)|regulation of protein stability (GO:0031647)|spindle assembly involved in female meiosis I (GO:0007057)|spindle stabilization (GO:0043146)	axon hillock (GO:0043203)|centrosome (GO:0005813)|cytosol (GO:0005829)|germinal vesicle (GO:0042585)|meiotic spindle (GO:0072687)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|histone serine kinase activity (GO:0035174)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)	p.?(1)		breast(2)|cervix(1)|endometrium(1)|large_intestine(4)|lung(9)|ovary(2)|prostate(1)|skin(2)	22			Colorectal(105;0.202)			ATTCAATTTACCTTAACAGGT	0.358																																					.	Melanoma(34;439 1292 51416 52695)|GBM(144;1525 2517 48902 51835)|Esophageal Squamous(191;569 2880 14195 30540)	Atlas-SNP	.											AURKA,NS,carcinoma,0,1	AURKA	42	.	1	Unknown(1)	lung(1)	c.42+1G>C						PASS	.						110	116	114					20																	54963211		2203	4300	6503	SO:0001630	splice_region_variant	6790	exon4			AATTTACCTTAAC	BC001280	CCDS13451.1	20q13	2012-07-23	2003-07-21	2003-07-23	ENSG00000087586	ENSG00000087586		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	11393	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 47", "Aurora-A kinase"	603072	"serine/threonine kinase 15", " serine/threonine kinase 6"	STK15, STK6		9174055, 9771714	Standard	NM_003600		Approved	BTAK, AurA, STK7, ARK1, PPP1R47, AIK	uc002xxi.1	O14965	OTTHUMG00000032796	ENST00000347343.2:c.42+1G>C	chr20.hg19:g.54963211C>G		123.0	1.0	.		125.0	8.0	.	NM_198434	E1P5F9|O60445|O75873|Q9BQD6|Q9UPG5	Splice_Site	SNP	ENST00000347343.2	hg19	CCDS13451.1	.	.	.	.	.	.	.	.	.	.	C	15.47	2.843515	0.51057	.	.	ENSG00000087586	ENST00000395909;ENST00000395914;ENST00000347343;ENST00000395915;ENST00000312783;ENST00000371356;ENST00000395913;ENST00000395911;ENST00000395907;ENST00000441357;ENST00000420474;ENST00000422322;ENST00000456249;ENST00000451915	.	.	.	4.53	4.53	0.55603	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.6225	0.56612	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	AURKA	54396618	1.000000	0.71417	1.000000	0.80357	0.767000	0.43475	3.235000	0.51328	2.329000	0.79093	0.585000	0.79938	.	.	.	.	none		0.358	AURKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079804.3	NM_003600	Intron	G	54963211	C	G	54963211	5	3	165	1	0	0	0	0	0	0	1	0	1221	521	18	4	1200	4	AURKA	20	54963211	Splice_Site	SNP	C	TCGA-F9-A7Q0-01A-11D-A35Z-10	23355028	54963211	8062309	16	9762											
HSPG2	3339	hgsc.bcm.edu	37	chr1	22180783	22180783	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttctccacacggcacacataTtctccagaatcagctggtga	11	10	7	13	1	3	2	1	1	2	1	5	2	3	2	2	2	1	2	2	2	2	3			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr1:22180783T>C	ENST00000374695.3	-	50	6421	c.6342A>G	c.(6340-6342)gaA>gaG	p.E2114E	HSPG2_ENST00000430507.1_Silent_p.E64E	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2114	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)	GGCACACATATTCTCCAGAAT	0.637																																					p.E2114E		Atlas-SNP	.											.	HSPG2	311	.	0			c.A6342G						PASS	.						24	22	22					1																	22180783		2196	4288	6484	SO:0001819	synonymous_variant	3339	exon50			CACATATTCTCCA	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.6342A>G	chr1.hg19:g.22180783T>C		97.0	0.0	.		73.0	33.0	.	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	hg19	CCDS30625.1																																																																																			.	.	.	none		0.637	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		C	22180783	T	C	22180783	2	2	166	1	0	0	0	0	0	0	0	1	7437	1490	52	3		3	HSPG2	1	22180783	Silent	SNP	T	TCGA-F9-A7VF-01A-11D-A33Q-10		22180783	227069838	1	9763											
HIVEP3	59269	hgsc.bcm.edu	37	chr1	41976929	41976929	+	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	caggagggacttcgggactcGgccttctgctggggtcagaa	7	8	16	10	2	2	1	1	0	1	1	4	4	2	4	1	6	1	1	1	6	1	2	rs146058477		TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr1:41976929G>T	ENST00000372583.1	-	9	7299	c.6414C>A	c.(6412-6414)gcC>gcA	p.A2138A	HIVEP3_ENST00000247584.5_Silent_p.A2138A|HIVEP3_ENST00000429157.2_Silent_p.A2137A|HIVEP3_ENST00000460604.1_5'UTR|HIVEP3_ENST00000372584.1_Silent_p.A2137A	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	2138	6 X 4 AA tandem repeats of S-P-X-[RK].				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)				TTCGGGACTCGGCCTTCTGCT	0.632																																					p.A2138A		Atlas-SNP	.											.	HIVEP3	235	.	0			c.C6414A						PASS	.						36	38	37					1																	41976929		2200	4299	6499	SO:0001819	synonymous_variant	59269	exon9			GGACTCGGCCTTC	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.6414C>A	chr1.hg19:g.41976929G>T		37.0	0.0	.		33.0	17.0	.	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Silent	SNP	ENST00000372583.1	hg19	CCDS463.1																																																																																			.	G|1.000;A|0.000	.	alt		0.632	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		T	41976929	G	T	41976929	2	4	166	1	0	0	0	0	0	0	0	1	7195	1103	39	4		4	HIVEP3	1	41976929	Silent	SNP	G	TCGA-F9-A7VF-01A-11D-A33Q-10	19796146	41976929	207273692	2	9764											
ZSWIM5	57643	hgsc.bcm.edu	37	chr1	45485775	45485775	+	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	gtcaccaaccatcgtaccatCtccctgcgtctccagttaag	9	10	6	16	2	3	0	1	0	2	0	6	0	3	0	5	0	3	2	5	0	3	2			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr1:45485775C>T	ENST00000359600.5	-	13	2863	c.2658G>A	c.(2656-2658)gaG>gaA	p.E886E		NM_020883.1	NP_065934.1	Q9P217	ZSWM5_HUMAN	zinc finger, SWIM-type containing 5	886						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)					ATCGTACCATCTCCCTGCGTC	0.552																																					p.E886E		Atlas-SNP	.											.	ZSWIM5	72	.	0			c.G2658A						PASS	.						90	88	89					1																	45485775		2052	4181	6233	SO:0001819	synonymous_variant	57643	exon13			TACCATCTCCCTG	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.2658G>A	chr1.hg19:g.45485775C>T		114.0	0.0	.		85.0	33.0	.	NM_020883	Q5SXQ9	Silent	SNP	ENST00000359600.5	hg19	CCDS41319.1																																																																																			.	.	.	none		0.552	ZSWIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024823.2	XM_046581		T	45485775	C	T	45485775	2	4	166	1	0	0	0	0	0	0	0	1	18256	912	32	2		2	ZSWIM5	1	45485775	Silent	SNP	C	TCGA-F9-A7VF-01A-11D-A33Q-10	3508846	45485775	203764846	3	9765											
DDX20	11218	hgsc.bcm.edu	37	chr1	112299342	112299342	+	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	tagctttggactctcttgttCttgaaaacttaagtacccag	10	15	7	9	0	2	1	0	1	2	0	3	2	2	2	1	1	3	3	1	1	5	7			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr1:112299342C>T	ENST00000369702.4	+	2	996	c.376C>T	c.(376-378)Ctt>Ttt	p.L126F	FAM212B_ENST00000412270.1_5'Flank|DDX20_ENST00000536167.1_Missense_Mutation_p.L126F|FAM212B_ENST00000444059.2_5'Flank	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	126	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				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)		CTCTCTTGTTCTTGAAAACTT	0.428																																					p.L126F		Atlas-SNP	.											.	DDX20	50	.	0			c.C376T						PASS	.						104	98	100					1																	112299342		2203	4300	6503	SO:0001583	missense	11218	exon2			CTTGTTCTTGAAA	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.376C>T	chr1.hg19:g.112299342C>T	ENSP00000358716:p.Leu126Phe	119.0	0.0	.		96.0	47.0	.	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Missense_Mutation	SNP	ENST00000369702.4	hg19	CCDS842.1	.	.	.	.	.	.	.	.	.	.	C	18.94	3.729711	0.69074	.	.	ENSG00000064703	ENST00000369702;ENST00000536167	T;T	0.35048	2.45;1.33	5.6	4.68	0.58851	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.064498	0.64402	D	0.000007	T	0.36248	0.0960	L	0.35341	1.055	0.49915	D	0.999835	D	0.71674	0.998	D	0.71870	0.975	T	0.27020	-1.0086	10	0.51188	T	0.08	-12.9842	13.7769	0.63059	0.1539:0.8461:0.0:0.0	.	126	Q9UHI6	DDX20_HUMAN	F	126	ENSP00000358716:L126F;ENSP00000439026:L126F	ENSP00000358716:L126F	L	+	1	0	DDX20	112100865	0.997000	0.39634	0.976000	0.42696	0.997000	0.91878	1.848000	0.39309	1.342000	0.45619	0.555000	0.69702	CTT	.	.	.	none		0.428	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204		T	112299342	C	T	112299342	3	4	166	1	0	0	0	0	1	0	0	0	4350	913	32	2	382	2	DDX20	1	112299342	Missense_Mutation	SNP	C	TCGA-F9-A7VF-01A-11D-A33Q-10	66813567	112299342	136951279	4	9766											
RFX5	5993	hgsc.bcm.edu	37	chr1	151317225	151317225	+	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	gataggcatcataaacacttTgctttggcagacaggtgtca	12	11	10	8	0	2	1	2	0	0	1	2	2	2	1	0	3	2	3	0	3	3	4			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr1:151317225T>A	ENST00000290524.4	-	6	510	c.332A>T	c.(331-333)cAa>cTa	p.Q111L	RFX5_ENST00000368870.2_Missense_Mutation_p.Q111L|RFX5_ENST00000478564.1_5'UTR|RFX5_ENST00000452513.2_Intron|RP11-126K1.8_ENST00000422153.1_RNA|RP11-126K1.6_ENST00000455503.1_RNA|RFX5_ENST00000452671.2_Missense_Mutation_p.Q111L	NM_000449.3|NM_001025603.1	NP_000440.1|NP_001020774.1	P48382	RFX5_HUMAN	regulatory factor X, 5 (influences HLA class II expression)	111					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)			ATAAACACTTTGCTTTGGCAG	0.542																																					p.Q111L		Atlas-SNP	.											.	RFX5	69	.	0			c.A332T						PASS	.						68	56	60					1																	151317225		2203	4300	6503	SO:0001583	missense	5993	exon6			ACACTTTGCTTTG		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.332A>T	chr1.hg19:g.151317225T>A	ENSP00000290524:p.Gln111Leu	124.0	0.0	.		123.0	54.0	.	NM_000449	B7Z848|D3DV19|E9PFU4|Q5VWC3	Missense_Mutation	SNP	ENST00000290524.4	hg19	CCDS994.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.666797	0.88251	.	.	ENSG00000143390	ENST00000290524;ENST00000368870;ENST00000436637;ENST00000452671;ENST00000392746;ENST00000422595;ENST00000450506;ENST00000458484;ENST00000430227;ENST00000412774	D;D;D;D;D;D;D;D;D	0.82803	-1.65;-1.65;-1.65;-1.65;-1.65;-1.65;-1.65;-1.65;-1.65	5.43	5.43	0.79202	Winged helix-turn-helix transcription repressor DNA-binding (1);DNA-binding RFX (1);	0.000000	0.85682	D	0.000000	D	0.88683	0.6503	M	0.74881	2.28	0.80722	D	1	D	0.69078	0.997	D	0.80764	0.994	D	0.90114	0.4194	10	0.72032	D	0.01	-13.3181	14.4364	0.67284	0.0:0.0:0.0:1.0	.	111	P48382	RFX5_HUMAN	L	111;111;3;111;111;111;111;111;111;111	ENSP00000290524:Q111L;ENSP00000357864:Q111L;ENSP00000390769:Q3L;ENSP00000389130:Q111L;ENSP00000376502:Q111L;ENSP00000399095:Q111L;ENSP00000398666:Q111L;ENSP00000409187:Q111L;ENSP00000387618:Q111L	ENSP00000290524:Q111L	Q	-	2	0	RFX5	149583849	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.068000	0.76748	2.279000	0.76181	0.533000	0.62120	CAA	.	.	.	none		0.542	RFX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034892.6	NM_000449		A	151317225	T	A	151317225	3	1	166	1	0	0	0	0	1	0	0	0	13279	1812	63	5	1542	5	RFX5	1	151317225	Missense_Mutation	SNP	T	TCGA-F9-A7VF-01A-11D-A33Q-10	39017883	151317225	97933396	5	9767											
FLG	2312	hgsc.bcm.edu	37	chr1	152284898	152284898	+	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	gttgtctcgtgcctgctcatGgtgggatccttgtcttactc	3	16	11	11	1	3	0	1	0	2	0	6	1	4	1	2	2	3	2	2	2	1	3			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr1:152284898G>T	ENST00000368799.1	-	3	2499	c.2464C>A	c.(2464-2466)Cat>Aat	p.H822N	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	822	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)			GCCTGCTCATGGTGGGATCCT	0.567									Ichthyosis																												p.H822N		Atlas-SNP	.											FLG,NS,lymphoid_neoplasm,0,1	FLG	900	.	0			c.C2464A						PASS	.						284	272	276					1																	152284898		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GCTCATGGTGGGA	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.2464C>A	chr1.hg19:g.152284898G>T	ENSP00000357789:p.His822Asn	103.0	0.0	.		95.0	33.0	.	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	-	4.331	0.060725	0.08339	.	.	ENSG00000143631	ENST00000368799	T	0.04015	3.73	3.3	-1.25	0.09405	.	.	.	.	.	T	0.01353	0.0044	L	0.58428	1.81	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45920	-0.9228	9	0.25106	T	0.35	.	2.5714	0.04796	0.2516:0.0:0.3484:0.3999	.	822	P20930	FILA_HUMAN	N	822	ENSP00000357789:H822N	ENSP00000357789:H822N	H	-	1	0	FLG	150551522	0.005000	0.15991	0.000000	0.03702	0.001000	0.01503	1.127000	0.31357	0.134000	0.18681	-0.415000	0.06103	CAT	.	.	.	none		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152284898	G	T	152284898	3	4	166	1	0	0	0	0	1	0	0	0	5929	1348	47	4	9725	4	FLG	1	152284898	Missense_Mutation	SNP	G	TCGA-F9-A7VF-01A-11D-A33Q-10	967673	152284898	96965723	6	9768											
F5	2153	hgsc.bcm.edu	37	chr1	169519125	169519125	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgtctctcatgatgtccaCgtcactgtagtatggtcttg	7	15	10	9	1	4	1	2	1	2	0	6	2	5	1	1	1	0	2	1	1	2	3			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr1:169519125C>T	ENST00000367797.3	-	10	1726	c.1525G>A	c.(1525-1527)Gtg>Atg	p.V509M	F5_ENST00000367796.3_Missense_Mutation_p.V509M|F5_ENST00000546081.1_3'UTR	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	509	F5/8 type A 2.|Plastocyanin-like 3.				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)	ATGATGTCCACGTCACTGTAG	0.438																																					p.V509M		Atlas-SNP	.											.	F5	301	.	0			c.G1525A						PASS	.						217	193	201					1																	169519125		2203	4300	6503	SO:0001583	missense	2153	exon10			TGTCCACGTCACT	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.1525G>A	chr1.hg19:g.169519125C>T	ENSP00000356771:p.Val509Met	152.0	0.0	.		120.0	43.0	.	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	hg19	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	C	31	5.096857	0.94197	.	.	ENSG00000198734	ENST00000367797;ENST00000367796	D;D	0.98567	-5.0;-5.0	5.71	5.71	0.89125	Cupredoxin (2);	0.124889	0.53938	D	0.000051	D	0.99354	0.9773	H	0.94582	3.555	0.40561	D	0.981212	D	0.89917	1.0	D	0.87578	0.998	D	0.98965	1.0799	9	0.87932	D	0	-6.2486	19.8398	0.96678	0.0:1.0:0.0:0.0	.	509	P12259	FA5_HUMAN	M	509	ENSP00000356771:V509M;ENSP00000356770:V509M	ENSP00000356770:V509M	V	-	1	0	F5	167785749	1.000000	0.71417	0.995000	0.50966	0.961000	0.63080	7.451000	0.80668	2.697000	0.92050	0.655000	0.94253	GTG	.	.	.	none		0.438	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		T	169519125	C	T	169519125	3	4	166	1	0	0	0	0	1	0	0	0	5350	536	19	1	5213	1	F5	1	169519125	Missense_Mutation	SNP	C	TCGA-F9-A7VF-01A-11D-A33Q-10	17234227	169519125	79731496	7	9769											
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160206448	160206448	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcgtttttagtaactggtcaTtggggagaggactgtagaac	10	12	14	5	1	1	2	1	0	0	2	1	4	1	3	0	4	2	3	0	4	4	6	rs200214529	byFrequency	TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr2:160206448T>C	ENST00000392783.2	-	28	5129	c.4634A>G	c.(4633-4635)aAt>aGt	p.N1545S	BAZ2B_ENST00000355831.2_Missense_Mutation_p.N1511S|BAZ2B_ENST00000343439.5_Missense_Mutation_p.N1445S|BAZ2B_ENST00000392782.1_Missense_Mutation_p.N1509S	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	1545					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						TAACTGGTCATTGGGGAGAGG	0.428													T|||	2	0.000399361	0	0	5008	,	,		20692	0.002		0	False		,,,				2504	0				p.N1545S		Atlas-SNP	.											.	BAZ2B	196	.	0			c.A4634G						PASS	.						159	154	156					2																	160206448		2019	4187	6206	SO:0001583	missense	29994	exon28			TGGTCATTGGGGA	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.4634A>G	chr2.hg19:g.160206448T>C	ENSP00000376534:p.Asn1545Ser	117.0	0.0	.		120.0	47.0	.	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	hg19	CCDS2209.2	.	.	.	.	.	.	.	.	.	.	T	7.084	0.570841	0.13623	.	.	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439	T;T;T;T	0.58060	0.43;0.42;0.43;0.36	6.17	3.83	0.44106	.	0.183181	0.25680	N	0.029005	T	0.40595	0.1123	L	0.41824	1.3	0.26418	N	0.976147	B;B	0.23377	0.081;0.084	B;B	0.20184	0.028;0.021	T	0.21930	-1.0231	10	0.15952	T	0.53	-11.6915	11.3102	0.49360	0.0:0.2045:0.0:0.7955	.	1509;1545	Q9UIF8-5;Q9UIF8	.;BAZ2B_HUMAN	S	1509;1545;1511;1445	ENSP00000376533:N1509S;ENSP00000376534:N1545S;ENSP00000348087:N1511S;ENSP00000339670:N1445S	ENSP00000339670:N1445S	N	-	2	0	BAZ2B	159914694	1.000000	0.71417	0.998000	0.56505	0.774000	0.43823	1.563000	0.36364	0.200000	0.20447	-1.139000	0.01908	AAT	.	.	.	weak		0.428	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			C	160206448	T	C	160206448	3	2	166	1	0	0	0	0	1	0	0	0	1332	1493	52	3	1912	3	BAZ2B	2	160206448	Missense_Mutation	SNP	T	TCGA-F9-A7VF-01A-11D-A33Q-10		160206448	82992925	8	9770											
XIRP2	129446	hgsc.bcm.edu	37	chr2	168105464	168105464	+	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	gattgcgcctcttataaaatCtcattcatttccagagagtt	11	15	6	9	1	3	1	2	0	2	1	5	3	4	1	2	0	1	1	2	0	3	6			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr2:168105464C>T	ENST00000409195.1	+	9	7651	c.7562C>T	c.(7561-7563)tCt>tTt	p.S2521F	XIRP2_ENST00000409273.1_Missense_Mutation_p.S2299F|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.S2521F	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2346					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						CTTATAAAATCTCATTCATTT	0.348																																					p.S2521F		Atlas-SNP	.											XIRP2,axilla,malignant_melanoma,0,1	XIRP2	914	.	0			c.C7562T						PASS	.						95	91	92					2																	168105464		1817	4068	5885	SO:0001583	missense	129446	exon9			TAAAATCTCATTC	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.7562C>T	chr2.hg19:g.168105464C>T	ENSP00000386840:p.Ser2521Phe	240.0	0.0	.		234.0	80.0	.	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	C	18.72	3.683539	0.68157	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.02890	4.12;4.12;4.13	6.07	5.15	0.70609	.	0.303615	0.35349	N	0.003270	T	0.05686	0.0149	M	0.65975	2.015	0.36927	D	0.891702	P;P;P	0.43287	0.702;0.802;0.802	B;B;B	0.36719	0.116;0.231;0.231	T	0.18272	-1.0342	10	0.72032	D	0.01	-15.1299	18.0572	0.89366	0.0:0.8695:0.1305:0.0	.	2346;2346;2299	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	F	2521;2521;2299	ENSP00000386840:S2521F;ENSP00000295237:S2521F;ENSP00000387255:S2299F	ENSP00000295237:S2521F	S	+	2	0	XIRP2	167813710	0.995000	0.38212	0.990000	0.47175	0.943000	0.58893	3.010000	0.49559	2.884000	0.98904	0.655000	0.94253	TCT	.	.	.	none		0.348	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		T	168105464	C	T	168105464	3	4	166	1	0	0	0	0	1	0	0	0	17442	913	32	2	7592	2	XIRP2	2	168105464	Missense_Mutation	SNP	C	TCGA-F9-A7VF-01A-11D-A33Q-10	7899016	168105464	75093909	9	9771											
TTN	7273	hgsc.bcm.edu	37	chr2	179460381	179460381	+	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	tcgggtaactgtatatgtcaCtggggtccatgctctgcggt	6	13	13	9	2	2	0	1	0	1	0	4	0	3	0	1	4	3	3	1	4	3	3			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr2:179460381C>T	ENST00000591111.1	-	245	53001	c.52777G>A	c.(52777-52779)Gtg>Atg	p.V17593M	TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V10361M|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.V10169M|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V16666M|TTN_ENST00000359218.5_Missense_Mutation_p.V10294M|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V19234M|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	17593	Fibronectin type-III 27. {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)			GTATATGTCACTGGGGTCCAT	0.453																																					p.V19234M		Atlas-SNP	.											.	TTN	18412	.	0			c.G57700A						PASS	.						73	67	69					2																	179460381		1902	4127	6029	SO:0001583	missense	7273	exon295			ATGTCACTGGGGT	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.52777G>A	chr2.hg19:g.179460381C>T	ENSP00000465570:p.Val17593Met	194.0	0.0	.		171.0	66.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	15.99	2.996350	0.54147	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.58358	0.34;0.34;0.34;0.34	5.9	5.9	0.94986	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.77765	0.4179	M	0.85630	2.765	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.79829	-0.1638	9	0.87932	D	0	.	20.2768	0.98488	0.0:1.0:0.0:0.0	.	10169;10294;10361;17593	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	M	16666;10169;10361;10294;10167	ENSP00000343764:V16666M;ENSP00000434586:V10169M;ENSP00000340554:V10361M;ENSP00000352154:V10294M	ENSP00000340554:V10361M	V	-	1	0	TTN	179168627	1.000000	0.71417	0.993000	0.49108	0.616000	0.37450	7.770000	0.85390	2.808000	0.96608	0.650000	0.86243	GTG	.	.	.	none		0.453	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179460381	C	T	179460381	3	4	166	1	0	0	0	0	1	0	0	0	16747	565	20	2	50551	2	TTN	2	179460381	Missense_Mutation	SNP	C	TCGA-F9-A7VF-01A-11D-A33Q-10	11354917	179460381	63738992	10	9772											
CCDC150	284992	hgsc.bcm.edu	37	chr2	197576887	197576887	+	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	agataaaagttaaacagctaGaagaacaagtacagtctttt	19	10	7	5	0	1	3	0	0	1	3	1	3	1	3	0	0	4	3	0	0	9	6			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr2:197576887G>C	ENST00000389175.4	+	16	1849	c.1714G>C	c.(1714-1716)Gaa>Caa	p.E572Q	CCDC150_ENST00000409270.1_5'Flank|CCDC150_ENST00000272831.7_Missense_Mutation_p.E240Q	NM_001080539.1	NP_001074008.1	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150	572										breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(14)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	33						TAAACAGCTAGAAGAACAAGT	0.259																																					p.E572Q		Atlas-SNP	.											.	CCDC150	96	.	0			c.G1714C						PASS	.						46	40	42					2																	197576887		1807	4062	5869	SO:0001583	missense	284992	exon16			CAGCTAGAAGAAC		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.1714G>C	chr2.hg19:g.197576887G>C	ENSP00000373827:p.Glu572Gln	165.0	0.0	.		167.0	65.0	.	NM_001080539	Q6P5U6|Q6P663|Q8N8V5	Missense_Mutation	SNP	ENST00000389175.4	hg19	CCDS46478.1	.	.	.	.	.	.	.	.	.	.	G	11.50	1.658115	0.29425	.	.	ENSG00000144395	ENST00000272831;ENST00000389175	T	0.44881	0.91	4.56	3.64	0.41730	.	0.347815	0.23865	N	0.043807	T	0.26882	0.0658	L	0.31294	0.92	0.80722	D	1	B;B	0.33318	0.154;0.408	B;B	0.31751	0.135;0.077	T	0.03922	-1.0992	10	0.18710	T	0.47	.	9.6745	0.40032	0.0:0.2311:0.7689:0.0	.	240;572	B4DZ03;Q8NCX0	.;CC150_HUMAN	Q	240;572	ENSP00000373827:E572Q	ENSP00000272831:E240Q	E	+	1	0	CCDC150	197285132	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.097000	0.50251	2.372000	0.80975	0.591000	0.81541	GAA	.	.	.	none		0.259	CCDC150-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335377.2	NM_001080539		C	197576887	G	C	197576887	3	2	166	1	0	0	0	0	1	0	0	0	2787	943	33	4	1776	4	CCDC150	2	197576887	Missense_Mutation	SNP	G	TCGA-F9-A7VF-01A-11D-A33Q-10	18116506	197576887	45622486	11	9773											
SCG2	7857	hgsc.bcm.edu	37	chr2	224463934	224463934	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagctgcttcagccccagAgatgaggaaaattaaaggga	15	7	12	7	0	1	3	1	2	0	1	1	6	1	5	2	2	3	2	2	2	5	2			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr2:224463934A>G	ENST00000305409.2	-	2	299	c.67T>C	c.(67-69)Tct>Cct	p.S23P		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)		TCAGCCCCAGAGATGAGGAAA	0.423																																					p.S23P		Atlas-SNP	.											.	SCG2	99	.	0			c.T67C						PASS	.						64	70	68					2																	224463934		2203	4299	6502	SO:0001583	missense	7857	exon2			CCCCAGAGATGAG	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.67T>C	chr2.hg19:g.224463934A>G	ENSP00000304133:p.Ser23Pro	225.0	0.0	.		195.0	75.0	.	NM_003469	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000305409.2	hg19	CCDS2457.1	.	.	.	.	.	.	.	.	.	.	A	7.472	0.646956	0.14516	.	.	ENSG00000171951	ENST00000305409;ENST00000450330;ENST00000421386;ENST00000433889	T;T;T	0.48522	2.64;0.81;0.82	5.59	4.4	0.53042	.	0.593410	0.18763	N	0.131840	T	0.29783	0.0744	N	0.12182	0.205	0.28756	N	0.901182	B	0.06786	0.001	B	0.06405	0.002	T	0.14811	-1.0459	10	0.32370	T	0.25	.	11.9761	0.53091	0.9309:0.0:0.0691:0.0	.	23	P13521	SCG2_HUMAN	P	23	ENSP00000304133:S23P;ENSP00000394702:S23P;ENSP00000415468:S23P	ENSP00000304133:S23P	S	-	1	0	SCG2	224172178	0.728000	0.28080	0.064000	0.19789	0.246000	0.25737	2.472000	0.45136	1.008000	0.39264	0.528000	0.53228	TCT	.	.	.	none		0.423	SCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256870.2	NM_003469		G	224463934	A	G	224463934	3	3	166	1	0	0	0	0	1	0	0	0	13904	304	11	3	1790	3	SCG2	2	224463934	Missense_Mutation	SNP	A	TCGA-F9-A7VF-01A-11D-A33Q-10	26887047	224463934	18735439	12	9774											
IL17RC	84818	hgsc.bcm.edu	37	chr3	9962215	9962215	+	Missense_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	cttcgaggctgccctagggaGtgaggtacgaatctggtcct	7	10	14	10	2	1	1	0	1	1	0	3	4	2	2	2	4	2	2	2	4	3	3			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr3:9962215G>A	ENST00000295981.3	+	6	937	c.719G>A	c.(718-720)aGt>aAt	p.S240N	IL17RC_ENST00000383812.4_Missense_Mutation_p.S169N|IL17RC_ENST00000455057.1_Missense_Mutation_p.S169N|RNU6-882P_ENST00000391025.1_RNA|IL17RC_ENST00000416074.2_Missense_Mutation_p.S40N|IL17RC_ENST00000403601.3_Missense_Mutation_p.S169N|IL17RC_ENST00000413608.1_Missense_Mutation_p.S169N|IL17RC_ENST00000498214.1_3'UTR	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	240					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						GCCCTAGGGAGTGAGGTACGA	0.597																																					p.S240N		Atlas-SNP	.											.	IL17RC	55	.	0			c.G719A						PASS	.						76	64	68					3																	9962215		2203	4299	6502	SO:0001583	missense	84818	exon6			TAGGGAGTGAGGT	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.719G>A	chr3.hg19:g.9962215G>A	ENSP00000295981:p.Ser240Asn	75.0	0.0	.		99.0	50.0	.	NM_153461	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Missense_Mutation	SNP	ENST00000295981.3	hg19	CCDS2590.1	.	.	.	.	.	.	.	.	.	.	G	9.495	1.101637	0.20632	.	.	ENSG00000163702	ENST00000383812;ENST00000438091;ENST00000295981;ENST00000436503;ENST00000403601;ENST00000416074;ENST00000455057;ENST00000413608	T;T;T;T;T;T;T;T	0.14391	2.51;2.51;2.51;2.51;2.51;2.51;2.51;2.51	5.5	2.71	0.32032	.	0.731779	0.12494	N	0.463996	T	0.09949	0.0244	L	0.29908	0.895	0.19300	N	0.999978	B;P;B;B;B;B;B;B;P	0.36315	0.435;0.547;0.148;0.148;0.231;0.231;0.231;0.255;0.547	B;B;B;B;B;B;B;B;B	0.33121	0.08;0.076;0.018;0.018;0.048;0.048;0.056;0.071;0.158	T	0.20338	-1.0278	10	0.49607	T	0.09	-1.0928	8.8918	0.35439	0.1168:0.5055:0.3777:0.0	.	169;40;169;169;169;169;169;240;169	Q8NAC3-4;F5H4Z2;E9PHG1;A8BWD5;E9PHJ6;A8BWC9;Q8NAC3-3;Q8NAC3;Q8NAC3-2	.;.;.;.;.;.;.;I17RC_HUMAN;.	N	169;144;240;144;169;40;169;169	ENSP00000373323:S169N;ENSP00000414609:S144N;ENSP00000295981:S240N;ENSP00000401128:S144N;ENSP00000384969:S169N;ENSP00000395315:S40N;ENSP00000407894:S169N;ENSP00000396064:S169N	ENSP00000295981:S240N	S	+	2	0	IL17RC	9937215	0.721000	0.28007	0.812000	0.32479	0.594000	0.36715	0.413000	0.21148	0.810000	0.34279	0.563000	0.77884	AGT	.	.	.	none		0.597	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732		A	9962215	G	A	9962215	3	1	166	1	0	0	0	0	1	0	0	0	7648	1029	36	2	741	2	IL17RC	3	9962215	Missense_Mutation	SNP	G	TCGA-F9-A7VF-01A-11D-A33Q-10		9962215	188060215	13	9775											
ATP2B2	491	hgsc.bcm.edu	37	chr3	10442753	10442753	+	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	tgaagaggccgtcggcagggAggaggtcacctggcaagagg	10	4	19	8	2	1	3	1	1	0	2	2	5	1	5	2	7	0	2	2	7	2	0			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr3:10442753A>T	ENST00000352432.4	-	4	734	c.665T>A	c.(664-666)cTc>cAc	p.L222H	ATP2B2_ENST00000360273.2_Missense_Mutation_p.L222H|ATP2B2_ENST00000343816.4_Missense_Mutation_p.L222H|ATP2B2_ENST00000397077.1_Missense_Mutation_p.L222H|ATP2B2_ENST00000383800.4_Missense_Mutation_p.L222H			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	222					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						GTCGGCAGGGAGGAGGTCACC	0.567																																					p.L222H	Ovarian(125;1619 1709 15675 19819 38835)	Atlas-SNP	.											.	ATP2B2	304	.	0			c.T665A						PASS	.						70	66	67					3																	10442753		2203	4300	6503	SO:0001583	missense	491	exon5			GCAGGGAGGAGGT	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"ATPases / P-type"	815	protein-coding gene	gene with protein product	"plasma membrane Ca2+ pump 2", "plasma membrane calcium-transporting ATPase 2"	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.665T>A	chr3.hg19:g.10442753A>T	ENSP00000324172:p.Leu222His	86.0	0.0	.		88.0	22.0	.	NM_001683	O00766|Q12994|Q16818	Missense_Mutation	SNP	ENST00000352432.4	hg19	CCDS33701.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.495893	0.85069	.	.	ENSG00000157087	ENST00000352432;ENST00000383800;ENST00000397077;ENST00000360273;ENST00000343816;ENST00000535386;ENST00000452124;ENST00000342354	D;D;D;D;D;D	0.91068	-2.78;-2.78;-2.78;-2.78;-2.78;-2.78	5.6	5.6	0.85130	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	D	0.96278	0.8786	M	0.90870	3.155	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	0.97158	0.9836	10	0.87932	D	0	-32.0976	15.7913	0.78367	1.0:0.0:0.0:0.0	.	222;234;222	Q01814-7;Q4LE63;Q01814	.;.;AT2B2_HUMAN	H	222;222;222;222;222;188;109;222	ENSP00000324172:L222H;ENSP00000373311:L222H;ENSP00000380267:L222H;ENSP00000353414:L222H;ENSP00000344677:L222H;ENSP00000414854:L109H	ENSP00000342954:L222H	L	-	2	0	ATP2B2	10417753	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	9.313000	0.96297	2.124000	0.65301	0.528000	0.53228	CTC	.	.	.	none		0.567	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683		T	10442753	A	T	10442753	3	4	166	1	0	0	0	0	1	0	0	0	1140	304	11	5	3142	5	ATP2B2	3	10442753	Missense_Mutation	SNP	A	TCGA-F9-A7VF-01A-11D-A33Q-10	480538	10442753	187579677	14	9776											
ATG7	10533	hgsc.bcm.edu	37	chr3	11374553	11374553	+	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	cgaagtgaagcttccagaaaTggcatttagcccaggtaatt	13	10	10	8	1	0	2	0	1	0	1	1	3	1	2	2	2	2	3	2	2	5	5			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr3:11374553T>A	ENST00000354449.3	+	9	900	c.875T>A	c.(874-876)aTg>aAg	p.M292K	ATG7_ENST00000446450.2_Missense_Mutation_p.M253K|ATG7_ENST00000354956.5_Missense_Mutation_p.M292K	NM_006395.2	NP_006386.1	O95352	ATG7_HUMAN	autophagy related 7	292					adult walking behavior (GO:0007628)|C-terminal protein lipidation (GO:0006501)|cardiac muscle cell development (GO:0055013)|cellular amino acid metabolic process (GO:0006520)|cellular protein modification process (GO:0006464)|cellular response to hyperoxia (GO:0071455)|cellular response to nitrogen starvation (GO:0006995)|cellular response to starvation (GO:0009267)|central nervous system neuron axonogenesis (GO:0021955)|cerebellar Purkinje cell layer development (GO:0021680)|cerebral cortex development (GO:0021987)|late nucleophagy (GO:0044805)|liver development (GO:0001889)|membrane fusion (GO:0061025)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of apoptotic process (GO:0043066)|negative stranded viral RNA replication (GO:0039689)|neurological system process (GO:0050877)|piecemeal microautophagy of nucleus (GO:0034727)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein modification process (GO:0031401)|post-embryonic development (GO:0009791)|protein catabolic process (GO:0030163)|protein lipidation (GO:0006497)|protein modification by small protein conjugation (GO:0032446)|protein transport (GO:0015031)|pyramidal neuron development (GO:0021860)|regulation of protein ubiquitination (GO:0031396)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|pre-autophagosomal structure (GO:0000407)	Atg12 activating enzyme activity (GO:0019778)|Atg8 activating enzyme (GO:0019779)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)|ubiquitin activating enzyme activity (GO:0004839)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(14)|prostate(1)|skin(2)|urinary_tract(1)	34						CTTCCAGAAATGGCATTTAGC	0.433																																					p.M292K		Atlas-SNP	.											.	ATG7	56	.	0			c.T875A						PASS	.						97	86	89					3																	11374553		2203	4300	6503	SO:0001583	missense	10533	exon9			CAGAAATGGCATT	AF094516	CCDS2605.1, CCDS46752.1, CCDS46753.1	3p25.3-p25.2	2014-02-18	2012-06-06	2005-09-11	ENSG00000197548	ENSG00000197548		"Ubiquitin-like modifier activating enzymes"	16935	protein-coding gene	gene with protein product	"ubiquitin-activating enzyme E1-like protein"	608760	"APG7 autophagy 7-like (S. cerevisiae)", "ATG7 autophagy related 7 homolog (S. cerevisiae)"	APG7L		10233149	Standard	NM_006395		Approved	GSA7, DKFZp434N0735	uc003bwc.3	O95352	OTTHUMG00000129740	ENST00000354449.3:c.875T>A	chr3.hg19:g.11374553T>A	ENSP00000346437:p.Met292Lys	91.0	0.0	.		110.0	27.0	.	NM_001136031	B4E170|E9PB95|Q7L8L0|Q9BWP2|Q9UFH4	Missense_Mutation	SNP	ENST00000354449.3	hg19	CCDS2605.1	.	.	.	.	.	.	.	.	.	.	T	13.39	2.222160	0.39300	.	.	ENSG00000197548	ENST00000446450;ENST00000354956;ENST00000354449	T;T;T	0.39787	1.07;1.07;1.06	5.46	5.46	0.80206	.	0.482455	0.22908	N	0.054170	T	0.22513	0.0543	N	0.16903	0.455	0.31387	N	0.678283	B;B;B	0.15930	0.015;0.012;0.007	B;B;B	0.20577	0.008;0.03;0.008	T	0.24476	-1.0159	10	0.06236	T	0.91	-9.8661	8.0007	0.30295	0.0:0.0725:0.1379:0.7896	.	253;292;292	E9PB95;O95352-2;O95352	.;.;ATG7_HUMAN	K	253;292;292	ENSP00000412580:M253K;ENSP00000347042:M292K;ENSP00000346437:M292K	ENSP00000346437:M292K	M	+	2	0	ATG7	11349553	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.115000	0.50391	2.063000	0.61619	0.482000	0.46254	ATG	.	.	.	none		0.433	ATG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251951.3	NM_006395		A	11374553	T	A	11374553	3	1	166	1	0	0	0	0	1	0	0	0	1101	1464	51	5	905	5	ATG7	3	11374553	Missense_Mutation	SNP	T	TCGA-F9-A7VF-01A-11D-A33Q-10	931800	11374553	186647877	15	9777											
RBM15B	29890	hgsc.bcm.edu	37	chr3	51431071	51431071	+	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	gagggggaccagggggtgatCagcagtctcctcaaagacca	11	5	15	10	0	3	2	2	1	1	1	4	4	3	3	3	4	1	1	3	4	1	0			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr3:51431071C>A	ENST00000323686.4	+	1	2341	c.2241C>A	c.(2239-2241)atC>atA	p.I747I		NM_013286.4	NP_037418.3	Q8NDT2	RB15B_HUMAN	RNA binding motif protein 15B	747	Interaction with Epstein-Barr virus BMLF1.|SPOC. {ECO:0000255|PROSITE- ProRule:PRU00249}.				mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|large_intestine(5)|lung(3)	12				BRCA - Breast invasive adenocarcinoma(193;0.000224)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		AGGGGGTGATCAGCAGTCTCC	0.567																																					p.I747I		Atlas-SNP	.											.	RBM15B	47	.	0			c.C2241A						PASS	.						67	73	71					3																	51431071		2203	4300	6503	SO:0001819	synonymous_variant	29890	exon1			GGTGATCAGCAGT	AL831838	CCDS33764.1	3p21.1	2013-02-12			ENSG00000179837	ENSG00000259956		"RNA binding motif (RRM) containing"	24303	protein-coding gene	gene with protein product		612602				16129689	Standard	NM_013286		Approved	HUMAGCGB, OTT3	uc003dbd.3	Q8NDT2	OTTHUMG00000156896	ENST00000323686.4:c.2241C>A	chr3.hg19:g.51431071C>A		79.0	0.0	.		125.0	75.0	.	NM_013286	A4QPG7|Q6QE19|Q9BV96	Silent	SNP	ENST00000323686.4	hg19	CCDS33764.1																																																																																			.	.	.	none		0.567	RBM15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346489.1	NM_013286		A	51431071	C	A	51431071	2	1	166	1	0	0	0	0	0	0	0	1	13130	816	29	4		4	RBM15B	3	51431071	Silent	SNP	C	TCGA-F9-A7VF-01A-11D-A33Q-10	40056518	51431071	146591359	16	9778											
STAB1	23166	hgsc.bcm.edu	37	chr3	52555381	52555381	+	Frame_Shift_Del	DEL	C	C	-																															cctaccccatccccagcttgCcctggcggccccagcagccc																										TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr3:52555381delC	ENST00000321725.6	+	56	5989	c.5913delC	c.(5911-5913)tgcfs	p.C1971fs		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	1971	Laminin EGF-like 2. {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)		CCCCAGCTTGCCCTGGCGGCC	0.637																																					p.C1971fs		Atlas-Indel,Pindel	.											.	STAB1	178	.	0			c.5912delG						PASS	.						98	95	96					3																	52555381		2203	4300	6503	SO:0001589	frameshift_variant	23166	exon56			.	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.5913delC	chr3.hg19:g.52555381delC	ENSP00000312946:p.Cys1971fs	41.0	0.0	0		55.0	30.0	0.545455	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Frame_Shift_Del	DEL	ENST00000321725.6	hg19	CCDS33768.1																																																																																			.	.	.	none		0.637	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		-	52555381	C	-	52555381	7	5	166	1	0	1	0	1	0	0	0	0	15249	747	26	0	6135	0	STAB1	3	52555381	Frame_Shift_Del	DEL	C	TCGA-F9-A7VF-01A-11D-A33Q-10	1124310	52555381	145467049	17	9779											
GRAMD1C	54762	hgsc.bcm.edu	37	chr3	113659165	113659165	+	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	catcgtttaaagggagtgctCcgagactccatagtgatgct	10	11	11	9	2	0	2	0	1	0	1	3	4	2	3	2	1	2	3	2	1	3	3			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr3:113659165C>G	ENST00000358160.4	+	17	2373	c.1881C>G	c.(1879-1881)ctC>ctG	p.L627L	GRAMD1C_ENST00000440446.2_Silent_p.L422L|GRAMD1C_ENST00000472026.1_Silent_p.L460L|GRAMD1C_ENST00000452134.2_Silent_p.L356L|GRAMD1C_ENST00000479212.1_3'UTR	NM_017577.4	NP_060047.3	Q8IYS0	GRM1C_HUMAN	GRAM domain containing 1C	627						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(2)|skin(3)	26						AGGGAGTGCTCCGAGACTCCA	0.413																																					p.L627L		Atlas-SNP	.											.	GRAMD1C	71	.	0			c.C1881G						PASS	.						133	134	134					3																	113659165		2203	4300	6503	SO:0001819	synonymous_variant	54762	exon17			AGTGCTCCGAGAC		CCDS33826.1, CCDS54625.1	3q13.31	2005-11-02			ENSG00000178075	ENSG00000178075			25252	protein-coding gene	gene with protein product						12975309	Standard	NM_017577		Approved	DKFZp434C0328	uc003eaq.4	Q8IYS0	OTTHUMG00000159340	ENST00000358160.4:c.1881C>G	chr3.hg19:g.113659165C>G		112.0	0.0	.		151.0	31.0	.	NM_017577	A8K9Y1|A8KA99|Q6AW94|Q6UWN1|Q8N6S0|Q9UF46	Silent	SNP	ENST00000358160.4	hg19	CCDS33826.1																																																																																			.	.	.	none		0.413	GRAMD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354733.1	NM_017577		G	113659165	C	G	113659165	2	3	166	1	0	0	0	0	0	0	0	1	6756	842	30	4		4	GRAMD1C	3	113659165	Silent	SNP	C	TCGA-F9-A7VF-01A-11D-A33Q-10	61103784	113659165	84363265	18	9780											
DVL3	1857	hgsc.bcm.edu	37	chr3	183888399	183888400	+	Frame_Shift_Ins	INS	-	-	C																															gcccccccatgctgatgatgINScccccgccgcccgcggccat																										TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr3:183888399_183888400insC	ENST00000313143.3	+	15	2255_2256	c.2007_2008insC	c.(2008-2010)cccfs	p.P670fs	EIF2B5_ENST00000444495.1_Intron|DVL3_ENST00000431765.1_Frame_Shift_Ins_p.P653fs	NM_004423.3	NP_004414.3	Q92997	DVL3_HUMAN	dishevelled segment polarity protein 3	670					canonical Wnt signaling pathway (GO:0060070)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|intracellular signal transduction (GO:0035556)|non-canonical Wnt signaling pathway (GO:0035567)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|outflow tract septum morphogenesis (GO:0003148)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	cell cortex (GO:0005938)	beta-catenin binding (GO:0008013)|frizzled binding (GO:0005109)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(6)|liver(1)|lung(13)|ovary(1)|prostate(1)	35	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.08e-34)|OV - Ovarian serous cystadenocarcinoma(80;1.31e-22)			TGCTGATGATGCCCCCGCCGCC	0.723																																					p.M669fs		Atlas-INDEL	.											.	DVL3	68	.	0			c.2007_2008insC						PASS	.																																			SO:0001589	frameshift_variant	1857	exon15			.	D86963	CCDS3253.1	3q27	2013-05-22	2013-05-22		ENSG00000161202	ENSG00000161202		"Dishevelled homologs"	3087	protein-coding gene	gene with protein product		601368	"dishevelled 3 (homologous to Drosophila dsh)", "dishevelled, dsh homolog 3 (Drosophila)"			8817329	Standard	NM_004423		Approved	KIAA0208	uc003fms.3	Q92997	OTTHUMG00000156841	ENST00000313143.3:c.2012dupC	chr3.hg19:g.183888404_183888404dupC	ENSP00000316054:p.Pro670fs	73.0	0.0	0		55.0	11.0	0.2	NM_004423	B4E3E5|D3DNT0|O14642|Q13531|Q8N5E9|Q92607	Frame_Shift_Ins	INS	ENST00000313143.3	hg19	CCDS3253.1																																																																																			.	.	.	none		0.723	DVL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346184.1	NM_004423		C	183888400	-	C	183888399	7	5	166	1	0	1	1	0	0	0	0	0	4839	1319	46	0	2065	0	DVL3	3	183888399	Frame_Shift_Ins	INS	-	TCGA-F9-A7VF-01A-11D-A33Q-10	70229234	183888399	14134031	19	9781											
FAM43A	131583	hgsc.bcm.edu	37	chr3	194408012	194408012	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acgcgcggctgcccaaggtcTtcgcctgggtgtaccggcac	5	7	14	15	5	1	0	0	0	1	0	2	0	1	0	3	4	2	3	3	4	2	2			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr3:194408012T>C	ENST00000329759.4	+	1	1391	c.457T>C	c.(457-459)Ttc>Ctc	p.F153L		NM_153690.4	NP_710157.2	Q8N2R8	FA43A_HUMAN	family with sequence similarity 43, member A	153										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)		GCCCAAGGTCTTCGCCTGGGT	0.706																																					p.F153L		Atlas-SNP	.											.	FAM43A	24	.	0			c.T457C						PASS	.						10	8	8					3																	194408012		2103	4161	6264	SO:0001583	missense	131583	exon1			AAGGTCTTCGCCT	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.457T>C	chr3.hg19:g.194408012T>C	ENSP00000371397:p.Phe153Leu	13.0	0.0	.		23.0	10.0	.	NM_153690	A3KME2|Q8IXP4|Q8WZ07	Missense_Mutation	SNP	ENST00000329759.4	hg19	CCDS33923.1	.	.	.	.	.	.	.	.	.	.	T	28.0	4.881997	0.91740	.	.	ENSG00000185112	ENST00000329759	T	0.74421	-0.84	5.07	5.07	0.68467	Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	D	0.82568	0.5065	L	0.53671	1.685	0.80722	D	1	D	0.71674	0.998	D	0.76071	0.987	D	0.83631	0.0145	10	0.54805	T	0.06	-20.3017	14.0316	0.64619	0.0:0.0:0.0:1.0	.	153	Q8N2R8	FA43A_HUMAN	L	153	ENSP00000371397:F153L	ENSP00000371397:F153L	F	+	1	0	FAM43A	195889301	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.573000	0.82421	1.913000	0.55393	0.379000	0.24179	TTC	.	.	.	none		0.706	FAM43A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342734.1	NM_153690		C	194408012	T	C	194408012	3	2	166	1	0	0	0	0	1	0	0	0	5569	1609	56	3	459	3	FAM43A	3	194408012	Missense_Mutation	SNP	T	TCGA-F9-A7VF-01A-11D-A33Q-10	10519613	194408012	3614418	20	9782											
MAEA	10296	hgsc.bcm.edu	37	chr4	1305935	1305935	+	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	gcgtggtggagaagctcagcGtcctcaagaggaaggttggt	9	8	17	7	2	2	2	2	0	0	2	3	4	3	3	1	5	2	2	1	5	3	1	rs146286709		TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr4:1305935G>C	ENST00000303400.4	+	2	301	c.238G>C	c.(238-240)Gtc>Ctc	p.V80L	MAEA_ENST00000505839.1_Missense_Mutation_p.V32L|MAEA_ENST00000510794.1_Missense_Mutation_p.V79L|MAEA_ENST00000505177.2_Missense_Mutation_p.V80L|MAEA_ENST00000264750.6_Missense_Mutation_p.V80L|MAEA_ENST00000514708.1_Missense_Mutation_p.V80L|MAEA_ENST00000452175.2_Missense_Mutation_p.V69L	NM_001017405.1	NP_001017405.1	Q7L5Y9	MAEA_HUMAN	macrophage erythroblast attacher	80	Extracellular and involved in cell to cell contact.				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)	GAAGCTCAGCGTCCTCAAGAG	0.627																																					p.V80L		Atlas-SNP	.											.	MAEA	39	.	0			c.G238C						PASS	.						35	38	37					4																	1305935		2203	4300	6503	SO:0001583	missense	10296	exon2			CTCAGCGTCCTCA	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.238G>C	chr4.hg19:g.1305935G>C	ENSP00000302830:p.Val80Leu	122.0	0.0	.		67.0	21.0	.	NM_005882	O95285|Q5JB54|Q6ZRD6|Q9BQ11|Q9H9V6|Q9H9Z4|Q9NW84	Missense_Mutation	SNP	ENST00000303400.4	hg19	CCDS33936.1	.	.	.	.	.	.	.	.	.	.	G	19.48	3.836364	0.71373	.	.	ENSG00000090316	ENST00000303400;ENST00000505177;ENST00000503653;ENST00000264750;ENST00000382947;ENST00000539495;ENST00000502558;ENST00000452175;ENST00000514708;ENST00000510794;ENST00000512842;ENST00000505839	T;T;T;T;T;T;T;T	0.47177	0.94;0.93;0.88;0.92;0.85;0.88;0.91;0.93	5.94	5.09	0.68999	.	0.054564	0.64402	D	0.000001	T	0.46908	0.1417	M	0.64404	1.975	0.38491	D	0.947969	B;B;B;B;B;B	0.27882	0.074;0.171;0.07;0.192;0.07;0.002	B;B;B;B;B;B	0.29077	0.057;0.081;0.098;0.094;0.076;0.012	T	0.43861	-0.9365	10	0.27785	T	0.31	-17.4029	15.5456	0.76097	0.0673:0.0:0.9327:0.0	.	79;80;80;80;80;80	B4DVN3;E7ESC7;Q7L5Y9-2;D6RIB6;Q7L5Y9-3;Q7L5Y9	.;.;.;.;.;MAEA_HUMAN	L	80;80;80;80;80;59;80;69;80;79;32;32	ENSP00000302830:V80L;ENSP00000422215:V80L;ENSP00000421644:V80L;ENSP00000264750:V80L;ENSP00000426903:V80L;ENSP00000411415:V69L;ENSP00000427512:V80L;ENSP00000426807:V79L	ENSP00000264750:V80L	V	+	1	0	MAEA	1295935	1.000000	0.71417	0.927000	0.36925	0.977000	0.68977	7.630000	0.83225	2.815000	0.96918	0.650000	0.86243	GTC	.	G|1.000;A|0.000	.	alt		0.627	MAEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359511.1	NM_005882		C	1305935	G	C	1305935	3	2	166	1	0	0	0	0	1	0	0	0	9160	1145	40	4	244	4	MAEA	4	1305935	Missense_Mutation	SNP	G	TCGA-F9-A7VF-01A-11D-A33Q-10		1305935	189848341	21	9783											
SH3TC1	54436	hgsc.bcm.edu	37	chr4	8229479	8229479	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcccgaggaggccctgccCttcctagagcggctgctgct	5	7	13	16	2	0	1	0	0	0	1	1	3	1	2	4	3	5	3	4	3	1	2			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr4:8229479C>T	ENST00000245105.3	+	12	2125	c.2058C>T	c.(2056-2058)ccC>ccT	p.P686P	SH3TC1_ENST00000539824.1_Silent_p.P610P	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	686										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						AGGCCCTGCCCTTCCTAGAGC	0.692																																					p.P686P	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											.	SH3TC1	105	.	0			c.C2058T						PASS	.						15	19	18					4																	8229479		2155	4213	6368	SO:0001819	synonymous_variant	54436	exon12			CCTGCCCTTCCTA	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.2058C>T	chr4.hg19:g.8229479C>T		87.0	0.0	.		42.0	13.0	.	NM_018986	Q4W5G5	Silent	SNP	ENST00000245105.3	hg19	CCDS3399.1																																																																																			.	.	.	none		0.692	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986		T	8229479	C	T	8229479	2	4	166	1	0	0	0	0	0	0	0	1	14274	668	24	2		2	SH3TC1	4	8229479	Silent	SNP	C	TCGA-F9-A7VF-01A-11D-A33Q-10	6923544	8229479	182924797	22	9784											
HS3ST1	9957	hgsc.bcm.edu	37	chr4	11401470	11401470	+	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	gatgatgatggtctgcggcaActgctgggcagagccgtttg	7	10	16	8	2	1	3	0	2	1	1	1	4	1	3	1	3	4	4	1	3	1	1	rs183663781		TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr4:11401470A>T	ENST00000002596.5	-	2	1334	c.160T>A	c.(160-162)Ttg>Atg	p.L54M		NM_005114.2	NP_005105.1	O14792	HS3S1_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	54					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						GTCTGCGGCAACTGCTGGGCA	0.701																																					p.L54M		Atlas-SNP	.											.	HS3ST1	41	.	0			c.T160A						PASS	.						31	28	29					4																	11401470		2202	4298	6500	SO:0001583	missense	9957	exon2			GCGGCAACTGCTG	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.160T>A	chr4.hg19:g.11401470A>T	ENSP00000002596:p.Leu54Met	49.0	0.0	.		30.0	13.0	.	NM_005114	B3KUA6|Q6PEY8	Missense_Mutation	SNP	ENST00000002596.5	hg19	CCDS3408.1	.	.	.	.	.	.	.	.	.	.	A	13.09	2.132217	0.37630	.	.	ENSG00000002587	ENST00000002596;ENST00000514690;ENST00000510712	T;T;T	0.59772	0.24;0.24;0.24	5.57	4.73	0.59995	.	0.328799	0.28754	N	0.014246	T	0.80093	0.4560	H	0.94886	3.595	0.50313	D	0.999861	D	0.67145	0.996	D	0.71414	0.973	D	0.83531	0.0091	10	0.72032	D	0.01	.	9.763	0.40543	0.1558:0.0:0.8442:0.0	.	54	O14792	HS3S1_HUMAN	M	54	ENSP00000002596:L54M;ENSP00000425673:L54M;ENSP00000422629:L54M	ENSP00000002596:L54M	L	-	1	2	HS3ST1	11010568	1.000000	0.71417	0.997000	0.53966	0.117000	0.20001	4.210000	0.58500	1.371000	0.46172	-0.132000	0.14878	TTG	.	A|0.999;C|0.001	.	alt		0.701	HS3ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207073.3	NM_005114		T	11401470	A	T	11401470	3	4	166	1	0	0	0	0	1	0	0	0	7370	40	2	5	767	5	HS3ST1	4	11401470	Missense_Mutation	SNP	A	TCGA-F9-A7VF-01A-11D-A33Q-10	3171991	11401470	179752806	23	9785											
COQ2	27235	hgsc.bcm.edu	37	chr4	84185397	84185397	+	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	cccttctttgttttgtctgtCttcttttctttccacaaatt	4	23	3	11	0	5	0	0	0	5	0	6	0	6	0	2	0	0	1	2	0	1	9			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr4:84185397C>T	ENST00000311469.4	-	7	1220	c.1221G>A	c.(1219-1221)aaG>aaA	p.K407K	COQ2_ENST00000439031.2_Silent_p.K370K	NM_015697.7	NP_056512.5	Q96H96	COQ2_HUMAN	coenzyme Q2 4-hydroxybenzoate polyprenyltransferase	357					cell death (GO:0008219)|glycerol metabolic process (GO:0006071)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	4-hydroxybenzoate decaprenyltransferase activity (GO:0002083)|4-hydroxybenzoate nonaprenyltransferase activity (GO:0047293)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|ovary(1)|skin(1)|stomach(1)	8		Hepatocellular(203;0.114)				TTTTGTCTGTCTTCTTTTCTT	0.284																																					p.K407K		Atlas-SNP	.											.	COQ2	22	.	0			c.G1221A						PASS	.						57	51	53					4																	84185397		1776	4061	5837	SO:0001819	synonymous_variant	27235	exon7			GTCTGTCTTCTTT		CCDS47090.1, CCDS47090.2	4q21.23	2013-05-23	2013-05-23				2.5.1.39		25223	protein-coding gene	gene with protein product	"4-hydroxybenzoate polyprenyltransferase"	609825	"coenzyme Q2 homolog, prenyltransferase (yeast)"			15153069, 17332895	Standard	NM_015697		Approved	CL640, FLJ26072	uc003hog.3	Q96H96		ENST00000311469.4:c.1221G>A	chr4.hg19:g.84185397C>T		249.0	0.0	.		201.0	71.0	.	NM_015697	O95331|Q1JQ78|Q684R2	Silent	SNP	ENST00000311469.4	hg19	CCDS47090.2																																																																																			.	.	.	none		0.284	COQ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363027.3	NM_015697		T	84185397	C	T	84185397	2	4	166	1	0	0	0	0	0	0	0	1	3747	912	32	2		2	COQ2	4	84185397	Silent	SNP	C	TCGA-F9-A7VF-01A-11D-A33Q-10	72783927	84185397	106968879	24	9786											
PCDH18	54510	hgsc.bcm.edu	37	chr4	138452939	138452940	+	Frame_Shift_Ins	INS	-	-	CT																															aactctatggaacagttcaaINSgtttttctggcacagttgtt																										TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr4:138452939_138452940insCT	ENST00000344876.4	-	1	689_690	c.303_304insAG	c.(301-306)aacttgfs	p.L102fs	PCDH18_ENST00000510305.1_Intron|PCDH18_ENST00000412923.2_Frame_Shift_Ins_p.L102fs|PCDH18_ENST00000511115.1_Intron|PCDH18_ENST00000507846.1_Intron	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	102	Cadherin 1. {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)					GAACAGTTCAAGTTTTTCTGGC	0.426																																					p.L102fs		Atlas-INDEL	.											.	PCDH18	229	.	0			c.304_305insAG						PASS	.																																			SO:0001589	frameshift_variant	54510	exon1			.	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.303_304insAG	chr4.hg19:g.138452939_138452940insCT	ENSP00000355082:p.Leu102fs	136.0	0.0	0		87.0	29.0	0.333333	NM_019035	A8K7K3|B7ZKT1|Q52LS2	Frame_Shift_Ins	INS	ENST00000344876.4	hg19	CCDS34064.1																																																																																			.	.	.	none		0.426	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		CT	138452940	-	CT	138452939	7	5	166	1	0	1	1	0	0	0	0	0	11520	69	3	0	3119	0	PCDH18	4	138452939	Frame_Shift_Ins	INS	-	TCGA-F9-A7VF-01A-11D-A33Q-10	54267542	138452939	52701337	25	9787	94	2									
PCDH18	54510	hgsc.bcm.edu	37	chr4	138452946	138452946	+	Silent	SNP	C	C	T																															atggaacagttcaagtttttCtggcacagttgttcacggtc																										TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr4:138452946C>T	ENST00000344876.4	-	1	683	c.297G>A	c.(295-297)caG>caA	p.Q99Q	PCDH18_ENST00000510305.1_Intron|PCDH18_ENST00000412923.2_Silent_p.Q99Q|PCDH18_ENST00000511115.1_Intron|PCDH18_ENST00000507846.1_Intron	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	99	Cadherin 1. {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)					TCAAGTTTTTCTGGCACAGTT	0.428																																					p.Q99Q		Atlas-SNP	.											PCDH18,NS,carcinoma,0,1	PCDH18	229	.	0			c.G297A						PASS	.						168	165	166					4																	138452946		2203	4300	6503	SO:0001819	synonymous_variant	54510	exon1			GTTTTTCTGGCAC	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.297G>A	chr4.hg19:g.138452946C>T		134.0	0.0	.		89.0	33.0	.	NM_019035	A8K7K3|B7ZKT1|Q52LS2	Silent	SNP	ENST00000344876.4	hg19	CCDS34064.1																																																																																			.	.	.	none		0.428	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		T	138452946	C	T	138452946	2	4	166	1	0	0	0	0	0	0	0	1	11520	912	32	2		2	PCDH18	4	138452946	Silent	SNP	C	TCGA-F9-A7VF-01A-11D-A33Q-10	7	138452946	52701330	26	9788	94	2									
PPID	5481	hgsc.bcm.edu	37	chr4	159634384	159634384	+	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	cttggctctatctgctgtctCaataacagcctttgaactgt	8	15	7	11	0	3	1	1	1	3	0	4	1	3	1	1	1	4	2	1	1	4	4			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr4:159634384C>A	ENST00000307720.3	-	7	888	c.781G>T	c.(781-783)Gag>Tag	p.E261*		NM_005038.2	NP_005029.1	Q08752	PPID_HUMAN	peptidylprolyl isomerase D	261	Interaction with HSP90AB1. {ECO:0000250}.				apoptotic process (GO:0006915)|cellular response to UV-A (GO:0071492)|chaperone-mediated protein folding (GO:0061077)|lipid particle organization (GO:0034389)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein secretion (GO:0050714)|positive regulation of viral genome replication (GO:0045070)|protein complex assembly (GO:0006461)|protein folding (GO:0006457)|protein transport (GO:0015031)|viral release from host cell (GO:0019076)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|estrogen receptor binding (GO:0030331)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|Hsp90 protein binding (GO:0051879)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|transcription factor binding (GO:0008134)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)	8	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0159)		TCTGCTGTCTCAATAACAGCC	0.398																																					p.E261X		Atlas-SNP	.											.	PPID	22	.	0			c.G781T						PASS	.						127	116	120					4																	159634384		2203	4300	6503	SO:0001587	stop_gained	5481	exon7			CTGTCTCAATAAC		CCDS3801.1	4q31.3	2013-01-10	2008-10-24		ENSG00000171497	ENSG00000171497		"Tetratricopeptide (TTC) repeat domain containing"	9257	protein-coding gene	gene with protein product	"cyclophilin 40"	601753	"peptidylprolyl isomerase D (cyclophilin D)"			8509368	Standard	NM_005038		Approved	CYP-40	uc003iqc.3	Q08752	OTTHUMG00000161927	ENST00000307720.3:c.781G>T	chr4.hg19:g.159634384C>A	ENSP00000303754:p.Glu261*	86.0	0.0	.		77.0	34.0	.	NM_005038	B2R9V2	Nonsense_Mutation	SNP	ENST00000307720.3	hg19	CCDS3801.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.650373	0.87958	.	.	ENSG00000171497	ENST00000307720	.	.	.	5.44	1.71	0.24356	.	0.331752	0.20962	N	0.082560	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	-16.4158	8.7939	0.34868	0.0:0.6398:0.2319:0.1282	.	.	.	.	X	261	.	ENSP00000303754:E261X	E	-	1	0	PPID	159853834	0.882000	0.30256	0.005000	0.12908	0.160000	0.22226	3.156000	0.50708	0.162000	0.19483	0.650000	0.86243	GAG	.	.	.	none		0.398	PPID-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366436.1	NM_005038		A	159634384	C	A	159634384	4	1	166	1	0	0	0	0	0	1	0	0	12331	835	29	4	347	4	PPID	4	159634384	Nonsense_Mutation	SNP	C	TCGA-F9-A7VF-01A-11D-A33Q-10	21181438	159634384	31519892	27	9789											
PKD2L2	27039	hgsc.bcm.edu	37	chr5	137271569	137271569	+	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	atggaaattcaagatgactaCcagcctgtcactcaagaaga	16	8	8	9	0	3	4	3	1	0	3	3	5	3	5	2	1	2	0	2	1	5	2			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr5:137271569C>G	ENST00000508883.1	+	13	1781	c.1755C>G	c.(1753-1755)taC>taG	p.Y585*	PKD2L2_ENST00000290431.5_Nonsense_Mutation_p.Y585*|PKD2L2_ENST00000502810.1_Nonsense_Mutation_p.Y563*|PKD2L2_ENST00000508638.1_Nonsense_Mutation_p.Y484*|PKD2L2_ENST00000350250.4_Nonsense_Mutation_p.Y551*			Q9NZM6	PK2L2_HUMAN	polycystic kidney disease 2-like 2	585					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)			AAGATGACTACCAGCCTGTCA	0.388																																					p.Y585X		Atlas-SNP	.											.	PKD2L2	68	.	0			c.C1755G						PASS	.						94	93	93					5																	137271569		1845	4093	5938	SO:0001587	stop_gained	27039	exon13			TGACTACCAGCCT	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.1755C>G	chr5.hg19:g.137271569C>G	ENSP00000424725:p.Tyr585*	62.0	0.0	.		56.0	22.0	.	NM_014386	A6NK98|B4DXD2|E9PC91|E9PDG4|Q86YB4|Q9UNJ0	Nonsense_Mutation	SNP	ENST00000508883.1	hg19		.	.	.	.	.	.	.	.	.	.	C	22.5	4.302549	0.81136	.	.	ENSG00000078795	ENST00000350250;ENST00000508638;ENST00000502810;ENST00000508883;ENST00000290431	.	.	.	5.43	1.56	0.23342	.	0.252794	0.27971	N	0.017101	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	-5.6504	8.3066	0.32047	0.0:0.6543:0.0:0.3457	.	.	.	.	X	551;484;563;585;585	.	ENSP00000290431:Y585X	Y	+	3	2	PKD2L2	137299468	1.000000	0.71417	0.999000	0.59377	0.954000	0.61252	0.387000	0.20718	0.347000	0.23924	0.655000	0.94253	TAC	.	.	.	none		0.388	PKD2L2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372521.1	NM_014386		G	137271569	C	G	137271569	4	3	166	1	0	0	0	0	0	1	0	0	11975	518	18	4	1805	4	PKD2L2	5	137271569	Nonsense_Mutation	SNP	C	TCGA-F9-A7VF-01A-11D-A33Q-10		137271569	43643691	28	9790											
F12	2161	hgsc.bcm.edu	37	chr5	176831557	176831557	+	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	cttgctcggcagtcacgttcCggtaggtggcctccgaggcc	4	9	14	14	4	1	0	1	0	0	0	4	1	3	0	4	5	1	4	4	5	1	3			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr5:176831557C>A	ENST00000253496.3	-	8	791	c.743G>T	c.(742-744)cGg>cTg	p.R248L	F12_ENST00000514943.1_5'Flank	NM_000505.3	NP_000496.2	P00748	FA12_HUMAN	coagulation factor XII (Hageman factor)	248	Kringle. {ECO:0000255|PROSITE- ProRule:PRU00121}.				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)	AGTCACGTTCCGGTAGGTGGC	0.736									Hereditary Angioedema		OREG0017088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R248L		Atlas-SNP	.											.	F12	35	.	0			c.G743T						PASS	.						11	14	13					5																	176831557		2173	4280	6453	SO:0001583	missense	2161	exon8	Familial Cancer Database	HAE, type I-III, Hereditary Angioneurotic Edema, HANE,	ACGTTCCGGTAGG	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.743G>T	chr5.hg19:g.176831557C>A	ENSP00000253496:p.Arg248Leu	42.0	0.0	.	1934	34.0	18.0	.	NM_000505	P78339	Missense_Mutation	SNP	ENST00000253496.3	hg19	CCDS34302.1	.	.	.	.	.	.	.	.	.	.	C	11.54	1.669323	0.29604	.	.	ENSG00000131187	ENST00000253496	T	0.66995	-0.24	5.31	1.21	0.21127	Kringle (4);Kringle-like fold (1);	1.106110	0.07016	N	0.825978	T	0.58032	0.2094	L	0.48260	1.515	0.18873	N	0.999988	B	0.24258	0.1	B	0.29785	0.107	T	0.51188	-0.8737	10	0.48119	T	0.1	.	3.2323	0.06752	0.1851:0.5144:0.0:0.3005	.	248	P00748	FA12_HUMAN	L	248	ENSP00000253496:R248L	ENSP00000253496:R248L	R	-	2	0	F12	176764163	0.000000	0.05858	0.502000	0.27614	0.140000	0.21249	0.283000	0.18846	0.366000	0.24427	0.561000	0.74099	CGG	.	.	.	none		0.736	F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373217.1			A	176831557	C	A	176831557	3	1	166	1	0	0	0	0	1	0	0	0	5341	652	23	4	1132	4	F12	5	176831557	Missense_Mutation	SNP	C	TCGA-F9-A7VF-01A-11D-A33Q-10	39559988	176831557	4083703	29	9791											
ITPR3	3710	hgsc.bcm.edu	37	chr6	33638181	33638181	+	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	agatctcccagcagctgggcGtggacctgattttcctgtgc	6	11	12	12	1	1	2	0	1	1	1	3	3	2	3	3	2	3	2	3	2	0	2			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr6:33638181G>T	ENST00000374316.5	+	20	3329	c.2269G>T	c.(2269-2271)Gtg>Ttg	p.V757L	ITPR3_ENST00000605930.1_Missense_Mutation_p.V757L			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	757					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)	GCAGCTGGGCGTGGACCTGAT	0.612																																					p.V757L		Atlas-SNP	.											.	ITPR3	409	.	0			c.G2269T						PASS	.						137	123	128					6																	33638181		2203	4300	6503	SO:0001583	missense	3710	exon19			CTGGGCGTGGACC	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.2269G>T	chr6.hg19:g.33638181G>T	ENSP00000363435:p.Val757Leu	67.0	0.0	.		52.0	46.0	.	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	hg19	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.297216	0.81025	.	.	ENSG00000096433	ENST00000374316	D	0.91577	-2.87	4.81	3.94	0.45596	.	0.073011	0.56097	D	0.000033	D	0.87629	0.6225	M	0.65975	2.015	0.42224	D	0.991862	P	0.47604	0.898	P	0.47645	0.553	D	0.86865	0.2032	10	0.46703	T	0.11	-20.5941	12.6317	0.56661	0.0805:0.0:0.9195:0.0	.	757	Q14573	ITPR3_HUMAN	L	757	ENSP00000363435:V757L	ENSP00000363435:V757L	V	+	1	0	ITPR3	33746159	1.000000	0.71417	0.847000	0.33407	0.987000	0.75469	4.668000	0.61568	1.012000	0.39366	0.563000	0.77884	GTG	.	.	.	none		0.612	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224		T	33638181	G	T	33638181	3	4	166	1	0	0	0	0	1	0	0	0	7929	1145	40	4	2343	4	ITPR3	6	33638181	Missense_Mutation	SNP	G	TCGA-F9-A7VF-01A-11D-A33Q-10		33638181	137476886	30	9792											
ACTB	60	hgsc.bcm.edu	37	chr7	5567773	5567773	+	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	atgtccacgtcacacttcatGatggagttgaaggtagtttc	10	13	10	8	1	2	2	2	2	0	0	4	3	3	3	1	2	0	3	1	2	2	4			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr7:5567773G>A	ENST00000331789.5	-	5	1037	c.846C>T	c.(844-846)atC>atT	p.I282I	ACTB_ENST00000464611.1_5'Flank|AC006483.1_ENST00000579427.1_RNA	NM_001101.3	NP_001092.1	P63261	ACTG_HUMAN	actin, beta	282					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)		CACACTTCATGATGGAGTTGA	0.567																																					p.I282I		Atlas-SNP	.											.	ACTB	45	.	0			c.C846T						PASS	.						150	146	148					7																	5567773		2203	4300	6503	SO:0001819	synonymous_variant	60	exon5			CTTCATGATGGAG	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.846C>T	chr7.hg19:g.5567773G>A		68.0	0.0	.		90.0	27.0	.	NM_001101	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Silent	SNP	ENST00000331789.5	hg19	CCDS5341.1																																																																																			.	.	.	none		0.567	ACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059589.4	NM_001101		A	5567773	G	A	5567773	2	1	166	1	0	0	0	0	0	0	0	1	193	1280	45	2		2	ACTB	7	5567773	Silent	SNP	G	TCGA-F9-A7VF-01A-11D-A33Q-10		5567773	153570890	31	9793											
C7orf63	79846	hgsc.bcm.edu	37	chr7	89903320	89903320	+	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	gggctttgaaggaagtatttAaaaatctgtttatgagaggt	13	14	12	2	0	1	2	0	2	1	1	1	4	1	3	0	3	0	3	0	3	7	6			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr7:89903320A>T	ENST00000389297.4	+	9	1131	c.880A>T	c.(880-882)Aaa>Taa	p.K294*	C7orf63_ENST00000497910.1_Nonsense_Mutation_p.K276*|C7orf63_ENST00000316089.8_Nonsense_Mutation_p.K294*	NM_001039706.2|NM_001160138.1	NP_001034795.2|NP_001153610.1	A5D8W1	CG063_HUMAN		294										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|prostate(3)	37						GGAAGTATTTAAAAATCTGTT	0.294																																					p.K294X		Atlas-SNP	.											.	C7orf63	158	.	0			c.A880T						PASS	.						56	53	54					7																	89903320		1801	4059	5860	SO:0001587	stop_gained	79846	exon9			GTATTTAAAAATC																												ENST00000389297.4:c.880A>T	chr7.hg19:g.89903320A>T	ENSP00000373948:p.Lys294*	208.0	1.0	.		272.0	140.0	.	NM_001039706	A3KMP9|B4DYW6|B4DZP7|B9EIM7|Q6V705|Q8IY89|Q9H7C2	Nonsense_Mutation	SNP	ENST00000389297.4	hg19	CCDS43613.2	.	.	.	.	.	.	.	.	.	.	A	19.61	3.859359	0.71834	.	.	ENSG00000105792	ENST00000389297;ENST00000316089;ENST00000497910;ENST00000457170	.	.	.	5.33	5.33	0.75918	.	0.542673	0.17704	N	0.164814	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.0252	8.6919	0.34271	0.909:0.0:0.091:0.0	.	.	.	.	X	294;294;276;234	.	ENSP00000321753:K294X	K	+	1	0	C7orf63	89741256	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	1.473000	0.35387	2.234000	0.73211	0.533000	0.62120	AAA	.	.	.	none		0.294	C7orf63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139891.4			T	89903320	A	T	89903320	4	4	166	1	0	0	0	0	0	1	0	0	2411	363	13	5	914	5	C7orf63	7	89903320	Nonsense_Mutation	SNP	A	TCGA-F9-A7VF-01A-11D-A33Q-10	84335547	89903320	69235343	32	9794											
CCDC132	55610	hgsc.bcm.edu	37	chr7	92905642	92905642	+	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	gtagtgacttaattactattCatatatctctcctttagatt	11	19	4	7	0	2	2	1	1	1	1	4	2	3	2	1	0	1	1	1	0	7	10			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr7:92905642C>T	ENST00000305866.5	+	12	1070				CCDC132_ENST00000544910.1_Intron|CCDC132_ENST00000251739.5_Missense_Mutation_p.H323Y|CCDC132_ENST00000535481.1_Intron|CCDC132_ENST00000317751.6_Intron|CCDC132_ENST00000541136.1_Intron	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)			AATTACTATTCATATATCTCT	0.284																																					p.H323Y		Atlas-SNP	.											.	CCDC132	136	.	0			c.C967T						PASS	.						77	77	77					7																	92905642		2203	4300	6503	SO:0001627	intron_variant	55610	exon12			ACTATTCATATAT	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.942+25C>T	chr7.hg19:g.92905642C>T		62.0	0.0	.		78.0	15.0	.	NM_024553	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	hg19	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	C	5.007	0.187013	0.09547	.	.	ENSG00000004766	ENST00000251739	.	.	.	4.54	-1.73	0.08081	.	.	.	.	.	T	0.36193	0.0958	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37244	-0.9714	7	0.87932	D	0	.	10.8309	0.46659	0.0:0.2665:0.0:0.7335	.	323	Q96JG6-2	.	Y	323	.	ENSP00000251739:H323Y	H	+	1	0	CCDC132	92743578	0.000000	0.05858	0.000000	0.03702	0.081000	0.17604	-0.406000	0.07187	-0.297000	0.08934	-0.140000	0.14226	CAT	.	.	.	none		0.284	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667		T	92905642	C	T	92905642	1	4	166	0	1	0	0	0	0	0	0	0	2769	826	29	2		2	CCDC132	7	92905642	Intron	SNP	C	TCGA-F9-A7VF-01A-11D-A33Q-10	3002322	92905642	66233021	33	9795											
TRIM56	81844	hgsc.bcm.edu	37	chr7	100732116	100732116	+	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	gcctggagacaagcggtcccCccggatcaccgggctctgtc	6	6	13	16	3	2	1	1	0	1	1	4	3	3	2	5	4	1	1	5	4	1	0			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr7:100732116C>T	ENST00000306085.6	+	3	1820	c.1523C>T	c.(1522-1524)cCc>cTc	p.P508L		NM_030961.1	NP_112223.1	Q9BRZ2	TRI56_HUMAN	tripartite motif containing 56	508					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)					AAGCGGTCCCCCCGGATCACC	0.647																																					p.P508L	Ovarian(89;1092 1379 22756 38989 39611)	Atlas-SNP	.											TRIM56_ENST00000306085,right_lower_lobe,carcinoma,0,2	TRIM56	123	.	0			c.C1523T						PASS	.						59	68	65					7																	100732116		2003	4161	6164	SO:0001583	missense	81844	exon3			GGTCCCCCCGGAT	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.1523C>T	chr7.hg19:g.100732116C>T	ENSP00000305161:p.Pro508Leu	67.0	0.0	.		98.0	32.0	.	NM_030961	Q6PJS5|Q86VT6|Q8N2H8|Q8NAC0|Q9H031	Missense_Mutation	SNP	ENST00000306085.6	hg19	CCDS43625.1	.	.	.	.	.	.	.	.	.	.	C	13.71	2.319380	0.41096	.	.	ENSG00000169871	ENST00000306085	T	0.53206	0.63	3.88	3.88	0.44766	Six-bladed beta-propeller, TolB-like (1);	.	.	.	.	T	0.49660	0.1570	N	0.19112	0.55	0.40985	D	0.984807	D	0.89917	1.0	D	0.80764	0.994	T	0.40440	-0.9563	9	0.29301	T	0.29	.	11.6346	0.51196	0.0:1.0:0.0:0.0	.	508	Q9BRZ2	TRI56_HUMAN	L	508	ENSP00000305161:P508L	ENSP00000305161:P508L	P	+	2	0	TRIM56	100518836	0.745000	0.28261	0.514000	0.27761	0.284000	0.27059	4.092000	0.57707	2.449000	0.82847	0.591000	0.81541	CCC	.	.	.	none		0.647	TRIM56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347185.1	NM_030961		T	100732116	C	T	100732116	3	4	166	1	0	0	0	0	1	0	0	0	16542	623	22	2	1525	2	TRIM56	7	100732116	Missense_Mutation	SNP	C	TCGA-F9-A7VF-01A-11D-A33Q-10	7826474	100732116	58406547	34	9796											
CHRM2	1129	hgsc.bcm.edu	37	chr7	136700128	136700128	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtaggggtgagaactgtggaGgatggggagtgctacattca	10	9	18	4	0	1	1	1	1	0	1	1	5	1	4	0	6	3	2	0	6	3	3			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr7:136700128G>A	ENST00000445907.2	+	3	1044	c.516G>A	c.(514-516)gaG>gaA	p.E172E	hsa-mir-490_ENST00000597642.1_RNA|CHRM2_ENST00000320658.5_Silent_p.E172E|CHRM2_ENST00000397608.3_Silent_p.E172E|hsa-mir-490_ENST00000439694.1_RNA|CHRM2_ENST00000402486.3_Silent_p.E172E|CHRM2_ENST00000401861.1_Silent_p.E172E|hsa-mir-490_ENST00000593789.1_RNA|hsa-mir-490_ENST00000598184.1_RNA|hsa-mir-490_ENST00000425981.2_RNA|CHRM2_ENST00000453373.1_Silent_p.E172E|hsa-mir-490_ENST00000592183.1_RNA|hsa-mir-490_ENST00000586239.1_RNA	NM_001006627.1|NM_001006629.1	NP_001006628.1|NP_001006630.1	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	172					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|nervous system development (GO:0007399)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|regulation of heart contraction (GO:0008016)|response to virus (GO:0009615)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(13)|liver(1)|lung(29)|ovary(4)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	68					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Bethanechol(DB01019)|Brompheniramine(DB00835)|Carbachol(DB00411)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Dimetindene(DB08801)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxacurium chloride(DB01135)|Doxepin(DB01142)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Rocuronium(DB00728)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	GAACTGTGGAGGATGGGGAGT	0.493																																					p.E172E		Atlas-SNP	.											CHRM2,NS,carcinoma,0,1	CHRM2	167	.	0			c.G516A						PASS	.						114	107	109					7																	136700128		2203	4300	6503	SO:0001819	synonymous_variant	1129	exon3			TGTGGAGGATGGG		CCDS5843.1	7q35-q36	2014-09-17			ENSG00000181072	ENSG00000181072		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1951	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 2"	118493					Standard	NM_000739		Approved		uc003vtl.1	P08172	OTTHUMG00000155658	ENST00000445907.2:c.516G>A	chr7.hg19:g.136700128G>A		64.0	0.0	.		101.0	25.0	.	NM_001006632	Q4VBK6|Q9P1X9	Silent	SNP	ENST00000445907.2	hg19	CCDS5843.1																																																																																			.	.	.	none		0.493	CHRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341010.1			A	136700128	G	A	136700128	2	1	166	1	0	0	0	0	0	0	0	1	3379	991	35	2		2	CHRM2	7	136700128	Silent	SNP	G	TCGA-F9-A7VF-01A-11D-A33Q-10	35968012	136700128	22438535	35	9797											
PLEC	5339	hgsc.bcm.edu	37	chr8	144990855	144990855	+	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	tggccggcctcgtagtagagCcagcccttcttcagggcctg	5	9	13	14	2	2	1	1	0	1	1	3	1	2	1	5	3	2	2	5	3	2	4			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr8:144990855C>A	ENST00000322810.4	-	32	13714	c.13545G>T	c.(13543-13545)tgG>tgT	p.W4515C	PLEC_ENST00000527096.1_Missense_Mutation_p.W4401C|PLEC_ENST00000354589.3_Missense_Mutation_p.W4378C|PLEC_ENST00000356346.3_Missense_Mutation_p.W4364C|PLEC_ENST00000436759.2_Missense_Mutation_p.W4405C|PLEC_ENST00000398774.2_Missense_Mutation_p.W4346C|PLEC_ENST00000357649.2_Missense_Mutation_p.W4382C|PLEC_ENST00000345136.3_Missense_Mutation_p.W4378C|PLEC_ENST00000354958.2_Missense_Mutation_p.W4356C	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	4515	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						CGTAGTAGAGCCAGCCCTTCT	0.687																																					p.W4515C		Atlas-SNP	.											.	PLEC	1144	.	0			c.G13545T						PASS	.						28	32	31					8																	144990855		2033	4179	6212	SO:0001583	missense	5339	exon32			GTAGAGCCAGCCC	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.13545G>T	chr8.hg19:g.144990855C>A	ENSP00000323856:p.Trp4515Cys	45.0	0.0	.		33.0	17.0	.	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	hg19	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	C	12.16	1.854233	0.32791	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34;-0.34;-0.34;-0.34;-0.34;-0.34	5.19	5.19	0.71726	.	0.000000	0.64402	U	0.000007	T	0.75606	0.3872	L	0.41492	1.28	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;P;D;D;D;D	0.66084	0.941;0.941;0.941;0.875;0.941;0.941;0.941;0.941	T	0.77797	-0.2453	10	0.87932	D	0	.	18.5216	0.90954	0.0:1.0:0.0:0.0	.	4405;4364;4356;4515;4346;4378;4382;4378	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	C	4378;4382;4378;4346;4515;4356;4364;4405;4401	ENSP00000344848:W4378C;ENSP00000350277:W4382C;ENSP00000346602:W4378C;ENSP00000381756:W4346C;ENSP00000323856:W4515C;ENSP00000347044:W4356C;ENSP00000348702:W4364C;ENSP00000388180:W4405C;ENSP00000434583:W4401C	ENSP00000323856:W4515C	W	-	3	0	PLEC	145062843	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.593000	0.82686	2.693000	0.91896	0.643000	0.83706	TGG	.	.	.	none		0.687	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		A	144990855	C	A	144990855	3	1	166	1	0	0	0	0	1	0	0	0	12059	740	26	4	513	4	PLEC	8	144990855	Missense_Mutation	SNP	C	TCGA-F9-A7VF-01A-11D-A33Q-10		144990855	1373167	36	9798											
GDA	9615	hgsc.bcm.edu	37	chr9	74828909	74828909	+	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	cgatcaaggaaactgagaggTaaaaggcccatttgtcttga	14	9	11	7	1	2	2	1	2	1	1	2	5	2	3	1	3	1	1	1	3	4	3			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr9:74828909T>A	ENST00000358399.3	+	5	671		c.e5+2		GDA_ENST00000545168.1_Splice_Site|GDA_ENST00000477618.1_Splice_Site|GDA_ENST00000376986.1_Splice_Site|GDA_ENST00000376989.3_Splice_Site|GDA_ENST00000238018.4_Splice_Site	NM_001242505.2|NM_001242506.2|NM_004293.4	NP_001229434.1|NP_001229435.1|NP_004284.1	Q9Y2T3	GUAD_HUMAN	guanine deaminase						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)		AACTGAGAGGTAAAAGGCCCA	0.438																																					.		Atlas-SNP	.											.	GDA	113	.	0			c.356+2T>A						PASS	.						106	100	102					9																	74828909		2203	4300	6503	SO:0001630	splice_region_variant	9615	exon5			GAGAGGTAAAAGG	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.578+2T>A	chr9.hg19:g.74828909T>A		134.0	0.0	.		106.0	45.0	.	NM_001242507	B4DTY5|Q5SZC7|Q9H335|Q9ULG2	Splice_Site	SNP	ENST00000358399.3	hg19	CCDS6641.1	.	.	.	.	.	.	.	.	.	.	T	13.64	2.296939	0.40594	.	.	ENSG00000119125	ENST00000545168;ENST00000238018;ENST00000376989;ENST00000376986;ENST00000358399;ENST00000414671	.	.	.	5.64	5.64	0.86602	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5087	0.75764	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	GDA	74018729	1.000000	0.71417	0.991000	0.47740	0.262000	0.26303	5.420000	0.66441	2.150000	0.67090	0.482000	0.46254	.	.	.	.	none		0.438	GDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052633.1		Intron	A	74828909	T	A	74828909	5	1	166	1	0	0	0	0	0	0	1	0	6313	1652	57	5	598	5	GDA	9	74828909	Splice_Site	SNP	T	TCGA-F9-A7VF-01A-11D-A33Q-10		74828909	66384522	37	9799											
PCSK5	5125	hgsc.bcm.edu	37	chr9	78710821	78710822	+	Missense_Mutation	DNP	GG	GG	CA																															aacaggggcggagaggcctcGgctctgtgtttgtttgggca																										TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr9:78710821_78710822GG>CA	ENST00000545128.1	+	8	1448_1449	c.910_911GG>CA	c.(910-912)GGc>CAc	p.G304H	PCSK5_ENST00000376767.3_Missense_Mutation_p.G304H|PCSK5_ENST00000376752.4_Missense_Mutation_p.G304H	NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	304	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						GAGAGGCCTCGGCTCTGTGTTT	0.495																																					p.G304R|p.G304D		Atlas-SNP	.											.	PCSK5	329	.	0			c.G910C|c.G911A						PASS	.																																			SO:0001583	missense	5125	exon8			GGCCTCGGCTCTG|GCCTCGGCTCTGT		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	Exception_encountered	chr9.hg19:g.78710821_78710822delinsCA	ENSP00000446280:p.Gly304His	99.0|101.0	0.0	.		81.0|82.0	32.0|31.0	.	NM_006200	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	hg19	CCDS55320.1																																																																																			.	.	.	none		0.495	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				CA	78710822	GG	CA	78710821	3	2	166	1	0	0	0	0	1	0	0	0	11610	1116	39	4	940	4	PCSK5	9	78710821	Missense_Mutation	DNP	GG	TCGA-F9-A7VF-01A-11D-A33Q-10	3881912	78710821	62502610	38	9800											
CDK5RAP2	55755	hgsc.bcm.edu	37	chr9	123216128	123216128	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgtcccagaagcagttccCgtaccactttcagaaggtct	9	11	9	12	1	2	2	1	0	1	2	4	2	4	2	3	1	2	4	3	1	3	4			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr9:123216128C>T	ENST00000349780.4	-	21	2578	c.2399G>A	c.(2398-2400)cGg>cAg	p.R800Q	CDK5RAP2_ENST00000360822.3_Missense_Mutation_p.R768Q|CDK5RAP2_ENST00000360190.4_Missense_Mutation_p.R800Q|CDK5RAP2_ENST00000359309.3_Missense_Mutation_p.R800Q	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	800					brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)			breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						AAGCAGTTCCCGTACCACTTT	0.468																																					p.R800Q		Atlas-SNP	.											.	CDK5RAP2	157	.	0			c.G2399A						PASS	.						68	64	65					9																	123216128		2202	4295	6497	SO:0001583	missense	55755	exon21			AGTTCCCGTACCA	BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"centrosomin"	608201	"microcephaly, primary autosomal recessive 3"	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.2399G>A	chr9.hg19:g.123216128C>T	ENSP00000343818:p.Arg800Gln	106.0	0.0	.		116.0	42.0	.	NM_018249	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Missense_Mutation	SNP	ENST00000349780.4	hg19	CCDS6823.1	.	.	.	.	.	.	.	.	.	.	C	5.025	0.190284	0.09547	.	.	ENSG00000136861	ENST00000360822;ENST00000359309;ENST00000349780;ENST00000360190;ENST00000416449	T;T;T;T;T	0.17854	3.92;3.83;3.95;3.86;2.25	5.79	3.0	0.34707	.	0.578394	0.16647	N	0.205372	T	0.09992	0.0245	N	0.17082	0.46	0.09310	N	1	B;B;B;B	0.15473	0.003;0.001;0.002;0.013	B;B;B;B	0.10450	0.005;0.001;0.002;0.003	T	0.29640	-1.0005	10	0.34782	T	0.22	.	7.8742	0.29584	0.0:0.6829:0.0:0.3171	.	569;800;800;194	Q6MZT4;Q96SN8-4;Q96SN8;B1AMJ5	.;.;CK5P2_HUMAN;.	Q	768;800;800;800;194	ENSP00000354065:R768Q;ENSP00000352258:R800Q;ENSP00000343818:R800Q;ENSP00000353317:R800Q;ENSP00000400395:R194Q	ENSP00000343818:R800Q	R	-	2	0	CDK5RAP2	122255949	0.000000	0.05858	0.008000	0.14137	0.005000	0.04900	0.005000	0.13129	0.381000	0.24851	-0.137000	0.14449	CGG	.	.	.	none		0.468	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249		T	123216128	C	T	123216128	3	4	166	1	0	0	0	0	1	0	0	0	3148	652	23	1	3354	1	CDK5RAP2	9	123216128	Missense_Mutation	SNP	C	TCGA-F9-A7VF-01A-11D-A33Q-10	44505307	123216128	17997303	39	9801											
BAT2L1	84726	hgsc.bcm.edu	37	chr9	134305606	134305606	+	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	tcgactctcagcctgtttgaTaagtataaaggaaaatcagt	14	12	8	7	1	2	1	2	1	1	0	4	3	2	2	1	1	1	2	1	1	6	4			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr9:134305606T>A	ENST00000357304.4	+	1	130	c.75T>A	c.(73-75)gaT>gaA	p.D25E	PRRC2B_ENST00000405995.1_Missense_Mutation_p.D25E|PRRC2B_ENST00000458550.1_Missense_Mutation_p.D25E	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	25							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						GCCTGTTTGATAAGTATAAAG	0.453																																					p.D25E		Atlas-SNP	.											.	PRRC2B	266	.	0			c.T75A						PASS	.						72	71	71					9																	134305606		1932	4130	6062	SO:0001583	missense	84726	exon1			GTTTGATAAGTAT	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.75T>A	chr9.hg19:g.134305606T>A	ENSP00000349856:p.Asp25Glu	139.0	0.0	.		135.0	64.0	.	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	hg19	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.342715	0.82022	.	.	ENSG00000130723	ENST00000405995;ENST00000541684;ENST00000357304;ENST00000458550	T;T;T	0.24151	1.87;1.87;1.87	6.17	1.26	0.21427	BAT2, N-terminal (1);	0.000000	0.41294	U	0.000904	T	0.44159	0.1280	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.22695	-1.0209	10	0.72032	D	0.01	-2.03	9.4094	0.38482	0.0:0.4505:0.0:0.5495	.	25	Q5JSZ5	PRC2B_HUMAN	E	25	ENSP00000384606:D25E;ENSP00000349856:D25E;ENSP00000398853:D25E	ENSP00000349856:D25E	D	+	3	2	PRRC2B	133295427	0.998000	0.40836	0.998000	0.56505	0.975000	0.68041	0.527000	0.22987	-0.031000	0.13781	-0.904000	0.02843	GAT	.	.	.	none		0.453	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	134305606	T	A	134305606	3	1	166	1	0	0	0	0	1	0	0	0	1320	1403	49	5	77	5	BAT2L1	9	134305606	Missense_Mutation	SNP	T	TCGA-F9-A7VF-01A-11D-A33Q-10	11089478	134305606	6907825	40	9802											
EBF3	253738	hgsc.bcm.edu	37	chr10	131757260	131757260	+	Nonsense_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	gggttcttgtcctggccctcGtagacgatggcctgcgcgag	4	10	15	12	4	1	1	0	0	1	1	3	3	2	1	3	3	1	2	3	3	1	3			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr10:131757260G>C	ENST00000355311.5	-	5	495	c.423C>G	c.(421-423)taC>taG	p.Y141*	EBF3_ENST00000368648.3_Nonsense_Mutation_p.Y141*			Q9H4W6	COE3_HUMAN	early B-cell factor 3	141					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)		CCTGGCCCTCGTAGACGATGG	0.726																																					p.Y141X		Atlas-SNP	.											.	EBF3	193	.	0			c.C423G						PASS	.						32	35	34					10																	131757260		2202	4300	6502	SO:0001587	stop_gained	253738	exon5			GCCCTCGTAGACG		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.423C>G	chr10.hg19:g.131757260G>C	ENSP00000347463:p.Tyr141*	108.0	0.0	.		94.0	45.0	.	NM_001005463	A0AUY1|Q5T6H9|Q9H4W5	Nonsense_Mutation	SNP	ENST00000355311.5	hg19		.	.	.	.	.	.	.	.	.	.	G	37	6.328482	0.97476	.	.	ENSG00000108001	ENST00000355311;ENST00000368648	.	.	.	4.32	-1.24	0.09435	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.657	9.1925	0.37209	0.4955:0.0:0.5045:0.0	.	.	.	.	X	141	.	ENSP00000347463:Y141X	Y	-	3	2	EBF3	131647250	0.853000	0.29707	0.992000	0.48379	0.997000	0.91878	-0.038000	0.12144	-0.300000	0.08895	0.561000	0.74099	TAC	.	.	.	none		0.726	EBF3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051015.2	NM_001005463		C	131757260	G	C	131757260	4	2	166	1	0	0	0	0	0	1	0	0	4884	1140	40	4	1280	4	EBF3	10	131757260	Nonsense_Mutation	SNP	G	TCGA-F9-A7VF-01A-11D-A33Q-10		131757260	3777487	41	9803											
SIGIRR	59307	hgsc.bcm.edu	37	chr11	407106	407106	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cggctcaggaaggcgtccgaAagcaccacgatgaggcgtcg	10	4	15	12	6	1	1	1	1	0	0	3	4	2	2	2	4	1	2	2	4	2	0			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr11:407106A>G	ENST00000431843.2	-	7	990	c.684T>C	c.(682-684)ctT>ctC	p.L228L	SIGIRR_ENST00000531205.1_Silent_p.L228L|SIGIRR_ENST00000332725.3_Silent_p.L228L|SIGIRR_ENST00000397632.3_Silent_p.L228L|SIGIRR_ENST00000382520.2_Silent_p.L228L|SIGIRR_ENST00000529486.1_5'Flank	NM_001135054.1	NP_001128526.1	Q6IA17	SIGIR_HUMAN	single immunoglobulin and toll-interleukin 1 receptor (TIR) domain	228	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				acute-phase response (GO:0006953)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				cervix(2)|endometrium(1)|liver(1)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	13		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)		AGGCGTCCGAAAGCACCACGA	0.751																																					p.L228L		Atlas-SNP	.											.	SIGIRR	22	.	0			c.T684C						PASS	.						10	12	12					11																	407106		2117	4206	6323	SO:0001819	synonymous_variant	59307	exon7			GTCCGAAAGCACC		CCDS31325.1	11p15.5	2013-01-11	2005-10-10					"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	30575	protein-coding gene	gene with protein product	"single immunoglobulin domain IL1R1 related"	605478				10346978	Standard	NM_021805		Approved	TIR8	uc001lpe.1	Q6IA17		ENST00000431843.2:c.684T>C	chr11.hg19:g.407106A>G		34.0	0.0	.		25.0	13.0	.	NM_001135053	Q3KQY2|Q6UXI3|Q9H733	Silent	SNP	ENST00000431843.2	hg19	CCDS31325.1																																																																																			.	.	.	none		0.751	SIGIRR-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383884.3	NM_021805		G	407106	A	G	407106	2	3	166	1	0	0	0	0	0	0	0	1	14317	1	1	3		3	SIGIRR	11	407106	Silent	SNP	A	TCGA-F9-A7VF-01A-11D-A33Q-10		407106	134599410	42	9804											
OR5T2	219464	hgsc.bcm.edu	37	chr11	56000203	56000203	+	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	tcataagccattgcagccaaGagaaagcattctgtggttcc	12	10	9	10	0	2	1	1	0	1	1	3	2	3	1	3	1	4	3	3	1	3	4			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr11:56000203G>A	ENST00000313264.4	-	1	534	c.459C>T	c.(457-459)ctC>ctT	p.L153L		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, 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)			endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					TTGCAGCCAAGAGAAAGCATT	0.418																																					p.L153L		Atlas-SNP	.											.	OR5T2	107	.	0			c.C459T						PASS	.						179	153	162					11																	56000203		2201	4296	6497	SO:0001819	synonymous_variant	219464	exon1			AGCCAAGAGAAAG	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.459C>T	chr11.hg19:g.56000203G>A		107.0	0.0	.		91.0	37.0	.	NM_001004746	B9EGX5|Q6IFC8	Silent	SNP	ENST00000313264.4	hg19	CCDS31523.1																																																																																			.	.	.	none		0.418	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746		A	56000203	G	A	56000203	2	1	166	1	0	0	0	0	0	0	0	1	11189	929	33	2		2	OR5T2	11	56000203	Silent	SNP	G	TCGA-F9-A7VF-01A-11D-A33Q-10	55593097	56000203	79006313	43	9805											
FAM86C	55199	hgsc.bcm.edu	37	chr11	71507154	71507154	+	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	caccagcgggctcctcaattCtacatggcccttaccgtctg	7	10	8	16	2	3	0	1	0	2	0	4	0	4	0	4	2	3	1	4	2	3	3			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr11:71507154C>A	ENST00000359244.4	+	4	376	c.353C>A	c.(352-354)tCt>tAt	p.S118Y	FAM86C1_ENST00000346333.6_Missense_Mutation_p.S84Y|FAM86C1_ENST00000426628.2_Missense_Mutation_p.S111Y	NM_018172.2	NP_060642.2	Q9NVL1	FA86C_HUMAN	family with sequence similarity 86, member C1	118										lung(1)	1						CTCCTCAATTCTACATGGCCC	0.642																																					p.S118Y		Atlas-SNP	.											.	FAM86C1	27	.	0			c.C353A						PASS	.						94	99	97					11																	71507154		2200	4293	6493	SO:0001583	missense	55199	exon4			TCAATTCTACATG	AK130709	CCDS8202.1, CCDS41686.1, CCDS44664.1	11q13.4	2011-07-07	2011-07-07	2011-07-07	ENSG00000158483	ENSG00000158483			25561	protein-coding gene	gene with protein product			"family with sequence similarity 86, member C"	FAM86C		12477932	Standard	NM_152563		Approved	FLJ10661, FLJ27199	uc001oqv.4	Q9NVL1	OTTHUMG00000160552	ENST00000359244.4:c.353C>A	chr11.hg19:g.71507154C>A	ENSP00000352182:p.Ser118Tyr	124.0	0.0	.		86.0	37.0	.	NM_018172	Q8N5D3	Missense_Mutation	SNP	ENST00000359244.4	hg19	CCDS41686.1	.	.	.	.	.	.	.	.	.	.	.	12.26	1.883348	0.33255	.	.	ENSG00000158483	ENST00000346333;ENST00000359244;ENST00000426628;ENST00000528685	T;T;T;T	0.25912	1.82;2.16;1.81;1.77	1.49	1.49	0.22878	.	.	.	.	.	T	0.29684	0.0741	N	0.24115	0.695	0.09310	N	0.999996	D;P;P	0.58970	0.984;0.952;0.952	D;B;B	0.63877	0.919;0.348;0.348	T	0.08411	-1.0723	9	0.87932	D	0	.	6.4456	0.21875	0.0:1.0:0.0:0.0	.	111;84;118	G3V0F7;Q9NVL1-2;Q9NVL1	.;.;FA86C_HUMAN	Y	84;118;111;84	ENSP00000325662:S84Y;ENSP00000352182:S118Y;ENSP00000391329:S111Y;ENSP00000436598:S84Y	ENSP00000325662:S84Y	S	+	2	0	FAM86C1	71184802	0.927000	0.31430	0.015000	0.15790	0.002000	0.02628	0.741000	0.26202	1.136000	0.42199	0.184000	0.17185	TCT	.	.	.	none		0.642	FAM86C1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361120.1	NM_152563		A	71507154	C	A	71507154	3	1	166	1	0	0	0	0	1	0	0	0	5653	913	32	4	452	4	FAM86C	11	71507154	Missense_Mutation	SNP	C	TCGA-F9-A7VF-01A-11D-A33Q-10	15506951	71507154	63499362	44	9806											
ABCC9	10060	hgsc.bcm.edu	37	chr12	21962796	21962797	+	Frame_Shift_Del	DEL	AG	AG	-																															ggaaatatacctagacctccAggtagagatttgaccatatt																										TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr12:21962796_21962797delAG	ENST00000261201.4	-	35	4303_4304	c.4304_4305delCT	c.(4303-4305)cctfs	p.P1435fs	ABCC9_ENST00000261200.4_Frame_Shift_Del_p.P1435fs|ABCC9_ENST00000345162.2_Frame_Shift_Del_p.P1399fs	NM_005691.2	NP_005682.2	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	1435	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				defense response to virus (GO:0051607)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	ATP-sensitive potassium channel complex (GO:0008282)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcomere (GO:0030017)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sulfonylurea receptor activity (GO:0008281)|transporter activity (GO:0005215)			NS(2)|breast(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|lung(56)|ovary(4)|pancreas(1)|prostate(4)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(5)	118					Adenosine triphosphate(DB00171)|Glyburide(DB01016)	CTAGACCTCCAGGTAGAGATTT	0.342																																					p.1435_1436del		Atlas-INDEL	.											.	ABCC9	411	.	0			c.4305_4306del						PASS	.																																			SO:0001589	frameshift_variant	10060	exon35			.	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.4304_4305delCT	chr12.hg19:g.21962796_21962797delAG	ENSP00000261201:p.Pro1435fs	35.0	0.0	0		32.0	13.0	0.40625	NM_020297	O60707	Frame_Shift_Del	DEL	ENST00000261201.4	hg19	CCDS8694.1																																																																																			.	.	.	none		0.342	ABCC9-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402230.1	NM_005691		-	21962797	AG	-	21962796	7	5	166	1	0	1	0	1	0	0	0	0	59	175	7	0	502	0	ABCC9	12	21962796	Frame_Shift_Del	DEL	AG	TCGA-F9-A7VF-01A-11D-A33Q-10		21962796	111889099	45	9807											
GIT2	9815	hgsc.bcm.edu	37	chr12	110390969	110390969	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatgccacgctgtcatagtcGggctgatcgttgtcttgact	6	13	12	10	3	2	2	1	2	1	0	4	3	2	2	1	1	1	3	1	1	1	3			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr12:110390969G>A	ENST00000355312.3	-	13	1169	c.1170C>T	c.(1168-1170)ccC>ccT	p.P390P	GIT2_ENST00000547815.1_Silent_p.P390P|GIT2_ENST00000343646.5_Intron|GIT2_ENST00000338373.5_Silent_p.P390P|GIT2_ENST00000551209.1_Silent_p.P389P|GIT2_ENST00000553118.1_Silent_p.P390P|GIT2_ENST00000356259.4_Silent_p.P390P|GIT2_ENST00000354574.4_Silent_p.P392P|GIT2_ENST00000320063.9_Silent_p.P390P|GIT2_ENST00000361006.5_Silent_p.P390P|TCHP_ENST00000550780.1_Intron|GIT2_ENST00000457474.2_Silent_p.P392P|GIT2_ENST00000360185.4_Silent_p.P390P	NM_057169.3	NP_476510.1	Q14161	GIT2_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 2	390					behavioral response to pain (GO:0048266)|regulation of ARF GTPase activity (GO:0032312)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.P390P(2)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(8)|skin(4)	27						TGTCATAGTCGGGCTGATCGT	0.468																																					p.P392P		Atlas-SNP	.											.	GIT2	81	.	2	Substitution - coding silent(2)	lung(2)	c.C1176T						PASS	.						259	209	226					12																	110390969		2203	4300	6503	SO:0001819	synonymous_variant	9815	exon14			ATAGTCGGGCTGA	AF124491	CCDS9138.1, CCDS9139.1, CCDS44968.1, CCDS44969.1, CCDS55884.1	12q24.1	2013-01-10	2008-09-05			ENSG00000139436		"ADP-ribosylation factor GTPase activating proteins", "Ankyrin repeat domain containing"	4273	protein-coding gene	gene with protein product		608564	"G protein-coupled receptor kinase interactor 2"			9826657, 10896954	Standard	NM_139201		Approved	KIAA0148	uc001tps.2	Q14161	OTTHUMG00000169313	ENST00000355312.3:c.1170C>T	chr12.hg19:g.110390969G>A		84.0	0.0	.		90.0	46.0	.	NM_001135213	Q86U59|Q96CI2|Q9BV91|Q9Y5V2	Silent	SNP	ENST00000355312.3	hg19	CCDS9138.1																																																																																			.	.	.	none		0.468	GIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403407.1	NM_057169		A	110390969	G	A	110390969	2	1	166	1	0	0	0	0	0	0	0	1	6404	1103	39	1		1	GIT2	12	110390969	Silent	SNP	G	TCGA-F9-A7VF-01A-11D-A33Q-10	88428173	110390969	23460926	46	9808											
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77732194	77732194	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcttctaatatagttggtgaAtgagaaagagctagaccctt	13	12	10	6	0	1	4	0	2	1	3	1	5	1	4	1	1	1	3	1	1	6	7			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr13:77732194A>G	ENST00000544440.2	-	45	6551	c.6534T>C	c.(6532-6534)caT>caC	p.H2178H	MYCBP2_ENST00000357337.6_Silent_p.H2178H|MYCBP2_ENST00000360084.5_5'UTR|MYCBP2_ENST00000407578.2_Silent_p.H2216H					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)		TAGTTGGTGAATGAGAAAGAG	0.333																																					p.H2216H		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.T6648C						PASS	.						86	87	87					13																	77732194		2203	4300	6503	SO:0001819	synonymous_variant	23077	exon45			TGGTGAATGAGAA	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.6534T>C	chr13.hg19:g.77732194A>G		100.0	0.0	.		101.0	36.0	.	NM_015057		Silent	SNP	ENST00000544440.2	hg19																																																																																				.	.	.	none		0.333	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		G	77732194	A	G	77732194	2	3	166	1	0	0	0	0	0	0	0	1	10025	98	4	3		3	MYCBP2	13	77732194	Silent	SNP	A	TCGA-F9-A7VF-01A-11D-A33Q-10		77732194	37437684	47	9809											
OR11H4	390442	hgsc.bcm.edu	37	chr14	20711302	20711302	+	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	1	0	0	0	0	0	0	0	0	tctatttcttcttttcactgGgaacaactgaatgtctcttt	8	19	5	9	0	5	1	1	1	4	0	6	2	5	2	0	1	2	0	0	1	4	6			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr14:20711302G>T	ENST00000315409.2	+	1	405	c.352G>T	c.(352-354)Gga>Tga	p.G118*		NM_001004479.1	NP_001004479.1	Q8NGC9	O11H4_HUMAN	olfactory receptor, family 11, subfamily H, member 4	118						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(3)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	29	all_cancers(95;0.000888)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0146)		CTTTTCACTGGGAACAACTGA	0.468																																					p.G118X		Atlas-SNP	.											.	OR11H4	63	.	0			c.G352T						PASS	.						103	106	105					14																	20711302		2203	4300	6503	SO:0001587	stop_gained	390442	exon1			TCACTGGGAACAA		CCDS32034.1	14q11.2	2013-09-24			ENSG00000176198	ENSG00000176198		"GPCR / Class A : Olfactory receptors"	15347	protein-coding gene	gene with protein product							Standard	NM_001004479		Approved		uc010tld.2	Q8NGC9	OTTHUMG00000170852	ENST00000315409.2:c.352G>T	chr14.hg19:g.20711302G>T	ENSP00000318997:p.Gly118*	91.0	0.0	.		68.0	4.0	.	NM_001004479	B2RNQ4|Q6IF07	Nonsense_Mutation	SNP	ENST00000315409.2	hg19	CCDS32034.1	.	.	.	.	.	.	.	.	.	.	G	34	5.411171	0.96072	.	.	ENSG00000176198	ENST00000315409	.	.	.	4.75	4.75	0.60458	.	0.000000	0.56097	D	0.000040	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-3.5741	15.2747	0.73732	0.0:0.0:1.0:0.0	.	.	.	.	X	118	.	ENSP00000318997:G118X	G	+	1	0	OR11H4	19781142	0.003000	0.15002	1.000000	0.80357	0.997000	0.91878	1.341000	0.33907	2.465000	0.83290	0.650000	0.86243	GGA	.	.	.	none		0.468	OR11H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410678.1			T	20711302	G	T	20711302	4	4	166	1	0	0	0	0	0	1	0	0	10935	1233	43	4	354	4	OR11H4	14	20711302	Nonsense_Mutation	SNP	G	TCGA-F9-A7VF-01A-11D-A33Q-10		20711302	86638238	48	9810											
MYH7	4625	hgsc.bcm.edu	37	chr14	23900190	23900190	+	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	ctttcagctggaaaataactCtggatttttccagaagatct	12	14	7	8	0	3	2	1	0	2	2	4	4	4	4	1	2	2	1	1	2	4	4			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr14:23900190C>T	ENST00000355349.3	-	10	977	c.815G>A	c.(814-816)aGa>aAa	p.R272K		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	272	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		GAAAATAACTCTGGATTTTTC	0.423																																					p.R272K		Atlas-SNP	.											.	MYH7	349	.	0			c.G815A						PASS	.						77	84	82					14																	23900190		2203	4300	6503	SO:0001583	missense	4625	exon10			ATAACTCTGGATT	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.815G>A	chr14.hg19:g.23900190C>T	ENSP00000347507:p.Arg272Lys	36.0	0.0	.		29.0	15.0	.	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	hg19	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	C	17.52	3.409375	0.62399	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	D	0.96716	-4.1	3.62	3.62	0.41486	Myosin head, motor domain (2);	.	.	.	.	D	0.98560	0.9519	H	0.99609	4.655	0.58432	D	0.999999	B	0.17038	0.02	B	0.39503	0.301	D	0.99930	1.1311	9	0.87932	D	0	.	15.4652	0.75394	0.0:1.0:0.0:0.0	.	272	P12883	MYH7_HUMAN	K	272	ENSP00000347507:R272K	ENSP00000347507:R272K	R	-	2	0	MYH7	22970030	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	7.395000	0.79876	1.862000	0.54008	0.305000	0.20034	AGA	.	.	.	none		0.423	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		T	23900190	C	T	23900190	3	4	166	1	0	0	0	0	1	0	0	0	10046	913	32	2	5116	2	MYH7	14	23900190	Missense_Mutation	SNP	C	TCGA-F9-A7VF-01A-11D-A33Q-10	3188888	23900190	83449350	49	9811											
ADCY4	196883	hgsc.bcm.edu	37	chr14	24798392	24798392	+	Missense_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	acgcatcttgaggccctcaaGcgaggacagcaagcctcctg	10	6	11	14	2	2	1	1	1	1	0	3	3	3	2	3	2	3	2	3	2	2	1			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr14:24798392G>A	ENST00000310677.4	-	11	1512	c.1399C>T	c.(1399-1401)Ctt>Ttt	p.L467F	ADCY4_ENST00000418030.2_Missense_Mutation_p.L467F|ADCY4_ENST00000554068.2_Missense_Mutation_p.L467F|ADCY4_ENST00000396747.3_Missense_Mutation_p.L160F	NM_001198568.1|NM_001198592.1|NM_139247.3	NP_001185497.1|NP_001185521.1|NP_640340.2	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4	467					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)		AGGCCCTCAAGCGAGGACAGC	0.602																																					p.L467F		Atlas-SNP	.											.	ADCY4	86	.	0			c.C1399T						PASS	.						132	115	121					14																	24798392		2203	4300	6503	SO:0001583	missense	196883	exon11			CCTCAAGCGAGGA	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.1399C>T	chr14.hg19:g.24798392G>A	ENSP00000312126:p.Leu467Phe	96.0	0.0	.		64.0	27.0	.	NM_001198592	B3KV74|D3DS75|Q17R40|Q6ZTM6|Q96ML7	Missense_Mutation	SNP	ENST00000310677.4	hg19	CCDS9627.1	.	.	.	.	.	.	.	.	.	.	G	10.60	1.396149	0.25205	.	.	ENSG00000129467	ENST00000310677;ENST00000554068;ENST00000418030;ENST00000396747	T;T;T;T	0.79749	-1.07;-1.07;-1.07;-1.3	4.75	3.86	0.44501	.	0.185106	0.26560	N	0.023685	T	0.60663	0.2286	N	0.08118	0	0.32417	N	0.549897	B	0.19706	0.038	B	0.23150	0.044	T	0.61840	-0.6980	10	0.46703	T	0.11	.	6.473	0.22020	0.0974:0.1841:0.7185:0.0	.	467	Q8NFM4	ADCY4_HUMAN	F	467;467;467;160	ENSP00000312126:L467F;ENSP00000452250:L467F;ENSP00000393177:L467F;ENSP00000379971:L160F	ENSP00000312126:L467F	L	-	1	0	ADCY4	23868232	0.755000	0.28372	0.993000	0.49108	0.802000	0.45316	0.530000	0.23036	1.223000	0.43536	0.655000	0.94253	CTT	.	.	.	none		0.602	ADCY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073200.4			A	24798392	G	A	24798392	3	1	166	1	0	0	0	0	1	0	0	0	296	971	34	2	1898	2	ADCY4	14	24798392	Missense_Mutation	SNP	G	TCGA-F9-A7VF-01A-11D-A33Q-10	898202	24798392	82551148	50	9812											
HEATR5A	25938	hgsc.bcm.edu	37	chr14	31771694	31771694	+	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	ctgaggaccccgattgtgagGtacaatatagtagggagaat	13	9	13	6	1	0	3	0	2	0	1	0	6	0	4	2	3	1	2	2	3	6	5			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr14:31771694G>A	ENST00000389961.3	-	32	5252	c.5253C>T	c.(5251-5253)taC>taT	p.Y1751Y	HEATR5A_ENST00000439727.1_Silent_p.Y1464Y|RP11-596D21.1_ENST00000551799.1_RNA|HEATR5A_ENST00000543095.2_Silent_p.Y1757Y|HEATR5A_ENST00000439348.1_Intron			Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	1751										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)		CGATTGTGAGGTACAATATAG	0.388																																					p.Y1757Y		Atlas-SNP	.											.	HEATR5A	181	.	0			c.C5271T						PASS	.						28	30	30					14																	31771694		1835	4085	5920	SO:0001819	synonymous_variant	25938	exon33			TGTGAGGTACAAT	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.5253C>T	chr14.hg19:g.31771694G>A		107.0	0.0	.		87.0	33.0	.	NM_015473	Q68DD8|Q6P3S5|Q6P5R9|Q9H8D7|Q9NXB7|Q9P2N0|Q9UFQ3	Silent	SNP	ENST00000389961.3	hg19																																																																																				.	.	.	none		0.388	HEATR5A-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015473		A	31771694	G	A	31771694	2	1	166	1	0	0	0	0	0	0	0	1	7038	1256	44	2		2	HEATR5A	14	31771694	Silent	SNP	G	TCGA-F9-A7VF-01A-11D-A33Q-10	6973302	31771694	75577846	51	9813											
CALM1	801	hgsc.bcm.edu	37	chr14	90870770	90870770	+	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	gaactacgtcacgtcatgacAaacttaggagaaaaactaac	18	7	7	9	2	2	2	2	1	0	1	2	4	2	2	0	1	5	0	0	1	7	3			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr14:90870770A>C	ENST00000356978.4	+	5	581	c.333A>C	c.(331-333)acA>acC	p.T111T	CALM1_ENST00000447653.3_Silent_p.T112T|RP11-471B22.2_ENST00000555853.1_RNA|CALM1_ENST00000553542.1_Silent_p.T75T|CALM1_ENST00000544280.2_Silent_p.T75T	NM_006888.4	NP_008819.1	P62158	CALM_HUMAN	calmodulin 1 (phosphorylase kinase, delta)	111	EF-hand 3. {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)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(1)	10		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.208)	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)	ACGTCATGACAAACTTAGGAG	0.383																																					p.T111T		Atlas-SNP	.											.	CALM1	16	.	0			c.A333C						PASS	.						136	125	129					14																	90870770		2203	4300	6503	SO:0001819	synonymous_variant	801	exon5			CATGACAAACTTA		CCDS9892.1	14q32.11	2013-02-25			ENSG00000198668	ENSG00000198668	2.7.11.19	"EF-hand domain containing", "Endogenous ligands"	1442	protein-coding gene	gene with protein product	"prepro-calmodulin 1"	114180		CALML2		6385987	Standard	NM_006888		Approved	CAMI, PHKD, DD132	uc001xyl.2	P62158	OTTHUMG00000171044	ENST00000356978.4:c.333A>C	chr14.hg19:g.90870770A>C		213.0	0.0	.		197.0	96.0	.	NM_006888	P02593|P70667|P99014|Q13942|Q53S29|Q61379|Q61380|Q96HK3	Silent	SNP	ENST00000356978.4	hg19	CCDS9892.1																																																																																			.	.	.	none		0.383	CALM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411346.1			C	90870770	A	C	90870770	2	2	166	1	0	0	0	0	0	0	0	1	2586	117	5	5		5	CALM1	14	90870770	Silent	SNP	A	TCGA-F9-A7VF-01A-11D-A33Q-10	59099076	90870770	16478770	52	9814											
HERC2	8924	hgsc.bcm.edu	37	chr15	28380665	28380665	+	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	ttcccatcttctgcctcaccCcaagagtaaacttctccttc	8	13	3	17	0	4	1	1	0	3	1	7	1	5	1	5	0	2	1	5	0	3	5			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr15:28380665C>G	ENST00000261609.7	-	79	12297	c.12189G>C	c.(12187-12189)tgG>tgC	p.W4063C		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)		CTGCCTCACCCCAAGAGTAAA	0.393																																					p.W4063C		Atlas-SNP	.											.	HERC2	501	.	0			c.G12189C						PASS	.						170	175	174					15																	28380665		2203	4300	6503	SO:0001583	missense	8924	exon79			CTCACCCCAAGAG	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.12189G>C	chr15.hg19:g.28380665C>G	ENSP00000261609:p.Trp4063Cys	156.0	0.0	.		134.0	54.0	.	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.203842	0.79127	.	.	ENSG00000128731	ENST00000261609	D	0.92348	-3.02	5.08	5.08	0.68730	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	D	0.000000	D	0.96494	0.8856	M	0.87097	2.86	0.80722	D	1	D	0.65815	0.995	D	0.69307	0.963	D	0.96907	0.9664	10	0.66056	D	0.02	.	18.8522	0.92237	0.0:1.0:0.0:0.0	.	4063	O95714	HERC2_HUMAN	C	4063	ENSP00000261609:W4063C	ENSP00000261609:W4063C	W	-	3	0	HERC2	26054260	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.762000	0.85270	2.515000	0.84797	0.557000	0.71058	TGG	.	.	.	none		0.393	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		G	28380665	C	G	28380665	3	3	166	1	0	0	0	0	1	0	0	0	7065	624	22	4	2375	4	HERC2	15	28380665	Missense_Mutation	SNP	C	TCGA-F9-A7VF-01A-11D-A33Q-10		28380665	74150727	53	9815											
RNF111	54778	hgsc.bcm.edu	37	chr15	59350658	59350658	+	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	tctgagcaggcctctgatacTgcttcagctgtcaccagtag	8	11	10	12	0	4	2	2	2	2	0	4	2	4	2	2	1	4	4	2	1	2	3			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr15:59350658T>A	ENST00000557998.1	+	5	1562	c.1275T>A	c.(1273-1275)acT>acA	p.T425T	RNF111_ENST00000434298.1_Silent_p.T425T|RNF111_ENST00000559209.1_Silent_p.T425T|RNF111_ENST00000348370.4_Silent_p.T425T|RNF111_ENST00000561186.1_Silent_p.T425T	NM_001270530.1	NP_001257459.1	Q6ZNA4	RN111_HUMAN	ring finger protein 111	425	Ser-rich.				gene expression (GO:0010467)|pattern specification process (GO:0007389)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein polyubiquitination (GO:0000209)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|SUMO polymer binding (GO:0032184)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35				all cancers(107;0.194)		CCTCTGATACTGCTTCAGCTG	0.448																																					p.T425T	NSCLC(72;983 1365 10746 34387 47081)	Atlas-SNP	.											.	RNF111	179	.	0			c.T1275A						PASS	.						257	256	256					15																	59350658		2192	4291	6483	SO:0001819	synonymous_variant	54778	exon5			TGATACTGCTTCA	AL157474	CCDS10169.1, CCDS58365.1, CCDS58366.1	15q21	2013-01-09			ENSG00000157450	ENSG00000157450		"RING-type (C3HC4) zinc fingers"	17384	protein-coding gene	gene with protein product		605840				11298452	Standard	NM_017610		Approved	ARK, Arkadia, FLJ38008, DKFZP761D081	uc002aft.4	Q6ZNA4	OTTHUMG00000132716	ENST00000557998.1:c.1275T>A	chr15.hg19:g.59350658T>A		99.0	0.0	.		80.0	27.0	.	NM_017610	C9JUS4|H0YN55|Q6P9A4|Q6ZMU2|Q7L428|Q7Z346|Q8N1P9|Q8WUA3|Q9NSR1	Silent	SNP	ENST00000557998.1	hg19	CCDS58366.1																																																																																			.	.	.	none		0.448	RNF111-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000416012.1	NM_017610		A	59350658	T	A	59350658	2	1	166	1	0	0	0	0	0	0	0	1	13438	1567	55	5		5	RNF111	15	59350658	Silent	SNP	T	TCGA-F9-A7VF-01A-11D-A33Q-10	30969993	59350658	43180734	54	9816											
LACTB	114294	hgsc.bcm.edu	37	chr15	63419075	63419075	+	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	aaggtttaggttatgctgatGttgagaaccgtgtaccatgt	10	14	12	5	1	0	2	0	2	0	1	0	3	0	2	2	2	3	5	2	2	5	5			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr15:63419075G>T	ENST00000261893.4	+	3	514	c.442G>T	c.(442-444)Gtt>Ttt	p.V148F	LACTB_ENST00000413507.2_Missense_Mutation_p.V148F|RPS27L_ENST00000559763.1_Intron	NM_032857.3	NP_116246.2	P83111	LACTB_HUMAN	lactamase, beta	148						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						TTATGCTGATGTTGAGAACCG	0.403																																					p.V148F	Melanoma(85;443 1381 6215 27308 35583)	Atlas-SNP	.											.	LACTB	29	.	0			c.G442T						PASS	.						112	105	107					15																	63419075		2203	4300	6503	SO:0001583	missense	114294	exon3			GCTGATGTTGAGA	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.442G>T	chr15.hg19:g.63419075G>T	ENSP00000261893:p.Val148Phe	142.0	0.0	.		90.0	42.0	.	NM_171846	P83096	Missense_Mutation	SNP	ENST00000261893.4	hg19	CCDS10182.1	.	.	.	.	.	.	.	.	.	.	G	17.45	3.393503	0.62066	.	.	ENSG00000103642	ENST00000261893;ENST00000413507	T;T	0.45668	0.89;0.89	5.44	3.56	0.40772	Beta-lactamase/transpeptidase-like (2);Beta-lactamase-related (1);	0.190607	0.46758	D	0.000272	T	0.49847	0.1581	L	0.58925	1.835	0.80722	D	1	P	0.48407	0.91	P	0.55161	0.77	T	0.43376	-0.9395	10	0.48119	T	0.1	-7.0724	8.4616	0.32931	0.2365:0.0:0.7635:0.0	.	148	P83111	LACTB_HUMAN	F	148	ENSP00000261893:V148F;ENSP00000392956:V148F	ENSP00000261893:V148F	V	+	1	0	LACTB	61206128	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	2.182000	0.42556	0.667000	0.31107	0.563000	0.77884	GTT	.	.	.	none		0.403	LACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256224.1	NM_032857		T	63419075	G	T	63419075	3	4	166	1	0	0	0	0	1	0	0	0	8604	1377	48	4	452	4	LACTB	15	63419075	Missense_Mutation	SNP	G	TCGA-F9-A7VF-01A-11D-A33Q-10	4068417	63419075	39112317	55	9817											
TRAP1	10131	hgsc.bcm.edu	37	chr16	3727498	3727498	+	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	caggcgacattcgtcactcaCccatctgaaagccactggta	11	8	8	14	2	3	1	2	1	1	0	4	2	3	1	2	2	1	1	2	2	2	2			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr16:3727498C>G	ENST00000246957.5	-	6	793		c.e6+1		TRAP1_ENST00000573872.1_Splice_Site|TRAP1_ENST00000538171.1_Splice_Site|TRAP1_ENST00000575671.1_Splice_Site	NM_016292.2	NP_057376.2	Q12931	TRAP1_HUMAN	TNF receptor-associated protein 1						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)				TCGTCACTCACCCATCTGAAA	0.552																																					.		Atlas-SNP	.											.	TRAP1	53	.	0			c.545+1G>C						PASS	.						67	63	65					16																	3727498		2197	4300	6497	SO:0001630	splice_region_variant	10131	exon6			CACTCACCCATCT	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.704+1G>C	chr16.hg19:g.3727498C>G		67.0	0.0	.		79.0	29.0	.	NM_001272049	B4DR68|D3DUC8|F5H897|O43642|O75235|Q9UHL5	Splice_Site	SNP	ENST00000246957.5	hg19	CCDS10508.1	.	.	.	.	.	.	.	.	.	.	C	13.10	2.137763	0.37728	.	.	ENSG00000126602	ENST00000246957;ENST00000538171	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.9543	0.92653	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TRAP1	3667499	1.000000	0.71417	1.000000	0.80357	0.115000	0.19883	7.385000	0.79763	2.714000	0.92807	0.655000	0.94253	.	.	.	.	none		0.552	TRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251586.2	NM_016292	Intron	G	3727498	C	G	3727498	5	3	166	1	0	0	0	0	0	0	1	0	16467	521	18	4	1461	4	TRAP1	16	3727498	Splice_Site	SNP	C	TCGA-F9-A7VF-01A-11D-A33Q-10		3727498	86627255	56	9818											
IL4R	3566	hgsc.bcm.edu	37	chr16	27375041	27375041	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgggcatctcagagaagagtAaatcctcatcatccttccat	12	10	7	12	1	3	2	3	0	1	2	7	3	6	2	3	1	0	2	3	1	3	2			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr16:27375041A>G	ENST00000395762.2	+	11	2627	c.2368A>G	c.(2368-2370)Aaa>Gaa	p.K790E	IL4R_ENST00000170630.2_Missense_Mutation_p.K790E|IL4R_ENST00000380922.3_Missense_Mutation_p.K775E|IL4R_ENST00000543915.2_Missense_Mutation_p.K790E	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	790	Poly-Ser.				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						AGAGAAGAGTAAATCCTCATC	0.597																																					p.K790E		Atlas-SNP	.											.	IL4R	70	.	0			c.A2368G						PASS	.						75	76	76					16																	27375041		2197	4300	6497	SO:0001583	missense	3566	exon11			AAGAGTAAATCCT	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.2368A>G	chr16.hg19:g.27375041A>G	ENSP00000379111:p.Lys790Glu	39.0	0.0	.		40.0	12.0	.	NM_000418	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Missense_Mutation	SNP	ENST00000395762.2	hg19	CCDS10629.1	.	.	.	.	.	.	.	.	.	.	A	16.46	3.128742	0.56721	.	.	ENSG00000077238	ENST00000395762;ENST00000543915;ENST00000380922;ENST00000170630	T;T;T;T	0.15372	2.43;2.43;2.43;2.43	5.0	1.38	0.22167	.	8.071550	0.00166	N	0.000000	T	0.28699	0.0711	M	0.62723	1.935	0.09310	N	1	D;D;D	0.52996	0.957;0.957;0.957	P;P;P	0.50537	0.643;0.643;0.643	T	0.08806	-1.0704	10	0.72032	D	0.01	.	5.1314	0.14913	0.5404:0.3644:0.0952:0.0	.	775;790;790	B4E076;B9EGC0;P24394	.;.;IL4RA_HUMAN	E	790;790;775;790	ENSP00000379111:K790E;ENSP00000441667:K790E;ENSP00000370309:K775E;ENSP00000170630:K790E	ENSP00000170630:K790E	K	+	1	0	IL4R	27282542	0.000000	0.05858	0.001000	0.08648	0.048000	0.14542	0.178000	0.16820	0.297000	0.22615	0.533000	0.62120	AAA	.	.	.	none		0.597	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4			G	27375041	A	G	27375041	3	3	166	1	0	0	0	0	1	0	0	0	7705	363	13	3	2420	3	IL4R	16	27375041	Missense_Mutation	SNP	A	TCGA-F9-A7VF-01A-11D-A33Q-10	23647543	27375041	62979712	57	9819											
HAS3	3038	hgsc.bcm.edu	37	chr16	69148783	69148783	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgggcattatcaaggccaccTacgcctgcttccttcggggc	6	10	11	14	2	1	0	1	0	0	0	3	0	2	0	4	4	2	2	4	4	3	4			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr16:69148783T>C	ENST00000306560.1	+	4	1432	c.1276T>C	c.(1276-1278)Tac>Cac	p.Y426H	HAS3_ENST00000569188.1_Missense_Mutation_p.Y426H|HAS3_ENST00000219322.3_Intron	NM_005329.2	NP_005320.2	O00219	HYAS3_HUMAN	hyaluronan synthase 3	426					carbohydrate metabolic process (GO:0005975)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|positive regulation of hyaluranon cable assembly (GO:1900106)|positive regulation of transcription, DNA-templated (GO:0045893)|small molecule metabolic process (GO:0044281)	hyaluranon cable (GO:0036117)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|urinary_tract(2)	16		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.0694)		CAAGGCCACCTACGCCTGCTT	0.547																																					p.Y426H		Atlas-SNP	.											.	HAS3	61	.	0			c.T1276C						PASS	.						120	111	114					16																	69148783		2198	4300	6498	SO:0001583	missense	3038	exon4			GCCACCTACGCCT	BC021853	CCDS10870.1, CCDS10871.1	16q22.1	2013-02-22			ENSG00000103044	ENSG00000103044	2.4.1.212	"Glycosyltransferase family 2 domain containing"	4820	protein-coding gene	gene with protein product		602428				9169154, 9083017	Standard	NM_005329		Approved		uc010cfh.3	O00219	OTTHUMG00000137562	ENST00000306560.1:c.1276T>C	chr16.hg19:g.69148783T>C	ENSP00000304440:p.Tyr426His	77.0	0.0	.		82.0	37.0	.	NM_005329	A8K5T5|Q8WTZ0|Q9NYP0	Missense_Mutation	SNP	ENST00000306560.1	hg19	CCDS10871.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.196679	0.79015	.	.	ENSG00000103044	ENST00000306560	T	0.50001	0.76	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.66587	0.2804	M	0.74647	2.275	0.58432	D	0.999992	D	0.67145	0.996	D	0.63381	0.914	T	0.65861	-0.6065	10	0.37606	T	0.19	-4.479	16.3021	0.82825	0.0:0.0:0.0:1.0	.	426	O00219	HAS3_HUMAN	H	426	ENSP00000304440:Y426H	ENSP00000304440:Y426H	Y	+	1	0	HAS3	67706284	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.991000	0.88244	2.326000	0.78906	0.533000	0.62120	TAC	.	.	.	none		0.547	HAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268898.2	NM_138612		C	69148783	T	C	69148783	3	2	166	1	0	0	0	0	1	0	0	0	6970	1522	53	3	1286	3	HAS3	16	69148783	Missense_Mutation	SNP	T	TCGA-F9-A7VF-01A-11D-A33Q-10	41773742	69148783	21205970	58	9820											
TRPV1	7442	hgsc.bcm.edu	37	chr17	3480920	3480920	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatgacggcatagatgcccAtctgctggaaaccgcgggtg	9	8	13	11	3	2	2	1	1	1	1	2	3	2	3	2	3	3	2	2	3	2	1			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr17:3480920A>G	ENST00000571088.1	-	11	1898	c.1685T>C	c.(1684-1686)aTg>aCg	p.M562T	TRPV1_ENST00000310522.5_Missense_Mutation_p.M502T|TRPV1_ENST00000425167.2_Missense_Mutation_p.M573T|TRPV1_ENST00000399759.3_Missense_Mutation_p.M562T|RP11-235E17.3_ENST00000573568.1_RNA|TRPV1_ENST00000399756.4_Missense_Mutation_p.M562T|TRPV1_ENST00000576351.1_Missense_Mutation_p.M552T|SHPK_ENST00000572705.1_Missense_Mutation_p.M562T|TRPV1_ENST00000174621.6_Missense_Mutation_p.M560T	NM_018727.5	NP_061197.4	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel, subfamily V, member 1	562					calcium ion transmembrane transport (GO:0070588)|cell surface receptor signaling pathway (GO:0007166)|cellular response to alkaloid (GO:0071312)|cellular response to ATP (GO:0071318)|chemosensory behavior (GO:0007635)|ion transmembrane transport (GO:0034220)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|calcium-release channel activity (GO:0015278)|excitatory extracellular ligand-gated ion channel activity (GO:0005231)|phosphoprotein binding (GO:0051219)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	17				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	ATAGATGCCCATCTGCTGGAA	0.572																																					p.M562T	Melanoma(38;962 1762 15789)	Atlas-SNP	.											.	TRPV1	99	.	0			c.T1685C						PASS	.						39	43	42					17																	3480920		1999	4150	6149	SO:0001583	missense	7442	exon11			ATGCCCATCTGCT	AJ272063	CCDS45576.1	17p13.2	2014-08-12	2002-01-29	2002-02-01	ENSG00000196689	ENSG00000262304		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12716	protein-coding gene	gene with protein product		602076	"vanilloid receptor subtype 1"	VR1		9349813, 11549313, 16382100	Standard	NM_018727		Approved		uc010vrt.2	Q8NER1	OTTHUMG00000177649	ENST00000571088.1:c.1685T>C	chr17.hg19:g.3480920A>G	ENSP00000461007:p.Met562Thr	129.0	0.0	.		129.0	39.0	.	NM_018727	A2RUA9|Q3LU47|Q9H0G9|Q9H303|Q9H304|Q9NQ74|Q9NY22	Missense_Mutation	SNP	ENST00000571088.1	hg19	CCDS45576.1	.	.	.	.	.	.	.	.	.	.	a	7.422	0.636933	0.14386	.	.	ENSG00000196689	ENST00000399759;ENST00000399756;ENST00000174621;ENST00000425167;ENST00000310522	D;D;D;D;D	0.90620	-2.7;-2.7;-2.7;-2.7;-2.7	5.22	5.22	0.72569	Ion transport (1);	0.035966	0.85682	D	0.000000	T	0.81908	0.4922	N	0.21508	0.67	0.58432	D	0.999998	B;B;B;B	0.22146	0.001;0.045;0.04;0.065	B;B;B;B	0.18871	0.006;0.008;0.023;0.015	T	0.76399	-0.2973	10	0.05833	T	0.94	-0.0301	14.5881	0.68342	1.0:0.0:0.0:0.0	.	562;560;502;573	Q8NER1;E7EQ80;E7ESJ2;E7EQ78	TRPV1_HUMAN;.;.;.	T	562;562;560;573;502	ENSP00000382661:M562T;ENSP00000382659:M562T;ENSP00000174621:M560T;ENSP00000409627:M573T;ENSP00000311692:M502T	ENSP00000174621:M560T	M	-	2	0	TRPV1	3427669	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	3.471000	0.53107	2.103000	0.63969	0.456000	0.33151	ATG	.	.	.	none		0.572	TRPV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438254.1	NM_018727		G	3480920	A	G	3480920	3	3	166	1	0	0	0	0	1	0	0	0	16607	217	8	3	531	3	TRPV1	17	3480920	Missense_Mutation	SNP	A	TCGA-F9-A7VF-01A-11D-A33Q-10		3480920	77714290	59	9821											
ZZEF1	23140	hgsc.bcm.edu	37	chr17	3947660	3947660	+	Frame_Shift_Del	DEL	T	T	-																															ctgatttcctcatgaacagcTctctttccctaaaaaaacaa																										TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr17:3947660delT	ENST00000381638.2	-	38	6148	c.6024delA	c.(6022-6024)agafs	p.R2008fs		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	2008							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						CATGAACAGCTCTCTTTCCCT	0.338																																					p.A2009fs		Atlas-Indel,Pindel	.											.	ZZEF1	195	.	0			c.6025delG						PASS	.						159	148	152					17																	3947660		2203	4300	6503	SO:0001589	frameshift_variant	23140	exon38			.	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.6024delA	chr17.hg19:g.3947660delT	ENSP00000371051:p.Arg2008fs	66.0	0.0	0		96.0	55.0	0.572917	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Frame_Shift_Del	DEL	ENST00000381638.2	hg19	CCDS11043.1																																																																																			.	.	.	none		0.338	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		-	3947660	T	-	3947660	7	5	166	1	0	1	0	1	0	0	0	0	18267	1548	54	0	2933	0	ZZEF1	17	3947660	Frame_Shift_Del	DEL	T	TCGA-F9-A7VF-01A-11D-A33Q-10	466740	3947660	77247550	60	9822											
SLC6A4	6532	hgsc.bcm.edu	37	chr17	28534784	28534784	+	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	ggctgatggccacccagcagAtcctccagaaccaccccggg	9	4	11	17	1	0	3	0	1	0	2	2	3	2	3	7	3	2	2	7	3	1	0			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr17:28534784A>T	ENST00000401766.2	-	12	2128	c.1616T>A	c.(1615-1617)aTc>aAc	p.I539N	RP11-354P11.4_ENST00000581633.1_RNA|SLC6A4_ENST00000261707.3_Missense_Mutation_p.I539N			P31645	SC6A4_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 4	539					brain morphogenesis (GO:0048854)|cellular response to cGMP (GO:0071321)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|memory (GO:0007613)|monoamine transport (GO:0015844)|negative regulation of cerebellar granule cell precursor proliferation (GO:0021941)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of organ growth (GO:0046621)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein homooligomerization (GO:0051260)|protein oligomerization (GO:0051259)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to toxic substance (GO:0009636)|serotonin transport (GO:0006837)|serotonin uptake (GO:0051610)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|thalamus development (GO:0021794)|vasoconstriction (GO:0042310)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|cocaine binding (GO:0019811)|monoamine transmembrane transporter activity (GO:0008504)|Rab GTPase binding (GO:0017137)|serotonin transmembrane transporter activity (GO:0015222)|serotonin:sodium symporter activity (GO:0005335)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(4)	25					Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexfenfluramine(DB01191)|Dexmethylphenidate(DB06701)|Dextromethorphan(DB00514)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fluoxetine(DB00472)|Fluvoxamine(DB00176)|Imipramine(DB00458)|Levomilnacipran(DB08918)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Pethidine(DB00454)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)	CACCCAGCAGATCCTCCAGAA	0.567																																					p.I539N		Atlas-SNP	.											.	SLC6A4	60	.	0			c.T1616A						PASS	.						86	73	77					17																	28534784		2203	4300	6503	SO:0001583	missense	6532	exon13			CAGCAGATCCTCC	L05568	CCDS11256.1	17q11.2	2014-01-30	2013-07-19		ENSG00000108576	ENSG00000108576		"Solute carriers"	11050	protein-coding gene	gene with protein product	"serotonin transporter 1"	182138	"solute carrier family 6 (neurotransmitter transporter, serotonin), member 4", "5-hydroxytryptamine (serotonin) transporter", "obsessive-compulsive disorder 1"	HTT, OCD1		7681602, 19806148	Standard	NM_001045		Approved	5-HTT, SERT1	uc002hey.5	P31645	OTTHUMG00000132751	ENST00000401766.2:c.1616T>A	chr17.hg19:g.28534784A>T	ENSP00000385822:p.Ile539Asn	110.0	0.0	.		141.0	87.0	.	NM_001045	Q5EE02	Missense_Mutation	SNP	ENST00000401766.2	hg19	CCDS11256.1	.	.	.	.	.	.	.	.	.	.	A	27.0	4.792743	0.90453	.	.	ENSG00000108576	ENST00000394821;ENST00000401766;ENST00000261707	T;T;T	0.76448	-1.02;-0.93;-0.93	5.64	5.64	0.86602	.	0.176744	0.50627	D	0.000118	D	0.86851	0.6032	M	0.88512	2.96	0.51233	D	0.999916	B	0.30542	0.284	P	0.45037	0.467	D	0.87665	0.2537	10	0.87932	D	0	.	15.0294	0.71694	1.0:0.0:0.0:0.0	.	539	P31645	SC6A4_HUMAN	N	581;539;539	ENSP00000378298:I581N;ENSP00000385822:I539N;ENSP00000261707:I539N	ENSP00000261707:I539N	I	-	2	0	SLC6A4	25558910	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.531000	0.81973	2.153000	0.67306	0.482000	0.46254	ATC	.	.	.	none		0.567	SLC6A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256115.3	NM_001045		T	28534784	A	T	28534784	3	4	166	1	0	0	0	0	1	0	0	0	14699	333	12	5	288	5	SLC6A4	17	28534784	Missense_Mutation	SNP	A	TCGA-F9-A7VF-01A-11D-A33Q-10	24587124	28534784	52660426	61	9823											
STAT5B	6777	hgsc.bcm.edu	37	chr17	40369252	40369259	+	Frame_Shift_Del	DEL	TCACCGAC	TCACCGAC	-																															gattgtaaatttttcttctgTcaccgactctgccccacgac																										TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	TCACCGAC	TCACCGAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr17:40369252_40369259delTCACCGAC	ENST00000293328.3	-	11	1467_1474	c.1299_1306delGTCGGTGA	c.(1297-1308)gagtcggtgacafs	p.ESVT433fs		NM_012448.3	NP_036580.2	P51692	STA5B_HUMAN	signal transducer and activator of transcription 5B	433					2-oxoglutarate metabolic process (GO:0006103)|acute-phase response (GO:0006953)|allantoin metabolic process (GO:0000255)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hormone stimulus (GO:0032870)|citrate metabolic process (GO:0006101)|creatine metabolic process (GO:0006600)|creatinine metabolic process (GO:0046449)|development of secondary female sexual characteristics (GO:0046543)|development of secondary male sexual characteristics (GO:0046544)|fatty acid metabolic process (GO:0006631)|female pregnancy (GO:0007565)|isoleucine metabolic process (GO:0006549)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|lipid storage (GO:0019915)|liver development (GO:0001889)|luteinization (GO:0001553)|natural killer cell differentiation (GO:0001779)|negative regulation of apoptotic process (GO:0043066)|negative regulation of erythrocyte differentiation (GO:0045647)|oxaloacetate metabolic process (GO:0006107)|Peyer's patch development (GO:0048541)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of cellular component movement (GO:0051272)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone metabolic process (GO:0042448)|prolactin signaling pathway (GO:0038161)|regulation of cell adhesion (GO:0030155)|regulation of epithelial cell differentiation (GO:0030856)|regulation of multicellular organism growth (GO:0040014)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to lipopolysaccharide (GO:0032496)|succinate metabolic process (GO:0006105)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|taurine metabolic process (GO:0019530)|transcription from RNA polymerase II promoter (GO:0006366)|valine metabolic process (GO:0006573)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|glucocorticoid receptor binding (GO:0035259)|protein dimerization activity (GO:0046983)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.S434L(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_cancers(22;4.15e-07)|all_epithelial(22;2.83e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.135)	Dasatinib(DB01254)	TTTTCTTCTGTCACCGACTCTGCCCCAC	0.438																																					p.434_436del		Atlas-Indel,Pindel	.											.	STAT5B	89	.	1	Substitution - Missense(1)	large_intestine(1)	c.1300_1307del						PASS	.																																			SO:0001589	frameshift_variant	6777	exon11			.	BC065227	CCDS11423.1	17q11.2	2014-09-17			ENSG00000173757	ENSG00000173757		"SH2 domain containing"	11367	protein-coding gene	gene with protein product		604260				8631883	Standard	NM_012448		Approved		uc002hzh.3	P51692	OTTHUMG00000150724	ENST00000293328.3:c.1299_1306delGTCGGTGA	chr17.hg19:g.40369252_40369259delTCACCGAC	ENSP00000293328:p.Glu433fs	132.0	0.0	0		172.0	73.0	0.424419	NM_012448	Q8WWS8	Frame_Shift_Del	DEL	ENST00000293328.3	hg19	CCDS11423.1																																																																																			.	.	.	none		0.438	STAT5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319797.1	NM_012448		-	40369259	TCACCGAC	-	40369252	7	5	166	1	0	1	0	1	0	0	0	0	15281	1667	58	0	1093	0	STAT5B	17	40369252	Frame_Shift_Del	DEL	TCACCGAC	TCGA-F9-A7VF-01A-11D-A33Q-10	11834468	40369252	40825958	62	9824											
DDX5	1655	hgsc.bcm.edu	37	chr17	62499923	62499923	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttaaaaatatatacttacaaTaggcccatcgcctctctcta	14	13	3	11	1	2	0	0	0	2	0	4	0	2	0	2	1	2	0	2	1	10	7			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr17:62499923T>C	ENST00000225792.5	-	5	906	c.505A>G	c.(505-507)Att>Gtt	p.I169V	DDX5_ENST00000450599.2_Missense_Mutation_p.I90V|MIR5047_ENST00000579212.1_RNA|DDX5_ENST00000578804.1_Missense_Mutation_p.I169V|CEP95_ENST00000556440.2_5'Flank|DDX5_ENST00000580026.1_5'Flank|MIR3064_ENST00000581130.1_RNA	NM_004396.3	NP_004387.1	P17844	DDX5_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 5	169	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)			ATACTTACAATAGGCCCATCG	0.353			T	ETV4	prostate																																p.I169V	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.A505G						PASS	.						63	65	64					17																	62499923		2203	4300	6503	SO:0001583	missense	1655	exon5			TTACAATAGGCCC	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.505A>G	chr17.hg19:g.62499923T>C	ENSP00000225792:p.Ile169Val	205.0	0.0	.		222.0	85.0	.	NM_004396	B4DLW8|B5BU21|D3DU32|E7ETL9|O75681|Q53Y61	Missense_Mutation	SNP	ENST00000225792.5	hg19	CCDS11659.1	.	.	.	.	.	.	.	.	.	.	T	13.09	2.133981	0.37630	.	.	ENSG00000108654	ENST00000540698;ENST00000450599;ENST00000225792	.	.	.	5.63	5.63	0.86233	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.085601	0.64402	D	0.000001	T	0.52468	0.1736	L	0.29908	0.895	0.80722	D	1	B;P;P	0.39831	0.036;0.69;0.69	B;B;B	0.42827	0.095;0.346;0.399	T	0.56559	-0.7959	9	0.56958	D	0.05	-15.0797	15.87	0.79108	0.0:0.0:0.0:1.0	.	90;169;169	B4DLW8;B5BUE6;P17844	.;.;DDX5_HUMAN	V	169;99;158	.	ENSP00000225792:I158V	I	-	1	0	DDX5	59930385	1.000000	0.71417	1.000000	0.80357	0.515000	0.34225	7.374000	0.79633	2.145000	0.66743	0.533000	0.62120	ATT	.	.	.	none		0.353	DDX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444030.1	NM_004396		C	62499923	T	C	62499923	3	2	166	1	0	0	0	0	1	0	0	0	4369	1406	49	3	1375	3	DDX5	17	62499923	Missense_Mutation	SNP	T	TCGA-F9-A7VF-01A-11D-A33Q-10	22130671	62499923	18695287	63	9825											
PRKAR1A	5573	hgsc.bcm.edu	37	chr17	66511650	66511650	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcaaagattctattgtgcAgttgtgcactgctcgacctg	8	13	10	10	1	2	1	1	0	1	1	3	2	2	1	1	0	3	5	1	0	2	4			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr17:66511650A>G	ENST00000589228.1	+	2	238	c.110A>G	c.(109-111)cAg>cGg	p.Q37R	PRKAR1A_ENST00000392711.1_Missense_Mutation_p.Q37R|PRKAR1A_ENST00000536854.2_Missense_Mutation_p.Q37R|PRKAR1A_ENST00000586397.1_Missense_Mutation_p.Q37R|PRKAR1A_ENST00000588188.2_Missense_Mutation_p.Q37R|PRKAR1A_ENST00000358598.2_Missense_Mutation_p.Q37R	NM_001276289.1|NM_001278433.1	NP_001263218.1|NP_001265362.1	P10644	KAP0_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, alpha	37	Dimerization and phosphorylation.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cardiac muscle cell proliferation (GO:0060038)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|female meiotic division (GO:0007143)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm formation (GO:0001707)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sarcomere organization (GO:0045214)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)			adrenal_gland(4)|breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(8)|soft_tissue(2)|stomach(2)|testis(1)|thyroid(2)|upper_aerodigestive_tract(1)	31	Breast(10;1.64e-13)					TCTATTGTGCAGTTGTGCACT	0.502			"T, Mis, N, F, S"	RET	papillary thyroid	"myxoma, endocrine, papillary thyroid"			Primary Pigmented Nodular Adrenocortical Disease, Familial;Carney Complex;Cardiac Myxomas, Familial Clustering of																												p.Q37R	Ovarian(167;637 1670 33025 39608 46699 51856)	Atlas-SNP	.	yes	"Dom, Rec"	yes	Carney complex	17	17q23-q24	5573	"protein kinase, cAMP-dependent, regulatory, type I, alpha (tissue specific extinguisher 1)"		"E, M"	.	PRKAR1A	48	.	0			c.A110G						PASS	.						84	68	73					17																	66511650		2203	4300	6503	SO:0001583	missense	5573	exon1	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2;Carney syndrome, NAME syndrome, LAMB syndrome, Familial Myxoma syndrome;	TTGTGCAGTTGTG		CCDS11678.1, CCDS62307.1	17q24.2	2014-09-17	2012-07-31		ENSG00000108946	ENSG00000108946	2.7.11.1		9388	protein-coding gene	gene with protein product	"Carney complex type 1"	188830	"tissue specific extinguisher 1"	PRKAR1, TSE1		3479018, 10973256	Standard	NM_212471		Approved	CNC1	uc002jhg.4	P10644	OTTHUMG00000180128	ENST00000589228.1:c.110A>G	chr17.hg19:g.66511650A>G	ENSP00000464977:p.Gln37Arg	55.0	0.0	.		68.0	37.0	.	NM_001276290	K7ER48|Q567S7	Missense_Mutation	SNP	ENST00000589228.1	hg19	CCDS11678.1	.	.	.	.	.	.	.	.	.	.	A	17.30	3.353606	0.61293	.	.	ENSG00000108946	ENST00000358598;ENST00000392711;ENST00000392710;ENST00000536854	T;T;T;T	0.78126	-1.15;-1.15;-1.15;-1.15	5.11	5.11	0.69529	cAMP-dependent protein kinase, regulatory subunit, type I/II alpha/beta (3);	0.000000	0.85682	D	0.000000	T	0.78426	0.4281	M	0.71206	2.165	0.58432	D	0.999999	B;B	0.22604	0.072;0.072	B;B	0.29176	0.099;0.099	T	0.76553	-0.2917	10	0.48119	T	0.1	-23.4732	14.8899	0.70600	1.0:0.0:0.0:0.0	.	37;37	B2R5T5;P10644	.;KAP0_HUMAN	R	37	ENSP00000351410:Q37R;ENSP00000376475:Q37R;ENSP00000376474:Q37R;ENSP00000445625:Q37R	ENSP00000351410:Q37R	Q	+	2	0	PRKAR1A	64023245	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	9.339000	0.96797	1.917000	0.55516	0.533000	0.62120	CAG	.	.	.	none		0.502	PRKAR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449884.1			G	66511650	A	G	66511650	3	3	166	1	0	0	0	0	1	0	0	0	12513	188	7	3	112	3	PRKAR1A	17	66511650	Missense_Mutation	SNP	A	TCGA-F9-A7VF-01A-11D-A33Q-10	4011727	66511650	14683560	64	9826											
EXOC7	23265	hgsc.bcm.edu	37	chr17	74097811	74097812	+	Missense_Mutation	DNP	AC	AC	CA																															ccacatggtagtagctgatgAcatggtccaggcaggacagc																										TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr17:74097811_74097812AC>CA	ENST00000335146.7	-	3	312_313	c.259_260GT>TG	c.(259-261)GTc>TGc	p.V87C	EXOC7_ENST00000406660.3_Missense_Mutation_p.V87C|EXOC7_ENST00000607838.1_Missense_Mutation_p.V87C|EXOC7_ENST00000589210.1_Missense_Mutation_p.V87C|EXOC7_ENST00000332065.5_Missense_Mutation_p.V87C|EXOC7_ENST00000411744.2_Missense_Mutation_p.V87C|EXOC7_ENST00000467929.2_Missense_Mutation_p.V46C|EXOC7_ENST00000405575.4_Missense_Mutation_p.V87C			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	87					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)			GTAGCTGATGACATGGTCCAGG	0.54																																					p.V87G|p.V87F		Atlas-SNP	.											.	EXOC7	47	.	0			c.T260G|c.G259T						PASS	.																																			SO:0001583	missense	23265	exon3			CTGATGACATGGT|TGATGACATGGTC	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.259_260delinsCA	chr17.hg19:g.74097811_74097812delinsCA	ENSP00000334100:p.Val87Cys	61.0|63.0	0.0	.		90.0|86.0	24.0|22.0	.	NM_001145298	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Missense_Mutation	SNP	ENST00000335146.7	hg19	CCDS45782.1																																																																																			.	.	.	none		0.54	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219		CA	74097812	AC	CA	74097811	3	2	166	1	0	0	0	0	1	0	0	0	5312	275	10	5	2019	5	EXOC7	17	74097811	Missense_Mutation	DNP	AC	TCGA-F9-A7VF-01A-11D-A33Q-10	7586161	74097811	7097399	65	9827											
HKR1	284459	hgsc.bcm.edu	37	chr19	37853726	37853726	+	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	ggctttacttggaagtcgaaCctctttacacatcagcggac	10	11	9	11	2	2	0	1	0	1	0	3	3	2	2	1	3	4	1	1	3	4	5			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr19:37853726C>T	ENST00000324411.4	+	6	1298	c.1029C>T	c.(1027-1029)aaC>aaT	p.N343N	HKR1_ENST00000392153.3_Silent_p.N324N|HKR1_ENST00000541583.2_Silent_p.N282N|HKR1_ENST00000591471.1_Silent_p.N70N|HKR1_ENST00000544914.1_Silent_p.N70N|HKR1_ENST00000591134.1_Intron|HKR1_ENST00000589392.1_Silent_p.N325N	NM_181786.2	NP_861451.1	P10072	HKR1_HUMAN	HKR1, GLI-Kruppel zinc finger family member	343					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)			GGAAGTCGAACCTCTTTACAC	0.488																																					p.N343N		Atlas-SNP	.											.	HKR1	74	.	0			c.C1029T						PASS	.						102	91	95					19																	37853726		2203	4300	6503	SO:0001819	synonymous_variant	284459	exon6			GTCGAACCTCTTT	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.1029C>T	chr19.hg19:g.37853726C>T		81.0	0.0	.		72.0	32.0	.	NM_181786	A8MRS7|Q6PJD0|Q9BSW9|Q9UM09	Silent	SNP	ENST00000324411.4	hg19	CCDS12502.1																																																																																			.	.	.	none		0.488	HKR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458375.1	NM_181786		T	37853726	C	T	37853726	2	4	166	1	0	0	0	0	0	0	0	1	7201	506	18	2		2	HKR1	19	37853726	Silent	SNP	C	TCGA-F9-A7VF-01A-11D-A33Q-10		37853726	21275257	66	9828											
IGFL3	388555	hgsc.bcm.edu	37	chr19	46623600	46623601	+	Missense_Mutation	DNP	AC	AC	GA																															ggggtttttatgggtacaggAcgtgcctcctgttcctatca																										TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr19:46623600_46623601AC>GA	ENST00000341415.2	-	4	388_389	c.364_365GT>TC	c.(364-366)GTc>TCc	p.V122S	AC007193.6_ENST00000597989.1_lincRNA	NM_207393.1	NP_997276.1	Q6UXB1	IGFL3_HUMAN	IGF-like family member 3	122						extracellular region (GO:0005576)				endometrium(1)|large_intestine(1)|lung(5)	7		Ovarian(192;0.0175)|all_neural(266;0.0476)		OV - Ovarian serous cystadenocarcinoma(262;0.00473)|GBM - Glioblastoma multiforme(486;0.0149)|Epithelial(262;0.239)		tgggtacaggacgTGCCTCCTG	0.455																																					p.V122A|p.V122F		Atlas-SNP	.											.	IGFL3	17	.	0			c.T365C|c.G364T						PASS	.																																			SO:0001583	missense	388555	exon4			TACAGGACGTGCC|ACAGGACGTGCCT	AY358434	CCDS33058.1	19q13.32	2006-07-14				ENSG00000188624			32930	protein-coding gene	gene with protein product		610546				14702039	Standard	NM_207393		Approved	UNQ483	uc002pea.1	Q6UXB1		ENST00000341415.2:c.364_365delinsGA	chr19.hg19:g.46623600_46623601delinsGA	ENSP00000344860:p.Val122Ser	93.0	0.0	.		71.0	32.0	.	NM_207393		Missense_Mutation	SNP	ENST00000341415.2	hg19	CCDS33058.1																																																																																			.	.	.	none		0.455	IGFL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421323.1	NM_207393		GA	46623601	AC	GA	46623600	3	3	166	1	0	0	0	0	1	0	0	0	7595	275	10	3	16	3	IGFL3	19	46623600	Missense_Mutation	DNP	AC	TCGA-F9-A7VF-01A-11D-A33Q-10	8769874	46623600	12505383	67	9829											
MAVS	57506	hgsc.bcm.edu	37	chr20	3842062	3842062	+	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	cccccacacctgctgcggccCacagcatcccctacaacagc	9	4	6	22	1	0	0	0	0	0	0	1	0	1	0	6	1	6	2	6	1	2	1			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr20:3842062C>A	ENST00000428216.2	+	4	504	c.376C>A	c.(376-378)Cac>Aac	p.H126N	MAVS_ENST00000358134.6_Intron|MAVS_ENST00000416600.2_5'UTR	NM_020746.4	NP_065797.2	Q7Z434	MAVS_HUMAN	mitochondrial antiviral signaling protein	126	Pro-rich.				activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|negative regulation of viral genome replication (GO:0045071)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of IP-10 production (GO:0071660)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of peroxisome organization (GO:1900063)|RIG-I signaling pathway (GO:0039529)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)	CARD domain binding (GO:0050700)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			autonomic_ganglia(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						TGCTGCGGCCCACAGCATCCC	0.637																																					p.H126N		Atlas-SNP	.											.	MAVS	34	.	0			c.C376A						PASS	.						73	73	73					20																	3842062		2203	4300	6503	SO:0001583	missense	57506	exon4			GCGGCCCACAGCA	DQ174270	CCDS33437.1, CCDS56176.1	20p13	2009-04-02			ENSG00000088888	ENSG00000088888			29233	protein-coding gene	gene with protein product	"virus-induced signaling adaptor", "IFN-B promoter stimulator 1", "CARD adaptor inducing IFN-beta"	609676				16125763, 16153868	Standard	NM_020746		Approved	VISA, KIAA1271, IPS-1, Cardif	uc002wjw.4	Q7Z434	OTTHUMG00000031765	ENST00000428216.2:c.376C>A	chr20.hg19:g.3842062C>A	ENSP00000401980:p.His126Asn	223.0	0.0	.		257.0	147.0	.	NM_020746	A8K6X0|B2BD33|B2BD34|F5H6C8|Q2HWT5|Q3I0Y2|Q5T7I6|Q86VY7|Q9H1H3|Q9H4Y1|Q9H8D3|Q9ULE9	Missense_Mutation	SNP	ENST00000428216.2	hg19	CCDS33437.1	.	.	.	.	.	.	.	.	.	.	C	13.68	2.309235	0.40895	.	.	ENSG00000088888	ENST00000428216	T	0.11604	2.76	3.84	3.84	0.44239	.	1.394380	0.04729	N	0.420774	T	0.18341	0.0440	L	0.43152	1.355	0.46061	D	0.998849	D	0.52996	0.957	P	0.51701	0.677	T	0.16897	-1.0387	10	0.17369	T	0.5	-2.9594	11.4651	0.50235	0.0:1.0:0.0:0.0	.	126	Q7Z434	MAVS_HUMAN	N	126	ENSP00000401980:H126N	ENSP00000401980:H126N	H	+	1	0	MAVS	3790062	0.078000	0.21339	0.024000	0.17045	0.017000	0.09413	1.020000	0.30027	2.148000	0.66965	0.591000	0.81541	CAC	.	.	.	none		0.637	MAVS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077784.3	NM_020746		A	3842062	C	A	3842062	3	1	166	1	0	0	0	0	1	0	0	0	9345	594	21	4	386	4	MAVS	20	3842062	Missense_Mutation	SNP	C	TCGA-F9-A7VF-01A-11D-A33Q-10		3842062	59183458	68	9830											
SLC13A3	64849	hgsc.bcm.edu	37	chr20	45216777	45216777	+	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	gatggcaaacatgcagaaaaGgatgaaaacagcctgttcgg	16	6	12	7	1	0	2	0	1	0	1	1	4	0	3	1	3	4	3	1	3	5	1			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr20:45216777G>T	ENST00000279027.4	-	8	1060	c.1042C>A	c.(1042-1044)Ctt>Att	p.L348I	SLC13A3_ENST00000413164.2_Missense_Mutation_p.L298I|SLC13A3_ENST00000435032.1_5'UTR|SLC13A3_ENST00000495082.1_Missense_Mutation_p.L301I|SLC13A3_ENST00000372121.1_Missense_Mutation_p.L298I|SLC13A3_ENST00000472148.1_Intron|SLC13A3_ENST00000464518.1_5'Flank|SLC13A3_ENST00000290317.5_Missense_Mutation_p.L301I|SLC13A3_ENST00000396360.1_Intron	NM_001193342.1|NM_022829.5	NP_001180271.1|NP_073740.2	Q8WWT9	S13A3_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	348					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-affinity sodium:dicarboxylate symporter activity (GO:0015362)			breast(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	ATGCAGAAAAGGATGAAAACA	0.592																																					p.L348I		Atlas-SNP	.											.	SLC13A3	88	.	0			c.C1042A						PASS	.						89	80	83					20																	45216777		2203	4300	6503	SO:0001583	missense	64849	exon8			AGAAAAGGATGAA	AF154121	CCDS13400.1, CCDS42886.1, CCDS54469.1, CCDS54470.1	20q13.12	2013-05-22			ENSG00000158296	ENSG00000158296		"Solute carriers"	14430	protein-coding gene	gene with protein product		606411				10794676, 10992006	Standard	NM_001011554		Approved	NADC3, SDCT2	uc002xsf.2	Q8WWT9	OTTHUMG00000033042	ENST00000279027.4:c.1042C>A	chr20.hg19:g.45216777G>T	ENSP00000279027:p.Leu348Ile	74.0	0.0	.		130.0	28.0	.	NM_022829	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Missense_Mutation	SNP	ENST00000279027.4	hg19	CCDS13400.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.89|11.89	1.774382|1.774382	0.31411|0.31411	.|.	.|.	ENSG00000158296|ENSG00000158296	ENST00000290317;ENST00000279027;ENST00000413164;ENST00000495082;ENST00000468915;ENST00000420568;ENST00000372121|ENST00000450298	T;T;T;T;T;T;T|.	0.12672|.	3.89;3.89;3.89;3.89;3.89;2.67;2.66|.	5.77|5.77	3.61|3.61	0.41365|0.41365	.|.	0.147589|.	0.64402|.	D|.	0.000011|.	T|T	0.29458|0.29458	0.0734|0.0734	N|N	0.05199|0.05199	-0.095|-0.095	0.80722|0.80722	D|D	1|1	B;B;B|.	0.26147|.	0.107;0.118;0.143|.	B;B;B|.	0.30943|.	0.053;0.075;0.122|.	T|T	0.06267|0.06267	-1.0836|-1.0836	10|5	0.28530|.	T|.	0.3|.	-5.8147|-5.8147	6.3165|6.3165	0.21194|0.21194	0.3814:0.0:0.6186:0.0|0.3814:0.0:0.6186:0.0	.|.	298;301;348|.	B4DIR8;F6WI18;Q8WWT9|.	.;.;S13A3_HUMAN|.	I|H	301;348;298;301;301;261;298|177	ENSP00000290317:L301I;ENSP00000279027:L348I;ENSP00000415852:L298I;ENSP00000419621:L301I;ENSP00000417784:L301I;ENSP00000395095:L261I;ENSP00000361193:L298I|.	ENSP00000279027:L348I|.	L|P	-|-	1|2	0|0	SLC13A3|SLC13A3	44650184|44650184	1.000000|1.000000	0.71417|0.71417	0.931000|0.931000	0.37212|0.37212	0.394000|0.394000	0.30568|0.30568	1.529000|1.529000	0.35996|0.35996	1.429000|1.429000	0.47314|0.47314	0.543000|0.543000	0.68304|0.68304	CTT|CCT	.	.	.	none		0.592	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2			T	45216777	G	T	45216777	3	4	166	1	0	0	0	0	1	0	0	0	14406	1000	35	4	790	4	SLC13A3	20	45216777	Missense_Mutation	SNP	G	TCGA-F9-A7VF-01A-11D-A33Q-10	41374715	45216777	17808743	69	9831											
BCAS1	8537	hgsc.bcm.edu	37	chr20	52612540	52612540	+	Missense_Mutation	SNP	T	T	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	ggtccccagggacagagcaaTccgcagttccaagttcttgt	9	9	11	12	1	1	1	0	0	1	1	4	2	4	2	4	2	1	4	4	2	2	3			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr20:52612540T>G	ENST00000395961.3	-	5	939	c.773A>C	c.(772-774)gAt>gCt	p.D258A	BCAS1_ENST00000371440.3_Missense_Mutation_p.D258A|BCAS1_ENST00000371435.2_Missense_Mutation_p.D258A|BCAS1_ENST00000434986.2_5'UTR	NM_003657.2	NP_003648.2	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1	258						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)			GACAGAGCAATCCGCAGTTCC	0.473																																					p.D258A		Atlas-SNP	.											.	BCAS1	77	.	0			c.A773C						PASS	.						148	122	131					20																	52612540		2203	4300	6503	SO:0001583	missense	8537	exon5			GAGCAATCCGCAG	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.773A>C	chr20.hg19:g.52612540T>G	ENSP00000379290:p.Asp258Ala	60.0	0.0	.		85.0	14.0	.	NM_003657	A0AVG5|Q68CZ3	Missense_Mutation	SNP	ENST00000395961.3	hg19	CCDS13444.1	.	.	.	.	.	.	.	.	.	.	T	5.880	0.346478	0.11126	.	.	ENSG00000064787	ENST00000448484;ENST00000371440;ENST00000448710;ENST00000395961;ENST00000371435	T;T;T;T	0.05081	3.5;3.5;3.5;3.5	6.03	-4.34	0.03666	.	0.949018	0.08921	N	0.874390	T	0.03011	0.0089	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.14012	0.009;0.009;0.003;0.008;0.008	B;B;B;B;B	0.13407	0.009;0.009;0.006;0.008;0.008	T	0.45542	-0.9254	10	0.37606	T	0.19	1.3367	7.6768	0.28490	0.1118:0.3398:0.0:0.5484	.	258;258;258;258;258	B2RCQ5;O75363-2;G3XAF7;A0AVG7;O75363	.;.;.;.;BCAS1_HUMAN	A	120;258;136;258;258	ENSP00000396361:D120A;ENSP00000360495:D258A;ENSP00000379290:D258A;ENSP00000360490:D258A	ENSP00000360490:D258A	D	-	2	0	BCAS1	52045947	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.527000	0.06200	-0.559000	0.06110	-0.912000	0.02778	GAT	.	.	.	none		0.473	BCAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079766.2	NM_003657		G	52612540	T	G	52612540	3	3	166	1	0	0	0	0	1	0	0	0	1350	1435	50	5	1013	5	BCAS1	20	52612540	Missense_Mutation	SNP	T	TCGA-F9-A7VF-01A-11D-A33Q-10	7395763	52612540	10412980	70	9832											
HSPA13	6782	hgsc.bcm.edu	37	chr21	15746238	15746238	+	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	tgaaagaggtcttcattaagGgtatcaaagagtttccgtga	13	12	11	5	1	3	4	2	2	1	2	4	4	4	4	1	2	0	2	1	2	4	4			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chr21:15746238G>T	ENST00000285667.3	-	5	1183	c.1116C>A	c.(1114-1116)acC>acA	p.T372T	HSPA13_ENST00000544452.1_Silent_p.T164T	NM_006948.4	NP_008879.3	P48723	HSP13_HUMAN	heat shock protein 70kDa family, member 13	372						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	13						CTTCATTAAGGGTATCAAAGA	0.403																																					p.T372T		Atlas-SNP	.											.	HSPA13	44	.	0			c.C1116A						PASS	.						143	154	150					21																	15746238		2203	4300	6503	SO:0001819	synonymous_variant	6782	exon5			ATTAAGGGTATCA		CCDS13567.1	21q11.1	2011-09-02	2008-06-17	2008-06-17	ENSG00000155304	ENSG00000155304		"Heat shock proteins / HSP70"	11375	protein-coding gene	gene with protein product		601100	"stress 70 protein chaperone, microsome-associated, 60kD", "stress 70 protein chaperone, microsome-associated, 60kDa"	STCH		8825657	Standard	NM_006948		Approved		uc002yjt.3	P48723	OTTHUMG00000074261	ENST00000285667.3:c.1116C>A	chr21.hg19:g.15746238G>T		107.0	0.0	.		113.0	42.0	.	NM_006948	B2R616|Q8NE40	Silent	SNP	ENST00000285667.3	hg19	CCDS13567.1																																																																																			.	.	.	none		0.403	HSPA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157815.1			T	15746238	G	T	15746238	2	4	166	1	0	0	0	0	0	0	0	1	7413	1219	43	4		4	HSPA13	21	15746238	Silent	SNP	G	TCGA-F9-A7VF-01A-11D-A33Q-10		15746238	32383657	71	9833											
MID1	4281	hgsc.bcm.edu	37	chrX	10535072	10535072	+	Frame_Shift_Del	DEL	C	C	-																															tcatgctccaagcacatcagCccccggatgtgagagtccgg																										TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chrX:10535072delC	ENST00000317552.4	-	2	916	c.516delG	c.(514-516)gggfs	p.G172fs	MID1_ENST00000380787.1_Frame_Shift_Del_p.G172fs|MID1_ENST00000453318.2_Frame_Shift_Del_p.G172fs|MID1_ENST00000380785.1_Frame_Shift_Del_p.G172fs|MID1_ENST00000380782.2_Frame_Shift_Del_p.G172fs|MID1_ENST00000380779.1_Frame_Shift_Del_p.G172fs|MID1_ENST00000380780.1_Frame_Shift_Del_p.G172fs	NM_000381.3|NM_033289.1	NP_000372.1|NP_150631.1	O15344	TRI18_HUMAN	midline 1	172					microtubule cytoskeleton organization (GO:0000226)|negative regulation of microtubule depolymerization (GO:0007026)|pattern specification process (GO:0007389)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein localization to microtubule (GO:0035372)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	ligase activity (GO:0016874)|microtubule binding (GO:0008017)|phosphoprotein binding (GO:0051219)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	26						AGCACATCAGCCCCCGGATGT	0.522																																					p.L173X		Atlas-Indel,Pindel	.											.	MID1	72	.	0			c.517delC						PASS	.						112	94	100					X																	10535072		2203	4300	6503	SO:0001589	frameshift_variant	4281	exon2			.	Y13667	CCDS14138.1, CCDS75952.1, CCDS75953.1	Xp22	2014-06-18	2014-06-18		ENSG00000101871	ENSG00000101871		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	7095	protein-coding gene	gene with protein product	"Opitz/BBB syndrome"	300552				9354791, 9425238	Standard	NM_001098624		Approved	OS, FXY, TRIM18, RNF59	uc004cti.4	O15344	OTTHUMG00000021127	ENST00000317552.4:c.516delG	chrX.hg19:g.10535072delC	ENSP00000312678:p.Gly172fs	150.0	0.0	0		68.0	45.0	0.661765	NM_033289	B2RCG2|O75361|Q9BZX5	Frame_Shift_Del	DEL	ENST00000317552.4	hg19	CCDS14138.1																																																																																			.	.	.	none		0.522	MID1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055738.1			-	10535072	C	-	10535072	7	5	166	1	0	1	0	1	0	0	0	0	9583	726	26	0	1523	0	MID1	23	10535072	Frame_Shift_Del	DEL	C	TCGA-F9-A7VF-01A-11D-A33Q-10		10535072	144735488	72	9834											
FIGF	2277	hgsc.bcm.edu	37	chrX	15364334	15364334	+	Missense_Mutation	SNP	T	T	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	aatgctttgcacatgctgttTtgccacttgcacatggtctg	7	15	9	10	0	1	0	0	0	1	0	1	0	1	0	1	1	5	5	1	1	1	4			TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chrX:15364334T>G	ENST00000297904.3	-	7	1415	c.986A>C	c.(985-987)aAa>aCa	p.K329T	FIGF_ENST00000488351.1_5'UTR	NM_004469.4	NP_004460.1	O43915	VEGFD_HUMAN	c-fos induced growth factor (vascular endothelial growth factor D)	329					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|induction of positive chemotaxis (GO:0050930)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mast cell chemotaxis (GO:0060754)|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)|platelet-derived growth factor receptor binding (GO:0005161)|vascular endothelial growth factor receptor binding (GO:0005172)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	17	Hepatocellular(33;0.183)					ACATGCTGTTTTGCCACTTGC	0.473																																					p.K329T		Atlas-SNP	.											.	FIGF	39	.	0			c.A986C						PASS	.						106	92	97					X																	15364334		2203	4300	6503	SO:0001583	missense	2277	exon7			GCTGTTTTGCCAC	AJ000185	CCDS14166.1	Xp22.31	2008-02-05			ENSG00000165197	ENSG00000165197			3708	protein-coding gene	gene with protein product		300091		VEGFD		9479493	Standard	NM_004469		Approved	VEGF-D	uc004cwt.2	O43915	OTTHUMG00000021175	ENST00000297904.3:c.986A>C	chrX.hg19:g.15364334T>G	ENSP00000297904:p.Lys329Thr	176.0	0.0	.		79.0	55.0	.	NM_004469	B2R7Z3	Missense_Mutation	SNP	ENST00000297904.3	hg19	CCDS14166.1	.	.	.	.	.	.	.	.	.	.	T	3.622	-0.077390	0.07184	.	.	ENSG00000165197	ENST00000297904	.	.	.	5.41	4.23	0.50019	.	0.098803	0.45606	N	0.000358	T	0.43567	0.1253	L	0.46157	1.445	0.33518	D	0.591948	P	0.52577	0.954	P	0.46452	0.517	T	0.54827	-0.8235	9	0.29301	T	0.29	-9.5606	9.854	0.41075	0.0:0.0817:0.0:0.9183	.	329	O43915	VEGFD_HUMAN	T	329	.	ENSP00000297904:K329T	K	-	2	0	FIGF	15274255	0.994000	0.37717	0.285000	0.24819	0.068000	0.16541	2.218000	0.42889	0.777000	0.33496	0.486000	0.48141	AAA	.	.	.	none		0.473	FIGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055859.1	NM_004469		G	15364334	T	G	15364334	3	3	166	1	0	0	0	0	1	0	0	0	5896	1841	64	5	82	5	FIGF	23	15364334	Missense_Mutation	SNP	T	TCGA-F9-A7VF-01A-11D-A33Q-10	4829262	15364334	139906226	73	9835											
LAMP2	3920	hgsc.bcm.edu	37	chrX	119565189	119565190	+	Frame_Shift_Ins	INS	-	-	AT																															tgcagattctaaaattgctcINSatatccagcatgatggtgct																										TCGA-F9-A7VF-01A-11D-A33Q-10	TCGA-F9-A7VF-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6f35b843-6207-45fa-b18f-ad0f104f9651	491d7fcd-e412-4f53-a19a-d5d51744cd81	g.chrX:119565189_119565190insAT	ENST00000200639.4	-	9	1357_1358	c.1221_1222insAT	c.(1219-1224)tatgagfs	p.E408fs	LAMP2_ENST00000434600.2_Intron|LAMP2_ENST00000538785.1_Intron			P13473	LAMP2_HUMAN	lysosomal-associated membrane protein 2	408					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						TAAAATTGCTCATATCCAGCAT	0.381																																					p.E408fs		Atlas-Indel,Pindel	.											.	LAMP2	101	.	0			c.1222_1223insAT						PASS	.																																			SO:0001589	frameshift_variant	3920	exon9			.	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.1220_1221dupAT	chrX.hg19:g.119565192_119565193dupAT	ENSP00000200639:p.Glu408fs	340.0	0.0	0		182.0	138.0	0.758242	NM_002294	A8K4X5|D3DTF0|Q16641|Q6Q3G8|Q96J30|Q99534|Q9UD93	Frame_Shift_Ins	INS	ENST00000200639.4	hg19	CCDS14599.1																																																																																			.	.	.	none		0.381	LAMP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058099.1			AT	119565190	-	AT	119565189	7	5	166	1	0	1	1	0	0	0	0	0	8625	835	29	0	161	0	LAMP2	23	119565189	Frame_Shift_Ins	INS	-	TCGA-F9-A7VF-01A-11D-A33Q-10	104200855	119565189	35705371	74	9836											
NCDN	23154	hgsc.bcm.edu	37	chr1	36029001	36029001	+	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	tgccacatcttcctcaacctCgtggtcaccgcaccggggct	6	9	9	17	3	3	0	2	0	1	0	5	0	4	0	5	3	2	2	5	3	1	1			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr1:36029001C>T	ENST00000373243.2	+	5	1967	c.1584C>T	c.(1582-1584)ctC>ctT	p.L528L	NCDN_ENST00000373253.3_Silent_p.L511L|NCDN_ENST00000356090.4_Silent_p.L528L	NM_014284.2	NP_055099.1	Q9UBB6	NCDN_HUMAN	neurochondrin	528					bone resorption (GO:0045453)|neuron projection development (GO:0031175)|regulation of neuronal synaptic plasticity (GO:0048168)	cytosol (GO:0005829)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|pancreas(1)|skin(2)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TCCTCAACCTCGTGGTCACCG	0.637																																					p.L528L		Atlas-SNP	.											.	NCDN	79	.	0			c.C1584T						PASS	.						73	72	73					1																	36029001		2203	4300	6503	SO:0001819	synonymous_variant	23154	exon5			CAACCTCGTGGTC	AB011179	CCDS392.1, CCDS30672.1	1p34.3	2008-02-05			ENSG00000020129	ENSG00000020129			17597	protein-coding gene	gene with protein product		608458				15007648	Standard	NM_014284		Approved	NCDN-1, NCDN-2	uc001bza.3	Q9UBB6	OTTHUMG00000059204	ENST00000373243.2:c.1584C>T	chr1.hg19:g.36029001C>T		51.0	0.0	.		52.0	22.0	.	NM_014284	D3DPR9|Q9UBY2|Q9Y4A6|Q9Y4D9	Silent	SNP	ENST00000373243.2	hg19	CCDS392.1	.	.	.	.	.	.	.	.	.	.	C	8.862	0.947208	0.18356	.	.	ENSG00000020129	ENST00000423723	.	.	.	4.71	-9.43	0.00607	.	.	.	.	.	T	0.48333	0.1494	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58381	-0.7646	4	.	.	.	.	10.1742	0.42929	0.0:0.1196:0.3934:0.4871	.	.	.	.	L	122	.	.	S	+	2	0	NCDN	35801588	0.002000	0.14202	0.817000	0.32601	0.960000	0.62799	-1.658000	0.01977	-1.527000	0.01758	-1.244000	0.01528	TCG	.	.	.	none		0.637	NCDN-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131298.1	NM_014284		T	36029001	C	T	36029001	2	4	167	1	0	0	0	0	0	0	0	1	10221	871	31	1		1	NCDN	1	36029001	Silent	SNP	C	TCGA-F9-A8NY-01A-11D-A35Z-10		36029001	213221620	1	9837											
ARHGAP29	9411	hgsc.bcm.edu	37	chr1	94668545	94668554	+	Splice_Site	DEL	CAAGTAGAGG	CAAGTAGAGG	-																															ttccatttcatttttccttcCaagtagaggctgtgaaaggt																										TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	CAAGTAGAGG	CAAGTAGAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr1:94668545_94668554delCAAGTAGAGG	ENST00000260526.6	-	10	1056_1065	c.874_883delCCTCTACTTG	c.(874-885)cctctacttgga>ga	p.PLLG292fs	ARHGAP29_ENST00000370217.3_Splice_Site_p.PLLG292fs	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	292					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)		TTTTTCCTTCCAAGTAGAGGCTGTGAAAGG	0.286																																					p.292_295del		Atlas-INDEL	.											.	ARHGAP29	132	.	0			c.875_884del						PASS	.																																			SO:0001630	splice_region_variant	9411	exon10			.		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.874-1CCTCTACTTG>-	chr1.hg19:g.94668545_94668554delCAAGTAGAGG		71.0	0.0	0		77.0	11.0	0.142857	NM_004815	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Frame_Shift_Del	DEL	ENST00000260526.6	hg19	CCDS748.1																																																																																			.	.	.	none		0.286	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815	Frame_Shift_Del	-	94668554	CAAGTAGAGG	-	94668545	8	5	167	1	0	1	0	1	0	0	1	0	878	603	21	0	2958	0	ARHGAP29	1	94668545	Splice_Site	DEL	CAAGTAGAGG	TCGA-F9-A8NY-01A-11D-A35Z-10	58639544	94668545	154582076	2	9838											
KCNC4	3749	hgsc.bcm.edu	37	chr1	110768794	110768794	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcgccgatggtagtgtcCggaaaggtatggcttcccaa	8	9	13	11	3	0	0	0	0	0	0	2	2	2	1	4	4	1	3	4	4	4	3	rs200184574		TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr1:110768794C>T	ENST00000369787.3	+	3	1840	c.1813C>T	c.(1813-1815)Cgg>Tgg	p.R605W	KCNC4_ENST00000438661.2_Missense_Mutation_p.R605W|KCNC4_ENST00000412512.2_Intron|KCNC4_ENST00000413138.3_Missense_Mutation_p.R605W	NM_004978.4	NP_004969.2	Q03721	KCNC4_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 4	605					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)		TGGTAGTGTCCGGAAAGGTAT	0.647																																					p.R605W		Atlas-SNP	.											.	KCNC4	113	.	0			c.C1813T						PASS	.						52	58	56					1																	110768794		2203	4300	6503	SO:0001583	missense	3749	exon3			AGTGTCCGGAAAG	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.1813C>T	chr1.hg19:g.110768794C>T	ENSP00000358802:p.Arg605Trp	66.0	0.0	.		77.0	36.0	.	NM_001039574	Q3MIM4|Q5TBI6	Missense_Mutation	SNP	ENST00000369787.3	hg19	CCDS821.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.656015	0.88056	.	.	ENSG00000116396	ENST00000369787;ENST00000413138;ENST00000438661	D;D;D	0.98221	-4.8;-4.63;-4.69	5.19	5.19	0.71726	.	0.134642	0.30723	N	0.009019	D	0.97579	0.9207	L	0.59436	1.845	0.43073	D	0.99471	D;D	0.71674	0.997;0.998	P;P	0.50754	0.551;0.649	D	0.98158	1.0445	10	0.87932	D	0	.	18.7013	0.91621	0.0:1.0:0.0:0.0	.	605;605	Q03721;Q03721-3	KCNC4_HUMAN;.	W	605	ENSP00000358802:R605W;ENSP00000388029:R605W;ENSP00000393655:R605W	ENSP00000358802:R605W	R	+	1	2	KCNC4	110570317	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.651000	0.61447	2.430000	0.82344	0.462000	0.41574	CGG	.	C|0.999;T|0.001	0.001	weak		0.647	KCNC4-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052146.2	NM_001039574		T	110768794	C	T	110768794	3	4	167	1	0	0	0	0	1	0	0	0	8024	643	23	1	1957	1	KCNC4	1	110768794	Missense_Mutation	SNP	C	TCGA-F9-A8NY-01A-11D-A35Z-10	16100249	110768794	138481827	3	9839											
IVNS1ABP	10625	hgsc.bcm.edu	37	chr1	185267408	185267411	+	Frame_Shift_Del	DEL	ACAA	ACAA	-																															aaccatcaaagccaccacatAcaaacagttttcctaaaaga																										TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	ACAA	ACAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr1:185267408_185267411delACAA	ENST00000367498.3	-	15	2307_2310	c.1685_1688delTTGT	c.(1684-1689)tttgtafs	p.FV562fs	IVNS1ABP_ENST00000459929.1_5'UTR|IVNS1ABP_ENST00000392007.3_Frame_Shift_Del_p.FV344fs	NM_006469.4	NP_006460.2	Q9Y6Y0	NS1BP_HUMAN	influenza virus NS1A binding protein	562					negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|response to virus (GO:0009615)|RNA splicing (GO:0008380)|transcription from RNA polymerase III promoter (GO:0006383)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|spliceosomal complex (GO:0005681)|transcription factor complex (GO:0005667)		p.F562fs*26(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(4)|prostate(2)	29						GCCACCACATACAAACAGTTTTCC	0.373																																					p.562_563del		Atlas-Indel,Pindel	.											.	IVNS1ABP	80	.	1	Deletion - Frameshift(1)	central_nervous_system(1)	c.1686_1689del						PASS	.																																			SO:0001589	frameshift_variant	10625	exon15			.	AB020657	CCDS1368.1	1q25.1-q31.1	2013-01-30			ENSG00000116679	ENSG00000116679		"Kelch-like", "BTB/POZ domain containing"	16951	protein-coding gene	gene with protein product	"kelch-like family member 39"	609209				9696811, 10048485	Standard	NM_006469		Approved	NS1-BP, HSPC068, NS-1, KIAA0850, ND1, KLHL39	uc001grl.3	Q9Y6Y0	OTTHUMG00000035384	ENST00000367498.3:c.1685_1688delTTGT	chr1.hg19:g.185267408_185267411delACAA	ENSP00000356468:p.Phe562fs	88.0	0.0	0		104.0	30.0	0.288462	NM_006469	A8K8R6|Q1G4T6|Q1G4T7|Q5TF75|Q6NW38|Q7LCG2|Q9NZX0|Q9Y480	Frame_Shift_Del	DEL	ENST00000367498.3	hg19	CCDS1368.1																																																																																			.	.	.	none		0.373	IVNS1ABP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085774.1	NM_006469		-	185267411	ACAA	-	185267408	7	5	167	1	0	1	0	1	0	0	0	0	7937	391	14	0	244	0	IVNS1ABP	1	185267408	Frame_Shift_Del	DEL	ACAA	TCGA-F9-A8NY-01A-11D-A35Z-10	74498614	185267408	63983213	4	9840											
AVPR1B	553	hgsc.bcm.edu	37	chr1	206225073	206225073	+	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	ctggctatcttcgttctgccGgtgaccatgctcacggcctg	4	12	11	14	3	3	1	1	1	2	0	4	1	3	1	3	3	2	3	3	3	1	3	rs150659663		TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr1:206225073G>T	ENST00000367126.4	+	1	1098	c.633G>T	c.(631-633)ccG>ccT	p.P211P	RP11-38J22.3_ENST00000425896.1_RNA	NM_000707.3	NP_000698.1	P47901	V1BR_HUMAN	arginine vasopressin receptor 1B	211					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)	TCGTTCTGCCGGTGACCATGC	0.617																																					p.P211P		Atlas-SNP	.											.	AVPR1B	47	.	0			c.G633T						PASS	.						57	55	56					1																	206225073		2202	4300	6502	SO:0001819	synonymous_variant	553	exon1			TCTGCCGGTGACC	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.633G>T	chr1.hg19:g.206225073G>T		71.0	0.0	.		93.0	4.0	.	NM_000707	B0M0J6|Q5TZ00	Silent	SNP	ENST00000367126.4	hg19	CCDS30994.1																																																																																			.	G|1.000;A|0.000	.	alt		0.617	AVPR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087996.1	NM_000707		T	206225073	G	T	206225073	2	4	167	1	0	0	0	0	0	0	0	1	1232	1103	39	4		4	AVPR1B	1	206225073	Silent	SNP	G	TCGA-F9-A8NY-01A-11D-A35Z-10	20957665	206225073	43025548	5	9841											
GRHL1	29841	hgsc.bcm.edu	37	chr2	10126281	10126281	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgtgaactgcttaagcacAgatttctcttcccagaaggg	10	12	9	10	0	2	3	0	1	2	2	4	3	3	3	1	1	3	2	1	1	3	3			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr2:10126281A>G	ENST00000324907.9	+	9	1276	c.1140A>G	c.(1138-1140)acA>acG	p.T380T	GRHL1_ENST00000405379.2_Silent_p.T380T|GRHL1_ENST00000324883.5_Silent_p.T191T	NM_198182.2	NP_937825.2	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1 (Drosophila)	380					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)		GCTTAAGCACAGATTTCTCTT	0.463																																					p.T380T		Atlas-SNP	.											.	GRHL1	95	.	0			c.A1140G						PASS	.						187	191	190					2																	10126281		2203	4300	6503	SO:0001819	synonymous_variant	29841	exon9			AAGCACAGATTTC	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.1140A>G	chr2.hg19:g.10126281A>G		67.0	0.0	.		113.0	28.0	.	NM_198182	A6NLA4|B2R7E4|B5MEC2|Q53T93|Q6NWN7|Q6NWN8|Q6NWN9|Q8NI33	Silent	SNP	ENST00000324907.9	hg19	CCDS33144.2																																																																																			.	.	.	none		0.463	GRHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323543.2	NM_014552		G	10126281	A	G	10126281	2	3	167	1	0	0	0	0	0	0	0	1	6770	175	7	3		3	GRHL1	2	10126281	Silent	SNP	A	TCGA-F9-A8NY-01A-11D-A35Z-10		10126281	233073092	6	9842											
MATN3	4148	hgsc.bcm.edu	37	chr2	20212199	20212199	+	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	gggcgcggccaggctcgctgGtcccggaagcgggcgcgccg	3	3	20	15	8	0	0	0	0	0	0	2	1	1	1	3	6	1	2	3	6	1	0			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr2:20212199G>C	ENST00000407540.3	-	1	256	c.194C>G	c.(193-195)aCc>aGc	p.T65S	MATN3_ENST00000421259.2_Missense_Mutation_p.T65S	NM_002381.4	NP_002372.1	O15232	MATN3_HUMAN	matrilin 3	65					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)					AGGCTCGCTGGTCCCGGAAGC	0.776																																					p.T65S		Atlas-SNP	.											.	MATN3	28	.	0			c.C194G						PASS	.						1	1	1					2																	20212199		306	662	968	SO:0001583	missense	4148	exon1			TCGCTGGTCCCGG	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.194C>G	chr2.hg19:g.20212199G>C	ENSP00000383894:p.Thr65Ser	162.0	0.0	.		107.0	26.0	.	NM_002381	B2CPU0|Q4ZG02	Missense_Mutation	SNP	ENST00000407540.3	hg19	CCDS46226.1	.	.	.	.	.	.	.	.	.	.	G	4.047	0.006311	0.07866	.	.	ENSG00000132031	ENST00000407540;ENST00000421259	T;T	0.78003	-1.14;-1.14	3.63	-4.48	0.03515	.	2.438210	0.02024	U	0.048018	T	0.56630	0.1998	N	0.22421	0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47182	-0.9137	10	0.08381	T	0.77	.	2.3036	0.04168	0.0979:0.2754:0.2087:0.418	.	65;65	B2CPU0;O15232	.;MATN3_HUMAN	S	65	ENSP00000383894:T65S;ENSP00000398753:T65S	ENSP00000383894:T65S	T	-	2	0	MATN3	20075680	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.729000	0.04920	-0.673000	0.05259	0.650000	0.86243	ACC	.	.	.	none		0.776	MATN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323925.1	NM_002381		C	20212199	G	C	20212199	3	2	167	1	0	0	0	0	1	0	0	0	9342	1261	44	4	1298	4	MATN3	2	20212199	Missense_Mutation	SNP	G	TCGA-F9-A8NY-01A-11D-A35Z-10	10085918	20212199	222987174	7	9843											
PTCD3	55037	hgsc.bcm.edu	37	chr2	86348656	86348656	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttggatttattgtgttactAtggtgaccaggagccctcaa	9	14	10	8	0	1	1	1	1	0	0	1	3	1	3	2	3	2	1	2	3	4	6	rs200261667		TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr2:86348656A>G	ENST00000254630.7	+	8	659	c.593A>G	c.(592-594)tAt>tGt	p.Y198C	PTCD3_ENST00000409277.3_Missense_Mutation_p.M157V|PTCD3_ENST00000465560.1_3'UTR	NM_017952.5	NP_060422.4	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3	198					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						TTGTGTTACTATGGTGACCAG	0.378																																					p.Y198C		Atlas-SNP	.											.	PTCD3	51	.	0			c.A593G						PASS	.						121	115	117					2																	86348656		2203	4300	6503	SO:0001583	missense	55037	exon8			GTTACTATGGTGA		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.593A>G	chr2.hg19:g.86348656A>G	ENSP00000254630:p.Tyr198Cys	86.0	0.0	.		87.0	30.0	.	NM_017952	A6NHD2|D6W5M1|Q597H0|Q658Y9|Q9BUZ8|Q9NWL0	Missense_Mutation	SNP	ENST00000254630.7	hg19	CCDS33235.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.96|10.96	1.498934|1.498934	0.26861|0.26861	.|.	.|.	ENSG00000132300|ENSG00000132300	ENST00000409783;ENST00000409277|ENST00000254630	T;T|T	0.46819|0.33438	0.92;0.86|1.41	5.14|5.14	2.71|2.71	0.32032|0.32032	.|.	.|0.110861	.|0.64402	.|D	.|0.000005	T|T	0.53658|0.53658	0.1810|0.1810	M|M	0.83603|0.83603	2.65|2.65	0.21064|0.21064	N|N	0.999791|0.999791	.|D	.|0.89917	.|1.0	.|D	.|0.91635	.|0.999	T|T	0.45542|0.45542	-0.9254|-0.9254	7|10	0.27082|0.38643	T|T	0.32|0.18	-13.7965|-13.7965	9.9922|9.9922	0.41879|0.41879	0.7303:0.0:0.0:0.2696|0.7303:0.0:0.0:0.2696	.|.	.|198	.|Q96EY7	.|PTCD3_HUMAN	V|C	157|198	ENSP00000386922:M157V;ENSP00000386462:M157V|ENSP00000254630:Y198C	ENSP00000386462:M157V|ENSP00000254630:Y198C	M|Y	+|+	1|2	0|0	PTCD3|PTCD3	86202167|86202167	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.853000|0.853000	0.48598|0.48598	4.855000|4.855000	0.62925|0.62925	0.348000|0.348000	0.23949|0.23949	-1.282000|-1.282000	0.01380|0.01380	ATG|TAT	.	.	.	weak		0.378	PTCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329854.1	NM_017952		G	86348656	A	G	86348656	3	3	167	1	0	0	0	0	1	0	0	0	12739	449	16	3	623	3	PTCD3	2	86348656	Missense_Mutation	SNP	A	TCGA-F9-A8NY-01A-11D-A35Z-10	66136457	86348656	156850717	8	9844											
FAM178B	51252	hgsc.bcm.edu	37	chr2	97559675	97559675	+	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	tcactcaccttgtggtctagCtcggcactagcctttggctg	5	13	10	13	1	3	0	2	0	1	0	4	0	3	0	2	3	2	3	2	3	2	4			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr2:97559675C>T	ENST00000417561.3	-	18	2207	c.2208G>A	c.(2206-2208)gaG>gaA	p.E736E	FAM178B_ENST00000490605.2_Silent_p.E588E|FAM178B_ENST00000470789.1_5'UTR|FAM178B_ENST00000327896.3_Silent_p.E556E|FAM178B_ENST00000393526.2_Silent_p.E28E			Q8IXR5	F178B_HUMAN	family with sequence similarity 178, member B	736										large_intestine(1)|ovary(1)	2						TGTGGTCTAGCTCGGCACTAG	0.627																																					p.E588E		Atlas-SNP	.											.	FAM178B	35	.	0			c.G1764A						PASS	.						107	91	97					2																	97559675		2203	4299	6502	SO:0001819	synonymous_variant	51252	exon14			GTCTAGCTCGGCA	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.2208G>A	chr2.hg19:g.97559675C>T		37.0	0.0	.		40.0	6.0	.	NM_001122646	A8MXN2|E9PD86|Q8IUY0|Q9P0P4	Silent	SNP	ENST00000417561.3	hg19																																																																																				.	.	.	none		0.627	FAM178B-202	KNOWN	basic	protein_coding	protein_coding		NM_016490		T	97559675	C	T	97559675	2	4	167	1	0	0	0	0	0	0	0	1	5508	796	28	2		2	FAM178B	2	97559675	Silent	SNP	C	TCGA-F9-A8NY-01A-11D-A35Z-10	11211019	97559675	145639698	9	9845											
CBLB	868	hgsc.bcm.edu	37	chr3	105459395	105459395	+	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	agggcttgttatgaggtatgGtctgtaagatattcccatcc	9	14	11	7	0	1	2	0	1	1	1	3	2	3	2	2	3	0	4	2	3	4	6			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr3:105459395G>T	ENST00000264122.4	-	7	1247	c.926C>A	c.(925-927)aCc>aAc	p.T309N	CBLB_ENST00000394027.3_Missense_Mutation_p.T331N|CBLB_ENST00000403724.1_Missense_Mutation_p.T309N|CBLB_ENST00000545639.1_3'UTR|CBLB_ENST00000405772.1_Missense_Mutation_p.T309N	NM_170662.3	NP_733762.2	Q13191	CBLB_HUMAN	Cbl proto-oncogene B, E3 ubiquitin protein ligase	309	Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.|SH2-like.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|negative regulation of T cell receptor signaling pathway (GO:0050860)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of T cell anergy (GO:0002669)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(2)|urinary_tract(2)	49						ATGAGGTATGGTCTGTAAGAT	0.418			Mis S		AML																																p.T309N	GBM(93;588 1337 9788 29341 43499)	Atlas-SNP	.		Rec	yes		3	3q13.11	868	Cas-Br-M (murine) ecotropic retroviral transforming sequence b		L	.	CBLB	118	.	0			c.C926A						PASS	.						150	126	134					3																	105459395		2203	4300	6503	SO:0001583	missense	868	exon7			GGTATGGTCTGTA	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.926C>A	chr3.hg19:g.105459395G>T	ENSP00000264122:p.Thr309Asn	67.0	0.0	.		72.0	17.0	.	NM_170662	A8K9S7|B7WNM4|Q13192|Q13193|Q3LIC0|Q63Z43|Q8IVC5	Missense_Mutation	SNP	ENST00000264122.4	hg19	CCDS2948.1	.	.	.	.	.	.	.	.	.	.	G	30	5.050656	0.93740	.	.	ENSG00000114423	ENST00000264122;ENST00000394027;ENST00000403724;ENST00000405772	D;D;D;D	0.81499	-1.5;-1.5;-1.5;-1.5	5.73	5.73	0.89815	Adaptor protein Cbl, PTB domain (1);SH2 motif (2);Adaptor protein Cbl, SH2-like (1);	0.000000	0.85682	D	0.000000	D	0.91009	0.7172	M	0.83603	2.65	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.97110	0.998;0.998;1.0	D	0.91572	0.5272	10	0.87932	D	0	-17.5729	19.9155	0.97058	0.0:0.0:1.0:0.0	.	331;309;309	E7ENW2;Q13191-3;Q13191	.;.;CBLB_HUMAN	N	309;331;309;309	ENSP00000264122:T309N;ENSP00000377595:T331N;ENSP00000384816:T309N;ENSP00000384938:T309N	ENSP00000264122:T309N	T	-	2	0	CBLB	106942085	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.465000	0.97660	2.699000	0.92147	0.650000	0.86243	ACC	.	.	.	none		0.418	CBLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319417.2	NM_170662		T	105459395	G	T	105459395	3	4	167	1	0	0	0	0	1	0	0	0	2703	1261	44	4	2074	4	CBLB	3	105459395	Missense_Mutation	SNP	G	TCGA-F9-A8NY-01A-11D-A35Z-10		105459395	92563035	10	9846											
HNRPDL	9987	hgsc.bcm.edu	37	chr4	83350691	83350691	+	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	tgggcccggcgcgccccctgCcgggcggagctgggagcgag	3	3	20	15	6	0	0	0	0	0	0	0	3	0	2	4	5	3	1	4	5	0	0	rs370944367		TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr4:83350691C>T	ENST00000295470.5	-	1	328	c.153G>A	c.(151-153)cgG>cgA	p.R51R	HNRNPDL_ENST00000602300.1_5'Flank|HNRNPDL_ENST00000514511.1_5'Flank|ENOPH1_ENST00000509635.1_5'Flank|HNRNPDL_ENST00000502762.1_Silent_p.R51R|HNRNPDL_ENST00000349655.4_5'Flank|ENOPH1_ENST00000273920.3_5'Flank	NM_001207000.1|NM_031372.3	NP_001193929.1|NP_112740.1	O14979	HNRDL_HUMAN	heterogeneous nuclear ribonucleoprotein D-like	51					regulation of gene expression (GO:0010468)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|single-stranded DNA binding (GO:0003697)										GCGCCCCCTGCCGGGCGGAGC	0.771													C|||	1	0.000199681	8e-04	0	5008	,	,		8953	0		0	False		,,,				2504	0				p.R51R		Atlas-SNP	.											.	HNRPDL	35	.	0			c.G153A						PASS	.	C	,	4,3044		0,4,1520	4	5	5		153,153	1.2	1	4		5	0,6810		0,0,3405	no	coding-synonymous,coding-synonymous	HNRPDL	NM_001207000.1,NM_031372.3	,	0,4,4925	TT,TC,CC		0.0,0.1312,0.0406	,	51/364,51/421	83350691	4,9854	1524	3405	4929	SO:0001819	synonymous_variant	9987	exon1			CCCCTGCCGGGCG	D89092	CCDS3593.1, CCDS75153.1	4q21.22	2013-06-12		2013-06-12	ENSG00000152795	ENSG00000152795		"RNA binding motif (RRM) containing"	5037	protein-coding gene	gene with protein product		607137		HNRPDL		10072754, 9524220	Standard	NM_001207000		Approved	JKTBP, laAUF1	uc003hmr.3	O14979	OTTHUMG00000130299	ENST00000295470.5:c.153G>A	chr4.hg19:g.83350691C>T		71.0	0.0	.		55.0	8.0	.	NM_031372	Q6SPF2|Q7KZ74|Q7KZ75|Q96IM0|Q96S43	Silent	SNP	ENST00000295470.5	hg19	CCDS3593.1																																																																																			.	.	.	weak		0.771	HNRNPDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252644.1	NM_005463		T	83350691	C	T	83350691	2	4	167	1	0	0	0	0	0	0	0	1	7283	726	26	2		2	HNRPDL	4	83350691	Silent	SNP	C	TCGA-F9-A8NY-01A-11D-A35Z-10		83350691	107803585	11	9847											
TRIML2	205860	hgsc.bcm.edu	37	chr4	189020257	189020257	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatgagctttaggaggctgcGgacctgttcagaagccctgg	8	9	15	9	1	1	2	1	1	0	1	1	5	1	4	2	4	3	3	2	4	2	3			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr4:189020257G>A	ENST00000512729.1	-	4	777	c.403C>T	c.(403-405)Cgc>Tgc	p.R135C	TRIML2_ENST00000326754.3_Missense_Mutation_p.R135C|TRIML2_ENST00000536972.1_Missense_Mutation_p.R185C	NM_173553.1	NP_775824.1	Q8N7C3	TRIMM_HUMAN	tripartite motif family-like 2	135					protein ubiquitination (GO:0016567)|response to retinoic acid (GO:0032526)		ligase activity (GO:0016874)			central_nervous_system(2)|kidney(1)|large_intestine(7)|lung(25)|prostate(3)|urinary_tract(1)	39		all_cancers(14;3.11e-44)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|all_hematologic(60;0.0202)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)		OV - Ovarian serous cystadenocarcinoma(60;1.79e-11)|BRCA - Breast invasive adenocarcinoma(30;4.52e-06)|GBM - Glioblastoma multiforme(59;1.62e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.0091)|READ - Rectum adenocarcinoma(43;0.163)		AGGAGGCTGCGGACCTGTTCA	0.483																																					p.R135C		Atlas-SNP	.											.	TRIML2	80	.	0			c.C403T						PASS	.						107	104	105					4																	189020257		2203	4300	6503	SO:0001583	missense	205860	exon4			GGCTGCGGACCTG	AK098667	CCDS3850.1	4q35.2	2014-02-12	2007-12-14		ENSG00000179046	ENSG00000179046			26378	protein-coding gene	gene with protein product	"SPRY domain containing 6"						Standard	NM_173553		Approved	FLJ25801, SPRYD6	uc003izl.2	Q8N7C3	OTTHUMG00000160225	ENST00000512729.1:c.403C>T	chr4.hg19:g.189020257G>A	ENSP00000422581:p.Arg135Cys	89.0	0.0	.		73.0	26.0	.	NM_173553	B7Z6J6	Missense_Mutation	SNP	ENST00000512729.1	hg19	CCDS3850.1	.	.	.	.	.	.	.	.	.	.	G	12.19	1.862400	0.32884	.	.	ENSG00000179046	ENST00000512729;ENST00000326754;ENST00000536972	T;T;T	0.58060	3.51;0.36;3.75	4.72	-6.47	0.01902	.	0.361572	0.20462	N	0.091871	T	0.18130	0.0435	N	0.04508	-0.205	0.09310	N	0.999996	B;B;B	0.12630	0.006;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.03761	-1.1006	10	0.44086	T	0.13	.	1.092	0.01665	0.2696:0.1336:0.3359:0.2609	.	185;135;135	B7Z6J6;B7ZLC3;Q8N7C3	.;.;TRIMM_HUMAN	C	135;135;185	ENSP00000422581:R135C;ENSP00000317498:R135C;ENSP00000441236:R185C	ENSP00000317498:R135C	R	-	1	0	TRIML2	189257251	0.000000	0.05858	0.006000	0.13384	0.172000	0.22775	-3.194000	0.00563	-0.991000	0.03476	-0.295000	0.09555	CGC	.	.	.	none		0.483	TRIML2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359733.1	NM_173553		A	189020257	G	A	189020257	3	1	167	1	0	0	0	0	1	0	0	0	16563	1116	39	1	776	1	TRIML2	4	189020257	Missense_Mutation	SNP	G	TCGA-F9-A8NY-01A-11D-A35Z-10	105669566	189020257	2134019	12	9848											
PCDHGA5	56110	hgsc.bcm.edu	37	chr5	140745680	140745680	+	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	tgaccaaggtggtagcggtgGacaaagattcaggccagaac	13	6	14	8	1	1	3	1	1	0	2	1	4	1	4	2	5	2	1	2	5	4	2			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr5:140745680G>A	ENST00000518069.1	+	1	1783	c.1783G>A	c.(1783-1785)Gac>Aac	p.D595N	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA4_ENST00000571252.1_Intron	NM_018918.2|NM_032054.1	NP_061741.1|NP_114443.1	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5	595	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)|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)			GGTAGCGGTGGACAAAGATTC	0.657																																					p.D595N		Atlas-SNP	.											.	PCDHGA5	215	.	0			c.G1783A						PASS	.						76	86	83					5																	140745680		2203	4300	6503	SO:0001583	missense	56110	exon1			GCGGTGGACAAAG	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.1783G>A	chr5.hg19:g.140745680G>A	ENSP00000429834:p.Asp595Asn	104.0	0.0	.		103.0	36.0	.	NM_032054	Q2M3F5|Q9Y5D2	Missense_Mutation	SNP	ENST00000518069.1	hg19	CCDS54925.1	.	.	.	.	.	.	.	.	.	.	.	18.72	3.685011	0.68157	.	.	ENSG00000253485	ENST00000518069	T	0.33654	1.4	4.58	4.58	0.56647	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.80253	0.4589	H	0.99946	5.015	0.40492	D	0.980553	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.91185	0.4979	9	0.87932	D	0	.	17.3301	0.87259	0.0:0.0:1.0:0.0	.	595;595	Q9Y5G8-2;Q9Y5G8	.;PCDG5_HUMAN	N	595	ENSP00000429834:D595N	ENSP00000429834:D595N	D	+	1	0	PCDHGA5	140725864	1.000000	0.71417	1.000000	0.80357	0.395000	0.30598	9.598000	0.98277	2.266000	0.75297	0.563000	0.77884	GAC	.	.	.	none		0.657	PCDHGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374742.1	NM_018918		A	140745680	G	A	140745680	3	1	167	1	0	0	0	0	1	0	0	0	11564	1174	41	2	1785	2	PCDHGA5	5	140745680	Missense_Mutation	SNP	G	TCGA-F9-A8NY-01A-11D-A35Z-10		140745680	40169580	13	9849											
C6orf108	23113	hgsc.bcm.edu	37	chr6	43193850	43193850	+	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	cccagctcatagcctacaccCaaggatggctgtgtcacttc	9	9	8	15	0	2	0	2	0	0	0	3	1	2	1	3	2	3	2	3	2	3	3			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr6:43193850C>T	ENST00000252050.4	+	0	7780				DNPH1_ENST00000230431.6_Silent_p.L99L|DNPH1_ENST00000393987.2_Silent_p.L99L|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						AGCCTACACCCAAGGATGGCT	0.607																																					p.L99L		Atlas-SNP	.											.	.	.	.	0			c.G297A						PASS	.						34	27	30					6																	43193850		2190	4285	6475	SO:0001628	intergenic_variant	10591	exon3			TACACCCAAGGAT	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		chr6.hg19:g.43193850C>T		33.0	0.0	.		41.0	16.0	.	NM_006443	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	hg19	CCDS4890.1																																																																																			.	.	.	none		0.607	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		T	43193850	C	T	43193850	1	4	167	0	1	0	0	0	0	0	0	0	2322	593	21	2		2	C6orf108	6	43193850	IGR	SNP	C	TCGA-F9-A8NY-01A-11D-A35Z-10		43193850	127921217	14	9850											
CDC5L	988	hgsc.bcm.edu	37	chr6	44355567	44355567	+	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	accctgccgccaagatgcctCgaattatgatcaaggggggc	10	7	12	12	2	1	2	1	1	0	1	2	3	1	2	4	3	2	0	4	3	4	1			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr6:44355567C>T	ENST00000371477.3	+	1	306	c.7C>T	c.(7-9)Cga>Tga	p.R3*		NM_001253.3	NP_001244.1	Q99459	CDC5L_HUMAN	cell division cycle 5-like	3	HTH myb-type 1. {ECO:0000255|PROSITE- ProRule:PRU00625}.				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)			CAAGATGCCTCGAATTATGAT	0.607																																					p.R3X		Atlas-SNP	.											.	CDC5L	86	.	0			c.C7T						PASS	.						29	29	29					6																	44355567		2200	4286	6486	SO:0001587	stop_gained	988	exon1			ATGCCTCGAATTA	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.7C>T	chr6.hg19:g.44355567C>T	ENSP00000360532:p.Arg3*	50.0	0.0	.		45.0	10.0	.	NM_001253	Q76N46|Q99974	Nonsense_Mutation	SNP	ENST00000371477.3	hg19	CCDS4912.1	.	.	.	.	.	.	.	.	.	.	C	42	9.432704	0.99169	.	.	ENSG00000096401	ENST00000371477	.	.	.	5.69	4.82	0.62117	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.9078	15.0684	0.72014	0.0:0.9308:0.0:0.0692	.	.	.	.	X	3	.	ENSP00000360532:R3X	R	+	1	2	CDC5L	44463545	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.562000	0.67346	2.674000	0.91012	0.650000	0.86243	CGA	.	.	.	none		0.607	CDC5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040743.1			T	44355567	C	T	44355567	4	4	167	1	0	0	0	0	0	1	0	0	3084	876	31	1	9	1	CDC5L	6	44355567	Nonsense_Mutation	SNP	C	TCGA-F9-A8NY-01A-11D-A35Z-10	1161717	44355567	126759500	15	9851											
MAP3K4	4216	hgsc.bcm.edu	37	chr6	161512563	161512563	+	Missense_Mutation	SNP	T	T	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	atgattcaggggtacaatttTggatttgaggtaggttcaaa	12	14	12	3	0	2	2	2	2	0	0	2	3	2	3	0	5	1	3	0	5	4	7			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr6:161512563T>G	ENST00000392142.4	+	12	3274	c.3126T>G	c.(3124-3126)ttT>ttG	p.F1042L	MAP3K4_ENST00000348824.7_Missense_Mutation_p.F1042L|MAP3K4_ENST00000366919.2_Missense_Mutation_p.F1042L|MAP3K4_ENST00000366920.2_Missense_Mutation_p.F1042L	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	1042					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)		GGTACAATTTTGGATTTGAGG	0.363																																					p.F1042L		Atlas-SNP	.											.	MAP3K4	364	.	0			c.T3126G						PASS	.						144	146	145					6																	161512563		2203	4300	6503	SO:0001583	missense	4216	exon12			CAATTTTGGATTT	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.3126T>G	chr6.hg19:g.161512563T>G	ENSP00000375986:p.Phe1042Leu	151.0	0.0	.		140.0	6.0	.	NM_006724	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Missense_Mutation	SNP	ENST00000392142.4	hg19	CCDS34565.1	.	.	.	.	.	.	.	.	.	.	T	18.30	3.593287	0.66219	.	.	ENSG00000085511	ENST00000366919;ENST00000392142;ENST00000540111;ENST00000366920;ENST00000348824	T;T;T;T	0.74421	-0.81;-0.84;-0.82;-0.79	5.17	-0.3	0.12804	.	0.000000	0.85682	D	0.000000	T	0.70360	0.3215	L	0.55834	1.745	0.58432	D	0.999996	P;P;D;D	0.76494	0.933;0.533;0.999;0.999	P;B;D;D	0.77557	0.85;0.083;0.99;0.986	T	0.67898	-0.5551	10	0.29301	T	0.29	-24.6745	9.7428	0.40429	0.0:0.2696:0.0:0.7304	.	1042;32;1042;1042	F5H538;Q9P1M2;Q9Y6R4-2;Q9Y6R4	.;.;.;M3K4_HUMAN	L	1042	ENSP00000355886:F1042L;ENSP00000375986:F1042L;ENSP00000355887:F1042L;ENSP00000297332:F1042L	ENSP00000297332:F1042L	F	+	3	2	MAP3K4	161432553	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	0.902000	0.28459	-0.197000	0.10350	-0.263000	0.10527	TTT	.	.	.	none		0.363	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			G	161512563	T	G	161512563	3	3	167	1	0	0	0	0	1	0	0	0	9259	1809	63	5	3172	5	MAP3K4	6	161512563	Missense_Mutation	SNP	T	TCGA-F9-A8NY-01A-11D-A35Z-10	117156996	161512563	9602504	16	9852											
PPP1R9A	55607	hgsc.bcm.edu	37	chr7	94540403	94540403	+	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	ggtcctgaagaaccttgtgcTgaaagtaaggcaatgccaaa	14	8	11	8	0	0	3	0	2	0	1	1	3	1	3	3	2	3	3	3	2	6	2			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr7:94540403T>G	ENST00000433881.1	+	2	1510	c.978T>G	c.(976-978)gcT>gcG	p.A326A	PPP1R9A_ENST00000424654.1_Silent_p.A326A|PPP1R9A_ENST00000433360.1_Silent_p.A326A|PPP1R9A_ENST00000456331.2_Silent_p.A326A|PPP1R9A_ENST00000340694.4_Silent_p.A326A|PPP1R9A_ENST00000289495.5_Silent_p.A326A			Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory subunit 9A	326					actin filament organization (GO:0007015)|calcium-mediated signaling (GO:0019722)|neuron projection development (GO:0031175)	cell junction (GO:0030054)|cortical actin cytoskeleton (GO:0030864)|dendritic spine (GO:0043197)|filopodium (GO:0030175)|growth cone (GO:0030426)|synapse (GO:0045202)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(11)|liver(2)|lung(22)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(8)|urinary_tract(5)	71	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)			AACCTTGTGCTGAAAGTAAGG	0.483										HNSCC(28;0.073)																											p.A326A		Atlas-SNP	.											.	PPP1R9A	264	.	0			c.T978G						PASS	.						75	76	76					7																	94540403		2203	4300	6503	SO:0001819	synonymous_variant	55607	exon2			TTGTGCTGAAAGT	AB033048	CCDS34683.1, CCDS55127.1, CCDS55128.1	7q21.3	2013-01-10	2011-10-04		ENSG00000158528	ENSG00000158528		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Sterile alpha motif (SAM) domain containing"	14946	protein-coding gene	gene with protein product		602468	"protein phosphatase 1, regulatory (inhibitor) subunit 9A"			10574462	Standard	NM_001166160		Approved	Neurabin-I, KIAA1222, FLJ20068	uc010lfj.3	Q9ULJ8	OTTHUMG00000155566	ENST00000433881.1:c.978T>G	chr7.hg19:g.94540403T>G		121.0	0.0	.		188.0	57.0	.	NM_017650	A1L494|B2RWQ1|E9PCA0|E9PCK6|E9PDX1|F8W7J9|O76059|Q9NXT2	Silent	SNP	ENST00000433881.1	hg19	CCDS34683.1																																																																																			.	.	.	none		0.483	PPP1R9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340662.1	NM_001166160		G	94540403	T	G	94540403	2	3	167	1	0	0	0	0	0	0	0	1	12388	1567	55	5		5	PPP1R9A	7	94540403	Silent	SNP	T	TCGA-F9-A8NY-01A-11D-A35Z-10		94540403	64598260	17	9853											
LAMB4	22798	hgsc.bcm.edu	37	chr7	107743597	107743597	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctggcagtcttcacacaCgcccccgctgaggccaccgc	6	6	11	18	3	2	1	1	1	1	0	2	1	2	1	4	2	1	3	4	2	0	1			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr7:107743597C>T	ENST00000388781.3	-	10	1155	c.1072G>A	c.(1072-1074)Gtg>Atg	p.V358M	LAMB4_ENST00000418464.1_Missense_Mutation_p.V358M|LAMB4_ENST00000414450.2_Missense_Mutation_p.V358M|LAMB4_ENST00000205386.4_Missense_Mutation_p.V358M|LAMB4_ENST00000388780.3_Missense_Mutation_p.V358M	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	358	Laminin EGF-like 2. {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						TCTTCACACACGCCCCCGCTG	0.592																																					p.V358M		Atlas-SNP	.											.	LAMB4	253	.	0			c.G1072A						PASS	.						52	42	45					7																	107743597		2203	4300	6503	SO:0001583	missense	22798	exon10			CACACACGCCCCC	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.1072G>A	chr7.hg19:g.107743597C>T	ENSP00000373433:p.Val358Met	56.0	0.0	.		67.0	29.0	.	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	hg19	CCDS34732.1	.	.	.	.	.	.	.	.	.	.	C	19.60	3.857613	0.71834	.	.	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000388780;ENST00000418464;ENST00000414450	T;T;T;T;T	0.62364	0.03;0.03;0.03;0.03;0.03	4.3	3.4	0.38934	EGF-like, laminin (3);	0.302038	0.23387	N	0.048736	T	0.66567	0.2802	M	0.74546	2.27	0.80722	D	1	D	0.57571	0.98	P	0.48089	0.566	T	0.71856	-0.4466	10	0.51188	T	0.08	.	12.9825	0.58572	0.0:0.9164:0.0:0.0835	.	358	A4D0S4	LAMB4_HUMAN	M	358	ENSP00000205386:V358M;ENSP00000373433:V358M;ENSP00000373432:V358M;ENSP00000402353:V358M;ENSP00000402265:V358M	ENSP00000205386:V358M	V	-	1	0	LAMB4	107530833	0.996000	0.38824	0.190000	0.23270	0.611000	0.37282	3.550000	0.53691	2.368000	0.80403	0.655000	0.94253	GTG	.	.	.	none		0.592	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		T	107743597	C	T	107743597	3	4	167	1	0	0	0	0	1	0	0	0	8620	536	19	1	4313	1	LAMB4	7	107743597	Missense_Mutation	SNP	C	TCGA-F9-A8NY-01A-11D-A35Z-10	13203194	107743597	51395066	18	9854											
CNOT4	4850	hgsc.bcm.edu	37	chr7	135095338	135095338	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtagatagctgaagaaaatTgggatttaatttatataatt	16	15	8	2	1	0	3	0	1	0	2	0	4	0	4	0	1	1	2	0	1	9	10			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr7:135095338T>C	ENST00000315544.5	-	7	1027	c.748A>G	c.(748-750)Aat>Gat	p.N250D	CNOT4_ENST00000451834.1_Missense_Mutation_p.N250D|CNOT4_ENST00000356162.4_Missense_Mutation_p.N250D|CNOT4_ENST00000361528.4_Missense_Mutation_p.N250D|CNOT4_ENST00000541284.1_Missense_Mutation_p.N250D|CNOT4_ENST00000428680.2_Missense_Mutation_p.N250D|CNOT4_ENST00000423368.2_Missense_Mutation_p.N250D|CNOT4_ENST00000414802.1_Missense_Mutation_p.N250D	NM_001190848.1	NP_001177777.1	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	250					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						TGAAGAAAATTGGGATTTAAT	0.343																																					p.N250D	Ovarian(51;766 1130 5502 35047 50875)	Atlas-SNP	.											.	CNOT4	146	.	0			c.A748G						PASS	.						104	105	104					7																	135095338		1808	4070	5878	SO:0001583	missense	4850	exon7			GAAAATTGGGATT	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.748A>G	chr7.hg19:g.135095338T>C	ENSP00000326731:p.Asn250Asp	52.0	0.0	.		94.0	32.0	.	NM_001190850	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Missense_Mutation	SNP	ENST00000315544.5	hg19	CCDS55166.1	.	.	.	.	.	.	.	.	.	.	T	15.97	2.988872	0.53934	.	.	ENSG00000080802	ENST00000541284;ENST00000451834;ENST00000423368;ENST00000262563;ENST00000361528;ENST00000414802;ENST00000356162;ENST00000428680;ENST00000315544	T;T;T;T;T;T;T;T	0.44083	0.95;0.94;0.96;0.94;0.96;0.96;0.93;0.95	5.52	5.52	0.82312	.	0.128185	0.64402	D	0.000001	T	0.28962	0.0719	N	0.19112	0.55	0.54753	D	0.999982	B;B;B;B;B;B	0.31817	0.031;0.053;0.031;0.023;0.187;0.341	B;B;B;B;B;B	0.27500	0.004;0.008;0.006;0.006;0.08;0.08	T	0.07462	-1.0771	10	0.30078	T	0.28	-6.89	15.644	0.77033	0.0:0.0:0.0:1.0	.	250;250;250;250;250;250	E7ET38;F8VQP3;O95628;O95628-2;O95628-4;O95628-8	.;.;CNOT4_HUMAN;.;.;.	D	250	ENSP00000445508:N250D;ENSP00000388491:N250D;ENSP00000406777:N250D;ENSP00000354673:N250D;ENSP00000416532:N250D;ENSP00000348485:N250D;ENSP00000399108:N250D;ENSP00000326731:N250D	ENSP00000262563:N250D	N	-	1	0	CNOT4	134745878	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.679000	0.68160	2.101000	0.63845	0.533000	0.62120	AAT	.	.	.	none		0.343	CNOT4-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_013316		C	135095338	T	C	135095338	3	2	167	1	0	0	0	0	1	0	0	0	3623	1812	63	3	1296	3	CNOT4	7	135095338	Missense_Mutation	SNP	T	TCGA-F9-A8NY-01A-11D-A35Z-10	27351741	135095338	24043325	19	9855											
TG	7038	hgsc.bcm.edu	37	chr8	133899367	133899367	+	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	tccttctcttcttgcaacatGctatctctgtgccagaagat	8	15	6	12	0	3	2	0	0	3	2	6	2	4	2	2	0	4	2	2	0	3	4			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr8:133899367G>T	ENST00000220616.4	+	9	1790	c.1750G>T	c.(1750-1752)Gct>Tct	p.A584S	TG_ENST00000377869.1_Missense_Mutation_p.A584S	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	584					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)		CTTGCAACATGCTATCTCTGT	0.453																																					p.A584S		Atlas-SNP	.											.	TG	416	.	0			c.G1750T						PASS	.						113	108	110					8																	133899367		2203	4300	6503	SO:0001583	missense	7038	exon9			CAACATGCTATCT	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.1750G>T	chr8.hg19:g.133899367G>T	ENSP00000220616:p.Ala584Ser	132.0	0.0	.		165.0	42.0	.	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	hg19	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	G	12.72	2.022056	0.35701	.	.	ENSG00000042832	ENST00000377869;ENST00000220616;ENST00000535932	T;T	0.66638	-0.22;-0.21	5.03	4.15	0.48705	.	0.194839	0.35615	N	0.003081	T	0.56688	0.2002	N	0.24115	0.695	0.21416	N	0.999696	D	0.53151	0.958	P	0.45276	0.475	T	0.55755	-0.8091	10	0.87932	D	0	.	14.0112	0.64498	0.0:0.0:0.8478:0.1522	.	584	P01266	THYG_HUMAN	S	584	ENSP00000367100:A584S;ENSP00000220616:A584S	ENSP00000220616:A584S	A	+	1	0	TG	133968549	0.995000	0.38212	0.618000	0.29105	0.017000	0.09413	3.676000	0.54612	1.326000	0.45319	-0.182000	0.12963	GCT	.	.	.	none		0.453	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		T	133899367	G	T	133899367	3	4	167	1	0	0	0	0	1	0	0	0	15825	1319	46	4	1784	4	TG	8	133899367	Missense_Mutation	SNP	G	TCGA-F9-A8NY-01A-11D-A35Z-10		133899367	12464655	20	9856											
TRAPPC9	83696	hgsc.bcm.edu	37	chr8	140743457	140743457	+	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	gccccgaggcaggccgactgGccggacggctgcacctgagc	6	3	16	16	4	0	1	0	1	0	0	0	4	0	2	5	5	2	3	5	5	0	0			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr8:140743457G>T	ENST00000438773.2	-	23	3427	c.3294C>A	c.(3292-3294)ggC>ggA	p.G1098G	TRAPPC9_ENST00000522504.1_5'UTR|TRAPPC9_ENST00000389328.4_Silent_p.G1196G|TRAPPC9_ENST00000389327.3_Silent_p.G1089G	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	1098					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						AGGCCGACTGGCCGGACGGCT	0.632																																					p.G1196G		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.C3588A						PASS	.						42	41	42					8																	140743457		2203	4300	6503	SO:0001819	synonymous_variant	83696	exon23			CGACTGGCCGGAC	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.3294C>A	chr8.hg19:g.140743457G>T		68.0	0.0	.		111.0	22.0	.	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Silent	SNP	ENST00000438773.2	hg19	CCDS55278.1	.	.	.	.	.	.	.	.	.	.	G	6.675	0.493107	0.12702	.	.	ENSG00000167632	ENST00000520857	.	.	.	4.93	0.802	0.18686	.	.	.	.	.	T	0.54967	0.1891	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48175	-0.9058	4	.	.	.	.	8.0787	0.30731	0.0:0.2238:0.4519:0.3243	.	.	.	.	T	942	.	.	P	-	1	0	TRAPPC9	140812639	0.997000	0.39634	0.970000	0.41538	0.693000	0.40251	0.337000	0.19841	0.442000	0.26555	0.655000	0.94253	CCA	.	.	.	none		0.632	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466		T	140743457	G	T	140743457	2	4	167	1	0	0	0	0	0	0	0	1	16477	1190	42	4		4	TRAPPC9	8	140743457	Silent	SNP	G	TCGA-F9-A8NY-01A-11D-A35Z-10	6844090	140743457	5620565	21	9857											
UHRF2	115426	hgsc.bcm.edu	37	chr9	6420922	6420922	+	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	tattttctagttggaaaatgGatataccttatttgattatg	12	19	7	3	0	1	1	0	1	1	0	1	3	1	3	1	2	1	1	1	2	8	10			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr9:6420922G>T	ENST00000276893.5	+	2	332	c.164G>T	c.(163-165)gGa>gTa	p.G55V	RP11-307L3.4_ENST00000411561.1_RNA|UHRF2_ENST00000381373.3_Missense_Mutation_p.G55V	NM_152896.2	NP_690856.1	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase	55	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)		TTGGAAAATGGATATACCTTA	0.343																																					p.G55V		Atlas-SNP	.											.	UHRF2	50	.	0			c.G164T						PASS	.						74	73	73					9																	6420922		2203	4300	6503	SO:0001583	missense	115426	exon2			AAAATGGATATAC	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.164G>T	chr9.hg19:g.6420922G>T	ENSP00000276893:p.Gly55Val	65.0	0.0	.		57.0	4.0	.	NM_152896	Q5VYR1|Q5VYR3|Q659C8|Q8TAG7	Missense_Mutation	SNP	ENST00000276893.5	hg19	CCDS6469.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.287390	0.80803	.	.	ENSG00000147854	ENST00000276893;ENST00000381373	T;T	0.74002	-0.8;-0.8	5.46	5.46	0.80206	Ubiquitin supergroup (1);Ubiquitin (2);	0.000000	0.85682	D	0.000000	D	0.88647	0.6493	M	0.87328	2.875	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90237	0.4283	10	0.87932	D	0	-16.5314	19.296	0.94122	0.0:0.0:1.0:0.0	.	55	Q96PU4	UHRF2_HUMAN	V	55	ENSP00000276893:G55V;ENSP00000370778:G55V	ENSP00000276893:G55V	G	+	2	0	UHRF2	6410922	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	8.448000	0.90335	2.548000	0.85928	0.467000	0.42956	GGA	.	.	.	none		0.343	UHRF2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051665.3	NM_152306		T	6420922	G	T	6420922	3	4	167	1	0	0	0	0	1	0	0	0	16982	1174	41	4	170	4	UHRF2	9	6420922	Missense_Mutation	SNP	G	TCGA-F9-A8NY-01A-11D-A35Z-10		6420922	134792509	22	9858											
DDX31	64794	hgsc.bcm.edu	37	chr9	135545507	135545507	+	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	cgggcgggtagggacaagacTaccgcgcgtgcccccgcctg	6	4	16	15	6	0	1	0	0	0	1	0	2	0	2	4	3	2	1	4	3	3	2			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr9:135545507T>A	ENST00000372159.3	-	1	281	c.130A>T	c.(130-132)Agt>Tgt	p.S44C	GTF3C4_ENST00000483873.2_5'UTR|DDX31_ENST00000310532.2_Missense_Mutation_p.S44C|DDX31_ENST00000372153.1_Missense_Mutation_p.S44C|GTF3C4_ENST00000372146.4_5'UTR|DDX31_ENST00000544003.1_5'Flank|DDX31_ENST00000480876.1_5'UTR	NM_022779.7	NP_073616.6	Q9H8H2	DDX31_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 31	44						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)		GGGACAAGACTACCGCGCGTG	0.701																																					p.S44C		Atlas-SNP	.											.	DDX31	76	.	0			c.A130T						PASS	.						8	8	8					9																	135545507		2143	4213	6356	SO:0001583	missense	64794	exon1			CAAGACTACCGCG	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.130A>T	chr9.hg19:g.135545507T>A	ENSP00000361232:p.Ser44Cys	62.0	0.0	.		69.0	31.0	.	NM_022779	Q5K6N2|Q5K6N3|Q5K6N4|Q5VZJ4|Q5VZJ9|Q96E91|Q96NY2|Q96SX5|Q9H5K6	Missense_Mutation	SNP	ENST00000372159.3	hg19	CCDS6951.1	.	.	.	.	.	.	.	.	.	.	T	6.961	0.547182	0.13312	.	.	ENSG00000125485	ENST00000372159;ENST00000372155;ENST00000372153;ENST00000310532	T;T;T	0.06768	4.12;3.66;3.26	0.235	-0.47	0.12131	.	.	.	.	.	T	0.03305	0.0096	N	0.08118	0	0.20403	N	0.999909	B;B;B	0.29341	0.242;0.037;0.022	B;B;B	0.12156	0.007;0.003;0.001	T	0.38908	-0.9639	8	0.72032	D	0.01	.	.	.	.	.	44;44;44	Q9H8H2-2;Q9H8H2-3;Q9H8H2	.;.;DDX31_HUMAN	C	44	ENSP00000361232:S44C;ENSP00000361226:S44C;ENSP00000310539:S44C	ENSP00000310539:S44C	S	-	1	0	DDX31	134535328	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.031000	0.01427	-0.750000	0.04740	-0.755000	0.03482	AGT	.	.	.	none		0.701	DDX31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054794.1	NM_138620		A	135545507	T	A	135545507	3	1	167	1	0	0	0	0	1	0	0	0	4358	1522	53	5	2512	5	DDX31	9	135545507	Missense_Mutation	SNP	T	TCGA-F9-A8NY-01A-11D-A35Z-10	129124585	135545507	5667924	23	9859											
PNPLA7	375775	hgsc.bcm.edu	37	chr9	140356049	140356049	+	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	atttcggcaaggtccgtgaaGgaggcgttgggacaggtgag	9	8	18	6	3	0	2	0	2	0	0	2	4	1	4	1	6	0	2	1	6	2	2			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr9:140356049G>T	ENST00000277531.4	-	32	3891	c.3705C>A	c.(3703-3705)tcC>tcA	p.S1235S	NSMF_ENST00000371474.3_5'Flank|PNPLA7_ENST00000406427.1_Silent_p.S1260S|NSMF_ENST00000371472.2_5'Flank|NSMF_ENST00000265663.7_5'Flank|NSMF_ENST00000371475.3_5'Flank|PNPLA7_ENST00000371457.1_Silent_p.S841S|PNPLA7_ENST00000492278.1_5'UTR|NSMF_ENST00000371473.3_5'Flank|NSMF_ENST00000392812.4_5'Flank|NSMF_ENST00000437259.1_5'Flank	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	1235					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)		GGTCCGTGAAGGAGGCGTTGG	0.647																																					p.S1260S		Atlas-SNP	.											.	PNPLA7	124	.	0			c.C3780A						PASS	.						92	66	75					9																	140356049		2202	4299	6501	SO:0001819	synonymous_variant	375775	exon33			CGTGAAGGAGGCG	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.3705C>A	chr9.hg19:g.140356049G>T		50.0	0.0	.		41.0	15.0	.	NM_001098537	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Silent	SNP	ENST00000277531.4	hg19	CCDS7045.1																																																																																			.	.	.	none		0.647	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286		T	140356049	G	T	140356049	2	4	167	1	0	0	0	0	0	0	0	1	12177	987	35	4		4	PNPLA7	9	140356049	Silent	SNP	G	TCGA-F9-A8NY-01A-11D-A35Z-10	4810542	140356049	857382	24	9860											
BICC1	80114	hgsc.bcm.edu	37	chr10	60566346	60566347	+	Frame_Shift_Ins	INS	-	-	TT																															ttctgtttcattttcaggcaINStttgactatgaacagaagaa																										TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr10:60566346_60566347insTT	ENST00000373886.3	+	16	2188_2189	c.2184_2185insTT	c.(2185-2187)tttfs	p.F729fs	BICC1_ENST00000263103.1_Frame_Shift_Ins_p.F355fs	NM_001080512.1	NP_001073981.1	Q9H694	BICC1_HUMAN	BicC family RNA binding protein 1	729					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						ATTTTCAGGCATTTGACTATGA	0.342																																					p.A728fs		Atlas-Indel,Pindel	.											.	BICC1	121	.	0			c.2184_2185insTT						PASS	.																																			SO:0001589	frameshift_variant	80114	exon16			.	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.2185_2186dupTT	chr10.hg19:g.60566347_60566348dupTT	ENSP00000362993:p.Phe729fs	148.0	0.0	0		196.0	43.0	0.219388	NM_001080512		Frame_Shift_Ins	INS	ENST00000373886.3	hg19	CCDS31206.1																																																																																			.	.	.	none		0.342	BICC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048150.2	NM_025044		TT	60566347	-	TT	60566346	7	5	167	1	0	1	1	0	0	0	0	0	1427	204	8	0	2246	0	BICC1	10	60566346	Frame_Shift_Ins	INS	-	TCGA-F9-A8NY-01A-11D-A35Z-10		60566346	74968401	25	9861											
LCOR	84458	hgsc.bcm.edu	37	chr10	98715228	98715228	+	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	tttggtaatgggttcacaaaCggagagcgcgcttagtaaaa	13	10	12	6	3	1	1	1	0	0	1	1	2	1	1	0	3	2	4	0	3	5	5	rs145573126		TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr10:98715228C>T	ENST00000371097.4	+	8	1397	c.851C>T	c.(850-852)aCg>aTg	p.T284M	LCOR_ENST00000498444.1_Intron|LCOR_ENST00000356016.3_Missense_Mutation_p.T284M|LCOR_ENST00000540664.1_Missense_Mutation_p.T284M|LCOR_ENST00000371103.3_Missense_Mutation_p.T284M			Q96JN0	LCOR_HUMAN	ligand dependent nuclear receptor corepressor	284					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(1)|large_intestine(3)|lung(1)|ovary(3)|prostate(1)|urinary_tract(1)	13		Colorectal(252;0.162)		Epithelial(162;4.43e-09)|all cancers(201;2.96e-07)		GGTTCACAAACGGAGAGCGCG	0.433																																					p.T284M		Atlas-SNP	.											.	LCOR	32	.	0			c.C851T						PASS	.	C	MET/THR,MET/THR,MET/THR	1,4405		0,1,2202	68	70	70		851,851,851	5.2	1	10	dbSNP_134	70	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	LCOR	NM_001170765.1,NM_001170766.1,NM_032440.3	81,81,81	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	,,	284/434,284/407,284/434	98715228	2,13004	2203	4300	6503	SO:0001583	missense	84458	exon8			CACAAACGGAGAG		CCDS7451.1, CCDS53561.1	10q24	2006-06-28			ENSG00000196233	ENSG00000196233			29503	protein-coding gene	gene with protein product		607698				12535528, 15193453	Standard	NM_001170765		Approved	MLR2, FLJ38026, KIAA1795		Q96JN0	OTTHUMG00000018841	ENST00000371097.4:c.851C>T	chr10.hg19:g.98715228C>T	ENSP00000360138:p.Thr284Met	138.0	0.0	.		216.0	12.0	.	NM_001170766	D3DR47|Q5VW16|Q7Z723|Q86T32|Q86T33|Q8N3L6	Missense_Mutation	SNP	ENST00000371097.4	hg19	CCDS7451.1	.	.	.	.	.	.	.	.	.	.	C	15.47	2.843438	0.51057	2.27E-4	1.16E-4	ENSG00000196233	ENST00000540664;ENST00000371103;ENST00000371097;ENST00000356016	.	.	.	5.24	5.24	0.73138	.	0.213748	0.48286	D	0.000197	T	0.59878	0.2226	N	0.08118	0	0.40355	D	0.979177	D;D	0.89917	0.999;1.0	D;D	0.70227	0.93;0.968	T	0.69558	-0.5113	9	0.59425	D	0.04	-2.5696	19.1864	0.93645	0.0:1.0:0.0:0.0	.	284;284	Q96JN0;Q96JN0-2	LCOR_HUMAN;.	M	284	.	ENSP00000348298:T284M	T	+	2	0	LCOR	98705218	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.913000	0.48790	2.606000	0.88127	0.650000	0.86243	ACG	.	C|1.000;T|0.000	0.000	weak		0.433	LCOR-009	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049628.2			T	98715228	C	T	98715228	3	4	167	1	0	0	0	0	1	0	0	0	8696	536	19	1	861	1	LCOR	10	98715228	Missense_Mutation	SNP	C	TCGA-F9-A8NY-01A-11D-A35Z-10	38148882	98715228	36819519	26	9862											
MUC2	4583	hgsc.bcm.edu	37	chr11	1093105	1093105	+	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	ccactacggtgaccccaaccCcaacacccaccggcacacag	12	2	6	21	2	0	1	0	1	0	0	0	1	0	1	7	2	3	1	7	2	3	1			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr11:1093105C>G	ENST00000441003.2	+	30	4951	c.4924C>G	c.(4924-4926)Cca>Gca	p.P1642A	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.P1609A	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)	gaccccaaccccaacacccac	0.632																																					p.P1642A		Atlas-SNP	.											.	MUC2	614	.	0			c.C4924G						PASS	.						61	114	96					11																	1093105		1798	3404	5202	SO:0001583	missense	4583	exon30			CCAACCCCAACAC	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.4924C>G	chr11.hg19:g.1093105C>G	ENSP00000415183:p.Pro1642Ala	20.0	0.0	.		19.0	4.0	.	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	C	4.060	0.008863	0.07912	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.13420	2.59;2.97	1.75	0.768	0.18487	.	51.722200	0.00166	U	0.000001	T	0.04048	0.0113	.	.	.	0.09310	N	1	P	0.37663	0.604	B	0.21546	0.035	T	0.28332	-1.0047	9	0.06099	T	0.92	.	4.0341	0.09722	0.0:0.7604:0.0:0.2396	.	1642	E7EUV1	.	A	1642;1609	ENSP00000415183:P1642A;ENSP00000351956:P1609A	ENSP00000351956:P1609A	P	+	1	0	MUC2	1083105	0.000000	0.05858	0.011000	0.14972	0.183000	0.23260	-0.982000	0.03762	0.104000	0.17725	0.121000	0.15741	CCA	.	.	.	none		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		G	1093105	C	G	1093105	3	3	167	1	0	0	0	0	1	0	0	0	9982	623	22	4	5042	4	MUC2	11	1093105	Missense_Mutation	SNP	C	TCGA-F9-A8NY-01A-11D-A35Z-10		1093105	133913411	27	9863											
CAND1	55832	hgsc.bcm.edu	37	chr12	67675700	67675700	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttttgataggtttatggctAcaaatgatttgatgacggaa	12	16	10	3	1	0	4	0	4	0	0	0	5	0	5	0	3	1	2	0	3	5	7			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr12:67675700A>G	ENST00000545606.1	+	2	516	c.79A>G	c.(79-81)Aca>Gca	p.T27A		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	27					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)		GTTTATGGCTACAAATGATTT	0.269																																					p.T27A		Atlas-SNP	.											.	CAND1	100	.	0			c.A79G						PASS	.						56	57	57					12																	67675700		2203	4300	6503	SO:0001583	missense	55832	exon2			ATGGCTACAAATG		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.79A>G	chr12.hg19:g.67675700A>G	ENSP00000442318:p.Thr27Ala	51.0	0.0	.		69.0	20.0	.	NM_018448	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Missense_Mutation	SNP	ENST00000545606.1	hg19	CCDS8977.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.043235	0.75732	.	.	ENSG00000111530	ENST00000545606;ENST00000299218;ENST00000540525	T;T	0.61392	0.11;0.11	5.88	5.88	0.94601	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.59307	0.2184	M	0.71871	2.18	0.80722	D	1	B	0.20988	0.05	B	0.25291	0.059	T	0.55573	-0.8120	9	.	.	.	-14.6611	15.9527	0.79855	1.0:0.0:0.0:0.0	.	27	Q86VP6	CAND1_HUMAN	A	27;27;3	ENSP00000442318:T27A;ENSP00000437594:T3A	.	T	+	1	0	CAND1	65961967	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.108000	0.94275	2.243000	0.73865	0.533000	0.62120	ACA	.	.	.	none		0.269	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448		G	67675700	A	G	67675700	3	3	167	1	0	0	0	0	1	0	0	0	2617	391	14	3	85	3	CAND1	12	67675700	Missense_Mutation	SNP	A	TCGA-F9-A8NY-01A-11D-A35Z-10		67675700	66176195	28	9864											
PHLDA1	22822	hgsc.bcm.edu	37	chr12	76424606	76424606	+	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	ctgcggctgcgaggggggctGctgctggaccaggtgctgct	3	8	19	11	2	0	0	0	0	0	0	0	2	0	1	1	6	6	6	1	6	0	0			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr12:76424606G>A	ENST00000266671.5	-	1	3106	c.916C>T	c.(916-918)Cag>Tag	p.Q306*	RP11-290L1.3_ENST00000552367.1_RNA|PHLDA1_ENST00000602540.1_Nonsense_Mutation_p.Q165*|RP11-290L1.2_ENST00000547721.1_RNA			Q8WV24	PHLA1_HUMAN	pleckstrin homology-like domain, family A, member 1	306					apoptotic process (GO:0006915)|FasL biosynthetic process (GO:0045210)|forebrain neuron differentiation (GO:0021879)|positive regulation of apoptotic process (GO:0043065)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	14		Colorectal(145;0.09)				gAGGGGGGCTGCTGCTGGACC	0.667																																					p.Q306X		Atlas-SNP	.											.	PHLDA1	39	.	0			c.C916T						PASS	.						24	25	24					12																	76424606		2198	4285	6483	SO:0001587	stop_gained	22822	exon1			GGGGCTGCTGCTG	Z50194	CCDS31861.1	12q15	2008-08-05				ENSG00000139289			8933	protein-coding gene	gene with protein product	"proline-histidine rich protein"	605335				12384558, 15037619	Standard	NM_007350		Approved	TDAG51, DT1P1B11, PHRIP	uc001sxu.3	Q8WV24		ENST00000266671.5:c.916C>T	chr12.hg19:g.76424606G>A	ENSP00000266671:p.Gln306*	25.0	0.0	.		37.0	11.0	.	NM_007350	A1A4G9|Q15184|Q2TAN2|Q9NZ17	Nonsense_Mutation	SNP	ENST00000266671.5	hg19	CCDS31861.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	54|54	21.720412|21.720412	0.99942|0.99942	.|.	.|.	ENSG00000139289|ENSG00000139289	ENST00000421361|ENST00000266671	.|.	.|.	.|.	5.03|5.03	5.03|5.03	0.67393|0.67393	.|.	.|0.187649	.|0.35615	.|N	.|0.003091	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|0.87932	.|D	.|0	.|-18.8753	11.6242|11.6242	0.51136|0.51136	0.0818:0.0:0.9182:0.0|0.0818:0.0:0.9182:0.0	.|.	.|.	.|.	.|.	.|X	-1|306	.|.	.|ENSP00000266671:Q306X	.|Q	-|-	.|1	.|0	PHLDA1|PHLDA1	74710873|74710873	1.000000|1.000000	0.71417|0.71417	0.983000|0.983000	0.44433|0.44433	0.915000|0.915000	0.54546|0.54546	3.829000|3.829000	0.55760|0.55760	2.630000|2.630000	0.89119|0.89119	0.561000|0.561000	0.74099|0.74099	.|CAG	.	.	.	none		0.667	PHLDA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405846.2	NM_007350		A	76424606	G	A	76424606	4	1	167	1	0	0	0	0	0	1	0	0	11855	1328	46	2	293	2	PHLDA1	12	76424606	Nonsense_Mutation	SNP	G	TCGA-F9-A8NY-01A-11D-A35Z-10	8748906	76424606	57427289	29	9865											
C12orf51	283450	hgsc.bcm.edu	37	chr12	112601434	112601434	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtcagcagctgcagggggAtgatggagcccaggccggcc	7	5	18	11	1	1	1	1	1	0	0	1	3	1	3	3	6	4	3	3	6	0	0			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr12:112601434A>G	ENST00000430131.2	-	73	12688	c.11543T>C	c.(11542-11544)aTc>aCc	p.I3848T	HECTD4_ENST00000550722.1_Missense_Mutation_p.I4124T|HECTD4_ENST00000377560.5_Missense_Mutation_p.I4098T|HECTD4_ENST00000549141.1_5'Flank			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3848	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)										CTGCAGGGGGATGATGGAGCC	0.647																																					p.I4136T		Atlas-SNP	.											.	.	.	.	0			c.T12407C						PASS	.						9	14	12					12																	112601434		1644	3264	4908	SO:0001583	missense	283450	exon74			AGGGGGATGATGG	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.11543T>C	chr12.hg19:g.112601434A>G	ENSP00000404379:p.Ile3848Thr	61.0	0.0	.		83.0	5.0	.	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	A	26.3	4.724471	0.89298	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722;ENST00000547085	T;T;T	0.61627	0.09;0.09;0.09	5.73	5.73	0.89815	HECT (4);	.	.	.	.	T	0.62441	0.2428	M	0.79258	2.445	0.58432	D	0.999996	P	0.34587	0.458	B	0.35413	0.202	T	0.67480	-0.5660	9	0.87932	D	0	.	16.0193	0.80468	1.0:0.0:0.0:0.0	.	3848	Q9Y4D8	K0614_HUMAN	T	4098;3848;4124;313	ENSP00000366783:I4098T;ENSP00000404379:I3848T;ENSP00000449784:I4124T	ENSP00000366783:I4098T	I	-	2	0	C12orf51	111085817	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.747000	0.91610	2.190000	0.69967	0.533000	0.62120	ATC	.	.	.	none		0.647	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		G	112601434	A	G	112601434	3	3	167	1	0	0	0	0	1	0	0	0	1698	333	12	3	459	3	C12orf51	12	112601434	Missense_Mutation	SNP	A	TCGA-F9-A8NY-01A-11D-A35Z-10	36176828	112601434	21250461	30	9866											
EP400	57634	hgsc.bcm.edu	37	chr12	132547084	132547084	+	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	ctcaggcagcagcagcagcaGcagcaacaacagcagcagca	15	1	11	14	0	1	0	1	0	0	0	1	0	1	0	0	1	11	10	0	1	2	0			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr12:132547084G>A	ENST00000333577.4	+	48	8389	c.8280G>A	c.(8278-8280)caG>caA	p.Q2760Q	EP400_ENST00000332482.4_Silent_p.Q2687Q|EP400_ENST00000330386.6_Silent_p.Q2643Q|EP400_ENST00000389561.2_Silent_p.Q2724Q|EP400_ENST00000389562.2_Silent_p.Q2723Q			Q96L91	EP400_HUMAN	E1A binding protein p400	2760	Interaction with ZNF42. {ECO:0000250}.|Poly-Gln.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		agcagcagcagcagcaacaac	0.557																																					p.Q2724Q		Atlas-SNP	.											.	EP400	370	.	0			c.G8172A						PASS	.						30	33	32					12																	132547084		2203	4298	6501	SO:0001819	synonymous_variant	57634	exon47			GCAGCAGCAGCAA	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.8280G>A	chr12.hg19:g.132547084G>A		78.0	0.0	.		110.0	8.0	.	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	hg19																																																																																				.	.	.	none		0.557	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		A	132547084	G	A	132547084	2	1	167	1	0	0	0	0	0	0	0	1	5151	962	34	2		2	EP400	12	132547084	Silent	SNP	G	TCGA-F9-A8NY-01A-11D-A35Z-10	19945650	132547084	1304811	31	9867											
IPO4	79711	hgsc.bcm.edu	37	chr14	24653966	24653966	+	Missense_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	gcagcgaggcctgggcagccGtagctgcaggatggaaggac	9	4	18	10	2	0	0	0	0	0	0	0	4	0	3	2	5	4	5	2	5	2	1			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr14:24653966G>A	ENST00000354464.6	-	16	1702	c.1526C>T	c.(1525-1527)aCg>aTg	p.T509M	RP11-468E2.2_ENST00000561419.1_3'UTR	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4	509					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)		CTGGGCAGCCGTAGCTGCAGG	0.617																																					p.T509M		Atlas-SNP	.											.	IPO4	74	.	0			c.C1526T						PASS	.						20	24	22					14																	24653966		2069	4195	6264	SO:0001583	missense	79711	exon16			GCAGCCGTAGCTG	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.1526C>T	chr14.hg19:g.24653966G>A	ENSP00000346453:p.Thr509Met	105.0	0.0	.		130.0	42.0	.	NM_024658	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Missense_Mutation	SNP	ENST00000354464.6	hg19	CCDS9616.1	.	.	.	.	.	.	.	.	.	.	G	12.98	2.101116	0.37048	.	.	ENSG00000196497	ENST00000354464;ENST00000399536	T	0.04862	3.54	5.28	4.36	0.52297	Armadillo-like helical (1);Armadillo-type fold (1);	0.240834	0.41097	D	0.000945	T	0.06735	0.0172	L	0.42245	1.32	0.30447	N	0.775618	B	0.21753	0.06	B	0.26202	0.067	T	0.02553	-1.1142	10	0.49607	T	0.09	-1.6031	7.7196	0.28725	0.0:0.1584:0.5713:0.2703	.	509	Q8TEX9	IPO4_HUMAN	M	509;185	ENSP00000346453:T509M	ENSP00000346453:T509M	T	-	2	0	IPO4	23723806	0.995000	0.38212	0.990000	0.47175	0.527000	0.34593	2.514000	0.45503	2.764000	0.94973	0.558000	0.71614	ACG	.	.	.	none		0.617	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658		A	24653966	G	A	24653966	3	1	167	1	0	0	0	0	1	0	0	0	7802	1145	40	1	1779	1	IPO4	14	24653966	Missense_Mutation	SNP	G	TCGA-F9-A8NY-01A-11D-A35Z-10		24653966	82695574	32	9868											
FLVCR2	55640	hgsc.bcm.edu	37	chr14	76107632	76107632	+	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	cttactcttggagcagccctCactggtgagttggagcctga	7	11	12	11	0	2	2	1	2	1	0	2	4	2	4	2	3	4	2	2	3	1	3			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr14:76107632C>T	ENST00000238667.4	+	8	1805	c.1449C>T	c.(1447-1449)ctC>ctT	p.L483L	FLVCR2_ENST00000553587.1_Intron|FLVCR2_ENST00000556856.1_Intron|FLVCR2_ENST00000555027.1_Silent_p.L198L|FLVCR2_ENST00000539311.1_Silent_p.L278L|FLVCR2_ENST00000556241.1_Intron	NM_017791.2	NP_060261.2	Q9UPI3	FLVC2_HUMAN	feline leukemia virus subgroup C cellular receptor family, member 2	483					heme transport (GO:0015886)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	heme binding (GO:0020037)|heme transporter activity (GO:0015232)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	15				BRCA - Breast invasive adenocarcinoma(234;0.029)		GAGCAGCCCTCACTGGTGAGT	0.527																																					p.L483L		Atlas-SNP	.											.	FLVCR2	39	.	0			c.C1449T						PASS	.						95	82	86					14																	76107632		2203	4300	6503	SO:0001819	synonymous_variant	55640	exon8			AGCCCTCACTGGT	AK000378	CCDS9844.1, CCDS55933.1	14q24.3	2013-05-22	2007-05-01	2007-05-01	ENSG00000119686	ENSG00000119686		"Solute carriers"	20105	protein-coding gene	gene with protein product		610865	"chromosome 14 open reading frame 58", "feline leukemia virus subgroup C cellular receptor 2"	C14orf58		16439531, 20206334	Standard	NM_017791		Approved	FLJ20371, MFSD7C	uc001xrs.2	Q9UPI3	OTTHUMG00000171487	ENST00000238667.4:c.1449C>T	chr14.hg19:g.76107632C>T		54.0	0.0	.		78.0	20.0	.	NM_017791	B7Z485|Q53ZT9|Q96JY3|Q9NX90	Silent	SNP	ENST00000238667.4	hg19	CCDS9844.1																																																																																			.	.	.	none		0.527	FLVCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413672.1	NM_017791		T	76107632	C	T	76107632	2	4	167	1	0	0	0	0	0	0	0	1	5953	813	29	2		2	FLVCR2	14	76107632	Silent	SNP	C	TCGA-F9-A8NY-01A-11D-A35Z-10	51453666	76107632	31241908	33	9869											
ATG2B	55102	hgsc.bcm.edu	37	chr14	96752216	96752216	+	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	caatcagaggtttcaccactGccggaggaatctggcgcaga	11	7	12	11	2	3	2	2	0	1	2	3	4	3	4	2	4	1	2	2	4	2	1			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr14:96752216G>C	ENST00000359933.4	-	42	7006	c.6113C>G	c.(6112-6114)gCa>gGa	p.A2038G		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	2038					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)		TTTCACCACTGCCGGAGGAAT	0.557																																					p.A2038G		Atlas-SNP	.											.	ATG2B	169	.	0			c.C6113G						PASS	.						99	82	88					14																	96752216		2203	4300	6503	SO:0001583	missense	55102	exon42			ACCACTGCCGGAG	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.6113C>G	chr14.hg19:g.96752216G>C	ENSP00000353010:p.Ala2038Gly	84.0	0.0	.		82.0	25.0	.	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	hg19	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	G	36	5.630816	0.96682	.	.	ENSG00000066739	ENST00000359933	T	0.12984	2.63	5.76	5.76	0.90799	Autophagy-related, C-terminal (1);	0.052478	0.85682	D	0.000000	T	0.33000	0.0848	M	0.67700	2.07	0.58432	D	0.999998	P	0.51147	0.942	P	0.54544	0.755	T	0.01235	-1.1410	10	0.87932	D	0	.	19.9759	0.97304	0.0:0.0:1.0:0.0	.	2038	Q96BY7	ATG2B_HUMAN	G	2038	ENSP00000353010:A2038G	ENSP00000353010:A2038G	A	-	2	0	ATG2B	95821969	1.000000	0.71417	0.165000	0.22776	0.954000	0.61252	9.450000	0.97607	2.713000	0.92767	0.655000	0.94253	GCA	.	.	.	none		0.557	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		C	96752216	G	C	96752216	3	2	167	1	0	0	0	0	1	0	0	0	1094	1319	46	4	127	4	ATG2B	14	96752216	Missense_Mutation	SNP	G	TCGA-F9-A8NY-01A-11D-A35Z-10	20644584	96752216	10597324	34	9870											
FRMD5	84978	hgsc.bcm.edu	37	chr15	44166102	44166102	+	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	ctcaggtgtcaatgagcaggCtcaccactgagcggattttg	9	10	12	10	1	3	2	3	2	0	0	3	3	3	3	1	3	2	2	1	3	1	2			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr15:44166102C>G	ENST00000417257.1	-	14	1870	c.1694G>C	c.(1693-1695)aGc>aCc	p.S565T	FRMD5_ENST00000484674.1_Missense_Mutation_p.E411D|FRMD5_ENST00000402883.1_Intron	NM_032892.3	NP_116281.2	Q7Z6J6	FRMD5_HUMAN	FERM domain containing 5	565						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(109;2.29e-15)|all_epithelial(112;9.98e-13)|Lung NSC(122;4.89e-08)|all_lung(180;5.08e-07)|Melanoma(134;0.0275)		all cancers(107;8.63e-20)|GBM - Glioblastoma multiforme(94;3.63e-06)		AATGAGCAGGCTCACCACTGA	0.542																																					p.S565T		Atlas-SNP	.											.	FRMD5	45	.	0			c.G1694C						PASS	.						46	47	47					15																	44166102		2198	4298	6496	SO:0001583	missense	84978	exon14			AGCAGGCTCACCA	BC007796	CCDS10107.2, CCDS73715.1, CCDS73716.1	15q15.3	2005-08-09			ENSG00000171877	ENSG00000171877			28214	protein-coding gene	gene with protein product							Standard	XM_005254729		Approved	MGC14161	uc001ztl.3	Q7Z6J6	OTTHUMG00000060475	ENST00000417257.1:c.1694G>C	chr15.hg19:g.44166102C>G	ENSP00000403067:p.Ser565Thr	86.0	0.0	.		103.0	41.0	.	NM_032892	Q8NBG4	Missense_Mutation	SNP	ENST00000417257.1	hg19	CCDS10107.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.92|12.92	2.082707|2.082707	0.36758|0.36758	.|.	.|.	ENSG00000171877|ENSG00000171877	ENST00000449926|ENST00000417257	D|D	0.84589|0.83163	-1.87|-1.69	5.3|5.3	5.3|5.3	0.74995|0.74995	.|.	.|0.247666	.|0.44688	.|D	.|0.000430	T|T	0.76608|0.76608	0.4011|0.4011	L|L	0.36672|0.36672	1.1|1.1	0.27650|0.27650	N|N	0.947438|0.947438	.|P;B	.|0.35272	.|0.493;0.361	.|B;B	.|0.32805	.|0.153;0.073	T|T	0.70288|0.70288	-0.4913|-0.4913	7|10	0.87932|0.34782	D|T	0|0.22	.|.	17.6986|17.6986	0.88289|0.88289	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|550;565	.|Q7Z6J6-2;Q7Z6J6	.|.;FRMD5_HUMAN	D|T	471|565	ENSP00000399684:E471D|ENSP00000403067:S565T	ENSP00000399684:E471D|ENSP00000403067:S565T	E|S	-|-	3|2	2|0	FRMD5|FRMD5	41953394|41953394	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.902000|2.902000	0.48703|0.48703	2.756000|2.756000	0.94617|0.94617	0.563000|0.563000	0.77884|0.77884	GAG|AGC	.	.	.	none		0.542	FRMD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133879.1	NM_032892		G	44166102	C	G	44166102	3	3	167	1	0	0	0	0	1	0	0	0	6060	797	28	4	22	4	FRMD5	15	44166102	Missense_Mutation	SNP	C	TCGA-F9-A8NY-01A-11D-A35Z-10		44166102	58365290	35	9871											
MAN2C1	4123	hgsc.bcm.edu	37	chr15	75653705	75653705	+	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	cgggagccatccaggccctcCcagaaaaatgtatggtgcta	11	7	11	12	1	0	1	0	0	0	1	2	2	2	2	4	3	2	2	4	3	4	2			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr15:75653705C>T	ENST00000267978.5	-	11	1282	c.1236G>A	c.(1234-1236)tgG>tgA	p.W412*	MAN2C1_ENST00000563622.1_Nonsense_Mutation_p.W313*|MAN2C1_ENST00000565683.1_Nonsense_Mutation_p.W412*|MAN2C1_ENST00000563539.1_5'Flank|MAN2C1_ENST00000569482.1_Nonsense_Mutation_p.W412*	NM_006715.3	NP_006706.2	Q9NTJ4	MA2C1_HUMAN	mannosidase, alpha, class 2C, member 1	412					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						CCAGGCCCTCCCAGAAAAATG	0.617																																					p.W412X		Atlas-SNP	.											.	MAN2C1	76	.	0			c.G1236A						PASS	.						28	29	29					15																	75653705		2179	4277	6456	SO:0001587	stop_gained	4123	exon11			GCCCTCCCAGAAA	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.1236G>A	chr15.hg19:g.75653705C>T	ENSP00000267978:p.Trp412*	80.0	0.0	.		80.0	34.0	.	NM_001256494	H3BMX2|H3BQY8|H3BUT6|Q13358|Q68EM8|Q9UL64	Nonsense_Mutation	SNP	ENST00000267978.5	hg19	CCDS32298.1	.	.	.	.	.	.	.	.	.	.	C	36	5.695842	0.96802	.	.	ENSG00000140400	ENST00000267978	.	.	.	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.9758	17.5661	0.87920	0.0:1.0:0.0:0.0	.	.	.	.	X	412	.	ENSP00000267978:W412X	W	-	3	0	MAN2C1	73440758	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	3.586000	0.53950	2.491000	0.84063	0.561000	0.74099	TGG	.	.	.	none		0.617	MAN2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419965.1			T	75653705	C	T	75653705	4	4	167	1	0	0	0	0	0	1	0	0	9225	624	22	2	1950	2	MAN2C1	15	75653705	Nonsense_Mutation	SNP	C	TCGA-F9-A8NY-01A-11D-A35Z-10	31487603	75653705	26877687	36	9872											
KRT27	342574	hgsc.bcm.edu	37	chr17	38935785	38935785	+	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	gggactgaagttcaatctcaAgggtttgaagagtgcgtttc	10	12	13	6	1	2	3	2	2	1	1	4	4	2	4	0	2	1	3	0	2	4	3			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr17:38935785A>T	ENST00000301656.3	-	5	981	c.941T>A	c.(940-942)cTt>cAt	p.L314H	KRT27_ENST00000540723.1_5'Flank	NM_181537.3	NP_853515.2			keratin 27											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				TTCAATCTCAAGGGTTTGAAG	0.453																																					p.L314H		Atlas-SNP	.											.	KRT27	41	.	0			c.T941A						PASS	.						72	66	68					17																	38935785		2203	4300	6503	SO:0001583	missense	342574	exon5			ATCTCAAGGGTTT	AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"-", "Intermediate filaments type I, keratins (acidic)"	30841	protein-coding gene	gene with protein product			"keratin 25C"	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.941T>A	chr17.hg19:g.38935785A>T	ENSP00000301656:p.Leu314His	123.0	0.0	.		182.0	37.0	.	NM_181537		Missense_Mutation	SNP	ENST00000301656.3	hg19	CCDS11375.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.632625	0.87660	.	.	ENSG00000171446	ENST00000301656	D	0.91464	-2.85	5.2	5.2	0.72013	Filament (1);	0.000000	0.43919	D	0.000520	D	0.96364	0.8814	M	0.93594	3.435	0.58432	D	0.999997	D	0.89917	1.0	D	0.81914	0.995	D	0.97365	0.9972	10	0.87932	D	0	.	14.5274	0.67897	1.0:0.0:0.0:0.0	.	314	Q7Z3Y8	K1C27_HUMAN	H	314	ENSP00000301656:L314H	ENSP00000301656:L314H	L	-	2	0	KRT27	36189311	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.072000	0.76777	2.092000	0.63282	0.482000	0.46254	CTT	.	.	.	none		0.453	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537		T	38935785	A	T	38935785	3	4	167	1	0	0	0	0	1	0	0	0	8471	72	3	5	454	5	KRT27	17	38935785	Missense_Mutation	SNP	A	TCGA-F9-A8NY-01A-11D-A35Z-10		38935785	42259425	37	9873											
CDR2L	30850	hgsc.bcm.edu	37	chr17	72998179	72998179	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgacggagaccattgagcGcctccaggctcaggtggagg	8	6	16	11	2	1	3	1	2	0	1	2	5	2	4	3	5	1	2	3	5	0	1	rs139957978		TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr17:72998179G>A	ENST00000337231.5	+	4	774	c.362G>A	c.(361-363)cGc>cAc	p.R121H		NM_014603.2	NP_055418.2	Q86X02	CDR2L_HUMAN	cerebellar degeneration-related protein 2-like	121												all_lung(278;0.226)					ACCATTGAGCGCCTCCAGGCT	0.662																																					p.R121H		Atlas-SNP	.											.	.	.	.	0			c.G362A						PASS	.	G	HIS/ARG	0,4406		0,0,2203	29	29	29		362	5.2	1	17	dbSNP_134	29	1,8583		0,1,4291	no	missense	CDR2L	NM_014603.2	29	0,1,6494	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	121/466	72998179	1,12989	2203	4292	6495	SO:0001583	missense	30850	exon4			TTGAGCGCCTCCA		CCDS11710.2	17q25.1	2006-03-28			ENSG00000109089	ENSG00000109089			29999	protein-coding gene	gene with protein product	"paraneoplastic antigen"						Standard	NM_014603		Approved	HUMPPA	uc002jml.4	Q86X02	OTTHUMG00000150435	ENST00000337231.5:c.362G>A	chr17.hg19:g.72998179G>A	ENSP00000336587:p.Arg121His	95.0	0.0	.		139.0	30.0	.	NM_014603	B4DFA7|Q15175	Missense_Mutation	SNP	ENST00000337231.5	hg19	CCDS11710.2	.	.	.	.	.	.	.	.	.	.	G	16.45	3.126558	0.56721	0.0	1.16E-4	ENSG00000109089	ENST00000337231	T	0.43688	0.94	5.22	5.22	0.72569	.	0.419993	0.28414	N	0.015421	T	0.42675	0.1213	L	0.44542	1.39	0.29647	N	0.844297	D	0.61697	0.99	P	0.44732	0.459	T	0.42932	-0.9422	10	0.44086	T	0.13	-14.3941	19.155	0.93506	0.0:0.0:1.0:0.0	.	121	Q86X02	CDR2L_HUMAN	H	121	ENSP00000336587:R121H	ENSP00000336587:R121H	R	+	2	0	CDR2L	70509774	1.000000	0.71417	1.000000	0.80357	0.575000	0.36095	3.159000	0.50731	2.609000	0.88269	0.563000	0.77884	CGC	.	G|1.000;A|0.000	0.000	weak		0.662	CDR2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318080.1	NM_014603		A	72998179	G	A	72998179	3	1	167	1	0	0	0	0	1	0	0	0	3175	1087	38	1	376	1	CDR2L	17	72998179	Missense_Mutation	SNP	G	TCGA-F9-A8NY-01A-11D-A35Z-10	34062394	72998179	8197031	38	9874											
TLE6	79816	hgsc.bcm.edu	37	chr19	2987356	2987356	+	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	ccgttgtcatggtgacagagCaggcaccaggcctggtgagt	8	8	15	10	1	1	3	1	2	0	1	1	3	1	3	3	4	1	3	3	4	0	1			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr19:2987356C>T	ENST00000246112.4	+	8	745	c.544C>T	c.(544-546)Cag>Tag	p.Q182*	TLE6_ENST00000478073.2_3'UTR|TLE6_ENST00000452088.1_Nonsense_Mutation_p.Q59*	NM_001143986.1	NP_001137458.1	Q9H808	TLE6_HUMAN	transducin-like enhancer of split 6	182					regulation of transcription, DNA-templated (GO:0006355)	cell cortex (GO:0005938)|nucleus (GO:0005634)|protein complex (GO:0043234)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|urinary_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGTGACAGAGCAGGCACCAGG	0.642																																					p.Q182X		Atlas-SNP	.											.	TLE6	68	.	0			c.C544T						PASS	.						91	83	86					19																	2987356		2203	4300	6503	SO:0001587	stop_gained	79816	exon8			ACAGAGCAGGCAC	AK024071	CCDS12100.1, CCDS45910.1	19p13.3	2014-03-07	2014-03-07		ENSG00000104953	ENSG00000104953		"WD repeat domain containing"	30788	protein-coding gene	gene with protein product		612399	"transducin-like enhancer of split 6 (E(sp1) homolog, Drosophila)"			11486032	Standard	NM_024760		Approved	FLJ14009, GRG6	uc002lwt.2	Q9H808	OTTHUMG00000156793	ENST00000246112.4:c.544C>T	chr19.hg19:g.2987356C>T	ENSP00000246112:p.Gln182*	56.0	0.0	.		41.0	13.0	.	NM_001143986	J3KMZ1	Nonsense_Mutation	SNP	ENST00000246112.4	hg19	CCDS45910.1	.	.	.	.	.	.	.	.	.	.	C	19.55	3.848293	0.71603	.	.	ENSG00000104953	ENST00000246112;ENST00000452088;ENST00000441927	.	.	.	2.21	1.17	0.20885	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	.	4.533	0.12015	0.0:0.8078:0.0:0.1922	.	.	.	.	X	182;59;59	.	ENSP00000246112:Q182X	Q	+	1	0	TLE6	2938356	0.000000	0.05858	0.004000	0.12327	0.231000	0.25187	-0.030000	0.12308	0.493000	0.27837	0.555000	0.69702	CAG	.	.	.	none		0.642	TLE6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345996.3	NM_024760		T	2987356	C	T	2987356	4	4	167	1	0	0	0	0	0	1	0	0	15954	711	25	2	570	2	TLE6	19	2987356	Nonsense_Mutation	SNP	C	TCGA-F9-A8NY-01A-11D-A35Z-10		2987356	56141627	39	9875											
ELOF1	84337	hgsc.bcm.edu	37	chr19	11664884	11664884	+	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	caagagatgactccggtgttGcgggcacggtccctgaaaca	10	7	13	11	3	0	3	0	2	0	1	2	4	2	3	2	3	2	2	2	3	2	1			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr19:11664884G>A	ENST00000252445.3	-	3	192	c.129C>T	c.(127-129)cgC>cgT	p.R43R	ELOF1_ENST00000591674.1_Silent_p.R50R|ELOF1_ENST00000590700.1_Silent_p.R43R|ELOF1_ENST00000586120.1_Silent_p.R43R|ELOF1_ENST00000586683.1_Silent_p.R43R|ELOF1_ENST00000591912.1_Silent_p.R43R|ELOF1_ENST00000589171.1_Silent_p.R43R|ELOF1_ENST00000587806.1_Silent_p.R64R	NM_032377.3	NP_115753.1	P60002	ELOF1_HUMAN	elongation factor 1 homolog (S. cerevisiae)	43					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(3)|lung(2)	5						CTCCGGTGTTGCGGGCACGGT	0.587																																					p.R43R		Atlas-SNP	.											.	ELOF1	10	.	0			c.C129T						PASS	.						126	118	121					19																	11664884		2203	4300	6503	SO:0001819	synonymous_variant	84337	exon3			GGTGTTGCGGGCA	AK001171	CCDS12264.1	19p13.2	2008-02-05	2006-02-13			ENSG00000130165			28691	protein-coding gene	gene with protein product			"elongation factor 1 homolog (ELF1, S. cerevisiae)"			12477932	Standard	NM_032377		Approved	MGC4549, ELF1	uc002mse.1	P60002		ENST00000252445.3:c.129C>T	chr19.hg19:g.11664884G>A		132.0	0.0	.		120.0	44.0	.	NM_032377	Q8R1J7|Q96II4	Silent	SNP	ENST00000252445.3	hg19	CCDS12264.1																																																																																			.	.	.	none		0.587	ELOF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458868.1	NM_032377		A	11664884	G	A	11664884	2	1	167	1	0	0	0	0	0	0	0	1	5074	1306	46	2		2	ELOF1	19	11664884	Silent	SNP	G	TCGA-F9-A8NY-01A-11D-A35Z-10	8677528	11664884	47464099	40	9876											
C20orf185	359710	hgsc.bcm.edu	37	chr20	31644491	31644491	+	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	gaggggtttttggcgttgtcGaggagctctctgggtgagtc	4	13	18	6	2	1	1	0	1	1	0	4	4	1	2	0	5	1	3	0	5	0	3			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr20:31644491G>A	ENST00000375494.3	+	2	268	c.268G>A	c.(268-270)Gag>Aag	p.E90K	AL121756.1_ENST00000579962.1_RNA	NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	90	Leu-rich.				innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TGGCGTTGTCGAGGAGCTCTC	0.582																																					p.E90K		Atlas-SNP	.											.	.	.	.	0			c.G268A						PASS	.						89	83	85					20																	31644491		2203	4300	6503	SO:0001583	missense	359710	exon2			GTTGTCGAGGAGC	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.268G>A	chr20.hg19:g.31644491G>A	ENSP00000364643:p.Glu90Lys	37.0	0.0	.		48.0	17.0	.	NM_182658	Q5TDX7	Missense_Mutation	SNP	ENST00000375494.3	hg19	CCDS13212.1	.	.	.	.	.	.	.	.	.	.	G	0.055	-1.238200	0.01493	.	.	ENSG00000186190	ENST00000375494	T	0.04360	3.64	4.5	-5.52	0.02560	.	0.754568	0.11974	N	0.511404	T	0.03305	0.0096	L	0.51422	1.61	0.09310	N	1	B	0.21309	0.054	B	0.17979	0.02	T	0.50329	-0.8841	10	0.02654	T	1	-7.8418	7.2066	0.25911	0.247:0.4926:0.2604:0.0	.	90	P59826	BPIB3_HUMAN	K	90	ENSP00000364643:E90K	ENSP00000364643:E90K	E	+	1	0	BPIFB3	31108152	0.003000	0.15002	0.000000	0.03702	0.017000	0.09413	-0.080000	0.11339	-0.746000	0.04766	-1.099000	0.02127	GAG	.	.	.	none		0.582	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658		A	31644491	G	A	31644491	3	1	167	1	0	0	0	0	1	0	0	0	2099	1059	37	1	274	1	C20orf185	20	31644491	Missense_Mutation	SNP	G	TCGA-F9-A8NY-01A-11D-A35Z-10		31644491	31381029	41	9877											
CCT8L2	150160	hgsc.bcm.edu	37	chr22	17072541	17072541	+	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	gccagtgtgagggtctcctcGtcgacctcccccaacaccac	7	7	9	18	2	1	1	0	1	1	0	5	2	2	1	6	1	1	0	6	1	1	0			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chr22:17072541G>A	ENST00000359963.3	-	1	1159	c.900C>T	c.(898-900)gaC>gaT	p.D300D		NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2	300					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)				GGGTCTCCTCGTCGACCTCCC	0.493																																					p.D300D		Atlas-SNP	.											CCT8L2,right_upper_lobe,carcinoma,0,1	CCT8L2	150	.	0			c.C900T						PASS	.						194	173	180					22																	17072541		2203	4300	6503	SO:0001819	synonymous_variant	150160	exon1			CTCCTCGTCGACC	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.900C>T	chr22.hg19:g.17072541G>A		157.0	0.0	.		78.0	40.0	.	NM_014406	A4QPH3|Q9UJS3	Silent	SNP	ENST00000359963.3	hg19	CCDS13738.1																																																																																			.	.	.	none		0.493	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280580.1			A	17072541	G	A	17072541	2	1	167	1	0	0	0	0	0	0	0	1	2963	1136	40	1		1	CCT8L2	22	17072541	Silent	SNP	G	TCGA-F9-A8NY-01A-11D-A35Z-10		17072541	34232025	42	9878											
HUWE1	10075	hgsc.bcm.edu	37	chrX	53616526	53616526	+	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	cctgattgactacttgcttcAgaatcatgtcacgataatct	11	14	6	10	1	4	3	3	2	1	1	4	4	4	3	1	0	2	1	1	0	3	5			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chrX:53616526A>T	ENST00000342160.3	-	35	4899	c.4442T>A	c.(4441-4443)cTg>cAg	p.L1481Q	HUWE1_ENST00000218328.8_Missense_Mutation_p.L1481Q|HUWE1_ENST00000262854.6_Missense_Mutation_p.L1481Q			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	1481					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						TACTTGCTTCAGAATCATGTC	0.453																																					p.L1481Q		Atlas-SNP	.											.	HUWE1	724	.	0			c.T4442A						PASS	.						188	164	172					X																	53616526		2203	4300	6503	SO:0001583	missense	10075	exon36			TGCTTCAGAATCA	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.4442T>A	chrX.hg19:g.53616526A>T	ENSP00000340648:p.Leu1481Gln	65.0	0.0	.		61.0	21.0	.	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	hg19	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.319177	0.81469	.	.	ENSG00000086758	ENST00000342160;ENST00000262854;ENST00000218328	T;T;T	0.60548	0.43;0.43;0.18	5.74	5.74	0.90152	Armadillo-like helical (1);	0.000000	0.64402	D	0.000006	T	0.66771	0.2823	L	0.34521	1.04	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.70342	-0.4898	10	0.87932	D	0	.	13.9311	0.63996	1.0:0.0:0.0:0.0	.	1481;1481	Q7Z6Z7;Q7Z6Z7-2	HUWE1_HUMAN;.	Q	1481	ENSP00000340648:L1481Q;ENSP00000262854:L1481Q;ENSP00000218328:L1481Q	ENSP00000218328:L1481Q	L	-	2	0	HUWE1	53633251	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.977000	0.93446	1.935000	0.56089	0.486000	0.48141	CTG	.	.	.	none		0.453	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		T	53616526	A	T	53616526	3	4	167	1	0	0	0	0	1	0	0	0	7468	188	7	5	8878	5	HUWE1	23	53616526	Missense_Mutation	SNP	A	TCGA-F9-A8NY-01A-11D-A35Z-10		53616526	101654034	43	9879											
AR	367	hgsc.bcm.edu	37	chrX	66766365	66766365	+	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	ggtgggggtggtggcggcggCggcggcggcggcggcggcgg	0	3	29	9	9	0	0	0	0	0	0	0	0	0	0	0	14	0	0	0	14	0	0			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chrX:66766365C>T	ENST00000374690.3	+	1	1901	c.1377C>T	c.(1375-1377)ggC>ggT	p.G459G	AR_ENST00000504326.1_Silent_p.G459G|AR_ENST00000396044.3_Silent_p.G459G|AR_ENST00000513847.1_3'UTR	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	457	Modulating.|Poly-Gly.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	gtggcggcggcggcggcggcg	0.756									Androgen Insensitivity Syndrome																												p.G459G		Atlas-SNP	.											.	AR	249	.	0			c.C1377T						PASS	.																																			SO:0001819	synonymous_variant	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	CGGCGGCGGCGGC	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.1377C>T	chrX.hg19:g.66766365C>T		256.0	0.0	.		181.0	20.0	.	NM_000044	A2RUN2|B1AKD7|Q9UD95	Silent	SNP	ENST00000374690.3	hg19	CCDS14387.1																																																																																			.	.	.	none		0.756	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		T	66766365	C	T	66766365	2	4	167	1	0	0	0	0	0	0	0	1	836	755	27	1		1	AR	23	66766365	Silent	SNP	C	TCGA-F9-A8NY-01A-11D-A35Z-10	13149839	66766365	88504195	44	9880											
PGAM4	441531	hgsc.bcm.edu	37	chrX	77225038	77225038	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttcgcctcctcgtggcccGccgggctcagatcggcgtcg	2	8	14	17	7	1	1	1	0	0	1	6	1	2	1	4	3	0	2	4	3	0	1			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chrX:77225038G>A	ENST00000458128.1	-	1	97	c.98C>T	c.(97-99)gCg>gTg	p.A33V	ATP7A_ENST00000350425.4_Intron|ATP7A_ENST00000341514.6_Intron|ATP7A_ENST00000343533.5_Intron	NM_001029891.2	NP_001025062.1	Q8N0Y7	PGAM4_HUMAN	phosphoglycerate mutase family member 4	33					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						CTCGTGGCCCGCCGGGCTCAG	0.637																																					p.A33V		Atlas-SNP	.											.	PGAM4	28	.	0			c.C98T						PASS	.						55	57	56					X																	77225038		2202	4294	6496	SO:0001583	missense	441531	exon1			TGGCCCGCCGGGC	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.98C>T	chrX.hg19:g.77225038G>A	ENSP00000412189:p.Ala33Val	158.0	0.0	.		154.0	51.0	.	NM_001029891	Q5JPN2|Q8NI24|Q8NI25|Q8NI26	Missense_Mutation	SNP	ENST00000458128.1	hg19	CCDS35338.1	.	.	.	.	.	.	.	.	.	.	G	11.85	1.761398	0.31228	.	.	ENSG00000226784	ENST00000458128	T	0.71579	-0.58	0.119	0.119	0.14685	Histidine phosphatase superfamily, clade-1 (2);	0.066185	0.64402	U	0.000014	T	0.40498	0.1119	N	0.05078	-0.115	0.28813	N	0.898138	B	0.06786	0.001	B	0.06405	0.002	T	0.20240	-1.0281	9	.	.	.	-18.5376	6.135	0.20227	4.0E-4:0.0:0.9996:0.0	.	33	Q8N0Y7	PGAM4_HUMAN	V	33	ENSP00000412189:A33V	.	A	-	2	0	PGAM4	77111694	0.000000	0.05858	0.426000	0.26672	0.444000	0.32077	-0.239000	0.08965	0.260000	0.21731	0.264000	0.19307	GCG	.	.	.	none		0.637	PGAM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128371.2	NM_001029891		A	77225038	G	A	77225038	3	1	167	1	0	0	0	0	1	0	0	0	11782	1087	38	1	670	1	PGAM4	23	77225038	Missense_Mutation	SNP	G	TCGA-F9-A8NY-01A-11D-A35Z-10	10458673	77225038	78045522	45	9881											
NRK	203447	hgsc.bcm.edu	37	chrX	105153848	105153848	+	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	aagatatctttaatcagcatGaggaagaattgagacaagtt	17	11	9	4	0	2	4	1	2	1	3	2	6	2	5	0	1	1	2	0	1	6	5			TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chrX:105153848G>C	ENST00000243300.9	+	13	2518	c.2215G>C	c.(2215-2217)Gag>Cag	p.E739Q	NRK_ENST00000428173.2_Missense_Mutation_p.E740Q	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	739					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						TAATCAGCATGAGGAAGAATT	0.393										HNSCC(51;0.14)																											p.E739Q		Atlas-SNP	.											.	NRK	321	.	0			c.G2215C						PASS	.						13	11	12					X																	105153848		1840	4056	5896	SO:0001583	missense	203447	exon13			CAGCATGAGGAAG	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.2215G>C	chrX.hg19:g.105153848G>C	ENSP00000434830:p.Glu739Gln	390.0	0.0	.		386.0	119.0	.	NM_198465	Q32ND6|Q5H9K2|Q6ZMP2	Missense_Mutation	SNP	ENST00000243300.9	hg19		.	.	.	.	.	.	.	.	.	.	G	12.75	2.032692	0.35893	.	.	ENSG00000123572	ENST00000243300;ENST00000428173	T;T	0.79141	-1.23;-1.24	4.27	4.27	0.50696	.	0.000000	0.49305	D	0.000143	T	0.80226	0.4584	L	0.29908	0.895	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.83275	0.996;0.986	T	0.81656	-0.0834	10	0.87932	D	0	.	10.9826	0.47504	0.0:0.0:1.0:0.0	.	407;739	Q7Z2Y5-2;Q7Z2Y5	.;NRK_HUMAN	Q	739;740	ENSP00000434830:E739Q;ENSP00000438378:E740Q	ENSP00000434830:E739Q	E	+	1	0	NRK	105040504	0.998000	0.40836	0.897000	0.35233	0.099000	0.18886	3.621000	0.54210	2.358000	0.79984	0.600000	0.82982	GAG	.	.	.	none		0.393	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465		C	105153848	G	C	105153848	3	2	167	1	0	0	0	0	1	0	0	0	10662	1291	45	4	2265	4	NRK	23	105153848	Missense_Mutation	SNP	G	TCGA-F9-A8NY-01A-11D-A35Z-10	27928810	105153848	50116712	46	9882											
ATP2B3	492	hgsc.bcm.edu	37	chrX	152826209	152826211	+	In_Frame_Del	DEL	TCT	TCT	-																															ctcagagcactacaccatcaTcttcaacacgttcgtcatga																										TCGA-F9-A8NY-01A-11D-A35Z-10	TCGA-F9-A8NY-10A-01D-A35Z-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	af2f02ad-e74d-4e56-98c2-b25edf27b998	49bd4b7d-d8c0-4ce3-adcf-81f81c37b6fd	g.chrX:152826209_152826211delTCT	ENST00000349466.2	+	18	3241_3243	c.2915_2917delTCT	c.(2914-2919)atcttc>atc	p.F973del	ATP2B3_ENST00000370181.2_In_Frame_Del_p.F959del|ATP2B3_ENST00000359149.3_In_Frame_Del_p.F973del|ATP2B3_ENST00000263519.4_In_Frame_Del_p.F973del|ATP2B3_ENST00000460549.1_3'UTR|ATP2B3_ENST00000393842.1_In_Frame_Del_p.F959del|ATP2B3_ENST00000370186.1_In_Frame_Del_p.F959del			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	973					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)					TACACCATCATCTTCAACACGTT	0.557																																					p.972_972del		Atlas-Indel,Pindel	.											.	ATP2B3	552	.	0			c.2914_2916del						PASS	.																																			SO:0001651	inframe_deletion	492	exon17			.	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.2915_2917delTCT	chrX.hg19:g.152826209_152826211delTCT	ENSP00000343886:p.Phe973del	143.0	0.0	0		129.0	50.0	0.387597	NM_001001344	B7WNR8|B7WNY5|Q12995|Q16858	In_Frame_Del	DEL	ENST00000349466.2	hg19	CCDS35440.1																																																																																			.	.	.	none		0.557	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060957.1	NM_021949		-	152826211	TCT	-	152826209	7	5	167	1	0	1	0	1	0	0	0	0	1141	1435	50	0	2981	0	ATP2B3	23	152826209	In_Frame_Del	DEL	TCT	TCGA-F9-A8NY-01A-11D-A35Z-10	47672361	152826209	2444351	47	9883											
HSPG2	3339	hgsc.bcm.edu	37	chr1	22166446	22166446	+	Missense_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	cctccacctgcttctgtgctGtgcctagtgcattctgagca	5	13	9	14	0	2	1	0	1	2	0	3	1	3	1	4	0	5	4	4	0	1	3			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr1:22166446G>A	ENST00000374695.3	-	72	9657	c.9578C>T	c.(9577-9579)aCa>aTa	p.T3193I		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	3193	Ig-like C2-type 17.				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)	CTTCTGTGCTGTGCCTAGTGC	0.572																																					p.T3193I		Atlas-SNP	.											.	HSPG2	311	.	0			c.C9578T						PASS	.						193	180	184					1																	22166446		2203	4300	6503	SO:0001583	missense	3339	exon72			TGTGCTGTGCCTA	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.9578C>T	chr1.hg19:g.22166446G>A	ENSP00000363827:p.Thr3193Ile	92.0	0.0	.		117.0	25.0	.	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	G	10.74	1.435771	0.25813	.	.	ENSG00000142798	ENST00000374695	T	0.68025	-0.3	5.69	2.83	0.33086	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.191721	0.25789	N	0.028294	T	0.57140	0.2033	L	0.48260	1.515	0.28557	N	0.911322	B;P	0.35174	0.004;0.488	B;B	0.37198	0.027;0.243	T	0.48614	-0.9020	10	0.26408	T	0.33	.	10.077	0.42366	0.2205:0.0:0.7795:0.0	.	1133;3193	Q59EG0;P98160	.;PGBM_HUMAN	I	3193	ENSP00000363827:T3193I	ENSP00000363827:T3193I	T	-	2	0	HSPG2	22039033	0.995000	0.38212	0.979000	0.43373	0.026000	0.11368	2.062000	0.41413	0.351000	0.24027	-0.251000	0.11542	ACA	.	.	.	none		0.572	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		A	22166446	G	A	22166446	3	1	168	1	0	0	0	0	1	0	0	0	7437	1377	48	2	3701	2	HSPG2	1	22166446	Missense_Mutation	SNP	G	TCGA-F9-A97G-01A-11D-A382-10		22166446	227084175	1	9884											
SRRM1	10250	hgsc.bcm.edu	37	chr1	24972473	24972473	+	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	agatgtggttctcttcctgcAgggaacaagtgcagaacagg	11	9	13	8	0	1	2	0	0	1	2	3	3	2	3	1	3	4	3	1	3	3	2			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr1:24972473A>G	ENST00000323848.9	+	2	336		c.e2-1		SRRM1_ENST00000374389.4_Splice_Site|SRRM1_ENST00000537199.1_5'Flank|SRRM1_ENST00000479034.1_Splice_Site|SRRM1_ENST00000447431.2_Splice_Site	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1						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)		CTCTTCCTGCAGGGAACAAGT	0.383																																					.	Ovarian(68;897 1494 3282 17478)	Atlas-SNP	.											.	SRRM1	81	.	0			c.22-2A>G						PASS	.						116	117	116					1																	24972473		2203	4300	6503	SO:0001630	splice_region_variant	10250	exon2			TCCTGCAGGGAAC	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.22-1A>G	chr1.hg19:g.24972473A>G		65.0	0.0	.		103.0	23.0	.	NM_005839	O60585|Q5VVN4	Splice_Site	SNP	ENST00000323848.9	hg19	CCDS255.1	.	.	.	.	.	.	.	.	.	.	A	19.37	3.815395	0.70912	.	.	ENSG00000133226	ENST00000323848;ENST00000447431;ENST00000374389	.	.	.	5.13	5.13	0.70059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2129	0.73241	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SRRM1	24845060	1.000000	0.71417	0.984000	0.44739	0.778000	0.44026	9.261000	0.95576	2.062000	0.61559	0.482000	0.46254	.	.	.	.	none		0.383	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839	Intron	G	24972473	A	G	24972473	5	3	168	1	0	0	0	0	0	0	1	0	15180	202	7	3	26	3	SRRM1	1	24972473	Splice_Site	SNP	A	TCGA-F9-A97G-01A-11D-A382-10	2806027	24972473	224278148	2	9885											
DLGAP3	58512	hgsc.bcm.edu	37	chr1	35350632	35350632	+	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	tggaactccctccggctcctGttctcggtgtccgaatctga	5	12	10	14	3	2	1	0	1	2	0	7	3	6	2	4	3	1	2	4	3	2	1	rs143986097		TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr1:35350632G>A	ENST00000373347.1	-	8	2215	c.1947C>T	c.(1945-1947)aaC>aaT	p.N649N	DLGAP3_ENST00000235180.4_Silent_p.N649N			O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated protein 3	649					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)				TCCGGCTCCTGTTCTCGGTGT	0.612																																					p.N649N		Atlas-SNP	.											.	DLGAP3	107	.	0			c.C1947T						PASS	.						102	98	100					1																	35350632		2203	4300	6503	SO:0001819	synonymous_variant	58512	exon6			GCTCCTGTTCTCG	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.1947C>T	chr1.hg19:g.35350632G>A		79.0	0.0	.		119.0	15.0	.	NM_001080418	Q5TDD5|Q9H3X7	Silent	SNP	ENST00000373347.1	hg19	CCDS30670.1																																																																																			.	G|1.000;C|0.000	.	alt		0.612	DLGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011554.1	NM_021234		A	35350632	G	A	35350632	2	1	168	1	0	0	0	0	0	0	0	1	4563	1368	48	2		2	DLGAP3	1	35350632	Silent	SNP	G	TCGA-F9-A97G-01A-11D-A382-10	10378159	35350632	213899989	3	9886											
KCNQ4	9132	hgsc.bcm.edu	37	chr1	41285146	41285146	+	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	ctcgctctggtgggggacggTgcgtgagggtctttgtaggg	3	11	20	7	3	2	1	0	1	2	0	3	2	2	2	0	6	1	2	0	6	1	2			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr1:41285146T>G	ENST00000347132.5	+	5	916		c.e5+2		KCNQ4_ENST00000509682.2_Splice_Site|KCNQ4_ENST00000506017.1_Splice_Site	NM_004700.3|NM_172163.2	NP_004691.2|NP_751895.1	P56696	KCNQ4_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 4						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)	TGGGGGACGGTGCGTGAGGGT	0.627																																					.		Atlas-SNP	.											.	KCNQ4	58	.	0			c.834+2T>G						PASS	.						105	94	98					1																	41285146		2203	4300	6503	SO:0001630	splice_region_variant	9132	exon5			GGACGGTGCGTGA	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.834+2T>G	chr1.hg19:g.41285146T>G		81.0	0.0	.		102.0	20.0	.	NM_172163	O96025	Splice_Site	SNP	ENST00000347132.5	hg19	CCDS456.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.604351	0.87157	.	.	ENSG00000117013	ENST00000347132;ENST00000509682;ENST00000443478	.	.	.	5.08	5.08	0.68730	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.801	0.57586	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	KCNQ4	41057733	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.040000	0.89188	1.907000	0.55213	0.460000	0.39030	.	.	.	.	none		0.627	KCNQ4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000020812.1	NM_004700	Intron	G	41285146	T	G	41285146	5	3	168	1	0	0	0	0	0	0	1	0	8092	1710	59	5	854	5	KCNQ4	1	41285146	Splice_Site	SNP	T	TCGA-F9-A97G-01A-11D-A382-10	5934514	41285146	207965475	4	9887											
PIK3R3	8503	hgsc.bcm.edu	37	chr1	46532743	46532743	+	Frame_Shift_Del	DEL	A	A	-																															cccggtgatagatctttattAacttattattgcctcccttc																										TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr1:46532743delA	ENST00000262741.5	-	4	1024	c.335delT	c.(334-336)ttafs	p.L112fs	PIK3R3_ENST00000372006.1_Frame_Shift_Del_p.L112fs|PIK3R3_ENST00000340332.6_Frame_Shift_Del_p.L76fs|PIK3R3_ENST00000420542.1_Frame_Shift_Del_p.L112fs|PIK3R3_ENST00000540385.1_Frame_Shift_Del_p.L158fs|PIK3R3_ENST00000354242.4_Frame_Shift_Del_p.L112fs|PIK3R3_ENST00000423209.1_Frame_Shift_Del_p.L112fs	NM_003629.3	NP_003620.3	Q92569	P55G_HUMAN	phosphoinositide-3-kinase, regulatory subunit 3 (gamma)	112	SH2 1. {ECO:0000255|PROSITE- ProRule:PRU00191}.				insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)			endometrium(1)|large_intestine(5)|lung(6)|prostate(2)	14	Acute lymphoblastic leukemia(166;0.155)				Isoprenaline(DB01064)	GATCTTTATTAACTTATTATT	0.388																																					p.L112fs		Atlas-Indel,Pindel	.											.	PIK3R3	41	.	0			c.336delA						PASS	.						166	158	161					1																	46532743		2203	4300	6503	SO:0001589	frameshift_variant	8503	exon4			.	BC021622	CCDS529.1	1p34.1	2013-02-14	2008-02-04		ENSG00000117461	ENSG00000117461		"SH2 domain containing"	8981	protein-coding gene	gene with protein product		606076				9524259	Standard	NM_003629		Approved	p55	uc001cpb.4	Q92569	OTTHUMG00000008096	ENST00000262741.5:c.335delT	chr1.hg19:g.46532743delA	ENSP00000262741:p.Leu112fs	153.0	0.0	0		185.0	38.0	0.205405	NM_003629	B2R9C1|D3DQ12|O60482|Q5T4P1|Q5T4P2	Frame_Shift_Del	DEL	ENST00000262741.5	hg19	CCDS529.1																																																																																			.	.	.	none		0.388	PIK3R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022171.1	NM_003629		-	46532743	A	-	46532743	7	5	168	1	0	1	0	1	0	0	0	0	11927	372	13	0	1078	0	PIK3R3	1	46532743	Frame_Shift_Del	DEL	A	TCGA-F9-A97G-01A-11D-A382-10	5247597	46532743	202717878	5	9888											
TBX15	6913	hgsc.bcm.edu	37	chr1	119427569	119427569	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagaggcgctcagtttttccGggcttgcagctagcctaggg	6	10	15	10	2	1	1	1	0	0	1	2	2	2	1	2	3	3	5	2	3	2	5			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr1:119427569G>A	ENST00000369429.3	-	8	1604	c.1595C>T	c.(1594-1596)cCg>cTg	p.P532L	TBX15_ENST00000207157.3_Missense_Mutation_p.P426L			Q96SF7	TBX15_HUMAN	T-box 15	532					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)		CAGTTTTTCCGGGCTTGCAGC	0.537																																					p.P426L		Atlas-SNP	.											.	TBX15	95	.	0			c.C1277T						PASS	.						92	85	87					1																	119427569		2203	4300	6503	SO:0001583	missense	6913	exon8			TTTTCCGGGCTTG	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.1595C>T	chr1.hg19:g.119427569G>A	ENSP00000358437:p.Pro532Leu	138.0	0.0	.		202.0	46.0	.	NM_152380	Q08E76|Q5JT54|Q5T9S7	Missense_Mutation	SNP	ENST00000369429.3	hg19		.	.	.	.	.	.	.	.	.	.	G	22.0	4.237026	0.79800	.	.	ENSG00000092607	ENST00000344218;ENST00000207157;ENST00000369429;ENST00000449873	D;D;D	0.92099	-2.92;-2.97;-1.78	5.3	5.3	0.74995	.	0.000000	0.64402	D	0.000015	D	0.93223	0.7841	L	0.34521	1.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.981;0.999	D	0.93973	0.7251	10	0.87932	D	0	.	19.143	0.93452	0.0:0.0:1.0:0.0	.	329;532	E9PCG3;Q96SF7	.;TBX15_HUMAN	L	329;426;532;260	ENSP00000207157:P426L;ENSP00000358437:P532L;ENSP00000398625:P260L	ENSP00000207157:P426L	P	-	2	0	TBX15	119229092	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.080000	0.94040	2.764000	0.94973	0.555000	0.69702	CCG	.	.	.	none		0.537	TBX15-002	PUTATIVE	not_organism_supported|upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000034351.1	NM_152380		A	119427569	G	A	119427569	3	1	168	1	0	0	0	0	1	0	0	0	15664	1116	39	1	217	1	TBX15	1	119427569	Missense_Mutation	SNP	G	TCGA-F9-A97G-01A-11D-A382-10	72894826	119427569	129823052	6	9889											
LHX4	89884	hgsc.bcm.edu	37	chr1	180240574	180240575	+	Missense_Mutation	DNP	AC	AC	GT																															tcacagccaagcagctggagAcattaaagaatgcatacaag																										TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr1:180240574_180240575AC>GT	ENST00000263726.2	+	4	755_756	c.511_512AC>GT	c.(511-513)ACa>GTa	p.T171V	RP5-1180C10.2_ENST00000440959.2_RNA|RP5-1180C10.2_ENST00000415414.1_RNA	NM_033343.3	NP_203129.1	Q969G2	LHX4_HUMAN	LIM homeobox 4	171					medial motor column neuron differentiation (GO:0021526)|motor neuron axon guidance (GO:0008045)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|placenta development (GO:0001890)|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)			endometrium(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)	16						GCAGCTGGAGACATTAAAGAAT	0.569																																					p.T171A|p.T171I		Atlas-SNP	.											.	LHX4	36	.	0			c.A511G|c.C512T						PASS	.																																			SO:0001583	missense	89884	exon4			CTGGAGACATTAA|TGGAGACATTAAA	AB037683	CCDS1338.1	1q25.3	2011-06-20			ENSG00000121454	ENSG00000121454		"Homeoboxes / LIM class"	21734	protein-coding gene	gene with protein product		602146				11844481, 11567216	Standard	NM_033343		Approved	Gsh4	uc001goe.2	Q969G2	OTTHUMG00000035115	Exception_encountered	chr1.hg19:g.180240574_180240575delinsGT	ENSP00000263726:p.Thr171Val	222.0|220.0	0.0	.		278.0|275.0	61.0|58.0	.	NM_033343	Q8NHE0|Q8NHM1|Q8TCJ1|Q8WWX2|Q969W2	Missense_Mutation	SNP	ENST00000263726.2	hg19	CCDS1338.1																																																																																			.	.	.	none		0.569	LHX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084995.2	NM_033343		GT	180240575	AC	GT	180240574	3	3	168	1	0	0	0	0	1	0	0	0	8780	275	10	3	525	3	LHX4	1	180240574	Missense_Mutation	DNP	AC	TCGA-F9-A97G-01A-11D-A382-10	60813005	180240574	69010047	7	9890											
HSD11B1	3290	hgsc.bcm.edu	37	chr1	209880345	209880347	+	In_Frame_Del	DEL	ATG	ATG	-																															cacttctttgaatctttttcAtgatgatattcaccatgtgc																								rs578197035		TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	ATG	ATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr1:209880345_209880347delATG	ENST00000367028.2	+	5	558_560	c.389_391delATG	c.(388-393)catgat>cat	p.D132del	HSD11B1_ENST00000367027.3_In_Frame_Del_p.D132del|RP1-28O10.1_ENST00000441672.1_RNA|HSD11B1_ENST00000261465.1_In_Frame_Del_p.D132del	NM_001206741.1	NP_001193670.1	P28845	DHI1_HUMAN	hydroxysteroid (11-beta) dehydrogenase 1	132					glucocorticoid biosynthetic process (GO:0006704)|lung development (GO:0030324)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	11-beta-hydroxysteroid dehydrogenase (NADP+) activity (GO:0070524)|11-beta-hydroxysteroid dehydrogenase [NAD(P)] activity (GO:0003845)			breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(9)	16				OV - Ovarian serous cystadenocarcinoma(81;1.04e-55)|Epithelial(68;1.57e-52)|all cancers(67;1.83e-46)|Colorectal(1306;0.115)	Prednisone(DB00635)	AATCTTTTTCATGATGATATTCA	0.443																																					p.130_130del		Atlas-Indel,Pindel	.											HSD11B1,NS,malignant_melanoma,0,1	HSD11B1	35	.	0			c.388_390del						PASS	.																																			SO:0001651	inframe_deletion	3290	exon4			.	BC012593	CCDS1489.1	1q32-q41	2011-09-20			ENSG00000117594	ENSG00000117594	1.1.1.146	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	5208	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 26C, member 1"	600713		HSD11B, HSD11		1885595, 19027726	Standard	NM_005525		Approved	SDR26C1	uc001hhk.3	P28845	OTTHUMG00000036481	ENST00000367028.2:c.389_391delATG	chr1.hg19:g.209880348_209880350delATG	ENSP00000355995:p.Asp132del	113.0	0.0	0		172.0	36.0	0.209302	NM_005525	B2R9Z1|D3DT89	In_Frame_Del	DEL	ENST00000367028.2	hg19	CCDS1489.1																																																																																			.	.	.	none		0.443	HSD11B1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088743.2	NM_005525		-	209880347	ATG	-	209880345	7	5	168	1	0	1	0	1	0	0	0	0	7382	217	8	0	403	0	HSD11B1	1	209880345	In_Frame_Del	DEL	ATG	TCGA-F9-A97G-01A-11D-A382-10	29639771	209880345	39370276	8	9891											
PLD5	200150	hgsc.bcm.edu	37	chr1	242511425	242511426	+	Frame_Shift_Ins	INS	-	-	T																															accgacatttattttggcaaINStttttttctgagagtccatc																										TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr1:242511425_242511426insT	ENST00000536534.2	-	2	549_550	c.308_309insA	c.(307-309)aatfs	p.N103fs	PLD5_ENST00000442594.2_Frame_Shift_Ins_p.I9fs|PLD5_ENST00000427495.1_Frame_Shift_Ins_p.N41fs			Q8N7P1	PLD5_HUMAN	phospholipase D family, member 5	103						integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(22)|ovary(6)|skin(3)|urinary_tract(1)	55	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)			TATTTTGGCAATTTTTTTCTGA	0.446																																					p.N103fs		Atlas-Indel,Pindel	.											.	PLD5	216	.	0			c.309_310insA						PASS	.																																			SO:0001589	frameshift_variant	200150	exon3			.	AK098092	CCDS1621.1, CCDS1621.2, CCDS55692.1	1q43	2008-02-05			ENSG00000180287	ENSG00000180287			26879	protein-coding gene	gene with protein product							Standard	NM_001195811		Approved	FLJ40773	uc001hzn.2	Q8N7P1	OTTHUMG00000039867	ENST00000536534.2:c.309dupA	chr1.hg19:g.242511432_242511432dupT	ENSP00000440896:p.Asn103fs	68.0	0.0	0		94.0	18.0	0.191489	NM_152666	A1KXV0|B7Z324|Q494U9|Q8NB22	Frame_Shift_Ins	INS	ENST00000536534.2	hg19	CCDS1621.2																																																																																			.	.	.	none		0.446	PLD5-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397213.2	NM_152666		T	242511426	-	T	242511425	7	5	168	1	0	1	1	0	0	0	0	0	12056	101	4	0	1344	0	PLD5	1	242511425	Frame_Shift_Ins	INS	-	TCGA-F9-A97G-01A-11D-A382-10	32631080	242511425	6739196	9	9892											
C2orf29	55571	hgsc.bcm.edu	37	chr2	101883275	101883275	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attaatgcagtcaagccagaTcactgagtatttctctgtcc	11	13	7	10	0	3	2	2	1	1	1	5	2	4	2	2	0	2	2	2	0	3	3			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr2:101883275T>C	ENST00000289382.3	+	5	1335	c.1172T>C	c.(1171-1173)aTc>aCc	p.I391T		NM_017546.4	NP_060016.3	Q9UKZ1	CNO11_HUMAN	CCR4-NOT transcription complex, subunit 11	391					cell proliferation (GO:0008283)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|nucleus (GO:0005634)											TCAAGCCAGATCACTGAGTAT	0.403																																					p.I391T		Atlas-SNP	.											.	.	.	.	0			c.T1172C						PASS	.						184	175	178					2																	101883275		2203	4300	6503	SO:0001583	missense	55571	exon5			GCCAGATCACTGA	AF103798	CCDS2050.1	2q12.1	2013-01-24	2013-01-24	2013-01-24	ENSG00000158435	ENSG00000158435			25217	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 29"	C2orf29		10497265, 23232451, 23303381	Standard	NM_017546		Approved	C40	uc002taw.4	Q9UKZ1	OTTHUMG00000130686	ENST00000289382.3:c.1172T>C	chr2.hg19:g.101883275T>C	ENSP00000289382:p.Ile391Thr	119.0	0.0	.		165.0	36.0	.	NM_017546	Q6P2M9|Q8N681	Missense_Mutation	SNP	ENST00000289382.3	hg19	CCDS2050.1	.	.	.	.	.	.	.	.	.	.	T	26.6	4.749354	0.89753	.	.	ENSG00000158435	ENST00000289382	.	.	.	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	D	0.83741	0.5320	M	0.87456	2.885	0.80722	D	1	D	0.67145	0.996	D	0.68192	0.956	D	0.86389	0.1734	9	0.66056	D	0.02	-28.9136	16.4237	0.83790	0.0:0.0:0.0:1.0	.	391	Q9UKZ1	CB029_HUMAN	T	391	.	ENSP00000289382:I391T	I	+	2	0	C2orf29	101249707	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.930000	0.87610	2.279000	0.76181	0.533000	0.62120	ATC	.	.	.	none		0.403	CNOT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253181.1	NM_017546		C	101883275	T	C	101883275	3	2	168	1	0	0	0	0	1	0	0	0	2163	1435	50	3	1190	3	C2orf29	2	101883275	Missense_Mutation	SNP	T	TCGA-F9-A97G-01A-11D-A382-10		101883275	141316098	10	9893											
LRP1B	53353	hgsc.bcm.edu	37	chr2	141272299	141272299	+	Missense_Mutation	SNP	T	T	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	tccaatgcttagaaatacatTtttgtgcggaacaagcaaat	15	12	7	7	1	0	1	0	0	0	1	1	2	1	2	1	1	5	2	1	1	7	4			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr2:141272299T>G	ENST00000389484.3	-	51	9163	c.8192A>C	c.(8191-8193)aAa>aCa	p.K2731T		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2731	LDL-receptor class A 16. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		AGAAATACATTTTTGTGCGGA	0.378										TSP Lung(27;0.18)																											p.K2731T	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.A8192C						PASS	.						110	103	105					2																	141272299		2203	4300	6503	SO:0001583	missense	53353	exon51			ATACATTTTTGTG	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.8192A>C	chr2.hg19:g.141272299T>G	ENSP00000374135:p.Lys2731Thr	126.0	0.0	.		226.0	57.0	.	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.994775	0.74703	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	T	0.40225	1.04	5.53	5.53	0.82687	.	0.000000	0.85682	U	0.000000	T	0.42698	0.1214	L	0.41573	1.285	0.42388	D	0.992517	P	0.43938	0.822	P	0.50270	0.636	T	0.19745	-1.0296	10	0.21014	T	0.42	.	11.074	0.48021	0.0:0.0724:0.0:0.9276	.	2731	Q9NZR2	LRP1B_HUMAN	T	2731;2669	ENSP00000374135:K2731T	ENSP00000374135:K2731T	K	-	2	0	LRP1B	140988769	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	3.870000	0.56070	2.219000	0.72066	0.533000	0.62120	AAA	.	.	.	none		0.378	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		G	141272299	T	G	141272299	3	3	168	1	0	0	0	0	1	0	0	0	8962	1841	64	5	5771	5	LRP1B	2	141272299	Missense_Mutation	SNP	T	TCGA-F9-A97G-01A-11D-A382-10	39389024	141272299	101927074	11	9894											
RQCD1	9125	hgsc.bcm.edu	37	chr2	219449436	219449436	+	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	tctccggctcaccagccttgGagttattggtaagttattag	8	14	10	9	1	2	0	1	0	1	0	3	1	2	1	3	3	1	4	3	3	4	6			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr2:219449436G>C	ENST00000273064.6	+	4	797	c.422G>C	c.(421-423)gGa>gCa	p.G141A	RQCD1_ENST00000295701.5_Missense_Mutation_p.G141A|RQCD1_ENST00000509807.2_Missense_Mutation_p.G141A|RQCD1_ENST00000542068.1_Missense_Mutation_p.G141A	NM_005444.2	NP_005435.1	Q92600	RCD1_HUMAN	RCD1 required for cell differentiation1 homolog (S. pombe)	141					cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of ligand-dependent nuclear receptor transcription coactivator activity (GO:2000327)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|sex differentiation (GO:0007548)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|prostate(3)|skin(1)	15		Renal(207;0.0915)		Epithelial(149;1.13e-06)|all cancers(144;0.000192)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ACCAGCCTTGGAGTTATTGGT	0.428																																					p.G141A		Atlas-SNP	.											.	RQCD1	32	.	0			c.G422C						PASS	.						179	184	182					2																	219449436		2203	4300	6503	SO:0001583	missense	9125	exon4			GCCTTGGAGTTAT	D87957	CCDS33379.1, CCDS63123.1	2q35	2010-04-23	2001-11-28		ENSG00000144580	ENSG00000144580			10445	protein-coding gene	gene with protein product	"cancer/testis antigen 129"	612054	"rcd1 (required for cell differentiation, S.pombe) homolog 1"			9447985	Standard	NM_001271634		Approved	RCD1, RCD1+, CNOT9, CT129	uc010zki.3	Q92600	OTTHUMG00000154750	ENST00000273064.6:c.422G>C	chr2.hg19:g.219449436G>C	ENSP00000273064:p.Gly141Ala	114.0	0.0	.		172.0	39.0	.	NM_001271634	B2RPI0|B5MDQ4|B7Z1E5|Q96IX4	Missense_Mutation	SNP	ENST00000273064.6	hg19	CCDS33379.1	.	.	.	.	.	.	.	.	.	.	G	32	5.123662	0.94429	.	.	ENSG00000144580	ENST00000273064;ENST00000509807;ENST00000542068;ENST00000295701	T;T;T;T	0.75154	-0.91;-0.91;-0.91;-0.91	5.22	5.22	0.72569	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.91918	0.7441	H	0.98133	4.155	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.997	D	0.94738	0.7916	10	0.87932	D	0	-1.8573	19.1489	0.93479	0.0:0.0:1.0:0.0	.	141;141;141	B7Z1E5;Q92600;B5MDQ4	.;RCD1_HUMAN;.	A	141	ENSP00000273064:G141A;ENSP00000441357:G141A;ENSP00000443687:G141A;ENSP00000295701:G141A	ENSP00000273064:G141A	G	+	2	0	RQCD1	219157680	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.613000	0.98350	2.587000	0.87381	0.563000	0.77884	GGA	.	.	.	none		0.428	RQCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336920.1	NM_005444		C	219449436	G	C	219449436	3	2	168	1	0	0	0	0	1	0	0	0	13683	1174	41	4	436	4	RQCD1	2	219449436	Missense_Mutation	SNP	G	TCGA-F9-A97G-01A-11D-A382-10	78177137	219449436	23749937	12	9895											
FLNB	2317	hgsc.bcm.edu	37	chr3	58107208	58107208	+	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	cccctacacagtggaggcctCgctgccaccagatcccagca	9	5	9	18	1	0	1	0	0	0	1	2	2	1	2	6	2	3	2	6	2	1	1			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr3:58107208C>T	ENST00000295956.4	+	20	3269	c.3104C>T	c.(3103-3105)tCg>tTg	p.S1035L	FLNB_ENST00000429972.2_Missense_Mutation_p.S1035L|FLNB_ENST00000490882.1_Missense_Mutation_p.S1035L|FLNB_ENST00000493452.1_Missense_Mutation_p.S866L|FLNB_ENST00000348383.5_Missense_Mutation_p.S1035L|FLNB_ENST00000358537.3_Missense_Mutation_p.S1035L|FLNB_ENST00000357272.4_Missense_Mutation_p.S1035L|FLNB_ENST00000419752.2_Missense_Mutation_p.S866L	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	1035					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)		GTGGAGGCCTCGCTGCCACCA	0.567																																					p.S1035L		Atlas-SNP	.											.	FLNB	430	.	0			c.C3104T						PASS	.						95	100	98					3																	58107208		2203	4300	6503	SO:0001583	missense	2317	exon20			AGGCCTCGCTGCC	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.3104C>T	chr3.hg19:g.58107208C>T	ENSP00000295956:p.Ser1035Leu	67.0	0.0	.		89.0	17.0	.	NM_001457	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	hg19	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	C	12.88	2.069850	0.36566	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	T;T;T;T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06;1.06;1.06;1.06	5.87	5.87	0.94306	Immunoglobulin E-set (2);	0.492477	0.22519	N	0.058991	T	0.22742	0.0549	N	0.02368	-0.58	0.33978	D	0.647678	B;B;B;B;B;B	0.31290	0.26;0.002;0.205;0.0;0.318;0.318	B;B;B;B;B;B	0.28465	0.039;0.001;0.09;0.002;0.028;0.028	T	0.23048	-1.0199	10	0.25106	T	0.35	.	20.2192	0.98319	0.0:1.0:0.0:0.0	.	1035;1035;866;866;1035;1035	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	L	1035;1035;1035;1035;1035;1035;866;866	ENSP00000295956:S1035L;ENSP00000420213:S1035L;ENSP00000351339:S1035L;ENSP00000415599:S1035L;ENSP00000232447:S1035L;ENSP00000349819:S1035L;ENSP00000418510:S866L;ENSP00000414532:S866L	ENSP00000295956:S1035L	S	+	2	0	FLNB	58082248	0.587000	0.26791	0.985000	0.45067	0.891000	0.51852	1.928000	0.40104	2.780000	0.95670	0.655000	0.94253	TCG	.	.	.	none		0.567	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457		T	58107208	C	T	58107208	3	4	168	1	0	0	0	0	1	0	0	0	5941	893	31	1	3182	1	FLNB	3	58107208	Missense_Mutation	SNP	C	TCGA-F9-A97G-01A-11D-A382-10		58107208	139915222	13	9896											
C3orf15	89876	hgsc.bcm.edu	37	chr3	119449132	119449132	+	Missense_Mutation	SNP	A	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	gcgtgaagagaatcagaatgAagtgaatatgaagcacttga	17	8	12	4	1	1	7	1	5	0	2	1	8	1	7	0	0	1	1	0	0	7	2			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr3:119449132A>C	ENST00000273390.5	+	8	1003	c.926A>C	c.(925-927)gAa>gCa	p.E309A		NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1	309						mitochondrion (GO:0005739)											AATCAGAATGAAGTGAATATG	0.413																																					p.E309A		Atlas-SNP	.											.	.	.	.	0			c.A926C						PASS	.						183	187	185					3																	119449132		2203	4300	6503	SO:0001583	missense	89876	exon8			AGAATGAAGTGAA	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.926A>C	chr3.hg19:g.119449132A>C	ENSP00000273390:p.Glu309Ala	204.0	0.0	.		226.0	41.0	.	NM_033364	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Missense_Mutation	SNP	ENST00000273390.5	hg19	CCDS2994.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.266006	0.80358	.	.	ENSG00000183833	ENST00000273390	T	0.23348	1.91	5.2	4.04	0.47022	.	0.399793	0.31821	N	0.007011	T	0.43500	0.1250	M	0.64676	1.99	0.80722	D	1	D;D;D;D;D	0.76494	0.986;0.991;0.967;0.999;0.998	P;D;P;D;D	0.70935	0.888;0.94;0.813;0.971;0.941	T	0.24404	-1.0161	10	0.41790	T	0.15	-18.7701	10.645	0.45615	0.9244:0.0:0.0756:0.0	.	309;70;247;309;309	Q7Z4T9;Q9UFB4;Q7Z4T9-3;Q4G0Y0;Q7Z4T9-7	AAT1_HUMAN;.;.;.;.	A	309	ENSP00000273390:E309A	ENSP00000273390:E309A	E	+	2	0	C3orf15	120931822	1.000000	0.71417	0.981000	0.43875	0.856000	0.48823	4.480000	0.60243	2.080000	0.62538	0.455000	0.32223	GAA	.	.	.	none		0.413	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364		C	119449132	A	C	119449132	3	2	168	1	0	0	0	0	1	0	0	0	2211	246	9	5	956	5	C3orf15	3	119449132	Missense_Mutation	SNP	A	TCGA-F9-A97G-01A-11D-A382-10	61341924	119449132	78573298	14	9897											
MRPL3	11222	hgsc.bcm.edu	37	chr3	131188617	131188617	+	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	aggccagactctgccaatatCctaaatgagaaaactaaagt	17	8	7	9	0	1	2	0	1	1	2	2	3	2	2	3	1	2	0	3	1	8	3			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr3:131188617C>T	ENST00000264995.3	-	8	886	c.739G>A	c.(739-741)Gat>Aat	p.D247N	MRPL3_ENST00000425847.2_Splice_Site_p.D274N	NM_007208.3	NP_009139.1	P09001	RM03_HUMAN	mitochondrial ribosomal protein L3	247					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	10						CTGCCAATATCCTAAATGAGA	0.308																																					p.D247N		Atlas-SNP	.											.	MRPL3	32	.	0			c.G739A						PASS	.						89	81	84					3																	131188617		2203	4300	6503	SO:0001630	splice_region_variant	11222	exon8			CAATATCCTAAAT	X06323	CCDS3071.1	3q21-q23	2012-09-13			ENSG00000114686	ENSG00000114686		"Mitochondrial ribosomal proteins / large subunits"	10379	protein-coding gene	gene with protein product		607118		RPML3		2891103	Standard	NM_007208		Approved	MRL3	uc003eoh.3	P09001	OTTHUMG00000159607	ENST00000264995.3:c.739-1G>A	chr3.hg19:g.131188617C>T		67.0	0.0	.		93.0	11.0	.	NM_007208	Q6IBT2	Missense_Mutation	SNP	ENST00000264995.3	hg19	CCDS3071.1	.	.	.	.	.	.	.	.	.	.	C	19.93	3.917664	0.73098	.	.	ENSG00000114686	ENST00000264995;ENST00000425847;ENST00000507669	T;T;T	0.44482	0.92;0.92;0.92	5.23	5.23	0.72850	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.090336	0.85682	D	0.000000	T	0.52240	0.1722	M	0.71581	2.175	0.58432	D	0.999997	B;B	0.25521	0.128;0.054	B;B	0.41174	0.349;0.245	T	0.56553	-0.7960	10	0.66056	D	0.02	-15.691	11.8044	0.52145	0.0:0.9145:0.0:0.0855	.	274;247	E7ETU7;P09001	.;RM03_HUMAN	N	247;274;142	ENSP00000264995:D247N;ENSP00000398536:D274N;ENSP00000422419:D142N	ENSP00000264995:D247N	D	-	1	0	MRPL3	132671307	1.000000	0.71417	1.000000	0.80357	0.836000	0.47400	3.794000	0.55492	2.435000	0.82474	0.650000	0.86243	GAT	.	.	.	none		0.308	MRPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356471.3	NM_007208	Missense_Mutation	T	131188617	C	T	131188617	5	4	168	1	0	0	0	0	0	0	1	0	9800	869	30	2	319	2	MRPL3	3	131188617	Splice_Site	SNP	C	TCGA-F9-A97G-01A-11D-A382-10	11739485	131188617	66833813	15	9898											
PLCH1	23007	hgsc.bcm.edu	37	chr3	155199731	155199731	+	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	atattcacaggttgttagagAaagattttctgattctccat	12	16	7	6	0	3	3	1	1	2	2	4	4	3	3	1	1	0	2	1	1	3	7			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr3:155199731A>T	ENST00000340059.7	-	23	4107	c.4108T>A	c.(4108-4110)Tct>Act	p.S1370T	PLCH1_ENST00000414191.1_Missense_Mutation_p.S1332T|PLCH1_ENST00000447496.2_3'UTR|PLCH1_ENST00000334686.6_Missense_Mutation_p.S1332T|PLCH1_ENST00000494598.1_Intron|PLCH1_ENST00000460012.1_Missense_Mutation_p.S1332T	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	1370					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)			GTTGTTAGAGAAAGATTTTCT	0.433																																					p.S1370T		Atlas-SNP	.											.	PLCH1	406	.	0			c.T4108A						PASS	.						44	48	47					3																	155199731		2203	4300	6503	SO:0001583	missense	23007	exon23			TTAGAGAAAGATT	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.4108T>A	chr3.hg19:g.155199731A>T	ENSP00000345988:p.Ser1370Thr	100.0	0.0	.		150.0	34.0	.	NM_001130960	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Missense_Mutation	SNP	ENST00000340059.7	hg19	CCDS46939.1	.	.	.	.	.	.	.	.	.	.	A	6.129	0.392091	0.11581	.	.	ENSG00000114805	ENST00000460012;ENST00000340059;ENST00000334686;ENST00000414191	T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98	5.47	1.81	0.25067	.	1.843090	0.02242	N	0.065897	T	0.64371	0.2592	L	0.27053	0.805	0.23386	N	0.997788	P;B	0.36837	0.571;0.435	B;B	0.35770	0.21;0.104	T	0.54029	-0.8354	10	0.33940	T	0.23	.	8.7404	0.34554	0.7078:0.0:0.2922:0.0	.	1332;1370	Q4KWH8-2;Q4KWH8	.;PLCH1_HUMAN	T	1332;1370;1332;1332	ENSP00000417502:S1332T;ENSP00000345988:S1370T;ENSP00000335469:S1332T;ENSP00000412977:S1332T	ENSP00000335469:S1332T	S	-	1	0	PLCH1	156682425	0.976000	0.34144	0.176000	0.23000	0.280000	0.26924	0.788000	0.26872	0.364000	0.24374	0.477000	0.44152	TCT	.	.	.	none		0.433	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996		T	155199731	A	T	155199731	3	4	168	1	0	0	0	0	1	0	0	0	12044	246	9	5	977	5	PLCH1	3	155199731	Missense_Mutation	SNP	A	TCGA-F9-A97G-01A-11D-A382-10	24011114	155199731	42822699	16	9899											
PHC3	80012	hgsc.bcm.edu	37	chr3	169831155	169831155	+	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	gaaacccacaaaccttcagcAatcatgtcttccatctctgt	12	11	4	14	0	4	0	2	0	2	0	6	1	5	0	3	0	3	1	3	0	3	2	rs532102572		TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr3:169831155A>T	ENST00000494943.1	-	11	2378	c.2310T>A	c.(2308-2310)atT>atA	p.I770I	PHC3_ENST00000467570.1_Silent_p.I729I|PHC3_ENST00000495893.2_Silent_p.I782I			Q8NDX5	PHC3_HUMAN	polyhomeotic homolog 3 (Drosophila)	770					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)			AACCTTCAGCAATCATGTCTT	0.353													A|||	1	0.000199681	0	0	5008	,	,		18415	0.001		0	False		,,,				2504	0				p.I782I		Atlas-SNP	.											.	PHC3	113	.	0			c.T2346A						PASS	.						89	82	85					3																	169831155		1852	4098	5950	SO:0001819	synonymous_variant	80012	exon11			TTCAGCAATCATG		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.2310T>A	chr3.hg19:g.169831155A>T		148.0	0.0	.		183.0	36.0	.	NM_024947	A2RRP9|Q5HYF0|Q6NSG2|Q8NFT7|Q8NFZ1|Q8TBM2|Q9H971|Q9H9I4	Silent	SNP	ENST00000494943.1	hg19																																																																																				.	.	.	none		0.353	PHC3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000352182.3	NM_024947		T	169831155	A	T	169831155	2	4	168	1	0	0	0	0	0	0	0	1	11825	126	5	5		5	PHC3	3	169831155	Silent	SNP	A	TCGA-F9-A97G-01A-11D-A382-10	14631424	169831155	28191275	17	9900											
PDE6B	5158	hgsc.bcm.edu	37	chr4	651194	651194	+	Missense_Mutation	SNP	A	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	acaccgacacctacgacaagAtgaacaagctggagaaccgc	16	3	9	13	3	0	3	0	1	0	2	0	6	0	3	3	1	4	1	3	1	5	1			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr4:651194A>C	ENST00000496514.1	+	10	1333	c.1312A>C	c.(1312-1314)Atg>Ctg	p.M438L	PDE6B_ENST00000255622.6_Missense_Mutation_p.M438L|PDE6B_ENST00000429163.2_Missense_Mutation_p.M159L|RP11-1191J2.2_ENST00000489312.1_RNA|RP11-1191J2.2_ENST00000468356.1_RNA			P35913	PDE6B_HUMAN	phosphodiesterase 6B, cGMP-specific, rod, beta	438					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)	CTACGACAAGATGAACAAGCT	0.612																																					p.M438L	GBM(71;463 1194 9848 25922 46834)	Atlas-SNP	.											.	PDE6B	80	.	0			c.A1312C						PASS	.						198	119	146					4																	651194		2203	4300	6503	SO:0001583	missense	5158	exon10			GACAAGATGAACA	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.1312A>C	chr4.hg19:g.651194A>C	ENSP00000420295:p.Met438Leu	332.0	0.0	.		427.0	74.0	.	NM_001145291	B7Z9T9|E7ETT3|Q53XN5|Q9BWH5|Q9UD49	Missense_Mutation	SNP	ENST00000496514.1	hg19	CCDS33932.1	.	.	.	.	.	.	.	.	.	.	A	14.75	2.629272	0.46944	.	.	ENSG00000133256	ENST00000255622;ENST00000496514;ENST00000429163	T;T;T	0.66995	-0.24;-0.24;-0.24	4.85	4.85	0.62838	GAF (1);	0.117165	0.85682	N	0.000000	T	0.64011	0.2560	M	0.67569	2.06	0.51482	D	0.999924	B;B	0.16802	0.011;0.019	B;B	0.23275	0.02;0.045	T	0.60835	-0.7184	10	0.30078	T	0.28	.	12.3767	0.55283	1.0:0.0:0.0:0.0	.	438;438	P35913;P35913-2	PDE6B_HUMAN;.	L	438;438;159	ENSP00000255622:M438L;ENSP00000420295:M438L;ENSP00000406334:M159L	ENSP00000255622:M438L	M	+	1	0	PDE6B	641194	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	4.760000	0.62235	1.804000	0.52760	0.367000	0.22151	ATG	.	.	.	none		0.612	PDE6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358109.1	NM_000283		C	651194	A	C	651194	3	2	168	1	0	0	0	0	1	0	0	0	11653	333	12	5	1350	5	PDE6B	4	651194	Missense_Mutation	SNP	A	TCGA-F9-A97G-01A-11D-A382-10		651194	190503082	18	9901											
SLC26A1	10861	hgsc.bcm.edu	37	chr4	982757	982759	+	In_Frame_Del	DEL	AGA	AGA	-																															cgaggaagcctcctctgctcAgaatgtctctcacaggcggg																										TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr4:982757_982759delAGA	ENST00000361661.2	-	4	2345_2347	c.1968_1970delTCT	c.(1966-1971)attctg>atg	p.656_657IL>M	IDUA_ENST00000453894.1_Intron|IDUA_ENST00000247933.4_Intron|SLC26A1_ENST00000513138.1_5'Flank|SLC26A1_ENST00000398520.2_Intron|SLC26A1_ENST00000398516.2_In_Frame_Del_p.656_657IL>M|IDUA_ENST00000509744.1_Intron	NM_213613.2	NP_998778.1	Q9H2B4	S26A1_HUMAN	solute carrier family 26 (anion exchanger), member 1	656	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|chloride transport (GO:0006821)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|oxalate transport (GO:0019532)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|chloride transmembrane transporter activity (GO:0015108)|oxalate transmembrane transporter activity (GO:0019531)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(1)|endometrium(4)|pancreas(1)|prostate(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			TCCTCTGCTCAGAATGTCTCTCA	0.68																																					p.657_657del		Atlas-Indel,Pindel	.											.	SLC26A1	44	.	0			c.1969_1971del						PASS	.																																			SO:0001651	inframe_deletion	10861	exon3			.	AF297659	CCDS33933.1, CCDS33934.1	4p16.3	2013-07-18	2013-07-18		ENSG00000145217	ENSG00000145217		"Solute carriers"	10993	protein-coding gene	gene with protein product		610130	"solute carrier family 26 (sulfate transporter), member 1"				Standard	NM_213613		Approved	SAT-1, EDM4	uc003gcc.3	Q9H2B4	OTTHUMG00000160003	ENST00000361661.2:c.1968_1970delTCT	chr4.hg19:g.982757_982759delAGA	ENSP00000354721:p.Ile656_Leu657delinsMet	178.0	0.0	0		177.0	40.0	0.225989	NM_022042	A8K9N2|Q7Z5R3|Q96BK0	In_Frame_Del	DEL	ENST00000361661.2	hg19	CCDS33934.1																																																																																			.	.	.	none		0.68	SLC26A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358783.1	NM_022042, NM_134425		-	982759	AGA	-	982757	7	5	168	1	0	1	0	1	0	0	0	0	14527	188	7	0	242	0	SLC26A1	4	982757	In_Frame_Del	DEL	AGA	TCGA-F9-A97G-01A-11D-A382-10	331563	982757	190171519	19	9902											
HGFAC	3083	hgsc.bcm.edu	37	chr4	3443797	3443797	+	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	ggccccttcctcctcctcctCctgctgctgctgctgctgcc	0	12	8	21	0	0	0	0	0	0	0	5	0	5	0	8	1	6	5	8	1	0	1	rs538844201	byFrequency	TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr4:3443797C>G	ENST00000382774.3	+	1	184	c.69C>G	c.(67-69)ctC>ctG	p.L23L	HGFAC_ENST00000511533.1_Silent_p.L23L	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	23					proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		TCCTCCTCCTCCTGCTGCTGC	0.716													C|||	2	0.000399361	8e-04	0	5008	,	,		13350	0		0	False		,,,				2504	0.001				p.L23L		Atlas-SNP	.											HGFAC,NS,carcinoma,0,2	HGFAC	69	.	0			c.C69G						PASS	.						13	16	15					4																	3443797		1723	3604	5327	SO:0001819	synonymous_variant	3083	exon1			CCTCCTCCTGCTG	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.69C>G	chr4.hg19:g.3443797C>G		50.0	0.0	.		68.0	3.0	.	NM_001528	Q14726|Q2M1W7|Q53X47	Silent	SNP	ENST00000382774.3	hg19	CCDS3369.1																																																																																			.	.	.	none		0.716	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3			G	3443797	C	G	3443797	2	3	168	1	0	0	0	0	0	0	0	1	7093	842	30	4		4	HGFAC	4	3443797	Silent	SNP	C	TCGA-F9-A97G-01A-11D-A382-10	2461040	3443797	187710479	20	9903											
LNX1	84708	hgsc.bcm.edu	37	chr4	54362470	54362470	+	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	tgctgcggaacttctgttcaCgcatcacagtcagccacagc	9	9	9	14	2	4	0	3	0	1	0	4	1	4	1	1	1	5	3	1	1	1	2			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr4:54362470C>A	ENST00000263925.7	-	6	1384	c.1070G>T	c.(1069-1071)cGt>cTt	p.R357L	FIP1L1_ENST00000507166.1_Intron|LNX1-AS1_ENST00000502373.1_RNA|LNX1_ENST00000306888.2_Missense_Mutation_p.R261L	NM_001126328.2	NP_001119800.1	Q8TBB1	LNX1_HUMAN	ligand of numb-protein X 1, E3 ubiquitin protein ligase	357	PDZ 1. {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)			CTTCTGTTCACGCATCACAGT	0.577																																					p.R357L		Atlas-SNP	.											.	LNX1	139	.	0			c.G1070T						PASS	.						51	52	51					4																	54362470		2203	4300	6503	SO:0001583	missense	84708	exon6			TGTTCACGCATCA	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.1070G>T	chr4.hg19:g.54362470C>A	ENSP00000263925:p.Arg357Leu	64.0	0.0	.		107.0	28.0	.	NM_001126328	Q4W5K7|Q8N4C2|Q96MJ7|Q9BY20	Missense_Mutation	SNP	ENST00000263925.7	hg19	CCDS47057.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.537618	0.85917	.	.	ENSG00000072201	ENST00000306888;ENST00000538207;ENST00000263925	T;T	0.13196	2.61;4.1	5.29	5.29	0.74685	PDZ/DHR/GLGF (3);	0.070422	0.64402	D	0.000001	T	0.53417	0.1795	H	0.96208	3.785	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.77557	0.927;0.99	T	0.68961	-0.5271	10	0.87932	D	0	.	19.1278	0.93393	0.0:1.0:0.0:0.0	.	357;261	Q8TBB1;Q8TBB1-2	LNX1_HUMAN;.	L	261;195;357	ENSP00000302879:R261L;ENSP00000263925:R357L	ENSP00000263925:R357L	R	-	2	0	LNX1	54057227	1.000000	0.71417	0.941000	0.38009	0.547000	0.35210	7.320000	0.79064	2.756000	0.94617	0.561000	0.74099	CGT	.	.	.	none		0.577	LNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219934.2			A	54362470	C	A	54362470	3	1	168	1	0	0	0	0	1	0	0	0	8872	536	19	4	1140	4	LNX1	4	54362470	Missense_Mutation	SNP	C	TCGA-F9-A97G-01A-11D-A382-10	50918673	54362470	136791806	21	9904											
CENPE	1062	hgsc.bcm.edu	37	chr4	104116296	104116296	+	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	catcttctcgaataattaaaGgtttcattttttgagtgcca	11	17	6	7	1	3	1	1	1	2	0	4	2	3	1	1	1	1	1	1	1	4	7			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr4:104116296G>A	ENST00000265148.3	-	5	541	c.452C>T	c.(451-453)cCt>cTt	p.P151L	CENPE_ENST00000380026.3_Missense_Mutation_p.P151L	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	151	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)|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)		AATAATTAAAGGTTTCATTTT	0.318																																					p.P151L		Atlas-SNP	.											.	CENPE	253	.	0			c.C452T						PASS	.						98	100	99					4																	104116296		2203	4291	6494	SO:0001583	missense	1062	exon5			ATTAAAGGTTTCA	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.452C>T	chr4.hg19:g.104116296G>A	ENSP00000265148:p.Pro151Leu	97.0	0.0	.		113.0	16.0	.	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	hg19	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.827249	0.90955	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026;ENST00000503705	T;T;T	0.75154	-0.91;-0.91;-0.91	5.94	5.94	0.96194	Kinesin, motor domain (4);	.	.	.	.	D	0.83133	0.5188	L	0.55017	1.72	0.80722	D	1	D;D	0.69078	0.991;0.997	D;D	0.72338	0.919;0.977	D	0.83582	0.0118	9	0.66056	D	0.02	.	15.5001	0.75691	0.0677:0.0:0.9323:0.0	.	151;151	Q02224-3;Q02224	.;CENPE_HUMAN	L	151	ENSP00000265148:P151L;ENSP00000369365:P151L;ENSP00000423981:P151L	ENSP00000265148:P151L	P	-	2	0	CENPE	104335745	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	8.966000	0.93397	2.820000	0.97059	0.650000	0.86243	CCT	.	.	.	none		0.318	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	104116296	G	A	104116296	3	1	168	1	0	0	0	0	1	0	0	0	3232	1000	35	2	7833	2	CENPE	4	104116296	Missense_Mutation	SNP	G	TCGA-F9-A97G-01A-11D-A382-10	49753826	104116296	87037980	22	9905											
MTRR	4552	hgsc.bcm.edu	37	chr5	7897216	7897229	+	Frame_Shift_Del	DEL	CTCATCTAAAGGTT	CTCATCTAAAGGTT	-																															ccttaagcatgggatcttaaCtcatctaaaggtttccttct																								rs114259126	byFrequency	TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	CTCATCTAAAGGTT	CTCATCTAAAGGTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr5:7897216_7897229delCTCATCTAAAGGTT	ENST00000264668.2	+	14	1919_1932	c.1889_1902delCTCATCTAAAGGTT	c.(1888-1902)actcatctaaaggttfs	p.THLKV630fs	MTRR_ENST00000440940.2_Frame_Shift_Del_p.THLKV603fs	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	630					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)	GGGATCTTAACTCATCTAAAGGTTTCCTTCTCAA	0.43																																					p.630_634del		Atlas-Indel,Pindel	.											.	MTRR	74	.	0			c.1888_1901del						PASS	.																																			SO:0001589	frameshift_variant	4552	exon14			.	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.1889_1902delCTCATCTAAAGGTT	chr5.hg19:g.7897216_7897229delCTCATCTAAAGGTT	ENSP00000264668:p.Thr630fs	189.0	0.0	0		257.0	47.0	0.182879	NM_024010	O60471|Q32MA9|Q7Z4M8	Frame_Shift_Del	DEL	ENST00000264668.2	hg19	CCDS3874.1																																																																																			.	.	.	none		0.43	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1			-	7897229	CTCATCTAAAGGTT	-	7897216	7	5	168	1	0	1	0	1	0	0	0	0	9968	565	20	0	1943	0	MTRR	5	7897216	Frame_Shift_Del	DEL	CTCATCTAAAGGTT	TCGA-F9-A97G-01A-11D-A382-10		7897216	173018044	23	9906											
PCSK1	5122	hgsc.bcm.edu	37	chr5	95759058	95759058	+	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	gtgattccactccaaaccatCatccagtacggtgataacaa	14	9	6	12	1	1	2	1	2	0	0	4	2	4	2	4	1	3	1	4	1	4	3			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr5:95759058C>T	ENST00000311106.3	-	4	739	c.502G>A	c.(502-504)Gat>Aat	p.D168N	CTD-2337A12.1_ENST00000502645.2_RNA|PCSK1_ENST00000508626.1_Missense_Mutation_p.D121N	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	168	Peptidase S8.				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)"	TCCAAACCATCATCCAGTACG	0.488																																					p.D168N		Atlas-SNP	.											.	PCSK1	93	.	0			c.G502A						PASS	.						188	138	155					5																	95759058		2203	4300	6503	SO:0001583	missense	5122	exon4			AACCATCATCCAG		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.502G>A	chr5.hg19:g.95759058C>T	ENSP00000308024:p.Asp168Asn	188.0	0.0	.		269.0	50.0	.	NM_000439	B7Z8T7|E9PHA1|P78478|Q92532	Missense_Mutation	SNP	ENST00000311106.3	hg19	CCDS4081.1	.	.	.	.	.	.	.	.	.	.	C	36	5.765100	0.96906	.	.	ENSG00000175426	ENST00000311106;ENST00000508626	D;D	0.88277	-2.36;-2.36	5.91	5.91	0.95273	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.000000	0.85682	D	0.000000	D	0.95182	0.8438	M	0.84219	2.685	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95088	0.8219	10	0.87932	D	0	-30.7254	19.8855	0.96910	0.0:1.0:0.0:0.0	.	168	P29120	NEC1_HUMAN	N	168;121	ENSP00000308024:D168N;ENSP00000421600:D121N	ENSP00000308024:D168N	D	-	1	0	PCSK1	95784814	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.442000	0.80503	2.796000	0.96246	0.655000	0.94253	GAT	.	.	.	none		0.488	PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1	NM_000439		T	95759058	C	T	95759058	3	4	168	1	0	0	0	0	1	0	0	0	11607	826	29	2	1803	2	PCSK1	5	95759058	Missense_Mutation	SNP	C	TCGA-F9-A97G-01A-11D-A382-10	87861842	95759058	85156202	24	9907											
FBN2	2201	hgsc.bcm.edu	37	chr5	127636522	127636522	+	Frame_Shift_Del	DEL	G	G	-																															ctcttaccaatgcagttctcGctttttacttcataccctgg																										TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr5:127636522delG	ENST00000508053.1	-	54	7127	c.6153delC	c.(6151-6153)agcfs	p.S2051fs	FBN2_ENST00000262464.4_Frame_Shift_Del_p.S2051fs			P35556	FBN2_HUMAN	fibrillin 2	2051	EGF-like 34; 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)		TGCAGTTCTCGCTTTTTACTT	0.463																																					p.E2052fs		Atlas-Indel,Pindel	.											.	FBN2	858	.	0			c.6154delG						PASS	.						122	113	116					5																	127636522		2203	4300	6503	SO:0001589	frameshift_variant	2201	exon48			.	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.6153delC	chr5.hg19:g.127636522delG	ENSP00000424571:p.Ser2051fs	72.0	0.0	0		94.0	18.0	0.191489	NM_001999	B4DU01|Q59ES6	Frame_Shift_Del	DEL	ENST00000508053.1	hg19	CCDS34222.1																																																																																			.	.	.	none		0.463	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		-	127636522	G	-	127636522	7	5	168	1	0	1	0	1	0	0	0	0	5710	1078	38	0	2657	0	FBN2	5	127636522	Frame_Shift_Del	DEL	G	TCGA-F9-A97G-01A-11D-A382-10	31877464	127636522	53278738	25	9908											
EGR1	1958	hgsc.bcm.edu	37	chr5	137801684	137801684	+	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	ggcggcgggggcggcagcaaCagcagcagcagcagcagcac	10	0	18	13	3	0	0	0	0	0	0	0	0	0	0	0	5	8	8	0	5	1	0			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr5:137801684C>G	ENST00000239938.4	+	1	506	c.234C>G	c.(232-234)aaC>aaG	p.N78K		NM_001964.2	NP_001955.1	P18146	EGR1_HUMAN	early growth response 1	78	Gly/Ser-rich.				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)			gcggcagcaacagcagcagca	0.726																																					p.N78K		Atlas-SNP	.											.,1	EGR1	52	.	0			c.C234G						PASS	.						11	11	11					5																	137801684		2140	4182	6322	SO:0001583	missense	1958	exon1			CAGCAACAGCAGC	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.234C>G	chr5.hg19:g.137801684C>G	ENSP00000239938:p.Asn78Lys	88.0	0.0	.		155.0	34.0	.	NM_001964		Missense_Mutation	SNP	ENST00000239938.4	hg19	CCDS4206.1	.	.	.	.	.	.	.	.	.	.	C	10.98	1.504003	0.26949	.	.	ENSG00000120738	ENST00000535792;ENST00000411801;ENST00000239938	T	0.07908	3.15	3.78	3.78	0.43462	.	0.356279	0.23859	N	0.043878	T	0.04679	0.0127	N	0.08118	0	0.22903	N	0.99859	B;B	0.17038	0.02;0.001	B;B	0.10450	0.005;0.002	T	0.35101	-0.9802	10	0.41790	T	0.15	.	10.9732	0.47450	0.0:1.0:0.0:0.0	.	78;78	B4DNX4;P18146	.;EGR1_HUMAN	K	78	ENSP00000239938:N78K	ENSP00000239938:N78K	N	+	3	2	EGR1	137829583	0.999000	0.42202	0.971000	0.41717	0.651000	0.38670	0.504000	0.22626	1.932000	0.55993	0.561000	0.74099	AAC	.	.	.	none		0.726	EGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251274.1	NM_001964		G	137801684	C	G	137801684	3	3	168	1	0	0	0	0	1	0	0	0	4973	477	17	4	236	4	EGR1	5	137801684	Missense_Mutation	SNP	C	TCGA-F9-A97G-01A-11D-A382-10	10165162	137801684	43113576	26	9909											
HECW1	23072	hgsc.bcm.edu	37	chr7	43547666	43547672	+	Frame_Shift_Del	DEL	ATGGCCT	ATGGCCT	-																															agggaaccttcaatcaggtgAtggcctattcgcggaaagag																								rs142279539	byFrequency	TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	ATGGCCT	ATGGCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr7:43547666_43547672delATGGCCT	ENST00000395891.2	+	23	4407_4413	c.3802_3808delATGGCCT	c.(3802-3810)atggcctatfs	p.MAY1268fs	AC011738.4_ENST00000436105.1_RNA|HECW1_ENST00000453890.1_Frame_Shift_Del_p.MAY1234fs	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1268					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						CAATCAGGTGATGGCCTATTCGCGGAA	0.536																																					p.1267_1269del		Atlas-INDEL	.											.	HECW1	540	.	0			c.3801_3807del						PASS	.																																			SO:0001589	frameshift_variant	23072	exon23			.	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.3802_3808delATGGCCT	chr7.hg19:g.43547666_43547672delATGGCCT	ENSP00000379228:p.Met1268fs	124.0	0.0	0		112.0	16.0	0.142857	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Frame_Shift_Del	DEL	ENST00000395891.2	hg19	CCDS5469.2																																																																																			.	.	.	none		0.536	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		-	43547672	ATGGCCT	-	43547666	7	5	168	1	0	1	0	1	0	0	0	0	7049	333	12	0	3884	0	HECW1	7	43547666	Frame_Shift_Del	DEL	ATGGCCT	TCGA-F9-A97G-01A-11D-A382-10		43547666	115590997	27	9910											
GUSB	2990	hgsc.bcm.edu	37	chr7	65441077	65441077	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgacacctggcaccttaagTtggccctgggtcccagtccc	6	9	10	16	0	0	1	0	1	0	0	2	1	2	1	5	3	0	2	5	3	1	2			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr7:65441077T>C	ENST00000304895.4	-	5	967	c.837A>G	c.(835-837)caA>caG	p.Q279Q	GUSB_ENST00000476486.1_5'UTR|GUSB_ENST00000421103.1_Intron|GUSB_ENST00000345660.6_Silent_p.Q279Q	NM_000181.3	NP_000172.2	P08236	BGLR_HUMAN	glucuronidase, beta	279					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-glucuronidase activity (GO:0004566)			breast(1)|cervix(2)|kidney(2)|large_intestine(4)|lung(10)|skin(1)	20						GCACCTTAAGTTGGCCCTGGG	0.527																																					p.Q279Q		Atlas-SNP	.											.	GUSB	52	.	0			c.A837G						PASS	.						82	68	73					7																	65441077		2203	4300	6503	SO:0001819	synonymous_variant	2990	exon5			CTTAAGTTGGCCC	M15182	CCDS5530.1, CCDS64665.1	7q11.21	2012-10-02			ENSG00000169919	ENSG00000169919	3.2.1.31		4696	protein-coding gene	gene with protein product		611499				3468507	Standard	NM_000181		Approved		uc003tun.3	P08236	OTTHUMG00000023735	ENST00000304895.4:c.837A>G	chr7.hg19:g.65441077T>C		47.0	0.0	.		67.0	17.0	.	NM_000181	B4E1F6|E9PCV0|Q549U0|Q96CL9	Silent	SNP	ENST00000304895.4	hg19	CCDS5530.1																																																																																			.	.	.	none		0.527	GUSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251637.3	NM_000181		C	65441077	T	C	65441077	2	2	168	1	0	0	0	0	0	0	0	1	6909	1722	60	3		3	GUSB	7	65441077	Silent	SNP	T	TCGA-F9-A97G-01A-11D-A382-10	21893411	65441077	93697586	28	9911											
YWHAG	7532	hgsc.bcm.edu	37	chr7	75959110	75959110	+	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	tagaagacggagtagttaagAgccaggcctaatcggatggg	13	7	15	6	2	0	3	0	0	0	3	1	5	0	5	2	4	1	2	2	4	5	4			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr7:75959110A>T	ENST00000307630.3	-	2	750	c.528T>A	c.(526-528)gcT>gcA	p.A176A		NM_012479.3	NP_036611.2	P61981	1433G_HUMAN	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma	176					apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway (GO:0097193)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein targeting (GO:0006605)|regulation of neuron differentiation (GO:0045664)|regulation of signal transduction (GO:0009966)|regulation of synaptic plasticity (GO:0048167)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	insulin-like growth factor receptor binding (GO:0005159)|poly(A) RNA binding (GO:0044822)|protein kinase C binding (GO:0005080)|protein kinase C inhibitor activity (GO:0008426)			endometrium(2)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	8						AGTAGTTAAGAGCCAGGCCTA	0.602																																					p.A176A		Atlas-SNP	.											.	YWHAG	24	.	0			c.T528A						PASS	.						167	165	165					7																	75959110		2203	4300	6503	SO:0001819	synonymous_variant	7532	exon2			GTTAAGAGCCAGG	AF142498	CCDS5584.1	7q11.23	2014-06-13	2013-12-03		ENSG00000170027	ENSG00000170027			12852	protein-coding gene	gene with protein product	"14-3-3 gamma", "protein phosphatase 1, regulatory subunit 170"	605356	"tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide"			10486217, 10433554	Standard	NM_012479		Approved	PPP1R170	uc011kgj.1	P61981	OTTHUMG00000022862	ENST00000307630.3:c.528T>A	chr7.hg19:g.75959110A>T		114.0	0.0	.		154.0	21.0	.	NM_012479	O70457|P35214|Q6FH52|Q9UDP2|Q9UN99	Silent	SNP	ENST00000307630.3	hg19	CCDS5584.1																																																																																			.	.	.	none		0.602	YWHAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253002.1	NM_012479		T	75959110	A	T	75959110	2	4	168	1	0	0	0	0	0	0	0	1	17515	291	11	5		5	YWHAG	7	75959110	Silent	SNP	A	TCGA-F9-A97G-01A-11D-A382-10	10518033	75959110	83179553	29	9912											
GPR37	2861	hgsc.bcm.edu	37	chr7	124387082	124387082	+	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	caaacaaaagtaacagccaaAataccaccacagtctcgcac	19	4	4	14	1	1	0	0	0	1	0	2	0	1	0	3	0	4	2	3	0	7	2			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr7:124387082A>T	ENST00000303921.2	-	2	1989	c.1339T>A	c.(1339-1341)Ttt>Att	p.F447I		NM_005302.3	NP_005293.1	O15354	GPR37_HUMAN	G protein-coupled receptor 37 (endothelin receptor type B-like)	447					dopamine biosynthetic process (GO:0042416)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotion involved in locomotory behavior (GO:0031987)|positive regulation of dopamine metabolic process (GO:0045964)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ubiquitin ligase complex (GO:0000151)	G-protein coupled receptor activity (GO:0004930)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						TAACAGCCAAAATACCACCAC	0.488																																					p.F447I		Atlas-SNP	.											.	GPR37	89	.	0			c.T1339A						PASS	.						163	137	146					7																	124387082		2203	4300	6503	SO:0001583	missense	2861	exon2			AGCCAAAATACCA		CCDS5792.1	7q31	2012-08-21			ENSG00000170775	ENSG00000170775		"GPCR / Class A : Orphans"	4494	protein-coding gene	gene with protein product		602583				9339362	Standard	NM_005302		Approved	EDNRBL, hET(B)R-LP, PAELR	uc003vli.4	O15354	OTTHUMG00000157197	ENST00000303921.2:c.1339T>A	chr7.hg19:g.124387082A>T	ENSP00000306449:p.Phe447Ile	56.0	0.0	.		75.0	19.0	.	NM_005302	A4D0Y6|O00348|O14768|Q8TD39	Missense_Mutation	SNP	ENST00000303921.2	hg19	CCDS5792.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.631183	0.87660	.	.	ENSG00000170775	ENST00000303921	T	0.71579	-0.58	5.73	5.73	0.89815	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000003	D	0.83403	0.5247	M	0.75615	2.305	0.58432	D	0.999999	D	0.71674	0.998	D	0.75020	0.985	D	0.85537	0.1213	10	0.87932	D	0	-24.2797	15.205	0.73173	1.0:0.0:0.0:0.0	.	447	O15354	GPR37_HUMAN	I	447	ENSP00000306449:F447I	ENSP00000306449:F447I	F	-	1	0	GPR37	124174318	1.000000	0.71417	0.817000	0.32601	0.986000	0.74619	9.339000	0.96797	2.179000	0.69175	0.533000	0.62120	TTT	.	.	.	none		0.488	GPR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347873.1	NM_005302		T	124387082	A	T	124387082	3	4	168	1	0	0	0	0	1	0	0	0	6698	14	1	5	506	5	GPR37	7	124387082	Missense_Mutation	SNP	A	TCGA-F9-A97G-01A-11D-A382-10	48427972	124387082	34751581	30	9913											
PODXL	5420	hgsc.bcm.edu	37	chr7	131241055	131241055	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcgacggcgacggcgacgAcggcagcagcggcggcgttg	6	2	20	13	11	0	0	0	0	0	0	0	4	0	0	0	6	2	3	0	6	0	1			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr7:131241055A>G	ENST00000378555.3	-	1	311	c.64T>C	c.(64-66)Tcg>Ccg	p.S22P	PODXL_ENST00000465001.1_Intron|PODXL_ENST00000322985.9_Missense_Mutation_p.S22P|PODXL_ENST00000537928.1_Missense_Mutation_p.S22P|PODXL_ENST00000541194.1_Missense_Mutation_p.S22P			O00592	PODXL_HUMAN	podocalyxin-like	22					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					gacggcgacgacggcagcagc	0.741																																					p.S22P		Atlas-SNP	.											.	PODXL	53	.	0			c.T64C						PASS	.						5	8	7					7																	131241055		1914	3836	5750	SO:0001583	missense	5420	exon1			GCGACGACGGCAG		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.64T>C	chr7.hg19:g.131241055A>G	ENSP00000367817:p.Ser22Pro	105.0	0.0	.		119.0	15.0	.	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Missense_Mutation	SNP	ENST00000378555.3	hg19	CCDS34755.1	.	.	.	.	.	.	.	.	.	.	A	10.93	1.488975	0.26686	.	.	ENSG00000128567	ENST00000541194;ENST00000537928;ENST00000378555;ENST00000322985	T;T;T;T	0.12774	2.82;2.65;2.82;2.85	.	.	.	.	7739.210000	0.00166	U	0.000000	T	0.08670	0.0215	N	0.14661	0.345	0.09310	N	0.999994	.	.	.	.	.	.	T	0.24728	-1.0152	6	0.29301	T	0.29	.	.	.	.	.	22;22	O00592-2;O00592	.;PODXL_HUMAN	P	22	ENSP00000440518:S22P;ENSP00000442655:S22P;ENSP00000367817:S22P;ENSP00000319782:S22P	ENSP00000319782:S22P	S	-	1	0	PODXL	130891595	0.001000	0.12720	0.027000	0.17364	0.027000	0.11550	0.743000	0.26231	0.056000	0.16144	0.055000	0.15244	TCG	.	.	.	none		0.741	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111		G	131241055	A	G	131241055	3	3	168	1	0	0	0	0	1	0	0	0	12187	275	10	3	1648	3	PODXL	7	131241055	Missense_Mutation	SNP	A	TCGA-F9-A97G-01A-11D-A382-10	6853973	131241055	27897608	31	9914											
PPP1R16A	84988	hgsc.bcm.edu	37	chr8	145726945	145726945	+	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	ggccgcacaatggccgagtaGggggctccccagtgcggcat	7	5	16	13	3	0	0	0	0	0	0	1	1	1	0	4	5	1	4	4	5	2	1			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr8:145726945G>T	ENST00000292539.4	+	11	2163	c.1246G>T	c.(1246-1248)Ggg>Tgg	p.G416W	PPP1R16A_ENST00000435887.1_Missense_Mutation_p.G416W|CTD-2517M22.14_ENST00000532766.1_RNA|GPT_ENST00000394955.2_5'Flank|CTD-2517M14.5_ENST00000569326.1_RNA|GPT_ENST00000528431.1_5'Flank			Q96I34	PP16A_HUMAN	protein phosphatase 1, regulatory subunit 16A	416						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)			TGGCCGAGTAGGGGGCTCCCC	0.657																																					p.G416W		Atlas-SNP	.											.	PPP1R16A	25	.	0			c.G1246T						PASS	.						28	25	26					8																	145726945		2184	4283	6467	SO:0001583	missense	84988	exon10			CGAGTAGGGGGCT		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.1246G>T	chr8.hg19:g.145726945G>T	ENSP00000292539:p.Gly416Trp	138.0	0.0	.		193.0	34.0	.	NM_032902	D3DWM5	Missense_Mutation	SNP	ENST00000292539.4	hg19	CCDS6429.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.9|21.9	4.219768|4.219768	0.79464|0.79464	.|.	.|.	ENSG00000160972|ENSG00000160972	ENST00000292539;ENST00000435887|ENST00000528430	T;T|.	0.72615|.	-0.67;-0.67|.	4.48|4.48	4.48|4.48	0.54585|0.54585	.|.	0.940914|.	0.08829|.	N|.	0.887657|.	T|.	0.55226|.	0.1907|.	L|L	0.59436|0.59436	1.845|1.845	0.20403|0.20403	N|N	0.999904|0.999904	D|.	0.67145|.	0.996|.	P|.	0.61658|.	0.892|.	T|.	0.49234|.	-0.8961|.	10|.	0.72032|.	D|.	0.01|.	.|.	14.6431|14.6431	0.68739|0.68739	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	416|.	Q96I34|.	PP16A_HUMAN|.	W|Y	416|83	ENSP00000292539:G416W;ENSP00000391126:G416W|.	ENSP00000292539:G416W|.	G|X	+|+	1|3	0|2	PPP1R16A|PPP1R16A	145697753|145697753	0.824000|0.824000	0.29247|0.29247	0.005000|0.005000	0.12908|0.12908	0.336000|0.336000	0.28762|0.28762	4.023000|4.023000	0.57211|0.57211	2.035000|2.035000	0.60131|0.60131	0.462000|0.462000	0.41574|0.41574	GGG|TAG	.	.	.	none		0.657	PPP1R16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382459.1	NM_032902		T	145726945	G	T	145726945	3	4	168	1	0	0	0	0	1	0	0	0	12375	1000	35	4	1284	4	PPP1R16A	8	145726945	Missense_Mutation	SNP	G	TCGA-F9-A97G-01A-11D-A382-10		145726945	637077	32	9915											
MORN5	254956	hgsc.bcm.edu	37	chr9	124929084	124929084	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtacatcctccctaccgaaAcaatatatgttggggaaatg	14	10	8	9	1	0	0	0	0	0	0	2	2	2	1	3	2	3	2	3	2	7	5			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr9:124929084A>G	ENST00000373764.3	+	2	147	c.85A>G	c.(85-87)Aca>Gca	p.T29A	MORN5_ENST00000486801.1_3'UTR|MORN5_ENST00000536616.1_Missense_Mutation_p.T29A	NM_198469.2	NP_940871.2	Q5VZ52	MORN5_HUMAN	MORN repeat containing 5	29										endometrium(3)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	9						CCCTACCGAAACAATATATGT	0.522																																					p.T29A		Atlas-SNP	.											.	MORN5	19	.	0			c.A85G						PASS	.						69	54	59					9																	124929084		2203	4300	6503	SO:0001583	missense	254956	exon2			ACCGAAACAATAT	AK128877	CCDS6836.1, CCDS75894.1	9q34.11	2008-06-23	2008-06-23	2008-06-23	ENSG00000185681	ENSG00000185681			17841	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 113", "chromosome 9 open reading frame 18"	C9orf113, C9orf18			Standard	XM_005251878		Approved	FLJ46909	uc004blw.2	Q5VZ52	OTTHUMG00000020599	ENST00000373764.3:c.85A>G	chr9.hg19:g.124929084A>G	ENSP00000362869:p.Thr29Ala	215.0	0.0	.		260.0	47.0	.	NM_198469	B7Z7I5|Q6ZQN1	Missense_Mutation	SNP	ENST00000373764.3	hg19	CCDS6836.1	.	.	.	.	.	.	.	.	.	.	A	14.95	2.688412	0.48097	.	.	ENSG00000185681	ENST00000373764;ENST00000536616;ENST00000418632	T;T;T	0.41758	0.99;0.99;0.99	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	T	0.44138	0.1279	L	0.38692	1.165	0.58432	D	0.999999	P;P;P	0.51057	0.693;0.941;0.751	B;P;P	0.51657	0.223;0.676;0.676	T	0.33650	-0.9860	10	0.44086	T	0.13	-16.1664	12.7975	0.57567	1.0:0.0:0.0:0.0	.	13;29;29	Q5T7S4;B7Z7I5;Q5VZ52	.;.;MORN5_HUMAN	A	29;29;13	ENSP00000362869:T29A;ENSP00000437483:T29A;ENSP00000409949:T13A	ENSP00000362869:T29A	T	+	1	0	MORN5	123968905	1.000000	0.71417	0.336000	0.25522	0.041000	0.13682	8.195000	0.89723	1.914000	0.55421	0.379000	0.24179	ACA	.	.	.	none		0.522	MORN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053910.2	NM_198469		G	124929084	A	G	124929084	3	3	168	1	0	0	0	0	1	0	0	0	9718	43	2	3	91	3	MORN5	9	124929084	Missense_Mutation	SNP	A	TCGA-F9-A97G-01A-11D-A382-10		124929084	16284347	33	9916											
TTF1	7270	hgsc.bcm.edu	37	chr9	135277608	135277625	+	In_Frame_Del	DEL	CAGAAAGCCAGGACTCCT	CAGAAAGCCAGGACTCCT	-																															aatttcaccccctggacccaCagaaagccaggactcctcct																										TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	CAGAAAGCCAGGACTCCT	CAGAAAGCCAGGACTCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr9:135277608_135277625delCAGAAAGCCAGGACTCCT	ENST00000334270.2	-	2	623_640	c.584_601delAGGAGTCCTGGCTTTCTG	c.(583-603)gaggagtcctggctttctgtg>gtg	p.EESWLS195del		NM_001205296.1|NM_007344.3	NP_001192225.1|NP_031370.2	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase I	195	N-terminal region (NRD). {ECO:0000250}.				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)		CCTGGACCCACAGAAAGCCAGGACTCCTCCTGGTGGGA	0.468																																					p.195_201del		Atlas-Indel,Pindel	.											.	TTF1	82	.	0			c.585_602del						PASS	.																																			SO:0001651	inframe_deletion	7270	exon2			.	BC050734	CCDS6948.1, CCDS75925.1	9q34.3	2008-02-05			ENSG00000125482	ENSG00000125482			12397	protein-coding gene	gene with protein product		600777				7597036	Standard	NM_007344		Approved		uc004cbl.3	Q15361	OTTHUMG00000020836	ENST00000334270.2:c.584_601delAGGAGTCCTGGCTTTCTG	chr9.hg19:g.135277608_135277625delCAGAAAGCCAGGACTCCT	ENSP00000333920:p.Glu195_Ser200del	62.0	0.0	0		69.0	10.0	0.144928	NM_007344	A1L160|Q4VXF3|Q58EY2|Q6P5T5	In_Frame_Del	DEL	ENST00000334270.2	hg19	CCDS6948.1																																																																																			.	.	.	none		0.468	TTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054784.2	NM_007344		-	135277625	CAGAAAGCCAGGACTCCT	-	135277608	7	5	168	1	0	1	0	1	0	0	0	0	16730	478	17	0	2156	0	TTF1	9	135277608	In_Frame_Del	DEL	CAGAAAGCCAGGACTCCT	TCGA-F9-A97G-01A-11D-A382-10	10348524	135277608	5935823	34	9917											
CACNA1B	774	hgsc.bcm.edu	37	chr9	140918184	140918185	+	Missense_Mutation	DNP	AC	AC	GT																															aggctgtggagaaggagaccAcggagaaggaggccacggag																								rs145816559|rs370787788	byFrequency	TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr9:140918184_140918185AC>GT	ENST00000371372.1	+	19	3134_3135	c.2989_2990AC>GT	c.(2989-2991)ACg>GTg	p.T997V	CACNA1B_ENST00000277549.5_Missense_Mutation_p.T189V|CACNA1B_ENST00000371367.5_5'UTR|CACNA1B_ENST00000371363.1_Missense_Mutation_p.T997V|CACNA1B_ENST00000545473.1_5'Flank|CACNA1B_ENST00000371355.4_Missense_Mutation_p.T998V|CACNA1B_ENST00000371357.1_Missense_Mutation_p.T998V|CACNA1B_ENST00000277551.2_Missense_Mutation_p.T997V	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	997					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)	p.T996_E1000delTTEKE(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	GAAGGAGACCACGGAGAAGGAG	0.718																																					p.T997A|p.T997M		Atlas-SNP	.											.	CACNA1B	266	.	1	Deletion - In frame(1)	breast(1)	c.A2989G|c.C2990T						PASS	.																																			SO:0001583	missense	774	exon19			GAGACCACGGAGA|AGACCACGGAGAA	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	Exception_encountered	chr9.hg19:g.140918184_140918185delinsGT	ENSP00000360423:p.Thr997Val	0.0|1.0	0.0	.		248.0|255.0	38.0|51.0	.	NM_001243812	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	hg19	CCDS59522.1																																																																																			.	.	.	none		0.718	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		GT	140918185	AC	GT	140918184	3	3	168	1	0	0	0	0	1	0	0	0	2541	159	6	3	3063	3	CACNA1B	9	140918184	Missense_Mutation	DNP	AC	TCGA-F9-A97G-01A-11D-A382-10	5640576	140918184	295247	35	9918											
DHDPSL	112817	hgsc.bcm.edu	37	chr10	99361640	99361640	+	Missense_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	tggggggcgtctgcgccctgGccaatgtcctgggggctcag	3	8	18	12	2	2	0	1	0	1	0	3	0	3	0	3	6	1	1	3	6	1	0			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr10:99361640G>A	ENST00000370646.4	+	6	1088	c.727G>A	c.(727-729)Gcc>Acc	p.A243T	PI4K2A_ENST00000370649.3_Missense_Mutation_p.A80T|HOGA1_ENST00000370647.4_Missense_Mutation_p.A80T|PI4K2A_ENST00000555577.1_Missense_Mutation_p.A80T	NM_138413.3	NP_612422.2	Q86XE5	HOGA1_HUMAN	4-hydroxy-2-oxoglutarate aldolase 1	243					4-hydroxyproline catabolic process (GO:0019470)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|oxalate metabolic process (GO:0033609)|pyruvate biosynthetic process (GO:0042866)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	4-hydroxy-2-oxoglutarate aldolase activity (GO:0008700)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|prostate(2)|skin(1)|stomach(1)	14						CTGCGCCCTGGCCAATGTCCT	0.637																																					p.A243T		Atlas-SNP	.											.	HOGA1	25	.	0			c.G727A						PASS	.						39	41	40					10																	99361640		2203	4300	6503	SO:0001583	missense	112817	exon6			GCCCTGGCCAATG	BC011916	CCDS7467.1, CCDS44469.1	10q24.1	2010-12-19	2010-12-19	2010-12-19	ENSG00000241935	ENSG00000241935			25155	protein-coding gene	gene with protein product	"dihydrodipicolinate synthetase homolog 2 (E. coli)", "N-acetylneuraminate pyruvate lyase 2 (putative)"	613597	"chromosome 10 open reading frame 65", "dihydrodipicolinate synthase-like, mitochondrial"	C10orf65, DHDPSL		20797690	Standard	NM_001134670		Approved	FLJ37472, DHDPS2, NPL2		Q86XE5	OTTHUMG00000018859	ENST00000370646.4:c.727G>A	chr10.hg19:g.99361640G>A	ENSP00000359680:p.Ala243Thr	101.0	0.0	.		106.0	27.0	.	NM_138413	A8K075|Q5T680|Q5T684|Q711P0|Q8N9F2|Q96EV5	Missense_Mutation	SNP	ENST00000370646.4	hg19	CCDS7467.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.604805|5.604805	0.96626|0.96626	.|.	.|.	ENSG00000241935;ENSG00000241935;ENSG00000155252;ENSG00000249967|ENSG00000241935	ENST00000370647;ENST00000370646;ENST00000555577;ENST00000370649|ENST00000370642	D;D;D;D|.	0.95035|.	-3.59;-3.59;-2.51;-2.51|.	5.07|5.07	5.07|5.07	0.68467|0.68467	Aldolase-type TIM barrel (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.84361|0.84361	0.5455|0.5455	M|M	0.89353|0.89353	3.025|3.025	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	0.993;1.0;1.0|.	D;D;D|.	0.81914|.	0.971;0.995;0.995|.	D|D	0.86967|0.86967	0.2095|0.2095	10|5	0.87932|.	D|.	0|.	-24.1425|-24.1425	18.8138|18.8138	0.92070|0.92070	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	80;80;243|.	E9PAM4;Q86XE5-3;Q86XE5|.	.;.;HOGA1_HUMAN|.	T|D	80;243;80;80|46	ENSP00000359681:A80T;ENSP00000359680:A243T;ENSP00000452243:A80T;ENSP00000359683:A80T|.	ENSP00000359680:A243T|.	A|G	+|+	1|2	0|0	PI4K2A;HOGA1;RP11-548K23.11|HOGA1	99351630|99351630	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	7.387000|7.387000	0.79785|0.79785	2.530000|2.530000	0.85305|0.85305	0.561000|0.561000	0.74099|0.74099	GCC|GGC	.	.	.	none		0.637	HOGA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049726.1	NM_138413		A	99361640	G	A	99361640	3	1	168	1	0	0	0	0	1	0	0	0	4482	1203	42	2	749	2	DHDPSL	10	99361640	Missense_Mutation	SNP	G	TCGA-F9-A97G-01A-11D-A382-10		99361640	36173107	36	9919											
ATRNL1	26033	hgsc.bcm.edu	37	chr10	117221517	117221517	+	Missense_Mutation	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	agatgatcgccaccatactgCcataaactttatagcaaacc	15	9	5	12	1	0	2	0	1	0	1	1	2	0	2	4	0	5	1	4	0	6	5			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr10:117221517C>T	ENST00000355044.3	+	22	3515	c.3389C>T	c.(3388-3390)gCc>gTc	p.A1130V	ATRNL1_ENST00000303745.7_Intron|ATRNL1_ENST00000423111.2_Missense_Mutation_p.A181V	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	1130					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)		CACCATACTGCCATAAACTTT	0.313																																					p.A1130V		Atlas-SNP	.											.	ATRNL1	219	.	0			c.C3389T						PASS	.						121	116	118					10																	117221517		2203	4299	6502	SO:0001583	missense	26033	exon22			ATACTGCCATAAA	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.3389C>T	chr10.hg19:g.117221517C>T	ENSP00000347152:p.Ala1130Val	105.0	0.0	.		81.0	18.0	.	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Missense_Mutation	SNP	ENST00000355044.3	hg19	CCDS7592.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.873727	0.91664	.	.	ENSG00000107518	ENST00000355044;ENST00000423111	T;T	0.53423	0.62;0.62	5.05	5.05	0.67936	.	0.103911	0.64402	D	0.000003	T	0.55878	0.1948	M	0.76433	2.335	0.80722	D	1	P;P	0.50443	0.799;0.935	B;P	0.45232	0.343;0.474	T	0.62877	-0.6761	10	0.51188	T	0.08	-10.1629	18.7909	0.91974	0.0:1.0:0.0:0.0	.	181;1130	B4DH41;Q5VV63	.;ATRN1_HUMAN	V	1130;181	ENSP00000347152:A1130V;ENSP00000409624:A181V	ENSP00000347152:A1130V	A	+	2	0	ATRNL1	117211507	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.704000	0.84595	2.522000	0.85027	0.650000	0.86243	GCC	.	.	.	none		0.313	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		T	117221517	C	T	117221517	3	4	168	1	0	0	0	0	1	0	0	0	1207	739	26	2	3475	2	ATRNL1	10	117221517	Missense_Mutation	SNP	C	TCGA-F9-A97G-01A-11D-A382-10	17859877	117221517	18313230	37	9920											
SBF2	81846	hgsc.bcm.edu	37	chr11	10011141	10011146	+	Splice_Site	DEL	AACTAG	AACTAG	-																															tctctacttcaaaggctaccAactaggaaaaagaatcaaat																										TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	AACTAG	AACTAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr11:10011141_10011146delAACTAG	ENST00000256190.8	-	13	1434_1435	c.1297_1298delCTAGTT	c.(1297-1299)cta>a	p.L433del		NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN	SET binding factor 2	433					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)		AAAGGCTACCAACTAGGAAAAAGAAT	0.316																																					p.433_433del		Atlas-Indel,Pindel	.											SBF2,colon,carcinoma,0,1	SBF2	146	.	0			c.1297_1299del						PASS	.																																			SO:0001630	splice_region_variant	81846	exon13			.	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.1297-1CTAGTT>-	chr11.hg19:g.10011141_10011146delAACTAG		80.0	0.0	0		84.0	11.0	0.130952	NM_030962	Q3MJF0|Q68DQ3|Q6P459|Q6PJD1|Q7Z325|Q7Z621|Q86VE2|Q96FE2|Q9C097	In_Frame_Del	DEL	ENST00000256190.8	hg19	CCDS31427.1																																																																																			.	.	.	none		0.316	SBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386911.2	NM_030962	In_Frame_Del	-	10011146	AACTAG	-	10011141	8	5	168	1	0	1	0	1	0	0	1	0	13872	144	5	0	4363	0	SBF2	11	10011141	Splice_Site	DEL	AACTAG	TCGA-F9-A97G-01A-11D-A382-10		10011141	124995375	38	9921											
PLEKHA7	144100	hgsc.bcm.edu	37	chr11	16812448	16812448	+	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	agctcaggctcactgacataCgaccgcagctccacctgtgg	9	7	10	15	2	2	1	2	1	0	0	3	2	3	1	3	2	3	4	3	2	1	1			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr11:16812448C>A	ENST00000355661.3	-	21	2959	c.2949G>T	c.(2947-2949)tcG>tcT	p.S983S	PLEKHA7_ENST00000332954.4_5'UTR|PLEKHA7_ENST00000532079.1_Intron|PLEKHA7_ENST00000531066.1_Silent_p.S983S|PLEKHA7_ENST00000448080.2_Silent_p.S984S			Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A member 7	983					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						CACTGACATACGACCGCAGCT	0.642																																					p.S983S		Atlas-SNP	.											.	PLEKHA7	120	.	0			c.G2949T						PASS	.						40	35	37					11																	16812448		2200	4294	6494	SO:0001819	synonymous_variant	144100	exon21			GACATACGACCGC	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.2949G>T	chr11.hg19:g.16812448C>A		123.0	0.0	.		163.0	29.0	.	NM_175058	B4DK33|B4DWC3|Q86VZ7	Silent	SNP	ENST00000355661.3	hg19	CCDS31434.1	.	.	.	.	.	.	.	.	.	.	C	8.196	0.797114	0.16327	.	.	ENSG00000166689	ENST00000530489	.	.	.	5.59	-11.2	0.00127	.	.	.	.	.	T	0.49541	0.1563	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.64791	-0.6324	4	.	.	.	-11.4593	11.8426	0.52364	0.0:0.3541:0.4355:0.2105	.	.	.	.	L	615	.	.	R	-	2	0	PLEKHA7	16769024	0.000000	0.05858	0.303000	0.25071	0.923000	0.55619	-2.377000	0.01069	-2.541000	0.00485	-0.265000	0.10407	CGT	.	.	.	none		0.642	PLEKHA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000387242.2	NM_175058		A	16812448	C	A	16812448	2	1	168	1	0	0	0	0	0	0	0	1	12068	523	19	4		4	PLEKHA7	11	16812448	Silent	SNP	C	TCGA-F9-A97G-01A-11D-A382-10	6801307	16812448	118194068	39	9922											
SYVN1	84447	hgsc.bcm.edu	37	chr11	64899012	64899012	+	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	tctcactctggaggtccacgGagtgcagcacatacttgatg	9	10	11	11	1	2	1	1	1	2	0	4	3	3	3	1	3	3	2	1	3	1	2	rs267603113		TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr11:64899012G>C	ENST00000377190.3	-	7	681	c.587C>G	c.(586-588)tCc>tGc	p.S196C	SYVN1_ENST00000294256.8_Missense_Mutation_p.S196C|SYVN1_ENST00000307289.6_Missense_Mutation_p.S145C|SYVN1_ENST00000526060.1_Missense_Mutation_p.S196C|SYVN1_ENST00000526121.1_5'UTR	NM_172230.2	NP_757385.1	Q86TM6	SYVN1_HUMAN	synovial apoptosis inhibitor 1, synoviolin	196					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						GAGGTCCACGGAGTGCAGCAC	0.552																																					p.S196C		Atlas-SNP	.											.	SYVN1	55	.	0			c.C587G						PASS	.						113	92	99					11																	64899012		2201	4297	6498	SO:0001583	missense	84447	exon7			TCCACGGAGTGCA	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.587C>G	chr11.hg19:g.64899012G>C	ENSP00000366395:p.Ser196Cys	76.0	0.0	.		87.0	12.0	.	NM_172230	Q8N3K3|Q8N6E8|Q96JL5|Q96PK3	Missense_Mutation	SNP	ENST00000377190.3	hg19	CCDS31605.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.118620	0.77323	.	.	ENSG00000162298	ENST00000377190;ENST00000294256;ENST00000434219;ENST00000307289;ENST00000526060;ENST00000531018;ENST00000528487	T;T;T;T;T;T	0.50277	0.75;0.75;0.75;0.75;0.75;0.75	4.76	4.76	0.60689	.	0.061993	0.64402	D	0.000004	T	0.57504	0.2058	L	0.36672	1.1	0.49798	D	0.999825	D;D;D	0.67145	0.996;0.994;0.989	D;D;P	0.66847	0.947;0.947;0.887	T	0.58978	-0.7540	10	0.54805	T	0.06	-34.3522	15.3234	0.74141	0.0:0.0:1.0:0.0	.	145;196;196	Q86TM6-2;Q86TM6-3;Q86TM6	.;.;SYVN1_HUMAN	C	196;196;196;145;196;136;181	ENSP00000366395:S196C;ENSP00000294256:S196C;ENSP00000302035:S145C;ENSP00000436984:S196C;ENSP00000431215:S136C;ENSP00000431720:S181C	ENSP00000294256:S196C	S	-	2	0	SYVN1	64655588	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	4.891000	0.63185	2.463000	0.83235	0.563000	0.77884	TCC	.	.	.	none		0.552	SYVN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385274.1	NM_032431		C	64899012	G	C	64899012	3	2	168	1	0	0	0	0	1	0	0	0	15499	1174	41	4	1306	4	SYVN1	11	64899012	Missense_Mutation	SNP	G	TCGA-F9-A97G-01A-11D-A382-10	48086564	64899012	70107504	40	9923											
KRTAP5-8	57830	hgsc.bcm.edu	37	chr11	71249532	71249532	+	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	ctgctgcaagccctgctgttCccagtccagctgctgtaagc	6	10	10	15	0	0	0	0	0	0	0	2	0	2	0	3	0	7	7	3	0	2	2	rs532438179|rs11234084|rs369043826	byFrequency	TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	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	chr11.hg19:g.71249532C>G	ENSP00000420723:p.Ser144Cys	73.0	0.0	.		102.0	6.0	.	NM_021046	Q6L8G7|Q6UTX6	Missense_Mutation	SNP	ENST00000398534.3	hg19	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	168	1	0	0	0	0	1	0	0	0	8574	855	30	4	433	4	KRTAP5-8	11	71249532	Missense_Mutation	SNP	C	TCGA-F9-A97G-01A-11D-A382-10	6350520	71249532	63756984	41	9924											
PRDM10	56980	hgsc.bcm.edu	37	chr11	129793159	129793159	+	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	ataccttaaattgcttcccaCaggtggaacacaggaagtct	13	10	8	10	0	1	0	0	0	1	0	2	2	2	2	2	3	3	1	2	3	5	4			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr11:129793159C>G	ENST00000360871.3	-	13	2249	c.2018G>C	c.(2017-2019)tGt>tCt	p.C673S	PRDM10_ENST00000526082.1_Missense_Mutation_p.C591S|PRDM10_ENST00000528746.1_Missense_Mutation_p.C647S|PRDM10_ENST00000358825.5_Missense_Mutation_p.C677S|PRDM10_ENST00000423662.2_Missense_Mutation_p.C591S|PRDM10_ENST00000304538.6_Missense_Mutation_p.C587S	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	677					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)		TTGCTTCCCACAGGTGGAACA	0.517											OREG0021513	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C677S		Atlas-SNP	.											.	PRDM10	120	.	0			c.G2030C						PASS	.						95	74	81					11																	129793159		2201	4297	6498	SO:0001583	missense	56980	exon14			TTCCCACAGGTGG	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.2018G>C	chr11.hg19:g.129793159C>G	ENSP00000354118:p.Cys673Ser	118.0	0.0	.	1575	122.0	40.0	.	NM_020228	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Missense_Mutation	SNP	ENST00000360871.3	hg19	CCDS8484.1	.	.	.	.	.	.	.	.	.	.	C	28.7	4.938669	0.92526	.	.	ENSG00000170325	ENST00000358825;ENST00000304538;ENST00000360871;ENST00000423662;ENST00000528746;ENST00000526082;ENST00000533431	D;D;D;D;D;D;D	0.99974	-10.2;-10.2;-10.2;-10.2;-10.2;-10.2;-10.2	6.16	6.16	0.99307	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	0.99981	0.9994	M	0.89715	3.055	0.80722	D	1	D;D;D;D;D;D	0.89917	0.997;0.996;0.997;0.996;1.0;0.996	D;D;D;D;D;D	0.87578	0.994;0.99;0.994;0.99;0.998;0.99	D	0.96873	0.9641	10	0.87932	D	0	-17.0242	20.8598	0.99761	0.0:1.0:0.0:0.0	.	587;673;677;591;587;591	B7ZL72;G3XAE5;Q9NQV6;Q9NQV6-5;Q9NQV6-2;Q9NQV6-1	.;.;PRD10_HUMAN;.;.;.	S	677;587;673;591;647;591;390	ENSP00000351686:C677S;ENSP00000302669:C587S;ENSP00000354118:C673S;ENSP00000398431:C591S;ENSP00000431262:C647S;ENSP00000432237:C591S;ENSP00000435940:C390S	ENSP00000302669:C587S	C	-	2	0	PRDM10	129298369	1.000000	0.71417	0.988000	0.46212	0.988000	0.76386	7.311000	0.78958	2.937000	0.99478	0.650000	0.86243	TGT	.	.	.	none		0.517	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437		G	129793159	C	G	129793159	3	3	168	1	0	0	0	0	1	0	0	0	12461	478	17	4	1488	4	PRDM10	11	129793159	Missense_Mutation	SNP	C	TCGA-F9-A97G-01A-11D-A382-10	58543627	129793159	5213357	42	9925											
TAS2R50	259296	hgsc.bcm.edu	37	chr12	11138793	11138793	+	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	ttgcaaagcttttatgtggaCcttggtgctgagatcttgcg	7	15	12	7	1	1	1	0	1	1	1	1	3	1	2	1	2	4	3	1	2	2	5			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr12:11138793C>T	ENST00000506868.1	-	1	718	c.667G>A	c.(667-669)Gtc>Atc	p.V223I	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176890.2	NP_795371.2	P59544	T2R50_HUMAN	taste receptor, type 2, member 50	223					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(4)|ovary(2)|pancreas(1)	17						TTTATGTGGACCTTGGTGCTG	0.438																																					p.V223I		Atlas-SNP	.											.	TAS2R50	37	.	0			c.G667A						PASS	.						157	154	155					12																	11138793		2203	4300	6503	SO:0001583	missense	259296	exon1			TGTGGACCTTGGT	AF494235	CCDS8638.1	12p13.2	2012-08-22			ENSG00000212126	ENSG00000212126		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18882	protein-coding gene	gene with protein product		609627				12379855, 12584440, 16175505	Standard	NM_176890		Approved	T2R51	uc001qzl.2	P59544	OTTHUMG00000162719	ENST00000506868.1:c.667G>A	chr12.hg19:g.11138793C>T	ENSP00000424040:p.Val223Ile	155.0	0.0	.		183.0	28.0	.	NM_176890	P59545|Q2M255|Q645Y0	Missense_Mutation	SNP	ENST00000506868.1	hg19	CCDS8638.1	.	.	.	.	.	.	.	.	.	.	C	12.25	1.882933	0.33255	.	.	ENSG00000212126	ENST00000506868	T	0.00824	5.65	2.19	-1.22	0.09494	.	1.058070	0.07508	U	0.908398	T	0.02230	0.0069	L	0.58810	1.83	0.09310	N	1	P	0.50156	0.932	P	0.52758	0.708	T	0.42447	-0.9451	10	0.49607	T	0.09	.	6.3225	0.21225	0.0:0.5837:0.0:0.4163	.	223	P59544	T2R50_HUMAN	I	223	ENSP00000424040:V223I	ENSP00000424040:V223I	V	-	1	0	TAS2R50	11030060	0.000000	0.05858	0.000000	0.03702	0.061000	0.15899	0.296000	0.19083	-0.526000	0.06383	0.313000	0.20887	GTC	.	.	.	none		0.438	TAS2R50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370192.2	NM_176890		T	11138793	C	T	11138793	3	4	168	1	0	0	0	0	1	0	0	0	15596	507	18	2	236	2	TAS2R50	12	11138793	Missense_Mutation	SNP	C	TCGA-F9-A97G-01A-11D-A382-10		11138793	122713102	43	9926											
KRT2	3849	hgsc.bcm.edu	37	chr12	53045631	53045632	+	In_Frame_Ins	INS	-	-	CGCCTCCAAAGCCGCTGC																															gccacctccaaagctgctgcINScgcctccaaaaccacctcct																										TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr12:53045631_53045632insCGCCTCCAAAGCCGCTGC	ENST00000309680.3	-	1	316_317	c.295_296insGCAGCGGCTTTGGAGGCG	c.(295-297)ggc>gGCAGCGGCTTTGGAGGCGgc	p.99_99G>GSGFGGG		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	99	Head.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		aaagctgctgccgcctccaaaa	0.619																																					p.G99delinsGSGFGGG		Atlas-INDEL	.											.	KRT2	94	.	0			c.296_297insGCAGCGGCTTTGGAGGCG						PASS	.																																			SO:0001652	inframe_insertion	3849	exon1			.		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"-", "Intermediate filaments type II, keratins (basic)"	6439	protein-coding gene	gene with protein product	"epidermal ichthyosis bullosa of Siemens"	600194	"keratin 2A (epidermal ichthyosis bullosa of Siemens)"	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.295_296insGCAGCGGCTTTGGAGGCG	chr12.hg19:g.53045631_53045632insCGCCTCCAAAGCCGCTGC	Exception_encountered	186.0	0.0	0		248.0	47.0	0.189516	NM_000423	Q4VAQ2	In_Frame_Ins	INS	ENST00000309680.3	hg19	CCDS8835.1																																																																																			.	.	.	none		0.619	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423		CGCCTCCAAAGCCGCTGC	53045632	-	CGCCTCCAAAGCCGCTGC	53045631	7	5	168	1	0	1	1	0	0	0	0	0	8464	739	26	0	1659	0	KRT2	12	53045631	In_Frame_Ins	INS	-	TCGA-F9-A97G-01A-11D-A382-10	41906838	53045631	80806264	44	9927											
ATP11A	23250	hgsc.bcm.edu	37	chr13	113479745	113479745	+	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	ctctgtccttttgttttagaTcgatgaatgcgttcctcatt	6	19	7	9	2	2	2	1	1	1	1	5	3	4	2	2	0	1	2	2	0	2	6			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr13:113479745T>A	ENST00000487903.1	+	11	962	c.874T>A	c.(874-876)Tcg>Acg	p.S292T	ATP11A_ENST00000283558.8_Splice_Site_p.S292T|ATP11A_ENST00000375630.2_Splice_Site_p.S292T|ATP11A_ENST00000375645.3_Splice_Site_p.S292T			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	292					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)				TTGTTTTAGATCGATGAATGC	0.453																																					p.S292T		Atlas-SNP	.											.	ATP11A	225	.	0			c.T874A						PASS	.						124	95	105					13																	113479745		2203	4300	6503	SO:0001630	splice_region_variant	23250	exon11			TTTAGATCGATGA	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.873-1T>A	chr13.hg19:g.113479745T>A		106.0	0.0	.		153.0	31.0	.	NM_032189	Q5VXT2	Missense_Mutation	SNP	ENST00000487903.1	hg19	CCDS32011.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.98|11.98	1.799891|1.799891	0.31869|0.31869	.|.	.|.	ENSG00000068650|ENSG00000068650	ENST00000418678|ENST00000487903;ENST00000375630;ENST00000375645;ENST00000283558	.|D;D;D;D	.|0.90788	.|-2.73;-2.73;-2.73;-2.73	5.2|5.2	5.2|5.2	0.72013|0.72013	.|ATPase, P-type, ATPase-associated domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.91975|0.91975	0.7458|0.7458	L|L	0.47190|0.47190	1.495|1.495	0.80722|0.80722	D|D	1|1	.|D;B;B	.|0.59357	.|0.985;0.107;0.004	.|P;B;B	.|0.62491	.|0.903;0.14;0.06	D|D	0.89626|0.89626	0.3852|0.3852	5|10	.|0.17832	.|T	.|0.49	.|.	15.1027|15.1027	0.72292|0.72292	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|292;292;292	.|E9PCW5;E9PEJ6;P98196	.|.;.;AT11A_HUMAN	K|T	266|292	.|ENSP00000420387:S292T;ENSP00000364781:S292T;ENSP00000364796:S292T;ENSP00000283558:S292T	.|ENSP00000283558:S292T	N|S	+|+	3|1	2|0	ATP11A|ATP11A	112527746|112527746	1.000000|1.000000	0.71417|0.71417	0.472000|0.472000	0.27241|0.27241	0.009000|0.009000	0.06853|0.06853	7.703000|7.703000	0.84585|0.84585	1.963000|1.963000	0.57068|0.57068	0.459000|0.459000	0.35465|0.35465	AAT|TCG	.	.	.	none		0.453	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205	Missense_Mutation	A	113479745	T	A	113479745	5	1	168	1	0	0	0	0	0	0	1	0	1119	1449	50	5	916	5	ATP11A	13	113479745	Splice_Site	SNP	T	TCGA-F9-A97G-01A-11D-A382-10		113479745	1690133	45	9928											
PPP2R3C	55012	hgsc.bcm.edu	37	chr14	35554933	35554940	+	Frame_Shift_Del	DEL	GAAGAGAG	GAAGAGAG	-																															attactgttgattaaatcctGaagagagattttcaaaggat																										TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	GAAGAGAG	GAAGAGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr14:35554933_35554940delGAAGAGAG	ENST00000261475.5	-	13	1571_1578	c.1218_1225delCTCTCTTC	c.(1216-1227)atctctcttcagfs	p.SLQ407fs		NM_017917.2	NP_060387.2	Q969Q6	P2R3C_HUMAN	protein phosphatase 2, regulatory subunit B'', gamma	407					activation of protein kinase activity (GO:0032147)|B cell homeostasis (GO:0001782)|positive regulation of B cell differentiation (GO:0045579)|regulation of antimicrobial humoral response (GO:0002759)|regulation of mitochondrial depolarization (GO:0051900)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.I406I(1)		central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)	15	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;8.62e-06)|LUAD - Lung adenocarcinoma(48;1.42e-05)|Epithelial(34;0.0177)|all cancers(34;0.0491)	GBM - Glioblastoma multiforme(112;0.0803)		ATTAAATCCTGAAGAGAGATTTTCAAAG	0.351																																					p.407_409del		Atlas-Indel,Pindel	.											.	PPP2R3C	44	.	1	Substitution - coding silent(1)	large_intestine(1)	c.1219_1226del						PASS	.																																			SO:0001589	frameshift_variant	55012	exon13			.	AK000651	CCDS9654.1	14q13.2	2010-06-18	2010-06-18	2007-01-22	ENSG00000092020	ENSG00000092020		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	17485	protein-coding gene	gene with protein product		615902	"chromosome 14 open reading frame 10", "protein phosphatase 2 (formerly 2A), regulatory subunit B'', gamma"	C14orf10		12167160, 16129705	Standard	NM_017917		Approved	FLJ20644, G4-1, G5PR	uc001wss.3	Q969Q6	OTTHUMG00000140224	ENST00000261475.5:c.1218_1225delCTCTCTTC	chr14.hg19:g.35554933_35554940delGAAGAGAG	ENSP00000261475:p.Ser407fs	107.0	0.0	0		97.0	15.0	0.154639	NM_017917	B4DEN7|D3DS97|D3DS98|Q5GJ55|Q5GJ56|Q6P4G2|Q86TZ3|Q9NWR9	Frame_Shift_Del	DEL	ENST00000261475.5	hg19	CCDS9654.1																																																																																			.	.	.	none		0.351	PPP2R3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276687.1	NM_017917		-	35554940	GAAGAGAG	-	35554933	7	5	168	1	0	1	0	1	0	0	0	0	12400	1299	45	0	140	0	PPP2R3C	14	35554933	Frame_Shift_Del	DEL	GAAGAGAG	TCGA-F9-A97G-01A-11D-A382-10		35554933	71794607	46	9929											
PLEKHG3	26030	hgsc.bcm.edu	37	chr14	65208230	65208230	+	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	gactccctcagctgtcagctCtccccagaagtggacatcag	9	8	9	15	0	4	1	3	0	1	1	6	3	5	2	3	1	2	2	3	1	1	0			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr14:65208230C>G	ENST00000394691.1	+	16	2142	c.1995C>G	c.(1993-1995)ctC>ctG	p.L665L	PLEKHG3_ENST00000471182.2_Silent_p.L198L|PLEKHG3_ENST00000484731.2_Silent_p.L170L|PLEKHG3_ENST00000247226.7_Silent_p.L609L			A1L390	PKHG3_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 3	665							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(5)|kidney(2)|large_intestine(1)|lung(14)|prostate(2)|skin(3)|urinary_tract(2)	29				all cancers(60;0.00802)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)|BRCA - Breast invasive adenocarcinoma(234;0.0485)		GCTGTCAGCTCTCCCCAGAAG	0.672																																					p.L609L		Atlas-SNP	.											.	PLEKHG3	89	.	0			c.C1827G						PASS	.						35	39	38					14																	65208230		2203	4299	6502	SO:0001819	synonymous_variant	26030	exon14			TCAGCTCTCCCCA	AB011171	CCDS32098.1	14q23.3	2013-01-10	2004-12-01	2004-12-01	ENSG00000126822	ENSG00000126822		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	20364	protein-coding gene	gene with protein product			"KIAA0599"	KIAA0599			Standard	XM_005267511		Approved	ARHGEF43	uc001xhp.2	A1L390	OTTHUMG00000029671	ENST00000394691.1:c.1995C>G	chr14.hg19:g.65208230C>G		60.0	0.0	.		85.0	18.0	.	NM_015549	A1L389|B5MEC9|O60339|Q6GMS3|Q6P4B1|Q7L3S3|Q86SW7|Q8TEF5|Q96EW6|Q9BT82	Silent	SNP	ENST00000394691.1	hg19																																																																																				.	.	.	none		0.672	PLEKHG3-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000412028.1	NM_015549		G	65208230	C	G	65208230	2	3	168	1	0	0	0	0	0	0	0	1	12077	900	32	4		4	PLEKHG3	14	65208230	Silent	SNP	C	TCGA-F9-A97G-01A-11D-A382-10	29653297	65208230	42141310	47	9930											
FOXN3	1112	hgsc.bcm.edu	37	chr14	89817056	89817056	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgggaggtgtattgaacaCgtgtgggtgtgggtgataag	8	11	20	2	1	0	2	0	2	0	0	0	3	0	3	0	5	1	1	0	5	3	3			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr14:89817056C>T	ENST00000345097.4	-	3	756	c.640G>A	c.(640-642)Gtg>Atg	p.V214M	FOXN3_ENST00000557258.1_Missense_Mutation_p.V214M|FOXN3_ENST00000555353.1_Missense_Mutation_p.V214M|RP11-356K23.1_ENST00000555407.1_RNA|FOXN3_ENST00000261302.5_Missense_Mutation_p.V214M|RP11-356K23.1_ENST00000556942.1_RNA|FOXN3_ENST00000555658.1_5'UTR	NM_001085471.1	NP_001078940.1	O00409	FOXN3_HUMAN	forkhead box N3	214					mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GTATTGAACACGTGTGGGTGT	0.433																																					p.V214M		Atlas-SNP	.											.	FOXN3	78	.	0			c.G640A						PASS	.						220	192	202					14																	89817056		2203	4300	6503	SO:0001583	missense	1112	exon3			TGAACACGTGTGG		CCDS32138.1, CCDS41977.1	14q32.11	2012-04-17	2007-05-02	2007-05-02	ENSG00000053254	ENSG00000053254		"Forkhead boxes"	1928	protein-coding gene	gene with protein product		602628	"chromosome 14 open reading frame 116", "checkpoint suppressor 1"	C14orf116, CHES1		9154802	Standard	NM_005197		Approved		uc001xxo.4	O00409	OTTHUMG00000170898	ENST00000345097.4:c.640G>A	chr14.hg19:g.89817056C>T	ENSP00000343288:p.Val214Met	171.0	0.0	.		206.0	34.0	.	NM_005197	Q96II7|Q9UIE7	Missense_Mutation	SNP	ENST00000345097.4	hg19	CCDS41977.1	.	.	.	.	.	.	.	.	.	.	C	18.26	3.584613	0.65992	.	.	ENSG00000053254	ENST00000345097;ENST00000261302;ENST00000557258;ENST00000555353;ENST00000553353	D;D;D;D	0.94828	-3.53;-3.53;-3.32;-3.32	5.03	5.03	0.67393	.	0.216604	0.37304	N	0.002141	D	0.93785	0.8013	L	0.51422	1.61	0.46901	D	0.999246	P;P	0.49783	0.624;0.928	B;P	0.47015	0.276;0.534	D	0.93504	0.6847	10	0.41790	T	0.15	.	18.3782	0.90442	0.0:1.0:0.0:0.0	.	214;214	O00409;O00409-2	FOXN3_HUMAN;.	M	214;214;214;214;65	ENSP00000343288:V214M;ENSP00000261302:V214M;ENSP00000452005:V214M;ENSP00000452227:V214M	ENSP00000261302:V214M	V	-	1	0	FOXN3	88886809	0.996000	0.38824	0.710000	0.30468	0.681000	0.39784	2.077000	0.41557	2.342000	0.79632	0.561000	0.74099	GTG	.	.	.	none		0.433	FOXN3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410902.2	NM_005197		T	89817056	C	T	89817056	3	4	168	1	0	0	0	0	1	0	0	0	6028	536	19	1	852	1	FOXN3	14	89817056	Missense_Mutation	SNP	C	TCGA-F9-A97G-01A-11D-A382-10	24608826	89817056	17532484	48	9931											
UBE3A	7337	hgsc.bcm.edu	37	chr15	25616011	25616011	+	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	caaaagggataagtggttttCgacaatccagggttttaaca	14	11	10	6	1	0	0	0	0	0	0	2	2	1	1	1	3	1	2	1	3	5	5			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr15:25616011C>T	ENST00000397954.2	-	4	1318	c.1319G>A	c.(1318-1320)cGa>cAa	p.R440Q	UBE3A_ENST00000438097.1_Missense_Mutation_p.R417Q|SNHG14_ENST00000554726.1_RNA|UBE3A_ENST00000232165.3_Missense_Mutation_p.R437Q|UBE3A_ENST00000566215.1_Missense_Mutation_p.R417Q|UBE3A_ENST00000428984.2_Missense_Mutation_p.R417Q			Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A	440	Interaction with HCV core protein.				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)		AAGTGGTTTTCGACAATCCAG	0.383																																					p.R440Q		Atlas-SNP	.											UBE3A,NS,adenocarcinoma,0,2	UBE3A	109	.	0			c.G1319A						PASS	.						35	35	35					15																	25616011		2202	4298	6500	SO:0001583	missense	7337	exon7			GGTTTTCGACAAT	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.1319G>A	chr15.hg19:g.25616011C>T	ENSP00000381045:p.Arg440Gln	80.0	0.0	.		100.0	20.0	.	NM_000462	A8K8Z9|P78355|Q93066|Q9UEP4|Q9UEP5|Q9UEP6|Q9UEP7|Q9UEP8|Q9UEP9	Missense_Mutation	SNP	ENST00000397954.2	hg19	CCDS45192.1	.	.	.	.	.	.	.	.	.	.	C	17.88	3.497612	0.64186	.	.	ENSG00000114062	ENST00000232165;ENST00000356465;ENST00000397954;ENST00000438097;ENST00000428984	T;T;T;T	0.72942	-0.7;-0.7;-0.7;-0.7	5.57	4.65	0.58169	.	0.052477	0.64402	N	0.000001	T	0.79907	0.4527	M	0.64170	1.965	0.54753	D	0.999988	D;D	0.69078	0.997;0.996	P;D	0.63033	0.747;0.91	T	0.80113	-0.1518	10	0.44086	T	0.13	.	14.5343	0.67950	0.0:0.9295:0.0:0.0705	.	437;440	Q05086-3;Q05086	.;UBE3A_HUMAN	Q	437;437;440;417;417	ENSP00000232165:R437Q;ENSP00000381045:R440Q;ENSP00000411258:R417Q;ENSP00000401265:R417Q	ENSP00000232165:R437Q	R	-	2	0	UBE3A	23167104	1.000000	0.71417	0.995000	0.50966	0.981000	0.71138	4.995000	0.63908	1.367000	0.46095	0.460000	0.39030	CGA	.	.	.	none		0.383	UBE3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000434203.1	NM_000462		T	25616011	C	T	25616011	3	4	168	1	0	0	0	0	1	0	0	0	16891	884	31	1	1340	1	UBE3A	15	25616011	Missense_Mutation	SNP	C	TCGA-F9-A97G-01A-11D-A382-10		25616011	76915381	49	9932											
THBS1	7057	hgsc.bcm.edu	37	chr15	39880740	39880740	+	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	cttacagtcaatggaggctgGggtccttggtcaccatggga	8	10	14	9	0	2	0	2	0	0	0	3	2	3	2	2	6	1	1	2	6	2	2			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr15:39880740G>T	ENST00000260356.5	+	10	1650	c.1485G>T	c.(1483-1485)tgG>tgT	p.W495C		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	495	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)		ATGGAGGCTGGGGTCCTTGGT	0.498																																					p.W495C		Atlas-SNP	.											.	THBS1	106	.	0			c.G1485T						PASS	.						65	64	64					15																	39880740		2200	4297	6497	SO:0001583	missense	7057	exon10			AGGCTGGGGTCCT		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.1485G>T	chr15.hg19:g.39880740G>T	ENSP00000260356:p.Trp495Cys	121.0	0.0	.		155.0	34.0	.	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	hg19	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.116990	0.77323	.	.	ENSG00000137801	ENST00000260356	T	0.62788	0.0	5.87	5.87	0.94306	.	0.000000	0.33792	N	0.004554	D	0.87665	0.6234	H	0.97440	4.005	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.91112	0.4923	10	0.72032	D	0.01	-18.5379	20.1976	0.98245	0.0:0.0:1.0:0.0	.	495	P07996	TSP1_HUMAN	C	495	ENSP00000260356:W495C	ENSP00000260356:W495C	W	+	3	0	THBS1	37668032	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.872000	0.87187	2.772000	0.95346	0.655000	0.94253	TGG	.	.	.	none		0.498	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		T	39880740	G	T	39880740	3	4	168	1	0	0	0	0	1	0	0	0	15865	1241	43	4	1519	4	THBS1	15	39880740	Missense_Mutation	SNP	G	TCGA-F9-A97G-01A-11D-A382-10	14264729	39880740	62650652	50	9933											
PLA2G4F	255189	hgsc.bcm.edu	37	chr15	42445858	42445858	+	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	cacctgcagctcttgtgaatCctacatggagggggagggag	9	8	15	9	0	1	1	0	1	1	0	2	4	2	4	2	4	3	2	2	4	2	2			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr15:42445858C>T	ENST00000382396.4	-	5	537	c.451G>A	c.(451-453)Gat>Aat	p.D151N	PLA2G4F_ENST00000397272.3_Splice_Site_p.D151N			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	151					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)		TCTTGTGAATCCTACATGGAG	0.552																																					p.D151N		Atlas-SNP	.											.	PLA2G4F	75	.	0			c.G451A						PASS	.						58	59	59					15																	42445858		2203	4299	6502	SO:0001630	splice_region_variant	255189	exon5			GTGAATCCTACAT		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.451-1G>A	chr15.hg19:g.42445858C>T		55.0	0.0	.		73.0	21.0	.	NM_213600	Q6ZMC8	Missense_Mutation	SNP	ENST00000382396.4	hg19	CCDS32204.1	.	.	.	.	.	.	.	.	.	.	C	1.958	-0.439473	0.04636	.	.	ENSG00000168907	ENST00000290497;ENST00000397272;ENST00000382396;ENST00000357924;ENST00000443825	T;T	0.62639	0.01;0.01	5.02	3.11	0.35812	C2 calcium/lipid-binding domain, CaLB (1);	0.308062	0.27375	N	0.019650	T	0.50531	0.1621	L	0.47716	1.5	0.34402	D	0.695385	B	0.15930	0.015	B	0.14023	0.01	T	0.53315	-0.8456	10	0.20519	T	0.43	-14.1627	9.8096	0.40815	0.0:0.8299:0.0:0.1701	.	151	Q68DD2	PA24F_HUMAN	N	147;151;151;151;151	ENSP00000380442:D151N;ENSP00000371833:D151N	ENSP00000290497:D147N	D	-	1	0	PLA2G4F	40233150	0.888000	0.30383	0.829000	0.32907	0.013000	0.08279	1.256000	0.32921	0.770000	0.33336	-0.140000	0.14226	GAT	.	.	.	none		0.552	PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600	Missense_Mutation	T	42445858	C	T	42445858	5	4	168	1	0	0	0	0	0	0	1	0	12013	869	30	2	2162	2	PLA2G4F	15	42445858	Splice_Site	SNP	C	TCGA-F9-A97G-01A-11D-A382-10	2565118	42445858	60085534	51	9934											
CHTF18	63922	hgsc.bcm.edu	37	chr16	847004	847006	+	In_Frame_Del	DEL	TTG	TTG	-																															cgagggtctgctggggggcaTtggggagaaaggggtgcacc																								rs200430443	byFrequency	TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	TTG	TTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr16:847004_847006delTTG	ENST00000262315.9	+	20	2708_2710	c.2645_2647delTTG	c.(2644-2649)attggg>agg	p.882_883IG>R	CHTF18_ENST00000317063.6_In_Frame_Del_p.1091_1092IG>R|CHTF18_ENST00000455171.2_In_Frame_Del_p.910_911IG>R	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	882					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)				CTGGGGGGCATTGGGGAGAAAGG	0.65																																					p.882_882del		Atlas-Indel,Pindel	.											.	CHTF18	52	.	0			c.2644_2646del						PASS	.																																			SO:0001651	inframe_deletion	63922	exon20			.	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.2645_2647delTTG	chr16.hg19:g.847004_847006delTTG	ENSP00000262315:p.Ile882_Gly883delinsArg	120.0	0.0	0		113.0	14.0	0.123894	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	In_Frame_Del	DEL	ENST00000262315.9	hg19	CCDS45371.1																																																																																			.	.	.	none		0.65	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092		-	847006	TTG	-	847004	7	5	168	1	0	1	0	1	0	0	0	0	3416	1493	52	0	2723	0	CHTF18	16	847004	In_Frame_Del	DEL	TTG	TCGA-F9-A97G-01A-11D-A382-10		847004	89507749	52	9935											
C16orf91	283951	hgsc.bcm.edu	37	chr16	1470405	1470405	+	Missense_Mutation	SNP	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	cacgaggaagcagctgagggGcagcaccttccaccagggcc	10	3	14	14	1	0	1	0	1	0	0	1	3	1	2	4	4	3	4	4	4	1	1			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr16:1470405G>A	ENST00000442039.2	-	2	317	c.241C>T	c.(241-243)Ccc>Tcc	p.P81S	C16orf91_ENST00000563974.1_Missense_Mutation_p.P14S|C16orf91_ENST00000310355.1_Missense_Mutation_p.P238S	NM_001272051.1	NP_001258980.1	Q4G0I0	CSMT1_HUMAN	chromosome 16 open reading frame 91	81						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(1)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	11						CAGCTGAGGGGCAGCACCTTC	0.627																																					p.P81S		Atlas-SNP	.											.	C16orf91	19	.	0			c.C241T						PASS	.						103	97	99					16																	1470405		2199	4300	6499	SO:0001583	missense	283951	exon2			TGAGGGGCAGCAC	BC023590	CCDS61789.1	16p13.3	2012-10-10			ENSG00000174109	ENSG00000174109			27558	protein-coding gene	gene with protein product	"cattle cerebrum and skeletal muscle-specific protein 1 family member"						Standard	NM_001272051		Approved	gs103, CCSMST1	uc002clr.4	Q4G0I0		ENST00000442039.2:c.241C>T	chr16.hg19:g.1470405G>A	ENSP00000413100:p.Pro81Ser	121.0	0.0	.		142.0	19.0	.	NM_001272051	Q96RZ0	Missense_Mutation	SNP	ENST00000442039.2	hg19		.	.	.	.	.	.	.	.	.	.	G	17.57	3.422356	0.62622	.	.	ENSG00000174109	ENST00000442039;ENST00000310355	.	.	.	5.31	5.31	0.75309	.	0.000000	0.64402	D	0.000005	T	0.79003	0.4373	.	.	.	0.43756	D	0.996266	D	0.89917	1.0	D	0.91635	0.999	T	0.81210	-0.1036	8	0.66056	D	0.02	-23.2505	14.4962	0.67688	0.0:0.0:1.0:0.0	.	81	Q4G0I0	CSMT1_HUMAN	S	81;238	.	ENSP00000311390:P238S	P	-	1	0	C16orf91	1410406	1.000000	0.71417	0.994000	0.49952	0.062000	0.15995	4.723000	0.61965	2.492000	0.84095	0.655000	0.94253	CCC	.	.	.	none		0.627	C16orf91-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432502.1	NM_001010878		A	1470405	G	A	1470405	3	1	168	1	0	0	0	0	1	0	0	0	1846	1203	42	2	364	2	C16orf91	16	1470405	Missense_Mutation	SNP	G	TCGA-F9-A97G-01A-11D-A382-10	623401	1470405	88884348	53	9936											
TMEM132E	124842	hgsc.bcm.edu	37	chr17	32956193	32956193	+	Silent	SNP	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	gagctgacggtcattcagcgGgatgtgcaagccatcctgcc	8	8	13	12	2	2	1	2	1	0	0	3	3	3	2	3	2	5	2	3	2	1	1			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr17:32956193G>A	ENST00000321639.5	+	5	1366	c.1038G>A	c.(1036-1038)cgG>cgA	p.R346R		NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	346						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57				BRCA - Breast invasive adenocarcinoma(366;0.231)		TCATTCAGCGGGATGTGCAAG	0.592																																					p.R346R		Atlas-SNP	.											.	TMEM132E	122	.	0			c.G1038A						PASS	.						58	47	51					17																	32956193		2203	4300	6503	SO:0001819	synonymous_variant	124842	exon5			TCAGCGGGATGTG	BN000149	CCDS11283.1	17q12	2012-11-01			ENSG00000181291	ENSG00000181291			26991	protein-coding gene	gene with protein product							Standard	NM_207313		Approved		uc002hif.3	Q6IEE7	OTTHUMG00000132927	ENST00000321639.5:c.1038G>A	chr17.hg19:g.32956193G>A		83.0	0.0	.		97.0	23.0	.	NM_207313	Q8WUF4|Q8WVA5	Silent	SNP	ENST00000321639.5	hg19	CCDS11283.1																																																																																			.	.	.	none		0.592	TMEM132E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256440.2	NM_207313		A	32956193	G	A	32956193	2	1	168	1	0	0	0	0	0	0	0	1	16060	1219	43	2		2	TMEM132E	17	32956193	Silent	SNP	G	TCGA-F9-A97G-01A-11D-A382-10		32956193	48239017	54	9937											
XYLT2	64132	hgsc.bcm.edu	37	chr17	48433616	48433616	+	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	aagccacaggacttcctccgGctgcaggtgcttgcccgagg	7	7	13	14	2	0	0	0	0	0	0	2	2	2	1	4	4	4	3	4	4	1	2			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr17:48433616G>T	ENST00000017003.2	+	7	1525	c.1476G>T	c.(1474-1476)cgG>cgT	p.R492R	XYLT2_ENST00000507602.1_Silent_p.R492R	NM_022167.2	NP_071450.2	Q9H1B5	XYLT2_HUMAN	xylosyltransferase II	492					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)					ACTTCCTCCGGCTGCAGGTGC	0.607																																					p.R492R		Atlas-SNP	.											.	XYLT2	51	.	0			c.G1476T						PASS	.						51	49	50					17																	48433616		2203	4300	6503	SO:0001819	synonymous_variant	64132	exon7			CCTCCGGCTGCAG	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.1476G>T	chr17.hg19:g.48433616G>T		52.0	0.0	.		80.0	18.0	.	NM_022167	Q6UY41|Q86V00	Silent	SNP	ENST00000017003.2	hg19	CCDS11563.1																																																																																			.	.	.	none		0.607	XYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367046.1	NM_022167		T	48433616	G	T	48433616	2	4	168	1	0	0	0	0	0	0	0	1	17476	1190	42	4		4	XYLT2	17	48433616	Silent	SNP	G	TCGA-F9-A97G-01A-11D-A382-10	15477423	48433616	32761594	55	9938											
LRRC59	55379	hgsc.bcm.edu	37	chr17	48472322	48472322	+	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	cagtttattacaagacagatCcaggatggtggcctttggaa	12	11	11	7	0	0	2	0	0	0	2	1	4	1	4	2	4	1	1	2	4	4	4			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr17:48472322C>G	ENST00000225972.7	-	2	368	c.133G>C	c.(133-135)Gat>Cat	p.D45H	RP1-117B12.4_ENST00000511627.1_RNA	NM_018509.3	NP_060979.2	Q96AG4	LRC59_HUMAN	leucine rich repeat containing 59	45						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	13	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)			CAAGACAGATCCAGGATGGTG	0.468																																					p.D45H		Atlas-SNP	.											.	LRRC59	23	.	0			c.G133C						PASS	.						114	95	101					17																	48472322		2203	4300	6503	SO:0001583	missense	55379	exon2			ACAGATCCAGGAT	AK025328	CCDS11566.1	17q21.33	2014-02-12	2006-01-12		ENSG00000108829	ENSG00000108829			28817	protein-coding gene	gene with protein product		614854				12477932	Standard	NM_018509		Approved	PRO1855, FLJ21675	uc002iqt.3	Q96AG4	OTTHUMG00000162079	ENST00000225972.7:c.133G>C	chr17.hg19:g.48472322C>G	ENSP00000225972:p.Asp45His	172.0	0.0	.		207.0	36.0	.	NM_018509	B2RE83|D3DTX8|Q9P189	Missense_Mutation	SNP	ENST00000225972.7	hg19	CCDS11566.1	.	.	.	.	.	.	.	.	.	.	C	30	5.055916	0.93793	.	.	ENSG00000108829	ENST00000225972	T	0.31510	1.49	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.58538	0.2129	M	0.76433	2.335	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.60979	-0.7155	10	0.62326	D	0.03	.	19.1981	0.93698	0.0:1.0:0.0:0.0	.	45	Q96AG4	LRC59_HUMAN	H	45	ENSP00000225972:D45H	ENSP00000225972:D45H	D	-	1	0	LRRC59	45827321	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.589000	0.82641	2.615000	0.88500	0.655000	0.94253	GAT	.	.	.	none		0.468	LRRC59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367117.2	NM_018509		G	48472322	C	G	48472322	3	3	168	1	0	0	0	0	1	0	0	0	9022	855	30	4	814	4	LRRC59	17	48472322	Missense_Mutation	SNP	C	TCGA-F9-A97G-01A-11D-A382-10	38706	48472322	32722888	56	9939											
SMAD4	4089	hgsc.bcm.edu	37	chr18	48575090	48575090	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggatttcctcatgtgatctAtgcccgtctctggaggtggc	6	13	12	10	1	3	1	1	1	2	0	5	3	4	3	2	4	1	0	2	4	1	2			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr18:48575090A>G	ENST00000342988.3	+	3	822	c.284A>G	c.(283-285)tAt>tGt	p.Y95C	SMAD4_ENST00000452201.2_Missense_Mutation_p.Y95C|SMAD4_ENST00000398417.2_Missense_Mutation_p.Y95C|SMAD4_ENST00000588745.1_Missense_Mutation_p.Y95C|RP11-729L2.2_ENST00000590722.2_3'UTR	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	95	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(4)|p.Y95S(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		CATGTGATCTATGCCCGTCTC	0.368																																					p.Y95C		Atlas-SNP	.											SMAD4,colon,carcinoma,+1,1	SMAD4	822	.	41	Whole gene deletion(36)|Unknown(4)|Substitution - Missense(1)	pancreas(27)|large_intestine(3)|stomach(3)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)|NS(1)	c.A284G						PASS	.						155	142	146					18																	48575090		2203	4300	6503	SO:0001583	missense	4089	exon3			TGATCTATGCCCG	U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"SMADs"	6770	protein-coding gene	gene with protein product		600993	"MAD, mothers against decapentaplegic homolog 4 (Drosophila)", "SMAD, mothers against DPP homolog 4 (Drosophila)"	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.284A>G	chr18.hg19:g.48575090A>G	ENSP00000341551:p.Tyr95Cys	140.0	0.0	.		130.0	28.0	.	NM_005359	A8K405	Missense_Mutation	SNP	ENST00000342988.3	hg19	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.409676	0.83340	.	.	ENSG00000141646	ENST00000452201;ENST00000342988;ENST00000544926;ENST00000398417	T;T;T	0.72615	-0.67;-0.67;-0.67	5.32	5.32	0.75619	MAD homology, MH1 (3);MAD homology 1, Dwarfin-type (2);	0.000000	0.85682	D	0.000000	D	0.83294	0.5223	M	0.75777	2.31	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85571	0.1234	10	0.87932	D	0	.	14.2563	0.66053	1.0:0.0:0.0:0.0	.	95	Q13485	SMAD4_HUMAN	C	95	ENSP00000409551:Y95C;ENSP00000341551:Y95C;ENSP00000381452:Y95C	ENSP00000341551:Y95C	Y	+	2	0	SMAD4	46829088	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.309000	0.96252	1.992000	0.58205	0.477000	0.44152	TAT	.	.	.	none		0.368	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		G	48575090	A	G	48575090	3	3	168	1	0	0	0	0	1	0	0	0	14773	449	16	3	290	3	SMAD4	18	48575090	Missense_Mutation	SNP	A	TCGA-F9-A97G-01A-11D-A382-10		48575090	29502158	57	9940											
ST8SIA3	51046	hgsc.bcm.edu	37	chr18	55021740	55021740	+	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	gtggaaatttaatcggacagCgtttttacatcaaaggtagg	13	12	11	5	2	1	0	1	0	0	0	2	2	1	2	0	4	2	2	0	4	5	6			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr18:55021740C>T	ENST00000324000.3	+	2	2321	c.287C>T	c.(286-288)gCg>gTg	p.A96V		NM_015879.2	NP_056963.2	O43173	SIA8C_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	96					cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycoprotein metabolic process (GO:0009100)|glycosphingolipid biosynthetic process (GO:0006688)|N-glycan processing (GO:0006491)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(16)|prostate(1)|skin(3)	36				READ - Rectum adenocarcinoma(59;0.19)|Colorectal(16;0.205)		AATCGGACAGCGTTTTTACAT	0.383																																					p.A96V		Atlas-SNP	.											.	ST8SIA3	73	.	0			c.C287T						PASS	.						103	102	103					18																	55021740		2203	4300	6503	SO:0001583	missense	51046	exon2			GGACAGCGTTTTT	AF004668	CCDS32834.1	18q21.31	2013-03-01	2005-02-07	2005-02-07	ENSG00000177511	ENSG00000177511		"Sialyltransferases"	14269	protein-coding gene	gene with protein product	"ST8Sia III"	609478	"sialyltransferase 8C (alpha2,3Galbeta1,4GlcNAcalpha 2,8-sialyltransferase)"	SIAT8C			Standard	NM_015879		Approved		uc002lgn.3	O43173	OTTHUMG00000180101	ENST00000324000.3:c.287C>T	chr18.hg19:g.55021740C>T	ENSP00000320431:p.Ala96Val	110.0	0.0	.		98.0	27.0	.	NM_015879	A8K0F2|Q6B085|Q9NS41	Missense_Mutation	SNP	ENST00000324000.3	hg19	CCDS32834.1	.	.	.	.	.	.	.	.	.	.	C	10.14	1.269186	0.23221	.	.	ENSG00000177511	ENST00000541833;ENST00000324000	T	0.48836	0.8	4.88	4.88	0.63580	.	0.101382	0.64402	D	0.000002	T	0.38081	0.1027	L	0.52573	1.65	0.80722	D	1	P	0.41710	0.76	B	0.30251	0.113	T	0.33548	-0.9864	10	0.30078	T	0.28	-29.0489	16.1712	0.81817	0.0:1.0:0.0:0.0	.	96	O43173	SIA8C_HUMAN	V	203;96	ENSP00000320431:A96V	ENSP00000320431:A96V	A	+	2	0	ST8SIA3	53172738	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.952000	0.75989	2.409000	0.81822	0.467000	0.42956	GCG	.	.	.	none		0.383	ST8SIA3-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449765.1	NM_015879		T	55021740	C	T	55021740	3	4	168	1	0	0	0	0	1	0	0	0	15245	768	27	1	293	1	ST8SIA3	18	55021740	Missense_Mutation	SNP	C	TCGA-F9-A97G-01A-11D-A382-10	6446650	55021740	23055508	58	9941											
ZFR2	23217	hgsc.bcm.edu	37	chr19	3827588	3827588	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggctcccgttgggctgcaCgcctgtcttctgggccgcct	1	10	14	16	4	2	0	0	0	2	0	3	0	3	0	4	3	1	4	4	3	0	2			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr19:3827588C>T	ENST00000262961.4	-	6	926	c.916G>A	c.(916-918)Gtg>Atg	p.V306M		NM_015174.1	NP_055989.1	Q9UPR6	ZFR2_HUMAN	zinc finger RNA binding protein 2	306							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00514)|STAD - Stomach adenocarcinoma(1328;0.19)		TTGGGCTGCACGCCTGTCTTC	0.701																																					p.V306M		Atlas-SNP	.											.	ZFR2	63	.	0			c.G916A						PASS	.						18	20	19					19																	3827588		1963	4109	6072	SO:0001583	missense	23217	exon6			GCTGCACGCCTGT	AB029009	CCDS45921.1, CCDS45922.1	19p13.3	2012-10-05	2008-03-25	2008-03-25	ENSG00000105278	ENSG00000105278			29189	protein-coding gene	gene with protein product			"KIAA1086"	KIAA1086		10470851	Standard	NM_015174		Approved		uc002lyw.2	Q9UPR6	OTTHUMG00000180918	ENST00000262961.4:c.916G>A	chr19.hg19:g.3827588C>T	ENSP00000262961:p.Val306Met	111.0	0.0	.		169.0	25.0	.	NM_015174		Missense_Mutation	SNP	ENST00000262961.4	hg19	CCDS45921.1	.	.	.	.	.	.	.	.	.	.	C	4.450	0.083351	0.08533	.	.	ENSG00000105278	ENST00000262961;ENST00000438164	T;T	0.15017	3.23;2.46	3.12	-6.24	0.02046	.	1.917410	0.03859	U	0.273735	T	0.17959	0.0431	M	0.61703	1.905	0.26249	N	0.978759	B	0.16166	0.016	B	0.14578	0.011	T	0.17684	-1.0361	10	0.44086	T	0.13	.	8.8172	0.35002	0.0:0.5586:0.2486:0.1928	.	306	Q9UPR6	ZFR2_HUMAN	M	306	ENSP00000262961:V306M;ENSP00000388974:V306M	ENSP00000262961:V306M	V	-	1	0	ZFR2	3778588	0.000000	0.05858	0.000000	0.03702	0.414000	0.31173	-0.677000	0.05215	-2.453000	0.00541	-0.873000	0.02984	GTG	.	.	.	none		0.701	ZFR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453648.2	NM_015174		T	3827588	C	T	3827588	3	4	168	1	0	0	0	0	1	0	0	0	17672	536	19	1	1959	1	ZFR2	19	3827588	Missense_Mutation	SNP	C	TCGA-F9-A97G-01A-11D-A382-10		3827588	55301395	59	9942											
AP1M2	10053	hgsc.bcm.edu	37	chr19	10692495	10692495	+	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	tcgtccagcaactcgtagacGatgacaaagttgtcccggat	11	9	10	11	4	0	2	0	1	0	1	4	4	2	3	2	1	2	3	2	1	3	2			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr19:10692495G>C	ENST00000250244.6	-	4	409	c.327C>G	c.(325-327)atC>atG	p.I109M	AP1M2_ENST00000590923.1_Missense_Mutation_p.I109M	NM_005498.4	NP_005489.2	Q9Y6Q5	AP1M2_HUMAN	adaptor-related protein complex 1, mu 2 subunit	109					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|protein targeting (GO:0006605)|regulation of defense response to virus by virus (GO:0050690)|vesicle targeting (GO:0006903)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)				endometrium(4)|large_intestine(1)|lung(1)|ovary(2)|urinary_tract(1)	9			Epithelial(33;1.58e-05)|all cancers(31;6.36e-05)			ACTCGTAGACGATGACAAAGT	0.567																																					p.I109M		Atlas-SNP	.											.	AP1M2	35	.	0			c.C327G						PASS	.						79	80	79					19																	10692495		2203	4300	6503	SO:0001583	missense	10053	exon4			GTAGACGATGACA	AF020797	CCDS45964.1	19p13.2	2008-10-07				ENSG00000129354			558	protein-coding gene	gene with protein product		607309				10338135	Standard	NM_005498		Approved	HSMU1B, mu2, AP1-mu2	uc002mpc.3	Q9Y6Q5		ENST00000250244.6:c.327C>G	chr19.hg19:g.10692495G>C	ENSP00000250244:p.Ile109Met	59.0	0.0	.		98.0	18.0	.	NM_005498	B2RDV5|Q9BSI8	Missense_Mutation	SNP	ENST00000250244.6	hg19	CCDS45964.1	.	.	.	.	.	.	.	.	.	.	g	16.45	3.126621	0.56721	.	.	ENSG00000129354	ENST00000250244	T	0.65732	-0.17	4.94	-3.21	0.05140	Longin-like (1);AP complex, mu/sigma subunit (1);	0.058938	0.64402	D	0.000002	T	0.74997	0.3790	M	0.89534	3.04	0.42849	D	0.994078	P;P	0.51449	0.805;0.945	P;P	0.59288	0.573;0.855	T	0.78370	-0.2230	10	0.72032	D	0.01	-35.9898	10.6557	0.45673	0.7224:0.0:0.2776:0.0	.	109;109	Q9Y6Q5-2;Q9Y6Q5	.;AP1M2_HUMAN	M	109	ENSP00000250244:I109M	ENSP00000250244:I109M	I	-	3	3	AP1M2	10553495	0.000000	0.05858	0.895000	0.35142	0.907000	0.53573	-1.827000	0.01704	-0.263000	0.09378	-0.350000	0.07774	ATC	.	.	.	none		0.567	AP1M2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452034.1			C	10692495	G	C	10692495	3	2	168	1	0	0	0	0	1	0	0	0	735	1048	37	4	980	4	AP1M2	19	10692495	Missense_Mutation	SNP	G	TCGA-F9-A97G-01A-11D-A382-10	6864907	10692495	48436488	60	9943											
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-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	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_ENST00000591462.1_Silent_p.E322E|PRKCSH_ENST00000587327.1_Silent_p.E322E|PRKCSH_ENST00000592741.1_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	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	chr19.hg19:g.11558370G>A		112.0	1.0	.		135.0	6.0	.	NM_001001329	A8K318|Q96BU9|Q96D06|Q9P0W9	Silent	SNP	ENST00000589838.1	hg19	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	168	1	0	0	0	0	0	0	0	1	12526	991	35	2		2	PRKCSH	19	11558370	Silent	SNP	G	TCGA-F9-A97G-01A-11D-A382-10	865875	11558370	47570613	61	9944											
FBXW9	84261	hgsc.bcm.edu	37	chr19	12805525	12805525	+	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	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-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr19:12805525G>T	ENST00000380339.3	-	3	597	c.561C>A	c.(559-561)ctC>ctA	p.L187L	FBXW9_ENST00000393261.3_Silent_p.L187L|FBXW9_ENST00000587955.1_Silent_p.L177L|FBXW9_ENST00000544494.1_De_novo_Start_OutOfFrame			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																																					p.L187L		Atlas-SNP	.											.	FBXW9	30	.	0			c.C561A						PASS	.						62	68	66					19																	12805525		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>A	chr19.hg19:g.12805525G>T		92.0	0.0	.		137.0	26.0	.	NM_032301	B3KVP7|Q9BT89	Silent	SNP	ENST00000380339.3	hg19																																																																																				.	G|0.921;C|0.079	.	alt		0.632	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301		T	12805525	G	T	12805525	2	4	168	1	0	0	0	0	0	0	0	1	5778	929	33	4		4	FBXW9	19	12805525	Silent	SNP	G	TCGA-F9-A97G-01A-11D-A382-10	1247155	12805525	46323458	62	9945											
PRNP	5621	hgsc.bcm.edu	37	chr20	4680620	4680620	+	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	ctttcctcatcttcctgataGtgggatgaggaaggtcttcc	7	14	10	10	0	3	2	1	2	2	0	6	4	6	4	3	3	0	0	3	3	2	4			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr20:4680620G>T	ENST00000379440.4	+	2	1041	c.754G>T	c.(754-756)Gtg>Ttg	p.V252L	PRNP_ENST00000430350.2_Missense_Mutation_p.V252L	NM_000311.3|NM_001080121.1|NM_001080122.1|NM_001080123.1|NM_001271561.1|NM_183079.2	NP_000302.1|NP_001073590.1|NP_001073591.1|NP_001073592.1|NP_001258490.1|NP_898902.1	F7VJQ1	APRIO_HUMAN	prion protein	0						integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)				central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	14						CTTCCTGATAGTGGGATGAGG	0.502																																					p.V252L		Atlas-SNP	.											.	PRNP	31	.	0			c.G754T						PASS	.						43	41	42					20																	4680620		2203	4300	6503	SO:0001583	missense	5621	exon2			CTGATAGTGGGAT	M13899	CCDS13080.1	20p13	2014-06-05	2008-07-28		ENSG00000171867	ENSG00000171867		"CD molecules"	9449	protein-coding gene	gene with protein product	"Creutzfeldt-Jakob disease", "Gerstmann-Strausler-Scheinker syndrome", "fatal familial insomnia", "p27-30"	176640	"prion protein (p27-30)"	PRIP, GSS, CJD			Standard	NM_000311		Approved	CD230, PRP, AltPrP	uc002wkw.4	F7VJQ1	OTTHUMG00000031786	ENST00000379440.4:c.754G>T	chr20.hg19:g.4680620G>T	ENSP00000368752:p.Val252Leu	133.0	0.0	.		167.0	33.0	.	NM_000311		Missense_Mutation	SNP	ENST00000379440.4	hg19	CCDS13080.1	.	.	.	.	.	.	.	.	.	.	G	17.58	3.424622	0.62733	.	.	ENSG00000171867	ENST00000379440;ENST00000430350;ENST00000444805	D;D	0.91894	-2.93;-2.93	5.1	5.1	0.69264	.	0.293440	0.24278	N	0.039928	D	0.94725	0.8298	L	0.57536	1.79	0.33382	D	0.575028	D;D	0.63046	0.992;0.992	D;D	0.77004	0.989;0.989	D	0.96382	0.9282	10	0.87932	D	0	-9.4323	13.8882	0.63721	0.0:0.0:1.0:0.0	.	252;284	P04156;O75942	PRIO_HUMAN;.	L	252;252;191	ENSP00000368752:V252L;ENSP00000399376:V252L	ENSP00000368752:V252L	V	+	1	0	PRNP	4628620	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	4.706000	0.61845	2.654000	0.90174	0.655000	0.94253	GTG	.	.	.	none		0.502	PRNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077820.2	NM_000311		T	4680620	G	T	4680620	3	4	168	1	0	0	0	0	1	0	0	0	12554	1029	36	4	756	4	PRNP	20	4680620	Missense_Mutation	SNP	G	TCGA-F9-A97G-01A-11D-A382-10		4680620	58344900	63	9946											
TRIOBP	11078	hgsc.bcm.edu	37	chr22	38119756	38119756	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctcccaacagaaccactcAacgagagaattccagaacat	16	6	5	14	1	2	3	1	0	1	3	4	5	3	3	3	0	4	0	3	0	5	1	rs71322688|rs67890459|rs201160789|rs77530465|rs55745992	byFrequency	TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr22:38119756A>G	ENST00000406386.3	+	7	1448	c.1193A>G	c.(1192-1194)cAa>cGa	p.Q398R		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	398					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.Q398R(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					AGAACCACTCAACGAGAGAAT	0.552																																					p.Q398R		Atlas-SNP	.											TRIOBP_ENST00000344404,NS,carcinoma,0,1	TRIOBP	262	.	1	Substitution - Missense(1)	lung(1)	c.A1193G						PASS	.						117	100	106					22																	38119756		1849	3515	5364	SO:0001583	missense	11078	exon7			CCACTCAACGAGA	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"Pleckstrin homology (PH) domain containing"	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1193A>G	chr22.hg19:g.38119756A>G	ENSP00000384312:p.Gln398Arg	73.0	0.0	.		83.0	6.0	.	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	hg19	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	A	7.038	0.561918	0.13498	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.33216	1.42	2.53	2.53	0.30540	.	.	.	.	.	T	0.27629	0.0679	L	0.44542	1.39	0.09310	N	0.99999	P	0.47604	0.898	P	0.47402	0.546	T	0.07578	-1.0765	9	0.21540	T	0.41	.	5.6825	0.17784	0.7186:0.2814:0.0:0.0	.	398	Q9H2D6	TARA_HUMAN	R	398	ENSP00000384312:Q398R	ENSP00000384312:Q398R	Q	+	2	0	TRIOBP	36449702	0.002000	0.14202	0.064000	0.19789	0.071000	0.16799	0.831000	0.27476	1.186000	0.42985	0.165000	0.16767	CAA	.	.	.	alt		0.552	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			G	38119756	A	G	38119756	3	3	168	1	0	0	0	0	1	0	0	0	16565	130	5	3	1211	3	TRIOBP	22	38119756	Missense_Mutation	SNP	A	TCGA-F9-A97G-01A-11D-A382-10		38119756	13184810	64	9947											
SHANK3	85358	hgsc.bcm.edu	37	chr22	51159397	51159397	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccccggcgcggatctgccaTccctacagccctcccgctcc	4	6	8	23	4	1	0	0	0	1	0	4	1	4	1	7	2	3	1	7	2	1	1			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chr22:51159397T>C	ENST00000414786.2	+	21	3321	c.3094T>C	c.(3094-3096)Tcc>Ccc	p.S1032P	SHANK3_ENST00000262795.3_Missense_Mutation_p.S1062P|SHANK3_ENST00000445220.2_Missense_Mutation_p.S1048P			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	1046					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)		GGATCTGCCATCCCTACAGCC	0.761																																					p.S1032P		Atlas-SNP	.											.	SHANK3	96	.	0			c.T3094C						PASS	.						8	11	10					22																	51159397		1831	3948	5779	SO:0001583	missense	85358	exon21			CTGCCATCCCTAC	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.3094T>C	chr22.hg19:g.51159397T>C	ENSP00000464552:p.Ser1032Pro	57.0	0.0	.		49.0	14.0	.	NM_033517	D7UT47|Q8TET3	Missense_Mutation	SNP	ENST00000414786.2	hg19		.	.	.	.	.	.	.	.	.	.	T	13.67	2.306121	0.40795	.	.	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.69175	-0.38;-0.38	4.24	4.24	0.50183	.	0.119241	0.64402	D	0.000016	T	0.73225	0.3560	M	0.63428	1.95	0.25860	N	0.983833	D;B;D	0.65815	0.963;0.013;0.995	P;B;P	0.56278	0.63;0.012;0.795	T	0.67090	-0.5758	10	0.62326	D	0.03	.	11.3209	0.49421	0.0:0.0:0.0:1.0	.	1046;1047;1062	D7UT47;Q9BYB0;F2Z3L0	.;SHAN3_HUMAN;.	P	1062;1048	ENSP00000442518:S1062P;ENSP00000446078:S1048P	ENSP00000442518:S1062P	S	+	1	0	SHANK3	49506263	1.000000	0.71417	0.988000	0.46212	0.602000	0.36980	3.791000	0.55469	1.563000	0.49615	0.260000	0.18958	TCC	.	.	.	none		0.761	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420		C	51159397	T	C	51159397	3	2	168	1	0	0	0	0	1	0	0	0	14279	1435	50	3	3270	3	SHANK3	22	51159397	Missense_Mutation	SNP	T	TCGA-F9-A97G-01A-11D-A382-10	13039641	51159397	145169	65	9948											
SLC16A2	6567	hgsc.bcm.edu	37	chrX	73641736	73641736	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acggtagagacccgcggcacCgcgcgcggcttccagcctcc	6	4	13	18	7	0	1	0	0	0	1	2	2	2	1	5	3	1	3	5	3	1	2			TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chrX:73641736C>T	ENST00000587091.1	+	1	441	c.264C>T	c.(262-264)acC>acT	p.T88T	SLC16A2_ENST00000276033.5_Silent_p.T162T	NM_006517.4	NP_006508.2	P36021	MOT8_HUMAN	solute carrier family 16, member 2 (thyroid hormone transporter)	88					monocarboxylic acid transport (GO:0015718)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)|transporter activity (GO:0005215)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|skin(2)	21					L-Leucine(DB00149)|L-Tryptophan(DB00150)|L-Tyrosine(DB00135)|Levothyroxine(DB00451)|Liotrix(DB01583)|Pyruvic acid(DB00119)	CCCGCGGCACCGCGCGCGGCT	0.692																																					p.T88T		Atlas-SNP	.											.	SLC16A2	54	.	0			c.C264T						PASS	.						13	15	14					X																	73641736		2187	4269	6456	SO:0001819	synonymous_variant	6567	exon1			CGGCACCGCGCGC		CCDS14426.1, CCDS14426.2	Xq13.2	2013-05-22	2012-03-20		ENSG00000147100	ENSG00000147100		"Solute carriers"	10923	protein-coding gene	gene with protein product		300095	"solute carrier family 16 (monocarboxylic acid transporters), member 2 (putative transporter)", "Allan-Herndon-Dudley syndrome", "solute carrier family 16 (monocarboxylic acid transporters), member 2", "mental retardation, X-linked 22", "solute carrier family 16, member 2 (monocarboxylic acid transporter 8)"	DXS128, AHDS, MRX22		7981683, 12871948, 15889350	Standard	NM_006517		Approved	XPCT, MCT8, MCT7	uc031tjy.1	P36021	OTTHUMG00000021857	ENST00000587091.1:c.264C>T	chrX.hg19:g.73641736C>T		72.0	0.0	.		110.0	37.0	.	NM_006517	Q7Z797	Silent	SNP	ENST00000587091.1	hg19	CCDS14426.2																																																																																			.	.	.	none		0.692	SLC16A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057266.3			T	73641736	C	T	73641736	2	4	168	1	0	0	0	0	0	0	0	1	14421	639	23	1		1	SLC16A2	23	73641736	Silent	SNP	C	TCGA-F9-A97G-01A-11D-A382-10		73641736	81628824	66	9949											
COL4A6	1288	hgsc.bcm.edu	37	chrX	107453231	107453231	+	Frame_Shift_Del	DEL	C	C	-																															cagtccaggcagcccaggatCcccctgagaaacaaaggcag																										TCGA-F9-A97G-01A-11D-A382-10	TCGA-F9-A97G-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b01862bd-0a0c-4961-a583-54646cad74e8	2cbd3338-65da-4ceb-9181-cf4bb8c86bc9	g.chrX:107453231delC	ENST00000372216.4	-	8	617	c.517delG	c.(517-519)gatfs	p.D173fs	COL4A6_ENST00000394872.2_Intron|COL4A6_ENST00000538570.1_Frame_Shift_Del_p.D172fs|COL4A6_ENST00000334504.7_Frame_Shift_Del_p.D172fs|COL4A6_ENST00000545689.1_Frame_Shift_Del_p.D172fs	NM_001847.2	NP_001838.2	Q14031	CO4A6_HUMAN	collagen, type IV, alpha 6	173	Triple-helical region.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(41)|ovary(7)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	92						AGCCCAGGATCCCCCTGAGAA	0.388									Alport syndrome with Diffuse Leiomyomatosis																												p.D173fs	Melanoma(87;1895 1945 2589 7165)	Atlas-Indel,Pindel	.											.	COL4A6	270	.	0			c.518delA						PASS	.						106	97	100					X																	107453231		2203	4300	6503	SO:0001589	frameshift_variant	1288	exon8	Familial Cancer Database		.	U04845	CCDS14541.1, CCDS14542.1, CCDS76008.1, CCDS76009.1, CCDS76010.1	Xq22	2014-09-17			ENSG00000197565	ENSG00000197565		"Collagens"	2208	protein-coding gene	gene with protein product		303631				8356449	Standard	NM_033641		Approved		uc004env.4	Q14031	OTTHUMG00000022179	ENST00000372216.4:c.517delG	chrX.hg19:g.107453231delC	ENSP00000361290:p.Asp173fs	522.0	0.0	0		621.0	271.0	0.436393	NM_001847	Q12823|Q14053|Q5JYH6|Q5JYH8|Q9NQM5|Q9NTX3|Q9UJ76|Q9UMG6|Q9Y4L4	Frame_Shift_Del	DEL	ENST00000372216.4	hg19	CCDS14541.1																																																																																			.	.	.	none		0.388	COL4A6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057875.2			-	107453231	C	-	107453231	7	5	168	1	0	1	0	1	0	0	0	0	3697	855	30	0	4710	0	COL4A6	23	107453231	Frame_Shift_Del	DEL	C	TCGA-F9-A97G-01A-11D-A382-10	33811495	107453231	47817329	67	9950											
ZNF684	127396	hgsc.bcm.edu	37	chr1	41012446	41012446	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tagacttacttaaatataatAgaagttatactgtagaaaac	19	13	5	4	0	0	3	0	0	0	3	0	3	0	3	0	0	3	2	0	0	13	9			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr1:41012446A>G	ENST00000372699.3	+	5	702	c.451A>G	c.(451-453)Aga>Gga	p.R151G	ZNF684_ENST00000493756.1_3'UTR	NM_152373.3	NP_689586.3	Q5T5D7	ZN684_HUMAN	zinc finger protein 684	151					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(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)			TAAATATAATAGAAGTTATAC	0.299																																					p.R151G		Atlas-SNP	.											.	ZNF684	37	.	0			c.A451G						PASS	.						35	39	38					1																	41012446		2197	4296	6493	SO:0001583	missense	127396	exon5			TATAATAGAAGTT		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.451A>G	chr1.hg19:g.41012446A>G	ENSP00000361784:p.Arg151Gly	40.0	0.0	.		50.0	35.0	.	NM_152373	Q2NKY4	Missense_Mutation	SNP	ENST00000372699.3	hg19	CCDS454.1	.	.	.	.	.	.	.	.	.	.	A	1.875	-0.459201	0.04508	.	.	ENSG00000117010	ENST00000372699	T	0.05717	3.4	3.87	0.211	0.15236	.	0.866547	0.09619	N	0.777770	T	0.06234	0.0161	L	0.41492	1.28	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37337	-0.9710	10	0.66056	D	0.02	.	7.0072	0.24844	0.6969:0.0:0.3031:0.0	.	151	Q5T5D7	ZN684_HUMAN	G	151	ENSP00000361784:R151G	ENSP00000361784:R151G	R	+	1	2	ZNF684	40785033	0.004000	0.15560	0.000000	0.03702	0.007000	0.05969	0.763000	0.26517	-0.060000	0.13132	-0.326000	0.08463	AGA	.	.	.	none		0.299	ZNF684-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019260.3	NM_152373		G	41012446	A	G	41012446	3	3	169	1	0	0	0	0	1	0	0	0	18103	412	15	3	465	3	ZNF684	1	41012446	Missense_Mutation	SNP	A	TCGA-G7-6789-01A-11D-1961-08		41012446	208238175	1	9951											
TNNI3K	100526835	hgsc.bcm.edu	37	chr1	74905226	74905226	+	Missense_Mutation	SNP	T	T	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	gcagtgcactcggtacaccaTcaaagcagatgtcttcagct	11	9	9	12	1	3	1	2	0	1	1	4	1	3	1	1	1	4	5	1	1	2	2			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr1:74905226T>G	ENST00000370899.3	+	22	2271	c.2234T>G	c.(2233-2235)aTc>aGc	p.I745S	FPGT-TNNI3K_ENST00000557284.2_Missense_Mutation_p.I758S|TNNI3K_ENST00000370891.2_Missense_Mutation_p.I745S|TNNI3K_ENST00000326637.3_Missense_Mutation_p.I644S	NM_001199327.1	NP_001186256			FPGT-TNNI3K readthrough																		CGGTACACCATCAAAGCAGAT	0.478																																					p.I745S		Atlas-SNP	.											.	.	.	.	0			c.T2234G						PASS	.						164	136	145					1																	74905226		2203	4300	6503	SO:0001583	missense	100526835	exon22			ACACCATCAAAGC			1p31.3	2014-03-14			ENSG00000259030	ENSG00000259030			42952	other	readthrough							Standard	NM_001112808		Approved		uc001dge.2		OTTHUMG00000166281	ENST00000370899.3:c.2234T>G	chr1.hg19:g.74905226T>G	ENSP00000359936:p.Ile745Ser	87.0	0.0	.		70.0	26.0	.	NM_001199327		Missense_Mutation	SNP	ENST00000370899.3	hg19		.	.	.	.	.	.	.	.	.	.	T	10.84	1.464750	0.26335	.	.	ENSG00000259030;ENSG00000259030;ENSG00000116783;ENSG00000116783	ENST00000370899;ENST00000557284;ENST00000370891;ENST00000326637	D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53	5.74	5.74	0.90152	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.056318	0.64402	D	0.000001	T	0.41328	0.1154	N	0.03983	-0.305	0.42989	D	0.994482	B;P;B	0.37276	0.183;0.589;0.372	B;B;B	0.32677	0.131;0.15;0.114	T	0.58451	-0.7634	10	0.08837	T	0.75	.	16.0467	0.80725	0.0:0.0:0.0:1.0	.	644;745;745	Q59H18;Q59H18-1;Q59H18-4	TNI3K_HUMAN;.;.	S	745;745;745;644	ENSP00000359936:I745S;ENSP00000450895:I745S;ENSP00000359928:I745S;ENSP00000322251:I644S	ENSP00000322251:I644S	I	+	2	0	RP11-653A5.2;AC093158.1	74677814	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	5.774000	0.68906	2.197000	0.70478	0.454000	0.30748	ATC	.	.	.	none		0.478	FPGT-TNNI3K-003	NOVEL	basic|appris_candidate|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000026438.3			G	74905226	T	G	74905226	3	3	169	1	0	0	0	0	1	0	0	0	16341	1435	50	5	2364	5	TNNI3K	1	74905226	Missense_Mutation	SNP	T	TCGA-G7-6789-01A-11D-1961-08	33892780	74905226	174345395	2	9952											
TDRD5	163589	hgsc.bcm.edu	37	chr1	179609042	179609042	+	Missense_Mutation	SNP	A	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	atgttttattcagccgggacAtctctgttgtgtaaggattt	8	17	10	6	1	2	0	1	0	1	0	3	2	2	2	1	2	1	3	1	2	2	6			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr1:179609042A>C	ENST00000367614.1	+	10	1948	c.1589A>C	c.(1588-1590)cAt>cCt	p.H530P	TDRD5_ENST00000294848.8_Missense_Mutation_p.H530P|TDRD5_ENST00000444136.1_Missense_Mutation_p.H530P	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	530	Tudor. {ECO:0000255|PROSITE- ProRule:PRU00211}.				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						CAGCCGGGACATCTCTGTTGT	0.418																																					p.H530P		Atlas-SNP	.											.	TDRD5	149	.	0			c.A1589C						PASS	.						206	197	200					1																	179609042		2203	4300	6503	SO:0001583	missense	163589	exon10			CGGGACATCTCTG	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.1589A>C	chr1.hg19:g.179609042A>C	ENSP00000356586:p.His530Pro	207.0	0.0	.		325.0	51.0	.	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	hg19	CCDS1332.1	.	.	.	.	.	.	.	.	.	.	A	18.16	3.562855	0.65538	.	.	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136	T;T;T	0.08984	3.03;3.03;3.03	5.33	4.19	0.49359	Tudor subgroup (1);Maternal tudor protein (1);Tudor domain (1);	0.062123	0.64402	D	0.000003	T	0.16727	0.0402	L	0.32530	0.975	0.35819	D	0.824489	D;D	0.76494	0.999;0.999	D;D	0.73380	0.977;0.98	T	0.09122	-1.0689	10	0.54805	T	0.06	-11.2483	10.2602	0.43423	0.9209:0.0:0.0791:0.0	.	530;530	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	P	530	ENSP00000356586:H530P;ENSP00000294848:H530P;ENSP00000406052:H530P	ENSP00000294848:H530P	H	+	2	0	TDRD5	177875665	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.266000	0.51569	0.854000	0.35336	0.533000	0.62120	CAT	.	.	.	none		0.418	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		C	179609042	A	C	179609042	3	2	169	1	0	0	0	0	1	0	0	0	15745	217	8	5	1623	5	TDRD5	1	179609042	Missense_Mutation	SNP	A	TCGA-G7-6789-01A-11D-1961-08	104703816	179609042	69641579	3	9953											
PTPRC	5788	hgsc.bcm.edu	37	chr1	198678927	198678927	+	Frame_Shift_Del	DEL	G	G	-																															ccacaagtttactaacgcaaGtaaaattattaaaacagatt																										TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr1:198678927delG	ENST00000367376.2	+	11	1310	c.1139delG	c.(1138-1140)agtfs	p.S380fs	PTPRC_ENST00000594404.1_Frame_Shift_Del_p.S219fs|PTPRC_ENST00000352140.3_Frame_Shift_Del_p.S332fs|PTPRC_ENST00000348564.6_Frame_Shift_Del_p.S221fs|PTPRC_ENST00000442510.2_Frame_Shift_Del_p.S382fs	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	380					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						ACTAACGCAAGTAAAATTATT	0.274																																					p.S382fs		Atlas-INDEL	.											.	PTPRC	229	.	0			c.1144delA						PASS	.						75	91	85					1																	198678927		2198	4265	6463	SO:0001589	frameshift_variant	5788	exon11			.	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.1139delG	chr1.hg19:g.198678927delG	ENSP00000356346:p.Ser380fs	141.0	0.0	0		225.0	24.0	0.106667	NM_002838	A8K7W6|Q16614|Q9H0Y6	Frame_Shift_Del	DEL	ENST00000367376.2	hg19																																																																																				.	.	.	none		0.274	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding				-	198678927	G	-	198678927	7	5	169	1	0	1	0	1	0	0	0	0	12810	1029	36	0	1188	0	PTPRC	1	198678927	Frame_Shift_Del	DEL	G	TCGA-G7-6789-01A-11D-1961-08	19069885	198678927	50571694	4	9954											
POLR1B	84172	hgsc.bcm.edu	37	chr2	113308552	113308559	+	Frame_Shift_Del	DEL	CTTTCTTC	CTTTCTTC	-																															atttaccgaaaagaactgttCtttcttcctttgggatttgc																										TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	CTTTCTTC	CTTTCTTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr2:113308552_113308559delCTTTCTTC	ENST00000263331.5	+	5	1315_1322	c.735_742delCTTTCTTC	c.(733-744)ttctttcttcctfs	p.FLP246fs	POLR1B_ENST00000417433.2_Frame_Shift_Del_p.FLP190fs|POLR1B_ENST00000537335.1_Frame_Shift_Del_p.FLP35fs|POLR1B_ENST00000541869.1_Frame_Shift_Del_p.FLP284fs|POLR1B_ENST00000409894.3_Frame_Shift_Del_p.FLP246fs	NM_019014.4	NP_061887.2	Q9H9Y6	RPA2_HUMAN	polymerase (RNA) I polypeptide B, 128kDa	246					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						AAGAACTGTTCTTTCTTCCTTTGGGATT	0.394																																					p.245_247del	Ovarian(16;256 576 9537 23969 41147)	Atlas-INDEL	.											.	POLR1B	95	.	0			c.734_741del						PASS	.																																			SO:0001589	frameshift_variant	84172	exon5			.	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.735_742delCTTTCTTC	chr2.hg19:g.113308552_113308559delCTTTCTTC	ENSP00000263331:p.Phe246fs	162.0	0.0	0		172.0	25.0	0.145349	NM_019014	B7Z6Y7|B7Z823|F5GZX4|F8W898|Q2TAM4|Q585T5|Q6ZRR2|Q9H9D3	Frame_Shift_Del	DEL	ENST00000263331.5	hg19	CCDS2097.1																																																																																			.	.	.	none		0.394	POLR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254083.1	NM_019014		-	113308559	CTTTCTTC	-	113308552	7	5	169	1	0	1	0	1	0	0	0	0	12217	912	32	0	753	0	POLR1B	2	113308552	Frame_Shift_Del	DEL	CTTTCTTC	TCGA-G7-6789-01A-11D-1961-08		113308552	129890821	5	9955											
ALPPL2	251	hgsc.bcm.edu	37	chr2	233272617	233272617	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcgccagccggcgcctacGcccacacggtgaaccgcaac	8	3	10	20	6	0	1	0	1	0	0	1	1	0	1	6	2	4	1	6	2	3	1	rs145892470		TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr2:233272617G>A	ENST00000295453.3	+	5	590	c.538G>A	c.(538-540)Gcc>Acc	p.A180T		NM_031313.2	NP_112603.2	P10696	PPBN_HUMAN	alkaline phosphatase, placental-like 2	180					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)	CGGCGCCTACGCCCACACGGT	0.627																																					p.A180T		Atlas-SNP	.											.	ALPPL2	36	.	0			c.G538A						PASS	.	G	THR/ALA	0,4406		0,0,2203	67	69	68		538	2.7	0.1	2	dbSNP_134	68	1,8597	1.2+/-3.3	0,1,4298	no	missense	ALPPL2	NM_031313.2	58	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	180/533	233272617	1,13003	2203	4299	6502	SO:0001583	missense	251	exon5			GCCTACGCCCACA	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.538G>A	chr2.hg19:g.233272617G>A	ENSP00000295453:p.Ala180Thr	137.0	0.0	.		170.0	26.0	.	NM_031313	A8KAF2|Q16727|Q53S81|Q96CM1	Missense_Mutation	SNP	ENST00000295453.3	hg19	CCDS2491.1	.	.	.	.	.	.	.	.	.	.	g	14.70	2.615024	0.46631	0.0	1.16E-4	ENSG00000163286	ENST00000295453	D	0.98400	-4.91	2.71	2.71	0.32032	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.057529	0.64402	D	0.000002	D	0.99118	0.9696	H	0.94306	3.52	0.45005	D	0.998024	D	0.89917	1.0	D	0.77004	0.989	D	0.99047	1.0826	10	0.87932	D	0	.	13.8099	0.63256	0.0:0.0:1.0:0.0	.	180	P10696	PPBN_HUMAN	T	180	ENSP00000295453:A180T	ENSP00000295453:A180T	A	+	1	0	ALPPL2	232980861	1.000000	0.71417	0.066000	0.19879	0.144000	0.21451	5.834000	0.69361	1.499000	0.48617	0.205000	0.17691	GCC	.	G|1.000;A|0.000	0.000	weak		0.627	ALPPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257034.2	NM_031313		A	233272617	G	A	233272617	3	1	169	1	0	0	0	0	1	0	0	0	549	1087	38	1	556	1	ALPPL2	2	233272617	Missense_Mutation	SNP	G	TCGA-G7-6789-01A-11D-1961-08	119964065	233272617	9926756	6	9956											
DNAH1	25981	hgsc.bcm.edu	37	chr3	52422876	52422876	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaggagacggtggagaacCtgcagtacatgctcaacaac	13	5	13	10	1	1	2	1	0	0	2	1	4	1	2	1	4	6	4	1	4	4	1			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr3:52422876C>T	ENST00000420323.2	+	59	9679	c.9418C>T	c.(9418-9420)Ctg>Ttg	p.L3140L		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	3205					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)		GGTGGAGAACCTGCAGTACAT	0.637																																					p.L3140L		Atlas-SNP	.											.	DNAH1	534	.	0			c.C9418T						PASS	.						59	71	67					3																	52422876		2151	4243	6394	SO:0001819	synonymous_variant	25981	exon59			GAGAACCTGCAGT	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.9418C>T	chr3.hg19:g.52422876C>T		70.0	0.0	.		60.0	39.0	.	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Silent	SNP	ENST00000420323.2	hg19	CCDS46842.1																																																																																			.	.	.	none		0.637	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		T	52422876	C	T	52422876	2	4	169	1	0	0	0	0	0	0	0	1	4599	680	24	2		2	DNAH1	3	52422876	Silent	SNP	C	TCGA-G7-6789-01A-11D-1961-08		52422876	145599554	7	9957											
ANKS1A	23294	hgsc.bcm.edu	37	chr6	35051232	35051232	+	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	aagaagatccccaccatcatCctgtccatcacatacaaagg	15	7	5	14	0	2	2	2	0	0	2	5	2	5	2	5	1	1	0	5	1	4	1	rs371531749		TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr6:35051232C>A	ENST00000360359.3	+	20	3084	c.2946C>A	c.(2944-2946)atC>atA	p.I982I	ANKS1A_ENST00000535627.1_Intron	NM_015245.2	NP_056060.2	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1A	982	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				ephrin receptor signaling pathway (GO:0048013)|neuron remodeling (GO:0016322)|substrate-dependent cell migration (GO:0006929)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleus (GO:0005634)				cervix(2)|endometrium(3)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						CCACCATCATCCTGTCCATCA	0.547																																					p.I982I		Atlas-SNP	.											.	ANKS1A	123	.	0			c.C2946A						PASS	.						232	185	201					6																	35051232		2203	4300	6503	SO:0001819	synonymous_variant	23294	exon20			CATCATCCTGTCC	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.2946C>A	chr6.hg19:g.35051232C>A		116.0	0.0	.		108.0	72.0	.	NM_015245	A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7	Silent	SNP	ENST00000360359.3	hg19	CCDS4798.1																																																																																			.	.	.	alt		0.547	ANKS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040262.1	XM_166478		A	35051232	C	A	35051232	2	1	169	1	0	0	0	0	0	0	0	1	688	845	30	4		4	ANKS1A	6	35051232	Silent	SNP	C	TCGA-G7-6789-01A-11D-1961-08		35051232	136063835	8	9958											
GSTK1	373156	hgsc.bcm.edu	37	chr7	142965268	142965268	+	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	accggatggagctgctggcgCacctgctgggtaagtaagtt	8	9	15	9	2	0	0	0	0	0	0	0	2	0	2	2	4	3	7	2	4	2	3			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr7:142965268C>T	ENST00000358406.5	+	7	693	c.622C>T	c.(622-624)Cac>Tac	p.H208Y	GSTK1_ENST00000409500.3_Missense_Mutation_p.H196Y|GSTK1_ENST00000443571.2_Missense_Mutation_p.H165Y|AC073342.12_ENST00000427392.1_RNA|GSTK1_ENST00000479303.1_Missense_Mutation_p.H264Y	NM_015917.2	NP_057001.1	Q9Y2Q3	GSTK1_HUMAN	glutathione S-transferase kappa 1	208					epithelial cell differentiation (GO:0030855)|glutathione metabolic process (GO:0006749)|oxidation-reduction process (GO:0055114)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|peroxisome (GO:0005777)	glutathione peroxidase activity (GO:0004602)|glutathione transferase activity (GO:0004364)|protein disulfide oxidoreductase activity (GO:0015035)|receptor binding (GO:0005102)			lung(4)	4	Melanoma(164;0.059)				Glutathione(DB00143)	GCTGCTGGCGCACCTGCTGGG	0.567																																					p.H264Y		Atlas-SNP	.											.	GSTK1	36	.	0			c.C790T						PASS	.						181	182	182					7																	142965268		2203	4300	6503	SO:0001583	missense	373156	exon6			CTGGCGCACCTGC		CCDS5877.1, CCDS47730.1, CCDS47731.1, CCDS47732.1	7q34	2012-06-21			ENSG00000197448	ENSG00000197448	2.5.1.18	"Glutathione S-transferases / Mitochondrial (kappa)"	16906	protein-coding gene	gene with protein product		602321				12720545, 14742434	Standard	NM_015917		Approved	GST13	uc003wcj.3	Q9Y2Q3	OTTHUMG00000152637	ENST00000358406.5:c.622C>T	chr7.hg19:g.142965268C>T	ENSP00000351181:p.His208Tyr	415.0	0.0	.		495.0	101.0	.	NM_001143679	B4DIH1|B4DSY2|Q6P4H0|Q7Z520|Q9P1S4	Missense_Mutation	SNP	ENST00000358406.5	hg19	CCDS5877.1	.	.	.	.	.	.	.	.	.	.	C	4.988	0.183556	0.09495	.	.	ENSG00000197448	ENST00000409500;ENST00000443571;ENST00000358406;ENST00000479303	.	.	.	5.78	-3.58	0.04597	DSBA-like thioredoxin domain (1);Thioredoxin-like fold (1);	1.302130	0.04873	N	0.446319	T	0.28167	0.0695	N	0.25380	0.74	0.09310	N	1	B;B;B;B	0.11235	0.0;0.0;0.004;0.002	B;B;B;B	0.14578	0.003;0.005;0.011;0.004	T	0.34825	-0.9813	9	0.08837	T	0.75	-3.554	12.5207	0.56058	0.0:0.6216:0.0:0.3784	.	196;165;264;208	Q9Y2Q3-3;Q9Y2Q3-4;Q9Y2Q3-2;Q9Y2Q3	.;.;.;GSTK1_HUMAN	Y	196;165;208;264	.	ENSP00000351181:H208Y	H	+	1	0	GSTK1	142675390	0.000000	0.05858	0.003000	0.11579	0.606000	0.37113	-1.201000	0.03026	-1.038000	0.03279	-0.259000	0.10710	CAC	.	.	.	none		0.567	GSTK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327091.1	NM_015917		T	142965268	C	T	142965268	3	4	169	1	0	0	0	0	1	0	0	0	6843	710	25	2	812	2	GSTK1	7	142965268	Missense_Mutation	SNP	C	TCGA-G7-6789-01A-11D-1961-08		142965268	16173395	9	9959											
CDKN2A	1029	hgsc.bcm.edu	37	chr9	21971120	21971120	+	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	ggcagcgtcgtgcacgggtcGggtgagagtggcggggtcgg	4	6	23	8	6	0	1	0	1	0	1	3	2	0	1	0	7	2	2	0	7	0	0	rs121913388		TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr9:21971120G>A	ENST00000304494.5	-	2	508	c.238C>T	c.(238-240)Cga>Tga	p.R80*	CDKN2A_ENST00000497750.1_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000479692.2_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000579755.1_Missense_Mutation_p.P94L|CDKN2A_ENST00000530628.2_Missense_Mutation_p.P94L|CDKN2A_ENST00000361570.3_Missense_Mutation_p.P135L|CDKN2A_ENST00000578845.2_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000494262.1_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000446177.1_Nonsense_Mutation_p.R80*|CDKN2A_ENST00000498628.2_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000498124.1_Nonsense_Mutation_p.R80*|CDKN2A_ENST00000579122.1_Nonsense_Mutation_p.R80*|RP11-145E5.5_ENST00000404796.2_Intron	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	80			R -> L (in a head and neck tumor).|R -> P (in CMM2; loss of CDK4 binding). {ECO:0000269|PubMed:19260062}.		cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.R80*(100)|p.?(44)|p.P135L(7)|p.L65fs*38(1)|p.T79fs*37(1)|p.0(1)|p.A76fs*64(1)|p.T79fs*65(1)|p.E61_L94del(1)|p.A68fs*3(1)|p.R80fs*34(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)		TGCACGGGTCGGGTGAGAGTG	0.726	R80*(HSC4_UPPER_AERODIGESTIVE_TRACT)|R80*(MEWO_SKIN)	17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																											p.R80X		Atlas-SNP	.											CDKN2A_ENST00000498124,bladder,carcinoma,0,7	CDKN2A	4810	.	1474	Whole gene deletion(1316)|Substitution - Nonsense(100)|Unknown(44)|Substitution - Missense(7)|Deletion - Frameshift(6)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(298)|skin(206)|central_nervous_system(168)|lung(150)|urinary_tract(91)|bone(76)|oesophagus(72)|upper_aerodigestive_tract(63)|soft_tissue(60)|pleura(51)|pancreas(37)|ovary(36)|kidney(32)|breast(32)|biliary_tract(16)|thyroid(15)|NS(14)|stomach(14)|large_intestine(7)|autonomic_ganglia(7)|meninges(7)|liver(6)|salivary_gland(4)|thymus(4)|vulva(3)|endometrium(3)|prostate(2)	c.C238T	GRCh37	CM014695	CDKN2A	M	rs121913388	PASS	.						11	14	13					9																	21971120		2172	4246	6418	SO:0001587	stop_gained	1029	exon2			CGGGTCGGGTGAG	L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.238C>T	chr9.hg19:g.21971120G>A	ENSP00000307101:p.Arg80*	40.0	0.0	.		38.0	26.0	.	NM_000077	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Nonsense_Mutation	SNP	ENST00000304494.5	hg19	CCDS6510.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	39|39	7.328457|7.328457	0.98214|0.98214	.|.	.|.	ENSG00000147889|ENSG00000147889	ENST00000361570;ENST00000530628|ENST00000304494;ENST00000446177	D;D|.	0.86497|.	-2.13;-2.02|.	5.93|5.93	5.01|5.01	0.66863|0.66863	.|.	0.000000|.	0.37136|.	N|.	0.002233|.	T|.	0.44561|.	0.1299|.	L|L	0.36672|0.36672	1.1|1.1	0.47511|0.47511	D|D	0.999443|0.999443	D|.	0.59357|.	0.985|.	B|.	0.40602|.	0.334|.	T|.	0.34825|.	-0.9813|.	10|.	0.13108|0.02654	T|T	0.6|1	-2.989|-2.989	8.7197|8.7197	0.34434|0.34434	0.0759:0.0:0.7715:0.1526|0.0759:0.0:0.7715:0.1526	.|.	135|.	Q8N726|.	CD2A2_HUMAN|.	L|X	135;94|80	ENSP00000355153:P135L;ENSP00000432664:P94L|.	ENSP00000355153:P135L|ENSP00000307101:R80X	P|R	-|-	2|1	0|2	CDKN2A|CDKN2A	21961120|21961120	0.995000|0.995000	0.38212|0.38212	1.000000|1.000000	0.80357|0.80357	0.899000|0.899000	0.52679|0.52679	2.363000|2.363000	0.44178|0.44178	1.464000|1.464000	0.47987|0.47987	0.650000|0.650000	0.86243|0.86243	CCG|CGA	.	.	.	weak		0.726	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077		A	21971120	G	A	21971120	4	1	169	1	0	0	0	0	0	1	0	0	3163	1125	39	1	240	1	CDKN2A	9	21971120	Nonsense_Mutation	SNP	G	TCGA-G7-6789-01A-11D-1961-08		21971120	119242311	10	9960											
BAT2L1	84726	hgsc.bcm.edu	37	chr9	134350415	134350415	+	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	agaagattaagcaggagctaGgggaggagagtacccggctg	13	5	17	6	1	0	3	0	0	0	3	0	6	0	5	1	5	3	4	1	5	4	3			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr9:134350415G>C	ENST00000357304.4	+	15	2954	c.2899G>C	c.(2899-2901)Ggg>Cgg	p.G967R	PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Intron|PRRC2B_ENST00000405995.1_Intron	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	967							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						GCAGGAGCTAGGGGAGGAGAG	0.582																																					p.G967R		Atlas-SNP	.											.	PRRC2B	266	.	0			c.G2899C						PASS	.						37	42	40					9																	134350415		2050	4189	6239	SO:0001583	missense	84726	exon15			GAGCTAGGGGAGG	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.2899G>C	chr9.hg19:g.134350415G>C	ENSP00000349856:p.Gly967Arg	19.0	0.0	.		12.0	6.0	.	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	hg19	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	G	11.07	1.531552	0.27387	.	.	ENSG00000130723	ENST00000357304;ENST00000418650	T	0.01918	4.56	5.87	4.98	0.66077	.	.	.	.	.	T	0.01627	0.0052	N	0.12182	0.205	0.80722	D	1	B;B	0.18166	0.026;0.004	B;B	0.18561	0.022;0.005	T	0.57985	-0.7716	8	.	.	.	.	9.9519	0.41645	0.152:0.0:0.848:0.0	.	263;967	Q5H9R5;Q5JSZ5	.;PRC2B_HUMAN	R	967;263	ENSP00000349856:G967R	.	G	+	1	0	PRRC2B	133340236	1.000000	0.71417	0.147000	0.22382	0.913000	0.54294	6.182000	0.71995	1.487000	0.48415	0.655000	0.94253	GGG	.	.	.	none		0.582	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	134350415	G	C	134350415	3	2	169	1	0	0	0	0	1	0	0	0	1320	1000	35	4	2957	4	BAT2L1	9	134350415	Missense_Mutation	SNP	G	TCGA-G7-6789-01A-11D-1961-08	112379295	134350415	6863016	11	9961											
C11orf70	85016	hgsc.bcm.edu	37	chr11	101937281	101937281	+	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	agctttcaatgtcattttttCatcggttatatgatgaagat	11	18	7	5	1	3	3	3	2	0	1	4	3	3	3	0	1	1	2	0	1	4	6			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr11:101937281C>G	ENST00000434758.2	+	4	362	c.334C>G	c.(334-336)Cat>Gat	p.H112D	C11orf70_ENST00000526781.1_Missense_Mutation_p.H112D|C11orf70_ENST00000534360.1_Intron	NM_032930.2	NP_116319.2	Q9BRQ4	CK070_HUMAN	chromosome 11 open reading frame 70	112										breast(1)|kidney(1)|lung(5)|ovary(1)|prostate(2)|skin(2)	12	all_epithelial(12;0.0137)	Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.0137)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0335)		GTCATTTTTTCATCGGTTATA	0.303																																					p.H112D		Atlas-SNP	.											.	C11orf70	33	.	0			c.C334G						PASS	.						107	101	103					11																	101937281		2200	4294	6494	SO:0001583	missense	85016	exon4			TTTTTTCATCGGT	AK094851	CCDS8313.1, CCDS8313.2, CCDS53698.1	11q22.1	2012-05-31			ENSG00000137691	ENSG00000137691			28188	protein-coding gene	gene with protein product							Standard	NM_032930		Approved	MGC13040	uc001pgp.3	Q9BRQ4	OTTHUMG00000167320	ENST00000434758.2:c.334C>G	chr11.hg19:g.101937281C>G	ENSP00000414390:p.His112Asp	72.0	0.0	.		66.0	37.0	.	NM_032930	E9PJU1	Missense_Mutation	SNP	ENST00000434758.2	hg19	CCDS8313.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.099|0.099	-1.155573|-1.155573	0.01686|0.01686	.|.	.|.	ENSG00000137691|ENSG00000137691	ENST00000529204|ENST00000434758;ENST00000526781;ENST00000423732	.|.	.|.	.|.	5.53|5.53	-5.51|-5.51	0.02568|0.02568	.|.	.|0.382417	.|0.32769	.|N	.|0.005664	T|T	0.04998|0.04998	0.0134|0.0134	N|N	0.00032|0.00032	-2.585|-2.585	0.80722|0.80722	D|D	1|1	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.46261|0.46261	-0.9204|-0.9204	6|9	0.87932|0.02654	D|T	0|1	-3.2945|-3.2945	9.2395|9.2395	0.37486|0.37486	0.1423:0.5247:0.3329:0.0|0.1423:0.5247:0.3329:0.0	.|.	.|112	.|Q9BRQ4	.|CK070_HUMAN	L|D	3|112;112;74	.|.	ENSP00000432322:F3L|ENSP00000392150:H74D	F|H	+|+	3|1	2|0	C11orf70|C11orf70	101442491|101442491	1.000000|1.000000	0.71417|0.71417	0.222000|0.222000	0.23844|0.23844	0.555000|0.555000	0.35460|0.35460	0.684000|0.684000	0.25364|0.25364	-0.778000|-0.778000	0.04566|0.04566	-0.474000|-0.474000	0.04947|0.04947	TTC|CAT	.	.	.	none		0.303	C11orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394144.1	NM_032930		G	101937281	C	G	101937281	3	3	169	1	0	0	0	0	1	0	0	0	1661	826	29	4	230	4	C11orf70	11	101937281	Missense_Mutation	SNP	C	TCGA-G7-6789-01A-11D-1961-08		101937281	33069235	12	9962											
FAR2	55711	hgsc.bcm.edu	37	chr12	29485566	29485566	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acgtgcgccagttgaactggTtggaatacattgaaaattat	13	12	10	6	2	0	2	0	2	0	0	0	3	0	3	1	2	3	2	1	2	6	5			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr12:29485566T>C	ENST00000536681.3	+	11	1537	c.1291T>C	c.(1291-1293)Ttg>Ctg	p.L431L	FAR2_ENST00000547116.1_Silent_p.L334L|FAR2_ENST00000182377.4_Silent_p.L431L	NM_001271783.1|NM_001271784.1	NP_001258712.1|NP_001258713.1	Q96K12	FACR2_HUMAN	fatty acyl CoA reductase 2	431					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	fatty-acyl-CoA reductase (alcohol-forming) activity (GO:0080019)|long-chain-fatty-acyl-CoA reductase activity (GO:0050062)			central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(15)|prostate(1)|stomach(1)	29						GTTGAACTGGTTGGAATACAT	0.398																																					p.L431L		Atlas-SNP	.											.	FAR2	60	.	0			c.T1291C						PASS	.						92	89	90					12																	29485566		2203	4300	6503	SO:0001819	synonymous_variant	55711	exon11			AACTGGTTGGAAT	AL136843	CCDS8717.1, CCDS61084.1	12p11.23	2013-07-30	2008-06-06	2008-06-06	ENSG00000064763	ENSG00000064763	1.2.1.-	"Short chain dehydrogenase/reductase superfamily / Atypical members"	25531	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 10E, member 2"		"male sterility domain containing 1"	MLSTD1		15220348, 15220349, 19027726	Standard	NM_001271783		Approved	FLJ10462, SDR10E2	uc001ris.5	Q96K12	OTTHUMG00000169320	ENST00000536681.3:c.1291T>C	chr12.hg19:g.29485566T>C		49.0	0.0	.		102.0	45.0	.	NM_018099	F8VV73|Q9H0D5|Q9NVW8	Silent	SNP	ENST00000536681.3	hg19	CCDS8717.1																																																																																			.	.	.	none		0.398	FAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403479.2	NM_018099		C	29485566	T	C	29485566	2	2	169	1	0	0	0	0	0	0	0	1	5682	1722	60	3		3	FAR2	12	29485566	Silent	SNP	T	TCGA-G7-6789-01A-11D-1961-08		29485566	104366329	13	9963											
SAV1	60485	hgsc.bcm.edu	37	chr14	51132011	51132012	+	Frame_Shift_Ins	INS	-	-	A																															ggccgctttctctgaccatcINSaaaaaaattgtctgaataat																										TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr14:51132011_51132012insA	ENST00000324679.4	-	2	783_784	c.420_421insT	c.(418-423)tttgatfs	p.D141fs	RP11-248J18.2_ENST00000602954.1_RNA	NM_021818.3	NP_068590.1	Q9H4B6	SAV1_HUMAN	salvador family WW domain containing protein 1	141					hair follicle development (GO:0001942)|hippo signaling (GO:0035329)|intestinal epithelial cell differentiation (GO:0060575)|keratinocyte differentiation (GO:0030216)|lung epithelial cell differentiation (GO:0060487)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of epithelial cell proliferation (GO:0050680)|positive regulation of apoptotic process (GO:0043065)|regulation of stem cell maintenance (GO:2000036)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)				breast(1)|kidney(2)|lung(2)|prostate(1)	6	all_epithelial(31;0.000611)|Breast(41;0.0333)					CTCTGACCATCAAAAAAATTGT	0.396																																					p.D141_G142delinsX		Atlas-INDEL	.											.	SAV1	18	.	0			c.421_422insT						PASS	.																																			SO:0001589	frameshift_variant	60485	exon2			.	AK023071	CCDS9701.1	14q13-q23	2014-04-14	2014-04-14		ENSG00000151748	ENSG00000151748			17795	protein-coding gene	gene with protein product	"WW domain-containing adaptor 45"	607203	"salvador homolog 1 (Drosophila)"			12202036, 11027580	Standard	NM_021818		Approved	WW45, WWP4, salvador	uc001wyh.2	Q9H4B6	OTTHUMG00000140293	ENST00000324679.4:c.421dupT	chr14.hg19:g.51132018_51132018dupA	ENSP00000324729:p.Asp141fs	78.0	0.0	0		63.0	35.0	0.555556	NM_021818	A8K4B8|D3DSB6|Q6IA58|Q9H949|Q9HAK9	Frame_Shift_Ins	INS	ENST00000324679.4	hg19	CCDS9701.1																																																																																			.	.	.	none		0.396	SAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276879.1			A	51132012	-	A	51132011	7	5	169	1	0	1	1	0	0	0	0	0	13869	826	29	0	746	0	SAV1	14	51132011	Frame_Shift_Ins	INS	-	TCGA-G7-6789-01A-11D-1961-08		51132011	56217529	14	9964											
RNF213	57674	hgsc.bcm.edu	37	chr17	78355391	78355391	+	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	ccagtgagggatccaaaaggCtttctgcagcagcacatcct	11	8	10	12	0	1	1	0	1	1	0	3	2	3	2	3	2	3	4	3	2	2	1			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr17:78355391C>G	ENST00000582970.1	+	57	13985	c.13842C>G	c.(13840-13842)ggC>ggG	p.G4614G	RNF213_ENST00000508628.2_Silent_p.G4663G|RNF213_ENST00000336301.6_Silent_p.G2687G|CTD-2047H16.4_ENST00000575034.1_RNA|CTD-2047H16.4_ENST00000572151.1_RNA|CTD-2047H16.4_ENST00000573394.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	4614					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)			ATCCAAAAGGCTTTCTGCAGC	0.562																																					p.G4614G		Atlas-SNP	.											.	RNF213	766	.	0			c.C13842G						PASS	.						109	94	99					17																	78355391		2203	4300	6503	SO:0001819	synonymous_variant	57674	exon57			AAAAGGCTTTCTG	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.13842C>G	chr17.hg19:g.78355391C>G		97.0	0.0	.		182.0	99.0	.	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	hg19	CCDS58606.1																																																																																			.	.	.	none		0.562	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		G	78355391	C	G	78355391	2	3	169	1	0	0	0	0	0	0	0	1	13490	784	28	4		4	RNF213	17	78355391	Silent	SNP	C	TCGA-G7-6789-01A-11D-1961-08		78355391	2839819	15	9965											
RPRD1A	55197	hgsc.bcm.edu	37	chr18	33606995	33606995	+	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	taatctgccagcaacatacaCgcatcctctaccattttgga	12	11	5	13	1	2	0	0	0	2	0	3	1	3	1	3	1	5	2	3	1	4	5	rs202026701		TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr18:33606995C>T	ENST00000399022.4	-	6	828	c.657G>A	c.(655-657)gcG>gcA	p.A219A	RPRD1A_ENST00000590898.1_Silent_p.A183A|RPRD1A_ENST00000319040.6_Silent_p.A219A|RPRD1A_ENST00000357384.4_Silent_p.A219A|RPRD1A_ENST00000337059.5_Silent_p.A183A|RPRD1A_ENST00000588737.1_Silent_p.A183A	NM_018170.3	NP_060640.2	Q96P16	RPR1A_HUMAN	regulation of nuclear pre-mRNA domain containing 1A	219					dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)	DNA-directed RNA polymerase II, holoenzyme (GO:0016591)		p.A219A(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|urinary_tract(2)	12						GCAACATACACGCATCCTCTA	0.373																																					p.A219A		Atlas-SNP	.											RPRD1A_ENST00000319040,NS,carcinoma,0,2	RPRD1A	30	.	1	Substitution - coding silent(1)	lung(1)	c.G657A						PASS	.	C		0,4406		0,0,2203	90	85	87		657	-5.7	1	18		87	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	RPRD1A	NM_018170.3		0,1,6501	TT,TC,CC		0.0116,0.0,0.0077		219/313	33606995	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	55197	exon6			CATACACGCATCC	AF419845	CCDS11917.1	18q12.2	2012-02-09	2008-08-15		ENSG00000141425	ENSG00000141425			25560	protein-coding gene	gene with protein product	"cyclin-dependent kinase 2B-inhibitor-related protein", "Cyclin-dependent kinase inhibitor 2B-related protein (p15INK4B-related protein)"	610347				12470661, 22231121	Standard	NM_018170		Approved	P15RS, FLJ10656, HsT3101	uc002kzg.3	Q96P16	OTTHUMG00000132591	ENST00000399022.4:c.657G>A	chr18.hg19:g.33606995C>T		103.0	0.0	.		73.0	45.0	.	NM_018170	A8KA42|B2RBA3|Q7Z5G8|Q96FY9|Q9NVL4	Silent	SNP	ENST00000399022.4	hg19	CCDS11917.1																																																																																			.	C|0.999;T|0.001	0.001	weak		0.373	RPRD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255802.1	NM_018170		T	33606995	C	T	33606995	2	4	169	1	0	0	0	0	0	0	0	1	13628	523	19	1		1	RPRD1A	18	33606995	Silent	SNP	C	TCGA-G7-6789-01A-11D-1961-08		33606995	44470253	16	9966											
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-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr19:879943G>C	ENST00000589119.1	-	7	1346	c.1347C>G	c.(1345-1347)caC>caG	p.H449Q	MED16_ENST00000269814.4_Missense_Mutation_p.H449Q|MED16_ENST00000312090.6_Missense_Mutation_p.H449Q|MED16_ENST00000325464.1_Missense_Mutation_p.H449Q|MED16_ENST00000395808.3_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	.	0			c.C1347G						PASS	.						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	chr19.hg19:g.879943G>C	ENSP00000464810:p.His449Gln	34.0	1.0	.		18.0	3.0	.	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Missense_Mutation	SNP	ENST00000589119.1	hg19	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	169	1	0	0	0	0	1	0	0	0	9441	1136	40	4	1322	4	MED16	19	879943	Missense_Mutation	SNP	G	TCGA-G7-6789-01A-11D-1961-08		879943	58249040	17	9967											
FCGBP	8857	hgsc.bcm.edu	37	chr19	40408648	40408648	+	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	ggcttctggaagtcatccttGgggtcgccgttgtagttccc	4	13	13	11	2	2	0	1	0	1	0	5	1	4	1	3	4	0	4	3	4	2	5			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chr19:40408648G>C	ENST00000221347.6	-	8	4198	c.4191C>G	c.(4189-4191)ccC>ccG	p.P1397P		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1397	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			AGTCATCCTTGGGGTCGCCGT	0.607																																					p.P1397P		Atlas-SNP	.											.	FCGBP	416	.	0			c.C4191G						PASS	.						121	108	112					19																	40408648		2203	4300	6503	SO:0001819	synonymous_variant	8857	exon8			ATCCTTGGGGTCG	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.4191C>G	chr19.hg19:g.40408648G>C		165.0	0.0	.		116.0	34.0	.	NM_003890	O95784	Silent	SNP	ENST00000221347.6	hg19	CCDS12546.1																																																																																			.	.	.	none		0.607	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		C	40408648	G	C	40408648	2	2	169	1	0	0	0	0	0	0	0	1	5785	1335	47	4		4	FCGBP	19	40408648	Silent	SNP	G	TCGA-G7-6789-01A-11D-1961-08	39528705	40408648	18720335	18	9968											
SLC6A14	11254	hgsc.bcm.edu	37	chrX	115573956	115573956	+	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	tgtttgcttcttttcaaagtGaactaccatggaaaaattgt	12	16	7	6	0	2	1	1	1	1	0	2	2	2	2	1	1	3	2	1	1	5	6			TCGA-G7-6789-01A-11D-1961-08	TCGA-G7-6789-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73b0f7f3-54f1-4030-b2a9-89bb6b4e6d3e	e2d58fed-dc32-460b-aae1-c39d371dfca5	g.chrX:115573956G>A	ENST00000371900.4	+	4	536	c.448G>A	c.(448-450)Gaa>Aaa	p.E150K		NM_007231.3	NP_009162.1	Q9UN76	S6A14_HUMAN	solute carrier family 6 (amino acid transporter), member 14	150					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)	TTTTCAAAGTGAACTACCATG	0.323																																					p.E150K		Atlas-SNP	.											.	SLC6A14	56	.	0			c.G448A						PASS	.						126	118	121					X																	115573956		2203	4297	6500	SO:0001583	missense	11254	exon4			CAAAGTGAACTAC	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.448G>A	chrX.hg19:g.115573956G>A	ENSP00000360967:p.Glu150Lys	191.0	0.0	.		140.0	83.0	.	NM_007231	Q5H942	Missense_Mutation	SNP	ENST00000371900.4	hg19	CCDS14570.1	.	.	.	.	.	.	.	.	.	.	G	5.346	0.249106	0.10130	.	.	ENSG00000087916	ENST00000371900	T	0.74526	-0.85	5.61	2.77	0.32553	.	0.454788	0.25045	N	0.033578	T	0.56171	0.1967	L	0.33339	1.005	0.22435	N	0.999103	B	0.02656	0.0	B	0.09377	0.004	T	0.35773	-0.9775	10	0.06625	T	0.88	.	8.3675	0.32395	0.0857:0.4534:0.4609:0.0	.	150	Q9UN76	S6A14_HUMAN	K	150	ENSP00000360967:E150K	ENSP00000360967:E150K	E	+	1	0	SLC6A14	115487984	0.371000	0.25056	0.448000	0.26945	0.981000	0.71138	1.623000	0.37008	0.143000	0.18926	-0.218000	0.12543	GAA	.	.	.	none		0.323	SLC6A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057986.1			A	115573956	G	A	115573956	3	1	169	1	0	0	0	0	1	0	0	0	14690	1291	45	2	462	2	SLC6A14	23	115573956	Missense_Mutation	SNP	G	TCGA-G7-6789-01A-11D-1961-08		115573956	39696604	19	9969											
JAK1	3716	hgsc.bcm.edu	37	chr1	65330541	65330541	+	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	aatgtgagtgatttcagggaAgtaagaaaaattgttccact	15	12	10	4	0	1	3	1	2	0	1	2	4	2	4	1	1	0	2	1	1	5	4			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr1:65330541A>T	ENST00000342505.4	-	8	1353	c.1105T>A	c.(1105-1107)Ttc>Atc	p.F369I		NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	369	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	ATTTCAGGGAAGTAAGAAAAA	0.368			Mis		ALL																																p.F369I		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.T1105A						PASS	.						156	150	152					1																	65330541		1885	4123	6008	SO:0001583	missense	3716	exon8			CAGGGAAGTAAGA	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.1105T>A	chr1.hg19:g.65330541A>T	ENSP00000343204:p.Phe369Ile	74.0	0.0	.		68.0	22.0	.	NM_002227	Q59GQ2|Q9UD26	Missense_Mutation	SNP	ENST00000342505.4	hg19	CCDS41346.1	.	.	.	.	.	.	.	.	.	.	A	27.8	4.861730	0.91433	.	.	ENSG00000162434	ENST00000342505	T	0.21191	2.02	5.55	5.55	0.83447	FERM domain (1);	.	.	.	.	T	0.25382	0.0617	M	0.85462	2.755	0.52099	D	0.999945	D	0.53619	0.961	P	0.47206	0.541	T	0.10042	-1.0647	9	0.28530	T	0.3	-5.6269	16.0013	0.80294	1.0:0.0:0.0:0.0	.	369	P23458	JAK1_HUMAN	I	369	ENSP00000343204:F369I	ENSP00000343204:F369I	F	-	1	0	JAK1	65103129	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.607000	0.90891	2.247000	0.74100	0.528000	0.53228	TTC	.	.	.	none		0.368	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		T	65330541	A	T	65330541	3	4	170	1	0	0	0	0	1	0	0	0	7944	72	3	5	2431	5	JAK1	1	65330541	Missense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08		65330541	183920080	1	9970											
SLC6A17	388662	hgsc.bcm.edu	37	chr1	110738291	110738291	+	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	ttgtcaccatgttcgatgacTactcggccaccctgccactc	7	11	7	16	2	1	1	1	1	0	0	4	2	1	1	4	1	2	1	4	1	1	3			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr1:110738291T>A	ENST00000331565.4	+	10	2061	c.1576T>A	c.(1576-1578)Tac>Aac	p.Y526N		NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	526					alanine transport (GO:0032328)|glycine transport (GO:0015816)|leucine transport (GO:0015820)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		GTTCGATGACTACTCGGCCAC	0.537																																					p.Y526N		Atlas-SNP	.											.	SLC6A17	86	.	0			c.T1576A						PASS	.						107	88	94					1																	110738291		2203	4300	6503	SO:0001583	missense	388662	exon10			GATGACTACTCGG		CCDS30799.1	1p13.2	2013-07-19	2013-07-19		ENSG00000197106	ENSG00000197106		"Solute carriers"	31399	protein-coding gene	gene with protein product		610299	"solute carrier family 6 (neurotransmitter transporter), member 17", "solute carrier family 6, member 17"				Standard	NM_001010898		Approved		uc009wfq.3	Q9H1V8	OTTHUMG00000011761	ENST00000331565.4:c.1576T>A	chr1.hg19:g.110738291T>A	ENSP00000330199:p.Tyr526Asn	73.0	0.0	.		75.0	32.0	.	NM_001010898	A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Missense_Mutation	SNP	ENST00000331565.4	hg19	CCDS30799.1	.	.	.	.	.	.	.	.	.	.	T	32	5.131369	0.94473	.	.	ENSG00000197106	ENST00000331565;ENST00000450985	D	0.81996	-1.56	5.65	5.65	0.86999	.	0.056027	0.64402	D	0.000001	D	0.92492	0.7616	M	0.93507	3.425	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.94407	0.7628	10	0.87932	D	0	.	15.8499	0.78921	0.0:0.0:0.0:1.0	.	526	Q9H1V8	S6A17_HUMAN	N	526	ENSP00000330199:Y526N	ENSP00000330199:Y526N	Y	+	1	0	SLC6A17	110539814	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.934000	0.87649	2.146000	0.66826	0.533000	0.62120	TAC	.	.	.	none		0.537	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2	XM_371280		A	110738291	T	A	110738291	3	1	170	1	0	0	0	0	1	0	0	0	14693	1522	53	5	1610	5	SLC6A17	1	110738291	Missense_Mutation	SNP	T	TCGA-G7-6790-01A-11D-1961-08	45407750	110738291	138512330	2	9971											
SIKE1	80143	hgsc.bcm.edu	37	chr1	115323170	115323170	+	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	cggcggccgcatcgtgctccCgtagcctctccagcagcgtc	4	7	12	18	6	1	0	0	0	1	0	5	0	2	0	4	2	4	4	4	2	1	1			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr1:115323170C>A	ENST00000060969.5	-	1	128	c.59G>T	c.(58-60)cGg>cTg	p.R20L	SIKE1_ENST00000506320.1_5'UTR|SIKE1_ENST00000369528.5_Missense_Mutation_p.R20L			Q9BRV8	SIKE1_HUMAN	suppressor of IKBKE 1	20					innate immune response (GO:0045087)	cytosol (GO:0005829)				endometrium(1)|kidney(2)|large_intestine(1)|lung(2)	6						ATCGTGCTCCCGTAGCCTCTC	0.687																																					p.R20L		Atlas-SNP	.											.	SIKE1	12	.	0			c.G59T						PASS	.						22	24	23					1																	115323170		2200	4298	6498	SO:0001583	missense	80143	exon1			TGCTCCCGTAGCC	AK024821	CCDS878.1, CCDS41371.1	1p13.1	2009-08-13			ENSG00000052723	ENSG00000052723			26119	protein-coding gene	gene with protein product	"suppressor of IKK epsilon"	611656				16281057	Standard	NM_025073		Approved	FLJ21168, SIKE	uc001efp.4	Q9BRV8	OTTHUMG00000012061	ENST00000060969.5:c.59G>T	chr1.hg19:g.115323170C>A	ENSP00000060969:p.Arg20Leu	53.0	0.0	.		57.0	5.0	.	NM_025073	Q5TEZ7|Q5TEZ9|Q68DZ4|Q9H778	Missense_Mutation	SNP	ENST00000060969.5	hg19	CCDS878.1	.	.	.	.	.	.	.	.	.	.	C	28.7	4.946346	0.92593	.	.	ENSG00000052723	ENST00000369528;ENST00000060969	.	.	.	5.39	5.39	0.77823	.	0.052522	0.64402	D	0.000001	T	0.24586	0.0596	L	0.39898	1.24	0.38578	D	0.950123	P;P	0.47191	0.891;0.8	B;B	0.41764	0.331;0.366	T	0.16247	-1.0409	9	0.48119	T	0.1	-15.9215	6.8936	0.24243	0.0:0.7981:0.0:0.2019	.	20;20	Q9BRV8-2;Q9BRV8	.;SIKE1_HUMAN	L	20	.	ENSP00000060969:R20L	R	-	2	0	SIKE1	115124693	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.668000	0.46816	2.791000	0.96007	0.655000	0.94253	CGG	.	.	.	none		0.687	SIKE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033401.1	NM_025073		A	115323170	C	A	115323170	3	1	170	1	0	0	0	0	1	0	0	0	14333	652	23	4	596	4	SIKE1	1	115323170	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08	4584879	115323170	133927451	3	9972											
TRIM46	80128	hgsc.bcm.edu	37	chr1	155148034	155148034	+	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	ccccagctccgagcccacctCtcctgcctccaccccttcca	5	7	4	25	1	1	0	0	0	1	0	5	1	4	0	11	0	3	1	11	0	0	1			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr1:155148034C>G	ENST00000334634.4	+	2	236	c.236C>G	c.(235-237)tCt>tGt	p.S79C	TRIM46_ENST00000368382.1_Missense_Mutation_p.S56C|KRTCAP2_ENST00000490672.1_5'Flank|TRIM46_ENST00000368385.4_Missense_Mutation_p.S79C|RP11-201K10.3_ENST00000473363.2_Intron|TRIM46_ENST00000468878.1_3'UTR|TRIM46_ENST00000545012.1_Intron|KRTCAP2_ENST00000295682.4_5'Flank|TRIM46_ENST00000543729.1_Missense_Mutation_p.S86C|TRIM46_ENST00000392451.2_Missense_Mutation_p.S79C|TRIM46_ENST00000368383.3_Missense_Mutation_p.S79C	NM_001256601.1|NM_001282378.1	NP_001243530.1|NP_001269307.1	Q7Z4K8	TRI46_HUMAN	tripartite motif containing 46	79						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)			GAGCCCACCTCTCCTGCCTCC	0.677																																					p.S79C		Atlas-SNP	.											.	TRIM46	79	.	0			c.C236G						PASS	.						56	55	55					1																	155148034		2203	4300	6503	SO:0001583	missense	80128	exon2			CCACCTCTCCTGC		CCDS1097.1, CCDS58033.1, CCDS60285.1, CCDS72932.1, CCDS72931.1	1q22	2013-01-09	2011-01-25		ENSG00000163462	ENSG00000163462		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19019	protein-coding gene	gene with protein product		600986	"tripartite motif-containing 46"				Standard	NM_025058		Approved	FLJ23229, TRIFIC	uc001fhs.2	Q7Z4K8	OTTHUMG00000035680	ENST00000334634.4:c.236C>G	chr1.hg19:g.155148034C>G	ENSP00000334657:p.Ser79Cys	118.0	0.0	.		97.0	19.0	.	NM_025058	A0AVI6|B1AVQ4|Q5VT60|Q5VT62|Q6NT17|Q6NT41|Q6ZRL7|Q9H5P2	Missense_Mutation	SNP	ENST00000334634.4	hg19	CCDS1097.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.448430	0.84101	.	.	ENSG00000163462	ENST00000543729;ENST00000430513;ENST00000368385;ENST00000392451;ENST00000368383;ENST00000368382;ENST00000334634	T;T;T;T;T;T	0.60672	0.75;0.5;0.69;0.42;0.17;0.23	4.53	4.53	0.55603	Zinc finger, RING-type (1);	0.348037	0.29205	N	0.012829	T	0.60856	0.2301	L	0.51422	1.61	0.47547	D	0.999457	D;B;D;D;B;D	0.89917	0.998;0.014;1.0;0.999;0.014;0.999	P;B;D;P;B;D	0.68765	0.889;0.033;0.96;0.867;0.033;0.924	T	0.58567	-0.7614	10	0.33141	T	0.24	.	15.1434	0.72630	0.0:1.0:0.0:0.0	.	66;79;66;56;79;79	F5H5Z2;Q5VT61;B7Z3S2;B1AVQ4;Q7Z4K8;Q7Z4K8-2	.;.;.;.;TRI46_HUMAN;.	C	86;66;79;79;79;56;79	ENSP00000442719:S86C;ENSP00000357369:S79C;ENSP00000376245:S79C;ENSP00000357367:S79C;ENSP00000357366:S56C;ENSP00000334657:S79C	ENSP00000334657:S79C	S	+	2	0	TRIM46	153414658	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.676000	0.74498	2.222000	0.72286	0.650000	0.86243	TCT	.	.	.	none		0.677	TRIM46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086728.1	NM_025058		G	155148034	C	G	155148034	3	3	170	1	0	0	0	0	1	0	0	0	16533	913	32	4	242	4	TRIM46	1	155148034	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08	39824864	155148034	94102587	4	9973											
F5	2153	hgsc.bcm.edu	37	chr1	169510915	169510916	+	Frame_Shift_Ins	INS	-	-	TT																															ggggtctgaagtagagtgcaINStttgatcagggtcttgaatg																										TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr1:169510915_169510916insTT	ENST00000367797.3	-	13	3613_3614	c.3412_3413insAA	c.(3412-3414)atgfs	p.M1138fs	F5_ENST00000367796.3_Frame_Shift_Ins_p.M1143fs	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	1138	B.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	AGTAGAGTGCATTTGATCAGGG	0.48																																					p.M1138fs		Atlas-INDEL	.											.	F5	301	.	0			c.3413_3414insAA						PASS	.																																			SO:0001589	frameshift_variant	2153	exon13			.	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.3411_3412dupAA	chr1.hg19:g.169510916_169510917dupTT	ENSP00000356771:p.Met1138fs	289.0	0.0	0		276.0	80.0	0.289855	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Frame_Shift_Ins	INS	ENST00000367797.3	hg19	CCDS1281.1																																																																																			.	.	.	none		0.48	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		TT	169510916	-	TT	169510915	7	5	170	1	0	1	1	0	0	0	0	0	5350	217	8	0	3313	0	F5	1	169510915	Frame_Shift_Ins	INS	-	TCGA-G7-6790-01A-11D-1961-08	14362881	169510915	79739706	5	9974											
RC3H1	149041	hgsc.bcm.edu	37	chr1	173916659	173916660	+	Frame_Shift_Del	DEL	GT	GT	-																															ggatgaggtcatcatcactgGtttctgctgctcttctctga																										TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	GT	GT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr1:173916659_173916660delGT	ENST00000367696.2	-	15	2935_2936	c.2584_2585delAC	c.(2584-2586)accfs	p.T862fs	RC3H1_ENST00000367694.2_Frame_Shift_Del_p.T862fs|RC3H1_ENST00000258349.4_Frame_Shift_Del_p.T862fs			Q5TC82	RC3H1_HUMAN	ring finger and CCCH-type domains 1	862					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						ATCATCACTGGTTTCTGCTGCT	0.45																																					p.862_862del		Atlas-INDEL	.											.	RC3H1	110	.	0			c.2585_2586del						PASS	.																																			SO:0001589	frameshift_variant	149041	exon14			.	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.2584_2585delAC	chr1.hg19:g.173916659_173916660delGT	ENSP00000356669:p.Thr862fs	153.0	0.0	0		130.0	29.0	0.223077	NM_172071	B3KVK1|Q5W180|Q5W181|Q8IVE6|Q8N9V1	Frame_Shift_Del	DEL	ENST00000367696.2	hg19	CCDS30940.1																																																																																			.	.	.	none		0.45	RC3H1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090733.2	NM_172071		-	173916660	GT	-	173916659	7	5	170	1	0	1	0	1	0	0	0	0	13179	1261	44	0	840	0	RC3H1	1	173916659	Frame_Shift_Del	DEL	GT	TCGA-G7-6790-01A-11D-1961-08	4405744	173916659	75333962	6	9975											
GREB1	9687	hgsc.bcm.edu	37	chr2	11706688	11706688	+	Frame_Shift_Del	DEL	G	G	-																															cctgcgggctttctcctcgtGggggtcaagtcccccagcct																										TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr2:11706688delG	ENST00000381486.2	+	4	660	c.360delG	c.(358-360)gtgfs	p.V120fs	GREB1_ENST00000234142.5_Frame_Shift_Del_p.V120fs|GREB1_ENST00000381483.2_Frame_Shift_Del_p.V120fs|GREB1_ENST00000389825.3_Frame_Shift_Del_p.V10fs|GREB1_ENST00000263834.5_Frame_Shift_Del_p.V120fs	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	120						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)		TTCTCCTCGTGGGGGTCAAGT	0.597																																					p.V120fs	Ovarian(39;850 945 2785 23371 33093)	Atlas-INDEL	.											GREB1_ENST00000381486,NS,carcinoma,+1,2	GREB1	308	.	0			c.359delT						PASS	.						98	91	93					2																	11706688		2203	4300	6503	SO:0001589	frameshift_variant	9687	exon4			.		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.360delG	chr2.hg19:g.11706688delG	ENSP00000370896:p.Val120fs	101.0	0.0	0		135.0	41.0	0.303704	NM_148903	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Frame_Shift_Del	DEL	ENST00000381486.2	hg19	CCDS42655.1																																																																																			.	.	.	none		0.597	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		-	11706688	G	-	11706688	7	5	170	1	0	1	0	1	0	0	0	0	6767	1335	47	0	370	0	GREB1	2	11706688	Frame_Shift_Del	DEL	G	TCGA-G7-6790-01A-11D-1961-08		11706688	231492685	7	9976											
NBAS	51594	hgsc.bcm.edu	37	chr2	15691634	15691634	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taccttgacatttcccaataAtggatgtaaaatcatctttt	13	16	4	8	0	2	1	1	1	1	0	3	2	3	2	2	1	1	1	2	1	5	7			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr2:15691634A>G	ENST00000281513.5	-	6	387	c.362T>C	c.(361-363)aTt>aCt	p.I121T	NBAS_ENST00000441750.1_Missense_Mutation_p.I121T	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	121					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						TTTCCCAATAATGGATGTAAA	0.299																																					p.I121T		Atlas-SNP	.											.	NBAS	246	.	0			c.T362C						PASS	.						41	40	41					2																	15691634		2201	4297	6498	SO:0001583	missense	51594	exon6			CCAATAATGGATG	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.362T>C	chr2.hg19:g.15691634A>G	ENSP00000281513:p.Ile121Thr	16.0	0.0	.		20.0	6.0	.	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	hg19	CCDS1685.1	.	.	.	.	.	.	.	.	.	.	A	9.005	0.980968	0.18812	.	.	ENSG00000151779	ENST00000441750;ENST00000281513	T;T	0.52526	0.66;0.66	5.66	5.66	0.87406	Quinoprotein amine dehydrogenase, beta chain-like (1);	0.283763	0.33854	N	0.004482	T	0.36026	0.0952	N	0.21448	0.665	0.23657	N	0.997182	B	0.06786	0.001	B	0.06405	0.002	T	0.36065	-0.9763	10	0.87932	D	0	.	13.4276	0.61035	1.0:0.0:0.0:0.0	.	121	A2RRP1	NBAS_HUMAN	T	121	ENSP00000413201:I121T;ENSP00000281513:I121T	ENSP00000281513:I121T	I	-	2	0	NBAS	15609085	1.000000	0.71417	0.995000	0.50966	0.472000	0.32918	4.934000	0.63491	2.144000	0.66660	0.477000	0.44152	ATT	.	.	.	none		0.299	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		G	15691634	A	G	15691634	3	3	170	1	0	0	0	0	1	0	0	0	10193	101	4	3	6941	3	NBAS	2	15691634	Missense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08	3984946	15691634	227507739	8	9977											
SMEK2	57223	hgsc.bcm.edu	37	chr2	55812212	55812212	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactctgctgagcttcttgcAttacaaactctcggaccata	10	12	6	13	1	3	1	0	1	3	0	4	2	3	2	1	1	5	3	1	1	3	4			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr2:55812212A>G	ENST00000345102.5	-	7	1509	c.1208T>C	c.(1207-1209)aTg>aCg	p.M403T	SMEK2_ENST00000407823.3_Missense_Mutation_p.M403T|SMEK2_ENST00000272313.5_Missense_Mutation_p.M403T	NM_001122964.1	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	403					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)			AGCTTCTTGCATTACAAACTC	0.368																																					p.M403T		Atlas-SNP	.											.	SMEK2	86	.	0			c.T1208C						PASS	.						114	111	112					2																	55812212		2203	4300	6503	SO:0001583	missense	57223	exon7			TCTTGCATTACAA	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.1208T>C	chr2.hg19:g.55812212A>G	ENSP00000339769:p.Met403Thr	77.0	0.0	.		134.0	29.0	.	NM_001122964	Q6P9B0|Q86XB8|Q9BQJ0|Q9BRK2|Q9H913|Q9P2G0	Missense_Mutation	SNP	ENST00000345102.5	hg19	CCDS46289.1	.	.	.	.	.	.	.	.	.	.	A	17.19	3.325891	0.60743	.	.	ENSG00000138041	ENST00000272313;ENST00000407823;ENST00000345102	T;T;T	0.40225	1.04;1.04;1.04	5.8	5.8	0.92144	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.46852	0.1414	M	0.66939	2.045	0.80722	D	1	B;B;B;B	0.25850	0.018;0.136;0.002;0.136	B;B;B;B	0.30782	0.071;0.082;0.005;0.12	T	0.40979	-0.9534	10	0.44086	T	0.13	-11.8434	16.134	0.81465	1.0:0.0:0.0:0.0	.	403;403;403;403	Q5MIZ7-2;Q5MIZ7;Q5MIZ7-3;B4DKA9	.;P4R3B_HUMAN;.;.	T	403	ENSP00000272313:M403T;ENSP00000385912:M403T;ENSP00000339769:M403T	ENSP00000272313:M403T	M	-	2	0	SMEK2	55665716	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.216000	0.71823	0.528000	0.53228	ATG	.	.	.	none		0.368	SMEK2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251483.1	NM_020463		G	55812212	A	G	55812212	3	3	170	1	0	0	0	0	1	0	0	0	14807	217	8	3	1385	3	SMEK2	2	55812212	Missense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08	40120578	55812212	187387161	9	9978											
ADD2	119	hgsc.bcm.edu	37	chr2	70903901	70903901	+	Intron	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	gaaggcaaacacgtttccccGccagtcaggggcagcctctg	9	6	12	14	2	2	0	1	0	1	0	3	1	3	0	4	3	2	3	4	3	2	1			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr2:70903901G>C	ENST00000264436.4	-	13	2038				ADD2_ENST00000413157.2_Silent_p.G540G|ADD2_ENST00000355733.3_Intron|ADD2_ENST00000430656.1_Silent_p.G556G|ADD2_ENST00000407644.2_Intron	NM_001617.3	NP_001608.1	P35612	ADDB_HUMAN	adducin 2 (beta)						actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|barbed-end actin filament capping (GO:0051016)|hemopoiesis (GO:0030097)|positive regulation of protein binding (GO:0032092)|protein complex assembly (GO:0006461)	cytoplasmic membrane-bounded vesicle (GO:0016023)|F-actin capping protein complex (GO:0008290)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(11)|lung(13)|ovary(3)|pancreas(1)|skin(2)	36						ACGTTTCCCCGCCAGTCAGGG	0.632																																					p.G556G		Atlas-SNP	.											ADD2_ENST00000430656,NS,carcinoma,0,1	ADD2	261	.	0			c.C1668G						PASS	.						36	39	38					2																	70903901		2203	4300	6503	SO:0001627	intron_variant	119	exon12			TTCCCCGCCAGTC	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.1593+26C>G	chr2.hg19:g.70903901G>C		55.0	0.0	.		47.0	2.0	.	NM_001185055	A8K4P2|B4DM17|D6W5G7|D6W5G8|Q13482|Q16412|Q59G82|Q5U5P4|Q6P0P2|Q6PGQ4|Q7Z688|Q7Z689|Q7Z690|Q7Z691	Silent	SNP	ENST00000264436.4	hg19	CCDS1906.1																																																																																			.	.	.	none		0.632	ADD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251918.4	NM_001617		C	70903901	G	C	70903901	1	2	170	0	1	0	0	0	0	0	0	0	305	1074	38	4		4	ADD2	2	70903901	Intron	SNP	G	TCGA-G7-6790-01A-11D-1961-08	15091689	70903901	172295472	10	9979											
GAD1	2571	hgsc.bcm.edu	37	chr2	171687570	171687570	+	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	ttgatcgctccaccaaggtgCtggactttcatcacccacac	9	10	7	15	1	2	1	2	1	0	0	4	2	3	2	3	2	1	2	3	2	1	2			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr2:171687570C>T	ENST00000358196.3	+	5	965	c.415C>T	c.(415-417)Ctg>Ttg	p.L139L	GAD1_ENST00000429023.1_3'UTR|GAD1_ENST00000375272.1_Silent_p.L139L|GAD1_ENST00000344257.5_Silent_p.L139L	NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	139					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						CACCAAGGTGCTGGACTTTCA	0.547																																					p.L139L		Atlas-SNP	.											.	GAD1	79	.	0			c.C415T						PASS	.						114	99	104					2																	171687570		2203	4300	6503	SO:0001819	synonymous_variant	2571	exon5			AAGGTGCTGGACT		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.415C>T	chr2.hg19:g.171687570C>T		137.0	0.0	.		128.0	63.0	.	NM_000817	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Silent	SNP	ENST00000358196.3	hg19	CCDS2239.1																																																																																			.	.	.	none		0.547	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2			T	171687570	C	T	171687570	2	4	170	1	0	0	0	0	0	0	0	1	6186	796	28	2		2	GAD1	2	171687570	Silent	SNP	C	TCGA-G7-6790-01A-11D-1961-08	100783669	171687570	71511803	11	9980											
TTN	7273	hgsc.bcm.edu	37	chr2	179419674	179419674	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagcatccactattaaggcgAtcggcatctttgatgagtat	11	13	9	8	2	1	2	0	2	1	0	3	3	2	2	1	2	1	3	1	2	4	5			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr2:179419674A>G	ENST00000591111.1	-	281	83813	c.83589T>C	c.(83587-83589)gaT>gaC	p.D27863D	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Silent_p.D20631D|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Silent_p.D29504D|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342992.6_Silent_p.D26936D|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000359218.5_Silent_p.D20564D|TTN_ENST00000460472.2_Silent_p.D20439D|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	27863	Ig-like 130.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TATTAAGGCGATCGGCATCTT	0.423																																					p.D29504D		Atlas-SNP	.											.	TTN	18412	.	0			c.T88512C						PASS	.						90	86	87					2																	179419674		1936	4131	6067	SO:0001819	synonymous_variant	7273	exon331			AAGGCGATCGGCA	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.83589T>C	chr2.hg19:g.179419674A>G		50.0	0.0	.		64.0	37.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.	.	none		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179419674	A	G	179419674	2	3	170	1	0	0	0	0	0	0	0	1	16747	330	12	3		3	TTN	2	179419674	Silent	SNP	A	TCGA-G7-6790-01A-11D-1961-08	7732104	179419674	63779699	12	9981											
TTN	7273	hgsc.bcm.edu	37	chr2	179650834	179650834	+	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	ggtctactgcagcaacaactGttgctacagcttcagccttt	9	12	8	12	0	2	0	1	0	1	0	2	0	2	0	1	1	9	5	1	1	4	5			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr2:179650834G>C	ENST00000591111.1	-	14	2335	c.2111C>G	c.(2110-2112)aCa>aGa	p.T704R	TTN_ENST00000360870.5_Missense_Mutation_p.T704R|TTN_ENST00000342175.6_Missense_Mutation_p.T658R|TTN_ENST00000589042.1_Missense_Mutation_p.T704R|TTN_ENST00000342992.6_Missense_Mutation_p.T704R|TTN_ENST00000359218.5_Missense_Mutation_p.T658R|TTN_ENST00000460472.2_Missense_Mutation_p.T658R			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)			AGCAACAACTGTTGCTACAGC	0.493																																					p.T704R		Atlas-SNP	.											.	TTN	18412	.	0			c.C2111G						PASS	.						53	55	54					2																	179650834		2203	4300	6503	SO:0001583	missense	7273	exon14			ACAACTGTTGCTA	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.2111C>G	chr2.hg19:g.179650834G>C	ENSP00000465570:p.Thr704Arg	66.0	0.0	.		110.0	56.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	16.74	3.207756	0.58343	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870;ENST00000436599	T;T;T;T;T;T	0.70399	-0.48;-0.26;-0.26;-0.27;0.29;0.24	5.99	5.99	0.97316	Ribonuclease H-like (1);	.	.	.	.	T	0.80303	0.4598	L	0.36672	1.1	0.43574	D	0.995901	D;D;D;D;D	0.89917	0.999;0.999;0.999;0.999;1.0	D;D;D;D;D	0.91635	0.996;0.996;0.996;0.996;0.999	T	0.80732	-0.1251	9	0.87932	D	0	.	20.4777	0.99188	0.0:0.0:1.0:0.0	.	658;658;658;704;704	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	R	704;658;658;658;658;704;208	ENSP00000343764:T704R;ENSP00000434586:T658R;ENSP00000340554:T658R;ENSP00000352154:T658R;ENSP00000354117:T704R;ENSP00000405517:T208R	ENSP00000340554:T658R	T	-	2	0	TTN	179359079	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.402000	0.79972	2.840000	0.97914	0.655000	0.94253	ACA	.	.	.	none		0.493	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179650834	G	C	179650834	3	2	170	1	0	0	0	0	1	0	0	0	16747	1377	48	4	109273	4	TTN	2	179650834	Missense_Mutation	SNP	G	TCGA-G7-6790-01A-11D-1961-08	231160	179650834	63548539	13	9982											
ZNF804A	91752	hgsc.bcm.edu	37	chr2	185801068	185801068	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccttcattttgcaagtttcaActtcagttatcttctgatgc	8	18	5	10	0	5	1	3	1	2	0	5	1	5	1	1	0	3	3	1	0	3	7			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr2:185801068A>G	ENST00000302277.6	+	4	1539	c.945A>G	c.(943-945)caA>caG	p.Q315Q		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	315							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						GCAAGTTTCAACTTCAGTTAT	0.333																																					p.Q315Q		Atlas-SNP	.											.	ZNF804A	322	.	0			c.A945G						PASS	.						33	32	33					2																	185801068		2203	4296	6499	SO:0001819	synonymous_variant	91752	exon4			GTTTCAACTTCAG	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.945A>G	chr2.hg19:g.185801068A>G		47.0	0.0	.		67.0	41.0	.	NM_194250	A7E253|Q6ZN26	Silent	SNP	ENST00000302277.6	hg19	CCDS2291.1																																																																																			.	.	.	none		0.333	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		G	185801068	A	G	185801068	2	3	170	1	0	0	0	0	0	0	0	1	18182	40	2	3		3	ZNF804A	2	185801068	Silent	SNP	A	TCGA-G7-6790-01A-11D-1961-08	6150234	185801068	57398305	14	9983											
PODXL2	50512	hgsc.bcm.edu	37	chr3	127379599	127379599	+	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	gagcagcatggggcccagctTgctgctgccttcagtcaccc	6	8	12	15	0	2	0	2	0	0	0	2	1	2	0	3	2	6	5	3	2	0	2			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr3:127379599T>A	ENST00000342480.6	+	3	767	c.728T>A	c.(727-729)tTg>tAg	p.L243*		NM_015720.2	NP_056535.1	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2	243					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						GGGCCCAGCTTGCTGCTGCCT	0.647																																					p.L243X		Atlas-SNP	.											.	PODXL2	53	.	0			c.T728A						PASS	.						51	57	55					3																	127379599		2203	4300	6503	SO:0001587	stop_gained	50512	exon3			CCAGCTTGCTGCT	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.728T>A	chr3.hg19:g.127379599T>A	ENSP00000345359:p.Leu243*	95.0	0.0	.		88.0	18.0	.	NM_015720	Q6UVY4|Q8WUV6	Nonsense_Mutation	SNP	ENST00000342480.6	hg19	CCDS3044.1	.	.	.	.	.	.	.	.	.	.	T	13.31	2.198338	0.38806	.	.	ENSG00000114631	ENST00000342480;ENST00000302192	.	.	.	4.67	-0.49	0.12049	.	0.719396	0.11780	N	0.530317	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.0789	7.8382	0.29382	0.0:0.3596:0.0:0.6404	.	.	.	.	X	243	.	ENSP00000304498:L243X	L	+	2	0	PODXL2	128862289	0.001000	0.12720	0.001000	0.08648	0.181000	0.23173	0.600000	0.24104	-0.256000	0.09473	0.402000	0.26972	TTG	.	.	.	none		0.647	PODXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356638.1	NM_015720		A	127379599	T	A	127379599	4	1	170	1	0	0	0	0	0	1	0	0	12188	1821	63	5	738	5	PODXL2	3	127379599	Nonsense_Mutation	SNP	T	TCGA-G7-6790-01A-11D-1961-08		127379599	70642831	15	9984											
XRN1	54464	hgsc.bcm.edu	37	chr3	142123863	142123863	+	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	cactatgttggtttcttttcCtctcttcctttttgagggag	4	20	8	9	0	2	1	0	1	2	0	5	2	4	2	2	2	0	2	2	2	1	8			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr3:142123863C>G	ENST00000264951.4	-	16	1886	c.1769G>C	c.(1768-1770)aGg>aCg	p.R590T	RNU6-1294P_ENST00000515995.1_RNA|XRN1_ENST00000392981.2_Missense_Mutation_p.R590T	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	590					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						GTTTCTTTTCCTCTCTTCCTT	0.408																																					p.R590T		Atlas-SNP	.											.	XRN1	138	.	0			c.G1769C						PASS	.						162	148	152					3																	142123863		2203	4300	6503	SO:0001583	missense	54464	exon16			CTTTTCCTCTCTT	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.1769G>C	chr3.hg19:g.142123863C>G	ENSP00000264951:p.Arg590Thr	76.0	0.0	.		82.0	35.0	.	NM_001042604	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Missense_Mutation	SNP	ENST00000264951.4	hg19	CCDS3123.1	.	.	.	.	.	.	.	.	.	.	C	13.86	2.363718	0.41902	.	.	ENSG00000114127	ENST00000264951;ENST00000392981	T;T	0.26373	1.74;1.74	5.53	2.35	0.29111	.	0.408805	0.27109	N	0.020895	T	0.15825	0.0381	L	0.31664	0.95	0.80722	D	1	B;P;B	0.34800	0.067;0.469;0.417	B;B;B	0.33121	0.024;0.158;0.142	T	0.05599	-1.0875	10	0.40728	T	0.16	-9.364	7.0395	0.25013	0.0:0.5382:0.0:0.4618	.	451;590;590	B3KW17;Q8IZH2-2;Q8IZH2	.;.;XRN1_HUMAN	T	590	ENSP00000264951:R590T;ENSP00000376707:R590T	ENSP00000264951:R590T	R	-	2	0	XRN1	143606553	1.000000	0.71417	0.999000	0.59377	0.961000	0.63080	1.245000	0.32790	0.691000	0.31592	-0.145000	0.13849	AGG	.	.	.	none		0.408	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001		G	142123863	C	G	142123863	3	3	170	1	0	0	0	0	1	0	0	0	17471	681	24	4	3459	4	XRN1	3	142123863	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08	14744264	142123863	55898567	16	9985											
FRYL	285527	hgsc.bcm.edu	37	chr4	48578146	48578146	+	Silent	SNP	T	T	C																															gtggaagatgacgatgttgcTgcactgcagcaaaggatcag																										TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr4:48578146T>C	ENST00000503238.1	-	21	2621	c.2622A>G	c.(2620-2622)gcA>gcG	p.A874A	FRYL_ENST00000537810.1_Silent_p.A874A|FRYL_ENST00000358350.4_Silent_p.A874A|FRYL_ENST00000507711.1_Silent_p.A874A|RNU5E-3P_ENST00000515913.1_RNA|FRYL_ENST00000264319.7_5'UTR			O94915	FRYL_HUMAN	FRY-like	874					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						ACGATGTTGCTGCACTGCAGC	0.473																																					p.A874A		Atlas-SNP	.											.	FRYL	242	.	0			c.A2622G						PASS	.						125	127	126					4																	48578146		1946	4149	6095	SO:0001819	synonymous_variant	285527	exon24			TGTTGCTGCACTG	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.2622A>G	chr4.hg19:g.48578146T>C		152.0	0.0	.		97.0	29.0	.	NM_015030	O95640|Q8WTZ5|Q9NT40	Silent	SNP	ENST00000503238.1	hg19	CCDS43227.1																																																																																			.	.	.	none		0.473	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			C	48578146	T	C	48578146	2	2	170	1	0	0	0	0	0	0	0	1	6071	1567	55	3		3	FRYL	4	48578146	Silent	SNP	T	TCGA-G7-6790-01A-11D-1961-08		48578146	142576130	17	9986	95	2									
FRYL	285527	hgsc.bcm.edu	37	chr4	48578148	48578148	+	Missense_Mutation	SNP	C	C	T																															ggaagatgacgatgttgctgCactgcagcaaaggatcagat																										TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr4:48578148C>T	ENST00000503238.1	-	21	2619	c.2620G>A	c.(2620-2622)Gca>Aca	p.A874T	FRYL_ENST00000537810.1_Missense_Mutation_p.A874T|FRYL_ENST00000358350.4_Missense_Mutation_p.A874T|FRYL_ENST00000507711.1_Missense_Mutation_p.A874T|RNU5E-3P_ENST00000515913.1_RNA|FRYL_ENST00000264319.7_5'UTR			O94915	FRYL_HUMAN	FRY-like	874					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						GATGTTGCTGCACTGCAGCAA	0.468																																					p.A874T		Atlas-SNP	.											.	FRYL	242	.	0			c.G2620A						PASS	.						122	124	124					4																	48578148		1943	4148	6091	SO:0001583	missense	285527	exon24			TTGCTGCACTGCA	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.2620G>A	chr4.hg19:g.48578148C>T	ENSP00000426064:p.Ala874Thr	148.0	0.0	.		97.0	27.0	.	NM_015030	O95640|Q8WTZ5|Q9NT40	Missense_Mutation	SNP	ENST00000503238.1	hg19	CCDS43227.1	.	.	.	.	.	.	.	.	.	.	C	15.58	2.875024	0.51695	.	.	ENSG00000075539	ENST00000503238;ENST00000358350;ENST00000537810;ENST00000507711	T;T;T;T	0.34859	2.35;2.35;2.35;1.34	5.14	5.14	0.70334	.	0.163703	0.41001	U	0.000974	T	0.19685	0.0473	N	0.08118	0	0.80722	D	1	B;B	0.25441	0.043;0.126	B;B	0.24701	0.011;0.055	T	0.09707	-1.0662	10	0.02654	T	1	.	18.6027	0.91255	0.0:1.0:0.0:0.0	.	874;874	F2Z2S2;O94915	.;FRYL_HUMAN	T	874	ENSP00000426064:A874T;ENSP00000351113:A874T;ENSP00000441114:A874T;ENSP00000421584:A874T	ENSP00000351113:A874T	A	-	1	0	FRYL	48272905	1.000000	0.71417	0.894000	0.35097	0.417000	0.31264	4.730000	0.62015	2.370000	0.80446	0.467000	0.42956	GCA	.	.	.	none		0.468	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			T	48578148	C	T	48578148	3	4	170	1	0	0	0	0	1	0	0	0	6071	710	25	2	6585	2	FRYL	4	48578148	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08	2	48578148	142576128	18	9987	95	2									
SHROOM3	57619	hgsc.bcm.edu	37	chr4	77675996	77675996	+	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	cagcccctgattttgcaaacCtgaagcactatcaaaaacag	15	8	6	12	0	1	2	1	2	0	0	1	2	1	2	3	0	5	2	3	0	5	3			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr4:77675996C>A	ENST00000296043.6	+	7	5313	c.4360C>A	c.(4360-4362)Ctg>Atg	p.L1454M	RP11-359D14.2_ENST00000452412.1_RNA	NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	1454					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)			TTTTGCAAACCTGAAGCACTA	0.567																																					p.L1454M		Atlas-SNP	.											.	SHROOM3	134	.	0			c.C4360A						PASS	.						52	54	54					4																	77675996		2203	4300	6503	SO:0001583	missense	57619	exon7			GCAAACCTGAAGC	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.4360C>A	chr4.hg19:g.77675996C>A	ENSP00000296043:p.Leu1454Met	73.0	0.0	.		57.0	21.0	.	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Missense_Mutation	SNP	ENST00000296043.6	hg19	CCDS3579.2	.	.	.	.	.	.	.	.	.	.	C	10.47	1.358823	0.24598	.	.	ENSG00000138771	ENST00000296043	T	0.22743	1.94	5.23	5.23	0.72850	.	1.171820	0.06113	N	0.667490	T	0.22820	0.0551	N	0.24115	0.695	0.09310	N	1	D	0.56521	0.976	P	0.47744	0.556	T	0.17837	-1.0356	10	0.33141	T	0.24	-1.3606	12.5341	0.56133	0.0:0.9214:0.0:0.0786	.	1454	Q8TF72	SHRM3_HUMAN	M	1454	ENSP00000296043:L1454M	ENSP00000296043:L1454M	L	+	1	2	SHROOM3	77895020	0.251000	0.23961	0.544000	0.28141	0.006000	0.05464	2.227000	0.42972	2.716000	0.92895	0.655000	0.94253	CTG	.	.	.	none		0.567	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859		A	77675996	C	A	77675996	3	1	170	1	0	0	0	0	1	0	0	0	14308	680	24	4	4386	4	SHROOM3	4	77675996	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08	29097848	77675996	113478280	19	9988											
SLC39A8	64116	hgsc.bcm.edu	37	chr4	103225511	103225511	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgacattatcaaaatggataTgtccattagcttctgtgaca	13	14	7	7	0	2	2	1	2	1	0	3	3	3	3	1	1	1	1	1	1	5	4			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr4:103225511T>C	ENST00000394833.2	-	5	1279	c.803A>G	c.(802-804)cAt>cGt	p.H268R	SLC39A8_ENST00000356736.4_Missense_Mutation_p.H268R|SLC39A8_ENST00000510255.1_5'Flank|SLC39A8_ENST00000424970.2_Missense_Mutation_p.H268R	NM_001135148.1|NM_022154.5	NP_001128620.1|NP_071437.3	Q9C0K1	S39A8_HUMAN	solute carrier family 39 (zinc transporter), member 8	268					transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)|plasma membrane (GO:0005886)	metal ion transmembrane transporter activity (GO:0046873)			large_intestine(1)|lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Hepatocellular(203;0.217)		all cancers(1;9.78e-10)|OV - Ovarian serous cystadenocarcinoma(123;1.52e-09)|GBM - Glioblastoma multiforme(1;0.000142)		AAAATGGATATGTCCATTAGC	0.363																																					p.H268R		Atlas-SNP	.											.	SLC39A8	24	.	0			c.A803G						PASS	.						158	138	145					4																	103225511		2203	4300	6503	SO:0001583	missense	64116	exon5			TGGATATGTCCAT		CCDS3656.1, CCDS47117.1	4q22-q24	2013-05-22			ENSG00000138821	ENSG00000138821		"Solute carriers"	20862	protein-coding gene	gene with protein product		608732	"solute carrier family 39 (metal ion transporter), member 8"			12504855, 12659941	Standard	NM_001135146		Approved	BIGM103	uc003hwc.2	Q9C0K1	OTTHUMG00000131120	ENST00000394833.2:c.803A>G	chr4.hg19:g.103225511T>C	ENSP00000378310:p.His268Arg	68.0	0.0	.		68.0	23.0	.	NM_022154	B4E2H3|Q96SM9|Q9BVC0|Q9NSA4	Missense_Mutation	SNP	ENST00000394833.2	hg19	CCDS3656.1	.	.	.	.	.	.	.	.	.	.	T	9.588	1.125353	0.20959	.	.	ENSG00000138821	ENST00000424970;ENST00000356736;ENST00000394833	T;T;T	0.44881	0.91;0.91;0.91	4.81	4.81	0.61882	.	0.460729	0.18153	U	0.150001	T	0.25938	0.0632	L	0.27053	0.805	0.33924	D	0.641179	B;B;B	0.32350	0.366;0.002;0.016	B;B;B	0.28385	0.089;0.003;0.048	T	0.32640	-0.9899	10	0.16896	T	0.51	-3.0995	9.2864	0.37760	0.1605:0.0:0.0:0.8395	.	268;268;201	B4E2H3;Q9C0K1;Q9C0K1-2	.;S39A8_HUMAN;.	R	268	ENSP00000394548:H268R;ENSP00000349174:H268R;ENSP00000378310:H268R	ENSP00000349174:H268R	H	-	2	0	SLC39A8	103444534	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	2.339000	0.43965	1.930000	0.55929	0.528000	0.53228	CAT	.	.	.	none		0.363	SLC39A8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253798.1	NM_022154		C	103225511	T	C	103225511	3	2	170	1	0	0	0	0	1	0	0	0	14637	1464	51	3	672	3	SLC39A8	4	103225511	Missense_Mutation	SNP	T	TCGA-G7-6790-01A-11D-1961-08	25549515	103225511	87928765	20	9989											
CTNNA1	1495	hgsc.bcm.edu	37	chr5	138266342	138266342	+	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	tggagatgacagactttaccCggtgagcagcaccccggccc	9	6	12	14	2	0	4	0	2	0	2	0	5	0	4	4	3	3	2	4	3	1	2			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr5:138266342C>T	ENST00000302763.7	+	15	2281	c.2191C>T	c.(2191-2193)Cga>Tga	p.R731*	CTNNA1_ENST00000518825.1_Splice_Site_p.R731*|CTNNA1_ENST00000540387.1_Splice_Site_p.R361*|CTNNA1_ENST00000355078.5_Splice_Site_p.R628*	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	731					adherens junction organization (GO:0034332)|aging (GO:0007568)|apical junction assembly (GO:0043297)|axon regeneration (GO:0031103)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular protein localization (GO:0034613)|cellular response to indole-3-methanol (GO:0071681)|epithelial cell-cell adhesion (GO:0090136)|establishment or maintenance of cell polarity (GO:0007163)|gap junction assembly (GO:0016264)|male gonad development (GO:0008584)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell motility (GO:2000146)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|negative regulation of neuroblast proliferation (GO:0007406)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of smoothened signaling pathway (GO:0045880)|protein heterooligomerization (GO:0051291)|response to estrogen (GO:0043627)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|catenin complex (GO:0016342)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|gamma-catenin binding (GO:0045295)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|vinculin binding (GO:0017166)	p.R731R(1)		NS(1)|breast(7)|cervix(2)|endometrium(4)|kidney(6)|large_intestine(16)|lung(9)|oesophagus(2)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	52			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AGACTTTACCCGGTGAGCAGC	0.582																																					p.R731X		Atlas-SNP	.											.	CTNNA1	114	.	1	Substitution - coding silent(1)	lung(1)	c.C2191T						PASS	.						134	129	130					5																	138266342		2203	4300	6503	SO:0001630	splice_region_variant	1495	exon15			TTTACCCGGTGAG	D13866	CCDS34243.1, CCDS75315.1	5q31.2	2008-02-05	2002-08-29			ENSG00000044115			2509	protein-coding gene	gene with protein product		116805	"catenin (cadherin-associated protein), alpha 1 (102kD)"			1924379	Standard	XM_005271898		Approved	CAP102	uc003ldh.3	P35221		ENST00000302763.7:c.2192+1C>T	chr5.hg19:g.138266342C>T		191.0	0.0	.		195.0	75.0	.	NM_001903	Q12795|Q8N1C0	Nonsense_Mutation	SNP	ENST00000302763.7	hg19	CCDS34243.1	.	.	.	.	.	.	.	.	.	.	C	36	5.632988	0.96682	.	.	ENSG00000044115	ENST00000355078;ENST00000302763;ENST00000537034;ENST00000541863;ENST00000518825;ENST00000540387;ENST00000520520	.	.	.	5.77	3.89	0.44902	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.7916	13.7731	0.63038	0.4172:0.5828:0.0:0.0	.	.	.	.	X	628;731;731;716;731;361;6	.	ENSP00000304669:R731X	R	+	1	2	CTNNA1	138294241	1.000000	0.71417	1.000000	0.80357	0.408000	0.30992	4.424000	0.59868	1.565000	0.49641	0.655000	0.94253	CGA	.	.	.	none		0.582	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903	Nonsense_Mutation	T	138266342	C	T	138266342	5	4	170	1	0	0	0	0	0	0	1	0	4014	666	23	1	2245	1	CTNNA1	5	138266342	Splice_Site	SNP	C	TCGA-G7-6790-01A-11D-1961-08		138266342	42648918	21	9990											
FAM71B	153745	hgsc.bcm.edu	37	chr5	156590094	156590094	+	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	gtggagatgaggggtcccacTgctggtccttcagttctttc	5	13	13	10	0	2	2	1	1	1	1	5	3	4	2	2	4	1	2	2	4	0	3			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr5:156590094T>A	ENST00000302938.4	-	2	1277	c.1182A>T	c.(1180-1182)gcA>gcT	p.A394A		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	394						nucleus (GO:0005634)				NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GGGGTCCCACTGCTGGTCCTT	0.552																																					p.A394A		Atlas-SNP	.											.	FAM71B	145	.	0			c.A1182T						PASS	.						62	65	64					5																	156590094		2203	4300	6503	SO:0001819	synonymous_variant	153745	exon2			TCCCACTGCTGGT		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.1182A>T	chr5.hg19:g.156590094T>A		103.0	0.0	.		92.0	36.0	.	NM_130899	Q1EDD9|Q8TC64|Q96LY8	Silent	SNP	ENST00000302938.4	hg19	CCDS4335.1																																																																																			.	.	.	none		0.552	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899		A	156590094	T	A	156590094	2	1	170	1	0	0	0	0	0	0	0	1	5615	1567	55	5		5	FAM71B	5	156590094	Silent	SNP	T	TCGA-G7-6790-01A-11D-1961-08	18323752	156590094	24325166	22	9991											
RPL10A	4736	hgsc.bcm.edu	37	chr6	35437266	35437267	+	Frame_Shift_Ins	INS	-	-	A																															acatggacatcgaggcgctgINSaaaaaactcaacaagaataa																										TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr6:35437266_35437267insA	ENST00000322203.6	+	4	297_298	c.270_271insA	c.(271-273)aaafs	p.K91fs	RPL10A_ENST00000467020.1_3'UTR	NM_007104.4	NP_009035.3	P62906	RL10A_HUMAN	ribosomal protein L10a	91					anatomical structure morphogenesis (GO:0009653)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|large_intestine(2)|ovary(1)	4						TCGAGGCGCTGAAAAAACTCAA	0.55																																					p.L90fs		Atlas-INDEL	.											.	RPL10A	13	.	0			c.270_271insA						PASS	.																																			SO:0001589	frameshift_variant	4736	exon4			.	U12404	CCDS4806.1	6p21.31	2011-04-06			ENSG00000198755	ENSG00000198755		"L ribosomal proteins"	10299	protein-coding gene	gene with protein product		615660		NEDD6		7609734, 9647638	Standard	NM_007104		Approved	Csa-19, L10A	uc003okp.1	P62906	OTTHUMG00000014566	ENST00000322203.6:c.276dupA	chr6.hg19:g.35437272_35437272dupA	ENSP00000363018:p.Lys91fs	52.0	0.0	0		44.0	12.0	0.272727	NM_007104	B2R801|P52859|P53025|Q5TZT6|Q8J013	Frame_Shift_Ins	INS	ENST00000322203.6	hg19	CCDS4806.1																																																																																			.	.	.	none		0.55	RPL10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040283.1	NM_007104		A	35437267	-	A	35437266	7	5	170	1	0	1	1	0	0	0	0	0	13568	1277	45	0	284	0	RPL10A	6	35437266	Frame_Shift_Ins	INS	-	TCGA-G7-6790-01A-11D-1961-08		35437266	135677801	23	9992											
FTSJD2	23070	hgsc.bcm.edu	37	chr6	37442389	37442389	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgccccgggacactctgctAtctgtggaaattgtgcatga	8	11	11	11	1	2	1	0	1	2	0	2	3	2	3	2	2	3	2	2	2	2	2			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr6:37442389A>G	ENST00000373451.4	+	18	2075	c.1911A>G	c.(1909-1911)ctA>ctG	p.L637L		NM_015050.2	NP_055865.1	Q8N1G2	CMTR1_HUMAN	cap methyltransferase 1	637					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)										ACACTCTGCTATCTGTGGAAA	0.572																																					p.L637L		Atlas-SNP	.											.	FTSJD2	64	.	0			c.A1911G						PASS	.						105	100	102					6																	37442389		2203	4300	6503	SO:0001819	synonymous_variant	23070	exon18			TCTGCTATCTGTG	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.1911A>G	chr6.hg19:g.37442389A>G		109.0	0.0	.		101.0	31.0	.	NM_015050	A8K949|Q14670|Q96FJ9	Silent	SNP	ENST00000373451.4	hg19	CCDS4835.1																																																																																			.	.	.	none		0.572	CMTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040408.1	NM_015050		G	37442389	A	G	37442389	2	3	170	1	0	0	0	0	0	0	0	1	6098	436	16	3		3	FTSJD2	6	37442389	Silent	SNP	A	TCGA-G7-6790-01A-11D-1961-08	2005123	37442389	133672678	24	9993											
RUNX2	860	hgsc.bcm.edu	37	chr6	45390445	45390445	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagcaacagcagcagcagcaAcagcagcagcagcagcagca	16	0	11	14	0	0	0	0	0	0	0	0	0	0	0	0	0	13	11	0	0	2	0	rs563987595	byFrequency	TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr6:45390445A>G	ENST00000371438.1	+	2	532	c.174A>G	c.(172-174)caA>caG	p.Q58Q	RP1-244F24.1_ENST00000606796.1_RNA|RUNX2_ENST00000371432.3_Silent_p.Q44Q|RUNX2_ENST00000371436.6_Silent_p.Q58Q|RUNX2_ENST00000541979.1_Silent_p.Q126Q|RUNX2_ENST00000465038.2_Silent_p.Q58Q|RUNX2_ENST00000359524.5_Silent_p.Q44Q|RUNX2_ENST00000576263.1_Silent_p.Q58Q|RUNX2_ENST00000352853.5_Silent_p.Q126Q	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	58	Poly-Gln.				BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						agcagcagcaacagcagcagc	0.731													A|||	6	0.00119808	0.0015	0	5008	,	,		8050	0.002		0	False		,,,				2504	0.002				p.Q58Q		Atlas-SNP	.											RUNX2_ENST00000352853,lower_third,carcinoma,0,2	RUNX2	128	.	0			c.A174G						PASS	.						16	24	21					6																	45390445		1589	3298	4887	SO:0001819	synonymous_variant	860	exon3			GCAGCAACAGCAG	AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.174A>G	chr6.hg19:g.45390445A>G		93.0	0.0	.		85.0	4.0	.	NM_001024630	O14614|O14615|O95181	Silent	SNP	ENST00000371438.1	hg19	CCDS43467.2																																																																																			.	.	.	none		0.731	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		G	45390445	A	G	45390445	2	3	170	1	0	0	0	0	0	0	0	1	13761	40	2	3		3	RUNX2	6	45390445	Silent	SNP	A	TCGA-G7-6790-01A-11D-1961-08	7948056	45390445	125724622	25	9994											
ADCY1	107	hgsc.bcm.edu	37	chr7	45747951	45747951	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccatctgtttacacctaggcTaagaagtccatctcctccca	10	11	5	15	0	2	1	0	0	2	1	5	1	4	1	5	1	1	2	5	1	4	4			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr7:45747951T>C	ENST00000297323.7	+	18	2842	c.2820T>C	c.(2818-2820)gcT>gcC	p.A940A		NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	940			A -> T (in dbSNP:rs45444695).		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)	ACACCTAGGCTAAGAAGTCCA	0.522																																					p.A940A		Atlas-SNP	.											.	ADCY1	187	.	0			c.T2820C						PASS	.						179	135	150					7																	45747951		2203	4300	6503	SO:0001819	synonymous_variant	107	exon18			CTAGGCTAAGAAG	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.2820T>C	chr7.hg19:g.45747951T>C		83.0	0.0	.		104.0	56.0	.	NM_021116	A4D2L8|Q75MI1	Silent	SNP	ENST00000297323.7	hg19	CCDS34631.1																																																																																			.	.	.	none		0.522	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2	NM_021116		C	45747951	T	C	45747951	2	2	170	1	0	0	0	0	0	0	0	1	292	1509	53	3		3	ADCY1	7	45747951	Silent	SNP	T	TCGA-G7-6790-01A-11D-1961-08		45747951	113390712	26	9995											
MLL5	55904	hgsc.bcm.edu	37	chr7	104717426	104717426	+	Missense_Mutation	SNP	T	T	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	ttagggttcagctccagagaTtgatccttcatctgatggtt	8	15	10	8	0	3	3	2	2	1	1	5	4	5	3	2	2	1	3	2	2	1	5			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr7:104717426T>G	ENST00000311117.3	+	10	1330	c.785T>G	c.(784-786)aTt>aGt	p.I262S	KMT2E_ENST00000257745.4_Missense_Mutation_p.I262S|KMT2E_ENST00000334877.4_Missense_Mutation_p.I262S|KMT2E_ENST00000334914.7_De_novo_Start_InFrame|KMT2E_ENST00000476671.1_Missense_Mutation_p.I262S	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	262					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										GCTCCAGAGATTGATCCTTCA	0.418																																					p.I262S		Atlas-SNP	.											.	MLL5	173	.	0			c.T785G						PASS	.						89	88	88					7																	104717426		2203	4300	6503	SO:0001583	missense	55904	exon9			CAGAGATTGATCC	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.785T>G	chr7.hg19:g.104717426T>G	ENSP00000312379:p.Ile262Ser	41.0	0.0	.		59.0	25.0	.	NM_018682	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	hg19	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	T	10.81	1.456010	0.26161	.	.	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745;ENST00000478990;ENST00000476671;ENST00000537308	D;D;D;D;D	0.95482	-2.85;-2.47;-2.85;-3.72;-3.22	6.07	4.92	0.64577	.	0.471220	0.25735	N	0.028644	D	0.92639	0.7661	L	0.44542	1.39	0.80722	D	1	D;B	0.54207	0.965;0.372	P;B	0.46758	0.526;0.083	D	0.89734	0.3928	10	0.08837	T	0.75	.	12.0897	0.53719	0.0:0.0668:0.0:0.9332	.	262;262	Q8IZD2;Q8IZD2-3	MLL5_HUMAN;.	S	262;262;262;262;262;120;262;196	ENSP00000312379:I262S;ENSP00000335599:I262S;ENSP00000257745:I262S;ENSP00000419883:I120S;ENSP00000417888:I262S	ENSP00000257745:I262S	I	+	2	0	MLL5	104504662	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.809000	0.38922	1.114000	0.41781	0.533000	0.62120	ATT	.	.	.	none		0.418	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			G	104717426	T	G	104717426	3	3	170	1	0	0	0	0	1	0	0	0	9631	1493	52	5	815	5	MLL5	7	104717426	Missense_Mutation	SNP	T	TCGA-G7-6790-01A-11D-1961-08	58969475	104717426	54421237	27	9996											
SMO	6608	hgsc.bcm.edu	37	chr7	128845571	128845571	+	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	cccagttcatggatggtgccCgccgagagatcgtctgccgt	6	9	13	13	4	2	1	1	0	1	1	3	4	2	2	4	2	2	1	4	2	0	1			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr7:128845571C>A	ENST00000249373.3	+	4	1148	c.868C>A	c.(868-870)Cgc>Agc	p.R290S		NM_005631.4	NP_005622.1	Q99835	SMO_HUMAN	smoothened, frizzled class receptor	290					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)	p.R290S(1)		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)	GGATGGTGCCCGCCGAGAGAT	0.587			Mis		skin basal cell																																p.R290S		Atlas-SNP	.		Dom	yes		7	7q31-q32	6608	smoothened homolog (Drosophila)		E	SMO,NS,malignant_melanoma,-1,2	SMO	145	.	1	Substitution - Missense(1)	lung(1)	c.C868A						PASS	.						58	58	58					7																	128845571		2203	4300	6503	SO:0001583	missense	6608	exon4			GGTGCCCGCCGAG	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.868C>A	chr7.hg19:g.128845571C>A	ENSP00000249373:p.Arg290Ser	90.0	0.0	.		115.0	5.0	.	NM_005631	A4D1K5	Missense_Mutation	SNP	ENST00000249373.3	hg19	CCDS5811.1	.	.	.	.	.	.	.	.	.	.	C	34	5.372657	0.95923	.	.	ENSG00000128602	ENST00000249373	D	0.82167	-1.58	5.57	5.57	0.84162	GPCR, family 2-like (1);	0.097576	0.64402	D	0.000001	D	0.91355	0.7273	M	0.78637	2.42	0.80722	D	1	D	0.69078	0.997	D	0.81914	0.995	D	0.92044	0.5643	10	0.87932	D	0	.	18.5223	0.90958	0.0:1.0:0.0:0.0	.	290	Q99835	SMO_HUMAN	S	290	ENSP00000249373:R290S	ENSP00000249373:R290S	R	+	1	0	SMO	128632807	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.997000	0.70646	2.620000	0.88729	0.491000	0.48974	CGC	.	.	.	none		0.587	SMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350986.1	NM_005631		A	128845571	C	A	128845571	3	1	170	1	0	0	0	0	1	0	0	0	14813	652	23	4	882	4	SMO	7	128845571	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08	24128145	128845571	30293092	28	9997											
COL14A1	7373	hgsc.bcm.edu	37	chr8	121237425	121237425	+	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	atctatgatgaaggacagtcAgagcctctgactggagtttt	11	12	11	7	0	3	4	1	3	2	1	3	6	3	6	1	2	1	1	1	2	2	3			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr8:121237425A>T	ENST00000297848.3	+	15	2106	c.1836A>T	c.(1834-1836)tcA>tcT	p.S612S	COL14A1_ENST00000247781.3_Silent_p.S517S|COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000309791.4_Silent_p.S612S|COL14A1_ENST00000537875.1_3'UTR	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1											NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			AAGGACAGTCAGAGCCTCTGA	0.418																																					p.S612S		Atlas-SNP	.											.	COL14A1	292	.	0			c.A1836T						PASS	.						76	75	76					8																	121237425		2203	4300	6503	SO:0001819	synonymous_variant	7373	exon15			ACAGTCAGAGCCT		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.1836A>T	chr8.hg19:g.121237425A>T		99.0	0.0	.		78.0	20.0	.	NM_021110		Silent	SNP	ENST00000297848.3	hg19	CCDS34938.1																																																																																			.	.	.	none		0.418	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		T	121237425	A	T	121237425	2	4	170	1	0	0	0	0	0	0	0	1	3673	175	7	5		5	COL14A1	8	121237425	Silent	SNP	A	TCGA-G7-6790-01A-11D-1961-08		121237425	25126597	29	9998											
CNTLN	54875	hgsc.bcm.edu	37	chr9	17332674	17332674	+	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	gactcagaagagctacagaaGctgagaaaagctgaaagaaa	20	4	11	6	0	1	6	1	2	0	5	1	8	1	6	0	0	4	3	0	0	7	1			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr9:17332674G>A	ENST00000380647.3	+	10	1674	c.1590G>A	c.(1588-1590)aaG>aaA	p.K530K	CNTLN_ENST00000262360.5_Silent_p.K530K|CNTLN_ENST00000425824.1_Silent_p.K530K			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	530					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)		AGCTACAGAAGCTGAGAAAAG	0.378																																					p.K530K		Atlas-SNP	.											.	CNTLN	128	.	0			c.G1590A						PASS	.						74	70	71					9																	17332674		1836	4082	5918	SO:0001819	synonymous_variant	54875	exon10			ACAGAAGCTGAGA	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.1590G>A	chr9.hg19:g.17332674G>A		69.0	0.0	.		71.0	17.0	.	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Silent	SNP	ENST00000380647.3	hg19	CCDS43789.1																																																																																			.	.	.	none		0.378	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		A	17332674	G	A	17332674	2	1	170	1	0	0	0	0	0	0	0	1	3641	962	34	2		2	CNTLN	9	17332674	Silent	SNP	G	TCGA-G7-6790-01A-11D-1961-08		17332674	123880757	30	9999											
ACO1	48	hgsc.bcm.edu	37	chr9	32448942	32448942	+	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	acgagcgcattcaccgcagtAacctggttgggatgggtgtg	8	9	15	9	3	1	0	1	0	0	0	1	2	1	1	2	3	2	4	2	3	1	3			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr9:32448942A>T	ENST00000309951.6	+	20	2557	c.2419A>T	c.(2419-2421)Aac>Tac	p.N807Y	ACO1_ENST00000379923.1_Missense_Mutation_p.N807Y|ACO1_ENST00000541043.1_Missense_Mutation_p.N708Y	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	807					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)		TCACCGCAGTAACCTGGTTGG	0.478																																					p.N807Y		Atlas-SNP	.											.	ACO1	149	.	0			c.A2419T						PASS	.						131	111	117					9																	32448942		2203	4300	6503	SO:0001583	missense	48	exon20			CGCAGTAACCTGG	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.2419A>T	chr9.hg19:g.32448942A>T	ENSP00000309477:p.Asn807Tyr	93.0	0.0	.		74.0	29.0	.	NM_002197	D3DRK7|Q14652|Q5VZA7	Missense_Mutation	SNP	ENST00000309951.6	hg19	CCDS6525.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.351925	0.82132	.	.	ENSG00000122729	ENST00000309951;ENST00000379923;ENST00000541043	T;T;T	0.61392	0.11;0.11;1.13	5.83	5.83	0.93111	Aconitase/3-isopropylmalate dehydratase, swivel (2);Aconitase A/isopropylmalate dehydratase small subunit, swivel (1);	0.000000	0.85682	D	0.000000	D	0.86711	0.5998	H	0.99600	4.65	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92343	0.5883	10	0.87932	D	0	-31.6045	15.1831	0.72975	1.0:0.0:0.0:0.0	.	807	P21399	ACOC_HUMAN	Y	807;807;708	ENSP00000309477:N807Y;ENSP00000369255:N807Y;ENSP00000438733:N708Y	ENSP00000309477:N807Y	N	+	1	0	ACO1	32438942	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.996000	0.63914	2.227000	0.72691	0.528000	0.53228	AAC	.	.	.	none		0.478	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197		T	32448942	A	T	32448942	3	4	170	1	0	0	0	0	1	0	0	0	146	362	13	5	2493	5	ACO1	9	32448942	Missense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08	15116268	32448942	108764489	31	10000											
HNRNPK	3190	hgsc.bcm.edu	37	chr9	86585225	86585225	+	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	tttaatccgctgaccaccttTgccaataatagatccagcca	12	11	5	13	1	0	2	0	1	0	1	2	2	2	2	6	0	2	1	6	0	4	5			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr9:86585225T>A	ENST00000376264.2	-	16	1471	c.1213A>T	c.(1213-1215)Aaa>Taa	p.K405*	HNRNPK_ENST00000351839.3_Nonsense_Mutation_p.K405*|RP11-575L7.8_ENST00000448389.1_RNA|MIR7-1_ENST00000384871.1_RNA|HNRNPK_ENST00000376263.3_Nonsense_Mutation_p.K405*|HNRNPK_ENST00000360384.5_Nonsense_Mutation_p.K405*|HNRNPK_ENST00000376281.4_Nonsense_Mutation_p.K405*	NM_002140.3|NM_031262.2	NP_002131.2|NP_112552.1	P61978	HNRPK_HUMAN	heterogeneous nuclear ribonucleoprotein K	405	2 X 22 AA approximate repeats.|5 X 4 AA repeats of G-X-G-G.|KH 3. {ECO:0000255|PROSITE- ProRule:PRU00117}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter (GO:0072369)|regulation of low-density lipoprotein particle clearance (GO:0010988)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|single-stranded DNA binding (GO:0003697)			endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|stomach(1)	19						TGACCACCTTTGCCAATAATA	0.368																																					p.K405X		Atlas-SNP	.											.	HNRNPK	49	.	0			c.A1213T						PASS	.						60	58	59					9																	86585225		2203	4300	6503	SO:0001587	stop_gained	3190	exon16			CACCTTTGCCAAT		CCDS6667.1, CCDS6668.1	9q21.32-q21.33	2011-10-24		2008-04-18	ENSG00000165119	ENSG00000165119			5044	protein-coding gene	gene with protein product	"transformation upregulated nuclear protein"	600712		HNRPK		8107114	Standard	NM_031263		Approved	CSBP, TUNP	uc004anf.4	P61978	OTTHUMG00000020107	ENST00000376264.2:c.1213A>T	chr9.hg19:g.86585225T>A	ENSP00000365440:p.Lys405*	60.0	0.0	.		71.0	24.0	.	NM_031262	Q07244|Q15671|Q59F98|Q5T6W4|Q60577|Q922Y7|Q96J62	Nonsense_Mutation	SNP	ENST00000376264.2	hg19	CCDS6667.1	.	.	.	.	.	.	.	.	.	.	T	38	7.091735	0.98059	.	.	ENSG00000165119	ENST00000376281;ENST00000376264;ENST00000376263;ENST00000376268;ENST00000351839;ENST00000435158;ENST00000360384;ENST00000376258	.	.	.	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.1915	15.5864	0.76485	0.0:0.0:0.0:1.0	.	.	.	.	X	405;405;405;405;405;370;405;400	.	ENSP00000317788:K405X	K	-	1	0	HNRNPK	85775045	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.510000	0.81708	2.142000	0.66516	0.482000	0.46254	AAA	.	.	.	none		0.368	HNRNPK-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052846.2			A	86585225	T	A	86585225	4	1	170	1	0	0	0	0	0	1	0	0	7276	1821	63	5	224	5	HNRNPK	9	86585225	Nonsense_Mutation	SNP	T	TCGA-G7-6790-01A-11D-1961-08	54136283	86585225	54628206	32	10001											
ADAMTS13	11093	hgsc.bcm.edu	37	chr9	136305491	136305491	+	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	ggatcggagggcgctatgtcGtggctgggaagatgagcatc	8	8	18	7	3	0	2	0	1	0	1	3	5	0	5	0	5	1	3	0	5	2	1			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr9:136305491G>C	ENST00000371929.3	+	16	2257	c.1813G>C	c.(1813-1815)Gtg>Ctg	p.V605L	ADAMTS13_ENST00000371916.1_3'UTR|ADAMTS13_ENST00000485925.1_3'UTR|ADAMTS13_ENST00000355699.2_Missense_Mutation_p.V605L|ADAMTS13_ENST00000356589.2_Missense_Mutation_p.V574L|ADAMTS13_ENST00000536611.1_Missense_Mutation_p.V277L	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	605	Spacer.				cell-matrix adhesion (GO:0007160)|glycoprotein metabolic process (GO:0009100)|integrin-mediated signaling pathway (GO:0007229)|peptide catabolic process (GO:0043171)|platelet activation (GO:0030168)|protein processing (GO:0016485)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to interleukin-4 (GO:0070670)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(4)	36				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		GCGCTATGTCGTGGCTGGGAA	0.627																																					p.V605L		Atlas-SNP	.											.	ADAMTS13	113	.	0			c.G1813C						PASS	.						139	98	112					9																	136305491		2203	4300	6503	SO:0001583	missense	11093	exon16			TATGTCGTGGCTG	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.1813G>C	chr9.hg19:g.136305491G>C	ENSP00000360997:p.Val605Leu	70.0	0.0	.		77.0	27.0	.	NM_139027	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Missense_Mutation	SNP	ENST00000371929.3	hg19	CCDS6970.1	.	.	.	.	.	.	.	.	.	.	G	14.87	2.663418	0.47572	.	.	ENSG00000160323	ENST00000371929;ENST00000355699;ENST00000356589;ENST00000536611	T;T;T;T	0.62788	0.04;0.0;0.06;0.49	5.21	4.31	0.51392	.	.	.	.	.	T	0.61912	0.2385	N	0.25825	0.765	0.41780	D	0.989816	D;D;D;D	0.89917	1.0;1.0;1.0;0.992	D;D;D;P	0.91635	0.997;0.999;0.99;0.742	T	0.59241	-0.7491	9	0.02654	T	1	.	12.261	0.54651	0.0833:0.0:0.9167:0.0	.	605;574;605;277	Q76LX8;Q76LX8-3;Q76LX8-2;Q9UGQ1	ATS13_HUMAN;.;.;.	L	605;605;574;277	ENSP00000360997:V605L;ENSP00000347927:V605L;ENSP00000348997:V574L;ENSP00000444504:V277L	ENSP00000347927:V605L	V	+	1	0	ADAMTS13	135295312	1.000000	0.71417	0.300000	0.25030	0.035000	0.12851	5.003000	0.63959	1.191000	0.43056	0.561000	0.74099	GTG	.	.	.	none		0.627	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025		C	136305491	G	C	136305491	3	2	170	1	0	0	0	0	1	0	0	0	258	1145	40	4	1875	4	ADAMTS13	9	136305491	Missense_Mutation	SNP	G	TCGA-G7-6790-01A-11D-1961-08	49720266	136305491	4907940	33	10002											
JMJD1C	221037	hgsc.bcm.edu	37	chr10	64968980	64968980	+	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	aggggtgggctgatgtagccAaggactgggagaattctatt	10	10	16	5	0	1	2	0	1	1	1	1	4	1	3	1	5	1	2	1	5	4	4			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr10:64968980A>T	ENST00000399262.2	-	9	2928	c.2710T>A	c.(2710-2712)Tgg>Agg	p.W904R	JMJD1C_ENST00000399251.1_Missense_Mutation_p.W685R|JMJD1C_ENST00000542921.1_Missense_Mutation_p.W722R|JMJD1C_ENST00000402544.1_Missense_Mutation_p.W685R	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	904					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)					TGATGTAGCCAAGGACTGGGA	0.433																																					p.W904R		Atlas-SNP	.											.	JMJD1C	347	.	0			c.T2710A						PASS	.						65	59	61					10																	64968980		1882	4108	5990	SO:0001583	missense	221037	exon9			GTAGCCAAGGACT	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.2710T>A	chr10.hg19:g.64968980A>T	ENSP00000382204:p.Trp904Arg	57.0	0.0	.		46.0	19.0	.	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	hg19	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.480118	0.84747	.	.	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000399251;ENST00000542921	T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.77624	0.4158	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.79105	-0.1940	10	0.66056	D	0.02	-4.4645	16.5655	0.84588	1.0:0.0:0.0:0.0	.	904;722	Q15652;A0T124	JHD2C_HUMAN;.	R	904;685;685;722	ENSP00000382204:W904R;ENSP00000384990:W685R;ENSP00000382195:W685R;ENSP00000444682:W722R	ENSP00000382195:W685R	W	-	1	0	JMJD1C	64638986	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.372000	0.90127	2.302000	0.77476	0.533000	0.62120	TGG	.	.	.	none		0.433	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		T	64968980	A	T	64968980	3	4	170	1	0	0	0	0	1	0	0	0	7957	130	5	5	4984	5	JMJD1C	10	64968980	Missense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08		64968980	70565767	34	10003											
LRRC4C	57689	hgsc.bcm.edu	37	chr11	40136275	40136275	+	Missense_Mutation	SNP	A	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	tgatgattttggtagtcttcAtgacctcatcaattcctggg	8	16	9	8	0	4	3	3	3	1	0	5	3	5	3	2	2	0	1	2	2	2	5			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr11:40136275A>C	ENST00000278198.2	-	2	3531	c.1568T>G	c.(1567-1569)aTg>aGg	p.M523R	LRRC4C_ENST00000530763.1_Missense_Mutation_p.M523R|LRRC4C_ENST00000528697.1_Missense_Mutation_p.M523R|LRRC4C_ENST00000527150.1_Missense_Mutation_p.M523R			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	523					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)				GGTAGTCTTCATGACCTCATC	0.478																																					p.M523R		Atlas-SNP	.											.	LRRC4C	190	.	0			c.T1568G						PASS	.						174	145	155					11																	40136275		2203	4300	6503	SO:0001583	missense	57689	exon7			GTCTTCATGACCT	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.1568T>G	chr11.hg19:g.40136275A>C	ENSP00000278198:p.Met523Arg	129.0	0.0	.		109.0	29.0	.	NM_001258419	A8K0T1|Q7L0N3	Missense_Mutation	SNP	ENST00000278198.2	hg19	CCDS31464.1	.	.	.	.	.	.	.	.	.	.	A	15.37	2.813848	0.50527	.	.	ENSG00000148948	ENST00000278198;ENST00000527150;ENST00000528697;ENST00000530763	T;T;T;T	0.38887	1.11;1.11;1.11;1.11	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	T	0.63319	0.2501	M	0.69358	2.11	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	T	0.65940	-0.6046	10	0.72032	D	0.01	.	15.6754	0.77316	1.0:0.0:0.0:0.0	.	523	Q9HCJ2	LRC4C_HUMAN	R	523	ENSP00000278198:M523R;ENSP00000436976:M523R;ENSP00000437132:M523R;ENSP00000434761:M523R	ENSP00000278198:M523R	M	-	2	0	LRRC4C	40092851	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.291000	0.77112	0.533000	0.62120	ATG	.	.	.	none		0.478	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929		C	40136275	A	C	40136275	3	2	170	1	0	0	0	0	1	0	0	0	9015	217	8	5	358	5	LRRC4C	11	40136275	Missense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08		40136275	94870241	35	10004											
ACCS	84680	hgsc.bcm.edu	37	chr11	44105011	44105011	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttgaggaggaaatgctgcTctggcgccgctttttggaca	7	12	13	9	2	1	1	0	1	1	0	1	4	1	4	1	4	2	3	1	4	1	3			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr11:44105011T>C	ENST00000263776.8	+	14	1726	c.1292T>C	c.(1291-1293)cTc>cCc	p.L431P		NM_001127219.1|NM_032592.3	NP_001120691.1|NP_115981.1	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)	431					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						GAAATGCTGCTCTGGCGCCGC	0.567																																					p.L431P	Esophageal Squamous(158;148 1889 8077 23160 41213)	Atlas-SNP	.											.	ACCS	64	.	0			c.T1292C						PASS	.						71	65	67					11																	44105011		2203	4300	6503	SO:0001583	missense	84680	exon14			TGCTGCTCTGGCG	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.1292T>C	chr11.hg19:g.44105011T>C	ENSP00000263776:p.Leu431Pro	62.0	0.0	.		68.0	13.0	.	NM_032592	B4E219|Q8WUL4|Q96LX5	Missense_Mutation	SNP	ENST00000263776.8	hg19	CCDS7907.1	.	.	.	.	.	.	.	.	.	.	T	16.09	3.025435	0.54683	.	.	ENSG00000110455	ENST00000263776	D	0.93488	-3.23	5.91	5.91	0.95273	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.073130	0.56097	D	0.000026	D	0.97942	0.9323	H	0.96943	3.91	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99297	1.0900	10	0.87932	D	0	-19.4821	16.0098	0.80391	0.0:0.0:0.0:1.0	.	431	Q96QU6	1A1L1_HUMAN	P	431	ENSP00000263776:L431P	ENSP00000263776:L431P	L	+	2	0	ACCS	44061587	0.997000	0.39634	0.041000	0.18516	0.142000	0.21351	7.315000	0.78998	2.254000	0.74563	0.533000	0.62120	CTC	.	.	.	none		0.567	ACCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389721.1	NM_032592		C	44105011	T	C	44105011	3	2	170	1	0	0	0	0	1	0	0	0	133	1551	54	3	1342	3	ACCS	11	44105011	Missense_Mutation	SNP	T	TCGA-G7-6790-01A-11D-1961-08	3968736	44105011	90901505	36	10005											
MLL2	8085	hgsc.bcm.edu	37	chr12	49434235	49434235	+	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	ggactggaagcgaggggtaaCgggtgatgggcaaaaagctt	12	6	18	5	2	0	1	0	1	0	0	0	4	0	3	0	6	3	3	0	6	4	2	rs375114492		TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr12:49434235C>T	ENST00000301067.7	-	31	7317	c.7318G>A	c.(7318-7320)Gtt>Att	p.V2440I		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2440	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)										CGAGGGGTAACGGGTGATGGG	0.622																																					p.V2440I		Atlas-SNP	.											.	MLL2	1173	.	0			c.G7318A						PASS	.	C	ILE/VAL	1,4177		0,1,2088	40	46	44		7318	5.2	0.8	12		44	0,8456		0,0,4228	no	missense	MLL2	NM_003482.3	29	0,1,6316	TT,TC,CC		0.0,0.0239,0.0079	probably-damaging	2440/5538	49434235	1,12633	2089	4228	6317	SO:0001583	missense	8085	exon31			GGGTAACGGGTGA	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.7318G>A	chr12.hg19:g.49434235C>T	ENSP00000301067:p.Val2440Ile	96.0	0.0	.		101.0	35.0	.	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	12.39	1.924285	0.34002	2.39E-4	0.0	ENSG00000167548	ENST00000301067	T	0.80033	-1.33	5.21	5.21	0.72293	.	0.000000	0.34002	N	0.004349	T	0.77136	0.4086	L	0.36672	1.1	0.26063	N	0.981323	D	0.57899	0.981	P	0.44772	0.46	T	0.74553	-0.3627	10	0.87932	D	0	.	17.9117	0.88936	0.0:1.0:0.0:0.0	.	2440	O14686	MLL2_HUMAN	I	2440	ENSP00000301067:V2440I	ENSP00000301067:V2440I	V	-	1	0	MLL2	47720502	0.544000	0.26441	0.785000	0.31869	0.974000	0.67602	3.934000	0.56553	2.596000	0.87737	0.591000	0.81541	GTT	.	.	.	weak		0.622	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			T	49434235	C	T	49434235	3	4	170	1	0	0	0	0	1	0	0	0	9628	536	19	1	9391	1	MLL2	12	49434235	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08		49434235	84417660	37	10006											
HNF1A	6927	hgsc.bcm.edu	37	chr12	121437343	121437343	+	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	ggcttcacacgccggcatctCaggccaccaccctccacgtc	7	6	8	20	3	2	0	2	0	1	0	5	0	3	0	5	3	0	2	5	3	0	1			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr12:121437343C>T	ENST00000257555.6	+	9	1907	c.1681C>T	c.(1681-1683)Cag>Tag	p.Q561*	HNF1A_ENST00000544413.1_Nonsense_Mutation_p.Q568*|HNF1A_ENST00000541395.1_Nonsense_Mutation_p.Q592*|RP11-216P16.2_ENST00000606238.1_RNA			P20823	HNF1A_HUMAN	HNF1 homeobox A	561					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)					GCCGGCATCTCAGGCCACCAC	0.701									Hepatic Adenoma, Familial Clustering of																												p.Q561X		Atlas-SNP	.											.	HNF1A	302	.	0			c.C1681T	GRCh37	CM056410	HNF1A	M		PASS	.						28	28	28					12																	121437343		2201	4300	6501	SO:0001587	stop_gained	6927	exon9	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	GCATCTCAGGCCA	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.1681C>T	chr12.hg19:g.121437343C>T	ENSP00000257555:p.Gln561*	42.0	0.0	.		37.0	10.0	.	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Nonsense_Mutation	SNP	ENST00000257555.6	hg19	CCDS9209.1	.	.	.	.	.	.	.	.	.	.	C	37	6.366855	0.97511	.	.	ENSG00000135100	ENST00000257555;ENST00000535125;ENST00000537424;ENST00000543027;ENST00000541395;ENST00000544413	.	.	.	5.8	5.8	0.92144	.	0.246461	0.28754	N	0.014249	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-4.9172	17.2189	0.86952	0.0:1.0:0.0:0.0	.	.	.	.	X	561;453;561;382;592;568	.	ENSP00000257555:Q561X	Q	+	1	0	HNF1A	119921726	0.929000	0.31497	0.953000	0.39169	0.944000	0.59088	3.336000	0.52113	2.741000	0.93983	0.650000	0.86243	CAG	.	.	.	none		0.701	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		T	121437343	C	T	121437343	4	4	170	1	0	0	0	0	0	1	0	0	7258	827	29	2	1715	2	HNF1A	12	121437343	Nonsense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08	72003108	121437343	12414552	38	10007											
EPSTI1	94240	hgsc.bcm.edu	37	chr13	43463356	43463357	+	Intron	DNP	CT	CT	TA																															aagtgacccaccttaggtgcCtcgaaaaaactaatagagaa																										TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr13:43463356_43463357CT>TA	ENST00000398762.3	-	12	948				EPSTI1_ENST00000313624.7_Intron|EPSTI1_ENST00000313640.7_Nonsense_Mutation_p.R324*			Q96J88	ESIP1_HUMAN	epithelial stromal interaction 1 (breast)											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)		CCTTAGGTGCCTCGAAAAAACT	0.292																																					p.R324K|p.R324W		Atlas-SNP	.											.	EPSTI1	47	.	0			c.G971A|c.A970T						PASS	.																																			SO:0001627	intron_variant	94240	exon12			AGGTGCCTCGAAA|GGTGCCTCGAAAA	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.949_949delinsTA	chr13.hg19:g.43463356_43463357delinsTA		47.0	0.0	.		27.0	16.0	.	NM_001002264	Q8IVC7|Q8NDQ7	Missense_Mutation	SNP	ENST00000398762.3	hg19	CCDS9387.1																																																																																			.	.	.	none		0.292	EPSTI1-010	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400321.1	NM_001002264		TA	43463357	CT	TA	43463356	1	4	170	0	1	0	0	0	0	0	0	0	5200	681	24	2		2	EPSTI1	13	43463356	Intron	DNP	CT	TCGA-G7-6790-01A-11D-1961-08		43463356	71706522	39	10008											
CCDC70	83446	hgsc.bcm.edu	37	chr13	52439743	52439743	+	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	ggactttccgaggcaagatcCatgctttccggggccagatc	8	9	12	12	2	0	2	0	0	0	2	4	4	3	3	4	4	1	2	4	4	1	2			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr13:52439743C>T	ENST00000242819.4	+	2	525	c.229C>T	c.(229-231)Cat>Tat	p.H77Y		NM_031290.2	NP_112580.2	Q6NSX1	CCD70_HUMAN	coiled-coil domain containing 70	77						extracellular region (GO:0005576)|plasma membrane (GO:0005886)				breast(1)|large_intestine(4)|lung(7)|skin(2)|urinary_tract(1)	15		Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.0107)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;2.4e-08)		AGGCAAGATCCATGCTTTCCG	0.463																																					p.H77Y		Atlas-SNP	.											.	CCDC70	31	.	0			c.C229T						PASS	.						58	65	62					13																	52439743		2203	4300	6503	SO:0001583	missense	83446	exon2			AAGATCCATGCTT		CCDS9431.1	13q14.3	2006-02-07			ENSG00000123171	ENSG00000123171			25303	protein-coding gene	gene with protein product						11230166	Standard	NM_031290		Approved	DKFZP434K1172, FLJ25853	uc001vfu.4	Q6NSX1	OTTHUMG00000016950	ENST00000242819.4:c.229C>T	chr13.hg19:g.52439743C>T	ENSP00000242819:p.His77Tyr	95.0	0.0	.		127.0	59.0	.	NM_031290	Q8N7A8|Q9H097	Missense_Mutation	SNP	ENST00000242819.4	hg19	CCDS9431.1	.	.	.	.	.	.	.	.	.	.	C	4.558	0.103562	0.08731	.	.	ENSG00000123171	ENST00000242819	T	0.20463	2.07	5.19	-0.626	0.11544	.	0.950993	0.08647	N	0.914676	T	0.13670	0.0331	N	0.22421	0.69	0.09310	N	1	B	0.18013	0.025	B	0.21708	0.036	T	0.35674	-0.9779	10	0.62326	D	0.03	-14.9052	6.1269	0.20184	0.4441:0.3965:0.0:0.1594	.	77	Q6NSX1	CCD70_HUMAN	Y	77	ENSP00000242819:H77Y	ENSP00000242819:H77Y	H	+	1	0	CCDC70	51337744	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.815000	0.04481	-0.051000	0.13334	-0.311000	0.09066	CAT	.	.	.	none		0.463	CCDC70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045033.2	NM_031290		T	52439743	C	T	52439743	3	4	170	1	0	0	0	0	1	0	0	0	2845	594	21	2	231	2	CCDC70	13	52439743	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08	8976387	52439743	62730135	40	10009											
PCDH8	5100	hgsc.bcm.edu	37	chr13	53418949	53418949	+	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	cagtgacgtgctcttacagaAggttgacatctgggctggtg	8	11	14	8	1	2	3	0	2	2	1	2	3	2	3	0	3	2	3	0	3	2	2			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr13:53418949A>T	ENST00000377942.3	-	3	3162	c.2959T>A	c.(2959-2961)Ttc>Atc	p.F987I	PCDH8_ENST00000338862.4_Missense_Mutation_p.F890I	NM_002590.3	NP_002581.2	O95206	PCDH8_HUMAN	protocadherin 8	987					cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|morphogenesis of embryonic epithelium (GO:0016331)|somitogenesis (GO:0001756)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(23)|ovary(1)|skin(1)|urinary_tract(1)	36		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.19e-08)		CTCTTACAGAAGGTTGACATC	0.602																																					p.F987I	GBM(36;25 841 9273 49207)	Atlas-SNP	.											.	PCDH8	95	.	0			c.T2959A						PASS	.						163	95	118					13																	53418949		2203	4300	6503	SO:0001583	missense	5100	exon3			TACAGAAGGTTGA	AF061573	CCDS9438.1, CCDS9439.1	13q21.1	2010-02-22			ENSG00000136099	ENSG00000136099		"Cadherins / Protocadherins : Non-clustered"	8660	protein-coding gene	gene with protein product		603580				9787079, 9315676	Standard	NM_002590		Approved	PAPC, ARCADLIN	uc001vhi.3	O95206	OTTHUMG00000016979	ENST00000377942.3:c.2959T>A	chr13.hg19:g.53418949A>T	ENSP00000367177:p.Phe987Ile	122.0	0.0	.		112.0	48.0	.	NM_002590	B4DMV7|Q5TAN1|Q5TAN2|Q8IYE9|Q96SF1	Missense_Mutation	SNP	ENST00000377942.3	hg19	CCDS9438.1	.	.	.	.	.	.	.	.	.	.	A	17.56	3.419256	0.62622	.	.	ENSG00000136099	ENST00000377942;ENST00000338862;ENST00000418407;ENST00000448969	T;T	0.56444	0.46;0.47	5.95	5.95	0.96441	.	0.000000	0.46442	D	0.000291	T	0.62816	0.2459	L	0.34521	1.04	0.52501	D	0.999954	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.994	T	0.59731	-0.7399	10	0.31617	T	0.26	.	16.4069	0.83677	1.0:0.0:0.0:0.0	.	890;987	O95206-2;O95206	.;PCDH8_HUMAN	I	987;890;513;830	ENSP00000367177:F987I;ENSP00000341350:F890I	ENSP00000341350:F890I	F	-	1	0	PCDH8	52316950	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.730000	0.91510	2.272000	0.75746	0.460000	0.39030	TTC	.	.	.	none		0.602	PCDH8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045108.2	NM_002590		T	53418949	A	T	53418949	3	4	170	1	0	0	0	0	1	0	0	0	11524	72	3	5	257	5	PCDH8	13	53418949	Missense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08	979206	53418949	61750929	41	10010											
ITGA11	22801	hgsc.bcm.edu	37	chr15	68631978	68631978	+	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	cgacggctcccagcagaaccCcatcctggcattggggaggg	8	5	14	14	2	0	1	0	0	0	1	2	3	2	2	4	5	2	3	4	5	1	1			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr15:68631978C>G	ENST00000315757.7	-	11	1222	c.1136G>C	c.(1135-1137)gGg>gCg	p.G379A	ITGA11_ENST00000423218.2_Missense_Mutation_p.G379A	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	379					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)	p.G379V(1)		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						CAGCAGAACCCCATCCTGGCA	0.597																																					p.G379A		Atlas-SNP	.											.	ITGA11	110	.	1	Substitution - Missense(1)	kidney(1)	c.G1136C						PASS	.						61	65	63					15																	68631978		2028	4187	6215	SO:0001583	missense	22801	exon11			AGAACCCCATCCT	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.1136G>C	chr15.hg19:g.68631978C>G	ENSP00000327290:p.Gly379Ala	100.0	0.0	.		84.0	19.0	.	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	hg19	CCDS45291.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.049868	0.75846	.	.	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000535491;ENST00000537153	T;T	0.77750	-1.12;-1.12	5.09	5.09	0.68999	.	0.141219	0.64402	D	0.000005	D	0.86690	0.5993	M	0.84511	2.7	0.54753	D	0.999988	D;D	0.59357	0.985;0.984	P;P	0.55871	0.786;0.736	D	0.87055	0.2149	10	0.38643	T	0.18	.	17.5593	0.87901	0.0:1.0:0.0:0.0	.	379;379	A8K8T0;Q9UKX5	.;ITA11_HUMAN	A	379;379;14;379	ENSP00000327290:G379A;ENSP00000403392:G379A	ENSP00000327290:G379A	G	-	2	0	ITGA11	66419032	1.000000	0.71417	0.983000	0.44433	0.842000	0.47809	7.818000	0.86416	2.391000	0.81399	0.555000	0.69702	GGG	.	.	.	none		0.597	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211		G	68631978	C	G	68631978	3	3	170	1	0	0	0	0	1	0	0	0	7881	623	22	4	2510	4	ITGA11	15	68631978	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08		68631978	33899414	42	10011											
SCAPER	49855	hgsc.bcm.edu	37	chr15	76673781	76673781	+	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	acgtaaactctgaatggccaCttggatggtattttgagtgt	10	14	11	6	1	1	2	0	2	1	0	1	3	1	3	1	3	1	2	1	3	4	5			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr15:76673781C>T	ENST00000563290.1	-	28	3738	c.3643G>A	c.(3643-3645)Gtg>Atg	p.V1215M	SCAPER_ENST00000538941.2_Missense_Mutation_p.V969M|SCAPER_ENST00000324767.7_Missense_Mutation_p.V1215M			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	1215						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						TGAATGGCCACTTGGATGGTA	0.443																																					p.V1215M		Atlas-SNP	.											.	SCAPER	160	.	0			c.G3643A						PASS	.						92	88	89					15																	76673781		1939	4133	6072	SO:0001583	missense	49855	exon27			TGGCCACTTGGAT	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.3643G>A	chr15.hg19:g.76673781C>T	ENSP00000454973:p.Val1215Met	59.0	0.0	.		50.0	11.0	.	NM_020843	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Missense_Mutation	SNP	ENST00000563290.1	hg19	CCDS53962.1	.	.	.	.	.	.	.	.	.	.	C	17.81	3.481299	0.63849	.	.	ENSG00000140386	ENST00000324767;ENST00000538941;ENST00000303521	T;T	0.32023	1.5;1.47	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.53334	0.1790	M	0.67953	2.075	0.51767	D	0.999932	D;D	0.65815	0.975;0.995	P;D	0.67231	0.793;0.95	T	0.53599	-0.8416	10	0.87932	D	0	.	15.5231	0.75881	0.0:0.8625:0.1375:0.0	.	1214;969	Q9BY12;F5H7X8	SCAPE_HUMAN;.	M	1215;969;1237	ENSP00000326924:V1215M;ENSP00000442190:V969M	ENSP00000303560:V1237M	V	-	1	0	SCAPER	74460836	1.000000	0.71417	0.920000	0.36463	0.589000	0.36550	5.651000	0.67951	2.740000	0.93945	0.650000	0.86243	GTG	.	.	.	none		0.443	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843		T	76673781	C	T	76673781	3	4	170	1	0	0	0	0	1	0	0	0	13891	565	20	2	579	2	SCAPER	15	76673781	Missense_Mutation	SNP	C	TCGA-G7-6790-01A-11D-1961-08	8041803	76673781	25857611	43	10012											
MYH13	8735	hgsc.bcm.edu	37	chr17	10227379	10227379	+	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	tctccttttcaactttcgtcAaggtcagctccaggtcatca	8	14	6	13	1	6	0	5	0	1	0	9	0	7	0	2	2	2	1	2	2	2	3			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr17:10227379A>T	ENST00000418404.3	-	22	3057	c.2894T>A	c.(2893-2895)tTg>tAg	p.L965*	MYH13_ENST00000252172.4_Nonsense_Mutation_p.L965*|RP11-401O9.3_ENST00000577743.1_RNA			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	965					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						AACTTTCGTCAAGGTCAGCTC	0.463																																					p.L965X		Atlas-SNP	.											.	MYH13	533	.	0			c.T2894A						PASS	.						106	105	106					17																	10227379		2195	4300	6495	SO:0001587	stop_gained	8735	exon23			TTCGTCAAGGTCA	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.2894T>A	chr17.hg19:g.10227379A>T	ENSP00000404570:p.Leu965*	70.0	0.0	.		105.0	68.0	.	NM_003802	O95252|Q9P0U8	Nonsense_Mutation	SNP	ENST00000418404.3	hg19	CCDS45613.1	.	.	.	.	.	.	.	.	.	.	A	42	9.641822	0.99227	.	.	ENSG00000006788	ENST00000252172;ENST00000418404	.	.	.	4.37	4.37	0.52481	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.0394	0.64665	1.0:0.0:0.0:0.0	.	.	.	.	X	965;591	.	ENSP00000252172:L965X	L	-	2	0	MYH13	10168104	1.000000	0.71417	0.965000	0.40720	0.705000	0.40729	8.981000	0.93465	1.950000	0.56595	0.533000	0.62120	TTG	.	.	.	none		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		T	10227379	A	T	10227379	4	4	170	1	0	0	0	0	0	1	0	0	10039	131	5	5	2998	5	MYH13	17	10227379	Nonsense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08		10227379	70967831	44	10013											
MYH8	4626	hgsc.bcm.edu	37	chr17	10309460	10309460	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttttcatctctcatttctTccagaagacccagaagtcca	11	14	4	12	0	4	3	2	0	2	3	7	3	6	3	3	0	0	0	3	0	2	4			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr17:10309460T>C	ENST00000403437.2	-	21	2424	c.2330A>G	c.(2329-2331)gAa>gGa	p.E777G	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	777	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						TCTCATTTCTTCCAGAAGACC	0.413									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																												p.E777G		Atlas-SNP	.											.	MYH8	346	.	0			c.A2330G						PASS	.						113	108	110					17																	10309460		2203	4300	6503	SO:0001583	missense	4626	exon21	Familial Cancer Database	Carney Complex Variant	ATTTCTTCCAGAA		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.2330A>G	chr17.hg19:g.10309460T>C	ENSP00000384330:p.Glu777Gly	90.0	0.0	.		101.0	54.0	.	NM_002472	Q14910	Missense_Mutation	SNP	ENST00000403437.2	hg19	CCDS11153.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.512766	0.85389	.	.	ENSG00000133020	ENST00000252173;ENST00000403437	T	0.75260	-0.92	5.22	5.22	0.72569	Myosin head, motor domain (1);	0.000000	0.42420	U	0.000719	D	0.92182	0.7521	H	0.99415	4.555	0.58432	D	0.999999	D	0.71674	0.998	D	0.74674	0.984	D	0.95289	0.8393	10	0.66056	D	0.02	.	15.2675	0.73672	0.0:0.0:0.0:1.0	.	777	P13535	MYH8_HUMAN	G	777	ENSP00000384330:E777G	ENSP00000252173:E777G	E	-	2	0	MYH8	10250185	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.825000	0.86693	2.205000	0.71048	0.528000	0.53228	GAA	.	.	.	none		0.413	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		C	10309460	T	C	10309460	3	2	170	1	0	0	0	0	1	0	0	0	10048	1783	62	3	3563	3	MYH8	17	10309460	Missense_Mutation	SNP	T	TCGA-G7-6790-01A-11D-1961-08	82081	10309460	70885750	45	10014											
STAC2	342667	hgsc.bcm.edu	37	chr17	37368584	37368584	+	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	tcgactggcaccaggccccgCttcttgccactgctgacgcg	5	8	11	17	4	1	1	0	1	1	0	2	2	1	1	4	2	2	3	4	2	0	2			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr17:37368584C>T	ENST00000333461.5	-	11	1566	c.1197G>A	c.(1195-1197)aaG>aaA	p.K399K		NM_198993.3	NP_945344.1	Q6ZMT1	STAC2_HUMAN	SH3 and cysteine rich domain 2	399					intracellular signal transduction (GO:0035556)		metal ion binding (GO:0046872)			NS(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|pancreas(1)|prostate(1)|skin(2)	17						CCAGGCCCCGCTTCTTGCCAC	0.622																																					p.K399K		Atlas-SNP	.											.	STAC2	47	.	0			c.G1197A						PASS	.						58	52	54					17																	37368584		2203	4300	6503	SO:0001819	synonymous_variant	342667	exon11			GCCCCGCTTCTTG	AJ608762	CCDS11335.1	17q21.2	2012-11-19			ENSG00000141750	ENSG00000141750			23990	protein-coding gene	gene with protein product							Standard	NM_198993		Approved	24b2	uc002hrs.3	Q6ZMT1	OTTHUMG00000179039	ENST00000333461.5:c.1197G>A	chr17.hg19:g.37368584C>T		35.0	0.0	.		60.0	14.0	.	NM_198993	Q32MA3	Silent	SNP	ENST00000333461.5	hg19	CCDS11335.1																																																																																			.	.	.	none		0.622	STAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444533.2	NM_198993		T	37368584	C	T	37368584	2	4	170	1	0	0	0	0	0	0	0	1	15252	796	28	2		2	STAC2	17	37368584	Silent	SNP	C	TCGA-G7-6790-01A-11D-1961-08	27059124	37368584	43826626	46	10015											
CAPS	8498	hgsc.bcm.edu	37	chr19	5914495	5914495	+	IGR	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	gcctcgggcatccagggcctGgccaggtgagctgtcccctc	4	7	14	16	1	0	1	0	1	0	0	4	1	2	1	6	4	1	2	6	4	0	0			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr19:5914495G>T	ENST00000340578.6	-	0	3233				AC104532.2_ENST00000588891.1_3'UTR|CAPS_ENST00000222125.5_Silent_p.L26L|CAPS_ENST00000452990.2_Silent_p.L26L|CAPS_ENST00000588776.1_Silent_p.L112L|AC104532.4_ENST00000591109.1_RNA	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						TCCAGGGCCTGGCCAGGTGAG	0.667																																					p.L26L		Atlas-SNP	.											.	CAPS	14	.	0			c.G78T						PASS	.						38	42	41					19																	5914495		2203	4300	6503	SO:0001628	intergenic_variant	828	exon2			GGGCCTGGCCAGG	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			chr19.hg19:g.5914495G>T		72.0	0.0	.		57.0	22.0	.	NM_080590	B2RAT8|O60405|O75759|O75760|Q9BT47|Q9UG74	Silent	SNP	ENST00000340578.6	hg19	CCDS42478.1																																																																																			.	.	.	none		0.667	RANBP3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452304.1	NM_007322		T	5914495	G	T	5914495	1	4	170	0	1	0	0	0	0	0	0	0	2639	1335	47	4		4	CAPS	19	5914495	IGR	SNP	G	TCGA-G7-6790-01A-11D-1961-08		5914495	53214488	47	10016											
C3	718	hgsc.bcm.edu	37	chr19	6709834	6709834	+	Missense_Mutation	SNP	T	T	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	caggctgccggtcttctgacTggccgctttttaccaccagc	5	11	10	15	2	2	1	0	1	2	0	2	1	2	1	4	3	3	2	4	3	1	4			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr19:6709834T>G	ENST00000245907.6	-	14	1798	c.1706A>C	c.(1705-1707)cAg>cCg	p.Q569P		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	569					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)	GTCTTCTGACTGGCCGCTTTT	0.637																																					p.Q569P		Atlas-SNP	.											C3,NS,carcinoma,0,1	C3	192	.	0			c.A1706C						PASS	.						51	52	52					19																	6709834		2203	4300	6503	SO:0001583	missense	718	exon14			TCTGACTGGCCGC	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.1706A>C	chr19.hg19:g.6709834T>G	ENSP00000245907:p.Gln569Pro	101.0	1.0	.		72.0	18.0	.	NM_000064	A7E236	Missense_Mutation	SNP	ENST00000245907.6	hg19	CCDS32883.1	.	.	.	.	.	.	.	.	.	.	T	7.093	0.572475	0.13623	.	.	ENSG00000125730	ENST00000245907	T	0.60548	0.18	5.15	-4.43	0.03568	Alpha-2-macroglobulin, N-terminal 2 (1);	1.754940	0.02473	N	0.087708	T	0.26991	0.0661	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.09143	-1.0688	10	0.15066	T	0.55	.	2.5674	0.04786	0.1135:0.1705:0.2356:0.4803	.	569	P01024	CO3_HUMAN	P	569	ENSP00000245907:Q569P	ENSP00000245907:Q569P	Q	-	2	0	C3	6660834	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.671000	0.01954	-0.737000	0.04824	-0.382000	0.06688	CAG	.	.	.	none		0.637	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		G	6709834	T	G	6709834	3	3	170	1	0	0	0	0	1	0	0	0	2206	1580	55	5	3397	5	C3	19	6709834	Missense_Mutation	SNP	T	TCGA-G7-6790-01A-11D-1961-08	795339	6709834	52419149	48	10017											
FCER2	2208	hgsc.bcm.edu	37	chr19	7755293	7755293	+	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	ctgcagagccccagcccaccTgctcctccgggctgtggatg	5	7	12	17	1	0	1	0	0	0	1	2	2	2	2	6	2	4	3	6	2	0	0			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr19:7755293T>A	ENST00000346664.5	-	9	832	c.620A>T	c.(619-621)cAg>cTg	p.Q207L	FCER2_ENST00000597921.1_Splice_Site_p.Q207L|FCER2_ENST00000360067.4_Splice_Site_p.Q206L	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)	207	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				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						CCAGCCCACCTGCTCCTCCGG	0.667																																					p.Q207L		Atlas-SNP	.											.	FCER2	19	.	0			c.A620T						PASS	.						43	46	45					19																	7755293		2203	4300	6503	SO:0001630	splice_region_variant	2208	exon9			CCCACCTGCTCCT	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.621+1A>T	chr19.hg19:g.7755293T>A		105.0	0.0	.		92.0	27.0	.	NM_002002		Missense_Mutation	SNP	ENST00000346664.5	hg19	CCDS12184.1	.	.	.	.	.	.	.	.	.	.	t	14.83	2.652954	0.47362	.	.	ENSG00000104921	ENST00000346664;ENST00000360067	T;T	0.16457	2.34;2.34	4.61	4.61	0.57282	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.33477	U	0.004865	T	0.37652	0.1011	M	0.66378	2.025	0.36695	D	0.879773	D	0.76494	0.999	D	0.87578	0.998	T	0.46843	-0.9162	10	0.87932	D	0	.	10.4446	0.44486	0.0:0.0:0.0:1.0	.	207	P06734	FCER2_HUMAN	L	207;206	ENSP00000264072:Q207L;ENSP00000353178:Q206L	ENSP00000264072:Q207L	Q	-	2	0	FCER2	7661293	1.000000	0.71417	1.000000	0.80357	0.567000	0.35839	3.912000	0.56386	1.733000	0.51620	0.382000	0.24955	CAG	.	.	.	none		0.667	FCER2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461832.1	NM_002002	Missense_Mutation	A	7755293	T	A	7755293	5	1	170	1	0	0	0	0	0	0	1	0	5783	1594	55	5	357	5	FCER2	19	7755293	Splice_Site	SNP	T	TCGA-G7-6790-01A-11D-1961-08	1045459	7755293	51373690	49	10018											
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11113781	11113781	+	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	gagtgggaagatcctcacagGcacagatgcccccaaagccg	12	4	12	13	1	1	2	1	0	0	2	2	4	2	3	4	2	2	1	4	2	2	0			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr19:11113781G>C	ENST00000429416.3	+	13	2170	c.1889G>C	c.(1888-1890)gGc>gCc	p.G630A	SMARCA4_ENST00000450717.3_Missense_Mutation_p.G630A|SMARCA4_ENST00000444061.3_Missense_Mutation_p.G630A|SMARCA4_ENST00000344626.4_Missense_Mutation_p.G630A|SMARCA4_ENST00000413806.3_Missense_Mutation_p.G630A|SMARCA4_ENST00000358026.2_Missense_Mutation_p.G630A|SMARCA4_ENST00000590574.1_Missense_Mutation_p.G630A|SMARCA4_ENST00000541122.2_Missense_Mutation_p.G630A|SMARCA4_ENST00000589677.1_Missense_Mutation_p.G630A	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	630					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)				ATCCTCACAGGCACAGATGCC	0.597			"F, N, Mis"		NSCLC																																p.G630A		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.G1889C						PASS	.						77	79	78					19																	11113781		2203	4300	6503	SO:0001583	missense	6597	exon12			TCACAGGCACAGA	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.1889G>C	chr19.hg19:g.11113781G>C	ENSP00000395654:p.Gly630Ala	148.0	0.0	.		111.0	28.0	.	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.862182	0.91511	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	T;T;T;T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83;-0.83;-0.83;-0.83	4.57	4.57	0.56435	BRK domain (2);	0.000000	0.85682	D	0.000000	T	0.79805	0.4509	L	0.58510	1.815	0.80722	D	1	P;P;P;P;D;P;P	0.54772	0.857;0.932;0.932;0.853;0.968;0.868;0.868	P;P;P;P;P;P;P	0.53760	0.597;0.708;0.708;0.734;0.699;0.708;0.708	T	0.82386	-0.0483	10	0.66056	D	0.02	-36.4878	16.6596	0.85238	0.0:0.0:1.0:0.0	.	630;630;630;630;630;630;630	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;A7E2E1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	A	630;630;694;630;630;630;630;630	ENSP00000395654:G630A;ENSP00000350720:G630A;ENSP00000343896:G630A;ENSP00000445036:G630A;ENSP00000392837:G630A;ENSP00000397783:G630A;ENSP00000414727:G630A	ENSP00000343896:G630A	G	+	2	0	SMARCA4	10974781	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	9.601000	0.98297	2.526000	0.85167	0.563000	0.77884	GGC	.	.	.	none		0.597	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		C	11113781	G	C	11113781	3	2	170	1	0	0	0	0	1	0	0	0	14783	1203	42	4	1931	4	SMARCA4	19	11113781	Missense_Mutation	SNP	G	TCGA-G7-6790-01A-11D-1961-08	3358488	11113781	48015202	50	10019											
RYR1	6261	hgsc.bcm.edu	37	chr19	38990577	38990577	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggaaccgcctgaagaaaaccGggtgcacctgggacacgcca	12	3	13	13	3	0	2	0	1	0	1	0	4	0	4	5	3	3	1	5	3	4	0	rs201584482		TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr19:38990577G>A	ENST00000359596.3	+	45	7244	c.7244G>A	c.(7243-7245)cGg>cAg	p.R2415Q	RYR1_ENST00000355481.4_Missense_Mutation_p.R2415Q|RYR1_ENST00000360985.3_Missense_Mutation_p.R2415Q			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2415	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GAAGAAAACCGGGTGCACCTG	0.632																																					p.R2415Q		Atlas-SNP	.											.	RYR1	708	.	0			c.G7244A						PASS	.						120	97	104					19																	38990577		2203	4300	6503	SO:0001583	missense	6261	exon45			AAAACCGGGTGCA	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.7244G>A	chr19.hg19:g.38990577G>A	ENSP00000352608:p.Arg2415Gln	109.0	0.0	.		105.0	35.0	.	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	15.00	2.704736	0.48412	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.97529	-4.42;-4.42;-4.42	3.99	3.99	0.46301	.	0.000000	0.64402	U	0.000007	D	0.95726	0.8610	L	0.48362	1.52	0.38108	D	0.937463	D;D	0.63046	0.992;0.985	P;B	0.48901	0.594;0.44	D	0.95492	0.8570	10	0.33141	T	0.24	.	15.0045	0.71501	0.0:0.0:1.0:0.0	.	2415;2415	P21817-2;P21817	.;RYR1_HUMAN	Q	2415	ENSP00000352608:R2415Q;ENSP00000347667:R2415Q;ENSP00000354254:R2415Q	ENSP00000347667:R2415Q	R	+	2	0	RYR1	43682417	0.992000	0.36948	1.000000	0.80357	0.705000	0.40729	2.287000	0.43505	2.045000	0.60652	0.297000	0.19635	CGG	.	.	.	weak		0.632	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	38990577	G	A	38990577	3	1	170	1	0	0	0	0	1	0	0	0	13781	1116	39	1	7422	1	RYR1	19	38990577	Missense_Mutation	SNP	G	TCGA-G7-6790-01A-11D-1961-08	27876796	38990577	20138406	51	10020											
MYH14	79784	hgsc.bcm.edu	37	chr19	50764757	50764757	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcgctggaactggaccccaAcctctaccgcgtgggacaga	9	5	13	14	3	1	1	0	0	1	1	1	4	1	4	4	4	3	1	4	4	3	1			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr19:50764757A>G	ENST00000596571.1	+	18	2327	c.2327A>G	c.(2326-2328)aAc>aGc	p.N776S	MYH14_ENST00000425460.1_Missense_Mutation_p.N784S|MYH14_ENST00000376970.2_Missense_Mutation_p.N809S|MYH14_ENST00000601313.1_Missense_Mutation_p.N817S|MYH14_ENST00000598205.1_Missense_Mutation_p.N784S|MYH14_ENST00000440075.2_Missense_Mutation_p.N817S|MYH14_ENST00000262269.8_Missense_Mutation_p.N817S			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	776	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)		CTGGACCCCAACCTCTACCGC	0.632																																					p.N817S		Atlas-SNP	.											.	MYH14	261	.	0			c.A2450G						PASS	.						40	44	42					19																	50764757		2011	4174	6185	SO:0001583	missense	79784	exon21			ACCCCAACCTCTA	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.2327A>G	chr19.hg19:g.50764757A>G	ENSP00000472819:p.Asn776Ser	85.0	0.0	.		74.0	20.0	.	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	hg19	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	A	16.39	3.111012	0.56398	.	.	ENSG00000105357	ENST00000301415;ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	D;D;D;D	0.87571	-2.27;-2.27;-2.27;-2.27	4.48	4.48	0.54585	Myosin head, motor domain (2);	.	.	.	.	D	0.82770	0.5109	L	0.47016	1.485	0.80722	D	1	B;B;B	0.29909	0.144;0.261;0.22	B;B;B	0.29176	0.03;0.099;0.06	T	0.82348	-0.0502	9	0.54805	T	0.06	.	12.0425	0.53460	1.0:0.0:0.0:0.0	.	817;776;784	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	S	776;817;809;784;776;817	ENSP00000406273:N817S;ENSP00000366169:N809S;ENSP00000407879:N784S;ENSP00000262269:N817S	ENSP00000262269:N817S	N	+	2	0	MYH14	55456569	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.830000	0.92063	2.028000	0.59812	0.454000	0.30748	AAC	.	.	.	none		0.632	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		G	50764757	A	G	50764757	3	3	170	1	0	0	0	0	1	0	0	0	10040	43	2	3	2528	3	MYH14	19	50764757	Missense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08	11774180	50764757	8364226	52	10021											
CEP250	11190	hgsc.bcm.edu	37	chr20	34092361	34092361	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagagctgagacatcagcAggaacgggagcagctgctgg	12	5	16	8	1	1	3	1	2	0	2	1	6	1	5	0	3	6	5	0	3	2	0			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr20:34092361A>G	ENST00000397527.1	+	30	6884	c.6164A>G	c.(6163-6165)cAg>cGg	p.Q2055R	CEP250_ENST00000342580.4_Missense_Mutation_p.Q1999R	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	2055	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)			AGACATCAGCAGGAACGGGAG	0.557																																					p.Q2055R		Atlas-SNP	.											.	CEP250	141	.	0			c.A6164G						PASS	.						29	31	30					20																	34092361		2203	4300	6503	SO:0001583	missense	11190	exon30			ATCAGCAGGAACG	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.6164A>G	chr20.hg19:g.34092361A>G	ENSP00000380661:p.Gln2055Arg	29.0	0.0	.		52.0	17.0	.	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	hg19	CCDS13255.1	.	.	.	.	.	.	.	.	.	.	A	7.149	0.583366	0.13749	.	.	ENSG00000126001	ENST00000397527;ENST00000342580;ENST00000422671	T;T;T	0.43688	2.96;2.95;0.94	4.83	1.33	0.21861	.	0.879228	0.09850	N	0.747749	T	0.14743	0.0356	N	0.00926	-1.1	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.29792	-1.0000	10	0.19147	T	0.46	.	8.6927	0.34275	0.6701:0.0:0.3299:0.0	.	2055	Q9BV73	CP250_HUMAN	R	2055;1999;543	ENSP00000380661:Q2055R;ENSP00000341541:Q1999R;ENSP00000395992:Q543R	ENSP00000341541:Q1999R	Q	+	2	0	CEP250	33555775	0.990000	0.36364	0.012000	0.15200	0.910000	0.53928	0.903000	0.28475	0.045000	0.15804	0.533000	0.62120	CAG	.	.	.	none		0.557	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		G	34092361	A	G	34092361	3	3	170	1	0	0	0	0	1	0	0	0	3254	188	7	3	6270	3	CEP250	20	34092361	Missense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08		34092361	28933159	53	10022											
ADNP	23394	hgsc.bcm.edu	37	chr20	49510230	49510230	+	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	cattgactgaccaacactgtAaccctggcctacagatttga	12	10	7	12	0	0	4	0	3	0	1	0	4	0	4	3	1	3	1	3	1	3	4			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr20:49510230A>T	ENST00000396029.3	-	5	1588	c.1021T>A	c.(1021-1023)Tac>Aac	p.Y341N	ADNP_ENST00000349014.3_Missense_Mutation_p.Y341N|ADNP_ENST00000396032.3_Missense_Mutation_p.Y341N|ADNP_ENST00000371602.4_Missense_Mutation_p.Y341N	NM_001282531.1|NM_015339.2	NP_001269460.1|NP_056154.1	Q9H2P0	ADNP_HUMAN	activity-dependent neuroprotector homeobox	341					negative regulation of neuron apoptotic process (GO:0043524)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|endometrium(7)|kidney(1)|large_intestine(13)|lung(7)|ovary(2)|prostate(2)|skin(2)	39						CCAACACTGTAACCCTGGCCT	0.443																																					p.Y341N		Atlas-SNP	.											.	ADNP	106	.	0			c.T1021A						PASS	.						137	123	128					20																	49510230		2203	4300	6503	SO:0001583	missense	23394	exon5			CACTGTAACCCTG	AF250860	CCDS13433.1	20q13.13	2011-06-20	2007-07-17		ENSG00000101126	ENSG00000101126		"Homeoboxes / ZF class"	15766	protein-coding gene	gene with protein product	"ADNP homeobox 1"	611386	"activity-dependent neuroprotector"			9872452, 11013255	Standard	NM_015339		Approved	KIAA0784, ADNP1	uc002xvu.1	Q9H2P0	OTTHUMG00000032737	ENST00000396029.3:c.1021T>A	chr20.hg19:g.49510230A>T	ENSP00000379346:p.Tyr341Asn	114.0	0.0	.		98.0	31.0	.	NM_015339	E1P5Y2|O94881|Q5BKU2|Q9UG34	Missense_Mutation	SNP	ENST00000396029.3	hg19	CCDS13433.1	.	.	.	.	.	.	.	.	.	.	A	12.89	2.072885	0.36566	.	.	ENSG00000101126	ENST00000371602;ENST00000349014;ENST00000396029;ENST00000396032	.	.	.	5.91	5.91	0.95273	.	0.295208	0.38663	N	0.001605	T	0.74665	0.3746	L	0.55990	1.75	0.42457	D	0.992773	D	0.76494	0.999	D	0.81914	0.995	T	0.72121	-0.4386	9	0.30078	T	0.28	-7.2492	16.3436	0.83110	1.0:0.0:0.0:0.0	.	341	Q9H2P0	ADNP_HUMAN	N	341	.	ENSP00000342905:Y341N	Y	-	1	0	ADNP	48943637	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	8.948000	0.93006	2.269000	0.75478	0.533000	0.62120	TAC	.	.	.	none		0.443	ADNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079705.2	NM_181442		T	49510230	A	T	49510230	3	4	170	1	0	0	0	0	1	0	0	0	323	362	13	5	2291	5	ADNP	20	49510230	Missense_Mutation	SNP	A	TCGA-G7-6790-01A-11D-1961-08	15417869	49510230	13515290	54	10023											
ADARB1	104	hgsc.bcm.edu	37	chr21	46596347	46596347	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgatcttgaacgaactgcGcccaggactcaagtatgact	12	9	10	10	2	2	3	1	3	1	0	2	6	2	4	1	1	3	1	1	1	4	2			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chr21:46596347G>A	ENST00000360697.3	+	2	746	c.731G>A	c.(730-732)cGc>cAc	p.R244H	ADARB1_ENST00000389863.4_Missense_Mutation_p.R244H|ADARB1_ENST00000437626.1_Intron|ADARB1_ENST00000348831.4_Missense_Mutation_p.R244H|ADARB1_ENST00000539173.1_Missense_Mutation_p.R244H			P78563	RED1_HUMAN	adenosine deaminase, RNA-specific, B1	244	DRBM 2. {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)			endometrium(4)|kidney(1)|large_intestine(3)|lung(8)|skin(1)	17				Colorectal(79;0.115)		AACGAACTGCGCCCAGGACTC	0.587																																					p.R244H		Atlas-SNP	.											ADARB1_ENST00000389863,colon,carcinoma,0,4	ADARB1	81	.	0			c.G731A						PASS	.						108	97	101					21																	46596347		2203	4300	6503	SO:0001583	missense	104	exon4			AACTGCGCCCAGG	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.731G>A	chr21.hg19:g.46596347G>A	ENSP00000353920:p.Arg244His	117.0	0.0	.		122.0	44.0	.	NM_001160230	A6NFK8|A6NJ84|C3TTQ1|C3TTQ2|C9JUP4|G5E9B4|O00395|O00465|O00691|O00692|P78555|Q4AE79|Q6P0M9|Q8NFD1	Missense_Mutation	SNP	ENST00000360697.3	hg19	CCDS33589.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.564135	0.86335	.	.	ENSG00000197381	ENST00000539173;ENST00000539917;ENST00000389863;ENST00000348831;ENST00000360697	T;T;T;T	0.77750	-1.12;-1.12;-1.12;-1.12	5.28	5.28	0.74379	Double-stranded RNA-binding (2);Double-stranded RNA-binding-like (1);	0.000000	0.85682	U	0.000000	D	0.86818	0.6024	M	0.75447	2.3	0.80722	D	1	P;D;D;B;P	0.61697	0.928;0.99;0.97;0.046;0.861	P;D;P;B;P	0.66716	0.521;0.946;0.877;0.04;0.521	D	0.85797	0.1371	10	0.38643	T	0.18	-42.4461	16.7859	0.85574	0.0:0.0:1.0:0.0	.	271;244;244;272;244	P78563-4;P78563;Q4AE77;G5E9B4;P78563-3	.;RED1_HUMAN;.;.;.	H	244	ENSP00000441897:R244H;ENSP00000374513:R244H;ENSP00000015877:R244H;ENSP00000353920:R244H	ENSP00000015877:R244H	R	+	2	0	ADARB1	45420775	1.000000	0.71417	1.000000	0.80357	0.762000	0.43233	9.347000	0.97059	2.633000	0.89246	0.655000	0.94253	CGC	.	.	.	none		0.587	ADARB1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206648.2	NM_015833		A	46596347	G	A	46596347	3	1	170	1	0	0	0	0	1	0	0	0	282	1087	38	1	737	1	ADARB1	21	46596347	Missense_Mutation	SNP	G	TCGA-G7-6790-01A-11D-1961-08		46596347	1533548	55	10024											
PNCK	139728	hgsc.bcm.edu	37	chrX	152937464	152937464	+	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	atgcggtcaaacagctcgccAcccgtcaccctgggggtgcc	7	6	12	16	3	2	0	2	0	0	0	3	0	2	0	4	3	4	1	4	3	1	0			TCGA-G7-6790-01A-11D-1961-08	TCGA-G7-6790-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ef807a92-f471-4d93-8ae9-24bbb846feaa	66cbb40f-14b3-40c0-a332-e8a8e21bca11	g.chrX:152937464A>T	ENST00000370150.1	-	5	463	c.285T>A	c.(283-285)ggT>ggA	p.G95G	PNCK_ENST00000393831.2_Silent_p.G95G|PNCK_ENST00000475172.1_5'UTR|PNCK_ENST00000370145.4_Silent_p.G112G|PNCK_ENST00000340888.3_Silent_p.G95G|PNCK_ENST00000447676.2_Silent_p.G178G|PNCK_ENST00000370142.1_Silent_p.G95G			Q6P2M8	KCC1B_HUMAN	pregnancy up-regulated nonubiquitous CaM kinase	95	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			breast(2)|lung(3)|skin(1)	6	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					ACAGCTCGCCACCCGTCACCC	0.657																																					p.G178G		Atlas-SNP	.											.	PNCK	70	.	0			c.T534A						PASS	.						39	35	36					X																	152937464		2203	4299	6502	SO:0001819	synonymous_variant	139728	exon5			CTCGCCACCCGTC	BC033746	CCDS35503.2, CCDS48189.1	Xq28	2013-10-14	2013-10-14		ENSG00000130822	ENSG00000130822			13415	protein-coding gene	gene with protein product		300680	"pregnancy upregulated non-ubiquitously expressed CaM kinase", "pregnancy up-regulated non-ubiquitously expressed CaM kinase"			12477932	Standard	NM_001039582		Approved	MGC45419, CaMK1b	uc011myu.2	Q6P2M8	OTTHUMG00000024216	ENST00000370150.1:c.285T>A	chrX.hg19:g.152937464A>T		30.0	0.0	.		21.0	10.0	.	NM_001039582	B4DJR8|B4E1A6|B7WPG0|D3DWU7|Q8N4R0	Silent	SNP	ENST00000370150.1	hg19																																																																																				.	.	.	none		0.657	PNCK-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000061044.2	NM_198452		T	152937464	A	T	152937464	2	4	170	1	0	0	0	0	0	0	0	1	12152	146	6	5		5	PNCK	23	152937464	Silent	SNP	A	TCGA-G7-6790-01A-11D-1961-08		152937464	2333096	56	10025											
DDX20	11218	hgsc.bcm.edu	37	chr1	112303729	112303729	+	Missense_Mutation	SNP	T	T	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	atttaatcaagctttagtctTttctaatttgcacagcaggt	11	17	6	7	0	3	0	1	0	2	0	3	0	3	0	0	1	3	3	0	1	4	8			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr1:112303729T>G	ENST00000369702.4	+	6	1564	c.944T>G	c.(943-945)tTt>tGt	p.F315C	DDX20_ENST00000475700.1_5'UTR|DDX20_ENST00000536167.1_3'UTR	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	315	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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)		GCTTTAGTCTTTTCTAATTTG	0.353																																					p.F315C		Atlas-SNP	.											.	DDX20	50	.	0			c.T944G						PASS	.						111	114	113					1																	112303729		2203	4300	6503	SO:0001583	missense	11218	exon6			TAGTCTTTTCTAA	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.944T>G	chr1.hg19:g.112303729T>G	ENSP00000358716:p.Phe315Cys	97.0	0.0	.		96.0	39.0	.	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Missense_Mutation	SNP	ENST00000369702.4	hg19	CCDS842.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.962407	0.74016	.	.	ENSG00000064703	ENST00000369702	T	0.11063	2.81	5.62	5.62	0.85841	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.43344	0.1243	H	0.98178	4.165	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.66106	-0.6006	10	0.87932	D	0	-23.1854	15.4768	0.75489	0.0:0.0:0.0:1.0	.	315	Q9UHI6	DDX20_HUMAN	C	315	ENSP00000358716:F315C	ENSP00000358716:F315C	F	+	2	0	DDX20	112105252	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.586000	0.82596	2.152000	0.67230	0.459000	0.35465	TTT	.	.	.	none		0.353	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204		G	112303729	T	G	112303729	3	3	171	1	0	0	0	0	1	0	0	0	4350	1841	64	5	966	5	DDX20	1	112303729	Missense_Mutation	SNP	T	TCGA-G7-6792-01A-21D-1961-08		112303729	136946892	1	10026											
DSTYK	25778	hgsc.bcm.edu	37	chr1	205132071	205132071	+	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	ctgtttgatttgctcccataGcatccttgtaactgacgacc	8	14	7	12	1	0	2	0	2	0	0	2	3	2	2	3	0	3	4	3	0	2	5			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr1:205132071G>A	ENST00000367162.3	-	5	1651	c.1621C>T	c.(1621-1623)Cta>Tta	p.L541L	DSTYK_ENST00000367160.4_Intron|DSTYK_ENST00000367161.3_Silent_p.L541L	NM_015375.2	NP_056190.1	Q6XUX3	DUSTY_HUMAN	dual serine/threonine and tyrosine protein kinase	541					cellular response to fibroblast growth factor stimulus (GO:0044344)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of kinase activity (GO:0033674)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(2)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(2)	14						TGCTCCCATAGCATCCTTGTA	0.418																																					p.L541L		Atlas-SNP	.											.	DSTYK	87	.	0			c.C1621T						PASS	.						205	191	196					1																	205132071		2203	4300	6503	SO:0001819	synonymous_variant	25778	exon5			CCCATAGCATCCT	AF068286	CCDS1451.1, CCDS1452.1	1q32	2008-12-18	2008-12-18	2008-12-18	ENSG00000133059	ENSG00000133059			29043	protein-coding gene	gene with protein product		612666	"receptor interacting protein kinase 5"	RIPK5		15178406	Standard	NM_015375		Approved	KIAA0472, DustyPK, RIP5	uc001hbw.3	Q6XUX3	OTTHUMG00000037102	ENST00000367162.3:c.1621C>T	chr1.hg19:g.205132071G>A		147.0	0.0	.		154.0	67.0	.	NM_199462	B7ZL64|O75060|Q17R94|Q5RKT0|Q6IN87|Q6P997|Q86Y03|Q9P1S5	Silent	SNP	ENST00000367162.3	hg19	CCDS1451.1																																																																																			.	.	.	none		0.418	DSTYK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090345.1	NM_015375		A	205132071	G	A	205132071	2	1	171	1	0	0	0	0	0	0	0	1	4787	962	34	2		2	DSTYK	1	205132071	Silent	SNP	G	TCGA-G7-6792-01A-21D-1961-08	92828342	205132071	44118550	2	10027											
ZFYVE20	64145	hgsc.bcm.edu	37	chr3	15116216	15116216	+	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	cgcacttcatccatgcggccCgcggccttggcctgcctgat	4	9	11	17	4	1	1	1	1	0	0	2	1	2	1	5	3	2	1	5	3	0	2			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr3:15116216C>A	ENST00000253699.3	-	14	2041	c.1428G>T	c.(1426-1428)gcG>gcT	p.A476A	ZFYVE20_ENST00000476527.2_Silent_p.A476A	NM_022340.2	NP_071735.2	Q9H1K0	RBNS5_HUMAN	zinc finger, FYVE domain containing 20	476	Necessary for the interaction with EHD1.|Necessary for the interaction with RAB4A.				blood coagulation (GO:0007596)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	endosome (GO:0005768)|endosome membrane (GO:0010008)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|skin(3)|stomach(1)|urinary_tract(2)	26						CCATGCGGCCCGCGGCCTTGG	0.617																																					p.A476A		Atlas-SNP	.											.	ZFYVE20	61	.	0			c.G1428T						PASS	.						74	69	70					3																	15116216		2203	4300	6503	SO:0001819	synonymous_variant	64145	exon14			GCGGCCCGCGGCC	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.1428G>T	chr3.hg19:g.15116216C>A		158.0	0.0	.		132.0	6.0	.	NM_022340	B4DWY8|C9J4P5|Q3KP30|Q59EY8|Q8NAQ1	Silent	SNP	ENST00000253699.3	hg19	CCDS2623.1																																																																																			.	.	.	none		0.617	ZFYVE20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252102.2	NM_022340		A	15116216	C	A	15116216	2	1	171	1	0	0	0	0	0	0	0	1	17678	639	23	4		4	ZFYVE20	3	15116216	Silent	SNP	C	TCGA-G7-6792-01A-21D-1961-08		15116216	182906214	3	10028											
CTDSPL	10217	hgsc.bcm.edu	37	chr3	38009318	38009318	+	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	tagtctcttttttctctagcCtattagtaatgctgatttta	8	21	5	7	0	2	1	0	1	2	0	4	1	2	1	1	0	2	2	1	0	6	10			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr3:38009318C>G	ENST00000273179.5	+	5	397	c.371C>G	c.(370-372)cCt>cGt	p.P124R	MIR26A1_ENST00000362205.1_RNA|CTDSPL_ENST00000310189.3_3'UTR|CTDSPL_ENST00000443503.2_Splice_Site_p.P113R	NM_001008392.1	NP_001008393.1	O15194	CTDSL_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like	124	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.					extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			breast(1)|endometrium(2)|large_intestine(4)|skin(1)	8		Melanoma(1037;0.0122)		KIRC - Kidney renal clear cell carcinoma(284;0.0729)|Kidney(284;0.0902)		TTTCTCTAGCCTATTAGTAAT	0.308											OREG0015472	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P124R		Atlas-SNP	.											.	CTDSPL	17	.	0			c.C371G						PASS	.						64	61	62					3																	38009318		2199	4299	6498	SO:0001630	splice_region_variant	10217	exon5			TCTAGCCTATTAG	D88153	CCDS33734.1, CCDS33735.1	3p21.3	2010-06-21	2003-10-27	2003-10-29	ENSG00000144677	ENSG00000144677	3.1.3.16	"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	16890	protein-coding gene	gene with protein product	"small CTD phosphatase 3", "HYA22 protein", "RB protein serine phosphatase from chromosome 3"	608592	"chromosome 3 open reading frame 8"	C3orf8		9179494, 12543795	Standard	NM_005808		Approved	HYA22, SCP3, PSR1, RBSP3	uc003chg.3	O15194	OTTHUMG00000155942	ENST00000273179.5:c.370-1C>G	chr3.hg19:g.38009318C>G		63.0	0.0	.	874	54.0	13.0	.	NM_001008392	Q3ZTU0|Q70KI4|Q7Z5Q2	Missense_Mutation	SNP	ENST00000273179.5	hg19	CCDS33734.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.625293	0.87560	.	.	ENSG00000144677	ENST00000443503;ENST00000273179;ENST00000447745	T;T;T	0.17213	2.29;2.29;2.29	5.15	5.15	0.70609	NLI interacting factor (3);Dullard phosphatase domain, eukaryotic (1);HAD-like domain (2);	0.049311	0.85682	D	0.000000	T	0.46756	0.1409	M	0.79926	2.475	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.992;0.995	T	0.49133	-0.8971	10	0.62326	D	0.03	-20.9054	19.0018	0.92837	0.0:1.0:0.0:0.0	.	113;124	O15194-2;O15194	.;CTDSL_HUMAN	R	113;124;13	ENSP00000398288:P113R;ENSP00000273179:P124R;ENSP00000407443:P13R	ENSP00000273179:P124R	P	+	2	0	CTDSPL	37984322	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.720000	0.84759	2.571000	0.86741	0.655000	0.94253	CCT	.	.	.	none		0.308	CTDSPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342392.1	NM_005808	Missense_Mutation	G	38009318	C	G	38009318	5	3	171	1	0	0	0	0	0	0	1	0	4007	695	24	4	389	4	CTDSPL	3	38009318	Splice_Site	SNP	C	TCGA-G7-6792-01A-21D-1961-08	22893102	38009318	160013112	4	10029											
FYCO1	79443	hgsc.bcm.edu	37	chr3	46008824	46008824	+	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	acccaagtgccggatgctggCctgctcggcctccagggagg	6	6	15	14	2	0	0	0	0	0	0	2	2	1	2	5	5	3	2	5	5	1	0			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr3:46008824C>T	ENST00000296137.2	-	8	2207	c.2002G>A	c.(2002-2004)Gcc>Acc	p.A668T	FYCO1_ENST00000535325.1_Missense_Mutation_p.A668T	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	668					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)		CGGATGCTGGCCTGCTCGGCC	0.632																																					p.A668T		Atlas-SNP	.											.	FYCO1	115	.	0			c.G2002A						PASS	.						48	53	52					3																	46008824		2203	4299	6502	SO:0001583	missense	79443	exon8			TGCTGGCCTGCTC	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.2002G>A	chr3.hg19:g.46008824C>T	ENSP00000296137:p.Ala668Thr	173.0	0.0	.		150.0	62.0	.	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	hg19	CCDS2734.1	.	.	.	.	.	.	.	.	.	.	C	14.80	2.644029	0.47258	.	.	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.21932	1.98;1.98	5.77	3.98	0.46160	.	0.365546	0.30492	N	0.009502	T	0.29355	0.0731	M	0.62723	1.935	0.25407	N	0.988398	D;D	0.60575	0.988;0.983	P;P	0.57204	0.815;0.766	T	0.12016	-1.0564	10	0.19147	T	0.46	-9.0348	5.1628	0.15070	0.0:0.5992:0.1506:0.2502	.	668;668	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	T	668	ENSP00000296137:A668T;ENSP00000441178:A668T	ENSP00000296137:A668T	A	-	1	0	FYCO1	45983828	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.289000	0.33307	0.786000	0.33708	0.655000	0.94253	GCC	.	.	.	none		0.632	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513		T	46008824	C	T	46008824	3	4	171	1	0	0	0	0	1	0	0	0	6132	739	26	2	2478	2	FYCO1	3	46008824	Missense_Mutation	SNP	C	TCGA-G7-6792-01A-21D-1961-08	7999506	46008824	152013606	5	10030											
FNIP2	57600	hgsc.bcm.edu	37	chr4	159825696	159825696	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtggctcaaatactcttataAgctaaagctcaggacagttc	13	11	8	9	0	3	0	2	0	1	0	4	1	3	1	0	2	3	4	0	2	6	5			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr4:159825696A>G	ENST00000264433.6	+	17	3420	c.3345A>G	c.(3343-3345)taA>taG	p.*1115*	C4orf45_ENST00000434826.2_Intron|FNIP2_ENST00000379346.3_Silent_p.*1138*|C4orf45_ENST00000508011.1_Intron	NM_020840.1	NP_065891.1	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	0					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)		TACTCTTATAAGCTAAAGCTC	0.388																																					p.X1115X		Atlas-SNP	.											.	FNIP2	90	.	0			c.A3345G						PASS	.						141	133	136					4																	159825696		1847	4095	5942	SO:0001819	synonymous_variant	57600	exon17			CTTATAAGCTAAA	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.3345A>G	chr4.hg19:g.159825696A>G		172.0	0.0	.		121.0	46.0	.	NM_020840	Q05DC3|Q96I31|Q9H994	Silent	SNP	ENST00000264433.6	hg19	CCDS47155.1																																																																																			.	.	.	none		0.388	FNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366602.1	NM_020840		G	159825696	A	G	159825696	2	3	171	1	0	0	0	0	0	0	0	1	5983	79	3	3		3	FNIP2	4	159825696	Silent	SNP	A	TCGA-G7-6792-01A-21D-1961-08		159825696	31328580	6	10031											
RBM27	54439	hgsc.bcm.edu	37	chr5	145610424	145610424	+	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	ttactataacaatcatagctCttccaattcttttggtcgaa	12	16	4	9	1	3	0	1	0	2	0	5	1	4	0	1	1	3	1	1	1	7	8			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr5:145610424C>A	ENST00000265271.5	+	6	960	c.794C>A	c.(793-795)tCt>tAt	p.S265Y	RBM27_ENST00000506502.1_Missense_Mutation_p.S265Y	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	265					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)			AATCATAGCTCTTCCAATTCT	0.428																																					p.S265Y		Atlas-SNP	.											.	RBM27	119	.	0			c.C794A						PASS	.						124	108	113					5																	145610424		1568	3582	5150	SO:0001583	missense	54439	exon6			ATAGCTCTTCCAA	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.794C>A	chr5.hg19:g.145610424C>A	ENSP00000265271:p.Ser265Tyr	118.0	0.0	.		97.0	37.0	.	NM_018989	Q8IYW9	Missense_Mutation	SNP	ENST00000265271.5	hg19	CCDS43378.1	.	.	.	.	.	.	.	.	.	.	C	14.96	2.690372	0.48097	.	.	ENSG00000091009	ENST00000265271	T	0.48201	0.82	5.56	5.56	0.83823	.	0.344763	0.28332	N	0.015722	T	0.36496	0.0969	N	0.22421	0.69	0.35199	D	0.774129	P;P	0.51653	0.454;0.947	B;B	0.41374	0.064;0.355	T	0.53514	-0.8428	10	0.59425	D	0.04	-7.8615	15.2609	0.73621	0.1489:0.8511:0.0:0.0	.	265;265	Q9P2N5;B3KY61	RBM27_HUMAN;.	Y	265	ENSP00000265271:S265Y	ENSP00000265271:S265Y	S	+	2	0	RBM27	145590617	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.339000	0.43965	2.614000	0.88457	0.563000	0.77884	TCT	.	.	.	none		0.428	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128		A	145610424	C	A	145610424	3	1	171	1	0	0	0	0	1	0	0	0	13140	913	32	4	816	4	RBM27	5	145610424	Missense_Mutation	SNP	C	TCGA-G7-6792-01A-21D-1961-08		145610424	35304836	7	10032											
ARSI	340075	hgsc.bcm.edu	37	chr5	149677576	149677576	+	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	gcggccagttgctgccccccGagaaagtctggccaccattg	7	7	12	15	2	1	1	0	0	1	1	1	2	1	1	6	2	2	2	6	2	1	2			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr5:149677576G>A	ENST00000328668.7	-	2	1490	c.911C>T	c.(910-912)tCg>tTg	p.S304L		NM_001012301.2	NP_001012301.1	Q5FYB1	ARSI_HUMAN	arylsulfatase family, member I	304					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)			GCTGCCCCCCGAGAAAGTCTG	0.587																																					p.S304L		Atlas-SNP	.											.	ARSI	65	.	0			c.C911T						PASS	.						36	32	34					5																	149677576		2199	4292	6491	SO:0001583	missense	340075	exon2			CCCCCCGAGAAAG	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.911C>T	chr5.hg19:g.149677576G>A	ENSP00000333395:p.Ser304Leu	94.0	0.0	.		71.0	28.0	.	NM_001012301	A1L3B0|B3KV22|B7XD03	Missense_Mutation	SNP	ENST00000328668.7	hg19	CCDS34275.1	.	.	.	.	.	.	.	.	.	.	G	17.33	3.361900	0.61403	.	.	ENSG00000183876	ENST00000328668;ENST00000515301	D;D	0.96745	-4.11;-4.11	4.46	4.46	0.54185	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.059421	0.64402	D	0.000001	D	0.92473	0.7610	N	0.25426	0.745	0.54753	D	0.999982	B	0.18166	0.026	B	0.18263	0.021	D	0.89036	0.3445	10	0.22109	T	0.4	.	17.6599	0.88189	0.0:0.0:1.0:0.0	.	304	Q5FYB1	ARSI_HUMAN	L	304;161	ENSP00000333395:S304L;ENSP00000426879:S161L	ENSP00000333395:S304L	S	-	2	0	ARSI	149657769	1.000000	0.71417	0.961000	0.40146	0.945000	0.59286	7.738000	0.84966	2.460000	0.83146	0.561000	0.74099	TCG	.	.	.	none		0.587	ARSI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373681.1	NM_001012301		A	149677576	G	A	149677576	3	1	171	1	0	0	0	0	1	0	0	0	994	1059	37	1	802	1	ARSI	5	149677576	Missense_Mutation	SNP	G	TCGA-G7-6792-01A-21D-1961-08	4067152	149677576	31237684	8	10033											
NDUFAF4	29078	hgsc.bcm.edu	37	chr6	97344647	97344647	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaagacacaggatctttggaAtcaacatacacatcttttag	15	11	7	8	0	3	1	1	0	2	1	3	4	3	3	0	2	2	0	0	2	5	4			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr6:97344647A>G	ENST00000316149.7	-	2	292	c.213T>C	c.(211-213)gaT>gaC	p.D71D	NDUFAF4_ENST00000489477.1_5'UTR	NM_014165.3	NP_054884.1	Q9P032	NDUF4_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 4	71					mitochondrial respiratory chain complex I assembly (GO:0032981)	mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)				large_intestine(5)|lung(3)|ovary(1)|skin(1)	10						GATCTTTGGAATCAACATACA	0.358																																					p.D71D		Atlas-SNP	.											.	NDUFAF4	16	.	0			c.T213C						PASS	.						148	149	149					6																	97344647		2203	4300	6503	SO:0001819	synonymous_variant	29078	exon2			TTTGGAATCAACA	AF161474	CCDS5037.1	6q16.3	2012-10-12	2012-05-08	2009-03-18	ENSG00000123545	ENSG00000123545		"Mitochondrial respiratory chain complex assembly factors"	21034	protein-coding gene	gene with protein product		611776	"chromosome 6 open reading frame 66", "NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 4"	C6orf66		11042152, 18179882	Standard	NM_014165		Approved	HSPC125, bA22L21.1, My013, HRPAP20	uc003pow.3	Q9P032	OTTHUMG00000015246	ENST00000316149.7:c.213T>C	chr6.hg19:g.97344647A>G		128.0	0.0	.		114.0	32.0	.	NM_014165	B2R4J5	Silent	SNP	ENST00000316149.7	hg19	CCDS5037.1																																																																																			.	.	.	none		0.358	NDUFAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041567.1	NM_014165		G	97344647	A	G	97344647	2	3	171	1	0	0	0	0	0	0	0	1	10284	98	4	3		3	NDUFAF4	6	97344647	Silent	SNP	A	TCGA-G7-6792-01A-21D-1961-08		97344647	73770420	9	10034											
PABPC1	26986	hgsc.bcm.edu	37	chr8	101719226	101719226	+	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	accgggcatattttggaatgCtgcattttaaagatgtgaat	12	14	10	5	1	0	2	0	1	0	1	0	3	0	3	1	2	2	3	1	2	5	5	rs112580522		TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr8:101719226C>G	ENST00000318607.5	-	10	2465		c.e10-1		PABPC1_ENST00000519004.1_Splice_Site|PABPC1_ENST00000522387.1_Splice_Site|PABPC1_ENST00000519596.1_Intron|AP001205.1_ENST00000579868.1_RNA	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)	p.?(1)		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)			TTTTGGAATGCTGCATTTTAA	0.413																																					.		Atlas-SNP	.											PABPC1,NS,carcinoma,0,1	PABPC1	76	.	1	Unknown(1)	lung(1)	c.1337-1G>C						PASS	.						39	41	40					8																	101719226		2203	4300	6503	SO:0001630	splice_region_variant	26986	exon11			GGAATGCTGCATT	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.1337-1G>C	chr8.hg19:g.101719226C>G		63.0	1.0	.		54.0	6.0	.	NM_002568	Q15097|Q93004	Splice_Site	SNP	ENST00000318607.5	hg19	CCDS6289.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.096182	0.76870	.	.	ENSG00000070756	ENST00000318607;ENST00000519004;ENST00000522387;ENST00000517403	.	.	.	6.04	6.04	0.98038	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.5891	0.99427	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PABPC1	101788402	1.000000	0.71417	0.998000	0.56505	0.957000	0.61999	5.388000	0.66249	2.876000	0.98609	0.650000	0.86243	.	.	G|1.000;|0.000	1.000	weak		0.413	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	Intron	G	101719226	C	G	101719226	5	3	171	1	0	0	0	0	0	0	1	0	11370	811	28	4	594	4	PABPC1	8	101719226	Splice_Site	SNP	C	TCGA-G7-6792-01A-21D-1961-08		101719226	44644796	10	10035											
TG	7038	hgsc.bcm.edu	37	chr8	133931710	133931710	+	Missense_Mutation	SNP	T	T	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	aacaggcagggagcttggccTgtgtcccatgtcctgtgggc	6	9	15	11	0	0	0	0	0	0	0	2	1	2	1	3	4	2	2	3	4	1	1			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr8:133931710T>G	ENST00000220616.4	+	21	4508	c.4468T>G	c.(4468-4470)Tgt>Ggt	p.C1490G	TG_ENST00000542445.1_5'UTR|TG_ENST00000377869.1_Missense_Mutation_p.C1490G	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1490					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)		GAGCTTGGCCTGTGTCCCATG	0.478																																					p.C1490G		Atlas-SNP	.											.	TG	416	.	0			c.T4468G						PASS	.						141	112	122					8																	133931710		2203	4300	6503	SO:0001583	missense	7038	exon21			TTGGCCTGTGTCC	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.4468T>G	chr8.hg19:g.133931710T>G	ENSP00000220616:p.Cys1490Gly	102.0	0.0	.		109.0	41.0	.	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	hg19	CCDS34944.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.60|16.60	3.168293|3.168293	0.57584|0.57584	.|.	.|.	ENSG00000042832|ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616|ENST00000519178	D;D|.	0.86865|.	-2.18;-2.18|.	5.52|5.52	5.52|5.52	0.82312|0.82312	Tyrosine-protein kinase ephrin type A/B receptor-like (1);|.	0.194939|.	0.36703|.	N|.	0.002444|.	T|T	0.80374|0.80374	0.4611|0.4611	H|H	0.97516|0.97516	4.02|4.02	0.28752|0.28752	N|N	0.90136|0.90136	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|T	0.80527|0.80527	-0.1343|-0.1343	10|5	0.87932|.	D|.	0|.	.|.	12.3216|12.3216	0.54987|0.54987	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1490|.	P01266|.	THYG_HUMAN|.	G|R	1490;296;1490|9	ENSP00000367100:C1490G;ENSP00000220616:C1490G|.	ENSP00000220616:C1490G|.	C|L	+|+	1|2	0|0	TG|TG	134000892|134000892	1.000000|1.000000	0.71417|0.71417	0.890000|0.890000	0.34922|0.34922	0.588000|0.588000	0.36517|0.36517	5.096000|5.096000	0.64535|0.64535	2.225000|2.225000	0.72522|0.72522	0.533000|0.533000	0.62120|0.62120	TGT|CTG	.	.	.	none		0.478	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		G	133931710	T	G	133931710	3	3	171	1	0	0	0	0	1	0	0	0	15825	1580	55	5	4550	5	TG	8	133931710	Missense_Mutation	SNP	T	TCGA-G7-6792-01A-21D-1961-08	32212484	133931710	12432312	11	10036											
ERLIN1	10613	hgsc.bcm.edu	37	chr10	101911987	101911987	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttccagtcctaatatctgaAtatttcaaagcacatgagga	14	12	6	9	0	2	2	1	2	1	0	4	3	4	3	2	1	1	1	2	1	5	5			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr10:101911987A>G	ENST00000421367.2	-	11	3655	c.948T>C	c.(946-948)taT>taC	p.Y316Y	ERLIN1_ENST00000407654.3_Silent_p.Y316Y	NM_001100626.1|NM_006459.3	NP_001094096.1|NP_006450.2	O75477	ERLN1_HUMAN	ER lipid raft associated 1	314					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)							Colorectal(252;0.234)		Epithelial(162;3.85e-10)|all cancers(201;3.25e-08)		TAATATCTGAATATTTCAAAG	0.443																																					p.Y316Y		Atlas-SNP	.											.	.	.	.	0			c.T948C						PASS	.						119	115	116					10																	101911987		2203	4300	6503	SO:0001819	synonymous_variant	10613	exon11			ATCTGAATATTTC	AF064093	CCDS7487.2	10q24.31	2014-03-03	2007-01-26	2007-01-26	ENSG00000107566	ENSG00000107566			16947	protein-coding gene	gene with protein product	"Band_7 23-211 Keo4 (Interim) similar to C.elegans protein C42C1.9"	611604	"chromosome 10 open reading frame 69", "SPFH domain family, member 1"	C10orf69, SPFH1		11118313, 16835267, 24482476	Standard	NM_006459		Approved	KE04, Erlin-1, SPG62	uc001kqo.4	O75477	OTTHUMG00000018900	ENST00000421367.2:c.948T>C	chr10.hg19:g.101911987A>G		127.0	0.0	.		132.0	50.0	.	NM_006459	B0QZ42|Q53HV0	Silent	SNP	ENST00000421367.2	hg19	CCDS7487.2																																																																																			.	.	.	none		0.443	ERLIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049840.2	NM_006459		G	101911987	A	G	101911987	2	3	171	1	0	0	0	0	0	0	0	1	5234	108	4	3		3	ERLIN1	10	101911987	Silent	SNP	A	TCGA-G7-6792-01A-21D-1961-08		101911987	33622760	12	10037											
PPFIBP2	8495	hgsc.bcm.edu	37	chr11	7669667	7669667	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacagagcgtgtgtgtgcaTggctggaggactttggcctg	6	10	17	8	1	0	1	0	0	0	1	0	3	0	3	1	4	2	3	1	4	0	1			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr11:7669667T>C	ENST00000299492.4	+	18	2084	c.1696T>C	c.(1696-1698)Tgg>Cgg	p.W566R	PPFIBP2_ENST00000533792.1_Missense_Mutation_p.W408R|PPFIBP2_ENST00000530181.1_Missense_Mutation_p.W423R|PPFIBP2_ENST00000530582.1_3'UTR|PPFIBP2_ENST00000528883.1_Missense_Mutation_p.W454R	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	566	SAM 1. {ECO:0000255|PROSITE- ProRule:PRU00184}.				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)		TGTGTGTGCATGGCTGGAGGA	0.547																																					p.W566R		Atlas-SNP	.											.	PPFIBP2	87	.	0			c.T1696C						PASS	.						165	124	138					11																	7669667		2201	4296	6497	SO:0001583	missense	8495	exon18			TGTGCATGGCTGG	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.1696T>C	chr11.hg19:g.7669667T>C	ENSP00000299492:p.Trp566Arg	140.0	0.0	.		117.0	44.0	.	NM_003621	B7Z433|E9PK77|O75337|Q8WW26	Missense_Mutation	SNP	ENST00000299492.4	hg19	CCDS31419.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.451254	0.84209	.	.	ENSG00000166387	ENST00000299492;ENST00000533792;ENST00000541115;ENST00000528883;ENST00000530181	T;T;T;T	0.61510	0.1;0.1;0.1;0.1	5.74	5.74	0.90152	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.000000	0.64402	D	0.000001	D	0.82660	0.5085	H	0.95114	3.625	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.87696	0.2557	10	0.87932	D	0	-9.1173	13.9867	0.64339	0.0:0.0:0.0:1.0	.	454;454;489;408;423;566	E9PK77;B7Z433;F5GWB0;E9PP16;E9PMU1;Q8ND30	.;.;.;.;.;LIPB2_HUMAN	R	566;408;489;454;423	ENSP00000299492:W566R;ENSP00000436498:W408R;ENSP00000435469:W454R;ENSP00000437321:W423R	ENSP00000299492:W566R	W	+	1	0	PPFIBP2	7626243	1.000000	0.71417	0.926000	0.36857	0.995000	0.86356	8.040000	0.89188	2.194000	0.70268	0.459000	0.35465	TGG	.	.	.	none		0.547	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621		C	7669667	T	C	7669667	3	2	171	1	0	0	0	0	1	0	0	0	12321	1464	51	3	1762	3	PPFIBP2	11	7669667	Missense_Mutation	SNP	T	TCGA-G7-6792-01A-21D-1961-08		7669667	127336849	13	10038											
B3GNT6	192134	hgsc.bcm.edu	37	chr11	76751585	76751585	+	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	cagcggccacgagggcatccTggcccttcggcgtgcagctt	5	7	14	15	4	0	0	0	0	0	0	2	1	1	0	3	4	3	3	3	4	0	2	rs11292199		TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr11:76751585T>C	ENST00000354301.5	+	4	1076	c.988T>C	c.(988-990)Tgg>Cgg	p.W330R	B3GNT6_ENST00000421061.1_Splice_Site|B3GNT6_ENST00000533140.1_Silent_p.P330P	NM_138706.3	NP_619651.3	O43505	B3GN1_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6 (core 3 synthase)	0					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|poly-N-acetyllactosamine biosynthetic process (GO:0030311)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity (GO:0008532)			central_nervous_system(1)|kidney(2)|lung(4)|prostate(1)	8						GAGGGCATCCTGGCCCTTCGG	0.697																																					.		Atlas-SNP	.											.,2	B3GNT6	27	.	0			c.988+1T>C						PASS	.						6	5	6					11																	76751585		1175	2610	3785	SO:0001630	splice_region_variant	192134	exon3			GCATCCTGGCCCT	AB073740	CCDS53681.1	11q13.4	2013-02-19			ENSG00000198488	ENSG00000198488		"Beta 3-glycosyltransferases"	24141	protein-coding gene	gene with protein product		615315				11821425	Standard	NM_138706		Approved	B3Gn-T6	uc021qnp.1	Q6ZMB0		ENST00000354301.5:c.988-1T>C	chr11.hg19:g.76751585T>C		0.0	0.0	.		5.0	3.0	.	NM_138706	Q4TTN0	Splice_Site	SNP	ENST00000354301.5	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	0.007|0.007	-1.936685|-1.936685	0.00484|0.00484	.|.	.|.	ENSG00000198488|ENSG00000198488	ENST00000354301;ENST00000421061|ENST00000354301	.|T	.|0.24538	.|1.85	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.11024	.|0.0269	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.26916	.|-1.0089	.|4	.|0.02654	.|T	.|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|R	-1|330	.|ENSP00000346256:W330R	.|ENSP00000346256:W330R	.|W	+|+	.|1	.|0	B3GNT6|B3GNT6	76429233|76429233	0.988000|0.988000	0.35896|0.35896	1.000000|1.000000	0.80357|0.80357	0.975000|0.975000	0.68041|0.68041	0.000000|0.000000	0.12993|0.12993	0.000000|0.000000	0.14550|0.14550	0.000000|0.000000	0.15137|0.15137	.|TGG	.	.	.	none		0.697	B3GNT6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_138706	Missense_Mutation	C	76751585	T	C	76751585	5	2	171	1	0	0	0	0	0	0	1	0	1261	1567	55	3	992	3	B3GNT6	11	76751585	Splice_Site	SNP	T	TCGA-G7-6792-01A-21D-1961-08	69081918	76751585	58254931	14	10039											
KLRK1	22914	hgsc.bcm.edu	37	chr12	10539567	10539567	+	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	gccatcgtgttgaaaaatcaCtcttcttcagatccaagtta	12	13	6	10	1	4	2	2	1	2	1	6	2	5	2	2	0	0	2	2	0	4	4			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr12:10539567C>T	ENST00000240618.6	-	3	223	c.83G>A	c.(82-84)aGt>aAt	p.S28N	KLRK1_ENST00000540818.1_Missense_Mutation_p.S28N|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	28					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						TGAAAAATCACTCTTCTTCAG	0.363																																					p.S28N		Atlas-SNP	.											.	.	.	.	0			c.G83A						PASS	.						171	159	163					12																	10539567		2203	4299	6502	SO:0001583	missense	0	exon8			AAATCACTCTTCT	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.83G>A	chr12.hg19:g.10539567C>T	ENSP00000240618:p.Ser28Asn	70.0	0.0	.		56.0	18.0	.	NM_001199805	A8K7K5|A8K7P4|Q9NR41	Missense_Mutation	SNP	ENST00000240618.6	hg19	CCDS8623.1	.	.	.	.	.	.	.	.	.	.	C	0.017	-1.506590	0.00992	.	.	ENSG00000213809	ENST00000240618;ENST00000540818	T;T	0.01430	4.9;4.9	4.09	-8.18	0.01053	.	2.508350	0.01286	N	0.009885	T	0.00998	0.0033	L	0.29908	0.895	0.09310	N	1	B;B;B	0.21520	0.0;0.0;0.057	B;B;B	0.15870	0.0;0.001;0.014	T	0.48958	-0.8988	10	0.11794	T	0.64	.	1.9441	0.03353	0.1238:0.2263:0.3731:0.2768	.	28;9;28	Q8WZ67;Q1HEA1;P26718	.;.;NKG2D_HUMAN	N	28	ENSP00000240618:S28N;ENSP00000446003:S28N	ENSP00000240618:S28N	S	-	2	0	KLRK1	10430834	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.256000	0.00538	-1.778000	0.01282	-1.161000	0.01788	AGT	.	.	.	none		0.363	KLRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400269.1	NM_007360		T	10539567	C	T	10539567	3	4	171	1	0	0	0	0	1	0	0	0	8430	565	20	2	591	2	KLRK1	12	10539567	Missense_Mutation	SNP	C	TCGA-G7-6792-01A-21D-1961-08		10539567	123312328	15	10040											
KRR1	11103	hgsc.bcm.edu	37	chr12	75895546	75895546	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttccttaggtggaataaaTgctttgtttctttcctcttg	6	21	7	7	0	2	0	0	0	2	0	4	1	4	1	2	2	1	2	2	2	4	8			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr12:75895546T>C	ENST00000229214.4	-	9	983	c.960A>G	c.(958-960)gcA>gcG	p.A320A	GLIPR1_ENST00000266659.3_3'UTR|KRR1_ENST00000438169.2_Silent_p.A263A	NM_007043.6	NP_008974.5	Q13601	KRR1_HUMAN	KRR1, small subunit (SSU) processome component, homolog (yeast)	320	Lys-rich.				rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(1)	11						GTGGAATAAATGCTTTGTTTC	0.279																																					p.A320A		Atlas-SNP	.											.	KRR1	37	.	0			c.A960G						PASS	.						125	123	124					12																	75895546		2203	4299	6502	SO:0001819	synonymous_variant	11103	exon9			AATAAATGCTTTG	U55766	CCDS9012.1	12q	2011-03-15	2006-05-18	2006-05-18	ENSG00000111615	ENSG00000111615			5176	protein-coding gene	gene with protein product		612817	"HIV-1 rev binding protein 2", "HIV-1 Rev binding protein 2"	HRB2		7505766, 11027267, 11359931, 8675026	Standard	NM_007043		Approved	RIP-1	uc001sxt.3	Q13601	OTTHUMG00000169759	ENST00000229214.4:c.960A>G	chr12.hg19:g.75895546T>C		87.0	0.0	.		73.0	21.0	.	NM_007043	A0FIK6|A0JLP0|B2R989|E7EUQ0|Q8NEA8|Q8TC37|Q96AT5	Silent	SNP	ENST00000229214.4	hg19	CCDS9012.1																																																																																			.	.	.	none		0.279	KRR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405727.1	NM_007043		C	75895546	T	C	75895546	2	2	171	1	0	0	0	0	0	0	0	1	8453	1451	51	3		3	KRR1	12	75895546	Silent	SNP	T	TCGA-G7-6792-01A-21D-1961-08	65355979	75895546	57956349	16	10041											
GNPTAB	79158	hgsc.bcm.edu	37	chr12	102159058	102159058	+	Frame_Shift_Del	DEL	A	A	-																															tctggtttgggagaaggatcActttatacaattcatgaaaa																										TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr12:102159058delA	ENST00000299314.7	-	13	1899	c.1637delT	c.(1636-1638)gtgfs	p.V546fs	RNU6-101P_ENST00000410323.1_RNA	NM_024312.4	NP_077288.2	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	546					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						GAGAAGGATCACTTTATACAA	0.358																																					p.V546fs		Atlas-INDEL	.											.	GNPTAB	120	.	0			c.1638delG						PASS	.						77	77	77					12																	102159058		2203	4300	6503	SO:0001589	frameshift_variant	79158	exon13			.	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.1637delT	chr12.hg19:g.102159058delA	ENSP00000299314:p.Val546fs	101.0	0.0	0		100.0	33.0	0.33	NM_024312	A2RRQ9|Q3ZQK2|Q6IPW5|Q86TQ2|Q96N13|Q9ULL2	Frame_Shift_Del	DEL	ENST00000299314.7	hg19	CCDS9088.1																																																																																			.	.	.	none		0.358	GNPTAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409182.1			-	102159058	A	-	102159058	7	5	171	1	0	1	0	1	0	0	0	0	6552	159	6	0	2169	0	GNPTAB	12	102159058	Frame_Shift_Del	DEL	A	TCGA-G7-6792-01A-21D-1961-08	26263512	102159058	31692837	17	10042											
ACACB	32	hgsc.bcm.edu	37	chr12	109692084	109692084	+	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	gacagagaaattgaattcctCccatccagagctccctacga	13	8	7	13	1	0	3	0	1	0	2	4	6	4	3	4	0	2	1	4	0	3	3			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr12:109692084C>T	ENST00000338432.7	+	44	6230	c.6111C>T	c.(6109-6111)ctC>ctT	p.L2037L	ACACB_ENST00000543201.1_Silent_p.L703L|ACACB_ENST00000377848.3_Silent_p.L2037L|ACACB_ENST00000377854.5_Silent_p.L1967L			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	2037	Carboxyltransferase.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	TTGAATTCCTCCCATCCAGAG	0.488																																					p.L2037L		Atlas-SNP	.											.	ACACB	330	.	0			c.C6111T						PASS	.						206	202	203					12																	109692084		2203	4300	6503	SO:0001819	synonymous_variant	32	exon43			ATTCCTCCCATCC	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.6111C>T	chr12.hg19:g.109692084C>T		321.0	0.0	.		240.0	95.0	.	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Silent	SNP	ENST00000338432.7	hg19	CCDS31898.1																																																																																			.	.	.	none		0.488	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		T	109692084	C	T	109692084	2	4	171	1	0	0	0	0	0	0	0	1	107	842	30	2		2	ACACB	12	109692084	Silent	SNP	C	TCGA-G7-6792-01A-21D-1961-08	7533026	109692084	24159811	18	10043											
CDAN1	146059	hgsc.bcm.edu	37	chr15	43024004	43024004	+	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	ccaagacggtgcccccagcaCcaccagggctctgacacatc	10	4	9	18	1	1	2	0	1	1	1	2	2	1	2	5	2	2	2	5	2	1	0			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr15:43024004C>T	ENST00000356231.3	-	11	1576	c.1553G>A	c.(1552-1554)gGt>gAt	p.G518D		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	518					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)		GCCCCCAGCACCACCAGGGCT	0.532																																					p.G518D		Atlas-SNP	.											.	CDAN1	70	.	0			c.G1553A						PASS	.						34	38	36					15																	43024004		2203	4299	6502	SO:0001583	missense	146059	exon11			CCAGCACCACCAG	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.1553G>A	chr15.hg19:g.43024004C>T	ENSP00000348564:p.Gly518Asp	80.0	0.0	.		94.0	26.0	.	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Missense_Mutation	SNP	ENST00000356231.3	hg19	CCDS32209.1	.	.	.	.	.	.	.	.	.	.	c	17.73	3.462735	0.63513	.	.	ENSG00000140326	ENST00000356231;ENST00000267892	D	0.86694	-2.16	5.85	4.9	0.64082	.	0.352932	0.32785	N	0.005652	D	0.88526	0.6460	L	0.41236	1.265	0.37581	D	0.919811	D	0.63046	0.992	P	0.57101	0.813	D	0.89548	0.3797	10	0.46703	T	0.11	-7.4334	16.3622	0.83271	0.1325:0.8675:0.0:0.0	.	518	Q8IWY9	CDAN1_HUMAN	D	518;516	ENSP00000348564:G518D	ENSP00000267892:G516D	G	-	2	0	CDAN1	40811296	0.601000	0.26907	0.996000	0.52242	0.629000	0.37895	3.677000	0.54619	2.773000	0.95371	0.651000	0.88453	GGT	.	.	.	none		0.532	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300		T	43024004	C	T	43024004	3	4	171	1	0	0	0	0	1	0	0	0	3056	507	18	2	2202	2	CDAN1	15	43024004	Missense_Mutation	SNP	C	TCGA-G7-6792-01A-21D-1961-08		43024004	59507388	19	10044											
LACTB	114294	hgsc.bcm.edu	37	chr15	63414861	63414861	+	Frame_Shift_Del	DEL	G	G	-																															gtgggcgcaccgggcatagtGgttggagtttctgtagatgg																										TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr15:63414861delG	ENST00000261893.4	+	2	456	c.384delG	c.(382-384)gtgfs	p.V129fs	LACTB_ENST00000413507.2_Frame_Shift_Del_p.V129fs	NM_032857.3	NP_116246.2	P83111	LACTB_HUMAN	lactamase, beta	129						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						CGGGCATAGTGGTTGGAGTTT	0.488																																					p.V128fs	Melanoma(85;443 1381 6215 27308 35583)	Atlas-INDEL	.											.	LACTB	29	.	0			c.383delT						PASS	.						169	148	155					15																	63414861		2203	4300	6503	SO:0001589	frameshift_variant	114294	exon2			.	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.384delG	chr15.hg19:g.63414861delG	ENSP00000261893:p.Val129fs	107.0	0.0	0		106.0	35.0	0.330189	NM_032857	P83096	Frame_Shift_Del	DEL	ENST00000261893.4	hg19	CCDS10182.1																																																																																			.	.	.	none		0.488	LACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256224.1	NM_032857		-	63414861	G	-	63414861	7	5	171	1	0	1	0	1	0	0	0	0	8604	1335	47	0	390	0	LACTB	15	63414861	Frame_Shift_Del	DEL	G	TCGA-G7-6792-01A-21D-1961-08	20390857	63414861	39116531	20	10045											
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43464597	43464598	+	Frame_Shift_Ins	INS	-	-	AA																															ttaccttggttagcagcatgINSaaaatcatatcactgttgtc																										TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr18:43464597_43464598insAA	ENST00000282041.5	-	30	5322_5323	c.5288_5289insTT	c.(5287-5289)ttcfs	p.F1763fs	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1763					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						TTAGCAGCATGAAAATCATATC	0.421																																					p.F1763fs		Atlas-INDEL	.											.	EPG5	199	.	0			c.5289_5290insTT						PASS	.																																			SO:0001589	frameshift_variant	57724	exon30			.	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.5287_5288dupTT	chr18.hg19:g.43464600_43464601dupAA	ENSP00000282041:p.Phe1763fs	143.0	0.0	0		121.0	39.0	0.322314	NM_020964	A2BDF3|Q9H8C8	Frame_Shift_Ins	INS	ENST00000282041.5	hg19	CCDS11926.2																																																																																			.	.	.	none		0.421	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		AA	43464598	-	AA	43464597	7	5	171	1	0	1	1	0	0	0	0	0	8256	1281	45	0	2510	0	KIAA1632	18	43464597	Frame_Shift_Ins	INS	-	TCGA-G7-6792-01A-21D-1961-08		43464597	34612651	21	10046											
TMPRSS9	360200	hgsc.bcm.edu	37	chr19	2421953	2421953	+	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	tgcgctcaggttaagaagccGggcgtgtacacgcgcatcac	9	7	13	12	5	2	1	2	0	0	1	2	1	2	1	1	2	3	4	1	2	3	2	rs537200343		TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr19:2421953G>T	ENST00000332578.3	+	13	2154	c.2154G>T	c.(2152-2154)ccG>ccT	p.P718P		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	718	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)		TTAAGAAGCCGGGCGTGTACA	0.632																																					p.P718P		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.G2154T						PASS	.						77	71	73					19																	2421953		2203	4300	6503	SO:0001819	synonymous_variant	360200	exon13			GAAGCCGGGCGTG	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.2154G>T	chr19.hg19:g.2421953G>T		178.0	0.0	.		120.0	7.0	.	NM_182973	Q6ZND6|Q7Z411	Silent	SNP	ENST00000332578.3	hg19	CCDS12088.1																																																																																			.	.	.	none		0.632	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973		T	2421953	G	T	2421953	2	4	171	1	0	0	0	0	0	0	0	1	16265	1103	39	4		4	TMPRSS9	19	2421953	Silent	SNP	G	TCGA-G7-6792-01A-21D-1961-08		2421953	56707030	22	10047											
CST9L	128821	hgsc.bcm.edu	37	chr20	23548869	23548869	+	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	tgctccttccaggaattcaaGatgtgccccagtctgtaggc	8	11	10	12	0	2	1	1	0	1	1	4	2	4	2	4	2	2	2	4	2	3	3			TCGA-G7-6792-01A-21D-1961-08	TCGA-G7-6792-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcb71dd8-5625-4d0c-9148-b70199b7f6f3	381c414c-def1-4d55-95b5-9071eaf29fa6	g.chr20:23548869G>T	ENST00000376979.3	-	1	517	c.219C>A	c.(217-219)atC>atA	p.I73I		NM_080610.2	NP_542177.1	Q9H4G1	CST9L_HUMAN	cystatin 9-like	73						extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	8	Colorectal(13;0.0431)|Lung NSC(19;0.235)					AGGAATTCAAGATGTGCCCCA	0.547																																					p.I73I		Atlas-SNP	.											.	CST9L	25	.	0			c.C219A						PASS	.						155	122	133					20																	23548869		2203	4300	6503	SO:0001819	synonymous_variant	128821	exon1			ATTCAAGATGTGC		CCDS13157.1	20p11.21	2012-08-14	2008-03-06		ENSG00000101435	ENSG00000101435			16233	protein-coding gene	gene with protein product			"cystatin 9 (mouse)-like"			20565543	Standard	NM_080610		Approved	bA218C14.1, CTES7B	uc002wtk.4	Q9H4G1	OTTHUMG00000032073	ENST00000376979.3:c.219C>A	chr20.hg19:g.23548869G>T		81.0	0.0	.		66.0	19.0	.	NM_080610	B2R5A1	Silent	SNP	ENST00000376979.3	hg19	CCDS13157.1																																																																																			.	.	.	none		0.547	CST9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078338.1	NM_080610		T	23548869	G	T	23548869	2	4	171	1	0	0	0	0	0	0	0	1	3982	932	33	4		4	CST9L	20	23548869	Silent	SNP	G	TCGA-G7-6792-01A-21D-1961-08		23548869	39476651	23	10048											
PIK3CD	5293	hgsc.bcm.edu	37	chr1	9782066	9782066	+	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	gcaaactgaaggccctgaatGacttcgtcaagctgagctct	11	9	10	11	1	2	4	1	4	1	0	3	4	2	4	1	1	3	3	1	1	4	1			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr1:9782066G>T	ENST00000377346.4	+	17	2284	c.2089G>T	c.(2089-2091)Gac>Tac	p.D697Y	PIK3CD_ENST00000543390.1_3'UTR|PIK3CD_ENST00000361110.2_Missense_Mutation_p.D721Y|PIK3CD_ENST00000536656.1_Missense_Mutation_p.D721Y	NM_005026.3	NP_005017.3	O00329	PK3CD_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta	697					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)	GGCCCTGAATGACTTCGTCAA	0.637											OREG0013082	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D697Y		Atlas-SNP	.											.	PIK3CD	86	.	0			c.G2089T						PASS	.						74	84	81					1																	9782066		2203	4300	6503	SO:0001583	missense	5293	exon17			CTGAATGACTTCG		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.2089G>T	chr1.hg19:g.9782066G>T	ENSP00000366563:p.Asp697Tyr	123.0	0.0	.	659	99.0	26.0	.	NM_005026	A6NCG0|G1FFP1|O15445|Q5SR49	Missense_Mutation	SNP	ENST00000377346.4	hg19	CCDS104.1	.	.	.	.	.	.	.	.	.	.	G	12.34	1.908660	0.33721	.	.	ENSG00000171608	ENST00000536656;ENST00000377346;ENST00000361110;ENST00000360563	D;D;D	0.82081	-1.57;-1.57;-1.57	5.4	4.48	0.54585	Protein kinase-like domain (1);	0.151853	0.64402	D	0.000020	D	0.86339	0.5909	L	0.55990	1.75	0.80722	D	1	P;D;P	0.65815	0.939;0.995;0.939	P;P;P	0.57620	0.615;0.824;0.707	D	0.87479	0.2419	10	0.87932	D	0	-44.469	13.397	0.60858	0.0756:0.0:0.9244:0.0	.	696;721;697	B7ZM44;Q5SR50;O00329	.;.;PK3CD_HUMAN	Y	721;697;721;721	ENSP00000446444:D721Y;ENSP00000366563:D697Y;ENSP00000354410:D721Y	ENSP00000353766:D721Y	D	+	1	0	PIK3CD	9704653	1.000000	0.71417	0.063000	0.19743	0.112000	0.19704	7.859000	0.86982	1.275000	0.44379	0.561000	0.74099	GAC	.	.	.	none		0.637	PIK3CD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004235.1	NM_005026		T	9782066	G	T	9782066	3	4	172	1	0	0	0	0	1	0	0	0	11922	1290	45	4	2147	4	PIK3CD	1	9782066	Missense_Mutation	SNP	G	TCGA-G7-6793-01A-11D-1961-08		9782066	239468555	1	10049											
TAS1R2	80834	hgsc.bcm.edu	37	chr1	19186021	19186021	+	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	taaggtgaacaatgcccttcAtgttggcatggagggagaag	12	9	14	6	0	1	2	1	1	0	1	1	4	1	3	1	4	2	2	1	4	4	3			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr1:19186021A>T	ENST00000375371.3	-	1	155	c.134T>A	c.(133-135)aTg>aAg	p.M45K	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	45					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)	AATGCCCTTCATGTTGGCATG	0.592																																					p.M45K		Atlas-SNP	.											.	TAS1R2	134	.	0			c.T134A						PASS	.						118	109	112					1																	19186021		2203	4300	6503	SO:0001583	missense	80834	exon1			CCCTTCATGTTGG		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.134T>A	chr1.hg19:g.19186021A>T	ENSP00000364520:p.Met45Lys	162.0	0.0	.		107.0	16.0	.	NM_152232	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	hg19	CCDS187.1	.	.	.	.	.	.	.	.	.	.	A	8.739	0.918447	0.17982	.	.	ENSG00000179002	ENST00000375371	D	0.88046	-2.33	4.47	2.07	0.26955	.	0.544004	0.13698	U	0.369069	T	0.74627	0.3741	N	0.22421	0.69	0.09310	N	0.999998	B	0.27068	0.167	B	0.18871	0.023	T	0.63093	-0.6714	10	0.52906	T	0.07	.	4.5956	0.12327	0.699:0.196:0.1051:0.0	.	45	Q8TE23	TS1R2_HUMAN	K	45	ENSP00000364520:M45K	ENSP00000364520:M45K	M	-	2	0	TAS1R2	19058608	0.239000	0.23836	0.384000	0.26145	0.776000	0.43924	1.724000	0.38064	0.201000	0.20466	0.260000	0.18958	ATG	.	.	.	none		0.592	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1			T	19186021	A	T	19186021	3	4	172	1	0	0	0	0	1	0	0	0	15575	217	8	5	2409	5	TAS1R2	1	19186021	Missense_Mutation	SNP	A	TCGA-G7-6793-01A-11D-1961-08	9403955	19186021	230064600	2	10050											
LRRC8C	84230	hgsc.bcm.edu	37	chr1	90180336	90180336	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaaacttaaaactctgaagaTtggaaaaaacagcctatctg	18	9	7	7	0	2	2	0	1	2	1	2	4	2	3	1	1	4	0	1	1	8	3			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr1:90180336T>C	ENST00000370454.4	+	3	2462	c.2207T>C	c.(2206-2208)aTt>aCt	p.I736T	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	736					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)		ACTCTGAAGATTGGAAAAAAC	0.353																																					p.I736T		Atlas-SNP	.											.	LRRC8C	73	.	0			c.T2207C						PASS	.						62	64	64					1																	90180336		2203	4300	6503	SO:0001583	missense	84230	exon3			TGAAGATTGGAAA		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.2207T>C	chr1.hg19:g.90180336T>C	ENSP00000359483:p.Ile736Thr	103.0	0.0	.		88.0	7.0	.	NM_032270	B3KXS9|Q29RV6|Q9H075	Missense_Mutation	SNP	ENST00000370454.4	hg19	CCDS725.1	.	.	.	.	.	.	.	.	.	.	T	12.90	2.077889	0.36662	.	.	ENSG00000171488	ENST00000370454	T	0.27402	1.67	5.87	5.87	0.94306	.	0.047961	0.85682	D	0.000000	T	0.25791	0.0628	M	0.69358	2.11	0.53688	D	0.99997	B	0.21821	0.061	B	0.27715	0.082	T	0.08953	-1.0697	10	0.87932	D	0	.	16.5764	0.84681	0.0:0.0:0.0:1.0	.	736	Q8TDW0	LRC8C_HUMAN	T	736	ENSP00000359483:I736T	ENSP00000359483:I736T	I	+	2	0	LRRC8C	89952924	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.655000	0.83696	2.371000	0.80710	0.533000	0.62120	ATT	.	.	.	none		0.353	LRRC8C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028435.2	NM_032270		C	90180336	T	C	90180336	3	2	172	1	0	0	0	0	1	0	0	0	9030	1493	52	3	2213	3	LRRC8C	1	90180336	Missense_Mutation	SNP	T	TCGA-G7-6793-01A-11D-1961-08	70994315	90180336	159070285	3	10051											
VAV3	10451	hgsc.bcm.edu	37	chr1	108307784	108307784	+	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	cactccactgcagtactgccCgtaaataaccaatctgaaag	14	8	6	13	1	1	1	0	1	1	0	2	1	2	1	3	0	4	3	3	0	6	3			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr1:108307784C>A	ENST00000370056.4	-	9	1109	c.835G>T	c.(835-837)Ggg>Tgg	p.G279W	VAV3_ENST00000343258.4_5'UTR|VAV3_ENST00000527011.1_Missense_Mutation_p.G279W|VAV3_ENST00000371846.4_Missense_Mutation_p.G214W	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	279	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				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)		CAGTACTGCCCGTAAATAACC	0.373																																					p.G279W		Atlas-SNP	.											.	VAV3	176	.	0			c.G835T						PASS	.						70	67	68					1																	108307784		2203	4300	6503	SO:0001583	missense	10451	exon9			ACTGCCCGTAAAT	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.835G>T	chr1.hg19:g.108307784C>A	ENSP00000359073:p.Gly279Trp	70.0	0.0	.		100.0	8.0	.	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	hg19	CCDS785.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.420776	0.83559	.	.	ENSG00000134215	ENST00000370056;ENST00000527011;ENST00000371846	T;T;T	0.64618	-0.11;-0.11;-0.11	5.55	5.55	0.83447	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	D	0.82421	0.5033	M	0.91459	3.21	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	0.85946	0.1461	10	0.87932	D	0	.	19.506	0.95116	0.0:1.0:0.0:0.0	.	279;279;214;279	B7ZLR1;E9PQ97;B4DHL6;Q9UKW4	.;.;.;VAV3_HUMAN	W	279;279;214	ENSP00000359073:G279W;ENSP00000432540:G279W;ENSP00000360912:G214W	ENSP00000359073:G279W	G	-	1	0	VAV3	108109307	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.354000	0.79424	2.611000	0.88343	0.585000	0.79938	GGG	.	.	.	none		0.373	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113		A	108307784	C	A	108307784	3	1	172	1	0	0	0	0	1	0	0	0	17145	652	23	4	1809	4	VAV3	1	108307784	Missense_Mutation	SNP	C	TCGA-G7-6793-01A-11D-1961-08	18127448	108307784	140942837	4	10052											
S100A3	6274	hgsc.bcm.edu	37	chr1	153520312	153520312	+	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	atttgttgtagtcacattccCgaaactcagtctgtgcaagg	10	13	9	9	1	3	0	2	0	1	0	4	1	4	0	1	1	2	3	1	1	3	4	rs566984814		TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr1:153520312C>A	ENST00000368713.3	-	3	348	c.152G>T	c.(151-153)cGg>cTg	p.R51L	S100A4_ENST00000481009.1_5'Flank|S100A4_ENST00000368714.1_Intron|S100A3_ENST00000368712.1_Missense_Mutation_p.R51L|S100A4_ENST00000368715.1_5'Flank|S100A4_ENST00000368716.4_5'Flank|S100A4_ENST00000354332.4_5'Flank	NM_002960.1	NP_002951.1	P33764	S10A3_HUMAN	S100 calcium binding protein A3	51	EF-hand 2.					cytoplasm (GO:0005737)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(1)|liver(1)|lung(1)	3	all_lung(78;5.98e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			GTCACATTCCCGAAACTCAGT	0.542																																					p.R51L		Atlas-SNP	.											S100A3,NS,carcinoma,0,1	S100A3	7	.	0			c.G152T						PASS	.						203	182	189					1																	153520312		2203	4300	6503	SO:0001583	missense	6274	exon3			CATTCCCGAAACT	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.152G>T	chr1.hg19:g.153520312C>A	ENSP00000357702:p.Arg51Leu	245.0	0.0	.		179.0	10.0	.	NM_002960	D3DV51|Q6FGE4	Missense_Mutation	SNP	ENST00000368713.3	hg19	CCDS1043.1	.	.	.	.	.	.	.	.	.	.	C	13.39	2.222659	0.39300	.	.	ENSG00000188015	ENST00000368713;ENST00000368712	T;T	0.13420	2.59;2.59	4.85	0.804	0.18697	EF-hand-like domain (1);	0.648330	0.14896	N	0.292117	T	0.04137	0.0115	L	0.51422	1.61	0.09310	N	1	B	0.28055	0.199	B	0.20577	0.03	T	0.32375	-0.9909	10	0.72032	D	0.01	.	7.4533	0.27250	0.0:0.6319:0.0:0.3681	.	51	P33764	S10A3_HUMAN	L	51	ENSP00000357702:R51L;ENSP00000357701:R51L	ENSP00000357701:R51L	R	-	2	0	S100A3	151786936	0.010000	0.17322	0.027000	0.17364	0.562000	0.35680	0.709000	0.25734	-0.041000	0.13558	-0.136000	0.14681	CGG	.	.	.	none		0.542	S100A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037726.1	NM_002960		A	153520312	C	A	153520312	3	1	172	1	0	0	0	0	1	0	0	0	13792	652	23	4	157	4	S100A3	1	153520312	Missense_Mutation	SNP	C	TCGA-G7-6793-01A-11D-1961-08	45212528	153520312	95730309	5	10053											
PRELP	5549	hgsc.bcm.edu	37	chr1	203455866	203455866	+	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	cccagatttgccccaacgacCtagtggcgttccatgacttc	8	10	8	15	2	0	2	0	1	0	1	2	3	1	2	5	1	2	1	5	1	2	4			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr1:203455866C>A	ENST00000343110.2	+	3	1133	c.1006C>A	c.(1006-1008)Cta>Ata	p.L336I		NM_002725.3|NM_201348.1	NP_002716.1|NP_958505.1	P51888	PRELP_HUMAN	proline/arginine-rich end leucine-rich repeat protein	336					carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			BRCA - Breast invasive adenocarcinoma(75;0.109)			CCCCAACGACCTAGTGGCGTT	0.567																																					p.L336I		Atlas-SNP	.											.	PRELP	63	.	0			c.C1006A						PASS	.						110	100	103					1																	203455866		2203	4300	6503	SO:0001583	missense	5549	exon3			AACGACCTAGTGG	BC032498	CCDS1438.1	1q32	2008-02-05	2005-07-24		ENSG00000188783	ENSG00000188783		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	9357	protein-coding gene	gene with protein product	"prolargin proteoglycan"	601914	"proline arginine-rich end leucine-rich repeat protein"				Standard	NM_002725		Approved	SLRR2A, prolargin	uc001gzt.3	P51888	OTTHUMG00000035911	ENST00000343110.2:c.1006C>A	chr1.hg19:g.203455866C>A	ENSP00000343924:p.Leu336Ile	142.0	0.0	.		125.0	36.0	.	NM_201348	Q6FG38	Missense_Mutation	SNP	ENST00000343110.2	hg19	CCDS1438.1	.	.	.	.	.	.	.	.	.	.	C	1.678	-0.507353	0.04231	.	.	ENSG00000188783	ENST00000343110	T	0.49139	0.79	5.45	1.38	0.22167	.	0.097389	0.42964	N	0.000628	T	0.26557	0.0649	N	0.24115	0.695	0.19775	N	0.999957	B	0.06786	0.001	B	0.12156	0.007	T	0.15607	-1.0431	10	0.18710	T	0.47	-7.7426	5.6324	0.17518	0.2531:0.5559:0.1222:0.0687	.	336	P51888	PRELP_HUMAN	I	336	ENSP00000343924:L336I	ENSP00000343924:L336I	L	+	1	2	PRELP	201722489	0.003000	0.15002	0.003000	0.11579	0.246000	0.25737	-0.032000	0.12266	0.005000	0.14708	-0.300000	0.09419	CTA	.	.	.	none		0.567	PRELP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087474.1	NM_002725		A	203455866	C	A	203455866	3	1	172	1	0	0	0	0	1	0	0	0	12483	680	24	4	1012	4	PRELP	1	203455866	Missense_Mutation	SNP	C	TCGA-G7-6793-01A-11D-1961-08	49935554	203455866	45794755	6	10054											
CKAP2L	150468	hgsc.bcm.edu	37	chr2	113513875	113513875	+	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	tctgaggtatacaaacttggCtggacttctgatcttgcttg	8	15	10	8	0	3	2	0	2	3	0	3	3	3	3	0	3	3	3	0	3	3	6			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr2:113513875C>T	ENST00000302450.6	-	4	1151	c.1073G>A	c.(1072-1074)aGc>aAc	p.S358N	CKAP2L_ENST00000481732.1_5'Flank|CKAP2L_ENST00000541405.1_Missense_Mutation_p.S193N	NM_152515.3	NP_689728.3	Q8IYA6	CKP2L_HUMAN	cytoskeleton associated protein 2-like	358						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						ACAAACTTGGCTGGACTTCTG	0.428																																					p.S358N		Atlas-SNP	.											.	CKAP2L	54	.	0			c.G1073A						PASS	.						149	144	145					2																	113513875		2203	4300	6503	SO:0001583	missense	150468	exon4			ACTTGGCTGGACT	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.1073G>A	chr2.hg19:g.113513875C>T	ENSP00000305204:p.Ser358Asn	191.0	0.0	.		175.0	64.0	.	NM_152515	A8K915|B4DZE3|B7ZAC6|F5H0M5|Q53QF8|Q53RS8|Q8N1J8	Missense_Mutation	SNP	ENST00000302450.6	hg19	CCDS2100.1	.	.	.	.	.	.	.	.	.	.	c	9.225	1.034367	0.19590	.	.	ENSG00000169607	ENST00000541405;ENST00000302450	T;T	0.11821	2.74;3.39	4.69	-4.0	0.04057	.	0.732493	0.12806	N	0.437566	T	0.04227	0.0117	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34925	-0.9809	10	0.24483	T	0.36	-1.0892	0.994	0.01462	0.2342:0.3464:0.1852:0.2342	.	358	Q8IYA6	CKP2L_HUMAN	N	193;358	ENSP00000438763:S193N;ENSP00000305204:S358N	ENSP00000305204:S358N	S	-	2	0	CKAP2L	113230346	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.718000	0.04980	-0.903000	0.03881	-0.911000	0.02809	AGC	.	.	.	none		0.428	CKAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254082.2	NM_152515		T	113513875	C	T	113513875	3	4	172	1	0	0	0	0	1	0	0	0	3445	797	28	2	1188	2	CKAP2L	2	113513875	Missense_Mutation	SNP	C	TCGA-G7-6793-01A-11D-1961-08		113513875	129685498	7	10055											
TTN	7273	hgsc.bcm.edu	37	chr2	179425266	179425266	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctaggggctcaccaacaccAtatttattaacaccagttac	13	11	5	12	0	2	0	1	0	1	0	2	0	2	0	3	2	3	2	3	2	6	6			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr2:179425266A>G	ENST00000591111.1	-	276	80894	c.80670T>C	c.(80668-80670)taT>taC	p.Y26890Y	TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.Y19658Y|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.Y19591Y|TTN_ENST00000460472.2_Silent_p.Y19466Y|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Silent_p.Y28531Y|TTN_ENST00000342992.6_Silent_p.Y25963Y|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA			Q8WZ42	TITIN_HUMAN	titin	26890	Fibronectin type-III 95. {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)			CACCAACACCATATTTATTAA	0.388																																					p.Y28531Y		Atlas-SNP	.											.	TTN	18412	.	0			c.T85593C						PASS	.						57	56	56					2																	179425266		1865	4100	5965	SO:0001819	synonymous_variant	7273	exon326			AACACCATATTTA	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.80670T>C	chr2.hg19:g.179425266A>G		72.0	0.0	.		60.0	20.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.	.	none		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179425266	A	G	179425266	2	3	172	1	0	0	0	0	0	0	0	1	16747	224	8	3		3	TTN	2	179425266	Silent	SNP	A	TCGA-G7-6793-01A-11D-1961-08	65911391	179425266	63774107	8	10056											
ITGA4	3676	hgsc.bcm.edu	37	chr2	182399601	182399601	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttatttcaccatagtgattaTttcaagtagcttgctacttg	10	18	6	7	0	2	1	2	1	0	0	2	1	2	1	1	0	3	3	1	0	6	9			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr2:182399601T>C	ENST00000397033.2	+	27	3372	c.2942T>C	c.(2941-2943)aTt>aCt	p.I981T		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	981					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)	ATAGTGATTATTTCAAGTAGC	0.313																																					p.I981T		Atlas-SNP	.											.	ITGA4	142	.	0			c.T2942C						PASS	.						148	140	143					2																	182399601		1850	4088	5938	SO:0001583	missense	3676	exon27			TGATTATTTCAAG		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.2942T>C	chr2.hg19:g.182399601T>C	ENSP00000380227:p.Ile981Thr	116.0	0.0	.		103.0	29.0	.	NM_000885	D3DPG4|Q7Z4L6	Missense_Mutation	SNP	ENST00000397033.2	hg19	CCDS42788.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.035378	0.75617	.	.	ENSG00000115232	ENST00000397033	T	0.74737	-0.87	6.17	6.17	0.99709	.	0.088153	0.85682	D	0.000000	T	0.78735	0.4330	M	0.78049	2.395	0.58432	D	0.999995	P	0.52577	0.954	P	0.45310	0.476	T	0.82464	-0.0444	10	0.87932	D	0	.	15.3933	0.74767	0.0:0.0:0.0:1.0	.	981	P13612	ITA4_HUMAN	T	981	ENSP00000380227:I981T	ENSP00000380227:I981T	I	+	2	0	ITGA4	182107846	1.000000	0.71417	0.171000	0.22900	0.989000	0.77384	5.141000	0.64814	2.371000	0.80710	0.533000	0.62120	ATT	.	.	.	none		0.313	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1			C	182399601	T	C	182399601	3	2	172	1	0	0	0	0	1	0	0	0	7885	1493	52	3	3048	3	ITGA4	2	182399601	Missense_Mutation	SNP	T	TCGA-G7-6793-01A-11D-1961-08	2974335	182399601	60799772	9	10057											
NBEAL1	65065	hgsc.bcm.edu	37	chr2	204058575	204058575	+	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	tgcagaagccaaccaaaataGacacttcaaccctaaacctg	17	6	5	13	0	1	2	1	0	0	2	1	2	1	2	4	0	5	1	4	0	8	3			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr2:204058575G>T	ENST00000449802.1	+	46	7225	c.6892G>T	c.(6892-6894)Gac>Tac	p.D2298Y		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	2298										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						AACCAAAATAGACACTTCAAC	0.343																																					p.D2298Y		Atlas-SNP	.											.	NBEAL1	266	.	0			c.G6892T						PASS	.						157	157	157					2																	204058575		1870	4098	5968	SO:0001583	missense	65065	exon46			AAAATAGACACTT	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.6892G>T	chr2.hg19:g.204058575G>T	ENSP00000399903:p.Asp2298Tyr	139.0	0.0	.		149.0	42.0	.	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	hg19	CCDS46495.1	.	.	.	.	.	.	.	.	.	.	G	17.83	3.486179	0.63962	.	.	ENSG00000144426	ENST00000449802;ENST00000414576	T;T	0.56776	0.44;1.1	5.43	5.43	0.79202	.	0.063926	0.64402	U	0.000013	T	0.66684	0.2814	M	0.77103	2.36	0.58432	D	0.999999	P	0.49862	0.929	P	0.51487	0.671	T	0.67385	-0.5684	10	0.39692	T	0.17	.	18.8378	0.92169	0.0:0.0:1.0:0.0	.	2298	Q6ZS30	NBEL1_HUMAN	Y	2298;313	ENSP00000399903:D2298Y;ENSP00000388466:D313Y	ENSP00000388466:D313Y	D	+	1	0	NBEAL1	203766820	1.000000	0.71417	0.973000	0.42090	0.900000	0.52787	9.028000	0.93712	2.550000	0.86006	0.650000	0.86243	GAC	.	.	.	none		0.343	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4			T	204058575	G	T	204058575	3	4	172	1	0	0	0	0	1	0	0	0	10195	942	33	4	7070	4	NBEAL1	2	204058575	Missense_Mutation	SNP	G	TCGA-G7-6793-01A-11D-1961-08	21658974	204058575	39140798	10	10058											
SLC9A10	285335	hgsc.bcm.edu	37	chr3	111918287	111918287	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctttgttttcacagtgacagCaatttctgggtgatcatact	9	16	8	8	0	3	2	2	2	1	0	3	2	3	2	0	1	2	2	0	1	2	5			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr3:111918287C>T	ENST00000305815.5	-	20	2656	c.2404G>A	c.(2404-2406)Gct>Act	p.A802T	SLC9C1_ENST00000487372.1_Missense_Mutation_p.A754T	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	802					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										ACAGTGACAGCAATTTCTGGG	0.279																																					p.A802T		Atlas-SNP	.											.	.	.	.	0			c.G2404A						PASS	.						73	73	73					3																	111918287		2201	4297	6498	SO:0001583	missense	285335	exon20			TGACAGCAATTTC	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"Solute carriers"	31401	protein-coding gene	gene with protein product	"sperm-NHE"	612738	"solute carrier family 9, isoform 10", "solute carrier family 9, member 10"	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.2404G>A	chr3.hg19:g.111918287C>T	ENSP00000306627:p.Ala802Thr	86.0	0.0	.		89.0	45.0	.	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	hg19	CCDS33817.1	.	.	.	.	.	.	.	.	.	.	C	15.97	2.990748	0.54041	.	.	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.80480	-1.35;-1.38	5.55	2.81	0.32909	.	0.221517	0.31577	N	0.007408	T	0.81264	0.4786	M	0.65498	2.005	0.27008	N	0.96476	P;D	0.59767	0.855;0.986	P;P	0.52909	0.713;0.655	T	0.71745	-0.4500	10	0.33940	T	0.23	.	7.6697	0.28451	0.0:0.7356:0.0:0.2644	.	754;802	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	T	802;754	ENSP00000306627:A802T;ENSP00000420688:A754T	ENSP00000306627:A802T	A	-	1	0	SLC9A10	113400977	0.902000	0.30710	0.686000	0.30086	0.473000	0.32948	1.823000	0.39062	0.310000	0.22990	-0.140000	0.14226	GCT	.	.	.	none		0.279	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061		T	111918287	C	T	111918287	3	4	172	1	0	0	0	0	1	0	0	0	14723	710	25	2	1169	2	SLC9A10	3	111918287	Missense_Mutation	SNP	C	TCGA-G7-6793-01A-11D-1961-08		111918287	86104143	11	10059											
TMCC1	23023	hgsc.bcm.edu	37	chr3	129390056	129390056	+	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	gatgctgccatcggtactggAggccactgcactggatgttt	7	11	13	10	1	0	0	0	0	0	0	1	3	0	2	2	4	4	4	2	4	1	2			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr3:129390056A>T	ENST00000393238.3	-	4	968	c.628T>A	c.(628-630)Tcc>Acc	p.S210T	TMCC1_ENST00000426664.2_Missense_Mutation_p.S96T|TMCC1_ENST00000329333.5_Missense_Mutation_p.S31T|TMCC1_ENST00000432054.2_5'UTR	NM_001017395.3	NP_001017395.2	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	210						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)			PLXND1/TMCC1(4)	breast(1)|endometrium(3)|large_intestine(8)|lung(12)|skin(1)	25						TCGGTACTGGAGGCCACTGCA	0.522																																					p.S210T		Atlas-SNP	.											.	TMCC1	105	.	0			c.T628A						PASS	.						86	82	83					3																	129390056		2203	4300	6503	SO:0001583	missense	23023	exon4			TACTGGAGGCCAC	AB018322	CCDS33855.1	3q21.3	2010-04-19	2005-07-13		ENSG00000172765	ENSG00000172765		"Transmembrane and coiled-coil domain containing"	29116	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 1"			9872452	Standard	NR_033361		Approved	KIAA0779	uc021xdy.1	O94876	OTTHUMG00000159579	ENST00000393238.3:c.628T>A	chr3.hg19:g.129390056A>T	ENSP00000376930:p.Ser210Thr	145.0	0.0	.		183.0	12.0	.	NM_001017395	A8K5Y3|B4DE04|Q68E06|Q8IXM8	Missense_Mutation	SNP	ENST00000393238.3	hg19	CCDS33855.1	.	.	.	.	.	.	.	.	.	.	A	17.31	3.356489	0.61293	.	.	ENSG00000172765	ENST00000393238;ENST00000426664;ENST00000329333	T;T;T	0.45276	1.5;1.49;0.9	5.86	5.86	0.93980	.	0.163105	0.56097	D	0.000032	T	0.27134	0.0665	N	0.12182	0.205	0.43385	D	0.995495	B;B	0.13145	0.007;0.002	B;B	0.09377	0.004;0.002	T	0.08472	-1.0720	10	0.20046	T	0.44	-7.6554	16.2449	0.82437	1.0:0.0:0.0:0.0	.	31;210	B4DE04;O94876	.;TMCC1_HUMAN	T	210;96;31	ENSP00000376930:S210T;ENSP00000389892:S96T;ENSP00000327349:S31T	ENSP00000327349:S31T	S	-	1	0	TMCC1	130872746	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.138000	0.77305	2.241000	0.73720	0.482000	0.46254	TCC	.	.	.	none		0.522	TMCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356418.2	NM_015008		T	129390056	A	T	129390056	3	4	172	1	0	0	0	0	1	0	0	0	16004	304	11	5	1345	5	TMCC1	3	129390056	Missense_Mutation	SNP	A	TCGA-G7-6793-01A-11D-1961-08	17471769	129390056	68632374	12	10060											
N4BP2	55728	hgsc.bcm.edu	37	chr4	40103811	40103811	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taggtgcagcagaaagtaaaAtaatggaaaaacgtcctgaa	19	7	10	5	1	0	2	0	1	0	1	1	3	1	3	1	2	3	3	1	2	8	3			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr4:40103811A>G	ENST00000261435.6	+	4	762	c.346A>G	c.(346-348)Ata>Gta	p.I116V		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	116					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						AGAAAGTAAAATAATGGAAAA	0.368																																					p.I116V		Atlas-SNP	.											.	N4BP2	166	.	0			c.A346G						PASS	.						92	90	91					4																	40103811		2203	4300	6503	SO:0001583	missense	55728	exon4			AGTAAAATAATGG	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.346A>G	chr4.hg19:g.40103811A>G	ENSP00000261435:p.Ile116Val	69.0	0.0	.		90.0	28.0	.	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	hg19	CCDS3457.1	.	.	.	.	.	.	.	.	.	.	A	0.424	-0.906575	0.02434	.	.	ENSG00000078177	ENST00000261435;ENST00000381804;ENST00000515550	T;T	0.79247	-1.25;-1.25	6.08	1.18	0.20946	.	0.531518	0.19034	N	0.124467	T	0.52451	0.1735	N	0.12746	0.255	0.09310	N	1	B;B	0.11235	0.004;0.002	B;B	0.14578	0.011;0.003	T	0.37291	-0.9712	10	0.02654	T	1	-6.4549	8.9819	0.35970	0.7223:0.0:0.2777:0.0	.	116;116	Q86UW6-2;Q86UW6	.;N4BP2_HUMAN	V	116;36;36	ENSP00000261435:I116V;ENSP00000422057:I36V	ENSP00000261435:I116V	I	+	1	0	N4BP2	39780206	0.971000	0.33674	0.507000	0.27676	0.442000	0.32017	0.597000	0.24059	0.543000	0.28864	0.482000	0.46254	ATA	.	.	.	none		0.368	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177		G	40103811	A	G	40103811	3	3	172	1	0	0	0	0	1	0	0	0	10117	101	4	3	352	3	N4BP2	4	40103811	Missense_Mutation	SNP	A	TCGA-G7-6793-01A-11D-1961-08		40103811	151050465	13	10061											
DAGLB	221955	hgsc.bcm.edu	37	chr7	6474439	6474439	+	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	ccgtactcgaaaaagcaaccCgagtatggtcgtctttccca	11	9	8	13	4	1	0	0	0	1	0	4	2	2	0	3	1	3	3	3	1	5	3			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr7:6474439C>A	ENST00000297056.6	-	4	801	c.632G>T	c.(631-633)cGg>cTg	p.R211L	DAGLB_ENST00000436575.1_Missense_Mutation_p.R170L|DAGLB_ENST00000425398.2_Intron|DAGLB_ENST00000421761.2_Intron|DAGLB_ENST00000479922.2_5'Flank|DAGLB_ENST00000428902.2_Missense_Mutation_p.R84L	NM_139179.3	NP_631918.3	Q8NCG7	DGLB_HUMAN	diacylglycerol lipase, beta	211					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|lipid catabolic process (GO:0016042)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|urinary_tract(2)	26		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.102)		AAAAGCAACCCGAGTATGGTC	0.463																																					p.R211L		Atlas-SNP	.											.	DAGLB	74	.	0			c.G632T						PASS	.						160	154	156					7																	6474439		2203	4300	6503	SO:0001583	missense	221955	exon4			GCAACCCGAGTAT	AF450090	CCDS5350.1, CCDS47536.1	7p22.1	2008-03-18			ENSG00000164535	ENSG00000164535	3.1.1.-		28923	protein-coding gene	gene with protein product		614016					Standard	NM_139179		Approved	KCCR13L, DAGLBETA	uc003sqa.3	Q8NCG7	OTTHUMG00000125513	ENST00000297056.6:c.632G>T	chr7.hg19:g.6474439C>A	ENSP00000297056:p.Arg211Leu	224.0	0.0	.		205.0	12.0	.	NM_139179	A4D2P3|B3KV90|B4DQU0|Q6PIX3|Q8N2N2|Q8N9S1|Q8TED3|Q8WXE6	Missense_Mutation	SNP	ENST00000297056.6	hg19	CCDS5350.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.898081	0.91962	.	.	ENSG00000164535	ENST00000297056;ENST00000436575;ENST00000471132;ENST00000428902	T;T	0.48836	0.81;0.8	5.23	5.23	0.72850	.	0.000000	0.64402	D	0.000001	T	0.56140	0.1965	M	0.84433	2.695	0.80722	D	1	P	0.41498	0.752	B	0.38842	0.283	T	0.64032	-0.6502	10	0.42905	T	0.14	.	18.8048	0.92032	0.0:1.0:0.0:0.0	.	211	Q8NCG7	DGLB_HUMAN	L	211;170;211;84	ENSP00000297056:R211L;ENSP00000404785:R170L	ENSP00000297056:R211L	R	-	2	0	DAGLB	6440964	1.000000	0.71417	0.088000	0.20740	0.980000	0.70556	4.539000	0.60657	2.431000	0.82371	0.491000	0.48974	CGG	.	.	.	none		0.463	DAGLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246840.2	NM_139179		A	6474439	C	A	6474439	3	1	172	1	0	0	0	0	1	0	0	0	4229	652	23	4	1434	4	DAGLB	7	6474439	Missense_Mutation	SNP	C	TCGA-G7-6793-01A-11D-1961-08		6474439	152664224	14	10062											
TSGA13	114960	hgsc.bcm.edu	37	chr7	130353922	130353922	+	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	gttgcggaaggcgctctcccCgggcgcggttctggtgggca	3	8	18	12	5	2	0	0	0	2	0	3	1	2	1	2	6	1	4	2	6	1	2			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr7:130353922C>A	ENST00000456951.1	-	9	1611	c.760G>T	c.(760-762)Ggg>Tgg	p.G254W	COPG2_ENST00000445977.2_5'Flank|TSGA13_ENST00000356588.3_Missense_Mutation_p.G254W			Q96PP4	TSG13_HUMAN	testis specific, 13	254										endometrium(1)|kidney(3)|large_intestine(3)|lung(6)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	18	Melanoma(18;0.0435)					GCGCTCTCCCCGGGCGCGGTT	0.592																																					p.G254W		Atlas-SNP	.											.	TSGA13	35	.	0			c.G760T						PASS	.						100	106	104					7																	130353922		2203	4300	6503	SO:0001583	missense	114960	exon8			TCTCCCCGGGCGC	AK093329	CCDS5824.1	7q32	2008-02-04			ENSG00000213265	ENSG00000213265			12369	protein-coding gene	gene with protein product							Standard	NM_052933		Approved		uc003vqi.3	Q96PP4	OTTHUMG00000154999	ENST00000456951.1:c.760G>T	chr7.hg19:g.130353922C>A	ENSP00000406047:p.Gly254Trp	282.0	0.0	.		191.0	8.0	.	NM_052933	B3KSC9	Missense_Mutation	SNP	ENST00000456951.1	hg19	CCDS5824.1	.	.	.	.	.	.	.	.	.	.	C	18.26	3.584905	0.65992	.	.	ENSG00000213265	ENST00000456951;ENST00000356588	.	.	.	5.51	5.51	0.81932	.	0.000000	0.49916	D	0.000130	T	0.66915	0.2838	L	0.34521	1.04	0.41776	D	0.989791	D	0.89917	1.0	D	0.97110	1.0	T	0.70029	-0.4984	9	0.87932	D	0	-16.3429	14.8978	0.70656	0.0:1.0:0.0:0.0	.	254	Q96PP4	TSG13_HUMAN	W	254	.	ENSP00000348996:G254W	G	-	1	0	TSGA13	130004462	0.467000	0.25831	0.776000	0.31678	0.138000	0.21146	3.831000	0.55776	2.585000	0.87301	0.561000	0.74099	GGG	.	.	.	none		0.592	TSGA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337997.1	NM_052933		A	130353922	C	A	130353922	3	1	172	1	0	0	0	0	1	0	0	0	16631	652	23	4	71	4	TSGA13	7	130353922	Missense_Mutation	SNP	C	TCGA-G7-6793-01A-11D-1961-08	123879483	130353922	28784741	15	10063											
PKN3	29941	hgsc.bcm.edu	37	chr9	131482023	131482023	+	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	accccggagttcctggctccCgaggtgctgacccaggaggc	6	6	14	15	2	0	1	0	1	0	0	2	4	2	3	5	5	1	3	5	5	0	1			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr9:131482023C>A	ENST00000291906.4	+	19	2577	c.2184C>A	c.(2182-2184)ccC>ccA	p.P728P	PKN3_ENST00000485301.1_3'UTR|ZDHHC12_ENST00000467312.1_5'Flank	NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	728	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						TCCTGGCTCCCGAGGTGCTGA	0.632																																					p.P728P		Atlas-SNP	.											.	PKN3	62	.	0			c.C2184A						PASS	.						144	151	149					9																	131482023		2203	4300	6503	SO:0001819	synonymous_variant	29941	exon19			GGCTCCCGAGGTG	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.2184C>A	chr9.hg19:g.131482023C>A		284.0	0.0	.		195.0	8.0	.	NM_013355	Q9UM03	Silent	SNP	ENST00000291906.4	hg19	CCDS6908.1																																																																																			.	.	.	none		0.632	PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054487.1	NM_013355		A	131482023	C	A	131482023	2	1	172	1	0	0	0	0	0	0	0	1	11988	639	23	4		4	PKN3	9	131482023	Silent	SNP	C	TCGA-G7-6793-01A-11D-1961-08		131482023	9731408	16	10064											
ITGA8	8516	hgsc.bcm.edu	37	chr10	15688933	15688933	+	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	gtgccagtgaggatctggggGtctctgaagaggagagagct	9	8	18	6	0	2	4	0	2	2	2	3	7	2	6	1	4	2	1	1	4	1	0			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr10:15688933G>A	ENST00000378076.3	-	12	1472	c.1119C>T	c.(1117-1119)gaC>gaT	p.D373D		NM_003638.1	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8	373					brain development (GO:0007420)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|metanephros development (GO:0001656)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|substrate adhesion-dependent cell spreading (GO:0034446)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|dendritic spine membrane (GO:0032591)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integrin alpha8-beta1 complex (GO:0034678)|integrin complex (GO:0008305)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	metal ion binding (GO:0046872)			NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	96						GGATCTGGGGGTCTCTGAAGA	0.483																																					p.D373D		Atlas-SNP	.											.	ITGA8	230	.	0			c.C1119T						PASS	.						122	109	113					10																	15688933		2203	4300	6503	SO:0001819	synonymous_variant	8516	exon12			CTGGGGGTCTCTG	L36531	CCDS31155.1	10p13	2010-03-23			ENSG00000077943	ENSG00000077943		"Integrins"	6144	protein-coding gene	gene with protein product		604063				7768999	Standard	XM_005252633		Approved		uc001ioc.1	P53708	OTTHUMG00000017733	ENST00000378076.3:c.1119C>T	chr10.hg19:g.15688933G>A		130.0	0.0	.		106.0	21.0	.	NM_003638	B0YJ31|Q5VX94	Silent	SNP	ENST00000378076.3	hg19	CCDS31155.1																																																																																			.	.	.	none		0.483	ITGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046987.1	NM_003638		A	15688933	G	A	15688933	2	1	172	1	0	0	0	0	0	0	0	1	7889	1252	44	2		2	ITGA8	10	15688933	Silent	SNP	G	TCGA-G7-6793-01A-11D-1961-08		15688933	119845814	17	10065											
CUBN	8029	hgsc.bcm.edu	37	chr10	16916468	16916468	+	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	gaataggcaggacttgtgatGattccagaagagaaattgaa	16	9	12	4	0	0	5	0	3	0	2	1	8	1	6	1	2	0	1	1	2	5	4			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr10:16916468G>T	ENST00000377833.4	-	58	9206	c.9141C>A	c.(9139-9141)atC>atA	p.I3047I		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	3047	CUB 23. {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)	GACTTGTGATGATTCCAGAAG	0.433																																					p.I3047I		Atlas-SNP	.											.	CUBN	515	.	0			c.C9141A						PASS	.						168	135	146					10																	16916468		2203	4300	6503	SO:0001819	synonymous_variant	8029	exon58			TGTGATGATTCCA	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.9141C>A	chr10.hg19:g.16916468G>T		101.0	0.0	.		89.0	24.0	.	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	hg19	CCDS7113.1																																																																																			.	.	.	none		0.433	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		T	16916468	G	T	16916468	2	4	172	1	0	0	0	0	0	0	0	1	4053	1280	45	4		4	CUBN	10	16916468	Silent	SNP	G	TCGA-G7-6793-01A-11D-1961-08	1227535	16916468	118618279	18	10066											
UBTD1	80019	hgsc.bcm.edu	37	chr10	99327795	99327795	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctgccttcgagggccgcaaGgagatctgggatgccctcaa	8	7	13	13	2	2	1	1	0	1	1	3	4	2	2	4	3	2	1	4	3	2	1			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr10:99327795G>A	ENST00000370664.3	+	2	531	c.195G>A	c.(193-195)aaG>aaA	p.K65K		NM_024954.3	NP_079230.1	Q9HAC8	UBTD1_HUMAN	ubiquitin domain containing 1	65										central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(1)|skin(1)	7		Colorectal(252;0.162)		Epithelial(162;3.04e-10)|all cancers(201;2.86e-08)		AGGGCCGCAAGGAGATCTGGG	0.632																																					p.K65K	Pancreas(100;169 2668 32720)	Atlas-SNP	.											.	UBTD1	19	.	0			c.G195A						PASS	.						87	86	86					10																	99327795		2203	4300	6503	SO:0001819	synonymous_variant	80019	exon2			CCGCAAGGAGATC	BC007331	CCDS7465.1	10q24.2	2005-09-22			ENSG00000165886	ENSG00000165886			25683	protein-coding gene	gene with protein product						12477932	Standard	NM_024954		Approved	FLJ11807	uc001knv.1	Q9HAC8	OTTHUMG00000018856	ENST00000370664.3:c.195G>A	chr10.hg19:g.99327795G>A		195.0	0.0	.		155.0	24.0	.	NM_024954	D3DR57|Q53HI3	Silent	SNP	ENST00000370664.3	hg19	CCDS7465.1																																																																																			.	.	.	none		0.632	UBTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049701.1	NM_024954		A	99327795	G	A	99327795	2	1	172	1	0	0	0	0	0	0	0	1	16919	991	35	2		2	UBTD1	10	99327795	Silent	SNP	G	TCGA-G7-6793-01A-11D-1961-08	82411327	99327795	36206952	19	10067											
TCF7L2	6934	hgsc.bcm.edu	37	chr10	114912175	114912175	+	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	cttcatatgcaactgtacccCggctggtccgcgcgggataa	8	9	11	13	4	1	0	1	0	0	0	2	1	2	1	3	3	3	3	3	3	4	4	rs149820593		TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr10:114912175C>A	ENST00000355995.4	+	11	1752	c.1245C>A	c.(1243-1245)ccC>ccA	p.P415P	TCF7L2_ENST00000466338.1_3'UTR|TCF7L2_ENST00000534894.1_Silent_p.P415P|TCF7L2_ENST00000352065.5_Silent_p.P392P|TCF7L2_ENST00000545257.1_Silent_p.P415P|TCF7L2_ENST00000369389.1_Silent_p.P126P|TCF7L2_ENST00000538897.1_Silent_p.P415P|TCF7L2_ENST00000542695.1_Silent_p.P131P|TCF7L2_ENST00000536810.1_Silent_p.P415P|TCF7L2_ENST00000355717.4_Silent_p.P439P|TCF7L2_ENST00000369397.4_Silent_p.P392P|TCF7L2_ENST00000369386.1_Silent_p.P58P|TCF7L2_ENST00000543371.1_Silent_p.P415P			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	415					blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		AACTGTACCCCGGCTGGTCCG	0.542			T	VTI1A	colorectal																																p.P439P		Atlas-SNP	.		Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	.	TCF7L2	298	.	0			c.C1317A						PASS	.						128	134	132					10																	114912175		2203	4300	6503	SO:0001819	synonymous_variant	6934	exon11			GTACCCCGGCTGG	X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.1245C>A	chr10.hg19:g.114912175C>A		258.0	0.0	.		204.0	9.0	.	NM_001146283	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Silent	SNP	ENST00000355995.4	hg19																																																																																				.	C|1.000;T|0.000	.	alt		0.542	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756		A	114912175	C	A	114912175	2	1	172	1	0	0	0	0	0	0	0	1	15710	639	23	4		4	TCF7L2	10	114912175	Silent	SNP	C	TCGA-G7-6793-01A-11D-1961-08	15584380	114912175	20622572	20	10068											
ATE1	11101	hgsc.bcm.edu	37	chr10	123658376	123658376	+	Intron	DEL	C	C	-																															ctcagtcttcccacattcatCgggtggatcctggtgtatgg																								rs150970157		TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr10:123658376delC	ENST00000224652.6	-	7	1028				ATE1_ENST00000540606.1_Frame_Shift_Del_p.D301fs|ATE1_ENST00000543447.1_Intron|ATE1_ENST00000481784.1_Intron|ATE1_ENST00000369040.3_Frame_Shift_Del_p.D212fs|ATE1_ENST00000369043.3_Frame_Shift_Del_p.D308fs|ATE1_ENST00000535655.1_Intron	NM_001001976.1	NP_001001976.1	O95260	ATE1_HUMAN	arginyltransferase 1						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)				CCACATTCATCGGGTGGATCC	0.423																																					p.D308fs		Atlas-INDEL	.											.	ATE1	67	.	0			c.923delA						PASS	.						189	157	168					10																	123658376		2203	4300	6503	SO:0001627	intron_variant	11101	exon7			.	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.942+1004G>-	chr10.hg19:g.123658376delC		82.0	0.0	0		73.0	11.0	0.150685	NM_007041	O95261|Q5SQQ3|Q8WW04	Frame_Shift_Del	DEL	ENST00000224652.6	hg19	CCDS31300.1																																																																																			.	.	.	none		0.423	ATE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001001976		-	123658376	C	-	123658376	6	5	172	0	1	1	0	1	0	0	0	0	1078	884	31	0		0	ATE1	10	123658376	Intron	DEL	C	TCGA-G7-6793-01A-11D-1961-08	8746201	123658376	11876371	21	10069											
CNIH2	254263	hgsc.bcm.edu	37	chr11	66049735	66049735	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acgcccctcccccagatcatAgcctttgatgagctgcggac	8	8	9	16	2	1	3	1	2	0	1	2	4	2	4	5	1	3	1	5	1	1	2			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr11:66049735A>G	ENST00000311445.6	+	2	345	c.87A>G	c.(85-87)atA>atG	p.I29M	CNIH2_ENST00000528852.1_Missense_Mutation_p.I29M|YIF1A_ENST00000526497.1_5'Flank|CNIH2_ENST00000530519.1_3'UTR	NM_182553.2	NP_872359.1	Q6PI25	CNIH2_HUMAN	cornichon family AMPA receptor auxiliary protein 2	29					intracellular signal transduction (GO:0035556)|localization within membrane (GO:0051668)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of membrane potential (GO:0042391)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				endometrium(1)|large_intestine(1)|lung(2)|prostate(1)	5						CCCAGATCATAGCCTTTGATG	0.597																																					p.I29M		Atlas-SNP	.											.	CNIH2	15	.	0			c.A87G						PASS	.						72	66	68					11																	66049735		2200	4295	6495	SO:0001583	missense	254263	exon2			GATCATAGCCTTT	BC047953	CCDS8131.1	11q13.2	2013-08-28	2013-08-28		ENSG00000174871	ENSG00000174871			28744	protein-coding gene	gene with protein product		611288	"cornichon homolog 2 (Drosophila)"			12477932	Standard	NM_182553		Approved	MGC50896, Cnil, CNIH-2	uc001ohi.2	Q6PI25	OTTHUMG00000166919	ENST00000311445.6:c.87A>G	chr11.hg19:g.66049735A>G	ENSP00000310003:p.Ile29Met	86.0	0.0	.		42.0	10.0	.	NM_182553		Missense_Mutation	SNP	ENST00000311445.6	hg19	CCDS8131.1	.	.	.	.	.	.	.	.	.	.	A	14.77	2.634157	0.47049	.	.	ENSG00000174871	ENST00000528852;ENST00000311445	T;T	0.55760	0.5;0.5	5.33	1.49	0.22878	.	0.000000	0.85682	D	0.000000	T	0.68869	0.3048	M	0.89478	3.035	0.58432	D	0.999998	D;D	0.71674	0.961;0.998	P;D	0.68483	0.791;0.958	T	0.68221	-0.5466	10	0.59425	D	0.04	-24.0482	4.9261	0.13894	0.3807:0.2295:0.0:0.3897	.	29;29	Q6PI25;E9PS15	CNIH2_HUMAN;.	M	29	ENSP00000432177:I29M;ENSP00000310003:I29M	ENSP00000310003:I29M	I	+	3	3	CNIH2	65806311	0.998000	0.40836	1.000000	0.80357	0.547000	0.35210	1.267000	0.33050	0.919000	0.36945	0.460000	0.39030	ATA	.	.	.	none		0.597	CNIH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000391892.1	NM_182553		G	66049735	A	G	66049735	3	3	172	1	0	0	0	0	1	0	0	0	3605	410	15	3	93	3	CNIH2	11	66049735	Missense_Mutation	SNP	A	TCGA-G7-6793-01A-11D-1961-08		66049735	68956781	22	10070											
EXPH5	23086	hgsc.bcm.edu	37	chr11	108380880	108380880	+	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	agaggtgtggctcaggttccCactccagagatgaagcactc	10	8	12	11	0	1	3	1	1	0	2	4	4	3	3	2	3	1	3	2	3	1	1			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr11:108380880C>T	ENST00000265843.4	-	6	5464	c.5354G>A	c.(5353-5355)tGg>tAg	p.W1785*	EXPH5_ENST00000428840.1_Nonsense_Mutation_p.W1709*|EXPH5_ENST00000443411.1_Nonsense_Mutation_p.W1597*|EXPH5_ENST00000525344.1_Nonsense_Mutation_p.W1778*	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1785					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)		CTCAGGTTCCCACTCCAGAGA	0.483																																					p.W1785X		Atlas-SNP	.											.	EXPH5	193	.	0			c.G5354A						PASS	.						89	96	94					11																	108380880		2201	4298	6499	SO:0001587	stop_gained	23086	exon6			GGTTCCCACTCCA		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.5354G>A	chr11.hg19:g.108380880C>T	ENSP00000265843:p.Trp1785*	188.0	0.0	.		107.0	46.0	.	NM_015065	Q2KHM1|Q9Y4D6	Nonsense_Mutation	SNP	ENST00000265843.4	hg19	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	C	41	8.551547	0.98859	.	.	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000439956;ENST00000526312	.	.	.	6.17	4.26	0.50523	.	0.766008	0.12354	N	0.476287	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	1.7662	10.3652	0.44019	0.0:0.497:0.431:0.0721	.	.	.	.	X	1785;1709;1597;1778;615;1709	.	ENSP00000265843:W1785X	W	-	2	0	EXPH5	107886090	0.060000	0.20803	0.159000	0.22649	0.035000	0.12851	0.897000	0.28390	0.883000	0.36040	0.655000	0.94253	TGG	.	.	.	none		0.483	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		T	108380880	C	T	108380880	4	4	172	1	0	0	0	0	0	1	0	0	5324	595	21	2	619	2	EXPH5	11	108380880	Nonsense_Mutation	SNP	C	TCGA-G7-6793-01A-11D-1961-08	42331145	108380880	26625636	23	10071											
NCAPD2	9918	hgsc.bcm.edu	37	chr12	6637024	6637024	+	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	acacagaggcagaactaatcCgtggcatctgcgagatggaa	14	6	12	9	2	1	3	0	0	1	3	2	5	2	4	1	3	2	2	1	3	3	1			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr12:6637024C>A	ENST00000315579.5	+	23	3788	c.2989C>A	c.(2989-2991)Cgt>Agt	p.R997S	NCAPD2_ENST00000542492.1_3'UTR|NCAPD2_ENST00000545962.1_Missense_Mutation_p.R952S	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	997					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)	p.R997C(1)		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						AGAACTAATCCGTGGCATCTG	0.493																																					p.R997S		Atlas-SNP	.											NCAPD2,NS,carcinoma,0,1	NCAPD2	99	.	1	Substitution - Missense(1)	endometrium(1)	c.C2989A						PASS	.						132	132	132					12																	6637024		2203	4300	6503	SO:0001583	missense	9918	exon23			CTAATCCGTGGCA	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.2989C>A	chr12.hg19:g.6637024C>A	ENSP00000325017:p.Arg997Ser	238.0	0.0	.		224.0	9.0	.	NM_014865	D3DUR4|Q8N6U3	Missense_Mutation	SNP	ENST00000315579.5	hg19	CCDS8548.1	.	.	.	.	.	.	.	.	.	.	C	17.42	3.385823	0.61956	.	.	ENSG00000010292	ENST00000315579;ENST00000382457;ENST00000545962;ENST00000535602	T;T;T	0.12672	2.66;2.66;2.66	5.95	5.95	0.96441	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.30103	0.0754	L	0.60455	1.87	0.58432	D	0.999997	D;B;D	0.57899	0.981;0.021;0.968	P;B;P	0.60886	0.88;0.051;0.66	T	0.00126	-1.2020	10	0.34782	T	0.22	-16.4149	15.1469	0.72662	0.1412:0.8588:0.0:0.0	.	952;958;997	F5GZJ1;B3KY03;Q15021	.;.;CND1_HUMAN	S	997;869;952;869	ENSP00000325017:R997S;ENSP00000371895:R869S;ENSP00000444417:R952S	ENSP00000325017:R997S	R	+	1	0	NCAPD2	6507285	1.000000	0.71417	0.954000	0.39281	0.127000	0.20565	3.691000	0.54720	2.824000	0.97209	0.655000	0.94253	CGT	.	.	.	none		0.493	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865		A	6637024	C	A	6637024	3	1	172	1	0	0	0	0	1	0	0	0	10212	652	23	4	3075	4	NCAPD2	12	6637024	Missense_Mutation	SNP	C	TCGA-G7-6793-01A-11D-1961-08		6637024	127214871	24	10072											
OR4N4	283694	hgsc.bcm.edu	37	chr15	22382930	22382930	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggctctgtggcttgggggttTtgtccactccattatccagg	4	14	13	10	0	1	0	0	0	1	0	4	0	4	0	3	5	0	3	3	5	1	4			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr15:22382930T>C	ENST00000328795.4	+	1	549	c.458T>C	c.(457-459)tTt>tCt	p.F153S	RP11-69H14.6_ENST00000558896.1_RNA	NM_001005241.2	NP_001005241.2	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N, member 4	153						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)		CTTGGGGGTTTTGTCCACTCC	0.527																																					p.F153S		Atlas-SNP	.											.	OR4N4	108	.	0			c.T458C						PASS	.						100	87	91					15																	22382930		2187	4254	6441	SO:0001583	missense	283694	exon1			GGGGTTTTGTCCA	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.458T>C	chr15.hg19:g.22382930T>C	ENSP00000332500:p.Phe153Ser	432.0	0.0	.		312.0	41.0	.	NM_001005241	Q6IEY3|Q6IF56	Missense_Mutation	SNP	ENST00000328795.4	hg19	CCDS32173.1	.	.	.	.	.	.	.	.	.	.	.	10.03	1.238759	0.22711	.	.	ENSG00000183706	ENST00000328795	T	0.00216	8.53	3.37	3.37	0.38596	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000117	T	0.00412	0.0013	M	0.62723	1.935	0.09310	N	1	D	0.67145	0.996	D	0.74348	0.983	T	0.47873	-0.9083	10	0.87932	D	0	-8.9888	10.041	0.42158	0.0:0.0:0.0:1.0	.	153	Q8N0Y3	OR4N4_HUMAN	S	153	ENSP00000332500:F153S	ENSP00000332500:F153S	F	+	2	0	OR4N4	19884294	0.006000	0.16342	0.918000	0.36340	0.103000	0.19146	1.078000	0.30754	1.522000	0.49001	0.332000	0.21555	TTT	.	.	.	none		0.527	OR4N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414922.1			C	22382930	T	C	22382930	3	2	172	1	0	0	0	0	1	0	0	0	11085	1841	64	3	460	3	OR4N4	15	22382930	Missense_Mutation	SNP	T	TCGA-G7-6793-01A-11D-1961-08		22382930	80148462	25	10073											
HERC1	8925	hgsc.bcm.edu	37	chr15	63955402	63955402	+	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	tgcacagagcggtataatccCgctcagaacaaaacaaaaaa	19	5	7	10	2	1	2	1	0	0	2	2	2	2	2	1	1	4	3	1	1	8	2			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr15:63955402C>A	ENST00000443617.2	-	44	8769	c.8682G>T	c.(8680-8682)gcG>gcT	p.A2894A		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	2894					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						GGTATAATCCCGCTCAGAACA	0.408																																					p.A2894A		Atlas-SNP	.											.	HERC1	624	.	0			c.G8682T						PASS	.						113	110	111					15																	63955402		1844	4089	5933	SO:0001630	splice_region_variant	8925	exon44			TAATCCCGCTCAG	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.8681-1G>T	chr15.hg19:g.63955402C>A		297.0	0.0	.		228.0	10.0	.	NM_003922	Q8IW65	Silent	SNP	ENST00000443617.2	hg19	CCDS45277.1																																																																																			.	.	.	none		0.408	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922	Silent	A	63955402	C	A	63955402	5	1	172	1	0	0	0	0	0	0	1	0	7064	666	23	4	6043	4	HERC1	15	63955402	Splice_Site	SNP	C	TCGA-G7-6793-01A-11D-1961-08	41572472	63955402	38575990	26	10074											
SMG1	23049	hgsc.bcm.edu	37	chr16	18856756	18856756	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggattattctgtacctcttTaaatggaatccagctgctcc	9	14	8	10	0	2	0	0	0	2	0	4	2	4	2	3	2	3	3	3	2	5	5			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr16:18856756T>C	ENST00000446231.2	-	39	6626	c.6214A>G	c.(6214-6216)Aaa>Gaa	p.K2072E	SMG1_ENST00000389467.3_Missense_Mutation_p.K2072E			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2072					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						TGTACCTCTTTAAATGGAATC	0.408																																					p.K2072E		Atlas-SNP	.											.	SMG1	401	.	0			c.A6214G						PASS	.						57	52	54					16																	18856756		1866	4105	5971	SO:0001583	missense	23049	exon39			CCTCTTTAAATGG	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.6214A>G	chr16.hg19:g.18856756T>C	ENSP00000402515:p.Lys2072Glu	58.0	0.0	.		62.0	33.0	.	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	hg19	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.237482	0.79800	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.80824	-1.42;-1.42	5.79	5.79	0.91817	Protein kinase-like domain (1);Armadillo-type fold (1);	0.080055	0.53938	D	0.000055	D	0.90249	0.6951	M	0.86178	2.8	0.80722	D	1	D;P	0.56035	0.974;0.743	D;B	0.67725	0.953;0.305	D	0.91308	0.5072	10	0.59425	D	0.04	.	16.1343	0.81471	0.0:0.0:0.0:1.0	.	1932;2072	Q96Q15-2;Q96Q15	.;SMG1_HUMAN	E	2072	ENSP00000402515:K2072E;ENSP00000374118:K2072E	ENSP00000374118:K2072E	K	-	1	0	SMG1	18764257	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.155000	0.71833	2.209000	0.71365	0.533000	0.62120	AAA	.	.	.	none		0.408	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		C	18856756	T	C	18856756	3	2	172	1	0	0	0	0	1	0	0	0	14808	1763	61	3	4871	3	SMG1	16	18856756	Missense_Mutation	SNP	T	TCGA-G7-6793-01A-11D-1961-08		18856756	71497997	27	10075											
PDILT	204474	hgsc.bcm.edu	37	chr16	20376785	20376785	+	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	tctttgtcaaagacgactacGttgaagttcttccccacgag	10	12	8	11	3	3	2	1	1	2	1	4	4	4	2	2	0	1	2	2	0	3	5			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr16:20376785G>A	ENST00000302451.4	-	9	1442	c.1194C>T	c.(1192-1194)aaC>aaT	p.N398N		NM_174924.1	NP_777584.1	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis expressed	398	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell migration (GO:0016477)|cell redox homeostasis (GO:0045454)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|spermatid development (GO:0007286)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(33)|prostate(3)|skin(1)|urinary_tract(1)	61						AGACGACTACGTTGAAGTTCT	0.448																																					p.N398N		Atlas-SNP	.											.	PDILT	120	.	0			c.C1194T						PASS	.						175	164	168					16																	20376785		2203	4300	6503	SO:0001819	synonymous_variant	204474	exon9			GACTACGTTGAAG		CCDS10584.1	16p12.3	2011-11-10	2009-02-23		ENSG00000169340	ENSG00000169340		"Protein disulfide isomerases"	27338	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 7", "protein disulfide isomerase-like protein of the testis"					15475357	Standard	NM_174924		Approved	PDIA7	uc002dhc.1	Q8N807	OTTHUMG00000131487	ENST00000302451.4:c.1194C>T	chr16.hg19:g.20376785G>A		176.0	0.0	.		163.0	39.0	.	NM_174924	Q8IVQ5	Silent	SNP	ENST00000302451.4	hg19	CCDS10584.1																																																																																			.	.	.	none		0.448	PDILT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254332.1	NM_174924		A	20376785	G	A	20376785	2	1	172	1	0	0	0	0	0	0	0	1	11681	1136	40	1		1	PDILT	16	20376785	Silent	SNP	G	TCGA-G7-6793-01A-11D-1961-08	1520029	20376785	69977968	28	10076											
AXIN2	8313	hgsc.bcm.edu	37	chr17	63533065	63533065	+	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	gcgacctgtctccttcctccCggggaagctgcagggcccca	5	7	12	17	2	1	0	0	0	1	0	4	2	3	1	6	3	2	2	6	3	1	1	rs376248072		TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr17:63533065C>A	ENST00000307078.5	-	7	2142	c.1829G>T	c.(1828-1830)cGg>cTg	p.R610L	AXIN2_ENST00000375702.5_Intron	NM_004655.3	NP_004646.3	Q9Y2T1	AXIN2_HUMAN	axin 2	610				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						TCCTTCCTCCCGGGGAAGCTG	0.687									Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome																												p.R610L		Atlas-SNP	.											AXIN2,NS,carcinoma,0,1	AXIN2	92	.	0			c.G1829T						PASS	.						63	62	63					17																	63533065		2203	4300	6503	SO:0001583	missense	8313	exon7	Familial Cancer Database	Oligodontia-Colorectal Cancer syndrome, Tooth Agenesis-Colorectal Cancer Syndrome	TCCTCCCGGGGAA	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	ENST00000307078.5:c.1829G>T	chr17.hg19:g.63533065C>A	ENSP00000302625:p.Arg610Leu	177.0	0.0	.		166.0	8.0	.	NM_004655	Q3MJ88|Q9H3M6|Q9UH84	Missense_Mutation	SNP	ENST00000307078.5	hg19	CCDS11662.1	.	.	.	.	.	.	.	.	.	.	C	11.57	1.679471	0.29783	.	.	ENSG00000168646	ENST00000307078	T	0.62232	0.04	5.24	3.07	0.35406	.	0.703317	0.14743	N	0.301042	T	0.43743	0.1261	N	0.08118	0	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.39583	-0.9607	10	0.48119	T	0.1	-6.532	15.2767	0.73748	0.0:0.5155:0.4845:0.0	.	610	Q9Y2T1	AXIN2_HUMAN	L	610	ENSP00000302625:R610L	ENSP00000302625:R610L	R	-	2	0	AXIN2	60963527	0.021000	0.18746	0.945000	0.38365	0.886000	0.51366	1.270000	0.33086	1.153000	0.42468	0.561000	0.74099	CGG	.	.	.	alt		0.687	AXIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445900.1	NM_004655		A	63533065	C	A	63533065	3	1	172	1	0	0	0	0	1	0	0	0	1237	652	23	4	722	4	AXIN2	17	63533065	Missense_Mutation	SNP	C	TCGA-G7-6793-01A-11D-1961-08		63533065	17662145	29	10077											
SLC26A11	284129	hgsc.bcm.edu	37	chr17	78219988	78219988	+	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	tcagtcgggggtgtgcacccCggcggggggcctggtgacgg	3	6	21	11	4	1	1	1	1	0	0	2	1	1	1	3	8	1	1	3	8	0	0			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr17:78219988C>A	ENST00000361193.3	+	12	1413	c.1133C>A	c.(1132-1134)cCg>cAg	p.P378Q	SLC26A11_ENST00000411502.3_Missense_Mutation_p.P378Q|SLC26A11_ENST00000546047.2_Missense_Mutation_p.P378Q|SLC26A11_ENST00000572725.1_Missense_Mutation_p.P378Q	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)			GTGTGCACCCCGGCGGGGGGC	0.667																																					p.P378Q		Atlas-SNP	.											SLC26A11,colon,carcinoma,0,1	SLC26A11	60	.	0			c.C1133A						PASS	.						49	59	56					17																	78219988		2200	4296	6496	SO:0001583	missense	284129	exon12			GCACCCCGGCGGG		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.1133C>A	chr17.hg19:g.78219988C>A	ENSP00000355384:p.Pro378Gln	232.0	0.0	.		223.0	11.0	.	NM_173626		Missense_Mutation	SNP	ENST00000361193.3	hg19	CCDS11771.2	.	.	.	.	.	.	.	.	.	.	C	14.53	2.562831	0.45694	.	.	ENSG00000181045	ENST00000411502;ENST00000546047;ENST00000361193	D;D;D	0.92858	-3.12;-3.12;-3.12	4.12	4.12	0.48240	Sulphate transporter (1);	0.000000	0.85682	D	0.000000	D	0.93307	0.7867	L	0.49778	1.585	0.58432	D	0.999999	D	0.89917	1.0	D	0.69654	0.965	D	0.92074	0.5667	10	0.40728	T	0.16	-23.4884	10.8479	0.46753	0.0:0.9073:0.0:0.0927	.	378	Q86WA9	S2611_HUMAN	Q	378	ENSP00000403998:P378Q;ENSP00000440724:P378Q;ENSP00000355384:P378Q	ENSP00000355384:P378Q	P	+	2	0	SLC26A11	75834583	0.955000	0.32602	0.990000	0.47175	0.148000	0.21650	2.113000	0.41902	2.270000	0.75569	0.491000	0.48974	CCG	.	.	.	none		0.667	SLC26A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257281.1			A	78219988	C	A	78219988	3	1	172	1	0	0	0	0	1	0	0	0	14529	652	23	4	1171	4	SLC26A11	17	78219988	Missense_Mutation	SNP	C	TCGA-G7-6793-01A-11D-1961-08	14686923	78219988	2975222	30	10078											
SYT5	6861	hgsc.bcm.edu	37	chr19	55685920	55685920	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggcacctcgaagctgaaagCttcgttgtaataggggttca	10	10	13	8	2	1	1	1	1	0	0	3	2	1	1	1	3	2	6	1	3	4	5			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr19:55685920C>T	ENST00000354308.3	-	8	1294	c.925G>A	c.(925-927)Gct>Act	p.A309T	CTD-2587H24.5_ENST00000591665.1_RNA|SYT5_ENST00000590851.1_Missense_Mutation_p.A305T|SYT5_ENST00000592935.1_5'Flank|SYT5_ENST00000537500.1_Missense_Mutation_p.A309T	NM_003180.2	NP_003171.2	O00445	SYT5_HUMAN	synaptotagmin V	309	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|energy reserve metabolic process (GO:0006112)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|dense core granule (GO:0031045)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|transporter activity (GO:0005215)			kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	18			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)		AAGCTGAAAGCTTCGTTGTAA	0.527																																					p.A309T		Atlas-SNP	.											.	SYT5	45	.	0			c.G925A						PASS	.						190	182	185					19																	55685920		2203	4300	6503	SO:0001583	missense	6861	exon8			TGAAAGCTTCGTT	X96783	CCDS12919.1, CCDS74455.1	19q13.42	2014-07-02			ENSG00000129990	ENSG00000129990		"Synaptotagmins"	11513	protein-coding gene	gene with protein product	"synaptotagmin 5"	600782				9177789	Standard	XM_006723338		Approved		uc002qjn.1	O00445	OTTHUMG00000180669	ENST00000354308.3:c.925G>A	chr19.hg19:g.55685920C>T	ENSP00000346265:p.Ala309Thr	282.0	0.0	.		248.0	62.0	.	NM_003180	B3KWJ8|B7Z300|Q86X72	Missense_Mutation	SNP	ENST00000354308.3	hg19	CCDS12919.1	.	.	.	.	.	.	.	.	.	.	C	16.51	3.144796	0.57044	.	.	ENSG00000129990	ENST00000537500;ENST00000354308;ENST00000543844	T;T	0.67345	-0.26;-0.26	3.42	1.23	0.21249	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.175642	0.49305	D	0.000147	T	0.38401	0.1039	N	0.03071	-0.42	0.38441	D	0.946694	B;B;B	0.27594	0.081;0.102;0.182	B;B;B	0.32465	0.146;0.026;0.092	T	0.23048	-1.0199	10	0.66056	D	0.02	.	5.0538	0.14522	0.4913:0.4025:0.0:0.1062	.	305;308;309	B7Z300;Q4FD32;O00445	.;.;SYT5_HUMAN	T	309;309;305	ENSP00000442896:A309T;ENSP00000346265:A309T	ENSP00000346265:A309T	A	-	1	0	SYT5	60377732	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	0.882000	0.28186	0.442000	0.26555	0.561000	0.74099	GCT	.	.	.	none		0.527	SYT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452501.1	NM_003180		T	55685920	C	T	55685920	3	4	172	1	0	0	0	0	1	0	0	0	15489	797	28	2	243	2	SYT5	19	55685920	Missense_Mutation	SNP	C	TCGA-G7-6793-01A-11D-1961-08		55685920	3443063	31	10079											
ZNF549	256051	hgsc.bcm.edu	37	chr19	58049607	58049607	+	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	tgatcaccatagaatccacaCgggagaaaggccttatgagt	14	8	10	9	1	1	4	1	2	0	2	2	5	2	4	3	2	0	0	3	2	4	2	rs531934209		TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr19:58049607C>G	ENST00000376233.3	+	4	1416	c.1235C>G	c.(1234-1236)aCg>aGg	p.T412R	ZNF549_ENST00000602149.1_Intron|ZNF550_ENST00000601415.1_Intron|ZNF549_ENST00000594943.1_Intron|ZNF549_ENST00000240719.3_Missense_Mutation_p.T399R	NM_001199295.1	NP_001186224	Q6P9A3	ZN549_HUMAN	zinc finger protein 549	412					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	21		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		AGAATCCACACGGGAGAAAGG	0.433																																					p.T412R		Atlas-SNP	.											.	ZNF549	118	.	0			c.C1235G						PASS	.						58	59	59					19																	58049607		2203	4300	6503	SO:0001583	missense	256051	exon4			TCCACACGGGAGA	AK092236	CCDS12952.1, CCDS56106.1	19q13.43	2013-01-08				ENSG00000121406		"Zinc fingers, C2H2-type", "-"	26632	protein-coding gene	gene with protein product						12477932	Standard	NM_153263		Approved	FLJ34917	uc002qpb.2	Q6P9A3		ENST00000376233.3:c.1235C>G	chr19.hg19:g.58049607C>G	ENSP00000365407:p.Thr412Arg	97.0	0.0	.		49.0	8.0	.	NM_001199295	B3KV91|O43336|Q8NAR4	Missense_Mutation	SNP	ENST00000376233.3	hg19	CCDS56106.1	.	.	.	.	.	.	.	.	.	.	C	16.55	3.153855	0.57259	.	.	ENSG00000121406	ENST00000240719;ENST00000376233	T;T	0.25749	1.78;1.78	2.35	-0.274	0.12910	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.37489	0.1005	L	0.46885	1.475	0.31073	N	0.712839	D;D	0.89917	1.0;1.0	D;D	0.87578	0.987;0.998	T	0.39683	-0.9602	9	0.72032	D	0.01	.	6.4994	0.22160	0.0:0.6894:0.1838:0.1268	.	412;399	Q6P9A3;Q6P9A3-2	ZN549_HUMAN;.	R	399;412	ENSP00000240719:T399R;ENSP00000365407:T412R	ENSP00000240719:T399R	T	+	2	0	ZNF549	62741419	0.892000	0.30473	0.923000	0.36655	0.989000	0.77384	2.036000	0.41165	0.319000	0.23209	0.585000	0.79938	ACG	.	.	.	none		0.433	ZNF549-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466780.1	NM_153263		G	58049607	C	G	58049607	3	3	172	1	0	0	0	0	1	0	0	0	17993	536	19	4	1206	4	ZNF549	19	58049607	Missense_Mutation	SNP	C	TCGA-G7-6793-01A-11D-1961-08	2363687	58049607	1079376	32	10080											
ZIK1	284307	hgsc.bcm.edu	37	chr19	58101980	58101980	+	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	catactggagaaaggccttgGgagtgcaatgaatgtggaaa	14	8	14	5	0	0	2	0	1	0	1	0	5	0	4	1	4	2	1	1	4	5	2	rs577749417		TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr19:58101980G>C	ENST00000597850.1	+	4	1016	c.801G>C	c.(799-801)tgG>tgC	p.W267C	ZIK1_ENST00000536878.2_Missense_Mutation_p.W254C|ZIK1_ENST00000307468.4_3'UTR|ZIK1_ENST00000599456.1_Missense_Mutation_p.W212C	NM_001010879.2	NP_001010879.2	Q3SY52	ZIK1_HUMAN	zinc finger protein interacting with K protein 1	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)			NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	34		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		AAAGGCCTTGGGAGTGCAATG	0.473																																					p.W267C		Atlas-SNP	.											.	ZIK1	94	.	0			c.G801C						PASS	.						58	59	58					19																	58101980		2203	4300	6503	SO:0001583	missense	284307	exon4			GCCTTGGGAGTGC	AK092538	CCDS33135.1	19q13.43	2013-01-08	2012-12-07		ENSG00000171649	ENSG00000171649		"Zinc fingers, C2H2-type", "-"	33104	protein-coding gene	gene with protein product			"zinc finger protein interacting with K protein 1 homolog (mouse)"				Standard	XM_005258769		Approved	ZNF762	uc002qpg.3	Q3SY52		ENST00000597850.1:c.801G>C	chr19.hg19:g.58101980G>C	ENSP00000472867:p.Trp267Cys	78.0	0.0	.		63.0	11.0	.	NM_001010879	O43339|Q3SY51|Q3SY53	Missense_Mutation	SNP	ENST00000597850.1	hg19	CCDS33135.1	.	.	.	.	.	.	.	.	.	.	G	14.31	2.497409	0.44455	.	.	ENSG00000171649	ENST00000536878;ENST00000356724;ENST00000307468	T	0.17691	2.26	3.37	-2.36	0.06663	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09992	0.0245	N	0.01438	-0.865	0.09310	N	0.999996	D;D	0.69078	0.997;0.993	P;P	0.60173	0.821;0.87	T	0.15178	-1.0446	9	0.87932	D	0	.	2.8351	0.05512	0.1183:0.0948:0.3259:0.4609	.	254;267	F5H435;Q3SY52	.;ZIK1_HUMAN	C	254;248;267	ENSP00000438487:W254C	ENSP00000303820:W267C	W	+	3	0	ZIK1	62793792	0.000000	0.05858	0.000000	0.03702	0.547000	0.35210	-1.932000	0.01554	-0.690000	0.05142	-0.182000	0.12963	TGG	.	.	.	none		0.473	ZIK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466791.1	NM_001010879		C	58101980	G	C	58101980	3	2	172	1	0	0	0	0	1	0	0	0	17695	1241	43	4	815	4	ZIK1	19	58101980	Missense_Mutation	SNP	G	TCGA-G7-6793-01A-11D-1961-08	52373	58101980	1027003	33	10081											
USP25	29761	hgsc.bcm.edu	37	chr21	17138432	17138432	+	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	cttcctggcaatgatagataCatcagtgtgggaagccaagc	12	9	11	9	0	1	2	1	1	0	1	2	3	2	3	2	2	3	1	2	2	5	3			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chr21:17138432C>G	ENST00000285679.6	+	3	609	c.240C>G	c.(238-240)taC>taG	p.Y80*	USP25_ENST00000285681.2_Nonsense_Mutation_p.Y80*|USP25_ENST00000351097.5_Nonsense_Mutation_p.Y80*|USP25_ENST00000400183.2_Nonsense_Mutation_p.Y80*	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	80	SUMO interaction domain (SIM).				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)		ATGATAGATACATCAGTGTGG	0.368																																					p.Y80X		Atlas-SNP	.											.	USP25	156	.	0			c.C240G						PASS	.						108	98	101					21																	17138432		2203	4300	6503	SO:0001587	stop_gained	29761	exon3			TAGATACATCAGT	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.240C>G	chr21.hg19:g.17138432C>G	ENSP00000285679:p.Tyr80*	80.0	0.0	.		97.0	4.0	.	NM_013396	C0LSZ0|Q6DHZ9|Q9H9W1	Nonsense_Mutation	SNP	ENST00000285679.6	hg19	CCDS33515.1	.	.	.	.	.	.	.	.	.	.	c	36	5.933887	0.97122	.	.	ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000351097;ENST00000400183	.	.	.	5.42	0.564	0.17302	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.7186	0.40289	0.0:0.6591:0.0:0.3409	.	.	.	.	X	80	.	ENSP00000285679:Y80X	Y	+	3	2	USP25	16060303	0.926000	0.31397	0.996000	0.52242	0.828000	0.46876	0.110000	0.15437	0.035000	0.15519	-0.993000	0.02533	TAC	.	.	.	none		0.368	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			G	17138432	C	G	17138432	4	3	172	1	0	0	0	0	0	1	0	0	17068	489	17	4	250	4	USP25	21	17138432	Nonsense_Mutation	SNP	C	TCGA-G7-6793-01A-11D-1961-08		17138432	30991463	34	10082											
RBBP7	5931	hgsc.bcm.edu	37	chrX	16864059	16864059	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcagtgtgtcctccatgaatAaactgttacaagaacaaaaa	17	9	7	8	0	0	2	0	1	0	1	2	2	2	2	2	0	3	2	2	0	8	2			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chrX:16864059A>G	ENST00000380087.2	-	11	1461	c.1101T>C	c.(1099-1101)ttT>ttC	p.F367F	RBBP7_ENST00000404022.1_Silent_p.F358F|RBBP7_ENST00000380084.4_Silent_p.F411F			Q16576	RBBP7_HUMAN	retinoblastoma binding protein 7	367					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)					CTCCATGAATAAACTGTTACA	0.363																																					p.F411F		Atlas-SNP	.											.	RBBP7	58	.	0			c.T1233C						PASS	.						59	54	56					X																	16864059		2203	4300	6503	SO:0001819	synonymous_variant	5931	exon11			ATGAATAAACTGT	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.1101T>C	chrX.hg19:g.16864059A>G		69.0	0.0	.		70.0	20.0	.	NM_001198719	Q5JP00	Silent	SNP	ENST00000380087.2	hg19	CCDS14179.1																																																																																			.	.	.	none		0.363	RBBP7-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055920.2	NM_002893		G	16864059	A	G	16864059	2	3	172	1	0	0	0	0	0	0	0	1	13117	359	13	3		3	RBBP7	23	16864059	Silent	SNP	A	TCGA-G7-6793-01A-11D-1961-08		16864059	138406501	35	10083											
ARHGEF6	9459	hgsc.bcm.edu	37	chrX	135825892	135825892	+	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	tcatcctcattagtctgcttAaagttgaatcttgcttttac	9	18	5	9	0	4	1	2	1	2	0	5	1	5	1	1	0	3	3	1	0	5	6			TCGA-G7-6793-01A-11D-1961-08	TCGA-G7-6793-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7ab802f1-4c29-4c65-9073-b2b17d3a7bba	33f384e6-bc1d-4ef9-8886-7319f51cd68b	g.chrX:135825892A>T	ENST00000250617.6	-	5	1718	c.513T>A	c.(511-513)ttT>ttA	p.F171L	ARHGEF6_ENST00000370620.1_Missense_Mutation_p.F17L|ARHGEF6_ENST00000535227.1_Missense_Mutation_p.F17L|ARHGEF6_ENST00000370622.1_Missense_Mutation_p.F17L	NM_004840.2	NP_004831.1	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	171	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell junction assembly (GO:0034329)|JNK cascade (GO:0007254)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|intracellular (GO:0005622)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(1)|lung(14)|prostate(1)	38	Acute lymphoblastic leukemia(192;0.000127)					TAGTCTGCTTAAAGTTGAATC	0.413																																					p.F171L		Atlas-SNP	.											.	ARHGEF6	111	.	0			c.T513A						PASS	.						193	158	170					X																	135825892		2203	4300	6503	SO:0001583	missense	9459	exon5			CTGCTTAAAGTTG	D13631	CCDS14660.1	Xq26	2013-01-10	2002-05-23		ENSG00000129675	ENSG00000129675		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	685	protein-coding gene	gene with protein product	"Rac/Cdc42 guanine exchange factor (GEF) 6", "PAK-interacting exchange factor, alpha", "rho guanine nucleotide exchange factor 6"	300267	"mental retardation, X-linked 46"	MRX46		7584048, 9659915	Standard	NM_004840		Approved	alphaPIX, Cool-2, KIAA0006, alpha-PIX, Cool2	uc004fab.3	Q15052	OTTHUMG00000022518	ENST00000250617.6:c.513T>A	chrX.hg19:g.135825892A>T	ENSP00000250617:p.Phe171Leu	189.0	0.0	.		171.0	50.0	.	NM_004840	A6NMW9|A8K6S7|B1AL37|Q15396|Q5JQ66|Q7Z3W1|Q86XH0	Missense_Mutation	SNP	ENST00000250617.6	hg19	CCDS14660.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.525856	0.85600	.	.	ENSG00000129675	ENST00000250617;ENST00000370620;ENST00000370622;ENST00000535736;ENST00000535227	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	6.08	2.47	0.30058	Src homology-3 domain (3);Variant SH3 (1);	0.000000	0.85682	D	0.000000	T	0.60869	0.2302	M	0.78916	2.43	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.994;0.996	T	0.58763	-0.7579	10	0.72032	D	0.01	.	8.7263	0.34471	0.7085:0.0:0.2915:0.0	.	17;171	B7Z3C7;Q15052	.;ARHG6_HUMAN	L	171;17;17;17;17	ENSP00000250617:F171L;ENSP00000359654:F17L;ENSP00000359656:F17L;ENSP00000439483:F17L	ENSP00000250617:F171L	F	-	3	2	ARHGEF6	135653558	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.119000	0.50422	0.071000	0.16664	0.486000	0.48141	TTT	.	.	.	none		0.413	ARHGEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058511.2	NM_004840		T	135825892	A	T	135825892	3	4	172	1	0	0	0	0	1	0	0	0	910	359	13	5	1889	5	ARHGEF6	23	135825892	Missense_Mutation	SNP	A	TCGA-G7-6793-01A-11D-1961-08	118961833	135825892	19444668	36	10084											
TPRG1L	127262	hgsc.bcm.edu	37	chr1	3544177	3544177	+	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	tgccactttcacagaacaccCgatggctggcgcagatgaga	11	7	11	12	2	1	3	1	1	0	3	1	5	1	3	2	2	2	2	2	2	1	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr1:3544177C>A	ENST00000378344.2	+	4	655	c.584C>A	c.(583-585)cCg>cAg	p.P195Q	TPRG1L_ENST00000344579.5_Missense_Mutation_p.P136Q|RP11-46F15.2_ENST00000435049.1_RNA	NM_182752.3	NP_877429.2	Q5T0D9	TPRGL_HUMAN	tumor protein p63 regulated 1-like	195						cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|synaptic vesicle (GO:0008021)				endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|prostate(1)	8	all_cancers(77;0.0119)|all_epithelial(69;0.00481)|Ovarian(185;0.0634)|Lung NSC(156;0.162)|all_lung(157;0.172)	all_epithelial(116;7.37e-22)|all_lung(118;8.23e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.41e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.83e-22)|GBM - Glioblastoma multiforme(42;4.77e-14)|Colorectal(212;1.12e-05)|COAD - Colon adenocarcinoma(227;5.61e-05)|Kidney(185;0.000351)|BRCA - Breast invasive adenocarcinoma(365;0.000688)|KIRC - Kidney renal clear cell carcinoma(229;0.00553)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.201)		ACAGAACACCCGATGGCTGGC	0.537																																					p.P195Q		Atlas-SNP	.											.	TPRG1L	24	.	0			c.C584A						PASS	.						144	145	145					1																	3544177		2203	4300	6503	SO:0001583	missense	127262	exon4			AACACCCGATGGC	BC019034	CCDS47.1	1p36.32	2008-02-05	2008-01-16	2008-01-16	ENSG00000158109	ENSG00000158109			27007	protein-coding gene	gene with protein product		611460	"family with sequence similarity 79, member A"	FAM79A		12477932	Standard	NM_182752		Approved	RP11-46F15.3, FLJ21811	uc001akm.3	Q5T0D9	OTTHUMG00000000609	ENST00000378344.2:c.584C>A	chr1.hg19:g.3544177C>A	ENSP00000367595:p.Pro195Gln	289.0	0.0	.		255.0	12.0	.	NM_182752	A8K1K4|Q8WV04	Missense_Mutation	SNP	ENST00000378344.2	hg19	CCDS47.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.343531	0.82022	.	.	ENSG00000158109	ENST00000378344;ENST00000456805;ENST00000344579	.	.	.	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	D	0.83248	0.5213	M	0.83223	2.63	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.86311	0.1686	9	0.87932	D	0	-0.7616	17.1228	0.86706	0.0:1.0:0.0:0.0	.	136;195	Q5T0D9-2;Q5T0D9	.;TPRGL_HUMAN	Q	195;152;136	.	ENSP00000339714:P136Q	P	+	2	0	TPRG1L	3534037	1.000000	0.71417	0.980000	0.43619	0.972000	0.66771	5.803000	0.69129	2.282000	0.76494	0.563000	0.77884	CCG	.	.	.	none		0.537	TPRG1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001466.1	NM_182752		A	3544177	C	A	3544177	3	1	173	1	0	0	0	0	1	0	0	0	16431	652	23	4	598	4	TPRG1L	1	3544177	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08		3544177	245706444	1	10085											
CC2D1B	200014	hgsc.bcm.edu	37	chr1	52819228	52819228	+	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	ccagaaccagccagttctcaGtgaccatctgcacatcctgg	10	8	8	15	0	2	2	1	1	2	1	4	2	3	2	5	1	3	2	5	1	1	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr1:52819228G>C	ENST00000371586.2	-	24	2678	c.2540C>G	c.(2539-2541)aCt>aGt	p.T847S	CC2D1B_ENST00000460261.1_5'UTR|RP11-155O18.6_ENST00000606527.1_RNA|CC2D1B_ENST00000284376.3_Missense_Mutation_p.T841S	NM_032449.2	NP_115825.1	Q5T0F9	C2D1B_HUMAN	coiled-coil and C2 domain containing 1B	847						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						CCAGTTCTCAGTGACCATCTG	0.592																																					p.T847S		Atlas-SNP	.											.	CC2D1B	73	.	0			c.C2540G						PASS	.						48	46	47					1																	52819228		2203	4300	6503	SO:0001583	missense	200014	exon24			TTCTCAGTGACCA	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.2540C>G	chr1.hg19:g.52819228G>C	ENSP00000360642:p.Thr847Ser	48.0	0.0	.		46.0	22.0	.	NM_032449	Q49AE8|Q5T0F8|Q5T0G0|Q6ZNQ1|Q96AP3|Q96I04|Q96JJ1	Missense_Mutation	SNP	ENST00000371586.2	hg19	CCDS30714.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.43|16.43	3.121445|3.121445	0.56613|0.56613	.|.	.|.	ENSG00000154222|ENSG00000154222	ENST00000450942|ENST00000371586;ENST00000284376	.|T;T	.|0.21543	.|2.0;2.0	4.97|4.97	4.06|4.06	0.47325|0.47325	.|.	.|0.215167	.|0.44483	.|D	.|0.000459	T|T	0.27524|0.27524	0.0676|0.0676	L|L	0.53249|0.53249	1.67|1.67	0.80722|0.80722	D|D	1|1	.|P;P	.|0.43477	.|0.808;0.757	.|P;B	.|0.46026	.|0.501;0.327	T|T	0.03051|0.03051	-1.1078|-1.1078	5|10	.|0.48119	.|T	.|0.1	-6.0069|-6.0069	13.5782|13.5782	0.61888|0.61888	0.0745:0.0:0.9255:0.0|0.0745:0.0:0.9255:0.0	.|.	.|841;847	.|Q5T0F9-2;Q5T0F9	.|.;C2D1B_HUMAN	V|S	761|847;841	.|ENSP00000360642:T847S;ENSP00000284376:T841S	.|ENSP00000284376:T841S	L|T	-|-	1|2	2|0	CC2D1B|CC2D1B	52591816|52591816	1.000000|1.000000	0.71417|0.71417	0.830000|0.830000	0.32933|0.32933	0.821000|0.821000	0.46438|0.46438	6.187000|6.187000	0.72039|0.72039	1.323000|1.323000	0.45263|0.45263	0.561000|0.561000	0.74099|0.74099	CTG|ACT	.	.	.	none		0.592	CC2D1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022189.1	NM_032449		C	52819228	G	C	52819228	3	2	173	1	0	0	0	0	1	0	0	0	2729	1029	36	4	40	4	CC2D1B	1	52819228	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08	49275051	52819228	196431393	2	10086											
DPYD	1806	hgsc.bcm.edu	37	chr1	98058809	98058809	+	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	tcttatattaacaaagccttTtctgaagacgatgaacacac	15	12	5	9	1	2	3	0	2	2	1	2	4	2	3	1	0	3	0	1	0	6	5			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr1:98058809T>A	ENST00000370192.3	-	10	1193	c.1093A>T	c.(1093-1095)Aaa>Taa	p.K365*		NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	365					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)	ACAAAGCCTTTTCTGAAGACG	0.448																																					p.K365X		Atlas-SNP	.											.	DPYD	219	.	0			c.A1093T						PASS	.						119	116	117					1																	98058809		2203	4300	6503	SO:0001587	stop_gained	1806	exon10			AGCCTTTTCTGAA	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.1093A>T	chr1.hg19:g.98058809T>A	ENSP00000359211:p.Lys365*	116.0	0.0	.		140.0	53.0	.	NM_000110	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Nonsense_Mutation	SNP	ENST00000370192.3	hg19	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	T	39	7.840231	0.98519	.	.	ENSG00000188641	ENST00000370192	.	.	.	6.17	6.17	0.99709	.	0.048348	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.3061	15.3933	0.74767	0.0:0.0:0.0:1.0	.	.	.	.	X	365	.	ENSP00000359211:K365X	K	-	1	0	DPYD	97831397	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.664000	0.68045	2.371000	0.80710	0.533000	0.62120	AAA	.	.	.	none		0.448	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110		A	98058809	T	A	98058809	4	1	173	1	0	0	0	0	0	1	0	0	4747	1850	64	5	2040	5	DPYD	1	98058809	Nonsense_Mutation	SNP	T	TCGA-G7-6795-01A-11D-1961-08	45239581	98058809	151191812	3	10087											
RHBG	57127	hgsc.bcm.edu	37	chr1	156347130	156347130	+	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	ccatggtcttcgtgggctttGgcttcctcatggtcttcctg	2	16	11	12	1	3	0	1	0	2	0	6	0	5	0	3	4	0	2	3	4	0	4			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr1:156347130G>C	ENST00000368249.1	+	2	264	c.226G>C	c.(226-228)Ggc>Cgc	p.G76R	RHBG_ENST00000537040.1_Intron|RHBG_ENST00000255013.3_Missense_Mutation_p.G7R|RHBG_ENST00000451864.2_Missense_Mutation_p.G7R|RHBG_ENST00000400992.2_Missense_Mutation_p.G7R|RHBG_ENST00000368246.2_Missense_Mutation_p.G76R	NM_001256396.1|NM_020407.4	NP_001243325.1|NP_065140.3	Q9H310	RHBG_HUMAN	Rh family, B glycoprotein (gene/pseudogene)	76			G -> D (in dbSNP:rs2245623). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.5}.		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)					CGTGGGCTTTGGCTTCCTCAT	0.637																																					p.G76R		Atlas-SNP	.											.	RHBG	133	.	0			c.G226C						PASS	.						142	144	143					1																	156347130		2203	4300	6503	SO:0001583	missense	57127	exon2			GGCTTTGGCTTCC	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.226G>C	chr1.hg19:g.156347130G>C	ENSP00000357232:p.Gly76Arg	207.0	0.0	.		147.0	47.0	.	NM_020407	A8K475|Q5SZW4|Q5SZW6|Q5SZW7|Q6P193|Q6YJI2|Q6YJI3	Missense_Mutation	SNP	ENST00000368249.1	hg19		.	.	.	.	.	.	.	.	.	.	G	29.7	5.031766	0.93575	.	.	ENSG00000132677	ENST00000368249;ENST00000368246;ENST00000400992;ENST00000255013;ENST00000451864	D;D;D;D;D	0.81579	-1.51;-1.51;-1.51;-1.51;-1.51	4.86	4.86	0.63082	Ammonium transporter AmtB-like (3);	0.000000	0.85682	D	0.000000	D	0.91744	0.7389	H	0.94582	3.555	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	0.93736	0.7046	10	0.87932	D	0	-6.6399	16.7188	0.85405	0.0:0.0:1.0:0.0	.	76;7;113	Q9H310;Q9H310-3;Q5SZW5	RHBG_HUMAN;.;.	R	76;76;7;7;7	ENSP00000357232:G76R;ENSP00000357229:G76R;ENSP00000383777:G7R;ENSP00000255013:G7R;ENSP00000389836:G7R	ENSP00000255013:G7R	G	+	1	0	RHBG	154613754	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.365000	0.73090	2.512000	0.84698	0.561000	0.74099	GGC	.	.	.	none		0.637	RHBG-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000060589.2	NM_001256395		C	156347130	G	C	156347130	3	2	173	1	0	0	0	0	1	0	0	0	13337	1348	47	4	232	4	RHBG	1	156347130	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08	58288321	156347130	92903491	4	10088											
ADAM17	6868	hgsc.bcm.edu	37	chr2	9645412	9645412	+	Missense_Mutation	SNP	T	T	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	ccctcgagttcccacaaactTtattgctgcgttcttgaaaa	10	13	6	12	2	1	1	0	1	1	0	3	2	2	1	2	0	3	3	2	0	4	6			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:9645412T>G	ENST00000310823.3	-	12	1609	c.1427A>C	c.(1426-1428)aAa>aCa	p.K476T	RP11-400L8.2_ENST00000480764.1_RNA|RP11-400L8.2_ENST00000472619.1_RNA	NM_003183.4	NP_003174.3	P78536	ADA17_HUMAN	ADAM metallopeptidase domain 17	476	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell motility (GO:0048870)|collagen catabolic process (GO:0030574)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|germinal center formation (GO:0002467)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil mediated immunity (GO:0002446)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of chemokine production (GO:0032722)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|proteolysis (GO:0006508)|regulation of mast cell apoptotic process (GO:0033025)|response to drug (GO:0042493)|response to high density lipoprotein particle (GO:0055099)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|wound healing, spreading of epidermal cells (GO:0035313)	actin cytoskeleton (GO:0015629)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|interleukin-6 receptor binding (GO:0005138)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|Notch binding (GO:0005112)|PDZ domain binding (GO:0030165)|zinc ion binding (GO:0008270)			breast(1)|cervix(4)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	28	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.225)		CCCACAAACTTTATTGCTGCG	0.438																																					p.K476T		Atlas-SNP	.											.	ADAM17	61	.	0			c.A1427C						PASS	.						178	155	163					2																	9645412		2203	4300	6503	SO:0001583	missense	6868	exon12			CAAACTTTATTGC	U69611	CCDS1665.1	2p25	2010-08-05	2008-07-31		ENSG00000151694	ENSG00000151694		"ADAM metallopeptidase domain containing", "CD molecules"	195	protein-coding gene	gene with protein product		603639	"tumor necrosis factor, alpha, converting enzyme"	TACE		9034190, 9574564	Standard	NM_003183		Approved	cSVP, CD156B	uc002qzu.3	P78536	OTTHUMG00000090425	ENST00000310823.3:c.1427A>C	chr2.hg19:g.9645412T>G	ENSP00000309968:p.Lys476Thr	120.0	0.0	.		154.0	72.0	.	NM_003183	O60226	Missense_Mutation	SNP	ENST00000310823.3	hg19	CCDS1665.1	.	.	.	.	.	.	.	.	.	.	T	12.83	2.056207	0.36277	.	.	ENSG00000151694	ENST00000310823	T	0.21191	2.02	5.66	3.33	0.38152	Blood coagulation inhibitor, Disintegrin (1);	0.226724	0.51477	D	0.000087	T	0.18718	0.0449	L	0.46670	1.46	0.80722	D	1	B;B	0.10296	0.003;0.003	B;B	0.12156	0.007;0.007	T	0.03325	-1.1048	10	0.48119	T	0.1	.	9.5244	0.39156	0.0:0.1409:0.0:0.8591	.	476;476	B2RNB2;P78536	.;ADA17_HUMAN	T	476	ENSP00000309968:K476T	ENSP00000309968:K476T	K	-	2	0	ADAM17	9562863	1.000000	0.71417	0.994000	0.49952	0.915000	0.54546	3.947000	0.56652	0.444000	0.26612	0.460000	0.39030	AAA	.	.	.	none		0.438	ADAM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206857.1			G	9645412	T	G	9645412	3	3	173	1	0	0	0	0	1	0	0	0	238	1841	64	5	1079	5	ADAM17	2	9645412	Missense_Mutation	SNP	T	TCGA-G7-6795-01A-11D-1961-08		9645412	233553961	5	10089											
MYCN	4613	hgsc.bcm.edu	37	chr2	16082320	16082321	+	Frame_Shift_Ins	INS	-	-	G																															ggccccgactcgacccccccINSgggggaggacatctggaaga																										TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:16082320_16082321insG	ENST00000281043.3	+	2	431_432	c.134_135insG	c.(133-138)ccggggfs	p.PG45fs	MYCNOS_ENST00000453400.1_RNA|MYCNOS_ENST00000448719.1_RNA|MYCNOS_ENST00000420452.1_RNA|MYCNOS_ENST00000419083.1_RNA|MYCNOS_ENST00000439180.1_RNA	NM_005378.4	NP_005369.2	P04198	MYCN_HUMAN	v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog	45					branching morphogenesis of an epithelial tube (GO:0048754)|cartilage condensation (GO:0001502)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|lung development (GO:0030324)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|positive regulation of cell death (GO:0010942)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin (GO:0000785)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	31	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)			TCGACCCCCCCGGGGGAGGACA	0.644			A		neuroblastoma																																p.P45fs		Atlas-INDEL	.		Dom	yes		2	2p24.1	4613	"v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)"		O	.	MYCN	63	.	0			c.134_135insG	GRCh37	CI084293	MYCN	I		PASS	.																																			SO:0001589	frameshift_variant	4613	exon2			.	BC002712	CCDS1687.1	2p24.3	2013-08-14	2013-07-09		ENSG00000134323	ENSG00000134323		"Basic helix-loop-helix proteins"	7559	protein-coding gene	gene with protein product		164840		NMYC			Standard	XM_006711886		Approved	bHLHe37, N-myc, MYCNOT	uc002rci.3	P04198	OTTHUMG00000039579	ENST00000281043.3:c.139dupG	chr2.hg19:g.16082325_16082325dupG	ENSP00000281043:p.Pro45fs	47.0	0.0	0		49.0	23.0	0.469388	NM_005378	Q53XS5|Q6LDT9	Frame_Shift_Ins	INS	ENST00000281043.3	hg19	CCDS1687.1																																																																																			.	.	.	none		0.644	MYCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095469.2	NM_005378		G	16082321	-	G	16082320	7	5	173	1	0	1	1	0	0	0	0	0	10028	652	23	0	136	0	MYCN	2	16082320	Frame_Shift_Ins	INS	-	TCGA-G7-6795-01A-11D-1961-08	6436908	16082320	227117053	6	10090											
APOB	338	hgsc.bcm.edu	37	chr2	21260848	21260848	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accagaaacaacacttgcttGgcttcttctgtctctggggg	8	12	10	11	0	3	1	0	0	3	1	4	1	3	1	1	3	3	2	1	3	2	4			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:21260848G>A	ENST00000233242.1	-	5	646	c.519C>T	c.(517-519)gcC>gcT	p.A173A	APOB_ENST00000399256.4_Silent_p.A173A	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	173	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)					ACACTTGCTTGGCTTCTTCTG	0.458																																					p.A173A		Atlas-SNP	.											.	APOB	761	.	0			c.C519T						PASS	.						128	129	129					2																	21260848		2203	4300	6503	SO:0001819	synonymous_variant	338	exon5			TTGCTTGGCTTCT	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.519C>T	chr2.hg19:g.21260848G>A		140.0	0.0	.		173.0	94.0	.	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.	.	none		0.458	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21260848	G	A	21260848	2	1	173	1	0	0	0	0	0	0	0	1	785	1335	47	2		2	APOB	2	21260848	Silent	SNP	G	TCGA-G7-6795-01A-11D-1961-08	5178528	21260848	221938525	7	10091											
ATAD2B	54454	hgsc.bcm.edu	37	chr2	24051776	24051776	+	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	tgacaattttggattccagtCcctggtatggatctgtaaga	10	14	10	7	0	1	2	0	1	1	1	3	4	3	4	2	3	0	2	2	3	3	5			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:24051776C>A	ENST00000238789.5	-	15	2105	c.1762G>T	c.(1762-1764)Gac>Tac	p.D588Y	ATAD2B_ENST00000474583.1_5'UTR	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	588						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGATTCCAGTCCCTGGTATGG	0.333																																					p.D588Y		Atlas-SNP	.											.	ATAD2B	110	.	0			c.G1762T						PASS	.						121	114	116					2																	24051776		1842	4090	5932	SO:0001583	missense	54454	exon15			TCCAGTCCCTGGT	AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"ATPases / AAA-type"	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.1762G>T	chr2.hg19:g.24051776C>A	ENSP00000238789:p.Asp588Tyr	97.0	0.0	.		138.0	59.0	.	NM_001242338	B9ZVQ5|Q6ZNA6|Q8N9E7	Missense_Mutation	SNP	ENST00000238789.5	hg19	CCDS46227.1	.	.	.	.	.	.	.	.	.	.	C	15.81	2.944509	0.53079	.	.	ENSG00000119778	ENST00000238789;ENST00000458510	D;D	0.94931	-3.56;-1.77	4.7	4.7	0.59300	.	.	.	.	.	D	0.95023	0.8389	L	0.60957	1.885	0.49299	D	0.999776	D	0.54047	0.964	P	0.53912	0.737	D	0.95210	0.8324	9	0.72032	D	0.01	.	14.2998	0.66339	0.1494:0.8506:0.0:0.0	.	588	Q9ULI0	ATD2B_HUMAN	Y	588;26	ENSP00000238789:D588Y;ENSP00000392764:D26Y	ENSP00000238789:D588Y	D	-	1	0	ATAD2B	23905280	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	3.884000	0.56175	2.551000	0.86045	0.650000	0.86243	GAC	.	.	.	none		0.333	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552		A	24051776	C	A	24051776	3	1	173	1	0	0	0	0	1	0	0	0	1072	855	30	4	2670	4	ATAD2B	2	24051776	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08	2790928	24051776	219147597	8	10092											
ITSN2	50618	hgsc.bcm.edu	37	chr2	24509153	24509155	+	In_Frame_Del	DEL	TTC	TTC	-																															ttttcaagagcatctaactgTtctttaagtctttggcataa																								rs201163358		TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:24509153_24509155delTTC	ENST00000355123.4	-	16	2232_2234	c.1789_1791delGAA	c.(1789-1791)gaadel	p.E597del	ITSN2_ENST00000361999.3_In_Frame_Del_p.E597del|ITSN2_ENST00000406921.3_In_Frame_Del_p.E597del	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	597					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)					CATCTAACTGTTCTTTAAGTCTT	0.286																																					p.597_598del		Atlas-INDEL	.											.	ITSN2	224	.	0			c.1790_1792del						PASS	.																																			SO:0001651	inframe_deletion	50618	exon16			.	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.1789_1791delGAA	chr2.hg19:g.24509153_24509155delTTC	ENSP00000347244:p.Glu597del	67.0	0.0	0		120.0	24.0	0.2	NM_006277	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	In_Frame_Del	DEL	ENST00000355123.4	hg19	CCDS1710.2																																																																																			.	.	.	none		0.286	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277		-	24509155	TTC	-	24509153	7	5	173	1	0	1	0	1	0	0	0	0	7934	1722	60	0	3453	0	ITSN2	2	24509153	In_Frame_Del	DEL	TTC	TCGA-G7-6795-01A-11D-1961-08	457377	24509153	218690220	9	10093											
AGBL5	60509	hgsc.bcm.edu	37	chr2	27291539	27291539	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcctctggagacaaaccagAggctgtcatggtaatcggga	11	8	13	9	1	2	2	1	0	1	2	4	4	3	3	2	4	1	2	2	4	2	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:27291539A>G	ENST00000360131.4	+	13	2441	c.2282A>G	c.(2281-2283)gAg>gGg	p.E761G		NM_021831.5	NP_068603.4	Q8NDL9	CBPC5_HUMAN	ATP/GTP binding protein-like 5	761					protein branching point deglutamylation (GO:0035611)|protein deglutamylation (GO:0035608)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	28	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GACAAACCAGAGGCTGTCATG	0.512																																					p.E761G		Atlas-SNP	.											.	AGBL5	126	.	0			c.A2282G						PASS	.						84	85	85					2																	27291539		2203	4300	6503	SO:0001583	missense	60509	exon13			AACCAGAGGCTGT	BC007415	CCDS1732.3, CCDS42665.1	2p23.3	2014-06-23			ENSG00000084693	ENSG00000084693			26147	protein-coding gene	gene with protein product	"cytosolic carboxypeptidase 5"	615900				24022482	Standard	NM_001035507		Approved	FLJ21839, CCP5	uc002rie.3	Q8NDL9	OTTHUMG00000128406	ENST00000360131.4:c.2282A>G	chr2.hg19:g.27291539A>G	ENSP00000353249:p.Glu761Gly	117.0	0.0	.		180.0	52.0	.	NM_021831	A2VDI7|B7WPG9|B7Z7I7|D6W548|Q53SW0|Q53SZ0|Q96IK8|Q9H6V0|Q9H8P8	Missense_Mutation	SNP	ENST00000360131.4	hg19	CCDS1732.3	.	.	.	.	.	.	.	.	.	.	A	10.83	1.459849	0.26248	.	.	ENSG00000084693	ENST00000360131	T	0.17370	2.28	5.61	4.46	0.54185	.	0.426245	0.25285	N	0.031768	T	0.10723	0.0262	N	0.19112	0.55	0.32634	N	0.521593	B	0.13145	0.007	B	0.09377	0.004	T	0.03641	-1.1017	10	0.87932	D	0	-0.026	7.4869	0.27439	0.9054:0.0:0.0946:0.0	.	761	Q8NDL9	CBPC5_HUMAN	G	761	ENSP00000353249:E761G	ENSP00000353249:E761G	E	+	2	0	AGBL5	27145043	1.000000	0.71417	1.000000	0.80357	0.237000	0.25408	2.781000	0.47750	2.123000	0.65237	0.459000	0.35465	GAG	.	.	.	none		0.512	AGBL5-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309033.1	NM_021831		G	27291539	A	G	27291539	3	3	173	1	0	0	0	0	1	0	0	0	378	304	11	3	2393	3	AGBL5	2	27291539	Missense_Mutation	SNP	A	TCGA-G7-6795-01A-11D-1961-08	2782386	27291539	215907834	10	10094											
SLC4A5	57835	hgsc.bcm.edu	37	chr2	74458396	74458396	+	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	gccaggaagacagagattccCgtcaggatgaagacgatgat	14	6	13	8	2	1	5	1	2	0	3	2	9	2	7	2	2	0	0	2	2	2	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:74458396C>A	ENST00000423644.1	-	24	3032	c.2635G>T	c.(2635-2637)Ggg>Tgg	p.G879W	SLC4A5_ENST00000394019.2_Silent_p.T938T|RP11-287D1.3_ENST00000451608.2_3'UTR|SLC4A5_ENST00000377632.1_Silent_p.T938T|SLC4A5_ENST00000346834.4_Silent_p.T938T|SLC4A5_ENST00000483195.1_5'UTR|SLC4A5_ENST00000357822.5_Silent_p.T938T|SLC4A5_ENST00000359484.4_Silent_p.T836T|SLC4A5_ENST00000377634.4_Silent_p.T938T|SLC4A5_ENST00000358683.4_Silent_p.T836T					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						CAGAGATTCCCGTCAGGATGA	0.562																																					p.T938T		Atlas-SNP	.											.	SLC4A5	215	.	0			c.G2814T						PASS	.						179	146	157					2																	74458396		2203	4300	6503	SO:0001583	missense	57835	exon20			GATTCCCGTCAGG	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	ENST00000423644.1:c.2635G>T	chr2.hg19:g.74458396C>A	ENSP00000395804:p.Gly879Trp	97.0	0.0	.		137.0	11.0	.	NM_021196		Silent	SNP	ENST00000423644.1	hg19		.	.	.	.	.	.	.	.	.	.	C	5.936	0.356646	0.11239	.	.	ENSG00000188687	ENST00000423644;ENST00000425249	T;T	0.74315	-0.83;-0.47	4.47	-8.36	0.00980	.	.	.	.	.	T	0.52996	0.1769	.	.	.	0.19575	N	0.999969	B	0.11235	0.004	B	0.09377	0.004	T	0.41070	-0.9529	8	0.59425	D	0.04	.	1.6798	0.02830	0.3015:0.1537:0.0994:0.4453	.	841	E7EQT3	.	W	879;841	ENSP00000395804:G879W;ENSP00000405678:G841W	ENSP00000395804:G879W	G	-	1	0	SLC4A5	74311904	0.000000	0.05858	0.373000	0.26003	0.924000	0.55760	-4.346000	0.00249	-2.458000	0.00538	-2.805000	0.00112	GGG	.	.	.	none		0.562	SLC4A5-204	KNOWN	basic	protein_coding	protein_coding				A	74458396	C	A	74458396	3	1	173	1	0	0	0	0	1	0	0	0	14670	639	23	4	627	4	SLC4A5	2	74458396	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08	47166857	74458396	168740977	11	10095											
SEMA4F	10505	hgsc.bcm.edu	37	chr2	74906851	74906851	+	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	gagtgactgcactcacccccCggcgggatggactggaggtg	7	6	16	12	2	1	1	1	1	0	0	1	5	1	4	3	5	1	1	3	5	0	0	rs367999393		TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:74906851C>A	ENST00000357877.2	+	14	1977	c.1828C>A	c.(1828-1830)Cgg>Agg	p.R610R	SEMA4F_ENST00000339773.5_Silent_p.R455R|SEMA4F_ENST00000473350.1_3'UTR	NM_004263.3	NP_004254.2	O95754	SEM4F_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F	610	Ig-like C2-type.				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						ACTCACCCCCCGGCGGGATGG	0.627																																					p.R610R		Atlas-SNP	.											.	SEMA4F	89	.	0			c.C1828A						PASS	.						73	72	73					2																	74906851		2203	4300	6503	SO:0001819	synonymous_variant	10505	exon14			ACCCCCCGGCGGG	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.1828C>A	chr2.hg19:g.74906851C>A		149.0	0.0	.		143.0	10.0	.	NM_004263	Q542Y7|Q9NS35	Silent	SNP	ENST00000357877.2	hg19	CCDS1955.1																																																																																			.	.	.	alt		0.627	SEMA4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252214.2	NM_004263		A	74906851	C	A	74906851	2	1	173	1	0	0	0	0	0	0	0	1	14048	643	23	4		4	SEMA4F	2	74906851	Silent	SNP	C	TCGA-G7-6795-01A-11D-1961-08	448455	74906851	168292522	12	10096											
SNRNP200	23020	hgsc.bcm.edu	37	chr2	96953697	96953697	+	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	caaatatcgctcgcatcaacCggccagccgactaagcaaag	14	5	8	14	4	1	0	1	0	0	0	3	1	1	0	3	1	3	3	3	1	5	2	rs397514574		TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:96953697C>A	ENST00000323853.5	-	25	3346	c.3269G>T	c.(3268-3270)cGg>cTg	p.R1090L	SNRNP200_ENST00000349783.5_Intron	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	1090	SEC63 1.		R -> L (in RP33). {ECO:0000269|PubMed:19710410}.		ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						TCGCATCAACCGGCCAGCCGA	0.502																																					p.R1090L		Atlas-SNP	.											.	SNRNP200	195	.	0			c.G3269T						PASS	.						126	111	116					2																	96953697		2203	4300	6503	SO:0001583	missense	23020	exon25			ATCAACCGGCCAG	AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"U5 snRNP specific protein, 200 KD"	601664	"activating signal cointegrator 1 complex subunit 3-like 1", "retinitis pigmentosa 33 (autosomal dominant)"	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.3269G>T	chr2.hg19:g.96953697C>A	ENSP00000317123:p.Arg1090Leu	170.0	0.0	.		191.0	9.0	.	NM_014014	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Missense_Mutation	SNP	ENST00000323853.5	hg19	CCDS2020.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.016736	0.93404	.	.	ENSG00000144028	ENST00000323853;ENST00000540328	T	0.70869	-0.52	5.3	5.3	0.74995	Sec63 domain (3);	0.000000	0.85682	D	0.000000	D	0.89473	0.6725	H	0.95850	3.73	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92387	0.5918	10	0.87932	D	0	-19.469	17.8872	0.88861	0.0:1.0:0.0:0.0	.	1090	O75643	U520_HUMAN	L	1090;765	ENSP00000317123:R1090L	ENSP00000317123:R1090L	R	-	2	0	SNRNP200	96317424	1.000000	0.71417	0.999000	0.59377	0.790000	0.44656	7.570000	0.82390	2.755000	0.94549	0.561000	0.74099	CGG	.	.	.	none		0.502	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252846.2	NM_014014		A	96953697	C	A	96953697	3	1	173	1	0	0	0	0	1	0	0	0	14865	652	23	4	3225	4	SNRNP200	2	96953697	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08	22046846	96953697	146245676	13	10097											
NEB	4703	hgsc.bcm.edu	37	chr2	152522655	152522655	+	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	tgctccacattcaaggcatcGggcaggagagtgtagtggtg	9	9	15	8	1	1	1	1	0	0	1	3	2	2	1	1	4	1	4	1	4	2	2	rs142074817	byFrequency	TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:152522655G>T	ENST00000172853.10	-	41	5127	c.4980C>A	c.(4978-4980)ccC>ccA	p.P1660P	NEB_ENST00000604864.1_Silent_p.P1660P|NEB_ENST00000397345.3_Silent_p.P1660P|NEB_ENST00000427231.2_Silent_p.P1660P|NEB_ENST00000603639.1_Silent_p.P1660P|NEB_ENST00000409198.1_Silent_p.P1660P			P20929	NEBU_HUMAN	nebulin	1660					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)		TCAAGGCATCGGGCAGGAGAG	0.488																																					p.P1660P		Atlas-SNP	.											.	NEB	1697	.	0			c.C4980A						PASS	.						268	262	264					2																	152522655		2077	4215	6292	SO:0001819	synonymous_variant	4703	exon41			GGCATCGGGCAGG	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.4980C>A	chr2.hg19:g.152522655G>T		227.0	0.0	.		248.0	10.0	.	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	hg19																																																																																				.	G|0.998;A|0.002	.	alt		0.488	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152522655	G	T	152522655	2	4	173	1	0	0	0	0	0	0	0	1	10309	1103	39	4		4	NEB	2	152522655	Silent	SNP	G	TCGA-G7-6795-01A-11D-1961-08	55568958	152522655	90676718	14	10098											
UBR3	130507	hgsc.bcm.edu	37	chr2	170843280	170843281	+	Frame_Shift_Ins	INS	-	-	T																															agatcgacctactggattagINSttgtactgttacaagcatcc																										TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:170843280_170843281insT	ENST00000272793.5	+	25	3810_3811	c.3760_3761insT	c.(3760-3762)gttfs	p.V1254fs	UBR3_ENST00000418381.1_Frame_Shift_Ins_p.V1254fs|UBR3_ENST00000392631.1_Frame_Shift_Ins_p.V75fs			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	1254					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						TACTGGATTAGTTGTACTGTTA	0.396																																					p.V1254fs		Atlas-INDEL	.											.	UBR3	182	.	0			c.3760_3761insT						PASS	.																																			SO:0001589	frameshift_variant	130507	exon25			.	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.3762dupT	chr2.hg19:g.170843282_170843282dupT	ENSP00000272793:p.Val1254fs	85.0	0.0	0		136.0	32.0	0.235294	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Frame_Shift_Ins	INS	ENST00000272793.5	hg19																																																																																				.	.	.	none		0.396	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070		T	170843281	-	T	170843280	7	5	173	1	0	1	1	0	0	0	0	0	16915	1029	36	0	3858	0	UBR3	2	170843280	Frame_Shift_Ins	INS	-	TCGA-G7-6795-01A-11D-1961-08	18320625	170843280	72356093	15	10099											
FRZB	2487	hgsc.bcm.edu	37	chr2	183699593	183699593	+	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	gatttagttgcgtgcttgccGggggttcgagttcctgccag	4	13	15	9	3	0	0	0	0	0	0	2	2	1	0	3	2	4	4	3	2	1	6			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:183699593G>T	ENST00000295113.4	-	6	1570	c.961C>A	c.(961-963)Cgg>Agg	p.R321R		NM_001463.3	NP_001454.2	Q92765	SFRP3_HUMAN	frizzled-related protein	321					brain development (GO:0007420)|cochlea morphogenesis (GO:0090103)|convergent extension involved in organogenesis (GO:0060029)|epithelium development (GO:0060429)|gonad development (GO:0008406)|mammary gland involution (GO:0060056)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell development (GO:0010721)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of hepatocyte differentiation (GO:0070367)|negative regulation of Wnt signaling pathway (GO:0030178)|neural crest cell differentiation (GO:0014033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fat cell differentiation (GO:0045600)|skeletal system development (GO:0001501)|somite development (GO:0061053)|vasculature development (GO:0001944)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)	21			OV - Ovarian serous cystadenocarcinoma(117;0.109)|Epithelial(96;0.231)			CGTGCTTGCCGGGGGTTCGAG	0.443																																					p.R321R		Atlas-SNP	.											.	FRZB	42	.	0			c.C961A						PASS	.						125	120	122					2																	183699593		2203	4300	6503	SO:0001819	synonymous_variant	2487	exon6			CTTGCCGGGGGTT	U24163	CCDS2286.1	2q32.1	2013-09-19			ENSG00000162998	ENSG00000162998		"Secreted frizzled-related proteins"	3959	protein-coding gene	gene with protein product		605083				8824257, 9118218	Standard	NM_001463		Approved	FRZB-PEN, FRZB1, SRFP3, FRP-3, SFRP3, FRE, FRITZ, FRZB-1, FZRB, hFIZ	uc002upa.2	Q92765	OTTHUMG00000132597	ENST00000295113.4:c.961C>A	chr2.hg19:g.183699593G>T		93.0	0.0	.		156.0	9.0	.	NM_001463	O00181|Q99686	Silent	SNP	ENST00000295113.4	hg19	CCDS2286.1																																																																																			.	.	.	none		0.443	FRZB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255808.1	NM_001463		T	183699593	G	T	183699593	2	4	173	1	0	0	0	0	0	0	0	1	6072	1115	39	4		4	FRZB	2	183699593	Silent	SNP	G	TCGA-G7-6795-01A-11D-1961-08	12856313	183699593	59499780	16	10100											
FAM171B	165215	hgsc.bcm.edu	37	chr2	187627072	187627072	+	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	gtccaaaggaaagccctcccCgcatcccagagcctggtttg	9	7	10	15	1	0	1	0	0	0	1	3	2	3	2	6	2	2	2	6	2	2	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:187627072C>A	ENST00000304698.5	+	8	2206	c.2003C>A	c.(2002-2004)cCg>cAg	p.P668Q		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	668						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						AAGCCCTCCCCGCATCCCAGA	0.483																																					p.P668Q		Atlas-SNP	.											FAM171B,NS,carcinoma,0,2	FAM171B	146	.	0			c.C2003A						PASS	.						77	86	83					2																	187627072		2203	4300	6503	SO:0001583	missense	165215	exon8			CCTCCCCGCATCC	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.2003C>A	chr2.hg19:g.187627072C>A	ENSP00000304108:p.Pro668Gln	166.0	0.0	.		212.0	11.0	.	NM_177454	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Missense_Mutation	SNP	ENST00000304698.5	hg19	CCDS33347.1	.	.	.	.	.	.	.	.	.	.	C	12.44	1.938791	0.34189	.	.	ENSG00000144369	ENST00000304698	T	0.37235	1.21	6.02	6.02	0.97574	.	0.110302	0.64402	D	0.000005	T	0.39963	0.1098	L	0.47016	1.485	0.37615	D	0.92108	P;P	0.36027	0.533;0.533	B;B	0.37091	0.241;0.241	T	0.41698	-0.9494	10	0.87932	D	0	-16.1339	20.547	0.99278	0.0:1.0:0.0:0.0	.	668;669	Q6P995;A8K122	F171B_HUMAN;.	Q	668	ENSP00000304108:P668Q	ENSP00000304108:P668Q	P	+	2	0	FAM171B	187335317	0.987000	0.35691	0.821000	0.32701	0.569000	0.35902	4.610000	0.61155	2.850000	0.98022	0.650000	0.86243	CCG	.	.	.	none		0.483	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454		A	187627072	C	A	187627072	3	1	173	1	0	0	0	0	1	0	0	0	5495	652	23	4	2033	4	FAM171B	2	187627072	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08	3927479	187627072	55572301	17	10101											
NDUFS1	4719	hgsc.bcm.edu	37	chr2	207006722	207006724	+	In_Frame_Del	DEL	AGA	AGA	-																															aacgtgggtttgtaccaaccAgaagaacaacatctgcctct																										TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:207006722_207006724delAGA	ENST00000233190.6	-	12	1469_1471	c.1203_1205delTCT	c.(1201-1206)cttctg>ctg	p.401_402LL>L	NDUFS1_ENST00000455934.2_In_Frame_Del_p.415_416LL>L|NDUFS1_ENST00000449699.1_In_Frame_Del_p.401_402LL>L|NDUFS1_ENST00000432169.1_In_Frame_Del_p.290_291LL>L|NDUFS1_ENST00000423725.1_In_Frame_Del_p.344_345LL>L|NDUFS1_ENST00000457011.1_In_Frame_Del_p.285_286LL>L|NDUFS1_ENST00000440274.1_In_Frame_Del_p.365_366LL>L	NM_005006.6	NP_004997.4	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)	401					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						TGTACCAACCAGAAGAACAACAT	0.325																																					p.416_416del		Atlas-INDEL	.											.	NDUFS1	82	.	0			c.1246_1248del						PASS	.																																			SO:0001651	inframe_deletion	4719	exon12			.		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.1203_1205delTCT	chr2.hg19:g.207006725_207006727delAGA	ENSP00000233190:p.Leu402del	101.0	0.0	0		138.0	21.0	0.152174	NM_001199984	B4DIN9|B4DJA0|B4DPG1|B4DUC1|E7ENF3|Q53TR8|Q8N1C4|Q8TCC9	In_Frame_Del	DEL	ENST00000233190.6	hg19	CCDS2366.1																																																																																			.	.	.	none		0.325	NDUFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256391.4	NM_005006		-	207006724	AGA	-	207006722	7	5	173	1	0	1	0	1	0	0	0	0	10298	188	7	0	1010	0	NDUFS1	2	207006722	In_Frame_Del	DEL	AGA	TCGA-G7-6795-01A-11D-1961-08	19379650	207006722	36192651	18	10102											
TNS1	7145	hgsc.bcm.edu	37	chr2	218713795	218713795	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccatctagtggcccctgcGtgtgtcccaccacctctgca	5	10	8	18	1	2	0	0	0	2	0	4	0	4	0	6	1	2	1	6	1	1	1	rs200862766		TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:218713795G>A	ENST00000171887.4	-	17	1522	c.1070C>T	c.(1069-1071)aCg>aTg	p.T357M	TNS1_ENST00000419504.1_Missense_Mutation_p.T357M|TNS1_ENST00000430930.1_Missense_Mutation_p.T357M|TNS1_ENST00000480665.1_5'UTR	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	357					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)		TGGCCCCTGCGTGTGTCCCAC	0.577																																					p.T357M		Atlas-SNP	.											.	TNS1	251	.	0			c.C1070T						PASS	.	G	MET/THR	0,4406		0,0,2203	89	89	89		1070	4.3	1	2		89	2,8598	2.2+/-6.3	0,2,4298	no	missense	TNS1	NM_022648.4	81	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	357/1736	218713795	2,13004	2203	4300	6503	SO:0001583	missense	7145	exon17			CCCTGCGTGTGTC	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.1070C>T	chr2.hg19:g.218713795G>A	ENSP00000171887:p.Thr357Met	189.0	0.0	.		198.0	38.0	.	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	hg19	CCDS2407.1	.	.	.	.	.	.	.	.	.	.	G	17.74	3.464168	0.63513	0.0	2.33E-4	ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930;ENST00000446903;ENST00000413554	D;D;D;D;D	0.96334	-3.5;-3.49;-3.51;-3.83;-3.98	5.22	4.34	0.51931	.	0.767219	0.12422	N	0.470300	D	0.95255	0.8461	M	0.83603	2.65	0.80722	D	1	P;B;B;P;P	0.43519	0.809;0.423;0.345;0.704;0.704	B;B;B;B;B	0.32090	0.14;0.053;0.05;0.09;0.09	D	0.94356	0.7583	10	0.66056	D	0.02	.	14.202	0.65710	0.0727:0.0:0.9273:0.0	.	357;411;357;357;357	B2RU35;A1L0S7;Q9HBL0;E9PGF5;E9PF55	.;.;TENS1_HUMAN;.;.	M	357;357;357;482;425	ENSP00000171887:T357M;ENSP00000408724:T357M;ENSP00000406016:T357M;ENSP00000405460:T482M;ENSP00000400383:T425M	ENSP00000171887:T357M	T	-	2	0	TNS1	218422040	1.000000	0.71417	0.991000	0.47740	0.969000	0.65631	7.726000	0.84824	1.404000	0.46819	0.655000	0.94253	ACG	.	G|0.999;A|0.001	0.001	weak		0.577	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		A	218713795	G	A	218713795	3	1	173	1	0	0	0	0	1	0	0	0	16355	1145	40	1	4205	1	TNS1	2	218713795	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08	11707073	218713795	24485578	19	10103											
UGT1A5	54579	hgsc.bcm.edu	37	chr2	234622277	234622277	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctgcaaagggtcaagaacAtgctctaccctctggccctg	9	9	9	14	0	3	1	1	0	2	1	4	1	4	1	3	2	4	2	3	2	4	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:234622277A>G	ENST00000373414.3	+	1	640	c.640A>G	c.(640-642)Atg>Gtg	p.M214V	UGT1A6_ENST00000480628.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000608381.1_Missense_Mutation_p.M214V|UGT1A10_ENST00000373445.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000305139.6_Intron			P35504	UD15_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A5	214						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			cervix(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|urinary_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;4.51e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000523)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.00645)		GGTCAAGAACATGCTCTACCC	0.483																																					p.M214V		Atlas-SNP	.											UGT1A5,NS,carcinoma,0,1	UGT1A5	66	.	0			c.A640G						PASS	.						209	197	201					2																	234622277		2203	4300	6503	SO:0001583	missense	54579	exon1			AAGAACATGCTCT	M84129	CCDS33404.1	2q37	2010-03-05	2005-07-20		ENSG00000240224	ENSG00000240224		"UDP glucuronosyltransferases"	12537	other	complex locus constituent		606430	"UDP glycosyltransferase 1 family, polypeptide A5"			9295054, 1339448	Standard	NM_019078		Approved	UGT1E		P35504	OTTHUMG00000059120	ENST00000373414.3:c.640A>G	chr2.hg19:g.234622277A>G	ENSP00000362513:p.Met214Val	352.0	1.0	.		368.0	195.0	.	NM_019078	B8K294	Missense_Mutation	SNP	ENST00000373414.3	hg19	CCDS33404.1	.	.	.	.	.	.	.	.	.	.	A	9.408	1.079672	0.20309	.	.	ENSG00000240224	ENST00000373414	T	0.61040	0.14	4.77	-0.524	0.11920	.	0.585446	0.20090	N	0.099480	T	0.34221	0.0890	N	0.25201	0.72	0.26978	N	0.965428	B;B	0.13594	0.008;0.008	B;B	0.23150	0.044;0.044	T	0.12604	-1.0541	10	0.45353	T	0.12	.	1.3681	0.02205	0.4274:0.2431:0.2117:0.1179	.	214;214	Q5DSZ9;P35504	.;UD15_HUMAN	V	214	ENSP00000362513:M214V	ENSP00000362513:M214V	M	+	1	0	UGT1A5	234287016	0.000000	0.05858	0.992000	0.48379	0.655000	0.38815	-0.882000	0.04174	-0.055000	0.13244	0.459000	0.35465	ATG	.	.	.	none		0.483	UGT1A5-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130985.1	NM_019078		G	234622277	A	G	234622277	3	3	173	1	0	0	0	0	1	0	0	0	16960	217	8	3	642	3	UGT1A5	2	234622277	Missense_Mutation	SNP	A	TCGA-G7-6795-01A-11D-1961-08	15908482	234622277	8577096	20	10104											
D2HGDH	728294	hgsc.bcm.edu	37	chr2	242695394	242695394	+	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	cctgcgcgcccgcctcggccCgcacgccaagcacgtggtgg	4	4	14	19	7	0	0	0	0	0	0	1	0	0	0	5	3	2	2	5	3	1	0			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr2:242695394C>A	ENST00000321264.4	+	9	1480	c.1271C>A	c.(1270-1272)cCg>cAg	p.P424Q	AC114730.7_ENST00000417267.1_RNA|D2HGDH_ENST00000403782.1_Missense_Mutation_p.P290Q|D2HGDH_ENST00000486953.1_3'UTR	NM_152783.3	NP_689996.4	Q8N465	D2HDH_HUMAN	D-2-hydroxyglutarate dehydrogenase	424					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular protein metabolic process (GO:0044267)|response to cobalt ion (GO:0032025)|response to manganese ion (GO:0010042)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	(R)-2-hydroxyglutarate dehydrogenase activity (GO:0051990)|flavin adenine dinucleotide binding (GO:0050660)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			breast(1)|endometrium(3)|lung(10)|skin(1)|urinary_tract(1)	16		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)		CGCCTCGGCCCGCACGCCAAG	0.706																																					p.P424Q		Atlas-SNP	.											D2HGDH,NS,malignant_melanoma,0,1	D2HGDH	39	.	0			c.C1271A						PASS	.						66	56	59					2																	242695394		2203	4296	6499	SO:0001583	missense	728294	exon9			TCGGCCCGCACGC	AK091725	CCDS33426.1, CCDS74684.1	2p25.3	2010-05-11			ENSG00000180902	ENSG00000180902	1.1.99.-		28358	protein-coding gene	gene with protein product		609186				15070399, 15609246	Standard	NM_152783		Approved	MGC25181, D2HGD, FLJ42195	uc002wce.1	Q8N465	OTTHUMG00000151474	ENST00000321264.4:c.1271C>A	chr2.hg19:g.242695394C>A	ENSP00000315351:p.Pro424Gln	107.0	0.0	.		132.0	7.0	.	NM_152783	B4E3L6|E7ENP2|Q6IQ24|Q8N5Q8	Missense_Mutation	SNP	ENST00000321264.4	hg19	CCDS33426.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.370|7.370	0.626555|0.626555	0.14257|0.14257	.|.	.|.	ENSG00000180902|ENSG00000180902	ENST00000321264;ENST00000403782;ENST00000542211|ENST00000445308	D;D|.	0.83075|.	-1.68;-1.68|.	5.31|5.31	2.19|2.19	0.27852|0.27852	FAD-linked oxidase-like, C-terminal (1);FAD-linked oxidase, C-terminal (1);|.	0.575624|.	0.18171|.	N|.	0.149454|.	T|T	0.18045|0.18045	0.0433|0.0433	N|N	0.13098|0.13098	0.295|0.295	0.09310|0.09310	N|N	1|1	B|.	0.10296|.	0.003|.	B|.	0.19666|.	0.026|.	T|T	0.20273|0.20273	-1.0280|-1.0280	10|5	0.22706|.	T|.	0.39|.	-15.5113|-15.5113	3.1273|3.1273	0.06412|0.06412	0.1851:0.541:0.1039:0.17|0.1851:0.541:0.1039:0.17	.|.	424|.	Q8N465|.	D2HDH_HUMAN|.	Q|S	424;290;44|223	ENSP00000315351:P424Q;ENSP00000384723:P290Q|.	ENSP00000315351:P424Q|.	P|R	+|+	2|1	0|0	D2HGDH|D2HGDH	242344067|242344067	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.021000|0.021000	0.10359|0.10359	-0.148000|-0.148000	0.10219|0.10219	0.618000|0.618000	0.30179|0.30179	0.467000|0.467000	0.42956|0.42956	CCG|CGC	.	.	.	none		0.706	D2HGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322794.2	NM_152783		A	242695394	C	A	242695394	3	1	173	1	0	0	0	0	1	0	0	0	4215	652	23	4	1301	4	D2HGDH	2	242695394	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08	8073117	242695394	503979	21	10105											
SYNPR	132204	hgsc.bcm.edu	37	chr3	63466530	63466530	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttttgcaatctttgcatttgCaacatgcggtggctattctg	7	17	9	8	1	2	0	0	0	2	0	2	0	2	0	0	2	5	4	0	2	3	6			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr3:63466530C>T	ENST00000295894.5	+	2	416	c.47C>T	c.(46-48)gCa>gTa	p.A16V	SYNPR_ENST00000465156.1_Missense_Mutation_p.A16V|SYNPR_ENST00000460711.1_Missense_Mutation_p.A27V|SYNPR_ENST00000479198.1_Missense_Mutation_p.A16V|SYNPR_ENST00000478300.1_Missense_Mutation_p.A36V|SYNPR_ENST00000478744.1_3'UTR|SYNPR-AS1_ENST00000488201.1_RNA	NM_144642.4	NP_653243.1	Q8TBG9	SYNPR_HUMAN	synaptoporin	16	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)			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)		TTTGCATTTGCAACATGCGGT	0.433																																					p.A36V	NSCLC(29;1052 1116 20025 32519)	Atlas-SNP	.											.	SYNPR	38	.	0			c.C107T						PASS	.						160	161	160					3																	63466530		1945	4146	6091	SO:0001583	missense	132204	exon3			CATTTGCAACATG	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.47C>T	chr3.hg19:g.63466530C>T	ENSP00000295894:p.Ala16Val	280.0	1.0	.		239.0	94.0	.	NM_001130003	B2R675|G5E9W4	Missense_Mutation	SNP	ENST00000295894.5	hg19	CCDS46860.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.408930	0.83340	.	.	ENSG00000163630	ENST00000478300;ENST00000295894;ENST00000479198;ENST00000460711;ENST00000465156	T;T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0;-1.0	5.38	5.38	0.77491	Marvel (1);MARVEL-like domain (1);	0.105267	0.64402	D	0.000004	D	0.87597	0.6217	M	0.90870	3.155	0.80722	D	1	D;D;D	0.60160	0.979;0.979;0.987	P;P;P	0.58013	0.831;0.831;0.74	D	0.90454	0.4441	10	0.87932	D	0	-3.3962	18.124	0.89580	0.0:1.0:0.0:0.0	.	27;16;36	B3KVD8;Q8TBG9;G5E9W4	.;SYNPR_HUMAN;.	V	36;16;16;27;16	ENSP00000418994:A36V;ENSP00000295894:A16V;ENSP00000418929:A16V;ENSP00000418701:A27V;ENSP00000418123:A16V	ENSP00000295894:A16V	A	+	2	0	SYNPR	63441570	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.523000	0.85059	0.650000	0.86243	GCA	.	.	.	none		0.433	SYNPR-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351787.1			T	63466530	C	T	63466530	3	4	173	1	0	0	0	0	1	0	0	0	15471	710	25	2	145	2	SYNPR	3	63466530	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08		63466530	134555900	22	10106											
TOPBP1	11073	hgsc.bcm.edu	37	chr3	133329894	133329895	+	Frame_Shift_Ins	INS	-	-	CT																															ctggattttttttctccatcINStcattgctgcaagtgctagt																										TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr3:133329894_133329895insCT	ENST00000260810.5	-	25	4257_4258	c.4126_4127insAG	c.(4126-4128)agafs	p.R1376fs		NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	1376					cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						TTTTCTCCATCTCATTGCTGCA	0.356								Other conserved DNA damage response genes																													p.R1376fs	Ovarian(21;193 658 4424 15423 17362)	Atlas-INDEL	.											.	TOPBP1	218	.	0			c.4127_4128insAG						PASS	.																																			SO:0001589	frameshift_variant	11073	exon25			.	AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.4126_4127insAG	chr3.hg19:g.133329894_133329895insCT	ENSP00000260810:p.Arg1376fs	230.0	0.0	0		249.0	88.0	0.353414	NM_007027	B7Z7W8|Q7LGC1|Q9UEB9	Frame_Shift_Ins	INS	ENST00000260810.5	hg19	CCDS46919.1																																																																																			.	.	.	none		0.356	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027		CT	133329895	-	CT	133329894	7	5	173	1	0	1	1	0	0	0	0	0	16381	913	32	0	457	0	TOPBP1	3	133329894	Frame_Shift_Ins	INS	-	TCGA-G7-6795-01A-11D-1961-08	69863364	133329894	64692536	23	10107											
P2RY1	5028	hgsc.bcm.edu	37	chr3	152553966	152553966	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgcagaggttcatctttcAtgtgaacctctatggcagca	10	12	9	10	0	4	2	2	1	2	1	4	2	4	2	1	2	3	4	1	2	2	3			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr3:152553966A>G	ENST00000305097.3	+	1	1231	c.395A>G	c.(394-396)cAt>cGt	p.H132R		NM_002563.3	NP_002554.1	P47900	P2RY1_HUMAN	purinergic receptor P2Y, G-protein coupled, 1	132					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)			TTCATCTTTCATGTGAACCTC	0.507																																					p.H132R		Atlas-SNP	.											.	P2RY1	49	.	0			c.A395G						PASS	.						79	76	77					3																	152553966		2203	4300	6503	SO:0001583	missense	5028	exon1			TCTTTCATGTGAA	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.395A>G	chr3.hg19:g.152553966A>G	ENSP00000304767:p.His132Arg	85.0	0.0	.		100.0	34.0	.	NM_002563		Missense_Mutation	SNP	ENST00000305097.3	hg19	CCDS3169.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.019475	0.75275	.	.	ENSG00000169860	ENST00000305097	T	0.71698	-0.59	5.76	5.76	0.90799	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.82944	0.5147	M	0.79475	2.455	0.80722	D	1	D	0.58268	0.982	D	0.62955	0.909	D	0.85045	0.0925	10	0.66056	D	0.02	.	15.2728	0.73717	1.0:0.0:0.0:0.0	.	132	P47900	P2RY1_HUMAN	R	132	ENSP00000304767:H132R	ENSP00000304767:H132R	H	+	2	0	P2RY1	154036656	1.000000	0.71417	0.987000	0.45799	0.981000	0.71138	9.210000	0.95106	2.186000	0.69663	0.533000	0.62120	CAT	.	.	.	none		0.507	P2RY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356943.1	NM_002563		G	152553966	A	G	152553966	3	3	173	1	0	0	0	0	1	0	0	0	11353	217	8	3	397	3	P2RY1	3	152553966	Missense_Mutation	SNP	A	TCGA-G7-6795-01A-11D-1961-08	19224072	152553966	45468464	24	10108											
SH3TC1	54436	hgsc.bcm.edu	37	chr4	8230107	8230107	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctgcgggtggctcgggacCtgggccagcaaaggaaccag	8	4	16	13	2	0	0	0	0	0	0	1	2	0	2	4	5	3	2	4	5	2	0			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr4:8230107C>T	ENST00000245105.3	+	12	2753	c.2686C>T	c.(2686-2688)Ctg>Ttg	p.L896L	SH3TC1_ENST00000539824.1_Silent_p.L820L	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	896										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						GGCTCGGGACCTGGGCCAGCA	0.692																																					p.L896L	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											.	SH3TC1	105	.	0			c.C2686T						PASS	.						37	43	41					4																	8230107		2203	4299	6502	SO:0001819	synonymous_variant	54436	exon12			CGGGACCTGGGCC	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.2686C>T	chr4.hg19:g.8230107C>T		102.0	0.0	.		116.0	57.0	.	NM_018986	Q4W5G5	Silent	SNP	ENST00000245105.3	hg19	CCDS3399.1																																																																																			.	.	.	none		0.692	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986		T	8230107	C	T	8230107	2	4	173	1	0	0	0	0	0	0	0	1	14274	680	24	2		2	SH3TC1	4	8230107	Silent	SNP	C	TCGA-G7-6795-01A-11D-1961-08		8230107	182924169	25	10109											
ACOX3	8310	hgsc.bcm.edu	37	chr4	8368755	8368755	+	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	actctggccaccaggatgccCgctccaacaccttgctttcc	7	9	7	18	1	1	0	0	0	1	0	3	1	3	1	6	2	3	2	6	2	1	2			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr4:8368755C>A	ENST00000356406.5	-	18	2113	c.2036G>T	c.(2035-2037)cGg>cTg	p.R679L	ACOX3_ENST00000503233.1_Missense_Mutation_p.R679L|ACOX3_ENST00000413009.2_3'UTR|ACOX3_ENST00000515797.1_5'UTR	NM_003501.2	NP_003492.2	O15254	ACOX3_HUMAN	acyl-CoA oxidase 3, pristanoyl	679					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(17)|prostate(1)|skin(3)|stomach(1)	42						CCAGGATGCCCGCTCCAACAC	0.483																																					p.R679L		Atlas-SNP	.											.	ACOX3	70	.	0			c.G2036T						PASS	.						105	97	99					4																	8368755		2203	4300	6503	SO:0001583	missense	8310	exon18			GATGCCCGCTCCA	Y11411	CCDS3401.1, CCDS47017.1	4p15.3	2010-04-30	2010-04-30		ENSG00000087008	ENSG00000087008	1.3.3.6		121	protein-coding gene	gene with protein product		603402	"acyl-Coenzyme A oxidase 3, pristanoyl"			9271077	Standard	NM_003501		Approved		uc003glc.4	O15254	OTTHUMG00000090509	ENST00000356406.5:c.2036G>T	chr4.hg19:g.8368755C>A	ENSP00000348775:p.Arg679Leu	93.0	0.0	.		128.0	8.0	.	NM_003501	Q96AJ8	Missense_Mutation	SNP	ENST00000356406.5	hg19	CCDS3401.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.543529	0.86022	.	.	ENSG00000087008	ENST00000356406;ENST00000503233	T;T	0.49720	0.77;0.77	5.16	5.16	0.70880	Acyl-CoA oxidase, C-terminal (1);Acyl-CoA dehydrogenase/oxidase C-terminal (1);	0.000000	0.64402	D	0.000002	T	0.74801	0.3764	M	0.91972	3.26	0.58432	D	0.99999	D	0.89917	1.0	D	0.97110	1.0	T	0.79313	-0.1855	10	0.46703	T	0.11	-25.9722	16.1529	0.81634	0.0:1.0:0.0:0.0	.	679	O15254	ACOX3_HUMAN	L	679	ENSP00000348775:R679L;ENSP00000421625:R679L	ENSP00000348775:R679L	R	-	2	0	ACOX3	8419655	0.997000	0.39634	0.064000	0.19789	0.008000	0.06430	5.682000	0.68182	2.411000	0.81874	0.655000	0.94253	CGG	.	.	.	none		0.483	ACOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206997.4			A	8368755	C	A	8368755	3	1	173	1	0	0	0	0	1	0	0	0	160	652	23	4	70	4	ACOX3	4	8368755	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08	138648	8368755	182785521	26	10110											
LAP3	51056	hgsc.bcm.edu	37	chr4	17586652	17586653	+	Missense_Mutation	DNP	AC	AC	GA																															gcttctgggcagaacttggcAcgccaattgatggagacgcc																										TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr4:17586652_17586653AC>GA	ENST00000226299.4	+	6	871_872	c.597_598AC>GA	c.(595-600)gcACgc>gcGAgc	p.R200S	AC006160.5_ENST00000511010.1_RNA|LAP3_ENST00000606142.1_Missense_Mutation_p.R169S	NM_015907.2	NP_056991.2	P28838	AMPL_HUMAN	leucine aminopeptidase 3	200					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						AGAACTTGGCACGCCAATTGAT	0.475																																					p.A199A|p.R200S		Atlas-SNP	.											.|LAP3,NS,carcinoma,0,1	LAP3	50	.	0			c.A597G|c.C598A						PASS	.																																			SO:0001583	missense	51056	exon6			CTTGGCACGCCAA|TTGGCACGCCAAT	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	Exception_encountered	chr4.hg19:g.17586652_17586653delinsGA	ENSP00000226299:p.Arg200Ser	66.0|69.0	0.0|1.0	.		89.0|91.0	23.0|24.0	.	NM_015907	B3KMQ3|Q6IAM6|Q6P0L6|Q9UQE3	Silent|Missense_Mutation	SNP	ENST00000226299.4	hg19	CCDS3422.1																																																																																			.	.	.	none		0.475	LAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250365.1			GA	17586653	AC	GA	17586652	3	3	173	1	0	0	0	0	1	0	0	0	8630	146	6	3	619	3	LAP3	4	17586652	Missense_Mutation	DNP	AC	TCGA-G7-6795-01A-11D-1961-08	9217897	17586652	173567624	27	10111											
CCDC110	256309	hgsc.bcm.edu	37	chr4	186382305	186382305	+	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	ttcaatatttcactgatttcCgactgtacctttaaaagata	13	16	4	8	1	2	2	2	1	0	1	3	3	3	2	2	0	1	1	2	0	6	8	rs141194686	byFrequency	TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr4:186382305C>A	ENST00000307588.3	-	5	321	c.246G>T	c.(244-246)tcG>tcT	p.S82S	CCDC110_ENST00000393540.3_Intron|CCDC110_ENST00000507501.1_5'UTR|CCDC110_ENST00000510617.1_Silent_p.S82S	NM_152775.3	NP_689988.1	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110	82						nucleus (GO:0005634)		p.S82S(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(9)	30		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)		CACTGATTTCCGACTGTACCT	0.289																																					p.S82S		Atlas-SNP	.											CCDC110,rectum,carcinoma,0,1	CCDC110	78	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G246T						PASS	.						90	89	89					4																	186382305		2203	4296	6499	SO:0001819	synonymous_variant	256309	exon5			GATTTCCGACTGT	AB080722	CCDS3843.1, CCDS47170.1	4q35.1	2010-12-24			ENSG00000168491	ENSG00000168491			28504	protein-coding gene	gene with protein product	"cancer/testis antigen 52"	609488				18160854	Standard	NM_152775		Approved	KM-HN-1, MGC33607, CT52	uc003ixu.4	Q8TBZ0	OTTHUMG00000160415	ENST00000307588.3:c.246G>T	chr4.hg19:g.186382305C>A		97.0	1.0	.		171.0	8.0	.	NM_152775	Q86YI9|Q8N7W0	Silent	SNP	ENST00000307588.3	hg19	CCDS3843.1																																																																																			.	C|0.999;T|0.001	.	alt		0.289	CCDC110-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360519.2	NM_152775		A	186382305	C	A	186382305	2	1	173	1	0	0	0	0	0	0	0	1	2749	639	23	4		4	CCDC110	4	186382305	Silent	SNP	C	TCGA-G7-6795-01A-11D-1961-08	168795653	186382305	4771971	28	10112											
WDR70	55100	hgsc.bcm.edu	37	chr5	37381726	37381726	+	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	aaaaaagctcgcacatttgaCttggaagcaatgtttgaaca	16	10	8	7	1	0	2	0	2	0	0	1	3	0	3	0	1	3	4	0	1	6	3			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr5:37381726C>T	ENST00000265107.4	+	3	270	c.114C>T	c.(112-114)gaC>gaT	p.D38D	WDR70_ENST00000504564.1_Silent_p.D38D	NM_018034.2	NP_060504.1	Q9NW82	WDR70_HUMAN	WD repeat domain 70	38							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)			GCACATTTGACTTGGAAGCAA	0.378																																					p.D38D		Atlas-SNP	.											.	WDR70	76	.	0			c.C114T						PASS	.						119	127	124					5																	37381726		2203	4300	6503	SO:0001819	synonymous_variant	55100	exon3			ATTTGACTTGGAA	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.114C>T	chr5.hg19:g.37381726C>T		166.0	0.0	.		220.0	71.0	.	NM_018034	Q9H053	Silent	SNP	ENST00000265107.4	hg19	CCDS34147.1																																																																																			.	.	.	none		0.378	WDR70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368294.1	NM_018034		T	37381726	C	T	37381726	2	4	173	1	0	0	0	0	0	0	0	1	17333	564	20	2		2	WDR70	5	37381726	Silent	SNP	C	TCGA-G7-6795-01A-11D-1961-08		37381726	143533534	29	10113											
SLCO4C1	353189	hgsc.bcm.edu	37	chr5	101599479	101599479	+	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	taagattgacatagcataacCggttcctagaagaagaacag	17	8	9	7	1	0	5	0	1	0	4	1	5	1	5	2	1	3	2	2	1	7	6			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr5:101599479C>A	ENST00000310954.6	-	4	1094	c.808G>T	c.(808-810)Ggt>Tgt	p.G270C		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)		ATAGCATAACCGGTTCCTAGA	0.378																																					p.G270C		Atlas-SNP	.											.	SLCO4C1	113	.	0			c.G808T						PASS	.						129	121	123					5																	101599479		2203	4300	6503	SO:0001583	missense	353189	exon4			CATAACCGGTTCC	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.808G>T	chr5.hg19:g.101599479C>A	ENSP00000309741:p.Gly270Cys	131.0	0.0	.		137.0	9.0	.	NM_180991		Missense_Mutation	SNP	ENST00000310954.6	hg19	CCDS34205.1	.	.	.	.	.	.	.	.	.	.	C	14.68	2.607691	0.46527	.	.	ENSG00000173930	ENST00000310954	T	0.80824	-1.42	5.24	5.24	0.73138	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.085636	0.49916	D	0.000129	D	0.85283	0.5661	M	0.66506	2.035	0.38375	D	0.944971	P	0.34546	0.456	P	0.45946	0.498	D	0.85158	0.0990	10	0.39692	T	0.17	.	19.1822	0.93628	0.0:1.0:0.0:0.0	.	270	Q6ZQN7	SO4C1_HUMAN	C	270	ENSP00000309741:G270C	ENSP00000309741:G270C	G	-	1	0	SLCO4C1	101627378	1.000000	0.71417	1.000000	0.80357	0.021000	0.10359	5.387000	0.66243	2.598000	0.87819	0.650000	0.86243	GGT	.	.	.	none		0.378	SLCO4C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370332.1	NM_180991		A	101599479	C	A	101599479	3	1	173	1	0	0	0	0	1	0	0	0	14743	652	23	4	1406	4	SLCO4C1	5	101599479	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08	64217753	101599479	79315781	30	10114											
PSD2	84249	hgsc.bcm.edu	37	chr5	139216448	139216448	+	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	agctggtggatgacaagttcGggacaggcacgaagaaggtg	12	6	17	6	2	0	2	0	1	0	1	1	5	0	4	0	5	1	3	0	5	3	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr5:139216448G>T	ENST00000274710.3	+	10	1661	c.1456G>T	c.(1456-1458)Ggg>Tgg	p.G486W		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	486					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGACAAGTTCGGGACAGGCAC	0.602																																					p.G486W		Atlas-SNP	.											.	PSD2	88	.	0			c.G1456T						PASS	.						164	148	154					5																	139216448		2203	4300	6503	SO:0001583	missense	84249	exon10			AAGTTCGGGACAG	AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"Pleckstrin homology (PH) domain containing"	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.1456G>T	chr5.hg19:g.139216448G>T	ENSP00000274710:p.Gly486Trp	152.0	0.0	.		108.0	8.0	.	NM_032289	D3DQD3|Q8N3J8	Missense_Mutation	SNP	ENST00000274710.3	hg19	CCDS4216.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.470024	0.84533	.	.	ENSG00000146005	ENST00000274710	T	0.13307	2.6	5.37	5.37	0.77165	.	0.053535	0.85682	D	0.000000	T	0.30262	0.0759	L	0.53249	1.67	0.58432	D	0.999998	D	0.67145	0.996	P	0.59288	0.855	T	0.01030	-1.1475	10	0.87932	D	0	.	17.2612	0.87070	0.0:0.0:1.0:0.0	.	486	Q9BQI7	PSD2_HUMAN	W	486	ENSP00000274710:G486W	ENSP00000274710:G486W	G	+	1	0	PSD2	139196632	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	7.214000	0.77958	2.524000	0.85096	0.555000	0.69702	GGG	.	.	.	none		0.602	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289		T	139216448	G	T	139216448	3	4	173	1	0	0	0	0	1	0	0	0	12657	1116	39	4	1490	4	PSD2	5	139216448	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08	37616969	139216448	41698812	31	10115											
APBB3	10307	hgsc.bcm.edu	37	chr5	139938231	139938231	+	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	caagaaaagagaagacacccCgctttcgaggggttgcccct	12	6	11	12	2	0	3	0	0	0	3	1	5	0	3	4	2	1	2	4	2	4	2			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr5:139938231C>A	ENST00000357560.4	-	13	1843	c.1400G>T	c.(1399-1401)cGg>cTg	p.R467L	SRA1_ENST00000336283.6_5'Flank|SRA1_ENST00000520427.1_5'Flank|APBB3_ENST00000356738.2_Missense_Mutation_p.R472L|APBB3_ENST00000508496.2_Missense_Mutation_p.R244L|APBB3_ENST00000358580.5_3'UTR|APBB3_ENST00000354402.5_Missense_Mutation_p.R474L|APBB3_ENST00000412920.3_Missense_Mutation_p.R465L	NM_006051.3|NM_133173.2	NP_006042.3|NP_573419.2	O95704	APBB3_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 3	467						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAAGACACCCCGCTTTCGAGG	0.607																																					p.R474L		Atlas-SNP	.											APBB3,NS,carcinoma,0,1	APBB3	34	.	0			c.G1421T						PASS	.						76	84	81					5																	139938231		2203	4300	6503	SO:0001583	missense	10307	exon12			ACACCCCGCTTTC	AB018247	CCDS4227.1, CCDS4228.1, CCDS4229.1, CCDS47279.1	5q31	2008-02-05			ENSG00000113108	ENSG00000113108			20708	protein-coding gene	gene with protein product		602711				9407065	Standard	NM_133172		Approved	FE65L2	uc003lgd.1	O95704	OTTHUMG00000129504	ENST00000357560.4:c.1400G>T	chr5.hg19:g.139938231C>A	ENSP00000350171:p.Arg467Leu	163.0	0.0	.		132.0	8.0	.	NM_006051	B3KQN9|Q08AG4|Q96Q18|Q9BYD4|Q9NYX6|Q9NYX7|Q9NYX8	Missense_Mutation	SNP	ENST00000357560.4	hg19	CCDS4229.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.308074	0.81247	.	.	ENSG00000113108	ENST00000356738;ENST00000354402;ENST00000357560;ENST00000508496;ENST00000412920	T;T;T;T;T	0.51574	1.74;1.73;1.74;0.7;1.74	5.03	5.03	0.67393	.	0.151653	0.37906	N	0.001888	T	0.55065	0.1897	L	0.27053	0.805	0.80722	D	1	D;D	0.76494	0.995;0.999	P;D	0.83275	0.878;0.996	T	0.52132	-0.8616	9	.	.	.	-17.5903	15.2742	0.73728	0.0:1.0:0.0:0.0	.	465;472	O95704-2;O95704-3	.;.	L	472;474;467;244;465	ENSP00000349177:R472L;ENSP00000346378:R474L;ENSP00000350171:R467L;ENSP00000444013:R244L;ENSP00000402591:R465L	.	R	-	2	0	APBB3	139918415	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	3.647000	0.54403	2.350000	0.79820	0.455000	0.32223	CGG	.	.	.	none		0.607	APBB3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251677.2	NM_006051		A	139938231	C	A	139938231	3	1	173	1	0	0	0	0	1	0	0	0	762	652	23	4	64	4	APBB3	5	139938231	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08	721783	139938231	40977029	32	10116											
MDGA1	266727	hgsc.bcm.edu	37	chr6	37622577	37622577	+	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	gggaggaaaatgcctgtaccCgtggtgttggtgagccggaa	9	8	17	7	2	0	1	0	1	0	0	0	4	0	4	3	5	3	2	3	5	4	2			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr6:37622577C>A	ENST00000434837.3	-	5	1889	c.711G>T	c.(709-711)acG>acT	p.T237T	MDGA1_ENST00000505425.1_Splice_Site_p.T237T|MDGA1_ENST00000297153.7_Splice_Site_p.T237T	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	237					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)		p.T237T(1)		central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						TGCCTGTACCCGTGGTGTTGG	0.602																																					p.T237T		Atlas-SNP	.											MDGA1,NS,carcinoma,0,2	MDGA1	104	.	1	Substitution - coding silent(1)	lung(1)	c.G711T						PASS	.						214	225	222					6																	37622577		2169	4258	6427	SO:0001630	splice_region_variant	266727	exon5			TGTACCCGTGGTG	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.712+1G>T	chr6.hg19:g.37622577C>A		282.0	2.0	.		263.0	12.0	.	NM_153487	A6NHG0|Q8NBE3	Silent	SNP	ENST00000434837.3	hg19	CCDS47417.1																																																																																			.	.	.	none		0.602	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3		Silent	A	37622577	C	A	37622577	5	1	173	1	0	0	0	0	0	0	1	0	9413	666	23	4	2208	4	MDGA1	6	37622577	Splice_Site	SNP	C	TCGA-G7-6795-01A-11D-1961-08		37622577	133492490	33	10117											
TULP4	56995	hgsc.bcm.edu	37	chr6	158873218	158873218	+	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	aacatcaagcctctgctcacCgtcagcttcacctcgggaga	10	8	8	15	2	5	1	4	0	1	1	6	2	5	1	3	1	4	2	3	1	2	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr6:158873218C>A	ENST00000367097.3	+	5	2134	c.777C>A	c.(775-777)acC>acA	p.T259T	TULP4_ENST00000367094.2_Silent_p.T259T	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	259					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)	p.T259T(1)		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)		CTCTGCTCACCGTCAGCTTCA	0.537																																					p.T259T		Atlas-SNP	.											.	TULP4	137	.	1	Substitution - coding silent(1)	lung(1)	c.C777A						PASS	.						185	148	161					6																	158873218		2203	4300	6503	SO:0001819	synonymous_variant	56995	exon5			GCTCACCGTCAGC		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.777C>A	chr6.hg19:g.158873218C>A		169.0	0.0	.		153.0	7.0	.	NM_020245	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Silent	SNP	ENST00000367097.3	hg19	CCDS34561.1																																																																																			.	.	.	none		0.537	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245		A	158873218	C	A	158873218	2	1	173	1	0	0	0	0	0	0	0	1	16788	639	23	4		4	TULP4	6	158873218	Silent	SNP	C	TCGA-G7-6795-01A-11D-1961-08	121250641	158873218	12241849	34	10118											
SLC13A1	6561	hgsc.bcm.edu	37	chr7	122765636	122765636	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actcaaccaatttctcctgtAggtgtagttttagtcagtgt	9	16	8	8	0	3	0	2	0	1	0	4	0	3	0	2	1	1	3	2	1	5	5			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr7:122765636A>G	ENST00000194130.2	-	11	1266	c.1227T>C	c.(1225-1227)ccT>ccC	p.P409P	SLC13A1_ENST00000539873.1_3'UTR	NM_022444.3	NP_071889.2	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 1	409					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)	TTTCTCCTGTAGGTGTAGTTT	0.368																																					p.P409P		Atlas-SNP	.											.	SLC13A1	110	.	0			c.T1227C						PASS	.						123	129	127					7																	122765636		2203	4300	6503	SO:0001819	synonymous_variant	6561	exon11			TCCTGTAGGTGTA		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.1227T>C	chr7.hg19:g.122765636A>G		192.0	0.0	.		384.0	147.0	.	NM_022444	Q9H5Z0	Silent	SNP	ENST00000194130.2	hg19	CCDS5786.1																																																																																			.	.	.	none		0.368	SLC13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347404.1	NM_022444		G	122765636	A	G	122765636	2	3	173	1	0	0	0	0	0	0	0	1	14404	407	15	3		3	SLC13A1	7	122765636	Silent	SNP	A	TCGA-G7-6795-01A-11D-1961-08		122765636	36373027	35	10119											
AKR1B15	441282	hgsc.bcm.edu	37	chr7	134260255	134260255	+	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	ttccagatcgagaggctcttGaacaaacctggactgaaata	14	9	9	9	1	1	4	0	2	1	2	3	6	2	5	2	2	2	1	2	2	4	3			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr7:134260255G>T	ENST00000457545.2	+	7	857	c.597G>T	c.(595-597)ttG>ttT	p.L199F	AKR1B15_ENST00000423958.1_Missense_Mutation_p.L171F	NM_001080538.2	NP_001074007.2	C9JRZ8	AK1BF_HUMAN	aldo-keto reductase family 1, member B15	199							oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|urinary_tract(1)	18						AGAGGCTCTTGAACAAACCTG	0.463																																					p.L199F		Atlas-SNP	.											.	AKR1B15	105	.	0			c.G597T						PASS	.						71	77	75					7																	134260255		2203	4300	6503	SO:0001583	missense	441282	exon7			GCTCTTGAACAAA		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.597G>T	chr7.hg19:g.134260255G>T	ENSP00000389289:p.Leu199Phe	164.0	0.0	.		265.0	97.0	.	NM_001080538	C9J3V2	Missense_Mutation	SNP	ENST00000457545.2	hg19	CCDS47715.2	.	.	.	.	.	.	.	.	.	.	G	14.27	2.484711	0.44147	.	.	ENSG00000227471	ENST00000457545;ENST00000423958	T;T	0.21031	2.03;2.03	3.82	0.986	0.19784	NADP-dependent oxidoreductase domain (3);	.	.	.	.	T	0.42832	0.1220	M	0.80508	2.5	0.47308	D	0.999386	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.23619	-1.0183	9	0.87932	D	0	.	7.683	0.28524	0.2865:0.0:0.7135:0.0	.	171;199	C9JRZ8-2;C9JRZ8	.;AK1BF_HUMAN	F	199;171	ENSP00000389289:L199F;ENSP00000397009:L171F	ENSP00000397009:L171F	L	+	3	2	AKR1B15	133910795	0.998000	0.40836	0.832000	0.32986	0.573000	0.36030	0.344000	0.19962	-0.004000	0.14419	0.543000	0.68304	TTG	.	.	.	none		0.463	AKR1B15-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339726.2			T	134260255	G	T	134260255	3	4	173	1	0	0	0	0	1	0	0	0	468	1281	45	4	615	4	AKR1B15	7	134260255	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08	11494619	134260255	24878408	36	10120											
BMP1	649	hgsc.bcm.edu	37	chr8	22058658	22058658	+	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	gccagctctgcagccccctcGgggacgcccccaccagctca	6	4	10	21	2	2	0	1	0	1	0	3	1	2	1	6	2	4	3	6	2	0	0			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr8:22058658G>T	ENST00000306385.5	+	16	2777				BMP1_ENST00000354870.5_Intron|BMP1_ENST00000306349.8_Missense_Mutation_p.R712L	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1						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)	p.R712L(1)		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)		CAGCCCCCTCGGGGACGCCCC	0.627																																					p.R712L		Atlas-SNP	.											BMP1_ENST00000306349,NS,carcinoma,0,1	BMP1	131	.	1	Substitution - Missense(1)	lung(1)	c.G2135T						PASS	.						67	81	76					8																	22058658		2203	4300	6503	SO:0001627	intron_variant	649	exon16			CCCCTCGGGGACG		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.2108-658G>T	chr8.hg19:g.22058658G>T		221.0	2.0	.		165.0	7.0	.	NM_001199	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Missense_Mutation	SNP	ENST00000306385.5	hg19	CCDS6026.1	.	.	.	.	.	.	.	.	.	.	G	18.14	3.557340	0.65425	.	.	ENSG00000168487	ENST00000306349	T	0.61627	0.09	4.16	4.16	0.48862	.	.	.	.	.	T	0.38321	0.1036	N	0.08118	0	0.80722	D	1	P;P	0.37612	0.602;0.458	B;B	0.37780	0.258;0.192	T	0.46331	-0.9199	9	0.62326	D	0.03	.	11.9617	0.53011	0.0:0.0:1.0:0.0	.	785;712	Q59F71;P13497-2	.;.	L	712	ENSP00000306121:R712L	ENSP00000306121:R712L	R	+	2	0	BMP1	22114603	0.999000	0.42202	1.000000	0.80357	0.990000	0.78478	3.757000	0.55212	1.854000	0.53819	0.407000	0.27541	CGG	.	.	.	none		0.627	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132		T	22058658	G	T	22058658	1	4	173	0	1	0	0	0	0	0	0	0	1456	1116	39	4		4	BMP1	8	22058658	Intron	SNP	G	TCGA-G7-6795-01A-11D-1961-08		22058658	124305364	37	10121											
TPD52	7163	hgsc.bcm.edu	37	chr8	80963849	80963851	+	In_Frame_Del	DEL	GAT	GAT	-																															cagcctgggataaggtttcaGatgtcttcttgtaactatat																										TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	GAT	GAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr8:80963849_80963851delGAT	ENST00000379097.3	-	4	779_781	c.417_419delATC	c.(415-420)acatct>act	p.S140del	TPD52_ENST00000379096.5_In_Frame_Del_p.S100del|TPD52_ENST00000520527.1_In_Frame_Del_p.S140del|TPD52_ENST00000517427.1_In_Frame_Del_p.S140del|TPD52_ENST00000537855.1_In_Frame_Del_p.S140del|TPD52_ENST00000519303.2_5'UTR|TPD52_ENST00000518937.1_In_Frame_Del_p.S100del|TPD52_ENST00000523395.1_5'Flank|TPD52_ENST00000448733.2_In_Frame_Del_p.S140del	NM_001025252.1	NP_001020423.1	P55327	TPD52_HUMAN	tumor protein D52	140					anatomical structure morphogenesis (GO:0009653)|B cell differentiation (GO:0030183)|positive regulation of cell proliferation (GO:0008284)|secretion (GO:0046903)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	8	all_epithelial(4;1.13e-09)|Lung NSC(7;9.71e-07)|all_lung(9;3.75e-06)	Lung NSC(129;3.55e-06)|all_lung(136;1.53e-05)|Acute lymphoblastic leukemia(644;0.158)	BRCA - Breast invasive adenocarcinoma(6;0.00181)|Epithelial(68;0.0149)|all cancers(69;0.0612)			TAAGGTTTCAGATGTCTTCTTGT	0.404																																					p.140_140del		Atlas-INDEL	.											.	TPD52	40	.	0			c.418_420del						PASS	.																																			SO:0001651	inframe_deletion	7163	exon4			.	U18914	CCDS34912.1, CCDS47879.1, CCDS55249.1, CCDS75757.1, CCDS75758.1, CCDS75759.1	8q21.13	2014-06-24			ENSG00000076554	ENSG00000076554			12005	protein-coding gene	gene with protein product		604068				7796418	Standard	NM_001287144		Approved	D52, hD52, N8L	uc003ybr.1	P55327	OTTHUMG00000164565	ENST00000379097.3:c.417_419delATC	chr8.hg19:g.80963849_80963851delGAT	ENSP00000368391:p.Ser140del	74.0	0.0	0		75.0	26.0	0.346667	NM_001025252	B7Z414|C9J502|D0UFD1|D0UFD2|D0UFD3|D0UFD4|D0UFD5|E5RKB4|Q13056|Q53EK8|Q6FGP3|Q6FGS3|Q86YZ2|Q9UCX8	In_Frame_Del	DEL	ENST00000379097.3	hg19	CCDS34912.1																																																																																			.	.	.	none		0.404	TPD52-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379539.2	NM_005079		-	80963851	GAT	-	80963849	7	5	173	1	0	1	0	1	0	0	0	0	16409	942	33	0	344	0	TPD52	8	80963849	In_Frame_Del	DEL	GAT	TCGA-G7-6795-01A-11D-1961-08	58905191	80963849	65400173	38	10122											
OXR1	55074	hgsc.bcm.edu	37	chr8	107718929	107718929	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctactggtactcctggtcacTtaagatctgatactgaacat	11	13	7	10	0	2	3	1	2	1	1	3	3	3	3	1	2	4	1	1	2	5	4			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr8:107718929T>C	ENST00000442977.2	+	8	1282	c.1183T>C	c.(1183-1185)Tta>Cta	p.L395L	OXR1_ENST00000312046.6_Silent_p.L387L|OXR1_ENST00000445937.1_Silent_p.L394L|OXR1_ENST00000452423.2_5'UTR|OXR1_ENST00000531443.1_Silent_p.L394L|OXR1_ENST00000517566.2_Silent_p.L394L|OXR1_ENST00000497705.1_Silent_p.L327L	NM_001198532.1	NP_001185461.1	Q8N573	OXR1_HUMAN	oxidation resistance 1	395					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)			TCCTGGTCACTTAAGATCTGA	0.368																																					p.L395L		Atlas-SNP	.											.	OXR1	190	.	0			c.T1183C						PASS	.						86	89	88					8																	107718929		2203	4300	6503	SO:0001819	synonymous_variant	55074	exon8			GGTCACTTAAGAT	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.1183T>C	chr8.hg19:g.107718929T>C		63.0	0.0	.		71.0	19.0	.	NM_001198532	A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7	Silent	SNP	ENST00000442977.2	hg19	CCDS56548.1																																																																																			.	.	.	none		0.368	OXR1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_181354		C	107718929	T	C	107718929	2	2	173	1	0	0	0	0	0	0	0	1	11341	1606	56	3		3	OXR1	8	107718929	Silent	SNP	T	TCGA-G7-6795-01A-11D-1961-08	26755080	107718929	38645093	39	10123											
COL22A1	169044	hgsc.bcm.edu	37	chr8	139737673	139737673	+	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	ggcctgggacaccagggggtCctggagggccctgtagagaa	8	5	18	10	0	0	1	0	0	0	1	1	4	1	3	4	6	0	1	4	6	2	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr8:139737673C>T	ENST00000303045.6	-	24	2596	c.2150G>A	c.(2149-2151)gGa>gAa	p.G717E	COL22A1_ENST00000435777.1_Missense_Mutation_p.G717E	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	717	Collagen-like 5.|Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			ACCAGGGGGTCCTGGAGGGCC	0.582										HNSCC(7;0.00092)																											p.G717E		Atlas-SNP	.											COL22A1,NS,carcinoma,0,1	COL22A1	390	.	0			c.G2150A						PASS	.						50	57	55					8																	139737673		2203	4300	6503	SO:0001583	missense	169044	exon24			GGGGGTCCTGGAG	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.2150G>A	chr8.hg19:g.139737673C>T	ENSP00000303153:p.Gly717Glu	131.0	0.0	.		127.0	44.0	.	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	hg19	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	C	16.16	3.043885	0.55110	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.99353	-5.77;-5.14	4.8	4.8	0.61643	.	0.000000	0.49305	D	0.000157	D	0.99722	0.9892	H	0.99719	4.725	0.52099	D	0.999949	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.96966	0.9705	10	0.87932	D	0	.	14.0818	0.64929	0.0:1.0:0.0:0.0	.	717;717	Q8NFW1-2;Q8NFW1	.;COMA1_HUMAN	E	717;717;430	ENSP00000303153:G717E;ENSP00000387655:G717E	ENSP00000303153:G717E	G	-	2	0	COL22A1	139806855	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	3.436000	0.52856	2.567000	0.86603	0.655000	0.94253	GGA	.	.	.	none		0.582	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		T	139737673	C	T	139737673	3	4	173	1	0	0	0	0	1	0	0	0	3683	855	30	2	2898	2	COL22A1	8	139737673	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08	32018744	139737673	6626349	40	10124											
KIAA0020	9933	hgsc.bcm.edu	37	chr9	2811557	2811557	+	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	aaatggattctaggagctccCgtctgcggacctctgtatct	8	12	10	11	2	4	0	0	0	4	0	5	3	5	3	2	3	2	2	2	3	3	3	rs2270889	byFrequency	TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr9:2811557C>A	ENST00000397885.2	-	15	1645	c.1439G>T	c.(1438-1440)cGg>cTg	p.R480L		NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	480	PUM-HD. {ECO:0000255|PROSITE- ProRule:PRU00318}.		R -> Q (in dbSNP:rs2270889).			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)		TAGGAGCTCCCGTCTGCGGAC	0.438																																					p.R480L		Atlas-SNP	.											.	KIAA0020	56	.	0			c.G1439T						PASS	.						99	97	98					9																	2811557		2203	4300	6503	SO:0001583	missense	9933	exon15			AGCTCCCGTCTGC	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.1439G>T	chr9.hg19:g.2811557C>A	ENSP00000380982:p.Arg480Leu	150.0	0.0	.		140.0	7.0	.	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Missense_Mutation	SNP	ENST00000397885.2	hg19	CCDS6448.2	.	.	.	.	.	.	.	.	.	.	C	17.99	3.523165	0.64747	.	.	ENSG00000080608	ENST00000397885	T	0.45668	0.89	5.97	4.9	0.64082	CPL (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.246724	0.42420	D	0.000701	T	0.37404	0.1002	L	0.48642	1.525	0.09310	N	1	B;P	0.38582	0.322;0.638	B;B	0.40741	0.258;0.339	T	0.29518	-1.0009	10	0.36615	T	0.2	-23.6222	10.0978	0.42486	0.0:0.8152:0.0:0.1848	.	340;480	B2RDG4;Q15397	.;K0020_HUMAN	L	480	ENSP00000380982:R480L	ENSP00000380982:R480L	R	-	2	0	KIAA0020	2801557	0.006000	0.16342	0.339000	0.25562	0.986000	0.74619	0.406000	0.21032	2.836000	0.97738	0.655000	0.94253	CGG	.	C|0.996;T|0.004	.	alt		0.438	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878		A	2811557	C	A	2811557	3	1	173	1	0	0	0	0	1	0	0	0	8159	652	23	4	523	4	KIAA0020	9	2811557	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08		2811557	138401874	41	10125											
ADD3	120	hgsc.bcm.edu	37	chr10	111860443	111860443	+	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	tgccagccaaggcgtgattaCcactcctcctcctcccagca	8	8	7	18	1	0	1	0	1	0	0	4	1	4	1	7	1	4	1	7	1	2	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr10:111860443C>G	ENST00000356080.4	+	2	399	c.32C>G	c.(31-33)aCc>aGc	p.T11S	ADD3_ENST00000497125.1_3'UTR|ADD3_ENST00000360162.3_Missense_Mutation_p.T11S|ADD3_ENST00000277900.8_Missense_Mutation_p.T11S	NM_016824.3	NP_058432.1	Q9UEY8	ADDG_HUMAN	adducin 3 (gamma)	11						cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	29		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)		GGCGTGATTACCACTCCTCCT	0.418																																					p.T11S		Atlas-SNP	.											.	ADD3	89	.	0			c.C32G						PASS	.						84	70	74					10																	111860443		2203	4300	6503	SO:0001583	missense	120	exon2			TGATTACCACTCC	U37122	CCDS7561.1, CCDS7562.1	10q25.2	2005-11-08			ENSG00000148700	ENSG00000148700			245	protein-coding gene	gene with protein product		601568		ADDL		8893809	Standard	XM_005269529		Approved		uc001kyv.3	Q9UEY8	OTTHUMG00000019032	ENST00000356080.4:c.32C>G	chr10.hg19:g.111860443C>G	ENSP00000348381:p.Thr11Ser	77.0	0.0	.		72.0	28.0	.	NM_001121	D3DRA8|O43243|Q5VU09|Q92773|Q9UEY7	Missense_Mutation	SNP	ENST00000356080.4	hg19	CCDS7561.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.165457	0.78339	.	.	ENSG00000148700	ENST00000360162;ENST00000356080;ENST00000277900	T;T;T	0.30714	1.52;1.52;1.52	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.47377	0.1442	M	0.76838	2.35	0.80722	D	1	P;B	0.51653	0.947;0.383	P;B	0.48400	0.576;0.155	T	0.32107	-0.9919	10	0.30078	T	0.28	-16.68	20.6397	0.99537	0.0:1.0:0.0:0.0	.	11;11	Q9UEY8;Q9UEY8-2	ADDG_HUMAN;.	S	11	ENSP00000353286:T11S;ENSP00000348381:T11S;ENSP00000277900:T11S	ENSP00000277900:T11S	T	+	2	0	ADD3	111850433	1.000000	0.71417	0.988000	0.46212	0.954000	0.61252	7.481000	0.81124	2.880000	0.98712	0.650000	0.86243	ACC	.	.	.	none		0.418	ADD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050289.1	NM_019903		G	111860443	C	G	111860443	3	3	173	1	0	0	0	0	1	0	0	0	306	507	18	4	34	4	ADD3	10	111860443	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08		111860443	23674304	42	10126											
MRVI1	10335	hgsc.bcm.edu	37	chr11	10647666	10647666	+	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	ttggcaagcactttctgcagCcgggggccaggttcttcagg	6	10	14	11	1	3	0	1	0	2	0	3	0	3	0	2	5	3	4	2	5	1	4			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr11:10647666C>G	ENST00000436272.1	-	8	1212	c.1134G>C	c.(1132-1134)cgG>cgC	p.R378R	MRVI1_ENST00000547195.1_Silent_p.R314R|MRVI1_ENST00000534266.2_Silent_p.R90R|MRVI1_ENST00000424001.1_Silent_p.R90R|MRVI1_ENST00000423302.2_Silent_p.R405R|MRVI1_ENST00000527509.2_Silent_p.R314R|MRVI1_ENST00000531107.1_Silent_p.R397R|MRVI1_ENST00000558540.1_Silent_p.R90R|MRVI1_ENST00000552103.1_Silent_p.R314R|MRVI1_ENST00000545852.1_Silent_p.R90R|MRVI1_ENST00000421747.1_Silent_p.R396R|MRVI1_ENST00000541483.1_Intron			Q9Y6F6	MRVI1_HUMAN	murine retrovirus integration site 1 homolog	378					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)		CTTTCTGCAGCCGGGGGCCAG	0.647																																					p.R405R		Atlas-SNP	.											.	MRVI1	113	.	0			c.G1215C						PASS	.						16	18	18					11																	10647666		1874	4079	5953	SO:0001819	synonymous_variant	10335	exon9			CTGCAGCCGGGGG	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.1134G>C	chr11.hg19:g.10647666C>G		42.0	0.0	.		30.0	11.0	.	NM_130385	B7Z3T4|B7Z6I2|B7Z9A3|E9PQY6|F5H6A1|J3KQZ7|Q17S00|Q9UNY1	Silent	SNP	ENST00000436272.1	hg19																																																																																				.	.	.	none		0.647	MRVI1-203	KNOWN	basic	protein_coding	protein_coding		NM_001098579		G	10647666	C	G	10647666	2	3	173	1	0	0	0	0	0	0	0	1	9860	726	26	4		4	MRVI1	11	10647666	Silent	SNP	C	TCGA-G7-6795-01A-11D-1961-08		10647666	124358850	43	10127											
HPS5	11234	hgsc.bcm.edu	37	chr11	18309441	18309441	+	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	aatatacaggacaacttaccGggtagcataaacaaccaaca	19	6	6	10	1	0	0	0	0	0	0	0	1	0	1	2	2	7	2	2	2	10	5			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr11:18309441G>A	ENST00000349215.3	-	17	2837	c.2560C>T	c.(2560-2562)Cgg>Tgg	p.R854W	HPS5_ENST00000537258.1_5'Flank|HPS5_ENST00000396253.3_Splice_Site_p.R740W|HPS5_ENST00000352460.3_5'UTR|HPS5_ENST00000438420.2_Splice_Site_p.R740W	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	854					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						ACAACTTACCGGGTAGCATAA	0.363									Hermansky-Pudlak syndrome																												p.R854W		Atlas-SNP	.											.	HPS5	70	.	0			c.C2560T						PASS	.						140	122	129					11																	18309441		2199	4293	6492	SO:0001630	splice_region_variant	11234	exon17	Familial Cancer Database	HPS, HPS1-8	CTTACCGGGTAGC	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.2561+1C>T	chr11.hg19:g.18309441G>A		53.0	0.0	.		53.0	24.0	.	NM_181507	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Missense_Mutation	SNP	ENST00000349215.3	hg19	CCDS7836.1	.	.	.	.	.	.	.	.	.	.	G	14.03	2.415187	0.42817	.	.	ENSG00000110756	ENST00000396253;ENST00000438420;ENST00000349215;ENST00000544218	D;D;D;D	0.88046	-2.33;-2.33;-2.33;-2.33	5.36	-0.639	0.11497	.	0.091394	0.85682	D	0.000000	D	0.90017	0.6883	M	0.66939	2.045	0.48830	D	0.999711	D	0.76494	0.999	D	0.65443	0.935	D	0.88319	0.2961	10	0.87932	D	0	.	10.3165	0.43740	0.0768:0.0:0.2154:0.7078	.	854	Q9UPZ3	HPS5_HUMAN	W	740;740;854;40	ENSP00000379552:R740W;ENSP00000399590:R740W;ENSP00000265967:R854W;ENSP00000441781:R40W	ENSP00000265967:R854W	R	-	1	2	HPS5	18266017	0.959000	0.32827	0.725000	0.30721	0.174000	0.22865	1.548000	0.36201	-0.008000	0.14320	-0.475000	0.04921	CGG	.	.	.	none		0.363	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507	Missense_Mutation	A	18309441	G	A	18309441	5	1	173	1	0	0	0	0	0	0	1	0	7349	1130	39	1	857	1	HPS5	11	18309441	Splice_Site	SNP	G	TCGA-G7-6795-01A-11D-1961-08	7661775	18309441	116697075	44	10128											
OR5M8	219484	hgsc.bcm.edu	37	chr11	56258788	56258788	+	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	agaggagaatttgtaattccCggcgactggtcagtcccagg	10	9	13	9	2	1	2	1	0	0	2	3	4	3	2	2	4	0	1	2	4	2	3	rs574852072	byFrequency	TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr11:56258788C>A	ENST00000327216.2	-	1	83	c.59G>T	c.(58-60)cGg>cTg	p.R20L		NM_001005282.1	NP_001005282.1	Q8NGP6	OR5M8_HUMAN	olfactory receptor, family 5, subfamily M, member 8	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(3)|kidney(3)|large_intestine(4)|lung(22)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	Esophageal squamous(21;0.00352)					TTGTAATTCCCGGCGACTGGT	0.483																																					p.R20L		Atlas-SNP	.											OR5M8,caecum,carcinoma,0,1	OR5M8	74	.	0			c.G59T						PASS	.						80	85	83					11																	56258788		2201	4296	6497	SO:0001583	missense	219484	exon1			AATTCCCGGCGAC	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.59G>T	chr11.hg19:g.56258788C>A	ENSP00000323354:p.Arg20Leu	134.0	1.0	.		131.0	7.0	.	NM_001005282	B2RNM5|Q6IEW3|Q96RB8	Missense_Mutation	SNP	ENST00000327216.2	hg19	CCDS31533.1	.	.	.	.	.	.	.	.	.	.	C	9.468	1.094793	0.20471	.	.	ENSG00000181371	ENST00000327216	T	0.00421	7.46	4.13	-7.18	0.01505	.	1.292630	0.06259	N	0.693636	T	0.00178	0.0005	N	0.05280	-0.08	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.39683	-0.9602	10	0.51188	T	0.08	0.1659	3.5083	0.07699	0.209:0.2522:0.4222:0.1166	.	20	Q8NGP6	OR5M8_HUMAN	L	20	ENSP00000323354:R20L	ENSP00000323354:R20L	R	-	2	0	OR5M8	56015364	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.691000	0.00198	-1.486000	0.01851	-1.292000	0.01352	CGG	.	.	.	none		0.483	OR5M8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391641.1	NM_001005282		A	56258788	C	A	56258788	3	1	173	1	0	0	0	0	1	0	0	0	11183	652	23	4	880	4	OR5M8	11	56258788	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08	37949347	56258788	78747728	45	10129											
NPAT	4863	hgsc.bcm.edu	37	chr11	108032024	108032024	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccggggcacaggtaaatcActactatcagcaagcctact	12	8	9	12	1	2	0	2	0	0	0	3	0	3	0	2	3	4	3	2	3	6	4			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr11:108032024A>G	ENST00000278612.8	-	17	3894	c.3789T>C	c.(3787-3789)agT>agC	p.S1263S		NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	1263					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)		CAGGTAAATCACTACTATCAG	0.443																																					p.S1263S		Atlas-SNP	.											.	NPAT	124	.	0			c.T3789C						PASS	.						107	105	106					11																	108032024		1852	4092	5944	SO:0001819	synonymous_variant	4863	exon17			TAAATCACTACTA	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.3789T>C	chr11.hg19:g.108032024A>G		164.0	0.0	.		132.0	54.0	.	NM_002519	A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	Silent	SNP	ENST00000278612.8	hg19	CCDS41710.1	.	.	.	.	.	.	.	.	.	.	A	0.009	-1.813585	0.00600	.	.	ENSG00000149308	ENST00000527296	.	.	.	3.92	-3.71	0.04424	.	.	.	.	.	T	0.35970	0.0950	.	.	.	0.44275	D	0.997137	.	.	.	.	.	.	T	0.37197	-0.9716	4	.	.	.	-0.1192	0.4805	0.00547	0.1833:0.2475:0.2586:0.3106	.	.	.	.	A	262	.	.	V	-	2	0	NPAT	107537234	0.001000	0.12720	0.012000	0.15200	0.023000	0.10783	-0.273000	0.08548	-0.420000	0.07427	-0.256000	0.11100	GTG	.	.	.	none		0.443	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389506.2	NM_002519		G	108032024	A	G	108032024	2	3	173	1	0	0	0	0	0	0	0	1	10573	156	6	3		3	NPAT	11	108032024	Silent	SNP	A	TCGA-G7-6795-01A-11D-1961-08	51773236	108032024	26974492	46	10130											
IGSF9B	22997	hgsc.bcm.edu	37	chr11	133790126	133790126	+	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	cataccaccgggtgtccaggCcaaatgtgctggggccgccg	7	6	14	14	3	0	0	0	0	0	0	1	0	1	0	6	4	2	1	6	4	2	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr11:133790126C>A	ENST00000321016.8	-	18	3724	c.3494G>T	c.(3493-3495)gGc>gTc	p.G1165V	IGSF9B_ENST00000533871.2_Missense_Mutation_p.G1165V			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	1165	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)		GGTGTCCAGGCCAAATGTGCT	0.692																																					p.G1165V		Atlas-SNP	.											.	IGSF9B	290	.	0			c.G3494T						PASS	.						30	34	33					11																	133790126		1905	4106	6011	SO:0001583	missense	22997	exon18			TCCAGGCCAAATG	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.3494G>T	chr11.hg19:g.133790126C>A	ENSP00000317980:p.Gly1165Val	108.0	0.0	.		99.0	39.0	.	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	hg19		.	.	.	.	.	.	.	.	.	.	C	15.82	2.946783	0.53186	.	.	ENSG00000080854	ENST00000321016;ENST00000533871	T;T	0.65364	0.18;-0.15	5.08	5.08	0.68730	.	0.000000	0.45606	D	0.000349	T	0.50205	0.1602	N	0.19112	0.55	0.58432	D	0.999991	P	0.35774	0.519	B	0.34418	0.182	T	0.57225	-0.7848	10	0.62326	D	0.03	.	18.0591	0.89371	0.0:1.0:0.0:0.0	.	1165	Q9UPX0	TUTLB_HUMAN	V	1165;1007	ENSP00000317980:G1165V;ENSP00000436552:G1007V	ENSP00000317980:G1165V	G	-	2	0	IGSF9B	133295336	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.261000	0.65496	2.358000	0.79984	0.455000	0.32223	GGC	.	.	.	none		0.692	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		A	133790126	C	A	133790126	3	1	173	1	0	0	0	0	1	0	0	0	7613	739	26	4	563	4	IGSF9B	11	133790126	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08	25758102	133790126	1216390	47	10131											
IGSF9B	22997	hgsc.bcm.edu	37	chr11	133794760	133794760	+	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	gctgggctcgctgatcagatCctgcatgacggccagaaccc	8	7	12	14	2	1	4	1	2	0	2	3	4	2	4	3	2	2	4	3	2	1	0			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr11:133794760C>T	ENST00000321016.8	-	15	2304	c.2074G>A	c.(2074-2076)Gat>Aat	p.D692N	IGSF9B_ENST00000533871.2_Missense_Mutation_p.D692N			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	692	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		CTGATCAGATCCTGCATGACG	0.587																																					p.D692N		Atlas-SNP	.											.	IGSF9B	290	.	0			c.G2074A						PASS	.						114	123	120					11																	133794760		2090	4217	6307	SO:0001583	missense	22997	exon15			TCAGATCCTGCAT	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.2074G>A	chr11.hg19:g.133794760C>T	ENSP00000317980:p.Asp692Asn	239.0	0.0	.		174.0	55.0	.	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	hg19		.	.	.	.	.	.	.	.	.	.	C	34	5.382681	0.95967	.	.	ENSG00000080854	ENST00000321016;ENST00000533871;ENST00000527648	T;T;T	0.56941	0.43;0.43;0.43	5.02	5.02	0.67125	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.41500	D	0.000871	T	0.64505	0.2604	L	0.46157	1.445	0.53005	D	0.999967	P	0.42518	0.782	P	0.56278	0.795	T	0.62353	-0.6872	10	0.42905	T	0.14	.	18.7177	0.91682	0.0:1.0:0.0:0.0	.	692	Q9UPX0	TUTLB_HUMAN	N	692;534;692	ENSP00000317980:D692N;ENSP00000436552:D534N;ENSP00000436576:D692N	ENSP00000317980:D692N	D	-	1	0	IGSF9B	133299970	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.637000	0.83313	2.493000	0.84123	0.655000	0.94253	GAT	.	.	.	none		0.587	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		T	133794760	C	T	133794760	3	4	173	1	0	0	0	0	1	0	0	0	7613	855	30	2	1995	2	IGSF9B	11	133794760	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08	4634	133794760	1211756	48	10132											
NACA	4666	hgsc.bcm.edu	37	chr12	57114205	57114205	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccactggaaaggcagccacaGtagcaggaactacctcattt	13	7	9	12	0	1	0	1	0	0	0	1	2	1	2	3	3	4	3	3	3	4	3			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr12:57114205G>A	ENST00000454682.1	-	3	1390	c.1109C>T	c.(1108-1110)aCt>aTt	p.T370I	NACA_ENST00000548563.1_Intron|NACA_ENST00000550952.1_Missense_Mutation_p.T370I|NACA_ENST00000551793.1_Intron|NACA_ENST00000546392.1_Intron|NACA_ENST00000356769.3_Intron|NACA_ENST00000552540.1_Intron|NACA_ENST00000393891.4_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	370	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						GGCAGCCACAGTAGCAGGAAC	0.488			T	BCL6	NHL																																p.T370I		Atlas-SNP	.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	NACA_ENST00000550952,NS,carcinoma,0,2	NACA	131	.	0			c.C1109T						PASS	.						60	55	56					12																	57114205		1568	3582	5150	SO:0001583	missense	4666	exon3			GCCACAGTAGCAG	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.1109C>T	chr12.hg19:g.57114205G>A	ENSP00000403817:p.Thr370Ile	42.0	0.0	.		46.0	27.0	.	NM_001113203		Missense_Mutation	SNP	ENST00000454682.1	hg19		.	.	.	.	.	.	.	.	.	.	G	14.65	2.598833	0.46318	.	.	ENSG00000196531	ENST00000454682;ENST00000550952	T;T	0.47869	0.83;0.9	3.29	3.29	0.37713	.	.	.	.	.	T	0.23171	0.0560	N	0.08118	0	0.09310	N	1	P;B	0.38978	0.652;0.358	B;B	0.30943	0.122;0.117	T	0.03750	-1.1007	9	0.26408	T	0.33	.	10.4563	0.44553	0.0:0.0:1.0:0.0	.	370;370	E9PAV3;F8VU71	.;.	I	370	ENSP00000403817:T370I;ENSP00000448035:T370I	ENSP00000403817:T370I	T	-	2	0	NACA	55400472	0.001000	0.12720	0.018000	0.16275	0.537000	0.34900	0.083000	0.14871	1.569000	0.49696	0.306000	0.20318	ACT	.	.	.	none		0.488	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594		A	57114205	G	A	57114205	3	1	173	1	0	0	0	0	1	0	0	0	10140	1029	36	2	5155	2	NACA	12	57114205	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08		57114205	76737690	49	10133											
MBD6	114785	hgsc.bcm.edu	37	chr12	57918527	57918527	+	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	agtggcacagagctgtcttcCttggagcaaacccggagcta	10	8	12	11	1	1	1	0	0	1	1	2	3	2	3	2	3	4	4	2	3	2	3			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr12:57918527C>A	ENST00000355673.3	+	4	494	c.138C>A	c.(136-138)tcC>tcA	p.S46S	MBD6_ENST00000431731.2_Silent_p.S46S|MBD6_ENST00000549231.1_3'UTR	NM_052897.3	NP_443129.3	Q96DN6	MBD6_HUMAN	methyl-CpG binding domain protein 6	46	MBD. {ECO:0000255|PROSITE- ProRule:PRU00338}.					chromocenter (GO:0010369)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|urinary_tract(1)	31						AGCTGTCTTCCTTGGAGCAAA	0.572																																					p.S46S		Atlas-SNP	.											.	MBD6	99	.	0			c.C138A						PASS	.						83	76	78					12																	57918527		2203	4300	6503	SO:0001819	synonymous_variant	114785	exon4			GTCTTCCTTGGAG	AB067474	CCDS8944.1	12q13.2	2008-02-05				ENSG00000166987			20445	protein-coding gene	gene with protein product						12529184	Standard	NM_052897		Approved	KIAA1887	uc001soj.1	Q96DN6		ENST00000355673.3:c.138C>A	chr12.hg19:g.57918527C>A		106.0	0.0	.		132.0	45.0	.	NM_052897	Q8N3M0|Q8NA81|Q96Q00	Silent	SNP	ENST00000355673.3	hg19	CCDS8944.1																																																																																			.	.	.	none		0.572	MBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407250.1			A	57918527	C	A	57918527	2	1	173	1	0	0	0	0	0	0	0	1	9355	668	24	4		4	MBD6	12	57918527	Silent	SNP	C	TCGA-G7-6795-01A-11D-1961-08	804322	57918527	75933368	50	10134											
CCDC70	83446	hgsc.bcm.edu	37	chr13	52439890	52439890	+	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	aaactttctggaaaaagtacCgcactttctggaaggaggat	14	10	10	7	1	2	0	0	0	2	0	2	4	2	4	1	4	2	2	1	4	5	3	rs17076052	byFrequency	TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr13:52439890C>A	ENST00000242819.4	+	2	672	c.376C>A	c.(376-378)Cgc>Agc	p.R126S		NM_031290.2	NP_112580.2	Q6NSX1	CCD70_HUMAN	coiled-coil domain containing 70	126			R -> C (in dbSNP:rs17076052).			extracellular region (GO:0005576)|plasma membrane (GO:0005886)				breast(1)|large_intestine(4)|lung(7)|skin(2)|urinary_tract(1)	15		Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.0107)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;2.4e-08)		GAAAAAGTACCGCACTTTCTG	0.468																																					p.R126S		Atlas-SNP	.											.	CCDC70	31	.	0			c.C376A						PASS	.						111	125	120					13																	52439890		2203	4300	6503	SO:0001583	missense	83446	exon2			AAGTACCGCACTT		CCDS9431.1	13q14.3	2006-02-07			ENSG00000123171	ENSG00000123171			25303	protein-coding gene	gene with protein product						11230166	Standard	NM_031290		Approved	DKFZP434K1172, FLJ25853	uc001vfu.4	Q6NSX1	OTTHUMG00000016950	ENST00000242819.4:c.376C>A	chr13.hg19:g.52439890C>A	ENSP00000242819:p.Arg126Ser	236.0	0.0	.		286.0	14.0	.	NM_031290	Q8N7A8|Q9H097	Missense_Mutation	SNP	ENST00000242819.4	hg19	CCDS9431.1	.	.	.	.	.	.	.	.	.	.	C	4.364	0.067073	0.08388	.	.	ENSG00000123171	ENST00000242819	T	0.21543	2.0	5.93	-0.542	0.11854	.	0.271361	0.25723	N	0.028737	T	0.18087	0.0434	M	0.65975	2.015	0.80722	P	0.0	P	0.35844	0.524	B	0.28465	0.09	T	0.16482	-1.0401	9	0.33940	T	0.23	-18.1723	11.3004	0.49302	0.6742:0.2599:0.0:0.0659	.	126	Q6NSX1	CCD70_HUMAN	S	126	ENSP00000242819:R126S	ENSP00000242819:R126S	R	+	1	0	CCDC70	51337891	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.113000	0.10774	-0.486000	0.06744	-2.156000	0.00330	CGC	.	C|0.927;T|0.073	.	alt		0.468	CCDC70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045033.2	NM_031290		A	52439890	C	A	52439890	3	1	173	1	0	0	0	0	1	0	0	0	2845	652	23	4	378	4	CCDC70	13	52439890	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08		52439890	62729988	51	10135											
UBR1	197131	hgsc.bcm.edu	37	chr15	43299382	43299382	+	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	ttctattttcacctcctgttCttcttggcaaaggatgcacg	7	16	7	11	1	4	0	1	0	3	0	5	1	5	1	2	2	1	3	2	2	2	7			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr15:43299382C>T	ENST00000290650.4	-	30	3388	c.3310G>A	c.(3310-3312)Gaa>Aaa	p.E1104K	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	1104					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)		ACCTCCTGTTCTTCTTGGCAA	0.473																																					p.E1104K		Atlas-SNP	.											.	UBR1	124	.	0			c.G3310A						PASS	.						128	115	119					15																	43299382		2203	4299	6502	SO:0001583	missense	197131	exon30			CCTGTTCTTCTTG		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.3310G>A	chr15.hg19:g.43299382C>T	ENSP00000290650:p.Glu1104Lys	121.0	0.0	.		137.0	49.0	.	NM_174916	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	hg19	CCDS10091.1	.	.	.	.	.	.	.	.	.	.	C	34	5.388214	0.95988	.	.	ENSG00000159459	ENST00000290650	T	0.55760	0.5	4.99	4.99	0.66335	Zinc finger, RING/FYVE/PHD-type (1);	0.050391	0.85682	D	0.000000	T	0.71829	0.3386	M	0.71206	2.165	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.71066	-0.4700	10	0.40728	T	0.16	-8.6741	18.4574	0.90725	0.0:1.0:0.0:0.0	.	1104	Q8IWV7	UBR1_HUMAN	K	1104	ENSP00000290650:E1104K	ENSP00000290650:E1104K	E	-	1	0	UBR1	41086674	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.320000	0.79064	2.593000	0.87608	0.655000	0.94253	GAA	.	.	.	none		0.473	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916		T	43299382	C	T	43299382	3	4	173	1	0	0	0	0	1	0	0	0	16913	922	32	2	2011	2	UBR1	15	43299382	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08		43299382	59232010	52	10136											
PKD1	5310	hgsc.bcm.edu	37	chr16	2155892	2155892	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagcacggtgaccagggccaAcgagtactcgatgacgtgct	10	6	13	12	4	0	2	0	2	0	0	1	4	0	2	2	2	4	3	2	2	2	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr16:2155892A>G	ENST00000262304.4	-	20	8045	c.7837T>C	c.(7837-7839)Ttg>Ctg	p.L2613L	PKD1_ENST00000423118.1_Silent_p.L2613L|PKD1_ENST00000561991.1_5'UTR	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	2613	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.		Missing (in PKD1; unknown pathological significance). {ECO:0000269|PubMed:11571556}.		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)	p.L2613L(1)		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						ACCAGGGCCAACGAGTACTCG	0.657																																					p.L2613L		Atlas-SNP	.											PKD1,NS,carcinoma,0,1	PKD1	184	.	1	Substitution - coding silent(1)	lung(1)	c.T7837C						PASS	.						46	45	45					16																	2155892		1400	2465	3865	SO:0001819	synonymous_variant	5310	exon20			GGGCCAACGAGTA	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.7837T>C	chr16.hg19:g.2155892A>G		44.0	0.0	.		36.0	4.0	.	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	hg19	CCDS32369.1																																																																																			.	.	.	none		0.657	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			G	2155892	A	G	2155892	2	3	173	1	0	0	0	0	0	0	0	1	11970	40	2	3		3	PKD1	16	2155892	Silent	SNP	A	TCGA-G7-6795-01A-11D-1961-08		2155892	88198861	53	10137											
ZFHX3	463	hgsc.bcm.edu	37	chr16	72992635	72992635	+	Silent	SNP	T	T	C																															tcctcctcctcctccgcctcTtcctcctcctcttcctcctc																										TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr16:72992635T>C	ENST00000268489.5	-	2	2082	c.1410A>G	c.(1408-1410)gaA>gaG	p.E470E	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	470	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)				cctccgcctcttcctcctcct	0.587																																					p.E470E		Atlas-SNP	.											.	ZFHX3	404	.	0			c.A1410G						PASS	.						38	42	40					16																	72992635		2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			CGCCTCTTCCTCC	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.1410A>G	chr16.hg19:g.72992635T>C		61.0	0.0	.		36.0	4.0	.	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	hg19	CCDS10908.1																																																																																			.	.	.	none		0.587	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		C	72992635	T	C	72992635	2	2	173	1	0	0	0	0	0	0	0	1	17646	1606	56	3		3	ZFHX3	16	72992635	Silent	SNP	T	TCGA-G7-6795-01A-11D-1961-08	70836743	72992635	17362118	54	10138	96	2									
ZFHX3	463	hgsc.bcm.edu	37	chr16	72992638	72992638	+	Silent	SNP	C	C	T																															tcctcctcctccgcctcttcCtcctcctcttcctcctccgc																										TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr16:72992638C>T	ENST00000268489.5	-	2	2079	c.1407G>A	c.(1405-1407)gaG>gaA	p.E469E	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	469	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)				ccgcctcttcctcctcctctt	0.587																																					p.E469E		Atlas-SNP	.											.	ZFHX3	404	.	0			c.G1407A						PASS	.						38	41	40					16																	72992638		2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			CTCTTCCTCCTCC	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.1407G>A	chr16.hg19:g.72992638C>T		59.0	0.0	.		38.0	9.0	.	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	hg19	CCDS10908.1																																																																																			.	.	.	none		0.587	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		T	72992638	C	T	72992638	2	4	173	1	0	0	0	0	0	0	0	1	17646	680	24	2		2	ZFHX3	16	72992638	Silent	SNP	C	TCGA-G7-6795-01A-11D-1961-08	3	72992638	17362115	55	10139	96	2									
METT10D	79066	hgsc.bcm.edu	37	chr17	2323643	2323643	+	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	cagcggcagcctcgccttccCgcagagcaggcccacagggg	7	3	14	17	3	0	1	0	0	0	1	2	1	1	1	4	4	3	3	4	4	0	1	rs201182820		TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:2323643C>A	ENST00000263092.6	-	10	1437	c.1310G>T	c.(1309-1311)cGg>cTg	p.R437L	METTL16_ENST00000571669.2_5'UTR|METTL16_ENST00000538844.1_Missense_Mutation_p.R219L	NM_024086.3	NP_076991.3	Q86W50	MET16_HUMAN	methyltransferase like 16	437							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						CTCGCCTTCCCGCAGAGCAGG	0.647																																					p.R437L		Atlas-SNP	.											.	METTL16	75	.	0			c.G1310T						PASS	.						54	61	59					17																	2323643		1828	4070	5898	SO:0001583	missense	79066	exon10			CCTTCCCGCAGAG	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.1310G>T	chr17.hg19:g.2323643C>A	ENSP00000263092:p.Arg437Leu	197.0	0.0	.		247.0	10.0	.	NM_024086	D3DTI8|Q86TE5|Q96T16|Q9BVG7	Missense_Mutation	SNP	ENST00000263092.6	hg19	CCDS42232.1	.	.	.	.	.	.	.	.	.	.	C	0.028	-1.357504	0.01245	.	.	ENSG00000127804	ENST00000263092;ENST00000537138;ENST00000538844	T;T	0.42131	1.0;0.98	4.96	-9.91	0.00458	.	1.656050	0.03445	N	0.209819	T	0.17152	0.0412	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.10800	-1.0614	10	0.20046	T	0.44	.	5.2765	0.15653	0.0792:0.3013:0.4229:0.1966	.	437	Q86W50	MET16_HUMAN	L	437;117;219	ENSP00000263092:R437L;ENSP00000443633:R219L	ENSP00000263092:R437L	R	-	2	0	METTL16	2270393	0.000000	0.05858	0.000000	0.03702	0.060000	0.15804	-2.154000	0.01285	-3.074000	0.00252	0.511000	0.50034	CGG	.	C|0.999;T|0.001	.	alt		0.647	METTL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437653.2	NM_024086		A	2323643	C	A	2323643	3	1	173	1	0	0	0	0	1	0	0	0	9497	652	23	4	382	4	METT10D	17	2323643	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08		2323643	78871567	56	10140											
RAP1GAP2	23108	hgsc.bcm.edu	37	chr17	2898695	2898695	+	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	aatcagtgtacacaacattcCgggacagggagatcatgttt	13	10	10	8	1	2	1	2	0	0	1	3	3	3	2	1	2	2	2	1	2	3	3			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:2898695C>A	ENST00000254695.8	+	13	1069	c.979C>A	c.(979-981)Cgg>Agg	p.R327R	RAP1GAP2_ENST00000542807.1_Silent_p.R327R|RAP1GAP2_ENST00000366401.4_Silent_p.R312R|RAP1GAP2_ENST00000540393.2_Silent_p.R308R	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	327	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				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						CACAACATTCCGGGACAGGGA	0.562																																					p.R327R		Atlas-SNP	.											.	RAP1GAP2	90	.	0			c.C979A						PASS	.						128	134	132					17																	2898695		2192	4300	6492	SO:0001819	synonymous_variant	23108	exon13			ACATTCCGGGACA	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.979C>A	chr17.hg19:g.2898695C>A		285.0	0.0	.		314.0	13.0	.	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Silent	SNP	ENST00000254695.8	hg19	CCDS45573.1																																																																																			.	.	.	none		0.562	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2			A	2898695	C	A	2898695	2	1	173	1	0	0	0	0	0	0	0	1	13051	643	23	4		4	RAP1GAP2	17	2898695	Silent	SNP	C	TCGA-G7-6795-01A-11D-1961-08	575052	2898695	78296515	57	10141											
MPRIP	23164	hgsc.bcm.edu	37	chr17	17030034	17030034	+	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	agcccacgacccttcctcagGgcaccatcaacatgaaccag	12	5	7	17	1	2	1	2	1	0	0	3	2	3	1	5	1	3	1	5	1	2	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:17030034G>A	ENST00000341712.4	+	4	286	c.286G>A	c.(286-288)Ggc>Agc	p.G96S	MPRIP_ENST00000395804.3_Missense_Mutation_p.G96S|MPRIP_ENST00000395811.5_Missense_Mutation_p.G96S|MPRIP_ENST00000444976.1_Missense_Mutation_p.G96S			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	96	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						CCTTCCTCAGGGCACCATCAA	0.602																																					p.G96S		Atlas-SNP	.											.	MPRIP	87	.	0			c.G286A						PASS	.						80	73	75					17																	17030034		2203	4300	6503	SO:0001583	missense	23164	exon4			CCTCAGGGCACCA	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.286G>A	chr17.hg19:g.17030034G>A	ENSP00000342379:p.Gly96Ser	96.0	0.0	.		127.0	36.0	.	NM_015134	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Missense_Mutation	SNP	ENST00000341712.4	hg19	CCDS32578.1	.	.	.	.	.	.	.	.	.	.	G	33	5.203730	0.95033	.	.	ENSG00000133030	ENST00000444976;ENST00000395811;ENST00000395804;ENST00000341712	D;D;D;D	0.95518	-3.73;-3.73;-3.73;-3.73	5.59	5.59	0.84812	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	.	.	.	.	D	0.97826	0.9286	M	0.80982	2.52	0.80722	D	1	D;D	0.89917	1.0;0.996	D;D	0.91635	0.999;0.993	D	0.98164	1.0448	9	0.66056	D	0.02	.	19.5944	0.95530	0.0:0.0:1.0:0.0	.	96;96	Q6WCQ1-2;Q6WCQ1	.;MPRIP_HUMAN	S	96	ENSP00000400189:G96S;ENSP00000379156:G96S;ENSP00000379149:G96S;ENSP00000342379:G96S	ENSP00000342379:G96S	G	+	1	0	MPRIP	16970759	1.000000	0.71417	0.993000	0.49108	0.756000	0.42949	9.414000	0.97362	2.642000	0.89623	0.561000	0.74099	GGC	.	.	.	none		0.602	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134		A	17030034	G	A	17030034	3	1	173	1	0	0	0	0	1	0	0	0	9750	1232	43	2	300	2	MPRIP	17	17030034	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08	14131339	17030034	64165176	58	10142											
PHF12	57649	hgsc.bcm.edu	37	chr17	27251080	27251080	+	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	tggttcctcatccacgtcaaTgatgtcttcgtcgacatcat	8	14	7	12	3	4	1	3	1	1	0	8	2	6	1	2	1	0	1	2	1	1	2			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:27251080T>A	ENST00000332830.4	-	4	1372	c.562A>T	c.(562-564)Att>Ttt	p.I188F	RP11-20B24.5_ENST00000582631.1_RNA|RP11-20B24.5_ENST00000580782.1_RNA|PHF12_ENST00000582655.1_5'UTR|PHF12_ENST00000577226.1_Missense_Mutation_p.I188F|PHF12_ENST00000268756.3_Missense_Mutation_p.I188F	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)			TCCACGTCAATGATGTCTTCG	0.602																																					p.I188F		Atlas-SNP	.											.	PHF12	69	.	0			c.A562T						PASS	.						83	65	71					17																	27251080		2203	4300	6503	SO:0001583	missense	57649	exon4			CGTCAATGATGTC	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.562A>T	chr17.hg19:g.27251080T>A	ENSP00000329933:p.Ile188Phe	63.0	0.0	.		89.0	51.0	.	NM_020889		Missense_Mutation	SNP	ENST00000332830.4	hg19	CCDS32598.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.962952	0.53507	.	.	ENSG00000109118	ENST00000332830;ENST00000378879;ENST00000268756	D;D;D	0.94793	-3.48;-3.52;-3.52	5.8	4.72	0.59763	.	0.213282	0.49305	D	0.000141	D	0.93527	0.7934	L	0.44542	1.39	0.46260	D	0.998956	D;D;B;D	0.57899	0.968;0.981;0.437;0.968	P;P;B;P	0.54026	0.474;0.74;0.068;0.474	D	0.91577	0.5276	10	0.36615	T	0.2	-19.0128	10.4673	0.44616	0.0:0.0766:0.0:0.9234	.	170;188;188;188	B4DFE2;Q96QT6-2;Q2TAK2;Q96QT6	.;.;.;PHF12_HUMAN	F	188	ENSP00000329933:I188F;ENSP00000368157:I188F;ENSP00000268756:I188F	ENSP00000268756:I188F	I	-	1	0	PHF12	24275206	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.241000	0.43097	1.031000	0.39867	0.533000	0.62120	ATT	.	.	.	none		0.602	PHF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255941.1	NM_020889		A	27251080	T	A	27251080	3	1	173	1	0	0	0	0	1	0	0	0	11830	1464	51	5	2526	5	PHF12	17	27251080	Missense_Mutation	SNP	T	TCGA-G7-6795-01A-11D-1961-08	10221046	27251080	53944130	59	10143											
GJC1	10052	hgsc.bcm.edu	37	chr17	42882624	42882624	+	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	ccctatcagaaaacccacctCaaacacggtccttgccagca	13	6	5	17	1	2	1	2	0	0	1	3	1	3	1	5	1	4	1	5	1	4	2			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:42882624C>G	ENST00000426548.1	-	3	831	c.562G>C	c.(562-564)Gag>Cag	p.E188Q	GJC1_ENST00000592524.1_Missense_Mutation_p.E188Q|GJC1_ENST00000330514.4_Missense_Mutation_p.E188Q|GJC1_ENST00000590758.1_Missense_Mutation_p.E188Q	NM_001080383.1|NM_005497.3	NP_001073852.1|NP_005488.2	P36383	CXG1_HUMAN	gap junction protein, gamma 1, 45kDa	188					atrial cardiac muscle cell action potential (GO:0086014)|cardiac muscle tissue development (GO:0048738)|cell development (GO:0048468)|cell-cell junction assembly (GO:0007043)|gap junction assembly (GO:0016264)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vasculogenesis (GO:0001570)|visual perception (GO:0007601)	connexon complex (GO:0005922)|endoplasmic reticulum membrane (GO:0005789)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)|ion channel activity (GO:0005216)			NS(1)|kidney(1)|large_intestine(5)|liver(1)|lung(10)|prostate(1)	19		Prostate(33;0.0959)				AAACCCACCTCAAACACGGTC	0.493																																					p.E188Q		Atlas-SNP	.											.	GJC1	45	.	0			c.G562C						PASS	.						188	173	178					17																	42882624		2203	4300	6503	SO:0001583	missense	10052	exon3			CCACCTCAAACAC	U03493	CCDS11487.1	17q21.31	2008-02-04	2007-11-06	2007-11-06		ENSG00000182963		"Ion channels / Gap junction proteins (connexins)"	4280	protein-coding gene	gene with protein product	"connexin 45"	608655	"gap junction protein, alpha 7, 45kDa"	GJA7		7966354	Standard	NM_005497		Approved	CX45	uc002ihl.3	P36383		ENST00000426548.1:c.562G>C	chr17.hg19:g.42882624C>G	ENSP00000411528:p.Glu188Gln	219.0	0.0	.		358.0	131.0	.	NM_005497	B3KW68|Q4VAY0	Missense_Mutation	SNP	ENST00000426548.1	hg19	CCDS11487.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.201522	0.79015	.	.	ENSG00000182963	ENST00000426548;ENST00000330514	D;D	0.97850	-4.57;-4.57	5.52	5.52	0.82312	Gap junction protein, cysteine-rich domain (1);	0.000000	0.85682	D	0.000000	D	0.99306	0.9757	H	0.98218	4.175	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98674	1.0689	10	0.87932	D	0	.	18.419	0.90582	0.0:1.0:0.0:0.0	.	188	P36383	CXG1_HUMAN	Q	188	ENSP00000411528:E188Q;ENSP00000333193:E188Q	ENSP00000333193:E188Q	E	-	1	0	GJC1	40238150	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.805000	0.86005	2.581000	0.87130	0.514000	0.50259	GAG	.	.	.	none		0.493	GJC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448661.1	NM_005497		G	42882624	C	G	42882624	3	3	173	1	0	0	0	0	1	0	0	0	6421	835	29	4	632	4	GJC1	17	42882624	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08	15631544	42882624	38312586	60	10144											
SAMD14	201191	hgsc.bcm.edu	37	chr17	48190273	48190273	+	Missense_Mutation	SNP	T	T	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	tcccctagctcttcttggccTcctgctctcggcgccggagc	2	11	10	18	3	3	0	0	0	3	0	6	1	5	1	5	3	3	2	5	3	1	3			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:48190273T>G	ENST00000330175.4	-	10	1555	c.1238A>C	c.(1237-1239)gAg>gCg	p.E413A	SAMD14_ENST00000503131.1_Missense_Mutation_p.E441A	NM_001257359.1	NP_001244288.1	Q8IZD0	SAM14_HUMAN	sterile alpha motif domain containing 14	413										breast(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	15						CTTCTTGGCCTCCTGCTCTCG	0.697																																					p.E441A		Atlas-SNP	.											.	SAMD14	36	.	0			c.A1322C						PASS	.						40	43	42					17																	48190273		2203	4300	6503	SO:0001583	missense	201191	exon11			TTGGCCTCCTGCT		CCDS11560.1, CCDS58562.1	17q21.33	2013-01-10				ENSG00000167100		"Sterile alpha motif (SAM) domain containing"	27312	protein-coding gene	gene with protein product						8619474	Standard	NM_174920		Approved	FLJ36890	uc002iqg.4	Q8IZD0		ENST00000330175.4:c.1238A>C	chr17.hg19:g.48190273T>G	ENSP00000329144:p.Glu413Ala	102.0	0.0	.		133.0	51.0	.	NM_174920	A5D8V1|Q8N2X0	Missense_Mutation	SNP	ENST00000330175.4	hg19	CCDS58562.1	.	.	.	.	.	.	.	.	.	.	T	16.48	3.134428	0.56828	.	.	ENSG00000167100	ENST00000330175;ENST00000285206;ENST00000503131	.	.	.	5.11	4.02	0.46733	.	0.370723	0.24490	N	0.038069	T	0.47544	0.1451	L	0.27053	0.805	0.27885	N	0.939546	D;B	0.63880	0.993;0.137	D;B	0.68192	0.956;0.046	T	0.37911	-0.9685	9	0.59425	D	0.04	-11.4398	10.0803	0.42386	0.0:0.0:0.1686:0.8313	.	413;441	Q8IZD0;Q8IZD0-2	SAM14_HUMAN;.	A	413;425;441	.	ENSP00000285206:E425A	E	-	2	0	SAMD14	45545272	0.996000	0.38824	1.000000	0.80357	0.862000	0.49288	2.701000	0.47094	0.773000	0.33404	0.379000	0.24179	GAG	.	.	.	none		0.697	SAMD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366661.1	NM_174920		G	48190273	T	G	48190273	3	3	173	1	0	0	0	0	1	0	0	0	13832	1551	54	5	19	5	SAMD14	17	48190273	Missense_Mutation	SNP	T	TCGA-G7-6795-01A-11D-1961-08	5307649	48190273	33004937	61	10145											
CACNA1G	8913	hgsc.bcm.edu	37	chr17	48669448	48669448	+	Missense_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	ttctggtggagggcttccagGcggaggtaacccactgctct	6	10	14	11	1	2	0	0	0	2	0	3	2	3	2	2	6	2	3	2	6	1	3			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:48669448G>A	ENST00000359106.5	+	13	2905	c.2905G>A	c.(2905-2907)Gcg>Acg	p.A969T	CACNA1G_ENST00000502264.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000514079.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000507609.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000513689.2_Missense_Mutation_p.A969T|CACNA1G_ENST00000507336.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000510115.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000507896.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000510366.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000416767.4_Missense_Mutation_p.A969T|CACNA1G_ENST00000505165.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000354983.4_Missense_Mutation_p.A969T|CACNA1G_ENST00000514717.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000515411.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000514181.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000512389.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000442258.2_Missense_Mutation_p.A969T|CACNA1G_ENST00000429973.2_Missense_Mutation_p.A969T|CACNA1G_ENST00000513964.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000507510.2_Missense_Mutation_p.A969T|CACNA1G_ENST00000360761.4_Missense_Mutation_p.A969T|CACNA1G_ENST00000503485.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000515765.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000515165.1_Missense_Mutation_p.A969T|CACNA1G_ENST00000358244.5_Missense_Mutation_p.A969T|CACNA1G_ENST00000352832.5_Missense_Mutation_p.A969T	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	969					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)	GGGCTTCCAGGCGGAGGTAAC	0.582																																					p.A969T		Atlas-SNP	.											.	CACNA1G	659	.	0			c.G2905A						PASS	.						50	55	53					17																	48669448		2071	4210	6281	SO:0001583	missense	8913	exon13			TTCCAGGCGGAGG	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.2905G>A	chr17.hg19:g.48669448G>A	ENSP00000352011:p.Ala969Thr	59.0	0.0	.		96.0	40.0	.	NM_001256360	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Missense_Mutation	SNP	ENST00000359106.5	hg19	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	g	14.26	2.482345	0.44147	.	.	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	0.97186	-4.13;-4.12;-4.28;-4.08;-4.13;-4.12;-4.16;-4.26;-4.22;-4.24;-4.25;-4.11;-4.12;-4.2;-4.12;-4.07;-4.16;-4.12;-4.12;-4.16;-4.12;-4.12;-4.16;-4.11;-4.16;-4.17	5.08	1.63	0.23807	.	0.106565	0.64402	N	0.000006	D	0.88142	0.6357	N	0.02916	-0.46	0.33790	D	0.625335	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.22080	0.064;0.0;0.0;0.0;0.0;0.001;0.001;0.0;0.001;0.019;0.0;0.001;0.002;0.0;0.001;0.001;0.007;0.0;0.0;0.001;0.001;0.002;0.0;0.001;0.001;0.013	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.25987	0.017;0.005;0.001;0.005;0.001;0.006;0.004;0.001;0.004;0.013;0.001;0.017;0.02;0.001;0.004;0.007;0.029;0.005;0.001;0.008;0.003;0.007;0.001;0.007;0.001;0.065	T	0.82715	-0.0320	10	0.23891	T	0.37	.	5.465	0.16637	0.6206:0.0:0.3794:0.0	.	969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969;969	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;.;.	T	969	ENSP00000353990:A969T;ENSP00000339302:A969T;ENSP00000392390:A969T;ENSP00000347078:A969T;ENSP00000409759:A969T;ENSP00000425522:A969T;ENSP00000426261:A969T;ENSP00000425451:A969T;ENSP00000422407:A969T;ENSP00000426814:A969T;ENSP00000427238:A969T;ENSP00000423112:A969T;ENSP00000420918:A969T;ENSP00000426172:A969T;ENSP00000423045:A969T;ENSP00000427173:A969T;ENSP00000426098:A969T;ENSP00000425698:A969T;ENSP00000426232:A969T;ENSP00000423317:A969T;ENSP00000350979:A969T;ENSP00000352011:A969T;ENSP00000414388:A969T;ENSP00000423155:A969T;ENSP00000422268:A969T;ENSP00000421518:A969T	ENSP00000339302:A969T	A	+	1	0	CACNA1G	46024447	1.000000	0.71417	0.982000	0.44146	0.980000	0.70556	2.660000	0.46749	0.553000	0.29044	0.462000	0.41574	GCG	.	.	.	none		0.582	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		A	48669448	G	A	48669448	3	1	173	1	0	0	0	0	1	0	0	0	2546	1203	42	2	2955	2	CACNA1G	17	48669448	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08	479175	48669448	32525762	62	10146											
TNRC6C	57690	hgsc.bcm.edu	37	chr17	76045567	76045567	+	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	aaaatatgggcaaccagaacGggaacccaacaggcacttta	17	5	9	10	1	0	1	0	0	0	1	0	2	0	2	2	3	4	2	2	3	8	3	rs143335497	byFrequency	TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:76045567G>T	ENST00000588061.1	+	5	1151	c.424G>T	c.(424-426)Ggg>Tgg	p.G142W	TNRC6C_ENST00000301624.4_Missense_Mutation_p.G142W|TNRC6C_ENST00000335749.4_Missense_Mutation_p.G142W|TNRC6C_ENST00000588847.1_Missense_Mutation_p.G142W|TNRC6C_ENST00000544502.1_Missense_Mutation_p.G142W|TNRC6C_ENST00000541771.1_Missense_Mutation_p.G142W			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	142	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)			CAACCAGAACGGGAACCCAAC	0.517																																					p.G142W		Atlas-SNP	.											.	TNRC6C	173	.	0			c.G424T						PASS	.						59	61	60					17																	76045567		2002	4187	6189	SO:0001583	missense	57690	exon4			CAGAACGGGAACC	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.424G>T	chr17.hg19:g.76045567G>T	ENSP00000468647:p.Gly142Trp	108.0	0.0	.		151.0	9.0	.	NM_018996	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Missense_Mutation	SNP	ENST00000588061.1	hg19	CCDS45798.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.988405	0.53934	.	.	ENSG00000078687	ENST00000455761;ENST00000395801;ENST00000335749;ENST00000301624;ENST00000541771;ENST00000544502	T;T;T;T	0.15603	2.41;2.42;2.42;2.41	5.36	5.36	0.76844	.	0.166883	0.52532	D	0.000071	T	0.39358	0.1075	L	0.50333	1.59	0.58432	D	0.999997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.997	T	0.06481	-1.0824	10	0.72032	D	0.01	-11.4286	19.277	0.94036	0.0:0.0:1.0:0.0	.	142;142;142	G3XAB8;Q9HCJ0-2;Q9HCJ0	.;.;TNR6C_HUMAN	W	142	ENSP00000336783:G142W;ENSP00000301624:G142W;ENSP00000440310:G142W;ENSP00000442421:G142W	ENSP00000301624:G142W	G	+	1	0	TNRC6C	73557162	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.622000	0.61240	2.782000	0.95742	0.655000	0.94253	GGG	.	G|0.999;A|0.001	.	alt		0.517	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996		T	76045567	G	T	76045567	3	4	173	1	0	0	0	0	1	0	0	0	16354	1116	39	4	426	4	TNRC6C	17	76045567	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08	27376119	76045567	5149643	63	10147											
TBC1D16	125058	hgsc.bcm.edu	37	chr17	77922704	77922704	+	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	cattgggattgtcttcccccCggaagaactggttgttccga	7	12	11	11	2	1	1	0	0	1	1	3	4	3	3	4	3	1	2	4	3	2	5	rs181752232	byFrequency	TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr17:77922704C>A	ENST00000310924.2	-	8	1623	c.1508G>T	c.(1507-1509)cGg>cTg	p.R503L	TBC1D16_ENST00000576768.1_Missense_Mutation_p.R128L|TBC1D16_ENST00000572862.1_Missense_Mutation_p.R141L|TBC1D16_ENST00000570373.1_Missense_Mutation_p.R142L|TBC1D16_ENST00000340848.7_Missense_Mutation_p.R141L	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	503	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(3)	28	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)			GTCTTCCCCCCGGAAGAACTG	0.572																																					p.R503L	Ovarian(14;397 562 4850 31922 49378)	Atlas-SNP	.											.	TBC1D16	48	.	0			c.G1508T						PASS	.						222	178	193					17																	77922704		2203	4300	6503	SO:0001583	missense	125058	exon8			TCCCCCCGGAAGA	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.1508G>T	chr17.hg19:g.77922704C>A	ENSP00000309794:p.Arg503Leu	140.0	0.0	.		219.0	11.0	.	NM_019020	B9A6L7|I3L1E0|I3L4U2|Q8N3Z4|Q96DH7	Missense_Mutation	SNP	ENST00000310924.2	hg19	CCDS11766.1	.	.	.	.	.	.	.	.	.	.	C	16.56	3.158742	0.57368	.	.	ENSG00000167291	ENST00000340848;ENST00000310924	T;T	0.10477	2.87;2.87	5.18	5.18	0.71444	Rab-GAP/TBC domain (4);	0.132210	0.50627	D	0.000114	T	0.20292	0.0488	L	0.59436	1.845	0.80722	D	1	P;B;B;B	0.38048	0.616;0.327;0.327;0.327	P;B;B;B	0.45138	0.471;0.258;0.258;0.299	T	0.00964	-1.1498	10	0.34782	T	0.22	-12.5599	18.692	0.91586	0.0:1.0:0.0:0.0	.	163;503;503;141	Q96DH7;Q8TBP0;B9A6L7;Q8N3Z4	.;TBC16_HUMAN;.;.	L	141;503	ENSP00000341517:R141L;ENSP00000309794:R503L	ENSP00000309794:R503L	R	-	2	0	TBC1D16	75537299	1.000000	0.71417	0.953000	0.39169	0.915000	0.54546	4.631000	0.61304	2.392000	0.81423	0.655000	0.94253	CGG	.	C|0.999;G|0.001	.	alt		0.572	TBC1D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437145.1	NM_019020		A	77922704	C	A	77922704	3	1	173	1	0	0	0	0	1	0	0	0	15617	652	23	4	815	4	TBC1D16	17	77922704	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08	1877137	77922704	3272506	64	10148											
DYM	54808	hgsc.bcm.edu	37	chr18	46645145	46645145	+	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	tttgcattatatcctgaaatGaaggatgagttcgaaattgt	13	15	9	4	1	0	3	0	3	0	0	2	5	1	4	1	1	1	2	1	1	5	5			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr18:46645145G>A	ENST00000269445.6	-	15	2172	c.1715C>T	c.(1714-1716)tCa>tTa	p.S572L	RP11-15F12.3_ENST00000585251.1_RNA|DYM_ENST00000442713.2_Missense_Mutation_p.S382L	NM_017653.3	NP_060123.3	Q7RTS9	DYM_HUMAN	dymeclin	572					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						ATCCTGAAATGAAGGATGAGT	0.353																																					p.S572L		Atlas-SNP	.											.	DYM	52	.	0			c.C1715T						PASS	.						136	120	126					18																	46645145		2203	4300	6503	SO:0001583	missense	54808	exon15			TGAAATGAAGGAT	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.1715C>T	chr18.hg19:g.46645145G>A	ENSP00000269445:p.Ser572Leu	63.0	0.0	.		70.0	22.0	.	NM_017653	A8K5I8|B2RCF9|B4DKI7|Q3ZTS8|Q6P2P5|Q8N2M0|Q9BVE9|Q9NPU7	Missense_Mutation	SNP	ENST00000269445.6	hg19	CCDS11937.1	.	.	.	.	.	.	.	.	.	.	G	31	5.094436	0.94149	.	.	ENSG00000141627	ENST00000442713;ENST00000269445	D;D	0.81908	-1.55;-1.55	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.86981	0.6064	L	0.48362	1.52	0.80722	D	1	P;D;P	0.56287	0.879;0.975;0.481	B;P;B	0.56648	0.399;0.803;0.22	D	0.87691	0.2554	10	0.66056	D	0.02	-11.3305	19.412	0.94677	0.0:0.0:1.0:0.0	.	382;394;572	Q7RTS9-2;Q9NXS9;Q7RTS9	.;.;DYM_HUMAN	L	382;572	ENSP00000395942:S382L;ENSP00000269445:S572L	ENSP00000269445:S572L	S	-	2	0	DYM	44899143	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.827000	0.99397	2.601000	0.87937	0.650000	0.86243	TCA	.	.	.	none		0.353	DYM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255912.3	NM_017653		A	46645145	G	A	46645145	3	1	173	1	0	0	0	0	1	0	0	0	4842	1294	45	2	306	2	DYM	18	46645145	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08		46645145	31432103	65	10149											
USHBP1	83878	hgsc.bcm.edu	37	chr19	17370111	17370111	+	Frame_Shift_Del	DEL	C	C	-																															cactgacctgtactgcaaggCcagatgcaatgctgtggcct																										TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr19:17370111delC	ENST00000252597.3	-	7	1206	c.1033delG	c.(1033-1035)gccfs	p.A345fs	USHBP1_ENST00000431146.2_Frame_Shift_Del_p.A281fs	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						TACTGCAAGGCCAGATGCAAT	0.602																																					p.A345fs		Atlas-INDEL	.											.	USHBP1	85	.	0			c.1034delC						PASS	.						53	49	50					19																	17370111		2203	4300	6503	SO:0001589	frameshift_variant	83878	exon7			.	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.1033delG	chr19.hg19:g.17370111delC	ENSP00000252597:p.Ala345fs	50.0	0.0	0		41.0	12.0	0.292683	NM_031941		Frame_Shift_Del	DEL	ENST00000252597.3	hg19	CCDS12353.1																																																																																			.	.	.	none		0.602	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941		-	17370111	C	-	17370111	7	5	173	1	0	1	0	1	0	0	0	0	17049	739	26	0	1106	0	USHBP1	19	17370111	Frame_Shift_Del	DEL	C	TCGA-G7-6795-01A-11D-1961-08		17370111	41758872	66	10150											
SSBP4	170463	hgsc.bcm.edu	37	chr19	18538728	18538728	+	Missense_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	cgtcttctgggacctgtactGcgcggcgcctgacagaagag	7	8	14	12	4	2	3	0	1	2	2	2	4	2	4	2	2	2	1	2	2	2	2			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr19:18538728G>A	ENST00000270061.7	+	4	509	c.215G>A	c.(214-216)tGc>tAc	p.C72Y	SSBP4_ENST00000348495.6_Missense_Mutation_p.C72Y|SSBP4_ENST00000598159.2_3'UTR	NM_032627.4	NP_116016.1	Q9BWG4	SSBP4_HUMAN	single stranded DNA binding protein 4	72						nucleus (GO:0005634)	single-stranded DNA binding (GO:0003697)			endometrium(2)|kidney(1)|skin(1)	4						GACCTGTACTGCGCGGCGCCT	0.667																																					p.C72Y		Atlas-SNP	.											.	SSBP4	19	.	0			c.G215A						PASS	.						77	70	72					19																	18538728		2203	4300	6503	SO:0001583	missense	170463	exon4			TGTACTGCGCGGC		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.215G>A	chr19.hg19:g.18538728G>A	ENSP00000270061:p.Cys72Tyr	163.0	0.0	.		107.0	40.0	.	NM_001009998	Q9BWW5	Missense_Mutation	SNP	ENST00000270061.7	hg19	CCDS12378.1	.	.	.	.	.	.	.	.	.	.	G	13.61	2.288142	0.40494	.	.	ENSG00000130511	ENST00000270061;ENST00000348495	.	.	.	3.7	3.7	0.42460	.	0.000000	0.85682	U	0.000000	T	0.58921	0.2156	L	0.57536	1.79	0.58432	D	0.999999	B;B	0.25048	0.048;0.117	B;B	0.27715	0.077;0.082	T	0.64193	-0.6465	9	0.72032	D	0.01	-16.1844	12.9926	0.58627	0.0:0.0:1.0:0.0	.	72;72	Q9BWW5;Q9BWG4	.;SSBP4_HUMAN	Y	72	.	ENSP00000270061:C72Y	C	+	2	0	SSBP4	18399728	1.000000	0.71417	0.932000	0.37286	0.036000	0.12997	8.730000	0.91510	1.883000	0.54544	0.561000	0.74099	TGC	.	.	.	none		0.667	SSBP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466348.3	NM_032627		A	18538728	G	A	18538728	3	1	173	1	0	0	0	0	1	0	0	0	15194	1319	46	2	229	2	SSBP4	19	18538728	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08	1168617	18538728	40590255	67	10151											
SLC25A42	284439	hgsc.bcm.edu	37	chr19	19218750	19218750	+	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	ccgcatctcgagagaagaggGgctgaagactctctaccatg	11	7	12	11	2	2	4	0	1	2	3	4	6	2	4	2	2	1	2	2	2	3	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr19:19218750G>T	ENST00000318596.7	+	7	696	c.545G>T	c.(544-546)gGg>gTg	p.G182V	SLC25A42_ENST00000600275.1_3'UTR	NM_178526.4	NP_848621.2	Q86VD7	S2542_HUMAN	solute carrier family 25, member 42	182					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)			AGAGAAGAGGGGCTGAAGACT	0.572																																					p.G182V		Atlas-SNP	.											.	SLC25A42	18	.	0			c.G545T						PASS	.						119	105	110					19																	19218750		2203	4300	6503	SO:0001583	missense	284439	exon7			AAGAGGGGCTGAA		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.545G>T	chr19.hg19:g.19218750G>T	ENSP00000326693:p.Gly182Val	139.0	0.0	.		134.0	51.0	.	NM_178526	D2T2J5|O14553|O43378	Missense_Mutation	SNP	ENST00000318596.7	hg19	CCDS32966.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.441353	0.83993	.	.	ENSG00000181035	ENST00000318596	D	0.95238	-3.65	5.26	5.26	0.73747	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.98701	0.9564	H	0.99435	4.565	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99686	1.1000	10	0.87932	D	0	-10.1963	17.8525	0.88751	0.0:0.0:1.0:0.0	.	182	Q86VD7	S2542_HUMAN	V	182	ENSP00000326693:G182V	ENSP00000326693:G182V	G	+	2	0	SLC25A42	19079750	1.000000	0.71417	0.987000	0.45799	0.753000	0.42808	8.259000	0.89855	2.449000	0.82847	0.491000	0.48974	GGG	.	.	.	none		0.572	SLC25A42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465931.1	NM_178526		T	19218750	G	T	19218750	3	4	173	1	0	0	0	0	1	0	0	0	14520	1232	43	4	567	4	SLC25A42	19	19218750	Missense_Mutation	SNP	G	TCGA-G7-6795-01A-11D-1961-08	680022	19218750	39910233	68	10152											
ZNF254	9534	hgsc.bcm.edu	37	chr19	24310237	24310237	+	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	tatggtcctcaaccctaactAgacataagaggatgcacact	14	9	7	11	0	1	2	1	0	0	2	2	3	2	3	2	2	3	1	2	2	5	4			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr19:24310237A>T	ENST00000357002.4	+	4	1550	c.1435A>T	c.(1435-1437)Aga>Tga	p.R479*	ZNF254_ENST00000342944.6_Nonsense_Mutation_p.R394*	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	479					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)				AACCCTAACTAGACATAAGAG	0.388																																					p.R479X		Atlas-SNP	.											.	ZNF254	88	.	0			c.A1435T						PASS	.						62	62	62					19																	24310237		2203	4299	6502	SO:0001587	stop_gained	9534	exon4			CTAACTAGACATA	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.1435A>T	chr19.hg19:g.24310237A>T	ENSP00000349494:p.Arg479*	107.0	0.0	.		74.0	21.0	.	NM_203282	A4QPC0|Q86XL7	Nonsense_Mutation	SNP	ENST00000357002.4	hg19	CCDS32983.1	.	.	.	.	.	.	.	.	.	.	A	35	5.491375	0.96339	.	.	ENSG00000213096	ENST00000342944;ENST00000357002	.	.	.	1.07	-2.07	0.07276	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	.	3.7155	0.08437	0.6048:0.3952:0.0:0.0	.	.	.	.	X	394;479	.	ENSP00000445527:R394X	R	+	1	2	ZNF254	24102077	0.000000	0.05858	0.040000	0.18447	0.918000	0.54935	-0.462000	0.06704	-0.565000	0.06061	0.248000	0.18094	AGA	.	.	.	none		0.388	ZNF254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466453.1	NM_004876		T	24310237	A	T	24310237	4	4	173	1	0	0	0	0	0	1	0	0	17810	412	15	5	1449	5	ZNF254	19	24310237	Nonsense_Mutation	SNP	A	TCGA-G7-6795-01A-11D-1961-08	5091487	24310237	34818746	69	10153											
SPINT2	10653	hgsc.bcm.edu	37	chr19	38774304	38774304	+	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	aaggtggtgggcagatgccgGgcctccatgcctaggtggtg	6	8	18	9	1	0	1	0	0	0	1	1	1	1	1	4	6	2	1	4	6	2	1			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr19:38774304G>T	ENST00000301244.7	+	2	579	c.144G>T	c.(142-144)cgG>cgT	p.R48R	SPINT2_ENST00000587090.1_5'UTR|SPINT2_ENST00000454580.3_Intron	NM_021102.3	NP_066925.1	O43291	SPIT2_HUMAN	serine peptidase inhibitor, Kunitz type, 2	48	BPTI/Kunitz inhibitor 1. {ECO:0000255|PROSITE-ProRule:PRU00031}.	Reactive bond. {ECO:0000250}.			cellular component movement (GO:0006928)|negative regulation of endopeptidase activity (GO:0010951)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			large_intestine(2)|lung(1)|ovary(1)	4	all_cancers(60;6.83e-07)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			GCAGATGCCGGGCCTCCATGC	0.562																																					p.R48R		Atlas-SNP	.											.	SPINT2	17	.	0			c.G144T						PASS	.						170	144	153					19																	38774304		2203	4300	6503	SO:0001819	synonymous_variant	10653	exon2			ATGCCGGGCCTCC	U78095	CCDS12510.1, CCDS54261.1	19q13.2	2010-05-12	2005-08-17		ENSG00000167642	ENSG00000167642			11247	protein-coding gene	gene with protein product	"placental bikunin"	605124	"serine protease inhibitor, Kunitz type, 2"			9115294, 9346890	Standard	NM_021102		Approved	Kop, HAI-2	uc002ohr.2	O43291		ENST00000301244.7:c.144G>T	chr19.hg19:g.38774304G>T		211.0	0.0	.		208.0	55.0	.	NM_021102	A8K667|B4DLU1|O00271|O14895|Q5TZQ3|Q969E0	Silent	SNP	ENST00000301244.7	hg19	CCDS12510.1																																																																																			.	.	.	none		0.562	SPINT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458151.2			T	38774304	G	T	38774304	2	4	173	1	0	0	0	0	0	0	0	1	15081	1219	43	4		4	SPINT2	19	38774304	Silent	SNP	G	TCGA-G7-6795-01A-11D-1961-08	14464067	38774304	20354679	70	10154											
ZNF471	57573	hgsc.bcm.edu	37	chr19	57037032	57037032	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagagatcacaccttgcccaAcatcagaaaactcatacagg	16	6	6	13	0	3	2	3	0	0	2	3	3	3	2	2	1	4	0	2	1	4	2			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr19:57037032A>G	ENST00000308031.5	+	5	1729	c.1596A>G	c.(1594-1596)caA>caG	p.Q532Q	ZNF471_ENST00000593197.1_Intron|ZNF471_ENST00000591537.1_3'UTR	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	532					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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)		ACCTTGCCCAACATCAGAAAA	0.398																																					p.Q532Q	Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)	Atlas-SNP	.											.	ZNF471	99	.	0			c.A1596G						PASS	.						105	111	109					19																	57037032		2203	4300	6503	SO:0001819	synonymous_variant	57573	exon5			TGCCCAACATCAG	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.1596A>G	chr19.hg19:g.57037032A>G		152.0	0.0	.		121.0	40.0	.	NM_020813	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Silent	SNP	ENST00000308031.5	hg19	CCDS12945.1																																																																																			.	.	.	none		0.398	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813		G	57037032	A	G	57037032	2	3	173	1	0	0	0	0	0	0	0	1	17942	40	2	3		3	ZNF471	19	57037032	Silent	SNP	A	TCGA-G7-6795-01A-11D-1961-08	18262728	57037032	2091951	71	10155											
C20orf70	140683	hgsc.bcm.edu	37	chr20	31761923	31761923	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctcatcctggatgtcaaagCtgaaccgatcgatgatggca	11	9	10	11	2	2	2	2	2	0	0	4	5	3	3	3	2	2	2	3	2	2	0			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr20:31761923C>T	ENST00000253362.2	+	4	487	c.341C>T	c.(340-342)gCt>gTt	p.A114V	BPIFA2_ENST00000354932.5_Missense_Mutation_p.A114V			Q96DR5	BPIA2_HUMAN	BPI fold containing family A, member 2	114						extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)										GATGTCAAAGCTGAACCGATC	0.507																																					p.A114V		Atlas-SNP	.											.	.	.	.	0			c.C341T						PASS	.						192	132	152					20																	31761923		2203	4300	6503	SO:0001583	missense	140683	exon4			TCAAAGCTGAACC	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.341C>T	chr20.hg19:g.31761923C>T	ENSP00000253362:p.Ala114Val	119.0	0.0	.		136.0	38.0	.	NM_080574	Q9BQQ0	Missense_Mutation	SNP	ENST00000253362.2	hg19	CCDS13214.1	.	.	.	.	.	.	.	.	.	.	C	1.293	-0.607118	0.03717	.	.	ENSG00000131050	ENST00000253362;ENST00000354932	T;T	0.04758	3.56;3.56	4.11	-1.34	0.09143	.	1.919610	0.02314	N	0.072384	T	0.03520	0.0101	N	0.20685	0.6	0.09310	N	1	P	0.39862	0.692	B	0.42692	0.395	T	0.35276	-0.9795	10	0.02654	T	1	-22.3913	3.4184	0.07384	0.1782:0.4121:0.0:0.4097	.	114	Q96DR5	BPIA2_HUMAN	V	114	ENSP00000253362:A114V;ENSP00000347012:A114V	ENSP00000253362:A114V	A	+	2	0	BPIFA2	31225584	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.978000	0.01494	-0.194000	0.10399	0.561000	0.74099	GCT	.	.	.	none		0.507	BPIFA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257117.1	NM_080574		T	31761923	C	T	31761923	3	4	173	1	0	0	0	0	1	0	0	0	2118	797	28	2	351	2	C20orf70	20	31761923	Missense_Mutation	SNP	C	TCGA-G7-6795-01A-11D-1961-08		31761923	31263597	72	10156											
GNAS	2778	hgsc.bcm.edu	37	chr20	57415512	57415512	+	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	accgagagcgagaccgagtcCgaaatcgagtccgagaccga	13	3	13	12	7	0	3	0	0	0	3	3	10	2	3	5	0	1	0	5	0	1	0			TCGA-G7-6795-01A-11D-1961-08	TCGA-G7-6795-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1af4c17e-514e-4b9d-bfcb-ed019430178f	0428b3c1-9f63-45bc-8457-3fffb9bcf9fb	g.chr20:57415512C>A	ENST00000313949.7	+	1	740	c.351C>A	c.(349-351)tcC>tcA	p.S117S	GNAS-AS1_ENST00000424094.2_RNA|GNAS-AS1_ENST00000598163.1_RNA|GNAS_ENST00000371098.2_Silent_p.S117S|GNAS-AS1_ENST00000443966.1_RNA|GNAS_ENST00000371075.3_Silent_p.S117S			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)			AGACCGAGTCCGAAATCGAGT	0.642			Mis		pituitary adenoma		"McCune-Albright syndrome; pseudohypoparathyroidism, type IA"			TSP Lung(22;0.16)																											p.S117S	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.C351A						PASS	.						101	94	96					20																	57415512		2203	4300	6503	SO:0001819	synonymous_variant	2778	exon1			CGAGTCCGAAATC	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	ENST00000313949.7:c.351C>A	chr20.hg19:g.57415512C>A		142.0	0.0	.		133.0	7.0	.	NM_016592	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Silent	SNP	ENST00000313949.7	hg19	CCDS13471.1																																																																																			.	.	.	none		0.642	GNAS-002	KNOWN	NMD_exception|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080418.7	NM_000516		A	57415512	C	A	57415512	2	1	173	1	0	0	0	0	0	0	0	1	6517	639	23	4		4	GNAS	20	57415512	Silent	SNP	C	TCGA-G7-6795-01A-11D-1961-08	25653589	57415512	5610008	73	10157											
RPL22	6146	hgsc.bcm.edu	37	chr1	6246873	6246873	+	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	tttttggtgagatatttcaaAtacctgcagagaaaggacac	14	12	9	6	0	1	2	1	1	0	2	1	5	1	3	1	2	2	1	1	2	4	5			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr1:6246873A>T	ENST00000234875.4	-	4	284	c.246T>A	c.(244-246)taT>taA	p.Y82*	RPL22_ENST00000484532.1_Intron|RPL22_ENST00000497965.1_Nonsense_Mutation_p.Y49*	NM_000983.3	NP_000974.1	P35268	RL22_HUMAN	ribosomal protein L22	82					alpha-beta T cell differentiation (GO:0046632)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	heparin binding (GO:0008201)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			kidney(1)|large_intestine(2)|lung(2)|skin(1)	6	Ovarian(185;0.0634)	all_cancers(23;2.78e-38)|all_epithelial(116;8.88e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.53e-38)|GBM - Glioblastoma multiforme(13;3.33e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.8e-19)|Colorectal(212;6.8e-08)|COAD - Colon adenocarcinoma(227;8.04e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		GATATTTCAAATACCTGCAGA	0.358			T	RUNX1	"AML, CML"																																p.Y82X		Atlas-SNP	.		Dom	yes		1	1p36.31	6146	ribosomal protein L22 (EAP)		L	.	RPL22	24	.	0			c.T246A						PASS	.						46	47	46					1																	6246873		2202	4300	6502	SO:0001587	stop_gained	6146	exon4			TTTCAAATACCTG	BC058887	CCDS58.1	1p36.31	2011-04-06			ENSG00000116251	ENSG00000116251		"L ribosomal proteins"	10315	protein-coding gene	gene with protein product		180474				8395054	Standard	NM_000983		Approved	EAP, L22	uc001amd.3	P35268	OTTHUMG00000000953	ENST00000234875.4:c.246T>A	chr1.hg19:g.6246873A>T	ENSP00000346088:p.Tyr82*	69.0	0.0	.		81.0	17.0	.	NM_000983	B2R495|Q6IBD1	Nonsense_Mutation	SNP	ENST00000234875.4	hg19	CCDS58.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.279556	0.80692	.	.	ENSG00000116251	ENST00000234875	.	.	.	5.43	4.31	0.51392	.	0.122602	0.56097	D	0.000023	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	2.2758	7.3535	0.26706	0.7815:0.0:0.2185:0.0	.	.	.	.	X	82	.	ENSP00000346088:Y82X	Y	-	3	2	RPL22	6169460	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.692000	0.47018	0.906000	0.36621	0.379000	0.24179	TAT	.	.	.	none		0.358	RPL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002830.1	NM_000983		T	6246873	A	T	6246873	4	4	174	1	0	0	0	0	0	1	0	0	13581	108	4	5	144	5	RPL22	1	6246873	Nonsense_Mutation	SNP	A	TCGA-G7-6796-01A-11D-1961-08		6246873	243003748	1	10158											
ARID1A	8289	hgsc.bcm.edu	37	chr1	27094329	27094329	+	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	agaagatcaccaagttgtatGagctgggtggtgagcctgag	11	9	15	6	0	1	5	1	3	0	2	1	5	1	5	2	2	2	3	2	2	3	2			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr1:27094329G>A	ENST00000324856.7	+	11	3408	c.3037G>A	c.(3037-3039)Gag>Aag	p.E1013K	ARID1A_ENST00000457599.2_Missense_Mutation_p.E1013K|ARID1A_ENST00000374152.2_Missense_Mutation_p.E630K	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1013					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)		CAAGTTGTATGAGCTGGGTGG	0.488			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.E1013K		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.G3037A						PASS	.						146	122	130					1																	27094329		2203	4300	6503	SO:0001583	missense	8289	exon11			TTGTATGAGCTGG	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.3037G>A	chr1.hg19:g.27094329G>A	ENSP00000320485:p.Glu1013Lys	159.0	0.0	.		142.0	32.0	.	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	hg19	CCDS285.1	.	.	.	.	.	.	.	.	.	.	G	36	5.703514	0.96812	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152	T;T;T	0.46819	0.86;0.86;0.86	5.17	5.17	0.71159	ARID/BRIGHT DNA-binding domain (2);	0.049842	0.85682	D	0.000000	T	0.64886	0.2639	L	0.59436	1.845	0.80722	D	1	D;D;D	0.67145	0.995;0.996;0.993	D;D;P	0.65323	0.909;0.934;0.861	T	0.64601	-0.6369	10	0.51188	T	0.08	-14.8758	18.8566	0.92255	0.0:0.0:1.0:0.0	.	1013;1013;667	O14497;O14497-2;Q4LE49	ARI1A_HUMAN;.;.	K	1013;1013;630	ENSP00000320485:E1013K;ENSP00000387636:E1013K;ENSP00000363267:E630K	ENSP00000320485:E1013K	E	+	1	0	ARID1A	26966916	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.657000	0.98554	2.678000	0.91216	0.655000	0.94253	GAG	.	.	.	none		0.488	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		A	27094329	G	A	27094329	3	1	174	1	0	0	0	0	1	0	0	0	913	1291	45	2	3079	2	ARID1A	1	27094329	Missense_Mutation	SNP	G	TCGA-G7-6796-01A-11D-1961-08	20847456	27094329	222156292	2	10159											
ADAR	103	hgsc.bcm.edu	37	chr1	154574720	154574720	+	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	cctgatcttggtagatactcAgttcctggaaatgtgaggaa	11	12	11	7	0	2	3	1	2	1	1	3	5	3	5	2	3	1	2	2	3	4	4			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr1:154574720A>T	ENST00000368474.4	-	2	597	c.398T>A	c.(397-399)cTg>cAg	p.L133Q	ADAR_ENST00000292205.5_Missense_Mutation_p.L176Q|ADAR_ENST00000368471.3_5'UTR|ADAR_ENST00000471068.1_5'UTR	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	133					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)		GTAGATACTCAGTTCCTGGAA	0.517																																					p.L133Q		Atlas-SNP	.											.	ADAR	113	.	0			c.T398A						PASS	.						65	67	66					1																	154574720		2203	4300	6503	SO:0001583	missense	103	exon2			ATACTCAGTTCCT	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.398T>A	chr1.hg19:g.154574720A>T	ENSP00000357459:p.Leu133Gln	150.0	0.0	.		102.0	25.0	.	NM_015840	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Missense_Mutation	SNP	ENST00000368474.4	hg19	CCDS1071.1	.	.	.	.	.	.	.	.	.	.	A	18.97	3.736498	0.69304	.	.	ENSG00000160710	ENST00000292205;ENST00000368474;ENST00000529168	T;T;T	0.79749	-1.3;-1.3;-1.3	4.47	4.47	0.54385	Winged helix-turn-helix transcription repressor DNA-binding (1);Double-stranded RNA-specific adenosine deaminase (DRADA) (2);	0.910334	0.09504	N	0.793175	D	0.86008	0.5830	M	0.63843	1.955	0.53688	D	0.999979	D;D;D	0.89917	0.998;1.0;0.999	D;D;D	0.85130	0.972;0.992;0.997	D	0.83933	0.0307	10	0.87932	D	0	-11.1093	13.8697	0.63610	1.0:0.0:0.0:0.0	.	133;133;133	P55265-3;P55265-2;P55265	.;.;DSRAD_HUMAN	Q	176;133;128	ENSP00000292205:L176Q;ENSP00000357459:L133Q;ENSP00000431794:L128Q	ENSP00000292205:L176Q	L	-	2	0	ADAR	152841344	1.000000	0.71417	0.166000	0.22797	0.666000	0.39218	6.906000	0.75719	1.992000	0.58205	0.402000	0.26972	CTG	.	.	.	none		0.517	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111		T	154574720	A	T	154574720	3	4	174	1	0	0	0	0	1	0	0	0	281	188	7	5	3338	5	ADAR	1	154574720	Missense_Mutation	SNP	A	TCGA-G7-6796-01A-11D-1961-08	127480391	154574720	94675901	3	10160											
FCRL4	83417	hgsc.bcm.edu	37	chr1	157559028	157559028	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcgcacagggttacttcgTggggagccccgggcctggca	7	6	16	12	3	0	0	0	0	0	0	1	1	0	1	3	5	3	3	3	5	2	2			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr1:157559028T>C	ENST00000271532.1	-	3	408	c.273A>G	c.(271-273)ccA>ccG	p.P91P	FCRL4_ENST00000448509.2_5'UTR	NM_031282.2	NP_112572.1	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4	91	Ig-like C2-type 1.				immune system process (GO:0002376)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(20)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	40	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.245)				GGTTACTTCGTGGGGAGCCCC	0.498																																					p.P91P		Atlas-SNP	.											.	FCRL4	95	.	0			c.A273G						PASS	.						74	79	77					1																	157559028		2203	4300	6503	SO:0001819	synonymous_variant	83417	exon3			ACTTCGTGGGGAG	AF343661	CCDS1166.1	1q21	2013-01-14			ENSG00000163518	ENSG00000163518		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18507	protein-coding gene	gene with protein product		605876				11290337, 11493702	Standard	NM_031282		Approved	FCRH4, IRTA1, IGFP2, CD307d	uc001fqw.3	Q96PJ5	OTTHUMG00000035488	ENST00000271532.1:c.273A>G	chr1.hg19:g.157559028T>C		154.0	0.0	.		165.0	32.0	.	NM_031282	Q96PJ3|Q96RE0	Silent	SNP	ENST00000271532.1	hg19	CCDS1166.1																																																																																			.	.	.	none		0.498	FCRL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086180.1	NM_031282		C	157559028	T	C	157559028	2	2	174	1	0	0	0	0	0	0	0	1	5804	1683	59	3		3	FCRL4	1	157559028	Silent	SNP	T	TCGA-G7-6796-01A-11D-1961-08	2984308	157559028	91691593	4	10161											
MPZL1	9019	hgsc.bcm.edu	37	chr1	167745333	167745333	+	Missense_Mutation	SNP	A	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	agagagtttgtcaccagttaAgcaggctcctcggaagtccc	10	9	11	11	1	1	1	1	0	0	1	4	3	3	2	3	2	1	4	3	2	2	2			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr1:167745333A>C	ENST00000359523.2	+	5	840	c.638A>C	c.(637-639)aAg>aCg	p.K213T	MPZL1_ENST00000403379.3_3'UTR|MPZL1_ENST00000474859.1_Intron|MPZL1_ENST00000392121.3_Intron	NM_003953.5|NM_024569.4	NP_003944.1|NP_078845.3	O95297	MPZL1_HUMAN	myelin protein zero-like 1	213					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)					TCACCAGTTAAGCAGGCTCCT	0.413																																					p.K213T		Atlas-SNP	.											.	MPZL1	25	.	0			c.A638C						PASS	.						76	74	75					1																	167745333		2203	4300	6503	SO:0001583	missense	9019	exon5			CAGTTAAGCAGGC	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.638A>C	chr1.hg19:g.167745333A>C	ENSP00000352513:p.Lys213Thr	99.0	0.0	.		93.0	12.0	.	NM_003953	B2REB9|B2REC0|Q5R332|Q8IX11|Q9BWZ3|Q9NYK4|Q9UL20	Missense_Mutation	SNP	ENST00000359523.2	hg19	CCDS1264.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.313200	0.81358	.	.	ENSG00000197965	ENST00000359523	D	0.96365	-3.99	5.28	5.28	0.74379	.	.	.	.	.	D	0.95370	0.8497	L	0.29908	0.895	0.33196	D	0.551469	D	0.71674	0.998	D	0.78314	0.991	D	0.94904	0.8059	8	0.33141	T	0.24	.	14.4968	0.67694	1.0:0.0:0.0:0.0	.	213	O95297	MPZL1_HUMAN	T	213	ENSP00000352513:K213T	ENSP00000352513:K213T	K	+	2	0	MPZL1	166011957	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.562000	0.53777	2.307000	0.77673	0.528000	0.53228	AAG	.	.	.	none		0.413	MPZL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083655.2	NM_024569		C	167745333	A	C	167745333	3	2	174	1	0	0	0	0	1	0	0	0	9756	72	3	5	656	5	MPZL1	1	167745333	Missense_Mutation	SNP	A	TCGA-G7-6796-01A-11D-1961-08	10186305	167745333	81505288	5	10162											
CACYBP	27101	hgsc.bcm.edu	37	chr1	174979129	174979129	+	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	ttctaaagaaaatttatgaaGatggagacgatgatatgaag	18	11	10	2	1	1	6	0	3	1	3	1	8	1	6	0	1	0	0	0	1	8	5			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr1:174979129G>T	ENST00000367679.2	+	6	1049	c.601G>T	c.(601-603)Gat>Tat	p.D201Y	CACYBP_ENST00000367681.2_Missense_Mutation_p.D158Y|MRPS14_ENST00000498253.1_5'Flank|CACYBP_ENST00000405362.1_Missense_Mutation_p.D158Y	NM_014412.2	NP_055227.1	Q9HB71	CYBP_HUMAN	calcyclin binding protein	201	Interaction with S100A6. {ECO:0000250}.|Interaction with SKP1.|SGS. {ECO:0000255|PROSITE- ProRule:PRU00386}.				aging (GO:0007568)|cardiac muscle cell differentiation (GO:0055007)|cellular response to calcium ion (GO:0071277)|negative regulation of cell death (GO:0060548)|positive regulation of DNA replication (GO:0045740)|response to growth hormone (GO:0060416)	beta-catenin destruction complex (GO:0030877)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|nuclear envelope lumen (GO:0005641)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(1)|prostate(1)	11						AATTTATGAAGATGGAGACGA	0.383																																					p.D201Y		Atlas-SNP	.											CACYBP,NS,carcinoma,0,1	CACYBP	23	.	0			c.G601T						PASS	.						86	85	85					1																	174979129		2203	4300	6503	SO:0001583	missense	27101	exon6			TATGAAGATGGAG	BC022352	CCDS1315.1, CCDS30942.1	1q24-q25	2008-02-05			ENSG00000116161	ENSG00000116161			30423	protein-coding gene	gene with protein product		606186				11389839, 12421809	Standard	XM_005245092		Approved	SIP, S100A6BP	uc001gkj.1	Q9HB71	OTTHUMG00000034941	ENST00000367679.2:c.601G>T	chr1.hg19:g.174979129G>T	ENSP00000356652:p.Asp201Tyr	60.0	0.0	.		68.0	17.0	.	NM_014412	B2ZWH2|B3KSF1|O60666|Q5R370|Q5R371	Missense_Mutation	SNP	ENST00000367679.2	hg19	CCDS1315.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.891415	0.91889	.	.	ENSG00000116161	ENST00000367681;ENST00000450101;ENST00000367679;ENST00000405362	T;T	0.58060	0.36;0.36	5.89	5.89	0.94794	SGS (2);HSP20-like chaperone (1);	0.132069	0.64402	D	0.000002	T	0.68091	0.2963	M	0.79258	2.445	0.80722	D	1	P	0.48589	0.912	P	0.50791	0.65	T	0.71031	-0.4710	10	0.72032	D	0.01	-24.1569	20.2561	0.98419	0.0:0.0:1.0:0.0	.	201	Q9HB71	CYBP_HUMAN	Y	158;174;201;158	ENSP00000356654:D158Y;ENSP00000385771:D158Y	ENSP00000356652:D201Y	D	+	1	0	CACYBP	173245752	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.296000	0.96104	2.797000	0.96272	0.563000	0.77884	GAT	.	.	.	none		0.383	CACYBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084583.3	NM_014412		T	174979129	G	T	174979129	3	4	174	1	0	0	0	0	1	0	0	0	2566	942	33	4	623	4	CACYBP	1	174979129	Missense_Mutation	SNP	G	TCGA-G7-6796-01A-11D-1961-08	7233796	174979129	74271492	6	10163											
NAV1	89796	hgsc.bcm.edu	37	chr1	201762968	201762968	+	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	gcctggtgaatatgacatccCgcctgcgacacctggcagag	9	7	12	13	2	0	3	0	2	0	1	1	4	1	3	4	2	1	1	4	2	2	1			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr1:201762968C>G	ENST00000367296.4	+	14	3790	c.3370C>G	c.(3370-3372)Cgc>Ggc	p.R1124G	NAV1_ENST00000469130.1_3'UTR|NAV1_ENST00000367302.1_Missense_Mutation_p.R1080G|NAV1_ENST00000367295.1_Missense_Mutation_p.R733G|NAV1_ENST00000295624.6_Missense_Mutation_p.R1124G|NAV1_ENST00000367300.3_Missense_Mutation_p.R1067G|NAV1_ENST00000367297.4_Missense_Mutation_p.R1116G|IPO9-AS1_ENST00000413035.1_RNA	NM_020443.4	NP_065176.3	Q8NEY1	NAV1_HUMAN	neuron navigator 1	1124					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						TATGACATCCCGCCTGCGACA	0.582																																					p.R1124G		Atlas-SNP	.											.	NAV1	143	.	0			c.C3370G						PASS	.						70	66	67					1																	201762968		2203	4300	6503	SO:0001583	missense	89796	exon14			ACATCCCGCCTGC	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.3370C>G	chr1.hg19:g.201762968C>G	ENSP00000356265:p.Arg1124Gly	88.0	0.0	.		99.0	5.0	.	NM_020443	A8MS88|Q5SVH1|Q5SVH2|Q5SVH3|Q5SVH7|Q5VUY9|Q8IVL2|Q96II1|Q9H7V9|Q9H9S9|Q9H9T5|Q9UGI1|Q9ULK7|Q9ULR9	Missense_Mutation	SNP	ENST00000367296.4	hg19	CCDS1414.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.5|27.5	4.841219|4.841219	0.91197|0.91197	.|.	.|.	ENSG00000134369|ENSG00000134369	ENST00000430015|ENST00000367302;ENST00000367296;ENST00000295624;ENST00000367297;ENST00000367300;ENST00000391966;ENST00000367295	.|D;D;D;D;D;D	.|0.94497	.|-3.44;-3.44;-3.44;-3.44;-3.44;-3.44	4.95|4.95	4.95|4.95	0.65309|0.65309	.|.	.|0.058638	.|0.64402	.|D	.|0.000002	D|D	0.97037|0.97037	0.9032|0.9032	M|M	0.73598|0.73598	2.24|2.24	0.58432|0.58432	D|D	0.999991|0.999991	.|D;D;D;D;D	.|0.89917	.|1.0;0.997;0.996;0.998;1.0	.|D;D;D;D;D	.|0.87578	.|0.998;0.932;0.948;0.991;0.998	D|D	0.97499|0.97499	1.0059|1.0059	5|10	.|0.72032	.|D	.|0.01	-24.902|-24.902	17.9873|17.9873	0.89159|0.89159	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1116;733;1124;624;1124	.|Q8NEY1-6;Q8NEY1-5;Q8NEY1;A8MYI2;Q8NEY1-3	.|.;.;NAV1_HUMAN;.;.	R|G	673|1080;1124;1124;1116;1067;624;733	.|ENSP00000356271:R1080G;ENSP00000356265:R1124G;ENSP00000295624:R1124G;ENSP00000356266:R1116G;ENSP00000356269:R1067G;ENSP00000356264:R733G	.|ENSP00000295624:R1124G	P|R	+|+	2|1	0|0	NAV1|NAV1	200029591|200029591	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.939000|0.939000	0.58152|0.58152	5.512000|5.512000	0.67030|0.67030	2.557000|2.557000	0.86248|0.86248	0.462000|0.462000	0.41574|0.41574	CCG|CGC	.	.	.	none		0.582	NAV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087013.1	NM_020443		G	201762968	C	G	201762968	3	3	174	1	0	0	0	0	1	0	0	0	10190	652	23	4	3481	4	NAV1	1	201762968	Missense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08	26783839	201762968	47487653	7	10164											
TRAF5	7188	hgsc.bcm.edu	37	chr1	211545951	211545952	+	Frame_Shift_Ins	INS	-	-	C																															gtccccgctttgtggctcatINStctgttttggagaatgccaa																										TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr1:211545951_211545952insC	ENST00000261464.5	+	11	1635_1636	c.1581_1582insC	c.(1582-1584)tctfs	p.S528fs	TRAF5_ENST00000336184.2_Frame_Shift_Ins_p.S528fs|TRAF5_ENST00000367004.3_Frame_Shift_Ins_p.S528fs|TRAF5_ENST00000427925.2_Frame_Shift_Ins_p.S422fs	NM_001033910.2	NP_001029082.1	O00463	TRAF5_HUMAN	TNF receptor-associated factor 5	528	Interaction with EIF2AK2/PKR.|MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				apoptotic process (GO:0006915)|positive regulation of cell proliferation (GO:0008284)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	CD40 receptor complex (GO:0035631)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)	signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				OV - Ovarian serous cystadenocarcinoma(81;0.00946)|all cancers(67;0.0808)|Epithelial(68;0.144)		TTGTGGCTCATTCTGTTTTGGA	0.465																																					p.H527fs		Atlas-INDEL	.											.	TRAF5	64	.	0			c.1581_1582insC						PASS	.																																			SO:0001589	frameshift_variant	7188	exon11			.	AB000509	CCDS1497.1	1q32	2008-02-05			ENSG00000082512	ENSG00000082512		"RING-type (C3HC4) zinc fingers"	12035	protein-coding gene	gene with protein product		602356				9126477	Standard	NM_001033910		Approved	RNF84	uc001hii.3	O00463	OTTHUMG00000036997	Exception_encountered	chr1.hg19:g.211545951_211545952insC	ENSP00000261464:p.Ser528fs	118.0	0.0	0		118.0	20.0	0.169492	NM_145759	B4DIS9|B4E0A2|Q6FHY1	Frame_Shift_Ins	INS	ENST00000261464.5	hg19	CCDS1497.1																																																																																			.	.	.	none		0.465	TRAF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089825.1	NM_004619		C	211545952	-	C	211545951	7	5	174	1	0	1	1	0	0	0	0	0	16456	1490	52	0	1619	0	TRAF5	1	211545951	Frame_Shift_Ins	INS	-	TCGA-G7-6796-01A-11D-1961-08	9782983	211545951	37704670	8	10165											
XDH	7498	hgsc.bcm.edu	37	chr2	31595113	31595113	+	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	cttgatcttggcgtgggcccGggtgctggtgaccagccgga	4	9	17	11	3	1	2	0	2	1	0	1	3	1	3	3	5	2	1	3	5	0	2	rs201668777	byFrequency	TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr2:31595113G>T	ENST00000379416.3	-	17	1885	c.1837C>A	c.(1837-1839)Cgg>Agg	p.R613R		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	613					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)	GCGTGGGCCCGGGTGCTGGTG	0.627																																					p.R613R	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.C1837A						PASS	.						98	104	102					2																	31595113		2203	4300	6503	SO:0001819	synonymous_variant	7498	exon17			GGGCCCGGGTGCT	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.1837C>A	chr2.hg19:g.31595113G>T		266.0	0.0	.		252.0	11.0	.	NM_000379	Q16681|Q16712|Q4PJ16	Silent	SNP	ENST00000379416.3	hg19	CCDS1775.1																																																																																			.	G|1.000;A|0.000	.	alt		0.627	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379		T	31595113	G	T	31595113	2	4	174	1	0	0	0	0	0	0	0	1	17438	1115	39	4		4	XDH	2	31595113	Silent	SNP	G	TCGA-G7-6796-01A-11D-1961-08		31595113	211604260	9	10166											
ABCA12	26154	hgsc.bcm.edu	37	chr2	215865500	215865500	+	Missense_Mutation	SNP	T	T	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	tcctgggagttccttccagtTtgcaattcaatgattgctct	7	16	8	10	0	2	1	1	1	1	0	5	2	5	2	3	1	2	4	3	1	2	5			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr2:215865500T>G	ENST00000272895.7	-	22	3327	c.3108A>C	c.(3106-3108)caA>caC	p.Q1036H	ABCA12_ENST00000389661.4_Missense_Mutation_p.Q718H	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1036					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)		TCCTTCCAGTTTGCAATTCAA	0.428																																					p.Q1036H	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.A3108C						PASS	.						125	130	128					2																	215865500		2203	4300	6503	SO:0001583	missense	26154	exon22			TCCAGTTTGCAAT	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.3108A>C	chr2.hg19:g.215865500T>G	ENSP00000272895:p.Gln1036His	166.0	0.0	.		183.0	41.0	.	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	hg19	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	T	14.43	2.533445	0.45073	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.95656	-3.77;-3.77	5.73	2.68	0.31781	.	0.087482	0.49916	D	0.000121	D	0.92456	0.7605	L	0.43152	1.355	0.80722	D	1	B;B	0.32467	0.136;0.372	B;B	0.38156	0.152;0.266	D	0.89343	0.3655	10	0.66056	D	0.02	.	8.1984	0.31411	0.0:0.731:0.0:0.269	.	1036;718	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	H	1036;718	ENSP00000272895:Q1036H;ENSP00000374312:Q718H	ENSP00000272895:Q1036H	Q	-	3	2	ABCA12	215573745	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.506000	0.45433	0.612000	0.30071	0.454000	0.30748	CAA	.	.	.	none		0.428	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		G	215865500	T	G	215865500	3	3	174	1	0	0	0	0	1	0	0	0	30	1838	64	5	4807	5	ABCA12	2	215865500	Missense_Mutation	SNP	T	TCGA-G7-6796-01A-11D-1961-08	184270387	215865500	27333873	10	10167											
C2orf62	375307	hgsc.bcm.edu	37	chr2	219222364	219222364	+	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	aggtgcagagagggaaatacCaggaaaaactcggcatgctg	15	5	14	7	1	0	1	0	0	0	1	1	4	0	3	1	4	4	3	1	4	4	1			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr2:219222364C>T	ENST00000289388.3	+	3	255	c.226C>T	c.(226-228)Cag>Tag	p.Q76*	AC021016.8_ENST00000411433.1_RNA	NM_198559.1	NP_940961.1	Q7Z7H3	CATIP_HUMAN		76					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Renal(207;0.0915)		Epithelial(149;8.08e-07)|all cancers(144;0.000146)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGGGAAATACCAGGAAAAACT	0.552																																					p.Q76X		Atlas-SNP	.											.	C2orf62	28	.	0			c.C226T						PASS	.						72	63	66					2																	219222364		2203	4300	6503	SO:0001587	stop_gained	375307	exon3			AAATACCAGGAAA																												ENST00000289388.3:c.226C>T	chr2.hg19:g.219222364C>T	ENSP00000289388:p.Gln76*	103.0	0.0	.		93.0	16.0	.	NM_198559		Nonsense_Mutation	SNP	ENST00000289388.3	hg19	CCDS2414.1	.	.	.	.	.	.	.	.	.	.	C	12.60	1.987633	0.35036	.	.	ENSG00000158428	ENST00000289388	.	.	.	4.56	-4.72	0.03269	.	1.478090	0.03845	N	0.271323	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-27.2458	4.8866	0.13706	0.2205:0.5606:0.0905:0.1283	.	.	.	.	X	76	.	ENSP00000289388:Q76X	Q	+	1	0	C2orf62	218930608	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	0.212000	0.17497	-0.542000	0.06249	-0.457000	0.05445	CAG	.	.	.	none		0.552	C2orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256771.1			T	219222364	C	T	219222364	4	4	174	1	0	0	0	0	0	1	0	0	2183	595	21	2	236	2	C2orf62	2	219222364	Nonsense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08	3356864	219222364	23977009	11	10168											
SP100	6672	hgsc.bcm.edu	37	chr2	231338157	231338157	+	Splice_Site	DEL	T	T	-																															caagcatctgacatgatgggTaaggctaccctagggtcttg																										TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr2:231338157delT	ENST00000264052.5	+	16	1901		c.e16+2		SP100_ENST00000409112.1_Splice_Site|SP100_ENST00000340126.4_Splice_Site	NM_003113.3	NP_003104.2	P23497	SP100_HUMAN	SP100 nuclear antigen						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)		ACATGATGGGTAAGGCTACCC	0.468																																					.		Atlas-INDEL	.											.	SP100	167	.	0			c.1546+1T>-						PASS	.						164	152	156					2																	231338157		2203	4300	6503	SO:0001630	splice_region_variant	6672	exon16			.	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.1546+2T>-	chr2.hg19:g.231338157delT		126.0	0.0	0		135.0	23.0	0.17037	NM_003113	B4DDX5|B8ZZD8|E7EUA7|E9PH61|F8WFE2|O75450|Q13343|Q8TE34|Q96F70|Q96T24|Q96T95|Q9NP33|Q9UE32	Splice_Site	DEL	ENST00000264052.5	hg19	CCDS2477.1																																																																																			.	.	.	none		0.468	SP100-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256914.2	NM_003113	Intron	-	231338157	T	-	231338157	8	5	174	1	0	1	0	1	0	0	1	0	14973	1652	57	0	1610	0	SP100	2	231338157	Splice_Site	DEL	T	TCGA-G7-6796-01A-11D-1961-08	12115793	231338157	11861216	12	10169											
SLC25A38	54977	hgsc.bcm.edu	37	chr3	39431018	39431018	+	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	atcaaggctttcctgtgtggCtccatcagtgggacctgctc	6	12	11	12	0	2	0	2	0	0	0	5	1	4	1	3	3	1	3	3	3	1	1			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr3:39431018C>T	ENST00000273158.4	+	2	479	c.102C>T	c.(100-102)ggC>ggT	p.G34G		NM_017875.2	NP_060345.2			solute carrier family 25, member 38									p.G34G(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(6)|skin(1)|stomach(1)	11				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		TCCTGTGTGGCTCCATCAGTG	0.522																																					p.G34G		Atlas-SNP	.											SLC25A38,colon,carcinoma,0,1	SLC25A38	25	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C102T						PASS	.						209	174	186					3																	39431018		2203	4300	6503	SO:0001819	synonymous_variant	54977	exon2			GTGTGGCTCCATC	BC013194	CCDS2685.1	3p22.1	2013-05-22			ENSG00000144659	ENSG00000144659		"Solute carriers"	26054	protein-coding gene	gene with protein product		610819				16949250	Standard	NM_017875		Approved	FLJ20551	uc003cjo.2	Q96DW6	OTTHUMG00000131289	ENST00000273158.4:c.102C>T	chr3.hg19:g.39431018C>T		126.0	0.0	.		116.0	27.0	.	NM_017875		Silent	SNP	ENST00000273158.4	hg19	CCDS2685.1																																																																																			.	.	.	none		0.522	SLC25A38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254057.3	NM_017875		T	39431018	C	T	39431018	2	4	174	1	0	0	0	0	0	0	0	1	14515	784	28	2		2	SLC25A38	3	39431018	Silent	SNP	C	TCGA-G7-6796-01A-11D-1961-08		39431018	158591412	13	10170											
TNFSF10	8743	hgsc.bcm.edu	37	chr3	172232704	172232704	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgccagcaggggctgttcaTactctcttcgtcattggggt	5	14	12	10	1	3	0	2	0	1	0	5	0	3	0	1	4	3	3	1	4	1	5			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr3:172232704T>C	ENST00000241261.2	-	2	339	c.217A>G	c.(217-219)Atg>Gtg	p.M73V	TNFSF10_ENST00000420541.2_Missense_Mutation_p.M73V	NM_003810.3	NP_003801.1	P50591	TNF10_HUMAN	tumor necrosis factor (ligand) superfamily, member 10	73					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|immune response (GO:0006955)|male gonad development (GO:0008584)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to insulin (GO:0032868)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)			breast(2)|cervix(1)|large_intestine(1)|lung(6)|ovary(1)|skin(4)	15	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.67e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)			GGGCTGTTCATACTCTCTTCG	0.502																																					p.M73V		Atlas-SNP	.											.	TNFSF10	30	.	0			c.A217G						PASS	.						144	137	140					3																	172232704		2203	4300	6503	SO:0001583	missense	8743	exon2			TGTTCATACTCTC	U37518	CCDS3219.1, CCDS54680.1	3q26	2006-09-20			ENSG00000121858	ENSG00000121858		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11925	protein-coding gene	gene with protein product		603598				8777713, 8663110	Standard	NM_003810		Approved	TRAIL, Apo-2L, TL2, CD253	uc003fid.3	P50591	OTTHUMG00000156917	ENST00000241261.2:c.217A>G	chr3.hg19:g.172232704T>C	ENSP00000241261:p.Met73Val	130.0	0.0	.		176.0	41.0	.	NM_003810	A1Y9B3	Missense_Mutation	SNP	ENST00000241261.2	hg19	CCDS3219.1	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.547137	0.00140	.	.	ENSG00000121858	ENST00000241261;ENST00000420541	D;T	0.86366	-2.11;1.59	5.61	-1.89	0.07689	.	0.989409	0.08265	N	0.972345	T	0.71804	0.3383	L	0.34521	1.04	0.09310	N	1	B;B	0.12630	0.006;0.001	B;B	0.11329	0.006;0.001	T	0.57136	-0.7863	10	0.05351	T	0.99	-3.1928	0.8408	0.01149	0.3634:0.1464:0.1187:0.3715	.	73;73	A1Y9B3;P50591	.;TNF10_HUMAN	V	73	ENSP00000241261:M73V;ENSP00000389931:M73V	ENSP00000241261:M73V	M	-	1	0	TNFSF10	173715398	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.552000	0.23376	-0.567000	0.06046	-0.256000	0.11100	ATG	.	.	.	none		0.502	TNFSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346601.1			C	172232704	T	C	172232704	3	2	174	1	0	0	0	0	1	0	0	0	16313	1406	49	3	644	3	TNFSF10	3	172232704	Missense_Mutation	SNP	T	TCGA-G7-6796-01A-11D-1961-08	132801686	172232704	25789726	14	10171											
ACOX3	8310	hgsc.bcm.edu	37	chr4	8372681	8372681	+	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	agtccagaacaaagtcaggaGgagcgatcacgtctaccagg	14	5	12	10	2	3	1	2	0	1	1	4	4	4	3	2	3	3	0	2	3	3	1			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr4:8372681G>A	ENST00000356406.5	-	17	2014	c.1937C>T	c.(1936-1938)cCt>cTt	p.P646L	ACOX3_ENST00000503233.1_Missense_Mutation_p.P646L|ACOX3_ENST00000413009.2_Silent_p.S623S|ACOX3_ENST00000515797.1_5'UTR	NM_003501.2	NP_003492.2	O15254	ACOX3_HUMAN	acyl-CoA oxidase 3, pristanoyl	646					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(17)|prostate(1)|skin(3)|stomach(1)	42						AAAGTCAGGAGGAGCGATCAC	0.562																																					p.P646L		Atlas-SNP	.											.	ACOX3	70	.	0			c.C1937T						PASS	.						120	104	109					4																	8372681		2203	4300	6503	SO:0001583	missense	8310	exon17			TCAGGAGGAGCGA	Y11411	CCDS3401.1, CCDS47017.1	4p15.3	2010-04-30	2010-04-30		ENSG00000087008	ENSG00000087008	1.3.3.6		121	protein-coding gene	gene with protein product		603402	"acyl-Coenzyme A oxidase 3, pristanoyl"			9271077	Standard	NM_003501		Approved		uc003glc.4	O15254	OTTHUMG00000090509	ENST00000356406.5:c.1937C>T	chr4.hg19:g.8372681G>A	ENSP00000348775:p.Pro646Leu	68.0	0.0	.		59.0	12.0	.	NM_003501	Q96AJ8	Missense_Mutation	SNP	ENST00000356406.5	hg19	CCDS3401.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.577015	0.86645	.	.	ENSG00000087008	ENST00000356406;ENST00000503233	T;T	0.38401	1.14;1.14	4.88	4.88	0.63580	Acyl-CoA oxidase, C-terminal (1);Acyl-CoA dehydrogenase/oxidase C-terminal (1);	0.069225	0.64402	N	0.000015	T	0.50718	0.1632	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.38628	-0.9652	9	0.11182	T	0.66	-18.1485	15.4924	0.75619	0.0:0.0:1.0:0.0	.	646	O15254	ACOX3_HUMAN	L	646	ENSP00000348775:P646L;ENSP00000421625:P646L	ENSP00000348775:P646L	P	-	2	0	ACOX3	8423581	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	6.945000	0.75947	2.226000	0.72624	0.549000	0.68633	CCT	.	.	.	none		0.562	ACOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206997.4			A	8372681	G	A	8372681	3	1	174	1	0	0	0	0	1	0	0	0	160	1000	35	2	173	2	ACOX3	4	8372681	Missense_Mutation	SNP	G	TCGA-G7-6796-01A-11D-1961-08		8372681	182781595	15	10172											
CENPC1	1060	hgsc.bcm.edu	37	chr4	68385012	68385012	+	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	tcaaaagtgtaagtctctctCttttgggcactagatggaat	11	14	9	7	0	3	1	1	0	2	1	5	2	3	2	0	2	0	2	0	2	5	4			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr4:68385012C>G	ENST00000273853.6	-	6	790	c.540G>C	c.(538-540)aaG>aaC	p.K180N		NM_001812.2	NP_001803.2	Q03188	CENPC_HUMAN	centromere protein C	180					chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	centromeric DNA binding (GO:0019237)|DNA binding (GO:0003677)										AAGTCTCTCTCTTTTGGGCAC	0.323																																					p.K180N		Atlas-SNP	.											.	CENPC1	66	.	0			c.G540C						PASS	.						88	83	84					4																	68385012		1809	4078	5887	SO:0001583	missense	1060	exon6			CTCTCTCTTTTGG	M95724	CCDS47063.1	4q13.2	2013-11-05	2013-07-03	2013-07-03	ENSG00000145241	ENSG00000145241			1854	protein-coding gene	gene with protein product		117141	"centromere protein C 1"	CENPC1		7959789	Standard	XR_245245		Approved	CENP-C, hcp-4, MIF2	uc003hdd.1	Q03188	OTTHUMG00000160735	ENST00000273853.6:c.540G>C	chr4.hg19:g.68385012C>G	ENSP00000273853:p.Lys180Asn	106.0	0.0	.		138.0	36.0	.	NM_001812	Q8IW27|Q9P0M5	Missense_Mutation	SNP	ENST00000273853.6	hg19	CCDS47063.1	.	.	.	.	.	.	.	.	.	.	C	10.84	1.463886	0.26335	.	.	ENSG00000145241	ENST00000273853	.	.	.	4.75	0.447	0.16608	.	0.626565	0.15039	N	0.283991	T	0.39226	0.1070	L	0.59436	1.845	0.28032	N	0.9341	D;D	0.65815	0.995;0.995	P;P	0.53954	0.738;0.738	T	0.30592	-0.9973	9	0.72032	D	0.01	-2.2885	2.5395	0.04722	0.3496:0.401:0.1533:0.0961	.	180;180	Q8IW27;Q03188	.;CENPC_HUMAN	N	180	.	ENSP00000273853:K180N	K	-	3	2	CENPC1	68067607	0.030000	0.19436	0.952000	0.39060	0.104000	0.19210	-0.627000	0.05521	0.173000	0.19788	-0.293000	0.09583	AAG	.	.	.	none		0.323	CENPC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362001.2			G	68385012	C	G	68385012	3	3	174	1	0	0	0	0	1	0	0	0	3231	912	32	4	2347	4	CENPC1	4	68385012	Missense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08	60012331	68385012	122769264	16	10173											
GC	2638	hgsc.bcm.edu	37	chr4	72629625	72629625	+	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	aagtgacagaggagcttgtcCgtaattagtggaatattccc	12	11	11	7	1	0	2	0	1	0	1	2	4	2	4	2	2	1	2	2	2	5	5	rs371509305		TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr4:72629625C>A	ENST00000273951.8	-	5	845	c.502G>T	c.(502-504)Gga>Tga	p.G168*	GC_ENST00000503472.1_5'UTR|GC_ENST00000513476.1_Nonsense_Mutation_p.G168*|GC_ENST00000504199.1_Nonsense_Mutation_p.G187*	NM_000583.3|NM_001204306.1	NP_000574.2|NP_001191235.1	P02774	VTDB_HUMAN	group-specific component (vitamin D binding protein)	168	Albumin 1. {ECO:0000255|PROSITE- ProRule:PRU00769}.			G -> E (in Ref. 1; AAA52173). {ECO:0000305}.	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)	GGAGCTTGTCCGTAATTAGTG	0.358																																					p.G187X		Atlas-SNP	.											.	GC	132	.	0			c.G559T						PASS	.						87	90	89					4																	72629625		2203	4300	6503	SO:0001587	stop_gained	2638	exon6			CTTGTCCGTAATT	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.502G>T	chr4.hg19:g.72629625C>A	ENSP00000273951:p.Gly168*	131.0	0.0	.		134.0	6.0	.	NM_001204307	B4DPP2|D6RAK8|Q16309|Q16310|Q53F31|Q6GTG1	Nonsense_Mutation	SNP	ENST00000273951.8	hg19	CCDS3550.1	.	.	.	.	.	.	.	.	.	.	C	37	6.603213	0.97697	.	.	ENSG00000145321	ENST00000273951;ENST00000504199;ENST00000513476	.	.	.	5.49	5.49	0.81192	.	0.123122	0.56097	D	0.000038	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	13.6514	0.62312	0.0:0.9245:0.0:0.0755	.	.	.	.	X	168;187;168	.	ENSP00000273951:G168X	G	-	1	0	GC	72848489	0.989000	0.36119	1.000000	0.80357	0.768000	0.43524	1.917000	0.39996	2.727000	0.93392	0.650000	0.86243	GGA	.	.	.	alt		0.358	GC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252167.2			A	72629625	C	A	72629625	4	1	174	1	0	0	0	0	0	1	0	0	6289	661	23	4	954	4	GC	4	72629625	Nonsense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08	4244613	72629625	118524651	17	10174											
RNF150	57484	hgsc.bcm.edu	37	chr4	141832440	141832440	+	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	tcgctggcacctgtgatctgGttggtgggtggacctcccag	4	11	15	11	1	1	1	0	1	1	0	3	2	2	2	3	5	0	3	3	5	0	1			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr4:141832440G>C	ENST00000515673.2	-	6	1089	c.1056C>G	c.(1054-1056)aaC>aaG	p.N352K	RNF150_ENST00000420921.2_Missense_Mutation_p.N211K|RNF150_ENST00000379512.2_Missense_Mutation_p.N211K|RNF150_ENST00000507500.1_Missense_Mutation_p.N352K|RNF150_ENST00000306799.3_Missense_Mutation_p.N310K			Q9ULK6	RN150_HUMAN	ring finger protein 150	352						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|large_intestine(10)|lung(7)|ovary(1)	19	all_hematologic(180;0.162)					CTGTGATCTGGTTGGTGGGTG	0.557																																					p.N352K		Atlas-SNP	.											.	RNF150	94	.	0			c.C1056G						PASS	.						100	93	95					4																	141832440		2203	4300	6503	SO:0001583	missense	57484	exon6			GATCTGGTTGGTG	AB033040	CCDS34065.1	4q31.1	2013-01-09			ENSG00000170153	ENSG00000170153		"RING-type (C3HC4) zinc fingers"	23138	protein-coding gene	gene with protein product						10574462	Standard	XM_005263150		Approved	KIAA1214	uc003iio.1	Q9ULK6	OTTHUMG00000161380	ENST00000515673.2:c.1056C>G	chr4.hg19:g.141832440G>C	ENSP00000425840:p.Asn352Lys	105.0	0.0	.		111.0	14.0	.	NM_020724	Q3T1D0|Q6ZNW6	Missense_Mutation	SNP	ENST00000515673.2	hg19	CCDS34065.1	.	.	.	.	.	.	.	.	.	.	G	17.78	3.474491	0.63737	.	.	ENSG00000170153	ENST00000379512;ENST00000420921;ENST00000306799;ENST00000515673;ENST00000507500;ENST00000506101	T;T;T;T;T;T	0.15139	2.45;2.45;2.49;3.47;3.48;2.51	5.74	0.749	0.18381	.	0.472179	0.23614	N	0.046304	T	0.16257	0.0391	L	0.29908	0.895	0.51767	D	0.999932	P;B;B	0.40970	0.734;0.294;0.415	P;B;B	0.47528	0.549;0.299;0.334	T	0.03103	-1.1072	10	0.46703	T	0.11	.	9.3149	0.37928	0.5802:0.0:0.4198:0.0	.	310;352;352	Q9ULK6-2;Q9ULK6-3;Q9ULK6	.;.;RN150_HUMAN	K	211;211;310;352;352;183	ENSP00000368827:N211K;ENSP00000394581:N211K;ENSP00000304321:N310K;ENSP00000425840:N352K;ENSP00000425568:N352K;ENSP00000425947:N183K	ENSP00000304321:N310K	N	-	3	2	RNF150	142051890	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	0.973000	0.29422	0.180000	0.19960	0.655000	0.94253	AAC	.	.	.	none		0.557	RNF150-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364739.2	XM_291090		C	141832440	G	C	141832440	3	2	174	1	0	0	0	0	1	0	0	0	13464	1252	44	4	268	4	RNF150	4	141832440	Missense_Mutation	SNP	G	TCGA-G7-6796-01A-11D-1961-08	69202815	141832440	49321836	18	10175											
SCAND3	114821	hgsc.bcm.edu	37	chr6	28554157	28554157	+	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	cactctcaggattatgctccCgcacccaagactggagctcc	9	8	8	16	1	1	1	1	0	1	1	4	3	3	3	3	2	2	3	3	2	2	1			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr6:28554157C>A	ENST00000452236.2	-	1	955	c.338G>T	c.(337-339)cGg>cTg	p.R113L	RP5-1186N24.3_ENST00000499525.1_RNA|SCAND3_ENST00000530247.1_Intron	NM_052923.1	NP_443155.1														NS(3)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(14)|liver(1)|lung(29)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)	71						ATTATGCTCCCGCACCCAAGA	0.527																																					p.R113L		Atlas-SNP	.											SCAND3,NS,carcinoma,0,1	SCAND3	156	.	0			c.G338T						PASS	.						123	130	128					6																	28554157		2203	4300	6503	SO:0001583	missense	114821	exon1			TGCTCCCGCACCC																												ENST00000452236.2:c.338G>T	chr6.hg19:g.28554157C>A	ENSP00000395259:p.Arg113Leu	267.0	0.0	.		236.0	11.0	.	NM_052923		Missense_Mutation	SNP	ENST00000452236.2	hg19	CCDS34355.1	.	.	.	.	.	.	.	.	.	.	C	16.04	3.009764	0.54361	.	.	ENSG00000232040	ENST00000452236	T	0.04551	3.6	3.46	1.66	0.24008	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	.	.	.	.	T	0.08670	0.0215	M	0.82056	2.57	0.25606	N	0.986544	D	0.71674	0.998	D	0.73708	0.981	T	0.11012	-1.0605	9	0.87932	D	0	.	5.6758	0.17747	0.0:0.6443:0.0:0.3557	.	113	Q6R2W3	SCND3_HUMAN	L	113	ENSP00000395259:R113L	ENSP00000395259:R113L	R	-	2	0	SCAND3	28662136	0.000000	0.05858	0.683000	0.30040	0.759000	0.43091	-0.482000	0.06544	0.291000	0.22468	0.655000	0.94253	CGG	.	.	.	none		0.527	SCAND3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000043551.3			A	28554157	C	A	28554157	3	1	174	1	0	0	0	0	1	0	0	0	13889	652	23	4	3655	4	SCAND3	6	28554157	Missense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08		28554157	142560910	19	10176											
LMBRD1	55788	hgsc.bcm.edu	37	chr6	70462182	70462182	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagtatcatcatcatcctttTcttcataatagaagtagaca	14	15	4	8	0	5	2	4	0	1	2	6	2	6	2	1	0	0	2	1	0	6	8			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr6:70462182T>C	ENST00000370577.3	-	4	603	c.374A>G	c.(373-375)gAa>gGa	p.E125G	LMBRD1_ENST00000370570.1_Missense_Mutation_p.E52G	NM_018368.3	NP_060838.3	Q9NUN5	LMBD1_HUMAN	LMBR1 domain containing 1	125					cobalamin metabolic process (GO:0009235)|insulin receptor internalization (GO:0038016)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein kinase B signaling (GO:0051898)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	clathrin-coated endocytic vesicle (GO:0045334)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cobalamin binding (GO:0031419)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	31						ATCATCCTTTTCTTCATAATA	0.294																																					p.E125G		Atlas-SNP	.											.	LMBRD1	61	.	0			c.A374G						PASS	.						54	56	56					6																	70462182		2197	4278	6475	SO:0001583	missense	55788	exon4			TCCTTTTCTTCAT	AF113224	CCDS4969.1	6q13	2011-05-12	2005-07-25	2005-07-25	ENSG00000168216	ENSG00000168216			23038	protein-coding gene	gene with protein product		612625	"chromosome 6 open reading frame 209"	C6orf209		19136951	Standard	NM_018368		Approved	FLJ11240, bA810I22.1, cblF	uc003pfa.3	Q9NUN5	OTTHUMG00000014985	ENST00000370577.3:c.374A>G	chr6.hg19:g.70462182T>C	ENSP00000359609:p.Glu125Gly	71.0	0.0	.		77.0	16.0	.	NM_018368	A8K204|E1P531|Q5VUN6|Q86Y70|Q96FW4|Q9BY56|Q9NZD6	Missense_Mutation	SNP	ENST00000370577.3	hg19	CCDS4969.1	.	.	.	.	.	.	.	.	.	.	T	16.36	3.102734	0.56183	.	.	ENSG00000168216	ENST00000370577;ENST00000370570	T;T	0.26067	1.76;1.76	5.33	4.15	0.48705	LMBR1-like membrane protein (1);	0.051951	0.85682	D	0.000000	T	0.19805	0.0476	M	0.85462	2.755	0.58432	D	0.999998	B	0.18968	0.032	B	0.22880	0.042	T	0.09487	-1.0672	10	0.39692	T	0.17	-12.1431	10.4775	0.44674	0.0:0.0797:0.0:0.9203	.	125	Q9NUN5	LMBD1_HUMAN	G	125;52	ENSP00000359609:E125G;ENSP00000359602:E52G	ENSP00000359602:E52G	E	-	2	0	LMBRD1	70518903	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.495000	0.66912	2.022000	0.59522	0.455000	0.32223	GAA	.	.	.	none		0.294	LMBRD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041124.1	NM_018368		C	70462182	T	C	70462182	3	2	174	1	0	0	0	0	1	0	0	0	8849	1783	62	3	1300	3	LMBRD1	6	70462182	Missense_Mutation	SNP	T	TCGA-G7-6796-01A-11D-1961-08	41908025	70462182	100652885	20	10177											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152673335	152673335	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgtgttctttccggacagTgctggtcagttccttcaact	6	15	9	11	1	3	0	2	0	1	0	5	1	5	1	2	2	2	3	2	2	1	4			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr6:152673335T>C	ENST00000367255.5	-	70	12008	c.11407A>G	c.(11407-11409)Act>Gct	p.T3803A	SYNE1_ENST00000448038.1_Missense_Mutation_p.T3788A|SYNE1_ENST00000341594.5_Missense_Mutation_p.T3774A|SYNE1_ENST00000265368.4_Missense_Mutation_p.T3803A|SYNE1_ENST00000423061.1_Missense_Mutation_p.T3788A	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3803					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)		TTCCGGACAGTGCTGGTCAGT	0.448										HNSCC(10;0.0054)																											p.T3803A		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A11407G						PASS	.						251	230	237					6																	152673335		2203	4300	6503	SO:0001583	missense	23345	exon70			GGACAGTGCTGGT	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.11407A>G	chr6.hg19:g.152673335T>C	ENSP00000356224:p.Thr3803Ala	217.0	0.0	.		261.0	44.0	.	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	T	9.518	1.107572	0.20714	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.34072	1.45;1.45;1.45;1.45;1.38	6.04	2.28	0.28536	.	0.339507	0.25194	N	0.032438	T	0.07638	0.0192	L	0.43152	1.355	0.09310	N	0.999998	B;B;B;B	0.09022	0.002;0.002;0.002;0.001	B;B;B;B	0.06405	0.001;0.001;0.001;0.002	T	0.39603	-0.9606	10	0.08837	T	0.75	.	4.3779	0.11279	0.2094:0.2204:0.0:0.5702	.	3803;3803;3803;3788	B7ZBC3;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	A	3803;3788;3803;3788;3774	ENSP00000356224:T3803A;ENSP00000396024:T3788A;ENSP00000265368:T3803A;ENSP00000390975:T3788A;ENSP00000341887:T3774A	ENSP00000265368:T3803A	T	-	1	0	SYNE1	152715028	0.076000	0.21285	0.602000	0.28890	0.876000	0.50452	0.615000	0.24329	0.155000	0.19261	0.460000	0.39030	ACT	.	.	.	none		0.448	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		C	152673335	T	C	152673335	3	2	174	1	0	0	0	0	1	0	0	0	15457	1696	59	3	15367	3	SYNE1	6	152673335	Missense_Mutation	SNP	T	TCGA-G7-6796-01A-11D-1961-08	82211153	152673335	18441732	21	10178											
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47898372	47898372	+	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	ccagactctggatatgagacCgatgagctcaagcctcactc	11	8	9	13	1	3	3	2	2	1	2	4	6	3	4	3	1	2	1	3	1	2	1	rs146609164	byFrequency	TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr7:47898372C>A	ENST00000289672.2	-	27	4311	c.4261G>T	c.(4261-4263)Ggt>Tgt	p.G1421C		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1421	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						GATATGAGACCGATGAGCTCA	0.483																																					p.G1421C		Atlas-SNP	.											.	PKD1L1	328	.	0			c.G4261T						PASS	.						135	131	133					7																	47898372		2203	4300	6503	SO:0001583	missense	168507	exon27			TGAGACCGATGAG	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.4261G>T	chr7.hg19:g.47898372C>A	ENSP00000289672:p.Gly1421Cys	98.0	0.0	.		121.0	7.0	.	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	hg19	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	C	8.989	0.977345	0.18812	.	.	ENSG00000158683	ENST00000289672	T	0.19250	2.16	5.03	0.111	0.14619	Egg jelly receptor, REJ-like (1);	2.019780	0.02131	N	0.056369	T	0.13628	0.0330	N	0.22421	0.69	0.09310	N	1	P	0.35600	0.511	B	0.31869	0.137	T	0.13872	-1.0493	10	0.39692	T	0.17	0.4077	4.0897	0.09963	0.3374:0.3834:0.2792:0.0	.	1421	Q8TDX9	PK1L1_HUMAN	C	1421	ENSP00000289672:G1421C	ENSP00000289672:G1421C	G	-	1	0	PKD1L1	47864897	0.013000	0.17824	0.000000	0.03702	0.005000	0.04900	0.268000	0.18571	-0.126000	0.11682	-0.171000	0.13296	GGT	.	C|1.000;T|0.000	.	alt		0.483	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		A	47898372	C	A	47898372	3	1	174	1	0	0	0	0	1	0	0	0	11971	652	23	4	4412	4	PKD1L1	7	47898372	Missense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08		47898372	111240291	22	10179											
C7orf42	55069	hgsc.bcm.edu	37	chr7	66410208	66410208	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tattcccgcaacgtcacccaTctgtactcaaccatcttagg	10	11	5	15	2	4	0	2	0	2	0	5	0	5	0	3	1	3	2	3	1	5	4			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr7:66410208T>C	ENST00000341567.4	+	3	660	c.405T>C	c.(403-405)caT>caC	p.H135H		NM_017994.4	NP_060464.1	Q9NWD8	TM248_HUMAN	transmembrane protein 248	135						integral component of membrane (GO:0016021)											ACGTCACCCATCTGTACTCAA	0.527																																					p.H135H		Atlas-SNP	.											.	.	.	.	0			c.T405C						PASS	.						107	105	106					7																	66410208		2203	4300	6503	SO:0001819	synonymous_variant	55069	exon3			CACCCATCTGTAC		CCDS5536.1	7q11.21	2012-05-30	2012-05-30	2012-05-30	ENSG00000106609	ENSG00000106609			25476	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 42"	C7orf42		12477932	Standard	XM_005250482		Approved	FLJ10099, FLJ13090	uc003tvk.3	Q9NWD8	OTTHUMG00000129553	ENST00000341567.4:c.405T>C	chr7.hg19:g.66410208T>C		244.0	0.0	.		247.0	43.0	.	NM_017994	Q53H07|Q96FR2	Silent	SNP	ENST00000341567.4	hg19	CCDS5536.1																																																																																			.	.	.	none		0.527	TMEM248-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251745.2	NM_017994		C	66410208	T	C	66410208	2	2	174	1	0	0	0	0	0	0	0	1	2394	1432	50	3		3	C7orf42	7	66410208	Silent	SNP	T	TCGA-G7-6796-01A-11D-1961-08	18511836	66410208	92728455	23	10180											
ING3	54556	hgsc.bcm.edu	37	chr7	120595620	120595620	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgttttcattcaggactactAtaaagctttggaagatgcag	12	14	9	6	0	2	1	2	0	0	1	2	3	2	3	0	2	3	3	0	2	5	7			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr7:120595620A>G	ENST00000315870.5	+	4	357	c.209A>G	c.(208-210)tAt>tGt	p.Y70C	ING3_ENST00000339121.5_Missense_Mutation_p.Y70C|ING3_ENST00000445699.1_Missense_Mutation_p.Y70C|ING3_ENST00000431467.1_Missense_Mutation_p.Y55C	NM_019071.2	NP_061944.2	Q9NXR8	ING3_HUMAN	inhibitor of growth family, member 3	70					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)					CAGGACTACTATAAAGCTTTG	0.303																																					p.Y70C		Atlas-SNP	.											.	ING3	36	.	0			c.A209G						PASS	.						78	79	78					7																	120595620		2203	4300	6503	SO:0001583	missense	54556	exon4			ACTACTATAAAGC	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.209A>G	chr7.hg19:g.120595620A>G	ENSP00000320566:p.Tyr70Cys	30.0	0.0	.		36.0	5.0	.	NM_019071	A8K790|O60394|Q567P3|Q6GMT3|Q7Z762|Q969G0|Q96DT4|Q9HC99|Q9P081	Missense_Mutation	SNP	ENST00000315870.5	hg19	CCDS5778.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.990024	0.74589	.	.	ENSG00000071243	ENST00000315870;ENST00000339121;ENST00000445699;ENST00000431467	D;D	0.95518	-3.7;-3.73	5.54	5.54	0.83059	Inhibitor of growth protein, N-terminal (1);	0.059163	0.64402	D	0.000001	D	0.96765	0.8944	M	0.73598	2.24	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.975;0.988;0.999;0.999	D;P;P;D;D	0.67900	0.911;0.739;0.811;0.912;0.954	D	0.95906	0.8919	10	0.38643	T	0.18	-21.6296	10.2439	0.43330	0.852:0.0:0.0:0.148	.	70;70;70;70;70	B7ZKQ7;Q5GRH6;Q9NXR8;Q9NXR8-2;C9JUT0	.;.;ING3_HUMAN;.;.	C	70;70;70;55	ENSP00000320566:Y70C;ENSP00000388506:Y55C	ENSP00000320566:Y70C	Y	+	2	0	ING3	120382856	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.966000	0.76073	2.230000	0.72887	0.528000	0.53228	TAT	.	.	.	none		0.303	ING3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280453.2	NM_019071		G	120595620	A	G	120595620	3	3	174	1	0	0	0	0	1	0	0	0	7744	449	16	3	223	3	ING3	7	120595620	Missense_Mutation	SNP	A	TCGA-G7-6796-01A-11D-1961-08	54185412	120595620	38543043	24	10181											
HIPK2	28996	hgsc.bcm.edu	37	chr7	139416356	139416356	+	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	ggcagtggcgacagtggcccCgcttgcattattctgaatca	8	10	12	11	2	2	1	1	1	1	0	2	2	2	1	2	3	1	3	2	3	2	3			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr7:139416356C>A	ENST00000406875.3	-	2	572	c.478G>T	c.(478-480)Ggg>Tgg	p.G160W	HIPK2_ENST00000428878.2_Missense_Mutation_p.G160W|HIPK2_ENST00000342645.6_Missense_Mutation_p.G160W	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	160	Transcriptional corepression. {ECO:0000250}.				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)			breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					ACAGTGGCCCCGCTTGCATTA	0.557																																					p.G160W		Atlas-SNP	.											.	HIPK2	192	.	0			c.G478T						PASS	.						139	121	126					7																	139416356		1568	3582	5150	SO:0001583	missense	28996	exon2			TGGCCCCGCTTGC	AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"homeodomain-interacting protein kinase 2"			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.478G>T	chr7.hg19:g.139416356C>A	ENSP00000385571:p.Gly160Trp	192.0	0.0	.		194.0	8.0	.	NM_022740	Q75MR7|Q8WWI4|Q9H2Y1	Missense_Mutation	SNP	ENST00000406875.3	hg19		.	.	.	.	.	.	.	.	.	.	C	15.42	2.827150	0.50739	.	.	ENSG00000064393	ENST00000406875;ENST00000428878;ENST00000342645	T;T;T	0.55413	0.52;0.55;0.55	5.41	4.53	0.55603	.	.	.	.	.	T	0.73164	0.3552	.	.	.	0.58432	D	0.999992	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.987	T	0.77707	-0.2487	8	0.87932	D	0	.	14.152	0.65392	0.0:0.9279:0.0:0.0721	.	160;160	Q9H2X6;Q9H2X6-3	HIPK2_HUMAN;.	W	160	ENSP00000385571:G160W;ENSP00000413724:G160W;ENSP00000343108:G160W	ENSP00000343108:G160W	G	-	1	0	HIPK2	139062842	1.000000	0.71417	0.935000	0.37517	0.365000	0.29674	7.677000	0.84024	1.277000	0.44412	-0.140000	0.14226	GGG	.	.	.	none		0.557	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740		A	139416356	C	A	139416356	3	1	174	1	0	0	0	0	1	0	0	0	7124	652	23	4	3174	4	HIPK2	7	139416356	Missense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08	18820736	139416356	19722307	25	10182											
MCPH1	79648	hgsc.bcm.edu	37	chr8	6302006	6302006	+	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	aaaggaagttggaaggatccAttaatgacattaaaagtgat	18	10	10	3	0	0	2	0	2	0	0	1	5	1	5	1	3	0	1	1	3	6	3			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr8:6302006A>T	ENST00000344683.5	+	8	839	c.763A>T	c.(763-765)Att>Ttt	p.I255F	MCPH1_ENST00000522905.1_Missense_Mutation_p.I207F|MCPH1_ENST00000519480.1_Missense_Mutation_p.I255F	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	255					cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)		AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		GGAAGGATCCATTAATGACAT	0.358																																					p.I255F	Colon(95;1448 1467 8277 34473 35819)	Atlas-SNP	.											.	MCPH1	65	.	0			c.A763T						PASS	.						129	122	124					8																	6302006		1883	4107	5990	SO:0001583	missense	79648	exon8			GGATCCATTAATG	AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"BRCT-repeat inhibitor of TERT expression 1"	607117	"microcephaly, primary autosomal recessive 1"			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.763A>T	chr8.hg19:g.6302006A>T	ENSP00000342924:p.Ile255Phe	89.0	0.0	.		89.0	23.0	.	NM_001172574	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Missense_Mutation	SNP	ENST00000344683.5	hg19	CCDS43689.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.579572	0.86645	.	.	ENSG00000147316	ENST00000344683;ENST00000519480;ENST00000522905	T;T;T	0.13778	2.56;2.56;2.56	5.26	-7.74	0.01241	.	1.774350	0.02525	N	0.092983	T	0.17492	0.0420	L	0.53249	1.67	0.09310	N	1	P;P;P	0.46784	0.884;0.867;0.884	P;P;P	0.52267	0.522;0.694;0.522	T	0.40289	-0.9571	10	0.32370	T	0.25	0.0924	3.4052	0.07338	0.3624:0.1106:0.4182:0.1088	.	207;255;255	E9PH63;Q8NEM0;E9PGU5	.;MCPH1_HUMAN;.	F	255;255;207	ENSP00000342924:I255F;ENSP00000430962:I255F;ENSP00000430768:I207F	ENSP00000342924:I255F	I	+	1	0	MCPH1	6289414	0.000000	0.05858	0.000000	0.03702	0.857000	0.48899	-0.113000	0.10774	-1.605000	0.01593	0.533000	0.62120	ATT	.	.	.	none		0.358	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596		T	6302006	A	T	6302006	3	4	174	1	0	0	0	0	1	0	0	0	9405	217	8	5	793	5	MCPH1	8	6302006	Missense_Mutation	SNP	A	TCGA-G7-6796-01A-11D-1961-08		6302006	140062016	26	10183											
IKBKB	3551	hgsc.bcm.edu	37	chr8	42173753	42173753	+	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	tggctgagcgactggagaagTggctgcaactgatgctgatg	9	9	16	7	1	0	4	0	3	0	1	0	6	0	4	0	3	4	4	0	3	2	0			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr8:42173753T>A	ENST00000520810.1	+	10	1012	c.826T>A	c.(826-828)Tgg>Agg	p.W276R	IKBKB_ENST00000379708.3_Missense_Mutation_p.W53R|IKBKB_ENST00000416505.2_Missense_Mutation_p.W217R|IKBKB_ENST00000520835.1_Missense_Mutation_p.W274R|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	276	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)	ACTGGAGAAGTGGCTGCAACT	0.562																																					p.W276R		Atlas-SNP	.											.	IKBKB	88	.	0			c.T826A						PASS	.						66	58	61					8																	42173753		2203	4300	6503	SO:0001583	missense	3551	exon10			GAGAAGTGGCTGC	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.826T>A	chr8.hg19:g.42173753T>A	ENSP00000430684:p.Trp276Arg	68.0	0.0	.		48.0	10.0	.	NM_001556	B4DZ30|B4E0U4|O75327	Missense_Mutation	SNP	ENST00000520810.1	hg19	CCDS6128.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.617138	0.87359	.	.	ENSG00000104365	ENST00000520810;ENST00000416505;ENST00000520835;ENST00000379708	T;T;T;T	0.64803	-0.12;-0.12;-0.12;1.78	5.27	5.27	0.74061	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.057892	0.85682	D	0.000000	T	0.78780	0.4337	M	0.75264	2.295	0.80722	D	1	P;D;P;D;D;D	0.89917	0.879;0.998;0.836;0.999;0.995;1.0	P;D;B;D;D;D	0.97110	0.745;0.987;0.425;0.987;0.988;1.0	T	0.81621	-0.0850	10	0.72032	D	0.01	.	15.1947	0.73078	0.0:0.0:0.0:1.0	.	217;274;53;227;276;276	B4E0U4;O14920-2;B3KRB7;Q59GL9;O14920;Q32ND9	.;.;.;.;IKKB_HUMAN;.	R	276;217;274;53	ENSP00000430684:W276R;ENSP00000404920:W217R;ENSP00000430868:W274R;ENSP00000369030:W53R	ENSP00000369030:W53R	W	+	1	0	IKBKB	42292910	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	6.228000	0.72288	1.994000	0.58287	0.460000	0.39030	TGG	.	.	.	none		0.562	IKBKB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377214.1			A	42173753	T	A	42173753	3	1	174	1	0	0	0	0	1	0	0	0	7618	1696	59	5	860	5	IKBKB	8	42173753	Missense_Mutation	SNP	T	TCGA-G7-6796-01A-11D-1961-08	35871747	42173753	104190269	27	10184											
CYP7A1	1581	hgsc.bcm.edu	37	chr8	59409487	59409487	+	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	tatgtgctttctgtgtgtccCgccttgtaagatctctgcca	5	16	9	11	1	2	1	0	0	2	1	4	1	3	1	3	0	2	2	3	0	2	4	rs201046553		TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr8:59409487C>A	ENST00000301645.3	-	3	721	c.584G>T	c.(583-585)cGg>cTg	p.R195L		NM_000780.3	NP_000771.2	P22680	CP7A1_HUMAN	cytochrome P450, family 7, subfamily A, polypeptide 1	195					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)	p.R195L(1)		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)				CTGTGTGTCCCGCCTTGTAAG	0.458									Neonatal Giant Cell Hepatitis																												p.R195L		Atlas-SNP	.											.	CYP7A1	76	.	1	Substitution - Missense(1)	lung(1)	c.G584T						PASS	.						136	129	131					8																	59409487		2203	4300	6503	SO:0001583	missense	1581	exon3	Familial Cancer Database	Neonatal Hemochromatosis	GTGTCCCGCCTTG	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.584G>T	chr8.hg19:g.59409487C>A	ENSP00000301645:p.Arg195Leu	163.0	0.0	.		176.0	9.0	.	NM_000780	P78454|Q3MIL8|Q7KZ19	Missense_Mutation	SNP	ENST00000301645.3	hg19	CCDS6171.1	.	.	.	.	.	.	.	.	.	.	c	7.189	0.591159	0.13812	.	.	ENSG00000167910	ENST00000301645	T	0.63913	-0.07	5.74	-2.23	0.06930	.	0.519770	0.23353	N	0.049112	T	0.31513	0.0799	N	0.08118	0	0.25011	N	0.991403	B	0.11235	0.004	B	0.14578	0.011	T	0.29941	-0.9995	10	0.08381	T	0.77	-0.7265	9.3325	0.38030	0.0:0.1223:0.4845:0.3932	.	195	P22680	CP7A1_HUMAN	L	195	ENSP00000301645:R195L	ENSP00000301645:R195L	R	-	2	0	CYP7A1	59572041	1.000000	0.71417	0.000000	0.03702	0.001000	0.01503	1.764000	0.38471	-0.158000	0.11040	-0.414000	0.06135	CGG	.	C|1.000;T|0.000	.	alt		0.458	CYP7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378190.1	NM_000780		A	59409487	C	A	59409487	3	1	174	1	0	0	0	0	1	0	0	0	4198	652	23	4	946	4	CYP7A1	8	59409487	Missense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08	17235734	59409487	86954535	28	10185											
FBXL6	26233	hgsc.bcm.edu	37	chr8	145579793	145579793	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagtgtatggcaccacttcTgggtcaaaaaggggctgccc	9	8	13	11	0	2	0	1	0	1	0	2	0	2	0	2	4	1	4	2	4	3	2			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr8:145579793T>C	ENST00000331890.5	-	8	1371	c.1307A>G	c.(1306-1308)cAg>cGg	p.Q436R	FBXL6_ENST00000526524.1_Intron|SLC52A2_ENST00000530047.1_5'Flank|FBXL6_ENST00000455319.2_Missense_Mutation_p.Q430R|SLC52A2_ENST00000540505.1_5'Flank|TMEM249_ENST00000531225.1_5'Flank|SLC52A2_ENST00000527078.1_5'Flank|TMEM249_ENST00000398633.3_5'Flank|SLC52A2_ENST00000402965.1_5'Flank|SLC52A2_ENST00000329994.2_5'Flank|SLC52A2_ENST00000532887.1_5'Flank	NM_012162.2	NP_036294.2	Q8N531	FBXL6_HUMAN	F-box and leucine-rich repeat protein 6	436					protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)		ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|lung(3)|ovary(1)	5	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;4.43e-40)|Epithelial(56;1.48e-39)|all cancers(56;1.49e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)			GCACCACTTCTGGGTCAAAAA	0.592																																					p.Q436R		Atlas-SNP	.											.	FBXL6	26	.	0			c.A1307G						PASS	.						70	77	74					8																	145579793		2203	4299	6502	SO:0001583	missense	26233	exon8			CACTTCTGGGTCA	AF174592	CCDS6422.1, CCDS47942.1	8q24.3	2011-06-09			ENSG00000182325	ENSG00000182325		"F-boxes / Leucine-rich repeats"	13603	protein-coding gene	gene with protein product		609076				10531035, 10531037	Standard	NM_012162		Approved	FBL6	uc003zcb.3	Q8N531	OTTHUMG00000165169	ENST00000331890.5:c.1307A>G	chr8.hg19:g.145579793T>C	ENSP00000330098:p.Gln436Arg	181.0	0.0	.		156.0	30.0	.	NM_012162	Q53G43|Q9H5W9|Q9UKC7	Missense_Mutation	SNP	ENST00000331890.5	hg19	CCDS6422.1	.	.	.	.	.	.	.	.	.	.	T	10.23	1.292836	0.23564	.	.	ENSG00000182325	ENST00000455319;ENST00000331890	T;T	0.24538	1.85;1.85	5.13	1.23	0.21249	.	0.612082	0.16879	N	0.195799	T	0.14141	0.0342	L	0.31207	0.915	0.22803	N	0.998711	B;B	0.14438	0.006;0.01	B;B	0.11329	0.003;0.006	T	0.32955	-0.9887	10	0.12766	T	0.61	-2.0714	6.0415	0.19736	0.0:0.403:0.0:0.597	.	436;430	Q8N531;Q8N531-2	FBXL6_HUMAN;.	R	430;436	ENSP00000403873:Q430R;ENSP00000330098:Q436R	ENSP00000330098:Q436R	Q	-	2	0	FBXL6	145550601	0.622000	0.27085	0.991000	0.47740	0.810000	0.45777	0.327000	0.19663	0.240000	0.21263	0.460000	0.39030	CAG	.	.	.	none		0.592	FBXL6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382413.1	NM_024555		C	145579793	T	C	145579793	3	2	174	1	0	0	0	0	1	0	0	0	5730	1580	55	3	320	3	FBXL6	8	145579793	Missense_Mutation	SNP	T	TCGA-G7-6796-01A-11D-1961-08	86170306	145579793	784229	29	10186											
KIN	22944	hgsc.bcm.edu	37	chr10	7825098	7825098	+	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	ctgaagccagcaatagttgtCtctgatgagattcggacata	12	11	10	8	1	1	3	0	3	1	1	3	5	1	4	1	1	2	2	1	1	4	4			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr10:7825098C>G	ENST00000379562.4	-	2	202	c.155G>C	c.(154-156)aGa>aCa	p.R52T	KIN_ENST00000543003.1_Intron|KIN_ENST00000535925.1_Missense_Mutation_p.R52T	NM_012311.3	NP_036443.1			Kin17 DNA and RNA binding protein											endometrium(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|skin(2)	19						CAATAGTTGTCTCTGATGAGA	0.328																																					p.R52T		Atlas-SNP	.											.	KIN	39	.	0			c.G155C						PASS	.						61	60	60					10																	7825098		2203	4298	6501	SO:0001583	missense	22944	exon2			AGTTGTCTCTGAT	AJ005273	CCDS7080.1	10p15-p14	2014-07-15	2014-07-15		ENSG00000151657	ENSG00000151657			6327	protein-coding gene	gene with protein product		601720	"antigenic determinant of recA protein (mouse) homolog", "KIN, antigenic determinant of recA protein homolog (mouse)"			1923796, 24140279	Standard	NM_012311		Approved	KIN17, Rts2	uc001ijt.3	O60870	OTTHUMG00000017634	ENST00000379562.4:c.155G>C	chr10.hg19:g.7825098C>G	ENSP00000368881:p.Arg52Thr	49.0	0.0	.		61.0	8.0	.	NM_012311		Missense_Mutation	SNP	ENST00000379562.4	hg19	CCDS7080.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.266664	0.80358	.	.	ENSG00000151657	ENST00000535925;ENST00000379562	.	.	.	6.06	4.18	0.49190	DNA/RNA-binding protein Kin17, conserved domain (1);	0.132739	0.64402	D	0.000002	T	0.81331	0.4800	H	0.95114	3.625	0.80722	D	1	B;B	0.22146	0.065;0.065	B;B	0.35470	0.203;0.203	T	0.80384	-0.1405	9	0.87932	D	0	-35.5448	10.9911	0.47549	0.13:0.8027:0.0:0.0672	.	52;52	B4DX32;O60870	.;KIN17_HUMAN	T	52	.	ENSP00000368881:R52T	R	-	2	0	KIN	7865104	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.693000	0.84214	0.846000	0.35142	0.650000	0.86243	AGA	.	.	.	none		0.328	KIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046683.2	NM_012311		G	7825098	C	G	7825098	3	3	174	1	0	0	0	0	1	0	0	0	8322	913	32	4	1074	4	KIN	10	7825098	Missense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08		7825098	127709649	30	10187											
PLCE1	51196	hgsc.bcm.edu	37	chr10	95849076	95849076	+	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	ctcttcccgctctctgaggtAcccaattttaccttgttaaa	8	15	5	13	1	2	1	0	1	2	0	4	1	3	1	3	1	2	3	3	1	5	6			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr10:95849076A>G	ENST00000371380.3	+	2	1441				PLCE1_ENST00000260766.3_Intron|RP11-429H9.4_ENST00000438899.1_RNA|PLCE1_ENST00000371385.3_Silent_p.V75V|PLCE1_ENST00000371375.1_Silent_p.V75V			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1						activation of MAPK activity (GO:0000187)|calcium-mediated signaling (GO:0019722)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|diacylglycerol biosynthetic process (GO:0006651)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerulus development (GO:0032835)|heart development (GO:0007507)|inositol phosphate metabolic process (GO:0043647)|inositol phosphate-mediated signaling (GO:0048016)|lipid catabolic process (GO:0016042)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipid metabolic process (GO:0006644)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of protein kinase activity (GO:0045859)|regulation of Ras protein signal transduction (GO:0046578)|regulation of smooth muscle contraction (GO:0006940)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|guanyl-nucleotide exchange factor activity (GO:0005085)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|Ras GTPase binding (GO:0017016)|receptor signaling protein activity (GO:0005057)			liver(1)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.0458)				TCTCTGAGGTACCCAATTTTA	0.502																																					p.V75V		Atlas-SNP	.											.	PLCE1	543	.	0			c.A225G						PASS	.						142	126	131					10																	95849076		1568	3582	5150	SO:0001627	intron_variant	51196	exon1			TGAGGTACCCAAT		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.1207-42855A>G	chr10.hg19:g.95849076A>G		198.0	0.0	.		169.0	66.0	.	NM_001165979	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Silent	SNP	ENST00000371380.3	hg19	CCDS41552.1																																																																																			.	.	.	none		0.502	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341		G	95849076	A	G	95849076	1	3	174	0	1	0	0	0	0	0	0	0	12041	378	14	3		3	PLCE1	10	95849076	Intron	SNP	A	TCGA-G7-6796-01A-11D-1961-08	88023978	95849076	39685671	31	10188											
BEST1	7439	hgsc.bcm.edu	37	chr11	61730354	61730354	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacatggatccttattgggcCttggaaaacaggtctgtcct	9	12	10	10	0	1	0	0	0	1	0	3	2	3	2	3	4	1	0	3	4	3	3			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr11:61730354C>T	ENST00000378043.4	+	10	2371	c.1728C>T	c.(1726-1728)gcC>gcT	p.A576A	FTH1_ENST00000529191.1_Intron|BEST1_ENST00000378042.3_Silent_p.A489A|BEST1_ENST00000449131.2_Silent_p.A516A|BEST1_ENST00000534553.1_3'UTR|FTH1_ENST00000529631.1_Intron|BEST1_ENST00000301774.9_Silent_p.A204A	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1	576					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						CTTATTGGGCCTTGGAAAACA	0.507																																					p.A576A		Atlas-SNP	.											.	BEST1	85	.	0			c.C1728T						PASS	.						120	130	126					11																	61730354		2202	4299	6501	SO:0001819	synonymous_variant	7439	exon10			TTGGGCCTTGGAA	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.1728C>T	chr11.hg19:g.61730354C>T		103.0	0.0	.		91.0	13.0	.	NM_004183	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Silent	SNP	ENST00000378043.4	hg19	CCDS31580.1																																																																																			.	.	.	none		0.507	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1	NM_004183		T	61730354	C	T	61730354	2	4	174	1	0	0	0	0	0	0	0	1	1404	668	24	2		2	BEST1	11	61730354	Silent	SNP	C	TCGA-G7-6796-01A-11D-1961-08		61730354	73276162	32	10189											
PARP11	57097	hgsc.bcm.edu	37	chr12	3921402	3921402	+	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	atataaattcacatagctccCgtctttggaaggaggtcgca	12	11	9	9	2	2	0	1	0	1	0	4	2	3	2	1	3	1	2	1	3	5	5			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr12:3921402C>A	ENST00000228820.4	-	8	1048	c.904G>T	c.(904-906)Ggg>Tgg	p.G302W	PARP11_ENST00000476985.1_Intron|PARP11_ENST00000447133.3_Missense_Mutation_p.G221W|PARP11_ENST00000397096.2_Intron|PARP11_ENST00000427057.2_Missense_Mutation_p.G221W	NM_020367.4	NP_065100.2	Q9NR21	PAR11_HUMAN	poly (ADP-ribose) polymerase family, member 11	295	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)			ACATAGCTCCCGTCTTTGGAA	0.398																																					p.G302W		Atlas-SNP	.											PARP11,NS,malignant_melanoma,0,1	PARP11	39	.	0			c.G904T						PASS	.						119	103	109					12																	3921402		2203	4300	6503	SO:0001583	missense	57097	exon8			AGCTCCCGTCTTT	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.904G>T	chr12.hg19:g.3921402C>A	ENSP00000228820:p.Gly302Trp	118.0	2.0	.		151.0	9.0	.	NM_020367	B4DRQ0|Q68DS1|Q8N5Y9	Missense_Mutation	SNP	ENST00000228820.4	hg19	CCDS8523.2	.	.	.	.	.	.	.	.	.	.	C	18.20	3.571674	0.65765	.	.	ENSG00000111224	ENST00000427057;ENST00000228820;ENST00000447133	T;T;T	0.14391	2.51;2.51;2.51	5.28	5.28	0.74379	Poly(ADP-ribose) polymerase, catalytic domain (2);	0.106561	0.64402	D	0.000004	T	0.40932	0.1137	M	0.81497	2.545	0.44985	D	0.998009	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.995;0.989;0.994	T	0.28267	-1.0049	10	0.87932	D	0	.	16.4627	0.84069	0.0:1.0:0.0:0.0	.	221;302;295	Q9NR21-2;Q9NR21-4;Q9NR21	.;.;PAR11_HUMAN	W	221;302;221	ENSP00000397058:G221W;ENSP00000228820:G302W;ENSP00000405385:G221W	ENSP00000228820:G302W	G	-	1	0	PARP11	3791663	0.987000	0.35691	1.000000	0.80357	0.999000	0.98932	2.777000	0.47717	2.747000	0.94245	0.650000	0.86243	GGG	.	.	.	none		0.398	PARP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344213.1			A	3921402	C	A	3921402	3	1	174	1	0	0	0	0	1	0	0	0	11463	652	23	4	116	4	PARP11	12	3921402	Missense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08		3921402	129930493	33	10190											
ABCC9	10060	hgsc.bcm.edu	37	chr12	21962862	21962862	+	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	tcccagagtctgtcatctgtGcatttgcactctggatctaa	8	14	8	11	0	5	1	1	0	4	1	6	2	6	2	1	1	2	2	1	1	1	2			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr12:21962862G>A	ENST00000261201.4	-	35	4238	c.4239C>T	c.(4237-4239)tgC>tgT	p.C1413C	ABCC9_ENST00000345162.2_Silent_p.C1377C|ABCC9_ENST00000261200.4_Silent_p.C1413C	NM_005691.2	NP_005682.2	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	1413	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				defense response to virus (GO:0051607)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	ATP-sensitive potassium channel complex (GO:0008282)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcomere (GO:0030017)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sulfonylurea receptor activity (GO:0008281)|transporter activity (GO:0005215)			NS(2)|breast(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|lung(56)|ovary(4)|pancreas(1)|prostate(4)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(5)	118					Adenosine triphosphate(DB00171)|Glyburide(DB01016)	TGTCATCTGTGCATTTGCACT	0.323																																					p.C1413C		Atlas-SNP	.											.	ABCC9	411	.	0			c.C4239T						PASS	.						83	85	84					12																	21962862		2203	4300	6503	SO:0001819	synonymous_variant	10060	exon35			ATCTGTGCATTTG	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.4239C>T	chr12.hg19:g.21962862G>A		94.0	0.0	.		127.0	24.0	.	NM_005691	O60707	Silent	SNP	ENST00000261201.4	hg19	CCDS8694.1																																																																																			.	.	.	none		0.323	ABCC9-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402230.1	NM_005691		A	21962862	G	A	21962862	2	1	174	1	0	0	0	0	0	0	0	1	59	1311	46	2		2	ABCC9	12	21962862	Silent	SNP	G	TCGA-G7-6796-01A-11D-1961-08	18041460	21962862	111889033	34	10191											
KIAA0528	9847	hgsc.bcm.edu	37	chr12	22666235	22666235	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtgaatcttaccctctgtTccaacgctgattgagtctgt	9	14	8	10	1	3	3	0	3	3	0	4	3	4	3	2	0	2	2	2	0	4	3			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr12:22666235T>C	ENST00000333957.4	-	9	1286	c.1031A>G	c.(1030-1032)gAa>gGa	p.E344G	C2CD5_ENST00000446597.1_Missense_Mutation_p.E344G|C2CD5_ENST00000396028.2_Missense_Mutation_p.E335G|C2CD5_ENST00000542676.1_Missense_Mutation_p.E344G|C2CD5_ENST00000545552.1_Missense_Mutation_p.E335G|C2CD5_ENST00000536386.1_Missense_Mutation_p.E335G|C2CD5_ENST00000544930.1_Missense_Mutation_p.E137G	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	344					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)										TACCCTCTGTTCCAACGCTGA	0.378																																					p.E344G		Atlas-SNP	.											.	.	.	.	0			c.A1031G						PASS	.						149	131	137					12																	22666235		2203	4300	6503	SO:0001583	missense	9847	exon9			CTCTGTTCCAACG	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.1031A>G	chr12.hg19:g.22666235T>C	ENSP00000334229:p.Glu344Gly	163.0	0.0	.		187.0	31.0	.	NM_014802	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Missense_Mutation	SNP	ENST00000333957.4	hg19	CCDS31758.1	.	.	.	.	.	.	.	.	.	.	T	19.42	3.824771	0.71143	.	.	ENSG00000111731	ENST00000333957;ENST00000446597;ENST00000536386;ENST00000396028;ENST00000542676;ENST00000545552;ENST00000544930;ENST00000544281	T;T;T;T;T;T;T;T	0.55234	0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53	5.0	3.85	0.44370	.	0.062767	0.64402	N	0.000006	T	0.65144	0.2663	L	0.57536	1.79	0.49915	D	0.999836	D;D;D;D;D;D	0.89917	0.999;0.992;1.0;0.992;1.0;0.979	D;P;D;P;D;P	0.85130	0.973;0.784;0.996;0.864;0.997;0.628	T	0.64045	-0.6499	10	0.51188	T	0.08	-22.0629	9.2812	0.37729	0.0:0.0816:0.0:0.9184	.	335;344;137;335;335;344	F5H2A1;B4DRN7;F5H3N1;B7ZLL0;Q86YS7-2;Q86YS7	.;.;.;.;.;K0528_HUMAN	G	344;344;335;335;344;335;137;96	ENSP00000334229:E344G;ENSP00000388756:E344G;ENSP00000439392:E335G;ENSP00000379345:E335G;ENSP00000441951:E344G;ENSP00000443204:E335G;ENSP00000445288:E137G;ENSP00000443479:E96G	ENSP00000334229:E344G	E	-	2	0	KIAA0528	22557502	1.000000	0.71417	0.988000	0.46212	0.978000	0.69477	7.272000	0.78516	0.920000	0.36970	0.528000	0.53228	GAA	.	.	.	none		0.378	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802		C	22666235	T	C	22666235	3	2	174	1	0	0	0	0	1	0	0	0	8189	1783	62	3	2039	3	KIAA0528	12	22666235	Missense_Mutation	SNP	T	TCGA-G7-6796-01A-11D-1961-08	703373	22666235	111185660	35	10192											
CAPRIN2	65981	hgsc.bcm.edu	37	chr12	30886574	30886574	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaactcacatgtcgttcctAccactgctttctcactacct	10	13	3	15	1	2	0	2	0	1	0	5	0	3	0	3	0	4	2	3	0	4	4			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr12:30886574A>G	ENST00000395805.2	-	5	1428	c.881T>C	c.(880-882)gTa>gCa	p.V294A	CAPRIN2_ENST00000538387.1_Intron|CAPRIN2_ENST00000308433.5_Intron|CAPRIN2_ENST00000417045.1_Missense_Mutation_p.V294A|CAPRIN2_ENST00000251071.5_Missense_Mutation_p.V294A|CAPRIN2_ENST00000298892.5_Missense_Mutation_p.V294A	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)					TGTCGTTCCTACCACTGCTTT	0.398																																					p.V294A		Atlas-SNP	.											.	CAPRIN2	109	.	0			c.T881C						PASS	.						164	143	150					12																	30886574		2203	4300	6503	SO:0001583	missense	65981	exon5			GTTCCTACCACTG	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.881T>C	chr12.hg19:g.30886574A>G	ENSP00000379150:p.Val294Ala	200.0	0.0	.		219.0	13.0	.	NM_023925		Missense_Mutation	SNP	ENST00000395805.2	hg19	CCDS55816.1	.	.	.	.	.	.	.	.	.	.	A	12.15	1.850529	0.32699	.	.	ENSG00000110888	ENST00000433722;ENST00000298892;ENST00000395805;ENST00000251071;ENST00000417045;ENST00000438006;ENST00000537108	T;T;T;T;T;T	0.21031	2.47;2.03;2.03;2.03;2.03;2.03	4.96	4.96	0.65561	.	0.276479	0.34460	N	0.003948	T	0.09730	0.0239	N	0.11201	0.11	0.80722	D	1	B;B;B;B;B	0.28783	0.142;0.222;0.029;0.049;0.013	B;B;B;B;B	0.28011	0.043;0.085;0.006;0.013;0.008	T	0.24977	-1.0145	10	0.15066	T	0.55	-12.678	7.5105	0.27571	0.8402:0.0:0.1598:0.0	.	294;294;294;294;294	Q149P6;Q6IMN6-3;Q6IMN6;Q6IMN6-2;E4NKG2	.;.;CAPR2_HUMAN;.;.	A	40;294;294;294;294;20;213	ENSP00000415407:V40A;ENSP00000298892:V294A;ENSP00000379150:V294A;ENSP00000251071:V294A;ENSP00000391479:V294A;ENSP00000438010:V213A	ENSP00000251071:V294A	V	-	2	0	CAPRIN2	30777841	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.311000	0.51919	2.069000	0.61940	0.533000	0.62120	GTA	.	.	.	none		0.398	CAPRIN2-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403322.2	NM_023925		G	30886574	A	G	30886574	3	3	174	1	0	0	0	0	1	0	0	0	2638	391	14	3	2558	3	CAPRIN2	12	30886574	Missense_Mutation	SNP	A	TCGA-G7-6796-01A-11D-1961-08	8220339	30886574	102965321	36	10193											
ARID2	196528	hgsc.bcm.edu	37	chr12	46246367	46246367	+	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	catcaaatcatagcagttccCgactcaggatcaaaagtatc	15	9	6	11	1	4	0	4	0	0	0	6	2	5	1	1	1	1	3	1	1	5	3			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr12:46246367C>A	ENST00000334344.6	+	15	4633	c.4461C>A	c.(4459-4461)ccC>ccA	p.P1487P	ARID2_ENST00000444670.1_Silent_p.P1097P|ARID2_ENST00000422737.1_Silent_p.P1338P|ARID2_ENST00000457135.1_Silent_p.P95P|ARID2_ENST00000479608.1_3'UTR	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1487					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)		TAGCAGTTCCCGACTCAGGAT	0.463			"N, S, F"		hepatocellular carcinoma																																p.P1487P		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.C4461A						PASS	.						113	107	109					12																	46246367		2203	4300	6503	SO:0001819	synonymous_variant	196528	exon15			AGTTCCCGACTCA		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.4461C>A	chr12.hg19:g.46246367C>A		171.0	0.0	.		172.0	8.0	.	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Silent	SNP	ENST00000334344.6	hg19	CCDS31783.1																																																																																			.	.	.	none		0.463	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		A	46246367	C	A	46246367	2	1	174	1	0	0	0	0	0	0	0	1	915	639	23	4		4	ARID2	12	46246367	Silent	SNP	C	TCGA-G7-6796-01A-11D-1961-08	15359793	46246367	87605528	37	10194											
KRT85	3891	hgsc.bcm.edu	37	chr12	52761009	52761009	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctatccggggcccgcaggAgcccaggttgcagaggctgc	7	5	16	13	2	0	1	0	0	0	1	1	2	1	2	3	5	4	5	3	5	1	2			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr12:52761009A>G	ENST00000257901.3	-	1	256	c.181T>C	c.(181-183)Tcc>Ccc	p.S61P	KRT85_ENST00000544265.1_5'Flank	NM_002283.3	NP_002274.1	P78386	KRT85_HUMAN	keratin 85	61	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)		GGCCCGCAGGAGCCCAGGTTG	0.716																																					p.S61P		Atlas-SNP	.											.	KRT85	78	.	0			c.T181C						PASS	.						18	23	21					12																	52761009		2197	4295	6492	SO:0001583	missense	3891	exon1			CGCAGGAGCCCAG	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.181T>C	chr12.hg19:g.52761009A>G	ENSP00000257901:p.Ser61Pro	79.0	0.0	.		58.0	11.0	.	NM_002283	Q9NSB1	Missense_Mutation	SNP	ENST00000257901.3	hg19	CCDS8824.1	.	.	.	.	.	.	.	.	.	.	A	5.873	0.345197	0.11126	.	.	ENSG00000135443	ENST00000257901	T	0.77877	-1.13	4.66	-2.96	0.05547	.	0.601870	0.15091	N	0.281064	T	0.51261	0.1664	N	0.12182	0.205	0.23563	N	0.997407	B	0.06786	0.001	B	0.10450	0.005	T	0.29488	-1.0010	10	0.40728	T	0.16	.	2.3992	0.04397	0.2911:0.4181:0.1687:0.1221	.	61	P78386	KRT85_HUMAN	P	61	ENSP00000257901:S61P	ENSP00000257901:S61P	S	-	1	0	KRT85	51047276	0.000000	0.05858	0.660000	0.29694	0.354000	0.29330	-0.238000	0.08977	-0.599000	0.05798	-0.366000	0.07423	TCC	.	.	.	none		0.716	KRT85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405184.1	NM_002283		G	52761009	A	G	52761009	3	3	174	1	0	0	0	0	1	0	0	0	8506	304	11	3	1378	3	KRT85	12	52761009	Missense_Mutation	SNP	A	TCGA-G7-6796-01A-11D-1961-08	6514642	52761009	81090886	38	10195											
SYCP3	50511	hgsc.bcm.edu	37	chr12	102127436	102127436	+	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	cagaaactgctgagaatattCttggttaagcttctgcctgt	10	14	9	8	0	2	2	0	1	2	2	2	3	2	2	1	1	4	3	1	1	4	5			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr12:102127436C>G	ENST00000392927.3	-	6	501	c.370G>C	c.(370-372)Gaa>Caa	p.E124Q	SYCP3_ENST00000266743.2_Missense_Mutation_p.E124Q|SYCP3_ENST00000392924.1_Missense_Mutation_p.E124Q	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	124	Gln-rich.				male meiosis I (GO:0007141)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(1)	11						TGAGAATATTCTTGGTTAAGC	0.308																																					p.E124Q		Atlas-SNP	.											.	SYCP3	19	.	0			c.G370C						PASS	.						110	102	105					12																	102127436		2203	4300	6503	SO:0001583	missense	50511	exon6			AATATTCTTGGTT	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.370G>C	chr12.hg19:g.102127436C>G	ENSP00000376658:p.Glu124Gln	73.0	0.0	.		89.0	12.0	.	NM_001177949		Missense_Mutation	SNP	ENST00000392927.3	hg19	CCDS9087.1	.	.	.	.	.	.	.	.	.	.	C	13.30	2.197243	0.38806	.	.	ENSG00000139351	ENST00000266743;ENST00000392927;ENST00000392924	.	.	.	5.95	5.01	0.66863	.	0.115967	0.64402	D	0.000019	T	0.72078	0.3416	M	0.67953	2.075	0.44247	D	0.997095	D	0.54397	0.966	P	0.56343	0.796	T	0.69698	-0.5075	9	0.34782	T	0.22	1.5322	15.6276	0.76874	0.1381:0.8619:0.0:0.0	.	124	Q8IZU3	SYCP3_HUMAN	Q	124	.	ENSP00000266743:E124Q	E	-	1	0	SYCP3	100651567	1.000000	0.71417	0.797000	0.32132	0.043000	0.13939	4.291000	0.59025	2.817000	0.96982	0.563000	0.77884	GAA	.	.	.	none		0.308	SYCP3-001	KNOWN	alternative_5_UTR|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316478.2	NM_153694		G	102127436	C	G	102127436	3	3	174	1	0	0	0	0	1	0	0	0	15446	922	32	4	356	4	SYCP3	12	102127436	Missense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08	49366427	102127436	31724459	39	10196											
USPL1	10208	hgsc.bcm.edu	37	chr13	31233386	31233386	+	Missense_Mutation	SNP	A	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	taaacttggagagtccgatgAagactgatattttcgatgag	13	12	11	5	2	0	5	0	3	0	2	2	8	1	5	1	1	1	0	1	1	4	5			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr13:31233386A>C	ENST00000255304.4	+	9	3514	c.3172A>C	c.(3172-3174)Aag>Cag	p.K1058Q		NM_005800.4	NP_005791.3	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	1058					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)		GAGTCCGATGAAGACTGATAT	0.373																																					p.K1058Q	Ovarian(60;318 1180 1554 28110 31601)	Atlas-SNP	.											.	USPL1	82	.	0			c.A3172C						PASS	.						93	94	93					13																	31233386		2202	4300	6502	SO:0001583	missense	10208	exon9			CCGATGAAGACTG	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.3172A>C	chr13.hg19:g.31233386A>C	ENSP00000255304:p.Lys1058Gln	92.0	0.0	.		110.0	20.0	.	NM_005800	Q14109|Q6AI45|Q8IY30|Q8IYE8	Missense_Mutation	SNP	ENST00000255304.4	hg19	CCDS9336.1	.	.	.	.	.	.	.	.	.	.	A	18.68	3.675070	0.67928	.	.	ENSG00000132952	ENST00000255304	T	0.26518	1.73	5.62	5.62	0.85841	.	0.083251	0.51477	D	0.000089	T	0.46870	0.1415	M	0.64997	1.995	0.25803	N	0.984481	D	0.67145	0.996	D	0.66497	0.944	T	0.43589	-0.9382	10	0.72032	D	0.01	-19.9681	14.3888	0.66963	1.0:0.0:0.0:0.0	.	1058	Q5W0Q7	USPL1_HUMAN	Q	1058	ENSP00000255304:K1058Q	ENSP00000255304:K1058Q	K	+	1	0	USPL1	30131386	0.983000	0.35010	0.930000	0.37139	0.675000	0.39556	4.229000	0.58625	2.143000	0.66587	0.455000	0.32223	AAG	.	.	.	none		0.373	USPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044369.1	NM_005800		C	31233386	A	C	31233386	3	2	174	1	0	0	0	0	1	0	0	0	17104	247	9	5	3202	5	USPL1	13	31233386	Missense_Mutation	SNP	A	TCGA-G7-6796-01A-11D-1961-08		31233386	83936492	40	10197											
ITM2B	9445	hgsc.bcm.edu	37	chr13	48833064	48833064	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaggaaacttacaaactgcaAcgcagagaaactattaaagg	20	6	8	7	1	0	1	0	0	0	1	0	3	0	2	0	2	6	2	0	2	9	3			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr13:48833064A>G	ENST00000378565.5	+	5	899	c.696A>G	c.(694-696)caA>caG	p.Q232Q	ITM2B_ENST00000378549.5_Silent_p.Q126Q	NM_021999.4	NP_068839.1	Q9Y287	ITM2B_HUMAN	integral membrane protein 2B	232					extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|nervous system development (GO:0007399)	endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle membrane (GO:0030660)|integral component of organelle membrane (GO:0031301)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|beta-amyloid binding (GO:0001540)			endometrium(1)|large_intestine(2)|lung(3)	6		all_cancers(8;2.2e-31)|all_epithelial(8;6.77e-15)|all_lung(13;9.67e-07)|all_hematologic(8;9.72e-06)|Lung NSC(96;8.3e-05)|Breast(56;0.000141)|Acute lymphoblastic leukemia(8;0.00045)|Prostate(109;0.000669)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;1.97e-06)		ACAAACTGCAACGCAGAGAAA	0.338																																					p.Q232Q		Atlas-SNP	.											.	ITM2B	24	.	0			c.A696G						PASS	.						85	78	81					13																	48833064		2203	4300	6503	SO:0001819	synonymous_variant	9445	exon5			ACTGCAACGCAGA	AF092128	CCDS9409.1	13q14.2	2012-10-10			ENSG00000136156	ENSG00000136156		"BRICHOS domain containing"	6174	protein-coding gene	gene with protein product	"BRICHOS domain containing 2B"	603904				9795190	Standard	NM_021999		Approved	BRI, E25B, E3-16, BRICD2B	uc001vbz.3	Q9Y287	OTTHUMG00000016894	ENST00000378565.5:c.696A>G	chr13.hg19:g.48833064A>G		54.0	0.0	.		83.0	13.0	.	NM_021999	Q5W0A3|Q96B24|Q9NYH1	Silent	SNP	ENST00000378565.5	hg19	CCDS9409.1																																																																																			.	.	.	none		0.338	ITM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044870.3	NM_021999		G	48833064	A	G	48833064	2	3	174	1	0	0	0	0	0	0	0	1	7920	40	2	3		3	ITM2B	13	48833064	Silent	SNP	A	TCGA-G7-6796-01A-11D-1961-08	17599678	48833064	66336814	41	10198											
BTBD7	55727	hgsc.bcm.edu	37	chr14	93708871	93708871	+	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	cccctgacatgggctggaccGgtactagcattttctggggc	6	10	13	12	1	1	1	0	1	1	0	1	2	1	2	3	5	2	3	3	5	2	4	rs145129249	byFrequency	TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr14:93708871G>T	ENST00000334746.5	-	11	3454	c.3147C>A	c.(3145-3147)acC>acA	p.T1049T	BTBD7_ENST00000393170.2_Silent_p.T623T|BTBD7_ENST00000554565.1_Silent_p.T698T	NM_001002860.2	NP_001002860.2	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7	1049					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)		GGGCTGGACCGGTACTAGCAT	0.507																																					p.T1049T		Atlas-SNP	.											.	BTBD7	112	.	0			c.C3147A						PASS	.						109	117	114					14																	93708871		2203	4300	6503	SO:0001819	synonymous_variant	55727	exon11			TGGACCGGTACTA	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.3147C>A	chr14.hg19:g.93708871G>T		251.0	0.0	.		176.0	8.0	.	NM_001002860	A8K5V7|Q69Z05|Q7Z308|Q86TS0|Q9HAA4|Q9NVM0	Silent	SNP	ENST00000334746.5	hg19	CCDS32146.1																																																																																			.	G|1.000;A|0.000	.	alt		0.507	BTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412701.1	NM_001002860		T	93708871	G	T	93708871	2	4	174	1	0	0	0	0	0	0	0	1	1548	1103	39	4		4	BTBD7	14	93708871	Silent	SNP	G	TCGA-G7-6796-01A-11D-1961-08		93708871	13640669	42	10199											
EDC4	23644	hgsc.bcm.edu	37	chr16	67910484	67910484	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gactctagcatttcaagcaaGgcccggggaagcaacaaggt	13	6	12	10	1	2	0	1	0	1	0	2	2	2	1	1	4	4	3	1	4	6	2			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr16:67910484G>A	ENST00000358933.5	+	3	572	c.333G>A	c.(331-333)aaG>aaA	p.K111K	AC040162.1_ENST00000408599.1_RNA|EDC4_ENST00000574770.1_3'UTR	NM_014329.4	NP_055144.3	Q6P2E9	EDC4_HUMAN	enhancer of mRNA decapping 4	111					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		TTTCAAGCAAGGCCCGGGGAA	0.537																																					p.K111K		Atlas-SNP	.											.	EDC4	101	.	0			c.G333A						PASS	.						76	65	69					16																	67910484		2198	4300	6498	SO:0001819	synonymous_variant	23644	exon3			AAGCAAGGCCCGG	U17474	CCDS10849.1	16q22.1	2008-02-05			ENSG00000038358	ENSG00000038358			17157	protein-coding gene	gene with protein product		606030				9067524	Standard	NM_014329		Approved	RCD-8, Ge-1, HEDLS	uc002eur.3	Q6P2E9	OTTHUMG00000137543	ENST00000358933.5:c.333G>A	chr16.hg19:g.67910484G>A		71.0	0.0	.		78.0	15.0	.	NM_014329	A6NGM1|A8K4T4|Q13025|Q13826|Q6ZR12|Q7Z6H7	Silent	SNP	ENST00000358933.5	hg19	CCDS10849.1																																																																																			.	.	.	none		0.537	EDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268874.2	NM_014329		A	67910484	G	A	67910484	2	1	174	1	0	0	0	0	0	0	0	1	4910	991	35	2		2	EDC4	16	67910484	Silent	SNP	G	TCGA-G7-6796-01A-11D-1961-08		67910484	22444269	43	10200											
GAN	8139	hgsc.bcm.edu	37	chr16	81388211	81388211	+	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	aatacctggagactcatttcCgagacgtcagcagcacggaa	13	7	10	11	3	2	2	2	0	0	2	3	5	3	3	2	2	3	2	2	2	3	2			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr16:81388211C>A	ENST00000568107.2	+	3	646	c.484C>A	c.(484-486)Cga>Aga	p.R162R		NM_022041.3	NP_071324.1	Q9H2C0	GAN_HUMAN	gigaxonin	162	BACK.				cell death (GO:0008219)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)	25		Colorectal(91;0.153)				GACTCATTTCCGAGACGTCAG	0.428																																					p.R162R	GBM(106;1239 1507 7582 9741 33976)	Atlas-SNP	.											.	GAN	59	.	0			c.C484A						PASS	.						161	146	151					16																	81388211		2202	4300	6502	SO:0001819	synonymous_variant	8139	exon3			CATTTCCGAGACG	AF291673	CCDS10935.1	16q24.1	2014-09-17	2008-08-01		ENSG00000261609	ENSG00000261609		"Kelch-like", "BTB/POZ domain containing"	4137	protein-coding gene	gene with protein product	"kelch-like family member 16"	605379	"giant axonal neuropathy (gigaxonin)"			9450783, 11062483	Standard	NM_022041		Approved	GAN1, KLHL16	uc002fgo.3	Q9H2C0	OTTHUMG00000137627	ENST00000568107.2:c.484C>A	chr16.hg19:g.81388211C>A		165.0	0.0	.		192.0	8.0	.	NM_022041		Silent	SNP	ENST00000568107.2	hg19	CCDS10935.1																																																																																			.	.	.	none		0.428	GAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269050.3			A	81388211	C	A	81388211	2	1	174	1	0	0	0	0	0	0	0	1	6239	644	23	4		4	GAN	16	81388211	Silent	SNP	C	TCGA-G7-6796-01A-11D-1961-08	13477727	81388211	8966542	44	10201											
TEKT1	83659	hgsc.bcm.edu	37	chr17	6718552	6718553	+	Frame_Shift_Ins	INS	-	-	A																															ttgttgagcgagaagcagatINSatcatctatggtcagggcca																										TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr17:6718552_6718553insA	ENST00000338694.2	-	5	687_688	c.558_559insT	c.(556-561)gatatcfs	p.I187fs	TEKT1_ENST00000535086.1_Frame_Shift_Ins_p.I41fs	NM_053285.1	NP_444515.1	Q969V4	TEKT1_HUMAN	tektin 1	187						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)				GAGAAGCAGATATCATCTATGG	0.48																																					p.I187fs		Atlas-INDEL	.											.	TEKT1	49	.	0			c.559_560insT						PASS	.																																			SO:0001589	frameshift_variant	83659	exon5			.		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.559dupT	chr17.hg19:g.6718553_6718553dupA	ENSP00000341346:p.Ile187fs	209.0	0.0	0		263.0	37.0	0.140684	NM_053285	D3DTM7	Frame_Shift_Ins	INS	ENST00000338694.2	hg19	CCDS11083.1																																																																																			.	.	.	none		0.48	TEKT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219867.2	NM_053285		A	6718553	-	A	6718552	7	5	174	1	0	1	1	0	0	0	0	0	15764	1406	49	0	713	0	TEKT1	17	6718552	Frame_Shift_Ins	INS	-	TCGA-G7-6796-01A-11D-1961-08		6718552	74476658	45	10202											
GLP2R	9340	hgsc.bcm.edu	37	chr17	9764494	9764494	+	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	ttgtaccctggggtttcgccCgtgcacacctggagaacaca	8	9	11	13	2	0	1	0	0	0	1	1	2	0	1	3	3	3	3	3	3	2	3			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr17:9764494C>A	ENST00000262441.5	+	8	1477	c.964C>A	c.(964-966)Cgt>Agt	p.R322S	GLP2R_ENST00000574745.1_Missense_Mutation_p.R142S	NM_004246.1	NP_004237.1	O95838	GLP2R_HUMAN	glucagon-like peptide 2 receptor	322					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|positive regulation of cell proliferation (GO:0008284)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|glucagon receptor activity (GO:0004967)			endometrium(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	44					Glucagon recombinant(DB00040)|Teduglutide(DB08900)	GGGTTTCGCCCGTGCACACCT	0.493																																					p.R322S		Atlas-SNP	.											.	GLP2R	90	.	0			c.C964A						PASS	.						198	180	186					17																	9764494		2203	4300	6503	SO:0001583	missense	9340	exon8			TTCGCCCGTGCAC	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.964C>A	chr17.hg19:g.9764494C>A	ENSP00000262441:p.Arg322Ser	227.0	0.0	.		245.0	10.0	.	NM_004246	Q4VAT3	Missense_Mutation	SNP	ENST00000262441.5	hg19	CCDS11150.1	.	.	.	.	.	.	.	.	.	.	C	8.206	0.799227	0.16397	.	.	ENSG00000065325	ENST00000396206;ENST00000304773;ENST00000262441	T	0.46451	0.87	5.24	5.24	0.73138	GPCR, family 2-like (1);	0.000000	0.40222	N	0.001141	T	0.65512	0.2698	M	0.86178	2.8	0.09310	N	1	D	0.69078	0.997	D	0.74348	0.983	T	0.61917	-0.6964	10	0.87932	D	0	.	11.1891	0.48675	0.2849:0.7151:0.0:0.0	.	322	O95838	GLP2R_HUMAN	S	322;297;322	ENSP00000262441:R322S	ENSP00000262441:R322S	R	+	1	0	GLP2R	9705219	0.948000	0.32251	0.788000	0.31933	0.475000	0.33008	2.876000	0.48498	2.706000	0.92434	0.655000	0.94253	CGT	.	.	.	none		0.493	GLP2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252601.4			A	9764494	C	A	9764494	3	1	174	1	0	0	0	0	1	0	0	0	6460	652	23	4	994	4	GLP2R	17	9764494	Missense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08	3045942	9764494	71430716	46	10203											
BRCA1	672	hgsc.bcm.edu	37	chr17	41244817	41244817	+	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	gatattagactcattctttcCttgattttcttccttttgtt	6	23	4	8	0	3	2	1	1	2	1	5	3	5	2	2	0	0	1	2	0	2	11	rs80357712|rs397509003|rs80357605|rs80357917		TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr17:41244817C>T	ENST00000357654.3	-	10	2849	c.2731G>A	c.(2731-2733)Gga>Aga	p.G911R	BRCA1_ENST00000493795.1_Missense_Mutation_p.G864R|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000471181.2_Missense_Mutation_p.G911R|BRCA1_ENST00000346315.3_Missense_Mutation_p.G911R|BRCA1_ENST00000309486.4_Missense_Mutation_p.G615R|BRCA1_ENST00000354071.3_Missense_Mutation_p.G911R	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	911					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)		TCATTCTTTCCTTGATTTTCT	0.398			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.G911R		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.G2731A						PASS	.						132	130	131					17																	41244817		2203	4300	6503	SO:0001583	missense	672	exon10	Familial Cancer Database		TCTTTCCTTGATT	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.2731G>A	chr17.hg19:g.41244817C>T	ENSP00000350283:p.Gly911Arg	145.0	0.0	.		146.0	24.0	.	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	hg19	CCDS11453.1	.	.	.	.	.	.	.	.	.	.	C	12.57	1.977264	0.34848	.	.	ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000354071;ENST00000346315;ENST00000309486;ENST00000471181;ENST00000493795	T;T;T;T;T;T	0.80566	-1.39;-1.39;-1.39;-1.39;-1.39;-1.39	4.85	2.8	0.32819	.	0.776431	0.11349	N	0.573162	D	0.84188	0.5417	M	0.65320	2	0.09310	N	1	B;B;B;B;D;B	0.59357	0.024;0.065;0.132;0.12;0.985;0.036	B;B;B;B;P;B	0.57371	0.046;0.046;0.261;0.22;0.819;0.043	T	0.71461	-0.4586	10	0.56958	D	0.05	.	8.2084	0.31469	0.0:0.7274:0.0:0.2726	.	911;870;911;911;911;911	E7EMP0;E7ERL4;Q5YLB2;E9PFC7;P38398;P38398-2	.;.;.;.;BRCA1_HUMAN;.	R	911;911;911;911;615;911;864	ENSP00000350283:G911R;ENSP00000326002:G911R;ENSP00000246907:G911R;ENSP00000310938:G615R;ENSP00000418960:G911R;ENSP00000418775:G864R	ENSP00000310938:G615R	G	-	1	0	BRCA1	38498343	0.001000	0.12720	0.001000	0.08648	0.134000	0.20937	0.961000	0.29267	0.582000	0.29556	0.484000	0.47621	GGA	.	.	.	none		0.398	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		T	41244817	C	T	41244817	3	4	174	1	0	0	0	0	1	0	0	0	1500	690	24	2	2986	2	BRCA1	17	41244817	Missense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08	31480323	41244817	39950393	47	10204											
ABCC3	8714	hgsc.bcm.edu	37	chr17	48735832	48735832	+	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	ccagcgctggctttctctccCgcctgtttttctggtggttc	1	16	10	14	2	2	0	0	0	2	0	5	0	3	0	3	3	1	4	3	3	0	4			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr17:48735832C>A	ENST00000285238.8	+	6	729	c.649C>A	c.(649-651)Cgc>Agc	p.R217S	ABCC3_ENST00000427699.1_Missense_Mutation_p.R217S	NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	217					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)	p.L215_F219delLSRLF(1)		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)	CTTTCTCTCCCGCCTGTTTTT	0.582																																					p.R217S		Atlas-SNP	.											ABCC3_ENST00000427699,rectum,carcinoma,0,2	ABCC3	138	.	1	Deletion - In frame(1)	prostate(1)	c.C649A						PASS	.						128	118	121					17																	48735832		2203	4300	6503	SO:0001583	missense	8714	exon6			CTCTCCCGCCTGT	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.649C>A	chr17.hg19:g.48735832C>A	ENSP00000285238:p.Arg217Ser	223.0	2.0	.		282.0	13.0	.	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Missense_Mutation	SNP	ENST00000285238.8	hg19	CCDS32681.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.037328	0.75617	.	.	ENSG00000108846	ENST00000427699;ENST00000285238	D;D	0.93019	-3.15;-3.15	5.92	4.96	0.65561	.	0.158362	0.42964	D	0.000632	D	0.94288	0.8165	M	0.77103	2.36	0.49483	D	0.999793	P;P	0.46987	0.866;0.888	B;P	0.53549	0.353;0.729	D	0.92427	0.5950	10	0.29301	T	0.29	-14.056	8.5005	0.33154	0.2579:0.6706:0.0:0.0715	.	217;217	O15438;O15438-5	MRP3_HUMAN;.	S	217	ENSP00000395160:R217S;ENSP00000285238:R217S	ENSP00000285238:R217S	R	+	1	0	ABCC3	46090831	0.028000	0.19301	1.000000	0.80357	0.985000	0.73830	1.110000	0.31147	1.515000	0.48885	0.561000	0.74099	CGC	.	.	.	none		0.582	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038		A	48735832	C	A	48735832	3	1	174	1	0	0	0	0	1	0	0	0	54	652	23	4	671	4	ABCC3	17	48735832	Missense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08	7491015	48735832	32459378	48	10205											
MSI2	124540	hgsc.bcm.edu	37	chr17	55754379	55754379	+	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	tgcaacggcctttacaaatgGataccattgagcaggtgctt	11	11	10	9	1	0	1	0	1	0	0	0	2	0	2	2	3	6	3	2	3	4	5			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr17:55754379G>A	ENST00000284073.2	+	13	1186	c.977G>A	c.(976-978)gGa>gAa	p.G326E	MSI2_ENST00000442934.2_Missense_Mutation_p.G265E|MSI2_ENST00000416426.2_Missense_Mutation_p.G322E	NM_138962.2	NP_620412.1	Q96DH6	MSI2H_HUMAN	musashi RNA-binding protein 2	326						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)		TTTACAAATGGATACCATTGA	0.458			T	HOXA9	CML																																p.G326E		Atlas-SNP	.		Dom	yes		17	17q23.2	124540	musashi homolog 2 (Drosophila)		L	.	MSI2	52	.	0			c.G977A						PASS	.						234	195	208					17																	55754379		2203	4300	6503	SO:0001583	missense	124540	exon13			CAAATGGATACCA	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.977G>A	chr17.hg19:g.55754379G>A	ENSP00000284073:p.Gly326Glu	173.0	0.0	.		252.0	80.0	.	NM_138962	Q7Z6M7|Q8N9T4	Missense_Mutation	SNP	ENST00000284073.2	hg19	CCDS11596.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.739690	0.89573	.	.	ENSG00000153944	ENST00000416426;ENST00000284073;ENST00000442934	D;T;T	0.89050	-2.46;0.62;1.01	4.87	4.87	0.63330	.	0.052819	0.85682	D	0.000000	D	0.93605	0.7958	M	0.64997	1.995	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.996;1.0	D	0.94391	0.7614	10	0.87932	D	0	.	18.0345	0.89296	0.0:0.0:1.0:0.0	.	322;326	B4DHE8;Q96DH6	.;MSI2H_HUMAN	E	322;326;265	ENSP00000414671:G322E;ENSP00000284073:G326E;ENSP00000392607:G265E	ENSP00000284073:G326E	G	+	2	0	MSI2	53109378	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.430000	0.97488	2.260000	0.74910	0.462000	0.41574	GGA	.	.	.	none		0.458	MSI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441813.1			A	55754379	G	A	55754379	3	1	174	1	0	0	0	0	1	0	0	0	9883	1174	41	2	1122	2	MSI2	17	55754379	Missense_Mutation	SNP	G	TCGA-G7-6796-01A-11D-1961-08	7018547	55754379	25440831	49	10206											
EXOC7	23265	hgsc.bcm.edu	37	chr17	74081426	74081426	+	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	ggtctggatctgctgctcaaTgtgctcccggtaggagcgct	5	11	14	11	2	3	0	1	0	2	0	4	2	4	2	1	4	4	5	1	4	2	1			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr17:74081426T>A	ENST00000335146.7	-	16	1887	c.1834A>T	c.(1834-1836)Att>Ttt	p.I612F	EXOC7_ENST00000591724.1_5'Flank|EXOC7_ENST00000411744.2_Missense_Mutation_p.I553F|EXOC7_ENST00000467929.2_Missense_Mutation_p.I533F|EXOC7_ENST00000332065.5_Missense_Mutation_p.I530F|EXOC7_ENST00000405575.4_Missense_Mutation_p.I584F|EXOC7_ENST00000607838.1_Missense_Mutation_p.I584F|EXOC7_ENST00000589210.1_Missense_Mutation_p.I561F			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	612					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)			TGCTGCTCAATGTGCTCCCGG	0.632																																					p.I612F		Atlas-SNP	.											.	EXOC7	47	.	0			c.A1834T						PASS	.						57	47	50					17																	74081426		2202	4300	6502	SO:0001583	missense	23265	exon16			GCTCAATGTGCTC	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.1834A>T	chr17.hg19:g.74081426T>A	ENSP00000334100:p.Ile612Phe	30.0	0.0	.		40.0	14.0	.	NM_001145297	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Missense_Mutation	SNP	ENST00000335146.7	hg19	CCDS45782.1	.	.	.	.	.	.	.	.	.	.	t	27.2	4.809754	0.90707	.	.	ENSG00000182473	ENST00000332065;ENST00000351709;ENST00000405575;ENST00000335146;ENST00000357231;ENST00000425372;ENST00000411744	.	.	.	4.43	4.43	0.53597	Cullin repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.76097	0.3940	M	0.78637	2.42	0.80722	D	1	B;B;P;P;D;B;P	0.58268	0.143;0.014;0.851;0.874;0.982;0.029;0.925	B;B;P;P;D;B;P	0.66497	0.109;0.109;0.635;0.731;0.944;0.043;0.803	T	0.75204	-0.3400	9	0.27082	T	0.32	-17.3693	13.7322	0.62794	0.0:0.0:0.0:1.0	.	553;584;533;498;612;530;561	Q9UPT5-5;Q9UPT5-6;B4DJ07;F5H1P1;Q9UPT5;Q9UPT5-2;Q9UPT5-1	.;.;.;.;EXOC7_HUMAN;.;.	F	530;450;584;612;561;498;553	.	ENSP00000333806:I530F	I	-	1	0	EXOC7	71593021	1.000000	0.71417	0.998000	0.56505	0.947000	0.59692	8.037000	0.88933	1.656000	0.50722	0.392000	0.25879	ATT	.	.	.	none		0.632	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219		A	74081426	T	A	74081426	3	1	174	1	0	0	0	0	1	0	0	0	5312	1464	51	5	393	5	EXOC7	17	74081426	Missense_Mutation	SNP	T	TCGA-G7-6796-01A-11D-1961-08	18327047	74081426	7113784	50	10207											
APCDD1	147495	hgsc.bcm.edu	37	chr18	10487626	10487626	+	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	ccccatggatgcggccacagCctcactgctcaacgtcttca	8	8	8	17	2	4	0	3	0	1	0	4	1	4	1	4	2	4	1	4	2	1	1			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr18:10487626C>G	ENST00000355285.5	+	5	1490	c.1136C>G	c.(1135-1137)gCc>gGc	p.A379G	APCDD1_ENST00000578882.1_Missense_Mutation_p.S175R	NM_153000.4	NP_694545.1			adenomatosis polyposis coli down-regulated 1											NS(1)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				READ - Rectum adenocarcinoma(15;0.08)		GCGGCCACAGCCTCACTGCTC	0.597																																					p.A379G		Atlas-SNP	.											.	APCDD1	57	.	0			c.C1136G						PASS	.						75	69	71					18																	10487626		2203	4300	6503	SO:0001583	missense	147495	exon5			CCACAGCCTCACT	AB056722	CCDS11849.1	18p11.21	2006-07-07			ENSG00000154856	ENSG00000154856			15718	protein-coding gene	gene with protein product		607479				12384519	Standard	NM_153000		Approved	B7323	uc002kom.4	Q8J025	OTTHUMG00000131635	ENST00000355285.5:c.1136C>G	chr18.hg19:g.10487626C>G	ENSP00000347433:p.Ala379Gly	135.0	0.0	.		95.0	15.0	.	NM_153000		Missense_Mutation	SNP	ENST00000355285.5	hg19	CCDS11849.1	.	.	.	.	.	.	.	.	.	.	C	13.22	2.172736	0.38413	.	.	ENSG00000154856	ENST00000355285;ENST00000423585	T	0.18502	2.21	5.06	5.06	0.68205	.	0.162880	0.56097	D	0.000037	T	0.29288	0.0729	M	0.63843	1.955	0.29806	N	0.832069	P	0.46952	0.887	P	0.47044	0.535	T	0.12656	-1.0539	10	0.87932	D	0	-34.4277	18.7893	0.91966	0.0:1.0:0.0:0.0	.	379	Q8J025	APCD1_HUMAN	G	379;430	ENSP00000347433:A379G	ENSP00000347433:A379G	A	+	2	0	APCDD1	10477626	1.000000	0.71417	0.981000	0.43875	0.968000	0.65278	5.655000	0.67981	2.496000	0.84212	0.561000	0.74099	GCC	.	.	.	none		0.597	APCDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254529.2	NM_153000		G	10487626	C	G	10487626	3	3	174	1	0	0	0	0	1	0	0	0	765	739	26	4	1154	4	APCDD1	18	10487626	Missense_Mutation	SNP	C	TCGA-G7-6796-01A-11D-1961-08		10487626	67589622	51	10208											
ST8SIA5	29906	hgsc.bcm.edu	37	chr18	44284579	44284579	+	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	atttcgtgcctcagctccagGcatcttgtggagttatattc	7	15	9	10	1	2	0	1	0	1	0	5	1	3	1	2	2	2	3	2	2	2	5			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr18:44284579G>T	ENST00000315087.7	-	2	840	c.180C>A	c.(178-180)tgC>tgA	p.C60*	ST8SIA5_ENST00000538168.1_Nonsense_Mutation_p.C96*|ST8SIA5_ENST00000590497.1_5'UTR|ST8SIA5_ENST00000536490.1_Intron	NM_013305.4	NP_037437.2	O15466	SIA8E_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	60					carbohydrate metabolic process (GO:0005975)|glycosphingolipid biosynthetic process (GO:0006688)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialyltransferase activity (GO:0008373)			kidney(1)|large_intestine(10)|lung(7)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	22						TCAGCTCCAGGCATCTTGTGG	0.512																																					p.C60X		Atlas-SNP	.											.	ST8SIA5	57	.	0			c.C180A						PASS	.						183	165	171					18																	44284579		2203	4300	6503	SO:0001587	stop_gained	29906	exon2			CTCCAGGCATCTT	U91641	CCDS11930.1	18q12.3	2013-03-01	2003-01-14	2005-02-07	ENSG00000101638	ENSG00000101638		"Sialyltransferases"	17827	protein-coding gene	gene with protein product	"ST8Sia V"	607162	"sialyltransferase 8E (alpha-2, 8-polysialytransferase)"	SIAT8E		9199191	Standard	XM_005258250		Approved		uc002lcj.1	O15466	OTTHUMG00000132643	ENST00000315087.7:c.180C>A	chr18.hg19:g.44284579G>T	ENSP00000321343:p.Cys60*	286.0	0.0	.		317.0	13.0	.	NM_013305	B7Z1K9|Q6IAW7	Nonsense_Mutation	SNP	ENST00000315087.7	hg19	CCDS11930.1	.	.	.	.	.	.	.	.	.	.	G	37	6.507977	0.97624	.	.	ENSG00000101638	ENST00000315087;ENST00000538168	.	.	.	4.48	1.66	0.24008	.	0.052875	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.5961	0.33716	0.2644:0.0:0.7356:0.0	.	.	.	.	X	60;96	.	ENSP00000321343:C60X	C	-	3	2	ST8SIA5	42538577	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.934000	0.48956	0.457000	0.26962	0.561000	0.74099	TGC	.	.	.	none		0.512	ST8SIA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255892.1	NM_013305		T	44284579	G	T	44284579	4	4	174	1	0	0	0	0	0	1	0	0	15247	1195	42	4	974	4	ST8SIA5	18	44284579	Nonsense_Mutation	SNP	G	TCGA-G7-6796-01A-11D-1961-08	33796953	44284579	33792669	52	10209											
VAV1	7409	hgsc.bcm.edu	37	chr19	6833546	6833546	+	Missense_Mutation	SNP	T	T	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	ccctgcatctcagaggtaccTtctatcagggctaccgctgc	7	10	9	15	1	3	1	2	0	2	1	4	1	3	1	3	2	4	4	3	2	3	4			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr19:6833546T>G	ENST00000602142.1	+	17	1700	c.1618T>G	c.(1618-1620)Ttc>Gtc	p.F540V	VAV1_ENST00000596764.1_Missense_Mutation_p.F508V|VAV1_ENST00000539284.1_Missense_Mutation_p.F443V|VAV1_ENST00000304076.2_Missense_Mutation_p.F540V|VAV1_ENST00000599806.1_Missense_Mutation_p.F485V	NM_005428.3	NP_005419.2	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	540					apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|reactive oxygen species metabolic process (GO:0072593)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(16)|lung(18)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	62						CAGAGGTACCTTCTATCAGGG	0.542																																					p.F540V		Atlas-SNP	.											.	VAV1	140	.	0			c.T1618G						PASS	.						94	96	95					19																	6833546		2203	4300	6503	SO:0001583	missense	7409	exon17			GGTACCTTCTATC		CCDS12174.1, CCDS59341.1, CCDS59342.1	19p13.2	2013-02-14	2007-07-25			ENSG00000141968		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12657	protein-coding gene	gene with protein product		164875	"vav 1 oncogene"	VAV		9438848	Standard	NM_005428		Approved		uc010xjh.2	P15498		ENST00000602142.1:c.1618T>G	chr19.hg19:g.6833546T>G	ENSP00000472929:p.Phe540Val	167.0	0.0	.		203.0	25.0	.	NM_005428	B4DVK9|M0QXX6|Q15860	Missense_Mutation	SNP	ENST00000602142.1	hg19	CCDS12174.1	.	.	.	.	.	.	.	.	.	.	T	17.11	3.306485	0.60305	.	.	ENSG00000141968	ENST00000304076;ENST00000539284	D;D	0.92647	-3.08;-3.08	4.73	4.73	0.59995	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);	0.055969	0.64402	D	0.000001	D	0.92954	0.7758	L	0.32530	0.975	0.58432	D	0.999999	D;D;D;D	0.89917	0.995;0.998;1.0;0.999	D;D;D;D	0.87578	0.94;0.982;0.998;0.996	D	0.93330	0.6700	10	0.62326	D	0.03	.	12.1658	0.54129	0.0:0.0:0.0:1.0	.	443;540;485;540	F5H5P4;B2R8B5;Q96D37;P15498	.;.;.;VAV_HUMAN	V	540;443	ENSP00000302269:F540V;ENSP00000443242:F443V	ENSP00000302269:F540V	F	+	1	0	VAV1	6784546	1.000000	0.71417	0.998000	0.56505	0.416000	0.31233	5.489000	0.66875	1.784000	0.52394	0.402000	0.26972	TTC	.	.	.	none		0.542	VAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458475.1			G	6833546	T	G	6833546	3	3	174	1	0	0	0	0	1	0	0	0	17143	1609	56	5	1684	5	VAV1	19	6833546	Missense_Mutation	SNP	T	TCGA-G7-6796-01A-11D-1961-08		6833546	52295437	53	10210											
ZNF132	7691	hgsc.bcm.edu	37	chr19	58945194	58945194	+	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	ctacactcgtaaggcttttcTccagtgtgaattctccagtg	8	14	8	11	1	2	1	0	1	2	0	5	1	2	1	2	1	1	2	2	1	3	5			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr19:58945194T>A	ENST00000254166.3	-	3	2017	c.1617A>T	c.(1615-1617)ggA>ggT	p.G539G	CTD-2619J13.17_ENST00000594816.1_lincRNA	NM_003433.3	NP_003424.3	P52740	ZN132_HUMAN	zinc finger protein 132	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)			NS(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(1)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0171)|Lung(386;0.182)		AAGGCTTTTCTCCAGTGTGAA	0.478																																					p.G539G		Atlas-SNP	.											.	ZNF132	56	.	0			c.A1617T						PASS	.						81	83	82					19																	58945194		2203	4300	6503	SO:0001819	synonymous_variant	7691	exon3			CTTTTCTCCAGTG	U09411	CCDS12980.1	19q13.4	2013-01-08	2006-06-13			ENSG00000131849		"Zinc fingers, C2H2-type", "-"	12916	protein-coding gene	gene with protein product		604074	"zinc finger protein 132 (clone pHZ-12)"			7557990	Standard	NM_003433		Approved	pHZ-12	uc002qst.4	P52740		ENST00000254166.3:c.1617A>T	chr19.hg19:g.58945194T>A		107.0	0.0	.		112.0	22.0	.	NM_003433	Q32MI9	Silent	SNP	ENST00000254166.3	hg19	CCDS12980.1																																																																																			.	.	.	none		0.478	ZNF132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467035.1	NM_003433		A	58945194	T	A	58945194	2	1	174	1	0	0	0	0	0	0	0	1	17734	1538	54	5		5	ZNF132	19	58945194	Silent	SNP	T	TCGA-G7-6796-01A-11D-1961-08	52111648	58945194	183789	54	10211											
SEC23B	10483	hgsc.bcm.edu	37	chr20	18496315	18496315	+	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	ttcctccagcttatggaggcAtatctgaggtgaatcaacct	10	12	9	10	0	2	2	1	2	1	0	4	3	4	3	3	3	2	2	3	3	4	3			TCGA-G7-6796-01A-11D-1961-08	TCGA-G7-6796-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d747a9f3-e148-4273-883e-8b64db6779a2	82db6745-95f5-4b86-acd4-8aeb5ec873db	g.chr20:18496315A>T	ENST00000336714.3	+	4	733	c.301A>T	c.(301-303)Ata>Tta	p.I101L	SEC23B_ENST00000494645.1_3'UTR|SEC23B_ENST00000262544.2_Missense_Mutation_p.I101L|SEC23B_ENST00000377475.3_Missense_Mutation_p.I101L|SEC23B_ENST00000377465.1_Missense_Mutation_p.I101L	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)	101					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						TTATGGAGGCATATCTGAGGT	0.348																																					p.I101L		Atlas-SNP	.											.	SEC23B	70	.	0			c.A301T						PASS	.						155	118	130					20																	18496315		2203	4300	6503	SO:0001583	missense	10483	exon4			GGAGGCATATCTG	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.301A>T	chr20.hg19:g.18496315A>T	ENSP00000338844:p.Ile101Leu	103.0	0.0	.		102.0	14.0	.	NM_032985	D3DW33|Q503A9|Q5W183|Q9BS15|Q9BSI2|Q9H1D7	Missense_Mutation	SNP	ENST00000336714.3	hg19	CCDS13137.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.215314	0.79352	.	.	ENSG00000101310	ENST00000450074;ENST00000336714;ENST00000262544;ENST00000377475;ENST00000377465	D;D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63;-1.63	5.04	5.04	0.67666	Zinc finger, Sec23/Sec24-type (1);	0.000000	0.85682	D	0.000000	D	0.86347	0.5911	M	0.81112	2.525	0.80722	D	1	P;P	0.41041	0.736;0.643	P;B	0.45577	0.486;0.271	D	0.87381	0.2357	10	0.49607	T	0.09	-22.3484	14.4009	0.67044	1.0:0.0:0.0:0.0	.	101;101	B4DJW8;Q15437	.;SC23B_HUMAN	L	101	ENSP00000403971:I101L;ENSP00000338844:I101L;ENSP00000262544:I101L;ENSP00000366695:I101L;ENSP00000366685:I101L	ENSP00000262544:I101L	I	+	1	0	SEC23B	18444315	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	8.929000	0.92859	2.241000	0.73720	0.528000	0.53228	ATA	.	.	.	none		0.348	SEC23B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078184.5			T	18496315	A	T	18496315	3	4	174	1	0	0	0	0	1	0	0	0	14005	217	8	5	311	5	SEC23B	20	18496315	Missense_Mutation	SNP	A	TCGA-G7-6796-01A-11D-1961-08		18496315	44529205	55	10212											
ZSCAN20	7579	hgsc.bcm.edu	37	chr1	33960785	33960785	+	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	agtgagcgctccaagctcatCacacaccagagagtgcacac	13	5	9	14	1	2	2	2	1	0	1	3	3	3	2	2	0	3	3	2	0	1	0			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr1:33960785C>T	ENST00000361328.3	+	8	2994	c.2841C>T	c.(2839-2841)atC>atT	p.I947I		NM_145238.3	NP_660281	P17040	ZSC20_HUMAN	zinc finger and SCAN domain containing 20	947					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)				CCAAGCTCATCACACACCAGA	0.527																																					p.I947I		Atlas-SNP	.											.	ZSCAN20	107	.	0			c.C2841T						PASS	.						82	96	91					1																	33960785		2167	4282	6449	SO:0001819	synonymous_variant	7579	exon8			GCTCATCACACAC	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.2841C>T	chr1.hg19:g.33960785C>T		108.0	0.0	.		39.0	36.0	.	NM_145238	A8K2D0|B1ALI4|B1ALI5|B1ALI6|Q6ZN23|Q96FA9|Q96H84	Silent	SNP	ENST00000361328.3	hg19	CCDS41300.1																																																																																			.	.	.	none		0.527	ZSCAN20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277003.2	NM_145238		T	33960785	C	T	33960785	2	4	175	1	0	0	0	0	0	0	0	1	18244	816	29	2		2	ZSCAN20	1	33960785	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08		33960785	215289836	1	10213											
URB2	9816	hgsc.bcm.edu	37	chr1	229770863	229770863	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaaggagctgtggtagcccAgttgtttgaggtcattcacc	8	11	13	9	1	2	1	2	1	0	0	2	3	2	2	2	3	2	4	2	3	2	4			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr1:229770863A>G	ENST00000258243.2	+	4	639	c.503A>G	c.(502-504)cAg>cGg	p.Q168R		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	168						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						GTGGTAGCCCAGTTGTTTGAG	0.582																																					p.Q168R		Atlas-SNP	.											.	URB2	152	.	0			c.A503G						PASS	.						68	55	59					1																	229770863		2203	4300	6503	SO:0001583	missense	9816	exon4			TAGCCCAGTTGTT	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.503A>G	chr1.hg19:g.229770863A>G	ENSP00000258243:p.Gln168Arg	105.0	0.0	.		26.0	21.0	.	NM_014777	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	hg19	CCDS31052.1	.	.	.	.	.	.	.	.	.	.	A	9.721	1.159761	0.21454	.	.	ENSG00000135763	ENST00000258243	T	0.09817	2.94	5.68	0.193	0.15139	.	0.485156	0.24580	N	0.037302	T	0.09512	0.0234	L	0.56769	1.78	0.22226	N	0.999273	P	0.35077	0.483	B	0.30251	0.113	T	0.20571	-1.0271	9	.	.	.	-5.5473	9.3827	0.38325	0.4958:0.3913:0.0:0.1129	.	168	Q14146	URB2_HUMAN	R	168	ENSP00000258243:Q168R	.	Q	+	2	0	URB2	227837486	0.984000	0.35163	0.009000	0.14445	0.428000	0.31595	1.413000	0.34725	0.129000	0.18514	0.528000	0.53228	CAG	.	.	.	none		0.582	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777		G	229770863	A	G	229770863	3	3	175	1	0	0	0	0	1	0	0	0	17037	188	7	3	513	3	URB2	1	229770863	Missense_Mutation	SNP	A	TCGA-G7-6797-01A-11D-1961-08	195810078	229770863	19479758	2	10214											
OR2T3	343173	hgsc.bcm.edu	37	chr1	248637423	248637423	+	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	tcatagtgctgctgctcttcGgtgcttccttctacacctac	5	15	7	14	1	3	0	1	0	2	0	5	0	4	0	2	1	6	4	2	1	3	6			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr1:248637423G>T	ENST00000359594.2	+	1	797	c.772G>T	c.(772-774)Ggt>Tgt	p.G258C		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, 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)			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)			GCTGCTCTTCGGTGCTTCCTT	0.547																																					p.G258C		Atlas-SNP	.											.	OR2T3	79	.	0			c.G772T						PASS	.						285	260	268					1																	248637423		2203	4300	6503	SO:0001583	missense	343173	exon1			CTCTTCGGTGCTT		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.772G>T	chr1.hg19:g.248637423G>T	ENSP00000352604:p.Gly258Cys	647.0	0.0	.		392.0	20.0	.	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	hg19	CCDS31117.1	.	.	.	.	.	.	.	.	.	.	g	11.47	1.647301	0.29246	.	.	ENSG00000196539	ENST00000359594	T	0.38722	1.12	2.37	2.37	0.29283	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.67163	0.2864	M	0.88450	2.955	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.55982	-0.8054	9	0.87932	D	0	.	10.4397	0.44457	0.0:0.0:1.0:0.0	.	258	Q8NH03	OR2T3_HUMAN	C	258	ENSP00000352604:G258C	ENSP00000352604:G258C	G	+	1	0	OR2T3	246704046	0.000000	0.05858	0.003000	0.11579	0.010000	0.07245	-0.435000	0.06931	1.014000	0.39417	0.186000	0.17326	GGT	.	.	.	none		0.547	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495		T	248637423	G	T	248637423	3	4	175	1	0	0	0	0	1	0	0	0	11030	1116	39	4	774	4	OR2T3	1	248637423	Missense_Mutation	SNP	G	TCGA-G7-6797-01A-11D-1961-08	18866560	248637423	613198	3	10215											
ROCK2	9475	hgsc.bcm.edu	37	chr2	11361482	11361482	+	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	tcaggtactacaggagctgcCgctattaaaagaaaagaaat	17	8	9	7	1	1	2	1	0	0	2	1	3	1	3	1	2	4	3	1	2	8	4			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr2:11361482C>A	ENST00000315872.6	-	9	1549	c.1101G>T	c.(1099-1101)acG>acT	p.T367T	ROCK2_ENST00000401753.1_Splice_Site_p.T124T	NM_004850.3	NP_004841.2	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein kinase 2	367	AGC-kinase C-terminal.|Interaction with PPP1R12A.				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)		CAGGAGCTGCCGCTATTAAAA	0.308																																					p.T367T		Atlas-SNP	.											ROCK2_ENST00000315872,NS,carcinoma,0,2	ROCK2	224	.	0			c.G1101T						PASS	.						62	66	65					2																	11361482		1828	4082	5910	SO:0001630	splice_region_variant	9475	exon9			AGCTGCCGCTATT	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.1100-1G>T	chr2.hg19:g.11361482C>A		137.0	0.0	.		145.0	7.0	.	NM_004850	Q53QZ0|Q53SJ7|Q9UQN5	Silent	SNP	ENST00000315872.6	hg19	CCDS42654.1																																																																																			.	.	.	none		0.308	ROCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313886.3		Silent	A	11361482	C	A	11361482	5	1	175	1	0	0	0	0	0	0	1	0	13531	666	23	4	3165	4	ROCK2	2	11361482	Splice_Site	SNP	C	TCGA-G7-6797-01A-11D-1961-08		11361482	231837891	4	10216											
APOB	338	hgsc.bcm.edu	37	chr2	21229324	21229324	+	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	tggtcaactgctcctttagcGgtagagtacagcattgaaga	11	11	11	8	1	1	3	1	1	0	2	2	3	2	3	1	2	5	4	1	2	5	5	rs558589282		TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr2:21229324G>T	ENST00000233242.1	-	26	10543	c.10416C>A	c.(10414-10416)acC>acA	p.T3472T		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3472	Heparin-binding.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.T3472T(2)		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)					CTCCTTTAGCGGTAGAGTACA	0.398																																					p.T3472T		Atlas-SNP	.											APOB,NS,carcinoma,0,1	APOB	761	.	2	Substitution - coding silent(2)	lung(2)	c.C10416A						PASS	.						102	103	102					2																	21229324		2203	4300	6503	SO:0001819	synonymous_variant	338	exon26			TTTAGCGGTAGAG	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.10416C>A	chr2.hg19:g.21229324G>T		166.0	0.0	.		135.0	12.0	.	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	hg19	CCDS1703.1																																																																																			.	.	.	none		0.398	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			T	21229324	G	T	21229324	2	4	175	1	0	0	0	0	0	0	0	1	785	1103	39	4		4	APOB	2	21229324	Silent	SNP	G	TCGA-G7-6797-01A-11D-1961-08	9867842	21229324	221970049	5	10217											
PSME4	23198	hgsc.bcm.edu	37	chr2	54147352	54147352	+	Frame_Shift_Del	DEL	C	C	-																															agacatttcaagttttccatCcccacaatgctggagtttga																										TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr2:54147352delC	ENST00000404125.1	-	19	2453	c.2398delG	c.(2398-2400)gatfs	p.D800fs	PSME4_ENST00000421748.2_Intron	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	800					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)			AGTTTTCCATCCCCACAATGC	0.383																																					p.D800fs		Atlas-INDEL	.											.	PSME4	247	.	0			c.2399delA						PASS	.						149	171	164					2																	54147352		2203	4300	6503	SO:0001589	frameshift_variant	23198	exon19			.	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.2398delG	chr2.hg19:g.54147352delC	ENSP00000384211:p.Asp800fs	456.0	0.0	0		468.0	189.0	0.403846	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Frame_Shift_Del	DEL	ENST00000404125.1	hg19	CCDS33197.2																																																																																			.	.	.	none		0.383	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		-	54147352	C	-	54147352	7	5	175	1	0	1	0	1	0	0	0	0	12719	855	30	0	3245	0	PSME4	2	54147352	Frame_Shift_Del	DEL	C	TCGA-G7-6797-01A-11D-1961-08	32918028	54147352	189052021	6	10218											
GFPT1	2673	hgsc.bcm.edu	37	chr2	69553334	69553334	+	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	atattcctcactctacagtcAcagatttggcaagattccgt	11	13	6	11	1	3	2	2	0	1	2	5	2	5	2	2	1	1	1	2	1	3	5			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr2:69553334A>T	ENST00000357308.4	-	20	2265	c.2087T>A	c.(2086-2088)gTg>gAg	p.V696E	GFPT1_ENST00000361060.5_Missense_Mutation_p.V678E	NM_001244710.1	NP_001231639.1	Q06210	GFPT1_HUMAN	glutamine--fructose-6-phosphate transaminase 1	696					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						CTCTACAGTCACAGATTTGGC	0.343																																					p.V696E		Atlas-SNP	.											.	GFPT1	38	.	0			c.T2087A						PASS	.						89	90	90					2																	69553334		2203	4300	6503	SO:0001583	missense	2673	exon20			ACAGTCACAGATT		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.2087T>A	chr2.hg19:g.69553334A>T	ENSP00000349860:p.Val696Glu	46.0	0.0	.		60.0	22.0	.	NM_001244710	Q53QE6|Q9BXF8	Missense_Mutation	SNP	ENST00000357308.4	hg19	CCDS58713.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.559990	0.86335	.	.	ENSG00000198380	ENST00000357308;ENST00000361060	T;T	0.77358	-1.09;-1.09	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	D	0.93684	0.7982	H	0.99732	4.735	0.80722	D	1	D	0.65815	0.995	D	0.85130	0.997	D	0.96269	0.9197	10	0.87932	D	0	-14.7507	14.9534	0.71091	1.0:0.0:0.0:0.0	.	678	Q06210-2	.	E	696;678	ENSP00000349860:V696E;ENSP00000354347:V678E	ENSP00000349860:V696E	V	-	2	0	GFPT1	69406838	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	9.082000	0.94059	2.302000	0.77476	0.533000	0.62120	GTG	.	.	.	none		0.343	GFPT1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				T	69553334	A	T	69553334	3	4	175	1	0	0	0	0	1	0	0	0	6352	159	6	5	16	5	GFPT1	2	69553334	Missense_Mutation	SNP	A	TCGA-G7-6797-01A-11D-1961-08	15405982	69553334	173646039	7	10219											
NCKAP5	344148	hgsc.bcm.edu	37	chr2	133541732	133541732	+	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	tgactcttggggcactggacCcagtccctcctgctgggcat	5	10	12	14	0	1	1	0	1	1	0	3	2	3	2	3	4	1	3	3	4	0	1			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr2:133541732C>G	ENST00000409261.1	-	14	3025	c.2652G>C	c.(2650-2652)tgG>tgC	p.W884C	NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000317721.6_Missense_Mutation_p.W884C|NCKAP5_ENST00000473859.1_5'Flank	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	884										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						GGCACTGGACCCAGTCCCTCC	0.577																																					p.W884C		Atlas-SNP	.											.	NCKAP5	322	.	0			c.G2652C						PASS	.						54	56	56					2																	133541732		1979	4160	6139	SO:0001583	missense	344148	exon14			CTGGACCCAGTCC	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.2652G>C	chr2.hg19:g.133541732C>G	ENSP00000387128:p.Trp884Cys	174.0	0.0	.		85.0	52.0	.	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	hg19	CCDS46418.1	.	.	.	.	.	.	.	.	.	.	c	11.53	1.664921	0.29604	.	.	ENSG00000176771	ENST00000409261;ENST00000317721	T;T	0.10860	2.83;2.83	5.1	4.18	0.49190	.	0.226096	0.22876	U	0.054566	T	0.20820	0.0501	L	0.32530	0.975	0.58432	D	0.999998	D	0.89917	1.0	D	0.70935	0.971	T	0.00448	-1.1733	10	0.48119	T	0.1	.	13.5162	0.61541	0.1547:0.8453:0.0:0.0	.	884	O14513	NCKP5_HUMAN	C	884	ENSP00000387128:W884C;ENSP00000380603:W884C	ENSP00000380603:W884C	W	-	3	0	NCKAP5	133258202	0.911000	0.30947	0.557000	0.28306	0.216000	0.24613	3.191000	0.50981	2.661000	0.90470	0.651000	0.88453	TGG	.	.	.	none		0.577	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		G	133541732	C	G	133541732	3	3	175	1	0	0	0	0	1	0	0	0	10230	624	22	4	3105	4	NCKAP5	2	133541732	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	63988398	133541732	109657641	8	10220											
ITM2C	81618	hgsc.bcm.edu	37	chr2	231741583	231741583	+	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	tcctgccagggtctgactgcGtaccatgatatctccctgga	7	11	10	13	1	2	2	0	2	2	0	4	3	3	3	4	2	3	1	4	2	2	2			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr2:231741583G>C	ENST00000326427.6	+	4	588	c.462G>C	c.(460-462)gcG>gcC	p.A154A	ITM2C_ENST00000326407.6_Intron|ITM2C_ENST00000492029.1_3'UTR|ITM2C_ENST00000335005.6_Silent_p.A107A|ITM2C_ENST00000409704.2_Silent_p.A92A	NM_030926.4	NP_112188.1	Q9NQX7	ITM2C_HUMAN	integral membrane protein 2C	154	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)		GTCTGACTGCGTACCATGATA	0.587																																					p.A154A		Atlas-SNP	.											.	ITM2C	17	.	0			c.G462C						PASS	.						147	126	133					2																	231741583		2203	4300	6503	SO:0001819	synonymous_variant	81618	exon4			GACTGCGTACCAT	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.462G>C	chr2.hg19:g.231741583G>C		169.0	0.0	.		107.0	50.0	.	NM_030926	B3KPG4|Q4G0A8|Q53H84|Q6IAE7|Q86VK5|Q8N288|Q8TAW0|Q9BUP8	Silent	SNP	ENST00000326427.6	hg19	CCDS2479.1																																																																																			.	.	.	none		0.587	ITM2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256954.2	NM_030926		C	231741583	G	C	231741583	2	2	175	1	0	0	0	0	0	0	0	1	7921	1132	40	4		4	ITM2C	2	231741583	Silent	SNP	G	TCGA-G7-6797-01A-11D-1961-08	98199851	231741583	11457790	9	10221											
CCR2	729230	hgsc.bcm.edu	37	chr3	46399085	46399085	+	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	gcggtgaagaagtcaccaccTtttttgattatgattacggt	10	14	10	7	2	1	4	1	3	0	1	1	4	1	4	2	2	1	0	2	2	4	5			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr3:46399085T>A	ENST00000400888.2	+	1	106	c.67T>A	c.(67-69)Ttt>Att	p.F23I	CCR2_ENST00000292301.4_Missense_Mutation_p.F23I|CCR2_ENST00000465202.1_Intron|CCR2_ENST00000445132.2_Missense_Mutation_p.F23I			P41597	CCR2_HUMAN	chemokine (C-C motif) receptor 2	23					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)		AGTCACCACCTTTTTTGATTA	0.478																																					p.F23I		Atlas-SNP	.											.	CCR2	103	.	0			c.T67A						PASS	.						195	172	179					3																	46399085		1568	3582	5150	SO:0001583	missense	729230	exon2			ACCACCTTTTTTG		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.67T>A	chr3.hg19:g.46399085T>A	ENSP00000383681:p.Phe23Ile	280.0	1.0	.		280.0	136.0	.	NM_001123041	A0AVQ3|B2RMT0|Q4VBL2	Missense_Mutation	SNP	ENST00000400888.2	hg19	CCDS43078.1	.	.	.	.	.	.	.	.	.	.	T	9.930	1.214490	0.22289	.	.	ENSG00000121807	ENST00000445132;ENST00000292301;ENST00000421659;ENST00000400888	T;T;T;T	0.68479	-0.33;-0.31;1.34;-0.31	4.62	-6.25	0.02039	.	6.783580	0.00397	N	0.000040	T	0.40743	0.1129	N	0.12746	0.255	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.15235	-1.0444	10	0.22109	T	0.4	.	2.8484	0.05550	0.3386:0.2093:0.3514:0.1007	.	23;23	P41597;Q4VBL2	CCR2_HUMAN;.	I	23	ENSP00000399285:F23I;ENSP00000292301:F23I;ENSP00000396736:F23I;ENSP00000383681:F23I	ENSP00000292301:F23I	F	+	1	0	CCR2	46374089	0.000000	0.05858	0.003000	0.11579	0.001000	0.01503	0.134000	0.15932	-0.799000	0.04439	-1.318000	0.01297	TTT	.	.	.	none		0.478	CCR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344292.1	NM_000647		A	46399085	T	A	46399085	3	1	175	1	0	0	0	0	1	0	0	0	2943	1609	56	5	69	5	CCR2	3	46399085	Missense_Mutation	SNP	T	TCGA-G7-6797-01A-11D-1961-08		46399085	151623345	10	10222											
SLC26A6	65010	hgsc.bcm.edu	37	chr3	48668741	48668741	+	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	tgcctgtggccccgatgagcTgtgggagaggacagagtcag	8	7	17	9	1	1	3	1	1	0	2	1	6	1	4	3	3	2	1	3	3	0	0			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr3:48668741T>C	ENST00000395550.2	-	8	951		c.e8-2		SLC26A6_ENST00000482282.1_5'Flank|SLC26A6_ENST00000383733.3_Splice_Site|SLC26A6_ENST00000337000.8_Splice_Site|SLC26A6_ENST00000455886.2_Splice_Site|SLC26A6_ENST00000358747.6_Splice_Site|SLC26A6_ENST00000420764.2_Splice_Site			Q9BXS9	S26A6_HUMAN	solute carrier family 26 (anion exchanger), member 6						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)		CCCGATGAGCTGTGGGAGAGG	0.577																																					.	NSCLC(13;369 479 28271 30152 44026)	Atlas-SNP	.											.	SLC26A6	45	.	0			c.841-2A>G						PASS	.						40	42	41					3																	48668741		2105	4230	6335	SO:0001630	splice_region_variant	65010	exon8			ATGAGCTGTGGGA	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.904-2A>G	chr3.hg19:g.48668741T>C		24.0	0.0	.		13.0	8.0	.	NM_001040454	B4DMZ1|Q548A7|Q96Q90|Q9NQU1	Splice_Site	SNP	ENST00000395550.2	hg19	CCDS43087.1	.	.	.	.	.	.	.	.	.	.	T	19.71	3.878586	0.72294	.	.	ENSG00000225697	ENST00000420764;ENST00000395550;ENST00000383733;ENST00000337000;ENST00000447978;ENST00000358747;ENST00000455886;ENST00000421649	.	.	.	5.71	5.71	0.89125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9886	0.80183	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC26A6	48643745	1.000000	0.71417	0.988000	0.46212	0.877000	0.50540	7.298000	0.78815	2.173000	0.68751	0.533000	0.62120	.	.	.	.	none		0.577	SLC26A6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345040.1	NM_022911	Intron	C	48668741	T	C	48668741	5	2	175	1	0	0	0	0	0	0	1	0	14534	1594	55	3	1469	3	SLC26A6	3	48668741	Splice_Site	SNP	T	TCGA-G7-6797-01A-11D-1961-08	2269656	48668741	149353689	11	10223											
ZMYND10	51364	hgsc.bcm.edu	37	chr3	50379017	50379017	+	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	accctcacctgcagcaatacCactcattctggcatcgtgag	10	9	7	15	1	3	1	2	1	1	0	4	1	3	1	3	1	3	3	3	1	2	2			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr3:50379017C>T	ENST00000231749.3	-	11	2507	c.1235G>A	c.(1234-1236)tGg>tAg	p.W412*	ZMYND10-AS1_ENST00000440013.1_RNA|RASSF1_ENST00000488024.1_5'Flank|RASSF1_ENST00000357043.2_5'Flank|ZMYND10_ENST00000360165.3_Nonsense_Mutation_p.W407*|RASSF1_ENST00000359365.4_5'Flank|ZMYND10_ENST00000490675.1_5'UTR	NM_015896.2	NP_056980.2	O75800	ZMY10_HUMAN	zinc finger, MYND-type containing 10	412	Interaction with LRRC6.				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)		GCAGCAATACCACTCATTCTG	0.572										TSP Lung(30;0.18)																											p.W412X		Atlas-SNP	.											.	ZMYND10	37	.	0			c.G1235A						PASS	.						138	129	132					3																	50379017		2203	4300	6503	SO:0001587	stop_gained	51364	exon11			CAATACCACTCAT	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.1235G>A	chr3.hg19:g.50379017C>T	ENSP00000231749:p.Trp412*	126.0	0.0	.		78.0	30.0	.	NM_015896	A6NK41|B3KU54|O14570|O75801|Q53FE6|Q8N4R6|Q8NDN6	Nonsense_Mutation	SNP	ENST00000231749.3	hg19	CCDS2825.1	.	.	.	.	.	.	.	.	.	.	C	37	6.249939	0.97412	.	.	ENSG00000004838	ENST00000231749;ENST00000360165	.	.	.	5.4	5.4	0.78164	.	0.053779	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.9405	19.525	0.95201	0.0:1.0:0.0:0.0	.	.	.	.	X	412;407	.	ENSP00000231749:W412X	W	-	2	0	ZMYND10	50354021	1.000000	0.71417	1.000000	0.80357	0.717000	0.41224	7.761000	0.85260	2.699000	0.92147	0.655000	0.94253	TGG	.	.	.	none		0.572	ZMYND10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346376.1	NM_015896		T	50379017	C	T	50379017	4	4	175	1	0	0	0	0	0	1	0	0	17717	595	21	2	95	2	ZMYND10	3	50379017	Nonsense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	1710276	50379017	147643413	12	10224											
C3orf63	23272	hgsc.bcm.edu	37	chr3	56658883	56658883	+	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	aaagactatgtgtcgttgctGtatgttctgagcctgaagtc	9	14	11	7	1	1	3	0	2	1	1	3	3	1	3	1	0	2	4	1	0	4	4			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr3:56658883G>C	ENST00000493960.2	-	22	4301	c.4291C>G	c.(4291-4293)Cag>Gag	p.Q1431E	FAM208A_ENST00000431842.2_Missense_Mutation_p.Q994E|FAM208A_ENST00000485156.1_Intron|FAM208A_ENST00000355628.5_Missense_Mutation_p.Q1370E	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	1431							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						TGTCGTTGCTGTATGTTCTGA	0.383																																					p.Q1431E		Atlas-SNP	.											.	FAM208A	113	.	0			c.C4291G						PASS	.						127	125	126					3																	56658883		2203	4300	6503	SO:0001583	missense	23272	exon22			GTTGCTGTATGTT	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.4291C>G	chr3.hg19:g.56658883G>C	ENSP00000417509:p.Gln1431Glu	121.0	0.0	.		147.0	58.0	.	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Missense_Mutation	SNP	ENST00000493960.2	hg19	CCDS46853.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.279138	0.80692	.	.	ENSG00000163946	ENST00000431842;ENST00000493960;ENST00000355628	T;T;T	0.53206	0.63;0.63;0.63	5.7	5.7	0.88788	.	0.000000	0.64402	D	0.000008	T	0.52613	0.1745	L	0.38838	1.175	0.47245	D	0.999367	P;B;D;B	0.61697	0.629;0.045;0.99;0.435	B;B;P;B	0.55011	0.382;0.094;0.766;0.104	T	0.54070	-0.8348	10	0.72032	D	0.01	-0.4466	14.6453	0.68756	0.0:0.0:0.8544:0.1456	.	1431;1370;994;1431	Q9UK61-3;Q9UK61-4;Q9UK61-2;Q9UK61	.;.;.;F208A_HUMAN	E	994;1431;1370	ENSP00000399410:Q994E;ENSP00000417509:Q1431E;ENSP00000347845:Q1370E	ENSP00000347845:Q1370E	Q	-	1	0	C3orf63	56633923	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.500000	0.81588	2.685000	0.91497	0.655000	0.94253	CAG	.	.	.	none		0.383	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224		C	56658883	G	C	56658883	3	2	175	1	0	0	0	0	1	0	0	0	2241	1386	48	4	793	4	C3orf63	3	56658883	Missense_Mutation	SNP	G	TCGA-G7-6797-01A-11D-1961-08	6279866	56658883	141363547	13	10225											
ACOX2	8309	hgsc.bcm.edu	37	chr3	58517532	58517532	+	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	accagggcatgggtggctgaCcgtcccactgagggcagaga	9	5	16	11	1	0	3	0	2	0	1	1	4	1	3	3	4	0	3	3	4	0	0			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr3:58517532C>A	ENST00000302819.5	-	6	882	c.591G>T	c.(589-591)cgG>cgT	p.R197R	ACOX2_ENST00000459701.2_Silent_p.R197R	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	197					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)		GGGTGGCTGACCGTCCCACTG	0.612																																					p.R197R		Atlas-SNP	.											.	ACOX2	53	.	0			c.G591T						PASS	.						57	50	52					3																	58517532		2203	4300	6503	SO:0001819	synonymous_variant	8309	exon6			GGCTGACCGTCCC	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.591G>T	chr3.hg19:g.58517532C>A		79.0	0.0	.		34.0	18.0	.	NM_003500	A6NF16|B2R8U5	Silent	SNP	ENST00000302819.5	hg19	CCDS33775.1																																																																																			.	.	.	none		0.612	ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1			A	58517532	C	A	58517532	2	1	175	1	0	0	0	0	0	0	0	1	159	494	18	4		4	ACOX2	3	58517532	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08	1858649	58517532	139504898	14	10226											
EPHA3	2042	hgsc.bcm.edu	37	chr3	89521663	89521663	+	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	atgtggatatcactaccttcCgcacaacaggtgactggctt	10	11	9	11	1	1	1	1	1	0	0	2	2	2	2	2	3	2	2	2	3	3	4	rs549868478	byFrequency	TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr3:89521663C>A	ENST00000336596.2	+	16	2965	c.2740C>A	c.(2740-2742)Cgc>Agc	p.R914S	EPHA3_ENST00000494014.1_Missense_Mutation_p.R914S	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	914	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.		R -> H (in dbSNP:rs17801309). {ECO:0000269|PubMed:17344846}.		cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		CACTACCTTCCGCACAACAGG	0.468										TSP Lung(6;0.00050)																											p.R914S		Atlas-SNP	.											.	EPHA3	501	.	0			c.C2740A						PASS	.						181	170	174					3																	89521663		2203	4300	6503	SO:0001583	missense	2042	exon16			ACCTTCCGCACAA	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.2740C>A	chr3.hg19:g.89521663C>A	ENSP00000337451:p.Arg914Ser	250.0	0.0	.		249.0	16.0	.	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	hg19	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	c	12.06	1.824931	0.32237	.	.	ENSG00000044524	ENST00000336596;ENST00000494014	D;T	0.83755	-1.76;-0.64	5.73	3.93	0.45458	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.328872	0.37012	N	0.002289	T	0.72542	0.3473	N	0.19112	0.55	0.26449	N	0.975649	B	0.28760	0.221	B	0.33521	0.165	T	0.59220	-0.7495	9	.	.	.	.	13.0963	0.59195	0.1289:0.7475:0.1236:0.0	.	914	P29320	EPHA3_HUMAN	S	914	ENSP00000337451:R914S;ENSP00000419190:R914S	.	R	+	1	0	EPHA3	89604353	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.492000	0.45311	0.772000	0.33382	-0.121000	0.15023	CGC	.	.	.	none		0.468	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		A	89521663	C	A	89521663	3	1	175	1	0	0	0	0	1	0	0	0	5170	652	23	4	2828	4	EPHA3	3	89521663	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	31004131	89521663	108500767	15	10227											
ZBTB11	27107	hgsc.bcm.edu	37	chr3	101370105	101370105	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tccttgctgttgtgctaataCataattaaccacttgcataa	12	15	5	9	0	0	0	0	0	0	0	1	0	1	0	2	0	5	4	2	0	5	8			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr3:101370105C>T	ENST00000312938.4	-	11	3647	c.3067G>A	c.(3067-3069)Gta>Ata	p.V1023I		NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	1023					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						TGTGCTAATACATAATTAACC	0.398																																					p.V1023I		Atlas-SNP	.											.	ZBTB11	77	.	0			c.G3067A						PASS	.						135	131	132					3																	101370105		2203	4300	6503	SO:0001583	missense	27107	exon11			CTAATACATAATT	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.3067G>A	chr3.hg19:g.101370105C>T	ENSP00000326200:p.Val1023Ile	181.0	0.0	.		168.0	70.0	.	NM_014415	Q2NKP9	Missense_Mutation	SNP	ENST00000312938.4	hg19	CCDS2943.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.982094	0.93044	.	.	ENSG00000066422	ENST00000312938	T	0.12672	2.66	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.28300	0.0699	L	0.32530	0.975	0.80722	D	1	D	0.76494	0.999	D	0.76071	0.987	T	0.00899	-1.1522	10	0.30078	T	0.28	-12.9426	19.5182	0.95174	0.0:1.0:0.0:0.0	.	1023	O95625	ZBT11_HUMAN	I	1023	ENSP00000326200:V1023I	ENSP00000326200:V1023I	V	-	1	0	ZBTB11	102852795	1.000000	0.71417	0.987000	0.45799	0.985000	0.73830	7.445000	0.80570	2.692000	0.91855	0.555000	0.69702	GTA	.	.	.	none		0.398	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415		T	101370105	C	T	101370105	3	4	175	1	0	0	0	0	1	0	0	0	17536	478	17	2	98	2	ZBTB11	3	101370105	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	11848442	101370105	96652325	16	10228											
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113376409	113376409	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagggatctgactgaccaTcatttgagtttggtcagaaa	12	11	12	6	0	3	4	2	3	1	1	3	6	3	6	1	3	0	1	1	3	1	2			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr3:113376409T>C	ENST00000478658.1	-	5	4137	c.4120A>G	c.(4120-4122)Atg>Gtg	p.M1374V	KIAA2018_ENST00000316407.4_Missense_Mutation_p.M1374V|KIAA2018_ENST00000491165.1_Intron			Q68DE3	K2018_HUMAN	KIAA2018	1374						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						TGACTGACCATCATTTGAGTT	0.468																																					p.M1374V		Atlas-SNP	.											.	KIAA2018	180	.	0			c.A4120G						PASS	.						105	102	103					3																	113376409		1991	4160	6151	SO:0001583	missense	205717	exon7			TGACCATCATTTG	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.4120A>G	chr3.hg19:g.113376409T>C	ENSP00000420721:p.Met1374Val	112.0	0.0	.		96.0	38.0	.	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Missense_Mutation	SNP	ENST00000478658.1	hg19	CCDS43133.1	.	.	.	.	.	.	.	.	.	.	T	10.68	1.417459	0.25552	.	.	ENSG00000176542	ENST00000316407;ENST00000478658	T;T	0.18338	2.22;2.22	5.68	4.46	0.54185	.	0.087940	0.85682	D	0.000000	T	0.13415	0.0325	L	0.32530	0.975	0.47862	D	0.999537	B	0.30406	0.278	B	0.30179	0.112	T	0.07404	-1.0774	10	0.37606	T	0.19	-12.1634	11.116	0.48259	0.0:0.0:0.3371:0.6629	.	1374	Q68DE3	K2018_HUMAN	V	1374	ENSP00000320794:M1374V;ENSP00000420721:M1374V	ENSP00000320794:M1374V	M	-	1	0	KIAA2018	114859099	1.000000	0.71417	1.000000	0.80357	0.752000	0.42762	2.543000	0.45752	2.169000	0.68431	0.402000	0.26972	ATG	.	.	.	none		0.468	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		C	113376409	T	C	113376409	3	2	175	1	0	0	0	0	1	0	0	0	8275	1435	50	3	2621	3	KIAA2018	3	113376409	Missense_Mutation	SNP	T	TCGA-G7-6797-01A-11D-1961-08	12006304	113376409	84646021	17	10229											
FSTL1	11167	hgsc.bcm.edu	37	chr3	120122159	120122159	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagctgagtttccaatcagcAttttcatcagacagttcaat	13	13	6	9	0	4	2	4	1	0	1	5	2	5	2	1	0	2	4	1	0	3	4			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr3:120122159A>G	ENST00000295633.3	-	8	980	c.624T>C	c.(622-624)aaT>aaC	p.N208N	FSTL1_ENST00000424703.2_Silent_p.N173N	NM_007085.4	NP_009016.1	Q12841	FSTL1_HUMAN	follistatin-like 1	208	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				BMP signaling pathway (GO:0030509)|response to starvation (GO:0042594)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|skin(1)	20				GBM - Glioblastoma multiforme(114;0.189)		TCCAATCAGCATTTTCATCAG	0.438																																					p.N208N		Atlas-SNP	.											.	FSTL1	43	.	0			c.T624C						PASS	.						106	106	106					3																	120122159		2203	4300	6503	SO:0001819	synonymous_variant	11167	exon8			ATCAGCATTTTCA	U06863	CCDS2998.1	3q13.33	2013-01-10			ENSG00000163430	ENSG00000163430		"EF-hand domain containing"	3972	protein-coding gene	gene with protein product		605547				7957230, 9786430	Standard	NM_007085		Approved	FRP, FSL1	uc003eds.3	Q12841	OTTHUMG00000159440	ENST00000295633.3:c.624T>C	chr3.hg19:g.120122159A>G		132.0	0.0	.		156.0	65.0	.	NM_007085	A8K523|B4DTT5|D3DN90|Q549Z0	Silent	SNP	ENST00000295633.3	hg19	CCDS2998.1																																																																																			.	.	.	none		0.438	FSTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355399.1	NM_007085		G	120122159	A	G	120122159	2	3	175	1	0	0	0	0	0	0	0	1	6084	214	8	3		3	FSTL1	3	120122159	Silent	SNP	A	TCGA-G7-6797-01A-11D-1961-08	6745750	120122159	77900271	18	10230											
ETV5	2119	hgsc.bcm.edu	37	chr3	185766603	185766603	+	Missense_Mutation	SNP	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	ggaaagccatggagaagaggGcatctgggtcacagacaaat	15	5	14	7	0	2	3	1	0	1	3	2	5	2	4	1	4	1	1	1	4	3	0			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr3:185766603G>A	ENST00000306376.5	-	13	1604	c.1358C>T	c.(1357-1359)gCc>gTc	p.A453V	ETV5_ENST00000434744.1_Missense_Mutation_p.A453V|ETV5_ENST00000480706.1_5'UTR|ETV5_ENST00000537818.1_Missense_Mutation_p.A495V	NM_004454.2	NP_004445.1	P41161	ETV5_HUMAN	ets variant 5	453					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)			GGAGAAGAGGGCATCTGGGTC	0.582			T	"TMPRSS2, SCL45A3"	Prostate																																p.A453V		Atlas-SNP	.		Dom	yes		3	3q28	2119	ets variant gene 5		E	.	ETV5	106	.	0			c.C1358T						PASS	.						70	61	64					3																	185766603		2203	4300	6503	SO:0001583	missense	2119	exon13			AAGAGGGCATCTG	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.1358C>T	chr3.hg19:g.185766603G>A	ENSP00000306894:p.Ala453Val	73.0	0.0	.		43.0	25.0	.	NM_004454	A6NH46|B7Z7D7|Q6IBN5	Missense_Mutation	SNP	ENST00000306376.5	hg19	CCDS33906.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.043894	0.93685	.	.	ENSG00000244405	ENST00000306376;ENST00000434744;ENST00000537818	T;T;T	0.54866	0.55;0.55;0.55	5.85	5.85	0.93711	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.69548	0.3123	L	0.49513	1.565	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.70149	-0.4951	10	0.87932	D	0	.	18.9349	0.92582	0.0:0.0:1.0:0.0	.	453;495	P41161;B7Z7D7	ETV5_HUMAN;.	V	453;453;495	ENSP00000306894:A453V;ENSP00000413755:A453V;ENSP00000441737:A495V	ENSP00000306894:A453V	A	-	2	0	ETV5	187249297	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.773000	0.95371	0.655000	0.94253	GCC	.	.	.	none		0.582	ETV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344947.1	NM_004454		A	185766603	G	A	185766603	3	1	175	1	0	0	0	0	1	0	0	0	5284	1203	42	2	178	2	ETV5	3	185766603	Missense_Mutation	SNP	G	TCGA-G7-6797-01A-11D-1961-08	65644444	185766603	12255827	19	10231											
SLC4A4	8671	hgsc.bcm.edu	37	chr4	72332250	72332250	+	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	ctcactattctgagcagcacCggacctgtcctagtttttga	8	13	8	12	1	2	2	1	2	1	0	3	3	3	3	3	1	2	3	3	1	2	5			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr4:72332250C>A	ENST00000264485.5	+	13	1704	c.1587C>A	c.(1585-1587)acC>acA	p.T529T	SLC4A4_ENST00000512686.1_Silent_p.T485T|SLC4A4_ENST00000351898.6_Silent_p.T529T|SLC4A4_ENST00000514331.1_3'UTR|SLC4A4_ENST00000425175.1_Silent_p.T529T|SLC4A4_ENST00000340595.3_Silent_p.T485T	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	529			T -> S (in pRTA-OA; decreased cotransporter activity). {ECO:0000269|PubMed:15930088, ECO:0000303|PubMed:17661077}.		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)	TGAGCAGCACCGGACCTGTCC	0.398																																					p.T529T		Atlas-SNP	.											.	SLC4A4	269	.	0			c.C1587A						PASS	.						150	142	145					4																	72332250		2203	4300	6503	SO:0001819	synonymous_variant	8671	exon13			CAGCACCGGACCT	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.1587C>A	chr4.hg19:g.72332250C>A		183.0	0.0	.		178.0	11.0	.	NM_001098484	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Silent	SNP	ENST00000264485.5	hg19	CCDS43236.1																																																																																			.	.	.	none		0.398	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		A	72332250	C	A	72332250	2	1	175	1	0	0	0	0	0	0	0	1	14669	639	23	4		4	SLC4A4	4	72332250	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08		72332250	118822026	20	10232											
ANK2	287	hgsc.bcm.edu	37	chr4	114177035	114177035	+	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	ctgcgcactgtggccactacCgtgtaaccaaactcctttta	9	11	7	14	2	0	0	0	0	0	0	1	0	1	0	4	1	4	2	4	1	4	4	rs143043717	byFrequency	TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr4:114177035C>A	ENST00000357077.4	+	11	1188	c.1135C>A	c.(1135-1137)Cgt>Agt	p.R379S	ANK2_ENST00000506722.1_Missense_Mutation_p.R358S|ANK2_ENST00000394537.3_Missense_Mutation_p.R379S|ANK2_ENST00000264366.6_Missense_Mutation_p.R379S	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	379					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.R379S(2)		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)		TGGCCACTACCGTGTAACCAA	0.507																																					p.R379S		Atlas-SNP	.											ANK2,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	ANK2	576	.	2	Substitution - Missense(2)	lung(1)|central_nervous_system(1)	c.C1135A						PASS	.						158	141	147					4																	114177035		2203	4300	6503	SO:0001583	missense	287	exon11			CACTACCGTGTAA	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.1135C>A	chr4.hg19:g.114177035C>A	ENSP00000349588:p.Arg379Ser	291.0	0.0	.		198.0	13.0	.	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	hg19	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.719331	0.89205	.	.	ENSG00000145362	ENST00000503271;ENST00000503423;ENST00000506722;ENST00000504454;ENST00000394537;ENST00000357077;ENST00000264366;ENST00000343056	T;T;T;T;T;T;T	0.63744	-0.06;-0.04;-0.04;-0.04;-0.04;-0.04;-0.04	5.91	5.91	0.95273	Ankyrin repeat-containing domain (3);	0.000000	0.56097	D	0.000026	T	0.64778	0.2629	N	0.05306	-0.075	0.80722	D	1	D;D;P;P;D	0.67145	0.984;0.973;0.929;0.885;0.996	P;P;B;P;D	0.79784	0.877;0.56;0.429;0.56;0.993	T	0.72711	-0.4211	10	0.59425	D	0.04	.	20.2896	0.98541	0.0:1.0:0.0:0.0	.	379;379;379;358;358	Q01484;Q01484-2;Q01484-4;Q01484-5;F8WEF9	ANK2_HUMAN;.;.;.;.	S	358;358;358;394;379;379;379;358	ENSP00000423799:R358S;ENSP00000421011:R358S;ENSP00000421067:R358S;ENSP00000424722:R394S;ENSP00000378044:R379S;ENSP00000349588:R379S;ENSP00000264366:R379S	ENSP00000264366:R379S	R	+	1	0	ANK2	114396484	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	5.021000	0.64072	2.794000	0.96219	0.655000	0.94253	CGT	.	C|1.000;T|0.000	.	alt		0.507	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		A	114177035	C	A	114177035	3	1	175	1	0	0	0	0	1	0	0	0	621	652	23	4	1202	4	ANK2	4	114177035	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	41844785	114177035	76977241	21	10233											
FAT4	79633	hgsc.bcm.edu	37	chr4	126369689	126369689	+	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	gaactgcattattctctttcGggtagaaattctgaaaaatt	13	15	7	6	1	2	2	0	1	2	1	4	3	2	2	0	1	2	2	0	1	6	6			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr4:126369689G>T	ENST00000394329.3	+	9	7531	c.7518G>T	c.(7516-7518)tcG>tcT	p.S2506S	FAT4_ENST00000335110.5_Silent_p.S804S	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2506	Cadherin 24. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						ATTCTCTTTCGGGTAGAAATT	0.423																																					p.S2506S		Atlas-SNP	.											FAT4_ENST00000394329,NS,carcinoma,0,2	FAT4	1752	.	0			c.G7518T						PASS	.						68	71	70					4																	126369689		2203	4299	6502	SO:0001819	synonymous_variant	79633	exon9			TCTTTCGGGTAGA	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.7518G>T	chr4.hg19:g.126369689G>T		123.0	0.0	.		165.0	8.0	.	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	hg19	CCDS3732.3																																																																																			.	.	.	none		0.423	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126369689	G	T	126369689	2	4	175	1	0	0	0	0	0	0	0	1	5699	1103	39	4		4	FAT4	4	126369689	Silent	SNP	G	TCGA-G7-6797-01A-11D-1961-08	12192654	126369689	64784587	22	10234											
FAT1	2195	hgsc.bcm.edu	37	chr4	187539870	187539870	+	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	gtcggcattggagccctcatCggcatcacttgcaagaactt	9	10	10	12	2	2	1	2	0	0	1	4	2	2	2	1	3	3	3	1	3	2	3			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr4:187539870C>A	ENST00000441802.2	-	10	8079	c.7870G>T	c.(7870-7872)Gat>Tat	p.D2624Y		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2624	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						GAGCCCTCATCGGCATCACTT	0.443										HNSCC(5;0.00058)																											p.D2624Y	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.G7870T						PASS	.						63	59	60					4																	187539870		1948	4127	6075	SO:0001583	missense	2195	exon10			CCTCATCGGCATC	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.7870G>T	chr4.hg19:g.187539870C>A	ENSP00000406229:p.Asp2624Tyr	79.0	0.0	.		84.0	37.0	.	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	hg19	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	14.70	2.612696	0.46631	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.74737	-0.87	5.2	5.2	0.72013	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.92675	0.7672	H	0.99090	4.425	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95297	0.8400	10	0.87932	D	0	.	19.2916	0.94102	0.0:1.0:0.0:0.0	.	2624	Q14517	FAT1_HUMAN	Y	2624;2626	ENSP00000406229:D2624Y	ENSP00000260147:D2626Y	D	-	1	0	FAT1	187776864	1.000000	0.71417	0.347000	0.25668	0.077000	0.17291	7.651000	0.83577	2.861000	0.98227	0.655000	0.94253	GAT	.	.	.	none		0.443	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		A	187539870	C	A	187539870	3	1	175	1	0	0	0	0	1	0	0	0	5696	884	31	4	5968	4	FAT1	4	187539870	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	61170181	187539870	3614406	23	10235											
FAT1	2195	hgsc.bcm.edu	37	chr4	187630250	187630250	+	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	ttggcctgttcgatgtgcacCgttagcttggccatgctgct	4	14	12	11	2	0	0	0	0	0	0	1	1	0	0	3	2	4	6	3	2	1	4	rs374978739		TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr4:187630250C>A	ENST00000441802.2	-	2	941	c.732G>T	c.(730-732)acG>acT	p.T244T		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	244	Cadherin 2. {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						CGATGTGCACCGTTAGCTTGG	0.512										HNSCC(5;0.00058)																											p.T244T	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.G732T						PASS	.						144	143	143					4																	187630250		2179	4286	6465	SO:0001819	synonymous_variant	2195	exon2			GTGCACCGTTAGC	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.732G>T	chr4.hg19:g.187630250C>A		277.0	0.0	.		226.0	11.0	.	NM_005245		Silent	SNP	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.	.	alt		0.512	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		A	187630250	C	A	187630250	2	1	175	1	0	0	0	0	0	0	0	1	5696	639	23	4		4	FAT1	4	187630250	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08	90380	187630250	3524026	24	10236											
RGS7BP	401190	hgsc.bcm.edu	37	chr5	63905047	63905047	+	Frame_Shift_Del	DEL	T	T	-																															tgagaagacggaagagaaggTtctttgggctgtgttgtctc																										TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr5:63905047delT	ENST00000334025.2	+	6	1068	c.742delT	c.(742-744)ttcfs	p.F249fs		NM_001029875.1|NM_001271890.1|NM_001271891.1	NP_001025046.1|NP_001258819.1|NP_001258820.1	Q6MZT1	R7BP_HUMAN	regulator of G-protein signaling 7 binding protein	249					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of signal transduction (GO:0009968)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)|stomach(1)	11		Lung NSC(810;0.000518)|Prostate(74;0.0435)|Ovarian(174;0.186)		Lung(70;0.147)		GAAGAGAAGGTTCTTTGGGCT	0.478																																					p.R247fs		Atlas-INDEL	.											.	RGS7BP	32	.	0			c.741delG						PASS	.						168	148	155					5																	63905047		2203	4300	6503	SO:0001589	frameshift_variant	401190	exon6			.	BX640900	CCDS34170.1	5q12.3	2008-02-05	2007-08-14		ENSG00000186479	ENSG00000186479			23271	protein-coding gene	gene with protein product		610890	"regulator of G-protein signalling 7 binding protein"			15632198	Standard	NM_001271890		Approved	R7BP	uc003jtj.4	Q6MZT1	OTTHUMG00000162293	ENST00000334025.2:c.742delT	chr5.hg19:g.63905047delT	ENSP00000334851:p.Phe249fs	121.0	0.0	0		101.0	38.0	0.376238	NM_001029875	B7Z3X1	Frame_Shift_Del	DEL	ENST00000334025.2	hg19	CCDS34170.1																																																																																			.	.	.	none		0.478	RGS7BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368464.1	NM_001029875		-	63905047	T	-	63905047	7	5	175	1	0	1	0	1	0	0	0	0	13324	1725	60	0	764	0	RGS7BP	5	63905047	Frame_Shift_Del	DEL	T	TCGA-G7-6797-01A-11D-1961-08		63905047	117010213	25	10237											
BHMT	635	hgsc.bcm.edu	37	chr5	78426827	78426828	+	Frame_Shift_Ins	INS	-	-	A																															aacccttcaatgtcaaagccINSagatggctggggagtgacca																										TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr5:78426827_78426828insA	ENST00000274353.5	+	8	1216_1217	c.1109_1110insA	c.(1108-1113)ccagatfs	p.D371fs	BHMT_ENST00000524080.1_Frame_Shift_Ins_p.D218fs|DMGDH_ENST00000520388.1_Intron	NM_001713.2	NP_001704.2	Q93088	BHMT1_HUMAN	betaine--homocysteine S-methyltransferase	371					amino-acid betaine catabolic process (GO:0006579)|amino-acid betaine metabolic process (GO:0006577)|cellular nitrogen compound metabolic process (GO:0034641)|L-methionine salvage (GO:0071267)|protein methylation (GO:0006479)|regulation of homocysteine metabolic process (GO:0050666)|response to organonitrogen compound (GO:0010243)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	betaine-homocysteine S-methyltransferase activity (GO:0047150)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)	29		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.88e-45)|Epithelial(54;8.07e-41)|all cancers(79;3.51e-36)	L-Methionine(DB00134)	ATGTCAAAGCCAGATGGCTGGG	0.495																																					p.P370fs		Atlas-INDEL	.											.	BHMT	53	.	0			c.1109_1110insA						PASS	.																																			SO:0001589	frameshift_variant	635	exon8			.	BC012616	CCDS4046.1	5q14.1	2012-09-20	2010-04-28		ENSG00000145692	ENSG00000145692	2.1.1.5		1047	protein-coding gene	gene with protein product	"betaine homocysteine methyltransferase"	602888				8798461, 9281325	Standard	NM_001713		Approved	BHMT1	uc003kfu.4	Q93088	OTTHUMG00000108157	ENST00000274353.5:c.1110dupA	chr5.hg19:g.78426828_78426828dupA	ENSP00000274353:p.Asp371fs	276.0	0.0	0		276.0	105.0	0.380435	NM_001713	Q9UNI9	Frame_Shift_Ins	INS	ENST00000274353.5	hg19	CCDS4046.1																																																																																			.	.	.	none		0.495	BHMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226961.1	NM_001713		A	78426828	-	A	78426827	7	5	175	1	0	1	1	0	0	0	0	0	1425	594	21	0	1139	0	BHMT	5	78426827	Frame_Shift_Ins	INS	-	TCGA-G7-6797-01A-11D-1961-08	14521780	78426827	102488433	26	10238											
PCDHB4	56131	hgsc.bcm.edu	37	chr5	140502471	140502471	+	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	ttctcaataaatgaagtcacGggagaaatactgttgaaaaa	18	10	8	5	1	2	3	2	2	1	1	3	4	2	3	0	1	1	1	0	1	8	4	rs375984500	byFrequency	TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr5:140502471G>T	ENST00000194152.1	+	1	891	c.891G>T	c.(889-891)acG>acT	p.T297T	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	297	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)			ATGAAGTCACGGGAGAAATAC	0.358																																					p.T297T		Atlas-SNP	.											.	PCDHB4	177	.	0			c.G891T						PASS	.						86	103	97					5																	140502471		2197	4298	6495	SO:0001819	synonymous_variant	56131	exon1			AGTCACGGGAGAA	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.891G>T	chr5.hg19:g.140502471G>T		239.0	0.0	.		275.0	14.0	.	NM_018938	Q4V761	Silent	SNP	ENST00000194152.1	hg19	CCDS4246.1																																																																																			.	.	.	alt		0.358	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938		T	140502471	G	T	140502471	2	4	175	1	0	0	0	0	0	0	0	1	11551	1103	39	4		4	PCDHB4	5	140502471	Silent	SNP	G	TCGA-G7-6797-01A-11D-1961-08	62075644	140502471	40412789	27	10239											
ECT2L	345930	hgsc.bcm.edu	37	chr6	139167797	139167797	+	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	acttcatgttaatatcatccCggattcctgcgtatgaggta	10	14	8	9	2	2	1	2	1	0	0	4	2	4	2	2	2	1	3	2	2	4	6	rs376022291		TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr6:139167797C>A	ENST00000423192.1	+	7	1047	c.886C>A	c.(886-888)Cgg>Agg	p.R296R	ECT2L_ENST00000367682.2_Silent_p.R296R|ECT2L_ENST00000541398.1_Silent_p.R227R			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	296							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						AATATCATCCCGGATTCCTGC	0.383			"N, Splice, Mis"		ETP ALL																																p.R296R		Atlas-SNP	.		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	.	ECT2L	75	.	0			c.C886A						PASS	.						227	218	221					6																	139167797		1940	4146	6086	SO:0001819	synonymous_variant	345930	exon7			TCATCCCGGATTC		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.886C>A	chr6.hg19:g.139167797C>A		395.0	0.0	.		497.0	20.0	.	NM_001195037	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Silent	SNP	ENST00000423192.1	hg19	CCDS43508.1																																																																																			.	.	.	alt		0.383	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706		A	139167797	C	A	139167797	2	1	175	1	0	0	0	0	0	0	0	1	4904	643	23	4		4	ECT2L	6	139167797	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08		139167797	31947270	28	10240											
AKAP12	9590	hgsc.bcm.edu	37	chr6	151626981	151626981	+	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	taaatggccagaaaggagccCtgaacggtcaaggagcccta	14	5	12	10	1	1	2	1	1	0	1	1	4	1	4	3	4	3	0	3	4	6	2			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr6:151626981C>G	ENST00000253332.1	+	2	451	c.262C>G	c.(262-264)Ctg>Gtg	p.L88V	AKAP12_ENST00000402676.2_Missense_Mutation_p.L88V			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	88					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		GAAAGGAGCCCTGAACGGTCA	0.552																																					p.L88V	Melanoma(141;1616 1805 10049 24534 51979)	Atlas-SNP	.											.	AKAP12	170	.	0			c.C262G						PASS	.						53	46	49					6																	151626981		2203	4300	6503	SO:0001583	missense	9590	exon3			GGAGCCCTGAACG	U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"A-kinase anchor proteins"	370	protein-coding gene	gene with protein product	"gravin", "Src-Suppressed C Kinase Substrate"	604698	"A kinase (PRKA) anchor protein (gravin) 12"			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.262C>G	chr6.hg19:g.151626981C>G	ENSP00000253332:p.Leu88Val	48.0	0.0	.		34.0	13.0	.	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	hg19	CCDS5229.1	.	.	.	.	.	.	.	.	.	.	C	0.285	-0.983780	0.02180	.	.	ENSG00000131016	ENST00000402676;ENST00000253332	T;T	0.08546	3.08;3.08	0.158	0.158	0.14942	.	.	.	.	.	T	0.01092	0.0036	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.48031	-0.9070	8	0.30854	T	0.27	.	.	.	.	.	88	Q02952	AKA12_HUMAN	V	88	ENSP00000384537:L88V;ENSP00000253332:L88V	ENSP00000253332:L88V	L	+	1	2	AKAP12	151668674	.	.	0.029000	0.17559	0.052000	0.14988	.	.	0.202000	0.20498	0.205000	0.17691	CTG	.	.	.	none		0.552	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1			G	151626981	C	G	151626981	3	3	175	1	0	0	0	0	1	0	0	0	448	680	24	4	268	4	AKAP12	6	151626981	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	12459184	151626981	19488086	29	10241											
PGAM2	5224	hgsc.bcm.edu	37	chr7	44105125	44105125	+	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	catcacgaggcggtgagtggCcatggtggcagcagggacca	9	5	17	10	2	1	1	1	1	0	0	1	3	1	2	2	6	1	2	2	6	0	0			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr7:44105125C>A	ENST00000297283.3	-	1	61	c.4G>T	c.(4-6)Gcc>Tcc	p.A2S	AC017116.11_ENST00000445938.1_RNA	NM_000290.3	NP_000281.2	P15259	PGAM2_HUMAN	phosphoglycerate mutase 2 (muscle)	2					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						CGGTGAGTGGCCATGGTGGCA	0.607																																					p.A2S		Atlas-SNP	.											.	PGAM2	20	.	0			c.G4T						PASS	.						62	54	57					7																	44105125		2203	4300	6503	SO:0001583	missense	5224	exon1			GAGTGGCCATGGT		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.4G>T	chr7.hg19:g.44105125C>A	ENSP00000297283:p.Ala2Ser	136.0	0.0	.		107.0	38.0	.	NM_000290		Missense_Mutation	SNP	ENST00000297283.3	hg19	CCDS34624.1	.	.	.	.	.	.	.	.	.	.	C	12.85	2.060303	0.36373	.	.	ENSG00000164708	ENST00000297283	T	0.80909	-1.43	5.93	-3.63	0.04529	.	0.487586	0.24258	N	0.040105	T	0.55162	0.1903	N	0.05554	-0.025	0.29035	N	0.885422	B	0.06786	0.001	B	0.10450	0.005	T	0.40979	-0.9534	10	0.45353	T	0.12	-11.1352	6.6092	0.22741	0.115:0.5762:0.2239:0.0848	.	2	P15259	PGAM2_HUMAN	S	2	ENSP00000297283:A2S	ENSP00000297283:A2S	A	-	1	0	PGAM2	44071650	0.648000	0.27313	0.979000	0.43373	0.986000	0.74619	-0.141000	0.10327	-0.536000	0.06298	0.650000	0.86243	GCC	.	.	.	none		0.607	PGAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339614.1			A	44105125	C	A	44105125	3	1	175	1	0	0	0	0	1	0	0	0	11781	739	26	4	769	4	PGAM2	7	44105125	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08		44105125	115033538	30	10242											
TMED4	222068	hgsc.bcm.edu	37	chr7	44621125	44621125	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggtcaccgggcgtgtgggAggtgaacgtgaagcggccct	7	7	18	9	4	1	2	1	2	0	0	1	3	1	3	2	5	2	0	2	5	2	0			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr7:44621125A>G	ENST00000457408.2	-	3	362	c.310T>C	c.(310-312)Tcc>Ccc	p.S104P	TMED4_ENST00000289577.5_Missense_Mutation_p.S104P|TMED4_ENST00000481238.1_Missense_Mutation_p.S104P|TMED4_ENST00000444131.2_5'UTR	NM_182547.2	NP_872353.2	Q7Z7H5	TMED4_HUMAN	transmembrane emp24 protein transport domain containing 4	104	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein transport (GO:0015031)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	signal transducer activity (GO:0004871)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)	6						GGCGTGTGGGAGGTGAACGTG	0.557																																					p.S104P		Atlas-SNP	.											.	TMED4	13	.	0			c.T310C						PASS	.						89	89	89					7																	44621125		2203	4300	6503	SO:0001583	missense	222068	exon3			TGTGGGAGGTGAA	BC035467	CCDS5493.1	7p13	2004-12-21			ENSG00000158604	ENSG00000158604			22301	protein-coding gene	gene with protein product		612038				12761501	Standard	NM_182547		Approved	HNLF	uc003tli.3	Q7Z7H5	OTTHUMG00000129210	ENST00000457408.2:c.310T>C	chr7.hg19:g.44621125A>G	ENSP00000404042:p.Ser104Pro	85.0	0.0	.		76.0	41.0	.	NM_182547	A4D2K8|B4DFJ4|Q56VW3|Q7Z432|Q8N2P6	Missense_Mutation	SNP	ENST00000457408.2	hg19	CCDS5493.1	.	.	.	.	.	.	.	.	.	.	A	34	5.340815	0.95783	.	.	ENSG00000158604	ENST00000457408;ENST00000289577;ENST00000419520;ENST00000481238	T;T;T	0.18502	2.21;2.21;2.21	5.22	5.22	0.72569	GOLD (2);	0.000000	0.85682	D	0.000000	T	0.51007	0.1649	M	0.93720	3.45	0.80722	D	1	D;D	0.76494	0.999;0.984	D;D	0.74348	0.983;0.962	T	0.63795	-0.6556	10	0.87932	D	0	-13.0927	13.1033	0.59233	1.0:0.0:0.0:0.0	.	104;104	Q7Z7H5-3;Q7Z7H5	.;TMED4_HUMAN	P	104;104;88;104	ENSP00000404042:S104P;ENSP00000289577:S104P;ENSP00000417443:S104P	ENSP00000289577:S104P	S	-	1	0	TMED4	44587650	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.944000	0.92980	2.191000	0.70037	0.533000	0.62120	TCC	.	.	.	none		0.557	TMED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251290.1	NM_182547		G	44621125	A	G	44621125	3	3	175	1	0	0	0	0	1	0	0	0	16018	304	11	3	385	3	TMED4	7	44621125	Missense_Mutation	SNP	A	TCGA-G7-6797-01A-11D-1961-08	516000	44621125	114517538	31	10243											
ADAM28	10863	hgsc.bcm.edu	37	chr8	24209520	24209520	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgagtcagatgaagccccaTgtgtatgatctgccagtaga	12	10	11	8	0	2	5	1	3	1	2	2	5	2	5	3	0	2	2	3	0	3	2			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr8:24209520T>C	ENST00000265769.4	+	21	2309	c.2199T>C	c.(2197-2199)caT>caC	p.H733H	RP11-624C23.1_ENST00000518988.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523700.1_RNA|ADAM28_ENST00000397649.3_Missense_Mutation_p.C482R	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	733					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)		TGAAGCCCCATGTGTATGATC	0.378																																					p.H733H	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											.	ADAM28	100	.	0			c.T2199C						PASS	.						117	114	115					8																	24209520		2203	4300	6503	SO:0001819	synonymous_variant	10863	exon21			GCCCCATGTGTAT	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.2199T>C	chr8.hg19:g.24209520T>C		116.0	0.0	.		135.0	56.0	.	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Silent	SNP	ENST00000265769.4	hg19	CCDS34865.1	.	.	.	.	.	.	.	.	.	.	T	7.970	0.748895	0.15710	.	.	ENSG00000042980	ENST00000397649;ENST00000521629	T	0.01745	4.66	4.14	-4.67	0.03319	.	.	.	.	.	T	0.01800	0.0057	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.42189	-0.9466	6	0.87932	D	0	.	2.3577	0.04300	0.1532:0.4266:0.1567:0.2635	.	.	.	.	R	482;366	ENSP00000380770:C482R	ENSP00000380770:C482R	C	+	1	0	ADAM28	24265465	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.317000	0.01122	-0.875000	0.04022	-0.347000	0.07816	TGT	.	.	.	none		0.378	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778		C	24209520	T	C	24209520	2	2	175	1	0	0	0	0	0	0	0	1	246	1461	51	3		3	ADAM28	8	24209520	Silent	SNP	T	TCGA-G7-6797-01A-11D-1961-08		24209520	122154502	32	10244											
C8orf41	80185	hgsc.bcm.edu	37	chr8	33369626	33369626	+	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	gcacctccctagcaacttccCgagatctcggagtggtccat	8	9	9	15	2	1	1	0	0	1	1	5	3	4	2	4	2	2	2	4	2	2	2			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr8:33369626C>A	ENST00000431156.2	-	2	1124	c.506G>T	c.(505-507)cGg>cTg	p.R169L	SNORD13_ENST00000459299.1_RNA|TTI2_ENST00000519356.1_5'Flank|TTI2_ENST00000360742.5_Missense_Mutation_p.R169L|TTI2_ENST00000520636.1_Missense_Mutation_p.R169L	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	169																	AGCAACTTCCCGAGATCTCGG	0.522																																					p.R169L		Atlas-SNP	.											.	.	.	.	0			c.G506T						PASS	.						149	145	147					8																	33369626		2203	4300	6503	SO:0001583	missense	80185	exon2			ACTTCCCGAGATC	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.506G>T	chr8.hg19:g.33369626C>A	ENSP00000411169:p.Arg169Leu	260.0	0.0	.		173.0	12.0	.	NM_001265581	D3DSV7|Q96IM2|Q9H5N4	Missense_Mutation	SNP	ENST00000431156.2	hg19	CCDS6090.1	.	.	.	.	.	.	.	.	.	.	C	3.157	-0.172868	0.06421	.	.	ENSG00000129696	ENST00000360742;ENST00000431156;ENST00000522668;ENST00000520636;ENST00000520397	T;T;T	0.76839	-0.71;-0.71;-1.05	4.66	-6.22	0.02058	.	0.588907	0.13846	N	0.358711	T	0.65668	0.2713	L	0.31926	0.97	0.09310	N	1	B;B;B	0.16396	0.014;0.017;0.014	B;B;B	0.18561	0.019;0.022;0.013	T	0.42103	-0.9471	10	0.54805	T	0.06	-4.8077	16.956	0.86259	0.0:0.749:0.0:0.251	.	169;169;169	E5RH83;Q6NXR4;E5RIH5	.;TTI2_HUMAN;.	L	169	ENSP00000353971:R169L;ENSP00000411169:R169L;ENSP00000428401:R169L	ENSP00000353971:R169L	R	-	2	0	C8orf41	33489168	0.000000	0.05858	0.000000	0.03702	0.411000	0.31082	-1.676000	0.01946	-1.280000	0.02402	-0.136000	0.14681	CGG	.	.	.	none		0.522	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115		A	33369626	C	A	33369626	3	1	175	1	0	0	0	0	1	0	0	0	2429	652	23	4	1048	4	C8orf41	8	33369626	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	9160106	33369626	112994396	33	10245											
XKR4	114786	hgsc.bcm.edu	37	chr8	56435874	56435874	+	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	gcttccctcgtgtccctggcCtgggccttggcctcctacca	2	11	10	18	1	0	0	0	0	0	0	4	0	3	0	7	3	1	1	7	3	1	3	rs4263738		TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr8:56435874C>G	ENST00000327381.6	+	3	1141	c.1041C>G	c.(1039-1041)gcC>gcG	p.A347A	RP11-628E19.2_ENST00000522918.1_RNA	NM_052898.1	NP_443130.1	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related family, member 4	347						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)			TGTCCCTGGCCTGGGCCTTGG	0.562																																					p.A347A		Atlas-SNP	.											.	XKR4	104	.	0			c.C1041G						PASS	.						62	57	59					8																	56435874		2203	4300	6503	SO:0001819	synonymous_variant	114786	exon3			CCTGGCCTGGGCC	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.1041C>G	chr8.hg19:g.56435874C>G		78.0	0.0	.		39.0	19.0	.	NM_052898	Q96PZ8	Silent	SNP	ENST00000327381.6	hg19	CCDS34893.1																																																																																			.	.	.	alt		0.562	XKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378129.2	NM_052898		G	56435874	C	G	56435874	2	3	175	1	0	0	0	0	0	0	0	1	17445	668	24	4		4	XKR4	8	56435874	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08	23066248	56435874	89928148	34	10246											
HNF4G	3174	hgsc.bcm.edu	37	chr8	76465335	76465335	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgttaagaaaattgcaagtaTtggtgatgtctgtgaatcta	13	14	10	4	1	2	3	0	2	2	1	2	3	2	3	0	1	1	3	0	1	7	5			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr8:76465335T>C	ENST00000354370.1	+	6	677	c.407T>C	c.(406-408)aTt>aCt	p.I136T	HNF4G_ENST00000396423.2_Missense_Mutation_p.I173T			Q14541	HNF4G_HUMAN	hepatocyte nuclear factor 4, gamma	136					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)			ATTGCAAGTATTGGTGATGTC	0.358																																					p.I173T		Atlas-SNP	.											.	HNF4G	111	.	0			c.T518C						PASS	.						120	109	113					8																	76465335		2203	4300	6503	SO:0001583	missense	3174	exon5			CAAGTATTGGTGA		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.407T>C	chr8.hg19:g.76465335T>C	ENSP00000346339:p.Ile136Thr	83.0	0.0	.		120.0	58.0	.	NM_004133	Q7Z2V9|Q9UH81|Q9UIS6	Missense_Mutation	SNP	ENST00000354370.1	hg19		.	.	.	.	.	.	.	.	.	.	T	17.96	3.517111	0.64634	.	.	ENSG00000164749	ENST00000354370;ENST00000396423	D;D	0.94723	-3.5;-3.5	5.4	5.4	0.78164	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (1);	0.102401	0.64402	D	0.000003	D	0.93769	0.8008	M	0.71036	2.16	0.58432	D	0.999998	B;B	0.10296	0.001;0.003	B;B	0.21151	0.02;0.033	D	0.91547	0.5254	10	0.66056	D	0.02	.	15.5943	0.76566	0.0:0.0:0.0:1.0	.	173;136	F1D8Q4;Q14541	.;HNF4G_HUMAN	T	136;173	ENSP00000346339:I136T;ENSP00000379701:I173T	ENSP00000346339:I136T	I	+	2	0	HNF4G	76627890	1.000000	0.71417	0.985000	0.45067	0.994000	0.84299	7.450000	0.80656	2.263000	0.75096	0.533000	0.62120	ATT	.	.	.	none		0.358	HNF4G-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000313914.2	NM_004133		C	76465335	T	C	76465335	3	2	175	1	0	0	0	0	1	0	0	0	7261	1493	52	3	536	3	HNF4G	8	76465335	Missense_Mutation	SNP	T	TCGA-G7-6797-01A-11D-1961-08	20029461	76465335	69898687	35	10247											
PTK2	5747	hgsc.bcm.edu	37	chr8	141745382	141745382	+	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	ttaagttcagtaaacctgggCcgcctgctggggtcataggc	8	10	13	10	1	2	0	2	0	0	0	2	0	2	0	3	4	2	3	3	4	4	4			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr8:141745382C>T	ENST00000522684.1	-	22	2227	c.1998G>A	c.(1996-1998)cgG>cgA	p.R666R	PTK2_ENST00000535192.1_Silent_p.R666R|PTK2_ENST00000519465.1_Silent_p.R294R|PTK2_ENST00000538769.1_Silent_p.R334R|PTK2_ENST00000340930.3_Silent_p.R666R|PTK2_ENST00000521059.1_Silent_p.R666R|MIR151A_ENST00000521276.1_RNA|PTK2_ENST00000395218.2_Silent_p.R666R|PTK2_ENST00000517887.1_Silent_p.R710R|PTK2_ENST00000519419.1_Silent_p.R710R	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	666	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell motility (GO:0048870)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|central nervous system neuron axonogenesis (GO:0021955)|embryo development (GO:0009790)|endothelial cell migration (GO:0043542)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|establishment of nucleus localization (GO:0040023)|extracellular matrix organization (GO:0030198)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|growth hormone receptor signaling pathway (GO:0060396)|heart morphogenesis (GO:0003007)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of organ growth (GO:0046621)|negative regulation of synapse assembly (GO:0051964)|netrin-activated signaling pathway (GO:0038007)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|placenta development (GO:0001890)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|regulation of endothelial cell migration (GO:0010594)|regulation of focal adhesion assembly (GO:0051893)|regulation of osteoblast differentiation (GO:0045667)|regulation of Rho GTPase activity (GO:0032319)|signal complex assembly (GO:0007172)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	apical plasma membrane (GO:0016324)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|stress fiber (GO:0001725)	actin binding (GO:0003779)|ATP binding (GO:0005524)|JUN kinase binding (GO:0008432)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(6)|lung(23)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	48	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			TAAACCTGGGCCGCCTGCTGG	0.532																																					p.R688R		Atlas-SNP	.											.	PTK2	311	.	0			c.G2064A						PASS	.						61	52	55					8																	141745382		2203	4300	6503	SO:0001819	synonymous_variant	5747	exon22			CCTGGGCCGCCTG	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.1998G>A	chr8.hg19:g.141745382C>T		41.0	0.0	.		29.0	15.0	.	NM_005607	B4E2N6|F5H4S4|Q14291|Q9UD85	Silent	SNP	ENST00000522684.1	hg19	CCDS6381.1	.	.	.	.	.	.	.	.	.	.	C	9.232	1.036008	0.19590	.	.	ENSG00000169398	ENST00000519654	.	.	.	5.51	3.39	0.38822	.	.	.	.	.	T	0.62171	0.2406	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60591	-0.7233	4	.	.	.	.	11.6247	0.51138	0.0:0.7826:0.0:0.2174	.	.	.	.	T	677	.	.	A	-	1	0	PTK2	141814564	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.429000	0.34903	1.340000	0.45581	-0.136000	0.14681	GCC	.	.	.	none		0.532	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607		T	141745382	C	T	141745382	2	4	175	1	0	0	0	0	0	0	0	1	12773	726	26	2		2	PTK2	8	141745382	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08	65280047	141745382	4618640	36	10248											
TBC1D13	54662	hgsc.bcm.edu	37	chr9	131565636	131565636	+	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	gtggagcggatcctgttcatCtacgccaagctcaaccctgg	8	9	11	13	2	3	0	2	0	1	0	4	2	4	2	3	3	4	2	3	3	3	2			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr9:131565636C>G	ENST00000372648.5	+	8	801	c.651C>G	c.(649-651)atC>atG	p.I217M	TBC1D13_ENST00000466056.1_3'UTR|TBC1D13_ENST00000539497.1_Missense_Mutation_p.I36M|TBC1D13_ENST00000223865.8_Intron	NM_018201.3	NP_060671.3	Q9NVG8	TBC13_HUMAN	TBC1 domain family, member 13	217	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	6						TCCTGTTCATCTACGCCAAGC	0.552																																					p.I217M		Atlas-SNP	.											.	TBC1D13	27	.	0			c.C651G						PASS	.						151	121	131					9																	131565636		2203	4300	6503	SO:0001583	missense	54662	exon8			GTTCATCTACGCC	AK001605	CCDS6911.1, CCDS69677.1	9q34.13	2013-07-09			ENSG00000107021	ENSG00000107021			25571	protein-coding gene	gene with protein product						22762500	Standard	XM_005252060		Approved	FLJ10743	uc010myj.3	Q9NVG8	OTTHUMG00000020760	ENST00000372648.5:c.651C>G	chr9.hg19:g.131565636C>G	ENSP00000361731:p.Ile217Met	109.0	0.0	.		65.0	34.0	.	NM_018201	A7E2E7|B3KW04|B9EGJ8|Q5T270|Q5T271	Missense_Mutation	SNP	ENST00000372648.5	hg19	CCDS6911.1	.	.	.	.	.	.	.	.	.	.	C	19.71	3.879150	0.72294	.	.	ENSG00000107021	ENST00000372648;ENST00000539497	T;T	0.12569	2.67;2.67	5.48	4.56	0.56223	Rab-GAP/TBC domain (4);	0.111120	0.64402	N	0.000011	T	0.29976	0.0750	M	0.78223	2.4	0.80722	D	1	D	0.55605	0.972	P	0.58721	0.844	T	0.02588	-1.1137	10	0.41790	T	0.15	-25.7081	8.7782	0.34776	0.0:0.769:0.1524:0.0786	.	217	Q9NVG8	TBC13_HUMAN	M	217;36	ENSP00000361731:I217M;ENSP00000437751:I36M	ENSP00000361731:I217M	I	+	3	3	TBC1D13	130605457	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	4.786000	0.62425	1.253000	0.44018	0.655000	0.94253	ATC	.	.	.	none		0.552	TBC1D13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054496.1	NM_018201		G	131565636	C	G	131565636	3	3	175	1	0	0	0	0	1	0	0	0	15614	903	32	4	681	4	TBC1D13	9	131565636	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08		131565636	9647795	37	10249											
MCM10	55388	hgsc.bcm.edu	37	chr10	13222572	13222572	+	Missense_Mutation	SNP	A	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	attgggtgacatttggggttAtattgaagaaggttacgcca	11	13	13	4	1	0	3	0	2	0	1	0	3	0	3	1	4	1	2	1	4	5	6			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr10:13222572A>C	ENST00000484800.2	+	7	1001	c.898A>C	c.(898-900)Ata>Cta	p.I300L	MCM10_ENST00000378694.1_Missense_Mutation_p.I299L|MCM10_ENST00000378714.3_Missense_Mutation_p.I299L			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	300	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						ATTTGGGGTTATATTGAAGAA	0.423																																					p.I300L		Atlas-SNP	.											.	MCM10	76	.	0			c.A898C						PASS	.						232	230	231					10																	13222572		2203	4300	6503	SO:0001583	missense	55388	exon7			GGGGTTATATTGA	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.898A>C	chr10.hg19:g.13222572A>C	ENSP00000418268:p.Ile300Leu	182.0	0.0	.		192.0	88.0	.	NM_182751	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Missense_Mutation	SNP	ENST00000484800.2	hg19	CCDS7096.1	.	.	.	.	.	.	.	.	.	.	A	10.70	1.422993	0.25639	.	.	ENSG00000065328	ENST00000378714;ENST00000361282;ENST00000484800;ENST00000378694	T;T;T	0.16073	2.38;2.37;2.37	5.82	5.82	0.92795	.	0.103877	0.64402	D	0.000003	T	0.16257	0.0391	N	0.26042	0.785	0.53688	D	0.999971	B;B;B	0.22683	0.037;0.073;0.008	B;B;B	0.30029	0.061;0.11;0.041	T	0.05683	-1.0870	10	0.36615	T	0.2	-11.6005	16.1814	0.81903	1.0:0.0:0.0:0.0	.	299;299;300	Q5T670;Q7L590-2;Q7L590	.;.;MCM10_HUMAN	L	299;300;300;299	ENSP00000367986:I299L;ENSP00000418268:I300L;ENSP00000367966:I299L	ENSP00000354945:I300L	I	+	1	0	MCM10	13262578	1.000000	0.71417	0.940000	0.37924	0.594000	0.36715	4.284000	0.58983	2.234000	0.73211	0.533000	0.62120	ATA	.	.	.	none		0.423	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751		C	13222572	A	C	13222572	3	2	175	1	0	0	0	0	1	0	0	0	9392	449	16	5	920	5	MCM10	10	13222572	Missense_Mutation	SNP	A	TCGA-G7-6797-01A-11D-1961-08		13222572	122312175	38	10250											
C10orf68	79741	hgsc.bcm.edu	37	chr10	33134884	33134884	+	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	ctacacaactgaagagtcacCgaggtaagagaaagaatttt	17	8	9	7	1	1	4	1	1	0	3	1	6	1	4	1	1	2	1	1	1	6	4	rs201575874	byFrequency	TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr10:33134884C>A	ENST00000375030.2	+	17	1825	c.1207C>A	c.(1207-1209)Cga>Aga	p.R403R	C10orf68_ENST00000375028.3_Silent_p.R448R|C10orf68_ENST00000375025.4_Silent_p.R508R			Q9H943	CJ068_HUMAN		444								p.R444R(1)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(4)	29						GAAGAGTCACCGAGGTAAGAG	0.333																																					p.R444R		Atlas-SNP	.											.	C10orf68	75	.	1	Substitution - coding silent(1)	lung(1)	c.C1330A						PASS	.						70	82	78					10																	33134884		2202	4295	6497	SO:0001819	synonymous_variant	79741	exon16			AGTCACCGAGGTA																												ENST00000375030.2:c.1207C>A	chr10.hg19:g.33134884C>A		219.0	0.0	.		297.0	14.0	.	NM_024688	B0QZ71|Q08AN7|Q8N7T7	Silent	SNP	ENST00000375030.2	hg19																																																																																				.	C|1.000;T|0.000	.	alt		0.333	C10orf68-001	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000313999.2			A	33134884	C	A	33134884	2	1	175	1	0	0	0	0	0	0	0	1	1615	644	23	4		4	C10orf68	10	33134884	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08	19912312	33134884	102399863	39	10251											
BMS1	9790	hgsc.bcm.edu	37	chr10	43315762	43315762	+	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	ttcgacctgggatgtacgtcCgcattgagattgaaaatgtt	10	13	11	7	3	0	2	0	2	0	1	2	5	1	3	2	1	1	3	2	1	3	5	rs397839854		TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr10:43315762C>A	ENST00000374518.5	+	16	2722	c.2659C>A	c.(2659-2661)Cgc>Agc	p.R887S		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	887					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						GATGTACGTCCGCATTGAGAT	0.458																																					p.R887S		Atlas-SNP	.											BMS1,colon,carcinoma,-1,1	BMS1	132	.	0			c.C2659A						PASS	.						135	131	132					10																	43315762		2203	4300	6503	SO:0001583	missense	9790	exon16			TACGTCCGCATTG	BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"BMS1-like, ribosome assembly protein (yeast)", "BMS1 homolog, ribosome assembly protein (yeast)"	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.2659C>A	chr10.hg19:g.43315762C>A	ENSP00000363642:p.Arg887Ser	158.0	0.0	.		130.0	7.0	.	NM_014753	Q5QPT5|Q86XJ9	Missense_Mutation	SNP	ENST00000374518.5	hg19	CCDS7199.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.075513	0.76415	.	.	ENSG00000165733	ENST00000374518	T	0.19669	2.13	5.05	5.05	0.67936	Ribosome biogenesis protein BMS1/TSR1, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.58047	0.2095	M	0.92459	3.31	0.58432	D	0.999998	D	0.76494	0.999	D	0.87578	0.998	T	0.69363	-0.5165	10	0.59425	D	0.04	.	18.4608	0.90737	0.0:1.0:0.0:0.0	.	887	Q14692	BMS1_HUMAN	S	887	ENSP00000363642:R887S	ENSP00000363642:R887S	R	+	1	0	BMS1	42635768	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.662000	0.61525	2.352000	0.79861	0.454000	0.30748	CGC	.	.	.	none		0.458	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753		A	43315762	C	A	43315762	3	1	175	1	0	0	0	0	1	0	0	0	1472	652	23	4	2717	4	BMS1	10	43315762	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	10180878	43315762	92218985	40	10252											
PCBD1	5092	hgsc.bcm.edu	37	chr10	72643783	72643783	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaaaggccggcacactcaTgggtgctcagcgtgatgtgg	8	8	15	10	2	2	2	2	2	0	0	2	2	2	2	1	4	2	2	1	4	1	0			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr10:72643783T>C	ENST00000299299.3	-	4	489	c.239A>G	c.(238-240)cAt>cGt	p.H80R	PCBD1_ENST00000493228.1_5'UTR	NM_000281.2	NP_000272.1	P61457	PHS_HUMAN	pterin-4 alpha-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha	80	Substrate binding. {ECO:0000250}.				cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein homotetramerization (GO:0051289)|regulation of protein homodimerization activity (GO:0043496)|small molecule metabolic process (GO:0044281)|tetrahydrobiopterin biosynthetic process (GO:0006729)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	4-alpha-hydroxytetrahydrobiopterin dehydratase activity (GO:0008124)|identical protein binding (GO:0042802)|phenylalanine 4-monooxygenase activity (GO:0004505)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(2)|large_intestine(1)	4						GGCACACTCATGGGTGCTCAG	0.512																																					p.H80R		Atlas-SNP	.											.	PCBD1	8	.	0			c.A239G						PASS	.						94	76	82					10																	72643783		2203	4300	6503	SO:0001583	missense	5092	exon4			CACTCATGGGTGC	BC006324	CCDS31217.1	10q22	2014-04-01	2007-11-06	2005-02-11	ENSG00000166228	ENSG00000166228	4.2.1.96		8646	protein-coding gene	gene with protein product	"Pterin-4a-carbinolamine dehydratase (dimerization cofactor of hepatic nuclear factor 1-alpha)", "pterin-4-alpha carbinolamine dehydratase", "dimerizing cofactor for HNF1"	126090	"6-pyruvoyl-tetrahydropterin synthase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1)", "pterin-4 alpha-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1)"	DCOH, PCBD		8486378	Standard	XM_005269877		Approved	PCD	uc001jrn.1	P61457	OTTHUMG00000018417	ENST00000299299.3:c.239A>G	chr10.hg19:g.72643783T>C	ENSP00000299299:p.His80Arg	62.0	0.0	.		61.0	20.0	.	NM_000281	P70519|P80095|Q9D930	Missense_Mutation	SNP	ENST00000299299.3	hg19	CCDS31217.1	.	.	.	.	.	.	.	.	.	.	T	17.38	3.375645	0.61735	.	.	ENSG00000166228	ENST00000299299	D	0.92752	-3.1	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.97801	0.9278	H	0.98333	4.205	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99478	1.0947	10	0.87932	D	0	.	15.9584	0.79906	0.0:0.0:0.0:1.0	.	80	P61457	PHS_HUMAN	R	80	ENSP00000299299:H80R	ENSP00000299299:H80R	H	-	2	0	PCBD1	72313789	1.000000	0.71417	0.978000	0.43139	0.159000	0.22180	7.474000	0.81024	2.165000	0.68154	0.528000	0.53228	CAT	.	.	.	none		0.512	PCBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048527.1	NM_000281		C	72643783	T	C	72643783	3	2	175	1	0	0	0	0	1	0	0	0	11505	1464	51	3	79	3	PCBD1	10	72643783	Missense_Mutation	SNP	T	TCGA-G7-6797-01A-11D-1961-08	29328021	72643783	62890964	41	10253											
TSG101	7251	hgsc.bcm.edu	37	chr11	18505434	18505434	+	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	tactacttcttgatctaaacGggtaaccatctcttccagtt	10	15	5	11	1	3	1	0	1	3	0	5	1	4	1	2	1	4	2	2	1	5	8			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr11:18505434G>T	ENST00000251968.3	-	8	1241	c.826C>A	c.(826-828)Cgt>Agt	p.R276S	TSG101_ENST00000536719.1_Missense_Mutation_p.R276S|TSG101_ENST00000357193.3_Missense_Mutation_p.R171S	NM_006292.3	NP_006283.1	Q99816	TS101_HUMAN	tumor susceptibility 101	276					cell cycle arrest (GO:0007050)|cell division (GO:0051301)|cellular protein modification process (GO:0006464)|endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|keratinocyte differentiation (GO:0030216)|membrane organization (GO:0061024)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell growth (GO:0001558)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|viral budding (GO:0046755)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|multivesicular body (GO:0005771)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transcription corepressor activity (GO:0003714)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)	p.R276S(2)|p.R276C(1)		kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	22						TGATCTAAACGGGTAACCATC	0.423																																					p.R276S	GBM(99;1348 1396 8611 26475 50572)	Atlas-SNP	.											TSG101,NS,carcinoma,0,1	TSG101	43	.	3	Substitution - Missense(3)	lung(2)|prostate(1)	c.C826A						PASS	.						188	186	187					11																	18505434		2199	4293	6492	SO:0001583	missense	7251	exon8			CTAAACGGGTAAC	U82130	CCDS7842.1	11p15	2013-08-22	2013-08-22		ENSG00000074319	ENSG00000074319			15971	protein-coding gene	gene with protein product		601387	"tumor susceptibility gene 10", "tumor susceptibility gene 101"	TSG10		9019400, 9241264	Standard	NM_006292		Approved	VPS23	uc001mor.3	Q99816	OTTHUMG00000167725	ENST00000251968.3:c.826C>A	chr11.hg19:g.18505434G>T	ENSP00000251968:p.Arg276Ser	321.0	1.0	.		291.0	12.0	.	NM_006292	Q9BUM5	Missense_Mutation	SNP	ENST00000251968.3	hg19	CCDS7842.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.730672	0.48939	.	.	ENSG00000074319	ENST00000536719;ENST00000251968;ENST00000357193	T;T;T	0.22539	1.95;1.95;1.95	5.46	5.46	0.80206	.	0.054589	0.64402	D	0.000001	T	0.28599	0.0708	M	0.79926	2.475	0.51233	D	0.999916	B	0.21071	0.051	B	0.14023	0.01	T	0.14504	-1.0470	10	0.14656	T	0.56	-5.396	17.4765	0.87660	0.0:0.0:1.0:0.0	.	276	Q99816	TS101_HUMAN	S	276;276;171	ENSP00000438471:R276S;ENSP00000251968:R276S;ENSP00000349721:R171S	ENSP00000251968:R276S	R	-	1	0	TSG101	18462010	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.714000	0.68422	2.561000	0.86390	0.462000	0.41574	CGT	.	.	.	none		0.423	TSG101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395906.1	NM_006292		T	18505434	G	T	18505434	3	4	175	1	0	0	0	0	1	0	0	0	16628	1116	39	4	358	4	TSG101	11	18505434	Missense_Mutation	SNP	G	TCGA-G7-6797-01A-11D-1961-08		18505434	116501082	42	10254											
OR4C13	283092	hgsc.bcm.edu	37	chr11	49974076	49974076	+	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	gtgttttctgtcatctacatCaacgccatgataggaaatgt	11	14	8	8	1	4	1	2	1	2	0	4	2	4	2	1	1	2	1	1	1	4	4			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr11:49974076C>A	ENST00000555099.1	+	1	134	c.102C>A	c.(100-102)atC>atA	p.I34I		NM_001001955.2	NP_001001955.2	Q8NGP0	OR4CD_HUMAN	olfactory receptor, family 4, subfamily C, member 13	34						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						TCATCTACATCAACGCCATGA	0.413																																					p.I34I		Atlas-SNP	.											.	OR4C13	96	.	0			c.C102A						PASS	.						206	190	195					11																	49974076		2201	4296	6497	SO:0001819	synonymous_variant	283092	exon1			CTACATCAACGCC	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.102C>A	chr11.hg19:g.49974076C>A		299.0	0.0	.		307.0	35.0	.	NM_001001955	A6NJJ3|B9EH30|Q6IF48|Q96R68	Silent	SNP	ENST00000555099.1	hg19	CCDS31495.1																																																																																			.	.	.	none		0.413	OR4C13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391103.1	NM_001001955		A	49974076	C	A	49974076	2	1	175	1	0	0	0	0	0	0	0	1	11054	816	29	4		4	OR4C13	11	49974076	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08	31468642	49974076	85032440	43	10255											
FAT3	120114	hgsc.bcm.edu	37	chr11	92086947	92086947	+	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	ctgactggggttcaccatacCgccatgaaagtgaggtcaat	11	9	11	10	1	2	3	2	3	0	0	2	3	2	3	3	3	1	1	3	3	3	2			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr11:92086947C>A	ENST00000298047.6	+	1	1686	c.1669C>A	c.(1669-1671)Cgc>Agc	p.R557S	FAT3_ENST00000541502.1_Missense_Mutation_p.R557S|FAT3_ENST00000525166.1_Missense_Mutation_p.R407S|FAT3_ENST00000409404.2_Missense_Mutation_p.R557S			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	557	Cadherin 5. {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)				TTCACCATACCGCCATGAAAG	0.418										TCGA Ovarian(4;0.039)																											p.R557S		Atlas-SNP	.											FAT3_ENST00000409404,right_upper_lobe,carcinoma,0,2	FAT3	1822	.	0			c.C1669A						PASS	.						80	81	80					11																	92086947		1845	4102	5947	SO:0001583	missense	120114	exon1			CCATACCGCCATG	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.1669C>A	chr11.hg19:g.92086947C>A	ENSP00000298047:p.Arg557Ser	153.0	0.0	.		149.0	7.0	.	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	C	14.21	2.466335	0.43839	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000541502;ENST00000525166	T;T;T;T	0.50001	0.76;0.76;0.76;0.76	5.82	5.82	0.92795	.	.	.	.	.	T	0.58119	0.2100	L	0.27053	0.805	0.48975	D	0.999731	D	0.89917	1.0	D	0.91635	0.999	T	0.53767	-0.8392	9	0.34782	T	0.22	.	19.0792	0.93175	0.0:1.0:0.0:0.0	.	557	Q8TDW7-3	.	S	557;557;557;407	ENSP00000298047:R557S;ENSP00000387040:R557S;ENSP00000443786:R557S;ENSP00000432586:R407S	ENSP00000298047:R557S	R	+	1	0	FAT3	91726595	1.000000	0.71417	0.997000	0.53966	0.585000	0.36419	6.184000	0.72008	2.755000	0.94549	0.591000	0.81541	CGC	.	.	.	none		0.418	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		A	92086947	C	A	92086947	3	1	175	1	0	0	0	0	1	0	0	0	5698	652	23	4	1671	4	FAT3	11	92086947	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	42112871	92086947	42919569	44	10256											
HEBP1	50865	hgsc.bcm.edu	37	chr12	13140120	13140120	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgccttcccgttcctcaaTcttaacgcttttgtcactgg	6	15	7	13	2	3	0	2	0	1	0	5	1	5	0	3	1	2	2	3	1	2	5			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr12:13140120T>C	ENST00000014930.4	-	3	522	c.364A>G	c.(364-366)Att>Gtt	p.I122V	HEBP1_ENST00000536942.1_Missense_Mutation_p.I122V|RP11-392P7.6_ENST00000499948.2_RNA	NM_015987.4	NP_057071.2	Q9NRV9	HEBP1_HUMAN	heme binding protein 1	122					circadian rhythm (GO:0007623)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	heme binding (GO:0020037)			breast(1)|endometrium(1)|large_intestine(3)|lung(1)|urinary_tract(1)	7		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.153)		CGTTCCTCAATCTTAACGCTT	0.483																																					p.I122V		Atlas-SNP	.											.	HEBP1	16	.	0			c.A364G						PASS	.						179	158	165					12																	13140120		2203	4300	6503	SO:0001583	missense	50865	exon3			CCTCAATCTTAAC	AF117615	CCDS31749.1	12p13.2	2014-01-30			ENSG00000013583	ENSG00000013583		"Endogenous ligands"	17176	protein-coding gene	gene with protein product		605826				10640688	Standard	NM_015987		Approved	HEBP, HBP	uc001rbd.3	Q9NRV9	OTTHUMG00000168771	ENST00000014930.4:c.364A>G	chr12.hg19:g.13140120T>C	ENSP00000014930:p.Ile122Val	211.0	0.0	.		187.0	75.0	.	NM_015987	A8K1G2|Q9Y5Z5	Missense_Mutation	SNP	ENST00000014930.4	hg19	CCDS31749.1	.	.	.	.	.	.	.	.	.	.	T	11.41	1.631678	0.29068	.	.	ENSG00000013583	ENST00000014930;ENST00000535636;ENST00000536942	T;T;T	0.25579	1.79;1.79;1.79	5.66	4.45	0.53987	Regulatory factor, effector, bacterial (1);	0.047188	0.85682	D	0.000000	T	0.33527	0.0866	M	0.77313	2.365	0.47737	D	0.9995	B	0.22746	0.074	B	0.32762	0.152	T	0.12192	-1.0557	10	0.27082	T	0.32	-5.125	12.5735	0.56352	0.1242:0.0:0.0:0.8758	.	122	Q9NRV9	HEBP1_HUMAN	V	122;51;122	ENSP00000014930:I122V;ENSP00000442020:I51V;ENSP00000441678:I122V	ENSP00000014930:I122V	I	-	1	0	HEBP1	13031387	1.000000	0.71417	0.882000	0.34594	0.210000	0.24377	3.727000	0.54984	2.283000	0.76528	0.533000	0.62120	ATT	.	.	.	none		0.483	HEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401001.1			C	13140120	T	C	13140120	3	2	175	1	0	0	0	0	1	0	0	0	7043	1435	50	3	213	3	HEBP1	12	13140120	Missense_Mutation	SNP	T	TCGA-G7-6797-01A-11D-1961-08		13140120	120711775	45	10257											
PPFIBP1	8496	hgsc.bcm.edu	37	chr12	27809595	27809595	+	Missense_Mutation	SNP	A	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	actagaagaaaaggaatctgAagtaaaaaggctacaagaaa	23	5	9	4	0	1	4	0	1	1	3	1	5	1	5	0	2	1	2	0	2	12	3	rs369414467		TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr12:27809595A>C	ENST00000318304.8	+	10	1119	c.836A>C	c.(835-837)gAa>gCa	p.E279A	PPFIBP1_ENST00000537927.1_Missense_Mutation_p.E126A|PPFIBP1_ENST00000228425.6_Missense_Mutation_p.E248A|PPFIBP1_ENST00000542629.1_Missense_Mutation_p.E248A	NM_001198916.1|NM_177444.2	NP_001185845.1|NP_803193	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)	279					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)					AAGGAATCTGAAGTAAAAAGG	0.313																																					p.E279A		Atlas-SNP	.											.	PPFIBP1	153	.	0			c.A836C						PASS	.						73	76	75					12																	27809595		2203	4299	6502	SO:0001583	missense	8496	exon10			AATCTGAAGTAAA	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.836A>C	chr12.hg19:g.27809595A>C	ENSP00000314724:p.Glu279Ala	113.0	0.0	.		176.0	79.0	.	NM_177444	O75336|Q86X70|Q9NY03|Q9ULJ0	Missense_Mutation	SNP	ENST00000318304.8	hg19	CCDS55812.1	.	.	.	.	.	.	.	.	.	.	A	14.99	2.699998	0.48307	.	.	ENSG00000110841	ENST00000543820;ENST00000545381;ENST00000540114;ENST00000537927;ENST00000318304;ENST00000542629;ENST00000228425	T;T;T;T;T;T	0.59083	0.29;0.62;0.71;1.19;1.2;1.61	5.05	5.05	0.67936	.	0.000000	0.35151	U	0.003420	T	0.56645	0.1999	L	0.38953	1.18	0.41614	D	0.988929	P;B;P;B	0.44776	0.828;0.044;0.843;0.073	P;B;B;B	0.49477	0.612;0.027;0.384;0.06	T	0.57940	-0.7724	10	0.42905	T	0.14	-26.9289	13.3332	0.60500	1.0:0.0:0.0:0.0	.	126;279;248;248	Q86W92-3;Q86W92;Q86W92-2;Q86W92-4	.;LIPB1_HUMAN;.;.	A	250;248;107;126;279;248;248	ENSP00000445822:E248A;ENSP00000444304:E107A;ENSP00000445425:E126A;ENSP00000314724:E279A;ENSP00000443442:E248A;ENSP00000228425:E248A	ENSP00000228425:E248A	E	+	2	0	PPFIBP1	27700862	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	6.463000	0.73530	2.022000	0.59522	0.533000	0.62120	GAA	.	.	.	alt		0.313	PPFIBP1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402877.1	NM_003622		C	27809595	A	C	27809595	3	2	175	1	0	0	0	0	1	0	0	0	12320	246	9	5	811	5	PPFIBP1	12	27809595	Missense_Mutation	SNP	A	TCGA-G7-6797-01A-11D-1961-08	14669475	27809595	106042300	46	10258											
GPD1	2819	hgsc.bcm.edu	37	chr12	50503242	50503242	+	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	gctgtgtacaaggtgtgctaCgagggccagccagtgggtga	8	8	17	8	1	0	1	0	1	0	0	0	2	0	1	2	3	4	3	2	3	3	2	rs116736822	byFrequency	TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr12:50503242C>G	ENST00000301149.3	+	8	1222	c.990C>G	c.(988-990)taC>taG	p.Y330*	COX14_ENST00000317943.2_5'Flank|GPD1_ENST00000548814.1_Nonsense_Mutation_p.Y307*|COX14_ENST00000550487.1_5'Flank|COX14_ENST00000550654.1_5'Flank|COX14_ENST00000548985.1_5'Flank|RP4-605O3.4_ENST00000552815.1_RNA	NM_001257199.1|NM_005276.3	NP_001244128.1|NP_005267.2	P21695	GPDA_HUMAN	glycerol-3-phosphate dehydrogenase 1 (soluble)	330					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						AGGTGTGCTACGAGGGCCAGC	0.577																																					p.Y330X	NSCLC(141;1402 1905 9497 13391 44868)	Atlas-SNP	.											.	GPD1	23	.	0			c.C990G						PASS	.						139	108	118					12																	50503242		2203	4300	6503	SO:0001587	stop_gained	2819	exon8			GTGCTACGAGGGC		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.990C>G	chr12.hg19:g.50503242C>G	ENSP00000301149:p.Tyr330*	135.0	0.0	.		87.0	26.0	.	NM_005276	F8W1L5|Q8N1B0	Nonsense_Mutation	SNP	ENST00000301149.3	hg19	CCDS8799.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.796601	0.90453	.	.	ENSG00000167588	ENST00000301149;ENST00000548814	.	.	.	4.99	-5.7	0.02421	.	0.125588	0.53938	D	0.000044	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.4578	14.9665	0.71198	0.0:0.6296:0.0:0.3704	.	.	.	.	X	330;307	.	ENSP00000301149:Y330X	Y	+	3	2	GPD1	48789509	0.008000	0.16893	0.884000	0.34674	0.899000	0.52679	-0.879000	0.04188	-1.358000	0.02177	-0.379000	0.06801	TAC	.	C|0.998;T|0.002	.	alt		0.577	GPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406018.1			G	50503242	C	G	50503242	4	3	175	1	0	0	0	0	0	1	0	0	6611	547	19	4	1020	4	GPD1	12	50503242	Nonsense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	22693647	50503242	83348653	47	10259											
KRT76	51350	hgsc.bcm.edu	37	chr12	53170736	53170736	+	Frame_Shift_Del	DEL	T	T	-																															accagcccctccaaaaccacTacctactcctctgccaccac																										TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr12:53170736delT	ENST00000332411.2	-	1	393	c.340delA	c.(340-342)agtfs	p.S114fs		NM_015848.4	NP_056932.2	Q01546	K22O_HUMAN	keratin 76	114	Head.				cytoskeleton organization (GO:0007010)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						ccaaaaccactacctactcct	0.607																																					p.S114fs		Atlas-INDEL	.											.	KRT76	72	.	0			c.341delG						PASS	.						268	276	273					12																	53170736		2203	4299	6502	SO:0001589	frameshift_variant	51350	exon1			.	M99063	CCDS8838.1	12q13.13	2013-06-25			ENSG00000185069	ENSG00000185069		"-", "Intermediate filaments type II, keratins (basic)"	24430	protein-coding gene	gene with protein product						1282112, 16831889	Standard	NM_015848		Approved	HUMCYT2A, KRT2B, KRT2P	uc001sax.3	Q01546	OTTHUMG00000169797	ENST00000332411.2:c.340delA	chr12.hg19:g.53170736delT	ENSP00000330101:p.Ser114fs	72.0	0.0	0		54.0	24.0	0.444444	NM_015848	B4DRR3|Q7Z795	Frame_Shift_Del	DEL	ENST00000332411.2	hg19	CCDS8838.1																																																																																			.	.	.	none		0.607	KRT76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405928.1	NM_015848		-	53170736	T	-	53170736	7	5	175	1	0	1	0	1	0	0	0	0	8496	1522	53	0	1612	0	KRT76	12	53170736	Frame_Shift_Del	DEL	T	TCGA-G7-6797-01A-11D-1961-08	2667494	53170736	80681159	48	10260											
LRIG3	121227	hgsc.bcm.edu	37	chr12	59271290	59271290	+	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	aaccacggctatgatcacgaCacccacagtggcccatccgt	11	6	8	16	3	1	1	1	1	0	0	2	2	2	1	4	2	1	1	4	2	2	1			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr12:59271290C>A	ENST00000320743.3	-	15	2714	c.2428G>T	c.(2428-2430)Gtc>Ttc	p.V810F	LRIG3_ENST00000379141.4_Missense_Mutation_p.V750F	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	810					otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)			LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			ATGATCACGACACCCACAGTG	0.562			T	ROS1	NSCLC																																p.V810F		Atlas-SNP	.		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	.	LRIG3	120	.	0			c.G2428T						PASS	.						212	121	152					12																	59271290		2203	4300	6503	SO:0001583	missense	121227	exon15			TCACGACACCCAC	AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"Immunoglobulin superfamily / I-set domain containing"	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.2428G>T	chr12.hg19:g.59271290C>A	ENSP00000326759:p.Val810Phe	98.0	0.0	.		61.0	39.0	.	NM_153377	Q6UXL7|Q8NC72	Missense_Mutation	SNP	ENST00000320743.3	hg19	CCDS8960.1	.	.	.	.	.	.	.	.	.	.	C	14.91	2.675366	0.47781	.	.	ENSG00000139263	ENST00000379141;ENST00000320743	T;T	0.61040	0.18;0.14	5.59	3.74	0.42951	.	0.494270	0.15041	N	0.283853	T	0.47414	0.1444	L	0.47716	1.5	0.39938	D	0.974378	P;P	0.39665	0.682;0.624	B;B	0.37508	0.252;0.154	T	0.36212	-0.9757	9	.	.	.	.	8.2502	0.31712	0.0:0.6658:0.0:0.3342	.	750;810	Q6UXM1-2;Q6UXM1	.;LRIG3_HUMAN	F	750;810	ENSP00000368436:V750F;ENSP00000326759:V810F	.	V	-	1	0	LRIG3	57557557	1.000000	0.71417	0.987000	0.45799	0.819000	0.46315	2.549000	0.45803	0.796000	0.33947	0.655000	0.94253	GTC	.	.	.	none		0.562	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377		A	59271290	C	A	59271290	3	1	175	1	0	0	0	0	1	0	0	0	8953	478	17	4	951	4	LRIG3	12	59271290	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	6100554	59271290	74580605	49	10261											
PLXNC1	10154	hgsc.bcm.edu	37	chr12	94613897	94613897	+	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	agaataaaagtcagcccaacCggacctgcacctgtagcatc	14	6	8	13	1	1	1	1	0	0	1	2	2	1	2	4	1	4	3	4	1	5	2	rs146510015		TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr12:94613897C>A	ENST00000258526.4	+	6	1909	c.1660C>A	c.(1660-1662)Cgg>Agg	p.R554R		NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	554					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.R554R(2)		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						TCAGCCCAACCGGACCTGCAC	0.458																																					p.R554R		Atlas-SNP	.											PLXNC1,NS,carcinoma,0,1	PLXNC1	135	.	2	Substitution - coding silent(2)	lung(2)	c.C1660A						PASS	.						147	156	153					12																	94613897		2203	4300	6503	SO:0001819	synonymous_variant	10154	exon6			CCCAACCGGACCT	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.1660C>A	chr12.hg19:g.94613897C>A		338.0	0.0	.		197.0	15.0	.	NM_005761	Q59H25	Silent	SNP	ENST00000258526.4	hg19	CCDS9049.1																																																																																			.	C|1.000;T|0.000	.	alt		0.458	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2			A	94613897	C	A	94613897	2	1	175	1	0	0	0	0	0	0	0	1	12133	643	23	4		4	PLXNC1	12	94613897	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08	35342607	94613897	39237998	50	10262											
ANKRD13A	88455	hgsc.bcm.edu	37	chr12	110457067	110457067	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaagccaaaaagcagggaagTtgagcggcggctcacaagcc	14	3	14	10	2	1	1	1	1	0	0	1	3	1	2	2	3	4	3	2	3	5	1			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr12:110457067T>C	ENST00000261739.4	+	6	834	c.668T>C	c.(667-669)gTt>gCt	p.V223A	ANKRD13A_ENST00000550404.1_3'UTR	NM_033121.1	NP_149112.1	Q8IZ07	AN13A_HUMAN	ankyrin repeat domain 13A	223						endosome (GO:0005768)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(8)|lung(3)|urinary_tract(1)	16						AGCAGGGAAGTTGAGCGGCGG	0.438																																					p.V223A		Atlas-SNP	.											.	ANKRD13A	39	.	0			c.T668C						PASS	.						76	76	76					12																	110457067		2203	4300	6503	SO:0001583	missense	88455	exon6			GGGAAGTTGAGCG	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.668T>C	chr12.hg19:g.110457067T>C	ENSP00000261739:p.Val223Ala	114.0	0.0	.		92.0	39.0	.	NM_033121	O60736	Missense_Mutation	SNP	ENST00000261739.4	hg19	CCDS9140.1	.	.	.	.	.	.	.	.	.	.	T	18.08	3.543716	0.65198	.	.	ENSG00000076513	ENST00000261738;ENST00000261739	T	0.65364	-0.15	5.83	5.83	0.93111	.	0.052948	0.85682	D	0.000000	T	0.73567	0.3603	M	0.72894	2.215	0.80722	D	1	D;D;D	0.56746	0.977;0.977;0.977	P;P;P	0.55011	0.766;0.766;0.766	T	0.77107	-0.2710	10	0.72032	D	0.01	-13.8298	15.3732	0.74584	0.0:0.0:0.0:1.0	.	223;223;223	B4DYP5;Q3ZTS7;Q8IZ07	.;.;AN13A_HUMAN	A	8;223	ENSP00000261739:V223A	ENSP00000261738:V8A	V	+	2	0	ANKRD13A	108941450	1.000000	0.71417	0.945000	0.38365	0.982000	0.71751	6.241000	0.72369	2.229000	0.72834	0.482000	0.46254	GTT	.	.	.	none		0.438	ANKRD13A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403430.1	NM_033121		C	110457067	T	C	110457067	3	2	175	1	0	0	0	0	1	0	0	0	641	1725	60	3	690	3	ANKRD13A	12	110457067	Missense_Mutation	SNP	T	TCGA-G7-6797-01A-11D-1961-08	15843170	110457067	23394828	51	10263											
SBNO1	55206	hgsc.bcm.edu	37	chr12	123780521	123780521	+	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	catagctgtttctgttggacCgcaagctgttgagactggtc	7	13	12	9	1	1	1	0	1	1	1	2	3	1	2	1	2	2	6	1	2	2	4			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr12:123780521C>A	ENST00000602398.1	-	32	4243	c.4116G>T	c.(4114-4116)gcG>gcT	p.A1372A	SBNO1_ENST00000420886.2_Silent_p.A1372A|SBNO1_ENST00000602750.1_Silent_p.A1371A|SBNO1_ENST00000267176.4_Silent_p.A1371A			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	1372					regulation of transcription, DNA-templated (GO:0006355)			p.A1371A(1)		NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		TCTGTTGGACCGCAAGCTGTT	0.428																																					p.A1372A		Atlas-SNP	.											.	SBNO1	138	.	1	Substitution - coding silent(1)	lung(1)	c.G4116T						PASS	.						350	312	325					12																	123780521		2203	4300	6503	SO:0001819	synonymous_variant	55206	exon31			TTGGACCGCAAGC	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"sno, strawberry notch homolog 1 (Drosophila)"				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.4116G>T	chr12.hg19:g.123780521C>A		367.0	0.0	.		297.0	15.0	.	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Silent	SNP	ENST00000602398.1	hg19	CCDS53844.1																																																																																			.	.	.	none		0.428	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183		A	123780521	C	A	123780521	2	1	175	1	0	0	0	0	0	0	0	1	13875	639	23	4		4	SBNO1	12	123780521	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08	13323454	123780521	10071374	52	10264											
C14orf101	54916	hgsc.bcm.edu	37	chr14	57075923	57075923	+	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	catcttaccttaatcacgccCggtggacctggggagaccag	9	8	11	13	2	2	1	1	0	1	1	2	3	2	2	4	4	1	0	4	4	2	2	rs140983222		TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr14:57075923C>A	ENST00000261556.6	+	6	858	c.736C>A	c.(736-738)Cgg>Agg	p.R246R	TMEM260_ENST00000538838.1_Silent_p.R246R|TMEM260_ENST00000536419.1_5'UTR	NM_017799.3	NP_060269.3	Q9NX78	TM260_HUMAN	transmembrane protein 260	246						integral component of membrane (GO:0016021)											TAATCACGCCCGGTGGACCTG	0.483																																					p.R246R		Atlas-SNP	.											.	.	.	.	0			c.C736A						PASS	.						207	199	202					14																	57075923		2203	4300	6503	SO:0001819	synonymous_variant	0	exon6			CACGCCCGGTGGA	AK000399	CCDS9727.2	14q22.2	2013-03-08	2013-03-08	2013-03-08	ENSG00000070269	ENSG00000070269			20185	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 101"	C14orf101			Standard	XR_245695		Approved	FLJ20392	uc001xcm.3	Q9NX78	OTTHUMG00000152337	ENST00000261556.6:c.736C>A	chr14.hg19:g.57075923C>A		497.0	0.0	.		311.0	14.0	.	NM_017799	A8KAN4|B3KPF5|Q86XE1	Silent	SNP	ENST00000261556.6	hg19	CCDS9727.2																																																																																			.	C|1.000;T|0.000	.	alt		0.483	TMEM260-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276924.1	NM_017799		A	57075923	C	A	57075923	2	1	175	1	0	0	0	0	0	0	0	1	1736	643	23	4		4	C14orf101	14	57075923	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08		57075923	50273617	53	10265											
SIX4	51804	hgsc.bcm.edu	37	chr14	61190290	61190290	+	Missense_Mutation	SNP	A	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	cgaagctgtggctctcgaggAtgctgtagagctcggggtag	7	9	17	8	3	1	1	0	0	1	1	3	4	1	2	0	4	3	6	0	4	3	2			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr14:61190290A>C	ENST00000216513.4	-	1	562	c.503T>G	c.(502-504)aTc>aGc	p.I168S		NM_017420.4	NP_059116.3	Q9UIU6	SIX4_HUMAN	SIX homeobox 4	168					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)		GCTCTCGAGGATGCTGTAGAG	0.692																																					p.I168S		Atlas-SNP	.											.	SIX4	69	.	0			c.T503G						PASS	.						13	14	14					14																	61190290		2190	4286	6476	SO:0001583	missense	51804	exon1			TCGAGGATGCTGT	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.503T>G	chr14.hg19:g.61190290A>C	ENSP00000216513:p.Ile168Ser	26.0	0.0	.		20.0	9.0	.	NM_017420	Q4QQH5|Q4V764	Missense_Mutation	SNP	ENST00000216513.4	hg19	CCDS9749.2	.	.	.	.	.	.	.	.	.	.	A	19.26	3.793861	0.70452	.	.	ENSG00000100625	ENST00000216513;ENST00000556952	D	0.94046	-3.34	3.63	3.63	0.41609	.	0.265948	0.36591	N	0.002504	D	0.93086	0.7799	M	0.70842	2.15	0.58432	D	0.999997	P;D	0.53312	0.84;0.959	P;P	0.47346	0.537;0.544	D	0.93446	0.6798	10	0.87932	D	0	.	12.4167	0.55498	1.0:0.0:0.0:0.0	.	160;168	G3V2N2;Q9UIU6	.;SIX4_HUMAN	S	168;160	ENSP00000216513:I168S	ENSP00000216513:I168S	I	-	2	0	SIX4	60260043	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.828000	0.92047	1.508000	0.48769	0.528000	0.53228	ATC	.	.	.	none		0.692	SIX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072397.2			C	61190290	A	C	61190290	3	2	175	1	0	0	0	0	1	0	0	0	14362	333	12	5	1854	5	SIX4	14	61190290	Missense_Mutation	SNP	A	TCGA-G7-6797-01A-11D-1961-08	4114367	61190290	46159250	54	10266											
IREB2	3658	hgsc.bcm.edu	37	chr15	78765688	78765688	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgggtcatcaaacccttttGttacatccatagatgttgtt	9	16	7	9	0	2	1	2	0	0	1	3	1	3	1	2	1	2	3	2	1	3	6			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr15:78765688G>A	ENST00000258886.8	+	8	1137	c.988G>A	c.(988-990)Gtt>Att	p.V330I	IREB2_ENST00000560440.1_Missense_Mutation_p.V330I	NM_004136.2	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2	330					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)		AAACCCTTTTGTTACATCCAT	0.373																																					p.V330I	NSCLC(200;764 2208 35157 49871 50830)	Atlas-SNP	.											.	IREB2	106	.	0			c.G988A						PASS	.						223	207	212					15																	78765688		2196	4293	6489	SO:0001583	missense	3658	exon8			CCTTTTGTTACAT	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.988G>A	chr15.hg19:g.78765688G>A	ENSP00000258886:p.Val330Ile	115.0	0.0	.		106.0	48.0	.	NM_004136	A8KAC7|E1CJT9|H0YKU0|Q13095|Q1HE21|Q59FQ7|Q8WVK6|Q9UF17	Missense_Mutation	SNP	ENST00000258886.8	hg19	CCDS10302.1	.	.	.	.	.	.	.	.	.	.	G	14.95	2.689480	0.48097	.	.	ENSG00000136381	ENST00000258886	T	0.23754	1.89	5.93	5.93	0.95920	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha (2);Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 2 (1);	0.252836	0.46442	D	0.000283	T	0.24928	0.0605	L	0.43646	1.37	0.27813	N	0.942089	B;B	0.20164	0.003;0.042	B;B	0.23150	0.032;0.044	T	0.26744	-1.0094	10	0.07813	T	0.8	.	20.3334	0.98727	0.0:0.0:1.0:0.0	.	330;330	P48200;Q8WVK6	IREB2_HUMAN;.	I	330	ENSP00000258886:V330I	ENSP00000258886:V330I	V	+	1	0	IREB2	76552743	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.095000	0.64529	2.818000	0.97014	0.591000	0.81541	GTT	.	.	.	none		0.373	IREB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290109.3	NM_004136		A	78765688	G	A	78765688	3	1	175	1	0	0	0	0	1	0	0	0	7833	1377	48	2	1018	2	IREB2	15	78765688	Missense_Mutation	SNP	G	TCGA-G7-6797-01A-11D-1961-08		78765688	23765704	55	10267											
STX4	6810	hgsc.bcm.edu	37	chr16	31046334	31046334	+	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	gctgatgagaactataactcCgtcaacacaagaatgagaaa	18	7	8	8	1	1	4	1	3	0	3	2	6	2	4	1	0	3	1	1	0	7	2			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr16:31046334C>A	ENST00000313843.3	+	5	666	c.351C>A	c.(349-351)tcC>tcA	p.S117S	STX4_ENST00000493902.1_3'UTR|STX4_ENST00000394998.1_Silent_p.S115S	NM_004604.3	NP_004595.2	Q12846	STX4_HUMAN	syntaxin 4	117					blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|neurotransmitter transport (GO:0006836)|platelet activation (GO:0030168)|post-Golgi vesicle-mediated transport (GO:0006892)|SNARE complex assembly (GO:0035493)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|membrane (GO:0016020)|myelin sheath adaxonal region (GO:0035749)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|SNARE complex (GO:0031201)|specific granule (GO:0042581)|trans-Golgi network (GO:0005802)|vacuole (GO:0005773)				NS(2)|breast(1)|large_intestine(3)|lung(3)	9						ACTATAACTCCGTCAACACAA	0.423																																					p.S117S		Atlas-SNP	.											.	STX4	28	.	0			c.C351A						PASS	.						78	85	83					16																	31046334		2197	4300	6497	SO:0001819	synonymous_variant	6810	exon5			TAACTCCGTCAAC	AF026007	CCDS10700.1, CCDS61916.1	16p11.2	2008-02-05	2006-04-25	2006-04-25	ENSG00000103496	ENSG00000103496			11439	protein-coding gene	gene with protein product		186591	"syntaxin 4A (placental)"	STX4A		8206394, 16339081	Standard	NM_001272095		Approved	p35-2	uc002eak.4	Q12846	OTTHUMG00000132404	ENST00000313843.3:c.351C>A	chr16.hg19:g.31046334C>A		169.0	0.0	.		220.0	9.0	.	NM_004604	A8MXY0|Q15525|Q6FHE8	Silent	SNP	ENST00000313843.3	hg19	CCDS10700.1																																																																																			.	.	.	none		0.423	STX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255538.3	NM_004604		A	31046334	C	A	31046334	2	1	175	1	0	0	0	0	0	0	0	1	15359	639	23	4		4	STX4	16	31046334	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08		31046334	59308419	56	10268											
CES3	23491	hgsc.bcm.edu	37	chr16	67000741	67000741	+	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	ttcctcatgggtgtcaacaaCcatgagttcagctggctcat	9	12	9	11	0	4	1	4	1	0	0	5	1	5	1	2	2	3	3	2	2	2	2			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr16:67000741C>A	ENST00000303334.4	+	8	1106	c.1035C>A	c.(1033-1035)aaC>aaA	p.N345K	CES3_ENST00000394037.1_Missense_Mutation_p.N345K|CES3_ENST00000543856.1_5'Flank	NM_024922.5	NP_079198.2	Q6UWW8	EST3_HUMAN	carboxylesterase 3	345						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	carboxylic ester hydrolase activity (GO:0052689)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(3)|skin(1)	24		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0488)|Epithelial(162;0.127)		GTGTCAACAACCATGAGTTCA	0.582																																					p.N345K		Atlas-SNP	.											.	CES3	56	.	0			c.C1035A						PASS	.						134	131	132					16																	67000741		2200	4300	6500	SO:0001583	missense	23491	exon8			CAACAACCATGAG	AK025389	CCDS10826.1, CCDS54022.1, CCDS54023.1	16q22.1	2014-05-13	2008-07-25		ENSG00000172828	ENSG00000172828		"Carboxylesterases"	1865	protein-coding gene	gene with protein product	"esterase 31", "brain carboxylesterase BR3"	605279	"carboxylesterase 3 (brain)"			10518925, 14581373, 15100172, 20931200	Standard	NM_001185176		Approved	FLJ21736, ES31	uc002eqt.3	Q6UWW8	OTTHUMG00000137525	ENST00000303334.4:c.1035C>A	chr16.hg19:g.67000741C>A	ENSP00000304782:p.Asn345Lys	248.0	0.0	.		223.0	85.0	.	NM_024922	B2Z3W9|F5H242|Q7Z6J1|Q9H6X7	Missense_Mutation	SNP	ENST00000303334.4	hg19	CCDS10826.1	.	.	.	.	.	.	.	.	.	.	C	12.62	1.991536	0.35131	.	.	ENSG00000172828	ENST00000303334;ENST00000394037	T;T	0.65549	-0.16;-0.16	3.97	-2.89	0.05665	Carboxylesterase, type B (1);	0.000000	0.43579	D	0.000560	T	0.40862	0.1134	N	0.20610	0.595	0.80722	D	1	P	0.37207	0.587	B	0.41174	0.349	T	0.33650	-0.9860	10	0.08179	T	0.78	.	11.2659	0.49110	0.0:0.6915:0.0:0.3085	.	345	Q6UWW8	EST3_HUMAN	K	345	ENSP00000304782:N345K;ENSP00000377602:N345K	ENSP00000304782:N345K	N	+	3	2	CES3	65558242	0.304000	0.24472	0.647000	0.29507	0.123000	0.20343	-0.234000	0.09028	-0.385000	0.07833	-0.809000	0.03173	AAC	.	.	.	none		0.582	CES3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268848.1	NM_024922		A	67000741	C	A	67000741	3	1	175	1	0	0	0	0	1	0	0	0	3273	506	18	4	1065	4	CES3	16	67000741	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	35954407	67000741	23354012	57	10269											
FAM65A	79567	hgsc.bcm.edu	37	chr16	67576026	67576026	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgggcatgcaccctacagtcGgactctgagccacatcagtg	9	8	11	13	1	2	1	1	1	1	0	3	2	2	2	2	2	3	2	2	2	1	1			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr16:67576026G>A	ENST00000379312.3	+	13	1470	c.1349G>A	c.(1348-1350)cGg>cAg	p.R450Q	FAM65A_ENST00000422602.2_Missense_Mutation_p.R466Q|CTD-2012K14.4_ENST00000564717.1_RNA|FAM65A_ENST00000042381.4_Missense_Mutation_p.R446Q|FAM65A_ENST00000540839.3_Missense_Mutation_p.R466Q|CTD-2012K14.2_ENST00000567122.1_RNA|CTD-2012K14.3_ENST00000563083.1_RNA|FAM65A_ENST00000428437.2_Missense_Mutation_p.R460Q	NM_001193522.1|NM_024519.3	NP_001180451.1|NP_078795.2	Q6ZS17	FA65A_HUMAN	family with sequence similarity 65, member A	450						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0474)|Epithelial(162;0.117)		CCCTACAGTCGGACTCTGAGC	0.632																																					p.R466Q		Atlas-SNP	.											.	FAM65A	104	.	0			c.G1397A						PASS	.						75	71	72					16																	67576026		2198	4300	6498	SO:0001583	missense	79567	exon13			ACAGTCGGACTCT	AK127792	CCDS10840.1, CCDS54026.1, CCDS54027.1, CCDS54028.1	16q22.1	2008-02-05			ENSG00000039523	ENSG00000039523			25836	protein-coding gene	gene with protein product						11572484	Standard	NM_001193522		Approved	FLJ13725	uc010vjp.2	Q6ZS17	OTTHUMG00000137536	ENST00000379312.3:c.1349G>A	chr16.hg19:g.67576026G>A	ENSP00000368614:p.Arg450Gln	139.0	0.0	.		155.0	35.0	.	NM_001193523	B4DEQ9|B4DIM2|E9PBS3|Q4G0A4|Q7Z5R7|Q8NDA4|Q96J39|Q96PV8|Q9H8D9	Missense_Mutation	SNP	ENST00000379312.3	hg19	CCDS54028.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.517558	0.85495	.	.	ENSG00000039523	ENST00000379312;ENST00000042381;ENST00000422602;ENST00000540839	T;T;T	0.32753	1.44;1.44;1.44	4.62	4.62	0.57501	.	0.467258	0.23181	N	0.051009	T	0.50137	0.1598	L	0.57536	1.79	0.54753	D	0.999984	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.998;0.998	T	0.39187	-0.9626	10	0.14252	T	0.57	-16.318	17.523	0.87792	0.0:0.0:1.0:0.0	.	460;466;450;466	B4DIM2;E9PBS3;Q6ZS17;B4DEQ9	.;.;FA65A_HUMAN;.	Q	450;446;466;460	ENSP00000368614:R450Q;ENSP00000042381:R446Q;ENSP00000400099:R466Q	ENSP00000042381:R446Q	R	+	2	0	FAM65A	66133527	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	7.569000	0.82380	2.149000	0.67028	0.442000	0.29010	CGG	.	.	.	none		0.632	FAM65A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268866.3	NM_024519		A	67576026	G	A	67576026	3	1	175	1	0	0	0	0	1	0	0	0	5606	1116	39	1	1383	1	FAM65A	16	67576026	Missense_Mutation	SNP	G	TCGA-G7-6797-01A-11D-1961-08	575285	67576026	22778727	58	10270											
CHMP1A	5119	hgsc.bcm.edu	37	chr16	89717999	89717999	+	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	tcttcactttggcctgctccGccttggagtccttctccgcc	2	14	8	17	2	3	0	1	0	2	0	6	1	5	1	6	2	1	1	6	2	0	4			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr16:89717999G>C	ENST00000397901.3	-	3	339	c.83C>G	c.(82-84)gCg>gGg	p.A28G	CHMP1A_ENST00000547614.1_5'UTR|CHMP1A_ENST00000550102.1_Missense_Mutation_p.A28G|CHMP1A_ENST00000253475.5_Silent_p.G21G|CHMP1A_ENST00000535997.2_5'UTR	NM_002768.3	NP_002759.2	Q9HD42	CHM1A_HUMAN	charged multivesicular body protein 1A	28					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)		GGCCTGCTCCGCCTTGGAGTC	0.572																																					p.A28G		Atlas-SNP	.											.	CHMP1A	15	.	0			c.C83G						PASS	.						76	85	82					16																	89717999		2034	4180	6214	SO:0001583	missense	5119	exon3			TGCTCCGCCTTGG	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.83C>G	chr16.hg19:g.89717999G>C	ENSP00000380998:p.Ala28Gly	89.0	0.0	.		75.0	43.0	.	NM_002768	A2RU09|Q14468|Q15779|Q96G31	Missense_Mutation	SNP	ENST00000397901.3	hg19	CCDS45552.1	.	.	.	.	.	.	.	.	.	.	G	14.21	2.467907	0.43839	.	.	ENSG00000131165	ENST00000397901;ENST00000550102	T;T	0.72505	-0.66;-0.66	4.81	2.69	0.31865	.	.	.	.	.	T	0.55768	0.1941	.	.	.	0.80722	D	1	B	0.15141	0.012	B	0.23419	0.046	T	0.46233	-0.9206	7	.	.	.	-3.1301	9.7579	0.40515	0.0779:0.141:0.7812:0.0	.	28	Q9HD42	CHM1A_HUMAN	G	28	ENSP00000380998:A28G;ENSP00000449243:A28G	.	A	-	2	0	CHMP1A	88245500	1.000000	0.71417	0.633000	0.29310	0.764000	0.43329	5.816000	0.69222	1.132000	0.42129	0.655000	0.94253	GCG	.	.	.	none		0.572	CHMP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404581.1	NM_002768		C	89717999	G	C	89717999	3	2	175	1	0	0	0	0	1	0	0	0	3354	1087	38	4	679	4	CHMP1A	16	89717999	Missense_Mutation	SNP	G	TCGA-G7-6797-01A-11D-1961-08	22141973	89717999	636754	59	10271											
FANCA	2175	hgsc.bcm.edu	37	chr16	89874755	89874755	+	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	tgtacgtgaagatgccacacCgcttcaagcaacaaagaact	15	7	8	11	2	1	3	1	1	0	2	1	3	1	3	2	0	5	3	2	0	6	2	rs143314367		TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr16:89874755C>A	ENST00000389301.3	-	6	573	c.543G>T	c.(541-543)gcG>gcT	p.A181A	FANCA_ENST00000389302.3_Silent_p.A181A|FANCA_ENST00000534992.1_Silent_p.A181A|FANCA_ENST00000563673.1_Silent_p.A181A|FANCA_ENST00000568369.1_Silent_p.A181A|FANCA_ENST00000543736.1_Silent_p.A149A	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)		p.A181A(1)		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)		GATGCCACACCGCTTCAAGCA	0.403			"D, Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.A181A		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"Fanconi anemia, complementation group A"		L	.	FANCA	99	.	1	Substitution - coding silent(1)	lung(1)	c.G543T						PASS	.						144	135	138					16																	89874755		2198	4300	6498	SO:0001819	synonymous_variant	2175	exon6	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CCACACCGCTTCA	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.543G>T	chr16.hg19:g.89874755C>A		206.0	0.0	.		368.0	15.0	.	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Silent	SNP	ENST00000389301.3	hg19	CCDS32515.1																																																																																			.	C|0.999;T|0.001	.	alt		0.403	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1			A	89874755	C	A	89874755	2	1	175	1	0	0	0	0	0	0	0	1	5669	639	23	4		4	FANCA	16	89874755	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08	156756	89874755	479998	60	10272											
SPAG5	10615	hgsc.bcm.edu	37	chr17	26911492	26911492	+	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	ccagaatctgcaactgagccCggagatctagaacaaaagta	16	6	9	10	1	2	4	0	1	2	3	2	5	2	4	2	1	4	2	2	1	7	2	rs140086700		TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr17:26911492C>A	ENST00000321765.5	-	12	2500	c.2168G>T	c.(2167-2169)cGg>cTg	p.R723L		NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	723	Gln-rich.|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)					CAACTGAGCCCGGAGATCTAG	0.493																																					p.R723L		Atlas-SNP	.											.	SPAG5	92	.	0			c.G2168T						PASS	.						147	139	142					17																	26911492		2203	4300	6503	SO:0001583	missense	10615	exon12			TGAGCCCGGAGAT	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.2168G>T	chr17.hg19:g.26911492C>A	ENSP00000323300:p.Arg723Leu	231.0	0.0	.		220.0	10.0	.	NM_006461	O95213|Q9BWE8|Q9NT17|Q9UFE6	Missense_Mutation	SNP	ENST00000321765.5	hg19	CCDS32594.1	.	.	.	.	.	.	.	.	.	.	C	12.99	2.103948	0.37145	.	.	ENSG00000076382	ENST00000321765;ENST00000536674	.	.	.	6.02	-4.11	0.03928	.	1.207820	0.05827	N	0.616907	T	0.19685	0.0473	N	0.14661	0.345	0.18873	N	0.999981	B	0.31193	0.312	B	0.26094	0.066	T	0.27123	-1.0083	9	0.62326	D	0.03	0.4992	8.2083	0.31469	0.0:0.5014:0.1246:0.374	.	723	Q96R06	SPAG5_HUMAN	L	723;220	.	ENSP00000323300:R723L	R	-	2	0	SPAG5	23935619	0.000000	0.05858	0.772000	0.31596	0.996000	0.88848	-2.533000	0.00942	-0.956000	0.03631	0.650000	0.86243	CGG	.	C|1.000;T|0.000	.	alt		0.493	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461		A	26911492	C	A	26911492	3	1	175	1	0	0	0	0	1	0	0	0	14994	652	23	4	1465	4	SPAG5	17	26911492	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08		26911492	54283718	61	10273											
ZNF207	7756	hgsc.bcm.edu	37	chr17	30696350	30696350	+	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	agttacctaagtatcaacgtAatcttcctcggccaggacag	12	10	8	11	2	2	0	1	0	1	0	4	1	3	1	3	2	2	3	3	2	5	5			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr17:30696350A>T	ENST00000321233.6	+	10	1307	c.1153A>T	c.(1153-1155)Aat>Tat	p.N385Y	ZNF207_ENST00000394673.2_Missense_Mutation_p.N370Y|ZNF207_ENST00000342555.6_Missense_Mutation_p.N404Y|ZNF207_ENST00000577908.1_Missense_Mutation_p.N401Y|ZNF207_ENST00000341711.6_Missense_Mutation_p.N302Y|ZNF207_ENST00000394670.4_Missense_Mutation_p.N401Y	NM_003457.3	NP_003448.1	O43670	ZN207_HUMAN	zinc finger protein 207	385	GLEBS.				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)			GTATCAACGTAATCTTCCTCG	0.502																																					p.N401Y		Atlas-SNP	.											.	ZNF207	32	.	0			c.A1201T						PASS	.						102	101	101					17																	30696350		2203	4300	6503	SO:0001583	missense	7756	exon11			CAACGTAATCTTC	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.1153A>T	chr17.hg19:g.30696350A>T	ENSP00000322777:p.Asn385Tyr	117.0	0.0	.		96.0	48.0	.	NM_001098507	A8K6Y6|E1P660|E1P661|E1P662|Q53XS9|Q96HW5|Q9BUQ7	Missense_Mutation	SNP	ENST00000321233.6	hg19	CCDS11271.1	.	.	.	.	.	.	.	.	.	.	A	15.02	2.710294	0.48517	.	.	ENSG00000010244	ENST00000394670;ENST00000394673;ENST00000394679;ENST00000321233;ENST00000341711;ENST00000342555	T;T	0.47177	0.87;0.85	5.55	5.55	0.83447	.	0.143629	0.64402	D	0.000010	T	0.60209	0.2251	L	0.40543	1.245	0.48762	D	0.999708	D;D;D;P;D	0.76494	0.972;0.972;0.972;0.924;0.999	P;P;P;P;D	0.83275	0.6;0.6;0.6;0.461;0.996	T	0.58137	-0.7689	10	0.37606	T	0.19	.	15.7019	0.77549	1.0:0.0:0.0:0.0	.	354;404;401;370;385	A8MTG3;Q59G94;E1P660;O43670-2;O43670	.;.;.;.;ZN207_HUMAN	Y	401;354;404;370;302;385	ENSP00000378165:N401Y;ENSP00000344913:N302Y	ENSP00000322777:N370Y	N	+	1	0	ZNF207	27720463	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.566000	0.67372	2.108000	0.64289	0.477000	0.44152	AAT	.	.	.	none		0.502	ZNF207-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256251.2			T	30696350	A	T	30696350	3	4	175	1	0	0	0	0	1	0	0	0	17777	362	13	5	1243	5	ZNF207	17	30696350	Missense_Mutation	SNP	A	TCGA-G7-6797-01A-11D-1961-08	3784858	30696350	50498860	62	10274											
PPM1D	8493	hgsc.bcm.edu	37	chr17	58740837	58740837	+	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	ctctgttaaactcaccatgcGacgcagacttaggggccaga	11	8	10	12	2	2	2	1	0	1	2	2	3	2	2	2	2	2	2	2	2	3	2	rs200809297		TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr17:58740837G>A	ENST00000305921.3	+	6	1974	c.1742G>A	c.(1741-1743)cGa>cAa	p.R581Q	RNU6-623P_ENST00000363143.1_RNA	NM_003620.3	NP_003611.1	O15297	PPM1D_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1D	581					G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of cell proliferation (GO:0008285)|peptidyl-threonine dephosphorylation (GO:0035970)|protein dephosphorylation (GO:0006470)|response to bacterium (GO:0009617)|response to radiation (GO:0009314)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	15	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;6.75e-12)|all cancers(12;1.96e-10)			CTCACCATGCGACGCAGACTT	0.443											OREG0031485	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.R581Q		Atlas-SNP	.											.	PPM1D	50	.	0			c.G1742A						PASS	.						85	82	83					17																	58740837		2203	4300	6503	SO:0001583	missense	8493	exon6			CCATGCGACGCAG	U78305	CCDS11625.1	17q23.3	2014-09-17	2010-03-05		ENSG00000170836	ENSG00000170836		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9277	protein-coding gene	gene with protein product	"wild-type p53-induced phosphatase 1", "protein phosphatase 2C, delta isoform"	605100	"protein phosphatase 1D magnesium-dependent, delta isoform"			9177166	Standard	NM_003620		Approved	Wip1, PP2C-DELTA	uc002iyt.2	O15297		ENST00000305921.3:c.1742G>A	chr17.hg19:g.58740837G>A	ENSP00000306682:p.Arg581Gln	109.0	0.0	.	1033	104.0	52.0	.	NM_003620	Q53XP4|Q6P991|Q8IVR6	Missense_Mutation	SNP	ENST00000305921.3	hg19	CCDS11625.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.564808	0.86439	.	.	ENSG00000170836	ENST00000305921	T	0.61158	0.13	5.98	5.01	0.66863	.	0.278410	0.34268	N	0.004118	T	0.66157	0.2761	L	0.34521	1.04	0.40466	D	0.980292	D	0.89917	1.0	D	0.63957	0.92	T	0.71721	-0.4507	10	0.87932	D	0	-2.6262	17.3117	0.87212	0.0:0.1253:0.8747:0.0	.	581	O15297	PPM1D_HUMAN	Q	581	ENSP00000306682:R581Q	ENSP00000306682:R581Q	R	+	2	0	PPM1D	56095619	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.144000	0.77357	1.522000	0.49001	0.591000	0.81541	CGA	.	G|0.999;A|0.001	0.001	weak		0.443	PPM1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449474.1	NM_003620		A	58740837	G	A	58740837	3	1	175	1	0	0	0	0	1	0	0	0	12347	1058	37	1	1764	1	PPM1D	17	58740837	Missense_Mutation	SNP	G	TCGA-G7-6797-01A-11D-1961-08	28044487	58740837	22454373	63	10275											
ANKRD12	23253	hgsc.bcm.edu	37	chr18	9275635	9275635	+	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	tgtactgttttgctggatgcCgaagtatacaatgtaccatt	10	15	9	7	1	0	0	0	0	0	0	0	2	0	1	2	1	5	5	2	1	6	7			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr18:9275635C>A	ENST00000262126.4	+	11	6117	c.5877C>A	c.(5875-5877)gcC>gcA	p.A1959A	ANKRD12_ENST00000400020.3_Silent_p.A1936A|ANKRD12_ENST00000383440.2_Silent_p.A1936A|snoU13_ENST00000459594.1_RNA	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1959						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						TGCTGGATGCCGAAGTATACA	0.363																																					p.A1959A		Atlas-SNP	.											ANKRD12,NS,carcinoma,0,1	ANKRD12	167	.	0			c.C5877A						PASS	.						163	148	153					18																	9275635		2203	4300	6503	SO:0001819	synonymous_variant	23253	exon11			GGATGCCGAAGTA	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"Ankyrin repeat domain containing"	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.5877C>A	chr18.hg19:g.9275635C>A		146.0	2.0	.		247.0	12.0	.	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Silent	SNP	ENST00000262126.4	hg19	CCDS11843.1																																																																																			.	.	.	none		0.363	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208		A	9275635	C	A	9275635	2	1	175	1	0	0	0	0	0	0	0	1	640	639	23	4		4	ANKRD12	18	9275635	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08		9275635	68801613	64	10276											
SMAD7	4092	hgsc.bcm.edu	37	chr18	46447887	46447887	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	taaactcgtggtcattgggcCgctgcaggctgtacgccttc	6	11	12	12	3	1	0	1	0	0	0	3	0	1	0	2	3	3	4	2	3	3	4			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr18:46447887C>T	ENST00000262158.2	-	4	1422	c.1136G>A	c.(1135-1137)cGg>cAg	p.R379Q	SMAD7_ENST00000591805.1_Missense_Mutation_p.R164Q|SMAD7_ENST00000589634.1_Missense_Mutation_p.R378Q|SMAD7_ENST00000585986.1_5'UTR	NM_001190821.1|NM_005904.3	NP_001177750.1|NP_005895.1	O15105	SMAD7_HUMAN	SMAD family member 7	379	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)					GTCATTGGGCCGCTGCAGGCT	0.582																																					p.R379Q		Atlas-SNP	.											.	SMAD7	22	.	0			c.G1136A						PASS	.						90	77	81					18																	46447887		2203	4300	6503	SO:0001583	missense	4092	exon4			TTGGGCCGCTGCA	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.1136G>A	chr18.hg19:g.46447887C>T	ENSP00000262158:p.Arg379Gln	91.0	0.0	.		66.0	25.0	.	NM_005904	B7Z773|K7EQ10|O14740|Q6DK23	Missense_Mutation	SNP	ENST00000262158.2	hg19	CCDS11936.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.380052	0.82682	.	.	ENSG00000101665	ENST00000545051;ENST00000262158	D	0.98792	-5.14	5.66	5.66	0.87406	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.97648	0.9229	N	0.05330	-0.07	0.80722	D	1	P;D	0.71674	0.68;0.998	B;D	0.79108	0.19;0.992	D	0.97332	0.9951	10	0.23891	T	0.37	.	19.7417	0.96234	0.0:1.0:0.0:0.0	.	379;191	O15105;B3KYA8	SMAD7_HUMAN;.	Q	164;379	ENSP00000262158:R379Q	ENSP00000262158:R379Q	R	-	2	0	SMAD7	44701885	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.972000	0.63756	2.658000	0.90341	0.591000	0.81541	CGG	.	.	.	none		0.582	SMAD7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255906.1	NM_005904		T	46447887	C	T	46447887	3	4	175	1	0	0	0	0	1	0	0	0	14776	652	23	1	148	1	SMAD7	18	46447887	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	37172252	46447887	31629361	65	10277											
SALL3	27164	hgsc.bcm.edu	37	chr18	76755171	76755171	+	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	tccagcgccgcacccaccatGatcaaaatggaagtgaacgg	13	5	10	13	3	1	2	1	2	0	0	2	3	2	3	4	2	2	1	4	2	4	0	rs371088522		TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr18:76755171G>C	ENST00000537592.2	+	2	3180	c.3180G>C	c.(3178-3180)atG>atC	p.M1060I	SALL3_ENST00000536229.3_Missense_Mutation_p.M855I|SALL3_ENST00000575389.2_Missense_Mutation_p.M988I	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	1060					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)		CACCCACCATGATCAAAATGG	0.612																																					p.M1060I		Atlas-SNP	.											.	SALL3	162	.	0			c.G3180C						PASS	.						64	64	64					18																	76755171		2203	4300	6503	SO:0001583	missense	27164	exon2			CACCATGATCAAA	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.3180G>C	chr18.hg19:g.76755171G>C	ENSP00000441823:p.Met1060Ile	119.0	0.0	.		100.0	4.0	.	NM_171999	Q9UGH1	Missense_Mutation	SNP	ENST00000537592.2	hg19	CCDS12013.1	.	.	.	.	.	.	.	.	.	.	G	9.680	1.148949	0.21288	.	.	ENSG00000256463	ENST00000537592;ENST00000536229;ENST00000543056	T	0.08370	3.1	5.1	3.24	0.37175	.	0.285135	0.29362	N	0.012368	T	0.07007	0.0178	N	0.20986	0.625	0.43617	D	0.995995	B;B	0.20887	0.002;0.049	B;B	0.14023	0.002;0.01	T	0.23084	-1.0198	10	0.35671	T	0.21	-20.2151	15.0906	0.72192	0.0:0.2696:0.7304:0.0	.	720;1060	F5GXY4;Q9BXA9	.;SALL3_HUMAN	I	1060;988;720	ENSP00000441823:M1060I	ENSP00000299466:M1060I	M	+	3	0	SALL3	74856159	1.000000	0.71417	0.871000	0.34182	0.073000	0.16967	3.010000	0.49559	0.505000	0.28104	0.561000	0.74099	ATG	.	.	.	alt		0.612	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999		C	76755171	G	C	76755171	3	2	175	1	0	0	0	0	1	0	0	0	13825	1290	45	4	3186	4	SALL3	18	76755171	Missense_Mutation	SNP	G	TCGA-G7-6797-01A-11D-1961-08	30307284	76755171	1322077	66	10278											
KCNN1	3780	hgsc.bcm.edu	37	chr19	18100536	18100536	+	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	tggccccaggtaaaaaacgcCgctgctaacgttctcaggga	11	7	11	12	3	1	0	1	0	1	0	2	1	1	1	3	3	3	4	3	3	4	3	rs377567043		TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr19:18100536C>A	ENST00000222249.9	+	8	1501	c.1182C>A	c.(1180-1182)gcC>gcA	p.A394A		NM_002248.3	NP_002239.2	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	394	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)	TAAAAAACGCCGCTGCTAACG	0.502																																					p.A394A		Atlas-SNP	.											.	KCNN1	74	.	0			c.C1182A						PASS	.						143	141	142					19																	18100536		1895	4132	6027	SO:0001819	synonymous_variant	3780	exon8			AAACGCCGCTGCT	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.1182C>A	chr19.hg19:g.18100536C>A		289.0	0.0	.		247.0	10.0	.	NM_002248	Q5KR10|Q6DJU4	Silent	SNP	ENST00000222249.9	hg19																																																																																				.	.	.	alt		0.502	KCNN1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471896.2	NM_002248		A	18100536	C	A	18100536	2	1	175	1	0	0	0	0	0	0	0	1	8085	639	23	4		4	KCNN1	19	18100536	Silent	SNP	C	TCGA-G7-6797-01A-11D-1961-08		18100536	41028447	67	10279											
GATAD2A	54815	hgsc.bcm.edu	37	chr19	19613195	19613195	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccccgaggtgtcctgcacaCgttcagtccgtcacccaaac	8	7	9	17	3	2	0	2	0	0	0	4	1	4	0	5	1	2	2	5	1	1	1			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr19:19613195C>T	ENST00000360315.3	+	11	1943	c.1631C>T	c.(1630-1632)aCg>aTg	p.T544M	GATAD2A_ENST00000358713.3_Missense_Mutation_p.T544M|GATAD2A_ENST00000429563.2_Missense_Mutation_p.T347M|GATAD2A_ENST00000537887.1_Missense_Mutation_p.T173M|GATAD2A_ENST00000252577.5_Missense_Mutation_p.T519M|GATAD2A_ENST00000404158.1_Missense_Mutation_p.T545M	NM_017660.3	NP_060130.3	Q86YP4	P66A_HUMAN	GATA zinc finger domain containing 2A	544					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						GTCCTGCACACGTTCAGTCCG	0.647																																					p.T544M		Atlas-SNP	.											.	GATAD2A	81	.	0			c.C1631T						PASS	.						76	79	78					19																	19613195		2203	4300	6503	SO:0001583	missense	54815	exon11			TGCACACGTTCAG	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.1631C>T	chr19.hg19:g.19613195C>T	ENSP00000353463:p.Thr544Met	182.0	0.0	.		93.0	36.0	.	NM_017660	B5MC40|Q7L3J2|Q96F28|Q9NPU2|Q9NXS1	Missense_Mutation	SNP	ENST00000360315.3	hg19	CCDS12402.2	.	.	.	.	.	.	.	.	.	.	C	16.57	3.160141	0.57368	.	.	ENSG00000167491	ENST00000360315;ENST00000252577;ENST00000537887;ENST00000404158;ENST00000358713;ENST00000429563	T;T;T;T	0.45668	1.43;1.48;1.43;0.89	5.23	5.23	0.72850	.	0.357947	0.31872	N	0.006930	T	0.56202	0.1969	L	0.47716	1.5	0.38138	D	0.938352	D;D;D	0.89917	0.994;0.998;1.0	P;P;P	0.61592	0.628;0.794;0.891	T	0.62248	-0.6894	10	0.72032	D	0.01	-26.0515	17.4151	0.87497	0.0:1.0:0.0:0.0	.	347;564;544	B4DKZ7;B5MC40;Q86YP4	.;.;P66A_HUMAN	M	544;519;173;564;544;347	ENSP00000353463:T544M;ENSP00000252577:T519M;ENSP00000351552:T544M;ENSP00000388416:T347M	ENSP00000252577:T519M	T	+	2	0	GATAD2A	19474195	1.000000	0.71417	0.929000	0.37066	0.486000	0.33341	4.956000	0.63645	2.452000	0.82932	0.585000	0.79938	ACG	.	.	.	none		0.647	GATAD2A-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326671.4	NM_017660		T	19613195	C	T	19613195	3	4	175	1	0	0	0	0	1	0	0	0	6267	536	19	1	1669	1	GATAD2A	19	19613195	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	1512659	19613195	39515788	68	10280											
ZNF573	126231	hgsc.bcm.edu	37	chr19	38230139	38230140	+	Nonsense_Mutation	DNP	CC	CC	AA																															gctaaaggcctttccgcattCcttgcattcatagggtttct																										TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr19:38230139_38230140CC>AA	ENST00000590414.2	-	4	1272_1273	c.1251_1252GG>TT	c.(1249-1254)aaGGaa>aaTTaa	p.417_418KE>N*	ZNF573_ENST00000392138.1_Nonsense_Mutation_p.330_331KE>N*|ZNF573_ENST00000339503.4_Nonsense_Mutation_p.359_360KE>N*|ZNF573_ENST00000536220.1_Nonsense_Mutation_p.329_330KE>N*|ZNF573_ENST00000357309.3_Nonsense_Mutation_p.329_330KE>N*			Q86YE8	ZN573_HUMAN	zinc finger protein 573	417					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|cervix(3)|endometrium(2)|large_intestine(8)|liver(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)|Lung(45;0.0813)|LUSC - Lung squamous cell carcinoma(53;0.146)			TTTCCGCATTCCTTGCATTCAT	0.376																																					p.E418X|p.K417N		Atlas-SNP	.											.	ZNF573	63	.	0			c.G1252T|c.G1251T						PASS	.																																			SO:0001587	stop_gained	126231	exon5			CGCATTCCTTGCA|GCATTCCTTGCAT	AK074539	CCDS12508.1, CCDS54260.1, CCDS59381.1	19q13.12	2013-09-20			ENSG00000189144	ENSG00000189144		"Zinc fingers, C2H2-type", "-"	26420	protein-coding gene	gene with protein product						12477932	Standard	NM_152360		Approved	FLJ30921	uc002ohe.3	Q86YE8	OTTHUMG00000048183	ENST00000590414.2:c.1251_1252delinsAA	chr19.hg19:g.38230139_38230140delinsAA	ENSP00000465020:p.K417_E418delinsN*	275.0|274.0	0.0	.		300.0|296.0	132.0	.	NM_001172690	B7WPE1|K7EJ45|Q6P1P1|Q7Z7Q3|Q8N2Q1|Q96BM3|Q96NH0	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000590414.2	hg19	CCDS59381.1																																																																																			.	.	.	none		0.376	ZNF573-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459773.2	NM_152360		AA	38230140	CC	AA	38230139	4	1	175	1	0	0	0	0	0	1	0	0	18017	864	30	4	749	4	ZNF573	19	38230139	Nonsense_Mutation	DNP	CC	TCGA-G7-6797-01A-11D-1961-08	18616944	38230139	20898844	69	10281											
PRR12	57479	hgsc.bcm.edu	37	chr19	50097991	50097991	+	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	cccacggagctcttcatctcGggtgccctgccgggttccag	4	9	12	16	3	3	0	1	0	2	0	5	1	4	1	4	3	3	2	4	3	0	2	rs527711314		TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr19:50097991G>C	ENST00000418929.2	+	4	411	c.399G>C	c.(397-399)tcG>tcC	p.S133S		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	0	Pro-rich.						DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		TCTTCATCTCGGGTGCCCTGC	0.662																																					p.S133S		Atlas-SNP	.											.	PRR12	157	.	0			c.G399C						PASS	.						27	32	31					19																	50097991		2036	4191	6227	SO:0001819	synonymous_variant	57479	exon4			CATCTCGGGTGCC	AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"KIAA1205"	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.399G>C	chr19.hg19:g.50097991G>C		72.0	0.0	.		30.0	15.0	.	NM_020719	E9PB06|Q8N4J6	Silent	SNP	ENST00000418929.2	hg19	CCDS46143.1																																																																																			.	.	.	none		0.662	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719		C	50097991	G	C	50097991	2	2	175	1	0	0	0	0	0	0	0	1	12594	1103	39	4		4	PRR12	19	50097991	Silent	SNP	G	TCGA-G7-6797-01A-11D-1961-08	11867852	50097991	9030992	70	10282											
NSFL1C	55968	hgsc.bcm.edu	37	chr20	1433207	1433207	+	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	gcttcacaaagtcctcgtccCgatggtcctccatatccaag	9	10	7	15	2	1	0	1	0	0	0	7	1	6	0	5	1	0	1	5	1	3	2	rs371393612		TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr20:1433207C>A	ENST00000216879.4	-	7	1583	c.716G>T	c.(715-717)cGg>cTg	p.R239L	NSFL1C_ENST00000350991.4_Missense_Mutation_p.R241L|NSFL1C_ENST00000476071.1_Missense_Mutation_p.R241L|NSFL1C_ENST00000353088.2_Missense_Mutation_p.R208L|NSFL1C_ENST00000461211.1_5'UTR|NSFL1C_ENST00000381658.4_Missense_Mutation_p.R128L	NM_016143.4	NP_057227.2	Q9UNZ2	NSF1C_HUMAN	NSFL1 (p97) cofactor (p47)	239	SEP. {ECO:0000255|PROSITE- ProRule:PRU00732}.					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)	p.R239Q(1)		breast(1)|large_intestine(5)|lung(6)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	16						GTCCTCGTCCCGATGGTCCTC	0.572																																					p.R239L		Atlas-SNP	.											NSFL1C,caecum,carcinoma,0,1	NSFL1C	38	.	1	Substitution - Missense(1)	large_intestine(1)	c.G716T						PASS	.						179	159	166					20																	1433207		2203	4300	6503	SO:0001583	missense	55968	exon7			TCGTCCCGATGGT	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.716G>T	chr20.hg19:g.1433207C>A	ENSP00000216879:p.Arg239Leu	285.0	2.0	.		345.0	19.0	.	NM_016143	A2A2L1|B2RD74|Q5JXA4|Q5JXA5|Q7Z533|Q9H102|Q9NVL9|Q9UI06	Missense_Mutation	SNP	ENST00000216879.4	hg19	CCDS13015.1	.	.	.	.	.	.	.	.	.	.	C	35	5.461733	0.96240	.	.	ENSG00000088833	ENST00000353088;ENST00000476071;ENST00000216879;ENST00000381658;ENST00000350991	T;T;T;T;T	0.50277	0.75;0.78;0.78;0.78;0.79	5.13	5.13	0.70059	SEP domain (4);	0.000000	0.85682	D	0.000000	T	0.67581	0.2908	M	0.66506	2.035	0.80722	D	1	D;D;D	0.67145	0.996;0.989;0.991	D;D;D	0.80764	0.992;0.99;0.994	T	0.69363	-0.5165	10	0.72032	D	0.01	-15.8878	17.2951	0.87168	0.0:1.0:0.0:0.0	.	208;128;239	Q9UNZ2-4;Q9UNZ2-6;Q9UNZ2	.;.;NSF1C_HUMAN	L	208;241;239;128;241	ENSP00000338643:R208L;ENSP00000418529:R241L;ENSP00000216879:R239L;ENSP00000371074:R128L;ENSP00000202584:R241L	ENSP00000216879:R239L	R	-	2	0	NSFL1C	1381207	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.754000	0.62191	2.824000	0.97209	0.655000	0.94253	CGG	.	.	.	alt		0.572	NSFL1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077525.2	NM_016143		A	1433207	C	A	1433207	3	1	175	1	0	0	0	0	1	0	0	0	10679	652	23	4	408	4	NSFL1C	20	1433207	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08		1433207	61592313	71	10283											
FAM113A	64773	hgsc.bcm.edu	37	chr20	2819363	2819363	+	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	acacccgctccaggttctccCggtagctctccattgagcag	7	9	9	16	2	2	1	0	1	2	0	5	1	3	1	4	2	2	5	4	2	1	3			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr20:2819363C>A	ENST00000360652.2	-	5	975	c.473G>T	c.(472-474)cGg>cTg	p.R158L	VPS16_ENST00000380469.3_5'Flank|VPS16_ENST00000380445.3_5'Flank|PCED1A_ENST00000356872.3_Missense_Mutation_p.R107L	NM_022760.4	NP_073597.2	Q9H1Q7	PED1A_HUMAN	PC-esterase domain containing 1A	158																	CAGGTTCTCCCGGTAGCTCTC	0.582																																					p.R158L		Atlas-SNP	.											FAM113A,colon,carcinoma,0,1	.	.	.	0			c.G473T						PASS	.						172	154	160					20																	2819363		2203	4300	6503	SO:0001583	missense	64773	exon5			TTCTCCCGGTAGC	AK026029	CCDS13035.1, CCDS59442.1	20p13	2012-06-11	2012-06-11	2012-06-11	ENSG00000132635	ENSG00000132635			16212	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 81", "family with sequence similarity 113, member A"	C20orf81, FAM113A		20056006	Standard	NM_022760		Approved	bA12M19.1, FLJ22376	uc002wgz.2	Q9H1Q7	OTTHUMG00000031716	ENST00000360652.2:c.473G>T	chr20.hg19:g.2819363C>A	ENSP00000353868:p.Arg158Leu	322.0	0.0	.		236.0	10.0	.	NM_022760	Q5JUA5|Q5JUA6|Q6PK19|Q86WF5|Q96CG7|Q9H1Q6|Q9H6D1	Missense_Mutation	SNP	ENST00000360652.2	hg19	CCDS13035.1	.	.	.	.	.	.	.	.	.	.	C	12.12	1.844032	0.32606	.	.	ENSG00000132635	ENST00000356872;ENST00000360652;ENST00000448755;ENST00000439542	T;T;T;T	0.20200	2.09;2.09;2.09;2.09	3.89	2.93	0.34026	Esterase, SGNH hydrolase-type (1);Esterase, SGNH hydrolase-type, subgroup (1);	0.151472	0.40908	D	0.000997	T	0.10723	0.0262	N	0.13235	0.315	0.39966	D	0.974729	B;B	0.24426	0.031;0.103	B;B	0.24701	0.034;0.055	T	0.12192	-1.0557	10	0.33141	T	0.24	-7.013	6.7152	0.23300	0.0:0.872:0.0:0.128	.	107;158	Q9H1Q7-2;Q9H1Q7	.;F113A_HUMAN	L	107;158;107;158	ENSP00000349334:R107L;ENSP00000353868:R158L;ENSP00000388935:R107L;ENSP00000401711:R158L	ENSP00000349334:R107L	R	-	2	0	FAM113A	2767363	0.494000	0.26043	0.922000	0.36590	0.442000	0.32017	0.684000	0.25364	2.205000	0.71048	0.462000	0.41574	CGG	.	.	.	none		0.582	PCED1A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077676.2	NM_022760		A	2819363	C	A	2819363	3	1	175	1	0	0	0	0	1	0	0	0	5405	652	23	4	907	4	FAM113A	20	2819363	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08	1386156	2819363	60206157	72	10284											
NF2	4771	hgsc.bcm.edu	37	chr22	30051666	30051666	+	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	gagcaccgaggccgagccagGtgaggcccattcattgttgg	8	7	15	11	2	1	1	1	1	0	0	1	4	1	1	4	4	2	2	4	4	0	3			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chr22:30051666G>A	ENST00000338641.4	+	6	1040		c.e6+1		NF2_ENST00000413209.2_Intron|NF2_ENST00000403435.1_Splice_Site|NF2_ENST00000397789.3_Splice_Site|NF2_ENST00000353887.4_Splice_Site|NF2_ENST00000361166.4_Splice_Site|NF2_ENST00000403999.3_Splice_Site|NF2_ENST00000361676.4_Splice_Site|NF2_ENST00000361452.4_Splice_Site|NF2_ENST00000347330.5_Intron|NF2_ENST00000334961.7_Splice_Site	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)						actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(5)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						GCCGAGCCAGGTGAGGCCCAT	0.408			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																												.		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	NF2_ENST00000403999,NS,carcinoma,0,5	NF2	1312	.	5	Unknown(5)	meninges(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)	c.599+1G>A	GRCh37	CS951487	NF2	S		PASS	.						83	87	85					22																	30051666		2203	4300	6503	SO:0001630	splice_region_variant	4771	exon6	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	AGCCAGGTGAGGC	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"A-kinase anchor proteins"	7773	protein-coding gene	gene with protein product	"moesin-ezrin-radixin like", "schwannomin"	607379	"neurofibromin 2 (bilateral acoustic neuroma)"			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.599+1G>A	chr22.hg19:g.30051666G>A		91.0	0.0	.		42.0	37.0	.	NM_016418	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Splice_Site	SNP	ENST00000338641.4	hg19	CCDS13861.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.954606	0.92726	.	.	ENSG00000186575	ENST00000338641;ENST00000403435;ENST00000361452;ENST00000397822;ENST00000403999;ENST00000334961;ENST00000353887;ENST00000397789;ENST00000361676;ENST00000361166	.	.	.	5.34	5.34	0.76211	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.036	0.92978	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NF2	28381666	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.653000	0.98506	2.484000	0.83849	0.555000	0.69702	.	.	.	.	none		0.408	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268	Intron	A	30051666	G	A	30051666	5	1	175	1	0	0	0	0	0	0	1	0	10364	1275	44	2	622	2	NF2	22	30051666	Splice_Site	SNP	G	TCGA-G7-6797-01A-11D-1961-08		30051666	21252900	73	10285											
NXF3	56000	hgsc.bcm.edu	37	chrX	102337711	102337711	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtatgttctcttcatggaCgtccagggaggcagccatgc	8	10	13	10	1	2	0	1	0	1	0	4	2	3	2	2	4	2	3	2	4	1	3			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chrX:102337711C>T	ENST00000395065.3	-	8	858	c.757G>A	c.(757-759)Gtc>Atc	p.V253I	NXF3_ENST00000425644.1_5'UTR|NXF3_ENST00000425463.2_Missense_Mutation_p.V164I	NM_022052.1	NP_071335.1	Q9H4D5	NXF3_HUMAN	nuclear RNA export factor 3	253					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						TCTTCATGGACGTCCAGGGAG	0.478																																					p.V253I		Atlas-SNP	.											.	NXF3	81	.	0			c.G757A						PASS	.						174	145	154					X																	102337711		2203	4300	6503	SO:0001583	missense	56000	exon8			CATGGACGTCCAG	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.757G>A	chrX.hg19:g.102337711C>T	ENSP00000378504:p.Val253Ile	155.0	1.0	.		91.0	87.0	.	NM_022052	B4DYS7|Q5H9I1|Q9H1A9	Missense_Mutation	SNP	ENST00000395065.3	hg19	CCDS14503.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.019|0.019	-1.461864|-1.461864	0.01062|0.01062	.|.	.|.	ENSG00000147206|ENSG00000147206	ENST00000427570|ENST00000395065;ENST00000425463	.|T;T	.|0.33865	.|1.39;1.39	3.64|3.64	1.2|1.2	0.21068|0.21068	.|.	.|0.308479	.|0.33364	.|N	.|0.004994	T|T	0.07638|0.07638	0.0192|0.0192	N|N	0.00686|0.00686	-1.255|-1.255	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.17852	.|0.024;0.011;0.004	.|B;B;B	.|0.10450	.|0.005;0.003;0.001	T|T	0.37314|0.37314	-0.9711|-0.9711	5|10	.|0.02654	.|T	.|1	-12.7344|-12.7344	4.8575|4.8575	0.13566|0.13566	0.0:0.2749:0.0:0.7251|0.0:0.2749:0.0:0.7251	.|.	.|253;149;253	.|B4DYI1;E9PEY7;Q9H4D5	.|.;.;NXF3_HUMAN	H|I	129|253;164	.|ENSP00000378504:V253I;ENSP00000404347:V164I	.|ENSP00000378504:V253I	R|V	-|-	2|1	0|0	NXF3|NXF3	102224367|102224367	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.923000|0.923000	0.28757|0.28757	0.139000|0.139000	0.18822|0.18822	-0.881000|-0.881000	0.02953|0.02953	CGT|GTC	.	.	.	none		0.478	NXF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057684.1	NM_022052		T	102337711	C	T	102337711	3	4	175	1	0	0	0	0	1	0	0	0	10792	536	19	1	886	1	NXF3	23	102337711	Missense_Mutation	SNP	C	TCGA-G7-6797-01A-11D-1961-08		102337711	52932849	74	10286											
DOCK11	139818	hgsc.bcm.edu	37	chrX	117731503	117731503	+	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	tacttgaatctgaatgatgcAgaatcaagaagggtaggaaa	17	9	11	4	0	2	5	1	3	1	2	2	6	2	6	0	2	2	2	0	2	8	3			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chrX:117731503A>T	ENST00000276202.7	+	21	2436	c.2373A>T	c.(2371-2373)gcA>gcT	p.A791A	DOCK11_ENST00000276204.6_Silent_p.A791A	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	791	DHR-1.				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						TGAATGATGCAGAATCAAGAA	0.398																																					p.A791A		Atlas-SNP	.											.	DOCK11	185	.	0			c.A2373T						PASS	.						92	82	85					X																	117731503		2203	4300	6503	SO:0001819	synonymous_variant	139818	exon21			TGATGCAGAATCA	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.2373A>T	chrX.hg19:g.117731503A>T		90.0	0.0	.		91.0	87.0	.	NM_144658	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Silent	SNP	ENST00000276202.7	hg19	CCDS35373.1																																																																																			.	.	.	none		0.398	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658		T	117731503	A	T	117731503	2	4	175	1	0	0	0	0	0	0	0	1	4688	175	7	5		5	DOCK11	23	117731503	Silent	SNP	A	TCGA-G7-6797-01A-11D-1961-08	15393792	117731503	37539057	75	10287											
KIAA1210	57481	hgsc.bcm.edu	37	chrX	118223094	118223094	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcttgatcttctaactggAtatgagaaggattcataaac	13	14	7	7	0	4	2	1	2	3	1	4	5	4	4	0	2	2	0	0	2	5	7			TCGA-G7-6797-01A-11D-1961-08	TCGA-G7-6797-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b1bd2e14-32b6-4c57-bad1-59c0591876c2	5df531ff-b58f-4f9b-8103-b154da29a87c	g.chrX:118223094A>G	ENST00000402510.2	-	11	2098	c.2099T>C	c.(2098-2100)aTc>aCc	p.I700T		NM_020721.1	NP_065772.1	Q9ULL0	K1210_HUMAN	KIAA1210	700										breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(31)|ovary(4)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	64						TTCTAACTGGATATGAGAAGG	0.443																																					p.I700T		Atlas-SNP	.											.	KIAA1210	171	.	0			c.T2099C						PASS	.						46	44	45					X																	118223094		1917	4125	6042	SO:0001583	missense	57481	exon11			AACTGGATATGAG	AB033036	CCDS48156.1	Xq24	2012-10-04			ENSG00000250423	ENSG00000250423			29218	protein-coding gene	gene with protein product						10574462	Standard	NM_020721		Approved		uc004era.4	Q9ULL0	OTTHUMG00000162980	ENST00000402510.2:c.2099T>C	chrX.hg19:g.118223094A>G	ENSP00000384670:p.Ile700Thr	57.0	0.0	.		58.0	50.0	.	NM_020721	B7ZCI8|Q5JPN4	Missense_Mutation	SNP	ENST00000402510.2	hg19	CCDS48156.1	.	.	.	.	.	.	.	.	.	.	A	12.44	1.939623	0.34189	.	.	ENSG00000250423	ENST00000402510	T	0.15952	2.38	4.42	-4.42	0.03579	.	.	.	.	.	T	0.07007	0.0178	N	0.24115	0.695	0.09310	N	1	B	0.28850	0.225	B	0.29176	0.099	T	0.40021	-0.9585	9	0.12103	T	0.63	.	0.4269	0.00465	0.264:0.1592:0.2924:0.2844	.	700	Q9ULL0	K1210_HUMAN	T	700	ENSP00000384670:I700T	ENSP00000384670:I700T	I	-	2	0	RP13-347D8.6	118107122	0.000000	0.05858	0.000000	0.03702	0.365000	0.29674	-1.161000	0.03144	-1.043000	0.03258	0.350000	0.21858	ATC	.	.	.	none		0.443	KIAA1210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371251.2	NM_020721		G	118223094	A	G	118223094	3	3	175	1	0	0	0	0	1	0	0	0	8221	333	12	3	3046	3	KIAA1210	23	118223094	Missense_Mutation	SNP	A	TCGA-G7-6797-01A-11D-1961-08	491591	118223094	37047466	76	10288											
C1orf173	127254	hgsc.bcm.edu	37	chr1	75114999	75114999	+	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	ctattatatgcagcaagtaaCctaaaatacaaaaataaaac	22	9	3	7	0	0	0	0	0	0	0	0	0	0	0	1	0	5	3	1	0	12	7			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr1:75114999C>A	ENST00000326665.5	-	2	242	c.24G>T	c.(22-24)ggG>ggT	p.G8G		NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		8										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						CAGCAAGTAACCTAAAATACA	0.353																																					p.G8G		Atlas-SNP	.											.	C1orf173	380	.	0			c.G24T						PASS	.						71	72	72					1																	75114999		2203	4300	6503	SO:0001630	splice_region_variant	127254	exon2			AAGTAACCTAAAA																												ENST00000326665.5:c.24-1G>T	chr1.hg19:g.75114999C>A		115.0	0.0	.		76.0	25.0	.	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Silent	SNP	ENST00000326665.5	hg19	CCDS30755.1																																																																																			.	.	.	none		0.353	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1		Silent	A	75114999	C	A	75114999	5	1	176	1	0	0	0	0	0	0	1	0	2016	521	18	4	4620	4	C1orf173	1	75114999	Splice_Site	SNP	C	TCGA-G7-7501-01A-11D-2201-08		75114999	174135622	1	10289											
INTS3	65123	hgsc.bcm.edu	37	chr1	153736638	153736638	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctgtccttgcttcctgcctAcaggagctcttcaaggccca	6	12	8	15	0	3	0	1	0	2	0	5	1	5	1	4	2	4	2	4	2	2	4			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr1:153736638A>G	ENST00000318967.2	+	18	2434	c.1866A>G	c.(1864-1866)ctA>ctG	p.L622L	INTS3_ENST00000456435.1_Silent_p.L416L|INTS3_ENST00000476843.1_3'UTR|INTS3_ENST00000512605.1_Silent_p.L416L|INTS3_ENST00000435409.2_Silent_p.L622L	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	623					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)			CTTCCTGCCTACAGGAGCTCT	0.572																																					p.L622L		Atlas-SNP	.											.	INTS3	83	.	0			c.A1866G						PASS	.						131	122	125					1																	153736638		2203	4300	6503	SO:0001819	synonymous_variant	65123	exon18			CTGCCTACAGGAG	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.1866A>G	chr1.hg19:g.153736638A>G		172.0	0.0	.		107.0	46.0	.	NM_023015	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Silent	SNP	ENST00000318967.2	hg19	CCDS1052.1																																																																																			.	.	.	none		0.572	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015		G	153736638	A	G	153736638	2	3	176	1	0	0	0	0	0	0	0	1	7786	378	14	3		3	INTS3	1	153736638	Silent	SNP	A	TCGA-G7-7501-01A-11D-2201-08	78621639	153736638	95513983	2	10290											
FAIM3	9214	hgsc.bcm.edu	37	chr1	207085119	207085119	+	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	tggttgtagctgggcgtctgGggcttgagcagcccctccag	4	10	16	11	1	1	1	0	1	1	0	2	1	2	1	3	4	3	5	3	4	1	3			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr1:207085119G>C	ENST00000367091.3	-	4	809	c.666C>G	c.(664-666)ccC>ccG	p.P222P	FAIM3_ENST00000420007.2_Silent_p.P222P|FAIM3_ENST00000442471.2_Silent_p.P110P|FAIM3_ENST00000528654.1_Intron	NM_005449.4	NP_005440.1	O60667	FAIM3_HUMAN	Fas apoptotic inhibitory molecule 3	222					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)					TGGGCGTCTGGGGCTTGAGCA	0.542											OREG0014185	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P222P		Atlas-SNP	.											.	FAIM3	36	.	0			c.C666G						PASS	.						92	91	91					1																	207085119		2203	4300	6503	SO:0001819	synonymous_variant	9214	exon4			CGTCTGGGGCTTG	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.666C>G	chr1.hg19:g.207085119G>C		137.0	0.0	.	2164	97.0	26.0	.	NM_005449	A8K7J2|B7Z6Z0|D9MWM3	Silent	SNP	ENST00000367091.3	hg19	CCDS1473.1																																																																																			.	.	.	none		0.542	FAIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088677.1	NM_005449		C	207085119	G	C	207085119	2	2	176	1	0	0	0	0	0	0	0	1	5381	1219	43	4		4	FAIM3	1	207085119	Silent	SNP	G	TCGA-G7-7501-01A-11D-2201-08	53348481	207085119	42165502	3	10291											
PIGR	5284	hgsc.bcm.edu	37	chr1	207105817	207105817	+	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	tcaccgacgttcttcctgtgCcgggctctggccacccccac	4	9	9	19	3	3	0	1	0	2	0	4	1	4	0	6	2	1	2	6	2	0	2			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr1:207105817C>G	ENST00000356495.4	-	8	2175	c.1992G>C	c.(1990-1992)cgG>cgC	p.R664R	PIGR_ENST00000487208.1_5'Flank	NM_002644.3	NP_002635.2	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor	664					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc receptor signaling pathway (GO:0038093)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|receptor clustering (GO:0043113)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	polymeric immunoglobulin receptor activity (GO:0001792)			central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						TCTTCCTGTGCCGGGCTCTGG	0.647																																					p.R664R		Atlas-SNP	.											.	PIGR	98	.	0			c.G1992C						PASS	.						72	75	74					1																	207105817		2203	4300	6503	SO:0001819	synonymous_variant	5284	exon8			CCTGTGCCGGGCT		CCDS1474.1	1q31-q41	2013-01-11			ENSG00000162896	ENSG00000162896		"Immunoglobulin superfamily / V-set domain containing"	8968	protein-coding gene	gene with protein product		173880					Standard	NM_002644		Approved		uc001hez.3	P01833	OTTHUMG00000036581	ENST00000356495.4:c.1992G>C	chr1.hg19:g.207105817C>G		157.0	0.0	.		97.0	34.0	.	NM_002644	Q68D81|Q8IZY7	Silent	SNP	ENST00000356495.4	hg19	CCDS1474.1																																																																																			.	.	.	none		0.647	PIGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088975.1	NM_002644		G	207105817	C	G	207105817	2	3	176	1	0	0	0	0	0	0	0	1	11904	726	26	4		4	PIGR	1	207105817	Silent	SNP	C	TCGA-G7-7501-01A-11D-2201-08	20698	207105817	42144804	4	10292											
OR2T1	26696	hgsc.bcm.edu	37	chr1	248569960	248569960	+	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	ctttcccttctgcaattcccGggagattaaccacttcttct	7	15	5	14	1	3	1	0	0	3	1	5	2	5	1	3	1	2	1	3	1	2	6	rs150412216	byFrequency	TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr1:248569960G>T	ENST00000366474.1	+	1	665	c.665G>T	c.(664-666)cGg>cTg	p.R222L		NM_030904.1	NP_112166.1	O43869	OR2T1_HUMAN	olfactory receptor, family 2, subfamily T, member 1	222						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			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)			TGCAATTCCCGGGAGATTAAC	0.517																																					p.R222L		Atlas-SNP	.											.	OR2T1	89	.	0			c.G665T						PASS	.						120	111	114					1																	248569960		2203	4300	6503	SO:0001583	missense	26696	exon1			ATTCCCGGGAGAT	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.665G>T	chr1.hg19:g.248569960G>T	ENSP00000355430:p.Arg222Leu	109.0	0.0	.		78.0	4.0	.	NM_030904	Q6IEZ9	Missense_Mutation	SNP	ENST00000366474.1	hg19	CCDS31115.1	.	.	.	.	.	.	.	.	.	.	g	16.46	3.129768	0.56721	.	.	ENSG00000175143	ENST00000366474	T	0.36157	1.27	4.84	0.732	0.18283	GPCR, rhodopsin-like superfamily (1);	0.254304	0.20520	U	0.090718	T	0.31734	0.0806	M	0.62209	1.925	0.09310	N	1	B	0.24576	0.106	B	0.34242	0.178	T	0.38067	-0.9678	10	0.59425	D	0.04	.	1.1502	0.01784	0.326:0.145:0.3802:0.1488	.	222	O43869	OR2T1_HUMAN	L	222	ENSP00000355430:R222L	ENSP00000355430:R222L	R	+	2	0	OR2T1	246636583	0.000000	0.05858	0.022000	0.16811	0.987000	0.75469	0.557000	0.23454	0.236000	0.21180	0.650000	0.86243	CGG	.	G|0.998;A|0.002	.	alt		0.517	OR2T1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097346.2			T	248569960	G	T	248569960	3	4	176	1	0	0	0	0	1	0	0	0	11023	1116	39	4	667	4	OR2T1	1	248569960	Missense_Mutation	SNP	G	TCGA-G7-7501-01A-11D-2201-08	41464143	248569960	680661	5	10293											
PLEKHB2	55041	hgsc.bcm.edu	37	chr2	131897791	131897791	+	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	cgtacccgccaggaactcaaGttgtctacgctgcgaatggg	9	8	12	12	4	2	0	1	0	1	0	2	2	2	1	2	2	4	3	2	2	5	3	rs143964327		TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr2:131897791G>C	ENST00000403716.1	+	7	1035	c.475G>C	c.(475-477)Gtt>Ctt	p.V159L	PLEKHB2_ENST00000439822.2_Missense_Mutation_p.K114N|PLEKHB2_ENST00000438882.2_Intron|PLEKHB2_ENST00000234115.6_Missense_Mutation_p.V158L|PLEKHB2_ENST00000303908.3_Intron|PLEKHB2_ENST00000404460.1_Intron|PLEKHB2_ENST00000409612.1_Missense_Mutation_p.V159L|PLEKHB2_ENST00000409158.1_Missense_Mutation_p.V167L|PLEKHB2_ENST00000538982.1_Missense_Mutation_p.V111L|PLEKHB2_ENST00000409279.1_Missense_Mutation_p.V159L	NM_001100623.1|NM_001267062.1|NM_001267063.1|NM_001267064.1|NM_001267065.1|NM_001267066.1|NM_017958.2	NP_001094093.1|NP_001253991.1|NP_001253992.1|NP_001253993.1|NP_001253994.1|NP_001253995.1|NP_060428.2	Q96CS7	PKHB2_HUMAN	pleckstrin homology domain containing, family B (evectins) member 2	159						endosome (GO:0005768)|membrane (GO:0016020)				large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.0828)		AGGAACTCAAGTTGTCTACGC	0.512																																					p.V167L		Atlas-SNP	.											.	PLEKHB2	47	.	0			c.G499C						PASS	.	G	LEU/VAL,LEU/VAL	1,4405	4.2+/-10.8	0,1,2202	62	57	59		475,472	3.9	1	2	dbSNP_134	59	0,8600		0,0,4300	no	missense,missense	PLEKHB2	NM_001100623.1,NM_017958.2	32,32	0,1,6502	CC,CG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	159/223,158/222	131897791	1,13005	2203	4300	6503	SO:0001583	missense	55041	exon7			ACTCAAGTTGTCT		CCDS2166.1, CCDS46413.1, CCDS58729.1, CCDS58730.1, CCDS74576.1, CCDS74577.1	2q22.1	2013-01-10			ENSG00000115762	ENSG00000115762		"Pleckstrin homology (PH) domain containing"	19236	protein-coding gene	gene with protein product						10200314	Standard	NM_017958		Approved	EVT2, FLJ20783	uc031rpd.1	Q96CS7	OTTHUMG00000131656	ENST00000403716.1:c.475G>C	chr2.hg19:g.131897791G>C	ENSP00000385892:p.Val159Leu	61.0	0.0	.		49.0	20.0	.	NM_001267065	B4DF08|B4DZ66|B8ZZN1|Q53FF1|Q53TH7|Q86W37|Q9BV75|Q9NWK1	Missense_Mutation	SNP	ENST00000403716.1	hg19	CCDS46413.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.16|16.16	3.043536|3.043536	0.55003|0.55003	2.27E-4|2.27E-4	0.0|0.0	ENSG00000115762|ENSG00000115762	ENST00000439822|ENST00000409158;ENST00000403716;ENST00000234115;ENST00000538982;ENST00000409612;ENST00000409279	.|.	.|.	.|.	4.81|4.81	3.91|3.91	0.45181|0.45181	.|.	.|.	.|.	.|.	.|.	T|T	0.61236|0.61236	0.2331|0.2331	M|M	0.76328|0.76328	2.33|2.33	0.43574|0.43574	D|D	0.995904|0.995904	B|B;B;B;B	0.30482|0.21905	0.281|0.036;0.061;0.036;0.062	B|B;B;B;B	0.32624|0.26094	0.149|0.03;0.066;0.03;0.03	T|T	0.56757|0.56757	-0.7926|-0.7926	8|8	0.17369|0.25106	T|T	0.5|0.35	.|.	12.1112|12.1112	0.53840|0.53840	0.0:0.0:0.8269:0.1731|0.0:0.0:0.8269:0.1731	.|.	114|158;158;159;167	B4DZ66|Q53FF1;Q96CS7-3;Q96CS7;B8ZZN1	.|.;.;PKHB2_HUMAN;.	N|L	114|167;159;158;111;159;159	.|.	ENSP00000389629:K114N|ENSP00000234115:V158L	K|V	+|+	3|1	2|0	PLEKHB2|PLEKHB2	131614261|131614261	0.999000|0.999000	0.42202|0.42202	0.982000|0.982000	0.44146|0.44146	0.843000|0.843000	0.47879|0.47879	1.275000|1.275000	0.33144|0.33144	0.993000|0.993000	0.38866|0.38866	0.650000|0.650000	0.86243|0.86243	AAG|GTT	.	G|1.000;C|0.000	0.000	weak		0.512	PLEKHB2-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331304.2	NM_017958		C	131897791	G	C	131897791	3	2	176	1	0	0	0	0	1	0	0	0	12072	1029	36	4	497	4	PLEKHB2	2	131897791	Missense_Mutation	SNP	G	TCGA-G7-7501-01A-11D-2201-08		131897791	111301582	6	10294											
TTN	7273	hgsc.bcm.edu	37	chr2	179567316	179567316	+	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	ggcatcatcaaaggacacttCacactcaaaggtggcagact	14	7	9	11	0	4	1	4	0	0	1	4	2	4	2	0	4	0	2	0	4	2	1			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr2:179567316C>A	ENST00000591111.1	-	105	29571	c.29347G>T	c.(29347-29349)Gaa>Taa	p.E9783*	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Nonsense_Mutation_p.E10100*|TTN-AS1_ENST00000431752.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Nonsense_Mutation_p.E8856*			Q8WZ42	TITIN_HUMAN	titin	13861	Ig-like 79.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAGGACACTTCACACTCAAAG	0.438																																					p.E10100X		Atlas-SNP	.											.	TTN	18412	.	0			c.G30298T						PASS	.						177	174	175					2																	179567316		2019	4185	6204	SO:0001587	stop_gained	7273	exon107			ACACTTCACACTC	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.29347G>T	chr2.hg19:g.179567316C>A	ENSP00000465570:p.Glu9783*	140.0	0.0	.		89.0	43.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	60	45.686615	0.99987	.	.	ENSG00000155657	ENST00000342992	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.8805	0.96895	0.0:1.0:0.0:0.0	.	.	.	.	X	8856	.	ENSP00000343764:E8856X	E	-	1	0	TTN	179275561	1.000000	0.71417	0.986000	0.45419	0.981000	0.71138	7.818000	0.86416	2.704000	0.92352	0.655000	0.94253	GAA	.	.	.	none		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179567316	C	A	179567316	4	1	176	1	0	0	0	0	0	1	0	0	16747	835	29	4	74255	4	TTN	2	179567316	Nonsense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08	47669525	179567316	63632057	7	10295											
HSPE1	3336	hgsc.bcm.edu	37	chr2	198365946	198365946	+	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	aacagtagtcgctgttggatCgggttctaaaggaaaggtaa	13	10	13	5	2	1	0	0	0	1	0	3	2	1	2	0	4	1	5	0	4	6	5			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr2:198365946C>G	ENST00000233893.5	+	2	595	c.152C>G	c.(151-153)tCg>tGg	p.S51W	HSPE1_ENST00000465573.1_Intron|HSPE1_ENST00000409468.1_Missense_Mutation_p.S51W|HSPD1_ENST00000345042.2_5'Flank|HSPD1_ENST00000388968.3_5'Flank|HSPE1_ENST00000409729.1_Intron|HSPD1_ENST00000544407.1_5'Flank|HSPE1-MOB4_ENST00000604458.1_Missense_Mutation_p.S51W	NM_002157.2	NP_002148.1	P61604	CH10_HUMAN	heat shock 10kDa protein 1	51					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|osteoblast differentiation (GO:0001649)|protein folding (GO:0006457)|response to unfolded protein (GO:0006986)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			lung(1)	1			Epithelial(96;0.225)			GCTGTTGGATCGGGTTCTAAA	0.408																																					p.S51W		Atlas-SNP	.											.	HSPE1	2	.	0			c.C152G						PASS	.						53	55	54					2																	198365946		2203	4300	6503	SO:0001583	missense	3336	exon2			TTGGATCGGGTTC	AF109872	CCDS2320.1	2q33.1	2013-10-17	2013-10-17		ENSG00000115541	ENSG00000115541		"Heat Shock Proteins / Chaperonins"	5269	protein-coding gene	gene with protein product	"chaperonin 10"	600141	"heat shock 10kD protein 1 (chaperonin 10)"			7914093, 7698325	Standard	NM_002157		Approved	CPN10, GROES		P61604	OTTHUMG00000132749	ENST00000233893.5:c.152C>G	chr2.hg19:g.198365946C>G	ENSP00000233893:p.Ser51Trp	38.0	0.0	.		23.0	10.0	.	NM_002157	O95421|Q04984|Q53X54|Q9UDH0	Missense_Mutation	SNP	ENST00000233893.5	hg19	CCDS2320.1	.	.	.	.	.	.	.	.	.	.	C	18.85	3.710542	0.68730	.	.	ENSG00000115541	ENST00000233893;ENST00000409468	.	.	.	5.37	5.37	0.77165	GroES-like (1);	0.221653	0.39475	U	0.001344	T	0.80813	0.4695	M	0.89214	3.015	0.58432	D	0.999999	D	0.60575	0.988	D	0.65573	0.936	D	0.84237	0.0470	9	0.72032	D	0.01	-11.1967	14.0187	0.64541	0.1511:0.8489:0.0:0.0	.	51	P61604	CH10_HUMAN	W	51	.	ENSP00000233893:S51W	S	+	2	0	HSPE1	198074191	0.720000	0.27996	0.637000	0.29366	0.705000	0.40729	3.596000	0.54024	2.530000	0.85305	0.557000	0.71058	TCG	.	.	.	none		0.408	HSPE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256112.1	NM_002157		G	198365946	C	G	198365946	3	3	176	1	0	0	0	0	1	0	0	0	7436	893	31	4	158	4	HSPE1	2	198365946	Missense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08	18798630	198365946	44833427	8	10296											
DNASE1L3	1776	hgsc.bcm.edu	37	chr3	58179114	58179114	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctggaagtcaaaaacacTgtttgacttgggaacaacag	14	11	9	7	0	2	1	1	1	1	0	2	3	2	3	0	2	3	1	0	2	5	3			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr3:58179114T>C	ENST00000394549.2	-	7	1073	c.757A>G	c.(757-759)Agt>Ggt	p.S253G	DNASE1L3_ENST00000486455.1_Missense_Mutation_p.S223G|DNASE1L3_ENST00000483681.1_Missense_Mutation_p.S253G|DNASE1L3_ENST00000318316.3_Missense_Mutation_p.S253G	NM_004944.3	NP_004935.1	Q13609	DNSL3_HUMAN	deoxyribonuclease I-like 3	253					apoptotic DNA fragmentation (GO:0006309)|developmental programmed cell death (GO:0010623)|DNA metabolic process (GO:0006259)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)|deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)			breast(2)|large_intestine(4)|lung(6)	12				BRCA - Breast invasive adenocarcinoma(55;0.00021)|KIRC - Kidney renal clear cell carcinoma(284;0.0445)|Kidney(284;0.0556)|OV - Ovarian serous cystadenocarcinoma(275;0.202)		TCAAAAACACTGTTTGACTTG	0.433																																					p.S253G	Esophageal Squamous(96;1069 1424 4841 43466 52325)	Atlas-SNP	.											.	DNASE1L3	36	.	0			c.A757G						PASS	.						111	99	103					3																	58179114		2203	4300	6503	SO:0001583	missense	1776	exon7			AAACACTGTTTGA	AF047354	CCDS2886.1, CCDS58836.1	3p14.3	2008-05-15			ENSG00000163687	ENSG00000163687			2959	protein-coding gene	gene with protein product	"DNase gamma"	602244				9205125, 9714828, 14646506	Standard	NM_004944		Approved	DNAS1L3, LSD	uc003djo.2	Q13609	OTTHUMG00000159153	ENST00000394549.2:c.757A>G	chr3.hg19:g.58179114T>C	ENSP00000378053:p.Ser253Gly	119.0	0.0	.		58.0	20.0	.	NM_004944	B2R8B1|B7Z707|O75803	Missense_Mutation	SNP	ENST00000394549.2	hg19	CCDS2886.1	.	.	.	.	.	.	.	.	.	.	T	10.36	1.327576	0.24080	.	.	ENSG00000163687	ENST00000486455;ENST00000450710;ENST00000318316;ENST00000483681;ENST00000394549	T;T;T;T	0.54071	0.59;0.59;0.59;0.59	5.7	-7.58	0.01313	Endonuclease/exonuclease/phosphatase (2);	1.174290	0.05847	N	0.620530	T	0.30324	0.0761	N	0.17723	0.515	0.09310	N	1	B;B;B	0.10296	0.001;0.003;0.001	B;B;B	0.09377	0.003;0.004;0.003	T	0.17684	-1.0361	10	0.21540	T	0.41	.	8.2569	0.31763	0.0:0.3088:0.2525:0.4387	.	223;253;253	B7Z707;E9PES0;Q13609	.;.;DNSL3_HUMAN	G	223;253;253;253;253	ENSP00000419052:S223G;ENSP00000316193:S253G;ENSP00000417047:S253G;ENSP00000378053:S253G	ENSP00000316193:S253G	S	-	1	0	DNASE1L3	58154154	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.785000	0.04628	-1.315000	0.02297	-0.290000	0.09829	AGT	.	.	.	none		0.433	DNASE1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353533.1	NM_004944		C	58179114	T	C	58179114	3	2	176	1	0	0	0	0	1	0	0	0	4665	1580	55	3	168	3	DNASE1L3	3	58179114	Missense_Mutation	SNP	T	TCGA-G7-7501-01A-11D-2201-08		58179114	139843316	9	10297											
HERC3	8916	hgsc.bcm.edu	37	chr4	89575198	89575198	+	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	tttaatttattctagatcgaGaatctccatgccatgtaaaa	14	15	5	7	1	2	2	0	0	2	2	4	3	2	2	2	0	1	1	2	0	6	7	rs35418561		TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr4:89575198G>T	ENST00000402738.1	+	7	930	c.691G>T	c.(691-693)Gaa>Taa	p.E231*	HERC3_ENST00000407637.1_Nonsense_Mutation_p.E231*|HERC3_ENST00000264345.3_Nonsense_Mutation_p.E231*	NM_001271602.1|NM_014606.1	NP_001258531.1|NP_055421.1	Q15034	HERC3_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 3	231					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|prostate(2)|skin(2)	45				OV - Ovarian serous cystadenocarcinoma(123;0.000319)		TCTAGATCGAGAATCTCCATG	0.368																																					p.E231X		Atlas-SNP	.											.	HERC3	82	.	0			c.G691T						PASS	.						87	88	88					4																	89575198		2203	4300	6503	SO:0001587	stop_gained	8916	exon7			GATCGAGAATCTC	D25215	CCDS34028.1	4q21	2012-02-23	2012-02-23		ENSG00000138641	ENSG00000138641			4876	protein-coding gene	gene with protein product		605200	"hect domain and RLD 3"			10702688	Standard	NM_014606		Approved	KIAA0032	uc003hrw.2	Q15034	OTTHUMG00000150436	ENST00000402738.1:c.691G>T	chr4.hg19:g.89575198G>T	ENSP00000385684:p.Glu231*	94.0	0.0	.		36.0	26.0	.	NM_014606	A8K1S5|Q8IXX3	Nonsense_Mutation	SNP	ENST00000402738.1	hg19	CCDS34028.1	.	.	.	.	.	.	.	.	.	.	G	36	5.963882	0.97151	.	.	ENSG00000138641	ENST00000402738;ENST00000407637;ENST00000264345	.	.	.	5.12	4.24	0.50183	.	0.168861	0.52532	D	0.000072	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12103	T	0.63	.	10.4986	0.44791	0.078:0.1468:0.7752:0.0	.	.	.	.	X	231	.	ENSP00000264345:E231X	E	+	1	0	HERC3	89794221	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	5.005000	0.63972	2.664000	0.90586	0.655000	0.94253	GAA	.	.	.	none		0.368	HERC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318081.2	NM_014606		T	89575198	G	T	89575198	4	4	176	1	0	0	0	0	0	1	0	0	7066	943	33	4	709	4	HERC3	4	89575198	Nonsense_Mutation	SNP	G	TCGA-G7-7501-01A-11D-2201-08		89575198	101579078	10	10298											
MYOZ3	91977	hgsc.bcm.edu	37	chr5	150050078	150050078	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctgggcaagaagctgagcGtgccccaggacctgatgatg	10	6	14	11	1	0	4	0	3	0	1	0	5	0	5	4	2	3	2	4	2	2	0	rs370373786		TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr5:150050078G>A	ENST00000297130.4	+	3	293	c.94G>A	c.(94-96)Gtg>Atg	p.V32M	MYOZ3_ENST00000517768.1_Missense_Mutation_p.V32M|CTC-345K18.2_ENST00000511626.2_RNA|MYOZ3_ENST00000520112.1_5'Flank	NM_001122853.2|NM_133371.4	NP_001116325.1|NP_588612.2			myozenin 3											large_intestine(2)|lung(1)|skin(2)	5		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GAAGCTGAGCGTGCCCCAGGA	0.612																																					p.V32M		Atlas-SNP	.											.	MYOZ3	21	.	0			c.G94A						PASS	.	G	MET/VAL,MET/VAL	1,4405	2.1+/-5.4	0,1,2202	50	39	43		94,94	2.9	1	5		43	0,8600		0,0,4300	no	missense,missense	MYOZ3	NM_001122853.1,NM_133371.3	21,21	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	32/252,32/252	150050078	1,13005	2203	4300	6503	SO:0001583	missense	91977	exon3			CTGAGCGTGCCCC	AF480443	CCDS4309.1	5q33.2	2008-07-18			ENSG00000164591	ENSG00000164591			18565	protein-coding gene	gene with protein product	"calsarcin 3", "FATZ related protein 3"	610735				11842093	Standard	NM_001122853		Approved	CS-3, CS3, FRP3	uc003lsr.3	Q8TDC0	OTTHUMG00000130077	ENST00000297130.4:c.94G>A	chr5.hg19:g.150050078G>A	ENSP00000297130:p.Val32Met	40.0	0.0	.		23.0	16.0	.	NM_001122853		Missense_Mutation	SNP	ENST00000297130.4	hg19	CCDS4309.1	.	.	.	.	.	.	.	.	.	.	G	15.40	2.820957	0.50633	2.27E-4	0.0	ENSG00000164591	ENST00000517768;ENST00000297130	T;T	0.70516	-0.49;-0.49	4.74	2.91	0.33838	.	0.542979	0.16126	N	0.228410	T	0.67268	0.2875	M	0.75777	2.31	0.80722	D	1	P	0.51653	0.947	B	0.41946	0.371	T	0.69771	-0.5055	10	0.72032	D	0.01	-16.886	7.231	0.26043	0.277:0.0:0.723:0.0	.	32	Q8TDC0	MYOZ3_HUMAN	M	32	ENSP00000428815:V32M;ENSP00000297130:V32M	ENSP00000297130:V32M	V	+	1	0	MYOZ3	150030271	0.186000	0.23225	0.968000	0.41197	0.985000	0.73830	0.833000	0.27504	1.116000	0.41820	0.555000	0.69702	GTG	.	.	.	weak		0.612	MYOZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252369.1	NM_001122853		A	150050078	G	A	150050078	3	1	176	1	0	0	0	0	1	0	0	0	10104	1145	40	1	100	1	MYOZ3	5	150050078	Missense_Mutation	SNP	G	TCGA-G7-7501-01A-11D-2201-08		150050078	30865182	11	10299											
HLA-DPB1	3115	hgsc.bcm.edu	37	chr6	33048613	33048613	+	Frame_Shift_Del	DEL	A	A	-																															ggcctgctgcggagtactggAacagccagaaggacatcctg																								rs41550319		TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr6:33048613delA	ENST00000418931.2	+	2	381	c.265delA	c.(265-267)aacfs	p.N89fs	HLA-DPB1_ENST00000471184.1_3'UTR|HLA-DPB1_ENST00000535465.1_Frame_Shift_Del_p.N89fs|HLA-DPA1_ENST00000419277.1_5'Flank	NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	89	Beta-1.		N -> H (in allele DPB1*02:03; dbSNP:rs41550319).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						GGAGTACTGGAACAGCCAGAA	0.657																																					p.W88X		Atlas-INDEL	.											.	HLA-DPB1	28	.	0			c.264delG						PASS	.						54	55	54					6																	33048613		1511	2709	4220	SO:0001589	frameshift_variant	3115	exon2			.		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.265delA	chr6.hg19:g.33048613delA	ENSP00000408146:p.Asn89fs	91.0	0.0	0		56.0	12.0	0.214286	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Frame_Shift_Del	DEL	ENST00000418931.2	hg19	CCDS4765.1																																																																																			.	.	.	none		0.657	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121		-	33048613	A	-	33048613	7	5	176	1	0	1	0	1	0	0	0	0	7210	246	9	0	271	0	HLA-DPB1	6	33048613	Frame_Shift_Del	DEL	A	TCGA-G7-7501-01A-11D-2201-08		33048613	138066454	12	10300											
KCNK5	8645	hgsc.bcm.edu	37	chr6	39159334	39159334	+	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	ggctgtgctccccttcacctGcagggccttccgggagtgtg	3	10	14	14	1	1	0	1	0	0	0	3	1	3	1	5	3	2	3	5	3	0	2			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr6:39159334G>A	ENST00000359534.3	-	5	1170	c.832C>T	c.(832-834)Cag>Tag	p.Q278*		NM_003740.3	NP_003731.1	O95279	KCNK5_HUMAN	potassium channel, subfamily K, member 5	278					excretion (GO:0007588)|potassium ion transport (GO:0006813)	integral component of plasma membrane (GO:0005887)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(4)|skin(3)	19						CCCTTCACCTGCAGGGCCTTC	0.547																																					p.Q278X		Atlas-SNP	.											.	KCNK5	57	.	0			c.C832T						PASS	.						100	105	104					6																	39159334		2203	4300	6503	SO:0001587	stop_gained	8645	exon5			TCACCTGCAGGGC	AF084830	CCDS4841.1	6p21	2012-03-07			ENSG00000164626	ENSG00000164626		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6280	protein-coding gene	gene with protein product		603493				9812978, 16382106	Standard	XM_005249456		Approved	K2p5.1, TASK-2	uc003oon.3	O95279	OTTHUMG00000014642	ENST00000359534.3:c.832C>T	chr6.hg19:g.39159334G>A	ENSP00000352527:p.Gln278*	252.0	0.0	.		150.0	47.0	.	NM_003740	B2RAQ6|B5TJL2|Q5VV76	Nonsense_Mutation	SNP	ENST00000359534.3	hg19	CCDS4841.1	.	.	.	.	.	.	.	.	.	.	G	35	5.470988	0.96274	.	.	ENSG00000164626	ENST00000359534	.	.	.	5.35	4.47	0.54385	.	1.406490	0.05067	N	0.481046	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	.	15.979	0.80091	0.0:0.1351:0.8649:0.0	.	.	.	.	X	278	.	ENSP00000352527:Q278X	Q	-	1	0	KCNK5	39267312	0.997000	0.39634	0.848000	0.33437	0.146000	0.21551	4.384000	0.59607	1.233000	0.43693	0.561000	0.74099	CAG	.	.	.	none		0.547	KCNK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040449.1	NM_003740		A	39159334	G	A	39159334	4	1	176	1	0	0	0	0	0	1	0	0	8076	1328	46	2	671	2	KCNK5	6	39159334	Nonsense_Mutation	SNP	G	TCGA-G7-7501-01A-11D-2201-08	6110721	39159334	131955733	13	10301											
C6orf150	115004	hgsc.bcm.edu	37	chr6	74135070	74135070	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agattgaattcaggaataaaAtaattctcaagtttttctgt	15	16	6	4	0	3	2	2	1	2	1	4	3	3	3	0	1	0	1	0	1	6	7			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr6:74135070A>G	ENST00000370315.3	-	5	1543	c.1449T>C	c.(1447-1449)taT>taC	p.Y483Y	MB21D1_ENST00000370318.1_Intron	NM_138441.2	NP_612450.2	Q8N884	CGAS_HUMAN	Mab-21 domain containing 1	483					activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|cyclic nucleotide biosynthetic process (GO:0009190)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of type I interferon production (GO:0032481)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cyclic-GMP-AMP synthase activity (GO:0061501)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|lung(1)	6						CAGGAATAAAATAATTCTCAA	0.373																																					p.Y483Y		Atlas-SNP	.											.	MB21D1	33	.	0			c.T1449C						PASS	.						54	54	54					6																	74135070		2203	4300	6503	SO:0001819	synonymous_variant	115004	exon5			AATAAAATAATTC	BC012928	CCDS4978.1	6q13	2011-02-23	2011-02-23	2011-02-23	ENSG00000164430	ENSG00000164430			21367	protein-coding gene	gene with protein product		613973	"chromosome 6 open reading frame 150"	C6orf150			Standard	NM_138441		Approved		uc003pgx.1	Q8N884	OTTHUMG00000015034	ENST00000370315.3:c.1449T>C	chr6.hg19:g.74135070A>G		73.0	0.0	.		39.0	17.0	.	NM_138441	L0L2J9|Q14CV6|Q32NC9|Q5SWL0|Q5SWL1|Q96E45	Silent	SNP	ENST00000370315.3	hg19	CCDS4978.1																																																																																			.	.	.	none		0.373	MB21D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041221.5	NM_138441		G	74135070	A	G	74135070	2	3	176	1	0	0	0	0	0	0	0	1	2339	108	4	3		3	C6orf150	6	74135070	Silent	SNP	A	TCGA-G7-7501-01A-11D-2201-08	34975736	74135070	96979997	14	10302											
TBP	6908	hgsc.bcm.edu	37	chr6	170871004	170871004	+	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	gagcaacaaaggcagcagcaGcaacaacaacagcagcagca	19	0	10	12	0	0	0	0	0	0	0	0	1	0	0	0	1	11	8	0	1	5	0			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr6:170871004G>A	ENST00000392092.2	+	3	459	c.180G>A	c.(178-180)caG>caA	p.Q60Q	TBP_ENST00000540980.1_Silent_p.Q40Q|TBP_ENST00000230354.6_Silent_p.Q60Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	60	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		Ggcagcagcagcaacaacaac	0.542																																					p.Q60Q		Atlas-SNP	.											.	TBP	58	.	0			c.G180A						PASS	.						43	45	44					6																	170871004		2203	4300	6503	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAACAA	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"General transcription factors"	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.180G>A	chr6.hg19:g.170871004G>A		94.0	0.0	.		71.0	5.0	.	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	hg19	CCDS5315.1																																																																																			.	.	.	none		0.542	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		A	170871004	G	A	170871004	2	1	176	1	0	0	0	0	0	0	0	1	15656	962	34	2		2	TBP	6	170871004	Silent	SNP	G	TCGA-G7-7501-01A-11D-2201-08	96735934	170871004	244063	15	10303											
C7orf59	389541	hgsc.bcm.edu	37	chr7	99746597	99746598	+	Start_Codon_Ins	INS	-	-	G																															ccagcaccgaagactgcgatINSggtgagtgaggacgcatgcg																										TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr7:99746597_99746598insG	ENST00000341942.5	+	0	68_69				LAMTOR4_ENST00000441173.1_Start_Codon_Ins	NM_001008395.2	NP_001008396.1	Q0VGL1	LTOR4_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 4						cellular response to amino acid stimulus (GO:0071230)|positive regulation of GTPase activity (GO:0043547)|positive regulation of TOR signaling (GO:0032008)|protein localization to lysosome (GO:0061462)|regulation of cell size (GO:0008361)	intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|Ragulator complex (GO:0071986)											AAGACTGCGATGGTGAGTGAGG	0.658																																					p.M1fs		Atlas-INDEL	.											.	.	.	.	0			c.2_3insG						PASS	.																																			SO:0001582	initiator_codon_variant	389541	exon1			.		CCDS34702.1	7q22	2012-09-24	2012-09-24	2012-09-24	ENSG00000188186	ENSG00000188186			33772	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 59"	C7orf59		22980980	Standard	NM_001008395		Approved		uc003utq.2	Q0VGL1	OTTHUMG00000154854	ENST00000341942.5:c.3dupG	chr7.hg19:g.99746599_99746599dupG		132.0	0.0	0		86.0	23.0	0.267442	NM_001008395		Frame_Shift_Ins	INS	ENST00000341942.5	hg19	CCDS34702.1																																																																																			.	.	.	none		0.658	LAMTOR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337373.2	NM_001008395		G	99746598	-	G	99746597	7	5	176	1	0	1	1	0	0	0	0	0	2408	1478	51	0	4	0	C7orf59	7	99746597	Start_Codon_Ins	INS	-	TCGA-G7-7501-01A-11D-2201-08		99746597	59392066	16	10304											
C7orf58	79974	hgsc.bcm.edu	37	chr7	120629777	120629777	+	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	ctcttctaccagactctgacCctccgagggtcgaggaagct	8	9	10	14	2	3	2	0	1	3	1	5	5	4	3	3	2	2	1	3	2	2	2			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr7:120629777C>G	ENST00000310396.5	+	2	569	c.102C>G	c.(100-102)acC>acG	p.T34T	CPED1_ENST00000450913.2_Silent_p.T34T|CPED1_ENST00000340646.5_Silent_p.T34T|CPED1_ENST00000495036.1_3'UTR	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	34						endoplasmic reticulum (GO:0005783)											AGACTCTGACCCTCCGAGGGT	0.587																																					p.T34T		Atlas-SNP	.											.	.	.	.	0			c.C102G						PASS	.						112	107	109					7																	120629777		2203	4300	6503	SO:0001819	synonymous_variant	79974	exon1			TCTGACCCTCCGA		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.102C>G	chr7.hg19:g.120629777C>G		146.0	0.0	.		86.0	36.0	.	NM_001105533	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Silent	SNP	ENST00000310396.5	hg19	CCDS34739.1																																																																																			.	.	.	none		0.587	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913		G	120629777	C	G	120629777	2	3	176	1	0	0	0	0	0	0	0	1	2407	610	22	4		4	C7orf58	7	120629777	Silent	SNP	C	TCGA-G7-7501-01A-11D-2201-08	20883180	120629777	38508886	17	10305											
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121679512	121679512	+	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	acattttcttttgcagagaaAatgtgatcagtactggcctg	11	14	9	7	0	2	2	1	1	1	1	2	3	2	2	1	1	2	2	1	1	3	5			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr7:121679512A>T	ENST00000393386.2	+	20	5918	c.5507A>T	c.(5506-5508)aAa>aTa	p.K1836I	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.K969I	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1836	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						TTGCAGAGAAAATGTGATCAG	0.423																																					p.K1836I		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.A5507T						PASS	.						84	83	84					7																	121679512		2203	4300	6503	SO:0001583	missense	5803	exon20			AGAGAAAATGTGA	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.5507A>T	chr7.hg19:g.121679512A>T	ENSP00000377047:p.Lys1836Ile	82.0	0.0	.		65.0	35.0	.	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	hg19	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	A	29.2	4.982726	0.93044	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	T;T	0.21361	2.01;2.01	5.88	5.88	0.94601	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	T	0.61553	0.2356	H	0.96460	3.825	0.80722	D	1	D;P;P	0.76494	0.999;0.503;0.674	D;P;P	0.85130	0.997;0.843;0.802	T	0.75169	-0.3412	10	0.87932	D	0	.	16.3015	0.82820	1.0:0.0:0.0:0.0	.	975;969;1836	P23471-2;C9JFM0;P23471	.;.;PTPRZ_HUMAN	I	1836;969	ENSP00000377047:K1836I;ENSP00000410000:K969I	ENSP00000377047:K1836I	K	+	2	0	PTPRZ1	121466748	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	6.195000	0.72088	2.239000	0.73571	0.533000	0.62120	AAA	.	.	.	none		0.423	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		T	121679512	A	T	121679512	3	4	176	1	0	0	0	0	1	0	0	0	12827	14	1	5	5585	5	PTPRZ1	7	121679512	Missense_Mutation	SNP	A	TCGA-G7-7501-01A-11D-2201-08	1049735	121679512	37459151	18	10306											
SF3B2	10992	hgsc.bcm.edu	37	chr11	65829382	65829382	+	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	aatgcccacaaggtccctccCccatggctgattgccatgca	9	8	8	16	0	0	1	0	1	0	0	2	1	2	1	5	2	3	2	5	2	2	1	rs559206953		TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr11:65829382C>A	ENST00000322535.6	+	16	1939	c.1890C>A	c.(1888-1890)ccC>ccA	p.P630P	SF3B2_ENST00000528302.1_Silent_p.P613P	NM_006842.2	NP_006833.2	Q13435	SF3B2_HUMAN	splicing factor 3b, subunit 2, 145kDa	630					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	41						AGGTCCCTCCCCCATGGCTGA	0.562																																					p.P630P		Atlas-SNP	.											.	SF3B2	85	.	0			c.C1890A						PASS	.						115	109	111					11																	65829382		2201	4295	6496	SO:0001819	synonymous_variant	10992	exon16			CCCTCCCCCATGG	U41371	CCDS31612.1	11q13	2010-07-21	2002-08-29		ENSG00000087365	ENSG00000087365			10769	protein-coding gene	gene with protein product		605591	"splicing factor 3b, subunit 2, 145kD"			8566756	Standard	XM_005273726		Approved	SAP145, SF3b1, Cus1, SF3b145	uc001ogy.1	Q13435	OTTHUMG00000166751	ENST00000322535.6:c.1890C>A	chr11.hg19:g.65829382C>A		64.0	0.0	.		38.0	20.0	.	NM_006842	A8K485|B4DT19|Q7L4T5|Q7Z627|Q969K1|Q96CM6|Q9BWD2	Silent	SNP	ENST00000322535.6	hg19	CCDS31612.1	.	.	.	.	.	.	.	.	.	.	C	6.177	0.400770	0.11696	.	.	ENSG00000087365	ENST00000530981	.	.	.	5.8	-0.975	0.10289	.	0.105145	0.64402	D	0.000003	T	0.53916	0.1826	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51212	-0.8734	6	0.87932	D	0	-15.3896	2.3521	0.04286	0.1231:0.3008:0.3612:0.2149	.	.	.	.	H	51	.	ENSP00000436757:P51H	P	+	2	0	SF3B2	65585958	0.832000	0.29368	0.923000	0.36655	0.530000	0.34684	-0.126000	0.10563	-0.166000	0.10890	0.650000	0.86243	CCC	.	.	.	none		0.562	SF3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391352.2			A	65829382	C	A	65829382	2	1	176	1	0	0	0	0	0	0	0	1	14164	610	22	4		4	SF3B2	11	65829382	Silent	SNP	C	TCGA-G7-7501-01A-11D-2201-08		65829382	69177134	19	10307											
ARAP1	116985	hgsc.bcm.edu	37	chr11	72406598	72406598	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccttcacctgggtcccacTggcagtgccagccacgcgca	7	6	11	17	2	1	0	1	0	0	0	2	0	2	0	5	2	3	2	5	2	0	1			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr11:72406598T>C	ENST00000393609.3	-	25	3698	c.3496A>G	c.(3496-3498)Agt>Ggt	p.S1166G	ARAP1_ENST00000393605.3_Missense_Mutation_p.S926G|ARAP1_ENST00000359373.5_Missense_Mutation_p.S1166G|ARAP1_ENST00000495878.1_5'UTR|ARAP1-AS1_ENST00000542022.1_RNA|ARAP1_ENST00000426523.1_Missense_Mutation_p.S921G|ARAP1_ENST00000334211.8_Missense_Mutation_p.S921G|ARAP1_ENST00000455638.2_Missense_Mutation_p.S1166G|ARAP1_ENST00000429686.1_Missense_Mutation_p.S860G	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	1166					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						TGGGTCCCACTGGCAGTGCCA	0.647																																					p.S1166G	Ovarian(102;1198 1520 13195 17913 37529)	Atlas-SNP	.											.	ARAP1	168	.	0			c.A3496G						PASS	.						46	44	45					11																	72406598		2200	4293	6493	SO:0001583	missense	116985	exon25			TCCCACTGGCAGT	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.3496A>G	chr11.hg19:g.72406598T>C	ENSP00000377233:p.Ser1166Gly	69.0	0.0	.		30.0	12.0	.	NM_001040118	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Missense_Mutation	SNP	ENST00000393609.3	hg19	CCDS41687.1	.	.	.	.	.	.	.	.	.	.	T	15.48	2.846485	0.51164	.	.	ENSG00000186635	ENST00000359373;ENST00000455638;ENST00000393605;ENST00000334211;ENST00000393609;ENST00000426523;ENST00000429686	T;T;T;T;T;T;T	0.07327	3.21;3.21;3.22;3.27;3.2;3.27;3.23	4.43	4.43	0.53597	.	0.300288	0.30419	N	0.009674	T	0.07007	0.0178	N	0.08118	0	0.34771	D	0.733746	B;P;P;B;B	0.50943	0.026;0.92;0.94;0.033;0.056	B;B;P;B;B	0.47402	0.01;0.422;0.546;0.028;0.031	T	0.35251	-0.9796	10	0.62326	D	0.03	.	12.6484	0.56748	0.0:0.0:0.0:1.0	.	921;860;1166;1166;926	E7EU13;B2RTS2;Q96P48-3;Q96P48;Q96P48-1	.;.;.;ARAP1_HUMAN;.	G	1166;1166;926;921;1166;921;860	ENSP00000352332:S1166G;ENSP00000390461:S1166G;ENSP00000377230:S926G;ENSP00000335506:S921G;ENSP00000377233:S1166G;ENSP00000392264:S921G;ENSP00000403127:S860G	ENSP00000335506:S921G	S	-	1	0	ARAP1	72084246	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.593000	0.67550	1.875000	0.54330	0.377000	0.23210	AGT	.	.	.	none		0.647	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118		C	72406598	T	C	72406598	3	2	176	1	0	0	0	0	1	0	0	0	838	1580	55	3	900	3	ARAP1	11	72406598	Missense_Mutation	SNP	T	TCGA-G7-7501-01A-11D-2201-08	6577216	72406598	62599918	20	10308											
CAPZA3	93661	hgsc.bcm.edu	37	chr12	18892035	18892035	+	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	gatactctctgacttgaatcTggtgatgtatcctaaattag	11	15	8	7	0	2	3	0	3	2	0	4	4	3	3	1	1	1	1	1	1	6	5			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr12:18892035T>A	ENST00000317658.3	+	1	991	c.833T>A	c.(832-834)cTg>cAg	p.L278Q	PLCZ1_ENST00000435379.1_5'Flank|PLCZ1_ENST00000539875.1_5'Flank|RP11-361I14.2_ENST00000536931.1_RNA|PLCZ1_ENST00000266505.7_5'Flank|PLCZ1_ENST00000447925.2_5'Flank	NM_033328.2	NP_201585.1	Q96KX2	CAZA3_HUMAN	capping protein (actin filament) muscle Z-line, alpha 3	278					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)				GACTTGAATCTGGTGATGTAT	0.393																																					p.L278Q		Atlas-SNP	.											.	CAPZA3	51	.	0			c.T833A						PASS	.						51	53	52					12																	18892035		2200	4287	6487	SO:0001583	missense	93661	exon1			TGAATCTGGTGAT	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.833T>A	chr12.hg19:g.18892035T>A	ENSP00000326238:p.Leu278Gln	135.0	0.0	.		83.0	35.0	.	NM_033328	Q969J0	Missense_Mutation	SNP	ENST00000317658.3	hg19	CCDS8681.1	.	.	.	.	.	.	.	.	.	.	T	15.41	2.824365	0.50739	.	.	ENSG00000177938	ENST00000317658	.	.	.	4.54	3.39	0.38822	.	0.000000	0.28088	U	0.016650	T	0.34395	0.0896	N	0.08118	0	0.33519	D	0.592145	P	0.49783	0.928	P	0.56612	0.802	T	0.50311	-0.8843	9	0.87932	D	0	-8.2508	7.6761	0.28486	0.0:0.0985:0.0:0.9015	.	278	Q96KX2	CAZA3_HUMAN	Q	278	.	ENSP00000326238:L278Q	L	+	2	0	CAPZA3	18783302	0.999000	0.42202	1.000000	0.80357	0.992000	0.81027	4.188000	0.58351	0.778000	0.33520	0.379000	0.24179	CTG	.	.	.	none		0.393	CAPZA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401902.1	NM_033328		A	18892035	T	A	18892035	3	1	176	1	0	0	0	0	1	0	0	0	2644	1580	55	5	835	5	CAPZA3	12	18892035	Missense_Mutation	SNP	T	TCGA-G7-7501-01A-11D-2201-08		18892035	114959860	21	10309											
MTUS2	23281	hgsc.bcm.edu	37	chr13	29600351	29600351	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcaaagaggtcaccacatctGttgctgaaaacaggaacctt	14	8	9	10	0	2	2	1	1	1	1	2	3	2	3	2	2	3	3	2	2	4	2			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr13:29600351G>A	ENST00000431530.3	+	1	1604	c.1546G>A	c.(1546-1548)Gtt>Att	p.V516I		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	506						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						CACCACATCTGTTGCTGAAAA	0.507																																					p.V516I		Atlas-SNP	.											.	MTUS2	279	.	0			c.G1546A						PASS	.						85	89	88					13																	29600351		1967	4155	6122	SO:0001583	missense	23281	exon1			ACATCTGTTGCTG	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.1546G>A	chr13.hg19:g.29600351G>A	ENSP00000392057:p.Val516Ile	79.0	0.0	.		56.0	25.0	.	NM_001033602	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Missense_Mutation	SNP	ENST00000431530.3	hg19	CCDS45022.1	.	.	.	.	.	.	.	.	.	.	g	11.63	1.695795	0.30052	.	.	ENSG00000132938	ENST00000431530	T	0.14266	2.52	5.39	1.52	0.23074	.	0.415389	0.20061	N	0.100094	T	0.10637	0.0260	L	0.51422	1.61	0.09310	N	1	B	0.23185	0.081	B	0.15484	0.013	T	0.25222	-1.0138	9	.	.	.	.	5.784	0.18322	0.2147:0.2602:0.5251:0.0	.	506	Q5JR59	MTUS2_HUMAN	I	516	ENSP00000392057:V516I	.	V	+	1	0	MTUS2	28498351	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.241000	0.18065	0.388000	0.25054	-0.175000	0.13238	GTT	.	.	.	none		0.507	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270		A	29600351	G	A	29600351	3	1	176	1	0	0	0	0	1	0	0	0	9973	1377	48	2	1548	2	MTUS2	13	29600351	Missense_Mutation	SNP	G	TCGA-G7-7501-01A-11D-2201-08		29600351	85569527	22	10310											
NBEA	26960	hgsc.bcm.edu	37	chr13	35733740	35733740	+	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	gaccttcccaatagtagtacAtcatttctctttgataaaat	13	15	4	9	0	2	1	1	1	1	0	4	2	3	1	2	0	1	2	2	0	6	7			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr13:35733740A>C	ENST00000400445.3	+	22	3966	c.3432A>C	c.(3430-3432)acA>acC	p.T1144T	NBEA_ENST00000310336.4_Silent_p.T1144T|NBEA_ENST00000379939.2_Silent_p.T1144T|NBEA_ENST00000540320.1_Silent_p.T1144T	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1144					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)		ATAGTAGTACATCATTTCTCT	0.333																																					p.T1144T		Atlas-SNP	.											.	NBEA	340	.	0			c.A3432C						PASS	.						48	44	45					13																	35733740		1841	4085	5926	SO:0001819	synonymous_variant	26960	exon22			TAGTACATCATTT	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.3432A>C	chr13.hg19:g.35733740A>C		33.0	0.0	.		34.0	5.0	.	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Silent	SNP	ENST00000400445.3	hg19	CCDS45026.1																																																																																			.	.	.	none		0.333	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		C	35733740	A	C	35733740	2	2	176	1	0	0	0	0	0	0	0	1	10194	204	8	5		5	NBEA	13	35733740	Silent	SNP	A	TCGA-G7-7501-01A-11D-2201-08	6133389	35733740	79436138	23	10311											
TXNDC16	57544	hgsc.bcm.edu	37	chr14	52907333	52907333	+	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	agtatttctgctttaccagtGtcaatattgcttttttatac	9	20	5	7	0	2	0	1	0	1	0	2	0	2	0	1	0	4	3	1	0	6	10			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr14:52907333G>C	ENST00000281741.4	-	19	2323	c.1952C>G	c.(1951-1953)aCa>aGa	p.T651R	TXNDC16_ENST00000554399.1_5'UTR	NM_001160047.1|NM_020784.2	NP_001153519.1|NP_065835.2	Q9P2K2	TXD16_HUMAN	thioredoxin domain containing 16	651					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)					CTTTACCAGTGTCAATATTGC	0.308																																					p.T651R		Atlas-SNP	.											.	TXNDC16	59	.	0			c.C1952G						PASS	.						81	77	78					14																	52907333		2203	4297	6500	SO:0001583	missense	57544	exon19			ACCAGTGTCAATA	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.1952C>G	chr14.hg19:g.52907333G>C	ENSP00000281741:p.Thr651Arg	44.0	0.0	.		39.0	4.0	.	NM_020784	A5PKW9|A7E260|A7MD07|B9EH67|Q9H9W7	Missense_Mutation	SNP	ENST00000281741.4	hg19	CCDS32083.1	.	.	.	.	.	.	.	.	.	.	G	0.336	-0.953307	0.02285	.	.	ENSG00000087301	ENST00000281741	T	0.28666	1.6	5.29	-2.77	0.05877	.	0.845265	0.10716	N	0.642273	T	0.10121	0.0248	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.29181	-1.0020	10	0.17832	T	0.49	-16.9969	0.0038	0.00000	0.287:0.2064:0.2084:0.2982	.	646;651	B7ZME4;Q9P2K2	.;TXD16_HUMAN	R	651	ENSP00000281741:T651R	ENSP00000281741:T651R	T	-	2	0	TXNDC16	51977083	0.000000	0.05858	0.000000	0.03702	0.143000	0.21401	-1.373000	0.02568	-0.539000	0.06273	-0.216000	0.12614	ACA	.	.	.	none		0.308	TXNDC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411681.1	XM_051699		C	52907333	G	C	52907333	3	2	176	1	0	0	0	0	1	0	0	0	16807	1377	48	4	537	4	TXNDC16	14	52907333	Missense_Mutation	SNP	G	TCGA-G7-7501-01A-11D-2201-08		52907333	54442207	24	10312											
MORF4L1	10933	hgsc.bcm.edu	37	chr15	79185887	79185887	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttgtcttcatagctctttTatcttcctgccaagaagaat	9	18	5	9	0	4	2	1	0	3	2	5	2	5	2	2	0	2	1	2	0	5	7			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr15:79185887T>C	ENST00000331268.5	+	10	868	c.664T>C	c.(664-666)Tat>Cat	p.Y222H	MORF4L1_ENST00000379535.4_Missense_Mutation_p.Y208H|MORF4L1_ENST00000426013.2_Missense_Mutation_p.Y183H|MORF4L1_ENST00000558746.1_Missense_Mutation_p.Y156H|MORF4L1_ENST00000559345.1_Missense_Mutation_p.Y95H|MORF4L1_ENST00000561171.1_Intron|MORF4L1_ENST00000558502.1_Missense_Mutation_p.Y95H	NM_206839.2	NP_996670.1	Q9UBU8	MO4L1_HUMAN	mortality factor 4 like 1	222	Interaction with RB1-1.|MRG. {ECO:0000255|PROSITE- ProRule:PRU00972}.|Sufficient for interaction with PHF12.|Sufficient for interaction with SIN3A.				cell proliferation (GO:0008283)|chromatin organization (GO:0006325)|double-strand break repair via homologous recombination (GO:0000724)|histone deacetylation (GO:0016575)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|Sin3 complex (GO:0016580)	chromatin binding (GO:0003682)|protein N-terminus binding (GO:0047485)			breast(1)|large_intestine(3)|lung(4)|prostate(1)|urinary_tract(1)	10						ATAGCTCTTTTATCTTCCTGC	0.299																																					p.Y222H		Atlas-SNP	.											.	MORF4L1	26	.	0			c.T664C						PASS	.						67	71	70					15																	79185887		2196	4288	6484	SO:0001583	missense	10933	exon10			CTCTTTTATCTTC	AF100615	CCDS10307.1, CCDS32304.1, CCDS58393.1	15q25.1	2009-07-13			ENSG00000185787	ENSG00000185787			16989	protein-coding gene	gene with protein product	"MORF-related gene on chromosome 15", "Esa1p-associated factor 3 homolog (S. cerevisiae)"	607303				8619474, 9110174	Standard	NM_006791		Approved	MRG15, MORFRG15, HsT17725, Eaf3, MEAF3	uc002bel.4	Q9UBU8	OTTHUMG00000143865	ENST00000331268.5:c.664T>C	chr15.hg19:g.79185887T>C	ENSP00000331310:p.Tyr222His	102.0	0.0	.		96.0	33.0	.	NM_206839	B4DKN6|B7Z6R1|D3DW88|O95899|Q5QTS1|Q6NVX8|Q86YT7|Q9HBP6|Q9NSW5	Missense_Mutation	SNP	ENST00000331268.5	hg19	CCDS10307.1	.	.	.	.	.	.	.	.	.	.	T	8.246	0.807960	0.16467	.	.	ENSG00000185787	ENST00000379535;ENST00000426013;ENST00000331268	T;T;T	0.09163	3.01;3.01;3.01	4.72	4.72	0.59763	.	0.113729	0.64402	D	0.000011	T	0.06005	0.0156	N	0.10874	0.06	0.39713	D	0.971363	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.27706	-1.0066	10	0.44086	T	0.13	-22.6224	8.8633	0.35272	0.1672:0.0:0.0:0.8328	.	183;222	Q9UBU8-2;Q9UBU8	.;MO4L1_HUMAN	H	208;183;222	ENSP00000368850:Y208H;ENSP00000408880:Y183H;ENSP00000331310:Y222H	ENSP00000331310:Y222H	Y	+	1	0	MORF4L1	76972942	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	4.625000	0.61262	1.902000	0.55061	0.459000	0.35465	TAT	.	.	.	none		0.299	MORF4L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000290131.4	NM_006791		C	79185887	T	C	79185887	3	2	176	1	0	0	0	0	1	0	0	0	9713	1754	61	3	702	3	MORF4L1	15	79185887	Missense_Mutation	SNP	T	TCGA-G7-7501-01A-11D-2201-08		79185887	23345505	25	10313											
FLYWCH2	114984	hgsc.bcm.edu	37	chr16	2946454	2946456	+	In_Frame_Del	DEL	CCC	CCC	-																															aggccctgggtcccgggatgCccctgcccgagcccagcgag																										TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	CCC	CCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr16:2946454_2946456delCCC	ENST00000396958.3	+	3	384_386	c.4_6delCCC	c.(4-6)cccdel	p.P2del	FLYWCH2_ENST00000293981.6_In_Frame_Del_p.P2del|FLYWCH2_ENST00000572006.1_In_Frame_Del_p.P2del	NM_001142500.1|NM_138439.2	NP_001135972.1|NP_612448.1	Q96CP2	FWCH2_HUMAN	FLYWCH family member 2	2							poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|lung(3)|ovary(1)|skin(1)	6						TCCCGGGATGCCCCTGCCCGAGC	0.67																																					p.1_2del		Atlas-INDEL	.											.	FLYWCH2	12	.	0			c.3_5del						PASS	.																																			SO:0001651	inframe_deletion	114984	exon3			.	BC014089	CCDS10482.1	16p13.3	2014-02-12	2007-06-21		ENSG00000162076	ENSG00000162076			25178	protein-coding gene	gene with protein product						12477932	Standard	NM_138439		Approved		uc010uwk.2	Q96CP2	OTTHUMG00000128962	ENST00000396958.3:c.4_6delCCC	chr16.hg19:g.2946454_2946456delCCC	ENSP00000380159:p.Pro2del	42.0	0.0	0		29.0	11.0	0.37931	NM_001142499		In_Frame_Del	DEL	ENST00000396958.3	hg19	CCDS10482.1																																																																																			.	.	.	none		0.67	FLYWCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250944.1	NM_138439		-	2946456	CCC	-	2946454	7	5	176	1	0	1	0	1	0	0	0	0	5955	739	26	0	6	0	FLYWCH2	16	2946454	In_Frame_Del	DEL	CCC	TCGA-G7-7501-01A-11D-2201-08		2946454	87408299	26	10314	97	3									
FLYWCH2	114984	hgsc.bcm.edu	37	chr16	2946458	2946458	+	Missense_Mutation	SNP	T	T	G																															cctgggtcccgggatgccccTgcccgagcccagcgagcagg																										TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr16:2946458T>G	ENST00000396958.3	+	3	388	c.8T>G	c.(7-9)cTg>cGg	p.L3R	FLYWCH2_ENST00000293981.6_Missense_Mutation_p.L3R|FLYWCH2_ENST00000572006.1_Missense_Mutation_p.L3R	NM_001142500.1|NM_138439.2	NP_001135972.1|NP_612448.1	Q96CP2	FWCH2_HUMAN	FLYWCH family member 2	3							poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|lung(3)|ovary(1)|skin(1)	6						GGGATGCCCCTGCCCGAGCCC	0.672																																					p.L3R		Atlas-SNP	.											.	FLYWCH2	12	.	0			c.T8G						PASS	.						28	35	32					16																	2946458		2197	4300	6497	SO:0001583	missense	114984	exon3			TGCCCCTGCCCGA	BC014089	CCDS10482.1	16p13.3	2014-02-12	2007-06-21		ENSG00000162076	ENSG00000162076			25178	protein-coding gene	gene with protein product						12477932	Standard	NM_138439		Approved		uc010uwk.2	Q96CP2	OTTHUMG00000128962	ENST00000396958.3:c.8T>G	chr16.hg19:g.2946458T>G	ENSP00000380159:p.Leu3Arg	45.0	0.0	.		33.0	11.0	.	NM_001142499		Missense_Mutation	SNP	ENST00000396958.3	hg19	CCDS10482.1	.	.	.	.	.	.	.	.	.	.	T	8.600	0.886580	0.17540	.	.	ENSG00000162076	ENST00000396958;ENST00000293981	.	.	.	3.6	2.48	0.30137	.	0.351696	0.16312	N	0.219949	T	0.25121	0.0610	L	0.32530	0.975	0.24368	N	0.994842	P	0.44044	0.825	B	0.39935	0.314	T	0.11470	-1.0586	9	0.87932	D	0	.	6.3825	0.21542	0.2172:0.0:0.0:0.7828	.	3	Q96CP2	FWCH2_HUMAN	R	3	.	ENSP00000293981:L3R	L	+	2	0	FLYWCH2	2886459	0.936000	0.31750	0.877000	0.34402	0.638000	0.38207	0.665000	0.25083	0.717000	0.32145	0.334000	0.21626	CTG	.	.	.	none		0.672	FLYWCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250944.1	NM_138439		G	2946458	T	G	2946458	3	3	176	1	0	0	0	0	1	0	0	0	5955	1580	55	5	10	5	FLYWCH2	16	2946458	Missense_Mutation	SNP	T	TCGA-G7-7501-01A-11D-2201-08	4	2946458	87408295	27	10315	97	3									
FLYWCH2	114984	hgsc.bcm.edu	37	chr16	2946461	2946461	+	Missense_Mutation	SNP	C	C	A																															gggtcccgggatgcccctgcCcgagcccagcgagcaggagg																										TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr16:2946461C>A	ENST00000396958.3	+	3	391	c.11C>A	c.(10-12)cCc>cAc	p.P4H	FLYWCH2_ENST00000293981.6_Missense_Mutation_p.P4H|FLYWCH2_ENST00000572006.1_Missense_Mutation_p.P4H	NM_001142500.1|NM_138439.2	NP_001135972.1|NP_612448.1	Q96CP2	FWCH2_HUMAN	FLYWCH family member 2	4							poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|lung(3)|ovary(1)|skin(1)	6						ATGCCCCTGCCCGAGCCCAGC	0.672																																					p.P4H		Atlas-SNP	.											.	FLYWCH2	12	.	0			c.C11A						PASS	.						28	36	33					16																	2946461		2197	4300	6497	SO:0001583	missense	114984	exon3			CCCTGCCCGAGCC	BC014089	CCDS10482.1	16p13.3	2014-02-12	2007-06-21		ENSG00000162076	ENSG00000162076			25178	protein-coding gene	gene with protein product						12477932	Standard	NM_138439		Approved		uc010uwk.2	Q96CP2	OTTHUMG00000128962	ENST00000396958.3:c.11C>A	chr16.hg19:g.2946461C>A	ENSP00000380159:p.Pro4His	49.0	0.0	.		40.0	14.0	.	NM_001142499		Missense_Mutation	SNP	ENST00000396958.3	hg19	CCDS10482.1	.	.	.	.	.	.	.	.	.	.	C	12.81	2.050286	0.36181	.	.	ENSG00000162076	ENST00000396958;ENST00000293981	.	.	.	3.6	3.6	0.41247	.	0.236227	0.22090	N	0.064771	T	0.45316	0.1336	L	0.34521	1.04	0.21697	N	0.999582	D	0.65815	0.995	P	0.57468	0.821	T	0.26121	-1.0112	9	0.87932	D	0	.	11.0322	0.47781	0.0:1.0:0.0:0.0	.	4	Q96CP2	FWCH2_HUMAN	H	4	.	ENSP00000293981:P4H	P	+	2	0	FLYWCH2	2886462	0.035000	0.19736	0.510000	0.27712	0.655000	0.38815	1.813000	0.38962	2.322000	0.78497	0.407000	0.27541	CCC	.	.	.	none		0.672	FLYWCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250944.1	NM_138439		A	2946461	C	A	2946461	3	1	176	1	0	0	0	0	1	0	0	0	5955	623	22	4	13	4	FLYWCH2	16	2946461	Missense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08	3	2946461	87408292	28	10316	97	3									
RBBP6	5930	hgsc.bcm.edu	37	chr16	24582258	24582258	+	Missense_Mutation	SNP	A	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	aaaaaacagatacaaagcgaActgtgattaaaacgatggaa	22	6	8	5	2	0	2	0	1	0	1	0	5	0	3	0	1	5	0	0	1	9	2			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr16:24582258A>C	ENST00000319715.4	+	18	4303	c.3871A>C	c.(3871-3873)Act>Cct	p.T1291P	RBBP6_ENST00000381039.3_Missense_Mutation_p.T451P|RBBP6_ENST00000348022.2_Missense_Mutation_p.T1257P	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1291					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)		TACAAAGCGAACTGTGATTAA	0.343																																					p.T1291P		Atlas-SNP	.											.	RBBP6	158	.	0			c.A3871C						PASS	.						44	43	43					16																	24582258		2197	4300	6497	SO:0001583	missense	5930	exon18			AAGCGAACTGTGA		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.3871A>C	chr16.hg19:g.24582258A>C	ENSP00000317872:p.Thr1291Pro	103.0	0.0	.		63.0	26.0	.	NM_006910	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Missense_Mutation	SNP	ENST00000319715.4	hg19	CCDS10621.1	.	.	.	.	.	.	.	.	.	.	A	16.89	3.248060	0.59103	.	.	ENSG00000122257	ENST00000381039;ENST00000319715;ENST00000348022	T;T;T	0.34667	1.35;1.46;1.36	5.6	5.6	0.85130	.	0.161807	0.42420	D	0.000707	T	0.49406	0.1555	L	0.32530	0.975	0.47621	D	0.999476	D;D;D	0.89917	1.0;0.999;0.998	D;D;D	0.87578	0.998;0.997;0.994	T	0.40794	-0.9544	10	0.35671	T	0.21	-16.9171	16.0786	0.80985	1.0:0.0:0.0:0.0	.	451;1257;1291	Q7Z6E9-4;Q7Z6E9-2;Q7Z6E9	.;.;RBBP6_HUMAN	P	451;1291;1257	ENSP00000370427:T451P;ENSP00000317872:T1291P;ENSP00000316291:T1257P	ENSP00000317872:T1291P	T	+	1	0	RBBP6	24489759	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.465000	0.80898	2.254000	0.74563	0.460000	0.39030	ACT	.	.	.	none		0.343	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910		C	24582258	A	C	24582258	3	2	176	1	0	0	0	0	1	0	0	0	13116	43	2	5	3995	5	RBBP6	16	24582258	Missense_Mutation	SNP	A	TCGA-G7-7501-01A-11D-2201-08	21635797	24582258	65772495	29	10317											
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-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr19:11558370G>A	ENST00000589838.1	+	10	966	c.966G>A	c.(964-966)gaG>gaA	p.E322E	PRKCSH_ENST00000412601.1_Silent_p.E322E|PRKCSH_ENST00000592741.1_Silent_p.E322E|PRKCSH_ENST00000587327.1_Silent_p.E322E|PRKCSH_ENST00000252455.2_Silent_p.E322E|PRKCSH_ENST00000591462.1_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	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	chr19.hg19:g.11558370G>A		19.0	2.0	.		13.0	4.0	.	NM_001001329	A8K318|Q96BU9|Q96D06|Q9P0W9	Silent	SNP	ENST00000589838.1	hg19	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	176	1	0	0	0	0	0	0	0	1	12526	991	35	2		2	PRKCSH	19	11558370	Silent	SNP	G	TCGA-G7-7501-01A-11D-2201-08		11558370	47570613	30	10318											
ZNF700	90592	hgsc.bcm.edu	37	chr19	12060128	12060128	+	Missense_Mutation	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	tgggaaagccttcagatctgCctcacagcttcgagtgcacg	9	9	11	12	2	3	1	2	0	1	1	4	3	3	2	2	1	4	2	2	1	1	2			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr19:12060128C>T	ENST00000254321.5	+	4	1432	c.1289C>T	c.(1288-1290)gCc>gTc	p.A430V	ZNF700_ENST00000482090.1_Missense_Mutation_p.A412V|CTD-2006C1.12_ENST00000586394.1_RNA|ZNF763_ENST00000590798.1_Intron|ZNF763_ENST00000591944.1_Intron|ZNF763_ENST00000538752.1_Intron	NM_001271848.1|NM_144566.1	NP_001258777.1|NP_653167.1	Q9H0M5	ZN700_HUMAN	zinc finger protein 700	430					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)		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						TTCAGATCTGCCTCACAGCTT	0.473																																					p.A433V		Atlas-SNP	.											.	ZNF700	81	.	0			c.C1298T						PASS	.						91	82	85					19																	12060128		2203	4300	6503	SO:0001583	missense	90592	exon4			GATCTGCCTCACA	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.1289C>T	chr19.hg19:g.12060128C>T	ENSP00000254321:p.Ala430Val	75.0	0.0	.		63.0	24.0	.	NM_001271848	B9EGU4	Missense_Mutation	SNP	ENST00000254321.5	hg19	CCDS32915.1	.	.	.	.	.	.	.	.	.	.	c	4.742	0.138029	0.09083	.	.	ENSG00000196757	ENST00000254321	T	0.34072	1.38	0.606	0.606	0.17559	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17450	0.0419	N	0.16708	0.43	0.09310	N	1	B	0.27910	0.193	B	0.21708	0.036	T	0.23868	-1.0176	9	0.17832	T	0.49	.	5.5675	0.17179	0.3178:0.6822:0.0:0.0	.	430	Q9H0M5	ZN700_HUMAN	V	430	ENSP00000254321:A430V	ENSP00000254321:A430V	A	+	2	0	ZNF700	11921128	0.000000	0.05858	0.001000	0.08648	0.090000	0.18270	-0.886000	0.04157	0.577000	0.29470	0.195000	0.17529	GCC	.	.	.	none		0.473	ZNF700-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344126.2	NM_144566		T	12060128	C	T	12060128	3	4	176	1	0	0	0	0	1	0	0	0	18116	739	26	2	1303	2	ZNF700	19	12060128	Missense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08	501758	12060128	47068855	31	10319											
PLEKHG2	64857	hgsc.bcm.edu	37	chr19	39914552	39914552	+	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	ccaatttgcctaagcaagacCttccgggcatccacgtttca	10	10	7	14	2	1	1	1	0	0	1	3	1	3	1	5	1	2	3	5	1	3	4			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr19:39914552C>G	ENST00000409794.3	+	19	3629	c.2779C>G	c.(2779-2781)Ctt>Gtt	p.L927V	PLEKHG2_ENST00000458508.2_Missense_Mutation_p.L868V|PLEKHG2_ENST00000409797.2_Intron|PLEKHG2_ENST00000425673.1_Missense_Mutation_p.L898V|PLEKHG2_ENST00000378550.1_Intron|CTB-60E11.4_ENST00000601124.1_lincRNA	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	927					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)			TAAGCAAGACCTTCCGGGCAT	0.577																																					p.L927V		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.C2779G						PASS	.						75	73	74					19																	39914552		2203	4300	6503	SO:0001583	missense	64857	exon19			CAAGACCTTCCGG	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.2779C>G	chr19.hg19:g.39914552C>G	ENSP00000386733:p.Leu927Val	108.0	0.0	.		80.0	32.0	.	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	hg19	CCDS33022.2	.	.	.	.	.	.	.	.	.	.	C	6.255	0.415175	0.11870	.	.	ENSG00000090924	ENST00000409794;ENST00000425673;ENST00000458508	T;T;T	0.69306	-0.26;-0.28;-0.39	4.94	2.56	0.30785	.	1.430940	0.04629	N	0.403390	T	0.50905	0.1643	N	0.08118	0	0.41040	D	0.985222	B;B;B	0.12630	0.003;0.002;0.006	B;B;B	0.06405	0.002;0.001;0.001	T	0.27606	-1.0069	10	0.72032	D	0.01	.	11.6779	0.51440	0.0:0.5758:0.4242:0.0	.	898;927;868	Q9H7P9-3;Q9H7P9;E7ESZ3	.;PKHG2_HUMAN;.	V	927;898;868	ENSP00000386733:L927V;ENSP00000392906:L898V;ENSP00000408857:L868V	ENSP00000386733:L927V	L	+	1	0	PLEKHG2	44606392	0.001000	0.12720	0.688000	0.30117	0.059000	0.15707	1.112000	0.31172	1.207000	0.43291	0.655000	0.94253	CTT	.	.	.	none		0.577	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835		G	39914552	C	G	39914552	3	3	176	1	0	0	0	0	1	0	0	0	12076	681	24	4	2849	4	PLEKHG2	19	39914552	Missense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08	27854424	39914552	19214431	32	10320											
ZNF45	7596	hgsc.bcm.edu	37	chr19	44418234	44418234	+	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	atttgaggcctggctgaagcCcttgccacactcctcacatt	8	11	8	14	0	1	2	1	2	0	0	2	2	2	2	4	2	2	1	4	2	1	3			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr19:44418234C>T	ENST00000269973.5	-	10	2444	c.1354G>A	c.(1354-1356)Ggc>Agc	p.G452S	ZNF45_ENST00000589703.1_Missense_Mutation_p.G452S|RP11-15A1.2_ENST00000586247.1_RNA	NM_003425.3	NP_003416.1	Q02386	ZNF45_HUMAN	zinc finger protein 45	452					gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	17						TGGCTGAAGCCCTTGCCACAC	0.483																																					p.G452S		Atlas-SNP	.											.	ZNF45	51	.	0			c.G1354A						PASS	.						62	63	63					19																	44418234		2203	4300	6503	SO:0001583	missense	7596	exon10			TGAAGCCCTTGCC	M67509	CCDS12632.1	19q13.2	2013-01-08	2005-01-11			ENSG00000124459		"Zinc fingers, C2H2-type", "-"	13111	protein-coding gene	gene with protein product		194554	"zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide)", "zinc finger protein 13"	ZNF13		9067431	Standard	NM_003425		Approved		uc002oxw.2	Q02386		ENST00000269973.5:c.1354G>A	chr19.hg19:g.44418234C>T	ENSP00000269973:p.Gly452Ser	128.0	0.0	.		71.0	23.0	.	NM_003425	P17016|P78472|Q9P1U9	Missense_Mutation	SNP	ENST00000269973.5	hg19	CCDS12632.1	.	.	.	.	.	.	.	.	.	.	C	14.96	2.692770	0.48202	.	.	ENSG00000124459	ENST00000269973	T	0.35421	1.31	3.62	3.62	0.41486	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.37178	N	0.002211	T	0.17023	0.0409	N	0.01122	-1.005	0.26498	N	0.974814	B	0.34349	0.45	B	0.42995	0.404	T	0.15464	-1.0436	10	0.44086	T	0.13	-11.8092	10.0287	0.42087	0.2022:0.7977:0.0:0.0	.	452	Q02386	ZNF45_HUMAN	S	452	ENSP00000269973:G452S	ENSP00000269973:G452S	G	-	1	0	ZNF45	49110074	0.000000	0.05858	0.984000	0.44739	0.830000	0.47004	0.090000	0.15025	2.030000	0.59900	0.462000	0.41574	GGC	.	.	.	none		0.483	ZNF45-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459919.1	NM_003425		T	44418234	C	T	44418234	3	4	176	1	0	0	0	0	1	0	0	0	17933	623	22	2	698	2	ZNF45	19	44418234	Missense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08	4503682	44418234	14710749	33	10321											
SLC8A2	6543	hgsc.bcm.edu	37	chr19	47969527	47969527	+	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	ccggctggcagcggtaggacCcctggcagccccctgtgctg	4	6	15	16	2	0	0	0	0	0	0	0	1	0	1	5	5	3	5	5	5	1	1			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr19:47969527C>T	ENST00000236877.6	-	2	529	c.134G>A	c.(133-135)gGg>gAg	p.G45E	SLC8A2_ENST00000542837.1_Intron|SLC8A2_ENST00000539381.1_Intron	NM_015063.2	NP_055878.1	Q9UPR5	NAC2_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 2	45					blood coagulation (GO:0007596)|cell communication (GO:0007154)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(5)|stomach(1)	31		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)		GCGGTAGGACCCCTGGCAGCC	0.731																																					p.G45E		Atlas-SNP	.											.	SLC8A2	77	.	0			c.G134A						PASS	.						10	9	9					19																	47969527		2191	4277	6468	SO:0001583	missense	6543	exon2			TAGGACCCCTGGC	AB029010	CCDS33065.1	19q13.32	2013-07-15	2008-09-02		ENSG00000118160	ENSG00000118160		"Solute carriers"	11069	protein-coding gene	gene with protein product		601901				8021246	Standard	NM_015063		Approved	NCX2, KIAA1087	uc002pgx.3	Q9UPR5	OTTHUMG00000183529	ENST00000236877.6:c.134G>A	chr19.hg19:g.47969527C>T	ENSP00000236877:p.Gly45Glu	10.0	0.0	.		9.0	7.0	.	NM_015063	B4DYQ9	Missense_Mutation	SNP	ENST00000236877.6	hg19	CCDS33065.1	.	.	.	.	.	.	.	.	.	.	C	14.41	2.525726	0.44969	.	.	ENSG00000118160	ENST00000236877	T	0.30448	1.53	4.25	3.19	0.36642	.	0.402651	0.22338	N	0.061364	T	0.23611	0.0571	L	0.51914	1.62	0.21782	N	0.999548	B	0.06786	0.001	B	0.06405	0.002	T	0.25433	-1.0132	10	0.10111	T	0.7	.	9.7772	0.40626	0.0:0.7898:0.2102:0.0	.	45	Q9UPR5	NAC2_HUMAN	E	45	ENSP00000236877:G45E	ENSP00000236877:G45E	G	-	2	0	SLC8A2	52661339	0.158000	0.22850	0.999000	0.59377	0.952000	0.60782	1.497000	0.35649	0.979000	0.38497	0.462000	0.41574	GGG	.	.	.	none		0.731	SLC8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466997.1			T	47969527	C	T	47969527	3	4	176	1	0	0	0	0	1	0	0	0	14720	623	22	2	2667	2	SLC8A2	19	47969527	Missense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08	3551293	47969527	11159456	34	10322											
NAPB	63908	hgsc.bcm.edu	37	chr20	23370612	23370612	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatctcaatggctttctggtActgctcaagctgggcagcat	8	12	11	10	0	3	0	2	0	2	0	4	1	3	0	0	3	4	6	0	3	3	2			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr20:23370612A>G	ENST00000377026.4	-	7	617	c.532T>C	c.(532-534)Tac>Cac	p.Y178H	NAPB_ENST00000432543.2_Missense_Mutation_p.Y139H|NAPB_ENST00000398425.3_Missense_Mutation_p.Y84H|NAPB_ENST00000472855.1_5'UTR	NM_001283018.1|NM_001283020.1|NM_022080.2	NP_001269947.1|NP_001269949.1|NP_071363.1	Q9H115	SNAB_HUMAN	N-ethylmaleimide-sensitive factor attachment protein, beta	178					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)					GCTTTCTGGTACTGCTCAAGC	0.398																																					p.Y178H		Atlas-SNP	.											.	NAPB	22	.	0			c.T532C						PASS	.						101	99	99					20																	23370612		2203	4300	6503	SO:0001583	missense	63908	exon7			TCTGGTACTGCTC	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.532T>C	chr20.hg19:g.23370612A>G	ENSP00000366225:p.Tyr178His	141.0	0.0	.		116.0	52.0	.	NM_022080	B4DK44|Q4G0M0|Q4G187|Q5JXF9|Q8N3C4	Missense_Mutation	SNP	ENST00000377026.4	hg19	CCDS13152.1	.	.	.	.	.	.	.	.	.	.	A	28.2	4.897519	0.91962	.	.	ENSG00000125814	ENST00000377026;ENST00000398425;ENST00000432543;ENST00000431864	T;T;T	0.48201	0.82;0.82;0.82	5.35	5.35	0.76521	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.77698	0.4169	H	0.97758	4.07	0.80722	D	1	D;D;D;D	0.65815	0.995;0.983;0.982;0.995	P;P;P;P	0.62435	0.902;0.82;0.848;0.902	D	0.86047	0.1523	10	0.87932	D	0	-17.6345	14.5087	0.67769	1.0:0.0:0.0:0.0	.	139;84;182;178	B4DK44;Q4G0M0;B4DIV0;Q9H115	.;.;.;SNAB_HUMAN	H	178;84;139;135	ENSP00000366225:Y178H;ENSP00000381459:Y84H;ENSP00000413600:Y139H	ENSP00000366225:Y178H	Y	-	1	0	NAPB	23318612	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	9.251000	0.95483	2.027000	0.59764	0.383000	0.25322	TAC	.	.	.	none		0.398	NAPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078317.2	NM_022080		G	23370612	A	G	23370612	3	3	176	1	0	0	0	0	1	0	0	0	10169	391	14	3	384	3	NAPB	20	23370612	Missense_Mutation	SNP	A	TCGA-G7-7501-01A-11D-2201-08		23370612	39654908	35	10323											
RIPK4	54101	hgsc.bcm.edu	37	chr21	43161570	43161570	+	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	cgtctgggcgttcacactcaCccccggctgcttggccagca	5	8	11	17	3	3	0	2	0	1	0	3	0	3	0	3	3	2	4	3	3	0	2			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr21:43161570C>A	ENST00000352483.2	-	9	1991	c.1927G>T	c.(1927-1929)Gtg>Ttg	p.V643L	RIPK4_ENST00000332512.3_Missense_Mutation_p.V595L|RIPK4_ENST00000542057.1_Missense_Mutation_p.V532L|RIPK4_ENST00000544709.1_Missense_Mutation_p.V532L|AP001615.9_ENST00000423276.1_RNA			P57078	RIPK4_HUMAN	receptor-interacting serine-threonine kinase 4	643					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						TTCACACTCACCCCCGGCTGC	0.682																																					p.V595L		Atlas-SNP	.											.	RIPK4	151	.	0			c.G1783T						PASS	.						55	55	55					21																	43161570		2203	4298	6501	SO:0001583	missense	54101	exon8			CACTCACCCCCGG	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.1927G>T	chr21.hg19:g.43161570C>A	ENSP00000330161:p.Val643Leu	146.0	0.0	.		91.0	29.0	.	NM_020639	Q96KH0	Missense_Mutation	SNP	ENST00000352483.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.44|18.44	3.625278|3.625278	0.66901|0.66901	.|.	.|.	ENSG00000183421|ENSG00000183421	ENST00000330470|ENST00000332512;ENST00000352483;ENST00000544709;ENST00000542057	.|T;T;T;T	.|0.65364	.|2.4;2.4;-0.15;-0.15	4.89|4.89	3.99|3.99	0.46301|0.46301	.|.	.|0.235579	.|0.28694	.|N	.|0.014447	T|T	0.51007|0.51007	0.1649|0.1649	L|L	0.28504|0.28504	0.86|0.86	0.35928|0.35928	D|D	0.832337|0.832337	.|B	.|0.33940	.|0.433	.|B	.|0.33454	.|0.164	T|T	0.62101|0.62101	-0.6925|-0.6925	6|10	0.39692|0.62326	T|D	0.17|0.03	-26.51|-26.51	14.2846|14.2846	0.66238|0.66238	0.0:0.8502:0.1498:0.0|0.0:0.8502:0.1498:0.0	.|.	.|595	.|P57078-2	.|.	V|L	331|595;643;532;532	.|ENSP00000332454:V595L;ENSP00000330161:V643L;ENSP00000441754:V532L;ENSP00000442901:V532L	ENSP00000330975:G331V|ENSP00000332454:V595L	G|V	-|-	2|1	0|0	RIPK4|RIPK4	42034639|42034639	0.982000|0.982000	0.34865|0.34865	0.944000|0.944000	0.38274|0.38274	0.671000|0.671000	0.39405|0.39405	4.763000|4.763000	0.62257|0.62257	1.021000|1.021000	0.39600|0.39600	0.591000|0.591000	0.81541|0.81541	GGT|GTG	.	.	.	none		0.682	RIPK4-201	KNOWN	basic	protein_coding	protein_coding		NM_020639		A	43161570	C	A	43161570	3	1	176	1	0	0	0	0	1	0	0	0	13396	507	18	4	575	4	RIPK4	21	43161570	Missense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08		43161570	4968325	36	10324											
CCT8L2	150160	hgsc.bcm.edu	37	chr22	17073382	17073382	+	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	ctggactcctcgggctctccCttgggttcagtgccagccgc	3	10	12	16	2	2	0	1	0	1	0	5	1	3	1	4	3	2	2	4	3	0	2			TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chr22:17073382C>T	ENST00000359963.3	-	1	318	c.59G>A	c.(58-60)aGg>aAg	p.R20K		NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2	20					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)				CGGGCTCTCCCTTGGGTTCAG	0.657																																					p.R20K		Atlas-SNP	.											.	CCT8L2	150	.	0			c.G59A						PASS	.						39	45	43					22																	17073382		2203	4300	6503	SO:0001583	missense	150160	exon1			CTCTCCCTTGGGT	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.59G>A	chr22.hg19:g.17073382C>T	ENSP00000353048:p.Arg20Lys	105.0	0.0	.		32.0	26.0	.	NM_014406	A4QPH3|Q9UJS3	Missense_Mutation	SNP	ENST00000359963.3	hg19	CCDS13738.1	.	.	.	.	.	.	.	.	.	.	c	0.015	-1.563933	0.00903	.	.	ENSG00000198445	ENST00000359963	T	0.55052	0.54	1.81	-1.91	0.07641	.	1.067860	0.07473	N	0.902516	T	0.23410	0.0566	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24333	-1.0163	10	0.02654	T	1	-1.1577	5.1497	0.15004	0.0:0.3187:0.0:0.6813	.	20	Q96SF2	TCPQM_HUMAN	K	20	ENSP00000353048:R20K	ENSP00000353048:R20K	R	-	2	0	CCT8L2	15453382	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-1.440000	0.02412	-0.377000	0.07930	0.393000	0.25936	AGG	.	.	.	none		0.657	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280580.1			T	17073382	C	T	17073382	3	4	176	1	0	0	0	0	1	0	0	0	2963	681	24	2	1618	2	CCT8L2	22	17073382	Missense_Mutation	SNP	C	TCGA-G7-7501-01A-11D-2201-08		17073382	34231184	37	10325											
TRPC5	7224	hgsc.bcm.edu	37	chrX	111090414	111090416	+	In_Frame_Del	DEL	TCA	TCA	-																															gctcatcgatagctctggttTcataatagaagtaaagctgg																										TCGA-G7-7501-01A-11D-2201-08	TCGA-G7-7501-10A-01D-2201-08	TCA	TCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	37a54336-f21c-4e13-b4bb-c370f1e563c9	6bab150d-1510-4c7a-bb5d-ff665290e36a	g.chrX:111090414_111090416delTCA	ENST00000262839.2	-	6	2544_2546	c.1626_1628delTGA	c.(1624-1629)tatgaa>taa	p.542_543YE>*		NM_012471.2	NP_036603.1	Q9UL62	TRPC5_HUMAN	transient receptor potential cation channel, subfamily C, member 5	542					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						AGCTCTGGTTTCATAATAGAAGT	0.433																																					p.543_543del		Atlas-INDEL	.											.	TRPC5	142	.	0			c.1627_1629del						PASS	.																																			SO:0001651	inframe_deletion	7224	exon6			.	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.1626_1628delTGA	chrX.hg19:g.111090414_111090416delTCA	ENSP00000262839:p.Tyr542_Glu543delins*	198.0	0.0	0		150.0	72.0	0.48	NM_012471	B2RP53|O75233|Q5JXY8|Q9Y514	In_Frame_Del	DEL	ENST00000262839.2	hg19	CCDS14561.1																																																																																			.	.	.	none		0.433	TRPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057945.1	NM_012471		-	111090416	TCA	-	111090414	7	5	176	1	0	1	0	1	0	0	0	0	16594	1783	62	0	1317	0	TRPC5	23	111090414	In_Frame_Del	DEL	TCA	TCGA-G7-7501-01A-11D-2201-08		111090414	44180146	38	10326											
PTAFR	5724	hgsc.bcm.edu	37	chr1	28477260	28477260	+	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	aagaaaaggcagccagccacGttgcacaggaatttggggag	14	5	14	8	1	0	1	0	0	0	1	0	3	0	3	2	4	3	3	2	4	4	2	rs146920734		TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr1:28477260G>A	ENST00000373857.3	-	2	907	c.273C>T	c.(271-273)aaC>aaT	p.N91N	PTAFR_ENST00000539896.1_Silent_p.N91N|PTAFR_ENST00000305392.3_Silent_p.N91N	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	91					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)		AGCCAGCCACGTTGCACAGGA	0.522																																					p.N91N		Atlas-SNP	.											.	PTAFR	30	.	0			c.C273T						PASS	.	G	,,,	3,4403	8.1+/-20.4	0,3,2200	158	133	141		273,273,273,273	-1.6	0.1	1	dbSNP_134	141	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTAFR	NM_000952.4,NM_001164721.1,NM_001164722.2,NM_001164723.2	,,,	0,4,6499	AA,AG,GG		0.0116,0.0681,0.0308	,,,	91/343,91/343,91/343,91/343	28477260	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	5724	exon3			AGCCACGTTGCAC	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.273C>T	chr1.hg19:g.28477260G>A		123.0	0.0	.		82.0	29.0	.	NM_001164723	A3KMC8|A8K2H5	Silent	SNP	ENST00000373857.3	hg19	CCDS318.1																																																																																			.	G|1.000;A|0.000	0.000	weak		0.522	PTAFR-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011258.1	NM_000952		A	28477260	G	A	28477260	2	1	177	1	0	0	0	0	0	0	0	1	12733	1136	40	1		1	PTAFR	1	28477260	Silent	SNP	G	TCGA-G7-7502-01A-11D-2201-08		28477260	220773361	1	10327											
MECR	51102	hgsc.bcm.edu	37	chr1	29520539	29520539	+	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	gctcttttgggatgatcacaTggtgagaatctgctttgaag	9	14	12	6	0	3	3	1	3	2	1	3	5	3	4	0	2	1	2	0	2	2	3			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr1:29520539T>A	ENST00000263702.6	-	10	1142	c.1117A>T	c.(1117-1119)Atg>Ttg	p.M373L	MECR_ENST00000373791.3_Missense_Mutation_p.M297L			Q9BV79	MECR_HUMAN	mitochondrial trans-2-enoyl-CoA reductase	373				M -> I (in Ref. 2; CAG32984). {ECO:0000305}.	fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)	11		Colorectal(325;0.000389)|Breast(348;0.00765)|Lung NSC(340;0.0081)|all_lung(284;0.00914)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.39e-07)|COAD - Colon adenocarcinoma(152;2.04e-05)|STAD - Stomach adenocarcinoma(196;0.0195)|BRCA - Breast invasive adenocarcinoma(304;0.053)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.137)		GATGATCACATGGTGAGAATC	0.597																																					p.M373L		Atlas-SNP	.											.	MECR	31	.	0			c.A1117T						PASS	.						87	89	88					1																	29520539		2203	4300	6503	SO:0001583	missense	51102	exon10			ATCACATGGTGAG		CCDS30659.1, CCDS30660.1	1p35.3	2012-09-20			ENSG00000116353	ENSG00000116353	1.3.1.38		19691	protein-coding gene	gene with protein product	"nuclear receptor binding factor 1", "mitochondrial 2-enoyl thioester reductase"	608205				9795230, 12654921	Standard	XM_005245885		Approved	CGI-63, NRBF1, FASN2B	uc001brq.1	Q9BV79	OTTHUMG00000059082	ENST00000263702.6:c.1117A>T	chr1.hg19:g.29520539T>A	ENSP00000263702:p.Met373Leu	138.0	0.0	.		100.0	34.0	.	NM_016011	B3KT72|Q5SYU0|Q5SYU1|Q5SYU2|Q6IBU9|Q9Y373	Missense_Mutation	SNP	ENST00000263702.6	hg19	CCDS30659.1	.	.	.	.	.	.	.	.	.	.	T	15.90	2.969746	0.53614	.	.	ENSG00000116353	ENST00000373791;ENST00000263702	T;T	0.03094	4.05;4.12	5.61	5.61	0.85477	.	0.129329	0.64402	D	0.000001	T	0.06325	0.0163	M	0.66939	2.045	0.49798	D	0.999822	B	0.12630	0.006	B	0.14578	0.011	T	0.27226	-1.0080	10	0.19147	T	0.46	.	13.7585	0.62950	0.0:0.0:0.0:1.0	.	373	Q9BV79	MECR_HUMAN	L	297;373	ENSP00000362896:M297L;ENSP00000263702:M373L	ENSP00000263702:M373L	M	-	1	0	MECR	29393126	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.236000	0.32683	2.143000	0.66587	0.533000	0.62120	ATG	.	.	.	none		0.597	MECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130740.1	NM_016011		A	29520539	T	A	29520539	3	1	177	1	0	0	0	0	1	0	0	0	9431	1464	51	5	8	5	MECR	1	29520539	Missense_Mutation	SNP	T	TCGA-G7-7502-01A-11D-2201-08	1043279	29520539	219730082	2	10328											
CDCA8	55143	hgsc.bcm.edu	37	chr1	38174030	38174030	+	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	tctgcagcagcatacggaccCacaaatgagacaccaaagtt	15	6	8	12	1	1	1	0	1	1	1	1	3	1	2	2	1	4	4	2	1	3	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr1:38174030C>T	ENST00000373055.1	+	10	1108	c.835C>T	c.(835-837)Cac>Tac	p.H279Y	CDCA8_ENST00000327331.2_Missense_Mutation_p.H279Y	NM_001256875.1|NM_018101.3	NP_001243804.1|NP_060571.1	Q53HL2	BOREA_HUMAN	cell division cycle associated 8	279					chromosome organization (GO:0051276)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)	chromocenter (GO:0010369)|chromosome passenger complex (GO:0032133)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|midbody (GO:0030496)|nucleolus (GO:0005730)|nucleus (GO:0005634)|protein complex (GO:0043234)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(3)|skin(1)|stomach(1)	11		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CATACGGACCCACAAATGAGA	0.483																																					p.H279Y		Atlas-SNP	.											.	CDCA8	25	.	0			c.C835T						PASS	.						131	125	127					1																	38174030		2203	4300	6503	SO:0001583	missense	55143	exon10			CGGACCCACAAAT	BG354581	CCDS424.1	1p34.3	2013-01-17			ENSG00000134690	ENSG00000134690			14629	protein-coding gene	gene with protein product	"borealin"	609977				12188893, 15260989	Standard	NM_001256875		Approved	FLJ12042, MESRGP, BOR, DasraB	uc001cbs.4	Q53HL2	OTTHUMG00000004320	ENST00000373055.1:c.835C>T	chr1.hg19:g.38174030C>T	ENSP00000362146:p.His279Tyr	88.0	0.0	.		67.0	16.0	.	NM_001256875	D3DPT4|Q53HN1|Q96AM3|Q9NVW5	Missense_Mutation	SNP	ENST00000373055.1	hg19	CCDS424.1	.	.	.	.	.	.	.	.	.	.	C	6.465	0.453973	0.12283	.	.	ENSG00000134690	ENST00000373055;ENST00000327331	T;T	0.46063	0.88;0.88	5.48	2.55	0.30701	.	1.036760	0.07555	N	0.916095	T	0.26159	0.0638	N	0.22421	0.69	0.25891	N	0.983472	B	0.02656	0.0	B	0.01281	0.0	T	0.27640	-1.0068	10	0.22706	T	0.39	-2.4563	3.8562	0.08976	0.1641:0.5775:0.1703:0.0881	.	279	Q53HL2	BOREA_HUMAN	Y	279	ENSP00000362146:H279Y;ENSP00000316121:H279Y	ENSP00000316121:H279Y	H	+	1	0	CDCA8	37946617	0.989000	0.36119	0.332000	0.25469	0.213000	0.24496	0.321000	0.19558	0.402000	0.25451	0.650000	0.86243	CAC	.	.	.	none		0.483	CDCA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012473.1	NM_018101		T	38174030	C	T	38174030	3	4	177	1	0	0	0	0	1	0	0	0	3094	594	21	2	873	2	CDCA8	1	38174030	Missense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08	8653491	38174030	211076591	3	10329											
LRRC40	55631	hgsc.bcm.edu	37	chr1	70671136	70671136	+	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	cctcgctgccttcaacagccCttggggtaccgaggtaccgc	6	8	11	16	3	1	0	1	0	0	0	2	1	1	0	5	3	5	3	5	3	3	4	rs368762009		TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr1:70671136C>G	ENST00000370952.3	-	1	167	c.88G>C	c.(88-90)Ggg>Cgg	p.G30R	SRSF11_ENST00000370950.3_5'Flank|SRSF11_ENST00000454435.2_5'Flank|SRSF11_ENST00000370951.1_5'Flank|SRSF11_ENST00000405432.1_5'Flank	NM_017768.4	NP_060238.3	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40	30						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						TTCAACAGCCCTTGGGGTACC	0.562																																					p.G30R		Atlas-SNP	.											.	LRRC40	66	.	0			c.G88C						PASS	.						91	82	85					1																	70671136		2203	4300	6503	SO:0001583	missense	55631	exon1			ACAGCCCTTGGGG		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.88G>C	chr1.hg19:g.70671136C>G	ENSP00000359990:p.Gly30Arg	107.0	0.0	.		82.0	8.0	.	NM_017768	Q9BTR7|Q9NSK1|Q9NXC1	Missense_Mutation	SNP	ENST00000370952.3	hg19	CCDS646.1	.	.	.	.	.	.	.	.	.	.	C	19.60	3.858799	0.71834	.	.	ENSG00000066557	ENST00000370952	T	0.25085	1.82	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	T	0.26702	0.0653	L	0.35854	1.095	0.58432	D	0.999997	D	0.89917	1.0	D	0.76575	0.988	T	0.01679	-1.1297	10	0.17832	T	0.49	.	14.1132	0.65137	0.0:1.0:0.0:0.0	.	30	Q9H9A6	LRC40_HUMAN	R	30	ENSP00000359990:G30R	ENSP00000359990:G30R	G	-	1	0	LRRC40	70443724	1.000000	0.71417	0.998000	0.56505	0.271000	0.26615	4.265000	0.58865	2.703000	0.92315	0.563000	0.77884	GGG	.	.	.	none		0.562	LRRC40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025914.1	NM_017768		G	70671136	C	G	70671136	3	3	177	1	0	0	0	0	1	0	0	0	9005	681	24	4	1780	4	LRRC40	1	70671136	Missense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08	32497106	70671136	178579485	4	10330											
OR6K2	81448	hgsc.bcm.edu	37	chr1	158669896	158669896	+	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	tgtgcaggccagacgcagcaCtgggaggaagtcacagaaga	13	4	15	9	1	1	3	1	0	0	3	1	5	1	5	1	3	2	3	1	3	2	0			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr1:158669896C>T	ENST00000359610.2	-	1	590	c.547G>A	c.(547-549)Gtg>Atg	p.V183M		NM_001005279.1	NP_001005279.1	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K, member 2	183						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|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)					AGACGCAGCACTGGGAGGAAG	0.478																																					p.V183M		Atlas-SNP	.											.	OR6K2	104	.	0			c.G547A						PASS	.						133	112	119					1																	158669896		2203	4300	6503	SO:0001583	missense	81448	exon1			GCAGCACTGGGAG	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.547G>A	chr1.hg19:g.158669896C>T	ENSP00000352626:p.Val183Met	132.0	0.0	.		105.0	35.0	.	NM_001005279	B9EH33|Q6IFR6	Missense_Mutation	SNP	ENST00000359610.2	hg19	CCDS30902.1	.	.	.	.	.	.	.	.	.	.	C	14.28	2.489601	0.44249	.	.	ENSG00000196171	ENST00000359610	T	0.00231	8.49	5.09	3.14	0.36123	GPCR, rhodopsin-like superfamily (1);	0.438834	0.16622	N	0.206443	T	0.00109	0.0003	M	0.66939	2.045	0.09310	N	1	B	0.31893	0.345	B	0.43360	0.417	T	0.34254	-0.9836	10	0.72032	D	0.01	-4.3506	3.0153	0.06058	0.2617:0.4934:0.1539:0.091	.	183	Q8NGY2	OR6K2_HUMAN	M	183	ENSP00000352626:V183M	ENSP00000352626:V183M	V	-	1	0	OR6K2	156936520	0.000000	0.05858	0.982000	0.44146	0.993000	0.82548	-1.509000	0.02264	1.348000	0.45733	0.655000	0.94253	GTG	.	.	.	none		0.478	OR6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059061.1	NM_001005279		T	158669896	C	T	158669896	3	4	177	1	0	0	0	0	1	0	0	0	11209	565	20	2	431	2	OR6K2	1	158669896	Missense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08	87998760	158669896	90580725	5	10331											
PAPPA2	60676	hgsc.bcm.edu	37	chr1	176740277	176740277	+	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	caaatatgaatgcaaaccagGgtactatgtggcagaaagtg	16	8	11	6	0	0	2	0	1	0	1	0	2	0	2	1	2	3	3	1	2	7	3			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr1:176740277G>T	ENST00000367662.3	+	17	5840	c.4676G>T	c.(4675-4677)gGg>gTg	p.G1559V		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	1559	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						TGCAAACCAGGGTACTATGTG	0.478																																					p.G1559V		Atlas-SNP	.											.	PAPPA2	665	.	0			c.G4676T						PASS	.						96	90	92					1																	176740277		2009	4181	6190	SO:0001583	missense	60676	exon17			AACCAGGGTACTA	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.4676G>T	chr1.hg19:g.176740277G>T	ENSP00000356634:p.Gly1559Val	120.0	0.0	.		75.0	18.0	.	NM_020318	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	ENST00000367662.3	hg19	CCDS41438.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.439678	0.83885	.	.	ENSG00000116183	ENST00000367662	T	0.77358	-1.09	5.53	5.53	0.82687	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	D	0.88544	0.6465	M	0.77313	2.365	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89575	0.3816	10	0.87932	D	0	-23.6151	18.0257	0.89268	0.0:0.0:1.0:0.0	.	1559	Q9BXP8	PAPP2_HUMAN	V	1559	ENSP00000356634:G1559V	ENSP00000356634:G1559V	G	+	2	0	PAPPA2	175006900	1.000000	0.71417	1.000000	0.80357	0.666000	0.39218	9.050000	0.93843	2.592000	0.87571	0.655000	0.94253	GGG	.	.	.	none		0.478	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			T	176740277	G	T	176740277	3	4	177	1	0	0	0	0	1	0	0	0	11440	1232	43	4	4791	4	PAPPA2	1	176740277	Missense_Mutation	SNP	G	TCGA-G7-7502-01A-11D-2201-08	18070381	176740277	72510344	6	10332											
FAM5B	57795	hgsc.bcm.edu	37	chr1	177250648	177250648	+	Missense_Mutation	SNP	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	ccctgtggaatatgagaccgGcaaactctgtagctaatggg	11	9	12	9	1	1	1	0	1	1	1	1	3	1	2	2	3	2	3	2	3	5	3			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr1:177250648G>A	ENST00000361539.4	+	8	2648	c.2336G>A	c.(2335-2337)gGc>gAc	p.G779D	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	779					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)											TATGAGACCGGCAAACTCTGT	0.537																																					p.G779D		Atlas-SNP	.											.	FAM5B	191	.	0			c.G2336A						PASS	.						68	73	71					1																	177250648		2203	4300	6503	SO:0001583	missense	57795	exon8			AGACCGGCAAACT		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.2336G>A	chr1.hg19:g.177250648G>A	ENSP00000354481:p.Gly779Asp	139.0	0.0	.		118.0	5.0	.	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	hg19	CCDS1320.1	.	.	.	.	.	.	.	.	.	.	G	14.91	2.676710	0.47886	.	.	ENSG00000198797	ENST00000536589;ENST00000361539	T	0.14266	2.52	5.05	5.05	0.67936	.	0.186815	0.46758	D	0.000278	T	0.13329	0.0323	N	0.22421	0.69	0.45183	D	0.998193	P;P	0.44429	0.835;0.759	P;B	0.44990	0.466;0.19	T	0.02668	-1.1126	10	0.52906	T	0.07	-23.4177	13.7174	0.62705	0.0:0.1546:0.8454:0.0	.	674;779	Q9C0B6-2;Q9C0B6	.;FAM5B_HUMAN	D	532;779	ENSP00000354481:G779D	ENSP00000354481:G779D	G	+	2	0	FAM5B	175517271	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	4.714000	0.61902	2.346000	0.79739	0.313000	0.20887	GGC	.	.	.	none		0.537	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165		A	177250648	G	A	177250648	3	1	177	1	0	0	0	0	1	0	0	0	5600	1203	42	2	2362	2	FAM5B	1	177250648	Missense_Mutation	SNP	G	TCGA-G7-7502-01A-11D-2201-08	510371	177250648	71999973	7	10333											
CFHR3	10878	hgsc.bcm.edu	37	chr1	196762616	196762617	+	Missense_Mutation	DNP	GA	GA	TT																															caagcagtgtgtcgggaaggGatagtggaataccccagatg																								rs149081467	byFrequency	TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr1:196762616_196762617GA>TT	ENST00000367425.4	+	6	1058_1059	c.966_967GA>TT	c.(964-969)ggGAta>ggTTta	p.I323L	CFHR3_ENST00000391985.3_Missense_Mutation_p.I262L	NM_021023.5	NP_066303.2	Q02985	FHR3_HUMAN	complement factor H-related 3	323	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.					blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	18						GTCGGGAAGGGATAGTGGAATA	0.381																																					p.G322G|p.I323L		Atlas-SNP	.											.	CFHR3	52	.	0			c.G966T|c.A967T						PASS	.																																			SO:0001583	missense	10878	exon6			GGAAGGGATAGTG|GAAGGGATAGTGG	X68679	CCDS30958.1, CCDS53453.1	1q32	2014-09-17		2006-02-28	ENSG00000116785	ENSG00000116785		"Complement system"	16980	protein-coding gene	gene with protein product	"complement factor H related 3"	605336		CFHL3		8428964, 10380701	Standard	NM_021023		Approved	FHR-3, HLF4, FHR3, DOWN16	uc001gtl.3	Q02985	OTTHUMG00000035929	Exception_encountered	chr1.hg19:g.196762616_196762617delinsTT	ENSP00000356395:p.Ile323Leu	140.0	0.0	.		124.0	9.0	.	NM_021023	B4DPR0|Q9UJ16	Silent|Missense_Mutation	SNP	ENST00000367425.4	hg19	CCDS30958.1																																																																																			.	G|0.998;C|0.002|.	.	alt|none		0.381	CFHR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087505.2	NM_021023		TT	196762617	GA	TT	196762616	3	4	177	1	0	0	0	0	1	0	0	0	3288	1161	41	4	988	4	CFHR3	1	196762616	Missense_Mutation	DNP	GA	TCGA-G7-7502-01A-11D-2201-08	19511968	196762616	52488005	8	10334											
KDM3A	55818	hgsc.bcm.edu	37	chr2	86716748	86716749	+	In_Frame_Ins	INS	-	-	GGG																															tggcacatatatgctgcaaaINSggacacggagaagataaggg																										TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr2:86716748_86716749insGGG	ENST00000409556.1	+	24	3904_3905	c.3539_3540insGGG	c.(3538-3543)aaggac>aaGGGggac	p.1180_1181KD>KGD	KDM3A_ENST00000542128.1_In_Frame_Ins_p.1128_1129KD>KGD|KDM3A_ENST00000409064.1_In_Frame_Ins_p.1180_1181KD>KGD|KDM3A_ENST00000312912.5_In_Frame_Ins_p.1180_1181KD>KGD			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	1180	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				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						TATGCTGCAAAGGACACGGAGA	0.406																																					p.K1180delinsKG	NSCLC(96;1150 1523 6936 46253 49736)	Atlas-INDEL	.											.	KDM3A	179	.	0			c.3539_3540insGGG						PASS	.																																			SO:0001652	inframe_insertion	55818	exon23			.	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	Exception_encountered	chr2.hg19:g.86716748_86716749insGGG	ENSP00000386660:p.Lys1180_Asp1181insGly	140.0	0.0	0		131.0	51.0	0.389313	NM_018433	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	In_Frame_Ins	INS	ENST00000409556.1	hg19	CCDS1990.1																																																																																			.	.	.	none		0.406	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433		GGG	86716749	-	GGG	86716748	7	5	177	1	0	1	1	0	0	0	0	0	8133	72	3	0	3625	0	KDM3A	2	86716748	In_Frame_Ins	INS	-	TCGA-G7-7502-01A-11D-2201-08		86716748	156482625	9	10335											
STK36	27148	hgsc.bcm.edu	37	chr2	219556970	219556970	+	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	caggttgtcttggatgggctCcttcatggcttgacagttcc	5	14	12	10	0	2	1	1	1	1	0	4	2	4	2	2	4	0	4	2	4	0	5			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr2:219556970C>G	ENST00000295709.3	+	15	2148	c.1869C>G	c.(1867-1869)ctC>ctG	p.L623L	STK36_ENST00000392105.3_Silent_p.L623L|STK36_ENST00000392106.2_Silent_p.L623L|STK36_ENST00000440309.1_Silent_p.L623L	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)		TGGATGGGCTCCTTCATGGCT	0.537																																					p.L623L		Atlas-SNP	.											.	STK36	111	.	0			c.C1869G						PASS	.						90	95	93					2																	219556970		2203	4300	6503	SO:0001819	synonymous_variant	27148	exon15			TGGGCTCCTTCAT	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.1869C>G	chr2.hg19:g.219556970C>G		110.0	0.0	.		133.0	70.0	.	NM_015690		Silent	SNP	ENST00000295709.3	hg19	CCDS2421.1																																																																																			.	.	.	none		0.537	STK36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256723.2			G	219556970	C	G	219556970	2	3	177	1	0	0	0	0	0	0	0	1	15314	842	30	4		4	STK36	2	219556970	Silent	SNP	C	TCGA-G7-7502-01A-11D-2201-08	132840222	219556970	23642403	10	10336											
ECEL1	9427	hgsc.bcm.edu	37	chr2	233350797	233350797	+	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	agtcgctcgatctcgcgcatGtcgaggcacgagcggaagaa	10	6	14	11	7	1	1	0	0	1	1	5	5	1	2	0	2	1	3	0	2	2	0			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr2:233350797G>A	ENST00000304546.1	-	2	777	c.567C>T	c.(565-567)gaC>gaT	p.D189D	ECEL1_ENST00000409941.1_Silent_p.D189D	NM_004826.2	NP_004817.2	O95672	ECEL1_HUMAN	endothelin converting enzyme-like 1	189					neuropeptide signaling pathway (GO:0007218)|respiratory system process (GO:0003016)	integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000771)|Lung(119;0.00213)|LUSC - Lung squamous cell carcinoma(224;0.00746)		TCTCGCGCATGTCGAGGCACG	0.746																																					p.D189D		Atlas-SNP	.											.	ECEL1	73	.	0			c.C567T						PASS	.																																			SO:0001819	synonymous_variant	9427	exon2			GCGCATGTCGAGG	Y16187	CCDS2493.1	2q37.1	2010-09-29			ENSG00000171551	ENSG00000171551			3147	protein-coding gene	gene with protein product	"damage induced neuronal endopeptidase"	605896				9931490, 11352565	Standard	NM_004826		Approved	XCE, DINE	uc002vsv.2	O95672	OTTHUMG00000133262	ENST00000304546.1:c.567C>T	chr2.hg19:g.233350797G>A		15.0	0.0	.		29.0	7.0	.	NM_004826	Q45UD9|Q53RF9|Q6UW86|Q86TH4|Q9NY95	Silent	SNP	ENST00000304546.1	hg19	CCDS2493.1																																																																																			.	.	.	none		0.746	ECEL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257039.2	NM_004826		A	233350797	G	A	233350797	2	1	177	1	0	0	0	0	0	0	0	1	4893	1368	48	2		2	ECEL1	2	233350797	Silent	SNP	G	TCGA-G7-7502-01A-11D-2201-08	13793827	233350797	9848576	11	10337											
JAGN1	84522	hgsc.bcm.edu	37	chr3	9934676	9934676	+	Missense_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	gctgctggttgctaagatgaGcgtgggacacctgaggctct	7	10	15	9	1	1	3	0	2	1	1	1	4	1	4	1	3	3	5	1	3	1	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr3:9934676G>A	ENST00000307768.4	+	2	336	c.167G>A	c.(166-168)aGc>aAc	p.S56N		NM_032492.3	NP_115881.3			jagunal homolog 1 (Drosophila)											breast(1)|central_nervous_system(1)|endometrium(4)|lung(3)|ovary(1)	10	Medulloblastoma(99;0.227)					GCTAAGATGAGCGTGGGACAC	0.512																																					p.S56N		Atlas-SNP	.											.	JAGN1	18	.	0			c.G167A						PASS	.						158	132	141					3																	9934676		2203	4300	6503	SO:0001583	missense	84522	exon2			AGATGAGCGTGGG	AK074760	CCDS2588.1	3p25.2	2010-03-23			ENSG00000171135	ENSG00000171135			26926	protein-coding gene	gene with protein product						12477932	Standard	NM_032492		Approved	GL009, FLJ14602	uc003btt.4	Q8N5M9	OTTHUMG00000128523	ENST00000307768.4:c.167G>A	chr3.hg19:g.9934676G>A	ENSP00000306106:p.Ser56Asn	86.0	0.0	.		79.0	20.0	.	NM_032492		Missense_Mutation	SNP	ENST00000307768.4	hg19	CCDS2588.1	.	.	.	.	.	.	.	.	.	.	G	10.74	1.434837	0.25813	.	.	ENSG00000171135	ENST00000307768;ENST00000543379	.	.	.	5.24	3.34	0.38264	.	0.446433	0.27754	N	0.017994	T	0.36220	0.0959	L	0.36672	1.1	0.20638	N	0.999878	B	0.17667	0.023	B	0.24541	0.054	T	0.21655	-1.0239	9	0.26408	T	0.33	-15.5227	10.1674	0.42888	0.0:0.1322:0.5948:0.2731	.	56	Q8N5M9	JAGN1_HUMAN	N	56	.	ENSP00000306106:S56N	S	+	2	0	JAGN1	9909676	0.775000	0.28604	0.992000	0.48379	0.966000	0.64601	1.530000	0.36007	0.514000	0.28300	0.313000	0.20887	AGC	.	.	.	none		0.512	JAGN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250335.1	NM_032492		A	9934676	G	A	9934676	3	1	177	1	0	0	0	0	1	0	0	0	7943	971	34	2	173	2	JAGN1	3	9934676	Missense_Mutation	SNP	G	TCGA-G7-7502-01A-11D-2201-08		9934676	188087754	12	10338											
DAG1	1605	hgsc.bcm.edu	37	chr3	49568641	49568641	+	Frame_Shift_Del	DEL	A	A	-																															aattagtgccggtggtgaatAacagactatttgacatgtcg																										TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr3:49568641delA	ENST00000539901.1	+	3	1255	c.697delA	c.(697-699)aacfs	p.N233fs	DAG1_ENST00000538711.1_Frame_Shift_Del_p.N233fs|DAG1_ENST00000541308.1_Frame_Shift_Del_p.N233fs|DAG1_ENST00000308775.2_Frame_Shift_Del_p.N233fs|DAG1_ENST00000545947.1_Frame_Shift_Del_p.N233fs|DAG1_ENST00000515359.2_Frame_Shift_Del_p.N233fs	NM_001177644.2	NP_001171115	Q14118	DAG1_HUMAN	dystroglycan 1 (dystrophin-associated glycoprotein 1)	233	Required for laminin recognition.				basement membrane organization (GO:0071711)|branching involved in salivary gland morphogenesis (GO:0060445)|calcium-dependent cell-matrix adhesion (GO:0016340)|commissural neuron axon guidance (GO:0071679)|cytoskeletal anchoring at plasma membrane (GO:0007016)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|microtubule anchoring (GO:0034453)|modulation by virus of host morphology or physiology (GO:0019048)|morphogenesis of an epithelial sheet (GO:0002011)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell migration (GO:0030336)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase B signaling (GO:0051898)|nerve maturation (GO:0021682)|NLS-bearing protein import into nucleus (GO:0006607)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell outer membrane (GO:0009279)|cell-cell adherens junction (GO:0005913)|contractile ring (GO:0070938)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystroglycan complex (GO:0016011)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|node of Ranvier (GO:0033268)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|alpha-actinin binding (GO:0051393)|calcium ion binding (GO:0005509)|laminin-1 binding (GO:0043237)|SH2 domain binding (GO:0042169)|structural constituent of muscle (GO:0008307)|tubulin binding (GO:0015631)|vinculin binding (GO:0017166)|virus receptor activity (GO:0001618)			NS(1)|autonomic_ganglia(2)|breast(2)|endometrium(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	23				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.00241)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		GGTGGTGAATAACAGACTATT	0.522																																					p.N232fs		Atlas-INDEL	.											.	DAG1	60	.	0			c.696delT						PASS	.						72	77	75					3																	49568641		2203	4300	6503	SO:0001589	frameshift_variant	1605	exon4			.	L19711	CCDS2799.1	3p21	2014-09-17			ENSG00000173402	ENSG00000173402			2666	protein-coding gene	gene with protein product	"alpha-dystroglycan", "dystrophin-associated glycoprotein-1", "beta-dystroglycan"	128239				7774920, 1741056	Standard	NM_001177643		Approved	A3a, 156DAG, AGRNR, DAG	uc021wyd.1	Q14118	OTTHUMG00000156869	ENST00000539901.1:c.697delA	chr3.hg19:g.49568641delA	ENSP00000439334:p.Asn233fs	67.0	0.0	0		49.0	10.0	0.204082	NM_001177642	A8K6M7|Q969J9	Frame_Shift_Del	DEL	ENST00000539901.1	hg19	CCDS2799.1																																																																																			.	.	.	none		0.522	DAG1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346326.1			-	49568641	A	-	49568641	7	5	177	1	0	1	0	1	0	0	0	0	4227	362	13	0	703	0	DAG1	3	49568641	Frame_Shift_Del	DEL	A	TCGA-G7-7502-01A-11D-2201-08	39633965	49568641	148453789	13	10339											
APEH	327	hgsc.bcm.edu	37	chr3	49720689	49720689	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggctcctgctctatcccaaaAgcacccacgcattatcagag	11	8	7	15	1	2	1	1	0	1	1	4	1	4	1	3	1	2	4	3	1	4	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr3:49720689A>G	ENST00000296456.5	+	22	2513	c.2113A>G	c.(2113-2115)Agc>Ggc	p.S705G	APEH_ENST00000438011.1_Missense_Mutation_p.S710G|AC099668.5_ENST00000563780.1_RNA	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase	705					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)		CTATCCCAAAAGCACCCACGC	0.557																																					p.S705G		Atlas-SNP	.											.	APEH	45	.	0			c.A2113G						PASS	.						188	196	193					3																	49720689		2203	4300	6503	SO:0001583	missense	327	exon22			CCCAAAAGCACCC	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.2113A>G	chr3.hg19:g.49720689A>G	ENSP00000296456:p.Ser705Gly	332.0	0.0	.		353.0	63.0	.	NM_001640	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	hg19	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	A	13.25	2.180168	0.38511	.	.	ENSG00000164062	ENST00000296456;ENST00000438011	T;T	0.32753	1.44;1.44	5.75	5.75	0.90469	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.129744	0.64402	D	0.000001	T	0.20129	0.0484	N	0.17278	0.47	0.37781	D	0.927029	B;B	0.10296	0.003;0.002	B;B	0.15052	0.012;0.006	T	0.08269	-1.0730	10	0.48119	T	0.1	-38.9892	10.7009	0.45926	0.9202:0.0:0.0798:0.0	.	710;705	C9JIF9;P13798	.;ACPH_HUMAN	G	705;710	ENSP00000296456:S705G;ENSP00000415862:S710G	ENSP00000296456:S705G	S	+	1	0	APEH	49695693	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	3.552000	0.53705	2.192000	0.70111	0.459000	0.35465	AGC	.	.	.	none		0.557	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			G	49720689	A	G	49720689	3	3	177	1	0	0	0	0	1	0	0	0	768	72	3	3	2199	3	APEH	3	49720689	Missense_Mutation	SNP	A	TCGA-G7-7502-01A-11D-2201-08	152048	49720689	148301741	14	10340											
ACY1	95	hgsc.bcm.edu	37	chr3	52022538	52022538	+	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	tgccattcttcctgtccctcAgaagtggatgcacccccaag	8	10	8	15	0	2	1	1	0	1	1	4	2	4	2	5	1	2	1	5	1	2	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr3:52022538A>C	ENST00000404366.2	+	13	1067		c.e13-1		ABHD14A-ACY1_ENST00000463937.1_Splice_Site|ACY1_ENST00000494103.1_Splice_Site|ACY1_ENST00000476351.1_Splice_Site|ACY1_ENST00000458031.2_Splice_Site|ACY1_ENST00000476854.1_Splice_Site	NM_000666.2|NM_001198895.1	NP_000657.1|NP_001185824.1	Q03154	ACY1_HUMAN	aminoacylase 1						cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aminoacylase activity (GO:0004046)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Acetylcysteine(DB06151)|L-Aspartic Acid(DB00128)	CCTGTCCCTCAGAAGTGGATG	0.562																																					.		Atlas-SNP	.											.	ACY1	35	.	0			c.817-2A>C						PASS	.						103	86	92					3																	52022538		2203	4300	6503	SO:0001630	splice_region_variant	95	exon12			TCCCTCAGAAGTG	L07548	CCDS2844.1, CCDS56261.1, CCDS56262.1, CCDS56263.1	3p21.2	2006-02-02			ENSG00000243989	ENSG00000243989	3.5.1.14		177	protein-coding gene	gene with protein product		104620				1707030, 6948533	Standard	NM_000666		Approved		uc003dcq.3	Q03154	OTTHUMG00000157815	ENST00000404366.2:c.922-1A>C	chr3.hg19:g.52022538A>C		72.0	0.0	.		74.0	17.0	.	NM_001198898	C9J6I6|C9J9D8|C9JWD4	Splice_Site	SNP	ENST00000404366.2	hg19	CCDS2844.1	.	.	.	.	.	.	.	.	.	.	A	13.72	2.321906	0.41096	.	.	ENSG00000114786;ENSG00000114786;ENSG00000114786;ENSG00000243989;ENSG00000243989;ENSG00000243989;ENSG00000243989	ENST00000458031;ENST00000463937;ENST00000232907;ENST00000476854;ENST00000476351;ENST00000494103;ENST00000404366	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0907	0.72192	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ACY1;RP11-155D18.11	51997578	1.000000	0.71417	0.993000	0.49108	0.278000	0.26855	8.943000	0.92975	2.048000	0.60808	0.459000	0.35465	.	.	.	.	none		0.562	ACY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349657.1	NM_000666	Intron	C	52022538	A	C	52022538	5	2	177	1	0	0	0	0	0	0	1	0	226	202	7	5	966	5	ACY1	3	52022538	Splice_Site	SNP	A	TCGA-G7-7502-01A-11D-2201-08	2301849	52022538	145999892	15	10341											
STAB1	23166	hgsc.bcm.edu	37	chr3	52554291	52554291	+	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	acccccatctctttctcctgCagccgaacgcgggccgtgag	6	8	10	17	4	2	1	0	1	2	0	4	2	2	1	5	1	3	1	5	1	1	1			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr3:52554291C>A	ENST00000321725.6	+	52	5560	c.5484C>A	c.(5482-5484)tgC>tgA	p.C1828*		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	1828	FAS1 6. {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)		CTTTCTCCTGCAGCCGAACGC	0.632																																					p.C1828X		Atlas-SNP	.											.	STAB1	178	.	0			c.C5484A						PASS	.						82	83	83					3																	52554291		2203	4300	6503	SO:0001587	stop_gained	23166	exon52			CTCCTGCAGCCGA	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.5484C>A	chr3.hg19:g.52554291C>A	ENSP00000312946:p.Cys1828*	165.0	0.0	.		160.0	17.0	.	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Nonsense_Mutation	SNP	ENST00000321725.6	hg19	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	C	40	8.313466	0.98754	.	.	ENSG00000010327	ENST00000321725	.	.	.	6.07	0.741	0.18336	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.5698	0.22533	0.1187:0.5434:0.0:0.3378	.	.	.	.	X	1828	.	ENSP00000312946:C1828X	C	+	3	2	STAB1	52529331	0.999000	0.42202	0.997000	0.53966	0.055000	0.15305	0.493000	0.22451	0.463000	0.27118	-0.126000	0.14955	TGC	.	.	.	none		0.632	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		A	52554291	C	A	52554291	4	1	177	1	0	0	0	0	0	1	0	0	15249	718	25	4	5690	4	STAB1	3	52554291	Nonsense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08	531753	52554291	145468139	16	10342											
MYH15	22989	hgsc.bcm.edu	37	chr3	108110610	108110610	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	attacccagactcctaccctGgattctagtttctggatttg	8	15	7	11	0	2	1	0	0	2	1	3	3	3	3	3	2	2	1	3	2	3	6			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr3:108110610G>A	ENST00000273353.3	-	38	5543	c.5487C>T	c.(5485-5487)tcC>tcT	p.S1829S		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1829						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						CTCCTACCCTGGATTCTAGTT	0.473																																					p.S1829S		Atlas-SNP	.											.	MYH15	223	.	0			c.C5487T						PASS	.						183	184	183					3																	108110610		1923	4132	6055	SO:0001819	synonymous_variant	22989	exon38			TACCCTGGATTCT	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.5487C>T	chr3.hg19:g.108110610G>A		207.0	0.0	.		213.0	38.0	.	NM_014981		Silent	SNP	ENST00000273353.3	hg19	CCDS43127.1																																																																																			.	.	.	none		0.473	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		A	108110610	G	A	108110610	2	1	177	1	0	0	0	0	0	0	0	1	10041	1335	47	2		2	MYH15	3	108110610	Silent	SNP	G	TCGA-G7-7502-01A-11D-2201-08	55556319	108110610	89911820	17	10343											
FAM162A	26355	hgsc.bcm.edu	37	chr3	122128621	122128621	+	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	gagactttaacaagcttgaaCttagaaaagaaagctcgtct	16	10	8	7	1	1	4	0	1	1	3	2	5	1	4	0	0	4	2	0	0	7	4			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr3:122128621C>T	ENST00000477892.1	+	5	492	c.408C>T	c.(406-408)aaC>aaT	p.N136N	FAM162A_ENST00000232125.5_Silent_p.N126N	NM_014367.3	NP_055182.3	Q96A26	F162A_HUMAN	family with sequence similarity 162, member A	136					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to hypoxia (GO:0071456)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|transformed cell apoptotic process (GO:0006927)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	6						CAAGCTTGAACTTAGAAAAGA	0.438																																					p.N136N		Atlas-SNP	.											.	FAM162A	18	.	0			c.C408T						PASS	.						108	98	101					3																	122128621		1886	4118	6004	SO:0001819	synonymous_variant	26355	exon5			CTTGAACTTAGAA	AF191020	CCDS43139.1	3q21.1	2008-06-05	2008-06-05	2008-06-05	ENSG00000114023	ENSG00000114023			17865	protein-coding gene	gene with protein product		608017	"chromosome 3 open reading frame 28"	C3orf28		11085516	Standard	NM_014367		Approved	E2IG5	uc003eez.3	Q96A26	OTTHUMG00000159494	ENST00000477892.1:c.408C>T	chr3.hg19:g.122128621C>T		150.0	0.0	.		126.0	55.0	.	NM_014367	Q9NRN6|Q9UJX8	Silent	SNP	ENST00000477892.1	hg19	CCDS43139.1	.	.	.	.	.	.	.	.	.	.	C	6.587	0.476718	0.12521	.	.	ENSG00000114023	ENST00000440333	.	.	.	5.44	3.65	0.41850	.	.	.	.	.	T	0.64080	0.2566	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.64732	-0.6338	5	0.72032	D	0.01	.	8.2172	0.31519	0.0:0.8217:0.0:0.1783	.	.	.	.	F	135	.	ENSP00000405770:L135F	L	+	1	0	FAM162A	123611311	0.995000	0.38212	1.000000	0.80357	0.745000	0.42441	1.364000	0.34171	0.857000	0.35407	0.655000	0.94253	CTT	.	.	.	none		0.438	FAM162A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355766.1	NM_014367		T	122128621	C	T	122128621	2	4	177	1	0	0	0	0	0	0	0	1	5478	564	20	2		2	FAM162A	3	122128621	Silent	SNP	C	TCGA-G7-7502-01A-11D-2201-08	14018011	122128621	75893809	18	10344											
ATR	545	hgsc.bcm.edu	37	chr3	142238533	142238533	+	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	ggtatttagatgaggttctaGtatttcccgaacatgctcag	10	14	10	7	1	2	2	1	1	1	1	3	3	3	2	1	2	2	4	1	2	5	7			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr3:142238533G>A	ENST00000350721.4	-	24	4481	c.4360C>T	c.(4360-4362)Cta>Tta	p.L1454L	ATR_ENST00000383101.3_Silent_p.L1390L	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	1454					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						TGAGGTTCTAGTATTTCCCGA	0.363								Other conserved DNA damage response genes																													p.L1454L		Atlas-SNP	.											.	ATR	285	.	0			c.C4360T						PASS	.						118	118	118					3																	142238533		2203	4300	6503	SO:0001819	synonymous_variant	545	exon24			GTTCTAGTATTTC	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.4360C>T	chr3.hg19:g.142238533G>A		170.0	0.0	.		152.0	32.0	.	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Silent	SNP	ENST00000350721.4	hg19	CCDS3124.1																																																																																			.	.	.	none		0.363	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		A	142238533	G	A	142238533	2	1	177	1	0	0	0	0	0	0	0	1	1204	1020	36	2		2	ATR	3	142238533	Silent	SNP	G	TCGA-G7-7502-01A-11D-2201-08	20109912	142238533	55783897	19	10345											
N4BP2	55728	hgsc.bcm.edu	37	chr4	40122970	40122970	+	Frame_Shift_Del	DEL	A	A	-																															taaaagcacgtttgttgaagAaagtgagcttaccagtgcag																										TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr4:40122970delA	ENST00000261435.6	+	9	3655	c.3239delA	c.(3238-3240)gaafs	p.E1080fs		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	1080					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						TTTGTTGAAGAAAGTGAGCTT	0.338																																					p.E1080fs		Atlas-INDEL	.											.	N4BP2	166	.	0			c.3238delG						PASS	.						75	81	79					4																	40122970		2201	4300	6501	SO:0001589	frameshift_variant	55728	exon9			.	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"BCL-3 binding protein"					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.3239delA	chr4.hg19:g.40122970delA	ENSP00000261435:p.Glu1080fs	101.0	0.0	0		96.0	25.0	0.260417	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Frame_Shift_Del	DEL	ENST00000261435.6	hg19	CCDS3457.1																																																																																			.	.	.	none		0.338	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177		-	40122970	A	-	40122970	7	5	177	1	0	1	0	1	0	0	0	0	10117	246	9	0	3265	0	N4BP2	4	40122970	Frame_Shift_Del	DEL	A	TCGA-G7-7502-01A-11D-2201-08		40122970	151031306	20	10346											
EHMT2	10919	hgsc.bcm.edu	37	chr6	31864742	31864742	+	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	ttccttctccagcagcagcgCccccatctcagcgggggcct	5	8	10	18	2	2	0	1	0	2	0	5	0	3	0	5	2	4	2	5	2	0	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr6:31864742C>A	ENST00000375537.4	-	2	73	c.67G>T	c.(67-69)Gcg>Tcg	p.A23S	EHMT2_ENST00000375530.4_Missense_Mutation_p.A23S|C2_ENST00000469372.1_5'Flank|EHMT2_ENST00000375528.4_Missense_Mutation_p.A80S|EHMT2_ENST00000395728.3_Missense_Mutation_p.A80S|EHMT2_ENST00000480912.1_5'Flank	NM_006709.3	NP_006700.3	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	23					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						AGCAGCAGCGCCCCCATCTCA	0.637																																					p.A23S		Atlas-SNP	.											.	EHMT2	45	.	0			c.G67T						PASS	.						129	130	130					6																	31864742		1511	2709	4220	SO:0001583	missense	10919	exon2			GCAGCGCCCCCAT	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.67G>T	chr6.hg19:g.31864742C>A	ENSP00000364687:p.Ala23Ser	202.0	0.0	.		137.0	37.0	.	NM_025256	B0UZY2|Q14349|Q5JP83|Q5JQ92|Q5JQA1|Q5JQG3|Q6PK06|Q96MH5|Q96QD0|Q9UQL8|Q9Y331	Missense_Mutation	SNP	ENST00000375537.4	hg19	CCDS4725.1	.	.	.	.	.	.	.	.	.	.	C	11.55	1.673198	0.29693	.	.	ENSG00000204371	ENST00000395728;ENST00000375528;ENST00000375530;ENST00000375537	T;T;T;T	0.76968	-0.73;-1.06;-0.98;-0.68	3.79	1.93	0.25924	.	0.364320	0.20081	N	0.099658	T	0.38957	0.1060	N	0.08118	0	0.22531	N	0.999013	B;P;B;B	0.50819	0.03;0.939;0.05;0.03	B;B;B;B	0.43867	0.017;0.434;0.025;0.002	T	0.32798	-0.9893	10	0.51188	T	0.08	.	5.6198	0.17451	0.0:0.7389:0.0:0.261	.	80;23;23;23	A2ABF8;Q96KQ7-3;Q96KQ7-2;Q96KQ7	.;.;.;EHMT2_HUMAN	S	80;80;23;23	ENSP00000379078:A80S;ENSP00000364678:A80S;ENSP00000364680:A23S;ENSP00000364687:A23S	ENSP00000364678:A80S	A	-	1	0	EHMT2	31972721	1.000000	0.71417	1.000000	0.80357	0.248000	0.25809	1.196000	0.32198	0.735000	0.32537	-0.361000	0.07541	GCG	.	.	.	none		0.637	EHMT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076355.5	NM_006709		A	31864742	C	A	31864742	3	1	177	1	0	0	0	0	1	0	0	0	4986	739	26	4	3673	4	EHMT2	6	31864742	Missense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08		31864742	139250325	21	10347											
BRD2	6046	hgsc.bcm.edu	37	chr6	32945266	32945266	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgcacaggagtttgctgcTgatgtacggcttatgttctc	7	14	12	8	1	1	1	0	1	1	0	2	3	1	2	0	2	4	7	0	2	2	4			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr6:32945266T>C	ENST00000374825.4	+	8	2949	c.1248T>C	c.(1246-1248)gcT>gcC	p.A416A	BRD2_ENST00000395287.1_Silent_p.A416A|BRD2_ENST00000374831.4_Silent_p.A416A|BRD2_ENST00000449085.2_Silent_p.A369A|BRD2_ENST00000443797.2_Silent_p.A296A|BRD2_ENST00000395289.2_Silent_p.A416A	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	416	Bromo 2. {ECO:0000255|PROSITE- ProRule:PRU00035}.				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						AGTTTGCTGCTGATGTACGGC	0.517																																					p.A416A		Atlas-SNP	.											.	BRD2	70	.	0			c.T1248C						PASS	.						279	225	244					6																	32945266		1511	2708	4219	SO:0001819	synonymous_variant	6046	exon8			TGCTGCTGATGTA	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.1248T>C	chr6.hg19:g.32945266T>C		228.0	0.0	.		158.0	41.0	.	NM_005104	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Silent	SNP	ENST00000374825.4	hg19	CCDS4762.1	.	.	.	.	.	.	.	.	.	.	T	9.651	1.141473	0.21205	.	.	ENSG00000204256	ENST00000449025	.	.	.	5.25	5.25	0.73442	.	.	.	.	.	T	0.55337	0.1914	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56360	-0.7992	4	.	.	.	-14.7189	13.1555	0.59514	0.0:0.0:0.0:1.0	.	.	.	.	P	422	.	.	L	+	2	0	BRD2	33053244	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	0.370000	0.20433	2.205000	0.71048	0.523000	0.50628	CTG	.	.	.	none		0.517	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2			C	32945266	T	C	32945266	2	2	177	1	0	0	0	0	0	0	0	1	1504	1567	55	3		3	BRD2	6	32945266	Silent	SNP	T	TCGA-G7-7502-01A-11D-2201-08	1080524	32945266	138169801	22	10348											
DNAH8	1769	hgsc.bcm.edu	37	chr6	38913344	38913344	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agctgagtaaacttccacaaTttgcagaaattatgaaccag	16	10	7	8	0	0	3	0	2	0	1	1	3	1	3	2	0	4	3	2	0	6	4			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr6:38913344T>C	ENST00000359357.3	+	78	11712	c.11458T>C	c.(11458-11460)Ttt>Ctt	p.F3820L	DNAH8_ENST00000449981.2_Missense_Mutation_p.F4037L|DNAH8_ENST00000441566.1_Missense_Mutation_p.F3784L|RP1-207H1.3_ENST00000416948.1_RNA			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	3820					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						ACTTCCACAATTTGCAGAAAT	0.488																																					p.F4037L		Atlas-SNP	.											.	DNAH8	1239	.	0			c.T12109C						PASS	.						96	95	96					6																	38913344		2203	4300	6503	SO:0001583	missense	1769	exon80			CCACAATTTGCAG	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.11458T>C	chr6.hg19:g.38913344T>C	ENSP00000352312:p.Phe3820Leu	134.0	0.0	.		114.0	35.0	.	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	T	26.7	4.762200	0.89932	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.10382	2.88;2.88;2.88	5.59	5.59	0.84812	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.30634	0.0771	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	T	0.20706	-1.0267	10	0.62326	D	0.03	.	15.7453	0.77936	0.0:0.0:0.0:1.0	.	3784;3820	Q96JB1-2;Q96JB1	.;DYH8_HUMAN	L	4025;4025;3820;3784	ENSP00000333363:F4025L;ENSP00000352312:F3820L;ENSP00000402294:F3784L	ENSP00000333363:F4025L	F	+	1	0	DNAH8	39021322	1.000000	0.71417	0.981000	0.43875	0.962000	0.63368	7.948000	0.87774	2.129000	0.65627	0.459000	0.35465	TTT	.	.	.	none		0.488	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		C	38913344	T	C	38913344	3	2	177	1	0	0	0	0	1	0	0	0	4609	1493	52	3	11760	3	DNAH8	6	38913344	Missense_Mutation	SNP	T	TCGA-G7-7502-01A-11D-2201-08	5968078	38913344	132201723	23	10349											
SLC35B2	347734	hgsc.bcm.edu	37	chr6	44224125	44224125	+	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	gcttcagggcctgccacatcGgggtggtctctgccgcctct	3	10	13	15	2	3	0	1	0	2	0	5	0	3	0	4	4	2	1	4	4	0	1			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr6:44224125G>C	ENST00000393812.3	-	3	457	c.314C>G	c.(313-315)cCg>cGg	p.P105R	SLC35B2_ENST00000393810.1_Intron|MIR4647_ENST00000583964.1_RNA|SLC35B2_ENST00000538577.1_Intron|SLC35B2_ENST00000537814.1_Intron|SLC35B2_ENST00000495706.1_5'UTR	NM_178148.2	NP_835361.1	Q8TB61	S35B2_HUMAN	solute carrier family 35 (adenosine 3'-phospho 5'-phosphosulfate transporter), member B2	105					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)			CTGCCACATCGGGGTGGTCTC	0.627																																					p.P105R		Atlas-SNP	.											.	SLC35B2	40	.	0			c.C314G						PASS	.						58	67	64					6																	44224125		2203	4300	6503	SO:0001583	missense	347734	exon3			CACATCGGGGTGG	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.314C>G	chr6.hg19:g.44224125G>C	ENSP00000377401:p.Pro105Arg	144.0	0.0	.		98.0	30.0	.	NM_178148	B4DDU9|F5H7Y9|Q2VY06|Q53GA3|Q5T9W1|Q5T9W2|Q7Z2G3|Q8NBK6|Q96AR6	Missense_Mutation	SNP	ENST00000393812.3	hg19	CCDS34462.1	.	.	.	.	.	.	.	.	.	.	G	11.82	1.752871	0.31046	.	.	ENSG00000157593	ENST00000393812;ENST00000341553	T	0.30714	1.52	4.26	3.35	0.38373	.	0.419213	0.26176	N	0.025884	T	0.08935	0.0221	N	0.14661	0.345	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.06826	-1.0805	10	0.22109	T	0.4	-29.8524	15.4721	0.75446	0.0:0.1512:0.8488:0.0	.	105	Q8TB61	S35B2_HUMAN	R	105	ENSP00000377401:P105R	ENSP00000342455:P105R	P	-	2	0	SLC35B2	44332103	1.000000	0.71417	0.889000	0.34880	0.859000	0.49053	7.270000	0.78493	2.191000	0.70037	0.561000	0.74099	CCG	.	.	.	none		0.627	SLC35B2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040724.2			C	44224125	G	C	44224125	3	2	177	1	0	0	0	0	1	0	0	0	14589	1116	39	4	992	4	SLC35B2	6	44224125	Missense_Mutation	SNP	G	TCGA-G7-7502-01A-11D-2201-08	5310781	44224125	126890942	24	10350											
MOXD1	26002	hgsc.bcm.edu	37	chr6	132694134	132694134	+	Missense_Mutation	SNP	A	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	cagatcactctcacagtgctAtcctggggatcagacatggg	10	9	11	11	0	3	2	3	0	1	2	5	3	4	3	1	3	1	1	1	3	1	1			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr6:132694134A>C	ENST00000367963.3	-	3	532	c.414T>G	c.(412-414)gaT>gaG	p.D138E	MOXD1_ENST00000336749.3_Missense_Mutation_p.D70E	NM_015529.2	NP_056344.2	Q6UVY6	MOXD1_HUMAN	monooxygenase, DBH-like 1	138	DOMON. {ECO:0000255|PROSITE- ProRule:PRU00246}.					endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(3)|skin(1)	37	Breast(56;0.0495)			OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)		TCACAGTGCTATCCTGGGGAT	0.458																																					p.D138E		Atlas-SNP	.											.	MOXD1	136	.	0			c.T414G						PASS	.						100	89	92					6																	132694134		2203	4300	6503	SO:0001583	missense	26002	exon3			AGTGCTATCCTGG	AY007239	CCDS5152.2	6q23.2	2010-09-24			ENSG00000079931	ENSG00000079931			21063	protein-coding gene	gene with protein product		609000				9751809	Standard	XM_006715456		Approved	DKFZP564G202, MOX, dJ248E1.1	uc003qdf.3	Q6UVY6	OTTHUMG00000055853	ENST00000367963.3:c.414T>G	chr6.hg19:g.132694134A>C	ENSP00000356940:p.Asp138Glu	120.0	0.0	.		103.0	31.0	.	NM_015529	Q5THU6|Q8NC97|Q8WV49|Q9H4M6|Q9Y4U3	Missense_Mutation	SNP	ENST00000367963.3	hg19	CCDS5152.2	.	.	.	.	.	.	.	.	.	.	A	4.845	0.157121	0.09236	.	.	ENSG00000079931	ENST00000367963;ENST00000336749	T;T	0.77750	-1.12;-1.12	5.3	0.0261	0.14148	DOMON domain (3);	0.440036	0.24074	N	0.041793	T	0.17195	0.0413	N	0.02129	-0.67	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.37842	-0.9688	10	0.02654	T	1	-26.2778	1.3667	0.02202	0.1886:0.3795:0.1103:0.3217	.	138;70	Q6UVY6;Q6UVY6-2	MOXD1_HUMAN;.	E	138;70	ENSP00000356940:D138E;ENSP00000336998:D70E	ENSP00000336998:D70E	D	-	3	2	MOXD1	132735827	0.665000	0.27466	0.999000	0.59377	0.974000	0.67602	-0.336000	0.07863	0.084000	0.17077	0.528000	0.53228	GAT	.	.	.	none		0.458	MOXD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000125837.1	NM_015529		C	132694134	A	C	132694134	3	2	177	1	0	0	0	0	1	0	0	0	9727	446	16	5	1467	5	MOXD1	6	132694134	Missense_Mutation	SNP	A	TCGA-G7-7502-01A-11D-2201-08	88470009	132694134	38420933	25	10351											
TXLNB	167838	hgsc.bcm.edu	37	chr6	139563747	139563747	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actggcagctcctctgctgcTgctcgtgggggctgcctact	3	11	13	14	1	1	0	0	0	1	0	3	0	2	0	2	3	6	6	2	3	1	1			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr6:139563747T>C	ENST00000358430.3	-	10	2203	c.1971A>G	c.(1969-1971)gcA>gcG	p.A657A	RP1-225E12.3_ENST00000585874.1_RNA	NM_153235.3	NP_694967.3	Q8N3L3	TXLNB_HUMAN	taxilin beta	657						cytoplasm (GO:0005737)				breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)		CCTCTGCTGCTGCTCGTGGGG	0.642																																					p.A657A		Atlas-SNP	.											.	TXLNB	96	.	0			c.A1971G						PASS	.						47	53	51					6																	139563747		2203	4300	6503	SO:0001819	synonymous_variant	167838	exon10			TGCTGCTGCTCGT		CCDS34545.1	6q23.3	2008-02-05	2005-07-29	2005-07-29	ENSG00000164440	ENSG00000164440			21617	protein-coding gene	gene with protein product		611438	"chromosome 6 open reading frame 198"	C6orf198		15184072	Standard	NM_153235		Approved	DKFZp451A175, MDP77, dJ522B19.2	uc021zfy.1	Q8N3L3	OTTHUMG00000015688	ENST00000358430.3:c.1971A>G	chr6.hg19:g.139563747T>C		142.0	0.0	.		131.0	42.0	.	NM_153235	Q5VTF3|Q76L25|Q86T52|Q8N3S2	Silent	SNP	ENST00000358430.3	hg19	CCDS34545.1																																																																																			.	.	.	none		0.642	TXLNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042458.1	NM_153235		C	139563747	T	C	139563747	2	2	177	1	0	0	0	0	0	0	0	1	16800	1567	55	3		3	TXLNB	6	139563747	Silent	SNP	T	TCGA-G7-7502-01A-11D-2201-08	6869613	139563747	31551320	26	10352											
HOXA10	3206	hgsc.bcm.edu	37	chr7	27211695	27211695	+	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	atattgaacagaaactccttCtccagctccagtgtctggtg	10	12	8	11	0	2	2	0	1	2	1	5	2	4	2	3	1	3	1	3	1	3	3			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr7:27211695C>T	ENST00000283921.4	-	2	1055	c.1056G>A	c.(1054-1056)gaG>gaA	p.E352E	MIR196B_ENST00000384852.1_RNA|RP1-170O19.20_ENST00000470747.4_Intron|HOXA10_ENST00000521421.1_5'UTR|HOXA9_ENST00000497089.1_5'Flank|HOXA10_ENST00000396344.4_Silent_p.E36E|HOXA-AS4_ENST00000519694.1_RNA|HOXA-AS4_ENST00000519935.1_RNA|RP1-170O19.20_ENST00000465941.1_Intron|HOXA-AS4_ENST00000523790.1_RNA	NM_018951.3	NP_061824.3	P31260	HXA10_HUMAN	homeobox A10	352					anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|male gonad development (GO:0008584)|multicellular organismal development (GO:0007275)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase binding (GO:0042826)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	9						GAAACTCCTTCTCCAGCTCCA	0.532																																					p.E352E		Atlas-SNP	.											.	HOXA10	55	.	0			c.G1056A						PASS	.						111	105	107					7																	27211695		2203	4300	6503	SO:0001819	synonymous_variant	3206	exon2			CTCCTTCTCCAGC		CCDS5410.2	7p15.2	2011-06-20	2005-12-22		ENSG00000253293	ENSG00000253293		"Homeoboxes / ANTP class : HOXL subclass"	5100	protein-coding gene	gene with protein product		142957	"homeo box A10"	HOX1H, HOX1		1973146, 1358459	Standard	NR_037939		Approved		uc011jzm.2	P31260	OTTHUMG00000023436	ENST00000283921.4:c.1056G>A	chr7.hg19:g.27211695C>T		130.0	0.0	.		182.0	80.0	.	NM_018951	O43370|O43605|Q15949|Q504T1	Silent	SNP	ENST00000283921.4	hg19	CCDS5410.2																																																																																			.	.	.	none		0.532	HOXA10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358724.2			T	27211695	C	T	27211695	2	4	177	1	0	0	0	0	0	0	0	1	7296	912	32	2		2	HOXA10	7	27211695	Silent	SNP	C	TCGA-G7-7502-01A-11D-2201-08		27211695	131926968	27	10353											
NRG1	3084	hgsc.bcm.edu	37	chr8	32463201	32463201	+	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	tcaccatcgtggaatcaaacGgtaagagatacctacggtat	14	9	9	9	3	2	1	2	0	0	1	3	3	2	2	2	3	3	2	2	3	6	4	rs78513616		TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr8:32463201G>A	ENST00000405005.3	+	3	400	c.400G>A	c.(400-402)Gag>Aag	p.E134K	NRG1_ENST00000287845.5_Splice_Site_p.A134T|NRG1_ENST00000287842.3_Splice_Site_p.E134K|NRG1_ENST00000519301.1_Splice_Site_p.A113T|NRG1_ENST00000341377.5_Splice_Site_p.E134K|NRG1_ENST00000356819.4_Splice_Site_p.E134K|NRG1_ENST00000523079.1_Splice_Site_p.E134K|NRG1_ENST00000338921.4_Splice_Site_p.E134K|NRG1_ENST00000521670.1_Splice_Site_p.E134K|NRG1_ENST00000520407.1_Splice_Site_p.A349T			Q02297	NRG1_HUMAN	neuregulin 1	134					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)		GGAATCAAACGGTAAGAGATA	0.398																																					p.A349T		Atlas-SNP	.											.	NRG1	260	.	0			c.G1045A						PASS	.	G	LYS/GLU,LYS/GLU,THR/ALA,LYS/GLU,LYS/GLU,THR/ALA,THR/ALA,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,THR/ALA,LYS/GLU	0,4406		0,0,2203	143	129	134		337,337,337,400,400,400,400,400,400,400,400,400,400,1045,400	5	1	8	dbSNP_131	134	1,8599	1.2+/-3.3	0,1,4299	no	missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice	NRG1	NM_001159995.1,NM_001159999.1,NM_001160001.1,NM_001160002.1,NM_001160004.1,NM_001160005.1,NM_001160007.1,NM_001160008.1,NM_004495.3,NM_013956.3,NM_013957.3,NM_013958.3,NM_013960.3,NM_013962.2,NM_013964.3	56,56,58,56,56,58,58,56,56,56,56,56,56,58,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	113/608,113/625,113/591,134/195,134/460,134/208,134/178,134/421,134/212,134/646,134/638,134/242,134/463,349/423,134/641	32463201	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	3084	exon3			TCAAACGGTAAGA	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.400+1G>A	chr8.hg19:g.32463201G>A		161.0	0.0	.		123.0	21.0	.	NM_013962	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Missense_Mutation	SNP	ENST00000405005.3	hg19	CCDS6085.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.01|13.01	2.108806|2.108806	0.37242|0.37242	0.0|0.0	1.16E-4|1.16E-4	ENSG00000157168|ENSG00000157168	ENST00000519301;ENST00000520407;ENST00000287845|ENST00000518104;ENST00000523534;ENST00000523079;ENST00000338921;ENST00000356819;ENST00000287840;ENST00000341377;ENST00000287842;ENST00000405005;ENST00000521670	T;T;T|T;T;T;T;T;T;T;T;T;T	0.75260|0.39997	-0.92;-0.83;-0.49|1.05;1.05;1.05;1.05;1.05;1.05;1.05;1.05;1.05;1.05	5.03|5.03	5.03|5.03	0.67393|0.67393	.|Immunoglobulin-like fold (1);	.|0.695834	.|0.14318	.|N	.|0.327222	T|T	0.54013|0.54013	0.1832|0.1832	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	B;B;B|P;P;P;P;D;P;P;P;P;D	0.32071|0.59767	0.355;0.11;0.22|0.76;0.776;0.614;0.76;0.986;0.733;0.589;0.857;0.863;0.964	B;B;B|B;B;B;B;D;B;B;B;B;P	0.23852|0.68192	0.049;0.01;0.016|0.038;0.079;0.053;0.038;0.956;0.077;0.054;0.165;0.115;0.454	T|T	0.38478|0.38478	-0.9659|-0.9659	9|10	0.02654|0.24483	T|T	1|0.36	-3.1604|-3.1604	16.914|16.914	0.86147|0.86147	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	134;133;349|134;134;133;134;134;134;134;134;134;134	F8W9E3;B0FWZ3;Q02297-9|E9PHH4;Q7RTW4;B0FYA9;B7Z4Z3;Q02297-4;Q02297-7;Q02297;Q02297-6;Q02297-3;Q02297-8	.;.;.|.;.;.;.;.;.;NRG1_HUMAN;.;.;.	T|K	113;349;134|113;202;134;134;134;134;134;134;134;134	ENSP00000429582:A113T;ENSP00000434640:A349T;ENSP00000287845:A134T|ENSP00000430053:E113K;ENSP00000429067:E202K;ENSP00000430120:E134K;ENSP00000343395:E134K;ENSP00000349275:E134K;ENSP00000287840:E134K;ENSP00000340497:E134K;ENSP00000287842:E134K;ENSP00000384620:E134K;ENSP00000428828:E134K	ENSP00000287845:A134T|ENSP00000287840:E134K	A|E	+|+	1|1	0|0	NRG1|NRG1	32582743|32582743	1.000000|1.000000	0.71417|0.71417	0.953000|0.953000	0.39169|0.39169	0.154000|0.154000	0.21943|0.21943	6.210000|6.210000	0.72176|0.72176	2.485000|2.485000	0.83878|0.83878	0.650000|0.650000	0.86243|0.86243	GCT|GAG	.	G|1.000;A|0.000	0.000	weak		0.398	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1		Missense_Mutation	A	32463201	G	A	32463201	5	1	177	1	0	0	0	0	0	0	1	0	10654	1130	39	1	1161	1	NRG1	8	32463201	Splice_Site	SNP	G	TCGA-G7-7502-01A-11D-2201-08		32463201	113900821	28	10354											
GPR124	25960	hgsc.bcm.edu	37	chr8	37692907	37692907	+	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	aatgtttctctgtcgtccttCcacatcaaggtgggcgctgg	6	13	11	11	2	2	0	1	0	1	0	6	0	4	0	2	3	0	2	2	3	2	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr8:37692907C>G	ENST00000412232.2	+	12	1837	c.1824C>G	c.(1822-1824)ttC>ttG	p.F608L	GPR124_ENST00000315215.7_Intron	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	608					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)			TGTCGTCCTTCCACATCAAGG	0.682																																					p.F608L		Atlas-SNP	.											.	GPR124	85	.	0			c.C1824G						PASS	.						19	23	22					8																	37692907		2201	4298	6499	SO:0001583	missense	25960	exon12			GTCCTTCCACATC	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.1824C>G	chr8.hg19:g.37692907C>G	ENSP00000406367:p.Phe608Leu	30.0	0.0	.		29.0	11.0	.	NM_032777	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Missense_Mutation	SNP	ENST00000412232.2	hg19	CCDS6097.2	.	.	.	.	.	.	.	.	.	.	C	7.845	0.722846	0.15439	.	.	ENSG00000020181	ENST00000416514;ENST00000412232	T	0.53857	0.6	5.29	1.44	0.22558	.	0.251562	0.38778	N	0.001564	T	0.36963	0.0986	N	0.17474	0.49	0.47698	D	0.999493	D	0.62365	0.991	P	0.51266	0.664	T	0.25745	-1.0123	10	0.06625	T	0.88	-18.4995	9.5253	0.39160	0.0:0.7051:0.0:0.2949	.	608	Q96PE1	GP124_HUMAN	L	601;608	ENSP00000406367:F608L	ENSP00000406367:F608L	F	+	3	2	GPR124	37812065	1.000000	0.71417	0.905000	0.35620	0.440000	0.31957	1.327000	0.33746	0.231000	0.21079	-0.140000	0.14226	TTC	.	.	.	none		0.682	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2			G	37692907	C	G	37692907	3	3	177	1	0	0	0	0	1	0	0	0	6645	854	30	4	1849	4	GPR124	8	37692907	Missense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08	5229706	37692907	108671115	29	10355											
GAPVD1	26130	hgsc.bcm.edu	37	chr9	128121733	128121733	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atatccagagattgtctaaaGtagtgactgcaaatcacaga	16	10	8	7	0	2	3	1	1	1	2	3	4	3	3	1	0	1	2	1	0	5	4	rs374403416		TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr9:128121733G>A	ENST00000495955.1	+	26	4350	c.4060G>A	c.(4060-4062)Gta>Ata	p.V1354I	GAPVD1_ENST00000265956.4_Missense_Mutation_p.V1328I|GAPVD1_ENST00000312123.9_Missense_Mutation_p.V1315I|GAPVD1_ENST00000394083.2_Missense_Mutation_p.V1288I|GAPVD1_ENST00000394104.2_Missense_Mutation_p.V1354I|GAPVD1_ENST00000470056.1_Missense_Mutation_p.V1309I|GAPVD1_ENST00000394105.2_Missense_Mutation_p.V1363I|GAPVD1_ENST00000297933.6_Missense_Mutation_p.V1336I			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	1354	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				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						ATTGTCTAAAGTAGTGACTGC	0.358																																					p.V1363I		Atlas-SNP	.											.	GAPVD1	124	.	0			c.G4087A						PASS	.	G	ILE/VAL	0,4406		0,0,2203	140	141	141		4087	6.2	1	9		141	1,8599	1.2+/-3.3	0,1,4299	no	missense	GAPVD1	NM_015635.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	1363/1488	128121733	1,13005	2203	4300	6503	SO:0001583	missense	26130	exon25			TCTAAAGTAGTGA		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.4060G>A	chr9.hg19:g.128121733G>A	ENSP00000419063:p.Val1354Ile	145.0	0.0	.		158.0	35.0	.	NM_015635	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Missense_Mutation	SNP	ENST00000495955.1	hg19		.	.	.	.	.	.	.	.	.	.	G	26.2	4.716877	0.89205	0.0	1.16E-4	ENSG00000165219	ENST00000470056;ENST00000394105;ENST00000394104;ENST00000265956;ENST00000394083;ENST00000495955;ENST00000297933;ENST00000312123;ENST00000438537	T;T;T;T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56;1.56;1.56;1.56	6.17	6.17	0.99709	Vacuolar sorting protein 9 (1);	0.000000	0.85682	D	0.000000	T	0.33352	0.0860	N	0.22421	0.69	0.80722	D	1	B;B;B;B;B;B	0.30870	0.118;0.23;0.298;0.298;0.298;0.188	B;B;B;B;B;B	0.42692	0.113;0.082;0.225;0.395;0.225;0.277	T	0.05194	-1.0900	10	0.25106	T	0.35	.	19.8676	0.96824	0.0:0.0:1.0:0.0	.	1354;369;1309;1315;1336;1363	Q14C86;B3KTX2;Q14C86-3;Q14C86-4;Q14C86-2;Q14C86-6	GAPD1_HUMAN;.;.;.;.;.	I	1309;1363;1354;1328;1288;1354;1336;1315;47	ENSP00000419767:V1309I;ENSP00000377665:V1363I;ENSP00000377664:V1354I;ENSP00000265956:V1328I;ENSP00000377645:V1288I;ENSP00000419063:V1354I;ENSP00000297933:V1336I;ENSP00000309582:V1315I	ENSP00000265956:V1328I	V	+	1	0	GAPVD1	127161554	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.476000	0.97823	2.941000	0.99782	0.655000	0.94253	GTA	.	.	.	weak		0.358	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1			A	128121733	G	A	128121733	3	1	177	1	0	0	0	0	1	0	0	0	6246	1029	36	2	4181	2	GAPVD1	9	128121733	Missense_Mutation	SNP	G	TCGA-G7-7502-01A-11D-2201-08		128121733	13091698	30	10356											
OLAH	55301	hgsc.bcm.edu	37	chr10	15107661	15107661	+	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	attaccttatggaatttggaGgcacccccaagcattttgct	10	13	8	10	0	0	0	0	0	0	0	0	2	0	2	3	3	3	3	3	3	4	5			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr10:15107661G>A	ENST00000378228.3	+	6	735	c.481G>A	c.(481-483)Ggc>Agc	p.G161S	OLAH_ENST00000378217.3_Missense_Mutation_p.G214S|OLAH_ENST00000485251.1_3'UTR	NM_001039702.2	NP_001034791.1	Q9NV23	SAST_HUMAN	oleoyl-ACP hydrolase	161					fatty acid biosynthetic process (GO:0006633)		myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)			endometrium(2)|large_intestine(1)|lung(14)|stomach(1)	18						GGAATTTGGAGGCACCCCCAA	0.408																																					p.G214S		Atlas-SNP	.											.	OLAH	45	.	0			c.G640A						PASS	.						83	77	79					10																	15107661		2203	4300	6503	SO:0001583	missense	55301	exon7			TTTGGAGGCACCC	AK001844	CCDS7106.1, CCDS31152.1	10p13	2010-11-23	2006-07-07	2006-07-07	ENSG00000152463	ENSG00000152463	3.1.2.14		25625	protein-coding gene	gene with protein product			"thioesterase domain containing 1"	THEDC1			Standard	NM_018324		Approved	FLJ11106, SAST	uc001inu.2	Q9NV23	OTTHUMG00000017724	ENST00000378228.3:c.481G>A	chr10.hg19:g.15107661G>A	ENSP00000367473:p.Gly161Ser	79.0	0.0	.		62.0	17.0	.	NM_018324	Q5VUB6|Q9NUW1	Missense_Mutation	SNP	ENST00000378228.3	hg19	CCDS31152.1	.	.	.	.	.	.	.	.	.	.	g	16.13	3.036095	0.54896	.	.	ENSG00000152463	ENST00000429028;ENST00000378228;ENST00000378217	.	.	.	5.03	4.12	0.48240	Thioesterase (1);	0.096919	0.64402	D	0.000001	D	0.84552	0.5497	M	0.92122	3.275	0.52099	D	0.999948	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.99	D	0.87441	0.2395	9	0.72032	D	0.01	-5.4247	12.2837	0.54779	0.0:0.0:0.8303:0.1697	.	161;214	Q9NV23;Q9NV23-2	SAST_HUMAN;.	S	161;161;214	.	ENSP00000367462:G214S	G	+	1	0	OLAH	15147667	1.000000	0.71417	0.972000	0.41901	0.162000	0.22319	1.630000	0.37081	1.222000	0.43521	0.557000	0.71058	GGC	.	.	.	none		0.408	OLAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046964.1	NM_018324		A	15107661	G	A	15107661	3	1	177	1	0	0	0	0	1	0	0	0	10858	1000	35	2	662	2	OLAH	10	15107661	Missense_Mutation	SNP	G	TCGA-G7-7502-01A-11D-2201-08		15107661	120427086	31	10357											
SLC5A12	159963	hgsc.bcm.edu	37	chr11	26725363	26725363	+	Missense_Mutation	SNP	A	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	aatatatgtagtcgagatccAtttgttgattgctctaatac	12	16	7	6	1	1	2	0	1	1	1	3	3	2	2	1	0	2	3	1	0	6	8			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr11:26725363A>C	ENST00000396005.3	-	5	966	c.657T>G	c.(655-657)aaT>aaG	p.N219K	SLC5A12_ENST00000280467.6_Missense_Mutation_p.N219K	NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	219					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						GTCGAGATCCATTTGTTGATT	0.368																																					p.N219K		Atlas-SNP	.											.	SLC5A12	134	.	0			c.T657G						PASS	.						230	218	222					11																	26725363		2203	4299	6502	SO:0001583	missense	159963	exon5			AGATCCATTTGTT	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.657T>G	chr11.hg19:g.26725363A>C	ENSP00000379326:p.Asn219Lys	244.0	0.0	.		172.0	56.0	.	NM_178498	Q86UC7	Missense_Mutation	SNP	ENST00000396005.3	hg19	CCDS7860.2	.	.	.	.	.	.	.	.	.	.	A	7.436	0.639686	0.14386	.	.	ENSG00000148942	ENST00000396005;ENST00000280467;ENST00000533617	D;D;D	0.87256	-2.23;-2.23;-2.23	5.07	3.9	0.45041	.	0.177263	0.47852	D	0.000209	T	0.81283	0.4790	L	0.48174	1.505	0.34755	D	0.732193	B;B	0.32467	0.055;0.372	B;B	0.36030	0.037;0.216	T	0.78191	-0.2300	10	0.22109	T	0.4	.	7.1583	0.25649	0.7866:0.0:0.0757:0.1378	.	219;219	Q1EHB4-2;Q1EHB4	.;SC5AC_HUMAN	K	219;219;31	ENSP00000379326:N219K;ENSP00000280467:N219K;ENSP00000435053:N31K	ENSP00000280467:N219K	N	-	3	2	SLC5A12	26681939	1.000000	0.71417	0.997000	0.53966	0.669000	0.39330	1.028000	0.30128	0.834000	0.34852	0.397000	0.26171	AAT	.	.	.	none		0.368	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498		C	26725363	A	C	26725363	3	2	177	1	0	0	0	0	1	0	0	0	14677	214	8	5	1243	5	SLC5A12	11	26725363	Missense_Mutation	SNP	A	TCGA-G7-7502-01A-11D-2201-08		26725363	108281153	32	10358											
AHNAK	79026	hgsc.bcm.edu	37	chr11	62293750	62293750	+	Frame_Shift_Del	DEL	G	G	-																															ttgggtcctttcaggtttaaGtcaatatcaggcatggagat																										TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr11:62293750delG	ENST00000378024.4	-	5	8413	c.8139delC	c.(8137-8139)gacfs	p.D2713fs	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	2713					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)				TCAGGTTTAAGTCAATATCAG	0.463																																					p.L2714X		Atlas-INDEL	.											.	AHNAK	532	.	0			c.8140delT						PASS	.						195	192	193					11																	62293750		2202	4299	6501	SO:0001589	frameshift_variant	79026	exon5			.	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.8139delC	chr11.hg19:g.62293750delG	ENSP00000367263:p.Asp2713fs	343.0	0.0	0		260.0	83.0	0.319231	NM_001620	A1A586	Frame_Shift_Del	DEL	ENST00000378024.4	hg19	CCDS31584.1																																																																																			.	.	.	none		0.463	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		-	62293750	G	-	62293750	7	5	177	1	0	1	0	1	0	0	0	0	414	1020	36	0	9653	0	AHNAK	11	62293750	Frame_Shift_Del	DEL	G	TCGA-G7-7502-01A-11D-2201-08	35568387	62293750	72712766	33	10359											
LRFN4	78999	hgsc.bcm.edu	37	chr11	66625625	66625625	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagctgggccgcatcgcgcCgggagccttcgacgacttcc	5	6	13	17	6	0	0	0	0	0	0	3	3	1	1	5	2	2	2	5	2	0	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr11:66625625C>T	ENST00000309602.4	+	1	653	c.410C>T	c.(409-411)cCg>cTg	p.P137L	PC_ENST00000393958.2_Intron|LRFN4_ENST00000393952.3_Missense_Mutation_p.P137L|PC_ENST00000393955.2_Intron|PC_ENST00000393960.1_Intron	NM_024036.4	NP_076941.2	Q6PJG9	LRFN4_HUMAN	leucine rich repeat and fibronectin type III domain containing 4	137						integral component of membrane (GO:0016021)				breast(1)|lung(1)|prostate(1)	3						CGCATCGCGCCGGGAGCCTTC	0.692																																					p.P137L		Atlas-SNP	.											.	LRFN4	25	.	0			c.C410T						PASS	.						49	54	52					11																	66625625		2200	4294	6494	SO:0001583	missense	78999	exon1			TCGCGCCGGGAGC	BC007718	CCDS8153.1	11q13.1	2013-02-11				ENSG00000173621		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	28456	protein-coding gene	gene with protein product	"fibronectin type III, immunoglobulin and leucine rich repeat domains 6"	612810				16495444, 16828986	Standard	NM_024036		Approved	MGC3103, SALM3., FIGLER6	uc001ojr.3	Q6PJG9		ENST00000309602.4:c.410C>T	chr11.hg19:g.66625625C>T	ENSP00000312535:p.Pro137Leu	117.0	0.0	.		66.0	18.0	.	NM_024036	Q4VBZ3|Q59GV4|Q8N644|Q9BWJ0	Missense_Mutation	SNP	ENST00000309602.4	hg19	CCDS8153.1	.	.	.	.	.	.	.	.	.	.	C	6.081	0.383217	0.11524	.	.	ENSG00000173621	ENST00000393952;ENST00000309602;ENST00000525479	T;T	0.60424	0.19;0.19	4.18	3.26	0.37387	.	0.304296	0.23951	N	0.042954	T	0.51227	0.1662	M	0.69358	2.11	0.24168	N	0.99564	P;B	0.34662	0.462;0.1	B;B	0.29862	0.105;0.108	T	0.50980	-0.8763	10	0.56958	D	0.05	.	9.9013	0.41348	0.0:0.8973:0.0:0.1027	.	137;137	E9PLQ1;Q6PJG9	.;LRFN4_HUMAN	L	137	ENSP00000377524:P137L;ENSP00000312535:P137L	ENSP00000312535:P137L	P	+	2	0	LRFN4	66382201	0.000000	0.05858	0.111000	0.21465	0.012000	0.07955	0.687000	0.25407	1.107000	0.41642	0.313000	0.20887	CCG	.	.	.	none		0.692	LRFN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393127.1	NM_024036		T	66625625	C	T	66625625	3	4	177	1	0	0	0	0	1	0	0	0	8947	652	23	1	412	1	LRFN4	11	66625625	Missense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08	4331875	66625625	68380891	34	10360											
LRP5	4041	hgsc.bcm.edu	37	chr11	68205929	68205929	+	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	ggcagaaatcaccaagccgcCctcagacgacagcccggccc	11	2	10	18	3	2	2	2	0	0	2	2	3	2	2	5	2	2	1	5	2	2	0			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr11:68205929C>T	ENST00000294304.7	+	20	4233	c.4127C>T	c.(4126-4128)cCc>cTc	p.P1376L		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	1376					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						ACCAAGCCGCCCTCAGACGAC	0.592																																					p.P1376L		Atlas-SNP	.											.	LRP5	136	.	0			c.C4127T						PASS	.						95	98	97					11																	68205929		2200	4294	6494	SO:0001583	missense	4041	exon20			AGCCGCCCTCAGA	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.4127C>T	chr11.hg19:g.68205929C>T	ENSP00000294304:p.Pro1376Leu	107.0	0.0	.		90.0	22.0	.	NM_002335	Q96TD6|Q9UES7|Q9UP66	Missense_Mutation	SNP	ENST00000294304.7	hg19	CCDS8181.1	.	.	.	.	.	.	.	.	.	.	C	12.86	2.065810	0.36470	.	.	ENSG00000162337	ENST00000294304	D	0.94000	-3.33	4.53	4.53	0.55603	.	0.139825	0.31495	U	0.007555	D	0.90889	0.7137	L	0.45137	1.4	0.43787	D	0.996329	B;B	0.24092	0.097;0.097	B;B	0.26094	0.066;0.066	D	0.88780	0.3270	10	0.49607	T	0.09	.	17.5404	0.87845	0.0:1.0:0.0:0.0	.	1376;1376	Q9UES7;O75197	.;LRP5_HUMAN	L	1376	ENSP00000294304:P1376L	ENSP00000294304:P1376L	P	+	2	0	LRP5	67962505	0.649000	0.27322	0.025000	0.17156	0.056000	0.15407	5.269000	0.65542	2.379000	0.81126	0.585000	0.79938	CCC	.	.	.	none		0.592	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335		T	68205929	C	T	68205929	3	4	177	1	0	0	0	0	1	0	0	0	8967	623	22	2	4205	2	LRP5	11	68205929	Missense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08	1580304	68205929	66800587	35	10361											
OR8D1	283159	hgsc.bcm.edu	37	chr11	124180474	124180474	+	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	tcgacgaaggacaagctgctGaggaaatagtacatgggggt	13	7	15	6	2	0	1	0	1	0	0	1	5	0	3	0	4	3	3	0	4	5	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr11:124180474G>T	ENST00000357821.2	-	1	259	c.189C>A	c.(187-189)ctC>ctA	p.L63L		NM_001002917.1	NP_001002917.1	Q8WZ84	OR8D1_HUMAN	olfactory receptor, family 8, subfamily D, 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)			kidney(1)|large_intestine(1)|lung(7)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0528)		ACAAGCTGCTGAGGAAATAGT	0.463																																					p.L63L		Atlas-SNP	.											.	OR8D1	53	.	0			c.C189A						PASS	.						87	81	83					11																	124180474		2201	4299	6500	SO:0001819	synonymous_variant	283159	exon1			GCTGCTGAGGAAA	AF238489	CCDS31706.1	11q25	2012-08-09			ENSG00000196341	ENSG00000196341		"GPCR / Class A : Olfactory receptors"	8481	protein-coding gene	gene with protein product				OR8D3			Standard	NM_001002917		Approved	OST004	uc010sag.2	Q8WZ84	OTTHUMG00000165977	ENST00000357821.2:c.189C>A	chr11.hg19:g.124180474G>T		119.0	0.0	.		89.0	4.0	.	NM_001002917	B2RNL4|Q6IEW1|Q8NGH0	Silent	SNP	ENST00000357821.2	hg19	CCDS31706.1																																																																																			.	.	.	none		0.463	OR8D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387285.1	NM_001002917		T	124180474	G	T	124180474	2	4	177	1	0	0	0	0	0	0	0	1	11238	1277	45	4		4	OR8D1	11	124180474	Silent	SNP	G	TCGA-G7-7502-01A-11D-2201-08	55974545	124180474	10826042	36	10362											
MLL2	8085	hgsc.bcm.edu	37	chr12	49433380	49433380	+	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	tggatctgctgccgaatcagCagctctcgtagtcgctggcg	6	10	13	12	4	3	0	1	0	2	0	5	2	3	1	1	2	4	5	1	2	2	1			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr12:49433380C>G	ENST00000301067.7	-	32	8066	c.8067G>C	c.(8065-8067)ctG>ctC	p.L2689L	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2689					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)										GCCGAATCAGCAGCTCTCGTA	0.577																																					p.L2689L		Atlas-SNP	.											.	MLL2	1173	.	0			c.G8067C						PASS	.						19	21	20					12																	49433380		1995	4182	6177	SO:0001819	synonymous_variant	8085	exon32			AATCAGCAGCTCT	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.8067G>C	chr12.hg19:g.49433380C>G		35.0	0.0	.		28.0	10.0	.	NM_003482	O14687	Silent	SNP	ENST00000301067.7	hg19	CCDS44873.1																																																																																			.	.	.	none		0.577	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			G	49433380	C	G	49433380	2	3	177	1	0	0	0	0	0	0	0	1	9628	697	25	4		4	MLL2	12	49433380	Silent	SNP	C	TCGA-G7-7502-01A-11D-2201-08		49433380	84418515	37	10363											
RPH3A	22895	hgsc.bcm.edu	37	chr12	113306301	113306301	+	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	aggtcctcccacagcctatgCctataaagaagaccaagccc	13	6	7	15	0	0	2	0	0	0	2	2	2	2	2	6	1	3	0	6	1	6	3			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr12:113306301C>A	ENST00000389385.4	+	8	1008	c.511C>A	c.(511-513)Cct>Act	p.P171T	RPH3A_ENST00000543106.2_Missense_Mutation_p.P171T|RPH3A_ENST00000549913.2_3'UTR|RPH3A_ENST00000415485.3_Missense_Mutation_p.P171T|RPH3A_ENST00000551052.1_Missense_Mutation_p.P167T|RPH3A_ENST00000548866.1_Missense_Mutation_p.P122T|RPH3A_ENST00000447659.2_Missense_Mutation_p.P122T|RPH3A_ENST00000420983.2_Missense_Mutation_p.P171T	NM_001143854.1|NM_014954.3	NP_001137326.1|NP_055769.2	Q9Y2J0	RP3A_HUMAN	rabphilin 3A	171	Pro-rich.				intracellular protein transport (GO:0006886)	cell junction (GO:0030054)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylinositol phosphate binding (GO:1901981)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)|ovary(3)|prostate(4)|skin(6)|urinary_tract(1)	47				BRCA - Breast invasive adenocarcinoma(302;0.00453)		ACAGCCTATGCCTATAAAGAA	0.602																																					p.P171T		Atlas-SNP	.											.	RPH3A	98	.	0			c.C511A						PASS	.						60	58	59					12																	113306301		2203	4300	6503	SO:0001583	missense	22895	exon8			CCTATGCCTATAA	AB023202	CCDS31904.1, CCDS44979.1	12q24.13	2014-07-02	2014-07-02		ENSG00000089169	ENSG00000089169		"Synaptotagmins"	17056	protein-coding gene	gene with protein product		612159	"rabphilin 3A homolog (mouse)"			10231032, 7822236	Standard	NM_014954		Approved	KIAA0985, rabphilin, exophilin-1	uc001ttz.3	Q9Y2J0	OTTHUMG00000169713	ENST00000389385.4:c.511C>A	chr12.hg19:g.113306301C>A	ENSP00000374036:p.Pro171Thr	55.0	0.0	.		63.0	13.0	.	NM_001143854	B7Z3C3|Q96AE0	Missense_Mutation	SNP	ENST00000389385.4	hg19	CCDS44979.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.653855	0.88056	.	.	ENSG00000089169	ENST00000543106;ENST00000551593;ENST00000389385;ENST00000447659;ENST00000551052;ENST00000415485;ENST00000548866;ENST00000420983	T;T;T;T;T;T;T	0.64438	-0.0;-0.0;-0.1;-0.0;-0.0;-0.1;-0.0	4.77	4.77	0.60923	Zinc finger, RING/FYVE/PHD-type (1);	0.000000	0.64402	D	0.000009	T	0.73521	0.3597	L	0.49126	1.545	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;0.996;0.998	T	0.70676	-0.4806	10	0.28530	T	0.3	.	16.5919	0.84767	0.0:1.0:0.0:0.0	.	122;171;171;167	F8VP47;B7Z9Z7;Q9Y2J0;Q9Y2J0-2	.;.;RP3A_HUMAN;.	T	171;171;171;122;167;171;122;171	ENSP00000440384:P171T;ENSP00000374036:P171T;ENSP00000413254:P122T;ENSP00000448297:P167T;ENSP00000405357:P171T;ENSP00000450347:P122T;ENSP00000408889:P171T	ENSP00000374036:P171T	P	+	1	0	RPH3A	111790684	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.916000	0.75776	2.213000	0.71641	0.655000	0.94253	CCT	.	.	.	none		0.602	RPH3A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405561.1	NM_014954		A	113306301	C	A	113306301	3	1	177	1	0	0	0	0	1	0	0	0	13564	739	26	4	533	4	RPH3A	12	113306301	Missense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08	63872921	113306301	20545594	38	10364											
CCDC62	84660	hgsc.bcm.edu	37	chr12	123286278	123286278	+	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	taattgaagccccaggccacAtgtctgacgtggagtggatg	10	9	13	9	1	1	2	0	2	1	0	1	4	1	4	3	3	1	0	3	3	2	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr12:123286278A>T	ENST00000253079.6	+	9	1929	c.1585A>T	c.(1585-1587)Atg>Ttg	p.M529L	CCDC62_ENST00000392440.2_Missense_Mutation_p.M290L|CCDC62_ENST00000392441.4_Missense_Mutation_p.M529L|CCDC62_ENST00000537566.1_Missense_Mutation_p.M290L	NM_201435.4	NP_958843.2	Q6P9F0	CCD62_HUMAN	coiled-coil domain containing 62	529					cellular response to estradiol stimulus (GO:0071392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(1)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.51e-06)|Epithelial(86;2.65e-05)|BRCA - Breast invasive adenocarcinoma(302;0.206)		CCCAGGCCACATGTCTGACGT	0.502																																					p.M529L		Atlas-SNP	.											.	CCDC62	119	.	0			c.A1585T						PASS	.						138	145	143					12																	123286278		2203	4300	6503	SO:0001583	missense	84660	exon9			GGCCACATGTCTG		CCDS9238.1	12q24.31	2009-08-18			ENSG00000130783	ENSG00000130783			30723	protein-coding gene	gene with protein product	"cancer/testis antigen 109"	613481				18563714, 19126643	Standard	NM_201435		Approved	TSP-NY, FLJ40344, CT109, ERAP75	uc001udc.3	Q6P9F0	OTTHUMG00000168764	ENST00000253079.6:c.1585A>T	chr12.hg19:g.123286278A>T	ENSP00000253079:p.Met529Leu	270.0	0.0	.		250.0	59.0	.	NM_201435	A8K8V1|B3KUP3|Q6ZVF2|Q86VJ0|Q9BYZ5	Missense_Mutation	SNP	ENST00000253079.6	hg19	CCDS9238.1	.	.	.	.	.	.	.	.	.	.	A	13.84	2.358511	0.41801	.	.	ENSG00000130783	ENST00000253079;ENST00000392441;ENST00000537566;ENST00000392440	T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01	5.73	-0.599	0.11645	.	0.206543	0.35805	N	0.002975	T	0.49609	0.1567	L	0.56769	1.78	0.18873	N	0.999988	B;B;B	0.21225	0.053;0.004;0.001	B;B;B	0.15484	0.013;0.006;0.001	T	0.44298	-0.9337	10	0.56958	D	0.05	-8.7087	4.9707	0.14113	0.4874:0.1609:0.3517:0.0	.	529;290;529	Q6P9F0-2;Q6P9F0-3;Q6P9F0	.;.;CCD62_HUMAN	L	529;529;290;290	ENSP00000253079:M529L;ENSP00000376236:M529L;ENSP00000445045:M290L;ENSP00000376235:M290L	ENSP00000253079:M529L	M	+	1	0	CCDC62	121852231	0.575000	0.26692	0.748000	0.31131	0.676000	0.39594	0.351000	0.20096	0.101000	0.17610	0.482000	0.46254	ATG	.	.	.	none		0.502	CCDC62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400930.1	NM_032573		T	123286278	A	T	123286278	3	4	177	1	0	0	0	0	1	0	0	0	2835	217	8	5	1619	5	CCDC62	12	123286278	Missense_Mutation	SNP	A	TCGA-G7-7502-01A-11D-2201-08	9979977	123286278	10565617	39	10365											
SLC15A4	121260	hgsc.bcm.edu	37	chr12	129283926	129283926	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcccattatggcactctgcAtggacttgggggcagctgag	8	9	14	10	0	1	1	0	1	1	0	1	2	1	2	1	4	3	4	1	4	1	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr12:129283926A>G	ENST00000266771.5	-	7	1490	c.1451T>C	c.(1450-1452)aTg>aCg	p.M484T	SLC15A4_ENST00000544112.1_Missense_Mutation_p.M147T|SLC15A4_ENST00000545031.1_Start_Codon_SNP_p.M1T	NM_145648.3	NP_663623.1	Q8N697	S15A4_HUMAN	solute carrier family 15 (oligopeptide transporter), member 4	484					ion transport (GO:0006811)|oligopeptide transport (GO:0006857)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	L-histidine transmembrane transporter activity (GO:0005290)|symporter activity (GO:0015293)			endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|skin(1)	22	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.69e-06)|Epithelial(86;1.17e-05)|all cancers(50;5.07e-05)		GGCACTCTGCATGGACTTGGG	0.512																																					p.M484T		Atlas-SNP	.											.	SLC15A4	41	.	0			c.T1451C						PASS	.						84	81	82					12																	129283926		2203	4300	6503	SO:0001583	missense	121260	exon7			CTCTGCATGGACT	AY038999	CCDS9264.1	12q24.32	2013-07-18	2013-07-18		ENSG00000139370	ENSG00000139370		"Solute carriers"	23090	protein-coding gene	gene with protein product		615806	"solute carrier family 15, member 4"			11741232	Standard	NM_145648		Approved	PHT1, PTR4	uc001uhu.2	Q8N697	OTTHUMG00000168415	ENST00000266771.5:c.1451T>C	chr12.hg19:g.129283926A>G	ENSP00000266771:p.Met484Thr	107.0	0.0	.		95.0	36.0	.	NM_145648	A6H8Y9|B3KTK1|Q71M34|Q7Z5F8|Q8TAH0	Missense_Mutation	SNP	ENST00000266771.5	hg19	CCDS9264.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.361060	0.82353	.	.	ENSG00000139370	ENST00000266771;ENST00000545031;ENST00000544112	T;T	0.05382	3.45;3.45	5.15	5.15	0.70609	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	T	0.28830	0.0715	M	0.85542	2.76	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.08249	-1.0731	10	0.87932	D	0	.	14.985	0.71342	1.0:0.0:0.0:0.0	.	484	Q8N697	S15A4_HUMAN	T	484;1;147	ENSP00000266771:M484T;ENSP00000439946:M147T	ENSP00000266771:M484T	M	-	2	0	SLC15A4	127849879	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.574000	0.90763	1.929000	0.55896	0.533000	0.62120	ATG	.	.	.	none		0.512	SLC15A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399663.1	NM_145648		G	129283926	A	G	129283926	3	3	177	1	0	0	0	0	1	0	0	0	14414	217	8	3	290	3	SLC15A4	12	129283926	Missense_Mutation	SNP	A	TCGA-G7-7502-01A-11D-2201-08	5997648	129283926	4567969	40	10366											
SLITRK1	114798	hgsc.bcm.edu	37	chr13	84453895	84453895	+	Missense_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	ttaacgtgggcgagatcctaGcgtacagctgagggcagatc	10	8	14	9	3	0	3	0	1	0	2	2	4	1	3	1	2	4	3	1	2	3	3			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr13:84453895G>A	ENST00000377084.2	-	1	2633	c.1748C>T	c.(1747-1749)gCt>gTt	p.A583V		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	583					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)		CGAGATCCTAGCGTACAGCTG	0.542																																					p.A583V		Atlas-SNP	.											.	SLITRK1	196	.	0			c.C1748T						PASS	.						94	80	85					13																	84453895		2203	4300	6503	SO:0001583	missense	114798	exon1			ATCCTAGCGTACA	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.1748C>T	chr13.hg19:g.84453895G>A	ENSP00000366288:p.Ala583Val	36.0	0.0	.		35.0	9.0	.	NM_052910	Q5U5I6|Q96SF9	Missense_Mutation	SNP	ENST00000377084.2	hg19	CCDS9464.1	.	.	.	.	.	.	.	.	.	.	G	7.865	0.726968	0.15439	.	.	ENSG00000178235	ENST00000377084	T	0.58797	0.31	5.22	4.36	0.52297	.	0.190710	0.45126	D	0.000397	T	0.58409	0.2120	M	0.76574	2.34	0.45261	D	0.998262	B	0.22541	0.071	B	0.25987	0.065	T	0.56595	-0.7953	10	0.30854	T	0.27	-10.4812	13.8324	0.63389	0.0:0.1548:0.8452:0.0	.	583	Q96PX8	SLIK1_HUMAN	V	583	ENSP00000366288:A583V	ENSP00000366288:A583V	A	-	2	0	SLITRK1	83351896	1.000000	0.71417	0.958000	0.39756	0.986000	0.74619	3.881000	0.56152	1.320000	0.45209	-0.175000	0.13238	GCT	.	.	.	none		0.542	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910		A	84453895	G	A	84453895	3	1	177	1	0	0	0	0	1	0	0	0	14755	971	34	2	346	2	SLITRK1	13	84453895	Missense_Mutation	SNP	G	TCGA-G7-7502-01A-11D-2201-08		84453895	30715983	41	10367											
UBAC2	337867	hgsc.bcm.edu	37	chr13	99890774	99890774	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcactgccagaagctctttgTgtatgaccttcacgcagtca	9	12	8	12	1	4	2	3	1	1	1	4	2	4	2	2	0	2	3	2	0	2	3			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr13:99890774T>C	ENST00000403766.3	+	2	260	c.125T>C	c.(124-126)gTg>gCg	p.V42A	UBAC2_ENST00000376440.2_Missense_Mutation_p.C84R	NM_001144072.1	NP_001137544.1	Q8NBM4	UBAC2_HUMAN	UBA domain containing 2	42					protein localization to endoplasmic reticulum (GO:0070972)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)	10	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					AAGCTCTTTGTGTATGACCTT	0.547																																					p.C84R		Atlas-SNP	.											.	UBAC2	23	.	0			c.T250C						PASS	.						222	221	222					13																	99890774		2203	4300	6503	SO:0001583	missense	337867	exon2			TCTTTGTGTATGA	AK055110	CCDS9490.1, CCDS45064.1	13q32.3	2012-02-01	2007-04-20	2007-04-20	ENSG00000134882	ENSG00000134882			20486	protein-coding gene	gene with protein product			"phosphoglycerate dehydrogenase like 1"	PHGDHL1			Standard	NM_177967		Approved	FLJ30548, RP11-178C10.1	uc001voa.4	Q8NBM4	OTTHUMG00000017267	ENST00000403766.3:c.125T>C	chr13.hg19:g.99890774T>C	ENSP00000383911:p.Val42Ala	442.0	0.0	.		334.0	83.0	.	NM_177967	B3KNV7|Q0VAB5|Q5W0W6|Q5W0W9|Q6GQR2|Q6P4B0|Q8N2E8|Q96NW2	Missense_Mutation	SNP	ENST00000403766.3	hg19	CCDS45064.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.11|13.11	2.139733|2.139733	0.37728|0.37728	.|.	.|.	ENSG00000134882|ENSG00000134882	ENST00000376440|ENST00000403766;ENST00000355700;ENST00000457666	.|T;T;T	.|0.45276	.|0.9;0.9;0.9	5.72|5.72	4.52|4.52	0.55395|0.55395	.|.	.|0.610304	.|0.17766	.|N	.|0.162736	T|T	0.25865|0.25865	0.0630|0.0630	.|.	.|.	.|.	0.37528|0.37528	D|D	0.917816|0.917816	B|B	0.18968|0.13594	0.032|0.008	B|B	0.13407|0.06405	0.009|0.002	T|T	0.12268|0.12268	-1.0554|-1.0554	6|8	.|.	.|.	.|.	-4.5461|-4.5461	5.6483|5.6483	0.17602|0.17602	0.1608:0.0847:0.0:0.7545|0.1608:0.0847:0.0:0.7545	.|.	84|42	Q8NBM4-2|Q8NBM4	.|UBAC2_HUMAN	R|A	84|42;42;48	.|ENSP00000383911:V42A;ENSP00000347928:V42A;ENSP00000402249:V48A	.|.	C|V	+|+	1|2	0|0	UBAC2|UBAC2	98688775|98688775	0.007000|0.007000	0.16637|0.16637	0.998000|0.998000	0.56505|0.56505	0.983000|0.983000	0.72400|0.72400	1.311000|1.311000	0.33562|0.33562	0.960000|0.960000	0.38005|0.38005	0.482000|0.482000	0.46254|0.46254	TGT|GTG	.	.	.	none		0.547	UBAC2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045588.1	NM_177967		C	99890774	T	C	99890774	3	2	177	1	0	0	0	0	1	0	0	0	16847	1696	59	3	291	3	UBAC2	13	99890774	Missense_Mutation	SNP	T	TCGA-G7-7502-01A-11D-2201-08	15436879	99890774	15279104	42	10368											
ERCC5	2073	hgsc.bcm.edu	37	chr13	103524734	103524734	+	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	ctgtgggggaaacctgatctCgacaaaattagagaatatcc	14	9	10	8	1	1	2	0	1	1	1	3	5	2	3	2	2	1	0	2	2	6	2	rs150671111		TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr13:103524734C>A	ENST00000355739.4	+	13	4288	c.2865C>A	c.(2863-2865)ctC>ctA	p.L955L	ERCC5_ENST00000375954.1_Silent_p.L188L|BIVM-ERCC5_ENST00000602836.1_Silent_p.R1381R	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	955					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)					AACCTGATCTCGACAAAATTA	0.438			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.L1409L		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.C4227A						PASS	.						58	55	56					13																	103524734		2203	4300	6503	SO:0001819	synonymous_variant	0	exon21	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	TGATCTCGACAAA	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.2865C>A	chr13.hg19:g.103524734C>A		60.0	0.0	.		52.0	4.0	.	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Silent	SNP	ENST00000355739.4	hg19	CCDS32004.1																																																																																			.	C|1.000;T|0.000	.	alt		0.438	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1			A	103524734	C	A	103524734	2	1	177	1	0	0	0	0	0	0	0	1	5218	871	31	4		4	ERCC5	13	103524734	Silent	SNP	C	TCGA-G7-7502-01A-11D-2201-08	3633960	103524734	11645144	43	10369											
CASC5	57082	hgsc.bcm.edu	37	chr15	40914067	40914068	+	Frame_Shift_Del	DEL	TT	TT	-																															gatgggaaaatgaatgtaaaTtgtaactcagttcctcatgt																										TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr15:40914067_40914068delTT	ENST00000346991.5	+	11	2073_2074	c.1683_1684delTT	c.(1681-1686)aattgtfs	p.NC561fs	CASC5_ENST00000527044.1_3'UTR|CASC5_ENST00000399668.2_Frame_Shift_Del_p.NC535fs			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	561	Interaction with BUB1 and BUB1B.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		TGAATGTAAATTGTAACTCAGT	0.371																																					p.561_561del		Atlas-INDEL	.											.	CASC5	269	.	0			c.1682_1683del						PASS	.																																			SO:0001589	frameshift_variant	57082	exon11			.	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.1683_1684delTT	chr15.hg19:g.40914067_40914068delTT	ENSP00000335463:p.Asn561fs	94.0	0.0	0		65.0	21.0	0.323077	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Frame_Shift_Del	DEL	ENST00000346991.5	hg19	CCDS42023.1																																																																																			.	.	.	none		0.371	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		-	40914068	TT	-	40914067	7	5	177	1	0	1	0	1	0	0	0	0	2665	1490	52	0	1721	0	CASC5	15	40914067	Frame_Shift_Del	DEL	TT	TCGA-G7-7502-01A-11D-2201-08		40914067	61617325	44	10370											
UBR1	197131	hgsc.bcm.edu	37	chr15	43276106	43276106	+	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	agactctacctgatagaagaCgaaccagatgtttctgtatc	13	11	8	9	1	2	5	0	1	2	4	3	6	2	5	2	0	2	2	2	0	5	4	rs536630830		TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr15:43276106C>G	ENST00000290650.4	-	37	4217	c.4139G>C	c.(4138-4140)cGt>cCt	p.R1380P	UBR1_ENST00000382177.2_3'UTR	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	1380					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)	p.R1380H(1)		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)		TGATAGAAGACGAACCAGATG	0.348																																					p.R1380P		Atlas-SNP	.											UBR1,NS,carcinoma,0,1	UBR1	124	.	1	Substitution - Missense(1)	prostate(1)	c.G4139C						PASS	.						71	63	66					15																	43276106		2203	4299	6502	SO:0001583	missense	197131	exon37			AGAAGACGAACCA		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.4139G>C	chr15.hg19:g.43276106C>G	ENSP00000290650:p.Arg1380Pro	40.0	0.0	.		41.0	2.0	.	NM_174916	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	hg19	CCDS10091.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.750814	0.89753	.	.	ENSG00000159459	ENST00000290650	T	0.49139	0.79	5.84	5.84	0.93424	.	0.289878	0.40554	N	0.001071	T	0.62684	0.2448	M	0.68952	2.095	0.80722	D	1	D	0.69078	0.997	P	0.56751	0.805	T	0.58222	-0.7674	10	0.33940	T	0.23	-22.8504	18.3196	0.90232	0.0:1.0:0.0:0.0	.	1380	Q8IWV7	UBR1_HUMAN	P	1380	ENSP00000290650:R1380P	ENSP00000290650:R1380P	R	-	2	0	UBR1	41063398	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	3.752000	0.55172	2.764000	0.94973	0.655000	0.94253	CGT	.	.	.	none		0.348	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916		G	43276106	C	G	43276106	3	3	177	1	0	0	0	0	1	0	0	0	16913	536	19	4	1154	4	UBR1	15	43276106	Missense_Mutation	SNP	C	TCGA-G7-7502-01A-11D-2201-08	2362039	43276106	59255286	45	10371											
SCAMP2	10066	hgsc.bcm.edu	37	chr15	75142970	75142970	+	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	ggagctgttgcccgagaaccAggccaggcaggcaagcaggt	10	4	16	11	1	0	1	0	0	0	1	0	3	0	2	3	5	4	5	3	5	2	1			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr15:75142970A>T	ENST00000268099.9	-	6	626	c.517T>A	c.(517-519)Tgg>Agg	p.W173R		NM_005697.3	NP_005688.2	O15127	SCAM2_HUMAN	secretory carrier membrane protein 2	173					post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|recycling endosome membrane (GO:0055038)|trans-Golgi network membrane (GO:0032588)|transport vesicle (GO:0030133)				kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	9						CCCGAGAACCAGGCCAGGCAG	0.562																																					p.W173R		Atlas-SNP	.											.	SCAMP2	18	.	0			c.T517A						PASS	.						123	112	115					15																	75142970		2197	4295	6492	SO:0001583	missense	10066	exon6			AGAACCAGGCCAG	AF005038	CCDS10271.1	15q23-q25	2013-02-21			ENSG00000140497	ENSG00000140497		"Secretory carrier membrane proteins"	10564	protein-coding gene	gene with protein product		606912				9378760	Standard	NM_005697		Approved		uc002azb.1	O15127	OTTHUMG00000142817	ENST00000268099.9:c.517T>A	chr15.hg19:g.75142970A>T	ENSP00000268099:p.Trp173Arg	123.0	0.0	.		93.0	21.0	.	NM_005697	B2RDF0|Q9BQE8	Missense_Mutation	SNP	ENST00000268099.9	hg19	CCDS10271.1	.	.	.	.	.	.	.	.	.	.	A	7.869	0.727707	0.15439	.	.	ENSG00000140497	ENST00000268099;ENST00000543345	T	0.16597	2.33	4.48	4.48	0.54585	.	0.307839	0.34802	N	0.003680	T	0.22513	0.0543	M	0.71036	2.16	0.30893	N	0.730139	B;B	0.21520	0.049;0.057	B;B	0.29267	0.035;0.1	T	0.10543	-1.0625	10	0.25751	T	0.34	.	13.2599	0.60098	1.0:0.0:0.0:0.0	.	173;142	O15127;B3KU14	SCAM2_HUMAN;.	R	173;142	ENSP00000268099:W173R	ENSP00000268099:W173R	W	-	1	0	SCAMP2	72930023	1.000000	0.71417	1.000000	0.80357	0.454000	0.32378	4.332000	0.59279	1.795000	0.52594	0.402000	0.26972	TGG	.	.	.	none		0.562	SCAMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286403.3	NM_005697		T	75142970	A	T	75142970	3	4	177	1	0	0	0	0	1	0	0	0	13884	188	7	5	488	5	SCAMP2	15	75142970	Missense_Mutation	SNP	A	TCGA-G7-7502-01A-11D-2201-08	31866864	75142970	27388422	46	10372											
ZSCAN2	54993	hgsc.bcm.edu	37	chr15	85159554	85159554	+	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	ttccagaaacagcttcctgcGtacatggctgccctgtgtga	8	11	10	12	1	0	2	0	1	0	1	2	2	2	2	3	1	5	3	3	1	2	3			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr15:85159554G>A	ENST00000448803.2	+	3	698				ZSCAN2_ENST00000327179.6_Intron|ZSCAN2_ENST00000546148.1_Intron|ZSCAN2_ENST00000541040.1_Intron|ZSCAN2_ENST00000358472.3_Intron|ZSCAN2_ENST00000538076.1_Intron|RP11-182J1.5_ENST00000542197.1_RNA|ZSCAN2_ENST00000485222.2_Intron|ZSCAN2_ENST00000379358.3_Missense_Mutation_p.V141I	NM_181877.3	NP_870992.2	Q7Z7L9	ZSCA2_HUMAN	zinc finger and SCAN domain containing 2						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)		agcttcctgcgtacatggctg	0.463																																					p.V141I		Atlas-SNP	.											.	ZSCAN2	43	.	0			c.G421A						PASS	.						170	139	149					15																	85159554		2203	4299	6502	SO:0001627	intron_variant	54993	exon3			TCCTGCGTACATG	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.407-4279G>A	chr15.hg19:g.85159554G>A		81.0	0.0	.		65.0	22.0	.	NM_001007072	A6NG83|B2RMQ9|Q6ZQY9|Q9NWU4	Missense_Mutation	SNP	ENST00000448803.2	hg19	CCDS10329.2	.	.	.	.	.	.	.	.	.	.	G	2.654	-0.281322	0.05642	.	.	ENSG00000176371	ENST00000379358	T	0.05855	3.38	1.85	-3.69	0.04450	.	.	.	.	.	T	0.03434	0.0099	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41787	-0.9489	8	0.38643	T	0.18	.	1.9006	0.03267	0.2148:0.1858:0.4349:0.1645	.	141	Q7Z7L9-4	.	I	141	ENSP00000368663:V141I	ENSP00000368663:V141I	V	+	1	0	ZSCAN2	82960558	0.000000	0.05858	0.000000	0.03702	0.060000	0.15804	-2.727000	0.00807	-1.295000	0.02357	-0.414000	0.06135	GTA	.	.	.	none		0.463	ZSCAN2-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396956.1	NM_017894		A	85159554	G	A	85159554	1	1	177	0	1	0	0	0	0	0	0	0	18243	1145	40	1		1	ZSCAN2	15	85159554	Intron	SNP	G	TCGA-G7-7502-01A-11D-2201-08	10016584	85159554	17371838	47	10373											
KIAA0556	23247	hgsc.bcm.edu	37	chr16	27761006	27761006	+	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	ccctcagtgccttcgaccgcTcccaccggggacgcatctcc	5	7	9	20	4	2	0	1	0	1	0	5	2	3	1	6	2	1	2	6	2	0	1			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr16:27761006T>A	ENST00000261588.4	+	16	2744	c.2725T>A	c.(2725-2727)Tcc>Acc	p.S909T		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	909						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						CTTCGACCGCTCCCACCGGGG	0.637																																					p.S909T		Atlas-SNP	.											.	KIAA0556	348	.	0			c.T2725A						PASS	.						63	60	61					16																	27761006		2197	4300	6497	SO:0001583	missense	23247	exon16			GACCGCTCCCACC	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.2725T>A	chr16.hg19:g.27761006T>A	ENSP00000261588:p.Ser909Thr	108.0	0.0	.		93.0	22.0	.	NM_015202	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	hg19	CCDS32415.1	.	.	.	.	.	.	.	.	.	.	T	18.42	3.620080	0.66787	.	.	ENSG00000047578	ENST00000261588	T	0.10382	2.88	4.7	3.58	0.41010	.	0.196895	0.45606	D	0.000352	T	0.10465	0.0256	L	0.53249	1.67	0.25290	N	0.989366	P	0.47545	0.897	P	0.45639	0.488	T	0.06373	-1.0830	10	0.06365	T	0.9	-22.2078	6.7315	0.23385	0.0:0.0832:0.161:0.7558	.	909	O60303	K0556_HUMAN	T	909	ENSP00000261588:S909T	ENSP00000261588:S909T	S	+	1	0	KIAA0556	27668507	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.876000	0.48498	0.738000	0.32606	0.533000	0.62120	TCC	.	.	.	none		0.637	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202		A	27761006	T	A	27761006	3	1	177	1	0	0	0	0	1	0	0	0	8190	1551	54	5	2787	5	KIAA0556	16	27761006	Missense_Mutation	SNP	T	TCGA-G7-7502-01A-11D-2201-08		27761006	62593747	48	10374											
SEZ6L2	26470	hgsc.bcm.edu	37	chr16	29884867	29884867	+	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	ccccagactcacaggcgcatTtggggaccctatcgctccac	8	7	9	17	2	1	1	1	0	0	1	3	2	2	2	4	3	0	2	4	3	1	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr16:29884867T>A	ENST00000308713.5	-	13	2815	c.2288A>T	c.(2287-2289)aAa>aTa	p.K763I	SEZ6L2_ENST00000537485.1_Missense_Mutation_p.K719I|SEZ6L2_ENST00000350527.3_Missense_Mutation_p.K693I|SEZ6L2_ENST00000346932.5_Missense_Mutation_p.K649I	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2	763	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|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						ACAGGCGCATTTGGGGACCCT	0.667																																					p.K763I		Atlas-SNP	.											.	SEZ6L2	137	.	0			c.A2288T						PASS	.						60	55	57					16																	29884867		2197	4300	6497	SO:0001583	missense	26470	exon13			GCGCATTTGGGGA	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.2288A>T	chr16.hg19:g.29884867T>A	ENSP00000312550:p.Lys763Ile	78.0	0.0	.		61.0	12.0	.	NM_001243332	B7Z1N0|F5H293|H7BXQ6|Q9BW82|Q9UJ45|Q9UJ46|Q9UJ47	Missense_Mutation	SNP	ENST00000308713.5	hg19	CCDS10659.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.145084	0.77888	.	.	ENSG00000174938	ENST00000350527;ENST00000308713;ENST00000346932;ENST00000537485	T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17	4.67	4.67	0.58626	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.49916	D	0.000135	T	0.66742	0.2820	L	0.28556	0.865	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;0.999;0.999;0.999;1.0	D;D;D;D;D;D	0.91635	0.997;0.999;0.996;0.998;0.998;0.999	T	0.63088	-0.6715	10	0.23891	T	0.37	.	13.1007	0.59218	0.0:0.0:0.0:1.0	.	719;763;649;693;763;693	F5H293;B7Z5L4;Q9BW82;Q6UXD5-2;Q6UXD5;Q6UXD5-3	.;.;.;.;SE6L2_HUMAN;.	I	693;763;649;719	ENSP00000310206:K693I;ENSP00000312550:K763I;ENSP00000319215:K649I;ENSP00000439412:K719I	ENSP00000312550:K763I	K	-	2	0	SEZ6L2	29792368	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.939000	0.70179	1.737000	0.51674	0.533000	0.62120	AAA	.	.	.	none		0.667	SEZ6L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255154.2	NM_012410		A	29884867	T	A	29884867	3	1	177	1	0	0	0	0	1	0	0	0	14157	1841	64	5	507	5	SEZ6L2	16	29884867	Missense_Mutation	SNP	T	TCGA-G7-7502-01A-11D-2201-08	2123861	29884867	60469886	49	10375											
HEATR3	55027	hgsc.bcm.edu	37	chr16	50104088	50104088	+	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	aatcatgatatttggttacaGtgtagtgctggactggattc	10	15	11	5	0	1	1	1	1	0	0	2	3	1	3	0	3	2	3	0	3	4	5			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr16:50104088G>A	ENST00000299192.7	+	4	590		c.e4-1		HEATR3_ENST00000285767.4_Splice_Site	NM_182922.2	NP_891552.1	Q7Z4Q2	HEAT3_HUMAN	HEAT repeat containing 3											cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						TTTGGTTACAGTGTAGTGCTG	0.383																																					.		Atlas-SNP	.											.	HEATR3	59	.	0			c.400-1G>A						PASS	.						86	83	84					16																	50104088		2198	4300	6498	SO:0001630	splice_region_variant	55027	exon4			GTTACAGTGTAGT	BC018730	CCDS10739.1	16q12.1	2008-02-05			ENSG00000155393	ENSG00000155393			26087	protein-coding gene	gene with protein product		614951				12477932	Standard	XM_005256013		Approved	FLJ20718	uc002efw.3	Q7Z4Q2	OTTHUMG00000133174	ENST00000299192.7:c.400-1G>A	chr16.hg19:g.50104088G>A		68.0	0.0	.		60.0	31.0	.	NM_182922	A8K1N4|Q8N525|Q8WV56|Q96CC9|Q9NWN7	Splice_Site	SNP	ENST00000299192.7	hg19	CCDS10739.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.012741	0.75161	.	.	ENSG00000155393	ENST00000285767;ENST00000299192	.	.	.	6.03	6.03	0.97812	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.545	0.95291	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	HEATR3	48661589	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.402000	0.73260	2.861000	0.98227	0.655000	0.94253	.	.	.	.	none		0.383	HEATR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256880.2	NM_182922	Intron	A	50104088	G	A	50104088	5	1	177	1	0	0	0	0	0	0	1	0	7036	1043	36	2	413	2	HEATR3	16	50104088	Splice_Site	SNP	G	TCGA-G7-7502-01A-11D-2201-08	20219221	50104088	40250665	50	10376											
AMFR	267	hgsc.bcm.edu	37	chr16	56401438	56401438	+	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	caggtctgatgctatctgacCgctggaagagaaacagtacc	12	8	11	10	1	2	3	0	2	2	1	2	5	2	4	2	2	3	3	2	2	4	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr16:56401438C>A	ENST00000290649.5	-	12	1727	c.1517G>T	c.(1516-1518)cGg>cTg	p.R506L		NM_001144.5	NP_001135.3	Q9UKV5	AMFR_HUMAN	autocrine motility factor receptor, E3 ubiquitin protein ligase	506					aging (GO:0007568)|cellular component movement (GO:0006928)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|learning or memory (GO:0007611)|protein oligomerization (GO:0051259)|protein polyubiquitination (GO:0000209)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)	dendrite (GO:0030425)|endoplasmic reticulum membrane (GO:0005789)|growth cone (GO:0030426)|Hrd1p ubiquitin ligase complex (GO:0000836)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	ligase activity (GO:0016874)|receptor activity (GO:0004872)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17						GCTATCTGACCGCTGGAAGAG	0.498																																					p.R506L	Pancreas(2;144 323 39528)	Atlas-SNP	.											.	AMFR	40	.	0			c.G1517T						PASS	.						248	233	238					16																	56401438		2198	4300	6498	SO:0001630	splice_region_variant	267	exon12			TCTGACCGCTGGA	L35233	CCDS10758.1	16q21	2013-01-09	2012-02-23		ENSG00000159461	ENSG00000159461		"RING-type (C3HC4) zinc fingers"	463	protein-coding gene	gene with protein product		603243	"autocrine motility factor receptor"			1649192	Standard	NM_001144		Approved	RNF45, gp78	uc002eiy.4	Q9UKV5	OTTHUMG00000133239	ENST00000290649.5:c.1516-1G>T	chr16.hg19:g.56401438C>A		360.0	0.0	.		398.0	100.0	.	NM_001144	P26442|Q8IZ70	Missense_Mutation	SNP	ENST00000290649.5	hg19	CCDS10758.1	.	.	.	.	.	.	.	.	.	.	C	14.69	2.611801	0.46631	.	.	ENSG00000159461	ENST00000290649	T	0.14391	2.51	5.8	5.8	0.92144	.	0.234971	0.44483	D	0.000455	T	0.15998	0.0385	M	0.63428	1.95	0.80722	D	1	B;P	0.37985	0.415;0.613	B;B	0.28709	0.089;0.093	T	0.02208	-1.1195	10	0.34782	T	0.22	-24.0104	18.2436	0.89977	0.0:1.0:0.0:0.0	.	506;155	Q9UKV5;Q1RN03	AMFR2_HUMAN;.	L	506	ENSP00000290649:R506L	ENSP00000290649:R506L	R	-	2	0	AMFR	54958939	1.000000	0.71417	1.000000	0.80357	0.452000	0.32318	3.487000	0.53222	2.735000	0.93741	0.655000	0.94253	CGG	.	.	.	none		0.498	AMFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256978.2		Missense_Mutation	A	56401438	C	A	56401438	5	1	177	1	0	0	0	0	0	0	1	0	571	666	23	4	426	4	AMFR	16	56401438	Splice_Site	SNP	C	TCGA-G7-7502-01A-11D-2201-08	6297350	56401438	33953315	51	10377											
GRB7	2886	hgsc.bcm.edu	37	chr17	37898588	37898588	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtctccacctcatcttagcAgctctccggaagacctttgc	7	12	7	15	1	4	1	1	0	3	1	6	2	4	2	4	1	3	2	4	1	2	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr17:37898588A>G	ENST00000309156.4	+	2	291	c.34A>G	c.(34-36)Agc>Ggc	p.S12G	GRB7_ENST00000445327.2_Missense_Mutation_p.S35G|GRB7_ENST00000578702.1_3'UTR|GRB7_ENST00000394209.2_Missense_Mutation_p.S12G|GRB7_ENST00000394204.1_Missense_Mutation_p.S12G|GRB7_ENST00000394211.3_Missense_Mutation_p.S12G|GRB7_ENST00000309185.3_Missense_Mutation_p.S12G	NM_005310.3	NP_005301.2	Q14451	GRB7_HUMAN	growth factor receptor-bound protein 7	12					blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|leukocyte migration (GO:0050900)|negative regulation of translation (GO:0017148)|positive regulation of cell migration (GO:0030335)|positive regulation of signal transduction (GO:0009967)|stress granule assembly (GO:0034063)	cell projection (GO:0042995)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;6.86e-60)|all cancers(3;1.65e-53)|BRCA - Breast invasive adenocarcinoma(8;2.03e-43)|STAD - Stomach adenocarcinoma(3;1.43e-12)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			TCATCTTAGCAGCTCTCCGGA	0.617																																					p.S35G		Atlas-SNP	.											.	GRB7	48	.	0			c.A103G						PASS	.						154	151	152					17																	37898588		2203	4300	6503	SO:0001583	missense	2886	exon2			CTTAGCAGCTCTC	D43772	CCDS11345.1, CCDS56028.1	17q12	2013-02-14			ENSG00000141738	ENSG00000141738		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	4567	protein-coding gene	gene with protein product		601522					Standard	NM_005310		Approved		uc021twu.1	Q14451	OTTHUMG00000133253	ENST00000309156.4:c.34A>G	chr17.hg19:g.37898588A>G	ENSP00000310771:p.Ser12Gly	295.0	0.0	.		250.0	100.0	.	NM_001242442	B2RAV1|B3KNL0|B3KWP9|B7WP75|J3KQM4|Q53YD3|Q92568|Q96DF9|Q9Y220	Missense_Mutation	SNP	ENST00000309156.4	hg19	CCDS11345.1	.	.	.	.	.	.	.	.	.	.	A	7.773	0.707831	0.15239	.	.	ENSG00000141738	ENST00000309185;ENST00000309156;ENST00000394211;ENST00000394209;ENST00000445327;ENST00000394204	T;T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86;0.86	4.61	4.61	0.57282	.	0.366448	0.26349	N	0.024892	T	0.38585	0.1046	L	0.47716	1.5	0.27860	N	0.940439	B;B	0.28971	0.229;0.043	B;B	0.29176	0.099;0.037	T	0.24404	-1.0161	10	0.21540	T	0.41	-25.7351	10.4148	0.44316	1.0:0.0:0.0:0.0	.	12;12	Q14451-2;Q14451	.;GRB7_HUMAN	G	12;12;12;12;35;12	ENSP00000311752:S12G;ENSP00000310771:S12G;ENSP00000377761:S12G;ENSP00000377759:S12G;ENSP00000403459:S35G;ENSP00000377754:S12G	ENSP00000310771:S12G	S	+	1	0	GRB7	35152114	1.000000	0.71417	0.981000	0.43875	0.110000	0.19582	4.739000	0.62080	1.718000	0.51419	0.459000	0.35465	AGC	.	.	.	none		0.617	GRB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257024.2	NM_005310		G	37898588	A	G	37898588	3	3	177	1	0	0	0	0	1	0	0	0	6766	188	7	3	36	3	GRB7	17	37898588	Missense_Mutation	SNP	A	TCGA-G7-7502-01A-11D-2201-08		37898588	43296622	52	10378											
SCRN2	90507	hgsc.bcm.edu	37	chr17	45915995	45915995	+	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	gccgtggtgcgaaagcctccCgagtccatacagataccact	10	7	10	14	3	0	1	0	0	0	1	2	3	2	1	5	1	4	0	5	1	3	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr17:45915995C>A	ENST00000290216.9	-	6	965	c.840G>T	c.(838-840)tcG>tcT	p.S280S	SCRN2_ENST00000584123.1_Silent_p.S288S|SCRN2_ENST00000407215.3_Silent_p.S280S	NM_001145023.1|NM_138355.3	NP_001138495.1|NP_612364.2	Q96FV2	SCRN2_HUMAN	secernin 2	280						extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)			cervix(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	14						GAAAGCCTCCCGAGTCCATAC	0.617																																					p.S280S		Atlas-SNP	.											.	SCRN2	35	.	0			c.G840T						PASS	.						105	87	93					17																	45915995		2203	4300	6503	SO:0001819	synonymous_variant	90507	exon6			GCCTCCCGAGTCC	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.840G>T	chr17.hg19:g.45915995C>A		78.0	0.0	.		94.0	4.0	.	NM_138355	A8K3N1|B7Z8S7|E9PBV5|Q96AC3|Q9BU04	Silent	SNP	ENST00000290216.9	hg19	CCDS11519.1																																																																																			.	.	.	none		0.617	SCRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441383.1	NM_138355		A	45915995	C	A	45915995	2	1	177	1	0	0	0	0	0	0	0	1	13952	639	23	4		4	SCRN2	17	45915995	Silent	SNP	C	TCGA-G7-7502-01A-11D-2201-08	8017407	45915995	35279215	53	10379											
CDK5RAP3	80279	hgsc.bcm.edu	37	chr17	46058013	46058013	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagtgaggaggcagatgtcCtgtctgtgagccagttccag	8	10	15	8	0	1	4	0	3	1	1	3	5	3	5	3	2	1	2	3	2	0	1			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr17:46058013C>T	ENST00000338399.4	+	12	1238	c.1132C>T	c.(1132-1134)Ctg>Ttg	p.L378L	CDK5RAP3_ENST00000578663.1_3'UTR|RP11-6N17.10_ENST00000578239.1_RNA|CDK5RAP3_ENST00000536708.2_Silent_p.L403L	NM_176096.1	NP_788276.1	Q96JB5	CK5P3_HUMAN	CDK5 regulatory subunit associated protein 3	378					brain development (GO:0007420)|protein ufmylation (GO:0071569)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of neuron differentiation (GO:0045664)	membrane (GO:0016020)	protein kinase binding (GO:0019901)			NS(1)|central_nervous_system(2)|cervix(3)|endometrium(3)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	18						GGCAGATGTCCTGTCTGTGAG	0.527																																					p.L378L		Atlas-SNP	.											.	CDK5RAP3	38	.	0			c.C1132T						PASS	.						182	184	183					17																	46058013		2092	4207	6299	SO:0001819	synonymous_variant	80279	exon12			GATGTCCTGTCTG	AF110322	CCDS42356.1, CCDS62232.1	17q21.2	2008-07-18				ENSG00000108465			18673	protein-coding gene	gene with protein product	"ischemic heart CDK5 activator-binding protein C53", "LXXLL/leucine-zipper-containing ARFbinding protein"	608202				10721722	Standard	NM_176096		Approved	MST016, FLJ13660, C53, IC53, HSF-27, OK/SW-cl.114, LZAP	uc010wlc.3	Q96JB5		ENST00000338399.4:c.1132C>T	chr17.hg19:g.46058013C>T		231.0	0.0	.		213.0	12.0	.	NM_176096	B7Z6N4|D3DTU1|D3DTU2|F5H3I5|Q53FA2|Q9H3F8|Q9H8G0|Q9HBR9	Silent	SNP	ENST00000338399.4	hg19	CCDS42356.1																																																																																			.	.	.	none		0.527	CDK5RAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442913.1	NM_176096		T	46058013	C	T	46058013	2	4	177	1	0	0	0	0	0	0	0	1	3149	680	24	2		2	CDK5RAP3	17	46058013	Silent	SNP	C	TCGA-G7-7502-01A-11D-2201-08	142018	46058013	35137197	54	10380											
RANBP3	8498	hgsc.bcm.edu	37	chr19	5941706	5941706	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagggcagtaatttccatctTctctgtcagaatctacagaa	12	12	8	9	0	4	2	1	0	3	2	6	3	5	2	1	1	1	2	1	1	4	4			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr19:5941706T>C	ENST00000340578.6	-	5	389	c.332A>G	c.(331-333)gAa>gGa	p.E111G	RANBP3_ENST00000591092.1_Missense_Mutation_p.E43G|RANBP3_ENST00000591124.1_5'UTR|RANBP3_ENST00000034275.8_Missense_Mutation_p.E43G|RANBP3_ENST00000541471.1_Intron|RANBP3_ENST00000439268.2_Missense_Mutation_p.E111G	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	111					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						ATTTCCATCTTCTCTGTCAGA	0.423																																					p.E111G		Atlas-SNP	.											.	RANBP3	36	.	0			c.A332G						PASS	.						161	152	155					19																	5941706		1912	4133	6045	SO:0001583	missense	8498	exon5			CCATCTTCTCTGT	Y08698	CCDS42477.1, CCDS42478.1, CCDS45935.1, CCDS74268.1	19p13.3	2008-02-05							9850	protein-coding gene	gene with protein product		603327				9637251	Standard	NM_007322		Approved		uc002mdw.3	Q9H6Z4		ENST00000340578.6:c.332A>G	chr19.hg19:g.5941706T>C	ENSP00000341483:p.Glu111Gly	159.0	0.0	.		99.0	30.0	.	NM_007322	B2RAT8|O60405|O75759|O75760|Q9BT47|Q9UG74	Missense_Mutation	SNP	ENST00000340578.6	hg19	CCDS42478.1	.	.	.	.	.	.	.	.	.	.	T	18.44	3.625162	0.66901	.	.	ENSG00000031823	ENST00000340578;ENST00000439268;ENST00000034275;ENST00000324807	T;T;T	0.38887	1.11;1.15;1.83	5.26	5.26	0.73747	.	0.096682	0.64402	D	0.000001	T	0.46171	0.1379	N	0.24115	0.695	0.80722	D	1	D;D;D;D	0.58268	0.97;0.982;0.982;0.97	P;P;P;P	0.60345	0.683;0.832;0.873;0.749	T	0.47114	-0.9142	10	0.54805	T	0.06	-17.7103	13.15	0.59484	0.0:0.0:0.0:1.0	.	43;43;111;111	B7Z7F3;Q9H6Z4-3;Q9H6Z4-2;Q9H6Z4	.;.;.;RANB3_HUMAN	G	111;111;43;42	ENSP00000341483:E111G;ENSP00000404837:E111G;ENSP00000034275:E43G	ENSP00000034275:E43G	E	-	2	0	RANBP3	5892706	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.699000	0.74613	1.996000	0.58369	0.533000	0.62120	GAA	.	.	.	none		0.423	RANBP3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452304.1	NM_007322		C	5941706	T	C	5941706	3	2	177	1	0	0	0	0	1	0	0	0	13042	1783	62	3	1423	3	RANBP3	19	5941706	Missense_Mutation	SNP	T	TCGA-G7-7502-01A-11D-2201-08		5941706	53187277	55	10381											
DNMT1	1786	hgsc.bcm.edu	37	chr19	10250732	10250732	+	Frame_Shift_Del	DEL	A	A	-																															acccgtttacctgaggaaggAaaccaccagagagtttttga																										TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr19:10250732delA	ENST00000340748.4	-	32	3983	c.3748delT	c.(3748-3750)tccfs	p.S1250fs	DNMT1_ENST00000589538.1_Intron|DNMT1_ENST00000359526.4_Frame_Shift_Del_p.S1266fs|DNMT1_ENST00000540357.1_Frame_Shift_Del_p.S1250fs			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	1250	Catalytic.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.|SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	CTGAGGAAGGAAACCACCAGA	0.612																																					p.S1266fs		Atlas-INDEL	.											.	DNMT1	148	.	0			c.3797delC						PASS	.						39	40	40					19																	10250732		2203	4300	6503	SO:0001589	frameshift_variant	1786	exon33			.	X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.3748delT	chr19.hg19:g.10250732delA	ENSP00000345739:p.Ser1250fs	84.0	0.0	0		51.0	10.0	0.196078	NM_001130823	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Frame_Shift_Del	DEL	ENST00000340748.4	hg19	CCDS12228.1																																																																																			.	.	.	none		0.612	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379		-	10250732	A	-	10250732	7	5	177	1	0	1	0	1	0	0	0	0	4677	246	9	0	1138	0	DNMT1	19	10250732	Frame_Shift_Del	DEL	A	TCGA-G7-7502-01A-11D-2201-08	4309026	10250732	48878251	56	10382											
ZNF101	94039	hgsc.bcm.edu	37	chr19	19789581	19789581	+	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	gagaatctgtaccaaaacctGgggattaagctaaggtaatc	15	9	10	7	0	1	1	0	0	1	1	2	3	1	2	2	3	3	3	2	3	7	4			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr19:19789581G>C	ENST00000592502.1	+	3	287	c.177G>C	c.(175-177)ctG>ctC	p.L59L	ZNF101_ENST00000415784.2_5'UTR|ZNF101_ENST00000444249.2_Missense_Mutation_p.W58S			Q8IZC7	ZN101_HUMAN	zinc finger protein 101	59	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)	17						ACCAAAACCTGGGGATTAAGC	0.333																																					p.L59L		Atlas-SNP	.											.	ZNF101	43	.	0			c.G177C						PASS	.						45	45	45					19																	19789581		2203	4300	6503	SO:0001819	synonymous_variant	94039	exon3			AAACCTGGGGATT	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.177G>C	chr19.hg19:g.19789581G>C		47.0	0.0	.		42.0	8.0	.	NM_033204	C9JU83|Q0VDG9	Silent	SNP	ENST00000592502.1	hg19	CCDS32971.1																																																																																			.	.	.	none		0.333	ZNF101-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460559.1	NM_033204		C	19789581	G	C	19789581	2	2	177	1	0	0	0	0	0	0	0	1	17726	1335	47	4		4	ZNF101	19	19789581	Silent	SNP	G	TCGA-G7-7502-01A-11D-2201-08	9538849	19789581	39339402	57	10383											
ZFP14	57677	hgsc.bcm.edu	37	chr19	36831515	36831515	+	Missense_Mutation	SNP	A	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	aagctgtgagtaactactaaAggtcttccaacattccatac	14	11	6	10	0	1	1	0	1	1	0	3	1	3	1	2	1	5	2	2	1	7	6			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr19:36831515A>C	ENST00000270001.7	-	5	1328	c.1213T>G	c.(1213-1215)Ttt>Gtt	p.F405V		NM_020917.2	NP_065968.1	Q9HCL3	ZFP14_HUMAN	ZFP14 zinc finger protein	405					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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)					TAACTACTAAAGGTCTTCCAA	0.408																																					p.F405V		Atlas-SNP	.											.	ZFP14	68	.	0			c.T1213G						PASS	.						115	106	109					19																	36831515		2203	4300	6503	SO:0001583	missense	57677	exon5			TACTAAAGGTCTT	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.1213T>G	chr19.hg19:g.36831515A>C	ENSP00000270001:p.Phe405Val	141.0	0.0	.		118.0	34.0	.	NM_020917	A7MD23	Missense_Mutation	SNP	ENST00000270001.7	hg19	CCDS33002.1	.	.	.	.	.	.	.	.	.	.	a	18.65	3.668655	0.67814	.	.	ENSG00000142065	ENST00000270001;ENST00000392172	T	0.46063	0.88	3.99	3.99	0.46301	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.46442	D	0.000284	T	0.67822	0.2934	M	0.88181	2.935	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	T	0.74919	-0.3500	10	0.87932	D	0	.	12.2842	0.54783	1.0:0.0:0.0:0.0	.	405;405	A8KAN8;Q9HCL3	.;ZFP14_HUMAN	V	405	ENSP00000270001:F405V	ENSP00000270001:F405V	F	-	1	0	ZFP14	41523355	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	5.755000	0.68750	1.794000	0.52575	0.523000	0.50628	TTT	.	.	.	none		0.408	ZFP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452528.1	NM_020917		C	36831515	A	C	36831515	3	2	177	1	0	0	0	0	1	0	0	0	17651	72	3	5	392	5	ZFP14	19	36831515	Missense_Mutation	SNP	A	TCGA-G7-7502-01A-11D-2201-08	17041934	36831515	22297468	58	10384											
ZNF776	284309	hgsc.bcm.edu	37	chr19	58265245	58265245	+	Frame_Shift_Del	DEL	T	T	-																															aaattcactagcaaaagtaaTagttttaataatcatcaggg																										TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr19:58265245delT	ENST00000317178.5	+	3	1010	c.747delT	c.(745-747)aatfs	p.N249fs		NM_173632.3	NP_775903.3	Q68DI1	ZN776_HUMAN	zinc finger protein 776	249					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(2)|kidney(13)|large_intestine(3)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	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;0.0256)		GCAAAAGTAATAGTTTTAATA	0.413																																					p.N249fs		Atlas-INDEL	.											.	ZNF776	115	.	0			c.746delA						PASS	.						63	64	64					19																	58265245		2203	4300	6503	SO:0001589	frameshift_variant	284309	exon3			.	AK095607	CCDS12962.2	19q13.43	2013-01-08			ENSG00000152443	ENSG00000152443		"Zinc fingers, C2H2-type", "-"	26765	protein-coding gene	gene with protein product							Standard	NM_173632		Approved	FLJ38288		Q68DI1	OTTHUMG00000156943	ENST00000317178.5:c.747delT	chr19.hg19:g.58265245delT	ENSP00000321812:p.Asn249fs	89.0	0.0	0		65.0	17.0	0.261538	NM_173632	Q6ZS36|Q8N968	Frame_Shift_Del	DEL	ENST00000317178.5	hg19	CCDS12962.2																																																																																			.	.	.	none		0.413	ZNF776-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346722.2	NM_173632		-	58265245	T	-	58265245	7	5	177	1	0	1	0	1	0	0	0	0	18161	1403	49	0	757	0	ZNF776	19	58265245	Frame_Shift_Del	DEL	T	TCGA-G7-7502-01A-11D-2201-08	21433730	58265245	863738	59	10385											
PLUNC	51297	hgsc.bcm.edu	37	chr20	31825663	31825663	+	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	gagtcccacaggtcttgcagGaagcttgacaaatggtgagt	11	9	13	8	0	1	2	0	2	1	0	2	4	2	3	1	3	2	2	1	3	2	2			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr20:31825663G>A	ENST00000354297.4	+	2	217	c.146G>A	c.(145-147)gGa>gAa	p.G49E	BPIFA1_ENST00000375413.4_Missense_Mutation_p.G49E|BPIFA1_ENST00000375422.2_Missense_Mutation_p.G49E	NM_130852.2	NP_570913.1	Q9NP55	BPIA1_HUMAN	BPI fold containing family A, member 1	49					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)										GGTCTTGCAGGAAGCTTGACA	0.557																																					p.G49E		Atlas-SNP	.											.	.	.	.	0			c.G146A						PASS	.						84	78	80					20																	31825663		2203	4300	6503	SO:0001583	missense	51297	exon2			TTGCAGGAAGCTT	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.146G>A	chr20.hg19:g.31825663G>A	ENSP00000346251:p.Gly49Glu	130.0	0.0	.		104.0	39.0	.	NM_016583	A8K9R3|E1P5M9|Q9NZT0	Missense_Mutation	SNP	ENST00000354297.4	hg19	CCDS13217.1	.	.	.	.	.	.	.	.	.	.	G	9.833	1.189055	0.21954	.	.	ENSG00000198183	ENST00000375422;ENST00000354297;ENST00000375413;ENST00000544328	T;T;T	0.11385	2.78;2.78;2.78	5.11	-0.843	0.10744	.	0.563694	0.17374	N	0.176573	T	0.06826	0.0174	L	0.39245	1.2	0.09310	N	1	B	0.24882	0.113	B	0.23419	0.046	T	0.43702	-0.9375	10	0.02654	T	1	0.4054	9.72	0.40297	0.0869:0.5908:0.3223:0.0	.	49	Q9NP55	BPIA1_HUMAN	E	49;49;49;35	ENSP00000364571:G49E;ENSP00000346251:G49E;ENSP00000364562:G49E	ENSP00000346251:G49E	G	+	2	0	BPIFA1	31289324	0.316000	0.24580	0.019000	0.16419	0.005000	0.04900	0.387000	0.20718	0.087000	0.17167	0.655000	0.94253	GGA	.	.	.	none		0.557	BPIFA1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078667.2	NM_130852		A	31825663	G	A	31825663	3	1	177	1	0	0	0	0	1	0	0	0	12122	1174	41	2	148	2	PLUNC	20	31825663	Missense_Mutation	SNP	G	TCGA-G7-7502-01A-11D-2201-08		31825663	31199857	60	10386											
C21orf7	56911	hgsc.bcm.edu	37	chr21	30547133	30547133	+	Frame_Shift_Del	DEL	T	T	-																															tgacggaggagaatcggacgTtgaggttggcccagtctcaa																										TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr21:30547133delT	ENST00000399947.2	+	9	926	c.649delT	c.(649-651)ttgfs	p.L217fs	MAP3K7CL_ENST00000341618.4_Frame_Shift_Del_p.L217fs|MAP3K7CL_ENST00000339024.4_Frame_Shift_Del_p.L117fs|MAP3K7CL_ENST00000399928.1_Frame_Shift_Del_p.L117fs|MAP3K7CL_ENST00000286791.5_3'UTR|MAP3K7CL_ENST00000399934.1_Frame_Shift_Del_p.L117fs|MAP3K7CL_ENST00000399935.2_Frame_Shift_Del_p.L117fs|MAP3K7CL_ENST00000545939.1_Frame_Shift_Del_p.L111fs|MAP3K7CL_ENST00000399926.1_Frame_Shift_Del_p.L117fs|MAP3K7CL_ENST00000399925.1_Frame_Shift_Del_p.L117fs	NM_020152.2	NP_064537.1	P57077	M3KCL_HUMAN	MAP3K7 C-terminal like	217						cytosol (GO:0005829)|nucleus (GO:0005634)											GAATCGGACGTTGAGGTTGGC	0.488																																					p.T216fs		Atlas-INDEL	.											.	.	.	.	0			c.648delG						PASS	.						115	106	109					21																	30547133		2203	4300	6503	SO:0001589	frameshift_variant	56911	exon9			.	AF269161	CCDS13584.1, CCDS68182.1, CCDS74775.1	21q22.3	2013-02-22	2013-02-22	2013-02-22	ENSG00000156265	ENSG00000156265			16457	protein-coding gene	gene with protein product		611110	"chromosome 21 open reading frame 7"	C21orf7			Standard	NM_020152		Approved	TAKL, TAK1L, TAKL-1, TAKL-2, TAKL-4	uc002ynf.3	P57077	OTTHUMG00000078806	ENST00000399947.2:c.649delT	chr21.hg19:g.30547133delT	ENSP00000382828:p.Leu217fs	71.0	0.0	0		65.0	19.0	0.292308	NM_020152	D3DSE0|Q8TCL9	Frame_Shift_Del	DEL	ENST00000399947.2	hg19	CCDS13584.1																																																																																			.	.	.	none		0.488	MAP3K7CL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000171865.2	NM_020152		-	30547133	T	-	30547133	7	5	177	1	0	1	0	1	0	0	0	0	2134	1722	60	0	675	0	C21orf7	21	30547133	Frame_Shift_Del	DEL	T	TCGA-G7-7502-01A-11D-2201-08		30547133	17582762	61	10387											
COL6A1	1291	hgsc.bcm.edu	37	chr21	47423886	47423886	+	Missense_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	accaggccctgctccgcggtGtcttccaccagacagtctcc	6	8	9	18	2	2	1	0	0	2	1	5	1	4	1	6	2	1	1	6	2	0	1			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr21:47423886G>A	ENST00000361866.3	+	35	3160	c.3046G>A	c.(3046-3048)Gtc>Atc	p.V1016I	COL6A1_ENST00000498614.1_3'UTR	NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	1016	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)		GCTCCGCGGTGTCTTCCACCA	0.662																																					p.V1016I		Atlas-SNP	.											.	COL6A1	101	.	0			c.G3046A						PASS	.						56	58	58					21																	47423886		2203	4300	6503	SO:0001583	missense	1291	exon35			CGCGGTGTCTTCC	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.3046G>A	chr21.hg19:g.47423886G>A	ENSP00000355180:p.Val1016Ile	150.0	0.0	.		150.0	63.0	.	NM_001848	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Missense_Mutation	SNP	ENST00000361866.3	hg19	CCDS13727.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.958303	0.73902	.	.	ENSG00000142156	ENST00000361866	D	0.91464	-2.85	4.83	4.83	0.62350	von Willebrand factor, type A (1);	0.000000	0.64402	D	0.000001	D	0.90376	0.6988	L	0.57536	1.79	0.58432	D	0.99999	D	0.52996	0.957	P	0.49752	0.621	D	0.88044	0.2783	10	0.08381	T	0.77	-40.0397	17.9387	0.89020	0.0:0.0:1.0:0.0	.	1016	P12109	CO6A1_HUMAN	I	1016	ENSP00000355180:V1016I	ENSP00000355180:V1016I	V	+	1	0	COL6A1	46248314	1.000000	0.71417	0.957000	0.39632	0.304000	0.27724	5.907000	0.69908	2.232000	0.73038	0.596000	0.82720	GTC	.	.	.	none		0.662	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848		A	47423886	G	A	47423886	3	1	177	1	0	0	0	0	1	0	0	0	3701	1377	48	2	3184	2	COL6A1	21	47423886	Missense_Mutation	SNP	G	TCGA-G7-7502-01A-11D-2201-08	16876753	47423886	706009	62	10388											
ARVCF	421	hgsc.bcm.edu	37	chr22	19966432	19966432	+	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	gtccacacctcaggcagcccGacgtgttcttgaagacagtt	9	9	10	13	2	2	2	1	1	1	1	3	3	3	2	3	1	1	3	3	1	1	3	rs542020914	byFrequency	TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr22:19966432G>A	ENST00000263207.3	-	7	1859	c.1568C>T	c.(1567-1569)tCg>tTg	p.S523L	ARVCF_ENST00000344269.3_Missense_Mutation_p.S460L|ARVCF_ENST00000401994.1_Missense_Mutation_p.S460L|ARVCF_ENST00000487793.1_5'Flank|ARVCF_ENST00000406259.1_Missense_Mutation_p.S523L|ARVCF_ENST00000406522.1_Missense_Mutation_p.S460L	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	523					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)					CAGGCAGCCCGACGTGTTCTT	0.622													G|||	2	0.000399361	0	0	5008	,	,		20460	0		0	False		,,,				2504	0.002				p.S523L		Atlas-SNP	.											.	ARVCF	54	.	0			c.C1568T						PASS	.						136	91	106					22																	19966432		2203	4300	6503	SO:0001583	missense	421	exon7			CAGCCCGACGTGT		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.1568C>T	chr22.hg19:g.19966432G>A	ENSP00000263207:p.Ser523Leu	60.0	0.0	.		42.0	8.0	.	NM_001670	B7WNV2	Missense_Mutation	SNP	ENST00000263207.3	hg19	CCDS13771.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.930425	0.92389	.	.	ENSG00000099889	ENST00000263207;ENST00000344269;ENST00000401994;ENST00000406522;ENST00000406259	T;T;T;T;T	0.38887	1.11;1.11;1.11;1.11;1.11	4.43	4.43	0.53597	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.64811	0.2632	M	0.75777	2.31	0.80722	D	1	P;D	0.89917	0.906;1.0	P;D	0.79108	0.475;0.992	T	0.66913	-0.5803	9	.	.	.	-14.4434	17.6161	0.88068	0.0:0.0:1.0:0.0	.	523;45	O00192;E7EV58	ARVC_HUMAN;.	L	523;460;460;460;523	ENSP00000263207:S523L;ENSP00000342042:S460L;ENSP00000384341:S460L;ENSP00000384732:S460L;ENSP00000385444:S523L	.	S	-	2	0	ARVCF	18346432	1.000000	0.71417	0.164000	0.22755	0.982000	0.71751	7.455000	0.80726	2.472000	0.83506	0.563000	0.77884	TCG	.	.	.	none		0.622	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670		A	19966432	G	A	19966432	3	1	177	1	0	0	0	0	1	0	0	0	1003	1059	37	1	1372	1	ARVCF	22	19966432	Missense_Mutation	SNP	G	TCGA-G7-7502-01A-11D-2201-08		19966432	31338134	63	10389											
C22orf13	83606	hgsc.bcm.edu	37	chr22	24938994	24938994	+	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	tcagctgtccaagtagacaaAgaggatgtcctcatctgtgc	11	10	10	10	0	3	2	2	0	1	2	5	3	5	3	2	1	2	2	2	1	3	1			TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr22:24938994A>T	ENST00000407471.3	-	6	893	c.703T>A	c.(703-705)Ttt>Att	p.F235I	GUCD1_ENST00000435822.1_Missense_Mutation_p.F234I|GUCD1_ENST00000402766.1_3'UTR|GUCD1_ENST00000447813.2_3'UTR|GUCD1_ENST00000490922.1_Intron|GUCD1_ENST00000404664.3_Missense_Mutation_p.F290I	NM_001284251.1	NP_001271180.1	Q96NT3	GUCD1_HUMAN	guanylyl cyclase domain containing 1	235																	AAGTAGACAAAGAGGATGTCC	0.637																																					p.F235I		Atlas-SNP	.											.	.	.	.	0			c.T703A						PASS	.						216	165	182					22																	24938994		2203	4300	6503	SO:0001583	missense	83606	exon6			AGACAAAGAGGAT	AK054681	CCDS33621.1, CCDS63426.1, CCDS63427.1, CCDS74831.1, CCDS74832.1, CCDS74833.1	22q11.2	2012-11-13	2012-11-13	2012-11-13	ENSG00000138867	ENSG00000138867			14237	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 13"	C22orf13		12477932	Standard	XM_005261761		Approved	MGC1842, LLN4	uc003aah.2	Q96NT3	OTTHUMG00000150728	ENST00000407471.3:c.703T>A	chr22.hg19:g.24938994A>T	ENSP00000386076:p.Phe235Ile	169.0	0.0	.		106.0	32.0	.	NM_031444	B5MCB8|B5MCL7|Q96Q79|Q9BU32	Missense_Mutation	SNP	ENST00000407471.3	hg19	CCDS33621.1	.	.	.	.	.	.	.	.	.	.	A	29.1	4.981630	0.93044	.	.	ENSG00000138867	ENST00000407471;ENST00000435822;ENST00000404664	.	.	.	5.37	5.37	0.77165	.	0.104223	0.64402	D	0.000003	T	0.70806	0.3266	M	0.69823	2.125	0.80722	D	1	P;P;P;P	0.47409	0.811;0.885;0.895;0.477	P;P;P;B	0.51324	0.489;0.666;0.629;0.327	T	0.72693	-0.4216	9	0.45353	T	0.12	-8.7496	14.5939	0.68392	1.0:0.0:0.0:0.0	.	290;298;191;235	B5MCL7;B4DH83;B4DL90;Q96NT3	.;.;.;CV013_HUMAN	I	235;234;290	.	ENSP00000381297:F234I	F	-	1	0	C22orf13	23268994	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.244000	0.78228	2.037000	0.60232	0.456000	0.33151	TTT	.	.	.	none		0.637	GUCD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319819.1	NM_031444		T	24938994	A	T	24938994	3	4	177	1	0	0	0	0	1	0	0	0	2137	72	3	5	23	5	C22orf13	22	24938994	Missense_Mutation	SNP	A	TCGA-G7-7502-01A-11D-2201-08	4972562	24938994	26365572	64	10390											
CSF2RB	1439	hgsc.bcm.edu	37	chr22	37334445	37334446	+	Missense_Mutation	DNP	GC	GC	TT																															aagcccccaggccaggctgtGccccaggtgcccgtcattca																								rs554053520		TCGA-G7-7502-01A-11D-2201-08	TCGA-G7-7502-10A-01D-2201-08	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ea718e65-433a-4e16-82fc-4f8e5be936af	2c767e98-3e53-4915-a687-2e67bc2cedc5	g.chr22:37334445_37334446GC>TT	ENST00000403662.3	+	14	2817_2818	c.2595_2596GC>TT	c.(2593-2598)gtGCcc>gtTTcc	p.P866S	CSF2RB_ENST00000406230.1_Missense_Mutation_p.P872S|CSF2RB_ENST00000536485.1_Missense_Mutation_p.P813S|CSF2RB_ENST00000262825.5_Missense_Mutation_p.P872S			P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	866					cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)|interleukin-5-mediated signaling pathway (GO:0038043)|respiratory gaseous exchange (GO:0007585)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	granulocyte macrophage colony-stimulating factor receptor complex (GO:0030526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(3)|pancreas(1)|skin(5)|upper_aerodigestive_tract(2)	42					Sargramostim(DB00020)	GCCAGGCTGTGCCCCAGGTGCC	0.589																																					p.V865V|p.P866S		Atlas-SNP	.											.	CSF2RB	104	.	0			c.G2595T|c.C2596T						PASS	.																																			SO:0001583	missense	1439	exon14			GGCTGTGCCCCAG|GCTGTGCCCCAGG	M59941	CCDS13936.1	22q12.3	2014-09-09			ENSG00000100368	ENSG00000100368		"CD molecules", "Fibronectin type III domain containing"	2436	protein-coding gene	gene with protein product		138981		IL3RB		1833064, 1424804	Standard	NM_000395		Approved	IL5RB, CD131	uc003aqa.4	P32927	OTTHUMG00000150546	Exception_encountered	chr22.hg19:g.37334445_37334446delinsTT	ENSP00000384053:p.Pro866Ser	189.0|187.0	0.0	.		161.0|165.0	37.0|38.0	.	NM_000395	Q5JZI1|Q6ICE0	Silent|Missense_Mutation	SNP	ENST00000403662.3	hg19	CCDS13936.1																																																																																			.	.	.	none		0.589	CSF2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318854.1	NM_000395		TT	37334446	GC	TT	37334445	3	4	177	1	0	0	0	0	1	0	0	0	3937	1306	46	4	2645	4	CSF2RB	22	37334445	Missense_Mutation	DNP	GC	TCGA-G7-7502-01A-11D-2201-08	12395451	37334445	13970121	65	10391											
PAQR7	164091	hgsc.bcm.edu	37	chr1	26189753	26189755	+	In_Frame_Del	DEL	TTG	TTG	-																															ggcctggtttctggatgtacTtgttatagcaggagccaatg																										TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	TTG	TTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr1:26189753_26189755delTTG	ENST00000374296.3	-	2	1242_1244	c.576_578delCAA	c.(574-579)aacaag>aag	p.N192del	RP1-125I3.2_ENST00000455431.1_RNA	NM_178422.5	NP_848509.1	Q86WK9	MPRA_HUMAN	progestin and adipoQ receptor family member VII	192					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)		CTGGATGTACTTGTTATAGCAGG	0.581																																					p.193_193del	Esophageal Squamous(111;1206 1556 18433 19151 38418)	Atlas-Indel,Pindel	.											.	PAQR7	23	.	0			c.577_579del						PASS	.																																			SO:0001651	inframe_deletion	164091	exon2			.		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.576_578delCAA	chr1.hg19:g.26189753_26189755delTTG	ENSP00000363414:p.Asn192del	105.0	0.0	0		105.0	44.0	0.419048	NM_178422	A2A2D3|Q5XKF9|Q86VE4	In_Frame_Del	DEL	ENST00000374296.3	hg19	CCDS267.1																																																																																			.	.	.	none		0.581	PAQR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019312.1	NM_178422		-	26189755	TTG	-	26189753	7	5	178	1	0	1	0	1	0	0	0	0	11447	1609	56	0	466	0	PAQR7	1	26189753	In_Frame_Del	DEL	TTG	TCGA-G7-A4TM-01A-11D-A31X-10		26189753	223060868	1	10392											
WASF2	10163	hgsc.bcm.edu	37	chr1	27736340	27736340	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccccggaggaggaggaggAgggggaggaggaggtgctcc	8	2	24	7	1	0	0	0	0	0	0	1	8	1	8	3	11	1	1	3	11	0	0	rs71584884		TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr1:27736340A>G	ENST00000430629.2	-	8	1400	c.1185T>C	c.(1183-1185)ccT>ccC	p.P395P	WASF2_ENST00000536657.1_Intron	NM_001201404.1|NM_006990.3	NP_001188333.1|NP_008921.1	Q9Y6W5	WASF2_HUMAN	WAS protein family, member 2	395	Poly-Pro.				actin cytoskeleton organization (GO:0030036)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of lamellipodium assembly (GO:0010592)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|SCAR complex (GO:0031209)	actin binding (GO:0003779)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	18		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0446)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.7e-08)|COAD - Colon adenocarcinoma(152;2e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00139)|KIRC - Kidney renal clear cell carcinoma(1967;0.00204)|STAD - Stomach adenocarcinoma(196;0.00325)|READ - Rectum adenocarcinoma(331;0.0481)		gaggaggaggagggggaggag	0.642																																					p.P395P		Atlas-SNP	.											.	WASF2	41	.	0			c.T1185C						PASS	.						51	53	52					1																	27736340		2203	4300	6503	SO:0001819	synonymous_variant	10163	exon8			AGGAGGAGGGGGA	AB026542	CCDS304.1, CCDS55582.1	1p36.11	2011-05-10			ENSG00000158195	ENSG00000158195			12733	protein-coding gene	gene with protein product		605875				10381382	Standard	NM_006990		Approved	WAVE2, SCAR2	uc001bof.2	Q9Y6W5	OTTHUMG00000003393	ENST00000430629.2:c.1185T>C	chr1.hg19:g.27736340A>G		108.0	0.0	.		132.0	7.0	.	NM_006990	B4DZN0|O60794|Q9UDY7	Silent	SNP	ENST00000430629.2	hg19	CCDS304.1																																																																																			.	A|0.500;T|0.500	.	alt		0.642	WASF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009516.1	NM_006990		G	27736340	A	G	27736340	2	3	178	1	0	0	0	0	0	0	0	1	17265	291	11	3		3	WASF2	1	27736340	Silent	SNP	A	TCGA-G7-A4TM-01A-11D-A31X-10	1546587	27736340	221514281	2	10393											
AHDC1	27245	hgsc.bcm.edu	37	chr1	27876672	27876673	+	Frame_Shift_Del	DEL	GT	GT	-																															ggaagtgggagatgctctggGtgtcgggggcctggtgcacc																										TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr1:27876672_27876673delGT	ENST00000247087.5	-	5	2550_2551	c.1954_1955delAC	c.(1954-1956)accfs	p.T652fs	AHDC1_ENST00000374011.2_Frame_Shift_Del_p.T652fs			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	652							DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		GATGCTCTGGGTGTCGGGGGCC	0.703																																					p.652_652del		Atlas-Indel,Pindel	.											.	AHDC1	98	.	0			c.1955_1956del						PASS	.																																			SO:0001589	frameshift_variant	27245	exon6			.	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.1954_1955delAC	chr1.hg19:g.27876674_27876675delGT	ENSP00000247087:p.Thr652fs	53.0	0.0	0		41.0	16.0	0.390244	NM_001029882	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Frame_Shift_Del	DEL	ENST00000247087.5	hg19	CCDS30652.1																																																																																			.	.	.	none		0.703	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3			-	27876673	GT	-	27876672	7	5	178	1	0	1	0	1	0	0	0	0	412	1261	44	0	2860	0	AHDC1	1	27876672	Frame_Shift_Del	DEL	GT	TCGA-G7-A4TM-01A-11D-A31X-10	140332	27876672	221373949	3	10394											
FOXJ3	22887	hgsc.bcm.edu	37	chr1	42744042	42744042	+	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	ccaaccactgccagcctctcTataatatgggaagttatcac	12	10	6	13	0	2	0	1	0	1	0	3	1	2	1	4	1	3	1	4	1	6	4			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr1:42744042T>A	ENST00000372572.1	-	5	657	c.346A>T	c.(346-348)Aga>Tga	p.R116*	FOXJ3_ENST00000361776.1_Nonsense_Mutation_p.R116*|FOXJ3_ENST00000372573.1_Nonsense_Mutation_p.R116*|FOXJ3_ENST00000545068.1_Nonsense_Mutation_p.R116*|FOXJ3_ENST00000361346.1_Nonsense_Mutation_p.R116*	NM_001198851.1	NP_001185780.1	Q9UPW0	FOXJ3_HUMAN	forkhead box J3	116					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				CCAGCCTCTCTATAATATGGG	0.313																																					p.R116X		Atlas-SNP	.											.	FOXJ3	59	.	0			c.A346T						PASS	.						70	71	70					1																	42744042		2203	4300	6503	SO:0001587	stop_gained	22887	exon3			CCTCTCTATAATA	AB028964	CCDS30689.1, CCDS55594.1	1p34.2	2008-04-10			ENSG00000198815	ENSG00000198815		"Forkhead boxes"	29178	protein-coding gene	gene with protein product							Standard	NM_014947		Approved	KIAA1041	uc001chf.3	Q9UPW0	OTTHUMG00000007026	ENST00000372572.1:c.346A>T	chr1.hg19:g.42744042T>A	ENSP00000361653:p.Arg116*	111.0	0.0	.		88.0	34.0	.	NM_001198852	A7MBL7|A7MD18|D3DPW2|Q9NSS7	Nonsense_Mutation	SNP	ENST00000372572.1	hg19	CCDS30689.1	.	.	.	.	.	.	.	.	.	.	T	40	8.346624	0.98769	.	.	ENSG00000198815	ENST00000372573;ENST00000372572;ENST00000361346;ENST00000361776;ENST00000545068;ENST00000445886;ENST00000454417	.	.	.	5.48	5.48	0.80851	.	0.066191	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.527	0.61601	0.0:0.0:0.0:1.0	.	.	.	.	X	116;116;116;116;116;116;73	.	ENSP00000354620:R116X	R	-	1	2	FOXJ3	42516629	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.242000	0.72376	2.082000	0.62665	0.374000	0.22700	AGA	.	.	.	none		0.313	FOXJ3-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000018310.1	NM_014947		A	42744042	T	A	42744042	4	1	178	1	0	0	0	0	0	1	0	0	6020	1530	53	5	1566	5	FOXJ3	1	42744042	Nonsense_Mutation	SNP	T	TCGA-G7-A4TM-01A-11D-A31X-10	14867370	42744042	206506579	4	10395											
RHOC	389	hgsc.bcm.edu	37	chr1	113244309	113244309	+	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	ctgatccggttcgccatgtcCcggccttcctcagaccgaac	6	9	9	17	4	1	2	1	1	0	1	5	3	4	2	6	2	1	1	6	2	1	2			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr1:113244309C>G	ENST00000285735.2	-	6	1644	c.435G>C	c.(433-435)cgG>cgC	p.R145R	RHOC_ENST00000369632.2_Silent_p.R145R|RHOC_ENST00000369636.2_Missense_Mutation_p.G125A|RHOC_ENST00000339083.7_Silent_p.R145R|RP11-426L16.10_ENST00000471038.2_5'Flank|RHOC_ENST00000369638.2_Silent_p.R145R|RHOC_ENST00000369642.3_Silent_p.R145R|RHOC_ENST00000369633.2_Silent_p.R145R|RHOC_ENST00000369637.1_Silent_p.R145R			P08134	RHOC_HUMAN	ras homolog family member C	145					apical junction assembly (GO:0043297)|axon guidance (GO:0007411)|cytokinesis (GO:0000910)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cleavage furrow (GO:0032154)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	9	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCGCCATGTCCCGGCCTTCCT	0.572																																					p.R145R		Atlas-SNP	.											.	RHOC	15	.	0			c.G435C						PASS	.						107	95	99					1																	113244309		2203	4300	6503	SO:0001819	synonymous_variant	389	exon6			CATGTCCCGGCCT	BC052808	CCDS854.1	1p13.1	2012-02-27	2012-02-27	2004-03-24	ENSG00000155366	ENSG00000155366			669	protein-coding gene	gene with protein product		165380	"ras homolog gene family, member C"	ARH9, ARHC		3283705	Standard	NM_001042678		Approved	RhoC	uc001ecp.1	P08134	OTTHUMG00000011905	ENST00000285735.2:c.435G>C	chr1.hg19:g.113244309C>G		184.0	0.0	.		153.0	59.0	.	NM_175744	B3KSW1|Q6ICN3	Silent	SNP	ENST00000285735.2	hg19	CCDS854.1	.	.	.	.	.	.	.	.	.	.	C	11.67	1.706628	0.30232	.	.	ENSG00000155366	ENST00000369636	T	0.71222	-0.55	5.13	2.24	0.28232	.	0.480686	0.15126	U	0.279101	T	0.46347	0.1388	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37911	-0.9685	7	0.25106	T	0.35	-8.222	4.4249	0.11498	0.0:0.4765:0.1577:0.3659	.	.	.	.	A	125	ENSP00000358650:G125A	ENSP00000358650:G125A	G	-	2	0	RHOC	113045832	0.998000	0.40836	1.000000	0.80357	0.865000	0.49528	0.626000	0.24492	0.196000	0.20367	-1.254000	0.01491	GGG	.	.	.	none		0.572	RHOC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032904.2	NM_175744		G	113244309	C	G	113244309	2	3	178	1	0	0	0	0	0	0	0	1	13349	610	22	4		4	RHOC	1	113244309	Silent	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10	70500267	113244309	136006312	5	10396											
CENPF	1063	hgsc.bcm.edu	37	chr1	214815619	214815619	+	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	atgtgaaatactgcaggctgAaaagtatgaactcgtaactg	15	10	10	6	1	0	3	0	3	0	0	1	3	0	3	0	1	4	4	0	1	7	3			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr1:214815619A>T	ENST00000366955.3	+	12	4106	c.3938A>T	c.(3937-3939)gAa>gTa	p.E1313V		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		CTGCAGGCTGAAAAGTATGAA	0.393																																					p.E1313V	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.A3938T						PASS	.						76	76	76					1																	214815619		2203	4300	6503	SO:0001583	missense	1063	exon12			AGGCTGAAAAGTA	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.3938A>T	chr1.hg19:g.214815619A>T	ENSP00000355922:p.Glu1313Val	204.0	0.0	.		169.0	81.0	.	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	hg19	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	A	11.63	1.694781	0.30052	.	.	ENSG00000117724	ENST00000366955	T	0.28255	1.62	4.77	3.61	0.41365	.	0.207947	0.24020	N	0.042296	T	0.51126	0.1656	.	.	.	0.34578	D	0.714136	D	0.89917	1.0	D	0.71414	0.973	T	0.63980	-0.6514	9	0.87932	D	0	.	9.1524	0.36971	0.9148:0.0:0.0852:0.0	.	1313	P49454	CENPF_HUMAN	V	1313	ENSP00000355922:E1313V	ENSP00000355922:E1313V	E	+	2	0	CENPF	212882242	1.000000	0.71417	0.077000	0.20336	0.052000	0.14988	5.178000	0.65037	0.631000	0.30412	0.418000	0.28097	GAA	.	.	.	none		0.393	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		T	214815619	A	T	214815619	3	4	178	1	0	0	0	0	1	0	0	0	3233	246	9	5	3980	5	CENPF	1	214815619	Missense_Mutation	SNP	A	TCGA-G7-A4TM-01A-11D-A31X-10	101571310	214815619	34435002	6	10397											
SLC3A1	6519	hgsc.bcm.edu	37	chr2	44539791	44539791	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtatgtcaacgtgatgaacAtgcttcttttcacactccct	10	14	6	11	1	3	2	2	2	1	0	4	2	4	2	1	0	3	2	1	0	3	4			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr2:44539791A>G	ENST00000260649.6	+	8	1475	c.1399A>G	c.(1399-1401)Atg>Gtg	p.M467V	SLC3A1_ENST00000409387.1_Missense_Mutation_p.M467V|SLC3A1_ENST00000409741.1_Missense_Mutation_p.M467V|SLC3A1_ENST00000409229.3_Missense_Mutation_p.M467V|SLC3A1_ENST00000409294.1_Missense_Mutation_p.M87V|SLC3A1_ENST00000409380.1_Missense_Mutation_p.M189V|SLC3A1_ENST00000409740.3_Missense_Mutation_p.M98V	NM_000341.3	NP_000332.2	Q07837	SLC31_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 1	467			M -> K (in CSNU). {ECO:0000269|PubMed:8054986}.|M -> T (in CSNU; loss of 80% of amino acid transport activity). {ECO:0000269|PubMed:11748844, ECO:0000269|PubMed:12234283, ECO:0000269|PubMed:8054986, ECO:0000269|PubMed:9186880}.		amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|basic amino acid transport (GO:0015802)|carbohydrate metabolic process (GO:0005975)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|vacuolar membrane (GO:0005774)	amino acid transmembrane transporter activity (GO:0015171)|basic amino acid transmembrane transporter activity (GO:0015174)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|L-cystine transmembrane transporter activity (GO:0015184)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(3)	26		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			L-Cystine(DB00138)	CGTGATGAACATGCTTCTTTT	0.408																																					p.M467V		Atlas-SNP	.											.	SLC3A1	62	.	0			c.A1399G						PASS	.						141	128	132					2																	44539791		2203	4300	6503	SO:0001583	missense	6519	exon8			ATGAACATGCTTC		CCDS1819.1	2p16.3	2013-07-19	2013-07-19		ENSG00000138079	ENSG00000138079		"Solute carriers"	11025	protein-coding gene	gene with protein product		104614	"solute carrier family 3 (cystine, dibasic and neutral amino acid transporters, activator of cystine, dibasic and neutral amino acid transport), member 1"			8486766, 9186880	Standard	NM_000341		Approved	CSNU1, D2H, RBAT, ATR1, NBAT	uc002ruc.4	Q07837	OTTHUMG00000128759	ENST00000260649.6:c.1399A>G	chr2.hg19:g.44539791A>G	ENSP00000260649:p.Met467Val	147.0	0.0	.		121.0	45.0	.	NM_000341	A8K0S1|O00658|Q15295|Q4J6B4|Q4J6B5|Q4J6B6|Q4J6B7|Q4J6B8|Q4J6B9|Q52M92|Q52M94	Missense_Mutation	SNP	ENST00000260649.6	hg19	CCDS1819.1	.	.	.	.	.	.	.	.	.	.	A	15.85	2.955494	0.53293	.	.	ENSG00000138079	ENST00000260649;ENST00000409387;ENST00000540334;ENST00000409741;ENST00000409229;ENST00000541289;ENST00000409380;ENST00000409294;ENST00000409740	D;D;D;D;D;D;D	0.99454	-5.92;-5.92;-5.92;-5.92;-5.92;-5.92;-5.92	5.82	4.64	0.57946	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);	0.036710	0.85682	D	0.000000	D	0.98710	0.9567	L	0.52364	1.645	0.58432	D	0.999999	B;B;P;P	0.44776	0.387;0.374;0.843;0.716	B;B;P;P	0.48815	0.194;0.194;0.591;0.511	D	0.97965	1.0340	10	0.51188	T	0.08	-23.3976	13.0393	0.58889	0.8655:0.1345:0.0:0.0	.	467;467;467;467	Q07837;B8ZZK1;Q4J6B5;Q4J6B6	SLC31_HUMAN;.;.;.	V	467;467;403;467;467;467;189;87;98	ENSP00000260649:M467V;ENSP00000387308:M467V;ENSP00000386954:M467V;ENSP00000386620:M467V;ENSP00000386709:M189V;ENSP00000386852:M87V;ENSP00000386677:M98V	ENSP00000260649:M467V	M	+	1	0	SLC3A1	44393295	1.000000	0.71417	1.000000	0.80357	0.792000	0.44763	5.273000	0.65564	0.987000	0.38709	0.477000	0.44152	ATG	.	.	.	none		0.408	SLC3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250676.1	NM_000341		G	44539791	A	G	44539791	3	3	178	1	0	0	0	0	1	0	0	0	14639	217	8	3	1429	3	SLC3A1	2	44539791	Missense_Mutation	SNP	A	TCGA-G7-A4TM-01A-11D-A31X-10		44539791	198659582	7	10398											
DCBLD2	131566	hgsc.bcm.edu	37	chr3	98600601	98600601	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcctagtacagtgtgtccAcatccatcacctttaaaaaa	13	10	7	11	0	1	0	1	0	0	0	3	0	3	0	4	1	1	1	4	1	5	4			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr3:98600601A>G	ENST00000326840.6	-	2	578	c.216T>C	c.(214-216)tgT>tgC	p.C72C	DCBLD2_ENST00000326857.9_Silent_p.C72C|DCBLD2_ENST00000469648.1_Intron	NM_080927.3	NP_563615.3	Q96PD2	DCBD2_HUMAN	discoidin, CUB and LCCL domain containing 2	72	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell adhesion (GO:0007155)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cell growth (GO:0030308)|wound healing (GO:0042060)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|stomach(2)	25						CAGTGTGTCCACATCCATCAC	0.363																																					p.C72C		Atlas-SNP	.											.	DCBLD2	62	.	0			c.T216C						PASS	.						127	119	121					3																	98600601		1874	4109	5983	SO:0001819	synonymous_variant	131566	exon2			GTGTCCACATCCA		CCDS46878.1	3q12.2	2006-04-12			ENSG00000057019	ENSG00000057019			24627	protein-coding gene	gene with protein product		608698				11447234	Standard	NM_080927		Approved	CLCP1, ESDN	uc003dtd.3	Q96PD2	OTTHUMG00000151985	ENST00000326840.6:c.216T>C	chr3.hg19:g.98600601A>G		186.0	0.0	.		144.0	51.0	.	NM_080927	B7WNL1|D3DN41|Q8N6M4|Q8TDX2	Silent	SNP	ENST00000326840.6	hg19	CCDS46878.1																																																																																			.	.	.	none		0.363	DCBLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324675.2	NM_080927		G	98600601	A	G	98600601	2	3	178	1	0	0	0	0	0	0	0	1	4283	157	6	3		3	DCBLD2	3	98600601	Silent	SNP	A	TCGA-G7-A4TM-01A-11D-A31X-10		98600601	99421829	8	10399											
EXOSC9	5393	hgsc.bcm.edu	37	chr4	122722615	122722615	+	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	ctctcaaactgcgaacgccgCttcctactccgtgccatcga	8	9	7	17	5	1	0	1	0	1	0	5	2	3	0	4	0	5	1	4	0	3	2	rs150604288		TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr4:122722615C>T	ENST00000243498.5	+	1	144	c.36C>T	c.(34-36)cgC>cgT	p.R12R	EXOSC9_ENST00000379663.3_Silent_p.R12R|EXOSC9_ENST00000509980.1_3'UTR|EXOSC9_ENST00000512454.1_5'Flank	NM_005033.2	NP_005024.2	Q06265	EXOS9_HUMAN	exosome component 9	12	ARE binding.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|immune response (GO:0006955)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear-transcribed mRNA catabolic process (GO:0000956)|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)|intermediate filament cytoskeleton (GO:0045111)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|AU-rich element binding (GO:0017091)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|urinary_tract(1)	16						GCGAACGCCGCTTCCTACTCC	0.582																																					p.R12R		Atlas-SNP	.											.	EXOSC9	51	.	0			c.C36T						PASS	.						84	82	83					4																	122722615		2203	4300	6503	SO:0001819	synonymous_variant	5393	exon1			ACGCCGCTTCCTA	M58460	CCDS3722.2, CCDS34057.1	4q27	2010-05-07	2004-06-16	2004-06-18	ENSG00000123737	ENSG00000123737	3.1.13.-		9137	protein-coding gene	gene with protein product	"polymyositis/scleroderma autoantigen 1 (75kD)"	606180	"polymyositis/scleroderma autoantigen 1, 75kDa"	PMSCL1			Standard	XR_427545		Approved	PM/Scl-75, Rrp45p, RRP45, p5, p6	uc003idz.3	Q06265	OTTHUMG00000128783	ENST00000243498.5:c.36C>T	chr4.hg19:g.122722615C>T		117.0	0.0	.		112.0	51.0	.	NM_001034194	Q12883|Q4W5P5|Q86Y41|Q86Y48	Silent	SNP	ENST00000243498.5	hg19	CCDS3722.2																																																																																			.	C|1.000;G|0.000	.	alt		0.582	EXOSC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250708.2	NM_005033		T	122722615	C	T	122722615	2	4	178	1	0	0	0	0	0	0	0	1	5323	784	28	2		2	EXOSC9	4	122722615	Silent	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10		122722615	68431661	9	10400											
RGNEF	64283	hgsc.bcm.edu	37	chr5	73207182	73207182	+	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	tttagtacaaatgtcatttaAcactttcaacaaactgaatc	16	14	3	8	0	2	1	2	1	0	0	3	1	2	1	0	0	4	1	0	0	7	6			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr5:73207182A>T	ENST00000426542.2	+	34	4750	c.4730A>T	c.(4729-4731)aAc>aTc	p.N1577I	ARHGEF28_ENST00000545377.1_Missense_Mutation_p.N1577I|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.N1264I|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.N1577I|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.N1577I|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.N1533I|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.N1577I|ARHGEF28_ENST00000512883.1_Missense_Mutation_p.N497I			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	1577	Interaction with microtubules. {ECO:0000250}.|Mediates cytoplasmic retention and interaction with MAPK8IP1. {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)										ATGTCATTTAACACTTTCAAC	0.363																																					p.N1577I		Atlas-SNP	.											.	.	.	.	0			c.A4730T						PASS	.						76	70	72					5																	73207182		1930	4126	6056	SO:0001583	missense	64283	exon35			CATTTAACACTTT		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.4730A>T	chr5.hg19:g.73207182A>T	ENSP00000412175:p.Asn1577Ile	166.0	0.0	.		132.0	45.0	.	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	hg19	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	A	15.30	2.793921	0.50102	.	.	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799;ENST00000512883	T;T;T;T;T;T;T;T	0.36157	2.92;2.93;2.88;2.62;2.93;2.88;2.72;1.27	5.3	5.3	0.74995	.	0.000000	0.35349	U	0.003279	T	0.53481	0.1799	M	0.69823	2.125	0.32983	D	0.52386	P;P;P;D;P	0.62365	0.692;0.916;0.951;0.991;0.95	B;P;P;D;P	0.64042	0.232;0.604;0.626;0.921;0.65	T	0.68356	-0.5430	10	0.87932	D	0	.	8.6768	0.34185	0.9063:0.0:0.0937:0.0	.	1264;1577;1577;497;1577	B5MDA3;Q8N1W1;E9PC75;D6RGZ3;Q8N1W1-4	.;RGNEF_HUMAN;.;.;.	I	1577;1577;1577;1533;1577;1577;1264;497	ENSP00000296794:N1577I;ENSP00000441913:N1577I;ENSP00000441436:N1577I;ENSP00000287898:N1533I;ENSP00000411459:N1577I;ENSP00000412175:N1577I;ENSP00000296799:N1264I;ENSP00000421081:N497I	ENSP00000287898:N1533I	N	+	2	0	RP11-428C6.1	73242938	0.998000	0.40836	0.986000	0.45419	0.532000	0.34746	3.430000	0.52807	2.006000	0.58801	0.443000	0.29094	AAC	.	.	.	none		0.363	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			T	73207182	A	T	73207182	3	4	178	1	0	0	0	0	1	0	0	0	13296	43	2	5	4864	5	RGNEF	5	73207182	Missense_Mutation	SNP	A	TCGA-G7-A4TM-01A-11D-A31X-10		73207182	107708078	10	10401											
MAML1	9794	hgsc.bcm.edu	37	chr5	179201053	179201053	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggccaacaggaccggggtgtGgctcagttccctggctccca	6	7	14	14	1	1	0	1	0	0	0	3	1	3	1	4	6	1	3	4	6	1	1			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr5:179201053G>A	ENST00000292599.3	+	5	2489	c.2226G>A	c.(2224-2226)gtG>gtA	p.V742V	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)			ACCGGGGTGTGGCTCAGTTCC	0.592																																					p.V742V		Atlas-SNP	.											.	MAML1	118	.	0			c.G2226A						PASS	.						54	55	55					5																	179201053		2203	4300	6503	SO:0001819	synonymous_variant	9794	exon5			GGGTGTGGCTCAG	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.2226G>A	chr5.hg19:g.179201053G>A		50.0	0.0	.		43.0	17.0	.	NM_014757		Silent	SNP	ENST00000292599.3	hg19	CCDS34315.1																																																																																			.	.	.	none		0.592	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757		A	179201053	G	A	179201053	2	1	178	1	0	0	0	0	0	0	0	1	9212	1335	47	2		2	MAML1	5	179201053	Silent	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10	105993871	179201053	1714207	11	10402											
DSP	1832	hgsc.bcm.edu	37	chr6	7584156	7584156	+	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	gacaacctgtgaccgtcactGagctagtagattctggtata	11	11	10	9	1	2	3	1	2	1	1	2	4	2	3	2	1	2	3	2	1	5	5			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr6:7584156G>C	ENST00000379802.3	+	24	7002	c.6661G>C	c.(6661-6663)Gag>Cag	p.E2221Q	DSP_ENST00000418664.2_Missense_Mutation_p.E1622Q	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2221	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)		GACCGTCACTGAGCTAGTAGA	0.458																																					p.E2221Q		Atlas-SNP	.											.	DSP	306	.	0			c.G6661C						PASS	.						119	109	112					6																	7584156		2203	4300	6503	SO:0001583	missense	1832	exon24			GTCACTGAGCTAG	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.6661G>C	chr6.hg19:g.7584156G>C	ENSP00000369129:p.Glu2221Gln	69.0	0.0	.		54.0	19.0	.	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	hg19	CCDS4501.1	.	.	.	.	.	.	.	.	.	.	G	16.06	3.015584	0.54468	.	.	ENSG00000096696	ENST00000379802;ENST00000418664	T;T	0.70399	-0.48;-0.48	5.62	5.62	0.85841	.	0.098059	0.45361	D	0.000376	T	0.74114	0.3674	L	0.48877	1.53	0.36056	D	0.841104	P;D	0.76494	0.526;0.999	B;P	0.60886	0.141;0.88	T	0.72440	-0.4293	10	0.41790	T	0.15	.	20.0281	0.97530	0.0:0.0:1.0:0.0	.	1669;2221	Q4LE79;P15924	.;DESP_HUMAN	Q	2221;1622	ENSP00000369129:E2221Q;ENSP00000396591:E1622Q	ENSP00000369129:E2221Q	E	+	1	0	DSP	7529155	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	6.483000	0.73617	2.818000	0.97014	0.655000	0.94253	GAG	.	.	.	none		0.458	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		C	7584156	G	C	7584156	3	2	178	1	0	0	0	0	1	0	0	0	4783	1291	45	4	6755	4	DSP	6	7584156	Missense_Mutation	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10		7584156	163530911	12	10403											
MLL3	58508	hgsc.bcm.edu	37	chr7	151874152	151874158	+	Frame_Shift_Del	DEL	TTTTTGG	TTTTTGG	-																															tttgttttcttgttccttttTttttggttcaacagatacac																								rs79763944|rs78116609		TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	TTTTTGG	TTTTTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr7:151874152_151874158delTTTTTGG	ENST00000262189.6	-	38	8598_8604	c.8380_8386delCCAAAAA	c.(8380-8388)ccaaaaaaafs	p.PKK2794fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.PKK2794fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2794					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)										TGTTCCTTTTTTTTTGGTTCAACAGAT	0.357																																					p.2794_2796del		Atlas-Indel,Pindel	.											.	MLL3	1564	.	0			c.8381_8387del						PASS	.																																			SO:0001589	frameshift_variant	58508	exon38			.	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.8380_8386delCCAAAAA	chr7.hg19:g.151874152_151874158delTTTTTGG	ENSP00000262189:p.Pro2794fs	69.0	0.0	0		95.0	30.0	0.315789	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	hg19	CCDS5931.1																																																																																			.	.	.	none		0.357	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			-	151874158	TTTTTGG	-	151874152	7	5	178	1	0	1	0	1	0	0	0	0	9629	1850	64	0	6437	0	MLL3	7	151874152	Frame_Shift_Del	DEL	TTTTTGG	TCGA-G7-A4TM-01A-11D-A31X-10		151874152	7264511	13	10404											
NAT1	9	hgsc.bcm.edu	37	chr8	18080420	18080420	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaacatggtgatagatttttTactatttagaataaggagta	16	15	8	2	0	0	3	0	1	0	2	0	4	0	4	0	2	2	1	0	2	8	9			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr8:18080420T>C	ENST00000517492.1	+	3	1502	c.864T>C	c.(862-864)ttT>ttC	p.F288F	NAT1_ENST00000535084.1_Silent_p.F288F|NAT1_ENST00000541942.1_Silent_p.F288F|NAT1_ENST00000539092.1_Silent_p.F288F|NAT1_ENST00000518029.1_Silent_p.F288F|NAT1_ENST00000545197.1_Silent_p.F350F|NAT1_ENST00000307719.4_Silent_p.F288F|NAT1_ENST00000520546.1_Silent_p.F288F			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)		ATAGATTTTTTACTATTTAGA	0.343																																					p.F350F		Atlas-SNP	.											.	NAT1	38	.	0			c.T1050C						PASS	.						28	30	29					8																	18080420		2185	4285	6470	SO:0001819	synonymous_variant	9	exon4			ATTTTTTACTATT	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.864T>C	chr8.hg19:g.18080420T>C		278.0	1.0	.		210.0	83.0	.	NM_001160176	C9JWA6|Q86SY5	Silent	SNP	ENST00000517492.1	hg19	CCDS6007.1																																																																																			.	.	.	none		0.343	NAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374828.1	NM_000662		C	18080420	T	C	18080420	2	2	178	1	0	0	0	0	0	0	0	1	10180	1751	61	3		3	NAT1	8	18080420	Silent	SNP	T	TCGA-G7-A4TM-01A-11D-A31X-10		18080420	128283602	14	10405											
CLTA	1211	hgsc.bcm.edu	37	chr9	36209297	36209297	+	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	gctttctacaaacaacccttCgctgacgtgattggttatgt	9	14	8	10	2	1	2	0	2	1	0	2	2	1	2	1	1	3	3	1	1	4	5			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr9:36209297C>T	ENST00000242285.6	+	5	639	c.519C>T	c.(517-519)ttC>ttT	p.F173F	CLTA_ENST00000396603.2_Silent_p.F173F|CLTA_ENST00000433436.2_Silent_p.F173F|CLTA_ENST00000470744.1_Intron|CLTA_ENST00000345519.5_Intron|CLTA_ENST00000538225.1_Intron|CLTA_ENST00000540080.1_Intron|CLTA_ENST00000466396.1_Silent_p.F121F			P09496	CLCA_HUMAN	clathrin, light chain A	173					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)			AACAACCCTTCGCTGACGTGA	0.403																																					p.F173F		Atlas-SNP	.											.	CLTA	18	.	0			c.C519T						PASS	.						191	165	174					9																	36209297		2203	4300	6503	SO:0001819	synonymous_variant	1211	exon5			ACCCTTCGCTGAC		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.519C>T	chr9.hg19:g.36209297C>T		128.0	0.0	.		89.0	38.0	.	NM_001076677	A8K4W3|B4DIN1|F5H6N3|Q2XPN5|Q53XZ1	Silent	SNP	ENST00000242285.6	hg19	CCDS6601.1																																																																																			.	.	.	none		0.403	CLTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052405.1	NM_007096		T	36209297	C	T	36209297	2	4	178	1	0	0	0	0	0	0	0	1	3566	883	31	1		1	CLTA	9	36209297	Silent	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10		36209297	105004134	15	10406											
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79318374	79318374	+	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	catttcccattcattgtcatGggtgacagcctgcaacgtaa	10	12	8	11	1	2	1	2	1	0	0	3	1	3	1	2	1	3	2	2	1	2	4			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr9:79318374G>A	ENST00000376718.3	-	9	8278	c.8155C>T	c.(8155-8157)Cat>Tat	p.H2719Y	PRUNE2_ENST00000428286.1_Missense_Mutation_p.H2360Y	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2719					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						TCATTGTCATGGGTGACAGCC	0.527																																					p.H2719Y		Atlas-SNP	.											.	PRUNE2	331	.	0			c.C8155T						PASS	.						102	83	89					9																	79318374		1568	3582	5150	SO:0001583	missense	158471	exon9			TGTCATGGGTGAC	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.8155C>T	chr9.hg19:g.79318374G>A	ENSP00000365908:p.His2719Tyr	63.0	0.0	.		51.0	32.0	.	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	hg19	CCDS47982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.75|17.75	3.465272|3.465272	0.63513|0.63513	.|.	.|.	ENSG00000106772|ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033|ENST00000426088	T;T|.	0.49720|.	0.77;0.78|.	5.89|5.89	5.89|5.89	0.94794|0.94794	.|.	0.102782|.	0.43747|.	D|.	0.000523|.	T|T	0.71187|0.71187	0.3310|0.3310	M|M	0.64997|0.64997	1.995|1.995	0.80722|0.80722	D|D	1|1	P;P|.	0.51653|.	0.898;0.947|.	B;B|.	0.43867|.	0.434;0.335|.	T|T	0.68957|0.68957	-0.5272|-0.5272	10|5	0.72032|.	D|.	0.01|.	-6.6465|-6.6465	14.0742|14.0742	0.64880|0.64880	0.0:0.1938:0.8062:0.0|0.0:0.1938:0.8062:0.0	.|.	2719;2719|.	Q8WUY3-3;Q8WUY3|.	.;PRUN2_HUMAN|.	Y|L	2719;2360;2718|2040	ENSP00000365908:H2719Y;ENSP00000397425:H2360Y|.	ENSP00000365908:H2719Y|.	H|P	-|-	1|2	0|0	PRUNE2|PRUNE2	78508194|78508194	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.640000|0.640000	0.38277|0.38277	4.226000|4.226000	0.58606|0.58606	2.814000|2.814000	0.96858|0.96858	0.586000|0.586000	0.80456|0.80456	CAT|CCA	.	.	.	none		0.527	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		A	79318374	G	A	79318374	3	1	178	1	0	0	0	0	1	0	0	0	12651	1348	47	2	1155	2	PRUNE2	9	79318374	Missense_Mutation	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10	43109077	79318374	61895057	16	10407											
WAPAL	23063	hgsc.bcm.edu	37	chr10	88227091	88227091	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtttcacagagccttcggAttttttctttaattttgttc	7	20	6	8	1	2	1	1	0	1	1	4	2	2	2	1	1	1	2	1	1	1	10			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr10:88227091A>G	ENST00000298767.5	-	9	2787	c.2315T>C	c.(2314-2316)aTc>aCc	p.I772T	WAPAL_ENST00000372075.1_Missense_Mutation_p.I39T|WAPAL_ENST00000263070.7_Missense_Mutation_p.I39T	NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	772	WAPL. {ECO:0000255|PROSITE- ProRule:PRU00603}.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)		p.I772T(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						GAGCCTTCGGATTTTTTCTTT	0.368																																					p.I772T		Atlas-SNP	.											WAPAL,NS,carcinoma,0,1	WAPAL	81	.	1	Substitution - Missense(1)	lung(1)	c.T2315C						PASS	.						180	167	171					10																	88227091		2203	4300	6503	SO:0001583	missense	23063	exon9			CTTCGGATTTTTT	AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"friend of EBNA2"	610754	"KIAA0261"	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.2315T>C	chr10.hg19:g.88227091A>G	ENSP00000298767:p.Ile772Thr	151.0	0.0	.		114.0	59.0	.	NM_015045	A7E2B5|Q5VSK5|Q8IX10|Q92549	Missense_Mutation	SNP	ENST00000298767.5	hg19	CCDS7375.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.484052	0.84854	.	.	ENSG00000062650	ENST00000342368;ENST00000298767;ENST00000372076;ENST00000372075;ENST00000263070	T	0.48201	0.82	5.99	5.99	0.97316	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.67316	0.2880	M	0.64997	1.995	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;0.99;0.998;0.996	T	0.69537	-0.5119	10	0.72032	D	0.01	.	16.4943	0.84223	1.0:0.0:0.0:0.0	.	766;810;772;809	B2RTX8;E9PH12;Q7Z5K2;Q7Z5K2-2	.;.;WAPL_HUMAN;.	T	857;772;857;39;39	ENSP00000298767:I772T	ENSP00000263070:I39T	I	-	2	0	WAPAL	88217071	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.336000	0.96533	2.291000	0.77112	0.533000	0.62120	ATC	.	.	.	none		0.368	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045		G	88227091	A	G	88227091	3	3	178	1	0	0	0	0	1	0	0	0	17260	333	12	3	1301	3	WAPAL	10	88227091	Missense_Mutation	SNP	A	TCGA-G7-A4TM-01A-11D-A31X-10		88227091	47307656	17	10408											
AHNAK	79026	hgsc.bcm.edu	37	chr11	62301415	62301415	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcacatccacagtgtaggcCgtgacccttctggtcactgt	7	11	10	13	1	3	1	2	1	1	0	4	1	4	1	3	2	0	1	3	2	1	2			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr11:62301415C>T	ENST00000378024.4	-	5	748	c.474G>A	c.(472-474)acG>acA	p.T158T	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	158					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)				CAGTGTAGGCCGTGACCCTTC	0.532																																					p.T158T		Atlas-SNP	.											.	AHNAK	532	.	0			c.G474A						PASS	.						136	119	124					11																	62301415		2202	4299	6501	SO:0001819	synonymous_variant	79026	exon5			GTAGGCCGTGACC	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.474G>A	chr11.hg19:g.62301415C>T		48.0	0.0	.		32.0	19.0	.	NM_001620	A1A586	Silent	SNP	ENST00000378024.4	hg19	CCDS31584.1																																																																																			.	.	.	none		0.532	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		T	62301415	C	T	62301415	2	4	178	1	0	0	0	0	0	0	0	1	414	639	23	1		1	AHNAK	11	62301415	Silent	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10		62301415	72705101	18	10409											
PIWIL4	143689	hgsc.bcm.edu	37	chr11	94341805	94341805	+	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	aaagatgcactcagcaaggaCgtgatggttgttggatgcgt	11	10	14	6	2	1	2	1	1	0	1	1	4	1	4	0	3	3	4	0	3	2	2			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr11:94341805C>T	ENST00000299001.6	+	15	2107	c.1896C>T	c.(1894-1896)gaC>gaT	p.D632D	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	632	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TCAGCAAGGACGTGATGGTTG	0.393																																					p.D632D		Atlas-SNP	.											PIWIL4,NS,carcinoma,0,1	PIWIL4	70	.	0			c.C1896T						PASS	.						269	236	247					11																	94341805		2201	4298	6499	SO:0001819	synonymous_variant	143689	exon15			CAAGGACGTGATG	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.1896C>T	chr11.hg19:g.94341805C>T		191.0	0.0	.		162.0	64.0	.	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Silent	SNP	ENST00000299001.6	hg19	CCDS31656.1																																																																																			.	.	.	none		0.393	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431		T	94341805	C	T	94341805	2	4	178	1	0	0	0	0	0	0	0	1	11967	535	19	1		1	PIWIL4	11	94341805	Silent	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10	32040390	94341805	40664711	19	10410											
FAM60A	58516	hgsc.bcm.edu	37	chr12	31448170	31448170	+	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	aaagaaagatggactaacatGattccagtttttttttgatc	14	15	7	5	0	0	4	0	2	0	2	2	5	1	5	1	1	1	1	1	1	3	6			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr12:31448170G>A	ENST00000337682.4	-	3	594	c.226C>T	c.(226-228)Cat>Tat	p.H76Y	FAM60A_ENST00000454658.2_Missense_Mutation_p.H76Y|FAM60A_ENST00000395766.1_5'UTR|FAM60A_ENST00000542983.1_5'UTR|FAM60A_ENST00000539409.1_Intron	NM_001135812.1	NP_001129284.1	Q9NP50	FA60A_HUMAN	family with sequence similarity 60, member A	76					negative regulation of cell migration (GO:0030336)	Sin3 complex (GO:0016580)				large_intestine(1)|lung(2)	3	all_cancers(9;5.22e-13)|all_epithelial(9;4e-13)|all_lung(12;1.2e-11)|Lung NSC(12;2.17e-09)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0207)|Lung SC(12;0.0592)|Esophageal squamous(101;0.162)					GGACTAACATGATTCCAGTTT	0.373																																					p.H76Y		Atlas-SNP	.											.	FAM60A	16	.	0			c.C226T						PASS	.						82	74	77					12																	31448170		2203	4300	6503	SO:0001583	missense	58516	exon4			TAACATGATTCCA	AF212220	CCDS8723.1	12p11.21	2012-11-30	2005-04-07	2005-04-07	ENSG00000139146	ENSG00000139146			30702	protein-coding gene	gene with protein product		615027	"chromosome 12 open reading frame 14"	C12orf14		11042152, 22984288, 22865885	Standard	NM_021238		Approved	TERA	uc001rke.3	Q9NP50	OTTHUMG00000168586	ENST00000337682.4:c.226C>T	chr12.hg19:g.31448170G>A	ENSP00000337477:p.His76Tyr	440.0	0.0	.		439.0	248.0	.	NM_021238	D3DUV8|Q9BSZ8	Missense_Mutation	SNP	ENST00000337682.4	hg19	CCDS8723.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.261331	0.80246	.	.	ENSG00000139146	ENST00000337682;ENST00000454658;ENST00000398170;ENST00000539004;ENST00000543615	T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06	4.22	4.22	0.49857	.	0.000000	0.85682	D	0.000000	T	0.80586	0.4651	M	0.82323	2.585	0.80722	D	1	D;D	0.76494	0.989;0.999	D;D	0.76575	0.969;0.988	D	0.84590	0.0666	10	0.87932	D	0	-1.1171	17.1323	0.86729	0.0:0.0:1.0:0.0	.	76;117	Q9NP50;B7Z287	FA60A_HUMAN;.	Y	76;76;117;76;76	ENSP00000337477:H76Y;ENSP00000393279:H76Y;ENSP00000443881:H76Y;ENSP00000437363:H76Y	ENSP00000337477:H76Y	H	-	1	0	FAM60A	31339437	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.457000	0.97630	2.343000	0.79666	0.561000	0.74099	CAT	.	.	.	none		0.373	FAM60A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400347.1	NM_021238		A	31448170	G	A	31448170	3	1	178	1	0	0	0	0	1	0	0	0	5602	1290	45	2	455	2	FAM60A	12	31448170	Missense_Mutation	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10		31448170	102403725	20	10411											
KCTD10	83892	hgsc.bcm.edu	37	chr12	109889450	109889450	+	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	gcgcttgatgtggatcctccGcacgcgctcgatccgctccc	4	9	11	17	6	0	1	0	1	0	0	5	3	4	2	4	1	0	4	4	1	0	1			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr12:109889450G>T	ENST00000228495.6	-	7	1173	c.892C>A	c.(892-894)Cgg>Agg	p.R298R	KCTD10_ENST00000424763.2_Silent_p.R117R|KCTD10_ENST00000540089.1_Silent_p.R117R|KCTD10_ENST00000540411.1_Silent_p.R272R|KCTD10_ENST00000538161.1_5'UTR	NM_031954.3	NP_114160.1	Q9H3F6	BACD3_HUMAN	potassium channel tetramerization domain containing 10	298					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						TGGATCCTCCGCACGCGCTCG	0.721																																					p.R298R		Atlas-SNP	.											KCTD10,NS,carcinoma,0,1	KCTD10	24	.	0			c.C892A						PASS	.						53	49	50					12																	109889450		2203	4300	6503	SO:0001819	synonymous_variant	83892	exon7			TCCTCCGCACGCG	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.892C>A	chr12.hg19:g.109889450G>T		41.0	0.0	.		55.0	4.0	.	NM_031954	Q53HN2|Q59FV1|Q6PL47|Q96SU0	Silent	SNP	ENST00000228495.6	hg19	CCDS9128.1	.	.	.	.	.	.	.	.	.	.	G	9.426	1.084203	0.20309	.	.	ENSG00000110906	ENST00000538161	.	.	.	4.97	4.05	0.47172	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-17.5015	11.8876	0.52610	0.0:0.0:0.6832:0.3168	.	.	.	.	X	263	.	.	C	-	3	2	KCTD10	108373833	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	5.414000	0.66405	1.407000	0.46875	0.655000	0.94253	TGC	.	.	.	none		0.721	KCTD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403099.1	NM_031954		T	109889450	G	T	109889450	2	4	178	1	0	0	0	0	0	0	0	1	8104	1086	38	4		4	KCTD10	12	109889450	Silent	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10	78441280	109889450	23962445	21	10412											
ELL3	80237	hgsc.bcm.edu	37	chr15	44067740	44067740	+	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	tacctcacttcccactgtgcCatgtgctcccttgaggatcc	6	12	7	16	0	1	1	1	1	0	0	4	2	4	2	5	1	3	1	5	1	1	3			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr15:44067740C>T	ENST00000319359.3	-	5	1193	c.552G>A	c.(550-552)atG>atA	p.M184I	RP11-296A16.1_ENST00000417761.2_3'UTR|ELL3_ENST00000497465.1_5'Flank|SERF2_ENST00000381359.1_5'Flank	NM_025165.2	NP_079441.1	Q9HB65	ELL3_HUMAN	elongation factor RNA polymerase II-like 3	184					DNA-templated transcription, elongation (GO:0006354)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epithelial to mesenchymal transition (GO:0010717)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	enhancer binding (GO:0035326)			cervix(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(1)	13		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;7.81e-07)		CCCACTGTGCCATGTGCTCCC	0.498											OREG0023092	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.M184I		Atlas-SNP	.											.	ELL3	38	.	0			c.G552A						PASS	.						154	133	140					15																	44067740		2198	4298	6496	SO:0001583	missense	80237	exon5			CTGTGCCATGTGC	AF276512	CCDS10102.1	15q15.1	2008-02-05			ENSG00000128886	ENSG00000128886			23113	protein-coding gene	gene with protein product		609885				10882741	Standard	NM_025165		Approved	FLJ22637	uc001zsw.1	Q9HB65	OTTHUMG00000059936	ENST00000319359.3:c.552G>A	chr15.hg19:g.44067740C>T	ENSP00000320346:p.Met184Ile	91.0	0.0	.	921	60.0	8.0	.	NM_025165	B3KQ66|B3KX08|Q6I9Z7|Q9H634	Missense_Mutation	SNP	ENST00000319359.3	hg19	CCDS10102.1	.	.	.	.	.	.	.	.	.	.	C	13.65	2.299310	0.40694	.	.	ENSG00000128886	ENST00000319359	T	0.29397	1.57	5.75	2.65	0.31530	.	0.896720	0.09670	N	0.771265	T	0.23492	0.0568	L	0.47716	1.5	0.28997	N	0.887675	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.06405	0.001;0.001;0.002	T	0.30707	-0.9969	10	0.19147	T	0.46	-31.8363	4.8606	0.13581	0.1517:0.6198:0.1467:0.0818	.	184;184;138	B3KX08;Q9HB65;B3KQ66	.;ELL3_HUMAN;.	I	184	ENSP00000320346:M184I	ENSP00000320346:M184I	M	-	3	0	ELL3	41855032	0.017000	0.18338	0.948000	0.38648	0.979000	0.70002	-0.179000	0.09768	0.734000	0.32515	0.555000	0.69702	ATG	.	.	.	none		0.498	ELL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133236.2	NM_025165		T	44067740	C	T	44067740	3	4	178	1	0	0	0	0	1	0	0	0	5066	594	21	2	669	2	ELL3	15	44067740	Missense_Mutation	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10		44067740	58463652	22	10413											
SGK269	79834	hgsc.bcm.edu	37	chr15	77450971	77450971	+	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	tgaagtgcagcccctgccatCttgcttcccaacaacagttc	9	10	7	15	0	1	1	0	1	1	0	3	1	2	1	4	0	6	3	4	0	3	3			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr15:77450971C>A	ENST00000560626.2	-	5	3680	c.3205G>T	c.(3205-3207)Gat>Tat	p.D1069Y	PEAK1_ENST00000312493.4_Missense_Mutation_p.D1069Y			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	1069					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										CCCCTGCCATCTTGCTTCCCA	0.473																																					p.D1069Y		Atlas-SNP	.											.	.	.	.	0			c.G3205T						PASS	.						127	119	122					15																	77450971		1933	4139	6072	SO:0001583	missense	0	exon6			TGCCATCTTGCTT		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.3205G>T	chr15.hg19:g.77450971C>A	ENSP00000452796:p.Asp1069Tyr	79.0	0.0	.		59.0	25.0	.	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Missense_Mutation	SNP	ENST00000560626.2	hg19	CCDS42062.1	.	.	.	.	.	.	.	.	.	.	C	15.41	2.826500	0.50739	.	.	ENSG00000173517	ENST00000312493	T	0.69685	-0.42	5.4	4.49	0.54785	.	0.667769	0.14142	N	0.338611	T	0.52092	0.1713	N	0.14661	0.345	0.28725	N	0.902826	P	0.44090	0.826	B	0.41723	0.365	T	0.50717	-0.8795	10	0.59425	D	0.04	-3.0393	12.2917	0.54823	0.0:0.9219:0.0:0.0781	.	1069	Q9H792	PEAK1_HUMAN	Y	1069	ENSP00000309230:D1069Y	ENSP00000309230:D1069Y	D	-	1	0	AC087465.1	75238026	1.000000	0.71417	0.993000	0.49108	0.748000	0.42578	4.715000	0.61909	1.275000	0.44379	0.563000	0.77884	GAT	.	.	.	none		0.473	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3			A	77450971	C	A	77450971	3	1	178	1	0	0	0	0	1	0	0	0	14224	913	32	4	2047	4	SGK269	15	77450971	Missense_Mutation	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10	33383231	77450971	25080421	23	10414											
CREBBP	1387	hgsc.bcm.edu	37	chr16	3860637	3860637	+	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	ttggtgactgaagtattcttGatatctgtagggaaggtggg	9	14	15	3	0	2	3	0	3	2	0	2	4	2	4	0	4	0	2	0	4	5	6			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr16:3860637G>A	ENST00000262367.5	-	3	1751	c.942C>T	c.(940-942)atC>atT	p.I314I	CREBBP_ENST00000382070.3_Silent_p.I314I	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	314	Interaction with SRCAP.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		AAGTATTCTTGATATCTGTAG	0.517			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.I314I		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.C942T						PASS	.						212	196	201					16																	3860637		2197	4300	6497	SO:0001819	synonymous_variant	1387	exon3			ATTCTTGATATCT	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.942C>T	chr16.hg19:g.3860637G>A		93.0	0.0	.		108.0	36.0	.	NM_001079846	D3DUC9|O00147|Q16376|Q4LE28	Silent	SNP	ENST00000262367.5	hg19	CCDS10509.1																																																																																			.	.	.	none		0.517	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		A	3860637	G	A	3860637	2	1	178	1	0	0	0	0	0	0	0	1	3863	1280	45	2		2	CREBBP	16	3860637	Silent	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10		3860637	86494116	24	10415											
ABCC1	4363	hgsc.bcm.edu	37	chr16	16180696	16180696	+	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	cccagggcgtgaacctgtctGggggccagaagcagcgcgtg	7	5	17	12	3	1	2	0	1	1	1	1	2	1	2	3	3	3	1	3	3	2	0			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr16:16180696G>A	ENST00000399410.3	+	18	2483	c.2308G>A	c.(2308-2310)Ggg>Agg	p.G770R	ABCC1_ENST00000345148.5_Missense_Mutation_p.G770R|ABCC1_ENST00000399408.2_Missense_Mutation_p.G770R|ABCC1_ENST00000346370.5_Intron|ABCC1_ENST00000351154.5_Missense_Mutation_p.G711R|ABCC1_ENST00000349029.5_Intron	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	770	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)	GAACCTGTCTGGGGGCCAGAA	0.587																																					p.G770R		Atlas-SNP	.											.	ABCC1	156	.	0			c.G2308A						PASS	.						60	71	68					16																	16180696		2181	4293	6474	SO:0001583	missense	4363	exon18			CTGTCTGGGGGCC	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.2308G>A	chr16.hg19:g.16180696G>A	ENSP00000382342:p.Gly770Arg	47.0	0.0	.		35.0	5.0	.	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Missense_Mutation	SNP	ENST00000399410.3	hg19	CCDS42122.1	.	.	.	.	.	.	.	.	.	.	G	33	5.195409	0.94960	.	.	ENSG00000103222	ENST00000399410;ENST00000399408;ENST00000351154;ENST00000345148;ENST00000536381	D;D;D;D	0.95205	-3.64;-3.64;-3.64;-3.64	5.38	5.38	0.77491	ABC transporter, conserved site (1);ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.98658	0.9550	H	0.99182	4.46	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.97110	0.993;0.978;1.0;1.0	D	0.99712	1.1007	10	0.87932	D	0	-31.1556	18.1249	0.89583	0.0:0.0:1.0:0.0	.	770;711;770;770	P33527-4;P33527-2;P33527;P33527-9	.;.;MRP1_HUMAN;.	R	770;770;711;770;444	ENSP00000382342:G770R;ENSP00000382340:G770R;ENSP00000263017:G711R;ENSP00000263014:G770R	ENSP00000263014:G770R	G	+	1	0	ABCC1	16088197	1.000000	0.71417	0.984000	0.44739	0.997000	0.91878	9.697000	0.98697	2.520000	0.84964	0.563000	0.77884	GGG	.	.	.	none		0.587	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996		A	16180696	G	A	16180696	3	1	178	1	0	0	0	0	1	0	0	0	49	1348	47	2	2378	2	ABCC1	16	16180696	Missense_Mutation	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10	12320059	16180696	74174057	25	10416											
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24788620	24788620	+	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	cagccagtcagaaagcagtgCtttaacaaatcaacagccac	16	6	7	12	0	2	1	2	0	0	1	2	1	2	1	2	0	6	2	2	0	4	2	rs201630200		TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr16:24788620C>G	ENST00000395799.3	+	5	659	c.530C>G	c.(529-531)gCt>gGt	p.A177G	TNRC6A_ENST00000315183.7_Missense_Mutation_p.A177G	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	177	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)		GAAAGCAGTGCTTTAACAAAT	0.433																																					p.A177G		Atlas-SNP	.											.	TNRC6A	171	.	0			c.C530G						PASS	.						137	141	140					16																	24788620		2064	4235	6299	SO:0001583	missense	27327	exon5			GCAGTGCTTTAAC	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.530C>G	chr16.hg19:g.24788620C>G	ENSP00000379144:p.Ala177Gly	57.0	0.0	.		59.0	24.0	.	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	hg19	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	C	14.14	2.446741	0.43429	.	.	ENSG00000090905	ENST00000315183;ENST00000395799	T;T	0.12774	2.65;2.65	5.72	4.72	0.59763	.	0.361735	0.29783	N	0.011217	T	0.11110	0.0271	N	0.19112	0.55	0.80722	D	1	B	0.20261	0.043	B	0.19946	0.027	T	0.17228	-1.0376	10	0.26408	T	0.33	-7.991	18.3586	0.90367	0.0:0.8717:0.1283:0.0	.	177	Q8NDV7	TNR6A_HUMAN	G	177	ENSP00000326900:A177G;ENSP00000379144:A177G	ENSP00000326900:A177G	A	+	2	0	TNRC6A	24696121	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.054000	0.49908	2.687000	0.91594	0.591000	0.81541	GCT	.	.	.	alt		0.433	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		G	24788620	C	G	24788620	3	3	178	1	0	0	0	0	1	0	0	0	16352	797	28	4	548	4	TNRC6A	16	24788620	Missense_Mutation	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10	8607924	24788620	65566133	26	10417											
COG4	25839	hgsc.bcm.edu	37	chr16	70548271	70548271	+	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	tcggctgagctcaatgaccgActtgtccaggcacaagtagc	10	8	11	12	2	1	2	1	2	0	0	3	3	2	2	2	2	2	4	2	2	3	2			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr16:70548271A>T	ENST00000323786.5	-	4	532	c.511T>A	c.(511-513)Tcg>Acg	p.S171T	COG4_ENST00000393612.4_Missense_Mutation_p.S167T|COG4_ENST00000564653.1_Missense_Mutation_p.S171T	NM_001195139.1|NM_015386.2	NP_001182068.1|NP_056201.2	Q9H9E3	COG4_HUMAN	component of oligomeric golgi complex 4	167					Golgi organization (GO:0007030)|Golgi vesicle prefusion complex stabilization (GO:0048213)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|pancreas(1)|prostate(2)	33		Ovarian(137;0.0694)				tcaatgaccgACTTGTCCAGG	0.468																																					p.S171T		Atlas-SNP	.											.	COG4	64	.	0			c.T511A						PASS	.						89	75	80					16																	70548271		2198	4300	6498	SO:0001583	missense	25839	exon4			TGACCGACTTGTC	AL050101	CCDS10892.2, CCDS73909.1	16q22.1	2013-09-20			ENSG00000103051	ENSG00000103051		"Components of oligomeric golgi complex"	18620	protein-coding gene	gene with protein product		606976				11980916	Standard	NM_015386		Approved	COD1, DKFZP586E1519	uc002ezc.3	Q9H9E3	OTTHUMG00000128515	ENST00000323786.5:c.511T>A	chr16.hg19:g.70548271A>T	ENSP00000315775:p.Ser171Thr	94.0	0.0	.		44.0	14.0	.	NM_015386	B4DMN8|C9JS23|Q96D40|Q9BRF0|Q9BVZ2|Q9H5Y4|Q9Y3W3	Missense_Mutation	SNP	ENST00000323786.5	hg19	CCDS10892.2	.	.	.	.	.	.	.	.	.	.	A	22.6	4.316795	0.81469	.	.	ENSG00000103051	ENST00000323786;ENST00000338984;ENST00000393612;ENST00000534772	T;T;T	0.46819	0.86;0.86;1.12	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.41305	0.1153	L	0.41961	1.31	0.80722	D	1	B;B	0.24368	0.057;0.102	B;B	0.20955	0.032;0.018	T	0.20706	-1.0267	10	0.25751	T	0.34	-5.8107	15.6224	0.76816	1.0:0.0:0.0:0.0	.	166;167	Q6PIW8;Q9H9E3	.;COG4_HUMAN	T	171;167;167;94	ENSP00000315775:S171T;ENSP00000377236:S167T;ENSP00000461912:S94T	ENSP00000315775:S171T	S	-	1	0	COG4	69105772	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.758000	0.91663	2.093000	0.63338	0.459000	0.35465	TCG	.	.	.	none		0.468	COG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250326.3			T	70548271	A	T	70548271	3	4	178	1	0	0	0	0	1	0	0	0	3662	275	10	5	1922	5	COG4	16	70548271	Missense_Mutation	SNP	A	TCGA-G7-A4TM-01A-11D-A31X-10	45759651	70548271	19806482	27	10418											
KIAA0100	9703	hgsc.bcm.edu	37	chr17	26943696	26943696	+	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	ttcatcatcttccacacttcGgccaggaaagaaaaagccca	14	8	6	13	1	3	1	2	0	1	1	5	2	4	2	3	2	1	0	3	2	3	3			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr17:26943696G>C	ENST00000528896.2	-	35	6171	c.6097C>G	c.(6097-6099)Cga>Gga	p.R2033G	KIAA0100_ENST00000389003.3_Missense_Mutation_p.R1890G|SGK494_ENST00000301037.5_5'Flank|KIAA0100_ENST00000579924.2_5'UTR|SPAG5-AS1_ENST00000554154.1_RNA|SPAG5-AS1_ENST00000414744.1_RNA|KIAA0100_ENST00000544884.1_Missense_Mutation_p.R1890G|SPAG5-AS1_ENST00000424210.1_RNA|RP11-192H23.4_ENST00000577790.1_5'Flank|SGK494_ENST00000469832.3_5'Flank|RP11-192H23.4_ENST00000534850.1_5'Flank	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	2033						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)					TCCACACTTCGGCCAGGAAAG	0.448																																					p.R2033G		Atlas-SNP	.											.	KIAA0100	175	.	0			c.C6097G						PASS	.						118	121	120					17																	26943696		2203	4300	6503	SO:0001583	missense	9703	exon35			CACTTCGGCCAGG	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.6097C>G	chr17.hg19:g.26943696G>C	ENSP00000436773:p.Arg2033Gly	117.0	0.0	.		140.0	85.0	.	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	hg19	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	G	17.82	3.483328	0.63962	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	T;T	0.46819	0.86;0.86	5.87	5.87	0.94306	FMP27,  C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.70605	0.3243	M	0.76170	2.325	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.67205	-0.5729	10	0.39692	T	0.17	.	20.1947	0.98239	0.0:0.0:1.0:0.0	.	2033	Q14667	K0100_HUMAN	G	2033;2003;2033;1890	ENSP00000436773:R2033G;ENSP00000446443:R1890G	ENSP00000005905:R2033G	R	-	1	2	KIAA0100	23967823	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	3.682000	0.54656	2.780000	0.95670	0.561000	0.74099	CGA	.	.	.	none		0.448	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		C	26943696	G	C	26943696	3	2	178	1	0	0	0	0	1	0	0	0	8161	1124	39	4	630	4	KIAA0100	17	26943696	Missense_Mutation	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10		26943696	54251514	28	10419											
HOXB4	3214	hgsc.bcm.edu	37	chr17	46654346	46654346	+	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	ggcgcgtgtaggcggtccgaGagcgcttgggctccccgccg	3	6	18	14	7	0	1	0	0	0	1	2	2	2	1	4	4	1	3	4	4	1	2			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr17:46654346G>T	ENST00000332503.5	-	2	2285	c.494C>A	c.(493-495)tCt>tAt	p.S165Y	HOXB3_ENST00000311626.4_5'Flank|MIR10A_ENST00000385043.1_RNA|HOXB3_ENST00000485909.2_5'Flank|HOXB3_ENST00000465120.3_Intron|HOXB3_ENST00000460160.1_Intron|HOXB-AS3_ENST00000465846.2_RNA|HOXB3_ENST00000490677.1_5'Flank|HOXB3_ENST00000498678.1_Intron|HOXB3_ENST00000472863.1_Intron|HOXB3_ENST00000552000.2_Intron|HOXB3_ENST00000476342.1_Intron|HOXB3_ENST00000489475.1_Intron	NM_024015.4	NP_076920.1	P17483	HXB4_HUMAN	homeobox B4	165					anterior/posterior pattern specification (GO:0009952)|bone marrow development (GO:0048539)|cell proliferation (GO:0008283)|definitive hemopoiesis (GO:0060216)|embryonic skeletal system morphogenesis (GO:0048704)|hematopoietic stem cell differentiation (GO:0060218)|morphogenesis of an epithelial sheet (GO:0002011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|somatic stem cell division (GO:0048103)|spleen development (GO:0048536)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|urinary_tract(2)	9						GGCGGTCCGAGAGCGCTTGGG	0.592																																					p.S165Y		Atlas-SNP	.											.	HOXB4	16	.	0			c.C494A						PASS	.						53	58	56					17																	46654346		2203	4300	6503	SO:0001583	missense	3214	exon2			GTCCGAGAGCGCT		CCDS11529.1	17q21.32	2011-06-20	2005-12-22		ENSG00000182742	ENSG00000182742		"Homeoboxes / ANTP class : HOXL subclass"	5115	protein-coding gene	gene with protein product		142965	"homeo box B4"	HOX2, HOX2F		1973146, 1358459	Standard	NM_024015		Approved		uc002inp.3	P17483	OTTHUMG00000159920	ENST00000332503.5:c.494C>A	chr17.hg19:g.46654346G>T	ENSP00000328928:p.Ser165Tyr	44.0	0.0	.		101.0	57.0	.	NM_024015	Q9NTA0	Missense_Mutation	SNP	ENST00000332503.5	hg19	CCDS11529.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.923509	0.92319	.	.	ENSG00000182742	ENST00000332503	D	0.96365	-3.99	5.27	5.27	0.74061	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.96836	0.8967	L	0.33710	1.025	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.97955	1.0334	10	0.87932	D	0	.	18.4966	0.90867	0.0:0.0:1.0:0.0	.	165	P17483	HXB4_HUMAN	Y	165	ENSP00000328928:S165Y	ENSP00000328928:S165Y	S	-	2	0	HOXB4	44009345	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	9.842000	0.99487	2.456000	0.83038	0.561000	0.74099	TCT	.	.	.	none		0.592	HOXB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358259.2			T	46654346	G	T	46654346	3	4	178	1	0	0	0	0	1	0	0	0	7310	942	33	4	265	4	HOXB4	17	46654346	Missense_Mutation	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10	19710650	46654346	34540864	29	10420											
KIAA0195	9772	hgsc.bcm.edu	37	chr17	73487468	73487468	+	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	tgttcttcagcgggaaggtgGagccccctcacagcagccat	8	8	12	13	1	3	0	2	0	1	0	3	2	3	2	3	3	4	2	3	3	1	2			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr17:73487468G>T	ENST00000314256.7	+	13	1712	c.1318G>T	c.(1318-1320)Gag>Tag	p.E440*	KIAA0195_ENST00000375248.5_Nonsense_Mutation_p.E450*|KIAA0195_ENST00000579208.1_Nonsense_Mutation_p.E91*	NM_014738.4	NP_055553.3	Q12767	K0195_HUMAN	KIAA0195	440						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)			CGGGAAGGTGGAGCCCCCTCA	0.602																																					p.E440X		Atlas-SNP	.											.	KIAA0195	102	.	0			c.G1318T						PASS	.						102	89	93					17																	73487468		2203	4300	6503	SO:0001587	stop_gained	9772	exon13			AAGGTGGAGCCCC		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.1318G>T	chr17.hg19:g.73487468G>T	ENSP00000313885:p.Glu440*	61.0	0.0	.		74.0	22.0	.	NM_014738	O75536|Q86XF1	Nonsense_Mutation	SNP	ENST00000314256.7	hg19	CCDS32732.1	.	.	.	.	.	.	.	.	.	.	G	31	5.089916	0.94149	.	.	ENSG00000177728	ENST00000314256;ENST00000375248	.	.	.	5.84	4.86	0.63082	.	0.100124	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	-25.239	16.9369	0.86205	0.0:0.1279:0.8721:0.0	.	.	.	.	X	440;450	.	ENSP00000313885:E440X	E	+	1	0	KIAA0195	70999063	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.741000	0.98843	1.465000	0.48006	0.591000	0.81541	GAG	.	.	.	none		0.602	KIAA0195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447303.1	NM_014738		T	73487468	G	T	73487468	4	4	178	1	0	0	0	0	0	1	0	0	8167	1175	41	4	1364	4	KIAA0195	17	73487468	Nonsense_Mutation	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10	26833122	73487468	7707742	30	10421											
ACER1	125981	hgsc.bcm.edu	37	chr19	6307219	6307219	+	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	ccagaagctgcaaagcagacGgtcactgatccagctggtca	12	6	11	12	1	2	3	2	1	0	2	3	3	3	3	2	2	4	4	2	2	2	0			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr19:6307219G>T	ENST00000301452.4	-	5	648	c.571C>A	c.(571-573)Cgt>Agt	p.R191S		NM_133492.2	NP_597999.1	Q8TDN7	ACER1_HUMAN	alkaline ceramidase 1	191					cell differentiation (GO:0030154)|cellular response to calcium ion (GO:0071277)|ceramide catabolic process (GO:0046514)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)|regulation of lipid metabolic process (GO:0019216)|response to alkaline pH (GO:0010446)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ceramidase activity (GO:0017040)|dihydroceramidase activity (GO:0071633)			NS(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|pancreas(1)	15						CAAAGCAGACGGTCACTGATC	0.542																																					p.R191S		Atlas-SNP	.											.	ACER1	38	.	0			c.C571A						PASS	.						89	86	87					19																	6307219		2203	4300	6503	SO:0001583	missense	125981	exon5			GCAGACGGTCACT	AF347024	CCDS12161.1	19p13.3	2013-01-25	2008-12-19	2008-12-19	ENSG00000167769	ENSG00000167769	3.5.1.23	"Alkaline ceramidase"	18356	protein-coding gene	gene with protein product		613491	"N-acylsphingosine amidohydrolase (alkaline ceramidase) 3"	ASAH3		12783875	Standard	NM_133492		Approved		uc002mel.2	Q8TDN7		ENST00000301452.4:c.571C>A	chr19.hg19:g.6307219G>T	ENSP00000301452:p.Arg191Ser	49.0	0.0	.		34.0	9.0	.	NM_133492		Missense_Mutation	SNP	ENST00000301452.4	hg19	CCDS12161.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.037897	0.75617	.	.	ENSG00000167769	ENST00000301452	T	0.47177	0.85	5.58	3.34	0.38264	.	0.000000	0.85682	D	0.000000	T	0.68668	0.3026	M	0.87900	2.915	0.80722	D	1	D	0.71674	0.998	D	0.63703	0.917	T	0.75932	-0.3143	10	0.87932	D	0	-21.1368	12.8258	0.57718	0.0:0.0:0.7048:0.2952	.	191	Q8TDN7	ACER1_HUMAN	S	191	ENSP00000301452:R191S	ENSP00000301452:R191S	R	-	1	0	ACER1	6258219	1.000000	0.71417	0.923000	0.36655	0.707000	0.40811	3.467000	0.53078	1.347000	0.45714	0.561000	0.74099	CGT	.	.	.	none		0.542	ACER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452982.1	NM_133492		T	6307219	G	T	6307219	3	4	178	1	0	0	0	0	1	0	0	0	138	1116	39	4	231	4	ACER1	19	6307219	Missense_Mutation	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10		6307219	52821764	31	10422											
ZNF529	57711	hgsc.bcm.edu	37	chr19	37038841	37038841	+	Frame_Shift_Del	DEL	T	T	-																															ggagttatctatcccaaaggTtttccaacattgattacatt																										TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr19:37038841delT	ENST00000591340.1	-	5	777	c.619delA	c.(619-621)accfs	p.T207fs	ZNF529_ENST00000334116.7_Frame_Shift_Del_p.T102fs	NM_020951.4	NP_066002.3	Q6P280	ZN529_HUMAN	zinc finger protein 529	207					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)					ATCCCAAAGGTTTTCCAACAT	0.313																																					p.T207fs		Atlas-Indel,Pindel	.											.	ZNF529	82	.	0			c.620delC						PASS	.						77	71	73					19																	37038841		1844	4087	5931	SO:0001589	frameshift_variant	57711	exon6			.	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.619delA	chr19.hg19:g.37038841delT	ENSP00000465578:p.Thr207fs	123.0	0.0	0		47.0	15.0	0.319149	NM_001145649	K7EKE1|Q9H731|Q9HCF7	Frame_Shift_Del	DEL	ENST00000591340.1	hg19	CCDS54256.1																																																																																			.	.	.	none		0.313	ZNF529-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452730.1	NM_020951		-	37038841	T	-	37038841	7	5	178	1	0	1	0	1	0	0	0	0	17982	1725	60	0	1076	0	ZNF529	19	37038841	Frame_Shift_Del	DEL	T	TCGA-G7-A4TM-01A-11D-A31X-10	30731622	37038841	22090142	32	10423											
CAPN12	147968	hgsc.bcm.edu	37	chr19	39226808	39226808	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagtcagcctcgtcgccggCgtgggcggtgctcggcacca	5	6	16	14	6	1	0	1	0	0	0	4	1	1	0	3	4	2	2	3	4	1	0			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr19:39226808C>T	ENST00000328867.4	-	12	1833	c.1525G>A	c.(1525-1527)Gcc>Acc	p.A509T	CTD-2540F13.2_ENST00000602255.1_RNA|CAPN12_ENST00000601953.1_Missense_Mutation_p.A360T	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	509	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)			TCGTCGCCGGCGTGGGCGGTG	0.731																																					p.A509T		Atlas-SNP	.											.	CAPN12	43	.	0			c.G1525A						PASS	.						5	7	6					19																	39226808		1560	2860	4420	SO:0001583	missense	147968	exon12			CGCCGGCGTGGGC	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.1525G>A	chr19.hg19:g.39226808C>T	ENSP00000331636:p.Ala509Thr	20.0	0.0	.		17.0	8.0	.	NM_144691		Missense_Mutation	SNP	ENST00000328867.4	hg19	CCDS12519.1	.	.	.	.	.	.	.	.	.	.	C	14.10	2.434611	0.43224	.	.	ENSG00000182472	ENST00000328867	D	0.87256	-2.23	3.72	2.48	0.30137	Peptidase C2, calpain, large subunit, domain III (2);Peptidase C2, calpain, domain III (1);	0.544531	0.18591	N	0.136731	T	0.80909	0.4714	L	0.55990	1.75	0.22266	N	0.999247	B	0.19331	0.035	B	0.12156	0.007	T	0.72204	-0.4361	10	0.87932	D	0	.	3.9299	0.09279	0.0:0.5899:0.2287:0.1814	.	509	Q6ZSI9	CAN12_HUMAN	T	509	ENSP00000331636:A509T	ENSP00000331636:A509T	A	-	1	0	CAPN12	43918648	0.987000	0.35691	0.077000	0.20336	0.396000	0.30629	2.272000	0.43373	0.658000	0.30925	0.484000	0.47621	GCC	.	.	.	none		0.731	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1			T	39226808	C	T	39226808	3	4	178	1	0	0	0	0	1	0	0	0	2627	768	27	1	674	1	CAPN12	19	39226808	Missense_Mutation	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10	2187967	39226808	19902175	33	10424											
CIC	23152	hgsc.bcm.edu	37	chr19	42795850	42795850	+	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	agccactgccactggtgagcCcgcccttctcagtacctgtg	6	9	10	16	1	1	1	1	1	1	0	2	1	1	1	5	1	4	1	5	1	1	2			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr19:42795850C>T	ENST00000575354.2	+	11	2879	c.2839C>T	c.(2839-2841)Ccg>Tcg	p.P947S	CIC_ENST00000160740.3_Missense_Mutation_p.P947S|CIC_ENST00000572681.2_Missense_Mutation_p.P1856S	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	947	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)				ACTGGTGAGCCCGCCCTTCTC	0.662			"Mis, F, S"		oligodendroglioma																																p.P947S		Atlas-SNP	.		Rec	yes		19	19q13.2	23152	capicua homolog		O	.	CIC	249	.	0			c.C2839T						PASS	.						46	52	50					19																	42795850		2048	4111	6159	SO:0001583	missense	23152	exon11			GTGAGCCCGCCCT	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.2839C>T	chr19.hg19:g.42795850C>T	ENSP00000458663:p.Pro947Ser	69.0	0.0	.		88.0	32.0	.	NM_015125	Q7LGI1|Q9UEG5|Q9Y6T1	Missense_Mutation	SNP	ENST00000575354.2	hg19	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	C	9.524	1.109082	0.20714	.	.	ENSG00000079432	ENST00000160740	.	.	.	4.32	3.28	0.37604	.	.	.	.	.	T	0.44138	0.1279	L	0.29908	0.895	0.35299	D	0.782869	B	0.13145	0.007	B	0.12156	0.007	T	0.52200	-0.8607	8	0.87932	D	0	-7.0964	9.1066	0.36701	0.0:0.8892:0.0:0.1108	.	947	Q96RK0	CIC_HUMAN	S	947	.	ENSP00000160740:P947S	P	+	1	0	CIC	47487690	1.000000	0.71417	0.980000	0.43619	0.928000	0.56348	3.631000	0.54280	1.014000	0.39417	0.462000	0.41574	CCG	.	.	.	none		0.662	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			T	42795850	C	T	42795850	3	4	178	1	0	0	0	0	1	0	0	0	3426	623	22	2	2881	2	CIC	19	42795850	Missense_Mutation	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10	3569042	42795850	16333133	34	10425											
ARFGEF2	10564	hgsc.bcm.edu	37	chr20	47587774	47587774	+	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	aatgcaatcaagcaatatctCtgtgtggccttgtccaaaaa	14	11	7	9	0	2	0	1	0	1	0	4	0	3	0	2	1	2	2	2	1	7	2			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr20:47587774C>G	ENST00000371917.4	+	10	1308	c.1308C>G	c.(1306-1308)ctC>ctG	p.L436L		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	436					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)			AGCAATATCTCTGTGTGGCCT	0.458																																					p.L436L	Esophageal Squamous(176;1738 1974 26285 33069 35354)	Atlas-SNP	.											.	ARFGEF2	160	.	0			c.C1308G						PASS	.						213	185	195					20																	47587774		2203	4300	6503	SO:0001819	synonymous_variant	10564	exon10			ATATCTCTGTGTG	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.1308C>G	chr20.hg19:g.47587774C>G		98.0	0.0	.		115.0	47.0	.	NM_006420	Q5TFT9|Q9NTS1	Silent	SNP	ENST00000371917.4	hg19	CCDS13411.1																																																																																			.	.	.	none		0.458	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420		G	47587774	C	G	47587774	2	3	178	1	0	0	0	0	0	0	0	1	853	900	32	4		4	ARFGEF2	20	47587774	Silent	SNP	C	TCGA-G7-A4TM-01A-11D-A31X-10		47587774	15437746	35	10426											
NCAM2	4685	hgsc.bcm.edu	37	chr21	22710734	22710734	+	Missense_Mutation	SNP	A	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	cctcacataatacagcttaaAaatgaaactacatatgagaa	20	9	4	8	0	1	2	1	2	0	1	1	3	1	2	1	0	4	1	1	0	9	5			TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chr21:22710734A>C	ENST00000400546.1	+	8	1173	c.924A>C	c.(922-924)aaA>aaC	p.K308N	NCAM2_ENST00000535285.1_Missense_Mutation_p.K333N|NCAM2_ENST00000284894.7_Missense_Mutation_p.K166N	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	308	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)		TACAGCTTAAAAATGAAACTA	0.388																																					p.K308N		Atlas-SNP	.											.	NCAM2	220	.	0			c.A924C						PASS	.						59	58	59					21																	22710734		1859	4085	5944	SO:0001583	missense	4685	exon8			GCTTAAAAATGAA		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.924A>C	chr21.hg19:g.22710734A>C	ENSP00000383392:p.Lys308Asn	188.0	0.0	.		148.0	61.0	.	NM_004540	A8MQ06|B7Z841|Q7Z7F2	Missense_Mutation	SNP	ENST00000400546.1	hg19	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	A	15.79	2.936147	0.52972	.	.	ENSG00000154654	ENST00000400546;ENST00000284894;ENST00000535285	T;T;T	0.69685	-0.42;-0.42;-0.42	5.8	3.37	0.38596	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.276736	0.45867	D	0.000323	T	0.67382	0.2887	L	0.39245	1.2	0.53688	D	0.999977	D;P;P	0.55800	0.973;0.776;0.618	P;P;B	0.56474	0.799;0.558;0.374	T	0.64761	-0.6331	10	0.49607	T	0.09	-16.2371	9.6438	0.39855	0.8549:0.0:0.1451:0.0	.	333;166;308	B7Z841;B7Z5K2;O15394	.;.;NCAM2_HUMAN	N	308;166;333	ENSP00000383392:K308N;ENSP00000284894:K166N;ENSP00000441887:K333N	ENSP00000284894:K166N	K	+	3	2	NCAM2	21632605	1.000000	0.71417	0.991000	0.47740	0.989000	0.77384	2.518000	0.45537	0.426000	0.26116	0.482000	0.46254	AAA	.	.	.	none		0.388	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		C	22710734	A	C	22710734	3	2	178	1	0	0	0	0	1	0	0	0	10210	11	1	5	954	5	NCAM2	21	22710734	Missense_Mutation	SNP	A	TCGA-G7-A4TM-01A-11D-A31X-10		22710734	25419161	36	10427											
BCOR	54880	hgsc.bcm.edu	37	chrX	39916463	39916463	+	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	gccatattcaaggaggtgtcGcacaatgttgagccagcccc	10	8	11	12	1	1	1	1	1	0	0	2	2	1	2	4	2	2	2	4	2	3	3	rs199676230		TCGA-G7-A4TM-01A-11D-A31X-10	TCGA-G7-A4TM-10B-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d7e8ac41-c79b-4372-92d4-4df7a9fdcdb7	e79e18b2-3037-4c27-bbeb-21d6df3720fb	g.chrX:39916463G>A	ENST00000378444.4	-	11	4768	c.4540C>T	c.(4540-4542)Cga>Tga	p.R1514*	BCOR_ENST00000397354.3_Nonsense_Mutation_p.R1480*|BCOR_ENST00000378455.4_Nonsense_Mutation_p.R1462*|BCOR_ENST00000342274.4_Nonsense_Mutation_p.R1480*|BCOR_ENST00000378463.1_Nonsense_Mutation_p.R357*	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	1514					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						AGGAGGTGTCGCACAATGTTG	0.512			"F, N, S, T"	RARA	"retinoblastoma, AML, APL(translocation)"		oculo-facio-cardio-dental genetic																														p.R1514X		Atlas-SNP	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	0			c.C4540T						PASS	.						154	104	121					X																	39916463		2202	4300	6502	SO:0001587	stop_gained	54880	exon11			GGTGTCGCACAAT	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.4540C>T	chrX.hg19:g.39916463G>A	ENSP00000367705:p.Arg1514*	78.0	0.0	.		89.0	4.0	.	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Nonsense_Mutation	SNP	ENST00000378444.4	hg19	CCDS48093.1	.	.	.	.	.	.	.	.	.	.	G	46	12.577683	0.99679	.	.	ENSG00000183337	ENST00000413905;ENST00000378463;ENST00000378455;ENST00000397354;ENST00000378444;ENST00000342274;ENST00000442018	.	.	.	5.46	3.67	0.42095	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.8224	10.3036	0.43667	0.0:0.2697:0.5875:0.1428	.	.	.	.	X	384;357;1462;1480;1514;1480;187	.	ENSP00000345923:R1480X	R	-	1	2	BCOR	39801407	1.000000	0.71417	0.702000	0.30337	0.988000	0.76386	4.473000	0.60196	0.479000	0.27511	0.600000	0.82982	CGA	.	G|0.999;C|0.001	.	alt		0.512	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		A	39916463	G	A	39916463	4	1	178	1	0	0	0	0	0	1	0	0	1386	1095	38	1	747	1	BCOR	23	39916463	Nonsense_Mutation	SNP	G	TCGA-G7-A4TM-01A-11D-A31X-10		39916463	115354097	37	10428											
TRIM63	84676	hgsc.bcm.edu	37	chr1	26392820	26392820	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcaggttcctctgcaggcCgtacactccgtgacgatcca	8	8	10	15	3	1	1	0	1	1	0	4	2	4	1	4	2	3	4	4	2	1	2			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr1:26392820C>T	ENST00000374272.3	-	2	409	c.271G>A	c.(271-273)Ggc>Agc	p.G91S	TRIM63_ENST00000483052.1_5'UTR	NM_032588.3	NP_115977.2	Q969Q1	TRI63_HUMAN	tripartite motif containing 63, E3 ubiquitin protein ligase	91	Interaction with TTN.				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)		CTCTGCAGGCCGTACACTCCG	0.632																																					p.G91S		Atlas-SNP	.											.	TRIM63	33	.	0			c.G271A						PASS	.						115	85	95					1																	26392820		2203	4300	6503	SO:0001583	missense	84676	exon2			GCAGGCCGTACAC	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.271G>A	chr1.hg19:g.26392820C>T	ENSP00000363390:p.Gly91Ser	82.0	0.0	.		48.0	23.0	.	NM_032588	B4DN95|Q5T2I1|Q96BD3|Q96KD9|Q9BYV4	Missense_Mutation	SNP	ENST00000374272.3	hg19	CCDS273.1	.	.	.	.	.	.	.	.	.	.	C	36	5.648865	0.96714	.	.	ENSG00000158022	ENST00000374272	T	0.28454	1.61	5.64	5.64	0.86602	Zinc finger, RING/FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	T	0.56601	0.1996	M	0.73430	2.235	0.80722	D	1	D	0.71674	0.998	D	0.64595	0.927	T	0.56823	-0.7915	10	0.54805	T	0.06	.	19.3141	0.94204	0.0:1.0:0.0:0.0	.	91	Q969Q1	TRI63_HUMAN	S	91	ENSP00000363390:G91S	ENSP00000363390:G91S	G	-	1	0	TRIM63	26265407	1.000000	0.71417	0.966000	0.40874	0.852000	0.48524	7.811000	0.86092	2.655000	0.90218	0.655000	0.94253	GGC	.	.	.	none		0.632	TRIM63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019750.1	NM_032588		T	26392820	C	T	26392820	3	4	179	1	0	0	0	0	1	0	0	0	16550	652	23	1	822	1	TRIM63	1	26392820	Missense_Mutation	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10		26392820	222857801	1	10429											
ATXN7L2	127002	hgsc.bcm.edu	37	chr1	110031587	110031587	+	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	tcccaaggagaagagcccagGgcgcaaggagcaagttctcg	12	4	14	11	2	1	2	0	0	1	2	3	4	2	3	2	3	2	3	2	3	4	1			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr1:110031587G>A	ENST00000369870.3	+	7	917	c.902G>A	c.(901-903)gGg>gAg	p.G301E		NM_153340.4	NP_699171.3	Q5T6C5	AT7L2_HUMAN	ataxin 7-like 2	301										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)	17		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0426)|Epithelial(280;0.0675)|READ - Rectum adenocarcinoma(129;0.0693)|all cancers(265;0.071)|LUSC - Lung squamous cell carcinoma(189;0.228)		AAGAGCCCAGGGCGCAAGGAG	0.647																																					p.G301E		Atlas-SNP	.											.	ATXN7L2	60	.	0			c.G902A						PASS	.						43	43	43					1																	110031587		2203	4300	6503	SO:0001583	missense	127002	exon7			GCCCAGGGCGCAA	BC037582	CCDS30794.1	1p13.2	2008-02-05			ENSG00000162650	ENSG00000162650			28713	protein-coding gene	gene with protein product						12477932	Standard	NM_153340		Approved	MGC46534, FLJ00381	uc001dxr.3	Q5T6C5	OTTHUMG00000011027	ENST00000369870.3:c.902G>A	chr1.hg19:g.110031587G>A	ENSP00000358886:p.Gly301Glu	77.0	0.0	.		74.0	42.0	.	NM_153340		Missense_Mutation	SNP	ENST00000369870.3	hg19	CCDS30794.1	.	.	.	.	.	.	.	.	.	.	G	11.29	1.594207	0.28445	.	.	ENSG00000162650	ENST00000369870;ENST00000541125	T	0.27890	1.64	5.97	3.96	0.45880	.	0.326224	0.26875	N	0.022059	T	0.07908	0.0198	L	0.36672	1.1	0.80722	D	1	P	0.38250	0.624	B	0.37267	0.245	T	0.06023	-1.0850	10	0.02654	T	1	-9.0894	9.0628	0.36444	0.0:0.3133:0.535:0.1516	.	301	Q5T6C5	AT7L2_HUMAN	E	301	ENSP00000358886:G301E	ENSP00000358886:G301E	G	+	2	0	ATXN7L2	109833110	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.864000	0.27926	1.496000	0.48567	0.655000	0.94253	GGG	.	.	.	none		0.647	ATXN7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030331.1	NM_153340		A	110031587	G	A	110031587	3	1	179	1	0	0	0	0	1	0	0	0	1217	1232	43	2	928	2	ATXN7L2	1	110031587	Missense_Mutation	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	83638767	110031587	139219034	2	10430											
BAT2L2	23215	hgsc.bcm.edu	37	chr1	171501480	171501480	+	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	atctgataccttaatgtttcAgcatccacctccagatcgac	11	12	5	13	1	2	2	1	1	1	1	5	3	4	2	4	0	2	2	4	0	2	3			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr1:171501480A>G	ENST00000338920.4	+	12	1485		c.e12-1		PRRC2C_ENST00000426496.2_Splice_Site|PRRC2C_ENST00000367742.3_Splice_Site|PRRC2C_ENST00000476522.1_Splice_Site|PRRC2C_ENST00000392078.3_Splice_Site	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C						hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										TTAATGTTTCAGCATCCACCT	0.438																																					.		Atlas-SNP	.											.	.	.	.	0			c.1249-2A>G						PASS	.						40	38	39					1																	171501480		2203	4300	6503	SO:0001630	splice_region_variant	23215	exon12			TGTTTCAGCATCC	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.1249-1A>G	chr1.hg19:g.171501480A>G		110.0	0.0	.		75.0	36.0	.	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Splice_Site	SNP	ENST00000338920.4	hg19	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	A	20.7	4.026744	0.75390	.	.	ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080;ENST00000483654	.	.	.	6.03	6.03	0.97812	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5582	0.84512	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PRRC2C	169768104	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	6.321000	0.72881	2.308000	0.77769	0.533000	0.62120	.	.	.	.	none		0.438	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172	Intron	G	171501480	A	G	171501480	5	3	179	1	0	0	0	0	0	0	1	0	1321	202	7	3	1289	3	BAT2L2	1	171501480	Splice_Site	SNP	A	TCGA-G7-A8LB-01A-11D-A35Z-10	61469893	171501480	77749141	3	10431											
CFHR2	3080	hgsc.bcm.edu	37	chr1	196927093	196927093	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcattcctgttgtcagtatAtgctccaggttcatcagttg	7	17	8	9	0	4	0	4	0	0	0	6	0	6	0	2	1	1	5	2	1	2	7			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr1:196927093A>G	ENST00000367415.5	+	4	603	c.503A>G	c.(502-504)tAt>tGt	p.Y168C	CFHR2_ENST00000496448.1_3'UTR|CFHR2_ENST00000367421.3_Missense_Mutation_p.Y168C|CFHR2_ENST00000476712.2_Missense_Mutation_p.Y152C	NM_005666.2	NP_005657.1	P36980	FHR2_HUMAN	complement factor H-related 2	168	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.					extracellular region (GO:0005576)				large_intestine(2)|ovary(1)|skin(3)	6						TTGTCAGTATATGCTCCAGGT	0.408																																					p.Y168C		Atlas-SNP	.											.	CFHR2	73	.	0			c.A503G						PASS	.						170	154	160					1																	196927093		2203	4300	6503	SO:0001583	missense	3080	exon4			CAGTATATGCTCC	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.503A>G	chr1.hg19:g.196927093A>G	ENSP00000356385:p.Tyr168Cys	264.0	0.0	.		183.0	85.0	.	NM_005666	Q14310|Q5T9T1	Missense_Mutation	SNP	ENST00000367415.5	hg19	CCDS30959.1	.	.	.	.	.	.	.	.	.	.	.	12.53	1.965546	0.34659	.	.	ENSG00000080910	ENST00000367421;ENST00000367415	T;T	0.69926	-0.44;-0.44	4.25	3.09	0.35607	Complement control module (2);Sushi/SCR/CCP (3);	0.922642	0.08792	N	0.893138	D	0.88683	0.6503	H	0.99299	4.505	0.09310	N	1	D	0.89917	1.0	D	0.71656	0.974	T	0.73046	-0.4106	10	0.87932	D	0	.	8.9845	0.35986	0.8122:0.1878:0.0:0.0	.	168	P36980	FHR2_HUMAN	C	168	ENSP00000356391:Y168C;ENSP00000356385:Y168C	ENSP00000356385:Y168C	Y	+	2	0	CFHR2	195193716	0.931000	0.31567	0.003000	0.11579	0.004000	0.04260	5.025000	0.64097	0.465000	0.27167	-0.604000	0.04097	TAT	.	.	.	none		0.408	CFHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088815.2	NM_005666		G	196927093	A	G	196927093	3	3	179	1	0	0	0	0	1	0	0	0	3287	449	16	3	517	3	CFHR2	1	196927093	Missense_Mutation	SNP	A	TCGA-G7-A8LB-01A-11D-A35Z-10	25425613	196927093	52323528	4	10432											
ZNF238	10472	hgsc.bcm.edu	37	chr1	244218407	244218407	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgagaggactcactcgggggAgaagccctacacatgcaccc	11	4	12	14	2	1	2	1	0	0	2	2	5	1	3	2	3	3	1	2	3	2	1			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr1:244218407A>G	ENST00000358704.4	+	2	1480	c.1331A>G	c.(1330-1332)gAg>gGg	p.E444G		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	435					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)										CACTCGGGGGAGAAGCCCTAC	0.632																																					p.E444G		Atlas-SNP	.											.	.	.	.	0			c.A1331G						PASS	.						69	71	70					1																	244218407		2203	4300	6503	SO:0001583	missense	10472	exon2			CGGGGGAGAAGCC	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.1331A>G	chr1.hg19:g.244218407A>G	ENSP00000351539:p.Glu444Gly	147.0	0.0	.		114.0	5.0	.	NM_205768	A8K5U3|Q13397|Q5VU40|Q8N463|Q9UD99	Missense_Mutation	SNP	ENST00000358704.4	hg19	CCDS1622.1	.	.	.	.	.	.	.	.	.	.	A	17.43	3.386591	0.61956	.	.	ENSG00000179456	ENST00000366538;ENST00000358704	T	0.27557	1.66	5.68	5.68	0.88126	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.55893	0.1949	M	0.71581	2.175	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.79108	0.992;0.986	T	0.59789	-0.7388	10	0.87932	D	0	.	15.9354	0.79698	1.0:0.0:0.0:0.0	.	435;444	Q99592;Q99592-2	ZN238_HUMAN;.	G	444	ENSP00000351539:E444G	ENSP00000351539:E444G	E	+	2	0	ZNF238	242285030	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.182000	0.69389	0.533000	0.62120	GAG	.	.	.	none		0.632	ZBTB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096513.2	NM_205768		G	244218407	A	G	244218407	3	3	179	1	0	0	0	0	1	0	0	0	17802	304	11	3	1337	3	ZNF238	1	244218407	Missense_Mutation	SNP	A	TCGA-G7-A8LB-01A-11D-A35Z-10	47291314	244218407	5032214	5	10433											
ATAD2B	54454	hgsc.bcm.edu	37	chr2	24086371	24086371	+	Frame_Shift_Del	DEL	T	T	-																															tggctgcattcattagctaaTgctctggcaaccaaggtttt																										TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr2:24086371delT	ENST00000238789.5	-	12	1702	c.1359delA	c.(1357-1359)gcafs	p.A453fs		NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	453						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CATTAGCTAATGCTCTGGCAA	0.398																																					p.L454X		Atlas-Indel,Pindel	.											.	ATAD2B	110	.	0			c.1360delT						PASS	.						34	32	33					2																	24086371		1837	4089	5926	SO:0001589	frameshift_variant	54454	exon12			.	AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"ATPases / AAA-type"	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.1359delA	chr2.hg19:g.24086371delT	ENSP00000238789:p.Ala453fs	208.0	0.0	0		191.0	91.0	0.47644	NM_017552	B9ZVQ5|Q6ZNA6|Q8N9E7	Frame_Shift_Del	DEL	ENST00000238789.5	hg19	CCDS46227.1																																																																																			.	.	.	none		0.398	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552		-	24086371	T	-	24086371	7	5	179	1	0	1	0	1	0	0	0	0	1072	1451	51	0	3085	0	ATAD2B	2	24086371	Frame_Shift_Del	DEL	T	TCGA-G7-A8LB-01A-11D-A35Z-10		24086371	219113002	6	10434											
MSH2	4436	hgsc.bcm.edu	37	chr2	47693891	47693892	+	Frame_Shift_Ins	INS	-	-	A																															aagaaaaagtccttcgtaacINSaataaaaactttagtactgt																								rs63750510|rs587779098		TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr2:47693891_47693892insA	ENST00000233146.2	+	10	1828_1829	c.1605_1606insA	c.(1606-1608)aatfs	p.N536fs	MSH2_ENST00000406134.1_Frame_Shift_Ins_p.N536fs|MSH2_ENST00000543555.1_Frame_Shift_Ins_p.N470fs	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	536					ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(2)		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)			TCCTTCGTAACAATAAAAACTT	0.347			"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.N535fs		Atlas-Indel,Pindel	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	.	MSH2	198	.	4	Whole gene deletion(2)|Unknown(2)	haematopoietic_and_lymphoid_tissue(3)|prostate(1)	c.1605_1606insA						PASS	.																																			SO:0001589	frameshift_variant	4436	exon10	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	.	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.1607dupA	chr2.hg19:g.47693893_47693893dupA	ENSP00000233146:p.Asn536fs	464.0	0.0	0		314.0	152.0	0.484076	NM_000251	B4E2Z2|O75488	Frame_Shift_Ins	INS	ENST00000233146.2	hg19	CCDS1834.1																																																																																			.	.	.	none		0.347	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3			A	47693892	-	A	47693891	7	5	179	1	0	1	1	0	0	0	0	0	9877	477	17	0	1643	0	MSH2	2	47693891	Frame_Shift_Ins	INS	-	TCGA-G7-A8LB-01A-11D-A35Z-10	23607520	47693891	195505482	7	10435											
RMND5A	64795	hgsc.bcm.edu	37	chr2	86968117	86968117	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgctgtaaaagaataaaggaTactgttcaaaaattggcctc	16	11	8	6	0	1	1	1	0	0	1	2	2	1	2	1	2	2	3	1	2	8	5			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr2:86968117T>C	ENST00000283632.4	+	2	705	c.210T>C	c.(208-210)gaT>gaC	p.D70D		NM_022780.3	NP_073617.1	Q9H871	RMD5A_HUMAN	required for meiotic nuclear division 5 homolog A (S. cerevisiae)	70										kidney(1)|liver(2)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	17						GAATAAAGGATACTGTTCAAA	0.388																																					p.D70D		Atlas-SNP	.											RMND5A,NS,carcinoma,0,1	RMND5A	33	.	0			c.T210C						PASS	.						98	92	94					2																	86968117		2201	4297	6498	SO:0001819	synonymous_variant	64795	exon2			AAAGGATACTGTT	BC012165	CCDS1991.1	2p11.2	2012-07-20			ENSG00000153561	ENSG00000153561			25850	protein-coding gene	gene with protein product	"GID complex subunit 2 homolog A"					12477932	Standard	NM_022780		Approved	FLJ13910, RMD5, GID2, GID2A	uc002srs.4	Q9H871	OTTHUMG00000130262	ENST00000283632.4:c.210T>C	chr2.hg19:g.86968117T>C		1255.0	0.0	.		971.0	225.0	.	NM_022780	D6W5M6|Q6NTF0|Q9H6W5|Q9H9H2	Silent	SNP	ENST00000283632.4	hg19	CCDS1991.1																																																																																			.	.	.	none		0.388	RMND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252591.2	NM_022780		C	86968117	T	C	86968117	2	2	179	1	0	0	0	0	0	0	0	1	13410	1403	49	3		3	RMND5A	2	86968117	Silent	SNP	T	TCGA-G7-A8LB-01A-11D-A35Z-10	39274226	86968117	156231256	8	10436											
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160295123	160295123	+	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	gattcagacgcaagaggtaaTggctggtgtattcttttttc	9	15	11	6	1	2	2	1	0	1	2	3	3	2	2	0	3	0	4	0	3	3	7			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr2:160295123T>A	ENST00000392783.2	-	8	1479	c.984A>T	c.(982-984)ccA>ccT	p.P328P	BAZ2B_ENST00000392782.1_Silent_p.P326P|BAZ2B_ENST00000355831.2_Silent_p.P328P|BAZ2B_ENST00000343439.5_Silent_p.P326P	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	328					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						CAAGAGGTAATGGCTGGTGTA	0.423																																					p.P328P		Atlas-SNP	.											.	BAZ2B	196	.	0			c.A984T						PASS	.						184	184	184					2																	160295123		1845	4101	5946	SO:0001819	synonymous_variant	29994	exon8			AGGTAATGGCTGG	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.984A>T	chr2.hg19:g.160295123T>A		62.0	0.0	.		56.0	31.0	.	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Silent	SNP	ENST00000392783.2	hg19	CCDS2209.2																																																																																			.	.	.	none		0.423	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			A	160295123	T	A	160295123	2	1	179	1	0	0	0	0	0	0	0	1	1332	1451	51	5		5	BAZ2B	2	160295123	Silent	SNP	T	TCGA-G7-A8LB-01A-11D-A35Z-10	73327006	160295123	82904250	9	10437											
TTC21B	79809	hgsc.bcm.edu	37	chr2	166785751	166785751	+	Missense_Mutation	SNP	A	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	gcaaaccttctaattgtgaaAagtgagtgtccaggacatca	14	10	9	8	0	2	2	1	2	1	0	3	3	3	3	2	1	1	1	2	1	4	3			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr2:166785751A>C	ENST00000243344.7	-	11	1417	c.1280T>G	c.(1279-1281)tTt>tGt	p.F427C		NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	427					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						TAATTGTGAAAAGTGAGTGTC	0.328																																					p.F427C		Atlas-SNP	.											.	TTC21B	130	.	0			c.T1280G						PASS	.						68	71	70					2																	166785751		2202	4299	6501	SO:0001583	missense	79809	exon11			TGTGAAAAGTGAG	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.1280T>G	chr2.hg19:g.166785751A>C	ENSP00000243344:p.Phe427Cys	355.0	0.0	.		316.0	137.0	.	NM_024753	A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Missense_Mutation	SNP	ENST00000243344.7	hg19	CCDS33315.1	.	.	.	.	.	.	.	.	.	.	a	17.10	3.304208	0.60305	.	.	ENSG00000123607	ENST00000243344	T	0.62498	0.02	5.38	5.38	0.77491	.	0.095949	0.64402	D	0.000001	T	0.79969	0.4538	M	0.84326	2.69	0.80722	D	1	D;D	0.89917	1.0;0.991	D;P	0.68192	0.956;0.798	T	0.82796	-0.0280	10	0.59425	D	0.04	-10.2853	15.6905	0.77446	1.0:0.0:0.0:0.0	.	427;427	Q7Z4L5-2;Q7Z4L5	.;TT21B_HUMAN	C	427	ENSP00000243344:F427C	ENSP00000243344:F427C	F	-	2	0	TTC21B	166493997	1.000000	0.71417	1.000000	0.80357	0.265000	0.26407	8.881000	0.92415	2.170000	0.68504	0.529000	0.55759	TTT	.	.	.	none		0.328	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333770.1	NM_024753		C	166785751	A	C	166785751	3	2	179	1	0	0	0	0	1	0	0	0	16700	14	1	5	2746	5	TTC21B	2	166785751	Missense_Mutation	SNP	A	TCGA-G7-A8LB-01A-11D-A35Z-10	6490628	166785751	76413622	10	10438											
TTN	7273	hgsc.bcm.edu	37	chr2	179476842	179476842	+	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	ccactttaggtcaacatgtcGttttgtcacatcaaccactg	10	13	6	12	1	3	0	3	0	0	0	4	0	3	0	2	1	2	1	2	1	3	4			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr2:179476842G>A	ENST00000591111.1	-	217	45597	c.45373C>T	c.(45373-45375)Cga>Tga	p.R15125*	TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000589042.1_Nonsense_Mutation_p.R16766*|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Nonsense_Mutation_p.R7893*|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Nonsense_Mutation_p.R7826*|TTN_ENST00000460472.2_Nonsense_Mutation_p.R7701*|TTN_ENST00000342992.6_Nonsense_Mutation_p.R14198*			Q8WZ42	TITIN_HUMAN	titin	15125	Fibronectin type-III 10. {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)			TCAACATGTCGTTTTGTCACA	0.403																																					p.R16766X		Atlas-SNP	.											.	TTN	18412	.	0			c.C50296T						PASS	.						106	94	98					2																	179476842		1874	4098	5972	SO:0001587	stop_gained	7273	exon267			CATGTCGTTTTGT	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.45373C>T	chr2.hg19:g.179476842G>A	ENSP00000465570:p.Arg15125*	109.0	0.0	.		99.0	44.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	59	37.731312	0.99984	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	.	.	.	6.17	0.537	0.17144	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	10.6047	0.45388	0.0:0.1944:0.2015:0.604	.	.	.	.	X	14198;7701;7893;7826;7701	.	ENSP00000340554:R7893X	R	-	1	2	TTN	179185087	1.000000	0.71417	0.988000	0.46212	0.995000	0.86356	1.702000	0.37836	0.136000	0.18733	0.655000	0.94253	CGA	.	.	.	none		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179476842	G	A	179476842	4	1	179	1	0	0	0	0	0	1	0	0	16747	1153	40	1	57781	1	TTN	2	179476842	Nonsense_Mutation	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	12691091	179476842	63722531	11	10439											
PID1	55022	hgsc.bcm.edu	37	chr2	230127427	230127427	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggctggaagtccaaaatgtAaaggttggcagggccacaca	14	6	13	8	0	0	0	0	0	0	0	1	1	1	1	2	5	0	4	2	5	5	2			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr2:230127427A>G	ENST00000392054.3	-	2	434	c.95T>C	c.(94-96)tTa>tCa	p.L32S	PID1_ENST00000392055.3_Intron|PID1_ENST00000409462.1_Intron	NM_017933.4	NP_060403.3	Q7Z2X4	PCLI1_HUMAN	phosphotyrosine interaction domain containing 1	0					cellular response to cytokine stimulus (GO:0071345)|cellular response to fatty acid (GO:0071398)|cellular response to interleukin-6 (GO:0071354)|cellular response to leptin stimulus (GO:0044320)|cellular response to tumor necrosis factor (GO:0071356)|energy reserve metabolic process (GO:0006112)|mitochondrion morphogenesis (GO:0070584)|negative regulation of ATP biosynthetic process (GO:2001170)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of glucose import in response to insulin stimulus (GO:2001274)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of mitochondrial DNA replication (GO:0090298)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of fat cell proliferation (GO:0070346)|positive regulation of gene expression (GO:0010628)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of mitochondrial fusion (GO:0010635)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of reactive oxygen species metabolic process (GO:2000377)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(4)|endometrium(3)|large_intestine(5)|lung(8)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	26		Renal(207;0.0112)|all_lung(227;0.0191)|Lung NSC(271;0.0851)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.171)		Epithelial(121;3.08e-11)|all cancers(144;2.28e-08)|LUSC - Lung squamous cell carcinoma(224;0.0145)|Lung(261;0.0189)		tccaaaatgtaaaggttggca	0.448																																					p.L32S		Atlas-SNP	.											.	PID1	43	.	0			c.T95C						PASS	.						154	158	156					2																	230127427		1327	2309	3636	SO:0001583	missense	55022	exon2			AAATGTAAAGGTT	AK096636	CCDS2471.1, CCDS42830.1	2q36.3	2007-02-02			ENSG00000153823	ENSG00000153823			26084	protein-coding gene	gene with protein product		612930				17124247, 16815647, 15221005	Standard	NM_001100818		Approved	NYGGF4, FLJ20701	uc002vps.4	Q7Z2X4	OTTHUMG00000133191	ENST00000392054.3:c.95T>C	chr2.hg19:g.230127427A>G	ENSP00000375907:p.Leu32Ser	86.0	0.0	.		49.0	18.0	.	NM_017933	B3KU82|Q68CJ2|Q6ZUS3|Q8IXL0|Q9NWP6	Missense_Mutation	SNP	ENST00000392054.3	hg19	CCDS2471.1	.	.	.	.	.	.	.	.	.	.	A	12.48	1.951464	0.34471	.	.	ENSG00000153823	ENST00000392054	.	.	.	2.79	1.6	0.23607	.	.	.	.	.	T	0.20820	0.0501	.	.	.	0.09310	N	1	B	0.29301	0.241	B	0.29440	0.102	T	0.21518	-1.0243	6	.	.	.	.	5.1959	0.15236	0.7417:0.0:0.0:0.2583	.	32	Q7Z2X4-2	.	S	32	.	.	L	-	2	0	PID1	229835671	0.008000	0.16893	0.001000	0.08648	0.001000	0.01503	0.637000	0.24659	0.484000	0.27630	0.379000	0.24179	TTA	.	.	.	none		0.448	PID1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331809.1	NM_017933		G	230127427	A	G	230127427	3	3	179	1	0	0	0	0	1	0	0	0	11889	372	13	3	663	3	PID1	2	230127427	Missense_Mutation	SNP	A	TCGA-G7-A8LB-01A-11D-A35Z-10	50650585	230127427	13071946	12	10440											
PLCD1	5333	hgsc.bcm.edu	37	chr3	38070995	38071000	+	Splice_Site	DEL	TCACCG	TCACCG	-																															ctcgcgcgggccaggcactcAccgtgcagggtcaggaagtc																								rs373017252		TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	TCACCG	TCACCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr3:38070995_38071000delTCACCG	ENST00000334661.4	-	1	253_257	c.31_35delCGGTGA	c.(31-36)cggtga>a	p.R*11del		NM_006225.3	NP_006216.2	P51178	PLCD1_HUMAN	phospholipase C, delta 1	11					angiogenesis (GO:0001525)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|labyrinthine layer blood vessel development (GO:0060716)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTPase activating protein binding (GO:0032794)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol phosphate binding (GO:1901981)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylserine binding (GO:0001786)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		CCAGGCACTCACCGTGCAGGGTCAGG	0.743																																					p.12_12del		Atlas-Indel,Pindel	.											.	PLCD1	87	.	0			c.34_34del						PASS	.																																			SO:0001630	splice_region_variant	5333	exon1			.		CCDS2671.1, CCDS46793.1	3p22-p21.3	2013-01-10			ENSG00000187091	ENSG00000187091	3.1.4.11	"EF-hand domain containing"	9060	protein-coding gene	gene with protein product		602142				9345909	Standard	NM_001130964		Approved		uc003chm.3	P51178	OTTHUMG00000130813	ENST00000334661.4:c.34+1CGGTGA>-	chr3.hg19:g.38070995_38071000delTCACCG		125.0	0.0	0		118.0	25.0	0.211864	NM_006225	B3KR14|Q86VN8	Frame_Shift_Del	DEL	ENST00000334661.4	hg19	CCDS2671.1																																																																																			.	.	.	none		0.743	PLCD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253359.2		In_Frame_Del	-	38071000	TCACCG	-	38070995	8	5	179	1	0	1	0	1	0	0	1	0	12038	173	6	0	2395	0	PLCD1	3	38070995	Splice_Site	DEL	TCACCG	TCGA-G7-A8LB-01A-11D-A35Z-10		38070995	159951435	13	10441											
SLC26A6	65010	hgsc.bcm.edu	37	chr3	48664425	48664425	+	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	cttcagtgtggacccatctgGggccttggagtcttcttgac	5	13	12	11	0	4	1	1	1	3	0	4	3	4	3	2	4	0	0	2	4	0	4			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr3:48664425G>T	ENST00000395550.2	-	18	2004	c.1957C>A	c.(1957-1959)Cca>Aca	p.P653T	SLC26A6_ENST00000420764.2_Missense_Mutation_p.P652T|SLC26A6_ENST00000455886.2_Missense_Mutation_p.P617T|SLC26A6_ENST00000383733.3_Missense_Mutation_p.P634T|SLC26A6_ENST00000337000.8_Missense_Mutation_p.P545T|SLC26A6_ENST00000358747.6_Missense_Mutation_p.P632T			Q9BXS9	S26A6_HUMAN	solute carrier family 26 (anion exchanger), member 6	653	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)		GACCCATCTGGGGCCTTGGAG	0.597																																					p.P653T	NSCLC(13;369 479 28271 30152 44026)	Atlas-SNP	.											.	SLC26A6	45	.	0			c.C1957A						PASS	.						110	117	114					3																	48664425		2002	4171	6173	SO:0001583	missense	65010	exon18			CATCTGGGGCCTT	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.1957C>A	chr3.hg19:g.48664425G>T	ENSP00000378920:p.Pro653Thr	87.0	0.0	.		94.0	59.0	.	NM_022911	B4DMZ1|Q548A7|Q96Q90|Q9NQU1	Missense_Mutation	SNP	ENST00000395550.2	hg19	CCDS43087.1	.	.	.	.	.	.	.	.	.	.	G	16.89	3.247190	0.59103	.	.	ENSG00000225697	ENST00000420764;ENST00000395550;ENST00000383733;ENST00000337000;ENST00000447978;ENST00000358747;ENST00000455886	D;D;D;D;D;D	0.93366	-3.03;-3.04;-3.12;-3.05;-3.03;-3.21	4.95	2.18	0.27775	Sulphate transporter/antisigma-factor antagonist STAS (3);	.	.	.	.	D	0.84813	0.5555	N	0.08118	0	0.18873	N	0.999989	P;B;P;B;P;B;B	0.43024	0.687;0.166;0.798;0.01;0.629;0.143;0.096	B;B;P;B;B;B;B	0.46299	0.439;0.138;0.511;0.015;0.446;0.142;0.089	T	0.75396	-0.3332	9	0.07030	T	0.85	.	8.6099	0.33795	0.3:0.0:0.7:0.0	.	617;647;545;634;652;653;4039	B4DMZ1;Q86YZ4;G3XAC1;Q9BXS9-2;Q548A7;Q9BXS9;Q5Y190	.;.;.;.;.;S26A6_HUMAN;.	T	652;653;634;545;647;632;617	ENSP00000404684:P652T;ENSP00000378920:P653T;ENSP00000373239:P634T;ENSP00000337648:P545T;ENSP00000351597:P632T;ENSP00000401066:P617T	ENSP00000337648:P545T	P	-	1	0	SLC26A6	48639429	0.629000	0.27146	0.606000	0.28943	0.890000	0.51754	0.329000	0.19698	0.234000	0.21139	0.491000	0.48974	CCA	.	.	.	none		0.597	SLC26A6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345040.1	NM_022911		T	48664425	G	T	48664425	3	4	179	1	0	0	0	0	1	0	0	0	14534	1232	43	4	338	4	SLC26A6	3	48664425	Missense_Mutation	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	10593430	48664425	149358005	14	10442											
SEMA3F	6405	hgsc.bcm.edu	37	chr3	50214250	50214250	+	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	actcgagtcagggaagggcaAgtgtccgtacgatcccaagc	11	6	13	11	3	1	0	1	0	0	0	4	3	3	1	2	2	2	2	2	2	4	1			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr3:50214250A>T	ENST00000002829.3	+	7	1083	c.599A>T	c.(598-600)aAg>aTg	p.K200M	SEMA3F_ENST00000413852.1_Missense_Mutation_p.K101M|SEMA3F_ENST00000434342.1_Missense_Mutation_p.K169M	NM_004186.3	NP_004177.3	Q13275	SEM3F_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F	200	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|negative regulation of axon extension involved in axon guidance (GO:0048843)|nerve development (GO:0021675)|neural crest cell migration (GO:0001755)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	extracellular space (GO:0005615)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|receptor activity (GO:0004872)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	17				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)		GGGAAGGGCAAGTGTCCGTAC	0.617																																					p.K200M		Atlas-SNP	.											.	SEMA3F	62	.	0			c.A599T						PASS	.						170	142	152					3																	50214250		2203	4300	6503	SO:0001583	missense	6405	exon7			AGGGCAAGTGTCC	U33920	CCDS2811.1	3p21.3	2013-01-11			ENSG00000001617	ENSG00000001617		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10728	protein-coding gene	gene with protein product	"sema IV"	601124				8786119, 8649831	Standard	NM_004186		Approved	SEMAK, Sema4	uc003cyj.3	Q13275	OTTHUMG00000156806	ENST00000002829.3:c.599A>T	chr3.hg19:g.50214250A>T	ENSP00000002829:p.Lys200Met	63.0	0.0	.		57.0	15.0	.	NM_004186	C9JQ85|Q13274|Q13372|Q15704|Q6GTR4	Missense_Mutation	SNP	ENST00000002829.3	hg19	CCDS2811.1	.	.	.	.	.	.	.	.	.	.	A	31	5.066774	0.93898	.	.	ENSG00000001617	ENST00000414301;ENST00000450338;ENST00000413852;ENST00000002829;ENST00000434342;ENST00000420831	T;T;T;T;T;T	0.12672	2.66;2.66;2.66;2.66;2.66;2.66	5.44	5.44	0.79542	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.141423	0.64402	D	0.000006	T	0.39911	0.1096	M	0.78801	2.425	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.31833	-0.9929	10	0.87932	D	0	.	15.4628	0.75373	1.0:0.0:0.0:0.0	.	169;200	C9JQ85;Q13275	.;SEM3F_HUMAN	M	169;169;101;200;169;133	ENSP00000392588:K169M;ENSP00000398399:K169M;ENSP00000388931:K101M;ENSP00000002829:K200M;ENSP00000409859:K169M;ENSP00000416356:K133M	ENSP00000002829:K200M	K	+	2	0	SEMA3F	50189254	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	7.120000	0.77153	2.190000	0.69967	0.459000	0.35465	AAG	.	.	.	none		0.617	SEMA3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345929.1	NM_004186		T	50214250	A	T	50214250	3	4	179	1	0	0	0	0	1	0	0	0	14042	72	3	5	621	5	SEMA3F	3	50214250	Missense_Mutation	SNP	A	TCGA-G7-A8LB-01A-11D-A35Z-10	1549825	50214250	147808180	15	10443											
CACNA2D3	55799	hgsc.bcm.edu	37	chr3	55018690	55018690	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tattttggtgtctgaagactAcacacaggtgagtgaaaatt	13	13	10	5	0	1	4	0	3	1	1	1	4	1	4	0	2	1	0	0	2	5	5			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr3:55018690A>G	ENST00000474759.1	+	30	2660	c.2612A>G	c.(2611-2613)tAc>tGc	p.Y871C	CACNA2D3_ENST00000415676.2_Missense_Mutation_p.Y871C|CACNA2D3_ENST00000288197.5_Missense_Mutation_p.Y871C|CACNA2D3_ENST00000490478.1_Missense_Mutation_p.Y777C	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	871						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)	TCTGAAGACTACACACAGGTG	0.343																																					p.Y871C		Atlas-SNP	.											.	CACNA2D3	159	.	0			c.A2612G						PASS	.						61	58	59					3																	55018690		1823	4082	5905	SO:0001583	missense	55799	exon30			AAGACTACACACA	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.2612A>G	chr3.hg19:g.55018690A>G	ENSP00000419101:p.Tyr871Cys	83.0	0.0	.		93.0	70.0	.	NM_018398	B2RPL6|Q9NY16|Q9NY18	Missense_Mutation	SNP	ENST00000474759.1	hg19	CCDS54598.1	.	.	.	.	.	.	.	.	.	.	A	17.15	3.316289	0.60524	.	.	ENSG00000157445	ENST00000415676;ENST00000474759;ENST00000288197;ENST00000490478;ENST00000398624	T;T;T;T	0.72942	-0.7;-0.7;-0.7;-0.7	5.95	5.95	0.96441	.	0.355700	0.30639	N	0.009197	T	0.67392	0.2888	L	0.27053	0.805	0.38988	D	0.95908	P	0.43477	0.808	P	0.48873	0.593	T	0.69442	-0.5144	10	0.38643	T	0.18	.	14.9948	0.71421	1.0:0.0:0.0:0.0	.	871	Q8IZS8	CA2D3_HUMAN	C	871;871;871;777;777	ENSP00000389506:Y871C;ENSP00000419101:Y871C;ENSP00000288197:Y871C;ENSP00000417279:Y777C	ENSP00000288197:Y871C	Y	+	2	0	CACNA2D3	54993730	0.999000	0.42202	1.000000	0.80357	0.999000	0.98932	3.801000	0.55545	2.279000	0.76181	0.533000	0.62120	TAC	.	.	.	none		0.343	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1			G	55018690	A	G	55018690	3	3	179	1	0	0	0	0	1	0	0	0	2552	391	14	3	2730	3	CACNA2D3	3	55018690	Missense_Mutation	SNP	A	TCGA-G7-A8LB-01A-11D-A35Z-10	4804440	55018690	143003740	16	10444											
GTPBP8	29083	hgsc.bcm.edu	37	chr3	112709865	112709865	+	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	gaatggcggcgcccgggctgCggctgggagcgggaagactc	6	4	20	11	5	0	1	0	0	0	1	1	4	0	3	1	6	2	2	1	6	2	0			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr3:112709865C>T	ENST00000383678.2	+	1	101	c.19C>T	c.(19-21)Cgg>Tgg	p.R7W	RP11-484K9.4_ENST00000609673.1_RNA|GTPBP8_ENST00000473129.1_5'Flank|GTPBP8_ENST00000383677.3_Missense_Mutation_p.R7W|GTPBP8_ENST00000467752.1_5'Flank	NM_014170.2	NP_054889.2	Q8N3Z3	GTPB8_HUMAN	GTP-binding protein 8 (putative)	7					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						GCCCGGGCTGCGGCTGGGAGC	0.632																																					p.R7W		Atlas-SNP	.											.	GTPBP8	22	.	0			c.C19T						PASS	.						15	22	20					3																	112709865		2168	4234	6402	SO:0001583	missense	29083	exon1			GGGCTGCGGCTGG	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.19C>T	chr3.hg19:g.112709865C>T	ENSP00000373176:p.Arg7Trp	77.0	0.0	.		55.0	25.0	.	NM_138485	A6NE99|A6NN11|A8K0P6|Q5I0Y4	Missense_Mutation	SNP	ENST00000383678.2	hg19	CCDS33820.1	.	.	.	.	.	.	.	.	.	.	C	17.98	3.521196	0.64747	.	.	ENSG00000163607	ENST00000383678;ENST00000383677;ENST00000305485	T;T	0.46819	0.86;0.91	5.85	-0.347	0.12617	.	0.697407	0.13168	N	0.408513	T	0.27313	0.0670	N	0.21583	0.68	0.09310	N	0.999991	B;B	0.11235	0.004;0.003	B;B	0.08055	0.003;0.002	T	0.13656	-1.0501	10	0.41790	T	0.15	0.1747	3.9332	0.09294	0.2516:0.39:0.0:0.3583	.	7;7	Q8N3Z3-2;Q8N3Z3	.;GTPB8_HUMAN	W	7	ENSP00000373176:R7W;ENSP00000373175:R7W	ENSP00000295864:R7W	R	+	1	2	GTPBP8	114192555	0.000000	0.05858	0.001000	0.08648	0.131000	0.20780	-1.774000	0.01784	-0.108000	0.12066	0.491000	0.48974	CGG	.	.	.	none		0.632	GTPBP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354260.2	NM_014170		T	112709865	C	T	112709865	3	4	179	1	0	0	0	0	1	0	0	0	6891	759	27	1	21	1	GTPBP8	3	112709865	Missense_Mutation	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10	57691175	112709865	85312565	17	10445											
ALDH1L1	10840	hgsc.bcm.edu	37	chr3	125844500	125844500	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgttcccggcagccaggcAggcagctgtcttccaggaca	7	8	13	13	1	1	0	0	0	1	0	3	1	3	1	3	4	2	5	3	4	0	2			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr3:125844500A>G	ENST00000393434.2	-	15	2108	c.1759T>C	c.(1759-1761)Tgc>Cgc	p.C587R	ALDH1L1_ENST00000472186.1_Missense_Mutation_p.C587R|ALDH1L1_ENST00000273450.3_Missense_Mutation_p.C597R|ALDH1L1_ENST00000452905.2_Missense_Mutation_p.C486R|ALDH1L1_ENST00000393431.2_3'UTR	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	587	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)	GCAGCCAGGCAGGCAGCTGTC	0.572																																					p.C597R		Atlas-SNP	.											.	ALDH1L1	138	.	0			c.T1789C						PASS	.						96	85	88					3																	125844500		2203	4300	6503	SO:0001583	missense	10840	exon15			CCAGGCAGGCAGC	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.1759T>C	chr3.hg19:g.125844500A>G	ENSP00000377083:p.Cys587Arg	154.0	1.0	.		144.0	102.0	.	NM_001270364	B4DG36|E9PBX3|Q68CS1	Missense_Mutation	SNP	ENST00000393434.2	hg19	CCDS3034.1	.	.	.	.	.	.	.	.	.	.	A	19.47	3.834548	0.71373	.	.	ENSG00000144908	ENST00000273450;ENST00000472186;ENST00000452905;ENST00000393434	T;T;T;T	0.08102	3.13;3.13;3.13;3.13	4.5	4.5	0.54988	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.85682	D	0.000000	T	0.25158	0.0611	M	0.68952	2.095	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.994;0.995	T	0.00797	-1.1562	10	0.87932	D	0	.	11.7788	0.52001	1.0:0.0:0.0:0.0	.	486;587	E9PBX3;O75891	.;AL1L1_HUMAN	R	597;587;486;587	ENSP00000273450:C597R;ENSP00000420293:C587R;ENSP00000395881:C486R;ENSP00000377083:C587R	ENSP00000273450:C597R	C	-	1	0	ALDH1L1	127327190	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	8.421000	0.90259	1.881000	0.54492	0.482000	0.46254	TGC	.	.	.	none		0.572	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190		G	125844500	A	G	125844500	3	3	179	1	0	0	0	0	1	0	0	0	494	188	7	3	985	3	ALDH1L1	3	125844500	Missense_Mutation	SNP	A	TCGA-G7-A8LB-01A-11D-A35Z-10	13134635	125844500	72177930	18	10446											
SENP2	59343	hgsc.bcm.edu	37	chr3	185341841	185341841	+	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	atagtgatctgaatcttttaGagtggacccatcacagcatg	12	12	9	8	0	3	3	1	2	2	1	3	4	3	4	1	1	1	1	1	1	3	3			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr3:185341841G>T	ENST00000296257.5	+	15	1822	c.1582G>T	c.(1582-1584)Gag>Tag	p.E528*	SENP2_ENST00000545472.1_Nonsense_Mutation_p.E518*|SENP2_ENST00000427465.2_Nonsense_Mutation_p.E352*	NM_021627.2	NP_067640.2	Q9HC62	SENP2_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 2	528	Protease.				cellular protein metabolic process (GO:0044267)|dorsal/ventral axis specification (GO:0009950)|heart development (GO:0007507)|labyrinthine layer development (GO:0060711)|mRNA transport (GO:0051028)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of protein binding (GO:0032091)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|protein transport (GO:0015031)|regulation of DNA endoreduplication (GO:0032875)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of Wnt signaling pathway (GO:0030111)|spongiotrophoblast layer development (GO:0060712)|trophoblast giant cell differentiation (GO:0060707)|Wnt signaling pathway (GO:0016055)	cytoplasmic vesicle (GO:0031410)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	SUMO-specific protease activity (GO:0016929)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(3)	12	all_cancers(143;1.28e-10)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			GAATCTTTTAGAGTGGACCCA	0.348																																					p.E528X		Atlas-SNP	.											.	SENP2	88	.	0			c.G1582T						PASS	.						140	134	136					3																	185341841		2203	4300	6503	SO:0001587	stop_gained	59343	exon15			CTTTTAGAGTGGA	AF151697	CCDS33902.1	3q28	2005-08-17	2005-08-17		ENSG00000163904	ENSG00000163904			23116	protein-coding gene	gene with protein product		608261	"SUMO1/sentrin/SMT3 specific protease 2"			11896061, 11489887	Standard	XM_005247690		Approved	SMT3IP2, KIAA1331, DKFZp762A2316, AXAM2	uc003fpn.3	Q9HC62	OTTHUMG00000156658	ENST00000296257.5:c.1582G>T	chr3.hg19:g.185341841G>T	ENSP00000296257:p.Glu528*	53.0	0.0	.		55.0	18.0	.	NM_021627	B4DQ42|Q8IW97|Q96SR2|Q9P2L5	Nonsense_Mutation	SNP	ENST00000296257.5	hg19	CCDS33902.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.221146	0.79464	.	.	ENSG00000163904	ENST00000545472;ENST00000296257;ENST00000437107;ENST00000427465;ENST00000444509	.	.	.	5.84	5.84	0.93424	.	0.059916	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	-29.0982	12.6115	0.56554	0.0:0.0:0.8347:0.1653	.	.	.	.	X	518;528;399;352;191	.	ENSP00000296257:E528X	E	+	1	0	SENP2	186824535	1.000000	0.71417	1.000000	0.80357	0.147000	0.21601	5.393000	0.66279	2.767000	0.95098	0.555000	0.69702	GAG	.	.	.	none		0.348	SENP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345159.1	NM_021627		T	185341841	G	T	185341841	4	4	179	1	0	0	0	0	0	1	0	0	14060	943	33	4	1640	4	SENP2	3	185341841	Nonsense_Mutation	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	59497341	185341841	12680589	19	10447											
POLN	353497	hgsc.bcm.edu	37	chr4	2210096	2210125	+	In_Frame_Del	DEL	GAGCTGATGCTCTTCTGTTTTTGGTCAGCA	GAGCTGATGCTCTTCTGTTTTTGGTCAGCA	-																															aacaacttgaaagagtcaatGagctgatgctcttctgtttt																								rs34459048	byFrequency	TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	GAGCTGATGCTCTTCTGTTTTTGGTCAGCA	GAGCTGATGCTCTTCTGTTTTTGGTCAGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr4:2210096_2210125delGAGCTGATGCTCTTCTGTTTTTGGTCAGCA	ENST00000511885.2	-	5	656_685	c.303_332delTGCTGACCAAAAACAGAAGAGCATCAGCTC	c.(301-333)tctgctgaccaaaaacagaagagcatcagctca>tca	p.101_111SADQKQKSISS>S	POLN_ENST00000382865.1_In_Frame_Del_p.101_111SADQKQKSISS>S|POLN_ENST00000515357.1_5'UTR			Q7Z5Q5	DPOLN_HUMAN	polymerase (DNA directed) nu	101					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)			AAGAGTCAATGAGCTGATGCTCTTCTGTTTTTGGTCAGCAGACAGCTGAT	0.396								DNA polymerases (catalytic subunits)																													p.102_111del		Atlas-Indel,Pindel	.											.	POLN	82	.	0			c.304_333del						PASS	.																																			SO:0001651	inframe_deletion	353497	exon3			.	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.303_332delTGCTGACCAAAAACAGAAGAGCATCAGCTC	chr4.hg19:g.2210096_2210125delGAGCTGATGCTCTTCTGTTTTTGGTCAGCA	ENSP00000435506:p.Ser101_Ser110del	71.0	0.0	0		38.0	13.0	0.342105	NM_181808	A2A336|B4E158|Q4TTW4|Q6ZNF4	In_Frame_Del	DEL	ENST00000511885.2	hg19	CCDS3360.1																																																																																			.	.	.	none		0.396	POLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205684.2	NM_181808		-	2210125	GAGCTGATGCTCTTCTGTTTTTGGTCAGCA	-	2210096	7	5	179	1	0	1	0	1	0	0	0	0	12214	1294	45	0	2458	0	POLN	4	2210096	In_Frame_Del	DEL	GAGCTGATGCTCTTCTGTTTTTGGTCAGCA	TCGA-G7-A8LB-01A-11D-A35Z-10		2210096	188944180	20	10448											
JAKMIP1	152789	hgsc.bcm.edu	37	chr4	6107649	6107649	+	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	gtgccgtcgctgctcctgctCgcgctccagcttcgcctcct	1	11	10	19	5	0	0	0	0	0	0	6	0	3	0	5	0	4	5	5	0	0	1			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr4:6107649C>T	ENST00000282924.5	-	3	660	c.175G>A	c.(175-177)Gag>Aag	p.E59K	JAKMIP1_ENST00000409831.1_Missense_Mutation_p.E59K|JAKMIP1_ENST00000457227.2_Intron|JAKMIP1_ENST00000409021.3_Missense_Mutation_p.E59K|JAKMIP1_ENST00000410077.2_Intron|JAKMIP1_ENST00000409371.3_Intron	NM_144720.3	NP_653321.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	59	Mediates association with microtubules.				cognition (GO:0050890)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|microtubule (GO:0005874)|ribonucleoprotein complex (GO:0030529)	GABA receptor binding (GO:0050811)|RNA binding (GO:0003723)			NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						TGCTCCTGCTCGCGCTCCAGC	0.667																																					p.E59K		Atlas-SNP	.											JAKMIP1_ENST00000409021,colon,carcinoma,0,2	JAKMIP1	250	.	0			c.G175A						PASS	.						27	27	27					4																	6107649		2164	4259	6423	SO:0001583	missense	152789	exon3			CCTGCTCGCGCTC	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.175G>A	chr4.hg19:g.6107649C>T	ENSP00000282924:p.Glu59Lys	92.0	0.0	.		33.0	14.0	.	NM_001099433	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Missense_Mutation	SNP	ENST00000282924.5	hg19	CCDS3385.1	.	.	.	.	.	.	.	.	.	.	C	31	5.078307	0.94000	.	.	ENSG00000152969	ENST00000409021;ENST00000418227;ENST00000425341;ENST00000282924;ENST00000409831	T;T;T	0.35789	1.29;1.29;1.29	3.93	3.93	0.45458	.	0.000000	0.64402	D	0.000007	T	0.60392	0.2265	M	0.79258	2.445	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.74023	0.92;0.982;0.92	T	0.67818	-0.5572	10	0.87932	D	0	.	15.4753	0.75474	0.0:1.0:0.0:0.0	.	59;59;59	F2Z2K5;Q96N16-2;Q96N16	.;.;JKIP1_HUMAN	K	59	ENSP00000386711:E59K;ENSP00000282924:E59K;ENSP00000386925:E59K	ENSP00000282924:E59K	E	-	1	0	JAKMIP1	6158550	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	7.172000	0.77604	2.166000	0.68216	0.484000	0.47621	GAG	.	.	.	none		0.667	JAKMIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246816.2	NM_144720		T	6107649	C	T	6107649	3	4	179	1	0	0	0	0	1	0	0	0	7947	893	31	1	2471	1	JAKMIP1	4	6107649	Missense_Mutation	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10	3897553	6107649	185046627	21	10449											
WDR19	57728	hgsc.bcm.edu	37	chr4	39191388	39191388	+	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	caaataagaccagccagttaGacaatggcatgaggtaagat	17	7	10	7	0	0	4	0	1	0	3	0	4	0	4	2	2	1	3	2	2	5	3			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr4:39191388G>C	ENST00000399820.3	+	4	431	c.277G>C	c.(277-279)Gac>Cac	p.D93H	WDR19_ENST00000506503.1_Missense_Mutation_p.D93H|WDR19_ENST00000288634.7_5'UTR	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	93					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						CAGCCAGTTAGACAATGGCAT	0.353																																					p.D93H		Atlas-SNP	.											.	WDR19	96	.	0			c.G277C						PASS	.						108	102	104					4																	39191388		1835	4094	5929	SO:0001583	missense	57728	exon4			CAGTTAGACAATG	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.277G>C	chr4.hg19:g.39191388G>C	ENSP00000382717:p.Asp93His	114.0	0.0	.		93.0	50.0	.	NM_025132	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Missense_Mutation	SNP	ENST00000399820.3	hg19	CCDS47042.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.522217	0.85600	.	.	ENSG00000157796	ENST00000399820;ENST00000509560;ENST00000506503;ENST00000399836	T;T;T	0.28069	3.43;1.63;3.43	5.94	5.94	0.96194	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.124661	0.64402	D	0.000001	T	0.59445	0.2194	M	0.83118	2.625	0.80722	D	1	D;D	0.61697	0.99;0.989	P;P	0.62382	0.897;0.901	T	0.59343	-0.7472	10	0.49607	T	0.09	-25.4728	20.3593	0.98849	0.0:0.0:1.0:0.0	.	93;93	Q8NEZ3;D6R9P6	WDR19_HUMAN;.	H	93;34;93;92	ENSP00000382717:D93H;ENSP00000426918:D34H;ENSP00000423491:D93H	ENSP00000382717:D93H	D	+	1	0	WDR19	38867783	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	9.397000	0.97276	2.822000	0.97130	0.557000	0.71058	GAC	.	.	.	none		0.353	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1			C	39191388	G	C	39191388	3	2	179	1	0	0	0	0	1	0	0	0	17291	942	33	4	291	4	WDR19	4	39191388	Missense_Mutation	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	33083739	39191388	151962888	22	10450											
KIAA1211	57482	hgsc.bcm.edu	37	chr4	57182299	57182299	+	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	aggcacagcagcaccggagaCagcgcggatgcagggccgcc	10	1	16	14	4	0	1	0	0	0	1	0	3	0	2	3	4	4	4	3	4	0	0			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr4:57182299C>T	ENST00000504228.1	+	6	2736	c.2631C>T	c.(2629-2631)gaC>gaT	p.D877D	KIAA1211_ENST00000264229.6_Silent_p.D877D|KIAA1211_ENST00000541073.1_Silent_p.D870D			Q6ZU35	K1211_HUMAN	KIAA1211	877										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)					GCACCGGAGACAGCGCGGATG	0.577																																					p.D877D		Atlas-SNP	.											.	KIAA1211	178	.	0			c.C2631T						PASS	.						39	48	45					4																	57182299		2186	4290	6476	SO:0001819	synonymous_variant	57482	exon8			CGGAGACAGCGCG	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.2631C>T	chr4.hg19:g.57182299C>T		79.0	0.0	.		62.0	31.0	.	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Silent	SNP	ENST00000504228.1	hg19	CCDS43230.1																																																																																			.	.	.	none		0.577	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722		T	57182299	C	T	57182299	2	4	179	1	0	0	0	0	0	0	0	1	8222	477	17	2		2	KIAA1211	4	57182299	Silent	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10	17990911	57182299	133971977	23	10451											
CNOT6L	246175	hgsc.bcm.edu	37	chr4	78665898	78665898	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actaatgatatctgcgtcacAgttaacaatttcttccataa	14	14	4	9	1	3	1	1	1	2	0	4	1	4	1	1	0	2	1	1	0	5	6			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr4:78665898A>G	ENST00000504123.1	-	7	821	c.691T>C	c.(691-693)Tgt>Cgt	p.C231R	CNOT6L_ENST00000506166.1_Intron|CNOT6L_ENST00000264903.4_Missense_Mutation_p.C231R			Q96LI5	CNO6L_HUMAN	CCR4-NOT transcription complex, subunit 6-like	231	Nuclease domain.				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						TCTGCGTCACAGTTAACAATT	0.383																																					p.C231R		Atlas-SNP	.											.	CNOT6L	57	.	0			c.T691C						PASS	.						67	61	63					4																	78665898		1872	4120	5992	SO:0001583	missense	246175	exon7			CGTCACAGTTAAC	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.691T>C	chr4.hg19:g.78665898A>G	ENSP00000424896:p.Cys231Arg	93.0	0.0	.		48.0	20.0	.	NM_144571	Q9UF92	Missense_Mutation	SNP	ENST00000504123.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.99|17.99	3.523382|3.523382	0.64747|0.64747	.|.	.|.	ENSG00000138767|ENSG00000138767	ENST00000504123;ENST00000264903;ENST00000512485|ENST00000515506	T;T;T|.	0.79940|.	-1.32;-1.32;-1.32|.	5.17|5.17	5.17|5.17	0.71159|0.71159	Endonuclease/exonuclease/phosphatase (2);|.	0.089945|.	0.85682|.	D|.	0.000000|.	T|T	0.39009|0.39009	0.1062|0.1062	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	P;B|.	0.40875|.	0.731;0.05|.	B;B|.	0.42692|.	0.395;0.125|.	T|T	0.32134|0.32134	-0.9918|-0.9918	10|5	0.33940|.	T|.	0.23|.	-18.9235|-18.9235	15.2936|15.2936	0.73885|0.73885	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	204;231|.	Q96LI5-2;Q96LI5|.	.;CNO6L_HUMAN|.	R|P	231;231;238|259	ENSP00000424896:C231R;ENSP00000264903:C231R;ENSP00000425571:C238R|.	ENSP00000264903:C231R|.	C|L	-|-	1|2	0|0	CNOT6L|CNOT6L	78884922|78884922	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.445000|7.445000	0.80570|0.80570	2.089000|2.089000	0.63090|0.63090	0.533000|0.533000	0.62120|0.62120	TGT|CTG	.	.	.	none		0.383	CNOT6L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000362515.1			G	78665898	A	G	78665898	3	3	179	1	0	0	0	0	1	0	0	0	3625	188	7	3	1000	3	CNOT6L	4	78665898	Missense_Mutation	SNP	A	TCGA-G7-A8LB-01A-11D-A35Z-10	21483599	78665898	112488378	24	10452											
C4orf29	80167	hgsc.bcm.edu	37	chr4	128930118	128930118	+	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	aatggaacagcaaatatagaCctgtatgcattcatcttgct	14	12	7	8	0	2	1	1	0	1	1	2	2	2	2	1	1	4	4	1	1	6	5			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr4:128930118C>G	ENST00000444616.1	+	5	569	c.322C>G	c.(322-324)Cct>Gct	p.P108A	C4orf29_ENST00000388795.5_Missense_Mutation_p.P26A|C4orf29_ENST00000398965.1_Missense_Mutation_p.P108A			Q0P651	CD029_HUMAN	chromosome 4 open reading frame 29	108						extracellular region (GO:0005576)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	8						CAAATATAGACCTGTATGCAT	0.294																																					p.P108A		Atlas-SNP	.											.	C4orf29	58	.	0			c.C322G						PASS	.						80	74	76					4																	128930118		1836	4092	5928	SO:0001583	missense	80167	exon5			TATAGACCTGTAT	AK024759	CCDS47131.1	4q28.2	2008-02-05			ENSG00000164074	ENSG00000164074			26111	protein-coding gene	gene with protein product						12477932	Standard	XM_006714318		Approved	FLJ21106	uc021xrt.1	Q0P651	OTTHUMG00000133304	ENST00000444616.1:c.322C>G	chr4.hg19:g.128930118C>G	ENSP00000397229:p.Pro108Ala	238.0	0.0	.		164.0	77.0	.	NM_001039717	A1A4W8|A1A4W9|Q9H7A7	Missense_Mutation	SNP	ENST00000444616.1	hg19		.	.	.	.	.	.	.	.	.	.	C	17.98	3.521110	0.64747	.	.	ENSG00000164074	ENST00000454347;ENST00000398965;ENST00000444616;ENST00000388795;ENST00000545758	.	.	.	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.77877	0.4196	M	0.66506	2.035	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.75502	-0.3295	9	0.33940	T	0.23	-28.3825	18.8831	0.92364	0.0:1.0:0.0:0.0	.	108	Q0P651	CD029_HUMAN	A	108;108;108;26;26	.	ENSP00000373447:P26A	P	+	1	0	C4orf29	129149568	1.000000	0.71417	0.621000	0.29145	0.249000	0.25844	7.215000	0.77966	2.521000	0.84997	0.650000	0.86243	CCT	.	.	.	none		0.294	C4orf29-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257098.1	NM_001039717		G	128930118	C	G	128930118	3	3	179	1	0	0	0	0	1	0	0	0	2261	507	18	4	336	4	C4orf29	4	128930118	Missense_Mutation	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10	50264220	128930118	62224158	25	10453											
ZNF366	167465	hgsc.bcm.edu	37	chr5	71739912	71739912	+	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	gagctgctggctctggggggCcaggccagggctgtagggct	4	7	20	10	0	1	0	0	0	1	0	1	1	1	0	2	7	2	6	2	7	1	1			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr5:71739912C>T	ENST00000318442.5	-	5	2396	c.1906G>A	c.(1906-1908)Gcc>Acc	p.A636T	RP11-389C8.2_ENST00000564956.1_RNA	NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	636	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)		CTCTGGGGGGCCAGGCCAGGG	0.652																																					p.A636T		Atlas-SNP	.											.	ZNF366	108	.	0			c.G1906A						PASS	.						104	119	114					5																	71739912		2203	4300	6503	SO:0001583	missense	167465	exon5			GGGGGGCCAGGCC	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.1906G>A	chr5.hg19:g.71739912C>T	ENSP00000313158:p.Ala636Thr	75.0	0.0	.		63.0	28.0	.	NM_152625	Q5HYI9|Q7RTV4	Missense_Mutation	SNP	ENST00000318442.5	hg19	CCDS4015.1	.	.	.	.	.	.	.	.	.	.	C	12.63	1.997047	0.35226	.	.	ENSG00000178175	ENST00000318442	T	0.08546	3.08	5.77	1.25	0.21368	.	1.473160	0.03691	N	0.247014	T	0.05502	0.0145	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.39035	-0.9633	10	0.25751	T	0.34	-1.5524	1.3046	0.02085	0.2362:0.3835:0.2159:0.1644	.	636	Q8N895	ZN366_HUMAN	T	636	ENSP00000313158:A636T	ENSP00000313158:A636T	A	-	1	0	ZNF366	71775668	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.858000	0.27845	0.421000	0.25980	-0.176000	0.13171	GCC	.	.	.	none		0.652	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3			T	71739912	C	T	71739912	3	4	179	1	0	0	0	0	1	0	0	0	17882	739	26	2	332	2	ZNF366	5	71739912	Missense_Mutation	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10		71739912	109175348	26	10454											
HMGCR	3156	hgsc.bcm.edu	37	chr5	74643113	74643113	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcttgttgaatgtcttgtgAttggagttggtaccatgtca	7	17	11	6	0	3	2	1	2	2	0	3	3	3	3	1	2	1	3	1	2	2	6			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr5:74643113A>G	ENST00000287936.4	+	6	691	c.535A>G	c.(535-537)Att>Gtt	p.I179V	HMGCR_ENST00000343975.5_Missense_Mutation_p.I179V|HMGCR_ENST00000511206.1_Missense_Mutation_p.I179V	NM_000859.2	NP_000850.1	P04035	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-CoA reductase	179	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				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)	ATGTCTTGTGATTGGAGTTGG	0.358																																					p.I179V		Atlas-SNP	.											.	HMGCR	53	.	0			c.A535G						PASS	.						310	283	292					5																	74643113		2203	4300	6503	SO:0001583	missense	3156	exon6			CTTGTGATTGGAG		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.535A>G	chr5.hg19:g.74643113A>G	ENSP00000287936:p.Ile179Val	131.0	0.0	.		91.0	37.0	.	NM_001130996	B7Z3Y9|Q8N190	Missense_Mutation	SNP	ENST00000287936.4	hg19	CCDS4027.1	.	.	.	.	.	.	.	.	.	.	A	19.17	3.775303	0.70107	.	.	ENSG00000113161	ENST00000511206;ENST00000544469;ENST00000287936;ENST00000343975	D;D;D	0.95690	-3.78;-3.78;-3.78	5.33	5.33	0.75918	Sterol-sensing domain (1);	0.000000	0.85682	D	0.000000	D	0.96605	0.8892	L	0.55017	1.72	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;0.999;1.0	D;D;D;D	0.87578	0.998;0.996;0.997;0.998	D	0.95694	0.8743	10	0.29301	T	0.29	-25.0512	14.959	0.71141	1.0:0.0:0.0:0.0	.	179;179;179;179	B2R649;A8KA27;P04035-2;P04035	.;.;.;HMDH_HUMAN	V	179;110;179;179	ENSP00000426745:I179V;ENSP00000287936:I179V;ENSP00000340816:I179V	ENSP00000287936:I179V	I	+	1	0	HMGCR	74678869	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.244000	0.95423	1.990000	0.58119	0.528000	0.53228	ATT	.	.	.	none		0.358	HMGCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219877.2			G	74643113	A	G	74643113	3	3	179	1	0	0	0	0	1	0	0	0	7238	333	12	3	553	3	HMGCR	5	74643113	Missense_Mutation	SNP	A	TCGA-G7-A8LB-01A-11D-A35Z-10	2903201	74643113	106272147	27	10455											
YTHDC2	64848	hgsc.bcm.edu	37	chr5	112860848	112860848	+	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	acttctgcctaaaacagaaaGaggaaatgtgtttgcagttg	14	11	10	6	0	1	2	0	0	1	2	1	3	1	3	1	1	3	3	1	1	4	4			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr5:112860848G>C	ENST00000161863.4	+	3	662	c.449G>C	c.(448-450)aGa>aCa	p.R150T	YTHDC2_ENST00000515883.1_Missense_Mutation_p.R150T	NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	150					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)		AAAACAGAAAGAGGAAATGTG	0.348																																					p.R150T		Atlas-SNP	.											.	YTHDC2	118	.	0			c.G449C						PASS	.						114	118	116					5																	112860848		2202	4300	6502	SO:0001583	missense	64848	exon3			CAGAAAGAGGAAA	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.449G>C	chr5.hg19:g.112860848G>C	ENSP00000161863:p.Arg150Thr	210.0	0.0	.		152.0	79.0	.	NM_022828	B2RP66	Missense_Mutation	SNP	ENST00000161863.4	hg19	CCDS4113.1	.	.	.	.	.	.	.	.	.	.	G	15.47	2.844331	0.51164	.	.	ENSG00000047188	ENST00000161863;ENST00000515883;ENST00000514720;ENST00000511372	T;T	0.07327	4.18;3.2	5.93	5.93	0.95920	.	0.157221	0.53938	D	0.000050	T	0.11836	0.0288	L	0.59436	1.845	0.38827	D	0.955758	B	0.26708	0.157	B	0.24394	0.053	T	0.02661	-1.1127	10	0.42905	T	0.14	.	15.4187	0.74995	0.068:0.0:0.932:0.0	.	150	Q9H6S0	YTDC2_HUMAN	T	150;150;90;60	ENSP00000161863:R150T;ENSP00000423101:R150T	ENSP00000161863:R150T	R	+	2	0	YTHDC2	112888747	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.170000	0.71920	2.805000	0.96524	0.655000	0.94253	AGA	.	.	.	none		0.348	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828		C	112860848	G	C	112860848	3	2	179	1	0	0	0	0	1	0	0	0	17509	942	33	4	459	4	YTHDC2	5	112860848	Missense_Mutation	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	38217735	112860848	68054412	28	10456											
JAKMIP2	9832	hgsc.bcm.edu	37	chr5	146991868	146991868	+	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	gttattgaatttgacacctaCcttttcttctaagtctttta	9	20	4	8	0	3	2	0	2	3	0	3	2	3	2	2	0	1	1	2	0	5	10			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr5:146991868C>T	ENST00000265272.5	-	20	2880		c.e20+1		JAKMIP2_ENST00000333010.6_Splice_Site|JAKMIP2_ENST00000507386.1_Splice_Site	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2							Golgi apparatus (GO:0005794)				NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTGACACCTACCTTTTCTTCT	0.308																																					.		Atlas-SNP	.											.	JAKMIP2	154	.	0			c.2349+1G>A						PASS	.						131	122	125					5																	146991868		2203	4300	6503	SO:0001630	splice_region_variant	9832	exon20			CACCTACCTTTTC	AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049			29067	protein-coding gene	gene with protein product		611197				9628581	Standard	NM_001270941		Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.2412+1G>A	chr5.hg19:g.146991868C>T		32.0	0.0	.		34.0	15.0	.	NM_001270934	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Splice_Site	SNP	ENST00000265272.5	hg19	CCDS4285.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.609318	0.87258	.	.	ENSG00000176049	ENST00000507386;ENST00000265272;ENST00000333010;ENST00000539401	.	.	.	5.34	5.34	0.76211	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4408	0.94820	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	JAKMIP2	146972061	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	7.249000	0.78278	2.677000	0.91161	0.655000	0.94253	.	.	.	.	none		0.308	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790	Intron	T	146991868	C	T	146991868	5	4	179	1	0	0	0	0	0	0	1	0	7948	521	18	2	27	2	JAKMIP2	5	146991868	Splice_Site	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10	34131020	146991868	33923392	29	10457											
NIPAL4	348938	hgsc.bcm.edu	37	chr5	156899945	156899945	+	Frame_Shift_Del	DEL	A	A	-																															catcaccagaagagaaacccAaagtatttataatccattcc																										TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr5:156899945delA	ENST00000311946.7	+	6	1494	c.1378delA	c.(1378-1380)aaafs	p.K460fs	ADAM19_ENST00000430702.2_Intron|NIPAL4_ENST00000435489.2_Frame_Shift_Del_p.K441fs	NM_001099287.1	NP_001092757.1	Q0D2K0	NIPA4_HUMAN	NIPA-like domain containing 4	460						integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(3)|endometrium(3)|kidney(1)|large_intestine(1)|lung(12)|prostate(1)|skin(1)	22						AGAGAAACCCAAAGTATTTAT	0.458																																					p.P459fs		Atlas-Indel,Pindel	.											.	NIPAL4	48	.	0			c.1377delC						PASS	.						46	46	46					5																	156899945		1887	4106	5993	SO:0001589	frameshift_variant	348938	exon6			.	AK026158	CCDS47328.1, CCDS54944.1	5q33.3	2009-03-24	2009-03-24		ENSG00000172548	ENSG00000172548			28018	protein-coding gene	gene with protein product	"ichthyin"	609383	"NIPA-like 4"			8619474, 9110174, 15317751	Standard	NM_001099287		Approved	ICHYN	uc003lwx.4	Q0D2K0	OTTHUMG00000163497	ENST00000311946.7:c.1378delA	chr5.hg19:g.156899945delA	ENSP00000311687:p.Lys460fs	31.0	0.0	0		27.0	13.0	0.481481	NM_001099287	A8S6F1|A8S6F5|A8S6F8|B4DLF3|Q0D2J8|Q0D2J9	Frame_Shift_Del	DEL	ENST00000311946.7	hg19	CCDS47328.1																																																																																			.	.	.	none		0.458	NIPAL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373789.1	NM_001099287		-	156899945	A	-	156899945	7	5	179	1	0	1	0	1	0	0	0	0	10434	131	5	0	1400	0	NIPAL4	5	156899945	Frame_Shift_Del	DEL	A	TCGA-G7-A8LB-01A-11D-A35Z-10	9908077	156899945	24015315	30	10458											
ZBTB12	221527	hgsc.bcm.edu	37	chr6	31868749	31868749	+	Missense_Mutation	SNP	T	T	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	tttctccaccacgtgctccaTctgcaggtaggaggcggctg	6	10	12	13	2	2	0	0	0	2	0	4	1	3	1	3	4	2	4	3	4	1	2			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr6:31868749T>G	ENST00000375527.2	-	2	509	c.334A>C	c.(334-336)Atg>Ctg	p.M112L	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	112					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						ACGTGCTCCATCTGCAGGTAG	0.567																																					p.M112L		Atlas-SNP	.											.	ZBTB12	25	.	0			c.A334C						PASS	.						80	75	76					6																	31868749		2203	4300	6503	SO:0001583	missense	221527	exon2			GCTCCATCTGCAG	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.334A>C	chr6.hg19:g.31868749T>G	ENSP00000364677:p.Met112Leu	100.0	0.0	.		63.0	37.0	.	NM_181842	B0UY00|Q5JQ98	Missense_Mutation	SNP	ENST00000375527.2	hg19	CCDS4727.1	.	.	.	.	.	.	.	.	.	.	T	26.9	4.784945	0.90282	.	.	ENSG00000204366	ENST00000375527	T	0.65178	-0.14	4.4	4.4	0.53042	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	U	0.000000	T	0.61813	0.2377	L	0.45422	1.42	0.49213	D	0.999769	P	0.40032	0.699	P	0.58130	0.833	T	0.67975	-0.5531	10	0.87932	D	0	.	12.6202	0.56600	0.0:0.0:0.0:1.0	.	112	Q9Y330	ZBT12_HUMAN	L	112	ENSP00000364677:M112L	ENSP00000364677:M112L	M	-	1	0	ZBTB12	31976728	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.186000	0.72026	1.615000	0.50252	0.433000	0.28618	ATG	.	.	.	none		0.567	ZBTB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076315.2	NM_181842		G	31868749	T	G	31868749	3	3	179	1	0	0	0	0	1	0	0	0	17537	1435	50	5	1049	5	ZBTB12	6	31868749	Missense_Mutation	SNP	T	TCGA-G7-A8LB-01A-11D-A35Z-10		31868749	139246318	31	10459											
HSD17B8	7923	hgsc.bcm.edu	37	chr6	33173952	33173953	+	Splice_Site	DEL	GG	GG	-																															ggacacttgggggaccctgaGggtgagcactgaatgtagtg																										TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr6:33173952_33173953delGG	ENST00000374662.3	+	7	720_721	c.693_694delGG	c.(691-696)gaggat>gaat	p.D232fs	HSD17B8_ENST00000469186.1_3'UTR|MIR219-1_ENST00000362166.1_RNA|RING1_ENST00000374656.4_5'Flank	NM_014234.4	NP_055049.1	Q92506	DHB8_HUMAN	hydroxysteroid (17-beta) dehydrogenase 8	232					androgen metabolic process (GO:0008209)|estrogen biosynthetic process (GO:0006703)|fatty acid biosynthetic process (GO:0006633)	mitochondrial envelope (GO:0005740)|mitochondrial matrix (GO:0005759)|plasma membrane (GO:0005886)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone dehydrogenase (NAD+) activity (GO:0047035)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(1)|urinary_tract(2)	9						GGGACCCTGAGGGTGAGCACTG	0.49																																					p.231_231del		Atlas-Indel,Pindel	.											.	HSD17B8	20	.	0			c.692_693del						PASS	.																																			SO:0001630	splice_region_variant	7923	exon7			.	D82061	CCDS4769.1	6p21.3	2011-09-14	2002-02-19	2002-02-22	ENSG00000204228	ENSG00000204228	1.1.1.62	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	3554	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 30C, member 1"	601417	"FabG (beta-ketoacyl-[acyl-carrier-protein] reductase, E coli) like (E. coli)"	FABGL		8812499, 19027726	Standard	NM_014234		Approved	HKE6, D6S2245E, RING2, KE6, H2-KE6, SDR30C1	uc003odi.2	Q92506	OTTHUMG00000031117	ENST00000374662.3:c.694+1GG>-	chr6.hg19:g.33173952_33173953delGG		149.0	0.0	0		82.0	42.0	0.512195	NM_014234	A6NLX7|Q5STP7|Q9UIQ1	Frame_Shift_Del	DEL	ENST00000374662.3	hg19	CCDS4769.1																																																																																			.	.	.	none		0.49	HSD17B8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076196.1	NM_014234	Frame_Shift_Del	-	33173953	GG	-	33173952	8	5	179	1	0	1	0	1	0	0	1	0	7396	1014	35	0	719	0	HSD17B8	6	33173952	Splice_Site	DEL	GG	TCGA-G7-A8LB-01A-11D-A35Z-10	1305203	33173952	137941115	32	10460											
ZNF318	24149	hgsc.bcm.edu	37	chr6	43305593	43305593	+	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	tacaccctataggtgatacaGaattttcttcacacactttc	12	14	4	11	0	2	2	1	1	1	1	3	2	2	2	1	1	2	0	1	1	5	8			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr6:43305593G>A	ENST00000361428.2	-	10	6220	c.6143C>T	c.(6142-6144)tCt>tTt	p.S2048F	ZNF318_ENST00000318149.3_Intron	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	2048					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)			AGGTGATACAGAATTTTCTTC	0.468																																					p.S2048F		Atlas-SNP	.											.	ZNF318	175	.	0			c.C6143T						PASS	.						91	82	85					6																	43305593		2203	4300	6503	SO:0001583	missense	24149	exon10			GATACAGAATTTT	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.6143C>T	chr6.hg19:g.43305593G>A	ENSP00000354964:p.Ser2048Phe	175.0	0.0	.		87.0	40.0	.	NM_014345	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Missense_Mutation	SNP	ENST00000361428.2	hg19	CCDS4895.2	.	.	.	.	.	.	.	.	.	.	G	8.914	0.959432	0.18507	.	.	ENSG00000171467	ENST00000361428	T	0.12774	2.65	5.2	3.27	0.37495	.	0.501221	0.19661	N	0.108975	T	0.10252	0.0251	L	0.32530	0.975	0.44485	D	0.99742	D	0.57571	0.98	P	0.56700	0.804	T	0.04203	-1.0969	10	0.54805	T	0.06	-4.6027	8.6883	0.34251	0.1987:0.0:0.8013:0.0	.	2048	Q5VUA4	ZN318_HUMAN	F	2048	ENSP00000354964:S2048F	ENSP00000354964:S2048F	S	-	2	0	ZNF318	43413571	1.000000	0.71417	0.884000	0.34674	0.096000	0.18686	1.868000	0.39509	1.432000	0.47375	0.655000	0.94253	TCT	.	.	.	none		0.468	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345		A	43305593	G	A	43305593	3	1	179	1	0	0	0	0	1	0	0	0	17848	942	33	2	700	2	ZNF318	6	43305593	Missense_Mutation	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	10131641	43305593	127809474	33	10461											
CAPN11	11131	hgsc.bcm.edu	37	chr6	44140108	44140108	+	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	actgctataccgcgtggtgcCcagaggacagagcttcaaga	11	7	12	11	2	1	3	1	0	0	3	1	4	1	4	2	2	4	2	2	2	3	3			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr6:44140108C>A	ENST00000398776.1	+	5	517	c.479C>A	c.(478-480)cCc>cAc	p.P160H	CAPN11_ENST00000542245.1_Missense_Mutation_p.P160H	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11	160	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)			breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CGCGTGGTGCCCAGAGGACAG	0.577											OREG0017466	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P160H		Atlas-SNP	.											.	CAPN11	66	.	0			c.C479A						PASS	.						22	23	23					6																	44140108		1939	4119	6058	SO:0001583	missense	11131	exon5			TGGTGCCCAGAGG	AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225		"EF-hand domain containing"	1478	protein-coding gene	gene with protein product		604822				10409436	Standard	NM_007058		Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.479C>A	chr6.hg19:g.44140108C>A	ENSP00000381758:p.Pro160His	74.0	0.0	.	921	69.0	40.0	.	NM_007058	B2RA64|Q5T3G1|Q8N4R5	Missense_Mutation	SNP	ENST00000398776.1	hg19	CCDS47436.1	.	.	.	.	.	.	.	.	.	.	C	18.84	3.708456	0.68615	.	.	ENSG00000137225	ENST00000398776;ENST00000542245	D;D	0.92752	-3.1;-3.1	4.05	4.05	0.47172	Peptidase C2, calpain, catalytic domain (3);	0.000000	0.49305	D	0.000159	D	0.97885	0.9305	H	0.99156	4.45	0.58432	D	0.999994	D	0.89917	1.0	D	0.97110	1.0	D	0.98911	1.0780	9	.	.	.	.	16.4876	0.84189	0.0:1.0:0.0:0.0	.	160	Q9UMQ6	CAN11_HUMAN	H	160	ENSP00000381758:P160H;ENSP00000441078:P160H	.	P	+	2	0	CAPN11	44248086	1.000000	0.71417	0.993000	0.49108	0.338000	0.28826	7.580000	0.82523	2.549000	0.85964	0.655000	0.94253	CCC	.	.	.	none		0.577	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3			A	44140108	C	A	44140108	3	1	179	1	0	0	0	0	1	0	0	0	2626	623	22	4	497	4	CAPN11	6	44140108	Missense_Mutation	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10	834515	44140108	126974959	34	10462											
RNGTT	8732	hgsc.bcm.edu	37	chr6	89614664	89614664	+	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	ttgggcaaaagtagcaactgCtgcttcgatactataggaaa	14	10	10	7	1	0	0	0	0	0	0	1	2	0	1	0	2	5	5	0	2	8	6			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr6:89614664C>A	ENST00000369485.4	-	6	640	c.454G>T	c.(454-456)Gca>Tca	p.A152S	RNGTT_ENST00000369475.3_Missense_Mutation_p.A152S|RNGTT_ENST00000265607.6_Missense_Mutation_p.A152S|RNGTT_ENST00000538899.1_Missense_Mutation_p.A92S	NM_003800.3	NP_003791.3	O60942	MCE1_HUMAN	RNA guanylyltransferase and 5'-phosphatase	152	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)		GTAGCAACTGCTGCTTCGATA	0.418																																					p.A152S		Atlas-SNP	.											.	RNGTT	52	.	0			c.G454T						PASS	.						94	95	94					6																	89614664		2203	4300	6503	SO:0001583	missense	8732	exon6			CAACTGCTGCTTC	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.454G>T	chr6.hg19:g.89614664C>A	ENSP00000358497:p.Ala152Ser	113.0	0.0	.		76.0	37.0	.	NM_003800	E1P513|E1P514|O43483|O60257|O60351|Q5TCW8|Q8WUM8	Missense_Mutation	SNP	ENST00000369485.4	hg19	CCDS5017.1	.	.	.	.	.	.	.	.	.	.	C	32	5.142079	0.94560	.	.	ENSG00000111880	ENST00000369485;ENST00000265607;ENST00000538899;ENST00000536746;ENST00000369475	D;D;D;D	0.92299	-3.01;-3.01;-3.01;-3.01	5.74	5.74	0.90152	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);	0.045290	0.85682	D	0.000000	D	0.96932	0.8998	M	0.92738	3.34	0.80722	D	1	D;D;D;D	0.63046	0.989;0.992;0.99;0.992	D;D;D;D	0.67900	0.94;0.954;0.923;0.954	D	0.97014	0.9738	10	0.66056	D	0.02	.	19.9357	0.97140	0.0:1.0:0.0:0.0	.	92;152;152;152	B4DSJ8;Q5TCW7;O60942-2;O60942	.;.;.;MCE1_HUMAN	S	152;152;92;123;152	ENSP00000358497:A152S;ENSP00000265607:A152S;ENSP00000442609:A92S;ENSP00000358487:A152S	ENSP00000265607:A152S	A	-	1	0	RNGTT	89671383	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.634000	0.83273	2.715000	0.92844	0.655000	0.94253	GCA	.	.	.	none		0.418	RNGTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041469.1			A	89614664	C	A	89614664	3	1	179	1	0	0	0	0	1	0	0	0	13516	797	28	4	1383	4	RNGTT	6	89614664	Missense_Mutation	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10	45474556	89614664	81500403	35	10463											
TRAF3IP2	10758	hgsc.bcm.edu	37	chr6	111880633	111880633	+	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	agggaaccacctgaagggtgGgcagaggcccccgtggagga	10	3	18	10	1	0	2	0	1	0	1	0	5	0	5	4	6	1	1	4	6	2	0			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr6:111880633G>T	ENST00000340026.6	-	10	2294	c.1700C>A	c.(1699-1701)cCc>cAc	p.P567H	TRAF3IP2_ENST00000368731.2_5'UTR|TRAF3IP2-AS1_ENST00000456352.2_RNA|TRAF3IP2_ENST00000359831.4_Missense_Mutation_p.P557H|TRAF3IP2-AS1_ENST00000442928.2_RNA|TRAF3IP2-AS1_ENST00000438298.2_RNA|TRAF3IP2_ENST00000392556.4_Missense_Mutation_p.P146H|TRAF3IP2-AS1_ENST00000449449.2_RNA|TRAF3IP2_ENST00000368735.1_Missense_Mutation_p.P102H|TRAF3IP2-AS1_ENST00000440395.1_RNA|TRAF3IP2-AS1_ENST00000532353.1_RNA|TRAF3IP2_ENST00000368761.5_Missense_Mutation_p.P558H			O43734	CIKS_HUMAN	TRAF3 interacting protein 2	567					B cell apoptotic process (GO:0001783)|humoral immune response (GO:0006959)|immunoglobulin secretion (GO:0048305)|intracellular signal transduction (GO:0035556)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)					central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	18		all_cancers(87;7.87e-06)|Acute lymphoblastic leukemia(125;3.61e-09)|all_hematologic(75;2.63e-07)|all_epithelial(87;0.0024)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.033)|all cancers(137;0.0412)|Epithelial(106;0.0732)		CTGAAGGGTGGGCAGAGGCCC	0.562																																					p.P558H		Atlas-SNP	.											.	TRAF3IP2	35	.	0			c.C1673A						PASS	.						90	91	90					6																	111880633		2203	4300	6503	SO:0001583	missense	10758	exon9			AGGGTGGGCAGAG	AF136405	CCDS5093.1, CCDS55049.1, CCDS55050.1	6q21	2008-09-05	2002-06-20	2005-04-13	ENSG00000056972	ENSG00000056972			1343	protein-coding gene	gene with protein product		607043	"chromosome 6 open reading frame 5", "chromosome 6 open reading frame 2"	C6orf4, C6orf5, C6orf6, C6orf2		10962033, 10962024	Standard	NR_028338		Approved	DKFZP586G0522, ACT1, CIKS	uc003pvf.4	O43734	OTTHUMG00000015379	ENST00000340026.6:c.1700C>A	chr6.hg19:g.111880633G>T	ENSP00000345984:p.Pro567His	97.0	0.0	.		67.0	34.0	.	NM_147686	B2RAY9|E1P555|Q5R3A3|Q7Z6Q1|Q7Z6Q2|Q7Z6Q3|Q9H5W2|Q9H6Y3|Q9NS14|Q9UG72	Missense_Mutation	SNP	ENST00000340026.6	hg19		.	.	.	.	.	.	.	.	.	.	G	22.0	4.233749	0.79688	.	.	ENSG00000056972	ENST00000392555;ENST00000368761;ENST00000392556;ENST00000340026;ENST00000359831;ENST00000368735	T;T;T	0.42900	0.98;0.98;0.96	6.17	6.17	0.99709	.	0.165337	0.56097	D	0.000040	T	0.54598	0.1868	L	0.43923	1.385	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.53315	-0.8456	10	0.87932	D	0	-0.0313	20.8794	0.99867	0.0:0.0:1.0:0.0	.	557	Q7Z6Q1	.	H	567;558;146;567;557;102	ENSP00000357750:P558H;ENSP00000345984:P567H;ENSP00000352889:P557H	ENSP00000345984:P567H	P	-	2	0	TRAF3IP2	111987326	1.000000	0.71417	1.000000	0.80357	0.530000	0.34684	4.822000	0.62686	2.941000	0.99782	0.655000	0.94253	CCC	.	.	.	none		0.562	TRAF3IP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000041841.2			T	111880633	G	T	111880633	3	4	179	1	0	0	0	0	1	0	0	0	16453	1232	43	4	28	4	TRAF3IP2	6	111880633	Missense_Mutation	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	22265969	111880633	59234434	36	10464											
TBP	6908	hgsc.bcm.edu	37	chr6	170871004	170871004	+	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	gagcaacaaaggcagcagcaGcaacaacaacagcagcagca	19	0	10	12	0	0	0	0	0	0	0	0	1	0	0	0	1	11	8	0	1	5	0			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr6:170871004G>A	ENST00000392092.2	+	3	459	c.180G>A	c.(178-180)caG>caA	p.Q60Q	TBP_ENST00000540980.1_Silent_p.Q40Q|TBP_ENST00000230354.6_Silent_p.Q60Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	60	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		Ggcagcagcagcaacaacaac	0.542																																					p.Q60Q		Atlas-SNP	.											.	TBP	58	.	0			c.G180A						PASS	.						43	45	44					6																	170871004		2203	4300	6503	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAACAA	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"General transcription factors"	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.180G>A	chr6.hg19:g.170871004G>A		58.0	0.0	.		47.0	4.0	.	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	hg19	CCDS5315.1																																																																																			.	.	.	none		0.542	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		A	170871004	G	A	170871004	2	1	179	1	0	0	0	0	0	0	0	1	15656	962	34	2		2	TBP	6	170871004	Silent	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	58990371	170871004	244063	37	10465											
TBP	6908	hgsc.bcm.edu	37	chr6	170871180	170871180	+	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	gggaacctcaggccaggcacCacagctcttccactcacaga	11	5	9	16	0	3	1	2	0	1	1	4	2	4	2	4	3	2	2	4	3	1	1			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr6:170871180C>A	ENST00000392092.2	+	3	635	c.356C>A	c.(355-357)cCa>cAa	p.P119Q	TBP_ENST00000540980.1_Missense_Mutation_p.P99Q|TBP_ENST00000230354.6_Missense_Mutation_p.P119Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	119					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)		GGCCAGGCACCACAGCTCTTC	0.622																																					p.P119Q		Atlas-SNP	.											.	TBP	58	.	0			c.C356A						PASS	.						136	126	129					6																	170871180		2203	4300	6503	SO:0001583	missense	6908	exon3			AGGCACCACAGCT	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.356C>A	chr6.hg19:g.170871180C>A	ENSP00000375942:p.Pro119Gln	131.0	0.0	.		103.0	51.0	.	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Missense_Mutation	SNP	ENST00000392092.2	hg19	CCDS5315.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.998609	0.74818	.	.	ENSG00000112592	ENST00000421512;ENST00000392092;ENST00000540980;ENST00000230354;ENST00000392091;ENST00000423353	T;T;T;T;T	0.65364	1.03;-0.15;-0.15;-0.15;1.03	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.49898	0.1584	L	0.29908	0.895	0.80722	D	1	D	0.54397	0.966	P	0.46479	0.518	T	0.57376	-0.7822	10	0.66056	D	0.02	-7.2007	19.3627	0.94446	0.0:1.0:0.0:0.0	.	119	P20226	TBP_HUMAN	Q	119;119;99;119;96;119	ENSP00000400008:P119Q;ENSP00000375942:P119Q;ENSP00000442132:P99Q;ENSP00000230354:P119Q;ENSP00000416482:P119Q	ENSP00000230354:P119Q	P	+	2	0	TBP	170713105	1.000000	0.71417	0.998000	0.56505	0.888000	0.51559	7.041000	0.76558	2.571000	0.86741	0.655000	0.94253	CCA	.	.	.	none		0.622	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		A	170871180	C	A	170871180	3	1	179	1	0	0	0	0	1	0	0	0	15656	594	21	4	362	4	TBP	6	170871180	Missense_Mutation	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10	176	170871180	243887	38	10466											
IQCE	23288	hgsc.bcm.edu	37	chr7	2625912	2625912	+	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	gtgccctcctgagcttgtccCggagtgtccaggagctcacg	5	9	13	14	2	1	1	1	1	0	0	4	3	4	3	4	2	3	2	4	2	0	1	rs547114342		TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr7:2625912C>A	ENST00000402050.2	+	12	1079	c.895C>A	c.(895-897)Cgg>Agg	p.R299R	IQCE_ENST00000404984.1_Silent_p.R248R|IQCE_ENST00000438376.2_Silent_p.R283R|IQCE_ENST00000325979.7_Silent_p.R234R	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	299						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)		GAGCTTGTCCCGGAGTGTCCA	0.592													C|||	1	0.000199681	0	0	5008	,	,		20372	0		0.001	False		,,,				2504	0				p.R299R		Atlas-SNP	.											.,1	IQCE	66	.	0			c.C895A						PASS	.						53	62	59					7																	2625912		2006	4165	6171	SO:0001819	synonymous_variant	23288	exon12			TTGTCCCGGAGTG	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.895C>A	chr7.hg19:g.2625912C>A		69.0	0.0	.		74.0	10.0	.	NM_152558	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Silent	SNP	ENST00000402050.2	hg19	CCDS43542.1																																																																																			.	.	.	none		0.592	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558		A	2625912	C	A	2625912	2	1	179	1	0	0	0	0	0	0	0	1	7813	643	23	4		4	IQCE	7	2625912	Silent	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10		2625912	156512751	39	10467											
INMT	11185	hgsc.bcm.edu	37	chr7	30795228	30795228	+	Missense_Mutation	SNP	T	T	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	ctgccctgtgcaaccttgccTcactgctcaagccgggtggc	5	9	11	16	1	2	0	2	0	0	0	2	0	2	0	4	2	6	2	4	2	2	1			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr7:30795228T>G	ENST00000013222.5	+	3	569	c.553T>G	c.(553-555)Tca>Gca	p.S185A	INMT_ENST00000484180.1_3'UTR|INMT-FAM188B_ENST00000458257.1_Intron|INMT_ENST00000409539.1_Missense_Mutation_p.S184A	NM_001199219.1|NM_006774.4	NP_001186148.1|NP_006765.4	O95050	INMT_HUMAN	indolethylamine N-methyltransferase	185					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						CAACCTTGCCTCACTGCTCAA	0.627																																					p.S185A		Atlas-SNP	.											.	INMT	38	.	0			c.T553G						PASS	.						117	99	105					7																	30795228		2203	4300	6503	SO:0001583	missense	11185	exon3			CTTGCCTCACTGC		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.553T>G	chr7.hg19:g.30795228T>G	ENSP00000013222:p.Ser185Ala	55.0	0.0	.		74.0	17.0	.	NM_006774	B8ZZ69|Q3KP49|Q9P1Y2|Q9UBY4|Q9UHQ0	Missense_Mutation	SNP	ENST00000013222.5	hg19	CCDS5430.1	.	.	.	.	.	.	.	.	.	.	T	12.65	2.001013	0.35320	.	.	ENSG00000241644	ENST00000013222;ENST00000409539	T;T	0.09817	2.94;2.94	3.67	-3.34	0.04943	.	2.476700	0.02010	N	0.046915	T	0.15176	0.0366	M	0.79614	2.46	0.09310	N	1	B;B	0.18741	0.03;0.03	B;B	0.21546	0.035;0.035	T	0.39231	-0.9624	10	0.35671	T	0.21	-21.5047	6.0673	0.19870	0.2462:0.0:0.5263:0.2275	.	184;185	B8ZZ69;O95050	.;INMT_HUMAN	A	185;184	ENSP00000013222:S185A;ENSP00000386961:S184A	ENSP00000013222:S185A	S	+	1	0	INMT	30761753	0.000000	0.05858	0.000000	0.03702	0.174000	0.22865	-1.235000	0.02928	-0.261000	0.09405	0.459000	0.35465	TCA	.	.	.	none		0.627	INMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214993.3	NM_006774		G	30795228	T	G	30795228	3	3	179	1	0	0	0	0	1	0	0	0	7752	1551	54	5	563	5	INMT	7	30795228	Missense_Mutation	SNP	T	TCGA-G7-A8LB-01A-11D-A35Z-10	28169316	30795228	128343435	40	10468											
DBF4	10926	hgsc.bcm.edu	37	chr7	87516694	87516695	+	Frame_Shift_Del	DEL	AA	AA	-																															aatgccttgtcatggggagtAaaaattcttcatattgatgg																										TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr7:87516694_87516695delAA	ENST00000265728.1	+	5	1005_1006	c.501_502delAA	c.(499-504)gtaaaafs	p.K168fs		NM_006716.3	NP_006707.1	Q9UBU7	DBF4A_HUMAN	DBF4 zinc finger	168	BRCT 2.				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)				CATGGGGAGTAAAAATTCTTCA	0.287																																					p.167_167del		Atlas-Indel,Pindel	.											.	DBF4	67	.	0			c.500_501del						PASS	.																																			SO:0001589	frameshift_variant	10926	exon5			.	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.501_502delAA	chr7.hg19:g.87516696_87516697delAA	ENSP00000265728:p.Lys168fs	200.0	0.0	0		223.0	131.0	0.587444	NM_006716	A4D1D8|A8K954|O75226|Q75MS6|Q75N01|Q9Y2M6	Frame_Shift_Del	DEL	ENST00000265728.1	hg19	CCDS5611.1																																																																																			.	.	.	none		0.287	DBF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253678.1	NM_006716		-	87516695	AA	-	87516694	7	5	179	1	0	1	0	1	0	0	0	0	4250	349	13	0	519	0	DBF4	7	87516694	Frame_Shift_Del	DEL	AA	TCGA-G7-A8LB-01A-11D-A35Z-10	56721466	87516694	71621969	41	10469											
DYNC1I1	1780	hgsc.bcm.edu	37	chr7	95668656	95668656	+	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	caggaattaactgccacatgGcagtgggcccaatcgacttt	11	9	10	11	1	0	0	0	0	0	0	1	2	0	1	2	3	2	1	2	3	3	2			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr7:95668656G>T	ENST00000324972.6	+	14	1676	c.1483G>T	c.(1483-1485)Gca>Tca	p.A495S	DYNC1I1_ENST00000457059.1_Missense_Mutation_p.A478S|DYNC1I1_ENST00000359388.4_Missense_Mutation_p.A458S|DYNC1I1_ENST00000497626.1_3'UTR|DYNC1I1_ENST00000447467.2_Missense_Mutation_p.A478S|DYNC1I1_ENST00000437599.1_Missense_Mutation_p.A475S|DYNC1I1_ENST00000537881.1_Missense_Mutation_p.A458S	NM_004411.4	NP_004402.1	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	495					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)			CTGCCACATGGCAGTGGGCCC	0.463																																					p.A495S		Atlas-SNP	.											.	DYNC1I1	111	.	0			c.G1483T						PASS	.						142	130	134					7																	95668656		2203	4300	6503	SO:0001583	missense	1780	exon14			CACATGGCAGTGG	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.1483G>T	chr7.hg19:g.95668656G>T	ENSP00000320130:p.Ala495Ser	127.0	0.0	.		140.0	89.0	.	NM_004411	B4DME3|F5H050|G5E9K1|Q8TBF7|Q9Y2X1	Missense_Mutation	SNP	ENST00000324972.6	hg19	CCDS5644.1	.	.	.	.	.	.	.	.	.	.	G	19.65	3.867794	0.72065	.	.	ENSG00000158560	ENST00000447467;ENST00000324972;ENST00000537881;ENST00000437599;ENST00000359388;ENST00000457059	T;T;T;T;T;T	0.57907	0.37;0.37;0.37;0.37;0.37;0.37	4.94	4.94	0.65067	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.47948	0.1473	N	0.10874	0.06	0.80722	D	1	P;P;P;P;B	0.40638	0.725;0.542;0.542;0.597;0.336	P;B;B;B;B	0.51777	0.679;0.327;0.327;0.401;0.155	T	0.38757	-0.9646	10	0.20046	T	0.44	-0.3946	18.7491	0.91806	0.0:0.0:1.0:0.0	.	478;475;478;495;458	Q7Z6M0;G5E9K1;O14576-2;O14576;O14576-3	.;.;.;DC1I1_HUMAN;.	S	478;495;458;475;458;478	ENSP00000392337:A478S;ENSP00000320130:A495S;ENSP00000438377:A458S;ENSP00000398118:A475S;ENSP00000352348:A458S;ENSP00000412444:A478S	ENSP00000320130:A495S	A	+	1	0	DYNC1I1	95506592	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.657000	0.98554	2.753000	0.94483	0.557000	0.71058	GCA	.	.	.	none		0.463	DYNC1I1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333432.1	NM_004411		T	95668656	G	T	95668656	3	4	179	1	0	0	0	0	1	0	0	0	4844	1203	42	4	1533	4	DYNC1I1	7	95668656	Missense_Mutation	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	8151962	95668656	63470007	42	10470											
ACTL6B	51412	hgsc.bcm.edu	37	chr7	100253150	100253150	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcttctctttgtccccctcCagctccagcccgcccccctc	2	12	4	23	1	2	0	0	0	2	0	7	0	5	0	8	0	2	1	8	0	0	3			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr7:100253150C>T	ENST00000160382.5	-	3	268	c.162G>A	c.(160-162)ctG>ctA	p.L54L		NM_016188.4	NP_057272.1	O94805	ACL6B_HUMAN	actin-like 6B	54	Essential for mediating its function in dendritic development; may contribute to neuronal-specific targeting. {ECO:0000250}.				chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|nervous system development (GO:0007399)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	structural constituent of cytoskeleton (GO:0005200)|transcription coactivator activity (GO:0003713)			endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|skin(1)	13	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					TGTCCCCCTCCAGCTCCAGCC	0.637																																					p.L54L		Atlas-SNP	.											.	ACTL6B	47	.	0			c.G162A						PASS	.						110	83	92					7																	100253150		2203	4300	6503	SO:0001819	synonymous_variant	51412	exon3			CCCCTCCAGCTCC	AB015906	CCDS5702.1	7q22	2008-02-01	2004-07-12	2004-07-14	ENSG00000077080	ENSG00000077080			160	protein-coding gene	gene with protein product		612458	"actin-like 6"	ACTL6		9799793	Standard	NM_016188		Approved	BAF53B	uc003uvy.3	O94805	OTTHUMG00000159661	ENST00000160382.5:c.162G>A	chr7.hg19:g.100253150C>T		51.0	0.0	.		65.0	22.0	.	NM_016188	A4D2D0|O75421	Silent	SNP	ENST00000160382.5	hg19	CCDS5702.1																																																																																			.	.	.	none		0.637	ACTL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356745.1	NM_016188		T	100253150	C	T	100253150	2	4	179	1	0	0	0	0	0	0	0	1	199	581	21	2		2	ACTL6B	7	100253150	Silent	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10	4584494	100253150	58885513	43	10471											
EXOC4	60412	hgsc.bcm.edu	37	chr7	133059613	133059615	+	In_Frame_Del	DEL	GAC	GAC	-																															aactgctggagttactgtttGacaagtttaatgctgtagcc																										TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	GAC	GAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr7:133059613_133059615delGAC	ENST00000253861.4	+	7	1068_1070	c.1039_1041delGAC	c.(1039-1041)gacdel	p.D347del	EXOC4_ENST00000393161.2_In_Frame_Del_p.D347del|EXOC4_ENST00000539845.1_In_Frame_Del_p.D246del	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	347					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)				GTTACTGTTTGACAAGTTTAATG	0.438																																					p.346_347del		Atlas-Indel,Pindel	.											.	EXOC4	118	.	0			c.1038_1040del						PASS	.																																			SO:0001651	inframe_deletion	60412	exon7			.	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.1039_1041delGAC	chr7.hg19:g.133059613_133059615delGAC	ENSP00000253861:p.Asp347del	65.0	0.0	0		63.0	38.0	0.603175	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	In_Frame_Del	DEL	ENST00000253861.4	hg19	CCDS5829.1																																																																																			.	.	.	none		0.438	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807		-	133059615	GAC	-	133059613	7	5	179	1	0	1	0	1	0	0	0	0	5308	1290	45	0	1065	0	EXOC4	7	133059613	In_Frame_Del	DEL	GAC	TCGA-G7-A8LB-01A-11D-A35Z-10	32806463	133059613	26079050	44	10472											
MYOM2	9172	hgsc.bcm.edu	37	chr8	2026963	2026963	+	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	gcatcagccgaccctccaggGtctctgatgcggtggctgca	6	8	13	14	2	2	1	1	1	1	0	4	2	3	1	3	3	3	3	3	3	0	0			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr8:2026963G>T	ENST00000262113.4	+	12	1552	c.1411G>T	c.(1411-1413)Gtc>Ttc	p.V471F	MYOM2_ENST00000523438.1_Intron	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	471	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		ACCCTCCAGGGTCTCTGATGC	0.542																																					p.V471F		Atlas-SNP	.											.	MYOM2	251	.	0			c.G1411T						PASS	.						138	147	144					8																	2026963		2203	4300	6503	SO:0001583	missense	9172	exon12			TCCAGGGTCTCTG		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.1411G>T	chr8.hg19:g.2026963G>T	ENSP00000262113:p.Val471Phe	103.0	0.0	.		67.0	34.0	.	NM_003970	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	hg19	CCDS5957.1	.	.	.	.	.	.	.	.	.	.	G	9.827	1.187293	0.21870	.	.	ENSG00000036448	ENST00000262113	T	0.60548	0.18	4.71	2.88	0.33553	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.264519	0.31721	N	0.007172	T	0.55242	0.1908	M	0.74881	2.28	0.80722	D	1	B	0.06786	0.001	B	0.11329	0.006	T	0.52711	-0.8539	10	0.46703	T	0.11	.	10.2016	0.43087	0.1646:0.0:0.8354:0.0	.	471	P54296	MYOM2_HUMAN	F	471	ENSP00000262113:V471F	ENSP00000262113:V471F	V	+	1	0	MYOM2	2014370	0.195000	0.23338	0.741000	0.31004	0.515000	0.34225	1.501000	0.35693	0.494000	0.27859	0.561000	0.74099	GTC	.	.	.	none		0.542	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970		T	2026963	G	T	2026963	3	4	179	1	0	0	0	0	1	0	0	0	10099	1261	44	4	1453	4	MYOM2	8	2026963	Missense_Mutation	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10		2026963	144337059	45	10473											
UBR5	51366	hgsc.bcm.edu	37	chr8	103273473	103273473	+	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	actggtatatttacaccattAggaatgagttcaacctgtga	13	13	8	7	0	1	2	1	2	0	0	1	3	1	3	2	2	2	2	2	2	6	6			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr8:103273473A>T	ENST00000520539.1	-	56	8463	c.7857T>A	c.(7855-7857)ccT>ccA	p.P2619P	UBR5_ENST00000220959.4_Silent_p.P2618P|UBR5_ENST00000518205.1_Silent_p.P347P|UBR5_ENST00000521922.1_Silent_p.P2612P	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	2619	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)			TTACACCATTAGGAATGAGTT	0.348																																					p.P2619P	Ovarian(131;96 1741 5634 7352 27489)	Atlas-SNP	.											.	UBR5	285	.	0			c.T7857A						PASS	.						152	130	138					8																	103273473		2203	4300	6503	SO:0001819	synonymous_variant	51366	exon56			ACCATTAGGAATG	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.7857T>A	chr8.hg19:g.103273473A>T		103.0	0.0	.		91.0	36.0	.	NM_015902	B2RP24|J3KMW7|O94970|Q9NPL3	Silent	SNP	ENST00000520539.1	hg19	CCDS34933.1																																																																																			.	.	.	none		0.348	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902		T	103273473	A	T	103273473	2	4	179	1	0	0	0	0	0	0	0	1	16917	407	15	5		5	UBR5	8	103273473	Silent	SNP	A	TCGA-G7-A8LB-01A-11D-A35Z-10	101246510	103273473	43090549	46	10474											
LRRC14	9684	hgsc.bcm.edu	37	chr8	145745846	145745846	+	Missense_Mutation	SNP	T	T	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	tgcgttcctgcgggaggcacTccgaagcagcgtgggcagcc	6	6	16	13	4	0	0	0	0	0	0	2	2	2	1	3	3	5	4	3	3	1	1			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr8:145745846T>G	ENST00000292524.1	+	3	700	c.554T>G	c.(553-555)cTc>cGc	p.L185R	RECQL4_ENST00000532237.1_5'Flank|RECQL4_ENST00000428558.2_5'Flank|LRRC14_ENST00000529022.1_Missense_Mutation_p.L185R	NM_001272036.1|NM_014665.2	NP_001258965.1|NP_055480.1	Q15048	LRC14_HUMAN	leucine rich repeat containing 14	185										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)			CGGGAGGCACTCCGAAGCAGC	0.711																																					p.L185R		Atlas-SNP	.											.	LRRC14	25	.	0			c.T554G						PASS	.						44	51	49					8																	145745846		2203	4297	6500	SO:0001583	missense	9684	exon4			AGGCACTCCGAAG	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.554T>G	chr8.hg19:g.145745846T>G	ENSP00000292524:p.Leu185Arg	46.0	0.0	.		31.0	14.0	.	NM_001272036	A8K0A8|D3DWM8	Missense_Mutation	SNP	ENST00000292524.1	hg19	CCDS6432.1	.	.	.	.	.	.	.	.	.	.	T	14.21	2.467258	0.43839	.	.	ENSG00000160959	ENST00000527730;ENST00000529022;ENST00000292524	T;T;T	0.23950	1.88;4.7;4.7	4.51	4.51	0.55191	.	0.414516	0.23716	N	0.045274	T	0.45094	0.1325	L	0.58101	1.795	0.50171	D	0.999857	D	0.89917	1.0	D	0.81914	0.995	T	0.39014	-0.9634	10	0.59425	D	0.04	.	11.7962	0.52102	0.0:0.0:0.0:1.0	.	185	Q15048	LRC14_HUMAN	R	185	ENSP00000436452:L185R;ENSP00000434768:L185R;ENSP00000292524:L185R	ENSP00000292524:L185R	L	+	2	0	LRRC14	145716654	0.497000	0.26067	0.055000	0.19348	0.133000	0.20885	3.701000	0.54793	1.893000	0.54813	0.379000	0.24179	CTC	.	.	.	none		0.711	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665		G	145745846	T	G	145745846	3	3	179	1	0	0	0	0	1	0	0	0	8975	1551	54	5	560	5	LRRC14	8	145745846	Missense_Mutation	SNP	T	TCGA-G7-A8LB-01A-11D-A35Z-10	42472373	145745846	618176	47	10475											
CDC37L1	55664	hgsc.bcm.edu	37	chr9	4701924	4701925	+	Frame_Shift_Ins	INS	-	-	T																															tgaagctttcaagtcaagagINStaagactttattctcaatca																										TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr9:4701924_4701925insT	ENST00000381854.3	+	6	1010_1011	c.808_809insT	c.(808-810)gtafs	p.V270fs	CDC37L1_ENST00000381858.1_Frame_Shift_Ins_p.V270fs	NM_017913.2	NP_060383.2	Q7L3B6	CD37L_HUMAN	cell division cycle 37-like 1	270	Interaction with Hsp70.|Self-association and interaction with Hsp90.					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)		CAAGTCAAGAGTAAGACTTTAT	0.332																																					p.V270fs		Atlas-Indel,Pindel	.											.	CDC37L1	19	.	0			c.808_809insT						PASS	.																																			SO:0001589	frameshift_variant	55664	exon6			.	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.809dupT	chr9.hg19:g.4701925_4701925dupT	ENSP00000371278:p.Val270fs	68.0	0.0	0		51.0	24.0	0.470588	NM_017913	B1AL70|Q9NWS3|Q9NX16	Frame_Shift_Ins	INS	ENST00000381854.3	hg19	CCDS6454.1																																																																																			.	.	.	none		0.332	CDC37L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051564.1	NM_017913		T	4701925	-	T	4701924	7	5	179	1	0	1	1	0	0	0	0	0	3071	1029	36	0	830	0	CDC37L1	9	4701924	Frame_Shift_Ins	INS	-	TCGA-G7-A8LB-01A-11D-A35Z-10		4701924	136511507	48	10476											
FREM1	158326	hgsc.bcm.edu	37	chr9	14776064	14776064	+	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	cggtcagctgaaggaggtcaGgggaaagcaggcccacggcc	10	3	17	11	2	2	1	2	1	0	0	2	3	2	3	2	7	2	2	2	7	2	0	rs369703203		TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr9:14776064G>A	ENST00000380880.3	-	25	5363	c.4580C>T	c.(4579-4581)cCt>cTt	p.P1527L	FREM1_ENST00000486223.1_5'Flank|FREM1_ENST00000380894.1_Missense_Mutation_p.P63L|FREM1_ENST00000380881.4_Missense_Mutation_p.P1528L|FREM1_ENST00000422223.2_Missense_Mutation_p.P1527L			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1527					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)		AAGGAGGTCAGGGGAAAGCAG	0.602																																					p.P1527L		Atlas-SNP	.											.	FREM1	261	.	0			c.C4580T						PASS	.						123	135	131					9																	14776064		2020	4176	6196	SO:0001583	missense	158326	exon26			AGGTCAGGGGAAA	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.4580C>T	chr9.hg19:g.14776064G>A	ENSP00000370262:p.Pro1527Leu	145.0	0.0	.		111.0	50.0	.	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	hg19	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	G	19.23	3.788320	0.70337	.	.	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380894;ENST00000380880	T;T;T;T	0.78003	0.66;0.66;-1.14;0.66	6.16	6.16	0.99307	.	0.207579	0.51477	D	0.000082	T	0.79964	0.4537	M	0.77103	2.36	0.80722	D	1	B;B	0.28378	0.075;0.209	B;B	0.24155	0.027;0.051	T	0.75207	-0.3399	10	0.37606	T	0.19	-4.5244	20.8598	0.99761	0.0:0.0:1.0:0.0	.	1527;63	Q5H8C1;B7ZBX4	FREM1_HUMAN;.	L	1528;1527;63;1527	ENSP00000370263:P1528L;ENSP00000412940:P1527L;ENSP00000370278:P63L;ENSP00000370262:P1527L	ENSP00000370262:P1527L	P	-	2	0	FREM1	14766064	1.000000	0.71417	0.949000	0.38748	0.644000	0.38419	7.598000	0.82745	2.937000	0.99478	0.650000	0.86243	CCT	.	.	.	alt		0.602	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		A	14776064	G	A	14776064	3	1	179	1	0	0	0	0	1	0	0	0	6051	1000	35	2	2011	2	FREM1	9	14776064	Missense_Mutation	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	10074140	14776064	126437367	49	10477											
MAMDC4	158056	hgsc.bcm.edu	37	chr9	139750216	139750216	+	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	ttgagtcccccgaggctgggGgctgggaggacgccagcgtg	5	6	19	11	3	0	1	0	1	0	0	1	4	1	3	3	5	1	2	3	5	0	1			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr9:139750216G>A	ENST00000317446.2	+	13	1554	c.1504G>A	c.(1504-1506)Ggc>Agc	p.G502S	MAMDC4_ENST00000485732.1_3'UTR|MAMDC4_ENST00000445819.1_Missense_Mutation_p.G502S	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)		CGAGGCTGGGGGCTGGGAGGA	0.701																																					p.G502S		Atlas-SNP	.											.	MAMDC4	117	.	0			c.G1504A						PASS	.						10	11	11					9																	139750216		2139	4234	6373	SO:0001583	missense	158056	exon13			GCTGGGGGCTGGG	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.1504G>A	chr9.hg19:g.139750216G>A	ENSP00000319388:p.Gly502Ser	101.0	0.0	.		63.0	44.0	.	NM_206920		Missense_Mutation	SNP	ENST00000317446.2	hg19	CCDS7010.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	17.14|17.14	3.313754|3.313754	0.60414|0.60414	.|.	.|.	ENSG00000177943|ENSG00000177943	ENST00000413647|ENST00000317446;ENST00000445819	.|T;T	.|0.02525	.|4.26;4.26	3.79|3.79	3.79|3.79	0.43588|0.43588	.|.	0.115488|0.115488	0.38548|0.38548	N|N	0.001648|0.001648	T|T	0.10594|0.10594	0.0259|0.0259	M|M	0.64997|0.64997	1.995|1.995	0.35799|0.35799	D|D	0.823021|0.823021	.|D	.|0.89917	.|1.0	.|D	.|0.77004	.|0.989	T|T	0.33497|0.33497	-0.9866|-0.9866	7|10	0.46703|0.22109	T|T	0.11|0.4	-31.4467|-31.4467	12.8395|12.8395	0.57793|0.57793	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|502	.|Q6UXC1-2	.|.	E|S	483|502	.|ENSP00000319388:G502S;ENSP00000411339:G502S	ENSP00000400009:G483E|ENSP00000319388:G502S	G|G	+|+	2|1	0|0	MAMDC4|MAMDC4	138870037|138870037	0.997000|0.997000	0.39634|0.39634	0.949000|0.949000	0.38748|0.38748	0.548000|0.548000	0.35241|0.35241	1.906000|1.906000	0.39887|0.39887	2.112000|2.112000	0.64535|0.64535	0.561000|0.561000	0.74099|0.74099	GGG|GGC	.	.	.	none		0.701	MAMDC4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254642.3	NM_206920		A	139750216	G	A	139750216	3	1	179	1	0	0	0	0	1	0	0	0	9211	1232	43	2	1554	2	MAMDC4	9	139750216	Missense_Mutation	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	124974152	139750216	1463215	50	10478											
DIP2C	22982	hgsc.bcm.edu	37	chr10	459976	459976	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcggccagttcgtgaccaCgcccagctgctctccgcgca	5	6	12	18	6	1	1	0	1	1	0	3	1	1	1	4	2	2	4	4	2	0	1			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr10:459976C>T	ENST00000280886.6	-	8	1021	c.934G>A	c.(934-936)Gtg>Atg	p.V312M	DIP2C_ENST00000381496.3_Missense_Mutation_p.V205M	NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	312						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)		TTCGTGACCACGCCCAGCTGC	0.622																																					p.V312M		Atlas-SNP	.											.	DIP2C	195	.	0			c.G934A						PASS	.						50	53	52					10																	459976		2203	4299	6502	SO:0001583	missense	22982	exon8			TGACCACGCCCAG	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.934G>A	chr10.hg19:g.459976C>T	ENSP00000280886:p.Val312Met	63.0	0.0	.		33.0	14.0	.	NM_014974	B4DPI5|Q5SS78	Missense_Mutation	SNP	ENST00000280886.6	hg19	CCDS7054.1	.	.	.	.	.	.	.	.	.	.	C	16.83	3.230399	0.58777	.	.	ENSG00000151240	ENST00000280886;ENST00000381496	T;T	0.47177	0.85;0.85	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.48978	0.1530	M	0.78456	2.415	0.54753	D	0.999987	P;P	0.46621	0.881;0.801	B;B	0.34536	0.185;0.097	T	0.61068	-0.7137	10	0.51188	T	0.08	-29.0514	18.7949	0.91990	0.0:1.0:0.0:0.0	.	205;312	E7EPU2;Q9Y2E4	.;DIP2C_HUMAN	M	312;205	ENSP00000280886:V312M;ENSP00000370907:V205M	ENSP00000280886:V312M	V	-	1	0	DIP2C	449976	1.000000	0.71417	0.525000	0.27900	0.278000	0.26855	7.776000	0.85560	2.427000	0.82271	0.655000	0.94253	GTG	.	.	.	none		0.622	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974		T	459976	C	T	459976	3	4	179	1	0	0	0	0	1	0	0	0	4531	536	19	1	3856	1	DIP2C	10	459976	Missense_Mutation	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10		459976	135074771	51	10479											
GDF2	2658	hgsc.bcm.edu	37	chr10	48416620	48416620	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accctcgtccccagctctgcAgtggcttcccctgtagggag	5	9	11	16	1	1	0	0	0	1	0	4	1	3	1	5	2	2	4	5	2	1	2			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr10:48416620A>G	ENST00000249598.1	-	1	233	c.74T>C	c.(73-75)cTg>cCg	p.L25P		NM_016204.1	NP_057288.1	Q9UK05	GDF2_HUMAN	growth differentiation factor 2	25					activin receptor signaling pathway (GO:0032924)|angiogenesis (GO:0001525)|blood vessel morphogenesis (GO:0048514)|BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to BMP stimulus (GO:0071773)|growth (GO:0040007)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of DNA replication (GO:0008156)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|ossification (GO:0001503)|osteoblast differentiation (GO:0001649)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(2)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	28						CCAGCTCTGCAGTGGCTTCCC	0.652																																					p.L25P		Atlas-SNP	.											.	GDF2	77	.	0			c.T74C						PASS	.						15	16	16					10																	48416620		2203	4300	6503	SO:0001583	missense	2658	exon1			CTCTGCAGTGGCT	AF156891	CCDS73118.1	10q11.22	2014-05-06			ENSG00000128802	ENSG00000263761		"Endogenous ligands"	4217	protein-coding gene	gene with protein product		605120				10849432	Standard	NM_016204		Approved	BMP-9, BMP9	uc001jfa.1	Q9UK05	OTTHUMG00000188320	ENST00000249598.1:c.74T>C	chr10.hg19:g.48416620A>G	ENSP00000249598:p.Leu25Pro	78.0	0.0	.		59.0	31.0	.	NM_016204	Q5VSQ9|Q9Y571	Missense_Mutation	SNP	ENST00000249598.1	hg19	CCDS7219.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.990617	0.74589	.	.	ENSG00000128802	ENST00000249598	T	0.81078	-1.45	5.69	5.69	0.88448	.	0.152498	0.44483	D	0.000444	D	0.84211	0.5422	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.84892	0.0837	10	0.51188	T	0.08	.	13.958	0.64162	1.0:0.0:0.0:0.0	.	25	Q9UK05	GDF2_HUMAN	P	25	ENSP00000249598:L25P	ENSP00000249598:L25P	L	-	2	0	GDF2	48036626	1.000000	0.71417	0.770000	0.31555	0.601000	0.36947	6.229000	0.72294	2.292000	0.77174	0.533000	0.62120	CTG	.	.	.	none		0.652	GDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047891.1	NM_016204		G	48416620	A	G	48416620	3	3	179	1	0	0	0	0	1	0	0	0	6321	188	7	3	1223	3	GDF2	10	48416620	Missense_Mutation	SNP	A	TCGA-G7-A8LB-01A-11D-A35Z-10	47956644	48416620	87118127	52	10480											
HERC4	26091	hgsc.bcm.edu	37	chr10	69804160	69804160	+	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	ctttctggtcacctttgttaCctgggtactctgatgcattc	5	17	8	11	0	3	1	1	1	2	0	4	1	3	1	2	2	3	3	2	2	2	5			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr10:69804160C>T	ENST00000395198.3	-	4	634		c.e4+1		HERC4_ENST00000373700.4_Splice_Site|HERC4_ENST00000395187.2_Intron|HERC4_ENST00000412272.2_Splice_Site	NM_022079.2	NP_071362.1	Q5GLZ8	HERC4_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 4						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						ACCTTTGTTACCTGGGTACTC	0.423																																					.		Atlas-SNP	.											.	HERC4	78	.	0			c.386+1G>A						PASS	.						118	95	103					10																	69804160		2203	4300	6503	SO:0001630	splice_region_variant	26091	exon5			TTGTTACCTGGGT	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.386+1G>A	chr10.hg19:g.69804160C>T		114.0	0.0	.		76.0	41.0	.	NM_022079	Q5GC98|Q5GC99|Q5GCA0|Q8IXP9|Q9HCH9	Splice_Site	SNP	ENST00000395198.3	hg19	CCDS41533.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.007526	0.93287	.	.	ENSG00000148634	ENST00000412272;ENST00000395198;ENST00000373700;ENST00000513996	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4692	0.94956	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	HERC4	69474166	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.757000	0.85209	2.596000	0.87737	0.591000	0.81541	.	.	.	.	none		0.423	HERC4-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359262.1	NM_015601	Intron	T	69804160	C	T	69804160	5	4	179	1	0	0	0	0	0	0	1	0	7067	521	18	2	2878	2	HERC4	10	69804160	Splice_Site	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10	21387540	69804160	65730587	53	10481											
UNC5B	219699	hgsc.bcm.edu	37	chr10	73051493	73051493	+	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	gccagcctcggttcccagcaGctcttgggcctgccccgaga	5	7	12	17	2	1	1	0	0	1	1	3	2	2	1	6	2	4	3	6	2	0	2			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr10:73051493G>T	ENST00000335350.6	+	10	2015	c.1599G>T	c.(1597-1599)caG>caT	p.Q533H	UNC5B_ENST00000373192.4_Missense_Mutation_p.Q522H	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	533					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						GTTCCCAGCAGCTCTTGGGCC	0.692																																					p.Q533H		Atlas-SNP	.											.	UNC5B	123	.	0			c.G1599T						PASS	.						32	33	33					10																	73051493		2203	4299	6502	SO:0001583	missense	219699	exon10			CCAGCAGCTCTTG	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.1599G>T	chr10.hg19:g.73051493G>T	ENSP00000334329:p.Gln533His	61.0	0.0	.		47.0	20.0	.	NM_170744	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Missense_Mutation	SNP	ENST00000335350.6	hg19	CCDS7309.1	.	.	.	.	.	.	.	.	.	.	g	10.59	1.392469	0.25118	.	.	ENSG00000107731	ENST00000335350;ENST00000373192	T;T	0.48522	0.87;0.81	4.24	2.12	0.27331	.	0.784528	0.11226	N	0.586193	T	0.23133	0.0559	N	0.03115	-0.41	0.21897	N	0.999482	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18555	-1.0333	10	0.23302	T	0.38	-12.9608	9.6384	0.39824	0.0:0.397:0.478:0.125	.	522;533	Q8IZJ1-2;Q8IZJ1	.;UNC5B_HUMAN	H	533;522	ENSP00000334329:Q533H;ENSP00000362288:Q522H	ENSP00000334329:Q533H	Q	+	3	2	UNC5B	72721499	0.976000	0.34144	1.000000	0.80357	0.891000	0.51852	0.354000	0.20146	0.866000	0.35629	0.556000	0.70494	CAG	.	.	.	none		0.692	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744		T	73051493	G	T	73051493	3	4	179	1	0	0	0	0	1	0	0	0	17004	962	34	4	1637	4	UNC5B	10	73051493	Missense_Mutation	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	3247333	73051493	62483254	54	10482											
BCCIP	56647	hgsc.bcm.edu	37	chr10	127512176	127512176	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaaagtggggttccgcagcCgccggatcccccagtccagc	7	5	14	15	3	0	0	0	0	0	0	3	2	3	2	6	4	2	2	6	4	1	1			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr10:127512176C>T	ENST00000278100.6	+	1	62	c.50C>T	c.(49-51)cCg>cTg	p.P17L	BCCIP_ENST00000368759.5_Missense_Mutation_p.P17L|UROS_ENST00000368797.4_5'Flank|BCCIP_ENST00000299130.3_Missense_Mutation_p.P17L|UROS_ENST00000368774.1_5'Flank|BCCIP_ENST00000429863.2_Missense_Mutation_p.P17L|UROS_ENST00000368778.3_5'Flank	NM_078468.2	NP_510868.1	Q9P287	BCCIP_HUMAN	BRCA2 and CDKN1A interacting protein	17					cell cycle (GO:0007049)|DNA repair (GO:0006281)|neuroendocrine cell differentiation (GO:0061101)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nucleus (GO:0005634)	kinase regulator activity (GO:0019207)|poly(A) RNA binding (GO:0044822)			breast(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(1)	8		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				GTTCCGCAGCCGCCGGATCCC	0.587																																					p.P17L		Atlas-SNP	.											.	BCCIP	48	.	0			c.C50T						PASS	.						105	107	106					10																	127512176		2203	4300	6503	SO:0001583	missense	56647	exon1			CGCAGCCGCCGGA	AB040451	CCDS7649.1, CCDS7650.1, CCDS7651.1	10q26.2	2008-05-14	2001-11-29		ENSG00000107949	ENSG00000107949			978	protein-coding gene	gene with protein product		611883	"BRCA2 and CDKN1A-interacting protein"			11313963, 10878006	Standard	NM_016567		Approved	BCCIPalpha, TOK-1	uc001ljd.4	Q9P287	OTTHUMG00000019237	ENST00000278100.6:c.50C>T	chr10.hg19:g.127512176C>T	ENSP00000278100:p.Pro17Leu	128.0	0.0	.		73.0	39.0	.	NM_016567	B3KP45|Q8ND15|Q96GC4|Q9P288	Missense_Mutation	SNP	ENST00000278100.6	hg19	CCDS7651.1	.	.	.	.	.	.	.	.	.	.	C	15.78	2.935205	0.52866	.	.	ENSG00000107949	ENST00000278100;ENST00000299130;ENST00000368759;ENST00000429863;ENST00000392718	T;T;T;T	0.60797	0.46;0.28;0.16;0.47	4.85	1.96	0.26148	.	0.504572	0.16759	N	0.200707	T	0.32734	0.0839	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.20459	0.013;0.013;0.045;0.022;0.004	B;B;B;B;B	0.13407	0.003;0.003;0.009;0.007;0.003	T	0.17868	-1.0355	10	0.48119	T	0.1	-2.3078	6.7389	0.23424	0.0:0.6895:0.0:0.3105	.	17;17;17;17;17	B4E318;B4DUS0;Q9P287-2;Q9P287-4;Q9P287	.;.;.;.;BCCIP_HUMAN	L	17	ENSP00000278100:P17L;ENSP00000299130:P17L;ENSP00000357748:P17L;ENSP00000394758:P17L	ENSP00000278100:P17L	P	+	2	0	BCCIP	127502166	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.163000	0.16520	0.120000	0.18254	-0.215000	0.12644	CCG	.	.	.	none		0.587	BCCIP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050941.1			T	127512176	C	T	127512176	3	4	179	1	0	0	0	0	1	0	0	0	1356	652	23	1	52	1	BCCIP	10	127512176	Missense_Mutation	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10	54460683	127512176	8022571	55	10483											
ACP2	53	hgsc.bcm.edu	37	chr11	47264636	47264637	+	Frame_Shift_Ins	INS	-	-	A																															gcttgttcaccattgtagacINSatccagtgccatttgcaggg																										TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr11:47264636_47264637insA	ENST00000256997.3	-	9	1010_1011	c.894_895insT	c.(892-897)gatgtcfs	p.V299fs	ACP2_ENST00000525230.1_5'UTR|ACP2_ENST00000533929.1_Frame_Shift_Ins_p.V271fs|ACP2_ENST00000527256.1_Frame_Shift_Ins_p.V267fs|ACP2_ENST00000537863.1_Frame_Shift_Ins_p.V112fs|ACP2_ENST00000529444.1_Frame_Shift_Ins_p.V236fs	NM_001610.2	NP_001601.1	P11117	PPAL_HUMAN	acid phosphatase 2, lysosomal	299					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						CCATTGTAGACATCCAGTGCCA	0.584																																					p.V299fs	Melanoma(90;262 1440 11488 44828 48531)	Atlas-Indel,Pindel	.											.	ACP2	36	.	0			c.895_896insT						PASS	.																																			SO:0001589	frameshift_variant	53	exon9			.	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.895dupT	chr11.hg19:g.47264637_47264637dupA	ENSP00000256997:p.Val299fs	89.0	0.0	0		58.0	26.0	0.448276	NM_001610	E9PCI1|Q561W5|Q9BTU7	Frame_Shift_Ins	INS	ENST00000256997.3	hg19	CCDS7928.1																																																																																			.	.	.	none		0.584	ACP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392022.2	NM_001610		A	47264637	-	A	47264636	7	5	179	1	0	1	1	0	0	0	0	0	163	478	17	0	388	0	ACP2	11	47264636	Frame_Shift_Ins	INS	-	TCGA-G7-A8LB-01A-11D-A35Z-10		47264636	87741880	56	10484											
MTMR2	8898	hgsc.bcm.edu	37	chr11	95657091	95657091	+	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	cgccgccggctgggagccaaGactctcgcagctcgagctct	6	6	13	16	5	2	1	0	0	2	1	4	3	2	2	3	2	3	4	3	2	1	0			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr11:95657091G>A	ENST00000346299.5	-	1	368	c.28C>T	c.(28-30)Ctt>Ttt	p.L10F	MTMR2_ENST00000484818.1_5'Flank|MTMR2_ENST00000409459.1_5'UTR|MTMR2_ENST00000352297.7_5'UTR|MTMR2_ENST00000393223.3_5'UTR	NM_016156.5	NP_057240.3	Q13614	MTMR2_HUMAN	myotubularin related protein 2	10	Ser-rich.				cell death (GO:0008219)|dendritic spine maintenance (GO:0097062)|inositol phosphate dephosphorylation (GO:0046855)|myelin assembly (GO:0032288)|negative regulation of endocytosis (GO:0045806)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of myelination (GO:0031642)|negative regulation of receptor catabolic process (GO:2000645)|negative regulation of receptor internalization (GO:0002091)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of early endosome to late endosome transport (GO:2000643)|protein dephosphorylation (GO:0006470)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endosome (GO:0005768)|neuronal postsynaptic density (GO:0097481)|nucleus (GO:0005634)|synaptic membrane (GO:0097060)|synaptic vesicle (GO:0008021)|vacuolar membrane (GO:0005774)	phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	19		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TGGGAGCCAAGACTCTCGCAG	0.701																																					p.L10F		Atlas-SNP	.											.	MTMR2	79	.	0			c.C28T						PASS	.						5	6	5					11																	95657091		2130	4130	6260	SO:0001583	missense	8898	exon1			AGCCAAGACTCTC	U58033	CCDS8305.1, CCDS8306.1	11q22	2014-09-17			ENSG00000087053	ENSG00000087053		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7450	protein-coding gene	gene with protein product		603557		CMT4B		8640223, 9736772	Standard	NM_016156		Approved	KIAA1073	uc001pfu.3	Q13614	OTTHUMG00000153837	ENST00000346299.5:c.28C>T	chr11.hg19:g.95657091G>A	ENSP00000345752:p.Leu10Phe	275.0	0.0	.		182.0	76.0	.	NM_016156	A6NN98|Q9UPS9	Missense_Mutation	SNP	ENST00000346299.5	hg19	CCDS8305.1	.	.	.	.	.	.	.	.	.	.	G	15.37	2.813946	0.50527	.	.	ENSG00000087053	ENST00000346299	D	0.95622	-3.76	4.49	2.5	0.30297	.	0.593190	0.14662	N	0.305920	D	0.91040	0.7181	L	0.29908	0.895	0.80722	D	1	D	0.56521	0.976	P	0.44597	0.454	D	0.88605	0.3152	10	0.66056	D	0.02	.	7.3712	0.26802	0.096:0.1696:0.7344:0.0	.	10	Q13614	MTMR2_HUMAN	F	10	ENSP00000345752:L10F	ENSP00000345752:L10F	L	-	1	0	MTMR2	95296739	1.000000	0.71417	0.968000	0.41197	0.179000	0.23085	2.766000	0.47629	1.044000	0.40200	0.561000	0.74099	CTT	.	.	.	none		0.701	MTMR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332620.1	NM_016156		A	95657091	G	A	95657091	3	1	179	1	0	0	0	0	1	0	0	0	9951	942	33	2	1963	2	MTMR2	11	95657091	Missense_Mutation	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	48392455	95657091	39349425	57	10485											
TMPRSS4	56649	hgsc.bcm.edu	37	chr11	117973872	117973872	+	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	ggcagcctctccacttcatcCcgaggaagcagctgtgtgac	8	8	11	14	1	2	1	1	1	1	0	4	3	3	2	3	2	3	3	3	2	1	1			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr11:117973872C>A	ENST00000437212.3	+	4	428	c.214C>A	c.(214-216)Ccg>Acg	p.P72T	TMPRSS4_ENST00000523251.1_Missense_Mutation_p.P32T|TMPRSS4_ENST00000522307.1_5'UTR|TMPRSS4_ENST00000534111.1_Missense_Mutation_p.P70T|TMPRSS4_ENST00000522824.1_Missense_Mutation_p.P72T			Q9NRS4	TMPS4_HUMAN	transmembrane protease, serine 4	72	LDL-receptor class A.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0431)|all_hematologic(192;0.164)|Breast(348;0.183)|all_neural(223;0.238)		BRCA - Breast invasive adenocarcinoma(274;4.16e-05)|Epithelial(105;0.00204)		CCACTTCATCCCGAGGAAGCA	0.592																																					p.P72T		Atlas-SNP	.											.	TMPRSS4	46	.	0			c.C214A						PASS	.						140	138	138					11																	117973872		2200	4296	6496	SO:0001583	missense	56649	exon4			TTCATCCCGAGGA	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.214C>A	chr11.hg19:g.117973872C>A	ENSP00000416037:p.Pro72Thr	81.0	0.0	.		43.0	21.0	.	NM_019894	A8MU84|B0YJB0|B7Z8C5|E7ERX8|Q5XKQ6|Q6UX37|Q9NZA5	Missense_Mutation	SNP	ENST00000437212.3	hg19	CCDS31684.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.901|7.901	0.734478|0.734478	0.15574|0.15574	.|.	.|.	ENSG00000137648|ENSG00000137648	ENST00000517544|ENST00000534111;ENST00000523251;ENST00000437212;ENST00000522824	.|D;D;D;D	.|0.91996	.|-2.95;-2.95;-2.95;-2.95	5.16|5.16	1.14|1.14	0.20703|0.20703	.|.	0.896737|0.896737	0.09414|0.09414	N|N	0.805430|0.805430	D|D	0.92951|0.92951	0.7757|0.7757	M|M	0.70108|0.70108	2.13|2.13	0.31916|0.31916	N|N	0.614078|0.614078	.|P;P;P;D	.|0.55172	.|0.87;0.949;0.859;0.97	.|B;P;B;P	.|0.51657	.|0.36;0.476;0.358;0.676	D|D	0.88864|0.88864	0.3328|0.3328	6|10	.|0.66056	.|D	.|0.02	.|.	9.626|9.626	0.39750|0.39750	0.0:0.6981:0.0:0.3019|0.0:0.6981:0.0:0.3019	.|.	.|47;32;72;70	.|B7Z900;E7ERX8;Q9NRS4;Q9NRS4-3	.|.;.;TMPS4_HUMAN;.	H|T	38|70;32;72;72	.|ENSP00000435184:P70T;ENSP00000429209:P32T;ENSP00000416037:P72T;ENSP00000430547:P72T	.|ENSP00000416037:P72T	P|P	+|+	2|1	0|0	TMPRSS4|TMPRSS4	117479082|117479082	0.360000|0.360000	0.24964|0.24964	0.448000|0.448000	0.26945|0.26945	0.048000|0.048000	0.14542|0.14542	0.926000|0.926000	0.28804|0.28804	0.203000|0.203000	0.20529|0.20529	-0.379000|-0.379000	0.06801|0.06801	CCC|CCG	.	.	.	none		0.592	TMPRSS4-004	KNOWN	non_canonical_polymorphism|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377328.2	NM_019894		A	117973872	C	A	117973872	3	1	179	1	0	0	0	0	1	0	0	0	16261	623	22	4	228	4	TMPRSS4	11	117973872	Missense_Mutation	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10	22316781	117973872	17032644	58	10486											
DDX6	1656	hgsc.bcm.edu	37	chr11	118635954	118635954	+	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	attatgtcatctcgtaaattGgttcctcctgtggttgccat	7	17	8	9	1	2	0	1	0	1	0	5	0	4	0	3	2	1	3	3	2	3	5			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr11:118635954G>T	ENST00000526070.2	-	6	969	c.609C>A	c.(607-609)acC>acA	p.T203T	DDX6_ENST00000264018.4_Silent_p.T203T|DDX6_ENST00000534980.1_Silent_p.T203T	NM_001257191.1	NP_001244120.1	P26196	DDX6_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 6	203	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cytoplasmic mRNA processing body assembly (GO:0033962)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)	13	all_hematologic(175;0.0839)	Renal(330;0.0183)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)|Hepatocellular(160;0.0893)|Breast(348;0.0979)|all_hematologic(192;0.103)		OV - Ovarian serous cystadenocarcinoma(223;3.39e-06)|BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Colorectal(284;0.0377)		CTCGTAAATTGGTTCCTCCTG	0.413			T	IGH@	B-NHL																																p.T203T		Atlas-SNP	.		Dom	yes		11	11q23.3	1656	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6		L	.	DDX6	64	.	0			c.C609A						PASS	.						351	341	344					11																	118635954		1896	4113	6009	SO:0001819	synonymous_variant	1656	exon6			TAAATTGGTTCCT	D17532	CCDS44751.1	11q23.3	2012-02-23	2012-02-23		ENSG00000110367	ENSG00000110367		"DEAD-boxes"	2747	protein-coding gene	gene with protein product		600326	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 6 (RNA helicase, 54kD)", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 6"	HLR2		1579499, 11839790	Standard	NM_004397		Approved	RCK	uc001pub.2	P26196	OTTHUMG00000166411	ENST00000526070.2:c.609C>A	chr11.hg19:g.118635954G>T		61.0	0.0	.		54.0	19.0	.	NM_004397	Q5D048	Silent	SNP	ENST00000526070.2	hg19	CCDS44751.1																																																																																			.	.	.	none		0.413	DDX6-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000389647.2	NM_004397		T	118635954	G	T	118635954	2	4	179	1	0	0	0	0	0	0	0	1	4379	1335	47	4		4	DDX6	11	118635954	Silent	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	662082	118635954	16370562	59	10487											
SLC6A12	6539	hgsc.bcm.edu	37	chr12	308000	308000	+	Missense_Mutation	SNP	T	T	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	ggaacaaatctggcttcaagTagtagatgatgccctggtag	12	10	12	7	0	2	2	1	1	1	1	2	3	2	3	1	3	2	4	1	3	6	4			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr12:308000T>G	ENST00000428720.1	-	8	1552	c.809A>C	c.(808-810)tAc>tCc	p.Y270S	SLC6A12_ENST00000536824.1_Missense_Mutation_p.Y270S|SLC6A12_ENST00000424061.2_Missense_Mutation_p.Y270S|SLC6A12_ENST00000359674.4_Missense_Mutation_p.Y270S|SLC6A12_ENST00000538272.1_5'UTR|SLC6A12_ENST00000397296.2_Missense_Mutation_p.Y270S	NM_001122848.2	NP_001116320.1	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 12	270					amino acid transport (GO:0006865)|cellular hyperosmotic response (GO:0071474)|cellular water homeostasis (GO:0009992)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|response to organic substance (GO:0010033)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)			TGGCTTCAAGTAGTAGATGAT	0.537																																					p.Y270S		Atlas-SNP	.											.	SLC6A12	60	.	0			c.A809C						PASS	.						148	123	132					12																	308000		2203	4300	6503	SO:0001583	missense	6539	exon8			TTCAAGTAGTAGA	L42300	CCDS8501.1	12p13	2013-07-19	2013-07-19		ENSG00000111181	ENSG00000111181		"Solute carriers"	11045	protein-coding gene	gene with protein product	"betaine/GABA transporter-1"	603080	"solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12"			7589472	Standard	NM_003044		Approved	BGT-1	uc009zdh.2	P48065	OTTHUMG00000090309	ENST00000428720.1:c.809A>C	chr12.hg19:g.308000T>G	ENSP00000388184:p.Tyr270Ser	225.0	0.0	.		221.0	125.0	.	NM_001122848	A0AV52|B2R992|D3DUN8	Missense_Mutation	SNP	ENST00000428720.1	hg19	CCDS8501.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.135276	0.77662	.	.	ENSG00000111181	ENST00000359674;ENST00000397296;ENST00000428720;ENST00000424061;ENST00000536824	T;T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07;-1.07	4.44	4.44	0.53790	.	0.000000	0.85682	D	0.000000	D	0.93154	0.7820	H	0.99464	4.58	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95722	0.8767	10	0.87932	D	0	.	14.0075	0.64473	0.0:0.0:0.0:1.0	.	270	P48065	S6A12_HUMAN	S	270	ENSP00000352702:Y270S;ENSP00000380464:Y270S;ENSP00000388184:Y270S;ENSP00000399136:Y270S;ENSP00000444268:Y270S	ENSP00000352702:Y270S	Y	-	2	0	SLC6A12	178261	1.000000	0.71417	0.994000	0.49952	0.740000	0.42216	7.796000	0.85898	1.762000	0.52044	0.533000	0.62120	TAC	.	.	.	none		0.537	SLC6A12-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206671.2	NM_003044		G	308000	T	G	308000	3	3	179	1	0	0	0	0	1	0	0	0	14688	1638	57	5	1071	5	SLC6A12	12	308000	Missense_Mutation	SNP	T	TCGA-G7-A8LB-01A-11D-A35Z-10		308000	133543895	60	10488											
DDX11	1663	hgsc.bcm.edu	37	chr12	31237572	31237572	+	Frame_Shift_Del	DEL	G	G	-																															cctgcagcagctgcagcacaGggtgcagctcaagtatgcag																										TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr12:31237572delG	ENST00000407793.2	+	4	700	c.449delG	c.(448-450)aggfs	p.R150fs	DDX11_ENST00000542838.1_Frame_Shift_Del_p.R150fs|DDX11_ENST00000350437.4_Frame_Shift_Del_p.R150fs|DDX11_ENST00000545668.1_Frame_Shift_Del_p.R150fs|DDX11_ENST00000251758.5_Frame_Shift_Del_p.R150fs|DDX11_ENST00000228264.6_Frame_Shift_Del_p.R124fs	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	150	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					CTGCAGCACAGGGTGCAGCTC	0.582										Multiple Myeloma(12;0.14)																											p.R150fs		Atlas-Indel,Pindel	.											.	DDX11	188	.	0			c.448delA						PASS	.						28	29	29					12																	31237572		2200	4271	6471	SO:0001589	frameshift_variant	1663	exon4			.	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"DEAD-boxes"	2736	protein-coding gene	gene with protein product	"CHL1-like helicase homolog (S. cerevisiae)"	601150	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)", "DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.449delG	chr12.hg19:g.31237572delG	ENSP00000384703:p.Arg150fs	355.0	0.0	0		340.0	85.0	0.25	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Frame_Shift_Del	DEL	ENST00000407793.2	hg19	CCDS44856.1																																																																																			.	.	.	none		0.582	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653		-	31237572	G	-	31237572	7	5	179	1	0	1	0	1	0	0	0	0	4345	1000	35	0	459	0	DDX11	12	31237572	Frame_Shift_Del	DEL	G	TCGA-G7-A8LB-01A-11D-A35Z-10	30929572	31237572	102614323	61	10489											
LRRK2	120892	hgsc.bcm.edu	37	chr12	40760813	40760813	+	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	tttgtttttgtaaaggaagcCttaaaaatgtcatgctggta	12	16	9	4	0	1	0	1	0	0	0	1	1	1	1	1	2	2	4	1	2	7	6			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr12:40760813C>A	ENST00000298910.7	+	50	7454	c.7396C>A	c.(7396-7398)Ctt>Att	p.L2466I		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	2466			L -> H (in PARK8). {ECO:0000269|PubMed:18213618}.		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)				TAAAGGAAGCCTTAAAAATGT	0.313																																					p.L2466I		Atlas-SNP	.											.	LRRK2	763	.	0			c.C7396A						PASS	.						63	66	65					12																	40760813		2203	4299	6502	SO:0001583	missense	120892	exon50			GGAAGCCTTAAAA	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.7396C>A	chr12.hg19:g.40760813C>A	ENSP00000298910:p.Leu2466Ile	336.0	0.0	.		454.0	152.0	.	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	hg19	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	C	8.406	0.843103	0.16963	.	.	ENSG00000188906	ENST00000298910	T	0.35605	1.3	5.42	5.42	0.78866	WD40 repeat-like-containing domain (1);	0.208934	0.43110	D	0.000601	T	0.28962	0.0719	L	0.45581	1.43	0.35294	D	0.782415	B;B	0.23185	0.081;0.081	B;B	0.17722	0.019;0.019	T	0.29027	-1.0025	10	0.19147	T	0.46	.	10.2613	0.43427	0.0:0.9098:0.0:0.0902	.	2466;2466	Q17RV3;Q5S007	.;LRRK2_HUMAN	I	2466	ENSP00000298910:L2466I	ENSP00000298910:L2466I	L	+	1	0	LRRK2	39047080	1.000000	0.71417	1.000000	0.80357	0.401000	0.30781	2.021000	0.41020	2.534000	0.85438	0.313000	0.20887	CTT	.	.	.	none		0.313	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		A	40760813	C	A	40760813	3	1	179	1	0	0	0	0	1	0	0	0	9040	681	24	4	7594	4	LRRK2	12	40760813	Missense_Mutation	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10	9523241	40760813	93091082	62	10490											
KCNH3	23416	hgsc.bcm.edu	37	chr12	49942954	49942955	+	Frame_Shift_Ins	INS	-	-	CGGTGAGCCC																															atctgcaccatgctcatcggINScggtgagcccggccgcgcgc																								rs369285416		TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr12:49942954_49942955insCGGTGAGCCC	ENST00000257981.6	+	8	1726_1727	c.1466_1467insCGGTGAGCCC	c.(1465-1470)ggcgccfs	p.A490fs		NM_012284.1	NP_036416.1	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 3	490					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36						ATGCTCATCGGCGGTGAGCCCG	0.688																																					p.G489fs		Atlas-Indel,Pindel	.											.	KCNH3	88	.	0			c.1466_1467insCGGTGAGCCC						PASS	.																																			SO:0001589	frameshift_variant	23416	exon8			.	AB022696	CCDS8786.1	12q13	2012-07-05				ENSG00000135519		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6252	protein-coding gene	gene with protein product		604527				10455180, 16382104	Standard	NM_012284		Approved	Kv12.2, BEC1, elk2	uc001ruh.1	Q9ULD8	OTTHUMG00000169517	Exception_encountered	chr12.hg19:g.49942955_49942964dupCGGTGAGCCC	ENSP00000257981:p.Ala490fs	68.0	0.0	0		61.0	10.0	0.163934	NM_012284	Q9UQ06	Frame_Shift_Ins	INS	ENST00000257981.6	hg19	CCDS8786.1																																																																																			.	.	.	none		0.688	KCNH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404571.2	NM_012284		CGGTGAGCCC	49942955	-	CGGTGAGCCC	49942954	7	5	179	1	0	1	1	0	0	0	0	0	8040	1203	42	0	1496	0	KCNH3	12	49942954	Frame_Shift_Ins	INS	-	TCGA-G7-A8LB-01A-11D-A35Z-10	9182141	49942954	83908941	63	10491											
LARP4	113251	hgsc.bcm.edu	37	chr12	50834282	50834282	+	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	tgataagctgtgagtttgcaCacaatagcaactggtatatc	13	12	9	7	0	0	2	0	2	0	0	1	2	0	2	0	1	4	5	0	1	6	5			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr12:50834282C>T	ENST00000398473.2	+	7	812	c.700C>T	c.(700-702)Cac>Tac	p.H234Y	LARP4_ENST00000429001.3_Missense_Mutation_p.H240Y|LARP4_ENST00000518561.1_Missense_Mutation_p.H164Y|LARP4_ENST00000522085.1_Missense_Mutation_p.H234Y|LARP4_ENST00000518444.1_Missense_Mutation_p.H233Y|LARP4_ENST00000347328.5_Missense_Mutation_p.H234Y|LARP4_ENST00000293618.8_Missense_Mutation_p.H234Y	NM_052879.4|NM_199188.2	NP_443111.4|NP_954658.2	Q71RC2	LARP4_HUMAN	La ribonucleoprotein domain family, member 4	234	RRM.				cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	23						TGAGTTTGCACACAATAGCAA	0.348																																					p.H234Y		Atlas-SNP	.											.	LARP4	58	.	0			c.C700T						PASS	.						99	88	91					12																	50834282		1863	4108	5971	SO:0001583	missense	113251	exon7			TTTGCACACAATA	AY004310	CCDS41782.1, CCDS44879.1, CCDS44880.1, CCDS44879.2, CCDS53789.1, CCDS53790.1	12q13.12	2005-08-09			ENSG00000161813	ENSG00000161813		"La ribonucleoprotein domain containing"	24320	protein-coding gene	gene with protein product						12477932	Standard	NM_052879		Approved	PP13296	uc001rwp.2	Q71RC2	OTTHUMG00000163724	ENST00000398473.2:c.700C>T	chr12.hg19:g.50834282C>T	ENSP00000381490:p.His234Tyr	453.0	0.0	.		653.0	404.0	.	NM_001170808	A8K6T1|E9PDG5|G3XAA8|G5E976|Q5CZ97|Q6ZV14|Q96NF9	Missense_Mutation	SNP	ENST00000398473.2	hg19	CCDS41782.1	.	.	.	.	.	.	.	.	.	.	C	12.43	1.935866	0.34189	.	.	ENSG00000161813	ENST00000293618;ENST00000429001;ENST00000398473;ENST00000441650;ENST00000522085;ENST00000398464;ENST00000518444;ENST00000518561;ENST00000520064;ENST00000347328	T;T;T;T;T;T;T	0.34275	1.37;1.37;1.37;1.37;1.37;1.37;1.37	5.23	5.23	0.72850	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.000000	0.85682	D	0.000000	T	0.45458	0.1343	N	0.25031	0.7	0.80722	D	1	D;B;D;P;D;D	0.89917	1.0;0.357;0.998;0.583;0.999;0.997	D;B;D;B;D;D	0.80764	0.99;0.155;0.994;0.233;0.968;0.947	T	0.18903	-1.0322	10	0.13853	T	0.58	.	19.1422	0.93450	0.0:1.0:0.0:0.0	.	135;233;234;234;234;240	Q71RC2-2;Q71RC2-3;G3XAA8;G5E976;Q71RC2;Q71RC2-4	.;.;.;.;LARP4_HUMAN;.	Y	234;240;234;164;234;234;233;164;135;234	ENSP00000293618:H234Y;ENSP00000415464:H240Y;ENSP00000381490:H234Y;ENSP00000429781:H234Y;ENSP00000429077:H233Y;ENSP00000430851:H164Y;ENSP00000340901:H234Y	ENSP00000293618:H234Y	H	+	1	0	LARP4	49120549	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.632000	0.83247	2.609000	0.88269	0.484000	0.47621	CAC	.	.	.	none		0.348	LARP4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374981.1	NM_052879		T	50834282	C	T	50834282	3	4	179	1	0	0	0	0	1	0	0	0	8637	478	17	2	726	2	LARP4	12	50834282	Missense_Mutation	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10	891328	50834282	83017613	64	10492											
C12orf66	144577	hgsc.bcm.edu	37	chr12	64615868	64615868	+	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	gccgccagcagcgacagccaGctgccccccgcgctcttgtt	5	6	11	19	4	1	0	0	0	1	0	1	1	1	0	6	0	5	4	6	0	0	2			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr12:64615868G>A	ENST00000398055.3	-	1	203	c.150C>T	c.(148-150)agC>agT	p.S50S	C12orf66_ENST00000311915.8_Silent_p.S50S|RPS11P6_ENST00000535684.1_RNA|C12orf66_ENST00000540673.1_5'UTR|C12orf66_ENST00000544871.1_Intron	NM_152440.4	NP_689653	Q96MD2	CL066_HUMAN	chromosome 12 open reading frame 66	50										central_nervous_system(1)|large_intestine(1)|lung(2)|ovary(1)	5						GCGACAGCCAGCTGCCCCCCG	0.617																																					p.S50S		Atlas-SNP	.											.	C12orf66	28	.	0			c.C150T						PASS	.						31	36	34					12																	64615868		1993	4166	6159	SO:0001819	synonymous_variant	144577	exon1			CAGCCAGCTGCCC		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.150C>T	chr12.hg19:g.64615868G>A		216.0	1.0	.		202.0	134.0	.	NM_152440	C9JX54|Q8IYA0	Silent	SNP	ENST00000398055.3	hg19	CCDS41803.1																																																																																			.	.	.	none		0.617	C12orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400921.1	NM_152440		A	64615868	G	A	64615868	2	1	179	1	0	0	0	0	0	0	0	1	1711	962	34	2		2	C12orf66	12	64615868	Silent	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	13781586	64615868	69236027	65	10493											
TRHDE	29953	hgsc.bcm.edu	37	chr12	73012751	73012751	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggattttcttccttggcatgCtgccagccgagctctttatc	5	15	9	12	1	2	0	0	0	2	0	4	2	3	1	3	2	4	3	3	2	1	6			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr12:73012751C>T	ENST00000261180.4	+	13	2363	c.2267C>T	c.(2266-2268)gCt>gTt	p.A756V		NM_013381.2	NP_037513.1	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	756					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						CCTTGGCATGCTGCCAGCCGA	0.353																																					p.A756V		Atlas-SNP	.											.	TRHDE	194	.	0			c.C2267T						PASS	.						53	57	56					12																	73012751		2201	4300	6501	SO:0001583	missense	29953	exon13			GGCATGCTGCCAG	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.2267C>T	chr12.hg19:g.73012751C>T	ENSP00000261180:p.Ala756Val	381.0	0.0	.		409.0	135.0	.	NM_013381	A5PL19|Q6UWJ4	Missense_Mutation	SNP	ENST00000261180.4	hg19	CCDS9004.1	.	.	.	.	.	.	.	.	.	.	C	35	5.481616	0.96307	.	.	ENSG00000072657	ENST00000261180	T	0.05649	3.41	5.77	5.77	0.91146	.	0.056300	0.64402	D	0.000001	T	0.09247	0.0228	L	0.35593	1.075	0.80722	D	1	B	0.30563	0.285	B	0.35073	0.195	T	0.28332	-1.0047	10	0.38643	T	0.18	.	20.3627	0.98863	0.0:1.0:0.0:0.0	.	756	Q9UKU6	TRHDE_HUMAN	V	756	ENSP00000261180:A756V	ENSP00000261180:A756V	A	+	2	0	TRHDE	71299018	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.160000	0.77495	2.885000	0.99019	0.655000	0.94253	GCT	.	.	.	none		0.353	TRHDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405380.1	NM_013381		T	73012751	C	T	73012751	3	4	179	1	0	0	0	0	1	0	0	0	16491	797	28	2	2317	2	TRHDE	12	73012751	Missense_Mutation	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10	8396883	73012751	60839144	66	10494											
APPL2	55198	hgsc.bcm.edu	37	chr12	105582149	105582149	+	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	tgtctcatcgcttcataaatCacttcagtagtgctgtctgt	8	16	7	10	1	5	0	4	0	2	0	7	0	5	0	0	0	1	3	0	0	3	4			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr12:105582149C>A	ENST00000258530.3	-	17	1761	c.1536G>T	c.(1534-1536)gtG>gtT	p.V512V	APPL2_ENST00000551662.1_Silent_p.V518V|APPL2_ENST00000539978.2_Silent_p.V469V	NM_001251904.1|NM_018171.3	NP_001238833.1|NP_060641.2	Q06481	APLP2_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 2	0					cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|midbrain development (GO:0030901)|neuromuscular process controlling balance (GO:0050885)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of protein binding (GO:0043393)|suckling behavior (GO:0001967)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						CTTCATAAATCACTTCAGTAG	0.423																																					p.V518V		Atlas-SNP	.											.	APPL2	69	.	0			c.G1554T						PASS	.						142	131	135					12																	105582149		2203	4300	6503	SO:0001819	synonymous_variant	55198	exon17			ATAAATCACTTCA	AY113704	CCDS9101.1, CCDS58275.1, CCDS58276.1	12q23.3	2014-08-12			ENSG00000136044	ENSG00000136044		"Pleckstrin homology (PH) domain containing"	18242	protein-coding gene	gene with protein product		606231				11431708, 17030088	Standard	NM_001251904		Approved	FLJ10659, DIP13B	uc010swu.1	Q8NEU8	OTTHUMG00000169853	ENST00000258530.3:c.1536G>T	chr12.hg19:g.105582149C>A		105.0	0.0	.		115.0	68.0	.	NM_001251904	B3KXX9|H7BXI4|Q13861|Q14594|Q14662|Q71U10|Q7M4L3|Q9BT36	Silent	SNP	ENST00000258530.3	hg19	CCDS9101.1																																																																																			.	.	.	none		0.423	APPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406238.3	NM_018171		A	105582149	C	A	105582149	2	1	179	1	0	0	0	0	0	0	0	1	818	813	29	4		4	APPL2	12	105582149	Silent	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10	32569398	105582149	28269746	67	10495											
C12orf51	283450	hgsc.bcm.edu	37	chr12	112620983	112620983	+	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	tgacatttccatcaattcatCttcaccatccaaacttgaca	13	13	2	13	0	4	2	3	2	1	0	6	2	6	2	3	0	1	0	3	0	2	4			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr12:112620983C>T	ENST00000430131.2	-	61	10746	c.9601G>A	c.(9601-9603)Gat>Aat	p.D3201N	HECTD4_ENST00000550722.1_Missense_Mutation_p.D3477N|HECTD4_ENST00000377560.5_Missense_Mutation_p.D3451N			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3201					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)										ATCAATTCATCTTCACCATCC	0.368																																					p.D3489N		Atlas-SNP	.											.	.	.	.	0			c.G10465A						PASS	.						181	176	178					12																	112620983		1837	4098	5935	SO:0001583	missense	283450	exon62			ATTCATCTTCACC	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.9601G>A	chr12.hg19:g.112620983C>T	ENSP00000404379:p.Asp3201Asn	130.0	0.0	.		137.0	55.0	.	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	C	27.9	4.870119	0.91587	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	T;T;T	0.51574	0.7;0.7;0.7	5.7	5.7	0.88788	.	.	.	.	.	T	0.33702	0.0872	N	0.14661	0.345	0.58432	D	0.999996	P	0.40970	0.734	B	0.34824	0.19	T	0.36359	-0.9751	9	0.87932	D	0	.	18.8233	0.92106	0.0:1.0:0.0:0.0	.	3201	Q9Y4D8	K0614_HUMAN	N	3451;3201;3477	ENSP00000366783:D3451N;ENSP00000404379:D3201N;ENSP00000449784:D3477N	ENSP00000366783:D3451N	D	-	1	0	C12orf51	111105366	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.994000	0.76251	2.687000	0.91594	0.655000	0.94253	GAT	.	.	.	none		0.368	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		T	112620983	C	T	112620983	3	4	179	1	0	0	0	0	1	0	0	0	1698	913	32	2	2449	2	C12orf51	12	112620983	Missense_Mutation	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10	7038834	112620983	21230912	68	10496											
TPCN1	53373	hgsc.bcm.edu	37	chr12	113704112	113704112	+	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	ggccctgctgctgctgctgcTctccctgtgcgaggcccccg	1	9	13	18	2	1	0	0	0	1	0	2	1	1	0	4	2	6	5	4	2	0	0			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr12:113704112T>A	ENST00000335509.6	+	4	679	c.365T>A	c.(364-366)cTc>cAc	p.L122H	TPCN1_ENST00000392569.4_Missense_Mutation_p.L54H|TPCN1_ENST00000541517.1_Missense_Mutation_p.L194H|TPCN1_ENST00000550785.1_Missense_Mutation_p.L194H	NM_017901.4	NP_060371.2	Q9ULQ1	TPC1_HUMAN	two pore segment channel 1	122					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						CTGCTGCTGCTCTCCCTGTGC	0.657																																					p.L194H		Atlas-SNP	.											.	TPCN1	109	.	0			c.T581A						PASS	.						201	208	206					12																	113704112		2203	4300	6503	SO:0001583	missense	53373	exon5			TGCTGCTCTCCCT	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.365T>A	chr12.hg19:g.113704112T>A	ENSP00000335300:p.Leu122His	43.0	0.0	.		45.0	11.0	.	NM_001143819	A7E258|Q86XS9|Q8NC20	Missense_Mutation	SNP	ENST00000335509.6	hg19	CCDS31908.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.823622	0.90873	.	.	ENSG00000186815	ENST00000552642;ENST00000552985;ENST00000335509;ENST00000552897;ENST00000550785;ENST00000541517;ENST00000392569;ENST00000552542;ENST00000548465	T;D;D;D;D	0.98602	-0.58;-4.88;-5.02;-5.02;-4.96	5.29	5.29	0.74685	.	0.000000	0.64402	D	0.000002	D	0.98801	0.9596	M	0.78456	2.415	0.58432	D	0.999996	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.997;1.0;1.0	D	0.99860	1.1082	10	0.87932	D	0	-27.5316	15.2318	0.73395	0.0:0.0:0.0:1.0	.	122;194;122	A5PKY2;Q9ULQ1-3;Q9ULQ1	.;.;TPC1_HUMAN	H	98;208;122;54;194;194;54;54;54	ENSP00000447569:L208H;ENSP00000335300:L122H;ENSP00000448083:L194H;ENSP00000438125:L194H;ENSP00000376350:L54H	ENSP00000335300:L122H	L	+	2	0	TPCN1	112188495	1.000000	0.71417	0.986000	0.45419	0.978000	0.69477	7.661000	0.83786	2.001000	0.58596	0.459000	0.35465	CTC	.	.	.	none		0.657	TPCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405156.3	NM_017901		A	113704112	T	A	113704112	3	1	179	1	0	0	0	0	1	0	0	0	16407	1551	54	5	595	5	TPCN1	12	113704112	Missense_Mutation	SNP	T	TCGA-G7-A8LB-01A-11D-A35Z-10	1083129	113704112	20147783	69	10497											
PIBF1	10464	hgsc.bcm.edu	37	chr13	73357620	73357620	+	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	taataaaaatgtctcgaaaaAtttcaaaggagtcaaaaaaa	23	9	5	4	1	3	0	2	0	1	0	4	2	3	1	0	1	0	0	0	1	10	3			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr13:73357620A>T	ENST00000326291.6	+	2	351	c.13A>T	c.(13-15)Att>Ttt	p.I5F	DIS3_ENST00000475871.1_5'Flank|DIS3_ENST00000545453.1_5'Flank|DIS3_ENST00000377767.4_5'Flank|DIS3_ENST00000377780.4_5'Flank	NM_006346.2	NP_006337.2	Q8WXW3	PIBF1_HUMAN	progesterone immunomodulatory binding factor 1	5						centrosome (GO:0005813)				breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24		Prostate(6;0.00191)|Breast(118;0.0736)|Acute lymphoblastic leukemia(28;0.0865)		GBM - Glioblastoma multiforme(99;0.000664)		GTCTCGAAAAATTTCAAAGGA	0.269																																					p.I5F		Atlas-SNP	.											.	PIBF1	65	.	0			c.A13T						PASS	.						44	49	47					13																	73357620		2203	4299	6502	SO:0001583	missense	10464	exon2			CGAAAAATTTCAA	AF330046	CCDS31991.1	13q21.33	2014-02-20	2007-10-17	2007-10-17	ENSG00000083535	ENSG00000083535			23352	protein-coding gene	gene with protein product	"progesterone-induced blocking factor 1"	607532	"chromosome 13 open reading frame 24"	C13orf24		11935316	Standard	NM_006346		Approved	CEP90	uc001vjc.3	Q8WXW3	OTTHUMG00000017071	ENST00000326291.6:c.13A>T	chr13.hg19:g.73357620A>T	ENSP00000317144:p.Ile5Phe	216.0	0.0	.		150.0	65.0	.	NM_006346	O95664|Q6U9V2|Q6UG50|Q86V07|Q96SF4	Missense_Mutation	SNP	ENST00000326291.6	hg19	CCDS31991.1	.	.	.	.	.	.	.	.	.	.	A	13.79	2.341787	0.41498	.	.	ENSG00000083535	ENST00000326291;ENST00000538949	T	0.24350	1.86	5.19	-2.11	0.07187	.	1.080480	0.06937	N	0.812077	T	0.17746	0.0426	L	0.44542	1.39	0.21697	N	0.999583	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.37454	-0.9705	10	0.48119	T	0.1	-1.1276	1.6908	0.02852	0.3442:0.242:0.2958:0.118	.	5;5	Q8WXW3;Q4G0R1	PIBF1_HUMAN;.	F	5	ENSP00000317144:I5F	ENSP00000317144:I5F	I	+	1	0	PIBF1	72255621	0.389000	0.25205	0.588000	0.28705	0.994000	0.84299	0.370000	0.20433	0.015000	0.14971	0.397000	0.26171	ATT	.	.	.	none		0.269	PIBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045255.1	NM_006346		T	73357620	A	T	73357620	3	4	179	1	0	0	0	0	1	0	0	0	11886	101	4	5	15	5	PIBF1	13	73357620	Missense_Mutation	SNP	A	TCGA-G7-A8LB-01A-11D-A35Z-10		73357620	41812258	70	10498											
SALL2	6297	hgsc.bcm.edu	37	chr14	21991632	21991632	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggggaaactccctgcccCggagactgtagattgctcgg	7	8	14	12	2	0	2	0	0	0	2	2	4	1	3	3	4	3	2	3	4	2	2			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr14:21991632C>T	ENST00000327430.3	-	2	2524	c.2230G>A	c.(2230-2232)Ggg>Agg	p.G744R	SALL2_ENST00000317492.5_Intron|SALL2_ENST00000450879.2_Missense_Mutation_p.G607R|AE000658.22_ENST00000535893.1_RNA|SALL2_ENST00000538754.1_Intron	NM_005407.1	NP_005398.1	Q9Y467	SALL2_HUMAN	spalt-like transcription factor 2	744					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(6)|urinary_tract(2)	43	all_cancers(95;0.000662)			GBM - Glioblastoma multiforme(265;0.0151)		CTCCCTGCCCCGGAGACTGTA	0.602																																					p.G744R		Atlas-SNP	.											.	SALL2	95	.	0			c.G2230A						PASS	.						55	48	51					14																	21991632		2203	4300	6503	SO:0001583	missense	6297	exon2			CTGCCCCGGAGAC	AB002358	CCDS32045.1	14q11.1-q12.1	2013-10-17	2013-10-17		ENSG00000165821	ENSG00000165821		"Zinc fingers, C2H2-type"	10526	protein-coding gene	gene with protein product		602219	"sal (Drosophila)-like 2", "sal-like 2 (Drosophila)"			8975705	Standard	XM_005267983		Approved	KIAA0360, Hsal2, ZNF795	uc001wbe.3	Q9Y467	OTTHUMG00000168826	ENST00000327430.3:c.2230G>A	chr14.hg19:g.21991632C>T	ENSP00000333537:p.Gly744Arg	61.0	0.0	.		38.0	15.0	.	NM_005407	B2RMX6|B9EGK8|Q8N656|Q9Y4G1	Missense_Mutation	SNP	ENST00000327430.3	hg19	CCDS32045.1	.	.	.	.	.	.	.	.	.	.	C	13.30	2.194957	0.38806	.	.	ENSG00000165821	ENST00000327430;ENST00000450879	T;T	0.04049	3.77;3.72	4.76	4.76	0.60689	.	0.204155	0.24504	N	0.037952	T	0.03651	0.0104	N	0.24115	0.695	0.20307	N	0.999917	B;B;B;B	0.28470	0.213;0.213;0.127;0.127	B;B;B;B	0.17433	0.012;0.018;0.012;0.012	T	0.35325	-0.9793	10	0.59425	D	0.04	-7.6456	8.8209	0.35025	0.0:0.8999:0.0:0.1001	.	607;607;505;744	B4DK65;E7EW59;B4DFD9;Q9Y467	.;.;.;SALL2_HUMAN	R	744;607	ENSP00000333537:G744R;ENSP00000396773:G607R	ENSP00000333537:G744R	G	-	1	0	SALL2	21061472	0.000000	0.05858	0.100000	0.21137	0.130000	0.20726	1.004000	0.29822	2.468000	0.83385	0.563000	0.77884	GGG	.	.	.	none		0.602	SALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401242.1	NM_005407		T	21991632	C	T	21991632	3	4	179	1	0	0	0	0	1	0	0	0	13824	652	23	1	797	1	SALL2	14	21991632	Missense_Mutation	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10		21991632	85357908	71	10499											
PSMB11	122706	hgsc.bcm.edu	37	chr14	23511771	23511771	+	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	gggtattacagcgggagctgCggcttcgggaactgagggag	8	7	19	7	3	0	1	0	1	0	0	1	4	0	4	0	5	5	3	0	5	3	3	rs376450654		TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr14:23511771C>T	ENST00000408907.2	+	1	396	c.337C>T	c.(337-339)Cgg>Tgg	p.R113W		NM_001099780.1	NP_001093250.1	A5LHX3	PSB11_HUMAN	proteasome (prosome, macropain) subunit, beta type, 11	113					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			endometrium(1)|kidney(2)|lung(4)	7	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00643)		GCGGGAGCTGCGGCTTCGGGA	0.597																																					p.R113W		Atlas-SNP	.											.	PSMB11	40	.	0			c.C337T						PASS	.	C	TRP/ARG	0,4212		0,0,2106	64	70	68		337	3.4	1	14		68	1,8443		0,1,4221	no	missense	PSMB11	NM_001099780.1	101	0,1,6327	TT,TC,CC		0.0118,0.0,0.0079	probably-damaging	113/301	23511771	1,12655	2106	4222	6328	SO:0001583	missense	122706	exon1			GAGCTGCGGCTTC		CCDS41923.1	14q11.2	2008-01-31				ENSG00000222028			31963	protein-coding gene	gene with protein product		611137				17540904	Standard	NM_001099780		Approved	beta5t	uc010ake.1	A5LHX3		ENST00000408907.2:c.337C>T	chr14.hg19:g.23511771C>T	ENSP00000386212:p.Arg113Trp	56.0	0.0	.		39.0	14.0	.	NM_001099780		Missense_Mutation	SNP	ENST00000408907.2	hg19	CCDS41923.1	.	.	.	.	.	.	.	.	.	.	C	17.84	3.487586	0.64074	0.0	1.18E-4	ENSG00000222028	ENST00000408907	T	0.36340	1.26	5.24	3.36	0.38483	.	0.000000	0.85682	D	0.000000	T	0.67059	0.2853	M	0.92367	3.3	0.42052	D	0.99112	D	0.89917	1.0	D	0.87578	0.998	T	0.74791	-0.3545	10	0.87932	D	0	0.0206	13.1646	0.59562	0.2911:0.7089:0.0:0.0	.	113	A5LHX3	PSB11_HUMAN	W	113	ENSP00000386212:R113W	ENSP00000386212:R113W	R	+	1	2	PSMB11	22581611	0.100000	0.21855	0.999000	0.59377	0.850000	0.48378	0.220000	0.17660	0.553000	0.29044	0.563000	0.77884	CGG	.	.	.	weak		0.597	PSMB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408294.1	NM_001099780		T	23511771	C	T	23511771	3	4	179	1	0	0	0	0	1	0	0	0	12686	759	27	1	339	1	PSMB11	14	23511771	Missense_Mutation	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10	1520139	23511771	83837769	72	10500											
MAP1A	4130	hgsc.bcm.edu	37	chr15	43818609	43818609	+	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	tactggagggggcaggatgtGgtccaggagtggcaagaaac	11	6	18	6	0	0	1	0	0	0	1	1	4	1	4	1	7	2	2	1	7	3	1			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr15:43818609G>T	ENST00000300231.5	+	4	5388	c.4938G>T	c.(4936-4938)gtG>gtT	p.V1646V	MAP1A_ENST00000399453.1_Silent_p.V1646V|MAP1A_ENST00000382031.1_Silent_p.V1884V			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1646					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)	GGCAGGATGTGGTCCAGGAGT	0.582																																					p.V1646V		Atlas-SNP	.											.	MAP1A	189	.	0			c.G4938T						PASS	.						45	59	54					15																	43818609		1974	4146	6120	SO:0001819	synonymous_variant	4130	exon4			GGATGTGGTCCAG	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.4938G>T	chr15.hg19:g.43818609G>T		124.0	0.0	.		73.0	4.0	.	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Silent	SNP	ENST00000300231.5	hg19	CCDS42031.1																																																																																			.	.	.	none		0.582	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373		T	43818609	G	T	43818609	2	4	179	1	0	0	0	0	0	0	0	1	9234	1335	47	4		4	MAP1A	15	43818609	Silent	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10		43818609	58712783	73	10501											
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1259111	1259111	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgctccagctggagcagccTgggccgtgcccccagcctca	5	5	13	18	2	1	0	1	0	0	0	2	1	2	1	6	2	5	3	6	2	0	0			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr16:1259111T>C	ENST00000348261.5	+	17	3691	c.3443T>C	c.(3442-3444)cTg>cCg	p.L1148P	CACNA1H_ENST00000358590.4_Missense_Mutation_p.L1148P|RP11-616M22.3_ENST00000564700.1_RNA|CACNA1H_ENST00000565831.1_Missense_Mutation_p.L1148P	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1148					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)	TGGAGCAGCCTGGGCCGTGCC	0.726																																					p.L1148P		Atlas-SNP	.											.	CACNA1H	317	.	0			c.T3443C						PASS	.						4	5	5					16																	1259111		1754	3783	5537	SO:0001583	missense	8912	exon17			GCAGCCTGGGCCG	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.3443T>C	chr16.hg19:g.1259111T>C	ENSP00000334198:p.Leu1148Pro	904.0	1.0	.		837.0	286.0	.	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	hg19	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	T	18.95	3.732137	0.69189	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.88586	-2.4;-2.4	3.9	3.9	0.45041	.	0.585053	0.15998	N	0.234441	D	0.93913	0.8052	M	0.80616	2.505	0.58432	D	0.999999	D;D	0.89917	1.0;0.999	D;D	0.80764	0.994;0.981	D	0.93697	0.7012	10	0.87932	D	0	.	11.9149	0.52759	0.0:0.0:0.0:1.0	.	1148;1148	O95180-2;O95180	.;CAC1H_HUMAN	P	1148	ENSP00000334198:L1148P;ENSP00000351401:L1148P	ENSP00000334198:L1148P	L	+	2	0	CACNA1H	1199112	1.000000	0.71417	1.000000	0.80357	0.627000	0.37826	7.552000	0.82192	1.399000	0.46721	0.402000	0.26972	CTG	.	.	.	none		0.726	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		C	1259111	T	C	1259111	3	2	179	1	0	0	0	0	1	0	0	0	2547	1580	55	3	3505	3	CACNA1H	16	1259111	Missense_Mutation	SNP	T	TCGA-G7-A8LB-01A-11D-A35Z-10		1259111	89095642	74	10502											
CCDC64B	146439	hgsc.bcm.edu	37	chr16	3080512	3080512	+	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	ctcctcgtgggtggtctgcaGtctgccctcacccttctcca	3	12	9	17	1	4	0	1	0	3	0	7	0	5	0	4	2	2	1	4	2	0	1			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr16:3080512G>C	ENST00000572449.1	-	5	762	c.700C>G	c.(700-702)Ctg>Gtg	p.L234V	CCDC64B_ENST00000389347.4_Missense_Mutation_p.L234V|CCDC64B_ENST00000573514.1_Missense_Mutation_p.L27V|RP11-473M20.5_ENST00000382225.3_RNA			A1A5D9	BICR2_HUMAN	coiled-coil domain containing 64B	234										breast(1)|endometrium(2)|large_intestine(1)	4						GTGGTCTGCAGTCTGCCCTCA	0.672																																					p.L234V		Atlas-SNP	.											.	CCDC64B	19	.	0			c.C700G						PASS	.						28	32	31					16																	3080512		2073	4210	6283	SO:0001583	missense	146439	exon4			TCTGCAGTCTGCC	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.700C>G	chr16.hg19:g.3080512G>C	ENSP00000459043:p.Leu234Val	27.0	0.0	.		26.0	16.0	.	NM_001103175	Q658L9	Missense_Mutation	SNP	ENST00000572449.1	hg19	CCDS45393.1	.	.	.	.	.	.	.	.	.	.	G	0.241	-1.013631	0.02095	.	.	ENSG00000162069	ENST00000389347	T	0.33865	1.39	5.15	4.17	0.49024	.	0.191847	0.34386	N	0.004017	T	0.12433	0.0302	N	0.01048	-1.04	0.09310	N	0.999994	B	0.22541	0.071	B	0.23716	0.048	T	0.16600	-1.0397	10	0.10902	T	0.67	-15.3767	12.8777	0.57999	0.0:0.2062:0.7938:0.0	.	234	A1A5D9	BICR2_HUMAN	V	234	ENSP00000373998:L234V	ENSP00000373998:L234V	L	-	1	2	CCDC64B	3020513	0.541000	0.26417	0.878000	0.34440	0.080000	0.17528	2.133000	0.42093	2.420000	0.82092	0.491000	0.48974	CTG	.	.	.	none		0.672	CCDC64B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436991.1			C	3080512	G	C	3080512	3	2	179	1	0	0	0	0	1	0	0	0	2838	1020	36	4	850	4	CCDC64B	16	3080512	Missense_Mutation	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	1821401	3080512	87274241	75	10503											
TMEM186	25880	hgsc.bcm.edu	37	chr16	8889985	8889985	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatcacatctgccatgggacAgtatgtgtcctgccgccagc	9	9	10	13	1	2	0	1	0	1	0	3	1	3	1	4	1	3	1	4	1	2	1			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr16:8889985A>G	ENST00000333050.6	-	2	499	c.466T>C	c.(466-468)Tgt>Cgt	p.C156R	PMM2_ENST00000268261.4_5'Flank|PMM2_ENST00000539622.1_5'Flank|TMEM186_ENST00000564869.1_Intron|PMM2_ENST00000537352.1_5'Flank|PMM2_ENST00000569958.1_5'Flank|PMM2_ENST00000566983.1_Intron	NM_015421.3	NP_056236.2	Q96B77	TM186_HUMAN	transmembrane protein 186	156						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	9						GCCATGGGACAGTATGTGTCC	0.542																																					p.C156R		Atlas-SNP	.											.	TMEM186	21	.	0			c.T466C						PASS	.						113	102	106					16																	8889985		2197	4300	6497	SO:0001583	missense	25880	exon2			TGGGACAGTATGT	BC015912	CCDS10535.1	16p13.2	2008-02-05	2007-02-08	2007-02-08	ENSG00000184857	ENSG00000184857			24530	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 51"	C16orf51		11230166	Standard	NM_015421		Approved	DKFZP564K2062	uc002cze.3	Q96B77	OTTHUMG00000129696	ENST00000333050.6:c.466T>C	chr16.hg19:g.8889985A>G	ENSP00000331640:p.Cys156Arg	80.0	0.0	.		86.0	53.0	.	NM_015421	B2RAY0|Q9Y4T4	Missense_Mutation	SNP	ENST00000333050.6	hg19	CCDS10535.1	.	.	.	.	.	.	.	.	.	.	A	9.941	1.217610	0.22373	.	.	ENSG00000184857	ENST00000333050	T	0.41065	1.01	5.28	4.18	0.49190	.	0.000000	0.49916	D	0.000123	T	0.52661	0.1748	L	0.57536	1.79	0.28050	N	0.933414	D	0.69078	0.997	D	0.65010	0.931	T	0.50189	-0.8857	10	0.72032	D	0.01	-17.9481	5.5333	0.16997	0.7659:0.0:0.0825:0.1516	.	156	Q96B77	TM186_HUMAN	R	156	ENSP00000331640:C156R	ENSP00000331640:C156R	C	-	1	0	TMEM186	8797486	1.000000	0.71417	0.061000	0.19648	0.343000	0.28985	2.999000	0.49473	0.850000	0.35239	0.402000	0.26972	TGT	.	.	.	none		0.542	TMEM186-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251903.1	NM_015421		G	8889985	A	G	8889985	3	3	179	1	0	0	0	0	1	0	0	0	16120	188	7	3	179	3	TMEM186	16	8889985	Missense_Mutation	SNP	A	TCGA-G7-A8LB-01A-11D-A35Z-10	5809473	8889985	81464768	76	10504											
UQCRC2	7385	hgsc.bcm.edu	37	chr16	21991981	21991981	+	Frame_Shift_Del	DEL	T	T	-																															catgccaccatccacagtccTtcagcagattgattcagtgg																										TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr16:21991981delT	ENST00000268379.4	+	13	2002	c.1238delT	c.(1237-1239)cttfs	p.L413fs	UQCRC2_ENST00000561553.1_Intron	NM_003366.2	NP_003357.2	P22695	QCR2_HUMAN	ubiquinol-cytochrome c reductase core protein II	413					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(4)|prostate(1)|skin(1)	15				GBM - Glioblastoma multiforme(48;0.0264)		TCCACAGTCCTTCAGCAGATT	0.408																																					p.L413fs	Colon(123;450 1645 12841 25393 45623)	Atlas-Indel,Pindel	.											.	UQCRC2	46	.	0			c.1237delC						PASS	.						144	136	139					16																	21991981		2198	4300	6498	SO:0001589	frameshift_variant	7385	exon13			.	J04973	CCDS10601.1	16p12	2011-07-04			ENSG00000140740	ENSG00000140740	1.10.2.2	"Mitochondrial respiratory chain complex / Complex III"	12586	protein-coding gene	gene with protein product		191329				8288258, 2547763	Standard	NM_003366		Approved	QCR2, UQCR2	uc002djx.3	P22695	OTTHUMG00000131585	ENST00000268379.4:c.1238delT	chr16.hg19:g.21991981delT	ENSP00000268379:p.Leu413fs	73.0	0.0	0		79.0	20.0	0.253165	NM_003366	B3KSN4|Q9BQ05	Frame_Shift_Del	DEL	ENST00000268379.4	hg19	CCDS10601.1																																																																																			.	.	.	none		0.408	UQCRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254466.1	NM_003366		-	21991981	T	-	21991981	7	5	179	1	0	1	0	1	0	0	0	0	17032	1609	56	0	1288	0	UQCRC2	16	21991981	Frame_Shift_Del	DEL	T	TCGA-G7-A8LB-01A-11D-A35Z-10	13101996	21991981	68362772	77	10505											
PALB2	79728	hgsc.bcm.edu	37	chr16	23646629	23646629	+	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	ggcaattggacatgcttcgtGttgttctaacataatattct	10	16	8	7	1	2	0	0	0	2	0	3	1	2	1	0	2	2	4	0	2	4	8			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr16:23646629G>C	ENST00000261584.4	-	4	1390	c.1238C>G	c.(1237-1239)aCa>aGa	p.T413R		NM_024675.3	NP_078951.2	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2	413	ChAM (Chromatin-association motif); required for chromatin association, mediates nucleosome association.|DNA-binding (with the preference D loop > dsDNA > ssDNA).				DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|inner cell mass cell proliferation (GO:0001833)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|post-anal tail morphogenesis (GO:0036342)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(3)	55				GBM - Glioblastoma multiforme(48;0.0167)		CATGCTTCGTGTTGTTCTAAC	0.413			"F, N, Mis"			"Wilms tumor, medulloblastoma, AML ,breast"		Involved in tolerance or repair of DNA crosslinks																													p.T413R		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.C1238G						PASS	.						80	83	82					16																	23646629		2197	4300	6497	SO:0001583	missense	79728	exon4			CTTCGTGTTGTTC		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.1238C>G	chr16.hg19:g.23646629G>C	ENSP00000261584:p.Thr413Arg	91.0	0.0	.		80.0	28.0	.	NM_024675	A6NIE1|Q8N7Y6|Q8ND31|Q9H6W1	Missense_Mutation	SNP	ENST00000261584.4	hg19	CCDS32406.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.376583	0.82682	.	.	ENSG00000083093	ENST00000261584	T	0.40756	1.02	5.67	5.67	0.87782	.	0.000000	0.64402	D	0.000003	T	0.65450	0.2692	M	0.72118	2.19	0.41484	D	0.988183	D	0.89917	1.0	D	0.97110	1.0	T	0.66937	-0.5797	10	0.72032	D	0.01	-18.1358	17.6312	0.88108	0.0:0.0:1.0:0.0	.	413	Q86YC2	PALB2_HUMAN	R	413	ENSP00000261584:T413R	ENSP00000261584:T413R	T	-	2	0	PALB2	23554130	1.000000	0.71417	0.991000	0.47740	0.957000	0.61999	6.967000	0.76079	2.836000	0.97738	0.655000	0.94253	ACA	.	.	.	none		0.413	PALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435287.2	NM_024675		C	23646629	G	C	23646629	3	2	179	1	0	0	0	0	1	0	0	0	11413	1377	48	4	2362	4	PALB2	16	23646629	Missense_Mutation	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	1654648	23646629	66708124	78	10506											
IL21R	50615	hgsc.bcm.edu	37	chr16	27448951	27448954	+	Frame_Shift_Del	DEL	ACAG	ACAG	-																															acattttcagtgtcaacatcAcagaccagtctggcaactac																										TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	ACAG	ACAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr16:27448951_27448954delACAG	ENST00000337929.3	+	4	768_771	c.295_298delACAG	c.(295-300)acagacfs	p.TD99fs	IL21R_ENST00000395754.4_Frame_Shift_Del_p.TD99fs|IL21R_ENST00000564089.1_Frame_Shift_Del_p.TD99fs|IL21R_ENST00000395755.1_Frame_Shift_Del_p.TD99fs	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	99	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)			breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						TGTCAACATCACAGACCAGTCTGG	0.559			T	BCL6	NHL																																p.120_121del		Atlas-Indel,Pindel	.		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	.	IL21R	95	.	0			c.360_363del						PASS	.																																			SO:0001589	frameshift_variant	50615	exon5			.	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.295_298delACAG	chr16.hg19:g.27448951_27448954delACAG	ENSP00000338010:p.Thr99fs	108.0	0.0	0		98.0	51.0	0.520408	NM_181079	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Frame_Shift_Del	DEL	ENST00000337929.3	hg19	CCDS10630.1																																																																																			.	.	.	none		0.559	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078		-	27448954	ACAG	-	27448951	7	5	179	1	0	1	0	1	0	0	0	0	7678	159	6	0	305	0	IL21R	16	27448951	Frame_Shift_Del	DEL	ACAG	TCGA-G7-A8LB-01A-11D-A35Z-10	3802322	27448951	62905802	79	10507											
PDPR	55066	hgsc.bcm.edu	37	chr16	70190776	70190776	+	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	gagctgagtgacttacatggGaagtgatgccaccagggcag	11	7	15	8	0	0	3	0	3	0	0	0	5	0	4	2	2	3	2	2	2	2	1			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr16:70190776G>C	ENST00000288050.4	+	19	3591	c.2634G>C	c.(2632-2634)ggG>ggC	p.G878G	RP11-296I10.3_ENST00000502126.1_RNA|RP11-296I10.3_ENST00000566989.1_RNA|PDPR_ENST00000568530.1_Silent_p.G878G|PDPR_ENST00000567046.1_Silent_p.G236G|PDPR_ENST00000398122.3_Silent_p.G778G|PDPR_ENST00000542659.1_Silent_p.G223G	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	878					cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		ACTTACATGGGAAGTGATGCC	0.582																																					p.G878G		Atlas-SNP	.											.	PDPR	66	.	0			c.G2634C						PASS	.						40	48	46					16																	70190776		2122	4228	6350	SO:0001819	synonymous_variant	55066	exon19			ACATGGGAAGTGA		CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857			30264	protein-coding gene	gene with protein product						9395502	Standard	NM_017990		Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.2634G>C	chr16.hg19:g.70190776G>C		66.0	0.0	.		93.0	36.0	.	NM_017990	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Silent	SNP	ENST00000288050.4	hg19	CCDS45520.1																																																																																			.	.	.	none		0.582	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1	NM_017990		C	70190776	G	C	70190776	2	2	179	1	0	0	0	0	0	0	0	1	11696	1161	41	4		4	PDPR	16	70190776	Silent	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	42741825	70190776	20163977	80	10508											
ATMIN	23300	hgsc.bcm.edu	37	chr16	81077147	81077147	+	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	cacttaatgcccttgtcagtAggaaccctgatcctcggcct	8	11	8	14	1	1	1	1	1	0	0	3	2	2	2	4	2	2	1	4	2	3	3			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr16:81077147A>T	ENST00000299575.4	+	4	1068	c.1044A>T	c.(1042-1044)gtA>gtT	p.V348V	ATMIN_ENST00000566488.1_Silent_p.V192V|ATMIN_ENST00000564241.1_Silent_p.V192V|ATMIN_ENST00000539819.1_3'UTR	NM_015251.2	NP_056066.2	O43313	ATMIN_HUMAN	ATM interactor	348	Required for formation of RAD51 foci.				cellular response to DNA damage stimulus (GO:0006974)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dynein binding (GO:0045502)|metal ion binding (GO:0046872)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	20						CCTTGTCAGTAGGAACCCTGA	0.512																																					p.V348V		Atlas-SNP	.											.	ATMIN	50	.	0			c.A1044T						PASS	.						52	52	52					16																	81077147		2202	4299	6501	SO:0001819	synonymous_variant	23300	exon4			GTCAGTAGGAACC	BC002701	CCDS32494.1, CCDS73917.1	16q23.2	2013-01-07			ENSG00000166454	ENSG00000166454		"Zinc fingers, C2H2-type"	29034	protein-coding gene	gene with protein product	"ATM/ATR-Substrate Chk2-Interacting Zn++-finger protein", "ATM INteracting protein"	614693				15933716, 17525732, 19001856	Standard	XM_005255866		Approved	ASCIZ, KIAA0431, ZNF822	uc002ffz.1	O43313	OTTHUMG00000176469	ENST00000299575.4:c.1044A>T	chr16.hg19:g.81077147A>T		82.0	0.0	.		120.0	42.0	.	NM_015251	A8K4H8|Q68DC9	Silent	SNP	ENST00000299575.4	hg19	CCDS32494.1																																																																																			.	.	.	none		0.512	ATMIN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432140.1	NM_015251		T	81077147	A	T	81077147	2	4	179	1	0	0	0	0	0	0	0	1	1110	407	15	5		5	ATMIN	16	81077147	Silent	SNP	A	TCGA-G7-A8LB-01A-11D-A35Z-10	10886371	81077147	9277606	81	10509											
ANKRD11	29123	hgsc.bcm.edu	37	chr16	89371696	89371696	+	Frame_Shift_Del	DEL	C	C	-																															gctcgctccctcacctccttCccgccatcgccacgctccag																										TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr16:89371696delC	ENST00000301030.4	-	4	604	c.144delG	c.(142-144)gggfs	p.G48fs	ANKRD11_ENST00000378330.2_Frame_Shift_Del_p.G48fs|ANKRD11_ENST00000567736.1_5'UTR|ANKRD11_ENST00000563291.1_Frame_Shift_Del_p.G48fs	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	48					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)		TCACCTCCTTCCCGCCATCGC	0.567																																					p.K49fs		Atlas-Indel,Pindel	.											.	ANKRD11	195	.	0			c.145delA						PASS	.						67	65	66					16																	89371696		2198	4300	6498	SO:0001589	frameshift_variant	29123	exon5			.	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.144delG	chr16.hg19:g.89371696delC	ENSP00000301030:p.Gly48fs	77.0	0.0	0		80.0	24.0	0.3	NM_001256182	Q6NTG1|Q6QMF8	Frame_Shift_Del	DEL	ENST00000301030.4	hg19	CCDS32513.1																																																																																			.	.	.	none		0.567	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		-	89371696	C	-	89371696	7	5	179	1	0	1	0	1	0	0	0	0	639	842	30	0	7887	0	ANKRD11	16	89371696	Frame_Shift_Del	DEL	C	TCGA-G7-A8LB-01A-11D-A35Z-10	8294549	89371696	983057	82	10510											
TRPV3	162514	hgsc.bcm.edu	37	chr17	3446887	3446887	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgcgcttcttcagccgcctcTttttcctcctctgctcttcc	1	17	5	18	2	5	0	1	0	4	0	8	0	8	0	5	0	3	2	5	0	0	5	rs372555157		TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr17:3446887T>C	ENST00000576742.1	-	5	668	c.347A>G	c.(346-348)aAg>aGg	p.K116R	TRPV3_ENST00000572519.1_Missense_Mutation_p.K116R|TRPV3_ENST00000301365.4_Missense_Mutation_p.K116R	NM_001258205.1|NM_145068.3	NP_001245134.1|NP_659505.1	Q8NET8	TRPV3_HUMAN	transient receptor potential cation channel, subfamily V, member 3	116					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|negative regulation of hair cycle (GO:0042636)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium channel activity (GO:0005262)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(12)|ovary(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	35					Menthol(DB00825)	CAGCCGCCTCTTTTTCCTCCT	0.552																																					p.K116R		Atlas-SNP	.											.	TRPV3	85	.	0			c.A347G						PASS	.						114	110	111					17																	3446887		2203	4300	6503	SO:0001583	missense	162514	exon5			CGCCTCTTTTTCC	AF514998	CCDS11029.1, CCDS58500.1	17p13.3	2013-01-10			ENSG00000167723	ENSG00000167723		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	18084	protein-coding gene	gene with protein product		607066				12016205, 12077606, 16382100	Standard	NM_001258205		Approved	VRL3	uc002fvr.3	Q8NET8	OTTHUMG00000090695	ENST00000576742.1:c.347A>G	chr17.hg19:g.3446887T>C	ENSP00000461518:p.Lys116Arg	70.0	0.0	.		75.0	50.0	.	NM_001258205	Q8NDW7|Q8NET9|Q8NFH2	Missense_Mutation	SNP	ENST00000576742.1	hg19	CCDS11029.1	.	.	.	.	.	.	.	.	.	.	T	8.300	0.819676	0.16607	.	.	ENSG00000167723	ENST00000381913;ENST00000301365;ENST00000430263	D	0.87334	-2.24	5.12	4.02	0.46733	.	0.077629	0.51477	D	0.000083	T	0.74268	0.3694	N	0.20986	0.625	0.22266	N	0.99924	B;B;B;B;B;B;B	0.06786	0.001;0.001;0.001;0.001;0.0;0.0;0.0	B;B;B;B;B;B;B	0.06405	0.001;0.002;0.002;0.002;0.001;0.001;0.001	T	0.55835	-0.8078	10	0.18276	T	0.48	-9.2531	6.5943	0.22664	0.0:0.1588:0.0:0.8412	.	100;100;116;100;116;116;116	E7EV24;B7ZKP9;Q2M3L1;B7ZKP6;Q8NET8-3;Q8NET8;Q8NET8-2	.;.;.;.;.;TRPV3_HUMAN;.	R	116;116;100	ENSP00000301365:K116R	ENSP00000301365:K116R	K	-	2	0	TRPV3	3393637	0.967000	0.33354	0.975000	0.42487	0.080000	0.17528	0.927000	0.28818	2.060000	0.61445	0.459000	0.35465	AAG	.	.	.	alt		0.552	TRPV3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207379.2	NM_145068		C	3446887	T	C	3446887	3	2	179	1	0	0	0	0	1	0	0	0	16609	1609	56	3	2081	3	TRPV3	17	3446887	Missense_Mutation	SNP	T	TCGA-G7-A8LB-01A-11D-A35Z-10		3446887	77748323	83	10511											
RAI1	10743	hgsc.bcm.edu	37	chr17	17697105	17697105	+	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	agctatgaccagcagcagcaGcagcagcagcagcagcagca	14	2	12	13	0	0	1	0	1	0	0	0	1	0	1	1	0	11	11	1	0	1	1	rs398124422|rs587780431		TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr17:17697105G>A	ENST00000353383.1	+	3	1312	c.843G>A	c.(841-843)caG>caA	p.Q281Q	RAI1_ENST00000261641.6_Silent_p.Q281Q	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	281	Gln-rich.|Poly-Gln.				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)		agcagcagcagcagcagcagc	0.632																																					p.Q281Q		Atlas-SNP	.											.	RAI1	121	.	0			c.G843A						PASS	.						20	25	24					17																	17697105		2020	4001	6021	SO:0001819	synonymous_variant	10743	exon3			GCAGCAGCAGCAG	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.843G>A	chr17.hg19:g.17697105G>A		73.0	0.0	.		87.0	4.0	.	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Silent	SNP	ENST00000353383.1	hg19	CCDS11188.1																																																																																			.	.	.	none		0.632	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665		A	17697105	G	A	17697105	2	1	179	1	0	0	0	0	0	0	0	1	13020	962	34	2		2	RAI1	17	17697105	Silent	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	14250218	17697105	63498105	84	10512											
DHX8	1659	hgsc.bcm.edu	37	chr17	41576230	41576230	+	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	tcttttggggggacttttagAtgaggaccttgagattgaat	9	15	13	4	0	1	4	0	3	1	2	1	7	1	6	1	4	0	0	1	4	2	6			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr17:41576230A>T	ENST00000262415.3	+	10	1373	c.1301A>T	c.(1300-1302)gAt>gTt	p.D434V	DHX8_ENST00000540306.1_Splice_Site_p.D434V	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	434					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)		GGACTTTTAGATGAGGACCTT	0.383																																					p.D434V	NSCLC(56;1548 1661 49258 49987)	Atlas-SNP	.											.	DHX8	98	.	0			c.A1301T						PASS	.						61	59	60					17																	41576230		2203	4300	6503	SO:0001630	splice_region_variant	1659	exon10			TTTTAGATGAGGA	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.1301-1A>T	chr17.hg19:g.41576230A>T		65.0	0.0	.		58.0	12.0	.	NM_004941		Missense_Mutation	SNP	ENST00000262415.3	hg19	CCDS11464.1	.	.	.	.	.	.	.	.	.	.	A	17.48	3.399319	0.62177	.	.	ENSG00000067596	ENST00000540306;ENST00000262415	T;T	0.03607	3.87;3.88	5.19	5.19	0.71726	.	0.050805	0.85682	D	0.000000	T	0.05593	0.0147	L	0.46741	1.465	0.80722	D	1	B;B	0.27140	0.169;0.114	B;B	0.32211	0.142;0.035	T	0.44221	-0.9342	9	.	.	.	.	13.9181	0.63914	1.0:0.0:0.0:0.0	.	434;434	F5H658;Q14562	.;DHX8_HUMAN	V	434	ENSP00000437886:D434V;ENSP00000262415:D434V	.	D	+	2	0	DHX8	38931756	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.937000	0.92936	1.962000	0.57031	0.459000	0.35465	GAT	.	.	.	none		0.383	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453485.1		Missense_Mutation	T	41576230	A	T	41576230	5	4	179	1	0	0	0	0	0	0	1	0	4517	347	12	5	1339	5	DHX8	17	41576230	Splice_Site	SNP	A	TCGA-G7-A8LB-01A-11D-A35Z-10	23879125	41576230	39618980	85	10513											
ADAM11	4185	hgsc.bcm.edu	37	chr17	42855411	42855411	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcccacgtccccacccaCgggggagacggagagatata	10	4	12	15	3	0	2	0	0	0	2	1	5	1	3	5	3	1	0	5	3	2	2	rs149116155		TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr17:42855411C>T	ENST00000200557.6	+	24	2331	c.2162C>T	c.(2161-2163)aCg>aTg	p.T721M	ADAM11_ENST00000535346.1_Missense_Mutation_p.T521M	NM_002390.4	NP_002381.2	O75078	ADA11_HUMAN	ADAM metallopeptidase domain 11	721					integrin-mediated signaling pathway (GO:0007229)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(15)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Prostate(33;0.0959)				TCCCCACCCACGGGGGAGACG	0.592																																					p.T721M		Atlas-SNP	.											.	ADAM11	118	.	0			c.C2162T						PASS	.	C	MET/THR	0,4406		0,0,2203	80	83	82		2162	4.9	1	17	dbSNP_134	82	1,8599	1.2+/-3.3	0,1,4299	no	missense	ADAM11	NM_002390.4	81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	721/770	42855411	1,13005	2203	4300	6503	SO:0001583	missense	4185	exon24			CACCCACGGGGGA	D17390	CCDS11486.1	17q21.3	2014-08-12	2005-08-18		ENSG00000073670			"ADAM metallopeptidase domain containing"	189	protein-coding gene	gene with protein product	"metalloproteinase-like, disintegrin-like, cysteine-rich protein"	155120	"a disintegrin and metalloproteinase domain 11"	MDC		8252040	Standard	XM_005257373		Approved		uc002ihh.3	O75078	OTTHUMG00000179038	ENST00000200557.6:c.2162C>T	chr17.hg19:g.42855411C>T	ENSP00000200557:p.Thr721Met	79.0	0.0	.		62.0	13.0	.	NM_002390	Q14808|Q14809|Q14810	Missense_Mutation	SNP	ENST00000200557.6	hg19	CCDS11486.1	.	.	.	.	.	.	.	.	.	.	C	15.88	2.964645	0.53507	0.0	1.16E-4	ENSG00000073670	ENST00000200557;ENST00000535346	T;T	0.02177	4.41;4.79	4.93	4.93	0.64822	.	0.182174	0.45126	D	0.000384	T	0.05640	0.0148	L	0.55990	1.75	0.48452	D	0.999652	P;D	0.60160	0.88;0.987	B;P	0.48227	0.357;0.571	T	0.28170	-1.0052	10	0.66056	D	0.02	.	16.9062	0.86128	0.0:1.0:0.0:0.0	.	521;721	B4DKD2;O75078	.;ADA11_HUMAN	M	721;521	ENSP00000200557:T721M;ENSP00000443773:T521M	ENSP00000200557:T721M	T	+	2	0	ADAM11	40210937	0.108000	0.22018	0.976000	0.42696	0.742000	0.42306	2.312000	0.43726	2.279000	0.76181	0.561000	0.74099	ACG	.	C|1.000;T|0.000	0.000	weak		0.592	ADAM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444531.1	NM_002390		T	42855411	C	T	42855411	3	4	179	1	0	0	0	0	1	0	0	0	235	536	19	1	2256	1	ADAM11	17	42855411	Missense_Mutation	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10	1279181	42855411	38339799	86	10514											
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43519695	43519695	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctcacatactgtgcccaaTggtcacttacataaccaaga	13	9	7	12	0	2	1	2	0	0	1	2	1	2	1	2	2	4	1	2	2	5	3			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr18:43519695T>C	ENST00000282041.5	-	10	2004	c.1970A>G	c.(1969-1971)cAt>cGt	p.H657R		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	657					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						CTGTGCCCAATGGTCACTTAC	0.403																																					p.H657R		Atlas-SNP	.											.	EPG5	199	.	0			c.A1970G						PASS	.						85	77	80					18																	43519695		1901	4121	6022	SO:0001583	missense	57724	exon10			GCCCAATGGTCAC	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.1970A>G	chr18.hg19:g.43519695T>C	ENSP00000282041:p.His657Arg	128.0	0.0	.		133.0	51.0	.	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	hg19	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	T	15.32	2.799468	0.50208	.	.	ENSG00000152223	ENST00000282041	T	0.11063	2.81	5.4	5.4	0.78164	.	0.430004	0.26832	N	0.022265	T	0.29716	0.0742	L	0.56769	1.78	0.53688	D	0.999979	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.00849	-1.1541	10	0.44086	T	0.13	-15.6279	15.423	0.75028	0.0:0.0:0.0:1.0	.	657;657	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	R	657	ENSP00000282041:H657R	ENSP00000282041:H657R	H	-	2	0	EPG5	41773693	1.000000	0.71417	0.998000	0.56505	0.049000	0.14656	7.318000	0.79029	2.037000	0.60232	0.379000	0.24179	CAT	.	.	.	none		0.403	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		C	43519695	T	C	43519695	3	2	179	1	0	0	0	0	1	0	0	0	8256	1464	51	3	5909	3	KIAA1632	18	43519695	Missense_Mutation	SNP	T	TCGA-G7-A8LB-01A-11D-A35Z-10		43519695	34557553	87	10515											
CDH19	28513	hgsc.bcm.edu	37	chr18	64235858	64235858	+	Missense_Mutation	SNP	T	T	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	atggcatatatgtcacctgtTctttcatcaatgataaaagt	13	15	6	7	0	4	1	3	1	1	0	4	1	4	1	1	1	0	2	1	1	5	5			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr18:64235858T>G	ENST00000540086.1	-	3	531	c.285A>C	c.(283-285)agA>agC	p.R95S	CDH19_ENST00000262150.2_Missense_Mutation_p.R95S	NM_001271028.1	NP_001257957.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	196	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)				TGTCACCTGTTCTTTCATCAA	0.428																																					p.R95S		Atlas-SNP	.											.	CDH19	141	.	0			c.A285C						PASS	.						116	112	114					18																	64235858		2203	4299	6502	SO:0001583	missense	28513	exon3			ACCTGTTCTTTCA	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.285A>C	chr18.hg19:g.64235858T>G	ENSP00000439593:p.Arg95Ser	66.0	0.0	.		104.0	69.0	.	NM_021153	O15098	Missense_Mutation	SNP	ENST00000540086.1	hg19	CCDS59325.1	.	.	.	.	.	.	.	.	.	.	T	11.37	1.618194	0.28801	.	.	ENSG00000071991	ENST00000262150;ENST00000540086;ENST00000454642	T;T	0.50277	0.75;0.75	5.87	-0.598	0.11649	Cadherin (5);Cadherin-like (1);	0.944409	0.09075	N	0.852351	T	0.22859	0.0552	N	0.16833	0.445	0.09310	N	1	B;B	0.22909	0.077;0.056	B;B	0.24394	0.019;0.053	T	0.23797	-1.0178	10	0.07990	T	0.79	.	1.9256	0.03316	0.127:0.3108:0.1313:0.4309	.	95;95	F5H1K0;Q9H159	.;CAD19_HUMAN	S	95;95;40	ENSP00000262150:R95S;ENSP00000439593:R95S	ENSP00000262150:R95S	R	-	3	2	CDH19	62386838	0.000000	0.05858	0.089000	0.20774	0.978000	0.69477	-2.192000	0.01245	-0.084000	0.12595	0.482000	0.46254	AGA	.	.	.	none		0.428	CDH19-005	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000442285.1	NM_021153		G	64235858	T	G	64235858	3	3	179	1	0	0	0	0	1	0	0	0	3106	1780	62	5	2073	5	CDH19	18	64235858	Missense_Mutation	SNP	T	TCGA-G7-A8LB-01A-11D-A35Z-10	20716163	64235858	13841390	88	10516											
ZNF236	7776	hgsc.bcm.edu	37	chr18	74617340	74617340	+	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	aaaaaacatttaagacttcaCtaaattgcaaaaagcacatg	21	9	4	7	0	1	1	1	0	0	1	1	1	1	1	0	0	3	2	0	0	8	5			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr18:74617340C>A	ENST00000253159.8	+	13	2458	c.2260C>A	c.(2260-2262)Cta>Ata	p.L754I	ZNF236_ENST00000320610.9_Missense_Mutation_p.L756I	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	754					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)		TAAGACTTCACTAAATTGCAA	0.423																																					p.L754I		Atlas-SNP	.											.	ZNF236	325	.	0			c.C2260A						PASS	.						57	54	55					18																	74617340		1827	4079	5906	SO:0001583	missense	7776	exon13			ACTTCACTAAATT	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.2260C>A	chr18.hg19:g.74617340C>A	ENSP00000253159:p.Leu754Ile	109.0	0.0	.		113.0	35.0	.	NM_007345	B2RTX9|Q9UL37	Missense_Mutation	SNP	ENST00000253159.8	hg19	CCDS42447.1	.	.	.	.	.	.	.	.	.	.	C	15.57	2.872028	0.51695	.	.	ENSG00000130856	ENST00000253159;ENST00000543926;ENST00000320610	T;T	0.07567	3.18;3.18	5.39	4.28	0.50868	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.084389	0.49916	D	0.000138	T	0.09113	0.0225	M	0.65975	2.015	0.20873	N	0.999835	P	0.44090	0.826	B	0.39152	0.292	T	0.25710	-1.0124	10	0.30854	T	0.27	.	6.6764	0.23095	0.0:0.7144:0.0:0.2856	.	754	Q9UL36	ZN236_HUMAN	I	754	ENSP00000253159:L754I;ENSP00000444524:L754I	ENSP00000253159:L754I	L	+	1	2	ZNF236	72746328	0.872000	0.30054	0.123000	0.21794	0.891000	0.51852	1.866000	0.39489	2.687000	0.91594	0.462000	0.41574	CTA	.	.	.	none		0.423	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1			A	74617340	C	A	74617340	3	1	179	1	0	0	0	0	1	0	0	0	17801	564	20	4	2310	4	ZNF236	18	74617340	Missense_Mutation	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10	10381482	74617340	3459908	89	10517											
CLEC4G	339390	hgsc.bcm.edu	37	chr19	7794389	7794389	+	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	gggctctccctggttccagtGgctacaggggggttgagtgg	4	10	18	9	0	1	1	0	1	1	0	3	1	2	1	2	7	1	4	2	7	1	3			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr19:7794389G>A	ENST00000328853.5	-	9	813	c.745C>T	c.(745-747)Cac>Tac	p.H249Y	CLEC4G_ENST00000598081.1_5'Flank	NM_001244856.1|NM_198492.3	NP_001231785.1|NP_940894.1	Q6UXB4	CLC4G_HUMAN	C-type lectin domain family 4, member G	249	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|cervix(2)|endometrium(1)|large_intestine(1)|lung(1)	6						TGGTTCCAGTGGCTACAGGGG	0.592																																					p.H249Y	Esophageal Squamous(146;540 1807 3349 19438 30853)	Atlas-SNP	.											.	CLEC4G	18	.	0			c.C745T						PASS	.						44	41	42					19																	7794389		2203	4300	6503	SO:0001630	splice_region_variant	339390	exon9			TCCAGTGGCTACA	AY358431	CCDS12185.1	19p13.2	2010-04-27	2008-11-04			ENSG00000182566		"C-type lectin domain containing"	24591	protein-coding gene	gene with protein product			"C-type lectin superfamily 4, member G"			12975309	Standard	NM_198492		Approved	UNQ431, LSECtin	uc002mhp.4	Q6UXB4		ENST00000328853.5:c.744-1C>T	chr19.hg19:g.7794389G>A		58.0	0.0	.		31.0	14.0	.	NM_198492		Missense_Mutation	SNP	ENST00000328853.5	hg19	CCDS12185.1	.	.	.	.	.	.	.	.	.	.	G	2.885	-0.230863	0.05983	.	.	ENSG00000182566	ENST00000328853;ENST00000381308	T	0.16324	2.35	5.46	-1.35	0.09114	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.887861	0.09337	N	0.816099	T	0.05090	0.0136	N	0.03177	-0.4	0.30480	N	0.772422	B	0.15141	0.012	B	0.16722	0.016	T	0.46803	-0.9165	10	0.07990	T	0.79	.	2.7461	0.05268	0.326:0.0:0.3351:0.3389	.	249	Q6UXB4	CLC4G_HUMAN	Y	249;133	ENSP00000327599:H249Y	ENSP00000327599:H249Y	H	-	1	0	CLEC4G	7700389	0.996000	0.38824	1.000000	0.80357	0.184000	0.23303	0.063000	0.14410	0.262000	0.21774	-0.181000	0.13052	CAC	.	.	.	none		0.592	CLEC4G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461989.1	NM_198492	Missense_Mutation	A	7794389	G	A	7794389	5	1	179	1	0	0	0	0	0	0	1	0	3519	1362	47	2	140	2	CLEC4G	19	7794389	Splice_Site	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10		7794389	51334594	90	10518											
MUC16	94025	hgsc.bcm.edu	37	chr19	8969402	8969403	+	Frame_Shift_Ins	INS	-	-	G																															gggtgctggagctgcttgttINSggttgataaactgatgactc																										TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr19:8969402_8969403insG	ENST00000397910.4	-	79	43144_43145	c.42941_42942insC	c.(42940-42942)ccafs	p.P14314fs	MUC16_ENST00000380951.5_Frame_Shift_Ins_p.P955fs	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	14409	SEA 15. {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						AGCTGCTTGTTGGTTGATAAAC	0.421																																					p.P14314fs		Atlas-Indel,Pindel	.											.	MUC16	4315	.	0			c.42942_42943insC						PASS	.																																			SO:0001589	frameshift_variant	94025	exon79			.	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.42942dupC	chr19.hg19:g.8969404_8969404dupG	ENSP00000381008:p.Pro14314fs	73.0	0.0	0		48.0	22.0	0.458333	NM_024690	Q6ZQW5|Q96RK2	Frame_Shift_Ins	INS	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.	.	none		0.421	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	8969403	-	G	8969402	7	5	179	1	0	1	1	0	0	0	0	0	9980	1799	63	0	605	0	MUC16	19	8969402	Frame_Shift_Ins	INS	-	TCGA-G7-A8LB-01A-11D-A35Z-10	1175013	8969402	50159581	91	10519											
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11123641	11123641	+	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	gcagatcaaaggtttggagtGgctggtgtccctgtacaaca	10	10	13	8	0	1	1	1	0	0	1	2	2	2	2	1	4	2	4	1	4	3	2			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr19:11123641G>C	ENST00000429416.3	+	17	2572	c.2291G>C	c.(2290-2292)tGg>tCg	p.W764S	RN7SL192P_ENST00000584303.1_RNA|SMARCA4_ENST00000444061.3_Missense_Mutation_p.W764S|SMARCA4_ENST00000589677.1_Missense_Mutation_p.W764S|SMARCA4_ENST00000590574.1_Missense_Mutation_p.W764S|SMARCA4_ENST00000541122.2_Missense_Mutation_p.W764S|SMARCA4_ENST00000358026.2_Missense_Mutation_p.W764S|CTC-215O4.4_ENST00000587831.1_RNA|SMARCA4_ENST00000413806.3_Missense_Mutation_p.W764S|SMARCA4_ENST00000450717.3_Missense_Mutation_p.W764S|SMARCA4_ENST00000344626.4_Missense_Mutation_p.W764S	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	764					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)				GGTTTGGAGTGGCTGGTGTCC	0.592			"F, N, Mis"		NSCLC																																p.W764S		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.G2291C						PASS	.						110	90	97					19																	11123641		2203	4300	6503	SO:0001583	missense	6597	exon16			TGGAGTGGCTGGT	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.2291G>C	chr19.hg19:g.11123641G>C	ENSP00000395654:p.Trp764Ser	142.0	0.0	.		83.0	34.0	.	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.452323	0.84209	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.95447	-3.71;-3.71;-3.71;-3.71;-3.71;-3.71;-3.71	4.73	4.73	0.59995	DEAD-like helicase (1);SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.98918	0.9633	H	0.99650	4.68	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.98997	1.0810	10	0.87932	D	0	-19.8408	16.6409	0.85098	0.0:0.0:1.0:0.0	.	764;764;764;764;764;764;764	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;A7E2E1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	S	764;764;828;764;764;764;764;764	ENSP00000395654:W764S;ENSP00000350720:W764S;ENSP00000343896:W764S;ENSP00000445036:W764S;ENSP00000392837:W764S;ENSP00000397783:W764S;ENSP00000414727:W764S	ENSP00000343896:W764S	W	+	2	0	SMARCA4	10984641	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.657000	0.98554	2.456000	0.83038	0.655000	0.94253	TGG	.	.	.	none		0.592	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		C	11123641	G	C	11123641	3	2	179	1	0	0	0	0	1	0	0	0	14783	1357	47	4	2349	4	SMARCA4	19	11123641	Missense_Mutation	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	2154239	11123641	48005342	92	10520											
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11141507	11141507	+	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	gcacccgggctggggggctcGgcctgaacctccagtcggca	5	5	16	15	3	0	1	0	1	0	0	3	1	1	1	4	6	1	4	4	6	1	0			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr19:11141507G>C	ENST00000429416.3	+	26	3765	c.3484G>C	c.(3484-3486)Ggc>Cgc	p.G1162R	SMARCA4_ENST00000444061.3_Missense_Mutation_p.G1162R|SMARCA4_ENST00000589677.1_Missense_Mutation_p.G1162R|SMARCA4_ENST00000590574.1_Missense_Mutation_p.G1162R|SMARCA4_ENST00000541122.2_Missense_Mutation_p.G1162R|SMARCA4_ENST00000358026.2_Missense_Mutation_p.G1162R|SMARCA4_ENST00000413806.3_Missense_Mutation_p.G1162R|SMARCA4_ENST00000450717.3_Missense_Mutation_p.G1162R|SMARCA4_ENST00000344626.4_Missense_Mutation_p.G1162R	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1162	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				TGGGGGGCTCGGCCTGAACCT	0.607			"F, N, Mis"		NSCLC																																p.G1162R		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,right_upper_lobe,carcinoma,0,2	SMARCA4	502	.	1	Unknown(1)	lung(1)	c.G3484C						PASS	.						24	25	25					19																	11141507		2197	4297	6494	SO:0001583	missense	6597	exon25			GGGCTCGGCCTGA	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.3484G>C	chr19.hg19:g.11141507G>C	ENSP00000395654:p.Gly1162Arg	83.0	0.0	.		46.0	18.0	.	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.744411	0.89663	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.97598	-4.45;-4.45;-4.45;-4.45;-4.45;-4.45;-4.45	4.59	4.59	0.56863	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.99381	0.9782	H	0.99982	5.21	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.97655	1.0157	10	0.87932	D	0	-37.1265	16.3247	0.82975	0.0:0.0:1.0:0.0	.	1162;1162;1162;1162;1162;382;1162;1162	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;A7E2E1;P51532	.;.;.;.;.;.;.;SMCA4_HUMAN	R	1162;1162;1226;1162;1162;1162;1162;1162	ENSP00000395654:G1162R;ENSP00000350720:G1162R;ENSP00000343896:G1162R;ENSP00000445036:G1162R;ENSP00000392837:G1162R;ENSP00000397783:G1162R;ENSP00000414727:G1162R	ENSP00000343896:G1162R	G	+	1	0	SMARCA4	11002507	1.000000	0.71417	0.957000	0.39632	0.994000	0.84299	9.356000	0.97091	2.389000	0.81357	0.563000	0.77884	GGC	.	.	.	none		0.607	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		C	11141507	G	C	11141507	3	2	179	1	0	0	0	0	1	0	0	0	14783	1116	39	4	3578	4	SMARCA4	19	11141507	Missense_Mutation	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	17866	11141507	47987476	93	10521											
LPPR2	64748	hgsc.bcm.edu	37	chr19	11470232	11470232	+	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	tgctgctgggcattgtgatcCtgcttgcttaccgcctggag	4	13	13	11	1	0	1	0	1	0	0	1	2	1	2	3	2	5	5	3	2	1	3			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr19:11470232C>A	ENST00000251473.5	+	4	467	c.91C>A	c.(91-93)Ctg>Atg	p.L31M	DKFZP761J1410_ENST00000591608.1_Intron|DKFZP761J1410_ENST00000586431.1_3'UTR	NM_001170635.1|NM_022737.2	NP_001164106.1|NP_073574.2																					CATTGTGATCCTGCTTGCTTA	0.612																																					p.L31M		Atlas-SNP	.											.	LPPR2	21	.	0			c.C91A						PASS	.						114	84	94					19																	11470232		2203	4300	6503	SO:0001583	missense	0	exon4			GTGATCCTGCTTG																												ENST00000251473.5:c.91C>A	chr19.hg19:g.11470232C>A	ENSP00000251473:p.Leu31Met	78.0	0.0	.		67.0	37.0	.	NM_022737		Missense_Mutation	SNP	ENST00000251473.5	hg19	CCDS12258.1	.	.	.	.	.	.	.	.	.	.	c	10.93	1.489114	0.26686	.	.	ENSG00000105520	ENST00000251473	T	0.42900	0.96	5.27	4.23	0.50019	.	0.088420	0.47455	D	0.000231	T	0.26521	0.0648	L	0.38838	1.175	0.80722	D	1	B	0.33379	0.41	B	0.25614	0.062	T	0.06534	-1.0821	10	0.27785	T	0.31	.	6.9598	0.24591	0.1712:0.7402:0.0:0.0886	.	31	Q96GM1	LPPR2_HUMAN	M	31	ENSP00000251473:L31M	ENSP00000251473:L31M	L	+	1	2	AC024575.1	11331232	1.000000	0.71417	1.000000	0.80357	0.729000	0.41735	1.458000	0.35223	1.229000	0.43630	0.443000	0.29094	CTG	.	.	.	none		0.612	DKFZP761J1410-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458779.1			A	11470232	C	A	11470232	3	1	179	1	0	0	0	0	1	0	0	0	8932	680	24	4	97	4	LPPR2	19	11470232	Missense_Mutation	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10	328725	11470232	47658751	94	10522											
UNC13A	23025	hgsc.bcm.edu	37	chr19	17759377	17759377	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtaggtgggcgtggtggccGtccacacttcgaagttgtgt	6	11	16	8	3	0	0	0	0	0	0	2	1	1	0	2	4	0	2	2	4	2	3			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr19:17759377G>A	ENST00000519716.2	-	16	1678	c.1679C>T	c.(1678-1680)aCg>aTg	p.T560M	UNC13A_ENST00000252773.7_Missense_Mutation_p.T560M|UNC13A_ENST00000550896.1_Missense_Mutation_p.T558M|UNC13A_ENST00000428389.2_Missense_Mutation_p.T648M|UNC13A_ENST00000551649.1_Missense_Mutation_p.T560M|UNC13A_ENST00000552293.1_Missense_Mutation_p.T560M	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	560					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						CGTGGTGGCCGTCCACACTTC	0.612																																					p.T560M		Atlas-SNP	.											.	UNC13A	299	.	0			c.C1679T						PASS	.						118	135	129					19																	17759377		2194	4299	6493	SO:0001583	missense	23025	exon15			GTGGCCGTCCACA	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.1679C>T	chr19.hg19:g.17759377G>A	ENSP00000429562:p.Thr560Met	77.0	0.0	.		61.0	31.0	.	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	hg19	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	g	22.5	4.301507	0.81136	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	D;D;D;D;D;D	0.93488	-3.23;-3.23;-3.23;-3.23;-3.23;-3.23	4.35	3.31	0.37934	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);	0.000000	0.85682	U	0.000000	D	0.96259	0.8780	M	0.85859	2.78	0.45621	D	0.998556	D	0.89917	1.0	D	0.76071	0.987	D	0.95845	0.8869	10	0.87932	D	0	-20.4176	10.261	0.43427	0.1017:0.0:0.8983:0.0	.	560	Q9UPW8	UN13A_HUMAN	M	560;648;560;560;560;558	ENSP00000429562:T560M;ENSP00000400409:T648M;ENSP00000252773:T560M;ENSP00000447236:T560M;ENSP00000447572:T560M;ENSP00000446831:T558M	ENSP00000252773:T560M	T	-	2	0	UNC13A	17620377	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.567000	0.98161	0.941000	0.37499	0.486000	0.48141	ACG	.	.	.	none		0.612	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		A	17759377	G	A	17759377	3	1	179	1	0	0	0	0	1	0	0	0	16996	1145	40	1	3544	1	UNC13A	19	17759377	Missense_Mutation	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	6289145	17759377	41369606	95	10523											
RINL	126432	hgsc.bcm.edu	37	chr19	39360598	39360598	+	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	cttaccttggttctcgcctcGagccaggcccgcatagacat	7	10	9	15	3	1	1	0	0	1	1	3	2	1	1	4	2	2	2	4	2	2	4			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr19:39360598G>T	ENST00000591812.1	-	9	1413	c.1327C>A	c.(1327-1329)Cga>Aga	p.R443R	RINL_ENST00000598904.1_Silent_p.R329R|CTC-360G5.6_ENST00000593830.1_RNA|RINL_ENST00000602238.1_5'Flank|RINL_ENST00000340740.3_Silent_p.R329R			Q6ZS11	RINL_HUMAN	Ras and Rab interactor-like	443	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)	actin cytoskeleton (GO:0015629)|cytoplasmic vesicle (GO:0031410)|ruffle (GO:0001726)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(3)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)|urinary_tract(2)	17						TTCTCGCCTCGAGCCAGGCCC	0.657											OREG0025454	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R443R		Atlas-SNP	.											.	RINL	32	.	0			c.C1327A						PASS	.																																			SO:0001819	synonymous_variant	126432	exon9			CGCCTCGAGCCAG	AK127808	CCDS12522.1, CCDS59386.1	19q13.2	2010-07-13			ENSG00000187994	ENSG00000187994			24795	protein-coding gene	gene with protein product							Standard	NM_001195833		Approved	FLJ45909	uc010xuo.2	Q6ZS11		ENST00000591812.1:c.1327C>A	chr19.hg19:g.39360598G>T		62.0	0.0	.	885	53.0	19.0	.	NM_001195833	B4DPG5	Silent	SNP	ENST00000591812.1	hg19	CCDS59386.1																																																																																			.	.	.	none		0.657	RINL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460433.1	NM_198445		T	39360598	G	T	39360598	2	4	179	1	0	0	0	0	0	0	0	1	13388	1066	37	4		4	RINL	19	39360598	Silent	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	21601221	39360598	19768385	96	10524											
LILRB5	10990	hgsc.bcm.edu	37	chr19	54758645	54758645	+	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	tagggctggacagcaggtagGggtaggacctgattgcgctg	8	8	18	7	1	0	1	0	1	0	0	0	3	0	3	1	6	2	5	1	6	3	4			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr19:54758645G>T	ENST00000316219.5	-	6	1315	c.1208C>A	c.(1207-1209)cCc>cAc	p.P403H	LILRB5_ENST00000345866.6_Missense_Mutation_p.P303H|LILRB5_ENST00000449561.2_Missense_Mutation_p.P403H|LILRB5_ENST00000450632.1_Missense_Mutation_p.P394H	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	403	Ig-like C2-type 4.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CAGCAGGTAGGGGTAGGACCT	0.582																																					p.P403H		Atlas-SNP	.											.	LILRB5	176	.	0			c.C1208A						PASS	.						128	104	112					19																	54758645		2203	4300	6503	SO:0001583	missense	10990	exon6			AGGTAGGGGTAGG	AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"Leukocyte immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.1208C>A	chr19.hg19:g.54758645G>T	ENSP00000320390:p.Pro403His	131.0	0.0	.		92.0	4.0	.	NM_001081442	Q8N760	Missense_Mutation	SNP	ENST00000316219.5	hg19	CCDS12885.1	.	.	.	.	.	.	.	.	.	.	G	11.78	1.741826	0.30865	.	.	ENSG00000105609	ENST00000316219;ENST00000450632;ENST00000449561;ENST00000345866	T;T;T;T	0.00940	5.52;5.52;5.52;5.52	2.54	0.34	0.15985	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.000000	0.32671	N	0.005791	T	0.05547	0.0146	M	0.93898	3.47	0.09310	N	1	B;D;D;D;D	0.89917	0.33;1.0;1.0;1.0;1.0	B;D;D;D;D	0.85130	0.145;0.996;0.997;0.995;0.992	T	0.13045	-1.0524	10	0.87932	D	0	.	4.5013	0.11865	0.337:0.0:0.663:0.0	.	394;294;303;403;403	C9JMK7;Q8NF80;O75023-2;O75023-3;O75023	.;.;.;.;LIRB5_HUMAN	H	403;394;403;303	ENSP00000320390:P403H;ENSP00000414225:P394H;ENSP00000406478:P403H;ENSP00000263430:P303H	ENSP00000320390:P403H	P	-	2	0	LILRB5	59450457	0.103000	0.21917	0.011000	0.14972	0.001000	0.01503	1.890000	0.39728	0.163000	0.19507	-0.242000	0.12053	CCC	.	.	.	none		0.582	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2			T	54758645	G	T	54758645	3	4	179	1	0	0	0	0	1	0	0	0	8801	1232	43	4	599	4	LILRB5	19	54758645	Missense_Mutation	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	15398047	54758645	4370338	97	10525											
TMX4	56255	hgsc.bcm.edu	37	chr20	8000101	8000101	+	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	tcacaatttcagcatccactCgccctccatcaccagcgtcc	9	9	4	19	2	3	0	3	0	0	0	7	0	6	0	5	0	2	1	5	0	1	1			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr20:8000101C>A	ENST00000246024.2	-	1	375	c.160G>T	c.(160-162)Gag>Tag	p.E54*	RP5-971N18.3_ENST00000457707.1_RNA|RP5-971N18.3_ENST00000607924.1_RNA	NM_021156.2	NP_066979.2	Q9H1E5	TMX4_HUMAN	thioredoxin-related transmembrane protein 4	54	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						AGCATCCACTCGCCCTCCATC	0.741																																					p.E54X		Atlas-SNP	.											.	TMX4	39	.	0			c.G160T						PASS	.						12	13	12					20																	8000101		2015	3902	5917	SO:0001587	stop_gained	56255	exon1			TCCACTCGCCCTC		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.160G>T	chr20.hg19:g.8000101C>A	ENSP00000246024:p.Glu54*	141.0	0.0	.		135.0	48.0	.	NM_021156	Q8N4P7|Q8NCC1|Q9UJA1|Q9ULQ8	Nonsense_Mutation	SNP	ENST00000246024.2	hg19	CCDS13101.1	.	.	.	.	.	.	.	.	.	.	C	37	6.588182	0.97684	.	.	ENSG00000125827	ENST00000246024;ENST00000527925	.	.	.	5.06	4.05	0.47172	.	0.179090	0.37577	N	0.002027	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	-11.8472	13.2749	0.60182	0.0:0.7474:0.2526:0.0	.	.	.	.	X	54	.	ENSP00000246024:E54X	E	-	1	0	TMX4	7948101	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.196000	0.32198	2.340000	0.79590	0.563000	0.77884	GAG	.	.	.	none		0.741	TMX4-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000077928.2	NM_021156		A	8000101	C	A	8000101	4	1	179	1	0	0	0	0	0	1	0	0	16281	893	31	4	921	4	TMX4	20	8000101	Nonsense_Mutation	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10		8000101	55025419	98	10526											
TM9SF4	9777	hgsc.bcm.edu	37	chr20	30720849	30720849	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtctttactgcttttctccCtgatgtgtgaaacaagcgcc	7	14	9	11	1	2	2	0	2	2	0	3	2	2	2	2	1	4	1	2	1	3	4			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr20:30720849C>T	ENST00000398022.2	+	2	284	c.49C>T	c.(49-51)Ctg>Ttg	p.L17L	TM9SF4_ENST00000217315.5_5'UTR	NM_014742.3	NP_055557.2	Q92544	TM9S4_HUMAN	transmembrane 9 superfamily protein member 4	17						integral component of membrane (GO:0016021)				central_nervous_system(2)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			GCTTTTCTCCCTGATGTGTGA	0.502																																					p.L17L		Atlas-SNP	.											.	TM9SF4	65	.	0			c.C49T						PASS	.						148	132	138					20																	30720849		2203	4300	6503	SO:0001819	synonymous_variant	9777	exon2			TTCTCCCTGATGT	BC021107	CCDS13196.2	20q11.21	2004-04-19			ENSG00000101337	ENSG00000101337			30797	protein-coding gene	gene with protein product						9039502	Standard	NM_014742		Approved	KIAA0255, dJ836N17.2	uc002wxj.2	Q92544	OTTHUMG00000032206	ENST00000398022.2:c.49C>T	chr20.hg19:g.30720849C>T		62.0	0.0	.		91.0	30.0	.	NM_014742	B0QYT7|Q9NUA3	Silent	SNP	ENST00000398022.2	hg19	CCDS13196.2																																																																																			.	.	.	none		0.502	TM9SF4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323568.1	NM_014742		T	30720849	C	T	30720849	2	4	179	1	0	0	0	0	0	0	0	1	15992	680	24	2		2	TM9SF4	20	30720849	Silent	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10	22720748	30720849	32304671	99	10527											
ARFGEF2	10564	hgsc.bcm.edu	37	chr20	47585740	47585740	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttctcccacgttctgcagaaGgatgccttccttgtgttccg	5	14	9	13	2	2	1	0	0	2	1	5	2	4	2	4	1	2	3	4	1	1	5			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr20:47585740G>A	ENST00000371917.4	+	9	1116	c.1116G>A	c.(1114-1116)aaG>aaA	p.K372K		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	372					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)			TTCTGCAGAAGGATGCCTTCC	0.552																																					p.K372K	Esophageal Squamous(176;1738 1974 26285 33069 35354)	Atlas-SNP	.											.	ARFGEF2	160	.	0			c.G1116A						PASS	.						225	149	175					20																	47585740		2203	4300	6503	SO:0001819	synonymous_variant	10564	exon9			GCAGAAGGATGCC	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.1116G>A	chr20.hg19:g.47585740G>A		150.0	0.0	.		183.0	8.0	.	NM_006420	Q5TFT9|Q9NTS1	Silent	SNP	ENST00000371917.4	hg19	CCDS13411.1																																																																																			.	.	.	none		0.552	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420		A	47585740	G	A	47585740	2	1	179	1	0	0	0	0	0	0	0	1	853	991	35	2		2	ARFGEF2	20	47585740	Silent	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	16864891	47585740	15439780	100	10528											
PCK1	5105	hgsc.bcm.edu	37	chr20	56138649	56138651	+	In_Frame_Del	DEL	AGA	AGA	-																															tataaccaaccctgagggtgAgaagaagtacctggcggccg																										TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr20:56138649_56138651delAGA	ENST00000319441.4	+	6	991_993	c.827_829delAGA	c.(826-831)gagaag>gag	p.K278del	PCK1_ENST00000543666.1_Intron|PCK1_ENST00000535860.1_In_Frame_Del_p.K146del	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	278					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			CCTGAGGGTGAGAAGAAGTACCT	0.562																																					p.276_276del		Atlas-Indel,Pindel	.											.	PCK1	95	.	0			c.826_828del						PASS	.																																			SO:0001651	inframe_deletion	5105	exon6			.		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.827_829delAGA	chr20.hg19:g.56138652_56138654delAGA	ENSP00000319814:p.Lys278del	106.0	0.0	0		136.0	40.0	0.294118	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	In_Frame_Del	DEL	ENST00000319441.4	hg19	CCDS13460.1																																																																																			.	.	.	none		0.562	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2			-	56138651	AGA	-	56138649	7	5	179	1	0	1	0	1	0	0	0	0	11588	304	11	0	845	0	PCK1	20	56138649	In_Frame_Del	DEL	AGA	TCGA-G7-A8LB-01A-11D-A35Z-10	8552909	56138649	6886871	101	10529											
ZC3H7B	23264	hgsc.bcm.edu	37	chr22	41721848	41721848	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgtggccgactacgctgccTctgaccaggtggccctgccc	5	7	12	17	3	1	1	0	1	1	0	1	2	1	1	5	3	3	1	5	3	1	1			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr22:41721848T>C	ENST00000352645.4	+	4	468	c.211T>C	c.(211-213)Tct>Cct	p.S71P	ZC3H7B_ENST00000351589.4_Missense_Mutation_p.S71P	NM_017590.4	NP_060060.3	Q9UGR2	Z3H7B_HUMAN	zinc finger CCCH-type containing 7B	71					viral process (GO:0016032)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	38						CTACGCTGCCTCTGACCAGGT	0.582																																					p.S71P		Atlas-SNP	.											.	ZC3H7B	82	.	0			c.T211C						PASS	.						65	47	53					22																	41721848		2203	4300	6503	SO:0001583	missense	23264	exon4			GCTGCCTCTGACC		CCDS14013.1	22q13.2	2013-01-10		2005-08-09	ENSG00000100403	ENSG00000100403		"Zinc fingers, CCCH-type domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30869	protein-coding gene	gene with protein product						10470851, 11230166	Standard	NM_017590		Approved	RoXaN, FLJ13787, DKFZp434K0920, KIAA1031	uc003azw.4	Q9UGR2	OTTHUMG00000150969	ENST00000352645.4:c.211T>C	chr22.hg19:g.41721848T>C	ENSP00000345793:p.Ser71Pro	134.0	0.0	.		137.0	90.0	.	NM_017590	A7YY88|B2RCA4|Q5TFX9|Q8TBT9|Q9H8B6|Q9UGQ9|Q9UGR0|Q9UGR1|Q9UK03|Q9UPW9	Missense_Mutation	SNP	ENST00000352645.4	hg19	CCDS14013.1	.	.	.	.	.	.	.	.	.	.	T	17.48	3.401268	0.62288	.	.	ENSG00000100403	ENST00000352645;ENST00000351589	T;T	0.60672	0.17;0.17	4.92	4.92	0.64577	Tetratricopeptide-like helical (1);	0.115329	0.64402	D	0.000012	T	0.72252	0.3437	L	0.58810	1.83	0.54753	D	0.999989	D;D	0.76494	0.999;0.999	D;D	0.87578	0.983;0.998	T	0.75717	-0.3220	10	0.87932	D	0	-17.5682	14.5596	0.68126	0.0:0.0:0.0:1.0	.	71;71	Q9UGR2-2;Q9UGR2	.;Z3H7B_HUMAN	P	71	ENSP00000345793:S71P;ENSP00000263243:S71P	ENSP00000263243:S71P	S	+	1	0	ZC3H7B	40051794	1.000000	0.71417	0.986000	0.45419	0.501000	0.33797	4.196000	0.58407	1.842000	0.53543	0.459000	0.35465	TCT	.	.	.	none		0.582	ZC3H7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320696.1	NM_017590		C	41721848	T	C	41721848	3	2	179	1	0	0	0	0	1	0	0	0	17585	1551	54	3	221	3	ZC3H7B	22	41721848	Missense_Mutation	SNP	T	TCGA-G7-A8LB-01A-11D-A35Z-10		41721848	9582718	102	10530											
GTSE1	51512	hgsc.bcm.edu	37	chr22	46704331	46704331	+	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	agcctccgttgcccacatctGagagtccctttgcctggagc	6	10	10	15	1	1	1	0	1	1	1	3	3	3	2	5	1	4	1	5	1	0	2			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr22:46704331G>A	ENST00000454366.1	+	4	465	c.253G>A	c.(253-255)Gag>Aag	p.E85K		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	66					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		GCCCACATCTGAGAGTCCCTT	0.507																																					p.E85K	GBM(153;542 1915 12487 29016 50495)	Atlas-SNP	.											.	GTSE1	100	.	0			c.G253A						PASS	.						103	114	110					22																	46704331		2203	4300	6503	SO:0001583	missense	51512	exon4			ACATCTGAGAGTC	AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.253G>A	chr22.hg19:g.46704331G>A	ENSP00000415430:p.Glu85Lys	126.0	0.0	.		118.0	68.0	.	NM_016426	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Missense_Mutation	SNP	ENST00000454366.1	hg19	CCDS14074.2	.	.	.	.	.	.	.	.	.	.	G	15.71	2.915009	0.52546	.	.	ENSG00000075218	ENST00000454366;ENST00000361934	T	0.08370	3.1	4.75	3.71	0.42584	.	1.192690	0.05519	N	0.561858	T	0.17023	0.0409	L	0.60455	1.87	0.09310	N	1	P	0.50819	0.939	P	0.46076	0.503	T	0.40776	-0.9545	10	0.45353	T	0.12	-1.6438	14.6257	0.68618	0.0:0.2767:0.7233:0.0	.	66	Q9NYZ3	GTSE1_HUMAN	K	85;45	ENSP00000415430:E85K	ENSP00000354634:E45K	E	+	1	0	GTSE1	45082995	0.032000	0.19561	0.002000	0.10522	0.012000	0.07955	2.316000	0.43761	1.287000	0.44583	0.655000	0.94253	GAG	.	.	.	none		0.507	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426		A	46704331	G	A	46704331	3	1	179	1	0	0	0	0	1	0	0	0	6892	1291	45	2	263	2	GTSE1	22	46704331	Missense_Mutation	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10	4982483	46704331	4600235	103	10531											
SHANK3	85358	hgsc.bcm.edu	37	chr22	51159620	51159620	+	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	tgcccgagagcgagctctggCctcccaggcgccctcccggt	4	6	13	18	4	1	1	0	0	1	1	3	3	3	1	5	3	3	1	5	3	0	0			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chr22:51159620C>T	ENST00000414786.2	+	21	3544	c.3317C>T	c.(3316-3318)gCc>gTc	p.A1106V	SHANK3_ENST00000262795.3_Missense_Mutation_p.A1136V|SHANK3_ENST00000445220.2_Missense_Mutation_p.A1122V			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	1120					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)		CGAGCTCTGGCCTCCCAGGCG	0.716																																					p.A1106V		Atlas-SNP	.											.	SHANK3	96	.	0			c.C3317T						PASS	.						8	10	10					22																	51159620		1962	4104	6066	SO:0001583	missense	85358	exon21			CTCTGGCCTCCCA	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.3317C>T	chr22.hg19:g.51159620C>T	ENSP00000464552:p.Ala1106Val	63.0	0.0	.		61.0	40.0	.	NM_033517	D7UT47|Q8TET3	Missense_Mutation	SNP	ENST00000414786.2	hg19		.	.	.	.	.	.	.	.	.	.	C	17.70	3.454930	0.63290	.	.	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.17213	2.29;2.29	4.3	4.3	0.51218	.	0.114429	0.64402	D	0.000012	T	0.13415	0.0325	L	0.47716	1.5	0.22511	N	0.999032	B;P;B	0.43750	0.276;0.816;0.16	B;B;B	0.28553	0.045;0.091;0.039	T	0.23726	-1.0180	10	0.66056	D	0.02	.	14.2694	0.66143	0.0:1.0:0.0:0.0	.	1120;1121;1136	D7UT47;Q9BYB0;F2Z3L0	.;SHAN3_HUMAN;.	V	1136;1122	ENSP00000442518:A1136V;ENSP00000446078:A1122V	ENSP00000442518:A1136V	A	+	2	0	SHANK3	49506486	1.000000	0.71417	0.999000	0.59377	0.961000	0.63080	5.241000	0.65384	1.949000	0.56562	0.462000	0.41574	GCC	.	.	.	none		0.716	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420		T	51159620	C	T	51159620	3	4	179	1	0	0	0	0	1	0	0	0	14279	739	26	2	3493	2	SHANK3	22	51159620	Missense_Mutation	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10	4455289	51159620	144946	104	10532											
NRK	203447	hgsc.bcm.edu	37	chrX	105199587	105199587	+	Missense_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	agctccaaagcaattatgatGtctaaaagtttccagtgatt	14	13	7	7	0	1	2	0	2	1	0	3	2	3	2	2	0	2	3	2	0	5	4			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chrX:105199587G>A	ENST00000243300.9	+	29	5047	c.4744G>A	c.(4744-4746)Gtc>Atc	p.V1582I	NRK_ENST00000428173.2_Missense_Mutation_p.V1583I|NRK_ENST00000540278.1_Missense_Mutation_p.V163I	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	1582					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						CAATTATGATGTCTAAAAGTT	0.363										HNSCC(51;0.14)																											p.V1582I		Atlas-SNP	.											.	NRK	321	.	0			c.G4744A						PASS	.						66	54	57					X																	105199587		1815	4062	5877	SO:0001583	missense	203447	exon29			TATGATGTCTAAA	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.4744G>A	chrX.hg19:g.105199587G>A	ENSP00000434830:p.Val1582Ile	136.0	0.0	.		92.0	87.0	.	NM_198465	Q32ND6|Q5H9K2|Q6ZMP2	Missense_Mutation	SNP	ENST00000243300.9	hg19		.	.	.	.	.	.	.	.	.	.	G	12.10	1.837299	0.32513	.	.	ENSG00000123572	ENST00000243300;ENST00000428173;ENST00000540278	T;T;T	0.79454	-1.26;-1.27;1.32	5.28	3.47	0.39725	.	0.153157	0.30732	N	0.008995	T	0.60444	0.2269	N	0.19112	0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.53892	-0.8374	10	0.87932	D	0	.	5.6294	0.17501	0.1834:0.0:0.6565:0.1601	.	163;1582	B7Z1I7;Q7Z2Y5	.;NRK_HUMAN	I	1582;1583;163	ENSP00000434830:V1582I;ENSP00000438378:V1583I;ENSP00000438148:V163I	ENSP00000434830:V1582I	V	+	1	0	NRK	105086243	0.551000	0.26497	0.730000	0.30809	0.001000	0.01503	1.968000	0.40500	0.510000	0.28216	-0.191000	0.12829	GTC	.	.	.	none		0.363	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465		A	105199587	G	A	105199587	3	1	179	1	0	0	0	0	1	0	0	0	10662	1377	48	2	4858	2	NRK	23	105199587	Missense_Mutation	SNP	G	TCGA-G7-A8LB-01A-11D-A35Z-10		105199587	50070973	105	10533											
RGAG1	57529	hgsc.bcm.edu	37	chrX	109694786	109694786	+	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	gtcatcgcttttaatgtcatCtccaggctctgaagtaatgt	9	15	8	9	1	4	1	2	1	2	0	6	1	4	1	1	1	0	3	1	1	3	3			TCGA-G7-A8LB-01A-11D-A35Z-10	TCGA-G7-A8LB-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f1beace3-f40d-4e2f-abff-815f257096c7	3c8d7f6b-ef32-4955-8113-91d246df62d4	g.chrX:109694786C>T	ENST00000465301.2	+	3	1187	c.941C>T	c.(940-942)tCt>tTt	p.S314F	RGAG1_ENST00000540313.1_Missense_Mutation_p.S314F	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	314										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						TTAATGTCATCTCCAGGCTCT	0.493																																					p.S314F		Atlas-SNP	.											.	RGAG1	168	.	0			c.C941T						PASS	.						249	222	231					X																	109694786		2203	4300	6503	SO:0001583	missense	57529	exon3			TGTCATCTCCAGG	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.941C>T	chrX.hg19:g.109694786C>T	ENSP00000419786:p.Ser314Phe	68.0	0.0	.		44.0	43.0	.	NM_020769	Q9P2M8	Missense_Mutation	SNP	ENST00000465301.2	hg19	CCDS14552.1	.	.	.	.	.	.	.	.	.	.	C	10.56	1.385067	0.25031	.	.	ENSG00000243978	ENST00000465301;ENST00000540313;ENST00000540483	T;T	0.47177	0.85;0.85	4.05	1.28	0.21552	.	1.603010	0.04115	N	0.315270	T	0.28699	0.0711	N	0.08118	0	0.09310	N	1	B	0.21225	0.053	B	0.24541	0.054	T	0.21518	-1.0243	9	.	.	.	1.2964	7.3573	0.26727	0.0:0.6769:0.0:0.3231	.	314	Q8NET4	RGAG1_HUMAN	F	314	ENSP00000419786:S314F;ENSP00000441452:S314F	.	S	+	2	0	RGAG1	109581442	0.001000	0.12720	0.000000	0.03702	0.008000	0.06430	-0.492000	0.06467	0.128000	0.18479	0.600000	0.82982	TCT	.	.	.	none		0.493	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		T	109694786	C	T	109694786	3	4	179	1	0	0	0	0	1	0	0	0	13287	913	32	2	943	2	RGAG1	23	109694786	Missense_Mutation	SNP	C	TCGA-G7-A8LB-01A-11D-A35Z-10	4495199	109694786	45575774	106	10534											
ZC3H12A	80149	hgsc.bcm.edu	37	chr1	37948521	37948521	+	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	gtccagctctctgctaacagAgagtgagcagtgcagcctgg	9	8	13	11	0	1	2	0	1	1	1	3	3	2	2	2	1	6	4	2	1	1	1			TCGA-G7-A8LC-01A-11D-A35Z-10	TCGA-G7-A8LC-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de876c49-d506-4de1-aad0-0136b35dd6f6	394bdf7b-2234-462d-839c-0a6177ffd570	g.chr1:37948521A>T	ENST00000373087.6	+	6	1225	c.1109A>T	c.(1108-1110)gAg>gTg	p.E370V		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)				CTGCTAACAGAGAGTGAGCAG	0.617																																					p.E370V		Atlas-SNP	.											.	ZC3H12A	58	.	0			c.A1109T						PASS	.						23	25	25					1																	37948521		2203	4300	6503	SO:0001583	missense	80149	exon6			TAACAGAGAGTGA		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.1109A>T	chr1.hg19:g.37948521A>T	ENSP00000362179:p.Glu370Val	233.0	0.0	.		104.0	71.0	.	NM_025079		Missense_Mutation	SNP	ENST00000373087.6	hg19	CCDS417.1	.	.	.	.	.	.	.	.	.	.	A	14.86	2.662428	0.47572	.	.	ENSG00000163874	ENST00000373087;ENST00000373082	T	0.25250	1.81	5.13	5.13	0.70059	.	1.008150	0.07957	N	0.981764	T	0.28830	0.0715	L	0.60455	1.87	0.36399	D	0.862973	P;B	0.38335	0.627;0.031	B;B	0.32928	0.155;0.014	T	0.27123	-1.0083	10	0.48119	T	0.1	-22.1084	13.5216	0.61572	1.0:0.0:0.0:0.0	.	165;370	B3KSD3;Q5D1E8	.;ZC12A_HUMAN	V	370	ENSP00000362179:E370V	ENSP00000362174:E370V	E	+	2	0	ZC3H12A	37721108	1.000000	0.71417	0.333000	0.25482	0.669000	0.39330	4.655000	0.61476	1.917000	0.55516	0.459000	0.35465	GAG	.	.	.	none		0.617	ZC3H12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012154.2	NM_025079		T	37948521	A	T	37948521	3	4	180	1	0	0	0	0	1	0	0	0	17573	304	11	5	1127	5	ZC3H12A	1	37948521	Missense_Mutation	SNP	A	TCGA-G7-A8LC-01A-11D-A35Z-10		37948521	211302100	1	10535											
C1orf26	54823	hgsc.bcm.edu	37	chr1	185159736	185159736	+	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	ctaaaatgctgtctccagcaCcaggaattattcccttgttc	10	13	6	12	0	1	0	0	0	1	0	4	1	2	1	3	1	2	3	3	1	4	5			TCGA-G7-A8LC-01A-11D-A35Z-10	TCGA-G7-A8LC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de876c49-d506-4de1-aad0-0136b35dd6f6	394bdf7b-2234-462d-839c-0a6177ffd570	g.chr1:185159736C>G	ENST00000367500.4	+	10	1650	c.1485C>G	c.(1483-1485)caC>caG	p.H495Q	SWT1_ENST00000367501.3_Missense_Mutation_p.H495Q	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	495	PINc.									breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						GTCTCCAGCACCAGGAATTAT	0.313																																					p.H495Q		Atlas-SNP	.											.	SWT1	88	.	0			c.C1485G						PASS	.						163	146	152					1																	185159736		2203	4300	6503	SO:0001583	missense	54823	exon10			CCAGCACCAGGAA	AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 26"	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.1485C>G	chr1.hg19:g.185159736C>G	ENSP00000356470:p.His495Gln	109.0	0.0	.		83.0	59.0	.	NM_017673	Q8NEK9|Q9BZQ7|Q9NXQ0	Missense_Mutation	SNP	ENST00000367500.4	hg19	CCDS1367.1	.	.	.	.	.	.	.	.	.	.	C	12.26	1.883969	0.33255	.	.	ENSG00000116668	ENST00000367501;ENST00000367500	T;T	0.16597	2.33;2.33	5.52	1.03	0.20045	Nucleotide binding protein, PINc (1);	0.064362	0.64402	D	0.000004	T	0.05593	0.0147	N	0.02011	-0.69	0.26460	N	0.97547	P	0.36048	0.534	B	0.32677	0.15	T	0.29058	-1.0024	10	0.72032	D	0.01	.	8.4892	0.33089	0.0:0.5494:0.0:0.4506	.	495	Q5T5J6	SWT1_HUMAN	Q	495	ENSP00000356471:H495Q;ENSP00000356470:H495Q	ENSP00000356470:H495Q	H	+	3	2	SWT1	183426359	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	0.853000	0.27777	0.291000	0.22468	-0.254000	0.11334	CAC	.	.	.	none		0.313	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673		G	185159736	C	G	185159736	3	3	180	1	0	0	0	0	1	0	0	0	2037	506	18	4	1519	4	C1orf26	1	185159736	Missense_Mutation	SNP	C	TCGA-G7-A8LC-01A-11D-A35Z-10	147211215	185159736	64090885	2	10536											
POLR1A	25885	hgsc.bcm.edu	37	chr2	86327152	86327152	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgtggcccaggtgcccagaaCagttgctgaagtcctgcacg	8	8	13	12	1	0	2	0	1	0	1	1	2	1	2	3	2	4	3	3	2	2	1			TCGA-G7-A8LC-01A-11D-A35Z-10	TCGA-G7-A8LC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de876c49-d506-4de1-aad0-0136b35dd6f6	394bdf7b-2234-462d-839c-0a6177ffd570	g.chr2:86327152C>T	ENST00000263857.6	-	2	599	c.221G>A	c.(220-222)tGt>tAt	p.C74Y	POLR1A_ENST00000409681.1_Missense_Mutation_p.C74Y			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	74					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						GTGCCCAGAACAGTTGCTGAA	0.567																																					p.C74Y		Atlas-SNP	.											.	POLR1A	137	.	0			c.G221A						PASS	.						90	95	93					2																	86327152		2027	4187	6214	SO:0001583	missense	25885	exon2			CCAGAACAGTTGC	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.221G>A	chr2.hg19:g.86327152C>T	ENSP00000263857:p.Cys74Tyr	111.0	0.0	.		129.0	6.0	.	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	hg19	CCDS42706.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.023496	0.75390	.	.	ENSG00000068654	ENST00000263857;ENST00000409681	T;T	0.30981	1.51;1.51	5.78	5.78	0.91487	RNA polymerase Rpb1, domain 1 (1);	0.000000	0.85682	D	0.000000	T	0.68540	0.3012	M	0.93328	3.405	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.76523	-0.2928	10	0.87932	D	0	-22.7322	19.9976	0.97389	0.0:1.0:0.0:0.0	.	74;74	B9ZVN9;O95602	.;RPA1_HUMAN	Y	74	ENSP00000263857:C74Y;ENSP00000386300:C74Y	ENSP00000263857:C74Y	C	-	2	0	POLR1A	86180663	1.000000	0.71417	0.998000	0.56505	0.929000	0.56500	7.268000	0.78473	2.737000	0.93849	0.563000	0.77884	TGT	.	.	.	none		0.567	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425		T	86327152	C	T	86327152	3	4	180	1	0	0	0	0	1	0	0	0	12216	478	17	2	5073	2	POLR1A	2	86327152	Missense_Mutation	SNP	C	TCGA-G7-A8LC-01A-11D-A35Z-10		86327152	156872221	3	10537											
SLC6A3	6531	hgsc.bcm.edu	37	chr5	1420693	1420693	+	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	actgtactcacagacgcctcGcagagccggtagaagtcaac	12	6	10	13	3	2	3	2	0	0	3	3	3	2	3	2	1	3	3	2	1	4	2			TCGA-G7-A8LC-01A-11D-A35Z-10	TCGA-G7-A8LC-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de876c49-d506-4de1-aad0-0136b35dd6f6	394bdf7b-2234-462d-839c-0a6177ffd570	g.chr5:1420693G>A	ENST00000270349.9	-	6	1045	c.918C>T	c.(916-918)tgC>tgT	p.C306C	SLC6A3_ENST00000453492.2_Silent_p.C306C	NM_001044.4	NP_001035.1	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 3	306					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)	CAGACGCCTCGCAGAGCCGGT	0.592																																					p.C306C		Atlas-SNP	.											.	SLC6A3	102	.	0			c.C918T						PASS	.						120	108	112					5																	1420693		2203	4300	6503	SO:0001819	synonymous_variant	6531	exon6			CGCCTCGCAGAGC		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.918C>T	chr5.hg19:g.1420693G>A		70.0	0.0	.		58.0	27.0	.	NM_001044	A2RUN4|Q14996	Silent	SNP	ENST00000270349.9	hg19	CCDS3863.1																																																																																			.	.	.	none		0.592	SLC6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253650.3	NM_001044		A	1420693	G	A	1420693	2	1	180	1	0	0	0	0	0	0	0	1	14698	1079	38	1		1	SLC6A3	5	1420693	Silent	SNP	G	TCGA-G7-A8LC-01A-11D-A35Z-10		1420693	179494567	4	10538											
SGK223	157285	hgsc.bcm.edu	37	chr8	8235196	8235196	+	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	ctgtccccggagggcgagcaCctttgatcactgtcatcctc	6	10	10	15	2	2	1	2	1	0	0	5	3	4	2	4	2	1	1	4	2	0	1			TCGA-G7-A8LC-01A-11D-A35Z-10	TCGA-G7-A8LC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de876c49-d506-4de1-aad0-0136b35dd6f6	394bdf7b-2234-462d-839c-0a6177ffd570	g.chr8:8235196C>A	ENST00000520004.1	-	3	987	c.723G>T	c.(721-723)agG>agT	p.R241S	SGK223_ENST00000330777.4_Missense_Mutation_p.R241S			Q86YV5	SG223_HUMAN		241							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										AGGGCGAGCACCTTTGATCAC	0.647																																					p.R241S	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.G723T						PASS	.						47	54	51					8																	8235196		1994	4165	6159	SO:0001583	missense	0	exon2			CGAGCACCTTTGA																												ENST00000520004.1:c.723G>T	chr8.hg19:g.8235196C>A	ENSP00000428054:p.Arg241Ser	130.0	0.0	.		77.0	8.0	.	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	hg19	CCDS43706.1	.	.	.	.	.	.	.	.	.	.	C	19.36	3.812405	0.70912	.	.	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.59224	0.28;0.28	5.55	4.61	0.57282	.	0.853255	0.09935	N	0.736705	T	0.60287	0.2257	L	0.29908	0.895	0.30458	N	0.774609	D	0.59357	0.985	P	0.58620	0.842	T	0.51568	-0.8689	10	0.28530	T	0.3	.	11.8792	0.52564	0.0:0.8245:0.1755:0.0	.	241	Q86YV5	SG223_HUMAN	S	241	ENSP00000330930:R241S;ENSP00000428054:R241S	ENSP00000330930:R241S	R	-	3	2	AC068353.1	8272606	0.832000	0.29368	1.000000	0.80357	0.860000	0.49131	1.246000	0.32803	2.780000	0.95670	0.655000	0.94253	AGG	.	.	.	none		0.647	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1			A	8235196	C	A	8235196	3	1	180	1	0	0	0	0	1	0	0	0	14223	506	18	4	3501	4	SGK223	8	8235196	Missense_Mutation	SNP	C	TCGA-G7-A8LC-01A-11D-A35Z-10		8235196	138128826	5	10539											
TRAPPC9	83696	hgsc.bcm.edu	37	chr8	140898201	140898201	+	Missense_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	cacactcgcctcgccactgcGcttcagggaggggtgagcct	6	7	13	15	3	1	1	1	1	0	0	3	2	1	2	3	3	2	1	3	3	0	1			TCGA-G7-A8LC-01A-11D-A35Z-10	TCGA-G7-A8LC-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de876c49-d506-4de1-aad0-0136b35dd6f6	394bdf7b-2234-462d-839c-0a6177ffd570	g.chr8:140898201G>A	ENST00000438773.2	-	21	3110	c.2977C>T	c.(2977-2979)Cgc>Tgc	p.R993C	TRAPPC9_ENST00000389328.4_Missense_Mutation_p.R1091C|TRAPPC9_ENST00000522504.1_5'UTR|TRAPPC9_ENST00000389327.3_Missense_Mutation_p.R984C	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	993					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						TCGCCACTGCGCTTCAGGGAG	0.617																																					p.R1091C		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.C3271T						PASS	.						24	23	24					8																	140898201		2195	4284	6479	SO:0001583	missense	83696	exon21			CACTGCGCTTCAG	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.2977C>T	chr8.hg19:g.140898201G>A	ENSP00000405060:p.Arg993Cys	381.0	0.0	.		204.0	153.0	.	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Missense_Mutation	SNP	ENST00000438773.2	hg19	CCDS55278.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.7|20.7	4.028987|4.028987	0.75504|0.75504	.|.	.|.	ENSG00000167632|ENSG00000167632	ENST00000520857|ENST00000389328;ENST00000389327;ENST00000438773	.|.	.|.	.|.	5.56|5.56	5.56|5.56	0.83823|0.83823	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.67581|0.67581	0.2908|0.2908	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.87578	.|0.998;0.997	T|T	0.67654|0.67654	-0.5615|-0.5615	5|9	.|0.49607	.|T	.|0.09	.|.	17.0314|17.0314	0.86462|0.86462	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|993;1091	.|Q96Q05;Q96Q05-2	.|TPPC9_HUMAN;.	V|C	836|1091;984;993	.|.	.|ENSP00000373978:R984C	A|R	-|-	2|1	0|0	TRAPPC9|TRAPPC9	140967383|140967383	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.577000|0.577000	0.36160|0.36160	5.425000|5.425000	0.66470|0.66470	2.620000|2.620000	0.88729|0.88729	0.655000|0.655000	0.94253|0.94253	GCG|CGC	.	.	.	none		0.617	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466		A	140898201	G	A	140898201	3	1	180	1	0	0	0	0	1	0	0	0	16477	1087	38	1	481	1	TRAPPC9	8	140898201	Missense_Mutation	SNP	G	TCGA-G7-A8LC-01A-11D-A35Z-10	132663005	140898201	5465821	6	10540											
DDI1	414301	hgsc.bcm.edu	37	chr11	103907571	103907571	+	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	atgctgatcaccgtgtactgCgtgcggagggacctctccga	7	9	13	12	4	2	1	1	1	1	0	3	4	2	3	3	2	4	2	3	2	1	1			TCGA-G7-A8LC-01A-11D-A35Z-10	TCGA-G7-A8LC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de876c49-d506-4de1-aad0-0136b35dd6f6	394bdf7b-2234-462d-839c-0a6177ffd570	g.chr11:103907571C>T	ENST00000302259.3	+	1	264	c.21C>T	c.(19-21)tgC>tgT	p.C7C	PDGFD_ENST00000302251.5_Intron|PDGFD_ENST00000393158.2_Intron	NM_001001711.2	NP_001001711.1	Q8WTU0	DDI1_HUMAN	DNA-damage inducible 1 homolog 1 (S. cerevisiae)	7	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.						aspartic-type endopeptidase activity (GO:0004190)	p.C7C(1)		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)		CCGTGTACTGCGTGCGGAGGG	0.682																																					p.C7C		Atlas-SNP	.											DDI1_ENST00000302259,colon,carcinoma,0,3	DDI1	222	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C21T						PASS	.						74	84	80					11																	103907571		2202	4299	6501	SO:0001819	synonymous_variant	414301	exon1			GTACTGCGTGCGG		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.21C>T	chr11.hg19:g.103907571C>T		87.0	0.0	.		113.0	47.0	.	NM_001001711	Q7Z4U6|Q8WTS3	Silent	SNP	ENST00000302259.3	hg19	CCDS31660.1	.	.	.	.	.	.	.	.	.	.	C	11.06	1.528853	0.27387	.	.	ENSG00000170962	ENST00000529268	T	0.27402	1.67	5.08	-10.2	0.00374	.	.	.	.	.	T	0.23171	0.0560	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50346	-0.8839	6	0.08599	T	0.76	-24.1506	19.4154	0.94694	0.0:0.7017:0.0:0.2983	.	.	.	.	T	62	ENSP00000432909:A62T	ENSP00000432909:A62T	A	-	1	0	PDGFD	103412781	0.972000	0.33761	0.139000	0.22197	0.856000	0.48823	0.059000	0.14322	-2.678000	0.00410	-0.742000	0.03525	GCA	.	.	.	none		0.682	DDI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387326.1	NM_001001711		T	103907571	C	T	103907571	2	4	180	1	0	0	0	0	0	0	0	1	4330	776	27	1		1	DDI1	11	103907571	Silent	SNP	C	TCGA-G7-A8LC-01A-11D-A35Z-10		103907571	31098945	7	10541											
SAV1	60485	hgsc.bcm.edu	37	chr14	51131967	51131967	+	Frame_Shift_Del	DEL	G	G	-																															ttgtattcataatatctgtaGtcttcatgtgcacgatctcc																										TCGA-G7-A8LC-01A-11D-A35Z-10	TCGA-G7-A8LC-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de876c49-d506-4de1-aad0-0136b35dd6f6	394bdf7b-2234-462d-839c-0a6177ffd570	g.chr14:51131967delG	ENST00000324679.4	-	2	828	c.465delC	c.(463-465)gacfs	p.D155fs	RP11-248J18.2_ENST00000602954.1_RNA	NM_021818.3	NP_068590.1	Q9H4B6	SAV1_HUMAN	salvador family WW domain containing protein 1	155					hair follicle development (GO:0001942)|hippo signaling (GO:0035329)|intestinal epithelial cell differentiation (GO:0060575)|keratinocyte differentiation (GO:0030216)|lung epithelial cell differentiation (GO:0060487)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of epithelial cell proliferation (GO:0050680)|positive regulation of apoptotic process (GO:0043065)|regulation of stem cell maintenance (GO:2000036)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)				breast(1)|kidney(2)|lung(2)|prostate(1)	6	all_epithelial(31;0.000611)|Breast(41;0.0333)					AATATCTGTAGTCTTCATGTG	0.383																																					p.Y156fs		Atlas-INDEL	.											.	SAV1	18	.	0			c.466delT						PASS	.						36	38	37					14																	51131967		2200	4290	6490	SO:0001589	frameshift_variant	60485	exon2			.	AK023071	CCDS9701.1	14q13-q23	2014-04-14	2014-04-14		ENSG00000151748	ENSG00000151748			17795	protein-coding gene	gene with protein product	"WW domain-containing adaptor 45"	607203	"salvador homolog 1 (Drosophila)"			12202036, 11027580	Standard	NM_021818		Approved	WW45, WWP4, salvador	uc001wyh.2	Q9H4B6	OTTHUMG00000140293	ENST00000324679.4:c.465delC	chr14.hg19:g.51131967delG	ENSP00000324729:p.Asp155fs	449.0	0.0	0		300.0	176.0	0.586667	NM_021818	A8K4B8|D3DSB6|Q6IA58|Q9H949|Q9HAK9	Frame_Shift_Del	DEL	ENST00000324679.4	hg19	CCDS9701.1																																																																																			.	.	.	none		0.383	SAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276879.1			-	51131967	G	-	51131967	7	5	180	1	0	1	0	1	0	0	0	0	13869	1020	36	0	702	0	SAV1	14	51131967	Frame_Shift_Del	DEL	G	TCGA-G7-A8LC-01A-11D-A35Z-10		51131967	56217573	8	10542	98	2									
SAV1	60485	hgsc.bcm.edu	37	chr14	51131969	51131969	+	Missense_Mutation	SNP	C	C	A																															gtattcataatatctgtagtCttcatgtgcacgatctccaa																										TCGA-G7-A8LC-01A-11D-A35Z-10	TCGA-G7-A8LC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de876c49-d506-4de1-aad0-0136b35dd6f6	394bdf7b-2234-462d-839c-0a6177ffd570	g.chr14:51131969C>A	ENST00000324679.4	-	2	826	c.463G>T	c.(463-465)Gac>Tac	p.D155Y	RP11-248J18.2_ENST00000602954.1_RNA	NM_021818.3	NP_068590.1	Q9H4B6	SAV1_HUMAN	salvador family WW domain containing protein 1	155					hair follicle development (GO:0001942)|hippo signaling (GO:0035329)|intestinal epithelial cell differentiation (GO:0060575)|keratinocyte differentiation (GO:0030216)|lung epithelial cell differentiation (GO:0060487)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of epithelial cell proliferation (GO:0050680)|positive regulation of apoptotic process (GO:0043065)|regulation of stem cell maintenance (GO:2000036)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)				breast(1)|kidney(2)|lung(2)|prostate(1)	6	all_epithelial(31;0.000611)|Breast(41;0.0333)					TATCTGTAGTCTTCATGTGCA	0.378																																					p.D155Y		Atlas-SNP	.											.	SAV1	18	.	0			c.G463T						PASS	.						38	40	39					14																	51131969		2199	4291	6490	SO:0001583	missense	60485	exon2			TGTAGTCTTCATG	AK023071	CCDS9701.1	14q13-q23	2014-04-14	2014-04-14		ENSG00000151748	ENSG00000151748			17795	protein-coding gene	gene with protein product	"WW domain-containing adaptor 45"	607203	"salvador homolog 1 (Drosophila)"			12202036, 11027580	Standard	NM_021818		Approved	WW45, WWP4, salvador	uc001wyh.2	Q9H4B6	OTTHUMG00000140293	ENST00000324679.4:c.463G>T	chr14.hg19:g.51131969C>A	ENSP00000324729:p.Asp155Tyr	454.0	1.0	.		303.0	177.0	.	NM_021818	A8K4B8|D3DSB6|Q6IA58|Q9H949|Q9HAK9	Missense_Mutation	SNP	ENST00000324679.4	hg19	CCDS9701.1	.	.	.	.	.	.	.	.	.	.	C	17.89	3.498931	0.64298	.	.	ENSG00000151748	ENST00000555720;ENST00000324679;ENST00000535862;ENST00000553731	T;T	0.52295	0.67;0.72	5.29	5.29	0.74685	.	0.090564	0.85682	D	0.000000	T	0.44850	0.1313	L	0.29908	0.895	0.51482	D	0.999924	P	0.50943	0.94	P	0.48030	0.564	T	0.22312	-1.0220	10	0.25751	T	0.34	-4.7833	17.9319	0.88999	0.0:1.0:0.0:0.0	.	155	Q9H4B6	SAV1_HUMAN	Y	87;155;122;39	ENSP00000451492:D87Y;ENSP00000324729:D155Y	ENSP00000324729:D155Y	D	-	1	0	SAV1	50201719	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	4.615000	0.61190	2.467000	0.83353	0.563000	0.77884	GAC	.	.	.	none		0.378	SAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276879.1			A	51131969	C	A	51131969	3	1	180	1	0	0	0	0	1	0	0	0	13869	913	32	4	704	4	SAV1	14	51131969	Missense_Mutation	SNP	C	TCGA-G7-A8LC-01A-11D-A35Z-10	2	51131969	56217571	9	10543	98	2									
YLPM1	56252	hgsc.bcm.edu	37	chr14	75276483	75276483	+	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	accagtacaacagactgttgAttatggccatggccgaggtg	11	9	12	9	1	0	2	0	1	0	1	0	3	0	2	3	3	2	2	3	3	3	3			TCGA-G7-A8LC-01A-11D-A35Z-10	TCGA-G7-A8LC-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de876c49-d506-4de1-aad0-0136b35dd6f6	394bdf7b-2234-462d-839c-0a6177ffd570	g.chr14:75276483A>T	ENST00000552421.1	+	6	2928	c.2804A>T	c.(2803-2805)gAt>gTt	p.D935V	YLPM1_ENST00000325680.7_Missense_Mutation_p.D1641V|YLPM1_ENST00000238571.3_Missense_Mutation_p.D1446V			P49750	YLPM1_HUMAN	YLP motif containing 1	1446	Arg-rich.				regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		CAGACTGTTGATTATGGCCAT	0.488																																					p.D1641V		Atlas-SNP	.											.	YLPM1	298	.	0			c.A4922T						PASS	.						57	53	54					14																	75276483		1963	4149	6112	SO:0001583	missense	56252	exon7			CTGTTGATTATGG	AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 169"		"chromosome 14 open reading frame 170"	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000552421.1:c.2804A>T	chr14.hg19:g.75276483A>T	ENSP00000447921:p.Asp935Val	208.0	1.0	.		133.0	82.0	.	NM_019589	P49752|Q96I64|Q9P1V7	Missense_Mutation	SNP	ENST00000552421.1	hg19		.	.	.	.	.	.	.	.	.	.	A	19.26	3.794011	0.70452	.	.	ENSG00000119596	ENST00000552421;ENST00000325680;ENST00000238571;ENST00000423680;ENST00000547879	.	.	.	5.32	5.32	0.75619	.	0.000000	0.64402	D	0.000010	T	0.66346	0.2780	L	0.29908	0.895	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.70615	-0.4823	9	0.87932	D	0	-10.8543	15.2838	0.73810	1.0:0.0:0.0:0.0	.	1446;1641	P49750-3;P49750-4	.;.	V	935;1641;1446;1354;50	.	ENSP00000238571:D1446V	D	+	2	0	YLPM1	74346236	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.204000	0.89741	2.001000	0.58596	0.482000	0.46254	GAT	.	.	.	none		0.488	YLPM1-008	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404450.1	NM_019589		T	75276483	A	T	75276483	3	4	180	1	0	0	0	0	1	0	0	0	17498	333	12	5	4948	5	YLPM1	14	75276483	Missense_Mutation	SNP	A	TCGA-G7-A8LC-01A-11D-A35Z-10	24144514	75276483	32073057	10	10544											
GPRC5C	55890	hgsc.bcm.edu	37	chr17	72443056	72443056	+	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	caggtgatgggcagtgccaaCtcgaccctgcgggctgaaga	9	6	15	11	2	0	3	0	2	0	1	1	4	0	3	2	3	3	2	2	3	2	0			TCGA-G7-A8LC-01A-11D-A35Z-10	TCGA-G7-A8LC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de876c49-d506-4de1-aad0-0136b35dd6f6	394bdf7b-2234-462d-839c-0a6177ffd570	g.chr17:72443056C>A	ENST00000392627.1	+	4	2476	c.1350C>A	c.(1348-1350)aaC>aaA	p.N450K	GPRC5C_ENST00000392629.2_Missense_Mutation_p.N417K|GPRC5C_ENST00000582873.1_3'UTR|GPRC5C_ENST00000342648.5_Missense_Mutation_p.N90K|GPRC5C_ENST00000481232.1_3'UTR	NM_022036.2	NP_071319.2	Q9NQ84	GPC5C_HUMAN	G protein-coupled receptor, class C, group 5, member C	405					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						GCAGTGCCAACTCGACCCTGC	0.612																																					p.N450K		Atlas-SNP	.											.	GPRC5C	92	.	0			c.C1350A						PASS	.						68	69	69					17																	72443056		2203	4300	6503	SO:0001583	missense	55890	exon4			TGCCAACTCGACC	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.1350C>A	chr17.hg19:g.72443056C>A	ENSP00000376403:p.Asn450Lys	117.0	0.0	.		98.0	4.0	.	NM_022036	B5BUN4|Q2NL85|Q9NZG5	Missense_Mutation	SNP	ENST00000392627.1	hg19	CCDS11699.1	.	.	.	.	.	.	.	.	.	.	C	19.74	3.884630	0.72410	.	.	ENSG00000170412	ENST00000392627;ENST00000342648;ENST00000262616;ENST00000392629;ENST00000392628	T	0.18810	2.19	5.59	2.49	0.30216	.	0.514125	0.20704	N	0.087204	T	0.34279	0.0892	L	0.44542	1.39	0.39978	D	0.974872	D;P;P;P	0.89917	1.0;0.919;0.842;0.902	D;B;B;B	0.76575	0.988;0.324;0.257;0.442	T	0.05419	-1.0886	10	0.72032	D	0.01	-19.0092	9.4257	0.38578	0.0:0.761:0.0:0.239	.	116;405;405;417	Q9NXI0;A8MXZ4;Q9NQ84;Q9NQ84-2	.;.;GPC5C_HUMAN;.	K	405;450;116;417;405	ENSP00000376405:N417K	ENSP00000262616:N116K	N	+	3	2	GPRC5C	69954651	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	1.637000	0.37155	0.301000	0.22738	0.561000	0.74099	AAC	.	.	.	none		0.612	GPRC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145094.2			A	72443056	C	A	72443056	3	1	180	1	0	0	0	0	1	0	0	0	6733	564	20	4	1372	4	GPRC5C	17	72443056	Missense_Mutation	SNP	C	TCGA-G7-A8LC-01A-11D-A35Z-10		72443056	8752154	11	10545											
POLRMT	5442	hgsc.bcm.edu	37	chr19	621197	621197	+	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	gccaatccaggccgtgcgggCcgagcgggcggccctgggcg	4	3	19	15	6	0	0	0	0	0	0	1	1	1	0	5	5	2	0	5	5	1	0			TCGA-G7-A8LC-01A-11D-A35Z-10	TCGA-G7-A8LC-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de876c49-d506-4de1-aad0-0136b35dd6f6	394bdf7b-2234-462d-839c-0a6177ffd570	g.chr19:621197C>G	ENST00000588649.2	-	10	2585	c.2501G>C	c.(2500-2502)gGc>gCc	p.G834A	LLNLR-299G3.1_ENST00000607288.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	834	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)		GCCGTGCGGGCCGAGCGGGCG	0.706																																					p.G834A		Atlas-SNP	.											.	POLRMT	91	.	0			c.G2501C						PASS	.						21	26	24					19																	621197		2196	4294	6490	SO:0001583	missense	5442	exon10			TGCGGGCCGAGCG		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.2501G>C	chr19.hg19:g.621197C>G	ENSP00000465759:p.Gly834Ala	112.0	0.0	.		87.0	5.0	.	NM_005035	O60370	Missense_Mutation	SNP	ENST00000588649.2	hg19	CCDS12036.1	.	.	.	.	.	.	.	.	.	.	.	17.17	3.322127	0.60634	.	.	ENSG00000099821	ENST00000215591	T	0.55413	0.52	4.41	4.41	0.53225	.	0.000000	0.85682	D	0.000000	T	0.82089	0.4961	H	0.97390	3.995	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89045	0.3451	10	0.87932	D	0	-42.5618	16.1611	0.81712	0.0:1.0:0.0:0.0	.	834	O00411	RPOM_HUMAN	A	834	ENSP00000215591:G834A	ENSP00000215591:G834A	G	-	2	0	POLRMT	572197	1.000000	0.71417	0.071000	0.20095	0.151000	0.21798	7.070000	0.76763	2.283000	0.76528	0.455000	0.32223	GGC	.	.	.	none		0.706	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035		G	621197	C	G	621197	3	3	180	1	0	0	0	0	1	0	0	0	12245	739	26	4	1239	4	POLRMT	19	621197	Missense_Mutation	SNP	C	TCGA-G7-A8LC-01A-11D-A35Z-10		621197	58507786	12	10546											
RBM10	8241	hgsc.bcm.edu	37	chrX	47030582	47030582	+	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	gaggaggaggaggaggaggaGgatgaggaggaggaggagaa	15	1	25	0	0	0	2	0	1	0	1	0	14	0	12	0	11	0	0	0	11	1	0			TCGA-G7-A8LC-01A-11D-A35Z-10	TCGA-G7-A8LC-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	de876c49-d506-4de1-aad0-0136b35dd6f6	394bdf7b-2234-462d-839c-0a6177ffd570	g.chrX:47030582G>T	ENST00000377604.3	+	4	1099	c.357G>T	c.(355-357)gaG>gaT	p.E119D	RBM10_ENST00000329236.7_Intron|RBM10_ENST00000345781.6_Intron	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	119	Poly-Glu.				3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						aggaggaggaggatgaggagg	0.662																																					p.E184D	Melanoma(171;120 2705 19495 39241)	Atlas-SNP	.											.	RBM10	117	.	0			c.G552T						PASS	.						20	19	19					X																	47030582		2202	4294	6496	SO:0001583	missense	8241	exon4			GGAGGAGGATGAG	U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"Zinc fingers, RAN-binding domain containing", "G patch domain containing", "RNA binding motif (RRM) containing"	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.357G>T	chrX.hg19:g.47030582G>T	ENSP00000366829:p.Glu119Asp	81.0	0.0	.		75.0	4.0	.	NM_001204468	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Missense_Mutation	SNP	ENST00000377604.3	hg19	CCDS14274.1	.	.	.	.	.	.	.	.	.	.	G	7.514	0.655267	0.14580	.	.	ENSG00000182872	ENST00000377604	T	0.11169	2.8	3.1	1.15	0.20763	Nucleotide-binding, alpha-beta plait (1);	0.859005	0.09469	N	0.797951	T	0.04815	0.0130	N	0.08118	0	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.38628	-0.9652	10	0.11182	T	0.66	-1.7872	6.9396	0.24486	0.0:0.0:0.4873:0.5127	.	184;119;119	Q7Z3D7;P98175-2;P98175	.;.;RBM10_HUMAN	D	119	ENSP00000366829:E119D	ENSP00000366829:E119D	E	+	3	2	RBM10	46915526	1.000000	0.71417	0.776000	0.31678	0.914000	0.54420	0.961000	0.29267	0.165000	0.19558	0.502000	0.49764	GAG	.	.	.	none		0.662	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676		T	47030582	G	T	47030582	3	4	180	1	0	0	0	0	1	0	0	0	13124	991	35	4	367	4	RBM10	23	47030582	Missense_Mutation	SNP	G	TCGA-G7-A8LC-01A-11D-A35Z-10		47030582	108239978	13	10547											
LMNA	4000	hgsc.bcm.edu	37	chr1	156084843	156084843	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caatgatcgcttggcggtctAcatcgaccgtgtgcgctcgc	6	10	12	13	6	1	1	0	1	1	0	4	2	1	1	1	2	2	2	1	2	2	2	rs58436778		TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr1:156084843A>G	ENST00000368300.4	+	1	346	c.134A>G	c.(133-135)tAc>tGc	p.Y45C	LMNA_ENST00000347559.2_Missense_Mutation_p.Y45C|LMNA_ENST00000361308.4_Missense_Mutation_p.Y45C|LMNA_ENST00000368301.2_Missense_Mutation_p.Y45C|LMNA_ENST00000368299.3_Missense_Mutation_p.Y45C	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C	45	Coil 1A.|Interaction with MLIP.|Rod.		Y -> C (in EDMD2; dbSNP:rs58436778). {ECO:0000269|PubMed:10939567, ECO:0000269|PubMed:20848652}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|endoplasmic reticulum unfolded protein response (GO:0030968)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle organ development (GO:0007517)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|positive regulation of cell aging (GO:0090343)|protein localization to nucleus (GO:0034504)|regulation of cell migration (GO:0030334)|regulation of protein localization to nucleus (GO:1900180)|sterol regulatory element binding protein import into nucleus (GO:0035105)|ventricular cardiac muscle cell development (GO:0055015)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|lamin filament (GO:0005638)|nuclear envelope (GO:0005635)|nuclear lamina (GO:0005652)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4)	10	Hepatocellular(266;0.158)					TTGGCGGTCTACATCGACCGT	0.657									Werner syndrome;Hutchinson-Gilford Progeria Syndrome																												p.Y45C		Atlas-SNP	.											.	LMNA	31	.	0			c.A134G	GRCh37	CM002044	LMNA	M	rs58436778	PASS	.						39	32	34					1																	156084843		2193	4298	6491	SO:0001583	missense	4000	exon1	Familial Cancer Database	WS, Adult Progeria;HGPS, Progeria	CGGTCTACATCGA	BC014507	CCDS1129.1, CCDS1131.1, CCDS58038.1, CCDS72941.1, CCDS72942.1	1q22	2014-09-17			ENSG00000160789	ENSG00000160789		"Intermediate filaments type V, lamins"	6636	protein-coding gene	gene with protein product		150330	"cardiomyopathy, dilated 1A (autosomal dominant)", "limb girdle muscular dystrophy 1B (autosomal dominant)", "progeria 1 (Hutchinson-Gilford type)", "lamin A/C-like 1"	LMN1, CMD1A, LGMD1B, PRO1, LMNL1		8511676, 8838815, 12702809	Standard	NM_005572		Approved	HGPS	uc001fni.3	P02545	OTTHUMG00000013961	ENST00000368300.4:c.134A>G	chr1.hg19:g.156084843A>G	ENSP00000357283:p.Tyr45Cys	231.0	0.0	.		316.0	93.0	.	NM_170707	B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2	Missense_Mutation	SNP	ENST00000368300.4	hg19	CCDS1129.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.501352	0.85176	.	.	ENSG00000160789	ENST00000368301;ENST00000347559;ENST00000361308;ENST00000368300;ENST00000368299;ENST00000292302;ENST00000392355	D;D;D;D;D	0.94613	-3.47;-3.47;-3.47;-3.47;-3.47	4.77	3.65	0.41850	Filament (1);	0.000000	0.52532	D	0.000066	D	0.97670	0.9236	H	0.97829	4.085	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.87578	0.997;0.998;0.996;0.995	D	0.97223	0.9879	10	0.87932	D	0	.	8.5522	0.33458	0.9076:0.0:0.0924:0.0	rs58436778	45;45;45;45	Q6UYC3;P02545;P02545-3;P02545-2	.;LMNA_HUMAN;.;.	C	45	ENSP00000357284:Y45C;ENSP00000292304:Y45C;ENSP00000355292:Y45C;ENSP00000357283:Y45C;ENSP00000357282:Y45C	ENSP00000292302:Y45C	Y	+	2	0	LMNA	154351467	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.097000	0.94193	0.860000	0.35481	0.379000	0.24179	TAC	.	.	.	weak		0.657	LMNA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039200.2	NM_170707		G	156084843	A	G	156084843	3	3	181	1	0	0	0	0	1	0	0	0	8855	391	14	3	136	3	LMNA	1	156084843	Missense_Mutation	SNP	A	TCGA-G7-A8LD-01A-11D-A35Z-10		156084843	93165778	1	10548											
XPR1	9213	hgsc.bcm.edu	37	chr1	180843054	180843054	+	Missense_Mutation	SNP	T	T	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	tggggacatcattgctactgTctttgccccacttgaggttt	6	15	10	10	0	2	1	1	1	1	0	2	2	2	2	2	3	3	2	2	3	1	5			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr1:180843054T>G	ENST00000367590.4	+	13	1982	c.1784T>G	c.(1783-1785)gTc>gGc	p.V595G	XPR1_ENST00000367589.3_Missense_Mutation_p.V530G	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1	595	EXS. {ECO:0000255|PROSITE- ProRule:PRU00712}.				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						ATTGCTACTGTCTTTGCCCCA	0.378																																					p.V595G		Atlas-SNP	.											.	XPR1	76	.	0			c.T1784G						PASS	.						117	101	107					1																	180843054		2203	4300	6503	SO:0001583	missense	9213	exon13			CTACTGTCTTTGC	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.1784T>G	chr1.hg19:g.180843054T>G	ENSP00000356562:p.Val595Gly	82.0	0.0	.		117.0	42.0	.	NM_004736	O95719|Q7L8K9|Q8IW20|Q9NT19|Q9UFB9	Missense_Mutation	SNP	ENST00000367590.4	hg19	CCDS1340.1	.	.	.	.	.	.	.	.	.	.	T	18.27	3.587089	0.66105	.	.	ENSG00000143324	ENST00000367590;ENST00000367589	T;T	0.48836	0.8;0.8	5.43	5.43	0.79202	EXS, C-terminal (2);	0.059107	0.64402	D	0.000002	T	0.50803	0.1637	M	0.70842	2.15	0.80722	D	1	B;B	0.28258	0.082;0.205	B;B	0.29176	0.059;0.099	T	0.54918	-0.8221	10	0.87932	D	0	-12.1075	15.1311	0.72523	0.0:0.0:0.0:1.0	.	530;595	Q9UBH6-2;Q9UBH6	.;XPR1_HUMAN	G	595;530	ENSP00000356562:V595G;ENSP00000356561:V530G	ENSP00000356561:V530G	V	+	2	0	XPR1	179109677	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	7.917000	0.87498	2.068000	0.61886	0.528000	0.53228	GTC	.	.	.	none		0.378	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084996.2	NM_004736		G	180843054	T	G	180843054	3	3	181	1	0	0	0	0	1	0	0	0	17463	1667	58	5	1834	5	XPR1	1	180843054	Missense_Mutation	SNP	T	TCGA-G7-A8LD-01A-11D-A35Z-10	24758211	180843054	68407567	2	10549											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228560567	228560567	+	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	aggtgaactgggcccccacgCaggcctggagatcacagagg	10	4	15	12	1	1	3	1	1	0	2	1	4	1	3	3	5	1	1	3	5	1	0			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr1:228560567C>G	ENST00000422127.1	+	94	22132	c.22088C>G	c.(22087-22089)gCa>gGa	p.A7363G	OBSCN_ENST00000570156.2_Missense_Mutation_p.A8320G|OBSCN_ENST00000366707.4_Missense_Mutation_p.A4997G	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7363					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)				GGCCCCCACGCAGGCCTGGAG	0.692																																					p.A8320G		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C24959G						PASS	.						16	20	18					1																	228560567		2187	4287	6474	SO:0001583	missense	84033	exon105			CCCACGCAGGCCT	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.22088C>G	chr1.hg19:g.228560567C>G	ENSP00000409493:p.Ala7363Gly	120.0	0.0	.		175.0	58.0	.	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	C	13.85	2.360250	0.41801	.	.	ENSG00000154358	ENST00000422127;ENST00000366707	T;T	0.62788	0.0;0.05	5.1	2.18	0.27775	.	.	.	.	.	T	0.38904	0.1058	L	0.27053	0.805	0.09310	N	0.99999	P	0.47106	0.89	B	0.35413	0.202	T	0.16988	-1.0384	9	0.32370	T	0.25	.	4.1869	0.10402	0.1709:0.563:0.0:0.2661	.	7363	Q5VST9	OBSCN_HUMAN	G	7363;4997	ENSP00000409493:A7363G;ENSP00000355668:A4997G	ENSP00000355668:A4997G	A	+	2	0	OBSCN	226627190	0.000000	0.05858	0.002000	0.10522	0.011000	0.07611	0.817000	0.27281	0.179000	0.19938	0.491000	0.48974	GCA	.	.	.	none		0.692	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		G	228560567	C	G	228560567	3	3	181	1	0	0	0	0	1	0	0	0	10819	710	25	4	23668	4	OBSCN	1	228560567	Missense_Mutation	SNP	C	TCGA-G7-A8LD-01A-11D-A35Z-10	47717513	228560567	20690054	3	10550											
CCDC104	112942	hgsc.bcm.edu	37	chr2	55772097	55772138	+	In_Frame_Del	DEL	AGGAGATTGCTTGCAGAGAAACTCAAAGAAGAAGTTATTAAT	AGGAGATTGCTTGCAGAGAAACTCAAAGAAGAAGTTATTAAT	-																															agaagcaaacattactaaagAggagattgcttgcagagaaa																								rs545373910|rs528334905		TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	AGGAGATTGCTTGCAGAGAAACTCAAAGAAGAAGTTATTAAT	AGGAGATTGCTTGCAGAGAAACTCAAAGAAGAAGTTATTAAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr2:55772097_55772138delAGGAGATTGCTTGCAGAGAAACTCAAAGAAGAAGTTATTAAT	ENST00000349456.4	+	10	1130_1171	c.982_1023delAGGAGATTGCTTGCAGAGAAACTCAAAGAAGAAGTTATTAAT	c.(982-1023)aggagattgcttgcagagaaactcaaagaagaagttattaatdel	p.RRLLAEKLKEEVIN328del	CCDC104_ENST00000339012.3_In_Frame_Del_p.RRLLAEKLKEEVIN353del|CCDC104_ENST00000407816.3_In_Frame_Del_p.RRLLAEKLKEEVIN299del			Q96G28	CFA36_HUMAN		328								p.I340T(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|liver(2)|lung(1)|ovary(2)	14			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			ATTACTAAAGAGGAGATTGCTTGCAGAGAAACTCAAAGAAGAAGTTATTAATAAGTAATAAT	0.293																																					p.327_341del		Atlas-Indel,Pindel	.											.	CCDC104	35	.	1	Substitution - Missense(1)	kidney(1)	c.981_1022del						PASS	.																																			SO:0001651	inframe_deletion	112942	exon10			.																												ENST00000349456.4:c.982_1023delAGGAGATTGCTTGCAGAGAAACTCAAAGAAGAAGTTATTAAT	chr2.hg19:g.55772097_55772138delAGGAGATTGCTTGCAGAGAAACTCAAAGAAGAAGTTATTAAT	ENSP00000295117:p.Arg328_Asn341del	750.0	0.0	0		541.0	78.0	0.144177	NM_080667	Q53SF0|Q53ST9|Q6UY34	In_Frame_Del	DEL	ENST00000349456.4	hg19	CCDS1854.2																																																																																			.	.	.	none		0.293	CCDC104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319610.2			-	55772138	AGGAGATTGCTTGCAGAGAAACTCAAAGAAGAAGTTATTAAT	-	55772097	7	5	181	1	0	1	0	1	0	0	0	0	2741	295	11	0	1020	0	CCDC104	2	55772097	In_Frame_Del	DEL	AGGAGATTGCTTGCAGAGAAACTCAAAGAAGAAGTTATTAAT	TCGA-G7-A8LD-01A-11D-A35Z-10		55772097	187427276	4	10551											
USP34	9736	hgsc.bcm.edu	37	chr2	61522309	61522309	+	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	ggaaatgcaattaccgtagaCtccctccttattcttctatt	10	15	5	11	1	2	1	0	0	2	1	4	2	4	2	3	1	2	2	3	1	6	7			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr2:61522309C>T	ENST00000398571.2	-	31	4447	c.4371G>A	c.(4369-4371)gaG>gaA	p.E1457E		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	1457					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)			TTACCGTAGACTCCCTCCTTA	0.323																																					p.E1457E		Atlas-SNP	.											.	USP34	334	.	0			c.G4371A						PASS	.						128	124	125					2																	61522309		1817	4082	5899	SO:0001819	synonymous_variant	9736	exon31			CGTAGACTCCCTC	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.4371G>A	chr2.hg19:g.61522309C>T		192.0	0.0	.		175.0	9.0	.	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Silent	SNP	ENST00000398571.2	hg19	CCDS42686.1																																																																																			.	.	.	none		0.323	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			T	61522309	C	T	61522309	2	4	181	1	0	0	0	0	0	0	0	1	17077	564	20	2		2	USP34	2	61522309	Silent	SNP	C	TCGA-G7-A8LD-01A-11D-A35Z-10	5750212	61522309	181677064	5	10552											
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125405341	125405341	+	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	tgttgtctgggcagaggacaAgatctggacatcagtgcagc	10	9	14	8	0	3	2	1	0	2	2	3	4	3	4	0	3	2	3	0	3	1	1			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr2:125405341A>T	ENST00000431078.1	+	13	2244	c.1880A>T	c.(1879-1881)aAg>aTg	p.K627M		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	627	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		GCAGAGGACAAGATCTGGACA	0.542																																					p.K627M		Atlas-SNP	.											.	CNTNAP5	405	.	0			c.A1880T						PASS	.						38	38	38					2																	125405341		2104	4237	6341	SO:0001583	missense	129684	exon13			AGGACAAGATCTG	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.1880A>T	chr2.hg19:g.125405341A>T	ENSP00000399013:p.Lys627Met	220.0	0.0	.		202.0	87.0	.	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	hg19	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	A	19.26	3.792842	0.70452	.	.	ENSG00000155052	ENST00000431078	T	0.21734	1.99	5.5	2.95	0.34219	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (2);	0.000000	0.53938	D	0.000058	T	0.46718	0.1407	M	0.82630	2.6	0.53688	D	0.999978	D	0.89917	1.0	D	0.87578	0.998	T	0.50092	-0.8868	10	0.59425	D	0.04	.	11.46	0.50204	0.7146:0.2854:0.0:0.0	.	627	Q8WYK1	CNTP5_HUMAN	M	627	ENSP00000399013:K627M	ENSP00000399013:K627M	K	+	2	0	CNTNAP5	125121811	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	6.020000	0.70826	0.905000	0.36596	0.459000	0.35465	AAG	.	.	.	none		0.542	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			T	125405341	A	T	125405341	3	4	181	1	0	0	0	0	1	0	0	0	3652	72	3	5	1930	5	CNTNAP5	2	125405341	Missense_Mutation	SNP	A	TCGA-G7-A8LD-01A-11D-A35Z-10	63883032	125405341	117794032	6	10553											
NCKAP5	344148	hgsc.bcm.edu	37	chr2	133540804	133540804	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccatgcttgctggattctTggagtcctctggcttagact	5	15	10	11	0	2	1	0	0	2	1	4	3	4	3	2	3	2	3	2	3	1	4			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr2:133540804T>C	ENST00000409261.1	-	14	3953	c.3580A>G	c.(3580-3582)Aag>Gag	p.K1194E	NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000317721.6_Missense_Mutation_p.K1194E|NCKAP5_ENST00000473859.1_5'Flank	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1194										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						GCTGGATTCTTGGAGTCCTCT	0.493																																					p.K1194E		Atlas-SNP	.											.	NCKAP5	322	.	0			c.A3580G						PASS	.						76	75	76					2																	133540804		1925	4142	6067	SO:0001583	missense	344148	exon14			GATTCTTGGAGTC	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.3580A>G	chr2.hg19:g.133540804T>C	ENSP00000387128:p.Lys1194Glu	93.0	0.0	.		114.0	22.0	.	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	hg19	CCDS46418.1	.	.	.	.	.	.	.	.	.	.	T	12.87	2.068687	0.36470	.	.	ENSG00000176771	ENST00000409261;ENST00000317721	T;T	0.09723	2.95;2.95	5.26	-2.18	0.07037	.	1.587860	0.04759	U	0.425865	T	0.04634	0.0126	N	0.19112	0.55	0.09310	N	1	B	0.29301	0.241	B	0.21917	0.037	T	0.29971	-0.9994	10	0.07175	T	0.84	.	1.3436	0.02159	0.246:0.3735:0.136:0.2446	.	1194	O14513	NCKP5_HUMAN	E	1194	ENSP00000387128:K1194E;ENSP00000380603:K1194E	ENSP00000380603:K1194E	K	-	1	0	NCKAP5	133257274	0.000000	0.05858	0.000000	0.03702	0.328000	0.28507	-1.569000	0.02142	0.017000	0.15025	0.533000	0.62120	AAG	.	.	.	none		0.493	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		C	133540804	T	C	133540804	3	2	181	1	0	0	0	0	1	0	0	0	10230	1821	63	3	2177	3	NCKAP5	2	133540804	Missense_Mutation	SNP	T	TCGA-G7-A8LD-01A-11D-A35Z-10	8135463	133540804	109658569	7	10554											
R3HDM1	23518	hgsc.bcm.edu	37	chr2	136399272	136399272	+	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	gatggtggcctaaatgggcaAgtcgcatctcctagcactag	10	9	12	10	1	1	0	0	0	1	0	3	1	1	0	2	3	1	3	2	3	5	3			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr2:136399272A>T	ENST00000264160.4	+	15	1756	c.1386A>T	c.(1384-1386)caA>caT	p.Q462H	R3HDM1_ENST00000443537.2_Intron|R3HDM1_ENST00000410054.1_Missense_Mutation_p.Q406H|R3HDM1_ENST00000409606.1_Missense_Mutation_p.Q462H|R3HDM1_ENST00000409478.1_Intron|R3HDM1_ENST00000329971.3_Intron	NM_001282798.1|NM_015361.2	NP_001269727.1|NP_056176.2	Q15032	R3HD1_HUMAN	R3H domain containing 1	462							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)		TAAATGGGCAAGTCGCATCTC	0.507																																					p.Q462H		Atlas-SNP	.											.	R3HDM1	84	.	0			c.A1386T						PASS	.						170	153	159					2																	136399272		2203	4300	6503	SO:0001583	missense	23518	exon15			TGGGCAAGTCGCA	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.1386A>T	chr2.hg19:g.136399272A>T	ENSP00000264160:p.Gln462His	73.0	0.0	.		87.0	19.0	.	NM_015361	A8K1V0|B3KXQ9|E9PBB4|E9PG42|G5E9G8|Q8IW32	Missense_Mutation	SNP	ENST00000264160.4	hg19	CCDS2177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.68|17.68	3.448457|3.448457	0.63178|0.63178	.|.	.|.	ENSG00000048991|ENSG00000048991	ENST00000264160;ENST00000410054;ENST00000409606|ENST00000429703	T;T;T|.	0.51574|.	0.7;0.7;0.7|.	5.57|5.57	4.35|4.35	0.52113|0.52113	.|.	0.325147|.	0.34652|.	N|.	0.003798|.	T|T	0.62171|0.62171	0.2406|0.2406	L|L	0.52905|0.52905	1.665|1.665	0.80722|0.80722	D|D	1|1	P;D;B|.	0.56521|.	0.877;0.976;0.412|.	B;P;B|.	0.48030|.	0.365;0.564;0.259|.	T|T	0.60642|0.60642	-0.7223|-0.7223	10|5	0.38643|.	T|.	0.18|.	-3.87|-3.87	12.3297|12.3297	0.55033|0.55033	0.859:0.141:0.0:0.0|0.859:0.141:0.0:0.0	.|.	462;406;462|.	E9PBB4;E9PG42;Q15032|.	.;.;R3HD1_HUMAN|.	H|C	462;406;462|151	ENSP00000264160:Q462H;ENSP00000386877:Q406H;ENSP00000387010:Q462H|.	ENSP00000264160:Q462H|.	Q|S	+|+	3|1	2|0	R3HDM1|R3HDM1	136115742|136115742	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.456000|2.456000	0.44997|0.44997	2.120000|2.120000	0.65058|0.65058	0.533000|0.533000	0.62120|0.62120	CAA|AGT	.	.	.	none		0.507	R3HDM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254659.1	NM_015361		T	136399272	A	T	136399272	3	4	181	1	0	0	0	0	1	0	0	0	12900	69	3	5	1436	5	R3HDM1	2	136399272	Missense_Mutation	SNP	A	TCGA-G7-A8LD-01A-11D-A35Z-10	2858468	136399272	106800101	8	10555											
KIF5C	3800	hgsc.bcm.edu	37	chr2	149853801	149853801	+	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	aaatgcacgaagtcagcttcCaggataaggagaaggaacat	17	6	11	7	1	1	1	1	0	0	1	2	5	2	3	1	3	3	2	1	3	5	2			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr2:149853801C>A	ENST00000435030.1	+	18	2415	c.2047C>A	c.(2047-2049)Cag>Aag	p.Q683K	KIF5C_ENST00000464066.1_3'UTR|KIF5C_ENST00000414838.2_Missense_Mutation_p.Q588K|KIF5C_ENST00000397413.1_Missense_Mutation_p.Q451K			O60282	KIF5C_HUMAN	kinesin family member 5C	683					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)		AGTCAGCTTCCAGGATAAGGA	0.413																																					p.Q683K		Atlas-SNP	.											.	KIF5C	166	.	0			c.C2047A						PASS	.						109	109	109					2																	149853801		2024	4196	6220	SO:0001583	missense	3800	exon18			AGCTTCCAGGATA	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.2047C>A	chr2.hg19:g.149853801C>A	ENSP00000393379:p.Gln683Lys	293.0	0.0	.		337.0	152.0	.	NM_004522	O95079|Q2YDC5	Missense_Mutation	SNP	ENST00000435030.1	hg19		.	.	.	.	.	.	.	.	.	.	C	7.928	0.740082	0.15642	.	.	ENSG00000168280	ENST00000435030;ENST00000414838;ENST00000334436;ENST00000397413	T;T;T	0.75260	-0.92;-0.92;-0.92	5.76	5.76	0.90799	.	0.201457	0.41938	D	0.000798	T	0.61035	0.2315	.	.	.	0.24214	N	0.995461	B;B	0.09022	0.0;0.002	B;B	0.09377	0.0;0.004	T	0.43702	-0.9375	8	.	.	.	.	14.6636	0.68891	0.1799:0.8201:0.0:0.0	.	683;249	O60282;Q3LIE3	KIF5C_HUMAN;.	K	683;588;586;451	ENSP00000393379:Q683K;ENSP00000410115:Q588K;ENSP00000380560:Q451K	.	Q	+	1	0	KIF5C	149562047	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.589000	0.46145	2.713000	0.92767	0.655000	0.94253	CAG	.	.	.	none		0.413	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522		A	149853801	C	A	149853801	3	1	181	1	0	0	0	0	1	0	0	0	8314	595	21	4	2039	4	KIF5C	2	149853801	Missense_Mutation	SNP	C	TCGA-G7-A8LD-01A-11D-A35Z-10	13454529	149853801	93345572	9	10556											
NCL	4691	hgsc.bcm.edu	37	chr2	232325488	232325488	+	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	atcctcttcttcatcttcatCctcagccacgttcttggctt	5	17	4	15	1	7	0	3	0	4	0	9	0	9	0	3	1	1	2	3	1	0	6			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr2:232325488C>G	ENST00000322723.4	-	4	943	c.703G>C	c.(703-705)Gat>Cat	p.D235H	SNORD82_ENST00000365530.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	235	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)		tcatcttcatcctcaGCCACG	0.453																																					p.D235H		Atlas-SNP	.											.	NCL	80	.	0			c.G703C						PASS	.						267	223	238					2																	232325488		2203	4300	6503	SO:0001583	missense	4691	exon4			CTTCATCCTCAGC		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.703G>C	chr2.hg19:g.232325488C>G	ENSP00000318195:p.Asp235His	75.0	0.0	.		72.0	9.0	.	NM_005381	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	Missense_Mutation	SNP	ENST00000322723.4	hg19	CCDS33397.1	.	.	.	.	.	.	.	.	.	.	C	11.88	1.771179	0.31320	.	.	ENSG00000115053	ENST00000322723	T	0.21932	1.98	5.46	5.46	0.80206	.	0.531595	0.21728	N	0.070002	T	0.21801	0.0525	L	0.43152	1.355	0.42567	D	0.993167	P	0.37955	0.612	B	0.37833	0.259	T	0.02333	-1.1175	10	0.66056	D	0.02	-6.147	13.9111	0.63866	0.1619:0.8381:0.0:0.0	.	235	P19338	NUCL_HUMAN	H	235	ENSP00000318195:D235H	ENSP00000318195:D235H	D	-	1	0	NCL	232033732	0.996000	0.38824	0.963000	0.40424	0.124000	0.20399	4.189000	0.58358	2.570000	0.86706	0.644000	0.83932	GAT	.	.	.	none		0.453	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381		G	232325488	C	G	232325488	3	3	181	1	0	0	0	0	1	0	0	0	10233	855	30	4	1473	4	NCL	2	232325488	Missense_Mutation	SNP	C	TCGA-G7-A8LD-01A-11D-A35Z-10	82471687	232325488	10873885	10	10557											
PER2	8864	hgsc.bcm.edu	37	chr2	239164455	239164455	+	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	tccttggtgaggcccagcttCttgaagggctccttctcttg	4	14	11	12	0	2	2	0	2	2	0	5	2	4	2	3	3	1	2	3	3	1	5			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr2:239164455C>T	ENST00000254657.3	-	18	2442	c.2163G>A	c.(2161-2163)aaG>aaA	p.K721K	PER2_ENST00000254658.3_3'UTR|AC096574.4_ENST00000456601.1_RNA	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	721	CSNK1E binding domain. {ECO:0000250}.				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)		GGCCCAGCTTCTTGAAGGGCT	0.562																																					p.K721K		Atlas-SNP	.											.	PER2	85	.	0			c.G2163A						PASS	.						84	89	87					2																	239164455		2203	4300	6503	SO:0001819	synonymous_variant	8864	exon18			CAGCTTCTTGAAG	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.2163G>A	chr2.hg19:g.239164455C>T		151.0	0.0	.		117.0	48.0	.	NM_022817	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Silent	SNP	ENST00000254657.3	hg19	CCDS2528.1																																																																																			.	.	.	none		0.562	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817		T	239164455	C	T	239164455	2	4	181	1	0	0	0	0	0	0	0	1	11737	912	32	2		2	PER2	2	239164455	Silent	SNP	C	TCGA-G7-A8LD-01A-11D-A35Z-10	6838967	239164455	4034918	11	10558											
HACL1	26061	hgsc.bcm.edu	37	chr3	15616583	15616583	+	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	acaattacatcagcaaattgCaaagccctattaaaaaaatt	20	10	3	8	0	1	0	1	0	0	0	1	0	1	0	1	0	4	2	1	0	9	5			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr3:15616583C>A	ENST00000321169.5	-	10	1177	c.810G>T	c.(808-810)ttG>ttT	p.L270F	HACL1_ENST00000435217.2_Intron|HACL1_ENST00000451445.2_Missense_Mutation_p.L188F|HACL1_ENST00000456194.2_Missense_Mutation_p.L243F|HACL1_ENST00000457447.2_Missense_Mutation_p.L244F	NM_012260.2	NP_036392.2	Q9UJ83	HACL1_HUMAN	2-hydroxyacyl-CoA lyase 1	270					cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carbon-carbon lyase activity (GO:0016830)|cofactor binding (GO:0048037)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|receptor binding (GO:0005102)|thiamine pyrophosphate binding (GO:0030976)			NS(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	16						CAGCAAATTGCAAAGCCCTAT	0.303																																					p.L270F		Atlas-SNP	.											.	HACL1	33	.	0			c.G810T						PASS	.						54	54	54					3																	15616583		2203	4300	6503	SO:0001583	missense	26061	exon10			AAATTGCAAAGCC	AJ131753	CCDS2627.1, CCDS68360.1, CCDS68361.1, CCDS68362.1	3p24.3	2009-01-14	2006-05-16	2006-05-16	ENSG00000131373	ENSG00000131373	4.1.-.-		17856	protein-coding gene	gene with protein product		604300	"2-hydroxyphytanoyl-CoA lyase"	HPCL		10468558, 15644336	Standard	NM_001284416		Approved	2-HPCL, PHYH2	uc003caf.3	Q9UJ83	OTTHUMG00000129862	ENST00000321169.5:c.810G>T	chr3.hg19:g.15616583C>A	ENSP00000323811:p.Leu270Phe	457.0	0.0	.		472.0	196.0	.	NM_012260	B4DWI1|B4DXI5|E9PEN4|Q9BV42|Q9P0A2	Missense_Mutation	SNP	ENST00000321169.5	hg19	CCDS2627.1	.	.	.	.	.	.	.	.	.	.	C	17.32	3.359593	0.61403	.	.	ENSG00000131373	ENST00000321169;ENST00000451445;ENST00000456194;ENST00000457447	T;T;T;T	0.50548	0.74;0.74;0.74;0.74	5.77	2.98	0.34508	Thiamine pyrophosphate enzyme, central domain (1);	0.000000	0.85682	D	0.000000	T	0.71256	0.3318	M	0.91920	3.255	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;1.0;1.0;0.999	T	0.72520	-0.4268	10	0.87932	D	0	.	9.0828	0.36563	0.0:0.6275:0.0:0.3725	.	188;244;243;270	B4DXI5;E9PEN4;B4DWI1;Q9UJ83	.;.;.;HACL1_HUMAN	F	270;188;243;244	ENSP00000323811:L270F;ENSP00000403656:L188F;ENSP00000390699:L243F;ENSP00000404883:L244F	ENSP00000323811:L270F	L	-	3	2	HACL1	15591587	1.000000	0.71417	0.978000	0.43139	0.995000	0.86356	1.302000	0.33459	0.340000	0.23745	0.650000	0.86243	TTG	.	.	.	none		0.303	HACL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252104.3	NM_012260		A	15616583	C	A	15616583	3	1	181	1	0	0	0	0	1	0	0	0	6948	709	25	4	958	4	HACL1	3	15616583	Missense_Mutation	SNP	C	TCGA-G7-A8LD-01A-11D-A35Z-10		15616583	182405847	12	10559											
BAP1	8314	hgsc.bcm.edu	37	chr3	52437709	52437709	+	Frame_Shift_Del	DEL	G	G	-																															tcattgctgggggtgggtgaGggctgcgagtgtgtgggcac																										TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr3:52437709delG	ENST00000460680.1	-	13	1923	c.1452delC	c.(1450-1452)cccfs	p.P484fs	BAP1_ENST00000296288.5_Frame_Shift_Del_p.P466fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	188					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		GGGTGGGTGAGGGCTGCGAGT	0.612			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.S485fs	GBM(101;493 1458 7992 21037 25532)	Atlas-Indel,Pindel	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	0			c.1453delT						PASS	.						42	45	44					3																	52437709		2203	4300	6503	SO:0001589	frameshift_variant	8314	exon13			.	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1452delC	chr3.hg19:g.52437709delG	ENSP00000417132:p.Pro484fs	74.0	0.0	0		44.0	36.0	0.818182	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Frame_Shift_Del	DEL	ENST00000460680.1	hg19	CCDS2853.1																																																																																			.	.	.	none		0.612	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			-	52437709	G	-	52437709	7	5	181	1	0	1	0	1	0	0	0	0	1311	987	35	0	757	0	BAP1	3	52437709	Frame_Shift_Del	DEL	G	TCGA-G7-A8LD-01A-11D-A35Z-10	36821126	52437709	145584721	13	10560											
COPB2	9276	hgsc.bcm.edu	37	chr3	139092573	139092573	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaccctcttagactggccaCgcaccataccctctccattc	8	10	5	18	1	2	2	0	1	2	1	4	2	2	2	5	1	1	1	5	1	2	3			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr3:139092573C>T	ENST00000333188.5	-	8	1010	c.829G>A	c.(829-831)Gtg>Atg	p.V277M	COPB2_ENST00000507777.1_Missense_Mutation_p.V248M	NM_004766.2	NP_004757.1	P35606	COPB2_HUMAN	coatomer protein complex, subunit beta 2 (beta prime)	277					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)	structural molecule activity (GO:0005198)	p.V277L(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	24						AGACTGGCCACGCACCATACC	0.433																																					p.V277M		Atlas-SNP	.											COPB2,NS,carcinoma,0,1	COPB2	80	.	1	Substitution - Missense(1)	endometrium(1)	c.G829A						PASS	.						156	128	138					3																	139092573		2203	4300	6503	SO:0001583	missense	9276	exon8			TGGCCACGCACCA	BC000326	CCDS3108.1	3q23	2013-01-10			ENSG00000184432	ENSG00000184432		"WD repeat domain containing"	2232	protein-coding gene	gene with protein product		606990				9858824	Standard	NM_004766		Approved	beta'-COP, betaprime-COP	uc003etf.4	P35606	OTTHUMG00000159959	ENST00000333188.5:c.829G>A	chr3.hg19:g.139092573C>T	ENSP00000329419:p.Val277Met	98.0	1.0	.		138.0	43.0	.	NM_004766	B4DZI8	Missense_Mutation	SNP	ENST00000333188.5	hg19	CCDS3108.1	.	.	.	.	.	.	.	.	.	.	C	17.05	3.290256	0.59976	.	.	ENSG00000184432	ENST00000333188;ENST00000507777	T;T	0.22743	2.07;1.94	5.1	5.1	0.69264	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (2);	0.000000	0.85682	D	0.000000	T	0.15392	0.0371	N	0.16016	0.355	0.80722	D	1	B	0.25272	0.122	B	0.19391	0.025	T	0.05920	-1.0856	10	0.41790	T	0.15	-2.1291	18.8549	0.92247	0.0:1.0:0.0:0.0	.	277	P35606	COPB2_HUMAN	M	277;248	ENSP00000329419:V277M;ENSP00000422295:V248M	ENSP00000329419:V277M	V	-	1	0	COPB2	140575263	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.942000	0.56614	2.512000	0.84698	0.655000	0.94253	GTG	.	.	.	none		0.433	COPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358495.2	NM_004766		T	139092573	C	T	139092573	3	4	181	1	0	0	0	0	1	0	0	0	3731	536	19	1	1951	1	COPB2	3	139092573	Missense_Mutation	SNP	C	TCGA-G7-A8LD-01A-11D-A35Z-10	86654864	139092573	58929857	14	10561											
ANK2	287	hgsc.bcm.edu	37	chr4	114257900	114257915	+	Frame_Shift_Del	DEL	AGATGCACCAACCTTA	AGATGCACCAACCTTA	-																															atgttgaatggttttgggggAgatgcaccaaccttaagatt																										TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	AGATGCACCAACCTTA	AGATGCACCAACCTTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr4:114257900_114257915delAGATGCACCAACCTTA	ENST00000357077.4	+	31	3812_3827	c.3759_3774delAGATGCACCAACCTTA	c.(3757-3774)ggagatgcaccaaccttafs	p.GDAPTL1253fs	ANK2_ENST00000509550.1_Frame_Shift_Del_p.GDAPTL429fs|ANK2_ENST00000504887.1_3'UTR|ANK2_ENST00000506722.1_Frame_Shift_Del_p.GDAPTL1244fs|ANK2_ENST00000264366.6_Frame_Shift_Del_p.GDAPTL1220fs|ANK2_ENST00000394537.3_Frame_Shift_Del_p.GDAPTL1253fs	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	1253	ZU5 2. {ECO:0000255|PROSITE- ProRule:PRU00485}.				atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.D1254D(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		GTTTTGGGGGAGATGCACCAACCTTAAGATTACTAT	0.38																																					p.1253_1258del		Atlas-Indel,Pindel	.											.	ANK2	576	.	1	Substitution - coding silent(1)	lung(1)	c.3758_3773del						PASS	.																																			SO:0001589	frameshift_variant	287	exon31			.	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.3759_3774delAGATGCACCAACCTTA	chr4.hg19:g.114257900_114257915delAGATGCACCAACCTTA	ENSP00000349588:p.Gly1253fs	158.0	0.0	0		66.0	41.0	0.621212	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Frame_Shift_Del	DEL	ENST00000357077.4	hg19	CCDS3702.1																																																																																			.	.	.	none		0.38	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		-	114257915	AGATGCACCAACCTTA	-	114257900	7	5	181	1	0	1	0	1	0	0	0	0	621	291	11	0	3946	0	ANK2	4	114257900	Frame_Shift_Del	DEL	AGATGCACCAACCTTA	TCGA-G7-A8LD-01A-11D-A35Z-10		114257900	76896376	15	10562											
FSTL4	23105	hgsc.bcm.edu	37	chr5	132556553	132556553	+	Missense_Mutation	SNP	T	T	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	atagaacatgtttcccacgcTgaggcctgggaggagcaaat	12	8	12	9	1	0	2	0	1	0	1	1	4	1	4	2	3	2	3	2	3	3	2			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr5:132556553T>G	ENST00000265342.7	-	12	1594	c.1345A>C	c.(1345-1347)Agc>Cgc	p.S449R	FSTL4_ENST00000507112.1_5'UTR|CTB-49A3.2_ENST00000509051.1_RNA|CTB-49A3.2_ENST00000502776.1_RNA	NM_015082.1	NP_055897.1	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	449						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(8)|skin(2)|upper_aerodigestive_tract(1)	23		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TTTCCCACGCTGAGGCCTGGG	0.562																																					p.S449R		Atlas-SNP	.											.	FSTL4	74	.	0			c.A1345C						PASS	.						110	98	102					5																	132556553		2203	4300	6503	SO:0001583	missense	23105	exon12			CCACGCTGAGGCC	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.1345A>C	chr5.hg19:g.132556553T>G	ENSP00000265342:p.Ser449Arg	120.0	0.0	.		109.0	43.0	.	NM_015082	Q8TBU0|Q9UPU1	Missense_Mutation	SNP	ENST00000265342.7	hg19	CCDS34238.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.057526	0.76074	.	.	ENSG00000053108	ENST00000265342;ENST00000360575	T	0.60299	0.2	5.35	4.18	0.49190	.	0.079177	0.85682	D	0.000000	T	0.68311	0.2987	L	0.53249	1.67	0.54753	D	0.999988	D;D	0.89917	1.0;0.996	D;D	0.74348	0.983;0.943	T	0.67385	-0.5684	10	0.48119	T	0.1	-13.6265	10.6069	0.45400	0.0:0.0757:0.0:0.9243	.	449;98	Q6MZW2;B3KPF3	FSTL4_HUMAN;.	R	449;280	ENSP00000265342:S449R	ENSP00000265342:S449R	S	-	1	0	FSTL4	132584452	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.123000	0.50453	0.980000	0.38523	0.482000	0.46254	AGC	.	.	.	none		0.562	FSTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370212.1	XM_048786		G	132556553	T	G	132556553	3	3	181	1	0	0	0	0	1	0	0	0	6086	1580	55	5	1203	5	FSTL4	5	132556553	Missense_Mutation	SNP	T	TCGA-G7-A8LD-01A-11D-A35Z-10		132556553	48358707	16	10563											
PCDHA9	9752	hgsc.bcm.edu	37	chr5	140229249	140229249	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaggttacctgctccctgaCgccccacgtccccttcaagc	6	8	8	19	2	1	1	1	1	0	0	3	1	3	1	6	1	3	3	6	1	2	2			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr5:140229249C>T	ENST00000532602.1	+	1	2202	c.1169C>T	c.(1168-1170)aCg>aTg	p.T390M	PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA9_ENST00000378122.3_Missense_Mutation_p.T390M|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	390	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(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)			TGCTCCCTGACGCCCCACGTC	0.562																																					p.T390M	Melanoma(55;1800 1972 14909)	Atlas-SNP	.											.	PCDHA9	373	.	0			c.C1169T						PASS	.						112	101	105					5																	140229249		2196	4274	6470	SO:0001583	missense	9752	exon1			CCCTGACGCCCCA	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.1169C>T	chr5.hg19:g.140229249C>T	ENSP00000436042:p.Thr390Met	177.0	0.0	.		194.0	84.0	.	NM_031857	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	hg19	CCDS54920.1	.	.	.	.	.	.	.	.	.	.	C	12.10	1.837550	0.32513	.	.	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.53206	0.63;0.63	3.6	0.613	0.17597	Cadherin (4);Cadherin-like (1);	0.730603	0.10108	U	0.715048	T	0.25121	0.0610	L	0.29908	0.895	0.09310	N	1	P;B	0.44260	0.83;0.421	B;B	0.33254	0.16;0.034	T	0.12218	-1.0556	10	0.33141	T	0.24	.	2.2108	0.03947	0.2563:0.4568:0.1254:0.1615	.	390;390	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	M	390	ENSP00000436042:T390M;ENSP00000367362:T390M	ENSP00000367362:T390M	T	+	2	0	PCDHA9	140209433	0.000000	0.05858	0.000000	0.03702	0.093000	0.18481	-2.560000	0.00921	-0.019000	0.14055	0.313000	0.20887	ACG	.	.	.	none		0.562	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		T	140229249	C	T	140229249	3	4	181	1	0	0	0	0	1	0	0	0	11538	536	19	1	1171	1	PCDHA9	5	140229249	Missense_Mutation	SNP	C	TCGA-G7-A8LD-01A-11D-A35Z-10	7672696	140229249	40686011	17	10564											
ZNF184	7738	hgsc.bcm.edu	37	chr6	27419747	27419747	+	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	tttcccacattctttacattCataagctttctcttgagtat	9	19	3	10	0	3	1	1	1	2	0	5	1	4	1	1	0	2	2	1	0	3	9			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr6:27419747C>G	ENST00000211936.6	-	6	1875	c.1591G>C	c.(1591-1593)Gaa>Caa	p.E531Q	ZNF184_ENST00000377419.1_Missense_Mutation_p.E531Q	NM_007149.2	NP_009080.2	Q99676	ZN184_HUMAN	zinc finger protein 184	531					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|kidney(9)|large_intestine(13)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						TCTTTACATTCATAAGCTTTC	0.383																																					p.E531Q		Atlas-SNP	.											.	ZNF184	89	.	0			c.G1591C						PASS	.						65	67	66					6																	27419747		2203	4299	6502	SO:0001583	missense	7738	exon6			TACATTCATAAGC	U66561	CCDS4624.1	6p21.3	2013-01-08	2006-06-28		ENSG00000096654	ENSG00000096654		"Zinc fingers, C2H2-type", "-"	12975	protein-coding gene	gene with protein product		602277	"zinc finger protein 184 (Kruppel-like)"				Standard	NM_007149		Approved		uc003nji.3	Q99676	OTTHUMG00000014478	ENST00000211936.6:c.1591G>C	chr6.hg19:g.27419747C>G	ENSP00000211936:p.Glu531Gln	46.0	0.0	.		54.0	12.0	.	NM_007149	B2R715|O60792|Q8TBA9	Missense_Mutation	SNP	ENST00000211936.6	hg19	CCDS4624.1	.	.	.	.	.	.	.	.	.	.	C	13.81	2.347859	0.41599	.	.	ENSG00000096654	ENST00000211936;ENST00000377419;ENST00000341087	T;T	0.35973	1.28;1.28	5.18	4.27	0.50696	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.50627	D	0.000106	T	0.10337	0.0253	N	0.11341	0.13	0.19300	N	0.99997	P	0.42961	0.795	B	0.42138	0.377	T	0.05305	-1.0893	10	0.48119	T	0.1	.	8.7945	0.34872	0.1669:0.6716:0.1615:0.0	.	531	Q99676	ZN184_HUMAN	Q	531;531;447	ENSP00000211936:E531Q;ENSP00000366636:E531Q	ENSP00000211936:E531Q	E	-	1	0	ZNF184	27527726	0.000000	0.05858	1.000000	0.80357	0.988000	0.76386	-1.449000	0.02392	2.696000	0.92011	0.591000	0.81541	GAA	.	.	.	none		0.383	ZNF184-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040146.1	NM_007149		G	27419747	C	G	27419747	3	3	181	1	0	0	0	0	1	0	0	0	17763	835	29	4	668	4	ZNF184	6	27419747	Missense_Mutation	SNP	C	TCGA-G7-A8LD-01A-11D-A35Z-10		27419747	143695320	18	10565											
TAF8	129685	hgsc.bcm.edu	37	chr6	42025251	42025251	+	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	cacacctacatcaaaactccGgtgagtgatgaagcactggg	13	7	10	11	1	1	3	1	3	0	0	2	3	2	3	2	2	3	1	2	2	4	1	rs554917914	byFrequency	TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr6:42025251G>A	ENST00000372977.3	+	5	507	c.489G>A	c.(487-489)ccG>ccA	p.P163P	TAF8_ENST00000494547.1_Splice_Site_p.P163P|TAF8_ENST00000482926.1_3'UTR|TAF8_ENST00000372982.4_Splice_Site_p.P163P|TAF8_ENST00000372978.3_Silent_p.P163P|TAF8_ENST00000456846.2_Splice_Site_p.P163P|TAF8_ENST00000465926.1_Splice_Site_p.P100P	NM_138572.2	NP_612639.2	Q7Z7C8	TAF8_HUMAN	TAF8 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 43kDa	163					cell differentiation (GO:0030154)|inner cell mass cell proliferation (GO:0001833)|maintenance of protein location in nucleus (GO:0051457)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fat cell differentiation (GO:0045598)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|transcription factor TFIID complex (GO:0005669)				endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	6	Colorectal(47;0.196)		STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00179)			TCAAAACTCCGGTGAGTGATG	0.572													G|||	3	0.000599042	0.0023	0	5008	,	,		16681	0		0	False		,,,				2504	0				p.P163P		Atlas-SNP	.											.	TAF8	25	.	0			c.G489A						PASS	.						66	68	68					6																	42025251		2003	4177	6180	SO:0001630	splice_region_variant	129685	exon5			AACTCCGGTGAGT	AK057383	CCDS43462.1	6p21.1	2008-10-23	2007-07-30	2007-07-30	ENSG00000137413	ENSG00000137413			17300	protein-coding gene	gene with protein product		609514	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 45/50kDa", "taube nuss homolog (mouse)"	TBN			Standard	NM_138572		Approved	FLJ32821, TAF(II)43	uc003ors.3	Q7Z7C8	OTTHUMG00000014692	ENST00000372977.3:c.489+1G>A	chr6.hg19:g.42025251G>A		112.0	0.0	.		78.0	67.0	.	NM_138572	Q5T0K1|Q8N4R9|Q96M52	Silent	SNP	ENST00000372977.3	hg19	CCDS43462.1																																																																																			.	.	.	none		0.572	TAF8-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000357901.1	NM_138572	Silent	A	42025251	G	A	42025251	5	1	181	1	0	0	0	0	0	0	1	0	15546	1130	39	1	507	1	TAF8	6	42025251	Splice_Site	SNP	G	TCGA-G7-A8LD-01A-11D-A35Z-10	14605504	42025251	129089816	19	10566											
SERAC1	84947	hgsc.bcm.edu	37	chr6	158565380	158565380	+	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	ggagaaaaaagcgaagatcaCtctcttcgcttcgtgccaaa	14	8	9	10	3	2	2	1	0	1	2	5	4	2	2	1	1	2	1	1	1	5	2			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr6:158565380C>T	ENST00000367104.3	-	7	691	c.560G>A	c.(559-561)aGt>aAt	p.S187N	SERAC1_ENST00000367102.2_Missense_Mutation_p.S187N|SERAC1_ENST00000367101.1_Missense_Mutation_p.S187N	NM_032861.3	NP_116250.3	Q96JX3	SRAC1_HUMAN	serine active site containing 1	187					extracellular matrix organization (GO:0030198)|GPI anchor metabolic process (GO:0006505)|intracellular protein transport (GO:0006886)|phospholipid biosynthetic process (GO:0008654)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)			endometrium(1)|kidney(2)|large_intestine(6)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	15		Breast(66;0.00519)|Ovarian(120;0.123)|Prostate(117;0.178)		OV - Ovarian serous cystadenocarcinoma(65;1.37e-18)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)		GCGAAGATCACTCTCTTCGCT	0.328																																					p.S187N		Atlas-SNP	.											.	SERAC1	31	.	0			c.G560A						PASS	.						85	87	87					6																	158565380		2203	4300	6503	SO:0001583	missense	84947	exon7			AGATCACTCTCTT	BC001705	CCDS5255.1	6q25.3	2003-05-12			ENSG00000122335	ENSG00000122335			21061	protein-coding gene	gene with protein product		614725					Standard	NM_032861		Approved	FLJ14917	uc003qrc.2	Q96JX3	OTTHUMG00000015905	ENST00000367104.3:c.560G>A	chr6.hg19:g.158565380C>T	ENSP00000356071:p.Ser187Asn	249.0	0.0	.		229.0	101.0	.	NM_032861	Q49AT1|Q5VTX3|Q6PKF3	Missense_Mutation	SNP	ENST00000367104.3	hg19	CCDS5255.1	.	.	.	.	.	.	.	.	.	.	C	14.81	2.645153	0.47258	.	.	ENSG00000122335	ENST00000367102;ENST00000367104;ENST00000367101	T;T;T	0.67865	-0.29;-0.29;-0.29	5.8	2.87	0.33458	Armadillo-like helical (1);	0.320817	0.37955	N	0.001871	T	0.38108	0.1028	L	0.44542	1.39	0.27038	N	0.964089	P	0.36465	0.554	B	0.30105	0.111	T	0.38478	-0.9659	10	0.56958	D	0.05	-16.1029	11.2274	0.48892	0.12:0.3136:0.5664:0.0	.	187	Q96JX3	SRAC1_HUMAN	N	187	ENSP00000356069:S187N;ENSP00000356071:S187N;ENSP00000356068:S187N	ENSP00000356068:S187N	S	-	2	0	SERAC1	158485368	0.990000	0.36364	0.998000	0.56505	0.997000	0.91878	1.940000	0.40223	2.227000	0.72691	0.460000	0.39030	AGT	.	.	.	none		0.328	SERAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042862.1	NM_032861		T	158565380	C	T	158565380	3	4	181	1	0	0	0	0	1	0	0	0	14087	565	20	2	1448	2	SERAC1	6	158565380	Missense_Mutation	SNP	C	TCGA-G7-A8LD-01A-11D-A35Z-10	116540129	158565380	12549687	20	10567											
DPY19L1	23333	hgsc.bcm.edu	37	chr7	34979806	34979806	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccattctataagttcttctTggggcaaattgctgaactcc	9	15	7	10	0	3	1	0	1	3	0	5	1	5	1	2	2	2	3	2	2	4	7			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr7:34979806T>C	ENST00000310974.4	-	19	1748	c.1604A>G	c.(1603-1605)cAa>cGa	p.Q535R	MIR548N_ENST00000408742.1_RNA	NM_015283.1	NP_056098.1	Q2PZI1	D19L1_HUMAN	dpy-19-like 1 (C. elegans)	535						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						AAGTTCTTCTTGGGGCAAATT	0.328																																					p.Q535R		Atlas-SNP	.											.	DPY19L1	56	.	0			c.A1604G						PASS	.						75	61	65					7																	34979806		1804	4072	5876	SO:0001583	missense	23333	exon19			TCTTCTTGGGGCA	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.1604A>G	chr7.hg19:g.34979806T>C	ENSP00000308695:p.Gln535Arg	52.0	0.0	.		47.0	15.0	.	NM_015283	O94954|Q4G151	Missense_Mutation	SNP	ENST00000310974.4	hg19	CCDS43567.1	.	.	.	.	.	.	.	.	.	.	T	16.76	3.210972	0.58343	.	.	ENSG00000173852	ENST00000310974	T	0.55930	0.49	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.72969	0.3527	M	0.84433	2.695	0.58432	D	0.999998	D	0.64830	0.994	D	0.76575	0.988	T	0.73075	-0.4097	10	0.24483	T	0.36	-10.8889	14.1743	0.65529	0.0:0.0:0.0:1.0	.	535	Q2PZI1	D19L1_HUMAN	R	535	ENSP00000308695:Q535R	ENSP00000308695:Q535R	Q	-	2	0	DPY19L1	34946331	1.000000	0.71417	0.990000	0.47175	0.069000	0.16628	7.972000	0.88022	2.009000	0.58944	0.482000	0.46254	CAA	.	.	.	none		0.328	DPY19L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337506.1			C	34979806	T	C	34979806	3	2	181	1	0	0	0	0	1	0	0	0	4742	1812	63	3	439	3	DPY19L1	7	34979806	Missense_Mutation	SNP	T	TCGA-G7-A8LD-01A-11D-A35Z-10		34979806	124158857	21	10568											
ZNF713	349075	hgsc.bcm.edu	37	chr7	56007671	56007671	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaatgtgagcaaactgttcGccacagtccttcatttagca	12	12	7	10	1	1	1	1	1	0	0	3	1	2	1	2	0	3	3	2	0	4	5	rs371670199		TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr7:56007671G>A	ENST00000429591.2	+	4	1303	c.1265G>A	c.(1264-1266)cGc>cAc	p.R422H	MRPS17_ENST00000426595.1_Intron	NM_182633.1	NP_872439.1	Q8N859	ZN713_HUMAN	zinc finger protein 713	422					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			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)			CAAACTGTTCGCCACAGTCCT	0.388													G|||	1	0.000199681	0	0	5008	,	,		16485	0		0.001	False		,,,				2504	0				p.R422H		Atlas-SNP	.											.	ZNF713	47	.	0			c.G1265A						PASS	.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	46	48	47		1265	2.7	0	7		47	0,8600		0,0,4300	no	missense	ZNF713	NM_182633.1	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	422/431	56007671	1,13005	2203	4300	6503	SO:0001583	missense	349075	exon4			CTGTTCGCCACAG	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.1265G>A	chr7.hg19:g.56007671G>A	ENSP00000416662:p.Arg422His	77.0	0.0	.		90.0	23.0	.	NM_182633		Missense_Mutation	SNP	ENST00000429591.2	hg19	CCDS34639.1	.	.	.	.	.	.	.	.	.	.	G	2.378	-0.342694	0.05243	2.27E-4	0.0	ENSG00000178665	ENST00000429591	T	0.06449	3.3	3.54	2.66	0.31614	.	0.625593	0.14282	N	0.329436	T	0.04679	0.0127	L	0.32530	0.975	0.09310	N	1	B	0.30824	0.296	B	0.22601	0.04	T	0.35871	-0.9771	10	0.72032	D	0.01	.	4.9192	0.13862	0.1194:0.2201:0.6605:0.0	.	422	Q8N859	ZN713_HUMAN	H	422	ENSP00000416662:R422H	ENSP00000416662:R422H	R	+	2	0	ZNF713	55975165	0.000000	0.05858	0.003000	0.11579	0.058000	0.15608	0.306000	0.19279	1.064000	0.40671	0.467000	0.42956	CGC	.	.	.	weak		0.388	ZNF713-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343297.1	NM_182633		A	56007671	G	A	56007671	3	1	181	1	0	0	0	0	1	0	0	0	18129	1087	38	1	1279	1	ZNF713	7	56007671	Missense_Mutation	SNP	G	TCGA-G7-A8LD-01A-11D-A35Z-10	21027865	56007671	103130992	22	10569											
MUC17	140453	hgsc.bcm.edu	37	chr7	100679220	100679220	+	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	taccagcatagcaatctcaaCgcctagtgaaggaagcactg	14	7	9	11	1	1	1	1	1	1	0	2	2	1	2	2	1	5	3	2	1	7	3	rs374713003		TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr7:100679220C>T	ENST00000306151.4	+	3	4587	c.4523C>T	c.(4522-4524)aCg>aTg	p.T1508M		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1508	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)					GCAATCTCAACGCCTAGTGAA	0.473																																					p.T1508M		Atlas-SNP	.											.	MUC17	804	.	0			c.C4523T						PASS	.	G	MET/THR	1,4405	2.1+/-5.4	0,1,2202	209	197	201		4523	-0.1	0	7		201	1,8599	1.2+/-3.3	0,1,4299	no	missense	MUC17	NM_001040105.1	81	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging	1508/4494	100679220	2,13004	2203	4300	6503	SO:0001583	missense	140453	exon3			TCTCAACGCCTAG	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.4523C>T	chr7.hg19:g.100679220C>T	ENSP00000302716:p.Thr1508Met	93.0	0.0	.		80.0	44.0	.	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	c	0.032	-1.330977	0.01298	2.27E-4	1.16E-4	ENSG00000169876	ENST00000306151	T	0.03330	3.97	0.922	-0.0705	0.13747	.	.	.	.	.	T	0.04092	0.0114	N	0.19112	0.55	0.09310	N	1	D	0.64830	0.994	P	0.53185	0.72	T	0.45454	-0.9260	9	0.32370	T	0.25	.	4.9293	0.13909	0.0:0.6094:0.3906:0.0	.	1508	Q685J3	MUC17_HUMAN	M	1508	ENSP00000302716:T1508M	ENSP00000302716:T1508M	T	+	2	0	MUC17	100465940	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.062000	0.14389	0.011000	0.14865	-1.865000	0.00557	ACG	.	.	.	weak		0.473	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		T	100679220	C	T	100679220	3	4	181	1	0	0	0	0	1	0	0	0	9981	536	19	1	4533	1	MUC17	7	100679220	Missense_Mutation	SNP	C	TCGA-G7-A8LD-01A-11D-A35Z-10	44671549	100679220	58459443	23	10570											
EPHB6	2051	hgsc.bcm.edu	37	chr7	142562074	142562074	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcctcctcctcctcctcCtcttcttcctctgcagcgtg	1	15	4	21	1	3	0	0	0	3	0	11	0	11	0	8	0	2	1	8	0	0	2			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr7:142562074C>T	ENST00000392957.2	+	7	1303	c.516C>T	c.(514-516)tcC>tcT	p.S172S	EPHB6_ENST00000411471.2_Intron|EPHB6_ENST00000442129.1_Silent_p.S172S	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	172	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.|Poly-Ser.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					cctcctcctcctcttcttcct	0.622																																					p.S172S		Atlas-SNP	.											.	EPHB6	168	.	0			c.C516T						PASS	.						83	98	93					7																	142562074		2200	4299	6499	SO:0001819	synonymous_variant	2051	exon7			CTCCTCCTCTTCT	D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"EPH receptors", "Sterile alpha motif (SAM) domain containing", "Fibronectin type III domain containing"	3396	protein-coding gene	gene with protein product		602757	"EphB6"				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.516C>T	chr7.hg19:g.142562074C>T		87.0	0.0	.		89.0	5.0	.	NM_004445	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Silent	SNP	ENST00000392957.2	hg19	CCDS5873.2																																																																																			.	.	.	none		0.622	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			T	142562074	C	T	142562074	2	4	181	1	0	0	0	0	0	0	0	1	5180	668	24	2		2	EPHB6	7	142562074	Silent	SNP	C	TCGA-G7-A8LD-01A-11D-A35Z-10	41882854	142562074	16576589	24	10571											
DPP6	1804	hgsc.bcm.edu	37	chr7	154598747	154598747	+	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	acaggcagtgcctctcctgtGacctggttgagaactgcacc	8	9	11	13	0	1	2	0	2	1	1	2	3	1	2	4	2	3	3	4	2	1	1			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr7:154598747G>T	ENST00000377770.3	+	16	1732	c.1591G>T	c.(1591-1593)Gac>Tac	p.D531Y	DPP6_ENST00000332007.3_Missense_Mutation_p.D469Y|DPP6_ENST00000404039.1_Missense_Mutation_p.D467Y|DPP6_ENST00000427557.1_Missense_Mutation_p.D424Y			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	531					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			CCTCTCCTGTGACCTGGTTGA	0.592																																					p.D531Y	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-SNP	.											.	DPP6	383	.	0			c.G1591T						PASS	.						138	142	141					7																	154598747		2134	4247	6381	SO:0001583	missense	1804	exon16			TCCTGTGACCTGG	M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"dipeptidylpeptidase VI", "dipeptidylpeptidase 6"			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.1591G>T	chr7.hg19:g.154598747G>T	ENSP00000367001:p.Asp531Tyr	50.0	0.0	.		60.0	11.0	.	NM_130797		Missense_Mutation	SNP	ENST00000377770.3	hg19		.	.	.	.	.	.	.	.	.	.	G	18.43	3.622636	0.66787	.	.	ENSG00000130226	ENST00000404039;ENST00000377770;ENST00000332007;ENST00000427557	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	4.8	4.8	0.61643	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.243493	0.39759	N	0.001271	T	0.53722	0.1814	M	0.74258	2.255	0.58432	D	0.999999	P;P;D;D	0.59357	0.943;0.954;0.985;0.985	P;P;P;P	0.61477	0.886;0.823;0.889;0.889	T	0.60089	-0.7331	10	0.72032	D	0.01	-38.514	16.667	0.85255	0.0:0.0:1.0:0.0	.	424;469;531;467	E9PDL2;P42658-2;P42658;E9PF59	.;.;DPP6_HUMAN;.	Y	467;531;469;424	ENSP00000385578:D467Y;ENSP00000367001:D531Y;ENSP00000328226:D469Y;ENSP00000397303:D424Y	ENSP00000328226:D469Y	D	+	1	0	DPP6	154229680	1.000000	0.71417	0.994000	0.49952	0.985000	0.73830	8.294000	0.89934	2.177000	0.69029	0.655000	0.94253	GAC	.	.	.	none		0.592	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797		T	154598747	G	T	154598747	3	4	181	1	0	0	0	0	1	0	0	0	4732	1290	45	4	1769	4	DPP6	7	154598747	Missense_Mutation	SNP	G	TCGA-G7-A8LD-01A-11D-A35Z-10	12036673	154598747	4539916	25	10572											
RIMS2	9699	hgsc.bcm.edu	37	chr8	104924348	104924348	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgcattttattaaataagcGtctaaaagatggaagtgtac	15	13	8	5	2	1	1	0	0	1	1	2	2	1	2	0	1	2	2	0	1	8	6	rs375138135		TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr8:104924348G>A	ENST00000436393.2	+	4	1335	c.1094G>A	c.(1093-1095)cGt>cAt	p.R365H	RIMS2_ENST00000262231.10_Missense_Mutation_p.R442H|RIMS2_ENST00000406091.3_Missense_Mutation_p.R587H|RIMS2_ENST00000507740.1_Missense_Mutation_p.R395H			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	665					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.R395H(1)|p.R670H(1)|p.R365H(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)			TTAAATAAGCGTCTAAAAGAT	0.353										HNSCC(12;0.0054)																											p.R587H		Atlas-SNP	.											RIMS2_ENST00000507740,NS,carcinoma,0,13	RIMS2	1357	.	3	Substitution - Missense(3)	large_intestine(3)	c.G1760A						PASS	.	G	HIS/ARG,HIS/ARG	1,3687		0,1,1843	119	116	117		1760,1184	5.9	1	8		117	1,8175		0,1,4087	no	missense,missense	RIMS2	NM_001100117.2,NM_014677.4	29,29	0,2,5930	AA,AG,GG		0.0122,0.0271,0.0169	probably-damaging,probably-damaging	587/1350,395/1164	104924348	2,11862	1844	4088	5932	SO:0001583	missense	9699	exon6			ATAAGCGTCTAAA	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.1094G>A	chr8.hg19:g.104924348G>A	ENSP00000390665:p.Arg365His	130.0	0.0	.		138.0	35.0	.	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	ENST00000436393.2	hg19		.	.	.	.	.	.	.	.	.	.	G	35	5.445035	0.96187	2.71E-4	1.22E-4	ENSG00000176406	ENST00000504942;ENST00000329869;ENST00000406091;ENST00000402998;ENST00000515551;ENST00000262231;ENST00000507740;ENST00000408894;ENST00000436393	T;T;T;T;T;T;T	0.21031	2.03;2.52;2.15;2.22;2.2;2.14;2.53	5.92	5.92	0.95590	PDZ/DHR/GLGF (1);	.	.	.	.	T	0.44644	0.1303	L	0.49778	1.585	0.80722	D	1	D;D;D;D;D	0.89917	0.998;0.997;0.999;0.998;1.0	D;D;D;D;D	0.81914	0.977;0.977;0.992;0.98;0.995	T	0.14254	-1.0479	9	0.66056	D	0.02	.	20.3343	0.98733	0.0:0.0:1.0:0.0	.	665;365;442;395;587	Q9UQ26;D6RA03;Q9UQ26-1;Q9UQ26-3;F8WD47	RIMS2_HUMAN;.;.;.;.	H	587;618;587;665;395;442;395;395;365	ENSP00000427018:R587H;ENSP00000384892:R587H;ENSP00000425205:R395H;ENSP00000262231:R442H;ENSP00000423559:R395H;ENSP00000386228:R395H;ENSP00000390665:R365H	ENSP00000262231:R442H	R	+	2	0	RIMS2	104993524	1.000000	0.71417	0.995000	0.50966	0.979000	0.70002	7.833000	0.86765	2.822000	0.97130	0.650000	0.86243	CGT	.	.	.	weak		0.353	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117		A	104924348	G	A	104924348	3	1	181	1	0	0	0	0	1	0	0	0	13381	1145	40	1	1908	1	RIMS2	8	104924348	Missense_Mutation	SNP	G	TCGA-G7-A8LD-01A-11D-A35Z-10		104924348	41439674	26	10573											
WDR67	93594	hgsc.bcm.edu	37	chr8	124109586	124109586	+	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	atttgtggtgcttggaagctAggcagctctttagaattatc	9	15	11	6	0	1	1	0	0	1	1	2	2	1	2	0	3	3	4	0	3	5	6			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr8:124109586A>C	ENST00000287380.1	+	6	826	c.736A>C	c.(736-738)Agg>Cgg	p.R246R	TBC1D31_ENST00000522420.1_Silent_p.R141R|TBC1D31_ENST00000327098.5_Silent_p.R246R|TBC1D31_ENST00000521676.1_Silent_p.R141R|TBC1D31_ENST00000378080.2_Silent_p.R141R|TBC1D31_ENST00000309336.3_Silent_p.R246R	NM_145647.3	NP_663622.2	Q96DN5	TBC31_HUMAN	TBC1 domain family, member 31	246						centrosome (GO:0005813)	Rab GTPase activator activity (GO:0005097)										CTTGGAAGCTAGGCAGCTCTT	0.423																																					p.R246R		Atlas-SNP	.											.	WDR67	97	.	0			c.A736C						PASS	.						131	118	122					8																	124109586		2203	4300	6503	SO:0001819	synonymous_variant	93594	exon6			GAAGCTAGGCAGC	AK094612	CCDS6338.1, CCDS47916.1	8q24.13	2013-07-10	2013-07-10	2013-07-10	ENSG00000156787	ENSG00000156787		"WD repeat domain containing"	30888	protein-coding gene	gene with protein product			"WD repeat domain 67"	WDR67		12477932	Standard	NM_001145088		Approved	MGC21654, Gm85	uc003ypp.2	Q96DN5	OTTHUMG00000165081	ENST00000287380.1:c.736A>C	chr8.hg19:g.124109586A>C		97.0	0.0	.		121.0	38.0	.	NM_001145088	B7ZL19|Q2M2J9|Q3MIR6|Q8TBP9	Silent	SNP	ENST00000287380.1	hg19	CCDS6338.1																																																																																			.	.	.	none		0.423	TBC1D31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381721.1	NM_145647		C	124109586	A	C	124109586	2	2	181	1	0	0	0	0	0	0	0	1	17330	411	15	5		5	WDR67	8	124109586	Silent	SNP	A	TCGA-G7-A8LD-01A-11D-A35Z-10	19185238	124109586	22254436	27	10574											
MAMDC2	256691	hgsc.bcm.edu	37	chr9	72728040	72728040	+	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	acaggatcacaccttcaagaGtgaactgggtgagctgggat	12	8	13	8	0	2	3	2	2	0	1	2	5	2	5	1	3	2	1	1	3	2	1			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr9:72728040G>C	ENST00000377182.4	+	5	1252	c.635G>C	c.(634-636)aGt>aCt	p.S212T	MAMDC2-AS1_ENST00000414515.3_RNA|MAMDC2-AS1_ENST00000591368.1_RNA	NM_153267.4	NP_694999.3	Q7Z304	MAMC2_HUMAN	MAM domain containing 2	212	MAM 2. {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						ACCTTCAAGAGTGAACTGGGT	0.493																																					p.S212T		Atlas-SNP	.											.	MAMDC2	55	.	0			c.G635C						PASS	.						84	76	79					9																	72728040		2203	4300	6503	SO:0001583	missense	256691	exon5			TCAAGAGTGAACT	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.635G>C	chr9.hg19:g.72728040G>C	ENSP00000366387:p.Ser212Thr	106.0	0.0	.		87.0	33.0	.	NM_153267	Q5VW47|Q8WX43|Q96BM4	Missense_Mutation	SNP	ENST00000377182.4	hg19	CCDS6631.1	.	.	.	.	.	.	.	.	.	.	G	7.048	0.563812	0.13498	.	.	ENSG00000165072	ENST00000377182	T	0.02140	4.43	5.72	2.73	0.32206	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.205916	0.64402	D	0.000017	T	0.01627	0.0052	N	0.24115	0.695	0.26934	N	0.966406	B	0.16603	0.018	B	0.20955	0.032	T	0.48175	-0.9058	10	0.06625	T	0.88	-7.9371	9.2328	0.37448	0.4469:0.0:0.5531:0.0	.	212	Q7Z304	MAMC2_HUMAN	T	212	ENSP00000366387:S212T	ENSP00000366387:S212T	S	+	2	0	MAMDC2	71917860	1.000000	0.71417	0.994000	0.49952	0.750000	0.42670	0.641000	0.24720	0.275000	0.22094	-0.379000	0.06801	AGT	.	.	.	none		0.493	MAMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052600.1	NM_153267		C	72728040	G	C	72728040	3	2	181	1	0	0	0	0	1	0	0	0	9210	1029	36	4	653	4	MAMDC2	9	72728040	Missense_Mutation	SNP	G	TCGA-G7-A8LD-01A-11D-A35Z-10		72728040	68485391	28	10575											
NOL8	55035	hgsc.bcm.edu	37	chr9	95077665	95077665	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaaagctcacagttttctctAtttttgaaagaagttttctt	11	18	6	6	0	3	2	1	1	2	1	4	3	3	2	0	0	1	3	0	0	4	8			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr9:95077665A>G	ENST00000535387.1	-	6	1241	c.1242T>C	c.(1240-1242)aaT>aaC	p.N414N	NOL8_ENST00000358855.4_Silent_p.N346N|NOL8_ENST00000545558.1_Silent_p.N414N|NOL8_ENST00000442668.2_Silent_p.N414N|NOL8_ENST00000542053.1_Silent_p.N346N					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						AGTTTTCTCTATTTTTGAAAG	0.313																																					p.N414N		Atlas-SNP	.											.	NOL8	118	.	0			c.T1242C						PASS	.						25	21	22					9																	95077665		1802	4054	5856	SO:0001819	synonymous_variant	55035	exon7			TTCTCTATTTTTG	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.1242T>C	chr9.hg19:g.95077665A>G		83.0	0.0	.		68.0	39.0	.	NM_017948		Silent	SNP	ENST00000535387.1	hg19	CCDS47993.1																																																																																			.	.	.	none		0.313	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948		G	95077665	A	G	95077665	2	3	181	1	0	0	0	0	0	0	0	1	10534	446	16	3		3	NOL8	9	95077665	Silent	SNP	A	TCGA-G7-A8LD-01A-11D-A35Z-10	22349625	95077665	46135766	29	10576											
KIAA1462	57608	hgsc.bcm.edu	37	chr10	30317816	30317816	+	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	atcaaagggaatgtactgaaCgaagccgtcataggcagtga	15	7	12	7	2	2	2	2	2	0	0	2	4	2	3	1	2	3	2	1	2	6	2			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr10:30317816C>T	ENST00000375377.1	-	3	1362	c.1261G>A	c.(1261-1263)Gtt>Att	p.V421I		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	421					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						ATGTACTGAACGAAGCCGTCA	0.517																																					p.V421I		Atlas-SNP	.											.	KIAA1462	162	.	0			c.G1261A						PASS	.						76	80	78					10																	30317816		1946	4138	6084	SO:0001583	missense	57608	exon3			ACTGAACGAAGCC	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.1261G>A	chr10.hg19:g.30317816C>T	ENSP00000364526:p.Val421Ile	107.0	0.0	.		104.0	9.0	.	NM_020848	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Missense_Mutation	SNP	ENST00000375377.1	hg19	CCDS41500.1	.	.	.	.	.	.	.	.	.	.	C	13.04	2.118022	0.37339	.	.	ENSG00000165757	ENST00000375377	T	0.16743	2.32	5.42	2.49	0.30216	.	0.321071	0.29900	N	0.010915	T	0.08980	0.0222	N	0.13327	0.33	0.32893	D	0.512148	D	0.60575	0.988	B	0.40636	0.335	T	0.22487	-1.0215	10	0.27785	T	0.31	-9.6829	10.3754	0.44079	0.0:0.7798:0.0:0.2202	.	421	Q9P266	K1462_HUMAN	I	421	ENSP00000364526:V421I	ENSP00000364526:V421I	V	-	1	0	KIAA1462	30357822	0.030000	0.19436	0.038000	0.18304	0.183000	0.23260	0.262000	0.18460	0.645000	0.30675	0.561000	0.74099	GTT	.	.	.	none		0.517	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848		T	30317816	C	T	30317816	3	4	181	1	0	0	0	0	1	0	0	0	8241	536	19	1	2826	1	KIAA1462	10	30317816	Missense_Mutation	SNP	C	TCGA-G7-A8LD-01A-11D-A35Z-10		30317816	105216931	30	10577											
PARD3	56288	hgsc.bcm.edu	37	chr10	34673133	34673133	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcacgaaaaagattttcatGttcagctttaccacctttct	11	15	4	11	1	4	1	3	0	1	1	4	2	4	1	2	0	2	2	2	0	3	6			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr10:34673133G>A	ENST00000374789.3	-	8	1265	c.940C>T	c.(940-942)Cat>Tat	p.H314Y	PARD3_ENST00000544292.1_Missense_Mutation_p.H44Y|PARD3_ENST00000340077.5_Missense_Mutation_p.H314Y|PARD3_ENST00000374776.1_Missense_Mutation_p.H314Y|PARD3_ENST00000374790.3_Missense_Mutation_p.H270Y|PARD3_ENST00000374773.1_Missense_Mutation_p.H314Y|PARD3_ENST00000545693.1_Missense_Mutation_p.H314Y|PARD3_ENST00000350537.4_Missense_Mutation_p.H314Y|PARD3_ENST00000545260.1_Missense_Mutation_p.H270Y|PARD3_ENST00000374788.3_Missense_Mutation_p.H314Y|PARD3_ENST00000346874.4_Missense_Mutation_p.H314Y|PARD3_ENST00000374794.3_Missense_Mutation_p.H270Y	NM_019619.3	NP_062565.2	Q8TEW0	PARD3_HUMAN	par-3 family cell polarity regulator	314	PDZ 1. {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)				AGATTTTCATGTTCAGCTTTA	0.388																																					p.H314Y		Atlas-SNP	.											.	PARD3	131	.	0			c.C940T						PASS	.						180	160	167					10																	34673133		2203	4300	6503	SO:0001583	missense	56288	exon8			TTTCATGTTCAGC	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.940C>T	chr10.hg19:g.34673133G>A	ENSP00000363921:p.His314Tyr	78.0	0.0	.		85.0	12.0	.	NM_001184788	F5H5T0|Q5T2U1|Q5VUA2|Q5VUA3|Q5VWV0|Q5VWV1|Q5VWV3|Q5VWV4|Q5VWV5|Q6IQ47|Q8TCZ9|Q8TEW1|Q8TEW2|Q8TEW3|Q96K28|Q96RM6|Q96RM7|Q9BY57|Q9BY58|Q9HC48|Q9NWL4|Q9NYE6	Missense_Mutation	SNP	ENST00000374789.3	hg19	CCDS7178.1	.	.	.	.	.	.	.	.	.	.	G	16.92	3.256229	0.59321	.	.	ENSG00000148498	ENST00000545693;ENST00000545260;ENST00000374789;ENST00000374788;ENST00000346874;ENST00000374794;ENST00000350537;ENST00000374790;ENST00000374776;ENST00000340077;ENST00000374773;ENST00000544292	T;T;T;T;T;T;T;T;T;T;T;T	0.26957	1.7;1.7;1.7;1.7;1.7;1.7;1.7;1.7;1.7;1.7;1.7;1.7	5.68	5.68	0.88126	PDZ/DHR/GLGF (3);	0.290697	0.40554	N	0.001075	T	0.19805	0.0476	N	0.08118	0	0.28529	N	0.91269	B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.22541	0.017;0.028;0.019;0.017;0.019;0.017;0.017;0.01;0.01;0.01;0.059;0.071;0.008;0.017	B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.28849	0.051;0.049;0.051;0.095;0.095;0.051;0.095;0.007;0.044;0.044;0.095;0.028;0.095;0.095	T	0.26849	-1.0091	10	0.87932	D	0	.	20.1615	0.98135	0.0:0.0:1.0:0.0	.	270;270;314;314;314;314;314;314;270;314;314;314;314;44	Q8TEW0-5;Q8TEW0-3;Q8TEW0-7;Q8TEW0-6;F5H5T0;Q8TEW0-4;Q8TEW0-2;Q8TEW0;Q5VWV2;Q6IQ47;Q8TEW0-8;Q8TEW0-9;Q8TEW0-10;F5GZI3	.;.;.;.;.;.;.;PARD3_HUMAN;.;.;.;.;.;.	Y	314;270;314;314;314;270;314;270;314;314;314;44	ENSP00000443147:H314Y;ENSP00000440857:H270Y;ENSP00000363921:H314Y;ENSP00000363920:H314Y;ENSP00000340591:H314Y;ENSP00000363926:H270Y;ENSP00000311986:H314Y;ENSP00000363922:H270Y;ENSP00000363908:H314Y;ENSP00000341844:H314Y;ENSP00000363905:H314Y;ENSP00000444429:H44Y	ENSP00000341844:H314Y	H	-	1	0	PARD3	34713139	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	7.220000	0.78008	2.835000	0.97688	0.650000	0.86243	CAT	.	.	.	none		0.388	PARD3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047527.1	NM_019619		A	34673133	G	A	34673133	3	1	181	1	0	0	0	0	1	0	0	0	11450	1377	48	2	3237	2	PARD3	10	34673133	Missense_Mutation	SNP	G	TCGA-G7-A8LD-01A-11D-A35Z-10	4355317	34673133	100861614	31	10578											
FGF4	2249	hgsc.bcm.edu	37	chr11	69588117	69588117	+	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	gggtgaccttcatggtgggcGacactcggttccccttcttg	4	12	13	12	2	2	1	1	1	1	0	4	2	3	1	3	4	0	1	3	4	0	4			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr11:69588117G>A	ENST00000168712.1	-	3	899	c.581C>T	c.(580-582)tCg>tTg	p.S194L	AP001888.1_ENST00000602104.1_5'Flank|FGF4_ENST00000538040.1_5'UTR	NM_002007.2	NP_001998.1	P08620	FGF4_HUMAN	fibroblast growth factor 4	194					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)	CATGGTGGGCGACACTCGGTT	0.612																																					p.S194L		Atlas-SNP	.											FGF4,NS,lymphoid_neoplasm,0,1	FGF4	13	.	0			c.C581T						PASS	.						178	149	159					11																	69588117		2200	4294	6494	SO:0001583	missense	2249	exon3			GTGGGCGACACTC	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.581C>T	chr11.hg19:g.69588117G>A	ENSP00000168712:p.Ser194Leu	221.0	0.0	.		174.0	82.0	.	NM_002007	B7U994	Missense_Mutation	SNP	ENST00000168712.1	hg19	CCDS8194.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.788207	0.90367	.	.	ENSG00000075388	ENST00000168712	D	0.81659	-1.52	5.81	5.81	0.92471	.	0.000000	0.41194	D	0.000936	D	0.90082	0.6902	M	0.78344	2.41	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	D	0.89179	0.3542	9	.	.	.	.	20.074	0.97736	0.0:0.0:1.0:0.0	.	194	P08620	FGF4_HUMAN	L	194	ENSP00000168712:S194L	.	S	-	2	0	FGF4	69297298	1.000000	0.71417	0.948000	0.38648	0.350000	0.29205	9.026000	0.93700	2.746000	0.94184	0.655000	0.94253	TCG	.	.	.	none		0.612	FGF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396834.2	NM_002007		A	69588117	G	A	69588117	3	1	181	1	0	0	0	0	1	0	0	0	5861	1059	37	1	43	1	FGF4	11	69588117	Missense_Mutation	SNP	G	TCGA-G7-A8LD-01A-11D-A35Z-10		69588117	65418399	32	10579											
MAML2	84441	hgsc.bcm.edu	37	chr11	95825257	95825257	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgttgctgctgctgctgctgTtgttgctgctgctgctgctg	0	17	14	10	0	0	0	0	0	0	0	0	0	0	0	0	0	10	13	0	0	0	3	rs575986134	byFrequency	TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr11:95825257T>C	ENST00000524717.1	-	2	3222	c.1938A>G	c.(1936-1938)caA>caG	p.Q646Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	646					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgctgctgttgttgctgct	0.517			T	"MECT1, CRTC3"	salivary gland mucoepidermoid								T|||	5	0.000998403	0	0	5008	,	,		17451	0.005		0	False		,,,				2504	0				p.Q646Q		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	MAML2,colon,carcinoma,0,1	MAML2	94	.	0			c.A1938G						PASS	.						37	42	40					11																	95825257		2095	4114	6209	SO:0001819	synonymous_variant	84441	exon2			CTGCTGTTGTTGC	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1938A>G	chr11.hg19:g.95825257T>C		70.0	1.0	.		53.0	3.0	.	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	hg19	CCDS44714.1																																																																																			.	.	.	none		0.517	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			C	95825257	T	C	95825257	2	2	181	1	0	0	0	0	0	0	0	1	9213	1722	60	3		3	MAML2	11	95825257	Silent	SNP	T	TCGA-G7-A8LD-01A-11D-A35Z-10	26237140	95825257	39181259	33	10580											
AVPR1A	552	hgsc.bcm.edu	37	chr12	63544413	63544413	+	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	gccagcagtacgctgctgttGcccagcacggccaccgcgaa	8	5	12	16	4	0	0	0	0	0	0	0	1	0	0	4	1	5	6	4	1	2	2			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr12:63544413G>C	ENST00000299178.2	-	1	309	c.204C>G	c.(202-204)ggC>ggG	p.G68G		NM_000706.4	NP_000697.1	P37288	V1AR_HUMAN	arginine vasopressin receptor 1A	68					activation of phospholipase C activity (GO:0007202)|blood circulation (GO:0008015)|calcium-mediated signaling (GO:0019722)|cellular response to water deprivation (GO:0042631)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of precursor metabolites and energy (GO:0006091)|grooming behavior (GO:0007625)|maternal aggressive behavior (GO:0002125)|maternal behavior (GO:0042711)|myotube differentiation (GO:0014902)|negative regulation of female receptivity (GO:0007621)|negative regulation of transmission of nerve impulse (GO:0051970)|penile erection (GO:0043084)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular pH reduction (GO:0032849)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of glutamate secretion (GO:0014049)|positive regulation of heart rate (GO:0010460)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of vasoconstriction (GO:0045907)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to corticosterone (GO:0051412)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|telencephalon development (GO:0021537)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	peptide hormone binding (GO:0017046)|protein kinase C binding (GO:0005080)|vasopressin receptor activity (GO:0005000)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(12)|prostate(2)|skin(1)	26			BRCA - Breast invasive adenocarcinoma(9;0.193)	GBM - Glioblastoma multiforme(28;0.0569)	Conivaptan(DB00872)|Desmopressin(DB00035)|Felypressin(DB00093)|Terlipressin(DB02638)|Tolvaptan(DB06212)|Vasopressin(DB00067)	CGCTGCTGTTGCCCAGCACGG	0.682																																					p.G68G		Atlas-SNP	.											.	AVPR1A	85	.	0			c.C204G						PASS	.						32	29	30					12																	63544413		2203	4298	6501	SO:0001819	synonymous_variant	552	exon1			GCTGTTGCCCAGC	L25615	CCDS8965.1	12q14-q15	2012-08-08				ENSG00000166148		"GPCR / Class A : Vasopressin and oxytocin receptors"	895	protein-coding gene	gene with protein product		600821		AVPR1		8106369	Standard	NM_000706		Approved		uc001sro.2	P37288		ENST00000299178.2:c.204C>G	chr12.hg19:g.63544413G>C		76.0	0.0	.		115.0	21.0	.	NM_000706		Silent	SNP	ENST00000299178.2	hg19	CCDS8965.1																																																																																			.	.	.	none		0.682	AVPR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406734.1			C	63544413	G	C	63544413	2	2	181	1	0	0	0	0	0	0	0	1	1231	1306	46	4		4	AVPR1A	12	63544413	Silent	SNP	G	TCGA-G7-A8LD-01A-11D-A35Z-10		63544413	70307482	34	10581											
SPERT	220082	hgsc.bcm.edu	37	chr13	46287523	46287523	+	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	gactacaacccgccgcgggtGcagctcagcgacgagatgtt	9	6	13	13	5	1	1	1	0	0	1	1	4	1	1	2	1	5	3	2	1	2	2			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr13:46287523G>A	ENST00000310521.1	+	3	443	c.363G>A	c.(361-363)gtG>gtA	p.V121V	SPERT_ENST00000378966.3_Silent_p.V85V	NM_152719.1	NP_689932.1	Q8NA61	SPERT_HUMAN	spermatid associated	121						cytoplasmic membrane-bounded vesicle (GO:0016023)				NS(1)|central_nervous_system(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	15		Breast(56;0.000819)|Lung NSC(96;0.00227)|Prostate(109;0.00703)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;7.26e-05)		CGCCGCGGGTGCAGCTCAGCG	0.627																																					p.V121V		Atlas-SNP	.											.	SPERT	54	.	0			c.G363A						PASS	.						63	67	66					13																	46287523		2203	4300	6503	SO:0001819	synonymous_variant	220082	exon3			GCGGGTGCAGCTC	AK093129	CCDS9399.1, CCDS66540.1	13q14.13	2010-03-23			ENSG00000174015	ENSG00000174015			30720	protein-coding gene	gene with protein product	"spermatid flower-like structure protein", "testis specific leucine zipper protein nurit", "chibby homolog 2 (Drosophila)"					12204287, 20096028	Standard	NM_001286341		Approved	NURIT, CBY2	uc001van.1	Q8NA61	OTTHUMG00000016861	ENST00000310521.1:c.363G>A	chr13.hg19:g.46287523G>A		144.0	0.0	.		76.0	62.0	.	NM_152719	A8K8I5|Q8NHV2	Silent	SNP	ENST00000310521.1	hg19	CCDS9399.1																																																																																			.	.	.	none		0.627	SPERT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044786.2	NM_152719		A	46287523	G	A	46287523	2	1	181	1	0	0	0	0	0	0	0	1	15051	1306	46	2		2	SPERT	13	46287523	Silent	SNP	G	TCGA-G7-A8LD-01A-11D-A35Z-10		46287523	68882355	35	10582											
KCNJ12	3768	hgsc.bcm.edu	37	chr17	21318791	21318791	+	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	gcgcaggtgccgcaaccgctTcgtcaagaagaatggccagt	10	6	13	12	4	1	2	1	0	0	2	2	2	1	2	3	2	2	3	3	2	4	1			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr17:21318791T>A	ENST00000583088.1	+	3	1032	c.137T>A	c.(136-138)tTc>tAc	p.F46Y	KCNJ12_ENST00000331718.5_Missense_Mutation_p.F46Y	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	46					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)	CGCAACCGCTTCGTCAAGAAG	0.612										Prostate(3;0.18)																											p.F46Y		Atlas-SNP	.											.	.	.	.	0			c.T137A						PASS	.						151	107	122					17																	21318791		2203	4300	6503	SO:0001583	missense	100134444	exon3			ACCGCTTCGTCAA	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.137T>A	chr17.hg19:g.21318791T>A	ENSP00000463778:p.Phe46Tyr	108.0	0.0	.		125.0	14.0	.	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	hg19	CCDS11219.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.075785	0.76415	.	.	ENSG00000184185	ENST00000331718	T	0.60424	0.19	5.33	5.33	0.75918	Potassium channel, inwardly rectifying, Kir, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.72391	0.3454	M	0.66939	2.045	0.58432	D	0.999999	D	0.89917	1.0	D	0.75484	0.986	T	0.69669	-0.5083	10	0.23891	T	0.37	.	15.3028	0.73966	0.0:0.0:0.0:1.0	.	46	Q14500	IRK12_HUMAN	Y	46	ENSP00000328150:F46Y	ENSP00000328150:F46Y	F	+	2	0	KCNJ12	21259384	1.000000	0.71417	0.997000	0.53966	0.978000	0.69477	7.898000	0.87363	2.027000	0.59764	0.482000	0.46254	TTC	.	.	.	none		0.612	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012		A	21318791	T	A	21318791	3	1	181	1	0	0	0	0	1	0	0	0	8053	1783	62	5	139	5	KCNJ12	17	21318791	Missense_Mutation	SNP	T	TCGA-G7-A8LD-01A-11D-A35Z-10		21318791	59876419	36	10583											
MYO9B	4650	hgsc.bcm.edu	37	chr19	17305947	17305947	+	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	tctgaagaaactgagaagacGctgcccagtgggagccccag	12	5	13	11	1	1	4	0	2	1	3	1	6	1	5	3	1	3	1	3	1	3	0			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr19:17305947G>T	ENST00000594824.1	+	22	3858	c.3711G>T	c.(3709-3711)acG>acT	p.T1237T	MYO9B_ENST00000397274.2_Silent_p.T1237T|MYO9B_ENST00000595618.1_Silent_p.T1237T			Q13459	MYO9B_HUMAN	myosin IXB	1237	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						CTGAGAAGACGCTGCCCAGTG	0.647																																					p.T1237T		Atlas-SNP	.											.	MYO9B	264	.	0			c.G3711T						PASS	.						20	26	25					19																	17305947		1929	4131	6060	SO:0001819	synonymous_variant	4650	exon22			GAAGACGCTGCCC		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.3711G>T	chr19.hg19:g.17305947G>T		162.0	0.0	.		116.0	5.0	.	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Silent	SNP	ENST00000594824.1	hg19																																																																																				.	.	.	none		0.647	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1			T	17305947	G	T	17305947	2	4	181	1	0	0	0	0	0	0	0	1	10092	1074	38	4		4	MYO9B	19	17305947	Silent	SNP	G	TCGA-G7-A8LD-01A-11D-A35Z-10		17305947	41823036	37	10584											
DMKN	93099	hgsc.bcm.edu	37	chr19	36004269	36004269	+	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	caggccatgtccaagggcctCcccaatatttgtcccagtgc	8	9	9	15	0	0	0	0	0	0	0	3	0	3	0	6	2	1	0	6	2	3	2			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr19:36004269C>T	ENST00000339686.3	-	1	285	c.109G>A	c.(109-111)Gag>Aag	p.E37K	DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000419602.1_Missense_Mutation_p.E37K|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000424570.2_Missense_Mutation_p.E37K|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000440396.1_Missense_Mutation_p.E37K|DMKN_ENST00000451297.2_Missense_Mutation_p.E37K|DMKN_ENST00000418261.1_Missense_Mutation_p.E37K|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000429837.1_Missense_Mutation_p.E37K|DMKN_ENST00000447113.2_Missense_Mutation_p.E37K|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000392206.2_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	37	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)			CCAAGGGCCTCCCCAATATTT	0.667																																					p.E37K		Atlas-SNP	.											.	DMKN	116	.	0			c.G109A						PASS	.						56	60	59					19																	36004269		2203	4300	6503	SO:0001583	missense	93099	exon1			GGGCCTCCCCAAT	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.109G>A	chr19.hg19:g.36004269C>T	ENSP00000342012:p.Glu37Lys	39.0	0.0	.		44.0	9.0	.	NM_001190347	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Missense_Mutation	SNP	ENST00000339686.3	hg19	CCDS12463.1	.	.	.	.	.	.	.	.	.	.	C	18.89	3.719708	0.68844	.	.	ENSG00000161249	ENST00000339686;ENST00000392207;ENST00000429837;ENST00000419602;ENST00000447113;ENST00000440396;ENST00000418261;ENST00000424570;ENST00000451297	T;T;T;T;T;T;T;T	0.19105	2.67;2.45;2.43;2.18;2.19;2.18;2.19;2.17	4.37	3.31	0.37934	.	.	.	.	.	T	0.37652	0.1011	L	0.59436	1.845	0.09310	N	1	D;P;P;D;D;D;D	0.58268	0.982;0.811;0.811;0.982;0.965;0.965;0.982	P;P;P;P;P;P;P	0.60789	0.82;0.879;0.879;0.82;0.709;0.709;0.82	T	0.11397	-1.0589	9	0.72032	D	0.01	-6.5769	11.2325	0.48920	0.1848:0.8152:0.0:0.0	.	37;37;37;37;37;37;37	E7EUS0;Q6E0U4-7;Q6E0U4-3;Q6E0U4-5;C9J4P6;Q6E0U4-4;Q6E0U4	.;.;.;.;.;.;DMKN_HUMAN	K	37	ENSP00000342012:E37K;ENSP00000405503:E37K;ENSP00000391036:E37K;ENSP00000394908:E37K;ENSP00000415277:E37K;ENSP00000414743:E37K;ENSP00000388404:E37K;ENSP00000409513:E37K	ENSP00000342012:E37K	E	-	1	0	DMKN	40696109	0.530000	0.26330	0.096000	0.21009	0.111000	0.19643	3.083000	0.50136	0.811000	0.34303	0.491000	0.48974	GAG	.	.	.	none		0.667	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317		T	36004269	C	T	36004269	3	4	181	1	0	0	0	0	1	0	0	0	4584	864	30	2	1702	2	DMKN	19	36004269	Missense_Mutation	SNP	C	TCGA-G7-A8LD-01A-11D-A35Z-10	18698322	36004269	23124714	38	10585											
PRMT1	3276	hgsc.bcm.edu	37	chr19	50185321	50185321	+	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	cggggcccgcaaggtcatcgGggtgagtctccagggtggcc	5	6	18	12	3	2	1	1	1	1	0	4	1	2	1	3	7	0	1	3	7	1	0			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr19:50185321G>A	ENST00000391851.4	+	3	422	c.293G>A	c.(292-294)gGg>gAg	p.G98E	MIR5088_ENST00000581740.1_RNA|PRMT1_ENST00000532489.1_Splice_Site_p.G70E|PRMT1_ENST00000454376.2_Splice_Site_p.G116E	NM_198318.4	NP_938074.2	Q99873	ANM1_HUMAN	protein arginine methyltransferase 1	106	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cell surface receptor signaling pathway (GO:0007166)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|negative regulation of megakaryocyte differentiation (GO:0045653)|neuron projection development (GO:0031175)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|protein methylation (GO:0006479)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|identical protein binding (GO:0042802)|methyltransferase activity (GO:0008168)|N-methyltransferase activity (GO:0008170)|poly(A) RNA binding (GO:0044822)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(2)	12		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00103)|GBM - Glioblastoma multiforme(134;0.012)		AAGGTCATCGGGGTGAGTCTC	0.677																																					p.G116E		Atlas-SNP	.											.	PRMT1	31	.	0			c.G347A						PASS	.						35	39	38					19																	50185321		2202	4299	6501	SO:0001630	splice_region_variant	3276	exon4			TCATCGGGGTGAG	D66904	CCDS42592.1, CCDS46145.1, CCDS74425.1	19q13	2014-06-12	2006-02-16	2006-02-16	ENSG00000126457	ENSG00000126457	2.1.1.125	"Protein arginine methyltransferases"	5187	protein-coding gene	gene with protein product		602950	"HMT1 (hnRNP methyltransferase, S. cerevisiae)-like 2", "HMT1 hnRNP methyltransferase-like 2 (S. cerevisiae)"	HRMT1L2		9545638	Standard	NM_001207042		Approved	HCP1, ANM1	uc010enf.2	Q99873	OTTHUMG00000167568	ENST00000391851.4:c.294+1G>A	chr19.hg19:g.50185321G>A		89.0	0.0	.		85.0	40.0	.	NM_001536	B4E3C3|G5E9B6|Q15529|Q2VP93|Q6LEU5|Q8WUW5|Q99872|Q99874|Q9NZ04|Q9NZ05|Q9NZ06	Missense_Mutation	SNP	ENST00000391851.4	hg19	CCDS42592.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.3|22.3	4.278157|4.278157	0.80692|0.80692	.|.	.|.	ENSG00000126457|ENSG00000126457	ENST00000529284;ENST00000532489;ENST00000527382;ENST00000534465;ENST00000391851;ENST00000449059;ENST00000454376;ENST00000529836;ENST00000526224;ENST00000527412|ENST00000524771	T;T;T;T;T;T;T;T;T|T	0.43294|0.43688	0.95;0.95;0.95;0.95;0.95;0.95;1.26;0.95;1.26|0.94	5.04|5.04	5.04|5.04	0.67666|0.67666	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.78272|0.78272	0.4257|0.4257	H|H	0.98525|0.98525	4.255|4.255	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.76494|.	0.999;0.999;0.999;0.999|.	D;D;D;D|.	0.76575|.	0.988;0.984;0.972;0.972|.	D|D	0.86699|0.86699	0.1928|0.1928	10|8	0.87932|0.87932	D|D	0|0	0.0459|0.0459	15.9171|15.9171	0.79527|0.79527	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	106;70;98;92|.	Q99873;E9PKG1;G5E9B6;Q99873-2|.	ANM1_HUMAN;.;.;.|.	E|R	70;70;70;70;98;92;116;92;70;95|126	ENSP00000432349:G70E;ENSP00000433556:G70E;ENSP00000432538:G70E;ENSP00000431957:G70E;ENSP00000375724:G98E;ENSP00000406162:G116E;ENSP00000437273:G92E;ENSP00000432788:G70E;ENSP00000436732:G95E|ENSP00000433480:G126R	ENSP00000375724:G98E|ENSP00000433480:G126R	G|G	+|+	2|1	0|0	PRMT1|PRMT1	54877133|54877133	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.455000|0.455000	0.32408|0.32408	9.271000|9.271000	0.95698|0.95698	2.629000|2.629000	0.89072|0.89072	0.643000|0.643000	0.83706|0.83706	GGG|GGA	.	.	.	none		0.677	PRMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395065.1	NM_001536	Missense_Mutation	A	50185321	G	A	50185321	5	1	181	1	0	0	0	0	0	0	1	0	12545	1246	43	2	361	2	PRMT1	19	50185321	Splice_Site	SNP	G	TCGA-G7-A8LD-01A-11D-A35Z-10	14181052	50185321	8943662	39	10586											
ZNF816A	125893	hgsc.bcm.edu	37	chr19	53453491	53453491	+	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	actgaaaactttgtcacattCttcacatttgtaaggtttct	11	17	5	8	0	4	1	2	1	2	0	4	1	4	1	0	1	1	2	0	1	3	6			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr19:53453491C>G	ENST00000357666.4	-	5	1837	c.1537G>C	c.(1537-1539)Gaa>Caa	p.E513Q	ZNF816_ENST00000434371.2_Intron|ZNF321P_ENST00000391777.3_Intron|ZNF816_ENST00000444460.2_Missense_Mutation_p.E513Q	NM_001031665.2	NP_001026835.1	Q0VGE8	ZN816_HUMAN	zinc finger protein 816	513					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|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						TTGTCACATTCTTCACATTTG	0.388																																					p.E513Q		Atlas-SNP	.											.	ZNF816	73	.	0			c.G1537C						PASS	.						104	106	105					19																	53453491		2203	4300	6503	SO:0001583	missense	125893	exon4			CACATTCTTCACA	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.1537G>C	chr19.hg19:g.53453491C>G	ENSP00000350295:p.Glu513Gln	74.0	0.0	.		68.0	7.0	.	NM_001202457	A8K7H5|Q3KR39|Q659B3	Missense_Mutation	SNP	ENST00000357666.4	hg19	CCDS33096.1	.	.	.	.	.	.	.	.	.	.	-	10.66	1.412249	0.25465	.	.	ENSG00000180257	ENST00000357666;ENST00000444460	T;T	0.07444	3.19;3.19	1.85	-1.03	0.10102	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08802	0.0218	N	0.04746	-0.17	0.09310	N	1	D	0.76494	0.999	D	0.75484	0.986	T	0.36407	-0.9749	9	0.36615	T	0.2	.	5.6179	0.17442	0.0:0.6528:0.2006:0.1466	.	513	Q0VGE8	ZN816_HUMAN	Q	513	ENSP00000350295:E513Q;ENSP00000403266:E513Q	ENSP00000350295:E513Q	E	-	1	0	ZNF816	58145303	0.000000	0.05858	0.013000	0.15412	0.291000	0.27294	-0.583000	0.05807	0.106000	0.17784	0.313000	0.20887	GAA	.	.	.	none		0.388	ZNF816-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396132.1	NM_001031665		G	53453491	C	G	53453491	3	3	181	1	0	0	0	0	1	0	0	0	18189	922	32	4	422	4	ZNF816A	19	53453491	Missense_Mutation	SNP	C	TCGA-G7-A8LD-01A-11D-A35Z-10	3268170	53453491	5675492	40	10587											
NLRP4	147945	hgsc.bcm.edu	37	chr19	56388499	56388499	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagctgttgtgtcgggctcTgacgcatacggattgccgct	5	11	14	11	4	1	1	0	1	1	0	2	2	1	2	1	2	3	6	1	2	1	3			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr19:56388499T>C	ENST00000301295.6	+	8	3085	c.2663T>C	c.(2662-2664)cTg>cCg	p.L888P	NLRP4_ENST00000587891.1_Missense_Mutation_p.L813P|NLRP4_ENST00000346986.5_Missense_Mutation_p.L832P	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	888					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)		TGTCGGGCTCTGACGCATACG	0.493																																					p.L888P		Atlas-SNP	.											.	NLRP4	331	.	0			c.T2663C						PASS	.						203	192	196					19																	56388499		2203	4300	6503	SO:0001583	missense	147945	exon8			GGGCTCTGACGCA	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.2663T>C	chr19.hg19:g.56388499T>C	ENSP00000301295:p.Leu888Pro	159.0	0.0	.		116.0	37.0	.	NM_134444	Q86W87|Q96AY6	Missense_Mutation	SNP	ENST00000301295.6	hg19	CCDS12936.1	.	.	.	.	.	.	.	.	.	.	T	14.24	2.477580	0.44044	.	.	ENSG00000160505	ENST00000301295;ENST00000346986	T;T	0.71103	-0.02;-0.54	3.91	3.91	0.45181	.	.	.	.	.	D	0.86928	0.6051	H	0.94222	3.51	0.19300	N	0.99997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.991;0.979	T	0.77395	-0.2604	9	0.87932	D	0	.	9.35	0.38131	0.0:0.0:0.0:1.0	.	832;813;888	Q96MN2-2;Q96MN2-3;Q96MN2	.;.;NALP4_HUMAN	P	888;832	ENSP00000301295:L888P;ENSP00000344787:L832P	ENSP00000301295:L888P	L	+	2	0	NLRP4	61080311	0.059000	0.20769	0.007000	0.13788	0.014000	0.08584	3.482000	0.53186	1.783000	0.52377	0.477000	0.44152	CTG	.	.	.	none		0.493	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444		C	56388499	T	C	56388499	3	2	181	1	0	0	0	0	1	0	0	0	10486	1580	55	3	2689	3	NLRP4	19	56388499	Missense_Mutation	SNP	T	TCGA-G7-A8LD-01A-11D-A35Z-10	2935008	56388499	2740484	41	10588											
LRRN4	164312	hgsc.bcm.edu	37	chr20	6031523	6031523	+	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	tgacagtccagctgctgcagGttgggggtcatcttgaaaat	9	11	13	8	0	2	2	1	2	1	0	3	2	3	2	1	3	3	4	1	3	2	2			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr20:6031523G>T	ENST00000378858.4	-	3	986	c.762C>A	c.(760-762)aaC>aaA	p.N254K		NM_152611.4	NP_689824.2	Q8WUT4	LRRN4_HUMAN	leucine rich repeat neuronal 4	254					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						GCTGCTGCAGGTTGGGGGTCA	0.552																																					p.N254K		Atlas-SNP	.											.	LRRN4	54	.	0			c.C762A						PASS	.						133	123	127					20																	6031523		2203	4300	6503	SO:0001583	missense	164312	exon3			CTGCAGGTTGGGG	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.762C>A	chr20.hg19:g.6031523G>T	ENSP00000368135:p.Asn254Lys	191.0	0.0	.		165.0	101.0	.	NM_152611	A8K258|Q5JWV6|Q9H419	Missense_Mutation	SNP	ENST00000378858.4	hg19	CCDS13097.1	.	.	.	.	.	.	.	.	.	.	G	12.65	2.001798	0.35320	.	.	ENSG00000125872	ENST00000378858	T	0.56444	0.46	5.68	2.15	0.27550	.	0.506545	0.19230	N	0.119428	T	0.41834	0.1176	L	0.41632	1.29	0.24473	N	0.994383	B;B	0.30146	0.27;0.027	B;B	0.34931	0.192;0.034	T	0.29579	-1.0007	10	0.36615	T	0.2	-7.2773	7.64	0.28288	0.1127:0.472:0.4153:0.0	.	254;254	Q6ZMD1;Q8WUT4	.;LRRN4_HUMAN	K	254	ENSP00000368135:N254K	ENSP00000368135:N254K	N	-	3	2	LRRN4	5979523	0.000000	0.05858	0.617000	0.29091	0.888000	0.51559	-0.500000	0.06405	0.740000	0.32651	0.491000	0.48974	AAC	.	.	.	none		0.552	LRRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077907.2	NM_152611		T	6031523	G	T	6031523	3	4	181	1	0	0	0	0	1	0	0	0	9044	1252	44	4	1472	4	LRRN4	20	6031523	Missense_Mutation	SNP	G	TCGA-G7-A8LD-01A-11D-A35Z-10		6031523	56993997	42	10589											
CD93	22918	hgsc.bcm.edu	37	chr20	23065706	23065706	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccccctctccaggaccgcccGgctcatagccaacccagcat	8	5	7	21	2	2	0	1	0	1	0	3	1	2	1	7	2	3	2	7	2	2	1	rs139005135		TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr20:23065706G>A	ENST00000246006.4	-	1	1271	c.1124C>T	c.(1123-1125)cCg>cTg	p.P375L		NM_012072.3	NP_036204.2	Q9NPY3	C1QR1_HUMAN	CD93 molecule	375	EGF-like 3; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				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)					AGGACCGCCCGGCTCATAGCC	0.632																																					p.P375L		Atlas-SNP	.											.	CD93	84	.	0			c.C1124T						PASS	.	G	LEU/PRO	0,4406		0,0,2203	41	43	42		1124	3.9	0.2	20	dbSNP_134	42	2,8598	2.2+/-6.3	0,2,4298	no	missense	CD93	NM_012072.3	98	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	375/653	23065706	2,13004	2203	4300	6503	SO:0001583	missense	22918	exon1			CCGCCCGGCTCAT	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.1124C>T	chr20.hg19:g.23065706G>A	ENSP00000246006:p.Pro375Leu	170.0	0.0	.		154.0	67.0	.	NM_012072	O00274	Missense_Mutation	SNP	ENST00000246006.4	hg19	CCDS13149.1	.	.	.	.	.	.	.	.	.	.	G	4.744	0.138295	0.09083	0.0	2.33E-4	ENSG00000125810	ENST00000246006	T	0.20332	2.08	4.89	3.94	0.45596	EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.203167	0.34879	N	0.003614	T	0.07324	0.0185	N	0.02158	-0.66	0.09310	N	0.999998	B	0.18968	0.032	B	0.09377	0.004	T	0.30966	-0.9960	10	0.22109	T	0.4	-10.0711	9.2402	0.37491	0.1733:0.0:0.8267:0.0	.	375	Q9NPY3	C1QR1_HUMAN	L	375	ENSP00000246006:P375L	ENSP00000246006:P375L	P	-	2	0	CD93	23013706	0.010000	0.17322	0.222000	0.23844	0.169000	0.22640	1.721000	0.38032	1.423000	0.47198	0.650000	0.86243	CCG	.	G|1.000;A|0.000	0.000	weak		0.632	CD93-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078312.2	NM_012072		A	23065706	G	A	23065706	3	1	181	1	0	0	0	0	1	0	0	0	3049	1116	39	1	842	1	CD93	20	23065706	Missense_Mutation	SNP	G	TCGA-G7-A8LD-01A-11D-A35Z-10	17034183	23065706	39959814	43	10590											
SIM2	6493	hgsc.bcm.edu	37	chr21	38115795	38115795	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcacaagaaactaggaaatTagtgaaacccaaaaatacca	21	6	5	9	0	1	2	1	1	0	1	1	3	1	3	2	1	3	0	2	1	9	3			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr21:38115795T>C	ENST00000290399.6	+	9	1719	c.1106T>C	c.(1105-1107)tTa>tCa	p.L369S	SIM2_ENST00000430056.3_Missense_Mutation_p.L369S	NM_005069.3	NP_005060.1	Q14190	SIM2_HUMAN	single-minded family bHLH transcription factor 2	369	Single-minded C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00632}.				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						ACTAGGAAATTAGTGAAACCC	0.498																																					p.L369S		Atlas-SNP	.											.	SIM2	55	.	0			c.T1106C						PASS	.						166	164	164					21																	38115795		2203	4300	6503	SO:0001583	missense	6493	exon9			GGAAATTAGTGAA		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.1106T>C	chr21.hg19:g.38115795T>C	ENSP00000290399:p.Leu369Ser	234.0	0.0	.		230.0	96.0	.	NM_005069	O60766|Q15470|Q15471|Q15472|Q15473|Q16532|Q2TBD8	Missense_Mutation	SNP	ENST00000290399.6	hg19	CCDS13646.1	.	.	.	.	.	.	.	.	.	.	T	0.039	-1.293915	0.01375	.	.	ENSG00000159263	ENST00000290399;ENST00000430056	T;T	0.24723	1.84;1.84	4.43	2.05	0.26809	Single-minded, C-terminal (2);	1.087690	0.07148	N	0.848635	T	0.10852	0.0265	N	0.04508	-0.205	0.09310	N	1	B;B	0.09022	0.0;0.002	B;B	0.09377	0.004;0.002	T	0.32534	-0.9903	10	0.08837	T	0.75	.	7.0238	0.24928	0.0:0.3703:0.0:0.6297	.	369;369	Q14190;Q14190-2	SIM2_HUMAN;.	S	369	ENSP00000290399:L369S;ENSP00000404176:L369S	ENSP00000290399:L369S	L	+	2	0	SIM2	37037665	0.999000	0.42202	0.232000	0.24009	0.491000	0.33493	1.380000	0.34351	0.659000	0.30945	0.334000	0.21626	TTA	.	.	.	none		0.498	SIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194692.1	NM_009586		C	38115795	T	C	38115795	3	2	181	1	0	0	0	0	1	0	0	0	14337	1764	61	3	1140	3	SIM2	21	38115795	Missense_Mutation	SNP	T	TCGA-G7-A8LD-01A-11D-A35Z-10		38115795	10014100	44	10591											
PCNT	5116	hgsc.bcm.edu	37	chr21	47831608	47831608	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcgacgattgccgagagaaAtttagaaatcgacgctctga	14	8	11	8	5	1	3	0	1	1	2	2	8	1	3	1	0	2	1	1	0	3	3			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chr21:47831608A>G	ENST00000359568.5	+	28	5728	c.5621A>G	c.(5620-5622)aAt>aGt	p.N1874S	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1874					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)					GCCGAGAGAAATTTAGAAATC	0.622																																					p.N1874S		Atlas-SNP	.											.	PCNT	283	.	0			c.A5621G						PASS	.						30	34	33					21																	47831608		2196	4292	6488	SO:0001583	missense	5116	exon28			AGAGAAATTTAGA	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.5621A>G	chr21.hg19:g.47831608A>G	ENSP00000352572:p.Asn1874Ser	130.0	0.0	.		125.0	56.0	.	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	hg19	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	A	14.47	2.545363	0.45280	.	.	ENSG00000160299	ENST00000359568	T	0.01464	4.86	5.07	5.07	0.68467	.	0.489448	0.15283	N	0.270570	T	0.01287	0.0042	N	0.08118	0	0.20764	N	0.99985	B;B	0.25272	0.122;0.074	B;B	0.21708	0.036;0.016	T	0.50600	-0.8809	10	0.13108	T	0.6	.	13.4209	0.60996	1.0:0.0:0.0:0.0	.	1756;1874	O95613-2;O95613	.;PCNT_HUMAN	S	1874	ENSP00000352572:N1874S	ENSP00000352572:N1874S	N	+	2	0	PCNT	46656036	0.995000	0.38212	0.015000	0.15790	0.019000	0.09904	2.831000	0.48144	2.219000	0.72066	0.533000	0.62120	AAT	.	.	.	none		0.622	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		G	47831608	A	G	47831608	3	3	181	1	0	0	0	0	1	0	0	0	11597	101	4	3	5731	3	PCNT	21	47831608	Missense_Mutation	SNP	A	TCGA-G7-A8LD-01A-11D-A35Z-10	9715813	47831608	298287	45	10592											
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-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	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	chrX.hg19:g.66765164A>T	ENSP00000363822:p.Gln59Leu	72.0	0.0	.		119.0	16.0	.	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	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	181	1	0	0	0	0	1	0	0	0	836	188	7	5	178	5	AR	23	66765164	Missense_Mutation	SNP	A	TCGA-G7-A8LD-01A-11D-A35Z-10		66765164	88505396	46	10593			1	23		2	2	59	N	GC_A	8.992788e-05
AR	367	hgsc.bcm.edu	37	chrX	66765222	66765223	+	Missense_Mutation	DNP	GC	GC	AG																															cagcagcagcagcagcagcaGcagcaagagactagccccag																										TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chrX:66765222_66765223GC>AG	ENST00000374690.3	+	1	758_759	c.234_235GC>AG	c.(232-237)caGCag>caAGag	p.Q79E	AR_ENST00000504326.1_Missense_Mutation_p.Q79E|AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.Q79E	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	78	Gln-rich.|Modulating.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	agcagcagcagcagcaagagac	0.653									Androgen Insensitivity Syndrome																												p.Q78Q|p.Q79E		Atlas-SNP	.											.	AR	249	.	0			c.G234A|c.C235G						PASS	.																																			SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	GCAGCAGCAGCAA|CAGCAGCAGCAAG	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	Exception_encountered	chrX.hg19:g.66765222_66765223delinsAG	ENSP00000363822:p.Gln79Glu	92.0|94.0	0.0	.		150.0|152.0	12.0	.	NM_000044	A2RUN2|B1AKD7|Q9UD95	Silent|Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1																																																																																			.	.	.	none		0.653	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		AG	66765223	GC	AG	66765222	3	1	181	1	0	0	0	0	1	0	0	0	836	962	34	2	236	2	AR	23	66765222	Missense_Mutation	DNP	GC	TCGA-G7-A8LD-01A-11D-A35Z-10	58	66765222	88505338	47	10594			1	23		2	2	59	N	GC_A	8.992788e-05
SMARCA1	6594	hgsc.bcm.edu	37	chrX	128652406	128652406	+	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	tttagcagcaagtttgagttGaaatgaagaaacgtttttct	13	15	9	4	1	1	4	0	3	1	1	1	4	1	4	0	0	3	5	0	0	5	6			TCGA-G7-A8LD-01A-11D-A35Z-10	TCGA-G7-A8LD-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	755a9884-f632-4260-bf9d-a84b5d86aa87	632fa524-d179-4f7e-9cbc-b57a32d1fb38	g.chrX:128652406G>A	ENST00000371122.4	-	2	322	c.193C>T	c.(193-195)Caa>Taa	p.Q65*	SMARCA1_ENST00000371123.1_Nonsense_Mutation_p.Q65*|SMARCA1_ENST00000478420.1_5'UTR|SMARCA1_ENST00000371121.3_Nonsense_Mutation_p.Q65*	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	65					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						AGTTTGAGTTGAAATGAAGAA	0.358																																					p.Q65X		Atlas-SNP	.											.	SMARCA1	126	.	0			c.C193T						PASS	.						92	79	83					X																	128652406		2202	4299	6501	SO:0001587	stop_gained	6594	exon2			TGAGTTGAAATGA	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.193C>T	chrX.hg19:g.128652406G>A	ENSP00000360163:p.Gln65*	253.0	0.0	.		213.0	193.0	.	NM_139035	Q5JV41|Q5JV42	Nonsense_Mutation	SNP	ENST00000371122.4	hg19	CCDS14612.1	.	.	.	.	.	.	.	.	.	.	G	36	5.879507	0.97062	.	.	ENSG00000102038	ENST00000371121;ENST00000371123;ENST00000371122;ENST00000450039	.	.	.	5.13	5.13	0.70059	.	0.574317	0.14333	N	0.326218	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	-2.2867	12.401	0.55412	0.0:0.1644:0.8356:0.0	.	.	.	.	X	65;65;65;44	.	ENSP00000360162:Q65X	Q	-	1	0	SMARCA1	128480087	1.000000	0.71417	0.998000	0.56505	0.922000	0.55478	5.851000	0.69481	2.092000	0.63282	0.513000	0.50165	CAA	.	.	.	none		0.358	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058206.1	NM_003069		A	128652406	G	A	128652406	4	1	181	1	0	0	0	0	0	1	0	0	14781	1299	45	2	3063	2	SMARCA1	23	128652406	Nonsense_Mutation	SNP	G	TCGA-G7-A8LD-01A-11D-A35Z-10	61887184	128652406	26618154	48	10595											
MTHFR	4524	hgsc.bcm.edu	37	chr1	11854058	11854058	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgtgagttgatggtgaggAtgccctggcggttcacccgc	5	10	16	10	2	1	3	1	3	0	0	1	4	1	4	2	4	1	3	2	4	0	2			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr1:11854058A>G	ENST00000376592.1	-	8	1564	c.1436T>C	c.(1435-1437)aTc>aCc	p.I479T	MTHFR_ENST00000376585.1_Missense_Mutation_p.I520T|MTHFR_ENST00000376583.3_Missense_Mutation_p.I520T|MTHFR_ENST00000376590.3_Missense_Mutation_p.I479T			P42898	MTHR_HUMAN	methylenetetrahydrofolate reductase (NAD(P)H)	479					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)	GATGGTGAGGATGCCCTGGCG	0.652																																					p.I479T		Atlas-SNP	.											.	MTHFR	65	.	0			c.T1436C						PASS	.						98	102	100					1																	11854058		2203	4300	6503	SO:0001583	missense	4524	exon9			GTGAGGATGCCCT	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.1436T>C	chr1.hg19:g.11854058A>G	ENSP00000365777:p.Ile479Thr	38.0	0.0	.		57.0	50.0	.	NM_005957	B2R7A6|Q5SNW6|Q5SNW9|Q7Z6M6|Q8IU73|Q9UQR2	Missense_Mutation	SNP	ENST00000376592.1	hg19	CCDS137.1	.	.	.	.	.	.	.	.	.	.	A	18.61	3.660655	0.67586	.	.	ENSG00000177000	ENST00000376592;ENST00000376583;ENST00000376590;ENST00000376585	T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22	4.71	4.71	0.59529	.	0.162118	0.56097	D	0.000037	T	0.68860	0.3047	M	0.81497	2.545	0.54753	D	0.999986	B;P	0.43938	0.072;0.822	B;B	0.40477	0.09;0.33	T	0.75605	-0.3260	10	0.72032	D	0.01	.	13.3979	0.60865	1.0:0.0:0.0:0.0	.	479;520	P42898;Q5SNW6	MTHR_HUMAN;.	T	479;520;479;520	ENSP00000365777:I479T;ENSP00000365767:I520T;ENSP00000365775:I479T;ENSP00000365770:I520T	ENSP00000365767:I520T	I	-	2	0	MTHFR	11776645	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	8.832000	0.92079	1.771000	0.52183	0.379000	0.24179	ATC	.	.	.	none		0.652	MTHFR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006538.1	NM_005957		G	11854058	A	G	11854058	3	3	182	1	0	0	0	0	1	0	0	0	9938	333	12	3	550	3	MTHFR	1	11854058	Missense_Mutation	SNP	A	TCGA-G7-A8LE-01A-11D-A35Z-10		11854058	237396563	1	10596											
GJB3	2707	hgsc.bcm.edu	37	chr1	35251060	35251060	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgcagcccctcgtcctccGccagccgagcttccacctgc	4	8	9	20	3	0	0	0	0	0	0	4	1	3	0	8	0	5	3	8	0	0	2			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr1:35251060G>A	ENST00000373366.2	+	2	1312	c.697G>A	c.(697-699)Gcc>Acc	p.A233T	GJB3_ENST00000373362.3_Missense_Mutation_p.A233T|RP1-34M23.5_ENST00000542839.1_RNA	NM_024009.2	NP_076872.1	O75712	CXB3_HUMAN	gap junction protein, beta 3, 31kDa	233					cell communication (GO:0007154)|in utero embryonic development (GO:0001701)|placenta development (GO:0001890)|sensory perception of sound (GO:0007605)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	connexon complex (GO:0005922)|cytoplasm (GO:0005737)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)	gap junction channel activity (GO:0005243)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(2)|prostate(3)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				CTCGTCCTCCGCCAGCCGAGC	0.632																																					p.A233T		Atlas-SNP	.											GJB3,NS,carcinoma,0,1	GJB3	40	.	0			c.G697A						PASS	.						31	31	31					1																	35251060		2202	4300	6502	SO:0001583	missense	2707	exon2			TCCTCCGCCAGCC	BC012918	CCDS384.1	1p34	2008-05-14	2007-01-16		ENSG00000188910	ENSG00000188910		"Ion channels / Gap junction proteins (connexins)"	4285	protein-coding gene	gene with protein product	"connexin 31"	603324	"gap junction protein, beta 3, 31kD (connexin 31)", "gap junction protein, beta 3, 31kDa (connexin 31)", "erythrokeratodermia variabilis"	DFNA2, EKV		9843210, 9704026	Standard	NM_024009		Approved	CX31	uc001bxy.3	O75712	OTTHUMG00000004051	ENST00000373366.2:c.697G>A	chr1.hg19:g.35251060G>A	ENSP00000362464:p.Ala233Thr	163.0	0.0	.		189.0	39.0	.	NM_001005752	B2R790|Q2TAZ8	Missense_Mutation	SNP	ENST00000373366.2	hg19	CCDS384.1	.	.	.	.	.	.	.	.	.	.	G	2.744	-0.261542	0.05791	.	.	ENSG00000188910	ENST00000373366;ENST00000373362;ENST00000543647	D;D	0.97752	-4.52;-4.52	5.03	-10.1	0.00402	.	2.095770	0.02337	N	0.074477	D	0.91009	0.7172	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	D	0.83820	0.0246	10	0.12430	T	0.62	.	10.795	0.46455	0.0789:0.0641:0.538:0.319	.	233	O75712	CXB3_HUMAN	T	233;233;217	ENSP00000362464:A233T;ENSP00000362460:A233T	ENSP00000362460:A233T	A	+	1	0	GJB3	35023647	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.581000	0.05820	-3.943000	0.00089	-2.233000	0.00290	GCC	.	.	.	none		0.632	GJB3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011559.1	NM_024009		A	35251060	G	A	35251060	3	1	182	1	0	0	0	0	1	0	0	0	6416	1087	38	1	699	1	GJB3	1	35251060	Missense_Mutation	SNP	G	TCGA-G7-A8LE-01A-11D-A35Z-10	23397002	35251060	213999561	2	10597											
DNM3	26052	hgsc.bcm.edu	37	chr1	172017810	172017810	+	Missense_Mutation	SNP	A	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	tagtcaagaaacagattgtaAagttgaaagggccttccttg	14	11	10	6	0	1	3	1	1	0	2	2	3	2	3	2	1	1	2	2	1	6	6			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr1:172017810A>C	ENST00000355305.5	+	10	1412	c.1255A>C	c.(1255-1257)Aag>Cag	p.K419Q	DNM3_ENST00000520906.1_Missense_Mutation_p.K419Q|DNM3_ENST00000367731.1_Missense_Mutation_p.K419Q|DNM3_ENST00000358155.4_Missense_Mutation_p.K419Q|DNM3_ENST00000367733.2_Missense_Mutation_p.K419Q			Q9UQ16	DYN3_HUMAN	dynamin 3	419					endocytosis (GO:0006897)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|synapse assembly (GO:0007416)	dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(16)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						ACAGATTGTAAAGTTGAAAGG	0.368																																					p.K419Q		Atlas-SNP	.											.	DNM3	85	.	0			c.A1255C						PASS	.						119	116	117					1																	172017810		1868	4101	5969	SO:0001583	missense	26052	exon10			ATTGTAAAGTTGA	AL136712	CCDS44276.1, CCDS60356.1	1q24.1	2013-01-10			ENSG00000197959	ENSG00000197959		"Pleckstrin homology (PH) domain containing"	29125	protein-coding gene	gene with protein product	"Dyna III"	611445				10048485	Standard	NM_015569		Approved	KIAA0820	uc001gie.4	Q9UQ16	OTTHUMG00000034913	ENST00000355305.5:c.1255A>C	chr1.hg19:g.172017810A>C	ENSP00000347457:p.Lys419Gln	218.0	0.0	.		318.0	246.0	.	NM_001136127	A9Z1Y1|O14982|O95555|Q1MTM8|Q5W129|Q6P2G1|Q9H0P3|Q9H548|Q9NQ68|Q9NQN6	Missense_Mutation	SNP	ENST00000355305.5	hg19		.	.	.	.	.	.	.	.	.	.	A	21.2	4.107156	0.77096	.	.	ENSG00000197959	ENST00000359070;ENST00000358155;ENST00000367733;ENST00000355305;ENST00000367731;ENST00000520906;ENST00000523513	T;T;T;T;T;T	0.73047	-0.71;-0.71;-0.71;-0.71;-0.71;-0.71	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.55768	0.1941	L	0.58669	1.825	0.54753	D	0.999988	B;P;B;B	0.36712	0.04;0.566;0.389;0.04	B;B;B;B	0.35278	0.199;0.198;0.198;0.14	T	0.60974	-0.7156	10	0.37606	T	0.19	.	15.0317	0.71713	1.0:0.0:0.0:0.0	.	419;419;419;419	E5RHK8;Q9UQ16-2;Q9UQ16-3;Q6P2G1	.;.;.;.	Q	419;419;419;419;419;419;309	ENSP00000350876:K419Q;ENSP00000356707:K419Q;ENSP00000347457:K419Q;ENSP00000356705:K419Q;ENSP00000429701:K419Q;ENSP00000429416:K309Q	ENSP00000347457:K419Q	K	+	1	0	DNM3	170284433	1.000000	0.71417	0.969000	0.41365	0.792000	0.44763	9.287000	0.95975	2.137000	0.66172	0.460000	0.39030	AAG	.	.	.	none		0.368	DNM3-003	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000084531.1	NM_015569		C	172017810	A	C	172017810	3	2	182	1	0	0	0	0	1	0	0	0	4675	15	1	5	1293	5	DNM3	1	172017810	Missense_Mutation	SNP	A	TCGA-G7-A8LE-01A-11D-A35Z-10	136766750	172017810	77232811	3	10598											
PNPT1	87178	hgsc.bcm.edu	37	chr2	55863466	55863466	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacggttgtagctggcgacTgaagcacttttcgagaaagc	10	9	12	10	3	0	2	0	1	0	1	1	4	0	2	1	2	3	4	1	2	3	4			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr2:55863466T>C	ENST00000447944.2	-	28	2344	c.2258A>G	c.(2257-2259)cAg>cGg	p.Q753R		NM_033109.3	NP_149100.2	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	753					cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA polyadenylation (GO:0097222)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA 5'-end processing (GO:0000964)|mitochondrial RNA catabolic process (GO:0000957)|mitochondrion morphogenesis (GO:0070584)|mitotic cell cycle arrest (GO:0071850)|mRNA catabolic process (GO:0006402)|negative regulation of growth (GO:0045926)|nuclear polyadenylation-dependent mRNA catabolic process (GO:0071042)|positive regulation of miRNA catabolic process (GO:2000627)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|positive regulation of mRNA catabolic process (GO:0061014)|protein homooligomerization (GO:0051260)|protein homotrimerization (GO:0070207)|regulation of cellular respiration (GO:0043457)|regulation of cellular senescence (GO:2000772)|RNA catabolic process (GO:0006401)|RNA import into mitochondrion (GO:0035927)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA polyadenylation (GO:0043631)|rRNA import into mitochondrion (GO:0035928)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrial degradosome (GO:0045025)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	3'-5'-exoribonuclease activity (GO:0000175)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|polyribonucleotide nucleotidyltransferase activity (GO:0004654)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			AGCTGGCGACTGAAGCACTTT	0.403																																					p.Q753R		Atlas-SNP	.											.	PNPT1	68	.	0			c.A2258G						PASS	.						95	85	88					2																	55863466		2203	4300	6503	SO:0001583	missense	87178	exon28			GGCGACTGAAGCA	BC053660	CCDS1856.1	2p15	2013-01-08			ENSG00000138035	ENSG00000138035			23166	protein-coding gene	gene with protein product	"polynucleotide phosphorylase", "3'-5' RNA exonuclease"	610316	"deafness, autosomal recessive 70"	DFNB70		12419256	Standard	NM_033109		Approved	PNPase, OLD35, old-35	uc002rzf.3	Q8TCS8	OTTHUMG00000129335	ENST00000447944.2:c.2258A>G	chr2.hg19:g.55863466T>C	ENSP00000400646:p.Gln753Arg	34.0	0.0	.		71.0	28.0	.	NM_033109	Q53SU0|Q68CN1|Q7Z7D1|Q8IWX1|Q96T05|Q9BRU3|Q9BVX0	Missense_Mutation	SNP	ENST00000447944.2	hg19	CCDS1856.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.665121	0.88251	.	.	ENSG00000138035	ENST00000447944	T	0.58358	0.34	5.95	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.52306	0.1726	L	0.34521	1.04	0.58432	D	0.999995	D	0.53462	0.96	P	0.53146	0.719	T	0.47699	-0.9097	10	0.35671	T	0.21	-4.4849	12.5042	0.55972	0.1252:0.0:0.0:0.8748	.	753	Q8TCS8	PNPT1_HUMAN	R	753	ENSP00000400646:Q753R	ENSP00000393953:Q753R	Q	-	2	0	PNPT1	55716970	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	7.397000	0.79903	1.050000	0.40346	0.533000	0.62120	CAG	.	.	.	none		0.403	PNPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251481.2	NM_033109		C	55863466	T	C	55863466	3	2	182	1	0	0	0	0	1	0	0	0	12180	1580	55	3	97	3	PNPT1	2	55863466	Missense_Mutation	SNP	T	TCGA-G7-A8LE-01A-11D-A35Z-10		55863466	187335907	4	10599											
LONRF2	164832	hgsc.bcm.edu	37	chr2	100916274	100916274	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagcgctgggtgctgttggaAggatgctttctaacgccttt	6	13	13	9	2	1	0	0	0	1	0	1	2	1	2	1	3	4	4	1	3	2	4			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr2:100916274A>G	ENST00000393437.3	-	5	1811	c.1172T>C	c.(1171-1173)cTt>cCt	p.L391P	LONRF2_ENST00000409647.1_Missense_Mutation_p.L148P	NM_198461.3	NP_940863.3	Q1L5Z9	LONF2_HUMAN	LON peptidase N-terminal domain and ring finger 2	391							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						TGCTGTTGGAAGGATGCTTTC	0.443																																					p.L391P		Atlas-SNP	.											.	LONRF2	62	.	0			c.T1172C						PASS	.						92	88	89					2																	100916274		2203	4300	6503	SO:0001583	missense	164832	exon5			GTTGGAAGGATGC	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.1172T>C	chr2.hg19:g.100916274A>G	ENSP00000377086:p.Leu391Pro	62.0	0.0	.		126.0	41.0	.	NM_198461	B9A006|Q6ZSR4	Missense_Mutation	SNP	ENST00000393437.3	hg19	CCDS2046.2	.	.	.	.	.	.	.	.	.	.	A	14.83	2.651892	0.47362	.	.	ENSG00000170500	ENST00000393437;ENST00000409647	D;D	0.86562	-2.01;-2.14	4.49	3.34	0.38264	.	0.158304	0.41938	D	0.000786	T	0.77356	0.4118	L	0.29908	0.895	0.28049	N	0.933432	B	0.11235	0.004	B	0.10450	0.005	T	0.65755	-0.6091	10	0.32370	T	0.25	-8.8817	8.0404	0.30519	0.9068:0.0:0.0932:0.0	.	391	Q1L5Z9	LONF2_HUMAN	P	391;148	ENSP00000377086:L391P;ENSP00000386823:L148P	ENSP00000377086:L391P	L	-	2	0	LONRF2	100282706	1.000000	0.71417	0.002000	0.10522	0.252000	0.25951	3.729000	0.54999	1.650000	0.50662	0.454000	0.30748	CTT	.	.	.	none		0.443	LONRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253161.2	NM_198461		G	100916274	A	G	100916274	3	3	182	1	0	0	0	0	1	0	0	0	8902	72	3	3	1124	3	LONRF2	2	100916274	Missense_Mutation	SNP	A	TCGA-G7-A8LE-01A-11D-A35Z-10	45052808	100916274	142283099	5	10600											
ZC3H6	376940	hgsc.bcm.edu	37	chr2	113074893	113074893	+	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	tattgtaccaaaggagagaaCtgcatttatatgcataatat	16	13	7	5	0	0	1	0	0	0	1	0	3	0	2	1	1	4	3	1	1	8	8			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr2:113074893C>G	ENST00000409871.1	+	7	1361	c.960C>G	c.(958-960)aaC>aaG	p.N320K	ZC3H6_ENST00000343936.4_Missense_Mutation_p.N320K	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	320							metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						AAGGAGAGAACTGCATTTATA	0.289																																					p.N320K		Atlas-SNP	.											.	ZC3H6	93	.	0			c.C960G						PASS	.						33	33	33					2																	113074893		1790	4047	5837	SO:0001583	missense	376940	exon7			AGAGAACTGCATT	AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"Zinc fingers, CCCH-type domain containing"	24762	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 6"	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.960C>G	chr2.hg19:g.113074893C>G	ENSP00000386764:p.Asn320Lys	317.0	0.0	.		522.0	184.0	.	NM_198581	A9JR71|Q6ZW96	Missense_Mutation	SNP	ENST00000409871.1	hg19	CCDS46393.1	.	.	.	.	.	.	.	.	.	.	C	15.41	2.824573	0.50739	.	.	ENSG00000188177	ENST00000409871;ENST00000343936;ENST00000542974	T;T	0.30714	1.52;1.52	5.44	3.24	0.37175	Zinc finger, CCCH-type (2);	0.049261	0.85682	D	0.000000	T	0.39517	0.1081	L	0.31526	0.94	0.53688	D	0.999975	D	0.76494	0.999	D	0.75484	0.986	T	0.15407	-1.0438	10	0.44086	T	0.13	-23.3467	11.1044	0.48194	0.0:0.8062:0.0:0.1938	.	320	P61129	ZC3H6_HUMAN	K	320;320;297	ENSP00000386764:N320K;ENSP00000340298:N320K	ENSP00000340298:N320K	N	+	3	2	ZC3H6	112791364	0.997000	0.39634	1.000000	0.80357	0.997000	0.91878	0.550000	0.23345	1.437000	0.47472	0.585000	0.79938	AAC	.	.	.	none		0.289	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581		G	113074893	C	G	113074893	3	3	182	1	0	0	0	0	1	0	0	0	17583	564	20	4	986	4	ZC3H6	2	113074893	Missense_Mutation	SNP	C	TCGA-G7-A8LE-01A-11D-A35Z-10	12158619	113074893	130124480	6	10601											
PAX8	7849	hgsc.bcm.edu	37	chr2	113999196	113999196	+	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	ctgccgctcaaatgggcactCgagcggctcgaggtggtgct	6	8	15	12	4	1	0	1	0	0	0	3	2	1	0	1	4	3	4	1	4	1	0	rs199890664		TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr2:113999196C>T	ENST00000429538.3	-	7	903	c.709G>A	c.(709-711)Gag>Aag	p.E237K	AC016683.6_ENST00000451179.1_RNA|AC016683.6_ENST00000556070.1_RNA|AC016683.6_ENST00000445745.1_RNA|PAX8_ENST00000263334.5_Missense_Mutation_p.E237K|AC016683.6_ENST00000422956.2_RNA|AC016683.6_ENST00000437551.1_RNA|AC016683.6_ENST00000436293.2_RNA|PAX8_ENST00000397647.3_Missense_Mutation_p.E237K|PAX8_ENST00000263335.7_Missense_Mutation_p.E237K|PAX8_ENST00000348715.5_Missense_Mutation_p.E237K|AC016683.6_ENST00000456685.1_RNA|RP11-65I12.1_ENST00000553319.1_RNA|AC016683.6_ENST00000553869.2_RNA|AC016683.6_ENST00000333145.5_RNA	NM_003466.3	NP_003457.1	Q06710	PAX8_HUMAN	paired box 8	237					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						AATGGGCACTCGAGCGGCTCG	0.632			T	PPARG	follicular thyroid		Thyroid dysgenesis																														p.E237K	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.G709A						PASS	.																																			SO:0001583	missense	7849	exon7			GGCACTCGAGCGG	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.709G>A	chr2.hg19:g.113999196C>T	ENSP00000395498:p.Glu237Lys	52.0	0.0	.		53.0	15.0	.	NM_013952	Q09155|Q16337|Q16338|Q16339|Q4ZG35|Q96J49	Missense_Mutation	SNP	ENST00000429538.3	hg19	CCDS46398.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.24|19.24	3.789645|3.789645	0.70337|0.70337	.|.	.|.	ENSG00000125618|ENSG00000125618	ENST00000263335;ENST00000397647;ENST00000348715;ENST00000429538;ENST00000263334|ENST00000468980	D;D;D;D;D|.	0.98633|.	-5.03;-5.04;-4.84;-4.29;-4.84|.	4.69|4.69	4.69|4.69	0.59074|0.59074	.|.	0.293300|.	0.36444|.	N|.	0.002600|.	T|T	0.72309|0.72309	0.3444|0.3444	M|M	0.66939|0.66939	2.045|2.045	0.48395|0.48395	D|D	0.999641|0.999641	P;P;P;D;D|.	0.69078|.	0.89;0.948;0.804;0.995;0.997|.	B;B;B;P;P|.	0.60236|.	0.117;0.325;0.039;0.871;0.811|.	T|T	0.72431|0.72431	-0.4296|-0.4296	10|5	0.87932|.	D|.	0|.	.|.	15.4542|15.4542	0.75299|0.75299	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	237;237;237;237;237|.	Q06710-2;Q06710-3;Q06710;Q06710-5;Q06710-4|.	.;.;PAX8_HUMAN;.;.|.	K|Q	237|22	ENSP00000263335:E237K;ENSP00000380768:E237K;ENSP00000314750:E237K;ENSP00000395498:E237K;ENSP00000263334:E237K|.	ENSP00000263334:E237K|.	E|R	-|-	1|2	0|0	PAX8|PAX8	113715666|113715666	1.000000|1.000000	0.71417|0.71417	0.935000|0.935000	0.37517|0.37517	0.537000|0.537000	0.34900|0.34900	6.414000|6.414000	0.73318|0.73318	2.334000|2.334000	0.79466|0.79466	0.650000|0.650000	0.86243|0.86243	GAG|CGA	.	C|0.999;G|0.001	.	alt		0.632	PAX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250353.5			T	113999196	C	T	113999196	3	4	182	1	0	0	0	0	1	0	0	0	11492	893	31	1	542	1	PAX8	2	113999196	Missense_Mutation	SNP	C	TCGA-G7-A8LE-01A-11D-A35Z-10	924303	113999196	129200177	7	10602											
NCKAP5	344148	hgsc.bcm.edu	37	chr2	133540450	133540451	+	Frame_Shift_Ins	INS	-	-	A																															gaagagttctgccgggtaagINSagaattgcctctctcggcgg																										TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr2:133540450_133540451insA	ENST00000409261.1	-	14	4306_4307	c.3933_3934insT	c.(3931-3936)tctcttfs	p.L1312fs	NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000473859.1_5'Flank|NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000317721.6_Frame_Shift_Ins_p.L1312fs	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1312										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						TGCCGGGTAAGAGAATTGCCTC	0.579																																					p.L1312fs		Atlas-Indel,Pindel	.											.	NCKAP5	322	.	0			c.3934_3935insT						PASS	.																																			SO:0001589	frameshift_variant	344148	exon14			.	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.3934dupT	chr2.hg19:g.133540451_133540451dupA	ENSP00000387128:p.Leu1312fs	114.0	0.0	0		167.0	70.0	0.419162	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Frame_Shift_Ins	INS	ENST00000409261.1	hg19	CCDS46418.1																																																																																			.	.	.	none		0.579	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		A	133540451	-	A	133540450	7	5	182	1	0	1	1	0	0	0	0	0	10230	942	33	0	1823	0	NCKAP5	2	133540450	Frame_Shift_Ins	INS	-	TCGA-G7-A8LE-01A-11D-A35Z-10	19541254	133540450	109658923	8	10603											
LRP2	4036	hgsc.bcm.edu	37	chr2	169997040	169997040	+	Missense_Mutation	SNP	A	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	tgcatggggggggcaggttgAtaggcagttcgatggctgca	7	9	19	6	1	0	1	0	1	0	0	1	2	0	1	0	7	2	7	0	7	1	3			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr2:169997040A>C	ENST00000263816.3	-	72	13409	c.13124T>G	c.(13123-13125)aTc>aGc	p.I4375S		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	4375					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)"	GGGCAGGTTGATAGGCAGTTC	0.542																																					p.I4375S		Atlas-SNP	.											.	LRP2	751	.	0			c.T13124G						PASS	.						56	52	53					2																	169997040		2203	4300	6503	SO:0001583	missense	4036	exon72			AGGTTGATAGGCA		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.13124T>G	chr2.hg19:g.169997040A>C	ENSP00000263816:p.Ile4375Ser	35.0	0.0	.		51.0	17.0	.	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	hg19	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	A	6.611	0.481057	0.12581	.	.	ENSG00000081479	ENST00000263816	D	0.89343	-2.5	5.92	3.55	0.40652	Growth factor, receptor (1);Epidermal growth factor-like (1);	0.636134	0.17247	N	0.181326	T	0.65186	0.2667	N	0.03967	-0.31	0.23120	N	0.998262	P	0.40144	0.704	B	0.33521	0.165	T	0.61098	-0.7131	10	0.09084	T	0.74	.	1.7437	0.02958	0.5346:0.0:0.1786:0.2868	.	4375	P98164	LRP2_HUMAN	S	4375	ENSP00000263816:I4375S	ENSP00000263816:I4375S	I	-	2	0	LRP2	169705286	1.000000	0.71417	0.008000	0.14137	0.035000	0.12851	5.532000	0.67154	1.044000	0.40200	-0.333000	0.08304	ATC	.	.	.	none		0.542	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		C	169997040	A	C	169997040	3	2	182	1	0	0	0	0	1	0	0	0	8963	333	12	5	875	5	LRP2	2	169997040	Missense_Mutation	SNP	A	TCGA-G7-A8LE-01A-11D-A35Z-10	36456590	169997040	73202333	9	10604											
HAT1	8520	hgsc.bcm.edu	37	chr2	172848147	172848147	+	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	gaaaatgtctcagaccagaaGaactgacaaaccagatgaac	19	5	8	9	0	1	6	1	2	1	4	2	7	1	6	2	0	3	0	2	0	6	0			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr2:172848147G>T	ENST00000264108.4	+	11	1177	c.1141G>T	c.(1141-1143)Gaa>Taa	p.E381*	SLC25A12_ENST00000472748.1_Intron|HAT1_ENST00000392584.1_Nonsense_Mutation_p.E296*	NM_003642.3	NP_003633.1	O14929	HAT1_HUMAN	histone acetyltransferase 1	381					chromatin organization (GO:0006325)|chromatin silencing at telomere (GO:0006348)|DNA packaging (GO:0006323)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4 acetylation (GO:0043967)|internal protein amino acid acetylation (GO:0006475)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	H4 histone acetyltransferase activity (GO:0010485)|histone acetyltransferase activity (GO:0004402)			breast(1)|kidney(1)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|prostate(1)	19			OV - Ovarian serous cystadenocarcinoma(117;0.216)			CAGACCAGAAGAACTGACAAA	0.358																																					p.E381X		Atlas-SNP	.											.	HAT1	40	.	0			c.G1141T						PASS	.						106	104	105					2																	172848147		2203	4300	6503	SO:0001587	stop_gained	8520	exon11			CCAGAAGAACTGA	AF030424	CCDS2245.1	2q31.2-q33.1	2011-07-01			ENSG00000128708	ENSG00000128708	2.3.1.48	"Chromatin-modifying enzymes / K-acetyltransferases"	4821	protein-coding gene	gene with protein product		603053				9427644	Standard	NM_003642		Approved	KAT1	uc002uhi.3	O14929	OTTHUMG00000132282	ENST00000264108.4:c.1141G>T	chr2.hg19:g.172848147G>T	ENSP00000264108:p.Glu381*	277.0	0.0	.		383.0	153.0	.	NM_003642	Q49A44|Q53QF0|Q53SU4|Q6P594|Q8WWB9	Nonsense_Mutation	SNP	ENST00000264108.4	hg19	CCDS2245.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.014466	0.93404	.	.	ENSG00000128708	ENST00000392584;ENST00000264108	.	.	.	5.94	5.05	0.67936	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-18.6532	15.5425	0.76066	0.0671:0.0:0.9329:0.0	.	.	.	.	X	296;381	.	ENSP00000264108:E381X	E	+	1	0	HAT1	172556393	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.368000	0.79567	2.807000	0.96579	0.591000	0.81541	GAA	.	.	.	none		0.358	HAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255377.1	NM_003642		T	172848147	G	T	172848147	4	4	182	1	0	0	0	0	0	1	0	0	6971	943	33	4	1183	4	HAT1	2	172848147	Nonsense_Mutation	SNP	G	TCGA-G7-A8LE-01A-11D-A35Z-10	2851107	172848147	70351226	10	10605											
NEUROD1	4760	hgsc.bcm.edu	37	chr2	182543486	182543486	+	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	tcctccttcttgtctgcctcGtgctcctcgtcctgagaact	3	15	7	16	2	2	1	0	1	2	1	8	2	6	1	5	0	3	1	5	0	1	2			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr2:182543486G>C	ENST00000295108.3	-	2	559	c.102C>G	c.(100-102)caC>caG	p.H34Q	NEUROD1_ENST00000496876.1_Intron|CERKL_ENST00000479558.1_Intron	NM_002500.4	NP_002491.2	Q13562	NDF1_HUMAN	neuronal differentiation 1	34					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.H34H(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)			TGTCTGCCTCGTGCTCCTCGT	0.587																																					p.H34Q		Atlas-SNP	.											NEUROD1,NS,carcinoma,0,1	NEUROD1	67	.	1	Substitution - coding silent(1)	lung(1)	c.C102G						PASS	.						109	85	93					2																	182543486		2203	4300	6503	SO:0001583	missense	4760	exon2			TGCCTCGTGCTCC	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.102C>G	chr2.hg19:g.182543486G>C	ENSP00000295108:p.His34Gln	59.0	0.0	.		76.0	30.0	.	NM_002500	B2R9I8|F1T0E1|O00343|Q13340|Q5U095|Q96TH0|Q99455|Q9UEC8	Missense_Mutation	SNP	ENST00000295108.3	hg19	CCDS2283.1	.	.	.	.	.	.	.	.	.	.	G	11.76	1.735132	0.30774	.	.	ENSG00000162992	ENST00000295108	D	0.94793	-3.52	5.37	-0.584	0.11702	.	0.307024	0.26665	N	0.023123	D	0.84065	0.5390	N	0.08118	0	0.36683	D	0.879175	B	0.06786	0.001	B	0.01281	0.0	T	0.71600	-0.4544	10	0.23891	T	0.37	-0.3395	9.7906	0.40704	0.451:0.0:0.549:0.0	.	34	Q13562	NDF1_HUMAN	Q	34	ENSP00000295108:H34Q	ENSP00000295108:H34Q	H	-	3	2	NEUROD1	182251731	0.991000	0.36638	0.994000	0.49952	0.988000	0.76386	0.165000	0.16564	-0.062000	0.13088	-0.157000	0.13467	CAC	.	.	.	none		0.587	NEUROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255792.2	NM_002500		C	182543486	G	C	182543486	3	2	182	1	0	0	0	0	1	0	0	0	10355	1136	40	4	972	4	NEUROD1	2	182543486	Missense_Mutation	SNP	G	TCGA-G7-A8LE-01A-11D-A35Z-10	9695339	182543486	60655887	11	10606											
BAP1	51533	hgsc.bcm.edu	37	chr3	52443594	52443594	+	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	gacatttgctctgaaggtcgTagatctcctccacttgcacc	8	12	8	13	1	2	2	0	1	2	1	5	3	3	2	3	1	2	3	3	1	2	3			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr3:52443594T>C	ENST00000327906.3	+	0	0				PHF7_ENST00000347025.2_5'Flank|BAP1_ENST00000460680.1_Missense_Mutation_p.Y33C|BAP1_ENST00000296288.5_Missense_Mutation_p.Y33C	NM_016483.4	NP_057567.3	Q9BWX1	PHF7_HUMAN	PHD finger protein 7							Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			breast(2)|large_intestine(4)|lung(3)	9				BRCA - Breast invasive adenocarcinoma(193;1.71e-05)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)|OV - Ovarian serous cystadenocarcinoma(275;0.0275)		CTGAAGGTCGTAGATCTCCTC	0.612																																					p.Y33C		Atlas-SNP	.											.	BAP1	371	.	0			c.A98G						PASS	.						220	229	226					3																	52443594		2203	4300	6503	SO:0001631	upstream_gene_variant	8314	exon3			AGGTCGTAGATCT	AY014283	CCDS2854.1, CCDS2855.1	3p21.31	2013-01-28			ENSG00000010318	ENSG00000010318		"Zinc fingers, PHD-type"	18458	protein-coding gene	gene with protein product						11042152, 11829468	Standard	NM_016483		Approved	NYD-SP6, HSPC226	uc003ddy.3	Q9BWX1	OTTHUMG00000158495		chr3.hg19:g.52443594T>C	Exception_encountered	106.0	0.0	.		111.0	5.0	.	NM_004656	K4DI82	Missense_Mutation	SNP	ENST00000327906.3	hg19	CCDS2854.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.803049	0.90623	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	T;T	0.53206	0.63;0.63	4.97	4.97	0.65823	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (3);	0.000000	0.85682	D	0.000000	T	0.73845	0.3639	M	0.90542	3.125	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80434	-0.1384	10	0.72032	D	0.01	-1.7504	14.6644	0.68896	0.0:0.0:0.0:1.0	.	33	Q92560	BAP1_HUMAN	C	33	ENSP00000417132:Y33C;ENSP00000296288:Y33C	ENSP00000296288:Y33C	Y	-	2	0	BAP1	52418634	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.825000	0.86693	1.875000	0.54330	0.533000	0.62120	TAC	.	.	.	none		0.612	PHF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351155.1	NM_016483		C	52443594	T	C	52443594	1	2	182	0	1	0	0	0	0	0	0	0	1311	1638	57	3		3	BAP1	3	52443594	5'Flank	SNP	T	TCGA-G7-A8LE-01A-11D-A35Z-10		52443594	145578836	12	10607											
TMEM45A	55076	hgsc.bcm.edu	37	chr3	100295846	100295846	+	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	tgctgaacgagaacaagaatCagaagaagaaatgtgacttt	18	8	10	5	1	1	7	1	2	0	5	1	8	1	7	0	0	3	1	0	0	7	1			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr3:100295846C>A	ENST00000323523.4	+	6	1125	c.812C>A	c.(811-813)tCa>tAa	p.S271*	TMEM45A_ENST00000403410.1_Nonsense_Mutation_p.S287*	NM_018004.1	NP_060474.1	Q9NWC5	TM45A_HUMAN	transmembrane protein 45A	271						integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)	11						GAACAAGAATCAGAAGAAGAA	0.368																																					p.S271X		Atlas-SNP	.											.	TMEM45A	35	.	0			c.C812A						PASS	.						99	106	104					3																	100295846		2203	4300	6503	SO:0001587	stop_gained	55076	exon6			AAGAATCAGAAGA	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.812C>A	chr3.hg19:g.100295846C>A	ENSP00000319009:p.Ser271*	43.0	0.0	.		83.0	28.0	.	NM_018004	Q53YW5	Nonsense_Mutation	SNP	ENST00000323523.4	hg19	CCDS2937.1	.	.	.	.	.	.	.	.	.	.	C	41	8.585272	0.98875	.	.	ENSG00000181458	ENST00000323523;ENST00000403410	.	.	.	6.17	5.22	0.72569	.	0.287576	0.35179	N	0.003392	.	.	.	.	.	.	0.45161	D	0.998178	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	-4.5576	12.3932	0.55370	0.0:0.9157:0.0:0.0843	.	.	.	.	X	271;287	.	ENSP00000319009:S271X	S	+	2	0	TMEM45A	101778536	0.993000	0.37304	1.000000	0.80357	0.901000	0.52897	2.320000	0.43797	1.463000	0.47967	0.655000	0.94253	TCA	.	.	.	none		0.368	TMEM45A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317571.1	NM_018004		A	100295846	C	A	100295846	4	1	182	1	0	0	0	0	0	1	0	0	16181	838	29	4	830	4	TMEM45A	3	100295846	Nonsense_Mutation	SNP	C	TCGA-G7-A8LE-01A-11D-A35Z-10	47852252	100295846	97726584	13	10608											
ZNF80	7634	hgsc.bcm.edu	37	chr3	113955534	113955536	+	In_Frame_Del	DEL	CTC	CTC	-																															gctgcactcatagggcttctCtccagtgtgaatctggcggt																										TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr3:113955534_113955536delCTC	ENST00000482457.2	-	1	889_891	c.386_388delGAG	c.(385-390)ggagag>gag	p.G129del	RP11-553L6.2_ENST00000493033.1_RNA|RP11-553L6.2_ENST00000481773.1_RNA	NM_007136.3	NP_009067.2	P51504	ZNF80_HUMAN	zinc finger protein 80	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)			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)				TAGGGCTTCTCTCCAGTGTGAAT	0.542																																					p.129_130del	GBM(23;986 1114 21716)	Atlas-Indel,Pindel	.											.	ZNF80	75	.	0			c.387_389del						PASS	.																																			SO:0001651	inframe_deletion	7634	exon1			.	X65233	CCDS2979.1	3q13.31	2013-01-08	2006-05-12		ENSG00000174255	ENSG00000174255		"Zinc fingers, C2H2-type"	13155	protein-coding gene	gene with protein product		194553	"zinc finger protein 80 (pT17)"			8478004	Standard	NM_007136		Approved	pT17	uc010hqo.3	P51504	OTTHUMG00000159332	ENST00000482457.2:c.386_388delGAG	chr3.hg19:g.113955534_113955536delCTC	ENSP00000417192:p.Gly129del	83.0	0.0	0		111.0	48.0	0.432432	NM_007136	Q6NSW4|Q6NT14	In_Frame_Del	DEL	ENST00000482457.2	hg19	CCDS2979.1																																																																																			.	.	.	none		0.542	ZNF80-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354696.2	NM_007136		-	113955536	CTC	-	113955534	7	5	182	1	0	1	0	1	0	0	0	0	18180	922	32	0	437	0	ZNF80	3	113955534	In_Frame_Del	DEL	CTC	TCGA-G7-A8LE-01A-11D-A35Z-10	13659688	113955534	84066896	14	10609											
EPHB3	2049	hgsc.bcm.edu	37	chr3	184299386	184299386	+	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	gacatgcggctgcagatgaaCcagacgctgcctgtgcaggt	9	7	14	11	2	0	3	0	1	0	2	0	4	0	3	2	2	5	4	2	2	1	0			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr3:184299386C>G	ENST00000330394.2	+	16	3425	c.2973C>G	c.(2971-2973)aaC>aaG	p.N991K	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	991					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)			TGCAGATGAACCAGACGCTGC	0.622																																					p.N991K		Atlas-SNP	.											.	EPHB3	114	.	0			c.C2973G						PASS	.						45	41	42					3																	184299386		2203	4300	6503	SO:0001583	missense	2049	exon16			GATGAACCAGACG	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.2973C>G	chr3.hg19:g.184299386C>G	ENSP00000332118:p.Asn991Lys	106.0	0.0	.		129.0	53.0	.	NM_004443	Q7Z740	Missense_Mutation	SNP	ENST00000330394.2	hg19	CCDS3268.1	.	.	.	.	.	.	.	.	.	.	C	13.55	2.269452	0.40095	.	.	ENSG00000182580	ENST00000330394	T	0.06142	3.34	4.36	4.36	0.52297	Sterile alpha motif/pointed domain (2);	0.098712	0.64402	D	0.000002	T	0.04272	0.0118	L	0.37561	1.115	0.58432	D	0.999999	P	0.43094	0.799	B	0.33339	0.162	T	0.50440	-0.8828	10	0.12103	T	0.63	.	10.4826	0.44702	0.0:0.9084:0.0:0.0916	.	991	P54753	EPHB3_HUMAN	K	991	ENSP00000332118:N991K	ENSP00000332118:N991K	N	+	3	2	EPHB3	185782080	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.060000	0.57477	2.378000	0.81104	0.643000	0.83706	AAC	.	.	.	none		0.622	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443		G	184299386	C	G	184299386	3	3	182	1	0	0	0	0	1	0	0	0	5178	506	18	4	3035	4	EPHB3	3	184299386	Missense_Mutation	SNP	C	TCGA-G7-A8LE-01A-11D-A35Z-10	70343852	184299386	13723044	15	10610											
LMLN	89782	hgsc.bcm.edu	37	chr3	197726166	197726166	+	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	atgactggttctcacactcaGaatcgagtactctctcgaat	11	12	7	11	2	3	2	2	1	2	1	7	4	3	2	0	1	1	2	0	1	3	2			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr3:197726166G>A	ENST00000330198.4	+	11	1207	c.1185G>A	c.(1183-1185)caG>caA	p.Q395Q	LMLN_ENST00000332636.5_Silent_p.Q343Q|LMLN_ENST00000482695.1_Silent_p.Q343Q|LMLN_ENST00000420910.2_Silent_p.Q395Q	NM_033029.3	NP_149018.2	Q96KR4	LMLN_HUMAN	leishmanolysin-like (metallopeptidase M8 family)	395					cell adhesion (GO:0007155)|mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)		CTCACACTCAGAATCGAGTAC	0.388																																					p.Q395Q		Atlas-SNP	.											.	LMLN	53	.	0			c.G1185A						PASS	.						103	98	100					3																	197726166		2203	4300	6503	SO:0001819	synonymous_variant	89782	exon11			CACTCAGAATCGA	AJ312398	CCDS3332.1, CCDS46988.1	3q29	2008-02-04			ENSG00000185621	ENSG00000185621	3.4.24.36		15991	protein-coding gene	gene with protein product		609380					Standard	NM_033029		Approved	Gp63, Msp	uc010iar.3	Q96KR4	OTTHUMG00000155375	ENST00000330198.4:c.1185G>A	chr3.hg19:g.197726166G>A		41.0	0.0	.		58.0	25.0	.	NM_001136049	B3LDG9|B3LDH0|C9J796|F8WB28|Q96KR5	Silent	SNP	ENST00000330198.4	hg19	CCDS3332.1																																																																																			.	.	.	none		0.388	LMLN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339701.1	NM_033029		A	197726166	G	A	197726166	2	1	182	1	0	0	0	0	0	0	0	1	8854	933	33	2		2	LMLN	3	197726166	Silent	SNP	G	TCGA-G7-A8LE-01A-11D-A35Z-10	13426780	197726166	296264	16	10611											
POU4F2	5458	hgsc.bcm.edu	37	chr4	147560484	147560484	+	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	ggcggcggcggcggcggcggCggcggcggaggccgaagcag	4	0	25	12	10	0	0	0	0	0	0	0	2	0	1	1	11	1	1	1	11	1	0			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr4:147560484C>A	ENST00000281321.3	+	1	440	c.192C>A	c.(190-192)ggC>ggA	p.G64G	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	64	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)					gcggcggcggcggcggcggag	0.771																																					p.G64G		Atlas-SNP	.											.	POU4F2	83	.	0			c.C192A						PASS	.						3	5	5					4																	147560484		1329	2897	4226	SO:0001819	synonymous_variant	5458	exon1			CGGCGGCGGCGGC	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.192C>A	chr4.hg19:g.147560484C>A		63.0	0.0	.		116.0	6.0	.	NM_004575	B1PJR6|B2RC84|Q13883|Q14987	Silent	SNP	ENST00000281321.3	hg19	CCDS34074.1																																																																																			.	.	.	none		0.771	POU4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367020.1	NM_004575		A	147560484	C	A	147560484	2	1	182	1	0	0	0	0	0	0	0	1	12286	755	27	4		4	POU4F2	4	147560484	Silent	SNP	C	TCGA-G7-A8LE-01A-11D-A35Z-10		147560484	43593792	17	10612											
NEK1	4750	hgsc.bcm.edu	37	chr4	170354709	170354709	+	Missense_Mutation	SNP	T	T	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	tacatactgagtttcctttgTttctttttcctcactaatcc	7	20	3	11	0	2	1	1	1	1	0	5	1	5	1	3	0	2	2	3	0	3	8			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr4:170354709T>G	ENST00000439128.2	-	27	3428	c.2788A>C	c.(2788-2790)Aca>Cca	p.T930P	NEK1_ENST00000507142.1_Missense_Mutation_p.T958P|NEK1_ENST00000511633.1_Missense_Mutation_p.T914P|NEK1_ENST00000512193.1_Missense_Mutation_p.T861P|NEK1_ENST00000510533.1_Missense_Mutation_p.T886P	NM_012224.2	NP_036356.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	930					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)		GTTTCCTTTGTTTCTTTTTCC	0.333																																					p.T958P		Atlas-SNP	.											.	NEK1	203	.	0			c.A2872C						PASS	.						174	163	166					4																	170354709		1841	4090	5931	SO:0001583	missense	4750	exon29			CCTTTGTTTCTTT	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.2788A>C	chr4.hg19:g.170354709T>G	ENSP00000408020:p.Thr930Pro	121.0	0.0	.		215.0	74.0	.	NM_001199397	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	Missense_Mutation	SNP	ENST00000439128.2	hg19	CCDS47162.1	.	.	.	.	.	.	.	.	.	.	t	10.02	1.235909	0.22626	.	.	ENSG00000137601	ENST00000439128;ENST00000511633;ENST00000510533;ENST00000507142;ENST00000512193	T;T;T;T;T	0.70045	-0.45;-0.43;-0.44;-0.43;-0.43	5.65	-8.11	0.01082	.	0.921323	0.09246	N	0.828579	T	0.45175	0.1329	N	0.22421	0.69	0.09310	N	1	B;B;B;P;B	0.40250	0.002;0.116;0.0;0.709;0.0	B;B;B;B;B	0.41299	0.004;0.124;0.001;0.353;0.0	T	0.46843	-0.9162	10	0.41790	T	0.15	.	6.4416	0.21853	0.0893:0.4493:0.0913:0.3701	.	861;914;958;886;930	Q96PY6-4;G5E9Z3;Q96PY6-3;Q96PY6-2;Q96PY6	.;.;.;.;NEK1_HUMAN	P	930;914;886;958;861	ENSP00000408020:T930P;ENSP00000423332:T914P;ENSP00000427653:T886P;ENSP00000424757:T958P;ENSP00000424938:T861P	ENSP00000408020:T930P	T	-	1	0	NEK1	170591284	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.517000	0.06275	-1.416000	0.02019	-2.057000	0.00402	ACA	.	.	.	none		0.333	NEK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363157.3			G	170354709	T	G	170354709	3	3	182	1	0	0	0	0	1	0	0	0	10328	1725	60	5	1020	5	NEK1	4	170354709	Missense_Mutation	SNP	T	TCGA-G7-A8LE-01A-11D-A35Z-10	22794225	170354709	20799567	18	10613											
FAT1	2195	hgsc.bcm.edu	37	chr4	187629813	187629814	+	In_Frame_Ins	INS	-	-	AAA																															ggaataagcaggaatggcctINSttaccatgaccacaggtgtg																										TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr4:187629813_187629814insAAA	ENST00000441802.2	-	2	1377_1378	c.1168_1169insTTT	c.(1168-1170)aag>aTTTag	p.390_390K>I*		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	390	Cadherin 3. {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						AGGAATGGCCTTTACCATGACC	0.386										HNSCC(5;0.00058)																											p.K390delinsIX	Colon(197;1040 2055 4143 4984 49344)	Atlas-Indel,Pindel	.											.	FAT1	500	.	0			c.1169_1170insTTT						PASS	.																																			SO:0001652	inframe_insertion	2195	exon2			.	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.1168_1169insTTT	chr4.hg19:g.187629813_187629814insAAA	ENSP00000406229:p.Lys390delinsIle*	47.0	0.0	0		82.0	34.0	0.414634	NM_005245		In_Frame_Ins	INS	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.	.	none		0.386	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		AAA	187629814	-	AAA	187629813	7	5	182	1	0	1	1	0	0	0	0	0	5696	1609	56	0	12701	0	FAT1	4	187629813	In_Frame_Ins	INS	-	TCGA-G7-A8LE-01A-11D-A35Z-10	17275104	187629813	3524463	19	10614											
AGXT2	64902	hgsc.bcm.edu	37	chr5	35014199	35014199	+	Missense_Mutation	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	ggaagccccagaagtgagagCccaaccttccaaatcctgtc	12	6	9	14	0	0	2	0	1	0	2	3	4	2	3	6	1	3	0	6	1	4	1			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr5:35014199C>T	ENST00000231420.6	-	10	1189	c.989G>A	c.(988-990)gGc>gAc	p.G330D		NM_031900.3	NP_114106.1	Q9BYV1	AGT2_HUMAN	alanine--glyoxylate aminotransferase 2	330					cellular nitrogen compound metabolic process (GO:0034641)|glycine biosynthetic process, by transamination of glyoxylate (GO:0019265)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|L-alanine catabolic process, by transamination (GO:0019481)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	(R)-3-amino-2-methylpropionate-pyruvate transaminase activity (GO:0047305)|alanine-glyoxylate transaminase activity (GO:0008453)|beta-alanine-pyruvate transaminase activity (GO:0016223)|pyridoxal phosphate binding (GO:0030170)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(18)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	41	all_lung(31;4.52e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)	GBM - Glioblastoma multiforme(108;0.181)	Glycine(DB00145)|L-Alanine(DB00160)|Pyruvic acid(DB00119)	GAAGTGAGAGCCCAACCTTCC	0.517																																					p.G330D		Atlas-SNP	.											.	AGXT2	89	.	0			c.G989A						PASS	.						123	109	114					5																	35014199		2203	4300	6503	SO:0001583	missense	64902	exon10			TGAGAGCCCAACC	AJ292204	CCDS3908.1	5p13	2010-05-07	2010-05-07		ENSG00000113492	ENSG00000113492	2.6.1.44		14412	protein-coding gene	gene with protein product	"beta-alanine-pyruvate aminotransferase", "beta-ALAAT II"	612471	"alanine-glyoxylate aminotransferase 2"			15240345	Standard	NM_031900		Approved	AGT2	uc003jjf.3	Q9BYV1	OTTHUMG00000090788	ENST00000231420.6:c.989G>A	chr5.hg19:g.35014199C>T	ENSP00000231420:p.Gly330Asp	163.0	0.0	.		183.0	73.0	.	NM_031900	B7ZM47|E9PDL7|Q53FB4|Q53FY7|Q53G03|Q5W7Q1	Missense_Mutation	SNP	ENST00000231420.6	hg19	CCDS3908.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.952520	0.92660	.	.	ENSG00000113492	ENST00000231420	D	0.94330	-3.4	5.88	5.88	0.94601	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.98532	0.9510	H	0.99487	4.59	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99293	1.0899	10	0.87932	D	0	-19.6355	19.8216	0.96599	0.0:1.0:0.0:0.0	.	330	Q9BYV1	AGT2_HUMAN	D	330	ENSP00000231420:G330D	ENSP00000231420:G330D	G	-	2	0	AGXT2	35049956	1.000000	0.71417	0.998000	0.56505	0.972000	0.66771	7.110000	0.77069	2.769000	0.95229	0.655000	0.94253	GGC	.	.	.	none		0.517	AGXT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207574.2	NM_031900		T	35014199	C	T	35014199	3	4	182	1	0	0	0	0	1	0	0	0	405	739	26	2	575	2	AGXT2	5	35014199	Missense_Mutation	SNP	C	TCGA-G7-A8LE-01A-11D-A35Z-10		35014199	145901061	20	10615											
TMEM174	134288	hgsc.bcm.edu	37	chr5	72469241	72469241	+	Frame_Shift_Del	DEL	G	G	-																															gggatcacattcactgtcatGggctggatcaaataccaagg																										TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr5:72469241delG	ENST00000296776.5	+	1	220	c.171delG	c.(169-171)atgfs	p.M57fs	TMEM174_ENST00000511737.1_3'UTR	NM_153217.2	NP_694949.1	Q8WUU8	TM174_HUMAN	transmembrane protein 174	57						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	7		Lung NSC(167;0.0378)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;1.46e-54)		TCACTGTCATGGGCTGGATCA	0.557																																					p.M57fs		Pindel	.											.	TMEM174	22	.	0			c.170delT						PASS	.						125	115	119					5																	72469241		2203	4300	6503	SO:0001589	frameshift_variant	134288	exon1			.	BC019346	CCDS4018.1	5q13.2	2008-02-05			ENSG00000164325	ENSG00000164325			28187	protein-coding gene	gene with protein product		614909				12477932	Standard	NM_153217		Approved	MGC13034, FLJ31268	uc010izc.3	Q8WUU8	OTTHUMG00000131268	ENST00000296776.5:c.171delG	chr5.hg19:g.72469241delG	ENSP00000296776:p.Met57fs	84.0	0.0	.		99.0	27.0	0.273	NM_153217	B2RDA0|Q96N81	Frame_Shift_Del	DEL	ENST00000296776.5	hg19	CCDS4018.1																																																																																			.	.	.	none		0.557	TMEM174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254036.1	NM_153217		-	72469241	G	-	72469241	7	5	182	1	0	1	0	1	0	0	0	0	16102	1348	47	0	173	0	TMEM174	5	72469241	Frame_Shift_Del	DEL	G	TCGA-G7-A8LE-01A-11D-A35Z-10	37455042	72469241	108446019	21	10616											
PCDHGA2	56113	hgsc.bcm.edu	37	chr5	140718667	140718667	+	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	gaagagatcgacagaggctcCttcgtaggcaacatcgccaa	13	6	11	11	3	0	2	0	0	0	2	4	5	1	2	2	2	1	3	2	2	4	2			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr5:140718667C>G	ENST00000394576.2	+	1	129	c.129C>G	c.(127-129)tcC>tcG	p.S43S	PCDHGA1_ENST00000517417.1_Intron	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	43	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			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)			ACAGAGGCTCCTTCGTAGGCA	0.607											OREG0016854	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S43S		Atlas-SNP	.											.	PCDHGA2	205	.	0			c.C129G						PASS	.						73	74	74					5																	140718667		2203	4300	6503	SO:0001819	synonymous_variant	56113	exon1			AGGCTCCTTCGTA	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.129C>G	chr5.hg19:g.140718667C>G		72.0	0.0	.	1658	77.0	34.0	.	NM_018915	Q52LL6|Q9Y5D5	Silent	SNP	ENST00000394576.2	hg19	CCDS47289.1																																																																																			.	.	.	none		0.607	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374738.1	NM_018915		G	140718667	C	G	140718667	2	3	182	1	0	0	0	0	0	0	0	1	11561	668	24	4		4	PCDHGA2	5	140718667	Silent	SNP	C	TCGA-G7-A8LE-01A-11D-A35Z-10	68249426	140718667	40196593	22	10617											
NR3C1	2908	hgsc.bcm.edu	37	chr5	142662143	142662143	+	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	tgacacttacttcatgcataGaatccaagagttttgtcagt	12	14	7	8	0	2	3	2	1	0	2	3	3	3	3	1	0	2	2	1	0	4	5			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr5:142662143G>C	ENST00000343796.2	-	8	3164	c.2171C>G	c.(2170-2172)tCt>tGt	p.S724C	NR3C1_ENST00000424646.2_Missense_Mutation_p.S698C|NR3C1_ENST00000503201.1_Missense_Mutation_p.S724C|NR3C1_ENST00000394464.2_Missense_Mutation_p.S724C|NR3C1_ENST00000416954.2_Missense_Mutation_p.S327C|NR3C1_ENST00000504572.1_Missense_Mutation_p.S725C|NR3C1_ENST00000231509.3_Missense_Mutation_p.S725C|NR3C1_ENST00000415690.2_Missense_Mutation_p.S724C|NR3C1_ENST00000394466.2_Missense_Mutation_p.S725C	NM_001018074.1|NM_001018075.1|NM_001018077.1	NP_001018084.1|NP_001018085.1|NP_001018087.1	P04150	GCR_HUMAN	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)	724	Interaction with CLOCK.|Steroid-binding.				adrenal gland development (GO:0030325)|chromatin modification (GO:0016568)|gene expression (GO:0010467)|glucocorticoid metabolic process (GO:0008211)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of glucocorticoid mediated signaling pathway (GO:1900170)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucocorticoid biosynthetic process (GO:0031946)|regulation of gluconeogenesis (GO:0006111)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	glucocorticoid receptor activity (GO:0004883)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|zinc ion binding (GO:0008270)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	35		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Alclometasone(DB00240)|Amcinonide(DB00288)|Beclomethasone(DB00394)|Betamethasone(DB00443)|Budesonide(DB01222)|Ciclesonide(DB01410)|Clobetasol propionate(DB01013)|Clocortolone(DB00838)|Cortisone acetate(DB01380)|Desonide(DB01260)|Desoximetasone(DB00547)|Dexamethasone(DB01234)|Diflorasone(DB00223)|Difluprednate(DB06781)|Fludrocortisone(DB00687)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Fluoxymesterone(DB01185)|Flurandrenolide(DB00846)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol(DB00873)|Medrysone(DB00253)|Megestrol acetate(DB00351)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Paramethasone(DB01384)|Prednicarbate(DB01130)|Prednisolone(DB00860)|Prednisone(DB00635)|Rimexolone(DB00896)|Spironolactone(DB00421)|Triamcinolone(DB00620)	TTCATGCATAGAATCCAAGAG	0.393																																					p.S725C		Atlas-SNP	.											NR3C1_ENST00000415690,NS,carcinoma,0,2	NR3C1	124	.	0			c.C2174G						PASS	.						107	103	104					5																	142662143		2203	4300	6503	SO:0001583	missense	2908	exon8			TGCATAGAATCCA	X03225	CCDS4278.1, CCDS34258.1, CCDS47298.1	5q31-q32	2013-01-16	2002-08-27		ENSG00000113580	ENSG00000113580		"Nuclear hormone receptors"	7978	protein-coding gene	gene with protein product		138040	"nuclear receptor subfamily 3, group C, member 1"	GRL		2867473	Standard	NM_001204258		Approved	GR	uc003lnb.3	P04150	OTTHUMG00000129677	ENST00000343796.2:c.2171C>G	chr5.hg19:g.142662143G>C	ENSP00000343205:p.Ser724Cys	77.0	0.0	.		93.0	37.0	.	NM_001024094	A0ZXF9|B0LPG8|D3DQF4|P04151|Q53EP5|Q6N0A4	Missense_Mutation	SNP	ENST00000343796.2	hg19	CCDS4278.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.611957	0.87258	.	.	ENSG00000113580	ENST00000394464;ENST00000343796;ENST00000361001;ENST00000415690;ENST00000424646;ENST00000504572;ENST00000394466;ENST00000231509;ENST00000416954;ENST00000503201	D;D;D;D;D;D;D;D;D	0.96967	-4.19;-4.19;-4.19;-4.19;-4.19;-4.19;-4.19;-4.19;-4.19	5.77	5.77	0.91146	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.97999	0.9341	M	0.70595	2.14	0.80722	D	1	D;P;D	0.89917	1.0;0.728;1.0	D;P;D	0.91635	0.997;0.55;0.999	D	0.98227	1.0481	10	0.72032	D	0.01	.	20.3626	0.98863	0.0:0.0:1.0:0.0	.	724;724;725	E5KQF5;P04150;E5KQF6	.;GCR_HUMAN;.	C	724;724;540;724;698;725;725;725;327;724	ENSP00000377977:S724C;ENSP00000343205:S724C;ENSP00000387672:S724C;ENSP00000405282:S698C;ENSP00000422518:S725C;ENSP00000377979:S725C;ENSP00000231509:S725C;ENSP00000404218:S327C;ENSP00000427672:S724C	ENSP00000231509:S725C	S	-	2	0	NR3C1	142642336	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.814000	0.86154	2.885000	0.99019	0.655000	0.94253	TCT	.	.	.	none		0.393	NR3C1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370829.1			C	142662143	G	C	142662143	3	2	182	1	0	0	0	0	1	0	0	0	10637	942	33	4	222	4	NR3C1	5	142662143	Missense_Mutation	SNP	G	TCGA-G7-A8LE-01A-11D-A35Z-10	1943476	142662143	38253117	23	10618											
CPEB4	80315	hgsc.bcm.edu	37	chr5	173372036	173372036	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtggggatcagcctcttcAtagtggcctgggttcacctc	5	11	12	13	1	4	0	3	0	1	0	5	1	4	1	4	4	1	1	4	4	1	3			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr5:173372036A>G	ENST00000265085.5	+	5	2803	c.1349A>G	c.(1348-1350)cAt>cGt	p.H450R	CPEB4_ENST00000517880.1_Missense_Mutation_p.H43R|CPEB4_ENST00000520867.1_Missense_Mutation_p.H425R|CPEB4_ENST00000519835.1_Missense_Mutation_p.H425R|CPEB4_ENST00000522336.1_Missense_Mutation_p.H60R|CPEB4_ENST00000334035.5_Missense_Mutation_p.H433R|CPEB4_ENST00000519467.1_3'UTR	NM_030627.2	NP_085130.2	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding protein 4	450					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)			CAGCCTCTTCATAGTGGCCTG	0.483																																					p.H450R		Atlas-SNP	.											.	CPEB4	54	.	0			c.A1349G						PASS	.						185	167	173					5																	173372036		2203	4300	6503	SO:0001583	missense	80315	exon5			CTCTTCATAGTGG	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.1349A>G	chr5.hg19:g.173372036A>G	ENSP00000265085:p.His450Arg	150.0	0.0	.		179.0	71.0	.	NM_030627	B7ZLQ7|Q7Z310|Q8N405|Q9C0J0	Missense_Mutation	SNP	ENST00000265085.5	hg19	CCDS4390.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.62|10.62	1.401584|1.401584	0.25291|0.25291	.|.	.|.	ENSG00000113742|ENSG00000113742	ENST00000265085;ENST00000520867;ENST00000334035;ENST00000519835;ENST00000522336;ENST00000517880|ENST00000519152	T;T;T;T|.	0.41400|.	1.0;1.02;1.01;1.02|.	5.37|5.37	4.18|4.18	0.49190|0.49190	Nucleotide-binding, alpha-beta plait (1);|.	0.218399|.	0.46758|.	D|.	0.000271|.	T|T	0.35393|0.35393	0.0930|0.0930	N|N	0.08118|0.08118	0|0	0.35285|0.35285	D|D	0.781681|0.781681	B;B;P;B;P|.	0.38565|.	0.033;0.099;0.484;0.037;0.637|.	B;B;B;B;B|.	0.42188|.	0.072;0.028;0.379;0.039;0.379|.	T|T	0.42172|0.42172	-0.9467|-0.9467	10|5	0.22706|.	T|.	0.39|.	-19.4622|-19.4622	12.5823|12.5823	0.56397|0.56397	0.8611:0.1389:0.0:0.0|0.8611:0.1389:0.0:0.0	.|.	425;433;425;60;450|.	B7ZLQ8;Q17RY0-2;E5RJM0;E5RFP2;Q17RY0|.	.;.;.;.;CPEB4_HUMAN|.	R|V	450;425;433;425;60;43|128	ENSP00000265085:H450R;ENSP00000429092:H425R;ENSP00000334533:H433R;ENSP00000429048:H425R|.	ENSP00000265085:H450R|.	H|I	+|+	2|1	0|0	CPEB4|CPEB4	173304642|173304642	1.000000|1.000000	0.71417|0.71417	0.952000|0.952000	0.39060|0.39060	0.975000|0.975000	0.68041|0.68041	3.862000|3.862000	0.56009|0.56009	0.960000|0.960000	0.38005|0.38005	0.533000|0.533000	0.62120|0.62120	CAT|ATA	.	.	.	none		0.483	CPEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252964.2	NM_030627		G	173372036	A	G	173372036	3	3	182	1	0	0	0	0	1	0	0	0	3805	217	8	3	1367	3	CPEB4	5	173372036	Missense_Mutation	SNP	A	TCGA-G7-A8LE-01A-11D-A35Z-10	30709893	173372036	7543224	24	10619											
OR2B2	81697	hgsc.bcm.edu	37	chr6	27879766	27879766	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgacggccaggagaagacatTctgtggaacccaaggccagg	12	5	14	10	1	1	3	0	1	1	2	1	5	1	4	3	5	1	0	3	5	3	1			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr6:27879766T>C	ENST00000303324.2	-	1	408	c.332A>G	c.(331-333)gAa>gGa	p.E111G		NM_033057.2	NP_149046.2	Q9GZK3	OR2B2_HUMAN	olfactory receptor, family 2, subfamily B, member 2	111						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(4)|large_intestine(5)|lung(10)|prostate(1)|urinary_tract(1)	22						GAGAAGACATTCTGTGGAACC	0.468																																					p.E111G		Atlas-SNP	.											.	OR2B2	54	.	0			c.A332G						PASS	.						111	100	104					6																	27879766		2203	4300	6503	SO:0001583	missense	81697	exon1			AGACATTCTGTGG	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.332A>G	chr6.hg19:g.27879766T>C	ENSP00000304419:p.Glu111Gly	107.0	0.0	.		134.0	54.0	.	NM_033057	B2RNH2|Q9GZL2|Q9Y299	Missense_Mutation	SNP	ENST00000303324.2	hg19	CCDS4641.1	.	.	.	.	.	.	.	.	.	.	T	14.88	2.666670	0.47677	.	.	ENSG00000168131	ENST00000303324	T	0.02197	4.4	4.52	4.52	0.55395	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39615	U	0.001307	T	0.10508	0.0257	H	0.94582	3.555	0.26114	N	0.980642	D	0.89917	1.0	D	0.85130	0.997	T	0.12400	-1.0549	10	0.87932	D	0	.	12.4261	0.55548	0.0:0.0:0.0:1.0	.	111	Q9GZK3	OR2B2_HUMAN	G	111	ENSP00000304419:E111G	ENSP00000304419:E111G	E	-	2	0	OR2B2	27987745	0.997000	0.39634	0.998000	0.56505	0.225000	0.24961	4.535000	0.60629	1.965000	0.57142	0.460000	0.39030	GAA	.	.	.	none		0.468	OR2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040163.1			C	27879766	T	C	27879766	3	2	182	1	0	0	0	0	1	0	0	0	10996	1783	62	3	745	3	OR2B2	6	27879766	Missense_Mutation	SNP	T	TCGA-G7-A8LE-01A-11D-A35Z-10		27879766	143235301	25	10620											
DST	667	hgsc.bcm.edu	37	chr6	56489406	56489406	+	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	agagtgaccagggcagtataTcgagtccttaggtccatgaa	12	9	12	8	1	0	3	0	2	0	1	3	4	2	3	3	2	0	2	3	2	4	3			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr6:56489406T>G	ENST00000361203.3	-	32	4225	c.4218A>C	c.(4216-4218)cgA>cgC	p.R1406R	DST_ENST00000370765.6_Silent_p.R1080R|DST_ENST00000370769.4_Silent_p.R1406R|DST_ENST00000370754.5_Silent_p.R1584R|DST_ENST00000312431.6_Silent_p.R1406R|DST_ENST00000446842.2_Silent_p.R1080R|DST_ENST00000421834.2_Silent_p.R1406R|DST_ENST00000518935.1_Silent_p.R1080R|DST_ENST00000244364.6_Silent_p.R1080R|DST_ENST00000370788.2_Silent_p.R1406R			Q03001	DYST_HUMAN	dystonin	1406					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)			GGGCAGTATATCGAGTCCTTA	0.363																																					p.R1080R		Atlas-SNP	.											.	DST	1427	.	0			c.A3240C						PASS	.						74	70	71					6																	56489406		2203	4300	6503	SO:0001819	synonymous_variant	667	exon22			AGTATATCGAGTC	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.4218A>C	chr6.hg19:g.56489406T>G		30.0	0.0	.		44.0	16.0	.	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	hg19		.	.	.	.	.	.	.	.	.	.	T	9.003	0.980520	0.18812	.	.	ENSG00000151914	ENST00000522360	.	.	.	5.1	-4.23	0.03789	.	.	.	.	.	T	0.06005	0.0156	.	.	.	.	.	.	.	.	.	.	.	.	T	0.33394	-0.9870	3	.	.	.	.	1.4079	0.02284	0.1521:0.2852:0.1726:0.3901	.	.	.	.	A	78	.	.	D	-	2	0	DST	56597365	0.033000	0.19621	0.550000	0.28217	0.932000	0.56968	-0.736000	0.04882	-0.663000	0.05331	-0.147000	0.13772	GAT	.	.	.	none		0.363	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		G	56489406	T	G	56489406	2	3	182	1	0	0	0	0	0	0	0	1	4785	1422	50	5		5	DST	6	56489406	Silent	SNP	T	TCGA-G7-A8LE-01A-11D-A35Z-10	28609640	56489406	114625661	26	10621											
FILIP1	27145	hgsc.bcm.edu	37	chr6	76024129	76024129	+	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	aattctttaactcgactcttGaccacctccaattcatttag	11	15	3	12	1	3	1	1	1	2	0	5	2	4	1	3	0	1	0	3	0	4	7			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr6:76024129G>T	ENST00000237172.7	-	5	1749	c.1419C>A	c.(1417-1419)gtC>gtA	p.V473V	FILIP1_ENST00000393004.2_Silent_p.V473V|FILIP1_ENST00000498523.1_5'UTR|FILIP1_ENST00000370020.1_Silent_p.V374V	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	473										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						CTCGACTCTTGACCACCTCCA	0.368																																					p.V473V		Atlas-SNP	.											.	FILIP1	173	.	0			c.C1419A						PASS	.						121	124	123					6																	76024129		2203	4300	6503	SO:0001819	synonymous_variant	27145	exon5			ACTCTTGACCACC	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.1419C>A	chr6.hg19:g.76024129G>T		43.0	0.0	.		73.0	4.0	.	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Silent	SNP	ENST00000237172.7	hg19	CCDS4984.1																																																																																			.	.	.	none		0.368	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		T	76024129	G	T	76024129	2	4	182	1	0	0	0	0	0	0	0	1	5901	1277	45	4		4	FILIP1	6	76024129	Silent	SNP	G	TCGA-G7-A8LE-01A-11D-A35Z-10	19534723	76024129	95090938	27	10622											
FAM26F	441168	hgsc.bcm.edu	37	chr6	116784681	116784681	+	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	agaatataacactccaagcaTgaaagagtggcagcaaattt	18	8	8	7	0	0	3	0	1	0	2	1	3	1	3	1	1	3	3	1	1	6	3			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr6:116784681T>A	ENST00000368605.1	+	3	856	c.761T>A	c.(760-762)aTg>aAg	p.M254K	RP1-93H18.6_ENST00000476099.1_RNA|FAM26F_ENST00000368606.3_Missense_Mutation_p.M82K	NM_001010919.1	NP_001010919.1	Q5R3K3	FA26F_HUMAN	family with sequence similarity 26, member F	254					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)		ACTCCAAGCATGAAAGAGTGG	0.388																																					p.I254N		Atlas-SNP	.											.	FAM26F	12	.	0			c.T761A						PASS	.						131	136	134					6																	116784681		2203	4300	6503	SO:0001583	missense	441168	exon3			CAAGCATGAAAGA	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.761T>A	chr6.hg19:g.116784681T>A	ENSP00000357594:p.Met254Lys	150.0	0.0	.		202.0	78.0	.	NM_001010919	B9EJB0|Q5R3K4	Missense_Mutation	SNP	ENST00000368605.1	hg19	CCDS34519.1	.	.	.	.	.	.	.	.	.	.	T	6.714	0.500482	0.12822	.	.	ENSG00000188820	ENST00000368606;ENST00000368605;ENST00000368604	T;T;T	0.28255	1.63;2.67;1.62	5.11	-6.95	0.01628	.	1.784060	0.02516	N	0.092072	T	0.05044	0.0135	L	0.44542	1.39	0.09310	N	1	B	0.11235	0.004	B	0.15870	0.014	T	0.14559	-1.0468	10	0.05959	T	0.93	2.8695	2.4451	0.04504	0.2029:0.3659:0.2782:0.153	.	254	Q5R3K3	FA26F_HUMAN	K	82;254;97	ENSP00000357595:M82K;ENSP00000357594:M254K;ENSP00000357593:M97K	ENSP00000357593:M97K	M	+	2	0	FAM26F	116891374	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.008000	0.12788	-0.776000	0.04578	-1.117000	0.02048	ATG	.	.	.	none		0.388	FAM26F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041946.1	NM_001010919		A	116784681	T	A	116784681	3	1	182	1	0	0	0	0	1	0	0	0	5558	1464	51	5	767	5	FAM26F	6	116784681	Missense_Mutation	SNP	T	TCGA-G7-A8LE-01A-11D-A35Z-10	40760552	116784681	54330386	28	10623											
SLC2A12	154091	hgsc.bcm.edu	37	chr6	134349788	134349788	+	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	ttgacaggtttcctggtccaTaaatcacagactcatccaag	12	11	7	11	0	2	2	2	1	0	1	5	2	5	2	3	2	0	1	3	2	3	3			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr6:134349788T>A	ENST00000275230.5	-	2	1330	c.1175A>T	c.(1174-1176)tAt>tTt	p.Y392F		NM_145176.2	NP_660159.1	Q8TD20	GTR12_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 12	392					glucose transport (GO:0015758)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			NS(1)|breast(1)|large_intestine(6)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	17	Breast(56;0.214)|Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0101)|GBM - Glioblastoma multiforme(68;0.0123)		TCCTGGTCCATAAATCACAGA	0.448																																					p.Y392F	Melanoma(122;1663 1672 14489 35294 41228)	Atlas-SNP	.											.	SLC2A12	43	.	0			c.A1175T						PASS	.						156	146	149					6																	134349788		2203	4300	6503	SO:0001583	missense	154091	exon2			GGTCCATAAATCA	AL035699	CCDS5169.1	6q23.2	2013-05-22			ENSG00000146411	ENSG00000146411		"Solute carriers"	18067	protein-coding gene	gene with protein product		610372				11780753, 11832379	Standard	XM_006715349		Approved	GLUT12, GLUT8	uc003qem.1	Q8TD20	OTTHUMG00000015611	ENST00000275230.5:c.1175A>T	chr6.hg19:g.134349788T>A	ENSP00000275230:p.Tyr392Phe	89.0	0.0	.		137.0	49.0	.	NM_145176	B3KV17|Q7Z6U3|Q96MR8	Missense_Mutation	SNP	ENST00000275230.5	hg19	CCDS5169.1	.	.	.	.	.	.	.	.	.	.	T	0.512	-0.866146	0.02590	.	.	ENSG00000146411	ENST00000275230	T	0.78364	-1.17	5.18	1.14	0.20703	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	7739.210000	0.00166	N	0.000000	T	0.45637	0.1352	L	0.34521	1.04	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.29274	-1.0017	10	0.11485	T	0.65	-1.6437	10.178	0.42950	0.3829:0.0:0.0:0.6171	.	392	Q8TD20	GTR12_HUMAN	F	392	ENSP00000275230:Y392F	ENSP00000275230:Y392F	Y	-	2	0	SLC2A12	134391481	0.096000	0.21769	0.009000	0.14445	0.007000	0.05969	2.836000	0.48183	-0.037000	0.13646	0.383000	0.25322	TAT	.	.	.	none		0.448	SLC2A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042302.1			A	134349788	T	A	134349788	3	1	182	1	0	0	0	0	1	0	0	0	14554	1406	49	5	694	5	SLC2A12	6	134349788	Missense_Mutation	SNP	T	TCGA-G7-A8LE-01A-11D-A35Z-10	17565107	134349788	36765279	29	10624											
MUC17	140453	hgsc.bcm.edu	37	chr7	100683876	100683876	+	Missense_Mutation	SNP	T	T	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	cagcaccacgccagtggccaTtcctgaggctagcacccttt	8	8	9	16	1	0	1	0	1	0	0	1	1	1	1	5	2	2	3	5	2	1	3	rs145514577		TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr7:100683876T>G	ENST00000306151.4	+	3	9243	c.9179T>G	c.(9178-9180)aTt>aGt	p.I3060S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3060	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)					CCAGTGGCCATTCCTGAGGCT	0.493													G|||	1	0.000199681	0	0	5008	,	,		25521	0		0.001	False		,,,				2504	0				p.I3060S		Atlas-SNP	.											MUC17,NS,carcinoma,0,1	MUC17	804	.	0			c.T9179G						PASS	.						275	283	280					7																	100683876		2203	4300	6503	SO:0001583	missense	140453	exon3			TGGCCATTCCTGA	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.9179T>G	chr7.hg19:g.100683876T>G	ENSP00000302716:p.Ile3060Ser	37.0	1.0	.		53.0	6.0	.	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	N	0.327	-0.958208	0.02267	.	.	ENSG00000169876	ENST00000306151	T	0.02197	4.4	0.814	-0.258	0.12975	.	.	.	.	.	T	0.00998	0.0033	N	0.03608	-0.345	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.48681	-0.9014	9	0.17369	T	0.5	.	3.7091	0.08413	0.0:0.5408:0.2591:0.2001	.	3060	Q685J3	MUC17_HUMAN	S	3060	ENSP00000302716:I3060S	ENSP00000302716:I3060S	I	+	2	0	MUC17	100470596	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-4.610000	0.00209	-0.661000	0.05345	-2.058000	0.00401	ATT	.	.	.	weak		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		G	100683876	T	G	100683876	3	3	182	1	0	0	0	0	1	0	0	0	9981	1493	52	5	9189	5	MUC17	7	100683876	Missense_Mutation	SNP	T	TCGA-G7-A8LE-01A-11D-A35Z-10		100683876	58454787	30	10625											
MET	4233	hgsc.bcm.edu	37	chr7	116423413	116423413	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttggtcttgccagagacatgTatgataaagaatactatagt	14	13	9	5	0	1	3	0	1	1	2	1	4	1	3	1	1	2	1	1	1	7	7	rs121913247		TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr7:116423413T>C	ENST00000318493.6	+	19	3929	c.3742T>C	c.(3742-3744)Tat>Cat	p.Y1248H	MET_ENST00000539704.1_Missense_Mutation_p.Y100H|MET_ENST00000397752.3_Missense_Mutation_p.Y1230H			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.Y1248H(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)			CAGAGACATGTATGATAAAGA	0.388			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.Y1248H		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,rectum,carcinoma,-2,1	MET	412	.	1	Substitution - Missense(1)	kidney(1)	c.T3742C	GRCh37	CM992180	MET	M	rs121913247	PASS	.						105	99	101					7																	116423413		1843	4095	5938	SO:0001583	missense	4233	exon19	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	GACATGTATGATA	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.3742T>C	chr7.hg19:g.116423413T>C	ENSP00000317272:p.Tyr1248His	110.0	1.0	.		242.0	129.0	.	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	T	18.43	3.622544	0.66787	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000539704	D;D;D	0.83075	-1.68;-1.68;-1.68	5.46	5.46	0.80206	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.90075	0.6900	M	0.68593	2.085	0.54753	D	0.999981	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.91155	0.4956	10	0.87932	D	0	.	15.824	0.78683	0.0:0.0:0.0:1.0	.	1248;1230	P08581-2;P08581	.;MET_HUMAN	H	1230;1248;100	ENSP00000380860:Y1230H;ENSP00000317272:Y1248H;ENSP00000445020:Y100H	ENSP00000317272:Y1248H	Y	+	1	0	MET	116210649	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.145000	0.71769	2.197000	0.70478	0.460000	0.39030	TAT	.	.	.	weak		0.388	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			C	116423413	T	C	116423413	3	2	182	1	0	0	0	0	1	0	0	0	9492	1638	57	3	3812	3	MET	7	116423413	Missense_Mutation	SNP	T	TCGA-G7-A8LE-01A-11D-A35Z-10	15739537	116423413	42715250	31	10626											
CTTNBP2	83992	hgsc.bcm.edu	37	chr7	117358121	117358122	+	Frame_Shift_Del	DEL	GG	GG	-																															taatagttgctgaaagtacaGggttgtttccagaactatca																										TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr7:117358121_117358122delGG	ENST00000160373.3	-	22	4787_4788	c.4696_4697delCC	c.(4696-4698)cctfs	p.P1566fs		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1566					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)		TGAAAGTACAGGGTTGTTTCCA	0.411																																					p.1566_1566del		Atlas-Indel,Pindel	.											.	CTTNBP2	200	.	0			c.4697_4698del						PASS	.																																			SO:0001589	frameshift_variant	83992	exon22			.		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.4696_4697delCC	chr7.hg19:g.117358121_117358122delGG	ENSP00000160373:p.Pro1566fs	155.0	0.0	0		252.0	142.0	0.563492	NM_033427	O43389|Q7LG11|Q9C0A5	Frame_Shift_Del	DEL	ENST00000160373.3	hg19	CCDS5774.1																																																																																			.	.	.	none		0.411	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		-	117358122	GG	-	117358121	7	5	182	1	0	1	0	1	0	0	0	0	4047	1000	35	0	302	0	CTTNBP2	7	117358121	Frame_Shift_Del	DEL	GG	TCGA-G7-A8LE-01A-11D-A35Z-10	934708	117358121	41780542	32	10627											
C7orf45	136263	hgsc.bcm.edu	37	chr7	129847790	129847790	+	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	tattttgggaggtagatcctCccccaatacctgtaaattgt	10	14	8	9	0	0	1	0	0	0	1	2	2	2	2	4	2	1	2	4	2	6	7	rs371191805		TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr7:129847790C>T	ENST00000297819.3	+	1	91	c.40C>T	c.(40-42)Ccc>Tcc	p.P14S	TMEM209_ENST00000462753.1_5'Flank|TMEM209_ENST00000473456.1_5'Flank|RP11-775D22.3_ENST00000483283.1_RNA|TMEM209_ENST00000336804.8_5'Flank|TMEM209_ENST00000397622.2_5'Flank	NM_145268.3	NP_660311.1	Q8WWF3	SSMM1_HUMAN	serine-rich single-pass membrane protein 1	14						integral component of membrane (GO:0016021)											GGTAGATCCTCCCCCAATACC	0.418																																					p.P14S		Atlas-SNP	.											.	.	.	.	0			c.C40T						PASS	.						207	196	200					7																	129847790		2203	4300	6503	SO:0001583	missense	0	exon1			GATCCTCCCCCAA	AK097635	CCDS5816.1	7q32.2	2013-03-08	2013-03-08	2013-03-08	ENSG00000165120	ENSG00000165120			29580	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 45"	C7orf45		12477932	Standard	NM_145268		Approved	FLJ40316	uc003vpp.3	Q8WWF3	OTTHUMG00000157844	ENST00000297819.3:c.40C>T	chr7.hg19:g.129847790C>T	ENSP00000297819:p.Pro14Ser	103.0	0.0	.		228.0	127.0	.	NM_145268		Missense_Mutation	SNP	ENST00000297819.3	hg19	CCDS5816.1	.	.	.	.	.	.	.	.	.	.	C	16.70	3.194977	0.58017	.	.	ENSG00000165120	ENST00000297819	T	0.61859	0.07	5.54	3.74	0.42951	.	0.325431	0.27206	N	0.020435	T	0.62600	0.2441	M	0.67953	2.075	0.36756	D	0.883021	D	0.55605	0.972	P	0.51806	0.68	T	0.70004	-0.4991	10	0.87932	D	0	-5.1446	8.6789	0.34196	0.0:0.8244:0.0:0.1756	.	14	Q8WWF3	CG045_HUMAN	S	14	ENSP00000297819:P14S	ENSP00000297819:P14S	P	+	1	0	C7orf45	129635026	0.971000	0.33674	0.986000	0.45419	0.468000	0.32798	2.491000	0.45303	0.831000	0.34780	-0.136000	0.14681	CCC	.	.	.	weak		0.418	SSMEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349768.1	NM_145268		T	129847790	C	T	129847790	3	4	182	1	0	0	0	0	1	0	0	0	2397	855	30	2	42	2	C7orf45	7	129847790	Missense_Mutation	SNP	C	TCGA-G7-A8LE-01A-11D-A35Z-10	12489669	129847790	29290873	33	10628											
C7orf34	3792	hgsc.bcm.edu	37	chr7	142636835	142636835	+	IGR	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	aaagatgggagccagacagaGaaaacgccctctgcaggtag	15	4	13	9	1	1	3	0	0	1	3	1	5	1	4	2	2	3	2	2	2	4	1			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr7:142636835G>C	ENST00000355265.2	-	0	2812				C7orf34_ENST00000409607.3_Missense_Mutation_p.E64D	NM_000420.2	NP_000411.1	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase						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)					GCCAGACAGAGAAAACGCCCT	0.547																																					p.E64D		Atlas-SNP	.											.	C7orf34	34	.	0			c.G192C						PASS	.						48	53	51					7																	142636835		2203	4300	6503	SO:0001628	intergenic_variant	135927	exon1			GACAGAGAAAACG	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		chr7.hg19:g.142636835G>C		94.0	0.0	.		170.0	84.0	.	NM_178829	B2RBV4|Q96RS8|Q99885	Missense_Mutation	SNP	ENST00000355265.2	hg19	CCDS34766.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	12.95|12.95	2.090470|2.090470	0.36855|0.36855	.|.	.|.	ENSG00000165131|ENSG00000165131	ENST00000409607|ENST00000458732	.|.	.|.	.|.	3.5|3.5	-3.57|-3.57	0.04612|0.04612	.|.	1.113020|1.113020	0.06947|0.06947	N|N	0.813873|0.813873	T|T	0.30386|0.30386	0.0763|0.0763	L|L	0.34521|0.34521	1.04|1.04	0.09310|0.09310	N|N	1|1	B|.	0.20550|.	0.046|.	B|.	0.18871|.	0.023|.	T|T	0.35126|0.35126	-0.9801|-0.9801	9|7	0.34782|0.46703	T|T	0.22|0.11	-5.1258|-5.1258	4.2209|4.2209	0.10558|0.10558	0.3996:0.332:0.2685:0.0|0.3996:0.332:0.2685:0.0	.|.	39|.	Q96L11|.	CG034_HUMAN|.	D|Q	64|70	.|.	ENSP00000386450:E64D|ENSP00000401055:E70Q	E|E	+|+	3|1	2|0	C7orf34|C7orf34	142346957|142346957	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	-1.159000|-1.159000	0.03150|0.03150	-0.937000|-0.937000	0.03719|0.03719	-0.387000|-0.387000	0.06579|0.06579	GAG|GAA	.	.	.	none		0.547	KEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347671.2	NM_000420		C	142636835	G	C	142636835	1	2	182	0	1	0	0	0	0	0	0	0	2391	933	33	4		4	C7orf34	7	142636835	IGR	SNP	G	TCGA-G7-A8LE-01A-11D-A35Z-10	12789045	142636835	16501828	34	10629											
TSPYL5	85453	hgsc.bcm.edu	37	chr8	98289181	98289181	+	Missense_Mutation	SNP	A	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	gaaatacgggttgcgatcgaAgtagaacttgattttgtagc	12	12	12	5	3	0	2	0	1	0	1	1	5	0	2	0	1	4	3	0	1	6	7			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr8:98289181A>C	ENST00000322128.3	-	1	995	c.892T>G	c.(892-894)Ttc>Gtc	p.F298V		NM_033512.2	NP_277047.2	Q86VY4	TSYL5_HUMAN	TSPY-like 5	298					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)					TTGCGATCGAAGTAGAACTTG	0.473																																					p.F298V		Atlas-SNP	.											.	TSPYL5	48	.	0			c.T892G						PASS	.						83	84	84					8																	98289181		2203	4300	6503	SO:0001583	missense	85453	exon1			GATCGAAGTAGAA	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.892T>G	chr8.hg19:g.98289181A>C	ENSP00000322802:p.Phe298Val	90.0	0.0	.		153.0	51.0	.	NM_033512	B3KRF0|Q9C0B3	Missense_Mutation	SNP	ENST00000322128.3	hg19	CCDS34927.1	.	.	.	.	.	.	.	.	.	.	A	18.29	3.590837	0.66219	.	.	ENSG00000180543	ENST00000322128	T	0.78364	-1.17	4.4	4.4	0.53042	.	0.000000	0.38492	N	0.001675	D	0.90232	0.6946	H	0.95224	3.64	0.58432	D	0.999994	D	0.76494	0.999	D	0.77557	0.99	D	0.91872	0.5508	10	0.87932	D	0	-13.9906	10.3132	0.43721	1.0:0.0:0.0:0.0	.	298	Q86VY4	TSYL5_HUMAN	V	298	ENSP00000322802:F298V	ENSP00000322802:F298V	F	-	1	0	TSPYL5	98358357	1.000000	0.71417	0.993000	0.49108	0.775000	0.43874	5.386000	0.66238	2.211000	0.71520	0.460000	0.39030	TTC	.	.	.	none		0.473	TSPYL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380611.1	NM_033512		C	98289181	A	C	98289181	3	2	182	1	0	0	0	0	1	0	0	0	16674	72	3	5	365	5	TSPYL5	8	98289181	Missense_Mutation	SNP	A	TCGA-G7-A8LE-01A-11D-A35Z-10		98289181	48074841	35	10630											
TG	7038	hgsc.bcm.edu	37	chr8	134024148	134024148	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgttgccttctctcctagtgTctctggactcgtggcagtcc	3	14	10	14	2	2	0	0	0	2	0	7	1	4	1	3	2	1	2	3	2	1	3			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr8:134024148T>C	ENST00000220616.4	+	36	6305	c.6265T>C	c.(6265-6267)Tct>Cct	p.S2089P	TG_ENST00000377869.1_Missense_Mutation_p.S2032P|TG_ENST00000519543.1_Missense_Mutation_p.S222P|TG_ENST00000522523.1_3'UTR|TG_ENST00000542445.1_Missense_Mutation_p.S459P	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2089					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)		TCTCCTAGTGTCTCTGGACTC	0.527																																					p.S2089P		Atlas-SNP	.											.	TG	416	.	0			c.T6265C						PASS	.						407	366	380					8																	134024148		2203	4300	6503	SO:0001583	missense	7038	exon36			CTAGTGTCTCTGG	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.6265T>C	chr8.hg19:g.134024148T>C	ENSP00000220616:p.Ser2089Pro	46.0	0.0	.		66.0	32.0	.	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	hg19	CCDS34944.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.504|8.504	0.864979|0.864979	0.17250|0.17250	.|.	.|.	ENSG00000042832|ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445;ENST00000519543|ENST00000519178	T;T;T;T|T	0.68903|0.68331	-0.15;-0.15;-0.36;-0.34|-0.32	5.58|5.58	-7.76|-7.76	0.01232|0.01232	.|.	0.909678|.	0.09285|.	N|.	0.823146|.	T|T	0.41650|0.41650	0.1168|0.1168	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	1|1	B;B;P|.	0.51240|.	0.08;0.024;0.943|.	B;B;P|.	0.44477|.	0.017;0.018;0.451|.	T|T	0.32268|0.32268	-0.9913|-0.9913	10|7	0.62326|0.23891	D|T	0.03|0.37	.|.	2.7412|2.7412	0.05254|0.05254	0.1687:0.1507:0.4783:0.2023|0.1687:0.1507:0.4783:0.2023	.|.	222;459;2089|.	E7EVM0;F5GWW5;P01266|.	.;.;THYG_HUMAN|.	P|A	2032;895;2089;459;222|544	ENSP00000367100:S2032P;ENSP00000220616:S2089P;ENSP00000441693:S459P;ENSP00000430430:S222P|ENSP00000430523:V544A	ENSP00000220616:S2089P|ENSP00000430523:V544A	S|V	+|+	1|2	0|0	TG|TG	134093330|134093330	0.000000|0.000000	0.05858|0.05858	0.003000|0.003000	0.11579|0.11579	0.055000|0.055000	0.15305|0.15305	-0.975000|-0.975000	0.03790|0.03790	-1.298000|-1.298000	0.02348|0.02348	0.460000|0.460000	0.39030|0.39030	TCT|GTC	.	.	.	none		0.527	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		C	134024148	T	C	134024148	3	2	182	1	0	0	0	0	1	0	0	0	15825	1667	58	3	6407	3	TG	8	134024148	Missense_Mutation	SNP	T	TCGA-G7-A8LE-01A-11D-A35Z-10	35734967	134024148	12339874	36	10631											
CIZ1	25792	hgsc.bcm.edu	37	chr9	130939947	130939947	+	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	gtggaggagacggagtcactGgggcgggggacaggtgtcag	8	5	22	6	2	2	1	2	0	0	1	2	5	2	4	0	8	0	0	0	8	0	0			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr9:130939947G>T	ENST00000393608.1	-	10	1918	c.1716C>A	c.(1714-1716)ccC>ccA	p.P572P	CIZ1_ENST00000277465.4_Silent_p.P544P|CIZ1_ENST00000541172.1_Silent_p.P471P|CIZ1_ENST00000372954.1_Silent_p.P492P|CIZ1_ENST00000538431.1_Silent_p.P572P|CIZ1_ENST00000476727.2_Intron|CIZ1_ENST00000372948.3_Silent_p.P516P|CIZ1_ENST00000325721.8_Silent_p.P543P|CIZ1_ENST00000372938.5_Silent_p.P572P|CIZ1_ENST00000357558.5_Silent_p.P544P	NM_012127.2	NP_036259.2	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1	572					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						CGGAGTCACTGGGGCGGGGGA	0.642																																					p.P602P		Atlas-SNP	.											.	CIZ1	75	.	0			c.C1806A						PASS	.						22	21	21					9																	130939947		2199	4297	6496	SO:0001819	synonymous_variant	25792	exon10			GTCACTGGGGCGG	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.1716C>A	chr9.hg19:g.130939947G>T		52.0	0.0	.		57.0	26.0	.	NM_001257975	A8K9J8|B4E131|B7ZAS8|Q5SYW3|Q5SYW5|Q8WU72|Q9H868|Q9NYM8|Q9UHK4|Q9Y3F9|Q9Y3G0	Silent	SNP	ENST00000393608.1	hg19	CCDS6894.1																																																																																			.	.	.	none		0.642	CIZ1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054399.1	NM_012127		T	130939947	G	T	130939947	2	4	182	1	0	0	0	0	0	0	0	1	3443	1335	47	4		4	CIZ1	9	130939947	Silent	SNP	G	TCGA-G7-A8LE-01A-11D-A35Z-10		130939947	10273484	37	10632											
PRKCQ	5588	hgsc.bcm.edu	37	chr10	6557092	6557092	+	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	aagccaatccgaagaaatggCgacatggttgcgccctggaa	13	6	12	10	3	0	1	0	0	0	1	1	4	1	2	3	3	2	1	3	3	5	1	rs201768145		TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr10:6557092C>T	ENST00000263125.5	-	2	105	c.6G>A	c.(4-6)tcG>tcA	p.S2S	PRKCQ_ENST00000539722.1_5'UTR|PRKCQ_ENST00000397176.2_Silent_p.S2S	NM_001282644.1|NM_006257.3	NP_001269573.1|NP_006248.1	Q04759	KPCT_HUMAN	protein kinase C, theta	2					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of T cell apoptotic process (GO:0070233)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of T-helper 2 cell activation (GO:2000570)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of transcription, DNA-templated (GO:0006355)|rhodopsin mediated signaling pathway (GO:0016056)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(2)	45					Tamoxifen(DB00675)	GAAGAAATGGCGACATGGTTG	0.478													C|||	1	0.000199681	0	0	5008	,	,		19940	0		0	False		,,,				2504	0.001				p.S2S	Ovarian(50;572 1126 10530 25349 30594)	Atlas-SNP	.											.	PRKCQ	113	.	0			c.G6A						PASS	.						64	66	65					10																	6557092		2203	4300	6503	SO:0001819	synonymous_variant	5588	exon2			AAATGGCGACATG	L07032	CCDS7079.1, CCDS55701.1, CCDS60482.1	10p15	2009-07-10			ENSG00000065675	ENSG00000065675	2.7.11.1		9410	protein-coding gene	gene with protein product		600448				8444877	Standard	NM_001282645		Approved		uc001ijj.2	Q04759	OTTHUMG00000017623	ENST00000263125.5:c.6G>A	chr10.hg19:g.6557092C>T		52.0	0.0	.		80.0	22.0	.	NM_006257	B4DF52|Q14DH6|Q3MJF1|Q64FY5|Q9H508|Q9H549	Silent	SNP	ENST00000263125.5	hg19	CCDS7079.1																																																																																			.	C|0.999;T|0.001	0.001	weak		0.478	PRKCQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046665.1	NM_006257		T	6557092	C	T	6557092	2	4	182	1	0	0	0	0	0	0	0	1	12525	755	27	1		1	PRKCQ	10	6557092	Silent	SNP	C	TCGA-G7-A8LE-01A-11D-A35Z-10		6557092	128977655	38	10633											
CBARA1	10367	hgsc.bcm.edu	37	chr10	74127978	74127978	+	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	gtttgggtaaagcgaagtccCaggcagtttcctgtgcacat	9	11	12	9	1	0	0	0	0	0	0	2	1	2	0	2	2	2	5	2	2	3	3			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr10:74127978C>G	ENST00000361114.5	-	12	1502	c.1406G>C	c.(1405-1407)tGg>tCg	p.W469S	MICU1_ENST00000398763.4_Missense_Mutation_p.W271S|MICU1_ENST00000401998.3_Missense_Mutation_p.W469S|MICU1_ENST00000418483.2_Missense_Mutation_p.W271S|MICU1_ENST00000398761.4_Missense_Mutation_p.W471S	NM_001195518.1|NM_006077.3	NP_001182447.1|NP_006068.2	Q9BPX6	MICU1_HUMAN	mitochondrial calcium uptake 1	469					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)										AGCGAAGTCCCAGGCAGTTTC	0.572																																					p.W469S		Atlas-SNP	.											.	.	.	.	0			c.G1406C						PASS	.						79	81	80					10																	74127978		1926	4143	6069	SO:0001583	missense	10367	exon12			AAGTCCCAGGCAG	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.1406G>C	chr10.hg19:g.74127978C>G	ENSP00000354415:p.Trp469Ser	56.0	0.0	.		86.0	39.0	.	NM_001195518	A8MV96|B3KN20|B4DJH9|B4DPI1|B5MBY3|D3YTJ3|O75785|Q9H9N6|Q9UFX0	Missense_Mutation	SNP	ENST00000361114.5	hg19	CCDS55715.1	.	.	.	.	.	.	.	.	.	.	C	17.87	3.496041	0.64186	.	.	ENSG00000107745	ENST00000361114;ENST00000398761;ENST00000401998;ENST00000418483;ENST00000398763	T;T;T;T;T	0.80738	-1.38;-1.41;-1.38;0.93;0.94	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.75451	0.3851	L	0.36672	1.1	0.80722	D	1	B;B;B	0.24882	0.074;0.074;0.113	B;B;B	0.17433	0.012;0.012;0.018	T	0.68800	-0.5313	10	0.38643	T	0.18	.	20.3312	0.98718	0.0:1.0:0.0:0.0	.	271;271;469	Q9BPX6-4;Q9BPX6-5;Q9BPX6	.;.;MICU1_HUMAN	S	469;471;469;271;271	ENSP00000354415:W469S;ENSP00000381745:W471S;ENSP00000384068:W469S;ENSP00000402470:W271S;ENSP00000381747:W271S	ENSP00000354415:W469S	W	-	2	0	MICU1	73797984	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	7.792000	0.85828	2.797000	0.96272	0.655000	0.94253	TGG	.	.	.	none		0.572	MICU1-002	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048586.1	NM_006077		G	74127978	C	G	74127978	3	3	182	1	0	0	0	0	1	0	0	0	2698	595	21	4	28	4	CBARA1	10	74127978	Missense_Mutation	SNP	C	TCGA-G7-A8LE-01A-11D-A35Z-10	67570886	74127978	61406769	39	10634											
TSPAN14	81619	hgsc.bcm.edu	37	chr10	82264502	82264502	+	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	agttggctggagttgtcttcCttggagtcgggctgtgggca	4	13	17	7	1	1	0	0	0	1	0	3	2	2	2	1	5	0	5	1	5	0	4			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr10:82264502C>A	ENST00000429989.3	+	3	323	c.100C>A	c.(100-102)Ctt>Att	p.L34I	TSPAN14_ENST00000341863.6_Missense_Mutation_p.L34I|TSPAN14_ENST00000481124.1_Intron|TSPAN14_ENST00000372156.1_Missense_Mutation_p.L34I|TSPAN14_ENST00000372164.3_Intron|TSPAN14_ENST00000372158.1_Missense_Mutation_p.L34I	NM_030927.2	NP_112189.2	Q8NG11	TSN14_HUMAN	tetraspanin 14	34					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)			AGTTGTCTTCCTTGGAGTCGG	0.512																																					p.L34I		Atlas-SNP	.											.	TSPAN14	29	.	0			c.C100A						PASS	.						210	176	188					10																	82264502		2203	4300	6503	SO:0001583	missense	81619	exon3			GTCTTCCTTGGAG	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.100C>A	chr10.hg19:g.82264502C>A	ENSP00000396270:p.Leu34Ile	108.0	0.0	.		128.0	51.0	.	NM_030927	A6NHE1|B4DHY6|D3DWD7|D3DWD8|Q567U7|Q9BU34|Q9H0U1	Missense_Mutation	SNP	ENST00000429989.3	hg19	CCDS7369.1	.	.	.	.	.	.	.	.	.	.	C	16.42	3.118747	0.56505	.	.	ENSG00000108219	ENST00000429989;ENST00000372160;ENST00000372158;ENST00000341863;ENST00000372156	T;T;T;T	0.80214	-1.35;-1.35;-1.35;-1.35	5.54	5.54	0.83059	.	0.056707	0.64402	D	0.000002	T	0.67590	0.2909	N	0.12569	0.235	0.54753	D	0.999986	B	0.14438	0.01	B	0.31245	0.126	T	0.63233	-0.6683	10	0.36615	T	0.2	-19.5088	10.4111	0.44294	0.0:0.9117:0.0:0.0883	.	34	Q8NG11	TSN14_HUMAN	I	34	ENSP00000396270:L34I;ENSP00000361231:L34I;ENSP00000344076:L34I;ENSP00000361229:L34I	ENSP00000344076:L34I	L	+	1	0	TSPAN14	82254482	1.000000	0.71417	0.997000	0.53966	0.964000	0.63967	2.970000	0.49240	2.623000	0.88846	0.561000	0.74099	CTT	.	.	.	none		0.512	TSPAN14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049081.2	NM_030927		A	82264502	C	A	82264502	3	1	182	1	0	0	0	0	1	0	0	0	16650	681	24	4	106	4	TSPAN14	10	82264502	Missense_Mutation	SNP	C	TCGA-G7-A8LE-01A-11D-A35Z-10	8136524	82264502	53270245	40	10635											
TCERG1L	256536	hgsc.bcm.edu	37	chr10	132896657	132896657	+	Missense_Mutation	SNP	T	T	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	cttttccttgtattcttcttTtattcttgtcttgacaaact	6	23	3	9	0	4	1	0	1	4	0	5	1	5	1	1	0	1	1	1	0	3	11			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr10:132896657T>G	ENST00000368642.4	-	11	1601	c.1516A>C	c.(1516-1518)Aaa>Caa	p.K506Q	RP11-462G8.3_ENST00000436942.1_RNA	NM_174937.3	NP_777597.2	Q5VWI1	TCRGL_HUMAN	transcription elongation regulator 1-like	506										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)		TATTCTTCTTTTATTCTTGTC	0.328																																					p.K506Q		Atlas-SNP	.											.	TCERG1L	91	.	0			c.A1516C						PASS	.						61	52	55					10																	132896657		2132	4211	6343	SO:0001583	missense	256536	exon11			CTTCTTTTATTCT	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.1516A>C	chr10.hg19:g.132896657T>G	ENSP00000357631:p.Lys506Gln	26.0	0.0	.		23.0	7.0	.	NM_174937	Q5VWI2|Q86XM8	Missense_Mutation	SNP	ENST00000368642.4	hg19	CCDS7662.2	.	.	.	.	.	.	.	.	.	.	T	14.93	2.683146	0.47991	.	.	ENSG00000176769	ENST00000368642	T	0.24723	1.84	4.71	4.71	0.59529	FF domain (2);	0.155083	0.40144	N	0.001180	T	0.23611	0.0571	L	0.33137	0.985	0.39116	D	0.961576	P	0.48764	0.915	B	0.44315	0.446	T	0.05370	-1.0889	10	0.49607	T	0.09	-6.5535	13.0047	0.58696	0.0:0.0:0.0:1.0	.	506	Q5VWI1	TCRGL_HUMAN	Q	506	ENSP00000357631:K506Q	ENSP00000357631:K506Q	K	-	1	0	TCERG1L	132786647	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	3.703000	0.54808	1.755000	0.51935	0.383000	0.25322	AAA	.	.	.	none		0.328	TCERG1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091619.2	NM_174937		G	132896657	T	G	132896657	3	3	182	1	0	0	0	0	1	0	0	0	15698	1850	64	5	252	5	TCERG1L	10	132896657	Missense_Mutation	SNP	T	TCGA-G7-A8LE-01A-11D-A35Z-10	50632155	132896657	2638090	41	10636											
LRDD	55367	hgsc.bcm.edu	37	chr11	801091	801091	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggaggggcccagtacaacaGgtgcaggcgggagcggtcca	10	3	18	10	2	0	0	0	0	0	0	1	2	1	2	2	7	4	2	2	7	2	1			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr11:801091G>A	ENST00000347755.5	-	10	1801	c.1660C>T	c.(1660-1662)Ctg>Ttg	p.L554L	PIDD_ENST00000411829.2_Silent_p.L554L|PIDD_ENST00000534649.1_5'Flank	NM_145886.3|NM_145887.3	NP_665893.2|NP_665894.2																					CAGTACAACAGGTGCAGGCGG	0.662																																					p.L554L		Atlas-SNP	.											.	PIDD	76	.	0			c.C1660T						PASS	.						29	23	25					11																	801091		2184	4289	6473	SO:0001819	synonymous_variant	55367	exon10			ACAACAGGTGCAG																												ENST00000347755.5:c.1660C>T	chr11.hg19:g.801091G>A		99.0	0.0	.		127.0	51.0	.	NM_145887		Silent	SNP	ENST00000347755.5	hg19	CCDS7716.1																																																																																			.	.	.	none		0.662	PIDD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257103.1			A	801091	G	A	801091	2	1	182	1	0	0	0	0	0	0	0	1	8943	991	35	2		2	LRDD	11	801091	Silent	SNP	G	TCGA-G7-A8LE-01A-11D-A35Z-10		801091	134205425	42	10637											
CDKN1C	1028	hgsc.bcm.edu	37	chr11	2906711	2906711	+	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	gatgtgctgcggagggacgcGtcggacatggcccggggctg	5	6	20	10	5	0	0	0	0	0	0	1	4	0	3	1	6	2	2	1	6	0	0			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr11:2906711G>T	ENST00000414822.3	-	1	400	c.9C>A	c.(7-9)gaC>gaA	p.D3E	CDKN1C_ENST00000313407.6_Intron|CDKN1C_ENST00000430149.2_Missense_Mutation_p.D3E|CDKN1C_ENST00000380725.1_Intron|CDKN1C_ENST00000440480.2_Intron	NM_000076.2	NP_000067.1	P49918	CDN1C_HUMAN	cyclin-dependent kinase inhibitor 1C (p57, Kip2)	3					adrenal gland development (GO:0030325)|aging (GO:0007568)|camera-type eye development (GO:0043010)|cell cycle arrest (GO:0007050)|digestive system development (GO:0055123)|embryonic placenta morphogenesis (GO:0060669)|genetic imprinting (GO:0071514)|kidney development (GO:0001822)|multicellular organism growth (GO:0035264)|myeloid cell differentiation (GO:0030099)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of kinase activity (GO:0033673)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron maturation (GO:0042551)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|skeletal system development (GO:0001501)|uterus development (GO:0060065)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)			central_nervous_system(1)|lung(1)	2		all_epithelial(84;0.000187)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|Breast(177;0.00328)|all_neural(188;0.00681)|all_lung(207;0.157)|Lung NSC(207;0.216)		BRCA - Breast invasive adenocarcinoma(625;0.0025)|LUSC - Lung squamous cell carcinoma(625;0.19)		GGAGGGACGCGTCGGACATGG	0.692																																					p.D3E	GBM(111;59 1151 2497 5746 16112 18241 29216)	Atlas-SNP	.											.	CDKN1C	4	.	0			c.C9A						PASS	.						10	9	9					11																	2906711		2081	4104	6185	SO:0001583	missense	1028	exon1			GGACGCGTCGGAC	D64137	CCDS7738.1, CCDS44519.1	11p15.5	2014-09-17	2004-02-13		ENSG00000129757	ENSG00000129757			1786	protein-coding gene	gene with protein product		600856	"Beckwith-Wiedemann syndrome"	BWCR, BWS		7729684	Standard	NM_000076		Approved	P57, KIP2	uc001lws.4	P49918	OTTHUMG00000010040	ENST00000414822.3:c.9C>A	chr11.hg19:g.2906711G>T	ENSP00000413720:p.Asp3Glu	145.0	0.0	.		158.0	62.0	.	NM_000076		Missense_Mutation	SNP	ENST00000414822.3	hg19	CCDS7738.1	.	.	.	.	.	.	.	.	.	.	G	16.57	3.160155	0.57368	.	.	ENSG00000129757	ENST00000414822;ENST00000430149	D;D	0.90900	-2.75;-2.75	2.34	1.37	0.22104	.	.	.	.	.	T	0.80839	0.4700	N	0.14661	0.345	0.80722	D	1	D	0.59357	0.985	B	0.42625	0.393	T	0.77595	-0.2529	9	0.72032	D	0.01	.	8.4056	0.32612	0.1313:0.0:0.8687:0.0	.	3	P49918	CDN1C_HUMAN	E	3	ENSP00000413720:D3E;ENSP00000411552:D3E	ENSP00000413720:D3E	D	-	3	2	CDKN1C	2863287	1.000000	0.71417	0.820000	0.32676	0.754000	0.42855	3.513000	0.53414	0.317000	0.23160	0.305000	0.20034	GAC	.	.	.	none		0.692	CDKN1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027774.2	NM_000076		T	2906711	G	T	2906711	3	4	182	1	0	0	0	0	1	0	0	0	3162	1136	40	4	949	4	CDKN1C	11	2906711	Missense_Mutation	SNP	G	TCGA-G7-A8LE-01A-11D-A35Z-10	2105620	2906711	132099805	43	10638											
NLRP14	338323	hgsc.bcm.edu	37	chr11	7063888	7063888	+	Missense_Mutation	SNP	A	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	gtctctaccagcagaggtttAagtatgttttttatctcaat	10	17	7	7	0	2	1	1	0	2	1	4	1	2	1	1	1	2	4	1	1	5	7			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr11:7063888A>C	ENST00000299481.4	+	4	977	c.631A>C	c.(631-633)Aag>Cag	p.K211Q		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	211	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)		GCAGAGGTTTAAGTATGTTTT	0.468																																					p.K211Q		Atlas-SNP	.											.	NLRP14	187	.	0			c.A631C						PASS	.						86	89	88					11																	7063888		2201	4296	6497	SO:0001583	missense	338323	exon4			AGGTTTAAGTATG	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.631A>C	chr11.hg19:g.7063888A>C	ENSP00000299481:p.Lys211Gln	157.0	0.0	.		244.0	87.0	.	NM_176822	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	hg19	CCDS7776.1	.	.	.	.	.	.	.	.	.	.	A	6.311	0.425450	0.11987	.	.	ENSG00000158077	ENST00000299481	T	0.81078	-1.45	4.47	-6.77	0.01727	NACHT nucleoside triphosphatase (1);	3.128170	0.00879	N	0.002112	T	0.63616	0.2526	N	0.11023	0.085	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.54221	-0.8326	10	0.35671	T	0.21	.	11.4429	0.50107	0.1819:0.0:0.6906:0.1275	.	211	Q86W24	NAL14_HUMAN	Q	211	ENSP00000299481:K211Q	ENSP00000299481:K211Q	K	+	1	0	NLRP14	7020464	0.000000	0.05858	0.000000	0.03702	0.201000	0.24016	-0.397000	0.07269	-1.362000	0.02166	-0.417000	0.06048	AAG	.	.	.	none		0.468	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822		C	7063888	A	C	7063888	3	2	182	1	0	0	0	0	1	0	0	0	10483	363	13	5	641	5	NLRP14	11	7063888	Missense_Mutation	SNP	A	TCGA-G7-A8LE-01A-11D-A35Z-10	4157177	7063888	127942628	44	10639											
SYT13	57586	hgsc.bcm.edu	37	chr11	45277403	45277403	+	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	gtctgggaacttgaggagggCacggggctgaacaggttccg	8	7	18	8	2	1	2	0	2	1	0	2	4	2	4	1	6	2	3	1	6	2	2			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr11:45277403C>T	ENST00000020926.3	-	2	334	c.223G>A	c.(223-225)Gcc>Acc	p.A75T	CTD-2560E9.5_ENST00000531663.1_RNA|CTD-2560E9.5_ENST00000534342.1_RNA	NM_001247987.1|NM_020826.2	NP_001234916.1|NP_065877.1	Q7L8C5	SYT13_HUMAN	synaptotagmin XIII	75					vesicle-mediated transport (GO:0016192)	integral component of plasma membrane (GO:0005887)|transport vesicle (GO:0030133)				breast(1)|large_intestine(3)|lung(16)|ovary(1)|skin(2)	23						TTGAGGAGGGCACGGGGCTGA	0.512																																					p.A75T		Atlas-SNP	.											.	SYT13	45	.	0			c.G223A						PASS	.						92	93	93					11																	45277403		2203	4299	6502	SO:0001583	missense	57586	exon2			GGAGGGCACGGGG	AB037848	CCDS31470.1	11p12-p11	2013-01-21			ENSG00000019505	ENSG00000019505		"Synaptotagmins"	14962	protein-coding gene	gene with protein product		607716				11171101	Standard	NM_020826		Approved	KIAA1427	uc001myq.2	Q7L8C5	OTTHUMG00000166504	ENST00000020926.3:c.223G>A	chr11.hg19:g.45277403C>T	ENSP00000020926:p.Ala75Thr	99.0	0.0	.		143.0	45.0	.	NM_020826	A8K4P4|D3DQP1|Q9BQS3|Q9H041|Q9P2C0	Missense_Mutation	SNP	ENST00000020926.3	hg19	CCDS31470.1	.	.	.	.	.	.	.	.	.	.	C	11.25	1.583492	0.28268	.	.	ENSG00000019505	ENST00000020926	T	0.07800	3.16	5.42	1.33	0.21861	.	0.374613	0.26542	N	0.023790	T	0.04634	0.0126	N	0.19112	0.55	0.18873	N	0.999988	B	0.14805	0.011	B	0.12837	0.008	T	0.40136	-0.9579	10	0.28530	T	0.3	.	5.7553	0.18170	0.0:0.5127:0.2665:0.2209	.	75	Q7L8C5	SYT13_HUMAN	T	75	ENSP00000020926:A75T	ENSP00000020926:A75T	A	-	1	0	SYT13	45233979	0.000000	0.05858	0.284000	0.24805	0.331000	0.28603	-0.652000	0.05366	0.051000	0.15978	-0.258000	0.10820	GCC	.	.	.	none		0.512	SYT13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390110.1	NM_020826		T	45277403	C	T	45277403	3	4	182	1	0	0	0	0	1	0	0	0	15481	710	25	2	1077	2	SYT13	11	45277403	Missense_Mutation	SNP	C	TCGA-G7-A8LE-01A-11D-A35Z-10	38213515	45277403	89729113	45	10640											
CLP1	10978	hgsc.bcm.edu	37	chr11	57427119	57427121	+	In_Frame_Del	DEL	TGA	TGA	-																															cgaaacaagaaattcaccttTgatgctggtgccaaggtggc																										TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr11:57427119_57427121delTGA	ENST00000302731.4	+	2	291_293	c.171_173delTGA	c.(169-174)tttgat>ttt	p.D58del	CLP1_ENST00000529430.1_In_Frame_Del_p.D69del|CLP1_ENST00000533682.1_In_Frame_Del_p.D58del|CLP1_ENST00000525602.1_In_Frame_Del_p.D58del	NM_001142597.1|NM_006831.2	NP_001136069.1|NP_006822.1	Q5KU26	COL12_HUMAN	cleavage and polyadenylation factor I subunit 1	0					carbohydrate mediated signaling (GO:0009756)|defense response (GO:0006952)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|protein homooligomerization (GO:0051260)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galactose binding (GO:0005534)|low-density lipoprotein particle binding (GO:0030169)|metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|stomach(1)	15						AATTCACCTTTGATGCTGGTGCC	0.517																																					p.57_58del		Atlas-Indel,Pindel	.											.	CLP1	40	.	0			c.170_172del						PASS	.																																			SO:0001651	inframe_deletion	10978	exon2			.	BC000446	CCDS7964.1, CCDS44600.1	11q12.1	2012-10-02	2012-10-02		ENSG00000172409	ENSG00000172409	2.7.1.78		16999	protein-coding gene	gene with protein product	"ATP/GTPbinding protein", "polyribonucleotide 5'-hydroxyl-kinase"	608757	"CLP1, cleavage and polyadenylation factor I subunit, homolog (S. cerevisiae)"			8896421, 11060040	Standard	NM_006831		Approved	HEAB, hClp1	uc001nkw.3	Q92989	OTTHUMG00000167146	ENST00000302731.4:c.171_173delTGA	chr11.hg19:g.57427119_57427121delTGA	ENSP00000304704:p.Asp58del	168.0	0.0	0		241.0	83.0	0.344398	NM_001142597	Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7	In_Frame_Del	DEL	ENST00000302731.4	hg19	CCDS44600.1																																																																																			.	.	.	none		0.517	CLP1-003	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000393465.1	NM_006831		-	57427121	TGA	-	57427119	7	5	182	1	0	1	0	1	0	0	0	0	3552	1809	63	0	173	0	CLP1	11	57427119	In_Frame_Del	DEL	TGA	TCGA-G7-A8LE-01A-11D-A35Z-10	12149716	57427119	77579397	46	10641											
C11orf24	53838	hgsc.bcm.edu	37	chr11	68029170	68029172	+	In_Frame_Del	DEL	CTT	CTT	-																															tagtccacctgggtgtagtcCttcttcttgtagctctcata																										TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr11:68029170_68029172delCTT	ENST00000304271.6	-	4	1693_1695	c.1291_1293delAAG	c.(1291-1293)aagdel	p.K431del	C11orf24_ENST00000533310.1_In_Frame_Del_p.K96del|C11orf24_ENST00000530166.1_5'Flank	NM_022338.3	NP_071733.1	Q96F05	CK024_HUMAN	chromosome 11 open reading frame 24	431						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						GGGTGTAGTCCTTCTTCTTGTAG	0.557																																					p.431_432del	NSCLC(21;855 905 4198 36694)	Atlas-Indel,Pindel	.											.	C11orf24	35	.	0			c.1292_1294del						PASS	.			5,4259		2,1,2129						5.3	1			94	2,8252		0,2,4125	no	coding	C11orf24	NM_022338.3		2,3,6254	A1A1,A1R,RR		0.0242,0.1173,0.0559				7,12511				SO:0001651	inframe_deletion	53838	exon4			.	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.1291_1293delAAG	chr11.hg19:g.68029176_68029178delCTT	ENSP00000307264:p.Lys431del	93.0	0.0	0		125.0	44.0	0.352	NM_022338	Q9H2K4	In_Frame_Del	DEL	ENST00000304271.6	hg19	CCDS8180.1																																																																																			.	.	.	none		0.557	C11orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394750.1	NM_022338		-	68029172	CTT	-	68029170	7	5	182	1	0	1	0	1	0	0	0	0	1637	680	24	0	60	0	C11orf24	11	68029170	In_Frame_Del	DEL	CTT	TCGA-G7-A8LE-01A-11D-A35Z-10	10602051	68029170	66977346	47	10642											
GDF3	9573	hgsc.bcm.edu	37	chr12	7842823	7842823	+	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	ggacagggatggctgctctcCttttccgagaagggtggcac	7	9	15	10	1	1	1	0	0	1	1	3	4	2	3	2	5	1	3	2	5	1	2			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr12:7842823C>G	ENST00000329913.3	-	2	793	c.746G>C	c.(745-747)aGg>aCg	p.R249T		NM_020634.1	NP_065685.1	Q9NR23	GDF3_HUMAN	growth differentiation factor 3	249					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						GGCTGCTCTCCTTTTCCGAGA	0.537																																					p.R249T		Atlas-SNP	.											.	GDF3	68	.	0			c.G746C						PASS	.						96	87	90					12																	7842823		2203	4300	6503	SO:0001583	missense	9573	exon2			GCTCTCCTTTTCC	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.746G>C	chr12.hg19:g.7842823C>G	ENSP00000331745:p.Arg249Thr	122.0	0.0	.		151.0	61.0	.	NM_020634	Q8NEJ4	Missense_Mutation	SNP	ENST00000329913.3	hg19	CCDS8581.1	.	.	.	.	.	.	.	.	.	.	C	9.046	0.990771	0.18966	.	.	ENSG00000184344	ENST00000329913	D	0.85171	-1.95	4.61	4.61	0.57282	Transforming growth factor-beta, C-terminal (1);	0.240498	0.47852	D	0.000210	D	0.91875	0.7428	M	0.90705	3.14	0.45366	D	0.998357	D	0.62365	0.991	D	0.63957	0.92	D	0.92487	0.5997	10	0.72032	D	0.01	.	9.051	0.36376	0.0:0.8988:0.0:0.1012	.	249	Q9NR23	GDF3_HUMAN	T	249	ENSP00000331745:R249T	ENSP00000331745:R249T	R	-	2	0	GDF3	7734090	0.177000	0.23109	0.988000	0.46212	0.114000	0.19823	0.441000	0.21611	2.285000	0.76669	0.561000	0.74099	AGG	.	.	.	none		0.537	GDF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399717.1			G	7842823	C	G	7842823	3	3	182	1	0	0	0	0	1	0	0	0	6322	681	24	4	352	4	GDF3	12	7842823	Missense_Mutation	SNP	C	TCGA-G7-A8LE-01A-11D-A35Z-10		7842823	126009072	48	10643											
OVCH1	341350	hgsc.bcm.edu	37	chr12	29608320	29608321	+	Missense_Mutation	DNP	GT	GT	CC																															attttcatgtctacatactaGtggcccaccagagtctccct																										TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	G|T	G|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr12:29608320_29608321GT>CC	ENST00000318184.5	-	20	2297_2298	c.2298_2299AC>GG	c.(2296-2301)ccACta>ccGGta	p.L767V	OVCH1-AS1_ENST00000551108.1_Intron|OVCH1-AS1_ENST00000549411.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	767	Peptidase S1 2. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					CTACATACTAGTGGCCCACCAG	0.455																																					p.L767V|p.P766P		Atlas-SNP	.											.	OVCH1	195	.	0			c.C2299G|c.A2298G						PASS	.																																			SO:0001583	missense	341350	exon20			ATACTAGTGGCCC|TACTAGTGGCCCA	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.2298_2299delinsCC	chr12.hg19:g.29608320_29608321delinsCC	ENSP00000326708:p.Leu767Val	247.0|243.0	0.0	.		339.0|335.0	123.0|121.0	.	NM_183378		Missense_Mutation|Silent	SNP	ENST00000318184.5	hg19																																																																																				.	.	.	none		0.455	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378		CC	29608321	GT	CC	29608320	3	2	182	1	0	0	0	0	1	0	0	0	11330	1020	36	4	1141	4	OVCH1	12	29608320	Missense_Mutation	DNP	GT	TCGA-G7-A8LE-01A-11D-A35Z-10	21765497	29608320	104243575	49	10644											
IPO8	10526	hgsc.bcm.edu	37	chr12	30792659	30792659	+	Missense_Mutation	SNP	A	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	ccaaaacaagttgaacgaagAgtggaatgcactagaagaca	19	5	10	7	1	0	4	0	1	0	3	0	6	0	5	1	1	3	2	1	1	8	2			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr12:30792659A>C	ENST00000256079.4	-	21	2617	c.2279T>G	c.(2278-2280)cTc>cGc	p.L760R	IPO8_ENST00000544829.1_Missense_Mutation_p.L555R	NM_006390.3	NP_006381.2	O15397	IPO8_HUMAN	importin 8	760					intracellular protein transport (GO:0006886)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	Ran GTPase binding (GO:0008536)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(16)|liver(1)|lung(22)|prostate(2)|skin(2)|urinary_tract(2)	52	all_lung(12;6.66e-10)|Lung NSC(12;4.84e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					TTGAACGAAGAGTGGAATGCA	0.403																																					p.L760R		Atlas-SNP	.											.	IPO8	105	.	0			c.T2279G						PASS	.						84	80	81					12																	30792659		2203	4300	6503	SO:0001583	missense	10526	exon21			ACGAAGAGTGGAA	U77494	CCDS8719.1, CCDS53773.1	12p11.21	2011-05-23	2003-03-11	2003-03-14	ENSG00000133704	ENSG00000133704		"Importins"	9853	protein-coding gene	gene with protein product		605600	"RAN binding protein 8"	RANBP8		9214382	Standard	NM_006390		Approved	IMP8	uc001rjd.3	O15397	OTTHUMG00000169172	ENST00000256079.4:c.2279T>G	chr12.hg19:g.30792659A>C	ENSP00000256079:p.Leu760Arg	55.0	0.0	.		87.0	41.0	.	NM_006390	B7Z7M3	Missense_Mutation	SNP	ENST00000256079.4	hg19	CCDS8719.1	.	.	.	.	.	.	.	.	.	.	A	12.82	2.052055	0.36181	.	.	ENSG00000133704	ENST00000256079;ENST00000545286;ENST00000544829	T;T	0.66638	-0.22;-0.22	5.27	4.12	0.48240	Armadillo-like helical (1);Armadillo-type fold (1);	0.064281	0.64402	D	0.000005	T	0.73148	0.3550	L	0.52573	1.65	0.80722	D	1	P;D;B	0.89917	0.629;1.0;0.212	B;D;B	0.91635	0.411;0.999;0.15	T	0.67776	-0.5583	10	0.15952	T	0.53	-8.69	10.8138	0.46562	0.9249:0.0:0.0751:0.0	.	555;236;760	B7Z7M3;Q59F59;O15397	.;.;IPO8_HUMAN	R	760;236;555	ENSP00000256079:L760R;ENSP00000444520:L555R	ENSP00000256079:L760R	L	-	2	0	IPO8	30683926	1.000000	0.71417	0.849000	0.33467	0.980000	0.70556	8.966000	0.93397	0.842000	0.35045	0.460000	0.39030	CTC	.	.	.	none		0.403	IPO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402700.2	NM_006390		C	30792659	A	C	30792659	3	2	182	1	0	0	0	0	1	0	0	0	7805	304	11	5	854	5	IPO8	12	30792659	Missense_Mutation	SNP	A	TCGA-G7-A8LE-01A-11D-A35Z-10	1184339	30792659	103059236	50	10645											
SLC2A13	114134	hgsc.bcm.edu	37	chr12	40158612	40158612	+	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	0	0	0	0	0	0	0	0	0	tatggagtagggcagaaattGtaagcccaaaatatatcttc	15	11	9	6	0	1	1	0	0	1	1	2	2	1	2	1	2	1	3	1	2	8	7			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr12:40158612G>C	ENST00000280871.4	-	8	1544	c.1494C>G	c.(1492-1494)taC>taG	p.Y498*		NM_052885.3	NP_443117.3	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 13	498					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	29		Lung NSC(34;0.105)|all_lung(34;0.123)				GGCAGAAATTGTAAGCCCAAA	0.343										HNSCC(50;0.14)																											p.Y498X		Atlas-SNP	.											.	SLC2A13	91	.	0			c.C1494G						PASS	.						130	147	141					12																	40158612		2203	4300	6503	SO:0001587	stop_gained	114134	exon8			GAAATTGTAAGCC	AJ315644	CCDS8736.2	12q12	2013-05-22			ENSG00000151229	ENSG00000151229		"Solute carriers"	15956	protein-coding gene	gene with protein product	"H(+)-myo-inositol symporter"	611036				11500374	Standard	NM_052885		Approved	HMIT	uc010skm.2	Q96QE2	OTTHUMG00000059743	ENST00000280871.4:c.1494C>G	chr12.hg19:g.40158612G>C	ENSP00000280871:p.Tyr498*	91.0	0.0	.		136.0	40.0	.	NM_052885	Q17S07	Nonsense_Mutation	SNP	ENST00000280871.4	hg19	CCDS8736.2	.	.	.	.	.	.	.	.	.	.	G	33	5.203671	0.95033	.	.	ENSG00000151229	ENST00000280871	.	.	.	5.12	1.25	0.21368	.	0.355074	0.30028	N	0.010593	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.089	8.9456	0.35756	0.5097:0.0:0.4903:0.0	.	.	.	.	X	498	.	ENSP00000280871:Y498X	Y	-	3	2	SLC2A13	38444879	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.673000	0.37534	0.197000	0.20387	-0.157000	0.13467	TAC	.	.	.	none		0.343	SLC2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132849.2			C	40158612	G	C	40158612	4	2	182	1	0	0	0	0	0	1	0	0	14555	1372	48	4	464	4	SLC2A13	12	40158612	Nonsense_Mutation	SNP	G	TCGA-G7-A8LE-01A-11D-A35Z-10	9365953	40158612	93693283	51	10646											
SLC2A13	114134	hgsc.bcm.edu	37	chr12	40441958	40441958	+	Frame_Shift_Del	DEL	A	A	-																															tggtgactaatcggcctcttAaattgggtggtgagacctcc																										TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr12:40441958delA	ENST00000280871.4	-	2	661	c.611delT	c.(610-612)ttafs	p.L204fs	SLC2A13_ENST00000380858.1_Frame_Shift_Del_p.L204fs	NM_052885.3	NP_443117.3	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 13	204					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	29		Lung NSC(34;0.105)|all_lung(34;0.123)				TCGGCCTCTTAAATTGGGTGG	0.418										HNSCC(50;0.14)																											p.L204fs		Atlas-Indel,Pindel	.											.	SLC2A13	91	.	0			c.612delA						PASS	.						163	155	158					12																	40441958		2203	4300	6503	SO:0001589	frameshift_variant	114134	exon2			.	AJ315644	CCDS8736.2	12q12	2013-05-22			ENSG00000151229	ENSG00000151229		"Solute carriers"	15956	protein-coding gene	gene with protein product	"H(+)-myo-inositol symporter"	611036				11500374	Standard	NM_052885		Approved	HMIT	uc010skm.2	Q96QE2	OTTHUMG00000059743	ENST00000280871.4:c.611delT	chr12.hg19:g.40441958delA	ENSP00000280871:p.Leu204fs	73.0	0.0	0		132.0	49.0	0.371212	NM_052885	Q17S07	Frame_Shift_Del	DEL	ENST00000280871.4	hg19	CCDS8736.2																																																																																			.	.	.	none		0.418	SLC2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132849.2			-	40441958	A	-	40441958	7	5	182	1	0	1	0	1	0	0	0	0	14555	372	13	0	1371	0	SLC2A13	12	40441958	Frame_Shift_Del	DEL	A	TCGA-G7-A8LE-01A-11D-A35Z-10	283346	40441958	93409937	52	10647											
MLL2	8085	hgsc.bcm.edu	37	chr12	49434397	49434397	+	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	agggggcggaggttggggccGaggagtcaatgggggctgag	7	5	24	5	2	1	1	1	1	0	0	1	4	1	3	1	9	0	2	1	9	1	1			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr12:49434397G>C	ENST00000301067.7	-	31	7155	c.7156C>G	c.(7156-7158)Cgg>Ggg	p.R2386G		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2386	Poly-Pro.|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)										GGTTGGGGCCGAGGAGTCAAT	0.642																																					p.R2386G		Atlas-SNP	.											MLL2_ENST00000301067,NS,carcinoma,0,2	MLL2	1173	.	0			c.C7156G						PASS	.						22	27	25					12																	49434397		2046	4195	6241	SO:0001583	missense	8085	exon31			GGGGCCGAGGAGT	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.7156C>G	chr12.hg19:g.49434397G>C	ENSP00000301067:p.Arg2386Gly	147.0	0.0	.		199.0	73.0	.	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	4.200	0.035884	0.08148	.	.	ENSG00000167548	ENST00000301067	D	0.84146	-1.81	5.21	3.18	0.36537	.	0.000000	0.34338	N	0.004047	D	0.85822	0.5786	L	0.48642	1.525	0.29050	N	0.884552	D	0.69078	0.997	P	0.54815	0.761	T	0.82159	-0.0595	10	0.87932	D	0	.	12.3552	0.55171	0.0:0.0:0.6054:0.3946	.	2386	O14686	MLL2_HUMAN	G	2386	ENSP00000301067:R2386G	ENSP00000301067:R2386G	R	-	1	2	MLL2	47720664	0.998000	0.40836	1.000000	0.80357	0.529000	0.34654	1.401000	0.34589	1.276000	0.44395	0.591000	0.81541	CGG	.	.	.	none		0.642	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			C	49434397	G	C	49434397	3	2	182	1	0	0	0	0	1	0	0	0	9628	1057	37	4	9553	4	MLL2	12	49434397	Missense_Mutation	SNP	G	TCGA-G7-A8LE-01A-11D-A35Z-10	8992439	49434397	84417498	53	10648											
RACGAP1	29127	hgsc.bcm.edu	37	chr12	50410456	50410456	+	Frame_Shift_Del	DEL	G	G	-																															aatctccacccggcgcacaaGctgctcaaacagattccgca																										TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr12:50410456delG	ENST00000427314.2	-	4	266	c.43delC	c.(43-45)cttfs	p.L15fs	RACGAP1_ENST00000434422.1_Frame_Shift_Del_p.L15fs|RACGAP1_ENST00000454520.2_Frame_Shift_Del_p.L15fs|RACGAP1_ENST00000551016.1_Frame_Shift_Del_p.L15fs|RACGAP1_ENST00000312377.5_Frame_Shift_Del_p.L15fs|RACGAP1_ENST00000547905.1_Frame_Shift_Del_p.L15fs	NM_013277.3	NP_037409.2			Rac GTPase activating protein 1											cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(6)	14						CGGCGCACAAGCTGCTCAAAC	0.438																																					p.L15fs		Atlas-Indel,Pindel	.											.	RACGAP1	36	.	0			c.44delT						PASS	.						134	143	140					12																	50410456		2203	4300	6503	SO:0001589	frameshift_variant	29127	exon4			.		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.43delC	chr12.hg19:g.50410456delG	ENSP00000404190:p.Leu15fs	53.0	0.0	0		76.0	39.0	0.513158	NM_013277		Frame_Shift_Del	DEL	ENST00000427314.2	hg19	CCDS8795.1																																																																																			.	.	.	none		0.438	RACGAP1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405997.1	NM_013277		-	50410456	G	-	50410456	7	5	182	1	0	1	0	1	0	0	0	0	12990	971	34	0	1919	0	RACGAP1	12	50410456	Frame_Shift_Del	DEL	G	TCGA-G7-A8LE-01A-11D-A35Z-10	976059	50410456	83441439	54	10649											
LRIG3	121227	hgsc.bcm.edu	37	chr12	59271539	59271539	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atctttggtccagttcagttTagggggagggcttcctccag	6	13	13	9	0	2	0	1	0	1	0	5	1	5	1	3	4	0	3	3	4	1	5			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr12:59271539T>C	ENST00000320743.3	-	15	2465	c.2179A>G	c.(2179-2181)Aaa>Gaa	p.K727E	LRIG3_ENST00000379141.4_Missense_Mutation_p.K667E	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	727	Ig-like C2-type 3.				otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)			LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			CAGTTCAGTTTAGGGGGAGGG	0.493			T	ROS1	NSCLC																																p.K727E		Atlas-SNP	.		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	.	LRIG3	120	.	0			c.A2179G						PASS	.						114	111	112					12																	59271539		2203	4300	6503	SO:0001583	missense	121227	exon15			TCAGTTTAGGGGG	AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"Immunoglobulin superfamily / I-set domain containing"	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.2179A>G	chr12.hg19:g.59271539T>C	ENSP00000326759:p.Lys727Glu	56.0	0.0	.		90.0	42.0	.	NM_153377	Q6UXL7|Q8NC72	Missense_Mutation	SNP	ENST00000320743.3	hg19	CCDS8960.1	.	.	.	.	.	.	.	.	.	.	T	9.226	1.034489	0.19590	.	.	ENSG00000139263	ENST00000379141;ENST00000320743	T;T	0.65732	-0.17;-0.17	5.59	1.51	0.23008	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.37715	N	0.001969	T	0.41558	0.1164	N	0.05554	-0.025	0.09310	N	1	B;B	0.23735	0.007;0.09	B;B	0.31442	0.038;0.13	T	0.28004	-1.0057	9	.	.	.	.	14.1036	0.65072	0.0:0.0:0.5152:0.4848	.	667;727	Q6UXM1-2;Q6UXM1	.;LRIG3_HUMAN	E	667;727	ENSP00000368436:K667E;ENSP00000326759:K727E	.	K	-	1	0	LRIG3	57557806	0.002000	0.14202	0.001000	0.08648	0.212000	0.24457	1.189000	0.32114	0.431000	0.26258	0.533000	0.62120	AAA	.	.	.	none		0.493	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377		C	59271539	T	C	59271539	3	2	182	1	0	0	0	0	1	0	0	0	8953	1763	61	3	1200	3	LRIG3	12	59271539	Missense_Mutation	SNP	T	TCGA-G7-A8LE-01A-11D-A35Z-10	8861083	59271539	74580356	55	10650											
NAV3	89795	hgsc.bcm.edu	37	chr12	78400770	78400770	+	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	gtttgcactgaaaaaccagtCaaagaagagaaggatcaggt	17	7	11	6	0	2	3	2	1	0	2	2	5	2	4	1	2	2	2	1	2	5	1			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr12:78400770C>A	ENST00000397909.2	+	8	1625	c.1452C>A	c.(1450-1452)gtC>gtA	p.V484V	NAV3_ENST00000536525.2_Silent_p.V484V|NAV3_ENST00000266692.7_Silent_p.V484V|NAV3_ENST00000228327.6_Silent_p.V484V			Q8IVL0	NAV3_HUMAN	neuron navigator 3	484						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						AAAAACCAGTCAAAGAAGAGA	0.408										HNSCC(70;0.22)																											p.V484V		Atlas-SNP	.											.	NAV3	506	.	0			c.C1452A						PASS	.						72	71	71					12																	78400770		1859	4097	5956	SO:0001819	synonymous_variant	89795	exon8			ACCAGTCAAAGAA	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.1452C>A	chr12.hg19:g.78400770C>A		170.0	0.0	.		292.0	109.0	.	NM_014903	Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	hg19																																																																																				.	.	.	none		0.408	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		A	78400770	C	A	78400770	2	1	182	1	0	0	0	0	0	0	0	1	10192	813	29	4		4	NAV3	12	78400770	Silent	SNP	C	TCGA-G7-A8LE-01A-11D-A35Z-10	19129231	78400770	55451125	56	10651											
SALL2	6297	hgsc.bcm.edu	37	chr14	21993091	21993091	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggaagaggaggaggaggaGgaagatgccagtgtcttgct	12	6	19	4	0	1	2	0	0	1	2	1	9	1	8	1	6	2	1	1	6	2	1			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr14:21993091G>A	ENST00000327430.3	-	2	1065	c.771C>T	c.(769-771)tcC>tcT	p.S257S	SALL2_ENST00000317492.5_Intron|AE000658.22_ENST00000535893.1_RNA|SALL2_ENST00000450879.2_Intron|SALL2_ENST00000538754.1_Intron	NM_005407.1	NP_005398.1	Q9Y467	SALL2_HUMAN	spalt-like transcription factor 2	257	Poly-Ser.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(6)|urinary_tract(2)	43	all_cancers(95;0.000662)			GBM - Glioblastoma multiforme(265;0.0151)		aggaggaggaggaagaTGCCA	0.582																																					p.S257S		Atlas-SNP	.											.	SALL2	95	.	0			c.C771T						PASS	.						48	47	48					14																	21993091		2203	4300	6503	SO:0001819	synonymous_variant	6297	exon2			GGAGGAGGAAGAT	AB002358	CCDS32045.1	14q11.1-q12.1	2013-10-17	2013-10-17		ENSG00000165821	ENSG00000165821		"Zinc fingers, C2H2-type"	10526	protein-coding gene	gene with protein product		602219	"sal (Drosophila)-like 2", "sal-like 2 (Drosophila)"			8975705	Standard	XM_005267983		Approved	KIAA0360, Hsal2, ZNF795	uc001wbe.3	Q9Y467	OTTHUMG00000168826	ENST00000327430.3:c.771C>T	chr14.hg19:g.21993091G>A		67.0	0.0	.		99.0	4.0	.	NM_005407	B2RMX6|B9EGK8|Q8N656|Q9Y4G1	Silent	SNP	ENST00000327430.3	hg19	CCDS32045.1																																																																																			.	.	.	none		0.582	SALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401242.1	NM_005407		A	21993091	G	A	21993091	2	1	182	1	0	0	0	0	0	0	0	1	13824	987	35	2		2	SALL2	14	21993091	Silent	SNP	G	TCGA-G7-A8LE-01A-11D-A35Z-10		21993091	85356449	57	10652											
RHBDL1	9028	hgsc.bcm.edu	37	chr16	726998	726998	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttcctgtgttacggggccCgcctcaacaagtgggtgctg	5	11	14	11	2	1	0	1	0	0	0	2	0	2	0	3	3	3	3	3	3	3	2			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr16:726998C>T	ENST00000219551.2	+	3	676	c.649C>T	c.(649-651)Cgc>Tgc	p.R217C	LA16c-313D11.9_ENST00000567091.1_RNA|RHBDL1_ENST00000352681.3_Missense_Mutation_p.R152C|LA16c-313D11.9_ENST00000571933.1_RNA			O75783	RHBL1_HUMAN	rhomboid, veinlet-like 1 (Drosophila)	217					signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(1)|lung(4)|urinary_tract(3)	9		Hepatocellular(780;0.0218)				TTACGGGGCCCGCCTCAACAA	0.682																																					p.R217C		Atlas-SNP	.											.	RHBDL1	14	.	0			c.C649T						PASS	.						63	67	66					16																	726998		2201	4298	6499	SO:0001583	missense	9028	exon3			GGGGCCCGCCTCA	Y17108	CCDS61779.1	16p13.3	2008-02-05	2001-11-28	2003-04-11	ENSG00000103269	ENSG00000103269			10007	protein-coding gene	gene with protein product		603264	"rhomboid (veinlet, Drosophila)-like"	RHBDL		9662444	Standard	NM_001278720		Approved	RRP	uc002cis.1	O75783	OTTHUMG00000121141	ENST00000219551.2:c.649C>T	chr16.hg19:g.726998C>T	ENSP00000219551:p.Arg217Cys	84.0	0.0	.		99.0	46.0	.	NM_003961	A2IDC0|A2IDC1|Q0VAX4|Q9NQ85	Missense_Mutation	SNP	ENST00000219551.2	hg19	CCDS10418.1	.	.	.	.	.	.	.	.	.	.	C	12.17	1.859017	0.32884	.	.	ENSG00000103269	ENST00000352681;ENST00000450775;ENST00000219551	T;T	0.33216	1.46;1.42	3.99	3.99	0.46301	.	0.143249	0.42964	D	0.000631	T	0.22399	0.0540	N	0.08118	0	0.46981	D	0.999279	D;D;D	0.61080	0.989;0.977;0.958	P;B;P	0.50617	0.54;0.439;0.646	T	0.05099	-1.0906	10	0.56958	D	0.05	-18.8892	10.2818	0.43543	0.1975:0.8025:0.0:0.0	.	152;217;152	B4DFK3;O75783;O75783-2	.;RHBL1_HUMAN;.	C	152;152;217	ENSP00000344206:R152C;ENSP00000219551:R217C	ENSP00000219551:R217C	R	+	1	0	RHBDL1	666999	0.811000	0.29063	0.683000	0.30040	0.029000	0.11900	1.737000	0.38197	2.062000	0.61559	0.557000	0.71058	CGC	.	.	.	none		0.682	RHBDL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000241619.1	NM_003961		T	726998	C	T	726998	3	4	182	1	0	0	0	0	1	0	0	0	13334	652	23	1	659	1	RHBDL1	16	726998	Missense_Mutation	SNP	C	TCGA-G7-A8LE-01A-11D-A35Z-10		726998	89627755	58	10653											
GSG2	83903	hgsc.bcm.edu	37	chr17	3629517	3629517	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaccttcaagactaaatgtaAcactcctgccatgaagcaaa	16	8	6	11	0	1	2	1	1	0	1	2	3	2	2	3	0	3	2	3	0	6	3			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr17:3629517A>G	ENST00000325418.4	+	1	2307	c.2288A>G	c.(2287-2289)aAc>aGc	p.N763S	ITGAE_ENST00000571185.1_Intron|ITGAE_ENST00000263087.4_Intron	NM_031965.2	NP_114171.2	Q8TF76	HASP_HUMAN	germ cell associated 2 (haspin)	763	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)										ACTAAATGTAACACTCCTGCC	0.443																																					p.N763S		Atlas-SNP	.											.	GSG2	48	.	0			c.A2288G						PASS	.						60	59	59					17																	3629517		2203	4300	6503	SO:0001583	missense	83903	exon1			AATGTAACACTCC	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.2288A>G	chr17.hg19:g.3629517A>G	ENSP00000325290:p.Asn763Ser	99.0	0.0	.		172.0	100.0	.	NM_031965	Q5U5K3|Q96MN1|Q9BXS7	Missense_Mutation	SNP	ENST00000325418.4	hg19	CCDS11036.1	.	.	.	.	.	.	.	.	.	.	A	7.407	0.633968	0.14322	.	.	ENSG00000177602	ENST00000325418	T	0.05649	3.41	5.51	0.132	0.14762	Domain of unknown function DUF3635 (1);Protein kinase, catalytic domain (1);	0.858738	0.10326	N	0.688158	T	0.04048	0.0113	N	0.16708	0.43	0.09310	N	1	B	0.21452	0.056	B	0.12837	0.008	T	0.40869	-0.9540	10	0.87932	D	0	-5.7401	5.8033	0.18426	0.3914:0.428:0.1806:0.0	.	763	Q8TF76	HASP_HUMAN	S	763	ENSP00000325290:N763S	ENSP00000325290:N763S	N	+	2	0	GSG2	3576266	0.000000	0.05858	0.010000	0.14722	0.907000	0.53573	-0.231000	0.09069	0.131000	0.18576	0.533000	0.62120	AAC	.	.	.	none		0.443	GSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207391.1	NM_031965		G	3629517	A	G	3629517	3	3	182	1	0	0	0	0	1	0	0	0	6829	43	2	3	2290	3	GSG2	17	3629517	Missense_Mutation	SNP	A	TCGA-G7-A8LE-01A-11D-A35Z-10		3629517	77565693	59	10654											
DHX33	56919	hgsc.bcm.edu	37	chr17	5354241	5354241	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtccagttgggcaatggcCgcctgaatgtgatctaaaga	11	9	13	8	1	1	3	0	2	1	1	2	3	2	3	3	3	0	2	3	3	4	2			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr17:5354241C>T	ENST00000225296.3	-	9	1610	c.1410G>A	c.(1408-1410)gcG>gcA	p.A470A	DHX33_ENST00000433302.3_Silent_p.A246A	NM_001199699.1|NM_020162.3	NP_001186628.1|NP_064547.2	Q9H6R0	DHX33_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 33	470					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						GGGCAATGGCCGCCTGAATGT	0.428																																					p.A470A		Atlas-SNP	.											.	DHX33	41	.	0			c.G1410A						PASS	.						124	119	120					17																	5354241		2203	4300	6503	SO:0001819	synonymous_variant	56919	exon9			AATGGCCGCCTGA	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.1410G>A	chr17.hg19:g.5354241C>T		117.0	0.0	.		195.0	43.0	.	NM_020162	B4DHF9|Q4G149|Q5CZ73|Q9H5M9	Silent	SNP	ENST00000225296.3	hg19	CCDS11072.1																																																																																			.	.	.	none		0.428	DHX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219826.2	NM_020162		T	5354241	C	T	5354241	2	4	182	1	0	0	0	0	0	0	0	1	4508	639	23	1		1	DHX33	17	5354241	Silent	SNP	C	TCGA-G7-A8LE-01A-11D-A35Z-10	1724724	5354241	75840969	60	10655											
ALOX12	239	hgsc.bcm.edu	37	chr17	6909258	6909258	+	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	cctactgctccctctgtcctCctgacgacctggctgaccgg	4	10	9	18	2	1	2	0	2	1	0	4	3	4	2	6	2	2	2	6	2	1	1			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr17:6909258C>A	ENST00000251535.6	+	10	1383	c.1330C>A	c.(1330-1332)Cct>Act	p.P444T	AC027763.2_ENST00000575727.1_Intron|AC027763.2_ENST00000399540.2_Intron|AC027763.2_ENST00000574377.1_Intron|AC027763.2_ENST00000399541.2_Intron|AC027763.2_ENST00000573939.1_Intron|RP11-589P10.7_ENST00000572547.1_RNA	NM_000697.2	NP_000688.2	P18054	LOX12_HUMAN	arachidonate 12-lipoxygenase	444	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				aging (GO:0007568)|arachidonic acid metabolic process (GO:0019369)|cellular component movement (GO:0006928)|cellular response to lipid (GO:0071396)|establishment of skin barrier (GO:0061436)|fatty acid oxidation (GO:0019395)|hepoxilin biosynthetic process (GO:0051122)|hepoxilin metabolic process (GO:0051121)|leukotriene A4 metabolic process (GO:1901751)|linoleic acid metabolic process (GO:0043651)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxin B4 biosynthetic process (GO:2001306)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of platelet aggregation (GO:0090331)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|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 endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of gene expression (GO:0010628)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|superoxide anion generation (GO:0042554)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|sarcolemma (GO:0042383)	arachidonate 12-lipoxygenase activity (GO:0004052)|hepoxilin A3 synthase activity (GO:0051120)|hepoxilin-epoxide hydrolase activity (GO:0047977)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(3)|urinary_tract(1)	19						CCTCTGTCCTCCTGACGACCT	0.617																																					p.P444T		Atlas-SNP	.											.	ALOX12	49	.	0			c.C1330A						PASS	.						71	69	70					17																	6909258		2203	4300	6503	SO:0001583	missense	239	exon10			TGTCCTCCTGACG	M35418	CCDS11084.1	17p13.1	2010-01-14			ENSG00000108839	ENSG00000108839	1.13.11.31	"Arachidonate lipoxygenases"	429	protein-coding gene	gene with protein product	"platelet 12-LOX"	152391				1570320	Standard	NM_000697		Approved	12S-LOX	uc002gdx.4	P18054	OTTHUMG00000102088	ENST00000251535.6:c.1330C>A	chr17.hg19:g.6909258C>A	ENSP00000251535:p.Pro444Thr	30.0	0.0	.		66.0	16.0	.	NM_000697	O95569|Q6ISF8|Q9UQM4	Missense_Mutation	SNP	ENST00000251535.6	hg19	CCDS11084.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.064434	0.76187	.	.	ENSG00000108839	ENST00000251535	D	0.89681	-2.55	5.3	5.3	0.74995	Lipoxygenase, C-terminal (3);	0.359698	0.28382	N	0.015542	D	0.94892	0.8349	M	0.91920	3.255	0.42564	D	0.993152	P	0.52842	0.956	P	0.59115	0.852	D	0.95770	0.8808	10	0.87932	D	0	-1.9879	16.4972	0.84248	0.0:1.0:0.0:0.0	.	444	P18054	LOX12_HUMAN	T	444	ENSP00000251535:P444T	ENSP00000251535:P444T	P	+	1	0	ALOX12	6849982	0.298000	0.24417	1.000000	0.80357	0.973000	0.67179	4.613000	0.61176	2.763000	0.94921	0.585000	0.79938	CCT	.	.	.	none		0.617	ALOX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219922.2			A	6909258	C	A	6909258	3	1	182	1	0	0	0	0	1	0	0	0	536	855	30	4	1368	4	ALOX12	17	6909258	Missense_Mutation	SNP	C	TCGA-G7-A8LE-01A-11D-A35Z-10	1555017	6909258	74285952	61	10656											
MPP2	4355	hgsc.bcm.edu	37	chr17	41960406	41960406	+	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	tttgaggccacagagtcgtgCgtctccaggagggactgggg	7	8	17	9	2	1	2	0	1	1	1	3	4	1	4	2	5	1	0	2	5	0	1	rs553317360		TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr17:41960406C>G	ENST00000461854.1	-	6	475	c.390G>C	c.(388-390)acG>acC	p.T130T	MPP2_ENST00000377184.3_Silent_p.T123T|MPP2_ENST00000473246.1_5'UTR|MPP2_ENST00000520305.1_5'UTR|MPP2_ENST00000536246.1_Silent_p.T95T|MPP2_ENST00000518766.1_Silent_p.T151T|MPP2_ENST00000269095.4_Silent_p.T106T|MPP2_ENST00000523501.1_Silent_p.T95T			Q14168	MPP2_HUMAN	membrane protein, palmitoylated 2 (MAGUK p55 subfamily member 2)	130	L27 2. {ECO:0000255|PROSITE- ProRule:PRU00365}.				nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			breast(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)		CAGAGTCGTGCGTCTCCAGGA	0.622													c|||	1	0.000199681	0	0	5008	,	,		14588	0		0	False		,,,				2504	0.001				p.T106T		Atlas-SNP	.											.	MPP2	67	.	0			c.G318C						PASS	.						30	28	29					17																	41960406		2203	4300	6503	SO:0001819	synonymous_variant	4355	exon5			GTCGTGCGTCTCC		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.390G>C	chr17.hg19:g.41960406C>G		59.0	0.0	.		122.0	13.0	.	NM_005374	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Silent	SNP	ENST00000461854.1	hg19																																																																																				.	.	.	none		0.622	MPP2-003	KNOWN	non_canonical_polymorphism|basic	protein_coding	protein_coding	OTTHUMT00000258388.2	NM_005374		G	41960406	C	G	41960406	2	3	182	1	0	0	0	0	0	0	0	1	9741	755	27	4		4	MPP2	17	41960406	Silent	SNP	C	TCGA-G7-A8LE-01A-11D-A35Z-10	35051148	41960406	39234804	62	10657											
SCRN2	90507	hgsc.bcm.edu	37	chr17	45915920	45915920	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatgggtctggcgtggcggtAagaaagtgcacgcagggctg	8	7	19	7	3	1	1	0	0	1	1	1	2	1	1	0	5	1	4	0	5	2	1			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr17:45915920A>G	ENST00000290216.9	-	6	1040	c.915T>C	c.(913-915)ctT>ctC	p.L305L	SCRN2_ENST00000407215.3_Silent_p.L305L|SCRN2_ENST00000584123.1_Silent_p.L313L	NM_001145023.1|NM_138355.3	NP_001138495.1|NP_612364.2	Q96FV2	SCRN2_HUMAN	secernin 2	305						extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)			cervix(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	14						GCGTGGCGGTAAGAAAGTGCA	0.597																																					p.L305L		Atlas-SNP	.											.	SCRN2	35	.	0			c.T915C						PASS	.						97	97	97					17																	45915920		2203	4300	6503	SO:0001819	synonymous_variant	90507	exon6			GGCGGTAAGAAAG	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.915T>C	chr17.hg19:g.45915920A>G		76.0	0.0	.		121.0	35.0	.	NM_138355	A8K3N1|B7Z8S7|E9PBV5|Q96AC3|Q9BU04	Silent	SNP	ENST00000290216.9	hg19	CCDS11519.1																																																																																			.	.	.	none		0.597	SCRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441383.1	NM_138355		G	45915920	A	G	45915920	2	3	182	1	0	0	0	0	0	0	0	1	13952	349	13	3		3	SCRN2	17	45915920	Silent	SNP	A	TCGA-G7-A8LE-01A-11D-A35Z-10	3955514	45915920	35279290	63	10658											
ESCO1	114799	hgsc.bcm.edu	37	chr18	19112541	19112541	+	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	tctggtaatgttgagcagcaCcaggctttttgcctttcaaa	9	14	9	9	0	2	1	1	1	1	0	2	1	2	1	2	2	3	5	2	2	2	5			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr18:19112541C>A	ENST00000269214.5	-	11	3205	c.2268G>T	c.(2266-2268)tgG>tgT	p.W756C		NM_052911.2	NP_443143.2	Q5FWF5	ESCO1_HUMAN	establishment of sister chromatid cohesion N-acetyltransferase 1	756					mitotic cell cycle (GO:0000278)|post-translational protein acetylation (GO:0034421)|regulation of DNA replication (GO:0006275)|sister chromatid cohesion (GO:0007062)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|transferase activity, transferring acyl groups (GO:0016746)			breast(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(10)|prostate(3)|upper_aerodigestive_tract(1)	35						TTGAGCAGCACCAGGCTTTTT	0.433																																					p.W756C		Atlas-SNP	.											.	ESCO1	89	.	0			c.G2268T						PASS	.						156	148	151					18																	19112541		2203	4300	6503	SO:0001583	missense	114799	exon11			GCAGCACCAGGCT	AL832041	CCDS32800.1	18q11.2	2013-05-02	2013-05-02		ENSG00000141446	ENSG00000141446			24645	protein-coding gene	gene with protein product		609674	"establishment of cohesion 1 homolog 1 (S. cerevisiae)"			11572484, 14576321, 15958495	Standard	NM_052911		Approved	ESO1, EFO1, KIAA1911	uc002kth.1	Q5FWF5		ENST00000269214.5:c.2268G>T	chr18.hg19:g.19112541C>A	ENSP00000269214:p.Trp756Cys	79.0	0.0	.		105.0	41.0	.	NM_052911	B0YJ11|B0YJ12|Q69YG4|Q69YS3|Q6IMD7|Q8N3Z5|Q8NBG2|Q96PX7	Missense_Mutation	SNP	ENST00000269214.5	hg19	CCDS32800.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.158408	0.78114	.	.	ENSG00000141446	ENST00000269214	T	0.60920	0.15	5.73	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.75664	0.3880	M	0.75615	2.305	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.76564	-0.2913	10	0.40728	T	0.16	-3.2526	16.7742	0.85546	0.0:0.8709:0.1291:0.0	.	756	Q5FWF5	ESCO1_HUMAN	C	756	ENSP00000269214:W756C	ENSP00000269214:W756C	W	-	3	0	ESCO1	17366539	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.818000	0.86416	1.409000	0.46915	-0.176000	0.13171	TGG	.	.	.	none		0.433	ESCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443942.1	NM_052911		A	19112541	C	A	19112541	3	1	182	1	0	0	0	0	1	0	0	0	5250	508	18	4	262	4	ESCO1	18	19112541	Missense_Mutation	SNP	C	TCGA-G7-A8LE-01A-11D-A35Z-10		19112541	58964707	64	10659											
VAV1	7409	hgsc.bcm.edu	37	chr19	6821672	6821672	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctgtcctggaccccgatcGcccagaacagggggatcatg	8	7	12	14	2	2	1	1	0	1	1	4	4	3	3	4	3	1	0	4	3	1	0			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr19:6821672G>A	ENST00000602142.1	+	3	443	c.361G>A	c.(361-363)Gcc>Acc	p.A121T	VAV1_ENST00000596764.1_Missense_Mutation_p.A121T|VAV1_ENST00000599806.1_Missense_Mutation_p.A66T|VAV1_ENST00000539284.1_Missense_Mutation_p.A56T|VAV1_ENST00000304076.2_Missense_Mutation_p.A121T	NM_005428.3	NP_005419.2	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	121					apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|reactive oxygen species metabolic process (GO:0072593)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(16)|lung(18)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	62						GACCCCGATCGCCCAGAACAG	0.632																																					p.A121T		Atlas-SNP	.											VAV1,caecum,carcinoma,0,2	VAV1	140	.	0			c.G361A						PASS	.						85	74	78					19																	6821672		2203	4300	6503	SO:0001583	missense	7409	exon3			CCGATCGCCCAGA		CCDS12174.1, CCDS59341.1, CCDS59342.1	19p13.2	2013-02-14	2007-07-25			ENSG00000141968		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12657	protein-coding gene	gene with protein product		164875	"vav 1 oncogene"	VAV		9438848	Standard	NM_005428		Approved		uc010xjh.2	P15498		ENST00000602142.1:c.361G>A	chr19.hg19:g.6821672G>A	ENSP00000472929:p.Ala121Thr	80.0	1.0	.		127.0	43.0	.	NM_005428	B4DVK9|M0QXX6|Q15860	Missense_Mutation	SNP	ENST00000602142.1	hg19	CCDS12174.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.189377	0.78789	.	.	ENSG00000141968	ENST00000304076;ENST00000539284	T;T	0.61274	0.12;0.12	4.34	4.34	0.51931	Calponin homology domain (2);	0.000000	0.85682	D	0.000000	T	0.71400	0.3335	L	0.60845	1.875	0.54753	D	0.999986	D;D;D;P	0.89917	1.0;1.0;0.972;0.917	D;D;P;P	0.87578	0.998;0.997;0.691;0.486	T	0.73418	-0.3989	10	0.54805	T	0.06	.	14.377	0.66884	0.0:0.0:1.0:0.0	.	56;121;66;121	F5H5P4;B2R8B5;Q96D37;P15498	.;.;.;VAV_HUMAN	T	121;56	ENSP00000302269:A121T;ENSP00000443242:A56T	ENSP00000302269:A121T	A	+	1	0	VAV1	6772672	1.000000	0.71417	0.939000	0.37840	0.766000	0.43426	5.226000	0.65299	2.256000	0.74724	0.561000	0.74099	GCC	.	.	.	none		0.632	VAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458475.1			A	6821672	G	A	6821672	3	1	182	1	0	0	0	0	1	0	0	0	17143	1087	38	1	371	1	VAV1	19	6821672	Missense_Mutation	SNP	G	TCGA-G7-A8LE-01A-11D-A35Z-10		6821672	52307311	65	10660											
MUC16	94025	hgsc.bcm.edu	37	chr19	8961960	8961960	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccttgctcaccaggacacCgcagatcaggcatgtgatga	10	9	10	12	1	2	3	2	2	0	1	3	4	3	4	3	2	1	3	3	2	0	2	rs200653636		TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr19:8961960C>T	ENST00000397910.4	-	83	43620	c.43417G>A	c.(43417-43419)Ggt>Agt	p.G14473S	MUC16_ENST00000380951.5_Missense_Mutation_p.G1114S	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	22118	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						ACCAGGACACCGCAGATCAGG	0.488													C|||	1	0.000199681	0	0.0014	5008	,	,		14224	0		0	False		,,,				2504	0				p.G14473S		Atlas-SNP	.											.	MUC16	4315	.	0			c.G43417A						PASS	.	T	SER/GLY	8,3914		0,8,1953	64	62	62		43417	1.3	0	19		62	1,8319		0,1,4159	yes	missense	MUC16	NM_024690.2	56	0,9,6112	TT,TC,CC		0.012,0.204,0.0735	probably-damaging	14473/14508	8961960	9,12233	1961	4160	6121	SO:0001583	missense	94025	exon83			GGACACCGCAGAT	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.43417G>A	chr19.hg19:g.8961960C>T	ENSP00000381008:p.Gly14473Ser	119.0	0.0	.		166.0	49.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	4.878	0.163110	0.09287	0.00204	1.2E-4	ENSG00000181143	ENST00000397910;ENST00000380951	T	0.01745	4.66	4.6	1.3	0.21679	.	.	.	.	.	T	0.01254	0.0041	N	0.14661	0.345	.	.	.	P;D	0.62365	0.645;0.991	B;P	0.44732	0.077;0.459	T	0.49735	-0.8908	8	0.13853	T	0.58	.	5.8157	0.18492	0.5313:0.3158:0.0:0.1529	.	22118;14473	Q8WXI7;B5ME49	MUC16_HUMAN;.	S	14473;1114	ENSP00000381008:G14473S	ENSP00000370338:G1114S	G	-	1	0	MUC16	8822960	0.824000	0.29247	0.012000	0.15200	0.002000	0.02628	1.549000	0.36212	0.064000	0.16427	-1.203000	0.01651	GGT	.	.	.	weak		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	8961960	C	T	8961960	3	4	182	1	0	0	0	0	1	0	0	0	9980	652	23	1	114	1	MUC16	19	8961960	Missense_Mutation	SNP	C	TCGA-G7-A8LE-01A-11D-A35Z-10	2140288	8961960	50167023	66	10661											
DPF1	8193	hgsc.bcm.edu	37	chr19	38704380	38704380	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtcatgttcaccgtgaattgTaaacacgaggggtgtcctgg	9	11	13	8	2	2	1	2	1	0	0	3	2	3	1	2	3	1	2	2	3	3	3			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr19:38704380T>C	ENST00000420980.2	-	9	890	c.864A>G	c.(862-864)ttA>ttG	p.L288L	DPF1_ENST00000416611.1_Silent_p.L306L|DPF1_ENST00000414789.1_Silent_p.L250L|DPF1_ENST00000456296.1_Silent_p.L306L|DPF1_ENST00000355526.4_Silent_p.L332L|DPF1_ENST00000412732.1_Silent_p.L250L	NM_004647.2	NP_004638.2	Q92782	DPF1_HUMAN	D4, zinc and double PHD fingers family 1	288					apoptotic process (GO:0006915)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nBAF complex (GO:0071565)	zinc ion binding (GO:0008270)			large_intestine(1)|lung(4)|ovary(1)|skin(1)	7	all_cancers(60;1.24e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CCGTGAATTGTAAACACGAGG	0.637																																					p.L332L		Atlas-SNP	.											.	DPF1	54	.	0			c.A996G						PASS	.						51	47	48					19																	38704380		2203	4300	6503	SO:0001819	synonymous_variant	8193	exon10			GAATTGTAAACAC	U43843	CCDS33008.2, CCDS46064.1, CCDS46065.1	19q13.12	2013-01-28			ENSG00000011332	ENSG00000011332		"Zinc fingers, PHD-type"	20225	protein-coding gene	gene with protein product		601670				8812431	Standard	XM_005259288		Approved	neuro-d4, NEUD4, BAF45b	uc002ohm.3	Q92782	OTTHUMG00000157164	ENST00000420980.2:c.864A>G	chr19.hg19:g.38704380T>C		127.0	0.0	.		152.0	58.0	.	NM_001135155	B3KSY8|Q08AJ0	Silent	SNP	ENST00000420980.2	hg19	CCDS33008.2	.	.	.	.	.	.	.	.	.	.	T	9.663	1.144758	0.21288	.	.	ENSG00000011332	ENST00000355526	.	.	.	4.04	1.9	0.25705	.	.	.	.	.	T	0.51176	0.1659	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35724	-0.9777	4	.	.	.	0.8287	4.4001	0.11383	0.0:0.1899:0.1719:0.6382	.	.	.	.	A	325	.	.	T	-	1	0	DPF1	43396220	1.000000	0.71417	0.999000	0.59377	0.965000	0.64279	1.619000	0.36965	0.135000	0.18707	0.369000	0.22263	ACA	.	.	.	none		0.637	DPF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347721.1			C	38704380	T	C	38704380	2	2	182	1	0	0	0	0	0	0	0	1	4718	1635	57	3		3	DPF1	19	38704380	Silent	SNP	T	TCGA-G7-A8LE-01A-11D-A35Z-10	29742420	38704380	20424603	67	10662											
CACNG8	59283	hgsc.bcm.edu	37	chr19	54485656	54485656	+	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	cgccgccgctcccgctctagCtcccgctccagcgagccgtc	3	6	10	22	7	1	0	0	0	1	0	5	1	4	0	6	0	3	4	6	0	1	1			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr19:54485656C>G	ENST00000270458.2	+	4	934	c.831C>G	c.(829-831)agC>agG	p.S277R	MIR935_ENST00000401179.1_RNA	NM_031895.5	NP_114101	Q8WXS5	CCG8_HUMAN	calcium channel, voltage-dependent, gamma subunit 8	277	Gly-rich.				calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			kidney(1)|large_intestine(3)|lung(8)|urinary_tract(1)	13	all_cancers(19;0.0385)|all_epithelial(19;0.0207)|all_lung(19;0.145)|Lung NSC(19;0.168)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.162)		CCCGCTCTAGCTCCCGCTCCA	0.766																																					p.S277R		Atlas-SNP	.											.	CACNG8	29	.	0			c.C831G						PASS	.						1	2	2					19																	54485656		1151	2686	3837	SO:0001583	missense	59283	exon4			CTCTAGCTCCCGC	AF288388	CCDS33104.1	19q13.4	2008-05-02			ENSG00000142408	ENSG00000142408		"Calcium channel subunits"	13628	protein-coding gene	gene with protein product		606900				11170751	Standard	NM_031895		Approved		uc002qcs.2	Q8WXS5	OTTHUMG00000064908	ENST00000270458.2:c.831C>G	chr19.hg19:g.54485656C>G	ENSP00000270458:p.Ser277Arg	19.0	0.0	.		22.0	7.0	.	NM_031895	Q9BXT0|Q9BY23	Missense_Mutation	SNP	ENST00000270458.2	hg19	CCDS33104.1	.	.	.	.	.	.	.	.	.	.	.	16.54	3.152958	0.57259	.	.	ENSG00000142408	ENST00000270458	T	0.53206	0.63	2.34	2.34	0.29019	.	0.139963	0.43110	U	0.000614	T	0.51873	0.1700	M	0.66297	2.02	0.33300	D	0.564723	D	0.59357	0.985	P	0.54889	0.763	T	0.61068	-0.7137	9	0.42905	T	0.14	.	5.3399	0.15979	0.0:0.8181:0.0:0.1819	.	277	Q8WXS5	CCG8_HUMAN	R	277	ENSP00000270458:S277R	ENSP00000270458:S277R	S	+	3	2	CACNG8	59177468	0.976000	0.34144	0.998000	0.56505	0.938000	0.57974	0.117000	0.15583	0.998000	0.38996	0.281000	0.19383	AGC	.	.	.	none		0.766	CACNG8-001	KNOWN	non_ATG_start|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139361.3			G	54485656	C	G	54485656	3	3	182	1	0	0	0	0	1	0	0	0	2565	796	28	4	845	4	CACNG8	19	54485656	Missense_Mutation	SNP	C	TCGA-G7-A8LE-01A-11D-A35Z-10	15781276	54485656	4643327	68	10663											
ZNF582	147948	hgsc.bcm.edu	37	chr19	56896344	56896344	+	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	ctggtcaaaagtgggcatttCttcatgtctgatgatcatct	9	15	9	8	0	6	2	3	2	3	0	6	2	6	2	0	2	0	1	0	2	2	2			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr19:56896344C>G	ENST00000301310.4	-	5	600	c.442G>C	c.(442-444)Gaa>Caa	p.E148Q	ZNF582_ENST00000586929.1_Missense_Mutation_p.E148Q|AC006116.12_ENST00000589671.1_RNA	NM_144690.1	NP_653291.1	Q96NG8	ZN582_HUMAN	zinc finger protein 582	148					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			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)		GTGGGCATTTCTTCATGTCTG	0.373																																					p.E148Q	Ovarian(183;1887 2032 4349 30507 51343)	Atlas-SNP	.											.	ZNF582	56	.	0			c.G442C						PASS	.						150	148	149					19																	56896344		2203	4300	6503	SO:0001583	missense	147948	exon5			GCATTTCTTCATG	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.442G>C	chr19.hg19:g.56896344C>G	ENSP00000301310:p.Glu148Gln	65.0	0.0	.		86.0	38.0	.	NM_144690	B4DQZ9|B7Z9R3|Q6PJT6	Missense_Mutation	SNP	ENST00000301310.4	hg19	CCDS33121.1	.	.	.	.	.	.	.	.	.	.	C	15.13	2.741982	0.49151	.	.	ENSG00000018869	ENST00000301310	T	0.06218	3.33	4.23	0.936	0.19488	.	0.214881	0.23477	N	0.047757	T	0.03053	0.0090	L	0.28054	0.825	0.09310	N	1	P;P	0.44877	0.845;0.845	B;B	0.36719	0.169;0.231	T	0.43653	-0.9378	10	0.15499	T	0.54	.	4.4024	0.11393	0.1595:0.5801:0.0:0.2603	.	148;179	Q96NG8;B4DQZ9	ZN582_HUMAN;.	Q	148	ENSP00000301310:E148Q	ENSP00000301310:E148Q	E	-	1	0	ZNF582	61588156	0.668000	0.27493	0.003000	0.11579	0.259000	0.26198	0.385000	0.20685	0.318000	0.23185	-0.282000	0.10007	GAA	.	.	.	none		0.373	ZNF582-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458387.2	NM_144690		G	56896344	C	G	56896344	3	3	182	1	0	0	0	0	1	0	0	0	18026	922	32	4	1115	4	ZNF582	19	56896344	Missense_Mutation	SNP	C	TCGA-G7-A8LE-01A-11D-A35Z-10	2410688	56896344	2232639	69	10664											
JAG1	182	hgsc.bcm.edu	37	chr20	10620302	10620302	+	Frame_Shift_Del	DEL	T	T	-																															ggctgcttggcaaaccgggcTttctgctggtgtttgtccat																										TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr20:10620302delT	ENST00000254958.5	-	26	4016	c.3501delA	c.(3499-3501)aaafs	p.K1167fs	JAG1_ENST00000423891.2_Frame_Shift_Del_p.K1008fs	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	1167					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						CAAACCGGGCTTTCTGCTGGT	0.493									Alagille Syndrome																												p.A1168fs		Atlas-Indel,Pindel	.											.	JAG1	213	.	0			c.3502delG						PASS	.						174	175	175					20																	10620302		2203	4300	6503	SO:0001589	frameshift_variant	182	exon26	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	.	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"CD molecules"	6188	protein-coding gene	gene with protein product		601920	"Alagille syndrome"	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.3501delA	chr20.hg19:g.10620302delT	ENSP00000254958:p.Lys1167fs	108.0	0.0	0		161.0	75.0	0.465839	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Frame_Shift_Del	DEL	ENST00000254958.5	hg19	CCDS13112.1																																																																																			.	.	.	none		0.493	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214		-	10620302	T	-	10620302	7	5	182	1	0	1	0	1	0	0	0	0	7941	1606	56	0	159	0	JAG1	20	10620302	Frame_Shift_Del	DEL	T	TCGA-G7-A8LE-01A-11D-A35Z-10		10620302	52405218	70	10665											
ABHD12	26090	hgsc.bcm.edu	37	chr20	25282895	25282895	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggctcttgtaaatgtattTgtgcctgtagccaaggtctg	8	14	12	7	0	2	0	0	0	2	0	2	0	2	0	2	2	2	4	2	2	5	5			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr20:25282895T>C	ENST00000339157.5	-	12	1389	c.1117A>G	c.(1117-1119)Aaa>Gaa	p.K373E	ABHD12_ENST00000376542.3_Missense_Mutation_p.K373E	NM_001042472.2	NP_001035937.1	Q8N2K0	ABD12_HUMAN	abhydrolase domain containing 12	373					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						TAAATGTATTTGTGCCTGTAG	0.537																																					p.K373E		Atlas-SNP	.											.	ABHD12	46	.	0			c.A1117G						PASS	.						132	118	122					20																	25282895		2203	4300	6503	SO:0001583	missense	26090	exon12			TGTATTTGTGCCT	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.1117A>G	chr20.hg19:g.25282895T>C	ENSP00000341408:p.Lys373Glu	70.0	0.0	.		90.0	38.0	.	NM_001042472	A6NED4|A6NJ90|A8K450|B4DE71|Q5T710|Q5T711|Q96CR1|Q9BX05|Q9NPX7|Q9UFV6	Missense_Mutation	SNP	ENST00000339157.5	hg19	CCDS42857.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.416495	0.83449	.	.	ENSG00000100997	ENST00000376542;ENST00000339157;ENST00000526543	T;T	0.19938	2.11;2.11	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.42720	0.1215	M	0.75264	2.295	0.80722	D	1	P;D;D	0.71674	0.745;0.996;0.998	P;P;D	0.63283	0.475;0.82;0.913	T	0.26121	-1.0112	10	0.30854	T	0.27	-20.5607	14.6085	0.68498	0.0:0.0:0.0:1.0	.	335;373;373	Q8N2K0-3;Q8N2K0;Q8N2K0-2	.;ABD12_HUMAN;.	E	373;373;335	ENSP00000365725:K373E;ENSP00000341408:K373E	ENSP00000341408:K373E	K	-	1	0	ABHD12	25230895	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	7.218000	0.77991	2.116000	0.64780	0.459000	0.35465	AAA	.	.	.	none		0.537	ABHD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078423.2	NM_015600		C	25282895	T	C	25282895	3	2	182	1	0	0	0	0	1	0	0	0	76	1821	63	3	149	3	ABHD12	20	25282895	Missense_Mutation	SNP	T	TCGA-G7-A8LE-01A-11D-A35Z-10	14662593	25282895	37742625	71	10666											
C22orf29	79680	hgsc.bcm.edu	37	chr22	19839753	19839753	+	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	ctgcccagatgggaatgcgaGggccctgctgacggcaccgg	7	5	16	13	3	0	2	0	1	0	1	0	4	0	3	3	4	3	2	3	4	1	0			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr22:19839753G>T	ENST00000405640.1	-	2	700	c.32C>A	c.(31-33)cCt>cAt	p.P11H	GNB1L_ENST00000329517.6_Intron|C22orf29_ENST00000407472.1_Missense_Mutation_p.P11H|GNB1L_ENST00000405009.1_Intron|GNB1L_ENST00000460402.1_Intron|C22orf29_ENST00000484072.1_Intron|C22orf29_ENST00000328554.4_Missense_Mutation_p.P11H|GNB1L_ENST00000403325.1_Intron			Q7L3V2	BOP_HUMAN	chromosome 22 open reading frame 29	11					mitochondrial outer membrane permeabilization (GO:0097345)|regulation of mitochondrial membrane potential (GO:0051881)	mitochondrion (GO:0005739)				NS(1)|large_intestine(1)|lung(3)|prostate(1)|urinary_tract(1)	7	Colorectal(54;0.0993)					GGGAATGCGAGGGCCCTGCTG	0.637																																					p.P11H		Atlas-SNP	.											.	C22orf29	23	.	0			c.C32A						PASS	.						55	55	55					22																	19839753		2203	4298	6501	SO:0001583	missense	79680	exon3			ATGCGAGGGCCCT	BX640998	CCDS13769.1	22q11.21	2006-07-05			ENSG00000215012	ENSG00000215012			26112	protein-coding gene	gene with protein product						12477932	Standard	NM_024627		Approved	FLJ21125	uc002zqh.3	Q7L3V2	OTTHUMG00000030314	ENST00000405640.1:c.32C>A	chr22.hg19:g.19839753G>T	ENSP00000384924:p.Pro11His	85.0	0.0	.		106.0	34.0	.	NM_024627	A8K5E7|D3DX21|Q6MZM8|Q6N000|Q9H7A0	Missense_Mutation	SNP	ENST00000405640.1	hg19	CCDS13769.1	.	.	.	.	.	.	.	.	.	.	G	13.62	2.291328	0.40494	.	.	ENSG00000215012	ENST00000407472;ENST00000328554;ENST00000405640;ENST00000416337	T;T;T;T	0.31769	1.48;1.48;1.48;1.48	3.69	3.69	0.42338	.	.	.	.	.	T	0.33323	0.0859	N	0.08118	0	0.23221	N	0.998095	D	0.89917	1.0	D	0.72625	0.978	T	0.18745	-1.0327	9	0.72032	D	0.01	-8.3753	11.2466	0.49000	0.0:0.0:1.0:0.0	.	11	Q7L3V2	CV029_HUMAN	H	11	ENSP00000386111:P11H;ENSP00000330596:P11H;ENSP00000384924:P11H;ENSP00000392994:P11H	ENSP00000330596:P11H	P	-	2	0	C22orf29	18219753	0.103000	0.21917	0.544000	0.28141	0.013000	0.08279	0.397000	0.20883	2.358000	0.79984	0.655000	0.94253	CCT	.	.	.	none		0.637	C22orf29-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317290.2	NM_024627		T	19839753	G	T	19839753	3	4	182	1	0	0	0	0	1	0	0	0	2143	1000	35	4	1066	4	C22orf29	22	19839753	Missense_Mutation	SNP	G	TCGA-G7-A8LE-01A-11D-A35Z-10		19839753	31464813	72	10667											
SSTR3	6753	hgsc.bcm.edu	37	chr22	37603060	37603060	+	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	agcacgaagagcgccaccacGgccaccaccatgcgcgtgac	11	2	11	17	5	0	2	0	1	0	1	0	3	0	2	5	1	3	1	5	1	1	0	rs144127697		TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chr22:37603060G>T	ENST00000328544.3	-	2	1316	c.783C>A	c.(781-783)gcC>gcA	p.A261A	SSTR3_ENST00000402501.1_Silent_p.A261A	NM_001051.3	NP_001042.1	P32745	SSR3_HUMAN	somatostatin receptor 3	261					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)	GCGCCACCACGGCCACCACCA	0.672																																					p.A261A		Atlas-SNP	.											.	SSTR3	42	.	0			c.C783A						PASS	.						70	57	61					22																	37603060		2203	4300	6503	SO:0001819	synonymous_variant	6753	exon2			CACCACGGCCACC		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.783C>A	chr22.hg19:g.37603060G>T		107.0	0.0	.		146.0	60.0	.	NM_001051	A8K550|Q53ZR7	Silent	SNP	ENST00000328544.3	hg19	CCDS13944.1																																																																																			.	G|1.000;A|0.000	.	alt		0.672	SSTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318802.1			T	37603060	G	T	37603060	2	4	182	1	0	0	0	0	0	0	0	1	15211	1103	39	4		4	SSTR3	22	37603060	Silent	SNP	G	TCGA-G7-A8LE-01A-11D-A35Z-10	17763307	37603060	13701506	73	10668											
HCFC1	3054	hgsc.bcm.edu	37	chrX	153216893	153216893	+	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	cacatcaaaccactggttttCcttcttcatgggggctttgc	7	14	8	12	0	3	0	2	0	1	0	4	0	4	0	2	3	2	2	2	3	1	5			TCGA-G7-A8LE-01A-11D-A35Z-10	TCGA-G7-A8LE-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f304b920-e25e-445a-b834-d54c241d029b	e8d9c96d-cf86-4b29-ba93-23c5e8b4bd28	g.chrX:153216893C>G	ENST00000310441.7	-	22	6391	c.5425G>C	c.(5425-5427)Gaa>Caa	p.E1809Q	HCFC1_ENST00000354233.3_Missense_Mutation_p.E1740Q|HCFC1_ENST00000369984.4_Missense_Mutation_p.E1854Q	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	1809	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)					CACTGGTTTTCCTTCTTCATG	0.542																																					p.E1809Q		Atlas-SNP	.											.	HCFC1	284	.	0			c.G5425C						PASS	.						217	225	222					X																	153216893		2051	4175	6226	SO:0001583	missense	3054	exon22			GGTTTTCCTTCTT		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.5425G>C	chrX.hg19:g.153216893C>G	ENSP00000309555:p.Glu1809Gln	38.0	0.0	.		46.0	33.0	.	NM_005334	Q6P4G5	Missense_Mutation	SNP	ENST00000310441.7	hg19	CCDS44020.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.10|19.10	3.761895|3.761895	0.69763|0.69763	.|.	.|.	ENSG00000172534|ENSG00000172534	ENST00000310441;ENST00000369984;ENST00000354233|ENST00000444191	T;T;T|.	0.03689|.	3.84;3.85;3.85|.	5.55|5.55	5.55|5.55	0.83447|0.83447	Fibronectin, type III (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74114|0.74114	0.3674|0.3674	M|M	0.68952|0.68952	2.095|2.095	0.47374|0.47374	D|D	0.999402|0.999402	D|.	0.64830|.	0.994|.	P|.	0.56960|.	0.81|.	T|T	0.73244|0.73244	-0.4044|-0.4044	10|5	0.41790|.	T|.	0.15|.	.|.	17.327|17.327	0.87251|0.87251	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1809|.	P51610|.	HCFC1_HUMAN|.	Q|A	1809;1854;1740|384	ENSP00000309555:E1809Q;ENSP00000359001:E1854Q;ENSP00000346174:E1740Q|.	ENSP00000309555:E1809Q|.	E|G	-|-	1|2	0|0	HCFC1|HCFC1	152870087|152870087	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.703000|0.703000	0.40648|0.40648	7.328000|7.328000	0.79160|0.79160	2.359000|2.359000	0.80004|0.80004	0.525000|0.525000	0.51046|0.51046	GAA|GGA	.	.	.	none		0.542	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061099.4	NM_005334		G	153216893	C	G	153216893	3	3	182	1	0	0	0	0	1	0	0	0	6998	864	30	4	702	4	HCFC1	23	153216893	Missense_Mutation	SNP	C	TCGA-G7-A8LE-01A-11D-A35Z-10		153216893	2053667	74	10669											
EPHB2	2048	hgsc.bcm.edu	37	chr1	23234542	23234542	+	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	cagacatgaactatgttcacCgtgacctggctgcccgcaac	10	8	9	14	2	1	3	1	2	0	1	1	3	1	3	3	1	3	3	3	1	3	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr1:23234542C>A	ENST00000400191.3	+	12	2251	c.2233C>A	c.(2233-2235)Cgt>Agt	p.R745S	EPHB2_ENST00000374627.1_Missense_Mutation_p.R740S|EPHB2_ENST00000374632.3_Missense_Mutation_p.R746S|EPHB2_ENST00000374630.3_Missense_Mutation_p.R745S	NM_004442.6|NM_017449.3	NP_004433.2|NP_059145.2	P29323	EPHB2_HUMAN	EPH receptor B2	745	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.R745C(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)		CTATGTTCACCGTGACCTGGC	0.557																																					p.R746S		Atlas-SNP	.											EPHB2,NS,carcinoma,-1,1	EPHB2	257	.	1	Substitution - Missense(1)	stomach(1)	c.C2236A						PASS	.						188	166	173					1																	23234542		2203	4300	6503	SO:0001583	missense	2048	exon12			GTTCACCGTGACC	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.2233C>A	chr1.hg19:g.23234542C>A	ENSP00000383053:p.Arg745Ser	199.0	1.0	.		140.0	6.0	.	NM_004442	O43477|Q5T0U6|Q5T0U7|Q5T0U8	Missense_Mutation	SNP	ENST00000400191.3	hg19		.	.	.	.	.	.	.	.	.	.	C	25.9	4.681019	0.88542	.	.	ENSG00000133216	ENST00000374625;ENST00000374630;ENST00000400191;ENST00000374632;ENST00000374627	T;T;T;T	0.74842	-0.88;-0.88;-0.88;-0.88	5.32	4.37	0.52481	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.89643	0.6774	H	0.95504	3.68	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.91974	0.5589	10	0.87932	D	0	.	14.3622	0.66779	0.1478:0.8522:0.0:0.0	.	687;745;763;746	A6NJM0;P29323;Q4LE53;P29323-3	.;EPHB2_HUMAN;.;.	S	687;745;745;746;740	ENSP00000363761:R745S;ENSP00000383053:R745S;ENSP00000363763:R746S;ENSP00000363758:R740S	ENSP00000363755:R687S	R	+	1	0	EPHB2	23107129	1.000000	0.71417	0.997000	0.53966	0.870000	0.49936	5.909000	0.69923	2.778000	0.95560	0.650000	0.86243	CGT	.	.	.	none		0.557	EPHB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000008060.2	NM_017449		A	23234542	C	A	23234542	3	1	183	1	0	0	0	0	1	0	0	0	5177	652	23	4	2282	4	EPHB2	1	23234542	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08		23234542	226016079	1	10670											
AGL	178	hgsc.bcm.edu	37	chr1	100346675	100346675	+	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	tccaagtactacaattgtttCtatggcatgttgtgctagtg	9	16	9	7	0	1	0	0	0	1	0	2	0	2	0	1	1	3	5	1	1	6	7			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr1:100346675C>G	ENST00000294724.4	+	15	2421	c.1943C>G	c.(1942-1944)tCt>tGt	p.S648C	AGL_ENST00000361302.3_Missense_Mutation_p.S632C|AGL_ENST00000370165.3_Missense_Mutation_p.S648C|AGL_ENST00000361522.4_Missense_Mutation_p.S631C|AGL_ENST00000370163.3_Missense_Mutation_p.S648C|AGL_ENST00000370161.2_Missense_Mutation_p.S632C|AGL_ENST00000361915.3_Missense_Mutation_p.S648C	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	648					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)		ACAATTGTTTCTATGGCATGT	0.368																																					p.S648C		Atlas-SNP	.											.	AGL	137	.	0			c.C1943G						PASS	.						180	165	170					1																	100346675		2203	4300	6503	SO:0001583	missense	178	exon15			TTGTTTCTATGGC	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.1943C>G	chr1.hg19:g.100346675C>G	ENSP00000294724:p.Ser648Cys	104.0	0.0	.		96.0	44.0	.	NM_000644	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Missense_Mutation	SNP	ENST00000294724.4	hg19	CCDS759.1	.	.	.	.	.	.	.	.	.	.	C	13.83	2.355191	0.41700	.	.	ENSG00000162688	ENST00000361915;ENST00000370165;ENST00000370163;ENST00000294724;ENST00000361302;ENST00000370161;ENST00000361522	D;D;D;D;D;D;D	0.84516	-1.86;-1.86;-1.86;-1.86;-1.86;-1.86;-1.86	6.01	6.01	0.97437	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.049923	0.85682	D	0.000000	D	0.89681	0.6785	M	0.62723	1.935	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.998	D;D;D	0.72625	0.978;0.978;0.95	D	0.90138	0.4211	10	0.87932	D	0	.	15.6295	0.76893	0.0:0.9327:0.0:0.0673	.	631;632;648	P35573-2;P35573-3;P35573	.;.;GDE_HUMAN	C	648;648;648;648;632;632;631	ENSP00000355106:S648C;ENSP00000359184:S648C;ENSP00000359182:S648C;ENSP00000294724:S648C;ENSP00000354971:S632C;ENSP00000359180:S632C;ENSP00000354635:S631C	ENSP00000294724:S648C	S	+	2	0	AGL	100119263	1.000000	0.71417	0.805000	0.32314	0.062000	0.15995	5.550000	0.67268	2.850000	0.98022	0.655000	0.94253	TCT	.	.	.	none		0.368	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028		G	100346675	C	G	100346675	3	3	183	1	0	0	0	0	1	0	0	0	384	913	32	4	2066	4	AGL	1	100346675	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08	77112133	100346675	148903946	2	10671											
BAT2L2	23215	hgsc.bcm.edu	37	chr1	171535917	171535917	+	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	aggagactaaagcagtctcaGaaatgtctactgaaatagga	17	8	10	6	0	2	3	1	1	2	2	3	5	2	4	0	2	2	1	0	2	6	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr1:171535917G>A	ENST00000338920.4	+	22	6724	c.6487G>A	c.(6487-6489)Gaa>Aaa	p.E2163K	PRRC2C_ENST00000426496.2_Missense_Mutation_p.E2163K|PRRC2C_ENST00000367742.3_Missense_Mutation_p.E2165K|PRRC2C_ENST00000392078.3_Missense_Mutation_p.E2165K	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	2163					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										AGCAGTCTCAGAAATGTCTAC	0.448																																					p.E2163K		Atlas-SNP	.											.	.	.	.	0			c.G6487A						PASS	.						77	69	71					1																	171535917		2203	4300	6503	SO:0001583	missense	23215	exon22			GTCTCAGAAATGT	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.6487G>A	chr1.hg19:g.171535917G>A	ENSP00000343629:p.Glu2163Lys	49.0	0.0	.		37.0	11.0	.	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	hg19	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	G	18.45	3.627687	0.66901	.	.	ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080	T;T;T;T	0.03124	4.25;4.04;4.27;4.27	5.6	5.6	0.85130	.	0.000000	0.46145	D	0.000303	T	0.10551	0.0258	L	0.59436	1.845	0.58432	D	0.999995	D	0.89917	1.0	D	0.85130	0.997	T	0.12372	-1.0550	10	0.36615	T	0.2	.	19.6251	0.95674	0.0:0.0:1.0:0.0	.	2163	Q9Y520-4	.	K	2165;2117;2163;2165;2163;1920	ENSP00000375928:E2165K;ENSP00000410219:E2163K;ENSP00000356716:E2165K;ENSP00000343629:E2163K	ENSP00000343629:E2163K	E	+	1	0	PRRC2C	169802541	1.000000	0.71417	0.992000	0.48379	0.510000	0.34073	9.236000	0.95360	2.636000	0.89361	0.655000	0.94253	GAA	.	.	.	none		0.448	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		A	171535917	G	A	171535917	3	1	183	1	0	0	0	0	1	0	0	0	1321	943	33	2	6569	2	BAT2L2	1	171535917	Missense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08	71189242	171535917	77714704	3	10672											
AGT	183	hgsc.bcm.edu	37	chr1	230841797	230841797	+	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	caggcaggcgctctcagtgaAgggcacttgagtcaccgaga	10	6	14	11	2	2	3	2	2	1	1	3	4	2	3	1	3	0	3	1	3	1	1			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr1:230841797A>T	ENST00000366667.4	-	3	1220	c.1006T>A	c.(1006-1008)Ttc>Atc	p.F336I		NM_000029.3	NP_000020.1	P01019	ANGT_HUMAN	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	336					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)		CTCTCAGTGAAGGGCACTTGA	0.562																																					p.F336I		Atlas-SNP	.											.	AGT	62	.	0			c.T1006A						PASS	.						110	104	106					1																	230841797		2203	4300	6503	SO:0001583	missense	183	exon3			CAGTGAAGGGCAC	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.1006T>A	chr1.hg19:g.230841797A>T	ENSP00000355627:p.Phe336Ile	146.0	0.0	.		126.0	57.0	.	NM_000029	Q16358|Q16359|Q96F91	Missense_Mutation	SNP	ENST00000366667.4	hg19	CCDS1585.1	.	.	.	.	.	.	.	.	.	.	A	8.200	0.797970	0.16327	.	.	ENSG00000135744	ENST00000366667;ENST00000430091	D	0.84800	-1.9	5.17	-4.42	0.03579	Serpin domain (3);	0.408163	0.24752	N	0.035897	T	0.66005	0.2746	N	0.14661	0.345	0.09310	N	1	B;B;B	0.26258	0.094;0.145;0.094	B;B;B	0.25140	0.044;0.058;0.044	T	0.54556	-0.8276	10	0.34782	T	0.22	.	7.5483	0.27781	0.1397:0.142:0.6158:0.1025	.	336;336;336	B0ZBE2;B2R5S1;P01019	.;.;ANGT_HUMAN	I	336;254	ENSP00000355627:F336I	ENSP00000355627:F336I	F	-	1	0	AGT	228908420	0.002000	0.14202	0.012000	0.15200	0.007000	0.05969	-0.319000	0.08039	-0.831000	0.04256	-0.250000	0.11733	TTC	.	.	.	none		0.562	AGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092102.1	NM_000029		T	230841797	A	T	230841797	3	4	183	1	0	0	0	0	1	0	0	0	399	72	3	5	463	5	AGT	1	230841797	Missense_Mutation	SNP	A	TCGA-GL-6846-01A-11D-1961-08	59305880	230841797	18408824	4	10673											
PUM2	23369	hgsc.bcm.edu	37	chr2	20518349	20518349	+	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	atcatccccaagaaatatgcCtttttgtccatcttttgttg	9	17	5	10	0	2	1	1	0	1	1	4	1	4	1	4	0	1	1	4	0	3	6			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr2:20518349C>T	ENST00000361078.2	-	2	131	c.109G>A	c.(109-111)Ggc>Agc	p.G37S	PUM2_ENST00000536417.1_Intron|PUM2_ENST00000319801.5_Missense_Mutation_p.G37S|PUM2_ENST00000338086.5_Missense_Mutation_p.G37S|PUM2_ENST00000420234.1_5'UTR|PUM2_ENST00000403432.1_Missense_Mutation_p.G37S			Q8TB72	PUM2_HUMAN	pumilio RNA-binding family member 2	37	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)					AGAAATATGCCTTTTTGTCCA	0.338																																					p.G37S		Atlas-SNP	.											.	PUM2	91	.	0			c.G109A						PASS	.						142	131	135					2																	20518349		2203	4300	6503	SO:0001583	missense	23369	exon2			ATATGCCTTTTTG	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.109G>A	chr2.hg19:g.20518349C>T	ENSP00000354370:p.Gly37Ser	108.0	0.0	.		91.0	35.0	.	NM_015317	B3KSL0|B4E2B6|D6W527|O00234|Q53TV7|Q8WY43|Q9HAN2	Missense_Mutation	SNP	ENST00000361078.2	hg19		.	.	.	.	.	.	.	.	.	.	C	16.75	3.210343	0.58343	.	.	ENSG00000055917	ENST00000338086;ENST00000361078;ENST00000319801;ENST00000403432;ENST00000442400	T;T;T;T	0.21031	2.03;2.31;2.21;2.03	5.74	0.167	0.15006	.	0.151206	0.64402	N	0.000016	T	0.17152	0.0412	L	0.49350	1.555	0.80722	D	1	B;B	0.20459	0.0;0.045	B;B	0.20184	0.001;0.028	T	0.05500	-1.0881	10	0.54805	T	0.06	-0.9827	7.59	0.28015	0.1096:0.6213:0.0:0.2691	.	37;37	B7ZL34;Q8TB72-3	.;.	S	37	ENSP00000338173:G37S;ENSP00000354370:G37S;ENSP00000326746:G37S;ENSP00000385992:G37S	ENSP00000326746:G37S	G	-	1	0	PUM2	20381830	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	3.338000	0.52128	0.071000	0.16664	-0.948000	0.02665	GGC	.	.	.	none		0.338	PUM2-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015317		T	20518349	C	T	20518349	3	4	183	1	0	0	0	0	1	0	0	0	12839	681	24	2	3161	2	PUM2	2	20518349	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08		20518349	222681024	5	10674											
ANKRD44	91526	hgsc.bcm.edu	37	chr2	197986231	197986231	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccattgtagcaggcgatgTgaagcgctgtatttccatag	9	12	12	8	2	0	1	0	1	0	0	2	2	2	1	2	1	2	4	2	1	4	5			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr2:197986231T>C	ENST00000328737.2	-	8	732	c.656A>G	c.(655-657)cAc>cGc	p.H219R	ANKRD44_ENST00000539527.1_Missense_Mutation_p.H172R|ANKRD44_ENST00000409153.1_Missense_Mutation_p.H244R|ANKRD44_ENST00000450567.1_Missense_Mutation_p.H219R|ANKRD44_ENST00000337207.5_Missense_Mutation_p.H219R|ANKRD44_ENST00000282272.8_Missense_Mutation_p.H236R|ANKRD44_ENST00000409919.1_Missense_Mutation_p.H244R			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	244										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)			GCAGGCGATGTGAAGCGCTGT	0.433																																					p.H244R		Atlas-SNP	.											.	ANKRD44	281	.	0			c.A731G						PASS	.						155	117	130					2																	197986231		2203	4300	6503	SO:0001583	missense	91526	exon8			GCGATGTGAAGCG	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.656A>G	chr2.hg19:g.197986231T>C	ENSP00000331516:p.His219Arg	54.0	0.0	.		50.0	18.0	.	NM_153697	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Missense_Mutation	SNP	ENST00000328737.2	hg19		.	.	.	.	.	.	.	.	.	.	T	22.1	4.245633	0.80024	.	.	ENSG00000065413	ENST00000424317;ENST00000282272;ENST00000328737;ENST00000450567;ENST00000337207;ENST00000409153;ENST00000539527;ENST00000409919	T;T;T;T;T;T;T;T	0.79554	-0.56;-0.56;-1.28;-1.28;-1.28;-0.56;-1.28;-1.28	5.14	5.14	0.70334	.	0.105903	0.64402	D	0.000004	D	0.90287	0.6962	M	0.85630	2.765	0.58432	D	0.999999	D;D	0.89917	1.0;0.99	D;D	0.81914	0.995;0.968	D	0.91903	0.5533	10	0.87932	D	0	.	15.4162	0.74970	0.0:0.0:0.0:1.0	.	172;244	F5H682;Q8N8A2-3	.;.	R	41;236;219;219;219;244;172;244	ENSP00000403415:H41R;ENSP00000282272:H236R;ENSP00000331516:H219R;ENSP00000402420:H219R;ENSP00000338794:H219R;ENSP00000387141:H244R;ENSP00000437825:H172R;ENSP00000387233:H244R	ENSP00000282272:H236R	H	-	2	0	ANKRD44	197694476	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	7.825000	0.86693	2.285000	0.76669	0.533000	0.62120	CAC	.	.	.	none		0.433	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697		C	197986231	T	C	197986231	3	2	183	1	0	0	0	0	1	0	0	0	672	1696	59	3	2179	3	ANKRD44	2	197986231	Missense_Mutation	SNP	T	TCGA-GL-6846-01A-11D-1961-08	177467882	197986231	45213142	6	10675											
FZD5	7855	hgsc.bcm.edu	37	chr2	208632800	208632800	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgaaggacggctggtagcAgggtaccgcgcagttgggca	9	6	17	9	3	0	1	0	1	0	0	0	2	0	2	1	5	2	7	1	5	3	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr2:208632800A>G	ENST00000295417.3	-	2	1217	c.664T>C	c.(664-666)Tgc>Cgc	p.C222R		NM_003468.3	NP_003459.2	Q13467	FZD5_HUMAN	frizzled class receptor 5	222					angiogenesis (GO:0001525)|anterior/posterior axis specification, embryo (GO:0008595)|apoptotic process (GO:0006915)|apoptotic process involved in morphogenesis (GO:0060561)|axonogenesis (GO:0007409)|brain development (GO:0007420)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|canonical Wnt signaling pathway (GO:0060070)|cell maturation (GO:0048469)|cellular response to molecule of bacterial origin (GO:0071219)|chorionic trophoblast cell differentiation (GO:0060718)|embryonic axis specification (GO:0000578)|embryonic camera-type eye development (GO:0031076)|gonad development (GO:0008406)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|neuron differentiation (GO:0030182)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic camera-type eye development (GO:0031077)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of chorionic trophoblast cell proliferation (GO:1901382)|regulation of tight junction assembly (GO:2000810)|Spemann organizer formation (GO:0060061)|syncytiotrophoblast cell differentiation involved in labyrinthine layer development (GO:0060715)|T cell differentiation in thymus (GO:0033077)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	cell projection (GO:0042995)|cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			NS(1)|kidney(1)|lung(1)|ovary(2)|prostate(1)|skin(1)	7				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.13)|Lung(261;0.134)		GGCTGGTAGCAGGGTACCGCG	0.632																																					p.C222R		Atlas-SNP	.											.	FZD5	22	.	0			c.T664C						PASS	.						54	52	52					2																	208632800		2203	4300	6503	SO:0001583	missense	7855	exon2			GGTAGCAGGGTAC	U43318	CCDS33366.1	2q33.3	2014-01-29	2014-01-29		ENSG00000163251	ENSG00000163251		"GPCR / Class F : Frizzled receptors"	4043	protein-coding gene	gene with protein product		601723	"frizzled (Drosophila) homolog 5", "chromosome 2 open reading frame 31", "frizzled homolog 5 (Drosophila)", "frizzled 5, seven transmembrane spanning receptor", "frizzled family receptor 5"	C2orf31		8626800, 11408929	Standard	NM_003468		Approved	HFZ5, DKFZP434E2135	uc002vcj.3	Q13467	OTTHUMG00000154790	ENST00000295417.3:c.664T>C	chr2.hg19:g.208632800A>G	ENSP00000354607:p.Cys222Arg	25.0	0.0	.		24.0	11.0	.	NM_003468	A8K2X1|B2RCZ1|Q53R22	Missense_Mutation	SNP	ENST00000295417.3	hg19	CCDS33366.1	.	.	.	.	.	.	.	.	.	.	A	18.80	3.701621	0.68501	.	.	ENSG00000163251	ENST00000295417	D	0.90197	-2.63	5.05	5.05	0.67936	.	0.051032	0.85682	D	0.000000	D	0.94706	0.8292	M	0.74647	2.275	0.80722	D	1	D	0.76494	0.999	D	0.76575	0.988	D	0.95299	0.8402	10	0.87932	D	0	.	14.4703	0.67512	1.0:0.0:0.0:0.0	.	222	Q13467	FZD5_HUMAN	R	222	ENSP00000354607:C222R	ENSP00000354607:C222R	C	-	1	0	FZD5	208341045	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	9.339000	0.96797	1.908000	0.55244	0.459000	0.35465	TGC	.	.	.	none		0.632	FZD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337060.1	NM_003468		G	208632800	A	G	208632800	3	3	183	1	0	0	0	0	1	0	0	0	6140	188	7	3	1097	3	FZD5	2	208632800	Missense_Mutation	SNP	A	TCGA-GL-6846-01A-11D-1961-08	10646569	208632800	34566573	7	10676											
CCDC13	152206	hgsc.bcm.edu	37	chr3	42777251	42777251	+	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	gctgtcgcactttggcctccCgctcagctaccatggcctgc	4	10	10	17	2	1	0	1	0	0	0	3	0	2	0	4	2	3	4	4	2	1	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr3:42777251C>A	ENST00000310232.6	-	10	1402	c.1319G>T	c.(1318-1320)cGg>cTg	p.R440L	CCDC13-AS1_ENST00000446950.1_RNA|CCDC13-AS1_ENST00000418161.1_RNA	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	440										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						TTTGGCCTCCCGCTCAGCTAC	0.602																																					p.R440L		Atlas-SNP	.											.	CCDC13	71	.	0			c.G1319T						PASS	.						119	104	109					3																	42777251		2203	4300	6503	SO:0001583	missense	152206	exon10			GCCTCCCGCTCAG	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.1319G>T	chr3.hg19:g.42777251C>A	ENSP00000309836:p.Arg440Leu	154.0	0.0	.		207.0	11.0	.	NM_144719		Missense_Mutation	SNP	ENST00000310232.6	hg19	CCDS2705.1	.	.	.	.	.	.	.	.	.	.	C	18.80	3.700694	0.68501	.	.	ENSG00000244607	ENST00000310232	T	0.27720	1.65	5.03	5.03	0.67393	.	0.085006	0.47852	D	0.000217	T	0.55353	0.1915	M	0.75447	2.3	0.38311	D	0.943263	D	0.89917	1.0	D	0.76071	0.987	T	0.57207	-0.7851	10	0.30078	T	0.28	.	17.144	0.86761	0.0:1.0:0.0:0.0	.	440	Q8IYE1	CCD13_HUMAN	L	440	ENSP00000309836:R440L	ENSP00000309836:R440L	R	-	2	0	CCDC13	42752255	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	4.131000	0.57970	2.345000	0.79718	0.511000	0.50034	CGG	.	.	.	none		0.602	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719		A	42777251	C	A	42777251	3	1	183	1	0	0	0	0	1	0	0	0	2767	652	23	4	856	4	CCDC13	3	42777251	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08		42777251	155245179	8	10677											
ALS2CL	259173	hgsc.bcm.edu	37	chr3	46713506	46713506	+	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	ccagcacctccagcttctccCgtgggtccaccgtggtcctg	4	9	10	18	2	1	0	0	0	1	0	5	0	4	0	7	2	2	2	7	2	0	1			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr3:46713506C>A	ENST00000318962.4	-	24	2635	c.2552G>T	c.(2551-2553)cGg>cTg	p.R851L	ALS2CL_ENST00000415953.1_Missense_Mutation_p.R851L|ALS2CL_ENST00000383742.3_Missense_Mutation_p.R198L	NM_147129.3	NP_667340.2	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like	851	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				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)		CAGCTTCTCCCGTGGGTCCAC	0.642																																					p.R851L		Atlas-SNP	.											.	ALS2CL	78	.	0			c.G2552T						PASS	.						96	89	92					3																	46713506		2203	4300	6503	SO:0001583	missense	259173	exon24			TTCTCCCGTGGGT	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.2552G>T	chr3.hg19:g.46713506C>A	ENSP00000313670:p.Arg851Leu	160.0	0.0	.		185.0	10.0	.	NM_001190707	Q32MA1|Q6AI56|Q6ZNC5|Q6ZNC7|Q6ZTL4|Q86YD2|Q8N9U1|Q8NAL7	Missense_Mutation	SNP	ENST00000318962.4	hg19	CCDS2743.1	.	.	.	.	.	.	.	.	.	.	C	18.61	3.660329	0.67586	.	.	ENSG00000178038	ENST00000318962;ENST00000415953;ENST00000383742	T;T;T	0.31510	1.49;1.49;1.49	5.29	5.29	0.74685	Vacuolar sorting protein 9 (2);	0.248448	0.27415	N	0.019472	T	0.27524	0.0676	N	0.22421	0.69	0.32113	N	0.589045	P	0.45283	0.855	P	0.48304	0.573	T	0.28138	-1.0053	10	0.51188	T	0.08	.	9.9532	0.41651	0.0:0.9073:0.0:0.0927	.	851	Q60I27	AL2CL_HUMAN	L	851;851;198	ENSP00000313670:R851L;ENSP00000413223:R851L;ENSP00000373248:R198L	ENSP00000313670:R851L	R	-	2	0	ALS2CL	46688510	0.665000	0.27466	0.923000	0.36655	0.988000	0.76386	2.220000	0.42908	2.465000	0.83290	0.650000	0.86243	CGG	.	.	.	none		0.642	ALS2CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250567.3	NM_147129		A	46713506	C	A	46713506	3	1	183	1	0	0	0	0	1	0	0	0	551	652	23	4	321	4	ALS2CL	3	46713506	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08	3936255	46713506	151308924	9	10678											
KIAA1407	57577	hgsc.bcm.edu	37	chr3	113721375	113721375	+	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	tcagctcgttgaattgctctCtcttccatagctagaaaata	11	14	6	10	1	3	2	1	1	2	1	6	2	4	2	1	0	3	4	1	0	6	6			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr3:113721375C>A	ENST00000295878.3	-	12	2135	c.1989G>T	c.(1987-1989)gaG>gaT	p.E663D	KIAA1407_ENST00000545063.1_3'UTR	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	663										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						GAATTGCTCTCTCTTCCATAG	0.318																																					p.E663D		Atlas-SNP	.											.	KIAA1407	80	.	0			c.G1989T						PASS	.						90	83	86					3																	113721375		2202	4299	6501	SO:0001583	missense	57577	exon12			TGCTCTCTCTTCC	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.1989G>T	chr3.hg19:g.113721375C>A	ENSP00000295878:p.Glu663Asp	51.0	0.0	.		108.0	34.0	.	NM_020817	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	hg19	CCDS2977.1	.	.	.	.	.	.	.	.	.	.	C	12.27	1.887102	0.33348	.	.	ENSG00000163617	ENST00000295878	T	0.35048	1.33	5.35	4.48	0.54585	.	1.585750	0.04130	N	0.317747	T	0.61299	0.2336	M	0.71581	2.175	0.80722	D	1	D	0.76494	0.999	D	0.71184	0.972	T	0.35101	-0.9802	10	0.59425	D	0.04	.	9.6228	0.39732	0.0:0.8395:0.0:0.1605	.	663	Q8NCU4	K1407_HUMAN	D	663	ENSP00000295878:E663D	ENSP00000295878:E663D	E	-	3	2	KIAA1407	115204065	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	0.489000	0.22387	1.635000	0.50512	0.655000	0.94253	GAG	.	.	.	none		0.318	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817		A	113721375	C	A	113721375	3	1	183	1	0	0	0	0	1	0	0	0	8236	912	32	4	845	4	KIAA1407	3	113721375	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08	67007869	113721375	84301055	10	10679											
POLQ	10721	hgsc.bcm.edu	37	chr3	121217327	121217327	+	Missense_Mutation	SNP	T	T	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	gagaccttgacgtttaccttTtatggatggccatttgtcga	8	15	10	8	2	0	2	0	1	0	1	1	5	0	3	3	2	1	1	3	2	2	6			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr3:121217327T>G	ENST00000264233.5	-	13	2278	c.2150A>C	c.(2149-2151)aAa>aCa	p.K717T		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	717					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)		CGTTTACCTTTTATGGATGGC	0.453								DNA polymerases (catalytic subunits)																													p.K717T	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.A2150C						PASS	.						164	147	153					3																	121217327		2203	4300	6503	SO:0001583	missense	10721	exon13			TACCTTTTATGGA	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.2150A>C	chr3.hg19:g.121217327T>G	ENSP00000264233:p.Lys717Thr	170.0	0.0	.		221.0	118.0	.	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	hg19	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.369837	0.82573	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.53857	0.6	5.83	5.83	0.93111	.	0.049703	0.85682	D	0.000000	T	0.69584	0.3127	M	0.85945	2.785	0.49582	D	0.999802	D	0.57257	0.979	P	0.58130	0.833	T	0.75199	-0.3402	10	0.87932	D	0	.	10.5218	0.44922	0.0:0.072:0.0:0.928	.	717	O75417	DPOLQ_HUMAN	T	340;717;853	ENSP00000264233:K717T	ENSP00000264233:K717T	K	-	2	0	POLQ	122700017	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.866000	0.69590	2.212000	0.71576	0.533000	0.62120	AAA	.	.	.	none		0.453	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		G	121217327	T	G	121217327	3	3	183	1	0	0	0	0	1	0	0	0	12215	1841	64	5	5694	5	POLQ	3	121217327	Missense_Mutation	SNP	T	TCGA-GL-6846-01A-11D-1961-08	7495952	121217327	76805103	11	10680											
IQCJ	654502	hgsc.bcm.edu	37	chr3	158980472	158980472	+	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	ttctccgacagcagcacaccCgtgagtgtcatgtttctttt	7	14	8	12	2	3	1	1	1	2	0	4	2	3	1	2	0	2	3	2	0	0	4			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr3:158980472C>A	ENST00000451172.1	+	4	396	c.291C>A	c.(289-291)ccC>ccA	p.P97P	IQCJ_ENST00000482126.1_Splice_Site_p.P70P|IQCJ-SCHIP1_ENST00000485419.1_Splice_Site_p.P97P|IQCJ-SCHIP1_ENST00000476809.1_Splice_Site_p.P70P|IQCJ-SCHIP1_ENST00000467442.1_3'UTR|IQCJ_ENST00000397832.2_Silent_p.P97P	NM_001042705.2	NP_001036170.1	Q1A5X6	IQCJ_HUMAN	IQ motif containing J	97										cervix(1)|endometrium(2)|large_intestine(2)|lung(10)	15			LUSC - Lung squamous cell carcinoma(72;0.00523)|Lung(72;0.00534)			GCAGCACACCCGTGAGTGTCA	0.517																																					p.P97P		Atlas-SNP	.											IQCJ-SCHIP1,NS,carcinoma,0,2	IQCJ	28	.	0			c.C291A						PASS	.						114	113	113					3																	158980472		2005	4175	6180	SO:0001630	splice_region_variant	654502	exon4			CACACCCGTGAGT	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+1C>A	chr3.hg19:g.158980472C>A		151.0	0.0	.		172.0	7.0	.	NM_001042705	B7ZMM2|B9EH97|Q1A5X5	Silent	SNP	ENST00000451172.1	hg19	CCDS46946.1																																																																																			.	.	.	none		0.517	IQCJ-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352395.1	NM_001042705.1	Silent	A	158980472	C	A	158980472	5	1	183	1	0	0	0	0	0	0	1	0	7819	666	23	4	305	4	IQCJ	3	158980472	Splice_Site	SNP	C	TCGA-GL-6846-01A-11D-1961-08	37763145	158980472	39041958	12	10681											
SEC62	7095	hgsc.bcm.edu	37	chr3	169706125	169706125	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgcaggctgttttgtagcCagtattcttctccttgctgt	4	17	11	9	0	2	0	0	0	2	0	3	0	2	0	2	2	3	6	2	2	2	7			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr3:169706125C>T	ENST00000337002.4	+	7	766	c.708C>T	c.(706-708)gcC>gcT	p.A236A	SEC62_ENST00000470355.1_3'UTR|SEC62_ENST00000480708.1_Silent_p.A236A|SEC62-AS1_ENST00000479626.1_RNA	NM_003262.3	NP_003253.1	Q99442	SEC62_HUMAN	SEC62 homolog (S. cerevisiae)	236					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						GTTTTGTAGCCAGTATTCTTC	0.433																																					p.A236A		Atlas-SNP	.											.	SEC62	27	.	0			c.C708T						PASS	.						208	189	195					3																	169706125		2203	4300	6503	SO:0001819	synonymous_variant	7095	exon7			TGTAGCCAGTATT	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.708C>T	chr3.hg19:g.169706125C>T		150.0	0.0	.		180.0	49.0	.	NM_003262	D3DNQ0|O00682|O00729	Silent	SNP	ENST00000337002.4	hg19	CCDS3210.1																																																																																			.	.	.	none		0.433	SEC62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352043.1			T	169706125	C	T	169706125	2	4	183	1	0	0	0	0	0	0	0	1	14017	581	21	2		2	SEC62	3	169706125	Silent	SNP	C	TCGA-GL-6846-01A-11D-1961-08	10725653	169706125	28316305	13	10682											
ACAP2	23527	hgsc.bcm.edu	37	chr3	195006526	195006526	+	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	ttattagtagaatattgaccTggctgtccataaagtccttc	11	15	7	8	0	0	2	0	1	0	1	3	2	2	2	3	1	0	2	3	1	7	7			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr3:195006526T>C	ENST00000326793.6	-	22	2465	c.2235A>G	c.(2233-2235)ccA>ccG	p.P745P		NM_012287.5	NP_036419.3	Q15057	ACAP2_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	745					cellular response to nerve growth factor stimulus (GO:1990090)|protein localization to endosome (GO:0036010)|regulation of ARF GTPase activity (GO:0032312)	endosome membrane (GO:0010008)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	27						AATATTGACCTGGCTGTCCAT	0.313																																					p.P745P		Atlas-SNP	.											.	ACAP2	72	.	0			c.A2235G						PASS	.						131	120	124					3																	195006526		2203	4299	6502	SO:0001630	splice_region_variant	23527	exon22			TTGACCTGGCTGT		CCDS33924.1	3q29	2013-01-10	2008-09-22	2008-09-22	ENSG00000114331	ENSG00000114331		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16469	protein-coding gene	gene with protein product		607766	"centaurin, beta 2"	CENTB2		11050434, 11062263	Standard	NM_012287		Approved	KIAA0041, CNT-B2	uc003fun.4	Q15057	OTTHUMG00000155885	ENST00000326793.6:c.2236+1A>G	chr3.hg19:g.195006526T>C		63.0	0.0	.		81.0	15.0	.	NM_012287	A8K2V4|Q8N5Z8|Q9UQR3	Silent	SNP	ENST00000326793.6	hg19	CCDS33924.1																																																																																			.	.	.	none		0.313	ACAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342126.2	NM_012287	Silent	C	195006526	T	C	195006526	5	2	183	1	0	0	0	0	0	0	1	0	119	1594	55	3	109	3	ACAP2	3	195006526	Splice_Site	SNP	T	TCGA-GL-6846-01A-11D-1961-08	25300401	195006526	3015904	14	10683											
LMLN	89782	hgsc.bcm.edu	37	chr3	197687145	197687145	+	Missense_Mutation	SNP	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	cgaatggggcggaggagtggGttactcgggctcaggcccgg	6	6	20	9	4	1	0	1	0	0	0	2	3	1	2	1	8	1	2	1	8	2	1			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr3:197687145G>A	ENST00000330198.4	+	1	75	c.53G>A	c.(52-54)gGt>gAt	p.G18D	IQCG_ENST00000480302.1_5'Flank|IQCG_ENST00000265239.6_5'Flank|LMLN_ENST00000482695.1_Silent_p.G6G|LMLN_ENST00000420910.2_Missense_Mutation_p.G18D|LMLN_ENST00000332636.5_Silent_p.G6G	NM_033029.3	NP_149018.2	Q96KR4	LMLN_HUMAN	leishmanolysin-like (metallopeptidase M8 family)	18					cell adhesion (GO:0007155)|mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)		GGAGGAGTGGGTTACTCGGGC	0.736																																					p.G18D		Atlas-SNP	.											.	LMLN	53	.	0			c.G53A						PASS	.						21	26	25					3																	197687145		2199	4297	6496	SO:0001583	missense	89782	exon1			GAGTGGGTTACTC	AJ312398	CCDS3332.1, CCDS46988.1	3q29	2008-02-04			ENSG00000185621	ENSG00000185621	3.4.24.36		15991	protein-coding gene	gene with protein product		609380					Standard	NM_033029		Approved	Gp63, Msp	uc010iar.3	Q96KR4	OTTHUMG00000155375	ENST00000330198.4:c.53G>A	chr3.hg19:g.197687145G>A	ENSP00000328829:p.Gly18Asp	47.0	0.0	.		61.0	13.0	.	NM_001136049	B3LDG9|B3LDH0|C9J796|F8WB28|Q96KR5	Missense_Mutation	SNP	ENST00000330198.4	hg19	CCDS3332.1	.	.	.	.	.	.	.	.	.	.	G	10.43	1.349097	0.24426	.	.	ENSG00000185621	ENST00000330198;ENST00000420910	T;T	0.45276	0.92;0.9	3.66	0.764	0.18465	.	0.675595	0.12533	N	0.460640	T	0.22044	0.0531	N	0.19112	0.55	0.09310	N	0.999994	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.16012	-1.0417	10	0.36615	T	0.2	-0.6469	2.1617	0.03827	0.1124:0.1977:0.4859:0.204	.	18;18	Q96KR4;F8WB28	LMLN_HUMAN;.	D	18	ENSP00000328829:G18D;ENSP00000410926:G18D	ENSP00000328829:G18D	G	+	2	0	LMLN	199171542	0.000000	0.05858	0.000000	0.03702	0.207000	0.24258	0.016000	0.13377	0.154000	0.19237	0.456000	0.33151	GGT	.	.	.	none		0.736	LMLN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339701.1	NM_033029		A	197687145	G	A	197687145	3	1	183	1	0	0	0	0	1	0	0	0	8854	1261	44	2	55	2	LMLN	3	197687145	Missense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08	2680619	197687145	335285	15	10684											
FRYL	285527	hgsc.bcm.edu	37	chr4	48598002	48598003	+	Frame_Shift_Del	DEL	TT	TT	-																															ttccagtgcaactcgagacaTtttcggatctttattctgtt																										TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr4:48598002_48598003delTT	ENST00000503238.1	-	11	1049_1050	c.1050_1051delAA	c.(1048-1053)aaaatgfs	p.KM350fs	FRYL_ENST00000507711.1_Frame_Shift_Del_p.KM350fs|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000506685.1_Frame_Shift_Del_p.KM56fs|FRYL_ENST00000358350.4_Frame_Shift_Del_p.KM350fs|FRYL_ENST00000537810.1_Frame_Shift_Del_p.KM350fs			O94915	FRYL_HUMAN	FRY-like	350					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						ACTCGAGACATTTTCGGATCTT	0.302																																					p.351_351del		Atlas-INDEL	.											.	FRYL	242	.	0			c.1051_1052del						PASS	.																																			SO:0001589	frameshift_variant	285527	exon14			.	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.1050_1051delAA	chr4.hg19:g.48598004_48598005delTT	ENSP00000426064:p.Lys350fs	54.0	0.0	0		64.0	18.0	0.28125	NM_015030	O95640|Q8WTZ5|Q9NT40	Frame_Shift_Del	DEL	ENST00000503238.1	hg19	CCDS43227.1																																																																																			.	.	.	none		0.302	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			-	48598003	TT	-	48598002	7	5	183	1	0	1	0	1	0	0	0	0	6071	1493	52	0	8194	0	FRYL	4	48598002	Frame_Shift_Del	DEL	TT	TCGA-GL-6846-01A-11D-1961-08		48598002	142556274	16	10685											
TET2	54790	hgsc.bcm.edu	37	chr4	106157461	106157461	+	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	tggaagaatgttttcatggtGaaaatcagtattcaaaatca	16	13	8	4	0	4	2	4	1	0	1	4	3	4	3	0	2	0	2	0	2	7	4			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr4:106157461G>T	ENST00000540549.1	+	3	3222	c.2362G>T	c.(2362-2364)Gaa>Taa	p.E788*	TET2_ENST00000305737.2_Nonsense_Mutation_p.E788*|TET2_ENST00000513237.1_Nonsense_Mutation_p.E809*|TET2_ENST00000380013.4_Nonsense_Mutation_p.E788*|TET2_ENST00000413648.2_Nonsense_Mutation_p.E788*|TET2_ENST00000394764.1_Nonsense_Mutation_p.E788*|TET2_ENST00000545826.1_Nonsense_Mutation_p.E788*			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	788	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)	p.E788K(1)|p.E788*(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)		TTTTCATGGTGAAAATCAGTA	0.393			"Mis N, F"		MDS																																p.E788X		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	TET2,NS,haematopoietic_neoplasm,0,2	TET2	1762	.	2	Substitution - Nonsense(1)|Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(2)	c.G2362T						PASS	.						57	60	59					4																	106157461		2203	4300	6503	SO:0001587	stop_gained	54790	exon3			CATGGTGAAAATC	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.2362G>T	chr4.hg19:g.106157461G>T	ENSP00000442788:p.Glu788*	43.0	0.0	.		49.0	24.0	.	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Nonsense_Mutation	SNP	ENST00000540549.1	hg19	CCDS47120.1	.	.	.	.	.	.	.	.	.	.	G	42	9.661685	0.99231	.	.	ENSG00000168769	ENST00000305737;ENST00000540549;ENST00000545826;ENST00000513237;ENST00000380013;ENST00000394764;ENST00000413648	.	.	.	5.91	5.91	0.95273	.	16.416400	0.00166	N	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	.	20.2985	0.98592	0.0:0.0:1.0:0.0	.	.	.	.	X	788;788;788;809;788;788;788	.	ENSP00000265149:E788X	E	+	1	0	TET2	106376910	1.000000	0.71417	0.997000	0.53966	0.985000	0.73830	4.534000	0.60622	2.793000	0.96121	0.655000	0.94253	GAA	.	.	.	none		0.393	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		T	106157461	G	T	106157461	4	4	183	1	0	0	0	0	0	1	0	0	15782	1291	45	4	2364	4	TET2	4	106157461	Nonsense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08	57559459	106157461	84996815	17	10686											
FAT1	2195	hgsc.bcm.edu	37	chr4	187530418	187530418	+	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	gagcttccttggttgccatcTataattgagtagtggatgtg	8	15	12	6	0	1	1	0	1	1	0	2	3	2	2	2	2	2	3	2	2	3	7			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr4:187530418T>A	ENST00000441802.2	-	16	10334	c.10125A>T	c.(10123-10125)atA>atT	p.I3375I		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	3375	Cadherin 31. {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						GGTTGCCATCTATAATTGAGT	0.478										HNSCC(5;0.00058)																											p.I3375I	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.A10125T						PASS	.						126	121	123					4																	187530418		1933	4136	6069	SO:0001819	synonymous_variant	2195	exon16			GCCATCTATAATT	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.10125A>T	chr4.hg19:g.187530418T>A		73.0	0.0	.		82.0	32.0	.	NM_005245		Silent	SNP	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.	.	none		0.478	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		A	187530418	T	A	187530418	2	1	183	1	0	0	0	0	0	0	0	1	5696	1512	53	5		5	FAT1	4	187530418	Silent	SNP	T	TCGA-GL-6846-01A-11D-1961-08	81372957	187530418	3623858	18	10687											
AGGF1	55109	hgsc.bcm.edu	37	chr5	76344781	76344781	+	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	agaaaaggatatggaacataCtctccgaatccctgaagttg	15	9	9	8	1	1	2	0	1	1	1	3	5	2	4	2	2	2	1	2	2	7	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr5:76344781C>A	ENST00000312916.7	+	8	1716	c.1334C>A	c.(1333-1335)aCt>aAt	p.T445N		NM_018046.4	NP_060516.2	Q8N302	AGGF1_HUMAN	angiogenic factor with G patch and FHA domains 1	445	FHA. {ECO:0000255|PROSITE- ProRule:PRU00086}.				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)		ATGGAACATACTCTCCGAATC	0.294																																					p.T445N		Atlas-SNP	.											.	AGGF1	71	.	0			c.C1334A						PASS	.						97	106	103					5																	76344781		2203	4295	6498	SO:0001583	missense	55109	exon8			AACATACTCTCCG	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.1334C>A	chr5.hg19:g.76344781C>A	ENSP00000316109:p.Thr445Asn	150.0	0.0	.		179.0	82.0	.	NM_018046	O00581|Q53YS3|Q9BU84|Q9NW66	Missense_Mutation	SNP	ENST00000312916.7	hg19	CCDS4035.1	.	.	.	.	.	.	.	.	.	.	C	16.10	3.028459	0.54790	.	.	ENSG00000164252	ENST00000312916	T	0.39592	1.07	4.64	4.64	0.57946	Forkhead-associated (FHA) domain (4);SMAD/FHA domain (1);	0.105294	0.64402	D	0.000003	T	0.41627	0.1167	N	0.17723	0.515	0.80722	D	1	P	0.51653	0.947	P	0.52424	0.698	T	0.36286	-0.9754	10	0.44086	T	0.13	-4.4424	16.8258	0.85930	0.0:1.0:0.0:0.0	.	445	Q8N302	AGGF1_HUMAN	N	445	ENSP00000316109:T445N	ENSP00000316109:T445N	T	+	2	0	AGGF1	76380537	1.000000	0.71417	0.987000	0.45799	0.743000	0.42351	7.194000	0.77789	2.285000	0.76669	0.305000	0.20034	ACT	.	.	.	none		0.294	AGGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219971.2	NM_018046		A	76344781	C	A	76344781	3	1	183	1	0	0	0	0	1	0	0	0	382	565	20	4	1364	4	AGGF1	5	76344781	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08		76344781	104570479	19	10688											
NME5	8382	hgsc.bcm.edu	37	chr5	137474383	137474383	+	Frame_Shift_Del	DEL	C	C	-																															ctaagaataatatcttgtatCtcctcctctttgtcaacaat																										TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr5:137474383delC	ENST00000265191.2	-	2	136	c.87delG	c.(85-87)gagfs	p.E29fs		NM_003551.2	NP_003542.1	P56597	NDK5_HUMAN	NME/NM23 family member 5	29					cilium assembly (GO:0042384)|CTP biosynthetic process (GO:0006241)|epithelial cilium movement (GO:0003351)|GTP biosynthetic process (GO:0006183)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|nucleoside metabolic process (GO:0009116)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)|ventricular system development (GO:0021591)	sperm flagellum (GO:0036126)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)			kidney(1)|large_intestine(1)|lung(2)|skin(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TATCTTGTATCTCCTCCTCTT	0.368																																					p.I30fs		Atlas-INDEL	.											.	NME5	15	.	0			c.88delA						PASS	.						140	128	132					5																	137474383		2203	4300	6503	SO:0001589	frameshift_variant	8382	exon2			.	Y14992	CCDS4197.1	5q31.2	2012-05-18	2012-05-18		ENSG00000112981	ENSG00000112981			7853	protein-coding gene	gene with protein product	"radial spoke 23 homolog (Chlamydomonas)"	603575	"non-metastatic cells 5, protein expressed in (nucleoside-diphosphate kinase)"			9742940, 19852809	Standard	NM_003551		Approved	nm23-H5, RSPH23	uc003lce.3	P56597	OTTHUMG00000129207	ENST00000265191.2:c.87delG	chr5.hg19:g.137474383delC	ENSP00000265191:p.Glu29fs	64.0	0.0	0		63.0	32.0	0.507937	NM_003551	B2R5G7	Frame_Shift_Del	DEL	ENST00000265191.2	hg19	CCDS4197.1																																																																																			.	.	.	none		0.368	NME5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251286.1	NM_003551		-	137474383	C	-	137474383	7	5	183	1	0	1	0	1	0	0	0	0	10501	912	32	0	571	0	NME5	5	137474383	Frame_Shift_Del	DEL	C	TCGA-GL-6846-01A-11D-1961-08	61129602	137474383	43440877	20	10689	99	2									
NME5	8382	hgsc.bcm.edu	37	chr5	137474385	137474386	+	Nonsense_Mutation	DNP	CC	CC	AG																															aagaataatatcttgtatctCctcctctttgtcaacaatat																										TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr5:137474385_137474386CC>AG	ENST00000265191.2	-	2	133_134	c.84_85GG>CT	c.(82-87)gaGGag>gaCTag	p.28_29EE>D*		NM_003551.2	NP_003542.1	P56597	NDK5_HUMAN	NME/NM23 family member 5	28					cilium assembly (GO:0042384)|CTP biosynthetic process (GO:0006241)|epithelial cilium movement (GO:0003351)|GTP biosynthetic process (GO:0006183)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|nucleoside metabolic process (GO:0009116)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)|ventricular system development (GO:0021591)	sperm flagellum (GO:0036126)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)			kidney(1)|large_intestine(1)|lung(2)|skin(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TCTTGTATCTCCTCCTCTTTGT	0.371																																					p.E29X|p.E28D		Atlas-SNP	.											NME5,NS,carcinoma,0,1|.	NME5	15	.	0			c.G85T|c.G84C						PASS	.																																			SO:0001587	stop_gained	8382	exon2			GTATCTCCTCCTC|TATCTCCTCCTCT	Y14992	CCDS4197.1	5q31.2	2012-05-18	2012-05-18		ENSG00000112981	ENSG00000112981			7853	protein-coding gene	gene with protein product	"radial spoke 23 homolog (Chlamydomonas)"	603575	"non-metastatic cells 5, protein expressed in (nucleoside-diphosphate kinase)"			9742940, 19852809	Standard	NM_003551		Approved	nm23-H5, RSPH23	uc003lce.3	P56597	OTTHUMG00000129207	ENST00000265191.2:c.84_85delinsAG	chr5.hg19:g.137474385_137474386delinsAG	ENSP00000265191:p.E28_E29delinsD*	67.0	2.0|0.0	.		66.0	33.0	.	NM_003551	B2R5G7	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000265191.2	hg19	CCDS4197.1																																																																																			.	.	.	none		0.371	NME5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251286.1	NM_003551		AG	137474386	CC	AG	137474385	4	1	183	1	0	0	0	0	0	1	0	0	10501	864	30	4	573	4	NME5	5	137474385	Nonsense_Mutation	DNP	CC	TCGA-GL-6846-01A-11D-1961-08	2	137474385	43440875	21	10690	99	2									
PCDH12	51294	hgsc.bcm.edu	37	chr5	141336615	141336615	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccttggtcagggtctgtggCggtcagttttatgagaagcg	6	12	16	7	2	3	1	2	1	1	1	3	2	3	1	1	4	1	1	1	4	2	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr5:141336615C>T	ENST00000231484.3	-	1	2012	c.802G>A	c.(802-804)Gcc>Acc	p.A268T	PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	268	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A268T(1)		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)			GGGTCTGTGGCGGTCAGTTTT	0.527																																					p.A268T		Atlas-SNP	.											PCDH12,bladder,carcinoma,0,2	PCDH12	133	.	1	Substitution - Missense(1)	large_intestine(1)	c.G802A						PASS	.						97	95	96					5																	141336615		2203	4300	6503	SO:0001583	missense	51294	exon1			CTGTGGCGGTCAG	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.802G>A	chr5.hg19:g.141336615C>T	ENSP00000231484:p.Ala268Thr	76.0	0.0	.		97.0	37.0	.	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	hg19	CCDS4269.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.727645	0.89390	.	.	ENSG00000113555	ENST00000231484	T	0.61392	0.11	5.32	5.32	0.75619	Cadherin (5);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.82190	0.4983	M	0.93283	3.4	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.86437	0.1764	10	0.87932	D	0	.	16.5409	0.84384	0.0:1.0:0.0:0.0	.	268	Q9NPG4	PCD12_HUMAN	T	268	ENSP00000231484:A268T	ENSP00000231484:A268T	A	-	1	0	PCDH12	141316799	1.000000	0.71417	0.991000	0.47740	0.932000	0.56968	7.651000	0.83577	2.767000	0.95098	0.655000	0.94253	GCC	.	.	.	none		0.527	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		T	141336615	C	T	141336615	3	4	183	1	0	0	0	0	1	0	0	0	11517	768	27	1	2768	1	PCDH12	5	141336615	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08	3862230	141336615	39578645	22	10691											
AGXT2L2	85007	hgsc.bcm.edu	37	chr5	177642285	177642285	+	Silent	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	ccagagcctcacctgacatcCccgacgatgggatgtttgat	9	9	10	13	2	1	3	1	2	0	1	2	6	2	4	5	1	1	1	5	1	0	1			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr5:177642285C>T	ENST00000308158.5	-	9	1308	c.1074G>A	c.(1072-1074)ggG>ggA	p.G358G	PHYKPL_ENST00000481811.1_5'UTR	NM_153373.2	NP_699204.1	Q8IUZ5	AT2L2_HUMAN	5-phosphohydroxy-L-lysine phospho-lyase	358						mitochondrion (GO:0005739)	lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)									L-Alanine(DB00160)	ACCTGACATCCCCGACGATGG	0.567																																					p.G358G		Atlas-SNP	.											.	AGXT2L2	51	.	0			c.G1074A						PASS	.						42	39	40					5																	177642285		2203	4300	6503	SO:0001819	synonymous_variant	85007	exon9			GACATCCCCGACG	BC037567	CCDS4434.1	5q35.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000175309	ENSG00000175309	4.2.3.134		28249	protein-coding gene	gene with protein product	"5-phosphonooxy-L-lysine phospho-lyase"	614683	"alanine-glyoxylate aminotransferase 2-like 2"	AGXT2L2		22241472	Standard	NM_153373		Approved	MGC15875	uc003miz.3	Q8IUZ5	OTTHUMG00000130892	ENST00000308158.5:c.1074G>A	chr5.hg19:g.177642285C>T		62.0	0.0	.		53.0	27.0	.	NM_153373	A8K7P6|B3KN36|D3DWP9|Q8WYS6|Q96HW8	Silent	SNP	ENST00000308158.5	hg19	CCDS4434.1																																																																																			.	.	.	none		0.567	PHYKPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253477.1	NM_032921		T	177642285	C	T	177642285	2	4	183	1	0	0	0	0	0	0	0	1	407	610	22	2		2	AGXT2L2	5	177642285	Silent	SNP	C	TCGA-GL-6846-01A-11D-1961-08	36305670	177642285	3272975	23	10692											
KCTD20	222658	hgsc.bcm.edu	37	chr6	36454734	36454734	+	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	tcatctataattatgtacaaCgccccttcatccagatgtca	12	13	4	12	1	4	1	3	0	1	1	5	1	5	1	3	0	2	1	3	0	5	5			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr6:36454734C>T	ENST00000373731.2	+	8	1433	c.1042C>T	c.(1042-1044)Cgc>Tgc	p.R348C	KCTD20_ENST00000449081.2_Missense_Mutation_p.R182C|KCTD20_ENST00000544295.1_Missense_Mutation_p.R102C|KCTD20_ENST00000474988.1_3'UTR|KCTD20_ENST00000536244.1_Missense_Mutation_p.R203C	NM_173562.3	NP_775833.2	Q7Z5Y7	KCD20_HUMAN	potassium channel tetramerization domain containing 20	348					protein homooligomerization (GO:0051260)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|skin(1)	15						TTATGTACAACGCCCCTTCAT	0.463																																					p.R348C		Atlas-SNP	.											.	KCTD20	37	.	0			c.C1042T						PASS	.						90	96	94					6																	36454734		2203	4300	6503	SO:0001583	missense	222658	exon8			GTACAACGCCCCT	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.1042C>T	chr6.hg19:g.36454734C>T	ENSP00000362836:p.Arg348Cys	182.0	0.0	.		119.0	45.0	.	NM_173562	B4DZD3|B4E2Q3|F5H3T3|Q5W105|Q69YQ7|Q8IZ55	Missense_Mutation	SNP	ENST00000373731.2	hg19	CCDS4821.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.701883	0.88924	.	.	ENSG00000112078	ENST00000373731;ENST00000544295;ENST00000449081;ENST00000536244	D;D;D;D	0.81996	-1.56;-1.56;-1.56;-1.56	6.03	6.03	0.97812	.	0.061169	0.64402	N	0.000003	D	0.87148	0.6105	L	0.53561	1.675	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	D	0.87043	0.2142	10	0.56958	D	0.05	-18.2215	15.2928	0.73879	0.14:0.86:0.0:0.0	.	182;348	Q7Z5Y7-2;Q7Z5Y7	.;KCD20_HUMAN	C	348;102;182;203	ENSP00000362836:R348C;ENSP00000440150:R102C;ENSP00000412205:R182C;ENSP00000439118:R203C	ENSP00000362836:R348C	R	+	1	0	KCTD20	36562712	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.971000	0.40530	2.861000	0.98227	0.655000	0.94253	CGC	.	.	.	none		0.463	KCTD20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040345.2	NM_173562		T	36454734	C	T	36454734	3	4	183	1	0	0	0	0	1	0	0	0	8115	536	19	1	1068	1	KCTD20	6	36454734	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08		36454734	134660333	24	10693											
ULBP1	80329	hgsc.bcm.edu	37	chr6	150289835	150289835	+	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	aaggcctggtggatgaaaggCcttttcttcactatgactgt	9	13	11	8	0	2	2	1	2	1	0	2	3	2	3	2	4	0	0	2	4	3	4			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr6:150289835C>A	ENST00000229708.3	+	2	221	c.178C>A	c.(178-180)Cct>Act	p.P60T		NM_025218.2	NP_079494.1	Q9BZM6	N2DL1_HUMAN	UL16 binding protein 1	60	MHC class I alpha-1 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)	anchored component of plasma membrane (GO:0046658)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	natural killer cell lectin-like receptor binding (GO:0046703)			large_intestine(3)|lung(5)|pancreas(1)|skin(1)	10		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.14e-11)		GGATGAAAGGCCTTTTCTTCA	0.453																																					p.P60T		Atlas-SNP	.											.	ULBP1	25	.	0			c.C178A						PASS	.						133	133	133					6																	150289835		2203	4300	6503	SO:0001583	missense	80329	exon2			GAAAGGCCTTTTC	AF304377	CCDS5223.1	6q25	2003-04-29			ENSG00000111981	ENSG00000111981			14893	protein-coding gene	gene with protein product		605697				11239445, 11827464	Standard	XM_005267151		Approved	RAET1I	uc003qnp.3	Q9BZM6	OTTHUMG00000015810	ENST00000229708.3:c.178C>A	chr6.hg19:g.150289835C>A	ENSP00000229708:p.Pro60Thr	213.0	0.0	.		192.0	90.0	.	NM_025218	Q5VY81|Q8IZW3|Q8IZX6	Missense_Mutation	SNP	ENST00000229708.3	hg19	CCDS5223.1	.	.	.	.	.	.	.	.	.	.	c	0.006	-2.109641	0.00353	.	.	ENSG00000111981	ENST00000367345;ENST00000229708	T;T	0.00682	5.86;5.86	2.2	-4.39	0.03611	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	0.00144	0.0004	N	0.11927	0.2	0.09310	N	1	B	0.10296	0.003	B	0.17098	0.017	T	0.45101	-0.9284	9	0.72032	D	0.01	.	1.2925	0.02063	0.2296:0.3696:0.2522:0.1487	.	60	Q9BZM6	N2DL1_HUMAN	T	60	ENSP00000356314:P60T;ENSP00000229708:P60T	ENSP00000229708:P60T	P	+	1	0	ULBP1	150331528	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-4.865000	0.00176	-2.597000	0.00453	-0.834000	0.03071	CCT	.	.	.	none		0.453	ULBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042677.2			A	150289835	C	A	150289835	3	1	183	1	0	0	0	0	1	0	0	0	16984	739	26	4	184	4	ULBP1	6	150289835	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08	113835101	150289835	20825232	25	10694											
MLLT4	4301	hgsc.bcm.edu	37	chr6	168344092	168344092	+	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	atttgcctaggatggacgtcTagctgcaggtgatcagctcc	8	11	12	10	1	2	1	1	1	1	0	3	3	3	3	2	3	4	3	2	3	2	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr6:168344092T>A	ENST00000447894.2	+	24	3155	c.3155T>A	c.(3154-3156)cTa>cAa	p.L1052Q	MLLT4_ENST00000366806.2_Missense_Mutation_p.L1052Q|MLLT4_ENST00000507679.1_3'UTR|MLLT4_ENST00000344191.4_Missense_Mutation_p.L1052Q|MLLT4_ENST00000400822.3_Missense_Mutation_p.L1051Q|MLLT4_ENST00000351017.4_Missense_Mutation_p.L1059Q|MLLT4_ENST00000392112.1_Missense_Mutation_p.L1035Q|MLLT4_ENST00000392108.3_Missense_Mutation_p.L1052Q			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	1052	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)		GATGGACGTCTAGCTGCAGGT	0.458			T	MLL	AL																																p.L1052Q		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.T3155A						PASS	.						244	221	229					6																	168344092		2203	4300	6503	SO:0001583	missense	4301	exon24			GACGTCTAGCTGC	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.3155T>A	chr6.hg19:g.168344092T>A	ENSP00000404595:p.Leu1052Gln	233.0	0.0	.		250.0	105.0	.	NM_001040000	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Missense_Mutation	SNP	ENST00000447894.2	hg19		.	.	.	.	.	.	.	.	.	.	T	23.7	4.441746	0.83993	.	.	ENSG00000130396	ENST00000344191;ENST00000351017;ENST00000392108;ENST00000366806;ENST00000392112;ENST00000341575;ENST00000400822;ENST00000447894	T;T;T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74;0.74;0.74	5.18	5.18	0.71444	PDZ/DHR/GLGF (4);	0.000000	0.64402	D	0.000010	T	0.76751	0.4031	H	0.97983	4.12	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;0.997	D	0.86288	0.1672	10	0.87932	D	0	-11.2076	15.0548	0.71904	0.0:0.0:0.0:1.0	.	1052;1051;1052;1036	P55196;P55196-5;P55196-6;P55196-2	AFAD_HUMAN;.;.;.	Q	1052;1059;1052;1052;1035;1052;1051;1052	ENSP00000341118:L1052Q;ENSP00000252692:L1059Q;ENSP00000375956:L1052Q;ENSP00000355771:L1052Q;ENSP00000375960:L1035Q;ENSP00000383623:L1051Q;ENSP00000404595:L1052Q	ENSP00000345834:L1052Q	L	+	2	0	MLLT4	168086941	1.000000	0.71417	0.015000	0.15790	0.985000	0.73830	7.440000	0.80464	1.954000	0.56735	0.528000	0.53228	CTA	.	.	.	none		0.458	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936		A	168344092	T	A	168344092	3	1	183	1	0	0	0	0	1	0	0	0	9636	1522	53	5	3249	5	MLLT4	6	168344092	Missense_Mutation	SNP	T	TCGA-GL-6846-01A-11D-1961-08	18054257	168344092	2770975	26	10695											
C7orf26	79034	hgsc.bcm.edu	37	chr7	6639834	6639834	+	Missense_Mutation	SNP	T	T	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	ggcgcctggggctgatcctcTtcgaccacatggtcccgctg	4	9	13	15	3	1	1	0	1	1	0	4	2	3	1	4	4	0	2	4	4	0	1			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr7:6639834T>G	ENST00000344417.5	+	4	1222	c.955T>G	c.(955-957)Ttc>Gtc	p.F319V	C7orf26_ENST00000359073.5_Missense_Mutation_p.F222V|C7orf26_ENST00000472693.1_3'UTR	NM_024067.2	NP_076972.2	Q96N11	CG026_HUMAN	chromosome 7 open reading frame 26	319										endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	11		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)		GCTGATCCTCTTCGACCACAT	0.582																																					p.F319V		Atlas-SNP	.											.	C7orf26	33	.	0			c.T955G						PASS	.						59	52	54					7																	6639834		2203	4300	6503	SO:0001583	missense	79034	exon4			ATCCTCTTCGACC	BC005121	CCDS5353.1	7p22.1	2011-11-24			ENSG00000146576	ENSG00000146576			21702	protein-coding gene	gene with protein product							Standard	NM_024067		Approved	MGC2718	uc003sqo.1	Q96N11	OTTHUMG00000125517	ENST00000344417.5:c.955T>G	chr7.hg19:g.6639834T>G	ENSP00000340220:p.Phe319Val	48.0	0.0	.		46.0	29.0	.	NM_024067	Q9BQ43	Missense_Mutation	SNP	ENST00000344417.5	hg19	CCDS5353.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.95|10.95	1.496091|1.496091	0.26774|0.26774	.|.	.|.	ENSG00000146576|ENSG00000146576	ENST00000344417;ENST00000359073|ENST00000445375	T;T|T	0.39997|0.40756	1.05;1.05|1.02	5.2|5.2	5.2|5.2	0.72013|0.72013	.|.	0.213127|.	0.53938|.	D|.	0.000054|.	T|T	0.30103|0.30103	0.0754|0.0754	N|N	0.19112|0.19112	0.55|0.55	0.29914|0.29914	N|N	0.823337|0.823337	B;B|.	0.17038|.	0.02;0.02|.	B;B|.	0.14023|.	0.004;0.01|.	T|T	0.12344|0.12344	-1.0551|-1.0551	10|7	0.14656|0.09084	T|T	0.56|0.74	-26.1927|-26.1927	13.6493|13.6493	0.62301|0.62301	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	222;319|.	Q96N11-2;Q96N11|.	.;CG026_HUMAN|.	V|R	319;222|56	ENSP00000340220:F319V;ENSP00000351974:F222V|ENSP00000390166:L56R	ENSP00000340220:F319V|ENSP00000390166:L56R	F|L	+|+	1|2	0|0	C7orf26|C7orf26	6606359|6606359	1.000000|1.000000	0.71417|0.71417	0.466000|0.466000	0.27168|0.27168	0.709000|0.709000	0.40893|0.40893	3.987000|3.987000	0.56944|0.56944	2.268000|2.268000	0.75426|0.75426	0.454000|0.454000	0.30748|0.30748	TTC|CTT	.	.	.	none		0.582	C7orf26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246844.2	NM_024067		G	6639834	T	G	6639834	3	3	183	1	0	0	0	0	1	0	0	0	2383	1609	56	5	969	5	C7orf26	7	6639834	Missense_Mutation	SNP	T	TCGA-GL-6846-01A-11D-1961-08		6639834	152498829	27	10696											
ASB4	51666	hgsc.bcm.edu	37	chr7	95125264	95125264	+	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	attgtgttaagatcctctgtGatcgtggggcaaagctcaat	10	13	11	7	1	2	2	1	1	1	1	4	2	3	2	1	2	1	3	1	2	3	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr7:95125264G>A	ENST00000325885.5	+	2	453	c.382G>A	c.(382-384)Gat>Aat	p.D128N	ASB4_ENST00000257621.4_3'UTR|ASB4_ENST00000428113.1_Missense_Mutation_p.D128N	NM_016116.2	NP_057200.1	Q9Y574	ASB4_HUMAN	ankyrin repeat and SOCS box containing 4	128					intracellular signal transduction (GO:0035556)|positive regulation of vasculogenesis (GO:2001214)|protein autoubiquitination (GO:0051865)	Cul2-RING ubiquitin ligase complex (GO:0031462)|Cul5-RING ubiquitin ligase complex (GO:0031466)	ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|pancreas(1)|prostate(1)|skin(2)	20	all_cancers(62;2.27e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.218)|all_lung(186;0.246)		STAD - Stomach adenocarcinoma(171;0.0151)			GATCCTCTGTGATCGTGGGGC	0.458																																					p.D128N		Atlas-SNP	.											.	ASB4	52	.	0			c.G382A						PASS	.						210	156	175					7																	95125264		2203	4300	6503	SO:0001583	missense	51666	exon2			CTCTGTGATCGTG	AF156779	CCDS5641.1, CCDS5642.1	7q21-q22	2013-01-10	2011-01-25		ENSG00000005981	ENSG00000005981		"Ankyrin repeat domain containing"	16009	protein-coding gene	gene with protein product		605761	"ankyrin repeat and SOCS box-containing 4"				Standard	NM_145872		Approved	ASB-4	uc011kij.2	Q9Y574	OTTHUMG00000153960	ENST00000325885.5:c.382G>A	chr7.hg19:g.95125264G>A	ENSP00000321388:p.Asp128Asn	101.0	0.0	.		112.0	23.0	.	NM_016116	A4D1H6|O14586|Q14D68|Q8TBT2	Missense_Mutation	SNP	ENST00000325885.5	hg19	CCDS5641.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.692526	0.30052	.	.	ENSG00000005981	ENST00000325885;ENST00000428113	T;T	0.65364	-0.15;-0.15	5.35	5.35	0.76521	Ankyrin repeat-containing domain (3);	0.260422	0.44688	D	0.000432	T	0.48822	0.1521	L	0.38531	1.155	0.33932	D	0.642157	B;B	0.15141	0.009;0.012	B;B	0.15052	0.012;0.011	T	0.56062	-0.8041	10	0.45353	T	0.12	-7.733	7.2877	0.26348	0.2046:0.0:0.7954:0.0	.	128;128	Q9Y574;Q14D68	ASB4_HUMAN;.	N	128	ENSP00000321388:D128N;ENSP00000397070:D128N	ENSP00000321388:D128N	D	+	1	0	ASB4	94963200	1.000000	0.71417	1.000000	0.80357	0.292000	0.27327	3.865000	0.56033	2.680000	0.91292	0.655000	0.94253	GAT	.	.	.	none		0.458	ASB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333225.2	NM_016116		A	95125264	G	A	95125264	3	1	183	1	0	0	0	0	1	0	0	0	1025	1290	45	2	388	2	ASB4	7	95125264	Missense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08	88485430	95125264	64013399	28	10697											
NRCAM	4897	hgsc.bcm.edu	37	chr7	107808822	107808822	+	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	gcagctgcagcagtaagattGctgatcctgggatttactgc	9	11	12	9	0	0	2	0	1	0	1	1	3	1	3	1	1	6	6	1	1	2	4			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr7:107808822G>A	ENST00000425651.2	-	26	3212	c.3213C>T	c.(3211-3213)agC>agT	p.S1071S	NRCAM_ENST00000379028.3_Silent_p.S1071S|NRCAM_ENST00000379024.4_Intron|NRCAM_ENST00000379022.4_Silent_p.S1071S|NRCAM_ENST00000413765.2_Intron|NRCAM_ENST00000351718.4_Intron	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	1071	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						CAGTAAGATTGCTGATCCTGG	0.363																																					p.S1071S		Atlas-SNP	.											.	NRCAM	267	.	0			c.C3213T						PASS	.						71	68	69					7																	107808822		1891	4119	6010	SO:0001819	synonymous_variant	4897	exon26			AAGATTGCTGATC		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.3213C>T	chr7.hg19:g.107808822G>A		66.0	0.0	.		81.0	27.0	.	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Silent	SNP	ENST00000425651.2	hg19	CCDS47686.1	.	.	.	.	.	.	.	.	.	.	G	9.798	1.179809	0.21787	.	.	ENSG00000091129	ENST00000445634	.	.	.	5.75	1.63	0.23807	.	.	.	.	.	T	0.55433	0.1920	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49624	-0.8920	4	.	.	.	.	7.8556	0.29480	0.0:0.3328:0.2964:0.3708	.	.	.	.	V	21	.	.	A	-	2	0	NRCAM	107596058	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.272000	0.33109	0.762000	0.33152	0.650000	0.86243	GCA	.	.	.	none		0.363	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		A	107808822	G	A	107808822	2	1	183	1	0	0	0	0	0	0	0	1	10651	1310	46	2		2	NRCAM	7	107808822	Silent	SNP	G	TCGA-GL-6846-01A-11D-1961-08	12683558	107808822	51329841	29	10698											
CHD7	55636	hgsc.bcm.edu	37	chr8	61654762	61654762	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactcggtgcagcagttccaTcaccacccctctactgctct	7	10	6	18	1	3	0	1	0	2	0	5	0	4	0	4	1	4	4	4	1	1	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr8:61654762T>C	ENST00000423902.2	+	2	1250	c.771T>C	c.(769-771)caT>caC	p.H257H	CHD7_ENST00000525508.1_Silent_p.H257H|CHD7_ENST00000524602.1_Silent_p.H257H	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	257					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			AGCAGTTCCATCACCACCCCT	0.582																																					p.H257H		Atlas-SNP	.											.	CHD7	534	.	0			c.T771C						PASS	.						119	122	121					8																	61654762		2099	4221	6320	SO:0001819	synonymous_variant	55636	exon2			GTTCCATCACCAC	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.771T>C	chr8.hg19:g.61654762T>C		258.0	1.0	.		218.0	89.0	.	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Silent	SNP	ENST00000423902.2	hg19	CCDS47865.1																																																																																			.	.	.	none		0.582	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		C	61654762	T	C	61654762	2	2	183	1	0	0	0	0	0	0	0	1	3332	1432	50	3		3	CHD7	8	61654762	Silent	SNP	T	TCGA-GL-6846-01A-11D-1961-08		61654762	84709260	30	10699											
BNC2	54796	hgsc.bcm.edu	37	chr9	16552614	16552615	+	In_Frame_Ins	INS	-	-	GAA																															tcctcttgcttcaggacgctINSgaagagacggtccagcagga																										TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr9:16552614_16552615insGAA	ENST00000380672.4	-	5	639_640	c.582_583insTTC	c.(580-585)ttcagc>ttcTTCagc	p.194_195insF	BNC2_ENST00000545497.1_In_Frame_Ins_p.99_100insF|BNC2_ENST00000380667.2_In_Frame_Ins_p.127_128insF|BNC2_ENST00000380666.2_In_Frame_Ins_p.194_195insF	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)		TTCAGGACGCTGAAGAGACGGT	0.55																																					p.S195delinsFS		Atlas-INDEL	.											BNC2,NS,carcinoma,0,1	BNC2	166	.	0			c.583_584insTTC						PASS	.																																			SO:0001652	inframe_insertion	54796	exon5			.	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.580_582dupTTC	chr9.hg19:g.16552615_16552617dupGAA	ENSP00000370047:p.Phe194_Phe194dup	90.0	0.0	0		77.0	17.0	0.220779	NM_017637		In_Frame_Ins	INS	ENST00000380672.4	hg19	CCDS6482.2																																																																																			.	.	.	none		0.55	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637		GAA	16552615	-	GAA	16552614	7	5	183	1	0	1	1	0	0	0	0	0	1475	1580	55	0	2728	0	BNC2	9	16552614	In_Frame_Ins	INS	-	TCGA-GL-6846-01A-11D-1961-08		16552614	124660817	31	10700											
GTF3C5	9328	hgsc.bcm.edu	37	chr9	135917679	135917680	+	Missense_Mutation	DNP	TT	TT	AA																															ccttggcatcatctccaccaTttacaaatttcagggtaact																										TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr9:135917679_135917680TT>AA	ENST00000372097.5	+	2	682_683	c.359_360TT>AA	c.(358-360)aTT>aAA	p.I120K	GTF3C5_ENST00000342018.8_Missense_Mutation_p.I120K|GTF3C5_ENST00000485692.1_Intron|GTF3C5_ENST00000372108.5_Missense_Mutation_p.I120K|GTF3C5_ENST00000372095.5_Intron|GTF3C5_ENST00000372099.6_Missense_Mutation_p.I111K	NM_012087.3	NP_036219.2	Q9Y5Q8	TF3C5_HUMAN	general transcription factor IIIC, polypeptide 5, 63kDa	120					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)	21				OV - Ovarian serous cystadenocarcinoma(145;4.01e-06)|Epithelial(140;4e-05)		ATCTCCACCATTTACAAATTTC	0.535																																					p.I120N|p.I120I		Atlas-SNP	.											.	GTF3C5	46	.	0			c.T359A|c.T360A						PASS	.																																			SO:0001583	missense	9328	exon2			CCACCATTTACAA|CACCATTTACAAA	AF133124	CCDS6958.1, CCDS48050.1, CCDS75927.1	9q34.13	2010-03-23	2002-08-29		ENSG00000148308	ENSG00000148308		"General transcription factors"	4668	protein-coding gene	gene with protein product	"transcription factor IIIC, 63 kD"	604890	"general transcription factor IIIC, polypeptide 5 (63kD)"			10373544	Standard	NM_012087		Approved	TFiiiC2-63, TFIIIC63, TFIIICepsilon	uc004ccj.4	Q9Y5Q8	OTTHUMG00000020856	Exception_encountered	chr9.hg19:g.135917679_135917680delinsAA	ENSP00000361169:p.Ile120Lys	120.0|119.0	0.0	.		97.0|94.0	36.0|35.0	.	NM_012087	A6NI44|A6NJB9|Q5T7U2|Q5T7U3|Q8N2U7|Q8N857|Q96GD9|Q9H4P2	Missense_Mutation|Silent	SNP	ENST00000372097.5	hg19	CCDS6958.1																																																																																			.	.	.	none		0.535	GTF3C5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054826.1	NM_001122823		AA	135917680	TT	AA	135917679	3	1	183	1	0	0	0	0	1	0	0	0	6883	1493	52	5	365	5	GTF3C5	9	135917679	Missense_Mutation	DNP	TT	TCGA-GL-6846-01A-11D-1961-08	119365065	135917679	5295752	32	10701											
CACNA1B	774	hgsc.bcm.edu	37	chr9	140943670	140943670	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctccctcctagatgatcgacTtgggactgctgcttcaccct	6	12	8	15	1	1	2	1	1	0	1	4	4	3	3	3	1	2	2	3	1	1	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr9:140943670T>C	ENST00000371372.1	+	24	3758	c.3613T>C	c.(3613-3615)Ttg>Ctg	p.L1205L	CACNA1B_ENST00000371355.4_Silent_p.L1206L|CACNA1B_ENST00000277551.2_Silent_p.L1205L|CACNA1B_ENST00000371357.1_Silent_p.L1206L|CACNA1B_ENST00000277549.5_Silent_p.L397L|CACNA1B_ENST00000371363.1_Silent_p.L1205L|CACNA1B_ENST00000545473.1_3'UTR	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	1205					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	GATGATCGACTTGGGACTGCT	0.527																																					p.L1205L		Atlas-SNP	.											.	CACNA1B	266	.	0			c.T3613C						PASS	.						177	173	174					9																	140943670		2047	4198	6245	SO:0001819	synonymous_variant	774	exon24			ATCGACTTGGGAC	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels", "EF-hand domain containing"	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.3613T>C	chr9.hg19:g.140943670T>C		89.0	0.0	.		88.0	38.0	.	NM_001243812	B1AQK5	Silent	SNP	ENST00000371372.1	hg19	CCDS59522.1																																																																																			.	.	.	none		0.527	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		C	140943670	T	C	140943670	2	2	183	1	0	0	0	0	0	0	0	1	2541	1606	56	3		3	CACNA1B	9	140943670	Silent	SNP	T	TCGA-GL-6846-01A-11D-1961-08	5025991	140943670	269761	33	10702											
DIP2C	22982	hgsc.bcm.edu	37	chr10	375449	375449	+	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	aggagcaaaacgtgtctcggActttgtactgactcacggca	11	9	11	10	3	2	1	1	1	1	0	3	3	2	3	0	3	3	3	0	3	3	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr10:375449A>T	ENST00000280886.6	-	30	3764	c.3677T>A	c.(3676-3678)gTc>gAc	p.V1226D		NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1226						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)		CGTGTCTCGGACTTTGTACTG	0.577																																					p.V1226D		Atlas-SNP	.											.	DIP2C	195	.	0			c.T3677A						PASS	.						64	55	58					10																	375449		2203	4300	6503	SO:0001583	missense	22982	exon30			TCTCGGACTTTGT	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.3677T>A	chr10.hg19:g.375449A>T	ENSP00000280886:p.Val1226Asp	32.0	0.0	.		54.0	24.0	.	NM_014974	B4DPI5|Q5SS78	Missense_Mutation	SNP	ENST00000280886.6	hg19	CCDS7054.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	34|34	5.376544|5.376544	0.95945|0.95945	.|.	.|.	ENSG00000151240|ENSG00000151240	ENST00000434695|ENST00000280886;ENST00000535541;ENST00000381503	.|T	.|0.51574	.|0.7	5.84|5.84	5.84|5.84	0.93424|0.93424	.|AMP-dependent synthetase/ligase (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.67211|0.67211	0.2869|0.2869	M|M	0.67397|0.67397	2.05|2.05	0.80722|0.80722	D|D	1|1	.|D	.|0.60575	.|0.988	.|D	.|0.71656	.|0.974	T|T	0.69749|0.69749	-0.5061|-0.5061	5|10	.|0.66056	.|D	.|0.02	-39.2182|-39.2182	16.2141|16.2141	0.82191|0.82191	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|1226	.|Q9Y2E4	.|DIP2C_HUMAN	R|D	31|1226;151;75	.|ENSP00000280886:V1226D	.|ENSP00000280886:V1226D	S|V	-|-	3|2	2|0	DIP2C|DIP2C	365449|365449	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.841000|0.841000	0.47740|0.47740	9.339000|9.339000	0.96797|0.96797	2.230000|2.230000	0.72887|0.72887	0.528000|0.528000	0.53228|0.53228	AGT|GTC	.	.	.	none		0.577	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974		T	375449	A	T	375449	3	4	183	1	0	0	0	0	1	0	0	0	4531	275	10	5	1025	5	DIP2C	10	375449	Missense_Mutation	SNP	A	TCGA-GL-6846-01A-11D-1961-08		375449	135159298	34	10703											
ZEB1	6935	hgsc.bcm.edu	37	chr10	31812949	31812949	+	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	accgcccaaaaagaaaatgcGgaagacagaaaatggaatgt	20	4	10	7	2	0	3	0	0	0	3	0	5	0	5	2	2	1	0	2	2	8	0	rs35653460		TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr10:31812949G>T	ENST00000320985.10	+	8	2800	c.2690G>T	c.(2689-2691)cGg>cTg	p.R897L	ZEB1_ENST00000560721.2_Missense_Mutation_p.R877L|ZEB1_ENST00000446923.2_Missense_Mutation_p.R881L|ZEB1_ENST00000542815.3_Missense_Mutation_p.R830L|ZEB1_ENST00000361642.5_Missense_Mutation_p.R898L			P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1	897					cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cellular response to amino acid stimulus (GO:0071230)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cochlea morphogenesis (GO:0090103)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain development (GO:0030900)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pattern specification process (GO:0007389)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mesenchymal cell proliferation (GO:0010464)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to activity (GO:0014823)|response to nutrient levels (GO:0031667)|semicircular canal morphogenesis (GO:0048752)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.R897Q(1)		NS(2)|breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(38)|ovary(3)|skin(6)|upper_aerodigestive_tract(4)	77		Prostate(175;0.0156)				AAGAAAATGCGGAAGACAGAA	0.373																																					p.R898L	Ovarian(40;423 959 14296 36701 49589)	Atlas-SNP	.											ZEB1,rectum,carcinoma,0,1	ZEB1	173	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2693T						PASS	.						111	111	111					10																	31812949		2203	4300	6503	SO:0001583	missense	6935	exon8			AAATGCGGAAGAC	AK091478	CCDS7169.1, CCDS44370.1, CCDS53505.1, CCDS53506.1, CCDS53507.1	10p11.22	2014-02-14	2007-02-15	2007-02-15	ENSG00000148516	ENSG00000148516		"Zinc fingers, C2H2-type", "Homeoboxes / ZF class"	11642	protein-coding gene	gene with protein product		189909	"transcription factor 8 (represses interleukin 2 expression)", "posterior polymorphous corneal dystrophy 3"	TCF8, PPCD3		1427828, 1840704, 15384081, 16252232	Standard	NM_001128128		Approved	BZP, ZEB, AREB6, NIL-2-A, Zfhep, Zfhx1a, FECD6	uc001ivu.4	P37275	OTTHUMG00000017907	ENST00000320985.10:c.2690G>T	chr10.hg19:g.31812949G>T	ENSP00000319248:p.Arg897Leu	140.0	0.0	.		147.0	59.0	.	NM_001174096	B4DJV0|B4DUW9|E9PCM7|F5H4I8|Q12924|Q13800|Q2KJ05|Q5T968|Q5VZ84|Q8NB68	Missense_Mutation	SNP	ENST00000320985.10	hg19	CCDS7169.1	.	.	.	.	.	.	.	.	.	.	G	19.18	3.777667	0.70107	.	.	ENSG00000148516	ENST00000542879;ENST00000537225;ENST00000361642;ENST00000546250;ENST00000542815;ENST00000320985;ENST00000437844;ENST00000543514;ENST00000446923	T;T;T;T;T	0.07327	3.2;3.2;3.2;3.2;3.2	5.72	4.8	0.61643	.	0.369405	0.21055	N	0.080939	T	0.15435	0.0372	L	0.27053	0.805	0.41478	D	0.988147	D;P;B;P;P	0.69078	0.997;0.826;0.208;0.826;0.826	D;B;B;B;B	0.69824	0.966;0.334;0.09;0.334;0.177	T	0.02901	-1.1096	10	0.52906	T	0.07	-12.9237	10.1047	0.42526	0.071:0.1383:0.7907:0.0	.	830;881;877;898;897	F5H4I8;E9PCM7;Q5VZ84;Q2KJ05;P37275	.;.;.;.;ZEB1_HUMAN	L	679;897;898;892;830;897;877;788;881	ENSP00000444282:R679L;ENSP00000354487:R898L;ENSP00000444891:R830L;ENSP00000319248:R897L;ENSP00000391612:R881L	ENSP00000319248:R897L	R	+	2	0	ZEB1	31852955	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.665000	0.68052	1.410000	0.46936	0.585000	0.79938	CGG	.	G|0.987;A|0.013	.	alt		0.373	ZEB1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419083.2	NM_030751		T	31812949	G	T	31812949	3	4	183	1	0	0	0	0	1	0	0	0	17635	1116	39	4	2734	4	ZEB1	10	31812949	Missense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08	31437500	31812949	103721798	35	10704											
SEC23IP	11196	hgsc.bcm.edu	37	chr10	121692658	121692658	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taatgaataccttttcgctcTtcagagtcacttatgctatt	10	17	5	9	1	3	2	2	1	1	1	4	2	3	2	1	0	2	2	1	0	5	8			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr10:121692658T>C	ENST00000369075.3	+	17	2972	c.2900T>C	c.(2899-2901)cTt>cCt	p.L967P	SEC23IP_ENST00000543134.1_Missense_Mutation_p.L756P|SEC23IP_ENST00000475542.1_3'UTR	NM_007190.3	NP_009121.1	Q9Y6Y8	S23IP_HUMAN	SEC23 interacting protein	967	DDHD. {ECO:0000255|PROSITE- ProRule:PRU00378}.				acrosome assembly (GO:0001675)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|single fertilization (GO:0007338)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear endoplasmic reticulum (GO:0097038)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	36		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		CTTTTCGCTCTTCAGAGTCAC	0.383																																					p.L967P		Atlas-SNP	.											.	SEC23IP	100	.	0			c.T2900C						PASS	.						128	125	126					10																	121692658		2203	4300	6503	SO:0001583	missense	11196	exon17			TCGCTCTTCAGAG	AB019435	CCDS7618.1	10q26.11-q26.12	2013-01-10			ENSG00000107651	ENSG00000107651		"Sterile alpha motif (SAM) domain containing"	17018	protein-coding gene	gene with protein product						10400679	Standard	NM_007190		Approved	p125	uc001leu.2	Q9Y6Y8	OTTHUMG00000019161	ENST00000369075.3:c.2900T>C	chr10.hg19:g.121692658T>C	ENSP00000358071:p.Leu967Pro	128.0	0.0	.		152.0	68.0	.	NM_007190	D3DRD2|Q8IXH5|Q9BUK5	Missense_Mutation	SNP	ENST00000369075.3	hg19	CCDS7618.1	.	.	.	.	.	.	.	.	.	.	T	18.64	3.667691	0.67814	.	.	ENSG00000107651	ENST00000369075;ENST00000543134	T;T	0.39406	1.08;1.12	5.28	4.14	0.48551	DDHD (2);	0.000000	0.85682	D	0.000000	T	0.65831	0.2729	M	0.86268	2.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.991;0.998	T	0.69254	-0.5193	10	0.62326	D	0.03	-23.9312	11.2264	0.48886	0.0:0.0726:0.0:0.9274	.	756;967	F5H0L8;Q9Y6Y8	.;S23IP_HUMAN	P	967;756	ENSP00000358071:L967P;ENSP00000438773:L756P	ENSP00000358071:L967P	L	+	2	0	SEC23IP	121682648	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	7.655000	0.83696	0.950000	0.37743	-0.256000	0.11100	CTT	.	.	.	none		0.383	SEC23IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050688.1			C	121692658	T	C	121692658	3	2	183	1	0	0	0	0	1	0	0	0	14006	1609	56	3	2966	3	SEC23IP	10	121692658	Missense_Mutation	SNP	T	TCGA-GL-6846-01A-11D-1961-08	89879709	121692658	13842089	36	10705											
DOCK1	1793	hgsc.bcm.edu	37	chr10	128788791	128788791	+	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	ttgaatggcgatcacaaattCtttctggaactctgcctcag	10	13	8	10	1	5	1	2	1	3	0	5	3	5	2	1	2	2	0	1	2	3	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr10:128788791C>G	ENST00000280333.6	+	6	506	c.397C>G	c.(397-399)Ctt>Gtt	p.L133V		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	133					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)		ATCACAAATTCTTTCTGGAAC	0.393																																					p.L133V		Atlas-SNP	.											.	DOCK1	188	.	0			c.C397G						PASS	.						109	103	105					10																	128788791		1909	4134	6043	SO:0001583	missense	1793	exon6			CAAATTCTTTCTG	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.397C>G	chr10.hg19:g.128788791C>G	ENSP00000280333:p.Leu133Val	48.0	0.0	.		29.0	12.0	.	NM_001380	A9Z1Z5	Missense_Mutation	SNP	ENST00000280333.6	hg19		.	.	.	.	.	.	.	.	.	.	C	14.43	2.532331	0.45073	.	.	ENSG00000150760	ENST00000280333	T	0.47177	0.85	4.5	4.5	0.54988	.	0.000000	0.64402	D	0.000001	T	0.47911	0.1471	L	0.61218	1.895	0.53688	D	0.999978	B;B	0.28850	0.122;0.225	B;B	0.26202	0.067;0.061	T	0.52366	-0.8585	10	0.51188	T	0.08	.	17.7282	0.88370	0.0:1.0:0.0:0.0	.	133;133	B2RUU3;Q14185	.;DOCK1_HUMAN	V	133	ENSP00000280333:L133V	ENSP00000280333:L133V	L	+	1	0	DOCK1	128678781	1.000000	0.71417	0.998000	0.56505	0.967000	0.64934	4.454000	0.60068	2.510000	0.84645	0.555000	0.69702	CTT	.	.	.	none		0.393	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380		G	128788791	C	G	128788791	3	3	183	1	0	0	0	0	1	0	0	0	4686	913	32	4	419	4	DOCK1	10	128788791	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08	7096133	128788791	6745956	37	10706											
OR56A1	120796	hgsc.bcm.edu	37	chr11	6048449	6048449	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggataggaatgggtgcagtAagaagcgcattccgcaccac	13	6	13	9	2	0	1	0	0	0	1	1	3	1	3	2	3	2	4	2	3	4	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr11:6048449A>G	ENST00000316650.5	-	1	522	c.486T>C	c.(484-486)ctT>ctC	p.L162L		NM_001001917.2	NP_001001917.2	Q8NGH5	O56A1_HUMAN	olfactory receptor, family 56, subfamily A, member 1	162						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)		TGGGTGCAGTAAGAAGCGCAT	0.498																																					p.L162L		Atlas-SNP	.											.	OR56A1	73	.	0			c.T486C						PASS	.						142	125	131					11																	6048449		2201	4296	6497	SO:0001819	synonymous_variant	120796	exon1			TGCAGTAAGAAGC	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.486T>C	chr11.hg19:g.6048449A>G		148.0	0.0	.		125.0	56.0	.	NM_001001917	B2RNI2|Q6IFL0	Silent	SNP	ENST00000316650.5	hg19	CCDS31405.1																																																																																			.	.	.	none		0.498	OR56A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383757.1	NM_001001917		G	6048449	A	G	6048449	2	3	183	1	0	0	0	0	0	0	0	1	11140	349	13	3		3	OR56A1	11	6048449	Silent	SNP	A	TCGA-GL-6846-01A-11D-1961-08		6048449	128958067	38	10707											
VWF	7450	hgsc.bcm.edu	37	chr12	6143881	6143881	+	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	agaacgtactggcactccccGgggaacaggtatttgagccc	10	7	12	12	2	0	2	0	1	0	1	1	3	1	3	3	4	4	3	3	4	4	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr12:6143881G>T	ENST00000261405.5	-	20	2912	c.2658C>A	c.(2656-2658)ccC>ccA	p.P886P		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	886	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)	GGCACTCCCCGGGGAACAGGT	0.602																																					p.P886P		Atlas-SNP	.											.	VWF	338	.	0			c.C2658A						PASS	.						154	126	136					12																	6143881		2203	4300	6503	SO:0001819	synonymous_variant	7450	exon20			CTCCCCGGGGAAC		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.2658C>A	chr12.hg19:g.6143881G>T		105.0	0.0	.		129.0	6.0	.	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	hg19	CCDS8539.1																																																																																			.	.	.	none		0.602	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		T	6143881	G	T	6143881	2	4	183	1	0	0	0	0	0	0	0	1	17258	1103	39	4		4	VWF	12	6143881	Silent	SNP	G	TCGA-GL-6846-01A-11D-1961-08		6143881	127708014	39	10708											
MLF2	8079	hgsc.bcm.edu	37	chr12	6859057	6859057	+	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	tgccgctcctcctggtccccCgtgcgatggtttcgggagcg	2	10	14	15	5	0	0	0	0	0	0	4	2	3	1	5	3	3	2	5	3	0	1	rs201104363	byFrequency	TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr12:6859057C>A	ENST00000203630.5	-	7	1160	c.516G>T	c.(514-516)acG>acT	p.T172T	MLF2_ENST00000539187.1_Silent_p.T172T|MLF2_ENST00000564181.1_5'Flank|MLF2_ENST00000435120.1_Silent_p.T172T|MLF2_ENST00000542154.1_Silent_p.T172T			Q15773	MLF2_HUMAN	myeloid leukemia factor 2	172					defense response (GO:0006952)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)		p.T172T(1)		kidney(2)|large_intestine(3)|lung(4)	9						CCTGGTCCCCCGTGCGATGGT	0.612																																					p.T172T		Atlas-SNP	.											MLF2,NS,carcinoma,0,1	MLF2	26	.	1	Substitution - coding silent(1)	lung(1)	c.G516T						PASS	.						109	91	97					12																	6859057		2203	4300	6503	SO:0001819	synonymous_variant	8079	exon7			GTCCCCCGTGCGA	U57342	CCDS8559.1	12p13.31	2014-09-11			ENSG00000089693	ENSG00000089693			7126	protein-coding gene	gene with protein product		601401				8661158	Standard	NM_005439		Approved	NTN4	uc010sfi.2	Q15773	OTTHUMG00000168717	ENST00000203630.5:c.516G>T	chr12.hg19:g.6859057C>A		109.0	0.0	.		131.0	6.0	.	NM_005439		Silent	SNP	ENST00000203630.5	hg19	CCDS8559.1	.	.	.	.	.	.	.	.	.	.	C	10.97	1.502929	0.26949	.	.	ENSG00000089693	ENST00000537126	.	.	.	5.83	-11.7	0.00046	.	.	.	.	.	T	0.63034	0.2477	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.80908	-0.1172	5	0.87932	D	0	.	11.3127	0.49372	0.0696:0.0898:0.1311:0.7095	.	.	.	.	L	183	.	ENSP00000439789:R183L	R	-	2	0	MLF2	6729318	0.000000	0.05858	0.093000	0.20910	0.970000	0.65996	-2.378000	0.01068	-3.057000	0.00258	-1.069000	0.02264	CGG	.	C|0.999;T|0.001	.	alt		0.612	MLF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400733.2			A	6859057	C	A	6859057	2	1	183	1	0	0	0	0	0	0	0	1	9623	639	23	4		4	MLF2	12	6859057	Silent	SNP	C	TCGA-GL-6846-01A-11D-1961-08	715176	6859057	126992838	40	10709											
KIAA0528	9847	hgsc.bcm.edu	37	chr12	22623804	22623804	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttttgtggtttgtaaagcCtgatttttgtcaaaagtgat	9	19	10	3	0	1	2	1	2	0	0	1	2	1	2	1	1	1	3	1	1	4	6			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr12:22623804C>T	ENST00000333957.4	-	21	2655	c.2400G>A	c.(2398-2400)caG>caA	p.Q800Q	C2CD5_ENST00000545552.1_Silent_p.Q813Q|C2CD5_ENST00000542676.1_Silent_p.Q800Q|C2CD5_ENST00000446597.1_Silent_p.Q800Q|C2CD5_ENST00000536386.1_Silent_p.Q802Q|C2CD5_ENST00000544930.1_Silent_p.Q615Q|C2CD5_ENST00000396028.2_Silent_p.Q791Q	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	800					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)										TTTGTAAAGCCTGATTTTTGT	0.343																																					p.Q800Q		Atlas-SNP	.											.	.	.	.	0			c.G2400A						PASS	.						159	149	152					12																	22623804		2203	4299	6502	SO:0001819	synonymous_variant	9847	exon21			TAAAGCCTGATTT	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.2400G>A	chr12.hg19:g.22623804C>T		78.0	0.0	.		93.0	27.0	.	NM_014802	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Silent	SNP	ENST00000333957.4	hg19	CCDS31758.1	.	.	.	.	.	.	.	.	.	.	C	8.519	0.868292	0.17250	.	.	ENSG00000111731	ENST00000539615	.	.	.	4.99	3.02	0.34903	.	.	.	.	.	T	0.47691	0.1459	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39881	-0.9592	4	.	.	.	-10.4578	4.4442	0.11589	0.0:0.6458:0.0:0.3542	.	.	.	.	K	84	.	.	R	-	2	0	KIAA0528	22515071	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.959000	0.40412	1.338000	0.45544	0.591000	0.81541	AGG	.	.	.	none		0.343	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802		T	22623804	C	T	22623804	2	4	183	1	0	0	0	0	0	0	0	1	8189	680	24	2		2	KIAA0528	12	22623804	Silent	SNP	C	TCGA-GL-6846-01A-11D-1961-08	15764747	22623804	111228091	41	10710											
ITGB7	3695	hgsc.bcm.edu	37	chr12	53586547	53586547	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catagtagccgtccaagcacTggcagcggttgcatttgcag	9	9	12	11	2	0	0	0	0	0	0	1	0	1	0	2	2	5	6	2	2	3	4			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr12:53586547T>C	ENST00000267082.5	-	13	2105	c.1874A>G	c.(1873-1875)cAg>cGg	p.Q625R	ITGB7_ENST00000550743.2_Intron|ITGB7_ENST00000338737.4_Intron|ITGB7_ENST00000422257.3_Missense_Mutation_p.Q625R	NM_000889.1	NP_000880.1	P26010	ITB7_HUMAN	integrin, beta 7	625	Cysteine-rich tandem repeats.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte tethering or rolling (GO:0050901)|multicellular organismal development (GO:0007275)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alpha4-beta7 complex (GO:0034669)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			NS(2)|breast(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GTCCAAGCACTGGCAGCGGTT	0.597																																					p.Q625R		Atlas-SNP	.											.	ITGB7	60	.	0			c.A1874G						PASS	.						117	95	102					12																	53586547		2203	4300	6503	SO:0001583	missense	3695	exon13			AAGCACTGGCAGC		CCDS8849.1	12q13.1	2010-03-23				ENSG00000139626		"Integrins"	6162	protein-coding gene	gene with protein product		147559				2040616	Standard	XM_005268851		Approved		uc001scc.3	P26010		ENST00000267082.5:c.1874A>G	chr12.hg19:g.53586547T>C	ENSP00000267082:p.Gln625Arg	75.0	0.0	.		106.0	65.0	.	NM_000889	Q9UCP7|Q9UCS7	Missense_Mutation	SNP	ENST00000267082.5	hg19	CCDS8849.1	.	.	.	.	.	.	.	.	.	.	T	13.89	2.372998	0.42105	.	.	ENSG00000139626	ENST00000422257;ENST00000267082	D;D	0.94046	-3.34;-3.34	5.13	5.13	0.70059	EGF, extracellular (1);	0.000000	0.40385	N	0.001119	D	0.87533	0.6201	N	0.20685	0.6	0.80722	D	1	P	0.40515	0.719	B	0.39258	0.295	D	0.86926	0.2070	10	0.30078	T	0.28	.	14.3146	0.66440	0.0:0.0:0.0:1.0	.	625	P26010	ITB7_HUMAN	R	625	ENSP00000408741:Q625R;ENSP00000267082:Q625R	ENSP00000267082:Q625R	Q	-	2	0	ITGB7	51872814	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	1.901000	0.39838	2.087000	0.62958	0.454000	0.30748	CAG	.	.	.	none		0.597	ITGB7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405821.2			C	53586547	T	C	53586547	3	2	183	1	0	0	0	0	1	0	0	0	7907	1580	55	3	538	3	ITGB7	12	53586547	Missense_Mutation	SNP	T	TCGA-GL-6846-01A-11D-1961-08	30962743	53586547	80265348	42	10711											
SHMT2	6472	hgsc.bcm.edu	37	chr12	57625342	57625342	+	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	cggagggttatcctggcaagAggtgagggctggagggcagt	8	7	20	6	1	0	2	0	1	0	1	1	4	1	4	1	7	0	4	1	7	2	1			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr12:57625342A>G	ENST00000328923.3	+	3	762	c.310A>G	c.(310-312)Aga>Gga	p.R104G	SHMT2_ENST00000554600.1_3'UTR|SHMT2_ENST00000553474.1_Splice_Site_p.R83G|SHMT2_ENST00000557487.1_Splice_Site_p.R104G|SHMT2_ENST00000449049.3_Splice_Site_p.R83G|SHMT2_ENST00000414700.3_Splice_Site_p.R83G|SHMT2_ENST00000393827.4_Intron	NM_001166356.1|NM_005412.5	NP_001159828.1|NP_005403.2	P34897	GLYM_HUMAN	serine hydroxymethyltransferase 2 (mitochondrial)	104					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)	TCCTGGCAAGAGGTGAGGGCT	0.597																																					p.R104G	Esophageal Squamous(150;1369 2416 49071 49364)	Atlas-SNP	.											.	SHMT2	40	.	0			c.A310G						PASS	.						55	52	53					12																	57625342		2203	4300	6503	SO:0001630	splice_region_variant	6472	exon3			GGCAAGAGGTGAG	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.311+1A>G	chr12.hg19:g.57625342A>G		58.0	0.0	.		92.0	4.0	.	NM_005412	B7Z9F1|E7EQ19|E7EU43|O00740|Q8N1A5	Missense_Mutation	SNP	ENST00000328923.3	hg19	CCDS8934.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.700417	0.88924	.	.	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	0.60920	0.15;0.15;0.15;0.15;0.15;0.15;0.15;0.15;0.15;0.15;0.15;0.15;0.15	4.71	4.71	0.59529	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.094386	0.64402	D	0.000001	D	0.85048	0.5608	H	0.98936	4.375	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.987	D	0.90665	0.4593	10	0.87932	D	0	.	13.611	0.62078	1.0:0.0:0.0:0.0	.	104;104	Q8N1A5;P34897	.;GLYM_HUMAN	G	104;104;104;83;83;83;83;83;83;83;83;83;83	ENSP00000333667:R104G;ENSP00000452315:R104G;ENSP00000452035:R104G;ENSP00000406881:R83G;ENSP00000450452:R83G;ENSP00000452161:R83G;ENSP00000450893:R83G;ENSP00000452045:R83G;ENSP00000452419:R83G;ENSP00000451968:R83G;ENSP00000452404:R83G;ENSP00000413770:R83G;ENSP00000451495:R83G	ENSP00000333667:R104G	R	+	1	2	SHMT2	55911609	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.024000	0.70857	2.128000	0.65567	0.459000	0.35465	AGA	.	.	.	none		0.597	SHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412525.2	NM_005412	Missense_Mutation	G	57625342	A	G	57625342	5	3	183	1	0	0	0	0	0	0	1	0	14299	318	11	3	320	3	SHMT2	12	57625342	Splice_Site	SNP	A	TCGA-GL-6846-01A-11D-1961-08	4038795	57625342	76226553	43	10712											
FSCB	84075	hgsc.bcm.edu	37	chr14	44975261	44975261	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaactttaacagaattctcCgcaactgcagtggctgcctc	10	11	8	12	1	1	2	0	1	1	1	3	2	1	2	2	1	5	3	2	1	4	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr14:44975261C>T	ENST00000340446.4	-	1	1221	c.930G>A	c.(928-930)gcG>gcA	p.A310A	RP11-163M18.1_ENST00000555433.1_RNA|RP11-163M18.1_ENST00000557465.1_RNA|RP11-163M18.1_ENST00000556228.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	310						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)		CAGAATTCTCCGCAACTGCAG	0.527																																					p.A310A		Atlas-SNP	.											.	FSCB	173	.	0			c.G930A						PASS	.						48	51	50					14																	44975261		2203	4300	6503	SO:0001819	synonymous_variant	84075	exon1			ATTCTCCGCAACT	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.930G>A	chr14.hg19:g.44975261C>T		88.0	0.0	.		88.0	38.0	.	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Silent	SNP	ENST00000340446.4	hg19	CCDS9679.1																																																																																			.	.	.	none		0.527	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135		T	44975261	C	T	44975261	2	4	183	1	0	0	0	0	0	0	0	1	6073	639	23	1		1	FSCB	14	44975261	Silent	SNP	C	TCGA-GL-6846-01A-11D-1961-08		44975261	62374279	44	10713											
TDP1	55775	hgsc.bcm.edu	37	chr14	90429932	90429932	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caggacatttgggacatgctGgataaagggaaccccttcca	12	8	11	10	0	0	0	0	0	0	0	1	4	1	4	3	4	2	1	3	4	3	3			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr14:90429932G>A	ENST00000335725.4	+	3	724	c.474G>A	c.(472-474)ctG>ctA	p.L158L	TDP1_ENST00000393452.3_Silent_p.L158L|TDP1_ENST00000555565.1_Intron|TDP1_ENST00000555880.1_Silent_p.L158L|TDP1_ENST00000393454.2_Silent_p.L158L|TDP1_ENST00000357382.3_5'UTR	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	158					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)		GGGACATGCTGGATAAAGGGA	0.512								Repair of DNA-protein crosslinks																													p.L158L		Atlas-SNP	.											.	TDP1	47	.	0			c.G474A						PASS	.						63	59	60					14																	90429932		2203	4300	6503	SO:0001819	synonymous_variant	55775	exon3			CATGCTGGATAAA	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.474G>A	chr14.hg19:g.90429932G>A		137.0	0.0	.		125.0	51.0	.	NM_018319	Q2HXX4|Q86TV8|Q96BK7|Q9NZM7|Q9NZM8	Silent	SNP	ENST00000335725.4	hg19	CCDS9888.1																																																																																			.	.	.	none		0.512	TDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411239.1	NM_018319		A	90429932	G	A	90429932	2	1	183	1	0	0	0	0	0	0	0	1	15740	1335	47	2		2	TDP1	14	90429932	Silent	SNP	G	TCGA-GL-6846-01A-11D-1961-08	45454671	90429932	16919608	45	10714											
SRRM2	23524	hgsc.bcm.edu	37	chr16	2814253	2814253	+	Missense_Mutation	SNP	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	atgaagagttaatggaggtgGtagagaagtctgaagaaccc	15	8	14	4	0	1	5	0	2	1	3	1	7	1	6	1	3	1	2	1	3	6	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr16:2814253G>A	ENST00000301740.8	+	11	4273	c.3724G>A	c.(3724-3726)Gta>Ata	p.V1242I		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	1242	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						AATGGAGGTGGTAGAGAAGTC	0.443																																					p.V1242I		Atlas-SNP	.											.	SRRM2	263	.	0			c.G3724A						PASS	.						106	113	111					16																	2814253		2198	4300	6498	SO:0001583	missense	23524	exon11			GAGGTGGTAGAGA	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.3724G>A	chr16.hg19:g.2814253G>A	ENSP00000301740:p.Val1242Ile	221.0	0.0	.		303.0	72.0	.	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	hg19	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	G	3.875	-0.027037	0.07589	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	T	0.24350	1.86	6.17	2.02	0.26589	.	0.793322	0.11547	N	0.553197	T	0.13713	0.0332	N	0.16478	0.41	0.09310	N	0.999996	B	0.06786	0.001	B	0.06405	0.002	T	0.33292	-0.9874	10	0.20519	T	0.43	0.1551	6.7948	0.23719	0.375:0.0:0.625:0.0	.	1242	Q9UQ35	SRRM2_HUMAN	I	1242;1242;494	ENSP00000301740:V1242I	ENSP00000301740:V1242I	V	+	1	0	SRRM2	2754254	0.001000	0.12720	0.868000	0.34077	0.982000	0.71751	-0.011000	0.12721	0.445000	0.26639	0.655000	0.94253	GTA	.	.	.	none		0.443	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			A	2814253	G	A	2814253	3	1	183	1	0	0	0	0	1	0	0	0	15181	1261	44	2	3762	2	SRRM2	16	2814253	Missense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08		2814253	87540500	46	10715											
SRCAP	10847	hgsc.bcm.edu	37	chr16	30735227	30735227	+	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	cctggacctccctccttggcAccatctggtgcttccccgtc	3	11	8	19	1	1	0	0	0	1	0	5	1	4	1	7	3	1	2	7	3	0	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr16:30735227A>C	ENST00000262518.4	+	25	4867	c.4482A>C	c.(4480-4482)gcA>gcC	p.A1494A	SRCAP_ENST00000395059.2_Silent_p.A1432A|SRCAP_ENST00000344771.4_Silent_p.A1336A	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1494	Pro-rich.			A -> Q (in Ref. 6; AAD39760). {ECO:0000305}.	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)			CCTCCTTGGCACCATCTGGTG	0.587																																					p.A1494A		Atlas-SNP	.											.	SRCAP	298	.	0			c.A4482C						PASS	.						113	102	106					16																	30735227		2197	4300	6497	SO:0001819	synonymous_variant	10847	exon25			CTTGGCACCATCT	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.4482A>C	chr16.hg19:g.30735227A>C		133.0	0.0	.		165.0	8.0	.	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Silent	SNP	ENST00000262518.4	hg19	CCDS10689.2																																																																																			.	.	.	none		0.587	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		C	30735227	A	C	30735227	2	2	183	1	0	0	0	0	0	0	0	1	15147	146	6	5		5	SRCAP	16	30735227	Silent	SNP	A	TCGA-GL-6846-01A-11D-1961-08	27920974	30735227	59619526	47	10716											
C16orf86	388284	hgsc.bcm.edu	37	chr16	67702137	67702137	+	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	ctgcggccgctgtaccagtaCgtcaactattgcaaccctga	9	9	9	14	3	1	1	1	1	0	0	1	1	1	1	3	1	6	4	3	1	5	4			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr16:67702137C>G	ENST00000403458.4	+	4	743	c.588C>G	c.(586-588)taC>taG	p.Y196*	ENKD1_ENST00000602409.1_5'Flank|ENKD1_ENST00000243878.4_5'Flank|ENKD1_ENST00000602644.1_5'Flank	NM_001012984.2	NP_001013002.2	Q6ZW13	CP086_HUMAN	chromosome 16 open reading frame 86	196										endometrium(2)|lung(4)	6		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.047)|all cancers(182;0.228)		TGTACCAGTACGTCAACTATT	0.667											OREG0023886	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y196X		Atlas-SNP	.											.	C16orf86	20	.	0			c.C588G						PASS	.						15	16	16					16																	67702137		2190	4293	6483	SO:0001587	stop_gained	388284	exon4			CCAGTACGTCAAC		CCDS32468.2	16q22.1	2008-10-30			ENSG00000159761	ENSG00000159761			33755	protein-coding gene	gene with protein product							Standard	NM_001012984		Approved	FLJ41802	uc002ety.3	Q6ZW13	OTTHUMG00000150527	ENST00000403458.4:c.588C>G	chr16.hg19:g.67702137C>G	ENSP00000384117:p.Tyr196*	25.0	0.0	.	1101	32.0	18.0	.	NM_001012984	B5MCW6	Nonsense_Mutation	SNP	ENST00000403458.4	hg19	CCDS32468.2	.	.	.	.	.	.	.	.	.	.	C	32	5.154005	0.94645	.	.	ENSG00000159761	ENST00000403458	.	.	.	5.95	2.97	0.34412	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.8901	9.6968	0.40163	0.0:0.7838:0.0:0.2162	.	.	.	.	X	196	.	ENSP00000384117:Y196X	Y	+	3	2	C16orf86	66259638	0.998000	0.40836	1.000000	0.80357	0.972000	0.66771	0.259000	0.18405	0.426000	0.26116	0.563000	0.77884	TAC	.	.	.	none		0.667	C16orf86-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318767.2	NM_001012984		G	67702137	C	G	67702137	4	3	183	1	0	0	0	0	0	1	0	0	1841	547	19	4	602	4	C16orf86	16	67702137	Nonsense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08	36966910	67702137	22652616	48	10717											
C16orf7	9605	hgsc.bcm.edu	37	chr16	89775318	89775318	+	Frame_Shift_Del	DEL	G	G	-																															tggggtgtggcctctggggtGgggcagtagtcttccgcaca																										TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr16:89775318delG	ENST00000389386.3	-	13	1768	c.1644delC	c.(1642-1644)cccfs	p.P548fs	VPS9D1_ENST00000565452.1_5'Flank|VPS9D1_ENST00000561976.1_Frame_Shift_Del_p.P478fs|VPS9D1-AS1_ENST00000562866.1_RNA	NM_004913.2	NP_004904.2	Q9Y2B5	VP9D1_HUMAN	VPS9 domain containing 1	548	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				ATP synthesis coupled proton transport (GO:0015986)		GTPase activator activity (GO:0005096)|transporter activity (GO:0005215)										CCTCTGGGGTGGGGCAGTAGT	0.682																																					p.T549fs		Atlas-INDEL	.											.	.	.	.	0			c.1645delA						PASS	.						13	16	15					16																	89775318		1928	4125	6053	SO:0001589	frameshift_variant	9605	exon13			.	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.1644delC	chr16.hg19:g.89775318delG	ENSP00000374037:p.Pro548fs	27.0	0.0	0		29.0	12.0	0.413793	NM_004913		Frame_Shift_Del	DEL	ENST00000389386.3	hg19	CCDS42220.1																																																																																			.	.	.	none		0.682	VPS9D1-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422508.1	NM_004913		-	89775318	G	-	89775318	7	5	183	1	0	1	0	1	0	0	0	0	1830	1335	47	0	263	0	C16orf7	16	89775318	Frame_Shift_Del	DEL	G	TCGA-GL-6846-01A-11D-1961-08	22073181	89775318	579435	49	10718											
SCARF1	8578	hgsc.bcm.edu	37	chr17	1538231	1538231	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggaccgcttcctctggtcTgactgccataggccctgtgg	4	10	12	15	2	2	1	0	1	2	0	3	2	3	2	5	4	1	1	5	4	1	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr17:1538231T>C	ENST00000263071.4	-	11	2363	c.2314A>G	c.(2314-2316)Aga>Gga	p.R772G	SCARF1_ENST00000348987.3_Missense_Mutation_p.R686G|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	772	Gly-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)		TCCTCTGGTCTGACTGCCATA	0.657																																					p.R772G		Atlas-SNP	.											.	SCARF1	46	.	0			c.A2314G						PASS	.						34	39	37					17																	1538231		2203	4298	6501	SO:0001583	missense	8578	exon11			CTGGTCTGACTGC	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.2314A>G	chr17.hg19:g.1538231T>C	ENSP00000263071:p.Arg772Gly	75.0	0.0	.		87.0	51.0	.	NM_003693	A8MQ05|O43701|Q8NHD2|Q8NHD3|Q8NHD4|Q8NHD5	Missense_Mutation	SNP	ENST00000263071.4	hg19	CCDS11007.1	.	.	.	.	.	.	.	.	.	.	t	9.073	0.997418	0.19043	.	.	ENSG00000074660	ENST00000263071;ENST00000348987	T;T	0.20463	2.07;2.77	4.68	-1.08	0.09936	.	0.960477	0.08537	N	0.931174	T	0.08980	0.0222	N	0.03608	-0.345	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.38993	-0.9635	10	0.24483	T	0.36	-2.2932	9.7539	0.40492	0.0:0.3094:0.0:0.6906	.	686;772	Q14162-2;Q14162	.;SREC_HUMAN	G	772;686	ENSP00000263071:R772G;ENSP00000323964:R686G	ENSP00000263071:R772G	R	-	1	2	SCARF1	1484981	0.000000	0.05858	0.004000	0.12327	0.092000	0.18411	-0.431000	0.06965	-0.332000	0.08489	0.450000	0.29827	AGA	.	.	.	none		0.657	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207081.4	NM_003693		C	1538231	T	C	1538231	3	2	183	1	0	0	0	0	1	0	0	0	13896	1588	55	3	182	3	SCARF1	17	1538231	Missense_Mutation	SNP	T	TCGA-GL-6846-01A-11D-1961-08		1538231	79656979	50	10719											
CAMKK1	84254	hgsc.bcm.edu	37	chr17	3788622	3788622	+	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	cctcgttctgccccaccaacCtctgcatctgagatggccac	7	9	7	18	1	3	1	0	1	3	1	4	2	3	1	6	1	3	2	6	1	1	1			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr17:3788622C>G	ENST00000348335.2	-	2	508	c.360G>C	c.(358-360)gaG>gaC	p.E120D	CAMKK1_ENST00000381771.2_Splice_Site_p.E120D|CAMKK1_ENST00000158166.5_Splice_Site_p.E120D|CAMKK1_ENST00000381769.2_Splice_Site_p.E147D	NM_032294.2	NP_115670.1	Q8N5S9	KKCC1_HUMAN	calcium/calmodulin-dependent protein kinase kinase 1, alpha	120					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)		CCCCACCAACCTCTGCATCTG	0.622																																					p.E120D		Atlas-SNP	.											.	CAMKK1	70	.	0			c.G360C						PASS	.						12	15	14					17																	3788622		2182	4265	6447	SO:0001630	splice_region_variant	84254	exon2			ACCAACCTCTGCA	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.360+1G>C	chr17.hg19:g.3788622C>G		39.0	0.0	.		46.0	14.0	.	NM_032294	Q9BQH3	Missense_Mutation	SNP	ENST00000348335.2	hg19	CCDS11038.1	.	.	.	.	.	.	.	.	.	.	C	11.57	1.677258	0.29783	.	.	ENSG00000004660	ENST00000381769;ENST00000348335;ENST00000381771;ENST00000158166	T;T;T;T	0.50548	0.74;0.74;0.74;0.74	5.57	5.57	0.84162	Protein kinase-like domain (1);	0.246503	0.41938	D	0.000799	T	0.31513	0.0799	N	0.19112	0.55	0.44316	D	0.997194	B;B	0.13145	0.007;0.002	B;B	0.14578	0.011;0.005	T	0.11494	-1.0585	9	.	.	.	-39.5364	12.0428	0.53462	0.1724:0.8276:0.0:0.0	.	120;120	F8W9H1;Q8N5S9	.;KKCC1_HUMAN	D	147;120;120;120	ENSP00000371188:E147D;ENSP00000323118:E120D;ENSP00000371190:E120D;ENSP00000158166:E120D	.	E	-	3	2	CAMKK1	3735371	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	2.413000	0.44618	2.632000	0.89209	0.491000	0.48974	GAG	.	.	.	none		0.622	CAMKK1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207456.1	NM_032294, NM_172206, NM_172207	Missense_Mutation	G	3788622	C	G	3788622	5	3	183	1	0	0	0	0	0	0	1	0	2608	695	24	4	1339	4	CAMKK1	17	3788622	Splice_Site	SNP	C	TCGA-GL-6846-01A-11D-1961-08	2250391	3788622	77406588	51	10720											
ZNF232	7775	hgsc.bcm.edu	37	chr17	5009512	5009512	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggacaacaagatgtgagttAtaaatgaaggttttaccaca	16	11	9	5	0	0	3	0	2	0	1	0	4	0	4	1	2	2	2	1	2	7	4			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr17:5009512A>G	ENST00000250076.3	-	5	1596	c.942T>C	c.(940-942)taT>taC	p.Y314Y	ZNF232_ENST00000416429.2_3'UTR|ZNF232_ENST00000575898.1_Silent_p.Y305Y|ZNF232_ENST00000575538.1_5'Flank	NM_014519.2	NP_055334.2	Q9UNY5	ZN232_HUMAN	zinc finger protein 232	287					transcription, DNA-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						GATGTGAGTTATAAATGAAGG	0.428																																					p.Y314Y		Atlas-SNP	.											.	ZNF232	42	.	0			c.T942C						PASS	.						111	110	111					17																	5009512		2203	4300	6503	SO:0001819	synonymous_variant	7775	exon5			TGAGTTATAAATG	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.942T>C	chr17.hg19:g.5009512A>G		136.0	0.0	.		188.0	47.0	.	NM_014519		Silent	SNP	ENST00000250076.3	hg19	CCDS11068.1																																																																																			.	.	.	none		0.428	ZNF232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216915.1	NM_014519		G	5009512	A	G	5009512	2	3	183	1	0	0	0	0	0	0	0	1	17797	456	16	3		3	ZNF232	17	5009512	Silent	SNP	A	TCGA-GL-6846-01A-11D-1961-08	1220890	5009512	76185698	52	10721											
SENP3	26168	hgsc.bcm.edu	37	chr17	7468055	7468055	+	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	tcagcaatgtgtgcagcatcGgggaccatgtggcccaggag	9	7	15	10	1	1	0	1	0	0	0	2	2	1	2	2	4	3	3	2	4	1	0	rs544419637		TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr17:7468055G>T	ENST00000429205.2	+	3	878	c.829G>T	c.(829-831)Ggg>Tgg	p.G277W	SENP3_ENST00000321337.7_Missense_Mutation_p.G277W|SENP3-EIF4A1_ENST00000579777.1_RNA|SENP3_ENST00000578868.1_3'UTR			Q9H4L4	SENP3_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 3	277						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)				GTGCAGCATCGGGGACCATGT	0.617																																					p.G277W		Atlas-SNP	.											.	SENP3	18	.	0			c.G829T						PASS	.						48	50	49					17																	7468055		1964	4161	6125	SO:0001583	missense	26168	exon3			AGCATCGGGGACC	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.829G>T	chr17.hg19:g.7468055G>T	ENSP00000403712:p.Gly277Trp	92.0	0.0	.		129.0	7.0	.	NM_015670	Q66K15|Q86VS7|Q96PS4|Q9Y3W9	Missense_Mutation	SNP	ENST00000429205.2	hg19		.	.	.	.	.	.	.	.	.	.	G	19.94	3.920082	0.73098	.	.	ENSG00000161956	ENST00000321337;ENST00000429205	T;T	0.57752	0.38;0.39	5.98	5.98	0.97165	.	0.000000	0.64402	D	0.000019	T	0.59432	0.2193	N	0.19112	0.55	0.42176	D	0.99166	D	0.89917	1.0	D	0.87578	0.998	T	0.60591	-0.7233	10	0.48119	T	0.1	-14.5285	15.9367	0.79717	0.0:0.0:1.0:0.0	.	277	Q9H4L4	SENP3_HUMAN	W	277	ENSP00000314029:G277W;ENSP00000403712:G277W	ENSP00000314029:G277W	G	+	1	0	SENP3	7408779	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.877000	0.69675	2.837000	0.97791	0.591000	0.81541	GGG	.	.	.	none		0.617	SENP3-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015670		T	7468055	G	T	7468055	3	4	183	1	0	0	0	0	1	0	0	0	14061	1116	39	4	835	4	SENP3	17	7468055	Missense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08	2458543	7468055	73727155	53	10722											
SLC13A2	9058	hgsc.bcm.edu	37	chr17	26818545	26818545	+	Missense_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	ccacctcacccagtgcatgaGcctgtgcgtgtgctactccg	6	9	10	16	2	1	1	1	1	0	0	2	1	2	1	5	0	5	2	5	0	1	1			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr17:26818545G>A	ENST00000314669.5	+	5	1085	c.665G>A	c.(664-666)aGc>aAc	p.S222N	SLC13A2_ENST00000537681.1_Missense_Mutation_p.S151N|SLC13A2_ENST00000444914.3_Missense_Mutation_p.S271N|SLC13A2_ENST00000545060.1_Missense_Mutation_p.S179N	NM_003984.3	NP_003975.1	Q13183	S13A2_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2	222					dicarboxylic acid transport (GO:0006835)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	low-affinity sodium:dicarboxylate symporter activity (GO:0015361)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_lung(13;0.000871)|Lung NSC(42;0.0027)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)	Succinic acid(DB00139)	CAGTGCATGAGCCTGTGCGTG	0.617																																					p.S271N		Atlas-SNP	.											.	SLC13A2	125	.	0			c.G812A						PASS	.						69	64	66					17																	26818545		2203	4300	6503	SO:0001583	missense	9058	exon5			GCATGAGCCTGTG	U26209	CCDS11231.1, CCDS54098.1	17p13.2	2013-05-22			ENSG00000007216	ENSG00000007216		"Solute carriers"	10917	protein-coding gene	gene with protein product		604148				8967342, 10343111	Standard	NM_001145975		Approved	NaDC-1	uc010wan.2	Q13183	OTTHUMG00000132523	ENST00000314669.5:c.665G>A	chr17.hg19:g.26818545G>A	ENSP00000316202:p.Ser222Asn	131.0	0.0	.		150.0	46.0	.	NM_001145975	B2RBI9|B4DPL1|E7ETH5|Q4VAR7	Missense_Mutation	SNP	ENST00000314669.5	hg19	CCDS11231.1	.	.	.	.	.	.	.	.	.	.	G	13.53	2.265898	0.40095	.	.	ENSG00000007216	ENST00000314669;ENST00000444914;ENST00000545060;ENST00000541739;ENST00000537681	T;T;T;T	0.03124	4.04;4.04;4.04;4.04	5.62	4.63	0.57726	.	0.200462	0.64402	D	0.000010	T	0.14227	0.0344	M	0.81341	2.54	0.42186	D	0.991709	D;B;B;B;B	0.65815	0.995;0.007;0.041;0.138;0.041	P;B;B;B;B	0.62560	0.904;0.098;0.081;0.073;0.081	T	0.01621	-1.1310	10	0.35671	T	0.21	-13.5366	9.6615	0.39958	0.0762:0.413:0.5108:0.0	.	179;271;178;151;222	F5GWV6;E7ETH5;B4E1M6;G3V1L2;Q13183	.;.;.;.;S13A2_HUMAN	N	222;271;179;178;151	ENSP00000316202:S222N;ENSP00000392411:S271N;ENSP00000441935:S179N;ENSP00000440802:S151N	ENSP00000316202:S222N	S	+	2	0	SLC13A2	23842672	1.000000	0.71417	1.000000	0.80357	0.705000	0.40729	2.293000	0.43558	1.346000	0.45694	0.557000	0.71058	AGC	.	.	.	none		0.617	SLC13A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255722.1	NM_003984		A	26818545	G	A	26818545	3	1	183	1	0	0	0	0	1	0	0	0	14405	971	34	2	830	2	SLC13A2	17	26818545	Missense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08	19350490	26818545	54376665	54	10723											
SPAG5	10615	hgsc.bcm.edu	37	chr17	26919846	26919846	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaatatcatgtcttgttgcTgccccagtggagatggtaca	10	12	10	9	0	2	1	1	0	1	1	2	2	2	1	2	2	3	3	2	2	3	4			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr17:26919846T>C	ENST00000321765.5	-	3	748	c.416A>G	c.(415-417)cAg>cGg	p.Q139R		NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	139					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)					GTCTTGTTGCTGCCCCAGTGG	0.453																																					p.Q139R		Atlas-SNP	.											.	SPAG5	92	.	0			c.A416G						PASS	.						190	176	180					17																	26919846		2203	4300	6503	SO:0001583	missense	10615	exon3			TGTTGCTGCCCCA	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.416A>G	chr17.hg19:g.26919846T>C	ENSP00000323300:p.Gln139Arg	185.0	0.0	.		253.0	145.0	.	NM_006461	O95213|Q9BWE8|Q9NT17|Q9UFE6	Missense_Mutation	SNP	ENST00000321765.5	hg19	CCDS32594.1	.	.	.	.	.	.	.	.	.	.	T	6.118	0.390021	0.11581	.	.	ENSG00000076382	ENST00000321765	T	0.25912	1.77	5.94	2.35	0.29111	.	0.760636	0.11855	N	0.522906	T	0.23210	0.0561	M	0.67953	2.075	0.25392	N	0.988515	P	0.49090	0.919	B	0.39738	0.308	T	0.32322	-0.9911	10	0.87932	D	0	-0.1373	3.1967	0.06635	0.1858:0.187:0.0:0.6271	.	139	Q96R06	SPAG5_HUMAN	R	139	ENSP00000323300:Q139R	ENSP00000323300:Q139R	Q	-	2	0	SPAG5	23943973	0.917000	0.31117	0.981000	0.43875	0.152000	0.21847	0.898000	0.28404	1.069000	0.40788	0.533000	0.62120	CAG	.	.	.	none		0.453	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461		C	26919846	T	C	26919846	3	2	183	1	0	0	0	0	1	0	0	0	14994	1580	55	3	3253	3	SPAG5	17	26919846	Missense_Mutation	SNP	T	TCGA-GL-6846-01A-11D-1961-08	101301	26919846	54275364	55	10724											
FAM20A	54757	hgsc.bcm.edu	37	chr17	66538845	66538846	+	Frame_Shift_Del	DEL	AA	AA	-																															agtactctacctggagagacAaagaaaacactctgcaggat																										TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr17:66538845_66538846delAA	ENST00000592554.1	-	6	1639_1640	c.917_918delTT	c.(916-918)tttfs	p.F306fs	PRKAR1A_ENST00000588188.2_Intron|AC079210.1_ENST00000600820.1_5'Flank|FAM20A_ENST00000226094.5_5'UTR	NM_001243746.1|NM_017565.3	NP_001230675.1|NP_060035.2	Q96MK3	FA20A_HUMAN	family with sequence similarity 20, member A	306					calcium ion homeostasis (GO:0055074)|enamel mineralization (GO:0070166)|tooth eruption (GO:0044691)	cell (GO:0005623)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)				cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(1)	9	Breast(10;1.64e-13)					CTGGAGAGACAAAGAAAACACT	0.525																																					p.306_307del		Atlas-INDEL	.											.	FAM20A	35	.	0			c.918_919del						PASS	.																																			SO:0001589	frameshift_variant	54757	exon6			.	AK056789	CCDS11679.1	17q24.2	2014-02-07			ENSG00000108950	ENSG00000108950			23015	protein-coding gene	gene with protein product		611062					Standard	NM_017565		Approved	DKFZp434F2322	uc002jho.3	Q96MK3	OTTHUMG00000180152	ENST00000592554.1:c.917_918delTT	chr17.hg19:g.66538845_66538846delAA	ENSP00000468308:p.Phe306fs	102.0	0.0	0		131.0	30.0	0.229008	NM_017565	B2RN47|B2RN49|Q9UF95	Frame_Shift_Del	DEL	ENST00000592554.1	hg19	CCDS11679.1																																																																																			.	.	.	none		0.525	FAM20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450029.2	NM_017565		-	66538846	AA	-	66538845	7	5	183	1	0	1	0	1	0	0	0	0	5541	127	5	0	731	0	FAM20A	17	66538845	Frame_Shift_Del	DEL	AA	TCGA-GL-6846-01A-11D-1961-08	39618999	66538845	14656365	56	10725											
CTAGE1	64693	hgsc.bcm.edu	37	chr18	19997258	19997258	+	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	ttgtatttctatctccaaccGttcttcattcgcttgaaatc	8	18	4	11	2	4	1	1	1	3	0	7	1	4	1	2	0	1	3	2	0	4	8	rs372127240		TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr18:19997258G>A	ENST00000525417.1	-	0	0				CTAGE1_ENST00000391403.2_Missense_Mutation_p.R173W			Q9HC47	CTGE1_HUMAN	cutaneous T-cell lymphoma-associated antigen 1							integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(19)|ovary(1)	27	all_cancers(21;0.000361)|all_epithelial(16;9.61e-06)|Colorectal(14;0.0533)|Lung NSC(20;0.0605)|Ovarian(2;0.116)|all_lung(20;0.135)					ATCTCCAACCGTTCTTCATTC	0.388																																					p.R173W		Atlas-SNP	.											CTAGE1_ENST00000391403,colon,carcinoma,0,2	CTAGE1	146	.	0			c.C517T						PASS	.	G	TRP/ARG	0,4314		0,0,2157	95	100	99		517	0.9	0	18		99	2,8574		0,2,4286	no	missense	CTAGE1	NM_172241.2	101	0,2,6443	AA,AG,GG		0.0233,0.0,0.0155	probably-damaging	173/746	19997258	2,12888	2157	4288	6445	SO:0001631	upstream_gene_variant	64693	exon1			CCAACCGTTCTTC	AF177229	CCDS45837.1	18q11.2	2010-05-26			ENSG00000212710	ENSG00000212710			24346	protein-coding gene	gene with protein product	"cutaneous T-cell lymphoma-associated antigen 1", "cutaneous T-cell lymphoma-associated antigen 2", "cancer/testis antigen family 21, member 1", "cancer/testis antigen family 21, member 2"	608856				11149944, 12839582	Standard	NM_172241		Approved	cTAGE-1, cTAGE-2, CTAGE, CT21.1, CT21.2	uc002ktv.1	Q96RT6			chr18.hg19:g.19997258G>A	Exception_encountered	253.0	0.0	.		169.0	71.0	.	NM_172241	B0YIZ3	Missense_Mutation	SNP	ENST00000525417.1	hg19		.	.	.	.	.	.	.	.	.	.	G	12.14	1.849249	0.32699	0.0	2.33E-4	ENSG00000212710	ENST00000391403	T	0.29655	1.56	0.909	0.909	0.19332	.	.	.	.	.	T	0.47581	0.1453	M	0.78637	2.42	0.09310	N	1	D	0.76494	0.999	D	0.64321	0.924	T	0.22941	-1.0202	8	.	.	.	.	5.2011	0.15264	0.0:0.0:1.0:0.0	.	173	Q96RT6	CTGE2_HUMAN	W	173	ENSP00000375220:R173W	.	R	-	1	2	CTAGE1	18251256	0.980000	0.34600	0.003000	0.11579	0.004000	0.04260	0.579000	0.23788	0.776000	0.33473	0.449000	0.29647	CGG	.	.	.	weak		0.388	CTAGE1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000386767.1	NM_022663, NM_172241		A	19997258	G	A	19997258	1	1	183	0	1	0	0	0	0	0	0	0	3994	1144	40	1		1	CTAGE1	18	19997258	5'Flank	SNP	G	TCGA-GL-6846-01A-11D-1961-08		19997258	58079990	57	10726											
LGI4	163175	hgsc.bcm.edu	37	chr19	35617247	35617247	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaagtggcgtgtggcatagAcatcctcggcctcggggatg	7	8	17	9	3	0	1	0	0	0	1	3	3	1	3	2	6	0	1	2	6	2	1			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr19:35617247A>G	ENST00000310123.3	-	8	1745	c.1226T>C	c.(1225-1227)gTc>gCc	p.V409A	LGI4_ENST00000493050.1_5'UTR|LGI4_ENST00000392225.3_Missense_Mutation_p.S435P	NM_139284.2	NP_644813.1	Q8N135	LGI4_HUMAN	leucine-rich repeat LGI family, member 4	409					adult locomotory behavior (GO:0008344)|glial cell proliferation (GO:0014009)|myelination in peripheral nervous system (GO:0022011)|neuron maturation (GO:0042551)	extracellular space (GO:0005615)				endometrium(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			TGTGGCATAGACATCCTCGGC	0.682																																					p.V409A		Atlas-SNP	.											.	LGI4	32	.	0			c.T1226C						PASS	.						35	32	33					19																	35617247		2203	4300	6503	SO:0001583	missense	163175	exon8			GCATAGACATCCT	AJ487519	CCDS12444.1	19q13.13	2008-07-03			ENSG00000153902	ENSG00000153902			18712	protein-coding gene	gene with protein product		608303				12023020	Standard	NM_139284		Approved		uc002nxx.2	Q8N135	OTTHUMG00000044558	ENST00000310123.3:c.1226T>C	chr19.hg19:g.35617247A>G	ENSP00000312273:p.Val409Ala	30.0	0.0	.		36.0	17.0	.	NM_139284	B2RN53|B9EGS7|Q5M8T1	Missense_Mutation	SNP	ENST00000310123.3	hg19	CCDS12444.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.1|21.1	4.097418|4.097418	0.76870|0.76870	.|.	.|.	ENSG00000153902|ENSG00000153902	ENST00000392225|ENST00000310123;ENST00000437421	T|T	0.68331|0.78595	-0.32|-1.19	4.66|4.66	4.66|4.66	0.58398|0.58398	.|.	.|0.000000	.|0.52532	.|D	.|0.000079	D|D	0.84261|0.84261	0.5433|0.5433	L|L	0.58583|0.58583	1.82|1.82	0.80722|0.80722	D|D	1|1	.|D;D	.|0.76494	.|0.999;0.999	.|D;D	.|0.85130	.|0.997;0.997	T|T	0.83349|0.83349	-0.0004|-0.0004	7|10	0.87932|0.37606	D|T	0|0.19	.|.	12.0653|12.0653	0.53583|0.53583	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|320;409	.|Q658V8;Q8N135	.|.;LGI4_HUMAN	P|A	435|409	ENSP00000376059:S435P|ENSP00000312273:V409A	ENSP00000376059:S435P|ENSP00000312273:V409A	S|V	-|-	1|2	0|0	LGI4|LGI4	40309087|40309087	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.386000|7.386000	0.79775|0.79775	1.745000|1.745000	0.51790|0.51790	0.477000|0.477000	0.44152|0.44152	TCT|GTC	.	.	.	none		0.682	LGI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103963.1			G	35617247	A	G	35617247	3	3	183	1	0	0	0	0	1	0	0	0	8761	275	10	3	395	3	LGI4	19	35617247	Missense_Mutation	SNP	A	TCGA-GL-6846-01A-11D-1961-08		35617247	23511736	58	10727											
ZNF546	339327	hgsc.bcm.edu	37	chr19	40520846	40520846	+	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	agaaaccctatgaatgtaagGaatgtgggaaggcttttatt	14	12	11	4	0	0	2	0	1	0	1	0	4	0	4	1	3	1	2	1	3	7	5			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr19:40520846G>A	ENST00000347077.4	+	7	1885	c.1669G>A	c.(1669-1671)Gaa>Aaa	p.E557K	ZNF546_ENST00000600094.1_Missense_Mutation_p.E531K|ZNF546_ENST00000596894.1_Intron	NM_178544.3	NP_848639.2	Q86UE3	ZN546_HUMAN	zinc finger protein 546	557					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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)					TGAATGTAAGGAATGTGGGAA	0.388																																					p.E557K		Atlas-SNP	.											.	ZNF546	93	.	0			c.G1669A						PASS	.						61	59	59					19																	40520846		2203	4300	6503	SO:0001583	missense	339327	exon7			TGTAAGGAATGTG	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.1669G>A	chr19.hg19:g.40520846G>A	ENSP00000339823:p.Glu557Lys	74.0	0.0	.		84.0	45.0	.	NM_178544	A8K913	Missense_Mutation	SNP	ENST00000347077.4	hg19	CCDS12548.1	.	.	.	.	.	.	.	.	.	.	g	15.69	2.907182	0.52333	.	.	ENSG00000187187	ENST00000347077;ENST00000392042	T	0.07327	3.2	3.0	-0.424	0.12321	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06781	0.0173	L	0.41415	1.275	0.09310	N	0.999998	B	0.06786	0.001	B	0.06405	0.002	T	0.35624	-0.9781	9	0.56958	D	0.05	.	4.6522	0.12601	0.23:0.1839:0.5862:0.0	.	557	Q86UE3	ZN546_HUMAN	K	557;166	ENSP00000339823:E557K	ENSP00000339823:E557K	E	+	1	0	ZNF546	45212686	0.001000	0.12720	0.990000	0.47175	0.997000	0.91878	0.499000	0.22546	-0.002000	0.14469	0.655000	0.94253	GAA	.	.	.	none		0.388	ZNF546-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462495.2	NM_178544		A	40520846	G	A	40520846	3	1	183	1	0	0	0	0	1	0	0	0	17990	1175	41	2	1687	2	ZNF546	19	40520846	Missense_Mutation	SNP	G	TCGA-GL-6846-01A-11D-1961-08	4903599	40520846	18608137	59	10728											
EGLN2	112398	hgsc.bcm.edu	37	chr19	41306603	41306603	+	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	gtggagagttacctgccctgTcccctgctcccctcctacca	5	10	8	18	0	0	1	0	0	0	1	3	2	3	1	8	1	4	2	8	1	2	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr19:41306603T>A	ENST00000593726.1	+	1	1154	c.126T>A	c.(124-126)tgT>tgA	p.C42*	RAB4B-EGLN2_ENST00000594136.1_3'UTR|CTC-490E21.12_ENST00000601627.1_5'Flank|EGLN2_ENST00000303961.4_Nonsense_Mutation_p.C42*|EGLN2_ENST00000406058.2_Nonsense_Mutation_p.C42*|EGLN2_ENST00000594140.1_5'Flank			Q96KS0	EGLN2_HUMAN	egl-9 family hypoxia-inducible factor 2	42					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)	ACCTGCCCTGTCCCCTGCTCC	0.652																																					p.C42X		Atlas-SNP	.											.	EGLN2	31	.	0			c.T126A						PASS	.						55	47	50					19																	41306603		2203	4300	6503	SO:0001587	stop_gained	112398	exon2			GCCCTGTCCCCTG	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.126T>A	chr19.hg19:g.41306603T>A	ENSP00000469686:p.Cys42*	56.0	0.0	.		52.0	15.0	.	NM_053046	A8K5S0|Q8WWY4|Q9BV14	Nonsense_Mutation	SNP	ENST00000593726.1	hg19	CCDS12567.1	.	.	.	.	.	.	.	.	.	.	T	38	6.815813	0.97861	.	.	ENSG00000171570	ENST00000303961;ENST00000406058	.	.	.	4.15	1.91	0.25777	.	0.092299	0.46758	D	0.000268	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.0525	7.5512	0.27798	0.0:0.1918:0.0:0.8082	.	.	.	.	X	42	.	ENSP00000307080:C42X	C	+	3	2	EGLN2	45998443	0.372000	0.25064	0.976000	0.42696	0.984000	0.73092	0.337000	0.19841	0.198000	0.20407	0.402000	0.26972	TGT	.	.	.	none		0.652	EGLN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463218.1			A	41306603	T	A	41306603	4	1	183	1	0	0	0	0	0	1	0	0	4971	1673	58	5	128	5	EGLN2	19	41306603	Nonsense_Mutation	SNP	T	TCGA-GL-6846-01A-11D-1961-08	785757	41306603	17822380	60	10729											
SLC24A3	57419	hgsc.bcm.edu	37	chr20	19665982	19665982	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaggatgatgatgaaggacCgtacacaccattcgacaccc	13	6	10	12	3	0	3	0	3	0	0	1	7	0	5	3	2	1	1	3	2	2	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr20:19665982C>T	ENST00000328041.6	+	12	1498	c.1301C>T	c.(1300-1302)cCg>cTg	p.P434L		NM_020689.3	NP_065740.2	Q9HC58	NCKX3_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 3	434					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						gatgaagGACCGTACACACCA	0.488																																					p.P434L		Atlas-SNP	.											.	SLC24A3	92	.	0			c.C1301T						PASS	.						166	142	150					20																	19665982		2203	4300	6503	SO:0001583	missense	57419	exon12			AAGGACCGTACAC	AF169257	CCDS13140.1	20p13	2013-05-22			ENSG00000185052	ENSG00000185052		"Solute carriers"	10977	protein-coding gene	gene with protein product		609839					Standard	NM_020689		Approved		uc002wrl.3	Q9HC58	OTTHUMG00000031993	ENST00000328041.6:c.1301C>T	chr20.hg19:g.19665982C>T	ENSP00000333519:p.Pro434Leu	102.0	0.0	.		106.0	41.0	.	NM_020689	B1AKV7|Q9BQJ9|Q9BQL7|Q9BQY3|Q9H519	Missense_Mutation	SNP	ENST00000328041.6	hg19	CCDS13140.1	.	.	.	.	.	.	.	.	.	.	C	13.61	2.287750	0.40494	.	.	ENSG00000185052	ENST00000328041	T	0.62498	0.02	5.67	5.67	0.87782	.	0.000000	0.64402	D	0.000001	T	0.62036	0.2395	M	0.61703	1.905	0.80722	D	1	B	0.17667	0.023	B	0.12837	0.008	T	0.56486	-0.7971	9	.	.	.	.	19.3646	0.94456	0.0:1.0:0.0:0.0	.	434	Q9HC58	NCKX3_HUMAN	L	434	ENSP00000333519:P434L	.	P	+	2	0	SLC24A3	19613982	1.000000	0.71417	0.833000	0.33012	0.408000	0.30992	7.465000	0.80898	2.668000	0.90789	0.563000	0.77884	CCG	.	.	.	none		0.488	SLC24A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078207.4	NM_020689		T	19665982	C	T	19665982	3	4	183	1	0	0	0	0	1	0	0	0	14480	652	23	1	1347	1	SLC24A3	20	19665982	Missense_Mutation	SNP	C	TCGA-GL-6846-01A-11D-1961-08		19665982	43359538	61	10730											
ARFGEF2	10564	hgsc.bcm.edu	37	chr20	47641990	47641990	+	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	aaggccttcaactccaattaCgagcagcggactgtcctgtg	10	9	10	12	2	1	0	1	0	0	0	3	2	3	1	3	2	4	1	3	2	4	2			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr20:47641990C>T	ENST00000371917.4	+	36	4896	c.4896C>T	c.(4894-4896)taC>taT	p.Y1632Y		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	1632					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)			ACTCCAATTACGAGCAGCGGA	0.473																																					p.Y1632Y	Esophageal Squamous(176;1738 1974 26285 33069 35354)	Atlas-SNP	.											.	ARFGEF2	160	.	0			c.C4896T						PASS	.						97	80	85					20																	47641990		2203	4300	6503	SO:0001819	synonymous_variant	10564	exon36			CAATTACGAGCAG	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.4896C>T	chr20.hg19:g.47641990C>T		90.0	0.0	.		66.0	27.0	.	NM_006420	Q5TFT9|Q9NTS1	Silent	SNP	ENST00000371917.4	hg19	CCDS13411.1																																																																																			.	.	.	none		0.473	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420		T	47641990	C	T	47641990	2	4	183	1	0	0	0	0	0	0	0	1	853	547	19	1		1	ARFGEF2	20	47641990	Silent	SNP	C	TCGA-GL-6846-01A-11D-1961-08	27976008	47641990	15383530	62	10731											
KRTAP10-3	386682	hgsc.bcm.edu	37	chr21	45978008	45978008	+	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	gagcacgtggggcggcagagGagggacacgcaggaggccgg	9	1	22	9	4	0	1	0	0	0	1	0	5	0	4	1	8	1	3	1	8	0	0			TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr21:45978008G>A	ENST00000391620.1	-	1	635	c.591C>T	c.(589-591)ctC>ctT	p.L197L	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198696.2	NP_941969.2	P60369	KR103_HUMAN	keratin associated protein 10-3	197	18 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				kidney(1)|lung(4)|prostate(1)|skin(1)	7						GGCGGCAGAGGAGGGACACGC	0.701																																					p.L197L		Atlas-SNP	.											.	KRTAP10-3	17	.	0			c.C591T						PASS	.						29	35	33					21																	45978008		2199	4295	6494	SO:0001819	synonymous_variant	386682	exon1			GCAGAGGAGGGAC	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.591C>T	chr21.hg19:g.45978008G>A		68.0	0.0	.		33.0	16.0	.	NM_198696	A3KN67|Q70LJ4	Silent	SNP	ENST00000391620.1	hg19	CCDS42956.1																																																																																			.	.	.	none		0.701	KRTAP10-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128031.1			A	45978008	G	A	45978008	2	1	183	1	0	0	0	0	0	0	0	1	8517	1161	41	2		2	KRTAP10-3	21	45978008	Silent	SNP	G	TCGA-GL-6846-01A-11D-1961-08		45978008	2151887	63	10732											
SMARCB1	6598	hgsc.bcm.edu	37	chr22	24175838	24175839	+	Frame_Shift_Ins	INS	-	-	T																															gtgcccactgctggagactcINStgacagacgctgagatggag																										TCGA-GL-6846-01A-11D-1961-08	TCGA-GL-6846-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	98a51f37-1d5f-4db0-b785-b751168bf46e	631ce65b-a92f-4c3c-b0eb-c2e13249edd7	g.chr22:24175838_24175839insT	ENST00000263121.7	+	8	1262_1263	c.1066_1067insT	c.(1066-1068)ctgfs	p.L356fs	SMARCB1_ENST00000407422.3_Frame_Shift_Ins_p.L347fs|SMARCB1_ENST00000407082.3_Frame_Shift_Ins_p.L310fs|SMARCB1_ENST00000344921.6_Frame_Shift_Ins_p.L365fs|DERL3_ENST00000464023.1_5'Flank	NM_003073.3	NP_003064.2	Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	356					ATP-dependent chromatin remodeling (GO:0043044)|blastocyst hatching (GO:0001835)|cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|DNA integration (GO:0015074)|DNA repair (GO:0006281)|mitotic cell cycle phase transition (GO:0044772)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	p53 binding (GO:0002039)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)	p.?(2)|p.L266_*386del(1)		bone(4)|central_nervous_system(198)|endometrium(4)|haematopoietic_and_lymphoid_tissue(25)|kidney(3)|large_intestine(5)|liver(2)|lung(5)|meninges(5)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|soft_tissue(194)	458		Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05)				GCTGGAGACTCTGACAGACGCT	0.629			"D, N, F, S"		malignant rhabdoid	malignant rhabdoid																															p.L356fs		Atlas-INDEL	.	yes	Rec	yes	Rhabdoid predisposition syndrome	22	22q11	6598	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1"		M	.	SMARCB1	586	.	3	Unknown(2)|Deletion - In frame(1)	central_nervous_system(3)	c.1066_1067insT						PASS	.																																			SO:0001589	frameshift_variant	6598	exon8			.	U04847	CCDS13817.1, CCDS46671.1	22q11.23	2014-09-17			ENSG00000099956	ENSG00000099956			11103	protein-coding gene	gene with protein product	"sucrose nonfermenting, yeast, homolog-like 1", "integrase interactor 1", "malignant rhabdoid tumor suppressor", "protein phosphatase 1, regulatory subunit 144"	601607		SNF5L1		7801128, 10319872, 10365963	Standard	NM_003073		Approved	BAF47, Ini1, Snr1, hSNFS, Sfh1p, RDT, PPP1R144	uc002zyb.3	Q12824	OTTHUMG00000150737	ENST00000263121.7:c.1067dupT	chr22.hg19:g.24175839_24175839dupT	ENSP00000263121:p.Leu356fs	149.0	0.0	0		111.0	91.0	0.81982	NM_003073	O75784|O95474|Q17S11|Q38GA1|Q76N08|Q9UBH2	Frame_Shift_Ins	INS	ENST00000263121.7	hg19	CCDS13817.1																																																																																			.	.	.	none		0.629	SMARCB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319872.1	NM_003073		T	24175839	-	T	24175838	7	5	183	1	0	1	1	0	0	0	0	0	14787	912	32	0	1096	0	SMARCB1	22	24175838	Frame_Shift_Ins	INS	-	TCGA-GL-6846-01A-11D-1961-08		24175838	27128728	64	10733											
MEGF6	1953	hgsc.bcm.edu	37	chr1	3511980	3511980	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtccgggcctccgtggtatAcacctgcctgtagcccatgt	5	10	12	14	2	0	0	0	0	0	0	2	0	2	0	6	3	3	2	6	3	3	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:3511980A>G	ENST00000356575.4	-	3	524	c.298T>C	c.(298-300)Tat>Cat	p.Y100H		NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	100	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.					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)		TCCGTGGTATACACCTGCCTG	0.632																																					p.Y100H	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.T298C						PASS	.						36	44	41					1																	3511980		2027	4179	6206	SO:0001583	missense	1953	exon3			TGGTATACACCTG	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.298T>C	chr1.hg19:g.3511980A>G	ENSP00000348982:p.Tyr100His	105.0	0.0	.		117.0	41.0	.	NM_001409	Q4AC86|Q5VV39	Missense_Mutation	SNP	ENST00000356575.4	hg19	CCDS41237.1	.	.	.	.	.	.	.	.	.	.	a	15.35	2.806840	0.50421	.	.	ENSG00000162591	ENST00000356575	D	0.85258	-1.96	3.92	3.92	0.45320	EMI domain (1);	0.000000	0.64402	U	0.000003	D	0.84991	0.5595	M	0.76574	2.34	0.39571	D	0.969271	D	0.53312	0.959	P	0.46076	0.503	D	0.86605	0.1869	10	0.59425	D	0.04	-38.3019	9.703	0.40198	1.0:0.0:0.0:0.0	.	100	O75095	MEGF6_HUMAN	H	100	ENSP00000348982:Y100H	ENSP00000348982:Y100H	Y	-	1	0	MEGF6	3501840	1.000000	0.71417	0.906000	0.35671	0.306000	0.27790	6.186000	0.72026	1.726000	0.51525	0.398000	0.26397	TAT	.	.	.	none		0.632	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409		G	3511980	A	G	3511980	3	3	184	1	0	0	0	0	1	0	0	0	9469	391	14	3	4467	3	MEGF6	1	3511980	Missense_Mutation	SNP	A	TCGA-GL-7773-01A-11D-2136-08		3511980	245738641	1	10734											
TCEB3	6924	hgsc.bcm.edu	37	chr1	24080614	24080614	+	Missense_Mutation	SNP	A	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	ctcttcaccccaggaagaagAagaagctggatttactgggc	12	8	11	10	0	2	3	1	0	1	3	2	5	2	5	2	3	2	1	2	3	5	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:24080614A>C	ENST00000418390.2	+	6	1911	c.1640A>C	c.(1639-1641)gAa>gCa	p.E547A	TCEB3_ENST00000609199.1_Missense_Mutation_p.E521A	NM_003198.2	NP_003189.2	Q14241	ELOA1_HUMAN	transcription elongation factor B (SIII), polypeptide 3 (110kDa, elongin A)	547					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)		CAGGAAGAAGAAGAAGCTGGA	0.473																																					p.E547A		Atlas-SNP	.											.	TCEB3	61	.	0			c.A1640C						PASS	.						107	99	102					1																	24080614		2203	4300	6503	SO:0001583	missense	6924	exon6			AAGAAGAAGAAGC	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.1640A>C	chr1.hg19:g.24080614A>C	ENSP00000395574:p.Glu547Ala	124.0	0.0	.		120.0	42.0	.	NM_003198	B2R7Q8|Q8IXH1	Missense_Mutation	SNP	ENST00000418390.2	hg19	CCDS239.2	.	.	.	.	.	.	.	.	.	.	A	23.4	4.405738	0.83230	.	.	ENSG00000011007	ENST00000418390	T	0.10382	2.88	5.71	5.71	0.89125	.	0.243724	0.31936	N	0.006831	T	0.15435	0.0372	M	0.70275	2.135	0.58432	D	0.999995	D	0.54397	0.966	B	0.42462	0.388	T	0.01269	-1.1400	10	0.72032	D	0.01	-23.7872	10.6424	0.45600	0.9197:0.0:0.0803:0.0	.	547	Q14241	ELOA1_HUMAN	A	547	ENSP00000395574:E547A	ENSP00000395574:E547A	E	+	2	0	TCEB3	23953201	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.929000	0.70096	2.179000	0.69175	0.379000	0.24179	GAA	.	.	.	none		0.473	TCEB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000008230.2	NM_003198		C	24080614	A	C	24080614	3	2	184	1	0	0	0	0	1	0	0	0	15693	246	9	5	1662	5	TCEB3	1	24080614	Missense_Mutation	SNP	A	TCGA-GL-7773-01A-11D-2136-08	20568634	24080614	225170007	2	10735											
PUM1	9698	hgsc.bcm.edu	37	chr1	31479871	31479871	+	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	ccaggcactgtctcgccattGatcacccaggaatattcctt	9	11	7	14	1	2	1	1	1	1	0	4	2	3	2	4	2	0	1	4	2	2	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:31479871G>C	ENST00000257075.5	-	4	604	c.511C>G	c.(511-513)Caa>Gaa	p.Q171E	PUM1_ENST00000423018.2_Intron|PUM1_ENST00000440538.2_Missense_Mutation_p.Q171E|PUM1_ENST00000424085.2_Intron|PUM1_ENST00000373742.2_Intron|PUM1_ENST00000426105.2_Missense_Mutation_p.Q171E|PUM1_ENST00000373741.4_Missense_Mutation_p.Q207E|PUM1_ENST00000373747.3_Missense_Mutation_p.Q171E	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	171					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)		TCTCGCCATTGATCACCCAGG	0.418																																					p.Q171E		Atlas-SNP	.											.	PUM1	107	.	0			c.C511G						PASS	.						301	283	289					1																	31479871		2203	4300	6503	SO:0001583	missense	9698	exon4			GCCATTGATCACC	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.511C>G	chr1.hg19:g.31479871G>C	ENSP00000257075:p.Gln171Glu	340.0	0.0	.		363.0	122.0	.	NM_014676	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Missense_Mutation	SNP	ENST00000257075.5	hg19	CCDS338.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	3.154|3.154	-0.173618|-0.173618	0.06421|0.06421	.|.	.|.	ENSG00000134644|ENSG00000134644	ENST00000257075;ENST00000373747;ENST00000426105;ENST00000440538;ENST00000373741;ENST00000543952|ENST00000525843	T;T;T;T;T|.	0.17691|.	2.26;2.53;2.54;2.54;2.53|.	5.26|5.26	5.26|5.26	0.73747|0.73747	.|.	0.000000|.	0.64402|.	D|.	0.000004|.	T|.	0.55800|.	0.1943|.	N|N	0.24115|0.24115	0.695|0.695	0.80722|0.80722	D|D	1|1	B;B;B;B|.	0.15473|.	0.002;0.013;0.001;0.001|.	B;B;B;B|.	0.12156|.	0.002;0.007;0.001;0.001|.	T|.	0.49513|.	-0.8932|.	10|.	0.05620|.	T|.	0.96|.	-4.9673|-4.9673	19.0513|19.0513	0.93046|0.93046	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	207;171;171;171|.	Q5T1Z8;Q14671-2;Q14671;E9PCJ0|.	.;.;PUM1_HUMAN;.|.	E|X	171;171;171;171;207;171|187	ENSP00000257075:Q171E;ENSP00000362852:Q171E;ENSP00000391723:Q171E;ENSP00000401777:Q171E;ENSP00000362846:Q207E|.	ENSP00000257075:Q171E|.	Q|S	-|-	1|2	0|0	PUM1|PUM1	31252458|31252458	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.482000|4.482000	0.60257|0.60257	2.736000|2.736000	0.93811|0.93811	0.557000|0.557000	0.71058|0.71058	CAA|TCA	.	.	.	none		0.418	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1			C	31479871	G	C	31479871	3	2	184	1	0	0	0	0	1	0	0	0	12838	1299	45	4	3131	4	PUM1	1	31479871	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	7399257	31479871	217770750	3	10736											
CDC20	991	hgsc.bcm.edu	37	chr1	43828621	43828621	+	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	tactgttctcatttgctccaGgtcacacatcccgggtcctg	6	13	8	14	1	2	0	2	0	1	0	6	0	5	0	3	2	2	2	3	2	1	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:43828621G>A	ENST00000372462.1	+	10	1524		c.e10-1		CDC20_ENST00000310955.6_Splice_Site|ELOVL1_ENST00000470769.1_5'Flank			Q12834	CDC20_HUMAN	cell division cycle 20						activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell cycle (GO:0007049)|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 cell proliferation (GO:0008284)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein ubiquitination (GO:0016567)|regulation of dendrite development (GO:0050773)|regulation of meiosis (GO:0040020)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|spindle (GO:0005819)	enzyme binding (GO:0019899)|protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	15	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				ATTTGCTCCAGGTCACACATC	0.532																																					.	Esophageal Squamous(137;1154 1759 10362 10401 46925)	Atlas-SNP	.											.	CDC20	34	.	0			c.1322-1G>A						PASS	.						72	70	70					1																	43828621		2203	4300	6503	SO:0001630	splice_region_variant	991	exon11			GCTCCAGGTCACA	U05340	CCDS484.1	1p34.1	2013-01-17	2013-01-17		ENSG00000117399	ENSG00000117399		"WD repeat domain containing"	1723	protein-coding gene	gene with protein product		603618	"CDC20 (cell division cycle 20, S. cerevisiae, homolog)", "CDC20 cell division cycle 20 homolog (S. cerevisiae)", "cell division cycle 20 homolog (S. cerevisiae)"			7513050, 9353311	Standard	NM_001255		Approved	p55CDC, CDC20A	uc001cix.3	Q12834	OTTHUMG00000007420	ENST00000372462.1:c.1322-1G>A	chr1.hg19:g.43828621G>A		112.0	0.0	.		146.0	61.0	.	NM_001255	B2R6Z6|D3DPJ1|Q5JUY4|Q9BW56|Q9UQI9	Splice_Site	SNP	ENST00000372462.1	hg19	CCDS484.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.972600	0.74246	.	.	ENSG00000117399	ENST00000437896;ENST00000310955;ENST00000372462	.	.	.	5.76	4.85	0.62838	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7097	0.69222	0.0697:0.0:0.9303:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CDC20	43601208	1.000000	0.71417	0.994000	0.49952	0.916000	0.54674	9.338000	0.96553	1.431000	0.47355	0.561000	0.74099	.	.	.	.	none		0.532	CDC20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019488.1	NM_001255	Intron	A	43828621	G	A	43828621	5	1	184	1	0	0	0	0	0	0	1	0	3061	1014	35	2	1359	2	CDC20	1	43828621	Splice_Site	SNP	G	TCGA-GL-7773-01A-11D-2136-08	12348750	43828621	205422000	4	10737											
STIL	6491	hgsc.bcm.edu	37	chr1	47717027	47717027	+	Frame_Shift_Del	DEL	T	T	-																															aggttctttactaagaaagcTggcttttcagtcaactgctg																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:47717027delT	ENST00000360380.3	-	18	4008	c.3645delA	c.(3643-3645)ccafs	p.P1215fs	STIL_ENST00000243182.6_Frame_Shift_Del_p.P1215fs|STIL_ENST00000371877.3_Frame_Shift_Del_p.P1216fs|STIL_ENST00000396221.2_Frame_Shift_Del_p.P1198fs|STIL_ENST00000337817.5_Frame_Shift_Del_p.P1215fs	NM_001282936.1	NP_001269865.1	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus	1215					cell proliferation (GO:0008283)|determination of left/right symmetry (GO:0007368)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|notochord development (GO:0030903)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	36		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)				CTAAGAAAGCTGGCTTTTCAG	0.423																																					p.A1217fs		Atlas-INDEL	.											.	STIL	91	.	0			c.3649delG						PASS	.						120	121	121					1																	47717027		2203	4300	6503	SO:0001589	frameshift_variant	6491	exon17			.	M74558	CCDS548.1, CCDS41329.1, CCDS72785.1, CCDS72786.1	1p32	2010-02-09	2005-11-29	2005-11-29	ENSG00000123473	ENSG00000123473			10879	protein-coding gene	gene with protein product		181590	"TAL1 (SCL) interrupting locus"	SIL		2209547	Standard	NM_003035		Approved	MCPH7	uc001crd.1	Q15468	OTTHUMG00000007851	ENST00000360380.3:c.3645delA	chr1.hg19:g.47717027delT	ENSP00000353544:p.Pro1215fs	117.0	0.0	0		175.0	71.0	0.405714	NM_001048166	Q5T0C5|Q68CN9	Frame_Shift_Del	DEL	ENST00000360380.3	hg19	CCDS548.1																																																																																			.	.	.	none		0.423	STIL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021649.2	NM_003035		-	47717027	T	-	47717027	7	5	184	1	0	1	0	1	0	0	0	0	15294	1567	55	0	222	0	STIL	1	47717027	Frame_Shift_Del	DEL	T	TCGA-GL-7773-01A-11D-2136-08	3888406	47717027	201533594	5	10738											
PRPF38A	84950	hgsc.bcm.edu	37	chr1	52881045	52881046	+	In_Frame_Ins	INS	-	-	AGT																															cagacacaggagccactcaaINSagtctcccgaaaggtaatga																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:52881045_52881046insAGT	ENST00000257181.9	+	9	1069_1070	c.883_884insAGT	c.(883-885)aag>aAGTag	p.295_296ins*	PRPF38A_ENST00000474048.1_3'UTR	NM_032864.3	NP_116253.2	Q8NAV1	PR38A_HUMAN	pre-mRNA processing factor 38A	295					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			cervix(2)|kidney(1)|large_intestine(2)|liver(1)|lung(2)|stomach(1)	9						GAGCCACTCAAAGTCTCCCGAA	0.401																																					p.K295delinsKX		Atlas-INDEL	.											.	PRPF38A	36	.	0			c.883_884insAGT						PASS	.																																			SO:0001652	inframe_insertion	84950	exon9			.	AK092038	CCDS567.1	1p32.3	2013-10-03	2013-10-03		ENSG00000134748	ENSG00000134748			25930	protein-coding gene	gene with protein product			"PRP38 pre-mRNA processing factor 38 (yeast) domain containing A"			12477932	Standard	NM_032864		Approved	FLJ14936, Prp38	uc001ctw.4	Q8NAV1	OTTHUMG00000008199	ENST00000257181.9:c.884_886dupAGT	chr1.hg19:g.52881046_52881048dupAGT	ENSP00000257181:p.Ser296*	53.0	0.0	0		51.0	19.0	0.372549	NM_032864	Q96JW1|Q9BVZ8	In_Frame_Ins	INS	ENST00000257181.9	hg19	CCDS567.1																																																																																			.	.	.	none		0.401	PRPF38A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022459.2	NM_032864		AGT	52881046	-	AGT	52881045	7	5	184	1	0	1	1	0	0	0	0	0	12577	15	1	0	917	0	PRPF38A	1	52881045	In_Frame_Ins	INS	-	TCGA-GL-7773-01A-11D-2136-08	5164018	52881045	196369576	6	10739											
DBT	1629	hgsc.bcm.edu	37	chr1	100680458	100680458	+	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	ctcggagcttaaccagttcaGtaaggtcaatctcatcacaa	13	10	7	11	1	4	0	4	0	1	0	6	1	4	1	1	2	2	3	1	2	4	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:100680458G>T	ENST00000370132.4	-	7	867	c.854C>A	c.(853-855)aCt>aAt	p.T285N	DBT_ENST00000370131.3_Missense_Mutation_p.T285N	NM_001918.3	NP_001909.3	P11182	ODB2_HUMAN	dihydrolipoamide branched chain transacylase E2	285					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity (GO:0043754)			NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(1)	19		all_epithelial(167;5.4e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0739)|all cancers(265;0.123)|COAD - Colon adenocarcinoma(174;0.154)|Lung(183;0.199)		AACCAGTTCAGTAAGGTCAAT	0.373																																					p.T285N		Atlas-SNP	.											.	DBT	39	.	0			c.C854A						PASS	.						77	73	75					1																	100680458		2203	4300	6503	SO:0001583	missense	1629	exon7			AGTTCAGTAAGGT	BC016675	CCDS767.1	1p31	2008-02-05	2004-11-15		ENSG00000137992	ENSG00000137992			2698	protein-coding gene	gene with protein product		248610	"dihydrolipoamide branched chain transacylase (E2 component of branched chain keto acid dehydrogenase complex; maple syrup urine disease)"			1420314, 1429740	Standard	NM_001918		Approved		uc001dta.3	P11182	OTTHUMG00000010921	ENST00000370132.4:c.854C>A	chr1.hg19:g.100680458G>T	ENSP00000359151:p.Thr285Asn	59.0	0.0	.		80.0	29.0	.	NM_001918	B2R811|Q5VVL8	Missense_Mutation	SNP	ENST00000370132.4	hg19	CCDS767.1	.	.	.	.	.	.	.	.	.	.	G	13.57	2.275507	0.40294	.	.	ENSG00000137992	ENST00000543138;ENST00000370132;ENST00000370131	T;T	0.51325	0.71;0.71	5.44	4.53	0.55603	2-oxoacid dehydrogenase acyltransferase, catalytic domain (1);Chloramphenicol acetyltransferase-like domain (1);	0.199950	0.51477	D	0.000096	T	0.38427	0.1040	M	0.81112	2.525	0.45634	D	0.99856	B;B	0.18310	0.002;0.027	B;B	0.24701	0.011;0.055	T	0.41875	-0.9484	10	0.42905	T	0.14	-14.8131	14.2831	0.66226	0.0716:0.0:0.9284:0.0	.	104;285	F5H1F9;P11182	.;ODB2_HUMAN	N	104;285;285	ENSP00000359151:T285N;ENSP00000359150:T285N	ENSP00000359150:T285N	T	-	2	0	DBT	100453046	1.000000	0.71417	0.998000	0.56505	0.945000	0.59286	3.303000	0.51858	1.299000	0.44798	0.655000	0.94253	ACT	.	.	.	none		0.373	DBT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030101.2	NM_001918		T	100680458	G	T	100680458	3	4	184	1	0	0	0	0	1	0	0	0	4260	1029	36	4	614	4	DBT	1	100680458	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	47799413	100680458	148570163	7	10740											
CELSR2	1952	hgsc.bcm.edu	37	chr1	109807126	109807126	+	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	gttaacagcctggatcccagCcatggggagagcatcaacgt	11	7	12	11	1	1	1	1	0	0	1	2	3	2	2	3	3	5	2	3	3	2	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:109807126C>A	ENST00000271332.3	+	11	5401	c.5340C>A	c.(5338-5340)agC>agA	p.S1780R		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	1780	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		TGGATCCCAGCCATGGGGAGA	0.617																																					p.S1780R	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.C5340A						PASS	.						162	141	148					1																	109807126		2203	4300	6503	SO:0001583	missense	1952	exon11			TCCCAGCCATGGG	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.5340C>A	chr1.hg19:g.109807126C>A	ENSP00000271332:p.Ser1780Arg	148.0	0.0	.		184.0	71.0	.	NM_001408	Q5T2Y7|Q92566	Missense_Mutation	SNP	ENST00000271332.3	hg19	CCDS796.1	.	.	.	.	.	.	.	.	.	.	C	11.57	1.677071	0.29783	.	.	ENSG00000143126	ENST00000271332	T	0.69435	-0.4	4.79	3.85	0.44370	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	.	.	.	.	T	0.34366	0.0895	L	0.36672	1.1	0.41718	D	0.989496	B	0.14438	0.01	B	0.09377	0.004	T	0.17776	-1.0358	9	0.15952	T	0.53	.	10.7084	0.45969	0.1481:0.709:0.1429:0.0	.	1780	Q9HCU4	CELR2_HUMAN	R	1780	ENSP00000271332:S1780R	ENSP00000271332:S1780R	S	+	3	2	CELSR2	109608649	0.905000	0.30787	0.998000	0.56505	0.796000	0.44982	1.567000	0.36407	1.193000	0.43086	0.561000	0.74099	AGC	.	.	.	none		0.617	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		A	109807126	C	A	109807126	3	1	184	1	0	0	0	0	1	0	0	0	3224	738	26	4	5382	4	CELSR2	1	109807126	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	9126668	109807126	139443495	8	10741											
CHIA	27159	hgsc.bcm.edu	37	chr1	111862962	111862962	+	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	ttctgtgctgtcagagccaaCggcctctaccccgtggcaaa	8	9	10	14	2	3	1	1	0	2	1	3	1	3	1	4	2	4	2	4	2	3	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:111862962C>T	ENST00000369740.1	+	12	1408	c.1305C>T	c.(1303-1305)aaC>aaT	p.N435N	CHIA_ENST00000343320.6_Silent_p.N435N|CHIA_ENST00000451398.2_Silent_p.N274N|CHIA_ENST00000353665.6_Silent_p.N274N|RP5-1125M8.2_ENST00000426321.1_RNA|CHIA_ENST00000483391.1_Silent_p.N274N|CHIA_ENST00000430615.1_Silent_p.N327N	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	435	Chitin-binding type-2. {ECO:0000255|PROSITE-ProRule:PRU00144}.				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)		TCAGAGCCAACGGCCTCTACC	0.597																																					p.N435N		Atlas-SNP	.											.	CHIA	115	.	0			c.C1305T						PASS	.						68	62	64					1																	111862962		2203	4300	6503	SO:0001819	synonymous_variant	27159	exon12			AGCCAACGGCCTC	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.1305C>T	chr1.hg19:g.111862962C>T		68.0	0.0	.		77.0	31.0	.	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Silent	SNP	ENST00000369740.1	hg19	CCDS41368.1																																																																																			.	.	.	none		0.597	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1			T	111862962	C	T	111862962	2	4	184	1	0	0	0	0	0	0	0	1	3344	535	19	1		1	CHIA	1	111862962	Silent	SNP	C	TCGA-GL-7773-01A-11D-2136-08	2055836	111862962	137387659	9	10742											
RSBN1	54665	hgsc.bcm.edu	37	chr1	114308975	114308975	+	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	actgatgaatgacatttctaGggatgaagtagatatcattg	14	13	10	4	0	2	5	1	4	1	1	2	6	2	6	0	1	0	1	0	1	5	5			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:114308975G>C	ENST00000261441.5	-	7	2099	c.2036C>G	c.(2035-2037)cCt>cGt	p.P679R	RSBN1_ENST00000369581.2_5'UTR	NM_018364.3	NP_060834.2	Q5VWQ0	RSBN1_HUMAN	round spermatid basic protein 1	679						nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(3)|urinary_tract(2)	29	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GACATTTCTAGGGATGAAGTA	0.443																																					p.P679R		Atlas-SNP	.											.	RSBN1	71	.	0			c.C2036G						PASS	.						102	94	97					1																	114308975		2203	4300	6503	SO:0001583	missense	54665	exon7			TTTCTAGGGATGA	AK002082	CCDS862.1	1p13.1	2008-02-05			ENSG00000081019	ENSG00000081019			25642	protein-coding gene	gene with protein product		615858				12477932	Standard	NM_018364		Approved	FLJ11220, ROSBIN	uc001edq.3	Q5VWQ0	OTTHUMG00000011938	ENST00000261441.5:c.2036C>G	chr1.hg19:g.114308975G>C	ENSP00000261441:p.Pro679Arg	114.0	0.0	.		177.0	70.0	.	NM_018364	A8K937|Q6AI21|Q8TC33|Q9HA80|Q9NUP6	Missense_Mutation	SNP	ENST00000261441.5	hg19	CCDS862.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.042164	0.75732	.	.	ENSG00000081019	ENST00000261441	.	.	.	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.81088	0.4750	M	0.77616	2.38	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.82230	-0.0560	9	0.87932	D	0	-8.3576	19.8965	0.96963	0.0:0.0:1.0:0.0	.	679	Q5VWQ0	RSBN1_HUMAN	R	679	.	ENSP00000261441:P679R	P	-	2	0	RSBN1	114110498	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.813000	0.99286	2.771000	0.95319	0.563000	0.77884	CCT	.	.	.	none		0.443	RSBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033022.2	NM_018364		C	114308975	G	C	114308975	3	2	184	1	0	0	0	0	1	0	0	0	13709	1000	35	4	376	4	RSBN1	1	114308975	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	2446013	114308975	134941646	10	10743											
FLG	2312	hgsc.bcm.edu	37	chr1	152276023	152276023	+	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	gggaccctgagtgtccagacCtatctaccgattgctcgtgg	7	10	12	12	2	1	2	0	1	1	1	3	4	2	3	4	2	2	1	4	2	2	3	rs367989347		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:152276023C>G	ENST00000368799.1	-	3	11374	c.11339G>C	c.(11338-11340)aGg>aCg	p.R3780T	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3780	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)			GTGTCCAGACCTATCTACCGA	0.577									Ichthyosis																												p.R3780T		Atlas-SNP	.											.	FLG	900	.	0			c.G11339C						PASS	.						359	347	351					1																	152276023		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CCAGACCTATCTA	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.11339G>C	chr1.hg19:g.152276023C>G	ENSP00000357789:p.Arg3780Thr	567.0	0.0	.		744.0	264.0	.	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	3.380	-0.126622	0.06795	.	.	ENSG00000143631	ENST00000368799	T	0.01599	4.74	2.62	1.67	0.24075	.	.	.	.	.	T	0.00637	0.0021	L	0.52364	1.645	0.09310	N	1	B	0.18013	0.025	B	0.10450	0.005	T	0.44802	-0.9304	9	0.14656	T	0.56	-2.2716	7.2143	0.25951	0.0:0.6727:0.3273:0.0	.	3780	P20930	FILA_HUMAN	T	3780	ENSP00000357789:R3780T	ENSP00000357789:R3780T	R	-	2	0	FLG	150542647	0.000000	0.05858	0.007000	0.13788	0.002000	0.02628	-0.617000	0.05584	0.644000	0.30656	0.552000	0.68991	AGG	.	.	.	none		0.577	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		G	152276023	C	G	152276023	3	3	184	1	0	0	0	0	1	0	0	0	5929	681	24	4	850	4	FLG	1	152276023	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	37967048	152276023	96974598	11	10744											
PBX1	5087	hgsc.bcm.edu	37	chr1	164781319	164781320	+	Frame_Shift_Ins	INS	-	-	GTATA																															tttatgctgccaaaacagctINSgtcactgctaccaatgtgtc																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:164781319_164781320insGTATA	ENST00000420696.2	+	6	1118_1119	c.930_931insGTATA	c.(931-933)gtcfs	p.-311fs	PBX1_ENST00000367897.1_Frame_Shift_Ins_p.-311fs|PBX1_ENST00000540246.1_Frame_Shift_Ins_p.-206fs|PBX1_ENST00000560641.1_Frame_Shift_Ins_p.-206fs|PBX1_ENST00000401534.1_Frame_Shift_Ins_p.-311fs|PBX1_ENST00000559240.1_Intron|PBX1_ENST00000540236.1_Frame_Shift_Ins_p.-311fs	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						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						CCAAAACAGCTGTCACTGCTAC	0.455			T	"TCF3, EWSR1"	"pre B-ALL, myoepithelioma"																																p.A310fs		Atlas-INDEL	.		Dom	yes		1	1q23	5087	pre-B-cell leukemia transcription factor 1		"L, M"	.	PBX1	60	.	0			c.930_931insGTATA						PASS	.																																			SO:0001589	frameshift_variant	5087	exon6			.	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	Exception_encountered	chr1.hg19:g.164781319_164781320insGTATA	ENSP00000405890:p.Val311fs	83.0	0.0	0		100.0	23.0	0.23	NM_001204963	B4DSC1|F5H4U9|Q5T488	Frame_Shift_Ins	INS	ENST00000420696.2	hg19	CCDS1246.1																																																																																			.	.	.	none		0.455	PBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082864.4	NM_002585		GTATA	164781320	-	GTATA	164781319	7	5	184	1	0	1	1	0	0	0	0	0	11499	1567	55	0	952	0	PBX1	1	164781319	Frame_Shift_Ins	INS	-	TCGA-GL-7773-01A-11D-2136-08	12505296	164781319	84469302	12	10745											
BAT2L2	23215	hgsc.bcm.edu	37	chr1	171527271	171527271	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accagctgtgctgaatgataTctctaagaaatgtaagttgc	13	12	9	7	0	1	3	0	2	1	1	2	3	1	3	1	0	3	4	1	0	5	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:171527271T>C	ENST00000338920.4	+	19	6251	c.6014T>C	c.(6013-6015)aTc>aCc	p.I2005T	PRRC2C_ENST00000426496.2_Missense_Mutation_p.I2005T|PRRC2C_ENST00000367742.3_Missense_Mutation_p.I2007T|PRRC2C_ENST00000392078.3_Missense_Mutation_p.I2007T	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	2005					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										CTGAATGATATCTCTAAGAAA	0.423																																					p.I2005T		Atlas-SNP	.											.	.	.	.	0			c.T6014C						PASS	.						63	62	62					1																	171527271		2203	4300	6503	SO:0001583	missense	23215	exon19			ATGATATCTCTAA	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.6014T>C	chr1.hg19:g.171527271T>C	ENSP00000343629:p.Ile2005Thr	77.0	0.0	.		85.0	34.0	.	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	hg19	CCDS1296.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.38|16.38	3.105838|3.105838	0.56291|0.56291	.|.	.|.	ENSG00000117523|ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080|ENST00000495585	T;T;T;T|.	0.03035|.	4.11;4.07;4.12;4.12|.	5.32|5.32	5.32|5.32	0.75619|0.75619	.|.	0.154856|.	0.29253|.	U|.	0.012694|.	T|T	0.58163|0.58163	0.2103|0.2103	L|L	0.51422|0.51422	1.61|1.61	0.45427|0.45427	D|D	0.998403|0.998403	B|.	0.30361|.	0.277|.	B|.	0.35470|.	0.203|.	T|T	0.58589|0.58589	-0.7610|-0.7610	10|5	0.66056|.	D|.	0.02|.	.|.	15.3486|15.3486	0.74363|0.74363	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	2005|.	Q9Y520-4|.	.|.	T|P	2007;1959;2005;2007;2005;1762|553	ENSP00000375928:I2007T;ENSP00000410219:I2005T;ENSP00000356716:I2007T;ENSP00000343629:I2005T|.	ENSP00000343629:I2005T|.	I|S	+|+	2|1	0|0	PRRC2C|PRRC2C	169793895|169793895	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.878000|0.878000	0.50629|0.50629	6.663000|6.663000	0.74431|0.74431	2.013000|2.013000	0.59113|0.59113	0.451000|0.451000	0.29950|0.29950	ATC|TCT	.	.	.	none		0.423	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		C	171527271	T	C	171527271	3	2	184	1	0	0	0	0	1	0	0	0	1321	1435	50	3	6084	3	BAT2L2	1	171527271	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	6745952	171527271	77723350	13	10746											
MRPS14	63931	hgsc.bcm.edu	37	chr1	174987712	174987712	+	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	tgaagctgatgaaggaaccaTctgaaagacagagacaaggg	17	5	13	6	0	1	6	0	4	1	2	1	8	1	7	1	2	2	1	1	2	5	0			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:174987712T>C	ENST00000476371.1	-	2	62	c.46A>G	c.(46-48)Atg>Gtg	p.M16V		NM_022100.2	NP_071383.1			mitochondrial ribosomal protein S14											large_intestine(2)|lung(5)|pancreas(1)|prostate(2)	10						GAAGGAACCATCTGAAAGACA	0.448																																					p.M16V		Atlas-SNP	.											.	MRPS14	20	.	0			c.A46G						PASS	.						98	85	89					1																	174987712		2203	4300	6503	SO:0001630	splice_region_variant	63931	exon2			GAACCATCTGAAA	AB051350	CCDS1316.1	1q25.1	2012-09-13			ENSG00000120333	ENSG00000120333		"Mitochondrial ribosomal proteins / small subunits"	14049	protein-coding gene	gene with protein product		611978					Standard	NR_037606		Approved	HSMRPS14	uc001gkk.3	O60783	OTTHUMG00000034878	ENST00000476371.1:c.46-1A>G	chr1.hg19:g.174987712T>C		72.0	0.0	.		88.0	35.0	.	NM_022100		Missense_Mutation	SNP	ENST00000476371.1	hg19	CCDS1316.1	.	.	.	.	.	.	.	.	.	.	T	0.064	-1.217425	0.01542	.	.	ENSG00000120333	ENST00000476371	.	.	.	5.67	-1.6	0.08426	.	0.671809	0.15704	N	0.248788	T	0.11707	0.0285	N	0.04043	-0.29	0.22745	N	0.998783	B	0.02656	0.0	B	0.01281	0.0	T	0.34601	-0.9822	9	0.02654	T	1	-0.3997	7.7061	0.28650	0.2345:0.5387:0.0:0.2267	.	16	O60783	RT14_HUMAN	V	16	.	ENSP00000420714:M16V	M	-	1	0	MRPS14	173254335	0.995000	0.38212	0.560000	0.28344	0.318000	0.28184	0.132000	0.15891	-0.280000	0.09154	-0.256000	0.11100	ATG	.	.	.	none		0.448	MRPS14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084416.2	NM_022100	Missense_Mutation	C	174987712	T	C	174987712	5	2	184	1	0	0	0	0	0	0	1	0	9831	1449	50	3	348	3	MRPS14	1	174987712	Splice_Site	SNP	T	TCGA-GL-7773-01A-11D-2136-08	3460441	174987712	74262909	14	10747											
TNR	7143	hgsc.bcm.edu	37	chr1	175355248	175355248	+	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	acacctcgtatcgggagccaGgccgcagggcctgcactgag	8	5	14	14	3	0	1	0	1	0	0	2	2	0	2	4	3	2	3	4	3	1	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:175355248G>C	ENST00000367674.2	-	8	2405	c.1697C>G	c.(1696-1698)cCt>cGt	p.P566R	TNR_ENST00000263525.2_Missense_Mutation_p.P566R			Q92752	TENR_HUMAN	tenascin R	566	Fibronectin type-III 3. {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)					TCGGGAGCCAGGCCGCAGGGC	0.612																																					p.P566R		Atlas-SNP	.											.	TNR	399	.	0			c.C1697G						PASS	.						63	60	61					1																	175355248		2203	4300	6503	SO:0001583	missense	7143	exon8			GAGCCAGGCCGCA	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.1697C>G	chr1.hg19:g.175355248G>C	ENSP00000356646:p.Pro566Arg	91.0	0.0	.		105.0	31.0	.	NM_003285	C9J563|Q15568|Q5R3G0	Missense_Mutation	SNP	ENST00000367674.2	hg19	CCDS1318.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.710158	0.68730	.	.	ENSG00000116147	ENST00000367674;ENST00000263525;ENST00000367673	T;T	0.68903	-0.36;-0.36	5.58	5.58	0.84498	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.84964	0.5589	M	0.86502	2.82	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86989	0.2109	10	0.72032	D	0.01	.	19.1714	0.93580	0.0:0.0:1.0:0.0	.	566	Q92752	TENR_HUMAN	R	566	ENSP00000356646:P566R;ENSP00000263525:P566R	ENSP00000263525:P566R	P	-	2	0	TNR	173621871	1.000000	0.71417	0.953000	0.39169	0.256000	0.26092	8.911000	0.92721	2.613000	0.88420	0.650000	0.86243	CCT	.	.	.	none		0.612	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		C	175355248	G	C	175355248	3	2	184	1	0	0	0	0	1	0	0	0	16350	1000	35	4	2443	4	TNR	1	175355248	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	367536	175355248	73895373	15	10748											
DHX9	1660	hgsc.bcm.edu	37	chr1	182856426	182856426	+	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	gctatagaggagtttcccgaGgtggctttagaggcaactct	9	11	13	8	1	1	2	0	0	1	2	2	4	2	3	1	4	1	4	1	4	4	5	rs571363823		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:182856426G>C	ENST00000367549.3	+	28	3780	c.3670G>C	c.(3670-3672)Ggt>Cgt	p.G1224R	DHX9_ENST00000485081.1_3'UTR	NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	1224	NTD.				ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						AGTTTCCCGAGGTGGCTTTAG	0.592																																					p.G1224R	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.G3670C						PASS	.						77	83	81					1																	182856426		1903	4120	6023	SO:0001583	missense	1660	exon28			TCCCGAGGTGGCT	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.3670G>C	chr1.hg19:g.182856426G>C	ENSP00000356520:p.Gly1224Arg	103.0	0.0	.		136.0	58.0	.	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Missense_Mutation	SNP	ENST00000367549.3	hg19	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	G	11.36	1.615017	0.28712	.	.	ENSG00000135829	ENST00000367549	D	0.98329	-4.87	3.88	2.96	0.34315	.	0.241496	0.34725	N	0.003731	D	0.94748	0.8305	L	0.27053	0.805	0.58432	D	0.999996	P;P	0.47106	0.89;0.83	P;P	0.44946	0.465;0.465	D	0.91260	0.5036	10	0.13470	T	0.59	.	9.1231	0.36799	0.1132:0.0:0.8868:0.0	.	503;1224	B3KU66;Q08211	.;DHX9_HUMAN	R	1224	ENSP00000356520:G1224R	ENSP00000356520:G1224R	G	+	1	0	DHX9	181123049	1.000000	0.71417	0.182000	0.23118	0.556000	0.35491	6.067000	0.71193	0.619000	0.30197	0.561000	0.74099	GGT	.	.	.	none		0.592	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		C	182856426	G	C	182856426	3	2	184	1	0	0	0	0	1	0	0	0	4518	1000	35	4	3776	4	DHX9	1	182856426	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	7501178	182856426	66394195	16	10749											
RGS18	64407	hgsc.bcm.edu	37	chr1	192128419	192128419	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcatgaagacacccgctcCagtagatctgggcacttggc	9	10	10	12	1	2	3	1	1	1	2	3	3	3	3	2	2	0	3	2	2	2	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:192128419C>T	ENST00000367460.3	+	2	370	c.189C>T	c.(187-189)tcC>tcT	p.S63S	RGS18_ENST00000481707.1_3'UTR	NM_130782.2	NP_570138.1	Q9NS28	RGS18_HUMAN	regulator of G-protein signaling 18	63					G-protein coupled receptor signaling pathway (GO:0007186)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			kidney(1)|large_intestine(2)|lung(15)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						ACACCCGCTCCAGTAGATCTG	0.363																																					p.S63S		Atlas-SNP	.											.	RGS18	54	.	0			c.C189T						PASS	.						46	50	48					1																	192128419		2203	4300	6503	SO:0001819	synonymous_variant	64407	exon2			CCGCTCCAGTAGA	AF268036	CCDS1374.1	1q31.2	2008-02-05	2007-08-14		ENSG00000150681	ENSG00000150681		"Regulators of G-protein signaling"	14261	protein-coding gene	gene with protein product		607192	"regulator of G-protein signalling 18"			11042171	Standard	NM_130782		Approved	RGS13	uc001gsg.3	Q9NS28	OTTHUMG00000035592	ENST00000367460.3:c.189C>T	chr1.hg19:g.192128419C>T		64.0	0.0	.		83.0	21.0	.	NM_130782	B2RD23	Silent	SNP	ENST00000367460.3	hg19	CCDS1374.1																																																																																			.	.	.	none		0.363	RGS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086382.1	NM_130782		T	192128419	C	T	192128419	2	4	184	1	0	0	0	0	0	0	0	1	13313	581	21	2		2	RGS18	1	192128419	Silent	SNP	C	TCGA-GL-7773-01A-11D-2136-08	9271993	192128419	57122202	17	10750											
SIPA1L2	57568	hgsc.bcm.edu	37	chr1	232649814	232649814	+	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	gagttggctcgagagagcgcAatccgcctgtcgccttcccc	6	8	12	15	4	0	1	0	0	0	1	4	4	2	1	5	1	1	3	5	1	1	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr1:232649814A>T	ENST00000366630.1	-	2	1630	c.1272T>A	c.(1270-1272)atT>atA	p.I424I	SIPA1L2_ENST00000262861.4_Silent_p.I424I			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	424					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)				GAGAGAGCGCAATCCGCCTGT	0.517																																					p.I424I		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.T1272A						PASS	.						138	137	138					1																	232649814		1984	4161	6145	SO:0001819	synonymous_variant	57568	exon1			GAGCGCAATCCGC	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.1272T>A	chr1.hg19:g.232649814A>T		170.0	0.0	.		251.0	101.0	.	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Silent	SNP	ENST00000366630.1	hg19	CCDS41474.1																																																																																			.	.	.	none		0.517	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		T	232649814	A	T	232649814	2	4	184	1	0	0	0	0	0	0	0	1	14343	126	5	5		5	SIPA1L2	1	232649814	Silent	SNP	A	TCGA-GL-7773-01A-11D-2136-08	40521395	232649814	16600807	18	10751											
RASGRP3	25780	hgsc.bcm.edu	37	chr2	33768640	33768640	+	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	ttcccaagaggactttgaaaGtatagctgccaattttccct	11	13	7	10	0	0	2	0	1	0	1	2	3	2	3	3	1	2	2	3	1	5	6			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr2:33768640G>C	ENST00000403687.3	+	13	2080	c.1340G>C	c.(1339-1341)aGt>aCt	p.S447T	RASGRP3_ENST00000482731.1_3'UTR|RASGRP3_ENST00000402538.3_Missense_Mutation_p.S447T|RASGRP3_ENST00000407811.1_Missense_Mutation_p.S446T	NM_001139488.1	NP_001132960.1	Q8IV61	GRP3_HUMAN	RAS guanyl releasing protein 3 (calcium and DAG-regulated)	447	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				MAPK cascade (GO:0000165)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)	guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap GTPase activator activity (GO:0046582)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)			large_intestine(3)|lung(3)|ovary(2)|pancreas(1)|stomach(2)	11	all_hematologic(175;0.115)					GACTTTGAAAGTATAGCTGCC	0.338																																					p.S447T		Atlas-SNP	.											.	RASGRP3	87	.	0			c.G1340C						PASS	.						100	93	95					2																	33768640		1824	4085	5909	SO:0001583	missense	25780	exon14			TTGAAAGTATAGC	AB020653	CCDS46256.1, CCDS54346.1	2p25.1-p24.1	2013-01-10			ENSG00000152689	ENSG00000152689		"EF-hand domain containing"	14545	protein-coding gene	gene with protein product		609531				10048485, 10934204	Standard	NM_170672		Approved	KIAA0846, GRP3	uc002roy.3	Q8IV61	OTTHUMG00000152124	ENST00000403687.3:c.1340G>C	chr2.hg19:g.33768640G>C	ENSP00000384192:p.Ser447Thr	39.0	0.0	.		39.0	18.0	.	NM_170672	D6W583|O94931|Q53SD7	Missense_Mutation	SNP	ENST00000403687.3	hg19	CCDS46256.1	.	.	.	.	.	.	.	.	.	.	G	16.90	3.250031	0.59212	.	.	ENSG00000152689	ENST00000402538;ENST00000403687;ENST00000407811	T;T;T	0.69175	-0.38;-0.38;-0.38	5.54	5.54	0.83059	EF-hand-like domain (1);	0.096408	0.64402	D	0.000002	T	0.66626	0.2808	N	0.14661	0.345	0.38135	D	0.938277	P;P	0.51240	0.943;0.885	P;P	0.59288	0.855;0.599	T	0.65961	-0.6041	10	0.23302	T	0.38	-3.5489	19.4767	0.94992	0.0:0.0:1.0:0.0	.	446;447	D6W583;Q8IV61	.;GRP3_HUMAN	T	447;447;446	ENSP00000385886:S447T;ENSP00000384192:S447T;ENSP00000383917:S446T	ENSP00000385886:S447T	S	+	2	0	RASGRP3	33622144	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.384000	0.52478	2.601000	0.87937	0.563000	0.77884	AGT	.	.	.	none		0.338	RASGRP3-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325462.2	NM_015376		C	33768640	G	C	33768640	3	2	184	1	0	0	0	0	1	0	0	0	13089	1029	36	4	1382	4	RASGRP3	2	33768640	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08		33768640	209430733	19	10752											
STRN	6801	hgsc.bcm.edu	37	chr2	37129786	37129786	+	Missense_Mutation	SNP	T	T	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	tttacaactgagtcctgattTttgtcatcttccctgtccgt	6	18	6	11	1	2	2	1	2	1	0	5	2	5	2	3	0	2	0	3	0	2	5			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr2:37129786T>G	ENST00000263918.4	-	5	608	c.600A>C	c.(598-600)aaA>aaC	p.K200N	STRN_ENST00000379213.2_Missense_Mutation_p.K188N	NM_003162.3	NP_003153.2	O43815	STRN_HUMAN	striatin, calmodulin binding protein	200					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)				AGTCCTGATTTTTGTCATCTT	0.393																																					p.K200N		Atlas-SNP	.											.	STRN	71	.	0			c.A600C						PASS	.						204	187	193					2																	37129786		2203	4300	6503	SO:0001583	missense	6801	exon5			CTGATTTTTGTCA	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.600A>C	chr2.hg19:g.37129786T>G	ENSP00000263918:p.Lys200Asn	224.0	0.0	.		224.0	92.0	.	NM_003162	Q3KP65|Q53TQ8|Q9NP38	Missense_Mutation	SNP	ENST00000263918.4	hg19	CCDS1784.1	.	.	.	.	.	.	.	.	.	.	T	14.10	2.434771	0.43224	.	.	ENSG00000115808	ENST00000263918;ENST00000538092;ENST00000379213	T;T	0.65732	-0.17;-0.17	5.25	4.1	0.47936	.	0.260012	0.36101	N	0.002786	T	0.52821	0.1758	L	0.47190	1.495	0.36799	D	0.885272	B;B	0.14012	0.009;0.001	B;B	0.12837	0.008;0.004	T	0.52682	-0.8543	10	0.32370	T	0.25	-7.8697	10.7081	0.45966	0.0:0.0746:0.0:0.9254	.	188;200	O43815-2;O43815	.;STRN_HUMAN	N	200;175;188	ENSP00000263918:K200N;ENSP00000368513:K188N	ENSP00000263918:K200N	K	-	3	2	STRN	36983290	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.314000	0.43743	0.848000	0.35191	0.533000	0.62120	AAA	.	.	.	none		0.393	STRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218568.1			G	37129786	T	G	37129786	3	3	184	1	0	0	0	0	1	0	0	0	15341	1838	64	5	1798	5	STRN	2	37129786	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	3361146	37129786	206069587	20	10753											
CNNM4	26504	hgsc.bcm.edu	37	chr2	97428005	97428005	+	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	aatattgtagatattctctaCgtcaaagacttggcctttgt	11	16	7	7	1	2	2	1	0	1	2	3	2	2	2	1	1	1	1	1	1	6	8			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr2:97428005C>A	ENST00000377075.2	+	1	1367	c.1269C>A	c.(1267-1269)taC>taA	p.Y423*		NM_020184.3	NP_064569.3	Q6P4Q7	CNNM4_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 4	423	CBS 1. {ECO:0000255|PROSITE- ProRule:PRU00703}.				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						ATATTCTCTACGTCAAAGACT	0.502																																					p.Y423X		Atlas-SNP	.											.	CNNM4	48	.	0			c.C1269A						PASS	.						149	146	147					2																	97428005		2203	4300	6503	SO:0001587	stop_gained	26504	exon1			TCTCTACGTCAAA	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.1269C>A	chr2.hg19:g.97428005C>A	ENSP00000366275:p.Tyr423*	217.0	0.0	.		209.0	74.0	.	NM_020184	B7Z1U0|C7SQM3|C7SQM4|C7SQM5|Q53RE5|Q9H9G3|Q9HCI0|Q9NRN1	Nonsense_Mutation	SNP	ENST00000377075.2	hg19	CCDS2024.2	.	.	.	.	.	.	.	.	.	.	C	35	5.425731	0.96131	.	.	ENSG00000158158	ENST00000377075	.	.	.	5.05	-5.28	0.02755	.	0.140382	0.49305	D	0.000151	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05721	T	0.95	.	9.3317	0.38025	0.1152:0.5507:0.0:0.3341	.	.	.	.	X	423	.	ENSP00000366275:Y423X	Y	+	3	2	CNNM4	96791732	0.008000	0.16893	0.908000	0.35775	0.975000	0.68041	-0.996000	0.03709	-1.113000	0.02981	-0.302000	0.09304	TAC	.	.	.	none		0.502	CNNM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252954.1	NM_020184		A	97428005	C	A	97428005	4	1	184	1	0	0	0	0	0	1	0	0	3617	547	19	4	1271	4	CNNM4	2	97428005	Nonsense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	60298219	97428005	145771368	21	10754											
TTN	7273	hgsc.bcm.edu	37	chr2	179599140	179599140	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcaccaacatctgcactattAaacgaaaagatctccagaca	17	8	4	12	1	3	2	1	0	2	2	4	3	3	2	2	0	3	1	2	0	6	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr2:179599140A>G	ENST00000591111.1	-	50	14684	c.14460T>C	c.(14458-14460)ttT>ttC	p.F4820F	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000342992.6_Silent_p.F3893F|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Silent_p.F5137F			Q8WZ42	TITIN_HUMAN	titin	12201	Ig-like 28.				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)			CTGCACTATTAAACGAAAAGA	0.373																																					p.F5137F		Atlas-SNP	.											.	TTN	18412	.	0			c.T15411C						PASS	.						170	159	162					2																	179599140		1893	4123	6016	SO:0001819	synonymous_variant	7273	exon52			ACTATTAAACGAA	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.14460T>C	chr2.hg19:g.179599140A>G		185.0	0.0	.		232.0	81.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.	.	none		0.373	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179599140	A	G	179599140	2	3	184	1	0	0	0	0	0	0	0	1	16747	359	13	3		3	TTN	2	179599140	Silent	SNP	A	TCGA-GL-7773-01A-11D-2136-08	82171135	179599140	63600233	22	10755											
ANKRD44	91526	hgsc.bcm.edu	37	chr2	197889959	197889959	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttagtagcaccagaatctgaTtcttcaaatccactgtttgt	11	15	6	9	0	3	2	1	1	2	1	4	2	4	2	2	0	1	3	2	0	4	5			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr2:197889959T>C	ENST00000328737.2	-	17	1684	c.1608A>G	c.(1606-1608)gaA>gaG	p.E536E	ANKRD44_ENST00000450567.1_Silent_p.E536E|ANKRD44_ENST00000282272.8_Silent_p.E553E|ANKRD44_ENST00000337207.5_Silent_p.E536E			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	561										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)			CAGAATCTGATTCTTCAAATC	0.388																																					p.E561E		Atlas-SNP	.											.	ANKRD44	281	.	0			c.A1683G						PASS	.						133	118	123					2																	197889959		2203	4300	6503	SO:0001819	synonymous_variant	91526	exon17			ATCTGATTCTTCA	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.1608A>G	chr2.hg19:g.197889959T>C		118.0	0.0	.		107.0	39.0	.	NM_001195144	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Silent	SNP	ENST00000328737.2	hg19																																																																																				.	.	.	none		0.388	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697		C	197889959	T	C	197889959	2	2	184	1	0	0	0	0	0	0	0	1	672	1490	52	3		3	ANKRD44	2	197889959	Silent	SNP	T	TCGA-GL-7773-01A-11D-2136-08	18290819	197889959	45309414	23	10756											
ALS2CR8	79800	hgsc.bcm.edu	37	chr2	203848266	203848266	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtaccatttctgtgagccaAgttaaacaagaacccaaaga	17	8	7	9	0	1	3	0	1	1	2	1	3	1	3	3	0	4	2	3	0	7	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr2:203848266A>G	ENST00000402905.3	+	16	2418	c.2097A>G	c.(2095-2097)caA>caG	p.Q699Q	CARF_ENST00000545253.1_Silent_p.Q611Q|WDR12_ENST00000477723.1_Intron|CARF_ENST00000414439.1_Silent_p.Q597Q|CARF_ENST00000545262.1_Silent_p.Q623Q|CARF_ENST00000428585.1_Silent_p.Q623Q|CARF_ENST00000320443.8_Silent_p.Q699Q|CARF_ENST00000438828.2_Silent_p.Q699Q	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	699					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)										CTGTGAGCCAAGTTAAACAAG	0.328																																					p.Q699Q		Atlas-SNP	.											.	ALS2CR8	56	.	0			c.A2097G						PASS	.						81	78	79					2																	203848266		1801	4076	5877	SO:0001819	synonymous_variant	79800	exon17			GAGCCAAGTTAAA	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.2097A>G	chr2.hg19:g.203848266A>G		111.0	0.0	.		93.0	33.0	.	NM_024744	B4E1W7|G3V1K7|Q8ND29|Q8WXC0|Q96J78|Q96Q38|Q96Q39|Q9H712	Silent	SNP	ENST00000402905.3	hg19	CCDS42801.1																																																																																			.	.	.	none		0.328	CARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335768.5	NM_001104586		G	203848266	A	G	203848266	2	3	184	1	0	0	0	0	0	0	0	1	555	69	3	3		3	ALS2CR8	2	203848266	Silent	SNP	A	TCGA-GL-7773-01A-11D-2136-08	5958307	203848266	39351107	24	10757											
CHL1	10752	hgsc.bcm.edu	37	chr3	407694	407695	+	Frame_Shift_Ins	INS	-	-	T																															ccaaattgcatatgcttgaaINSttacattgtgaaagcaaatg																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr3:407694_407695insT	ENST00000256509.2	+	15	2289_2290	c.1647_1648insT	c.(1648-1650)ttafs	p.L550fs	CHL1-AS1_ENST00000417612.1_RNA|CHL1_ENST00000397491.2_Frame_Shift_Ins_p.L534fs|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)		ATATGCTTGAATTACATTGTGA	0.361																																					p.E549fs		Atlas-INDEL	.											.	CHL1	242	.	0			c.1647_1648insT						PASS	.																																			SO:0001589	frameshift_variant	10752	exon13			.	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.1649dupT	chr3.hg19:g.407696_407696dupT	ENSP00000256509:p.Leu550fs	71.0	0.0	0		87.0	36.0	0.413793	NM_001253388	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Frame_Shift_Ins	INS	ENST00000256509.2	hg19	CCDS2556.1																																																																																			.	.	.	none		0.361	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614		T	407695	-	T	407694	7	5	184	1	0	1	1	0	0	0	0	0	3351	98	4	0	1697	0	CHL1	3	407694	Frame_Shift_Ins	INS	-	TCGA-GL-7773-01A-11D-2136-08		407694	197614736	25	10758											
CAMP	820	hgsc.bcm.edu	37	chr3	48266893	48266893	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggattttttgcggaatctTgtacccaggacagagtccta	11	12	10	8	1	1	1	0	0	1	1	2	4	2	4	2	3	2	1	2	3	4	6			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr3:48266893T>C	ENST00000576243.1	+	4	632	c.492T>C	c.(490-492)ctT>ctC	p.L164L	CAMP_ENST00000296435.2_Silent_p.L167L			P49913	CAMP_HUMAN	cathelicidin antimicrobial peptide	164					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)		TGCGGAATCTTGTACCCAGGA	0.453																																					p.L167L		Atlas-SNP	.											.	CAMP	12	.	0			c.T501C						PASS	.						103	113	109					3																	48266893		2203	4300	6503	SO:0001819	synonymous_variant	820	exon4			GAATCTTGTACCC	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.492T>C	chr3.hg19:g.48266893T>C		164.0	0.0	.		225.0	83.0	.	NM_004345	Q71SN9	Silent	SNP	ENST00000576243.1	hg19																																																																																				.	.	.	none		0.453	CAMP-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_004345		C	48266893	T	C	48266893	2	2	184	1	0	0	0	0	0	0	0	1	2612	1799	63	3		3	CAMP	3	48266893	Silent	SNP	T	TCGA-GL-7773-01A-11D-2136-08	47859199	48266893	149755537	26	10759											
IQCF2	389123	hgsc.bcm.edu	37	chr3	51897303	51897303	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccactggcaatgccacaacTgccagacctgcgctctcctc	8	7	8	18	1	1	1	0	0	1	1	3	1	1	1	5	1	4	2	5	1	2	0			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr3:51897303T>C	ENST00000333127.3	+	3	441	c.412T>C	c.(412-414)Tgc>Cgc	p.C138R	IQCF2_ENST00000429548.1_3'UTR	NM_203424.1	NP_982248.1	Q8IXL9	IQCF2_HUMAN	IQ motif containing F2	138										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)		ATGCCACAACTGCCAGACCTG	0.577																																					p.C138R		Atlas-SNP	.											.	IQCF2	21	.	0			c.T412C						PASS	.						120	113	116					3																	51897303		2203	4300	6503	SO:0001583	missense	389123	exon3			CACAACTGCCAGA	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.412T>C	chr3.hg19:g.51897303T>C	ENSP00000329904:p.Cys138Arg	204.0	0.0	.		180.0	12.0	.	NM_203424		Missense_Mutation	SNP	ENST00000333127.3	hg19	CCDS2835.1	.	.	.	.	.	.	.	.	.	.	T	19.99	3.928595	0.73327	.	.	ENSG00000184345	ENST00000333127	T	0.34859	1.34	5.22	5.22	0.72569	.	0.202993	0.36101	N	0.002800	T	0.52125	0.1715	L	0.58810	1.83	0.48696	D	0.999697	D	0.71674	0.998	D	0.64144	0.922	T	0.54761	-0.8245	10	0.87932	D	0	-16.5932	11.6771	0.51436	0.0:0.0:0.0:1.0	.	138	Q8IXL9	IQCF2_HUMAN	R	138	ENSP00000329904:C138R	ENSP00000329904:C138R	C	+	1	0	IQCF2	51872343	0.999000	0.42202	1.000000	0.80357	0.986000	0.74619	3.496000	0.53288	2.311000	0.77944	0.528000	0.53228	TGC	.	.	.	none		0.577	IQCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346594.1	NM_203424		C	51897303	T	C	51897303	3	2	184	1	0	0	0	0	1	0	0	0	7815	1580	55	3	422	3	IQCF2	3	51897303	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	3630410	51897303	146125127	27	10760											
LRTM1	57408	hgsc.bcm.edu	37	chr3	54952818	54952823	+	In_Frame_Del	DEL	CAGGAA	CAGGAA	-																															cgaggacactggatcaggagCaggaagagggcagggctggt																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	CAGGAA	CAGGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr3:54952818_54952823delCAGGAA	ENST00000273286.5	-	3	863_868	c.701_706delTTCCTG	c.(700-708)cttcctgct>cct	p.234_236LPA>P	CACNA2D3_ENST00000474759.1_Intron|CACNA2D3_ENST00000288197.5_Intron|CACNA2D3_ENST00000415676.2_Intron|CACNA2D3_ENST00000490478.1_Intron|LRTM1_ENST00000493075.1_In_Frame_Del_p.158_160LPA>P	NM_020678.2	NP_065729.1	Q9HBL6	LRTM1_HUMAN	leucine-rich repeats and transmembrane domains 1	234	LRRCT.					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)		GGATCAGGAGCAGGAAGAGGGCAGGG	0.597																																					p.234_236del		Atlas-INDEL	.											.	LRTM1	52	.	0			c.702_707del						PASS	.																																			SO:0001651	inframe_deletion	57408	exon3			.	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.701_706delTTCCTG	chr3.hg19:g.54952818_54952823delCAGGAA	ENSP00000273286:p.Leu234_Ala236delinsPro	38.0	0.0	0		43.0	14.0	0.325581	NM_020678	Q8IUU2	In_Frame_Del	DEL	ENST00000273286.5	hg19	CCDS2876.1																																																																																			.	.	.	none		0.597	LRTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351399.1	NM_020678		-	54952823	CAGGAA	-	54952818	7	5	184	1	0	1	0	1	0	0	0	0	9051	710	25	0	335	0	LRTM1	3	54952818	In_Frame_Del	DEL	CAGGAA	TCGA-GL-7773-01A-11D-2136-08	3055515	54952818	143069612	28	10761											
ARHGEF3	50650	hgsc.bcm.edu	37	chr3	56779418	56779418	+	Missense_Mutation	SNP	T	T	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	ctggactcggtgatcttgctTtttgtggtccagcagagctt	5	15	12	9	1	1	2	0	1	1	1	3	3	2	3	1	3	3	3	1	3	0	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr3:56779418T>G	ENST00000296315.3	-	7	853	c.685A>C	c.(685-687)Aag>Cag	p.K229Q	ARHGEF3_ENST00000495373.1_Missense_Mutation_p.K229Q|ARHGEF3_ENST00000413728.2_Missense_Mutation_p.K235Q|ARHGEF3_ENST00000497267.1_Missense_Mutation_p.K200Q|ARHGEF3_ENST00000338458.4_Missense_Mutation_p.K261Q|ARHGEF3_ENST00000496106.1_Missense_Mutation_p.K235Q	NM_019555.2	NP_062455.1	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor (GEF) 3	229	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of 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)		TGATCTTGCTTTTTGTGGTCC	0.478																																					p.K261Q		Atlas-SNP	.											.	ARHGEF3	128	.	0			c.A781C						PASS	.						161	169	166					3																	56779418		2203	4300	6503	SO:0001583	missense	50650	exon10			CTTGCTTTTTGTG	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.685A>C	chr3.hg19:g.56779418T>G	ENSP00000296315:p.Lys229Gln	229.0	0.0	.		238.0	82.0	.	NM_001128615	A8K5U7|Q4FZB6|Q4QQI5|Q4QQQ0|Q59F00|Q6NUN3|Q7Z4U2|Q7Z5T2|Q9H7T4	Missense_Mutation	SNP	ENST00000296315.3	hg19	CCDS2878.1	.	.	.	.	.	.	.	.	.	.	T	28.7	4.943519	0.92593	.	.	ENSG00000163947	ENST00000296315;ENST00000338458;ENST00000413728;ENST00000496106;ENST00000497267;ENST00000495373	T;T;T;T;T;T	0.32272	1.46;1.46;1.46;1.46;1.46;1.46	5.85	5.85	0.93711	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	T	0.61813	0.2377	M	0.89601	3.045	0.80722	D	1	D;D;D;D;D;D;D	0.69078	0.966;0.968;0.992;0.984;0.98;0.997;0.98	P;P;P;P;P;D;P	0.63192	0.712;0.571;0.591;0.713;0.665;0.912;0.665	T	0.70669	-0.4808	10	0.87932	D	0	-14.323	16.5479	0.84454	0.0:0.0:0.0:1.0	.	235;200;27;229;261;229;235	E9PG37;E7EU49;Q9NR81-4;C9J586;Q9NR81-2;Q9NR81;Q9NR81-3	.;.;.;.;.;ARHG3_HUMAN;.	Q	229;261;235;235;200;229	ENSP00000296315:K229Q;ENSP00000341071:K261Q;ENSP00000410922:K235Q;ENSP00000420420:K235Q;ENSP00000418826:K200Q;ENSP00000417986:K229Q	ENSP00000296315:K229Q	K	-	1	0	ARHGEF3	56754458	1.000000	0.71417	0.996000	0.52242	0.983000	0.72400	8.040000	0.89188	2.371000	0.80710	0.533000	0.62120	AAG	.	.	.	none		0.478	ARHGEF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352431.2	NM_019555		G	56779418	T	G	56779418	3	3	184	1	0	0	0	0	1	0	0	0	904	1850	64	5	911	5	ARHGEF3	3	56779418	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	1826600	56779418	141243012	29	10762											
C3orf14	57415	hgsc.bcm.edu	37	chr3	62317065	62317065	+	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	cttccacggcctgaggtggtTtctcttgaggtgagcatctt	5	14	12	10	1	2	3	0	3	2	0	4	3	3	3	2	4	1	2	2	4	0	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr3:62317065T>A	ENST00000494481.1	+	5	557	c.243T>A	c.(241-243)gtT>gtA	p.V81V	C3orf14_ENST00000542214.1_Silent_p.V81V|C3orf14_ENST00000232519.5_Silent_p.V81V|C3orf14_ENST00000462069.1_Silent_p.V81V|PTPRG-AS1_ENST00000495542.1_RNA|PTPRG-AS1_ENST00000490916.1_RNA			Q9HBI5	CC014_HUMAN	chromosome 3 open reading frame 14	81										central_nervous_system(1)|large_intestine(1)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(55;0.00023)|KIRC - Kidney renal clear cell carcinoma(15;0.00877)|Kidney(15;0.0101)		CTGAGGTGGTTTCTCTTGAGG	0.393																																					p.V81V		Atlas-SNP	.											.	C3orf14	10	.	0			c.T243A						PASS	.						102	101	102					3																	62317065		2203	4300	6503	SO:0001819	synonymous_variant	57415	exon4			GGTGGTTTCTCTT	AF236158	CCDS2896.1	3p14.2	2011-11-29			ENSG00000114405	ENSG00000114405			25024	protein-coding gene	gene with protein product						12477932	Standard	XM_005265338		Approved	HT021	uc003dlg.3	Q9HBI5	OTTHUMG00000158704	ENST00000494481.1:c.243T>A	chr3.hg19:g.62317065T>A		112.0	0.0	.		147.0	57.0	.	NM_020685	B2R9U0	Silent	SNP	ENST00000494481.1	hg19	CCDS2896.1																																																																																			.	.	.	none		0.393	C3orf14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351807.1	NM_020685		A	62317065	T	A	62317065	2	1	184	1	0	0	0	0	0	0	0	1	2210	1828	64	5		5	C3orf14	3	62317065	Silent	SNP	T	TCGA-GL-7773-01A-11D-2136-08	5537647	62317065	135705365	30	10763											
CPOX	1371	hgsc.bcm.edu	37	chr3	98309567	98309567	+	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	ataacagagctcacgcccatAgcacaaaatggcaatttacc	16	7	6	12	1	1	1	1	0	0	1	1	1	1	1	2	1	4	3	2	1	6	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr3:98309567A>T	ENST00000264193.2	-	3	938	c.720T>A	c.(718-720)gcT>gcA	p.A240A		NM_000097.5	NP_000088.3	P36551	HEM6_HUMAN	coproporphyrinogen oxidase	240					heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to arsenic-containing substance (GO:0046685)|response to insecticide (GO:0017085)|response to iron ion (GO:0010039)|response to lead ion (GO:0010288)|response to methylmercury (GO:0051597)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	coproporphyrinogen oxidase activity (GO:0004109)|protein homodimerization activity (GO:0042803)|structural constituent of eye lens (GO:0005212)			endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(1)	16						TCACGCCCATAGCACAAAATG	0.388																																					p.A240A	Esophageal Squamous(75;7 1223 22300 43648 48951)	Atlas-SNP	.											.	CPOX	34	.	0			c.T720A						PASS	.						82	78	79					3																	98309567		2203	4300	6503	SO:0001819	synonymous_variant	1371	exon3			GCCCATAGCACAA	BC017210	CCDS2932.1	3q12	2012-10-02		2004-01-30		ENSG00000080819	1.3.3.3		2321	protein-coding gene	gene with protein product	"coproporphyria"	612732	"coproporphyrinogen oxidase (coproporphyria, harderoporphyria)"	CPO		7757079, 8407975	Standard	NM_000097		Approved	CPX, HCP	uc003dsx.3	P36551		ENST00000264193.2:c.720T>A	chr3.hg19:g.98309567A>T		99.0	0.0	.		88.0	22.0	.	NM_000097	A8K275|B4DSD5|Q14060|Q53F08|Q8IZ45|Q96AF3	Silent	SNP	ENST00000264193.2	hg19	CCDS2932.1																																																																																			.	.	.	none		0.388	CPOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358900.1	NM_000097		T	98309567	A	T	98309567	2	4	184	1	0	0	0	0	0	0	0	1	3823	407	15	5		5	CPOX	3	98309567	Silent	SNP	A	TCGA-GL-7773-01A-11D-2136-08	35992502	98309567	99712863	31	10764											
ZBTB20	26137	hgsc.bcm.edu	37	chr3	114057877	114057878	+	Frame_Shift_Del	DEL	AT	AT	-																															cgtcagacacatgcatcctcAtgtggtcgttgaactgctcg																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr3:114057877_114057878delAT	ENST00000474710.1	-	5	2378_2379	c.2200_2201delAT	c.(2200-2202)atgfs	p.M734fs	ZBTB20_ENST00000393785.2_Frame_Shift_Del_p.M661fs|ZBTB20_ENST00000357258.3_Frame_Shift_Del_p.M661fs|ZBTB20_ENST00000464560.1_Frame_Shift_Del_p.M661fs|ZBTB20_ENST00000462705.1_Frame_Shift_Del_p.M661fs|ZBTB20_ENST00000481632.1_Frame_Shift_Del_p.M661fs|ZBTB20_ENST00000471418.1_Frame_Shift_Del_p.M661fs	NM_001164342.1	NP_001157814.1	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20	734						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)		ATGCATCCTCATGTGGTCGTTG	0.48																																					p.734_734del	NSCLC(69;748 1344 9802 11203 30933)	Atlas-INDEL	.											.	ZBTB20	157	.	0			c.2201_2202del						PASS	.																																			SO:0001589	frameshift_variant	26137	exon5			.	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.2200_2201delAT	chr3.hg19:g.114057877_114057878delAT	ENSP00000419153:p.Met734fs	124.0	0.0	0		141.0	56.0	0.397163	NM_001164342	Q63HP6|Q8N6R5|Q9Y410	Frame_Shift_Del	DEL	ENST00000474710.1	hg19	CCDS54626.1																																																																																			.	.	.	none		0.48	ZBTB20-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354951.1	NM_015642		-	114057878	AT	-	114057877	7	5	184	1	0	1	0	1	0	0	0	0	17541	217	8	0	28	0	ZBTB20	3	114057877	Frame_Shift_Del	DEL	AT	TCGA-GL-7773-01A-11D-2136-08	15748310	114057877	83964553	32	10765											
MCM2	4171	hgsc.bcm.edu	37	chr3	127340566	127340566	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagtgagctcttcaggatgAacaagttcagccacgacctg	12	8	10	11	1	3	2	2	2	1	0	3	4	3	3	2	1	3	2	2	1	2	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr3:127340566A>G	ENST00000265056.7	+	16	2909	c.2665A>G	c.(2665-2667)Aac>Gac	p.N889D	MCM2_ENST00000468414.1_3'UTR	NM_004526.2	NP_004517.2	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	889					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						CTTCAGGATGAACAAGTTCAG	0.498																																					p.N889D		Atlas-SNP	.											.	MCM2	79	.	0			c.A2665G						PASS	.						100	95	96					3																	127340566		2203	4300	6503	SO:0001583	missense	4171	exon16			AGGATGAACAAGT	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.2665A>G	chr3.hg19:g.127340566A>G	ENSP00000265056:p.Asn889Asp	77.0	0.0	.		82.0	4.0	.	NM_004526	Q14577|Q15023|Q8N2V1|Q969W7|Q96AE1|Q9BRM7	Missense_Mutation	SNP	ENST00000265056.7	hg19	CCDS3043.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.42|19.42	3.824506|3.824506	0.71143|0.71143	.|.	.|.	ENSG00000073111|ENSG00000073111	ENST00000265056;ENST00000539922;ENST00000543142|ENST00000491422	T|.	0.02421|.	4.3|.	5.38|5.38	4.22|4.22	0.49857|0.49857	.|.	0.132166|.	0.64402|.	D|.	0.000002|.	T|.	0.74261|.	0.3693|.	M|M	0.81239|0.81239	2.535|2.535	0.80722|0.80722	D|D	1|1	P;P;B|.	0.38788|.	0.51;0.647;0.419|.	B;P;P|.	0.50896|.	0.282;0.653;0.455|.	T|.	0.74717|.	-0.3571|.	10|.	0.51188|.	T|.	0.08|.	-40.2853|-40.2853	12.3561|12.3561	0.55176|0.55176	0.8518:0.1482:0.0:0.0|0.8518:0.1482:0.0:0.0	.|.	939;759;889|.	F5H1E9;B4DSV5;P49736|.	.;.;MCM2_HUMAN|.	D|W	889;793;939|820	ENSP00000265056:N889D|.	ENSP00000265056:N889D|.	N|X	+|+	1|3	0|0	MCM2|MCM2	128823256|128823256	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.487000|0.487000	0.33371|0.33371	5.837000|5.837000	0.69381|0.69381	0.882000|0.882000	0.36016|0.36016	0.260000|0.260000	0.18958|0.18958	AAC|TGA	.	.	.	none		0.498	MCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356612.1			G	127340566	A	G	127340566	3	3	184	1	0	0	0	0	1	0	0	0	9393	246	9	3	2727	3	MCM2	3	127340566	Missense_Mutation	SNP	A	TCGA-GL-7773-01A-11D-2136-08	13282689	127340566	70681864	33	10766											
PLSCR2	57047	hgsc.bcm.edu	37	chr3	146167110	146167110	+	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	cttaaaaacccagaccagtgCttagaaatcctgccaaccac	15	7	5	14	0	0	2	0	0	0	2	1	2	1	2	5	0	4	1	5	0	6	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr3:146167110C>T	ENST00000497985.1	-	8	1186	c.747G>A	c.(745-747)aaG>aaA	p.K249K	PLSCR2_ENST00000336685.2_Silent_p.K176K	NM_001199978.1	NP_001186907.1	Q9NRY7	PLS2_HUMAN	phospholipid scramblase 2	249					phospholipid scrambling (GO:0017121)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phospholipid scramblase activity (GO:0017128)			endometrium(2)|large_intestine(5)|lung(7)|stomach(1)	15						CAGACCAGTGCTTAGAAATCC	0.328																																					p.K249K		Atlas-SNP	.											.	PLSCR2	68	.	0			c.G747A						PASS	.						128	130	130					3																	146167110		2203	4300	6503	SO:0001819	synonymous_variant	57047	exon8			CCAGTGCTTAGAA		CCDS56284.1, CCDS3134.1, CCDS75029.1	3q24	2008-07-18			ENSG00000163746	ENSG00000163746			16494	protein-coding gene	gene with protein product		607610				10930526	Standard	NM_001199978		Approved		uc003evw.2	Q9NRY7	OTTHUMG00000159429	ENST00000497985.1:c.747G>A	chr3.hg19:g.146167110C>T		164.0	0.0	.		228.0	90.0	.	NM_001199978	B4DXC3|J3KR76|Q0VAQ1|Q6NSW9|Q7Z4L7	Silent	SNP	ENST00000497985.1	hg19	CCDS56284.1																																																																																			.	.	.	none		0.328	PLSCR2-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000355264.1	NM_020359		T	146167110	C	T	146167110	2	4	184	1	0	0	0	0	0	0	0	1	12117	796	28	2		2	PLSCR2	3	146167110	Silent	SNP	C	TCGA-GL-7773-01A-11D-2136-08	18826544	146167110	51855320	34	10767											
MCCC1	56922	hgsc.bcm.edu	37	chr3	182789038	182789038	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cggctttaatcatgacaggaTagccaattctcctggcgtgt	9	12	10	10	2	2	1	1	1	1	0	3	2	2	2	2	3	1	1	2	3	3	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr3:182789038T>C	ENST00000265594.4	-	6	745	c.599A>G	c.(598-600)tAt>tGt	p.Y200C	MCCC1_ENST00000539926.1_Missense_Mutation_p.Y65C|MCCC1_ENST00000492597.1_Missense_Mutation_p.Y91C	NM_020166.3	NP_064551.3	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-CoA carboxylase 1 (alpha)	200	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.				biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(17)|ovary(1)|pancreas(2)|prostate(1)|skin(2)	40	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	CATGACAGGATAGCCAATTCT	0.463																																					p.Y200C		Atlas-SNP	.											.	MCCC1	87	.	0			c.A599G						PASS	.						100	101	101					3																	182789038		2203	4300	6503	SO:0001583	missense	56922	exon6			ACAGGATAGCCAA	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.599A>G	chr3.hg19:g.182789038T>C	ENSP00000265594:p.Tyr200Cys	103.0	0.0	.		129.0	30.0	.	NM_020166	Q59ES4|Q9H959|Q9NS97	Missense_Mutation	SNP	ENST00000265594.4	hg19	CCDS3241.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.081996	0.76528	.	.	ENSG00000078070	ENST00000265594;ENST00000492597;ENST00000392616;ENST00000539926;ENST00000476176;ENST00000448585;ENST00000541636	D;D;D;D	0.98400	-4.91;-4.91;-4.91;-4.91	5.9	5.9	0.94986	ATP-grasp fold (1);ATP-grasp fold, subdomain 1 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);Biotin carboxylation domain (1);	0.053830	0.85682	D	0.000000	D	0.99242	0.9736	H	0.94698	3.57	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.73708	0.975;0.975;0.981	D	0.99032	1.0821	10	0.87932	D	0	.	16.3322	0.83039	0.0:0.0:0.0:1.0	.	153;91;200	E9PG35;E9PHF7;Q96RQ3	.;.;MCCA_HUMAN	C	200;91;50;65;153;153;91	ENSP00000265594:Y200C;ENSP00000419898:Y91C;ENSP00000441253:Y65C;ENSP00000420433:Y153C	ENSP00000265594:Y200C	Y	-	2	0	MCCC1	184271732	1.000000	0.71417	0.605000	0.28930	0.929000	0.56500	5.693000	0.68264	2.251000	0.74343	0.528000	0.53228	TAT	.	.	.	none		0.463	MCCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350775.1	NM_020166		C	182789038	T	C	182789038	3	2	184	1	0	0	0	0	1	0	0	0	9381	1406	49	3	1634	3	MCCC1	3	182789038	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	36621928	182789038	15233392	35	10768											
CDKL2	8999	hgsc.bcm.edu	37	chr4	76529105	76529105	+	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	tccagcaaacacaggattttTattaaaaagctcctgatgcc	14	11	6	10	0	0	1	0	1	0	0	2	2	2	2	3	1	4	2	3	1	5	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr4:76529105T>A	ENST00000429927.2	-	6	1394	c.691A>T	c.(691-693)Aaa>Taa	p.K231*	CDKL2_ENST00000307465.4_Nonsense_Mutation_p.K231*	NM_003948.3	NP_003939.1	Q92772	CDKL2_HUMAN	cyclin-dependent kinase-like 2 (CDC2-related kinase)	231	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				sex differentiation (GO:0007548)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)			breast(3)|endometrium(1)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(2)|stomach(2)	22			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			ACAGGATTTTTATTAAAAAGC	0.388																																					p.K231X		Atlas-SNP	.											.	CDKL2	58	.	0			c.A691T						PASS	.						86	89	88					4																	76529105		2203	4300	6503	SO:0001587	stop_gained	8999	exon6			GATTTTTATTAAA	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.691A>T	chr4.hg19:g.76529105T>A	ENSP00000412365:p.Lys231*	127.0	0.0	.		113.0	46.0	.	NM_003948	B2R695	Nonsense_Mutation	SNP	ENST00000429927.2	hg19	CCDS3570.1	.	.	.	.	.	.	.	.	.	.	T	42	9.693897	0.99240	.	.	ENSG00000138769	ENST00000429927;ENST00000307465	.	.	.	5.14	3.9	0.45041	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-24.029	11.3921	0.49820	0.0:0.0:0.1508:0.8492	.	.	.	.	X	231	.	ENSP00000306340:K231X	K	-	1	0	CDKL2	76748129	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	4.829000	0.62737	2.164000	0.68074	0.460000	0.39030	AAA	.	.	.	none		0.388	CDKL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252409.2	NM_003948		A	76529105	T	A	76529105	4	1	184	1	0	0	0	0	0	1	0	0	3156	1763	61	5	814	5	CDKL2	4	76529105	Nonsense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08		76529105	114625171	36	10769											
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123202841	123202841	+	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	gttcttaaattcagtgccatGttagatggtatagccattgg	10	15	10	6	0	2	1	1	0	1	1	2	1	2	1	2	2	2	3	2	2	5	7	rs115036597		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr4:123202841G>C	ENST00000264501.4	+	52	9322	c.8949G>C	c.(8947-8949)atG>atC	p.M2983I	KIAA1109_ENST00000388738.3_Missense_Mutation_p.M2983I|KIAA1109_ENST00000455637.1_Missense_Mutation_p.M2983I			Q2LD37	K1109_HUMAN	KIAA1109	2983					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						TCAGTGCCATGTTAGATGGTA	0.383																																					p.M2983I		Atlas-SNP	.											.	KIAA1109	424	.	0			c.G8949C						PASS	.						121	113	116					4																	123202841		1831	4099	5930	SO:0001583	missense	84162	exon50			TGCCATGTTAGAT	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.8949G>C	chr4.hg19:g.123202841G>C	ENSP00000264501:p.Met2983Ile	124.0	0.0	.		160.0	57.0	.	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	5.047|5.047	0.194277|0.194277	0.09599|0.09599	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637|ENST00000419325	T;T;T|.	0.20069|.	2.69;2.69;2.1|.	5.46|5.46	5.46|5.46	0.80206|0.80206	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.33990|0.33990	0.0882|0.0882	N|N	0.04090|0.04090	-0.28|-0.28	0.43073|0.43073	D|D	0.994713|0.994713	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.08055|.	0.003;0.001|.	T|T	0.28138|0.28138	-1.0053|-1.0053	10|5	0.05436|.	T|.	0.98|.	.|.	12.6377|12.6377	0.56692|0.56692	0.0759:0.0:0.9241:0.0|0.0759:0.0:0.9241:0.0	.|.	2983;2983|.	Q2LD37-6;Q2LD37|.	.;K1109_HUMAN|.	I|L	2983|941	ENSP00000264501:M2983I;ENSP00000373390:M2983I;ENSP00000389925:M2983I|.	ENSP00000264501:M2983I|.	M|V	+|+	3|1	0|0	KIAA1109|KIAA1109	123422291|123422291	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	6.528000|6.528000	0.73807|0.73807	2.572000|2.572000	0.86782|0.86782	0.591000|0.591000	0.81541|0.81541	ATG|GTT	.	G|0.999;T|0.001	.	alt		0.383	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		C	123202841	G	C	123202841	3	2	184	1	0	0	0	0	1	0	0	0	8215	1377	48	4	9147	4	KIAA1109	4	123202841	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	46673736	123202841	67951435	37	10770											
MTRR	4552	hgsc.bcm.edu	37	chr5	7878202	7878202	+	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	ggacagaccttgtgaagtcaGagctgctacacattgaatct	12	10	10	9	0	2	4	1	2	1	2	2	5	2	5	1	1	3	2	1	1	3	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr5:7878202G>T	ENST00000264668.2	+	5	658	c.628G>T	c.(628-630)Gag>Tag	p.E210*	MTRR_ENST00000341013.6_3'UTR|MTRR_ENST00000440940.2_Nonsense_Mutation_p.E183*	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	210	Hinge.				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)	TGTGAAGTCAGAGCTGCTACA	0.478																																					p.E210X		Atlas-SNP	.											.	MTRR	74	.	0			c.G628T						PASS	.						82	77	78					5																	7878202		2203	4300	6503	SO:0001587	stop_gained	4552	exon5			AAGTCAGAGCTGC	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.628G>T	chr5.hg19:g.7878202G>T	ENSP00000264668:p.Glu210*	64.0	0.0	.		57.0	19.0	.	NM_024010	O60471|Q32MA9|Q7Z4M8	Nonsense_Mutation	SNP	ENST00000264668.2	hg19	CCDS3874.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.92|11.92	1.783157|1.783157	0.31593|0.31593	.|.	.|.	ENSG00000124275|ENSG00000124275	ENST00000264668;ENST00000440940|ENST00000514220	.|.	.|.	.|.	5.91|5.91	3.14|3.14	0.36123|0.36123	.|.	1.215660|.	0.05458|.	N|.	0.550635|.	.|T	.|0.49898	.|0.1584	.|.	.|.	.|.	0.18873|0.18873	N|N	0.999986|0.999986	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.38394	.|-0.9663	.|4	0.18276|.	T|.	0.48|.	-19.4083|-19.4083	15.3298|15.3298	0.74200|0.74200	0.0:0.4006:0.5994:0.0|0.0:0.4006:0.5994:0.0	.|.	.|.	.|.	.|.	X|I	210;183|111	.|.	ENSP00000264668:E210X|.	E|R	+|+	1|2	0|0	MTRR|MTRR	7931202|7931202	0.022000|0.022000	0.18835|0.18835	0.000000|0.000000	0.03702|0.03702	0.014000|0.014000	0.08584|0.08584	1.921000|1.921000	0.40035|0.40035	0.387000|0.387000	0.25024|0.25024	-0.127000|-0.127000	0.14921|0.14921	GAG|AGA	.	.	.	none		0.478	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1			T	7878202	G	T	7878202	4	4	184	1	0	0	0	0	0	1	0	0	9968	943	33	4	646	4	MTRR	5	7878202	Nonsense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08		7878202	173037058	38	10771											
RNASEN	29102	hgsc.bcm.edu	37	chr5	31515239	31515239	+	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	tccttgattgaggtatagttCttgtctttgccagaactctg	7	17	9	8	0	3	3	0	2	3	1	4	3	4	3	2	1	2	2	2	1	3	7			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr5:31515239C>G	ENST00000511367.2	-	7	1390	c.1146G>C	c.(1144-1146)aaG>aaC	p.K382N	DROSHA_ENST00000442743.1_Missense_Mutation_p.K345N|DROSHA_ENST00000513349.1_Missense_Mutation_p.K345N|DROSHA_ENST00000344624.3_Missense_Mutation_p.K382N	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	382					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						AGGTATAGTTCTTGTCTTTGC	0.478																																					p.K382N		Atlas-SNP	.											DROSHA,colon,carcinoma,0,1	DROSHA	130	.	0			c.G1146C						PASS	.						160	152	154					5																	31515239		1868	4097	5965	SO:0001583	missense	29102	exon7			ATAGTTCTTGTCT	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.1146G>C	chr5.hg19:g.31515239C>G	ENSP00000425979:p.Lys382Asn	148.0	0.0	.		178.0	63.0	.	NM_013235	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Missense_Mutation	SNP	ENST00000511367.2	hg19	CCDS47195.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.68|16.68	3.189775|3.189775	0.57909|0.57909	.|.	.|.	ENSG00000113360|ENSG00000113360	ENST00000512076|ENST00000511367;ENST00000344624;ENST00000442743;ENST00000513349;ENST00000265075;ENST00000382188;ENST00000512302	.|T;T;T;T;T	.|0.59083	.|0.29;0.29;0.29;0.29;0.29	5.64|5.64	4.78|4.78	0.61160|0.61160	.|.	.|0.048766	.|0.85682	.|D	.|0.000000	T|T	0.54303|0.54303	0.1850|0.1850	N|N	0.19112|0.19112	0.55|0.55	0.44098|0.44098	D|D	0.996864|0.996864	.|D;B;B	.|0.54964	.|0.969;0.421;0.421	.|P;B;B	.|0.55824	.|0.785;0.154;0.154	T|T	0.55560|0.55560	-0.8122|-0.8122	5|10	.|0.44086	.|T	.|0.13	-27.3211|-27.3211	11.1936|11.1936	0.48700|0.48700	0.0:0.8412:0.0:0.1588|0.0:0.8412:0.0:0.1588	.|.	.|314;345;382	.|Q9NRR4-2;E7EMP9;Q9NRR4	.|.;.;RNC_HUMAN	Q|N	144|382;382;345;345;307;338;149	.|ENSP00000425979:K382N;ENSP00000339845:K382N;ENSP00000409335:K345N;ENSP00000424161:K345N;ENSP00000428782:K149N	.|ENSP00000265075:K307N	E|K	-|-	1|3	0|2	DROSHA|DROSHA	31550996|31550996	0.980000|0.980000	0.34600|0.34600	0.968000|0.968000	0.41197|0.41197	0.798000|0.798000	0.45092|0.45092	0.552000|0.552000	0.23376|0.23376	1.395000|1.395000	0.46643|0.46643	0.561000|0.561000	0.74099|0.74099	GAA|AAG	.	.	.	none		0.478	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235		G	31515239	C	G	31515239	3	3	184	1	0	0	0	0	1	0	0	0	13430	912	32	4	3094	4	RNASEN	5	31515239	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	23637037	31515239	149400021	39	10772											
CHD1	1105	hgsc.bcm.edu	37	chr5	98192299	98192299	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acttgaccggtggtctgaatGtaaccgatgatctgagtgag	10	11	13	7	2	2	5	0	5	2	0	2	6	2	5	2	2	1	1	2	2	2	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr5:98192299G>A	ENST00000284049.3	-	35	5067	c.4918C>T	c.(4918-4920)Cat>Tat	p.H1640Y		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	1640	3 X 5 AA repeats of H-S-D-H-R.				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)	TGGTCTGAATGTAACCGATGA	0.428																																					p.H1640Y		Atlas-SNP	.											.	CHD1	137	.	0			c.C4918T						PASS	.						136	128	131					5																	98192299		2203	4299	6502	SO:0001583	missense	1105	exon35			CTGAATGTAACCG	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.4918C>T	chr5.hg19:g.98192299G>A	ENSP00000284049:p.His1640Tyr	68.0	0.0	.		45.0	29.0	.	NM_001270	Q17RZ3	Missense_Mutation	SNP	ENST00000284049.3	hg19	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	G	4.283	0.051605	0.08291	.	.	ENSG00000153922	ENST00000422663;ENST00000284049	D	0.89875	-2.58	5.21	5.21	0.72293	.	0.000000	0.34386	U	0.004006	D	0.86079	0.5847	M	0.65498	2.005	0.38271	D	0.942164	B	0.27882	0.192	B	0.22880	0.042	T	0.82969	-0.0193	10	0.02654	T	1	.	18.7493	0.91807	0.0:0.0:1.0:0.0	.	1640	O14646	CHD1_HUMAN	Y	230;1640	ENSP00000284049:H1640Y	ENSP00000284049:H1640Y	H	-	1	0	CHD1	98220199	1.000000	0.71417	0.970000	0.41538	0.993000	0.82548	2.914000	0.48797	2.407000	0.81776	0.655000	0.94253	CAT	.	.	.	none		0.428	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270		A	98192299	G	A	98192299	3	1	184	1	0	0	0	0	1	0	0	0	3325	1377	48	2	218	2	CHD1	5	98192299	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	66677060	98192299	82722961	40	10773											
PCDHGB2	56103	hgsc.bcm.edu	37	chr5	140741729	140741729	+	Missense_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	agaggtattgccagacctcaGcgaccgccgggagccctctg	8	6	13	14	3	2	2	1	0	1	2	2	4	2	3	5	2	3	1	5	2	1	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr5:140741729G>A	ENST00000522605.1	+	1	2027	c.2027G>A	c.(2026-2028)aGc>aAc	p.S676N	PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_5'Flank|PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018923.2|NM_032096.1	NP_061746.1|NP_115267.1	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2	676					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)			CCAGACCTCAGCGACCGCCGG	0.602																																					p.S676N		Atlas-SNP	.											.	PCDHGB2	196	.	0			c.G2027A						PASS	.						54	59	57					5																	140741729		2031	4196	6227	SO:0001583	missense	56103	exon1			ACCTCAGCGACCG	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.2027G>A	chr5.hg19:g.140741729G>A	ENSP00000429018:p.Ser676Asn	67.0	0.0	.		68.0	44.0	.	NM_018923	Q3MIJ3|Q9UN65	Missense_Mutation	SNP	ENST00000522605.1	hg19	CCDS54924.1	.	.	.	.	.	.	.	.	.	.	.	9.065	0.995573	0.19043	.	.	ENSG00000253910	ENST00000522605	T	0.51071	0.72	4.95	3.13	0.36017	.	.	.	.	.	T	0.39937	0.1097	L	0.53617	1.68	0.09310	N	1	B;B	0.24618	0.005;0.107	B;B	0.22601	0.021;0.04	T	0.22977	-1.0201	9	0.21014	T	0.42	.	9.109	0.36716	0.242:0.0:0.758:0.0	.	676;676	Q9Y5G2-2;Q9Y5G2	.;PCDGE_HUMAN	N	676	ENSP00000429018:S676N	ENSP00000429018:S676N	S	+	2	0	PCDHGB2	140721913	0.000000	0.05858	0.045000	0.18777	0.027000	0.11550	0.655000	0.24933	1.220000	0.43490	0.454000	0.30748	AGC	.	.	.	none		0.602	PCDHGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374741.1	NM_018923		A	140741729	G	A	140741729	3	1	184	1	0	0	0	0	1	0	0	0	11570	971	34	2	2029	2	PCDHGB2	5	140741729	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	42549430	140741729	40173531	41	10774											
F12	2161	hgsc.bcm.edu	37	chr5	176829362	176829363	+	Frame_Shift_Del	DEL	GC	GC	-																															gtgtagacgcctggcttgttGcggtcaccacagcccgatcc																								rs375101670		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr5:176829362_176829363delGC	ENST00000253496.3	-	14	1826_1827	c.1778_1779delGC	c.(1777-1779)cgcfs	p.R593fs	F12_ENST00000514943.1_5'Flank|PFN3_ENST00000358571.2_5'Flank	NM_000505.3	NP_000496.2	P00748	FA12_HUMAN	coagulation factor XII (Hageman factor)	593	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|plasma kallikrein-kinin cascade (GO:0002353)|positive regulation of blood coagulation (GO:0030194)|positive regulation of fibrinolysis (GO:0051919)|positive regulation of plasminogen activation (GO:0010756)|protein autoprocessing (GO:0016540)|protein processing (GO:0016485)|response to misfolded protein (GO:0051788)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	misfolded protein binding (GO:0051787)|serine-type aminopeptidase activity (GO:0070009)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	12	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Ethanolamine Oleate(DB06689)	CTGGCTTGTTGCGGTCACCACA	0.619									Hereditary Angioedema																												p.593_594del		Atlas-INDEL	.											.	F12	35	.	0			c.1779_1780del						PASS	.																																			SO:0001589	frameshift_variant	2161	exon14	Familial Cancer Database	HAE, type I-III, Hereditary Angioneurotic Edema, HANE,	.	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.1778_1779delGC	chr5.hg19:g.176829362_176829363delGC	ENSP00000253496:p.Arg593fs	41.0	0.0	0		44.0	13.0	0.295455	NM_000505	P78339	Frame_Shift_Del	DEL	ENST00000253496.3	hg19	CCDS34302.1																																																																																			.	.	.	none		0.619	F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373217.1			-	176829363	GC	-	176829362	7	5	184	1	0	1	0	1	0	0	0	0	5341	1306	46	0	72	0	F12	5	176829362	Frame_Shift_Del	DEL	GC	TCGA-GL-7773-01A-11D-2136-08	36087633	176829362	4085898	42	10775											
FLT4	2324	hgsc.bcm.edu	37	chr5	180030377	180030377	+	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	ggtcacagccacattctggcCaggtcctttacagctgccaa	9	9	9	14	0	2	0	1	0	1	0	3	0	3	0	4	3	4	1	4	3	2	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr5:180030377C>T	ENST00000261937.6	-	30	3985	c.3907G>A	c.(3907-3909)Ggc>Agc	p.G1303S		NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	1303					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)	ACATTCTGGCCAGGTCCTTTA	0.617																																					p.G1303S	Colon(97;1075 1466 27033 27547 35871)	Atlas-SNP	.											.	FLT4	356	.	0			c.G3907A						PASS	.						24	26	25					5																	180030377		2203	4300	6503	SO:0001583	missense	2324	exon30			TCTGGCCAGGTCC	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.3907G>A	chr5.hg19:g.180030377C>T	ENSP00000261937:p.Gly1303Ser	27.0	0.0	.		47.0	17.0	.	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Missense_Mutation	SNP	ENST00000261937.6	hg19	CCDS4457.1	.	.	.	.	.	.	.	.	.	.	C	9.313	1.056047	0.19907	.	.	ENSG00000037280	ENST00000261937	T	0.75050	-0.9	4.62	2.77	0.32553	.	.	.	.	.	T	0.50292	0.1607	L	0.27053	0.805	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.42015	-0.9476	9	0.02654	T	1	.	1.1998	0.01882	0.2134:0.4115:0.2083:0.1668	.	1303	P35916	VGFR3_HUMAN	S	1303	ENSP00000261937:G1303S	ENSP00000261937:G1303S	G	-	1	0	FLT4	179962983	0.001000	0.12720	0.010000	0.14722	0.901000	0.52897	0.037000	0.13840	1.051000	0.40369	0.471000	0.43371	GGC	.	.	.	none		0.617	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4			T	180030377	C	T	180030377	3	4	184	1	0	0	0	0	1	0	0	0	5951	594	21	2	188	2	FLT4	5	180030377	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	3201015	180030377	884883	43	10776											
CDKAL1	54901	hgsc.bcm.edu	37	chr6	20548882	20548882	+	Missense_Mutation	SNP	T	T	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	ggggttgttctcataataatTcagatggagaatatatggct	12	14	11	4	0	2	2	2	0	1	2	3	3	2	2	0	4	0	3	0	4	5	7			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr6:20548882T>G	ENST00000378610.1	+	2	242	c.232T>G	c.(232-234)Tca>Gca	p.S78A	CDKAL1_ENST00000378624.4_Intron|CDKAL1_ENST00000274695.4_Missense_Mutation_p.S78A			Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein 1-like 1	78	MTTase N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00780}.				maintenance of translational fidelity (GO:1990145)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|N6-threonylcarbomyladenosine methylthiotransferase activity (GO:0035598)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|stomach(1)	29	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			TCATAATAATTCAGATGGAGA	0.294																																					p.S78A		Atlas-SNP	.											.	CDKAL1	55	.	0			c.T232G						PASS	.						80	85	83					6																	20548882		2203	4300	6503	SO:0001583	missense	54901	exon4			AATAATTCAGATG	AK000349	CCDS4546.1	6p22.2	2008-02-05			ENSG00000145996	ENSG00000145996			21050	protein-coding gene	gene with protein product		611259					Standard	NM_017774		Approved	FLJ20342	uc003ndd.2	Q5VV42	OTTHUMG00000014340	ENST00000378610.1:c.232T>G	chr6.hg19:g.20548882T>G	ENSP00000367873:p.Ser78Ala	127.0	0.0	.		171.0	68.0	.	NM_017774	A8K6S0|Q6P385|Q6ZR27|Q9NXB3	Missense_Mutation	SNP	ENST00000378610.1	hg19	CCDS4546.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.515717	0.85389	.	.	ENSG00000145996	ENST00000274695;ENST00000378610	T;T	0.43688	0.94;0.94	5.81	5.81	0.92471	Methylthiotransferase, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.49372	0.1553	L	0.52823	1.66	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.83275	0.951;0.996	T	0.39313	-0.9620	10	0.24483	T	0.36	.	16.1708	0.81812	0.0:0.0:0.0:1.0	.	78;78	Q5VV42;Q5VV42-3	CDKAL_HUMAN;.	A	78	ENSP00000274695:S78A;ENSP00000367873:S78A	ENSP00000274695:S78A	S	+	1	0	CDKAL1	20656861	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.400000	0.79949	2.225000	0.72522	0.533000	0.62120	TCA	.	.	.	none		0.294	CDKAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039986.1	NM_017774		G	20548882	T	G	20548882	3	3	184	1	0	0	0	0	1	0	0	0	3154	1783	62	5	238	5	CDKAL1	6	20548882	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08		20548882	150566185	44	10777											
COL9A1	1297	hgsc.bcm.edu	37	chr6	71003975	71003975	+	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	aaagattcaatcctgttgcaGtcaacaaaaagagtagcact	17	9	7	8	0	2	2	2	0	0	2	3	2	3	2	1	0	3	4	1	0	6	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr6:71003975G>A	ENST00000357250.6	-	5	749	c.591C>T	c.(589-591)gaC>gaT	p.D197D	COL9A1_ENST00000370496.3_Silent_p.D197D	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	197	Laminin G-like.|Nonhelical region (NC4).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|organ morphogenesis (GO:0009887)|tissue homeostasis (GO:0001894)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(44)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)	80						TCCTGTTGCAGTCAACAAAAA	0.433																																					p.D197D		Atlas-SNP	.											.	COL9A1	228	.	0			c.C591T						PASS	.						128	124	125					6																	71003975		2203	4300	6503	SO:0001819	synonymous_variant	1297	exon5			GTTGCAGTCAACA		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.591C>T	chr6.hg19:g.71003975G>A		135.0	0.0	.		215.0	73.0	.	NM_001851	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Silent	SNP	ENST00000357250.6	hg19	CCDS4971.1																																																																																			.	.	.	none		0.433	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2			A	71003975	G	A	71003975	2	1	184	1	0	0	0	0	0	0	0	1	3709	1020	36	2		2	COL9A1	6	71003975	Silent	SNP	G	TCGA-GL-7773-01A-11D-2136-08	50455093	71003975	100111092	45	10778											
BACH2	60468	hgsc.bcm.edu	37	chr6	90660214	90660214	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcacagagagggaggctgcaGggtgagcccccgctcccgtc	7	5	15	14	2	1	2	1	1	0	1	3	4	2	3	3	3	2	3	3	3	0	0			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr6:90660214G>A	ENST00000257749.4	-	7	2318	c.1611C>T	c.(1609-1611)ccC>ccT	p.P537P	BACH2_ENST00000343122.3_Silent_p.P537P|RP3-512E2.2_ENST00000445838.1_RNA|BACH2_ENST00000537989.1_Silent_p.P537P|RP3-512E2.2_ENST00000413986.1_RNA	NM_021813.2	NP_068585.1	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 2	537						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)		GGAGGCTGCAGGGTGAGCCCC	0.612																																					p.P537P		Atlas-SNP	.											.	BACH2	224	.	0			c.C1611T						PASS	.						69	68	68					6																	90660214		2203	4300	6503	SO:0001819	synonymous_variant	60468	exon7			GCTGCAGGGTGAG	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.1611C>T	chr6.hg19:g.90660214G>A		68.0	0.0	.		102.0	40.0	.	NM_021813	E1P518|Q59H70|Q5T793|Q9NTS5	Silent	SNP	ENST00000257749.4	hg19	CCDS5026.1																																																																																			.	.	.	none		0.612	BACH2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041522.2	NM_021813		A	90660214	G	A	90660214	2	1	184	1	0	0	0	0	0	0	0	1	1284	987	35	2		2	BACH2	6	90660214	Silent	SNP	G	TCGA-GL-7773-01A-11D-2136-08	19656239	90660214	80454853	46	10779											
PREP	5550	hgsc.bcm.edu	37	chr6	105776878	105776878	+	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	gtagcataagaccaagaagtTggacctgacacaagctatcc	15	7	9	10	0	0	3	0	1	0	2	1	4	1	4	3	1	2	4	3	1	6	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr6:105776878T>A	ENST00000369110.3	-	9	1231	c.1039A>T	c.(1039-1041)Aac>Tac	p.N347Y		NM_002726.4	NP_002717.3	P48147	PPCE_HUMAN	prolyl endopeptidase	347					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(2)|large_intestine(7)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)	ACCAAGAAGTTGGACCTGACA	0.413																																					p.N347Y		Atlas-SNP	.											.	PREP	65	.	0			c.A1039T						PASS	.						71	73	73					6																	105776878		2203	4300	6503	SO:0001583	missense	5550	exon9			AGAAGTTGGACCT		CCDS5053.1	6q22	2008-02-05			ENSG00000085377	ENSG00000085377	3.4.21.26		9358	protein-coding gene	gene with protein product		600400				7959018	Standard	NM_002726		Approved		uc003prc.3	P48147	OTTHUMG00000015297	ENST00000369110.3:c.1039A>T	chr6.hg19:g.105776878T>A	ENSP00000358106:p.Asn347Tyr	67.0	0.0	.		91.0	35.0	.	NM_002726	Q8N6D4	Missense_Mutation	SNP	ENST00000369110.3	hg19	CCDS5053.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.627037	0.87560	.	.	ENSG00000085377	ENST00000369110	T	0.47528	0.84	5.48	5.48	0.80851	Peptidase S9A, oligopeptidase, N-terminal (1);Peptidase S9A/B/C, oligopeptidase, N-terminal beta-propeller (2);	0.123452	0.85682	D	0.000000	T	0.60143	0.2246	M	0.83223	2.63	0.58432	D	0.999996	D	0.54047	0.964	P	0.57009	0.811	T	0.67860	-0.5561	10	0.72032	D	0.01	-30.1871	15.8535	0.78956	0.0:0.0:0.0:1.0	.	347	P48147	PPCE_HUMAN	Y	347	ENSP00000358106:N347Y	ENSP00000358106:N347Y	N	-	1	0	PREP	105883571	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.655000	0.83696	2.207000	0.71202	0.459000	0.35465	AAC	.	.	.	none		0.413	PREP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041658.1			A	105776878	T	A	105776878	3	1	184	1	0	0	0	0	1	0	0	0	12484	1812	63	5	1121	5	PREP	6	105776878	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	15116664	105776878	65338189	47	10780											
SEMA3A	10371	hgsc.bcm.edu	37	chr7	83631283	83631283	+	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	gcactcacccgaaaaactgtCatttcttccagcagaacctc	12	9	5	15	1	3	1	2	0	1	1	5	2	4	1	3	0	3	2	3	0	3	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr7:83631283C>A	ENST00000265362.4	-	12	1754	c.1440G>T	c.(1438-1440)atG>atT	p.M480I	SEMA3A_ENST00000436949.1_Missense_Mutation_p.M480I	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	480	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						GAAAAACTGTCATTTCTTCCA	0.428																																					p.M480I		Atlas-SNP	.											SEMA3A,NS,carcinoma,0,1	SEMA3A	121	.	0			c.G1440T						PASS	.						130	118	122					7																	83631283		2203	4300	6503	SO:0001583	missense	10371	exon12			AACTGTCATTTCT	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.1440G>T	chr7.hg19:g.83631283C>A	ENSP00000265362:p.Met480Ile	73.0	0.0	.		79.0	22.0	.	NM_006080		Missense_Mutation	SNP	ENST00000265362.4	hg19	CCDS5599.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.665855	0.88251	.	.	ENSG00000075213	ENST00000265362;ENST00000436949	T;T	0.09073	3.02;3.02	5.36	5.36	0.76844	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.09113	0.0225	N	0.10809	0.05	0.80722	D	1	P	0.42039	0.769	P	0.47162	0.54	T	0.46303	-0.9201	10	0.28530	T	0.3	.	19.4559	0.94889	0.0:1.0:0.0:0.0	.	480	Q14563	SEM3A_HUMAN	I	480	ENSP00000265362:M480I;ENSP00000415260:M480I	ENSP00000265362:M480I	M	-	3	0	SEMA3A	83469219	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.722000	0.84778	2.669000	0.90835	0.591000	0.81541	ATG	.	.	.	none		0.428	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		A	83631283	C	A	83631283	3	1	184	1	0	0	0	0	1	0	0	0	14037	826	29	4	899	4	SEMA3A	7	83631283	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08		83631283	75507380	48	10781											
SLC25A13	10165	hgsc.bcm.edu	37	chr7	95818645	95818645	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagttaaagggcagagttccCtcttccagaggagcaatccg	12	8	11	10	1	1	2	0	0	1	2	4	3	4	3	3	2	1	4	3	2	4	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr7:95818645C>T	ENST00000265631.5	-	9	1030	c.894G>A	c.(892-894)gaG>gaA	p.E298E	SLC25A13_ENST00000416240.2_Silent_p.E298E|SLC25A13_ENST00000542654.1_Silent_p.E190E			Q9UJS0	CMC2_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 13	298					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)	GCAGAGTTCCCTCTTCCAGAG	0.458																																					p.E298E		Atlas-SNP	.											.	SLC25A13	131	.	0			c.G894A						PASS	.						93	91	91					7																	95818645		2203	4300	6503	SO:0001819	synonymous_variant	10165	exon9			AGTTCCCTCTTCC	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.894G>A	chr7.hg19:g.95818645C>T		48.0	0.0	.		54.0	23.0	.	NM_001160210	O14566|O14575|Q546F9|Q9NZW1|Q9UNI7	Silent	SNP	ENST00000265631.5	hg19	CCDS5645.1																																																																																			.	.	.	none		0.458	SLC25A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059395.2	NM_014251		T	95818645	C	T	95818645	2	4	184	1	0	0	0	0	0	0	0	1	14488	680	24	2		2	SLC25A13	7	95818645	Silent	SNP	C	TCGA-GL-7773-01A-11D-2136-08	12187362	95818645	63320018	49	10782											
RP1L1	94137	hgsc.bcm.edu	37	chr8	10466983	10466983	+	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	cctgcaggccccagcgtgctCggagctcagccaccgcactg	6	5	12	18	3	1	0	1	0	0	0	2	1	1	1	5	2	5	4	5	2	0	0			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr8:10466983C>A	ENST00000382483.3	-	4	4848	c.4625G>T	c.(4624-4626)cGa>cTa	p.R1542L		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1622					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)		CCAGCGTGCTCGGAGCTCAGC	0.647																																					p.R1542L		Atlas-SNP	.											.	RP1L1	453	.	0			c.G4625T						PASS	.						22	26	25					8																	10466983		2119	4242	6361	SO:0001583	missense	94137	exon4			CGTGCTCGGAGCT	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.4625G>T	chr8.hg19:g.10466983C>A	ENSP00000371923:p.Arg1542Leu	47.0	0.0	.		62.0	19.0	.	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	hg19	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	C	9.421	1.083074	0.20309	.	.	ENSG00000183638	ENST00000382483	T	0.07327	3.2	5.32	-0.24	0.13047	.	0.320649	0.17484	U	0.172610	T	0.03959	0.0111	L	0.29908	0.895	0.09310	N	1	P	0.44309	0.832	B	0.31442	0.13	T	0.40365	-0.9567	10	0.66056	D	0.02	-2.2884	3.8382	0.08903	0.175:0.3157:0.0:0.5092	.	1542	A6NKC6	.	L	1542	ENSP00000371923:R1542L	ENSP00000371923:R1542L	R	-	2	0	RP1L1	10504393	0.988000	0.35896	0.001000	0.08648	0.017000	0.09413	2.285000	0.43487	0.252000	0.21531	0.491000	0.48974	CGA	.	.	.	none		0.647	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			A	10466983	C	A	10466983	3	1	184	1	0	0	0	0	1	0	0	0	13546	884	31	4	2581	4	RP1L1	8	10466983	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08		10466983	135897039	50	10783											
CA13	377677	hgsc.bcm.edu	37	chr8	86180770	86180770	+	Missense_Mutation	SNP	T	T	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	catcctgggactactggacaTatcctggttctcttacagtt	8	14	8	11	0	1	0	0	0	1	0	4	2	3	2	2	3	2	2	2	3	3	5			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr8:86180770T>G	ENST00000321764.3	+	6	885	c.583T>G	c.(583-585)Tat>Gat	p.Y195D	CA13_ENST00000517298.1_3'UTR	NM_198584.2	NP_940986.1	Q8N1Q1	CAH13_HUMAN	carbonic anhydrase XIII	195					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)	CTACTGGACATATCCTGGTTC	0.398																																					p.Y195D		Atlas-SNP	.											.	CA13	26	.	0			c.T583G						PASS	.						180	163	169					8																	86180770		2203	4300	6503	SO:0001583	missense	377677	exon6			TGGACATATCCTG	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.583T>G	chr8.hg19:g.86180770T>G	ENSP00000318912:p.Tyr195Asp	145.0	0.0	.		166.0	64.0	.	NM_198584		Missense_Mutation	SNP	ENST00000321764.3	hg19	CCDS6236.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.582688	0.86748	.	.	ENSG00000185015	ENST00000321764	D	0.83914	-1.78	5.5	5.5	0.81552	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.000000	0.85682	D	0.000000	D	0.95401	0.8507	H	0.99689	4.705	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97404	0.9998	10	0.87932	D	0	-19.1625	14.5856	0.68322	0.0:0.0:0.0:1.0	.	195	Q8N1Q1	CAH13_HUMAN	D	195	ENSP00000318912:Y195D	ENSP00000318912:Y195D	Y	+	1	0	CA13	86368022	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	7.311000	0.78958	2.104000	0.64026	0.383000	0.25322	TAT	.	.	.	none		0.398	CA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381066.1	NM_198584		G	86180770	T	G	86180770	3	3	184	1	0	0	0	0	1	0	0	0	2516	1406	49	5	605	5	CA13	8	86180770	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	75713787	86180770	60183252	51	10784											
EFR3A	23167	hgsc.bcm.edu	37	chr8	132982859	132982859	+	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	tccaaagacaatgatgagaaGattgtgcagaatgctatcat	16	10	9	6	0	1	5	1	2	0	4	2	6	2	5	1	0	2	2	1	0	5	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr8:132982859G>T	ENST00000254624.5	+	10	1353	c.1128G>T	c.(1126-1128)aaG>aaT	p.K376N	EFR3A_ENST00000519656.1_Missense_Mutation_p.K340N|EFR3A_ENST00000334503.4_Missense_Mutation_p.K376N	NM_015137.4	NP_055952.2	Q14156	EFR3A_HUMAN	EFR3 homolog A (S. cerevisiae)	376						extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|skin(1)|stomach(2)	35	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)			ATGATGAGAAGATTGTGCAGA	0.378																																					p.K376N		Atlas-SNP	.											.	EFR3A	96	.	0			c.G1128T						PASS	.						124	124	124					8																	132982859		2203	4300	6503	SO:0001583	missense	23167	exon10			TGAGAAGATTGTG	D63477	CCDS34942.2	8q24.22	2008-10-23			ENSG00000132294	ENSG00000132294			28970	protein-coding gene	gene with protein product		611798				15363888	Standard	NM_015137		Approved	KIAA0143	uc003yte.3	Q14156	OTTHUMG00000150552	ENST00000254624.5:c.1128G>T	chr8.hg19:g.132982859G>T	ENSP00000254624:p.Lys376Asn	141.0	0.0	.		182.0	56.0	.	NM_015137	A7MD19|Q2VPK2|Q63HL7|Q68DX1|Q6IQ18	Missense_Mutation	SNP	ENST00000254624.5	hg19	CCDS34942.2	.	.	.	.	.	.	.	.	.	.	G	14.63	2.592563	0.46214	.	.	ENSG00000132294	ENST00000254624;ENST00000377917;ENST00000334503;ENST00000519656	T;T;T	0.67345	3.52;3.52;-0.26	5.56	4.68	0.58851	Armadillo-like helical (1);Armadillo-type fold (1);	0.045081	0.85682	D	0.000000	T	0.58764	0.2145	L	0.47190	1.495	0.38491	D	0.947988	B	0.28512	0.214	B	0.30782	0.12	T	0.59563	-0.7431	10	0.39692	T	0.17	-19.1717	10.108	0.42546	0.073:0.0:0.789:0.138	.	376	Q14156	EFR3A_HUMAN	N	376;376;376;340	ENSP00000254624:K376N;ENSP00000334769:K376N;ENSP00000428086:K340N	ENSP00000254624:K376N	K	+	3	2	EFR3A	133052041	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.792000	0.47837	1.342000	0.45619	0.585000	0.79938	AAG	.	.	.	none		0.378	EFR3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318886.1	NM_015137		T	132982859	G	T	132982859	3	4	184	1	0	0	0	0	1	0	0	0	4960	933	33	4	1166	4	EFR3A	8	132982859	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	46802089	132982859	13381163	52	10785											
KIAA0020	9933	hgsc.bcm.edu	37	chr9	2810352	2810352	+	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	ttcatagcctaccttctctcCcattttctttcatcttttta	6	21	1	13	0	5	0	2	0	3	0	7	0	6	0	3	0	2	0	3	0	3	10			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr9:2810352C>G	ENST00000397885.2	-	16	1921	c.1715G>C	c.(1714-1716)gGg>gCg	p.G572A		NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	572						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)		ACCTTCTCTCCCATTTTCTTT	0.393																																					p.G572A		Atlas-SNP	.											.	KIAA0020	56	.	0			c.G1715C						PASS	.						225	188	201					9																	2810352		2203	4300	6503	SO:0001583	missense	9933	exon16			TCTCTCCCATTTT	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.1715G>C	chr9.hg19:g.2810352C>G	ENSP00000380982:p.Gly572Ala	65.0	0.0	.		91.0	21.0	.	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Missense_Mutation	SNP	ENST00000397885.2	hg19	CCDS6448.2	.	.	.	.	.	.	.	.	.	.	C	11.75	1.731430	0.30684	.	.	ENSG00000080608	ENST00000397885	T	0.50548	0.74	5.95	5.05	0.67936	CPL (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.046170	0.85682	D	0.000000	T	0.48607	0.1509	M	0.73962	2.25	0.45528	D	0.998487	B;B	0.12013	0.005;0.001	B;B	0.15870	0.014;0.006	T	0.44682	-0.9312	10	0.21014	T	0.42	-18.5072	14.8914	0.70611	0.0:0.7295:0.2705:0.0	.	432;572	B2RDG4;Q15397	.;K0020_HUMAN	A	572	ENSP00000380982:G572A	ENSP00000380982:G572A	G	-	2	0	KIAA0020	2800352	1.000000	0.71417	0.326000	0.25389	0.569000	0.35902	2.906000	0.48735	1.521000	0.48983	0.650000	0.86243	GGG	.	.	.	none		0.393	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878		G	2810352	C	G	2810352	3	3	184	1	0	0	0	0	1	0	0	0	8159	623	22	4	243	4	KIAA0020	9	2810352	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08		2810352	138403079	53	10786											
PRSS3	5646	hgsc.bcm.edu	37	chr9	33798069	33798069	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccggctggggcaacactcTgagctttggtggtgagtggg	5	10	17	9	1	1	2	0	2	1	0	2	2	2	2	1	6	2	3	1	6	1	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr9:33798069T>C	ENST00000361005.5	+	3	614	c.614T>C	c.(613-615)cTg>cCg	p.L205P	RP11-133O22.6_ENST00000454429.2_RNA|PRSS3_ENST00000429677.3_Missense_Mutation_p.L141P|PRSS3_ENST00000342836.4_Missense_Mutation_p.L162P|PRSS3_ENST00000379405.3_Missense_Mutation_p.L148P	NM_007343.3	NP_031369	P35030	TRY3_HUMAN	protease, serine, 3	205	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)			GGCAACACTCTGAGCTTTGGT	0.572																																					p.L205P		Atlas-SNP	.											.	PRSS3	79	.	0			c.T614C						PASS	.						130	111	117					9																	33798069		2203	4300	6503	SO:0001583	missense	5646	exon3			ACACTCTGAGCTT		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.614T>C	chr9.hg19:g.33798069T>C	ENSP00000354280:p.Leu205Pro	129.0	0.0	.		174.0	52.0	.	NM_007343	A8CED1|A8CED3|A9Z1Y4|E7ES07|F8W7P3|P15951|Q15665|Q5VXV0|Q6ISJ4|Q9UQV3	Missense_Mutation	SNP	ENST00000361005.5	hg19	CCDS47958.1	.	.	.	.	.	.	.	.	.	.	T	10.01	1.233504	0.22626	.	.	ENSG00000010438	ENST00000361005;ENST00000457896;ENST00000342836;ENST00000429677;ENST00000379405	D;D;D;D;D	0.88664	-2.41;-2.41;-2.41;-2.41;-2.41	3.61	-1.02	0.10135	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.210916	0.40908	D	0.000985	D	0.83248	0.5213	L	0.27053	0.805	0.58432	D	0.999996	P;P;P	0.52170	0.477;0.951;0.649	P;P;P	0.55785	0.589;0.784;0.485	T	0.76798	-0.2826	10	0.45353	T	0.12	.	2.3719	0.04332	0.3669:0.2296:0.0:0.4035	.	148;205;162	P35030-3;P35030;P35030-4	.;TRY3_HUMAN;.	P	205;160;162;141;148	ENSP00000354280:L205P;ENSP00000401249:L160P;ENSP00000340889:L162P;ENSP00000401828:L141P;ENSP00000368715:L148P	ENSP00000340889:L162P	L	+	2	0	PRSS3	33788069	0.949000	0.32298	0.976000	0.42696	0.018000	0.09664	1.089000	0.30890	-0.026000	0.13895	-0.753000	0.03488	CTG	.	.	.	none		0.572	PRSS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052121.1	NM_002771		C	33798069	T	C	33798069	3	2	184	1	0	0	0	0	1	0	0	0	12632	1580	55	3	668	3	PRSS3	9	33798069	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	30987717	33798069	107415362	54	10787											
SEMA4D	10507	hgsc.bcm.edu	37	chr9	92007357	92007357	+	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	ccgttcagccaagggattgcAtattctgtcctcagaggact	9	11	10	11	1	3	1	2	0	1	1	4	3	4	3	3	2	2	2	3	2	2	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr9:92007357A>T	ENST00000450295.1	-	8	1379	c.603T>A	c.(601-603)taT>taA	p.Y201*	SEMA4D_ENST00000420987.1_Nonsense_Mutation_p.Y201*|SEMA4D_ENST00000339861.4_Nonsense_Mutation_p.Y201*|SEMA4D_ENST00000455551.2_Nonsense_Mutation_p.Y201*|SEMA4D_ENST00000356444.2_Nonsense_Mutation_p.Y201*|SEMA4D_ENST00000422704.2_Nonsense_Mutation_p.Y201*|SEMA4D_ENST00000438547.2_Nonsense_Mutation_p.Y201*|SEMA4D_ENST00000343780.4_Nonsense_Mutation_p.Y201*			Q92854	SEM4D_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	201	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|immune response (GO:0006955)|leukocyte aggregation (GO:0070486)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ossification involved in bone maturation (GO:0043931)|positive regulation of cell migration (GO:0030335)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)|regulation of dendrite morphogenesis (GO:0048814)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(8)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34						AAGGGATTGCATATTCTGTCC	0.488																																					p.Y201X		Atlas-SNP	.											.	SEMA4D	81	.	0			c.T603A						PASS	.						125	112	117					9																	92007357		2203	4300	6503	SO:0001587	stop_gained	10507	exon10			GATTGCATATTCT	U60800	CCDS6685.1, CCDS47991.1	9q22-q31	2013-01-11			ENSG00000187764	ENSG00000187764		"Semaphorins", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10732	protein-coding gene	gene with protein product	"M-sema G"	601866	"chromosome 9 open reading frame 164"	SEMAJ, C9orf164		8876214, 8969198	Standard	NM_006378		Approved	CD100, coll-4, FLJ39737	uc004aqo.1	Q92854	OTTHUMG00000020185	ENST00000450295.1:c.603T>A	chr9.hg19:g.92007357A>T	ENSP00000416523:p.Tyr201*	138.0	0.0	.		139.0	40.0	.	NM_006378	B2RPM6|Q7Z5S4|Q8N8B0	Nonsense_Mutation	SNP	ENST00000450295.1	hg19	CCDS6685.1	.	.	.	.	.	.	.	.	.	.	G	38	6.945547	0.97956	.	.	ENSG00000187764	ENST00000339861;ENST00000420987;ENST00000455551;ENST00000343780;ENST00000450295;ENST00000438547;ENST00000356444;ENST00000422704	.	.	.	5.92	-9.64	0.00541	.	0.057514	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	23.1558	0.99980	0.8226:0.0:0.1774:0.0	.	.	.	.	X	201	.	ENSP00000344923:Y201X	Y	-	3	2	SEMA4D	91197177	0.023000	0.18921	0.008000	0.14137	0.015000	0.08874	-0.722000	0.04958	-2.623000	0.00438	-1.874000	0.00550	TAT	.	.	.	none		0.488	SEMA4D-018	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342411.1	NM_006378		T	92007357	A	T	92007357	4	4	184	1	0	0	0	0	0	1	0	0	14047	224	8	5	2591	5	SEMA4D	9	92007357	Nonsense_Mutation	SNP	A	TCGA-GL-7773-01A-11D-2136-08	58209288	92007357	49206074	55	10788											
NUP214	8021	hgsc.bcm.edu	37	chr9	134019822	134019822	+	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	gagcccccactgtgttctccTttggttcttcatctttgaag	5	16	8	12	0	4	1	1	1	3	0	5	2	4	1	3	1	1	2	3	1	1	5			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr9:134019822T>A	ENST00000359428.5	+	12	1594	c.1450T>A	c.(1450-1452)Ttt>Att	p.F484I	RP11-544A12.4_ENST00000589540.1_RNA|RP11-544A12.4_ENST00000590461.1_RNA|RP11-544A12.4_ENST00000586290.1_RNA|RP11-544A12.4_ENST00000587408.1_RNA|RP11-544A12.4_ENST00000587264.1_RNA|NUP214_ENST00000411637.2_Missense_Mutation_p.F484I|NUP214_ENST00000451030.1_Missense_Mutation_p.F484I|RP11-544A12.4_ENST00000415391.2_RNA|RP11-544A12.4_ENST00000588378.1_RNA|RP11-544A12.4_ENST00000589667.1_RNA			P35658	NU214_HUMAN	nucleoporin 214kDa	484	11 X 5 AA approximate repeats.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		TGTGTTCTCCTTTGGTTCTTC	0.582			T	"DEK, SET, ABL1"	"AML, T-ALL"																																p.F484I	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.T1450A						PASS	.						222	224	223					9																	134019822		2203	4300	6503	SO:0001583	missense	8021	exon12			TTCTCCTTTGGTT	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.1450T>A	chr9.hg19:g.134019822T>A	ENSP00000352400:p.Phe484Ile	413.0	0.0	.		479.0	161.0	.	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	hg19	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.429164	0.83776	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899	T;T;T	0.79653	-1.29;-1.29;-1.29	5.79	5.79	0.91817	.	0.000000	0.42053	D	0.000772	T	0.72867	0.3514	N	0.08118	0	0.45554	D	0.998503	D;D	0.56287	0.975;0.975	P;P	0.51516	0.591;0.672	T	0.77928	-0.2404	10	0.52906	T	0.07	-18.8096	13.8602	0.63554	0.0:0.0:0.0:1.0	.	484;484	P35658-4;P35658	.;NU214_HUMAN	I	484;484;484;484;77	ENSP00000352400:F484I;ENSP00000396576:F484I;ENSP00000405014:F484I	ENSP00000352400:F484I	F	+	1	0	NUP214	133009643	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	3.193000	0.50997	2.201000	0.70794	0.533000	0.62120	TTT	.	.	.	none		0.582	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		A	134019822	T	A	134019822	3	1	184	1	0	0	0	0	1	0	0	0	10769	1609	56	5	1496	5	NUP214	9	134019822	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	42012465	134019822	7193609	56	10789											
PFKFB3	5209	hgsc.bcm.edu	37	chr10	6258717	6258717	+	Missense_Mutation	SNP	C	C	A																															agaggagacacatgatccttCattttgccaaagaaaatgac																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr10:6258717C>A	ENST00000379775.4	+	5	745	c.415C>A	c.(415-417)Cat>Aat	p.H139N	PFKFB3_ENST00000379785.1_Missense_Mutation_p.H139N|PFKFB3_ENST00000379789.4_Missense_Mutation_p.H119N|PFKFB3_ENST00000360521.2_Missense_Mutation_p.H139N|PFKFB3_ENST00000540253.1_Missense_Mutation_p.H153N|PFKFB3_ENST00000317350.4_Missense_Mutation_p.H139N|PFKFB3_ENST00000536985.1_Missense_Mutation_p.H119N|PFKFB3_ENST00000379782.3_Missense_Mutation_p.H139N	NM_004566.3	NP_004557.1	Q16875	F263_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	139	6-phosphofructo-2-kinase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|liver(2)|lung(10)|ovary(3)|upper_aerodigestive_tract(1)	22						CATGATCCTTCATTTTGCCAA	0.463																																					p.H139N		Atlas-SNP	.											.	PFKFB3	82	.	0			c.C415A						PASS	.						215	210	211					10																	6258717		2203	4300	6503	SO:0001583	missense	5209	exon5			ATCCTTCATTTTG		CCDS7078.1, CCDS44353.1, CCDS60479.1	10p15.1	2008-05-14			ENSG00000170525	ENSG00000170525			8874	protein-coding gene	gene with protein product		605319				9146922, 10072580	Standard	NM_004566		Approved		uc001ije.3	Q16875	OTTHUMG00000017621	ENST00000379775.4:c.415C>A	chr10.hg19:g.6258717C>A	ENSP00000369100:p.His139Asn	254.0	0.0	.		206.0	49.0	.	NM_004566	B7Z955|O43622|O75902|Q5VX15|Q5VX18|Q5VX19	Missense_Mutation	SNP	ENST00000379775.4	hg19	CCDS7078.1	.	.	.	.	.	.	.	.	.	.	C	5.826	0.336691	0.11013	.	.	ENSG00000170525	ENST00000536985;ENST00000379789;ENST00000540253;ENST00000317350;ENST00000379785;ENST00000379782;ENST00000360521;ENST00000379775;ENST00000358499	.	.	.	5.71	1.54	0.23209	6-phosphofructo-2-kinase (1);	0.496023	0.24935	N	0.034432	T	0.06554	0.0168	N	0.00408	-1.53	0.20403	N	0.999904	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	0.40905	-0.9538	9	0.05620	T	0.96	-18.1641	9.3897	0.38365	0.3959:0.419:0.1851:0.0	.	153;139;139;119	B7Z955;Q16875-2;Q16875;Q5VX15	.;.;F263_HUMAN;.	N	119;119;153;139;139;139;139;139;139	.	ENSP00000369105:H139N	H	+	1	0	PFKFB3	6298723	0.021000	0.18746	0.983000	0.44433	0.868000	0.49771	0.284000	0.18864	0.716000	0.32124	0.591000	0.81541	CAT	.	.	.	none		0.463	PFKFB3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046647.1			A	6258717	C	A	6258717	3	1	184	1	0	0	0	0	1	0	0	0	11769	826	29	4	453	4	PFKFB3	10	6258717	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08		6258717	129276030	57	10790	100	2									
PFKFB3	5209	hgsc.bcm.edu	37	chr10	6258719	6258719	+	Missense_Mutation	SNP	T	T	A																															aggagacacatgatccttcaTtttgccaaagaaaatgactt																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr10:6258719T>A	ENST00000379775.4	+	5	747	c.417T>A	c.(415-417)caT>caA	p.H139Q	PFKFB3_ENST00000379785.1_Missense_Mutation_p.H139Q|PFKFB3_ENST00000379789.4_Missense_Mutation_p.H119Q|PFKFB3_ENST00000360521.2_Missense_Mutation_p.H139Q|PFKFB3_ENST00000540253.1_Missense_Mutation_p.H153Q|PFKFB3_ENST00000317350.4_Missense_Mutation_p.H139Q|PFKFB3_ENST00000536985.1_Missense_Mutation_p.H119Q|PFKFB3_ENST00000379782.3_Missense_Mutation_p.H139Q	NM_004566.3	NP_004557.1	Q16875	F263_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	139	6-phosphofructo-2-kinase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|liver(2)|lung(10)|ovary(3)|upper_aerodigestive_tract(1)	22						TGATCCTTCATTTTGCCAAAG	0.468																																					p.H139Q		Atlas-SNP	.											.	PFKFB3	82	.	0			c.T417A						PASS	.						212	207	209					10																	6258719		2203	4300	6503	SO:0001583	missense	5209	exon5			CCTTCATTTTGCC		CCDS7078.1, CCDS44353.1, CCDS60479.1	10p15.1	2008-05-14			ENSG00000170525	ENSG00000170525			8874	protein-coding gene	gene with protein product		605319				9146922, 10072580	Standard	NM_004566		Approved		uc001ije.3	Q16875	OTTHUMG00000017621	ENST00000379775.4:c.417T>A	chr10.hg19:g.6258719T>A	ENSP00000369100:p.His139Gln	244.0	0.0	.		201.0	47.0	.	NM_004566	B7Z955|O43622|O75902|Q5VX15|Q5VX18|Q5VX19	Missense_Mutation	SNP	ENST00000379775.4	hg19	CCDS7078.1	.	.	.	.	.	.	.	.	.	.	T	7.097	0.573259	0.13623	.	.	ENSG00000170525	ENST00000536985;ENST00000379789;ENST00000540253;ENST00000317350;ENST00000379785;ENST00000379782;ENST00000360521;ENST00000379775;ENST00000358499	.	.	.	5.71	0.992	0.19819	6-phosphofructo-2-kinase (1);	0.496023	0.24935	N	0.034432	T	0.13586	0.0329	N	0.01168	-0.975	0.30946	N	0.72524	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.003;0.0;0.0;0.0	T	0.24512	-1.0158	9	0.13470	T	0.59	-18.1641	10.2567	0.43401	0.0:0.3897:0.0:0.6103	.	153;139;139;119	B7Z955;Q16875-2;Q16875;Q5VX15	.;.;F263_HUMAN;.	Q	119;119;153;139;139;139;139;139;139	.	ENSP00000369105:H139Q	H	+	3	2	PFKFB3	6298725	0.869000	0.29996	0.999000	0.59377	0.820000	0.46376	-0.073000	0.11468	0.448000	0.26722	-0.376000	0.06991	CAT	.	.	.	none		0.468	PFKFB3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046647.1			A	6258719	T	A	6258719	3	1	184	1	0	0	0	0	1	0	0	0	11769	1490	52	5	455	5	PFKFB3	10	6258719	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	2	6258719	129276028	58	10791	100	2									
PRPF18	8559	hgsc.bcm.edu	37	chr10	13653627	13653627	+	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	ttcttcaggcgcttggagagTccttagggaaaggcgatgat	9	11	14	7	2	2	2	1	1	1	1	3	5	3	3	1	4	0	1	1	4	2	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr10:13653627T>A	ENST00000378572.3	+	6	683	c.523T>A	c.(523-525)Tcc>Acc	p.S175T		NM_003675.3	NP_003666.1	Q99633	PRP18_HUMAN	pre-mRNA processing factor 18	175					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						GCTTGGAGAGTCCTTAGGGAA	0.423																																					p.S175T		Atlas-SNP	.											.	PRPF18	32	.	0			c.T523A						PASS	.						128	119	122					10																	13653627		2203	4300	6503	SO:0001583	missense	8559	exon6			GGAGAGTCCTTAG	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.523T>A	chr10.hg19:g.13653627T>A	ENSP00000367835:p.Ser175Thr	119.0	0.0	.		105.0	39.0	.	NM_003675	Q5T9P9|Q9BUI9	Missense_Mutation	SNP	ENST00000378572.3	hg19	CCDS7100.1	.	.	.	.	.	.	.	.	.	.	T	12.27	1.886622	0.33348	.	.	ENSG00000165630	ENST00000378572;ENST00000417658;ENST00000320054;ENST00000378544	.	.	.	5.59	5.59	0.84812	Prp18 (2);	0.105608	0.64402	D	0.000003	T	0.41419	0.1158	N	0.16478	0.41	0.45295	D	0.998291	B	0.06786	0.001	B	0.04013	0.001	T	0.28681	-1.0036	9	0.15499	T	0.54	-14.6828	15.7693	0.78152	0.0:0.0:0.0:1.0	.	175	Q99633	PRP18_HUMAN	T	175;169;160;169	.	ENSP00000367824:S160T	S	+	1	0	PRPF18	13693633	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	4.281000	0.58965	2.125000	0.65367	0.459000	0.35465	TCC	.	.	.	none		0.423	PRPF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046879.1			A	13653627	T	A	13653627	3	1	184	1	0	0	0	0	1	0	0	0	12573	1667	58	5	545	5	PRPF18	10	13653627	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	7394908	13653627	121881120	59	10792											
CUBN	8029	hgsc.bcm.edu	37	chr10	16941136	16941136	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaaaattctgaggccagtgAggggatctgattgtaccatt	11	11	13	6	0	2	3	0	3	2	0	2	5	2	5	2	4	1	1	2	4	3	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr10:16941136A>G	ENST00000377833.4	-	54	8522	c.8457T>C	c.(8455-8457)ccT>ccC	p.P2819P		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2819	CUB 21. {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)	GAGGCCAGTGAGGGGATCTGA	0.398																																					p.P2819P		Atlas-SNP	.											.	CUBN	515	.	0			c.T8457C						PASS	.						129	121	124					10																	16941136		2203	4300	6503	SO:0001819	synonymous_variant	8029	exon54			CCAGTGAGGGGAT	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.8457T>C	chr10.hg19:g.16941136A>G		111.0	0.0	.		103.0	44.0	.	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	hg19	CCDS7113.1																																																																																			.	.	.	none		0.398	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		G	16941136	A	G	16941136	2	3	184	1	0	0	0	0	0	0	0	1	4053	291	11	3		3	CUBN	10	16941136	Silent	SNP	A	TCGA-GL-7773-01A-11D-2136-08	3287509	16941136	118593611	60	10793											
NRAP	4892	hgsc.bcm.edu	37	chr10	115365937	115365939	+	Splice_Site	TNP	GTC	GTC	TAA																															taagtaacaaaagggcttacGtcactcaggttggctgcatt																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G|T|C	G|T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr10:115365937_115365939GTC>TAA	ENST00000359988.3	-	33	4049_4051	c.3805_3807GAC>TTA	c.(3805-3807)GAC>TTA	p.D1269L	NRAP_ENST00000369358.4_Splice_Site_p.D1277L|NRAP_ENST00000360478.3_Splice_Site_p.D1234L|NRAP_ENST00000369360.3_Splice_Site_p.D1242L	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)		AAGGGCTTACGTCACTCAGGTTG	0.478																																					p.D1269E|p.D1269V|p.D1269Y		Atlas-SNP	.											.	NRAP	208	.	0			c.C3807A|c.A3806T|c.G3805T						PASS	.																																			SO:0001630	splice_region_variant	4892	exon33			GCTTACGTCACTC|CTTACGTCACTCA|TTACGTCACTCAG		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.3807+1GAC>TTA	chr10.hg19:g.115365937GTC>TAA		63.0	0.0	.		82.0|84.0|84.0	24.0|24.0|25.0	.	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	hg19	CCDS7579.1																																																																																			.	.	.	none		0.478	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	Missense_Mutation	TAA	115365939	GTC	TAA	115365937	5	4	184	1	0	0	0	0	0	0	1	0	10645	1159	40	4	1425	4	NRAP	10	115365937	Splice_Site	TNP	GTC	TCGA-GL-7773-01A-11D-2136-08	98424801	115365937	20168810	61	10794											
MPEG1	219972	hgsc.bcm.edu	37	chr11	58978386	58978386	+	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	gctgcagcccctcctgacagAccaccaccatccccatggat	9	6	7	19	0	0	2	0	1	0	1	2	3	2	3	8	1	2	2	8	1	0	0			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr11:58978386A>T	ENST00000361050.3	-	1	2038	c.1953T>A	c.(1951-1953)ggT>ggA	p.G651G		NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	651						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)				CTCCTGACAGACCACCACCAT	0.577																																					p.G651G		Atlas-SNP	.											.	MPEG1	72	.	0			c.T1953A						PASS	.						100	108	105					11																	58978386		2014	4161	6175	SO:0001819	synonymous_variant	219972	exon1			TGACAGACCACCA	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.1953T>A	chr11.hg19:g.58978386A>T		174.0	0.0	.		180.0	58.0	.	NM_001039396	Q2M1T6|Q8TEF8	Silent	SNP	ENST00000361050.3	hg19	CCDS41650.1																																																																																			.	.	.	none		0.577	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396		T	58978386	A	T	58978386	2	4	184	1	0	0	0	0	0	0	0	1	9730	262	10	5		5	MPEG1	11	58978386	Silent	SNP	A	TCGA-GL-7773-01A-11D-2136-08		58978386	76028130	62	10795											
FLRT1	28992	hgsc.bcm.edu	37	chr11	63885635	63885635	+	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	ccgtaccgcgccaaagaagaGtacgtggtccacactatctt	11	8	9	13	4	1	2	0	0	1	2	2	2	2	2	4	1	2	2	4	1	5	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr11:63885635G>A	ENST00000255681.6	-	3	584				RP11-21A7A.3_ENST00000543817.1_RNA|FLRT1_ENST00000246841.3_Silent_p.E632E	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						CCAAAGAAGAGTACGTGGTCC	0.607																																					p.E632E		Atlas-SNP	.											.	FLRT1	46	.	0			c.G1896A						PASS	.						79	69	72					11																	63885635		2201	4297	6498	SO:0001627	intron_variant	23769	exon2			AGAAGAGTACGTG	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+33075C>T	chr11.hg19:g.63885635G>A		126.0	0.0	.		139.0	58.0	.	NM_013280	Q9UH96	Silent	SNP	ENST00000255681.6	hg19	CCDS8056.1																																																																																			.	.	.	none		0.607	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067		A	63885635	G	A	63885635	1	1	184	0	1	0	0	0	0	0	0	0	5945	1020	36	2		2	FLRT1	11	63885635	Intron	SNP	G	TCGA-GL-7773-01A-11D-2136-08	4907249	63885635	71120881	63	10796											
PC	5091	hgsc.bcm.edu	37	chr11	66617172	66617172	+	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	gtggcagtgaagtccttgaaGtgggcaaacacatcggggta	11	8	15	7	1	0	2	0	2	0	0	2	2	1	2	1	4	1	3	1	4	4	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr11:66617172G>C	ENST00000393958.2	-	20	3150	c.3057C>G	c.(3055-3057)caC>caG	p.H1019Q	PC_ENST00000393955.2_Missense_Mutation_p.H1019Q|PC_ENST00000529047.1_Missense_Mutation_p.H139Q|PC_ENST00000393960.1_Missense_Mutation_p.H1019Q|PC_ENST00000528224.1_5'UTR	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	1019					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)	AGTCCTTGAAGTGGGCAAACA	0.577																																					p.H1019Q		Atlas-SNP	.											.	PC	116	.	0			c.C3057G						PASS	.						107	86	93					11																	66617172		2200	4295	6495	SO:0001583	missense	5091	exon20			CTTGAAGTGGGCA	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.3057C>G	chr11.hg19:g.66617172G>C	ENSP00000377530:p.His1019Gln	81.0	0.0	.		97.0	26.0	.	NM_000920	B4DN00|Q16705	Missense_Mutation	SNP	ENST00000393958.2	hg19	CCDS8152.1	.	.	.	.	.	.	.	.	.	.	G	10.71	1.427583	0.25726	.	.	ENSG00000173599	ENST00000529047;ENST00000393955;ENST00000393958;ENST00000393960	D;D;D;D	0.95377	-1.52;-3.69;-3.69;-3.69	4.89	-4.28	0.03732	Carboxylase, conserved domain (1);	0.231260	0.33515	N	0.004840	T	0.79505	0.4457	N	0.00859	-1.14	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.59568	-0.7430	10	0.34782	T	0.22	-8.0574	7.3499	0.26684	0.0864:0.6092:0.163:0.1415	.	1019	P11498	PYC_HUMAN	Q	139;1019;1019;1019	ENSP00000435905:H139Q;ENSP00000377527:H1019Q;ENSP00000377530:H1019Q;ENSP00000377532:H1019Q	ENSP00000377527:H1019Q	H	-	3	2	PC	66373748	0.988000	0.35896	0.454000	0.27019	0.803000	0.45373	0.243000	0.18106	-0.607000	0.05738	0.462000	0.41574	CAC	.	.	.	none		0.577	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716		C	66617172	G	C	66617172	3	2	184	1	0	0	0	0	1	0	0	0	11504	1020	36	4	491	4	PC	11	66617172	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	2731537	66617172	68389344	64	10797											
FUT4	2526	hgsc.bcm.edu	37	chr11	94278647	94278649	+	In_Frame_Del	DEL	TTT	TTT	-																															accgtgccaactacgagcgcTttgtgccccgcggcgccttc																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	TTT	TTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr11:94278647_94278649delTTT	ENST00000358752.2	+	1	1631_1633	c.1348_1350delTTT	c.(1348-1350)tttdel	p.F450del	RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA	NM_002033.3	NP_002024.1	P22083	FUT4_HUMAN	fucosyltransferase 4 (alpha (1,3) fucosyltransferase, myeloid-specific)	450					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)				CTACGAGCGCTTTGTGCCCCGCG	0.655																																					p.449_450del		Atlas-INDEL	.											.	FUT4	17	.	0			c.1347_1349del						PASS	.																																			SO:0001651	inframe_deletion	2526	exon1			.		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.1348_1350delTTT	chr11.hg19:g.94278647_94278649delTTT	ENSP00000351602:p.Phe450del	58.0	0.0	0		73.0	25.0	0.342466	NM_002033	B2RMS0	In_Frame_Del	DEL	ENST00000358752.2	hg19	CCDS8301.1																																																																																			.	.	.	none		0.655	FUT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396327.2	NM_002033		-	94278649	TTT	-	94278647	7	5	184	1	0	1	0	1	0	0	0	0	6113	1609	56	0	1350	0	FUT4	11	94278647	In_Frame_Del	DEL	TTT	TCGA-GL-7773-01A-11D-2136-08	27661475	94278647	40727869	65	10798											
DRD2	1813	hgsc.bcm.edu	37	chr11	113288847	113288847	+	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	tgaatcctgctgaatttccaCtcacctaccacctggggaca	10	10	7	14	0	1	2	1	2	0	0	3	3	3	3	5	2	2	1	5	2	3	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr11:113288847C>T	ENST00000362072.3	-	3	641	c.297G>A	c.(295-297)gaG>gaA	p.E99E	DRD2_ENST00000355319.2_Silent_p.E99E|DRD2_ENST00000346454.3_Silent_p.E99E|DRD2_ENST00000535984.1_5'UTR|DRD2_ENST00000542968.1_Silent_p.E99E|DRD2_ENST00000538967.1_Silent_p.E99E|DRD2_ENST00000544518.1_Silent_p.E98E	NM_000795.3	NP_000786.1	P14416	DRD2_HUMAN	dopamine receptor D2	99					activation of protein kinase activity (GO:0032147)|adenohypophysis development (GO:0021984)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adult walking behavior (GO:0007628)|arachidonic acid secretion (GO:0050482)|associative learning (GO:0008306)|auditory behavior (GO:0031223)|axonogenesis (GO:0007409)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|branching morphogenesis of a nerve (GO:0048755)|cellular calcium ion homeostasis (GO:0006874)|cerebral cortex GABAergic interneuron migration (GO:0021853)|circadian regulation of gene expression (GO:0032922)|dopamine metabolic process (GO:0042417)|feeding behavior (GO:0007631)|G-protein coupled receptor internalization (GO:0002031)|grooming behavior (GO:0007625)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|long-term memory (GO:0007616)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of circadian sleep/wake cycle, sleep (GO:0042321)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of insulin secretion (GO:0046676)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein secretion (GO:0050709)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|neuron-neuron synaptic transmission (GO:0007270)|orbitofrontal cortex development (GO:0021769)|peristalsis (GO:0030432)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|pigmentation (GO:0043473)|positive regulation of cytokinesis (GO:0032467)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of dopamine uptake involved in synaptic transmission (GO:0051586)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of receptor internalization (GO:0002092)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of urine volume (GO:0035810)|prepulse inhibition (GO:0060134)|protein localization (GO:0008104)|regulation of cAMP metabolic process (GO:0030814)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of heart rate (GO:0002027)|regulation of locomotion involved in locomotory behavior (GO:0090325)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of potassium ion transport (GO:0043266)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, GABAergic (GO:0032228)|release of sequestered calcium ion into cytosol (GO:0051209)|response to amphetamine (GO:0001975)|response to axon injury (GO:0048678)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to histamine (GO:0034776)|response to hypoxia (GO:0001666)|response to inactivity (GO:0014854)|response to iron ion (GO:0010039)|response to light stimulus (GO:0009416)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to toxic substance (GO:0009636)|sensory perception of smell (GO:0007608)|striatum development (GO:0021756)|synapse assembly (GO:0007416)|synaptic transmission, dopaminergic (GO:0001963)|temperature homeostasis (GO:0001659)|visual learning (GO:0008542)|Wnt signaling pathway (GO:0016055)	acrosomal vesicle (GO:0001669)|axon (GO:0030424)|axon terminus (GO:0043679)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|sperm flagellum (GO:0036126)|synaptic vesicle membrane (GO:0030672)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity, coupled via Gi/Go (GO:0001591)|drug binding (GO:0008144)|identical protein binding (GO:0042802)|potassium channel regulator activity (GO:0015459)			endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(18)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	39		all_cancers(61;3.91e-16)|all_epithelial(67;2.95e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000977)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0494)		BRCA - Breast invasive adenocarcinoma(274;5.77e-06)|Epithelial(105;6.66e-05)|all cancers(92;0.000307)|OV - Ovarian serous cystadenocarcinoma(223;0.216)	Acepromazine(DB01614)|Acetophenazine(DB01063)|Alizapride(DB01425)|Amantadine(DB00915)|Amisulpride(DB06288)|Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Desipramine(DB01151)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Droperidol(DB00450)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Memantine(DB01043)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Metoclopramide(DB01233)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sertindole(DB06144)|Sulpiride(DB00391)|Tetrabenazine(DB04844)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	TGAATTTCCACTCACCTACCA	0.532																																					p.E99E		Atlas-SNP	.											.	DRD2	98	.	0			c.G297A						PASS	.						171	121	138					11																	113288847		2201	4296	6497	SO:0001819	synonymous_variant	1813	exon3			TTTCCACTCACCT	M29066	CCDS8361.1, CCDS8362.1	11q22-q23	2012-08-08						"GPCR / Class A : Dopamine receptors"	3023	protein-coding gene	gene with protein product		126450					Standard	NM_000795		Approved		uc001poa.4	P14416		ENST00000362072.3:c.297G>A	chr11.hg19:g.113288847C>T		65.0	0.0	.		65.0	18.0	.	NM_016574	Q9NZR3|Q9UPA9	Silent	SNP	ENST00000362072.3	hg19	CCDS8361.1																																																																																			.	.	.	none		0.532	DRD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395834.1	NM_000795		T	113288847	C	T	113288847	2	4	184	1	0	0	0	0	0	0	0	1	4759	564	20	2		2	DRD2	11	113288847	Silent	SNP	C	TCGA-GL-7773-01A-11D-2136-08	19010200	113288847	21717669	66	10799											
IGSF9B	22997	hgsc.bcm.edu	37	chr11	133816079	133816079	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccgtcactgggtggatcaCgtcgcatcgcaggaccacgc	7	7	12	15	5	2	0	2	0	0	0	5	2	3	2	2	3	0	2	2	3	0	0			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr11:133816079C>T	ENST00000321016.8	-	2	369	c.139G>A	c.(139-141)Gtg>Atg	p.V47M	IGSF9B_ENST00000533871.2_Missense_Mutation_p.V47M			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	47	Ig-like 1.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		GGGTGGATCACGTCGCATCGC	0.627																																					p.V47M		Atlas-SNP	.											.	IGSF9B	290	.	0			c.G139A						PASS	.						50	57	54					11																	133816079		2145	4233	6378	SO:0001583	missense	22997	exon2			GGATCACGTCGCA	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.139G>A	chr11.hg19:g.133816079C>T	ENSP00000317980:p.Val47Met	38.0	0.0	.		46.0	12.0	.	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	hg19		.	.	.	.	.	.	.	.	.	.	C	32	5.124674	0.94429	.	.	ENSG00000080854	ENST00000321016;ENST00000527648;ENST00000533160;ENST00000526663	T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23	5.41	5.41	0.78517	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.56097	D	0.000025	T	0.82144	0.4973	M	0.75884	2.315	0.58432	D	0.999999	D	0.89917	1.0	D	0.74023	0.982	D	0.84066	0.0377	10	0.87932	D	0	.	18.8177	0.92084	0.0:1.0:0.0:0.0	.	47	Q9UPX0	TUTLB_HUMAN	M	47;47;37;94	ENSP00000317980:V47M;ENSP00000436576:V47M;ENSP00000434026:V37M;ENSP00000435989:V94M	ENSP00000317980:V47M	V	-	1	0	IGSF9B	133321289	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	7.684000	0.84104	2.544000	0.85801	0.655000	0.94253	GTG	.	.	.	none		0.627	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		T	133816079	C	T	133816079	3	4	184	1	0	0	0	0	1	0	0	0	7613	536	19	1	3982	1	IGSF9B	11	133816079	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	20527232	133816079	1190437	67	10800											
CLEC1B	51266	hgsc.bcm.edu	37	chr12	10145838	10145838	+	Frame_Shift_Del	DEL	A	A	-																															gggtgcattttcccattatgAaaataagcacaattcatatt																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr12:10145838delA	ENST00000298527.6	-	6	773	c.594delT	c.(592-594)tttfs	p.F198fs	CLEC1B_ENST00000348658.4_Frame_Shift_Del_p.F165fs|CLEC1B_ENST00000428126.2_Frame_Shift_Del_p.F165fs	NM_016509.3	NP_057593.3	Q9P126	CLC1B_HUMAN	C-type lectin domain family 1, member B	198	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|platelet formation (GO:0030220)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(12)|stomach(1)|urinary_tract(1)	19						TCCCATTATGAAAATAAGCAC	0.373																																					p.H199fs		Atlas-INDEL	.											.	CLEC1B	39	.	0			c.595delC						PASS	.						136	123	127					12																	10145838		1852	4085	5937	SO:0001589	frameshift_variant	51266	exon6			.	AF124841	CCDS41751.1, CCDS41752.1	12p13.31	2006-04-12				ENSG00000165682		"C-type lectin domain containing"	24356	protein-coding gene	gene with protein product		606783				10671229, 11745369	Standard	NM_016509		Approved	CLEC2	uc001qwu.3	Q9P126		ENST00000298527.6:c.594delT	chr12.hg19:g.10145838delA	ENSP00000298527:p.Phe198fs	127.0	0.0	0		191.0	72.0	0.376963	NM_016509	Q6UWX7|Q8NHR6	Frame_Shift_Del	DEL	ENST00000298527.6	hg19	CCDS41752.1																																																																																			.	.	.	none		0.373	CLEC1B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399922.1	NM_016509		-	10145838	A	-	10145838	7	5	184	1	0	1	0	1	0	0	0	0	3508	243	9	0	99	0	CLEC1B	12	10145838	Frame_Shift_Del	DEL	A	TCGA-GL-7773-01A-11D-2136-08		10145838	123706057	68	10801											
KLRK1	22914	hgsc.bcm.edu	37	chr12	10541382	10541382	+	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	aaacataccccagctgtgtcGagacctccgaccacgaatcc	12	6	7	16	3	0	1	0	0	0	1	3	4	2	1	6	0	3	1	6	0	3	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr12:10541382G>A	ENST00000240618.6	-	2	168	c.28C>T	c.(28-30)Cga>Tga	p.R10*	KLRK1_ENST00000540818.1_Nonsense_Mutation_p.R10*|KLRC4-KLRK1_ENST00000539300.1_3'UTR|RP11-277P12.20_ENST00000500682.1_RNA	NM_001199805.1|NM_007360.3	NP_001186734.1|NP_031386.2	P26718	NKG2D_HUMAN	killer cell lectin-like receptor subfamily K, member 1	10					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						CAGCTGTGTCGAGACCTCCGA	0.388																																					p.R10X		Atlas-SNP	.											.	.	.	.	0			c.C28T						PASS	.						101	92	95					12																	10541382		2203	4300	6503	SO:0001587	stop_gained	0	exon7			TGTGTCGAGACCT	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.28C>T	chr12.hg19:g.10541382G>A	ENSP00000240618:p.Arg10*	98.0	0.0	.		111.0	47.0	.	NM_001199805	A8K7K5|A8K7P4|Q9NR41	Nonsense_Mutation	SNP	ENST00000240618.6	hg19	CCDS8623.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.601701	0.87055	.	.	ENSG00000213809	ENST00000240618;ENST00000540818	.	.	.	3.92	2.04	0.26737	.	1.508560	0.03947	N	0.287889	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	.	4.7229	0.12927	0.1127:0.0:0.657:0.2303	.	.	.	.	X	10	.	ENSP00000240618:R10X	R	-	1	2	KLRK1	10432649	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	-0.084000	0.11268	0.589000	0.29677	0.637000	0.83480	CGA	.	.	.	none		0.388	KLRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400269.1	NM_007360		A	10541382	G	A	10541382	4	1	184	1	0	0	0	0	0	1	0	0	8430	1066	37	1	650	1	KLRK1	12	10541382	Nonsense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	395544	10541382	123310513	69	10802											
LRP6	4040	hgsc.bcm.edu	37	chr12	12318144	12318144	+	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	gccagtcagtccagtaaacaTagtcacccaacaaagtaaat	17	7	6	11	0	2	0	2	0	0	0	3	0	3	0	3	0	2	2	3	0	7	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr12:12318144T>A	ENST00000261349.4	-	8	1707	c.1631A>T	c.(1630-1632)tAt>tTt	p.Y544F	LRP6_ENST00000543091.1_Missense_Mutation_p.Y544F	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	544	Beta-propeller 2.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				CCAGTAAACATAGTCACCCAA	0.433																																					p.Y544F		Atlas-SNP	.											.	LRP6	170	.	0			c.A1631T						PASS	.						149	150	150					12																	12318144		2203	4300	6503	SO:0001583	missense	4040	exon8			TAAACATAGTCAC	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.1631A>T	chr12.hg19:g.12318144T>A	ENSP00000261349:p.Tyr544Phe	195.0	0.0	.		215.0	83.0	.	NM_002336	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	hg19	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	T	9.879	1.200963	0.22121	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.91295	-2.82;-2.82	4.98	3.81	0.43845	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.56097	D	0.000032	T	0.81767	0.4892	N	0.21583	0.68	0.51767	D	0.999935	B;B	0.06786	0.001;0.001	B;B	0.10450	0.001;0.005	T	0.71820	-0.4477	10	0.11794	T	0.64	.	11.3882	0.49798	0.1355:0.0:0.0:0.8645	.	544;544	F5H7J9;O75581	.;LRP6_HUMAN	F	544	ENSP00000261349:Y544F;ENSP00000442472:Y544F	ENSP00000261349:Y544F	Y	-	2	0	LRP6	12209411	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	1.571000	0.36450	0.834000	0.34852	0.377000	0.23210	TAT	.	.	.	none		0.433	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			A	12318144	T	A	12318144	3	1	184	1	0	0	0	0	1	0	0	0	8969	1406	49	5	3274	5	LRP6	12	12318144	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	1776762	12318144	121533751	70	10803											
FAR2	55711	hgsc.bcm.edu	37	chr12	29469910	29469910	+	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	cgggcccctgccattatctaTgactgctatctgcggctcac	6	11	9	15	2	3	1	1	1	2	0	3	1	3	1	3	2	3	2	3	2	3	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr12:29469910T>A	ENST00000536681.3	+	9	1338	c.1092T>A	c.(1090-1092)taT>taA	p.Y364*	FAR2_ENST00000547116.1_Nonsense_Mutation_p.Y267*|FAR2_ENST00000182377.4_Nonsense_Mutation_p.Y364*|RP11-996F15.2_ENST00000553105.1_RNA	NM_001271783.1|NM_001271784.1	NP_001258712.1|NP_001258713.1	Q96K12	FACR2_HUMAN	fatty acyl CoA reductase 2	364					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	fatty-acyl-CoA reductase (alcohol-forming) activity (GO:0080019)|long-chain-fatty-acyl-CoA reductase activity (GO:0050062)			central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(15)|prostate(1)|stomach(1)	29						CCATTATCTATGACTGCTATC	0.502																																					p.Y364X		Atlas-SNP	.											.	FAR2	60	.	0			c.T1092A						PASS	.						133	136	135					12																	29469910		2203	4300	6503	SO:0001587	stop_gained	55711	exon9			TATCTATGACTGC	AL136843	CCDS8717.1, CCDS61084.1	12p11.23	2013-07-30	2008-06-06	2008-06-06	ENSG00000064763	ENSG00000064763	1.2.1.-	"Short chain dehydrogenase/reductase superfamily / Atypical members"	25531	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 10E, member 2"		"male sterility domain containing 1"	MLSTD1		15220348, 15220349, 19027726	Standard	NM_001271783		Approved	FLJ10462, SDR10E2	uc001ris.5	Q96K12	OTTHUMG00000169320	ENST00000536681.3:c.1092T>A	chr12.hg19:g.29469910T>A	ENSP00000443291:p.Tyr364*	325.0	0.0	.		358.0	142.0	.	NM_018099	F8VV73|Q9H0D5|Q9NVW8	Nonsense_Mutation	SNP	ENST00000536681.3	hg19	CCDS8717.1	.	.	.	.	.	.	.	.	.	.	T	38	7.075542	0.98048	.	.	ENSG00000064763	ENST00000536681;ENST00000182377;ENST00000547116	.	.	.	4.44	-3.57	0.04612	.	0.075218	0.56097	D	0.000033	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	-5.8079	11.3024	0.49314	0.0:0.5138:0.0:0.4862	.	.	.	.	X	364;364;267	.	ENSP00000182377:Y364X	Y	+	3	2	FAR2	29361177	0.039000	0.19947	0.980000	0.43619	0.940000	0.58332	-0.830000	0.04410	-0.596000	0.05821	0.383000	0.25322	TAT	.	.	.	none		0.502	FAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403479.2	NM_018099		A	29469910	T	A	29469910	4	1	184	1	0	0	0	0	0	1	0	0	5682	1471	51	5	1122	5	FAR2	12	29469910	Nonsense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	17151766	29469910	104381985	71	10804											
LRRK2	120892	hgsc.bcm.edu	37	chr12	40758851	40758851	+	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	gtcatgatgacagcacagctAggcaagtttctttcctttag	10	13	9	9	0	2	2	1	2	1	0	3	2	3	2	1	1	2	4	1	1	3	5			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr12:40758851A>G	ENST00000298910.7	+	49	7447	c.7389A>G	c.(7387-7389)ctA>ctG	p.L2463L		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	2463					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)				CAGCACAGCTAGGCAAGTTTC	0.343																																					p.L2463L		Atlas-SNP	.											.	LRRK2	763	.	0			c.A7389G						PASS	.						66	63	64					12																	40758851		2203	4298	6501	SO:0001630	splice_region_variant	120892	exon49			ACAGCTAGGCAAG	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.7390+1A>G	chr12.hg19:g.40758851A>G		73.0	0.0	.		96.0	34.0	.	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Silent	SNP	ENST00000298910.7	hg19	CCDS31774.1																																																																																			.	.	.	none		0.343	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513	Silent	G	40758851	A	G	40758851	5	3	184	1	0	0	0	0	0	0	1	0	9040	434	15	3	7583	3	LRRK2	12	40758851	Splice_Site	SNP	A	TCGA-GL-7773-01A-11D-2136-08	11288941	40758851	93093044	72	10805											
ANO6	196527	hgsc.bcm.edu	37	chr12	45803213	45803213	+	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	taaccccacgatgggaacagGactaccatctgcagcctatg	12	7	9	13	1	1	0	0	0	1	0	1	3	1	2	4	2	5	1	4	2	4	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr12:45803213G>T	ENST00000320560.8	+	16	2156	c.1954G>T	c.(1954-1956)Gac>Tac	p.D652Y	ANO6_ENST00000441606.2_Missense_Mutation_p.D634Y|ANO6_ENST00000423947.3_Missense_Mutation_p.D673Y|ANO6_ENST00000426898.2_3'UTR|ANO6_ENST00000425752.2_Missense_Mutation_p.D652Y|ANO6_ENST00000435642.1_Missense_Mutation_p.D652Y	NM_001025356.2	NP_001020527.2	Q4KMQ2	ANO6_HUMAN	anoctamin 6	652					activation of blood coagulation via clotting cascade (GO:0002543)|blood coagulation (GO:0007596)|bone mineralization involved in bone maturation (GO:0035630)|calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|phosphatidylserine exposure on blood platelet (GO:0097045)|phospholipid scrambling (GO:0017121)|positive regulation of endothelial cell apoptotic process (GO:2000353)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)|voltage-gated chloride channel activity (GO:0005247)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						ATGGGAACAGGACTACCATCT	0.353																																					p.D673Y		Atlas-SNP	.											.	ANO6	163	.	0			c.G2017T						PASS	.						124	124	124					12																	45803213		2203	4300	6503	SO:0001583	missense	196527	exon17			GAACAGGACTACC	AL832340	CCDS31782.1, CCDS44865.1, CCDS44866.1, CCDS55819.1	12q12-q13.11	2014-09-17	2008-08-28	2008-08-28				"Ion channels / Chloride channels : Calcium activated : Anoctamins"	25240	protein-coding gene	gene with protein product		608663	"transmembrane protein 16F"	TMEM16F		15067359, 24692353	Standard	NM_001025356		Approved	DKFZp313M0720	uc010slf.2	Q4KMQ2	OTTHUMG00000169564	ENST00000320560.8:c.1954G>T	chr12.hg19:g.45803213G>T	ENSP00000320087:p.Asp652Tyr	161.0	0.0	.		168.0	58.0	.	NM_001204803	A6NNM6|B9EGG0|E7ENK4|E9PB30|E9PCT2|Q8N3Q2	Missense_Mutation	SNP	ENST00000320560.8	hg19	CCDS31782.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.754633	0.89843	.	.	ENSG00000177119	ENST00000425752;ENST00000423947;ENST00000435642;ENST00000320560;ENST00000441606	T;T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17;-0.17	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	D	0.83991	0.5374	M	0.91872	3.25	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.97110	1.0;0.999;1.0;0.995	D	0.87659	0.2533	10	0.87932	D	0	.	19.0047	0.92846	0.0:0.0:1.0:0.0	.	634;673;652;652	E9PB30;B9EGG0;E9PCT2;Q4KMQ2	.;.;.;ANO6_HUMAN	Y	652;673;652;652;634	ENSP00000391417:D652Y;ENSP00000409126:D673Y;ENSP00000413840:D652Y;ENSP00000320087:D652Y;ENSP00000413137:D634Y	ENSP00000320087:D652Y	D	+	1	0	ANO6	44089480	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.813000	0.99286	2.652000	0.90054	0.655000	0.94253	GAC	.	.	.	none		0.353	ANO6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404822.1	XM_113743		T	45803213	G	T	45803213	3	4	184	1	0	0	0	0	1	0	0	0	701	1174	41	4	2036	4	ANO6	12	45803213	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	5044362	45803213	88048682	73	10806											
ATP7B	540	hgsc.bcm.edu	37	chr13	52548876	52548876	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttccggaccttgccttcaatGgagctgacacaggactggca	9	9	11	12	1	1	1	1	1	0	0	2	4	2	4	3	4	2	2	3	4	1	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr13:52548876G>A	ENST00000242839.4	-	2	636	c.480C>T	c.(478-480)tcC>tcT	p.S160S	ATP7B_ENST00000400366.3_Silent_p.S160S|ATP7B_ENST00000344297.5_Silent_p.S160S|ATP7B_ENST00000482841.1_5'UTR|ATP7B_ENST00000542656.1_Silent_p.S128S|ATP7B_ENST00000400370.3_Silent_p.S160S|ATP7B_ENST00000418097.2_Silent_p.S160S|ATP7B_ENST00000448424.2_Silent_p.S160S	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	160	HMA 2. {ECO:0000255|PROSITE- ProRule:PRU00280}.				cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	TGCCTTCAATGGAGCTGACAC	0.562									Wilson disease																												p.S160S		Atlas-SNP	.											.	ATP7B	123	.	0			c.C480T						PASS	.						47	49	48					13																	52548876		2045	4186	6231	SO:0001819	synonymous_variant	540	exon2	Familial Cancer Database		TTCAATGGAGCTG	U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"ATPases / P-type"	870	protein-coding gene	gene with protein product	"Wilson disease", "copper pump 2", "copper-transporting ATPase 2"	606882	"ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.480C>T	chr13.hg19:g.52548876G>A		71.0	0.0	.		72.0	23.0	.	NM_001243182	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Silent	SNP	ENST00000242839.4	hg19	CCDS41892.1																																																																																			.	.	.	none		0.562	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053		A	52548876	G	A	52548876	2	1	184	1	0	0	0	0	0	0	0	1	1191	1335	47	2		2	ATP7B	13	52548876	Silent	SNP	G	TCGA-GL-7773-01A-11D-2136-08		52548876	62621002	74	10807											
CDC16	8881	hgsc.bcm.edu	37	chr13	115022697	115022697	+	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	gtcggcgtggttgcatttcaGaatggagagtaagtactgga	10	11	15	5	2	1	2	1	0	0	2	2	4	1	3	0	4	2	4	0	4	3	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr13:115022697G>T	ENST00000356221.3	+	13	1350	c.1242G>T	c.(1240-1242)caG>caT	p.Q414H	CDC16_ENST00000252458.6_Intron|CDC16_ENST00000360383.3_Missense_Mutation_p.Q414H|CDC16_ENST00000252457.5_Missense_Mutation_p.Q413H|CDC16_ENST00000375308.1_Missense_Mutation_p.Q320H|CDC16_ENST00000375310.1_Missense_Mutation_p.Q320H|CDC16_ENST00000375312.3_Intron			Q13042	CDC16_HUMAN	cell division cycle 16	414					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)			TTGCATTTCAGAATGGAGAGT	0.438																																					p.Q414H		Atlas-SNP	.											.	CDC16	50	.	0			c.G1242T						PASS	.						121	114	116					13																	115022697		2203	4300	6503	SO:0001583	missense	8881	exon13			ATTTCAGAATGGA	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.1242G>T	chr13.hg19:g.115022697G>T	ENSP00000348554:p.Gln414His	142.0	0.0	.		166.0	53.0	.	NM_003903	A2A365|Q5T8C8|Q96AE6|Q9Y564	Missense_Mutation	SNP	ENST00000356221.3	hg19	CCDS9542.2	.	.	.	.	.	.	.	.	.	.	G	12.89	2.074396	0.36566	.	.	ENSG00000130177	ENST00000360383;ENST00000356221;ENST00000375310;ENST00000252457;ENST00000375308	T;T;T;T;T	0.55413	0.52;0.52;0.52;0.52;0.52	5.94	-2.27	0.06846	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.064378	0.64402	D	0.000003	T	0.27866	0.0686	N	0.12182	0.205	0.80722	D	1	B;B	0.23540	0.018;0.087	B;B	0.11329	0.006;0.006	T	0.07328	-1.0778	9	.	.	.	-19.2092	13.2551	0.60074	0.6016:0.0:0.3984:0.0	.	413;414	Q13042-2;Q13042	.;CDC16_HUMAN	H	414;414;320;413;320	ENSP00000353549:Q414H;ENSP00000348554:Q414H;ENSP00000364459:Q320H;ENSP00000252457:Q413H;ENSP00000364457:Q320H	.	Q	+	3	2	CDC16	114040799	1.000000	0.71417	0.983000	0.44433	0.942000	0.58702	0.794000	0.26958	-0.384000	0.07845	-0.142000	0.14014	CAG	.	.	.	none		0.438	CDC16-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276737.1	NM_003903		T	115022697	G	T	115022697	3	4	184	1	0	0	0	0	1	0	0	0	3060	933	33	4	1292	4	CDC16	13	115022697	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	62473821	115022697	147181	75	10808											
TINF2	26277	hgsc.bcm.edu	37	chr14	24709984	24709984	+	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	ggaagatgtgtgccaggcttGgcttttggcaggggattgtg	6	12	18	5	0	0	1	0	0	0	1	0	3	0	3	1	6	1	3	1	6	1	4	rs201135568		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr14:24709984G>C	ENST00000267415.7	-	6	1043	c.702C>G	c.(700-702)gcC>gcG	p.A234A	TINF2_ENST00000558566.1_3'UTR|TINF2_ENST00000558510.1_5'Flank|TINF2_ENST00000540705.1_Silent_p.A199A|TINF2_ENST00000538777.1_Silent_p.A20A|TINF2_ENST00000559019.1_3'UTR|TINF2_ENST00000399423.4_Silent_p.A234A	NM_001099274.1	NP_001092744.1	Q9BSI4	TINF2_HUMAN	TERF1 (TRF1)-interacting nuclear factor 2	234					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)		TGCCAGGCTTGGCTTTTGGCA	0.552									Congenital Dyskeratosis;Ataxia Pancytopenia syndrome																												p.A234A		Atlas-SNP	.											.	TINF2	61	.	0			c.C702G						PASS	.						149	144	146					14																	24709984		1996	4158	6154	SO:0001819	synonymous_variant	26277	exon6	Familial Cancer Database	Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita;Myelocerebellar disorder	AGGCTTGGCTTTT	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.702C>G	chr14.hg19:g.24709984G>C		150.0	0.0	.		143.0	35.0	.	NM_001099274	B3W5Q7|Q9H904|Q9UHC2	Silent	SNP	ENST00000267415.7	hg19	CCDS41936.1																																																																																			.	G|1.000;A|0.000	.	alt		0.552	TINF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415406.2			C	24709984	G	C	24709984	2	2	184	1	0	0	0	0	0	0	0	1	15935	1335	47	4		4	TINF2	14	24709984	Silent	SNP	G	TCGA-GL-7773-01A-11D-2136-08		24709984	82639556	76	10809											
HSPA2	3306	hgsc.bcm.edu	37	chr14	65008125	65008125	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcggccatcgcctacggcctGgacaagaagggctgcgcggg	7	4	17	13	5	0	1	0	0	0	1	1	2	0	2	3	5	2	1	3	5	3	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr14:65008125G>A	ENST00000394709.1	+	2	634	c.558G>A	c.(556-558)ctG>ctA	p.L186L	HSPA2_ENST00000247207.6_Silent_p.L186L|RP11-973N13.4_ENST00000554918.1_RNA|HSPA2_ENST00000554883.1_3'UTR			P54652	HSP72_HUMAN	heat shock 70kDa protein 2	186					male meiosis (GO:0007140)|male meiosis I (GO:0007141)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle (GO:0031662)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)|spermatid development (GO:0007286)|synaptonemal complex disassembly (GO:0070194)	blood microparticle (GO:0072562)|CatSper complex (GO:0036128)|cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycolipid binding (GO:0051861)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00515)|OV - Ovarian serous cystadenocarcinoma(108;0.00584)|BRCA - Breast invasive adenocarcinoma(234;0.045)		CCTACGGCCTGGACAAGAAGG	0.642																																					p.L186L	Pancreas(136;1211 1835 24894 31984 38227)	Atlas-SNP	.											.	HSPA2	83	.	0			c.G558A						PASS	.						67	75	72					14																	65008125		2203	4300	6503	SO:0001819	synonymous_variant	3306	exon1			CGGCCTGGACAAG	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.558G>A	chr14.hg19:g.65008125G>A		160.0	0.0	.		154.0	45.0	.	NM_021979	Q15508|Q53XM3|Q9UE78	Silent	SNP	ENST00000394709.1	hg19	CCDS9766.1																																																																																			.	.	.	none		0.642	HSPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280651.1			A	65008125	G	A	65008125	2	1	184	1	0	0	0	0	0	0	0	1	7418	1335	47	2		2	HSPA2	14	65008125	Silent	SNP	G	TCGA-GL-7773-01A-11D-2136-08	40298141	65008125	42341415	77	10810											
HSPA2	3306	hgsc.bcm.edu	37	chr14	65008173	65008173	+	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	aagaacgtgctcatctttgaCctgggcggtggcactttcga	8	11	12	10	3	2	2	1	1	1	1	3	3	2	2	1	3	2	2	1	3	2	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr14:65008173C>A	ENST00000394709.1	+	2	682	c.606C>A	c.(604-606)gaC>gaA	p.D202E	HSPA2_ENST00000247207.6_Missense_Mutation_p.D202E|RP11-973N13.4_ENST00000554918.1_RNA|HSPA2_ENST00000554883.1_3'UTR			P54652	HSP72_HUMAN	heat shock 70kDa protein 2	202					male meiosis (GO:0007140)|male meiosis I (GO:0007141)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle (GO:0031662)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)|spermatid development (GO:0007286)|synaptonemal complex disassembly (GO:0070194)	blood microparticle (GO:0072562)|CatSper complex (GO:0036128)|cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycolipid binding (GO:0051861)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00515)|OV - Ovarian serous cystadenocarcinoma(108;0.00584)|BRCA - Breast invasive adenocarcinoma(234;0.045)		TCATCTTTGACCTGGGCGGTG	0.642																																					p.D202E	Pancreas(136;1211 1835 24894 31984 38227)	Atlas-SNP	.											.	HSPA2	83	.	0			c.C606A						PASS	.						98	106	103					14																	65008173		2203	4300	6503	SO:0001583	missense	3306	exon1			CTTTGACCTGGGC	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.606C>A	chr14.hg19:g.65008173C>A	ENSP00000378199:p.Asp202Glu	169.0	0.0	.		200.0	58.0	.	NM_021979	Q15508|Q53XM3|Q9UE78	Missense_Mutation	SNP	ENST00000394709.1	hg19	CCDS9766.1	.	.	.	.	.	.	.	.	.	.	C	19.26	3.793970	0.70452	.	.	ENSG00000126803	ENST00000394709;ENST00000247207	T;T	0.49720	0.77;0.77	5.22	5.22	0.72569	Heat shock protein 70, conserved site (1);	0.000000	0.56097	U	0.000034	D	0.87026	0.6075	H	0.99998	5.51	0.44736	D	0.997733	D	0.89917	1.0	D	0.91635	0.999	D	0.94368	0.7593	10	0.87932	D	0	-12.6764	18.774	0.91902	0.0:1.0:0.0:0.0	.	202	P54652	HSP72_HUMAN	E	202	ENSP00000378199:D202E;ENSP00000247207:D202E	ENSP00000247207:D202E	D	+	3	2	HSPA2	64077926	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.963000	0.56773	2.422000	0.82143	0.563000	0.77884	GAC	.	.	.	none		0.642	HSPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280651.1			A	65008173	C	A	65008173	3	1	184	1	0	0	0	0	1	0	0	0	7418	506	18	4	608	4	HSPA2	14	65008173	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	48	65008173	42341367	78	10811											
ADAM20	8748	hgsc.bcm.edu	37	chr14	70991146	70991146	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctccacataaccatggtagTagcagtcatcctggatgaag	12	9	9	11	0	1	1	1	1	0	0	3	2	3	2	4	2	2	3	4	2	4	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr14:70991146T>C	ENST00000256389.3	-	2	723	c.479A>G	c.(478-480)tAc>tGc	p.Y160C	RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003814.4	NP_003805.3	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20	110					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(2)	27			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)		ACCATGGTAGTAGCAGTCATC	0.498																																					p.Y160C		Atlas-SNP	.											.	ADAM20	59	.	0			c.A479G						PASS	.						145	102	117					14																	70991146		2203	4300	6503	SO:0001583	missense	8748	exon2			TGGTAGTAGCAGT	AF029899	CCDS32111.1	14q24.2	2012-04-30	2005-08-18		ENSG00000134007	ENSG00000134007		"ADAM metallopeptidase domain containing"	199	protein-coding gene	gene with protein product		603712	"a disintegrin and metalloproteinase domain 20"			9469942	Standard	NM_003814		Approved		uc001xme.3	O43506	OTTHUMG00000167548	ENST00000256389.3:c.479A>G	chr14.hg19:g.70991146T>C	ENSP00000256389:p.Tyr160Cys	123.0	0.0	.		161.0	71.0	.	NM_003814	Q6GTZ1|Q9UKJ9	Missense_Mutation	SNP	ENST00000256389.3	hg19	CCDS32111.1	.	.	.	.	.	.	.	.	.	.	T	10.77	1.444114	0.25987	.	.	ENSG00000134007	ENST00000256389	T	0.07444	3.19	4.14	1.61	0.23674	Peptidase M12B, propeptide (1);	0.000000	0.35555	N	0.003123	T	0.39600	0.1084	H	0.98133	4.155	0.26202	N	0.979437	D	0.89917	1.0	D	0.79108	0.992	T	0.41179	-0.9523	10	0.87932	D	0	.	9.3882	0.38356	0.4926:0.0:0.0:0.5074	.	110	O43506	ADA20_HUMAN	C	160	ENSP00000256389:Y160C	ENSP00000256389:Y160C	Y	-	2	0	ADAM20	70060899	1.000000	0.71417	0.998000	0.56505	0.115000	0.19883	1.990000	0.40717	0.202000	0.20498	-0.336000	0.08194	TAC	.	.	.	none		0.498	ADAM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395004.2			C	70991146	T	C	70991146	3	2	184	1	0	0	0	0	1	0	0	0	242	1638	57	3	1855	3	ADAM20	14	70991146	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	5982973	70991146	36358394	79	10812											
C14orf174	161394	hgsc.bcm.edu	37	chr14	77844646	77844646	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccagaggagatgcaaagaaaGgcaactgaggagaaagggac	18	2	15	6	0	0	5	0	1	0	4	0	8	0	6	1	4	2	2	1	4	4	0			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr14:77844646G>A	ENST00000216471.4	+	1	1171	c.885G>A	c.(883-885)aaG>aaA	p.K295K	TMED8_ENST00000216468.7_5'Flank|SAMD15_ENST00000533095.2_Intron	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	295										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						TGCAAAGAAAGGCAACTGAGG	0.493																																					p.K295K		Atlas-SNP	.											.	SAMD15	60	.	0			c.G885A						PASS	.						81	83	82					14																	77844646		2203	4300	6503	SO:0001819	synonymous_variant	161394	exon1			AAGAAAGGCAACT	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.885G>A	chr14.hg19:g.77844646G>A		126.0	0.0	.		123.0	47.0	.	NM_001010860	Q2M3P3	Silent	SNP	ENST00000216471.4	hg19	CCDS32126.1																																																																																			.	.	.	none		0.493	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860		A	77844646	G	A	77844646	2	1	184	1	0	0	0	0	0	0	0	1	1761	991	35	2		2	C14orf174	14	77844646	Silent	SNP	G	TCGA-GL-7773-01A-11D-2136-08	6853500	77844646	29504894	80	10813											
NRXN3	9369	hgsc.bcm.edu	37	chr14	79423648	79423648	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caacgagtggcacaccgttcGggtggtgcggagaggaaaaa	12	5	16	8	4	0	1	0	0	0	1	1	4	0	2	1	5	2	2	1	5	3	1	rs367857290		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr14:79423648G>A	ENST00000554719.1	+	8	1711	c.1220G>A	c.(1219-1221)cGg>cAg	p.R407Q	NRXN3_ENST00000335750.5_Missense_Mutation_p.R407Q	NM_004796.4	NP_004787.2	Q9HDB5	NRX3B_HUMAN	neurexin 3	177					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)	p.R407P(1)		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)		CACACCGTTCGGGTGGTGCGG	0.473																																					p.R407Q		Atlas-SNP	.											NRXN3,NS,carcinoma,0,1	NRXN3	342	.	1	Substitution - Missense(1)	lung(1)	c.G1220A						PASS	.	G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	276	241	253		1220	3.8	1	14		253	0,8600		0,0,4300	no	missense	NRXN3	NM_004796.4	43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	407/1062	79423648	1,13005	2203	4300	6503	SO:0001583	missense	9369	exon8			CCGTTCGGGTGGT	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.1220G>A	chr14.hg19:g.79423648G>A	ENSP00000451648:p.Arg407Gln	150.0	0.0	.		172.0	65.0	.	NM_004796	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Missense_Mutation	SNP	ENST00000554719.1	hg19	CCDS9870.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.774869	0.90108	2.27E-4	0.0	ENSG00000021645	ENST00000330071;ENST00000332068;ENST00000554719;ENST00000335750	T;T	0.77877	-1.13;-1.13	5.64	3.82	0.43975	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.206569	0.42821	N	0.000657	D	0.86772	0.6013	.	.	.	0.54753	D	0.999982	D;D	0.89917	1.0;0.974	D;B	0.87578	0.998;0.406	D	0.86484	0.1793	8	.	.	.	.	12.5919	0.56447	0.135:0.0:0.865:0.0	.	780;407	Q9Y4C0;Q9Y4C0-3	NRX3A_HUMAN;.	Q	780;769;407;407	ENSP00000451648:R407Q;ENSP00000338349:R407Q	.	R	+	2	0	NRXN3	78493401	1.000000	0.71417	0.985000	0.45067	0.985000	0.73830	4.901000	0.63259	0.860000	0.35481	0.650000	0.86243	CGG	.	.	.	weak		0.473	NRXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413787.1	NM_001105250		A	79423648	G	A	79423648	3	1	184	1	0	0	0	0	1	0	0	0	10674	1116	39	1	1242	1	NRXN3	14	79423648	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	1579002	79423648	27925892	81	10814											
C14orf49	161176	hgsc.bcm.edu	37	chr14	95903278	95903278	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttcctcaggagctgggagAaatcttcatggctcccttct	8	12	10	11	0	4	1	2	0	2	1	6	3	6	2	2	3	1	3	2	3	1	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr14:95903278A>G	ENST00000334258.5	-	14	2431	c.2417T>C	c.(2416-2418)tTc>tCc	p.F806S	SYNE3_ENST00000554873.1_Missense_Mutation_p.F563S|SYNE3_ENST00000557275.1_Missense_Mutation_p.F801S	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	806					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						GAGCTGGGAGAAATCTTCATG	0.517																																					p.F806S		Atlas-SNP	.											.	SYNE3	130	.	0			c.T2417C						PASS	.						100	96	97					14																	95903278		2203	4300	6503	SO:0001583	missense	161176	exon14			TGGGAGAAATCTT	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.2417T>C	chr14.hg19:g.95903278A>G	ENSP00000334308:p.Phe806Ser	135.0	0.0	.		145.0	68.0	.	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	hg19	CCDS9935.1	.	.	.	.	.	.	.	.	.	.	A	12.57	1.978684	0.34942	.	.	ENSG00000176438	ENST00000334258;ENST00000554873;ENST00000557275	T;T;T	0.15372	3.48;2.43;3.5	5.13	-6.79	0.01715	.	1.951040	0.02897	N	0.134895	T	0.13157	0.0319	M	0.62723	1.935	0.09310	N	1	B;B	0.22211	0.066;0.04	B;B	0.17979	0.02;0.01	T	0.23226	-1.0194	10	0.23891	T	0.37	-0.2886	0.1537	0.00096	0.2263:0.2228:0.217:0.3339	.	801;806	Q6ZMZ3-2;Q6ZMZ3	.;SYNE3_HUMAN	S	806;563;801	ENSP00000334308:F806S;ENSP00000452154:F563S;ENSP00000450562:F801S	ENSP00000334308:F806S	F	-	2	0	C14orf49	94973031	0.011000	0.17503	0.000000	0.03702	0.134000	0.20937	0.178000	0.16820	-1.516000	0.01782	0.459000	0.35465	TTC	.	.	.	none		0.517	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592		G	95903278	A	G	95903278	3	3	184	1	0	0	0	0	1	0	0	0	1778	246	9	3	526	3	C14orf49	14	95903278	Missense_Mutation	SNP	A	TCGA-GL-7773-01A-11D-2136-08	16479630	95903278	11446262	82	10815											
BEGAIN	57596	hgsc.bcm.edu	37	chr14	101012903	101012903	+	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	cgcagctcgatctccaggtaGtggcgcgtggagtcgaactc	7	8	14	12	5	1	0	0	0	1	0	5	3	1	1	1	3	2	3	1	3	2	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr14:101012903G>A	ENST00000355173.2	-	3	182	c.111C>T	c.(109-111)caC>caT	p.H37H	BEGAIN_ENST00000443071.2_Silent_p.H37H|BEGAIN_ENST00000554747.1_5'UTR|BEGAIN_ENST00000556751.1_5'UTR	NM_020836.3	NP_065887.1	Q9BUH8	BEGIN_HUMAN	brain-enriched guanylate kinase-associated	37						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)				TCTCCAGGTAGTGGCGCGTGG	0.692																																					p.H37H	NSCLC(159;1889 2010 9965 27479 40101)	Atlas-SNP	.											.	BEGAIN	32	.	0			c.C111T						PASS	.						74	69	71					14																	101012903		2203	4300	6503	SO:0001819	synonymous_variant	57596	exon3			CAGGTAGTGGCGC	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.111C>T	chr14.hg19:g.101012903G>A		127.0	0.0	.		124.0	44.0	.	NM_020836	Q9NPU3|Q9P282	Silent	SNP	ENST00000355173.2	hg19	CCDS9962.1																																																																																			.	.	.	none		0.692	BEGAIN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414329.1	NM_020836		A	101012903	G	A	101012903	2	1	184	1	0	0	0	0	0	0	0	1	1397	1020	36	2		2	BEGAIN	14	101012903	Silent	SNP	G	TCGA-GL-7773-01A-11D-2136-08	5109625	101012903	6336637	83	10816											
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105408067	105408067	+	Frame_Shift_Del	DEL	T	T	-																															ctgcctttgggcctttcaggTccagcttggggcccttgacg																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr14:105408067delT	ENST00000333244.5	-	7	13840	c.13721delA	c.(13720-13722)gacfs	p.D4574fs	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4574						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)			GCCTTTCAGGTCCAGCTTGGG	0.627																																					p.D4574fs		Atlas-INDEL	.											.	AHNAK2	719	.	0			c.13722delC						PASS	.						124	134	131					14																	105408067		1916	4122	6038	SO:0001589	frameshift_variant	113146	exon7			.	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.13721delA	chr14.hg19:g.105408067delT	ENSP00000353114:p.Asp4574fs	307.0	0.0	0		302.0	94.0	0.311258	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Frame_Shift_Del	DEL	ENST00000333244.5	hg19	CCDS45177.1																																																																																			.	.	.	none		0.627	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		-	105408067	T	-	105408067	7	5	184	1	0	1	0	1	0	0	0	0	415	1667	58	0	3670	0	AHNAK2	14	105408067	Frame_Shift_Del	DEL	T	TCGA-GL-7773-01A-11D-2136-08	4395164	105408067	1941473	84	10817											
HERC2	8924	hgsc.bcm.edu	37	chr15	28431846	28431846	+	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	tgagaccatggattttacaaTcgattcctgagctcctgcac	10	12	8	11	1	0	2	0	2	0	1	3	5	2	3	3	1	3	2	3	1	2	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr15:28431846T>A	ENST00000261609.7	-	56	8810	c.8702A>T	c.(8701-8703)gAt>gTt	p.D2901V		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)		GATTTTACAATCGATTCCTGA	0.423																																					p.D2901V		Atlas-SNP	.											.	HERC2	501	.	0			c.A8702T						PASS	.						84	74	77					15																	28431846		2203	4300	6503	SO:0001583	missense	8924	exon56			TTACAATCGATTC	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.8702A>T	chr15.hg19:g.28431846T>A	ENSP00000261609:p.Asp2901Val	54.0	0.0	.		71.0	27.0	.	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.315805	0.81469	.	.	ENSG00000128731	ENST00000261609	T	0.70164	-0.46	5.0	5.0	0.66597	Anaphase-promoting complex, subunit 10/DOC domain (1);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	T	0.81721	0.4882	M	0.77103	2.36	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.84597	0.0670	10	0.87932	D	0	.	15.0231	0.71647	0.0:0.0:0.0:1.0	.	2901	O95714	HERC2_HUMAN	V	2901	ENSP00000261609:D2901V	ENSP00000261609:D2901V	D	-	2	0	HERC2	26105441	1.000000	0.71417	0.496000	0.27539	0.859000	0.49053	7.997000	0.88414	2.000000	0.58554	0.528000	0.53228	GAT	.	.	.	none		0.423	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		A	28431846	T	A	28431846	3	1	184	1	0	0	0	0	1	0	0	0	7065	1435	50	5	5954	5	HERC2	15	28431846	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08		28431846	74099546	85	10818											
ZNF770	54989	hgsc.bcm.edu	37	chr15	35274327	35274327	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acagattgacaagtctttctTattcactgaattatcaatgc	13	15	5	8	0	4	3	2	2	2	1	4	3	4	3	0	0	1	0	0	0	5	5			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr15:35274327T>C	ENST00000356321.4	-	3	1653	c.1309A>G	c.(1309-1311)Aag>Gag	p.K437E		NM_014106.3	NP_054825.2	Q6IQ21	ZN770_HUMAN	zinc finger protein 770	437					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)		AAGTCTTTCTTATTCACTGAA	0.348																																					p.K437E		Atlas-SNP	.											.	ZNF770	64	.	0			c.A1309G						PASS	.						82	84	83					15																	35274327		2201	4297	6498	SO:0001583	missense	54989	exon3			CTTTCTTATTCAC	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.1309A>G	chr15.hg19:g.35274327T>C	ENSP00000348673:p.Lys437Glu	117.0	0.0	.		167.0	65.0	.	NM_014106	Q6ZMZ6|Q9NWV2	Missense_Mutation	SNP	ENST00000356321.4	hg19	CCDS10042.1	.	.	.	.	.	.	.	.	.	.	T	4.829	0.154043	0.09185	.	.	ENSG00000198146	ENST00000356321	T	0.09073	3.02	5.49	5.49	0.81192	.	0.394233	0.25414	N	0.030860	T	0.07052	0.0179	N	0.14661	0.345	0.22996	N	0.998451	B	0.23937	0.094	B	0.22386	0.039	T	0.31194	-0.9952	10	0.87932	D	0	-3.5887	15.7623	0.78096	0.0:0.0:0.0:1.0	.	437	Q6IQ21	ZN770_HUMAN	E	437	ENSP00000348673:K437E	ENSP00000348673:K437E	K	-	1	0	ZNF770	33061619	1.000000	0.71417	0.997000	0.53966	0.123000	0.20343	3.570000	0.53834	2.311000	0.77944	0.533000	0.62120	AAG	.	.	.	none		0.348	ZNF770-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251896.2	NM_014106		C	35274327	T	C	35274327	3	2	184	1	0	0	0	0	1	0	0	0	18155	1763	61	3	770	3	ZNF770	15	35274327	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	6842481	35274327	67257065	86	10819											
BAHD1	22893	hgsc.bcm.edu	37	chr15	40758294	40758294	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttgccgccatgtctatgacTtccgccacgggcgcatcctt	5	12	9	15	4	1	1	0	1	1	0	3	1	3	1	5	1	1	1	5	1	1	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr15:40758294T>C	ENST00000416165.1	+	7	2379	c.2308T>C	c.(2308-2310)Ttc>Ctc	p.F770L	BAHD1_ENST00000561234.1_Missense_Mutation_p.F769L|RP11-64K12.8_ENST00000559730.1_RNA|BAHD1_ENST00000560846.1_Missense_Mutation_p.F767L	NM_014952.3	NP_055767.3	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1	770	BAH. {ECO:0000255|PROSITE- ProRule:PRU00370}.				heterochromatin assembly (GO:0031507)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|chromosome (GO:0005694)	chromatin binding (GO:0003682)			NS(1)|endometrium(6)|kidney(3)|large_intestine(3)|lung(10)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	28		all_cancers(109;8.28e-19)|all_epithelial(112;2.64e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.46e-06)|BRCA - Breast invasive adenocarcinoma(123;0.08)		TGTCTATGACTTCCGCCACGG	0.632																																					p.F770L		Atlas-SNP	.											.	BAHD1	68	.	0			c.T2308C						PASS	.						98	101	100					15																	40758294		2203	4300	6503	SO:0001583	missense	22893	exon7			TATGACTTCCGCC	AL833923	CCDS10058.1, CCDS73705.1	15q14	2005-11-10			ENSG00000140320	ENSG00000140320			29153	protein-coding gene	gene with protein product		613880				10231032	Standard	XM_005254229		Approved	KIAA0945	uc001zlu.2	Q8TBE0	OTTHUMG00000129982	ENST00000416165.1:c.2308T>C	chr15.hg19:g.40758294T>C	ENSP00000396976:p.Phe770Leu	200.0	0.0	.		249.0	103.0	.	NM_014952	Q8NDF7|Q9Y2F4	Missense_Mutation	SNP	ENST00000416165.1	hg19	CCDS10058.1	.	.	.	.	.	.	.	.	.	.	T	29.4	5.000543	0.93227	.	.	ENSG00000140320	ENST00000416165	D	0.85339	-1.97	5.6	5.6	0.85130	Bromo adjacent homology (BAH) domain (3);	0.000000	0.85682	D	0.000000	D	0.91965	0.7455	M	0.76328	2.33	0.80722	D	1	D;D;D	0.89917	0.996;1.0;1.0	D;D;D	0.87578	0.917;0.998;0.997	D	0.92808	0.6262	10	0.72032	D	0.01	-16.7549	15.7888	0.78332	0.0:0.0:0.0:1.0	.	767;770;769	Q8TBE0-3;Q8TBE0;Q8TBE0-2	.;BAHD1_HUMAN;.	L	770	ENSP00000396976:F770L	ENSP00000396976:F770L	F	+	1	0	BAHD1	38545586	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.040000	0.89188	2.144000	0.66660	0.460000	0.39030	TTC	.	.	.	none		0.632	BAHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252248.1	NM_014952		C	40758294	T	C	40758294	3	2	184	1	0	0	0	0	1	0	0	0	1297	1609	56	3	2330	3	BAHD1	15	40758294	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	5483967	40758294	61773098	87	10820											
MYO5C	55930	hgsc.bcm.edu	37	chr15	52498142	52498142	+	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	gcaattcttattctgctgtgGactattatgcttcatgaatt	9	18	7	7	0	3	1	1	1	2	0	3	2	3	2	0	1	2	3	0	1	5	7			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr15:52498142G>T	ENST00000261839.7	-	37	4569	c.4408C>A	c.(4408-4410)Cca>Aca	p.P1470T	RP11-430B1.2_ENST00000560518.1_lincRNA	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	1470	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)		TTCTGCTGTGGACTATTATGC	0.269																																					p.P1470T		Atlas-SNP	.											.	MYO5C	162	.	0			c.C4408A						PASS	.						57	49	52					15																	52498142		1789	4055	5844	SO:0001583	missense	55930	exon37			GCTGTGGACTATT	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.4408C>A	chr15.hg19:g.52498142G>T	ENSP00000261839:p.Pro1470Thr	47.0	0.0	.		47.0	19.0	.	NM_018728	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	hg19	CCDS42036.1	.	.	.	.	.	.	.	.	.	.	G	17.87	3.494477	0.64186	.	.	ENSG00000128833	ENST00000261839	T	0.16897	2.31	5.21	4.27	0.50696	Dilute (1);	0.061993	0.64402	D	0.000004	T	0.32010	0.0815	M	0.72118	2.19	0.80722	D	1	D	0.56035	0.974	P	0.52957	0.714	T	0.09228	-1.0684	10	0.33940	T	0.23	.	15.7715	0.78173	0.0:0.1365:0.8635:0.0	.	1470	Q9NQX4	MYO5C_HUMAN	T	1470	ENSP00000261839:P1470T	ENSP00000261839:P1470T	P	-	1	0	MYO5C	50285434	1.000000	0.71417	0.959000	0.39883	0.903000	0.53119	3.298000	0.51818	1.376000	0.46267	0.555000	0.69702	CCA	.	.	.	none		0.269	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728		T	52498142	G	T	52498142	3	4	184	1	0	0	0	0	1	0	0	0	10087	1174	41	4	840	4	MYO5C	15	52498142	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	11739848	52498142	50033250	88	10821											
PML	5371	hgsc.bcm.edu	37	chr15	74327953	74327953	+	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	catcctgcccagctgcaaagGggcatcagcccaccccaccg	9	4	9	19	1	1	0	1	0	0	0	2	0	2	0	6	2	4	3	6	2	1	0			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr15:74327953G>A	ENST00000268058.3	+	7	1806				PML_ENST00000359928.4_Intron|PML_ENST00000435786.2_3'UTR|PML_ENST00000436891.3_3'UTR|PML_ENST00000569965.1_Intron|PML_ENST00000395135.3_Intron|PML_ENST00000395132.2_Intron|PML_ENST00000354026.6_Silent_p.R669R|PML_ENST00000268059.6_Silent_p.R717R|PML_ENST00000563500.1_3'UTR|PML_ENST00000564428.1_Intron|PML_ENST00000565898.1_Intron	NM_033238.2	NP_150241.2	P29590	PML_HUMAN	promyelocytic leukemia						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to interleukin-4 (GO:0071353)|cellular senescence (GO:0090398)|circadian regulation of gene expression (GO:0032922)|common-partner SMAD protein phosphorylation (GO:0007182)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|entrainment of circadian clock by photoperiod (GO:0043153)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|maintenance of protein location in nucleus (GO:0051457)|myeloid cell differentiation (GO:0030099)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation in response to oxidative stress (GO:0032938)|negative regulation of viral release from host cell (GO:1902187)|PML body organization (GO:0030578)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of histone deacetylation (GO:0031065)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)|regulation of calcium ion transport into cytosol (GO:0010522)|regulation of circadian rhythm (GO:0042752)|regulation of double-strand break repair (GO:2000779)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of protein phosphorylation (GO:0001932)|regulation of transcription, DNA-templated (GO:0006355)|response to cytokine (GO:0034097)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|retinoic acid receptor signaling pathway (GO:0048384)|SMAD protein import into nucleus (GO:0007184)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	cobalt ion binding (GO:0050897)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|SUMO binding (GO:0032183)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	31						AGCTGCAAAGGGGCATCAGCC	0.622			T	"RARA, PAX5"	"APL, ALL"																																p.R717R		Atlas-SNP	.		Dom	yes		15	15q22	5371	promyelocytic leukemia		L	.	PML	169	.	0			c.G2151A						PASS	.						64	63	64					15																	74327953		2198	4297	6495	SO:0001627	intron_variant	5371	exon8			GCAAAGGGGCATC	AB208950	CCDS10255.1, CCDS10256.1, CCDS10257.1, CCDS10258.1, CCDS45297.1, CCDS45298.1, CCDS45299.1, CCDS45300.1, CCDS58386.1	15q24.1	2011-04-21			ENSG00000140464	ENSG00000140464		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	9113	protein-coding gene	gene with protein product		102578					Standard	NM_033244		Approved	MYL, TRIM19, RNF71	uc002awv.3	P29590	OTTHUMG00000137607	ENST00000268058.3:c.1710+1082G>A	chr15.hg19:g.74327953G>A		119.0	0.0	.		128.0	39.0	.	NM_033239	E9PBR7|P29591|P29592|P29593|Q00755|Q15959|Q59FP9|Q8WUA0|Q96S41|Q9BPW2|Q9BWP7|Q9BZX6|Q9BZX7|Q9BZX8|Q9BZX9|Q9BZY0|Q9BZY2|Q9BZY3	Silent	SNP	ENST00000268058.3	hg19	CCDS10255.1																																																																																			.	.	.	none		0.622	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269021.3	NM_002675		A	74327953	G	A	74327953	1	1	184	0	1	0	0	0	0	0	0	0	12142	1223	43	2		2	PML	15	74327953	Intron	SNP	G	TCGA-GL-7773-01A-11D-2136-08	21829811	74327953	28203439	89	10822											
AXIN1	8312	hgsc.bcm.edu	37	chr16	338194	338194	+	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	acggcctcgtcctctcgaacCtcctcaaacaccaccccaca	10	6	4	21	3	2	0	1	0	1	0	6	1	4	0	7	1	2	0	7	1	2	0			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr16:338194C>A	ENST00000262320.3	-	11	2888	c.2517G>T	c.(2515-2517)gaG>gaT	p.E839D	AXIN1_ENST00000354866.3_Missense_Mutation_p.E803D	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	839	DIX. {ECO:0000255|PROSITE- ProRule:PRU00069}.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				CCTCTCGAACCTCCTCAAACA	0.587																																					p.E839D		Atlas-SNP	.											.	AXIN1	290	.	0			c.G2517T						PASS	.						233	174	194					16																	338194		2203	4300	6503	SO:0001583	missense	8312	exon11			TCGAACCTCCTCA	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.2517G>T	chr16.hg19:g.338194C>A	ENSP00000262320:p.Glu839Asp	166.0	0.0	.		170.0	47.0	.	NM_003502	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Missense_Mutation	SNP	ENST00000262320.3	hg19	CCDS10405.1	.	.	.	.	.	.	.	.	.	.	c	14.73	2.621324	0.46736	.	.	ENSG00000103126	ENST00000262320;ENST00000354866	T;T	0.61274	0.12;0.12	4.62	-0.702	0.11265	DIX (3);	0.000000	0.85682	D	0.000000	T	0.73528	0.3598	M	0.89534	3.04	0.50171	D	0.999859	D;D	0.89917	0.999;1.0	D;D	0.91635	0.998;0.999	T	0.70432	-0.4873	10	0.72032	D	0.01	-11.9016	5.4595	0.16610	0.1225:0.5288:0.0:0.3487	.	803;839	O15169-2;O15169	.;AXIN1_HUMAN	D	839;803	ENSP00000262320:E839D;ENSP00000346935:E803D	ENSP00000262320:E839D	E	-	3	2	AXIN1	278195	0.998000	0.40836	0.424000	0.26647	0.122000	0.20287	0.667000	0.25112	-0.105000	0.12132	-0.224000	0.12420	GAG	.	.	.	none		0.587	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			A	338194	C	A	338194	3	1	184	1	0	0	0	0	1	0	0	0	1236	680	24	4	75	4	AXIN1	16	338194	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08		338194	90016559	90	10823											
GLYR1	84656	hgsc.bcm.edu	37	chr16	4864623	4864623	+	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	cgggggttcttcccagacggGccccctcctggatgaacaaa	8	7	12	14	2	1	2	0	1	1	1	3	3	3	3	4	4	1	1	4	4	2	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr16:4864623G>C	ENST00000321919.9	-	11	1008	c.932C>G	c.(931-933)gCc>gGc	p.A311G	GLYR1_ENST00000436648.5_Missense_Mutation_p.A230G|GLYR1_ENST00000591451.1_Missense_Mutation_p.A305G|GLYR1_ENST00000381983.3_Missense_Mutation_p.A294G	NM_032569.3	NP_115958	Q49A26	GLYR1_HUMAN	glyoxylate reductase 1 homolog (Arabidopsis)	311					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						TCCCAGACGGGCCCCCTCCTG	0.577																																					p.A311G		Atlas-SNP	.											.	GLYR1	49	.	0			c.C932G						PASS	.						42	41	41					16																	4864623		2197	4300	6497	SO:0001583	missense	84656	exon11			AGACGGGCCCCCT	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.932C>G	chr16.hg19:g.4864623G>C	ENSP00000322716:p.Ala311Gly	43.0	0.0	.		61.0	17.0	.	NM_032569	B4DL47|C9JJ40|C9JJ60|Q5U632|Q6P1Q2|Q6V3W7|Q9BTI1|Q9BXK2	Missense_Mutation	SNP	ENST00000321919.9	hg19	CCDS10524.1	.	.	.	.	.	.	.	.	.	.	G	32	5.124490	0.94429	.	.	ENSG00000140632	ENST00000321919;ENST00000381983;ENST00000436648	T;T;T	0.73789	-0.49;-0.48;-0.78	5.33	5.33	0.75918	6-phosphogluconate dehydrogenase, NADP-binding (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.86887	0.6041	M	0.79926	2.475	0.80722	D	1	B;P;B;D	0.58620	0.262;0.512;0.173;0.983	B;P;B;D	0.79784	0.418;0.548;0.341;0.993	D	0.86708	0.1934	10	0.46703	T	0.11	-16.0047	18.1572	0.89696	0.0:0.0:1.0:0.0	.	230;305;294;311	Q49A26-5;Q49A26-3;Q49A26-2;Q49A26	.;.;.;GLYR1_HUMAN	G	311;294;230	ENSP00000322716:A311G;ENSP00000371413:A294G;ENSP00000390276:A230G	ENSP00000322716:A311G	A	-	2	0	GLYR1	4804624	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.422000	0.97458	2.654000	0.90174	0.561000	0.74099	GCC	.	.	.	none		0.577	GLYR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251717.2	NM_032569		C	4864623	G	C	4864623	3	2	184	1	0	0	0	0	1	0	0	0	6490	1203	42	4	753	4	GLYR1	16	4864623	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	4526429	4864623	85490130	91	10824											
NTAN1	123803	hgsc.bcm.edu	37	chr16	15133833	15133833	+	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	atttgaaactcactggtcctCctgctaaagttcgcgcagca	10	11	8	12	2	1	1	1	1	0	0	4	1	3	1	2	1	3	4	2	1	3	3			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr16:15133833C>G	ENST00000287706.3	-	8	724	c.632G>C	c.(631-633)gGa>gCa	p.G211A	PDXDC1_ENST00000535621.2_Intron	NM_001270766.1|NM_173474.3	NP_001257695.1|NP_775745.1	Q96AB6	NTAN1_HUMAN	N-terminal asparagine amidase	211					adult locomotory behavior (GO:0008344)|memory (GO:0007613)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-N-terminal asparagine amidohydrolase activity (GO:0008418)			endometrium(1)|large_intestine(4)|lung(3)	8						CACTGGTCCTCCTGCTAAAGT	0.433																																					p.G211A		Atlas-SNP	.											.	NTAN1	21	.	0			c.G632C						PASS	.						112	122	119					16																	15133833		2197	4300	6497	SO:0001583	missense	123803	exon8			GGTCCTCCTGCTA	AF092440	CCDS10558.1, CCDS73832.1	16p13	2008-02-05			ENSG00000157045	ENSG00000157045			29909	protein-coding gene	gene with protein product		615367				8910481	Standard	NM_173474		Approved		uc002ddd.4	Q96AB6	OTTHUMG00000129849	ENST00000287706.3:c.632G>C	chr16.hg19:g.15133833C>G	ENSP00000287706:p.Gly211Ala	277.0	0.0	.		286.0	106.0	.	NM_173474	Q7Z4Z0	Missense_Mutation	SNP	ENST00000287706.3	hg19	CCDS10558.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.344058	0.82022	.	.	ENSG00000157045	ENST00000287706	T	0.29655	1.56	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.62417	0.2426	M	0.85041	2.73	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.67369	-0.5688	10	0.72032	D	0.01	-20.0269	18.5814	0.91172	0.0:1.0:0.0:0.0	.	211	Q96AB6	NTAN1_HUMAN	A	211	ENSP00000287706:G211A	ENSP00000287706:G211A	G	-	2	0	NTAN1	15041334	1.000000	0.71417	0.987000	0.45799	0.810000	0.45777	5.601000	0.67606	2.630000	0.89119	0.650000	0.86243	GGA	.	.	.	none		0.433	NTAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252089.1	NM_173474		G	15133833	C	G	15133833	3	3	184	1	0	0	0	0	1	0	0	0	10702	855	30	4	312	4	NTAN1	16	15133833	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	10269210	15133833	75220920	92	10825											
XPO6	23214	hgsc.bcm.edu	37	chr16	28181133	28181133	+	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	gcttccgcaactcctccttcCgagccacactgaggtcctca	7	9	7	18	2	1	1	1	1	0	0	6	2	6	1	6	1	2	2	6	1	1	2	rs558020059		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr16:28181133C>A	ENST00000304658.5	-	5	1003	c.503G>T	c.(502-504)cGg>cTg	p.R168L	XPO6_ENST00000565698.1_Missense_Mutation_p.R154L	NM_015171.3	NP_055986.1	Q96QU8	XPO6_HUMAN	exportin 6	168					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						CTCCTCCTTCCGAGCCACACT	0.572																																					p.R168L		Atlas-SNP	.											XPO6_ENST00000304658,NS,carcinoma,0,2	XPO6	177	.	0			c.G503T						PASS	.						59	62	61					16																	28181133		2001	4169	6170	SO:0001583	missense	23214	exon5			TCCTTCCGAGCCA	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.503G>T	chr16.hg19:g.28181133C>A	ENSP00000302790:p.Arg168Leu	95.0	1.0	.		149.0	8.0	.	NM_015171	A1L3W4|D3DWF9|Q2YDX3|Q53G88|Q68G50|Q76N88|Q96CP8|Q9BT21	Missense_Mutation	SNP	ENST00000304658.5	hg19	CCDS42135.1	.	.	.	.	.	.	.	.	.	.	C	36	5.708014	0.96821	.	.	ENSG00000169180	ENST00000304658	T	0.54071	0.59	5.75	5.75	0.90469	Exportin-1/Importin-beta-like (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.72740	0.3498	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.995	T	0.74754	-0.3558	10	0.87932	D	0	-19.7624	17.4387	0.87559	0.0:1.0:0.0:0.0	.	168;168	B7ZM10;Q96QU8	.;XPO6_HUMAN	L	168	ENSP00000302790:R168L	ENSP00000302790:R168L	R	-	2	0	XPO6	28088634	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.792000	0.85828	2.696000	0.92011	0.655000	0.94253	CGG	.	.	.	none		0.572	XPO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433732.1	XM_055195		A	28181133	C	A	28181133	3	1	184	1	0	0	0	0	1	0	0	0	17460	652	23	4	2954	4	XPO6	16	28181133	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	13047300	28181133	62173620	93	10826											
SH2B1	25970	hgsc.bcm.edu	37	chr16	28880661	28880661	+	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	gagagtctacccagccaggaCctgctgcttggacccagcga	9	6	12	14	1	1	1	0	0	1	1	1	5	1	3	4	2	5	2	4	2	1	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr16:28880661C>A	ENST00000322610.8	+	7	1705	c.1266C>A	c.(1264-1266)gaC>gaA	p.D422E	SH2B1_ENST00000545570.1_Missense_Mutation_p.D112E|SH2B1_ENST00000337120.5_Missense_Mutation_p.D422E|SH2B1_ENST00000395532.4_Missense_Mutation_p.D422E|SH2B1_ENST00000359285.5_Missense_Mutation_p.D422E|SH2B1_ENST00000538342.1_Missense_Mutation_p.D86E|SH2B1_ENST00000563674.1_Intron			Q9NRF2	SH2B1_HUMAN	SH2B adaptor protein 1	422	Interaction with JAK2 (low-affinity binding; independent of JAK2 phosphorylation). {ECO:0000250}.				blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|intracellular signal transduction (GO:0035556)|lamellipodium assembly (GO:0030032)|positive regulation of mitosis (GO:0045840)|regulation of DNA biosynthetic process (GO:2000278)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25						CCAGCCAGGACCTGCTGCTTG	0.632																																					p.D422E		Atlas-SNP	.											.	SH2B1	160	.	0			c.C1266A						PASS	.						50	48	48					16																	28880661		2197	4300	6497	SO:0001583	missense	25970	exon5			CCAGGACCTGCTG	AK055104	CCDS32424.1, CCDS53996.1, CCDS53997.1	16p11.2	2013-02-14						"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	30417	protein-coding gene	gene with protein product	"SH2-B homolog"	608937				11827956, 10594240	Standard	NM_001145812		Approved	FLJ30542, SH2B	uc002drl.3	Q9NRF2		ENST00000322610.8:c.1266C>A	chr16.hg19:g.28880661C>A	ENSP00000321221:p.Asp422Glu	96.0	0.0	.		96.0	35.0	.	NM_001145796	A8K2R7|Q96FK3|Q96SX3|Q9NRF1|Q9NRF3|Q9P2P7|Q9Y3Y3	Missense_Mutation	SNP	ENST00000322610.8	hg19	CCDS53996.1	.	.	.	.	.	.	.	.	.	.	C	10.69	1.420802	0.25639	.	.	ENSG00000178188	ENST00000322610;ENST00000545570;ENST00000359285;ENST00000538342;ENST00000395532;ENST00000337120	T;T;T;T;T;T	0.42131	0.98;1.71;1.01;1.6;1.0;1.0	5.17	-9.53	0.00575	.	0.393219	0.23983	N	0.042660	T	0.11836	0.0288	N	0.03608	-0.345	0.22112	N	0.999357	B;B;B;B;B	0.06786	0.0;0.0;0.0;0.001;0.0	B;B;B;B;B	0.06405	0.0;0.001;0.001;0.002;0.001	T	0.09207	-1.0685	10	0.27082	T	0.32	-14.1712	6.2599	0.20893	0.0853:0.4877:0.1844:0.2426	.	86;112;422;422;422	B4DLN5;F5GXU7;Q9NRF2-2;Q9NRF2-3;Q9NRF2	.;.;.;.;SH2B1_HUMAN	E	422;112;422;86;422;422	ENSP00000321221:D422E;ENSP00000440354:D112E;ENSP00000352232:D422E;ENSP00000438784:D86E;ENSP00000378903:D422E;ENSP00000337163:D422E	ENSP00000321221:D422E	D	+	3	2	SH2B1	28788162	0.011000	0.17503	0.821000	0.32701	0.889000	0.51656	-2.120000	0.01323	-1.453000	0.01928	-0.373000	0.07131	GAC	.	.	.	none		0.632	SH2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000432666.1	NM_015503		A	28880661	C	A	28880661	3	1	184	1	0	0	0	0	1	0	0	0	14240	506	18	4	1280	4	SH2B1	16	28880661	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	699528	28880661	61474092	94	10827											
RABEP2	79874	hgsc.bcm.edu	37	chr16	28925762	28925762	+	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	aggaggagatggaggcgctgTcatcgcagttgtgagcgaag	10	7	18	6	3	1	2	1	1	0	1	2	6	1	4	0	4	1	3	0	4	1	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr16:28925762T>A	ENST00000358201.4	-	5	1277	c.689A>T	c.(688-690)gAc>gTc	p.D230V	RABEP2_ENST00000561803.1_5'Flank|RABEP2_ENST00000357573.6_Missense_Mutation_p.D230V|RABEP2_ENST00000544477.1_Missense_Mutation_p.D159V	NM_024816.2	NP_079092.2	Q9H5N1	RABE2_HUMAN	rabaptin, RAB GTPase binding effector protein 2	230					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						GGAGGCGCTGTCATCGCAGTT	0.682																																					p.D230V	Pancreas(66;639 1284 10093 31061 49099)	Atlas-SNP	.											.	RABEP2	48	.	0			c.A689T						PASS	.						24	30	28					16																	28925762		2041	4205	6246	SO:0001583	missense	79874	exon5			GCGCTGTCATCGC	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.689A>T	chr16.hg19:g.28925762T>A	ENSP00000350934:p.Asp230Val	46.0	0.0	.		48.0	11.0	.	NM_024816		Missense_Mutation	SNP	ENST00000358201.4	hg19	CCDS42140.1	.	.	.	.	.	.	.	.	.	.	T	19.65	3.867523	0.72065	.	.	ENSG00000177548	ENST00000358201;ENST00000357573;ENST00000544477	T;T;T	0.70516	-0.33;-0.49;-0.27	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.74906	0.3778	L	0.29908	0.895	0.53005	D	0.999965	D;D;D;D	0.89917	0.999;1.0;0.998;0.999	D;D;D;D	0.87578	0.996;0.998;0.994;0.996	T	0.77653	-0.2507	10	0.87932	D	0	-35.9958	11.3244	0.49440	0.0:0.0:0.0:1.0	.	159;230;230;230	B4DHR0;Q9H5N1-2;Q49AT6;Q9H5N1	.;.;.;RABE2_HUMAN	V	230;230;159	ENSP00000350934:D230V;ENSP00000350186:D230V;ENSP00000442798:D159V	ENSP00000350186:D230V	D	-	2	0	RABEP2	28833263	1.000000	0.71417	0.997000	0.53966	0.848000	0.48234	5.481000	0.66826	1.933000	0.56026	0.379000	0.24179	GAC	.	.	.	none		0.682	RABEP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432691.1	NM_024816		A	28925762	T	A	28925762	3	1	184	1	0	0	0	0	1	0	0	0	12975	1667	58	5	1056	5	RABEP2	16	28925762	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	45101	28925762	61428991	95	10828											
RNF40	9810	hgsc.bcm.edu	37	chr16	30775599	30775599	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaggaggtggagctggagcTgcaaggccgaatggagttct	9	8	18	6	1	1	1	0	1	1	0	1	6	1	5	1	6	3	4	1	6	2	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr16:30775599T>C	ENST00000324685.6	+	5	977	c.542T>C	c.(541-543)cTg>cCg	p.L181P	C16orf93_ENST00000545825.1_5'Flank|C16orf93_ENST00000543610.1_5'Flank|RNF40_ENST00000563683.1_Missense_Mutation_p.L181P|C16orf93_ENST00000541260.1_5'Flank|RNF40_ENST00000357890.5_Missense_Mutation_p.L181P|RNF40_ENST00000402121.3_Intron	NM_001207033.1|NM_014771.3	NP_001193962.1|NP_055586	O75150	BRE1B_HUMAN	ring finger protein 40, E3 ubiquitin protein ligase	181					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)			GAGCTGGAGCTGCAAGGCCGA	0.632																																					p.L181P		Atlas-SNP	.											.	RNF40	83	.	0			c.T542C						PASS	.						69	56	60					16																	30775599		2197	4300	6497	SO:0001583	missense	9810	exon5			TGGAGCTGCAAGG	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.542T>C	chr16.hg19:g.30775599T>C	ENSP00000325677:p.Leu181Pro	20.0	0.0	.		36.0	11.0	.	NM_014771	Q6AHZ6|Q6N005|Q7L3T6|Q8N615|Q96T18|Q9BSV9|Q9HC82	Missense_Mutation	SNP	ENST00000324685.6	hg19	CCDS10691.1	.	.	.	.	.	.	.	.	.	.	T	17.57	3.423101	0.62733	.	.	ENSG00000103549	ENST00000324685;ENST00000357890;ENST00000452273	T;T	0.60920	0.76;0.15	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000001	T	0.78349	0.4269	M	0.82323	2.585	0.80722	D	1	D;B;B	0.76494	0.999;0.09;0.024	D;B;B	0.85130	0.997;0.06;0.038	T	0.81540	-0.0886	10	0.87932	D	0	-13.9353	15.6114	0.76721	0.0:0.0:0.0:1.0	.	181;181;181	O75150-4;A8K6K1;O75150	.;.;BRE1B_HUMAN	P	181;181;30	ENSP00000325677:L181P;ENSP00000350563:L181P	ENSP00000325677:L181P	L	+	2	0	RNF40	30683100	1.000000	0.71417	1.000000	0.80357	0.822000	0.46500	6.959000	0.76031	2.326000	0.78906	0.533000	0.62120	CTG	.	.	.	none		0.632	RNF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255524.2	NM_014771		C	30775599	T	C	30775599	3	2	184	1	0	0	0	0	1	0	0	0	13506	1580	55	3	556	3	RNF40	16	30775599	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	1849837	30775599	59579154	96	10829											
ITGAM	3684	hgsc.bcm.edu	37	chr16	31340556	31340556	+	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	tttctcccttcagccatgggGtctccactaaatatctcaac	9	13	5	14	0	4	0	2	0	3	0	7	0	4	0	3	2	2	0	3	2	4	4	rs199790913		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr16:31340556G>T	ENST00000287497.8	+	24	2875	c.2800G>T	c.(2800-2802)Gtc>Ttc	p.V934F	ITGAM_ENST00000544665.3_Missense_Mutation_p.V935F			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	934					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)			endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						CAGCCATGGGGTCTCCACTAA	0.542																																					p.V935F		Atlas-SNP	.											.	ITGAM	137	.	0			c.G2803T						PASS	.	G	PHE/VAL,PHE/VAL	0,3888		0,0,1944	71	70	70		2803,2800	-6.6	0	16		70	1,8303		0,1,4151	yes	missense,missense	ITGAM	NM_001145808.1,NM_000632.3	50,50	0,1,6095	TT,TG,GG		0.012,0.0,0.0082	benign,benign	935/1154,934/1153	31340556	1,12191	1944	4152	6096	SO:0001583	missense	3684	exon24			CATGGGGTCTCCA	J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"CD molecules", "Complement system", "Integrins"	6149	protein-coding gene	gene with protein product		120980	"integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.2800G>T	chr16.hg19:g.31340556G>T	ENSP00000287497:p.Val934Phe	31.0	0.0	.		28.0	10.0	.	NM_001145808	Q4VAK0|Q4VAK1|Q4VAK2	Missense_Mutation	SNP	ENST00000287497.8	hg19	CCDS45470.1	.	.	.	.	.	.	.	.	.	.	G	14.20	2.464821	0.43839	0.0	1.2E-4	ENSG00000169896	ENST00000544665;ENST00000287497	T;T	0.44083	0.93;0.93	4.87	-6.59	0.01830	Integrin alpha-2 (1);	.	.	.	.	T	0.31513	0.0799	L	0.44542	1.39	0.09310	N	1	B;B	0.34181	0.44;0.44	B;B	0.41619	0.361;0.361	T	0.41574	-0.9501	9	0.59425	D	0.04	.	1.9836	0.03432	0.3427:0.3574:0.1793:0.1206	.	934;934	Q4VAK1;P11215	.;ITAM_HUMAN	F	935;934	ENSP00000441691:V935F;ENSP00000287497:V934F	ENSP00000287497:V934F	V	+	1	0	ITGAM	31248057	0.000000	0.05858	0.000000	0.03702	0.074000	0.17049	-0.727000	0.04931	-1.560000	0.01686	-0.903000	0.02851	GTC	.	.	.	weak		0.542	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632		T	31340556	G	T	31340556	3	4	184	1	0	0	0	0	1	0	0	0	7894	1261	44	4	2897	4	ITGAM	16	31340556	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	564957	31340556	59014197	97	10830											
PHKB	5257	hgsc.bcm.edu	37	chr16	47684490	47684490	+	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	attaaacaatattggaaaatGcatggacgtccacttttcct	14	13	6	8	1	0	0	0	0	0	0	2	2	2	2	2	2	2	1	2	2	6	5			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr16:47684490G>T	ENST00000323584.5	+	19	1857	c.1833G>T	c.(1831-1833)atG>atT	p.M611I	PHKB_ENST00000299167.8_Missense_Mutation_p.M611I|PHKB_ENST00000566044.1_Missense_Mutation_p.M604I|PHKB_ENST00000455779.1_Missense_Mutation_p.M604I	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	611					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				ATTGGAAAATGCATGGACGTC	0.408																																					p.M611I		Atlas-SNP	.											.	PHKB	298	.	0			c.G1833T						PASS	.						137	120	126					16																	47684490		2201	4300	6501	SO:0001583	missense	5257	exon19			GAAAATGCATGGA		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.1833G>T	chr16.hg19:g.47684490G>T	ENSP00000313504:p.Met611Ile	140.0	0.0	.		120.0	40.0	.	NM_000293	Q8N4T5	Missense_Mutation	SNP	ENST00000323584.5	hg19	CCDS10729.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.004653	0.74932	.	.	ENSG00000102893	ENST00000299167;ENST00000455779;ENST00000323584	D;D	0.90900	-2.75;-2.75	5.86	5.86	0.93980	Glycoside hydrolase 15-related (1);	0.036486	0.85682	D	0.000000	D	0.91432	0.7296	M	0.73598	2.24	0.80722	D	1	B;B	0.26902	0.036;0.163	B;B	0.29862	0.098;0.108	D	0.88208	0.2888	10	0.44086	T	0.13	-27.2635	20.1813	0.98205	0.0:0.0:1.0:0.0	.	611;604	Q93100;Q93100-4	KPBB_HUMAN;.	I	604;604;611	ENSP00000414345:M604I;ENSP00000313504:M611I	ENSP00000299167:M604I	M	+	3	0	PHKB	46241991	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.172000	0.94808	2.777000	0.95525	0.591000	0.81541	ATG	.	.	.	none		0.408	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1			T	47684490	G	T	47684490	3	4	184	1	0	0	0	0	1	0	0	0	11852	1319	46	4	1966	4	PHKB	16	47684490	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	16343934	47684490	42670263	98	10831											
SKAP1	8631	hgsc.bcm.edu	37	chr17	46423341	46423341	+	Frame_Shift_Del	DEL	T	T	-																															gagtcccgctgtgattatcaTcagagctgtcctgtccaatg																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr17:46423341delT	ENST00000336915.6	-	4	275	c.206delA	c.(205-207)gatfs	p.D70fs	SKAP1_ENST00000584924.1_Frame_Shift_Del_p.D70fs	NM_001075099.1|NM_003726.3	NP_001068567.1|NP_003717.3	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1	70					positive regulation of signal transduction (GO:0009967)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|SH2 domain binding (GO:0042169)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)			large_intestine(1)|lung(10)|prostate(2)|skin(4)|urinary_tract(1)	18						GTGATTATCATCAGAGCTGTC	0.438																																					p.D69fs		Atlas-INDEL	.											.	SKAP1	41	.	0			c.207delT						PASS	.						80	70	73					17																	46423341		2203	4300	6503	SO:0001589	frameshift_variant	8631	exon4			.	Y11215	CCDS32674.1	17q21.32	2013-01-10	2006-09-28	2006-09-28		ENSG00000141293		"Pleckstrin homology (PH) domain containing"	15605	protein-coding gene	gene with protein product		604969	"src family associated phosphoprotein 1"	SCAP1		9195899	Standard	NM_003726		Approved	SKAP55	uc002ini.1	Q86WV1		ENST00000336915.6:c.206delA	chr17.hg19:g.46423341delT	ENSP00000338171:p.Asp70fs	55.0	0.0	0		67.0	30.0	0.447761	NM_001075099	D3DTV1|O15268	Frame_Shift_Del	DEL	ENST00000336915.6	hg19	CCDS32674.1																																																																																			.	.	.	none		0.438	SKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443432.1	NM_003726		-	46423341	T	-	46423341	7	5	184	1	0	1	0	1	0	0	0	0	14368	1435	50	0	909	0	SKAP1	17	46423341	Frame_Shift_Del	DEL	T	TCGA-GL-7773-01A-11D-2136-08		46423341	34771869	99	10832											
HELZ	9931	hgsc.bcm.edu	37	chr17	65134124	65134125	+	Missense_Mutation	DNP	TG	TG	GA																															cagcacgtattctaaacactTgatcagcatatggagtcacc																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr17:65134124_65134125TG>GA	ENST00000358691.5	-	22	3041_3042	c.2875_2876CA>TC	c.(2875-2877)CAa>TCa	p.Q959S	HELZ_ENST00000580168.1_Missense_Mutation_p.Q960S	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	959						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)					TCTAAACACTTGATCAGCATAT	0.401																																					p.Q959P|p.Q959X		Atlas-SNP	.											.	HELZ	160	.	0			c.A2876C|c.C2875T						PASS	.																																			SO:0001583	missense	9931	exon22			AACACTTGATCAG|ACACTTGATCAGC	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.2875_2876delinsGA	chr17.hg19:g.65134124_65134125delinsGA	ENSP00000351524:p.Gln959Ser	174.0|173.0	0.0	.		203.0|197.0	74.0	.	NM_014877	I6L9H4	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000358691.5	hg19	CCDS42374.1																																																																																			.	.	.	none		0.401	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		GA	65134125	TG	GA	65134124	3	3	184	1	0	0	0	0	1	0	0	0	7056	1812	63	5	3000	5	HELZ	17	65134124	Missense_Mutation	DNP	TG	TCGA-GL-7773-01A-11D-2136-08	18710783	65134124	16061086	100	10833											
COG1	9382	hgsc.bcm.edu	37	chr17	71197359	71197359	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actccccttcaaataagcacAtccactttgagtacaacatg	14	10	4	13	0	1	1	1	1	0	0	3	1	3	1	3	0	3	2	3	0	4	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr17:71197359A>G	ENST00000299886.4	+	7	1473	c.1393A>G	c.(1393-1395)Atc>Gtc	p.I465V		NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	465					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)			AAATAAGCACATCCACTTTGA	0.522																																					p.I465V		Atlas-SNP	.											.	COG1	46	.	0			c.A1393G						PASS	.						161	147	152					17																	71197359		2203	4300	6503	SO:0001583	missense	9382	exon7			AAGCACATCCACT		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.1393A>G	chr17.hg19:g.71197359A>G	ENSP00000299886:p.Ile465Val	187.0	0.0	.		195.0	69.0	.	NM_018714	Q9NPV9|Q9P2G6	Missense_Mutation	SNP	ENST00000299886.4	hg19	CCDS11692.1	.	.	.	.	.	.	.	.	.	.	A	6.539	0.467704	0.12402	.	.	ENSG00000166685	ENST00000438720;ENST00000299886	T;T	0.19938	2.11;2.11	5.28	-4.74	0.03249	.	0.662686	0.16490	N	0.212142	T	0.08714	0.0216	N	0.17674	0.51	0.09310	N	0.999994	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.40924	-0.9537	10	0.07990	T	0.79	-9.3358	8.8132	0.34981	0.3346:0.2123:0.4531:0.0	.	465;465;465	E9PBL8;Q8WTW3;Q4G0L8	.;COG1_HUMAN;.	V	465	ENSP00000400111:I465V;ENSP00000299886:I465V	ENSP00000299886:I465V	I	+	1	0	COG1	68708954	0.000000	0.05858	0.363000	0.25875	0.372000	0.29890	-0.711000	0.05019	-0.776000	0.04578	-0.250000	0.11733	ATC	.	.	.	none		0.522	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441638.1			G	71197359	A	G	71197359	3	3	184	1	0	0	0	0	1	0	0	0	3659	217	8	3	1419	3	COG1	17	71197359	Missense_Mutation	SNP	A	TCGA-GL-7773-01A-11D-2136-08	6063235	71197359	9997851	101	10834											
KIAA0802	23255	hgsc.bcm.edu	37	chr18	8813134	8813135	+	Frame_Shift_Ins	INS	-	-	T																															atccatcacagcgagaagaaINSctggaaccgggagaaggtgg																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr18:8813134_8813135insT	ENST00000306329.11	+	10	3719_3720	c.3719_3720insT	c.(3718-3723)aactggfs	p.W1241fs	SOGA2_ENST00000306285.7_Frame_Shift_Ins_p.W275fs|SOGA2_ENST00000359865.3_Frame_Shift_Ins_p.W922fs|SOGA2_ENST00000400050.3_Frame_Shift_Ins_p.W881fs|SOGA2_ENST00000517570.1_Frame_Shift_Ins_p.W881fs|SOGA2_ENST00000518815.1_Frame_Shift_Ins_p.W275fs																							AGCGAGAAGAACTGGAACCGGG	0.574																																					p.N921fs		Atlas-INDEL	.											.	.	.	.	0			c.2762_2763insT						PASS	.																																			SO:0001589	frameshift_variant	23255	exon12			.																												Exception_encountered	chr18.hg19:g.8813134_8813135insT	ENSP00000305027:p.Trp1241fs	37.0	0.0	0		26.0	14.0	0.538462	NM_015210		Frame_Shift_Ins	INS	ENST00000306329.11	hg19																																																																																				.	.	.	none		0.574	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1			T	8813135	-	T	8813134	7	5	184	1	0	1	1	0	0	0	0	0	8201	43	2	0	2800	0	KIAA0802	18	8813134	Frame_Shift_Ins	INS	-	TCGA-GL-7773-01A-11D-2136-08		8813134	69264114	102	10835	101	2									
KIAA0802	23255	hgsc.bcm.edu	37	chr18	8813135	8813135	+	Silent	SNP	C	C	T																															atccatcacagcgagaagaaCtggaaccgggagaaggtgga																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr18:8813135C>T	ENST00000306329.11	+	10	3720	c.3720C>T	c.(3718-3720)aaC>aaT	p.N1240N	SOGA2_ENST00000306285.7_Silent_p.N274N|SOGA2_ENST00000359865.3_Silent_p.N921N|SOGA2_ENST00000400050.3_Silent_p.N880N|SOGA2_ENST00000517570.1_Silent_p.N880N|SOGA2_ENST00000518815.1_Silent_p.N274N																							GCGAGAAGAACTGGAACCGGG	0.572																																					p.N921N		Atlas-SNP	.											.	.	.	.	0			c.C2763T						PASS	.						45	44	44					18																	8813135		2203	4300	6503	SO:0001819	synonymous_variant	23255	exon12			GAAGAACTGGAAC																												ENST00000306329.11:c.3720C>T	chr18.hg19:g.8813135C>T		36.0	0.0	.		26.0	14.0	.	NM_015210		Silent	SNP	ENST00000306329.11	hg19																																																																																				.	.	.	none		0.572	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1			T	8813135	C	T	8813135	2	4	184	1	0	0	0	0	0	0	0	1	8201	564	20	2		2	KIAA0802	18	8813135	Silent	SNP	C	TCGA-GL-7773-01A-11D-2136-08	1	8813135	69264113	103	10836	101	2									
ZNF599	148103	hgsc.bcm.edu	37	chr19	35250173	35250173	+	Missense_Mutation	SNP	T	T	A																															tgggtaaaagcctttccacaTtctctacaaacatagggctt																								rs375598988		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr19:35250173T>A	ENST00000329285.8	-	4	1906	c.1533A>T	c.(1531-1533)gaA>gaT	p.E511D		NM_001007248.2	NP_001007249.1	Q96NL3	ZN599_HUMAN	zinc finger protein 599	511					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|skin(1)	24	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			CCTTTCCACATTCTCTACAAA	0.418																																					p.E511D		Atlas-SNP	.											.	ZNF599	72	.	0			c.A1533T						PASS	.						116	117	116					19																	35250173		2203	4300	6503	SO:0001583	missense	148103	exon4			TCCACATTCTCTA	AK055225	CCDS32991.1	19q13.13	2013-01-08				ENSG00000153896		"Zinc fingers, C2H2-type", "-"	26408	protein-coding gene	gene with protein product							Standard	NM_001007248		Approved	FLJ30663	uc010edn.1	Q96NL3		ENST00000329285.8:c.1533A>T	chr19.hg19:g.35250173T>A	ENSP00000333802:p.Glu511Asp	136.0	0.0	.		173.0	71.0	.	NM_001007248	Q569K0|Q5PRG1	Missense_Mutation	SNP	ENST00000329285.8	hg19	CCDS32991.1	.	.	.	.	.	.	.	.	.	.	T	4.110	0.018610	0.07959	.	.	ENSG00000153896	ENST00000392231;ENST00000329285;ENST00000392229	T	0.07444	3.19	2.52	1.45	0.22620	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07143	0.0181	L	0.50993	1.605	0.58432	D	0.999999	B	0.06786	0.001	B	0.11329	0.006	T	0.24905	-1.0147	9	0.45353	T	0.12	.	2.0678	0.03606	0.2607:0.1492:0.0:0.5901	.	511	Q96NL3	ZN599_HUMAN	D	510;511;285	ENSP00000333802:E511D	ENSP00000333802:E511D	E	-	3	2	ZNF599	39942013	0.000000	0.05858	0.906000	0.35671	0.133000	0.20885	-1.206000	0.03011	0.357000	0.24183	0.482000	0.46254	GAA	.	.	.	alt		0.418	ZNF599-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460648.2	XM_086046		A	35250173	T	A	35250173	3	1	184	1	0	0	0	0	1	0	0	0	18041	1490	52	5	237	5	ZNF599	19	35250173	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08		35250173	23878810	104	10837	102	2									
ZNF599	148103	hgsc.bcm.edu	37	chr19	35250175	35250175	+	Nonsense_Mutation	SNP	C	C	A																															ggtaaaagcctttccacattCtctacaaacatagggcttct																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr19:35250175C>A	ENST00000329285.8	-	4	1904	c.1531G>T	c.(1531-1533)Gaa>Taa	p.E511*		NM_001007248.2	NP_001007249.1	Q96NL3	ZN599_HUMAN	zinc finger protein 599	511					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|skin(1)	24	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			TTTCCACATTCTCTACAAACA	0.418																																					p.E511X		Atlas-SNP	.											.	ZNF599	72	.	0			c.G1531T						PASS	.						115	117	116					19																	35250175		2203	4300	6503	SO:0001587	stop_gained	148103	exon4			CACATTCTCTACA	AK055225	CCDS32991.1	19q13.13	2013-01-08				ENSG00000153896		"Zinc fingers, C2H2-type", "-"	26408	protein-coding gene	gene with protein product							Standard	NM_001007248		Approved	FLJ30663	uc010edn.1	Q96NL3		ENST00000329285.8:c.1531G>T	chr19.hg19:g.35250175C>A	ENSP00000333802:p.Glu511*	142.0	0.0	.		176.0	71.0	.	NM_001007248	Q569K0|Q5PRG1	Nonsense_Mutation	SNP	ENST00000329285.8	hg19	CCDS32991.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.544924	0.86022	.	.	ENSG00000153896	ENST00000392231;ENST00000329285;ENST00000392229	.	.	.	2.52	2.52	0.30459	.	.	.	.	.	.	.	.	.	.	.	0.19300	N	0.999974	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	11.1742	0.48590	0.0:1.0:0.0:0.0	.	.	.	.	X	510;511;285	.	ENSP00000333802:E511X	E	-	1	0	ZNF599	39942015	0.000000	0.05858	0.726000	0.30738	0.087000	0.18053	0.077000	0.14738	1.711000	0.51337	0.591000	0.81541	GAA	.	.	.	none		0.418	ZNF599-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460648.2	XM_086046		A	35250175	C	A	35250175	4	1	184	1	0	0	0	0	0	1	0	0	18041	922	32	4	239	4	ZNF599	19	35250175	Nonsense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	2	35250175	23878808	105	10838	102	2									
SALL4	57167	hgsc.bcm.edu	37	chr20	50407897	50407897	+	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	tgcttgtagagggccgcctcGtctttgggtttgacatccac	5	13	12	11	2	1	2	0	1	1	1	3	2	2	2	3	2	1	3	3	2	1	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr20:50407897G>C	ENST00000217086.4	-	2	1236	c.1125C>G	c.(1123-1125)gaC>gaG	p.D375E	SALL4_ENST00000371539.3_Intron|SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000395997.3_Missense_Mutation_p.D375E	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	375					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						GGGCCGCCTCGTCTTTGGGTT	0.547																																					p.D375E		Atlas-SNP	.											.	SALL4	168	.	0			c.C1125G						PASS	.						78	76	77					20																	50407897		2203	4300	6503	SO:0001583	missense	57167	exon2			CGCCTCGTCTTTG	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.1125C>G	chr20.hg19:g.50407897G>C	ENSP00000217086:p.Asp375Glu	134.0	0.0	.		128.0	45.0	.	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Missense_Mutation	SNP	ENST00000217086.4	hg19	CCDS13438.1	.	.	.	.	.	.	.	.	.	.	G	4.854	0.158821	0.09236	.	.	ENSG00000101115	ENST00000217086;ENST00000395997	T;T	0.08807	3.05;3.34	5.29	-5.33	0.02713	.	0.000000	0.47852	D	0.000204	T	0.08044	0.0201	L	0.29908	0.895	0.80722	D	1	B;D	0.69078	0.028;0.997	B;D	0.76575	0.006;0.988	T	0.49781	-0.8903	10	0.02654	T	1	-53.0902	4.1442	0.10209	0.5133:0.168:0.2268:0.0919	.	375;375	A2A2D8;Q9UJQ4	.;SALL4_HUMAN	E	375	ENSP00000217086:D375E;ENSP00000379319:D375E	ENSP00000217086:D375E	D	-	3	2	SALL4	49841304	0.000000	0.05858	0.608000	0.28969	0.091000	0.18340	-1.867000	0.01646	-0.896000	0.03915	-1.581000	0.00855	GAC	.	.	.	none		0.547	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			C	50407897	G	C	50407897	3	2	184	1	0	0	0	0	1	0	0	0	13826	1136	40	4	2048	4	SALL4	20	50407897	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08		50407897	12617623	106	10839											
RGL4	266747	hgsc.bcm.edu	37	chr22	24034222	24034222	+	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	cagatctggagctttgatgaGgaagctgctcacaaatctgc	11	10	11	9	0	3	3	1	2	2	1	3	5	3	5	0	2	4	3	0	2	2	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr22:24034222G>A	ENST00000290691.5	+	1	1175	c.5G>A	c.(4-6)aGg>aAg	p.R2K	AP000347.2_ENST00000417194.1_RNA|KB-1572G7.2_ENST00000421064.1_RNA|GUSBP11_ENST00000455485.1_RNA|RGL4_ENST00000401461.1_Intron	NM_153615.1	NP_705843.1	Q8IZJ4	RGDSR_HUMAN	ral guanine nucleotide dissociation stimulator-like 4	2					small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)	guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(3)	15						GCTTTGATGAGGAAGCTGCTC	0.607																																					p.R2K		Atlas-SNP	.											.	RGL4	29	.	0			c.G5A						PASS	.						59	58	58					22																	24034222		2203	4300	6503	SO:0001583	missense	266747	exon1			TGATGAGGAAGCT		CCDS13811.1	22q11.23	2008-02-22			ENSG00000159496	ENSG00000159496			31911	protein-coding gene	gene with protein product	"RalGDS related oncogene"	612214				9178890, 10851075	Standard	NM_153615		Approved	Rgr	uc002zxn.3	Q8IZJ4	OTTHUMG00000150711	ENST00000290691.5:c.5G>A	chr22.hg19:g.24034222G>A	ENSP00000290691:p.Arg2Lys	109.0	0.0	.		88.0	5.0	.	NM_153615	Q495L8	Missense_Mutation	SNP	ENST00000290691.5	hg19	CCDS13811.1	.	.	.	.	.	.	.	.	.	.	g	8.750	0.921142	0.17982	.	.	ENSG00000159496	ENST00000290691;ENST00000382833;ENST00000423392	T;T	0.32023	1.47;1.47	1.77	-2.54	0.06307	.	7.772780	0.01150	U	0.006397	T	0.18215	0.0437	N	0.14661	0.345	0.09310	N	1	B;B	0.09022	0.002;0.0	B;B	0.08055	0.003;0.0	T	0.27536	-1.0071	10	0.87932	D	0	.	4.1084	0.10047	0.1754:0.4809:0.3436:0.0	.	2;2	E9PH87;Q8IZJ4	.;RGDSR_HUMAN	K	2	ENSP00000290691:R2K;ENSP00000402142:R2K	ENSP00000290691:R2K	R	+	2	0	RGL4	22364222	0.139000	0.22563	0.000000	0.03702	0.001000	0.01503	-0.102000	0.10956	-0.558000	0.06118	-0.386000	0.06593	AGG	.	.	.	none		0.607	RGL4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319711.1	NM_153615		A	24034222	G	A	24034222	3	1	184	1	0	0	0	0	1	0	0	0	13292	1000	35	2	7	2	RGL4	22	24034222	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08		24034222	27270344	107	10840											
MICALL1	85377	hgsc.bcm.edu	37	chr22	38328888	38328888	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcggcgagagtccgagctcAtctatgtgtgagtccccccg	6	9	13	13	4	2	2	1	1	1	1	4	4	4	2	4	1	2	1	4	1	1	1			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr22:38328888A>G	ENST00000215957.6	+	12	2353	c.2227A>G	c.(2227-2229)Atc>Gtc	p.I743V	MICALL1_ENST00000402631.1_3'UTR	NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1	743	Necessary and sufficient to associate with tubular recycling endosome membranes, mediate phosphatidic acid- binding and membrane tubulation.|RAB-binding domain (RBD); mediates the interaction with RAB13 and RAB35 and intramolecular interaction with the CH domain.				endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|neuron projection development (GO:0031175)|protein localization to endosome (GO:0036010)|protein targeting to membrane (GO:0006612)|receptor-mediated endocytosis (GO:0006898)|retrograde transport, endosome to plasma membrane (GO:1990126)|slow endocytic recycling (GO:0032458)	extrinsic component of membrane (GO:0019898)|late endosome (GO:0005770)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	24	Melanoma(58;0.045)					GTCCGAGCTCATCTATGTGTG	0.582																																					p.I743V		Atlas-SNP	.											.	MICALL1	53	.	0			c.A2227G						PASS	.						68	63	65					22																	38328888		2203	4300	6503	SO:0001583	missense	85377	exon12			GAGCTCATCTATG	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.2227A>G	chr22.hg19:g.38328888A>G	ENSP00000215957:p.Ile743Val	67.0	0.0	.		77.0	31.0	.	NM_033386	Q5TI16|Q7RTP5|Q8N3N8|Q9BVL9|Q9BY92|Q9UH43|Q9UH44|Q9UH45	Missense_Mutation	SNP	ENST00000215957.6	hg19	CCDS13961.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.26|13.26	2.184944|2.184944	0.38609|0.38609	.|.	.|.	ENSG00000100139|ENSG00000100139	ENST00000454685|ENST00000215957;ENST00000402631;ENST00000424008	.|T;T;T	.|0.39406	.|1.08;1.08;1.08	5.47|5.47	4.37|4.37	0.52481|0.52481	.|Domain of unknown function DUF3585 (1);	.|0.102897	.|0.43919	.|D	.|0.000508	T|T	0.16854|0.16854	0.0405|0.0405	N|N	0.02960|0.02960	-0.455|-0.455	0.40194|0.40194	D|D	0.97743|0.97743	.|B	.|0.34329	.|0.449	.|B	.|0.34873	.|0.191	T|T	0.09796|0.09796	-1.0658|-1.0658	5|10	.|0.19147	.|T	.|0.46	.|.	6.8248|6.8248	0.23876|0.23876	0.7709:0.1531:0.076:0.0|0.7709:0.1531:0.076:0.0	.|.	.|743	.|Q8N3F8	.|MILK1_HUMAN	R|V	318|743;170;57	.|ENSP00000215957:I743V;ENSP00000384608:I170V;ENSP00000416766:I57V	.|ENSP00000215957:I743V	H|I	+|+	2|1	0|0	MICALL1|MICALL1	36658834|36658834	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	5.031000|5.031000	0.64134|0.64134	2.070000|2.070000	0.61991|0.61991	0.482000|0.482000	0.46254|0.46254	CAT|ATC	.	.	.	none		0.582	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319545.4	NM_033386		G	38328888	A	G	38328888	3	3	184	1	0	0	0	0	1	0	0	0	9580	217	8	3	2273	3	MICALL1	22	38328888	Missense_Mutation	SNP	A	TCGA-GL-7773-01A-11D-2136-08	14294666	38328888	12975678	108	10841											
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-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chr22:40816901C>G	ENST00000355630.3	-	10	1421	c.831G>C	c.(829-831)caG>caC	p.Q277H	MKL1_ENST00000396617.3_Missense_Mutation_p.Q277H|MKL1_ENST00000407029.1_Missense_Mutation_p.Q277H|MKL1_ENST00000402042.1_Missense_Mutation_p.Q227H	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	chr22.hg19:g.40816901C>G	ENSP00000347847:p.Gln277His	59.0	0.0	.		72.0	4.0	.	NM_020831	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Missense_Mutation	SNP	ENST00000355630.3	hg19	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	184	1	0	0	0	0	1	0	0	0	9608	796	28	4	1988	4	MKL1	22	40816901	Missense_Mutation	SNP	C	TCGA-GL-7773-01A-11D-2136-08	2488013	40816901	10487665	109	10842											
ARMCX1	51309	hgsc.bcm.edu	37	chrX	100808732	100808733	+	Frame_Shift_Ins	INS	-	-	T																															cttacaatgcccttaataacINSttgagtgtgaacgcagaaaa																										TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chrX:100808732_100808733insT	ENST00000372829.3	+	4	1190_1191	c.819_820insT	c.(820-822)ttgfs	p.L274fs		NM_016608.1	NP_057692.1	Q9P291	ARMX1_HUMAN	armadillo repeat containing, X-linked 1	274						integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(2)|ovary(3)|pancreas(1)|urinary_tract(1)	19						CCCTTAATAACTTGAGTGTGAA	0.426																																					p.N273fs		Atlas-INDEL	.											.	ARMCX1	67	.	0			c.819_820insT						PASS	.																																			SO:0001589	frameshift_variant	51309	exon4			.	AB039670	CCDS14487.1	Xq21.33-q22.2	2014-03-21			ENSG00000126947	ENSG00000126947		"Armadillo repeat containing"	18073	protein-coding gene	gene with protein product		300362				11162520, 16221301, 22569362	Standard	NM_016608		Approved	ALEX1, GASP7	uc004ehv.3	Q9P291	OTTHUMG00000022033	ENST00000372829.3:c.821dupT	chrX.hg19:g.100808734_100808734dupT	ENSP00000361917:p.Leu274fs	96.0	0.0	0		103.0	44.0	0.427184	NM_016608	Q53HK2|Q9H2Q0	Frame_Shift_Ins	INS	ENST00000372829.3	hg19	CCDS14487.1																																																																																			.	.	.	none		0.426	ARMCX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057561.1	NM_016608		T	100808733	-	T	100808732	7	5	184	1	0	1	1	0	0	0	0	0	959	564	20	0	821	0	ARMCX1	23	100808732	Frame_Shift_Ins	INS	-	TCGA-GL-7773-01A-11D-2136-08		100808732	54461828	110	10843											
PLS3	5358	hgsc.bcm.edu	37	chrX	114883786	114883786	+	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	ctagaagaatcggagccagaGtgtatgctctccctgaagac	12	8	11	10	1	1	5	0	1	1	4	3	6	1	6	2	1	2	2	2	1	5	2			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chrX:114883786G>C	ENST00000420625.2	+	16	1932	c.1798G>C	c.(1798-1800)Gtg>Ctg	p.V600L	PLS3_ENST00000537301.1_Missense_Mutation_p.V587L|PLS3_ENST00000543070.1_Missense_Mutation_p.V194L|PLS3_ENST00000355899.3_Missense_Mutation_p.V600L|PLS3_ENST00000289290.3_Missense_Mutation_p.V564L|PLS3_ENST00000539310.1_Missense_Mutation_p.V555L	NM_001136025.3|NM_001172335.1|NM_001282338.1	NP_001129497.1|NP_001165806.1|NP_001269267.1	P13797	PLST_HUMAN	plastin 3	600	Actin-binding 2.|CH 4. {ECO:0000255|PROSITE- ProRule:PRU00044}.				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						CGGAGCCAGAGTGTATGCTCT	0.433																																					p.V600L	Colon(160;1047 1864 8490 12969 29601)	Atlas-SNP	.											.	PLS3	60	.	0			c.G1798C						PASS	.						161	136	145					X																	114883786		2203	4300	6503	SO:0001583	missense	5358	exon16			GCCAGAGTGTATG	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.1798G>C	chrX.hg19:g.114883786G>C	ENSP00000398945:p.Val600Leu	156.0	0.0	.		183.0	72.0	.	NM_005032	A8K579|B1AQ09|B4DGB4|B7Z6M1|Q86YI6	Missense_Mutation	SNP	ENST00000420625.2	hg19	CCDS14568.1	.	.	.	.	.	.	.	.	.	.	G	12.11	1.840800	0.32513	.	.	ENSG00000102024	ENST00000355899;ENST00000537301;ENST00000289290;ENST00000420625;ENST00000539310;ENST00000543070	D;D;D;D;D;D	0.95001	-3.58;-3.58;-3.58;-3.58;-3.58;-3.58	5.59	5.59	0.84812	Calponin homology domain (5);	0.053518	0.85682	D	0.000000	D	0.95367	0.8496	M	0.81942	2.565	0.80722	D	1	B;B;B	0.21606	0.02;0.058;0.009	B;B;B	0.39771	0.309;0.306;0.215	D	0.93807	0.7106	10	0.87932	D	0	-7.9383	10.9343	0.47237	0.0886:0.0:0.9114:0.0	.	573;587;600	B4DPW9;B4DGB4;P13797	.;.;PLST_HUMAN	L	600;587;564;600;555;194	ENSP00000348163:V600L;ENSP00000445105:V587L;ENSP00000289290:V564L;ENSP00000398945:V600L;ENSP00000445339:V555L;ENSP00000439260:V194L	ENSP00000289290:V564L	V	+	1	0	PLS3	114790042	1.000000	0.71417	0.983000	0.44433	0.191000	0.23601	7.881000	0.87252	2.494000	0.84150	0.594000	0.82650	GTG	.	.	.	none		0.433	PLS3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057976.2			C	114883786	G	C	114883786	3	2	184	1	0	0	0	0	1	0	0	0	12115	1029	36	4	1856	4	PLS3	23	114883786	Missense_Mutation	SNP	G	TCGA-GL-7773-01A-11D-2136-08	14075054	114883786	40386774	111	10844											
WDR44	54521	hgsc.bcm.edu	37	chrX	117526750	117526750	+	Missense_Mutation	SNP	T	T	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	cccggactgttagccatagaTcaagtactaccggaagaatc	13	8	9	11	2	1	2	1	0	0	2	2	4	1	4	3	2	3	2	3	2	7	4			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chrX:117526750T>G	ENST00000254029.3	+	4	737	c.342T>G	c.(340-342)gaT>gaG	p.D114E	WDR44_ENST00000493448.1_3'UTR|WDR44_ENST00000371825.3_Missense_Mutation_p.D114E|WDR44_ENST00000371822.5_Missense_Mutation_p.D89E	NM_019045.4	NP_061918.3	Q5JSH3	WDR44_HUMAN	WD repeat domain 44	114	Binding activity.					endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	33						TAGCCATAGATCAAGTACTAC	0.403																																					p.D114E		Atlas-SNP	.											.	WDR44	188	.	0			c.T342G						PASS	.						88	83	85					X																	117526750		2203	4300	6503	SO:0001583	missense	54521	exon4			CATAGATCAAGTA	AK001978	CCDS14572.1, CCDS55482.1, CCDS55483.1	Xq24	2013-01-09			ENSG00000131725	ENSG00000131725		"WD repeat domain containing"	30512	protein-coding gene	gene with protein product						12477932	Standard	NM_019045		Approved	DKFZp686L20145, RPH11, RAB11BP	uc004eqn.3	Q5JSH3	OTTHUMG00000022254	ENST00000254029.3:c.342T>G	chrX.hg19:g.117526750T>G	ENSP00000254029:p.Asp114Glu	159.0	0.0	.		190.0	78.0	.	NM_001184965	B4DSE9|F8W913|Q0JS52|Q0JTF3|Q5JSH2|Q6ZSC1|Q7Z365|Q7Z3P6|Q8NAU8|Q8NHU5|Q9NUV4	Missense_Mutation	SNP	ENST00000254029.3	hg19	CCDS14572.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.058|0.058	-1.232190|-1.232190	0.01505|0.01505	.|.	.|.	ENSG00000131725|ENSG00000131725	ENST00000371822;ENST00000254029;ENST00000371825|ENST00000371848	T;T;T|.	0.71579|.	-0.58;0.02;0.15|.	5.68|5.68	0.195|0.195	0.15151|0.15151	.|.	0.637812|.	0.17319|.	N|.	0.178592|.	T|T	0.09949|0.09949	0.0244|0.0244	N|N	0.04508|0.04508	-0.205|-0.205	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	0.26326|0.26326	-1.0106|-1.0106	10|5	0.08179|.	T|.	0.78|.	-1.0257|-1.0257	1.5608|1.5608	0.02594|0.02594	0.3214:0.0908:0.3459:0.2419|0.3214:0.0908:0.3459:0.2419	.|.	89;114;114|.	F8W913;Q5JSH3-2;Q5JSH3|.	.;.;WDR44_HUMAN|.	E|A	89;114;114|14	ENSP00000360887:D89E;ENSP00000254029:D114E;ENSP00000360890:D114E|.	ENSP00000254029:D114E|.	D|S	+|+	3|1	2|0	WDR44|WDR44	117410778|117410778	0.397000|0.397000	0.25270|0.25270	0.074000|0.074000	0.20217|0.20217	0.110000|0.110000	0.19582|0.19582	0.688000|0.688000	0.25422|0.25422	-0.017000|-0.017000	0.14103|0.14103	0.486000|0.486000	0.48141|0.48141	GAT|TCA	.	.	.	none		0.403	WDR44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058001.1	NM_019045		G	117526750	T	G	117526750	3	3	184	1	0	0	0	0	1	0	0	0	17308	1432	50	5	356	5	WDR44	23	117526750	Missense_Mutation	SNP	T	TCGA-GL-7773-01A-11D-2136-08	2642964	117526750	37743810	112	10845											
THOC2	57187	hgsc.bcm.edu	37	chrX	122801090	122801090	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgccaatcaccaatctttaAtaaggcttccaacaagccaa	15	10	4	12	0	2	0	1	0	1	0	3	0	3	0	4	1	3	1	4	1	7	5			TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chrX:122801090A>G	ENST00000245838.8	-	11	1088	c.1057T>C	c.(1057-1059)Tta>Cta	p.L353L	THOC2_ENST00000355725.4_Silent_p.L353L|THOC2_ENST00000491737.1_Silent_p.L238L	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	353					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						CCAATCTTTAATAAGGCTTCC	0.378																																					p.L353L		Atlas-SNP	.											.	THOC2	310	.	0			c.T1057C						PASS	.						138	121	127					X																	122801090		1869	4097	5966	SO:0001819	synonymous_variant	57187	exon11			TCTTTAATAAGGC	AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"THO complex subunits"	19073	protein-coding gene	gene with protein product		300395	"chromosome X open reading frame 3"	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.1057T>C	chrX.hg19:g.122801090A>G		155.0	0.0	.		171.0	64.0	.	NM_001081550	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Silent	SNP	ENST00000245838.8	hg19	CCDS43988.1																																																																																			.	.	.	none		0.378	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3			G	122801090	A	G	122801090	2	3	184	1	0	0	0	0	0	0	0	1	15877	98	4	3		3	THOC2	23	122801090	Silent	SNP	A	TCGA-GL-7773-01A-11D-2136-08	5274340	122801090	32469470	113	10846											
ATP2B3	492	hgsc.bcm.edu	37	chrX	152826336	152826336	+	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	accatcgttttgggcactttCgggattcaggtaggaggggc	7	11	15	8	2	1	0	1	0	0	0	3	2	1	2	1	6	0	3	1	6	1	5	rs181539158		TCGA-GL-7773-01A-11D-2136-08	TCGA-GL-7773-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	10a0f4f1-391f-4eff-9dc9-023a2993549c	06b70c78-6523-4956-a2b4-dd78e80cad60	g.chrX:152826336C>T	ENST00000349466.2	+	18	3368	c.3042C>T	c.(3040-3042)ttC>ttT	p.F1014F	ATP2B3_ENST00000393842.1_Silent_p.F1000F|ATP2B3_ENST00000263519.4_Silent_p.F1014F|ATP2B3_ENST00000359149.3_Silent_p.F1014F|ATP2B3_ENST00000370186.1_Silent_p.F1000F|ATP2B3_ENST00000370181.2_Silent_p.F1000F			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	1014					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)	p.F1014F(5)|p.F1014L(3)|p.F1000F(2)|p.F1000L(1)		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)					TGGGCACTTTCGGGATTCAGG	0.572													C|||	1	0.000264901	8e-04	0	3775	,	,		13946	0		0	False		,,,				2504	0				p.F1014F		Atlas-SNP	.											.	ATP2B3	552	.	11	Substitution - coding silent(7)|Substitution - Missense(4)	lung(4)|breast(4)|large_intestine(3)	c.C3042T						PASS	.						194	141	159					X																	152826336		2203	4300	6503	SO:0001819	synonymous_variant	492	exon17			CACTTTCGGGATT	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.3042C>T	chrX.hg19:g.152826336C>T		114.0	0.0	.		106.0	50.0	.	NM_001001344	B7WNR8|B7WNY5|Q12995|Q16858	Silent	SNP	ENST00000349466.2	hg19	CCDS35440.1																																																																																			.	C|1.000;A|0.000	.	alt		0.572	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060957.1	NM_021949		T	152826336	C	T	152826336	2	4	184	1	0	0	0	0	0	0	0	1	1141	883	31	1		1	ATP2B3	23	152826336	Silent	SNP	C	TCGA-GL-7773-01A-11D-2136-08	30025246	152826336	2444224	114	10847											
CC2D1B	200014	hgsc.bcm.edu	37	chr1	52820569	52820569	+	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	ggatcaccctcttgaagcccCggtggtttcggttgatgttt	5	14	12	10	2	2	2	1	2	1	0	3	3	2	3	3	4	1	3	3	4	1	4			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr1:52820569C>A	ENST00000371586.2	-	22	2438	c.2300G>T	c.(2299-2301)cGg>cTg	p.R767L	CC2D1B_ENST00000438831.1_Missense_Mutation_p.R142L|CC2D1B_ENST00000460261.1_5'UTR|CC2D1B_ENST00000284376.3_Missense_Mutation_p.R761L|RP11-155O18.6_ENST00000606527.1_RNA	NM_032449.2	NP_115825.1	Q5T0F9	C2D1B_HUMAN	coiled-coil and C2 domain containing 1B	767	C2.					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						CTTGAAGCCCCGGTGGTTTCG	0.532																																					p.R767L		Atlas-SNP	.											CC2D1B,NS,carcinoma,0,1	CC2D1B	73	.	0			c.G2300T						PASS	.						135	130	131					1																	52820569		2203	4300	6503	SO:0001583	missense	200014	exon22			AAGCCCCGGTGGT	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.2300G>T	chr1.hg19:g.52820569C>A	ENSP00000360642:p.Arg767Leu	124.0	0.0	.		74.0	3.0	.	NM_032449	Q49AE8|Q5T0F8|Q5T0G0|Q6ZNQ1|Q96AP3|Q96I04|Q96JJ1	Missense_Mutation	SNP	ENST00000371586.2	hg19	CCDS30714.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	36|36	5.756100|5.756100	0.96898|0.96898	.|.	.|.	ENSG00000154222|ENSG00000154222	ENST00000438021;ENST00000450942|ENST00000371586;ENST00000284376;ENST00000371573;ENST00000438831	.|T;T;T	.|0.27256	.|1.68;1.68;1.68	5.65|5.65	5.65|5.65	0.86999|0.86999	.|C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.58892|0.58892	0.2154|0.2154	M|M	0.84846|0.84846	2.72|2.72	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	0.62421|0.62421	-0.6858|-0.6858	5|10	.|0.87932	.|D	.|0	-19.4104|-19.4104	19.9142|19.9142	0.97043|0.97043	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|547;761;767	.|Q5T0G1;Q5T0F9-2;Q5T0F9	.|.;.;C2D1B_HUMAN	W|L	548;681|767;761;675;142	.|ENSP00000360642:R767L;ENSP00000284376:R761L;ENSP00000406300:R142L	.|ENSP00000284376:R761L	G|R	-|-	1|2	0|0	CC2D1B|CC2D1B	52593157|52593157	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.249000|7.249000	0.78278|0.78278	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	GGG|CGG	.	.	.	none		0.532	CC2D1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022189.1	NM_032449		A	52820569	C	A	52820569	3	1	185	1	0	0	0	0	1	0	0	0	2729	652	23	4	288	4	CC2D1B	1	52820569	Missense_Mutation	SNP	C	TCGA-GL-7966-01A-11D-2201-08		52820569	196430052	1	10848											
EVI5	7813	hgsc.bcm.edu	37	chr1	93160869	93160869	+	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	gtctgcccattagcttacctCagacataaagatatcaaata	15	11	5	10	0	3	2	2	0	1	2	3	2	3	2	2	0	3	1	2	0	7	5			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr1:93160869C>G	ENST00000370331.1	-	7	1048	c.1039G>C	c.(1039-1041)Gag>Cag	p.E347Q	EVI5_ENST00000540033.1_Missense_Mutation_p.E347Q|EVI5_ENST00000543509.1_Missense_Mutation_p.E347Q	NM_005665.4	NP_005656.4	O60447	EVI5_HUMAN	ecotropic viral integration site 5	347	Dimerization.|Interaction with alpha-tubulin, gamma- tubulin, BIRC5 and FBXO5.|Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|retrograde transport, endosome to Golgi (GO:0042147)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|skin(1)	38		all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203)		Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211)		TAGCTTACCTCAGACATAAAG	0.423																																					p.E347Q		Atlas-SNP	.											.	EVI5	94	.	0			c.G1039C						PASS	.						107	109	108					1																	93160869		2203	4300	6503	SO:0001583	missense	7813	exon7			TTACCTCAGACAT	AF008915	CCDS30774.1	1p22	2013-07-09			ENSG00000067208	ENSG00000067208			3501	protein-coding gene	gene with protein product	"neuroblastoma stage 4S gene"	602942				9618176	Standard	XM_005271180		Approved	NB4S	uc001dox.3	O60447	OTTHUMG00000010895	ENST00000370331.1:c.1039G>C	chr1.hg19:g.93160869C>G	ENSP00000359356:p.Glu347Gln	135.0	0.0	.		66.0	7.0	.	NM_005665	A6NKX8|B9A6J0|Q9H1Y9	Missense_Mutation	SNP	ENST00000370331.1	hg19	CCDS30774.1	.	.	.	.	.	.	.	.	.	.	C	31	5.084339	0.94100	.	.	ENSG00000067208	ENST00000370331;ENST00000540033;ENST00000543509	T;T;T	0.14766	2.48;2.48;2.48	5.94	5.94	0.96194	Rab-GAP/TBC domain (4);	0.045268	0.85682	D	0.000000	T	0.34424	0.0897	M	0.83223	2.63	0.80722	D	1	D;D	0.60575	0.986;0.988	P;P	0.62560	0.844;0.904	T	0.13282	-1.0515	10	0.87932	D	0	-17.0097	20.3552	0.98837	0.0:1.0:0.0:0.0	.	347;347	F5H4R0;O60447	.;EVI5_HUMAN	Q	347	ENSP00000359356:E347Q;ENSP00000440826:E347Q;ENSP00000445019:E347Q	ENSP00000359356:E347Q	E	-	1	0	EVI5	92933457	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.760000	0.85248	2.812000	0.96745	0.557000	0.71058	GAG	.	.	.	none		0.423	EVI5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030047.1	NM_005665		G	93160869	C	G	93160869	3	3	185	1	0	0	0	0	1	0	0	0	5291	835	29	4	1441	4	EVI5	1	93160869	Missense_Mutation	SNP	C	TCGA-GL-7966-01A-11D-2201-08	40340300	93160869	156089752	2	10849											
OR6Y1	391112	hgsc.bcm.edu	37	chr1	158517503	158517503	+	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	gggtagcgtagtggattacaAatggctacatagcggtcaaa	13	9	13	6	2	1	0	1	0	0	0	1	1	1	1	0	4	4	3	0	4	7	5			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr1:158517503A>T	ENST00000302617.3	-	1	392	c.393T>A	c.(391-393)atT>atA	p.I131I		NM_001005189.1	NP_001005189.1	Q8NGX8	OR6Y1_HUMAN	olfactory receptor, family 6, subfamily Y, member 1	131						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			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)					GTGGATTACAAATGGCTACAT	0.473																																					p.I131I		Atlas-SNP	.											.	OR6Y1	73	.	0			c.T393A						PASS	.						100	85	90					1																	158517503		2202	4300	6502	SO:0001819	synonymous_variant	391112	exon1			ATTACAAATGGCT	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.393T>A	chr1.hg19:g.158517503A>T		100.0	0.0	.		104.0	8.0	.	NM_001005189	Q6IFS0	Silent	SNP	ENST00000302617.3	hg19	CCDS30899.1																																																																																			.	.	.	none		0.473	OR6Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051844.1	NM_001005189		T	158517503	A	T	158517503	2	4	185	1	0	0	0	0	0	0	0	1	11220	10	1	5		5	OR6Y1	1	158517503	Silent	SNP	A	TCGA-GL-7966-01A-11D-2201-08	65356634	158517503	90733118	3	10850											
NUAK2	81788	hgsc.bcm.edu	37	chr1	205274389	205274389	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttcactaggatcttatggTcatgcccatcaaagggcatg	10	12	10	9	0	4	0	3	0	1	0	4	1	4	1	1	3	1	2	1	3	3	3			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr1:205274389T>C	ENST00000367157.3	-	6	887	c.761A>G	c.(760-762)gAc>gGc	p.D254G		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)			GATCTTATGGTCATGCCCATC	0.572																																					p.D254G		Atlas-SNP	.											.	NUAK2	107	.	0			c.A761G						PASS	.						98	83	88					1																	205274389		2203	4300	6503	SO:0001583	missense	81788	exon6			TTATGGTCATGCC	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.761A>G	chr1.hg19:g.205274389T>C	ENSP00000356125:p.Asp254Gly	87.0	0.0	.		69.0	17.0	.	NM_030952		Missense_Mutation	SNP	ENST00000367157.3	hg19	CCDS1453.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.895395	0.91962	.	.	ENSG00000163545	ENST00000367157	T	0.26373	1.74	5.73	5.73	0.89815	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	0.47093	D	0.000245	T	0.38983	0.1061	L	0.41124	1.26	0.80722	D	1	D	0.63046	0.992	P	0.59056	0.851	T	0.13710	-1.0499	10	0.62326	D	0.03	.	15.683	0.77388	0.0:0.0:0.0:1.0	.	254	Q9H093	NUAK2_HUMAN	G	254	ENSP00000356125:D254G	ENSP00000356125:D254G	D	-	2	0	NUAK2	203541012	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	8.040000	0.89188	2.188000	0.69820	0.459000	0.35465	GAC	.	.	.	none		0.572	NUAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090390.1	NM_030952		C	205274389	T	C	205274389	3	2	185	1	0	0	0	0	1	0	0	0	10720	1667	58	3	1133	3	NUAK2	1	205274389	Missense_Mutation	SNP	T	TCGA-GL-7966-01A-11D-2201-08	46756886	205274389	43976232	4	10851											
C1orf55	163859	hgsc.bcm.edu	37	chr1	226180666	226180666	+	Missense_Mutation	SNP	A	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	tctcgattggttgtcttctcAatctgagcaccaagtgctcg	7	14	9	11	2	4	1	1	1	4	0	7	2	4	1	1	1	2	3	1	1	2	3			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr1:226180666A>C	ENST00000272091.7	-	3	294	c.276T>G	c.(274-276)atT>atG	p.I92M		NM_152608.3	NP_689821.3	Q6IQ49	SDE2_HUMAN	SDE2 telomere maintenance homolog (S. pombe)	92																	TTGTCTTCTCAATCTGAGCAC	0.428																																					p.I92M		Atlas-SNP	.											.	.	.	.	0			c.T276G						PASS	.						85	76	79					1																	226180666		1868	4101	5969	SO:0001583	missense	163859	exon3			CTTCTCAATCTGA	BC071563	CCDS41473.1	1q42.12	2012-06-26	2012-06-26	2012-06-26	ENSG00000143751	ENSG00000143751			26643	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 55"	C1orf55		21333630	Standard	NM_152608		Approved	FLJ35382	uc001hpu.4	Q6IQ49	OTTHUMG00000037504	ENST00000272091.7:c.276T>G	chr1.hg19:g.226180666A>C	ENSP00000272091:p.Ile92Met	89.0	0.0	.		69.0	25.0	.	NM_152608	A8K4P3|Q5TD36|Q6ZS26|Q8NAG7	Missense_Mutation	SNP	ENST00000272091.7	hg19	CCDS41473.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.5|20.5	3.994098|3.994098	0.74703|0.74703	.|.	.|.	ENSG00000143751|ENSG00000143751	ENST00000272091;ENST00000366818|ENST00000366817	T|T	0.42131|0.49139	0.98|0.79	5.86|5.86	2.21|2.21	0.28008|0.28008	.|.	0.046995|.	0.85682|.	D|.	0.000000|.	T|T	0.41488|0.41488	0.1161|0.1161	L|L	0.41356|0.41356	1.27|1.27	0.29942|0.29942	N|N	0.82101|0.82101	D;D|.	0.89917|.	1.0;0.998|.	D;D|.	0.91635|.	0.999;0.978|.	T|T	0.45071|0.45071	-0.9286|-0.9286	10|7	0.15066|0.87932	T|D	0.55|0	-11.6814|-11.6814	4.9973|4.9973	0.14245|0.14245	0.6408:0.0:0.1288:0.2305|0.6408:0.0:0.1288:0.2305	.|.	80;92|.	Q6IQ49-2;Q6IQ49|.	.;CA055_HUMAN|.	M|W	92;80|41	ENSP00000272091:I92M|ENSP00000355782:L41W	ENSP00000272091:I92M|ENSP00000355782:L41W	I|L	-|-	3|2	3|0	C1orf55|C1orf55	224247289|224247289	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	1.520000|1.520000	0.35899|0.35899	0.119000|0.119000	0.18210|0.18210	0.529000|0.529000	0.55759|0.55759	ATT|TTG	.	.	.	none		0.428	SDE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091310.1	NM_152608		C	226180666	A	C	226180666	3	2	185	1	0	0	0	0	1	0	0	0	2049	126	5	5	1099	5	C1orf55	1	226180666	Missense_Mutation	SNP	A	TCGA-GL-7966-01A-11D-2201-08	20906277	226180666	23069955	5	10852											
FH	2271	hgsc.bcm.edu	37	chr1	241663812	241663812	+	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	gatcctttctgtattggcctGgattcccaccacgcagtttt	6	15	8	12	1	1	0	0	0	1	0	3	2	3	1	4	2	0	3	4	2	1	6			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr1:241663812G>A	ENST00000366560.3	-	9	1353	c.1315C>T	c.(1315-1317)Cag>Tag	p.Q439*		NM_000143.3	NP_000134.2	P07954	FUMH_HUMAN	fumarate hydratase	439					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)		GTATTGGCCTGGATTCCCACC	0.413			"Mis, N, F"			"lieomyomatosis, renal"			Hereditary Leiomyomatosis and Renal Cell Cancer																												p.Q439X	Melanoma(148;1573 2486 7381 46575)	Atlas-SNP	.	yes	Rec		hereditary leiomyomatosis and renal cell cancer	1	1q42.1	2271	fumarate hydratase		"E, M"	.	FH	64	.	0			c.C1315T						PASS	.						149	143	145					1																	241663812		2203	4298	6501	SO:0001587	stop_gained	2271	exon9	Familial Cancer Database	HLRCC, Reed syndrome, Hereditary Multiple Leiomyomata of Skin and Uterus	TGGCCTGGATTCC	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.1315C>T	chr1.hg19:g.241663812G>A	ENSP00000355518:p.Gln439*	195.0	0.0	.		218.0	91.0	.	NM_000143	B1ANK7	Nonsense_Mutation	SNP	ENST00000366560.3	hg19	CCDS1617.1	.	.	.	.	.	.	.	.	.	.	G	36	5.942978	0.97128	.	.	ENSG00000091483	ENST00000366560	.	.	.	5.71	5.71	0.89125	.	0.221640	0.47093	D	0.000245	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	-13.6944	17.3485	0.87316	0.0:0.0:1.0:0.0	.	.	.	.	X	439	.	ENSP00000355518:Q439X	Q	-	1	0	FH	239730435	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.437000	0.52863	2.697000	0.92050	0.655000	0.94253	CAG	.	.	.	none		0.413	FH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095490.1	NM_000143		A	241663812	G	A	241663812	4	1	185	1	0	0	0	0	0	1	0	0	5882	1357	47	2	225	2	FH	1	241663812	Nonsense_Mutation	SNP	G	TCGA-GL-7966-01A-11D-2201-08	15483146	241663812	7586809	6	10853											
TAF1B	9014	hgsc.bcm.edu	37	chr2	10059757	10059763	+	Frame_Shift_Del	DEL	GCACACT	GCACACT	-																															gaatctacagaaacaatttaGcacactggtcgagtcaacag																								rs59159809		TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	GCACACT	GCACACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr2:10059757_10059763delGCACACT	ENST00000263663.5	+	14	1561_1567	c.1373_1379delGCACACT	c.(1372-1380)agcacactgfs	p.STL458fs	TAF1B_ENST00000396242.3_Frame_Shift_Del_p.STL203fs	NM_005680.2	NP_005671	Q53T94	TAF1B_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa	458					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)					AAACAATTTAGCACACTGGTCGAGTCA	0.391																																					p.458_460del		Atlas-INDEL	.											.	TAF1B	62	.	0			c.1372_1378del						PASS	.																																			SO:0001589	frameshift_variant	9014	exon14			.	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.1373_1379delGCACACT	chr2.hg19:g.10059757_10059763delGCACACT	ENSP00000263663:p.Ser458fs	123.0	0.0	0		101.0	17.0	0.168317	NM_005680	B4DI42|F8WD72|Q15574|Q8WVC3	Frame_Shift_Del	DEL	ENST00000263663.5	hg19	CCDS33143.1																																																																																			.	.	.	none		0.391	TAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323426.2	NM_005680		-	10059763	GCACACT	-	10059757	7	5	185	1	0	1	0	1	0	0	0	0	15532	971	34	0	1427	0	TAF1B	2	10059757	Frame_Shift_Del	DEL	GCACACT	TCGA-GL-7966-01A-11D-2201-08		10059757	233139616	7	10854											
SCN2A	6326	hgsc.bcm.edu	37	chr2	166201262	166201262	+	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	atttccaatgattgtgaactCccacgctggcacatgcatga	11	11	8	11	1	0	3	0	3	0	0	2	3	2	3	2	1	2	3	2	1	2	2			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr2:166201262C>G	ENST00000375437.2	+	16	3050	c.2760C>G	c.(2758-2760)ctC>ctG	p.L920L	SCN2A_ENST00000283256.6_Silent_p.L920L|SCN2A_ENST00000357398.3_Silent_p.L920L|SCN2A_ENST00000375427.2_Silent_p.L920L	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	920					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)	ATTGTGAACTCCCACGCTGGC	0.488																																					p.L920L		Atlas-SNP	.											.	SCN2A	589	.	0			c.C2760G						PASS	.						231	208	216					2																	166201262		2203	4300	6503	SO:0001819	synonymous_variant	6326	exon15			TGAACTCCCACGC	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.2760C>G	chr2.hg19:g.166201262C>G		199.0	0.0	.		182.0	26.0	.	NM_001040143	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Silent	SNP	ENST00000375437.2	hg19	CCDS33314.1																																																																																			.	.	.	none		0.488	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		G	166201262	C	G	166201262	2	3	185	1	0	0	0	0	0	0	0	1	13929	842	30	4		4	SCN2A	2	166201262	Silent	SNP	C	TCGA-GL-7966-01A-11D-2201-08	156141505	166201262	76998111	8	10855											
XIRP2	129446	hgsc.bcm.edu	37	chr2	168105759	168105759	+	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	ggctctcaaagtaatgctcgGatactaggagtgtgttctga	10	12	12	7	1	2	1	1	1	2	0	4	3	2	3	0	3	2	4	0	3	4	4			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr2:168105759G>A	ENST00000409195.1	+	9	7946	c.7857G>A	c.(7855-7857)cgG>cgA	p.R2619R	XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000295237.9_Silent_p.R2619R|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409273.1_Silent_p.R2397R|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409756.2_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2444					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						GTAATGCTCGGATACTAGGAG	0.458																																					p.R2619R		Atlas-SNP	.											.	XIRP2	914	.	0			c.G7857A						PASS	.						88	85	86					2																	168105759		1909	4120	6029	SO:0001819	synonymous_variant	129446	exon9			TGCTCGGATACTA	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.7857G>A	chr2.hg19:g.168105759G>A		134.0	0.0	.		147.0	41.0	.	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	hg19	CCDS42769.1																																																																																			.	.	.	none		0.458	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		A	168105759	G	A	168105759	2	1	185	1	0	0	0	0	0	0	0	1	17442	1161	41	2		2	XIRP2	2	168105759	Silent	SNP	G	TCGA-GL-7966-01A-11D-2201-08	1904497	168105759	75093614	9	10856											
SESTD1	91404	hgsc.bcm.edu	37	chr2	179986590	179986590	+	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	catcctttccataggcccagGatgcctgattggagatctga	9	11	10	11	0	1	3	0	2	1	1	3	5	3	4	4	3	1	0	4	3	1	3			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr2:179986590G>A	ENST00000428443.3	-	13	1665	c.1349C>T	c.(1348-1350)tCc>tTc	p.S450F		NM_178123.4	NP_835224.3	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	450							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)			ATAGGCCCAGGATGCCTGATT	0.393																																					p.S450F		Atlas-SNP	.											.	SESTD1	66	.	0			c.C1349T						PASS	.						109	106	107					2																	179986590		2203	4300	6503	SO:0001583	missense	91404	exon13			GCCCAGGATGCCT	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.1349C>T	chr2.hg19:g.179986590G>A	ENSP00000415332:p.Ser450Phe	76.0	0.0	.		84.0	26.0	.	NM_178123	Q53R38|Q53SP3|Q5GM69|Q8N6M1|Q96LQ2	Missense_Mutation	SNP	ENST00000428443.3	hg19	CCDS33338.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.547863	0.86022	.	.	ENSG00000187231	ENST00000428443	T	0.06371	3.31	5.18	5.18	0.71444	.	0.102206	0.64402	D	0.000001	T	0.06280	0.0162	N	0.24115	0.695	0.80722	D	1	P	0.50943	0.94	B	0.41571	0.36	T	0.50268	-0.8848	9	.	.	.	-0.0059	18.0499	0.89344	0.0:0.0:1.0:0.0	.	450	Q86VW0	SESD1_HUMAN	F	450	ENSP00000415332:S450F	.	S	-	2	0	SESTD1	179694835	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.023000	0.93683	2.584000	0.87258	0.467000	0.42956	TCC	.	.	.	none		0.393	SESTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335916.2	NM_178123		A	179986590	G	A	179986590	3	1	185	1	0	0	0	0	1	0	0	0	14140	1174	41	2	765	2	SESTD1	2	179986590	Missense_Mutation	SNP	G	TCGA-GL-7966-01A-11D-2201-08	11880831	179986590	63212783	10	10857											
ABCB6	10058	hgsc.bcm.edu	37	chr2	220074990	220074990	+	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	cagccatccttgatgacgagGatctggtcagcattgaccac	10	9	10	12	1	2	3	1	3	1	0	3	5	3	4	3	2	2	1	3	2	0	2			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr2:220074990G>A	ENST00000265316.3	-	18	2698	c.2382C>T	c.(2380-2382)atC>atT	p.I794I	ABCB6_ENST00000439002.2_Silent_p.I748I	NM_005689.2	NP_005680.1	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 6 (Langereis blood group)	794	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				brain development (GO:0007420)|cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|porphyrin-containing compound biosynthetic process (GO:0006779)|skin development (GO:0043588)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial envelope (GO:0005740)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|efflux transmembrane transporter activity (GO:0015562)|heme binding (GO:0020037)|heme transporter activity (GO:0015232)|heme-transporting ATPase activity (GO:0015439)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	34		Renal(207;0.0474)		Epithelial(149;1.22e-06)|all cancers(144;0.000201)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGATGACGAGGATCTGGTCAG	0.562																																					p.I794I		Atlas-SNP	.											.	ABCB6	76	.	0			c.C2382T						PASS	.						102	97	99					2																	220074990		2203	4300	6503	SO:0001819	synonymous_variant	10058	exon18			GACGAGGATCTGG	AF070598	CCDS2436.1	2q36	2014-08-27	2014-08-27		ENSG00000115657	ENSG00000115657		"ATP binding cassette transporters / subfamily B"	47	protein-coding gene	gene with protein product	"ATP-binding cassette half-transporter"	605452	"ATP-binding cassette, sub-family B (MDR/TAP), member 6"			8894702, 9110174	Standard	NM_005689		Approved	EST45597, umat, MTABC3	uc002vkc.2	Q9NP58	OTTHUMG00000133131	ENST00000265316.3:c.2382C>T	chr2.hg19:g.220074990G>A		129.0	0.0	.		126.0	8.0	.	NM_005689	O75542|Q49A66|Q59GQ5|Q6ZME6|Q96ME8|Q9HAQ6|Q9HAQ7	Silent	SNP	ENST00000265316.3	hg19	CCDS2436.1	.	.	.	.	.	.	.	.	.	.	G	9.909	1.208939	0.22205	.	.	ENSG00000115657	ENST00000295750	.	.	.	4.83	0.378	0.16204	.	.	.	.	.	T	0.56062	0.1960	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49579	-0.8925	4	.	.	.	-23.7644	9.3287	0.38008	0.3743:0.0:0.6257:0.0	.	.	.	.	F	642	.	.	S	-	2	0	ABCB6	219783234	1.000000	0.71417	0.992000	0.48379	0.984000	0.73092	0.893000	0.28336	0.171000	0.19730	-0.145000	0.13849	TCC	.	.	.	none		0.562	ABCB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256820.2	NM_005689		A	220074990	G	A	220074990	2	1	185	1	0	0	0	0	0	0	0	1	45	1164	41	2		2	ABCB6	2	220074990	Silent	SNP	G	TCGA-GL-7966-01A-11D-2201-08	40088400	220074990	23124383	11	10858											
CNOT10	25904	hgsc.bcm.edu	37	chr3	32766999	32766999	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttgcatccattttgccatgaGcaagcacaatttgggaatat	12	13	8	8	0	0	1	0	1	0	0	1	2	1	2	2	1	4	3	2	1	4	5			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr3:32766999G>A	ENST00000328834.5	+	9	1236	c.920G>A	c.(919-921)aGc>aAc	p.S307N	CNOT10_ENST00000454516.2_Missense_Mutation_p.S367N|CNOT10_ENST00000538368.1_Missense_Mutation_p.S79N|CNOT10_ENST00000463697.1_3'UTR|CNOT10_ENST00000331889.6_Missense_Mutation_p.S307N	NM_015442.2	NP_056257.1	Q9H9A5	CNO10_HUMAN	CCR4-NOT transcription complex, subunit 10	307					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(3)	23						TTTGCCATGAGCAAGCACAAT	0.393																																					p.S367N		Atlas-SNP	.											.	CNOT10	57	.	0			c.G1100A						PASS	.						148	145	146					3																	32766999		2203	4300	6503	SO:0001583	missense	25904	exon9			CCATGAGCAAGCA	BC002928	CCDS2655.1, CCDS58821.1, CCDS58822.1	3p23	2013-01-10			ENSG00000182973	ENSG00000182973		"Tetratricopeptide (TTC) repeat domain containing"	23817	protein-coding gene	gene with protein product							Standard	NR_046352		Approved	FLJ12890, FLJ13165	uc011axj.2	Q9H9A5	OTTHUMG00000130748	ENST00000328834.5:c.920G>A	chr3.hg19:g.32766999G>A	ENSP00000330060:p.Ser307Asn	177.0	0.0	.		133.0	8.0	.	NM_001256742	B7Z7L1|F8WAF2|Q9BU30|Q9H5J7|Q9H8X1|Q9H9W0|Q9HAH3|Q9UFJ2	Missense_Mutation	SNP	ENST00000328834.5	hg19	CCDS2655.1	.	.	.	.	.	.	.	.	.	.	G	18.74	3.689299	0.68271	.	.	ENSG00000182973	ENST00000331889;ENST00000328834;ENST00000540405;ENST00000538368;ENST00000454516	T;T;T;T	0.61859	0.07;0.07;0.07;0.07	5.52	5.52	0.82312	Tetratricopeptide-like helical (1);	0.043732	0.85682	D	0.000000	T	0.39279	0.1072	N	0.03608	-0.345	0.47037	D	0.999297	B;B;B;B	0.17465	0.022;0.011;0.019;0.014	B;B;B;B	0.19946	0.027;0.012;0.019;0.02	T	0.23013	-1.0200	10	0.39692	T	0.17	-16.0206	19.4425	0.94827	0.0:0.0:1.0:0.0	.	367;307;306;307	F8WAF2;Q9H9A5-3;Q9H9A5-2;Q9H9A5	.;.;.;CNOTA_HUMAN	N	307;307;207;79;367	ENSP00000329376:S307N;ENSP00000330060:S307N;ENSP00000442552:S79N;ENSP00000399862:S367N	ENSP00000330060:S307N	S	+	2	0	CNOT10	32742003	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.348000	0.97062	2.594000	0.87642	0.655000	0.94253	AGC	.	.	.	none		0.393	CNOT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253248.2	NM_015442		A	32766999	G	A	32766999	3	1	185	1	0	0	0	0	1	0	0	0	3620	971	34	2	954	2	CNOT10	3	32766999	Missense_Mutation	SNP	G	TCGA-GL-7966-01A-11D-2201-08		32766999	165255431	12	10859											
TAS2R1	50834	hgsc.bcm.edu	37	chr5	9629374	9629374	+	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	aggatgaagaacagaaagatGaaccttctgatgtgaaactt	17	9	10	5	0	1	7	0	4	1	3	1	8	1	8	1	1	3	0	1	1	5	2			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr5:9629374G>A	ENST00000382492.2	-	1	1089	c.771C>T	c.(769-771)ttC>ttT	p.F257F	CTD-2001E22.1_ENST00000504182.2_RNA	NM_019599.2	NP_062545.1	Q9NYW7	TA2R1_HUMAN	taste receptor, type 2, member 1	257					chemosensory behavior (GO:0007635)|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)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(19)|ovary(3)|prostate(1)|skin(1)|stomach(1)	39						ACAGAAAGATGAACCTTCTGA	0.378																																					p.F257F		Atlas-SNP	.											.	TAS2R1	84	.	0			c.C771T						PASS	.						97	101	100					5																	9629374		2203	4300	6503	SO:0001819	synonymous_variant	50834	exon1			AAAGATGAACCTT	AF227129	CCDS3876.1	5p15	2012-08-22			ENSG00000169777	ENSG00000169777		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14909	protein-coding gene	gene with protein product		604796				10761934, 10766242	Standard	NM_019599		Approved	T2R1, TRB7	uc003jem.1	Q9NYW7	OTTHUMG00000090500	ENST00000382492.2:c.771C>T	chr5.hg19:g.9629374G>A		103.0	0.0	.		85.0	7.0	.	NM_019599	Q646G8	Silent	SNP	ENST00000382492.2	hg19	CCDS3876.1																																																																																			.	.	.	none		0.378	TAS2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206988.2			A	9629374	G	A	9629374	2	1	185	1	0	0	0	0	0	0	0	1	15577	1281	45	2		2	TAS2R1	5	9629374	Silent	SNP	G	TCGA-GL-7966-01A-11D-2201-08		9629374	171285886	13	10860											
SHROOM1	134549	hgsc.bcm.edu	37	chr5	132161119	132161119	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacccaggcattcccgcgcCggcccaccgccccgacccac	6	3	8	24	5	1	0	1	0	0	0	2	1	2	0	8	2	0	1	8	2	0	1			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr5:132161119C>T	ENST00000378679.3	-	4	1518	c.714G>A	c.(712-714)ccG>ccA	p.P238P	SHROOM1_ENST00000319854.3_Silent_p.P238P|SHROOM1_ENST00000488072.1_5'Flank|SHROOM1_ENST00000378676.1_Silent_p.P238P	NM_001172700.1	NP_001166171.1	Q2M3G4	SHRM1_HUMAN	shroom family member 1	238					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)			ATTCCCGCGCCGGCCCACCGC	0.682																																					p.P238P		Atlas-SNP	.											.	SHROOM1	35	.	0			c.G714A						PASS	.																																			SO:0001819	synonymous_variant	134549	exon1			CCGCGCCGGCCCA	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.714G>A	chr5.hg19:g.132161119C>T		25.0	0.0	.		11.0	8.0	.	NM_133456	B7WP40|B7ZL01|Q8TDP0|Q8TF41	Silent	SNP	ENST00000378679.3	hg19	CCDS54902.1																																																																																			.	.	.	none		0.682	SHROOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133033.1	NM_133456		T	132161119	C	T	132161119	2	4	185	1	0	0	0	0	0	0	0	1	14306	639	23	1		1	SHROOM1	5	132161119	Silent	SNP	C	TCGA-GL-7966-01A-11D-2201-08	122531745	132161119	48754141	14	10861											
MTHFD1L	25902	hgsc.bcm.edu	37	chr6	151358132	151358132	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttgcccatctgcatggcaaAgacccacctttctctatctc	8	13	5	15	0	3	1	0	0	3	1	5	1	3	1	3	1	2	2	3	1	2	3			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr6:151358132A>G	ENST00000367321.3	+	26	3000	c.2726A>G	c.(2725-2727)aAg>aGg	p.K909R	AL133260.1_ENST00000408542.1_RNA	NM_001242767.1|NM_001242768.1|NM_015440.4	NP_001229696.1|NP_001229697.1|NP_056255.2	Q6UB35	C1TM_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like	909	Formyltetrahydrofolate synthetase.				folic acid-containing compound biosynthetic process (GO:0009396)|folic acid-containing compound metabolic process (GO:0006760)|formate metabolic process (GO:0015942)|one-carbon metabolic process (GO:0006730)|oxidation-reduction process (GO:0055114)|tetrahydrofolate interconversion (GO:0035999)|tetrahydrofolate metabolic process (GO:0046653)	membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	29		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)		TGCATGGCAAAGACCCACCTT	0.463																																					p.K910R		Atlas-SNP	.											.	MTHFD1L	75	.	0			c.A2729G						PASS	.						85	79	81					6																	151358132		2203	4300	6503	SO:0001583	missense	25902	exon26			TGGCAAAGACCCA	BC017477	CCDS5228.1, CCDS56457.1, CCDS75535.1, CCDS75536.1	6q25.1	2010-07-19	2004-12-13	2004-12-14	ENSG00000120254	ENSG00000120254	6.3.4.3		21055	protein-coding gene	gene with protein product	"10-formyl-THF synthetase", "mitochondrial C1-tetrahydrofolate synthase", "monofunctional C1-tetrahydrofolate synthase, mitochondrial"	611427	"formyltetrahydrofolate synthetase domain containing 1"	FTHFSDC1		18804703	Standard	NM_015440		Approved	DKFZP586G1517, FLJ21145	uc021zgs.1	Q6UB35	OTTHUMG00000015828	ENST00000367321.3:c.2726A>G	chr6.hg19:g.151358132A>G	ENSP00000356290:p.Lys909Arg	116.0	0.0	.		87.0	6.0	.	NM_001242767	Q2TBF3|Q8WVW0|Q96HG8|Q9H789|Q9UFU8	Missense_Mutation	SNP	ENST00000367321.3	hg19	CCDS5228.1	.	.	.	.	.	.	.	.	.	.	A	28.8	4.951688	0.92660	.	.	ENSG00000120254	ENST00000367321;ENST00000453602;ENST00000450635	T;T;T	0.39787	1.06;1.06;1.06	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.73297	0.3569	H	0.97918	4.105	0.80722	D	1	D;D;D	0.89917	1.0;0.994;1.0	D;D;D	0.91635	0.999;0.914;0.999	D	0.84465	0.0596	10	0.72032	D	0.01	.	15.1893	0.73032	1.0:0.0:0.0:0.0	.	910;664;909	B7ZM99;B2RD24;Q6UB35	.;.;C1TM_HUMAN	R	909;34;8	ENSP00000356290:K909R;ENSP00000391022:K34R;ENSP00000399804:K8R	ENSP00000356290:K909R	K	+	2	0	MTHFD1L	151399825	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.339000	0.96797	1.974000	0.57490	0.533000	0.62120	AAG	.	.	.	none		0.463	MTHFD1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042699.1	NM_015440		G	151358132	A	G	151358132	3	3	185	1	0	0	0	0	1	0	0	0	9935	72	3	3	2828	3	MTHFD1L	6	151358132	Missense_Mutation	SNP	A	TCGA-GL-7966-01A-11D-2201-08		151358132	19756935	15	10862											
NOBOX	135935	hgsc.bcm.edu	37	chr7	144098145	144098145	+	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	ctttagggacttacctgagcGgtatagggttcgtgtctttt	6	16	12	7	2	1	1	0	1	1	0	2	2	1	2	1	3	2	2	1	3	4	8			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr7:144098145G>T	ENST00000467773.1	-	4	837	c.838C>A	c.(838-840)Cgc>Agc	p.R280S	NOBOX_ENST00000223140.5_Missense_Mutation_p.R195S|NOBOX_ENST00000483238.1_Missense_Mutation_p.R280S	NM_001080413.3	NP_001073882.3	O60393	NOBOX_HUMAN	NOBOX oogenesis homeobox	280					oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.R280G(2)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	26	Melanoma(164;0.14)					TTACCTGAGCGGTATAGGGTT	0.542																																					p.R280S		Atlas-SNP	.											NOBOX_ENST00000467773,NS,carcinoma,0,2	NOBOX	130	.	2	Substitution - Missense(2)	kidney(2)	c.C838A						PASS	.						76	72	73					7																	144098145		1844	4092	5936	SO:0001583	missense	135935	exon4			CTGAGCGGTATAG			7q35	2011-06-20			ENSG00000106410	ENSG00000106410		"Homeoboxes / PRD class"	22448	protein-coding gene	gene with protein product	"newborn ovary homeobox-encoding gene"	610934				11804785, 16597639	Standard	NM_001080413		Approved	OG2, Og2x	uc022aoj.1	O60393	OTTHUMG00000158051	ENST00000467773.1:c.838C>A	chr7.hg19:g.144098145G>T	ENSP00000419457:p.Arg280Ser	59.0	1.0	.		27.0	2.0	.	NM_001080413	A6NCD3|A8MZN5	Missense_Mutation	SNP	ENST00000467773.1	hg19		.	.	.	.	.	.	.	.	.	.	G	14.32	2.499271	0.44455	.	.	ENSG00000106410	ENST00000483238;ENST00000467773;ENST00000223140;ENST00000555556	D;D;D	0.94828	-3.53;-3.53;-3.53	5.15	5.15	0.70609	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.135341	0.49305	D	0.000145	T	0.79776	0.4504	N	0.00007	-3.155	0.36532	D	0.870806	P	0.50819	0.939	P	0.56865	0.808	D	0.84935	0.0862	10	0.15066	T	0.55	-31.9255	13.9985	0.64419	0.0:0.0:1.0:0.0	.	280	O60393	NOBOX_HUMAN	S	280;280;195;69	ENSP00000419565:R280S;ENSP00000419457:R280S;ENSP00000223140:R195S	ENSP00000223140:R195S	R	-	1	0	NOBOX	143729078	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	2.884000	0.48562	2.671000	0.90904	0.650000	0.86243	CGC	.	.	.	none		0.542	NOBOX-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000350095.1	XM_001134420		T	144098145	G	T	144098145	3	4	185	1	0	0	0	0	1	0	0	0	10519	1116	39	4	1169	4	NOBOX	7	144098145	Missense_Mutation	SNP	G	TCGA-GL-7966-01A-11D-2201-08		144098145	15040518	16	10863											
KIAA1984	84960	hgsc.bcm.edu	37	chr9	139694856	139694856	+	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	cccagatcatccgccagctgGagaacaacatcgagaagaca	15	4	9	13	2	1	4	1	0	0	4	3	6	2	4	3	1	3	1	3	1	3	0	rs544497218	byFrequency	TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr9:139694856G>A	ENST00000338005.6	+	5	489	c.454G>A	c.(454-456)Gag>Aag	p.E152K	RP11-216L13.18_ENST00000471502.1_RNA|RP11-216L13.19_ENST00000415992.1_RNA|KIAA1984_ENST00000371682.3_3'UTR|RP11-216L13.17_ENST00000456614.2_Missense_Mutation_p.E182K	NM_001039374.4	NP_001034463.4	Q5T5S1	CC183_HUMAN		152										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)		CCGCCAGCTGGAGAACAACAT	0.602													G|||	3	0.000599042	0	0	5008	,	,		10479	0		0	False		,,,				2504	0.0031				p.E152K		Atlas-SNP	.											.	KIAA1984	39	.	0			c.G454A						PASS	.																																			SO:0001583	missense	84960	exon5			CAGCTGGAGAACA																												ENST00000338005.6:c.454G>A	chr9.hg19:g.139694856G>A	ENSP00000338013:p.Glu152Lys	20.0	0.0	.		17.0	6.0	.	NM_001039374	B2RP89|C9JD38|Q6P2D9|Q8NAI4|Q8TF18	Missense_Mutation	SNP	ENST00000338005.6	hg19	CCDS43906.1	.	.	.	.	.	.	.	.	.	.	G	31	5.059818	0.93846	.	.	ENSG00000213213	ENST00000423962;ENST00000338005	T	0.31510	1.49	4.19	4.19	0.49359	.	0.000000	0.41823	U	0.000810	T	0.50086	0.1595	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.49360	-0.8948	10	0.48119	T	0.1	-24.9723	12.0196	0.53336	0.0:0.0:1.0:0.0	.	152	Q5T5S1	K1984_HUMAN	K	152	ENSP00000338013:E152K	ENSP00000338013:E152K	E	+	1	0	KIAA1984	138814677	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	3.494000	0.53273	1.873000	0.54277	0.305000	0.20034	GAG	.	.	.	none		0.602	KIAA1984-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354899.1			A	139694856	G	A	139694856	3	1	185	1	0	0	0	0	1	0	0	0	8273	1175	41	2	472	2	KIAA1984	9	139694856	Missense_Mutation	SNP	G	TCGA-GL-7966-01A-11D-2201-08		139694856	1518575	17	10864											
PUS3	83480	hgsc.bcm.edu	37	chr11	125766029	125766029	+	Frame_Shift_Del	DEL	T	T	-																															gaaatcaaatgcacgcttagTttttccagctcctgctgaat																										TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr11:125766029delT	ENST00000530811.1	-	1	196	c.151delA	c.(151-153)actfs	p.T51fs	HYLS1_ENST00000356438.3_Intron|HYLS1_ENST00000425380.2_Intron|PUS3_ENST00000227474.3_Frame_Shift_Del_p.T51fs|HYLS1_ENST00000526028.1_Intron			Q9BZE2	PUS3_HUMAN	pseudouridylate synthase 3	51					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)		GCACGCTTAGTTTTTCCAGCT	0.448																																					p.T51fs		Atlas-INDEL	.											.	PUS3	33	.	0			c.152delC						PASS	.						230	226	227					11																	125766029		2201	4299	6500	SO:0001589	frameshift_variant	83480	exon2			.	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.151delA	chr11.hg19:g.125766029delT	ENSP00000432386:p.Thr51fs	255.0	0.0	0		244.0	18.0	0.0737705	NM_031307	B2RAM0|Q96D17|Q96J23|Q96NB4	Frame_Shift_Del	DEL	ENST00000530811.1	hg19	CCDS8466.1																																																																																			.	.	.	none		0.448	PUS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386783.1	NM_031307		-	125766029	T	-	125766029	7	5	185	1	0	1	0	1	0	0	0	0	12845	1725	60	0	1306	0	PUS3	11	125766029	Frame_Shift_Del	DEL	T	TCGA-GL-7966-01A-11D-2201-08		125766029	9240487	18	10865											
GLB1L2	89944	hgsc.bcm.edu	37	chr11	134241359	134241359	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggattcttggactacaagacAacgaagattgctgtccccct	11	10	9	11	1	1	2	0	0	1	2	2	5	2	4	2	2	3	1	2	2	4	4			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr11:134241359A>G	ENST00000535456.2	+	14	1589	c.1401A>G	c.(1399-1401)acA>acG	p.T467T	GLB1L2_ENST00000389881.3_Silent_p.T467T|GLB1L2_ENST00000529077.1_3'UTR|GLB1L2_ENST00000339772.7_Silent_p.T467T	NM_138342.3	NP_612351.2	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2	467					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)		ACTACAAGACAACGAAGATTG	0.542																																					p.T467T		Atlas-SNP	.											.	GLB1L2	79	.	0			c.A1401G						PASS	.						161	159	160					11																	134241359		2201	4297	6498	SO:0001819	synonymous_variant	89944	exon14			CAAGACAACGAAG		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.1401A>G	chr11.hg19:g.134241359A>G		216.0	0.0	.		210.0	79.0	.	NM_138342	A6NCE6|Q6UX60|Q8NC62|Q8NCB3|Q8NCJ1|Q96HP3	Silent	SNP	ENST00000535456.2	hg19	CCDS31724.1	.	.	.	.	.	.	.	.	.	.	A	4.458	0.084834	0.08583	.	.	ENSG00000149328	ENST00000525089	.	.	.	4.72	-9.38	0.00623	.	.	.	.	.	T	0.13457	0.0326	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.17961	-1.0352	4	.	.	.	-3.4454	0.6104	0.00760	0.3795:0.1978:0.2259:0.1968	.	.	.	.	D	406	.	.	N	+	1	0	GLB1L2	133746569	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-3.622000	0.00412	-1.622000	0.01560	-1.291000	0.01355	AAC	.	.	.	none		0.542	GLB1L2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393629.2	NM_138342		G	134241359	A	G	134241359	2	3	185	1	0	0	0	0	0	0	0	1	6436	117	5	3		3	GLB1L2	11	134241359	Silent	SNP	A	TCGA-GL-7966-01A-11D-2201-08	8475330	134241359	765157	19	10866											
ULK1	8408	hgsc.bcm.edu	37	chr12	132395297	132395297	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgtacccaagctcggggtcCggcagcagctccagcagcag	8	5	13	15	3	0	0	0	0	0	0	4	0	2	0	3	3	6	7	3	3	2	1	rs571147302		TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr12:132395297C>T	ENST00000321867.4	+	12	1251	c.900C>T	c.(898-900)tcC>tcT	p.S300S		NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	300	Interaction with GABARAP and GABARAPL2.|Poly-Ser.				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)		GCTCGGGGTCCGGCAGCAGCT	0.662													T|||	1	0.000199681	8e-04	0	5008	,	,		14232	0		0	False		,,,				2504	0				p.S300S		Atlas-SNP	.											.	ULK1	92	.	0			c.C900T						PASS	.						76	67	70					12																	132395297		2203	4299	6502	SO:0001819	synonymous_variant	8408	exon12			GGGGTCCGGCAGC	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.900C>T	chr12.hg19:g.132395297C>T		95.0	0.0	.		81.0	31.0	.	NM_003565	Q9UQ28	Silent	SNP	ENST00000321867.4	hg19	CCDS9274.1																																																																																			.	.	.	none		0.662	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3			T	132395297	C	T	132395297	2	4	185	1	0	0	0	0	0	0	0	1	16987	639	23	1		1	ULK1	12	132395297	Silent	SNP	C	TCGA-GL-7966-01A-11D-2201-08		132395297	1456598	20	10867											
SNURF	8926	hgsc.bcm.edu	37	chr15	25207297	25207297	+	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	agacgaactacagaacagcaCgtaccagaggtggaagtcca	16	4	11	10	2	0	3	0	0	0	3	1	5	1	4	2	2	5	2	2	2	5	2			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr15:25207297C>T	ENST00000577949.1	+	2	114	c.51C>T	c.(49-51)caC>caT	p.H17H	SNURF_ENST00000338094.6_Silent_p.H17H|SNRPN_ENST00000554227.2_5'UTR|SNURF_ENST00000551312.2_Silent_p.H17H|SNRPN_ENST00000577565.1_5'UTR|SNRPN_ENST00000400100.1_5'UTR|SNURF_ENST00000338327.4_Silent_p.H17H|SNRPN_ENST00000400098.1_5'UTR|SNRPN_ENST00000390687.4_5'UTR|SNRPN_ENST00000553597.1_3'UTR|SNRPN_ENST00000400097.1_5'UTR|SNRPN_ENST00000346403.6_5'UTR			Q9Y675	SNURF_HUMAN	SNRPN upstream reading frame	17						nucleus (GO:0005634)				breast(2)|large_intestine(2)|lung(1)	5		all_cancers(20;1.4e-21)|Breast(32;0.000625)		all cancers(64;3.48e-07)|Epithelial(43;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0142)		CAGAACAGCACGTACCAGAGG	0.448																																					p.H17H		Atlas-SNP	.											.	SNURF	17	.	0			c.C51T						PASS	.						154	124	134					15																	25207297		2203	4300	6503	SO:0001819	synonymous_variant	8926	exon2			ACAGCACGTACCA		CCDS10016.1	15q11.2	2013-08-27			ENSG00000214265	ENSG00000214265			11171	protein-coding gene	gene with protein product						10318933	Standard	NM_022804		Approved		uc001ywu.3	Q9Y675	OTTHUMG00000129181	ENST00000577949.1:c.51C>T	chr15.hg19:g.25207297C>T		129.0	0.0	.		74.0	5.0	.	NM_005678	A6NCW2	Silent	SNP	ENST00000577949.1	hg19	CCDS10016.1																																																																																			.	.	.	none		0.448	SNURF-005	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446300.1	NM_005678		T	25207297	C	T	25207297	2	4	185	1	0	0	0	0	0	0	0	1	14891	535	19	1		1	SNURF	15	25207297	Silent	SNP	C	TCGA-GL-7966-01A-11D-2201-08		25207297	77324095	21	10868											
B2M	567	hgsc.bcm.edu	37	chr15	45003781	45003782	+	Frame_Shift_Del	DEL	CT	CT	-																															ccttagctgtgctcgcgctaCtctctctttctggcctggag																										TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr15:45003781_45003782delCT	ENST00000558401.1	+	1	107_108	c.37_38delCT	c.(37-39)ctcfs	p.L13fs	PATL2_ENST00000558573.1_5'Flank|B2M_ENST00000559916.1_Frame_Shift_Del_p.L13fs|B2M_ENST00000544417.1_Frame_Shift_Del_p.L13fs	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	99	.	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	chr15.hg19:g.45003787_45003788delCT	ENSP00000452780:p.Leu13fs	104.0	0.0	0		58.0	10.0	0.172414	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Frame_Shift_Del	DEL	ENST00000558401.1	hg19	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	185	1	0	1	0	1	0	0	0	0	1244	565	20	0	39	0	B2M	15	45003781	Frame_Shift_Del	DEL	CT	TCGA-GL-7966-01A-11D-2201-08	19796484	45003781	57527611	22	10869											
UACA	55075	hgsc.bcm.edu	37	chr15	70987423	70987423	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcaaacactcaagattcccCtttgaggtcacaacatggaa	14	10	6	11	0	3	2	3	1	0	1	4	3	4	3	2	2	2	0	2	2	4	3			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr15:70987423C>T	ENST00000322954.6	-	3	419	c.234G>A	c.(232-234)aaG>aaA	p.K78K	UACA_ENST00000560441.1_Silent_p.K65K|UACA_ENST00000539319.1_Silent_p.K78K|UACA_ENST00000379983.2_Silent_p.K65K	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	78					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						CAAGATTCCCCTTTGAGGTCA	0.353																																					p.K78K		Atlas-SNP	.											.	UACA	235	.	0			c.G234A						PASS	.						91	83	86					15																	70987423		2199	4297	6496	SO:0001819	synonymous_variant	55075	exon3			ATTCCCCTTTGAG	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.234G>A	chr15.hg19:g.70987423C>T		44.0	0.0	.		27.0	18.0	.	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Silent	SNP	ENST00000322954.6	hg19	CCDS10235.1																																																																																			.	.	.	none		0.353	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			T	70987423	C	T	70987423	2	4	185	1	0	0	0	0	0	0	0	1	16836	680	24	2		2	UACA	15	70987423	Silent	SNP	C	TCGA-GL-7966-01A-11D-2201-08	25983642	70987423	31543969	23	10870											
KIAA0753	9851	hgsc.bcm.edu	37	chr17	6531560	6531560	+	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	acctatcctgggatgaggctGaagtcccggatcatgggtgg	8	9	15	9	1	1	2	1	2	0	0	3	4	3	4	3	5	0	1	3	5	2	1			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr17:6531560G>A	ENST00000361413.3	-	3	953	c.595C>T	c.(595-597)Cag>Tag	p.Q199*	KIAA0753_ENST00000542606.1_5'UTR|KIAA0753_ENST00000572370.1_5'UTR	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	199						centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		GGATGAGGCTGAAGTCCCGGA	0.483																																					p.Q199X		Atlas-SNP	.											.	KIAA0753	63	.	0			c.C595T						PASS	.						129	131	131					17																	6531560		2023	4175	6198	SO:0001587	stop_gained	9851	exon3			GAGGCTGAAGTCC		CCDS42247.1	17p13.1	2014-04-04			ENSG00000198920	ENSG00000198920			29110	protein-coding gene	gene with protein product						24613305	Standard	NM_014804		Approved		uc002gde.4	Q2KHM9	OTTHUMG00000177928	ENST00000361413.3:c.595C>T	chr17.hg19:g.6531560G>A	ENSP00000355250:p.Gln199*	179.0	0.0	.		157.0	9.0	.	NM_014804	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Nonsense_Mutation	SNP	ENST00000361413.3	hg19	CCDS42247.1	.	.	.	.	.	.	.	.	.	.	G	32	5.129961	0.94473	.	.	ENSG00000198920	ENST00000361413	.	.	.	5.34	-0.77	0.11005	.	0.864801	0.09963	N	0.733125	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-2.5116	10.7147	0.46005	0.0:0.5544:0.3039:0.1417	.	.	.	.	X	199	.	ENSP00000355250:Q199X	Q	-	1	0	KIAA0753	6472284	0.004000	0.15560	0.007000	0.13788	0.294000	0.27393	0.211000	0.17474	0.282000	0.22254	0.655000	0.94253	CAG	.	.	.	none		0.483	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804		A	6531560	G	A	6531560	4	1	185	1	0	0	0	0	0	1	0	0	8198	1299	45	2	2376	2	KIAA0753	17	6531560	Nonsense_Mutation	SNP	G	TCGA-GL-7966-01A-11D-2201-08		6531560	74663650	24	10871											
TRPV2	51393	hgsc.bcm.edu	37	chr17	16340169	16340169	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggatggtgcctctgaggaaaActatgtgcccgtccagctcc	8	9	12	12	1	1	1	0	1	1	0	3	3	3	3	4	3	4	1	4	3	3	1			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr17:16340169A>G	ENST00000338560.7	+	15	2660	c.2261A>G	c.(2260-2262)aAc>aGc	p.N754S	C17orf76-AS1_ENST00000470491.2_RNA|C17orf76-AS1_ENST00000487066.1_RNA|C17orf76-AS1_ENST00000491009.1_RNA|C17orf76-AS1_ENST00000580180.1_RNA|C17orf76-AS1_ENST00000472367.1_RNA|C17orf76-AS1_ENST00000365172.1_RNA|C17orf76-AS1_ENST00000460249.1_RNA|C17orf76-AS1_ENST00000584177.1_RNA|C17orf76-AS1_ENST00000477249.2_RNA|TRPV2_ENST00000577397.1_Missense_Mutation_p.N324S|C17orf76-AS1_ENST00000492250.1_RNA|C17orf76-AS1_ENST00000481898.1_RNA|C17orf76-AS1_ENST00000475947.2_RNA|C17orf76-AS1_ENST00000582911.1_RNA|C17orf76-AS1_ENST00000478103.2_RNA|C17orf76-AS1_ENST00000581718.1_RNA|C17orf76-AS1_ENST00000484836.1_RNA|C17orf76-AS1_ENST00000578380.2_RNA|C17orf76-AS1_ENST00000581913.1_RNA|C17orf76-AS1_ENST00000584926.1_RNA|C17orf76-AS1_ENST00000481027.1_RNA|C17orf76-AS1_ENST00000583400.2_RNA|C17orf76-AS1_ENST00000475953.1_RNA|C17orf76-AS1_ENST00000584141.1_RNA|C17orf76-AS1_ENST00000580770.1_RNA|C17orf76-AS1_ENST00000483140.1_RNA|C17orf76-AS1_ENST00000480811.1_RNA|C17orf76-AS1_ENST00000579473.1_RNA	NM_016113.4	NP_057197.2	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel, subfamily V, member 2	754					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|positive regulation of axon extension (GO:0045773)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|response to temperature stimulus (GO:0009266)|sensory perception (GO:0007600)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|growth cone membrane (GO:0032584)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|ion channel activity (GO:0005216)|ion transmembrane transporter activity (GO:0015075)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|stomach(3)	28				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		TCTGAGGAAAACTATGTGCCC	0.562																																					p.N754S		Atlas-SNP	.											.	TRPV2	74	.	0			c.A2261G						PASS	.						154	134	141					17																	16340169		2203	4300	6503	SO:0001583	missense	51393	exon15			AGGAAAACTATGT	AF129112	CCDS32576.1	17p11.2	2013-01-10			ENSG00000187688	ENSG00000187688		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	18082	protein-coding gene	gene with protein product		606676				10201375, 16382100	Standard	NM_016113		Approved	VRL, VRL-1, VRL1	uc002gpy.3	Q9Y5S1	OTTHUMG00000058989	ENST00000338560.7:c.2261A>G	chr17.hg19:g.16340169A>G	ENSP00000342222:p.Asn754Ser	156.0	0.0	.		145.0	58.0	.	NM_016113	A6NML2|A8K0Z0|Q9Y670	Missense_Mutation	SNP	ENST00000338560.7	hg19	CCDS32576.1	.	.	.	.	.	.	.	.	.	.	A	5.819	0.335390	0.11013	.	.	ENSG00000187688	ENST00000338560	D	0.87334	-2.24	3.83	3.83	0.44106	.	0.576086	0.16403	N	0.215935	T	0.72740	0.3498	N	0.08118	0	0.19775	N	0.999956	B	0.09022	0.002	B	0.09377	0.004	T	0.61093	-0.7132	10	0.34782	T	0.22	-56.024	9.2873	0.37764	1.0:0.0:0.0:0.0	.	754	Q9Y5S1	TRPV2_HUMAN	S	754	ENSP00000342222:N754S	ENSP00000342222:N754S	N	+	2	0	TRPV2	16280894	0.920000	0.31207	0.964000	0.40570	0.094000	0.18550	2.141000	0.42168	1.972000	0.57404	0.459000	0.35465	AAC	.	.	.	none		0.562	TRPV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130464.2	NM_016113		G	16340169	A	G	16340169	3	3	185	1	0	0	0	0	1	0	0	0	16608	43	2	3	2315	3	TRPV2	17	16340169	Missense_Mutation	SNP	A	TCGA-GL-7966-01A-11D-2201-08	9808609	16340169	64855041	25	10872											
STARD3	10948	hgsc.bcm.edu	37	chr17	37809843	37809854	+	In_Frame_Del	DEL	CCTCCCTGGGCT	CCTCCCTGGGCT	-																															gcgcagcctgcctgccgtggCctccctgggctcctcactgt																								rs371019835		TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	CCTCCCTGGGCT	CCTCCCTGGGCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr17:37809843_37809854delCCTCCCTGGGCT	ENST00000336308.5	+	2	277_288	c.59_70delCCTCCCTGGGCT	c.(58-72)gcctccctgggctcc>gcc	p.SLGS21del	STARD3_ENST00000544210.2_In_Frame_Del_p.SLGS21del|STARD3_ENST00000578232.1_Intron|STARD3_ENST00000394250.4_In_Frame_Del_p.SLGS21del|STARD3_ENST00000580611.1_In_Frame_Del_p.SLGS21del	NM_001165937.1|NM_006804.3	NP_001159409.1|NP_006795.3	Q14849	STAR3_HUMAN	StAR-related lipid transfer (START) domain containing 3	21					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)			CCTGCCGTGGCCTCCCTGGGCTCCTCACTGTC	0.684											OREG0024381	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.20_23del		Atlas-INDEL	.											.	STARD3	33	.	0			c.58_69del						PASS	.																																			SO:0001651	inframe_deletion	10948	exon2			.		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.59_70delCCTCCCTGGGCT	chr17.hg19:g.37809843_37809854delCCTCCCTGGGCT	ENSP00000337446:p.Ser21_Ser24del	76.0	0.0	0	873	60.0	20.0	0.333333	NM_006804	A8MXA4|B4DUY1|F5H0G2|Q53Y53|Q96HM9	In_Frame_Del	DEL	ENST00000336308.5	hg19	CCDS11341.1																																																																																			.	.	.	none		0.684	STARD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256933.1			-	37809854	CCTCCCTGGGCT	-	37809843	7	5	185	1	0	1	0	1	0	0	0	0	15269	739	26	0	61	0	STARD3	17	37809843	In_Frame_Del	DEL	CCTCCCTGGGCT	TCGA-GL-7966-01A-11D-2201-08	21469674	37809843	43385367	26	10873											
SYT4	6860	hgsc.bcm.edu	37	chr18	40853736	40853736	+	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	atagaatgtaaaggtctcatCaaaagctggatccaaggttt	15	11	9	6	0	2	1	2	0	1	1	4	2	3	2	1	3	1	3	1	3	7	3			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr18:40853736C>G	ENST00000255224.3	-	2	1026	c.658G>C	c.(658-660)Gat>Cat	p.D220H	SYT4_ENST00000586678.1_Intron|SYT4_ENST00000590752.1_Missense_Mutation_p.D202H	NM_020783.3	NP_065834.1	Q9H2B2	SYT4_HUMAN	synaptotagmin IV	220	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Phospholipid binding. {ECO:0000305}.				exocytosis (GO:0006887)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of vesicle fusion (GO:0031339)|neurotransmitter secretion (GO:0007269)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44						AAGGTCTCATCAAAAGCTGGA	0.403																																					p.D220H	NSCLC(85;81 1419 2855 22820 35912)	Atlas-SNP	.											.	SYT4	162	.	0			c.G658C						PASS	.						111	108	109					18																	40853736		2203	4300	6503	SO:0001583	missense	6860	exon2			TCTCATCAAAAGC	BC036538	CCDS11922.1	18q12.3	2013-01-21			ENSG00000132872	ENSG00000132872		"Synaptotagmins"	11512	protein-coding gene	gene with protein product		600103				8058779	Standard	NM_020783		Approved	KIAA1342, HsT1192	uc002law.3	Q9H2B2	OTTHUMG00000132610	ENST00000255224.3:c.658G>C	chr18.hg19:g.40853736C>G	ENSP00000255224:p.Asp220His	147.0	0.0	.		68.0	30.0	.	NM_020783	B4DEU3|Q9P2K4	Missense_Mutation	SNP	ENST00000255224.3	hg19	CCDS11922.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.319387	0.81469	.	.	ENSG00000132872	ENST00000255224;ENST00000442661	T	0.09163	3.01	5.87	5.87	0.94306	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.043597	0.85682	D	0.000000	T	0.33265	0.0857	M	0.64260	1.97	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.69142	0.962;0.962	T	0.00357	-1.1792	10	0.87932	D	0	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	202;220	B4DEU3;Q9H2B2	.;SYT4_HUMAN	H	220;25	ENSP00000255224:D220H	ENSP00000255224:D220H	D	-	1	0	SYT4	39107734	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.729000	0.84864	2.941000	0.99782	0.655000	0.94253	GAT	.	.	.	none		0.403	SYT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255851.2	NM_020783		G	40853736	C	G	40853736	3	3	185	1	0	0	0	0	1	0	0	0	15488	826	29	4	631	4	SYT4	18	40853736	Missense_Mutation	SNP	C	TCGA-GL-7966-01A-11D-2201-08		40853736	37223512	27	10874											
SERPINB10	5273	hgsc.bcm.edu	37	chr18	61585305	61585305	+	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	acttaaaacagccaatgcgaTatatggagagaaaacgtatg	18	8	9	6	2	0	1	0	0	0	1	0	4	0	2	1	1	4	1	1	1	8	4			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr18:61585305T>A	ENST00000238508.3	+	4	400	c.341T>A	c.(340-342)aTa>aAa	p.I114K		NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10	114					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)				GCCAATGCGATATATGGAGAG	0.363																																					p.I114K		Atlas-SNP	.											.	SERPINB10	53	.	0			c.T341A						PASS	.						103	94	97					18																	61585305		2203	4300	6503	SO:0001583	missense	5273	exon3			ATGCGATATATGG	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.341T>A	chr18.hg19:g.61585305T>A	ENSP00000238508:p.Ile114Lys	83.0	0.0	.		44.0	6.0	.	NM_005024	Q4VAX4|Q4VAX7	Missense_Mutation	SNP	ENST00000238508.3	hg19	CCDS11990.1	.	.	.	.	.	.	.	.	.	.	T	9.136	1.012671	0.19277	.	.	ENSG00000242550	ENST00000238508	D	0.84370	-1.84	5.83	3.43	0.39272	Serpin domain (3);	0.694589	0.14087	N	0.342276	D	0.88555	0.6468	H	0.94771	3.58	0.09310	N	1	B	0.27316	0.175	B	0.28465	0.09	T	0.83166	-0.0096	10	0.87932	D	0	.	9.1438	0.36919	0.0:0.1534:0.0:0.8466	.	114	P48595	SPB10_HUMAN	K	114	ENSP00000238508:I114K	ENSP00000238508:I114K	I	+	2	0	SERPINB10	59736285	0.002000	0.14202	0.004000	0.12327	0.109000	0.19521	1.191000	0.32138	1.037000	0.40024	-0.274000	0.10170	ATA	.	.	.	none		0.363	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134012.3	NM_005024		A	61585305	T	A	61585305	3	1	185	1	0	0	0	0	1	0	0	0	14110	1406	49	5	351	5	SERPINB10	18	61585305	Missense_Mutation	SNP	T	TCGA-GL-7966-01A-11D-2201-08	20731569	61585305	16491943	28	10875											
C19orf50	79036	hgsc.bcm.edu	37	chr19	18679377	18679377	+	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	cgaggacctgtcccatgtccAgcctggctccccagccatca	7	7	9	18	1	1	0	1	0	0	0	4	2	4	1	7	2	2	1	7	2	0	0			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr19:18679377A>T	ENST00000602094.1	+	5	1927	c.467A>T	c.(466-468)cAg>cTg	p.Q156L	KXD1_ENST00000539106.1_Missense_Mutation_p.Q156L|KXD1_ENST00000595073.1_Missense_Mutation_p.Q156L|AC005253.4_ENST00000593791.1_RNA|KXD1_ENST00000540691.1_Missense_Mutation_p.Q156L|KXD1_ENST00000222307.4_Missense_Mutation_p.Q156L|KXD1_ENST00000601630.1_Missense_Mutation_p.Q175L|KXD1_ENST00000599319.1_Missense_Mutation_p.Q156L			Q9BQD3	KXDL1_HUMAN	KxDL motif containing 1	156					vesicle-mediated transport (GO:0016192)	BLOC-1 complex (GO:0031083)											TCCCATGTCCAGCCTGGCTCC	0.657																																					p.Q156L		Atlas-SNP	.											C19orf50,caecum,carcinoma,0,1	.	.	.	0			c.A467T						PASS	.						96	89	92					19																	18679377		2203	4300	6503	SO:0001583	missense	79036	exon6			ATGTCCAGCCTGG	AK098346	CCDS12381.1	19p13.11	2011-11-24	2011-11-24	2011-11-24	ENSG00000105700	ENSG00000105700			28420	protein-coding gene	gene with protein product		615178	"chromosome 19 open reading frame 50"	C19orf50		21159114	Standard	NM_001171948		Approved	FLJ25480, MGC2749, KXDL	uc002njo.3	Q9BQD3		ENST00000602094.1:c.467A>T	chr19.hg19:g.18679377A>T	ENSP00000472836:p.Gln156Leu	151.0	0.0	.		141.0	9.0	.	NM_001171948	O76098	Missense_Mutation	SNP	ENST00000602094.1	hg19	CCDS12381.1	.	.	.	.	.	.	.	.	.	.	A	12.86	2.064988	0.36470	.	.	ENSG00000105700	ENST00000540691;ENST00000539106;ENST00000222307	T;T;T	0.45276	0.9;0.9;0.9	4.59	-4.19	0.03835	.	0.517276	0.21501	N	0.073525	T	0.21590	0.0520	N	0.22421	0.69	0.09310	N	1	B	0.11235	0.004	B	0.09377	0.004	T	0.05699	-1.0869	10	0.59425	D	0.04	-5.0797	6.0241	0.19646	0.4521:0.2352:0.3127:0.0	.	156	Q9BQD3	CS050_HUMAN	L	156	ENSP00000443549:Q156L;ENSP00000438903:Q156L;ENSP00000222307:Q156L	ENSP00000222307:Q156L	Q	+	2	0	C19orf50	18540377	0.002000	0.14202	0.000000	0.03702	0.040000	0.13550	0.014000	0.13333	-0.954000	0.03640	-0.345000	0.07892	CAG	.	.	.	none		0.657	KXD1-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465107.1	NM_024069		T	18679377	A	T	18679377	3	4	185	1	0	0	0	0	1	0	0	0	1934	188	7	5	481	5	C19orf50	19	18679377	Missense_Mutation	SNP	A	TCGA-GL-7966-01A-11D-2201-08		18679377	40449606	29	10876											
TCFL5	10732	hgsc.bcm.edu	37	chr20	61490803	61490806	+	Frame_Shift_Del	DEL	AGAA	AGAA	-																															ttcaatttcttgctgataacAgaaagaaaatgctctaggca																										TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	AGAA	AGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr20:61490803_61490806delAGAA	ENST00000335351.3	-	3	996_999	c.904_907delTTCT	c.(904-909)ttctgtfs	p.FC302fs	TCFL5_ENST00000217162.5_Frame_Shift_Del_p.FC254fs	NM_006602.2	NP_006593.2	Q9UL49	TCFL5_HUMAN	transcription factor-like 5 (basic helix-loop-helix)	302					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|urinary_tract(1)	9	Breast(26;5.68e-08)					TGCTGATAACAGAAAGAAAATGCT	0.387																																					p.302_303del		Atlas-INDEL	.											.	TCFL5	43	.	0			c.905_908del						PASS	.																																			SO:0001589	frameshift_variant	10732	exon3			.	AB012124	CCDS13506.1	20q13.33	2013-09-19			ENSG00000101190	ENSG00000101190		"Basic helix-loop-helix proteins"	11646	protein-coding gene	gene with protein product	"HPV-16 E2 binding protein 1"	604745				9763657	Standard	XM_005260185		Approved	Figlb, E2BP-1, CHA, bHLHe82	uc002ydp.3	Q9UL49	OTTHUMG00000032939	ENST00000335351.3:c.904_907delTTCT	chr20.hg19:g.61490807_61490810delAGAA	ENSP00000334294:p.Phe302fs	228.0	0.0	0		210.0	74.0	0.352381	NM_006602	O94771|Q9BYW0	Frame_Shift_Del	DEL	ENST00000335351.3	hg19	CCDS13506.1																																																																																			.	.	.	none		0.387	TCFL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080079.2	NM_006602		-	61490806	AGAA	-	61490803	7	5	185	1	0	1	0	1	0	0	0	0	15711	188	7	0	611	0	TCFL5	20	61490803	Frame_Shift_Del	DEL	AGAA	TCGA-GL-7966-01A-11D-2201-08		61490803	1534717	30	10877											
LSS	4047	hgsc.bcm.edu	37	chr21	47615617	47615617	+	Missense_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	ggtaggtctgccccatacagGcgaaggcctccaggccaaac	10	5	12	14	1	1	0	0	0	1	0	2	1	2	0	5	5	3	1	5	5	4	2			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr21:47615617G>A	ENST00000397728.3	-	19	1868	c.1790C>T	c.(1789-1791)gCc>gTc	p.A597V	LSS_ENST00000356396.4_Missense_Mutation_p.A597V|LSS_ENST00000522411.1_Missense_Mutation_p.A586V|LSS_ENST00000457828.2_Missense_Mutation_p.A517V|AP001468.1_ENST00000594486.1_5'Flank	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	597					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)	p.A597V(1)		cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	21	Breast(49;0.214)					CCCCATACAGGCGAAGGCCTC	0.582																																					p.A597V	Pancreas(114;955 2313 34923 50507)	Atlas-SNP	.											LSS,trunk,malignant_melanoma,0,1	LSS	50	.	1	Substitution - Missense(1)	skin(1)	c.C1790T						PASS	.						127	109	115					21																	47615617		2203	4300	6503	SO:0001583	missense	4047	exon19			ATACAGGCGAAGG	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.1790C>T	chr21.hg19:g.47615617G>A	ENSP00000380837:p.Ala597Val	118.0	0.0	.		67.0	51.0	.	NM_001001438	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Missense_Mutation	SNP	ENST00000397728.3	hg19	CCDS13733.1	.	.	.	.	.	.	.	.	.	.	G	18.98	3.738473	0.69304	.	.	ENSG00000160285	ENST00000356396;ENST00000457828;ENST00000397728;ENST00000522411	T;T;T;T	0.25749	1.78;1.78;1.78;1.78	5.61	5.61	0.85477	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.098347	0.64402	D	0.000001	T	0.31670	0.0804	L	0.39692	1.235	0.80722	D	1	D;D	0.62365	0.979;0.991	B;P	0.49922	0.393;0.626	T	0.01205	-1.1419	10	0.19590	T	0.45	.	19.224	0.93810	0.0:0.0:1.0:0.0	.	586;597	E9PEI9;P48449	.;ERG7_HUMAN	V	597;517;597;586	ENSP00000348762:A597V;ENSP00000409191:A517V;ENSP00000380837:A597V;ENSP00000429133:A586V	ENSP00000348762:A597V	A	-	2	0	LSS	46440045	1.000000	0.71417	1.000000	0.80357	0.709000	0.40893	9.232000	0.95325	2.633000	0.89246	0.655000	0.94253	GCC	.	.	.	none		0.582	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2			A	47615617	G	A	47615617	3	1	185	1	0	0	0	0	1	0	0	0	9072	1203	42	2	424	2	LSS	21	47615617	Missense_Mutation	SNP	G	TCGA-GL-7966-01A-11D-2201-08		47615617	514278	31	10878											
NF2	4771	hgsc.bcm.edu	37	chr22	30061052	30061052	+	Splice_Site	DEL	T	T	-																															aaagcttcgtgttaataagcTggtaagttgagatcctggtt																										TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr22:30061052delT	ENST00000338641.4	+	9	1325	c.884delT	c.(883-885)ctg>cg	p.L295fs	NF2_ENST00000403435.1_Splice_Site_p.L295fs|NF2_ENST00000397789.3_Splice_Site_p.L295fs|NF2_ENST00000361166.4_Splice_Site_p.L295fs|NF2_ENST00000334961.7_Splice_Site_p.L212fs|NF2_ENST00000413209.2_Intron|NF2_ENST00000361676.4_Splice_Site_p.L253fs|NF2_ENST00000353887.4_Splice_Site_p.L212fs|NF2_ENST00000361452.4_Splice_Site_p.L254fs|NF2_ENST00000403999.3_Splice_Site_p.L295fs|NF2_ENST00000347330.5_Splice_Site_p.L136fs	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	295	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(3)|p.F271_L295del(1)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						GTTAATAAGCTGGTAAGTTGA	0.333			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																												p.L295X		Atlas-INDEL	.	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	.	NF2	1312	.	4	Unknown(3)|Deletion - In frame(1)	central_nervous_system(2)|large_intestine(1)|stomach(1)	c.883delC	GRCh37	CD070492	NF2	D		PASS	.						111	103	106					22																	30061052		2202	4300	6502	SO:0001630	splice_region_variant	4771	exon9	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	.	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"A-kinase anchor proteins"	7773	protein-coding gene	gene with protein product	"moesin-ezrin-radixin like", "schwannomin"	607379	"neurofibromin 2 (bilateral acoustic neuroma)"			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.885+1T>-	chr22.hg19:g.30061052delT		28.0	0.0	0		24.0	18.0	0.75	NM_181832	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Frame_Shift_Del	DEL	ENST00000338641.4	hg19	CCDS13861.1																																																																																			.	.	.	none		0.333	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268	Frame_Shift_Del	-	30061052	T	-	30061052	8	5	185	1	0	1	0	1	0	0	1	0	10364	1594	55	0	918	0	NF2	22	30061052	Splice_Site	DEL	T	TCGA-GL-7966-01A-11D-2201-08		30061052	21243514	32	10879											
APOL3	80833	hgsc.bcm.edu	37	chr22	36556768	36556768	+	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	agatccagctgttctgagctGtgtggatcccacctccagcc	7	10	10	14	0	1	2	0	1	1	1	4	3	4	3	5	1	3	3	5	1	0	1	rs11089781	byFrequency	TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr22:36556768G>T	ENST00000349314.2	-	1	209	c.172C>A	c.(172-174)Cag>Aag	p.Q58K	APOL3_ENST00000361710.2_5'UTR|APOL3_ENST00000424878.2_5'UTR|APOL3_ENST00000397293.2_5'UTR|APOL3_ENST00000397287.2_5'UTR	NM_145640.2	NP_663615.1	O95236	APOL3_HUMAN	apolipoprotein L, 3	58					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						GTTCTGAGCTGTGTGGATCCC	0.512																																					p.Q58K		Atlas-SNP	.											.	APOL3	60	.	0			c.C172A						PASS	.						149	122	131					22																	36556768		2203	4300	6503	SO:0001583	missense	80833	exon1			TGAGCTGTGTGGA	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.172C>A	chr22.hg19:g.36556768G>T	ENSP00000344577:p.Gln58Lys	144.0	0.0	.		75.0	11.0	.	NM_145640	B1AHI4|B1AHI5|Q5U5N4|Q9BQ82|Q9BQA3	Missense_Mutation	SNP	ENST00000349314.2	hg19	CCDS13922.1	.	.	.	.	.	.	.	.	.	.	G	5.735	0.320098	0.10845	.	.	ENSG00000128284	ENST00000349314;ENST00000531095	T;T	0.60672	3.74;0.17	2.76	1.71	0.24356	.	680.984000	0.00751	U	0.001072	T	0.34890	0.0913	N	0.08118	0	0.23879	N	0.99658	P	0.43477	0.808	B	0.33799	0.17	T	0.40040	-0.9584	10	0.51188	T	0.08	.	6.0512	0.19787	0.1475:0.0:0.8525:0.0	.	58	O95236	APOL3_HUMAN	K	58;22	ENSP00000344577:Q58K;ENSP00000432271:Q22K	ENSP00000344577:Q58K	Q	-	1	0	APOL3	34886714	0.000000	0.05858	0.006000	0.13384	0.005000	0.04900	-0.640000	0.05440	0.726000	0.32339	0.603000	0.83216	CAG	.	G|0.932;A|0.068	.	alt		0.512	APOL3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319268.1	NM_145641		T	36556768	G	T	36556768	3	4	185	1	0	0	0	0	1	0	0	0	807	1386	48	4	1048	4	APOL3	22	36556768	Missense_Mutation	SNP	G	TCGA-GL-7966-01A-11D-2201-08	6495716	36556768	14747798	33	10880											
CACNG2	10369	hgsc.bcm.edu	37	chr22	37098492	37098492	+	Frame_Shift_Del	DEL	T	T	-																															ggtttcattctcactgacacTtttggtcttgcaaacccctc																										TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chr22:37098492delT	ENST00000300105.6	-	1	1111	c.130delA	c.(130-132)agtfs	p.S44fs	RP1-293L6.1_ENST00000430281.1_RNA	NM_006078.3	NP_006069.1	Q9Y698	CCG2_HUMAN	calcium channel, voltage-dependent, gamma subunit 2	44					membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|neuromuscular junction development (GO:0007528)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	18						TCACTGACACTTTTGGTCTTG	0.488																																					p.S44fs		Atlas-INDEL	.											.	CACNG2	43	.	0			c.131delG						PASS	.						266	225	239					22																	37098492		2203	4300	6503	SO:0001589	frameshift_variant	10369	exon1			.	AF096322	CCDS13931.1	22q13.1	2006-08-01			ENSG00000166862	ENSG00000166862		"Calcium channel subunits"	1406	protein-coding gene	gene with protein product		602911					Standard	NM_006078		Approved	stargazin, MGC138502, MGC138504	uc003aps.2	Q9Y698	OTTHUMG00000030612	ENST00000300105.6:c.130delA	chr22.hg19:g.37098492delT	ENSP00000300105:p.Ser44fs	266.0	0.0	0		174.0	120.0	0.689655	NM_006078	Q2M1M1|Q5TGT3|Q9UGZ7	Frame_Shift_Del	DEL	ENST00000300105.6	hg19	CCDS13931.1																																																																																			.	.	.	none		0.488	CACNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075500.2			-	37098492	T	-	37098492	7	5	185	1	0	1	0	1	0	0	0	0	2559	1609	56	0	857	0	CACNG2	22	37098492	Frame_Shift_Del	DEL	T	TCGA-GL-7966-01A-11D-2201-08	541724	37098492	14206074	34	10881											
ATP2B3	492	hgsc.bcm.edu	37	chrX	152823737	152823737	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggtggctgtgatcgtggcCttcacaggtgcctgcattac	5	12	14	10	1	1	1	1	1	0	0	2	1	1	1	2	4	3	2	2	4	1	2			TCGA-GL-7966-01A-11D-2201-08	TCGA-GL-7966-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	458fa5d9-d07d-4869-8e72-52b7318d7810	b720a727-863a-4225-99b2-bb5cd03e11bd	g.chrX:152823737C>T	ENST00000349466.2	+	16	2927	c.2601C>T	c.(2599-2601)gcC>gcT	p.A867A	ATP2B3_ENST00000460549.1_3'UTR|ATP2B3_ENST00000393842.1_Silent_p.A853A|ATP2B3_ENST00000359149.3_Silent_p.A867A|ATP2B3_ENST00000263519.4_Silent_p.A867A|ATP2B3_ENST00000370186.1_Silent_p.A853A|ATP2B3_ENST00000370181.2_Silent_p.A853A			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	867					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)					TGATCGTGGCCTTCACAGGTG	0.582																																					p.A867A		Atlas-SNP	.											.	ATP2B3	552	.	0			c.C2601T						PASS	.						181	128	146					X																	152823737		2203	4300	6503	SO:0001819	synonymous_variant	492	exon15			CGTGGCCTTCACA	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.2601C>T	chrX.hg19:g.152823737C>T		208.0	0.0	.		133.0	8.0	.	NM_001001344	B7WNR8|B7WNY5|Q12995|Q16858	Silent	SNP	ENST00000349466.2	hg19	CCDS35440.1																																																																																			.	.	.	none		0.582	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060957.1	NM_021949		T	152823737	C	T	152823737	2	4	185	1	0	0	0	0	0	0	0	1	1141	668	24	2		2	ATP2B3	23	152823737	Silent	SNP	C	TCGA-GL-7966-01A-11D-2201-08		152823737	2446823	35	10882											
IPO13	9670	hgsc.bcm.edu	37	chr1	44423086	44423086	+	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	ttccccagcacacagaggccCtcctctacggcttccaatcc	8	8	6	19	1	1	1	0	0	1	1	5	1	5	1	6	2	2	2	6	2	2	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr1:44423086C>A	ENST00000372343.3	+	7	2067	c.1405C>A	c.(1405-1407)Ctc>Atc	p.L469I	IPO13_ENST00000492152.1_3'UTR	NM_014652.3	NP_055467.3	O94829	IPO13_HUMAN	importin 13	469					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)				CACAGAGGCCCTCCTCTACGG	0.572																																					p.L469I		Atlas-SNP	.											.	IPO13	86	.	0			c.C1405A						PASS	.						109	99	103					1																	44423086		2203	4300	6503	SO:0001583	missense	9670	exon7			GAGGCCCTCCTCT	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.1405C>A	chr1.hg19:g.44423086C>A	ENSP00000361418:p.Leu469Ile	153.0	0.0	.		69.0	54.0	.	NM_014652	D3DPY4|Q5T4X3|Q7LC04|Q96HS3|Q9H8N3|Q9UFR1	Missense_Mutation	SNP	ENST00000372343.3	hg19	CCDS503.1	.	.	.	.	.	.	.	.	.	.	C	15.39	2.818926	0.50633	.	.	ENSG00000117408	ENST00000372343	T	0.66995	-0.24	5.69	4.78	0.61160	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000002	T	0.53351	0.1791	L	0.47716	1.5	0.80722	D	1	P	0.37663	0.604	B	0.35550	0.205	T	0.49312	-0.8953	10	0.22109	T	0.4	16.3773	7.0228	0.24924	0.0:0.7119:0.0:0.2881	.	469	O94829	IPO13_HUMAN	I	469	ENSP00000361418:L469I	ENSP00000361418:L469I	L	+	1	0	IPO13	44195673	0.942000	0.31987	1.000000	0.80357	0.991000	0.79684	1.613000	0.36900	1.420000	0.47138	0.561000	0.74099	CTC	.	.	.	none		0.572	IPO13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022846.1	NM_014652		A	44423086	C	A	44423086	3	1	186	1	0	0	0	0	1	0	0	0	7801	681	24	4	1431	4	IPO13	1	44423086	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08		44423086	204827535	1	10883											
SLC30A1	7779	hgsc.bcm.edu	37	chr1	211749303	211749308	+	In_Frame_Del	DEL	ATCTAA	ATCTAA	-																															attacaacacaaagagttggAtctaaatatagcacccagca																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	ATCTAA	ATCTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr1:211749303_211749308delATCTAA	ENST00000367001.4	-	2	1075_1080	c.946_951delTTAGAT	c.(946-951)ttagatdel	p.LD316del		NM_021194.2	NP_067017.2	Q9Y6M5	ZNT1_HUMAN	solute carrier family 30 (zinc transporter), member 1	316					cadmium ion transmembrane transport (GO:0070574)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|cellular zinc ion homeostasis (GO:0006882)|detoxification of cadmium ion (GO:0071585)|in utero embryonic development (GO:0001701)|negative regulation of calcium ion import (GO:0090281)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of zinc ion transmembrane import (GO:0071584)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	calcium channel inhibitor activity (GO:0019855)|zinc ion transmembrane transporter activity (GO:0005385)	p.D317Y(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(3)|prostate(1)	11				OV - Ovarian serous cystadenocarcinoma(81;0.00535)|GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.0604)|Epithelial(68;0.0978)		AAAGAGTTGGATCTAAATATAGCACC	0.364																																					p.316_318del		Atlas-INDEL	.											.	SLC30A1	27	.	1	Substitution - Missense(1)	large_intestine(1)	c.947_952del						PASS	.																																			SO:0001651	inframe_deletion	7779	exon2			.	AF323590	CCDS1499.1	1q32.3	2013-05-22			ENSG00000170385	ENSG00000170385		"Solute carriers"	11012	protein-coding gene	gene with protein product		609521		ZNT1			Standard	NM_021194		Approved	ZRC1	uc001hio.1	Q9Y6M5	OTTHUMG00000036995	ENST00000367001.4:c.946_951delTTAGAT	chr1.hg19:g.211749303_211749308delATCTAA	ENSP00000355968:p.Leu316_Asp317del	214.0	0.0	0		95.0	72.0	0.757895	NM_021194	Q0VAK9|Q9BZF6	In_Frame_Del	DEL	ENST00000367001.4	hg19	CCDS1499.1																																																																																			.	.	.	none		0.364	SLC30A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104738.2			-	211749308	ATCTAA	-	211749303	7	5	186	1	0	1	0	1	0	0	0	0	14566	330	12	0	576	0	SLC30A1	1	211749303	In_Frame_Del	DEL	ATCTAA	TCGA-GL-8500-01A-11D-2396-08	167326217	211749303	37501318	2	10884											
RRP15	51018	hgsc.bcm.edu	37	chr1	218480910	218480910	+	Missense_Mutation	SNP	T	T	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	gaaagatttcatcagtgtttTgagagggatggatggaagta	13	12	14	2	0	2	2	2	1	0	2	2	7	2	5	0	3	0	2	0	3	3	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr1:218480910T>G	ENST00000366932.3	+	4	671	c.641T>G	c.(640-642)tTg>tGg	p.L214W		NM_016052.3	NP_057136.2	Q9Y3B9	RRP15_HUMAN	ribosomal RNA processing 15 homolog (S. cerevisiae)	214						mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)			ACBD6/RRP15(2)	NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	14				all cancers(67;0.0315)|OV - Ovarian serous cystadenocarcinoma(81;0.0411)|GBM - Glioblastoma multiforme(131;0.06)|Epithelial(68;0.248)		ATCAGTGTTTTGAGAGGGATG	0.373																																					p.L214W		Atlas-SNP	.											.	RRP15	33	.	0			c.T641G						PASS	.						109	106	107					1																	218480910		2203	4300	6503	SO:0001583	missense	51018	exon4			GTGTTTTGAGAGG		CCDS1520.2	1q41	2008-02-05			ENSG00000067533	ENSG00000067533			24255	protein-coding gene	gene with protein product		611193	"KIAA0507"	KIAA0507		15769876	Standard	NM_016052		Approved	CGI-115	uc001hlj.3	Q9Y3B9	OTTHUMG00000039494	ENST00000366932.3:c.641T>G	chr1.hg19:g.218480910T>G	ENSP00000355899:p.Leu214Trp	59.0	0.0	.		28.0	24.0	.	NM_016052		Missense_Mutation	SNP	ENST00000366932.3	hg19	CCDS1520.2	.	.	.	.	.	.	.	.	.	.	T	28.0	4.883907	0.91814	.	.	ENSG00000067533	ENST00000366932	T	0.56275	0.47	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.78329	0.4266	M	0.90759	3.145	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	T	0.83015	-0.0170	10	0.87932	D	0	.	16.5764	0.84681	0.0:0.0:0.0:1.0	.	214	Q9Y3B9	RRP15_HUMAN	W	214	ENSP00000355899:L214W	ENSP00000355899:L214W	L	+	2	0	RRP15	216547533	1.000000	0.71417	0.940000	0.37924	0.987000	0.75469	7.935000	0.87658	2.371000	0.80710	0.533000	0.62120	TTG	.	.	.	none		0.373	RRP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095284.1	NM_016052		G	218480910	T	G	218480910	3	3	186	1	0	0	0	0	1	0	0	0	13700	1821	63	5	655	5	RRP15	1	218480910	Missense_Mutation	SNP	T	TCGA-GL-8500-01A-11D-2396-08	6731607	218480910	30769711	3	10885											
GALNT2	2590	hgsc.bcm.edu	37	chr1	230385000	230385000	+	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	agaaggtcccggcaggggaaCccagtcgcccctataaagta	12	5	12	12	2	0	1	0	0	0	1	2	2	1	2	4	4	1	2	4	4	6	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr1:230385000C>A	ENST00000366672.4	+	9	960	c.888C>A	c.(886-888)aaC>aaA	p.N296K	GALNT2_ENST00000543760.1_Missense_Mutation_p.N258K|GALNT2_ENST00000541865.1_Missense_Mutation_p.N206K	NM_004481.3	NP_004472.1	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2	296					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)				GGCAGGGGAACCCAGTCGCCC	0.567																																					p.N296K		Atlas-SNP	.											.	GALNT2	83	.	0			c.C888A						PASS	.						68	73	71					1																	230385000		2203	4300	6503	SO:0001583	missense	2590	exon9			GGGGAACCCAGTC	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.888C>A	chr1.hg19:g.230385000C>A	ENSP00000355632:p.Asn296Lys	74.0	0.0	.		29.0	18.0	.	NM_004481	A8K1Y3|B7Z8V8|C5HU00|Q9NPY4	Missense_Mutation	SNP	ENST00000366672.4	hg19	CCDS1582.1	.	.	.	.	.	.	.	.	.	.	C	12.77	2.038196	0.35989	.	.	ENSG00000143641	ENST00000543760;ENST00000366672;ENST00000543291;ENST00000541865	T;T;T	0.59638	0.25;0.25;0.25	4.99	0.378	0.16204	Glycosyl transferase, family 2 (1);	0.000000	0.85682	D	0.000000	T	0.39118	0.1066	L	0.28649	0.875	0.80722	D	1	B;B	0.27882	0.192;0.063	B;B	0.20577	0.03;0.018	T	0.21690	-1.0238	10	0.66056	D	0.02	.	8.1747	0.31275	0.0:0.5081:0.0:0.4919	.	296;258	Q10471;G3V1S6	GALT2_HUMAN;.	K	258;296;177;206	ENSP00000445017:N258K;ENSP00000355632:N296K;ENSP00000444346:N206K	ENSP00000355632:N296K	N	+	3	2	GALNT2	228451623	0.998000	0.40836	0.988000	0.46212	0.888000	0.51559	0.520000	0.22878	0.244000	0.21351	-0.373000	0.07131	AAC	.	.	.	none		0.567	GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092158.1	NM_004481		A	230385000	C	A	230385000	3	1	186	1	0	0	0	0	1	0	0	0	6220	506	18	4	922	4	GALNT2	1	230385000	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	11904090	230385000	18865621	4	10886											
RGS7	6000	hgsc.bcm.edu	37	chr1	241094065	241094065	+	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	atttgatggccaaaaataggGggtctgcggaatgaaaagaa	16	8	13	4	1	1	3	0	2	1	1	1	4	1	4	1	4	1	0	1	4	7	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr1:241094065G>C	ENST00000407727.1	-	5	336	c.337C>G	c.(337-339)Ccc>Gcc	p.P113A	RGS7_ENST00000366564.1_Missense_Mutation_p.P113A|RGS7_ENST00000331110.7_Missense_Mutation_p.P87A|RGS7_ENST00000366565.1_Missense_Mutation_p.P113A|RGS7_ENST00000366562.4_Missense_Mutation_p.P113A|RGS7_ENST00000366563.1_Missense_Mutation_p.P113A|RGS7_ENST00000348120.2_Intron|RGS7_ENST00000401882.1_Intron|RGS7_ENST00000446183.2_Missense_Mutation_p.P29A			P49802	RGS7_HUMAN	regulator of G-protein signaling 7	113					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)			CAAAAATAGGGGGTCTGCGGA	0.383																																					p.P113A		Atlas-SNP	.											.	RGS7	308	.	0			c.C337G						PASS	.						102	114	110					1																	241094065		2203	4300	6503	SO:0001583	missense	6000	exon6			AATAGGGGGTCTG	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.337C>G	chr1.hg19:g.241094065G>C	ENSP00000384428:p.Pro113Ala	173.0	0.0	.		81.0	68.0	.	NM_002924	Q5T3H4|Q8TD66|Q8TD67|Q8WW09|Q9UNU7|Q9Y6B9	Missense_Mutation	SNP	ENST00000407727.1	hg19		.	.	.	.	.	.	.	.	.	.	G	25.7	4.660563	0.88154	.	.	ENSG00000182901	ENST00000331110;ENST00000366565;ENST00000366564;ENST00000366563;ENST00000446183;ENST00000366562;ENST00000407727	T;T;T;T;T;T;T	0.47177	1.16;1.1;1.14;1.13;0.85;1.14;1.11	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.74604	0.3738	M	0.88640	2.97	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;0.998;0.994;0.999;0.996	T	0.78907	-0.2019	10	0.87932	D	0	-3.1678	17.2744	0.87111	0.0:0.0:1.0:0.0	.	29;87;113;113;113	B7Z223;B7Z257;P49802-2;P49802-5;P49802-3	.;.;.;.;.	A	87;113;113;113;29;113;113	ENSP00000331485:P87A;ENSP00000355523:P113A;ENSP00000355522:P113A;ENSP00000355521:P113A;ENSP00000390138:P29A;ENSP00000355520:P113A;ENSP00000384428:P113A	ENSP00000331485:P87A	P	-	1	0	RGS7	239160688	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	9.000000	0.93564	2.769000	0.95229	0.655000	0.94253	CCC	.	.	.	none		0.383	RGS7-204	KNOWN	basic	protein_coding	protein_coding		NM_002924		C	241094065	G	C	241094065	3	2	186	1	0	0	0	0	1	0	0	0	13323	1232	43	4	1178	4	RGS7	1	241094065	Missense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08	10709065	241094065	8156556	5	10887											
VPS24	51652	hgsc.bcm.edu	37	chr2	86790455	86790455	+	Frame_Shift_Del	DEL	T	T	-																															tgggcggcttctcctgggtcTttccaaacagccccatgacg																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr2:86790455delT	ENST00000263856.4	-	1	145	c.17delA	c.(16-18)aagfs	p.K6fs	CHMP3_ENST00000439940.2_Intron|RNF103-CHMP3_ENST00000604011.1_Intron|CHMP3_ENST00000409727.1_Frame_Shift_Del_p.K6fs|CHMP3_ENST00000409225.2_5'UTR|AC015971.2_ENST00000597638.1_RNA|AC015971.2_ENST00000439077.1_RNA	NM_001193517.1|NM_016079.3	NP_001180446.1|NP_057163.1	Q9Y3E7	CHMP3_HUMAN	charged multivesicular body protein 3	6	Intramolecular interaction with C- terminus.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|endosomal transport (GO:0016197)|membrane organization (GO:0061024)|positive regulation of viral release from host cell (GO:1902188)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)											CTCCTGGGTCTTTCCAAACAG	0.632																																					p.K6fs		Atlas-INDEL	.											.	.	.	.	0			c.18delG						PASS	.						120	123	122					2																	86790455		2203	4300	6503	SO:0001589	frameshift_variant	51652	exon1			.	AF219226	CCDS33236.1, CCDS42707.1, CCDS54375.1	2p11.2	2011-09-21	2011-09-21	2011-09-21	ENSG00000115561	ENSG00000115561		"Charged multivesicular body proteins"	29865	protein-coding gene	gene with protein product		610052	"vacuolar protein sorting 24 (yeast)", "vacuolar protein sorting 24 homolog (S. cerevisiae)"	VPS24		11549700, 12878588	Standard	NM_016079		Approved	NEDF, CGI-149		Q9Y3E7	OTTHUMG00000153189	ENST00000263856.4:c.17delA	chr2.hg19:g.86790455delT	ENSP00000263856:p.Lys6fs	223.0	0.0	0		219.0	93.0	0.424658	NM_001193517	A8K3W0|B4DG34|B8ZZM0|B8ZZX5|Q3ZTS9|Q53S71|Q53SU5|Q9NZ51	Frame_Shift_Del	DEL	ENST00000263856.4	hg19	CCDS33236.1																																																																																			.	.	.	none		0.632	CHMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330015.2	NM_016079		-	86790455	T	-	86790455	7	5	186	1	0	1	0	1	0	0	0	0	17207	1609	56	0	675	0	VPS24	2	86790455	Frame_Shift_Del	DEL	T	TCGA-GL-8500-01A-11D-2396-08		86790455	156408918	6	10888											
SLC40A1	30061	hgsc.bcm.edu	37	chr2	190428363	190428363	+	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	gactgacagagattatgggcAcagattcaggacttgtctcc	11	10	11	9	0	2	3	1	1	1	2	3	6	2	4	1	2	0	1	1	2	1	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr2:190428363A>T	ENST00000261024.2	-	7	1775	c.1349T>A	c.(1348-1350)gTg>gAg	p.V450E		NM_014585.5	NP_055400.1	Q9NP59	S40A1_HUMAN	solute carrier family 40 (iron-regulated transporter), member 1	450					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)			GATTATGGGCACAGATTCAGG	0.368																																					p.V450E		Atlas-SNP	.											.	SLC40A1	51	.	0			c.T1349A						PASS	.						78	80	80					2																	190428363		2203	4300	6503	SO:0001583	missense	30061	exon7			ATGGGCACAGATT	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.1349T>A	chr2.hg19:g.190428363A>T	ENSP00000261024:p.Val450Glu	118.0	0.0	.		95.0	40.0	.	NM_014585	Q6FI62|Q7Z4F8|Q8IVB2|Q9NRL0	Missense_Mutation	SNP	ENST00000261024.2	hg19	CCDS2299.1	.	.	.	.	.	.	.	.	.	.	A	13.30	2.195338	0.38806	.	.	ENSG00000138449	ENST00000261024	D	0.92397	-3.03	6.02	0.296	0.15757	Major facilitator superfamily domain, general substrate transporter (1);	0.667620	0.15785	N	0.244735	T	0.81245	0.4782	N	0.16368	0.405	0.22827	N	0.998683	B	0.02656	0.0	B	0.06405	0.002	T	0.61237	-0.7103	10	0.02654	T	1	-0.1187	12.0936	0.53742	0.5205:0.0:0.0:0.4795	.	450	Q9NP59	S40A1_HUMAN	E	450	ENSP00000261024:V450E	ENSP00000261024:V450E	V	-	2	0	SLC40A1	190136608	0.973000	0.33851	0.001000	0.08648	0.433000	0.31745	1.091000	0.30915	-0.201000	0.10284	0.528000	0.53228	GTG	.	.	.	none		0.368	SLC40A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255916.2			T	190428363	A	T	190428363	3	4	186	1	0	0	0	0	1	0	0	0	14641	159	6	5	374	5	SLC40A1	2	190428363	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	103637908	190428363	52771010	7	10889											
HECW2	57520	hgsc.bcm.edu	37	chr2	197187250	197187250	+	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	ggactggaatggttagtttcCccagaaaacgcttgatgatg	11	11	12	7	1	0	3	0	2	0	1	1	5	1	5	2	3	1	3	2	3	4	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr2:197187250C>T	ENST00000260983.3	-	7	1018	c.836G>A	c.(835-837)gGg>gAg	p.G279E	HECW2_ENST00000409111.1_5'UTR	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	279	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				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						GGTTAGTTTCCCCAGAAAACG	0.413																																					p.G279E		Atlas-SNP	.											.	HECW2	239	.	0			c.G836A						PASS	.						123	126	125					2																	197187250		2203	4300	6503	SO:0001583	missense	57520	exon7			AGTTTCCCCAGAA	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.836G>A	chr2.hg19:g.197187250C>T	ENSP00000260983:p.Gly279Glu	223.0	0.0	.		194.0	77.0	.	NM_020760	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Missense_Mutation	SNP	ENST00000260983.3	hg19	CCDS33354.1	.	.	.	.	.	.	.	.	.	.	C	33	5.280284	0.95489	.	.	ENSG00000138411	ENST00000260983	T	0.77489	-1.1	5.49	5.49	0.81192	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.221358	0.47093	D	0.000253	D	0.88496	0.6452	M	0.75447	2.3	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88816	0.3295	10	0.87932	D	0	.	19.6359	0.95733	0.0:1.0:0.0:0.0	.	279	Q9P2P5	HECW2_HUMAN	E	279	ENSP00000260983:G279E	ENSP00000260983:G279E	G	-	2	0	HECW2	196895495	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.635000	0.83286	2.878000	0.98634	0.650000	0.86243	GGG	.	.	.	none		0.413	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760		T	197187250	C	T	197187250	3	4	186	1	0	0	0	0	1	0	0	0	7050	623	22	2	3974	2	HECW2	2	197187250	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	6758887	197187250	46012123	8	10890											
ABCB6	10058	hgsc.bcm.edu	37	chr2	220075814	220075814	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caactccaatgtgagaccggAgagaggcctgggtcacctag	11	6	13	11	1	1	2	1	1	0	2	2	5	2	3	4	3	1	0	4	3	3	1	rs387906909		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr2:220075814A>G	ENST00000265316.3	-	15	2301	c.1985T>C	c.(1984-1986)cTc>cCc	p.L662P	ABCB6_ENST00000439002.2_Missense_Mutation_p.L616P	NM_005689.2	NP_005680.1	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 6 (Langereis blood group)	662	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				brain development (GO:0007420)|cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|porphyrin-containing compound biosynthetic process (GO:0006779)|skin development (GO:0043588)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial envelope (GO:0005740)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|efflux transmembrane transporter activity (GO:0015562)|heme binding (GO:0020037)|heme transporter activity (GO:0015232)|heme-transporting ATPase activity (GO:0015439)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	34		Renal(207;0.0474)		Epithelial(149;1.22e-06)|all cancers(144;0.000201)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GTGAGACCGGAGAGAGGCCTG	0.582																																					p.L662P		Atlas-SNP	.											.	ABCB6	76	.	0			c.T1985C						PASS	.						108	106	106					2																	220075814		2203	4300	6503	SO:0001583	missense	10058	exon15			GACCGGAGAGAGG	AF070598	CCDS2436.1	2q36	2014-08-27	2014-08-27		ENSG00000115657	ENSG00000115657		"ATP binding cassette transporters / subfamily B"	47	protein-coding gene	gene with protein product	"ATP-binding cassette half-transporter"	605452	"ATP-binding cassette, sub-family B (MDR/TAP), member 6"			8894702, 9110174	Standard	NM_005689		Approved	EST45597, umat, MTABC3	uc002vkc.2	Q9NP58	OTTHUMG00000133131	ENST00000265316.3:c.1985T>C	chr2.hg19:g.220075814A>G	ENSP00000265316:p.Leu662Pro	183.0	0.0	.		142.0	55.0	.	NM_005689	O75542|Q49A66|Q59GQ5|Q6ZME6|Q96ME8|Q9HAQ6|Q9HAQ7	Missense_Mutation	SNP	ENST00000265316.3	hg19	CCDS2436.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.9|20.9	4.065625|4.065625	0.76187|0.76187	.|.	.|.	ENSG00000115657|ENSG00000115657	ENST00000265316;ENST00000439002|ENST00000295750	D;D|.	0.92299|.	-3.01;-3.01|.	4.7|4.7	4.7|4.7	0.59300|0.59300	ATPase, AAA+ type, core (1);ABC transporter-like (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.79885|0.79885	0.4523|0.4523	M|M	0.89478|0.89478	3.035|3.035	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.83275|.	0.994;0.996|.	D|D	0.83833|0.83833	0.0253|0.0253	10|5	0.87932|.	D|.	0|.	-18.3339|-18.3339	14.286|14.286	0.66247|0.66247	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	616;662|.	Q9NP58-4;Q9NP58|.	.;ABCB6_HUMAN|.	P|P	662;616|510	ENSP00000265316:L662P;ENSP00000394333:L616P|.	ENSP00000265316:L662P|.	L|S	-|-	2|1	0|0	ABCB6|ABCB6	219784058|219784058	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.828000|0.828000	0.46876|0.46876	8.912000|8.912000	0.92726|0.92726	2.084000|2.084000	0.62774|0.62774	0.528000|0.528000	0.53228|0.53228	CTC|TCC	.	.	.	none		0.582	ABCB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256820.2	NM_005689		G	220075814	A	G	220075814	3	3	186	1	0	0	0	0	1	0	0	0	45	304	11	3	563	3	ABCB6	2	220075814	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	22888564	220075814	23123559	9	10891											
SEC13	6396	hgsc.bcm.edu	37	chr3	10342967	10342967	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgctcgttctgctggcccTctgtcactgatgctgatacg	5	13	10	13	2	3	2	1	2	2	0	4	2	3	2	1	1	4	4	1	1	1	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr3:10342967T>C	ENST00000350697.3	-	9	1072	c.947A>G	c.(946-948)gAg>gGg	p.E316G	SEC13_ENST00000383801.2_Missense_Mutation_p.E362G|SEC13_ENST00000397117.1_Intron|SEC13_ENST00000492602.1_Intron|SEC13_ENST00000337354.4_Missense_Mutation_p.E319G|SEC13_ENST00000397109.3_Missense_Mutation_p.E302G	NM_183352.1	NP_899195.1	P55735	SEC13_HUMAN	SEC13 homolog (S. cerevisiae)	316					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)				NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	17						CTGCTGGCCCTCTGTCACTGA	0.612																																					p.E316G		Atlas-SNP	.											.	SEC13	35	.	0			c.A947G						PASS	.						120	96	104					3																	10342967		2203	4300	6503	SO:0001583	missense	6396	exon9			TGGCCCTCTGTCA		CCDS2599.1, CCDS46751.1, CCDS63540.1	3p25-p24	2013-01-10	2006-11-07	2006-11-07	ENSG00000157020	ENSG00000157020		"WD repeat domain containing"	10697	protein-coding gene	gene with protein product		600152	"SEC13 (S. cerevisiae)-like 1", "SEC13-like 1 (S. cerevisiae)"	D3S1231E, SEC13L1		7987303	Standard	NM_183352		Approved	SEC13R, npp-20	uc003bvn.3	P55735	OTTHUMG00000128671	ENST00000350697.3:c.947A>G	chr3.hg19:g.10342967T>C	ENSP00000312122:p.Glu316Gly	130.0	0.0	.		98.0	40.0	.	NM_183352	A8MV37|B4DXJ1|Q5BJF0|Q9BRM6|Q9BUG7	Missense_Mutation	SNP	ENST00000350697.3	hg19	CCDS2599.1	.	.	.	.	.	.	.	.	.	.	T	17.66	3.444051	0.63067	.	.	ENSG00000157020	ENST00000397109;ENST00000337354;ENST00000350697;ENST00000383801	T;T;T;T	0.69806	0.84;-0.3;-0.43;-0.37	5.23	5.23	0.72850	.	0.288120	0.41001	D	0.000976	T	0.53706	0.1813	L	0.36672	1.1	0.54753	D	0.999984	P;B	0.34522	0.455;0.0	B;B	0.30105	0.111;0.0	T	0.53229	-0.8468	10	0.27785	T	0.31	.	13.0995	0.59212	0.0:0.0:0.0:1.0	.	362;316	B4DXJ1;P55735	.;SEC13_HUMAN	G	302;319;316;362	ENSP00000380298:E302G;ENSP00000336566:E319G;ENSP00000312122:E316G;ENSP00000373312:E362G	ENSP00000336566:E319G	E	-	2	0	SEC13	10317967	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	7.914000	0.87478	1.971000	0.57363	0.533000	0.62120	GAG	.	.	.	none		0.612	SEC13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250563.3			C	10342967	T	C	10342967	3	2	186	1	0	0	0	0	1	0	0	0	13993	1551	54	3	25	3	SEC13	3	10342967	Missense_Mutation	SNP	T	TCGA-GL-8500-01A-11D-2396-08		10342967	187679463	10	10892											
MLH1	4292	hgsc.bcm.edu	37	chr3	37042512	37042512	+	Missense_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	tgcagtcctttgaggatttaGccagtatttctacctatggc	8	15	9	9	0	1	1	0	1	1	0	2	2	2	2	3	2	3	2	3	2	4	7	rs63750133		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr3:37042512G>A	ENST00000231790.2	+	3	490	c.274G>A	c.(274-276)Gcc>Acc	p.A92T	MLH1_ENST00000536378.1_5'UTR|MLH1_ENST00000458205.2_5'UTR|MLH1_ENST00000492474.1_3'UTR|MLH1_ENST00000455445.2_5'UTR|MLH1_ENST00000539477.1_5'UTR|MLH1_ENST00000435176.1_5'UTR	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	92					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)			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						TGAGGATTTAGCCAGTATTTC	0.348		1	"D, Mis, N, F, S"		"colorectal, endometrial, ovarian, CNS"	"colorectal, endometrial, ovarian, CNS"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.A92T		Atlas-SNP	.	yes	Rec	yes	"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	3	3p21.3	4292	E.coli MutL homolog gene		"E, O"	.	MLH1	226	.	0			c.G274A						PASS	.						152	151	152					3																	37042512		2203	4300	6503	SO:0001583	missense	4292	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	GATTTAGCCAGTA	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.274G>A	chr3.hg19:g.37042512G>A	ENSP00000231790:p.Ala92Thr	111.0	0.0	.		82.0	41.0	.	NM_000249	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	hg19	CCDS2663.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.195561	0.38806	.	.	ENSG00000076242	ENST00000231790;ENST00000436867;ENST00000537937	D	0.94537	-3.45	5.91	4.11	0.48088	DNA mismatch repair protein, N-terminal (1);ATPase-like, ATP-binding domain (4);	0.269957	0.37669	N	0.001984	D	0.84683	0.5526	N	0.04018	-0.295	0.80722	D	1	B;B	0.16166	0.016;0.009	B;B	0.25405	0.06;0.038	T	0.75434	-0.3319	10	0.20046	T	0.44	-6.4566	8.0469	0.30555	0.0732:0.0:0.6432:0.2836	.	92;92	Q53GX1;P40692	.;MLH1_HUMAN	T	92;58;58	ENSP00000231790:A92T	ENSP00000231790:A92T	A	+	1	0	MLH1	37017516	1.000000	0.71417	0.962000	0.40283	0.992000	0.81027	1.745000	0.38278	0.829000	0.34733	-0.169000	0.13324	GCC	.	.	.	alt		0.348	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249		A	37042512	G	A	37042512	3	1	186	1	0	0	0	0	1	0	0	0	9624	971	34	2	284	2	MLH1	3	37042512	Missense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08	26699545	37042512	160979918	11	10893											
XYLB	9942	hgsc.bcm.edu	37	chr3	38404484	38404484	+	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	ggcttcgacttctctcaagtCctagccttgtccggggcggg	4	11	13	13	3	2	0	1	0	1	0	6	1	4	0	3	4	1	1	3	4	2	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr3:38404484C>G	ENST00000207870.3	+	4	357	c.267C>G	c.(265-267)gtC>gtG	p.V89V	XYLB_ENST00000542835.1_Intron	NM_005108.3	NP_005099.2	O75191	XYLB_HUMAN	xylulokinase homolog (H. influenzae)	89					carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|D-xylose metabolic process (GO:0042732)|generation of precursor metabolites and energy (GO:0006091)|xylulose catabolic process (GO:0005998)|xylulose metabolic process (GO:0005997)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|xylulokinase activity (GO:0004856)			endometrium(3)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(1)|prostate(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.00372)|Kidney(284;0.00405)		TCTCTCAAGTCCTAGCCTTGT	0.532																																					p.V89V		Atlas-SNP	.											.	XYLB	50	.	0			c.C267G						PASS	.						108	108	108					3																	38404484		2203	4300	6503	SO:0001819	synonymous_variant	9942	exon4			TCAAGTCCTAGCC	AB015046	CCDS2678.1	3p22-p21.3	2006-12-18	2001-12-04		ENSG00000093217	ENSG00000093217			12839	protein-coding gene	gene with protein product		604049	"xylulokinase (H. influenzae) homolog"			9763671	Standard	NM_005108		Approved	FLJ10343, FLJ12539	uc003cic.2	O75191	OTTHUMG00000131294	ENST00000207870.3:c.267C>G	chr3.hg19:g.38404484C>G		116.0	0.0	.		109.0	48.0	.	NM_005108	B2RAW4|B4DDT2|B9EH64	Silent	SNP	ENST00000207870.3	hg19	CCDS2678.1																																																																																			.	.	.	none		0.532	XYLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254062.2	NM_005108		G	38404484	C	G	38404484	2	3	186	1	0	0	0	0	0	0	0	1	17474	842	30	4		4	XYLB	3	38404484	Silent	SNP	C	TCGA-GL-8500-01A-11D-2396-08	1361972	38404484	159617946	12	10894											
SMARCC1	6599	hgsc.bcm.edu	37	chr3	47716999	47716999	+	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	tcttggagtaaatgtcagtaCggagaccaaagttctgcaaa	14	10	10	7	1	3	1	1	0	2	1	3	3	3	2	1	2	2	4	1	2	5	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr3:47716999C>G	ENST00000254480.5	-	18	1924	c.1805G>C	c.(1804-1806)cGt>cCt	p.R602P	SMARCC1_ENST00000425518.1_5'UTR	NM_003074.3	NP_003065.3	Q92922	SMRC1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	602					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|insulin receptor signaling pathway (GO:0008286)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)	p.R602H(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(15)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)		AATGTCAGTACGGAGACCAAA	0.363																																					p.R602P		Atlas-SNP	.											SMARCC1,NS,carcinoma,0,1	SMARCC1	85	.	1	Substitution - Missense(1)	endometrium(1)	c.G1805C						PASS	.						151	143	146					3																	47716999		2203	4300	6503	SO:0001583	missense	6599	exon18			TCAGTACGGAGAC	U66615	CCDS2758.1	3p21.31	2008-05-15			ENSG00000173473	ENSG00000173473			11104	protein-coding gene	gene with protein product		601732				8804307	Standard	NM_003074		Approved	BAF155, SRG3, Rsc8, CRACC1	uc003crq.2	Q92922	OTTHUMG00000133519	ENST00000254480.5:c.1805G>C	chr3.hg19:g.47716999C>G	ENSP00000254480:p.Arg602Pro	49.0	0.0	.		49.0	2.0	.	NM_003074	Q17RS0|Q6P172|Q8IWH2	Missense_Mutation	SNP	ENST00000254480.5	hg19	CCDS2758.1	.	.	.	.	.	.	.	.	.	.	C	32	5.154800	0.94686	.	.	ENSG00000173473	ENST00000254480	T	0.51574	0.7	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.72867	0.3514	M	0.83012	2.62	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	T	0.75153	-0.3418	10	0.87932	D	0	-16.3291	19.1586	0.93522	0.0:1.0:0.0:0.0	.	602	Q92922	SMRC1_HUMAN	P	602	ENSP00000254480:R602P	ENSP00000254480:R602P	R	-	2	0	SMARCC1	47692003	1.000000	0.71417	0.991000	0.47740	0.919000	0.55068	7.614000	0.82996	2.873000	0.98535	0.563000	0.77884	CGT	.	.	.	none		0.363	SMARCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257491.1			G	47716999	C	G	47716999	3	3	186	1	0	0	0	0	1	0	0	0	14788	536	19	4	1556	4	SMARCC1	3	47716999	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	9312515	47716999	150305431	13	10895											
SLC38A3	10991	hgsc.bcm.edu	37	chr3	50257565	50257565	+	RNA	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcttgagcttcatcatcAttgactgggcctcagggacc	8	11	11	11	0	4	3	4	3	0	0	4	4	4	4	2	2	2	2	2	2	0	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr3:50257565A>G	ENST00000420502.1	+	0	1624									solute carrier family 38, member 3											breast(1)|cervix(1)|endometrium(1)|lung(3)	6				BRCA - Breast invasive adenocarcinoma(193;0.000275)|KIRC - Kidney renal clear cell carcinoma(197;0.00548)|Kidney(197;0.00615)		CTTCATCATCATTGACTGGGC	0.557																																					p.I491V		Atlas-SNP	.											.	SLC38A3	22	.	0			c.A1471G						PASS	.						93	88	89					3																	50257565		2026	4180	6206			10991	exon16			ATCATCATTGACT	U49082	CCDS74940.1	3p21.3	2013-05-22			ENSG00000188338	ENSG00000188338		"Solute carriers"	18044	protein-coding gene	gene with protein product		604437				10619430, 10823827	Standard	XM_006712954		Approved	G17, SN1	uc003cyn.4	Q99624	OTTHUMG00000156764		chr3.hg19:g.50257565A>G		14.0	0.0	.		13.0	10.0	.	NM_006841		Missense_Mutation	SNP	ENST00000420502.1	hg19																																																																																				.	.	.	none		0.557	SLC38A3-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000345635.2	NM_006841		G	50257565	A	G	50257565	1	3	186	0	1	0	0	0	0	0	0	0	14618	217	8	3		3	SLC38A3	3	50257565	RNA	SNP	A	TCGA-GL-8500-01A-11D-2396-08	2540566	50257565	147764865	14	10896											
ABHD10	55347	hgsc.bcm.edu	37	chr3	111700691	111700691	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaccttccaaacctggcttAtaagaagctaaaaggcaaaa	18	7	7	9	0	0	2	0	0	0	2	1	2	1	2	3	2	2	3	3	2	8	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr3:111700691A>G	ENST00000273359.3	+	2	230	c.203A>G	c.(202-204)tAt>tGt	p.Y68C	ABHD10_ENST00000494817.1_Missense_Mutation_p.Y68C|ABHD10_ENST00000534857.1_Intron	NM_018394.2	NP_060864.1	Q9NUJ1	ABHDA_HUMAN	abhydrolase domain containing 10	68					glucuronoside catabolic process (GO:0019391)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			large_intestine(2)|lung(7)|skin(1)	10						AACCTGGCTTATAAGAAGCTA	0.378																																					p.Y68C		Atlas-SNP	.											.	ABHD10	20	.	0			c.A203G						PASS	.						126	123	124					3																	111700691		2203	4300	6503	SO:0001583	missense	55347	exon2			TGGCTTATAAGAA	AL713726	CCDS2963.1, CCDS63718.1	3q13.2	2012-03-26			ENSG00000144827	ENSG00000144827		"Abhydrolase domain containing"	25656	protein-coding gene	gene with protein product						22294686	Standard	NM_018394		Approved	FLJ11342	uc003dyk.5	Q9NUJ1	OTTHUMG00000159280	ENST00000273359.3:c.203A>G	chr3.hg19:g.111700691A>G	ENSP00000273359:p.Tyr68Cys	136.0	0.0	.		140.0	62.0	.	NM_001272069	B7Z6A8|C9IZX5|D3DN63|Q8TCF9	Missense_Mutation	SNP	ENST00000273359.3	hg19	CCDS2963.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.190688	0.78789	.	.	ENSG00000144827	ENST00000273359;ENST00000494817	T	0.48836	0.8	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.69115	0.3075	M	0.77820	2.39	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.72962	-0.4132	10	0.62326	D	0.03	-30.1278	14.7236	0.69326	1.0:0.0:0.0:0.0	.	68	Q9NUJ1	ABHDA_HUMAN	C	68	ENSP00000273359:Y68C	ENSP00000273359:Y68C	Y	+	2	0	ABHD10	113183381	1.000000	0.71417	0.953000	0.39169	0.988000	0.76386	8.935000	0.92923	2.117000	0.64856	0.459000	0.35465	TAT	.	.	.	none		0.378	ABHD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354326.1	NM_018394		G	111700691	A	G	111700691	3	3	186	1	0	0	0	0	1	0	0	0	74	449	16	3	209	3	ABHD10	3	111700691	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	61443126	111700691	86321739	15	10897											
ZMAT3	64393	hgsc.bcm.edu	37	chr3	178785387	178785387	+	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	ctcccctcccttcgataactCttcttcccctgcaagaggca	7	11	5	18	1	2	1	0	0	2	1	6	2	5	1	5	1	2	2	5	1	2	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr3:178785387C>A	ENST00000311417.2	-	2	895	c.154G>T	c.(154-156)Gag>Tag	p.E52*	ZMAT3_ENST00000432729.1_Nonsense_Mutation_p.E52*	NM_022470.3	NP_071915.1			zinc finger, matrin-type 3											breast(1)|endometrium(1)|large_intestine(6)|lung(2)|ovary(2)|prostate(1)|skin(1)	14	all_cancers(143;3.31e-18)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;6.74e-27)|GBM - Glioblastoma multiforme(14;0.00448)|BRCA - Breast invasive adenocarcinoma(182;0.0527)			TTCGATAACTCTTCTTCCCCT	0.552																																					p.E52X		Atlas-SNP	.											ZMAT3,NS,carcinoma,0,1	ZMAT3	42	.	0			c.G154T						PASS	.						123	116	119					3																	178785387		2203	4300	6503	SO:0001587	stop_gained	64393	exon2			ATAACTCTTCTTC	AK122768	CCDS3224.1, CCDS46962.1	3q26.32	2012-10-05	2010-09-15		ENSG00000172667	ENSG00000172667		"Zinc fingers, matrin-type"	29983	protein-coding gene	gene with protein product		606452				9400996, 11689294	Standard	NM_022470		Approved	WIG1, MGC10613, FLJ12296, WIG-1, PAG608	uc003fjg.3	Q9HA38	OTTHUMG00000157290	ENST00000311417.2:c.154G>T	chr3.hg19:g.178785387C>A	ENSP00000311221:p.Glu52*	161.0	0.0	.		123.0	45.0	.	NM_022470		Nonsense_Mutation	SNP	ENST00000311417.2	hg19	CCDS3224.1	.	.	.	.	.	.	.	.	.	.	C	44	11.170319	0.99525	.	.	ENSG00000172667	ENST00000311417;ENST00000432729;ENST00000414084	.	.	.	5.86	5.86	0.93980	.	0.278038	0.40554	N	0.001064	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	-15.196	20.1931	0.98233	0.0:1.0:0.0:0.0	.	.	.	.	X	52	.	ENSP00000311221:E52X	E	-	1	0	ZMAT3	180268081	1.000000	0.71417	0.999000	0.59377	0.928000	0.56348	5.278000	0.65592	2.771000	0.95319	0.563000	0.77884	GAG	.	.	.	none		0.552	ZMAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348336.2	NM_152240		A	178785387	C	A	178785387	4	1	186	1	0	0	0	0	0	1	0	0	17705	922	32	4	735	4	ZMAT3	3	178785387	Nonsense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	67084696	178785387	19237043	16	10898											
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123229112	123229112	+	Frame_Shift_Del	DEL	T	T	-																															aattatcaaaagctgtgctgTtttggctgaattataaggcc																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr4:123229112delT	ENST00000264501.4	+	58	10223	c.9850delT	c.(9850-9852)tttfs	p.F3284fs	KIAA1109_ENST00000455637.1_Frame_Shift_Del_p.F3284fs|KIAA1109_ENST00000388738.3_Frame_Shift_Del_p.F3284fs			Q2LD37	K1109_HUMAN	KIAA1109	3284					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						AGCTGTGCTGTTTTGGCTGAA	0.343																																					p.L3283fs		Atlas-INDEL	.											.	KIAA1109	424	.	0			c.9849delG						PASS	.						132	129	130					4																	123229112		1827	4092	5919	SO:0001589	frameshift_variant	84162	exon56			.	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.9850delT	chr4.hg19:g.123229112delT	ENSP00000264501:p.Phe3284fs	193.0	0.0	0		171.0	65.0	0.380117	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Frame_Shift_Del	DEL	ENST00000264501.4	hg19	CCDS43267.1																																																																																			.	.	.	none		0.343	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		-	123229112	T	-	123229112	7	5	186	1	0	1	0	1	0	0	0	0	8215	1725	60	0	10072	0	KIAA1109	4	123229112	Frame_Shift_Del	DEL	T	TCGA-GL-8500-01A-11D-2396-08		123229112	67925164	17	10899											
SPOCK3	50859	hgsc.bcm.edu	37	chr4	167713322	167713322	+	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	tcaaatttagaaatcttactGcttctctcaggcctcagcaa	12	13	5	11	0	5	1	3	0	2	1	6	1	5	1	1	1	3	2	1	1	5	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr4:167713322G>T	ENST00000357154.3	-	8	854	c.717C>A	c.(715-717)agC>agA	p.S239R	SPOCK3_ENST00000541637.1_Splice_Site_p.S141R|SPOCK3_ENST00000535728.1_Intron|SPOCK3_ENST00000511269.1_Splice_Site_p.S236R|SPOCK3_ENST00000502330.1_Splice_Site_p.S239R|SPOCK3_ENST00000512648.1_Splice_Site_p.S236R|SPOCK3_ENST00000506886.1_Splice_Site_p.S239R|SPOCK3_ENST00000541354.1_Splice_Site_p.S119R|SPOCK3_ENST00000510741.1_Intron|SPOCK3_ENST00000511531.1_Splice_Site_p.S239R|SPOCK3_ENST00000504953.1_Splice_Site_p.S236R|SPOCK3_ENST00000421836.2_Splice_Site_p.S188R|SPOCK3_ENST00000507137.1_5'UTR|SPOCK3_ENST00000512681.1_Splice_Site_p.S141R|SPOCK3_ENST00000357545.4_Splice_Site_p.S236R|SPOCK3_ENST00000534949.1_Splice_Site_p.S143R	NM_016950.2	NP_058646.2	Q9BQ16	TICN3_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3	239					negative regulation of endopeptidase activity (GO:0010951)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|metalloendopeptidase inhibitor activity (GO:0008191)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	38	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		AAATCTTACTGCTTCTCTCAG	0.373																																					p.S239R		Atlas-SNP	.											.	SPOCK3	90	.	0			c.C717A						PASS	.						101	84	90					4																	167713322		2203	4300	6503	SO:0001630	splice_region_variant	50859	exon8			CTTACTGCTTCTC	AJ001454	CCDS34095.1, CCDS54817.1, CCDS56343.1, CCDS56344.1, CCDS56346.1, CCDS56347.1, CCDS58931.1, CCDS75207.1	4q32.3	2011-10-10			ENSG00000196104	ENSG00000196104			13565	protein-coding gene	gene with protein product		607989				11751414	Standard	NM_001204352		Approved	testican-3	uc003iri.1	Q9BQ16	OTTHUMG00000161190	ENST00000357154.3:c.718+1C>A	chr4.hg19:g.167713322G>T		75.0	0.0	.		60.0	4.0	.	NM_016950	B2R7M7|B3KR67|B4DGK5|B4DHB4|B4DHV3|B4DI46|B4DJY3|E7EP61|F5H099|O75705|Q6UW53|Q96Q26	Missense_Mutation	SNP	ENST00000357154.3	hg19	CCDS54817.1	.	.	.	.	.	.	.	.	.	.	G	14.33	2.504073	0.44558	.	.	ENSG00000196104	ENST00000357154;ENST00000357545;ENST00000504953;ENST00000506886;ENST00000511531;ENST00000502330;ENST00000541354;ENST00000512681;ENST00000511269;ENST00000421836;ENST00000541637;ENST00000534949;ENST00000512648;ENST00000510403	T;T;T;T;T;T;T;T;T;T;T;T;T;D	0.87412	1.48;1.49;1.49;1.48;1.48;1.48;1.4;0.92;1.49;1.29;0.92;1.18;2.2;-2.25	5.33	4.47	0.54385	SPARC/Testican, calcium-binding domain (1);EF-hand-like domain (1);	0.410761	0.26800	N	0.022422	D	0.89350	0.6690	L	0.59436	1.845	0.37036	D	0.896894	D;D;D;D;D;D;D	0.64830	0.959;0.967;0.958;0.994;0.967;0.98;0.984	P;P;P;D;P;P;P	0.63192	0.629;0.664;0.821;0.912;0.587;0.711;0.81	D	0.87800	0.2624	10	0.27082	T	0.32	-13.9637	9.7077	0.40225	0.2078:0.0:0.7921:0.0	.	141;143;188;248;239;236;239	B4DGK5;F5H099;B4DHB4;B4DFW5;Q9BQ16-2;Q9BQ16-1;Q9BQ16	.;.;.;.;.;.;TICN3_HUMAN	R	239;236;236;239;239;239;119;141;236;188;141;143;236;118	ENSP00000349677:S239R;ENSP00000350153:S236R;ENSP00000425570:S236R;ENSP00000420920:S239R;ENSP00000423421:S239R;ENSP00000423606:S239R;ENSP00000444789:S119R;ENSP00000426318:S141R;ENSP00000425502:S236R;ENSP00000411344:S188R;ENSP00000445430:S141R;ENSP00000438142:S143R;ENSP00000426177:S236R;ENSP00000423176:S118R	ENSP00000349677:S239R	S	-	3	2	SPOCK3	167949897	1.000000	0.71417	1.000000	0.80357	0.565000	0.35776	2.196000	0.42686	2.650000	0.89964	0.563000	0.77884	AGC	.	.	.	none		0.373	SPOCK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364091.1		Missense_Mutation	T	167713322	G	T	167713322	5	4	186	1	0	0	0	0	0	0	1	0	15093	1333	46	4	613	4	SPOCK3	4	167713322	Splice_Site	SNP	G	TCGA-GL-8500-01A-11D-2396-08	44484210	167713322	23440954	18	10900											
MOCS2	4338	hgsc.bcm.edu	37	chr5	52397195	52397196	+	Frame_Shift_Ins	INS	-	-	T																															aaggaaatcatacccaagtcINStatggaacactgctatgtgt																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr5:52397195_52397196insT	ENST00000396954.3	-	5	1047_1048	c.370_371insA	c.(370-372)agafs	p.R124fs	MOCS2_ENST00000361377.4_Intron|MOCS2_ENST00000508922.1_3'UTR|MOCS2_ENST00000582677.1_Intron|MOCS2_ENST00000584946.1_3'UTR|MOCS2_ENST00000510818.2_3'UTR|MOCS2_ENST00000527216.1_3'UTR|MOCS2_ENST00000450852.3_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)				ATACCCAAGTCTATGGAACACT	0.342																																					p.R124fs		Atlas-INDEL	.											.	MOCS2	28	.	0			c.371_372insA						PASS	.																																			SO:0001589	frameshift_variant	4338	exon5			.	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.371dupA	chr5.hg19:g.52397196_52397196dupT	ENSP00000380157:p.Arg124fs	175.0	0.0	0		175.0	83.0	0.474286	NM_004531		Frame_Shift_Ins	INS	ENST00000396954.3	hg19	CCDS3958.1																																																																																			.	.	.	none		0.342	MOCS2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214053.3	NM_183418		T	52397196	-	T	52397195	7	5	186	1	0	1	1	0	0	0	0	0	9698	913	32	0	207	0	MOCS2	5	52397195	Frame_Shift_Ins	INS	-	TCGA-GL-8500-01A-11D-2396-08		52397195	128518065	19	10901											
RGNEF	64283	hgsc.bcm.edu	37	chr5	73205322	73205322	+	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	cctgtctctcggccactctaTcctccgaggcggccccttgc	3	10	9	19	3	2	0	0	0	2	0	6	1	4	0	6	3	1	0	6	3	1	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr5:73205322T>A	ENST00000426542.2	+	33	4267	c.4247T>A	c.(4246-4248)aTc>aAc	p.I1416N	ARHGEF28_ENST00000296799.4_Missense_Mutation_p.I1103N|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.I1416N|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.I1372N|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.I1416N|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.I1416N|ARHGEF28_ENST00000512883.1_Missense_Mutation_p.I336N|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.I1416N			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	1416					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)										GGCCACTCTATCCTCCGAGGC	0.622																																					p.I1416N		Atlas-SNP	.											.	.	.	.	0			c.T4247A						PASS	.						21	25	24					5																	73205322		2019	4181	6200	SO:0001583	missense	64283	exon34			ACTCTATCCTCCG		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.4247T>A	chr5.hg19:g.73205322T>A	ENSP00000412175:p.Ile1416Asn	30.0	0.0	.		20.0	10.0	.	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	hg19	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	T	0.004	-2.374983	0.00207	.	.	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799;ENST00000512883	T;T;T;T;T;T;T;T	0.23348	1.91;1.91;1.91;1.91;1.91;1.91;1.91;1.91	0.55	0.55	0.17219	.	.	.	.	.	T	0.11324	0.0276	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.23990	0.002;0.023;0.04;0.004;0.095	B;B;B;B;B	0.23018	0.0;0.014;0.021;0.006;0.043	T	0.32481	-0.9905	8	0.27082	T	0.32	.	.	.	.	.	1103;1416;1416;336;1416	B5MDA3;Q8N1W1;E9PC75;D6RGZ3;Q8N1W1-4	.;RGNEF_HUMAN;.;.;.	N	1416;1416;1416;1372;1416;1416;1103;336	ENSP00000296794:I1416N;ENSP00000441913:I1416N;ENSP00000441436:I1416N;ENSP00000287898:I1372N;ENSP00000411459:I1416N;ENSP00000412175:I1416N;ENSP00000296799:I1103N;ENSP00000421081:I336N	ENSP00000287898:I1372N	I	+	2	0	RP11-428C6.1	73241078	0.000000	0.05858	0.009000	0.14445	0.029000	0.11900	0.015000	0.13355	0.464000	0.27142	0.454000	0.30748	ATC	.	.	.	none		0.622	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			A	73205322	T	A	73205322	3	1	186	1	0	0	0	0	1	0	0	0	13296	1435	50	5	4377	5	RGNEF	5	73205322	Missense_Mutation	SNP	T	TCGA-GL-8500-01A-11D-2396-08	20808127	73205322	107709938	20	10902											
SEMA6A	57556	hgsc.bcm.edu	37	chr5	115822558	115822558	+	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	tgagagtctccaggaactgaGcagttcaagcgcgccttcag	10	8	12	11	2	3	2	2	2	1	1	4	4	3	3	2	1	3	2	2	1	2	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr5:115822558G>A	ENST00000343348.6	-	10	1636	c.849C>T	c.(847-849)tgC>tgT	p.C283C	CTB-118N6.3_ENST00000510682.1_RNA|SEMA6A_ENST00000257414.8_Silent_p.C283C|SEMA6A_ENST00000503962.1_5'Flank|CTB-118N6.3_ENST00000514214.1_RNA|CTB-118N6.3_ENST00000508640.1_RNA|SEMA6A_ENST00000510263.1_Silent_p.C283C	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	283	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)		CAGGAACTGAGCAGTTCAAGC	0.463																																					p.C283C		Atlas-SNP	.											.	SEMA6A	93	.	0			c.C849T						PASS	.						110	110	110					5																	115822558		2009	4214	6223	SO:0001819	synonymous_variant	57556	exon10			AACTGAGCAGTTC	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.849C>T	chr5.hg19:g.115822558G>A		136.0	0.0	.		137.0	59.0	.	NM_020796	Q9P2H9	Silent	SNP	ENST00000343348.6	hg19	CCDS47256.1																																																																																			.	.	.	none		0.463	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371270.1	NM_020796		A	115822558	G	A	115822558	2	1	186	1	0	0	0	0	0	0	0	1	14052	963	34	2		2	SEMA6A	5	115822558	Silent	SNP	G	TCGA-GL-8500-01A-11D-2396-08	42617236	115822558	65092702	21	10903											
LOC153328	153328	hgsc.bcm.edu	37	chr5	135178132	135178132	+	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	cagtgtcatcgttggccaccCtctggacacagtcaaggtac	9	9	10	13	1	3	0	2	0	1	0	4	1	3	1	2	3	1	2	2	3	2	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr5:135178132C>A	ENST00000420621.1	+	2	246	c.74C>A	c.(73-75)cCt>cAt	p.P25H	SLC25A48_ENST00000433282.2_5'UTR|SLC25A48_ENST00000412661.2_Missense_Mutation_p.P25H|SLC25A48_ENST00000274513.5_Missense_Mutation_p.P25H|SLC25A48_ENST00000425402.1_Missense_Mutation_p.P25H			Q6ZT89	S2548_HUMAN	solute carrier family 25, member 48	25					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	10						GTTGGCCACCCTCTGGACACA	0.507																																					p.P25H		Atlas-SNP	.											.	SLC25A48	37	.	0			c.C74A						PASS	.						141	154	150					5																	135178132		2131	4257	6388	SO:0001583	missense	153328	exon2			GCCACCCTCTGGA		CCDS43366.2	5q31.1	2013-05-22			ENSG00000145832	ENSG00000145832		"Solute carriers"	30451	protein-coding gene	gene with protein product	"HCC-down-regulated mitochondrial carrier protein"					15322095, 19303656	Standard	NM_145282		Approved	FLJ44862, HDMCP	uc003lba.3	Q6ZT89	OTTHUMG00000157007	ENST00000420621.1:c.74C>A	chr5.hg19:g.135178132C>A	ENSP00000407973:p.Pro25His	180.0	0.0	.		204.0	69.0	.	NM_145282	Q8TAV9	Missense_Mutation	SNP	ENST00000420621.1	hg19		.	.	.	.	.	.	.	.	.	.	C	18.21	3.574438	0.65878	.	.	ENSG00000145832	ENST00000425402;ENST00000274513;ENST00000420621;ENST00000412661	D;D;D;D	0.96885	-4.16;-4.16;-4.16;-4.16	4.46	4.46	0.54185	.	0.000000	0.85682	D	0.000000	D	0.98912	0.9631	H	0.98918	4.37	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.98808	1.0742	10	0.87932	D	0	-31.2085	14.3274	0.66530	0.0:1.0:0.0:0.0	.	25;25	Q6ZT89-3;Q6ZT89-2	.;.	H	25	ENSP00000408750:P25H;ENSP00000274513:P25H;ENSP00000407973:P25H;ENSP00000413049:P25H	ENSP00000274513:P25H	P	+	2	0	SLC25A48	135206031	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	4.217000	0.58547	2.480000	0.83734	0.563000	0.77884	CCT	.	.	.	none		0.507	SLC25A48-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_145282		A	135178132	C	A	135178132	3	1	186	1	0	0	0	0	1	0	0	0	8878	681	24	4	80	4	LOC153328	5	135178132	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	19355574	135178132	45737128	22	10904											
HSPA9	3313	hgsc.bcm.edu	37	chr5	137904733	137904733	+	Frame_Shift_Del	DEL	T	T	-																															ggacaattttaaagggaacaTttttactgtaagacacaaaa																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr5:137904733delT	ENST00000297185.3	-	5	541	c.416delA	c.(415-417)aatfs	p.N139fs	HSPA9_ENST00000501917.2_5'Flank	NM_004134.6	NP_004125.3	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 (mortalin)	139					cellular protein metabolic process (GO:0044267)|negative regulation of apoptotic process (GO:0043066)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(1)|kidney(4)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AAAGGGAACATTTTTACTGTA	0.403																																					p.N139fs		Atlas-INDEL	.											.	HSPA9	49	.	0			c.417delT						PASS	.						61	61	61					5																	137904733		2203	4300	6503	SO:0001589	frameshift_variant	3313	exon5			.	L11066	CCDS4208.1	5q31.1	2011-09-02	2006-10-31	2006-10-31	ENSG00000113013	ENSG00000113013		"Heat shock proteins / HSP70"	5244	protein-coding gene	gene with protein product		600548	"heat shock 70kDa protein 9B (mortalin-2)"	HSPA9B		7684501	Standard	NM_004134		Approved	GRP75, PBP74, mot-2, mthsp75	uc003ldf.3	P38646	OTTHUMG00000129206	ENST00000297185.3:c.416delA	chr5.hg19:g.137904733delT	ENSP00000297185:p.Asn139fs	100.0	0.0	0		103.0	40.0	0.38835	NM_004134	B2RCM1|P30036|P31932|Q1HB43|Q53H23|Q6GU03|Q9BWB7|Q9UC56	Frame_Shift_Del	DEL	ENST00000297185.3	hg19	CCDS4208.1																																																																																			.	.	.	none		0.403	HSPA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251285.1	NM_004134		-	137904733	T	-	137904733	7	5	186	1	0	1	0	1	0	0	0	0	7424	1493	52	0	1675	0	HSPA9	5	137904733	Frame_Shift_Del	DEL	T	TCGA-GL-8500-01A-11D-2396-08	2726601	137904733	43010527	23	10905											
RANBP17	64901	hgsc.bcm.edu	37	chr5	170323085	170323085	+	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	acactgcataataggagtaaTaatcctttctgaattgactc	14	13	6	8	0	1	2	0	2	1	0	3	3	2	3	1	1	1	2	1	1	5	6			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr5:170323085T>A	ENST00000523189.1	+	5	619	c.455T>A	c.(454-456)aTa>aAa	p.I152K		NM_022897.3	NP_075048.1	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	152					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)			ATAGGAGTAATAATCCTTTCT	0.388			T	TRD@	ALL																																p.I152K		Atlas-SNP	.		Dom	yes		5	5q34	64901	RAN binding protein 17		L	.	RANBP17	108	.	0			c.T455A						PASS	.						116	109	111					5																	170323085		2203	4300	6503	SO:0001583	missense	64901	exon5			GAGTAATAATCCT	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.455T>A	chr5.hg19:g.170323085T>A	ENSP00000427975:p.Ile152Lys	90.0	0.0	.		106.0	43.0	.	NM_022897	Q8IU74	Missense_Mutation	SNP	ENST00000523189.1	hg19	CCDS34287.1	.	.	.	.	.	.	.	.	.	.	.	4.832	0.154664	0.09236	.	.	ENSG00000204764	ENST00000523189	T	0.65916	-0.18	5.14	5.14	0.70334	Armadillo-type fold (1);	0.271232	0.32343	N	0.006225	T	0.29620	0.0739	N	0.02181	-0.65	0.49213	D	0.999766	B;B	0.19583	0.004;0.037	B;B	0.13407	0.007;0.009	T	0.35201	-0.9798	10	0.02654	T	1	-4.1259	11.0057	0.47633	0.0:0.0:0.156:0.844	.	152;202	Q9H2T7;B4DQG2	RBP17_HUMAN;.	K	152	ENSP00000427975:I152K	ENSP00000373770:I152K	I	+	2	0	RANBP17	170255663	0.998000	0.40836	0.997000	0.53966	0.968000	0.65278	3.161000	0.50747	2.072000	0.62099	0.460000	0.39030	ATA	.	.	.	none		0.388	RANBP17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372036.1	NM_022897		A	170323085	T	A	170323085	3	1	186	1	0	0	0	0	1	0	0	0	13040	1406	49	5	473	5	RANBP17	5	170323085	Missense_Mutation	SNP	T	TCGA-GL-8500-01A-11D-2396-08	32418352	170323085	10592175	24	10906											
SLC17A4	10050	hgsc.bcm.edu	37	chr6	25773825	25773825	+	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	ttttagtctcttatttctgtGaatactggcttttttatacc	7	22	5	7	0	2	1	0	1	2	0	3	1	2	1	1	1	2	1	1	1	6	9			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr6:25773825G>A	ENST00000377905.4	+	8	1029	c.910G>A	c.(910-912)Gaa>Aaa	p.E304K	SLC17A4_ENST00000397076.2_Missense_Mutation_p.E74K|SLC17A4_ENST00000439485.2_Intron	NM_005495.2	NP_005486.1	Q9Y2C5	S17A4_HUMAN	solute carrier family 17, member 4	304					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						TTATTTCTGTGAATACTGGCT	0.443																																					p.E304K		Atlas-SNP	.											.	SLC17A4	79	.	0			c.G910A						PASS	.						163	144	150					6																	25773825		2203	4300	6503	SO:0001583	missense	10050	exon8			TTCTGTGAATACT	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.910G>A	chr6.hg19:g.25773825G>A	ENSP00000367137:p.Glu304Lys	89.0	0.0	.		92.0	36.0	.	NM_005495	B4DDV9|E7EPE8|E7EU17|Q32MB7|Q32MB8	Missense_Mutation	SNP	ENST00000377905.4	hg19	CCDS4564.1	.	.	.	.	.	.	.	.	.	.	G	17.76	3.468242	0.63625	.	.	ENSG00000146039	ENST00000377905;ENST00000397076	T;T	0.58797	0.41;0.31	5.34	0.672	0.17935	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.890844	0.09592	N	0.781378	T	0.40645	0.1125	M	0.73598	2.24	0.09310	N	1	P;B	0.38048	0.616;0.082	B;B	0.40901	0.343;0.158	T	0.40365	-0.9567	10	0.54805	T	0.06	.	7.4701	0.27344	0.1347:0.4004:0.4649:0.0	.	74;304	E7EU17;Q9Y2C5	.;S17A4_HUMAN	K	304;74	ENSP00000367137:E304K;ENSP00000380266:E74K	ENSP00000367137:E304K	E	+	1	0	SLC17A4	25881804	0.000000	0.05858	0.079000	0.20413	0.976000	0.68499	-0.078000	0.11375	0.167000	0.19631	0.655000	0.94253	GAA	.	.	.	none		0.443	SLC17A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040068.1			A	25773825	G	A	25773825	3	1	186	1	0	0	0	0	1	0	0	0	14432	1291	45	2	936	2	SLC17A4	6	25773825	Missense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08		25773825	145341242	25	10907											
MUC21	394263	hgsc.bcm.edu	37	chr6	30955264	30955264	+	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	gggccaacacagccaccaacTctgggtccagtgtgacctct	9	7	10	15	0	2	1	0	1	2	0	3	1	3	1	5	2	3	0	5	2	2	0			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr6:30955264T>A	ENST00000376296.3	+	2	1553	c.1312T>A	c.(1312-1314)Tct>Act	p.S438T	MUC21_ENST00000486149.2_De_novo_Start_OutOfFrame	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	438	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						AGCCACCAACTCTGGGTCCAG	0.577																																					p.S438T		Atlas-SNP	.											.	MUC21	98	.	0			c.T1312A						PASS	.						124	120	122					6																	30955264		2203	4300	6503	SO:0001583	missense	394263	exon2			ACCAACTCTGGGT	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.1312T>A	chr6.hg19:g.30955264T>A	ENSP00000365473:p.Ser438Thr	211.0	0.0	.		179.0	75.0	.	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	hg19	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	t	7.419	0.636395	0.14386	.	.	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.02015	4.5	3.96	-1.72	0.08107	.	.	.	.	.	T	0.00328	0.0010	N	0.12746	0.255	0.09310	N	1	B	0.15473	0.013	B	0.17722	0.019	T	0.42275	-0.9461	9	0.07325	T	0.83	0.2489	4.0719	0.09885	0.5071:0.2625:0.0:0.2303	.	438	Q5SSG8	MUC21_HUMAN	T	288;438	ENSP00000365473:S438T	ENSP00000365473:S438T	S	+	1	0	MUC21	31063243	0.002000	0.14202	0.000000	0.03702	0.004000	0.04260	0.031000	0.13710	-0.390000	0.07774	-0.468000	0.05107	TCT	.	.	.	none		0.577	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909		A	30955264	T	A	30955264	3	1	186	1	0	0	0	0	1	0	0	0	9984	1551	54	5	1318	5	MUC21	6	30955264	Missense_Mutation	SNP	T	TCGA-GL-8500-01A-11D-2396-08	5181439	30955264	140159803	26	10908											
MCM3	4172	hgsc.bcm.edu	37	chr6	52141973	52141973	+	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	aagcacataccgcagaagctGagacttggcaacggatgggt	13	6	13	9	2	0	2	0	1	0	2	0	4	0	3	1	3	4	4	1	3	4	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr6:52141973G>C	ENST00000229854.7	-	8	1133	c.1057C>G	c.(1057-1059)Cag>Gag	p.Q353E	MCM3_ENST00000476448.1_5'UTR|MCM3_ENST00000596288.1_Missense_Mutation_p.Q398E|MCM3_ENST00000419835.2_Missense_Mutation_p.Q307E			P25205	MCM3_HUMAN	minichromosome maintenance complex component 3	353	MCM.				DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	alpha DNA polymerase:primase complex (GO:0005658)|centrosome (GO:0005813)|intracellular membrane-bounded organelle (GO:0043231)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.Q353K(1)		endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Lung NSC(77;0.0931)					CGCAGAAGCTGAGACTTGGCA	0.597																																					p.Q398E		Atlas-SNP	.											MCM3,pharynx,carcinoma,0,1	MCM3	63	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.C1192G						PASS	.						60	58	59					6																	52141973		2203	4300	6503	SO:0001583	missense	4172	exon8			GAAGCTGAGACTT	X62153	CCDS4940.1, CCDS4940.2, CCDS75468.1	6p12	2008-02-05	2007-04-04		ENSG00000112118	ENSG00000112118			6945	protein-coding gene	gene with protein product		602693	"minichromosome maintenance deficient (S. cerevisiae) 3", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae)"			1549468	Standard	NM_002388		Approved		uc011dwu.2	P25205	OTTHUMG00000014844	ENST00000229854.7:c.1057C>G	chr6.hg19:g.52141973G>C	ENSP00000229854:p.Gln353Glu	65.0	0.0	.		39.0	12.0	.	NM_002388	B4DWW4|Q92660|Q9BTR3|Q9NUE7	Missense_Mutation	SNP	ENST00000229854.7	hg19		.	.	.	.	.	.	.	.	.	.	G	32	5.114750	0.94339	.	.	ENSG00000112118	ENST00000229854;ENST00000419835	T;T	0.10960	2.82;2.82	5.36	5.36	0.76844	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.44726	0.1307	H	0.97131	3.945	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.996	T	0.63510	-0.6621	10	0.87932	D	0	-17.9504	19.2924	0.94105	0.0:0.0:1.0:0.0	.	307;353	B4DUQ9;P25205	.;MCM3_HUMAN	E	353;307	ENSP00000229854:Q353E;ENSP00000388647:Q307E	ENSP00000229854:Q353E	Q	-	1	0	MCM3	52249932	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.657000	0.98554	2.783000	0.95769	0.655000	0.94253	CAG	.	.	.	none		0.597	MCM3-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470784.1			C	52141973	G	C	52141973	3	2	186	1	0	0	0	0	1	0	0	0	9394	1299	45	4	1409	4	MCM3	6	52141973	Missense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08	21186709	52141973	118973094	27	10909											
FERD3L	222894	hgsc.bcm.edu	37	chr7	19184646	19184646	+	Frame_Shift_Del	DEL	T	T	-																															ggcctcgttgaggttgaacaTccgcttcctttcgcggatgt																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr7:19184646delT	ENST00000275461.3	-	1	398	c.340delA	c.(340-342)atgfs	p.M114fs	AC003986.5_ENST00000452700.1_RNA	NM_152898.2	NP_690862.1	Q96RJ6	FER3L_HUMAN	Fer3-like bHLH transcription factor	114	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cell development (GO:0048468)|floor plate development (GO:0033504)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of neurogenesis (GO:0050767)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(4)|large_intestine(8)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	35						AGGTTGAACATCCGCTTCCTT	0.612																																					p.M114fs		Atlas-INDEL	.											.	FERD3L	63	.	0			c.341delT						PASS	.						103	83	90					7																	19184646		2203	4300	6503	SO:0001589	frameshift_variant	222894	exon1			.	AF369897	CCDS5368.1	7p21.3	2013-10-17	2013-10-17		ENSG00000146618	ENSG00000146618		"Basic helix-loop-helix proteins"	16660	protein-coding gene	gene with protein product			"Fer3-like (Drosophila)"			11472856, 12217327	Standard	NM_152898		Approved	NATO3, N-TWIST, bHLHa31	uc003suo.1	Q96RJ6	OTTHUMG00000090823	ENST00000275461.3:c.340delA	chr7.hg19:g.19184646delT	ENSP00000275461:p.Met114fs	64.0	0.0	0		80.0	26.0	0.325	NM_152898	Q495K0	Frame_Shift_Del	DEL	ENST00000275461.3	hg19	CCDS5368.1																																																																																			.	.	.	none		0.612	FERD3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207627.1			-	19184646	T	-	19184646	7	5	186	1	0	1	0	1	0	0	0	0	5823	1435	50	0	164	0	FERD3L	7	19184646	Frame_Shift_Del	DEL	T	TCGA-GL-8500-01A-11D-2396-08		19184646	139954017	28	10910											
SEMA3D	223117	hgsc.bcm.edu	37	chr7	84636164	84636164	+	Frame_Shift_Del	DEL	G	G	-																															tctggatataccatttaataGttgcttgttgggatttaggt																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr7:84636164delG	ENST00000284136.6	-	16	1905	c.1862delC	c.(1861-1863)actfs	p.T621fs	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	621	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						CCATTTAATAGTTGCTTGTTG	0.388																																					p.T621fs	Ovarian(63;442 1191 17318 29975 31528)	Atlas-INDEL	.											.	SEMA3D	177	.	0			c.1863delT						PASS	.						214	198	203					7																	84636164		2203	4300	6503	SO:0001589	frameshift_variant	223117	exon16			.	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.1862delC	chr7.hg19:g.84636164delG	ENSP00000284136:p.Thr621fs	276.0	0.0	0		441.0	305.0	0.69161	NM_152754	A6NK46|Q6UW77|Q8NCQ1	Frame_Shift_Del	DEL	ENST00000284136.6	hg19	CCDS34676.1																																																																																			.	.	.	none		0.388	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754		-	84636164	G	-	84636164	7	5	186	1	0	1	0	1	0	0	0	0	14040	1029	36	0	479	0	SEMA3D	7	84636164	Frame_Shift_Del	DEL	G	TCGA-GL-8500-01A-11D-2396-08	65451518	84636164	74502499	29	10911											
KIAA1549	57670	hgsc.bcm.edu	37	chr7	138597164	138597164	+	Missense_Mutation	SNP	A	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	gaatcctcagtacttctttgAttgctgtaatgatgtactcc	9	16	7	9	0	2	2	1	2	1	0	4	3	4	2	2	0	3	4	2	0	4	6			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr7:138597164A>C	ENST00000422774.1	-	3	2969	c.2921T>G	c.(2920-2922)aTc>aGc	p.I974S	KIAA1549_ENST00000242365.4_Missense_Mutation_p.I924S|KIAA1549_ENST00000440172.1_Missense_Mutation_p.I974S			Q9HCM3	K1549_HUMAN	KIAA1549	974						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						TACTTCTTTGATTGCTGTAAT	0.463			O	BRAF	pilocytic astrocytoma																																p.I974S	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549	314	.	0			c.T2921G						PASS	.						149	145	146					7																	138597164		2032	4201	6233	SO:0001583	missense	57670	exon3			TCTTTGATTGCTG		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.2921T>G	chr7.hg19:g.138597164A>C	ENSP00000416040:p.Ile974Ser	71.0	0.0	.		71.0	43.0	.	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	hg19	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.284165	0.80803	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.32515	1.45;1.46;1.46	5.38	5.38	0.77491	.	0.071830	0.56097	D	0.000028	T	0.45994	0.1370	L	0.36672	1.1	0.51482	D	0.999929	D;D	0.89917	1.0;1.0	D;D	0.77004	0.975;0.989	T	0.44544	-0.9321	10	0.87932	D	0	.	14.7359	0.69414	1.0:0.0:0.0:0.0	.	974;974	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	S	974;924;974	ENSP00000406661:I974S;ENSP00000242365:I924S;ENSP00000416040:I974S	ENSP00000242365:I924S	I	-	2	0	KIAA1549	138247704	1.000000	0.71417	0.998000	0.56505	0.977000	0.68977	7.162000	0.77515	2.254000	0.74563	0.533000	0.62120	ATC	.	.	.	none		0.463	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			C	138597164	A	C	138597164	3	2	186	1	0	0	0	0	1	0	0	0	8251	333	12	5	3003	5	KIAA1549	7	138597164	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	53961000	138597164	20541499	30	10912											
ATP6V0E2	155066	hgsc.bcm.edu	37	chr7	149576654	149576654	+	3'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	ggatgtcctgctccaataccCgcactgctctggagtttgcc	6	11	10	14	1	1	0	0	0	1	0	3	2	3	2	4	2	4	4	4	2	2	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr7:149576654C>G	ENST00000425642.2	+	0	519				ATP6V0E2_ENST00000479613.1_Missense_Mutation_p.P151R|ATP6V0E2_ENST00000421974.2_Missense_Mutation_p.P177R|RP11-445N20.3_ENST00000608912.1_lincRNA|ATP6V0E2_ENST00000456496.2_3'UTR|ATP6V0E2_ENST00000606024.1_Missense_Mutation_p.P128R|ATP6V0E2-AS1_ENST00000464939.1_RNA			Q8NHE4	VA0E2_HUMAN	ATPase, H+ transporting V0 subunit e2						ATP hydrolysis coupled proton transport (GO:0015991)|cell growth (GO:0016049)|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)|vacuolar acidification (GO:0007035)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)	ATPase activity, coupled to transmembrane movement of ions (GO:0042625)|hydrogen ion transmembrane transporter activity (GO:0015078)			lung(1)	1			OV - Ovarian serous cystadenocarcinoma(82;0.00256)			CTCCAATACCCGCACTGCTCT	0.637																																					p.P177R		Atlas-SNP	.											.	ATP6V0E2	12	.	0			c.C530G						PASS	.						61	69	66					7																	149576654		1987	4159	6146	SO:0001624	3_prime_UTR_variant	155066	exon3			AATACCCGCACTG	AK057700	CCDS47742.1, CCDS55181.1	7q36.1	2010-04-21	2006-10-12	2006-10-12	ENSG00000171130	ENSG00000171130		"ATPases / V-type"	21723	protein-coding gene	gene with protein product		611019	"chromosome 7 open reading frame 32", "ATPase, H+ transporting V0 subunit E isoform 2-like (rat)"	C7orf32, ATP6V0E2L			Standard	XM_005249958		Approved		uc003wgs.3	Q8NHE4	OTTHUMG00000158094	ENST00000425642.2:c.*250C>G	chr7.hg19:g.149576654C>G		25.0	0.0	.		28.0	19.0	.	NM_001100592	A2T863|A2T8L7|B5MDP5|J3KQW7|Q6MZW1|Q75L47|Q7Z4R7|Q8N7I8	Missense_Mutation	SNP	ENST00000425642.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	12.45|12.45	1.941217|1.941217	0.34283|0.34283	.|.	.|.	ENSG00000171130|ENSG00000171130	ENST00000421974;ENST00000425642;ENST00000479613|ENST00000307445	.|.	.|.	.|.	2.78|2.78	1.89|1.89	0.25635|0.25635	.|.	.|.	.|.	.|.	.|.	T|T	0.19725|0.19725	0.0474|0.0474	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	P;P|.	0.44090|.	0.826;0.742|.	B;B|.	0.37422|.	0.249;0.238|.	T|T	0.19160|0.19160	-1.0314|-1.0314	8|6	0.72032|0.87932	D|D	0.01|0	.|.	5.6822|5.6822	0.17782|0.17782	0.0:0.8483:0.0:0.1517|0.0:0.8483:0.0:0.1517	.|.	177;151|.	E9PAS2;Q8NHE4-3|.	.;.|.	R|G	177;128;151|96	.|.	ENSP00000411672:P177R|ENSP00000304519:R96G	P|R	+|+	2|1	0|0	ATP6V0E2|ATP6V0E2	149207587|149207587	0.000000|0.000000	0.05858|0.05858	0.003000|0.003000	0.11579|0.11579	0.005000|0.005000	0.04900|0.04900	0.044000|0.044000	0.13992|0.13992	0.750000|0.750000	0.32877|0.32877	0.467000|0.467000	0.42956|0.42956	CCG|CGC	.	.	.	none		0.637	ATP6V0E2-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470874.1	NM_145230		G	149576654	C	G	149576654	1	3	186	0	1	0	0	0	0	0	0	0	1176	652	23	4		4	ATP6V0E2	7	149576654	3'UTR	SNP	C	TCGA-GL-8500-01A-11D-2396-08	10979490	149576654	9562009	31	10913											
NEIL2	252969	hgsc.bcm.edu	37	chr8	11637150	11637150	+	Frame_Shift_Del	DEL	A	A	-																															tagatttgatctagatgaagAaatggggccccctggcagca																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr8:11637150delA	ENST00000284503.6	+	3	781	c.182delA	c.(181-183)gaafs	p.E61fs	NEIL2_ENST00000403422.3_5'UTR|NEIL2_ENST00000455213.2_Frame_Shift_Del_p.E61fs|NEIL2_ENST00000528323.1_Intron|NEIL2_ENST00000436750.3_Frame_Shift_Del_p.E61fs	NM_145043.2	NP_659480.1	Q969S2	NEIL2_HUMAN	nei endonuclease VIII-like 2 (E. coli)	61					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)		CTAGATGAAGAAATGGGGCCC	0.527								Base excision repair (BER), DNA glycosylases																													p.E61fs		Atlas-INDEL	.											.	NEIL2	14	.	0			c.181delG						PASS	.						59	75	70					8																	11637150		2203	4300	6503	SO:0001589	frameshift_variant	252969	exon3			.	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.182delA	chr8.hg19:g.11637150delA	ENSP00000284503:p.Glu61fs	183.0	0.0	0		190.0	91.0	0.478947	NM_001135746	B4DFR7|Q7Z3Q7|Q8N842|Q8NG52	Frame_Shift_Del	DEL	ENST00000284503.6	hg19	CCDS5984.1																																																																																			.	.	.	none		0.527	NEIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207583.3	NM_145043		-	11637150	A	-	11637150	7	5	186	1	0	1	0	1	0	0	0	0	10326	246	9	0	193	0	NEIL2	8	11637150	Frame_Shift_Del	DEL	A	TCGA-GL-8500-01A-11D-2396-08		11637150	134726872	32	10914											
LYN	4067	hgsc.bcm.edu	37	chr8	56922610	56922610	+	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	gaccaacgtttgactacttaCagagcgtcctggatgatttc	10	12	9	10	2	0	3	0	2	0	1	2	5	1	4	2	1	4	1	2	1	3	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr8:56922610C>A	ENST00000519728.1	+	13	1776	c.1480C>A	c.(1480-1482)Cag>Aag	p.Q494K	LYN_ENST00000520220.2_Missense_Mutation_p.Q473K	NM_002350.3	NP_002341.1	P07948	LYN_HUMAN	LYN proto-oncogene, Src family tyrosine kinase	494	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)	TGACTACTTACAGAGCGTCCT	0.527																																					p.Q494K		Atlas-SNP	.											.	LYN	54	.	0			c.C1480A						PASS	.						102	94	96					8																	56922610		2203	4300	6503	SO:0001583	missense	4067	exon13			TACTTACAGAGCG	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.1480C>A	chr8.hg19:g.56922610C>A	ENSP00000428924:p.Gln494Lys	125.0	0.0	.		103.0	39.0	.	NM_002350	A0AVQ5	Missense_Mutation	SNP	ENST00000519728.1	hg19	CCDS6162.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.672813	0.88445	.	.	ENSG00000254087	ENST00000519728;ENST00000520220	T;T	0.10573	2.86;2.86	5.95	5.95	0.96441	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	0.13500	0.0327	N	0.12422	0.21	0.80722	D	1	P;P	0.41265	0.744;0.59	P;B	0.48189	0.57;0.415	T	0.08106	-1.0738	10	0.54805	T	0.06	.	20.3932	0.98965	0.0:1.0:0.0:0.0	.	564;494	Q6NUK7;P07948	.;LYN_HUMAN	K	494;473	ENSP00000428924:Q494K;ENSP00000428424:Q473K	ENSP00000428924:Q494K	Q	+	1	0	LYN	57085164	1.000000	0.71417	0.967000	0.41034	0.879000	0.50718	7.818000	0.86416	2.824000	0.97209	0.655000	0.94253	CAG	.	.	.	none		0.527	LYN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378155.1	NM_002350		A	56922610	C	A	56922610	3	1	186	1	0	0	0	0	1	0	0	0	9114	479	17	4	1526	4	LYN	8	56922610	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	45285460	56922610	89441412	33	10915											
GEM	2669	hgsc.bcm.edu	37	chr8	95262646	95262646	+	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	cgcctggctttcctgggcatGctctccttccttttctggta	2	16	9	14	1	2	0	0	0	2	0	5	0	4	0	4	3	1	4	4	3	1	5			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr8:95262646G>A	ENST00000297596.2	-	5	1047	c.783C>T	c.(781-783)agC>agT	p.S261S	GEM_ENST00000396194.2_Silent_p.S261S	NM_005261.3	NP_005252.1	P55040	GEM_HUMAN	GTP binding protein overexpressed in skeletal muscle	261					cell surface receptor signaling pathway (GO:0007166)|chromosome organization (GO:0051276)|immune response (GO:0006955)|metaphase plate congression (GO:0051310)|mitotic nuclear division (GO:0007067)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic side of plasma membrane (GO:0009898)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|spindle midzone (GO:0051233)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	22	Breast(36;4.65e-06)	Myeloproliferative disorder(644;0.204)	BRCA - Breast invasive adenocarcinoma(8;0.00691)			TCCTGGGCATGCTCTCCTTCC	0.552																																					p.S261S	GBM(125;80 1653 28655 32188 47338)|Esophageal Squamous(19;97 579 13602 49091 51766)	Atlas-SNP	.											.	GEM	40	.	0			c.C783T						PASS	.						96	87	90					8																	95262646		2203	4300	6503	SO:0001819	synonymous_variant	2669	exon5			GGGCATGCTCTCC		CCDS6261.1	8q13-q21	2014-05-09	2001-11-28		ENSG00000164949	ENSG00000164949			4234	protein-coding gene	gene with protein product	"kinase-inducible Ras-like protein"	600164	"GTP-binding protein overexpressed in skeletal muscle"			7912851, 11956230	Standard	NM_005261		Approved	KIR	uc003ygj.3	P55040	OTTHUMG00000164392	ENST00000297596.2:c.783C>T	chr8.hg19:g.95262646G>A		83.0	0.0	.		67.0	25.0	.	NM_181702	B2RA31	Silent	SNP	ENST00000297596.2	hg19	CCDS6261.1																																																																																			.	.	.	none		0.552	GEM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378566.1	NM_181702		A	95262646	G	A	95262646	2	1	186	1	0	0	0	0	0	0	0	1	6336	1310	46	2		2	GEM	8	95262646	Silent	SNP	G	TCGA-GL-8500-01A-11D-2396-08	38340036	95262646	51101376	34	10916											
RAD54B	25788	hgsc.bcm.edu	37	chr8	95419720	95419720	+	Frame_Shift_Del	DEL	T	T	-																															tttggaaatcattctgtctaTtttcctttgaacttggttta																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr8:95419720delT	ENST00000336148.5	-	5	852	c.728delA	c.(727-729)aatfs	p.N243fs		NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)	243					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)			ATTCTGTCTATTTTCCTTTGA	0.353								Direct reversal of damage;Homologous recombination																													p.N243fs		Atlas-INDEL	.											.	RAD54B	88	.	0			c.729delT						PASS	.						79	78	79					8																	95419720		2203	4300	6503	SO:0001589	frameshift_variant	25788	exon5			.	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.728delA	chr8.hg19:g.95419720delT	ENSP00000336606:p.Asn243fs	99.0	0.0	0		116.0	58.0	0.5	NM_012415	F6WBS8	Frame_Shift_Del	DEL	ENST00000336148.5	hg19	CCDS6262.1																																																																																			.	.	.	none		0.353	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415		-	95419720	T	-	95419720	7	5	186	1	0	1	0	1	0	0	0	0	13005	1493	52	0	2048	0	RAD54B	8	95419720	Frame_Shift_Del	DEL	T	TCGA-GL-8500-01A-11D-2396-08	157074	95419720	50944302	35	10917											
BNC2	54796	hgsc.bcm.edu	37	chr9	16552664	16552664	+	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	gcacaggcactgcttgtgtcCcatagagcatcaggctgctg	8	9	12	12	0	1	1	1	0	0	1	2	1	2	1	1	2	3	6	1	2	1	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr9:16552664C>T	ENST00000380672.4	-	5	590	c.533G>A	c.(532-534)gGg>gAg	p.G178E	BNC2_ENST00000380667.2_Missense_Mutation_p.G111E|BNC2_ENST00000380666.2_Missense_Mutation_p.G178E|BNC2_ENST00000545497.1_Missense_Mutation_p.G83E	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)		TGCTTGTGTCCCATAGAGCAT	0.567																																					p.G178E		Atlas-SNP	.											.	BNC2	166	.	0			c.G533A						PASS	.						138	106	117					9																	16552664		2203	4300	6503	SO:0001583	missense	54796	exon5			TGTGTCCCATAGA	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.533G>A	chr9.hg19:g.16552664C>T	ENSP00000370047:p.Gly178Glu	96.0	0.0	.		97.0	4.0	.	NM_017637		Missense_Mutation	SNP	ENST00000380672.4	hg19	CCDS6482.2	.	.	.	.	.	.	.	.	.	.	C	25.1	4.601586	0.87055	.	.	ENSG00000173068	ENST00000380672;ENST00000418777;ENST00000456672;ENST00000436939;ENST00000380667;ENST00000545497;ENST00000544198;ENST00000380666;ENST00000540340;ENST00000451290	T;T;T;T;T	0.03580	3.88;3.88;3.88;3.88;3.88	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.20861	0.0502	M	0.76328	2.33	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.998;0.999;0.999;1.0;0.998;0.999	T	0.00010	-1.2450	10	0.87932	D	0	-18.731	20.4366	0.99092	0.0:1.0:0.0:0.0	.	83;111;215;178;4;136;178	F5H586;B1APH0;Q06HC4;Q6ZN30-2;B4E3J2;Q5H9S4;Q6ZN30	.;.;.;.;.;.;BNC2_HUMAN	E	178;135;215;206;111;83;4;178;178;101	ENSP00000370047:G178E;ENSP00000408370:G135E;ENSP00000370042:G111E;ENSP00000444640:G83E;ENSP00000370041:G178E	ENSP00000370041:G178E	G	-	2	0	BNC2	16542664	1.000000	0.71417	0.969000	0.41365	0.352000	0.29268	7.818000	0.86416	2.837000	0.97791	0.591000	0.81541	GGG	.	.	.	none		0.567	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637		T	16552664	C	T	16552664	3	4	186	1	0	0	0	0	1	0	0	0	1475	623	22	2	2778	2	BNC2	9	16552664	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08		16552664	124660767	36	10918											
OR13J1	392309	hgsc.bcm.edu	37	chr9	35869823	35869823	+	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	aggaagtcttcgctgaccgaCgtgttgccgcatgccagctt	7	10	12	12	4	1	1	0	1	1	0	2	3	1	2	3	1	3	4	3	1	1	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr9:35869823C>T	ENST00000377981.2	-	1	638	c.576G>A	c.(574-576)acG>acA	p.T192T		NM_001004487.1	NP_001004487.1	Q8NGT2	O13J1_HUMAN	olfactory receptor, family 13, subfamily J, member 1	192						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(1)|lung(3)|skin(1)	6	all_epithelial(49;0.169)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00494)|STAD - Stomach adenocarcinoma(86;0.194)			CGCTGACCGACGTGTTGCCGC	0.597																																					p.T192T		Atlas-SNP	.											.	OR13J1	37	.	0			c.G576A						PASS	.						69	57	61					9																	35869823		2203	4300	6503	SO:0001819	synonymous_variant	392309	exon1			GACCGACGTGTTG		CCDS35011.1	9p13.3	2013-09-24			ENSG00000168828	ENSG00000168828		"GPCR / Class A : Olfactory receptors"	15108	protein-coding gene	gene with protein product							Standard	NM_001004487		Approved		uc011lph.2	Q8NGT2	OTTHUMG00000019879	ENST00000377981.2:c.576G>A	chr9.hg19:g.35869823C>T		89.0	0.0	.		56.0	18.0	.	NM_001004487	B2RN66|Q6IF20|Q96R40	Silent	SNP	ENST00000377981.2	hg19	CCDS35011.1																																																																																			.	.	.	none		0.597	OR13J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052381.1			T	35869823	C	T	35869823	2	4	186	1	0	0	0	0	0	0	0	1	10951	523	19	1		1	OR13J1	9	35869823	Silent	SNP	C	TCGA-GL-8500-01A-11D-2396-08	19317159	35869823	105343608	37	10919											
SECISBP2	79048	hgsc.bcm.edu	37	chr9	91965762	91965762	+	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	caactgtgagaagatacagtCaaaaggtaaaggcacagtgt	17	7	11	6	0	1	2	1	1	0	2	1	3	1	2	0	2	2	2	0	2	7	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr9:91965762C>T	ENST00000375807.3	+	14	2179	c.2108C>T	c.(2107-2109)tCa>tTa	p.S703L	SECISBP2_ENST00000339901.4_Missense_Mutation_p.S630L|SECISBP2_ENST00000534113.2_Missense_Mutation_p.S635L	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	703					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						AAGATACAGTCAAAAGGTAAA	0.498																																					p.S703L		Atlas-SNP	.											.	SECISBP2	64	.	0			c.C2108T						PASS	.						68	69	69					9																	91965762		2203	4300	6503	SO:0001583	missense	79048	exon14			TACAGTCAAAAGG	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.2108C>T	chr9.hg19:g.91965762C>T	ENSP00000364965:p.Ser703Leu	75.0	0.0	.		67.0	34.0	.	NM_024077	F8W892|Q5HYY1|Q8IYC0|Q9H0A1	Missense_Mutation	SNP	ENST00000375807.3	hg19	CCDS6683.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.299315	0.81136	.	.	ENSG00000187742	ENST00000375807;ENST00000395669;ENST00000339901;ENST00000534113	T;T;T	0.57273	0.41;0.41;0.41	4.84	4.84	0.62591	Ribosomal protein L7Ae/L30e/S12e/Gadd45 (1);	0.000000	0.85682	D	0.000000	T	0.69342	0.3100	L	0.52905	1.665	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	0.70695	-0.4801	10	0.59425	D	0.04	-12.0495	18.4955	0.90864	0.0:1.0:0.0:0.0	.	710;630;703	Q59H19;Q96T21-2;Q96T21	.;.;SEBP2_HUMAN	L	703;709;630;635	ENSP00000364965:S703L;ENSP00000364959:S630L;ENSP00000436650:S635L	ENSP00000364959:S630L	S	+	2	0	SECISBP2	91155582	1.000000	0.71417	0.991000	0.47740	0.546000	0.35178	7.314000	0.78988	2.686000	0.91538	0.561000	0.74099	TCA	.	.	.	none		0.498	SECISBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052990.3	NM_024077		T	91965762	C	T	91965762	3	4	186	1	0	0	0	0	1	0	0	0	14019	838	29	2	2162	2	SECISBP2	9	91965762	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	56095939	91965762	49247669	38	10920											
RAD23B	5887	hgsc.bcm.edu	37	chr9	110091836	110091836	+	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	tcttccagttaaaggcattaGgatttcctgaaggacttgtg	10	14	10	7	0	1	1	0	1	1	0	3	3	3	3	2	3	0	2	2	3	4	5			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr9:110091836G>A	ENST00000358015.3	+	10	1480	c.1129G>A	c.(1129-1131)Gga>Aga	p.G377R	RAD23B_ENST00000416373.2_Missense_Mutation_p.G305R	NM_001244713.1|NM_002874.4	NP_001231642.1|NP_002865.1	P54727	RD23B_HUMAN	RAD23 homolog B (S. cerevisiae)	377	UBA 2. {ECO:0000255|PROSITE- ProRule:PRU00212}.				DNA repair (GO:0006281)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|XPC complex (GO:0071942)	damaged DNA binding (GO:0003684)|polyubiquitin binding (GO:0031593)|single-stranded DNA binding (GO:0003697)			breast(3)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						AAAGGCATTAGGATTTCCTGA	0.328								Direct reversal of damage;Nucleotide excision repair (NER)																													p.G377R		Atlas-SNP	.											RAD23B,colon,carcinoma,0,1	RAD23B	31	.	0			c.G1129A						PASS	.						71	73	72					9																	110091836		2203	4300	6503	SO:0001583	missense	5887	exon10			GCATTAGGATTTC		CCDS6769.1, CCDS59138.1	9q31.2	2008-07-21	2001-11-28		ENSG00000119318	ENSG00000119318			9813	protein-coding gene	gene with protein product	"XP-C repair complementing protein", "XP-C repair complementing complex 58 kDa"	600062	"RAD23 (S. cerevisiae) homolog B"			7851894, 8168482	Standard	NM_002874		Approved	HHR23B, P58, HR23B	uc004bde.3	P54727	OTTHUMG00000020446	ENST00000358015.3:c.1129G>A	chr9.hg19:g.110091836G>A	ENSP00000350708:p.Gly377Arg	114.0	0.0	.		102.0	33.0	.	NM_002874	B3KWK8|G5E9P0|Q7Z5K8|Q8WUB0	Missense_Mutation	SNP	ENST00000358015.3	hg19	CCDS6769.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.086513	0.76642	.	.	ENSG00000119318	ENST00000358015;ENST00000416373	D;D	0.93019	-3.15;-3.15	5.27	5.27	0.74061	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (2);Ubiquitin-associated/translation elongation factor EF1B, N-terminal (1);UBA-like (1);	0.000000	0.85682	D	0.000000	D	0.97804	0.9279	H	0.94503	3.545	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.994	D	0.98693	1.0697	10	0.87932	D	0	-3.6232	19.2454	0.93901	0.0:0.0:1.0:0.0	.	356;377	B7Z4W4;P54727	.;RD23B_HUMAN	R	377;305	ENSP00000350708:G377R;ENSP00000405623:G305R	ENSP00000350708:G377R	G	+	1	0	RAD23B	109131657	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.439000	0.97543	2.623000	0.88846	0.563000	0.77884	GGA	.	.	.	none		0.328	RAD23B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053548.1	NM_002874		A	110091836	G	A	110091836	3	1	186	1	0	0	0	0	1	0	0	0	12996	1001	35	2	1167	2	RAD23B	9	110091836	Missense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08	18126074	110091836	31121595	39	10921											
RABGAP1	23637	hgsc.bcm.edu	37	chr9	125751642	125751642	+	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	tacaaaatcctcttctgtgtCagagggcatgatggaactcc	11	11	9	10	0	3	2	1	1	2	1	5	3	5	3	2	2	2	1	2	2	4	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr9:125751642C>T	ENST00000373647.4	+	5	791	c.657C>T	c.(655-657)gtC>gtT	p.V219V		NM_012197.3	NP_036329.3	Q9Y3P9	RBGP1_HUMAN	RAB GTPase activating protein 1	219	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						TCTTCTGTGTCAGAGGGCATG	0.413																																					p.V219V		Atlas-SNP	.											.	RABGAP1	164	.	0			c.C657T						PASS	.						117	115	116					9																	125751642		2203	4300	6503	SO:0001819	synonymous_variant	23637	exon5			CTGTGTCAGAGGG	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.657C>T	chr9.hg19:g.125751642C>T		119.0	0.0	.		90.0	44.0	.	NM_012197	B9A6L2|Q05CW2|Q6ZMY1|Q9HA28|Q9P0E2|Q9UG67	Silent	SNP	ENST00000373647.4	hg19	CCDS6848.2																																																																																			.	.	.	none		0.413	RABGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053976.3	NM_012197		T	125751642	C	T	125751642	2	4	186	1	0	0	0	0	0	0	0	1	12977	813	29	2		2	RABGAP1	9	125751642	Silent	SNP	C	TCGA-GL-8500-01A-11D-2396-08	15659806	125751642	15461789	40	10922											
MLLT10	8028	hgsc.bcm.edu	37	chr10	22022934	22022934	+	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	accaactggcaattaatggcAttgtaggagctttaaatggg	13	11	11	6	0	0	0	0	0	0	0	0	1	0	1	1	4	2	4	1	4	6	5			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr10:22022934A>T	ENST00000307729.7	+	20	2912	c.2734A>T	c.(2734-2736)Att>Ttt	p.I912F	MLLT10_ENST00000377072.3_Missense_Mutation_p.I928F|MLLT10_ENST00000446906.2_Missense_Mutation_p.I912F|MLLT10_ENST00000377059.3_Missense_Mutation_p.I912F			P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10	912					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6						AATTAATGGCATTGTAGGAGC	0.498			T	"MLL, PICALM, CDK6"	AL																																p.I928F		Atlas-SNP	.		Dom	yes		10	10p12	8028	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10 (AF10)"		L	MLLT10_ENST00000377072,NS,carcinoma,0,2	MLLT10	183	.	0			c.A2782T						PASS	.						105	92	96					10																	22022934		2203	4300	6503	SO:0001583	missense	8028	exon21			AATGGCATTGTAG	U13948	CCDS7135.1, CCDS55706.1, CCDS55707.1, CCDS55708.1	10p12	2013-01-28	2001-11-28		ENSG00000078403	ENSG00000078403		"Zinc fingers, PHD-type"	16063	protein-coding gene	gene with protein product		602409	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 10"			7888665	Standard	NM_004641		Approved	AF10	uc021pny.1	P55197	OTTHUMG00000017799	ENST00000307729.7:c.2734A>T	chr10.hg19:g.22022934A>T	ENSP00000307411:p.Ile912Phe	86.0	0.0	.		78.0	33.0	.	NM_004641	B1ANA8|Q5JT37|Q5VX90|Q66K63	Missense_Mutation	SNP	ENST00000307729.7	hg19	CCDS55708.1	.	.	.	.	.	.	.	.	.	.	A	17.10	3.302680	0.60195	.	.	ENSG00000078403	ENST00000377072;ENST00000446906;ENST00000307729;ENST00000396529;ENST00000377059	T;T;T;T	0.19938	2.21;2.22;2.11;2.22	4.55	4.55	0.56014	.	0.178156	0.48767	D	0.000174	T	0.33731	0.0873	L	0.55481	1.735	0.58432	D	0.999998	D;P;D;P	0.65815	0.96;0.745;0.995;0.883	P;B;P;B	0.56163	0.59;0.169;0.793;0.231	T	0.06954	-1.0798	10	0.56958	D	0.05	.	12.4706	0.55785	1.0:0.0:0.0:0.0	.	607;912;912;928	Q5HYC6;E9PBP4;Q5VX90;P55197	.;.;.;AF10_HUMAN	F	928;912;912;747;912	ENSP00000366272:I928F;ENSP00000401406:I912F;ENSP00000307411:I912F;ENSP00000366258:I912F	ENSP00000307411:I912F	I	+	1	0	MLLT10	22062940	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.644000	0.67902	1.686000	0.51046	0.455000	0.32223	ATT	.	.	.	none		0.498	MLLT10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047136.1			T	22022934	A	T	22022934	3	4	186	1	0	0	0	0	1	0	0	0	9633	217	8	5	2860	5	MLLT10	10	22022934	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08		22022934	113511813	41	10923											
ANXA11	311	hgsc.bcm.edu	37	chr10	81927005	81927005	+	Missense_Mutation	SNP	A	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	agcctttcatggccttccgcAggacctcggcatctcgcagg	6	9	11	15	3	2	0	1	0	1	0	5	1	3	1	4	4	1	3	4	4	0	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr10:81927005A>C	ENST00000438331.1	-	7	1108	c.626T>G	c.(625-627)cTg>cGg	p.L209R	ANXA11_ENST00000265447.4_Missense_Mutation_p.L209R|ANXA11_ENST00000372231.3_Missense_Mutation_p.L209R|ANXA11_ENST00000537102.1_Missense_Mutation_p.L176R|ANXA11_ENST00000535999.1_Missense_Mutation_p.L209R|ANXA11_ENST00000422982.3_Missense_Mutation_p.L209R|ANXA11_ENST00000360615.4_Missense_Mutation_p.L209R	NM_145869.1	NP_665876.1	P50995	ANX11_HUMAN	annexin A11	209					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)			GGCCTTCCGCAGGACCTCGGC	0.577																																					p.L209R		Atlas-SNP	.											.	ANXA11	32	.	0			c.T626G						PASS	.						66	61	63					10																	81927005		2203	4300	6503	SO:0001583	missense	311	exon6			TTCCGCAGGACCT	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.626T>G	chr10.hg19:g.81927005A>C	ENSP00000398610:p.Leu209Arg	70.0	0.0	.		61.0	31.0	.	NM_145868	B4DVE7	Missense_Mutation	SNP	ENST00000438331.1	hg19	CCDS7364.1	.	.	.	.	.	.	.	.	.	.	.	26.1	4.707456	0.89018	.	.	ENSG00000122359	ENST00000372231;ENST00000422982;ENST00000438331;ENST00000372234;ENST00000360615;ENST00000265447;ENST00000535999;ENST00000424188;ENST00000537102	T;T;T;T;T;T;T	0.18338	2.22;2.22;2.22;2.22;2.22;2.22;2.22	5.31	5.31	0.75309	.	0.000000	0.64402	D	0.000001	T	0.61924	0.2386	H	0.99498	4.595	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.995;0.995	T	0.78922	-0.2013	10	0.87932	D	0	.	13.5153	0.61537	1.0:0.0:0.0:0.0	.	309;209;209	B7Z6L0;Q5T0G8;P50995	.;.;ANX11_HUMAN	R	209;209;209;209;209;209;209;116;176	ENSP00000361305:L209R;ENSP00000404412:L209R;ENSP00000398610:L209R;ENSP00000353827:L209R;ENSP00000265447:L209R;ENSP00000441748:L209R;ENSP00000441400:L176R	ENSP00000265447:L209R	L	-	2	0	ANXA11	81916985	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	8.792000	0.91856	2.151000	0.67156	0.459000	0.35465	CTG	.	.	.	none		0.577	ANXA11-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049044.1	NM_145869		C	81927005	A	C	81927005	3	2	186	1	0	0	0	0	1	0	0	0	716	188	7	5	935	5	ANXA11	10	81927005	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	59904071	81927005	53607742	42	10924											
SLC35F2	54733	hgsc.bcm.edu	37	chr11	107677532	107677532	+	Missense_Mutation	SNP	A	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	ccacggcgatgaagtggatcActctgtatcttgcatgaaga	11	10	11	9	2	3	3	1	2	2	1	3	5	3	4	1	2	1	2	1	2	3	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr11:107677532A>C	ENST00000525815.1	-	4	905	c.485T>G	c.(484-486)gTg>gGg	p.V162G	SLC35F2_ENST00000429869.1_Missense_Mutation_p.V162G|SLC35F2_ENST00000375682.4_Missense_Mutation_p.V115G|SLC35F2_ENST00000265836.7_Missense_Mutation_p.V14G|SLC35F2_ENST00000525071.1_Missense_Mutation_p.V162G	NM_017515.4	NP_059985.2	Q8IXU6	S35F2_HUMAN	solute carrier family 35, member F2	162					transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(61;9.46e-06)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;0.000111)|all_hematologic(158;0.000315)|all_epithelial(67;0.00197)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)|Epithelial(105;0.000105)|all cancers(92;0.00217)		GAAGTGGATCACTCTGTATCT	0.463																																					p.V162G		Atlas-SNP	.											.	SLC35F2	29	.	0			c.T485G						PASS	.						137	136	136					11																	107677532		1983	4179	6162	SO:0001583	missense	54733	exon4			TGGATCACTCTGT		CCDS41709.1	11q22.3	2013-05-22			ENSG00000110660	ENSG00000110660		"Solute carriers"	23615	protein-coding gene	gene with protein product						9119394	Standard	NM_017515		Approved	FLJ13018	uc001pjq.3	Q8IXU6	OTTHUMG00000166366	ENST00000525815.1:c.485T>G	chr11.hg19:g.107677532A>C	ENSP00000436785:p.Val162Gly	100.0	0.0	.		81.0	32.0	.	NM_017515	Q14963|Q5JPA8|Q6ZRQ3|Q9H947	Missense_Mutation	SNP	ENST00000525815.1	hg19	CCDS41709.1	.	.	.	.	.	.	.	.	.	.	A	16.47	3.133031	0.56828	.	.	ENSG00000110660	ENST00000525815;ENST00000525071;ENST00000265836;ENST00000375682;ENST00000429869	T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53	4.86	4.86	0.63082	.	0.341161	0.28140	N	0.016457	T	0.72211	0.3432	L	0.53249	1.67	0.50467	D	0.999875	P;P	0.42296	0.605;0.775	B;P	0.46208	0.405;0.507	T	0.75836	-0.3177	10	0.66056	D	0.02	.	14.4886	0.67634	1.0:0.0:0.0:0.0	.	162;162	E9PJD1;Q8IXU6	.;S35F2_HUMAN	G	162;162;14;115;162	ENSP00000436785:V162G;ENSP00000434307:V162G;ENSP00000364834:V115G;ENSP00000393571:V162G	ENSP00000265836:V14G	V	-	2	0	SLC35F2	107182742	1.000000	0.71417	1.000000	0.80357	0.534000	0.34807	3.837000	0.55820	1.824000	0.53156	0.533000	0.62120	GTG	.	.	.	none		0.463	SLC35F2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389417.1	NM_017515		C	107677532	A	C	107677532	3	2	186	1	0	0	0	0	1	0	0	0	14602	159	6	5	659	5	SLC35F2	11	107677532	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08		107677532	27328984	43	10925											
SIDT2	51092	hgsc.bcm.edu	37	chr11	117058116	117058118	+	In_Frame_Del	DEL	TTC	TTC	-																															caccctcgagtcctggctgaTtcttttcctggcagttcccc																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr11:117058116_117058118delTTC	ENST00000324225.4	+	11	1569_1571	c.1038_1040delTTC	c.(1036-1041)gattct>gat	p.S347del	SIDT2_ENST00000431081.2_In_Frame_Del_p.S351del	NM_001040455.1	NP_001035545.1	Q8NBJ9	SIDT2_HUMAN	SID1 transmembrane family, member 2	347					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)		TCCTGGCTGATTCTTTTCCTGGC	0.517																																					p.346_347del		Atlas-INDEL	.											.	SIDT2	82	.	0			c.1037_1039del						PASS	.																																			SO:0001651	inframe_deletion	51092	exon11			.	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.1038_1040delTTC	chr11.hg19:g.117058116_117058118delTTC	ENSP00000314023:p.Ser347del	170.0	0.0	0		153.0	58.0	0.379085	NM_001040455	Q8NBY7|Q9Y357	In_Frame_Del	DEL	ENST00000324225.4	hg19	CCDS31682.1																																																																																			.	.	.	none		0.517	SIDT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392836.1	NM_015996		-	117058118	TTC	-	117058116	7	5	186	1	0	1	0	1	0	0	0	0	14316	1490	52	0	1080	0	SIDT2	11	117058116	In_Frame_Del	DEL	TTC	TCGA-GL-8500-01A-11D-2396-08	9380584	117058116	17948400	44	10926											
SLC6A12	6539	hgsc.bcm.edu	37	chr12	308019	308019	+	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	gtagtagatgatgccctggtAggctccgggaagggtgacac	9	8	16	8	1	0	3	0	2	0	1	1	4	1	4	2	4	1	4	2	4	4	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr12:308019A>T	ENST00000428720.1	-	8	1533	c.790T>A	c.(790-792)Tac>Aac	p.Y264N	SLC6A12_ENST00000397296.2_Missense_Mutation_p.Y264N|SLC6A12_ENST00000536824.1_Missense_Mutation_p.Y264N|SLC6A12_ENST00000359674.4_Missense_Mutation_p.Y264N|SLC6A12_ENST00000424061.2_Missense_Mutation_p.Y264N|SLC6A12_ENST00000538272.1_5'UTR	NM_001122848.2	NP_001116320.1	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 12	264					amino acid transport (GO:0006865)|cellular hyperosmotic response (GO:0071474)|cellular water homeostasis (GO:0009992)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|response to organic substance (GO:0010033)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)			ATGCCCTGGTAGGCTCCGGGA	0.562																																					p.Y264N		Atlas-SNP	.											.	SLC6A12	60	.	0			c.T790A						PASS	.						143	119	127					12																	308019		2203	4300	6503	SO:0001583	missense	6539	exon8			CCTGGTAGGCTCC	L42300	CCDS8501.1	12p13	2013-07-19	2013-07-19		ENSG00000111181	ENSG00000111181		"Solute carriers"	11045	protein-coding gene	gene with protein product	"betaine/GABA transporter-1"	603080	"solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12"			7589472	Standard	NM_003044		Approved	BGT-1	uc009zdh.2	P48065	OTTHUMG00000090309	ENST00000428720.1:c.790T>A	chr12.hg19:g.308019A>T	ENSP00000388184:p.Tyr264Asn	104.0	0.0	.		128.0	69.0	.	NM_001122848	A0AV52|B2R992|D3DUN8	Missense_Mutation	SNP	ENST00000428720.1	hg19	CCDS8501.1	.	.	.	.	.	.	.	.	.	.	A	8.181	0.793882	0.16327	.	.	ENSG00000111181	ENST00000359674;ENST00000397296;ENST00000428720;ENST00000424061;ENST00000536824	T;T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83;-0.83	4.44	3.19	0.36642	.	0.450623	0.22962	N	0.053522	T	0.74245	0.3691	L	0.52905	1.665	0.09310	N	1	P	0.34800	0.469	P	0.48901	0.594	T	0.62163	-0.6912	10	0.28530	T	0.3	.	6.6378	0.22893	0.6374:0.2349:0.0:0.1277	.	264	P48065	S6A12_HUMAN	N	264	ENSP00000352702:Y264N;ENSP00000380464:Y264N;ENSP00000388184:Y264N;ENSP00000399136:Y264N;ENSP00000444268:Y264N	ENSP00000352702:Y264N	Y	-	1	0	SLC6A12	178280	0.021000	0.18746	0.919000	0.36401	0.166000	0.22503	0.594000	0.24014	1.762000	0.52044	0.533000	0.62120	TAC	.	.	.	none		0.562	SLC6A12-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206671.2	NM_003044		T	308019	A	T	308019	3	4	186	1	0	0	0	0	1	0	0	0	14688	420	15	5	1090	5	SLC6A12	12	308019	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08		308019	133543876	45	10927											
KDM5A	5927	hgsc.bcm.edu	37	chr12	401948	401948	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccttgcagggcctttggcAgttctgtgctgcgcacacag	5	11	13	12	1	1	0	0	0	1	0	2	0	2	0	2	2	3	5	2	2	0	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr12:401948A>G	ENST00000399788.2	-	27	5205	c.4843T>C	c.(4843-4845)Tgc>Cgc	p.C1615R	KDM5A_ENST00000382815.4_Missense_Mutation_p.C1615R|KDM5A_ENST00000540838.1_5'UTR	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	1615					chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|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 coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						GGCCTTTGGCAGTTCTGTGCT	0.468			T	NUP98	AML																																p.C1615R		Atlas-SNP	.		Dom	yes		12	12p11	5927	"lysine (K)-specific demethylase 5A, JARID1A"		L	.	KDM5A	307	.	0			c.T4843C						PASS	.						118	119	119					12																	401948		2033	4195	6228	SO:0001583	missense	5927	exon27			TTTGGCAGTTCTG		CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	9886	protein-coding gene	gene with protein product		180202	"retinoblastoma-binding protein 2", "Jumonji, AT rich interactive domain 1A (RBBP2-like)", "jumonji, AT rich interactive domain 1A"	RBBP2, JARID1A		1857421	Standard	NM_001042603		Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.4843T>C	chr12.hg19:g.401948A>G	ENSP00000382688:p.Cys1615Arg	137.0	0.0	.		151.0	48.0	.	NM_001042603	A8MV76|Q4LE72|Q86XZ1	Missense_Mutation	SNP	ENST00000399788.2	hg19	CCDS41736.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.219116	0.79464	.	.	ENSG00000073614	ENST00000399788;ENST00000382815	D;D	0.99667	-6.34;-3.28	5.48	5.48	0.80851	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.150326	0.64402	D	0.000005	D	0.99354	0.9773	L	0.59436	1.845	0.80722	D	1	D;D	0.64830	0.99;0.994	P;P	0.60682	0.758;0.878	D	0.98834	1.0752	10	0.87932	D	0	-9.1245	15.575	0.76368	1.0:0.0:0.0:0.0	.	1615;1615	P29375;P29375-2	KDM5A_HUMAN;.	R	1615	ENSP00000382688:C1615R;ENSP00000372265:C1615R	ENSP00000372265:C1615R	C	-	1	0	KDM5A	272209	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.313000	0.96297	2.080000	0.62538	0.528000	0.53228	TGC	.	.	.	none		0.468	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397812.1	NM_005056		G	401948	A	G	401948	3	3	186	1	0	0	0	0	1	0	0	0	8140	188	7	3	237	3	KDM5A	12	401948	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	93929	401948	133449947	46	10928											
C12orf5	57103	hgsc.bcm.edu	37	chr12	4461705	4461705	+	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	agtgttccttaccagccactCtgagcagatctgaacttatg	10	12	8	11	0	2	3	0	2	2	1	3	3	3	3	3	0	4	2	3	0	3	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr12:4461705C>G	ENST00000179259.4	+	6	728	c.661C>G	c.(661-663)Ctg>Gtg	p.L221V		NM_020375.2	NP_065108.1	Q9NQ88	TIGAR_HUMAN	chromosome 12 open reading frame 5	221					intestinal epithelial cell development (GO:0060576)|negative regulation of macromitophagy (GO:1901525)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|response to gamma radiation (GO:0010332)|response to xenobiotic stimulus (GO:0009410)	intracellular (GO:0005622)	fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			endometrium(1)|large_intestine(1)|lung(5)|skin(3)	10			all cancers(3;1.15e-07)|Colorectal(7;0.00165)|OV - Ovarian serous cystadenocarcinoma(31;0.00596)|COAD - Colon adenocarcinoma(12;0.0229)|GBM - Glioblastoma multiforme(3;0.0266)|STAD - Stomach adenocarcinoma(119;0.206)			ACCAGCCACTCTGAGCAGATC	0.423																																					p.L221V	Colon(1;100 192 35375 49454 52532)	Atlas-SNP	.											.	C12orf5	28	.	0			c.C661G						PASS	.						100	89	93					12																	4461705		2203	4300	6503	SO:0001583	missense	57103	exon6			GCCACTCTGAGCA	AJ272206	CCDS8525.1	12p13.32	2014-05-29	2009-11-24	2009-11-24	ENSG00000078237	ENSG00000078237	3.1.3.46		1185	protein-coding gene	gene with protein product	"TP53-induced glycolysis and apoptosis regulator"	610775				16140933, 16839880, 18945750, 19713938	Standard	NM_020375		Approved	TIGAR	uc001qmp.3	Q9NQ88		ENST00000179259.4:c.661C>G	chr12.hg19:g.4461705C>G	ENSP00000179259:p.Leu221Val	136.0	0.0	.		125.0	49.0	.	NM_020375	B2R840	Missense_Mutation	SNP	ENST00000179259.4	hg19	CCDS8525.1	.	.	.	.	.	.	.	.	.	.	C	3.030	-0.199744	0.06219	.	.	ENSG00000078237	ENST00000179259	T	0.80738	-1.41	5.86	-2.23	0.06930	.	0.842330	0.10652	N	0.649789	T	0.68659	0.3025	L	0.43152	1.355	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.54609	-0.8268	10	0.40728	T	0.16	-13.6183	6.2439	0.20805	0.0912:0.2965:0.4592:0.1531	.	221	Q9NQ88	TIGAR_HUMAN	V	221	ENSP00000179259:L221V	ENSP00000179259:L221V	L	+	1	2	C12orf5	4331966	0.005000	0.15991	0.000000	0.03702	0.066000	0.16364	-0.080000	0.11339	-0.333000	0.08476	-0.219000	0.12488	CTG	.	.	.	none		0.423	C12orf5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398290.1	NM_020375		G	4461705	C	G	4461705	3	3	186	1	0	0	0	0	1	0	0	0	1696	912	32	4	683	4	C12orf5	12	4461705	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	4059757	4461705	129390190	47	10929											
GPR162	27239	hgsc.bcm.edu	37	chr12	6933600	6933600	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctccaagatcggcctcggctTtggcgtttgcttcagcctct	4	13	10	14	3	2	1	1	0	1	1	5	1	3	1	3	3	2	3	3	3	1	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr12:6933600T>C	ENST00000311268.3	+	2	1323	c.536T>C	c.(535-537)tTt>tCt	p.F179S	GPR162_ENST00000382315.3_Intron|GPR162_ENST00000428545.2_Intron	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162	179						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(2)|skin(1)	18						GGCCTCGGCTTTGGCGTTTGC	0.597																																					p.F179S		Atlas-SNP	.											.	GPR162	55	.	0			c.T536C						PASS	.						86	82	84					12																	6933600		2203	4300	6503	SO:0001583	missense	27239	exon2			TCGGCTTTGGCGT	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.536T>C	chr12.hg19:g.6933600T>C	ENSP00000311528:p.Phe179Ser	131.0	0.0	.		97.0	39.0	.	NM_019858	Q16664|Q59EH5|Q66K56	Missense_Mutation	SNP	ENST00000311268.3	hg19	CCDS8563.1	.	.	.	.	.	.	.	.	.	.	T	19.89	3.910599	0.72983	.	.	ENSG00000250510	ENST00000311268	T	0.72051	-0.62	4.33	3.19	0.36642	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.59321	0.2185	L	0.34521	1.04	0.80722	D	1	P;B	0.41624	0.757;0.156	B;B	0.40602	0.334;0.053	T	0.60234	-0.7303	9	0.87932	D	0	.	9.5237	0.39152	0.0:0.0841:0.0:0.9159	.	179;179	B7Z3U3;Q16538	.;GP162_HUMAN	S	179	ENSP00000311528:F179S	ENSP00000311528:F179S	F	+	2	0	GPR162	6803861	1.000000	0.71417	0.747000	0.31113	0.888000	0.51559	7.858000	0.86971	0.722000	0.32252	0.402000	0.26972	TTT	.	.	.	none		0.597	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	NM_019858		C	6933600	T	C	6933600	3	2	186	1	0	0	0	0	1	0	0	0	6673	1841	64	3	557	3	GPR162	12	6933600	Missense_Mutation	SNP	T	TCGA-GL-8500-01A-11D-2396-08	2471895	6933600	126918295	48	10930											
ITPR2	3709	hgsc.bcm.edu	37	chr12	26809443	26809443	+	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	ggtttatggccagatactggCgatccaagcacatccttgca	10	10	10	11	1	0	1	0	0	0	1	2	2	2	1	3	3	3	3	3	3	3	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr12:26809443C>G	ENST00000381340.3	-	19	2647	c.2231G>C	c.(2230-2232)cGc>cCc	p.R744P		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	744					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)	CAGATACTGGCGATCCAAGCA	0.453																																					p.R744P		Atlas-SNP	.											.	ITPR2	270	.	0			c.G2231C						PASS	.						68	70	69					12																	26809443		2001	4179	6180	SO:0001583	missense	3709	exon19			TACTGGCGATCCA	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.2231G>C	chr12.hg19:g.26809443C>G	ENSP00000370744:p.Arg744Pro	91.0	0.0	.		85.0	27.0	.	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	hg19	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.758328	0.89843	.	.	ENSG00000123104	ENST00000381340	D	0.95656	-3.77	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	D	0.97949	0.9325	M	0.87381	2.88	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98818	1.0746	10	0.87932	D	0	.	18.0329	0.89290	0.0:1.0:0.0:0.0	.	744	Q14571	ITPR2_HUMAN	P	744	ENSP00000370744:R744P	ENSP00000370744:R744P	R	-	2	0	ITPR2	26700710	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.596000	0.82721	2.546000	0.85860	0.655000	0.94253	CGC	.	.	.	none		0.453	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		G	26809443	C	G	26809443	3	3	186	1	0	0	0	0	1	0	0	0	7928	768	27	4	6030	4	ITPR2	12	26809443	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	19875843	26809443	107042452	49	10931											
DIP2B	57609	hgsc.bcm.edu	37	chr12	51092173	51092173	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcaatgaatggattgagctAtggggtaatacgggtcaata	13	11	12	5	1	2	2	2	2	0	0	2	3	2	3	0	4	2	2	0	4	7	5			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr12:51092173A>G	ENST00000301180.5	+	18	2145	c.2111A>G	c.(2110-2112)tAt>tGt	p.Y704C		NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	704						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						GGATTGAGCTATGGGGTAATA	0.463																																					p.Y704C		Atlas-SNP	.											.	DIP2B	167	.	0			c.A2111G						PASS	.						108	101	103					12																	51092173		2203	4300	6503	SO:0001583	missense	57609	exon18			TGAGCTATGGGGT	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.2111A>G	chr12.hg19:g.51092173A>G	ENSP00000301180:p.Tyr704Cys	117.0	0.0	.		104.0	38.0	.	NM_173602	Q6B011|Q8N1L5|Q8NB38	Missense_Mutation	SNP	ENST00000301180.5	hg19	CCDS31799.1	.	.	.	.	.	.	.	.	.	.	A	19.81	3.896459	0.72639	.	.	ENSG00000066084	ENST00000301180	T	0.23552	1.9	5.2	5.2	0.72013	AMP-dependent synthetase/ligase (1);	0.113362	0.64402	D	0.000011	T	0.45498	0.1345	M	0.71581	2.175	0.42957	D	0.994399	D	0.63880	0.993	D	0.64687	0.928	T	0.38714	-0.9648	10	0.40728	T	0.16	-14.3821	11.1177	0.48270	0.8536:0.0:0.0:0.1464	.	704	Q9P265	DIP2B_HUMAN	C	704	ENSP00000301180:Y704C	ENSP00000301180:Y704C	Y	+	2	0	DIP2B	49378440	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.169000	0.77578	2.184000	0.69523	0.482000	0.46254	TAT	.	.	.	none		0.463	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602		G	51092173	A	G	51092173	3	3	186	1	0	0	0	0	1	0	0	0	4530	449	16	3	2181	3	DIP2B	12	51092173	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	24282730	51092173	82759722	50	10932											
ESPL1	9700	hgsc.bcm.edu	37	chr12	53680427	53680427	+	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	caccattaataaaaagtgtcCctggctcagagccctctaag	13	9	7	12	0	2	1	1	0	1	1	3	1	3	1	3	1	1	1	3	1	5	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr12:53680427C>A	ENST00000257934.4	+	18	3998	c.3907C>A	c.(3907-3909)Cct>Act	p.P1303T	ESPL1_ENST00000552462.1_Missense_Mutation_p.P1303T	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	1303					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						AAAAAGTGTCCCTGGCTCAGA	0.527																																					p.P1303T	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											.	ESPL1	158	.	0			c.C3907A						PASS	.						42	44	44					12																	53680427		2203	4300	6503	SO:0001583	missense	9700	exon18			AGTGTCCCTGGCT	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.3907C>A	chr12.hg19:g.53680427C>A	ENSP00000257934:p.Pro1303Thr	103.0	0.0	.		79.0	40.0	.	NM_012291		Missense_Mutation	SNP	ENST00000257934.4	hg19	CCDS8852.1	.	.	.	.	.	.	.	.	.	.	C	0.020	-1.435949	0.01108	.	.	ENSG00000135476	ENST00000257934;ENST00000552671;ENST00000552462	T;T	0.11385	2.78;2.78	5.26	1.4	0.22301	.	0.405202	0.29501	N	0.011979	T	0.05273	0.0140	N	0.21583	0.68	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.42050	-0.9474	10	0.14252	T	0.57	.	3.9836	0.09506	0.1566:0.4565:0.3028:0.0841	.	1303	Q14674	ESPL1_HUMAN	T	1303;978;1303	ENSP00000257934:P1303T;ENSP00000449831:P1303T	ENSP00000257934:P1303T	P	+	1	0	ESPL1	51966694	0.000000	0.05858	0.000000	0.03702	0.056000	0.15407	-0.007000	0.12810	0.093000	0.17368	0.561000	0.74099	CCT	.	.	.	none		0.527	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291		A	53680427	C	A	53680427	3	1	186	1	0	0	0	0	1	0	0	0	5255	623	22	4	3973	4	ESPL1	12	53680427	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	2588254	53680427	80171468	51	10933											
GLIPR1L2	144321	hgsc.bcm.edu	37	chr12	75785104	75785104	+	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	agctgcggggcgacgtcattCcccgagggtctaacttgcgc	6	8	14	13	5	2	0	1	0	1	0	3	2	3	0	2	3	4	1	2	3	1	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr12:75785104C>A	ENST00000550916.1	+	1	255	c.208C>A	c.(208-210)Ccc>Acc	p.P70T	GLIPR1L2_ENST00000378689.2_Missense_Mutation_p.P70T|GLIPR1L2_ENST00000320460.4_Missense_Mutation_p.P70T|GLIPR1L2_ENST00000547164.1_Missense_Mutation_p.P70T|GLIPR1L2_ENST00000441218.1_5'Flank|GLIPR1L2_ENST00000435775.1_Missense_Mutation_p.P70T|GLIPR1L2_ENST00000378692.3_5'UTR|CAPS2_ENST00000442339.2_5'Flank	NM_001270396.1	NP_001257325.1	Q4G1C9	GRPL2_HUMAN	GLI pathogenesis-related 1 like 2	70	SCP.					integral component of membrane (GO:0016021)				kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16						CGACGTCATTCCCCGAGGGTC	0.567											OREG0021999	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P70T		Atlas-SNP	.											.	GLIPR1L2	54	.	0			c.C208A						PASS	.						104	80	88					12																	75785104		2203	4300	6503	SO:0001583	missense	144321	exon1			GTCATTCCCCGAG	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.208C>A	chr12.hg19:g.75785104C>A	ENSP00000448248:p.Pro70Thr	92.0	0.0	.	1163	81.0	39.0	.	NM_152436	Q6MZS1|Q8N6N0|Q8NA43	Missense_Mutation	SNP	ENST00000550916.1	hg19	CCDS58258.1	.	.	.	.	.	.	.	.	.	.	C	12.33	1.906693	0.33628	.	.	ENSG00000180481	ENST00000550916;ENST00000435775;ENST00000378689;ENST00000320460;ENST00000547164	T;T;T;T;T	0.14516	2.5;2.5;2.5;2.5;2.5	3.68	3.68	0.42216	CAP domain (3);	0.000000	0.85682	D	0.000000	T	0.41880	0.1178	M	0.90425	3.115	0.48288	D	0.999624	D;D	0.89917	0.997;1.0	P;D	0.87578	0.897;0.998	T	0.49062	-0.8978	10	0.87932	D	0	.	11.1954	0.48709	0.0:1.0:0.0:0.0	.	70;70	Q4G1C9;Q4G1C9-2	GRPL2_HUMAN;.	T	70	ENSP00000448248:P70T;ENSP00000398328:P70T;ENSP00000367960:P70T;ENSP00000317385:P70T;ENSP00000447980:P70T	ENSP00000317385:P70T	P	+	1	0	GLIPR1L2	74071371	0.067000	0.21026	0.025000	0.17156	0.007000	0.05969	2.883000	0.48554	2.352000	0.79861	0.585000	0.79938	CCC	.	.	.	none		0.567	GLIPR1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405718.1	NM_152436		A	75785104	C	A	75785104	3	1	186	1	0	0	0	0	1	0	0	0	6450	855	30	4	210	4	GLIPR1L2	12	75785104	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	22104677	75785104	58066791	52	10934											
CUL4A	8451	hgsc.bcm.edu	37	chr13	113915023	113915023	+	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	agatgagaaagactcttggtCataatcttctagtttctgaa	13	14	8	6	0	5	4	1	2	4	3	5	5	5	4	0	1	0	1	0	1	4	5			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr13:113915023C>G	ENST00000375440.4	+	19	2218	c.2134C>G	c.(2134-2136)Cat>Gat	p.H712D	CUL4A_ENST00000326335.4_Missense_Mutation_p.H612D|CUL4A_ENST00000375441.3_Missense_Mutation_p.H612D|CUL4A_ENST00000451881.1_Missense_Mutation_p.H612D	NM_001008895.1	NP_001008895.1	Q13619	CUL4A_HUMAN	cullin 4A	712					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)			GACTCTTGGTCATAATCTTCT	0.328																																					p.H712D		Atlas-SNP	.											.	CUL4A	50	.	0			c.C2134G						PASS	.						75	74	74					13																	113915023		2203	4300	6503	SO:0001583	missense	8451	exon19			CTTGGTCATAATC	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.2134C>G	chr13.hg19:g.113915023C>G	ENSP00000364589:p.His712Asp	43.0	0.0	.		31.0	14.0	.	NM_001008895	A2A2W2|O75834|Q589T6|Q5TC62|Q6UP08|Q9UP17	Missense_Mutation	SNP	ENST00000375440.4	hg19	CCDS41908.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.332500	0.81801	.	.	ENSG00000139842	ENST00000375441;ENST00000451881;ENST00000326335;ENST00000375440	T;T;T;T	0.79454	-1.27;-1.27;-1.27;-1.18	5.52	5.52	0.82312	Cullin protein, neddylation domain (2);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.93588	0.7953	H	0.99011	4.4	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.95979	0.8976	10	0.87932	D	0	-35.2623	19.4327	0.94778	0.0:1.0:0.0:0.0	.	712;712	Q13619;A8MSH7	CUL4A_HUMAN;.	D	612;612;612;712	ENSP00000364590:H612D;ENSP00000389118:H612D;ENSP00000322132:H612D;ENSP00000364589:H712D	ENSP00000322132:H612D	H	+	1	0	CUL4A	112963024	1.000000	0.71417	0.165000	0.22776	0.878000	0.50629	5.612000	0.67681	2.594000	0.87642	0.561000	0.74099	CAT	.	.	.	none		0.328	CUL4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045888.3	NM_003589		G	113915023	C	G	113915023	3	3	186	1	0	0	0	0	1	0	0	0	4059	826	29	4	2208	4	CUL4A	13	113915023	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08		113915023	1254855	53	10935											
LAMP1	3916	hgsc.bcm.edu	37	chr13	113963979	113963979	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatgacctttgacctgccaTcagatgccacagtggtgctc	9	10	9	13	0	1	3	1	2	0	1	2	3	1	3	4	1	3	1	4	1	0	1			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr13:113963979T>C	ENST00000332556.4	+	3	399	c.205T>C	c.(205-207)Tca>Cca	p.S69P	LAMP1_ENST00000397181.3_Missense_Mutation_p.S69P	NM_005561.3	NP_005552.3	P11279	LAMP1_HUMAN	lysosomal-associated membrane protein 1	69	First lumenal domain.				autophagic cell death (GO:0048102)|autophagy (GO:0006914)|establishment of protein localization to organelle (GO:0072594)|Golgi to lysosome transport (GO:0090160)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|protein stabilization (GO:0050821)|regulation of organelle transport along microtubule (GO:1902513)	alveolar lamellar body (GO:0097208)|cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|phagolysosome membrane (GO:0061474)|sarcolemma (GO:0042383)	enzyme binding (GO:0019899)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|skin(1)|stomach(2)	16	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)			TGACCTGCCATCAGATGCCAC	0.423																																					p.S69P		Atlas-SNP	.											.	LAMP1	41	.	0			c.T205C						PASS	.						89	92	91					13																	113963979		1960	4142	6102	SO:0001583	missense	3916	exon3			CTGCCATCAGATG	J03263	CCDS41909.1	13q34	2011-11-24			ENSG00000185896	ENSG00000185896		"CD molecules"	6499	protein-coding gene	gene with protein product		153330					Standard	NM_005561		Approved	CD107a	uc001vtm.1	P11279	OTTHUMG00000017380	ENST00000332556.4:c.205T>C	chr13.hg19:g.113963979T>C	ENSP00000333298:p.Ser69Pro	110.0	0.0	.		115.0	45.0	.	NM_005561	B4DWL3|Q8WU33|Q96I40|Q9BRD2|Q9NP13	Missense_Mutation	SNP	ENST00000332556.4	hg19	CCDS41909.1	.	.	.	.	.	.	.	.	.	.	T	10.74	1.434683	0.25813	.	.	ENSG00000185896	ENST00000332556;ENST00000397181	T;T	0.32023	1.47;1.88	5.15	-10.3	0.00346	.	1.186920	0.05805	N	0.612961	T	0.19366	0.0465	L	0.51914	1.62	0.09310	N	1	B;B	0.15141	0.012;0.004	B;B	0.14578	0.011;0.004	T	0.10064	-1.0646	10	0.26408	T	0.33	-1.3993	4.2226	0.10565	0.0888:0.4046:0.2957:0.2108	.	69;69	B4DWL3;P11279	.;LAMP1_HUMAN	P	69	ENSP00000333298:S69P;ENSP00000415354:S69P	ENSP00000333298:S69P	S	+	1	0	LAMP1	113011980	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.754000	0.00790	-2.251000	0.00700	-0.479000	0.04858	TCA	.	.	.	none		0.423	LAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045876.2			C	113963979	T	C	113963979	3	2	186	1	0	0	0	0	1	0	0	0	8624	1435	50	3	215	3	LAMP1	13	113963979	Missense_Mutation	SNP	T	TCGA-GL-8500-01A-11D-2396-08	48956	113963979	1205899	54	10936											
SDCCAG1	9147	hgsc.bcm.edu	37	chr14	50292672	50292672	+	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	tcttttctgctgacttgaatGcctatttatagaaaagagtt	11	17	7	6	0	2	4	0	2	2	2	2	4	2	4	1	0	2	2	1	0	6	8	rs370101877		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr14:50292672G>A	ENST00000298310.5	-	16	1939	c.1490C>T	c.(1489-1491)gCa>gTa	p.A497V	NEMF_ENST00000545773.1_Splice_Site_p.A455V|NEMF_ENST00000546046.1_Splice_Site_p.A497V|AL627171.2_ENST00000595378.1_3'UTR|NEMF_ENST00000556925.1_5'UTR			O60524	NEMF_HUMAN	nuclear export mediator factor	497					nuclear export (GO:0051168)	nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(13)|liver(1)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	36						TGACTTGAATGCCTATTTATA	0.269																																					p.A497V		Atlas-SNP	.											.	NEMF	79	.	0			c.C1490T						PASS	.	G	VAL/ALA	0,4400		0,0,2200	96	91	93		1490	5.3	1	14		93	1,8591	1.2+/-3.3	0,1,4295	no	missense-near-splice	NEMF	NM_004713.3	64	0,1,6495	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	497/1077	50292672	1,12991	2200	4296	6496	SO:0001630	splice_region_variant	9147	exon16			TTGAATGCCTATT	AF039687	CCDS9694.1	14q21.3	2012-11-19	2011-01-31	2011-01-31	ENSG00000165525	ENSG00000165525			10663	protein-coding gene	gene with protein product		608378	"serologically defined colon cancer antigen 1"	SDCCAG1		9610721, 10575219	Standard	XR_429334		Approved	NY-CO-1, FLJ10051	uc001wxc.3	O60524	OTTHUMG00000170857	ENST00000298310.5:c.1489-1C>T	chr14.hg19:g.50292672G>A		47.0	0.0	.		23.0	17.0	.	NM_004713	A0JLQ3|B3KSK1|B4DDL3|B4DHA9|B4E3F3|Q32Q66|Q8WW70|Q9NWG1	Missense_Mutation	SNP	ENST00000298310.5	hg19	CCDS9694.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.985467	0.93044	0.0	1.16E-4	ENSG00000165525	ENST00000298310;ENST00000545773;ENST00000546046;ENST00000534912;ENST00000555970	T;T;T;T	0.47528	0.84;0.84;0.84;0.84	5.34	5.34	0.76211	Fibronectin-binding A, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.73892	0.3645	M	0.86864	2.845	0.80722	D	1	D;D;D;D;D	0.69078	0.997;0.994;0.985;0.997;0.995	D;D;D;D;D	0.73380	0.966;0.966;0.943;0.966;0.98	T	0.77086	-0.2718	10	0.54805	T	0.06	-18.6685	19.4564	0.94892	0.0:0.0:1.0:0.0	.	497;268;472;455;497	O60524-3;F5H639;O60524-5;O60524-4;O60524	.;.;.;.;NEMF_HUMAN	V	497;455;497;268;455	ENSP00000298310:A497V;ENSP00000438309:A455V;ENSP00000441016:A497V;ENSP00000452540:A455V	ENSP00000298310:A497V	A	-	2	0	NEMF	49362422	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.484000	0.90445	2.684000	0.91462	0.644000	0.83932	GCA	.	.	.	weak		0.269	NEMF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410798.1	NM_004713	Missense_Mutation	A	50292672	G	A	50292672	5	1	186	1	0	0	0	0	0	0	1	0	13970	1333	46	2	1812	2	SDCCAG1	14	50292672	Splice_Site	SNP	G	TCGA-GL-8500-01A-11D-2396-08		50292672	57056868	55	10937											
DLGAP5	9787	hgsc.bcm.edu	37	chr14	55655750	55655751	+	Frame_Shift_Ins	INS	-	-	AT																															tccaaggttggaatgtttacINSatctttcaaaccaaagtgtc																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr14:55655750_55655751insAT	ENST00000247191.2	-	2	363_364	c.147_148insAT	c.(145-150)gatgtafs	p.V50fs	DLGAP5_ENST00000395425.2_Frame_Shift_Ins_p.V50fs	NM_014750.4	NP_055565.3	Q15398	DLGP5_HUMAN	discs, large (Drosophila) homolog-associated protein 5	50					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|dephosphorylation (GO:0016311)|mitotic chromosome movement towards spindle pole (GO:0007079)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|spindle pole centrosome (GO:0031616)	phosphoprotein phosphatase activity (GO:0004721)			biliary_tract(1)|breast(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	44						GGAATGTTTACATCTTTCAAAC	0.347																																					p.V50fs		Atlas-INDEL	.											.	DLGAP5	84	.	0			c.148_149insAT						PASS	.																																			SO:0001589	frameshift_variant	9787	exon2			.	D13633	CCDS9723.1, CCDS53897.1	14q22.3	2008-05-30	2008-05-30	2008-05-30	ENSG00000126787	ENSG00000126787			16864	protein-coding gene	gene with protein product			"discs, large homolog 7 (Drosophila)"	DLG7		7584026, 7584028	Standard	NM_014750		Approved	KIAA0008, DLG1, HURP	uc001xbs.3	Q15398	OTTHUMG00000140310	ENST00000247191.2:c.146_147dupAT	chr14.hg19:g.55655751_55655752dupAT	ENSP00000247191:p.Val50fs	58.0	0.0	0		43.0	28.0	0.651163	NM_014750	A8MTM6|B4DRM8|Q86T11|Q8NG58	Frame_Shift_Ins	INS	ENST00000247191.2	hg19	CCDS9723.1																																																																																			.	.	.	none		0.347	DLGAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276908.2	NM_014750		AT	55655751	-	AT	55655750	7	5	186	1	0	1	1	0	0	0	0	0	4565	478	17	0	2559	0	DLGAP5	14	55655750	Frame_Shift_Ins	INS	-	TCGA-GL-8500-01A-11D-2396-08	5363078	55655750	51693790	56	10938											
PPM1A	5494	hgsc.bcm.edu	37	chr14	60712638	60712638	+	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	taatgaaaagagagaaaagaAgaatggggaagagaagggca	22	3	15	1	0	0	6	0	1	0	5	0	9	0	7	0	3	0	1	0	3	9	1			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr14:60712638A>G	ENST00000529574.1	+	0	164				CTD-2184C24.2_ENST00000553775.1_RNA|CTD-2184C24.2_ENST00000529171.1_RNA|PPM1A_ENST00000325642.3_Missense_Mutation_p.R25G|CTD-2184C24.2_ENST00000532515.1_RNA|CTD-2184C24.2_ENST00000553269.1_RNA			P35813	PPM1A_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1A						cell cycle arrest (GO:0007050)|dephosphorylation (GO:0016311)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|N-terminal protein myristoylation (GO:0006499)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|protein dephosphorylation (GO:0006470)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|voltage-gated calcium channel complex (GO:0005891)	calmodulin-dependent protein phosphatase activity (GO:0033192)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)|R-SMAD binding (GO:0070412)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(1)|large_intestine(8)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(108;0.046)		agagaaaagaagaatggggaa	0.408																																					p.R25G		Atlas-SNP	.											.	PPM1A	72	.	0			c.A73G						PASS	.						79	77	78					14																	60712638		1568	3578	5146	SO:0001623	5_prime_UTR_variant	5494	exon1			AAAAGAAGAATGG	S87759	CCDS9744.1, CCDS9745.1, CCDS45120.1	14q23.1	2013-01-24	2010-03-05		ENSG00000100614	ENSG00000100614	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9275	protein-coding gene	gene with protein product	"phosphatase 2C alpha", "protein phosphatase 2C, alpha isoform"	606108	"protein phosphatase 1A (formerly 2C), magnesium-dependent, alpha isoform"			1311954	Standard	NM_177952		Approved	MGC9201, PP2Calpha, PP2CA	uc001xew.4	P35813	OTTHUMG00000140333	ENST00000529574.1:c.-234A>G	chr14.hg19:g.60712638A>G		12.0	0.0	.		4.0	4.0	.	NM_177952	B5BU11|J3KNM0|O75551	Missense_Mutation	SNP	ENST00000529574.1	hg19	CCDS9744.1	.	.	.	.	.	.	.	.	.	.	A	10.67	1.415786	0.25552	.	.	ENSG00000100614	ENST00000325642	T	0.33438	1.41	3.86	0.196	0.15159	.	.	.	.	.	T	0.14141	0.0342	N	0.08118	0	0.09310	N	0.999997	.	.	.	.	.	.	T	0.23297	-1.0192	7	0.87932	D	0	.	2.3945	0.04386	0.5595:0.0:0.2316:0.2089	.	.	.	.	G	25	ENSP00000327255:R25G	ENSP00000327255:R25G	R	+	1	2	PPM1A	59782391	0.006000	0.16342	0.001000	0.08648	0.216000	0.24613	-0.020000	0.12525	0.023000	0.15187	0.172000	0.16884	AGA	.	.	.	none		0.408	PPM1A-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding		NM_021003		G	60712638	A	G	60712638	1	3	186	0	1	0	0	0	0	0	0	0	12345	64	3	3		3	PPM1A	14	60712638	5'UTR	SNP	A	TCGA-GL-8500-01A-11D-2396-08	5056888	60712638	46636902	57	10939											
DISP2	85455	hgsc.bcm.edu	37	chr15	40661086	40661086	+	Frame_Shift_Del	DEL	A	A	-																															accagacccagctcttctacAatgaggtcagccactggctg																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr15:40661086delA	ENST00000267889.3	+	8	2860	c.2773delA	c.(2773-2775)aatfs	p.N925fs	RP11-64K12.4_ENST00000558421.1_RNA|LINC00594_ENST00000561261.1_lincRNA	NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	925					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)		GCTCTTCTACAATGAGGTCAG	0.602																																					p.Y924X		Atlas-INDEL	.											.	DISP2	86	.	0			c.2772delC						PASS	.						53	58	56					15																	40661086		2203	4300	6503	SO:0001589	frameshift_variant	85455	exon8			.	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.2773delA	chr15.hg19:g.40661086delA	ENSP00000267889:p.Asn925fs	138.0	0.0	0		98.0	40.0	0.408163	NM_033510	Q6AHW3|Q9C0C1	Frame_Shift_Del	DEL	ENST00000267889.3	hg19	CCDS10056.1																																																																																			.	.	.	none		0.602	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510		-	40661086	A	-	40661086	7	5	186	1	0	1	0	1	0	0	0	0	4542	130	5	0	2803	0	DISP2	15	40661086	Frame_Shift_Del	DEL	A	TCGA-GL-8500-01A-11D-2396-08		40661086	61870306	58	10940											
MYO5A	4644	hgsc.bcm.edu	37	chr15	52606371	52606371	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttcttcaaactcattaacTggagtatacaaattcaacac	15	13	3	10	0	4	0	3	0	1	0	4	1	4	1	0	1	4	1	0	1	6	6			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr15:52606371T>C	ENST00000399231.3	-	40	5607	c.5364A>G	c.(5362-5364)ccA>ccG	p.P1788P	MYO5A_ENST00000356338.6_Silent_p.P1761P|MYO5A_ENST00000358212.6_Silent_p.P1813P|MYO5A_ENST00000553916.1_Silent_p.P1786P|MYO5A_ENST00000399233.2_Silent_p.P1785P	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1788	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.				actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		ACTCATTAACTGGAGTATACA	0.348																																					p.P1788P		Atlas-SNP	.											.	MYO5A	145	.	0			c.A5364G						PASS	.						88	81	83					15																	52606371		1810	4082	5892	SO:0001819	synonymous_variant	4644	exon40			ATTAACTGGAGTA		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.5364A>G	chr15.hg19:g.52606371T>C		88.0	0.0	.		82.0	29.0	.	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Silent	SNP	ENST00000399231.3	hg19	CCDS42037.1																																																																																			.	.	.	none		0.348	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259		C	52606371	T	C	52606371	2	2	186	1	0	0	0	0	0	0	0	1	10085	1567	55	3		3	MYO5A	15	52606371	Silent	SNP	T	TCGA-GL-8500-01A-11D-2396-08	11945285	52606371	49925021	59	10941											
SRRM2	23524	hgsc.bcm.edu	37	chr16	2812806	2812806	+	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	cgcatttcttcaaggcggagCaggtctctctcttcaccacg	7	11	9	14	3	5	0	2	0	3	0	7	1	5	1	1	3	1	2	1	3	1	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr16:2812806C>G	ENST00000301740.8	+	11	2826	c.2277C>G	c.(2275-2277)agC>agG	p.S759R		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	759	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						CAAGGCGGAGCAGGTCTCTCT	0.473																																					p.S759R		Atlas-SNP	.											.	SRRM2	263	.	0			c.C2277G						PASS	.						119	123	122					16																	2812806		2198	4300	6498	SO:0001583	missense	23524	exon11			GCGGAGCAGGTCT	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.2277C>G	chr16.hg19:g.2812806C>G	ENSP00000301740:p.Ser759Arg	237.0	0.0	.		285.0	170.0	.	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	hg19	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	C	8.634	0.894431	0.17613	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933;ENST00000426305	T	0.26373	1.74	5.62	4.67	0.58626	.	0.000000	0.85682	D	0.000000	T	0.32526	0.0832	L	0.27053	0.805	0.33222	D	0.554776	D	0.65815	0.995	P	0.59115	0.852	T	0.48747	-0.9008	10	0.87932	D	0	-13.5853	12.4668	0.55764	0.0:0.9183:0.0:0.0817	.	759	Q9UQ35	SRRM2_HUMAN	R	759;759;11;724	ENSP00000301740:S759R	ENSP00000301740:S759R	S	+	3	2	SRRM2	2752807	0.982000	0.34865	1.000000	0.80357	0.796000	0.44982	0.846000	0.27682	1.367000	0.46095	0.655000	0.94253	AGC	.	.	.	none		0.473	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			G	2812806	C	G	2812806	3	3	186	1	0	0	0	0	1	0	0	0	15181	709	25	4	2315	4	SRRM2	16	2812806	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08		2812806	87541947	60	10942											
PRKCB	5579	hgsc.bcm.edu	37	chr16	23848699	23848699	+	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	tccttctgcttttgcaggggCttcgggaagcagggattcca	6	12	13	10	1	1	0	0	0	1	0	4	2	3	2	2	4	3	4	2	4	1	5			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr16:23848699C>T	ENST00000321728.7	+	2	352	c.177C>T	c.(175-177)ggC>ggT	p.G59G	PRKCB_ENST00000498058.1_Intron|PRKCB_ENST00000303531.7_Silent_p.G59G	NM_212535.2	NP_997700.1	P05771	KPCB_HUMAN	protein kinase C, beta	59					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)	TTTGCAGGGGCTTCGGGAAGC	0.552																																					p.G59G		Atlas-SNP	.											.	PRKCB	383	.	0			c.C177T						PASS	.						113	123	120					16																	23848699		2197	4300	6497	SO:0001819	synonymous_variant	5579	exon2			CAGGGGCTTCGGG	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.177C>T	chr16.hg19:g.23848699C>T		337.0	1.0	.		342.0	202.0	.	NM_212535	C5IFJ8|D3DWF5|O43744|P05127|Q15138|Q93060|Q9UE49|Q9UE50|Q9UEH8|Q9UJ30|Q9UJ33	Silent	SNP	ENST00000321728.7	hg19	CCDS10618.1																																																																																			.	.	.	none		0.552	PRKCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254504.2	NM_212535		T	23848699	C	T	23848699	2	4	186	1	0	0	0	0	0	0	0	1	12518	784	28	2		2	PRKCB	16	23848699	Silent	SNP	C	TCGA-GL-8500-01A-11D-2396-08	21035893	23848699	66506054	61	10943											
ZC3H18	124245	hgsc.bcm.edu	37	chr16	88653085	88653085	+	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	cgtcccacctgccggttcttCatgaaaggtaattgtctgcg	7	12	10	12	3	3	1	1	1	2	0	4	1	4	1	3	2	2	2	3	2	2	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr16:88653085C>T	ENST00000301011.5	+	3	881	c.681C>T	c.(679-681)ttC>ttT	p.F227F	ZC3H18_ENST00000452588.2_Silent_p.F227F	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	227						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)		GCCGGTTCTTCATGAAAGGTA	0.587																																					p.F227F	Ovarian(121;375 2276 20373 38669)	Atlas-SNP	.											.	ZC3H18	90	.	0			c.C681T						PASS	.						112	88	96					16																	88653085		2198	4300	6498	SO:0001819	synonymous_variant	124245	exon3			GTTCTTCATGAAA	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.681C>T	chr16.hg19:g.88653085C>T		44.0	0.0	.		74.0	18.0	.	NM_144604	Q96DG4|Q96MP7	Silent	SNP	ENST00000301011.5	hg19	CCDS10967.1																																																																																			.	.	.	none		0.587	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1	NM_144604		T	88653085	C	T	88653085	2	4	186	1	0	0	0	0	0	0	0	1	17580	825	29	2		2	ZC3H18	16	88653085	Silent	SNP	C	TCGA-GL-8500-01A-11D-2396-08	64804386	88653085	1701668	62	10944											
SAT2	112483	hgsc.bcm.edu	37	chr17	7530935	7530935	+	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	gtctccctccttggcctctcGgatccgcacggaagccatcc	5	9	9	18	3	2	0	0	0	2	0	7	2	5	2	6	3	1	1	6	3	1	1			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr17:7530935G>A	ENST00000269298.5	-	1	238	c.19C>T	c.(19-21)Cga>Tga	p.R7*	SAT2_ENST00000573566.1_Nonsense_Mutation_p.R7*|SHBG_ENST00000575314.1_Intron|SHBG_ENST00000570547.1_Intron|SHBG_ENST00000572182.1_Intron|SHBG_ENST00000576478.1_Intron|SHBG_ENST00000574539.1_Intron|SHBG_ENST00000380450.4_5'Flank|SAT2_ENST00000380466.2_5'UTR|SHBG_ENST00000416273.3_5'Flank|SHBG_ENST00000572262.1_Intron|SHBG_ENST00000340624.5_5'Flank|SHBG_ENST00000575903.1_5'Flank|SHBG_ENST00000441599.2_5'Flank|SHBG_ENST00000576728.1_Intron	NM_133491.3	NP_597998.1	Q96F10	SAT2_HUMAN	spermidine/spermine N1-acetyltransferase family member 2	7	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				nor-spermidine metabolic process (GO:0046204)|putrescine acetylation (GO:0032920)|putrescine catabolic process (GO:0009447)|spermidine acetylation (GO:0032918)|spermine acetylation (GO:0032919)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	diamine N-acetyltransferase activity (GO:0004145)	p.?(1)		kidney(1)|large_intestine(2)	3				READ - Rectum adenocarcinoma(115;0.166)	Spermine(DB00127)	TTGGCCTCTCGGATCCGCACG	0.632																																					p.R7X		Atlas-SNP	.											.	SAT2	8	.	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.C19T						PASS	.						50	45	47					17																	7530935		2203	4300	6503	SO:0001587	stop_gained	112483	exon1			CCTCTCGGATCCG	AF348524	CCDS11116.1	17p13.2	2011-11-16	2008-01-07		ENSG00000141504	ENSG00000141504	2.3.1.57		23160	protein-coding gene	gene with protein product	"diamine N-acetyltransferase 2"	611463	"spermidine/spermine N1-acetyltransferase 2"			15283699, 17558023	Standard	NM_133491		Approved	SSAT2	uc002gic.2	Q96F10	OTTHUMG00000108152	ENST00000269298.5:c.19C>T	chr17.hg19:g.7530935G>A	ENSP00000269298:p.Arg7*	77.0	0.0	.		58.0	18.0	.	NM_133491		Nonsense_Mutation	SNP	ENST00000269298.5	hg19	CCDS11116.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.441041|6.441041	0.97568|0.97568	.|.	.|.	ENSG00000141504|ENSG00000141504	ENST00000380466|ENST00000269298	.|.	.|.	.|.	4.71|4.71	4.71|4.71	0.59529|0.59529	.|.	0.000000|.	0.31963|.	U|.	0.006786|.	T|.	0.34658|.	0.0905|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.15752|.	-1.0426|.	6|.	0.72032|0.02654	D|T	0.01|1	-13.2823|-13.2823	13.0369|13.0369	0.58877|0.58877	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	L|X	80|7	.|.	ENSP00000369833:P80L|ENSP00000269298:R7X	P|R	-|-	2|1	0|2	SAT2|SAT2	7471660|7471660	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.852000|0.852000	0.48524|0.48524	3.025000|3.025000	0.49681|0.49681	2.453000|2.453000	0.82957|0.82957	0.655000|0.655000	0.94253|0.94253	CCG|CGA	.	.	.	none		0.632	SAT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440078.1	NM_133491		A	7530935	G	A	7530935	4	1	186	1	0	0	0	0	0	1	0	0	13865	1124	39	1	517	1	SAT2	17	7530935	Nonsense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08		7530935	73664275	63	10945											
LINGO3	645191	hgsc.bcm.edu	37	chr19	2290213	2290213	+	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	aggatggtggtgaggtcgagCggcgcgcgcagggccgccag	6	4	21	10	6	0	1	0	1	0	0	1	3	0	2	2	6	1	1	2	6	0	0			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr19:2290213C>T	ENST00000585527.1	-	1	1810	c.1563G>A	c.(1561-1563)ccG>ccA	p.P521P	LINGO3_ENST00000404279.1_Silent_p.P521P			P0C6S8	LIGO3_HUMAN	leucine rich repeat and Ig domain containing 3	521						integral component of membrane (GO:0016021)				lung(1)|urinary_tract(1)	2						TGAGGTCGAGCGGCGCGCGCA	0.706																																					p.P521P		Atlas-SNP	.											.	LINGO3	19	.	0			c.G1563A						PASS	.						20	25	24					19																	2290213		2039	4177	6216	SO:0001819	synonymous_variant	645191	exon2			GTCGAGCGGCGCG	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.1563G>A	chr19.hg19:g.2290213C>T		47.0	0.0	.		59.0	23.0	.	NM_001101391		Silent	SNP	ENST00000585527.1	hg19	CCDS45905.1																																																																																			.	.	.	none		0.706	LINGO3-001	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451291.2	NM_001101391		T	2290213	C	T	2290213	2	4	186	1	0	0	0	0	0	0	0	1	8823	755	27	1		1	LINGO3	19	2290213	Silent	SNP	C	TCGA-GL-8500-01A-11D-2396-08		2290213	56838770	64	10946											
ZNF557	79230	hgsc.bcm.edu	37	chr19	7075688	7075688	+	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	ctgtcttccctgttcccagcCtctcagcgagaaggacacac	8	9	8	16	1	2	1	1	0	2	1	5	3	4	2	3	1	2	1	3	1	1	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr19:7075688C>G	ENST00000439035.2	+	4	273	c.33C>G	c.(31-33)gcC>gcG	p.A11A	ZNF557_ENST00000414706.1_Silent_p.A18A|ZNF557_ENST00000252840.6_Silent_p.A18A			Q8N988	ZN557_HUMAN	zinc finger protein 557	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)			endometrium(6)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17				Lung(535;0.179)		TGTTCCCAGCCTCTCAGCGAG	0.532																																					p.A18A		Atlas-SNP	.											.	ZNF557	40	.	0			c.C54G						PASS	.						132	139	136					19																	7075688		2203	4300	6503	SO:0001630	splice_region_variant	79230	exon4			CCCAGCCTCTCAG	AK095524	CCDS42485.1, CCDS45945.1	19p13.2	2013-09-20			ENSG00000130544	ENSG00000130544		"Zinc fingers, C2H2-type", "-"	28632	protein-coding gene	gene with protein product						12477932	Standard	NM_024341		Approved	MGC4054	uc002mgc.3	Q8N988	OTTHUMG00000181977	ENST00000439035.2:c.32-1C>G	chr19.hg19:g.7075688C>G		140.0	0.0	.		108.0	52.0	.	NM_001044387	Q6PEJ3|Q9BTZ1	Silent	SNP	ENST00000439035.2	hg19	CCDS45945.1																																																																																			.	.	.	none		0.532	ZNF557-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458502.1	NM_024341	Silent	G	7075688	C	G	7075688	5	3	186	1	0	0	0	0	0	0	1	0	18000	695	24	4	60	4	ZNF557	19	7075688	Splice_Site	SNP	C	TCGA-GL-8500-01A-11D-2396-08	4785475	7075688	52053295	65	10947											
CACNA1A	773	hgsc.bcm.edu	37	chr19	13346025	13346025	+	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	tagggacacgacactcacctGcatcccaatgatggcataga	13	7	9	12	1	1	2	1	1	0	1	2	4	2	3	2	2	1	2	2	2	3	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr19:13346025G>A	ENST00000360228.5	-	33	5130	c.5131C>T	c.(5131-5133)Cag>Tag	p.Q1711*	CACNA1A_ENST00000573710.2_Nonsense_Mutation_p.Q1712*|CACNA1A_ENST00000574822.1_5'UTR	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1712					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)	ACACTCACCTGCATCCCAATG	0.557											OREG0025293	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q1712X		Atlas-SNP	.											.	CACNA1A	715	.	0			c.C5134T						PASS	.						44	48	47					19																	13346025		2021	4185	6206	SO:0001587	stop_gained	773	exon33			TCACCTGCATCCC	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.5131C>T	chr19.hg19:g.13346025G>A	ENSP00000353362:p.Gln1711*	21.0	0.0	.	686	15.0	5.0	.	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Nonsense_Mutation	SNP	ENST00000360228.5	hg19	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	G	48	14.471052	0.99797	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	.	.	.	5.17	5.17	0.71159	.	0.140928	0.48767	D	0.000167	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.4899	0.87700	0.0:0.0:1.0:0.0	.	.	.	.	X	1711;1717;1712;1712	.	ENSP00000317661:Q1712X	Q	-	1	0	CACNA1A	13207025	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.808000	0.99193	2.411000	0.81874	0.644000	0.83932	CAG	.	.	.	none		0.557	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		A	13346025	G	A	13346025	4	1	186	1	0	0	0	0	0	1	0	0	2540	1328	46	2	2550	2	CACNA1A	19	13346025	Nonsense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08	6270337	13346025	45782958	66	10948											
ZNF461	92283	hgsc.bcm.edu	37	chr19	37147417	37147417	+	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	ttcccttgctccaatgaggaGattacggctggcttagaaac	10	11	10	10	1	0	3	0	1	0	2	2	4	2	3	2	3	3	3	2	3	4	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr19:37147417G>C	ENST00000588268.1	-	4	392	c.165C>G	c.(163-165)atC>atG	p.I55M	ZNF461_ENST00000360357.4_Missense_Mutation_p.I55M	NM_153257.2	NP_694989.2	Q8TAF7	ZN461_HUMAN	zinc finger protein 461	55	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(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)			CCAATGAGGAGATTACGGCTG	0.443																																					p.I55M		Atlas-SNP	.											.	ZNF461	73	.	0			c.C165G						PASS	.						72	74	73					19																	37147417		2068	4232	6300	SO:0001583	missense	92283	exon4			TGAGGAGATTACG	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.165C>G	chr19.hg19:g.37147417G>C	ENSP00000467931:p.Ile55Met	94.0	0.0	.		78.0	32.0	.	NM_153257	A8K9W9|Q6VSF7|Q9ULZ8	Missense_Mutation	SNP	ENST00000588268.1	hg19	CCDS54257.1	.	.	.	.	.	.	.	.	.	.	G	13.67	2.306002	0.40795	.	.	ENSG00000197808	ENST00000396893;ENST00000360357	T	0.00912	5.55	3.27	-0.373	0.12516	Krueppel-associated box (3);	.	.	.	.	T	0.05090	0.0136	M	0.88704	2.975	0.09310	N	1	D;D	0.64830	0.994;0.994	D;D	0.76071	0.987;0.987	T	0.14364	-1.0475	9	0.87932	D	0	.	5.9972	0.19501	0.3696:0.0:0.6304:0.0	.	55;55	B4DRP8;Q8TAF7	.;ZN461_HUMAN	M	55	ENSP00000353515:I55M	ENSP00000353515:I55M	I	-	3	3	ZNF461	41839257	0.882000	0.30256	0.011000	0.14972	0.955000	0.61496	0.417000	0.21214	-0.071000	0.12886	0.585000	0.79938	ATC	.	.	.	none		0.443	ZNF461-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453202.1	NM_153257		C	37147417	G	C	37147417	3	2	186	1	0	0	0	0	1	0	0	0	17937	932	33	4	1538	4	ZNF461	19	37147417	Missense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08	23801392	37147417	21981566	67	10949											
ERCC2	2068	hgsc.bcm.edu	37	chr19	45868315	45868315	+	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	gtaacctcatagaatcggcaGtggggcaggctggtgtcatg	9	9	15	8	1	2	1	2	0	0	1	3	1	2	1	1	5	1	4	1	5	3	2	rs139263710		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr19:45868315G>A	ENST00000391945.4	-	6	539	c.462C>T	c.(460-462)caC>caT	p.H154H	ERCC2_ENST00000485403.2_Silent_p.H130H|ERCC2_ENST00000391940.4_Silent_p.H130H|ERCC2_ENST00000221481.6_Intron|ERCC2_ENST00000391944.3_Intron	NM_000400.3	NP_000391.1	P18074	ERCC2_HUMAN	excision repair cross-complementation group 2	154	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				7-methylguanosine mRNA capping (GO:0006370)|aging (GO:0007568)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|central nervous system myelin formation (GO:0032289)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|embryonic cleavage (GO:0040016)|erythrocyte maturation (GO:0043249)|extracellular matrix organization (GO:0030198)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|hair follicle maturation (GO:0048820)|hematopoietic stem cell differentiation (GO:0060218)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|MMXD complex (GO:0071817)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		AGAATCGGCAGTGGGGCAGGC	0.637			"Mis, N, F, S"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.H154H		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.C462T						PASS	.						61	55	57					19																	45868315		2203	4300	6503	SO:0001819	synonymous_variant	2068	exon6	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	TCGGCAGTGGGGC		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.462C>T	chr19.hg19:g.45868315G>A		60.0	0.0	.		50.0	23.0	.	NM_000400	Q2TB78|Q2YDY2|Q7KZU6|Q8N721	Silent	SNP	ENST00000391945.4	hg19	CCDS33049.1																																																																																			.	G|1.000;C|0.000	.	alt		0.637	ERCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109626.2	NM_000400		A	45868315	G	A	45868315	2	1	186	1	0	0	0	0	0	0	0	1	5215	1020	36	2		2	ERCC2	19	45868315	Silent	SNP	G	TCGA-GL-8500-01A-11D-2396-08	8720898	45868315	13260668	68	10950											
BAX	581	hgsc.bcm.edu	37	chr19	49464330	49464330	+	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	agatcatcagatgtggtctaTaatgcgttttccttacgtgt	9	16	9	7	2	3	2	2	0	1	2	4	2	4	2	1	1	2	1	1	1	3	5			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr19:49464330T>C	ENST00000345358.7	+	5	526				BAX_ENST00000354470.3_Intron|BAX_ENST00000539787.1_Intron|BAX_ENST00000391871.3_Intron|BAX_ENST00000293288.8_Silent_p.Y211Y|CTD-2639E6.9_ENST00000599784.1_lincRNA|BAX_ENST00000415969.2_Intron	NM_138761.3|NM_138764.4	NP_620116.1|NP_620119.2	Q07812	BAX_HUMAN	BCL2-associated X protein						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|apoptotic process involved in patterning of blood vessels (GO:1902262)|apoptotic signaling pathway (GO:0097190)|B cell apoptotic process (GO:0001783)|B cell homeostasis (GO:0001782)|B cell homeostatic proliferation (GO:0002358)|B cell negative selection (GO:0002352)|B cell receptor apoptotic signaling pathway (GO:1990117)|blood vessel remodeling (GO:0001974)|cellular response to organic substance (GO:0071310)|cellular response to UV (GO:0034644)|cerebral cortex development (GO:0021987)|development of secondary sexual characteristics (GO:0045136)|ectopic germ cell programmed cell death (GO:0035234)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|establishment or maintenance of transmembrane electrochemical gradient (GO:0010248)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|fertilization (GO:0009566)|germ cell development (GO:0007281)|glycosphingolipid metabolic process (GO:0006687)|homeostasis of number of cells within a tissue (GO:0048873)|hypothalamus development (GO:0021854)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion morphogenesis (GO:0070584)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein binding (GO:0032091)|neuron apoptotic process (GO:0051402)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of apoptotic DNA fragmentation (GO:1902512)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of developmental pigmentation (GO:0048087)|positive regulation of endoplasmic reticulum unfolded protein response (GO:1900103)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|post-embryonic camera-type eye morphogenesis (GO:0048597)|protein homooligomerization (GO:0051260)|protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:0001844)|protein oligomerization (GO:0051259)|regulation of cell cycle (GO:0051726)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of mitochondrial membrane permeability involved in programmed necrotic cell death (GO:1902445)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of nitrogen utilization (GO:0006808)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|release of cytochrome c from mitochondria (GO:0001836)|release of matrix enzymes from mitochondria (GO:0032976)|response to axon injury (GO:0048678)|response to gamma radiation (GO:0010332)|response to salt stress (GO:0009651)|response to toxic substance (GO:0009636)|retina development in camera-type eye (GO:0060041)|retinal cell apoptotic process (GO:1990009)|retinal cell programmed cell death (GO:0046666)|Sertoli cell proliferation (GO:0060011)|spermatid differentiation (GO:0048515)|T cell homeostatic proliferation (GO:0001777)|thymocyte apoptotic process (GO:0070242)|transformed cell apoptotic process (GO:0006927)|vagina development (GO:0060068)|viral process (GO:0016032)	BAX complex (GO:0097144)|Bcl-2 family protein complex (GO:0097136)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrial permeability transition pore complex (GO:0005757)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|pore complex (GO:0046930)	BH3 domain binding (GO:0051434)|channel activity (GO:0015267)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(4)	17		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000159)|all cancers(93;0.00047)|GBM - Glioblastoma multiforme(486;0.018)|Epithelial(262;0.0279)		ATGTGGTCTATAATGCGTTTT	0.567																																					p.Y211Y		Atlas-SNP	.											.	BAX	69	.	0			c.T633C						PASS	.						89	63	72					19																	49464330		2176	4278	6454	SO:0001627	intron_variant	581	exon5			GGTCTATAATGCG		CCDS12742.1, CCDS12743.1, CCDS12744.1, CCDS12745.1, CCDS12745.2	19q13.3-q13.4	2014-03-07			ENSG00000087088	ENSG00000087088			959	protein-coding gene	gene with protein product		600040				8358790	Standard	NM_138761		Approved	BCL2L4	uc002plf.1	Q07812	OTTHUMG00000160476	ENST00000345358.7:c.474+159T>C	chr19.hg19:g.49464330T>C		83.0	0.0	.		96.0	45.0	.	NM_004324	A8K4W1|P55269|Q07814|Q07815|Q8WZ49|Q9NR76|Q9NYG7|Q9UCZ6|Q9UCZ7|Q9UQD6	Silent	SNP	ENST00000345358.7	hg19	CCDS12742.1																																																																																			.	.	.	none		0.567	BAX-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360767.1	NM_138763		C	49464330	T	C	49464330	1	2	186	0	1	0	0	0	0	0	0	0	1328	1413	49	3		3	BAX	19	49464330	Intron	SNP	T	TCGA-GL-8500-01A-11D-2396-08	3596015	49464330	9664653	69	10951											
ZNF321	399669	hgsc.bcm.edu	37	chr19	53432286	53432286	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaaattctttgggatgtcAaaattaaggaggcattgatg	15	12	11	3	0	2	2	1	1	1	1	2	4	2	4	0	3	0	1	0	3	5	4			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr19:53432286A>G	ENST00000391777.3	-	4	693	c.572T>C	c.(571-573)tTg>tCg	p.L191S	ZNF816_ENST00000434371.2_Missense_Mutation_p.L191S|ZNF816_ENST00000549216.1_Missense_Mutation_p.L122S|ZNF816-ZNF321P_ENST00000313956.4_RNA			Q8N8H1	ZN321_HUMAN	zinc finger protein 321, pseudogene	122										endometrium(1)|large_intestine(1)|lung(1)|ovary(1)	4						TTGGGATGTCAAAATTAAGGA	0.373																																					p.L191S		Atlas-SNP	.											.	.	.	.	0			c.T572C						PASS	.						94	100	98					19																	53432286		2185	4293	6478	SO:0001583	missense	100529240	exon4			GATGTCAAAATTA	AK096828		19q13.4	2013-01-08	2011-04-19	2011-04-19	ENSG00000221874	ENSG00000221874			13827	pseudogene	pseudogene			"zinc finger protein 321"	ZNF321			Standard	NR_037805		Approved	MGC35402		Q8N8H1	OTTHUMG00000167760	ENST00000391777.3:c.572T>C	chr19.hg19:g.53432286A>G	ENSP00000375656:p.Leu191Ser	214.0	0.0	.		200.0	89.0	.	NM_001202473	B7ZB38|Q68DZ0|Q86SS5	Missense_Mutation	SNP	ENST00000391777.3	hg19	CCDS56101.1	.	.	.	.	.	.	.	.	.	.	g	0.886	-0.727124	0.03158	.	.	ENSG00000180257;ENSG00000180257;ENSG00000221874	ENST00000549216;ENST00000434371;ENST00000391777	T;T;T	0.01252	5.1;5.95;5.95	1.78	-0.553	0.11815	.	.	.	.	.	T	0.00412	0.0013	N	0.00337	-1.62	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46512	-0.9186	9	0.02654	T	1	.	4.0322	0.09714	0.4322:0.0:0.5678:0.0	.	122	Q8N8H1	ZN321_HUMAN	S	122;191;191	ENSP00000449832:L122S;ENSP00000438519:L191S;ENSP00000375656:L191S	ENSP00000375656:L191S	L	-	2	0	ZNF321P;ZNF816	58124098	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	0.088000	0.14979	0.107000	0.17824	-1.981000	0.00455	TTG	.	.	.	none		0.373	ZNF321P-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000396130.1	NR_037805		G	53432286	A	G	53432286	3	3	186	1	0	0	0	0	1	0	0	0	17852	131	5	3	133	3	ZNF321	19	53432286	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	3967956	53432286	5696697	70	10952											
NLRP9	338321	hgsc.bcm.edu	37	chr19	56244868	56244868	+	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	gacaggtttccttctcccatAtgagttgaaatgtttccttc	8	16	7	10	0	1	2	0	2	1	0	5	3	3	2	3	1	0	3	3	1	2	6			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr19:56244868A>T	ENST00000332836.2	-	2	356	c.329T>A	c.(328-330)aTa>aAa	p.I110K		NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	110						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)		CTTCTCCCATATGAGTTGAAA	0.363																																					p.I110K		Atlas-SNP	.											.	NLRP9	163	.	0			c.T329A						PASS	.						122	122	122					19																	56244868		2203	4300	6503	SO:0001583	missense	338321	exon2			TCCCATATGAGTT	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.329T>A	chr19.hg19:g.56244868A>T	ENSP00000331857:p.Ile110Lys	149.0	0.0	.		124.0	57.0	.	NM_176820	B2RN12|Q86W27	Missense_Mutation	SNP	ENST00000332836.2	hg19	CCDS12934.1	.	.	.	.	.	.	.	.	.	.	A	14.52	2.559517	0.45590	.	.	ENSG00000185792	ENST00000332836;ENST00000333452	T	0.73897	-0.79	3.4	3.4	0.38934	.	.	.	.	.	T	0.60996	0.2312	L	0.39898	1.24	0.18873	N	0.999985	P	0.42827	0.791	B	0.36719	0.231	T	0.49925	-0.8887	9	0.29301	T	0.29	.	8.4613	0.32929	1.0:0.0:0.0:0.0	.	110	Q7RTR0	NALP9_HUMAN	K	110	ENSP00000331857:I110K	ENSP00000331857:I110K	I	-	2	0	NLRP9	60936680	0.004000	0.15560	0.004000	0.12327	0.074000	0.17049	1.274000	0.33132	1.588000	0.49971	0.524000	0.50904	ATA	.	.	.	none		0.363	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1	NM_176820		T	56244868	A	T	56244868	3	4	186	1	0	0	0	0	1	0	0	0	10491	449	16	5	2678	5	NLRP9	19	56244868	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	2812582	56244868	2884115	71	10953											
MZF1	7593	hgsc.bcm.edu	37	chr19	59073766	59073766	+	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	cccaggccgcactcaccgcaGtggtagggcttttcgccggt	5	8	13	15	4	1	0	1	0	0	0	2	0	1	0	4	4	0	4	4	4	1	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr19:59073766G>T	ENST00000215057.2	-	6	2438	c.1878C>A	c.(1876-1878)caC>caA	p.H626Q	AC016629.8_ENST00000600726.1_RNA|AC016629.8_ENST00000593642.1_RNA|MZF1_ENST00000599369.1_Missense_Mutation_p.H626Q|MZF1_ENST00000594234.1_3'UTR|AC016629.8_ENST00000600534.1_RNA	NM_001267033.1|NM_198055.1	NP_001253962.1|NP_932172.1	P28698	MZF1_HUMAN	myeloid zinc finger 1	626					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0443)|all cancers(4;7.92e-14)|Epithelial(4;5.57e-11)|OV - Ovarian serous cystadenocarcinoma(4;1.13e-09)|GBM - Glioblastoma multiforme(193;0.0108)|Lung(386;0.182)		ACTCACCGCAGTGGTAGGGCT	0.682																																					p.H626Q		Atlas-SNP	.											.	MZF1	37	.	0			c.C1878A						PASS	.						33	25	28					19																	59073766		2201	4300	6501	SO:0001583	missense	7593	exon6			ACCGCAGTGGTAG	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.1878C>A	chr19.hg19:g.59073766G>T	ENSP00000215057:p.His626Gln	16.0	0.0	.		17.0	11.0	.	NM_198055	M0QXU0|Q7Z729|Q96I71|Q9NRY0|Q9UBW2	Missense_Mutation	SNP	ENST00000215057.2	hg19	CCDS12988.1	.	.	.	.	.	.	.	.	.	.	G	8.359	0.832673	0.16820	.	.	ENSG00000099326	ENST00000215057	T	0.16073	2.37	3.21	2.17	0.27698	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.732947	0.11236	N	0.585150	T	0.04272	0.0118	N	0.00315	-1.66	0.25952	N	0.982731	B	0.27286	0.174	B	0.34722	0.188	T	0.43540	-0.9385	10	0.15499	T	0.54	-9.8517	4.7075	0.12856	0.1258:0.2248:0.6494:0.0	.	626	P28698	MZF1_HUMAN	Q	626	ENSP00000215057:H626Q	ENSP00000215057:H626Q	H	-	3	2	MZF1	63765578	0.000000	0.05858	0.908000	0.35775	0.900000	0.52787	-0.753000	0.04792	0.925000	0.37094	-0.379000	0.06801	CAC	.	.	.	none		0.682	MZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467112.1	NM_198055		T	59073766	G	T	59073766	3	4	186	1	0	0	0	0	1	0	0	0	10115	1020	36	4	330	4	MZF1	19	59073766	Missense_Mutation	SNP	G	TCGA-GL-8500-01A-11D-2396-08	2828898	59073766	55217	72	10954											
CPXM1	56265	hgsc.bcm.edu	37	chr20	2776796	2776796	+	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	cggccctcggcccagcccacCagctctgaaccctgccgggc	5	4	11	21	3	1	1	0	1	1	0	2	1	1	1	6	3	4	1	6	3	1	0			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr20:2776796C>G	ENST00000380605.2	-	10	1318	c.1254G>C	c.(1252-1254)ctG>ctC	p.L418L		NM_001184699.1|NM_019609.4	NP_001171628.1|NP_062555.1	Q96SM3	CPXM1_HUMAN	carboxypeptidase X (M14 family), member 1	418					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						CCCAGCCCACCAGCTCTGAAC	0.602																																					p.L418L		Atlas-SNP	.											.	CPXM1	107	.	0			c.G1254C						PASS	.						56	59	58					20																	2776796		2203	4300	6503	SO:0001819	synonymous_variant	56265	exon10			GCCCACCAGCTCT	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.1254G>C	chr20.hg19:g.2776796C>G		101.0	0.0	.		83.0	32.0	.	NM_001184699	Q6P4G8|Q6UW65|Q9NUB5	Silent	SNP	ENST00000380605.2	hg19	CCDS13033.1																																																																																			.	.	.	none		0.602	CPXM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077643.2	NM_019609		G	2776796	C	G	2776796	2	3	186	1	0	0	0	0	0	0	0	1	3839	581	21	4		4	CPXM1	20	2776796	Silent	SNP	C	TCGA-GL-8500-01A-11D-2396-08		2776796	60248724	73	10955											
HUNK	30811	hgsc.bcm.edu	37	chr21	33371363	33371363	+	Missense_Mutation	SNP	A	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	ctatgatgggcatcggacagAtgttaaggaagcgccatcag	12	8	13	8	2	1	2	1	1	0	1	2	4	1	4	1	3	1	2	1	3	3	2			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr21:33371363A>C	ENST00000270112.2	+	11	2371	c.2011A>C	c.(2011-2013)Atg>Ctg	p.M671L		NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	671					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						CATCGGACAGATGTTAAGGAA	0.617																																					p.M671L		Atlas-SNP	.											.	HUNK	74	.	0			c.A2011C						PASS	.						54	60	58					21																	33371363		2203	4300	6503	SO:0001583	missense	30811	exon11			GGACAGATGTTAA	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.2011A>C	chr21.hg19:g.33371363A>C	ENSP00000270112:p.Met671Leu	143.0	0.0	.		114.0	36.0	.	NM_014586		Missense_Mutation	SNP	ENST00000270112.2	hg19	CCDS13610.1	.	.	.	.	.	.	.	.	.	.	A	15.78	2.935668	0.52972	.	.	ENSG00000142149	ENST00000270112	T	0.68181	-0.31	4.21	4.21	0.49690	.	0.165227	0.51477	D	0.000092	T	0.64148	0.2572	L	0.29908	0.895	0.45354	D	0.998345	P	0.40970	0.734	P	0.50825	0.651	T	0.60727	-0.7206	10	0.25751	T	0.34	-32.4647	13.4793	0.61326	1.0:0.0:0.0:0.0	.	671	P57058	HUNK_HUMAN	L	671	ENSP00000270112:M671L	ENSP00000270112:M671L	M	+	1	0	HUNK	32293234	1.000000	0.71417	0.997000	0.53966	0.204000	0.24138	5.843000	0.69424	1.767000	0.52121	0.482000	0.46254	ATG	.	.	.	none		0.617	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192782.1	NM_014586		C	33371363	A	C	33371363	3	2	186	1	0	0	0	0	1	0	0	0	7465	333	12	5	2053	5	HUNK	21	33371363	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08		33371363	14758532	74	10956											
TTC3	7267	hgsc.bcm.edu	37	chr21	38568034	38568035	+	Frame_Shift_Ins	INS	-	-	T																															ggccaagggcttgtgacttcINStgcaagcgacgtgactggaa																										TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr21:38568034_38568035insT	ENST00000399017.2	+	42	8023_8024	c.5276_5277insT	c.(5275-5280)tctgcafs	p.A1760fs	TTC3_ENST00000355666.1_Frame_Shift_Ins_p.A1760fs|TTC3-AS1_ENST00000424733.1_RNA|TTC3_ENST00000354749.2_Frame_Shift_Ins_p.A1760fs|TTC3_ENST00000479930.1_3'UTR	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1760					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)				CTTGTGACTTCTGCAAGCGACG	0.569																																					p.S1759fs	Ovarian(38;194 1649 35661)	Atlas-INDEL	.											.	TTC3	182	.	0			c.5276_5277insT						PASS	.																																			SO:0001589	frameshift_variant	7267	exon42			.	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.5277dupT	chr21.hg19:g.38568035_38568035dupT	ENSP00000381981:p.Ala1760fs	340.0	0.0	0		305.0	129.0	0.422951	NM_003316	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Frame_Shift_Ins	INS	ENST00000399017.2	hg19	CCDS13651.1																																																																																			.	.	.	none		0.569	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			T	38568035	-	T	38568034	7	5	186	1	0	1	1	0	0	0	0	0	16709	913	32	0	5438	0	TTC3	21	38568034	Frame_Shift_Ins	INS	-	TCGA-GL-8500-01A-11D-2396-08	5196671	38568034	9561861	75	10957											
MICAL3	57553	hgsc.bcm.edu	37	chr22	18293513	18293513	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcctcctgcttggcctgtcTccgagctgccttttgcacac	3	13	8	17	1	1	0	0	0	1	0	4	1	3	0	5	1	4	3	5	1	0	3			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr22:18293513T>C	ENST00000441493.2	-	28	5864	c.5512A>G	c.(5512-5514)Aga>Gga	p.R1838G	XXbac-B461K10.4_ENST00000476405.1_RNA|MICAL3_ENST00000580469.1_5'UTR	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	1838					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)		TTGGCCTGTCTCCGAGCTGCC	0.572																																					p.R1838G		Atlas-SNP	.											.	MICAL3	53	.	0			c.A5512G						PASS	.						92	98	96					22																	18293513		2184	4283	6467	SO:0001583	missense	57553	exon28			CCTGTCTCCGAGC	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.5512A>G	chr22.hg19:g.18293513T>C	ENSP00000416015:p.Arg1838Gly	68.0	0.0	.		76.0	26.0	.	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Missense_Mutation	SNP	ENST00000441493.2	hg19	CCDS46659.1	.	.	.	.	.	.	.	.	.	.	T	16.19	3.051801	0.55218	.	.	ENSG00000093100	ENST00000441493	T	0.68025	-0.3	4.81	4.81	0.61882	.	0.102956	0.64402	D	0.000009	T	0.70631	0.3246	L	0.34521	1.04	0.80722	D	1	D	0.63880	0.993	D	0.72338	0.977	T	0.69146	-0.5222	9	.	.	.	.	11.1121	0.48239	0.0:0.0:0.1547:0.8453	.	1838	Q7RTP6	MICA3_HUMAN	G	1838	ENSP00000416015:R1838G	.	R	-	1	2	XXbac-B461K10.4	16673513	0.999000	0.42202	1.000000	0.80357	0.995000	0.86356	2.991000	0.49409	1.799000	0.52666	0.379000	0.24179	AGA	.	.	.	none		0.572	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			C	18293513	T	C	18293513	3	2	186	1	0	0	0	0	1	0	0	0	9578	1559	54	3	516	3	MICAL3	22	18293513	Missense_Mutation	SNP	T	TCGA-GL-8500-01A-11D-2396-08		18293513	33011053	76	10958											
POLR2F	5435	hgsc.bcm.edu	37	chr22	38355418	38355418	+	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	caggccaaccagaagcgaatCaccacaccatacatgaccaa	17	3	6	15	1	1	2	1	1	0	1	1	3	1	2	5	1	3	0	5	1	5	1			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr22:38355418C>G	ENST00000442738.2	+	3	281	c.156C>G	c.(154-156)atC>atG	p.I52M	POLR2F_ENST00000460648.1_Intron|POLR2F_ENST00000470701.1_Missense_Mutation_p.I47M|POLR2F_ENST00000606538.1_Missense_Mutation_p.I52M|POLR2F_ENST00000488684.1_Nonsense_Mutation_p.S72*|POLR2F_ENST00000407936.1_Missense_Mutation_p.I52M|POLR2F_ENST00000405557.1_Missense_Mutation_p.I52M	NM_021974.3	NP_068809.1	P61218	RPAB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide F	52					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)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			breast(1)|urinary_tract(2)	3	Melanoma(58;0.045)					AGAAGCGAATCACCACACCAT	0.577																																					p.I52M		Atlas-SNP	.											.	POLR2F	13	.	0			c.C156G						PASS	.						187	170	176					22																	38355418		2203	4300	6503	SO:0001583	missense	5435	exon3			GCGAATCACCACA		CCDS13963.1	22q13.1	2013-01-21			ENSG00000100142	ENSG00000100142		"RNA polymerase subunits"	9193	protein-coding gene	gene with protein product	"DNA directed RNA polymerase II 14.4 kda polypeptide"	604414				8786150	Standard	XR_112241		Approved	RPB6, HRBP14.4	uc010gxi.3	P61218	OTTHUMG00000151160	ENST00000442738.2:c.156C>G	chr22.hg19:g.38355418C>G	ENSP00000403852:p.Ile52Met	294.0	0.0	.		230.0	99.0	.	NM_021974	P41584|Q6IAY3	Missense_Mutation	SNP	ENST00000442738.2	hg19	CCDS13963.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.242366	0.79912	.	.	ENSG00000100142	ENST00000442738;ENST00000407936;ENST00000405557	.	.	.	4.98	4.98	0.66077	RNA polymerase subunit, RPB6/omega (1);	0.000000	0.85682	D	0.000000	T	0.67353	0.2884	L	0.60455	1.87	0.80722	D	1	B	0.11235	0.004	B	0.25140	0.058	T	0.65656	-0.6115	9	0.54805	T	0.06	.	18.6213	0.91322	0.0:1.0:0.0:0.0	.	52	P61218	RPAB2_HUMAN	M	52	.	ENSP00000384112:I52M	I	+	3	3	POLR2F	36685364	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.564000	0.53791	2.467000	0.83353	0.655000	0.94253	ATC	.	.	.	none		0.577	POLR2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321570.1	NM_021974		G	38355418	C	G	38355418	3	3	186	1	0	0	0	0	1	0	0	0	12226	816	29	4	166	4	POLR2F	22	38355418	Missense_Mutation	SNP	C	TCGA-GL-8500-01A-11D-2396-08	20061905	38355418	12949148	77	10959											
KDELR3	11015	hgsc.bcm.edu	37	chr22	38875733	38875733	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttggcctttccttccttgaaAactacagtttcactctgctg	7	16	6	12	0	2	1	1	1	1	0	4	1	4	1	3	1	3	2	3	1	3	6			TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	g.chr22:38875733A>G	ENST00000216014.4	+	3	500	c.328A>G	c.(328-330)Aac>Gac	p.N110D	KDELR3_ENST00000471268.1_3'UTR|KDELR3_ENST00000409006.3_Missense_Mutation_p.N110D	NM_006855.2	NP_006846.1	O43731	ERD23_HUMAN	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3	110					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein retention in ER lumen (GO:0006621)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ER retention sequence binding (GO:0046923)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)	13	Melanoma(58;0.0286)					CTTCCTTGAAAACTACAGTTT	0.473																																					p.N110D	Ovarian(11;103 529 24120 28493 32980)	Atlas-SNP	.											.	KDELR3	39	.	0			c.A328G						PASS	.						226	234	231					22																	38875733		2203	4300	6503	SO:0001583	missense	11015	exon3			CTTGAAAACTACA	AL035081	CCDS13972.1, CCDS46705.1	22q13	2008-05-02			ENSG00000100196	ENSG00000100196			6306	protein-coding gene	gene with protein product							Standard	NM_006855		Approved		uc003avu.3	O43731	OTTHUMG00000153520	ENST00000216014.4:c.328A>G	chr22.hg19:g.38875733A>G	ENSP00000216014:p.Asn110Asp	418.0	0.0	.		386.0	171.0	.	NM_016657	A8K7T7|B8ZZ26|O95557|Q4V750|Q4V767|Q53FP4|Q53GK1	Missense_Mutation	SNP	ENST00000216014.4	hg19	CCDS13972.1	.	.	.	.	.	.	.	.	.	.	A	27.4	4.824209	0.90955	.	.	ENSG00000100196	ENST00000216014;ENST00000409006	T;T	0.29142	1.58;1.58	4.39	4.39	0.52855	.	0.000000	0.85682	D	0.000000	T	0.58750	0.2144	M	0.89287	3.02	0.80722	D	1	D;D	0.58970	0.984;0.98	D;P	0.64410	0.925;0.823	T	0.66937	-0.5797	10	0.54805	T	0.06	.	13.8085	0.63248	1.0:0.0:0.0:0.0	.	110;110	O43731;O43731-2	ERD23_HUMAN;.	D	110	ENSP00000216014:N110D;ENSP00000386918:N110D	ENSP00000216014:N110D	N	+	1	0	KDELR3	37205679	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	8.916000	0.92745	1.854000	0.53819	0.533000	0.62120	AAC	.	.	.	none		0.473	KDELR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331474.1			G	38875733	A	G	38875733	3	3	186	1	0	0	0	0	1	0	0	0	8128	14	1	3	338	3	KDELR3	22	38875733	Missense_Mutation	SNP	A	TCGA-GL-8500-01A-11D-2396-08	520315	38875733	12428833	78	10960											
RIMS3	9783	hgsc.bcm.edu	37	chr1	41107442	41107442	+	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	aggcccacgatggccaccatCttggcacccaggctgctccg	7	6	11	17	2	1	0	0	0	1	0	2	1	2	0	5	4	1	3	5	4	0	1			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr1:41107442C>T	ENST00000372684.3	-	3	625	c.156G>A	c.(154-156)aaG>aaA	p.K52K	RIMS3_ENST00000372683.1_Silent_p.K52K	NM_014747.2	NP_055562.2	Q9UJD0	RIMS3_HUMAN	regulating synaptic membrane exocytosis 3	52					calcium ion-dependent exocytosis (GO:0017156)|neurotransmitter transport (GO:0006836)|regulation of membrane potential (GO:0042391)	cell junction (GO:0030054)|presynaptic active zone (GO:0048786)				NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.47e-17)			TGGCCACCATCTTGGCACCCA	0.662																																					p.K52K		Atlas-SNP	.											.	RIMS3	44	.	0			c.G156A						PASS	.						50	46	47					1																	41107442		2203	4300	6503	SO:0001819	synonymous_variant	9783	exon3			CACCATCTTGGCA	BC003103	CCDS30687.1	1p34.2	2013-09-19			ENSG00000117016	ENSG00000117016			21292	protein-coding gene	gene with protein product		611600				12620390, 10748113	Standard	NM_014747		Approved	RIM3, NIM3	uc001cfu.1	Q9UJD0	OTTHUMG00000007453	ENST00000372684.3:c.156G>A	chr1.hg19:g.41107442C>T		60.0	0.0	.		88.0	18.0	.	NM_014747	D3DPV8|Q92511|X5D7U7	Silent	SNP	ENST00000372684.3	hg19	CCDS30687.1																																																																																			.	.	.	none		0.662	RIMS3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019585.1	NM_014747		T	41107442	C	T	41107442	2	4	187	1	0	0	0	0	0	0	0	1	13382	912	32	2		2	RIMS3	1	41107442	Silent	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10		41107442	208143179	1	10961											
LRRC42	115353	hgsc.bcm.edu	37	chr1	54417869	54417876	+	Frame_Shift_Del	DEL	AAGAGAAG	AAGAGAAG	-																															ggaagacgacactgcacggaAagagaagactgatcatttca																										TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	AAGAGAAG	AAGAGAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr1:54417869_54417876delAAGAGAAG	ENST00000371370.3	+	3	718_725	c.197_204delAAGAGAAG	c.(196-204)aaagagaagfs	p.KEK66fs	LRRC42_ENST00000319223.4_Frame_Shift_Del_p.KEK66fs	NM_001256409.1	NP_001243338.1	Q9Y546	LRC42_HUMAN	leucine rich repeat containing 42	66										breast(2)|kidney(1)|large_intestine(1)|lung(5)	9						ACTGCACGGAAAGAGAAGACTGATCATT	0.514																																					p.66_68del		Atlas-Indel,Pindel	.											.	LRRC42	29	.	0			c.196_203del						PASS	.																																			SO:0001589	frameshift_variant	115353	exon2			.	AK075201	CCDS585.1	1p33-p32.1	2014-02-12			ENSG00000116212	ENSG00000116212			28792	protein-coding gene	gene with protein product						12477932	Standard	NM_001256409		Approved	MGC8974	uc001cwj.2	Q9Y546	OTTHUMG00000008436	ENST00000371370.3:c.197_204delAAGAGAAG	chr1.hg19:g.54417869_54417876delAAGAGAAG	ENSP00000360421:p.Lys66fs	155.0	0.0	0		111.0	13.0	0.117117	NM_052940	D3DQ46|Q8N2Q8	Frame_Shift_Del	DEL	ENST00000371370.3	hg19	CCDS585.1																																																																																			.	.	.	none		0.514	LRRC42-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023250.1	NM_052940		-	54417876	AAGAGAAG	-	54417869	7	5	187	1	0	1	0	1	0	0	0	0	9007	14	1	0	199	0	LRRC42	1	54417869	Frame_Shift_Del	DEL	AAGAGAAG	TCGA-GL-A4EM-01A-11D-A25F-10	13310427	54417869	194832752	2	10962											
SLC25A44	9673	hgsc.bcm.edu	37	chr1	156169658	156169658	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catggaggacaaacgcaacaTccagatcatcgagtgggaac	15	5	11	10	2	1	1	1	0	0	1	3	5	2	4	1	3	3	1	1	3	3	0			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr1:156169658T>C	ENST00000359511.4	+	2	192	c.20T>C	c.(19-21)aTc>aCc	p.I7T	SLC25A44_ENST00000469537.1_3'UTR|SLC25A44_ENST00000423538.2_Missense_Mutation_p.I7T	NM_014655.2	NP_055470.1	Q96H78	S2544_HUMAN	solute carrier family 25, member 44	7					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)					AAACGCAACATCCAGATCATC	0.507																																					p.I7T		Atlas-SNP	.											.	SLC25A44	30	.	0			c.T20C						PASS	.						153	142	146					1																	156169658		2203	4300	6503	SO:0001583	missense	9673	exon2			GCAACATCCAGAT	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	ENST00000359511.4:c.20T>C	chr1.hg19:g.156169658T>C	ENSP00000352497:p.Ile7Thr	179.0	0.0	.		123.0	16.0	.	NM_014655	O75034	Missense_Mutation	SNP	ENST00000359511.4	hg19	CCDS1133.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.365339	0.82463	.	.	ENSG00000160785	ENST00000359511;ENST00000423538;ENST00000412949	T;T	0.80824	-1.42;-1.34	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.85517	0.5715	M	0.79123	2.44	0.80722	D	1	D;D;D	0.63046	0.992;0.986;0.986	P;P;P	0.61477	0.858;0.889;0.889	D	0.87847	0.2655	10	0.72032	D	0.01	-27.8219	13.6089	0.62063	0.0:0.0:0.0:1.0	.	7;7;7	E9PGQ0;B4DGC4;Q96H78	.;.;S2544_HUMAN	T	7	ENSP00000352497:I7T;ENSP00000407560:I7T	ENSP00000352497:I7T	I	+	2	0	SLC25A44	154436282	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.778000	0.85637	2.108000	0.64289	0.528000	0.53228	ATC	.	.	.	none		0.507	SLC25A44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040856.1	NM_014655		C	156169658	T	C	156169658	3	2	187	1	0	0	0	0	1	0	0	0	14522	1435	50	3	22	3	SLC25A44	1	156169658	Missense_Mutation	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10	101751789	156169658	93080963	3	10963											
OR6K6	128371	hgsc.bcm.edu	37	chr1	158724869	158724869	+	Frame_Shift_Del	DEL	T	T	-																															gccctgcacacccctttgtaTttctttatcagtgtcctctc																										TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr1:158724869delT	ENST00000368144.2	+	1	360	c.264delT	c.(262-264)tatfs	p.Y88fs		NM_001005184.1	NP_001005184.1	Q8NGW6	OR6K6_HUMAN	olfactory receptor, family 6, subfamily K, member 6	88						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(5)|lung(17)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_hematologic(112;0.0378)					CCCCTTTGTATTTCTTTATCA	0.463																																					p.Y88fs		Atlas-Indel,Pindel	.											.	OR6K6	81	.	0			c.263delA						PASS	.						156	157	157					1																	158724869		2203	4300	6503	SO:0001589	frameshift_variant	128371	exon1			.	BK004198	CCDS30904.1	1q23.1	2012-08-09			ENSG00000180433	ENSG00000180433		"GPCR / Class A : Olfactory receptors"	15033	protein-coding gene	gene with protein product							Standard	NM_001005184		Approved		uc001fsw.1	Q8NGW6	OTTHUMG00000022772	ENST00000368144.2:c.264delT	chr1.hg19:g.158724869delT	ENSP00000357126:p.Tyr88fs	150.0	0.0	0		151.0	16.0	0.10596	NM_001005184	B9EIM8|Q5VUU9|Q6IFR4	Frame_Shift_Del	DEL	ENST00000368144.2	hg19	CCDS30904.1																																																																																			.	.	.	none		0.463	OR6K6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059065.2	NM_001005184		-	158724869	T	-	158724869	7	5	187	1	0	1	0	1	0	0	0	0	11211	1500	52	0	266	0	OR6K6	1	158724869	Frame_Shift_Del	DEL	T	TCGA-GL-A4EM-01A-11D-A25F-10	2555211	158724869	90525752	4	10964											
HMCN1	83872	hgsc.bcm.edu	37	chr1	186024754	186024754	+	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	acaggccgttatgtgtgtgtTgctgtgaatgtagcaggaat	9	13	14	5	1	0	1	0	1	0	0	0	2	0	2	1	2	2	5	1	2	4	3			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr1:186024754T>A	ENST00000271588.4	+	45	7321	c.7092T>A	c.(7090-7092)gtT>gtA	p.V2364V	HMCN1_ENST00000367492.2_Silent_p.V2364V	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2364	Ig-like C2-type 21.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						ATGTGTGTGTTGCTGTGAATG	0.418																																					p.V2364V		Atlas-SNP	.											.	HMCN1	797	.	0			c.T7092A						PASS	.						152	137	142					1																	186024754		2203	4300	6503	SO:0001819	synonymous_variant	83872	exon45			GTGTGTTGCTGTG	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.7092T>A	chr1.hg19:g.186024754T>A		331.0	0.0	.		258.0	43.0	.	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.	.	none		0.418	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186024754	T	A	186024754	2	1	187	1	0	0	0	0	0	0	0	1	7227	1799	63	5		5	HMCN1	1	186024754	Silent	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10	27299885	186024754	63225867	5	10965											
PPP1R15B	84919	hgsc.bcm.edu	37	chr1	204379087	204379089	+	In_Frame_Del	DEL	CTA	CTA	-																															gttctggggattataaggatCtacactgcagaaagagttcc																								rs200631983		TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	CTA	CTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr1:204379087_204379089delCTA	ENST00000367188.4	-	1	1830_1832	c.1451_1453delTAG	c.(1450-1455)gtagat>gat	p.V484del	RP11-739N20.2_ENST00000443515.1_RNA	NM_032833.3	NP_116222.3	Q5SWA1	PR15B_HUMAN	protein phosphatase 1, regulatory subunit 15B	484					ER overload response (GO:0006983)|regulation of translation (GO:0006417)|response to hydrogen peroxide (GO:0042542)	protein phosphatase type 1 complex (GO:0000164)	protein serine/threonine phosphatase activity (GO:0004722)			breast(3)|cervix(1)|kidney(4)|large_intestine(3)|lung(16)|ovary(1)|pancreas(2)|skin(1)|urinary_tract(3)	34	all_cancers(21;0.0032)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.179)|all_epithelial(62;0.193)|Prostate(682;0.227)		all cancers(3;1.14e-29)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.139)			TTATAAGGATCTACACTGCAGAA	0.448																																					p.484_485del		Atlas-Indel,Pindel	.											.	PPP1R15B	67	.	0			c.1452_1454del						PASS	.																																			SO:0001651	inframe_deletion	84919	exon1			.	AK027650	CCDS1445.1	1q32.1	2012-04-17	2011-10-04		ENSG00000158615	ENSG00000158615		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14951	protein-coding gene	gene with protein product		613257	"protein phosphatase 1, regulatory (inhibitor) subunit 15B"			11948623	Standard	XM_005245551		Approved	FLJ14744	uc001hav.4	Q5SWA1	OTTHUMG00000036105	ENST00000367188.4:c.1451_1453delTAG	chr1.hg19:g.204379087_204379089delCTA	ENSP00000356156:p.Val484del	60.0	0.0	0		67.0	12.0	0.179104	NM_032833	Q53GQ4|Q658M2|Q6P156|Q96SN1	In_Frame_Del	DEL	ENST00000367188.4	hg19	CCDS1445.1																																																																																			.	.	.	none		0.448	PPP1R15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087974.1	NM_032833		-	204379089	CTA	-	204379087	7	5	187	1	0	1	0	1	0	0	0	0	12374	913	32	0	696	0	PPP1R15B	1	204379087	In_Frame_Del	DEL	CTA	TCGA-GL-A4EM-01A-11D-A25F-10	18354333	204379087	44871534	6	10966											
USH2A	7399	hgsc.bcm.edu	37	chr1	215820886	215820886	+	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	tctttttgggtggtgaaactGatccactcggaagccgtact	8	13	11	9	2	1	2	0	2	1	0	3	3	2	3	2	3	3	1	2	3	3	3			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr1:215820886G>T	ENST00000307340.3	-	67	15155	c.14769C>A	c.(14767-14769)atC>atA	p.I4923I	USH2A_ENST00000366943.2_Silent_p.I4923I	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	4923	Fibronectin type-III 34. {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)		TGGTGAAACTGATCCACTCGG	0.532										HNSCC(13;0.011)																											p.I4923I		Atlas-SNP	.											.	USH2A	1168	.	0			c.C14769A						PASS	.						93	76	81					1																	215820886		2203	4300	6503	SO:0001819	synonymous_variant	7399	exon67			GAAACTGATCCAC	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.14769C>A	chr1.hg19:g.215820886G>T		196.0	0.0	.		165.0	25.0	.	NM_206933	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	hg19	CCDS31025.1																																																																																			.	.	.	none		0.532	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	215820886	G	T	215820886	2	4	187	1	0	0	0	0	0	0	0	1	17048	1280	45	4		4	USH2A	1	215820886	Silent	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	11441799	215820886	33429735	7	10967											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228462497	228462497	+	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	aggacgcgggccagatcaccGtggaggctgagggcgcctca	8	4	17	12	4	2	2	2	1	0	1	2	4	2	4	3	5	0	1	3	5	0	0			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr1:228462497G>C	ENST00000422127.1	+	20	5952	c.5908G>C	c.(5908-5910)Gtg>Ctg	p.V1970L	RP5-1139B12.3_ENST00000602529.1_RNA|OBSCN_ENST00000570156.2_Missense_Mutation_p.V2345L|RP5-1139B12.3_ENST00000602947.1_RNA|OBSCN_ENST00000359599.6_Missense_Mutation_p.V817L|OBSCN_ENST00000284548.11_Missense_Mutation_p.V1970L|OBSCN_ENST00000366707.4_5'UTR|RP5-1139B12.2_ENST00000602517.1_RNA|OBSCN_ENST00000366709.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1970	Ig-like 19.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CCAGATCACCGTGGAGGCTGA	0.652																																					p.V2345L		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G7033C						PASS	.						27	33	31					1																	228462497		2133	4237	6370	SO:0001583	missense	84033	exon24			ATCACCGTGGAGG	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.5908G>C	chr1.hg19:g.228462497G>C	ENSP00000409493:p.Val1970Leu	47.0	0.0	.		104.0	18.0	.	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	10.37	1.331260	0.24167	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000359599	T;T;T	0.76448	1.01;1.01;-1.02	5.49	3.61	0.41365	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.425981	0.22964	N	0.053513	T	0.73393	0.3581	L	0.51914	1.62	0.48571	D	0.999671	B;P	0.44816	0.002;0.844	B;B	0.44085	0.005;0.44	T	0.69339	-0.5171	10	0.36615	T	0.2	.	11.1091	0.48221	0.0696:0.129:0.8014:0.0	.	1970;1970	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	L	1970;1970;817	ENSP00000284548:V1970L;ENSP00000409493:V1970L;ENSP00000352613:V817L	ENSP00000284548:V1970L	V	+	1	0	OBSCN	226529120	0.981000	0.34729	0.000000	0.03702	0.005000	0.04900	6.186000	0.72026	0.679000	0.31345	0.555000	0.69702	GTG	.	.	.	none		0.652	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		C	228462497	G	C	228462497	3	2	187	1	0	0	0	0	1	0	0	0	10819	1145	40	4	5982	4	OBSCN	1	228462497	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	12641611	228462497	20788124	8	10968											
PKDCC	91461	hgsc.bcm.edu	37	chr2	42281437	42281445	+	In_Frame_Del	DEL	AATGCCTAC	AATGCCTAC	-																															acgagaagcggaacctctatAatgcctacaggtgacctcca																								rs55733961|rs371967754	byFrequency	TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	AATGCCTAC	AATGCCTAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr2:42281437_42281445delAATGCCTAC	ENST00000294964.5	+	3	1204_1212	c.1024_1032delAATGCCTAC	c.(1024-1032)aatgcctacdel	p.NAY342del		NM_138370.2	NP_612379.2			protein kinase domain containing, cytoplasmic											breast(2)|kidney(1)|lung(5)	8						GAACCTCTATAATGCCTACAGGTGACCTC	0.617																																					p.341_344del		Atlas-Indel,Pindel	.											.	PKDCC	21	.	0			c.1023_1031del						PASS	.																																			SO:0001651	inframe_deletion	91461	exon3			.		CCDS33186.2	2p21	2014-01-28	2012-12-07		ENSG00000162878	ENSG00000162878			25123	protein-coding gene	gene with protein product	"vertebrate lonesome kinase"	614150	"protein kinase domain containing, cytoplasmic homolog (mouse)"			19097194, 19465597	Standard	NM_138370		Approved	SgK493, Vlk	uc002rsg.3	Q504Y2	OTTHUMG00000152303	ENST00000294964.5:c.1024_1032delAATGCCTAC	chr2.hg19:g.42281437_42281445delAATGCCTAC	ENSP00000294964:p.Asn342_Tyr344del	208.0	0.0	0		199.0	16.0	0.080402	NM_138370		In_Frame_Del	DEL	ENST00000294964.5	hg19	CCDS33186.2																																																																																			.	.	.	none		0.617	PKDCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325745.3			-	42281445	AATGCCTAC	-	42281437	7	5	187	1	0	1	0	1	0	0	0	0	11976	362	13	0	1034	0	PKDCC	2	42281437	In_Frame_Del	DEL	AATGCCTAC	TCGA-GL-A4EM-01A-11D-A25F-10		42281437	200917936	9	10969											
NCKAP1	10787	hgsc.bcm.edu	37	chr2	183826949	183826949	+	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	gagatttcgagcttgtttggCcatttcatctaggaacatat	10	15	9	7	1	2	1	1	0	1	1	3	4	2	2	1	2	2	2	1	2	3	6	rs533229025		TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr2:183826949C>T	ENST00000361354.4	-	18	2191	c.1819G>A	c.(1819-1821)Gcc>Acc	p.A607T	NCKAP1_ENST00000360982.2_Missense_Mutation_p.A613T	NM_013436.3	NP_038464.1	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1	607					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)			GCTTGTTTGGCCATTTCATCT	0.348																																					p.A613T		Atlas-SNP	.											.	NCKAP1	105	.	0			c.G1837A						PASS	.						154	142	146					2																	183826949		2203	4300	6503	SO:0001583	missense	10787	exon19			GTTTGGCCATTTC	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.1819G>A	chr2.hg19:g.183826949C>T	ENSP00000355348:p.Ala607Thr	141.0	0.0	.		99.0	4.0	.	NM_205842	O60329|Q53QN5|Q53S94|Q53Y35	Missense_Mutation	SNP	ENST00000361354.4	hg19	CCDS2287.1	.	.	.	.	.	.	.	.	.	.	C	35	5.540632	0.96474	.	.	ENSG00000061676	ENST00000361354;ENST00000360982	T;T	0.34667	1.35;1.35	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.64962	0.2646	M	0.84846	2.72	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.73708	0.981;0.967	T	0.67356	-0.5691	10	0.41790	T	0.15	-6.6139	18.773	0.91899	0.0:1.0:0.0:0.0	.	607;613	Q9Y2A7;Q9Y2A7-2	NCKP1_HUMAN;.	T	607;613	ENSP00000355348:A607T;ENSP00000354251:A613T	ENSP00000354251:A613T	A	-	1	0	NCKAP1	183535194	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.794000	0.85869	2.517000	0.84864	0.655000	0.94253	GCC	.	.	.	none		0.348	NCKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255867.2	NM_205842		T	183826949	C	T	183826949	3	4	187	1	0	0	0	0	1	0	0	0	10228	739	26	2	1623	2	NCKAP1	2	183826949	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	141545512	183826949	59372424	10	10970											
IKZF2	22807	hgsc.bcm.edu	37	chr2	213872808	213872808	+	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	tgaatcgcatgagcttttccCctggaagggagtgggaggtg	8	10	16	7	1	0	2	0	2	0	0	2	5	1	5	2	4	1	2	2	4	2	2			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr2:213872808C>A	ENST00000434687.1	-	9	1166	c.857G>T	c.(856-858)gGg>gTg	p.G286V	IKZF2_ENST00000374319.4_Splice_Site_p.G260V|IKZF2_ENST00000413091.3_3'UTR|AC079610.1_ENST00000415387.1_RNA|IKZF2_ENST00000457361.1_Splice_Site_p.G286V|IKZF2_ENST00000342002.2_Splice_Site_p.G292V|IKZF2_ENST00000374327.4_Splice_Site_p.G141V|IKZF2_ENST00000421754.2_Splice_Site_p.G212V|IKZF2_ENST00000451136.2_Splice_Site_p.G214V			Q9UKS7	IKZF2_HUMAN	IKAROS family zinc finger 2 (Helios)	286					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)		GAGCTTTTCCCCTGGAAGGGA	0.373																																					p.G286V		Atlas-SNP	.											.	IKZF2	71	.	0			c.G857T						PASS	.						35	35	35					2																	213872808		2203	4300	6503	SO:0001630	splice_region_variant	22807	exon8			TTTTCCCCTGGAA	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.857-1G>T	chr2.hg19:g.213872808C>A		119.0	0.0	.		71.0	12.0	.	NM_016260	Q53YJ5|Q6PQC5|Q6PQC6|Q6PQC7|Q6PQC8|Q6PQD0|Q6PQD1|Q8N6S1	Missense_Mutation	SNP	ENST00000434687.1	hg19	CCDS2395.1	.	.	.	.	.	.	.	.	.	.	C	16.55	3.154388	0.57259	.	.	ENSG00000030419	ENST00000457361;ENST00000342002;ENST00000434687;ENST00000374319;ENST00000451136;ENST00000421754;ENST00000374327	T;T;T;T;T;T;T	0.24350	2.74;2.71;2.74;2.88;2.86;3.06;1.86	5.83	5.83	0.93111	.	0.072285	0.64402	D	0.000018	T	0.60090	0.2242	M	0.88979	2.995	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;0.998;0.999;0.999	T	0.66248	-0.5971	10	0.87932	D	0	.	18.2957	0.90145	0.0:1.0:0.0:0.0	.	214;212;141;260;286;64	C9JCG7;C9JTM9;F5H8M1;Q9UKS7-2;Q9UKS7;Q96LD7	.;.;.;.;IKZF2_HUMAN;.	V	286;292;286;260;214;212;141	ENSP00000410447:G286V;ENSP00000342876:G292V;ENSP00000412869:G286V;ENSP00000363439:G260V;ENSP00000395203:G214V;ENSP00000399574:G212V;ENSP00000363447:G141V	ENSP00000342876:G292V	G	-	2	0	IKZF2	213581053	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	5.731000	0.68554	2.750000	0.94351	0.655000	0.94253	GGG	.	.	.	none		0.373	IKZF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256593.3	NM_016260	Missense_Mutation	A	213872808	C	A	213872808	5	1	187	1	0	0	0	0	0	0	1	0	7622	637	22	4	727	4	IKZF2	2	213872808	Splice_Site	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	30045859	213872808	29326565	11	10971											
PER2	8864	hgsc.bcm.edu	37	chr2	239162231	239162231	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gacacgggccccccagatccGgtgctctcagatgagtctcg	7	7	12	15	3	2	3	1	1	2	2	5	4	3	3	4	2	1	1	4	2	0	0	rs566281173	byFrequency	TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr2:239162231G>A	ENST00000254657.3	-	19	2712	c.2433C>T	c.(2431-2433)acC>acT	p.T811T	AC096574.4_ENST00000456601.1_RNA|PER2_ENST00000254658.3_3'UTR	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	811					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)		CCCCAGATCCGGTGCTCTCAG	0.572													g|||	2	0.000399361	0	0	5008	,	,		14310	0		0	False		,,,				2504	0.002				p.T811T		Atlas-SNP	.											.	PER2	85	.	0			c.C2433T						PASS	.						12	15	14					2																	239162231		2199	4298	6497	SO:0001819	synonymous_variant	8864	exon19			AGATCCGGTGCTC	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.2433C>T	chr2.hg19:g.239162231G>A		35.0	0.0	.		53.0	12.0	.	NM_022817	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Silent	SNP	ENST00000254657.3	hg19	CCDS2528.1																																																																																			.	.	.	none		0.572	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817		A	239162231	G	A	239162231	2	1	187	1	0	0	0	0	0	0	0	1	11737	1103	39	1		1	PER2	2	239162231	Silent	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	25289423	239162231	4037142	12	10972											
DNAH1	25981	hgsc.bcm.edu	37	chr3	52429465	52429465	+	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	ccaaaaagctctctgccatcTccctgggccaggggcaggtc	8	7	11	15	0	2	0	0	0	2	0	5	0	2	0	4	4	2	2	4	4	2	0			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr3:52429465T>A	ENST00000420323.2	+	69	11371	c.11110T>A	c.(11110-11112)Tcc>Acc	p.S3704T		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	3769					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)		CTCTGCCATCTCCCTGGGCCA	0.627																																					p.S3704T		Atlas-SNP	.											.	DNAH1	534	.	0			c.T11110A						PASS	.						36	38	37					3																	52429465		1924	4124	6048	SO:0001583	missense	25981	exon69			GCCATCTCCCTGG	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.11110T>A	chr3.hg19:g.52429465T>A	ENSP00000401514:p.Ser3704Thr	207.0	0.0	.		199.0	36.0	.	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	hg19	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	T	19.51	3.840907	0.71488	.	.	ENSG00000114841	ENST00000420323;ENST00000273600	T	0.14022	2.54	4.38	4.38	0.52667	.	0.000000	0.64402	D	0.000005	T	0.57110	0.2031	H	0.99435	4.565	0.45366	D	0.998355	D;D	0.89917	1.0;0.99	D;D	0.85130	0.997;0.979	T	0.76963	-0.2764	10	0.87932	D	0	.	13.7712	0.63026	0.0:0.0:0.0:1.0	.	3704;3769	C9JXH6;Q9P2D7-2	.;.	T	3704;457	ENSP00000401514:S3704T	ENSP00000273600:S457T	S	+	1	0	DNAH1	52404505	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.531000	0.81973	1.837000	0.53436	0.533000	0.62120	TCC	.	.	.	none		0.627	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		A	52429465	T	A	52429465	3	1	187	1	0	0	0	0	1	0	0	0	4599	1551	54	5	11380	5	DNAH1	3	52429465	Missense_Mutation	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10		52429465	145592965	13	10973											
EPHA3	2042	hgsc.bcm.edu	37	chr3	89478285	89478285	+	Missense_Mutation	SNP	A	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	ttatgattgtcacagaatacAtggagaatggttccttggat	12	14	10	5	0	1	3	1	1	0	2	2	5	2	4	1	3	1	1	1	3	4	5			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr3:89478285A>C	ENST00000336596.2	+	12	2329	c.2104A>C	c.(2104-2106)Atg>Ctg	p.M702L	EPHA3_ENST00000494014.1_Missense_Mutation_p.M702L	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	702	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)		CACAGAATACATGGAGAATGG	0.299										TSP Lung(6;0.00050)																											p.M702L		Atlas-SNP	.											.	EPHA3	501	.	0			c.A2104C						PASS	.						111	116	114					3																	89478285		2203	4299	6502	SO:0001583	missense	2042	exon12			GAATACATGGAGA	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.2104A>C	chr3.hg19:g.89478285A>C	ENSP00000337451:p.Met702Leu	74.0	0.0	.		77.0	11.0	.	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	hg19	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.781520	0.90282	.	.	ENSG00000044524	ENST00000336596;ENST00000494014	T;T	0.62639	0.01;0.01	5.68	5.68	0.88126	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	0.70228	0.3200	L	0.39020	1.185	0.80722	D	1	P	0.50710	0.938	D	0.65773	0.938	T	0.67964	-0.5534	9	.	.	.	.	16.2237	0.82280	1.0:0.0:0.0:0.0	.	702	P29320	EPHA3_HUMAN	L	702	ENSP00000337451:M702L;ENSP00000419190:M702L	.	M	+	1	0	EPHA3	89560975	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.287000	0.95975	2.289000	0.77006	0.482000	0.46254	ATG	.	.	.	none		0.299	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		C	89478285	A	C	89478285	3	2	187	1	0	0	0	0	1	0	0	0	5170	217	8	5	2176	5	EPHA3	3	89478285	Missense_Mutation	SNP	A	TCGA-GL-A4EM-01A-11D-A25F-10	37048820	89478285	108544145	14	10974											
CP	1356	hgsc.bcm.edu	37	chr3	148924070	148924070	+	Missense_Mutation	SNP	T	T	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	aacatgcttcccacggatatTatcctttgatgaagacttgt	11	14	7	9	1	0	3	0	2	0	1	2	4	2	4	2	1	2	1	2	1	4	5			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr3:148924070T>G	ENST00000264613.6	-	6	1355	c.1093A>C	c.(1093-1095)Aat>Cat	p.N365H		NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	365					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)	CCACGGATATTATCCTTTGAT	0.408																																					p.N365H		Atlas-SNP	.											.	CP	112	.	0			c.A1093C						PASS	.						140	137	138					3																	148924070		2203	4300	6503	SO:0001583	missense	1356	exon6			GGATATTATCCTT	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.1093A>C	chr3.hg19:g.148924070T>G	ENSP00000264613:p.Asn365His	135.0	0.0	.		112.0	10.0	.	NM_000096	Q14063|Q2PP18|Q9UKS4	Missense_Mutation	SNP	ENST00000264613.6	hg19	CCDS3141.1	.	.	.	.	.	.	.	.	.	.	T	11.00	1.511691	0.27036	.	.	ENSG00000047457	ENST00000264613;ENST00000494544	D;D	0.99239	-5.04;-5.61	5.81	-5.54	0.02544	.	1.443030	0.03609	N	0.234542	D	0.97785	0.9273	L	0.53249	1.67	0.09310	N	1	B;B;B;B	0.28128	0.0;0.201;0.0;0.0	B;B;B;B	0.24848	0.0;0.056;0.0;0.0	D	0.94485	0.7696	10	0.39692	T	0.17	0.0553	13.1324	0.59391	0.0:0.1357:0.1004:0.7639	.	365;365;365;365	A5PL27;A8K5A4;P00450;Q1L857	.;.;CERU_HUMAN;.	H	365;148	ENSP00000264613:N365H;ENSP00000420545:N148H	ENSP00000264613:N365H	N	-	1	0	CP	150406760	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.776000	0.04674	-1.021000	0.03350	-0.242000	0.12053	AAT	.	.	.	none		0.408	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096		G	148924070	T	G	148924070	3	3	187	1	0	0	0	0	1	0	0	0	3789	1754	61	5	2160	5	CP	3	148924070	Missense_Mutation	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10	59445785	148924070	49098360	15	10975											
CPZ	8532	hgsc.bcm.edu	37	chr4	8621250	8621250	+	Missense_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	gcccgacccgctccgggcgcGcaggcagccctcggccgacg	4	2	15	20	8	0	0	0	0	0	0	2	2	1	0	5	3	1	3	5	3	0	0	rs144042196		TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr4:8621250G>A	ENST00000360986.4	+	11	2039	c.1865G>A	c.(1864-1866)cGc>cAc	p.R622H	CPZ_ENST00000429646.2_Missense_Mutation_p.R230H|CPZ_ENST00000382480.2_Missense_Mutation_p.R485H|CPZ_ENST00000315782.6_Missense_Mutation_p.R611H	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	622					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						CTCCGGGCGCGCAGGCAGCCC	0.672																																					p.R622H		Atlas-SNP	.											.	CPZ	95	.	0			c.G1865A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG	0,4402		0,0,2201	28	31	30		1865,1454,1832	2.1	0.1	4	dbSNP_134	30	1,8595	1.2+/-3.3	0,1,4297	yes	missense,missense,missense	CPZ	NM_001014447.2,NM_001014448.2,NM_003652.3	29,29,29	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign	622/653,485/516,611/642	8621250	1,12997	2201	4298	6499	SO:0001583	missense	8532	exon11			GGGCGCGCAGGCA	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.1865G>A	chr4.hg19:g.8621250G>A	ENSP00000354255:p.Arg622His	3.0	0.0	.		8.0	5.0	.	NM_001014447	O00520|Q96MX2	Missense_Mutation	SNP	ENST00000360986.4	hg19	CCDS33953.1	.	.	.	.	.	.	.	.	.	.	G	14.91	2.677115	0.47886	0.0	1.16E-4	ENSG00000109625	ENST00000360986;ENST00000382480;ENST00000315782;ENST00000429646	T;T;T;T	0.58940	0.62;1.98;0.3;1.86	4.82	2.09	0.27110	.	0.624251	0.13588	U	0.376803	T	0.51873	0.1700	M	0.62723	1.935	0.09310	N	0.999999	B;B	0.18013	0.025;0.006	B;B	0.10450	0.005;0.001	T	0.46610	-0.9179	10	0.46703	T	0.11	-25.7306	8.9438	0.35747	0.2406:0.0:0.7594:0.0	.	611;622	Q66K79-2;Q66K79	.;CBPZ_HUMAN	H	622;485;611;230	ENSP00000354255:R622H;ENSP00000371920:R485H;ENSP00000315074:R611H;ENSP00000403981:R230H	ENSP00000315074:R611H	R	+	2	0	CPZ	8672150	0.003000	0.15002	0.094000	0.20943	0.121000	0.20230	0.793000	0.26944	0.448000	0.26722	0.462000	0.41574	CGC	.	G|1.000;A|0.000	0.000	weak		0.672	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652		A	8621250	G	A	8621250	3	1	187	1	0	0	0	0	1	0	0	0	3841	1087	38	1	1907	1	CPZ	4	8621250	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10		8621250	182533026	16	10976											
GRID2	2895	hgsc.bcm.edu	37	chr4	94690404	94690404	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgacatggacatcctgaagCacaaatggtggcctaagaat	14	8	11	8	0	0	3	0	2	0	1	1	4	1	4	2	3	1	1	2	3	4	1			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr4:94690404C>T	ENST00000282020.4	+	15	2662	c.2404C>T	c.(2404-2406)Cac>Tac	p.H802Y	GRID2_ENST00000510992.1_Missense_Mutation_p.H707Y	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	802					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)		CATCCTGAAGCACAAATGGTG	0.483																																					p.H802Y		Atlas-SNP	.											.	GRID2	233	.	0			c.C2404T						PASS	.						124	117	119					4																	94690404		2203	4300	6503	SO:0001583	missense	2895	exon15			CTGAAGCACAAAT	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.2404C>T	chr4.hg19:g.94690404C>T	ENSP00000282020:p.His802Tyr	168.0	0.0	.		156.0	21.0	.	NM_001510	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Missense_Mutation	SNP	ENST00000282020.4	hg19	CCDS3637.1	.	.	.	.	.	.	.	.	.	.	C	19.45	3.829280	0.71258	.	.	ENSG00000152208	ENST00000282020;ENST00000510992	T;T	0.26957	1.7;1.7	5.17	5.17	0.71159	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.054536	0.64402	D	0.000001	T	0.16514	0.0397	N	0.08118	0	0.58432	D	0.999992	B;B	0.30584	0.286;0.286	B;B	0.26693	0.072;0.072	T	0.11324	-1.0592	10	0.87932	D	0	.	18.7052	0.91635	0.0:1.0:0.0:0.0	.	707;802	E9PH24;O43424	.;GRID2_HUMAN	Y	802;707	ENSP00000282020:H802Y;ENSP00000421257:H707Y	ENSP00000282020:H802Y	H	+	1	0	GRID2	94909427	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.713000	0.54882	2.415000	0.81967	0.650000	0.86243	CAC	.	.	.	none		0.483	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2			T	94690404	C	T	94690404	3	4	187	1	0	0	0	0	1	0	0	0	6779	710	25	2	2462	2	GRID2	4	94690404	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	86069154	94690404	96463872	17	10977											
ZCCHC10	54819	hgsc.bcm.edu	37	chr5	132342536	132342536	+	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	gggcctatgtaggtattttcTttttcctgtgcattcataag	7	18	9	7	0	2	0	1	0	1	0	3	0	3	0	2	2	1	3	2	2	4	9			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr5:132342536T>G	ENST00000509437.1	-	3	191	c.184A>C	c.(184-186)Aga>Cga	p.R62R	ZCCHC10_ENST00000509008.1_Silent_p.R40R|ZCCHC10_ENST00000508080.1_5'UTR|ZCCHC10_ENST00000513848.1_Silent_p.R40R|ZCCHC10_ENST00000513541.1_Silent_p.R62R|ZCCHC10_ENST00000324170.3_Silent_p.R40R|ZCCHC10_ENST00000355372.2_Silent_p.R62R			Q8TBK6	ZCH10_HUMAN	zinc finger, CCHC domain containing 10	62							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGGTATTTTCTTTTTCCTGTG	0.338																																					p.R40R		Atlas-SNP	.											.	ZCCHC10	7	.	0			c.A118C						PASS	.						91	83	85					5																	132342536		2201	4298	6499	SO:0001819	synonymous_variant	54819	exon2			ATTTTCTTTTTCC	BC005211	CCDS4165.1, CCDS75300.1, CCDS75301.1, CCDS75302.1	5q31.1	2008-05-02			ENSG00000155329	ENSG00000155329		"Zinc fingers, CCHC domain containing"	25954	protein-coding gene	gene with protein product						12477932	Standard	XM_005272024		Approved	FLJ20094	uc003kyg.3	Q8TBK6	OTTHUMG00000129013	ENST00000509437.1:c.184A>C	chr5.hg19:g.132342536T>G		108.0	0.0	.		153.0	16.0	.	NM_017665	Q9NXR4	Silent	SNP	ENST00000509437.1	hg19																																																																																				.	.	.	none		0.338	ZCCHC10-004	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000370163.1	NM_017665		G	132342536	T	G	132342536	2	3	187	1	0	0	0	0	0	0	0	1	17591	1617	56	5		5	ZCCHC10	5	132342536	Silent	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10		132342536	48572724	18	10978											
COL12A1	1303	hgsc.bcm.edu	37	chr6	75860944	75860944	+	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	atctgccacattgtatgcatGggtatcatcaggatcagttg	10	13	10	8	0	4	0	3	0	1	0	4	1	4	1	1	2	2	4	1	2	2	4			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr6:75860944G>T	ENST00000322507.8	-	21	4369	c.4060C>A	c.(4060-4062)Cat>Aat	p.H1354N	COL12A1_ENST00000416123.2_Missense_Mutation_p.H1354N|COL12A1_ENST00000345356.6_Missense_Mutation_p.H190N|COL12A1_ENST00000483888.2_Missense_Mutation_p.H1354N	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1354	VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TTGTATGCATGGGTATCATCA	0.368																																					p.H1354N		Atlas-SNP	.											.	COL12A1	385	.	0			c.C4060A						PASS	.						171	170	170					6																	75860944		1901	4128	6029	SO:0001583	missense	1303	exon21			ATGCATGGGTATC	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.4060C>A	chr6.hg19:g.75860944G>T	ENSP00000325146:p.His1354Asn	100.0	0.0	.		100.0	16.0	.	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	hg19	CCDS43482.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.98|18.98	3.738638|3.738638	0.69304|0.69304	.|.	.|.	ENSG00000111799|ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888|ENST00000419671	D;D;D;D|.	0.84516|.	-1.86;-1.86;-1.86;-1.86|.	5.6|5.6	5.6|5.6	0.85130|0.85130	von Willebrand factor, type A (3);|.	0.072196|.	0.64402|.	D|.	0.000020|.	T|T	0.57548|0.57548	0.2061|0.2061	M|M	0.63169|0.63169	1.94|1.94	0.49915|0.49915	D|D	0.999831|0.999831	B;D|.	0.60575|.	0.345;0.988|.	B;D|.	0.64237|.	0.199;0.923|.	T|T	0.57289|0.57289	-0.7837|-0.7837	10|5	0.66056|.	D|.	0.02|.	.|.	12.886|12.886	0.58045|0.58045	0.0744:0.0:0.9256:0.0|0.0744:0.0:0.9256:0.0	.|.	190;1354|.	Q99715-2;Q99715|.	.;COCA1_HUMAN|.	N|Q	1354;1354;190;1354;1354|95	ENSP00000325146:H1354N;ENSP00000305147:H190N;ENSP00000412864:H1354N;ENSP00000421216:H1354N|.	ENSP00000325146:H1354N|.	H|P	-|-	1|2	0|0	COL12A1|COL12A1	75917664|75917664	1.000000|1.000000	0.71417|0.71417	0.509000|0.509000	0.27700|0.27700	0.925000|0.925000	0.55904|0.55904	7.690000|7.690000	0.84178|0.84178	2.631000|2.631000	0.89168|0.89168	0.655000|0.655000	0.94253|0.94253	CAT|CCA	.	.	.	none		0.368	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		T	75860944	G	T	75860944	3	4	187	1	0	0	0	0	1	0	0	0	3671	1348	47	4	5315	4	COL12A1	6	75860944	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10		75860944	95254123	19	10979											
MYO6	4646	hgsc.bcm.edu	37	chr6	76602272	76602272	+	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	agtggaggcacagctggcccGacagaaggaggaggaatccc	12	3	16	10	1	0	1	0	0	0	1	1	6	1	5	2	6	1	2	2	6	2	0	rs529167250		TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr6:76602272G>C	ENST00000369977.3	+	28	3111	c.2972G>C	c.(2971-2973)cGa>cCa	p.R991P	MYO6_ENST00000369981.3_Missense_Mutation_p.R991P|MYO6_ENST00000369985.4_Missense_Mutation_p.R991P|MYO6_ENST00000369975.1_Missense_Mutation_p.R991P	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	991	Glu-rich.				actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		CAGCTGGCCCGACAGAAGGAG	0.532																																					p.R991P		Atlas-SNP	.											.	MYO6	124	.	0			c.G2972C						PASS	.						100	109	106					6																	76602272		2203	4300	6503	SO:0001583	missense	4646	exon28			TGGCCCGACAGAA	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.2972G>C	chr6.hg19:g.76602272G>C	ENSP00000358994:p.Arg991Pro	88.0	0.0	.		97.0	15.0	.	NM_004999	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Missense_Mutation	SNP	ENST00000369977.3	hg19	CCDS34487.1	.	.	.	.	.	.	.	.	.	.	G	9.868	1.198055	0.22037	.	.	ENSG00000196586	ENST00000428345;ENST00000369981;ENST00000369985;ENST00000369977;ENST00000369975;ENST00000430435	T;T;T;T;T	0.58060	2.07;2.59;2.59;2.07;0.36	5.75	3.97	0.46021	.	0.350255	0.33477	N	0.004873	T	0.55210	0.1906	L	0.61218	1.895	0.09310	N	1	B;D	0.62365	0.086;0.991	B;D	0.67548	0.049;0.952	T	0.50939	-0.8768	10	0.72032	D	0.01	.	11.8787	0.52562	0.1401:0.0:0.8599:0.0	.	991;991	Q9UM54-2;Q9UM54-1	.;.	P	991;991;991;991;991;54	ENSP00000358998:R991P;ENSP00000359002:R991P;ENSP00000358994:R991P;ENSP00000358992:R991P;ENSP00000399406:R54P	ENSP00000358992:R991P	R	+	2	0	MYO6	76658992	0.031000	0.19500	0.018000	0.16275	0.286000	0.27126	0.655000	0.24933	1.448000	0.47680	0.491000	0.48974	CGA	.	.	.	none		0.532	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999		C	76602272	G	C	76602272	3	2	187	1	0	0	0	0	1	0	0	0	10088	1058	37	4	3078	4	MYO6	6	76602272	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	741328	76602272	94512795	20	10980											
C6orf167	253714	hgsc.bcm.edu	37	chr6	97629854	97629854	+	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	tcatcccaaccaaaaagttgAataattgatataactggctg	16	11	6	8	0	1	2	1	2	0	0	2	2	2	2	2	1	2	2	2	1	7	5			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr6:97629854A>T	ENST00000275053.4	-	16	2575	c.2310T>A	c.(2308-2310)atT>atA	p.I770I	MMS22L_ENST00000369251.2_Silent_p.I730I	NM_198468.2	NP_940870.2	Q6ZRQ5	MMS22_HUMAN	MMS22-like, DNA repair protein	770					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						CAAAAAGTTGAATAATTGATA	0.373																																					p.I770I		Atlas-SNP	.											.	MMS22L	102	.	0			c.T2310A						PASS	.						174	169	171					6																	97629854		2203	4300	6503	SO:0001819	synonymous_variant	253714	exon16			AAGTTGAATAATT		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.2310T>A	chr6.hg19:g.97629854A>T		78.0	0.0	.		67.0	10.0	.	NM_198468	D6R9Y8|D6RBQ4|E1P529|Q5THT2|Q68CQ6|Q68D32	Silent	SNP	ENST00000275053.4	hg19	CCDS5039.1																																																																																			.	.	.	none		0.373	MMS22L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041573.3	NM_198468		T	97629854	A	T	97629854	2	4	187	1	0	0	0	0	0	0	0	1	2344	242	9	5		5	C6orf167	6	97629854	Silent	SNP	A	TCGA-GL-A4EM-01A-11D-A25F-10	21027582	97629854	73485213	21	10981											
SERINC1	57515	hgsc.bcm.edu	37	chr6	122777747	122777747	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tacagctttatagccaaccaAaatgttacaagggacaacac	17	8	6	10	0	0	0	0	0	0	0	0	1	0	1	2	1	6	2	2	1	9	5			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr6:122777747A>G	ENST00000339697.4	-	3	334	c.250T>C	c.(250-252)Ttg>Ctg	p.L84L		NM_020755.2	NP_065806.1	Q9NRX5	SERC1_HUMAN	serine incorporator 1	84					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)		TAGCCAACCAAAATGTTACAA	0.333																																					p.L84L		Atlas-SNP	.											.	SERINC1	39	.	0			c.T250C						PASS	.						125	110	115					6																	122777747		2203	4300	6503	SO:0001819	synonymous_variant	57515	exon3			CAACCAAAATGTT	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.250T>C	chr6.hg19:g.122777747A>G		78.0	0.0	.		74.0	13.0	.	NM_020755	B3KY69|E1P565|O75655|Q7Z2F5|Q8TAG1|Q9NTH8|Q9ULG7	Silent	SNP	ENST00000339697.4	hg19	CCDS5125.1																																																																																			.	.	.	none		0.333	SERINC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042031.2	NM_020755		G	122777747	A	G	122777747	2	3	187	1	0	0	0	0	0	0	0	1	14092	11	1	3		3	SERINC1	6	122777747	Silent	SNP	A	TCGA-GL-A4EM-01A-11D-A25F-10	25147893	122777747	48337320	22	10982											
SP4	6671	hgsc.bcm.edu	37	chr7	21469335	21469335	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caaattcaaatcaatccaacTagtagttcatctctacagga	16	11	4	10	0	4	0	3	0	1	0	6	1	5	1	1	1	2	2	1	1	7	5			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr7:21469335T>C	ENST00000222584.3	+	3	770	c.552T>C	c.(550-552)acT>acC	p.T184T		NM_003112.3	NP_003103.2	Q02446	SP4_HUMAN	Sp4 transcription factor	184					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						TCAATCCAACTAGTAGTTCAT	0.398																																					p.T184T		Atlas-SNP	.											.	SP4	91	.	0			c.T552C						PASS	.						77	74	75					7																	21469335		2203	4300	6503	SO:0001819	synonymous_variant	6671	exon3			TCCAACTAGTAGT		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.552T>C	chr7.hg19:g.21469335T>C		64.0	0.0	.		71.0	15.0	.	NM_003112	O60402|Q32M52	Silent	SNP	ENST00000222584.3	hg19	CCDS5373.1																																																																																			.	.	.	none		0.398	SP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211617.2	NM_003112		C	21469335	T	C	21469335	2	2	187	1	0	0	0	0	0	0	0	1	14979	1509	53	3		3	SP4	7	21469335	Silent	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10		21469335	137669328	23	10983											
MYO1G	64005	hgsc.bcm.edu	37	chr7	45010552	45010552	+	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	agcggagcacgaggtcccggGgtgtggccgtcagctcagcc	6	5	17	13	4	2	0	2	0	0	0	3	2	3	1	3	5	4	2	3	5	0	0			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr7:45010552G>T	ENST00000258787.7	-	8	1089	c.953C>A	c.(952-954)cCc>cAc	p.P318H		NM_033054.2	NP_149043.2	B0I1T2	MYO1G_HUMAN	myosin IG	318	Myosin motor.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|skin(4)	28						GAGGTCCCGGGGTGTGGCCGT	0.657																																					p.P318H		Atlas-SNP	.											.	MYO1G	86	.	0			c.C953A						PASS	.						57	47	50					7																	45010552		2202	4300	6502	SO:0001583	missense	64005	exon8			TCCCGGGGTGTGG	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.953C>A	chr7.hg19:g.45010552G>T	ENSP00000258787:p.Pro318His	24.0	0.0	.		87.0	12.0	.	NM_033054	Q8TEI9|Q8TES2|Q96BE2|Q96RI5|Q96RI6	Missense_Mutation	SNP	ENST00000258787.7	hg19	CCDS34629.1	.	.	.	.	.	.	.	.	.	.	G	16.27	3.075212	0.55646	.	.	ENSG00000136286	ENST00000258787	D	0.87029	-2.2	5.3	4.36	0.52297	Myosin head, motor domain (2);	0.183757	0.26598	N	0.023498	D	0.86871	0.6037	L	0.42744	1.35	0.09310	N	1	P;P	0.50528	0.936;0.848	P;P	0.53401	0.725;0.722	T	0.79472	-0.1789	10	0.46703	T	0.11	.	11.939	0.52890	0.0:0.2921:0.7079:0.0	.	318;318	B0I1T2-4;B0I1T2	.;MYO1G_HUMAN	H	318	ENSP00000258787:P318H	ENSP00000258787:P318H	P	-	2	0	MYO1G	44977077	0.000000	0.05858	0.428000	0.26697	0.808000	0.45660	0.514000	0.22786	2.649000	0.89929	0.655000	0.94253	CCC	.	.	.	none		0.657	MYO1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341832.2			T	45010552	G	T	45010552	3	4	187	1	0	0	0	0	1	0	0	0	10081	1232	43	4	2163	4	MYO1G	7	45010552	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	23541217	45010552	114128111	24	10984											
TMC1	117531	hgsc.bcm.edu	37	chr9	75355127	75355127	+	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	taagatgatgatggccaaggTaggtatttttatagttgtct	11	16	11	3	0	1	3	0	2	1	1	1	3	1	3	1	3	0	3	1	3	6	8			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr9:75355127T>C	ENST00000297784.5	+	9	993		c.e9+2		TMC1_ENST00000340019.3_Splice_Site|TMC1_ENST00000396237.3_Splice_Site	NM_138691.2	NP_619636.2	Q8TDI8	TMC1_HUMAN	transmembrane channel-like 1						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						ATGGCCAAGGTAGGTATTTTT	0.358																																					.	Pancreas(75;173 1345 14232 34245 43413)	Atlas-SNP	.											.	TMC1	87	.	0			c.453+2T>C						PASS	.						105	108	107					9																	75355127		2203	4300	6503	SO:0001630	splice_region_variant	117531	exon9			CCAAGGTAGGTAT	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.453+2T>C	chr9.hg19:g.75355127T>C		76.0	0.0	.		73.0	16.0	.	NM_138691	A8MVZ2|B1AM91	Splice_Site	SNP	ENST00000297784.5	hg19	CCDS6643.1	.	.	.	.	.	.	.	.	.	.	T	13.49	2.251532	0.39797	.	.	ENSG00000165091	ENST00000297784;ENST00000340019;ENST00000396235;ENST00000537917;ENST00000538054;ENST00000542143;ENST00000396237	.	.	.	5.62	5.62	0.85841	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2221	0.54439	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	TMC1	74544947	1.000000	0.71417	0.998000	0.56505	0.532000	0.34746	3.240000	0.51368	2.133000	0.65898	0.533000	0.62120	.	.	.	.	none		0.358	TMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052655.1		Intron	C	75355127	T	C	75355127	5	2	187	1	0	0	0	0	0	0	1	0	15996	1652	57	3	473	3	TMC1	9	75355127	Splice_Site	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10		75355127	65858304	25	10985											
COBRA1	25920	hgsc.bcm.edu	37	chr9	140158762	140158762	+	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	agcaagagggcgcgggagctGcaggggtttctcgatggcgt	7	7	19	8	4	1	1	0	0	1	1	2	3	1	2	0	5	3	4	0	5	1	1			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr9:140158762G>A	ENST00000343053.4	+	6	1186	c.849G>A	c.(847-849)ctG>ctA	p.L283L		NM_015456.3	NP_056271.2	Q8WX92	NELFB_HUMAN	negative elongation factor complex member B	283					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)											CGCGGGAGCTGCAGGGGTTTC	0.672																																					p.L283L		Atlas-SNP	.											.	.	.	.	0			c.G849A						PASS	.						63	61	62					9																	140158762		2201	4299	6500	SO:0001819	synonymous_variant	25920	exon6			GGAGCTGCAGGGG	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.849G>A	chr9.hg19:g.140158762G>A		25.0	0.0	.		37.0	8.0	.	NM_015456	A2BFA3|Q96EW5|Q9H9R4|Q9ULN8|Q9Y3W0	Silent	SNP	ENST00000343053.4	hg19	CCDS7040.1																																																																																			.	.	.	none		0.672	NELFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254710.1	NM_015456		A	140158762	G	A	140158762	2	1	187	1	0	0	0	0	0	0	0	1	3657	1306	46	2		2	COBRA1	9	140158762	Silent	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	64803635	140158762	1054669	26	10986											
C10orf18	54906	hgsc.bcm.edu	37	chr10	5781661	5781661	+	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	ggattagcataaatagtgttCaaccagaaaataccacagcg	17	8	8	8	1	1	1	1	0	0	1	1	2	1	2	2	1	4	2	2	1	8	5			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr10:5781661C>T	ENST00000328090.5	+	13	2153	c.1528C>T	c.(1528-1530)Caa>Taa	p.Q510*	RP11-336A10.2_ENST00000411512.2_RNA	NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	510																	AAATAGTGTTCAACCAGAAAA	0.383																																					p.Q510X		Atlas-SNP	.											.	.	.	.	0			c.C1528T						PASS	.						99	93	95					10																	5781661		1895	4126	6021	SO:0001587	stop_gained	54906	exon13			AGTGTTCAACCAG	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.1528C>T	chr10.hg19:g.5781661C>T	ENSP00000328426:p.Gln510*	134.0	0.0	.		112.0	6.0	.	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Nonsense_Mutation	SNP	ENST00000328090.5	hg19	CCDS41485.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	37|37	6.453755|6.453755	0.97581|0.97581	.|.	.|.	ENSG00000108021|ENSG00000108021	ENST00000328090|ENST00000380270	.|.	.|.	.|.	5.72|5.72	3.81|3.81	0.43845|0.43845	.|.	0.212671|.	0.33144|.	N|.	0.005222|.	.|T	.|0.63920	.|0.2552	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.69379	.|-0.5161	.|3	0.25106|.	T|.	0.35|.	.|.	13.9222|13.9222	0.63940|0.63940	0.0:0.556:0.444:0.0|0.0:0.556:0.444:0.0	.|.	.|.	.|.	.|.	X|L	510|208	.|.	ENSP00000328426:Q510X|.	Q|S	+|+	1|2	0|0	C10orf18|C10orf18	5821667|5821667	0.722000|0.722000	0.28017|0.28017	0.029000|0.029000	0.17559|0.17559	0.010000|0.010000	0.07245|0.07245	1.851000|1.851000	0.39338|0.39338	0.699000|0.699000	0.31761|0.31761	-0.274000|-0.274000	0.10170|0.10170	CAA|TCA	.	.	.	none		0.383	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782		T	5781661	C	T	5781661	4	4	187	1	0	0	0	0	0	1	0	0	1598	827	29	2	1566	2	C10orf18	10	5781661	Nonsense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10		5781661	129753086	27	10987											
EPC1	80314	hgsc.bcm.edu	37	chr10	32573863	32573863	+	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	agatttgtccgaggtatttgTttctgaggtattggcaaact	9	16	11	5	1	1	2	0	1	1	1	2	3	2	2	1	3	1	4	1	3	3	6			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr10:32573863T>A	ENST00000263062.8	-	10	1776	c.1507A>T	c.(1507-1509)Aca>Tca	p.T503S	EPC1_ENST00000319778.6_Missense_Mutation_p.T503S|EPC1_ENST00000375110.2_Missense_Mutation_p.T453S|RP11-166N17.3_ENST00000419441.1_RNA	NM_025209.2	NP_079485.1	Q9H2F5	EPC1_HUMAN	enhancer of polycomb homolog 1 (Drosophila)	503					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(5)|urinary_tract(1)	24		Prostate(175;0.0199)				GAGGTATTTGTTTCTGAGGTA	0.423																																					p.T503S		Atlas-SNP	.											.	EPC1	74	.	0			c.A1507T						PASS	.						145	139	141					10																	32573863		2203	4300	6503	SO:0001583	missense	80314	exon10			TATTTGTTTCTGA	AF277374	CCDS7172.1, CCDS60511.1, CCDS73083.1	10p11	2005-12-12			ENSG00000120616	ENSG00000120616			19876	protein-coding gene	gene with protein product		610999				10976108	Standard	NM_025209		Approved	Epl1	uc001iwg.2	Q9H2F5	OTTHUMG00000017925	ENST00000263062.8:c.1507A>T	chr10.hg19:g.32573863T>A	ENSP00000263062:p.Thr503Ser	140.0	0.0	.		119.0	21.0	.	NM_025209	B4DSC3|D3DRX7|Q5VW54|Q5VW56|Q5VW58|Q8NAQ4|Q8NE21|Q96LF4|Q96RR6|Q9H7T7	Missense_Mutation	SNP	ENST00000263062.8	hg19	CCDS7172.1	.	.	.	.	.	.	.	.	.	.	T	16.87	3.240893	0.58995	.	.	ENSG00000120616	ENST00000375110;ENST00000319778;ENST00000263062	T;T;T	0.16743	2.32;2.32;2.32	6.07	4.93	0.64822	.	0.132659	0.64402	D	0.000002	T	0.19485	0.0468	L	0.56769	1.78	0.37213	D	0.904872	B;B;B	0.26512	0.019;0.003;0.151	B;B;B	0.27796	0.031;0.027;0.083	T	0.06391	-1.0829	10	0.25106	T	0.35	-3.2229	13.751	0.62908	0.0:0.0:0.1278:0.8721	.	453;503;503	Q9H2F5-3;Q9H2F5-2;Q9H2F5	.;.;EPC1_HUMAN	S	453;503;503	ENSP00000364251:T453S;ENSP00000318559:T503S;ENSP00000263062:T503S	ENSP00000263062:T503S	T	-	1	0	EPC1	32613869	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.783000	0.68982	1.080000	0.41073	0.533000	0.62120	ACA	.	.	.	none		0.423	EPC1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047484.1			A	32573863	T	A	32573863	3	1	187	1	0	0	0	0	1	0	0	0	5162	1725	60	5	1027	5	EPC1	10	32573863	Missense_Mutation	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10	26792202	32573863	102960884	28	10988											
MBL2	4153	hgsc.bcm.edu	37	chr10	54527970	54527970	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccactggccatttttcagtAgcaatacacaatcttcatca	12	13	4	12	0	4	0	3	0	1	0	5	0	5	0	2	1	2	2	2	1	4	5			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr10:54527970A>G	ENST00000373968.3	-	4	738	c.674T>C	c.(673-675)cTa>cCa	p.L225P		NM_000242.2	NP_000233.1	P11226	MBL2_HUMAN	mannose-binding lectin (protein C) 2, soluble	225	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				acute-phase response (GO:0006953)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|complement activation, lectin pathway (GO:0001867)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response (GO:0045087)|killing by host of symbiont cells (GO:0051873)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of viral process (GO:0048525)|opsonization (GO:0008228)|positive regulation of phagocytosis (GO:0050766)|response to oxidative stress (GO:0006979)	cell surface (GO:0009986)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium-dependent protein binding (GO:0048306)|mannose binding (GO:0005537)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21						ATTTTTCAGTAGCAATACACA	0.502																																					p.L225P		Atlas-SNP	.											.	MBL2	55	.	0			c.T674C						PASS	.						379	337	351					10																	54527970		2202	4300	6502	SO:0001583	missense	4153	exon4			TTCAGTAGCAATA	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.674T>C	chr10.hg19:g.54527970A>G	ENSP00000363079:p.Leu225Pro	263.0	0.0	.		219.0	39.0	.	NM_000242	Q4VB12|Q4VB13|Q4VB14|Q5SQS3|Q86SI4|Q96KE4|Q96TF7|Q96TF8|Q96TF9	Missense_Mutation	SNP	ENST00000373968.3	hg19	CCDS7247.1	.	.	.	.	.	.	.	.	.	.	A	17.66	3.444961	0.63178	.	.	ENSG00000165471	ENST00000373968	T	0.24350	1.86	5.13	5.13	0.70059	C-type lectin fold (1);C-type lectin, conserved site (1);C-type lectin-like (1);C-type lectin (3);	1.028080	0.07735	N	0.945891	T	0.66137	0.2759	H	0.95611	3.695	0.22811	N	0.99871	D	0.89917	1.0	D	0.85130	0.997	T	0.56805	-0.7918	10	0.87932	D	0	-1.5247	13.1902	0.59706	1.0:0.0:0.0:0.0	.	225	P11226	MBL2_HUMAN	P	225	ENSP00000363079:L225P	ENSP00000363079:L225P	L	-	2	0	MBL2	54197976	0.066000	0.20996	0.003000	0.11579	0.002000	0.02628	4.043000	0.57354	2.048000	0.60808	0.482000	0.46254	CTA	.	.	.	none		0.502	MBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048115.1	NM_000242		G	54527970	A	G	54527970	3	3	187	1	0	0	0	0	1	0	0	0	9357	420	15	3	76	3	MBL2	10	54527970	Missense_Mutation	SNP	A	TCGA-GL-A4EM-01A-11D-A25F-10	21954107	54527970	81006777	29	10989											
CCDC86	79080	hgsc.bcm.edu	37	chr11	60609627	60609627	+	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	ccgttaaggcgcagccgacgGctgggaggcctaaggcccga	8	4	16	13	5	0	0	0	0	0	0	0	3	0	1	4	5	1	3	4	5	2	2			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr11:60609627G>T	ENST00000227520.5	+	1	84	c.30G>T	c.(28-30)cgG>cgT	p.R10R	RP11-804A23.4_ENST00000538705.1_RNA|RP11-804A23.2_ENST00000539897.1_RNA	NM_024098.3	NP_077003.1	Q9H6F5	CCD86_HUMAN	coiled-coil domain containing 86	10					viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(2)|liver(2)|lung(2)|urinary_tract(3)	10						GCAGCCGACGGCTGGGAGGCC	0.642																																					p.R10R		Atlas-SNP	.											.	CCDC86	24	.	0			c.G30T						PASS	.						15	16	15					11																	60609627		2187	4274	6461	SO:0001819	synonymous_variant	79080	exon1			CCGACGGCTGGGA	AK025974	CCDS7993.1	11q12.2	2006-03-16			ENSG00000110104	ENSG00000110104			28359	protein-coding gene	gene with protein product		611293					Standard	NM_024098		Approved	MGC2574	uc001nqa.2	Q9H6F5	OTTHUMG00000167706	ENST00000227520.5:c.30G>T	chr11.hg19:g.60609627G>T		71.0	0.0	.		98.0	18.0	.	NM_024098	B4DY99	Silent	SNP	ENST00000227520.5	hg19	CCDS7993.1																																																																																			.	.	.	none		0.642	CCDC86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395743.1	NM_024098		T	60609627	G	T	60609627	2	4	187	1	0	0	0	0	0	0	0	1	2863	1190	42	4		4	CCDC86	11	60609627	Silent	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10		60609627	74396889	30	10990											
RNASEH2C	84153	hgsc.bcm.edu	37	chr11	65487867	65487867	+	Frame_Shift_Del	DEL	C	C	-																															cctctccccgtagacagcggCcccgaaacgacacttcgagt																								rs554234154		TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr11:65487867delC	ENST00000308418.4	-	2	382	c.194delG	c.(193-195)ggcfs	p.G65fs	RNASEH2C_ENST00000527610.1_Frame_Shift_Del_p.G65fs|RNASEH2C_ENST00000528220.1_5'UTR	NM_032193.3	NP_115569.2	Q8TDP1	RNH2C_HUMAN	ribonuclease H2, subunit C	65					RNA catabolic process (GO:0006401)	nucleus (GO:0005634)|ribonuclease H2 complex (GO:0032299)				cervix(1)	1						TAGACAGCGGCCCCGAAACGA	0.677																																					p.G65fs		Atlas-Indel,Pindel	.											.	RNASEH2C	3	.	0			c.195delC						PASS	.						41	48	46					11																	65487867		2201	4296	6497	SO:0001589	frameshift_variant	84153	exon2			.	AF312034	CCDS8111.1	11q13.1	2014-09-17							24116	protein-coding gene	gene with protein product	"Aicardi-Goutieres syndrome 3"	610330				8244390, 16845400	Standard	NM_032193		Approved	AYP1, AGS3	uc001ofn.3	Q8TDP1		ENST00000308418.4:c.194delG	chr11.hg19:g.65487867delC	ENSP00000308193:p.Gly65fs	67.0	0.0	0		76.0	16.0	0.210526	NM_032193	Q9H7F5	Frame_Shift_Del	DEL	ENST00000308418.4	hg19	CCDS8111.1																																																																																			.	.	.	none		0.677	RNASEH2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390693.2	NM_032193		-	65487867	C	-	65487867	7	5	187	1	0	1	0	1	0	0	0	0	13427	739	26	0	312	0	RNASEH2C	11	65487867	Frame_Shift_Del	DEL	C	TCGA-GL-A4EM-01A-11D-A25F-10	4878240	65487867	69518649	31	10991											
SF3B2	10992	hgsc.bcm.edu	37	chr11	65835416	65835416	+	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	tgatcccattgtccttcgcaGaagtgagacacctcagctct	9	11	8	13	1	2	3	1	2	1	2	5	4	4	3	3	0	1	2	3	0	1	2			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr11:65835416G>T	ENST00000322535.6	+	20	2379		c.e20-1		RP11-1167A19.2_ENST00000529036.1_Intron|SF3B2_ENST00000528302.1_Splice_Site|PACS1_ENST00000320580.4_5'Flank	NM_006842.2	NP_006833.2	Q13435	SF3B2_HUMAN	splicing factor 3b, subunit 2, 145kDa						gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	41						GTCCTTCGCAGAAGTGAGACA	0.522											OREG0021094	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-SNP	.											.	SF3B2	85	.	0			c.2331-1G>T						PASS	.						128	127	127					11																	65835416		2201	4295	6496	SO:0001630	splice_region_variant	10992	exon20			TTCGCAGAAGTGA	U41371	CCDS31612.1	11q13	2010-07-21	2002-08-29		ENSG00000087365	ENSG00000087365			10769	protein-coding gene	gene with protein product		605591	"splicing factor 3b, subunit 2, 145kD"			8566756	Standard	XM_005273726		Approved	SAP145, SF3b1, Cus1, SF3b145	uc001ogy.1	Q13435	OTTHUMG00000166751	ENST00000322535.6:c.2331-1G>T	chr11.hg19:g.65835416G>T		94.0	0.0	.	1087	92.0	4.0	.	NM_006842	A8K485|B4DT19|Q7L4T5|Q7Z627|Q969K1|Q96CM6|Q9BWD2	Splice_Site	SNP	ENST00000322535.6	hg19	CCDS31612.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.076483	0.76415	.	.	ENSG00000087365	ENST00000528302;ENST00000322535;ENST00000355456	.	.	.	5.76	5.76	0.90799	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.4726	0.87650	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SF3B2	65591992	1.000000	0.71417	1.000000	0.80357	0.752000	0.42762	9.236000	0.95360	2.719000	0.93026	0.555000	0.69702	.	.	.	.	none		0.522	SF3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391352.2		Intron	T	65835416	G	T	65835416	5	4	187	1	0	0	0	0	0	0	1	0	14164	956	33	4	2408	4	SF3B2	11	65835416	Splice_Site	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	347549	65835416	69171100	32	10992											
PANX1	24145	hgsc.bcm.edu	37	chr11	93911576	93911576	+	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	ctctttgcgatcctcctgtaCctgcccccgctgttctggcg	2	13	9	17	3	2	0	0	0	2	0	4	1	4	0	5	1	3	3	5	1	1	3			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr11:93911576C>G	ENST00000227638.3	+	3	748	c.363C>G	c.(361-363)taC>taG	p.Y121*	PANX1_ENST00000436171.2_Nonsense_Mutation_p.Y121*	NM_015368.3	NP_056183.2	Q96RD7	PANX1_HUMAN	pannexin 1	121					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)	TCCTCCTGTACCTGCCCCCGC	0.463																																					p.Y121X		Atlas-SNP	.											.	PANX1	38	.	0			c.C363G						PASS	.						167	127	141					11																	93911576		2201	4298	6499	SO:0001587	stop_gained	24145	exon3			CCTGTACCTGCCC	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.363C>G	chr11.hg19:g.93911576C>G	ENSP00000227638:p.Tyr121*	191.0	0.0	.		184.0	41.0	.	NM_015368	O75968|Q543A0|Q6UW26|Q96AM9|Q96L77|Q96RS5	Nonsense_Mutation	SNP	ENST00000227638.3	hg19	CCDS8296.1	.	.	.	.	.	.	.	.	.	.	C	38	6.963806	0.97967	.	.	ENSG00000110218	ENST00000227638;ENST00000436171	.	.	.	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-27.6852	13.9642	0.64199	0.0:0.9245:0.0:0.0755	.	.	.	.	X	121	.	ENSP00000227638:Y121X	Y	+	3	2	PANX1	93551224	1.000000	0.71417	1.000000	0.80357	0.682000	0.39822	0.922000	0.28734	2.402000	0.81655	0.563000	0.77884	TAC	.	.	.	none		0.463	PANX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396121.1	NM_015368		G	93911576	C	G	93911576	4	3	187	1	0	0	0	0	0	1	0	0	11427	518	18	4	373	4	PANX1	11	93911576	Nonsense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	28076160	93911576	41094940	33	10993											
LPCAT3	10162	hgsc.bcm.edu	37	chr12	7125633	7125633	+	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	tctgacgcgcccagggacgtCgccaacttgttaaggctcag	8	8	12	13	4	2	1	1	1	1	0	3	2	2	2	2	2	1	2	2	2	2	2			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr12:7125633C>T	ENST00000261407.4	-	1	181	c.96G>A	c.(94-96)gcG>gcA	p.A32A	C1S_ENST00000406697.1_Intron	NM_005768.5	NP_005759.4	Q6P1A2	MBOA5_HUMAN	lysophosphatidylcholine acyltransferase 3	32					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|regulation of plasma lipoprotein particle levels (GO:0097006)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(2)	17						CCAGGGACGTCGCCAACTTGT	0.662																																					p.A32A		Atlas-SNP	.											.	LPCAT3	33	.	0			c.G96A						PASS	.						49	48	49					12																	7125633		2202	4299	6501	SO:0001819	synonymous_variant	10162	exon1			GGACGTCGCCAAC	U72515	CCDS8572.1	12p13.31	2010-05-12	2008-06-24	2008-06-24	ENSG00000111684	ENSG00000111684			30244	protein-coding gene	gene with protein product		611950	"O-acyltransferase (membrane bound) domain containing 5", "membrane bound O-acyltransferase domain containing 5"	OACT5, MBOAT5		8723724, 9074930, 18195019	Standard	NM_005768		Approved	C3F, nessy	uc001qsi.3	Q6P1A2	OTTHUMG00000168970	ENST00000261407.4:c.96G>A	chr12.hg19:g.7125633C>T		122.0	0.0	.		143.0	39.0	.	NM_005768	B2RDH0|B7Z3N3|Q7KZS1|Q92980|Q9BW40	Silent	SNP	ENST00000261407.4	hg19	CCDS8572.1																																																																																			.	.	.	none		0.662	LPCAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401812.1	NM_005768		T	7125633	C	T	7125633	2	4	187	1	0	0	0	0	0	0	0	1	8919	871	31	1		1	LPCAT3	12	7125633	Silent	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10		7125633	126726262	34	10994											
SCN8A	6334	hgsc.bcm.edu	37	chr12	52188171	52188171	+	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	ccagaacaaaatccaaggaaTcgtctttgattttgtcactc	13	12	6	10	1	2	2	1	1	1	1	5	3	3	3	2	1	1	0	2	1	5	3			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr12:52188171T>A	ENST00000354534.6	+	26	4719	c.4541T>A	c.(4540-4542)aTc>aAc	p.I1514N	SCN8A_ENST00000545061.1_Missense_Mutation_p.I1473N	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit	1514					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)	ATCCAAGGAATCGTCTTTGAT	0.428																																					p.I1514N		Atlas-SNP	.											.	SCN8A	331	.	0			c.T4541A						PASS	.						132	127	129					12																	52188171		1982	4186	6168	SO:0001583	missense	6334	exon26			AAGGAATCGTCTT	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.4541T>A	chr12.hg19:g.52188171T>A	ENSP00000346534:p.Ile1514Asn	82.0	0.0	.		72.0	25.0	.	NM_014191	B9VWG8|O95788|Q9NYX2|Q9UPB2	Missense_Mutation	SNP	ENST00000354534.6	hg19	CCDS44891.1	.	.	.	.	.	.	.	.	.	.	t	11.59	1.684148	0.29872	.	.	ENSG00000196876	ENST00000354534;ENST00000545061;ENST00000355133	D;D;D	0.96073	-3.9;-3.87;-3.75	4.96	4.96	0.65561	.	0.387189	0.31821	N	0.007009	D	0.92051	0.7481	L	0.60455	1.87	0.23050	N	0.998375	B	0.06786	0.001	B	0.01281	0.0	D	0.83764	0.0216	10	0.66056	D	0.02	.	3.8457	0.08934	0.0:0.1628:0.1988:0.6384	.	1514	Q9UQD0	SCN8A_HUMAN	N	1514;1473;1473	ENSP00000346534:I1514N;ENSP00000440360:I1473N;ENSP00000347255:I1473N	ENSP00000346534:I1514N	I	+	2	0	SCN8A	50474438	0.009000	0.17119	0.680000	0.29994	0.997000	0.91878	1.516000	0.35856	2.228000	0.72767	0.524000	0.50904	ATC	.	.	.	none		0.428	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404372.3	NM_014191		A	52188171	T	A	52188171	3	1	187	1	0	0	0	0	1	0	0	0	13937	1435	50	5	4639	5	SCN8A	12	52188171	Missense_Mutation	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10	45062538	52188171	81663724	35	10995											
KRT84	3890	hgsc.bcm.edu	37	chr12	52779218	52779218	+	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	aggtgatgacactccgactaCcaaagctgccaaggccccgg	11	5	11	14	2	0	2	0	2	0	0	1	3	1	2	5	3	3	1	5	3	3	1	rs148258545		TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr12:52779218C>G	ENST00000257951.3	-	1	218	c.152G>C	c.(151-153)gGt>gCt	p.G51A	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	51	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)		ACTCCGACTACCAAAGCTGCC	0.582																																					p.G51A		Atlas-SNP	.											.	KRT84	61	.	0			c.G152C						PASS	.						75	80	78					12																	52779218		2203	4300	6503	SO:0001583	missense	3890	exon1			CGACTACCAAAGC	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.152G>C	chr12.hg19:g.52779218C>G	ENSP00000257951:p.Gly51Ala	166.0	0.0	.		164.0	35.0	.	NM_033045	B2RA43|Q6ISB0|Q701L6	Missense_Mutation	SNP	ENST00000257951.3	hg19	CCDS8825.1	.	.	.	.	.	.	.	.	.	.	C	13.89	2.370922	0.42003	.	.	ENSG00000161849	ENST00000257951	D	0.84944	-1.92	5.06	4.15	0.48705	.	0.143814	0.32563	N	0.005926	D	0.87269	0.6135	M	0.86420	2.815	0.34114	D	0.663369	B	0.15141	0.012	B	0.12156	0.007	D	0.89533	0.3787	10	0.66056	D	0.02	.	15.849	0.78912	0.0:0.864:0.136:0.0	.	51	Q9NSB2	KRT84_HUMAN	A	51	ENSP00000257951:G51A	ENSP00000257951:G51A	G	-	2	0	KRT84	51065485	0.946000	0.32159	0.968000	0.41197	0.853000	0.48598	2.037000	0.41174	1.466000	0.48025	0.543000	0.68304	GGT	.	C|1.000;T|0.000	.	alt		0.582	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045		G	52779218	C	G	52779218	3	3	187	1	0	0	0	0	1	0	0	0	8505	507	18	4	1686	4	KRT84	12	52779218	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	591047	52779218	81072677	36	10996											
C12orf29	91298	hgsc.bcm.edu	37	chr12	88442035	88442035	+	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	atcgccatcatcttggcttaTgctggccaattccagatact	9	13	7	12	1	2	1	1	0	1	1	4	1	3	1	3	2	2	2	3	2	3	4			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr12:88442035T>A	ENST00000356891.3	+	7	1017	c.814T>A	c.(814-816)Tgc>Agc	p.C272S		NM_001009894.2	NP_001009894.2	Q8N999	CL029_HUMAN	chromosome 12 open reading frame 29	272					hematopoietic progenitor cell differentiation (GO:0002244)					large_intestine(3)|lung(1)|ovary(1)	5						TCTTGGCTTATGCTGGCCAAT	0.363																																					p.C272S		Atlas-SNP	.											.	C12orf29	18	.	0			c.T814A						PASS	.						126	108	114					12																	88442035		2203	4300	6503	SO:0001583	missense	91298	exon7			GGCTTATGCTGGC	AL137488	CCDS31866.1	12q21.32	2012-05-30			ENSG00000133641	ENSG00000133641			25322	protein-coding gene	gene with protein product						14702039	Standard	NM_001009894		Approved	DKFZp434N2030	uc001tao.3	Q8N999	OTTHUMG00000169870	ENST00000356891.3:c.814T>A	chr12.hg19:g.88442035T>A	ENSP00000349358:p.Cys272Ser	91.0	0.0	.		141.0	41.0	.	NM_001009894	Q569K5|Q6AWA8|Q6PEK5|Q8IYQ5|Q9NT75	Missense_Mutation	SNP	ENST00000356891.3	hg19	CCDS31866.1	.	.	.	.	.	.	.	.	.	.	.	3.780	-0.045871	0.07452	.	.	ENSG00000133641	ENST00000356891	T	0.50001	0.76	5.41	1.98	0.26296	.	0.784752	0.12584	N	0.456148	T	0.27278	0.0669	L	0.34521	1.04	0.26278	N	0.978315	B	0.02656	0.0	B	0.04013	0.001	T	0.32851	-0.9891	10	0.02654	T	1	0.2767	4.1297	0.10143	0.1564:0.353:0.0:0.4906	.	272	Q8N999	CL029_HUMAN	S	272	ENSP00000349358:C272S	ENSP00000349358:C272S	C	+	1	0	C12orf29	86966166	0.225000	0.23685	0.998000	0.56505	0.994000	0.84299	0.223000	0.17719	0.109000	0.17891	0.533000	0.62120	TGC	.	.	.	none		0.363	C12orf29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406335.1	NM_001009894		A	88442035	T	A	88442035	3	1	187	1	0	0	0	0	1	0	0	0	1682	1464	51	5	840	5	C12orf29	12	88442035	Missense_Mutation	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10	35662817	88442035	45409860	37	10997											
RPH3A	22895	hgsc.bcm.edu	37	chr12	113333603	113333603	+	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	agtttttctatgacatcaaaCacagtgacctggcaaagaag	15	10	8	8	0	2	3	1	2	1	1	2	3	2	3	1	1	1	2	1	1	4	3			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr12:113333603C>A	ENST00000389385.4	+	21	2376	c.1879C>A	c.(1879-1881)Cac>Aac	p.H627N	RPH3A_ENST00000548866.1_Missense_Mutation_p.H578N|RPH3A_ENST00000447659.2_Missense_Mutation_p.H578N|RPH3A_ENST00000420983.2_Missense_Mutation_p.H627N|RPH3A_ENST00000543106.2_Missense_Mutation_p.H627N|RPH3A_ENST00000549913.2_3'UTR|RPH3A_ENST00000551052.1_Missense_Mutation_p.H623N|RPH3A_ENST00000415485.3_Missense_Mutation_p.H627N	NM_001143854.1|NM_014954.3	NP_001137326.1|NP_055769.2	Q9Y2J0	RP3A_HUMAN	rabphilin 3A	627	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				intracellular protein transport (GO:0006886)	cell junction (GO:0030054)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylinositol phosphate binding (GO:1901981)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)|ovary(3)|prostate(4)|skin(6)|urinary_tract(1)	47				BRCA - Breast invasive adenocarcinoma(302;0.00453)		TGACATCAAACACAGTGACCT	0.473																																					p.H627N		Atlas-SNP	.											.	RPH3A	98	.	0			c.C1879A						PASS	.						97	78	84					12																	113333603		2203	4300	6503	SO:0001583	missense	22895	exon21			ATCAAACACAGTG	AB023202	CCDS31904.1, CCDS44979.1	12q24.13	2014-07-02	2014-07-02		ENSG00000089169	ENSG00000089169		"Synaptotagmins"	17056	protein-coding gene	gene with protein product		612159	"rabphilin 3A homolog (mouse)"			10231032, 7822236	Standard	NM_014954		Approved	KIAA0985, rabphilin, exophilin-1	uc001ttz.3	Q9Y2J0	OTTHUMG00000169713	ENST00000389385.4:c.1879C>A	chr12.hg19:g.113333603C>A	ENSP00000374036:p.His627Asn	96.0	0.0	.		101.0	11.0	.	NM_001143854	B7Z3C3|Q96AE0	Missense_Mutation	SNP	ENST00000389385.4	hg19	CCDS44979.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.599097	0.87055	.	.	ENSG00000089169	ENST00000543106;ENST00000389385;ENST00000447659;ENST00000551052;ENST00000415485;ENST00000548866;ENST00000420983;ENST00000549913	T;T;T;T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34;-0.34;-0.34;-0.34	5.42	5.42	0.78866	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);Synaptotagmin (1);	0.000000	0.64402	D	0.000007	T	0.70684	0.3252	N	0.19112	0.55	0.80722	D	1	D;D;D	0.89917	1.0;0.995;0.997	D;D;D	0.77004	0.989;0.972;0.977	T	0.68637	-0.5356	10	0.27785	T	0.31	.	18.006	0.89209	0.0:1.0:0.0:0.0	.	578;627;623	F8VP47;Q9Y2J0;Q9Y2J0-2	.;RP3A_HUMAN;.	N	627;627;578;623;627;578;627;279	ENSP00000440384:H627N;ENSP00000374036:H627N;ENSP00000413254:H578N;ENSP00000448297:H623N;ENSP00000405357:H627N;ENSP00000450347:H578N;ENSP00000408889:H627N	ENSP00000374036:H627N	H	+	1	0	RPH3A	111817986	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	5.703000	0.68340	2.550000	0.86006	0.655000	0.94253	CAC	.	.	.	none		0.473	RPH3A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405561.1	NM_014954		A	113333603	C	A	113333603	3	1	187	1	0	0	0	0	1	0	0	0	13564	478	17	4	1953	4	RPH3A	12	113333603	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	24891568	113333603	20518292	38	10998											
FREM2	341640	hgsc.bcm.edu	37	chr13	39262352	39262352	+	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	tggagctgcgttcacgagggGctcctgtgggcagccctgct	4	9	16	12	2	1	0	1	0	0	0	2	2	2	1	2	4	4	5	2	4	0	1			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr13:39262352G>C	ENST00000280481.7	+	1	1087	c.871G>C	c.(871-873)Gct>Cct	p.A291P		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	291					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)		TTCACGAGGGGCTCCTGTGGG	0.617																																					p.A291P		Atlas-SNP	.											.	FREM2	385	.	0			c.G871C						PASS	.						57	56	56					13																	39262352		2203	4300	6503	SO:0001583	missense	341640	exon1			CGAGGGGCTCCTG	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.871G>C	chr13.hg19:g.39262352G>C	ENSP00000280481:p.Ala291Pro	116.0	0.0	.		107.0	22.0	.	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	hg19	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	G	12.34	1.909632	0.33721	.	.	ENSG00000150893	ENST00000280481	T	0.19532	2.14	5.93	0.756	0.18421	.	0.690381	0.13204	N	0.405691	T	0.16685	0.0401	L	0.39898	1.24	0.22675	N	0.998866	B	0.10296	0.003	B	0.10450	0.005	T	0.21655	-1.0239	10	0.62326	D	0.03	.	8.0541	0.30596	0.138:0.0:0.6112:0.2508	.	291	Q5SZK8	FREM2_HUMAN	P	291	ENSP00000280481:A291P	ENSP00000280481:A291P	A	+	1	0	FREM2	38160352	0.752000	0.28338	0.027000	0.17364	0.945000	0.59286	1.457000	0.35212	-0.207000	0.10187	0.555000	0.69702	GCT	.	.	.	none		0.617	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		C	39262352	G	C	39262352	3	2	187	1	0	0	0	0	1	0	0	0	6052	1203	42	4	873	4	FREM2	13	39262352	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10		39262352	75907526	39	10999											
RAB15	376267	hgsc.bcm.edu	37	chr14	65418357	65418362	+	In_Frame_Del	DEL	GTATCT	GTATCT	-																															tactgctttgtgatggtctgGtatctctcctgccctgcagt																										TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	GTATCT	GTATCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr14:65418357_65418362delGTATCT	ENST00000533601.2	-	3	542_547	c.205_210delAGATAC	c.(205-210)agatacdel	p.RY69del	CHURC1-FNTB_ENST00000549987.1_Intron|RAB15_ENST00000267512.5_In_Frame_Del_p.RY69del|FNTB_ENST00000542227.1_Intron|FNTB_ENST00000447296.2_Intron|RAB15_ENST00000426039.3_In_Frame_Del_p.RY23del|RAB15_ENST00000436278.2_In_Frame_Del_p.RY23del			P59190	RAB15_HUMAN	RAB15, member RAS oncogene family	69					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	GTP binding (GO:0005525)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)	8				all cancers(60;0.00136)|OV - Ovarian serous cystadenocarcinoma(108;0.00593)|BRCA - Breast invasive adenocarcinoma(234;0.0102)		TGATGGTCTGGTATCTCTCCTGCCCT	0.592																																					p.69_71del		Atlas-Indel,Pindel	.											.	RAB15	23	.	0			c.206_211del						PASS	.																																			SO:0001651	inframe_deletion	376267	exon3			.	BC014511	CCDS9768.1	14q23.2	2012-02-28	2012-02-28		ENSG00000139998	ENSG00000139998		"RAB, member RAS oncogene"	20150	protein-coding gene	gene with protein product						11697911	Standard	NM_198686		Approved		uc001xhz.2	P59190	OTTHUMG00000142810	ENST00000533601.2:c.205_210delAGATAC	chr14.hg19:g.65418357_65418362delGTATCT	ENSP00000434103:p.Arg69_Tyr70del	189.0	0.0	0		148.0	19.0	0.128378	NM_198686	G5EMR7|Q86TX7|Q8IW89	In_Frame_Del	DEL	ENST00000533601.2	hg19																																																																																				.	.	.	none		0.592	RAB15-003	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000390443.2	NM_198686		-	65418362	GTATCT	-	65418357	7	5	187	1	0	1	0	1	0	0	0	0	12914	1256	44	0	436	0	RAB15	14	65418357	In_Frame_Del	DEL	GTATCT	TCGA-GL-A4EM-01A-11D-A25F-10		65418357	41931183	40	11000											
PLEKHH1	57475	hgsc.bcm.edu	37	chr14	68038953	68038953	+	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	agcctgagcacaaactgcagCgcacctcatcctactccacc	11	6	6	18	1	1	1	1	1	0	0	3	1	3	1	5	0	6	3	5	0	2	1			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr14:68038953C>A	ENST00000329153.5	+	11	1819	c.1687C>A	c.(1687-1689)Cgc>Agc	p.R563S		NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	563						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)		CAAACTGCAGCGCACCTCATC	0.662																																					p.R563S		Atlas-SNP	.											.	PLEKHH1	118	.	0			c.C1687A						PASS	.						29	32	31					14																	68038953		2079	4209	6288	SO:0001583	missense	57475	exon11			CTGCAGCGCACCT	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.1687C>A	chr14.hg19:g.68038953C>A	ENSP00000330278:p.Arg563Ser	29.0	0.0	.		37.0	10.0	.	NM_020715	A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	ENST00000329153.5	hg19	CCDS45128.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.966478	0.74131	.	.	ENSG00000054690	ENST00000329153	T	0.73789	-0.78	4.61	3.68	0.42216	.	0.000000	0.85682	D	0.000000	T	0.79650	0.4482	M	0.64997	1.995	0.80722	D	1	P;D	0.61080	0.911;0.989	P;P	0.60012	0.486;0.867	T	0.76963	-0.2764	10	0.30854	T	0.27	.	11.6328	0.51185	0.2994:0.7006:0.0:0.0	.	78;563	Q9ULM0-2;Q9ULM0	.;PKHH1_HUMAN	S	563	ENSP00000330278:R563S	ENSP00000330278:R563S	R	+	1	0	PLEKHH1	67108706	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.483000	0.45233	2.387000	0.81309	0.555000	0.69702	CGC	.	.	.	none		0.662	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054		A	68038953	C	A	68038953	3	1	187	1	0	0	0	0	1	0	0	0	12083	768	27	4	1725	4	PLEKHH1	14	68038953	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	2620596	68038953	39310587	41	11001											
EML5	161436	hgsc.bcm.edu	37	chr14	89105224	89105224	+	Missense_Mutation	SNP	T	T	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	tgaggcacagaatatcatcaTtatgttcctgataaaaactc	15	12	6	8	0	2	3	2	2	0	1	4	3	3	3	1	1	1	2	1	1	6	4			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr14:89105224T>G	ENST00000380664.5	-	30	4240	c.4241A>C	c.(4240-4242)aAt>aCt	p.N1414T	EML5_ENST00000352093.5_Missense_Mutation_p.N1376T|EML5_ENST00000554922.1_Missense_Mutation_p.N1422T			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	1414						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						AATATCATCATTATGTTCCTG	0.333																																					p.N1422T		Atlas-SNP	.											.	EML5	141	.	0			c.A4265C						PASS	.						81	71	74					14																	89105224		1809	4079	5888	SO:0001583	missense	161436	exon31			TCATCATTATGTT	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.4241A>C	chr14.hg19:g.89105224T>G	ENSP00000370039:p.Asn1414Thr	50.0	0.0	.		72.0	12.0	.	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	hg19	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	T	2.398	-0.338242	0.05278	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.04234	3.67;3.67;3.67	5.38	3.04	0.35103	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.114168	0.64402	D	0.000016	T	0.01029	0.0034	N	0.00332	-1.63	0.31575	N	0.655785	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.38112	-0.9676	10	0.02654	T	1	-24.3174	5.3744	0.16156	0.0:0.1523:0.1491:0.6985	.	1422;1414	Q05BV3-5;Q05BV3	.;EMAL5_HUMAN	T	1422;1376;1414	ENSP00000451998:N1422T;ENSP00000298315:N1376T;ENSP00000370039:N1414T	ENSP00000298315:N1376T	N	-	2	0	EML5	88174977	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.975000	0.40569	0.884000	0.36064	0.482000	0.46254	AAT	.	.	.	none		0.333	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			G	89105224	T	G	89105224	3	3	187	1	0	0	0	0	1	0	0	0	5102	1493	52	5	1720	5	EML5	14	89105224	Missense_Mutation	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10	21066271	89105224	18244316	42	11002											
WDR20	91833	hgsc.bcm.edu	37	chr14	102689211	102689211	+	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	gccagttctccaggtggaacTgtagtgtagcgacctcactg	8	10	12	11	1	2	0	1	0	1	0	3	2	2	1	3	2	2	3	3	2	3	3			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr14:102689211T>A	ENST00000335263.5	+	4	1817	c.1737T>A	c.(1735-1737)acT>acA	p.T579T	WDR20_ENST00000556807.1_Silent_p.T518T	NM_181291.2	NP_851808.1	Q8TBZ3	WDR20_HUMAN	WD repeat domain 20	0										breast(1)|large_intestine(2)|lung(4)|prostate(1)	8						CAGGTGGAACTGTAGTGTAGC	0.602																																					p.T579T		Atlas-SNP	.											.	WDR20	35	.	0			c.T1737A						PASS	.						148	116	126					14																	102689211		2203	4300	6503	SO:0001819	synonymous_variant	91833	exon4			TGGAACTGTAGTG	BC028387	CCDS9968.1, CCDS9969.1, CCDS9970.1, CCDS55942.1, CCDS55943.1, CCDS55944.1, CCDS55945.1	14q32.31	2013-01-09				ENSG00000140153		"WD repeat domain containing"	19667	protein-coding gene	gene with protein product							Standard	NM_181291		Approved	DMR, MGC33177, FLJ33659	uc010txu.2	Q8TBZ3		ENST00000335263.5:c.1737T>A	chr14.hg19:g.102689211T>A		221.0	0.0	.		232.0	42.0	.	NM_181291	B4DN18|E7EUY8|F8W9S4|G3V2F8|G3V5R0|H0YJJ1|Q86TU2|Q8NCN7|Q8WXX2|Q9UF86	Silent	SNP	ENST00000335263.5	hg19	CCDS9968.1																																																																																			.	.	.	none		0.602	WDR20-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414960.1	NM_181291		A	102689211	T	A	102689211	2	1	187	1	0	0	0	0	0	0	0	1	17292	1567	55	5		5	WDR20	14	102689211	Silent	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10	13583987	102689211	4660329	43	11003											
BAHD1	22893	hgsc.bcm.edu	37	chr15	40751142	40751142	+	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	cagccgtgaccgtgatcgtgCtactgggggctggtcctcct	4	10	14	13	3	0	2	0	2	0	0	3	2	2	2	4	3	3	2	4	3	1	1			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr15:40751142C>A	ENST00000416165.1	+	2	550	c.479C>A	c.(478-480)gCt>gAt	p.A160D	BAHD1_ENST00000561234.1_Missense_Mutation_p.A160D|BAHD1_ENST00000560846.1_Missense_Mutation_p.A160D	NM_014952.3	NP_055767.3	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1	160					heterochromatin assembly (GO:0031507)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|chromosome (GO:0005694)	chromatin binding (GO:0003682)			NS(1)|endometrium(6)|kidney(3)|large_intestine(3)|lung(10)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	28		all_cancers(109;8.28e-19)|all_epithelial(112;2.64e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.46e-06)|BRCA - Breast invasive adenocarcinoma(123;0.08)		CGTGATCGTGCTACTGGGGGC	0.672																																					p.A160D		Atlas-SNP	.											.	BAHD1	68	.	0			c.C479A						PASS	.						22	29	26					15																	40751142		2197	4296	6493	SO:0001583	missense	22893	exon2			ATCGTGCTACTGG	AL833923	CCDS10058.1, CCDS73705.1	15q14	2005-11-10			ENSG00000140320	ENSG00000140320			29153	protein-coding gene	gene with protein product		613880				10231032	Standard	XM_005254229		Approved	KIAA0945	uc001zlu.2	Q8TBE0	OTTHUMG00000129982	ENST00000416165.1:c.479C>A	chr15.hg19:g.40751142C>A	ENSP00000396976:p.Ala160Asp	26.0	0.0	.		44.0	10.0	.	NM_014952	Q8NDF7|Q9Y2F4	Missense_Mutation	SNP	ENST00000416165.1	hg19	CCDS10058.1	.	.	.	.	.	.	.	.	.	.	C	9.014	0.983230	0.18889	.	.	ENSG00000140320	ENST00000416165	T	0.18338	2.22	5.11	0.82	0.18793	.	0.394096	0.23881	N	0.043645	T	0.09291	0.0229	N	0.08118	0	0.09310	N	1	P;B;P	0.36909	0.573;0.437;0.573	B;B;B	0.41894	0.369;0.203;0.369	T	0.26121	-1.0112	10	0.36615	T	0.2	-3.895	7.9432	0.29971	0.0:0.6539:0.1214:0.2247	.	160;160;160	Q8TBE0-3;Q8TBE0;Q8TBE0-2	.;BAHD1_HUMAN;.	D	160	ENSP00000396976:A160D	ENSP00000396976:A160D	A	+	2	0	BAHD1	38538434	0.840000	0.29493	0.037000	0.18230	0.004000	0.04260	1.548000	0.36201	0.311000	0.23014	-0.182000	0.12963	GCT	.	.	.	none		0.672	BAHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252248.1	NM_014952		A	40751142	C	A	40751142	3	1	187	1	0	0	0	0	1	0	0	0	1297	797	28	4	481	4	BAHD1	15	40751142	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10		40751142	61780250	44	11004											
UBR1	197131	hgsc.bcm.edu	37	chr15	43378432	43378432	+	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	ataaaaatcaacttgctgatCccaccactaaaagaaaagaa	21	7	4	9	0	1	3	1	1	0	2	2	3	2	3	2	0	2	1	2	0	9	3			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr15:43378432C>T	ENST00000290650.4	-	2	166	c.88G>A	c.(88-90)Gat>Aat	p.D30N	UBR1_ENST00000382177.2_Missense_Mutation_p.D30N	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	30					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)		ACTTGCTGATCCCACCACTAA	0.358																																					p.D30N		Atlas-SNP	.											.	UBR1	124	.	0			c.G88A						PASS	.						47	50	49					15																	43378432		2203	4299	6502	SO:0001583	missense	197131	exon2			GCTGATCCCACCA		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.88G>A	chr15.hg19:g.43378432C>T	ENSP00000290650:p.Asp30Asn	37.0	0.0	.		30.0	6.0	.	NM_174916	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	hg19	CCDS10091.1	.	.	.	.	.	.	.	.	.	.	C	10.76	1.442186	0.25987	.	.	ENSG00000159459	ENST00000290650;ENST00000382177;ENST00000546274	T;T	0.70045	0.39;-0.45	5.41	3.39	0.38822	.	0.425163	0.24730	N	0.036070	T	0.42539	0.1207	N	0.08118	0	0.32678	N	0.515941	B;P	0.35433	0.147;0.501	B;B	0.25140	0.045;0.058	T	0.48958	-0.8988	10	0.17832	T	0.49	-13.2485	17.5354	0.87829	0.0:0.7515:0.2485:0.0	.	30;30	B4DYL2;Q8IWV7	.;UBR1_HUMAN	N	30	ENSP00000290650:D30N;ENSP00000371612:D30N	ENSP00000290650:D30N	D	-	1	0	UBR1	41165724	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	1.711000	0.37930	1.277000	0.44412	0.561000	0.74099	GAT	.	.	.	none		0.358	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916		T	43378432	C	T	43378432	3	4	187	1	0	0	0	0	1	0	0	0	16913	855	30	2	5345	2	UBR1	15	43378432	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	2627290	43378432	59152960	45	11005											
NEDD4	4734	hgsc.bcm.edu	37	chr15	56207639	56207639	+	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	tggatagacaggaaatatttGgataagctcctcccaatgaa	15	10	9	7	0	0	2	0	1	0	1	2	5	2	5	2	3	1	1	2	3	6	4	rs543656596		TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr15:56207639G>T	ENST00000508342.1	-	1	1690	c.1391C>A	c.(1390-1392)cCa>cAa	p.P464Q	NEDD4_ENST00000435532.3_Intron|NEDD4_ENST00000338963.2_Missense_Mutation_p.P464Q|NEDD4_ENST00000506154.1_Missense_Mutation_p.P464Q	NM_001284338.1	NP_001271267.1	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	464					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)		GGAAATATTTGGATAAGCTCC	0.363																																					p.P464Q		Atlas-SNP	.											.	NEDD4	167	.	0			c.C1391A						PASS	.						135	137	136					15																	56207639		2193	4292	6485	SO:0001583	missense	4734	exon1			ATATTTGGATAAG	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.1391C>A	chr15.hg19:g.56207639G>T	ENSP00000424827:p.Pro464Gln	107.0	0.0	.		98.0	4.0	.	NM_198400	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Missense_Mutation	SNP	ENST00000508342.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.98|16.98	3.271215|3.271215	0.59649|0.59649	.|.	.|.	ENSG00000069869|ENSG00000069869	ENST00000508342;ENST00000338963;ENST00000506154|ENST00000508871	T;T;T|.	0.18338|.	2.25;2.22;2.25|.	5.46|5.46	4.48|4.48	0.54585|0.54585	.|.	7.228800|.	0.02135|.	U|.	0.056683|.	T|T	0.41143|0.41143	0.1146|0.1146	L|L	0.39633|0.39633	1.23|1.23	0.25741|0.25741	N|N	0.98517|0.98517	B;B;B|.	0.19331|.	0.035;0.02;0.035|.	B;B;B|.	0.20767|.	0.031;0.014;0.031|.	T|T	0.22695|0.22695	-1.0209|-1.0209	10|5	0.34782|.	T|.	0.22|.	.|.	11.2909|11.2909	0.49250|0.49250	0.0:0.0:0.6725:0.3275|0.0:0.0:0.6725:0.3275	.|.	464;464;464|.	P46934-2;P46934;P46934-3|.	.;NEDD4_HUMAN;.|.	Q|K	464|72	ENSP00000424827:P464Q;ENSP00000345530:P464Q;ENSP00000422705:P464Q|.	ENSP00000345530:P464Q|.	P|Q	-|-	2|1	0|0	NEDD4|NEDD4	53994931|53994931	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	3.131000|3.131000	0.50515|0.50515	2.580000|2.580000	0.87095|0.87095	0.460000|0.460000	0.39030|0.39030	CCA|CAA	.	.	.	none		0.363	NEDD4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000359817.1	NM_198400		T	56207639	G	T	56207639	3	4	187	1	0	0	0	0	1	0	0	0	10317	1348	47	4	2668	4	NEDD4	15	56207639	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	12829207	56207639	46323753	46	11006											
POLG	5428	hgsc.bcm.edu	37	chr15	89872222	89872222	+	Frame_Shift_Del	DEL	G	G	-																															gacttctggccttgctttgtGgggggctggaccttgtgttt																								rs551973680		TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr15:89872222delG	ENST00000268124.5	-	4	1308	c.975delC	c.(973-975)cccfs	p.P325fs	POLG_ENST00000442287.2_Frame_Shift_Del_p.P325fs	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	325					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)			CTTGCTTTGTGGGGGGCTGGA	0.602								DNA polymerases (catalytic subunits)																													p.T326fs	Colon(73;648 1203 11348 18386 27782)	Atlas-Indel,Pindel	.											.	POLG	75	.	0			c.976delA						PASS	.						91	80	83					15																	89872222		2200	4299	6499	SO:0001589	frameshift_variant	5428	exon4			.	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.975delC	chr15.hg19:g.89872222delG	ENSP00000268124:p.Pro325fs	164.0	0.0	0		149.0	19.0	0.127517	NM_001126131	Q8NFM2|Q92515	Frame_Shift_Del	DEL	ENST00000268124.5	hg19	CCDS10350.1																																																																																			.	.	.	none		0.602	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000312854.2	NM_002693		-	89872222	G	-	89872222	7	5	187	1	0	1	0	1	0	0	0	0	12207	1335	47	0	2824	0	POLG	15	89872222	Frame_Shift_Del	DEL	G	TCGA-GL-A4EM-01A-11D-A25F-10	33664583	89872222	12659170	47	11007											
MMP25	64386	hgsc.bcm.edu	37	chr16	3100091	3100091	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcggggctggtcaggcggcGtcgccggtacgctctgagcg	3	6	20	12	7	2	1	1	1	1	0	3	1	2	1	1	7	2	3	1	7	1	1	rs146181243		TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr16:3100091G>A	ENST00000336577.4	+	3	551	c.314G>A	c.(313-315)cGt>cAt	p.R105H	MMP25_ENST00000570755.1_3'UTR|RP11-473M20.7_ENST00000576250.1_RNA	NM_022468.4	NP_071913.1	Q9H239	MMP28_HUMAN	matrix metallopeptidase 25	120					negative regulation of macrophage chemotaxis (GO:0010760)	cytoplasm (GO:0005737)|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(2)|lung(7)|prostate(1)|skin(1)	14					Marimastat(DB00786)	GTCAGGCGGCGTCGCCGGTAC	0.701																																					p.R105H	NSCLC(147;665 1067 3888 6863 19894 30469 40247 45633 51336)	Atlas-SNP	.											.	MMP25	35	.	0			c.G314A						PASS	.	G	HIS/ARG	1,4393	2.1+/-5.4	0,1,2196	54	59	57		314	5.1	0.1	16	dbSNP_134	57	0,8596		0,0,4298	no	missense	MMP25	NM_022468.4	29	0,1,6494	AA,AG,GG		0.0,0.0228,0.0077	probably-damaging	105/563	3100091	1,12989	2197	4298	6495	SO:0001583	missense	64386	exon3			GGCGGCGTCGCCG	AF145442	CCDS10492.1	16p13.3	2008-02-05	2005-08-08			ENSG00000008516			14246	protein-coding gene	gene with protein product		608482	"matrix metalloproteinase 25", "matrix metallopeptidase-like 1"	MMPL1, MMP20		10628838, 10706098	Standard	NM_022468		Approved	MT6-MMP	uc002cth.3	Q9NPA2		ENST00000336577.4:c.314G>A	chr16.hg19:g.3100091G>A	ENSP00000337816:p.Arg105His	0.0	0.0	.		22.0	9.0	.	NM_022468	Q96F04|Q96TE2	Missense_Mutation	SNP	ENST00000336577.4	hg19	CCDS10492.1	.	.	.	.	.	.	.	.	.	.	G	12.93	2.085309	0.36758	2.28E-4	0.0	ENSG00000008516	ENST00000336577;ENST00000325800	T	0.19105	2.17	5.06	5.06	0.68205	Metallopeptidase, catalytic domain (1);	0.000000	0.34802	U	0.003670	T	0.19725	0.0474	M	0.62088	1.915	0.09310	N	0.999994	P;D	0.57571	0.796;0.98	B;B	0.37833	0.124;0.259	T	0.39820	-0.9595	10	0.72032	D	0.01	.	9.5362	0.39224	0.0975:0.0:0.9025:0.0	.	29;105	O43923;Q9NPA2	.;MMP25_HUMAN	H	105;32	ENSP00000337816:R105H	ENSP00000324953:R32H	R	+	2	0	MMP25	3040092	0.997000	0.39634	0.093000	0.20910	0.166000	0.22503	5.754000	0.68743	2.356000	0.79943	0.655000	0.94253	CGT	.	G|1.000;A|0.000	0.000	weak		0.701	MMP25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437116.1	NM_022468		A	3100091	G	A	3100091	3	1	187	1	0	0	0	0	1	0	0	0	9669	1145	40	1	324	1	MMP25	16	3100091	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10		3100091	87254662	48	11008											
ANKS4B	257629	hgsc.bcm.edu	37	chr16	21245180	21245180	+	Frame_Shift_Del	DEL	A	A	-																															tcctactctcttggcagcctAccatgggaacttggaagccc																										TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr16:21245180delA	ENST00000311620.5	+	1	195	c.122delA	c.(121-123)tacfs	p.Y41fs		NM_145865.2	NP_665872.2	Q8N8V4	ANS4B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 4B	41					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)		TTGGCAGCCTACCATGGGAAC	0.463																																					p.Y41fs		Atlas-Indel,Pindel	.											.	ANKS4B	43	.	0			c.121delT						PASS	.						128	125	126					16																	21245180		1902	4118	6020	SO:0001589	frameshift_variant	257629	exon1			.	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.122delA	chr16.hg19:g.21245180delA	ENSP00000308772:p.Tyr41fs	141.0	0.0	0		144.0	47.0	0.326389	NM_145865		Frame_Shift_Del	DEL	ENST00000311620.5	hg19	CCDS42130.1																																																																																			.	.	.	none		0.463	ANKS4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436535.1	NM_145865		-	21245180	A	-	21245180	7	5	187	1	0	1	0	1	0	0	0	0	691	391	14	0	124	0	ANKS4B	16	21245180	Frame_Shift_Del	DEL	A	TCGA-GL-A4EM-01A-11D-A25F-10	18145089	21245180	69109573	49	11009											
COG8	84342	hgsc.bcm.edu	37	chr16	69368509	69368509	+	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	gcagatcattgaaggcaaccAgaatattgttgagaaagcag	16	8	11	6	0	1	4	1	2	0	3	1	5	1	4	1	1	2	4	1	1	5	4			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr16:69368509A>T	ENST00000306875.4	-	3	1442	c.1328T>A	c.(1327-1329)cTg>cAg	p.L443Q	RP11-343C2.12_ENST00000562949.1_Missense_Mutation_p.L89Q|COG8_ENST00000562081.1_Missense_Mutation_p.L443Q	NM_032382.4	NP_115758.3	Q96MW5	COG8_HUMAN	component of oligomeric golgi complex 8	443					protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|kidney(1)|large_intestine(2)|ovary(2)|skin(1)	9						GAAGGCAACCAGAATATTGTT	0.597																																					p.L443Q		Atlas-SNP	.											.	COG8	32	.	0			c.T1328A						PASS	.						68	65	66					16																	69368509		2198	4300	6498	SO:0001583	missense	84342	exon3			GCAACCAGAATAT	AK025968	CCDS10876.1	16q22.1	2011-05-31			ENSG00000213380	ENSG00000213380		"Components of oligomeric golgi complex"	18623	protein-coding gene	gene with protein product		606979				11980916	Standard	NM_032382		Approved	FLJ22315, DOR1	uc002ewy.2	Q96MW5	OTTHUMG00000154277	ENST00000306875.4:c.1328T>A	chr16.hg19:g.69368509A>T	ENSP00000305459:p.Leu443Gln	167.0	0.0	.		153.0	27.0	.	NM_032382	Q0VAK2|Q8WVV6|Q9H6F8	Missense_Mutation	SNP	ENST00000306875.4	hg19	CCDS10876.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.556094	0.86231	.	.	ENSG00000213380	ENST00000306875	T	0.61859	0.07	5.86	5.86	0.93980	.	0.085303	0.56097	D	0.000029	T	0.73860	0.3641	M	0.74881	2.28	0.80722	D	1	D;D	0.61080	0.989;0.989	P;P	0.61328	0.887;0.887	T	0.76305	-0.3008	10	0.56958	D	0.05	-1.8093	16.2605	0.82541	1.0:0.0:0.0:0.0	.	470;443	B4DYU2;Q96MW5	.;COG8_HUMAN	Q	443	ENSP00000305459:L443Q	ENSP00000305459:L443Q	L	-	2	0	COG8	67926010	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	8.903000	0.92573	2.237000	0.73441	0.460000	0.39030	CTG	.	.	.	none		0.597	COG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268948.2	NM_032382		T	69368509	A	T	69368509	3	4	187	1	0	0	0	0	1	0	0	0	3666	188	7	5	522	5	COG8	16	69368509	Missense_Mutation	SNP	A	TCGA-GL-A4EM-01A-11D-A25F-10	48123329	69368509	20986244	50	11010											
CHRNB1	1140	hgsc.bcm.edu	37	chr17	7350850	7350850	+	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	cttccccttcgactggcagaAttgcactatggtgttcagct	7	13	9	12	1	1	1	1	0	0	1	3	2	2	1	2	2	2	4	2	2	2	5			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr17:7350850A>T	ENST00000306071.2	+	6	558	c.491A>T	c.(490-492)aAt>aTt	p.N164I	RP11-104H15.10_ENST00000575331.1_RNA|CHRNB1_ENST00000576360.1_Missense_Mutation_p.N92I|CHRNB1_ENST00000536404.2_Missense_Mutation_p.N92I	NM_000747.2	NP_000738.2	P11230	ACHB_HUMAN	cholinergic receptor, nicotinic, beta 1 (muscle)	164					behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|neurological system process (GO:0050877)|neuromuscular synaptic transmission (GO:0007274)|postsynaptic membrane organization (GO:0001941)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|ligand-gated ion channel activity (GO:0015276)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|ovary(3)	23		Prostate(122;0.157)			Galantamine(DB00674)	GACTGGCAGAATTGCACTATG	0.567																																					p.N164I		Atlas-SNP	.											.	CHRNB1	46	.	0			c.A491T						PASS	.						126	112	117					17																	7350850		2203	4300	6503	SO:0001583	missense	1140	exon6			GGCAGAATTGCAC	X14830	CCDS11106.1	17p13.1	2012-02-11	2006-02-01		ENSG00000170175	ENSG00000170175		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1961	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 1 (muscle)"	100710	"cholinergic receptor, nicotinic, beta polypeptide 1 (muscle)"	CHRNB			Standard	NM_000747		Approved		uc002ghb.3	P11230	OTTHUMG00000108139	ENST00000306071.2:c.491A>T	chr17.hg19:g.7350850A>T	ENSP00000304290:p.Asn164Ile	171.0	0.0	.		166.0	21.0	.	NM_000747	B7Z5H1|Q8IZ46|Q96FB8	Missense_Mutation	SNP	ENST00000306071.2	hg19	CCDS11106.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.331856	0.81801	.	.	ENSG00000170175	ENST00000306071;ENST00000536404	T;T	0.80480	-1.38;-1.38	4.96	4.96	0.65561	Neurotransmitter-gated ion-channel ligand-binding (3);Neurotransmitter-gated ion-channel, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.86335	0.5908	M	0.69248	2.105	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.86860	0.2029	10	0.87932	D	0	.	7.3997	0.26956	0.9015:0.0:0.0985:0.0	.	164	P11230	ACHB_HUMAN	I	164;92	ENSP00000304290:N164I;ENSP00000439209:N92I	ENSP00000304290:N164I	N	+	2	0	CHRNB1	7291574	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.939000	0.92951	1.863000	0.54032	0.459000	0.35465	AAT	.	.	.	none		0.567	CHRNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226942.3			T	7350850	A	T	7350850	3	4	187	1	0	0	0	0	1	0	0	0	3392	101	4	5	513	5	CHRNB1	17	7350850	Missense_Mutation	SNP	A	TCGA-GL-A4EM-01A-11D-A25F-10		7350850	73844360	51	11011											
AMAC1L3	643664	hgsc.bcm.edu	37	chr17	7386013	7386013	+	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	gctgctgggctctgtgccagGcctctttgtgctgcagcccc	2	11	13	15	0	2	0	0	0	2	0	2	0	2	0	4	2	5	5	4	2	0	1			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr17:7386013G>C	ENST00000412468.2	+	2	825	c.710G>C	c.(709-711)gGc>gCc	p.G237A	POLR2A_ENST00000572844.1_5'Flank|ZBTB4_ENST00000311403.4_Intron|POLR2A_ENST00000322644.6_5'Flank	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	237						integral component of membrane (GO:0016021)											TCTGTGCCAGGCCTCTTTGTG	0.612																																					p.G237A		Atlas-SNP	.											POLR2A_ENST00000412468,NS,carcinoma,0,1	.	.	.	0			c.G710C						PASS	.						52	52	52					17																	7386013		2203	4297	6500	SO:0001583	missense	643664	exon2			TGCCAGGCCTCTT		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.710G>C	chr17.hg19:g.7386013G>C	ENSP00000396523:p.Gly237Ala	158.0	0.0	.		183.0	25.0	.	NM_001102614		Missense_Mutation	SNP	ENST00000412468.2	hg19	CCDS45603.1	.	.	.	.	.	.	.	.	.	.	G	3.103	-0.184272	0.06340	.	.	ENSG00000181222	ENST00000412468	T	0.49720	0.77	4.06	3.07	0.35406	.	.	.	.	.	T	0.21631	0.0521	N	0.08118	0	0.25938	N	0.982908	B	0.09022	0.002	B	0.14578	0.011	T	0.27468	-1.0073	9	0.02654	T	1	-1.8186	7.3041	0.26436	0.0:0.1871:0.6199:0.193	.	237	P0C7Q6	S35G6_HUMAN	A	237	ENSP00000396523:G237A	ENSP00000396523:G237A	G	+	2	0	SLC35G6	7326737	0.975000	0.34042	0.271000	0.24616	0.720000	0.41350	2.298000	0.43602	0.827000	0.34685	0.467000	0.42956	GGC	.	.	.	none		0.612	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614		C	7386013	G	C	7386013	3	2	187	1	0	0	0	0	1	0	0	0	561	1203	42	4	716	4	AMAC1L3	17	7386013	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	35163	7386013	73809197	52	11012											
UTP6	55813	hgsc.bcm.edu	37	chr17	30219812	30219812	+	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	agagccaaagttgaacatcgTcctgcaagaaaagcaatgta	17	7	9	8	1	0	3	0	1	0	2	2	3	1	3	2	0	4	4	2	0	7	2			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr17:30219812T>C	ENST00000261708.4	-	5	451	c.314A>G	c.(313-315)gAc>gGc	p.D105G	UTP6_ENST00000490218.2_5'UTR	NM_018428.2	NP_060898.2	Q9NYH9	UTP6_HUMAN	UTP6, small subunit (SSU) processome component, homolog (yeast)	105					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)				TTGAACATCGTCCTGCAAGAA	0.378																																					p.D105G		Atlas-SNP	.											.	UTP6	46	.	0			c.A314G						PASS	.						116	93	101					17																	30219812		2203	4300	6503	SO:0001630	splice_region_variant	55813	exon5			ACATCGTCCTGCA	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.313-1A>G	chr17.hg19:g.30219812T>C		76.0	0.0	.		76.0	10.0	.	NM_018428	Q8IX96|Q96BL2|Q9NQ91	Missense_Mutation	SNP	ENST00000261708.4	hg19	CCDS11269.1	.	.	.	.	.	.	.	.	.	.	T	13.02	2.111575	0.37242	.	.	ENSG00000108651	ENST00000261708	T	0.36699	1.24	5.44	5.44	0.79542	.	0.233979	0.51477	D	0.000100	T	0.24084	0.0583	N	0.21617	0.685	0.54753	D	0.999983	B;B	0.29766	0.129;0.256	B;B	0.24155	0.021;0.051	T	0.06698	-1.0812	10	0.15952	T	0.53	-22.7625	15.1464	0.72657	0.0:0.0:0.0:1.0	.	105;105	B4DSL9;Q9NYH9	.;UTP6_HUMAN	G	105	ENSP00000261708:D105G	ENSP00000261708:D105G	D	-	2	0	UTP6	27243925	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	3.602000	0.54066	2.057000	0.61298	0.454000	0.30748	GAC	.	.	.	none		0.378	UTP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256265.2	NM_018428	Missense_Mutation	C	30219812	T	C	30219812	5	2	187	1	0	0	0	0	0	0	1	0	17114	1681	58	3	1539	3	UTP6	17	30219812	Splice_Site	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10	22833799	30219812	50975398	53	11013											
CLTC	1213	hgsc.bcm.edu	37	chr17	57760151	57760152	+	Frame_Shift_Del	DEL	AG	AG	-																															aacagtactcgaacatggaaAgaggtaatctaaacccaagt																								rs111452880		TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr17:57760151_57760152delAG	ENST00000269122.3	+	23	4036_4037	c.3762_3763delAG	c.(3760-3765)aaagagfs	p.E1255fs	CLTC_ENST00000393043.1_Frame_Shift_Del_p.E1255fs|CLTC_ENST00000579456.1_Frame_Shift_Del_p.E192fs	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	1255	Heavy chain arm.|Involved in binding clathrin light chain. {ECO:0000250}.|Proximal segment.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					GAACATGGAAAGAGGTAATCTA	0.386			T	"ALK, TFE3"	"ALCL, renal "																																p.1254_1254del		Atlas-Indel,Pindel	.		Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	.	CLTC	124	.	0			c.3761_3762del						PASS	.																																			SO:0001589	frameshift_variant	1213	exon23			.	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.3762_3763delAG	chr17.hg19:g.57760153_57760154delAG	ENSP00000269122:p.Glu1255fs	68.0	0.0	0		90.0	21.0	0.233333	NM_004859	D3DU00|Q6N0A0|Q86TF2	Frame_Shift_Del	DEL	ENST00000269122.3	hg19	CCDS32696.1																																																																																			.	.	.	none		0.386	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859		-	57760152	AG	-	57760151	7	5	187	1	0	1	0	1	0	0	0	0	3568	69	3	0	3852	0	CLTC	17	57760151	Frame_Shift_Del	DEL	AG	TCGA-GL-A4EM-01A-11D-A25F-10	27540339	57760151	23435059	54	11014											
SLC25A19	60386	hgsc.bcm.edu	37	chr17	73273550	73273550	+	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	agctccactgccacaaagcaGgttttggaggttctctgaac	10	10	10	11	0	1	1	0	1	1	0	3	2	2	2	2	3	4	4	2	3	2	3			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr17:73273550G>C	ENST00000402418.3	-	5	1567	c.658C>G	c.(658-660)Ctg>Gtg	p.L220V	SLC25A19_ENST00000320362.3_Missense_Mutation_p.L220V|SLC25A19_ENST00000580994.1_Missense_Mutation_p.L220V|SLC25A19_ENST00000416858.2_Missense_Mutation_p.L220V|SLC25A19_ENST00000375261.4_Missense_Mutation_p.L163V|SLC25A19_ENST00000442286.2_Missense_Mutation_p.L220V			Q9HC21	TPC_HUMAN	solute carrier family 25 (mitochondrial thiamine pyrophosphate carrier), member 19	220					deoxynucleotide transport (GO:0030302)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	deoxynucleotide transmembrane transporter activity (GO:0030233)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9	all_cancers(13;5.98e-08)|all_epithelial(9;1.16e-08)|Breast(9;3.1e-08)		all cancers(21;6.82e-07)|Epithelial(20;6.86e-06)			CCACAAAGCAGGTTTTGGAGG	0.512																																					p.L220V		Atlas-SNP	.											.	SLC25A19	25	.	0			c.C658G						PASS	.						83	75	78					17																	73273550		2203	4300	6503	SO:0001583	missense	60386	exon6			AAAGCAGGTTTTG		CCDS11720.1	17q25.1	2013-05-22	2007-03-08		ENSG00000125454	ENSG00000125454		"Solute carriers"	14409	protein-coding gene	gene with protein product		606521	"solute carrier family 25 (mitochondrial deoxynucleotide carrier), member 19", "microcephaly, Amish"	MCPHA		11474176, 11226231, 19798730	Standard	NM_021734		Approved	DNC, MUP1, TPC	uc002jnw.4	Q9HC21		ENST00000402418.3:c.658C>G	chr17.hg19:g.73273550G>C	ENSP00000385312:p.Leu220Val	104.0	0.0	.		105.0	27.0	.	NM_001126122	E9PF74|Q6V9R7	Missense_Mutation	SNP	ENST00000402418.3	hg19	CCDS11720.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.031943	0.54790	.	.	ENSG00000125454	ENST00000416858;ENST00000442286;ENST00000320362;ENST00000402418;ENST00000375261	D;D;D;D;D	0.81499	-1.5;-1.5;-1.5;-1.5;-1.5	5.35	2.3	0.28687	Mitochondrial carrier domain (2);	0.067029	0.64402	D	0.000011	D	0.82435	0.5036	L	0.45581	1.43	0.45930	D	0.998765	D;P	0.61697	0.99;0.935	P;P	0.62014	0.897;0.513	T	0.81187	-0.1047	10	0.62326	D	0.03	-13.3282	9.0336	0.36273	0.3003:0.0:0.6997:0.0	.	163;220	E9PF74;Q9HC21	.;TPC_HUMAN	V	220;220;220;220;163	ENSP00000397818:L220V;ENSP00000402202:L220V;ENSP00000319574:L220V;ENSP00000385312:L220V;ENSP00000364410:L163V	ENSP00000319574:L220V	L	-	1	2	SLC25A19	70785145	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	4.657000	0.61490	0.648000	0.30732	-0.157000	0.13467	CTG	.	.	.	none		0.512	SLC25A19-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447282.1	NM_021734		C	73273550	G	C	73273550	3	2	187	1	0	0	0	0	1	0	0	0	14494	991	35	4	312	4	SLC25A19	17	73273550	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10	15513399	73273550	7921660	55	11015											
RNF213	57674	hgsc.bcm.edu	37	chr17	78321624	78321624	+	Frame_Shift_Del	DEL	C	C	-																															gtgtacaaacactttcccatCcccctcattaaccggctgga																										TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr17:78321624delC	ENST00000582970.1	+	29	9632	c.9489delC	c.(9487-9489)atcfs	p.I3163fs	RNF213_ENST00000336301.6_Frame_Shift_Del_p.I1236fs|RNF213_ENST00000508628.2_Frame_Shift_Del_p.I3212fs	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3163					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)			ACTTTCCCATCCCCCTCATTA	0.542																																					p.I3163fs		Atlas-Indel,Pindel	.											.	RNF213	766	.	0			c.9488delT						PASS	.						67	62	63					17																	78321624		2203	4300	6503	SO:0001589	frameshift_variant	57674	exon29			.	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.9489delC	chr17.hg19:g.78321624delC	ENSP00000464087:p.Ile3163fs	153.0	0.0	0		180.0	48.0	0.266667	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Frame_Shift_Del	DEL	ENST00000582970.1	hg19	CCDS58606.1																																																																																			.	.	.	none		0.542	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		-	78321624	C	-	78321624	7	5	187	1	0	1	0	1	0	0	0	0	13490	845	30	0	9918	0	RNF213	17	78321624	Frame_Shift_Del	DEL	C	TCGA-GL-A4EM-01A-11D-A25F-10	5048074	78321624	2873586	56	11016											
CC2D1A	54862	hgsc.bcm.edu	37	chr19	14028999	14028999	+	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	ctgccgctagacacttccgcGtggctaaggtgcgtccagcc	6	8	12	15	4	0	1	0	0	0	1	2	1	2	1	4	2	3	2	4	2	2	3	rs368763604		TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr19:14028999G>T	ENST00000318003.7	+	7	1106	c.865G>T	c.(865-867)Gtg>Ttg	p.V289L	CC2D1A_ENST00000589606.1_Missense_Mutation_p.V289L	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	289	Pro-rich.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			ACACTTCCGCGTGGCTAAGGT	0.632																																					p.V289L		Atlas-SNP	.											.	CC2D1A	67	.	0			c.G865T						PASS	.						9	11	10					19																	14028999		2035	4174	6209	SO:0001583	missense	54862	exon7			TTCCGCGTGGCTA	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.865G>T	chr19.hg19:g.14028999G>T	ENSP00000313601:p.Val289Leu	67.0	0.0	.		156.0	32.0	.	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Missense_Mutation	SNP	ENST00000318003.7	hg19	CCDS42512.1	.	.	.	.	.	.	.	.	.	.	G	11.85	1.760509	0.31137	.	.	ENSG00000132024	ENST00000318003;ENST00000397486	T	0.23147	1.92	5.38	4.32	0.51571	Domain of unknown function DM14 (1);	0.244121	0.35291	N	0.003314	T	0.20007	0.0481	L	0.47716	1.5	0.34644	D	0.72099	P;B;P	0.43909	0.543;0.33;0.821	B;B;B	0.36719	0.198;0.126;0.231	T	0.30679	-0.9970	10	0.30854	T	0.27	-20.8199	10.4966	0.44780	0.0918:0.0:0.9082:0.0	.	289;289;43	Q6P1N0-2;Q6P1N0;C9J1T8	.;C2D1A_HUMAN;.	L	289;43	ENSP00000313601:V289L	ENSP00000313601:V289L	V	+	1	0	CC2D1A	13889999	0.936000	0.31750	0.936000	0.37596	0.192000	0.23643	1.812000	0.38952	1.235000	0.43724	0.655000	0.94253	GTG	.	.	.	alt		0.632	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721		T	14028999	G	T	14028999	3	4	187	1	0	0	0	0	1	0	0	0	2728	1145	40	4	891	4	CC2D1A	19	14028999	Missense_Mutation	SNP	G	TCGA-GL-A4EM-01A-11D-A25F-10		14028999	45099984	57	11017											
GRAMD1A	57655	hgsc.bcm.edu	37	chr19	35505160	35505160	+	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	ctccagccagacagtgacccCggtggctgaacccccgagca	9	4	11	17	2	0	3	0	2	0	1	1	4	1	3	6	2	3	2	6	2	1	0			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr19:35505160C>G	ENST00000317991.5	+	10	1130	c.938C>G	c.(937-939)cCg>cGg	p.P313R	GRAMD1A_ENST00000599564.1_Missense_Mutation_p.P400R|GRAMD1A_ENST00000411896.2_Missense_Mutation_p.P306R|GRAMD1A_ENST00000504615.2_Missense_Mutation_p.P79R|CTD-2527I21.14_ENST00000605640.1_RNA	NM_020895.3	NP_065946.2	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A	313						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)			ACAGTGACCCCGGTGGCTGAA	0.652																																					p.P313R		Atlas-SNP	.											.	GRAMD1A	39	.	0			c.C938G						PASS	.						48	61	57					19																	35505160		2097	4240	6337	SO:0001583	missense	57655	exon10			TGACCCCGGTGGC	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.938C>G	chr19.hg19:g.35505160C>G	ENSP00000441032:p.Pro313Arg	72.0	0.0	.		168.0	21.0	.	NM_020895	A6NKY7|Q8NC77|Q9P1Z5	Missense_Mutation	SNP	ENST00000317991.5	hg19	CCDS42546.1	.	.	.	.	.	.	.	.	.	.	C	18.05	3.536733	0.65085	.	.	ENSG00000089351	ENST00000453966;ENST00000504615;ENST00000317991;ENST00000411896	T;T;T	0.47177	0.85;1.89;1.9	4.44	4.44	0.53790	.	0.367080	0.24580	N	0.037308	T	0.54647	0.1871	L	0.34521	1.04	0.50039	D	0.999843	P;D;D;D;D	0.76494	0.484;0.997;0.999;0.964;0.997	B;P;D;P;D	0.75484	0.215;0.901;0.986;0.694;0.963	T	0.44174	-0.9345	10	0.18276	T	0.48	.	14.5907	0.68362	0.0:1.0:0.0:0.0	.	313;313;79;306;400	Q96CP6-3;Q96CP6;B3KQF7;Q96CP6-2;F5GZ02	.;GRM1A_HUMAN;.;.;.	R	400;79;313;306	ENSP00000423728:P79R;ENSP00000441032:P313R;ENSP00000439267:P306R	ENSP00000441032:P313R	P	+	2	0	GRAMD1A	40197000	0.272000	0.24172	0.963000	0.40424	0.951000	0.60555	1.956000	0.40382	2.309000	0.77851	0.491000	0.48974	CCG	.	.	.	none		0.652	GRAMD1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461557.1	NM_020895		G	35505160	C	G	35505160	3	3	187	1	0	0	0	0	1	0	0	0	6754	652	23	4	976	4	GRAMD1A	19	35505160	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	21476161	35505160	23623823	58	11018											
ZNF154	7710	hgsc.bcm.edu	37	chr19	58213806	58213806	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attgagactgtagcttttgcTaaaggatttcccacattcac	11	14	7	9	0	1	1	1	1	0	1	2	3	2	2	1	1	2	3	1	1	3	7			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr19:58213806T>C	ENST00000512439.2	-	3	707	c.511A>G	c.(511-513)Agc>Ggc	p.S171G	ZNF154_ENST00000426889.1_Missense_Mutation_p.S171G|AC003006.7_ENST00000599221.1_Intron|ZNF551_ENST00000596085.1_Intron|AC003006.7_ENST00000594684.1_Intron			Q13106	ZN154_HUMAN	zinc finger protein 154	171					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			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)		TAGCTTTTGCTAAAGGATTTC	0.433																																					p.S171G		Atlas-SNP	.											.	ZNF154	34	.	0			c.A511G						PASS	.						215	215	215					19																	58213806		2165	4285	6450	SO:0001583	missense	7710	exon3			TTTTGCTAAAGGA	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.511A>G	chr19.hg19:g.58213806T>C	ENSP00000421258:p.Ser171Gly	335.0	0.0	.		296.0	41.0	.	NM_001085384	A7MCY3|Q8IVG7|Q8NAR0	Missense_Mutation	SNP	ENST00000512439.2	hg19	CCDS42639.1	.	.	.	.	.	.	.	.	.	.	T	15.85	2.953447	0.53293	.	.	ENSG00000179909	ENST00000512439;ENST00000426889;ENST00000396157	T;T	0.07688	3.17;3.17	3.03	2.0	0.26442	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08044	0.0201	L	0.55834	1.745	0.09310	N	1	B	0.15141	0.012	B	0.04013	0.001	T	0.34825	-0.9813	9	0.52906	T	0.07	.	2.5259	0.04691	0.2336:0.1338:0.0:0.6326	.	171	Q13106	ZN154_HUMAN	G	171;171;42	ENSP00000421258:S171G;ENSP00000442370:S171G	ENSP00000440907:S42G	S	-	1	0	ZNF154	62905618	0.001000	0.12720	0.015000	0.15790	0.941000	0.58515	0.218000	0.17622	0.559000	0.29153	0.459000	0.35465	AGC	.	.	.	none		0.433	ZNF154-002	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277102.2			C	58213806	T	C	58213806	3	2	187	1	0	0	0	0	1	0	0	0	17747	1522	53	3	806	3	ZNF154	19	58213806	Missense_Mutation	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10	22708646	58213806	915177	59	11019											
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-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr19:58385793C>T	ENST00000435989.2	-	3	1199	c.965G>A	c.(964-966)aGa>aAa	p.R322K	ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597342.1_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	chr19.hg19:g.58385793C>T	ENSP00000410545:p.Arg322Lys	81.0	0.0	.		106.0	14.0	.	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	hg19	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	187	1	0	0	0	0	1	0	0	0	18188	913	32	2	1606	2	ZNF814	19	58385793	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10	171987	58385793	743190	60	11020											
C20orf117	140710	hgsc.bcm.edu	37	chr20	35443624	35443624	+	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	tgagaaggactcctgctgttCcttgacagagcacccgagga	10	8	12	11	1	0	3	0	2	0	2	2	7	2	5	3	2	2	3	3	2	1	2			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chr20:35443624C>T	ENST00000357779.3	-	5	1833	c.1507G>A	c.(1507-1509)Gaa>Aaa	p.E503K	SOGA1_ENST00000456801.2_Missense_Mutation_p.E344K|SOGA1_ENST00000279034.6_Missense_Mutation_p.E503K|SOGA1_ENST00000237536.4_Missense_Mutation_p.E741K			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	503					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						TCCTGCTGTTCCTTGACAGAG	0.577																																					p.E741K		Atlas-SNP	.											.	SOGA1	136	.	0			c.G2221A						PASS	.						84	95	91					20																	35443624		2173	4275	6448	SO:0001583	missense	140710	exon5			GCTGTTCCTTGAC	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.1507G>A	chr20.hg19:g.35443624C>T	ENSP00000350424:p.Glu503Lys	98.0	0.0	.		85.0	17.0	.	NM_080627	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Missense_Mutation	SNP	ENST00000357779.3	hg19		.	.	.	.	.	.	.	.	.	.	C	18.14	3.556991	0.65425	.	.	ENSG00000149639	ENST00000237536;ENST00000279034;ENST00000456801;ENST00000357779	T;T;T;T	0.22743	1.99;1.94;1.98;1.98	5.72	5.72	0.89469	.	0.594212	0.17064	N	0.188438	T	0.45677	0.1354	M	0.63843	1.955	0.52501	D	0.999954	D	0.89917	1.0	D	0.87578	0.998	T	0.04991	-1.0913	10	0.27082	T	0.32	-37.714	18.6578	0.91460	0.0:1.0:0.0:0.0	.	503	O94964-4	.	K	741;503;344;503	ENSP00000237536:E741K;ENSP00000279034:E503K;ENSP00000413886:E344K;ENSP00000350424:E503K	ENSP00000237536:E741K	E	-	1	0	KIAA0889	34877038	1.000000	0.71417	0.999000	0.59377	0.042000	0.13812	3.774000	0.55341	2.706000	0.92434	0.561000	0.74099	GAA	.	.	.	none		0.577	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181		T	35443624	C	T	35443624	3	4	187	1	0	0	0	0	1	0	0	0	2085	864	30	2	2870	2	C20orf117	20	35443624	Missense_Mutation	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10		35443624	27581896	61	11021											
FOXO4	4303	hgsc.bcm.edu	37	chrX	70316474	70316474	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agccgtccccgctcctgcacCtggccccttccccgaccaga	5	6	8	22	3	0	1	0	0	0	1	3	2	3	1	10	1	2	2	10	1	0	1			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chrX:70316474C>T	ENST00000374259.3	+	1	428	c.96C>T	c.(94-96)acC>acT	p.T32T	FOXO4_ENST00000341558.3_Silent_p.T32T|FOXO4_ENST00000466874.1_3'UTR	NM_001170931.1|NM_005938.3	NP_001164402.1|NP_005929.2	P98177	FOXO4_HUMAN	forkhead box O4	32				QSRPRSCTWP -> RAVPLLHLA (in Ref. 1; CAA72156). {ECO:0000305}.	cell cycle arrest (GO:0007050)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|mitotic G2 DNA damage checkpoint (GO:0007095)|muscle organ development (GO:0007517)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of smooth muscle cell differentiation (GO:0051151)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)	18	Renal(35;0.156)					GCTCCTGCACCTGGCCCCTTC	0.637																																					p.T32T		Atlas-SNP	.											.	FOXO4	60	.	0			c.C96T						PASS	.						24	27	26					X																	70316474		1951	4125	6076	SO:0001819	synonymous_variant	4303	exon1			CTGCACCTGGCCC		CCDS43969.1, CCDS55440.1	Xq13.1	2008-02-05	2007-05-02	2007-05-02	ENSG00000184481	ENSG00000184481		"Forkhead boxes"	7139	protein-coding gene	gene with protein product		300033	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 7", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 7"	MLLT7		7529552	Standard	NM_005938		Approved	AFX1	uc004dys.2	P98177	OTTHUMG00000021789	ENST00000374259.3:c.96C>T	chrX.hg19:g.70316474C>T		84.0	0.0	.		96.0	23.0	.	NM_005938	B7WPJ7|O43821|Q13720|Q3KPF1|Q8TDK9	Silent	SNP	ENST00000374259.3	hg19	CCDS43969.1																																																																																			.	.	.	none		0.637	FOXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057115.1	NM_005938		T	70316474	C	T	70316474	2	4	187	1	0	0	0	0	0	0	0	1	6032	668	24	2		2	FOXO4	23	70316474	Silent	SNP	C	TCGA-GL-A4EM-01A-11D-A25F-10		70316474	84954086	62	11022											
OCRL	4952	hgsc.bcm.edu	37	chrX	128678970	128678970	+	Missense_Mutation	SNP	T	T	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	gcatgagaaggaacagcatgTtcaagatatcattcctataa	16	10	8	7	0	2	2	2	1	0	2	3	4	3	3	1	1	2	3	1	1	6	5			TCGA-GL-A4EM-01A-11D-A25F-10	TCGA-GL-A4EM-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7815397b-aa39-4b79-bcaa-6859a3f115f8	4bc53b4e-8334-46ff-aaab-4e5a0f30177b	g.chrX:128678970T>G	ENST00000371113.4	+	3	320	c.155T>G	c.(154-156)gTt>gGt	p.V52G	OCRL_ENST00000486673.1_3'UTR|OCRL_ENST00000357121.5_Missense_Mutation_p.V52G	NM_000276.3	NP_000267.2	Q01968	OCRL_HUMAN	oculocerebrorenal syndrome of Lowe	52	PH.				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						GAACAGCATGTTCAAGATATC	0.348																																					p.V52G		Atlas-SNP	.											.	OCRL	117	.	0			c.T155G						PASS	.						178	153	162					X																	128678970		2203	4300	6503	SO:0001583	missense	4952	exon3			AGCATGTTCAAGA	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.155T>G	chrX.hg19:g.128678970T>G	ENSP00000360154:p.Val52Gly	49.0	0.0	.		37.0	14.0	.	NM_000276	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	Missense_Mutation	SNP	ENST00000371113.4	hg19	CCDS35393.1	.	.	.	.	.	.	.	.	.	.	T	12.47	1.946658	0.34377	.	.	ENSG00000122126	ENST00000371113;ENST00000357121	D;D	0.94376	-3.41;-3.41	5.36	3.03	0.35002	.	0.751295	0.12380	N	0.473987	D	0.84938	0.5583	N	0.14661	0.345	0.47341	D	0.999398	B;B	0.19200	0.034;0.02	B;B	0.19946	0.027;0.019	T	0.80174	-0.1492	10	0.42905	T	0.14	.	5.7638	0.18215	0.0:0.1888:0.0:0.8112	.	52;52	Q01968-2;Q01968	.;OCRL_HUMAN	G	52	ENSP00000360154:V52G;ENSP00000349635:V52G	ENSP00000349635:V52G	V	+	2	0	OCRL	128506651	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.736000	0.26130	1.780000	0.52325	0.417000	0.27973	GTT	.	.	.	none		0.348	OCRL-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058917.1	NM_000276		G	128678970	T	G	128678970	3	3	187	1	0	0	0	0	1	0	0	0	10830	1725	60	5	165	5	OCRL	23	128678970	Missense_Mutation	SNP	T	TCGA-GL-A4EM-01A-11D-A25F-10	58362496	128678970	26591590	63	11023											
TTC4	7268	hgsc.bcm.edu	37	chr1	55183223	55183223	+	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	tttaaagaaaaagactacaaGaaagctgtaatttcatacac	20	10	5	6	0	1	3	1	0	0	3	1	3	1	3	0	0	3	2	0	0	9	6			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr1:55183223G>C	ENST00000371281.3	+	3	375	c.288G>C	c.(286-288)aaG>aaC	p.K96N	MROH7-TTC4_ENST00000414150.2_Missense_Mutation_p.R1332T|TTC4_ENST00000371284.5_3'UTR	NM_004623.4	NP_004614.3	O95801	TTC4_HUMAN	tetratricopeptide repeat domain 4	96										breast(2)|endometrium(3)|kidney(1)|lung(2)|stomach(1)	9						AAGACTACAAGAAAGCTGTAA	0.368																																					p.K96N		Atlas-SNP	.											.	TTC4	21	.	0			c.G288C						PASS	.						64	63	64					1																	55183223		2203	4300	6503	SO:0001583	missense	7268	exon3			CTACAAGAAAGCT		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.288G>C	chr1.hg19:g.55183223G>C	ENSP00000360329:p.Lys96Asn	176.0	0.0	.		156.0	55.0	.	NM_004623	Q53Y95|Q5TA96|Q9H3I2	Missense_Mutation	SNP	ENST00000371281.3	hg19	CCDS596.1	.	.	.	.	.	.	.	.	.	.	G	14.07	2.424330	0.43020	.	.	ENSG00000243725	ENST00000371281;ENST00000371284	T	0.61040	0.14	3.97	1.82	0.25136	Elongated TPR repeat-containing domain (1);Tetratricopeptide repeat-containing (1);	.	.	.	.	T	0.42877	0.1222	L	0.38838	1.175	0.46185	D	0.998919	B;P	0.34977	0.058;0.478	B;B	0.34824	0.056;0.19	T	0.19549	-1.0302	9	0.45353	T	0.12	-17.6511	6.6318	0.22861	0.303:0.0:0.697:0.0	.	96;107	O95801;Q5TA95	TTC4_HUMAN;.	N	96;107	ENSP00000360329:K96N	ENSP00000360329:K96N	K	+	3	2	TTC4	54955811	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.484000	0.45242	0.311000	0.23014	0.563000	0.77884	AAG	.	.	.	none		0.368	TTC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027432.1	NM_004623		C	55183223	G	C	55183223	3	2	188	1	0	0	0	0	1	0	0	0	16722	933	33	4	298	4	TTC4	1	55183223	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10		55183223	194067398	1	11024											
ALG6	29929	hgsc.bcm.edu	37	chr1	63868011	63868011	+	Frame_Shift_Del	DEL	A	A	-																															tcatagtctcctatgtgcatAtgtgtaagtttttctttctt																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr1:63868011delA	ENST00000371108.4	+	4	559	c.254delA	c.(253-255)tatfs	p.Y85fs	ALG6_ENST00000263440.4_Frame_Shift_Del_p.Y85fs	NM_013339.3	NP_037471.2	Q9Y672	ALG6_HUMAN	ALG6, alpha-1,3-glucosyltransferase	85					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						CTATGTGCATATGTGTAAGTT	0.353																																					p.Y85fs		Atlas-Indel,Pindel	.											.	ALG6	33	.	0			c.253delT						PASS	.						118	114	116					1																	63868011		2202	4300	6502	SO:0001589	frameshift_variant	29929	exon4			.	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.254delA	chr1.hg19:g.63868011delA	ENSP00000360149:p.Tyr85fs	41.0	0.0	0		37.0	19.0	0.513514	NM_013339	B3KMU2|Q5SXR9|Q9H3I0	Frame_Shift_Del	DEL	ENST00000371108.4	hg19	CCDS30735.1																																																																																			.	.	.	none		0.353	ALG6-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025330.2	NM_013339		-	63868011	A	-	63868011	7	5	188	1	0	1	0	1	0	0	0	0	522	449	16	0	264	0	ALG6	1	63868011	Frame_Shift_Del	DEL	A	TCGA-GL-A59R-01A-11D-A26P-10	8684788	63868011	185382610	2	11025											
ASH1L	55870	hgsc.bcm.edu	37	chr1	155313421	155313421	+	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	ttcttccaaagcttctcaatGcgaaagatgtcaagtttatc	12	14	6	9	1	3	1	2	0	2	1	6	2	4	1	1	0	2	2	1	0	5	5			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr1:155313421G>A	ENST00000368346.3	-	23	8748	c.8109C>T	c.(8107-8109)cgC>cgT	p.R2703R	ASH1L_ENST00000392403.3_Silent_p.R2698R|MIR555_ENST00000384987.1_RNA			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	2703	BAH. {ECO:0000255|PROSITE- ProRule:PRU00370}.				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)			GCTTCTCAATGCGAAAGATGT	0.493																																					p.R2698R		Atlas-SNP	.											.	ASH1L	279	.	0			c.C8094T						PASS	.						114	109	110					1																	155313421		2203	4300	6503	SO:0001819	synonymous_variant	55870	exon23			CTCAATGCGAAAG	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.8109C>T	chr1.hg19:g.155313421G>A		186.0	0.0	.		177.0	64.0	.	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Silent	SNP	ENST00000368346.3	hg19																																																																																				.	.	.	none		0.493	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		A	155313421	G	A	155313421	2	1	188	1	0	0	0	0	0	0	0	1	1041	1306	46	2		2	ASH1L	1	155313421	Silent	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	91445410	155313421	93937200	3	11026											
LMNA	4000	hgsc.bcm.edu	37	chr1	156107474	156107474	+	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	atgcgcaagctggtgcgctcAgtgactgtggttgaggacga	8	9	16	8	3	1	2	1	2	0	0	1	4	1	3	0	3	3	4	0	3	1	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr1:156107474A>C	ENST00000368300.4	+	10	1850	c.1638A>C	c.(1636-1638)tcA>tcC	p.S546S	LMNA_ENST00000347559.2_Intron|LMNA_ENST00000392353.3_Silent_p.S465S|LMNA_ENST00000448611.2_Silent_p.S434S|LMNA_ENST00000368301.2_Silent_p.S546S|LMNA_ENST00000361308.4_Silent_p.S546S|LMNA_ENST00000368297.1_Silent_p.S465S|LMNA_ENST00000368299.3_Silent_p.S546S|LMNA_ENST00000496738.1_3'UTR|LMNA_ENST00000473598.2_Silent_p.S447S	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C	546	Tail.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|endoplasmic reticulum unfolded protein response (GO:0030968)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle organ development (GO:0007517)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|positive regulation of cell aging (GO:0090343)|protein localization to nucleus (GO:0034504)|regulation of cell migration (GO:0030334)|regulation of protein localization to nucleus (GO:1900180)|sterol regulatory element binding protein import into nucleus (GO:0035105)|ventricular cardiac muscle cell development (GO:0055015)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|lamin filament (GO:0005638)|nuclear envelope (GO:0005635)|nuclear lamina (GO:0005652)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4)	10	Hepatocellular(266;0.158)					TGGTGCGCTCAGTGACTGTGG	0.622									Werner syndrome;Hutchinson-Gilford Progeria Syndrome																												p.S546S		Atlas-SNP	.											.	LMNA	31	.	0			c.A1638C						PASS	.						64	45	51					1																	156107474		2174	4254	6428	SO:0001819	synonymous_variant	4000	exon10	Familial Cancer Database	WS, Adult Progeria;HGPS, Progeria	GCGCTCAGTGACT	BC014507	CCDS1129.1, CCDS1131.1, CCDS58038.1, CCDS72941.1, CCDS72942.1	1q22	2014-09-17			ENSG00000160789	ENSG00000160789		"Intermediate filaments type V, lamins"	6636	protein-coding gene	gene with protein product		150330	"cardiomyopathy, dilated 1A (autosomal dominant)", "limb girdle muscular dystrophy 1B (autosomal dominant)", "progeria 1 (Hutchinson-Gilford type)", "lamin A/C-like 1"	LMN1, CMD1A, LGMD1B, PRO1, LMNL1		8511676, 8838815, 12702809	Standard	NM_005572		Approved	HGPS	uc001fni.3	P02545	OTTHUMG00000013961	ENST00000368300.4:c.1638A>C	chr1.hg19:g.156107474A>C		74.0	0.0	.		77.0	29.0	.	NM_170707	B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2	Silent	SNP	ENST00000368300.4	hg19	CCDS1129.1																																																																																			.	.	.	none		0.622	LMNA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039200.2	NM_170707		C	156107474	A	C	156107474	2	2	188	1	0	0	0	0	0	0	0	1	8855	175	7	5		5	LMNA	1	156107474	Silent	SNP	A	TCGA-GL-A59R-01A-11D-A26P-10	794053	156107474	93143147	4	11027											
C1orf125	126859	hgsc.bcm.edu	37	chr1	179339155	179339155	+	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	atgtctggcatcaccctgttCgaaggaataaattcaaatac	14	11	7	9	1	3	0	2	0	1	0	4	2	3	1	1	2	1	2	1	2	6	4	rs577148644		TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr1:179339155C>G	ENST00000367618.3	+	4	703	c.316C>G	c.(316-318)Cga>Gga	p.R106G	AXDND1_ENST00000457238.2_Missense_Mutation_p.R106G|AXDND1_ENST00000461179.2_3'UTR	NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	106										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						TCACCCTGTTCGAAGGAATAA	0.438																																					p.R106G		Atlas-SNP	.											.	AXDND1	142	.	0			c.C316G						PASS	.						80	72	75					1																	179339155		2203	4300	6503	SO:0001583	missense	126859	exon4			CCTGTTCGAAGGA	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.316C>G	chr1.hg19:g.179339155C>G	ENSP00000356590:p.Arg106Gly	104.0	0.0	.		106.0	44.0	.	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Missense_Mutation	SNP	ENST00000367618.3	hg19	CCDS30948.1	.	.	.	.	.	.	.	.	.	.	C	11.71	1.720207	0.30503	.	.	ENSG00000162779	ENST00000509175;ENST00000367618;ENST00000360322;ENST00000507383;ENST00000457238;ENST00000508285;ENST00000511889;ENST00000434088	T;T;T	0.52057	1.9;0.68;2.02	5.39	3.47	0.39725	.	0.176693	0.38605	N	0.001628	T	0.45256	0.1333	L	0.41710	1.295	0.19775	N	0.99996	D;D	0.53619	0.961;0.961	P;P	0.51453	0.67;0.67	T	0.34279	-0.9835	10	0.87932	D	0	0.9492	6.752	0.23491	0.1744:0.7348:0.0:0.0909	.	64;106	E9PCJ4;Q5T1B0	.;AXDN1_HUMAN	G	64;106;64;64;106;106;64;40	ENSP00000356590:R106G;ENSP00000416712:R106G;ENSP00000391716:R40G	ENSP00000353471:R64G	R	+	1	2	AXDND1	177605778	0.879000	0.30193	0.432000	0.26747	0.923000	0.55619	1.441000	0.35035	0.605000	0.29947	0.453000	0.30009	CGA	.	.	.	none		0.438	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696		G	179339155	C	G	179339155	3	3	188	1	0	0	0	0	1	0	0	0	1995	876	31	4	326	4	C1orf125	1	179339155	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	23231681	179339155	69911466	5	11028											
CAPN13	92291	hgsc.bcm.edu	37	chr2	30987162	30987162	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atagtgcagatcggaataggAtccgagcagcctgggaggga	12	6	16	7	2	0	1	0	0	0	1	2	6	1	5	2	4	3	2	2	4	3	2			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr2:30987162A>G	ENST00000295055.8	-	6	711	c.535T>C	c.(535-537)Tcc>Ccc	p.S179P	CAPN13_ENST00000465960.2_5'UTR|CAPN13_ENST00000534090.2_Missense_Mutation_p.S179P	NM_144575.2	NP_653176.2	Q6MZZ7	CAN13_HUMAN	calpain 13	179	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	30	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					TCGGAATAGGATCCGAGCAGC	0.577																																					p.S179P		Atlas-SNP	.											.	CAPN13	70	.	0			c.T535C						PASS	.						50	51	51					2																	30987162		2104	4217	6321	SO:0001583	missense	92291	exon6			AATAGGATCCGAG		CCDS46252.1	2p22-p21	2008-02-05			ENSG00000162949	ENSG00000162949			16663	protein-coding gene	gene with protein product		610228				11675017	Standard	NM_144575		Approved	FLJ23523	uc021vfm.1	Q6MZZ7	OTTHUMG00000152053	ENST00000295055.8:c.535T>C	chr2.hg19:g.30987162A>G	ENSP00000295055:p.Ser179Pro	102.0	0.0	.		136.0	55.0	.	NM_144575	Q17RF0|Q580X1|Q8TE80	Missense_Mutation	SNP	ENST00000295055.8	hg19	CCDS46252.1	.	.	.	.	.	.	.	.	.	.	A	18.41	3.618329	0.66787	.	.	ENSG00000162949	ENST00000295055;ENST00000534090	D;D	0.89552	-2.53;-2.53	5.22	5.22	0.72569	Peptidase C2, calpain, catalytic domain (3);	0.000000	0.85682	D	0.000000	D	0.96439	0.8838	H	0.97265	3.97	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97655	1.0157	10	0.72032	D	0.01	.	14.0703	0.64856	1.0:0.0:0.0:0.0	.	179	Q6MZZ7	CAN13_HUMAN	P	179	ENSP00000295055:S179P;ENSP00000431298:S179P	ENSP00000295055:S179P	S	-	1	0	CAPN13	30840666	1.000000	0.71417	0.951000	0.38953	0.450000	0.32258	4.956000	0.63645	1.970000	0.57323	0.379000	0.24179	TCC	.	.	.	none		0.577	CAPN13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325101.2	NM_144575		G	30987162	A	G	30987162	3	3	188	1	0	0	0	0	1	0	0	0	2628	333	12	3	1542	3	CAPN13	2	30987162	Missense_Mutation	SNP	A	TCGA-GL-A59R-01A-11D-A26P-10		30987162	212212211	6	11029											
XPO1	7514	hgsc.bcm.edu	37	chr2	61705989	61705989	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttctggaatctcatgtggaTtaaagatgccagggacagac	12	10	11	8	0	2	2	1	0	2	2	3	5	2	5	1	3	1	0	1	3	3	2			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr2:61705989T>C	ENST00000401558.2	-	25	3909	c.3182A>G	c.(3181-3183)aAt>aGt	p.N1061S	RP11-355B11.2_ENST00000603199.1_RNA|XPO1_ENST00000406957.1_Missense_Mutation_p.N1061S|XPO1_ENST00000404992.2_Missense_Mutation_p.N1061S|RP11-355B11.2_ENST00000603028.1_RNA|RP11-355B11.2_ENST00000578974.2_RNA|RP11-355B11.2_ENST00000603652.1_RNA	NM_003400.3	NP_003391.1	O14980	XPO1_HUMAN	exportin 1	1061					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)			CTCATGTGGATTAAAGATGCC	0.393			Mis		CLL																																p.N1061S		Atlas-SNP	.	-'	Dom	yes		2	2p15	7514	"exportin 1 (CRM1 homolog, yeast)"		L	.	XPO1	108	.	0			c.A3182G						PASS	.						137	137	137					2																	61705989		2203	4300	6503	SO:0001583	missense	7514	exon25			TGTGGATTAAAGA	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.3182A>G	chr2.hg19:g.61705989T>C	ENSP00000384863:p.Asn1061Ser	68.0	0.0	.		42.0	20.0	.	NM_003400	A6NL14|A8K1K5|D6W5E2|Q63HP8|Q68CP3|Q99433	Missense_Mutation	SNP	ENST00000401558.2	hg19	CCDS33205.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.120462	0.77323	.	.	ENSG00000082898	ENST00000401558;ENST00000404992;ENST00000406957	.	.	.	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.78007	0.4216	M	0.79258	2.445	0.58432	D	0.999996	D;D	0.76494	0.994;0.999	P;D	0.69307	0.888;0.963	T	0.76534	-0.2924	9	0.28530	T	0.3	-21.4772	15.9952	0.80234	0.0:0.0:0.0:1.0	.	708;1061	B3KWD0;O14980	.;XPO1_HUMAN	S	1061	.	ENSP00000384863:N1061S	N	-	2	0	XPO1	61559493	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.005000	0.88553	2.172000	0.68678	0.533000	0.62120	AAT	.	.	.	none		0.393	XPO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325872.3	NM_003400		C	61705989	T	C	61705989	3	2	188	1	0	0	0	0	1	0	0	0	17457	1493	52	3	37	3	XPO1	2	61705989	Missense_Mutation	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	30718827	61705989	181493384	7	11030											
FAM161A	84140	hgsc.bcm.edu	37	chr2	62067237	62067237	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttctccgttcttctttttgcTtgactaaatcatggtaaagg	8	18	7	8	1	4	1	1	1	3	0	5	1	4	1	1	2	1	3	1	2	4	8			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr2:62067237T>C	ENST00000405894.3	-	3	1003	c.902A>G	c.(901-903)aAg>aGg	p.K301R	FAM161A_ENST00000404929.1_Missense_Mutation_p.K301R	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	301					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						TTCTTTTTGCTTGACTAAATC	0.418																																					p.K301R		Atlas-SNP	.											.	FAM161A	200	.	0			c.A902G						PASS	.						166	149	154					2																	62067237		1847	4095	5942	SO:0001583	missense	84140	exon3			TTTTGCTTGACTA		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.902A>G	chr2.hg19:g.62067237T>C	ENSP00000385893:p.Lys301Arg	67.0	0.0	.		46.0	21.0	.	NM_032180	B4DJV7|Q9H8R2	Missense_Mutation	SNP	ENST00000405894.3	hg19	CCDS42687.2	.	.	.	.	.	.	.	.	.	.	T	13.72	2.322375	0.41096	.	.	ENSG00000170264	ENST00000404929;ENST00000405894	T;T	0.22336	1.96;1.96	5.41	4.26	0.50523	.	0.176973	0.44902	D	0.000408	T	0.22205	0.0535	L	0.52573	1.65	0.29380	N	0.863369	B;B	0.30563	0.285;0.074	B;B	0.34931	0.192;0.064	T	0.10314	-1.0635	10	0.44086	T	0.13	-18.3941	10.8689	0.46872	0.0:0.0746:0.0:0.9254	.	301;301	Q3B820;Q3B820-3	F161A_HUMAN;.	R	301	ENSP00000385158:K301R;ENSP00000385893:K301R	ENSP00000385158:K301R	K	-	2	0	FAM161A	61920741	1.000000	0.71417	0.997000	0.53966	0.900000	0.52787	2.205000	0.42770	0.884000	0.36064	0.533000	0.62120	AAG	.	.	.	none		0.418	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180		C	62067237	T	C	62067237	3	2	188	1	0	0	0	0	1	0	0	0	5476	1609	56	3	1096	3	FAM161A	2	62067237	Missense_Mutation	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	361248	62067237	181132136	8	11031											
RTKN	6242	hgsc.bcm.edu	37	chr2	74656034	74656034	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgcactgctgccagggtgAgtgtggtgtgagccaagagg	7	9	17	8	0	0	3	0	2	0	1	0	3	0	3	2	3	4	2	2	3	1	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr2:74656034A>G	ENST00000233330.6	-	7	958	c.641T>C	c.(640-642)cTc>cCc	p.L214P	RTKN_ENST00000272430.5_Missense_Mutation_p.L264P|RTKN_ENST00000305557.5_Missense_Mutation_p.L251P	NM_001015056.1	NP_001015056.1			rhotekin											endometrium(3)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	16						TGCCAGGGTGAGTGTGGTGTG	0.552																																					p.L264P		Atlas-SNP	.											.	RTKN	80	.	0			c.T791C						PASS	.						192	128	150					2																	74656034		2203	4300	6503	SO:0001583	missense	6242	exon7			AGGGTGAGTGTGG	AF049227	CCDS1941.1, CCDS33226.1, CCDS42699.1	2p13.1	2013-01-10			ENSG00000114993	ENSG00000114993		"Pleckstrin homology (PH) domain containing"	10466	protein-coding gene	gene with protein product		602288				9073523, 10940294	Standard	XM_005264478		Approved	B5	uc002sle.3	Q9BST9	OTTHUMG00000129955	ENST00000233330.6:c.641T>C	chr2.hg19:g.74656034A>G	ENSP00000233330:p.Leu214Pro	249.0	0.0	.		232.0	68.0	.	NM_001015055		Missense_Mutation	SNP	ENST00000233330.6	hg19	CCDS42699.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.545730	0.86022	.	.	ENSG00000114993	ENST00000305557;ENST00000272430;ENST00000233330	T;T;T	0.65178	-0.14;-0.14;-0.14	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.78291	0.4260	M	0.76170	2.325	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.81055	-0.1106	10	0.87932	D	0	.	13.6415	0.62253	1.0:0.0:0.0:0.0	.	264;251	Q9BST9;Q9BST9-2	RTKN_HUMAN;.	P	251;264;214	ENSP00000305298:L251P;ENSP00000272430:L264P;ENSP00000233330:L214P	ENSP00000233330:L214P	L	-	2	0	RTKN	74509542	1.000000	0.71417	0.991000	0.47740	0.971000	0.66376	8.673000	0.91186	2.128000	0.65567	0.459000	0.35465	CTC	.	.	.	none		0.552	RTKN-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000328236.3	NM_001015055		G	74656034	A	G	74656034	3	3	188	1	0	0	0	0	1	0	0	0	13735	304	11	3	924	3	RTKN	2	74656034	Missense_Mutation	SNP	A	TCGA-GL-A59R-01A-11D-A26P-10	12588797	74656034	168543339	9	11032											
DNAH6	1768	hgsc.bcm.edu	37	chr2	84846836	84846836	+	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	ttcttgtcaaatgatgaactTctggagattttggcccagac	10	14	9	8	0	3	4	1	2	2	2	3	5	3	4	1	2	1	0	1	2	2	5			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr2:84846836T>G	ENST00000237449.6	+	23	3608	c.3600T>G	c.(3598-3600)ctT>ctG	p.L1200L	DNAH6_ENST00000398278.2_Silent_p.L1200L|DNAH6_ENST00000389394.3_Silent_p.L1200L			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	1200	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						ATGATGAACTTCTGGAGATTT	0.383																																					p.L1200L		Atlas-SNP	.											.	DNAH6	194	.	0			c.T3600G						PASS	.						138	114	121					2																	84846836		692	1591	2283	SO:0001819	synonymous_variant	1768	exon24			TGAACTTCTGGAG	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.3600T>G	chr2.hg19:g.84846836T>G		67.0	0.0	.		54.0	23.0	.	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	hg19	CCDS46348.1																																																																																			.	.	.	none		0.383	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		G	84846836	T	G	84846836	2	3	188	1	0	0	0	0	0	0	0	1	4607	1770	62	5		5	DNAH6	2	84846836	Silent	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	10190802	84846836	158352537	10	11033											
NEB	4703	hgsc.bcm.edu	37	chr2	152390040	152390040	+	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	ccatgttgcagaaacatcttGgcactagatttatattttct	11	16	6	8	0	2	2	0	0	2	2	2	2	2	2	1	1	2	3	1	1	4	8			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr2:152390040G>T	ENST00000172853.10	-	115	16462				NEB_ENST00000397345.3_Silent_p.A7111A|NEB_ENST00000604864.1_Intron|NEB_ENST00000427231.2_Intron|NEB_ENST00000603639.1_Silent_p.A7111A|NEB_ENST00000409198.1_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)		GAAACATCTTGGCACTAGATT	0.413																																					p.A7146A		Atlas-SNP	.											.	NEB	1697	.	0			c.C21438A						PASS	.						182	146	157					2																	152390040		692	1591	2283	SO:0001627	intron_variant	4703	exon144			CATCTTGGCACTA	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+688C>A	chr2.hg19:g.152390040G>T		76.0	0.0	.		56.0	4.0	.	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	hg19																																																																																				.	.	.	none		0.413	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152390040	G	T	152390040	1	4	188	0	1	0	0	0	0	0	0	0	10309	1335	47	4		4	NEB	2	152390040	Intron	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	67543204	152390040	90809333	11	11034											
AGPS	8540	hgsc.bcm.edu	37	chr2	178257747	178257747	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccacggccactcccgccgCgcaggagtcgggcaccatcc	6	3	12	20	5	0	0	0	0	0	0	3	1	2	1	6	3	0	2	6	3	0	0			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr2:178257747C>T	ENST00000264167.4	+	1	376	c.230C>T	c.(229-231)gCg>gTg	p.A77V	NFE2L2_ENST00000464747.1_5'Flank|AGPS_ENST00000409888.1_Missense_Mutation_p.A77V|AC074286.1_ENST00000397057.2_RNA	NM_003659.3	NP_003650.1	O00116	ADAS_HUMAN	alkylglycerone phosphate synthase	77					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)			ACTCCCGCCGCGCAGGAGTCG	0.692																																					p.A77V		Atlas-SNP	.											.	AGPS	56	.	0			c.C230T						PASS	.						2	2	2					2																	178257747		1370	2704	4074	SO:0001583	missense	8540	exon1			CCGCCGCGCAGGA	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.230C>T	chr2.hg19:g.178257747C>T	ENSP00000264167:p.Ala77Val	51.0	0.0	.		53.0	31.0	.	NM_003659	A5D8U9|Q2TU35	Missense_Mutation	SNP	ENST00000264167.4	hg19	CCDS2275.1	.	.	.	.	.	.	.	.	.	.	C	18.28	3.589519	0.66105	.	.	ENSG00000018510	ENST00000264167;ENST00000409888	D	0.97328	-4.34	4.57	3.7	0.42460	.	0.000000	0.45126	D	0.000391	D	0.91543	0.7329	L	0.38531	1.155	0.23751	N	0.996949	P	0.38745	0.645	B	0.22386	0.039	D	0.84254	0.0479	10	0.29301	T	0.29	.	9.702	0.40192	0.0:0.902:0.0:0.098	.	77	O00116	ADAS_HUMAN	V	77	ENSP00000264167:A77V	ENSP00000264167:A77V	A	+	2	0	AGPS	177965993	0.089000	0.21612	0.781000	0.31783	0.978000	0.69477	0.687000	0.25407	1.138000	0.42230	0.655000	0.94253	GCG	.	.	.	none		0.692	AGPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255730.2			T	178257747	C	T	178257747	3	4	188	1	0	0	0	0	1	0	0	0	394	768	27	1	232	1	AGPS	2	178257747	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	25867707	178257747	64941626	12	11035											
TTN	7273	hgsc.bcm.edu	37	chr2	179598544	179598545	+	Missense_Mutation	DNP	AC	AC	CA																															aaatgggctctgaccctctcAcagcagcttgcagggtaacg																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr2:179598544_179598545AC>CA	ENST00000591111.1	-	51	14844_14845	c.14620_14621GT>TG	c.(14620-14622)GTg>TGg	p.V4874W	TTN_ENST00000342992.6_Missense_Mutation_p.V3947W|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.V5191W			Q8WZ42	TITIN_HUMAN	titin	12256	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)			TGACCCTCTCACAGCAGCTTGC	0.426																																					p.V5191G|p.V5191L		Atlas-SNP	.											.	TTN	18412	.	0			c.T15572G|c.G15571T						PASS	.																																			SO:0001583	missense	7273	exon53			CCTCTCACAGCAG|CTCTCACAGCAGC	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.14620_14621delinsCA	chr2.hg19:g.179598544_179598545delinsCA	ENSP00000465570:p.Val4874Trp	154.0|156.0	0.0	.		151.0	66.0|65.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19																																																																																				.	.	.	none		0.426	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		CA	179598545	AC	CA	179598544	3	2	188	1	0	0	0	0	1	0	0	0	16747	159	6	5	89197	5	TTN	2	179598544	Missense_Mutation	DNP	AC	TCGA-GL-A59R-01A-11D-A26P-10	1340797	179598544	63600829	13	11036											
FSIP2	401024	hgsc.bcm.edu	37	chr2	186672719	186672719	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atttatctccaaaagtaagaTtaaacttgtaccacccacca	16	11	3	11	0	1	1	0	0	1	1	2	1	1	1	4	0	2	2	4	0	7	6	rs377239551		TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr2:186672719T>C	ENST00000424728.1	+	17	18686	c.18686T>C	c.(18685-18687)aTt>aCt	p.I6229T	FSIP2_ENST00000343098.5_Missense_Mutation_p.I6318T			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	6229										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						AAAAGTAAGATTAAACTTGTA	0.308																																					p.I6318T		Atlas-SNP	.											.	FSIP2	251	.	0			c.T18953C						PASS	.	T	THR/ILE	0,3640		0,0,1820	32	29	30		18953	5.1	1	2		30	1,8109		0,1,4054	no	missense	FSIP2	NM_173651.2	89	0,1,5874	CC,CT,TT		0.0123,0.0,0.0085	probably-damaging	6318/6997	186672719	1,11749	1820	4055	5875	SO:0001583	missense	401024	exon17			GTAAGATTAAACT	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.18686T>C	chr2.hg19:g.186672719T>C	ENSP00000401306:p.Ile6229Thr	111.0	0.0	.		152.0	14.0	.	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Missense_Mutation	SNP	ENST00000424728.1	hg19		.	.	.	.	.	.	.	.	.	.	T	15.95	2.984130	0.53827	0.0	1.23E-4	ENSG00000188738	ENST00000343098;ENST00000424728	T;T	0.60797	0.16;0.16	5.07	5.07	0.68467	.	0.235594	0.29737	N	0.011328	T	0.61825	0.2378	L	0.52011	1.625	0.34264	D	0.680189	.	.	.	.	.	.	T	0.74544	-0.3630	8	0.72032	D	0.01	.	11.132	0.48351	0.0:0.0:0.0:1.0	.	.	.	.	T	6318;6229	ENSP00000344403:I6318T;ENSP00000401306:I6229T	ENSP00000344403:I6318T	I	+	2	0	FSIP2	186380964	1.000000	0.71417	0.983000	0.44433	0.928000	0.56348	3.872000	0.56085	2.130000	0.65690	0.397000	0.26171	ATT	.	.	.	weak		0.308	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		C	186672719	T	C	186672719	3	2	188	1	0	0	0	0	1	0	0	0	6082	1493	52	3	19019	3	FSIP2	2	186672719	Missense_Mutation	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	7074175	186672719	56526654	14	11037											
SF3B1	23451	hgsc.bcm.edu	37	chr2	198265131	198265131	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaagagcattaaccactgTgccaaagccgttcaacatta	14	8	7	12	1	1	1	1	0	0	1	1	1	1	1	4	0	5	2	4	0	5	3			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr2:198265131T>C	ENST00000335508.6	-	19	2837	c.2746A>G	c.(2746-2748)Aca>Gca	p.T916A	SF3B1_ENST00000462613.1_5'Flank	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	916					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)			TTAACCACTGTGCCAAAGCCG	0.358			Mis		myelodysplastic syndrome																																p.T916A		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1	1038	.	0			c.A2746G						PASS	.						97	95	95					2																	198265131		2203	4300	6503	SO:0001583	missense	23451	exon19			CCACTGTGCCAAA	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.2746A>G	chr2.hg19:g.198265131T>C	ENSP00000335321:p.Thr916Ala	178.0	0.0	.		176.0	77.0	.	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	hg19	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	T	15.50	2.851230	0.51270	.	.	ENSG00000115524	ENST00000335508	.	.	.	5.87	5.87	0.94306	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.57695	0.2071	L	0.48174	1.505	0.80722	D	1	B	0.14012	0.009	B	0.21360	0.034	T	0.51903	-0.8646	9	0.29301	T	0.29	.	16.5764	0.84681	0.0:0.0:0.0:1.0	.	916	O75533	SF3B1_HUMAN	A	916	.	ENSP00000335321:T916A	T	-	1	0	SF3B1	197973376	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.910000	0.87451	2.371000	0.80710	0.533000	0.62120	ACA	.	.	.	none		0.358	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			C	198265131	T	C	198265131	3	2	188	1	0	0	0	0	1	0	0	0	14162	1696	59	3	1196	3	SF3B1	2	198265131	Missense_Mutation	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	11592412	198265131	44934242	15	11038											
RAF1	5894	hgsc.bcm.edu	37	chr3	12653543	12653543	+	Frame_Shift_Del	DEL	T	T	-																															aaggcagtcatgcaagctcaTtccatttcgcacattgacct																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr3:12653543delT	ENST00000251849.4	-	3	665	c.226delA	c.(226-228)atgfs	p.M76fs	RAF1_ENST00000542177.1_Intron|RAF1_ENST00000442415.2_Frame_Shift_Del_p.M76fs|RAF1_ENST00000534997.1_5'Flank	NM_002880.3	NP_002871.1	P04049	RAF1_HUMAN	Raf-1 proto-oncogene, serine/threonine kinase	76	RBD. {ECO:0000255|PROSITE- ProRule:PRU00262}.				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)	TGCAAGCTCATTCCATTTCGC	0.498			T	SRGAP3	pilocytic astrocytoma				Noonan syndrome																												p.M76fs		Atlas-Indel,Pindel	.		Dom	yes		3	3p25	5894	v-raf-1 murine leukemia viral oncogene homolog 1		M	.	RAF1	66	.	0			c.227delT						PASS	.						154	137	143					3																	12653543		2203	4300	6503	SO:0001589	frameshift_variant	5894	exon3	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	.	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.226delA	chr3.hg19:g.12653543delT	ENSP00000251849:p.Met76fs	126.0	0.0	0		118.0	55.0	0.466102	NM_002880	B0LPH8|B2R5N3|Q15278|Q9UC20	Frame_Shift_Del	DEL	ENST00000251849.4	hg19	CCDS2612.1																																																																																			.	.	.	none		0.498	RAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252015.2	NM_002880		-	12653543	T	-	12653543	7	5	188	1	0	1	0	1	0	0	0	0	13015	1493	52	0	1780	0	RAF1	3	12653543	Frame_Shift_Del	DEL	T	TCGA-GL-A59R-01A-11D-A26P-10		12653543	185368887	16	11039											
SCN11A	11280	hgsc.bcm.edu	37	chr3	38966961	38966961	+	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	acacggaaggtacgcaggggCaatagtttgatggtgattcc	11	9	14	7	2	0	2	0	2	0	0	1	3	1	3	1	5	1	4	1	5	4	4			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr3:38966961C>G	ENST00000302328.3	-	5	855	c.657G>C	c.(655-657)ttG>ttC	p.L219F	SCN11A_ENST00000444237.2_Missense_Mutation_p.L219F|SCN11A_ENST00000450244.1_Missense_Mutation_p.L219F|SCN11A_ENST00000456224.3_Missense_Mutation_p.L219F	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	219					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)	TACGCAGGGGCAATAGTTTGA	0.463																																					p.L219F		Atlas-SNP	.											.	SCN11A	296	.	0			c.G657C						PASS	.						162	136	145					3																	38966961		2203	4300	6503	SO:0001583	missense	11280	exon5			CAGGGGCAATAGT	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.657G>C	chr3.hg19:g.38966961C>G	ENSP00000307599:p.Leu219Phe	132.0	0.0	.		141.0	53.0	.	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Missense_Mutation	SNP	ENST00000302328.3	hg19	CCDS33737.1	.	.	.	.	.	.	.	.	.	.	C	15.35	2.808991	0.50421	.	.	ENSG00000168356	ENST00000302328;ENST00000450244;ENST00000456224;ENST00000444237	D;D;D;D	0.97404	-4.37;-4.37;-4.37;-4.37	4.79	-4.0	0.04057	Ion transport (1);	0.225617	0.39210	N	0.001423	D	0.94515	0.8234	L	0.55481	1.735	0.09310	N	1	P	0.50819	0.939	P	0.49192	0.602	D	0.89878	0.4028	10	0.87932	D	0	.	5.7293	0.18030	0.0:0.2152:0.3973:0.3874	.	219	Q9UI33	SCNBA_HUMAN	F	219	ENSP00000307599:L219F;ENSP00000400945:L219F;ENSP00000416757:L219F;ENSP00000408028:L219F	ENSP00000307599:L219F	L	-	3	2	SCN11A	38941965	0.002000	0.14202	0.003000	0.11579	0.008000	0.06430	-1.047000	0.03521	-0.513000	0.06496	0.467000	0.42956	TTG	.	.	.	none		0.463	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		G	38966961	C	G	38966961	3	3	188	1	0	0	0	0	1	0	0	0	13926	709	25	4	4806	4	SCN11A	3	38966961	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	26313418	38966961	159055469	17	11040											
PLXNB1	5364	hgsc.bcm.edu	37	chr3	48465285	48465285	+	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	acacactcgagatacataggCacgaaaagctctagactgag	16	6	9	10	2	1	3	0	1	1	2	2	5	1	3	0	1	2	2	0	1	5	3			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr3:48465285C>T	ENST00000358536.4	-	3	1005	c.736G>A	c.(736-738)Gcc>Acc	p.A246T	PLXNB1_ENST00000448774.2_Intron|PLXNB1_ENST00000358459.4_Missense_Mutation_p.A246T|PLXNB1_ENST00000456774.1_Missense_Mutation_p.A246T|PLXNB1_ENST00000296440.6_Missense_Mutation_p.A246T	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	246	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GATACATAGGCACGAAAAGCT	0.607																																					p.A246T		Atlas-SNP	.											.	PLXNB1	150	.	0			c.G736A						PASS	.						62	58	59					3																	48465285		2202	4300	6502	SO:0001583	missense	5364	exon3			CATAGGCACGAAA	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"Plexins"	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.736G>A	chr3.hg19:g.48465285C>T	ENSP00000351338:p.Ala246Thr	218.0	0.0	.		188.0	81.0	.	NM_001130082	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Missense_Mutation	SNP	ENST00000358536.4	hg19	CCDS2765.1	.	.	.	.	.	.	.	.	.	.	C	0.009	-1.836487	0.00579	.	.	ENSG00000164050	ENST00000296440;ENST00000358459;ENST00000358536;ENST00000456774	T;T;T;T	0.02944	4.1;4.1;4.1;4.1	4.41	2.58	0.30949	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.176749	0.38436	N	0.001699	T	0.00666	0.0022	N	0.00201	-1.865	0.80722	D	1	B;B	0.12013	0.001;0.005	B;B	0.10450	0.005;0.004	T	0.41324	-0.9515	10	0.07325	T	0.83	.	4.5893	0.12299	0.0:0.2937:0.3661:0.3403	.	246;246	O43157;O43157-2	PLXB1_HUMAN;.	T	246	ENSP00000296440:A246T;ENSP00000351242:A246T;ENSP00000351338:A246T;ENSP00000414199:A246T	ENSP00000296440:A246T	A	-	1	0	PLXNB1	48440289	0.995000	0.38212	0.188000	0.23233	0.006000	0.05464	2.590000	0.46154	0.308000	0.22923	-0.229000	0.12294	GCC	.	.	.	none		0.607	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673		T	48465285	C	T	48465285	3	4	188	1	0	0	0	0	1	0	0	0	12130	710	25	2	5815	2	PLXNB1	3	48465285	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	9498324	48465285	149557145	18	11041											
NISCH	11188	hgsc.bcm.edu	37	chr3	52505969	52505969	+	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	ctcgggcacatcctggacttCacctgtcgccttaagtacct	7	11	8	15	2	1	0	1	0	0	0	4	1	2	1	4	2	1	2	4	2	2	3			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr3:52505969C>T	ENST00000479054.1	+	6	621	c.549C>T	c.(547-549)ttC>ttT	p.F183F	NISCH_ENST00000420808.2_Silent_p.F183F|NISCH_ENST00000345716.4_Silent_p.F183F|NISCH_ENST00000488380.1_Silent_p.F183F			Q9Y2I1	NISCH_HUMAN	nischarin	183	Necessary for homooligomerization and targeting to endosomes.				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)	TCCTGGACTTCACCTGTCGCC	0.632											OREG0015615	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F183F		Atlas-SNP	.											.	NISCH	97	.	0			c.C549T						PASS	.						59	60	60					3																	52505969		2203	4300	6503	SO:0001819	synonymous_variant	11188	exon5			GGACTTCACCTGT	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.549C>T	chr3.hg19:g.52505969C>T		323.0	0.0	.	985	284.0	18.0	.	NM_001276293	C9J245|Q6PGP3|Q6PIB4|Q7L8M3|Q7Z2X6|Q9UES6|Q9UEU4|Q9UFW3	Silent	SNP	ENST00000479054.1	hg19	CCDS33767.1																																																																																			.	.	.	none		0.632	NISCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351357.1	NM_007184		T	52505969	C	T	52505969	2	4	188	1	0	0	0	0	0	0	0	1	10439	825	29	2		2	NISCH	3	52505969	Silent	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	4040684	52505969	145516461	19	11042											
SKIL	6498	hgsc.bcm.edu	37	chr3	170078913	170078913	+	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	tggcagtgcctttgaagtggAgcatgaatgcctaggcaaat	11	10	13	7	0	0	2	0	2	0	0	0	3	0	3	2	3	3	3	2	3	4	2			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr3:170078913A>T	ENST00000458537.3	+	1	1503	c.794A>T	c.(793-795)gAg>gTg	p.E265V	SKIL_ENST00000259119.4_Missense_Mutation_p.E265V|SKIL_ENST00000413427.2_Missense_Mutation_p.E265V|SKIL_ENST00000426052.2_Missense_Mutation_p.E245V	NM_001145097.2|NM_001248008.1|NM_005414.4	NP_001138569.1|NP_001234937.1|NP_005405.2	P12757	SKIL_HUMAN	SKI-like proto-oncogene	265					blastocyst formation (GO:0001825)|cell cycle arrest (GO:0007050)|gene expression (GO:0010467)|lens fiber cell differentiation (GO:0070306)|lymphocyte homeostasis (GO:0002260)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of axonogenesis (GO:0050772)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|protein heterotrimerization (GO:0070208)|protein homotrimerization (GO:0070207)|regulation of apoptotic process (GO:0042981)|response to antibiotic (GO:0046677)|response to cytokine (GO:0034097)|response to growth factor (GO:0070848)|skeletal muscle tissue development (GO:0007519)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|protein complex binding (GO:0032403)|protein domain specific binding (GO:0019904)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	25	all_cancers(22;7.13e-23)|all_epithelial(15;9.95e-28)|all_lung(20;1.23e-16)|Lung NSC(18;5.15e-16)|Ovarian(172;0.000337)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			TTTGAAGTGGAGCATGAATGC	0.453																																					p.E265V		Atlas-SNP	.											.	SKIL	67	.	0			c.A794T						PASS	.						147	129	135					3																	170078913		2203	4300	6503	SO:0001583	missense	6498	exon1			AAGTGGAGCATGA	X15217	CCDS33890.1, CCDS46953.1, CCDS46954.1	3q26	2014-06-25	2014-06-25		ENSG00000136603	ENSG00000136603		"SKI transcriptional corepressors"	10897	protein-coding gene	gene with protein product		165340	"SKI-like oncogene"			2762147	Standard	NM_005414		Approved	SNO, SnoN, SnoA	uc003fgw.3	P12757	OTTHUMG00000158831	ENST00000458537.3:c.794A>T	chr3.hg19:g.170078913A>T	ENSP00000415243:p.Glu265Val	187.0	0.0	.		190.0	66.0	.	NM_001248008	A6NGT1|B4DT50|O00464|P12756|Q07501	Missense_Mutation	SNP	ENST00000458537.3	hg19	CCDS33890.1	.	.	.	.	.	.	.	.	.	.	A	17.14	3.312956	0.60414	.	.	ENSG00000136603	ENST00000259119;ENST00000426052;ENST00000413427;ENST00000458537	D;D;D;D	0.91464	-2.85;-2.85;-2.83;-2.85	5.51	5.51	0.81932	SAND domain-like (2);c-SKI Smad4-binding (1);	0.221987	0.48286	D	0.000184	D	0.92038	0.7477	L	0.33485	1.01	0.52099	D	0.999943	D;D	0.89917	0.998;1.0	D;D	0.97110	0.969;1.0	D	0.90522	0.4489	10	0.25751	T	0.34	-22.9066	15.6712	0.77279	1.0:0.0:0.0:0.0	.	265;265	P12757-3;P12757	.;SKIL_HUMAN	V	265;245;265;265	ENSP00000259119:E265V;ENSP00000406520:E245V;ENSP00000400193:E265V;ENSP00000415243:E265V	ENSP00000259119:E265V	E	+	2	0	SKIL	171561607	1.000000	0.71417	1.000000	0.80357	0.454000	0.32378	8.962000	0.93254	2.111000	0.64477	0.524000	0.50904	GAG	.	.	.	none		0.453	SKIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352351.4	NM_005414		T	170078913	A	T	170078913	3	4	188	1	0	0	0	0	1	0	0	0	14371	304	11	5	796	5	SKIL	3	170078913	Missense_Mutation	SNP	A	TCGA-GL-A59R-01A-11D-A26P-10	117572944	170078913	27943517	20	11043											
RUFY3	22902	hgsc.bcm.edu	37	chr4	71629308	71629308	+	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	acaaaataaatccttctgggGgcctctagaactggtagaaa	15	9	9	8	0	2	2	0	0	2	2	3	2	3	2	2	3	1	1	2	3	8	4			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr4:71629308G>A	ENST00000226328.4	+	3	955	c.392G>A	c.(391-393)gGg>gAg	p.G131E	RUFY3_ENST00000536664.1_Missense_Mutation_p.G115E|RUFY3_ENST00000381006.3_Missense_Mutation_p.G131E|RUFY3_ENST00000417478.2_Missense_Mutation_p.G191E|RUFY3_ENST00000502653.1_Missense_Mutation_p.G78E	NM_014961.3	NP_055776.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3	131	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)				endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			TCCTTCTGGGGGCCTCTAGAA	0.368																																					p.G191E		Atlas-SNP	.											.	RUFY3	61	.	0			c.G572A						PASS	.						37	41	40					4																	71629308		2195	4298	6493	SO:0001583	missense	22902	exon3			TCTGGGGGCCTCT	AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189		"Zinc fingers, FYVE domain containing"	30285	protein-coding gene	gene with protein product	"single axon-related 1"	611194				17439943	Standard	NM_001130709		Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910	ENST00000226328.4:c.392G>A	chr4.hg19:g.71629308G>A	ENSP00000226328:p.Gly131Glu	184.0	0.0	.		104.0	50.0	.	NM_001130709	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	Missense_Mutation	SNP	ENST00000226328.4	hg19	CCDS3547.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.907015	0.92107	.	.	ENSG00000018189	ENST00000503876;ENST00000417478;ENST00000381006;ENST00000226328;ENST00000536664;ENST00000513597;ENST00000502653	T;T;T;T;T;T;T	0.11712	2.75;2.75;2.75;2.75;2.75;2.75;2.75	5.13	5.13	0.70059	RUN (2);	0.000000	0.85682	D	0.000000	T	0.32823	0.0842	M	0.64997	1.995	0.80722	D	1	D;P;B;P	0.59767	0.986;0.498;0.397;0.956	D;P;P;D	0.76071	0.987;0.744;0.679;0.95	T	0.02093	-1.1215	10	0.72032	D	0.01	-9.749	18.944	0.92615	0.0:0.0:1.0:0.0	.	115;131;131;191	B4DKC2;Q7L099-3;Q7L099;Q7L099-2	.;.;RUFY3_HUMAN;.	E	67;191;131;131;115;67;78	ENSP00000426734:G67E;ENSP00000399771:G191E;ENSP00000370394:G131E;ENSP00000226328:G131E;ENSP00000443652:G115E;ENSP00000425574:G67E;ENSP00000425400:G78E	ENSP00000226328:G131E	G	+	2	0	RUFY3	71848172	1.000000	0.71417	0.979000	0.43373	0.957000	0.61999	9.744000	0.98853	2.569000	0.86673	0.591000	0.81541	GGG	.	.	.	none		0.368	RUFY3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252161.2	NM_014961		A	71629308	G	A	71629308	3	1	188	1	0	0	0	0	1	0	0	0	13753	1232	43	2	764	2	RUFY3	4	71629308	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10		71629308	119524968	21	11044											
NSUN2	54888	hgsc.bcm.edu	37	chr5	6600168	6600168	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acgtcattgtctggctgtccGgtgctggctgcactctcatt	4	14	11	12	2	3	0	2	0	2	0	5	0	4	0	1	3	2	4	1	3	0	2			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr5:6600168G>A	ENST00000264670.6	-	19	2486	c.2175C>T	c.(2173-2175)acC>acT	p.T725T	NSUN2_ENST00000506139.1_Silent_p.T690T|NSUN2_ENST00000539938.1_Silent_p.T489T	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	725					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						CTGGCTGTCCGGTGCTGGCTG	0.537																																					p.T725T		Atlas-SNP	.											.	NSUN2	82	.	0			c.C2175T						PASS	.						182	148	160					5																	6600168		2203	4300	6503	SO:0001819	synonymous_variant	54888	exon19			CTGTCCGGTGCTG	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.2175C>T	chr5.hg19:g.6600168G>A		125.0	0.0	.		146.0	64.0	.	NM_017755	A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Silent	SNP	ENST00000264670.6	hg19	CCDS3869.1																																																																																			.	.	.	none		0.537	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755		A	6600168	G	A	6600168	2	1	188	1	0	0	0	0	0	0	0	1	10685	1103	39	1		1	NSUN2	5	6600168	Silent	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10		6600168	174315092	22	11045											
FASTKD3	79072	hgsc.bcm.edu	37	chr5	7867451	7867451	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatcctccggggtaaatgttTccaatttttcaccttgaagt	9	16	7	9	1	1	1	1	1	0	0	4	1	4	1	4	2	0	2	4	2	5	6			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr5:7867451T>C	ENST00000264669.5	-	2	882	c.746A>G	c.(745-747)gAa>gGa	p.E249G	MTRR_ENST00000341013.6_5'Flank|MTRR_ENST00000502509.1_Intron|MTRR_ENST00000264668.2_5'Flank|FASTKD3_ENST00000513658.1_Intron|MTRR_ENST00000440940.2_5'Flank	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	249					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						GGTAAATGTTTCCAATTTTTC	0.368																																					p.E249G		Atlas-SNP	.											.	FASTKD3	88	.	0			c.A746G						PASS	.						80	85	83					5																	7867451		2203	4300	6503	SO:0001583	missense	79072	exon2			AATGTTTCCAATT	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.746A>G	chr5.hg19:g.7867451T>C	ENSP00000264669:p.Glu249Gly	31.0	0.0	.		32.0	11.0	.	NM_024091	Q9BVD3	Missense_Mutation	SNP	ENST00000264669.5	hg19	CCDS3873.1	.	.	.	.	.	.	.	.	.	.	T	17.00	3.275390	0.59649	.	.	ENSG00000124279	ENST00000264669	T	0.29142	1.58	4.85	3.65	0.41850	.	0.369914	0.32055	N	0.006643	T	0.31327	0.0793	M	0.72118	2.19	0.23421	N	0.997719	P	0.40144	0.704	B	0.36719	0.231	T	0.14531	-1.0469	10	0.38643	T	0.18	-20.1472	11.6008	0.51001	0.0:0.0:0.1494:0.8506	.	249	Q14CZ7	FAKD3_HUMAN	G	249	ENSP00000264669:E249G	ENSP00000264669:E249G	E	-	2	0	FASTKD3	7920451	0.203000	0.23435	0.094000	0.20943	0.730000	0.41778	2.603000	0.46266	0.835000	0.34877	0.528000	0.53228	GAA	.	.	.	none		0.368	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091		C	7867451	T	C	7867451	3	2	188	1	0	0	0	0	1	0	0	0	5694	1783	62	3	1266	3	FASTKD3	5	7867451	Missense_Mutation	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	1267283	7867451	173047809	23	11046											
PCDHB10	56126	hgsc.bcm.edu	37	chr5	140573409	140573413	+	Frame_Shift_Del	DEL	ACCCA	ACCCA	-																															accgtcactgacttggggacAcccaggctgaaaaccgagca																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	ACCCA	ACCCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr5:140573409_140573413delACCCA	ENST00000239446.4	+	1	1468_1472	c.1284_1288delACCCA	c.(1282-1290)acacccaggfs	p.PR429fs		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	429	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(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)			ACTTGGGGACACCCAGGCTGAAAAC	0.532																																					p.428_429del		Pindel	.											.	PCDHB10	177	.	0			c.1283_1287del						PASS	.																																			SO:0001589	frameshift_variant	56126	exon1			.	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"Cadherins / Protocadherins : Clustered"	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.1284_1288delACCCA	chr5.hg19:g.140573409_140573413delACCCA	ENSP00000239446:p.Pro429fs	188.0	0.0	.		145.0	23.0	0.159	NM_018930	Q96T99	Frame_Shift_Del	DEL	ENST00000239446.4	hg19	CCDS4252.1																																																																																			.	.	.	none		0.532	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		-	140573413	ACCCA	-	140573409	7	5	188	1	0	1	0	1	0	0	0	0	11542	146	6	0	1286	0	PCDHB10	5	140573409	Frame_Shift_Del	DEL	ACCCA	TCGA-GL-A59R-01A-11D-A26P-10	132705958	140573409	40341851	24	11047											
DOM3Z	1797	hgsc.bcm.edu	37	chr6	31938842	31938842	+	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	ggctgccagctgccagccctCctgccgctcatacggtgtcg	4	8	12	17	3	1	0	1	0	0	0	3	0	2	0	5	2	6	3	5	2	1	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr6:31938842C>T	ENST00000375349.3	-	3	850	c.439G>A	c.(439-441)Gag>Aag	p.E147K	DXO_ENST00000478221.1_5'UTR|DXO_ENST00000375356.3_Missense_Mutation_p.E147K|STK19_ENST00000375331.2_5'Flank|DXO_ENST00000337523.5_Missense_Mutation_p.E147K|STK19_ENST00000375333.2_5'Flank			O77932	DXO_HUMAN	decapping exoribonuclease	147					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)										TGCCAGCCCTCCTGCCGCTCA	0.642																																					p.E147K		Atlas-SNP	.											.	DOM3Z	20	.	0			c.G439A						PASS	.						81	91	88					6																	31938842		1508	2708	4216	SO:0001583	missense	1797	exon3			AGCCCTCCTGCCG	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.439G>A	chr6.hg19:g.31938842C>T	ENSP00000364498:p.Glu147Lys	90.0	0.0	.		88.0	34.0	.	NM_005510	A2CER3|B0UZ80|O15004|O78127|O78128|Q5ST60|Q6IPZ2|Q9NPK4	Missense_Mutation	SNP	ENST00000375349.3	hg19	CCDS4732.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.568158	0.86439	.	.	ENSG00000204348	ENST00000337523;ENST00000375349;ENST00000375356	T;T;T	0.19532	2.14;2.14;2.14	4.91	4.03	0.46877	.	0.054459	0.64402	D	0.000001	T	0.24547	0.0595	L	0.53249	1.67	0.49483	D	0.999795	P;D	0.76494	0.951;0.999	P;P	0.62298	0.487;0.9	T	0.01591	-1.1317	10	0.29301	T	0.29	-10.6299	14.2192	0.65815	0.0:0.849:0.151:0.0	.	147;147	F8WC68;O77932	.;DOM3Z_HUMAN	K	147	ENSP00000337759:E147K;ENSP00000364498:E147K;ENSP00000364505:E147K	ENSP00000337759:E147K	E	-	1	0	DOM3Z	32046821	1.000000	0.71417	0.983000	0.44433	0.793000	0.44817	7.160000	0.77495	1.266000	0.44231	-0.305000	0.09177	GAG	.	.	.	none		0.642	DXO-006	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076592.3			T	31938842	C	T	31938842	3	4	188	1	0	0	0	0	1	0	0	0	4707	864	30	2	771	2	DOM3Z	6	31938842	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10		31938842	139176225	25	11048											
PGK2	5232	hgsc.bcm.edu	37	chr6	49753793	49753793	+	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	agtgtctccaccccctataaCagtgatgcagcccttggaag	10	9	9	13	0	1	1	0	1	1	0	2	2	1	2	4	1	3	1	4	1	3	3			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr6:49753793C>G	ENST00000304801.3	-	1	1260	c.1108G>C	c.(1108-1110)Gtt>Ctt	p.V370L		NM_138733.4	NP_620061.2	P07205	PGK2_HUMAN	phosphoglycerate kinase 2	370					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)					CCCCCTATAACAGTGATGCAG	0.498																																					p.V370L		Atlas-SNP	.											.	PGK2	87	.	0			c.G1108C						PASS	.						155	152	153					6																	49753793		2203	4300	6503	SO:0001583	missense	5232	exon1			CTATAACAGTGAT	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.1108G>C	chr6.hg19:g.49753793C>G	ENSP00000305995:p.Val370Leu	195.0	0.0	.		189.0	53.0	.	NM_138733	B2R6Y8|Q9H107	Missense_Mutation	SNP	ENST00000304801.3	hg19	CCDS4930.1	.	.	.	.	.	.	.	.	.	.	C	13.46	2.243598	0.39697	.	.	ENSG00000170950	ENST00000304801	D	0.93712	-3.27	4.81	2.39	0.29439	Phosphoglycerate kinase, C-terminal (1);	0.100392	0.64402	D	0.000003	D	0.84347	0.5452	L	0.56199	1.76	0.22719	N	0.998819	B	0.14805	0.011	B	0.28553	0.091	T	0.79105	-0.1940	10	0.87932	D	0	-12.902	7.2513	0.26150	0.0:0.2024:0.0:0.7976	.	370	P07205	PGK2_HUMAN	L	370	ENSP00000305995:V370L	ENSP00000305995:V370L	V	-	1	0	PGK2	49861752	1.000000	0.71417	0.998000	0.56505	0.921000	0.55340	3.605000	0.54088	0.407000	0.25591	-0.295000	0.09555	GTT	.	.	.	none		0.498	PGK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040872.1			G	49753793	C	G	49753793	3	3	188	1	0	0	0	0	1	0	0	0	11798	478	17	4	149	4	PGK2	6	49753793	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	17814951	49753793	121361274	26	11049											
TRAF3IP2	10758	hgsc.bcm.edu	37	chr6	111912891	111912891	+	Frame_Shift_Del	DEL	A	A	-																															cattgattacgtttttccatAaatgaaaactgatgctctgc																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr6:111912891delA	ENST00000340026.6	-	3	1020	c.426delT	c.(424-426)tttfs	p.F142fs	TRAF3IP2_ENST00000368761.5_Frame_Shift_Del_p.F133fs|TRAF3IP2_ENST00000392556.4_5'UTR|TRAF3IP2-AS1_ENST00000532353.1_RNA|TRAF3IP2_ENST00000359831.4_Frame_Shift_Del_p.F133fs			O43734	CIKS_HUMAN	TRAF3 interacting protein 2	142	Mediates interaction with TRAF6.				B cell apoptotic process (GO:0001783)|humoral immune response (GO:0006959)|immunoglobulin secretion (GO:0048305)|intracellular signal transduction (GO:0035556)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)					central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	18		all_cancers(87;7.87e-06)|Acute lymphoblastic leukemia(125;3.61e-09)|all_hematologic(75;2.63e-07)|all_epithelial(87;0.0024)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.033)|all cancers(137;0.0412)|Epithelial(106;0.0732)		GTTTTTCCATAAATGAAAACT	0.512																																					p.M134fs		Atlas-Indel,Pindel	.											.	TRAF3IP2	35	.	0			c.400delA						PASS	.						51	50	50					6																	111912891		2203	4300	6503	SO:0001589	frameshift_variant	10758	exon2			.	AF136405	CCDS5093.1, CCDS55049.1, CCDS55050.1	6q21	2008-09-05	2002-06-20	2005-04-13	ENSG00000056972	ENSG00000056972			1343	protein-coding gene	gene with protein product		607043	"chromosome 6 open reading frame 5", "chromosome 6 open reading frame 2"	C6orf4, C6orf5, C6orf6, C6orf2		10962033, 10962024	Standard	NR_028338		Approved	DKFZP586G0522, ACT1, CIKS	uc003pvf.4	O43734	OTTHUMG00000015379	ENST00000340026.6:c.426delT	chr6.hg19:g.111912891delA	ENSP00000345984:p.Phe142fs	82.0	0.0	0		86.0	32.0	0.372093	NM_001164281	B2RAY9|E1P555|Q5R3A3|Q7Z6Q1|Q7Z6Q2|Q7Z6Q3|Q9H5W2|Q9H6Y3|Q9NS14|Q9UG72	Frame_Shift_Del	DEL	ENST00000340026.6	hg19																																																																																				.	.	.	none		0.512	TRAF3IP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000041841.2			-	111912891	A	-	111912891	7	5	188	1	0	1	0	1	0	0	0	0	16453	359	13	0	1330	0	TRAF3IP2	6	111912891	Frame_Shift_Del	DEL	A	TCGA-GL-A59R-01A-11D-A26P-10	62159098	111912891	59202176	27	11050											
GIGYF1	64599	hgsc.bcm.edu	37	chr7	100279805	100279805	+	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	caggcaggaacggatataatCgtggacatcatagggggatt	13	8	14	6	2	1	0	1	0	0	0	2	4	1	4	0	6	1	1	0	6	4	4			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr7:100279805C>T	ENST00000275732.5	-	22	4024	c.2815G>A	c.(2815-2817)Gat>Aat	p.D939N	GIGYF1_ENST00000471340.2_5'Flank	NM_022574.4	NP_072096.2	O75420	PERQ1_HUMAN	GRB10 interacting GYF protein 1	939					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)					CGGATATAATCGTGGACATCA	0.597																																					p.D939N		Atlas-SNP	.											.	GIGYF1	113	.	0			c.G2815A						PASS	.						74	79	77					7																	100279805		2203	4300	6503	SO:0001583	missense	64599	exon22			TATAATCGTGGAC	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.2815G>A	chr7.hg19:g.100279805C>T	ENSP00000275732:p.Asp939Asn	50.0	0.0	.		81.0	5.0	.	NM_022574	Q6Y7W7|Q8WZ38	Missense_Mutation	SNP	ENST00000275732.5	hg19	CCDS34708.1	.	.	.	.	.	.	.	.	.	.	.	17.25	3.341351	0.60963	.	.	ENSG00000146830	ENST00000539430;ENST00000275732	D	0.84223	-1.82	5.14	5.14	0.70334	.	0.053328	0.64402	D	0.000001	T	0.78748	0.4332	L	0.59912	1.85	0.51482	D	0.999924	P	0.47409	0.895	B	0.25506	0.061	D	0.83414	0.0029	10	0.59425	D	0.04	-21.0708	16.146	0.81569	0.0:1.0:0.0:0.0	.	939	O75420	PERQ1_HUMAN	N	658;939	ENSP00000275732:D939N	ENSP00000275732:D939N	D	-	1	0	GIGYF1	100117741	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	4.780000	0.62382	2.672000	0.90937	0.555000	0.69702	GAT	.	.	.	none		0.597	GIGYF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347205.2	NM_022574		T	100279805	C	T	100279805	3	4	188	1	0	0	0	0	1	0	0	0	6384	884	31	1	304	1	GIGYF1	7	100279805	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10		100279805	58858858	28	11051											
FOXP2	93986	hgsc.bcm.edu	37	chr7	114302186	114302186	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tagaaaatgttaaaggagcaGtatggactgtggatgaagta	16	10	13	2	0	0	2	0	1	0	1	0	5	0	5	0	3	1	4	0	3	8	4			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr7:114302186G>A	ENST00000393494.2	+	14	1993	c.1714G>A	c.(1714-1716)Gta>Ata	p.V572I	FOXP2_ENST00000393498.2_Missense_Mutation_p.V551I|FOXP2_ENST00000393500.3_3'UTR|FOXP2_ENST00000408937.3_Missense_Mutation_p.V597I|FOXP2_ENST00000350908.4_Missense_Mutation_p.V572I|FOXP2_ENST00000393489.3_Missense_Mutation_p.V480I|FOXP2_ENST00000403559.4_Missense_Mutation_p.V589I|FOXP2_ENST00000393491.3_Missense_Mutation_p.V387I			O15409	FOXP2_HUMAN	forkhead box P2	572					camera-type eye development (GO:0043010)|caudate nucleus development (GO:0021757)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|growth (GO:0040007)|lung alveolus development (GO:0048286)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of mesenchymal cell proliferation (GO:0002053)|post-embryonic development (GO:0009791)|putamen development (GO:0021758)|righting reflex (GO:0060013)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|vocal learning (GO:0042297)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						TAAAGGAGCAGTATGGACTGT	0.393																																					p.V597I		Atlas-SNP	.											.	FOXP2	133	.	0			c.G1789A						PASS	.						139	129	133					7																	114302186		2203	4300	6503	SO:0001583	missense	93986	exon15			GGAGCAGTATGGA	U80741	CCDS5760.1, CCDS5761.1, CCDS43635.1, CCDS5761.2, CCDS55154.1	7q31	2008-07-18			ENSG00000128573	ENSG00000128573		"Forkhead boxes"	13875	protein-coding gene	gene with protein product	"trinucleotide repeat containing 10", "forkhead/winged-helix transcription factor", "speech and language disorder 1", "CAG repeat protein 44"	605317		TNRC10, SPCH1		11586359, 9225980	Standard	NM_014491		Approved	CAGH44	uc003vgz.3	O15409	OTTHUMG00000023131	ENST00000393494.2:c.1714G>A	chr7.hg19:g.114302186G>A	ENSP00000377132:p.Val572Ile	157.0	0.0	.		245.0	53.0	.	NM_148898	A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	Missense_Mutation	SNP	ENST00000393494.2	hg19	CCDS5760.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.967741	0.74131	.	.	ENSG00000128573	ENST00000393494;ENST00000408937;ENST00000403559;ENST00000350908;ENST00000393498;ENST00000393489;ENST00000393491	D;D;D;D;D;D	0.95447	-3.71;-3.71;-3.71;-3.71;-3.71;-3.71	5.65	5.65	0.86999	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.85682	D	0.000000	D	0.97692	0.9243	M	0.76838	2.35	0.80722	D	1	P;P;D;P;P	0.67145	0.92;0.92;0.996;0.92;0.902	D;D;D;D;D	0.70227	0.935;0.956;0.968;0.935;0.927	D	0.97929	1.0319	10	0.87932	D	0	.	20.0965	0.97849	0.0:0.0:1.0:0.0	.	571;589;387;572;597	B7ZLK5;B4DLD9;Q0PRL4;O15409;O15409-4	.;.;.;FOXP2_HUMAN;.	I	572;597;589;572;549;480;387	ENSP00000377132:V572I;ENSP00000386200:V597I;ENSP00000385069:V589I;ENSP00000265436:V572I;ENSP00000377129:V480I;ENSP00000377130:V387I	ENSP00000265436:V572I	V	+	1	0	FOXP2	114089422	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	9.813000	0.99286	2.824000	0.97209	0.655000	0.94253	GTA	.	.	.	none		0.393	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1	NM_014491		A	114302186	G	A	114302186	3	1	188	1	0	0	0	0	1	0	0	0	6034	1029	36	2	1931	2	FOXP2	7	114302186	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	14022381	114302186	44836477	29	11052											
MET	4233	hgsc.bcm.edu	37	chr7	116415114	116415115	+	Missense_Mutation	DNP	GT	GT	AG																															tccaggcagtgcagcatgtaGtgattgggcccagtagcctg																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G|T	G|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr7:116415114_116415115GT>AG	ENST00000318493.6	+	15	3449_3450	c.3262_3263GT>AG	c.(3262-3264)GTg>AGg	p.V1088R	MET_ENST00000397752.3_Missense_Mutation_p.V1070R|MET_ENST00000539704.1_5'Flank			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.V1088E(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)			GCAGCATGTAGTGATTGGGCCC	0.431			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.V1088M|p.V1088G		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	Substitution - Missense(1)	kidney(1)	c.G3262A|c.T3263G						PASS	.																																			SO:0001583	missense	4233	exon15	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	CATGTAGTGATTG|ATGTAGTGATTGG	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	Exception_encountered	chr7.hg19:g.116415114_116415115delinsAG	ENSP00000317272:p.Val1088Arg	133.0|132.0	0.0	.		205.0|202.0	127.0|125.0	.	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1																																																																																			.	.	.	none		0.431	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			AG	116415115	GT	AG	116415114	3	1	188	1	0	0	0	0	1	0	0	0	9492	1029	36	2	3316	2	MET	7	116415114	Missense_Mutation	DNP	GT	TCGA-GL-A59R-01A-11D-A26P-10	2112928	116415114	42723549	30	11053											
AASS	10157	hgsc.bcm.edu	37	chr7	121717970	121717971	+	Missense_Mutation	DNP	CA	CA	AG																															tgaaaagccattgatgtcccCataagccacaagatcaatcg																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr7:121717970_121717971CA>AG	ENST00000393376.1	-	22	2678_2679	c.2583_2584TG>CT	c.(2581-2586)taTGgg>taCTgg	p.G862W	AASS_ENST00000473553.1_5'UTR|AASS_ENST00000417368.2_Missense_Mutation_p.G862W			Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase	862	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						TTGATGTCCCCATAAGCCACAA	0.436																																					p.G862W|p.Y861Y		Atlas-SNP	.											.	AASS	123	.	0			c.G2584T|c.T2583C						PASS	.																																			SO:0001583	missense	10157	exon23			TGTCCCCATAAGC|GTCCCCATAAGCC	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.2583_2584delinsAG	chr7.hg19:g.121717970_121717971delinsAG	ENSP00000377040:p.Gly862Trp	143.0|145.0	0.0	.		222.0	21.0	.	NM_005763	O95462	Missense_Mutation|Silent	SNP	ENST00000393376.1	hg19	CCDS5783.1																																																																																			.	.	.	none		0.436	AASS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347300.1	NM_005763		AG	121717971	CA	AG	121717970	3	1	188	1	0	0	0	0	1	0	0	0	24	594	21	4	204	4	AASS	7	121717970	Missense_Mutation	DNP	CA	TCGA-GL-A59R-01A-11D-A26P-10	5302856	121717970	37420693	31	11054											
KIAA1549	57670	hgsc.bcm.edu	37	chr7	138566237	138566237	+	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	cttcagaggtcctggcagtgGcgctggctcatgaataatca	9	10	12	10	1	3	2	3	1	0	1	4	2	4	2	1	4	0	3	1	4	2	2			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr7:138566237G>T	ENST00000422774.1	-	11	4174	c.4126C>A	c.(4126-4128)Cca>Aca	p.P1376T	KIAA1549_ENST00000242365.4_Missense_Mutation_p.P1326T|KIAA1549_ENST00000440172.1_Missense_Mutation_p.P1376T			Q9HCM3	K1549_HUMAN	KIAA1549	1376						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						CCTGGCAGTGGCGCTGGCTCA	0.512			O	BRAF	pilocytic astrocytoma																																p.P1376T	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549	314	.	0			c.C4126A						PASS	.						115	121	119					7																	138566237		2083	4214	6297	SO:0001583	missense	57670	exon11			GCAGTGGCGCTGG		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.4126C>A	chr7.hg19:g.138566237G>T	ENSP00000416040:p.Pro1376Thr	196.0	0.0	.		259.0	71.0	.	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	hg19	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.101871	0.76983	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.25912	1.77;1.77;1.79	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.51227	0.1662	M	0.65975	2.015	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;0.999	T	0.38067	-0.9678	10	0.41790	T	0.15	.	18.5236	0.90963	0.0:0.0:1.0:0.0	.	1376;160;1376;160	Q9HCM3;Q9HCM3-4;Q9HCM3-2;Q9HCM3-3	K1549_HUMAN;.;.;.	T	1376;1326;1376	ENSP00000406661:P1376T;ENSP00000242365:P1326T;ENSP00000416040:P1376T	ENSP00000242365:P1326T	P	-	1	0	KIAA1549	138216777	1.000000	0.71417	0.686000	0.30086	0.849000	0.48306	7.124000	0.77185	2.716000	0.92895	0.655000	0.94253	CCA	.	.	.	none		0.512	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			T	138566237	G	T	138566237	3	4	188	1	0	0	0	0	1	0	0	0	8251	1203	42	4	1766	4	KIAA1549	7	138566237	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	16848267	138566237	20572426	32	11055											
ANK1	286	hgsc.bcm.edu	37	chr8	41547822	41547822	+	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	gtacttcatcgccttgcgcaGaaacgacagggaccctcccg	9	7	10	15	4	1	1	1	0	0	1	3	3	2	2	3	1	3	2	3	1	2	3			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr8:41547822G>A	ENST00000347528.4	-	33	4110	c.4027C>T	c.(4027-4029)Ctg>Ttg	p.L1343L	ANK1_ENST00000265709.8_Silent_p.L1384L|ANK1_ENST00000289734.7_Silent_p.L1343L|ANK1_ENST00000396942.1_Silent_p.L1343L|ANK1_ENST00000396945.1_Silent_p.L1343L|ANK1_ENST00000352337.4_Silent_p.L1343L|ANK1_ENST00000379758.2_Silent_p.L1343L	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	1343	UPA domain. {ECO:0000250}.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			GCCTTGCGCAGAAACGACAGG	0.597																																					p.L1384L		Atlas-SNP	.											.	ANK1	497	.	0			c.C4150T						PASS	.						133	112	119					8																	41547822		2203	4300	6503	SO:0001819	synonymous_variant	286	exon34			TGCGCAGAAACGA	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.4027C>T	chr8.hg19:g.41547822G>A		146.0	0.0	.		136.0	57.0	.	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Silent	SNP	ENST00000347528.4	hg19	CCDS6119.1	.	.	.	.	.	.	.	.	.	.	G	8.890	0.953747	0.18431	.	.	ENSG00000029534	ENST00000520299	.	.	.	5.08	4.2	0.49525	.	.	.	.	.	T	0.55210	0.1906	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52734	-0.8536	4	.	.	.	.	6.0089	0.19562	0.1621:0.0:0.6843:0.1536	.	.	.	.	F	664	.	.	S	-	2	0	ANK1	41666979	1.000000	0.71417	0.884000	0.34674	0.838000	0.47535	1.678000	0.37586	1.352000	0.45808	0.563000	0.77884	TCT	.	.	.	none		0.597	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		A	41547822	G	A	41547822	2	1	188	1	0	0	0	0	0	0	0	1	620	933	33	2		2	ANK1	8	41547822	Silent	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10		41547822	104816200	33	11056											
ZBTB10	65986	hgsc.bcm.edu	37	chr8	81412103	81412103	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagctatcttcaaatgagTgaagttgttcaaacttgccg	11	12	9	9	1	3	2	2	2	1	0	3	2	3	2	2	0	3	3	2	0	4	5			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr8:81412103T>C	ENST00000430430.1	+	3	2126	c.1347T>C	c.(1345-1347)agT>agC	p.S449S	ZBTB10_ENST00000455036.3_Silent_p.S449S|ZBTB10_ENST00000426744.2_Silent_p.S449S|ZBTB10_ENST00000379091.4_Silent_p.S157S	NM_001277145.1	NP_001264074.1	Q96DT7	ZBT10_HUMAN	zinc finger and BTB domain containing 10	449					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(4)	20	all_cancers(3;1.68e-09)|all_epithelial(4;5.13e-11)|Lung NSC(7;1.75e-07)|all_lung(9;7.38e-07)|Breast(3;2.96e-06)		BRCA - Breast invasive adenocarcinoma(6;0.000434)|Epithelial(68;0.00486)|all cancers(69;0.0296)			TTCAAATGAGTGAAGTTGTTC	0.373																																					p.S449S		Atlas-SNP	.											.	ZBTB10	51	.	0			c.T1347C						PASS	.						88	81	83					8																	81412103		1826	4092	5918	SO:0001819	synonymous_variant	65986	exon2			AATGAGTGAAGTT	AK022814	CCDS47880.1, CCDS64920.1	8q13-q21.1	2013-01-09			ENSG00000205189	ENSG00000205189		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	30953	protein-coding gene	gene with protein product						12477932	Standard	NM_001105539		Approved	RINZF, FLJ12752	uc003ybx.5	Q96DT7	OTTHUMG00000155016	ENST00000430430.1:c.1347T>C	chr8.hg19:g.81412103T>C		83.0	0.0	.		67.0	21.0	.	NM_023929	A4FVD0|Q86W96|Q8IXI9|Q96MH9	Silent	SNP	ENST00000430430.1	hg19	CCDS47880.1																																																																																			.	.	.	none		0.373	ZBTB10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338055.2	NM_023929		C	81412103	T	C	81412103	2	2	188	1	0	0	0	0	0	0	0	1	17535	1693	59	3		3	ZBTB10	8	81412103	Silent	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	39864281	81412103	64951919	34	11057											
WWP1	11059	hgsc.bcm.edu	37	chr8	87447714	87447715	+	Frame_Shift_Ins	INS	-	-	AATTTTT																															cacaaattgcttatgaacgcINSggctttaggtggaagcttgc																								rs139712565		TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr8:87447714_87447715insAATTTTT	ENST00000517970.1	+	15	1942_1943	c.1635_1636insAATTTTT	c.(1636-1638)ggcfs	p.G546fs	WWP1_ENST00000341922.2_Frame_Shift_Ins_p.G416fs|WWP1_ENST00000265428.4_Frame_Shift_Ins_p.G546fs|WWP1_ENST00000349423.2_Frame_Shift_Ins_p.G328fs	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	546					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						CTTATGAACGCGGCTTTAGGTG	0.302																																					p.R545fs		Atlas-INDEL	.											.	WWP1	97	.	0			c.1635_1636insAATTTTT						PASS	.																																			SO:0001589	frameshift_variant	11059	exon15			.	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	Exception_encountered	chr8.hg19:g.87447714_87447715insAATTTTT	ENSP00000427793:p.Gly546fs	172.0	0.0	0		120.0	17.0	0.141667	NM_007013	O00307|Q5YLC1|Q96BP4	Frame_Shift_Ins	INS	ENST00000517970.1	hg19	CCDS6242.1																																																																																			.	.	.	none		0.302	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013		AATTTTT	87447715	-	AATTTTT	87447714	7	5	188	1	0	1	1	0	0	0	0	0	17427	755	27	0	1685	0	WWP1	8	87447714	Frame_Shift_Ins	INS	-	TCGA-GL-A59R-01A-11D-A26P-10	6035611	87447714	58916308	35	11058	103	2									
WWP1	11059	hgsc.bcm.edu	37	chr8	87447715	87447715	+	Frame_Shift_Del	DEL	G	G	-																															cacaaattgcttatgaacgcGgctttaggtggaagcttgct																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr8:87447715delG	ENST00000517970.1	+	15	1943	c.1636delG	c.(1636-1638)ggcfs	p.G546fs	WWP1_ENST00000341922.2_Frame_Shift_Del_p.G416fs|WWP1_ENST00000265428.4_Frame_Shift_Del_p.G546fs|WWP1_ENST00000349423.2_Frame_Shift_Del_p.G328fs	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	546					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						TTATGAACGCGGCTTTAGGTG	0.303																																					p.R545fs		Pindel	.											.	WWP1	97	.	0			c.1635delC						PASS	.						90	91	91					8																	87447715		2203	4300	6503	SO:0001589	frameshift_variant	11059	exon15			.	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.1636delG	chr8.hg19:g.87447715delG	ENSP00000427793:p.Gly546fs	172.0	0.0	.		119.0	15.0	0.126	NM_007013	O00307|Q5YLC1|Q96BP4	Frame_Shift_Del	DEL	ENST00000517970.1	hg19	CCDS6242.1																																																																																			.	.	.	none		0.303	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013		-	87447715	G	-	87447715	7	5	188	1	0	1	0	1	0	0	0	0	17427	1116	39	0	1686	0	WWP1	8	87447715	Frame_Shift_Del	DEL	G	TCGA-GL-A59R-01A-11D-A26P-10	1	87447715	58916307	36	11059	103	2									
JAK2	3717	hgsc.bcm.edu	37	chr9	5078361	5078361	+	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	caaaaatattctgcttatcaGagaagaagacaggaagacag	19	7	9	6	0	2	4	1	0	1	4	2	6	2	5	0	1	1	1	0	1	7	3			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr9:5078361G>T	ENST00000381652.3	+	16	2542	c.2048G>T	c.(2047-2049)aGa>aTa	p.R683I	JAK2_ENST00000539801.1_Missense_Mutation_p.R683I|JAK2_ENST00000544510.1_Missense_Mutation_p.R534I|AL161450.1_ENST00000601793.1_Intron	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	683	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	p.R683T(2)|p.I682_R683insTG(1)|p.R683K(1)|p.I682_D686>(1)	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)	CTGCTTATCAGAGAAGAAGAC	0.363		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial																												p.R683I		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	JAK2,colon,carcinoma,-1,3	JAK2	35466	.	5	Substitution - Missense(3)|Insertion - In frame(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(5)	c.G2048T						PASS	.						149	163	158					9																	5078361		2203	4300	6503	SO:0001583	missense	3717	exon16	Familial Cancer Database		TTATCAGAGAAGA		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.2048G>T	chr9.hg19:g.5078361G>T	ENSP00000371067:p.Arg683Ile	66.0	1.0	.		71.0	25.0	.	NM_004972	O14636|O75297	Missense_Mutation	SNP	ENST00000381652.3	hg19	CCDS6457.1	.	.	.	.	.	.	.	.	.	.	G	32	5.158488	0.94686	.	.	ENSG00000096968	ENST00000539801;ENST00000381652;ENST00000544510	D;D;D	0.83163	-1.69;-1.69;-1.69	5.55	5.55	0.83447	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	0.92381	0.7582	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92930	0.6363	10	0.87932	D	0	-24.9121	19.4912	0.95050	0.0:0.0:1.0:0.0	.	683	O60674	JAK2_HUMAN	I	683;683;534	ENSP00000440387:R683I;ENSP00000371067:R683I;ENSP00000443103:R534I	ENSP00000371067:R683I	R	+	2	0	JAK2	5068361	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.371000	0.97162	2.771000	0.95319	0.561000	0.74099	AGA	.	.	.	none		0.363	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			T	5078361	G	T	5078361	3	4	188	1	0	0	0	0	1	0	0	0	7945	942	33	4	2102	4	JAK2	9	5078361	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10		5078361	136135070	37	11060											
DDX58	23586	hgsc.bcm.edu	37	chr9	32459420	32459420	+	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	gccaaggctttgcactttctGcagagcagttttttattttc	7	17	8	9	0	1	1	0	0	1	1	2	1	1	1	1	1	3	5	1	1	2	7			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr9:32459420G>T	ENST00000379883.2	-	17	2587	c.2430C>A	c.(2428-2430)tgC>tgA	p.C810*	DDX58_ENST00000379882.1_Nonsense_Mutation_p.C765*|DDX58_ENST00000542096.1_Nonsense_Mutation_p.C739*|DDX58_ENST00000379868.1_Nonsense_Mutation_p.C607*	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	810	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)		TGCACTTTCTGCAGAGCAGTT	0.388																																					p.C810X		Atlas-SNP	.											.	DDX58	82	.	0			c.C2430A						PASS	.						184	166	172					9																	32459420		2203	4300	6503	SO:0001587	stop_gained	23586	exon17			CTTTCTGCAGAGC	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.2430C>A	chr9.hg19:g.32459420G>T	ENSP00000369213:p.Cys810*	57.0	0.0	.		47.0	4.0	.	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Nonsense_Mutation	SNP	ENST00000379883.2	hg19	CCDS6526.1	.	.	.	.	.	.	.	.	.	.	G	38	7.254024	0.98168	.	.	ENSG00000107201	ENST00000379882;ENST00000379883;ENST00000379868;ENST00000542096	.	.	.	4.79	-0.4	0.12411	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.0038	9.3509	0.38138	0.719:0.0:0.281:0.0	.	.	.	.	X	765;810;607;739	.	ENSP00000369197:C607X	C	-	3	2	DDX58	32449420	0.540000	0.26410	0.928000	0.36995	0.005000	0.04900	0.443000	0.21644	0.069000	0.16605	0.655000	0.94253	TGC	.	.	.	none		0.388	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314		T	32459420	G	T	32459420	4	4	188	1	0	0	0	0	0	1	0	0	4377	1311	46	4	355	4	DDX58	9	32459420	Nonsense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	27381059	32459420	108754011	38	11061											
VPS13A	23230	hgsc.bcm.edu	37	chr9	79820297	79820297	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgaagccgtattggaagaaAtttatttacttatagtgcct	12	16	8	5	1	0	2	0	1	0	1	0	3	0	3	2	1	3	1	2	1	8	9			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr9:79820297A>G	ENST00000360280.3	+	4	516	c.256A>G	c.(256-258)Att>Gtt	p.I86V	VPS13A_ENST00000376636.3_Missense_Mutation_p.I86V|VPS13A_ENST00000357409.5_Missense_Mutation_p.I86V|VPS13A_ENST00000376634.4_Missense_Mutation_p.I86V	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	86					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						ATTGGAAGAAATTTATTTACT	0.229																																					p.I86V		Atlas-SNP	.											.	VPS13A	735	.	0			c.A256G						PASS	.						38	44	42					9																	79820297		2194	4279	6473	SO:0001583	missense	23230	exon4			GAAGAAATTTATT	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.256A>G	chr9.hg19:g.79820297A>G	ENSP00000353422:p.Ile86Val	59.0	0.0	.		55.0	34.0	.	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	hg19	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	A	8.130	0.782854	0.16189	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.80304	-1.36;-1.36;-1.36;-1.36	5.62	4.48	0.54585	.	0.063343	0.64402	D	0.000008	T	0.55593	0.1930	N	0.04880	-0.145	0.80722	D	1	B;B;B;B	0.24882	0.012;0.113;0.046;0.046	B;B;B;B	0.25614	0.018;0.062;0.027;0.027	T	0.51980	-0.8636	10	0.02654	T	1	.	7.951	0.30014	0.7743:0.0:0.2257:0.0	.	86;86;86;86	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	V	86	ENSP00000365821:I86V;ENSP00000365823:I86V;ENSP00000353422:I86V;ENSP00000349985:I86V	ENSP00000349985:I86V	I	+	1	0	VPS13A	79010117	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	4.485000	0.60279	0.952000	0.37798	0.477000	0.44152	ATT	.	.	.	none		0.229	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		G	79820297	A	G	79820297	3	3	188	1	0	0	0	0	1	0	0	0	17201	101	4	3	270	3	VPS13A	9	79820297	Missense_Mutation	SNP	A	TCGA-GL-A59R-01A-11D-A26P-10	47360877	79820297	61393134	39	11062											
CTSL2	1515	hgsc.bcm.edu	37	chr9	99799669	99799669	+	Missense_Mutation	SNP	T	T	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	caacccatcatctgcctgaaTtcttcattggtcttcaagga	10	13	6	12	0	6	1	3	1	3	0	6	2	6	2	2	2	2	0	2	2	3	4			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr9:99799669T>G	ENST00000259470.5	-	4	510	c.261A>C	c.(259-261)gaA>gaC	p.E87D	CTSV_ENST00000479932.1_5'UTR|CTSV_ENST00000538255.1_Missense_Mutation_p.E87D	NM_001333.3	NP_001324.2	O60911	CATL2_HUMAN	cathepsin V	87					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|autophagic cell death (GO:0048102)|catagen (GO:0042637)|cellular response to starvation (GO:0009267)|decidualization (GO:0046697)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|multicellular organismal aging (GO:0010259)|negative regulation of keratinocyte proliferation (GO:0010839)|nerve development (GO:0021675)|protein autoprocessing (GO:0016540)|regulation of actin cytoskeleton reorganization (GO:2000249)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to gonadotropin (GO:0034698)|Sertoli cell differentiation (GO:0060008)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|microvillus (GO:0005902)|neuron projection (GO:0043005)|nucleolus (GO:0005730)|perikaryon (GO:0043204)	aminopeptidase activity (GO:0004177)|cysteine-type carboxypeptidase activity (GO:0016807)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|peptide binding (GO:0042277)										TCTGCCTGAATTCTTCATTGG	0.418																																					p.E87D		Atlas-SNP	.											.	CTSL2	40	.	0			c.A261C						PASS	.						100	100	100					9																	99799669		2203	4300	6503	SO:0001583	missense	1515	exon4			CCTGAATTCTTCA	Y14734	CCDS6723.1	9q22.33	2013-06-27	2013-06-27	2013-06-27	ENSG00000136943	ENSG00000136943		"Cathepsins"	2538	protein-coding gene	gene with protein product		603308	"cathepsin L2"	CTSL2		9563472, 10029531	Standard	NM_001201575		Approved	CTSU	uc004awt.3	O60911	OTTHUMG00000020314	ENST00000259470.5:c.261A>C	chr9.hg19:g.99799669T>G	ENSP00000259470:p.Glu87Asp	108.0	0.0	.		114.0	55.0	.	NM_001201575	O60233|Q2TB86|Q5T1U0	Missense_Mutation	SNP	ENST00000259470.5	hg19	CCDS6723.1	.	.	.	.	.	.	.	.	.	.	T	19.18	3.776996	0.70107	.	.	ENSG00000136943	ENST00000259470;ENST00000538255	D;D	0.94092	-3.35;-3.35	3.81	2.68	0.31781	Proteinase inhibitor I29, cathepsin propeptide (2);	0.000000	0.85682	D	0.000000	D	0.97356	0.9135	H	0.97365	3.99	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96055	0.9034	9	.	.	.	.	7.4637	0.27310	0.0:0.1067:0.0:0.8933	.	87;87	B2R717;O60911	.;CATL2_HUMAN	D	87	ENSP00000259470:E87D;ENSP00000445052:E87D	.	E	-	3	2	CTSL2	98839490	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	0.938000	0.28965	0.848000	0.35191	0.459000	0.35465	GAA	.	.	.	none		0.418	CTSV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053301.2	NM_001333		G	99799669	T	G	99799669	3	3	188	1	0	0	0	0	1	0	0	0	4041	1490	52	5	763	5	CTSL2	9	99799669	Missense_Mutation	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	19979372	99799669	41413762	40	11063											
DHTKD1	55526	hgsc.bcm.edu	37	chr10	12162862	12162863	+	Frame_Shift_Ins	INS	-	-	T																															cacttgcaccagcatgaagaINStatcctcgccaagaccttcg																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr10:12162862_12162863insT	ENST00000263035.4	+	17	2797_2798	c.2735_2736insT	c.(2734-2739)gatatcfs	p.I913fs		NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	913					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)			CAGCATGAAGATATCCTCGCCA	0.5																																					p.D912fs		Atlas-Indel,Pindel	.											.	DHTKD1	104	.	0			c.2735_2736insT						PASS	.																																			SO:0001589	frameshift_variant	55526	exon17			.	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.2736dupT	chr10.hg19:g.12162863_12162863dupT	ENSP00000263035:p.Ile913fs	94.0	0.0	0		90.0	37.0	0.411111	NM_018706	Q68CU5|Q9BUM8|Q9HCE2	Frame_Shift_Ins	INS	ENST00000263035.4	hg19	CCDS7087.1																																																																																			.	.	.	none		0.5	DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046777.1	NM_018706		T	12162863	-	T	12162862	7	5	188	1	0	1	1	0	0	0	0	0	4502	333	12	0	2801	0	DHTKD1	10	12162862	Frame_Shift_Ins	INS	-	TCGA-GL-A59R-01A-11D-A26P-10		12162862	123371885	41	11064											
JMJD1C	221037	hgsc.bcm.edu	37	chr10	64968540	64968540	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acagaccgtaatggttccatAaaagcttttctttctaattc	12	15	5	9	1	2	1	0	0	2	1	4	1	3	1	2	1	1	3	2	1	4	8			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr10:64968540A>G	ENST00000399262.2	-	10	3107	c.2889T>C	c.(2887-2889)ttT>ttC	p.F963F	JMJD1C_ENST00000399251.1_Silent_p.F744F|JMJD1C_ENST00000542921.1_Silent_p.F781F|JMJD1C_ENST00000402544.1_Silent_p.F744F	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	963					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)					ATGGTTCCATAAAAGCTTTTC	0.348																																					p.F963F		Atlas-SNP	.											.	JMJD1C	347	.	0			c.T2889C						PASS	.						49	45	46					10																	64968540		1815	4081	5896	SO:0001819	synonymous_variant	221037	exon10			TTCCATAAAAGCT	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.2889T>C	chr10.hg19:g.64968540A>G		29.0	0.0	.		28.0	11.0	.	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Silent	SNP	ENST00000399262.2	hg19	CCDS41532.1																																																																																			.	.	.	none		0.348	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		G	64968540	A	G	64968540	2	3	188	1	0	0	0	0	0	0	0	1	7957	359	13	3		3	JMJD1C	10	64968540	Silent	SNP	A	TCGA-GL-A59R-01A-11D-A26P-10	52805678	64968540	70566207	42	11065											
P4HA1	5033	hgsc.bcm.edu	37	chr10	74810906	74810906	+	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	tttctttggtgtagttttctGatcagattggtcatctgaag	7	19	10	5	0	5	3	2	2	3	1	5	3	5	3	0	2	0	2	0	2	2	6			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr10:74810906G>A	ENST00000307116.2	-	7	921	c.805C>T	c.(805-807)Cag>Tag	p.Q269*	P4HA1_ENST00000394890.2_Nonsense_Mutation_p.Q269*|P4HA1_ENST00000440381.1_Nonsense_Mutation_p.Q269*|P4HA1_ENST00000373008.2_Nonsense_Mutation_p.Q269*|P4HA1_ENST00000412021.2_Nonsense_Mutation_p.Q269*|P4HA1_ENST00000263556.3_Nonsense_Mutation_p.Q269*			P13674	P4HA1_HUMAN	prolyl 4-hydroxylase, alpha polypeptide I	269					collagen fibril organization (GO:0030199)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|procollagen-proline 4-dioxygenase complex (GO:0016222)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|procollagen-proline 4-dioxygenase activity (GO:0004656)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	15	Prostate(51;0.0198)				Hydralazine(DB01275)|L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	GTAGTTTTCTGATCAGATTGG	0.388																																					p.Q269X	Colon(147;367 2405 2662 52127)	Atlas-SNP	.											.	P4HA1	86	.	0			c.C805T						PASS	.						217	213	214					10																	74810906		2203	4300	6503	SO:0001587	stop_gained	5033	exon7			TTTTCTGATCAGA		CCDS7320.1, CCDS41537.1, CCDS44432.1	10q21.3-q23.1	2008-12-09	2008-12-09		ENSG00000122884	ENSG00000122884	1.14.11.2		8546	protein-coding gene	gene with protein product	"collagen prolyl 4-hydroxylase alpha(I)"	176710	"procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide I"	P4HA		2556027	Standard	NM_001017962		Approved	C-P4Halpha(I)	uc001jtg.3	P13674	OTTHUMG00000018449	ENST00000307116.2:c.805C>T	chr10.hg19:g.74810906G>A	ENSP00000307318:p.Gln269*	76.0	0.0	.		65.0	34.0	.	NM_001142596	C9JL12|Q15082|Q15083|Q5VSQ5	Nonsense_Mutation	SNP	ENST00000307116.2	hg19		.	.	.	.	.	.	.	.	.	.	G	38	6.748289	0.97809	.	.	ENSG00000122884	ENST00000307116;ENST00000373008;ENST00000412021;ENST00000394890;ENST00000263556;ENST00000440381	.	.	.	5.67	4.75	0.60458	.	0.628969	0.17058	N	0.188667	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	-9.1782	14.0861	0.64957	0.0:0.0:0.6736:0.3264	.	.	.	.	X	269	.	ENSP00000263556:Q269X	Q	-	1	0	P4HA1	74480912	0.668000	0.27493	1.000000	0.80357	0.995000	0.86356	0.893000	0.28336	1.363000	0.46019	0.557000	0.71058	CAG	.	.	.	none		0.388	P4HA1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000048601.1	NM_000917		A	74810906	G	A	74810906	4	1	188	1	0	0	0	0	0	1	0	0	11363	1299	45	2	910	2	P4HA1	10	74810906	Nonsense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	9842366	74810906	60723841	43	11066											
FAM35A	54537	hgsc.bcm.edu	37	chr10	88911776	88911776	+	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	ctcgaacgcagtagataagtCaaggtctgaagcagcagtta	14	8	11	8	2	2	2	1	1	1	1	3	3	2	2	0	1	3	5	0	1	6	3			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr10:88911776C>G	ENST00000298784.1	+	3	779	c.665C>G	c.(664-666)tCa>tGa	p.S222*	RN7SL733P_ENST00000582253.1_RNA|FAM35A_ENST00000298786.4_Nonsense_Mutation_p.S222*	NM_019054.2	NP_061927.2	Q86V20	FA35A_HUMAN	family with sequence similarity 35, member A	222										endometrium(2)|kidney(2)|large_intestine(5)|lung(1)|ovary(2)|prostate(2)|skin(2)	16						GTAGATAAGTCAAGGTCTGAA	0.398																																					p.S222X	Ovarian(175;703 2004 25460 32514 43441)	Atlas-SNP	.											.	FAM35A	48	.	0			c.C665G						PASS	.						34	35	35					10																	88911776		2197	4290	6487	SO:0001587	stop_gained	54537	exon3			ATAAGTCAAGGTC	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.665C>G	chr10.hg19:g.88911776C>G	ENSP00000298784:p.Ser222*	134.0	0.0	.		113.0	40.0	.	NM_019054	O95885|Q9H991	Nonsense_Mutation	SNP	ENST00000298784.1	hg19	CCDS7383.1	.	.	.	.	.	.	.	.	.	.	c	26.2	4.712906	0.89112	.	.	ENSG00000122376	ENST00000298786;ENST00000298784;ENST00000358313	.	.	.	4.09	4.09	0.47781	.	0.374206	0.21967	N	0.066511	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-1.042	14.7247	0.69336	0.0:1.0:0.0:0.0	.	.	.	.	X	222	.	ENSP00000298784:S222X	S	+	2	0	FAM35A	88901756	0.031000	0.19500	0.008000	0.14137	0.139000	0.21198	3.315000	0.51951	2.134000	0.65973	0.537000	0.68136	TCA	.	.	.	none		0.398	FAM35A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049196.2	NM_019054		G	88911776	C	G	88911776	4	3	188	1	0	0	0	0	0	1	0	0	5560	838	29	4	667	4	FAM35A	10	88911776	Nonsense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	14100870	88911776	46622971	44	11067											
TDRD1	56165	hgsc.bcm.edu	37	chr10	115947630	115947635	+	In_Frame_Del	DEL	AATTTG	AATTTG	-																															ttaatgtgatgtcaagaaatAatttggaagcacctccttgt																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	AATTTG	AATTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr10:115947630_115947635delAATTTG	ENST00000369280.1	+	2	500_505	c.40_45delAATTTG	c.(40-45)aatttgdel	p.NL14del	TDRD1_ENST00000369282.1_In_Frame_Del_p.NL14del|TDRD1_ENST00000369281.2_In_Frame_Del_p.NL14del|TDRD1_ENST00000422662.1_5'UTR|TDRD1_ENST00000251864.2_In_Frame_Del_p.NL14del			Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	14					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ cell development (GO:0007281)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)	metal ion binding (GO:0046872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(5)	48		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		GTCAAGAAATAATTTGGAAGCACCTC	0.345																																					p.13_15del		Atlas-Indel,Pindel	.											.	TDRD1	126	.	0			c.39_44del						PASS	.																																			SO:0001651	inframe_deletion	56165	exon2			.	AF285606	CCDS7588.1	10q26.11	2013-01-23			ENSG00000095627	ENSG00000095627		"Tudor domain containing"	11712	protein-coding gene	gene with protein product	"cancer/testis antigen 41.1"	605796				11279525	Standard	NM_198795		Approved	CT41.1	uc001lbg.1	Q9BXT4	OTTHUMG00000019083	ENST00000369280.1:c.40_45delAATTTG	chr10.hg19:g.115947630_115947635delAATTTG	ENSP00000358286:p.Asn14_Leu15del	95.0	0.0	0		70.0	20.0	0.285714	NM_198795	A6NEN3|A6NMN2|B3KVI4|B4E2L5|D3DRC2|Q4G0Y8|Q6P518|Q9H7B3	In_Frame_Del	DEL	ENST00000369280.1	hg19																																																																																				.	.	.	none		0.345	TDRD1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050457.2			-	115947635	AATTTG	-	115947630	7	5	188	1	0	1	0	1	0	0	0	0	15742	362	13	0	42	0	TDRD1	10	115947630	In_Frame_Del	DEL	AATTTG	TCGA-GL-A59R-01A-11D-A26P-10	27035854	115947630	19587117	45	11068											
ACCSL	390110	hgsc.bcm.edu	37	chr11	44079985	44079985	+	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	cacaaccgcagctctggcctCtatgtctggatcaacttgaa	10	10	8	13	1	4	1	1	1	3	0	4	2	4	2	2	2	3	2	2	2	4	2			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr11:44079985C>T	ENST00000378832.1	+	12	1502	c.1446C>T	c.(1444-1446)ctC>ctT	p.L482L		NM_001031854.2	NP_001027025.2	Q4AC99	1A1L2_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)-like	482					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(14)|ovary(5)|pancreas(1)|skin(2)	34						GCTCTGGCCTCTATGTCTGGA	0.532																																					p.L482L		Atlas-SNP	.											.	ACCSL	57	.	0			c.C1446T						PASS	.						134	136	135					11																	44079985		1985	4152	6137	SO:0001819	synonymous_variant	390110	exon12			TGGCCTCTATGTC		CCDS41636.1	11p11.2	2008-11-26			ENSG00000205126	ENSG00000205126			34391	protein-coding gene	gene with protein product							Standard	NM_001031854		Approved		uc001mxw.1	Q4AC99	OTTHUMG00000166426	ENST00000378832.1:c.1446C>T	chr11.hg19:g.44079985C>T		116.0	0.0	.		128.0	60.0	.	NM_001031854		Silent	SNP	ENST00000378832.1	hg19	CCDS41636.1																																																																																			.	.	.	none		0.532	ACCSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389717.1	NM_001031854		T	44079985	C	T	44079985	2	4	188	1	0	0	0	0	0	0	0	1	134	900	32	2		2	ACCSL	11	44079985	Silent	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10		44079985	90926531	46	11069											
CNTF	1270	hgsc.bcm.edu	37	chr11	58391968	58391968	+	Frame_Shift_Del	DEL	T	T	-																															atcccagcacgtgggagccaTtatattgctaacaacaagaa																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr11:58391968delT	ENST00000361987.4	+	2	656	c.576delT	c.(574-576)catfs	p.H192fs	ZFP91-CNTF_ENST00000389919.4_3'UTR	NM_000614.3	NP_000605.1	P26441	CNTF_HUMAN	ciliary neurotrophic factor	192					ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|growth (GO:0040007)|muscle organ morphogenesis (GO:0048644)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of photoreceptor cell differentiation (GO:0046533)|neuron development (GO:0048666)|positive regulation of cell proliferation (GO:0008284)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of retinal cell programmed cell death (GO:0046668)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor activity (GO:0008083)|interleukin-6 receptor binding (GO:0005138)			NS(1)|breast(1)|kidney(2)|large_intestine(4)|lung(1)|ovary(1)	10		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				GTGGGAGCCATTATATTGCTA	0.468																																					p.H192fs		Atlas-Indel,Pindel	.											.	CNTF	22	.	0			c.575delA						PASS	.						84	88	86					11																	58391968		2201	4295	6496	SO:0001589	frameshift_variant	1270	exon2			.	BC068030	CCDS31554.1	11q12	2011-07-21			ENSG00000242689	ENSG00000242689			2169	protein-coding gene	gene with protein product		118945				1840538, 1714745	Standard	NM_000614		Approved	HCNTF	uc001nna.4	P26441	OTTHUMG00000137476	ENST00000361987.4:c.576delT	chr11.hg19:g.58391968delT	ENSP00000355370:p.His192fs	73.0	0.0	0		68.0	28.0	0.411765	NM_000614	B2RAB2	Frame_Shift_Del	DEL	ENST00000361987.4	hg19	CCDS31554.1																																																																																			.	.	.	none		0.468	CNTF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268673.1	NM_000614		-	58391968	T	-	58391968	7	5	188	1	0	1	0	1	0	0	0	0	3639	1490	52	0	582	0	CNTF	11	58391968	Frame_Shift_Del	DEL	T	TCGA-GL-A59R-01A-11D-A26P-10	14311983	58391968	76614548	47	11070											
RELA	5970	hgsc.bcm.edu	37	chr11	65425828	65425840	+	Frame_Shift_Del	DEL	GGAGACACGCACA	GGAGACACGCACA	-																															gaaggccgccgcagctgcatGgagacacgcacaggagcctg																								rs375033007		TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	GGAGACACGCACA	GGAGACACGCACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr11:65425828_65425840delGGAGACACGCACA	ENST00000406246.3	-	8	1056_1068	c.795_807delTGTGCGTGTCTCC	c.(793-807)cctgtgcgtgtctccfs	p.PVRVS265fs	RELA_ENST00000308639.9_Frame_Shift_Del_p.PVRVS262fs|RELA_ENST00000525693.1_Frame_Shift_Del_p.PVRVS265fs	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	265	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				acetaldehyde metabolic process (GO:0006117)|aging (GO:0007568)|cellular defense response (GO:0006968)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|Fc-epsilon receptor signaling pathway (GO:0038095)|hair follicle development (GO:0001942)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|liver development (GO:0001889)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of Schwann cell differentiation (GO:0014040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to amino acid (GO:0043200)|response to cAMP (GO:0051591)|response to cobalamin (GO:0033590)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to interleukin-1 (GO:0070555)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to muramyl dipeptide (GO:0032495)|response to organic substance (GO:0010033)|response to progesterone (GO:0032570)|response to UV-B (GO:0010224)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phosphate ion binding (GO:0042301)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|repressing transcription factor binding (GO:0070491)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(11)|ovary(1)|urinary_tract(1)	19						GCAGCTGCATGGAGACACGCACAGGAGCCTGCA	0.634																																					p.266_270del		Atlas-Indel,Pindel	.											.	RELA	44	.	0			c.796_808del						PASS	.																																			SO:0001589	frameshift_variant	5970	exon8			.	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.795_807delTGTGCGTGTCTCC	chr11.hg19:g.65425828_65425840delGGAGACACGCACA	ENSP00000384273:p.Pro265fs	110.0	0.0	0		78.0	18.0	0.230769	NM_001243985	Q6GTV1|Q6SLK1	Frame_Shift_Del	DEL	ENST00000406246.3	hg19	CCDS31609.1																																																																																			.	.	.	none		0.634	RELA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390457.2	NM_021975		-	65425840	GGAGACACGCACA	-	65425828	7	5	188	1	0	1	0	1	0	0	0	0	13229	1335	47	0	864	0	RELA	11	65425828	Frame_Shift_Del	DEL	GGAGACACGCACA	TCGA-GL-A59R-01A-11D-A26P-10	7033860	65425828	69580688	48	11071											
MYO7A	4647	hgsc.bcm.edu	37	chr11	76893004	76893004	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtctccttcaggacctggAgcgagggcggagggagatgg	7	8	18	8	2	2	1	1	0	1	1	3	6	2	4	2	6	1	0	2	6	0	2			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr11:76893004A>G	ENST00000409709.3	+	24	3184	c.2912A>G	c.(2911-2913)gAg>gGg	p.E971G	MYO7A_ENST00000409619.2_Missense_Mutation_p.E960G|MYO7A_ENST00000409893.1_Missense_Mutation_p.E971G|MYO7A_ENST00000458637.2_Missense_Mutation_p.E971G	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	971					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						CAGGACCTGGAGCGAGGGCGG	0.592																																					p.E971G		Atlas-SNP	.											.	MYO7A	164	.	0			c.A2912G						PASS	.						50	59	56					11																	76893004		2084	4201	6285	SO:0001583	missense	4647	exon24			ACCTGGAGCGAGG	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.2912A>G	chr11.hg19:g.76893004A>G	ENSP00000386331:p.Glu971Gly	71.0	0.0	.		94.0	4.0	.	NM_001127179	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	hg19	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	.	18.27	3.586425	0.66105	.	.	ENSG00000137474	ENST00000409709;ENST00000409893;ENST00000458637;ENST00000409619;ENST00000545136;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000343419;ENST00000458169	D;D;D;D;D	0.89617	-2.5;-2.54;-2.51;-2.53;-2.29	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	D	0.89054	0.6606	M	0.81802	2.56	0.80722	D	1	B;B;B;B	0.29835	0.258;0.087;0.011;0.023	B;B;B;B	0.28784	0.043;0.094;0.068;0.043	D	0.87356	0.2341	10	0.36615	T	0.2	.	15.3587	0.74453	1.0:0.0:0.0:0.0	.	971;960;971;971	B9A012;B9A011;F8VUN5;Q13402	.;.;.;MYO7A_HUMAN	G	971;971;971;960;182;970;970;847;970;152	ENSP00000386331:E971G;ENSP00000386689:E971G;ENSP00000392185:E971G;ENSP00000386635:E960G;ENSP00000417017:E152G	ENSP00000345075:E847G	E	+	2	0	MYO7A	76570652	1.000000	0.71417	0.998000	0.56505	0.830000	0.47004	8.887000	0.92456	2.028000	0.59812	0.448000	0.29417	GAG	.	.	.	none		0.592	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		G	76893004	A	G	76893004	3	3	188	1	0	0	0	0	1	0	0	0	10089	304	11	3	3002	3	MYO7A	11	76893004	Missense_Mutation	SNP	A	TCGA-GL-A59R-01A-11D-A26P-10	11467176	76893004	58113512	49	11072											
EXPH5	23086	hgsc.bcm.edu	37	chr11	108381026	108381026	+	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	gcttccctgaggctggtgaaTgtgatgggtgatggggctcc	5	11	17	8	0	0	4	0	4	0	0	2	4	2	4	2	5	0	3	2	5	1	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr11:108381026T>G	ENST00000265843.4	-	6	5318	c.5208A>C	c.(5206-5208)acA>acC	p.T1736T	EXPH5_ENST00000525344.1_Silent_p.T1729T|EXPH5_ENST00000443411.1_Silent_p.T1548T|EXPH5_ENST00000428840.1_Silent_p.T1660T	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1736					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)		GGCTGGTGAATGTGATGGGTG	0.468																																					p.T1736T		Atlas-SNP	.											.	EXPH5	193	.	0			c.A5208C						PASS	.						85	91	89					11																	108381026		2201	4298	6499	SO:0001819	synonymous_variant	23086	exon6			GGTGAATGTGATG		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.5208A>C	chr11.hg19:g.108381026T>G		101.0	0.0	.		108.0	41.0	.	NM_015065	Q2KHM1|Q9Y4D6	Silent	SNP	ENST00000265843.4	hg19	CCDS8341.1																																																																																			.	.	.	none		0.468	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		G	108381026	T	G	108381026	2	3	188	1	0	0	0	0	0	0	0	1	5324	1451	51	5		5	EXPH5	11	108381026	Silent	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	31488022	108381026	26625490	50	11073											
MCAM	4162	hgsc.bcm.edu	37	chr11	119182661	119182661	+	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	tttccagcacctggcctgtcTgggatgagagatgggtcaga	8	10	14	9	0	2	3	1	1	1	2	3	5	3	4	3	3	1	1	3	3	0	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr11:119182661T>A	ENST00000264036.4	-	10	1158		c.e10-2		MCAM_ENST00000392814.1_Splice_Site|MCAM_ENST00000530144.2_5'Flank	NM_006500.2	NP_006491.2	P43121	MUC18_HUMAN	melanoma cell adhesion molecule						anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|glomerular filtration (GO:0003094)|vascular wound healing (GO:0061042)	external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|skin(1)	22		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.78e-05)		CTGGCCTGTCTGGGATGAGAG	0.632																																					.		Atlas-SNP	.											.	MCAM	57	.	0			c.1144-2A>T						PASS	.						90	93	92					11																	119182661		2199	4295	6494	SO:0001630	splice_region_variant	4162	exon11			CCTGTCTGGGATG	X68264	CCDS31690.1	11q23.3	2013-01-29				ENSG00000076706		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6934	protein-coding gene	gene with protein product	"Gicerin"	155735				2602381, 10702685	Standard	XM_005271552		Approved	MUC18, CD146	uc001pwf.3	P43121		ENST00000264036.4:c.1144-2A>T	chr11.hg19:g.119182661T>A		39.0	0.0	.		29.0	15.0	.	NM_006500	O95812|Q59E86|Q6PHR3|Q6ZTR2	Splice_Site	SNP	ENST00000264036.4	hg19	CCDS31690.1	.	.	.	.	.	.	.	.	.	.	T	15.24	2.776310	0.49786	.	.	ENSG00000076706	ENST00000264036;ENST00000392814	.	.	.	4.73	4.73	0.59995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.4953	0.33125	0.0:0.0:0.1965:0.8035	.	.	.	.	.	-1	.	.	.	-	.	.	MCAM	118687871	1.000000	0.71417	0.979000	0.43373	0.886000	0.51366	4.238000	0.58688	1.973000	0.57446	0.379000	0.24179	.	.	.	.	none		0.632	MCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388332.2		Intron	A	119182661	T	A	119182661	5	1	188	1	0	0	0	0	0	0	1	0	9375	1594	55	5	826	5	MCAM	11	119182661	Splice_Site	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	10801635	119182661	15823855	51	11074											
SLC2A14	144195	hgsc.bcm.edu	37	chr12	7984344	7984344	+	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	tgtccgtcaaagttttattgAtaaattcctttatgatctgc	10	18	6	7	1	2	2	1	2	1	0	4	2	4	2	2	0	1	1	2	0	5	7			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr12:7984344A>T	ENST00000543909.1	-	9	956	c.197T>A	c.(196-198)aTc>aAc	p.I66N	SLC2A14_ENST00000396589.2_Missense_Mutation_p.I66N|SLC2A14_ENST00000542546.1_Intron|SLC2A14_ENST00000539924.1_Missense_Mutation_p.I81N|SLC2A14_ENST00000542505.1_Intron|SLC2A14_ENST00000535295.1_Intron|SLC2A14_ENST00000431042.2_Missense_Mutation_p.I43N|SLC2A14_ENST00000340749.5_Missense_Mutation_p.I43N			Q8TDB8	GTR14_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 14	66					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)		AGTTTTATTGATAAATTCCTT	0.458											OREG0021654	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I66N		Atlas-SNP	.											.	SLC2A14	78	.	0			c.T197A						PASS	.						89	86	87					12																	7984344		2203	4300	6503	SO:0001583	missense	144195	exon5			TTATTGATAAATT	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.197T>A	chr12.hg19:g.7984344A>T	ENSP00000440480:p.Ile66Asn	129.0	0.0	.	645	191.0	61.0	.	NM_153449	B3KVB5|B3KWW7|B7Z844|B7ZAC3|Q6UY84|Q8TDB9	Missense_Mutation	SNP	ENST00000543909.1	hg19	CCDS8585.1	.	.	.	.	.	.	.	.	.	.	A	13.77	2.337198	0.41398	.	.	ENSG00000173262	ENST00000340749;ENST00000543909;ENST00000431042;ENST00000396589;ENST00000539924;ENST00000546234;ENST00000542782;ENST00000535344;ENST00000537557;ENST00000535266;ENST00000542916;ENST00000535383	T;T;T;T;T;T;T;T;T;T;T;T	0.81163	-1.46;-1.46;-1.46;-1.46;-1.46;-1.46;-1.46;-1.46;-1.46;-1.46;-0.83;-0.83	3.6	3.6	0.41247	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.322524	0.33496	N	0.004853	D	0.84325	0.5447	M	0.70595	2.14	0.31524	N	0.662021	P;P;B	0.45428	0.858;0.81;0.093	P;P;B	0.57009	0.811;0.575;0.102	D	0.84462	0.0594	10	0.72032	D	0.01	.	6.4066	0.21668	0.781:0.0:0.0:0.219	.	81;43;66	B7ZAC3;Q8TDB8-2;Q8TDB8	.;.;GTR14_HUMAN	N	43;66;43;66;81;43;43;43;66;66;43;43	ENSP00000340450:I43N;ENSP00000440480:I66N;ENSP00000407287:I43N;ENSP00000379834:I66N;ENSP00000445929:I81N;ENSP00000440043:I43N;ENSP00000438312:I43N;ENSP00000443217:I43N;ENSP00000440044:I66N;ENSP00000437653:I66N;ENSP00000442402:I43N;ENSP00000443076:I43N	ENSP00000340450:I43N	I	-	2	0	SLC2A14	7875611	0.995000	0.38212	0.015000	0.15790	0.012000	0.07955	1.901000	0.39838	1.391000	0.46566	0.477000	0.44152	ATC	.	.	.	none		0.458	SLC2A14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399836.2	NM_153449		T	7984344	A	T	7984344	3	4	188	1	0	0	0	0	1	0	0	0	14556	333	12	5	1397	5	SLC2A14	12	7984344	Missense_Mutation	SNP	A	TCGA-GL-A59R-01A-11D-A26P-10		7984344	125867551	52	11075											
BCL2L14	79370	hgsc.bcm.edu	37	chr12	12247627	12247628	+	Frame_Shift_Del	DEL	CT	CT	-																															gataaggctttgatgggccaCttccaggatgggctgtccta																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr12:12247627_12247628delCT	ENST00000308721.5	+	5	914_915	c.708_709delCT	c.(706-711)cacttcfs	p.F237fs	BCL2L14_ENST00000589718.1_Frame_Shift_Del_p.F237fs|BCL2L14_ENST00000396369.1_Intron|BCL2L14_ENST00000586576.1_Frame_Shift_Del_p.F270fs|BCL2L14_ENST00000396367.1_Frame_Shift_Del_p.F237fs|BCL2L14_ENST00000266434.4_3'UTR	NM_138723.1	NP_620049.1	Q9BZR8	B2L14_HUMAN	BCL2-like 14 (apoptosis facilitator)	237					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular organelle (GO:0043229)|membrane (GO:0016020)	protein kinase binding (GO:0019901)			large_intestine(1)|lung(2)|skin(3)	6		Prostate(47;0.0872)		BRCA - Breast invasive adenocarcinoma(232;0.154)		TGATGGGCCACTTCCAGGATGG	0.49																																					p.236_236del		Atlas-Indel,Pindel	.											.	BCL2L14	47	.	0			c.707_708del						PASS	.																																			SO:0001589	frameshift_variant	79370	exon5			.	AF281254	CCDS8645.1, CCDS8646.1	12p13-p12	2014-03-07			ENSG00000121380	ENSG00000121380			16657	protein-coding gene	gene with protein product		606126				11054413	Standard	NM_030766		Approved	BCLG, BCL-G	uc001rac.3	Q9BZR8	OTTHUMG00000159528	ENST00000308721.5:c.708_709delCT	chr12.hg19:g.12247627_12247628delCT	ENSP00000309132:p.Phe237fs	203.0	0.0	0		276.0	71.0	0.257246	NM_138723	A8KAD0|Q96QR5|Q9BZR7	Frame_Shift_Del	DEL	ENST00000308721.5	hg19	CCDS8645.1																																																																																			.	.	.	none		0.49	BCL2L14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355994.3	NM_030766		-	12247628	CT	-	12247627	7	5	188	1	0	1	0	1	0	0	0	0	1372	564	20	0	807	0	BCL2L14	12	12247627	Frame_Shift_Del	DEL	CT	TCGA-GL-A59R-01A-11D-A26P-10	4263283	12247627	121604268	53	11076											
LRP6	4040	hgsc.bcm.edu	37	chr12	12274330	12274330	+	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	ggtgtggtggggggtgcaaaGtgccggtagctatatggcct	6	10	19	6	1	0	0	0	0	0	0	0	0	0	0	2	7	3	3	2	7	4	3			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr12:12274330G>C	ENST00000261349.4	-	23	4648	c.4572C>G	c.(4570-4572)caC>caG	p.H1524Q	BCL2L14_ENST00000396369.1_Intron|LRP6_ENST00000543091.1_Missense_Mutation_p.H1479Q	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1524					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)				GGGGTGCAAAGTGCCGGTAGC	0.463																																					p.H1524Q		Atlas-SNP	.											.	LRP6	170	.	0			c.C4572G						PASS	.						99	103	101					12																	12274330		2203	4300	6503	SO:0001583	missense	4040	exon23			TGCAAAGTGCCGG	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.4572C>G	chr12.hg19:g.12274330G>C	ENSP00000261349:p.His1524Gln	120.0	0.0	.		166.0	37.0	.	NM_002336	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	hg19	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	G	12.94	2.088550	0.36855	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.92911	-3.07;-3.13	5.86	4.96	0.65561	.	0.000000	0.64402	D	0.000004	D	0.89663	0.6780	L	0.43152	1.355	0.54753	D	0.999989	D;P	0.54207	0.965;0.607	P;B	0.47981	0.563;0.177	D	0.88842	0.3313	10	0.52906	T	0.07	.	9.8375	0.40977	0.2372:0.0:0.7628:0.0	.	1479;1524	F5H7J9;O75581	.;LRP6_HUMAN	Q	1524;1479	ENSP00000261349:H1524Q;ENSP00000442472:H1479Q	ENSP00000261349:H1524Q	H	-	3	2	LRP6	12165597	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.704000	0.37857	2.780000	0.95670	0.643000	0.83706	CAC	.	.	.	none		0.463	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			C	12274330	G	C	12274330	3	2	188	1	0	0	0	0	1	0	0	0	8969	1020	36	4	273	4	LRP6	12	12274330	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	26703	12274330	121577565	54	11077											
ARID2	196528	hgsc.bcm.edu	37	chr12	46244883	46244883	+	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	ctgccatgtcgtcgtcctctAcccctcaatcacagggacca	8	9	7	17	2	3	0	2	0	1	0	6	1	4	1	5	1	2	0	5	1	2	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr12:46244883A>T	ENST00000334344.6	+	15	3149	c.2977A>T	c.(2977-2979)Acc>Tcc	p.T993S	ARID2_ENST00000422737.1_Missense_Mutation_p.T844S|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000444670.1_Missense_Mutation_p.T603S|ARID2_ENST00000457135.1_5'Flank	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	993	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)		GTCGTCCTCTACCCCTCAATC	0.498			"N, S, F"		hepatocellular carcinoma																																p.T993S		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.A2977T						PASS	.						246	213	224					12																	46244883		2203	4300	6503	SO:0001583	missense	196528	exon15			TCCTCTACCCCTC		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.2977A>T	chr12.hg19:g.46244883A>T	ENSP00000335044:p.Thr993Ser	248.0	0.0	.		393.0	114.0	.	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Missense_Mutation	SNP	ENST00000334344.6	hg19	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	A	5.023	0.189957	0.09547	.	.	ENSG00000189079	ENST00000334344;ENST00000549153;ENST00000338636;ENST00000422737;ENST00000444670	T	0.33438	1.41	5.66	2.06	0.26882	.	0.394387	0.30593	N	0.009288	T	0.17746	0.0426	N	0.19112	0.55	0.80722	D	1	B;B;B	0.26147	0.143;0.143;0.104	B;B;B	0.30572	0.117;0.075;0.039	T	0.06041	-1.0849	10	0.31617	T	0.26	-1.4259	6.2264	0.20710	0.6727:0.124:0.2032:0.0	.	993;603;993	Q68CP9-3;F8W108;Q68CP9	.;.;ARID2_HUMAN	S	993;110;110;844;603	ENSP00000335044:T993S	ENSP00000335044:T993S	T	+	1	0	ARID2	44531150	0.976000	0.34144	0.996000	0.52242	0.380000	0.30137	1.302000	0.33459	0.425000	0.26087	0.379000	0.24179	ACC	.	.	.	none		0.498	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		T	46244883	A	T	46244883	3	4	188	1	0	0	0	0	1	0	0	0	915	391	14	5	3035	5	ARID2	12	46244883	Missense_Mutation	SNP	A	TCGA-GL-A59R-01A-11D-A26P-10	33970553	46244883	87607012	55	11078											
NAV3	89795	hgsc.bcm.edu	37	chr12	78591182	78591182	+	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	aattgtaaatacaacaaatgGtatgcttatcaaatattctg	17	14	5	5	0	2	0	1	0	1	0	2	0	2	0	0	1	3	3	0	1	10	7			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr12:78591182G>C	ENST00000397909.2	+	35	6619		c.e35+1		NAV3_ENST00000266692.7_Splice_Site|NAV3_ENST00000541270.1_5'Flank|NAV3_ENST00000536525.2_Splice_Site|NAV3_ENST00000228327.6_Splice_Site			Q8IVL0	NAV3_HUMAN	neuron navigator 3							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						ACAACAAATGGTATGCTTATC	0.284										HNSCC(70;0.22)																											.		Atlas-SNP	.											.	NAV3	506	.	0			c.6380+1G>C						PASS	.						83	73	76					12																	78591182		1798	4068	5866	SO:0001630	splice_region_variant	89795	exon34			CAAATGGTATGCT	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.6446+1G>C	chr12.hg19:g.78591182G>C		21.0	0.0	.		27.0	13.0	.	NM_014903	Q8NFW7|Q9Y2E7	Splice_Site	SNP	ENST00000397909.2	hg19		.	.	.	.	.	.	.	.	.	.	G	25.5	4.648927	0.87958	.	.	ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692;ENST00000378640;ENST00000552895;ENST00000550788	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8339	0.96646	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NAV3	77115313	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.813000	0.99286	2.751000	0.94390	0.655000	0.94253	.	.	.	.	none		0.284	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	Intron	C	78591182	G	C	78591182	5	2	188	1	0	0	0	0	0	0	1	0	10192	1275	44	4	6515	4	NAV3	12	78591182	Splice_Site	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	32346299	78591182	55260713	56	11079											
ATXN2	6311	hgsc.bcm.edu	37	chr12	111926345	111926345	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgctgggctggaagtctgAaccccttgggaagtgacctc	8	9	13	11	0	1	2	0	2	1	0	2	4	1	4	3	3	2	2	3	3	3	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr12:111926345A>G	ENST00000377617.3	-	15	2816	c.2655T>C	c.(2653-2655)gtT>gtC	p.V885V	ATXN2_ENST00000535949.1_Silent_p.V596V|ATXN2_ENST00000608853.1_Silent_p.V725V|AC002395.1_ENST00000581907.1_RNA|ATXN2_ENST00000389153.4_Silent_p.V620V|ATXN2_ENST00000542287.2_Silent_p.V620V|ATXN2_ENST00000550104.1_Silent_p.V885V	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	885					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						TGGAAGTCTGAACCCCTTGGG	0.498																																					p.V885V		Atlas-SNP	.											.	ATXN2	99	.	0			c.T2655C						PASS	.						122	117	119					12																	111926345		2203	4300	6503	SO:0001819	synonymous_variant	6311	exon15			AGTCTGAACCCCT	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.2655T>C	chr12.hg19:g.111926345A>G		99.0	0.0	.		154.0	85.0	.	NM_002973	A6NLD4|Q6ZQZ7|Q99493	Silent	SNP	ENST00000377617.3	hg19	CCDS31902.1																																																																																			.	.	.	none		0.498	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973		G	111926345	A	G	111926345	2	3	188	1	0	0	0	0	0	0	0	1	1211	233	9	3		3	ATXN2	12	111926345	Silent	SNP	A	TCGA-GL-A59R-01A-11D-A26P-10	33335163	111926345	21925550	57	11080											
CIT	11113	hgsc.bcm.edu	37	chr12	120158284	120158284	+	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	ttcaaacactttgactcaccTttttctttttagcaggttgg	8	18	6	9	0	3	1	2	1	1	0	3	1	3	1	1	2	2	2	1	2	2	8			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr12:120158284T>C	ENST00000261833.7	-	29	3765	c.3713A>G	c.(3712-3714)aAg>aGg	p.K1238R	CIT_ENST00000537607.1_5'UTR|CIT_ENST00000392521.2_Splice_Site_p.K1280R	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	1238	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)		TTGACTCACCTTTTTCTTTTT	0.373																																					p.K1280R		Atlas-SNP	.											.	CIT	535	.	0			c.A3839G						PASS	.						136	130	132					12																	120158284		2203	4299	6502	SO:0001630	splice_region_variant	11113	exon30			CTCACCTTTTTCT	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.3714+1A>G	chr12.hg19:g.120158284T>C		127.0	0.0	.		163.0	88.0	.	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	hg19	CCDS9192.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.70|18.70	3.680696|3.680696	0.68042|0.68042	.|.	.|.	ENSG00000122966|ENSG00000122966	ENST00000392521;ENST00000261833|ENST00000392520	T;T|.	0.69806|.	-0.42;-0.43|.	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72070|0.72070	0.3415|0.3415	M|M	0.62723|0.62723	1.935|1.935	0.80722|0.80722	D|D	1|1	B;D;P|.	0.69078|.	0.355;0.997;0.734|.	B;D;B|.	0.73380|.	0.1;0.98;0.203|.	T|T	0.70880|0.70880	-0.4752|-0.4752	10|5	0.24483|.	T|.	0.36|.	.|.	16.1193|16.1193	0.81336|0.81336	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1280;1238;771|.	Q2M5E1;O14578;O14578-3|.	.;CTRO_HUMAN;.|.	R|G	1280;1238|866	ENSP00000376306:K1280R;ENSP00000261833:K1238R|.	ENSP00000261833:K1238R|.	K|R	-|-	2|1	0|2	CIT|CIT	118642667|118642667	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.040000|8.040000	0.89188|0.89188	2.204000|2.204000	0.70986|0.70986	0.528000|0.528000	0.53228|0.53228	AAG|AGG	.	.	.	none		0.373	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174	Missense_Mutation	C	120158284	T	C	120158284	5	2	188	1	0	0	0	0	0	0	1	0	3440	1623	56	3	2446	3	CIT	12	120158284	Splice_Site	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10	8231939	120158284	13693611	58	11081											
KIAA0564	23078	hgsc.bcm.edu	37	chr13	42440068	42440068	+	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	attaaacatatatctttaacCatgtgagactgcatcatttc	14	15	4	8	0	2	1	1	1	1	1	3	2	2	1	1	0	3	1	1	0	5	6			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr13:42440068C>T	ENST00000379310.3	-	11	1385	c.1317G>A	c.(1315-1317)atG>atA	p.M439I	VWA8_ENST00000281496.6_Missense_Mutation_p.M439I	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	439						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										TATCTTTAACCATGTGAGACT	0.418																																					p.M439I		Atlas-SNP	.											.	.	.	.	0			c.G1317A						PASS	.						146	148	147					13																	42440068		2203	4300	6503	SO:0001583	missense	23078	exon11			TTTAACCATGTGA	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"KIAA0564"	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.1317G>A	chr13.hg19:g.42440068C>T	ENSP00000368612:p.Met439Ile	75.0	0.0	.		73.0	36.0	.	NM_015058	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Missense_Mutation	SNP	ENST00000379310.3	hg19	CCDS41881.1	.	.	.	.	.	.	.	.	.	.	C	12.78	2.040196	0.35989	.	.	ENSG00000102763	ENST00000251030;ENST00000379310;ENST00000281496;ENST00000398857	T;T	0.38401	1.14;1.14	5.3	5.3	0.74995	ATPase, AAA+ type, core (1);	0.109015	0.64402	D	0.000017	T	0.33381	0.0861	L	0.46157	1.445	0.43467	D	0.995671	B	0.02656	0.0	B	0.09377	0.004	T	0.17471	-1.0368	10	0.11182	T	0.66	.	19.3149	0.94208	0.0:1.0:0.0:0.0	.	439	A3KMH1	K0564_HUMAN	I	343;439;439;439	ENSP00000368612:M439I;ENSP00000281496:M439I	ENSP00000251030:M343I	M	-	3	0	KIAA0564	41338068	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.386000	0.52492	2.631000	0.89168	0.563000	0.77884	ATG	.	.	.	none		0.418	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058		T	42440068	C	T	42440068	3	4	188	1	0	0	0	0	1	0	0	0	8192	594	21	2	4544	2	KIAA0564	13	42440068	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10		42440068	72729810	59	11082											
SIX4	51804	hgsc.bcm.edu	37	chr14	61186919	61186919	+	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	aactccactgggtccctgaaTaaaagaatttccattaagga	15	10	7	9	0	0	2	0	1	0	1	3	3	3	3	3	2	1	0	3	2	6	3			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr14:61186919T>A	ENST00000216513.4	-	2	1167	c.1108A>T	c.(1108-1110)Att>Ttt	p.I370F		NM_017420.4	NP_059116.3	Q9UIU6	SIX4_HUMAN	SIX homeobox 4	370					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)		GGTCCCTGAATAAAAGAATTT	0.398																																					p.I370F		Atlas-SNP	.											.	SIX4	69	.	0			c.A1108T						PASS	.						79	76	77					14																	61186919		2203	4300	6503	SO:0001583	missense	51804	exon2			CCTGAATAAAAGA	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.1108A>T	chr14.hg19:g.61186919T>A	ENSP00000216513:p.Ile370Phe	110.0	0.0	.		103.0	37.0	.	NM_017420	Q4QQH5|Q4V764	Missense_Mutation	SNP	ENST00000216513.4	hg19	CCDS9749.2	.	.	.	.	.	.	.	.	.	.	T	13.45	2.239521	0.39598	.	.	ENSG00000100625	ENST00000216513;ENST00000554079;ENST00000556952	D;T	0.91792	-2.91;0.56	5.72	5.72	0.89469	.	0.297103	0.34178	N	0.004182	D	0.86464	0.5939	N	0.19112	0.55	0.47698	D	0.999492	P;P	0.49090	0.919;0.454	B;B	0.43575	0.424;0.153	D	0.86816	0.2001	10	0.41790	T	0.15	.	12.7402	0.57249	0.0:0.0:0.146:0.854	.	362;370	G3V2N2;Q9UIU6	.;SIX4_HUMAN	F	370;43;362	ENSP00000216513:I370F;ENSP00000451537:I43F	ENSP00000216513:I370F	I	-	1	0	SIX4	60256672	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.761000	0.55242	2.194000	0.70268	0.533000	0.62120	ATT	.	.	.	none		0.398	SIX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072397.2			A	61186919	T	A	61186919	3	1	188	1	0	0	0	0	1	0	0	0	14362	1406	49	5	1245	5	SIX4	14	61186919	Missense_Mutation	SNP	T	TCGA-GL-A59R-01A-11D-A26P-10		61186919	46162621	60	11083											
GPHN	10243	hgsc.bcm.edu	37	chr14	67647539	67647539	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtaatcaaatgagcagccGtctgatgagcatgcgcagtg	12	8	13	8	2	2	3	1	3	1	0	2	3	2	3	1	1	4	4	1	1	2	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr14:67647539G>A	ENST00000315266.5	+	22	3217	c.2096G>A	c.(2095-2097)cGt>cAt	p.R699H	GPHN_ENST00000543237.1_Missense_Mutation_p.R745H|GPHN_ENST00000478722.1_Missense_Mutation_p.R732H|GPHN_ENST00000305960.9_Missense_Mutation_p.R668H|GPHN_ENST00000544752.2_3'UTR	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	699	MPT adenylyltransferase.				establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycine receptor clustering (GO:0072579)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|molybdopterin adenylyltransferase activity (GO:0061598)|molybdopterin molybdotransferase activity (GO:0061599)|transferase activity (GO:0016740)			large_intestine(8)|liver(1)|ovary(2)|stomach(1)	12		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		ATGAGCAGCCGTCTGATGAGC	0.458			T	MLL	AL																																p.R732H		Atlas-SNP	.		Dom	yes		14	14q24	10243	gephyrin (GPH)		L	.	GPHN	79	.	0			c.G2195A						PASS	.						128	105	113					14																	67647539		2203	4300	6503	SO:0001583	missense	10243	exon23			GCAGCCGTCTGAT	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.2096G>A	chr14.hg19:g.67647539G>A	ENSP00000312771:p.Arg699His	123.0	0.0	.		125.0	58.0	.	NM_020806	Q9H4E9|Q9P2G2	Missense_Mutation	SNP	ENST00000315266.5	hg19	CCDS32103.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.934351	0.73442	.	.	ENSG00000171723	ENST00000315266;ENST00000478722;ENST00000543237;ENST00000305960	.	.	.	5.83	4.93	0.64822	MoeA, C-terminal, domain IV (3);	0.102725	0.64402	D	0.000004	T	0.79476	0.4452	M	0.81112	2.525	0.80722	D	1	P;D;D;D	0.89917	0.953;1.0;0.978;1.0	B;D;P;D	0.87578	0.379;0.998;0.75;0.998	T	0.80308	-0.1437	9	0.51188	T	0.08	-7.1864	15.3438	0.74317	0.0681:0.0:0.9319:0.0	.	668;745;699;732	F8W7D6;F5H039;Q9NQX3;Q9NQX3-2	.;.;GEPH_HUMAN;.	H	699;732;745;668	.	ENSP00000303019:R668H	R	+	2	0	GPHN	66717292	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.843000	0.86859	2.768000	0.95171	0.467000	0.42956	CGT	.	.	.	none		0.458	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806		A	67647539	G	A	67647539	3	1	188	1	0	0	0	0	1	0	0	0	6617	1145	40	1	2285	1	GPHN	14	67647539	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	6460620	67647539	39702001	61	11084											
EML5	161436	hgsc.bcm.edu	37	chr14	89171882	89171883	+	Frame_Shift_Ins	INS	-	-	T																															tcagaatccagttctggaacINSatcagacagatctgaatctg																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr14:89171882_89171883insT	ENST00000380664.5	-	12	1874_1875	c.1875_1876insA	c.(1873-1878)gatgttfs	p.V626fs	EML5_ENST00000352093.5_Frame_Shift_Ins_p.V626fs|EML5_ENST00000554922.1_Frame_Shift_Ins_p.V626fs			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	626						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						AGTTCTGGAACATCAGACAGAT	0.337																																					p.V626fs		Atlas-Indel,Pindel	.											.	EML5	141	.	0			c.1876_1877insA						PASS	.																																			SO:0001589	frameshift_variant	161436	exon12			.	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.1875_1876insA	chr14.hg19:g.89171882_89171883insT	ENSP00000370039:p.Val626fs	32.0	0.0	0		41.0	18.0	0.439024	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Frame_Shift_Ins	INS	ENST00000380664.5	hg19	CCDS45148.1																																																																																			.	.	.	none		0.337	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			T	89171883	-	T	89171882	7	5	188	1	0	1	1	0	0	0	0	0	5102	478	17	0	4185	0	EML5	14	89171882	Frame_Shift_Ins	INS	-	TCGA-GL-A59R-01A-11D-A26P-10	21524343	89171882	18177658	62	11085											
RYR3	6263	hgsc.bcm.edu	37	chr15	34130027	34130027	+	Frame_Shift_Del	DEL	A	A	-																															agaattccagaaggccatggAagggcaaaaacagtacacgc																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr15:34130027delA	ENST00000389232.4	+	89	11916	c.11846delA	c.(11845-11847)gaafs	p.E3949fs	RYR3_ENST00000415757.3_Frame_Shift_Del_p.E3944fs	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3949					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)		AAGGCCATGGAAGGGCAAAAA	0.403																																					p.E3949fs		Atlas-Indel,Pindel	.											.	RYR3	760	.	0			c.11845delG						PASS	.						108	103	104					15																	34130027		1895	4111	6006	SO:0001589	frameshift_variant	6263	exon89			.		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.11846delA	chr15.hg19:g.34130027delA	ENSP00000373884:p.Glu3949fs	85.0	0.0	0		83.0	45.0	0.542169	NM_001036	O15175|Q15412	Frame_Shift_Del	DEL	ENST00000389232.4	hg19	CCDS45210.1																																																																																			.	.	.	none		0.403	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			-	34130027	A	-	34130027	7	5	188	1	0	1	0	1	0	0	0	0	13783	246	9	0	12200	0	RYR3	15	34130027	Frame_Shift_Del	DEL	A	TCGA-GL-A59R-01A-11D-A26P-10		34130027	68401365	63	11086											
CASKIN1	57524	hgsc.bcm.edu	37	chr16	2239295	2239295	+	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	cgtcttccccgagttgtccaCcatgcacgggttagactggt	6	11	11	13	3	1	1	0	0	1	1	3	2	3	1	4	2	1	3	4	2	1	3			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr16:2239295C>A	ENST00000343516.6	-	5	522	c.430G>T	c.(430-432)Gtg>Ttg	p.V144L		NM_020764.3	NP_065815.1	Q8WXD9	CSKI1_HUMAN	CASK interacting protein 1	144					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						GAGTTGTCCACCATGCACGGG	0.697																																					p.V144L		Atlas-SNP	.											.	CASKIN1	130	.	0			c.G430T						PASS	.						39	52	47					16																	2239295		2114	4208	6322	SO:0001583	missense	57524	exon5			TGTCCACCATGCA	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.430G>T	chr16.hg19:g.2239295C>A	ENSP00000345436:p.Val144Leu	81.0	0.0	.		77.0	4.0	.	NM_020764	Q9P2P0	Missense_Mutation	SNP	ENST00000343516.6	hg19	CCDS42103.1	.	.	.	.	.	.	.	.	.	.	C	16.12	3.032936	0.54790	.	.	ENSG00000167971	ENST00000343516	T	0.64438	-0.1	3.46	3.46	0.39613	Ankyrin repeat-containing domain (3);	.	.	.	.	T	0.42291	0.1196	N	0.13327	0.33	0.42422	D	0.992647	B	0.25105	0.118	B	0.29353	0.101	T	0.44190	-0.9344	9	0.56958	D	0.05	-19.1703	5.5157	0.16906	0.0:0.7694:0.0:0.2306	.	144	Q8WXD9	CSKI1_HUMAN	L	144	ENSP00000345436:V144L	ENSP00000345436:V144L	V	-	1	0	CASKIN1	2179296	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.807000	0.38902	1.954000	0.56735	0.561000	0.74099	GTG	.	.	.	none		0.697	CASKIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435055.1	NM_020764		A	2239295	C	A	2239295	3	1	188	1	0	0	0	0	1	0	0	0	2668	507	18	4	3929	4	CASKIN1	16	2239295	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10		2239295	88115458	64	11087											
TMEM159	57146	hgsc.bcm.edu	37	chr16	21185458	21185458	+	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	tccagcctcatcagctgctgGttttctcccaggtaaataca	9	12	7	13	0	3	0	2	0	1	0	5	0	4	0	3	2	4	4	3	2	3	4			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr16:21185458G>C	ENST00000233047.4	+	4	861	c.393G>C	c.(391-393)tgG>tgC	p.W131C	TMEM159_ENST00000572599.1_Missense_Mutation_p.W131C|TMEM159_ENST00000451578.2_Missense_Mutation_p.W155C|TMEM159_ENST00000572258.1_Intron|TMEM159_ENST00000261388.3_Missense_Mutation_p.W131C			Q96B96	TM159_HUMAN	transmembrane protein 159	131						integral component of membrane (GO:0016021)				large_intestine(3)|lung(2)|ovary(1)	6				GBM - Glioblastoma multiforme(48;0.0972)		TCAGCTGCTGGTTTTCTCCCA	0.428																																					p.W131C		Atlas-SNP	.											.	TMEM159	14	.	0			c.G393C						PASS	.						121	98	106					16																	21185458		2200	4300	6500	SO:0001583	missense	57146	exon4			CTGCTGGTTTTCT	AF070596	CCDS10595.1	16p12.2	2008-02-05			ENSG00000011638	ENSG00000011638			30136	protein-coding gene	gene with protein product		611304				8619474, 9110174, 15589683	Standard	NM_020422		Approved	promethin	uc002dif.4	Q96B96	OTTHUMG00000131559	ENST00000233047.4:c.393G>C	chr16.hg19:g.21185458G>C	ENSP00000233047:p.Trp131Cys	113.0	0.0	.		127.0	59.0	.	NM_020422	A6NMA9|B4DEC1|O00323	Missense_Mutation	SNP	ENST00000233047.4	hg19	CCDS10595.1	.	.	.	.	.	.	.	.	.	.	G	12.84	2.059590	0.36373	.	.	ENSG00000011638	ENST00000233047;ENST00000261388;ENST00000451578	T;T;T	0.25579	1.8;1.8;1.79	6.07	6.07	0.98685	.	0.371511	0.26467	N	0.024208	T	0.49338	0.1551	M	0.64997	1.995	0.58432	D	0.999993	D;D	0.76494	0.999;0.999	D;D	0.65874	0.939;0.912	T	0.38950	-0.9637	10	0.72032	D	0.01	-19.3257	18.139	0.89633	0.0:0.0:1.0:0.0	.	155;131	B4DEC1;Q96B96	.;TM159_HUMAN	C	131;131;155	ENSP00000233047:W131C;ENSP00000261388:W131C;ENSP00000409879:W155C	ENSP00000233047:W131C	W	+	3	0	TMEM159	21092959	1.000000	0.71417	1.000000	0.80357	0.655000	0.38815	3.746000	0.55127	2.885000	0.99019	0.650000	0.86243	TGG	.	.	.	none		0.428	TMEM159-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254421.1	NM_020422		C	21185458	G	C	21185458	3	2	188	1	0	0	0	0	1	0	0	0	16086	1270	44	4	403	4	TMEM159	16	21185458	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	18946163	21185458	69169295	65	11088											
ZP2	7783	hgsc.bcm.edu	37	chr16	21214557	21214557	+	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	taagtagaactgatggagtaGgcatttttcagataactgaa	15	12	10	4	0	1	4	1	2	0	2	1	5	1	5	0	2	2	3	0	2	6	6			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr16:21214557G>T	ENST00000574002.1	-	11	1470	c.988C>A	c.(988-990)Cta>Ata	p.L330I	ZP2_ENST00000574091.1_Missense_Mutation_p.L330I|AF001550.7_ENST00000572747.1_RNA|ZP2_ENST00000219593.4_Missense_Mutation_p.L330I			Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 (sperm receptor)	330					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)		TGATGGAGTAGGCATTTTTCA	0.483																																					p.L330I		Atlas-SNP	.											.	ZP2	92	.	0			c.C988A						PASS	.						107	102	103					16																	21214557		2200	4300	6500	SO:0001583	missense	7783	exon10			GGAGTAGGCATTT	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.988C>A	chr16.hg19:g.21214557G>T	ENSP00000460971:p.Leu330Ile	62.0	0.0	.		54.0	31.0	.	NM_003460	B2R7J2|Q4VAN9|Q4VAP0|Q4VAP1	Missense_Mutation	SNP	ENST00000574002.1	hg19	CCDS10596.1	.	.	.	.	.	.	.	.	.	.	G	14.40	2.523709	0.44866	.	.	ENSG00000103310	ENST00000219593	T	0.76316	-1.01	5.97	2.76	0.32466	.	0.485326	0.18994	N	0.125524	T	0.77267	0.4105	M	0.75447	2.3	0.19575	N	0.999964	P;P	0.51351	0.944;0.944	P;P	0.47981	0.563;0.563	T	0.66685	-0.5861	10	0.32370	T	0.25	-6.6445	7.7511	0.28898	0.1328:0.292:0.5752:0.0	.	330;330	Q4VAP1;Q05996	.;ZP2_HUMAN	I	330	ENSP00000219593:L330I	ENSP00000219593:L330I	L	-	1	2	ZP2	21122058	0.879000	0.30193	0.975000	0.42487	0.291000	0.27294	0.880000	0.28159	1.513000	0.48852	0.655000	0.94253	CTA	.	.	.	none		0.483	ZP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207365.2			T	21214557	G	T	21214557	3	4	188	1	0	0	0	0	1	0	0	0	18228	991	35	4	1289	4	ZP2	16	21214557	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	29099	21214557	69140196	66	11089											
SETD1A	9739	hgsc.bcm.edu	37	chr16	30976286	30976286	+	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	agctgagcgcttcccaccttCttacacctcctacctgcccc	6	10	5	20	1	1	1	0	1	1	0	3	1	3	1	7	0	5	2	7	0	2	4			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr16:30976286C>A	ENST00000262519.8	+	7	1909	c.1223C>A	c.(1222-1224)tCt>tAt	p.S408Y		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	408	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						TTCCCACCTTCTTACACCTCC	0.662																																					p.S408Y		Atlas-SNP	.											.	SETD1A	143	.	0			c.C1223A						PASS	.						57	66	63					16																	30976286		2197	4300	6497	SO:0001583	missense	9739	exon7			CACCTTCTTACAC	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.1223C>A	chr16.hg19:g.30976286C>A	ENSP00000262519:p.Ser408Tyr	64.0	0.0	.		63.0	19.0	.	NM_014712	A6NP62|Q6PIF3|Q8TAJ6	Missense_Mutation	SNP	ENST00000262519.8	hg19	CCDS32435.1	.	.	.	.	.	.	.	.	.	.	C	13.26	2.182646	0.38511	.	.	ENSG00000099381	ENST00000262519	D	0.94497	-3.44	5.64	5.64	0.86602	.	0.197187	0.45361	D	0.000366	D	0.93979	0.8072	L	0.36672	1.1	0.26055	N	0.981439	D	0.67145	0.996	P	0.56700	0.804	D	0.89234	0.3579	10	0.72032	D	0.01	.	12.5755	0.56362	0.0:0.92:0.0:0.08	.	408	O15047	SET1A_HUMAN	Y	408	ENSP00000262519:S408Y	ENSP00000262519:S408Y	S	+	2	0	SETD1A	30883787	1.000000	0.71417	1.000000	0.80357	0.548000	0.35241	3.742000	0.55097	2.648000	0.89879	0.561000	0.74099	TCT	.	.	.	none		0.662	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712		A	30976286	C	A	30976286	3	1	188	1	0	0	0	0	1	0	0	0	14143	913	32	4	1245	4	SETD1A	16	30976286	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	9761729	30976286	59378467	67	11090											
THAP11	57215	hgsc.bcm.edu	37	chr16	67876718	67876718	+	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	ccgctgcgcggcgtcaatgaGcgcaaagtagcgcgcagacc	9	4	14	14	7	1	2	1	1	0	1	1	2	1	2	2	1	3	4	2	1	3	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr16:67876718G>T	ENST00000303596.1	+	1	506	c.261G>T	c.(259-261)gaG>gaT	p.E87D	CENPT_ENST00000562787.1_Intron	NM_020457.2	NP_065190.2	Q96EK4	THA11_HUMAN	THAP domain containing 11	87					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|urinary_tract(1)	8		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118)		GCGTCAATGAGCGCAAAGTAG	0.687																																					p.E87D		Atlas-SNP	.											.	THAP11	27	.	0			c.G261T						PASS	.						18	19	18					16																	67876718		2197	4296	6493	SO:0001583	missense	57215	exon1			CAATGAGCGCAAA	AB015338	CCDS10847.1	16q22.1	2013-01-25			ENSG00000168286	ENSG00000168286		"THAP (C2CH-type zinc finger) domain containing"	23194	protein-coding gene	gene with protein product		609119				12575992, 8325628	Standard	NM_020457		Approved	HRIHFB2206, CTG-B45d, CTG-B43a	uc002euo.3	Q96EK4	OTTHUMG00000137546	ENST00000303596.1:c.261G>T	chr16.hg19:g.67876718G>T	ENSP00000304689:p.Glu87Asp	47.0	0.0	.		28.0	12.0	.	NM_020457	A4UCT5|A8K002|O94795	Missense_Mutation	SNP	ENST00000303596.1	hg19	CCDS10847.1	.	.	.	.	.	.	.	.	.	.	G	17.35	3.368381	0.61513	.	.	ENSG00000168286	ENST00000303596	T	0.33216	1.42	5.4	4.31	0.51392	.	0.000000	0.85682	D	0.000000	T	0.41880	0.1178	L	0.32530	0.975	0.51767	D	0.999939	D	0.63880	0.993	D	0.70016	0.967	T	0.26121	-1.0112	10	0.54805	T	0.06	-16.1311	11.7789	0.52001	0.1059:0.0:0.8941:0.0	.	87	Q96EK4	THA11_HUMAN	D	87	ENSP00000304689:E87D	ENSP00000304689:E87D	E	+	3	2	THAP11	66434219	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.044000	0.57361	1.155000	0.42497	0.563000	0.77884	GAG	.	.	.	none		0.687	THAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268879.1	NM_020457		T	67876718	G	T	67876718	3	4	188	1	0	0	0	0	1	0	0	0	15855	962	34	4	263	4	THAP11	16	67876718	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	36900432	67876718	22478035	68	11091											
LGALS9	3965	hgsc.bcm.edu	37	chr17	25967635	25967635	+	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	agactggcttcagtggaaatGacattgccttccacttcaac	11	11	8	11	0	2	2	2	1	0	1	3	3	3	3	2	2	2	1	2	2	2	4			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr17:25967635G>A	ENST00000395473.2	+	3	1637	c.169G>A	c.(169-171)Gac>Aac	p.D57N	LGALS9_ENST00000313648.6_Missense_Mutation_p.D57N|AC015688.3_ENST00000584605.1_3'UTR|LGALS9_ENST00000413914.2_Intron|LGALS9_ENST00000310394.5_Missense_Mutation_p.D57N|LGALS9_ENST00000302228.5_Missense_Mutation_p.D57N|LGALS9_ENST00000448970.2_3'UTR	NM_009587.2	NP_033665.1	O00182	LEG9_HUMAN	lectin, galactoside-binding, soluble, 9	57	Galectin 1. {ECO:0000255|PROSITE- ProRule:PRU00639}.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|galactose binding (GO:0005534)|signal transducer activity (GO:0004871)			endometrium(3)|large_intestine(2)|lung(12)|skin(1)	18	Lung NSC(42;0.0103)		BRCA - Breast invasive adenocarcinoma(3;0.0141)	UCEC - Uterine corpus endometrioid carcinoma (53;0.155)		CAGTGGAAATGACATTGCCTT	0.527																																					p.D57N	Melanoma(106;677 1527 28724 29571 46552)|Ovarian(193;263 2088 2118 29005 43023)	Atlas-SNP	.											.	LGALS9	29	.	0			c.G169A						PASS	.						124	118	120					17																	25967635		2203	4300	6503	SO:0001583	missense	3965	exon3			GGAAATGACATTG	AB006782	CCDS11222.1, CCDS32592.1	17q11.2	2013-03-28	2008-07-25		ENSG00000168961	ENSG00000168961		"Lectins, galactoside-binding"	6570	protein-coding gene	gene with protein product	"galectin 9"	601879				9045665	Standard	NM_009587		Approved	LGALS9A	uc002gzp.3	O00182	OTTHUMG00000179831	ENST00000395473.2:c.169G>A	chr17.hg19:g.25967635G>A	ENSP00000378856:p.Asp57Asn	609.0	0.0	.		819.0	207.0	.	NM_009587	A7VJG6|O14532|O75028|Q3B8N1|Q53FQ0|Q9NQ58	Missense_Mutation	SNP	ENST00000395473.2	hg19	CCDS11222.1	.	.	.	.	.	.	.	.	.	.	G	9.418	1.082274	0.20309	.	.	ENSG00000168961	ENST00000395473;ENST00000302228;ENST00000310394;ENST00000313648;ENST00000448970	T;T;T;T	0.14022	2.54;2.54;2.54;2.54	3.94	0.839	0.18907	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.459334	0.24325	N	0.039518	T	0.12774	0.0310	L	0.50993	1.605	0.58432	D	0.999995	B;P;P	0.42871	0.1;0.792;0.624	B;B;B	0.42319	0.084;0.383;0.203	T	0.06570	-1.0819	10	0.42905	T	0.14	.	7.4254	0.27096	0.3157:0.0:0.6843:0.0	.	57;57;57	F8W9W4;Q3B8N1;O00182	.;.;LEG9_HUMAN	N	57	ENSP00000378856:D57N;ENSP00000306228:D57N;ENSP00000312259:D57N;ENSP00000318214:D57N	ENSP00000306228:D57N	D	+	1	0	LGALS9	22991762	0.637000	0.27216	0.459000	0.27081	0.622000	0.37654	0.741000	0.26202	0.460000	0.27045	0.586000	0.80456	GAC	.	.	.	none		0.527	LGALS9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255583.1	NM_009587		A	25967635	G	A	25967635	3	1	188	1	0	0	0	0	1	0	0	0	8755	1290	45	2	179	2	LGALS9	17	25967635	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10		25967635	55227575	69	11092											
WIPI1	55062	hgsc.bcm.edu	37	chr17	66440668	66440668	+	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	ggaatatccaggagggtcttCaacagcttcatgtctttaat	11	13	9	8	0	4	0	2	0	2	0	5	2	5	2	1	3	2	1	1	3	4	5			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr17:66440668C>T	ENST00000262139.5	-	4	395	c.396G>A	c.(394-396)ttG>ttA	p.L132L	WIPI1_ENST00000589459.1_5'UTR|WIPI1_ENST00000546360.1_Silent_p.L50L	NM_017983.5	NP_060453.3	Q5MNZ9	WIPI1_HUMAN	WD repeat domain, phosphoinositide interacting 1	132					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						GGAGGGTCTTCAACAGCTTCA	0.433																																					p.L132L		Atlas-SNP	.											.	WIPI1	46	.	0			c.G396A						PASS	.						150	137	142					17																	66440668		2203	4300	6503	SO:0001819	synonymous_variant	55062	exon4			GGTCTTCAACAGC		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.396G>A	chr17.hg19:g.66440668C>T		74.0	0.0	.		119.0	31.0	.	NM_017983	Q8IXM5|Q9NWF8	Silent	SNP	ENST00000262139.5	hg19	CCDS11677.1																																																																																			.	.	.	none		0.433	WIPI1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448739.1	NM_017983		T	66440668	C	T	66440668	2	4	188	1	0	0	0	0	0	0	0	1	17382	825	29	2		2	WIPI1	17	66440668	Silent	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	40473033	66440668	14754542	70	11093											
RBBP8	5932	hgsc.bcm.edu	37	chr18	20562277	20562277	+	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	tcattttctggcgttaaccgGctacgaagaaaggagaaccc	12	9	10	10	3	2	2	1	0	1	2	2	4	2	2	2	3	3	2	2	3	5	4			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr18:20562277G>A	ENST00000399722.2	+	7	876	c.525G>A	c.(523-525)cgG>cgA	p.R175R	RBBP8_ENST00000327155.5_Silent_p.R175R|RBBP8_ENST00000360790.5_Silent_p.R175R|RBBP8_ENST00000399725.2_Silent_p.R175R	NM_203291.1	NP_976036.1	Q99708	COM1_HUMAN	retinoblastoma binding protein 8	175					blastocyst hatching (GO:0001835)|cell cycle checkpoint (GO:0000075)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|G2 DNA damage checkpoint (GO:0031572)|meiotic nuclear division (GO:0007126)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	damaged DNA binding (GO:0003684)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			central_nervous_system(1)|cervix(2)|endometrium(5)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	24	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)		OV - Ovarian serous cystadenocarcinoma(1;0.00196)			GCGTTAACCGGCTACGAAGAA	0.433								Homologous recombination																													p.R175R		Atlas-SNP	.											.	RBBP8	138	.	0			c.G525A						PASS	.						174	154	161					18																	20562277		2203	4300	6503	SO:0001819	synonymous_variant	5932	exon7			TAACCGGCTACGA	AF043431	CCDS11874.1, CCDS11875.1	18q11.2	2012-11-05	2001-11-28		ENSG00000101773	ENSG00000101773			9891	protein-coding gene	gene with protein product	"CTBP-interacting protein"	604124	"retinoblastoma-binding protein 8", "Seckel syndrome 2"	SCKL2		9721205, 17965729, 21998596	Standard	NM_002894		Approved	CtIP, RIM, COM1	uc002ktw.3	Q99708	OTTHUMG00000131769	ENST00000399722.2:c.525G>A	chr18.hg19:g.20562277G>A		112.0	0.0	.		138.0	44.0	.	NM_203292	A6NKN2|A8K8W6|E7ETY1|O75371|Q8NHQ3	Silent	SNP	ENST00000399722.2	hg19	CCDS11875.1																																																																																			.	.	.	none		0.433	RBBP8-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446387.1	NM_203291		A	20562277	G	A	20562277	2	1	188	1	0	0	0	0	0	0	0	1	13118	1190	42	2		2	RBBP8	18	20562277	Silent	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10		20562277	57514971	71	11094											
TRPM4	54795	hgsc.bcm.edu	37	chr19	49714007	49714007	+	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	gccgagcggaagctgctaacGtgggaatcggtgcataagga	11	6	16	8	4	0	0	0	0	0	0	1	4	0	3	1	4	5	3	1	4	4	2			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr19:49714007G>T	ENST00000252826.5	+	22	3495	c.3369G>T	c.(3367-3369)acG>acT	p.T1123T	TRPM4_ENST00000355712.5_Silent_p.T769T|TRPM4_ENST00000427978.2_Silent_p.T978T	NM_017636.3	NP_060106.2	Q8TD43	TRPM4_HUMAN	transient receptor potential cation channel, subfamily M, member 4	1123	Calmodulin-binding.				calcium ion transmembrane transport (GO:0070588)|cardiac conduction (GO:0061337)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|protein sumoylation (GO:0016925)|regulation of membrane potential (GO:0042391)|regulation of T cell cytokine production (GO:0002724)|transmembrane transport (GO:0055085)|vasoconstriction (GO:0042310)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)			breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(18)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	49		all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15)		all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751)		AGCTGCTAACGTGGGAATCGG	0.622																																					p.T1123T		Atlas-SNP	.											.	TRPM4	119	.	0			c.G3369T						PASS	.						38	44	42					19																	49714007		2203	4300	6503	SO:0001819	synonymous_variant	54795	exon22			GCTAACGTGGGAA	AK000048	CCDS33073.1, CCDS56098.1	19q13.3	2011-12-14				ENSG00000130529		"Voltage-gated ion channels / Transient receptor potential cation channels"	17993	protein-coding gene	gene with protein product		606936				11535825, 16382100	Standard	NM_017636		Approved	FLJ20041	uc002pmw.3	Q8TD43		ENST00000252826.5:c.3369G>T	chr19.hg19:g.49714007G>T		186.0	0.0	.		125.0	41.0	.	NM_017636	A2RU25|Q7Z5D9|Q96L84|Q9NXV1	Silent	SNP	ENST00000252826.5	hg19	CCDS33073.1																																																																																			.	.	.	none		0.622	TRPM4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465543.2	NM_017636		T	49714007	G	T	49714007	2	4	188	1	0	0	0	0	0	0	0	1	16600	1132	40	4		4	TRPM4	19	49714007	Silent	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10		49714007	9414976	72	11095											
TMC4	147798	hgsc.bcm.edu	37	chr19	54669261	54669261	+	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	ctgtagctggtcagagcctcGgactccgccagcagtgtctg	6	9	13	13	2	2	1	1	0	1	1	4	2	3	2	3	2	3	3	3	2	1	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr19:54669261G>T	ENST00000376591.4	-	6	986	c.855C>A	c.(853-855)tcC>tcA	p.S285S	TMC4_ENST00000416963.1_5'Flank|TMC4_ENST00000476013.2_Intron|TMC4_ENST00000301187.4_Silent_p.S279S	NM_001145303.1|NM_144686.2	NP_001138775|NP_653287.2	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4	285					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(7)|large_intestine(4)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	22	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					TCAGAGCCTCGGACTCCGCCA	0.652																																					p.S285S		Atlas-SNP	.											.	TMC4	89	.	0			c.C855A						PASS	.						32	30	31					19																	54669261		2202	4299	6501	SO:0001819	synonymous_variant	147798	exon6			AGCCTCGGACTCC	AY236492	CCDS12882.1, CCDS46174.1	19q13.42	2008-02-05			ENSG00000167608	ENSG00000167608			22998	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005277069		Approved		uc010erf.3	Q7Z404	OTTHUMG00000066485	ENST00000376591.4:c.855C>A	chr19.hg19:g.54669261G>T		67.0	0.0	.		52.0	25.0	.	NM_001145303	Q7Z5M3|Q8N5E4|Q8TBS7	Silent	SNP	ENST00000376591.4	hg19	CCDS46174.1																																																																																			.	.	.	none		0.652	TMC4-011	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000156164.2			T	54669261	G	T	54669261	2	4	188	1	0	0	0	0	0	0	0	1	15999	1103	39	4		4	TMC4	19	54669261	Silent	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	4955254	54669261	4459722	73	11096											
CSE1L	1434	hgsc.bcm.edu	37	chr20	47705894	47705895	+	Frame_Shift_Ins	INS	-	-	TT																															taaattttgaggaggctttgINStttttggtgtttactgaaat																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr20:47705894_47705895insTT	ENST00000262982.2	+	18	2055_2056	c.1932_1933insTT	c.(1933-1935)tttfs	p.F645fs	CSE1L_ENST00000542325.1_Frame_Shift_Ins_p.F428fs|CSE1L_ENST00000396192.3_Frame_Shift_Ins_p.F589fs	NM_001256135.1|NM_001316.3	NP_001243064.1|NP_001307.2	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like (yeast)	645					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	importin-alpha export receptor activity (GO:0008262)			breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(11)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	35			BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)			AGGAGGCTTTGTTTTTGGTGTT	0.312																																					p.L644fs		Atlas-Indel,Pindel	.											.	CSE1L	83	.	0			c.1932_1933insTT						PASS	.																																			SO:0001589	frameshift_variant	1434	exon18			.	U33286	CCDS13412.1, CCDS58773.1	20q13	2013-05-01	2001-11-28		ENSG00000124207	ENSG00000124207		"Exportins"	2431	protein-coding gene	gene with protein product	"cellular apoptosis susceptibility"	601342	"chromosome segregation 1 (yeast homolog)-like"			8963895, 7479798	Standard	NM_001316		Approved	CAS, XPO2, CSE1	uc002xty.4	P55060	OTTHUMG00000033046	ENST00000262982.2:c.1935_1936dupTT	chr20.hg19:g.47705897_47705898dupTT	ENSP00000262982:p.Phe645fs	73.0	0.0	0		64.0	15.0	0.234375	NM_001316	A3RLL6|B2R5T4|E1P5Y0|F8W904|O75432|Q32M40|Q9H5B7|Q9NTS0|Q9UP98|Q9UP99|Q9UPA0	Frame_Shift_Ins	INS	ENST00000262982.2	hg19	CCDS13412.1																																																																																			.	.	.	none		0.312	CSE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080345.2	NM_001316		TT	47705895	-	TT	47705894	7	5	188	1	0	1	1	0	0	0	0	0	3932	1368	48	0	1998	0	CSE1L	20	47705894	Frame_Shift_Ins	INS	-	TCGA-GL-A59R-01A-11D-A26P-10		47705894	15319626	74	11097											
CASS4	57091	hgsc.bcm.edu	37	chr20	55033659	55033659	+	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	atcctccgtggcagcagtcaCctctgcagcctgctcaagga	8	8	10	15	1	3	0	2	0	1	0	5	1	5	1	4	2	4	4	4	2	1	0			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr20:55033659C>A	ENST00000360314.3	+	7	2442	c.2217C>A	c.(2215-2217)caC>caA	p.H739Q	CASS4_ENST00000371336.3_Missense_Mutation_p.H739Q|CASS4_ENST00000434344.1_Missense_Mutation_p.H302Q|AL121914.1_ENST00000390795.2_RNA	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	739					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						GCAGCAGTCACCTCTGCAGCC	0.642																																					p.H739Q		Atlas-SNP	.											.	CASS4	121	.	0			c.C2217A						PASS	.						61	50	53					20																	55033659		2203	4300	6503	SO:0001583	missense	57091	exon6			CAGTCACCTCTGC	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.2217C>A	chr20.hg19:g.55033659C>A	ENSP00000353462:p.His739Gln	106.0	0.0	.		94.0	11.0	.	NM_020356	E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Missense_Mutation	SNP	ENST00000360314.3	hg19	CCDS33492.1	.	.	.	.	.	.	.	.	.	.	C	11.41	1.631149	0.28978	.	.	ENSG00000087589	ENST00000360314;ENST00000371336;ENST00000434344	T;T;T	0.22336	1.96;1.96;1.96	5.91	1.54	0.23209	CAS family, DUF3513 (1);	0.511945	0.22918	N	0.054044	T	0.15305	0.0369	L	0.32530	0.975	0.32062	N	0.595525	B;B;B	0.22983	0.078;0.023;0.065	B;B;B	0.23275	0.045;0.013;0.033	T	0.18650	-1.0330	10	0.12430	T	0.62	-9.0912	15.118	0.72419	0.0882:0.3522:0.5595:0.0	.	685;302;739	B4DII4;Q9NQ75-3;Q9NQ75	.;.;CASS4_HUMAN	Q	739;739;302	ENSP00000353462:H739Q;ENSP00000360387:H739Q;ENSP00000410027:H302Q	ENSP00000353462:H739Q	H	+	3	2	CASS4	54467066	1.000000	0.71417	0.288000	0.24862	0.859000	0.49053	1.083000	0.30815	0.372000	0.24591	0.655000	0.94253	CAC	.	.	.	none		0.642	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079789.2	NM_020356		A	55033659	C	A	55033659	3	1	188	1	0	0	0	0	1	0	0	0	2685	506	18	4	2239	4	CASS4	20	55033659	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	7327765	55033659	7991861	75	11098											
SLCO4A1	28231	hgsc.bcm.edu	37	chr20	61300283	61300283	+	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	agtgggcttctctccgcaggGggcatcccggggcccatcgc	4	7	15	15	3	1	0	0	0	1	0	5	0	3	0	3	5	0	3	3	5	0	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr20:61300283G>A	ENST00000370507.1	+	10	1974	c.1878G>A	c.(1876-1878)ggG>ggA	p.G626G	RP11-93B14.5_ENST00000451648.1_RNA|RP11-93B14.5_ENST00000411824.1_RNA|RP11-93B14.5_ENST00000433126.1_RNA|SLCO4A1_ENST00000217159.1_Splice_Site_p.G626G|SLCO4A1_ENST00000470412.1_3'UTR			Q96BD0	SO4A1_HUMAN	solute carrier organic anion transporter family, member 4A1	626					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)	TCTCCGCAGGGGGCATCCCGG	0.662											OREG0026115	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G626G	Pancreas(168;741 2006 10379 40139 45334)	Atlas-SNP	.											.	SLCO4A1	65	.	0			c.G1878A						PASS	.						29	32	31					20																	61300283		2202	4299	6501	SO:0001630	splice_region_variant	28231	exon11			CGCAGGGGGCATC	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.1877-1G>A	chr20.hg19:g.61300283G>A		19.0	0.0	.	1052	20.0	14.0	.	NM_016354	Q9H4T7|Q9H4T8|Q9H8P2|Q9NWX8|Q9UI35|Q9UIG7	Silent	SNP	ENST00000370507.1	hg19	CCDS13501.1																																																																																			.	.	.	none		0.662	SLCO4A1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080048.2	NM_016354	Silent	A	61300283	G	A	61300283	5	1	188	1	0	0	0	0	0	0	1	0	14742	1246	43	2	1916	2	SLCO4A1	20	61300283	Splice_Site	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10	6266624	61300283	1725237	76	11099											
KRTAP19-7	337974	hgsc.bcm.edu	37	chr21	31933587	31933587	+	Frame_Shift_Del	DEL	A	A	-																															gccgtagcctaggcctccatAgtagctgccggagtagctca																								rs149420565		TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr21:31933587delA	ENST00000334849.2	-	1	46	c.22delT	c.(22-24)tatfs	p.Y8fs		NM_181614.1	NP_853645.1	Q3SYF9	KR197_HUMAN	keratin associated protein 19-7	8						intermediate filament (GO:0005882)				endometrium(1)|large_intestine(1)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	11						AGGCCTCCATAGTAGCTGCCG	0.522																																					p.Y8fs		Atlas-Indel,Pindel	.											.	KRTAP19-7	23	.	0			c.23delA						PASS	.						123	106	111					21																	31933587		2203	4300	6503	SO:0001589	frameshift_variant	337974	exon1			.	AP001708	CCDS13599.1	21q22.1	2006-03-13			ENSG00000244362	ENSG00000244362		"Keratin associated proteins"	18942	protein-coding gene	gene with protein product						12359730	Standard	NM_181614		Approved	KAP19.7	uc011adb.2	Q3SYF9	OTTHUMG00000057785	ENST00000334849.2:c.22delT	chr21.hg19:g.31933587delA	ENSP00000334696:p.Tyr8fs	198.0	0.0	0		220.0	104.0	0.472727	NM_181614	Q08EP7	Frame_Shift_Del	DEL	ENST00000334849.2	hg19	CCDS13599.1																																																																																			.	.	.	none		0.522	KRTAP19-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128237.2			-	31933587	A	-	31933587	7	5	188	1	0	1	0	1	0	0	0	0	8541	420	15	0	172	0	KRTAP19-7	21	31933587	Frame_Shift_Del	DEL	A	TCGA-GL-A59R-01A-11D-A26P-10		31933587	16196308	77	11100											
COL18A1	80781	hgsc.bcm.edu	37	chr21	46875643	46875643	+	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	ccaccacacacgtgacccccCggaatggttccacagagcca	11	4	8	18	2	0	2	0	1	0	1	1	3	1	3	7	2	1	1	7	2	1	1	rs375087150		TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr21:46875643C>G	ENST00000359759.4	+	1	220	c.199C>G	c.(199-201)Cgg>Ggg	p.R67G	COL18A1_ENST00000355480.5_Missense_Mutation_p.R67G|COL18A1_ENST00000400337.2_Intron			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	67					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)		CGTGACCCCCCGGAATGGTTC	0.647																																					p.R67G		Atlas-SNP	.											.	COL18A1	129	.	0			c.C199G						PASS	.						53	68	63					21																	46875643		2077	4200	6277	SO:0001583	missense	80781	exon1			ACCCCCCGGAATG		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.199C>G	chr21.hg19:g.46875643C>G	ENSP00000352798:p.Arg67Gly	159.0	0.0	.		131.0	60.0	.	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	hg19		.	.	.	.	.	.	.	.	.	.	C	10.16	1.275053	0.23307	.	.	ENSG00000182871	ENST00000355480;ENST00000359759;ENST00000539645	T;T	0.38077	1.16;1.16	3.61	0.181	0.15073	Domain of unknown function DUF959, collagen XVIII, N-terminal (1);	1.949970	0.03091	N	0.159750	T	0.22627	0.0546	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.28522	-1.0041	10	0.72032	D	0.01	.	4.007	0.09605	0.0:0.3657:0.3946:0.2397	.	67;67	P39060;P39060-1	COIA1_HUMAN;.	G	67	ENSP00000347665:R67G;ENSP00000352798:R67G	ENSP00000347665:R67G	R	+	1	2	COL18A1	45700071	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.084000	0.14891	0.253000	0.21552	-0.339000	0.08088	CGG	.	.	.	alt		0.647	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			G	46875643	C	G	46875643	3	3	188	1	0	0	0	0	1	0	0	0	3677	643	23	4	315	4	COL18A1	21	46875643	Missense_Mutation	SNP	C	TCGA-GL-A59R-01A-11D-A26P-10	14942056	46875643	1254252	78	11101											
GAB4	128954	hgsc.bcm.edu	37	chr22	17488934	17488934	+	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	cggggccacttccgggccacGaagacaaaggcgcaaatgcc	11	3	13	14	4	0	1	0	0	0	1	1	2	1	1	4	4	1	1	4	4	3	1			TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr22:17488934G>A	ENST00000400588.1	-	1	178	c.71C>T	c.(70-72)tCg>tTg	p.S24L	GAB4_ENST00000523144.1_5'Flank	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	24										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)				TCCGGGCCACGAAGACAAAGG	0.682																																					p.S24L		Atlas-SNP	.											.	GAB4	95	.	0			c.C71T						PASS	.						16	19	18					22																	17488934		2097	4219	6316	SO:0001583	missense	128954	exon1			GGCCACGAAGACA	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.71C>T	chr22.hg19:g.17488934G>A	ENSP00000383431:p.Ser24Leu	49.0	0.0	.		46.0	14.0	.	NM_001037814		Missense_Mutation	SNP	ENST00000400588.1	hg19	CCDS42976.1	.	.	.	.	.	.	.	.	.	.	G	10.22	1.290327	0.23478	.	.	ENSG00000215568	ENST00000400588	T	0.10288	2.89	0.637	0.637	0.17735	.	.	.	.	.	T	0.04634	0.0126	N	0.08118	0	0.09310	N	1	P	0.44241	0.829	B	0.40134	0.32	T	0.37244	-0.9714	8	0.14656	T	0.56	.	.	.	.	.	24	Q2WGN9	GAB4_HUMAN	L	24	ENSP00000383431:S24L	ENSP00000383431:S24L	S	-	2	0	GAB4	15868934	0.001000	0.12720	0.007000	0.13788	0.022000	0.10575	-0.092000	0.11129	0.591000	0.29711	0.313000	0.20887	TCG	.	.	.	none		0.682	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882		A	17488934	G	A	17488934	3	1	188	1	0	0	0	0	1	0	0	0	6158	1059	37	1	1693	1	GAB4	22	17488934	Missense_Mutation	SNP	G	TCGA-GL-A59R-01A-11D-A26P-10		17488934	33815632	79	11102											
EP300	2033	hgsc.bcm.edu	37	chr22	41558757	41558757	+	Frame_Shift_Del	DEL	A	A	-																															aaagaacaattttccaagagAaaaaatgacacactggatcc																										TCGA-GL-A59R-01A-11D-A26P-10	TCGA-GL-A59R-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c504d5a9-29b0-4b7e-ac7b-5e543449a0f4	b95ff063-202c-47ad-a9fa-d2f922585ae7	g.chr22:41558757delA	ENST00000263253.7	+	21	4921	c.3702delA	c.(3700-3702)agafs	p.R1234fs		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1234					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.Y1198_L1243del(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						TTTCCAAGAGAAAAAATGACA	0.368			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.R1234fs		Atlas-Indel,Pindel	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300	367	.	1	Deletion - In frame(1)	breast(1)	c.3701delG						PASS	.						120	114	116					22																	41558757		2203	4300	6503	SO:0001589	frameshift_variant	2033	exon21	Familial Cancer Database	Broad Thumb-Hallux syndrome	.	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.3702delA	chr22.hg19:g.41558757delA	ENSP00000263253:p.Arg1234fs	134.0	0.0	0		132.0	51.0	0.386364	NM_001429	B1AKC2	Frame_Shift_Del	DEL	ENST00000263253.7	hg19	CCDS14010.1																																																																																			.	.	.	none		0.368	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		-	41558757	A	-	41558757	7	5	188	1	0	1	0	1	0	0	0	0	5150	243	9	0	3784	0	EP300	22	41558757	Frame_Shift_Del	DEL	A	TCGA-GL-A59R-01A-11D-A26P-10	24069823	41558757	9745809	80	11103											
PADI4	23569	hgsc.bcm.edu	37	chr1	17674521	17674521	+	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	aaggaacagaggcctgaaggAgtttcccatcaaacgcgtga	14	6	12	9	2	1	3	1	2	0	1	2	5	2	5	2	3	2	1	2	3	4	1			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:17674521A>T	ENST00000375448.4	+	10	1159	c.1133A>T	c.(1132-1134)gAg>gTg	p.E378V	AC004824.2_ENST00000602074.1_Intron|PADI4_ENST00000487048.1_3'UTR	NM_012387.2	NP_036519.2	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV	378					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)	GGCCTGAAGGAGTTTCCCATC	0.567																																					p.E378V		Atlas-SNP	.											.	PADI4	70	.	0			c.A1133T						PASS	.						99	89	92					1																	17674521		2203	4300	6503	SO:0001583	missense	23569	exon10			TGAAGGAGTTTCC	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.1133A>T	chr1.hg19:g.17674521A>T	ENSP00000364597:p.Glu378Val	129.0	0.0	.		83.0	26.0	.	NM_012387	A8K392|B2RBW0|Q5VTZ8|Q70SX4	Missense_Mutation	SNP	ENST00000375448.4	hg19	CCDS180.1	.	.	.	.	.	.	.	.	.	.	-	15.98	2.991445	0.54041	.	.	ENSG00000159339	ENST00000375448	T	0.25414	1.8	4.85	4.85	0.62838	Protein-arginine deiminase, C-terminal (1);	0.357378	0.28883	N	0.013830	T	0.23649	0.0572	N	0.13235	0.315	0.39431	D	0.967088	B;P	0.47191	0.04;0.891	B;P	0.51550	0.091;0.673	T	0.05920	-1.0856	10	0.41790	T	0.15	-11.7468	11.9518	0.52959	1.0:0.0:0.0:0.0	.	378;378	A8K392;Q9UM07	.;PADI4_HUMAN	V	378	ENSP00000364597:E378V	ENSP00000364597:E378V	E	+	2	0	PADI4	17547108	1.000000	0.71417	0.970000	0.41538	0.890000	0.51754	6.131000	0.71670	2.042000	0.60477	0.423000	0.28283	GAG	.	.	.	none		0.567	PADI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006799.1	NM_012387		T	17674521	A	T	17674521	3	4	189	1	0	0	0	0	1	0	0	0	11387	304	11	5	1171	5	PADI4	1	17674521	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10		17674521	231576100	1	11104											
RWDD3	25950	hgsc.bcm.edu	37	chr1	95710051	95710051	+	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	aaccagaaactggcagtggcAgtgaaaagtgtactttttca	14	10	10	7	0	1	2	1	1	0	1	1	2	1	2	1	2	3	3	1	2	5	3	rs138509057		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:95710051A>T	ENST00000370202.4	+	2	446	c.370A>T	c.(370-372)Agt>Tgt	p.S124C	RWDD3_ENST00000263893.6_Missense_Mutation_p.S124C|RWDD3_ENST00000495272.1_3'UTR|RP11-57H12.6_ENST00000604534.1_3'UTR|RP11-57H12.5_ENST00000444665.1_RNA|RWDD3_ENST00000429514.2_Missense_Mutation_p.S109C	NM_001199682.1|NM_015485.4	NP_001186611.1|NP_056300	Q9Y3V2	RWDD3_HUMAN	RWD domain containing 3	124					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of hypoxia-inducible factor-1alpha signaling pathway (GO:1902073)|positive regulation of protein sumoylation (GO:0033235)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.S124R(1)		kidney(1)|large_intestine(2)|lung(6)|ovary(1)	10		all_epithelial(167;5.99e-05)|all_lung(203;0.00168)|Lung NSC(277;0.00769)		all cancers(265;0.112)|Epithelial(280;0.229)		TGGCAGTGGCAGTGAAAAGTG	0.438																																					p.S124C		Atlas-SNP	.											RWDD3,rectum,carcinoma,0,1	RWDD3	24	.	1	Substitution - Missense(1)	large_intestine(1)	c.A370T						PASS	.						107	102	104					1																	95710051		1947	4130	6077	SO:0001583	missense	25950	exon2			AGTGGCAGTGAAA	BC010936	CCDS41357.1, CCDS44177.1	1p22.1	2012-12-07			ENSG00000122481	ENSG00000122481			21393	protein-coding gene	gene with protein product		615875				11230166	Standard	NM_015485		Approved	DKFZP566K023	uc009wdu.3	Q9Y3V2	OTTHUMG00000010910	ENST00000370202.4:c.370A>T	chr1.hg19:g.95710051A>T	ENSP00000359221:p.Ser124Cys	133.0	2.0	.		111.0	32.0	.	NM_015485	A6NP44|A8K9F0|C9J9L7|C9JI45|Q08AJ7|Q6FID3|Q9BX35	Missense_Mutation	SNP	ENST00000370202.4	hg19	CCDS41357.1	.	.	.	.	.	.	.	.	.	.	A	3.798	-0.042270	0.07452	.	.	ENSG00000122481	ENST00000370202;ENST00000429514;ENST00000263893	T;T;T	0.34859	1.34;1.38;1.35	5.38	-5.53	0.02552	.	1.677590	0.02325	N	0.073392	T	0.09202	0.0227	L	0.40543	1.245	0.09310	N	1	B;B;B;B;B	0.11235	0.001;0.001;0.0;0.004;0.0	B;B;B;B;B	0.09377	0.001;0.001;0.0;0.004;0.001	T	0.27191	-1.0081	10	0.52906	T	0.07	0.4062	0.9194	0.01311	0.2608:0.2714:0.1228:0.345	.	109;124;124;109;124	E7ES73;Q9Y3V2;D3DT49;Q9Y3V2-3;Q9Y3V2-2	.;RWDD3_HUMAN;.;.;.	C	124;109;124	ENSP00000359221:S124C;ENSP00000397398:S109C;ENSP00000263893:S124C	ENSP00000263893:S124C	S	+	1	0	RWDD3	95482639	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.566000	0.05922	-0.478000	0.06823	-0.274000	0.10170	AGT	.	.	.	none		0.438	RWDD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030078.1	NM_015485		T	95710051	A	T	95710051	3	4	189	1	0	0	0	0	1	0	0	0	13770	188	7	5	376	5	RWDD3	1	95710051	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	78035530	95710051	153540570	2	11105											
LPPR4	9890	hgsc.bcm.edu	37	chr1	99764611	99764611	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgttcatgtatttggattaTgctctacagctctcattaca	9	17	7	8	0	3	0	2	0	2	0	4	1	3	1	0	1	4	4	0	1	4	6			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:99764611T>C	ENST00000370185.3	+	4	1056	c.559T>C	c.(559-561)Tgc>Cgc	p.C187R	LPPR4_ENST00000370184.1_Missense_Mutation_p.C29R|LPPR4_ENST00000457765.1_Missense_Mutation_p.C187R	NM_014839.4	NP_055654.2	Q7Z2D5	LPPR4_HUMAN		187					axonogenesis (GO:0007409)|inner ear development (GO:0048839)|phospholipid dephosphorylation (GO:0046839)	integral component of plasma membrane (GO:0005887)	lipid phosphatase activity (GO:0042577)|phosphatidate phosphatase activity (GO:0008195)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(39)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	72		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)		ATTTGGATTATGCTCTACAGC	0.363																																					p.C187R		Atlas-SNP	.											.	LPPR4	143	.	0			c.T559C						PASS	.						150	133	138					1																	99764611		2203	4300	6503	SO:0001583	missense	0	exon4			GGATTATGCTCTA																												ENST00000370185.3:c.559T>C	chr1.hg19:g.99764611T>C	ENSP00000359204:p.Cys187Arg	97.0	0.0	.		103.0	39.0	.	NM_001166252	E7EPS1|O75043|Q5T9R9|Q86XQ5|Q8N3F1|Q96MP0	Missense_Mutation	SNP	ENST00000370185.3	hg19	CCDS757.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.012287	0.75046	.	.	ENSG00000117600	ENST00000370185;ENST00000457765;ENST00000263178;ENST00000370184	T;T;T	0.52057	0.68;0.68;0.68	5.41	5.41	0.78517	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.63920	0.2552	M	0.78637	2.42	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.69636	-0.5092	10	0.72032	D	0.01	-30.56	15.7585	0.78058	0.0:0.0:0.0:1.0	.	187;187	E7EPS1;Q7Z2D5	.;LPPR4_HUMAN	R	187;187;187;29	ENSP00000359204:C187R;ENSP00000394913:C187R;ENSP00000359203:C29R	ENSP00000263178:C187R	C	+	1	0	RP4-788L13.1	99537199	1.000000	0.71417	0.955000	0.39395	0.578000	0.36192	6.235000	0.72332	2.191000	0.70037	0.528000	0.53228	TGC	.	.	.	none		0.363	LPPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029670.2			C	99764611	T	C	99764611	3	2	189	1	0	0	0	0	1	0	0	0	8934	1464	51	3	573	3	LPPR4	1	99764611	Missense_Mutation	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10	4054560	99764611	149486010	3	11106											
NUP210L	91181	hgsc.bcm.edu	37	chr1	154033038	154033049	+	In_Frame_Del	DEL	ATGTAAGTGATG	ATGTAAGTGATG	-																															caacagagctttctgcttccAtgtaagtgatggtgacaaca																								rs368673993		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	ATGTAAGTGATG	ATGTAAGTGATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:154033038_154033049delATGTAAGTGATG	ENST00000368559.3	-	20	2888_2899	c.2817_2828delCATCACTTACAT	c.(2815-2829)accatcacttacatg>acg	p.ITYM940del	NUP210L_ENST00000271854.3_In_Frame_Del_p.ITYM940del	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	940					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)			TTCTGCTTCCATGTAAGTGATGGTGACAACAC	0.415																																					p.940_943del		Atlas-Indel,Pindel	.											.	NUP210L	181	.	0			c.2818_2829del						PASS	.																																			SO:0001651	inframe_deletion	91181	exon20			.	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.2817_2828delCATCACTTACAT	chr1.hg19:g.154033038_154033049delATGTAAGTGATG	ENSP00000357547:p.Ile940_Met943del	99.0	0.0	0		64.0	14.0	0.21875	NM_207308	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	In_Frame_Del	DEL	ENST00000368559.3	hg19	CCDS41399.1																																																																																			.	.	.	none		0.415	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308		-	154033049	ATGTAAGTGATG	-	154033038	7	5	189	1	0	1	0	1	0	0	0	0	10768	217	8	0	2922	0	NUP210L	1	154033038	In_Frame_Del	DEL	ATGTAAGTGATG	TCGA-GL-A59T-01A-21D-A28G-10	54268427	154033038	95217583	4	11107											
KCNN3	3782	hgsc.bcm.edu	37	chr1	154842253	154842253	+	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	gctgctgctgaagctgcggaGgctgaggctgcagcgagggt	6	7	19	9	2	0	2	0	2	0	0	0	4	0	3	0	4	6	7	0	4	1	0			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:154842253G>T	ENST00000271915.4	-	1	503	c.188C>A	c.(187-189)cCt>cAt	p.P63H	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	63	Gln-rich.|Pro-rich.				potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	aagctgcggaggctgaggctg	0.697																																					p.P63H		Atlas-SNP	.											.	KCNN3	141	.	0			c.C188A						PASS	.						6	4	5					1																	154842253		1984	3925	5909	SO:0001583	missense	3782	exon1			TGCGGAGGCTGAG	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.188C>A	chr1.hg19:g.154842253G>T	ENSP00000271915:p.Pro63His	81.0	0.0	.		62.0	15.0	.	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Missense_Mutation	SNP	ENST00000271915.4	hg19	CCDS30880.1	.	.	.	.	.	.	.	.	.	.	g	11.14	1.552427	0.27739	.	.	ENSG00000143603	ENST00000271915;ENST00000539103	T	0.56275	0.47	5.07	3.18	0.36537	.	1.727610	0.03258	N	0.182822	T	0.18551	0.0445	N	0.08118	0	0.80722	D	1	.	.	.	.	.	.	T	0.11372	-1.0590	8	0.33141	T	0.24	-4.1487	6.4327	0.21807	0.0918:0.0:0.7284:0.1798	.	.	.	.	H	63;158	ENSP00000271915:P63H	ENSP00000271915:P63H	P	-	2	0	KCNN3	153108877	0.863000	0.29885	1.000000	0.80357	0.998000	0.95712	1.873000	0.39558	0.823000	0.34589	0.563000	0.77884	CCT	.	.	.	none		0.697	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		T	154842253	G	T	154842253	3	4	189	1	0	0	0	0	1	0	0	0	8087	1000	35	4	2061	4	KCNN3	1	154842253	Missense_Mutation	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	809215	154842253	94408368	5	11108											
THBS3	7059	hgsc.bcm.edu	37	chr1	155172114	155172114	+	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	ctgtgtgcccttgtaccctcGaggacaggcctcacagtgga	7	9	12	13	1	1	0	1	0	0	0	2	3	1	2	3	3	2	1	3	3	1	2			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:155172114G>A	ENST00000368378.3	-	9	1056	c.1036C>T	c.(1036-1038)Cga>Tga	p.R346*	RP11-263K19.4_ENST00000422665.1_RNA|RP11-263K19.4_ENST00000454348.1_RNA|THBS3_ENST00000457183.2_Nonsense_Mutation_p.R226*|RP11-263K19.4_ENST00000430312.1_RNA|RP11-263K19.4_ENST00000447623.1_RNA|RP11-263K19.4_ENST00000436772.1_RNA|RP11-263K19.4_ENST00000453136.1_RNA|THBS3_ENST00000486260.1_5'UTR|THBS3_ENST00000541990.1_5'UTR|THBS3_ENST00000541576.1_5'Flank	NM_001252607.1|NM_007112.4	NP_001239536.1|NP_009043.1	P49746	TSP3_HUMAN	thrombospondin 3	346	EGF-like 1; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				bone trabecula formation (GO:0060346)|cell-matrix adhesion (GO:0007160)|growth plate cartilage development (GO:0003417)|ossification involved in bone maturation (GO:0043931)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(6)|endometrium(4)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(3)	48	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			TTGTACCCTCGAGGACAGGCC	0.602																																					p.R346X		Atlas-SNP	.											.	THBS3	70	.	0			c.C1036T						PASS	.						96	90	92					1																	155172114		2203	4300	6503	SO:0001587	stop_gained	7059	exon9			ACCCTCGAGGACA	L38969	CCDS1099.1, CCDS58034.1, CCDS72937.1	1q21	2008-02-05			ENSG00000169231	ENSG00000169231			11787	protein-coding gene	gene with protein product		188062				1601886	Standard	NM_007112		Approved		uc001fix.3	P49746	OTTHUMG00000035710	ENST00000368378.3:c.1036C>T	chr1.hg19:g.155172114G>A	ENSP00000357362:p.Arg346*	193.0	0.0	.		151.0	41.0	.	NM_007112	B1AVR8|B4DQ20|Q8WV34	Nonsense_Mutation	SNP	ENST00000368378.3	hg19	CCDS1099.1	.	.	.	.	.	.	.	.	.	.	G	34	5.316567	0.95655	.	.	ENSG00000169231	ENST00000368378;ENST00000457183;ENST00000428962	.	.	.	5.44	5.44	0.79542	.	0.674441	0.14773	N	0.299266	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	3.2614	16.8112	0.85720	0.0:0.0:1.0:0.0	.	.	.	.	X	346;226;196	.	ENSP00000357362:R346X	R	-	1	2	THBS3	153438738	0.461000	0.25783	0.082000	0.20525	0.937000	0.57800	3.403000	0.52615	2.837000	0.97791	0.655000	0.94253	CGA	.	.	.	none		0.602	THBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086856.1	NM_007112		A	155172114	G	A	155172114	4	1	189	1	0	0	0	0	0	1	0	0	15867	1066	37	1	1894	1	THBS3	1	155172114	Nonsense_Mutation	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	329861	155172114	94078507	6	11109											
PAPPA2	60676	hgsc.bcm.edu	37	chr1	176525851	176525851	+	Silent	SNP	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	ccggctgccccatgggtaggGgatagtcctattgggcaatc	7	9	14	11	1	0	0	0	0	0	0	2	1	1	1	4	5	1	3	4	5	4	4			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:176525851G>A	ENST00000367662.3	+	2	1557	c.393G>A	c.(391-393)ggG>ggA	p.G131G	PAPPA2_ENST00000367661.3_Silent_p.G131G	NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	131					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						CATGGGTAGGGGATAGTCCTA	0.537																																					p.G131G		Atlas-SNP	.											.	PAPPA2	665	.	0			c.G393A						PASS	.						114	115	114					1																	176525851		2073	4228	6301	SO:0001819	synonymous_variant	60676	exon2			GGTAGGGGATAGT	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.393G>A	chr1.hg19:g.176525851G>A		148.0	0.0	.		152.0	12.0	.	NM_021936	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Silent	SNP	ENST00000367662.3	hg19	CCDS41438.1																																																																																			.	.	.	none		0.537	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			A	176525851	G	A	176525851	2	1	189	1	0	0	0	0	0	0	0	1	11440	1219	43	2		2	PAPPA2	1	176525851	Silent	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	21353737	176525851	72724770	7	11110											
SYT2	127833	hgsc.bcm.edu	37	chr1	202566051	202566052	+	Frame_Shift_Del	DEL	AG	AG	-																															ctatggcttcgttcttgcccAgcttgtcatagtccagcacg																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:202566051_202566052delAG	ENST00000367267.1	-	9	1285_1286	c.1093_1094delCT	c.(1093-1095)ctgfs	p.L365fs	SYT2_ENST00000367268.4_Frame_Shift_Del_p.L365fs	NM_001136504.1	NP_001129976.1	Q8N9I0	SYT2_HUMAN	synaptotagmin II	365	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)	GTTCTTGCCCAGCTTGTCATAG	0.584																																					p.365_365del		Atlas-Indel,Pindel	.											.	SYT2	51	.	0			c.1094_1095del						PASS	.																																			SO:0001589	frameshift_variant	127833	exon9			.	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.1093_1094delCT	chr1.hg19:g.202566051_202566052delAG	ENSP00000356236:p.Leu365fs	134.0	0.0	0		122.0	32.0	0.262295	NM_001136504	Q496K5|Q8NBE5	Frame_Shift_Del	DEL	ENST00000367267.1	hg19	CCDS1427.1																																																																																			.	.	.	none		0.584	SYT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099157.1	NM_177402		-	202566052	AG	-	202566051	7	5	189	1	0	1	0	1	0	0	0	0	15486	188	7	0	169	0	SYT2	1	202566051	Frame_Shift_Del	DEL	AG	TCGA-GL-A59T-01A-21D-A28G-10	26040200	202566051	46684570	8	11111											
AHCTF1	25909	hgsc.bcm.edu	37	chr1	247053281	247053281	+	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	actataccttgataaacgctCaaacttctgtcgacgactgg	12	11	7	11	3	2	1	1	1	1	0	3	3	2	1	1	1	3	1	1	1	5	5			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:247053281C>T	ENST00000391829.2	-	17	2254	c.2131G>A	c.(2131-2133)Gag>Aag	p.E711K	AHCTF1_ENST00000366508.1_Missense_Mutation_p.E746K|AHCTF1_ENST00000326225.3_Missense_Mutation_p.E720K|AHCTF1_ENST00000470300.1_5'UTR			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	711	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)	p.E711Q(1)		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)			GATAAACGCTCAAACTTCTGT	0.338																																					p.E720K	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											AHCTF1,bladder,carcinoma,0,1	AHCTF1	187	.	1	Substitution - Missense(1)	urinary_tract(1)	c.G2158A						PASS	.						114	120	118					1																	247053281		2203	4300	6503	SO:0001583	missense	25909	exon17			AACGCTCAAACTT		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.2131G>A	chr1.hg19:g.247053281C>T	ENSP00000375705:p.Glu711Lys	60.0	0.0	.		47.0	13.0	.	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Missense_Mutation	SNP	ENST00000391829.2	hg19		.	.	.	.	.	.	.	.	.	.	C	10.35	1.327003	0.24080	.	.	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	T;T;T	0.33438	1.41;1.41;1.41	5.61	3.62	0.41486	.	0.132552	0.52532	D	0.000063	T	0.33323	0.0859	M	0.63428	1.95	0.40661	D	0.982126	P;P	0.48503	0.911;0.605	B;B	0.43867	0.434;0.121	T	0.21211	-1.0252	10	0.34782	T	0.22	-9.9643	12.8931	0.58082	0.0:0.8042:0.1258:0.07	.	746;711	Q8WYP5-2;Q8WYP5	.;ELYS_HUMAN	K	746;720;711	ENSP00000355464:E746K;ENSP00000355465:E720K;ENSP00000375705:E711K	ENSP00000355465:E720K	E	-	1	0	AHCTF1	245119904	1.000000	0.71417	0.890000	0.34922	0.002000	0.02628	3.403000	0.52615	1.379000	0.46325	0.579000	0.79373	GAG	.	.	.	none		0.338	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446		T	247053281	C	T	247053281	3	4	189	1	0	0	0	0	1	0	0	0	408	835	29	2	4749	2	AHCTF1	1	247053281	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	44487230	247053281	2197340	9	11112											
DNMT3A	1788	hgsc.bcm.edu	37	chr2	25505312	25505312	+	Frame_Shift_Del	DEL	G	G	-																															ctggtgctgaggactcacccGcttctgcaggggctcctcgg																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr2:25505312delG	ENST00000264709.3	-	4	783	c.446delC	c.(445-447)gcgfs	p.A149fs	DNMT3A_ENST00000406659.3_Frame_Shift_Del_p.A149fs|DNMT3A_ENST00000321117.5_Frame_Shift_Del_p.A149fs	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	149					C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGACTCACCCGCTTCTGCAGG	0.637			"Mis, F, N, S"		AML																																p.A149fs		Atlas-Indel,Pindel	.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	.	DNMT3A	1807	.	0			c.447delG						PASS	.						14	17	16					2																	25505312		2202	4299	6501	SO:0001589	frameshift_variant	1788	exon4			.		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.446delC	chr2.hg19:g.25505312delG	ENSP00000264709:p.Ala149fs	115.0	0.0	0		146.0	67.0	0.458904	NM_175630	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Frame_Shift_Del	DEL	ENST00000264709.3	hg19	CCDS33157.1																																																																																			.	.	.	none		0.637	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552		-	25505312	G	-	25505312	7	5	189	1	0	1	0	1	0	0	0	0	4678	1087	38	0	2505	0	DNMT3A	2	25505312	Frame_Shift_Del	DEL	G	TCGA-GL-A59T-01A-21D-A28G-10		25505312	217694061	10	11113											
ZC3H6	376940	hgsc.bcm.edu	37	chr2	113089251	113089251	+	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	tagattatggaatacaaaaaGtgatcttcatcaaaatacag	19	11	6	5	0	3	2	2	1	1	1	3	3	3	3	0	1	2	0	0	1	9	5			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr2:113089251G>C	ENST00000409871.1	+	12	3157	c.2756G>C	c.(2755-2757)aGt>aCt	p.S919T	ZC3H6_ENST00000343936.4_Missense_Mutation_p.S919T|AC115115.2_ENST00000607612.1_RNA	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	919							metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						AATACAAAAAGTGATCTTCAT	0.388																																					p.S919T		Atlas-SNP	.											.	ZC3H6	93	.	0			c.G2756C						PASS	.						65	59	61					2																	113089251		1855	4101	5956	SO:0001583	missense	376940	exon12			CAAAAAGTGATCT	AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"Zinc fingers, CCCH-type domain containing"	24762	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 6"	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.2756G>C	chr2.hg19:g.113089251G>C	ENSP00000386764:p.Ser919Thr	74.0	0.0	.		74.0	26.0	.	NM_198581	A9JR71|Q6ZW96	Missense_Mutation	SNP	ENST00000409871.1	hg19	CCDS46393.1	.	.	.	.	.	.	.	.	.	.	G	9.984	1.229069	0.22542	.	.	ENSG00000188177	ENST00000409871;ENST00000343936	T;T	0.15487	2.42;2.42	5.94	5.06	0.68205	.	0.469384	0.26776	N	0.022560	T	0.14485	0.0350	L	0.54323	1.7	0.22389	N	0.999144	P	0.35433	0.501	B	0.26770	0.073	T	0.19679	-1.0298	10	0.39692	T	0.17	-2.4342	9.1318	0.36850	0.2286:0.0:0.7714:0.0	.	919	P61129	ZC3H6_HUMAN	T	919	ENSP00000386764:S919T;ENSP00000340298:S919T	ENSP00000340298:S919T	S	+	2	0	ZC3H6	112805722	0.931000	0.31567	0.994000	0.49952	0.985000	0.73830	1.552000	0.36244	1.512000	0.48834	0.591000	0.81541	AGT	.	.	.	none		0.388	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581		C	113089251	G	C	113089251	3	2	189	1	0	0	0	0	1	0	0	0	17583	1029	36	4	2802	4	ZC3H6	2	113089251	Missense_Mutation	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	87583939	113089251	130110122	11	11114											
FAP	2191	hgsc.bcm.edu	37	chr2	163046173	163046173	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaaagatcttactaatttcAtctacttcaagtttcttaat	14	18	2	7	0	5	1	2	0	3	1	5	1	5	1	0	0	2	1	0	0	7	8			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr2:163046173A>G	ENST00000188790.4	-	18	1749	c.1542T>C	c.(1540-1542)gaT>gaC	p.D514D	FAP_ENST00000443424.1_Silent_p.D489D	NM_004460.2	NP_004451.2			fibroblast activation protein, alpha											NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(34)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(4)	63						TACTAATTTCATCTACTTCAA	0.284																																					p.D514D		Atlas-SNP	.											.	FAP	122	.	0			c.T1542C						PASS	.						58	59	58					2																	163046173		2190	4274	6464	SO:0001819	synonymous_variant	2191	exon18			AATTTCATCTACT	U09278	CCDS33311.1	2q23	2008-02-05			ENSG00000078098	ENSG00000078098			3590	protein-coding gene	gene with protein product	"seprase"	600403				9247085, 14707457	Standard	NM_004460		Approved	DPPIV	uc002ucd.3	Q12884	OTTHUMG00000153890	ENST00000188790.4:c.1542T>C	chr2.hg19:g.163046173A>G		72.0	0.0	.		84.0	50.0	.	NM_004460		Silent	SNP	ENST00000188790.4	hg19	CCDS33311.1																																																																																			.	.	.	none		0.284	FAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332852.2			G	163046173	A	G	163046173	2	3	189	1	0	0	0	0	0	0	0	1	5680	214	8	3		3	FAP	2	163046173	Silent	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	49956922	163046173	80153200	12	11115											
LRP2	4036	hgsc.bcm.edu	37	chr2	170096143	170096143	+	Frame_Shift_Del	DEL	A	A	-																															tgctggctacaagagcctagAatatcacattcatctatgtc																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr2:170096143delA	ENST00000263816.3	-	26	4473	c.4188delT	c.(4186-4188)attfs	p.I1396fs		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1396	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"	AAGAGCCTAGAATATCACATT	0.438																																					p.L1397X		Atlas-Indel,Pindel	.											.	LRP2	751	.	0			c.4189delC						PASS	.						145	138	141					2																	170096143		2203	4300	6503	SO:0001589	frameshift_variant	4036	exon26			.		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.4188delT	chr2.hg19:g.170096143delA	ENSP00000263816:p.Ile1396fs	196.0	0.0	0		211.0	15.0	0.0710901	NM_004525	O00711|Q16215	Frame_Shift_Del	DEL	ENST00000263816.3	hg19	CCDS2232.1																																																																																			.	.	.	none		0.438	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		-	170096143	A	-	170096143	7	5	189	1	0	1	0	1	0	0	0	0	8963	242	9	0	9995	0	LRP2	2	170096143	Frame_Shift_Del	DEL	A	TCGA-GL-A59T-01A-21D-A28G-10	7049970	170096143	73103230	13	11116											
FN1	2335	hgsc.bcm.edu	37	chr2	216232592	216232592	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcaactactcactagatgAatcacatctgaaatgaccac	17	8	5	11	0	3	4	2	3	1	1	3	4	3	4	1	0	3	1	1	0	6	2			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr2:216232592A>G	ENST00000359671.1	-	41	7004	c.6739T>C	c.(6739-6741)Tca>Cca	p.S2247P	FN1_ENST00000357867.4_Missense_Mutation_p.S2037P|FN1_ENST00000346544.3_Intron|FN1_ENST00000421182.1_Missense_Mutation_p.S2101P|FN1_ENST00000345488.5_Missense_Mutation_p.S2045P|FN1_ENST00000446046.1_Missense_Mutation_p.S2191P|FN1_ENST00000356005.4_Missense_Mutation_p.S2157P|FN1_ENST00000443816.1_Missense_Mutation_p.S2126P|FN1_ENST00000354785.4_Missense_Mutation_p.S2338P|FN1_ENST00000357009.2_3'UTR|FN1_ENST00000336916.4_Missense_Mutation_p.S2216P|FN1_ENST00000432072.2_Missense_Mutation_p.S2128P|FN1_ENST00000323926.6_Missense_Mutation_p.S2307P			P02751	FINC_HUMAN	fibronectin 1	2247	Fibrin-binding 2.|Fibronectin type-I 10. {ECO:0000255|PROSITE-ProRule:PRU00478}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	TCACTAGATGAATCACATCTG	0.458																																					p.S2338P		Atlas-SNP	.											.	FN1	521	.	0			c.T7012C						PASS	.						115	90	98					2																	216232592		2203	4300	6503	SO:0001583	missense	2335	exon42			TAGATGAATCACA		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.6739T>C	chr2.hg19:g.216232592A>G	ENSP00000352696:p.Ser2247Pro	131.0	0.0	.		155.0	50.0	.	NM_212482	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	hg19		.	.	.	.	.	.	.	.	.	.	A	20.4	3.977481	0.74360	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000345488;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005;ENST00000456923	T;T;T;T;T;T;T;T;T;T;T;T	0.66638	-0.22;1.16;1.37;-0.05;1.65;1.31;1.1;1.08;0.57;-0.11;0.61;0.54	5.67	5.67	0.87782	Fibronectin, type I (2);Complement control module (1);	0.000000	0.56097	D	0.000034	T	0.79811	0.4510	L	0.61218	1.895	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.995;0.992;1.0;0.992;0.995;0.995;0.999;0.999	D;D;D;D;D;D;D;D;D;D;D	0.91635	0.998;0.989;0.998;0.993;0.985;0.999;0.985;0.993;0.993;0.998;0.995	T	0.80269	-0.1453	10	0.49607	T	0.09	.	15.8986	0.79356	1.0:0.0:0.0:0.0	.	2128;2307;2037;2157;2191;2216;2248;2101;2126;2338;2247	P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15;P02751	.;.;.;.;.;.;.;.;.;.;FINC_HUMAN	P	2101;2307;2216;2037;2338;2248;2247;2045;2191;2126;2128;2157;964	ENSP00000394423:S2101P;ENSP00000323534:S2307P;ENSP00000338200:S2216P;ENSP00000350534:S2037P;ENSP00000346839:S2338P;ENSP00000352696:S2247P;ENSP00000273049:S2045P;ENSP00000410422:S2191P;ENSP00000415018:S2126P;ENSP00000399538:S2128P;ENSP00000348285:S2157P;ENSP00000416139:S964P	ENSP00000265313:S2248P	S	-	1	0	FN1	215940837	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.339000	0.96797	2.156000	0.67533	0.477000	0.44152	TCA	.	.	.	none		0.458	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		G	216232592	A	G	216232592	3	3	189	1	0	0	0	0	1	0	0	0	5969	246	9	3	441	3	FN1	2	216232592	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	46136449	216232592	26966781	14	11117											
EFHD1	80303	hgsc.bcm.edu	37	chr2	233498655	233498656	+	Frame_Shift_Ins	INS	-	-	AC																															ctgcagggtcttcaacccctINSacacggagttcccggagttc																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr2:233498655_233498656insAC	ENST00000264059.3	+	1	718_719	c.241_242insAC	c.(241-243)tacfs	p.Y81fs	EFHD1_ENST00000409613.1_Intron	NM_025202.3	NP_079478.1	Q9BUP0	EFHD1_HUMAN	EF-hand domain family, member D1	81					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)		CTTCAACCCCTACACGGAGTTC	0.708																																					p.Y81fs		Atlas-Indel,Pindel	.											.	EFHD1	28	.	0			c.241_242insAC						PASS	.																																			SO:0001589	frameshift_variant	80303	exon1			.		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.244_245dupAC	chr2.hg19:g.233498658_233498659dupAC	ENSP00000264059:p.Tyr81fs	22.0	0.0	0		28.0	13.0	0.464286	NM_025202	B2RD83|E9PFH3|Q9BTF8|Q9H8I2|Q9HBQ0	Frame_Shift_Ins	INS	ENST00000264059.3	hg19	CCDS2497.1																																																																																			.	.	.	none		0.708	EFHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257040.2	NM_025202		AC	233498656	-	AC	233498655	7	5	189	1	0	1	1	0	0	0	0	0	4950	1522	53	0	243	0	EFHD1	2	233498655	Frame_Shift_Ins	INS	-	TCGA-GL-A59T-01A-21D-A28G-10	17266063	233498655	9700718	15	11118											
CNTN4	152330	hgsc.bcm.edu	37	chr3	3080674	3080675	+	Frame_Shift_Ins	INS	-	-	TA																															ggcagcaaatctgaactggtINStataacctgggaggtaaatg																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr3:3080674_3080675insTA	ENST00000397461.1	+	18	2534_2535	c.2150_2151insTA	c.(2149-2154)gttatafs	p.VI717fs	CNTN4_ENST00000427331.1_Frame_Shift_Ins_p.VI717fs|CNTN4_ENST00000418658.1_Frame_Shift_Ins_p.VI717fs|CNTN4_ENST00000358480.3_Frame_Shift_Ins_p.VI498fs|CNTN4-AS1_ENST00000442749.2_RNA|CNTN4_ENST00000397459.2_Frame_Shift_Ins_p.VI389fs|CNTN4_ENST00000448906.2_Frame_Shift_Ins_p.VI389fs	NM_001206955.1	NP_001193884.1	Q8IWV2	CNTN4_HUMAN	contactin 4	717	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		TCTGAACTGGTTATAACCTGGG	0.45																																					p.V717fs		Atlas-Indel,Pindel	.											.	CNTN4	335	.	0			c.2150_2151insTA						PASS	.																																			SO:0001589	frameshift_variant	152330	exon19			.	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.2153_2154dupTA	chr3.hg19:g.3080677_3080678dupTA	ENSP00000380602:p.Val717fs	153.0	0.0	0		158.0	10.0	0.0632911	NM_175607	B2RAX3|Q8IX14|Q8TC35	Frame_Shift_Ins	INS	ENST00000397461.1	hg19	CCDS43041.1																																																																																			.	.	.	none		0.45	CNTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239236.2			TA	3080675	-	TA	3080674	7	5	189	1	0	1	1	0	0	0	0	0	3645	1725	60	0	2212	0	CNTN4	3	3080674	Frame_Shift_Ins	INS	-	TCGA-GL-A59T-01A-21D-A28G-10		3080674	194941756	16	11119											
FBXL2	25827	hgsc.bcm.edu	37	chr3	33415410	33415410	+	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	agcctcaacttgcagtcctgCtcagtaagtagcgtgccttt	8	12	9	12	1	2	0	2	0	0	0	3	0	3	0	3	0	6	4	3	0	3	4			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr3:33415410C>T	ENST00000484457.1	+	9	745	c.654C>T	c.(652-654)tgC>tgT	p.C218C	FBXL2_ENST00000283627.6_3'UTR|FBXL2_ENST00000538892.1_Silent_p.C150C|FBXL2_ENST00000446237.3_5'UTR|FBXL2_ENST00000507198.1_Silent_p.C150C|FBXL2_ENST00000542085.1_5'UTR|FBXL2_ENST00000538181.1_Silent_p.C134C	NM_012157.3	NP_036289.3			F-box and leucine-rich repeat protein 2											endometrium(2)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|urinary_tract(1)	15						TGCAGTCCTGCTCAGTAAGTA	0.498																																					p.C218C		Atlas-SNP	.											.	FBXL2	44	.	0			c.C654T						PASS	.						152	145	147					3																	33415410		2203	4300	6503	SO:0001819	synonymous_variant	25827	exon9			GTCCTGCTCAGTA	AF174589	CCDS2658.1, CCDS54560.1	3p22.3	2011-06-09			ENSG00000153558	ENSG00000153558		"F-boxes / Leucine-rich repeats"	13598	protein-coding gene	gene with protein product		605652				10508920, 10531035	Standard	NM_012157		Approved	FBL2, FBL3	uc003cfp.3	Q9UKC9	OTTHUMG00000130745	ENST00000484457.1:c.654C>T	chr3.hg19:g.33415410C>T		132.0	0.0	.		139.0	64.0	.	NM_012157		Silent	SNP	ENST00000484457.1	hg19	CCDS2658.1																																																																																			.	.	.	none		0.498	FBXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253245.2	NM_012157		T	33415410	C	T	33415410	2	4	189	1	0	0	0	0	0	0	0	1	5723	805	28	2		2	FBXL2	3	33415410	Silent	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	30334736	33415410	164607020	17	11120											
PARP14	54625	hgsc.bcm.edu	37	chr3	122437696	122437696	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagagaaaagaaaaaaacAgttgatgtcaaaattaatca	23	7	8	3	0	2	3	2	1	0	2	2	5	2	4	0	1	1	1	0	1	8	2	rs377210300		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr3:122437696A>G	ENST00000474629.2	+	14	4964	c.4698A>G	c.(4696-4698)acA>acG	p.T1566T	PARP14_ENST00000475640.1_3'UTR	NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1566	WWE. {ECO:0000255|PROSITE- ProRule:PRU00248}.				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)		AGAAAAAAACAGTTGATGTCA	0.373																																					p.T1566T		Atlas-SNP	.											.	PARP14	242	.	0			c.A4698G						PASS	.	A		0,3790		0,0,1895	88	87	87		4698	-5.7	0	3		87	1,8247		0,1,4123	no	coding-synonymous	PARP14	NM_017554.2		0,1,6018	GG,GA,AA		0.0121,0.0,0.0083		1566/1802	122437696	1,12037	1895	4124	6019	SO:0001819	synonymous_variant	54625	exon14			AAAAACAGTTGAT	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.4698A>G	chr3.hg19:g.122437696A>G		99.0	0.0	.		150.0	39.0	.	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Silent	SNP	ENST00000474629.2	hg19	CCDS46894.1																																																																																			.	.	.	weak		0.373	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		G	122437696	A	G	122437696	2	3	189	1	0	0	0	0	0	0	0	1	11465	175	7	3		3	PARP14	3	122437696	Silent	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	89022286	122437696	75584734	18	11121											
NDUFB5	4711	hgsc.bcm.edu	37	chr3	179322636	179322636	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agtttgttgcggcgggtttcGgttactgcggtggcagctct	3	14	16	8	4	1	0	0	0	1	0	2	0	1	0	0	5	4	6	0	5	1	4			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr3:179322636G>A	ENST00000259037.3	+	1	147	c.33G>A	c.(31-33)tcG>tcA	p.S11S	MRPL47_ENST00000259038.2_5'Flank|NDUFB5_ENST00000493866.1_Silent_p.S11S|MRPL47_ENST00000476781.1_5'Flank|MRPL47_ENST00000392659.2_5'Flank|NDUFB5_ENST00000472629.1_Silent_p.S11S	NM_002492.3	NP_002483.1	O43674	NDUB5_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5, 16kDa	11					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			endometrium(1)|lung(6)|skin(1)	8	all_cancers(143;9.62e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.18)			GGCGGGTTTCGGTTACTGCGG	0.617																																					p.S11S		Atlas-SNP	.											.	NDUFB5	22	.	0			c.G33A						PASS	.						36	36	36					3																	179322636		2203	4300	6503	SO:0001819	synonymous_variant	4711	exon1			GGTTTCGGTTACT	AF047181	CCDS3234.1, CCDS56297.1, CCDS75054.1	3q27.1	2011-07-04	2002-08-29		ENSG00000136521	ENSG00000136521		"Mitochondrial respiratory chain complex / Complex I"	7700	protein-coding gene	gene with protein product	"complex I SGDH subunit"	603841	"NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5 (16kD, SGDH)"			9425316	Standard	NM_002492		Approved	SGDH, CI-SGDH, MGC12314	uc003fkc.3	O43674	OTTHUMG00000157480	ENST00000259037.3:c.33G>A	chr3.hg19:g.179322636G>A		125.0	0.0	.		107.0	34.0	.	NM_002492	Q561V6	Silent	SNP	ENST00000259037.3	hg19	CCDS3234.1	.	.	.	.	.	.	.	.	.	.	G	15.68	2.903796	0.52333	.	.	ENSG00000136521	ENST00000482604	.	.	.	5.75	1.95	0.26073	.	.	.	.	.	T	0.56093	0.1962	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48340	-0.9044	5	0.40728	T	0.16	-3.1698	6.2744	0.20973	0.2212:0.1325:0.6463:0.0	.	.	.	.	Q	8	.	ENSP00000419099:R3Q	R	+	2	0	NDUFB5	180805330	0.998000	0.40836	0.993000	0.49108	0.016000	0.09150	0.145000	0.16157	0.148000	0.19059	-0.133000	0.14855	CGG	.	.	.	none		0.617	NDUFB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348937.2	NM_002492		A	179322636	G	A	179322636	2	1	189	1	0	0	0	0	0	0	0	1	10291	1103	39	1		1	NDUFB5	3	179322636	Silent	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	56884940	179322636	18699794	19	11122											
KLHL6	89857	hgsc.bcm.edu	37	chr3	183226047	183226047	+	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	gacccagctcatcacggtctCaaacacctgagcctcctcgg	9	7	8	17	2	3	1	3	1	1	0	6	2	4	1	4	2	3	1	4	2	1	0			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr3:183226047C>T	ENST00000341319.3	-	3	744	c.709G>A	c.(709-711)Gag>Aag	p.E237K		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	237	BACK.				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)			ATCACGGTCTCAAACACCTGa	0.547																																					p.E237K		Atlas-SNP	.											.	KLHL6	100	.	0			c.G709A						PASS	.						135	114	121					3																	183226047		2203	4300	6503	SO:0001583	missense	89857	exon3			CGGTCTCAAACAC	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.709G>A	chr3.hg19:g.183226047C>T	ENSP00000341342:p.Glu237Lys	199.0	0.0	.		277.0	69.0	.	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Missense_Mutation	SNP	ENST00000341319.3	hg19	CCDS3245.2	.	.	.	.	.	.	.	.	.	.	C	36	5.904004	0.97087	.	.	ENSG00000172578	ENST00000341319	T	0.69685	-0.42	5.87	5.87	0.94306	BTB/Kelch-associated (2);	0.043908	0.85682	D	0.000000	D	0.83083	0.5177	M	0.79343	2.45	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.82400	-0.0476	10	0.54805	T	0.06	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	237	Q8WZ60	KLHL6_HUMAN	K	237	ENSP00000341342:E237K	ENSP00000341342:E237K	E	-	1	0	KLHL6	184708741	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.445000	0.80570	2.941000	0.99782	0.655000	0.94253	GAG	.	.	.	none		0.547	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446		T	183226047	C	T	183226047	3	4	189	1	0	0	0	0	1	0	0	0	8400	835	29	2	1176	2	KLHL6	3	183226047	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	3903411	183226047	14796383	20	11123											
TMPRSS11F	389208	hgsc.bcm.edu	37	chr4	68930403	68930403	+	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	attaggttgaaactgctcacCatcatctacaatggatccaa	14	11	6	10	0	3	1	2	1	1	0	4	2	4	2	2	2	3	2	2	2	5	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr4:68930403C>A	ENST00000356291.2	-	8	1074	c.1015G>T	c.(1015-1017)Gga>Tga	p.G339*	RP11-35D5.1_ENST00000600441.1_RNA|UBA6-AS1_ENST00000500538.2_RNA|UBA6-AS1_ENST00000499180.2_RNA|UBA6-AS1_ENST00000511571.1_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	339	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						AACTGCTCACCATCATCTACA	0.363																																					p.G339X		Atlas-SNP	.											.	TMPRSS11F	79	.	0			c.G1015T						PASS	.						68	68	68					4																	68930403		2203	4300	6503	SO:0001630	splice_region_variant	389208	exon8			GCTCACCATCATC	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.1015+1G>T	chr4.hg19:g.68930403C>A		69.0	0.0	.		40.0	14.0	.	NM_207407	A8MXX2	Nonsense_Mutation	SNP	ENST00000356291.2	hg19	CCDS3520.1	.	.	.	.	.	.	.	.	.	.	C	37	6.372005	0.97515	.	.	ENSG00000198092	ENST00000356291	.	.	.	5.92	5.92	0.95590	.	0.000000	0.53938	D	0.000048	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8344	0.78787	0.0:1.0:0.0:0.0	.	.	.	.	X	339	.	.	G	-	1	0	TMPRSS11F	68612998	1.000000	0.71417	1.000000	0.80357	0.731000	0.41821	4.819000	0.62664	2.822000	0.97130	0.650000	0.86243	GGA	.	.	.	none		0.363	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407	Nonsense_Mutation	A	68930403	C	A	68930403	5	1	189	1	0	0	0	0	0	0	1	0	16255	608	21	4	313	4	TMPRSS11F	4	68930403	Splice_Site	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10		68930403	122223873	21	11124											
SLC12A7	10723	hgsc.bcm.edu	37	chr5	1093744	1093744	+	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	agcttgttgagcagcgaggaCaccatggggttactgtccat	9	10	13	9	1	0	1	0	1	0	0	1	3	1	2	2	3	4	4	2	3	1	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr5:1093744C>A	ENST00000264930.5	-	3	289	c.246G>T	c.(244-246)gtG>gtT	p.V82V		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	82					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)	GCAGCGAGGACACCATGGGGT	0.682																																					p.V82V		Atlas-SNP	.											.	SLC12A7	97	.	0			c.G246T						PASS	.						111	75	87					5																	1093744		2202	4299	6501	SO:0001819	synonymous_variant	10723	exon3			CGAGGACACCATG	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.246G>T	chr5.hg19:g.1093744C>A		235.0	0.0	.		163.0	47.0	.	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Silent	SNP	ENST00000264930.5	hg19	CCDS34129.1																																																																																			.	.	.	none		0.682	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598		A	1093744	C	A	1093744	2	1	189	1	0	0	0	0	0	0	0	1	14401	465	17	4		4	SLC12A7	5	1093744	Silent	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10		1093744	179821516	22	11125											
NSD1	64324	hgsc.bcm.edu	37	chr5	176562915	176562915	+	Missense_Mutation	SNP	T	T	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	acattacaatagaagagcaaTtaaactcaataaatttatct	20	12	3	6	0	2	2	1	0	1	2	2	2	2	2	0	0	3	1	0	0	11	6	rs374083142		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr5:176562915T>G	ENST00000439151.2	+	2	856	c.811T>G	c.(811-813)Tta>Gta	p.L271V	NSD1_ENST00000354179.4_Intron|NSD1_ENST00000347982.4_Intron|NSD1_ENST00000361032.4_Missense_Mutation_p.L271V|NSD1_ENST00000511258.1_Intron	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	271					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)		AGAAGAGCAATTAAACTCAAT	0.383			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.L271V		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.T811G						PASS	.						66	67	67					5																	176562915		2203	4300	6503	SO:0001583	missense	64324	exon2	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	GAGCAATTAAACT	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.811T>G	chr5.hg19:g.176562915T>G	ENSP00000395929:p.Leu271Val	105.0	0.0	.		91.0	31.0	.	NM_022455	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	hg19	CCDS4412.1	.	.	.	.	.	.	.	.	.	.	T	12.12	1.841288	0.32513	.	.	ENSG00000165671	ENST00000439151;ENST00000361032	D;D	0.94576	-3.23;-3.46	5.19	5.19	0.71726	.	0.186195	0.26485	N	0.024119	D	0.88633	0.6489	N	0.14661	0.345	0.80722	D	1	B;B;B	0.30634	0.288;0.19;0.137	B;B;B	0.30572	0.117;0.055;0.051	D	0.88112	0.2826	10	0.72032	D	0.01	.	12.6728	0.56876	0.0:0.0:0.0:1.0	.	271;271;271	Q96L73-3;Q96L73;Q6PJ64	.;NSD1_HUMAN;.	V	271	ENSP00000395929:L271V;ENSP00000354310:L271V	ENSP00000354310:L271V	L	+	1	2	NSD1	176495521	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.025000	0.57225	2.189000	0.69895	0.533000	0.62120	TTA	.	.	.	alt		0.383	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		G	176562915	T	G	176562915	3	3	189	1	0	0	0	0	1	0	0	0	10676	1490	52	5	813	5	NSD1	5	176562915	Missense_Mutation	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10	175469171	176562915	4352345	23	11126											
MRPS10	55173	hgsc.bcm.edu	37	chr6	42176601	42176601	+	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	aaattcaagctatacctttgTtacttccatggcaacccctt	11	14	4	12	0	1	0	1	0	0	0	2	0	2	0	4	1	4	3	4	1	6	7			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr6:42176601T>A	ENST00000053468.3	-	6	532	c.517A>T	c.(517-519)Aca>Tca	p.T173S		NM_018141.3	NP_060611.2	P82664	RT10_HUMAN	mitochondrial ribosomal protein S10	173						mitochondrion (GO:0005739)|ribosome (GO:0005840)				endometrium(1)|lung(1)	2	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00528)			TATACCTTTGTTACTTCCATG	0.443																																					p.T173S		Atlas-SNP	.											.	MRPS10	9	.	0			c.A517T						PASS	.						103	98	100					6																	42176601		2203	4300	6503	SO:0001583	missense	55173	exon6			CCTTTGTTACTTC		CCDS4866.1	6p21.1	2012-09-13			ENSG00000048544	ENSG00000048544		"Mitochondrial ribosomal proteins / small subunits"	14502	protein-coding gene	gene with protein product		611976				11279123	Standard	NM_018141		Approved	FLJ10567	uc003osa.4	P82664	OTTHUMG00000014694	ENST00000053468.3:c.517A>T	chr6.hg19:g.42176601T>A	ENSP00000053468:p.Thr173Ser	178.0	0.0	.		152.0	45.0	.	NM_018141	B2RE89|Q9H3E5|Q9NVR3	Missense_Mutation	SNP	ENST00000053468.3	hg19	CCDS4866.1	.	.	.	.	.	.	.	.	.	.	T	19.87	3.906883	0.72868	.	.	ENSG00000048544	ENST00000053468	.	.	.	5.78	5.78	0.91487	.	0.094475	0.64402	D	0.000001	T	0.49047	0.1534	L	0.41415	1.275	0.46901	D	0.999243	D	0.53462	0.96	P	0.52454	0.699	T	0.46456	-0.9190	9	0.32370	T	0.25	-7.8115	15.0972	0.72244	0.0:0.0:0.0:1.0	.	173	P82664	RT10_HUMAN	S	173	.	ENSP00000053468:T173S	T	-	1	0	MRPS10	42284579	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	7.043000	0.76572	2.200000	0.70718	0.460000	0.39030	ACA	.	.	.	none		0.443	MRPS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040547.1			A	42176601	T	A	42176601	3	1	189	1	0	0	0	0	1	0	0	0	9828	1725	60	5	96	5	MRPS10	6	42176601	Missense_Mutation	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10		42176601	128938466	24	11127											
EEF1A1	1915	hgsc.bcm.edu	37	chr6	74227601	74227601	+	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	tccagcagccttcttgtccaCtgctttgatgacacccaccg	7	11	7	16	1	1	2	0	2	1	0	3	2	3	2	5	0	3	2	5	0	0	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr6:74227601C>T	ENST00000316292.9	-	7	2312	c.1321G>A	c.(1321-1323)Gtg>Atg	p.V441M	EEF1A1_ENST00000491404.1_Intron|EEF1A1_ENST00000331523.2_Missense_Mutation_p.V441M|EEF1A1_ENST00000309268.6_Missense_Mutation_p.V441M	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1	441					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation elongation factor activity (GO:0003746)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						TTCTTGTCCACTGCTTTGATG	0.443											OREG0003893	type=REGULATORY REGION|Gene=BC038897|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.V441M		Atlas-SNP	.											.	EEF1A1	56	.	0			c.G1321A						PASS	.						29	30	30					6																	74227601		2203	4296	6499	SO:0001583	missense	1915	exon8			TGTCCACTGCTTT	BC019669	CCDS4980.1	6q14.1	2010-06-30	2004-11-19		ENSG00000156508	ENSG00000156508			3189	protein-coding gene	gene with protein product		130590	"leukocyte receptor cluster (LRC) member 7"	EF1A, EEF1A, LENG7		8812466, 10941842	Standard	NM_001402		Approved	EE1A1	uc003phj.3	P68104	OTTHUMG00000015031	ENST00000316292.9:c.1321G>A	chr6.hg19:g.74227601C>T	ENSP00000339063:p.Val441Met	172.0	0.0	.	1151	101.0	25.0	.	NM_001402	P04719|P04720|Q6IQ15	Missense_Mutation	SNP	ENST00000316292.9	hg19	CCDS4980.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.352587	0.82132	.	.	ENSG00000156508	ENST00000316292;ENST00000309268;ENST00000331523;ENST00000391977	T;T;T	0.52526	0.66;0.66;0.66	4.81	4.81	0.61882	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal (2);Translation elongation factor EFTu/EF1A, C-terminal (2);	0.072938	0.53938	U	0.000048	T	0.68229	0.2978	H	0.94462	3.54	0.80722	D	1	D;D;D	0.55172	0.97;0.97;0.97	P;P;P	0.54590	0.756;0.756;0.756	T	0.79850	-0.1629	10	0.87932	D	0	.	18.3119	0.90203	0.0:1.0:0.0:0.0	.	441;441;441	P68104;Q6IPS9;Q5VTE0	EF1A1_HUMAN;.;EF1A3_HUMAN	M	441;441;441;420	ENSP00000339063:V441M;ENSP00000339053:V441M;ENSP00000330054:V441M	ENSP00000339053:V441M	V	-	1	0	EEF1A1	74284322	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.405000	0.80007	2.381000	0.81170	0.556000	0.70494	GTG	.	.	.	none		0.443	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041210.2	NM_001402		T	74227601	C	T	74227601	3	4	189	1	0	0	0	0	1	0	0	0	4925	565	20	2	71	2	EEF1A1	6	74227601	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	32051000	74227601	96887466	25	11128											
RIPPLY2	134701	hgsc.bcm.edu	37	chr6	84563845	84563845	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccctggaatgaccgcagcCtcaggaaagctttaccaatt	11	8	10	12	1	1	1	1	1	0	0	1	3	1	3	4	3	3	2	4	3	4	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr6:84563845C>T	ENST00000369689.1	+	3	355	c.204C>T	c.(202-204)gcC>gcT	p.A68A	RIPPLY2_ENST00000369687.1_Silent_p.A10A	NM_001009994.1	NP_001009994.1	Q5TAB7	RIPP2_HUMAN	ripply transcriptional repressor 2	68					bone morphogenesis (GO:0060349)|determination of left/right symmetry (GO:0007368)|Notch signaling pathway (GO:0007219)|ossification (GO:0001503)|post-anal tail morphogenesis (GO:0036342)|regulation of gene expression (GO:0010468)|somite rostral/caudal axis specification (GO:0032525)|somitogenesis (GO:0001756)	nucleus (GO:0005634)				large_intestine(2)|lung(4)|urinary_tract(1)	7						TGACCGCAGCCTCAGGAAAGC	0.592																																					p.A68A		Atlas-SNP	.											.	RIPPLY2	17	.	0			c.C204T						PASS	.						102	96	98					6																	84563845		2203	4300	6503	SO:0001819	synonymous_variant	134701	exon3			CGCAGCCTCAGGA	BC130460	CCDS34493.1	6q14.2	2013-07-23	2013-07-23	2008-05-07	ENSG00000203877	ENSG00000203877			21390	protein-coding gene	gene with protein product		609891	"chromosome 6 open reading frame 159", "ripply2 homolog (zebrafish)"	C6orf159			Standard	NM_001009994		Approved	dJ237I15.1	uc003pke.3	Q5TAB7	OTTHUMG00000015117	ENST00000369689.1:c.204C>T	chr6.hg19:g.84563845C>T		163.0	0.0	.		132.0	13.0	.	NM_001009994	Q5TAB6	Silent	SNP	ENST00000369689.1	hg19	CCDS34493.1																																																																																			.	.	.	none		0.592	RIPPLY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041360.1	NM_001009994		T	84563845	C	T	84563845	2	4	189	1	0	0	0	0	0	0	0	1	13398	668	24	2		2	RIPPLY2	6	84563845	Silent	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	10336244	84563845	86551222	26	11129											
IGF2R	3482	hgsc.bcm.edu	37	chr6	160494272	160494272	+	Frame_Shift_Del	DEL	G	G	-																															ctttggacagaccaggattaGcgtgggcaaggccaacaaga																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr6:160494272delG	ENST00000356956.1	+	34	4866	c.4718delG	c.(4717-4719)agcfs	p.S1573fs		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	1573					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)	ACCAGGATTAGCGTGGGCAAG	0.547																																					p.S1573fs		Pindel	.											.	IGF2R	251	.	0			c.4717delA						PASS	.						146	128	134					6																	160494272		2203	4300	6503	SO:0001589	frameshift_variant	3482	exon34			.	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.4718delG	chr6.hg19:g.160494272delG	ENSP00000349437:p.Ser1573fs	248.0	0.0	.		226.0	54.0	0.239	NM_000876	Q7Z7G9|Q96PT5	Frame_Shift_Del	DEL	ENST00000356956.1	hg19	CCDS5273.1																																																																																			.	.	.	none		0.547	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		-	160494272	G	-	160494272	7	5	189	1	0	1	0	1	0	0	0	0	7583	971	34	0	4852	0	IGF2R	6	160494272	Frame_Shift_Del	DEL	G	TCGA-GL-A59T-01A-21D-A28G-10	75930427	160494272	10620795	27	11130											
GATAD1	57798	hgsc.bcm.edu	37	chr7	92083893	92083893	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctactatgctcaaatcagAggttttatccaggaccagta	12	11	7	11	0	2	1	2	0	0	1	3	2	3	2	3	2	2	3	3	2	5	5			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr7:92083893A>G	ENST00000287957.3	+	4	790	c.513A>G	c.(511-513)agA>agG	p.R171R	AC007566.10_ENST00000427458.1_RNA	NM_021167.4	NP_066990.3	Q8WUU5	GATD1_HUMAN	GATA zinc finger domain containing 1	171						nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|lung(3)	6	all_cancers(62;1.63e-10)|all_epithelial(64;8.33e-10)|Breast(17;0.00311)|all_lung(186;0.0498)|Lung NSC(181;0.0676)		STAD - Stomach adenocarcinoma(171;4.51e-05)|GBM - Glioblastoma multiforme(5;8.83e-05)|all cancers(6;0.000136)|Lung(22;0.123)|Epithelial(20;0.179)|LUSC - Lung squamous cell carcinoma(200;0.225)			CTCAAATCAGAGGTTTTATCC	0.458																																					p.R171R		Atlas-SNP	.											.	GATAD1	10	.	0			c.A513G						PASS	.						193	183	186					7																	92083893		2203	4300	6503	SO:0001819	synonymous_variant	57798	exon4			AATCAGAGGTTTT		CCDS5625.1	7q21-q22	2014-09-17			ENSG00000157259	ENSG00000157259		"GATA zinc finger domain containing"	29941	protein-coding gene	gene with protein product	"ocular development associated gene"	614518				12062807	Standard	NM_021167		Approved	ODAG, RG083M05.2, FLJ22489	uc003ulx.2	Q8WUU5	OTTHUMG00000131201	ENST00000287957.3:c.513A>G	chr7.hg19:g.92083893A>G		148.0	0.0	.		136.0	63.0	.	NM_021167	B2RE37|D6W5Q5|Q8N5Y5|Q99995|Q9H689	Silent	SNP	ENST00000287957.3	hg19	CCDS5625.1																																																																																			.	.	.	none		0.458	GATAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253929.2	NM_021167		G	92083893	A	G	92083893	2	3	189	1	0	0	0	0	0	0	0	1	6266	301	11	3		3	GATAD1	7	92083893	Silent	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10		92083893	67054770	28	11131											
PDK4	5166	hgsc.bcm.edu	37	chr7	95217131	95217131	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgttcaactgttgcccgcaTtgcattctaaaacaaagcaa	13	11	7	10	1	2	0	1	0	1	0	2	0	2	0	1	0	5	5	1	0	5	5			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr7:95217131T>C	ENST00000005178.5	-	8	975	c.778A>G	c.(778-780)Atg>Gtg	p.M260V		NM_002612.3	NP_002603.1	Q16654	PDK4_HUMAN	pyruvate dehydrogenase kinase, isozyme 4	260	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.				cellular metabolic process (GO:0044237)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|negative regulation of anoikis (GO:2000811)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|reactive oxygen species metabolic process (GO:0072593)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of bone resorption (GO:0045124)|regulation of cellular ketone metabolic process (GO:0010565)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose metabolic process (GO:0010906)|regulation of pH (GO:0006885)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	15	all_cancers(62;1.06e-10)|all_epithelial(64;1.04e-09)|Lung NSC(181;0.128)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0151)			GTTGCCCGCATTGCATTCTAA	0.363																																					p.M260V		Atlas-SNP	.											.	PDK4	42	.	0			c.A778G						PASS	.						74	74	74					7																	95217131		2203	4300	6503	SO:0001583	missense	5166	exon8			CCCGCATTGCATT	U54617	CCDS5643.1	7q21.3-q22.1	2008-07-18	2005-11-16		ENSG00000004799	ENSG00000004799			8812	protein-coding gene	gene with protein product		602527	"pyruvate dehydrogenase kinase, isoenzyme 4"			7499431	Standard	NM_002612		Approved		uc003uoa.3	Q16654	OTTHUMG00000153977	ENST00000005178.5:c.778A>G	chr7.hg19:g.95217131T>C	ENSP00000005178:p.Met260Val	86.0	0.0	.		99.0	4.0	.	NM_002612		Missense_Mutation	SNP	ENST00000005178.5	hg19	CCDS5643.1	.	.	.	.	.	.	.	.	.	.	T	16.21	3.058332	0.55325	.	.	ENSG00000004799	ENST00000005178;ENST00000542888	T	0.46451	0.87	5.34	5.34	0.76211	Signal transduction histidine kinase, core (1);ATPase-like, ATP-binding domain (4);	0.000000	0.85682	D	0.000000	T	0.54431	0.1858	L	0.41027	1.25	0.80722	D	1	D	0.56968	0.978	D	0.64237	0.923	T	0.57705	-0.7765	10	0.87932	D	0	.	15.6388	0.76977	0.0:0.0:0.0:1.0	.	260	Q16654	PDK4_HUMAN	V	260;224	ENSP00000005178:M260V	ENSP00000005178:M260V	M	-	1	0	PDK4	95055067	1.000000	0.71417	1.000000	0.80357	0.357000	0.29423	4.977000	0.63792	2.154000	0.67381	0.482000	0.46254	ATG	.	.	.	none		0.363	PDK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333298.1	NM_002612		C	95217131	T	C	95217131	3	2	189	1	0	0	0	0	1	0	0	0	11685	1493	52	3	473	3	PDK4	7	95217131	Missense_Mutation	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10	3133238	95217131	63921532	29	11132											
KIF13B	23303	hgsc.bcm.edu	37	chr8	28984648	28984650	+	In_Frame_Del	DEL	CTC	CTC	-																															tagaaacttacatggaaggtCtcatgtgttctgggggctct																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr8:28984648_28984650delCTC	ENST00000524189.1	-	25	3249_3251	c.3211_3213delGAG	c.(3211-3213)gagdel	p.E1071del	CTD-2647L4.1_ENST00000523661.1_RNA	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	1071					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)		CATGGAAGGTCTCATGTGTTCTG	0.424																																					p.1071_1072del		Atlas-INDEL	.											.	KIF13B	192	.	0			c.3212_3214del						PASS	.																																			SO:0001651	inframe_deletion	23303	exon25			.	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.3211_3213delGAG	chr8.hg19:g.28984648_28984650delCTC	ENSP00000427900:p.Glu1071del	128.0	0.0	0		97.0	10.0	0.103093	NM_015254	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	In_Frame_Del	DEL	ENST00000524189.1	hg19	CCDS55217.1																																																																																			.	.	.	none		0.424	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1			-	28984650	CTC	-	28984648	7	5	189	1	0	1	0	1	0	0	0	0	8282	912	32	0	2331	0	KIF13B	8	28984648	In_Frame_Del	DEL	CTC	TCGA-GL-A59T-01A-21D-A28G-10		28984648	117379374	30	11133	104	2									
KIF13B	23303	hgsc.bcm.edu	37	chr8	28984652	28984654	+	In_Frame_Del	DEL	TGT	TGT	-																															aacttacatggaaggtctcaTgtgttctgggggctctgagc																								rs536929811		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr8:28984652_28984654delTGT	ENST00000524189.1	-	25	3245_3247	c.3207_3209delACA	c.(3205-3210)acacat>act	p.H1070del	CTD-2647L4.1_ENST00000523661.1_RNA	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	1070					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)		GAAGGTCTCATGTGTTCTGGGGG	0.429																																					p.1070_1070del		Atlas-INDEL	.											.	KIF13B	192	.	0			c.3208_3210del						PASS	.																																			SO:0001651	inframe_deletion	23303	exon25			.	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.3207_3209delACA	chr8.hg19:g.28984652_28984654delTGT	ENSP00000427900:p.His1070del	126.0	0.0	0		99.0	10.0	0.10101	NM_015254	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	In_Frame_Del	DEL	ENST00000524189.1	hg19	CCDS55217.1																																																																																			.	.	.	none		0.429	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1			-	28984654	TGT	-	28984652	7	5	189	1	0	1	0	1	0	0	0	0	8282	1464	51	0	2335	0	KIF13B	8	28984652	In_Frame_Del	DEL	TGT	TCGA-GL-A59T-01A-21D-A28G-10	4	28984652	117379370	31	11134	104	2									
WHSC1L1	54904	hgsc.bcm.edu	37	chr8	38175506	38175506	+	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	ttcctcaatcgctgcggagaCggagctgtcactgaatctga	9	10	11	11	3	3	3	2	2	1	1	5	5	4	4	1	2	2	2	1	2	2	1			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr8:38175506C>T	ENST00000317025.8	-	9	2373				WHSC1L1_ENST00000525081.1_5'UTR|WHSC1L1_ENST00000316985.3_Missense_Mutation_p.V636I|WHSC1L1_ENST00000527502.1_Intron|WHSC1L1_ENST00000433384.2_Intron	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1						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)			GCTGCGGAGACGGAGCTGTCA	0.537			T	NUP98	AML																																p.V636I		Atlas-SNP	.		Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	.	WHSC1L1	137	.	0			c.G1906A						PASS	.						90	82	85					8																	38175506		2203	4300	6503	SO:0001627	intron_variant	54904	exon10			CGGAGACGGAGCT	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.1855+906G>A	chr8.hg19:g.38175506C>T		72.0	0.0	.		79.0	28.0	.	NM_017778	B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	Missense_Mutation	SNP	ENST00000317025.8	hg19	CCDS43729.1	.	.	.	.	.	.	.	.	.	.	C	15.44	2.835251	0.50951	.	.	ENSG00000147548	ENST00000316985	T	0.64438	-0.1	6.17	5.29	0.74685	.	.	.	.	.	T	0.50752	0.1634	.	.	.	0.21499	N	0.999666	B	0.14805	0.011	B	0.10450	0.005	T	0.33033	-0.9884	8	0.40728	T	0.16	.	11.9912	0.53176	0.0:0.9189:0.0:0.0811	.	636	Q9BZ95-3	.	I	636	ENSP00000313410:V636I	ENSP00000313410:V636I	V	-	1	0	WHSC1L1	38294663	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.355000	0.44107	2.941000	0.99782	0.655000	0.94253	GTC	.	.	.	none		0.537	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	NM_023034		T	38175506	C	T	38175506	1	4	189	0	1	0	0	0	0	0	0	0	17375	536	19	1		1	WHSC1L1	8	38175506	Intron	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	9190854	38175506	108188516	32	11135											
JAK2	3717	hgsc.bcm.edu	37	chr9	5126752	5126752	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctcctttagggatctagcTcttcgagtggatcaaataag	10	12	9	10	1	3	0	1	0	2	0	5	3	4	2	2	2	1	1	2	2	4	5			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr9:5126752T>C	ENST00000381652.3	+	25	3854	c.3360T>C	c.(3358-3360)gcT>gcC	p.A1120A	JAK2_ENST00000544510.1_Silent_p.A971A|JAK2_ENST00000487310.1_3'UTR|JAK2_ENST00000539801.1_Silent_p.A1120A	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	1120	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	GGGATCTAGCTCTTCGAGTGG	0.348		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial																												p.A1120A		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.T3360C						PASS	.						79	74	76					9																	5126752		2203	4299	6502	SO:0001819	synonymous_variant	3717	exon25	Familial Cancer Database		TCTAGCTCTTCGA		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.3360T>C	chr9.hg19:g.5126752T>C		76.0	0.0	.		58.0	45.0	.	NM_004972	O14636|O75297	Silent	SNP	ENST00000381652.3	hg19	CCDS6457.1																																																																																			.	.	.	none		0.348	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			C	5126752	T	C	5126752	2	2	189	1	0	0	0	0	0	0	0	1	7945	1538	54	3		3	JAK2	9	5126752	Silent	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10		5126752	136086679	33	11136											
DAPK1	1612	hgsc.bcm.edu	37	chr9	90321821	90321821	+	Missense_Mutation	SNP	T	T	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	tgggggggtacaaggaaagcTtcagcagcatcatgtgcttc	10	9	14	8	0	2	0	2	0	0	0	3	1	2	1	0	4	5	5	0	4	3	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr9:90321821T>G	ENST00000408954.3	+	26	4170	c.3835T>G	c.(3835-3837)Ttc>Gtc	p.F1279V	DAPK1_ENST00000491893.1_Missense_Mutation_p.F1213V|DAPK1_ENST00000358077.5_Missense_Mutation_p.F1279V|DAPK1_ENST00000469640.2_Missense_Mutation_p.F1304V|DAPK1_ENST00000472284.1_Missense_Mutation_p.F1279V	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	1279					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						CAAGGAAAGCTTCAGCAGCAT	0.567									Chronic Lymphocytic Leukemia, Familial Clustering of																												p.F1279V		Atlas-SNP	.											.	DAPK1	329	.	0			c.T3835G						PASS	.						54	62	60					9																	90321821		2131	4237	6368	SO:0001583	missense	1612	exon26	Familial Cancer Database	Familial CLL	GAAAGCTTCAGCA	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.3835T>G	chr9.hg19:g.90321821T>G	ENSP00000386135:p.Phe1279Val	132.0	0.0	.		108.0	79.0	.	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	hg19	CCDS43842.1	.	.	.	.	.	.	.	.	.	.	T	18.91	3.723375	0.68959	.	.	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	T;T;T;T;T	0.63255	0.05;0.05;0.03;0.05;-0.03	5.66	5.66	0.87406	.	0.000000	0.56097	D	0.000040	T	0.77552	0.4147	M	0.66939	2.045	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.998	D;D;D	0.83275	0.987;0.996;0.987	T	0.77534	-0.2552	10	0.45353	T	0.12	.	16.2026	0.82095	0.0:0.0:0.0:1.0	.	1213;1279;1279	B7ZLE7;P53355-3;P53355	.;.;DAPK1_HUMAN	V	1279;1279;1304;1279;1213	ENSP00000350785:F1279V;ENSP00000417076:F1279V;ENSP00000418885:F1304V;ENSP00000386135:F1279V;ENSP00000419026:F1213V	ENSP00000350785:F1279V	F	+	1	0	DAPK1	89511641	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.997000	0.88414	2.285000	0.76669	0.533000	0.62120	TTC	.	.	.	none		0.567	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938		G	90321821	T	G	90321821	3	3	189	1	0	0	0	0	1	0	0	0	4237	1609	56	5	3933	5	DAPK1	9	90321821	Missense_Mutation	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10	85195069	90321821	50891610	34	11137											
RAPGEF1	2889	hgsc.bcm.edu	37	chr9	134505712	134505712	+	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	atggtgagcctgaccagctcCtacccccacaagaaaaaggc	13	5	9	14	0	0	3	0	2	0	1	1	3	1	3	5	2	3	1	5	2	4	1			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr9:134505712C>T	ENST00000372189.3	-	6	724		c.e6-1		RAPGEF1_ENST00000372190.3_Splice_Site|RAPGEF1_ENST00000481260.1_Intron|RAPGEF1_ENST00000372195.1_Splice_Site	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1						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)		TGACCAGCTCCTACCCCCACA	0.592																																					.		Atlas-SNP	.											.	RAPGEF1	126	.	0			c.601-1G>A						PASS	.						57	65	62					9																	134505712		2074	4208	6282	SO:0001630	splice_region_variant	2889	exon7			CAGCTCCTACCCC	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.601-1G>A	chr9.hg19:g.134505712C>T		87.0	0.0	.		97.0	9.0	.	NM_005312	Q5JUE4|Q8IV73	Splice_Site	SNP	ENST00000372189.3	hg19	CCDS48047.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.006457	0.74932	.	.	ENSG00000107263	ENST00000266110;ENST00000372195;ENST00000429421;ENST00000372189;ENST00000372190;ENST00000411834;ENST00000337036;ENST00000357686	.	.	.	5.45	5.45	0.79879	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0057	0.80362	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RAPGEF1	133495533	1.000000	0.71417	0.996000	0.52242	0.758000	0.43043	6.814000	0.75236	2.549000	0.85964	0.655000	0.94253	.	.	.	.	none		0.592	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312	Intron	T	134505712	C	T	134505712	5	4	189	1	0	0	0	0	0	0	1	0	13056	695	24	2	2709	2	RAPGEF1	9	134505712	Splice_Site	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	44183891	134505712	6707719	35	11138											
KIN	22944	hgsc.bcm.edu	37	chr10	7811178	7811178	+	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	cacgcaatccataaactgtaCctccatgatttcatccagtg	12	11	5	13	1	1	1	1	1	0	0	4	1	4	1	4	0	2	2	4	0	4	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr10:7811178C>T	ENST00000379562.4	-	8	846		c.e8+1		KIN_ENST00000535925.1_Splice_Site|KIN_ENST00000543003.1_Splice_Site|KIN_ENST00000463666.1_5'Flank	NM_012311.3	NP_036443.1			Kin17 DNA and RNA binding protein											endometrium(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|skin(2)	19						ATAAACTGTACCTCCATGATT	0.343																																					.		Atlas-SNP	.											.	KIN	39	.	0			c.798+1G>A						PASS	.						99	99	99					10																	7811178		2203	4300	6503	SO:0001630	splice_region_variant	22944	exon9			ACTGTACCTCCAT	AJ005273	CCDS7080.1	10p15-p14	2014-07-15	2014-07-15		ENSG00000151657	ENSG00000151657			6327	protein-coding gene	gene with protein product		601720	"antigenic determinant of recA protein (mouse) homolog", "KIN, antigenic determinant of recA protein homolog (mouse)"			1923796, 24140279	Standard	NM_012311		Approved	KIN17, Rts2	uc001ijt.3	O60870	OTTHUMG00000017634	ENST00000379562.4:c.798+1G>A	chr10.hg19:g.7811178C>T		21.0	0.0	.		23.0	8.0	.	NM_012311		Splice_Site	SNP	ENST00000379562.4	hg19	CCDS7080.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.955761	0.73902	.	.	ENSG00000151657	ENST00000535925;ENST00000379562;ENST00000543003	.	.	.	5.12	5.12	0.69794	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.75	0.85483	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KIN	7851184	1.000000	0.71417	0.995000	0.50966	0.891000	0.51852	5.846000	0.69444	2.363000	0.80096	0.650000	0.86243	.	.	.	.	none		0.343	KIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046683.2	NM_012311	Intron	T	7811178	C	T	7811178	5	4	189	1	0	0	0	0	0	0	1	0	8322	521	18	2	406	2	KIN	10	7811178	Splice_Site	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10		7811178	127723569	36	11139											
OAT	4942	hgsc.bcm.edu	37	chr10	126100644	126100644	+	Frame_Shift_Del	DEL	T	T	-																															ggttggagggccttggactgTttttttagttgcaacagatg																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr10:126100644delT	ENST00000368845.5	-	2	189	c.97delA	c.(97-99)acafs	p.T33fs	OAT_ENST00000539214.1_Intron	NM_000274.3	NP_000265.1	P04181	OAT_HUMAN	ornithine aminotransferase	33					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-proline biosynthetic process (GO:0055129)|protein hexamerization (GO:0034214)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ornithine-oxo-acid transaminase activity (GO:0004587)|pyridoxal phosphate binding (GO:0030170)			endometrium(2)|large_intestine(1)|lung(2)	5		all_lung(145;0.0271)|Lung NSC(174;0.0436)|Colorectal(57;0.102)|all_neural(114;0.116)			L-Ornithine(DB00129)	CCTTGGACTGTTTTTTTAGTT	0.433																																					p.T33fs		Atlas-Indel,Pindel	.											.	OAT	25	.	0			c.98delC						PASS	.						88	81	83					10																	126100644		2203	4300	6503	SO:0001589	frameshift_variant	4942	exon2			.	BC016928	CCDS7639.1, CCDS53586.1	10q26	2014-09-17	2010-01-20		ENSG00000065154	ENSG00000065154	2.6.1.13		8091	protein-coding gene	gene with protein product	"Ornithine aminotransferase", "ornithine aminotransferase precursor", "gyrate atrophy"	613349				1682785	Standard	NM_000274		Approved	HOGA	uc001lhp.3	P04181	OTTHUMG00000019213	ENST00000368845.5:c.97delA	chr10.hg19:g.126100644delT	ENSP00000357838:p.Thr33fs	99.0	0.0	0		96.0	27.0	0.28125	NM_000274	D3DRF0|Q16068|Q16069|Q68CS0|Q6IAV9|Q9UD03	Frame_Shift_Del	DEL	ENST00000368845.5	hg19	CCDS7639.1																																																																																			.	.	.	none		0.433	OAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050863.1	NM_000274		-	126100644	T	-	126100644	7	5	189	1	0	1	0	1	0	0	0	0	10810	1725	60	0	1258	0	OAT	10	126100644	Frame_Shift_Del	DEL	T	TCGA-GL-A59T-01A-21D-A28G-10	118289466	126100644	9434103	37	11140											
MUC2	4583	hgsc.bcm.edu	37	chr11	1093292	1093292	+	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	atcgacacccatcaccaccaCcactacggtgaccccaaccc	12	4	4	21	2	1	1	1	1	0	0	2	2	1	1	7	1	2	0	7	1	2	1			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:1093292C>T	ENST00000441003.2	+	30	5138	c.5111C>T	c.(5110-5112)aCc>aTc	p.T1704I	MUC2_ENST00000359061.5_Missense_Mutation_p.T1671I|MUC2_ENST00000333592.6_5'Flank|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)	atcaccaccaccactacggtg	0.637																																					p.T1704I		Atlas-SNP	.											.	MUC2	614	.	0			c.C5111T						PASS	.						107	156	138					11																	1093292		1878	3453	5331	SO:0001583	missense	4583	exon30			CCACCACCACTAC	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.5111C>T	chr11.hg19:g.1093292C>T	ENSP00000415183:p.Thr1704Ile	97.0	0.0	.		107.0	7.0	.	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	C	2.150	-0.394632	0.04899	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.11063	2.81;2.84	1.6	-2.66	0.06077	.	2.760050	0.04005	U	0.297091	T	0.06416	0.0165	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.36286	-0.9754	9	0.36615	T	0.2	.	2.477	0.04578	0.4942:0.3128:0.0:0.1931	.	1704	E7EUV1	.	I	1704;1671	ENSP00000415183:T1704I;ENSP00000351956:T1671I	ENSP00000351956:T1671I	T	+	2	0	MUC2	1083292	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.330000	0.19715	-0.514000	0.06488	0.184000	0.17185	ACC	.	.	.	none		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1093292	C	T	1093292	3	4	189	1	0	0	0	0	1	0	0	0	9982	507	18	2	5229	2	MUC2	11	1093292	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10		1093292	133913224	38	11141											
MPEG1	219972	hgsc.bcm.edu	37	chr11	58978564	58978564	+	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	gccgggtgaaaggtgggagcCtggcagggggcagggaccct	7	4	21	9	1	0	1	0	1	0	0	0	3	0	3	3	7	1	2	3	7	1	0			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:58978564C>T	ENST00000361050.3	-	1	1860	c.1775G>A	c.(1774-1776)aGg>aAg	p.R592K		NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	592						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)				AGGTGGGAGCCTGGCAGGGGG	0.582																																					p.R592K		Atlas-SNP	.											.	MPEG1	72	.	0			c.G1775A						PASS	.						87	97	93					11																	58978564		1945	4123	6068	SO:0001583	missense	219972	exon1			GGGAGCCTGGCAG	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.1775G>A	chr11.hg19:g.58978564C>T	ENSP00000354335:p.Arg592Lys	96.0	0.0	.		104.0	39.0	.	NM_001039396	Q2M1T6|Q8TEF8	Missense_Mutation	SNP	ENST00000361050.3	hg19	CCDS41650.1	.	.	.	.	.	.	.	.	.	.	C	14.82	2.648686	0.47258	.	.	ENSG00000197629	ENST00000361050	T	0.23147	1.92	5.69	5.69	0.88448	.	0.109255	0.64402	D	0.000015	T	0.42154	0.1190	L	0.61387	1.9	0.34323	D	0.686779	D	0.60575	0.988	P	0.54759	0.76	T	0.52601	-0.8554	10	0.44086	T	0.13	-27.9243	16.7224	0.85413	0.0:1.0:0.0:0.0	.	592	Q2M385	MPEG1_HUMAN	K	592	ENSP00000354335:R592K	ENSP00000354335:R592K	R	-	2	0	MPEG1	58735140	0.678000	0.27586	1.000000	0.80357	0.942000	0.58702	0.292000	0.19011	2.682000	0.91365	0.655000	0.94253	AGG	.	.	.	none		0.582	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396		T	58978564	C	T	58978564	3	4	189	1	0	0	0	0	1	0	0	0	9730	681	24	2	379	2	MPEG1	11	58978564	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	57885272	58978564	76027952	39	11142											
PYGM	5837	hgsc.bcm.edu	37	chr11	64517951	64517951	+	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	cacattggccccgtccatggTgccaatggtcagagccccgt	7	8	11	15	2	1	1	1	0	0	1	2	1	2	1	6	3	2	0	6	3	1	1			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:64517951T>A	ENST00000164139.3	-	17	2472	c.2074A>T	c.(2074-2076)Acc>Tcc	p.T692S	PYGM_ENST00000462303.1_5'Flank|PYGM_ENST00000377432.3_Missense_Mutation_p.T604S	NM_005609.2	NP_005600.1	P11217	PYGM_HUMAN	phosphorylase, glycogen, muscle	692					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						CCGTCCATGGTGCCAATGGTC	0.567																																					p.T692S		Atlas-SNP	.											.	PYGM	77	.	0			c.A2074T						PASS	.						167	151	157					11																	64517951		2201	4297	6498	SO:0001583	missense	5837	exon17			CCATGGTGCCAAT		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.2074A>T	chr11.hg19:g.64517951T>A	ENSP00000164139:p.Thr692Ser	156.0	0.0	.		114.0	38.0	.	NM_005609	A0AVK1|A6NDY6	Missense_Mutation	SNP	ENST00000164139.3	hg19	CCDS8079.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.903517	0.92035	.	.	ENSG00000068976	ENST00000377432;ENST00000164139;ENST00000540450	D;D	0.95342	-3.68;-3.68	4.91	4.91	0.64330	.	0.000000	0.52532	D	0.000074	D	0.96895	0.8986	M	0.93854	3.465	0.80722	D	1	P;P	0.48407	0.91;0.91	P;P	0.52386	0.697;0.697	D	0.97609	1.0128	10	0.87932	D	0	-39.6172	12.5412	0.56172	0.0:0.0:0.0:1.0	.	604;692	A6NDY6;P11217	.;PYGM_HUMAN	S	604;692;673	ENSP00000366650:T604S;ENSP00000164139:T692S	ENSP00000164139:T692S	T	-	1	0	PYGM	64274527	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.832000	0.86757	2.073000	0.62155	0.454000	0.30748	ACC	.	.	.	none		0.567	PYGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143254.2	NM_005609		A	64517951	T	A	64517951	3	1	189	1	0	0	0	0	1	0	0	0	12875	1696	59	5	470	5	PYGM	11	64517951	Missense_Mutation	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10	5539387	64517951	70488565	40	11143											
NUMA1	4926	hgsc.bcm.edu	37	chr11	71733436	71733436	+	Frame_Shift_Del	DEL	G	G	-																															ctgggacttttggagctcatGgtagagtggtataagagcag																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:71733436delG	ENST00000393695.3	-	7	652	c.321delC	c.(319-321)accfs	p.T107fs	RP11-849H4.4_ENST00000502284.1_RNA|NUMA1_ENST00000351960.6_Frame_Shift_Del_p.T107fs|NUMA1_ENST00000358965.6_Frame_Shift_Del_p.T107fs	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						TGGAGCTCATGGTAGAGTGGT	0.517			T	RARA	APL																																p.M108X		Atlas-Indel,Pindel	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.322delA						PASS	.						155	158	157					11																	71733436		2200	4293	6493	SO:0001589	frameshift_variant	4926	exon7			.	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.321delC	chr11.hg19:g.71733436delG	ENSP00000377298:p.Thr107fs	85.0	0.0	0		68.0	21.0	0.308824	NM_006185		Frame_Shift_Del	DEL	ENST00000393695.3	hg19	CCDS31633.1																																																																																			.	.	.	none		0.517	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1			-	71733436	G	-	71733436	7	5	189	1	0	1	0	1	0	0	0	0	10757	1335	47	0	6110	0	NUMA1	11	71733436	Frame_Shift_Del	DEL	G	TCGA-GL-A59T-01A-21D-A28G-10	7215485	71733436	63273080	41	11144											
CHCHD8	51287	hgsc.bcm.edu	37	chr11	73584202	73584202	+	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	tcttgcctcctctgcagctcCtcttgccgcctcgcctgctg	1	13	8	19	2	3	0	0	0	3	0	6	0	5	0	6	0	5	3	6	0	0	2			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:73584202C>A	ENST00000355693.4	-	2	469	c.222G>T	c.(220-222)gaG>gaT	p.E74D	COA4_ENST00000537289.1_Missense_Mutation_p.E74D|COA4_ENST00000541455.1_Missense_Mutation_p.E83D|COA4_ENST00000537581.1_5'Flank|COA4_ENST00000545127.1_Missense_Mutation_p.E74D	NM_016565.2	NP_057649.2	Q9NYJ1	COA4_HUMAN	cytochrome c oxidase assembly factor 4 homolog (S. cerevisiae)	74						mitochondrion (GO:0005739)											TCTGCAGCTCCTCTTGCCGCC	0.612																																					p.E74D		Atlas-SNP	.											.	.	.	.	0			c.G222T						PASS	.						108	81	90					11																	73584202		2200	4293	6493	SO:0001583	missense	51287	exon2			CAGCTCCTCTTGC	AF242180	CCDS8225.1	11q13.4	2013-10-18	2012-10-15	2012-10-15		ENSG00000181924		"Coiled-coil-helix-coiled-coil-helix domain containing", "Mitochondrial respiratory chain complex assembly factors"	24604	protein-coding gene	gene with protein product		608016	"coiled-coil-helix-coiled-coil-helix domain containing 8"	CHCHD8		11085516, 20624914	Standard	NM_016565		Approved	E2IG2, CMC3	uc001ouj.3	Q9NYJ1		ENST00000355693.4:c.222G>T	chr11.hg19:g.73584202C>A	ENSP00000347919:p.Glu74Asp	85.0	0.0	.		77.0	9.0	.	NM_016565	B2RAA0|Q69YU4	Missense_Mutation	SNP	ENST00000355693.4	hg19	CCDS8225.1	.	.	.	.	.	.	.	.	.	.	C	16.99	3.273202	0.59649	.	.	ENSG00000181924	ENST00000355693;ENST00000545127;ENST00000541455;ENST00000537289	.	.	.	6.02	2.73	0.32206	.	0.000000	0.85682	D	0.000000	T	0.34048	0.0884	.	.	.	0.33160	D	0.546821	P	0.39665	0.682	B	0.34038	0.174	T	0.50890	-0.8774	8	0.59425	D	0.04	-24.9482	8.1718	0.31260	0.0:0.6617:0.0:0.3383	.	74	Q9NYJ1	CHCH8_HUMAN	D	74;74;83;74	.	ENSP00000347919:E74D	E	-	3	2	CHCHD8	73261850	0.857000	0.29778	0.996000	0.52242	0.388000	0.30384	0.299000	0.19138	0.879000	0.35944	0.655000	0.94253	GAG	.	.	.	none		0.612	COA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397878.1	NM_016565		A	73584202	C	A	73584202	3	1	189	1	0	0	0	0	1	0	0	0	3324	680	24	4	45	4	CHCHD8	11	73584202	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	1850766	73584202	61422314	42	11145											
PRCP	5547	hgsc.bcm.edu	37	chr11	82560214	82560214	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggatgtcctgagaagttaaTgggctgcataagtgaagggc	11	10	15	5	0	0	2	0	2	0	1	1	4	1	3	1	3	1	3	1	3	4	2			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:82560214T>C	ENST00000313010.3	-	6	992	c.798A>G	c.(796-798)ccA>ccG	p.P266P	PRCP_ENST00000393399.2_Silent_p.P287P|PRCP_ENST00000535099.1_Silent_p.P161P	NM_005040.2	NP_005031.1	P42785	PCP_HUMAN	prolylcarboxypeptidase (angiotensinase C)	266	SKS domain.				angiogenesis involved in wound healing (GO:0060055)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|energy homeostasis (GO:0097009)|glucose homeostasis (GO:0042593)|negative regulation of systemic arterial blood pressure (GO:0003085)|plasma kallikrein-kinin cascade (GO:0002353)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of thyroid hormone mediated signaling pathway (GO:0002155)	basal part of cell (GO:0045178)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	serine-type carboxypeptidase activity (GO:0004185)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	17						GAGAAGTTAATGGGCTGCATA	0.443																																					p.P287P		Atlas-SNP	.											.	PRCP	69	.	0			c.A861G						PASS	.						115	108	110					11																	82560214		2203	4300	6503	SO:0001819	synonymous_variant	5547	exon7			AGTTAATGGGCTG	BC001500, BI827978, L13977	CCDS8262.1, CCDS41695.1	11q14	2005-10-04				ENSG00000137509			9344	protein-coding gene	gene with protein product		176785				8344943	Standard	NM_199418		Approved	PCP, HUMPCP	uc001ozr.3	P42785		ENST00000313010.3:c.798A>G	chr11.hg19:g.82560214T>C		82.0	0.0	.		88.0	18.0	.	NM_199418	A8MU24|B2R7B7|B3KRK5|B5BU34	Silent	SNP	ENST00000313010.3	hg19	CCDS8262.1																																																																																			.	.	.	none		0.443	PRCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391792.1	NM_005040		C	82560214	T	C	82560214	2	2	189	1	0	0	0	0	0	0	0	1	12459	1451	51	3		3	PRCP	11	82560214	Silent	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10	8976012	82560214	52446302	43	11146											
DDX10	1662	hgsc.bcm.edu	37	chr11	108559718	108559718	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtgagctgcagcaaaaaataAgtgtgctgtattcctttttg	11	14	10	6	0	0	1	0	1	0	0	1	1	1	1	1	0	4	5	1	0	5	5			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:108559718A>G	ENST00000322536.3	+	7	1033	c.904A>G	c.(904-906)Agt>Ggt	p.S302G	DDX10_ENST00000526794.1_Missense_Mutation_p.S302G	NM_004398.2	NP_004389.2	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	302	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				metabolic process (GO:0008152)		ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			breast(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|prostate(2)	27		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		GCAAAAAATAAGTGTGCTGTA	0.373			T	NUP98	AML*																																p.S302G		Atlas-SNP	.		Dom	yes		11	11q22-q23	1662	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10		L	.	DDX10	70	.	0			c.A904G						PASS	.						194	193	193					11																	108559718		2201	4298	6499	SO:0001583	missense	1662	exon7			AAAATAAGTGTGC	U28042	CCDS8342.1	11q22-q23	2005-10-11	2003-06-13		ENSG00000178105	ENSG00000178105		"DEAD-boxes"	2735	protein-coding gene	gene with protein product		601235	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 10 (RNA helicase)"			8660968	Standard	NM_004398		Approved	HRH-J8	uc001pkm.3	Q13206	OTTHUMG00000166540	ENST00000322536.3:c.904A>G	chr11.hg19:g.108559718A>G	ENSP00000314348:p.Ser302Gly	112.0	0.0	.		79.0	4.0	.	NM_004398	B2RCQ3|Q5BJD8	Missense_Mutation	SNP	ENST00000322536.3	hg19	CCDS8342.1	.	.	.	.	.	.	.	.	.	.	A	8.380	0.837213	0.16891	.	.	ENSG00000178105	ENST00000322536;ENST00000456020;ENST00000526794	T;T	0.04809	3.55;3.55	5.61	5.61	0.85477	Helicase, C-terminal (1);	0.171976	0.64402	D	0.000008	T	0.04092	0.0114	N	0.16130	0.375	0.30844	N	0.735378	B;B	0.20887	0.049;0.049	B;B	0.16722	0.016;0.016	T	0.20505	-1.0273	10	0.27082	T	0.32	-11.3262	15.8096	0.78547	1.0:0.0:0.0:0.0	.	302;302	Q13206;E9PIF2	DDX10_HUMAN;.	G	302;208;302	ENSP00000314348:S302G;ENSP00000432032:S302G	ENSP00000314348:S302G	S	+	1	0	DDX10	108064928	1.000000	0.71417	1.000000	0.80357	0.015000	0.08874	6.272000	0.72575	2.132000	0.65825	0.533000	0.62120	AGT	.	.	.	none		0.373	DDX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390343.1	NM_004398		G	108559718	A	G	108559718	3	3	189	1	0	0	0	0	1	0	0	0	4344	72	3	3	930	3	DDX10	11	108559718	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	25999504	108559718	26446798	44	11147											
SLC37A4	51399	hgsc.bcm.edu	37	chr11	118895661	118895661	+	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	0	0	0	0	0	0	0	tcggcccatcttggtgcggaTgtttcgtaggaggaagaagg	8	10	16	7	3	1	1	0	0	1	1	3	4	1	4	1	6	1	2	1	6	3	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:118895661T>C	ENST00000533632.1	+	0	1759				SLC37A4_ENST00000545985.1_Missense_Mutation_p.I417V|SLC37A4_ENST00000330775.7_Missense_Mutation_p.I438V|SLC37A4_ENST00000538950.1_Missense_Mutation_p.I344V|SLC37A4_ENST00000357590.5_Missense_Mutation_p.I439V|TRAPPC4_ENST00000533058.1_Missense_Mutation_p.C226R|SLC37A4_ENST00000525102.1_5'UTR	NM_016146.4	NP_057230.1	Q9Y296	TPPC4_HUMAN	trafficking protein particle complex 4						dendrite development (GO:0016358)|ER to Golgi vesicle-mediated transport (GO:0006888)|extracellular matrix organization (GO:0030198)	cis-Golgi network (GO:0005801)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi stack (GO:0005795)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)|TRAPP complex (GO:0030008)				NS(1)|endometrium(1)|large_intestine(2)|lung(1)	5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.58e-05)		TTGGTGCGGATGTTTCGTAGG	0.597																																					p.I439V		Atlas-SNP	.											.	SLC37A4	19	.	0			c.A1315G						PASS	.						43	51	48					11																	118895661		2020	4175	6195	SO:0001628	intergenic_variant	2542	exon12			TGCGGATGTTTCG	AF078862	CCDS8407.1	11q23.3	2011-10-10				ENSG00000196655		"Trafficking protein particle complex"	19943	protein-coding gene	gene with protein product		610971				10810093	Standard	NM_016146		Approved	TRS23, SBDN, PTD009	uc010ryo.2	Q9Y296			chr11.hg19:g.118895661T>C		180.0	0.0	.		125.0	41.0	.	NM_001164278	A8K3A5|B4DME1	Missense_Mutation	SNP	ENST00000533632.1	hg19	CCDS8407.1	.	.	.	.	.	.	.	.	.	.	T	14.52	2.560807	0.45590	.	.	ENSG00000196655	ENST00000533058	T	0.50001	0.76	5.27	5.27	0.74061	.	.	.	.	.	T	0.52370	0.1730	L	0.36672	1.1	0.50171	D	0.999855	.	.	.	.	.	.	T	0.56147	-0.8027	7	0.87932	D	0	-22.4876	15.3661	0.74523	0.0:0.0:0.0:1.0	.	.	.	.	R	226	ENSP00000432920:C226R	ENSP00000432920:C226R	C	+	1	0	TRAPPC4	118400871	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	7.309000	0.78937	2.226000	0.72624	0.459000	0.35465	TGT	.	.	.	none		0.597	TRAPPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389332.1	NM_016146		C	118895661	T	C	118895661	1	2	189	0	1	0	0	0	0	0	0	0	14613	1464	51	3		3	SLC37A4	11	118895661	IGR	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10	10335943	118895661	16110855	45	11148											
NCAPD2	9918	hgsc.bcm.edu	37	chr12	6637492	6637492	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggactcctcatctgtatgcTcggtaagagacccctcacaa	10	10	8	13	1	3	1	2	0	1	1	5	3	4	2	3	2	1	3	3	2	3	2			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr12:6637492T>C	ENST00000315579.5	+	25	4096	c.3297T>C	c.(3295-3297)gcT>gcC	p.A1099A	NCAPD2_ENST00000545962.1_Silent_p.A1054A	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	1099					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						ATCTGTATGCTCGGTAAGAGA	0.577																																					p.A1099A		Atlas-SNP	.											.	NCAPD2	99	.	0			c.T3297C						PASS	.						139	143	142					12																	6637492		2203	4300	6503	SO:0001819	synonymous_variant	9918	exon25			GTATGCTCGGTAA	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.3297T>C	chr12.hg19:g.6637492T>C		146.0	0.0	.		134.0	31.0	.	NM_014865	D3DUR4|Q8N6U3	Silent	SNP	ENST00000315579.5	hg19	CCDS8548.1																																																																																			.	.	.	none		0.577	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865		C	6637492	T	C	6637492	2	2	189	1	0	0	0	0	0	0	0	1	10212	1538	54	3		3	NCAPD2	12	6637492	Silent	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10		6637492	127214403	46	11149											
A2M	2	hgsc.bcm.edu	37	chr12	9243036	9243036	+	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	cgcttgttccttctccactgGgacagctaggaaggcgggag	7	9	14	11	2	1	0	0	0	1	0	3	3	2	3	2	4	1	3	2	4	2	4			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr12:9243036G>T	ENST00000318602.7	-	20	2819	c.2512C>A	c.(2512-2514)Cca>Aca	p.P838T		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	838					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)	TTCTCCACTGGGACAGCTAGG	0.537																																					p.P838T		Atlas-SNP	.											.	A2M	180	.	0			c.C2512A						PASS	.						97	100	99					12																	9243036		2130	4272	6402	SO:0001583	missense	2	exon20			CCACTGGGACAGC	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.2512C>A	chr12.hg19:g.9243036G>T	ENSP00000323929:p.Pro838Thr	120.0	0.0	.		93.0	4.0	.	NM_000014	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Missense_Mutation	SNP	ENST00000318602.7	hg19	CCDS44827.1	.	.	.	.	.	.	.	.	.	.	G	12.82	2.053189	0.36181	.	.	ENSG00000175899	ENST00000318602;ENST00000540099	T	0.13778	2.56	5.08	5.08	0.68730	.	0.243635	0.35805	N	0.002961	T	0.41305	0.1153	M	0.87758	2.905	0.41736	D	0.989588	D	0.62365	0.991	D	0.63703	0.917	T	0.38735	-0.9647	10	0.37606	T	0.19	.	17.397	0.87449	0.0:0.0:1.0:0.0	.	838	P01023	A2MG_HUMAN	T	838;853	ENSP00000323929:P838T	ENSP00000323929:P838T	P	-	1	0	A2M	9134303	1.000000	0.71417	0.518000	0.27811	0.038000	0.13279	5.993000	0.70616	2.512000	0.84698	0.655000	0.94253	CCA	.	.	.	none		0.537	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014		T	9243036	G	T	9243036	3	4	189	1	0	0	0	0	1	0	0	0	4	1232	43	4	1980	4	A2M	12	9243036	Missense_Mutation	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	2605544	9243036	124608859	47	11150											
LARP4	113251	hgsc.bcm.edu	37	chr12	50847398	50847398	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caccaacagtactcggtctaTagtattgtgcctcagtcttg	9	13	8	11	1	3	0	1	0	2	0	4	0	3	0	2	1	3	2	2	1	5	6			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr12:50847398T>C	ENST00000398473.2	+	9	1072	c.960T>C	c.(958-960)taT>taC	p.Y320Y	LARP4_ENST00000347328.5_Intron|LARP4_ENST00000518444.1_Silent_p.Y319Y|LARP4_ENST00000293618.8_Silent_p.Y320Y|LARP4_ENST00000518561.1_Silent_p.Y250Y|LARP4_ENST00000429001.3_Silent_p.Y326Y|LARP4_ENST00000522085.1_Silent_p.Y320Y	NM_052879.4|NM_199188.2	NP_443111.4|NP_954658.2	Q71RC2	LARP4_HUMAN	La ribonucleoprotein domain family, member 4	320					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	23						ACTCGGTCTATAGTATTGTGC	0.373																																					p.Y320Y		Atlas-SNP	.											.	LARP4	58	.	0			c.T960C						PASS	.						208	181	190					12																	50847398		1906	4126	6032	SO:0001819	synonymous_variant	113251	exon9			GGTCTATAGTATT	AY004310	CCDS41782.1, CCDS44879.1, CCDS44880.1, CCDS44879.2, CCDS53789.1, CCDS53790.1	12q13.12	2005-08-09			ENSG00000161813	ENSG00000161813		"La ribonucleoprotein domain containing"	24320	protein-coding gene	gene with protein product						12477932	Standard	NM_052879		Approved	PP13296	uc001rwp.2	Q71RC2	OTTHUMG00000163724	ENST00000398473.2:c.960T>C	chr12.hg19:g.50847398T>C		121.0	0.0	.		178.0	44.0	.	NM_001170808	A8K6T1|E9PDG5|G3XAA8|G5E976|Q5CZ97|Q6ZV14|Q96NF9	Silent	SNP	ENST00000398473.2	hg19	CCDS41782.1																																																																																			.	.	.	none		0.373	LARP4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374981.1	NM_052879		C	50847398	T	C	50847398	2	2	189	1	0	0	0	0	0	0	0	1	8637	1413	49	3		3	LARP4	12	50847398	Silent	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10	41604362	50847398	83004497	48	11151											
NPFF	8620	hgsc.bcm.edu	37	chr12	53900627	53900627	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aattcagcccctctccagccCggggactcagccattcattc	8	9	7	17	1	4	0	3	0	1	0	6	1	4	1	5	2	3	0	5	2	1	3	rs199569723		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr12:53900627C>T	ENST00000267017.3	-	3	438	c.275G>A	c.(274-276)cGg>cAg	p.R92Q	RP11-793H13.10_ENST00000591834.1_3'UTR|NPFF_ENST00000609999.1_Missense_Mutation_p.R95Q	NM_003717.2	NP_003708.1	O15130	NPFF_HUMAN	neuropeptide FF-amide peptide precursor	92					acute inflammatory response to antigenic stimulus (GO:0002438)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of appetite (GO:0032099)|negative regulation of heart rate (GO:0010459)|negative regulation of insulin secretion (GO:0046676)|neuropeptide signaling pathway (GO:0007218)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane depolarization (GO:0003254)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|response to morphine (GO:0043278)|somatostatin secretion (GO:0070253)|spinal cord development (GO:0021510)|synaptic transmission (GO:0007268)|vasopressin secretion (GO:0030103)	axon terminus (GO:0043679)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|perikaryon (GO:0043204)|vesicle (GO:0031982)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(1)|prostate(1)|urinary_tract(1)	3						CTCTCCAGCCCGGGGACTCAG	0.552																																					p.R92Q		Atlas-SNP	.											.	NPFF	9	.	0			c.G275A						PASS	.						111	114	113					12																	53900627		2203	4300	6503	SO:0001583	missense	8620	exon3			CCAGCCCGGGGAC	AF005271	CCDS8862.1	12q13.13	2013-02-26			ENSG00000139574	ENSG00000139574		"Endogenous ligands"	7901	protein-coding gene	gene with protein product		604643				9224703	Standard	NM_003717		Approved	FMRFAL	uc001sdw.1	O15130	OTTHUMG00000169856	ENST00000267017.3:c.275G>A	chr12.hg19:g.53900627C>T	ENSP00000267017:p.Arg92Gln	58.0	0.0	.		76.0	10.0	.	NM_003717	Q3SXL4	Missense_Mutation	SNP	ENST00000267017.3	hg19	CCDS8862.1	.	.	.	.	.	.	.	.	.	.	C	10.28	1.306772	0.23821	.	.	ENSG00000139574	ENST00000267017	T	0.54279	0.58	4.52	-1.46	0.08800	.	0.173981	0.36555	N	0.002528	T	0.36441	0.0967	L	0.49126	1.545	0.09310	N	1	B	0.23490	0.086	B	0.17722	0.019	T	0.13737	-1.0498	10	0.38643	T	0.18	-7.5784	3.979	0.09487	0.3493:0.371:0.0:0.2797	.	92	O15130	NPFF_HUMAN	Q	92	ENSP00000267017:R92Q	ENSP00000267017:R92Q	R	-	2	0	NPFF	52186894	0.048000	0.20356	0.008000	0.14137	0.980000	0.70556	0.139000	0.16036	-0.071000	0.12886	0.491000	0.48974	CGG	.	.	.	weak		0.552	NPFF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406301.1	NM_003717		T	53900627	C	T	53900627	3	4	189	1	0	0	0	0	1	0	0	0	10583	652	23	1	70	1	NPFF	12	53900627	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	3053229	53900627	79951268	49	11152											
ATP5G2	517	hgsc.bcm.edu	37	chr12	54062935	54062935	+	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	ggtccaacttatcttacctgGcataaccaatgatgaggctc	11	11	8	11	0	1	2	0	2	1	0	3	2	2	2	3	3	3	2	3	3	5	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr12:54062935G>T	ENST00000549164.1	-	4	495	c.308C>A	c.(307-309)gCc>gAc	p.A103D	ATP5G2_ENST00000602871.1_Missense_Mutation_p.A103D|ATP5G2_ENST00000338662.5_Missense_Mutation_p.A119D|ATP5G2_ENST00000394349.3_Missense_Mutation_p.A160D|ATP5G2_ENST00000550241.1_5'UTR			Q06055	AT5G2_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C2 (subunit 9)	103					ATP hydrolysis coupled proton transport (GO:0015991)|ATP synthesis coupled proton transport (GO:0015986)|response to ethanol (GO:0045471)	integral component of membrane (GO:0016021)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045263)	hydrogen ion transmembrane transporter activity (GO:0015078)|lipid binding (GO:0008289)|transporter activity (GO:0005215)			kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	6						ATCTTACCTGGCATAACCAAT	0.498																																					p.A160D		Atlas-SNP	.											.	ATP5G2	16	.	0			c.C479A						PASS	.						81	79	80					12																	54062935		2203	4300	6503	SO:0001583	missense	517	exon4			TACCTGGCATAAC	X69908	CCDS8863.2, CCDS31812.1	12q13.13	2012-10-12	2010-06-11		ENSG00000135390	ENSG00000135390		"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	842	protein-coding gene	gene with protein product		603193	"ATP synthase, H+ transporting, mitochondrial F0 complex, subunit c (subunit 9), isoform 2", "ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C2 (subunit 9)"			8328972	Standard	NM_005176		Approved		uc001sec.3	Q06055	OTTHUMG00000133442	ENST00000549164.1:c.308C>A	chr12.hg19:g.54062935G>T	ENSP00000447317:p.Ala103Asp	65.0	0.0	.		89.0	4.0	.	NM_005176	B3KQQ6	Missense_Mutation	SNP	ENST00000549164.1	hg19		.	.	.	.	.	.	.	.	.	.	G	34	5.341976	0.95783	.	.	ENSG00000135390	ENST00000394349;ENST00000549164;ENST00000338662	T;T;T	0.57752	0.38;0.38;0.38	5.14	5.14	0.70334	ATPase, F0/V0 complex, subunit C (3);	0.000000	0.85682	D	0.000000	D	0.83454	0.5258	H	0.98682	4.3	0.80722	D	1	D;D;D	0.76494	0.998;0.995;0.999	D;D;D	0.75020	0.971;0.964;0.985	D	0.89594	0.3830	10	0.87932	D	0	.	17.9104	0.88932	0.0:0.0:1.0:0.0	.	103;119;160	Q06055;Q06055-3;Q06055-2	AT5G2_HUMAN;.;.	D	160;103;119	ENSP00000377878:A160D;ENSP00000447317:A103D;ENSP00000340315:A119D	ENSP00000340315:A119D	A	-	2	0	ATP5G2	52349202	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.496000	0.97967	2.847000	0.97988	0.655000	0.94253	GCC	.	.	.	none		0.498	ATP5G2-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000407403.1	NM_005176		T	54062935	G	T	54062935	3	4	189	1	0	0	0	0	1	0	0	0	1154	1203	42	4	125	4	ATP5G2	12	54062935	Missense_Mutation	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	162308	54062935	79788960	50	11153											
CEP290	80184	hgsc.bcm.edu	37	chr12	88514780	88514780	+	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	ataaaaatacataccgattcAtaatcttttaacctcttcag	16	14	2	9	1	4	0	2	0	2	0	4	1	4	0	2	0	3	0	2	0	7	8			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr12:88514780A>C	ENST00000552810.1	-	14	1696	c.1353T>G	c.(1351-1353)taT>taG	p.Y451*	CEP290_ENST00000309041.7_Nonsense_Mutation_p.Y451*|CEP290_ENST00000397838.3_5'UTR	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	451					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						ATACCGATTCATAATCTTTTA	0.363																																					p.Y451X		Atlas-SNP	.											.	CEP290	195	.	0			c.T1353G						PASS	.						89	86	87					12																	88514780		1837	4077	5914	SO:0001587	stop_gained	80184	exon14			CGATTCATAATCT	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.1353T>G	chr12.hg19:g.88514780A>C	ENSP00000448012:p.Tyr451*	12.0	0.0	.		18.0	10.0	.	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Nonsense_Mutation	SNP	ENST00000552810.1	hg19	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	A	41	8.542306	0.98857	.	.	ENSG00000198707	ENST00000552810;ENST00000309041;ENST00000536998;ENST00000545139	.	.	.	5.61	4.42	0.53409	.	0.147782	0.46758	D	0.000264	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	.	5.4776	0.16704	0.7324:0.0:0.1371:0.1305	.	.	.	.	X	451;451;451;353	.	ENSP00000308021:Y451X	Y	-	3	2	CEP290	87038911	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.199000	0.58426	2.137000	0.66172	0.482000	0.46254	TAT	.	.	.	none		0.363	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		C	88514780	A	C	88514780	4	2	189	1	0	0	0	0	0	1	0	0	3255	224	8	5	6250	5	CEP290	12	88514780	Nonsense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	34451845	88514780	45337115	51	11154											
ANKS1B	56899	hgsc.bcm.edu	37	chr12	99640158	99640158	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	actcttgatgttttctcattGgaaggataggcaatgagatc	11	14	10	6	0	2	2	1	2	2	1	4	5	2	4	0	3	0	2	0	3	3	5			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr12:99640158G>A	ENST00000547776.2	-	13	2240	c.2241C>T	c.(2239-2241)tcC>tcT	p.S747S	ANKS1B_ENST00000329257.7_Silent_p.S747S|ANKS1B_ENST00000550833.1_5'Flank|ANKS1B_ENST00000547010.1_Silent_p.S327S	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	747						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)		TTTTCTCATTGGAAGGATAGG	0.413																																					p.S747S		Atlas-SNP	.											.	ANKS1B	180	.	0			c.C2241T						PASS	.						92	87	89					12																	99640158		1912	4102	6014	SO:0001819	synonymous_variant	56899	exon13			CTCATTGGAAGGA	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.2241C>T	chr12.hg19:g.99640158G>A		198.0	0.0	.		231.0	112.0	.	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Silent	SNP	ENST00000547776.2	hg19	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	G	7.433	0.639208	0.14386	.	.	ENSG00000185046	ENST00000550778	.	.	.	5.21	-7.15	0.01521	.	.	.	.	.	T	0.38401	0.1039	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45977	-0.9224	4	.	.	.	-6.1946	3.8547	0.08970	0.0906:0.3375:0.3258:0.2461	.	.	.	.	L	19	.	.	P	-	2	0	ANKS1B	98164289	0.194000	0.23325	0.127000	0.21898	0.969000	0.65631	-1.051000	0.03507	-0.833000	0.04245	0.462000	0.41574	CCA	.	.	.	none		0.413	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140		A	99640158	G	A	99640158	2	1	189	1	0	0	0	0	0	0	0	1	689	1335	47	2		2	ANKS1B	12	99640158	Silent	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	11125378	99640158	34211737	52	11155											
FAM161B	145483	hgsc.bcm.edu	37	chr14	74409353	74409353	+	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	actagaggaggcgataggggAagaggccatctggagcatgt	12	6	17	6	1	1	2	0	0	1	2	1	6	1	5	1	6	1	1	1	6	3	2			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr14:74409353A>T	ENST00000534936.1	-	4	1096	c.991T>A	c.(991-993)Tcc>Acc	p.S331T	FAM161B_ENST00000286544.3_Missense_Mutation_p.S394T			Q96MY7	F161B_HUMAN	family with sequence similarity 161, member B	331										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)	21						GCGATAGGGGAAGAGGCCATC	0.532																																					p.S394T		Atlas-SNP	.											.	FAM161B	67	.	0			c.T1180A						PASS	.						88	96	94					14																	74409353		2203	4300	6503	SO:0001583	missense	145483	exon4			TAGGGGAAGAGGC	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.991T>A	chr14.hg19:g.74409353A>T	ENSP00000445326:p.Ser331Thr	114.0	0.0	.		72.0	18.0	.	NM_152445	B7Z882|J3KNA2	Missense_Mutation	SNP	ENST00000534936.1	hg19		.	.	.	.	.	.	.	.	.	.	A	16.34	3.096005	0.56075	.	.	ENSG00000156050	ENST00000286544;ENST00000534936	T;T	0.21361	2.01;2.01	5.5	4.34	0.51931	.	0.392302	0.25786	N	0.028306	T	0.38719	0.1051	M	0.79475	2.455	0.29528	N	0.852984	D	0.61697	0.99	P	0.61722	0.893	T	0.35475	-0.9787	10	0.09843	T	0.71	-10.2675	12.0316	0.53401	0.5426:0.4574:0.0:0.0	.	331	Q96MY7	F161B_HUMAN	T	394;331	ENSP00000286544:S394T;ENSP00000445326:S331T	ENSP00000286544:S394T	S	-	1	0	FAM161B	73479106	0.652000	0.27349	1.000000	0.80357	0.874000	0.50279	1.334000	0.33827	1.081000	0.41110	0.533000	0.62120	TCC	.	.	.	none		0.532	FAM161B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_152445		T	74409353	A	T	74409353	3	4	189	1	0	0	0	0	1	0	0	0	5477	246	9	5	976	5	FAM161B	14	74409353	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10		74409353	32940187	53	11156											
C14orf49	161176	hgsc.bcm.edu	37	chr14	95906070	95906070	+	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	catcaccagccagccctgcgCttccaccagggacagctggg	8	5	11	17	1	1	0	1	0	0	0	2	1	2	1	5	2	4	2	5	2	0	1			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr14:95906070C>T	ENST00000334258.5	-	12	2139	c.2125G>A	c.(2125-2127)Gcg>Acg	p.A709T	SYNE3_ENST00000554873.1_Missense_Mutation_p.A466T|SYNE3_ENST00000557275.1_Missense_Mutation_p.A709T	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	709					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						CAGCCCTGCGCTTCCACCAGG	0.637																																					p.A709T		Atlas-SNP	.											.	SYNE3	130	.	0			c.G2125A						PASS	.						44	47	46					14																	95906070		2203	4300	6503	SO:0001583	missense	161176	exon12			CCTGCGCTTCCAC	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.2125G>A	chr14.hg19:g.95906070C>T	ENSP00000334308:p.Ala709Thr	181.0	0.0	.		137.0	7.0	.	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	hg19	CCDS9935.1	.	.	.	.	.	.	.	.	.	.	C	14.87	2.663059	0.47572	.	.	ENSG00000176438	ENST00000334258;ENST00000554873;ENST00000557275	T;T;T	0.52295	0.67;0.67;0.67	5.34	5.34	0.76211	.	0.171047	0.27932	N	0.017272	T	0.46034	0.1372	L	0.50333	1.59	0.80722	D	1	P;P	0.50369	0.919;0.934	P;P	0.48598	0.447;0.583	T	0.26573	-1.0099	10	0.12430	T	0.62	-23.2732	11.6332	0.51187	0.1774:0.8226:0.0:0.0	.	709;709	Q6ZMZ3-2;Q6ZMZ3	.;SYNE3_HUMAN	T	709;466;709	ENSP00000334308:A709T;ENSP00000452154:A466T;ENSP00000450562:A709T	ENSP00000334308:A709T	A	-	1	0	C14orf49	94975823	0.218000	0.23608	0.039000	0.18376	0.023000	0.10783	1.454000	0.35178	2.507000	0.84556	0.561000	0.74099	GCG	.	.	.	none		0.637	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592		T	95906070	C	T	95906070	3	4	189	1	0	0	0	0	1	0	0	0	1778	797	28	2	826	2	C14orf49	14	95906070	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10	21496717	95906070	11443470	54	11157											
TBC1D24	57465	hgsc.bcm.edu	37	chr16	2550436	2550436	+	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	gccgctcgccacttcaacctGccctccaagaccgagtccat	8	7	7	19	3	1	1	1	0	0	1	4	2	3	1	7	0	2	1	7	0	2	1			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr16:2550436G>T	ENST00000293970.5	+	7	1603	c.1470G>T	c.(1468-1470)ctG>ctT	p.L490L	TBC1D24_ENST00000567020.1_Silent_p.L484L|TBC1D24_ENST00000434757.2_Silent_p.L490L|RP11-20I23.1_ENST00000564543.1_Intron	NM_001199107.1	NP_001186036.1	Q9ULP9	TBC24_HUMAN	TBC1 domain family, member 24	490	TLD.				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						ACTTCAACCTGCCCTCCAAGA	0.692																																					p.L490L		Atlas-SNP	.											.	TBC1D24	35	.	0			c.G1470T						PASS	.						12	17	15					16																	2550436		2057	4196	6253	SO:0001819	synonymous_variant	57465	exon7			CAACCTGCCCTCC	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.1470G>T	chr16.hg19:g.2550436G>T		314.0	0.0	.		269.0	58.0	.	NM_001199107	A0JNW3|B9A6M6|Q2KJ08	Silent	SNP	ENST00000293970.5	hg19	CCDS55980.1																																																																																			.	.	.	none		0.692	TBC1D24-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000435637.1	NM_020705		T	2550436	G	T	2550436	2	4	189	1	0	0	0	0	0	0	0	1	15626	1306	46	4		4	TBC1D24	16	2550436	Silent	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10		2550436	87804317	55	11158											
TCAP	8557	hgsc.bcm.edu	37	chr17	37821723	37821723	+	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	tccacacggcccgaggagggGtgagtgtgggtctgctagag	7	7	18	9	2	1	2	0	1	1	1	2	4	2	3	2	5	1	1	2	5	1	1	rs113187448		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr17:37821723G>A	ENST00000309889.2	+	1	1283		c.e1+1		PNMT_ENST00000394246.1_5'Flank|TCAP_ENST00000578283.1_Splice_Site|PNMT_ENST00000269582.2_5'Flank|PNMT_ENST00000581428.1_5'Flank			O15273	TELT_HUMAN	titin-cap						adult heart development (GO:0007512)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of mechanical stimulus (GO:0050982)|detection of muscle stretch (GO:0035995)|muscle filament sliding (GO:0030049)|otic vesicle formation (GO:0030916)|protein complex assembly (GO:0006461)|response to muscle stretch (GO:0035994)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle contraction (GO:0003009)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)	cytosol (GO:0005829)|I band (GO:0031674)|Z disc (GO:0030018)	FATZ binding (GO:0051373)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)			kidney(1)|lung(1)	2	all_cancers(6;6.59e-85)|all_epithelial(6;2.89e-103)|Breast(7;1.05e-86)|Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;3.87e-45)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			CCGAGGAGGGGTGAGTGTGGG	0.627																																					.		Atlas-SNP	.											.	TCAP	12	.	0			c.110+1G>A						PASS	.						67	64	65					17																	37821723		2203	4300	6503	SO:0001630	splice_region_variant	8557	exon1			GGAGGGGTGAGTG	AJ000491	CCDS11342.1	17q12	2014-09-17	2012-09-20		ENSG00000173991	ENSG00000173991			11610	protein-coding gene	gene with protein product	"19 kDa sarcomeric protein"	604488	"limb girdle muscular dystrophy 2G (autosomal recessive)", "titin-cap (telethonin)"	LGMD2G		9350988, 9817758	Standard	NM_003673		Approved	T-cap, TELE, telethonin, CMD1N	uc002hsh.3	O15273	OTTHUMG00000133215	ENST00000309889.2:c.110+1G>A	chr17.hg19:g.37821723G>A		87.0	0.0	.		134.0	32.0	.	NM_003673	Q96L27	Splice_Site	SNP	ENST00000309889.2	hg19	CCDS11342.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.194985	0.38806	.	.	ENSG00000173991	ENST00000309889	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.5082	0.95130	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TCAP	35075249	1.000000	0.71417	1.000000	0.80357	0.117000	0.20001	7.443000	0.80521	2.710000	0.92621	0.563000	0.77884	.	.	.	.	alt		0.627	TCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256942.1	NM_003673	Intron	A	37821723	G	A	37821723	5	1	189	1	0	0	0	0	0	0	1	0	15678	1275	44	2	113	2	TCAP	17	37821723	Splice_Site	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10		37821723	43373487	56	11159											
RPTOR	57521	hgsc.bcm.edu	37	chr17	78811724	78811724	+	Missense_Mutation	SNP	A	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	cctctgttctctccgcaggcAagcctgggacctggctgttg	4	11	12	14	1	2	0	0	0	2	0	4	1	3	1	4	3	1	5	4	3	1	2			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr17:78811724A>C	ENST00000306801.3	+	10	1501	c.1139A>C	c.(1138-1140)cAa>cCa	p.Q380P	RPTOR_ENST00000544334.2_Missense_Mutation_p.Q380P|RPTOR_ENST00000537330.1_Missense_Mutation_p.Q195P|RPTOR_ENST00000575542.1_3'UTR	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	380					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						CTCCGCAGGCAAGCCTGGGAC	0.612																																					p.Q380P		Atlas-SNP	.											.	RPTOR	122	.	0			c.A1139C						PASS	.						111	77	89					17																	78811724		2203	4300	6503	SO:0001583	missense	57521	exon10			GCAGGCAAGCCTG		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.1139A>C	chr17.hg19:g.78811724A>C	ENSP00000307272:p.Gln380Pro	108.0	0.0	.		174.0	36.0	.	NM_001163034	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Missense_Mutation	SNP	ENST00000306801.3	hg19	CCDS11773.1	.	.	.	.	.	.	.	.	.	.	A	16.94	3.260139	0.59321	.	.	ENSG00000141564	ENST00000537330;ENST00000306801;ENST00000544334	T;T	0.46819	0.86;0.86	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.66218	0.2767	M	0.79475	2.455	0.80722	D	1	D;B;D	0.56521	0.96;0.168;0.976	D;B;B	0.64237	0.923;0.086;0.438	T	0.68526	-0.5385	10	0.46703	T	0.11	.	13.1464	0.59463	1.0:0.0:0.0:0.0	.	380;195;380	F5H7J5;F5GXV9;Q8N122	.;.;RPTOR_HUMAN	P	195;380;380	ENSP00000307272:Q380P;ENSP00000442479:Q380P	ENSP00000307272:Q380P	Q	+	2	0	RPTOR	76426319	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	8.087000	0.89521	1.990000	0.58119	0.455000	0.32223	CAA	.	.	.	none		0.612	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761		C	78811724	A	C	78811724	3	2	189	1	0	0	0	0	1	0	0	0	13678	130	5	5	1177	5	RPTOR	17	78811724	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	40990001	78811724	2383486	57	11160											
RTTN	25914	hgsc.bcm.edu	37	chr18	67863855	67863855	+	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	aggcgatgctttccatctccAaaggccagtttcaacagaga	12	9	9	11	1	2	1	1	0	1	1	4	3	3	1	3	2	2	2	3	2	2	2	rs2365902		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr18:67863855A>T	ENST00000255674.6	-	7	1009	c.723T>A	c.(721-723)ttT>ttA	p.F241L	RTTN_ENST00000437017.1_Missense_Mutation_p.F241L|RTTN_ENST00000454359.1_Missense_Mutation_p.F241L	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	241				F -> FG (in Ref. 1; AK096404 and 3; CAH18659). {ECO:0000305}.	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)				TTCCATCTCCAAAGGCCAGTT	0.448																																					p.F241L		Atlas-SNP	.											.,1	RTTN	184	.	0			c.T723A						PASS	.						69	66	67					18																	67863855		1859	4099	5958	SO:0001583	missense	25914	exon7			ATCTCCAAAGGCC	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.723T>A	chr18.hg19:g.67863855A>T	ENSP00000255674:p.Phe241Leu	110.0	1.0	.		81.0	7.0	.	NM_173630	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Missense_Mutation	SNP	ENST00000255674.6	hg19	CCDS42443.1	.	.	.	.	.	.	.	.	.	.	A	14.03	2.412496	0.42817	.	.	ENSG00000176225	ENST00000255674;ENST00000454359;ENST00000437017	T;T;T	0.62364	3.75;0.03;0.03	5.21	-1.64	0.08318	Armadillo-like helical (1);Armadillo-type fold (2);	0.168056	0.41396	D	0.000882	T	0.45256	0.1333	L	0.57536	1.79	0.28531	N	0.912606	B;B	0.11235	0.003;0.004	B;B	0.13407	0.004;0.009	T	0.40098	-0.9581	10	0.06625	T	0.88	.	5.9129	0.19039	0.4745:0.0:0.3977:0.1277	.	241;241	Q86VV8-2;Q86VV8	.;RTTN_HUMAN	L	241	ENSP00000255674:F241L;ENSP00000402352:F241L;ENSP00000399520:F241L	ENSP00000255674:F241L	F	-	3	2	RTTN	66014835	0.504000	0.26123	0.928000	0.36995	0.995000	0.86356	-0.014000	0.12656	-0.284000	0.09102	0.528000	0.53228	TTT	.	.	.	weak		0.448	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630		T	67863855	A	T	67863855	3	4	189	1	0	0	0	0	1	0	0	0	13750	127	5	5	6129	5	RTTN	18	67863855	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10		67863855	10213393	58	11161											
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-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	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	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	chr19.hg19:g.11558370G>A		203.0	0.0	.		115.0	6.0	.	NM_001001329	A8K318|Q96BU9|Q96D06|Q9P0W9	Silent	SNP	ENST00000589838.1	hg19	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	189	1	0	0	0	0	0	0	0	1	12526	991	35	2		2	PRKCSH	19	11558370	Silent	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10		11558370	47570613	59	11162											
GRWD1	83743	hgsc.bcm.edu	37	chr19	48953775	48953775	+	Frame_Shift_Del	DEL	G	G	-																															tgcccttgactggtccccccGggtgaccggtgagtccctgg																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr19:48953775delG	ENST00000253237.5	+	4	907	c.674delG	c.(673-675)cggfs	p.R225fs		NM_031485.3	NP_113673.3	Q9BQ67	GRWD1_HUMAN	glutamate-rich WD repeat containing 1	225						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|stomach(1)	19		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;0.000206)|all cancers(93;0.000207)|Epithelial(262;0.0125)|GBM - Glioblastoma multiforme(486;0.0222)		TGGTCCCCCCGGGTGACCGGT	0.667																																					p.R225fs		Pindel	.											.	GRWD1	41	.	0			c.673delC						PASS	.						34	37	36					19																	48953775		2203	4300	6503	SO:0001589	frameshift_variant	83743	exon4			.	AF337808	CCDS12720.1	19q13.33	2013-05-21				ENSG00000105447		"WD repeat domain containing"	21270	protein-coding gene	gene with protein product	regulator of ribosome biogenesis 1 homolog (S. cerevisiae)	610597				15885502	Standard	NM_031485		Approved	WDR28, GRWD, RRB1	uc002pjd.2	Q9BQ67		ENST00000253237.5:c.674delG	chr19.hg19:g.48953775delG	ENSP00000253237:p.Arg225fs	51.0	0.0	.		54.0	12.0	0.222	NM_031485	Q8TF59	Frame_Shift_Del	DEL	ENST00000253237.5	hg19	CCDS12720.1																																																																																			.	.	.	none		0.667	GRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466122.1	NM_031485		-	48953775	G	-	48953775	7	5	189	1	0	1	0	1	0	0	0	0	6818	1116	39	0	688	0	GRWD1	19	48953775	Frame_Shift_Del	DEL	G	TCGA-GL-A59T-01A-21D-A28G-10	37395405	48953775	10175208	60	11163											
ZNF615	284370	hgsc.bcm.edu	37	chr19	52496371	52496372	+	Missense_Mutation	DNP	GC	GC	AT																															attttccacattcagtacatGcaaaggaagtctttcctgtg																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr19:52496371_52496372GC>AT	ENST00000602063.1	-	6	2306_2307	c.1957_1958GC>AT	c.(1957-1959)GCa>ATa	p.A653I	ZNF615_ENST00000391795.3_Missense_Mutation_p.A658I|ZNF615_ENST00000594083.1_Missense_Mutation_p.A664I|ZNF615_ENST00000598071.1_Missense_Mutation_p.A664I|ZNF615_ENST00000376716.5_Missense_Mutation_p.A653I			Q8N8J6	ZN615_HUMAN	zinc finger protein 615	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)|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)		TTCAGTACATGCAAAGGAAGTC	0.406																																					p.A664V|p.A664T		Atlas-SNP	.											.	ZNF615	111	.	0			c.C1991T|c.G1990A						PASS	.																																			SO:0001583	missense	284370	exon7			GTACATGCAAAGG|TACATGCAAAGGA	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.1957_1958delinsAT	chr19.hg19:g.52496371_52496372delinsAT	ENSP00000473089:p.Ala653Ile	144.0	0.0	.		132.0|134.0	40.0|41.0	.	NM_001199324	B7ZKW9|Q2M2Y6|Q5CZB0|Q6ZMT7|Q6ZRB3	Missense_Mutation	SNP	ENST00000602063.1	hg19	CCDS12846.1																																																																																			.	.	.	none		0.406	ZNF615-009	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462391.1	NM_198480		AT	52496372	GC	AT	52496371	3	1	189	1	0	0	0	0	1	0	0	0	18052	1319	46	2	241	2	ZNF615	19	52496371	Missense_Mutation	DNP	GC	TCGA-GL-A59T-01A-21D-A28G-10	3542596	52496371	6632612	61	11164											
ZNF160	90338	hgsc.bcm.edu	37	chr19	53572249	53572249	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgaaggctttcccacacTcattacacttgtaaggtttc	10	13	6	12	0	1	1	1	1	0	0	3	1	2	1	1	2	1	3	1	2	3	5			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr19:53572249T>C	ENST00000429604.1	-	7	1953	c.1538A>G	c.(1537-1539)gAg>gGg	p.E513G	ZNF160_ENST00000599056.1_Missense_Mutation_p.E513G|ZNF160_ENST00000418871.1_Missense_Mutation_p.E513G|ZNF160_ENST00000601421.1_Missense_Mutation_p.E477G	NM_001102603.1|NM_198893.2	NP_001096073.1|NP_942596.1	Q9HCG1	ZN160_HUMAN	zinc finger protein 160	513					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)		TTTCCCACACTCATTACACTT	0.403																																					p.E513G		Atlas-SNP	.											.	ZNF160	75	.	0			c.A1538G						PASS	.						103	103	103					19																	53572249		2203	4300	6503	SO:0001583	missense	90338	exon7			CCACACTCATTAC	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.1538A>G	chr19.hg19:g.53572249T>C	ENSP00000406201:p.Glu513Gly	51.0	0.0	.		49.0	16.0	.	NM_001102603	Q14589|Q504Q8|Q96JC5|Q9BVY9|Q9H7N6	Missense_Mutation	SNP	ENST00000429604.1	hg19	CCDS12859.1	.	.	.	.	.	.	.	.	.	.	T	11.15	1.552720	0.27739	.	.	ENSG00000170949	ENST00000429604;ENST00000418871	T;T	0.07444	3.19;3.19	2.47	0.0174	0.14112	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.20780	0.0500	M	0.64080	1.96	0.09310	N	1	D	0.89917	1.0	D	0.76575	0.988	T	0.07908	-1.0748	9	0.87932	D	0	.	6.7782	0.23630	0.363:0.0:0.0:0.637	.	513	Q9HCG1	ZN160_HUMAN	G	513	ENSP00000406201:E513G;ENSP00000409597:E513G	ENSP00000409597:E513G	E	-	2	0	ZNF160	58264061	0.000000	0.05858	0.002000	0.10522	0.354000	0.29330	0.114000	0.15520	-0.237000	0.09739	0.459000	0.35465	GAG	.	.	.	none		0.403	ZNF160-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463994.2	NM_033288		C	53572249	T	C	53572249	3	2	189	1	0	0	0	0	1	0	0	0	17751	1551	54	3	922	3	ZNF160	19	53572249	Missense_Mutation	SNP	T	TCGA-GL-A59T-01A-21D-A28G-10	1075878	53572249	5556734	62	11165											
C20orf30	29058	hgsc.bcm.edu	37	chr20	5086868	5086868	+	Missense_Mutation	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	agcctgacagcaggagggagCctataataatgagaaaggcg	15	5	14	7	1	0	2	0	2	0	1	0	5	0	4	2	3	3	1	2	3	4	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr20:5086868C>T	ENST00000379286.2	-	4	608	c.188G>A	c.(187-189)gGc>gAc	p.G63D	TMEM230_ENST00000379279.2_Missense_Mutation_p.G63D|TMEM230_ENST00000379283.2_Missense_Mutation_p.G63D|TMEM230_ENST00000342308.5_Missense_Mutation_p.G126D|TMEM230_ENST00000202834.7_Missense_Mutation_p.G63D|TMEM230_ENST00000492419.1_5'UTR|TMEM230_ENST00000379277.2_Missense_Mutation_p.G63D	NM_001009924.1	NP_001009924.1	Q96A57	TM230_HUMAN	transmembrane protein 230	63						integral component of membrane (GO:0016021)											CAGGAGGGAGCCTATAATAAT	0.453																																					p.G126D		Atlas-SNP	.											.	.	.	.	0			c.G377A						PASS	.						66	66	66					20																	5086868		2203	4300	6503	SO:0001583	missense	29058	exon4			AGGGAGCCTATAA	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.188G>A	chr20.hg19:g.5086868C>T	ENSP00000368588:p.Gly63Asp	178.0	0.0	.		93.0	6.0	.	NM_001009923	B2RDM8|D3DVZ9|Q0VGC8|Q5TDS5|Q96ES2|Q9P0A7	Missense_Mutation	SNP	ENST00000379286.2	hg19	CCDS13086.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.392086	0.83011	.	.	ENSG00000089063	ENST00000379283;ENST00000342308;ENST00000379299;ENST00000202834;ENST00000379286;ENST00000379279;ENST00000379277;ENST00000379276	T	0.60299	0.2	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.80879	0.4708	M	0.90145	3.09	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.81914	0.964;0.995;0.993	D	0.84375	0.0546	10	0.87932	D	0	-27.0491	17.8394	0.88711	0.0:1.0:0.0:0.0	.	63;63;126	Q5JWB9;Q96A57;Q96A57-2	.;CT030_HUMAN;.	D	63;126;63;63;63;63;63;63	ENSP00000341364:G126D	ENSP00000202834:G63D	G	-	2	0	C20orf30	5034868	1.000000	0.71417	1.000000	0.80357	0.471000	0.32888	7.104000	0.77024	2.854000	0.98071	0.655000	0.94253	GGC	.	.	.	none		0.453	TMEM230-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077846.1			T	5086868	C	T	5086868	3	4	189	1	0	0	0	0	1	0	0	0	2112	739	26	2	182	2	C20orf30	20	5086868	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10		5086868	57938652	63	11166											
PLCB4	5332	hgsc.bcm.edu	37	chr20	9440354	9440354	+	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	cccacagtgctgaggagcaaGaaatccgagacctgcacctc	12	5	10	14	1	0	3	0	1	0	2	2	5	1	4	4	1	3	3	4	1	2	0			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr20:9440354G>A	ENST00000378493.1	+	31	3124	c.3109G>A	c.(3109-3111)Gaa>Aaa	p.E1037K	PLCB4_ENST00000278655.4_Missense_Mutation_p.E1037K|PLCB4_ENST00000378501.2_Missense_Mutation_p.E1037K|PLCB4_ENST00000334005.3_Missense_Mutation_p.E1037K|PLCB4_ENST00000414679.2_Missense_Mutation_p.E1049K|PLCB4_ENST00000378473.3_Missense_Mutation_p.E1049K|PLCB4_ENST00000492632.1_Intron			Q15147	PLCB4_HUMAN	phospholipase C, beta 4	1037					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						TGAGGAGCAAGAAATCCGAGA	0.502																																					p.E1049K		Atlas-SNP	.											.	PLCB4	204	.	0			c.G3145A						PASS	.						64	53	57					20																	9440354		2203	4300	6503	SO:0001583	missense	5332	exon34			GAGCAAGAAATCC		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.3109G>A	chr20.hg19:g.9440354G>A	ENSP00000367754:p.Glu1037Lys	72.0	0.0	.		71.0	23.0	.	NM_001172646	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	Missense_Mutation	SNP	ENST00000378493.1	hg19	CCDS13105.1	.	.	.	.	.	.	.	.	.	.	G	18.17	3.565149	0.65651	.	.	ENSG00000101333	ENST00000334005;ENST00000378473;ENST00000278655;ENST00000378493;ENST00000378501;ENST00000414679	T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96	5.51	5.51	0.81932	.	0.055638	0.64402	D	0.000001	T	0.44829	0.1312	L	0.50333	1.59	0.53688	D	0.999974	B;B;B;P	0.37824	0.042;0.021;0.083;0.609	B;B;B;P	0.44860	0.013;0.014;0.011;0.462	T	0.29027	-1.0025	10	0.35671	T	0.21	.	12.7258	0.57170	0.0753:0.0:0.9247:0.0	.	1049;884;1037;1037	E2QRH8;Q15147-2;Q15147;Q15147-4	.;.;PLCB4_HUMAN;.	K	1037;1049;1037;1037;1037;885	ENSP00000334105:E1037K;ENSP00000367734:E1049K;ENSP00000278655:E1037K;ENSP00000367754:E1037K;ENSP00000367762:E1037K;ENSP00000390616:E885K	ENSP00000278655:E1037K	E	+	1	0	PLCB4	9388354	1.000000	0.71417	0.997000	0.53966	0.965000	0.64279	7.421000	0.80204	2.578000	0.87016	0.561000	0.74099	GAA	.	.	.	none		0.502	PLCB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077948.2			A	9440354	G	A	9440354	3	1	189	1	0	0	0	0	1	0	0	0	12037	943	33	2	3271	2	PLCB4	20	9440354	Missense_Mutation	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	4353486	9440354	53585166	64	11167											
MYH7B	57644	hgsc.bcm.edu	37	chr20	33567508	33567512	+	Frame_Shift_Del	DEL	TCGCT	TCGCT	-																															ctgcagcccatgaacccgccTcgcttcgacttactggagga																								rs539864476|rs572570454	byFrequency	TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	TCGCT	TCGCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr20:33567508_33567512delTCGCT	ENST00000262873.7	+	5	461_465	c.369_373delTCGCT	c.(367-375)cctcgcttcfs	p.RF124fs		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	82	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)			TGAACCCGCCTCGCTTCGACTTACT	0.629																																					p.123_124del		Atlas-Indel,Pindel	.											.	MYH7B	145	.	0			c.368_372del						PASS	.																																			SO:0001589	frameshift_variant	57644	exon7			.	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.369_373delTCGCT	chr20.hg19:g.33567508_33567512delTCGCT	ENSP00000262873:p.Arg124fs	81.0	0.0	0		76.0	29.0	0.381579	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Frame_Shift_Del	DEL	ENST00000262873.7	hg19	CCDS42869.1																																																																																			.	.	.	none		0.629	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884		-	33567512	TCGCT	-	33567508	7	5	189	1	0	1	0	1	0	0	0	0	10047	1538	54	0	387	0	MYH7B	20	33567508	Frame_Shift_Del	DEL	TCGCT	TCGA-GL-A59T-01A-21D-A28G-10	24127154	33567508	29458012	65	11168											
APP	351	hgsc.bcm.edu	37	chr21	27328004	27328004	+	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	acatgctcgaaatgctttagGgtgtgctgtctgtccttctg	6	15	11	9	1	2	0	0	0	2	0	4	1	3	0	1	1	3	3	1	1	2	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr21:27328004G>C	ENST00000346798.3	-	12	1557	c.1524C>G	c.(1522-1524)acC>acG	p.T508T	APP_ENST00000357903.3_Silent_p.T489T|APP_ENST00000358918.3_Silent_p.T508T|APP_ENST00000359726.3_Silent_p.T452T|APP_ENST00000439274.2_Silent_p.T452T|APP_ENST00000348990.5_Silent_p.T433T|APP_ENST00000354192.3_Silent_p.T377T|APP_ENST00000440126.3_Silent_p.T484T|APP_ENST00000448388.2_Silent_p.T398T	NM_000484.3	NP_000475.1	P05067	A4_HUMAN	amyloid beta (A4) precursor protein	508	Heparin-binding.				adult locomotory behavior (GO:0008344)|axon cargo transport (GO:0008088)|axon midline choice point recognition (GO:0016199)|axonogenesis (GO:0007409)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|collateral sprouting in absence of injury (GO:0048669)|dendrite development (GO:0016358)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|ionotropic glutamate receptor signaling pathway (GO:0035235)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|mRNA polyadenylation (GO:0006378)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron differentiation (GO:0045665)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of multicellular organism growth (GO:0040014)|regulation of protein binding (GO:0043393)|regulation of synapse structure and activity (GO:0050803)|regulation of translation (GO:0006417)|response to oxidative stress (GO:0006979)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|suckling behavior (GO:0001967)|synaptic growth at neuromuscular junction (GO:0051124)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|ciliary rootlet (GO:0035253)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endosome (GO:0005768)|ER to Golgi transport vesicle (GO:0030134)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|receptor complex (GO:0043235)|spindle midzone (GO:0051233)|synapse (GO:0045202)	acetylcholine receptor binding (GO:0033130)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|peptidase activator activity (GO:0016504)|PTB domain binding (GO:0051425)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			endometrium(5)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(209;0.00295)				AATGCTTTAGGGTGTGCTGTC	0.483																																					p.T508T		Atlas-SNP	.											.	APP	90	.	0			c.C1524G						PASS	.						229	180	196					21																	27328004		2203	4300	6503	SO:0001819	synonymous_variant	351	exon12			CTTTAGGGTGTGC	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.1524C>G	chr21.hg19:g.27328004G>C		202.0	0.0	.		168.0	43.0	.	NM_000484	B2R5V1|B4DII8|D3DSD1|D3DSD2|D3DSD3|P09000|P78438|Q13764|Q13778|Q13793|Q16011|Q16014|Q16019|Q16020|Q6GSC0|Q8WZ99|Q9BT38|Q9UC33|Q9UCA9|Q9UCB6|Q9UCC8|Q9UCD1|Q9UQ58	Silent	SNP	ENST00000346798.3	hg19	CCDS13576.1	.	.	.	.	.	.	.	.	.	.	G	8.763	0.923954	0.18056	.	.	ENSG00000142192	ENST00000448850	.	.	.	5.45	3.65	0.41850	.	.	.	.	.	T	0.55970	0.1954	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50816	-0.8783	4	.	.	.	-24.9633	7.0758	0.25203	0.3229:0.0:0.6771:0.0	.	.	.	.	A	411	.	.	P	-	1	0	APP	26249875	0.782000	0.28689	0.975000	0.42487	0.811000	0.45836	-0.105000	0.10907	0.869000	0.35703	0.655000	0.94253	CCT	.	.	.	none		0.483	APP-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171340.1	NM_000484		C	27328004	G	C	27328004	2	2	189	1	0	0	0	0	0	0	0	1	815	1219	43	4		4	APP	21	27328004	Silent	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10		27328004	20801891	66	11169											
DIP2A	23181	hgsc.bcm.edu	37	chr21	47985760	47985761	+	Frame_Shift_Del	DEL	TG	TG	-																															tgggcaaggaccggctacctTggcttccttcggcgaacaga																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr21:47985760_47985761delTG	ENST00000417564.2	+	36	4320_4321	c.4299_4300delTG	c.(4297-4302)cttggcfs	p.G1434fs	DIP2A_ENST00000400274.1_Frame_Shift_Del_p.G1430fs|DIP2A_ENST00000318711.7_Frame_Shift_Del_p.G1435fs|DIP2A_ENST00000479654.1_3'UTR			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	1434					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)		CCGGCTACCTTGGCTTCCTTCG	0.614																																					p.1433_1433del		Pindel	.											.	DIP2A	332	.	0			c.4298_4299del						PASS	.																																			SO:0001589	frameshift_variant	23181	exon36			.	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.4299_4300delTG	chr21.hg19:g.47985760_47985761delTG	ENSP00000392066:p.Gly1434fs	139.0	0.0	.		117.0	27.0	0.231	NM_015151	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Frame_Shift_Del	DEL	ENST00000417564.2	hg19	CCDS46655.1																																																																																			.	.	.	none		0.614	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151		-	47985761	TG	-	47985760	7	5	189	1	0	1	0	1	0	0	0	0	4529	1799	63	0	4554	0	DIP2A	21	47985760	Frame_Shift_Del	DEL	TG	TCGA-GL-A59T-01A-21D-A28G-10	20657756	47985760	144135	67	11170											
ARVCF	421	hgsc.bcm.edu	37	chr22	19967613	19967613	+	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	cccgccagcgcggctccttgCgggcgctatccactgagggc	4	6	14	17	5	0	1	0	1	0	0	2	1	2	1	4	3	2	2	4	3	1	2	rs376884775		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr22:19967613C>A	ENST00000263207.3	-	6	1340	c.1049G>T	c.(1048-1050)cGc>cTc	p.R350L	ARVCF_ENST00000344269.3_Missense_Mutation_p.R287L|ARVCF_ENST00000406259.1_Missense_Mutation_p.R350L|ARVCF_ENST00000401994.1_Missense_Mutation_p.R287L|ARVCF_ENST00000487793.1_5'Flank|ARVCF_ENST00000406522.1_Missense_Mutation_p.R287L	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	350					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)					CGGCTCCTTGCGGGCGCTATC	0.726																																					p.R350L		Atlas-SNP	.											.	ARVCF	54	.	0			c.G1049T						PASS	.						5	7	6					22																	19967613		2043	3993	6036	SO:0001583	missense	421	exon6			TCCTTGCGGGCGC		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.1049G>T	chr22.hg19:g.19967613C>A	ENSP00000263207:p.Arg350Leu	51.0	0.0	.		34.0	14.0	.	NM_001670	B7WNV2	Missense_Mutation	SNP	ENST00000263207.3	hg19	CCDS13771.1	.	.	.	.	.	.	.	.	.	.	C	32	5.120544	0.94385	.	.	ENSG00000099889	ENST00000263207;ENST00000344269;ENST00000401994;ENST00000406522;ENST00000406259	T;T;T;T;T	0.69435	-0.4;-0.34;-0.34;-0.34;-0.4	5.35	4.33	0.51752	Armadillo-like helical (1);	0.049736	0.85682	D	0.000000	T	0.61788	0.2375	L	0.38838	1.175	0.80722	D	1	P	0.49090	0.919	P	0.46850	0.529	T	0.60747	-0.7202	9	.	.	.	-18.2472	14.2537	0.66038	0.0:0.9281:0.0:0.0719	.	350	O00192	ARVC_HUMAN	L	350;287;287;287;350	ENSP00000263207:R350L;ENSP00000342042:R287L;ENSP00000384341:R287L;ENSP00000384732:R287L;ENSP00000385444:R350L	.	R	-	2	0	ARVCF	18347613	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.598000	0.67585	1.406000	0.46857	0.655000	0.94253	CGC	.	.	.	alt		0.726	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670		A	19967613	C	A	19967613	3	1	189	1	0	0	0	0	1	0	0	0	1003	768	27	4	1895	4	ARVCF	22	19967613	Missense_Mutation	SNP	C	TCGA-GL-A59T-01A-21D-A28G-10		19967613	31336953	68	11171											
CACNA1I	8911	hgsc.bcm.edu	37	chr22	40055466	40055466	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatgcatatttttggctgcAagttcagcctccgcacggac	8	11	11	11	2	1	0	1	0	0	0	2	2	2	2	2	3	3	5	2	3	2	4			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr22:40055466A>G	ENST00000402142.3	+	13	2359	c.2359A>G	c.(2359-2361)Aag>Gag	p.K787E	CACNA1I_ENST00000407673.1_Missense_Mutation_p.K752E|CACNA1I_ENST00000400164.3_Missense_Mutation_p.K752E|CACNA1I_ENST00000404898.1_Missense_Mutation_p.K752E|CACNA1I_ENST00000336649.4_Missense_Mutation_p.K793E|CACNA1I_ENST00000401624.1_Missense_Mutation_p.K787E	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	787					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	TTTTGGCTGCAAGTTCAGCCT	0.552																																					p.K787E		Atlas-SNP	.											.	CACNA1I	264	.	0			c.A2359G						PASS	.						51	52	52					22																	40055466		2095	4208	6303	SO:0001583	missense	8911	exon13			GGCTGCAAGTTCA	AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.2359A>G	chr22.hg19:g.40055466A>G	ENSP00000385019:p.Lys787Glu	222.0	0.0	.		179.0	64.0	.	NM_021096	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Missense_Mutation	SNP	ENST00000402142.3	hg19	CCDS46710.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.813895	0.90790	.	.	ENSG00000100346	ENST00000402142;ENST00000404898;ENST00000401624;ENST00000407673;ENST00000336649;ENST00000400164	D;D;D;D;D;D	0.98400	-4.91;-4.91;-4.91;-4.91;-4.91;-4.91	4.3	4.3	0.51218	Ion transport (1);	0.048588	0.85682	D	0.000000	D	0.98544	0.9514	M	0.69185	2.1	0.58432	D	0.999994	D;D;D;D	0.76494	0.999;0.998;0.999;0.999	D;D;D;D	0.85130	0.995;0.948;0.997;0.996	D	0.99593	1.0976	10	0.87932	D	0	.	13.8843	0.63699	1.0:0.0:0.0:0.0	.	752;787;752;787	Q9P0X4-3;Q9P0X4-2;Q9P0X4-4;Q9P0X4	.;.;.;CAC1I_HUMAN	E	787;752;787;752;793;752	ENSP00000385019:K787E;ENSP00000384093:K752E;ENSP00000383887:K787E;ENSP00000385680:K752E;ENSP00000337829:K793E;ENSP00000383028:K752E	ENSP00000337829:K793E	K	+	1	0	CACNA1I	38385412	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.849000	0.92178	1.920000	0.55613	0.459000	0.35465	AAG	.	.	.	none		0.552	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406		G	40055466	A	G	40055466	3	3	189	1	0	0	0	0	1	0	0	0	2548	131	5	3	2409	3	CACNA1I	22	40055466	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	20087853	40055466	11249100	69	11172											
WNT7B	7477	hgsc.bcm.edu	37	chr22	46319111	46319112	+	Frame_Shift_Ins	INS	-	-	C																															acttctccttcagcaggtggINScccacctctcggaacttggg																										TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr22:46319111_46319112insC	ENST00000339464.4	-	4	1048_1049	c.674_675insG	c.(673-675)ggcfs	p.G225fs	WNT7B_ENST00000409496.3_Frame_Shift_Ins_p.G229fs|WNT7B_ENST00000410089.1_Frame_Shift_Ins_p.G209fs	NM_058238.2	NP_478679.1	P56706	WNT7B_HUMAN	wingless-type MMTV integration site family, member 7B	225					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)		TCAGCAGGTGGCCCACCTCTCG	0.649																																					p.G225fs		Atlas-INDEL	.											.	WNT7B	45	.	0			c.675_676insG						PASS	.																																			SO:0001589	frameshift_variant	7477	exon4			.	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.675dupG	chr22.hg19:g.46319114_46319114dupC	ENSP00000341032:p.Gly225fs	164.0	0.0	0		184.0	14.0	0.076087	NM_058238	B8A596|Q96Q12	Frame_Shift_Ins	INS	ENST00000339464.4	hg19	CCDS33667.1																																																																																			.	.	.	none		0.649	WNT7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336418.1	NM_058238		C	46319112	-	C	46319111	7	5	189	1	0	1	1	0	0	0	0	0	17407	1190	42	0	378	0	WNT7B	22	46319111	Frame_Shift_Ins	INS	-	TCGA-GL-A59T-01A-21D-A28G-10	6263645	46319111	4985455	70	11173											
PKDREJ	10343	hgsc.bcm.edu	37	chr22	46654194	46654194	+	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	gcctcggattcggacgatctGgtcatgtatcctctgcattt	6	14	10	11	3	3	0	1	0	2	0	6	3	4	2	2	3	1	2	2	3	1	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr22:46654194G>A	ENST00000253255.5	-	1	5025	c.5026C>T	c.(5026-5028)Cag>Tag	p.Q1676*		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	1676					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)		CGGACGATCTGGTCATGTATC	0.418																																					p.Q1676X		Atlas-SNP	.											.	PKDREJ	195	.	0			c.C5026T						PASS	.						200	166	178					22																	46654194		2203	4300	6503	SO:0001587	stop_gained	10343	exon1			CGATCTGGTCATG	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.5026C>T	chr22.hg19:g.46654194G>A	ENSP00000253255:p.Gln1676*	68.0	0.0	.		66.0	27.0	.	NM_006071	B1AJY3|O95850	Nonsense_Mutation	SNP	ENST00000253255.5	hg19	CCDS14073.1	.	.	.	.	.	.	.	.	.	.	g	42	9.331670	0.99138	.	.	ENSG00000130943	ENST00000253255	.	.	.	4.95	-3.76	0.04359	.	1.756340	0.02965	N	0.143633	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	-0.9396	3.1764	0.06570	0.1516:0.388:0.2844:0.1761	.	.	.	.	X	1676	.	ENSP00000253255:Q1676X	Q	-	1	0	PKDREJ	45032858	0.000000	0.05858	0.000000	0.03702	0.449000	0.32228	0.053000	0.14184	-0.308000	0.08792	0.298000	0.19748	CAG	.	.	.	none		0.418	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		A	46654194	G	A	46654194	4	1	189	1	0	0	0	0	0	1	0	0	11977	1357	47	2	1739	2	PKDREJ	22	46654194	Nonsense_Mutation	SNP	G	TCGA-GL-A59T-01A-21D-A28G-10	335083	46654194	4650372	71	11174											
TTC38	55020	hgsc.bcm.edu	37	chr22	46677589	46677589	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaaggatgggttggaattcAtgcagcactcagagaccttc	11	10	11	9	0	3	1	3	0	0	1	4	4	3	3	1	3	2	3	1	3	2	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr22:46677589A>G	ENST00000381031.3	+	7	785	c.709A>G	c.(709-711)Atg>Gtg	p.M237V	TTC38_ENST00000445282.2_Missense_Mutation_p.M179V	NM_017931.2	NP_060401	Q5R3I4	TTC38_HUMAN	tetratricopeptide repeat domain 38	237						extracellular vesicular exosome (GO:0070062)				endometrium(4)|large_intestine(3)|lung(4)|ovary(1)	12						GTTGGAATTCATGCAGCACTC	0.512																																					p.M237V		Atlas-SNP	.											.	TTC38	40	.	0			c.A709G						PASS	.						125	128	127					22																	46677589		2092	4220	6312	SO:0001583	missense	55020	exon7			GAATTCATGCAGC		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.709A>G	chr22.hg19:g.46677589A>G	ENSP00000370419:p.Met237Val	116.0	0.0	.		88.0	31.0	.	NM_017931	Q8WV27|Q9NWP8	Missense_Mutation	SNP	ENST00000381031.3	hg19	CCDS43030.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.079821	0.76528	.	.	ENSG00000075234	ENST00000381031;ENST00000445282	T;T	0.75704	1.62;-0.96	5.79	5.79	0.91817	Tetratricopeptide-like helical (1);	0.072520	0.85682	D	0.000000	D	0.84320	0.5446	M	0.79693	2.465	0.58432	D	0.999992	D;D	0.62365	0.991;0.962	P;P	0.59171	0.853;0.523	D	0.84956	0.0874	10	0.42905	T	0.14	-12.5636	15.3166	0.74085	1.0:0.0:0.0:0.0	.	179;237	E7ES35;Q5R3I4	.;TTC38_HUMAN	V	237;179	ENSP00000370419:M237V;ENSP00000393960:M179V	ENSP00000370419:M237V	M	+	1	0	TTC38	45056253	1.000000	0.71417	1.000000	0.80357	0.785000	0.44390	4.319000	0.59197	2.207000	0.71202	0.533000	0.62120	ATG	.	.	.	none		0.512	TTC38-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318469.1	NM_017931		G	46677589	A	G	46677589	3	3	189	1	0	0	0	0	1	0	0	0	16718	217	8	3	735	3	TTC38	22	46677589	Missense_Mutation	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	23395	46677589	4626977	72	11175											
WWC3	55841	hgsc.bcm.edu	37	chrX	10062249	10062249	+	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	gtggacttccctcaccatgtAggcgtgcctggcgatgctgg	5	10	14	12	2	1	0	1	0	0	0	2	2	2	1	3	4	2	2	3	4	1	2			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chrX:10062249A>T	ENST00000380861.4	+	7	976	c.585A>T	c.(583-585)gtA>gtT	p.V195V	WWC3_ENST00000454666.1_Silent_p.V195V	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	195					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						CTCACCATGTAGGCGTGCCTG	0.577																																					p.V195V		Atlas-SNP	.											.	WWC3	142	.	0			c.A585T						PASS	.						144	125	132					X																	10062249		2203	4300	6503	SO:0001819	synonymous_variant	55841	exon7			CCATGTAGGCGTG	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.585A>T	chrX.hg19:g.10062249A>T		92.0	0.0	.		80.0	8.0	.	NM_015691	A8KA96|Q659C1|Q9BTQ1	Silent	SNP	ENST00000380861.4	hg19	CCDS14136.1																																																																																			.	.	.	none		0.577	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691		T	10062249	A	T	10062249	2	4	189	1	0	0	0	0	0	0	0	1	17425	407	15	5		5	WWC3	23	10062249	Silent	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10		10062249	145208311	73	11176											
HUWE1	10075	hgsc.bcm.edu	37	chrX	53584383	53584383	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtcatttgacttagatgcAgtacactgcaaaaagaaggg	15	9	11	6	0	1	3	1	1	0	2	1	4	1	3	0	1	3	3	0	1	5	3			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chrX:53584383A>G	ENST00000342160.3	-	59	8623	c.8166T>C	c.(8164-8166)acT>acC	p.T2722T	MIR98_ENST00000606724.1_RNA|MIRLET7F2_ENST00000385277.1_RNA|HUWE1_ENST00000262854.6_Silent_p.T2722T			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	2722					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						ACTTAGATGCAGTACACTGCA	0.428																																					p.T2722T		Atlas-SNP	.											.	HUWE1	724	.	0			c.T8166C						PASS	.						137	122	127					X																	53584383		2203	4300	6503	SO:0001819	synonymous_variant	10075	exon60			AGATGCAGTACAC	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.8166T>C	chrX.hg19:g.53584383A>G		53.0	0.0	.		41.0	31.0	.	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Silent	SNP	ENST00000342160.3	hg19	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	A	8.337	0.827732	0.16749	.	.	ENSG00000086758	ENST00000427052	.	.	.	5.64	0.708	0.18144	.	.	.	.	.	T	0.22126	0.0533	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.22695	-1.0209	4	.	.	.	.	3.0889	0.06286	0.3857:0.0:0.3048:0.3095	.	.	.	.	R	1756	.	.	C	-	1	0	HUWE1	53601108	0.001000	0.12720	0.177000	0.23020	0.915000	0.54546	0.717000	0.25851	0.266000	0.21894	0.486000	0.48141	TGC	.	.	.	none		0.428	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		G	53584383	A	G	53584383	2	3	189	1	0	0	0	0	0	0	0	1	7468	175	7	3		3	HUWE1	23	53584383	Silent	SNP	A	TCGA-GL-A59T-01A-21D-A28G-10	43522134	53584383	101686177	74	11177											
KIAA0562	9731	hgsc.bcm.edu	37	chr1	3742942	3742942	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcgcgacttacttatctagAtagtgctcatccgggattcc	9	12	9	11	3	2	1	1	0	1	1	4	3	4	2	2	1	3	1	2	1	4	5			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr1:3742942A>G	ENST00000378230.3	-	17	2571	c.2247T>C	c.(2245-2247)taT>taC	p.Y749Y		NM_014704.3	NP_055519.1	O60308	CE104_HUMAN	centrosomal protein 104kDa	749						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						ACTTATCTAGATAGTGCTCAT	0.463																																					p.Y749Y		Atlas-SNP	.											.	CEP104	79	.	0			c.T2247C						PASS	.						84	79	80					1																	3742942		2203	4300	6503	SO:0001819	synonymous_variant	9731	exon17			ATCTAGATAGTGC	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.2247T>C	chr1.hg19:g.3742942A>G		114.0	0.0	.		113.0	48.0	.	NM_014704	Q5JSQ3|Q5SR24|Q5SR25|Q6PKF5|Q86W32|Q86X14	Silent	SNP	ENST00000378230.3	hg19	CCDS30571.1	.	.	.	.	.	.	.	.	.	.	A	0.033	-1.320509	0.01320	.	.	ENSG00000116198	ENST00000438539	.	.	.	4.52	-0.637	0.11504	.	.	.	.	.	T	0.31451	0.0797	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.30822	-0.9965	4	.	.	.	.	7.5619	0.27855	0.5592:0.0:0.4408:0.0	.	.	.	.	T	46	.	.	I	-	2	0	CEP104	3732802	0.000000	0.05858	0.001000	0.08648	0.188000	0.23474	-0.889000	0.04144	-0.294000	0.08973	-0.408000	0.06270	ATC	.	.	.	none		0.463	CEP104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009747.3	NM_014704		G	3742942	A	G	3742942	2	3	190	1	0	0	0	0	0	0	0	1	8191	340	12	3		3	KIAA0562	1	3742942	Silent	SNP	A	TCGA-GL-A9DC-01A-11D-A36X-10		3742942	245507679	1	11178											
PRAMEF2	65122	hgsc.bcm.edu	37	chr1	12918882	12918890	+	In_Frame_Del	DEL	ACCGAGACT	ACCGAGACT	-																															aggatgagcatccaggccccAccgagactactggagctggc																								rs149417814|rs17404792|rs138447851	byFrequency	TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	ACCGAGACT	ACCGAGACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr1:12918882_12918890delACCGAGACT	ENST00000240189.2	+	2	105_113	c.18_26delACCGAGACT	c.(16-27)ccaccgagacta>cca	p.PRL7del		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	7					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)		TCCAGGCCCCACCGAGACTACTGGAGCTG	0.55																																					p.6_9del		Atlas-Indel,Pindel	.											.	PRAMEF2	85	.	0			c.17_25del						PASS	.																																			SO:0001651	inframe_deletion	65122	exon2			.		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.18_26delACCGAGACT	chr1.hg19:g.12918882_12918890delACCGAGACT	ENSP00000240189:p.Pro7_Leu9del	179.0	0.0	0		208.0	73.0	0.350962	NM_023014		In_Frame_Del	DEL	ENST00000240189.2	hg19	CCDS149.1																																																																																			.	.	.	none		0.55	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014		-	12918890	ACCGAGACT	-	12918882	7	5	190	1	0	1	0	1	0	0	0	0	12445	146	6	0	20	0	PRAMEF2	1	12918882	In_Frame_Del	DEL	ACCGAGACT	TCGA-GL-A9DC-01A-11D-A36X-10	9175940	12918882	236331739	2	11179											
SFPQ	6421	hgsc.bcm.edu	37	chr1	35650120	35650120	+	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	cctctaccatatcctgctggAgttccaggccccattcctct	6	12	6	17	0	2	0	0	0	2	0	5	1	5	1	7	2	2	2	7	2	2	4			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr1:35650120A>T	ENST00000357214.5	-	10	2159	c.2061T>A	c.(2059-2061)acT>acA	p.T687T		NM_005066.2	NP_005057.1	P23246	SFPQ_HUMAN	splicing factor proline/glutamine-rich	687					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)				ATCCTGCTGGAGTTCCAGGCC	0.488			T	TFE3	papillary renal cell																																p.T687T		Atlas-SNP	.		Dom	yes		1	1p34.3	6421	splicing factor proline/glutamine rich(polypyrimidine tract binding protein associated)		E	.	SFPQ	51	.	0			c.T2061A						PASS	.						128	127	128					1																	35650120		2203	4300	6503	SO:0001819	synonymous_variant	6421	exon10			TGCTGGAGTTCCA	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.2061T>A	chr1.hg19:g.35650120A>T		100.0	0.0	.		114.0	53.0	.	NM_005066	P30808|Q5SZ71	Silent	SNP	ENST00000357214.5	hg19	CCDS388.1																																																																																			.	.	.	none		0.488	SFPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011984.4	NM_005066		T	35650120	A	T	35650120	2	4	190	1	0	0	0	0	0	0	0	1	14173	291	11	5		5	SFPQ	1	35650120	Silent	SNP	A	TCGA-GL-A9DC-01A-11D-A36X-10	22731238	35650120	213600501	3	11180											
ZMPSTE24	10269	hgsc.bcm.edu	37	chr1	40724001	40724001	+	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	tgccggccgagaagcgtatcTtcggggccgtgctgctcttt	4	11	14	12	5	2	1	0	0	2	1	3	2	2	1	3	3	4	3	3	3	2	3			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr1:40724001T>A	ENST00000372759.3	+	1	223	c.58T>A	c.(58-60)Ttc>Atc	p.F20I	RP1-39G22.7_ENST00000567508.1_RNA|ZMPSTE24_ENST00000479131.1_3'UTR	NM_005857.4	NP_005848.2	O75844	FACE1_HUMAN	zinc metallopeptidase STE24	20					CAAX-box protein processing (GO:0071586)|nuclear envelope organization (GO:0006998)|prenylated protein catabolic process (GO:0030327)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metalloexopeptidase activity (GO:0008235)			endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	16	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;6.3e-18)			GAAGCGTATCTTCGGGGCCGT	0.627																																					p.F20I		Atlas-SNP	.											.	ZMPSTE24	50	.	0			c.T58A						PASS	.						123	106	112					1																	40724001		2203	4300	6503	SO:0001583	missense	10269	exon1			CGTATCTTCGGGG	Y13834	CCDS449.1	1p34	2014-09-17	2012-12-10		ENSG00000084073	ENSG00000084073	3.4.24.84		12877	protein-coding gene	gene with protein product	"Hutchinson-Gilford progeria syndrome", "CAAX prenyl protease 1 homolog"	606480	"zinc metalloproteinase (STE24 homolog, yeast)", "zinc metallopeptidase (STE24 homolog, yeast)", "zinc metallopeptidase STE24 homolog (S. cerevisiae)"			10373325, 9700155, 16671095	Standard	NM_005857		Approved	FACE-1, Ste24p, STE24, HGPS, PRO1	uc001cfg.4	O75844	OTTHUMG00000005762	ENST00000372759.3:c.58T>A	chr1.hg19:g.40724001T>A	ENSP00000361845:p.Phe20Ile	64.0	0.0	.		74.0	25.0	.	NM_005857	B3KQI7|D3DPU7|Q8NDZ8|Q9UBQ2	Missense_Mutation	SNP	ENST00000372759.3	hg19	CCDS449.1	.	.	.	.	.	.	.	.	.	.	T	36	5.971807	0.97162	.	.	ENSG00000084073	ENST00000372759	T	0.00902	5.56	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.04452	0.0122	M	0.71036	2.16	0.80722	D	1	D	0.69078	0.997	P	0.62560	0.904	T	0.36866	-0.9730	10	0.59425	D	0.04	-16.1505	15.3325	0.74226	0.0:0.0:0.0:1.0	.	20	O75844	FACE1_HUMAN	I	20	ENSP00000361845:F20I	ENSP00000361845:F20I	F	+	1	0	ZMPSTE24	40496588	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	7.016000	0.76393	2.026000	0.59711	0.533000	0.62120	TTC	.	.	.	none		0.627	ZMPSTE24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015766.1			A	40724001	T	A	40724001	3	1	190	1	0	0	0	0	1	0	0	0	17710	1609	56	5	60	5	ZMPSTE24	1	40724001	Missense_Mutation	SNP	T	TCGA-GL-A9DC-01A-11D-A36X-10	5073881	40724001	208526620	4	11181											
FOXD2	2306	hgsc.bcm.edu	37	chr1	47905188	47905188	+	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	tgctgactgctccggccctgGctcccgttgctggccacatt	3	11	11	16	2	0	1	0	1	0	0	2	1	2	1	4	3	3	5	4	3	0	2			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr1:47905188G>C	ENST00000334793.5	+	1	3500	c.1381G>C	c.(1381-1383)Gct>Cct	p.A461P		NM_004474.3	NP_004465.3	O60548	FOXD2_HUMAN	forkhead box D2	461	Ala-rich.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(4)	4				READ - Rectum adenocarcinoma(2;0.0908)		TCCGGCCCTGGCTCCCGTTGC	0.721																																					p.A461P		Atlas-SNP	.											.	FOXD2	16	.	0			c.G1381C						PASS	.						5	6	5					1																	47905188		2041	4122	6163	SO:0001583	missense	2306	exon1			GCCCTGGCTCCCG	AF042832	CCDS30708.1	1p34-p32	2008-02-05			ENSG00000186564	ENSG00000186564		"Forkhead boxes"	3803	protein-coding gene	gene with protein product		602211		FKHL17		9403061, 12621056	Standard	NM_004474		Approved	FREAC9	uc001crm.3	O60548	OTTHUMG00000007950	ENST00000334793.5:c.1381G>C	chr1.hg19:g.47905188G>C	ENSP00000335493:p.Ala461Pro	53.0	0.0	.		78.0	6.0	.	NM_004474	Q5SVZ3	Missense_Mutation	SNP	ENST00000334793.5	hg19	CCDS30708.1	.	.	.	.	.	.	.	.	.	.	G	14.12	2.439685	0.43326	.	.	ENSG00000186564	ENST00000334793	T	0.57436	0.4	4.46	2.37	0.29283	.	1.733230	0.03641	U	0.239565	T	0.44850	0.1313	L	0.29908	0.895	0.32396	N	0.552538	B	0.09022	0.002	B	0.08055	0.003	T	0.46303	-0.9201	10	0.72032	D	0.01	.	9.3432	0.38093	0.2205:0.0:0.7795:0.0	.	461	O60548	FOXD2_HUMAN	P	461	ENSP00000335493:A461P	ENSP00000335493:A461P	A	+	1	0	FOXD2	47677775	1.000000	0.71417	0.993000	0.49108	0.782000	0.44232	2.417000	0.44653	1.039000	0.40074	0.561000	0.74099	GCT	.	.	.	none		0.721	FOXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021831.1	NM_004474		C	47905188	G	C	47905188	3	2	190	1	0	0	0	0	1	0	0	0	6004	1203	42	4	1383	4	FOXD2	1	47905188	Missense_Mutation	SNP	G	TCGA-GL-A9DC-01A-11D-A36X-10	7181187	47905188	201345433	5	11182											
DCST2	127579	hgsc.bcm.edu	37	chr1	155005652	155005652	+	Frame_Shift_Del	DEL	G	G	-																															ccacaggctacagcctcgctGgcccgggtgaagttgcgtag																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr1:155005652delG	ENST00000368424.3	-	2	415	c.357delC	c.(355-357)gccfs	p.A119fs	DCST1_ENST00000392480.1_5'Flank|DCST1_ENST00000368419.2_5'Flank|DCST1_ENST00000423025.2_5'Flank|DCST2_ENST00000295536.5_Frame_Shift_Del_p.A119fs|DCST1_ENST00000295542.1_5'Flank	NM_144622.2	NP_653223.2	Q5T1A1	DCST2_HUMAN	DC-STAMP domain containing 2	119						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)			CAGCCTCGCTGGCCCGGGTGA	0.617																																					p.S120fs		Atlas-Indel,Pindel	.											.	DCST2	80	.	0			c.358delA						PASS	.						52	50	51					1																	155005652		2203	4300	6503	SO:0001589	frameshift_variant	127579	exon2			.	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.357delC	chr1.hg19:g.155005652delG	ENSP00000357409:p.Ala119fs	204.0	0.0	0		235.0	112.0	0.476596	NM_144622	Q2M2R2|Q8N810|Q96M03	Frame_Shift_Del	DEL	ENST00000368424.3	hg19	CCDS1082.2																																																																																			.	.	.	none		0.617	DCST2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090953.3	NM_144622		-	155005652	G	-	155005652	7	5	190	1	0	1	0	1	0	0	0	0	4305	1335	47	0	2020	0	DCST2	1	155005652	Frame_Shift_Del	DEL	G	TCGA-GL-A9DC-01A-11D-A36X-10	107100464	155005652	94244969	6	11183											
BCAN	63827	hgsc.bcm.edu	37	chr1	156622136	156622136	+	Missense_Mutation	SNP	A	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	atatgaagatgaagaagagaAagaggaggaagaagaagagg	22	3	16	0	0	0	9	0	2	0	7	0	12	0	11	0	3	0	0	0	3	8	1			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr1:156622136A>C	ENST00000329117.5	+	8	1730	c.1394A>C	c.(1393-1395)aAa>aCa	p.K465T	BCAN_ENST00000361588.5_Missense_Mutation_p.K465T|RP11-284F21.7_ENST00000448869.1_RNA	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	465	Glu-rich.				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)					gaagaagagaaagaggaggaa	0.542																																					p.K465T		Atlas-SNP	.											.	BCAN	174	.	0			c.A1394C						PASS	.						26	26	26					1																	156622136		2203	4300	6503	SO:0001583	missense	63827	exon8			AAGAGAAAGAGGA	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.1394A>C	chr1.hg19:g.156622136A>C	ENSP00000331210:p.Lys465Thr	118.0	0.0	.		126.0	63.0	.	NM_198427	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Missense_Mutation	SNP	ENST00000329117.5	hg19	CCDS1149.1	.	.	.	.	.	.	.	.	.	.	A	0.144	-1.098712	0.01843	.	.	ENSG00000132692	ENST00000255029;ENST00000329117;ENST00000361588	T;T	0.14766	2.48;3.22	3.69	-0.137	0.13469	.	3.115980	0.01588	N	0.021411	T	0.01765	0.0056	N	0.14661	0.345	0.09310	N	1	B;B	0.26400	0.148;0.0	B;B	0.24155	0.051;0.001	T	0.33548	-0.9864	10	0.11485	T	0.65	0.0752	3.617	0.08081	0.3722:0.3192:0.0:0.3087	.	465;465	Q96GW7;Q96GW7-2	PGCB_HUMAN;.	T	404;465;465	ENSP00000331210:K465T;ENSP00000354925:K465T	ENSP00000255029:K404T	K	+	2	0	BCAN	154888760	0.005000	0.15991	0.003000	0.11579	0.429000	0.31625	0.189000	0.17037	-0.229000	0.09854	0.454000	0.30748	AAA	.	.	.	none		0.542	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948		C	156622136	A	C	156622136	3	2	190	1	0	0	0	0	1	0	0	0	1345	14	1	5	1420	5	BCAN	1	156622136	Missense_Mutation	SNP	A	TCGA-GL-A9DC-01A-11D-A36X-10	1616484	156622136	92628485	7	11184											
LAMC1	3915	hgsc.bcm.edu	37	chr1	183090998	183090998	+	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	gcctctcaggttacagaagaGaaactcctaatcttggacca	13	9	8	11	0	2	2	1	0	2	2	4	4	3	3	3	2	2	1	3	2	4	3			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr1:183090998G>A	ENST00000258341.4	+	12	2388	c.2131G>A	c.(2131-2133)Gaa>Aaa	p.E711K		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	711	Laminin EGF-like 5; second part. {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						TTACAGAAGAGAAACTCCTAA	0.532																																					p.E711K		Atlas-SNP	.											.	LAMC1	176	.	0			c.G2131A						PASS	.						171	152	159					1																	183090998		2203	4300	6503	SO:0001583	missense	3915	exon12			AGAAGAGAAACTC	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.2131G>A	chr1.hg19:g.183090998G>A	ENSP00000258341:p.Glu711Lys	53.0	0.0	.		69.0	33.0	.	NM_002293	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	hg19	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	G	18.95	3.731851	0.69189	.	.	ENSG00000135862	ENST00000258341	T	0.30182	1.54	5.17	5.17	0.71159	EGF-like, laminin (1);	0.309234	0.36444	N	0.002581	T	0.38931	0.1059	M	0.84846	2.72	0.48632	D	0.999681	P	0.44627	0.839	B	0.39379	0.298	T	0.48198	-0.9056	10	0.10636	T	0.68	.	18.6846	0.91559	0.0:0.0:1.0:0.0	.	711	P11047	LAMC1_HUMAN	K	711	ENSP00000258341:E711K	ENSP00000258341:E711K	E	+	1	0	LAMC1	181357621	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.571000	0.53841	2.402000	0.81655	0.655000	0.94253	GAA	.	.	.	none		0.532	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293		A	183090998	G	A	183090998	3	1	190	1	0	0	0	0	1	0	0	0	8621	943	33	2	2177	2	LAMC1	1	183090998	Missense_Mutation	SNP	G	TCGA-GL-A9DC-01A-11D-A36X-10	26468862	183090998	66159623	8	11185											
PLXNA2	5362	hgsc.bcm.edu	37	chr1	208390905	208390905	+	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	gccagcaggcggttctcagaGtagtcaatgatgagcagctt	10	9	13	9	1	2	3	2	2	1	1	3	3	2	3	1	2	3	5	1	2	2	3			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr1:208390905G>A	ENST00000367033.3	-	2	1120	c.363C>T	c.(361-363)taC>taT	p.Y121Y		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	121	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		GGTTCTCAGAGTAGTCAATGA	0.572																																					p.Y121Y		Atlas-SNP	.											.	PLXNA2	178	.	0			c.C363T						PASS	.						102	105	104					1																	208390905		2203	4300	6503	SO:0001819	synonymous_variant	5362	exon2			CTCAGAGTAGTCA	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.363C>T	chr1.hg19:g.208390905G>A		125.0	0.0	.		144.0	69.0	.	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Silent	SNP	ENST00000367033.3	hg19	CCDS31013.1																																																																																			.	.	.	none		0.572	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		A	208390905	G	A	208390905	2	1	190	1	0	0	0	0	0	0	0	1	12127	1024	36	2		2	PLXNA2	1	208390905	Silent	SNP	G	TCGA-GL-A9DC-01A-11D-A36X-10	25299907	208390905	40859716	9	11186											
KCNH1	3756	hgsc.bcm.edu	37	chr1	211093156	211093156	+	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	gccagacccattaaactggtAaggggtgccaatgtccatcg	11	8	11	11	1	0	1	0	0	0	1	2	1	1	1	4	3	2	1	4	3	4	2			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr1:211093156A>T	ENST00000271751.4	-	7	1315	c.1288T>A	c.(1288-1290)Tac>Aac	p.Y430N	KCNH1_ENST00000367007.4_Missense_Mutation_p.Y403N			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	430					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)		TTAAACTGGTAAGGGGTGCCA	0.507																																					p.Y430N		Atlas-SNP	.											.	KCNH1	199	.	0			c.T1288A						PASS	.						190	169	176					1																	211093156		2203	4300	6503	SO:0001583	missense	3756	exon7			ACTGGTAAGGGGT	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.1288T>A	chr1.hg19:g.211093156A>T	ENSP00000271751:p.Tyr430Asn	224.0	0.0	.		214.0	108.0	.	NM_172362	B1AQ26|O76035|Q14CL3	Missense_Mutation	SNP	ENST00000271751.4	hg19	CCDS1496.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.521034	0.85495	.	.	ENSG00000143473	ENST00000271751;ENST00000367007	D;D	0.99186	-5.44;-5.53	5.8	5.8	0.92144	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99130	0.9700	M	0.76574	2.34	0.80722	D	1	D;D	0.58970	0.984;0.984	D;D	0.68483	0.958;0.958	D	0.99651	1.0991	10	0.87932	D	0	.	15.3272	0.74176	1.0:0.0:0.0:0.0	.	403;430	Q14CL3;O95259	.;KCNH1_HUMAN	N	430;403	ENSP00000271751:Y430N;ENSP00000355974:Y403N	ENSP00000271751:Y430N	Y	-	1	0	KCNH1	209159779	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.999000	0.93557	2.219000	0.72066	0.533000	0.62120	TAC	.	.	.	none		0.507	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238		T	211093156	A	T	211093156	3	4	190	1	0	0	0	0	1	0	0	0	8038	362	13	5	1701	5	KCNH1	1	211093156	Missense_Mutation	SNP	A	TCGA-GL-A9DC-01A-11D-A36X-10	2702251	211093156	38157465	10	11187											
PTPN14	5784	hgsc.bcm.edu	37	chr1	214588010	214588010	+	Frame_Shift_Del	DEL	A	A	-																															ctagccgaatcacctggtccAatgtacatcgtaatcgccct																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr1:214588010delA	ENST00000366956.5	-	4	598	c.404delT	c.(403-405)ttgfs	p.L135fs	PTPN14_ENST00000543945.1_Frame_Shift_Del_p.L135fs	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	135	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)			NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		CACCTGGTCCAATGTACATCG	0.423																																					p.L135fs	Colon(92;557 1424 24372 34121 40073)	Atlas-Indel,Pindel	.											.	PTPN14	168	.	0			c.405delG						PASS	.						287	259	269					1																	214588010		2203	4300	6503	SO:0001589	frameshift_variant	5784	exon4			.	X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.404delT	chr1.hg19:g.214588010delA	ENSP00000355923:p.Leu135fs	80.0	0.0	0		76.0	34.0	0.447368	NM_005401	Q5VSI0	Frame_Shift_Del	DEL	ENST00000366956.5	hg19	CCDS1514.1																																																																																			.	.	.	none		0.423	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401		-	214588010	A	-	214588010	7	5	190	1	0	1	0	1	0	0	0	0	12794	131	5	0	3223	0	PTPN14	1	214588010	Frame_Shift_Del	DEL	A	TCGA-GL-A9DC-01A-11D-A36X-10	3494854	214588010	34662611	11	11188											
TMEM63A	9725	hgsc.bcm.edu	37	chr1	226050526	226050526	+	Missense_Mutation	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	gtagcacagctgcacatcaaCcacctcacacgtgggatacg	12	6	9	14	2	2	0	2	0	0	0	2	1	2	1	2	1	5	4	2	1	3	2			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr1:226050526C>T	ENST00000366835.3	-	11	1042	c.772G>A	c.(772-774)Gtt>Att	p.V258I	TMEM63A_ENST00000474478.1_5'UTR|TMEM63A_ENST00000537914.1_5'UTR	NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	258					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)					TGCACATCAACCACCTCACAC	0.577																																					p.V258I		Atlas-SNP	.											.	TMEM63A	75	.	0			c.G772A						PASS	.						109	78	88					1																	226050526		2203	4300	6503	SO:0001583	missense	9725	exon11			CATCAACCACCTC		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.772G>A	chr1.hg19:g.226050526C>T	ENSP00000355800:p.Val258Ile	134.0	0.0	.		187.0	67.0	.	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Missense_Mutation	SNP	ENST00000366835.3	hg19	CCDS31042.1	.	.	.	.	.	.	.	.	.	.	C	7.629	0.678465	0.14841	.	.	ENSG00000196187	ENST00000366835	T	0.44482	0.92	5.84	4.91	0.64330	Nucleotide-binding, alpha-beta plait (1);	0.632722	0.17914	N	0.157757	T	0.39009	0.1062	L	0.48362	1.52	0.80722	D	1	B	0.20550	0.046	B	0.17098	0.017	T	0.13710	-1.0499	10	0.38643	T	0.18	-16.8033	15.0439	0.71813	0.0:0.7315:0.2685:0.0	.	258	O94886	TM63A_HUMAN	I	258	ENSP00000355800:V258I	ENSP00000355800:V258I	V	-	1	0	TMEM63A	224117149	0.573000	0.26676	1.000000	0.80357	0.258000	0.26162	0.886000	0.28241	1.448000	0.47680	0.561000	0.74099	GTT	.	.	.	none		0.577	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698		T	226050526	C	T	226050526	3	4	190	1	0	0	0	0	1	0	0	0	16202	507	18	2	1707	2	TMEM63A	1	226050526	Missense_Mutation	SNP	C	TCGA-GL-A9DC-01A-11D-A36X-10	11462516	226050526	23200095	12	11189											
NCOA1	8648	hgsc.bcm.edu	37	chr2	24930212	24930212	+	Frame_Shift_Del	DEL	A	A	-																															gactttcagatggagacagtAaatactctcaaaccagtcac																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr2:24930212delA	ENST00000406961.1	+	13	2525	c.1873delA	c.(1873-1875)aaafs	p.K625fs	NCOA1_ENST00000395856.3_Frame_Shift_Del_p.K625fs|NCOA1_ENST00000288599.5_Frame_Shift_Del_p.K625fs|NCOA1_ENST00000538539.1_Frame_Shift_Del_p.K625fs|NCOA1_ENST00000405141.1_Frame_Shift_Del_p.K625fs|NCOA1_ENST00000348332.3_Frame_Shift_Del_p.K625fs|NCOA1_ENST00000407230.1_Frame_Shift_Del_p.K474fs			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	625	Ser-rich.				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)					TGGAGACAGTAAATACTCTCA	0.418			T	PAX3	alveolar rhadomyosarcoma																																p.S624fs		Atlas-Indel,Pindel	.		Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	NCOA1	210	.	0			c.1872delT						PASS	.						52	50	51					2																	24930212		2203	4300	6503	SO:0001589	frameshift_variant	8648	exon11			.	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.1873delA	chr2.hg19:g.24930212delA	ENSP00000385216:p.Lys625fs	204.0	0.0	0		206.0	78.0	0.378641	NM_147223	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Frame_Shift_Del	DEL	ENST00000406961.1	hg19	CCDS1712.1																																																																																			.	.	.	none		0.418	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223		-	24930212	A	-	24930212	7	5	190	1	0	1	0	1	0	0	0	0	10235	363	13	0	1907	0	NCOA1	2	24930212	Frame_Shift_Del	DEL	A	TCGA-GL-A9DC-01A-11D-A36X-10		24930212	218269161	13	11190											
PLEKHH2	130271	hgsc.bcm.edu	37	chr2	43986044	43986044	+	Missense_Mutation	SNP	T	T	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	tttctttttttttaggcagcTttgccagcgactttcaacca	7	18	6	10	1	2	0	1	0	1	0	2	1	2	0	2	1	4	2	2	1	2	8			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr2:43986044T>G	ENST00000282406.4	+	27	4057	c.3947T>G	c.(3946-3948)cTt>cGt	p.L1316R		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	1316	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				tttAGGCAGCTTTGCCAGCGA	0.423																																					p.L1316R		Atlas-SNP	.											.	PLEKHH2	156	.	0			c.T3947G						PASS	.						36	35	35					2																	43986044		2203	4300	6503	SO:0001583	missense	130271	exon27			GGCAGCTTTGCCA	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.3947T>G	chr2.hg19:g.43986044T>G	ENSP00000282406:p.Leu1316Arg	55.0	0.0	.		50.0	26.0	.	NM_172069	Q5JPJ6|Q6P4Q1|Q8N3Q3	Missense_Mutation	SNP	ENST00000282406.4	hg19	CCDS1812.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.580076	0.86645	.	.	ENSG00000152527	ENST00000282406	T	0.81415	-1.49	5.66	5.66	0.87406	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	0.89976	0.6871	M	0.81497	2.545	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91227	0.5011	10	0.72032	D	0.01	-17.0245	15.8843	0.79232	0.0:0.0:0.0:1.0	.	1316	Q8IVE3	PKHH2_HUMAN	R	1316	ENSP00000282406:L1316R	ENSP00000282406:L1316R	L	+	2	0	PLEKHH2	43839548	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	7.698000	0.84413	2.164000	0.68074	0.533000	0.62120	CTT	.	.	.	none		0.423	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069		G	43986044	T	G	43986044	3	3	190	1	0	0	0	0	1	0	0	0	12084	1609	56	5	4049	5	PLEKHH2	2	43986044	Missense_Mutation	SNP	T	TCGA-GL-A9DC-01A-11D-A36X-10	19055832	43986044	199213329	14	11191											
EPAS1	2034	hgsc.bcm.edu	37	chr2	46605215	46605215	+	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	gtgccaccagcagcagcagcAgctgctccacggtgagcagc	9	4	13	15	1	0	1	0	1	0	0	1	1	1	1	3	1	9	7	3	1	0	0			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr2:46605215A>T	ENST00000263734.3	+	10	1942	c.1432A>T	c.(1432-1434)Agc>Tgc	p.S478C		NM_001430.4	NP_001421.2	Q99814	EPAS1_HUMAN	endothelial PAS domain protein 1	478	Poly-Ser.				angiogenesis (GO:0001525)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|erythrocyte differentiation (GO:0030218)|lung development (GO:0030324)|mitochondrion organization (GO:0007005)|myoblast fate commitment (GO:0048625)|norepinephrine metabolic process (GO:0042415)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart rate (GO:0002027)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|surfactant homeostasis (GO:0043129)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|histone acetyltransferase binding (GO:0035035)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	LUSC - Lung squamous cell carcinoma(58;0.151)			CAGCAGCAGCAGCTGCTCCAC	0.652																																					p.S478C		Atlas-SNP	.											.	EPAS1	83	.	0			c.A1432T						PASS	.						10	10	10					2																	46605215		2180	4275	6455	SO:0001583	missense	2034	exon10			AGCAGCAGCTGCT	U81984	CCDS1825.1	2p21-p16	2013-05-21			ENSG00000116016	ENSG00000116016		"Basic helix-loop-helix proteins"	3374	protein-coding gene	gene with protein product	"HIF-1 alpha-like factor"	603349				9000051, 9079689, 18378852	Standard	NM_001430		Approved	MOP2, PASD2, HIF2A, HLF, bHLHe73	uc002ruv.3	Q99814	OTTHUMG00000128818	ENST00000263734.3:c.1432A>T	chr2.hg19:g.46605215A>T	ENSP00000263734:p.Ser478Cys	113.0	0.0	.		125.0	5.0	.	NM_001430	Q86VA2|Q99630	Missense_Mutation	SNP	ENST00000263734.3	hg19	CCDS1825.1	.	.	.	.	.	.	.	.	.	.	A	18.75	3.689835	0.68271	.	.	ENSG00000116016	ENST00000263734	T	0.56444	0.46	5.58	3.23	0.37069	.	0.981388	0.08371	N	0.956092	T	0.67287	0.2877	M	0.76574	2.34	0.37050	D	0.897573	D	0.62365	0.991	P	0.59288	0.855	T	0.59553	-0.7433	10	0.37606	T	0.19	.	9.6414	0.39842	0.8591:0.0:0.1409:0.0	.	478	Q99814	EPAS1_HUMAN	C	478	ENSP00000263734:S478C	ENSP00000263734:S478C	S	+	1	0	EPAS1	46458719	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	4.474000	0.60203	0.427000	0.26145	0.533000	0.62120	AGC	.	.	.	none		0.652	EPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250752.2	NM_001430		T	46605215	A	T	46605215	3	4	190	1	0	0	0	0	1	0	0	0	5152	188	7	5	1470	5	EPAS1	2	46605215	Missense_Mutation	SNP	A	TCGA-GL-A9DC-01A-11D-A36X-10	2619171	46605215	196594158	15	11192											
KCMF1	56888	hgsc.bcm.edu	37	chr2	85276536	85276536	+	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	gacgttctgcaggaggacagCttaattcctctggcccttcc	7	11	10	13	1	2	0	0	0	2	0	4	3	4	2	3	3	2	3	3	3	1	4			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr2:85276536C>A	ENST00000409785.4	+	6	1008	c.649C>A	c.(649-651)Ctt>Att	p.L217I		NM_020122.4	NP_064507.3	Q9P0J7	KCMF1_HUMAN	potassium channel modulatory factor 1	217							ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			ovary(3)	3						AGGAGGACAGCTTAATTCCTC	0.478																																					p.L217I		Atlas-SNP	.											.	KCMF1	38	.	0			c.C649A						PASS	.						111	117	115					2																	85276536		2131	4242	6373	SO:0001583	missense	56888	exon6			GGACAGCTTAATT	AF155652	CCDS46350.1	2p11.2	2010-11-23			ENSG00000176407	ENSG00000176407		"Zinc fingers, ZZ-type"	20589	protein-coding gene	gene with protein product		614719					Standard	NM_020122		Approved	DEBT91, PCMF, DKFZP434L1021, ZZZ1	uc002sox.4	Q9P0J7	OTTHUMG00000153004	ENST00000409785.4:c.649C>A	chr2.hg19:g.85276536C>A	ENSP00000386738:p.Leu217Ile	123.0	0.0	.		109.0	47.0	.	NM_020122	Q4ZG04|Q53SC7|Q9BWK2|Q9H8P5|Q9UFE8	Missense_Mutation	SNP	ENST00000409785.4	hg19	CCDS46350.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.844635	0.51164	.	.	ENSG00000176407	ENST00000409785	T	0.48522	0.81	5.96	5.96	0.96718	Drought induced 19/ RING finger protein 114 (1);	0.111308	0.64402	D	0.000008	T	0.32526	0.0832	N	0.08118	0	0.44966	D	0.997988	B	0.15930	0.015	B	0.21360	0.034	T	0.08513	-1.0718	10	0.37606	T	0.19	-15.8537	17.9158	0.88950	0.0:1.0:0.0:0.0	.	217	Q9P0J7	KCMF1_HUMAN	I	217	ENSP00000386738:L217I	ENSP00000386738:L217I	L	+	1	0	KCMF1	85130047	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.484000	0.53201	2.832000	0.97577	0.655000	0.94253	CTT	.	.	.	none		0.478	KCMF1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328942.4	NM_020122		A	85276536	C	A	85276536	3	1	190	1	0	0	0	0	1	0	0	0	8007	797	28	4	671	4	KCMF1	2	85276536	Missense_Mutation	SNP	C	TCGA-GL-A9DC-01A-11D-A36X-10	38671321	85276536	157922837	16	11193											
KDM3A	55818	hgsc.bcm.edu	37	chr2	86709141	86709141	+	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	aaatccagcacagtcctccaTacgtttaacagcacaatttt	14	11	4	12	1	0	0	0	0	0	0	3	0	3	0	3	0	4	3	3	0	4	5	rs144469383	byFrequency	TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr2:86709141T>A	ENST00000409556.1	+	18	2966	c.2601T>A	c.(2599-2601)caT>caA	p.H867Q	KDM3A_ENST00000312912.5_Missense_Mutation_p.H867Q|KDM3A_ENST00000409064.1_Missense_Mutation_p.H867Q|KDM3A_ENST00000542128.1_Missense_Mutation_p.H815Q			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	867					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						CAGTCCTCCATACGTTTAACA	0.383																																					p.H867Q	NSCLC(96;1150 1523 6936 46253 49736)	Atlas-SNP	.											.	KDM3A	179	.	0			c.T2601A						PASS	.						157	147	150					2																	86709141		2203	4300	6503	SO:0001583	missense	55818	exon17			CCTCCATACGTTT	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.2601T>A	chr2.hg19:g.86709141T>A	ENSP00000386660:p.His867Gln	278.0	0.0	.		316.0	121.0	.	NM_001146688	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Missense_Mutation	SNP	ENST00000409556.1	hg19	CCDS1990.1	.	.	.	.	.	.	.	.	.	.	T	0.181	-1.061940	0.01950	.	.	ENSG00000115548	ENST00000409556;ENST00000540058;ENST00000312912;ENST00000409064;ENST00000542128	T;T;T;T	0.57107	0.42;0.42;0.42;0.42	5.8	-4.8	0.03190	.	0.158851	0.45606	N	0.000360	T	0.21347	0.0514	N	0.11560	0.145	0.20489	N	0.999898	B;B	0.13145	0.007;0.004	B;B	0.20577	0.03;0.013	T	0.21861	-1.0233	10	0.12103	T	0.63	.	4.2025	0.10473	0.1625:0.1718:0.0861:0.5796	.	815;867	F5H070;Q9Y4C1	.;KDM3A_HUMAN	Q	867;867;867;867;815	ENSP00000386660:H867Q;ENSP00000323659:H867Q;ENSP00000386516:H867Q;ENSP00000438324:H815Q	ENSP00000323659:H867Q	H	+	3	2	KDM3A	86562652	0.737000	0.28175	0.337000	0.25536	0.581000	0.36288	-0.439000	0.06897	-2.060000	0.00893	-2.501000	0.00191	CAT	.	T|1.000;C|0.000	.	alt		0.383	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433		A	86709141	T	A	86709141	3	1	190	1	0	0	0	0	1	0	0	0	8133	1403	49	5	2663	5	KDM3A	2	86709141	Missense_Mutation	SNP	T	TCGA-GL-A9DC-01A-11D-A36X-10	1432605	86709141	156490232	17	11194											
RNF103	7844	hgsc.bcm.edu	37	chr2	86839326	86839326	+	Frame_Shift_Del	DEL	T	T	-																															gtgcctgtacgtattccaaaTcttgacacctttttaaccat																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr2:86839326delT	ENST00000237455.4	-	3	1406	c.438delA	c.(436-438)agafs	p.R146fs	AC015971.2_ENST00000597638.1_RNA|AC015971.2_ENST00000424788.1_RNA|AC015971.2_ENST00000426549.1_RNA|RNF103_ENST00000477307.1_5'UTR|CHMP3_ENST00000439940.2_Intron|RNF103-CHMP3_ENST00000604011.1_Intron|AC015971.2_ENST00000439077.1_RNA	NM_001198951.1|NM_005667.3	NP_001185880.1|NP_005658.1	O00237	RN103_HUMAN	ring finger protein 103	146					central nervous system development (GO:0007417)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(7)|skin(2)	25						GTATTCCAAATCTTGACACCT	0.378																																					p.F147fs		Atlas-Indel,Pindel	.											.	RNF103	58	.	0			c.439delT						PASS	.						133	126	128					2																	86839326		2203	4300	6503	SO:0001589	frameshift_variant	7844	exon3			.	D76444	CCDS33237.1	2p11.2	2013-01-09	2003-05-14	2003-05-16	ENSG00000239305	ENSG00000239305		"RING-type (C3HC4) zinc fingers"	12859	protein-coding gene	gene with protein product		602507	"zinc finger protein 103 homolog (mouse)"	ZFP103		9070305	Standard	NM_005667		Approved	hkf-1, KF1	uc021vkg.1	O00237	OTTHUMG00000153197	ENST00000237455.4:c.438delA	chr2.hg19:g.86839326delT	ENSP00000237455:p.Arg146fs	130.0	0.0	0		137.0	59.0	0.430657	NM_005667	A6NFV6|B2RAG4|Q53SU6|Q8IVB9	Frame_Shift_Del	DEL	ENST00000237455.4	hg19	CCDS33237.1																																																																																			.	.	.	none		0.378	RNF103-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330041.2	NM_005667		-	86839326	T	-	86839326	7	5	190	1	0	1	0	1	0	0	0	0	13436	1432	50	0	1627	0	RNF103	2	86839326	Frame_Shift_Del	DEL	T	TCGA-GL-A9DC-01A-11D-A36X-10	130185	86839326	156360047	18	11195											
CNNM3	26505	hgsc.bcm.edu	37	chr2	97494855	97494855	+	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	accaggctccttggtgagaaGaccaccacagcggcaggtga	11	5	13	12	1	0	3	0	2	0	2	1	4	1	3	4	4	1	2	4	4	1	1			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr2:97494855G>C	ENST00000305510.3	+	7	2071	c.2043G>C	c.(2041-2043)aaG>aaC	p.K681N	CNNM3_ENST00000480035.1_3'UTR|CNNM3_ENST00000377060.3_Missense_Mutation_p.K633N|ANKRD23_ENST00000476975.1_Intron	NM_017623.4	NP_060093.3	Q8NE01	CNNM3_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 3	681					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			NS(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(2)|skin(1)|urinary_tract(2)	13						TTGGTGAGAAGACCACCACAG	0.612																																					p.K681N		Atlas-SNP	.											.	CNNM3	33	.	0			c.G2043C						PASS	.						69	70	70					2																	97494855		2203	4300	6503	SO:0001583	missense	26505	exon7			TGAGAAGACCACC	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.2043G>C	chr2.hg19:g.97494855G>C	ENSP00000305449:p.Lys681Asn	119.0	0.0	.		123.0	67.0	.	NM_017623	B3KX67|Q8TBV4|Q96IW4|Q9NRK4|Q9NXW6	Missense_Mutation	SNP	ENST00000305510.3	hg19	CCDS2025.1	.	.	.	.	.	.	.	.	.	.	G	10.77	1.445374	0.25987	.	.	ENSG00000168763	ENST00000377060;ENST00000424641;ENST00000305510	D;D	0.91740	-2.58;-2.9	5.56	3.74	0.42951	.	0.845028	0.10091	N	0.717179	D	0.86981	0.6064	L	0.38531	1.155	0.58432	D	0.999996	B;B	0.27823	0.016;0.19	B;B	0.28709	0.015;0.093	T	0.76650	-0.2881	10	0.25106	T	0.35	-13.8197	8.2356	0.31625	0.2409:0.0:0.7591:0.0	.	633;681	Q8NE01-2;Q8NE01	.;CNNM3_HUMAN	N	633;633;681	ENSP00000366260:K633N;ENSP00000305449:K681N	ENSP00000305449:K681N	K	+	3	2	CNNM3	96858582	0.992000	0.36948	0.489000	0.27452	0.352000	0.29268	3.142000	0.50601	0.684000	0.31448	0.655000	0.94253	AAG	.	.	.	none		0.612	CNNM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252952.2	NM_017623		C	97494855	G	C	97494855	3	2	190	1	0	0	0	0	1	0	0	0	3616	933	33	4	2069	4	CNNM3	2	97494855	Missense_Mutation	SNP	G	TCGA-GL-A9DC-01A-11D-A36X-10	10655529	97494855	145704518	19	11196											
ZC3H6	376940	hgsc.bcm.edu	37	chr2	113089842	113089843	+	Missense_Mutation	DNP	AC	AC	GG																															gccagctgacccacaggcggAcgttcccaggagttctggta																								rs371812950		TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr2:113089842_113089843AC>GG	ENST00000409871.1	+	12	3748_3749	c.3347_3348AC>GG	c.(3346-3348)gAC>gGG	p.D1116G	ZC3H6_ENST00000343936.4_Missense_Mutation_p.D1116G|AC115115.2_ENST00000607612.1_RNA	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	1116							metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						CCACAGGCGGACGTTCCCAGGA	0.535																																					p.D1116G|p.D1116E		Atlas-SNP	.											.	ZC3H6	93	.	0			c.A3347G|c.C3348G						PASS	.																																			SO:0001583	missense	376940	exon12			AGGCGGACGTTCC|GGCGGACGTTCCC	AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"Zinc fingers, CCCH-type domain containing"	24762	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 6"	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	Exception_encountered	chr2.hg19:g.113089842_113089843delinsGG	ENSP00000386764:p.Asp1116Gly	276.0|274.0	0.0	.		360.0|225.0	152.0|20.0	.	NM_198581	A9JR71|Q6ZW96	Missense_Mutation	SNP	ENST00000409871.1	hg19	CCDS46393.1																																																																																			.	.	.	none|alt		0.535	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581		GG	113089843	AC	GG	113089842	3	3	190	1	0	0	0	0	1	0	0	0	17583	275	10	3	3393	3	ZC3H6	2	113089842	Missense_Mutation	DNP	AC	TCGA-GL-A9DC-01A-11D-A36X-10	15594987	113089842	130109531	20	11197											
GLI2	2736	hgsc.bcm.edu	37	chr2	121746958	121746958	+	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	agctccggcaccgtagacgcCctggccagccaggtgaagcc	8	4	13	16	3	0	2	0	1	0	1	1	2	1	2	6	3	3	3	6	3	2	1			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr2:121746958C>G	ENST00000452319.1	+	14	3528	c.3468C>G	c.(3466-3468)gcC>gcG	p.A1156A	GLI2_ENST00000314490.11_Intron|GLI2_ENST00000361492.4_Silent_p.A1156A					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)				CCGTAGACGCCCTGGCCAGCC	0.617																																					p.A1156A		Atlas-SNP	.											.	GLI2	187	.	0			c.C3468G						PASS	.						27	25	26					2																	121746958		2177	4259	6436	SO:0001819	synonymous_variant	2736	exon13			AGACGCCCTGGCC		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.3468C>G	chr2.hg19:g.121746958C>G		94.0	0.0	.		104.0	42.0	.	NM_005270		Silent	SNP	ENST00000452319.1	hg19	CCDS33283.1																																																																																			.	.	.	none		0.617	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		G	121746958	C	G	121746958	2	3	190	1	0	0	0	0	0	0	0	1	6445	610	22	4		4	GLI2	2	121746958	Silent	SNP	C	TCGA-GL-A9DC-01A-11D-A36X-10	8657116	121746958	121452415	21	11198											
TTN	7273	hgsc.bcm.edu	37	chr2	179478924	179478924	+	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	tccttgacggtggatgagagCttgtgccacacttcactatc	8	12	10	11	1	1	2	1	2	0	1	3	4	2	3	2	2	2	1	2	2	1	4	rs539513077		TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr2:179478924C>G	ENST00000591111.1	-	212	44501	c.44277G>C	c.(44275-44277)aaG>aaC	p.K14759N	TTN_ENST00000342992.6_Missense_Mutation_p.K13832N|RP11-171I2.4_ENST00000605334.1_lincRNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.K7527N|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.K16400N|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.K7460N|TTN_ENST00000460472.2_Missense_Mutation_p.K7335N|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	14759	Fibronectin type-III 6. {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)			TGGATGAGAGCTTGTGCCACA	0.443																																					p.K16400N		Atlas-SNP	.											.	TTN	18412	.	0			c.G49200C						PASS	.						153	142	145					2																	179478924		2003	4177	6180	SO:0001583	missense	7273	exon262			TGAGAGCTTGTGC	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.44277G>C	chr2.hg19:g.179478924C>G	ENSP00000465570:p.Lys14759Asn	152.0	0.0	.		162.0	56.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	11.16	1.557484	0.27827	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56776	0.44;0.44;0.44;0.44	5.77	3.99	0.46301	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.61912	0.2385	L	0.42581	1.335	0.41869	D	0.990264	D;D;D;D	0.71674	0.997;0.997;0.997;0.998	D;D;D;D	0.69824	0.918;0.918;0.918;0.966	T	0.63817	-0.6551	9	0.87932	D	0	.	10.5973	0.45345	0.0:0.7432:0.0:0.2568	.	7335;7460;7527;14759	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	N	13832;7335;7527;7460;7335	ENSP00000343764:K13832N;ENSP00000434586:K7335N;ENSP00000340554:K7527N;ENSP00000352154:K7460N	ENSP00000340554:K7527N	K	-	3	2	TTN	179187169	0.975000	0.34042	1.000000	0.80357	0.974000	0.67602	0.227000	0.17795	0.914000	0.36822	-0.136000	0.14681	AAG	.	.	.	none		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179478924	C	G	179478924	3	3	190	1	0	0	0	0	1	0	0	0	16747	796	28	4	58897	4	TTN	2	179478924	Missense_Mutation	SNP	C	TCGA-GL-A9DC-01A-11D-A36X-10	57731966	179478924	63720449	22	11199											
CTDSPL	10217	hgsc.bcm.edu	37	chr3	38017370	38017370	+	Frame_Shift_Del	DEL	C	C	-																															tcccctgcctcatacatcttCcatcctgagaatgcagtaag																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr3:38017370delC	ENST00000273179.5	+	7	716	c.690delC	c.(688-690)ttcfs	p.F230fs	CTDSPL_ENST00000443503.2_Frame_Shift_Del_p.F219fs|CTDSPL_ENST00000310189.3_3'UTR	NM_001008392.1	NP_001008393.1	O15194	CTDSL_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like	230	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.					extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			breast(1)|endometrium(2)|large_intestine(4)|skin(1)	8		Melanoma(1037;0.0122)		KIRC - Kidney renal clear cell carcinoma(284;0.0729)|Kidney(284;0.0902)		CATACATCTTCCATCCTGAGA	0.507																																					p.F230fs		Atlas-Indel,Pindel	.											.	CTDSPL	17	.	0			c.689delT						PASS	.						93	92	92					3																	38017370		2203	4300	6503	SO:0001589	frameshift_variant	10217	exon7			.	D88153	CCDS33734.1, CCDS33735.1	3p21.3	2010-06-21	2003-10-27	2003-10-29	ENSG00000144677	ENSG00000144677	3.1.3.16	"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	16890	protein-coding gene	gene with protein product	"small CTD phosphatase 3", "HYA22 protein", "RB protein serine phosphatase from chromosome 3"	608592	"chromosome 3 open reading frame 8"	C3orf8		9179494, 12543795	Standard	NM_005808		Approved	HYA22, SCP3, PSR1, RBSP3	uc003chg.3	O15194	OTTHUMG00000155942	ENST00000273179.5:c.690delC	chr3.hg19:g.38017370delC	ENSP00000273179:p.Phe230fs	74.0	0.0	0		96.0	30.0	0.3125	NM_001008392	Q3ZTU0|Q70KI4|Q7Z5Q2	Frame_Shift_Del	DEL	ENST00000273179.5	hg19	CCDS33734.1																																																																																			.	.	.	none		0.507	CTDSPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342392.1	NM_005808		-	38017370	C	-	38017370	7	5	190	1	0	1	0	1	0	0	0	0	4007	854	30	0	716	0	CTDSPL	3	38017370	Frame_Shift_Del	DEL	C	TCGA-GL-A9DC-01A-11D-A36X-10		38017370	160005060	23	11200											
C3orf71	646450	hgsc.bcm.edu	37	chr3	48956576	48956576	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgtcgccggcacgttgtcCgagcattacccgccgtcagc	5	7	11	18	7	1	0	1	0	0	0	3	1	2	0	5	1	3	3	5	1	1	2			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr3:48956576C>T	ENST00000408959.2	-	1	242	c.7G>A	c.(7-9)Gga>Aga	p.G3R	ARIH2_ENST00000356401.4_Intron|ARIH2_ENST00000449376.1_Intron|ARIH2_ENST00000490095.1_Intron	NM_001123040.1	NP_001116512.1	Q8N7S6	ARI2O_HUMAN	ariadne homolog 2 opposite strand	3						integral component of membrane (GO:0016021)											GCACGTTGTCCGAGCATTACC	0.751																																					p.G3R		Atlas-SNP	.											.	.	.	.	0			c.G7A						PASS	.						4	5	4					3																	48956576		961	2282	3243	SO:0001583	missense	646450	exon1			GTTGTCCGAGCAT	DA461567	CCDS43088.1	3p21.31	2012-10-08	2012-10-08	2012-10-08	ENSG00000221883	ENSG00000221883			34425	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 71"	C3orf71			Standard	NM_001123040		Approved		uc010hkk.1	Q8N7S6	OTTHUMG00000156672	ENST00000408959.2:c.7G>A	chr3.hg19:g.48956576C>T	ENSP00000386193:p.Gly3Arg	39.0	0.0	.		52.0	20.0	.	NM_001123040		Missense_Mutation	SNP	ENST00000408959.2	hg19	CCDS43088.1	.	.	.	.	.	.	.	.	.	.	C	11.75	1.731212	0.30684	.	.	ENSG00000221883	ENST00000408959	.	.	.	3.3	-5.21	0.02815	.	.	.	.	.	T	0.14917	0.0360	N	0.08118	0	0.09310	N	0.999995	B	0.22604	0.072	B	0.19391	0.025	T	0.23084	-1.0198	8	0.87932	D	0	.	3.7894	0.08713	0.2267:0.3251:0.0:0.4482	.	3	Q8N7S6	CC071_HUMAN	R	3	.	ENSP00000386193:G3R	G	-	1	0	C3orf71	48931580	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.310000	0.08135	-1.121000	0.02949	0.561000	0.74099	GGA	.	.	.	none		0.751	ARIH2OS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345247.1	NM_001123040		T	48956576	C	T	48956576	3	4	190	1	0	0	0	0	1	0	0	0	2245	661	23	1	869	1	C3orf71	3	48956576	Missense_Mutation	SNP	C	TCGA-GL-A9DC-01A-11D-A36X-10	10939206	48956576	149065854	24	11201											
PRKCD	5580	hgsc.bcm.edu	37	chr3	53221398	53221398	+	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	tgtggactgcagtttctacaCagcaagggcatcatttacag	11	11	10	9	0	2	0	1	0	1	0	2	1	2	1	0	2	4	4	0	2	3	4			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr3:53221398C>G	ENST00000394729.2	+	14	1723	c.1395C>G	c.(1393-1395)caC>caG	p.H465Q	PRKCD_ENST00000330452.3_Missense_Mutation_p.H465Q	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)	AGTTTCTACACAGCAAGGGCA	0.557																																					p.H465Q		Atlas-SNP	.											.	PRKCD	124	.	0			c.C1395G						PASS	.						120	117	118					3																	53221398		2203	4300	6503	SO:0001583	missense	5580	exon14			TCTACACAGCAAG		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.1395C>G	chr3.hg19:g.53221398C>G	ENSP00000378217:p.His465Gln	67.0	0.0	.		58.0	23.0	.	NM_212539	B0KZ81|B2R834|Q15144|Q86XJ6	Missense_Mutation	SNP	ENST00000394729.2	hg19	CCDS2870.1	.	.	.	.	.	.	.	.	.	.	C	18.99	3.740330	0.69304	.	.	ENSG00000163932	ENST00000394729;ENST00000330452	D;D	0.84516	-1.86;-1.86	5.47	4.59	0.56863	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	0.92489	0.7615	M	0.88105	2.93	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.92943	0.6374	10	0.87932	D	0	.	10.5386	0.45020	0.0:0.8413:0.0:0.1587	.	465	Q05655	KPCD_HUMAN	Q	465	ENSP00000378217:H465Q;ENSP00000331602:H465Q	ENSP00000331602:H465Q	H	+	3	2	PRKCD	53196438	1.000000	0.71417	0.974000	0.42286	0.968000	0.65278	1.343000	0.33930	1.285000	0.44548	0.591000	0.81541	CAC	.	.	.	none		0.557	PRKCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257818.1			G	53221398	C	G	53221398	3	3	190	1	0	0	0	0	1	0	0	0	12519	477	17	4	1445	4	PRKCD	3	53221398	Missense_Mutation	SNP	C	TCGA-GL-A9DC-01A-11D-A36X-10	4264822	53221398	144801032	25	11202											
C3orf63	23272	hgsc.bcm.edu	37	chr3	56694972	56694972	+	Frame_Shift_Del	DEL	A	A	-																															acctaagtatgtttccttatAaaacagtgctggagggattt																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr3:56694972delA	ENST00000493960.2	-	10	1244	c.1234delT	c.(1234-1236)tatfs	p.Y412fs	FAM208A_ENST00000355628.5_Frame_Shift_Del_p.Y412fs|FAM208A_ENST00000431842.2_Frame_Shift_Del_p.Y16fs	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	412							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						GTTTCCTTATAAAACAGTGCT	0.289																																					p.Y412fs		Atlas-Indel,Pindel	.											.	FAM208A	113	.	0			c.1235delA						PASS	.						112	112	112					3																	56694972		2202	4298	6500	SO:0001589	frameshift_variant	23272	exon10			.	AF180425	CCDS2877.1, CCDS46853.1	3p14.3	2011-09-14	2011-09-14	2011-09-14	ENSG00000163946	ENSG00000163946			30314	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 63"	C3orf63		10470851, 11149944	Standard	NM_015224		Approved	se89-1, RAP140, KIAA1105	uc003die.4	Q9UK61	OTTHUMG00000158827	ENST00000493960.2:c.1234delT	chr3.hg19:g.56694972delA	ENSP00000417509:p.Tyr412fs	148.0	0.0	0		152.0	58.0	0.381579	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Frame_Shift_Del	DEL	ENST00000493960.2	hg19	CCDS46853.1																																																																																			.	.	.	none		0.289	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224		-	56694972	A	-	56694972	7	5	190	1	0	1	0	1	0	0	0	0	2241	362	13	0	3898	0	C3orf63	3	56694972	Frame_Shift_Del	DEL	A	TCGA-GL-A9DC-01A-11D-A36X-10	3473574	56694972	141327458	26	11203											
CADPS	8618	hgsc.bcm.edu	37	chr3	62423814	62423814	+	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	tatgtacatctcctcattgaCcttatcacgcaggacatcct	10	13	5	13	1	3	1	2	1	1	0	5	2	4	2	3	1	1	2	3	1	3	4			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr3:62423814C>T	ENST00000383710.4	-	28	4091	c.3742G>A	c.(3742-3744)Gtc>Atc	p.V1248I	CADPS_ENST00000283269.9_Missense_Mutation_p.V1209I|CADPS_ENST00000357948.3_Missense_Mutation_p.V1169I	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	1248	Mediates targeting and association with DCVs. {ECO:0000250}.				catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		TCCTCATTGACCTTATCACGC	0.448																																					p.V1248I		Atlas-SNP	.											.	CADPS	387	.	0			c.G3742A						PASS	.						95	91	92					3																	62423814		2203	4300	6503	SO:0001583	missense	8618	exon28			CATTGACCTTATC	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.3742G>A	chr3.hg19:g.62423814C>T	ENSP00000373215:p.Val1248Ile	227.0	0.0	.		263.0	94.0	.	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Missense_Mutation	SNP	ENST00000383710.4	hg19	CCDS46858.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.10|12.10	1.835491|1.835491	0.32421|0.32421	.|.	.|.	ENSG00000163618|ENSG00000163618	ENST00000466621|ENST00000383709;ENST00000383710;ENST00000357948;ENST00000283269	.|T;T;T	.|0.30448	.|1.53;1.53;1.53	5.65|5.65	5.65|5.65	0.86999|0.86999	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.30572|0.30572	0.0769|0.0769	L|L	0.40543|0.40543	1.245|1.245	0.80722|0.80722	D|D	1|1	.|B;B;B;B	.|0.23377	.|0.084;0.001;0.002;0.058	.|B;B;B;B	.|0.26614	.|0.071;0.007;0.004;0.065	T|T	0.04115|0.04115	-1.0976|-1.0976	5|10	.|0.24483	.|T	.|0.36	.|.	19.7806|19.7806	0.96414|0.96414	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1169;1209;1248;1253	.|Q9ULU8-2;Q9ULU8-3;Q9ULU8;Q9ULU8-4	.|.;.;CAPS1_HUMAN;.	D|I	148|1254;1248;1169;1209	.|ENSP00000373215:V1248I;ENSP00000350632:V1169I;ENSP00000283269:V1209I	.|ENSP00000283269:V1209I	G|V	-|-	2|1	0|0	CADPS|CADPS	62398854|62398854	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	5.978000|5.978000	0.70501|0.70501	2.668000|2.668000	0.90789|0.90789	0.644000|0.644000	0.83932|0.83932	GGT|GTC	.	.	.	none		0.448	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394		T	62423814	C	T	62423814	3	4	190	1	0	0	0	0	1	0	0	0	2572	507	18	2	331	2	CADPS	3	62423814	Missense_Mutation	SNP	C	TCGA-GL-A9DC-01A-11D-A36X-10	5728842	62423814	135598616	27	11204											
FNDC3B	64778	hgsc.bcm.edu	37	chr3	172065011	172065011	+	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	tgcctttccagagtcctgatAgttctggtgctgacatctca	7	14	9	11	0	2	3	1	2	2	1	5	3	4	3	3	1	2	2	3	1	1	3			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr3:172065011A>T	ENST00000336824.4	+	21	2473	c.2374A>T	c.(2374-2376)Agt>Tgt	p.S792C	FNDC3B_ENST00000416957.1_Missense_Mutation_p.S792C|FNDC3B_ENST00000415807.2_Missense_Mutation_p.S792C	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	792	Fibronectin type-III 6. {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)		GAGTCCTGATAGTTCTGGTGC	0.403																																					p.S792C		Atlas-SNP	.											.	FNDC3B	118	.	0			c.A2374T						PASS	.						125	125	125					3																	172065011		2203	4300	6503	SO:0001583	missense	64778	exon21			CCTGATAGTTCTG	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.2374A>T	chr3.hg19:g.172065011A>T	ENSP00000338523:p.Ser792Cys	89.0	0.0	.		97.0	47.0	.	NM_001135095	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Missense_Mutation	SNP	ENST00000336824.4	hg19	CCDS3217.1	.	.	.	.	.	.	.	.	.	.	A	9.703	1.154942	0.21371	.	.	ENSG00000075420	ENST00000415807;ENST00000336824;ENST00000416957	T;T;T	0.59224	0.28;0.28;0.28	6.03	3.61	0.41365	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.383662	0.37348	N	0.002126	T	0.34571	0.0902	N	0.13168	0.305	0.80722	D	1	B	0.06786	0.001	B	0.15484	0.013	T	0.06391	-1.0829	10	0.24483	T	0.36	-7.0432	5.9877	0.19444	0.5632:0.0:0.0696:0.3671	.	792	Q53EP0	FND3B_HUMAN	C	792	ENSP00000411242:S792C;ENSP00000338523:S792C;ENSP00000389094:S792C	ENSP00000338523:S792C	S	+	1	0	FNDC3B	173547705	1.000000	0.71417	0.140000	0.22221	0.895000	0.52256	1.823000	0.39062	0.499000	0.27970	0.533000	0.62120	AGT	.	.	.	none		0.403	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763		T	172065011	A	T	172065011	3	4	190	1	0	0	0	0	1	0	0	0	5977	420	15	5	2452	5	FNDC3B	3	172065011	Missense_Mutation	SNP	A	TCGA-GL-A9DC-01A-11D-A36X-10	109641197	172065011	25957419	28	11205											
RNF168	165918	hgsc.bcm.edu	37	chr3	196215554	196215554	+	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	gaactggctgatagtcatcaGctatttcatatcaaaaaaga	16	11	7	7	0	4	2	4	1	0	1	4	3	4	2	0	1	2	2	0	1	7	4	rs144091604		TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr3:196215554G>T	ENST00000318037.3	-	2	896	c.302C>A	c.(301-303)gCt>gAt	p.A101D		NM_152617.3	NP_689830.2	Q8IYW5	RN168_HUMAN	ring finger protein 168, E3 ubiquitin protein ligase	101					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone H2A K63-linked ubiquitination (GO:0070535)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K13 ubiquitination (GO:0036351)|histone H2A-K15 ubiquitination (GO:0036352)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|negative regulation of translational elongation (GO:0045900)|positive regulation of DNA repair (GO:0045739)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)	20	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)		ATAGTCATCAGCTATTTCATA	0.308																																					p.A101D		Atlas-SNP	.											.	RNF168	49	.	0			c.C302A						PASS	.						64	67	66					3																	196215554		2203	4300	6503	SO:0001630	splice_region_variant	165918	exon2			TCATCAGCTATTT	AK054732	CCDS3317.1	3q29	2014-09-17	2012-02-23		ENSG00000163961	ENSG00000163961		"RING-type (C3HC4) zinc fingers"	26661	protein-coding gene	gene with protein product		612688	"ring finger protein 168"			12477932	Standard	NM_152617		Approved	FLJ35794	uc003fwq.3	Q8IYW5	OTTHUMG00000155582	ENST00000318037.3:c.302-1C>A	chr3.hg19:g.196215554G>T		223.0	0.0	.		249.0	106.0	.	NM_152617	Q8NA67|Q96NS4	Missense_Mutation	SNP	ENST00000318037.3	hg19	CCDS3317.1	.	.	.	.	.	.	.	.	.	.	G	6.047	0.377061	0.11466	.	.	ENSG00000163961	ENST00000318037	T	0.08102	3.13	5.75	-1.81	0.07882	.	0.268702	0.26130	N	0.026166	T	0.05364	0.0142	L	0.40543	1.245	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.39961	-0.9588	10	0.20046	T	0.44	.	5.8089	0.18456	0.3866:0.3711:0.2423:0.0	.	101	Q8IYW5	RN168_HUMAN	D	101	ENSP00000320898:A101D	ENSP00000320898:A101D	A	-	2	0	RNF168	197699951	1.000000	0.71417	0.021000	0.16686	0.172000	0.22775	0.859000	0.27858	-0.536000	0.06298	-0.225000	0.12378	GCT	.	G|1.000;A|0.000	.	alt		0.308	RNF168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340778.1	NM_152617	Missense_Mutation	T	196215554	G	T	196215554	5	4	190	1	0	0	0	0	0	0	1	0	13472	985	34	4	1433	4	RNF168	3	196215554	Splice_Site	SNP	G	TCGA-GL-A9DC-01A-11D-A36X-10	24150543	196215554	1806876	29	11206											
WDR19	57728	hgsc.bcm.edu	37	chr4	39206803	39206804	+	Frame_Shift_Ins	INS	-	-	T																															tgcttggcaagaaaactttgINSttttttttaaatctgaatga																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr4:39206803_39206804insT	ENST00000399820.3	+	8	787_788	c.633_634insT	c.(634-636)tttfs	p.F212fs	WDR19_ENST00000506503.1_Frame_Shift_Ins_p.F212fs|WDR19_ENST00000288634.7_Frame_Shift_Ins_p.F52fs	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	212					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						AGAAAACTTTGTTTTTTTTAAA	0.361																																					p.L211fs		Atlas-Indel,Pindel	.											.,2	WDR19	96	.	0			c.633_634insT						PASS	.																																			SO:0001589	frameshift_variant	57728	exon8			.	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.641dupT	chr4.hg19:g.39206811_39206811dupT	ENSP00000382717:p.Phe212fs	62.0	0.0	0		72.0	30.0	0.416667	NM_025132	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Frame_Shift_Ins	INS	ENST00000399820.3	hg19	CCDS47042.1																																																																																			.	.	.	none		0.361	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1			T	39206804	-	T	39206803	7	5	190	1	0	1	1	0	0	0	0	0	17291	1368	48	0	663	0	WDR19	4	39206803	Frame_Shift_Ins	INS	-	TCGA-GL-A9DC-01A-11D-A36X-10		39206803	151947473	30	11207											
WDFY3	23001	hgsc.bcm.edu	37	chr4	85598373	85598374	+	Missense_Mutation	DNP	CA	CA	AG																															tctggcagaagagctgaccaCagttcctgcaatggtgtcgt																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr4:85598373_85598374CA>AG	ENST00000295888.4	-	67	10842_10843	c.10435_10436TG>CT	c.(10435-10437)TGt>CTt	p.C3479L	WDFY3_ENST00000322366.6_Missense_Mutation_p.C3462L	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	3479	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)		GAGCTGACCACAGTTCCTGCAA	0.45																																					p.C3479F|p.C3479R		Atlas-SNP	.											.	WDFY3	314	.	0			c.G10436T|c.T10435C						PASS	.																																			SO:0001583	missense	23001	exon67			TGACCACAGTTCC|GACCACAGTTCCT	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.10435_10436delinsAG	chr4.hg19:g.85598373_85598374delinsAG	ENSP00000295888:p.Cys3479Leu	127.0	0.0	.		154.0|155.0	69.0|71.0	.	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	hg19	CCDS3609.1																																																																																			.	.	.	none		0.45	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		AG	85598374	CA	AG	85598373	3	1	190	1	0	0	0	0	1	0	0	0	17282	478	17	4	152	4	WDFY3	4	85598373	Missense_Mutation	DNP	CA	TCGA-GL-A9DC-01A-11D-A36X-10	46391570	85598373	105555903	31	11208											
ADH6	130	hgsc.bcm.edu	37	chr4	100128709	100128709	+	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	acaaccacacagaccccataGctctcattgcaggaggcgag	13	5	9	14	1	1	1	1	0	1	1	2	3	1	2	3	2	3	2	3	2	2	2			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr4:100128709G>T	ENST00000237653.7	-	7	1242	c.858C>A	c.(856-858)agC>agA	p.S286R	ADH6_ENST00000394897.1_Intron|RP11-696N14.1_ENST00000500358.2_RNA|ADH6_ENST00000394899.2_Missense_Mutation_p.S286R|ADH6_ENST00000407820.2_Missense_Mutation_p.S77R|ADH6_ENST00000504257.1_5'Flank|RP11-696N14.1_ENST00000506160.1_RNA|RP11-696N14.1_ENST00000506454.1_RNA	NM_000672.3	NP_000663	P28332	ADH6_HUMAN	alcohol dehydrogenase 6 (class V)	286					ethanol oxidation (GO:0006069)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|ethanol binding (GO:0035276)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(2)	20				OV - Ovarian serous cystadenocarcinoma(123;3.58e-08)	Abacavir(DB01048)	AGACCCCATAGCTCTCATTGC	0.463																																					p.S286R		Atlas-SNP	.											.	ADH6	74	.	0			c.C858A						PASS	.						108	103	105					4																	100128709		2203	4300	6503	SO:0001583	missense	130	exon7			CCCATAGCTCTCA	AK092768	CCDS3647.1, CCDS43255.1	4q23	2008-02-05			ENSG00000172955	ENSG00000172955	1.1.1.1	"Alcohol dehydrogenases"	255	protein-coding gene	gene with protein product		103735				1881901	Standard	NM_000672		Approved	ADH-5	uc003huo.2	P28332	OTTHUMG00000131024	ENST00000237653.7:c.858C>A	chr4.hg19:g.100128709G>T	ENSP00000237653:p.Ser286Arg	127.0	0.0	.		150.0	61.0	.	NM_000672	B3KS45|Q58F53	Missense_Mutation	SNP	ENST00000237653.7	hg19	CCDS3647.1	.	.	.	.	.	.	.	.	.	.	G	10.36	1.328806	0.24167	.	.	ENSG00000172955	ENST00000394899;ENST00000407820;ENST00000237653;ENST00000508558	T;T;T;T	0.06528	3.29;3.29;3.29;3.29	3.8	0.95	0.19572	Alcohol dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	0.328356	0.36703	N	0.002444	T	0.08802	0.0218	L	0.28740	0.885	0.09310	N	1	P;P;D	0.56746	0.908;0.94;0.977	P;P;P	0.58873	0.752;0.656;0.847	T	0.14117	-1.0484	10	0.87932	D	0	-9.2534	4.2097	0.10505	0.1775:0.0:0.5047:0.3178	.	163;286;286	B4DPD8;P28332;P28332-2	.;ADH6_HUMAN;.	R	286;77;286;222	ENSP00000378359:S286R;ENSP00000384997:S77R;ENSP00000237653:S286R;ENSP00000426187:S222R	ENSP00000237653:S286R	S	-	3	2	ADH6	100347732	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.031000	0.12287	0.201000	0.20466	-0.251000	0.11542	AGC	.	.	.	none		0.463	ADH6-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253665.1	NM_000672		T	100128709	G	T	100128709	3	4	190	1	0	0	0	0	1	0	0	0	312	962	34	4	285	4	ADH6	4	100128709	Missense_Mutation	SNP	G	TCGA-GL-A9DC-01A-11D-A36X-10	14530336	100128709	91025567	32	11209											
SLC12A7	10723	hgsc.bcm.edu	37	chr5	1087135	1087135	+	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	agcgagcgcgatatcatgtaGtaggacccgccagctgcgga	10	6	14	11	5	1	0	1	0	0	0	1	4	1	2	2	2	4	3	2	2	3	3			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr5:1087135G>A	ENST00000264930.5	-	6	601	c.558C>T	c.(556-558)taC>taT	p.Y186Y		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	186					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)	ATATCATGTAGTAGGACCCGC	0.637																																					p.Y186Y		Atlas-SNP	.											.	SLC12A7	97	.	0			c.C558T						PASS	.						23	24	24					5																	1087135		2199	4298	6497	SO:0001819	synonymous_variant	10723	exon6			CATGTAGTAGGAC	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.558C>T	chr5.hg19:g.1087135G>A		144.0	0.0	.		180.0	88.0	.	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Silent	SNP	ENST00000264930.5	hg19	CCDS34129.1																																																																																			.	.	.	none		0.637	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598		A	1087135	G	A	1087135	2	1	190	1	0	0	0	0	0	0	0	1	14401	1024	36	2		2	SLC12A7	5	1087135	Silent	SNP	G	TCGA-GL-A9DC-01A-11D-A36X-10		1087135	179828125	33	11210											
C5orf49	134121	hgsc.bcm.edu	37	chr5	7831994	7831994	+	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	caatgtgcccaaagccgggtTccttgaggctggggatgtcg	7	9	15	10	2	0	1	0	1	0	0	2	2	1	2	3	4	2	2	3	4	2	2			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr5:7831994T>A	ENST00000399810.2	-	3	881	c.413A>T	c.(412-414)gAa>gTa	p.E138V	C5orf49_ENST00000509627.1_Missense_Mutation_p.E136V	NM_001089584.2	NP_001083053.1	A4QMS7	CE049_HUMAN	chromosome 5 open reading frame 49	138										large_intestine(3)|lung(5)|skin(1)	9						AAAGCCGGGTTCCTTGAGGCT	0.587																																					p.E138V		Atlas-SNP	.											.	C5orf49	27	.	0			c.A413T						PASS	.						109	117	115					5																	7831994		2013	4171	6184	SO:0001583	missense	134121	exon3			CCGGGTTCCTTGA		CCDS43300.1	5p15.31	2008-07-16			ENSG00000215217	ENSG00000215217			27028	protein-coding gene	gene with protein product						12477932	Standard	NM_001089584		Approved	LOC134121	uc003jea.5	A4QMS7	OTTHUMG00000161897	ENST00000399810.2:c.413A>T	chr5.hg19:g.7831994T>A	ENSP00000382708:p.Glu138Val	83.0	0.0	.		87.0	32.0	.	NM_001089584		Missense_Mutation	SNP	ENST00000399810.2	hg19	CCDS43300.1	.	.	.	.	.	.	.	.	.	.	T	3.625	-0.076646	0.07184	.	.	ENSG00000215217	ENST00000399810;ENST00000509627	T;T	0.26067	1.76;1.76	5.0	-9.72	0.00515	.	.	.	.	.	T	0.14787	0.0357	L	0.29908	0.895	0.09310	N	1	B	0.15473	0.013	B	0.13407	0.009	T	0.28364	-1.0046	9	0.36615	T	0.2	-10.2664	11.0233	0.47730	0.0:0.237:0.1945:0.5685	.	138	A4QMS7	CE049_HUMAN	V	138;136	ENSP00000382708:E138V;ENSP00000426019:E136V	ENSP00000382708:E138V	E	-	2	0	C5orf49	7884994	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-2.342000	0.01099	-1.768000	0.01298	-1.349000	0.01238	GAA	.	.	.	none		0.587	C5orf49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000366322.1	NM_001089584		A	7831994	T	A	7831994	3	1	190	1	0	0	0	0	1	0	0	0	2309	1783	62	5	34	5	C5orf49	5	7831994	Missense_Mutation	SNP	T	TCGA-GL-A9DC-01A-11D-A36X-10	6744859	7831994	173083266	34	11211											
RAI14	26064	hgsc.bcm.edu	37	chr5	34688329	34688329	+	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	atgcagcctacatatctcccGtggctttcagctaaggagaa	11	10	9	11	1	2	1	1	0	1	1	3	2	2	1	2	2	4	3	2	2	4	4			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr5:34688329G>A	ENST00000265109.3	+	2	323				RAI14_ENST00000503673.1_Intron|RAI14_ENST00000428746.2_Intron|RAI14_ENST00000506376.1_Intron|RAI14_ENST00000515799.1_Silent_p.P7P|RAI14_ENST00000512629.1_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)					CATATCTCCCGTGGCTTTCAG	0.448																																					p.P7P		Atlas-SNP	.											.	RAI14	100	.	0			c.G21A						PASS	.						98	85	89					5																	34688329		692	1591	2283	SO:0001627	intron_variant	26064	exon4			TCTCCCGTGGCTT	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+1269G>A	chr5.hg19:g.34688329G>A		139.0	0.0	.		155.0	54.0	.	NM_001145525	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Silent	SNP	ENST00000265109.3	hg19	CCDS34142.1																																																																																			.	.	.	none		0.448	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577		A	34688329	G	A	34688329	1	1	190	0	1	0	0	0	0	0	0	0	13021	1132	40	1		1	RAI14	5	34688329	Intron	SNP	G	TCGA-GL-A9DC-01A-11D-A36X-10	26856335	34688329	146226931	35	11212											
WDR41	55255	hgsc.bcm.edu	37	chr5	76732151	76732151	+	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	tgaacatgaagtagcattttCttgctgctttttaacaggtt	10	17	8	6	0	1	2	0	2	1	0	1	2	1	2	0	1	5	5	0	1	4	8			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr5:76732151C>T	ENST00000296679.4	-	12	1537	c.1162G>A	c.(1162-1164)Gaa>Aaa	p.E388K	WDR41_ENST00000512033.1_5'Flank|WDR41_ENST00000414719.2_Missense_Mutation_p.E134K|WDR41_ENST00000507029.1_Missense_Mutation_p.E333K	NM_018268.2	NP_060738.2	Q9HAD4	WDR41_HUMAN	WD repeat domain 41	388						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)		GTAGCATTTTCTTGCTGCTTT	0.393																																					p.E388K		Atlas-SNP	.											.	WDR41	29	.	0			c.G1162A						PASS	.						174	149	158					5																	76732151		2203	4300	6503	SO:0001583	missense	55255	exon12			CATTTTCTTGCTG	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.1162G>A	chr5.hg19:g.76732151C>T	ENSP00000296679:p.Glu388Lys	127.0	0.0	.		114.0	55.0	.	NM_018268	B4DT55|Q7Z792|Q8IWG3|Q8IXA9|Q8NDA7|Q9NV62	Missense_Mutation	SNP	ENST00000296679.4	hg19	CCDS4038.1	.	.	.	.	.	.	.	.	.	.	C	16.18	3.049649	0.55218	.	.	ENSG00000164253	ENST00000296679;ENST00000414719;ENST00000515253;ENST00000507029	T;T;T;T	0.51071	0.73;1.54;0.72;1.98	5.65	5.65	0.86999	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.224635	0.45606	D	0.000357	T	0.52224	0.1721	L	0.32530	0.975	0.58432	D	0.999996	D;D;D	0.58268	0.982;0.982;0.982	P;P;P	0.53760	0.664;0.664;0.734	T	0.41520	-0.9504	9	.	.	.	-26.7881	19.7233	0.96151	0.0:1.0:0.0:0.0	.	333;134;388	B4DT55;B4E2L4;Q9HAD4	.;.;WDR41_HUMAN	K	388;134;323;333	ENSP00000296679:E388K;ENSP00000392931:E134K;ENSP00000426499:E323K;ENSP00000424287:E333K	.	E	-	1	0	WDR41	76767907	1.000000	0.71417	0.994000	0.49952	0.210000	0.24377	6.532000	0.73825	2.653000	0.90120	0.563000	0.77884	GAA	.	.	.	none		0.393	WDR41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220014.2	NM_018268		T	76732151	C	T	76732151	3	4	190	1	0	0	0	0	1	0	0	0	17306	922	32	2	225	2	WDR41	5	76732151	Missense_Mutation	SNP	C	TCGA-GL-A9DC-01A-11D-A36X-10	42043822	76732151	104183109	36	11213											
MSH3	4437	hgsc.bcm.edu	37	chr5	79950745	79950745	+	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	ccgcagcgcccccagcgcccCcagctcccgccttcccgccc	3	3	8	27	5	0	0	0	0	0	0	2	0	2	0	9	0	3	2	9	0	0	1	rs144629981|rs3045983|rs557874766	byFrequency	TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr5:79950745C>G	ENST00000265081.6	+	1	279	c.199C>G	c.(199-201)Cca>Gca	p.P67A	DHFR_ENST00000513048.1_5'Flank|DHFR_ENST00000505337.1_5'Flank|DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000439211.2_5'UTR|DHFR_ENST00000504396.1_5'Flank	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	67					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)		CCCAGCGCCCCCAGCTCCCGC	0.731								Mismatch excision repair (MMR)					C|||	1091	0.217851	0.2678	0.1916	5008	,	,		6483	0.0476		0.2356	False		,,,				2504	0.3262				p.P67A	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											MSH3,NS,carcinoma,0,1	MSH3	129	.	0			c.C199G						PASS	.						3	4	3					5																	79950745		1702	3410	5112	SO:0001583	missense	4437	exon1			GCGCCCCCAGCTC	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.199C>G	chr5.hg19:g.79950745C>G	ENSP00000265081:p.Pro67Ala	51.0	0.0	.		79.0	12.0	.	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	hg19	CCDS34195.1	.	.	.	.	.	.	.	.	.	.	C	6.333	0.429466	0.11987	.	.	ENSG00000113318	ENST00000265081;ENST00000535995	D	0.85484	-1.99	.	.	.	.	.	.	.	.	T	0.70150	0.3191	N	0.19112	0.55	0.19945	N	0.999946	B	0.18741	0.03	B	0.17098	0.017	T	0.53507	-0.8429	6	.	.	.	0.6693	.	.	.	.	67	P20585	MSH3_HUMAN	A	67;58	ENSP00000265081:P67A	.	P	+	1	0	MSH3	79986501	0.560000	0.26570	0.857000	0.33713	0.119000	0.20118	0.055000	0.14229	0.064000	0.16427	0.064000	0.15345	CCA	.	.	.	none		0.731	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		G	79950745	C	G	79950745	3	3	190	1	0	0	0	0	1	0	0	0	9878	623	22	4	201	4	MSH3	5	79950745	Missense_Mutation	SNP	C	TCGA-GL-A9DC-01A-11D-A36X-10	3218594	79950745	100964515	37	11214											
PCDHA12	56137	hgsc.bcm.edu	37	chr5	140256290	140256290	+	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	tactcgttggtgctggacagCgccctggaccgcgagagcgt	6	8	15	12	5	0	1	0	0	0	1	1	4	0	3	2	3	4	2	2	3	1	2	rs369536692		TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr5:140256290C>T	ENST00000398631.2	+	1	1233	c.1233C>T	c.(1231-1233)agC>agT	p.S411S	PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	411	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S411S(1)		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)			TGCTGGACAGCGCCCTGGACC	0.607													.|||	1	0.000199681	8e-04	0	5008	,	,		19945	0		0	False		,,,				2504	0				p.S411S	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											PCDHA12,NS,NS,0,1	PCDHA12	196	.	1	Substitution - coding silent(1)	NS(1)	c.C1233T						PASS	.	C	,,,,,,,,,,,,,,,	5,4401	9.9+/-24.2	0,5,2198	196	189	192		,,,1233,,,,,,,,,,,,1233	0.6	0	5		192	0,8600		0,0,4300	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	,,,,,,,,,,,,,,,	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	,,,,,,,,,,,,,,,	,,,411/942,,,,,,,,,,,,411/793	140256290	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	56137	exon1			GGACAGCGCCCTG	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.1233C>T	chr5.hg19:g.140256290C>T		163.0	0.0	.		153.0	72.0	.	NM_018903	O75278|Q2M1N8	Silent	SNP	ENST00000398631.2	hg19	CCDS47285.1																																																																																			.	.	.	weak		0.607	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		T	140256290	C	T	140256290	2	4	190	1	0	0	0	0	0	0	0	1	11529	767	27	1		1	PCDHA12	5	140256290	Silent	SNP	C	TCGA-GL-A9DC-01A-11D-A36X-10	60305545	140256290	40658970	38	11215											
NDST1	3340	hgsc.bcm.edu	37	chr5	149927825	149927825	+	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	tggccctaaagtacaccttcCatgaggtgattaccgccggc	9	9	10	13	2	0	2	0	2	0	0	1	2	1	2	5	3	2	1	5	3	4	4			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr5:149927825C>T	ENST00000261797.6	+	12	2693	c.2191C>T	c.(2191-2193)Cat>Tat	p.H731Y	NDST1_ENST00000523767.1_Intron	NM_001543.4	NP_001534.1	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	731	Heparan sulfate N-sulfotransferase 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)			GTACACCTTCCATGAGGTGAT	0.617																																					p.H731Y		Atlas-SNP	.											.	NDST1	79	.	0			c.C2191T						PASS	.						88	61	70					5																	149927825		2203	4300	6503	SO:0001583	missense	3340	exon12			ACCTTCCATGAGG	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.2191C>T	chr5.hg19:g.149927825C>T	ENSP00000261797:p.His731Tyr	85.0	0.0	.		92.0	47.0	.	NM_001543	Q96E57	Missense_Mutation	SNP	ENST00000261797.6	hg19	CCDS34277.1	.	.	.	.	.	.	.	.	.	.	C	9.808	1.182455	0.21870	.	.	ENSG00000070614	ENST00000261797	D	0.81579	-1.51	4.91	4.91	0.64330	Sulfotransferase domain (1);	0.136269	0.64402	D	0.000002	T	0.56381	0.1981	N	0.01789	-0.72	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.60125	-0.7324	10	0.02654	T	1	.	18.4857	0.90828	0.0:1.0:0.0:0.0	.	731	P52848	NDST1_HUMAN	Y	731	ENSP00000261797:H731Y	ENSP00000261797:H731Y	H	+	1	0	NDST1	149908018	1.000000	0.71417	0.998000	0.56505	0.929000	0.56500	2.653000	0.46691	2.434000	0.82447	0.655000	0.94253	CAT	.	.	.	none		0.617	NDST1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374314.2	NM_001543		T	149927825	C	T	149927825	3	4	190	1	0	0	0	0	1	0	0	0	10262	594	21	2	2233	2	NDST1	5	149927825	Missense_Mutation	SNP	C	TCGA-GL-A9DC-01A-11D-A36X-10	9671535	149927825	30987435	39	11216											
TNIP1	10318	hgsc.bcm.edu	37	chr5	150443282	150443283	+	In_Frame_Ins	INS	-	-	ATA																															tgccggagcctggtcgcttcINScatctgggactcttccaaaa																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr5:150443282_150443283insATA	ENST00000389378.2	-	3	750_751	c.162_163insTAT	c.(160-165)atggaa>atgTATgaa	p.54_55ME>MYE	TNIP1_ENST00000523338.1_In_Frame_Ins_p.54_55ME>MYE|TNIP1_ENST00000315050.7_In_Frame_Ins_p.54_55ME>MYE|TNIP1_ENST00000522226.1_In_Frame_Ins_p.54_55ME>MYE|TNIP1_ENST00000521591.1_In_Frame_Ins_p.54_55ME>MYE|TNIP1_ENST00000523200.1_In_Frame_Ins_p.54_55ME>MYE|TNIP1_ENST00000524280.1_In_Frame_Ins_p.54_55ME>MYE|TNIP1_ENST00000518977.1_In_Frame_Ins_p.54_55ME>MYE|TNIP1_ENST00000520931.1_In_Frame_Ins_p.1_2ME>MYE	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	54					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)			CTGGTCGCTTCCATCTGGGACT	0.589																																					p.E55delinsYE		Atlas-INDEL	.											.	TNIP1	51	.	0			c.163_164insTAT						PASS	.																																			SO:0001652	inframe_insertion	10318	exon3			.	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.162_163insTAT	chr5.hg19:g.150443282_150443283insATA	ENSP00000374029:p.Met54_Glu55insTyr	79.0	0.0	0		68.0	18.0	0.264706	NM_001252385	A4F1W8|A4F1W9|A4F1X2|A4F1X4|A4F1X5|A4F1X6|A4F1X7|A4F1X9|B7Z699|E7EPY1|E7ET96|O76008|Q05KP3|Q05KP4|Q6N077|Q96EL9|Q99833|Q9H1J3	In_Frame_Ins	INS	ENST00000389378.2	hg19	CCDS34280.1																																																																																			.	.	.	none		0.589	TNIP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374914.1	NM_006058		ATA	150443283	-	ATA	150443282	7	5	190	1	0	1	1	0	0	0	0	0	16326	864	30	0	1811	0	TNIP1	5	150443282	In_Frame_Ins	INS	-	TCGA-GL-A9DC-01A-11D-A36X-10	515457	150443282	30471978	40	11217	105	3									
TNIP1	10318	hgsc.bcm.edu	37	chr5	150443283	150443286	+	Frame_Shift_Del	DEL	CATC	CATC	-																															tgccggagcctggtcgcttcCatctgggactcttccaaaag																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	CATC	CATC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr5:150443283_150443286delCATC	ENST00000389378.2	-	3	747_750	c.159_162delGATG	c.(157-162)cagatgfs	p.QM53fs	TNIP1_ENST00000523338.1_Frame_Shift_Del_p.QM53fs|TNIP1_ENST00000315050.7_Frame_Shift_Del_p.QM53fs|TNIP1_ENST00000522226.1_Frame_Shift_Del_p.QM53fs|TNIP1_ENST00000521591.1_Frame_Shift_Del_p.QM53fs|TNIP1_ENST00000523200.1_Frame_Shift_Del_p.QM53fs|TNIP1_ENST00000524280.1_Frame_Shift_Del_p.QM53fs|TNIP1_ENST00000518977.1_Frame_Shift_Del_p.QM53fs|TNIP1_ENST00000520931.1_Start_Codon_Del	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	53					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)			TGGTCGCTTCCATCTGGGACTCTT	0.588																																					p.54_55del		Pindel	.											.	TNIP1	51	.	0			c.160_163del						PASS	.																																			SO:0001589	frameshift_variant	10318	exon3			.	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.159_162delGATG	chr5.hg19:g.150443283_150443286delCATC	ENSP00000374029:p.Gln53fs	77.0	0.0	.		66.0	14.0	0.212	NM_001252385	A4F1W8|A4F1W9|A4F1X2|A4F1X4|A4F1X5|A4F1X6|A4F1X7|A4F1X9|B7Z699|E7EPY1|E7ET96|O76008|Q05KP3|Q05KP4|Q6N077|Q96EL9|Q99833|Q9H1J3	Frame_Shift_Del	DEL	ENST00000389378.2	hg19	CCDS34280.1																																																																																			.	.	.	none		0.588	TNIP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374914.1	NM_006058		-	150443286	CATC	-	150443283	7	5	190	1	0	1	0	1	0	0	0	0	16326	594	21	0	1812	0	TNIP1	5	150443283	Frame_Shift_Del	DEL	CATC	TCGA-GL-A9DC-01A-11D-A36X-10	1	150443283	30471977	41	11218	105	3									
TNIP1	10318	hgsc.bcm.edu	37	chr5	150443286	150443286	+	Silent	SNP	C	C	T																															cggagcctggtcgcttccatCtgggactcttccaaaagctc																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr5:150443286C>T	ENST00000389378.2	-	3	747	c.159G>A	c.(157-159)caG>caA	p.Q53Q	TNIP1_ENST00000523338.1_Silent_p.Q53Q|TNIP1_ENST00000315050.7_Silent_p.Q53Q|TNIP1_ENST00000522226.1_Silent_p.Q53Q|TNIP1_ENST00000521591.1_Silent_p.Q53Q|TNIP1_ENST00000523200.1_Silent_p.Q53Q|TNIP1_ENST00000524280.1_Silent_p.Q53Q|TNIP1_ENST00000518977.1_Silent_p.Q53Q|TNIP1_ENST00000520931.1_5'UTR	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	53					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)			TCGCTTCCATCTGGGACTCTT	0.587																																					p.Q53Q		Atlas-SNP	.											.	TNIP1	51	.	0			c.G159A						PASS	.						71	74	73					5																	150443286		2203	4300	6503	SO:0001819	synonymous_variant	10318	exon3			TTCCATCTGGGAC	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.159G>A	chr5.hg19:g.150443286C>T		75.0	0.0	.		64.0	20.0	.	NM_001252385	A4F1W8|A4F1W9|A4F1X2|A4F1X4|A4F1X5|A4F1X6|A4F1X7|A4F1X9|B7Z699|E7EPY1|E7ET96|O76008|Q05KP3|Q05KP4|Q6N077|Q96EL9|Q99833|Q9H1J3	Silent	SNP	ENST00000389378.2	hg19	CCDS34280.1																																																																																			.	.	.	none		0.587	TNIP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374914.1	NM_006058		T	150443286	C	T	150443286	2	4	190	1	0	0	0	0	0	0	0	1	16326	912	32	2		2	TNIP1	5	150443286	Silent	SNP	C	TCGA-GL-A9DC-01A-11D-A36X-10	3	150443286	30471974	42	11219	105	3									
PKHD1	5314	hgsc.bcm.edu	37	chr6	51613145	51613145	+	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	ccacaacgttgccatggaggTtgatgtcctttacctggttc	7	13	10	11	1	0	1	0	1	0	0	2	2	1	2	4	3	3	3	4	3	2	5			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr6:51613145T>A	ENST00000371117.3	-	58	9544	c.9269A>T	c.(9268-9270)aAc>aTc	p.N3090I	PKHD1_ENST00000340994.4_Missense_Mutation_p.N3090I	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3090					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)					GCCATGGAGGTTGATGTCCTT	0.512																																					p.N3090I		Atlas-SNP	.											.	PKHD1	927	.	0			c.A9269T						PASS	.						217	188	198					6																	51613145		2203	4300	6503	SO:0001583	missense	5314	exon58			TGGAGGTTGATGT	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.9269A>T	chr6.hg19:g.51613145T>A	ENSP00000360158:p.Asn3090Ile	95.0	0.0	.		106.0	47.0	.	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	T	0.870	-0.732173	0.03135	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	T;T	0.79653	-1.29;-1.19	5.72	-11.4	0.00090	Pectin lyase fold/virulence factor (1);	1.979650	0.02080	N	0.052295	T	0.33206	0.0855	N	0.17723	0.515	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.12156	0.004;0.001;0.007	T	0.35176	-0.9799	10	0.18710	T	0.47	.	2.4497	0.04515	0.2549:0.1962:0.4045:0.1445	.	3090;3090;3090	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	I	3090	ENSP00000360158:N3090I;ENSP00000341097:N3090I	ENSP00000341097:N3090I	N	-	2	0	PKHD1	51721104	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.765000	0.01799	-1.898000	0.01100	-0.313000	0.08912	AAC	.	.	.	none		0.512	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51613145	T	A	51613145	3	1	190	1	0	0	0	0	1	0	0	0	11978	1725	60	5	3034	5	PKHD1	6	51613145	Missense_Mutation	SNP	T	TCGA-GL-A9DC-01A-11D-A36X-10		51613145	119501922	43	11220											
SYNCRIP	10492	hgsc.bcm.edu	37	chr6	86324737	86324740	+	Frame_Shift_Del	DEL	CTCG	CTCG	-																															ttgggcacctcctctcgcacCtcgaacgcctcttgctgatc																								rs371636541		TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	CTCG	CTCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr6:86324737_86324740delCTCG	ENST00000369622.3	-	11	2106_2109	c.1606_1609delCGAG	c.(1606-1611)cgaggtfs	p.RG536fs	RP11-321N4.5_ENST00000503906.1_Frame_Shift_Del_p.FE71fs|SYNCRIP_ENST00000355238.6_Frame_Shift_Del_p.RG536fs	NM_001159675.1|NM_006372.4	NP_001153147.1|NP_006363.4	O60506	HNRPQ_HUMAN	synaptotagmin binding, cytoplasmic RNA interacting protein	536	8 X 3 AA repeats of R-G-G.|Interaction with APOBEC1.|Interaction with SMN.				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)		CCTCTCGCACCTCGAACGCCTCTT	0.623																																					p.536_537del		Atlas-Indel,Pindel	.											.	SYNCRIP	80	.	0			c.1607_1610del						PASS	.																																			SO:0001589	frameshift_variant	10492	exon11			.	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.1606_1609delCGAG	chr6.hg19:g.86324737_86324740delCTCG	ENSP00000358635:p.Arg536fs	83.0	0.0	0		98.0	37.0	0.377551	NM_001159677	E1P501|E1P502|Q53H05|Q5TCG2|Q5TCG3|Q8IW78|Q8N599|Q96LC1|Q96LC2|Q9Y583	Frame_Shift_Del	DEL	ENST00000369622.3	hg19	CCDS5005.1																																																																																			.	.	.	none		0.623	SYNCRIP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041396.1	NM_006372		-	86324740	CTCG	-	86324737	7	5	190	1	0	1	0	1	0	0	0	0	15456	681	24	0	312	0	SYNCRIP	6	86324737	Frame_Shift_Del	DEL	CTCG	TCGA-GL-A9DC-01A-11D-A36X-10	34711592	86324737	84790330	44	11221											
TCP10L2	401285	hgsc.bcm.edu	37	chr6	167591988	167591988	+	Frame_Shift_Del	DEL	G	G	-																															ccagcacccactggaaggccGactcccggtgcagaaagacg																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr6:167591988delG	ENST00000366832.2	+	5	746	c.615delG	c.(613-615)ccgfs	p.P205fs		NM_001145121.1	NP_001138593.1	B9ZVM9	TCP2L_HUMAN	t-complex 10-like 2	205										endometrium(1)|kidney(2)|lung(3)	6						CTGGAAGGCCGACTCCCGGTG	0.522																																					p.P205fs		Atlas-Indel,Pindel	.											TCP10L2_ENST00000366832,NS,carcinoma,0,2	TCP10L2	41	.	0			c.614delC						PASS	.						229	205	212					6																	167591988		692	1590	2282	SO:0001589	frameshift_variant	401285	exon5			.		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.615delG	chr6.hg19:g.167591988delG	ENSP00000355797:p.Pro205fs	620.0	0.0	0		647.0	129.0	0.199382	NM_001145121		Frame_Shift_Del	DEL	ENST00000366832.2	hg19	CCDS47514.1																																																																																			.	.	.	none		0.522	TCP10L2-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043112.5	XR_040749		-	167591988	G	-	167591988	7	5	190	1	0	1	0	1	0	0	0	0	15724	1045	37	0	629	0	TCP10L2	6	167591988	Frame_Shift_Del	DEL	G	TCGA-GL-A9DC-01A-11D-A36X-10	81267251	167591988	3523079	45	11222											
EIF2AK1	27102	hgsc.bcm.edu	37	chr7	6068606	6068606	+	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	taggatgtctgtgcaggccaGaccaaagtctcctattttta	10	13	9	9	0	2	1	0	0	2	1	3	2	2	2	3	2	1	1	3	2	4	5			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr7:6068606G>C	ENST00000199389.6	-	12	1536	c.1390C>G	c.(1390-1392)Ctg>Gtg	p.L464V	EIF2AK1_ENST00000536084.1_Missense_Mutation_p.L340V|ANKRD61_ENST00000409061.1_5'Flank	NM_001134335.1|NM_014413.3	NP_001127807.1|NP_055228.2	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 1	464	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of cell proliferation (GO:0008285)|negative regulation of hemoglobin biosynthetic process (GO:0046986)|negative regulation of translational initiation by iron (GO:0045993)|protein autophosphorylation (GO:0046777)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|response to external stimulus (GO:0009605)|response to stress (GO:0006950)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	27		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)		GTGCAGGCCAGACCAAAGTCT	0.383																																					p.L464V		Atlas-SNP	.											.	EIF2AK1	76	.	0			c.C1390G						PASS	.						100	96	97					7																	6068606		2203	4300	6503	SO:0001583	missense	27102	exon12			AGGCCAGACCAAA	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.1390C>G	chr7.hg19:g.6068606G>C	ENSP00000199389:p.Leu464Val	107.0	0.0	.		108.0	43.0	.	NM_014413	A8K2R2|Q549K6|Q8NBW3|Q9HC02|Q9NYE0|Q9P0V6|Q9P1J5|Q9P2H8|Q9UHG4	Missense_Mutation	SNP	ENST00000199389.6	hg19	CCDS5345.1	.	.	.	.	.	.	.	.	.	.	G	16.24	3.067812	0.55539	.	.	ENSG00000086232	ENST00000199389;ENST00000536084;ENST00000426957	T;T	0.33438	1.54;1.41	4.85	3.06	0.35304	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000005	T	0.51312	0.1667	M	0.75777	2.31	0.47511	D	0.999445	D;D;P	0.89917	1.0;0.998;0.937	D;D;P	0.80764	0.994;0.924;0.85	T	0.50440	-0.8828	10	0.87932	D	0	-13.4813	9.2919	0.37791	0.2527:0.0:0.7473:0.0	.	340;463;464	B4DIP4;Q9BQI3-2;Q9BQI3	.;.;E2AK1_HUMAN	V	464;340;91	ENSP00000199389:L464V;ENSP00000445784:L340V	ENSP00000199389:L464V	L	-	1	2	EIF2AK1	6035132	0.991000	0.36638	0.999000	0.59377	0.991000	0.79684	2.311000	0.43717	0.486000	0.27676	-0.266000	0.10368	CTG	.	.	.	none		0.383	EIF2AK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207373.2	NM_014413		C	6068606	G	C	6068606	3	2	190	1	0	0	0	0	1	0	0	0	4998	933	33	4	518	4	EIF2AK1	7	6068606	Missense_Mutation	SNP	G	TCGA-GL-A9DC-01A-11D-A36X-10		6068606	153070057	46	11223											
HOXA11	3207	hgsc.bcm.edu	37	chr7	27224287	27224287	+	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	tcggcgctcttgtccccgggGtagtcggaggaggcgaggtt	4	9	18	10	5	1	0	0	0	1	0	4	3	2	2	2	7	0	3	2	7	1	3			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr7:27224287G>A	ENST00000006015.3	-	1	548	c.477C>T	c.(475-477)taC>taT	p.Y159Y	RP1-170O19.14_ENST00000523331.1_lincRNA|HOXA11-AS_ENST00000522674.1_RNA|HOXA11-AS_ENST00000522863.1_RNA|HOXA11-AS_ENST00000520395.1_RNA|HOXA11-AS_ENST00000520360.1_RNA	NM_005523.5	NP_005514.1	P31270	HXA11_HUMAN	homeobox A11	159					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						TGTCCCCGGGGTAGTCGGAGG	0.697			T	NUP98	CML																																p.Y159Y		Atlas-SNP	.		Dom	yes		7	7p15-p14.2	3207	homeo box A11		L	.	HOXA11	29	.	0			c.C477T						PASS	.						13	15	14					7																	27224287		2177	4275	6452	SO:0001819	synonymous_variant	3207	exon1			CCCGGGGTAGTCG		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.477C>T	chr7.hg19:g.27224287G>A		132.0	0.0	.		139.0	53.0	.	NM_005523	A4D190	Silent	SNP	ENST00000006015.3	hg19	CCDS5411.1	.	.	.	.	.	.	.	.	.	.	G	13.10	2.135477	0.37728	.	.	ENSG00000005073	ENST00000517402	.	.	.	5.25	4.36	0.52297	.	.	.	.	.	T	0.56381	0.1981	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53899	-0.8373	4	.	.	.	.	6.6845	0.23138	0.2056:0.1362:0.6583:0.0	.	.	.	.	I	129	.	.	T	-	2	0	HOXA11	27190812	0.993000	0.37304	1.000000	0.80357	0.990000	0.78478	1.028000	0.30128	2.436000	0.82500	0.655000	0.94253	ACC	.	.	.	none		0.697	HOXA11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358754.1			A	27224287	G	A	27224287	2	1	190	1	0	0	0	0	0	0	0	1	7297	1256	44	2		2	HOXA11	7	27224287	Silent	SNP	G	TCGA-GL-A9DC-01A-11D-A36X-10	21155681	27224287	131914376	47	11224											
CALCR	799	hgsc.bcm.edu	37	chr7	93055856	93055856	+	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	cctcccccaacgctggttccActgaattttgaattgggccc	7	11	8	15	1	0	2	0	2	0	0	2	2	2	2	5	2	1	2	5	2	3	4			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr7:93055856A>T	ENST00000394441.1	-	13	1552	c.1237T>A	c.(1237-1239)Tgg>Agg	p.W413R	CALCR_ENST00000359558.2_Missense_Mutation_p.W447R|CALCR_ENST00000360249.4_Missense_Mutation_p.W429R|CALCR_ENST00000421592.1_Missense_Mutation_p.W429R|CALCR_ENST00000426151.1_Missense_Mutation_p.W413R	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor	447					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)	CGCTGGTTCCACTGAATTTTG	0.542																																					p.W447R		Atlas-SNP	.											.	CALCR	200	.	0			c.T1339A						PASS	.						46	51	50					7																	93055856		2203	4300	6503	SO:0001583	missense	799	exon16			GGTTCCACTGAAT	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.1237T>A	chr7.hg19:g.93055856A>T	ENSP00000377959:p.Trp413Arg	97.0	0.0	.		124.0	55.0	.	NM_001164737	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Missense_Mutation	SNP	ENST00000394441.1	hg19	CCDS5631.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.937626	0.73557	.	.	ENSG00000004948	ENST00000359558;ENST00000360249;ENST00000421592;ENST00000394441;ENST00000426151	T;T;T;T;T	0.62498	0.02;0.02;0.02;0.02;0.02	4.57	4.57	0.56435	.	.	.	.	.	T	0.68659	0.3025	L	0.45228	1.405	0.51482	D	0.999925	D;P	0.71674	0.998;0.613	D;B	0.72075	0.976;0.248	T	0.66106	-0.6006	9	0.33141	T	0.24	.	10.4932	0.44762	1.0:0.0:0.0:0.0	.	447;413	F5H605;A4D1G6	.;.	R	447;429;429;413;413	ENSP00000352561:W447R;ENSP00000353385:W429R;ENSP00000399552:W429R;ENSP00000377959:W413R;ENSP00000389295:W413R	ENSP00000352561:W447R	W	-	1	0	CALCR	92893792	1.000000	0.71417	0.495000	0.27527	0.014000	0.08584	6.514000	0.73746	2.055000	0.61198	0.477000	0.44152	TGG	.	.	.	none		0.542	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742		T	93055856	A	T	93055856	3	4	190	1	0	0	0	0	1	0	0	0	2581	159	6	5	191	5	CALCR	7	93055856	Missense_Mutation	SNP	A	TCGA-GL-A9DC-01A-11D-A36X-10	65831569	93055856	66082807	48	11225											
FAM200A	221786	hgsc.bcm.edu	37	chr7	99145242	99145243	+	Frame_Shift_Ins	INS	-	-	T																															aattaacagttttcactgcaINStttttcaatacatccatcag																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr7:99145242_99145243insT	ENST00000449309.1	-	2	1167_1168	c.788_789insA	c.(787-789)aatfs	p.N263fs		NM_145111.3	NP_659802.1	Q8TCP9	F200A_HUMAN	family with sequence similarity 200, member A	263						integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			endometrium(1)|kidney(5)|large_intestine(2)|ovary(2)|skin(1)	11						ttttcactgcatttttcaatac	0.366																																					p.N263fs		Atlas-Indel,Pindel	.											.	FAM200A	27	.	0			c.789_790insA						PASS	.																																			SO:0001589	frameshift_variant	221786	exon2			.		CCDS5668.1	7q22.1	2010-02-22	2010-02-22	2010-02-22	ENSG00000221909	ENSG00000221909			25401	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 38"	C7orf38		10607616	Standard	NM_145111		Approved	FLJ36794, DKFZp727G131	uc003ura.3	Q8TCP9	OTTHUMG00000156723	ENST00000449309.1:c.789dupA	chr7.hg19:g.99145247_99145247dupT	ENSP00000411372:p.Asn263fs	93.0	0.0	0		125.0	54.0	0.432	NM_145111	A4D293|A8K3V9|B2RD92|C9J6A8|D6W5T2|Q8N9P3	Frame_Shift_Ins	INS	ENST00000449309.1	hg19	CCDS5668.1																																																																																			.	.	.	none		0.366	FAM200A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345467.1	NM_145111		T	99145243	-	T	99145242	7	5	190	1	0	1	1	0	0	0	0	0	5540	214	8	0	936	0	FAM200A	7	99145242	Frame_Shift_Ins	INS	-	TCGA-GL-A9DC-01A-11D-A36X-10	6089386	99145242	59993421	49	11226											
AP1S1	1174	hgsc.bcm.edu	37	chr7	100802348	100802349	+	Missense_Mutation	DNP	GC	GC	CT																															ccgccctcccaggtgtgcgaGctggacatcatcttcaactt																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr7:100802348_100802349GC>CT	ENST00000337619.5	+	4	418_419	c.300_301GC>CT	c.(298-303)gaGCtg>gaCTtg	p.E100D	MIR4653_ENST00000585107.1_RNA	NM_001283.3	NP_001274.1	P61966	AP1S1_HUMAN	adaptor-related protein complex 1, sigma 1 subunit	100					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)|receptor-mediated endocytosis (GO:0006898)|regulation of defense response to virus by virus (GO:0050690)|response to virus (GO:0009615)|viral process (GO:0016032)	AP-1 adaptor complex (GO:0030121)|coated pit (GO:0005905)|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)	protein transporter activity (GO:0008565)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)	8	Lung NSC(181;0.168)|all_lung(186;0.215)					AGGTGTGCGAGCTGGACATCAT	0.559																																					p.E100D|p.L101L		Atlas-SNP	.											.	AP1S1	22	.	0			c.G300C|c.C301T						PASS	.																																			SO:0001583	missense	1174	exon4			GTGCGAGCTGGAC|TGCGAGCTGGACA	AB015319	CCDS47669.1	7q22.1	2014-02-04			ENSG00000106367	ENSG00000106367			559	protein-coding gene	gene with protein product	"clathrin-associated/assembly/adaptor protein, small 1 (19kD)", "clathrin coat assembly protein AP19", "sigma1A subunit of AP-1 clathrin adaptor complex", "AP-1 complex subunit sigma-1A", "sigma1A-adaptin", "golgi adaptor HA1/AP1 adaptin sigma-1A subunit", "clathrin assembly protein complex 1 sigma-1A small chain", "HA1 19 kDa subunit"	603531	"erythrokeratodermia variabilis 3 (Kamouraska type)"	CLAPS1, EKV3		9653655, 9733768, 19057675	Standard	NM_001283		Approved	AP19, SIGMA1A, WUGSC:H_DJ0747G18.2	uc003uxv.4	P61966	OTTHUMG00000157103	Exception_encountered	chr7.hg19:g.100802348_100802349delinsCT	ENSP00000336666:p.Glu100Asp	31.0	0.0	.		46.0|48.0	15.0|16.0	.	NM_001283	B2R5D8|P82267|Q00382|Q53YA7|Q9BTN4|Q9UDW9	Missense_Mutation|Silent	SNP	ENST00000337619.5	hg19	CCDS47669.1																																																																																			.	.	.	none		0.559	AP1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347439.1	NM_001283		CT	100802349	GC	CT	100802348	3	2	190	1	0	0	0	0	1	0	0	0	736	962	34	4	314	4	AP1S1	7	100802348	Missense_Mutation	DNP	GC	TCGA-GL-A9DC-01A-11D-A36X-10	1657106	100802348	58336315	50	11227											
DOCK4	9732	hgsc.bcm.edu	37	chr7	111535707	111535707	+	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	tgagtgccatctggaagagtCctaccatcttcttgcatcag	9	12	9	11	0	4	2	1	1	3	1	5	3	5	3	3	1	3	1	3	1	2	3			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr7:111535707C>A	ENST00000437633.1	-	16	1804	c.1548G>T	c.(1546-1548)agG>agT	p.R516S	DOCK4_ENST00000476846.1_5'UTR|DOCK4_ENST00000428084.1_Missense_Mutation_p.R516S	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	516	DHR-1.				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)				CTGGAAGAGTCCTACCATCTT	0.413																																					p.R516S		Atlas-SNP	.											.	DOCK4	365	.	0			c.G1548T						PASS	.						228	209	215					7																	111535707		2001	4180	6181	SO:0001583	missense	9732	exon16			AAGAGTCCTACCA		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.1548G>T	chr7.hg19:g.111535707C>A	ENSP00000404179:p.Arg516Ser	112.0	0.0	.		173.0	74.0	.	NM_014705	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	hg19	CCDS47688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.45|19.45	3.830388|3.830388	0.71258|0.71258	.|.	.|.	ENSG00000128512|ENSG00000128512	ENST00000445943|ENST00000352877;ENST00000428084;ENST00000437633;ENST00000342288;ENST00000544250	.|T;T	.|0.14266	.|2.52;2.52	5.88|5.88	4.99|4.99	0.66335|0.66335	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.15955|0.15955	0.0384|0.0384	L|L	0.38175|0.38175	1.15|1.15	0.80722|0.80722	D|D	1|1	.|P;P;P	.|0.37548	.|0.599;0.599;0.599	.|B;P;B	.|0.45167	.|0.356;0.472;0.356	T|T	0.01065|0.01065	-1.1463|-1.1463	5|10	.|0.44086	.|T	.|0.13	.|.	10.7911|10.7911	0.46434|0.46434	0.0:0.8056:0.0:0.1944|0.0:0.8056:0.0:0.1944	.|.	.|516;516;516	.|Q149N2;Q149N5;Q8N1I0	.|.;.;DOCK4_HUMAN	V|S	504|504;516;516;504;515	.|ENSP00000410746:R516S;ENSP00000404179:R516S	.|ENSP00000345432:R504S	G|R	-|-	2|3	0|2	DOCK4|DOCK4	111322943|111322943	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	1.605000|1.605000	0.36815|0.36815	2.781000|2.781000	0.95711|0.95711	0.591000|0.591000	0.81541|0.81541	GGA|AGG	.	.	.	none		0.413	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705		A	111535707	C	A	111535707	3	1	190	1	0	0	0	0	1	0	0	0	4691	854	30	4	4500	4	DOCK4	7	111535707	Missense_Mutation	SNP	C	TCGA-GL-A9DC-01A-11D-A36X-10	10733359	111535707	47602956	51	11228											
PRKAG2	51422	hgsc.bcm.edu	37	chr7	151478467	151478467	+	Missense_Mutation	SNP	T	T	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	gagggccggggctgggggccTctggagaagaaccctttgga	7	6	19	9	1	1	2	0	0	1	2	1	5	1	3	3	7	1	1	3	7	2	1			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr7:151478467T>G	ENST00000287878.4	-	3	741	c.237A>C	c.(235-237)agA>agC	p.R79S	PRKAG2_ENST00000461529.1_5'UTR|PRKAG2_ENST00000392801.2_Missense_Mutation_p.R35S	NM_016203.3	NP_057287.2	Q9UGJ0	AAKG2_HUMAN	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	79					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)	GCTGGGGGCCTCTGGAGAAGA	0.642																																					p.R79S		Atlas-SNP	.											.	PRKAG2	86	.	0			c.A237C						PASS	.						13	16	15					7																	151478467		2202	4297	6499	SO:0001583	missense	51422	exon3			GGGGCCTCTGGAG	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.237A>C	chr7.hg19:g.151478467T>G	ENSP00000287878:p.Arg79Ser	92.0	0.0	.		130.0	54.0	.	NM_016203	Q53Y07|Q6NUI0|Q75MP4|Q9NUZ9|Q9UDN8|Q9ULX8	Missense_Mutation	SNP	ENST00000287878.4	hg19	CCDS5928.1	.	.	.	.	.	.	.	.	.	.	T	14.23	2.472139	0.43942	.	.	ENSG00000106617	ENST00000287878;ENST00000392801	D;D	0.90069	-2.29;-2.61	4.6	-0.604	0.11626	.	0.174068	0.43579	D	0.000545	T	0.80513	0.4637	L	0.27053	0.805	0.80722	D	1	P;B	0.46142	0.873;0.099	B;B	0.42361	0.385;0.027	T	0.75668	-0.3238	10	0.59425	D	0.04	.	9.7457	0.40446	0.0:0.3953:0.0:0.6047	.	79;79	Q8NCK6;Q9UGJ0	.;AAKG2_HUMAN	S	79;35	ENSP00000287878:R79S;ENSP00000376549:R35S	ENSP00000287878:R79S	R	-	3	2	PRKAG2	151109400	0.952000	0.32445	0.998000	0.56505	0.938000	0.57974	0.152000	0.16302	-0.121000	0.11787	-0.464000	0.05259	AGA	.	.	.	none		0.642	PRKAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348440.2	NM_016203		G	151478467	T	G	151478467	3	3	190	1	0	0	0	0	1	0	0	0	12511	1548	54	5	1528	5	PRKAG2	7	151478467	Missense_Mutation	SNP	T	TCGA-GL-A9DC-01A-11D-A36X-10	39942760	151478467	7660196	52	11229											
RBM33	155435	hgsc.bcm.edu	37	chr7	155530893	155530893	+	Frame_Shift_Del	DEL	A	A	-																															ccattcactcagccaggaccAgcatttaatcagcaaggaca																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr7:155530893delA	ENST00000401878.3	+	11	1731	c.1533delA	c.(1531-1533)ccafs	p.P511fs		NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33	511	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)		AGCCAGGACCAGCATTTAATC	0.572																																					p.P511fs		Atlas-Indel,Pindel	.											.	RBM33	157	.	0			c.1532delC						PASS	.						116	123	121					7																	155530893		2083	4230	6313	SO:0001589	frameshift_variant	155435	exon11			.	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.1533delA	chr7.hg19:g.155530893delA	ENSP00000384160:p.Pro511fs	143.0	0.0	0		165.0	77.0	0.466667	NM_053043	A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	Frame_Shift_Del	DEL	ENST00000401878.3	hg19	CCDS5941.2																																																																																			.	.	.	none		0.572	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317225.3	NM_001008408		-	155530893	A	-	155530893	7	5	190	1	0	1	0	1	0	0	0	0	13143	175	7	0	1575	0	RBM33	7	155530893	Frame_Shift_Del	DEL	A	TCGA-GL-A9DC-01A-11D-A36X-10	4052426	155530893	3607770	53	11230											
CSMD1	64478	hgsc.bcm.edu	37	chr8	3063031	3063031	+	Missense_Mutation	SNP	T	T	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	caaggacatccttaccgaatTcctttggtaccgtgatggaa	11	11	9	10	2	0	1	0	1	0	0	2	4	2	3	4	3	2	1	4	3	5	4	rs548826533		TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr8:3063031T>G	ENST00000520002.1	-	32	5537	c.4982A>C	c.(4981-4983)gAa>gCa	p.E1661A	CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000602723.1_Missense_Mutation_p.E1661A|CSMD1_ENST00000539096.1_Missense_Mutation_p.E1660A|CSMD1_ENST00000400186.3_Missense_Mutation_p.E1661A|CSMD1_ENST00000542608.1_Missense_Mutation_p.E1660A|CSMD1_ENST00000537824.1_Missense_Mutation_p.E1660A|CSMD1_ENST00000602557.1_Missense_Mutation_p.E1661A			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1661	CUB 10. {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)		CTTACCGAATTCCTTTGGTAC	0.383																																					p.E1660A		Atlas-SNP	.											.	CSMD1	1469	.	0			c.A4979C						PASS	.						69	66	67					8																	3063031		1842	4093	5935	SO:0001583	missense	64478	exon31			CCGAATTCCTTTG			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.4982A>C	chr8.hg19:g.3063031T>G	ENSP00000430733:p.Glu1661Ala	54.0	0.0	.		67.0	22.0	.	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.	.	.	.	.	.	.	.	.	.	T	15.03	2.713104	0.48517	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.60171	0.21;0.21;0.21;0.21;0.21	5.28	5.28	0.74379	CUB (5);	0.071868	0.56097	D	0.000031	T	0.66218	0.2767	L	0.31845	0.965	0.58432	D	0.999992	D;P;P	0.69078	0.997;0.537;0.84	D;B;P	0.80764	0.994;0.309;0.557	T	0.66204	-0.5982	10	0.41790	T	0.15	.	15.5029	0.75713	0.0:0.0:0.0:1.0	.	1661;1661;1661	E5RIG2;Q96PZ7;Q96PZ7-4	.;CSMD1_HUMAN;.	A	1661;1661;1523;1660;1660;1660	ENSP00000383047:E1661A;ENSP00000430733:E1661A;ENSP00000441462:E1660A;ENSP00000446243:E1660A;ENSP00000441675:E1660A	ENSP00000320445:E1523A	E	-	2	0	CSMD1	3050438	1.000000	0.71417	0.990000	0.47175	0.474000	0.32979	7.809000	0.86057	2.115000	0.64714	0.533000	0.62120	GAA	.	.	.	none		0.383	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		G	3063031	T	G	3063031	3	3	190	1	0	0	0	0	1	0	0	0	3946	1783	62	5	5875	5	CSMD1	8	3063031	Missense_Mutation	SNP	T	TCGA-GL-A9DC-01A-11D-A36X-10		3063031	143300991	54	11231											
KIAA0146	23514	hgsc.bcm.edu	37	chr8	48647877	48647877	+	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	ttatcactgcagagctacgaAgtgaagagtgtcctcggaaa	13	9	11	8	2	1	3	1	1	0	2	3	5	2	4	1	1	3	2	1	1	5	2			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr8:48647877A>T	ENST00000297423.4	+	20	2997	c.2613A>T	c.(2611-2613)gaA>gaT	p.E871D	SPIDR_ENST00000521214.1_3'UTR|SPIDR_ENST00000541342.1_Missense_Mutation_p.E801D|SPIDR_ENST00000518060.1_Missense_Mutation_p.K95M|SPIDR_ENST00000518074.1_Missense_Mutation_p.S812C|SPIDR_ENST00000517693.1_Missense_Mutation_p.E346D	NM_001080394.2|NM_001282916.1	NP_001073863.1|NP_001269845.1	Q14159	SPIDR_HUMAN	scaffolding protein involved in DNA repair	871					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)											AGAGCTACGAAGTGAAGAGTG	0.517																																					p.E871D		Atlas-SNP	.											.	KIAA0146	64	.	0			c.A2613T						PASS	.						184	195	191					8																	48647877		1971	4147	6118	SO:0001583	missense	23514	exon20			CTACGAAGTGAAG	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.2613A>T	chr8.hg19:g.48647877A>T	ENSP00000297423:p.Glu871Asp	193.0	0.0	.		214.0	90.0	.	NM_001080394	B4DFV2|B4E0Y6|Q96BI5	Missense_Mutation	SNP	ENST00000297423.4	hg19	CCDS43737.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	12.91|12.91|12.91	2.078043|2.078043|2.078043	0.36662|0.36662|0.36662	.|.|.	.|.|.	ENSG00000164808|ENSG00000164808|ENSG00000164808	ENST00000297423;ENST00000541342;ENST00000519141;ENST00000517693;ENST00000519362;ENST00000517619|ENST00000518060|ENST00000518074;ENST00000519401	.|.|.	.|.|.	.|.|.	5.73|5.73|5.73	1.97|1.97|1.97	0.26223|0.26223|0.26223	.|.|.	0.109030|.|.	0.64402|.|.	D|.|.	0.000010|.|.	T|T|T	0.58991|0.58991|0.58991	0.2161|0.2161|0.2161	L|L|L	0.40543|0.40543|0.40543	1.245|1.245|1.245	0.35176|0.35176|0.35176	D|D|D	0.771997|0.771997|0.771997	D;D;D;D|.|D	0.89917|.|0.89917	1.0;0.986;1.0;1.0|.|1.0	D;P;D;D|.|D	0.85130|.|0.73380	0.997;0.706;0.997;0.997|.|0.98	T|T|T	0.63310|0.63310|0.63310	-0.6666|-0.6666|-0.6666	9|6|8	0.38643|0.87932|0.40728	T|D|T	0.18|0|0.16	.|.|.	9.6477|9.6477|9.6477	0.39877|0.39877|0.39877	0.6588:0.0:0.3412:0.0|0.6588:0.0:0.3412:0.0|0.6588:0.0:0.3412:0.0	.|.|.	361;376;801;871|.|812	B4DZY2;B4DWT8;B4DFV2;Q14159|.|B4E0Y6	.;.;.;K0146_HUMAN|.|.	D|M|C	871;801;376;346;346;73|95|812;497	.|.|.	ENSP00000297423:E871D|ENSP00000429448:K95M|ENSP00000429487:S812C	E|K|S	+|+|+	3|2|1	2|0|0	KIAA0146|KIAA0146|KIAA0146	48810430|48810430|48810430	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.066000|0.066000|0.066000	0.16364|0.16364|0.16364	0.996000|0.996000|0.996000	0.29719|0.29719|0.29719	0.432000|0.432000|0.432000	0.26286|0.26286|0.26286	-0.558000|-0.558000|-0.558000	0.04189|0.04189|0.04189	GAA|AAG|AGT	.	.	.	none		0.517	SPIDR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377611.1	NM_001080394		T	48647877	A	T	48647877	3	4	190	1	0	0	0	0	1	0	0	0	8164	69	3	5	2691	5	KIAA0146	8	48647877	Missense_Mutation	SNP	A	TCGA-GL-A9DC-01A-11D-A36X-10	45584846	48647877	97716145	55	11232											
NSMAF	8439	hgsc.bcm.edu	37	chr8	59510054	59510055	+	Frame_Shift_Ins	INS	-	-	C																															aatagttgttttggtgtctgINScccaaattccaagatttgcg																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr8:59510054_59510055insC	ENST00000038176.3	-	21	1895_1896	c.1683_1684insG	c.(1681-1686)gggcagfs	p.Q562fs	NSMAF_ENST00000427130.2_Frame_Shift_Ins_p.Q593fs	NM_003580.3	NP_003571.2	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation associated factor	562	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.				ceramide metabolic process (GO:0006672)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)|sphingomyelin phosphodiesterase activator activity (GO:0016230)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	38		all_lung(136;0.174)|Lung NSC(129;0.2)				TTTGGTGTCTGCCCAAATTCCA	0.441																																					p.Q593fs		Atlas-Indel,Pindel	.											.	NSMAF	156	.	0			c.1777_1778insG						PASS	.																																			SO:0001589	frameshift_variant	8439	exon21			.	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.1684dupG	chr8.hg19:g.59510057_59510057dupC	ENSP00000038176:p.Gln562fs	96.0	0.0	0		114.0	47.0	0.412281	NM_001144772	B4DFB0|E9PCH0|Q8IW26	Frame_Shift_Ins	INS	ENST00000038176.3	hg19	CCDS6173.1																																																																																			.	.	.	none		0.441	NSMAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378384.1	NM_003580		C	59510055	-	C	59510054	7	5	190	1	0	1	1	0	0	0	0	0	10681	1328	46	0	1113	0	NSMAF	8	59510054	Frame_Shift_Ins	INS	-	TCGA-GL-A9DC-01A-11D-A36X-10	10862177	59510054	86853968	56	11233											
KLHL38	340359	hgsc.bcm.edu	37	chr8	124659249	124659249	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacgagtttctggaaatgtgAtaaacctgagggagagagag	14	8	14	5	1	1	4	0	2	1	2	1	8	1	5	1	2	1	1	1	2	3	2			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr8:124659249A>G	ENST00000325995.7	-	2	1379	c.1356T>C	c.(1354-1356)taT>taC	p.Y452Y	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	452										breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						TGGAAATGTGATAAACCTGAG	0.438																																					p.Y452Y		Atlas-SNP	.											.	KLHL38	81	.	0			c.T1356C						PASS	.						160	154	156					8																	124659249		1937	4136	6073	SO:0001819	synonymous_variant	340359	exon2			AATGTGATAAACC		CCDS43766.1	8q24.13	2013-02-22	2013-02-22		ENSG00000175946	ENSG00000175946		"Kelch-like", "BTB/POZ domain containing"	34435	protein-coding gene	gene with protein product			"kelch-like 38 (Drosophila)"				Standard	NM_001081675		Approved	C8ORFK36	uc003yqs.1	Q2WGJ6	OTTHUMG00000164983	ENST00000325995.7:c.1356T>C	chr8.hg19:g.124659249A>G		118.0	0.0	.		124.0	52.0	.	NM_001081675	A0PK12	Silent	SNP	ENST00000325995.7	hg19	CCDS43766.1																																																																																			.	.	.	none		0.438	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1			G	124659249	A	G	124659249	2	3	190	1	0	0	0	0	0	0	0	1	8397	340	12	3		3	KLHL38	8	124659249	Silent	SNP	A	TCGA-GL-A9DC-01A-11D-A36X-10	65149195	124659249	21704773	57	11234											
TRPM6	140803	hgsc.bcm.edu	37	chr9	77407562	77407564	+	In_Frame_Del	DEL	ATT	ATT	-																															tataaaaccaaaacttgacaAttggagcactgtagaactca																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	ATT	ATT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr9:77407562_77407564delATT	ENST00000360774.1	-	19	2751_2753	c.2514_2516delAAT	c.(2512-2517)ccaatt>cct	p.I839del	TRPM6_ENST00000376864.4_In_Frame_Del_p.I839del|TRPM6_ENST00000451710.3_In_Frame_Del_p.I839del|TRPM6_ENST00000361255.3_In_Frame_Del_p.I834del|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000449912.2_In_Frame_Del_p.I834del|TRPM6_ENST00000376871.3_Intron	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	839					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						AAACTTGACAATTGGAGCACTGT	0.394																																					p.839_839del		Atlas-INDEL	.											.	TRPM6	377	.	0			c.2515_2517del						PASS	.																																			SO:0001651	inframe_deletion	140803	exon19			.	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.2514_2516delAAT	chr9.hg19:g.77407562_77407564delATT	ENSP00000354006:p.Ile839del	137.0	0.0	0		113.0	51.0	0.451327	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	In_Frame_Del	DEL	ENST00000360774.1	hg19	CCDS6647.1																																																																																			.	.	.	none		0.394	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		-	77407564	ATT	-	77407562	7	5	190	1	0	1	0	1	0	0	0	0	16602	101	4	0	3636	0	TRPM6	9	77407562	In_Frame_Del	DEL	ATT	TCGA-GL-A9DC-01A-11D-A36X-10		77407562	63805869	58	11235	106	2									
TRPM6	140803	hgsc.bcm.edu	37	chr9	77407567	77407567	+	Frame_Shift_Del	DEL	A	A	-																															aaccaaaacttgacaattggAgcactgtagaactcatagac																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr9:77407567delA	ENST00000360774.1	-	19	2748	c.2511delT	c.(2509-2511)gctfs	p.A837fs	TRPM6_ENST00000376864.4_Frame_Shift_Del_p.A837fs|TRPM6_ENST00000451710.3_Frame_Shift_Del_p.A837fs|TRPM6_ENST00000361255.3_Frame_Shift_Del_p.A832fs|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000449912.2_Frame_Shift_Del_p.A832fs|TRPM6_ENST00000376871.3_Intron	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	837					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						TGACAATTGGAGCACTGTAGA	0.408																																					p.P838fs		Atlas-INDEL	.											.	TRPM6	377	.	0			c.2512delC						PASS	.						149	130	136					9																	77407567		2203	4300	6503	SO:0001589	frameshift_variant	140803	exon19			.	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.2511delT	chr9.hg19:g.77407567delA	ENSP00000354006:p.Ala837fs	135.0	0.0	0		120.0	55.0	0.458333	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Frame_Shift_Del	DEL	ENST00000360774.1	hg19	CCDS6647.1																																																																																			.	.	.	none		0.408	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		-	77407567	A	-	77407567	7	5	190	1	0	1	0	1	0	0	0	0	16602	291	11	0	3641	0	TRPM6	9	77407567	Frame_Shift_Del	DEL	A	TCGA-GL-A9DC-01A-11D-A36X-10	5	77407567	63805864	59	11236	106	2									
BICC1	80114	hgsc.bcm.edu	37	chr10	60560753	60560753	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtccctccaaggtttcctgTgccaaaaggcagacagtgga	10	9	11	11	0	0	1	0	0	0	1	3	2	3	2	4	3	1	2	4	3	3	1			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr10:60560753T>C	ENST00000373886.3	+	14	1966	c.1962T>C	c.(1960-1962)tgT>tgC	p.C654C	BICC1_ENST00000263103.1_Silent_p.C280C	NM_001080512.1	NP_001073981.1	Q9H694	BICC1_HUMAN	BicC family RNA binding protein 1	654					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						AGGTTTCCTGTGCCAAAAGGC	0.408																																					p.C654C		Atlas-SNP	.											.	BICC1	121	.	0			c.T1962C						PASS	.						130	118	122					10																	60560753		2203	4300	6503	SO:0001819	synonymous_variant	80114	exon14			TTCCTGTGCCAAA	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.1962T>C	chr10.hg19:g.60560753T>C		115.0	0.0	.		114.0	41.0	.	NM_001080512		Silent	SNP	ENST00000373886.3	hg19	CCDS31206.1																																																																																			.	.	.	none		0.408	BICC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048150.2	NM_025044		C	60560753	T	C	60560753	2	2	190	1	0	0	0	0	0	0	0	1	1427	1702	59	3		3	BICC1	10	60560753	Silent	SNP	T	TCGA-GL-A9DC-01A-11D-A36X-10		60560753	74973994	60	11237											
CC2D2B	387707	hgsc.bcm.edu	37	chr10	97784670	97784670	+	Intron	SNP	T	T	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	tagaagatctaaggaataggTactgtgttttcccctaatct	12	14	8	7	0	2	2	0	0	2	2	3	3	3	3	2	2	1	2	2	2	7	7			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr10:97784670T>A	ENST00000344386.3	+	8	944				ENTPD1-AS1_ENST00000458228.1_RNA|RP11-690P14.4_ENST00000475252.2_Intron|ENTPD1-AS1_ENST00000452728.1_RNA|CC2D2B_ENST00000410012.2_Splice_Site|ENTPD1-AS1_ENST00000416301.1_RNA|ENTPD1-AS1_ENST00000454638.1_RNA|ENTPD1-AS1_ENST00000451364.1_RNA|CC2D2B_ENST00000371198.2_Intron|ENTPD1-AS1_ENST00000449197.1_RNA	NM_001001732.3	NP_001001732.2	Q6DHV5	C2D2B_HUMAN	coiled-coil and C2 domain containing 2B											large_intestine(1)|lung(7)|ovary(1)|urinary_tract(1)	10		Colorectal(252;0.158)		Epithelial(162;7.08e-08)|all cancers(201;2.71e-06)		AAGGAATAGGTACTGTGTTTT	0.363																																					.		Atlas-SNP	.											.	CC2D2B	46	.	0			c.839+2T>A						PASS	.						312	273	285					10																	97784670		692	1591	2283	SO:0001627	intron_variant	387707	exon10			AATAGGTACTGTG	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.780+5089T>A	chr10.hg19:g.97784670T>A		153.0	0.0	.		155.0	77.0	.	NM_001159747	A2A3E9|B4DYD4|E9PCC3|Q5VUS0	Splice_Site	SNP	ENST00000344386.3	hg19	CCDS41555.1	.	.	.	.	.	.	.	.	.	.	T	15.03	2.713349	0.48517	.	.	ENSG00000188649	ENST00000451649;ENST00000410012	.	.	.	6.17	6.17	0.99709	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3455	0.66658	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	CC2D2B	97774660	1.000000	0.71417	0.958000	0.39756	0.348000	0.29142	4.719000	0.61937	2.371000	0.80710	0.533000	0.62120	.	.	.	.	none		0.363	CC2D2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049573.3	NM_001001732		A	97784670	T	A	97784670	1	1	190	0	1	0	0	0	0	0	0	0	2731	1652	57	5		5	CC2D2B	10	97784670	Intron	SNP	T	TCGA-GL-A9DC-01A-11D-A36X-10	37223917	97784670	37750077	61	11238											
RRP12	23223	hgsc.bcm.edu	37	chr10	99141485	99141485	+	Missense_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	gcagtaccttgaggctctgcGtagcagcagtcagcacttgc	8	9	12	12	1	2	1	1	1	1	0	2	1	2	1	1	1	6	7	1	1	2	4			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr10:99141485G>A	ENST00000370992.4	-	11	1418	c.1307C>T	c.(1306-1308)aCg>aTg	p.T436M	RRP12_ENST00000536831.1_Missense_Mutation_p.T154M|RRP12_ENST00000315563.6_Missense_Mutation_p.T336M|RRP12_ENST00000414986.1_Missense_Mutation_p.T375M	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	436						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.T436M(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		GAGGCTCTGCGTAGCAGCAGT	0.597																																					p.T436M		Atlas-SNP	.											RRP12,colon,carcinoma,+1,1	RRP12	97	.	1	Substitution - Missense(1)	ovary(1)	c.C1307T						PASS	.						69	58	62					10																	99141485		2203	4300	6503	SO:0001583	missense	23223	exon11			CTCTGCGTAGCAG		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.1307C>T	chr10.hg19:g.99141485G>A	ENSP00000360031:p.Thr436Met	293.0	0.0	.		363.0	173.0	.	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Missense_Mutation	SNP	ENST00000370992.4	hg19	CCDS7457.1	.	.	.	.	.	.	.	.	.	.	G	19.78	3.891743	0.72524	.	.	ENSG00000052749	ENST00000370992;ENST00000315563;ENST00000414986;ENST00000536831	T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13	5.7	5.7	0.88788	Armadillo-like helical (1);Armadillo-type fold (1);	0.223488	0.48767	D	0.000171	T	0.73337	0.3574	L	0.56769	1.78	0.42336	D	0.992316	D;B;D;D	0.76494	0.999;0.139;0.998;0.998	P;B;P;P	0.59424	0.8;0.052;0.857;0.724	T	0.67699	-0.5603	10	0.22706	T	0.39	-17.4342	19.8221	0.96602	0.0:0.0:1.0:0.0	.	375;336;154;436	E9PCK7;Q5JTH9-2;F5H456;Q5JTH9	.;.;.;RRP12_HUMAN	M	436;336;375;154	ENSP00000360031:T436M;ENSP00000324315:T336M;ENSP00000414863:T375M;ENSP00000446184:T154M	ENSP00000324315:T336M	T	-	2	0	RRP12	99131475	1.000000	0.71417	0.998000	0.56505	0.242000	0.25591	9.563000	0.98148	2.684000	0.91462	0.563000	0.77884	ACG	.	.	.	none		0.597	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179		A	99141485	G	A	99141485	3	1	190	1	0	0	0	0	1	0	0	0	13699	1145	40	1	2682	1	RRP12	10	99141485	Missense_Mutation	SNP	G	TCGA-GL-A9DC-01A-11D-A36X-10	1356815	99141485	36393262	62	11239											
PSTK	118672	hgsc.bcm.edu	37	chr10	124740027	124740027	+	Missense_Mutation	SNP	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	cgagaacatcagaggaaccgGcagcgacgggccgcggaaac	13	1	15	12	6	1	2	1	0	0	2	1	6	1	4	2	4	4	1	2	4	3	0			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr10:124740027G>A	ENST00000368887.3	+	1	472	c.32G>A	c.(31-33)gGc>gAc	p.G11D	PSTK_ENST00000405485.1_Missense_Mutation_p.G11D	NM_153336.2	NP_699167.2	Q8IV42	PSTK_HUMAN	phosphoseryl-tRNA kinase	11					selenocysteine incorporation (GO:0001514)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|tRNA binding (GO:0000049)			endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|skin(1)|stomach(2)	13		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.0686)|COAD - Colon adenocarcinoma(40;0.0725)		AGAGGAACCGGCAGCGACGGG	0.701											OREG0020597	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G11D		Atlas-SNP	.											.	PSTK	34	.	0			c.G32A						PASS	.						18	21	20					10																	124740027		2194	4282	6476	SO:0001583	missense	118672	exon1			GAACCGGCAGCGA	AK127173	CCDS7633.1	10q26.13	2007-04-17	2007-04-17	2007-04-17	ENSG00000179988	ENSG00000179988			28578	protein-coding gene	gene with protein product		611310	"chromosome 10 open reading frame 89"	C10orf89		15317934	Standard	NM_153336		Approved	MGC35392	uc001lgy.1	Q8IV42	OTTHUMG00000019191	ENST00000368887.3:c.32G>A	chr10.hg19:g.124740027G>A	ENSP00000357882:p.Gly11Asp	142.0	0.0	.	1536	165.0	80.0	.	NM_153336	Q6ZSS9	Missense_Mutation	SNP	ENST00000368887.3	hg19	CCDS7633.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.314|8.314	0.822752|0.822752	0.16678|0.16678	.|.	.|.	ENSG00000179988|ENSG00000179988	ENST00000406217|ENST00000368887;ENST00000405485	.|T;T	.|0.43688	.|0.94;0.98	3.99|3.99	-3.11|-3.11	0.05299|0.05299	.|.	.|1.236170	.|0.06046	.|N	.|0.655665	T|T	0.27169|0.27169	0.0666|0.0666	L|L	0.34521|0.34521	1.04|1.04	0.09310|0.09310	N|N	1|1	.|B	.|0.06786	.|0.001	.|B	.|0.08055	.|0.003	T|T	0.17715|0.17715	-1.0360|-1.0360	5|10	.|0.22109	.|T	.|0.4	-0.0124|-0.0124	5.4915|5.4915	0.16779|0.16779	0.5242:0.1624:0.3135:0.0|0.5242:0.1624:0.3135:0.0	.|.	.|11	.|Q8IV42	.|PSTK_HUMAN	T|D	12|11	.|ENSP00000357882:G11D;ENSP00000384764:G11D	.|ENSP00000357882:G11D	A|G	+|+	1|2	0|0	PSTK|PSTK	124730017|124730017	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.038000|0.038000	0.13279|0.13279	-0.052000|-0.052000	0.11865|0.11865	-1.010000|-1.010000	0.03396|0.03396	0.655000|0.655000	0.94253|0.94253	GCA|GGC	.	.	.	none		0.701	PSTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050811.1	NM_153336		A	124740027	G	A	124740027	3	1	190	1	0	0	0	0	1	0	0	0	12730	1203	42	2	34	2	PSTK	10	124740027	Missense_Mutation	SNP	G	TCGA-GL-A9DC-01A-11D-A36X-10	25598542	124740027	10794720	63	11240											
OR51S1	119692	hgsc.bcm.edu	37	chr11	4869827	4869827	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agaaccacaaataggctgtaGgctgcaccccaagcttctgg	12	7	10	12	0	1	1	0	0	1	1	1	1	1	1	3	3	3	5	3	3	5	3			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr11:4869827G>A	ENST00000322101.2	-	1	687	c.612C>T	c.(610-612)gcC>gcT	p.A204A	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004758.1	NP_001004758.1	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S, member 1	204						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)		ATAGGCTGTAGGCTGCACCCC	0.532																																					p.A204A		Atlas-SNP	.											.	OR51S1	83	.	0			c.C612T						PASS	.						77	83	81					11																	4869827		2201	4298	6499	SO:0001819	synonymous_variant	119692	exon1			GCTGTAGGCTGCA	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.612C>T	chr11.hg19:g.4869827G>A		140.0	0.0	.		176.0	64.0	.	NM_001004758	B9EGZ1|Q6IFI2	Silent	SNP	ENST00000322101.2	hg19	CCDS31362.1																																																																																			.	.	.	none		0.532	OR51S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142179.1	NM_001004758		A	4869827	G	A	4869827	2	1	190	1	0	0	0	0	0	0	0	1	11112	987	35	2		2	OR51S1	11	4869827	Silent	SNP	G	TCGA-GL-A9DC-01A-11D-A36X-10		4869827	130136689	64	11241											
USP47	55031	hgsc.bcm.edu	37	chr11	11924349	11924349	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttttgttacaaaccagcaaAaagagagcaattgaaaccac	18	8	7	8	0	0	2	0	1	0	1	0	3	0	2	2	0	5	4	2	0	6	4			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr11:11924349A>G	ENST00000399455.2	+	7	861	c.741A>G	c.(739-741)aaA>aaG	p.K247K	USP47_ENST00000339865.5_Silent_p.K159K|USP47_ENST00000527733.1_Silent_p.K227K|USP47_ENST00000539466.1_5'UTR	NM_001282659.1	NP_001269588.1	Q96K76	UBP47_HUMAN	ubiquitin specific peptidase 47	247	USP.				base-excision repair (GO:0006284)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell growth (GO:0030307)|response to drug (GO:0042493)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-specific protease activity (GO:0004843)|WD40-repeat domain binding (GO:0071987)			breast(4)|endometrium(7)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46				Epithelial(150;0.000339)		AAACCAGCAAAAAGAGAGCAA	0.348																																					p.K159K		Atlas-SNP	.											.	USP47	91	.	0			c.A477G						PASS	.						125	118	120					11																	11924349		1818	4070	5888	SO:0001819	synonymous_variant	55031	exon5			CAGCAAAAAGAGA	AK027362	CCDS41619.1, CCDS60725.1	11p15.2	2008-02-05	2005-08-08		ENSG00000170242	ENSG00000170242		"Ubiquitin-specific peptidases"	20076	protein-coding gene	gene with protein product		614460	"Trf (TATA binding protein-related factor)-proximal homolog (Drosophila)", "ubiquitin specific protease 47"			12838346	Standard	XM_005252997		Approved		uc001mjr.3	Q96K76	OTTHUMG00000165685	ENST00000399455.2:c.741A>G	chr11.hg19:g.11924349A>G		484.0	0.0	.		594.0	252.0	.	NM_017944	B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1	Silent	SNP	ENST00000399455.2	hg19																																																																																				.	.	.	none		0.348	USP47-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000385853.2	NM_017944		G	11924349	A	G	11924349	2	3	190	1	0	0	0	0	0	0	0	1	17090	11	1	3		3	USP47	11	11924349	Silent	SNP	A	TCGA-GL-A9DC-01A-11D-A36X-10	7054522	11924349	123082167	65	11242											
GLYATL1	92292	hgsc.bcm.edu	37	chr11	58722267	58722267	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgactgatgacatggattcaTacacaaacgtatatcgtatg	14	12	8	7	2	1	3	1	3	0	0	2	4	1	4	0	1	2	2	0	1	5	5			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr11:58722267T>C	ENST00000317391.4	+	6	551	c.211T>C	c.(211-213)Tac>Cac	p.Y71H	GLYATL1_ENST00000300079.5_Missense_Mutation_p.Y102H|RP11-142C4.6_ENST00000533954.1_RNA	NM_001220494.1	NP_001207423.1	Q969I3	GLYL1_HUMAN	glycine-N-acyltransferase-like 1	71						mitochondrion (GO:0005739)	glutamine N-acyltransferase activity (GO:0047946)|glycine N-acyltransferase activity (GO:0047961)			NS(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|skin(4)|urinary_tract(1)	34					Glycine(DB00145)	CATGGATTCATACACAAACGT	0.368																																					p.Y102H		Atlas-SNP	.											.	GLYATL1	89	.	0			c.T304C						PASS	.						94	88	90					11																	58722267		2201	4295	6496	SO:0001583	missense	92292	exon5			GATTCATACACAA	AK091965	CCDS31556.1, CCDS55768.1	11q12.1	2014-08-12			ENSG00000166840	ENSG00000166840			30519	protein-coding gene	gene with protein product		614761				12477932	Standard	NM_080661		Approved	MGC15397, FLJ34646	uc001nnh.2	Q969I3	OTTHUMG00000167221	ENST00000317391.4:c.211T>C	chr11.hg19:g.58722267T>C	ENSP00000322223:p.Tyr71His	283.0	0.0	.		294.0	119.0	.	NM_080661	A6NDT0|Q7Z510|Q8NAW8	Missense_Mutation	SNP	ENST00000317391.4	hg19	CCDS55768.1	.	.	.	.	.	.	.	.	.	.	.	11.71	1.719568	0.30503	.	.	ENSG00000166840	ENST00000526351;ENST00000317391;ENST00000532726;ENST00000300079	T;T;T;T	0.23147	1.92;1.92;1.92;1.92	2.37	1.19	0.21007	Acyl-CoA N-acyltransferase (1);Glycine N-acyltransferase, N-terminal (1);	0.782658	0.10400	U	0.679322	T	0.39489	0.1080	M	0.67397	2.05	0.09310	N	0.999999	D;D	0.67145	0.995;0.996	P;P	0.61722	0.829;0.893	T	0.16778	-1.0391	9	.	.	.	.	4.1384	0.10181	0.0:0.1862:0.0:0.8138	.	102;71	Q969I3-2;Q969I3	.;GLYL1_HUMAN	H	94;71;71;102	ENSP00000434652:Y94H;ENSP00000322223:Y71H;ENSP00000436116:Y71H;ENSP00000300079:Y102H	.	Y	+	1	0	GLYATL1	58478843	0.166000	0.22962	0.001000	0.08648	0.037000	0.13140	1.220000	0.32491	0.172000	0.19760	0.164000	0.16699	TAC	.	.	.	none		0.368	GLYATL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393783.1	NM_080661		C	58722267	T	C	58722267	3	2	190	1	0	0	0	0	1	0	0	0	6487	1406	49	3	322	3	GLYATL1	11	58722267	Missense_Mutation	SNP	T	TCGA-GL-A9DC-01A-11D-A36X-10	46797918	58722267	76284249	66	11243											
WDR74	54663	hgsc.bcm.edu	37	chr11	62600570	62600570	+	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	ctctgtgtcttctaggggcaCcttgttgggttcttgaggct	3	16	13	9	0	4	1	0	1	4	0	4	1	4	1	1	4	0	4	1	4	1	6			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr11:62600570C>A	ENST00000525239.1	-	12	1549	c.1012G>T	c.(1012-1014)Gtg>Ttg	p.V338L	WDR74_ENST00000529106.1_Missense_Mutation_p.V338L|WDR74_ENST00000311713.7_Missense_Mutation_p.V319L|RP11-727F15.9_ENST00000535867.1_RNA|STX5_ENST00000294179.3_5'Flank|WDR74_ENST00000525752.1_Missense_Mutation_p.V281L|WDR74_ENST00000540620.1_5'Flank|STX5_ENST00000377897.4_5'Flank|WDR74_ENST00000278856.4_Missense_Mutation_p.V338L|RP11-727F15.9_ENST00000535817.1_RNA|STX5_ENST00000394690.1_5'Flank|STX5_ENST00000541317.1_5'Flank			Q6RFH5	WDR74_HUMAN	WD repeat domain 74	338					blastocyst formation (GO:0001825)|RNA metabolic process (GO:0016070)	nucleolus (GO:0005730)|nucleus (GO:0005634)				kidney(2)|large_intestine(1)|liver(1)|lung(3)|ovary(1)	8						TCTAGGGGCACCTTGTTGGGT	0.587																																					p.V338L		Atlas-SNP	.											.	WDR74	36	.	0			c.G1012T						PASS	.						70	69	69					11																	62600570		1871	4104	5975	SO:0001583	missense	54663	exon12			GGGGCACCTTGTT		CCDS44630.1	11q12.3	2013-01-09				ENSG00000133316		"WD repeat domain containing"	25529	protein-coding gene	gene with protein product							Standard	NM_018093		Approved	FLJ10439	uc001nvm.2	Q6RFH5		ENST00000525239.1:c.1012G>T	chr11.hg19:g.62600570C>A	ENSP00000432119:p.Val338Leu	95.0	0.0	.		83.0	35.0	.	NM_018093	A8K8G5|Q9BRC9|Q9H6X8|Q9NVY2	Missense_Mutation	SNP	ENST00000525239.1	hg19	CCDS44630.1	.	.	.	.	.	.	.	.	.	.	C	2.862	-0.235939	0.05944	.	.	ENSG00000133316	ENST00000311713;ENST00000529106;ENST00000525239;ENST00000278856;ENST00000535048;ENST00000525752	T	0.43294	0.95	4.97	0.918	0.19386	.	0.666571	0.13764	N	0.364341	T	0.25382	0.0617	L	0.36672	1.1	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.18209	-1.0344	10	0.27785	T	0.31	-0.0311	1.6117	0.02695	0.1606:0.4701:0.1821:0.1872	.	281;338;319	E9PS41;Q6RFH5;Q6RFH5-2	.;WDR74_HUMAN;.	L	319;338;338;338;134;281	ENSP00000432113:V281L	ENSP00000278856:V338L	V	-	1	0	WDR74	62357146	0.000000	0.05858	0.000000	0.03702	0.337000	0.28794	0.091000	0.15046	0.011000	0.14865	0.655000	0.94253	GTG	.	.	.	none		0.587	WDR74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395678.1	NM_018093		A	62600570	C	A	62600570	3	1	190	1	0	0	0	0	1	0	0	0	17336	507	18	4	149	4	WDR74	11	62600570	Missense_Mutation	SNP	C	TCGA-GL-A9DC-01A-11D-A36X-10	3878303	62600570	72405946	67	11244											
ARAP1	116985	hgsc.bcm.edu	37	chr11	72408128	72408132	+	Frame_Shift_Del	DEL	CTGCT	CTGCT	-																															gaggaaacatcatccacgtgCtgctcgccctccttgaggtg																								rs377204604		TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	CTGCT	CTGCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr11:72408128_72408132delCTGCT	ENST00000393609.3	-	22	3264_3268	c.3062_3066delAGCAG	c.(3061-3066)gagcagfs	p.EQ1021fs	ARAP1_ENST00000359373.5_Frame_Shift_Del_p.EQ1021fs|ARAP1_ENST00000455638.2_Frame_Shift_Del_p.EQ1021fs|ARAP1_ENST00000429686.1_Frame_Shift_Del_p.EQ715fs|ARAP1_ENST00000426523.1_Frame_Shift_Del_p.EQ776fs|ARAP1_ENST00000334211.8_Frame_Shift_Del_p.EQ776fs|ARAP1_ENST00000393605.3_Frame_Shift_Del_p.EQ781fs|ARAP1_ENST00000495878.1_5'UTR	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	1021	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				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						CATCCACGTGCTGCTCGCCCTCCTT	0.649																																					p.1021_1023del	Ovarian(102;1198 1520 13195 17913 37529)	Atlas-Indel,Pindel	.											.	ARAP1	168	.	0			c.3063_3067del						PASS	.																																			SO:0001589	frameshift_variant	116985	exon22			.	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.3062_3066delAGCAG	chr11.hg19:g.72408128_72408132delCTGCT	ENSP00000377233:p.Glu1021fs	84.0	0.0	0		69.0	24.0	0.347826	NM_001040118	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Frame_Shift_Del	DEL	ENST00000393609.3	hg19	CCDS41687.1																																																																																			.	.	.	none		0.649	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118		-	72408132	CTGCT	-	72408128	7	5	190	1	0	1	0	1	0	0	0	0	838	796	28	0	1342	0	ARAP1	11	72408128	Frame_Shift_Del	DEL	CTGCT	TCGA-GL-A9DC-01A-11D-A36X-10	9807558	72408128	62598388	68	11245											
DDX10	1662	hgsc.bcm.edu	37	chr11	108593893	108593893	+	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	cctacttcaatgagaaaatgTccatccttcaaaaaggtgga	15	10	7	9	0	2	1	2	1	0	1	4	3	4	2	3	2	1	0	3	2	6	3			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr11:108593893T>A	ENST00000322536.3	+	13	1798	c.1669T>A	c.(1669-1671)Tcc>Acc	p.S557T	DDX10_ENST00000526794.1_Missense_Mutation_p.S557T	NM_004398.2	NP_004389.2	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	557					metabolic process (GO:0008152)		ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			breast(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|prostate(2)	27		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		TGAGAAAATGTCCATCCTTCA	0.433			T	NUP98	AML*																																p.S557T		Atlas-SNP	.		Dom	yes		11	11q22-q23	1662	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10		L	.	DDX10	70	.	0			c.T1669A						PASS	.						68	67	67					11																	108593893		2201	4298	6499	SO:0001583	missense	1662	exon13			AAAATGTCCATCC	U28042	CCDS8342.1	11q22-q23	2005-10-11	2003-06-13		ENSG00000178105	ENSG00000178105		"DEAD-boxes"	2735	protein-coding gene	gene with protein product		601235	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 10 (RNA helicase)"			8660968	Standard	NM_004398		Approved	HRH-J8	uc001pkm.3	Q13206	OTTHUMG00000166540	ENST00000322536.3:c.1669T>A	chr11.hg19:g.108593893T>A	ENSP00000314348:p.Ser557Thr	131.0	0.0	.		127.0	58.0	.	NM_004398	B2RCQ3|Q5BJD8	Missense_Mutation	SNP	ENST00000322536.3	hg19	CCDS8342.1	.	.	.	.	.	.	.	.	.	.	T	10.97	1.501157	0.26861	.	.	ENSG00000178105	ENST00000322536;ENST00000456020;ENST00000526794	T;T	0.41065	1.01;1.02	4.9	3.68	0.42216	.	0.222920	0.38959	N	0.001508	T	0.17492	0.0420	N	0.08118	0	0.26714	N	0.970905	B;B	0.19583	0.013;0.037	B;B	0.16289	0.01;0.015	T	0.13548	-1.0505	10	0.13853	T	0.58	-9.0985	5.0685	0.14594	0.1615:0.0897:0.0:0.7488	.	557;557	Q13206;E9PIF2	DDX10_HUMAN;.	T	557;463;557	ENSP00000314348:S557T;ENSP00000432032:S557T	ENSP00000314348:S557T	S	+	1	0	DDX10	108099103	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	2.025000	0.41059	1.954000	0.56735	0.397000	0.26171	TCC	.	.	.	none		0.433	DDX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390343.1	NM_004398		A	108593893	T	A	108593893	3	1	190	1	0	0	0	0	1	0	0	0	4344	1667	58	5	1719	5	DDX10	11	108593893	Missense_Mutation	SNP	T	TCGA-GL-A9DC-01A-11D-A36X-10	36185765	108593893	26412623	69	11246											
DDX25	29118	hgsc.bcm.edu	37	chr11	125791201	125791201	+	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	gggcggacggggcgctttggGaaaaaaggccttgccttcaa	9	7	16	9	3	1	0	1	0	0	0	1	2	1	2	2	6	1	1	2	6	4	3			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr11:125791201G>C	ENST00000263576.6	+	11	1472	c.1317G>C	c.(1315-1317)ggG>ggC	p.G439G	DDX25_ENST00000525943.1_3'UTR|RP11-680F20.9_ENST00000533033.2_RNA	NM_013264.4	NP_037396.3	Q9UHL0	DDX25_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 25	439	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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)		GGCGCTTTGGGAAAAAAGGCC	0.493																																					p.G439G		Atlas-SNP	.											.	DDX25	65	.	0			c.G1317C						PASS	.						46	45	46					11																	125791201		1922	4128	6050	SO:0001819	synonymous_variant	29118	exon11			CTTTGGGAAAAAA	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.1317G>C	chr11.hg19:g.125791201G>C		98.0	0.0	.		129.0	61.0	.	NM_013264	B2R6Z0|Q5XVN2|Q86W81|Q8IYP1	Silent	SNP	ENST00000263576.6	hg19	CCDS44766.1																																																																																			.	.	.	none		0.493	DDX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386736.3	NM_013264		C	125791201	G	C	125791201	2	2	190	1	0	0	0	0	0	0	0	1	4354	1161	41	4		4	DDX25	11	125791201	Silent	SNP	G	TCGA-GL-A9DC-01A-11D-A36X-10	17197308	125791201	9215315	70	11247											
SRPR	6734	hgsc.bcm.edu	37	chr11	126134972	126134972	+	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	tgtagggcactcaaacgccgGgtgtgtgtacgcagctgctc	7	9	14	11	3	1	0	1	0	0	0	2	0	1	0	1	2	4	6	1	2	3	2			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr11:126134972G>T	ENST00000332118.6	-	11	1561	c.1407C>A	c.(1405-1407)acC>acA	p.T469T	SRPR_ENST00000530680.1_5'Flank|SRPR_ENST00000532259.1_Silent_p.T441T	NM_003139.3	NP_003130.2	P08240	SRPR_HUMAN	signal recognition particle receptor (docking protein)	469					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)		TCAAACGCCGGGTGTGTGTAC	0.547																																					p.T469T		Atlas-SNP	.											.	SRPR	60	.	0			c.C1407A						PASS	.						67	61	63					11																	126134972		2201	4299	6500	SO:0001819	synonymous_variant	6734	exon11			ACGCCGGGTGTGT	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.1407C>A	chr11.hg19:g.126134972G>T		103.0	0.0	.		88.0	35.0	.	NM_003139	A6NIB3|B2R5Z8|B4E0H3|E9PJS4|Q9BVJ4	Silent	SNP	ENST00000332118.6	hg19	CCDS31717.1																																																																																			.	.	.	none		0.547	SRPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386425.2	NM_003139		T	126134972	G	T	126134972	2	4	190	1	0	0	0	0	0	0	0	1	15174	1219	43	4		4	SRPR	11	126134972	Silent	SNP	G	TCGA-GL-A9DC-01A-11D-A36X-10	343771	126134972	8871544	71	11248											
ACSM4	341392	hgsc.bcm.edu	37	chr12	7459269	7459269	+	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	ccctgtggcctgcagagaggAgaccgtttggccgtgattct	6	10	14	11	2	1	3	0	1	1	2	1	5	1	3	4	3	1	2	4	3	0	2			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr12:7459269A>T	ENST00000399422.4	+	2	390	c.342A>T	c.(340-342)ggA>ggT	p.G114G		NM_001080454.1	NP_001073923.1	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member 4	114					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						TGCAGAGAGGAGACCGTTTGG	0.522																																					p.G114G		Atlas-SNP	.											.	ACSM4	98	.	0			c.A342T						PASS	.						77	85	83					12																	7459269		2093	4251	6344	SO:0001819	synonymous_variant	341392	exon2			GAGAGGAGACCGT		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.342A>T	chr12.hg19:g.7459269A>T		128.0	0.0	.		240.0	161.0	.	NM_001080454	A8MTI6	Silent	SNP	ENST00000399422.4	hg19	CCDS44825.1																																																																																			.	.	.	none		0.522	ACSM4-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337866.2	NM_001080454		T	7459269	A	T	7459269	2	4	190	1	0	0	0	0	0	0	0	1	186	291	11	5		5	ACSM4	12	7459269	Silent	SNP	A	TCGA-GL-A9DC-01A-11D-A36X-10		7459269	126392626	72	11249											
CAPZA3	93661	hgsc.bcm.edu	37	chr12	18891585	18891585	+	Missense_Mutation	SNP	A	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	tctgtgcgccttaaaactgtAtgtgaatgaccactatccaa	12	12	7	10	1	1	2	0	2	1	0	2	2	2	2	3	0	2	1	3	0	6	3			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr12:18891585A>C	ENST00000317658.3	+	1	541	c.383A>C	c.(382-384)tAt>tCt	p.Y128S	PLCZ1_ENST00000266505.7_5'Flank|PLCZ1_ENST00000539875.1_5'Flank|PLCZ1_ENST00000435379.1_5'Flank|RP11-361I14.2_ENST00000536931.1_RNA|PLCZ1_ENST00000447925.2_5'Flank	NM_033328.2	NP_201585.1	Q96KX2	CAZA3_HUMAN	capping protein (actin filament) muscle Z-line, alpha 3	128					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)				TTAAAACTGTATGTGAATGAC	0.388																																					p.Y128S		Atlas-SNP	.											.	CAPZA3	51	.	0			c.A383C						PASS	.						90	82	84					12																	18891585		2203	4300	6503	SO:0001583	missense	93661	exon1			AACTGTATGTGAA	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.383A>C	chr12.hg19:g.18891585A>C	ENSP00000326238:p.Tyr128Ser	166.0	0.0	.		239.0	144.0	.	NM_033328	Q969J0	Missense_Mutation	SNP	ENST00000317658.3	hg19	CCDS8681.1	.	.	.	.	.	.	.	.	.	.	A	12.78	2.040528	0.35989	.	.	ENSG00000177938	ENST00000317658	.	.	.	4.43	4.43	0.53597	.	0.000000	0.64402	D	0.000001	T	0.77412	0.4126	M	0.78049	2.395	0.52099	D	0.999946	D	0.76494	0.999	D	0.87578	0.998	T	0.80264	-0.1455	9	0.87932	D	0	-1.4926	11.1782	0.48612	1.0:0.0:0.0:0.0	.	128	Q96KX2	CAZA3_HUMAN	S	128	.	ENSP00000326238:Y128S	Y	+	2	0	CAPZA3	18782852	0.995000	0.38212	0.801000	0.32222	0.378000	0.30076	5.493000	0.66899	1.876000	0.54355	0.379000	0.24179	TAT	.	.	.	none		0.388	CAPZA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401902.1	NM_033328		C	18891585	A	C	18891585	3	2	190	1	0	0	0	0	1	0	0	0	2644	449	16	5	385	5	CAPZA3	12	18891585	Missense_Mutation	SNP	A	TCGA-GL-A9DC-01A-11D-A36X-10	11432316	18891585	114960310	73	11250											
GOLT1B	51026	hgsc.bcm.edu	37	chr12	21661461	21661461	+	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	gttggcctttgataggcatgAtcttcgaaatttatggattt	9	17	10	5	1	1	2	0	2	1	0	2	4	1	3	1	3	0	2	1	3	3	7			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr12:21661461A>T	ENST00000229314.5	+	3	371	c.262A>T	c.(262-264)Atc>Ttc	p.I88F	GOLT1B_ENST00000540141.1_Missense_Mutation_p.I88F|GOLT1B_ENST00000535593.1_Intron|GOLT1B_ENST00000542038.1_Missense_Mutation_p.I24F	NM_016072.4	NP_057156.1	Q9Y3E0	GOT1B_HUMAN	golgi transport 1B	88	Phe-rich.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein transport (GO:0015031)|signal transduction (GO:0007165)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	signal transducer activity (GO:0004871)			large_intestine(2)|lung(3)	5						GATAGGCATGATCTTCGAAAT	0.333																																					p.I88F		Atlas-SNP	.											.	GOLT1B	13	.	0			c.A262T						PASS	.						112	111	111					12																	21661461		2203	4298	6501	SO:0001583	missense	51026	exon3			GGCATGATCTTCG	AB097020	CCDS8689.1	12p13.1	2010-06-24	2010-06-24		ENSG00000111711	ENSG00000111711			20175	protein-coding gene	gene with protein product		615078	"golgi transport 1 homolog B (S. cerevisiae)"			12414650, 10810093	Standard	NM_016072		Approved	CGI-141, YMR292W, GOT1	uc001rez.2	Q9Y3E0	OTTHUMG00000169133	ENST00000229314.5:c.262A>T	chr12.hg19:g.21661461A>T	ENSP00000229314:p.Ile88Phe	104.0	0.0	.		183.0	105.0	.	NM_016072	B2R4R4|Q54A40|Q6I9W6|Q9P1R9	Missense_Mutation	SNP	ENST00000229314.5	hg19	CCDS8689.1	.	.	.	.	.	.	.	.	.	.	A	15.33	2.800809	0.50315	.	.	ENSG00000111711	ENST00000542038;ENST00000540141;ENST00000229314	T;T;T	0.47869	0.83;0.83;0.83	5.9	5.9	0.94986	.	0.055804	0.64402	D	0.000001	T	0.44746	0.1308	M	0.64170	1.965	0.58432	D	0.999993	B	0.10296	0.003	B	0.20767	0.031	T	0.42716	-0.9435	10	0.46703	T	0.11	-9.0019	8.6254	0.33886	0.8585:0.0:0.1415:0.0	.	88	Q9Y3E0	GOT1B_HUMAN	F	24;88;88	ENSP00000446231:I24F;ENSP00000437351:I88F;ENSP00000229314:I88F	ENSP00000229314:I88F	I	+	1	0	GOLT1B	21552728	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.462000	0.53042	2.251000	0.74343	0.528000	0.53228	ATC	.	.	.	none		0.333	GOLT1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402384.2	NM_016072		T	21661461	A	T	21661461	3	4	190	1	0	0	0	0	1	0	0	0	6578	333	12	5	272	5	GOLT1B	12	21661461	Missense_Mutation	SNP	A	TCGA-GL-A9DC-01A-11D-A36X-10	2769876	21661461	112190434	74	11251											
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	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	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-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.G12D	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	Atlas-SNP	.		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"L, E, M, O"	KRAS_ENST00000256078,NS,adenocarcinoma,0,66	KRAS	30930	.	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	c.G35A						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>A	chr12.hg19:g.25398284C>T	ENSP00000256078:p.Gly12Asp	177.0	0.0	.		272.0	141.0	.	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT	.	.	.	weak		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398284	C	T	25398284	3	4	190	1	0	0	0	0	1	0	0	0	8445	507	18	2	671	2	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-GL-A9DC-01A-11D-A36X-10	3736823	25398284	108453611	75	11252											
C12orf40	283461	hgsc.bcm.edu	37	chr12	40034792	40034792	+	Frame_Shift_Del	DEL	A	A	-																															caagcaggaaagaagaaagcAaaaggtaaagaaaaagtgtt																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr12:40034792delA	ENST00000324616.5	+	2	213	c.59delA	c.(58-60)caafs	p.Q20fs	C12orf40_ENST00000405531.3_Frame_Shift_Del_p.Q20fs|C12orf40_ENST00000398716.1_5'UTR	NM_001031748.2	NP_001026918.2	Q86WS4	CL040_HUMAN	chromosome 12 open reading frame 40	20										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						AGAAGAAAGCAAAAGGTAAAG	0.353																																					p.Q20fs		Atlas-Indel,Pindel	.											.	C12orf40	118	.	0			c.58delC						PASS	.						76	75	76					12																	40034792		1815	4075	5890	SO:0001589	frameshift_variant	283461	exon2			.	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.59delA	chr12.hg19:g.40034792delA	ENSP00000317671:p.Gln20fs	95.0	0.0	0		197.0	42.0	0.213198	NM_001031748	B7WNU1|Q8IXY6|Q8N818|V9HW02	Frame_Shift_Del	DEL	ENST00000324616.5	hg19	CCDS41770.1																																																																																			.	.	.	none		0.353	C12orf40-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257664.2	NM_173599		-	40034792	A	-	40034792	7	5	190	1	0	1	0	1	0	0	0	0	1688	130	5	0	65	0	C12orf40	12	40034792	Frame_Shift_Del	DEL	A	TCGA-GL-A9DC-01A-11D-A36X-10	14636508	40034792	93817103	76	11253											
MYF6	4618	hgsc.bcm.edu	37	chr12	81101509	81101509	+	Missense_Mutation	SNP	A	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	ggaggagaacatgatgatggAcctttttgaaactggctcct	11	11	12	7	0	0	4	0	3	0	1	1	7	1	6	2	4	2	1	2	4	2	2			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr12:81101509A>C	ENST00000228641.3	+	1	233	c.11A>C	c.(10-12)gAc>gCc	p.D4A		NM_002469.2	NP_002460.1	P23409	MYF6_HUMAN	myogenic factor 6 (herculin)	4					muscle cell differentiation (GO:0042692)|muscle cell fate commitment (GO:0042693)|muscle tissue morphogenesis (GO:0060415)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle tissue development (GO:0007519)|skeletal muscle tissue regeneration (GO:0043403)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|skin(1)	26						ATGATGATGGACCTTTTTGAA	0.468																																					p.D4A		Atlas-SNP	.											.	MYF6	74	.	0			c.A11C						PASS	.						115	122	120					12																	81101509		2203	4300	6503	SO:0001583	missense	4618	exon1			TGATGGACCTTTT		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.11A>C	chr12.hg19:g.81101509A>C	ENSP00000228641:p.Asp4Ala	71.0	0.0	.		137.0	77.0	.	NM_002469	B2R898|Q53X80|Q6FHI9	Missense_Mutation	SNP	ENST00000228641.3	hg19	CCDS9019.1	.	.	.	.	.	.	.	.	.	.	A	19.76	3.887817	0.72410	.	.	ENSG00000111046	ENST00000228641	T	0.79352	-1.26	5.46	5.46	0.80206	Myogenic basic muscle-specific protein (2);	0.000000	0.85682	D	0.000000	D	0.84074	0.5392	L	0.51422	1.61	0.80722	D	1	D	0.71674	0.998	D	0.64877	0.93	D	0.85751	0.1343	10	0.72032	D	0.01	.	15.5368	0.76011	1.0:0.0:0.0:0.0	.	4	P23409	MYF6_HUMAN	A	4	ENSP00000228641:D4A	ENSP00000228641:D4A	D	+	2	0	MYF6	79625640	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.730000	0.91510	2.090000	0.63153	0.533000	0.62120	GAC	.	.	.	none		0.468	MYF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407756.1	NM_002469		C	81101509	A	C	81101509	3	2	190	1	0	0	0	0	1	0	0	0	10035	275	10	5	13	5	MYF6	12	81101509	Missense_Mutation	SNP	A	TCGA-GL-A9DC-01A-11D-A36X-10	41066717	81101509	52750386	77	11254											
PLXNC1	10154	hgsc.bcm.edu	37	chr12	94543226	94543226	+	Missense_Mutation	SNP	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	ggtgtcgtgccacccgcaggGctcgacggccggcgtggtgt	3	7	18	13	6	0	0	0	0	0	0	2	1	0	0	3	5	1	2	3	5	0	0			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr12:94543226G>A	ENST00000258526.4	+	1	728	c.479G>A	c.(478-480)gGc>gAc	p.G160D		NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	160	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						CACCCGCAGGGCTCGACGGCC	0.741																																					p.G160D		Atlas-SNP	.											.	PLXNC1	135	.	0			c.G479A						PASS	.						2	2	2					12																	94543226		1355	2986	4341	SO:0001583	missense	10154	exon1			CGCAGGGCTCGAC	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.479G>A	chr12.hg19:g.94543226G>A	ENSP00000258526:p.Gly160Asp	16.0	0.0	.		38.0	7.0	.	NM_005761	Q59H25	Missense_Mutation	SNP	ENST00000258526.4	hg19	CCDS9049.1	.	.	.	.	.	.	.	.	.	.	G	17.50	3.404871	0.62288	.	.	ENSG00000136040	ENST00000258526	T	0.04551	3.6	4.87	4.87	0.63330	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (2);	0.352781	0.24001	N	0.042462	T	0.16300	0.0392	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.00503	-1.1701	10	0.39692	T	0.17	.	12.2042	0.54342	0.0:0.0:0.8298:0.1702	.	160	O60486	PLXC1_HUMAN	D	160	ENSP00000258526:G160D	ENSP00000258526:G160D	G	+	2	0	PLXNC1	93067357	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.442000	0.52900	2.233000	0.73108	0.561000	0.74099	GGC	.	.	.	none		0.741	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2			A	94543226	G	A	94543226	3	1	190	1	0	0	0	0	1	0	0	0	12133	1203	42	2	481	2	PLXNC1	12	94543226	Missense_Mutation	SNP	G	TCGA-GL-A9DC-01A-11D-A36X-10	13441717	94543226	39308669	78	11255											
ATP2A2	488	hgsc.bcm.edu	37	chr12	110760813	110760813	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttagttggtgacaaagttccTgctgatataaggttaacttc	11	15	9	6	0	0	2	0	2	0	0	2	2	1	2	1	2	2	4	1	2	5	7			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr12:110760813T>C	ENST00000539276.2	+	6	589	c.480T>C	c.(478-480)ccT>ccC	p.P160P	ATP2A2_ENST00000395494.2_Intron|ATP2A2_ENST00000550248.2_3'UTR|ATP2A2_ENST00000308664.6_Silent_p.P160P			P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	160			P -> L (in DD).		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						ACAAAGTTCCTGCTGATATAA	0.323																																					p.P160P		Atlas-SNP	.											.	ATP2A2	78	.	0			c.T480C						PASS	.						82	84	83					12																	110760813		2203	4300	6503	SO:0001819	synonymous_variant	488	exon6			AGTTCCTGCTGAT		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.480T>C	chr12.hg19:g.110760813T>C		104.0	0.0	.		171.0	55.0	.	NM_001681	A6NDN7|B4DF05|P16614|Q86VJ2	Silent	SNP	ENST00000539276.2	hg19	CCDS9144.1																																																																																			.	.	.	none		0.323	ATP2A2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403539.1	NM_001681		C	110760813	T	C	110760813	2	2	190	1	0	0	0	0	0	0	0	1	1137	1567	55	3		3	ATP2A2	12	110760813	Silent	SNP	T	TCGA-GL-A9DC-01A-11D-A36X-10	16217587	110760813	23091082	79	11256											
TAOK3	51347	hgsc.bcm.edu	37	chr12	118681252	118681252	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctttcaagtaacagccttTgtactcaatagtattaggat	12	16	6	7	0	3	0	2	0	1	0	3	1	3	1	1	1	3	3	1	1	7	8			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr12:118681252T>C	ENST00000392533.3	-	5	752	c.262A>G	c.(262-264)Aaa>Gaa	p.K88E	TAOK3_ENST00000419821.2_Missense_Mutation_p.K88E	NM_016281.3	NP_057365.3	Q9H2K8	TAOK3_HUMAN	TAO kinase 3	88	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|MAPK cascade (GO:0000165)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of JNK cascade (GO:0046329)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)|transferase activity (GO:0016740)			central_nervous_system(1)|lung(5)|skin(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TAACAGCCTTTGTACTCAATA	0.289																																					p.K88E		Atlas-SNP	.											.	TAOK3	151	.	0			c.A262G						PASS	.						72	70	71					12																	118681252		2202	4294	6496	SO:0001583	missense	51347	exon5			AGCCTTTGTACTC	AF135158	CCDS9188.1	12q	2007-08-03				ENSG00000135090			18133	protein-coding gene	gene with protein product						10559204, 10924369	Standard	NM_016281		Approved	JIK, DPK, MAP3K18	uc001twy.4	Q9H2K8		ENST00000392533.3:c.262A>G	chr12.hg19:g.118681252T>C	ENSP00000376317:p.Lys88Glu	103.0	0.0	.		183.0	110.0	.	NM_016281	Q658N1|Q8IUM4|Q9HC79|Q9NZM9|Q9UHG7	Missense_Mutation	SNP	ENST00000392533.3	hg19	CCDS9188.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.38|14.38	2.517362|2.517362	0.44763|0.44763	.|.	.|.	ENSG00000135090|ENSG00000135090	ENST00000419821;ENST00000392533;ENST00000535570;ENST00000541186|ENST00000538601	T;T;T;T|T	0.24908|0.74315	1.83;1.83;1.83;1.83|-0.83	5.05|5.05	5.05|5.05	0.67936|0.67936	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|T	0.68504|0.68504	0.3008|0.3008	N|N	0.13235|0.13235	0.315|0.315	0.80722|0.80722	D|D	1|1	B|.	0.28636|.	0.218|.	P|.	0.44990|.	0.466|.	T|T	0.74472|0.74472	-0.3654|-0.3654	10|7	0.87932|0.87932	D|D	0|0	.|.	14.9553|14.9553	0.71107|0.71107	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	88|.	Q9H2K8|.	TAOK3_HUMAN|.	E|R	88|1	ENSP00000416374:K88E;ENSP00000376317:K88E;ENSP00000443465:K88E;ENSP00000438820:K88E|ENSP00000437389:Q1R	ENSP00000376317:K88E|ENSP00000437389:Q1R	K|Q	-|-	1|2	0|0	TAOK3|TAOK3	117165635|117165635	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	7.719000|7.719000	0.84751|0.84751	2.119000|2.119000	0.64992|0.64992	0.533000|0.533000	0.62120|0.62120	AAA|CAA	.	.	.	none		0.289	TAOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401456.2	NM_016281		C	118681252	T	C	118681252	3	2	190	1	0	0	0	0	1	0	0	0	15561	1821	63	3	2502	3	TAOK3	12	118681252	Missense_Mutation	SNP	T	TCGA-GL-A9DC-01A-11D-A36X-10	7920439	118681252	15170643	80	11257											
EP400	57634	hgsc.bcm.edu	37	chr12	132547081	132547081	+	Silent	SNP	G	G	A																															cttctcaggcagcagcagcaGcagcagcaacaacagcagca																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr12:132547081G>A	ENST00000333577.4	+	48	8386	c.8277G>A	c.(8275-8277)caG>caA	p.Q2759Q	EP400_ENST00000330386.6_Silent_p.Q2642Q|EP400_ENST00000332482.4_Silent_p.Q2686Q|EP400_ENST00000389561.2_Silent_p.Q2723Q|EP400_ENST00000389562.2_Silent_p.Q2722Q			Q96L91	EP400_HUMAN	E1A binding protein p400	2759	Interaction with ZNF42. {ECO:0000250}.|Poly-Gln.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		agcagcagcagcagcagcaac	0.562																																					p.Q2723Q		Atlas-SNP	.											.	EP400	370	.	0			c.G8169A						PASS	.						33	35	34					12																	132547081		2203	4300	6503	SO:0001819	synonymous_variant	57634	exon47			GCAGCAGCAGCAG	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"trinucleotide repeat containing 12"	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8277G>A	chr12.hg19:g.132547081G>A		91.0	0.0	.		157.0	7.0	.	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	hg19																																																																																				.	.	.	none		0.562	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		A	132547081	G	A	132547081	2	1	190	1	0	0	0	0	0	0	0	1	5151	962	34	2		2	EP400	12	132547081	Silent	SNP	G	TCGA-GL-A9DC-01A-11D-A36X-10	13865829	132547081	1304814	81	11258	107	2									
EP400	57634	hgsc.bcm.edu	37	chr12	132547084	132547084	+	Silent	SNP	G	G	A																															ctcaggcagcagcagcagcaGcagcaacaacagcagcagca																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr12:132547084G>A	ENST00000333577.4	+	48	8389	c.8280G>A	c.(8278-8280)caG>caA	p.Q2760Q	EP400_ENST00000330386.6_Silent_p.Q2643Q|EP400_ENST00000332482.4_Silent_p.Q2687Q|EP400_ENST00000389561.2_Silent_p.Q2724Q|EP400_ENST00000389562.2_Silent_p.Q2723Q			Q96L91	EP400_HUMAN	E1A binding protein p400	2760	Interaction with ZNF42. {ECO:0000250}.|Poly-Gln.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		agcagcagcagcagcaacaac	0.557																																					p.Q2724Q		Atlas-SNP	.											.	EP400	370	.	0			c.G8172A						PASS	.						30	33	32					12																	132547084		2203	4298	6501	SO:0001819	synonymous_variant	57634	exon47			GCAGCAGCAGCAA	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.8280G>A	chr12.hg19:g.132547084G>A		93.0	0.0	.		162.0	9.0	.	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	hg19																																																																																				.	.	.	none		0.557	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		A	132547084	G	A	132547084	2	1	190	1	0	0	0	0	0	0	0	1	5151	962	34	2		2	EP400	12	132547084	Silent	SNP	G	TCGA-GL-A9DC-01A-11D-A36X-10	3	132547084	1304811	82	11259	107	2									
FOXO1	2308	hgsc.bcm.edu	37	chr13	41134273	41134273	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgcacagttatactgactcAtacctccataactcgactta	12	11	5	13	2	1	1	1	1	0	0	3	2	2	1	2	0	3	2	2	0	5	5			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr13:41134273A>G	ENST00000379561.5	-	2	1739	c.1355T>C	c.(1354-1356)aTg>aCg	p.M452T	FOXO1_ENST00000473775.1_5'Flank	NM_002015.3	NP_002006.2	Q12778	FOXO1_HUMAN	forkhead box O1	452	Required for interaction with RUNX2. {ECO:0000250}.|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)		ATACTGACTCATACCTCCATA	0.463																																					p.M452T		Atlas-SNP	.											.	FOXO1	110	.	0			c.T1355C						PASS	.						102	87	92					13																	41134273		2203	4300	6503	SO:0001583	missense	2308	exon2			TGACTCATACCTC		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.1355T>C	chr13.hg19:g.41134273A>G	ENSP00000368880:p.Met452Thr	69.0	0.0	.		91.0	42.0	.	NM_002015	O43523|Q5VYC7|Q6NSK6	Missense_Mutation	SNP	ENST00000379561.5	hg19	CCDS9371.1	.	.	.	.	.	.	.	.	.	.	A	10.99	1.508445	0.27036	.	.	ENSG00000150907	ENST00000379561	D	0.93906	-3.31	5.78	5.78	0.91487	.	0.369149	0.30742	N	0.008980	D	0.91412	0.7290	L	0.61218	1.895	0.39378	D	0.966211	B	0.14805	0.011	B	0.12837	0.008	D	0.88343	0.2976	10	0.20519	T	0.43	-0.5556	15.295	0.73898	1.0:0.0:0.0:0.0	.	452	Q12778	FOXO1_HUMAN	T	452	ENSP00000368880:M452T	ENSP00000368880:M452T	M	-	2	0	FOXO1	40032273	0.998000	0.40836	0.321000	0.25320	0.301000	0.27625	7.027000	0.76463	2.220000	0.72140	0.533000	0.62120	ATG	.	.	.	none		0.463	FOXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044634.3	NM_002015		G	41134273	A	G	41134273	3	3	190	1	0	0	0	0	1	0	0	0	6030	217	8	3	616	3	FOXO1	13	41134273	Missense_Mutation	SNP	A	TCGA-GL-A9DC-01A-11D-A36X-10		41134273	74035605	83	11260											
ALG11	440138	hgsc.bcm.edu	37	chr13	52598354	52598354	+	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	catttttcttggctgggaagCtctaatgcagtgtgttcctg	6	16	11	8	0	2	0	0	0	2	0	3	1	3	1	1	2	2	4	1	2	2	5			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr13:52598354C>G	ENST00000521508.1	+	3	493	c.488C>G	c.(487-489)gCt>gGt	p.A163G	ALG11_ENST00000523764.1_Intron|ALG11_ENST00000519151.1_3'UTR|UTP14C_ENST00000521776.2_5'Flank	NM_001004127.2	NP_001004127.2	Q2TAA5	ALG11_HUMAN	ALG11, alpha-1,2-mannosyltransferase	163					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)		GGCTGGGAAGCTCTAATGCAG	0.413																																					p.A163G		Atlas-SNP	.											.	ALG11	39	.	0			c.C488G						PASS	.						182	169	173					13																	52598354		2203	4300	6503	SO:0001583	missense	440138	exon3			GGGAAGCTCTAAT	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.488C>G	chr13.hg19:g.52598354C>G	ENSP00000430236:p.Ala163Gly	100.0	0.0	.		100.0	43.0	.	NM_001004127	A5PLP3|B4DKW9|Q5TAN9|Q6DKI6|Q96FI7	Missense_Mutation	SNP	ENST00000521508.1	hg19	CCDS31977.1	.	.	.	.	.	.	.	.	.	.	C	18.89	3.719490	0.68844	.	.	ENSG00000253710	ENST00000521508	T	0.69685	-0.42	5.94	5.94	0.96194	.	0.000000	0.85682	U	0.000000	T	0.74612	0.3739	M	0.82630	2.6	0.80722	D	1	P	0.49090	0.919	B	0.43331	0.416	T	0.78947	-0.2003	10	0.62326	D	0.03	.	20.3736	0.98901	0.0:1.0:0.0:0.0	.	163	Q2TAA5	ALG11_HUMAN	G	163	ENSP00000430236:A163G	ENSP00000430236:A163G	A	+	2	0	ALG11	51496355	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	7.438000	0.80431	2.820000	0.97059	0.650000	0.86243	GCT	.	.	.	none		0.413	ALG11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045050.1	NM_001004127		G	52598354	C	G	52598354	3	3	190	1	0	0	0	0	1	0	0	0	513	797	28	4	498	4	ALG11	13	52598354	Missense_Mutation	SNP	C	TCGA-GL-A9DC-01A-11D-A36X-10	11464081	52598354	62571524	84	11261											
FERMT2	10979	hgsc.bcm.edu	37	chr14	53386039	53386039	+	Missense_Mutation	SNP	A	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	ccaagttctcttcttttcccAccagagagcatggtcagacc	9	11	7	14	0	3	2	1	0	2	2	5	3	4	2	4	1	1	2	4	1	1	4			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr14:53386039A>C	ENST00000395631.2	-	3	409	c.193T>G	c.(193-195)Tgg>Ggg	p.W65G	FERMT2_ENST00000343279.4_Missense_Mutation_p.W65G|FERMT2_ENST00000399304.3_Missense_Mutation_p.W65G|FERMT2_ENST00000341590.3_Missense_Mutation_p.W65G|FERMT2_ENST00000553373.1_Missense_Mutation_p.W65G			Q96AC1	FERM2_HUMAN	fermitin family member 2	65	Interaction with membranes containing phosphatidylinositol phosphate.				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|focal adhesion assembly (GO:0048041)|integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|protein localization to membrane (GO:0072657)|regulation of cell shape (GO:0008360)|substrate adhesion-dependent cell spreading (GO:0034446)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|stress fiber (GO:0001725)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)		ERO1L/FERMT2(2)	NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	20	Breast(41;0.0342)					TTCTTTTCCCACCAGAGAGCA	0.363																																					p.W65G		Atlas-SNP	.											.	FERMT2	59	.	0			c.T193G						PASS	.						119	111	114					14																	53386039		2203	4300	6503	SO:0001583	missense	10979	exon3			TTTCCCACCAGAG	Z24725	CCDS9713.1, CCDS45107.1, CCDS45108.1	14q22.1	2013-01-10	2010-06-24	2007-12-14	ENSG00000073712	ENSG00000073712		"Fermitins", "Pleckstrin homology (PH) domain containing"	15767	protein-coding gene	gene with protein product	"kindlin-2"	607746	"pleckstrin homology domain containing, family C (with FERM domain) member 1", "fermitin family homolog 2 (Drosophila)"	PLEKHC1		8175911, 12697302	Standard	NM_006832		Approved	mig-2, KIND2, UNC112B	uc001xac.3	Q96AC1	OTTHUMG00000140309	ENST00000395631.2:c.193T>G	chr14.hg19:g.53386039A>C	ENSP00000378993:p.Trp65Gly	150.0	0.0	.		168.0	60.0	.	NM_001135000	B5TJY2|Q14840|Q86TY7	Missense_Mutation	SNP	ENST00000395631.2	hg19	CCDS9713.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.140592	0.77775	.	.	ENSG00000073712	ENST00000395631;ENST00000341590;ENST00000554152;ENST00000343279;ENST00000553373;ENST00000399304;ENST00000555692;ENST00000554712	T;T;T;T;T;T;T;T	0.14893	2.47;2.47;2.47;2.47;2.47;2.47;2.47;2.47	5.82	5.82	0.92795	.	0.063724	0.64402	D	0.000002	T	0.47303	0.1438	M	0.86268	2.805	0.80722	D	1	P;P;P	0.50710	0.938;0.791;0.897	D;P;P	0.67725	0.953;0.812;0.898	T	0.52434	-0.8576	10	0.87932	D	0	.	16.1966	0.82029	1.0:0.0:0.0:0.0	.	65;65;65	Q96AC1-2;Q96AC1;B5TJY2	.;FERM2_HUMAN;.	G	65;65;7;65;65;65;21;65	ENSP00000378993:W65G;ENSP00000340391:W65G;ENSP00000450741:W7G;ENSP00000342858:W65G;ENSP00000451084:W65G;ENSP00000382243:W65G;ENSP00000452472:W21G;ENSP00000450506:W65G	ENSP00000340391:W65G	W	-	1	0	FERMT2	52455789	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.232000	0.73038	0.528000	0.53228	TGG	.	.	.	none		0.363	FERMT2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276907.2	NM_006832		C	53386039	A	C	53386039	3	2	190	1	0	0	0	0	1	0	0	0	5825	159	6	5	1938	5	FERMT2	14	53386039	Missense_Mutation	SNP	A	TCGA-GL-A9DC-01A-11D-A36X-10		53386039	53963501	85	11262											
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102431117	102431140	+	In_Frame_Del	DEL	TGCAGAAGCACCTGCGCAAGCTGG	TGCAGAAGCACCTGCGCAAGCTGG	-																															tgtggcggacgtgtcggtgcTgcagaagcacctgcgcaagc																								rs369058949		TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	TGCAGAAGCACCTGCGCAAGCTGG	TGCAGAAGCACCTGCGCAAGCTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr14:102431117_102431140delTGCAGAAGCACCTGCGCAAGCTGG	ENST00000360184.4	+	1	253_276	c.89_112delTGCAGAAGCACCTGCGCAAGCTGG	c.(88-114)ctgcagaagcacctgcgcaagctggtg>ctg	p.QKHLRKLV31del		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	31					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						GTGTCGGTGCTGCAGAAGCACCTGCGCAAGCTGGTGCCGCTGCT	0.714																																					p.30_37del		Atlas-Indel,Pindel	.											.	DYNC1H1	395	.	0			c.88_111del						PASS	.																																			SO:0001651	inframe_deletion	1778	exon1			.	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.89_112delTGCAGAAGCACCTGCGCAAGCTGG	chr14.hg19:g.102431117_102431140delTGCAGAAGCACCTGCGCAAGCTGG	ENSP00000348965:p.Gln31_Val38del	93.0	0.0	0		106.0	36.0	0.339623	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	In_Frame_Del	DEL	ENST00000360184.4	hg19	CCDS9966.1																																																																																			.	.	.	none		0.714	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		-	102431140	TGCAGAAGCACCTGCGCAAGCTGG	-	102431117	7	5	190	1	0	1	0	1	0	0	0	0	4843	1580	55	0	91	0	DYNC1H1	14	102431117	In_Frame_Del	DEL	TGCAGAAGCACCTGCGCAAGCTGG	TCGA-GL-A9DC-01A-11D-A36X-10	49045078	102431117	4918423	86	11263											
GABRG3	2567	hgsc.bcm.edu	37	chr15	27777821	27777821	+	Frame_Shift_Del	DEL	T	T	-																															attccgtttactggcaggaaTttgaagatacctgtgtctat																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr15:27777821delT	ENST00000333743.6	+	10	1452	c.1198delT	c.(1198-1200)tttfs	p.F400fs	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	400					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)	CTGGCAGGAATTTGAAGATAC	0.453																																					p.E399fs	NSCLC(114;800 1656 7410 37729 45293)	Atlas-Indel,Pindel	.											.	GABRG3	115	.	0			c.1197delA						PASS	.						91	94	93					15																	27777821		1976	4150	6126	SO:0001589	frameshift_variant	2567	exon10			.		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.1198delT	chr15.hg19:g.27777821delT	ENSP00000331912:p.Phe400fs	129.0	0.0	0		160.0	33.0	0.20625	NM_033223	G3V594|Q9HD46|Q9NYT2	Frame_Shift_Del	DEL	ENST00000333743.6	hg19	CCDS45195.1																																																																																			.	.	.	none		0.453	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2			-	27777821	T	-	27777821	7	5	190	1	0	1	0	1	0	0	0	0	6180	1493	52	0	1236	0	GABRG3	15	27777821	Frame_Shift_Del	DEL	T	TCGA-GL-A9DC-01A-11D-A36X-10		27777821	74753571	87	11264											
SLC12A6	9990	hgsc.bcm.edu	37	chr15	34551060	34551067	+	Frame_Shift_Del	DEL	TGTTCCTT	TGTTCCTT	-																															tgatgttttctgcctcttcaTgttcctttgctccttgagtc																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	TGTTCCTT	TGTTCCTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr15:34551060_34551067delTGTTCCTT	ENST00000354181.3	-	5	982_989	c.490_497delAAGGAACA	c.(490-498)aaggaacatfs	p.KEH164fs	SLC12A6_ENST00000558589.1_Frame_Shift_Del_p.KEH155fs|RP11-1084A12.2_ENST00000559867.1_RNA|SLC12A6_ENST00000451844.2_Frame_Shift_Del_p.KEH25fs|SLC12A6_ENST00000560164.1_Frame_Shift_Del_p.KEH25fs|SLC12A6_ENST00000560611.1_Frame_Shift_Del_p.KEH164fs|SLC12A6_ENST00000558667.1_Frame_Shift_Del_p.KEH164fs|SLC12A6_ENST00000397707.2_Frame_Shift_Del_p.KEH149fs|SLC12A6_ENST00000290209.5_Frame_Shift_Del_p.KEH113fs|SLC12A6_ENST00000458406.2_Frame_Shift_Del_p.KEH105fs|SLC12A6_ENST00000397702.2_Frame_Shift_Del_p.KEH105fs			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	164					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)	TGCCTCTTCATGTTCCTTTGCTCCTTGA	0.447																																					p.164_166del		Atlas-Indel,Pindel	.											.	SLC12A6	205	.	0			c.491_498del						PASS	.																																			SO:0001589	frameshift_variant	9990	exon4			.	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.490_497delAAGGAACA	chr15.hg19:g.34551060_34551067delTGTTCCTT	ENSP00000346112:p.Lys164fs	108.0	0.0	0		113.0	17.0	0.150442	NM_133647	A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Frame_Shift_Del	DEL	ENST00000354181.3	hg19	CCDS58352.1																																																																																			.	.	.	none		0.447	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135		-	34551067	TGTTCCTT	-	34551060	7	5	190	1	0	1	0	1	0	0	0	0	14400	1464	51	0	3043	0	SLC12A6	15	34551060	Frame_Shift_Del	DEL	TGTTCCTT	TCGA-GL-A9DC-01A-11D-A36X-10	6773239	34551060	67980332	88	11265											
GTF2A2	2958	hgsc.bcm.edu	37	chr15	59942867	59942867	+	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	gattcaggaaaatatccttaCcctgaaattgactctgttcc	12	13	6	10	0	2	2	1	2	1	0	4	4	4	3	3	1	1	1	3	1	5	5			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr15:59942867C>A	ENST00000396060.2	-	3	359		c.e3+1		GTF2A2_ENST00000396061.1_Splice_Site|AC092755.4_ENST00000441746.1_RNA|GTF2A2_ENST00000396064.3_Splice_Site|GTF2A2_ENST00000396063.1_Splice_Site|GTF2A2_ENST00000267869.4_Intron|GTF2A2_ENST00000484743.1_Intron	NM_004492.2	NP_004483.1	P52657	T2AG_HUMAN	general transcription factor IIA, 2, 12kDa						gene expression (GO:0010467)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|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)	cell junction (GO:0030054)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIA complex (GO:0005672)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			central_nervous_system(2)|kidney(2)|lung(1)	5						AATATCCTTACCCTGAAATTG	0.398																																					.		Atlas-SNP	.											.	GTF2A2	9	.	0			c.177+1G>T						PASS	.						76	71	73					15																	59942867		2190	4290	6480	SO:0001630	splice_region_variant	2958	exon4			TCCTTACCCTGAA	BC001919	CCDS10173.1	15q21.3	2010-03-23	2002-08-29		ENSG00000140307	ENSG00000140307		"General transcription factors"	4647	protein-coding gene	gene with protein product		600519	"general transcription factor IIA, 2 (12kD subunit)"			7958899	Standard	NM_004492		Approved	TFIIA, HsT18745	uc002agg.3	P52657	OTTHUMG00000132725	ENST00000396060.2:c.177+1G>T	chr15.hg19:g.59942867C>A		75.0	0.0	.		87.0	26.0	.	NM_004492	A8MYQ7|Q6FGB5	Splice_Site	SNP	ENST00000396060.2	hg19	CCDS10173.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.498010	0.85069	.	.	ENSG00000140307	ENST00000396060;ENST00000396064;ENST00000396063;ENST00000396061	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.1601	0.93527	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GTF2A2	57730159	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.172000	0.77604	2.523000	0.85059	0.555000	0.69702	.	.	.	.	none		0.398	GTF2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256067.2	NM_004492	Intron	A	59942867	C	A	59942867	5	1	190	1	0	0	0	0	0	0	1	0	6861	521	18	4	163	4	GTF2A2	15	59942867	Splice_Site	SNP	C	TCGA-GL-A9DC-01A-11D-A36X-10	25391807	59942867	42588525	89	11266											
CRAMP1L	57585	hgsc.bcm.edu	37	chr16	1691167	1691167	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgacaagaatgcaacaaagcTgaatgaactcattcaggttg	16	9	9	7	0	2	4	2	3	0	1	2	4	2	4	0	1	4	3	0	1	6	2			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr16:1691167T>C	ENST00000397412.3	+	6	905	c.806T>C	c.(805-807)cTg>cCg	p.L269P	CRAMP1L_ENST00000436138.3_Missense_Mutation_p.L266P|LA16c-431H6.6_ENST00000454337.1_Silent_p.A73A|CRAMP1L_ENST00000293925.5_Missense_Mutation_p.L269P			Q96RY5	CRML_HUMAN	Crm, cramped-like (Drosophila)	269						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						GCAACAAAGCTGAATGAACTC	0.368																																					p.L269P		Atlas-SNP	.											.	CRAMP1L	60	.	0			c.T806C						PASS	.						137	136	137					16																	1691167		1865	4115	5980	SO:0001583	missense	57585	exon5			CAAAGCTGAATGA	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.806T>C	chr16.hg19:g.1691167T>C	ENSP00000380559:p.Leu269Pro	82.0	0.0	.		110.0	39.0	.	NM_020825	A8MZL1|B1AJY1|Q8NDN1|Q9P2C1	Missense_Mutation	SNP	ENST00000397412.3	hg19	CCDS10440.2	.	.	.	.	.	.	.	.	.	.	T	16.10	3.026242	0.54683	.	.	ENSG00000007545	ENST00000397412;ENST00000293925;ENST00000436138	.	.	.	5.46	5.46	0.80206	.	0.000000	0.64402	D	0.000020	T	0.77585	0.4152	M	0.67700	2.07	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.79680	-0.1702	9	0.62326	D	0.03	-8.9801	15.5282	0.75928	0.0:0.0:0.0:1.0	.	269	Q96RY5	CRML_HUMAN	P	269;269;266	.	ENSP00000293925:L269P	L	+	2	0	CRAMP1L	1631168	1.000000	0.71417	0.997000	0.53966	0.667000	0.39255	7.618000	0.83043	2.076000	0.62316	0.459000	0.35465	CTG	.	.	.	none		0.368	CRAMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157297.4			C	1691167	T	C	1691167	3	2	190	1	0	0	0	0	1	0	0	0	3848	1580	55	3	824	3	CRAMP1L	16	1691167	Missense_Mutation	SNP	T	TCGA-GL-A9DC-01A-11D-A36X-10		1691167	88663586	90	11267											
NUDT16L1	84309	hgsc.bcm.edu	37	chr16	4743827	4743827	+	Frame_Shift_Del	DEL	G	G	-																															cgtgccacgccatgctgtacGccgccaaccctgggcagctc																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr16:4743827delG	ENST00000304301.6	+	1	133	c.100delG	c.(100-102)gccfs	p.A35fs	NUDT16L1_ENST00000405142.1_Frame_Shift_Del_p.A35fs|NUDT16L1_ENST00000586252.1_Frame_Shift_Del_p.A35fs|NUDT16L1_ENST00000586536.1_Frame_Shift_Del_p.A35fs	NM_032349.3	NP_115725.1	Q9BRJ7	SDOS_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 16-like 1	35						cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)|poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)			endometrium(1)|large_intestine(1)|lung(1)|skin(1)	4						CATGCTGTACGCCGCCAACCC	0.736																																					p.Y33X		Atlas-INDEL	.											.	NUDT16L1	13	.	0			c.99delC						PASS	.						18	17	17					16																	4743827		2174	4289	6463	SO:0001589	frameshift_variant	84309	exon1			.	BC006223	CCDS10519.1, CCDS59257.1	16p13.3	2008-02-05			ENSG00000168101	ENSG00000168101		"Nudix motif containing"	28154	protein-coding gene	gene with protein product						11805099	Standard	NM_032349		Approved	SDOS	uc002cxe.3	Q9BRJ7	OTTHUMG00000129471	ENST00000304301.6:c.100delG	chr16.hg19:g.4743827delG	ENSP00000306670:p.Ala35fs	81.0	0.0	0		142.0	77.0	0.542253	NM_001193452	Q8NAI2	Frame_Shift_Del	DEL	ENST00000304301.6	hg19	CCDS10519.1																																																																																			.	.	.	none		0.736	NUDT16L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251634.1	NM_032349		-	4743827	G	-	4743827	7	5	190	1	0	1	0	1	0	0	0	0	10740	1087	38	0	102	0	NUDT16L1	16	4743827	Frame_Shift_Del	DEL	G	TCGA-GL-A9DC-01A-11D-A36X-10	3052660	4743827	85610926	91	11268											
C17orf81	23587	hgsc.bcm.edu	37	chr17	7162047	7162047	+	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	acaaggaaatgtagtttagtAtctggtcacgggagagaaaa	16	9	12	4	1	2	1	1	0	1	1	2	4	2	3	0	3	0	3	0	3	7	4			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr17:7162047A>G	ENST00000396628.2	+	6	952				RP1-4G17.5_ENST00000577138.1_Intron|ELP5_ENST00000396627.2_Intron|ELP5_ENST00000354429.2_Intron|ELP5_ENST00000356683.2_Silent_p.V260V|ELP5_ENST00000574993.1_Silent_p.V260V	NM_203414.1	NP_981959.1	Q8TE02	ELP5_HUMAN	elongator acetyltransferase complex subunit 5						chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Elongator holoenzyme complex (GO:0033588)|nucleus (GO:0005634)											GTAGTTTAGTATCTGGTCACG	0.527																																					p.V260V		Atlas-SNP	.											.	.	.	.	0			c.A780G						PASS	.						92	100	98					17																	7162047		2203	4300	6503	SO:0001627	intron_variant	23587	exon7			TTTAGTATCTGGT	BC002762	CCDS11094.1, CCDS11095.1	17p13.1	2012-08-14	2012-08-08	2012-08-08	ENSG00000170291	ENSG00000170291		"Elongator acetyltransferase complex subunits"	30617	protein-coding gene	gene with protein product	"dermal papilla derived protein 6", "S-phase 2 protein"	615019	"chromosome 17 open reading frame 81"	C17orf81		22854966	Standard	NM_203415		Approved	DERP6	uc002gfi.1	Q8TE02	OTTHUMG00000177974	ENST00000396628.2:c.735+45A>G	chr17.hg19:g.7162047A>G		119.0	0.0	.		176.0	95.0	.	NM_203413	A8K1M5|D3DTN9|Q659B6|Q7Z2T4|Q8TDR9|Q9BUB2|Q9Y2Q4	Silent	SNP	ENST00000396628.2	hg19	CCDS11094.1																																																																																			.	.	.	none		0.527	ELP5-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440111.1	NM_015362		G	7162047	A	G	7162047	1	3	190	0	1	0	0	0	0	0	0	0	1888	436	16	3		3	C17orf81	17	7162047	Intron	SNP	A	TCGA-GL-A9DC-01A-11D-A36X-10		7162047	74033163	92	11269											
SLC47A1	55244	hgsc.bcm.edu	37	chr17	19480761	19480761	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catccacaggacggcgctaaAttgtccaggaaacagctggt	12	7	11	11	2	0	0	0	0	0	0	2	2	2	2	2	4	2	2	2	4	3	2			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr17:19480761A>G	ENST00000270570.4	+	17	1694	c.1608A>G	c.(1606-1608)aaA>aaG	p.K536K	RP11-1113L8.1_ENST00000574267.1_RNA|AC025627.7_ENST00000420951.1_RNA|SLC47A1_ENST00000436810.2_3'UTR|SLC47A1_ENST00000457293.1_Silent_p.K536K|SLC47A1_ENST00000571335.1_Silent_p.K282K|SLC47A1_ENST00000575023.1_Silent_p.K234K|SLC47A1_ENST00000395585.1_Silent_p.K536K	NM_018242.2	NP_060712.2	Q96FL8	S47A1_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 1	536					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)	ACGGCGCTAAATTGTCCAGGA	0.507																																					p.K536K		Atlas-SNP	.											.	SLC47A1	55	.	0			c.A1608G						PASS	.						144	148	147					17																	19480761		2203	4300	6503	SO:0001819	synonymous_variant	55244	exon17			CGCTAAATTGTCC		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.1608A>G	chr17.hg19:g.19480761A>G		133.0	0.0	.		226.0	124.0	.	NM_018242	Q53HF5|Q6PD77|Q86VL4|Q9NVA3	Silent	SNP	ENST00000270570.4	hg19	CCDS11209.1																																																																																			.	.	.	none		0.507	SLC47A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132250.1	NM_018242		G	19480761	A	G	19480761	2	3	190	1	0	0	0	0	0	0	0	1	14660	98	4	3		3	SLC47A1	17	19480761	Silent	SNP	A	TCGA-GL-A9DC-01A-11D-A36X-10	12318714	19480761	61714449	93	11270											
MED13	9969	hgsc.bcm.edu	37	chr17	60061702	60061702	+	Missense_Mutation	SNP	T	T	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	cccactagaatttgacaattTtcaggcttatagacataaga	15	12	6	8	0	1	4	1	1	0	3	1	4	1	4	1	1	0	1	1	1	6	7			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr17:60061702T>G	ENST00000397786.2	-	15	2794	c.2718A>C	c.(2716-2718)gaA>gaC	p.E906D		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	906					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						TTTGACAATTTTCAGGCTTAT	0.353																																					p.E906D		Atlas-SNP	.											.	MED13	181	.	0			c.A2718C						PASS	.						59	55	56					17																	60061702		1797	4068	5865	SO:0001583	missense	9969	exon15			ACAATTTTCAGGC	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.2718A>C	chr17.hg19:g.60061702T>G	ENSP00000380888:p.Glu906Asp	137.0	0.0	.		200.0	63.0	.	NM_005121	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	hg19	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	T	18.17	3.563848	0.65651	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	T	0.74632	-0.86	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.82907	0.5139	M	0.65975	2.015	0.54753	D	0.999982	D	0.64830	0.994	D	0.70716	0.97	D	0.83879	0.0278	10	0.56958	D	0.05	-17.933	10.3148	0.43729	0.0:0.1158:0.0:0.8842	.	906	Q9UHV7	MED13_HUMAN	D	906;905	ENSP00000380888:E906D	ENSP00000262436:E905D	E	-	3	2	MED13	57416484	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.904000	0.39868	2.225000	0.72522	0.528000	0.53228	GAA	.	.	.	none		0.353	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		G	60061702	T	G	60061702	3	3	190	1	0	0	0	0	1	0	0	0	9437	1838	64	5	3870	5	MED13	17	60061702	Missense_Mutation	SNP	T	TCGA-GL-A9DC-01A-11D-A36X-10	40580941	60061702	21133508	94	11271											
FAM20A	54757	hgsc.bcm.edu	37	chr17	66533874	66533874	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcaggtgcaaaagtgttttcTtttttatcctgaaaagacaa	13	14	8	6	0	1	2	0	1	1	1	2	2	2	2	1	1	1	3	1	1	6	5			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr17:66533874T>C	ENST00000592554.1	-	11	2092	c.1370A>G	c.(1369-1371)aAg>aGg	p.K457R	FAM20A_ENST00000226094.5_5'UTR|PRKAR1A_ENST00000588188.2_Intron	NM_001243746.1|NM_017565.3	NP_001230675.1|NP_060035.2	Q96MK3	FA20A_HUMAN	family with sequence similarity 20, member A	457					calcium ion homeostasis (GO:0055074)|enamel mineralization (GO:0070166)|tooth eruption (GO:0044691)	cell (GO:0005623)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)				cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(1)	9	Breast(10;1.64e-13)					AAGTGTTTTCTTTTTTATCCT	0.448																																					p.K457R		Atlas-SNP	.											.	FAM20A	35	.	0			c.A1370G						PASS	.						48	45	46					17																	66533874		2203	4300	6503	SO:0001583	missense	54757	exon11			GTTTTCTTTTTTA	AK056789	CCDS11679.1	17q24.2	2014-02-07			ENSG00000108950	ENSG00000108950			23015	protein-coding gene	gene with protein product		611062					Standard	NM_017565		Approved	DKFZp434F2322	uc002jho.3	Q96MK3	OTTHUMG00000180152	ENST00000592554.1:c.1370A>G	chr17.hg19:g.66533874T>C	ENSP00000468308:p.Lys457Arg	76.0	0.0	.		116.0	28.0	.	NM_017565	B2RN47|B2RN49|Q9UF95	Missense_Mutation	SNP	ENST00000592554.1	hg19	CCDS11679.1	.	.	.	.	.	.	.	.	.	.	T	8.231	0.804584	0.16467	.	.	ENSG00000108950	ENST00000226094;ENST00000375556	.	.	.	5.81	-2.2	0.06994	.	0.468058	0.27831	N	0.017669	T	0.19046	0.0457	N	0.04686	-0.185	0.26802	N	0.969185	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.001	T	0.14117	-1.0484	9	0.19147	T	0.46	-13.7073	14.1661	0.65477	0.0:0.5689:0.0:0.4311	.	457;319	Q96MK3;B7Z4Y3	FA20A_HUMAN;.	R	457;61	.	ENSP00000226094:K457R	K	-	2	0	FAM20A	64045469	0.995000	0.38212	0.890000	0.34922	0.794000	0.44872	0.337000	0.19841	-0.737000	0.04824	-0.375000	0.07067	AAG	.	.	.	none		0.448	FAM20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450029.2	NM_017565		C	66533874	T	C	66533874	3	2	190	1	0	0	0	0	1	0	0	0	5541	1609	56	3	259	3	FAM20A	17	66533874	Missense_Mutation	SNP	T	TCGA-GL-A9DC-01A-11D-A36X-10	6472172	66533874	14661336	95	11272											
LGALS3BP	3959	hgsc.bcm.edu	37	chr17	76969173	76969173	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggatgaccgtgtggccacAgaagcccagggcgtcctcgc	8	5	14	14	3	0	2	0	1	0	1	2	3	1	3	4	3	1	0	4	3	1	0			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr17:76969173A>G	ENST00000262776.3	-	5	816	c.508T>C	c.(508-510)Tgt>Cgt	p.C170R	LGALS3BP_ENST00000585407.1_Missense_Mutation_p.C170R|LGALS3BP_ENST00000591778.1_Intron	NM_005567.3	NP_005558.1	Q08380	LG3BP_HUMAN	lectin, galactoside-binding, soluble, 3 binding protein	170	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				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)			GTGTGGCCACAGAAGCCCAGG	0.642																																					p.C170R	GBM(89;1105 1755 18102 21513)	Atlas-SNP	.											.	LGALS3BP	47	.	0			c.T508C						PASS	.						54	41	46					17																	76969173		2203	4300	6503	SO:0001583	missense	3959	exon5			GGCCACAGAAGCC	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.508T>C	chr17.hg19:g.76969173A>G	ENSP00000262776:p.Cys170Arg	63.0	0.0	.		119.0	29.0	.	NM_005567	Q7M4S0|Q9UCH8|Q9UCH9|Q9UCI0	Missense_Mutation	SNP	ENST00000262776.3	hg19	CCDS11759.1	.	.	.	.	.	.	.	.	.	.	A	13.38	2.219105	0.39201	.	.	ENSG00000108679	ENST00000262776;ENST00000536190	T	0.19938	2.11	3.04	3.04	0.35103	BTB/POZ-like (1);BTB/POZ fold (2);	0.000000	0.38778	N	0.001580	T	0.30603	0.0770	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.02115	-1.1211	10	0.44086	T	0.13	.	7.8817	0.29627	1.0:0.0:0.0:0.0	.	170	Q08380	LG3BP_HUMAN	R	170;158	ENSP00000262776:C170R	ENSP00000262776:C170R	C	-	1	0	LGALS3BP	74480768	0.986000	0.35501	0.287000	0.24848	0.283000	0.27025	5.780000	0.68956	1.661000	0.50771	0.459000	0.35465	TGT	.	.	.	none		0.642	LGALS3BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437785.3	NM_005567		G	76969173	A	G	76969173	3	3	190	1	0	0	0	0	1	0	0	0	8751	188	7	3	1257	3	LGALS3BP	17	76969173	Missense_Mutation	SNP	A	TCGA-GL-A9DC-01A-11D-A36X-10	10435299	76969173	4226037	96	11273											
FSCN2	25794	hgsc.bcm.edu	37	chr17	79495707	79495707	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagacctgggtgctggaaccCgacccaggacaaggcacggc	10	3	14	14	2	0	1	0	0	0	1	0	4	0	3	3	5	2	2	3	5	2	0	rs184519759	byFrequency	TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr17:79495707C>T	ENST00000417245.2	+	1	286	c.150C>T	c.(148-150)ccC>ccT	p.P50P	RP13-766D20.2_ENST00000442532.1_RNA|RP13-766D20.2_ENST00000430912.1_RNA|FSCN2_ENST00000334850.7_Silent_p.P50P	NM_001077182.2|NM_012418.3	NP_001070650.1|NP_036550.1	O14926	FSCN2_HUMAN	fascin actin-bundling protein 2, retinal	50					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)			TGCTGGAACCCGACCCAGGAC	0.647																																					p.P50P		Atlas-SNP	.											.	FSCN2	35	.	0			c.C150T						PASS	.						18	19	18					17																	79495707		1985	4159	6144	SO:0001819	synonymous_variant	25794	exon1			GGAACCCGACCCA	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.150C>T	chr17.hg19:g.79495707C>T		122.0	0.0	.		191.0	61.0	.	NM_001077182	A0AVC4|A8MRA6	Silent	SNP	ENST00000417245.2	hg19	CCDS45811.1																																																																																			.	C|0.997;G|0.003	.	alt		0.647	FSCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394746.1	NM_012418		T	79495707	C	T	79495707	2	4	190	1	0	0	0	0	0	0	0	1	6075	639	23	1		1	FSCN2	17	79495707	Silent	SNP	C	TCGA-GL-A9DC-01A-11D-A36X-10	2526534	79495707	1699503	97	11274											
SIRT7	51547	hgsc.bcm.edu	37	chr17	79875730	79875730	+	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	tcctgccgccgcttcaggccCtcgcgccgccggctccggcc	1	6	12	22	7	1	0	1	0	0	0	4	0	3	0	8	3	1	2	8	3	0	1			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr17:79875730C>G	ENST00000328666.6	-	2	269	c.207G>C	c.(205-207)gaG>gaC	p.E69D		NM_016538.2	NP_057622.1	Q9NRC8	SIR7_HUMAN	sirtuin 7	69	Arg-rich.				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)			GCTTCAGGCCCTCGCGCCGCC	0.796																																					p.E69D		Atlas-SNP	.											.	SIRT7	37	.	0			c.G207C						PASS	.						1	1	1					17																	79875730		661	1650	2311	SO:0001583	missense	51547	exon2			CAGGCCCTCGCGC	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.207G>C	chr17.hg19:g.79875730C>G	ENSP00000329466:p.Glu69Asp	21.0	0.0	.		30.0	18.0	.	NM_016538	A8K2K0|B3KSU8|Q3MIK4|Q9NSZ6|Q9NUS6	Missense_Mutation	SNP	ENST00000328666.6	hg19	CCDS11792.1	.	.	.	.	.	.	.	.	.	.	C	12.88	2.069771	0.36566	.	.	ENSG00000187531	ENST00000328666;ENST00000536038	T	0.16897	2.31	3.6	3.6	0.41247	.	0.545275	0.19339	N	0.116697	T	0.09949	0.0244	N	0.20685	0.6	0.80722	D	1	B	0.14012	0.009	B	0.12156	0.007	T	0.12682	-1.0538	10	0.12766	T	0.61	-22.0401	10.329	0.43812	0.0:0.8966:0.0:0.1034	.	69	Q9NRC8	SIRT7_HUMAN	D	69;52	ENSP00000329466:E69D	ENSP00000329466:E69D	E	-	3	2	SIRT7	77469022	0.998000	0.40836	1.000000	0.80357	0.311000	0.27955	0.921000	0.28718	1.826000	0.53198	0.195000	0.17529	GAG	.	.	.	none		0.796	SIRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439961.1	NM_016538		G	79875730	C	G	79875730	3	3	190	1	0	0	0	0	1	0	0	0	14356	680	24	4	1031	4	SIRT7	17	79875730	Missense_Mutation	SNP	C	TCGA-GL-A9DC-01A-11D-A36X-10	380023	79875730	1319480	98	11275											
PIAS2	9063	hgsc.bcm.edu	37	chr18	44416418	44416418	+	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	tgtagatagagggcagcatcAaaacactgcagatgtgtaca	15	8	11	7	0	1	3	1	0	0	3	1	3	1	3	0	1	4	5	0	1	5	3			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr18:44416418A>T	ENST00000585916.1	-	9	1103	c.1104T>A	c.(1102-1104)ttT>ttA	p.F368L	PIAS2_ENST00000545673.1_Missense_Mutation_p.F78L|PIAS2_ENST00000324794.7_Missense_Mutation_p.F368L	NM_004671.3	NP_004662.2	O75928	PIAS2_HUMAN	protein inhibitor of activated STAT, 2	368					androgen receptor signaling pathway (GO:0030521)|negative regulation of androgen receptor signaling pathway (GO:0060766)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein sumoylation (GO:0016925)|regulation of osteoblast differentiation (GO:0045667)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|SUMO ligase activity (GO:0019789)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	22						GGGCAGCATCAAAACACTGCA	0.413																																					p.F368L		Atlas-SNP	.											.	PIAS2	85	.	0			c.T1104A						PASS	.						125	111	116					18																	44416418		2203	4300	6503	SO:0001583	missense	9063	exon9			AGCATCAAAACAC	AF077953	CCDS32824.1, CCDS32825.1	18q12.1-q12.3	2011-10-11				ENSG00000078043		"Zinc fingers, MIZ-type"	17311	protein-coding gene	gene with protein product	"zinc finger, MIZ-type containing 4"	603567				9724754, 9256341	Standard	NM_004671		Approved	PIASX-BETA, miz, PIASX-ALPHA, ZMIZ4	uc002lck.3	O75928		ENST00000585916.1:c.1104T>A	chr18.hg19:g.44416418A>T	ENSP00000465676:p.Phe368Leu	181.0	0.0	.		205.0	15.0	.	NM_173206	O75927|Q96BT5|Q96KE3	Missense_Mutation	SNP	ENST00000585916.1	hg19	CCDS32824.1	.	.	.	.	.	.	.	.	.	.	A	19.77	3.889121	0.72524	.	.	ENSG00000078043	ENST00000398654;ENST00000262161;ENST00000398651;ENST00000545673;ENST00000324794	T;T	0.78595	-1.18;-1.19	5.52	3.17	0.36434	Zinc finger, MIZ-type (2);	0.000000	0.85682	D	0.000000	D	0.91317	0.7262	H	0.98314	4.2	0.80722	D	1	D;D;D;D;D	0.89917	0.997;1.0;0.999;1.0;0.999	D;D;D;D;D	0.91635	0.98;0.999;0.997;0.988;0.996	D	0.91010	0.4849	10	0.87932	D	0	-18.4406	8.3757	0.32442	0.7133:0.0:0.2867:0.0	.	78;372;368;368;368	B4DGW0;O75928-3;Q2TA77;O75928-2;O75928	.;.;.;.;PIAS2_HUMAN	L	368;368;364;78;368	ENSP00000443238:F78L;ENSP00000317163:F368L	ENSP00000262161:F368L	F	-	3	2	PIAS2	42670416	0.993000	0.37304	1.000000	0.80357	0.937000	0.57800	0.637000	0.24659	0.925000	0.37094	-0.467000	0.05162	TTT	.	.	.	none		0.413	PIAS2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445656.2	NM_004671		T	44416418	A	T	44416418	3	4	190	1	0	0	0	0	1	0	0	0	11883	127	5	5	860	5	PIAS2	18	44416418	Missense_Mutation	SNP	A	TCGA-GL-A9DC-01A-11D-A36X-10		44416418	33660830	99	11276											
ZNF407	55628	hgsc.bcm.edu	37	chr18	72352965	72352973	+	Splice_Site	DEL	ATCAAAACC	ATCAAAACC	-																															ttatgttaaatttactcaggAtcaaaaccattcaagtgcaa																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	ATCAAAACC	ATCAAAACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr18:72352965_72352973delATCAAAACC	ENST00000299687.5	+	2	4689_4697	c.4689_4697delATCAAAACC	c.(4687-4698)ggatcaaaacca>gga	p.SKP1564del	ZNF407_ENST00000577538.1_Splice_Site_p.SKP1564del|ZNF407_ENST00000309902.6_Splice_Site_p.SKP1564del|ZNF407_ENST00000582337.1_Splice_Site_p.SKP1564del	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	1564					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)		TTTACTCAGGATCAAAACCATTCAAGTGC	0.349																																					p.1563_1566del		Atlas-Indel,Pindel	.											.	ZNF407	231	.	0			c.4688_4696del						PASS	.																																			SO:0001630	splice_region_variant	55628	exon2			.	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.4688-1ATCAAAACC>-	chr18.hg19:g.72352965_72352973delATCAAAACC		222.0	0.0	0		214.0	70.0	0.327103	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	In_Frame_Del	DEL	ENST00000299687.5	hg19	CCDS45885.1																																																																																			.	.	.	none		0.349	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	In_Frame_Del	-	72352973	ATCAAAACC	-	72352965	8	5	190	1	0	1	0	1	0	0	1	0	17899	347	12	0	4695	0	ZNF407	18	72352965	Splice_Site	DEL	ATCAAAACC	TCGA-GL-A9DC-01A-11D-A36X-10	27936547	72352965	5724283	100	11277											
DIRAS1	148252	hgsc.bcm.edu	37	chr19	2717307	2717307	+	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	atgttccggcgcgtctccagCgtcagcagctcctggaagag	7	8	13	13	4	2	1	1	0	1	1	5	2	4	2	3	2	3	3	3	2	1	1			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr19:2717307C>T	ENST00000323469.4	-	2	681	c.498G>A	c.(496-498)acG>acA	p.T166T	DIRAS1_ENST00000585334.1_Silent_p.T166T	NM_145173.3	NP_660156.1	O95057	DIRA1_HUMAN	DIRAS family, GTP-binding RAS-like 1	166					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)		GCGTCTCCAGCGTCAGCAGCT	0.612																																					p.T166T		Atlas-SNP	.											.	DIRAS1	26	.	0			c.G498A						PASS	.						122	113	116					19																	2717307		2203	4300	6503	SO:0001819	synonymous_variant	148252	exon2			CTCCAGCGTCAGC	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.498G>A	chr19.hg19:g.2717307C>T		30.0	0.0	.		26.0	11.0	.	NM_145173		Silent	SNP	ENST00000323469.4	hg19	CCDS12092.1																																																																																			.	.	.	none		0.612	DIRAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451350.1			T	2717307	C	T	2717307	2	4	190	1	0	0	0	0	0	0	0	1	4532	755	27	1		1	DIRAS1	19	2717307	Silent	SNP	C	TCGA-GL-A9DC-01A-11D-A36X-10		2717307	56411676	101	11278											
PRKCSH	5589	hgsc.bcm.edu	37	chr19	11558367	11558367	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggaggaggaggaggaggaGgaggaagaagaggctgaaga	16	1	23	1	0	0	4	0	1	0	3	0	13	0	12	0	9	0	1	0	9	3	0			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr19:11558367G>A	ENST00000589838.1	+	10	963	c.963G>A	c.(961-963)gaG>gaA	p.E321E	PRKCSH_ENST00000591462.1_Silent_p.E321E|PRKCSH_ENST00000252455.2_Silent_p.E321E|PRKCSH_ENST00000592741.1_Silent_p.E321E|PRKCSH_ENST00000587327.1_Silent_p.E321E|PRKCSH_ENST00000412601.1_Silent_p.E321E			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	321	Glu-rich (acidic).				cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|N-glycan processing (GO:0006491)|negative regulation of neuron projection development (GO:0010977)|nitrogen compound metabolic process (GO:0006807)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein N-linked glycosylation via asparagine (GO:0018279)|renal system development (GO:0072001)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|phosphoprotein binding (GO:0051219)|protein kinase C binding (GO:0005080)|RNA binding (GO:0003723)	p.E321_E322delEE(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(3)	19						aggaggaggaggaggaagaag	0.632																																					p.E321E		Atlas-SNP	.											.	PRKCSH	55	.	1	Deletion - In frame(1)	central_nervous_system(1)	c.G963A						PASS	.						28	28	28					19																	11558367		2200	4298	6498	SO:0001819	synonymous_variant	5589	exon11			GGAGGAGGAGGAA		CCDS32911.1, CCDS45977.1, CCDS74286.1	19p13.2	2014-01-30			ENSG00000130175	ENSG00000130175	2.7.11.1	"EF-hand domain containing"	9411	protein-coding gene	gene with protein product		177060	"polycystic liver disease"	G19P1, PCLD, PLD1		12529853	Standard	NM_002743		Approved		uc002mrt.3	P14314	OTTHUMG00000182029	ENST00000589838.1:c.963G>A	chr19.hg19:g.11558367G>A		101.0	0.0	.		114.0	10.0	.	NM_001001329	A8K318|Q96BU9|Q96D06|Q9P0W9	Silent	SNP	ENST00000589838.1	hg19	CCDS32911.1																																																																																			.	.	.	none		0.632	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1			A	11558367	G	A	11558367	2	1	190	1	0	0	0	0	0	0	0	1	12526	991	35	2		2	PRKCSH	19	11558367	Silent	SNP	G	TCGA-GL-A9DC-01A-11D-A36X-10	8841060	11558367	47570616	102	11279											
ZNF823	55552	hgsc.bcm.edu	37	chr19	11833785	11833785	+	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	ttacatttataaggtccatcTccatggtgtgccgccatgtg	8	14	9	10	1	1	0	0	0	1	0	3	0	2	0	4	2	2	0	4	2	3	4			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr19:11833785T>G	ENST00000341191.6	-	4	717	c.564A>C	c.(562-564)ggA>ggC	p.G188G	ZNF823_ENST00000545749.1_Silent_p.G6G|CTC-499B15.6_ENST00000586983.1_RNA	NM_001080493.2	NP_001073962.1	P16415	ZN823_HUMAN	zinc finger protein 823	188					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)	26						AAGGTCCATCTCCATGGTGTG	0.443										HNSCC(68;0.2)																											p.G188G		Atlas-SNP	.											.	ZNF823	104	.	0			c.A564C						PASS	.						93	99	97					19																	11833785		2199	4298	6497	SO:0001819	synonymous_variant	55552	exon4			TCCATCTCCATGG	X51760	CCDS45981.1	19p13.2	2013-01-08			ENSG00000197933	ENSG00000197933		"Zinc fingers, C2H2-type", "-"	30936	protein-coding gene	gene with protein product	"ZFP 36 for a zinc finger protein"						Standard	XM_006722789		Approved	HSZFP36	uc002msm.2	P16415	OTTHUMG00000156528	ENST00000341191.6:c.564A>C	chr19.hg19:g.11833785T>G		146.0	0.0	.		152.0	69.0	.	NM_001080493	A0PJL4|B7Z8D4|Q6P4A9	Silent	SNP	ENST00000341191.6	hg19	CCDS45981.1																																																																																			.	.	.	none		0.443	ZNF823-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344516.2	NM_001080493		G	11833785	T	G	11833785	2	3	190	1	0	0	0	0	0	0	0	1	18191	1538	54	5		5	ZNF823	19	11833785	Silent	SNP	T	TCGA-GL-A9DC-01A-11D-A36X-10	275418	11833785	47295198	103	11280											
SPHK2	56848	hgsc.bcm.edu	37	chr19	49132774	49132774	+	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	cggcctggtgcacctgtgctGggtgcgtagcggcatctcgc	3	9	16	13	4	1	0	0	0	1	0	2	0	1	0	2	4	4	4	2	4	1	1			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr19:49132774G>A	ENST00000245222.4	+	7	2075	c.1709G>A	c.(1708-1710)tGg>tAg	p.W570*	SPHK2_ENST00000599029.1_Nonsense_Mutation_p.W534*|SPHK2_ENST00000600537.1_Nonsense_Mutation_p.W511*|SPHK2_ENST00000599748.1_Nonsense_Mutation_p.W534*|SPHK2_ENST00000443164.1_Nonsense_Mutation_p.W632*|SPHK2_ENST00000598088.1_Nonsense_Mutation_p.W570*|SPHK2_ENST00000340932.3_Nonsense_Mutation_p.W532*	NM_001204158.2|NM_001243876.1|NM_020126.4	NP_001191087.1|NP_001230805.1|NP_064511.2	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2	570					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)		CACCTGTGCTGGGTGCGTAGC	0.667																																					p.W570X		Atlas-SNP	.											.	SPHK2	62	.	0			c.G1709A						PASS	.						27	24	25					19																	49132774		2200	4297	6497	SO:0001587	stop_gained	56848	exon7			TGTGCTGGGTGCG	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.1709G>A	chr19.hg19:g.49132774G>A	ENSP00000245222:p.Trp570*	56.0	0.0	.		60.0	22.0	.	NM_020126	A0T4C8|B4DU87|Q9BRN1|Q9H0Q2|Q9NWU7	Nonsense_Mutation	SNP	ENST00000245222.4	hg19	CCDS12727.1	.	.	.	.	.	.	.	.	.	.	G	39	7.795158	0.98495	.	.	ENSG00000063176	ENST00000245222;ENST00000406269;ENST00000340932;ENST00000443164	.	.	.	4.49	4.49	0.54785	.	0.199237	0.44285	D	0.000466	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	-5.8616	10.1564	0.42825	0.0:0.0:0.8006:0.1993	.	.	.	.	X	570;543;532;632	.	ENSP00000245222:W570X	W	+	2	0	SPHK2	53824586	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	1.194000	0.32174	2.492000	0.84095	0.555000	0.69702	TGG	.	.	.	none		0.667	SPHK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466153.1			A	49132774	G	A	49132774	4	1	190	1	0	0	0	0	0	1	0	0	15059	1357	47	2	1731	2	SPHK2	19	49132774	Nonsense_Mutation	SNP	G	TCGA-GL-A9DC-01A-11D-A36X-10	37298989	49132774	9996209	104	11281											
HRC	3270	hgsc.bcm.edu	37	chr19	49657747	49657747	+	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	atcatcatcatcatcatcatCatcatcgtcatcttcttcat	11	16	1	13	1	12	0	10	0	2	0	13	0	12	0	0	0	0	0	0	0	0	2			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr19:49657747C>A	ENST00000252825.4	-	1	934	c.748G>T	c.(748-750)Gat>Tat	p.D250Y	HRC_ENST00000595625.1_Missense_Mutation_p.D250Y	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	250	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Asp-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		tcatcatcatcatcatcgtca	0.498																																					p.D250Y	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.G748T						PASS	.						138	100	113					19																	49657747		2203	4300	6503	SO:0001583	missense	3270	exon1			CATCATCATCATC		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.748G>T	chr19.hg19:g.49657747C>A	ENSP00000252825:p.Asp250Tyr	22.0	0.0	.		25.0	11.0	.	NM_002152	Q504Y6	Missense_Mutation	SNP	ENST00000252825.4	hg19	CCDS12759.1	.	.	.	.	.	.	.	.	.	.	N	12.91	2.079771	0.36662	.	.	ENSG00000130528	ENST00000252825;ENST00000434964	T	0.39787	1.06	2.35	1.24	0.21308	.	.	.	.	.	T	0.51873	0.1700	L	0.55990	1.75	0.34621	D	0.718578	D	0.56968	0.978	D	0.64144	0.922	T	0.60188	-0.7312	9	0.51188	T	0.08	.	8.641	0.33976	0.0:0.761:0.239:0.0	.	250	P23327	SRCH_HUMAN	Y	250;220	ENSP00000252825:D250Y	ENSP00000252825:D250Y	D	-	1	0	HRC	54349559	0.014000	0.17966	0.052000	0.19188	0.167000	0.22549	1.033000	0.30191	0.309000	0.22966	0.394000	0.25966	GAT	.	.	.	none		0.498	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		A	49657747	C	A	49657747	3	1	190	1	0	0	0	0	1	0	0	0	7359	826	29	4	1375	4	HRC	19	49657747	Missense_Mutation	SNP	C	TCGA-GL-A9DC-01A-11D-A36X-10	524973	49657747	9471236	105	11282											
POLD1	5424	hgsc.bcm.edu	37	chr19	50918121	50918121	+	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	gaagcgctacgcgggcctgcTcttctcctcccggcccgacg	4	7	12	18	6	2	0	0	0	2	0	4	2	3	0	4	2	3	2	4	2	2	2			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr19:50918121T>A	ENST00000440232.2	+	20	2491	c.2438T>A	c.(2437-2439)cTc>cAc	p.L813H	POLD1_ENST00000599857.1_Missense_Mutation_p.L813H|POLD1_ENST00000595904.1_Missense_Mutation_p.L839H|CTD-2545M3.6_ENST00000599632.1_5'Flank	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	813					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		GCGGGCCTGCTCTTCTCCTCC	0.662								DNA polymerases (catalytic subunits)			OREG0025635	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L813H		Atlas-SNP	.											.	POLD1	174	.	0			c.T2438A						PASS	.						55	53	54					19																	50918121		2203	4300	6503	SO:0001583	missense	5424	exon20			GCCTGCTCTTCTC		CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"DNA polymerases"	9175	protein-coding gene	gene with protein product	"CDC2 homolog (S. cerevisiae)"	174761	"polymerase (DNA directed), delta 1, catalytic subunit (125kD)"	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.2438T>A	chr19.hg19:g.50918121T>A	ENSP00000406046:p.Leu813His	73.0	0.0	.	973	99.0	44.0	.	NM_002691	Q8NER3|Q96H98	Missense_Mutation	SNP	ENST00000440232.2	hg19	CCDS12795.1	.	.	.	.	.	.	.	.	.	.	T	12.00	1.806200	0.31961	.	.	ENSG00000062822	ENST00000440232;ENST00000376930	T	0.18502	2.21	4.84	4.84	0.62591	DNA polymerase, palm domain (1);DNA-directed DNA polymerase, family B, multifunctional domain (1);	0.219677	0.39909	N	0.001224	T	0.30008	0.0751	M	0.80847	2.515	0.37207	D	0.90462	B;P	0.37731	0.407;0.607	B;P	0.46208	0.309;0.507	T	0.34304	-0.9834	10	0.87932	D	0	-38.3143	8.1304	0.31024	0.2888:0.0:0.0:0.7112	.	839;813	E7EVW0;P28340	.;DPOD1_HUMAN	H	813;814	ENSP00000406046:L813H	ENSP00000366129:L814H	L	+	2	0	POLD1	55609933	1.000000	0.71417	0.998000	0.56505	0.006000	0.05464	4.017000	0.57167	1.970000	0.57323	0.449000	0.29647	CTC	.	.	.	none		0.662	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1			A	50918121	T	A	50918121	3	1	190	1	0	0	0	0	1	0	0	0	12197	1551	54	5	2512	5	POLD1	19	50918121	Missense_Mutation	SNP	T	TCGA-GL-A9DC-01A-11D-A36X-10	1260374	50918121	8210862	106	11283											
VN1R2	317701	hgsc.bcm.edu	37	chr19	53762550	53762564	+	In_Frame_Del	DEL	TCTCCTGGGAACAGA	TCTCCTGGGAACAGA	-																															acaatctctaccccaactctTctcctgggaacagagccatc																								rs61732642|rs146904187	byFrequency	TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	TCTCCTGGGAACAGA	TCTCCTGGGAACAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr19:53762550_53762564delTCTCCTGGGAACAGA	ENST00000341702.3	+	1	1006_1020	c.922_936delTCTCCTGGGAACAGA	c.(922-936)tctcctgggaacagadel	p.SPGNR308del	VN1R2_ENST00000598458.1_3'UTR	NM_173856.2	NP_776255.2	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	308					response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)	p.G310G(1)		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)		CCCCAACTCTTCTCCTGGGAACAGAGCCATCCAAA	0.479																																					p.307_312del		Atlas-Indel,Pindel	.											.	VN1R2	71	.	1	Substitution - coding silent(1)	skin(1)	c.921_935del						PASS	.																																			SO:0001651	inframe_deletion	317701	exon1			.	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.922_936delTCTCCTGGGAACAGA	chr19.hg19:g.53762550_53762564delTCTCCTGGGAACAGA	ENSP00000351244:p.Ser308_Arg312del	105.0	0.0	0		131.0	39.0	0.29771	NM_173856	A1L411|Q8TDU4	In_Frame_Del	DEL	ENST00000341702.3	hg19	CCDS12862.1																																																																																			.	.	.	none		0.479	VN1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464285.1	NM_173856		-	53762564	TCTCCTGGGAACAGA	-	53762550	7	5	190	1	0	1	0	1	0	0	0	0	17191	1783	62	0	924	0	VN1R2	19	53762550	In_Frame_Del	DEL	TCTCCTGGGAACAGA	TCGA-GL-A9DC-01A-11D-A36X-10	2844429	53762550	5366433	107	11284											
ZNF331	55422	hgsc.bcm.edu	37	chr19	54080924	54080924	+	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	ttcaattgtggctatcacctCactcagcacgagagaatcca	12	10	7	12	1	4	1	4	0	0	1	5	3	5	1	2	1	1	2	2	1	3	3			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr19:54080924C>T	ENST00000253144.9	+	7	2443	c.1110C>T	c.(1108-1110)ctC>ctT	p.L370L	ZNF331_ENST00000512387.1_Silent_p.L370L|ZNF331_ENST00000513265.1_3'UTR|ZNF331_ENST00000411977.2_Silent_p.L370L|ZNF331_ENST00000449416.1_Silent_p.L370L|ZNF331_ENST00000513999.1_Silent_p.L370L|ZNF331_ENST00000511154.1_Silent_p.L370L|ZNF331_ENST00000511593.2_Silent_p.L370L	NM_001253801.1|NM_018555.5	NP_001240730.1|NP_061025.5	Q9NQX6	ZN331_HUMAN	zinc finger protein 331	370					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	10				GBM - Glioblastoma multiforme(134;0.00555)		GCTATCACCTCACTCAGCACG	0.507			T	?	follicular thyroid adenoma																																p.L370L		Atlas-SNP	.		Dom	yes		19	19q13.3-q13.4	55422	zinc finger protein 331		E	.	ZNF331	66	.	0			c.C1110T						PASS	.						100	88	92					19																	54080924		2203	4300	6503	SO:0001819	synonymous_variant	55422	exon5			TCACCTCACTCAG	AF251515	CCDS33102.1	19q13	2013-12-10				ENSG00000130844		"Zinc fingers, C2H2-type", "-"	15489	protein-coding gene	gene with protein product	"rearranged in thyroid adenomas"	606043					Standard	NM_001079906		Approved	RITA, ZNF463, ZNF361	uc021uzh.1	Q9NQX6		ENST00000253144.9:c.1110C>T	chr19.hg19:g.54080924C>T		212.0	0.0	.		254.0	115.0	.	NM_001253801	Q96GJ4	Silent	SNP	ENST00000253144.9	hg19	CCDS33102.1																																																																																			.	.	.	none		0.507	ZNF331-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371366.1	NM_018555		T	54080924	C	T	54080924	2	4	190	1	0	0	0	0	0	0	0	1	17861	813	29	2		2	ZNF331	19	54080924	Silent	SNP	C	TCGA-GL-A9DC-01A-11D-A36X-10	318374	54080924	5048059	108	11285											
SAPS1	22870	hgsc.bcm.edu	37	chr19	55748303	55748303	+	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	tctcatcgtcagcattgaggGagaaggtgatgttggctgtc	8	12	14	7	1	2	3	2	2	1	1	5	4	2	3	0	3	1	3	0	3	1	2			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr19:55748303G>A	ENST00000412770.2	-	16	2353	c.1787C>T	c.(1786-1788)tCc>tTc	p.S596F	AC010327.1_ENST00000581390.1_RNA|PPP6R1_ENST00000587283.1_Missense_Mutation_p.S596F	NM_014931.3	NP_055746.3	Q9UPN7	PP6R1_HUMAN	protein phosphatase 6, regulatory subunit 1	596					regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)	protein phosphatase binding (GO:0019903)			breast(1)	1						AGCATTGAGGGAGAAGGTGAT	0.622																																					p.S596F		Atlas-SNP	.											.	PPP6R1	63	.	0			c.C1787T						PASS	.						91	94	93					19																	55748303		2113	4217	6330	SO:0001583	missense	22870	exon16			TTGAGGGAGAAGG	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.1787C>T	chr19.hg19:g.55748303G>A	ENSP00000414202:p.Ser596Phe	167.0	0.0	.		165.0	67.0	.	NM_014931	Q2M2H3|Q504V2|Q6NVJ6|Q9BU97	Missense_Mutation	SNP	ENST00000412770.2	hg19	CCDS46186.1	.	.	.	.	.	.	.	.	.	.	G	18.96	3.733755	0.69189	.	.	ENSG00000105063	ENST00000412770	T	0.49432	0.78	4.7	4.7	0.59300	.	0.000000	0.56097	D	0.000023	T	0.60051	0.2239	L	0.46157	1.445	0.38613	D	0.950959	D	0.64830	0.994	P	0.61328	0.887	T	0.65940	-0.6046	10	0.87932	D	0	-37.8255	16.9293	0.86186	0.0:0.0:1.0:0.0	.	596	Q9UPN7	PP6R1_HUMAN	F	596	ENSP00000414202:S596F	ENSP00000414202:S596F	S	-	2	0	PPP6R1	60440115	1.000000	0.71417	1.000000	0.80357	0.822000	0.46500	1.831000	0.39141	2.613000	0.88420	0.467000	0.42956	TCC	.	.	.	none		0.622	PPP6R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452663.1	NM_014931		A	55748303	G	A	55748303	3	1	190	1	0	0	0	0	1	0	0	0	13849	1174	41	2	894	2	SAPS1	19	55748303	Missense_Mutation	SNP	G	TCGA-GL-A9DC-01A-11D-A36X-10	1667379	55748303	3380680	109	11286											
C20orf4	25980	hgsc.bcm.edu	37	chr20	34832729	34832729	+	Missense_Mutation	SNP	A	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	ggtcagaagcagccatgatgAagcaccacaccctctacatc	13	6	8	14	0	2	3	1	2	1	1	3	3	2	3	3	1	4	2	3	1	3	1			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr20:34832729A>C	ENST00000373932.3	+	3	1214	c.868A>C	c.(868-870)Aag>Cag	p.K290Q	AAR2_ENST00000320849.4_Missense_Mutation_p.K290Q|AAR2_ENST00000397286.3_Missense_Mutation_p.K290Q	NM_015511.3	NP_056326.2	Q9Y312	AAR2_HUMAN	AAR2 splicing factor homolog (S. cerevisiae)	290																	AGCCATGATGAAGCACCACAC	0.522																																					p.K290Q		Atlas-SNP	.											.	.	.	.	0			c.A868C						PASS	.						237	189	206					20																	34832729		2203	4300	6503	SO:0001583	missense	25980	exon3			ATGATGAAGCACC		CCDS13273.1	20q11.23	2012-07-20	2012-07-20	2012-07-20	ENSG00000131043	ENSG00000131043			15886	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 4"	C20orf4			Standard	NM_015511		Approved	bA234K24.2	uc002xfc.3	Q9Y312	OTTHUMG00000032380	ENST00000373932.3:c.868A>C	chr20.hg19:g.34832729A>C	ENSP00000363043:p.Lys290Gln	122.0	0.0	.		133.0	56.0	.	NM_001271874	E1P5S7|Q9H4F9|Q9P1P3|Q9UFK9	Missense_Mutation	SNP	ENST00000373932.3	hg19	CCDS13273.1	.	.	.	.	.	.	.	.	.	.	A	12.67	2.007091	0.35415	.	.	ENSG00000131043	ENST00000397286;ENST00000320849;ENST00000373932	T;T;T	0.46819	0.86;0.86;0.86	6.03	4.94	0.65067	.	0.280019	0.46442	D	0.000292	T	0.29749	0.0743	N	0.25245	0.725	0.35498	D	0.79959	B;B	0.26902	0.163;0.029	B;B	0.30029	0.11;0.029	T	0.31971	-0.9924	10	0.14656	T	0.56	.	6.9997	0.24803	0.7752:0.1505:0.0743:0.0	.	290;290	A2A2Q9;Q9Y312	.;CT004_HUMAN	Q	290	ENSP00000380455:K290Q;ENSP00000313674:K290Q;ENSP00000363043:K290Q	ENSP00000313674:K290Q	K	+	1	0	C20orf4	34296143	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	3.832000	0.55783	2.308000	0.77769	0.533000	0.62120	AAG	.	.	.	none		0.522	AAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079001.2	NM_015511		C	34832729	A	C	34832729	3	2	190	1	0	0	0	0	1	0	0	0	2113	247	9	5	874	5	C20orf4	20	34832729	Missense_Mutation	SNP	A	TCGA-GL-A9DC-01A-11D-A36X-10		34832729	28192791	110	11287											
BCAS1	8537	hgsc.bcm.edu	37	chr20	52569985	52569991	+	Frame_Shift_Del	DEL	AGCCCCC	AGCCCCC	-																															acctaccaggcctttaaagaAgcccccaagggactgctgcc																								rs200870946|rs375030303	byFrequency	TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	AGCCCCC	AGCCCCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr20:52569985_52569991delAGCCCCC	ENST00000395961.3	-	11	1826_1832	c.1660_1666delGGGGGCT	c.(1660-1668)gggggcttcfs	p.GGF554fs	BCAS1_ENST00000434986.2_Frame_Shift_Del_p.GGF220fs|BCAS1_ENST00000371435.2_Frame_Shift_Del_p.GGF476fs|BCAS1_ENST00000371440.3_Frame_Shift_Del_p.GGF563fs	NM_003657.2	NP_003648.2	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1	554						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)			CCTTTAAAGAAGCCCCCAAGGGACTGC	0.527																																					p.554_556del		Atlas-Indel,Pindel	.											.	BCAS1	77	.	0			c.1661_1667del						PASS	.																																			SO:0001589	frameshift_variant	8537	exon11			.	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.1660_1666delGGGGGCT	chr20.hg19:g.52569985_52569991delAGCCCCC	ENSP00000379290:p.Gly554fs	61.0	0.0	0		68.0	19.0	0.279412	NM_003657	A0AVG5|Q68CZ3	Frame_Shift_Del	DEL	ENST00000395961.3	hg19	CCDS13444.1																																																																																			.	.	.	none		0.527	BCAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079766.2	NM_003657		-	52569991	AGCCCCC	-	52569985	7	5	190	1	0	1	0	1	0	0	0	0	1350	72	3	0	96	0	BCAS1	20	52569985	Frame_Shift_Del	DEL	AGCCCCC	TCGA-GL-A9DC-01A-11D-A36X-10	17737256	52569985	10455535	111	11288											
CSF2RB	1439	hgsc.bcm.edu	37	chr22	37333782	37333782	+	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	caactggtccctctggcccaGgcgatgggaccaggacaggc	8	5	14	14	1	1	0	0	0	1	0	2	3	2	2	3	6	1	0	3	6	1	0			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr22:37333782G>T	ENST00000403662.3	+	14	2154	c.1932G>T	c.(1930-1932)caG>caT	p.Q644H	CSF2RB_ENST00000536485.1_Missense_Mutation_p.Q591H|CSF2RB_ENST00000262825.5_Missense_Mutation_p.Q650H|CSF2RB_ENST00000406230.1_Missense_Mutation_p.Q650H			P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	644					cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)|interleukin-5-mediated signaling pathway (GO:0038043)|respiratory gaseous exchange (GO:0007585)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	granulocyte macrophage colony-stimulating factor receptor complex (GO:0030526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(3)|pancreas(1)|skin(5)|upper_aerodigestive_tract(2)	42					Sargramostim(DB00020)	CTCTGGCCCAGGCGATGGGAC	0.701																																					p.Q644H		Atlas-SNP	.											.	CSF2RB	104	.	0			c.G1932T						PASS	.						8	9	9					22																	37333782		2169	4247	6416	SO:0001583	missense	1439	exon14			GGCCCAGGCGATG	M59941	CCDS13936.1	22q12.3	2014-09-09			ENSG00000100368	ENSG00000100368		"CD molecules", "Fibronectin type III domain containing"	2436	protein-coding gene	gene with protein product		138981		IL3RB		1833064, 1424804	Standard	NM_000395		Approved	IL5RB, CD131	uc003aqa.4	P32927	OTTHUMG00000150546	ENST00000403662.3:c.1932G>T	chr22.hg19:g.37333782G>T	ENSP00000384053:p.Gln644His	74.0	0.0	.		105.0	38.0	.	NM_000395	Q5JZI1|Q6ICE0	Missense_Mutation	SNP	ENST00000403662.3	hg19	CCDS13936.1	.	.	.	.	.	.	.	.	.	.	G	14.33	2.503380	0.44558	.	.	ENSG00000100368	ENST00000403662;ENST00000539104;ENST00000262825;ENST00000406230;ENST00000536485	D;D;D;D	0.93426	-2.71;-3.22;-3.22;-3.22	5.12	3.0	0.34707	.	0.556068	0.15041	N	0.283883	D	0.94984	0.8377	M	0.71581	2.175	0.27457	N	0.953266	D;D	0.89917	1.0;1.0	D;D	0.77557	0.99;0.978	D	0.87687	0.2551	10	0.22706	T	0.39	-24.6502	8.2995	0.32006	0.1892:0.0:0.8108:0.0	.	650;644	P32927-2;P32927	.;IL3RB_HUMAN	H	644;644;650;650;591	ENSP00000384053:Q644H;ENSP00000262825:Q650H;ENSP00000385271:Q650H;ENSP00000440003:Q591H	ENSP00000262825:Q650H	Q	+	3	2	CSF2RB	35663728	0.988000	0.35896	0.966000	0.40874	0.362000	0.29581	0.976000	0.29462	1.161000	0.42604	0.557000	0.71058	CAG	.	.	.	none		0.701	CSF2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318854.1	NM_000395		T	37333782	G	T	37333782	3	4	190	1	0	0	0	0	1	0	0	0	3937	991	35	4	1982	4	CSF2RB	22	37333782	Missense_Mutation	SNP	G	TCGA-GL-A9DC-01A-11D-A36X-10		37333782	13970784	112	11289											
SREBF2	6721	hgsc.bcm.edu	37	chr22	42280845	42280846	+	Splice_Site	DNP	GG	GG	AT																															gtctgtttctgcccaccctaGggaagcttcctgcaggatcc																										TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chr22:42280845_42280846GG>AT	ENST00000361204.4	+	11	2204_2205	c.2038_2039GG>AT	c.(2038-2040)GGg>ATg	p.G680M		NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	680					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						GCCCACCCTAGGGAAGCTTCCT	0.535																																					.|p.G680V		Atlas-SNP	.											.	SREBF2	99	.	0			c.2039-1G>A|c.G2039T						PASS	.																																			SO:0001630	splice_region_variant	6721	exon11			ACCCTAGGGAAGC|CCCTAGGGAAGCT	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	Exception_encountered	chr22.hg19:g.42280845_42280846delinsAT		126.0|124.0	0.0	.		132.0	64.0|62.0	.	NM_004599	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Splice_Site|Missense_Mutation	SNP	ENST00000361204.4	hg19	CCDS14023.1																																																																																			.	.	.	none		0.535	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599	Missense_Mutation	AT	42280846	GG	AT	42280845	5	1	190	1	0	0	0	0	0	0	1	0	15154	1014	35	2	2080	2	SREBF2	22	42280845	Splice_Site	DNP	GG	TCGA-GL-A9DC-01A-11D-A36X-10	4947063	42280845	9023721	113	11290											
KDM5C	8242	hgsc.bcm.edu	37	chrX	53223343	53223343	+	Missense_Mutation	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	taggcatatccttgccactgCcctctctgagggggtcagaa	8	10	11	12	0	2	2	1	1	1	1	4	2	3	2	3	3	2	1	3	3	3	3			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chrX:53223343C>T	ENST00000375401.3	-	23	4548	c.4016G>A	c.(4015-4017)gGc>gAc	p.G1339D	KDM5C_ENST00000375379.3_Missense_Mutation_p.G1339D|KDM5C_ENST00000404049.3_Missense_Mutation_p.G1338D|KDM5C_ENST00000375383.3_Missense_Mutation_p.G1298D|KDM5C_ENST00000452825.3_Missense_Mutation_p.G1272D	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	1339					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						CTTGCCACTGCCCTCTCTGAG	0.612			"N, F, S"		clear cell renal carcinoma																																p.G1339D		Atlas-SNP	.		Rec	yes		X	Xp11.22-p11.21	8242	lysine (K)-specific demethylase 5C (JARID1C)		E	.	KDM5C	385	.	0			c.G4016A						PASS	.						22	20	21					X																	53223343		2201	4299	6500	SO:0001583	missense	8242	exon23			CCACTGCCCTCTC	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.4016G>A	chrX.hg19:g.53223343C>T	ENSP00000364550:p.Gly1339Asp	201.0	0.0	.		237.0	108.0	.	NM_004187	B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Missense_Mutation	SNP	ENST00000375401.3	hg19	CCDS14351.1	.	.	.	.	.	.	.	.	.	.	c	0.196	-1.048772	0.01981	.	.	ENSG00000126012	ENST00000452825;ENST00000375401;ENST00000404049;ENST00000375379;ENST00000375383	D;D;D;D;D	0.85773	-2.03;-1.71;-1.71;-1.73;-1.86	4.76	3.9	0.45041	.	0.400598	0.27631	N	0.018501	T	0.72087	0.3417	L	0.34521	1.04	0.26500	N	0.974785	B;B;B	0.11235	0.004;0.004;0.004	B;B;B	0.13407	0.009;0.003;0.003	T	0.53933	-0.8368	10	0.02654	T	1	-4.4102	8.1117	0.30917	0.0:0.8839:0.0:0.1161	.	1272;1338;1339	F5H3T1;B0QZ44;P41229	.;.;KDM5C_HUMAN	D	1272;1339;1338;1339;1298	ENSP00000445176:G1272D;ENSP00000364550:G1339D;ENSP00000385394:G1338D;ENSP00000364528:G1339D;ENSP00000364532:G1298D	ENSP00000364528:G1339D	G	-	2	0	KDM5C	53240068	1.000000	0.71417	1.000000	0.80357	0.827000	0.46813	1.338000	0.33873	0.825000	0.34637	0.507000	0.49892	GGC	.	.	.	none		0.612	KDM5C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056737.2	NM_004187		T	53223343	C	T	53223343	3	4	190	1	0	0	0	0	1	0	0	0	8142	739	26	2	780	2	KDM5C	23	53223343	Missense_Mutation	SNP	C	TCGA-GL-A9DC-01A-11D-A36X-10		53223343	102047217	114	11291											
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-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	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	chrX.hg19:g.66765164A>T	ENSP00000363822:p.Gln59Leu	181.0	0.0	.		263.0	18.0	.	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	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	190	1	0	0	0	0	1	0	0	0	836	188	7	5	178	5	AR	23	66765164	Missense_Mutation	SNP	A	TCGA-GL-A9DC-01A-11D-A36X-10	13541821	66765164	88505396	115	11292											
MAGT1	84061	hgsc.bcm.edu	37	chrX	77131066	77131066	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttgttagtccattccatcAgctgactaaccttttcagat	9	17	5	10	0	2	2	2	1	0	1	4	2	4	2	3	0	2	2	3	0	2	7			TCGA-GL-A9DC-01A-11D-A36X-10	TCGA-GL-A9DC-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dbe2fec-20a5-4107-a6b3-b91b4646f2cb	ac49247f-bdb9-4f02-b075-ac3855d5a824	g.chrX:77131066A>G	ENST00000373336.3	-	2	160	c.131T>C	c.(130-132)cTg>cCg	p.L44P	MAGT1_ENST00000358075.6_Missense_Mutation_p.L76P			Q9H0U3	MAGT1_HUMAN	magnesium transporter 1	44					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						CCATTCCATCAGCTGACTAAC	0.388																																					p.L76P		Atlas-SNP	.											.	MAGT1	51	.	0			c.T227C						PASS	.						174	163	167					X																	77131066		2203	4296	6499	SO:0001583	missense	84061	exon2			TCCATCAGCTGAC		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	ENST00000373336.3:c.131T>C	chrX.hg19:g.77131066A>G	ENSP00000362433:p.Leu44Pro	141.0	0.0	.		167.0	71.0	.	NM_032121	B2RAR4|D3DTE3|Q53G00|Q6P577|Q8NBN6	Missense_Mutation	SNP	ENST00000373336.3	hg19		.	.	.	.	.	.	.	.	.	.	A	23.4	4.407210	0.83230	.	.	ENSG00000102158	ENST00000358075;ENST00000373336	T;T	0.26067	1.76;1.76	5.69	5.69	0.88448	.	0.063289	0.64402	U	0.000008	T	0.54886	0.1886	M	0.82823	2.61	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.75484	0.977;0.986	T	0.61946	-0.6958	10	0.87932	D	0	-6.7821	14.9683	0.71213	1.0:0.0:0.0:0.0	.	44;76	Q9H0U3;B4DH58	MAGT1_HUMAN;.	P	76;44	ENSP00000354649:L76P;ENSP00000362433:L44P	ENSP00000354649:L76P	L	-	2	0	MAGT1	77017722	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.859000	0.92264	1.917000	0.55516	0.486000	0.48141	CTG	.	.	.	none		0.388	MAGT1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000057302.2	NM_032121		G	77131066	A	G	77131066	3	3	190	1	0	0	0	0	1	0	0	0	9203	188	7	3	912	3	MAGT1	23	77131066	Missense_Mutation	SNP	A	TCGA-GL-A9DC-01A-11D-A36X-10	10365902	77131066	78139494	116	11293											
MFN2	9927	hgsc.bcm.edu	37	chr1	12052714	12052714	+	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	aggcatcagtgaggtgctggCtcggaggcacatgaaagtgg	10	7	17	7	1	1	2	1	2	0	0	2	3	1	3	0	6	1	4	0	6	1	0			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr1:12052714C>T	ENST00000235329.5	+	4	600	c.278C>T	c.(277-279)gCt>gTt	p.A93V	MFN2_ENST00000444836.1_Missense_Mutation_p.A93V	NM_014874.3	NP_055689.1	O95140	MFN2_HUMAN	mitofusin 2	93	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)		GAGGTGCTGGCTCGGAGGCAC	0.527																																					p.A93V		Atlas-SNP	.											.	MFN2	83	.	0			c.C278T						PASS	.						242	220	228					1																	12052714		2203	4300	6503	SO:0001583	missense	9927	exon4			TGCTGGCTCGGAG	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.278C>T	chr1.hg19:g.12052714C>T	ENSP00000235329:p.Ala93Val	169.0	0.0	.		153.0	29.0	.	NM_014874	A8K1B3|O95572|Q5JXC3|Q5JXC4|Q9H131|Q9NSX8	Missense_Mutation	SNP	ENST00000235329.5	hg19	CCDS30587.1	.	.	.	.	.	.	.	.	.	.	C	17.89	3.498702	0.64298	.	.	ENSG00000116688	ENST00000444836;ENST00000235329;ENST00000412236	D;D;D	0.95482	-3.72;-3.72;-3.63	5.5	5.5	0.81552	.	0.106729	0.64402	D	0.000006	D	0.93452	0.7911	L	0.50333	1.59	0.80722	D	1	B	0.20671	0.047	B	0.16289	0.015	D	0.90115	0.4195	10	0.32370	T	0.25	-25.6319	18.3893	0.90477	0.0:1.0:0.0:0.0	.	93	O95140	MFN2_HUMAN	V	93	ENSP00000416338:A93V;ENSP00000235329:A93V;ENSP00000412023:A93V	ENSP00000235329:A93V	A	+	2	0	MFN2	11975301	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.487000	0.81328	2.588000	0.87417	0.561000	0.74099	GCT	.	.	.	none		0.527	MFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006859.2	NM_014874		T	12052714	C	T	12052714	3	4	191	1	0	0	0	0	1	0	0	0	9531	797	28	2	284	2	MFN2	1	12052714	Missense_Mutation	SNP	C	TCGA-GL-A9DD-01A-11D-A36X-10		12052714	237197907	1	11294											
CROCC	9696	hgsc.bcm.edu	37	chr1	17256398	17256398	+	Frame_Shift_Del	DEL	C	C	-																															agacgcaggagcccagggggCtggtacggcagagcgtggag																										TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr1:17256398delC	ENST00000375541.5	+	4	478	c.409delC	c.(409-411)ctgfs	p.L137fs	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		GCCCAGGGGGCTGGTACGGCA	0.711																																					p.G136fs		Atlas-INDEL	.											.	CROCC	185	.	0			c.408delG						PASS	.						9	11	10					1																	17256398		2172	4244	6416	SO:0001589	frameshift_variant	9696	exon4			.	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"rootletin, ciliary rootlet protein"	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.409delC	chr1.hg19:g.17256398delC	ENSP00000364691:p.Leu137fs	54.0	0.0	0		54.0	10.0	0.185185	NM_014675		Frame_Shift_Del	DEL	ENST00000375541.5	hg19	CCDS30616.1																																																																																			.	.	.	none		0.711	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675		-	17256398	C	-	17256398	7	5	191	1	0	1	0	1	0	0	0	0	3895	796	28	0	423	0	CROCC	1	17256398	Frame_Shift_Del	DEL	C	TCGA-GL-A9DD-01A-11D-A36X-10	5203684	17256398	231994223	2	11295											
SFRS4	6429	hgsc.bcm.edu	37	chr1	29486974	29486974	+	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	acaaaggtctttgccattcaGttcataaacagcatcatctg	13	12	6	10	0	5	0	3	0	2	0	5	0	5	0	1	1	3	2	1	1	3	4			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr1:29486974G>C	ENST00000373795.4	-	2	397	c.163C>G	c.(163-165)Ctg>Gtg	p.L55V	SRSF4_ENST00000546138.1_Missense_Mutation_p.L55V|SRSF4_ENST00000466448.1_5'UTR	NM_005626.4	NP_005617.2	Q08170	SRSF4_HUMAN	serine/arginine-rich splicing factor 4	55	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|hematopoietic progenitor cell differentiation (GO:0002244)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(1)	27						TTGCCATTCAGTTCATAAACA	0.458																																					p.L55V		Atlas-SNP	.											.	SRSF4	44	.	0			c.C163G						PASS	.						191	166	175					1																	29486974		2203	4300	6503	SO:0001583	missense	6429	exon2			CATTCAGTTCATA	BC002781	CCDS333.1	1p35.3	2013-02-12	2010-06-22	2010-06-22	ENSG00000116350	ENSG00000116350		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10786	protein-coding gene	gene with protein product	"SR splicing factor 4"	601940	"splicing factor, arginine/serine-rich 4"	SFRS4		8321209, 20516191	Standard	NM_005626		Approved	SRP75	uc001bro.3	Q08170	OTTHUMG00000003663	ENST00000373795.4:c.163C>G	chr1.hg19:g.29486974G>C	ENSP00000362900:p.Leu55Val	184.0	0.0	.		205.0	33.0	.	NM_005626	Q5VXP1|Q9BUA4|Q9UEB5	Missense_Mutation	SNP	ENST00000373795.4	hg19	CCDS333.1	.	.	.	.	.	.	.	.	.	.	G	14.92	2.678755	0.47886	.	.	ENSG00000116350	ENST00000373795;ENST00000434636;ENST00000546138	T;T	0.80653	1.82;-1.4	5.23	3.34	0.38264	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.070031	0.64402	D	0.000017	D	0.86318	0.5904	M	0.74258	2.255	0.54753	D	0.999987	D;D	0.67145	0.995;0.996	D;D	0.72982	0.947;0.979	D	0.85670	0.1294	10	0.87932	D	0	.	6.2158	0.20653	0.1568:0.0:0.6966:0.1466	.	55;55	F6T1J1;Q08170	.;SRSF4_HUMAN	V	55	ENSP00000362900:L55V;ENSP00000444600:L55V	ENSP00000362900:L55V	L	-	1	2	SRSF4	29359561	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.066000	0.50002	1.203000	0.43233	0.561000	0.74099	CTG	.	.	.	none		0.458	SRSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010392.1	NM_005626		C	29486974	G	C	29486974	3	2	191	1	0	0	0	0	1	0	0	0	14192	1020	36	4	1341	4	SFRS4	1	29486974	Missense_Mutation	SNP	G	TCGA-GL-A9DD-01A-11D-A36X-10	12230576	29486974	219763647	3	11296											
FAM151A	338094	hgsc.bcm.edu	37	chr1	55080373	55080373	+	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	acagagaggcgaacactcacTgtgtggcattgacctcagtt	11	9	11	10	1	2	2	2	1	0	1	2	4	2	2	1	2	1	2	1	2	1	2			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr1:55080373T>C	ENST00000302250.2	-	4	735	c.575A>G	c.(574-576)cAg>cGg	p.Q192R	ACOT11_ENST00000371316.3_Intron|FAM151A_ENST00000371304.2_Splice_Site_p.Q192R	NM_176782.2	NP_788954.2	Q8WW52	F151A_HUMAN	family with sequence similarity 151, member A	192						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						GAACACTCACTGTGTGGCATT	0.542																																					p.Q192R		Atlas-SNP	.											.	FAM151A	58	.	0			c.A575G						PASS	.						129	100	110					1																	55080373		2203	4300	6503	SO:0001630	splice_region_variant	338094	exon4			ACTCACTGTGTGG	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.575+1A>G	chr1.hg19:g.55080373T>C		136.0	0.0	.		127.0	24.0	.	NM_176782	Q5VUG5|Q6DKH5|Q6UWV0|Q8NAX9|Q96KY5	Missense_Mutation	SNP	ENST00000302250.2	hg19	CCDS594.1	.	.	.	.	.	.	.	.	.	.	T	5.034	0.191930	0.09547	.	.	ENSG00000162391	ENST00000302250;ENST00000371304;ENST00000294370	T;T	0.10960	2.82;2.82	3.7	-0.227	0.13102	.	0.539876	0.18021	N	0.154258	T	0.05044	0.0135	N	0.12663	0.25	0.58432	D	0.999999	B	0.15141	0.012	B	0.18561	0.022	T	0.43376	-0.9395	9	.	.	.	-4.4951	8.1077	0.30896	0.0:0.4413:0.0:0.5587	.	192	Q8WW52	F151A_HUMAN	R	192	ENSP00000306888:Q192R;ENSP00000360353:Q192R	.	Q	-	2	0	FAM151A	54852961	0.001000	0.12720	0.846000	0.33378	0.520000	0.34377	-0.605000	0.05661	-0.116000	0.11893	0.379000	0.24179	CAG	.	.	.	none		0.542	FAM151A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027342.1	NM_176782	Missense_Mutation	C	55080373	T	C	55080373	5	2	191	1	0	0	0	0	0	0	1	0	5462	1594	55	3	1202	3	FAM151A	1	55080373	Splice_Site	SNP	T	TCGA-GL-A9DD-01A-11D-A36X-10	25593399	55080373	194170248	4	11297											
SLC44A5	204962	hgsc.bcm.edu	37	chr1	75669452	75669452	+	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	gattttcctcctggaaaatcTtcagcaaaggttgactcaca	12	12	7	10	0	3	1	2	1	1	0	5	3	5	2	2	2	1	2	2	2	3	4			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr1:75669452T>A	ENST00000370859.3	-	24	2259	c.2114A>T	c.(2113-2115)aAg>aTg	p.K705M		NM_001130058.1	NP_001123530.1	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5	705					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(13)|lung(35)|ovary(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61						CTGGAAAATCTTCAGCAAAGG	0.408																																					p.K705M		Atlas-SNP	.											.	SLC44A5	231	.	0			c.A2114T						PASS	.						203	201	202					1																	75669452		692	1591	2283	SO:0001583	missense	204962	exon24			AAAATCTTCAGCA	BC034580	CCDS667.1, CCDS44164.1	1p31.1	2013-05-22			ENSG00000137968	ENSG00000137968		"Solute carriers"	28524	protein-coding gene	gene with protein product						15715662	Standard	NM_152697		Approved	MGC34032, CTL5	uc001dgu.3	Q8NCS7	OTTHUMG00000009721	ENST00000370859.3:c.2114A>T	chr1.hg19:g.75669452T>A	ENSP00000359896:p.Lys705Met	82.0	0.0	.		89.0	15.0	.	NM_001130058	B5MCU3|Q4G0K0|Q8NA44|Q8NB86	Missense_Mutation	SNP	ENST00000370859.3	hg19	CCDS44164.1	.	.	.	.	.	.	.	.	.	.	T	14.64	2.595748	0.46318	.	.	ENSG00000137968	ENST00000370859;ENST00000536707	T	0.12255	2.7	5.53	5.53	0.82687	.	.	.	.	.	T	0.28034	0.0691	M	0.77616	2.38	0.80722	D	1	D;P;D	0.60160	0.987;0.868;0.984	P;P;P	0.62649	0.806;0.729;0.905	T	0.03278	-1.1053	9	0.59425	D	0.04	.	15.9488	0.79817	0.0:0.0:0.0:1.0	.	744;705;744	B7Z470;Q8NCS7-2;F5GYS0	.;.;.	M	705;744	ENSP00000359896:K705M	ENSP00000359896:K705M	K	-	2	0	SLC44A5	75442040	0.843000	0.29541	0.999000	0.59377	0.388000	0.30384	1.986000	0.40677	2.227000	0.72691	0.533000	0.62120	AAG	.	.	.	none		0.408	SLC44A5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026823.3	NM_152697		A	75669452	T	A	75669452	3	1	191	1	0	0	0	0	1	0	0	0	14652	1609	56	5	43	5	SLC44A5	1	75669452	Missense_Mutation	SNP	T	TCGA-GL-A9DD-01A-11D-A36X-10	20589079	75669452	173581169	5	11298											
C1orf59	113802	hgsc.bcm.edu	37	chr1	109192980	109192980	+	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	acaccagtaaactccacagaGtaatcatagcgatttgccac	15	8	6	12	1	1	1	1	0	0	1	2	2	2	1	3	0	3	2	3	0	4	4			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr1:109192980G>A	ENST00000370032.5	-	7	1029	c.609C>T	c.(607-609)taC>taT	p.Y203Y	HENMT1_ENST00000402983.1_Silent_p.Y203Y|HENMT1_ENST00000493676.1_5'UTR|HENMT1_ENST00000370031.1_Silent_p.Y203Y	NM_144584.2	NP_653185.2	Q5T8I9	HENMT_HUMAN	HEN1 methyltransferase homolog 1 (Arabidopsis)	203					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						ACTCCACAGAGTAATCATAGC	0.423																																					p.Y203Y		Atlas-SNP	.											.	HENMT1	38	.	0			c.C609T						PASS	.						91	85	87					1																	109192980		2203	4300	6503	SO:0001819	synonymous_variant	113802	exon7			CACAGAGTAATCA		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.609C>T	chr1.hg19:g.109192980G>A		84.0	0.0	.		85.0	15.0	.	NM_144584	A8MRR6|B1AM16|B1AM17|Q96EJ7|Q96NN0	Silent	SNP	ENST00000370032.5	hg19	CCDS787.1																																																																																			.	.	.	none		0.423	HENMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030592.1	NM_144584		A	109192980	G	A	109192980	2	1	191	1	0	0	0	0	0	0	0	1	2053	1024	36	2		2	C1orf59	1	109192980	Silent	SNP	G	TCGA-GL-A9DD-01A-11D-A36X-10	33523528	109192980	140057641	6	11299											
ASH1L	55870	hgsc.bcm.edu	37	chr1	155449729	155449729	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcggataattgttttcattaAttgtccattgtttctcttgg	7	20	8	6	1	2	0	1	0	1	0	4	1	3	1	1	2	0	2	1	2	2	9			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr1:155449729A>G	ENST00000368346.3	-	3	3571	c.2932T>C	c.(2932-2934)Tta>Cta	p.L978L	ASH1L_ENST00000392403.3_Silent_p.L978L			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	978					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)			GTTTTCATTAATTGTCCATTG	0.323																																					p.L978L		Atlas-SNP	.											.	ASH1L	279	.	0			c.T2932C						PASS	.						62	64	63					1																	155449729		2202	4300	6502	SO:0001819	synonymous_variant	55870	exon3			TCATTAATTGTCC	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.2932T>C	chr1.hg19:g.155449729A>G		55.0	0.0	.		57.0	12.0	.	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Silent	SNP	ENST00000368346.3	hg19																																																																																				.	.	.	none		0.323	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		G	155449729	A	G	155449729	2	3	191	1	0	0	0	0	0	0	0	1	1041	98	4	3		3	ASH1L	1	155449729	Silent	SNP	A	TCGA-GL-A9DD-01A-11D-A36X-10	46256749	155449729	93800892	7	11300											
LMNA	4000	hgsc.bcm.edu	37	chr1	156105104	156105104	+	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	tcagccagctccagaagcagGtgataccccacctcacccct	10	6	7	18	0	2	2	2	1	0	1	3	2	3	2	7	1	4	2	7	1	2	1	rs267607588		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr1:156105104G>A	ENST00000368300.4	+	5	1148		c.e5+1		LMNA_ENST00000448611.2_Splice_Site|LMNA_ENST00000392353.3_Splice_Site|LMNA_ENST00000368297.1_Splice_Site|LMNA_ENST00000368301.2_Splice_Site|LMNA_ENST00000368299.3_Splice_Site|LMNA_ENST00000361308.4_Splice_Site|LMNA_ENST00000496738.1_Splice_Site|LMNA_ENST00000473598.2_Splice_Site|LMNA_ENST00000347559.2_Splice_Site	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C						activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|endoplasmic reticulum unfolded protein response (GO:0030968)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle organ development (GO:0007517)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|positive regulation of cell aging (GO:0090343)|protein localization to nucleus (GO:0034504)|regulation of cell migration (GO:0030334)|regulation of protein localization to nucleus (GO:1900180)|sterol regulatory element binding protein import into nucleus (GO:0035105)|ventricular cardiac muscle cell development (GO:0055015)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|lamin filament (GO:0005638)|nuclear envelope (GO:0005635)|nuclear lamina (GO:0005652)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4)	10	Hepatocellular(266;0.158)					CCAGAAGCAGGTGATACCCCA	0.672									Werner syndrome;Hutchinson-Gilford Progeria Syndrome																												.		Atlas-SNP	.											.	LMNA	31	.	0			c.936+1G>A						PASS	.						22	25	24					1																	156105104		2202	4299	6501	SO:0001630	splice_region_variant	4000	exon5	Familial Cancer Database	WS, Adult Progeria;HGPS, Progeria	AAGCAGGTGATAC	BC014507	CCDS1129.1, CCDS1131.1, CCDS58038.1, CCDS72941.1, CCDS72942.1	1q22	2014-09-17			ENSG00000160789	ENSG00000160789		"Intermediate filaments type V, lamins"	6636	protein-coding gene	gene with protein product		150330	"cardiomyopathy, dilated 1A (autosomal dominant)", "limb girdle muscular dystrophy 1B (autosomal dominant)", "progeria 1 (Hutchinson-Gilford type)", "lamin A/C-like 1"	LMN1, CMD1A, LGMD1B, PRO1, LMNL1		8511676, 8838815, 12702809	Standard	NM_005572		Approved	HGPS	uc001fni.3	P02545	OTTHUMG00000013961	ENST00000368300.4:c.936+1G>A	chr1.hg19:g.156105104G>A		147.0	0.0	.		165.0	34.0	.	NM_170707	B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2	Splice_Site	SNP	ENST00000368300.4	hg19	CCDS1129.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.186744	0.78789	.	.	ENSG00000160789	ENST00000368301;ENST00000347559;ENST00000361308;ENST00000368300;ENST00000368299;ENST00000292302;ENST00000392355;ENST00000448611;ENST00000368297;ENST00000473598;ENST00000392353	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.1117	0.86676	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	LMNA	154371728	1.000000	0.71417	0.999000	0.59377	0.821000	0.46438	9.781000	0.99029	2.653000	0.90120	0.563000	0.77884	.	.	.	.	alt		0.672	LMNA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039200.2	NM_170707	Intron	A	156105104	G	A	156105104	5	1	191	1	0	0	0	0	0	0	1	0	8855	1275	44	2	955	2	LMNA	1	156105104	Splice_Site	SNP	G	TCGA-GL-A9DD-01A-11D-A36X-10	655375	156105104	93145517	8	11301											
IQGAP3	128239	hgsc.bcm.edu	37	chr1	156510499	156510499	+	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	gaggactggtgggccccataCctgcagagtgatccggttct	7	9	14	11	1	1	2	0	1	1	1	2	4	2	3	4	4	2	2	4	4	1	2			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr1:156510499C>A	ENST00000361170.2	-	23	2750		c.e23+1		IQGAP3_ENST00000498755.1_5'Flank	NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3						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)					GGGCCCCATACCTGCAGAGTG	0.512																																					.		Atlas-SNP	.											.	IQGAP3	146	.	0			c.2739+1G>T						PASS	.						149	101	117					1																	156510499		2203	4300	6503	SO:0001630	splice_region_variant	128239	exon24			CCCATACCTGCAG	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.2739+1G>T	chr1.hg19:g.156510499C>A		86.0	0.0	.		64.0	10.0	.	NM_178229	Q5T3H8	Splice_Site	SNP	ENST00000361170.2	hg19	CCDS1144.1	.	.	.	.	.	.	.	.	.	.	C	17.08	3.297384	0.60086	.	.	ENSG00000183856	ENST00000361170	.	.	.	4.71	4.71	0.59529	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1956	0.73084	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	IQGAP3	154777123	1.000000	0.71417	1.000000	0.80357	0.555000	0.35460	7.633000	0.83260	2.435000	0.82474	0.591000	0.81541	.	.	.	.	none		0.512	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229	Intron	A	156510499	C	A	156510499	5	1	191	1	0	0	0	0	0	0	1	0	7823	521	18	4	2219	4	IQGAP3	1	156510499	Splice_Site	SNP	C	TCGA-GL-A9DD-01A-11D-A36X-10	405395	156510499	92740122	9	11302											
RSAD2	91543	hgsc.bcm.edu	37	chr2	7035978	7035978	+	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	tcctggatgttggtgtagaaGaagctataaaattcagtgga	13	12	12	4	0	1	2	1	0	0	2	2	4	2	4	1	3	1	3	1	3	6	5			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr2:7035978G>A	ENST00000382040.3	+	6	1127	c.991G>A	c.(991-993)Gaa>Aaa	p.E331K	RSAD2_ENST00000541728.1_Missense_Mutation_p.E224K	NM_080657.4	NP_542388.2			radical S-adenosyl methionine domain containing 2											endometrium(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(1)	20	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			OV - Ovarian serous cystadenocarcinoma(76;0.191)		TGGTGTAGAAGAAGCTATAAA	0.413																																					p.E331K		Atlas-SNP	.											.	RSAD2	38	.	0			c.G991A						PASS	.						86	83	84					2																	7035978		2203	4300	6503	SO:0001583	missense	91543	exon6			GTAGAAGAAGCTA	AF442151	CCDS1656.1	2p25.2	2008-02-05			ENSG00000134321	ENSG00000134321			30908	protein-coding gene	gene with protein product		607810				11752458	Standard	NM_080657		Approved	cig5, viperin, vig1	uc002qyp.1	Q8WXG1	OTTHUMG00000090352	ENST00000382040.3:c.991G>A	chr2.hg19:g.7035978G>A	ENSP00000371471:p.Glu331Lys	113.0	0.0	.		96.0	19.0	.	NM_080657		Missense_Mutation	SNP	ENST00000382040.3	hg19	CCDS1656.1	.	.	.	.	.	.	.	.	.	.	G	11.75	1.730833	0.30684	.	.	ENSG00000134321	ENST00000382040;ENST00000541728	T	0.29397	1.57	5.57	4.67	0.58626	.	0.234163	0.49916	N	0.000122	T	0.17662	0.0424	N	0.19112	0.55	0.40643	D	0.981964	B	0.06786	0.001	B	0.08055	0.003	T	0.08330	-1.0727	10	0.13108	T	0.6	-20.1755	10.0238	0.42059	0.0715:0.1391:0.7894:0.0	.	331	Q8WXG1	RSAD2_HUMAN	K	331;224	ENSP00000371471:E331K	ENSP00000371471:E331K	E	+	1	0	RSAD2	6953429	0.982000	0.34865	0.642000	0.29436	0.977000	0.68977	1.644000	0.37228	1.459000	0.47892	0.655000	0.94253	GAA	.	.	.	none		0.413	RSAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206724.2	NM_080657		A	7035978	G	A	7035978	3	1	191	1	0	0	0	0	1	0	0	0	13708	943	33	2	1013	2	RSAD2	2	7035978	Missense_Mutation	SNP	G	TCGA-GL-A9DD-01A-11D-A36X-10		7035978	236163395	10	11303											
SFRS7	6432	hgsc.bcm.edu	37	chr2	38977271	38977271	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttaaaggaccataataacTgaaagccctttctaactctc	14	12	4	11	0	3	1	0	1	3	0	4	2	3	2	2	1	3	0	2	1	6	5			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr2:38977271T>C	ENST00000313117.6	-	2	331	c.94A>G	c.(94-96)Agt>Ggt	p.S32G	SRSF7_ENST00000409276.1_Missense_Mutation_p.S32G|SRSF7_ENST00000446327.2_Missense_Mutation_p.S32G|GEMIN6_ENST00000409011.1_5'Flank	NM_001031684.2|NM_001195446.1	NP_001026854.1|NP_001182375.1	Q16629	SRSF7_HUMAN	serine/arginine-rich splicing factor 7	32	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						CCATAATAACTGAAAGCCCTT	0.428																																					p.S32G		Atlas-SNP	.											SRSF7,NS,carcinoma,0,1	SRSF7	29	.	0			c.A94G						PASS	.						117	114	115					2																	38977271		2203	4300	6503	SO:0001583	missense	6432	exon2			AATAACTGAAAGC	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.94A>G	chr2.hg19:g.38977271T>C	ENSP00000325905:p.Ser32Gly	127.0	2.0	.		114.0	15.0	.	NM_001195446	B4DLU6|G5E9M3|Q564D3	Missense_Mutation	SNP	ENST00000313117.6	hg19	CCDS33183.1	.	.	.	.	.	.	.	.	.	.	T	6.752	0.507676	0.12883	.	.	ENSG00000115875	ENST00000313117;ENST00000446327;ENST00000409276	T;T;T	0.17854	2.25;2.25;2.25	6.07	6.07	0.98685	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.10937	0.0267	N	0.05158	-0.105	0.80722	D	1	B;B	0.14438	0.008;0.01	B;B	0.20184	0.017;0.028	T	0.19745	-1.0296	10	0.36615	T	0.2	.	16.6407	0.85098	0.0:0.0:0.0:1.0	.	32;32	G5E9M3;Q16629	.;SRSF7_HUMAN	G	32	ENSP00000325905:S32G;ENSP00000402264:S32G;ENSP00000386806:S32G	ENSP00000325905:S32G	S	-	1	0	SRSF7	38830775	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.754000	0.47532	2.326000	0.78906	0.533000	0.62120	AGT	.	.	.	none		0.428	SRSF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219889.2	NM_001031684		C	38977271	T	C	38977271	3	2	191	1	0	0	0	0	1	0	0	0	14195	1580	55	3	650	3	SFRS7	2	38977271	Missense_Mutation	SNP	T	TCGA-GL-A9DD-01A-11D-A36X-10	31941293	38977271	204222102	11	11304											
SLC8A1	6546	hgsc.bcm.edu	37	chr2	40657412	40657412	+	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	gaaagacttaatcgccgcatGttgtacatgacacttccaac	13	10	7	11	2	0	2	0	1	0	1	2	3	1	2	2	0	2	3	2	0	4	4			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr2:40657412G>A	ENST00000403092.1	-	2	42	c.9C>T	c.(7-9)aaC>aaT	p.N3N	SLC8A1_ENST00000402441.1_Silent_p.N3N|SLC8A1_ENST00000405269.1_Silent_p.N3N|SLC8A1_ENST00000542024.1_Silent_p.N3N|SLC8A1_ENST00000406785.2_Silent_p.N3N|SLC8A1_ENST00000332839.4_Silent_p.N3N|SLC8A1_ENST00000406391.2_Silent_p.N3N|SLC8A1_ENST00000405901.3_Silent_p.N3N|SLC8A1_ENST00000542756.1_Silent_p.N3N|SLC8A1_ENST00000408028.2_Silent_p.N3N			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1	3					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)	ATCGCCGCATGTTGTACATGA	0.418																																					p.N3N		Atlas-SNP	.											.	SLC8A1	221	.	0			c.C9T						PASS	.						60	56	58					2																	40657412		2203	4300	6503	SO:0001819	synonymous_variant	6546	exon1			CCGCATGTTGTAC		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.9C>T	chr2.hg19:g.40657412G>A		66.0	0.0	.		66.0	18.0	.	NM_001252624	A8K6N1|D6W595|O95849|Q4QQG6|Q587I6|Q59GN4|Q9UBL8|Q9UD55|Q9UDN1|Q9UDN2|Q9UKX6	Silent	SNP	ENST00000403092.1	hg19	CCDS1806.1																																																																																			.	.	.	none		0.418	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	NM_021097		A	40657412	G	A	40657412	2	1	191	1	0	0	0	0	0	0	0	1	14719	1368	48	2		2	SLC8A1	2	40657412	Silent	SNP	G	TCGA-GL-A9DD-01A-11D-A36X-10	1680141	40657412	202541961	12	11305											
THNSL2	55258	hgsc.bcm.edu	37	chr2	88474889	88474889	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caggagctccagatgacaacGgtgctgaagcagaacgtaca	14	5	12	10	2	0	4	0	2	0	2	1	5	1	5	1	2	6	4	1	2	4	1			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr2:88474889G>A	ENST00000324166.5	+	3	2231	c.540G>A	c.(538-540)acG>acA	p.T180T	THNSL2_ENST00000402102.1_Silent_p.T180T|THNSL2_ENST00000343544.4_Silent_p.T180T|THNSL2_ENST00000449349.1_Silent_p.T148T|THNSL2_ENST00000358591.2_Silent_p.T180T|THNSL2_ENST00000496844.1_3'UTR|THNSL2_ENST00000377254.3_Silent_p.T180T	NM_018271.4	NP_060741.3	Q86YJ6	THNS2_HUMAN	threonine synthase-like 2 (S. cerevisiae)	180					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						AGATGACAACGGTGCTGAAGC	0.517																																					p.T180T		Atlas-SNP	.											.	THNSL2	66	.	0			c.G540A						PASS	.						154	112	126					2																	88474889		2203	4300	6503	SO:0001819	synonymous_variant	55258	exon3			GACAACGGTGCTG		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.540G>A	chr2.hg19:g.88474889G>A		189.0	0.0	.		187.0	28.0	.	NM_018271	B3KTB1|B5MDX8|B7WPF8|D9ZZB8|Q6P2M7|Q6PI27|Q9NV54	Silent	SNP	ENST00000324166.5	hg19	CCDS2002.2																																																																																			.	.	.	none		0.517	THNSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252662.1	NM_018271		A	88474889	G	A	88474889	2	1	191	1	0	0	0	0	0	0	0	1	15875	1103	39	1		1	THNSL2	2	88474889	Silent	SNP	G	TCGA-GL-A9DD-01A-11D-A36X-10	47817477	88474889	154724484	13	11306											
AFF3	3899	hgsc.bcm.edu	37	chr2	100266104	100266104	+	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	gtacctgtcagagagagcgcGgagagccgttctctgagctg	8	8	15	10	3	2	4	1	1	1	3	3	6	2	4	2	1	4	3	2	1	1	2			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr2:100266104G>C	ENST00000409236.2	-	11	1280	c.1168C>G	c.(1168-1170)Cgc>Ggc	p.R390G	AFF3_ENST00000409579.1_Missense_Mutation_p.R415G|AFF3_ENST00000356421.2_Missense_Mutation_p.R415G|AFF3_ENST00000317233.4_Missense_Mutation_p.R390G			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	390					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)	p.R415C(2)		NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						GAGAGAGCGCGGAGAGCCGTT	0.363																																					p.R415G		Atlas-SNP	.											AFF3,scalp,carcinoma,0,2	AFF3	164	.	2	Substitution - Missense(2)	endometrium(1)|skin(1)	c.C1243G						PASS	.						87	101	96					2																	100266104		2203	4300	6503	SO:0001583	missense	3899	exon12			GAGCGCGGAGAGC	U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"lymphoid nuclear protein related to AF4"	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.1168C>G	chr2.hg19:g.100266104G>C	ENSP00000387207:p.Arg390Gly	372.0	0.0	.		359.0	85.0	.	NM_001025108	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Missense_Mutation	SNP	ENST00000409236.2	hg19	CCDS42723.1	.	.	.	.	.	.	.	.	.	.	G	14.60	2.585306	0.46110	.	.	ENSG00000144218	ENST00000317233;ENST00000356421;ENST00000409579;ENST00000409236;ENST00000433370;ENST00000444786;ENST00000432288	T;T;T;T	0.70516	-0.49;-0.49;-0.49;-0.49	6.08	6.08	0.98989	.	0.160493	0.29594	N	0.011704	T	0.70219	0.3199	L	0.36672	1.1	0.40959	D	0.984609	P;P;P	0.44946	0.846;0.549;0.493	P;B;B	0.48304	0.573;0.282;0.119	T	0.65948	-0.6044	10	0.27785	T	0.31	.	18.844	0.92196	0.0:0.0:1.0:0.0	.	543;390;415	B7Z4I6;P51826;P51826-2	.;AFF3_HUMAN;.	G	390;415;415;390;390;543;415	ENSP00000317421:R390G;ENSP00000348793:R415G;ENSP00000386834:R415G;ENSP00000387207:R390G	ENSP00000317421:R390G	R	-	1	0	AFF3	99632536	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	4.444000	0.60001	2.894000	0.99253	0.655000	0.94253	CGC	.	.	.	none		0.363	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285		C	100266104	G	C	100266104	3	2	191	1	0	0	0	0	1	0	0	0	358	1116	39	4	2564	4	AFF3	2	100266104	Missense_Mutation	SNP	G	TCGA-GL-A9DD-01A-11D-A36X-10	11791215	100266104	142933269	14	11307											
CCDC115	84317	hgsc.bcm.edu	37	chr2	131096793	131096793	+	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	ggaggctggctatgtctgcgGccagctgcaggcctggagga	6	7	18	10	1	1	0	0	0	1	0	1	3	1	3	2	7	3	4	2	7	1	1			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr2:131096793G>T	ENST00000259229.2	-	5	666	c.443C>A	c.(442-444)gCc>gAc	p.A148D	CCDC115_ENST00000437688.2_3'UTR|CCDC115_ENST00000409127.1_Missense_Mutation_p.A143D	NM_032357.2	NP_115733.2	Q96NT0	CC115_HUMAN	coiled-coil domain containing 115	148						endosome (GO:0005768)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(1)	7	Colorectal(110;0.1)					TATGTCTGCGGCCAGCTGCAG	0.577																																					p.A148D		Atlas-SNP	.											.	CCDC115	19	.	0			c.C443A						PASS	.						44	42	43					2																	131096793		2203	4300	6503	SO:0001583	missense	84317	exon5			TCTGCGGCCAGCT	AK054693	CCDS2159.1	2q21.1	2010-12-24			ENSG00000136710	ENSG00000136710			28178	protein-coding gene	gene with protein product		613734				21118521	Standard	XM_005263825		Approved	MGC12981, FLJ30131, ccp1	uc002tqy.1	Q96NT0	OTTHUMG00000131631	ENST00000259229.2:c.443C>A	chr2.hg19:g.131096793G>T	ENSP00000259229:p.Ala148Asp	49.0	0.0	.		42.0	5.0	.	NM_032357	B4DJ47|Q9BR88	Missense_Mutation	SNP	ENST00000259229.2	hg19	CCDS2159.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.937236	0.73557	.	.	ENSG00000136710	ENST00000259229;ENST00000409127	D;D	0.96802	-4.13;-4.13	4.0	4.0	0.46444	.	0.067301	0.64402	D	0.000010	D	0.97595	0.9212	M	0.79475	2.455	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.97354	0.9965	10	0.66056	D	0.02	.	11.8974	0.52663	0.0:0.0:1.0:0.0	.	148;143	Q96NT0;B8ZZ99	CC115_HUMAN;.	D	148;143	ENSP00000259229:A148D;ENSP00000387301:A143D	ENSP00000259229:A148D	A	-	2	0	CCDC115	130813263	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	3.833000	0.55790	2.520000	0.84964	0.591000	0.81541	GCC	.	.	.	none		0.577	CCDC115-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254524.2	NM_032357		T	131096793	G	T	131096793	3	4	191	1	0	0	0	0	1	0	0	0	2754	1203	42	4	103	4	CCDC115	2	131096793	Missense_Mutation	SNP	G	TCGA-GL-A9DD-01A-11D-A36X-10	30830689	131096793	112102580	15	11308											
LRP1B	53353	hgsc.bcm.edu	37	chr2	141641491	141641491	+	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	ccacttcgatttggtccagaTtgctgtctatccagtatatg	8	15	8	10	1	1	1	0	0	1	1	4	2	3	1	3	1	1	2	3	1	3	6			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr2:141641491T>A	ENST00000389484.3	-	25	5035	c.4064A>T	c.(4063-4065)aAt>aTt	p.N1355I		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1355					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)		TTGGTCCAGATTGCTGTCTAT	0.512										TSP Lung(27;0.18)																											p.N1355I	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.A4064T						PASS	.						184	175	178					2																	141641491		2203	4300	6503	SO:0001583	missense	53353	exon25			TCCAGATTGCTGT	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.4064A>T	chr2.hg19:g.141641491T>A	ENSP00000374135:p.Asn1355Ile	81.0	0.0	.		115.0	17.0	.	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	27.8	4.859686	0.91433	.	.	ENSG00000168702	ENST00000389484;ENST00000544579;ENST00000434794	D;D	0.84298	-1.83;-1.83	5.64	5.64	0.86602	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.89522	0.6739	L	0.45051	1.395	0.80722	D	1	D;D	0.89917	0.989;1.0	D;D	0.91635	0.965;0.999	D	0.89616	0.3845	10	0.49607	T	0.09	.	16.1404	0.81517	0.0:0.0:0.0:1.0	.	538;1355	Q96NT6;Q9NZR2	.;LRP1B_HUMAN	I	1355;1293;500	ENSP00000374135:N1355I;ENSP00000413239:N500I	ENSP00000374135:N1355I	N	-	2	0	LRP1B	141357961	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.926000	0.87569	2.261000	0.74972	0.533000	0.62120	AAT	.	.	.	none		0.512	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141641491	T	A	141641491	3	1	191	1	0	0	0	0	1	0	0	0	8962	1493	52	5	10003	5	LRP1B	2	141641491	Missense_Mutation	SNP	T	TCGA-GL-A9DD-01A-11D-A36X-10	10544698	141641491	101557882	16	11309											
COL5A2	1290	hgsc.bcm.edu	37	chr2	189916160	189916160	+	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	tccccacgaagacctggaggTccctccttcccgggttcccc	5	8	9	19	2	0	1	0	0	0	1	5	3	5	2	8	3	0	1	8	3	1	2			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr2:189916160T>A	ENST00000374866.3	-	42	3091	c.2817A>T	c.(2815-2817)ggA>ggT	p.G939G		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	939					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)			GACCTGGAGGTCCCTCCTTCC	0.612																																					p.G939G		Atlas-SNP	.											.	COL5A2	230	.	0			c.A2817T						PASS	.						48	50	49					2																	189916160		2203	4300	6503	SO:0001819	synonymous_variant	1290	exon42			TGGAGGTCCCTCC	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.2817A>T	chr2.hg19:g.189916160T>A		90.0	0.0	.		120.0	26.0	.	NM_000393	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Silent	SNP	ENST00000374866.3	hg19	CCDS33350.1																																																																																			.	.	.	none		0.612	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393		A	189916160	T	A	189916160	2	1	191	1	0	0	0	0	0	0	0	1	3699	1654	58	5		5	COL5A2	2	189916160	Silent	SNP	T	TCGA-GL-A9DD-01A-11D-A36X-10	48274669	189916160	53283213	17	11310											
DNAH7	56171	hgsc.bcm.edu	37	chr2	196915964	196915964	+	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	cttgaacttttctttgctggCtaatttctcctgtgtgaaaa	8	18	7	8	0	2	2	0	2	2	0	3	2	2	2	1	1	2	2	1	1	4	6			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr2:196915964C>T	ENST00000312428.6	-	3	188	c.88G>A	c.(88-90)Gcc>Acc	p.A30T	DNAH7_ENST00000410072.1_Missense_Mutation_p.A30T	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	30	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						TCTTTGCTGGCTAATTTCTCC	0.328																																					p.A30T		Atlas-SNP	.											.	DNAH7	512	.	0			c.G88A						PASS	.						167	163	164					2																	196915964		1817	4070	5887	SO:0001583	missense	56171	exon3			TGCTGGCTAATTT	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.88G>A	chr2.hg19:g.196915964C>T	ENSP00000311273:p.Ala30Thr	87.0	0.0	.		76.0	18.0	.	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	hg19	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	C	2.570	-0.299741	0.05532	.	.	ENSG00000118997	ENST00000312428;ENST00000410072;ENST00000312446;ENST00000427816	T;T	0.21734	1.99;2.89	4.13	-2.63	0.06133	.	1.029540	0.07754	N	0.949060	T	0.07954	0.0199	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39623	-0.9605	10	0.09843	T	0.71	.	5.1125	0.14817	0.5731:0.2462:0.0:0.1807	.	30	Q8WXX0	DYH7_HUMAN	T	30;30;30;5	ENSP00000311273:A30T;ENSP00000386260:A30T	ENSP00000311273:A30T	A	-	1	0	DNAH7	196624209	0.000000	0.05858	0.002000	0.10522	0.009000	0.06853	-3.248000	0.00541	-0.544000	0.06232	-0.314000	0.08810	GCC	.	.	.	none		0.328	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		T	196915964	C	T	196915964	3	4	191	1	0	0	0	0	1	0	0	0	4608	797	28	2	12238	2	DNAH7	2	196915964	Missense_Mutation	SNP	C	TCGA-GL-A9DD-01A-11D-A36X-10	6999804	196915964	46283409	18	11311											
PARD3B	117583	hgsc.bcm.edu	37	chr2	206110541	206110541	+	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	tcactcattggctggacaaaAatcgggtaagaaattccttg	13	11	9	8	1	2	1	2	0	0	1	4	2	3	2	1	3	0	2	1	3	4	4			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr2:206110541A>T	ENST00000406610.2	+	16	2387	c.2180A>T	c.(2179-2181)aAa>aTa	p.K727I	PARD3B_ENST00000351153.1_Missense_Mutation_p.K727I|PARD3B_ENST00000462231.1_Missense_Mutation_p.K727I|PARD3B_ENST00000358768.2_Missense_Mutation_p.K665I|PARD3B_ENST00000349953.3_Missense_Mutation_p.K727I	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	727					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)		GCTGGACAAAAATCGGGTAAG	0.403																																					p.K727I		Atlas-SNP	.											.	PARD3B	314	.	0			c.A2180T						PASS	.						155	147	149					2																	206110541		1830	4086	5916	SO:0001583	missense	117583	exon16			GACAAAAATCGGG	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.2180A>T	chr2.hg19:g.206110541A>T	ENSP00000385848:p.Lys727Ile	164.0	0.0	.		173.0	41.0	.	NM_205863	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	Missense_Mutation	SNP	ENST00000406610.2	hg19		.	.	.	.	.	.	.	.	.	.	A	16.30	3.083825	0.55861	.	.	ENSG00000116117	ENST00000406610;ENST00000358768;ENST00000351153;ENST00000349953	T;T;T;T	0.30981	1.63;1.63;1.51;1.63	5.85	1.19	0.21007	.	0.449872	0.21999	N	0.066026	T	0.29588	0.0738	L	0.29908	0.895	0.23376	N	0.99781	P;P;P;P;P	0.47604	0.898;0.836;0.604;0.579;0.828	P;B;P;B;P	0.51355	0.667;0.368;0.52;0.43;0.555	T	0.09840	-1.0656	10	0.72032	D	0.01	.	9.4325	0.38620	0.5621:0.0:0.4379:0.0	.	727;727;727;665;727	Q8TEW8-3;Q8TEW8;E9PE87;Q8TEW8-2;Q8TEW8-5	.;PAR3L_HUMAN;.;.;.	I	727;665;727;727	ENSP00000385848:K727I;ENSP00000351618:K665I;ENSP00000317261:K727I;ENSP00000340280:K727I	ENSP00000340280:K727I	K	+	2	0	PARD3B	205818786	0.977000	0.34250	0.991000	0.47740	0.724000	0.41520	0.829000	0.27449	0.532000	0.28657	0.533000	0.62120	AAA	.	.	.	none		0.403	PARD3B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000335992.1	NM_057177		T	206110541	A	T	206110541	3	4	191	1	0	0	0	0	1	0	0	0	11451	14	1	5	2242	5	PARD3B	2	206110541	Missense_Mutation	SNP	A	TCGA-GL-A9DD-01A-11D-A36X-10	9194577	206110541	37088832	19	11312											
ACADL	33	hgsc.bcm.edu	37	chr2	211057576	211057576	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccaacctccatggagctgtAcacagtcgtaagctacacta	12	8	7	14	1	0	0	0	0	0	0	2	1	1	1	3	1	5	4	3	1	5	4			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr2:211057576A>G	ENST00000233710.3	-	10	1378	c.1151T>C	c.(1150-1152)gTa>gCa	p.V384A	AC006994.2_ENST00000412065.1_RNA	NM_001608.3	NP_001599.1	P28330	ACADL_HUMAN	acyl-CoA dehydrogenase, long chain	384					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)		ATGGAGCTGTACACAGTCGTA	0.373																																					p.V384A		Atlas-SNP	.											.	ACADL	38	.	0			c.T1151C						PASS	.						96	87	90					2																	211057576		2203	4300	6503	SO:0001583	missense	33	exon10			AGCTGTACACAGT	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.1151T>C	chr2.hg19:g.211057576A>G	ENSP00000233710:p.Val384Ala	87.0	0.0	.		92.0	15.0	.	NM_001608	B2R8T3|Q8IUN8	Missense_Mutation	SNP	ENST00000233710.3	hg19	CCDS2389.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.048038	0.75846	.	.	ENSG00000115361	ENST00000233710	D	0.96522	-4.04	6.03	6.03	0.97812	Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);	0.189851	0.46442	D	0.000297	D	0.96457	0.8844	M	0.83774	2.66	0.52099	D	0.999949	B	0.20368	0.044	B	0.28305	0.088	D	0.94543	0.7747	10	0.87932	D	0	.	16.2316	0.82347	1.0:0.0:0.0:0.0	.	384	P28330	ACADL_HUMAN	A	384	ENSP00000233710:V384A	ENSP00000233710:V384A	V	-	2	0	ACADL	210765821	1.000000	0.71417	0.627000	0.29227	0.960000	0.62799	6.551000	0.73909	2.308000	0.77769	0.533000	0.62120	GTA	.	.	.	none		0.373	ACADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256561.2	NM_001608		G	211057576	A	G	211057576	3	3	191	1	0	0	0	0	1	0	0	0	112	391	14	3	149	3	ACADL	2	211057576	Missense_Mutation	SNP	A	TCGA-GL-A9DD-01A-11D-A36X-10	4947035	211057576	32141797	20	11313											
ARMC9	80210	hgsc.bcm.edu	37	chr2	232081381	232081381	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agctggatgaaaagatttccTacttcaaaacctacctggag	14	10	8	9	0	1	2	1	1	0	1	2	4	2	4	3	2	4	1	3	2	6	4			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr2:232081381T>C	ENST00000349938.4	+	5	573	c.379T>C	c.(379-381)Tac>Cac	p.Y127H	ARMC9_ENST00000483477.1_3'UTR	NM_001271466.1|NM_025139.4	NP_001258395.1|NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9	127						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)		AAAGATTTCCTACTTCAAAAC	0.483																																					p.Y127H		Atlas-SNP	.											.	ARMC9	129	.	0			c.T379C						PASS	.						185	169	174					2																	232081381		2203	4300	6503	SO:0001583	missense	80210	exon5			ATTTCCTACTTCA	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.379T>C	chr2.hg19:g.232081381T>C	ENSP00000258417:p.Tyr127His	118.0	0.0	.		143.0	33.0	.	NM_025139	Q53TI3|Q6P162|Q7L594|Q86WG2|Q96JF9|Q9H9R8	Missense_Mutation	SNP	ENST00000349938.4	hg19	CCDS2484.1	.	.	.	.	.	.	.	.	.	.	T	7.414	0.635408	0.14322	.	.	ENSG00000135931	ENST00000349938;ENST00000359743;ENST00000440107	T;T	0.18174	2.23;2.23	5.5	4.31	0.51392	.	0.480617	0.21657	N	0.071085	T	0.08268	0.0206	N	0.11560	0.145	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.37103	-0.9720	10	0.15952	T	0.53	-6.7602	8.7057	0.34354	0.0:0.2153:0.0:0.7847	.	127	Q7Z3E5	ARMC9_HUMAN	H	127	ENSP00000258417:Y127H;ENSP00000387391:Y127H	ENSP00000258417:Y127H	Y	+	1	0	ARMC9	231789625	0.006000	0.16342	0.432000	0.26747	0.931000	0.56810	1.657000	0.37366	0.880000	0.35969	0.533000	0.62120	TAC	.	.	.	none		0.483	ARMC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256966.3	NM_025139		C	232081381	T	C	232081381	3	2	191	1	0	0	0	0	1	0	0	0	958	1522	53	3	393	3	ARMC9	2	232081381	Missense_Mutation	SNP	T	TCGA-GL-A9DD-01A-11D-A36X-10	21023805	232081381	11117992	21	11314											
ZNF619	285267	hgsc.bcm.edu	37	chr3	40523745	40523745	+	Intron	SNP	T	T	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	aactgcagggggctttcctcTggatacagagagaactgaga	12	8	13	8	0	1	3	0	1	1	3	2	6	2	4	1	3	4	2	1	3	3	2			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr3:40523745T>A	ENST00000314686.5	+	3	485				ZNF619_ENST00000447116.2_Missense_Mutation_p.L68Q|ZNF619_ENST00000521353.1_Missense_Mutation_p.L68Q|ZNF619_ENST00000520737.1_Intron|ZNF619_ENST00000432264.2_Intron|ZNF619_ENST00000522736.1_Intron|ZNF619_ENST00000456778.1_Intron|ZNF619_ENST00000429348.2_Intron			Q8N2I2	ZN619_HUMAN	zinc finger protein 619						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		GGCTTTCCTCTGGATACAGAG	0.502																																					p.L68Q		Atlas-SNP	.											.	ZNF619	57	.	0			c.T203A						PASS	.						72	70	71					3																	40523745		692	1591	2283	SO:0001627	intron_variant	285267	exon4			TTCCTCTGGATAC	AK075245	CCDS46801.1, CCDS46802.1, CCDS46803.1	3p21.33	2013-01-08			ENSG00000177873	ENSG00000177873		"Zinc fingers, C2H2-type", "-"	26910	protein-coding gene	gene with protein product							Standard	NM_001145083		Approved	FLJ90764	uc011azb.2	Q8N2I2	OTTHUMG00000131391	ENST00000314686.5:c.80+238T>A	chr3.hg19:g.40523745T>A		48.0	0.0	.		83.0	24.0	.	NM_001145082	B4E271|C9JRN5|D4PHA2|E9PCD9	Missense_Mutation	SNP	ENST00000314686.5	hg19		.	.	.	.	.	.	.	.	.	.	T	12.37	1.917530	0.33815	.	.	ENSG00000177873	ENST00000447116;ENST00000521353	T;T	0.07114	3.22;3.22	3.52	3.52	0.40303	.	.	.	.	.	T	0.11196	0.0273	N	0.08118	0	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.32375	-0.9909	9	0.39692	T	0.17	.	10.3183	0.43751	0.0:0.0:0.0:1.0	.	68	E9PCD9	.	Q	68	ENSP00000411132:L68Q;ENSP00000430705:L68Q	ENSP00000411132:L68Q	L	+	2	0	ZNF619	40498749	0.000000	0.05858	0.065000	0.19835	0.018000	0.09664	-0.630000	0.05502	1.366000	0.46076	0.460000	0.39030	CTG	.	.	.	none		0.502	ZNF619-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000254180.2	NM_173656		A	40523745	T	A	40523745	1	1	191	0	1	0	0	0	0	0	0	0	18055	1580	55	5		5	ZNF619	3	40523745	Intron	SNP	T	TCGA-GL-A9DD-01A-11D-A36X-10		40523745	157498685	22	11315											
ROBO1	6091	hgsc.bcm.edu	37	chr3	78710202	78710202	+	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	tcttccagggttttggcaaaCttgatttcactatctgctcc	7	16	7	11	0	3	1	1	1	2	0	5	1	5	1	2	2	2	3	2	2	2	6	rs536774102		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr3:78710202C>T	ENST00000464233.1	-	16	2411	c.2298G>A	c.(2296-2298)aaG>aaA	p.K766K	ROBO1_ENST00000467549.1_Silent_p.K730K|ROBO1_ENST00000436010.2_Silent_p.K727K|ROBO1_ENST00000495273.1_Silent_p.K730K	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	766	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		TTTTGGCAAACTTGATTTCAC	0.343																																					p.K766K		Atlas-SNP	.											.	ROBO1	833	.	0			c.G2298A						PASS	.						95	89	91					3																	78710202		1834	4091	5925	SO:0001819	synonymous_variant	6091	exon16			GGCAAACTTGATT	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.2298G>A	chr3.hg19:g.78710202C>T		99.0	0.0	.		112.0	30.0	.	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Silent	SNP	ENST00000464233.1	hg19	CCDS54611.1																																																																																			.	.	.	none		0.343	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		T	78710202	C	T	78710202	2	4	191	1	0	0	0	0	0	0	0	1	13526	564	20	2		2	ROBO1	3	78710202	Silent	SNP	C	TCGA-GL-A9DD-01A-11D-A36X-10	38186457	78710202	119312228	23	11316											
C3orf22	152065	hgsc.bcm.edu	37	chr3	126270916	126270916	+	Frame_Shift_Del	DEL	C	C	-																															cgtgttcgagtcgtttgtgaCctcccagggctgcaggggct																										TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr3:126270916delC	ENST00000318225.2	-	3	517	c.139delG	c.(139-141)gtcfs	p.V47fs		NM_152533.1	NP_689746.1	Q8N5N4	CC022_HUMAN	chromosome 3 open reading frame 22	47										large_intestine(1)|lung(3)|ovary(2)|prostate(1)	7				GBM - Glioblastoma multiforme(114;0.147)		TCGTTTGTGACCTCCCAGGGC	0.617																																					p.V47fs		Atlas-Indel,Pindel	.											.	C3orf22	17	.	0			c.140delT						PASS	.						94	83	87					3																	126270916		2203	4300	6503	SO:0001589	frameshift_variant	152065	exon3			.		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.139delG	chr3.hg19:g.126270916delC	ENSP00000316644:p.Val47fs	45.0	0.0	0		61.0	18.0	0.295082	NM_152533	B3KUS9	Frame_Shift_Del	DEL	ENST00000318225.2	hg19	CCDS3040.1																																																																																			.	.	.	none		0.617	C3orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370231.2	NM_152533		-	126270916	C	-	126270916	7	5	191	1	0	1	0	1	0	0	0	0	2217	507	18	0	294	0	C3orf22	3	126270916	Frame_Shift_Del	DEL	C	TCGA-GL-A9DD-01A-11D-A36X-10	47560714	126270916	71751514	24	11317											
NMD3	51068	hgsc.bcm.edu	37	chr3	160967299	160967299	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcgtcgtagaaactggaaaTtgaaagagcttgcaagagag	16	7	13	5	2	0	4	0	1	0	3	1	6	0	5	0	1	4	3	0	1	5	3			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr3:160967299T>C	ENST00000460469.1	+	13	1716	c.1261T>C	c.(1261-1263)Ttg>Ctg	p.L421L	NMD3_ENST00000472947.1_Silent_p.L421L|NMD3_ENST00000351193.2_Silent_p.L421L			Q96D46	NMD3_HUMAN	NMD3 ribosome export adaptor	421					protein transport (GO:0015031)|ribosomal large subunit export from nucleus (GO:0000055)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|ribosomal large subunit binding (GO:0043023)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(10)|ovary(1)|skin(1)|urinary_tract(2)	25			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)			AAACTGGAAATTGAAAGAGCT	0.353																																					p.L421L		Atlas-SNP	.											.	NMD3	49	.	0			c.T1261C						PASS	.						76	75	75					3																	160967299		2203	4300	6503	SO:0001819	synonymous_variant	51068	exon14			TGGAAATTGAAAG	BC013317	CCDS3194.1	3q26.1	2013-08-06	2013-08-06		ENSG00000169251	ENSG00000169251			24250	protein-coding gene	gene with protein product		611021	"NMD3 homolog (S. cerevisiae)"			10810093, 23782956, 12773398	Standard	NM_015938		Approved	CGI-07	uc003feb.1	Q96D46	OTTHUMG00000159063	ENST00000460469.1:c.1261T>C	chr3.hg19:g.160967299T>C		304.0	0.0	.		337.0	57.0	.	NM_015938	D3DNM7|Q9Y2Z6	Silent	SNP	ENST00000460469.1	hg19	CCDS3194.1																																																																																			.	.	.	none		0.353	NMD3-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353114.1	NM_015938		C	160967299	T	C	160967299	2	2	191	1	0	0	0	0	0	0	0	1	10495	1490	52	3		3	NMD3	3	160967299	Silent	SNP	T	TCGA-GL-A9DD-01A-11D-A36X-10	34696383	160967299	37055131	25	11318											
HTR3D	200909	hgsc.bcm.edu	37	chr3	183756708	183756709	+	Frame_Shift_Ins	INS	-	-	T																															gccctgctcttccgcctctaINScctgctcttcatggcctcct																										TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr3:183756708_183756709insT	ENST00000382489.3	+	8	1310_1311	c.1310_1311insT	c.(1309-1314)tacctgfs	p.L438fs	HTR3D_ENST00000428798.2_Frame_Shift_Ins_p.L388fs|HTR3D_ENST00000453435.1_Frame_Shift_Ins_p.L217fs|HTR3D_ENST00000334128.2_Frame_Shift_Ins_p.L263fs	NM_001163646.1	NP_001157118.1	Q70Z44	5HT3D_HUMAN	5-hydroxytryptamine (serotonin) receptor 3D, ionotropic	438					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)			large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)	10	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;6.23e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Ergoloid mesylate(DB01049)	TTCCGCCTCTACCTGCTCTTCA	0.589																																					p.Y437fs		Atlas-Indel,Pindel	.											.	HTR3D	65	.	0			c.1310_1311insT						PASS	.																																			SO:0001589	frameshift_variant	200909	exon8			.	AY159812	CCDS3249.1, CCDS46966.1, CCDS54685.1	3q27	2012-05-22	2012-02-03		ENSG00000186090	ENSG00000186090		"5-HT (serotonin) receptors", "Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"	24004	protein-coding gene	gene with protein product		610122	"5-hydroxytryptamine (serotonin) receptor 3 family member D"			12801637	Standard	NM_001145143		Approved		uc011bqv.2	Q70Z44	OTTHUMG00000156858	Exception_encountered	chr3.hg19:g.183756708_183756709insT	ENSP00000371929:p.Leu438fs	139.0	0.0	0		140.0	33.0	0.235714	NM_001163646	C9J2I6|J3QT78|Q495N5|Q495N6|Q7Z6B3	Frame_Shift_Ins	INS	ENST00000382489.3	hg19	CCDS54685.1																																																																																			.	.	.	none		0.589	HTR3D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346289.1	NM_182537		T	183756709	-	T	183756708	7	5	191	1	0	1	1	0	0	0	0	0	7454	391	14	0	1510	0	HTR3D	3	183756708	Frame_Shift_Ins	INS	-	TCGA-GL-A9DD-01A-11D-A36X-10	22789409	183756708	14265722	26	11319											
ALG3	10195	hgsc.bcm.edu	37	chr3	183963295	183963295	+	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	atcaagaagacaagcagcaaGgtagccaggtagagcacagc	17	3	12	9	0	1	3	1	0	0	3	1	3	1	3	1	2	5	5	1	2	6	2			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr3:183963295G>C	ENST00000397676.3	-	3	435	c.405C>G	c.(403-405)acC>acG	p.T135T	ALG3_ENST00000455059.1_Silent_p.T95T|ALG3_ENST00000463495.1_5'Flank|ALG3_ENST00000445626.2_Silent_p.T87T|EIF2B5_ENST00000444495.1_Intron|ALG3_ENST00000418734.2_Silent_p.T79T	NM_005787.5	NP_005778.1	Q92685	ALG3_HUMAN	ALG3, alpha-1,3- mannosyltransferase	135					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)			CAAGCAGCAAGGTAGCCAGGT	0.567																																					p.T135T		Atlas-SNP	.											.	ALG3	48	.	0			c.C405G						PASS	.						62	64	64					3																	183963295		2121	4233	6354	SO:0001819	synonymous_variant	10195	exon3			CAGCAAGGTAGCC	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.405C>G	chr3.hg19:g.183963295G>C		146.0	0.0	.		159.0	45.0	.	NM_005787	A8JZZ6|Q9BT71	Silent	SNP	ENST00000397676.3	hg19	CCDS46968.1																																																																																			.	.	.	none		0.567	ALG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346033.1	NM_005787		C	183963295	G	C	183963295	2	2	191	1	0	0	0	0	0	0	0	1	520	987	35	4		4	ALG3	3	183963295	Silent	SNP	G	TCGA-GL-A9DD-01A-11D-A36X-10	206587	183963295	14059135	27	11320											
SENP5	205564	hgsc.bcm.edu	37	chr3	196613001	196613001	+	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	tggacagcagtgctgtggtgAaggggacgaactctcatgtg	9	9	16	7	1	1	1	1	1	1	0	2	4	1	3	0	4	3	2	0	4	2	0			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr3:196613001A>T	ENST00000323460.5	+	2	1198	c.949A>T	c.(949-951)Aag>Tag	p.K317*	SENP5_ENST00000419026.1_Intron|SENP5_ENST00000445299.2_Nonsense_Mutation_p.K317*	NM_152699.4	NP_689912.2	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	317					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)		TGCTGTGGTGAAGGGGACGAA	0.512																																					p.K317X	Ovarian(47;891 1095 11174 13858 51271)	Atlas-SNP	.											.	SENP5	68	.	0			c.A949T						PASS	.						107	94	98					3																	196613001		2203	4300	6503	SO:0001587	stop_gained	205564	exon2			GTGGTGAAGGGGA	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.949A>T	chr3.hg19:g.196613001A>T	ENSP00000327197:p.Lys317*	53.0	0.0	.		75.0	28.0	.	NM_152699	B4DY82|Q96SA5	Nonsense_Mutation	SNP	ENST00000323460.5	hg19	CCDS3322.1	.	.	.	.	.	.	.	.	.	.	A	38	6.956467	0.97964	.	.	ENSG00000119231	ENST00000323460;ENST00000445299	.	.	.	5.37	4.22	0.49857	.	0.349524	0.27429	N	0.019408	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.1768	9.6073	0.39641	0.9168:0.0:0.0832:0.0	.	.	.	.	X	317	.	ENSP00000327197:K317X	K	+	1	0	SENP5	198097398	0.999000	0.42202	0.999000	0.59377	0.954000	0.61252	3.305000	0.51873	0.992000	0.38840	0.533000	0.62120	AAG	.	.	.	none		0.512	SENP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340524.1	NM_152699		T	196613001	A	T	196613001	4	4	191	1	0	0	0	0	0	1	0	0	14062	247	9	5	951	5	SENP5	3	196613001	Nonsense_Mutation	SNP	A	TCGA-GL-A9DD-01A-11D-A36X-10	12649706	196613001	1409429	28	11321											
SPON2	10417	hgsc.bcm.edu	37	chr4	1165650	1165650	+	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	ctgtacttacccagcagcgaAgaccactgcgcaggggggcg	9	5	14	13	3	0	1	0	0	0	1	0	2	0	1	2	3	5	3	2	3	3	2			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr4:1165650A>T	ENST00000290902.5	-	2	542	c.210T>A	c.(208-210)tcT>tcA	p.S70S	SPON2_ENST00000431380.1_Silent_p.S70S	NM_012445.3	NP_036577	Q9BUD6	SPON2_HUMAN	spondin 2, extracellular matrix protein	70	Spondin. {ECO:0000255|PROSITE- ProRule:PRU00364}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|pancreas(1)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(23;0.00805)	UCEC - Uterine corpus endometrioid carcinoma (64;0.139)|Colorectal(103;0.19)		CCAGCAGCGAAGACCACTGCG	0.687																																					p.S70S		Atlas-SNP	.											.	SPON2	22	.	0			c.T210A						PASS	.						47	65	59					4																	1165650		2192	4292	6484	SO:0001819	synonymous_variant	10417	exon2			CAGCGAAGACCAC	AB027466	CCDS3347.1	4p16.3	2008-07-29			ENSG00000159674	ENSG00000159674			11253	protein-coding gene	gene with protein product	"Mindin", "M-spondin"	605918				10512675, 15094111	Standard	NM_012445		Approved	DIL1	uc003gco.4	Q9BUD6	OTTHUMG00000089002	ENST00000290902.5:c.210T>A	chr4.hg19:g.1165650A>T		120.0	0.0	.		76.0	18.0	.	NM_012445	D3DVN9|Q4W5N4|Q9ULW1	Silent	SNP	ENST00000290902.5	hg19	CCDS3347.1																																																																																			.	.	.	none		0.687	SPON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202080.2			T	1165650	A	T	1165650	2	4	191	1	0	0	0	0	0	0	0	1	15095	59	3	5		5	SPON2	4	1165650	Silent	SNP	A	TCGA-GL-A9DD-01A-11D-A36X-10		1165650	189988626	29	11322											
MAN2B2	23324	hgsc.bcm.edu	37	chr4	6576972	6576972	+	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	ctggctgccgctgctggcacCgctcctgttgctgcgaccgc	2	9	13	17	4	0	0	0	0	0	0	1	1	1	0	4	2	4	7	4	2	0	1			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr4:6576972C>A	ENST00000285599.3	+	1	71	c.35C>A	c.(34-36)cCg>cAg	p.P12Q	MAN2B2_ENST00000504248.1_Missense_Mutation_p.P12Q	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	12					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						CTGCTGGCACCGCTCCTGTTG	0.746																																					p.P12Q		Atlas-SNP	.											.	MAN2B2	80	.	0			c.C35A						PASS	.						4	5	5					4																	6576972		1999	3945	5944	SO:0001583	missense	23324	exon1			TGGCACCGCTCCT	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.35C>A	chr4.hg19:g.6576972C>A	ENSP00000285599:p.Pro12Gln	63.0	0.0	.		76.0	18.0	.	NM_015274	Q66MP2|Q86T67	Missense_Mutation	SNP	ENST00000285599.3	hg19	CCDS33951.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	1.365|1.365	-0.587738|-0.587738	0.03799|0.03799	.|.	.|.	ENSG00000013288|ENSG00000013288	ENST00000285599;ENST00000504248|ENST00000505907	T;D|.	0.83673|.	-1.31;-1.75|.	2.46|2.46	-4.92|-4.92	0.03075|0.03075	.|.	2.051680|.	0.02792|.	N|.	0.122182|.	T|T	0.08403|0.08403	0.0209|0.0209	N|N	0.02142|0.02142	-0.665|-0.665	0.09310|0.09310	N|N	1|1	B;B;B|.	0.06786|.	0.0;0.0;0.001|.	B;B;B|.	0.06405|.	0.001;0.001;0.002|.	T|T	0.09357|0.09357	-1.0678|-1.0678	10|5	0.13108|.	T|.	0.6|.	.|.	3.8561|3.8561	0.08976|0.08976	0.3608:0.3061:0.0:0.3331|0.3608:0.3061:0.0:0.3331	.|.	12;12;12|.	E9PCD7;Q9Y2E5;Q9Y2E5-2|.	.;MA2B2_HUMAN;.|.	Q|S	12|11	ENSP00000285599:P12Q;ENSP00000423129:P12Q|.	ENSP00000285599:P12Q|.	P|R	+|+	2|1	0|0	MAN2B2|MAN2B2	6627873|6627873	0.003000|0.003000	0.15002|0.15002	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.090000|0.090000	0.15025|0.15025	-3.717000|-3.717000	0.00116|0.00116	-2.834000|-2.834000	0.00106|0.00106	CCG|CGC	.	.	.	none		0.746	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274		A	6576972	C	A	6576972	3	1	191	1	0	0	0	0	1	0	0	0	9224	652	23	4	37	4	MAN2B2	4	6576972	Missense_Mutation	SNP	C	TCGA-GL-A9DD-01A-11D-A36X-10	5411322	6576972	184577304	30	11323											
TLR1	7096	hgsc.bcm.edu	37	chr4	38800432	38800432	+	Frame_Shift_Del	DEL	A	A	-																															attaacatgaagataatggcAaaatggaagatgctagtcat																										TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr4:38800432delA	ENST00000502213.2	-	3	250	c.21delT	c.(19-21)tttfs	p.F7fs	TLR1_ENST00000308979.2_Frame_Shift_Del_p.F7fs			Q15399	TLR1_HUMAN	toll-like receptor 1	7					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						AGATAATGGCAAAATGGAAGA	0.328																																					p.A8fs	GBM(5;216 373 40795 46382)	Atlas-Indel,Pindel	.											.	TLR1	70	.	0			c.22delG						PASS	.						33	36	35					4																	38800432		2194	4292	6486	SO:0001589	frameshift_variant	7096	exon4			.	U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"CD molecules"	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.21delT	chr4.hg19:g.38800432delA	ENSP00000421259:p.Phe7fs	285.0	0.0	0		317.0	70.0	0.22082	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Frame_Shift_Del	DEL	ENST00000502213.2	hg19	CCDS33973.1																																																																																			.	.	.	none		0.328	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3			-	38800432	A	-	38800432	7	5	191	1	0	1	0	1	0	0	0	0	15961	127	5	0	2343	0	TLR1	4	38800432	Frame_Shift_Del	DEL	A	TCGA-GL-A9DD-01A-11D-A36X-10	32223460	38800432	152353844	31	11324											
SEC31A	22872	hgsc.bcm.edu	37	chr4	83748748	83748748	+	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	ccaacgggttcatgattggtGatgtgatgggaacaggaggc	10	9	16	6	1	1	3	1	3	0	0	1	5	1	5	1	5	2	1	1	5	2	2			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr4:83748748G>T	ENST00000395310.2	-	24	3247	c.3065C>A	c.(3064-3066)tCa>tAa	p.S1022*	SEC31A_ENST00000509142.1_Nonsense_Mutation_p.S908*|SEC31A_ENST00000505472.1_Nonsense_Mutation_p.S1053*|SEC31A_ENST00000432794.1_Nonsense_Mutation_p.S1035*|SEC31A_ENST00000505984.1_Nonsense_Mutation_p.S968*|SEC31A_ENST00000348405.4_Nonsense_Mutation_p.S983*|SEC31A_ENST00000326950.5_Nonsense_Mutation_p.S983*|SEC31A_ENST00000355196.2_Nonsense_Mutation_p.S1022*|SEC31A_ENST00000443462.2_Nonsense_Mutation_p.S1002*|SEC31A_ENST00000513858.1_Nonsense_Mutation_p.S869*|SEC31A_ENST00000311785.7_Nonsense_Mutation_p.S908*|SEC31A_ENST00000500777.2_Nonsense_Mutation_p.S869*|SEC31A_ENST00000264405.5_Nonsense_Mutation_p.S771*|SEC31A_ENST00000508502.1_Nonsense_Mutation_p.S1007*|SEC31A_ENST00000448323.1_Nonsense_Mutation_p.S1022*	NM_001077207.2|NM_001077208.2|NM_014933.3	NP_001070675.1|NP_001070676.1|NP_055748.2	O94979	SC31A_HUMAN	SEC31 homolog A (S. cerevisiae)	1022	Interaction with PDCD6.|Pro-rich.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|response to calcium ion (GO:0051592)	COPII vesicle coat (GO:0030127)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|vesicle coat (GO:0030120)	calcium-dependent protein binding (GO:0048306)		SEC31A/ALK(3)|SEC31A/JAK2(4)	breast(1)	1		Hepatocellular(203;0.114)				CATGATTGGTGATGTGATGGG	0.458																																					p.S1022X		Atlas-SNP	.											.	SEC31A	227	.	0			c.C3065A						PASS	.						171	165	167					4																	83748748		2203	4300	6503	SO:0001587	stop_gained	22872	exon24			ATTGGTGATGTGA	AB018358	CCDS3596.1, CCDS3597.1, CCDS43244.1, CCDS47088.1, CCDS54773.1, CCDS75155.1, CCDS75156.1	4q21.3	2013-01-10	2006-10-05	2006-09-07	ENSG00000138674	ENSG00000138674		"WD repeat domain containing"	17052	protein-coding gene	gene with protein product		610257	"SEC31-like 1 (S. cerevisiae)", "Sec31 homolog A (S. cerevisiae)"	SEC31L1		10048485, 10788476	Standard	NM_001077206		Approved	KIAA0905, ABP125, ABP130	uc003hnh.3	O94979	OTTHUMG00000130297	ENST00000395310.2:c.3065C>A	chr4.hg19:g.83748748G>T	ENSP00000378721:p.Ser1022*	143.0	0.0	.		155.0	28.0	.	NM_001077207	B4DIW6|B7ZKZ7|B7ZL00|H7C2W3|Q17RR5|Q5H9P6|Q5XG74|Q659G7|Q6ZU90|Q7LCX9|Q86TJ0|Q8IZH4|Q9P048|Q9P0A6|Q9UM05|Q9UM06	Nonsense_Mutation	SNP	ENST00000395310.2	hg19	CCDS3596.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.07|15.07	2.725353|2.725353	0.48833|0.48833	.|.	.|.	ENSG00000138674|ENSG00000138674	ENST00000503937|ENST00000348405;ENST00000513858;ENST00000395310;ENST00000443462;ENST00000509142;ENST00000432794;ENST00000448323;ENST00000326950;ENST00000311785;ENST00000505472;ENST00000500777;ENST00000508502;ENST00000355196;ENST00000264405;ENST00000505984	.|.	.|.	.|.	5.77|5.77	4.9|4.9	0.64082|0.64082	.|.	.|0.201050	.|0.44097	.|D	.|0.000483	T|.	0.54287|.	0.1849|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.54450|.	-0.8292|.	3|.	.|0.12766	.|T	.|0.61	-2.6138|-2.6138	15.9381|15.9381	0.79734|0.79734	0.0:0.0:0.8639:0.1361|0.0:0.0:0.8639:0.1361	.|.	.|.	.|.	.|.	N|X	185|983;869;1022;1002;908;1035;1022;983;908;1053;869;1007;1022;771;968	.|.	.|ENSP00000264405:S771X	H|S	-|-	1|2	0|0	SEC31A|SEC31A	83967772|83967772	1.000000|1.000000	0.71417|0.71417	0.652000|0.652000	0.29579|0.29579	0.106000|0.106000	0.19336|0.19336	7.795000|7.795000	0.85887|0.85887	1.377000|1.377000	0.46286|0.46286	0.655000|0.655000	0.94253|0.94253	CAC|TCA	.	.	.	none		0.458	SEC31A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252640.1	NM_016211		T	83748748	G	T	83748748	4	4	191	1	0	0	0	0	0	1	0	0	14011	1294	45	4	613	4	SEC31A	4	83748748	Nonsense_Mutation	SNP	G	TCGA-GL-A9DD-01A-11D-A36X-10	44948316	83748748	107405528	32	11325											
ARHGAP24	83478	hgsc.bcm.edu	37	chr4	86916509	86916510	+	Frame_Shift_Ins	INS	-	-	C																															aatctccctccctgagaactINSccaactcctgtcgctcttct																										TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr4:86916509_86916510insC	ENST00000395184.1	+	9	2168_2169	c.1702_1703insC	c.(1702-1704)tccfs	p.S568fs	ARHGAP24_ENST00000264343.4_Frame_Shift_Ins_p.S475fs|ARHGAP24_ENST00000395183.2_Frame_Shift_Ins_p.S473fs	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	568					activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)			breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		CCCTGAGAACTCCAACTCCTGT	0.53																																					p.S568fs		Atlas-INDEL	.											.,2	ARHGAP24	116	.	0			c.1702_1703insC						PASS	.																																			SO:0001589	frameshift_variant	83478	exon9			.	AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	25361	protein-coding gene	gene with protein product		610586				11230166, 15254788	Standard	NM_001042669		Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.1704dupC	chr4.hg19:g.86916511_86916511dupC	ENSP00000378611:p.Ser568fs	112.0	0.0	0		101.0	14.0	0.138614	NM_001025616	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	Frame_Shift_Ins	INS	ENST00000395184.1	hg19	CCDS34025.1																																																																																			.	.	.	none		0.53	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252815.2	NM_031305		C	86916510	-	C	86916509	7	5	191	1	0	1	1	0	0	0	0	0	873	1551	54	0	1848	0	ARHGAP24	4	86916509	Frame_Shift_Ins	INS	-	TCGA-GL-A9DD-01A-11D-A36X-10	3167761	86916509	104237767	33	11326											
USP53	54532	hgsc.bcm.edu	37	chr4	120190931	120190931	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctattgaacagaaaaacttActttcttcacaaaggaaaga	18	10	6	7	0	2	3	1	1	1	2	2	4	2	4	0	1	3	1	0	1	7	5			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr4:120190931A>G	ENST00000274030.6	+	15	2553	c.1374A>G	c.(1372-1374)ttA>ttG	p.L458L	USP53_ENST00000450251.1_Silent_p.L458L	NM_019050.2	NP_061923.2			ubiquitin specific peptidase 53											breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	27						AGAAAAACTTACTTTCTTCAC	0.318																																					p.L458L		Atlas-SNP	.											.	USP53	69	.	0			c.A1374G						PASS	.						98	100	99					4																	120190931		1802	4058	5860	SO:0001819	synonymous_variant	54532	exon14			AAACTTACTTTCT	BC017382	CCDS43265.1	4q26	2010-05-12	2005-08-08		ENSG00000145390	ENSG00000145390		"Ubiquitin-specific peptidases"	29255	protein-coding gene	gene with protein product			"ubiquitin specific protease 53"			10718198, 14715245	Standard	NM_019050		Approved	KIAA1350	uc003ics.4	Q70EK8	OTTHUMG00000161331	ENST00000274030.6:c.1374A>G	chr4.hg19:g.120190931A>G		489.0	0.0	.		524.0	54.0	.	NM_019050		Silent	SNP	ENST00000274030.6	hg19	CCDS43265.1																																																																																			.	.	.	none		0.318	USP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364564.2	XM_052597		G	120190931	A	G	120190931	2	3	191	1	0	0	0	0	0	0	0	1	17096	388	14	3		3	USP53	4	120190931	Silent	SNP	A	TCGA-GL-A9DD-01A-11D-A36X-10	33274422	120190931	70963345	34	11327											
FAT1	2195	hgsc.bcm.edu	37	chr4	187629592	187629593	+	Frame_Shift_Ins	INS	-	-	A																															gctttgtacgctgtctgggtINSaaattcagggggattgctat																										TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr4:187629592_187629593insA	ENST00000441802.2	-	2	1598_1599	c.1389_1390insT	c.(1387-1392)tttaccfs	p.T464fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	464	Cadherin 4. {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						GCTGTCTGGGTAAATTCAGGGG	0.48										HNSCC(5;0.00058)																											p.T464fs	Colon(197;1040 2055 4143 4984 49344)	Atlas-Indel,Pindel	.											.	FAT1	500	.	0			c.1390_1391insT						PASS	.																																			SO:0001589	frameshift_variant	2195	exon2			.	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.1390dupT	chr4.hg19:g.187629595_187629595dupA	ENSP00000406229:p.Thr464fs	109.0	0.0	0		103.0	25.0	0.242718	NM_005245		Frame_Shift_Ins	INS	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.	.	none		0.48	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		A	187629593	-	A	187629592	7	5	191	1	0	1	1	0	0	0	0	0	5696	1638	57	0	12480	0	FAT1	4	187629592	Frame_Shift_Ins	INS	-	TCGA-GL-A9DD-01A-11D-A36X-10	67438661	187629592	3524684	35	11328											
RNASEN	29102	hgsc.bcm.edu	37	chr5	31526232	31526232	+	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	agatggtgttctccctcggtCataatcagatctgtaccggc	8	12	10	11	2	4	2	2	0	2	2	6	2	4	2	2	3	1	2	2	3	2	3			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr5:31526232C>A	ENST00000511367.2	-	4	1052	c.808G>T	c.(808-810)Gac>Tac	p.D270Y	DROSHA_ENST00000513349.1_Missense_Mutation_p.D270Y|DROSHA_ENST00000504361.1_5'Flank|DROSHA_ENST00000344624.3_Missense_Mutation_p.D270Y|DROSHA_ENST00000442743.1_Missense_Mutation_p.D270Y	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	270	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						CTCCCTCGGTCATAATCAGAT	0.587																																					p.D270Y		Atlas-SNP	.											.	DROSHA	130	.	0			c.G808T						PASS	.						101	104	103					5																	31526232		2082	4213	6295	SO:0001583	missense	29102	exon4			CTCGGTCATAATC	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.808G>T	chr5.hg19:g.31526232C>A	ENSP00000425979:p.Asp270Tyr	82.0	0.0	.		78.0	17.0	.	NM_013235	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Missense_Mutation	SNP	ENST00000511367.2	hg19	CCDS47195.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.56|10.56	1.384535|1.384535	0.25031|0.25031	.|.	.|.	ENSG00000113360|ENSG00000113360	ENST00000511367;ENST00000344624;ENST00000442743;ENST00000513349;ENST00000265075;ENST00000382188;ENST00000512302|ENST00000512076	T;T;T;T;T|.	0.51574|.	0.7;0.7;0.7;0.7;0.97|.	4.55|4.55	4.55|4.55	0.56014|0.56014	.|.	0.187574|.	0.43919|.	D|.	0.000519|.	T|.	0.49457|.	0.1558|.	N|N	0.24115|0.24115	0.695|0.695	0.58432|0.58432	D|D	0.999992|0.999992	P;B;B|.	0.48503|.	0.911;0.38;0.38|.	P;B;B|.	0.47705|.	0.555;0.125;0.125|.	T|.	0.42050|.	-0.9474|.	10|.	0.21540|.	T|.	0.41|.	-5.2075|-5.2075	12.0196|12.0196	0.53336|0.53336	0.0:0.9169:0.0:0.083|0.0:0.9169:0.0:0.083	.|.	270;270;270|.	Q9NRR4-2;E7EMP9;Q9NRR4|.	.;.;RNC_HUMAN|.	Y|L	270;270;270;270;263;263;68|99	ENSP00000425979:D270Y;ENSP00000339845:D270Y;ENSP00000409335:D270Y;ENSP00000424161:D270Y;ENSP00000428782:D68Y|.	ENSP00000265075:D263Y|.	D|X	-|-	1|2	0|2	DROSHA|DROSHA	31561989|31561989	0.998000|0.998000	0.40836|0.40836	0.449000|0.449000	0.26957|0.26957	0.080000|0.080000	0.17528|0.17528	4.622000|4.622000	0.61240|0.61240	2.348000|2.348000	0.79779|0.79779	0.650000|0.650000	0.86243|0.86243	GAC|TGA	.	.	.	none		0.587	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235		A	31526232	C	A	31526232	3	1	191	1	0	0	0	0	1	0	0	0	13430	826	29	4	3444	4	RNASEN	5	31526232	Missense_Mutation	SNP	C	TCGA-GL-A9DD-01A-11D-A36X-10		31526232	149389028	36	11329											
WDR41	55255	hgsc.bcm.edu	37	chr5	76758982	76758982	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttctcttcacaagattccaAggaaggaaatgtaataatag	16	12	7	6	0	2	1	1	0	1	1	4	3	3	3	1	2	0	1	1	2	7	6			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr5:76758982A>G	ENST00000296679.4	-	4	661	c.286T>C	c.(286-288)Ttg>Ctg	p.L96L	WDR41_ENST00000507029.1_Silent_p.L41L|WDR41_ENST00000414719.2_5'UTR	NM_018268.2	NP_060738.2	Q9HAD4	WDR41_HUMAN	WD repeat domain 41	96						lysosomal membrane (GO:0005765)		p.L96V(1)		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)		CAAGATTCCAAGGAAGGAAAT	0.343																																					p.L96L		Atlas-SNP	.											WDR41,colon,carcinoma,0,1	WDR41	29	.	1	Substitution - Missense(1)	large_intestine(1)	c.T286C						PASS	.						120	122	121					5																	76758982		2203	4300	6503	SO:0001819	synonymous_variant	55255	exon4			ATTCCAAGGAAGG	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.286T>C	chr5.hg19:g.76758982A>G		118.0	0.0	.		97.0	17.0	.	NM_018268	B4DT55|Q7Z792|Q8IWG3|Q8IXA9|Q8NDA7|Q9NV62	Silent	SNP	ENST00000296679.4	hg19	CCDS4038.1																																																																																			.	.	.	none		0.343	WDR41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220014.2	NM_018268		G	76758982	A	G	76758982	2	3	191	1	0	0	0	0	0	0	0	1	17306	69	3	3		3	WDR41	5	76758982	Silent	SNP	A	TCGA-GL-A9DD-01A-11D-A36X-10	45232750	76758982	104156278	37	11330											
WDR36	134430	hgsc.bcm.edu	37	chr5	110448824	110448824	+	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	gtgctgcgatggattgctctAttaggacttgggaccttcct	6	14	12	9	1	1	0	0	0	1	0	2	4	2	3	2	3	3	2	2	3	2	5	rs562223310		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr5:110448824A>T	ENST00000513710.2	+	16	1940	c.1936A>T	c.(1936-1938)Att>Ttt	p.I646F	WDR36_ENST00000506538.2_Missense_Mutation_p.I646F			Q8NI36	WDR36_HUMAN	WD repeat domain 36	646					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)		GGATTGCTCTATTAGGACTTG	0.289																																					p.I646F		Atlas-SNP	.											.	WDR36	111	.	0			c.A1936T						PASS	.						150	151	150					5																	110448824		2202	4300	6502	SO:0001583	missense	134430	exon16			TGCTCTATTAGGA	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.1936A>T	chr5.hg19:g.110448824A>T	ENSP00000424628:p.Ile646Phe	97.0	0.0	.		90.0	21.0	.	NM_139281	A2RUS4|Q68E02|Q8N1Q2	Missense_Mutation	SNP	ENST00000513710.2	hg19	CCDS4102.1	.	.	.	.	.	.	.	.	.	.	A	18.13	3.555751	0.65425	.	.	ENSG00000134987	ENST00000506538;ENST00000513710	T;T	0.70045	-0.45;-0.45	6.06	-9.14	0.00701	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.194328	0.56097	D	0.000029	T	0.72145	0.3424	M	0.91140	3.18	0.80722	D	1	P	0.43885	0.82	P	0.45474	0.482	T	0.81883	-0.0728	10	0.87932	D	0	-5.945	17.9341	0.89007	0.4286:0.0:0.5714:0.0	.	646	Q8NI36	WDR36_HUMAN	F	646	ENSP00000423067:I646F;ENSP00000424628:I646F	ENSP00000423067:I646F	I	+	1	0	WDR36	110476723	0.102000	0.21896	0.359000	0.25824	0.804000	0.45430	0.737000	0.26144	-1.830000	0.01199	-1.986000	0.00452	ATT	.	.	.	none		0.289	WDR36-008	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000373504.3	NM_139281		T	110448824	A	T	110448824	3	4	191	1	0	0	0	0	1	0	0	0	17302	449	16	5	1998	5	WDR36	5	110448824	Missense_Mutation	SNP	A	TCGA-GL-A9DD-01A-11D-A36X-10	33689842	110448824	70466436	38	11331											
PCDHGC3	5098	hgsc.bcm.edu	37	chr5	140857767	140857767	+	Missense_Mutation	SNP	T	T	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	aaatctcaccttttatctacTtctttctctaatcctggttt	8	20	2	11	0	4	0	1	0	4	0	7	0	5	0	2	1	1	1	2	1	4	7			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr5:140857767T>G	ENST00000308177.3	+	1	2188	c.2084T>G	c.(2083-2085)cTt>cGt	p.L695R	PCDHGB6_ENST00000520790.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	695					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)			TTTTATCTACTTCTTTCTCTA	0.483											OREG0016865	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L695R		Atlas-SNP	.											.	PCDHGC3	173	.	0			c.T2084G						PASS	.						159	198	185					5																	140857767		2203	4300	6503	SO:0001583	missense	5098	exon1			ATCTACTTCTTTC	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.2084T>G	chr5.hg19:g.140857767T>G	ENSP00000312070:p.Leu695Arg	80.0	0.0	.	1659	86.0	18.0	.	NM_032402	O60622|Q08192|Q9Y5C4	Missense_Mutation	SNP	ENST00000308177.3	hg19	CCDS4261.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.433275	0.83776	.	.	ENSG00000240184	ENST00000308177	T	0.51574	0.7	5.55	5.55	0.83447	.	.	.	.	.	T	0.56171	0.1967	L	0.29908	0.895	0.32577	N	0.529007	D;D	0.76494	0.996;0.999	P;D	0.67548	0.823;0.952	T	0.66044	-0.6021	9	0.87932	D	0	.	14.0843	0.64944	0.0:0.0:0.0:1.0	.	695;695	Q9UN70;Q9UN70-2	PCDGK_HUMAN;.	R	695	ENSP00000312070:L695R	ENSP00000312070:L695R	L	+	2	0	PCDHGC3	140837951	0.992000	0.36948	1.000000	0.80357	0.989000	0.77384	4.297000	0.59061	2.326000	0.78906	0.533000	0.62120	CTT	.	.	.	none		0.483	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588		G	140857767	T	G	140857767	3	3	191	1	0	0	0	0	1	0	0	0	11576	1609	56	5	2086	5	PCDHGC3	5	140857767	Missense_Mutation	SNP	T	TCGA-GL-A9DD-01A-11D-A36X-10	30408943	140857767	40057493	39	11332											
C5orf25	375484	hgsc.bcm.edu	37	chr5	175772284	175772294	+	Frame_Shift_Del	DEL	GAGAAGCAGAT	GAGAAGCAGAT	-																															acatcacagtggtagacgtaGagaagcagattgaggccttc																								rs116804795		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	GAGAAGCAGAT	GAGAAGCAGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr5:175772284_175772294delGAGAAGCAGAT	ENST00000443967.1	+	12	2862_2872	c.2455_2465delGAGAAGCAGAT	c.(2455-2466)gagaagcagattfs	p.EKQI819fs	KIAA1191_ENST00000393728.2_5'Flank|SIMC1_ENST00000332772.4_Frame_Shift_Del_p.EKQI280fs|RP11-843P14.2_ENST00000508187.1_RNA|SIMC1_ENST00000430704.2_Frame_Shift_Del_p.EKQI404fs|SIMC1_ENST00000341199.6_Frame_Shift_Del_p.EKQI404fs			Q8NDZ2	SIMC1_HUMAN	SUMO-interacting motifs containing 1	819							SUMO polymer binding (GO:0032184)										GGTAGACGTAGAGAAGCAGATTGAGGCCTTC	0.502																																					p.403_407del		Atlas-Indel,Pindel	.											.	.	.	.	0			c.1209_1219del						PASS	.																																			SO:0001589	frameshift_variant	375484	exon9			.	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.2455_2465delGAGAAGCAGAT	chr5.hg19:g.175772284_175772294delGAGAAGCAGAT	ENSP00000406571:p.Glu819fs	187.0	0.0	0		182.0	25.0	0.137363	NM_198567	J3KQQ8|Q6NXN8|Q6ZTU4|Q8IZ15	Frame_Shift_Del	DEL	ENST00000443967.1	hg19																																																																																				.	.	.	none		0.502	SIMC1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000253155.2	NM_198567		-	175772294	GAGAAGCAGAT	-	175772284	7	5	191	1	0	1	0	1	0	0	0	0	2290	943	33	0	1244	0	C5orf25	5	175772284	Frame_Shift_Del	DEL	GAGAAGCAGAT	TCGA-GL-A9DD-01A-11D-A36X-10	34914517	175772284	5142976	40	11333											
MTCH1	23787	hgsc.bcm.edu	37	chr6	36936732	36936732	+	Missense_Mutation	SNP	A	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	ccggcggaaaagcaggctggAgcctcggaagagctggccct	9	4	16	12	3	0	1	0	0	0	1	1	4	0	4	3	6	3	3	3	6	3	0			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr6:36936732A>C	ENST00000373627.5	-	12	1241	c.1117T>G	c.(1117-1119)Tcc>Gcc	p.S373A	MTCH1_ENST00000373616.5_Missense_Mutation_p.S356A|MTCH1_ENST00000471737.1_5'UTR	NM_001271641.1	NP_001258570.1	Q9NZJ7	MTCH1_HUMAN	mitochondrial carrier 1	373					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|neuronal ion channel clustering (GO:0045161)|positive regulation of apoptotic process (GO:0043065)|regulation of signal transduction (GO:0009966)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	6						AGCAGGCTGGAGCCTCGGAAG	0.562																																					p.S373A		Atlas-SNP	.											.	MTCH1	24	.	0			c.T1117G						PASS	.						78	70	73					6																	36936732		2203	4300	6503	SO:0001583	missense	23787	exon12			GGCTGGAGCCTCG	AF151822	CCDS4828.1, CCDS64411.1	6p21.2	2013-05-22	2011-05-19		ENSG00000137409	ENSG00000137409		"Solute carriers"	17586	protein-coding gene	gene with protein product	"solute carrier family 25, member 49"	610449	"mitochondrial carrier homolog 1 (C. elegans)"			12377771	Standard	NM_014341		Approved	CGI-64, PSAP, SLC25A49	uc003ond.2	Q9NZJ7	OTTHUMG00000014614	ENST00000373627.5:c.1117T>G	chr6.hg19:g.36936732A>C	ENSP00000362730:p.Ser373Ala	91.0	0.0	.		69.0	16.0	.	NM_001271641	A8KAX5|B2RCE3|Q6PK60|Q6UX45|Q7L465|Q9BW23|Q9NZR6|Q9UJZ5	Missense_Mutation	SNP	ENST00000373627.5	hg19		.	.	.	.	.	.	.	.	.	.	A	17.75	3.465220	0.63513	.	.	ENSG00000137409	ENST00000373616;ENST00000373627;ENST00000337855	T;T	0.77229	-1.08;-1.08	5.16	5.16	0.70880	Mitochondrial carrier domain (2);	2.951400	0.01758	N	0.030350	T	0.79233	0.4411	L	0.44542	1.39	0.80722	D	1	D;D	0.56521	0.976;0.974	P;D	0.67725	0.86;0.953	T	0.67146	-0.5744	10	0.20046	T	0.44	.	13.5751	0.61868	1.0:0.0:0.0:0.0	.	373;356	Q9NZJ7;Q9NZJ7-2	MTCH1_HUMAN;.	A	356;373;292	ENSP00000362718:S356A;ENSP00000362730:S373A	ENSP00000338712:S292A	S	-	1	0	MTCH1	37044710	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.964000	0.76061	1.955000	0.56771	0.533000	0.62120	TCC	.	.	.	none		0.562	MTCH1-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040396.1	NM_014341		C	36936732	A	C	36936732	3	2	191	1	0	0	0	0	1	0	0	0	9920	304	11	5	56	5	MTCH1	6	36936732	Missense_Mutation	SNP	A	TCGA-GL-A9DD-01A-11D-A36X-10		36936732	134178335	41	11334											
CYP39A1	51302	hgsc.bcm.edu	37	chr6	46604152	46604152	+	Missense_Mutation	SNP	A	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	attatcttttgcagatttacAtgcttttatatctggaatgt	10	20	6	5	0	2	1	0	0	2	1	2	2	2	2	0	1	3	2	0	1	5	8			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr6:46604152A>C	ENST00000275016.2	-	5	909	c.706T>G	c.(706-708)Tgt>Ggt	p.C236G		NM_016593.3	NP_057677.2	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A, polypeptide 1	236					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						GCAGATTTACATGCTTTTATA	0.254																																					p.C236G		Atlas-SNP	.											.	CYP39A1	41	.	0			c.T706G						PASS	.						48	49	49					6																	46604152		2201	4291	6492	SO:0001583	missense	51302	exon5			ATTTACATGCTTT	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.706T>G	chr6.hg19:g.46604152A>C	ENSP00000275016:p.Cys236Gly	163.0	0.0	.		155.0	27.0	.	NM_016593	Q5VTT0|Q96FW5	Missense_Mutation	SNP	ENST00000275016.2	hg19	CCDS4916.1	.	.	.	.	.	.	.	.	.	.	A	6.429	0.447325	0.12223	.	.	ENSG00000146233	ENST00000275016	T	0.67698	-0.28	6.04	-4.27	0.03744	.	1.033410	0.07651	N	0.931975	T	0.13841	0.0335	N	0.08118	0	0.09310	N	1	B;B	0.13145	0.003;0.007	B;B	0.11329	0.004;0.006	T	0.09885	-1.0654	10	0.15066	T	0.55	1.0091	1.0259	0.01527	0.2813:0.1006:0.277:0.3411	.	216;236	B7Z786;Q9NYL5	.;CP39A_HUMAN	G	236	ENSP00000275016:C236G	ENSP00000275016:C236G	C	-	1	0	CYP39A1	46712111	0.000000	0.05858	0.000000	0.03702	0.575000	0.36095	-0.191000	0.09601	-0.304000	0.08843	0.459000	0.35465	TGT	.	.	.	none		0.254	CYP39A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040787.1			C	46604152	A	C	46604152	3	2	191	1	0	0	0	0	1	0	0	0	4179	217	8	5	735	5	CYP39A1	6	46604152	Missense_Mutation	SNP	A	TCGA-GL-A9DD-01A-11D-A36X-10	9667420	46604152	124510915	42	11335											
EYS	346007	hgsc.bcm.edu	37	chr6	64574111	64574111	+	Frame_Shift_Del	DEL	G	G	-																															ggggtccagacctcccatatGggcagaggcagacaatatct																										TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr6:64574111delG	ENST00000370621.3	-	36	7722	c.7196delC	c.(7195-7197)ccafs	p.P2399fs	EYS_ENST00000370616.2_Frame_Shift_Del_p.P2399fs|EYS_ENST00000503581.1_Frame_Shift_Del_p.P2399fs			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	2399	EGF-like 23. {ECO:0000255|PROSITE- ProRule:PRU00076}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						CCTCCCATATGGGCAGAGGCA	0.468																																					p.P2399fs		Atlas-Indel,Pindel	.											.	EYS	527	.	0			c.7197delA						PASS	.						112	94	99					6																	64574111		692	1591	2283	SO:0001589	frameshift_variant	346007	exon36			.		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"chromosome 6 open reading frame 180", "EGF-like-domain, multiple 11", "retinitis pigmentosa 25 (autosomal recessive)", "EGF-like-domain, multiple 10", "chromosome 6 open reading frame 178", "chromosome 6 open reading frame 179"	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.7196delC	chr6.hg19:g.64574111delG	ENSP00000359655:p.Pro2399fs	77.0	0.0	0		93.0	19.0	0.204301	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Frame_Shift_Del	DEL	ENST00000370621.3	hg19																																																																																				.	.	.	none		0.468	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		-	64574111	G	-	64574111	7	5	191	1	0	1	0	1	0	0	0	0	5334	1348	47	0	2270	0	EYS	6	64574111	Frame_Shift_Del	DEL	G	TCGA-GL-A9DD-01A-11D-A36X-10	17969959	64574111	106540956	43	11336											
MDN1	23195	hgsc.bcm.edu	37	chr6	90405588	90405588	+	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	acatgctggaaggcctggctGctcccaagcagcagctgctc	8	7	12	14	0	0	0	0	0	0	0	2	1	1	1	2	3	6	7	2	3	2	0			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr6:90405588G>T	ENST00000369393.3	-	61	9622	c.9507C>A	c.(9505-9507)agC>agA	p.S3169R	MDN1_ENST00000428876.1_Missense_Mutation_p.S3169R			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	3169					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)		AGGCCTGGCTGCTCCCAAGCA	0.642																																					p.S3169R		Atlas-SNP	.											.	MDN1	478	.	0			c.C9507A						PASS	.						39	41	41					6																	90405588		2203	4300	6503	SO:0001583	missense	23195	exon61			CTGGCTGCTCCCA	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.9507C>A	chr6.hg19:g.90405588G>T	ENSP00000358400:p.Ser3169Arg	104.0	0.0	.		111.0	23.0	.	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	hg19	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	G	6.555	0.470722	0.12461	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03124	4.04;4.04	5.19	0.217	0.15264	.	0.622155	0.16894	N	0.195186	T	0.00468	0.0015	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43988	-0.9357	10	0.19147	T	0.46	.	2.3682	0.04324	0.2946:0.148:0.4511:0.1064	.	3169	Q9NU22	MDN1_HUMAN	R	3169	ENSP00000358400:S3169R;ENSP00000413970:S3169R	ENSP00000358400:S3169R	S	-	3	2	MDN1	90462309	0.940000	0.31905	0.015000	0.15790	0.809000	0.45718	0.326000	0.19646	-0.277000	0.09193	-0.140000	0.14226	AGC	.	.	.	none		0.642	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			T	90405588	G	T	90405588	3	4	191	1	0	0	0	0	1	0	0	0	9422	1310	46	4	7451	4	MDN1	6	90405588	Missense_Mutation	SNP	G	TCGA-GL-A9DD-01A-11D-A36X-10	25831477	90405588	80709479	44	11337											
AKD1	221264	hgsc.bcm.edu	37	chr6	109954291	109954291	+	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	tcttctgatgaaagacagtaGattttacctagaaaacttaa	16	13	6	6	0	2	5	0	2	2	3	2	5	2	5	1	0	2	1	1	0	7	6			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr6:109954291G>T	ENST00000424296.2	-	12	1165	c.1089C>A	c.(1087-1089)atC>atA	p.I363I	AK9_ENST00000341338.6_5'UTR|AK9_ENST00000285397.5_Silent_p.I363I|AK9_ENST00000368948.2_Silent_p.I363I	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	363					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)										AAAGACAGTAGATTTTACCTA	0.338																																					p.I363I		Atlas-SNP	.											.	AKD1	223	.	0			c.C1089A						PASS	.						82	77	79					6																	109954291		2203	4300	6503	SO:0001819	synonymous_variant	221264	exon12			ACAGTAGATTTTA	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.1089C>A	chr6.hg19:g.109954291G>T		77.0	0.0	.		103.0	33.0	.	NM_145025	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Silent	SNP	ENST00000424296.2	hg19	CCDS55048.1																																																																																			.	.	.	none		0.338	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128		T	109954291	G	T	109954291	2	4	191	1	0	0	0	0	0	0	0	1	460	932	33	4		4	AKD1	6	109954291	Silent	SNP	G	TCGA-GL-A9DD-01A-11D-A36X-10	19548703	109954291	61160776	45	11338											
KATNA1	11104	hgsc.bcm.edu	37	chr6	149944285	149944285	+	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	ctttcttttcacgacaacgaAcagctttccctctgtcattg	8	15	5	13	2	4	0	2	0	2	0	5	2	5	0	1	0	3	1	1	0	2	5			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr6:149944285A>T	ENST00000335647.5	-	3	499	c.455T>A	c.(454-456)gTt>gAt	p.V152D	KATNA1_ENST00000494504.1_5'Flank|KATNA1_ENST00000367411.2_Missense_Mutation_p.V152D|KATNA1_ENST00000335643.8_Missense_Mutation_p.V152D					katanin p60 (ATPase containing) subunit A 1											endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	12		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;2.95e-12)|GBM - Glioblastoma multiforme(68;0.173)		ACGACAACGAACAGCTTTCCC	0.358																																					p.V152D		Atlas-SNP	.											.	KATNA1	34	.	0			c.T455A						PASS	.						176	141	153					6																	149944285		2203	4300	6503	SO:0001583	missense	11104	exon4			CAACGAACAGCTT	AF056022	CCDS5217.1, CCDS56456.1	6q24.3	2011-01-25	2011-01-25		ENSG00000186625	ENSG00000186625		"ATPases / AAA-type"	6216	protein-coding gene	gene with protein product		606696	"katanin p60 (ATPase-containing) subunit A 1"			9658175	Standard	NM_007044		Approved		uc003qms.3	O75449	OTTHUMG00000015787	ENST00000335647.5:c.455T>A	chr6.hg19:g.149944285A>T	ENSP00000335106:p.Val152Asp	93.0	0.0	.		92.0	12.0	.	NM_007044		Missense_Mutation	SNP	ENST00000335647.5	hg19	CCDS5217.1	.	.	.	.	.	.	.	.	.	.	A	13.73	2.324241	0.41197	.	.	ENSG00000186625	ENST00000335647;ENST00000335643;ENST00000367411;ENST00000444282;ENST00000420200	D;D;D;D	0.95853	-3.39;-3.52;-3.39;-3.83	5.88	4.72	0.59763	.	0.523100	0.21943	N	0.066860	D	0.86707	0.5997	L	0.33485	1.01	0.58432	D	0.999999	B;P;B	0.35656	0.025;0.514;0.012	B;B;B	0.34242	0.028;0.178;0.028	D	0.84247	0.0475	9	.	.	.	.	12.0234	0.53356	0.9325:0.0:0.0675:0.0	.	152;152;152	A8K7S5;O75449-2;O75449	.;.;KTNA1_HUMAN	D	152	ENSP00000335106:V152D;ENSP00000335180:V152D;ENSP00000356381:V152D;ENSP00000390322:V152D	.	V	-	2	0	KATNA1	149985978	1.000000	0.71417	0.889000	0.34880	0.996000	0.88848	5.934000	0.70138	1.044000	0.40200	0.482000	0.46254	GTT	.	.	.	none		0.358	KATNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042641.2	NM_007044		T	149944285	A	T	149944285	3	4	191	1	0	0	0	0	1	0	0	0	7991	43	2	5	1052	5	KATNA1	6	149944285	Missense_Mutation	SNP	A	TCGA-GL-A9DD-01A-11D-A36X-10	39989994	149944285	21170782	46	11339											
ZNF479	90827	hgsc.bcm.edu	37	chr7	57187920	57187920	+	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	gtctctctccagtatgaattCtcttgtggatagtaagtgct	8	16	9	8	0	3	1	0	1	3	0	6	2	3	2	1	1	1	3	1	1	4	5	rs572783904		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr7:57187920C>G	ENST00000331162.4	-	5	1472	c.1202G>C	c.(1201-1203)aGa>aCa	p.R401T		NM_033273.1	NP_150376.1	Q96JC4	ZN479_HUMAN	zinc finger protein 479	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)	p.R401I(1)		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)			AGTATGAATTCTCTTGTGGAT	0.438																																					p.R401T		Atlas-SNP	.											ZNF479,colon,carcinoma,0,1	ZNF479	193	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1202C						PASS	.						14	12	13					7																	57187920		1821	3902	5723	SO:0001583	missense	90827	exon5			TGAATTCTCTTGT	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.1202G>C	chr7.hg19:g.57187920C>G	ENSP00000333776:p.Arg401Thr	241.0	1.0	.		307.0	80.0	.	NM_033273		Missense_Mutation	SNP	ENST00000331162.4	hg19	CCDS43590.1	.	.	.	.	.	.	.	.	.	.	c	8.487	0.861161	0.17178	.	.	ENSG00000185177	ENST00000331162	T	0.02421	4.3	0.946	-0.375	0.12509	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03136	0.0092	L	0.56340	1.77	0.24060	N	0.996018	P	0.50066	0.931	B	0.41088	0.347	T	0.33471	-0.9867	9	0.66056	D	0.02	.	2.1182	0.03719	0.2948:0.4775:0.0:0.2278	.	401	Q96JC4	ZN479_HUMAN	T	401	ENSP00000333776:R401T	ENSP00000333776:R401T	R	-	2	0	ZNF479	57191862	0.001000	0.12720	0.012000	0.15200	0.012000	0.07955	1.404000	0.34623	-1.303000	0.02332	-1.323000	0.01288	AGA	.	.	.	none		0.438	ZNF479-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345302.1	XM_291202		G	57187920	C	G	57187920	3	3	191	1	0	0	0	0	1	0	0	0	17945	913	32	4	376	4	ZNF479	7	57187920	Missense_Mutation	SNP	C	TCGA-GL-A9DD-01A-11D-A36X-10		57187920	101950743	47	11340											
GTF2IRD1	9569	hgsc.bcm.edu	37	chr7	73953047	73953047	+	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	ggcgggctgaggccgatcaaAattgagccagaggatctgga	11	6	16	8	2	2	3	1	2	1	1	2	6	2	5	2	5	1	1	2	5	2	1			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr7:73953047A>T	ENST00000265755.3	+	13	1878	c.1485A>T	c.(1483-1485)aaA>aaT	p.K495N	GTF2IRD1_ENST00000489094.1_3'UTR|GTF2IRD1_ENST00000455841.2_Missense_Mutation_p.K527N|GTF2IRD1_ENST00000476977.1_Missense_Mutation_p.K495N|GTF2IRD1_ENST00000424337.2_Missense_Mutation_p.K495N	NM_005685.3|NM_016328.2	NP_005676.3|NP_057412.1	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1	495					multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transition between slow and fast fiber (GO:0014886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						GGCCGATCAAAATTGAGCCAG	0.592																																					p.K527N		Atlas-SNP	.											.	GTF2IRD1	91	.	0			c.A1581T						PASS	.						70	70	70					7																	73953047		2203	4300	6503	SO:0001583	missense	9569	exon13			GATCAAAATTGAG	AF151354	CCDS5571.1, CCDS47613.1, CCDS56492.1	7q11.23	2008-04-18	2002-01-14		ENSG00000006704	ENSG00000006704			4661	protein-coding gene	gene with protein product	"binding factor for early enhancer"	604318	"GTF2I repeat domain-containing 1"	WBSCR11		9774679, 10198167	Standard	NM_016328		Approved	MusTRD1, RBAP2, GTF3, WBSCR12, BEN, Cream1	uc010lbq.3	Q9UHL9	OTTHUMG00000023782	ENST00000265755.3:c.1485A>T	chr7.hg19:g.73953047A>T	ENSP00000265755:p.Lys495Asn	72.0	0.0	.		49.0	8.0	.	NM_001199207	O95444|Q6DSU6|Q75MX7|Q86UM3|Q8WVC4|Q9UHK8|Q9UI91	Missense_Mutation	SNP	ENST00000265755.3	hg19	CCDS5571.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.323217	0.81580	.	.	ENSG00000006704	ENST00000265755;ENST00000455841;ENST00000424337;ENST00000476977	T;T;T;T	0.52754	0.68;0.67;0.71;0.65	4.8	2.34	0.29019	.	0.000000	0.85682	D	0.000000	T	0.60741	0.2292	M	0.65498	2.005	0.50632	D	0.999881	D;P;D;D	0.71674	0.998;0.792;0.967;0.98	D;B;P;P	0.78314	0.991;0.255;0.662;0.818	T	0.60702	-0.7211	10	0.87932	D	0	-14.944	7.1506	0.25608	0.7434:0.0:0.2566:0.0	.	527;495;495;495	Q6DSU6;E9PFE2;Q9UHL9;Q9UHL9-2	.;.;GT2D1_HUMAN;.	N	495;527;495;495	ENSP00000265755:K495N;ENSP00000397566:K527N;ENSP00000408477:K495N;ENSP00000418383:K495N	ENSP00000265755:K495N	K	+	3	2	GTF2IRD1	73590983	1.000000	0.71417	0.998000	0.56505	0.921000	0.55340	1.323000	0.33701	0.762000	0.33152	0.459000	0.35465	AAA	.	.	.	none		0.592	GTF2IRD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252654.2	NM_016328		T	73953047	A	T	73953047	3	4	191	1	0	0	0	0	1	0	0	0	6875	11	1	5	1531	5	GTF2IRD1	7	73953047	Missense_Mutation	SNP	A	TCGA-GL-A9DD-01A-11D-A36X-10	16765127	73953047	85185616	48	11341											
MUC17	140453	hgsc.bcm.edu	37	chr7	100683876	100683876	+	Missense_Mutation	SNP	T	T	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	cagcaccacgccagtggccaTtcctgaggctagcacccttt	8	8	9	16	1	0	1	0	1	0	0	1	1	1	1	5	2	2	3	5	2	1	3	rs145514577		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr7:100683876T>G	ENST00000306151.4	+	3	9243	c.9179T>G	c.(9178-9180)aTt>aGt	p.I3060S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3060	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)					CCAGTGGCCATTCCTGAGGCT	0.493													G|||	1	0.000199681	0	0	5008	,	,		25521	0		0.001	False		,,,				2504	0				p.I3060S		Atlas-SNP	.											MUC17,NS,carcinoma,0,1	MUC17	804	.	0			c.T9179G						PASS	.						275	283	280					7																	100683876		2203	4300	6503	SO:0001583	missense	140453	exon3			TGGCCATTCCTGA	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.9179T>G	chr7.hg19:g.100683876T>G	ENSP00000302716:p.Ile3060Ser	42.0	2.0	.		57.0	5.0	.	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	N	0.327	-0.958208	0.02267	.	.	ENSG00000169876	ENST00000306151	T	0.02197	4.4	0.814	-0.258	0.12975	.	.	.	.	.	T	0.00998	0.0033	N	0.03608	-0.345	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.48681	-0.9014	9	0.17369	T	0.5	.	3.7091	0.08413	0.0:0.5408:0.2591:0.2001	.	3060	Q685J3	MUC17_HUMAN	S	3060	ENSP00000302716:I3060S	ENSP00000302716:I3060S	I	+	2	0	MUC17	100470596	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-4.610000	0.00209	-0.661000	0.05345	-2.058000	0.00401	ATT	.	.	.	weak		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		G	100683876	T	G	100683876	3	3	191	1	0	0	0	0	1	0	0	0	9981	1493	52	5	9189	5	MUC17	7	100683876	Missense_Mutation	SNP	T	TCGA-GL-A9DD-01A-11D-A36X-10	26730829	100683876	58454787	49	11342											
MOGAT3	346606	hgsc.bcm.edu	37	chr7	100844043	100844043	+	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	tcacccatgaagaggaaagtGagcacatattggtaggcgcc	13	7	12	9	1	1	3	1	2	0	1	1	4	1	4	2	3	1	2	2	3	4	3			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr7:100844043G>A	ENST00000223114.4	-	1	259	c.93C>T	c.(91-93)ctC>ctT	p.L31L	MOGAT3_ENST00000379423.3_Silent_p.L31L|MOGAT3_ENST00000440203.2_Silent_p.L31L	NM_178176.2	NP_835470.1	Q86VF5	MOGT3_HUMAN	monoacylglycerol O-acyltransferase 3	31					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)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(10)|ovary(3)	22	Lung NSC(181;0.168)|all_lung(186;0.215)					AGAGGAAAGTGAGCACATATT	0.592																																					p.L31L		Atlas-SNP	.											.	MOGAT3	72	.	0			c.C93T						PASS	.						93	72	79					7																	100844043		2203	4300	6503	SO:0001819	synonymous_variant	346606	exon1			GAAAGTGAGCACA	AY229854	CCDS5714.1, CCDS75643.1	7q22	2012-09-06			ENSG00000106384	ENSG00000106384	2.3.1.20, 2.3.1.22		23249	protein-coding gene	gene with protein product		610184				12618427, 14970677	Standard	XM_005250309		Approved	DC7, MGAT3	uc003uyc.3	Q86VF5	OTTHUMG00000023328	ENST00000223114.4:c.93C>T	chr7.hg19:g.100844043G>A		89.0	0.0	.		78.0	13.0	.	NM_178176	Q496A6|Q496A7|Q496A8|Q9UDW7	Silent	SNP	ENST00000223114.4	hg19	CCDS5714.1																																																																																			.	.	.	none		0.592	MOGAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059649.3	NM_178176		A	100844043	G	A	100844043	2	1	191	1	0	0	0	0	0	0	0	1	9703	1277	45	2		2	MOGAT3	7	100844043	Silent	SNP	G	TCGA-GL-A9DD-01A-11D-A36X-10	160167	100844043	58294620	50	11343											
RINT1	60561	hgsc.bcm.edu	37	chr7	105187490	105187490	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttggtttcatgagagccacaGttaaattctggcataaaatt	13	14	8	6	0	2	1	1	1	1	1	2	2	2	1	1	2	1	3	1	2	4	6			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr7:105187490G>A	ENST00000257700.2	+	5	880	c.649G>A	c.(649-651)Gtt>Att	p.V217I		NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	217					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						GAGAGCCACAGTTAAATTCTG	0.403																																					p.V217I		Atlas-SNP	.											.	RINT1	65	.	0			c.G649A						PASS	.						108	98	102					7																	105187490		2203	4300	6503	SO:0001583	missense	60561	exon5			GCCACAGTTAAAT	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.649G>A	chr7.hg19:g.105187490G>A	ENSP00000257700:p.Val217Ile	147.0	0.0	.		184.0	54.0	.	NM_021930	Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Missense_Mutation	SNP	ENST00000257700.2	hg19	CCDS34726.1	.	.	.	.	.	.	.	.	.	.	G	14.82	2.650241	0.47362	.	.	ENSG00000135249	ENST00000257700	T	0.22336	1.96	5.26	4.38	0.52667	.	0.189193	0.46442	N	0.000290	T	0.19644	0.0472	L	0.48362	1.52	0.49687	D	0.999815	B	0.22346	0.068	B	0.13407	0.009	T	0.02567	-1.1140	10	0.30078	T	0.28	-10.9031	13.7518	0.62912	0.0749:0.0:0.9251:0.0	.	217	Q6NUQ1	RINT1_HUMAN	I	217	ENSP00000257700:V217I	ENSP00000257700:V217I	V	+	1	0	RINT1	104974726	1.000000	0.71417	0.884000	0.34674	0.970000	0.65996	4.771000	0.62318	1.205000	0.43262	0.563000	0.77884	GTT	.	.	.	none		0.403	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	NM_021930		A	105187490	G	A	105187490	3	1	191	1	0	0	0	0	1	0	0	0	13389	1029	36	2	667	2	RINT1	7	105187490	Missense_Mutation	SNP	G	TCGA-GL-A9DD-01A-11D-A36X-10	4343447	105187490	53951173	51	11344											
NAA38	84316	hgsc.bcm.edu	37	chr7	117828344	117828344	+	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	ctttacagggaacactgaaaGgttttgaccagaccattaat	14	11	8	8	0	0	3	0	2	0	1	0	4	0	4	2	2	2	1	2	2	4	5			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr7:117828344G>A	ENST00000249299.2	+	3	277	c.85G>A	c.(85-87)Ggt>Agt	p.G29S	NAA38_ENST00000422760.1_Missense_Mutation_p.G8S|NAA38_ENST00000424702.1_Missense_Mutation_p.G29S	NM_016200.4	NP_057284.1	Q9BRA0	LSMD1_HUMAN	N(alpha)-acetyltransferase 38, NatC auxiliary subunit	69					negative regulation of apoptotic process (GO:0043066)	cytoplasm (GO:0005737)|NatC complex (GO:0031417)|nucleus (GO:0005634)		p.G29S(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	8						AACACTGAAAGGTTTTGACCA	0.363																																					p.G29S		Atlas-SNP	.											NAA38,mouth,carcinoma,0,1	NAA38	16	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.G85A						PASS	.						83	85	84					7																	117828344		2203	4300	6503	SO:0001583	missense	51691	exon3			CTGAAAGGTTTTG		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.85G>A	chr7.hg19:g.117828344G>A	ENSP00000249299:p.Gly29Ser	68.0	0.0	.		86.0	28.0	.	NM_016200	Q8N4M0	Missense_Mutation	SNP	ENST00000249299.2	hg19	CCDS5775.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.916546	0.92249	.	.	ENSG00000128534	ENST00000249299;ENST00000424702;ENST00000422760;ENST00000411938	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	5.69	4.78	0.61160	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	T	0.61850	0.2380	.	.	.	0.80722	D	1	D	0.71674	0.998	D	0.79108	0.992	T	0.57670	-0.7771	9	0.32370	T	0.25	-19.584	16.7642	0.85520	0.0:0.1285:0.8715:0.0	.	29	O95777	NAA38_HUMAN	S	29;29;8;40	ENSP00000249299:G29S;ENSP00000395263:G29S;ENSP00000403811:G8S;ENSP00000408267:G40S	ENSP00000249299:G29S	G	+	1	0	NAA38	117615580	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.359000	0.79477	2.687000	0.91594	0.650000	0.86243	GGT	.	.	.	none		0.363	NAA38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346774.2	NM_032356		A	117828344	G	A	117828344	3	1	191	1	0	0	0	0	1	0	0	0	10131	1000	35	2	95	2	NAA38	7	117828344	Missense_Mutation	SNP	G	TCGA-GL-A9DD-01A-11D-A36X-10	12640854	117828344	41310319	52	11345											
MGAM	8972	hgsc.bcm.edu	37	chr7	141720863	141720863	+	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	tcacagcagaatatcagacaTctaatcgtttccactttaag	14	12	5	10	1	3	2	2	0	1	2	5	2	4	2	1	0	1	2	1	0	4	5			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr7:141720863T>A	ENST00000549489.2	+	5	633	c.538T>A	c.(538-540)Tct>Act	p.S180T	MGAM_ENST00000475668.2_Missense_Mutation_p.S180T	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	180					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)	ATATCAGACATCTAATCGTTT	0.348																																					p.S180T		Atlas-SNP	.											.	MGAM	767	.	0			c.T538A						PASS	.						99	89	92					7																	141720863		1829	4082	5911	SO:0001583	missense	8972	exon5			CAGACATCTAATC	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.538T>A	chr7.hg19:g.141720863T>A	ENSP00000447378:p.Ser180Thr	86.0	0.0	.		123.0	17.0	.	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	hg19	CCDS47727.1	.	.	.	.	.	.	.	.	.	.	T	11.14	1.550895	0.27739	.	.	ENSG00000257335	ENST00000465654;ENST00000549489;ENST00000475668;ENST00000548812	T;D	0.85702	-0.79;-2.02	5.22	2.71	0.32032	Glycoside hydrolase-type carbohydrate-binding (1);	0.138996	0.33875	N	0.004470	T	0.76814	0.4040	L	0.49640	1.575	0.09310	N	1	B	0.10296	0.003	B	0.11329	0.006	T	0.59273	-0.7485	10	0.21014	T	0.42	.	6.3621	0.21435	0.1454:0.0:0.3461:0.5085	.	180	O43451	MGA_HUMAN	T	180;180;180;57	ENSP00000419372:S180T;ENSP00000447378:S180T	ENSP00000316431:S57T	S	+	1	0	MGAM	141367332	0.000000	0.05858	0.748000	0.31131	0.979000	0.70002	-1.353000	0.02617	0.985000	0.38656	0.460000	0.39030	TCT	.	.	.	none		0.348	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			A	141720863	T	A	141720863	3	1	191	1	0	0	0	0	1	0	0	0	9548	1435	50	5	552	5	MGAM	7	141720863	Missense_Mutation	SNP	T	TCGA-GL-A9DD-01A-11D-A36X-10	23892519	141720863	17417800	53	11346											
ZNF786	136051	hgsc.bcm.edu	37	chr7	148767517	148767517	+	Nonstop_Mutation	SNP	A	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	tggatgtcccactctgcctcAactccaatcggcctctatca	8	11	6	16	1	4	0	2	0	2	0	7	1	6	1	4	2	2	0	4	2	3	1			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr7:148767517A>C	ENST00000491431.1	-	4	2411	c.2347T>G	c.(2347-2349)Tga>Gga	p.*783G	ZNF786_ENST00000451334.3_Nonstop_Mutation_p.*746G|ZNF786_ENST00000316286.9_Nonstop_Mutation_p.*697G	NM_152411.3	NP_689624.2	Q8N393	ZN786_HUMAN	zinc finger protein 786	0					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|cervix(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(2)	26	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			ACTCTGCCTCAACTCCAATCG	0.498																																					p.X783G		Atlas-SNP	.											.	ZNF786	69	.	0			c.T2347G						PASS	.						270	264	266					7																	148767517		2011	4186	6197	SO:0001578	stop_lost	136051	exon4			TGCCTCAACTCCA	AK095701, AL834510	CCDS47738.1	7q36.1	2013-01-08			ENSG00000197362	ENSG00000197362		"Zinc fingers, C2H2-type", "-"	21806	protein-coding gene	gene with protein product							Standard	NM_152411		Approved	DKFZp762I137	uc003wfh.2	Q8N393	OTTHUMG00000158975	ENST00000491431.1:c.2347T>G	chr7.hg19:g.148767517A>C	ENSP00000417470:p.*783Argext*9	67.0	0.0	.		91.0	34.0	.	NM_152411	A1A568|B4DMI1	Missense_Mutation	SNP	ENST00000491431.1	hg19	CCDS47738.1	.	.	.	.	.	.	.	.	.	.	A	13.42	2.232594	0.39498	.	.	ENSG00000197362	ENST00000316286;ENST00000491431;ENST00000451334	.	.	.	4.62	4.62	0.57501	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.3575	0.43974	1.0:0.0:0.0:0.0	.	.	.	.	G	697;783;746	.	.	X	-	1	0	ZNF786	148398450	0.027000	0.19231	0.997000	0.53966	0.787000	0.44495	1.219000	0.32479	1.954000	0.56735	0.482000	0.46254	TGA	.	.	.	none		0.498	ZNF786-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352751.1	NM_152411		C	148767517	A	C	148767517	4	2	191	1	0	0	0	0	0	0	0	0	18170	143	5	5	5	5	ZNF786	7	148767517	Nonstop_Mutation	SNP	A	TCGA-GL-A9DD-01A-11D-A36X-10	7046654	148767517	10371146	54	11347											
ABP1	26	hgsc.bcm.edu	37	chr7	150554944	150554944	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcaactgtctacaattatgaTtacatttgggactttatctt	11	18	5	7	0	3	1	1	1	2	0	3	2	3	2	0	1	3	0	0	1	6	7			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr7:150554944T>C	ENST00000493429.1	+	4	1970	c.1386T>C	c.(1384-1386)gaT>gaC	p.D462D	AOC1_ENST00000467291.1_Silent_p.D462D|AOC1_ENST00000360937.4_Silent_p.D462D|AOC1_ENST00000416793.2_Silent_p.D462D			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	462					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)	ACAATTATGATTACATTTGGG	0.527																																					p.D462D		Atlas-SNP	.											.	ABP1	92	.	0			c.T1386C						PASS	.						71	78	76					7																	150554944		2077	4222	6299	SO:0001819	synonymous_variant	26	exon2			TTATGATTACATT	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.1386T>C	chr7.hg19:g.150554944T>C		51.0	0.0	.		63.0	23.0	.	NM_001091	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Silent	SNP	ENST00000493429.1	hg19	CCDS43679.1																																																																																			.	.	.	none		0.527	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091		C	150554944	T	C	150554944	2	2	191	1	0	0	0	0	0	0	0	1	98	1490	52	3		3	ABP1	7	150554944	Silent	SNP	T	TCGA-GL-A9DD-01A-11D-A36X-10	1787427	150554944	8583719	55	11348											
MLL3	58508	hgsc.bcm.edu	37	chr7	151856014	151856014	+	Frame_Shift_Del	DEL	C	C	-																															ttctcctcttcgtcctttttCcttttctttgagcgaggtgc																										TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr7:151856014delC	ENST00000262189.6	-	44	11822	c.11604delG	c.(11602-11604)aggfs	p.R3868fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.R3868fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	3868					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)										CGTCCTTTTTCCTTTTCTTTG	0.463																																					p.K3869fs		Atlas-Indel,Pindel	.											.	MLL3	1564	.	0			c.11605delA						PASS	.						356	320	332					7																	151856014		2203	4300	6503	SO:0001589	frameshift_variant	58508	exon44			.	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.11604delG	chr7.hg19:g.151856014delC	ENSP00000262189:p.Arg3868fs	63.0	0.0	0		98.0	14.0	0.142857	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	hg19	CCDS5931.1																																																																																			.	.	.	none		0.463	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			-	151856014	C	-	151856014	7	5	191	1	0	1	0	1	0	0	0	0	9629	854	30	0	3195	0	MLL3	7	151856014	Frame_Shift_Del	DEL	C	TCGA-GL-A9DD-01A-11D-A36X-10	1301070	151856014	7282649	56	11349											
TNFRSF10D	8793	hgsc.bcm.edu	37	chr8	23012460	23012460	+	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	gtctgctggggaacttcgtcCtgccgggggatggtggcaga	5	9	18	9	2	1	1	0	0	1	1	3	3	2	3	2	6	3	2	2	6	1	1			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr8:23012460C>A	ENST00000312584.3	-	2	277	c.183G>T	c.(181-183)caG>caT	p.Q61H		NM_003840.4	NP_003831.2	Q9UBN6	TR10D_HUMAN	tumor necrosis factor receptor superfamily, member 10d, decoy with truncated death domain	61					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)		GAACTTCGTCCTGCCGGGGGA	0.582																																					p.Q61H		Atlas-SNP	.											.	TNFRSF10D	21	.	0			c.G183T						PASS	.						55	49	51					8																	23012460		2203	4300	6503	SO:0001583	missense	8793	exon2			TTCGTCCTGCCGG	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.183G>T	chr8.hg19:g.23012460C>A	ENSP00000310263:p.Gln61His	73.0	0.0	.		78.0	13.0	.	NM_003840	B2R8W0|Q9Y6Q4	Missense_Mutation	SNP	ENST00000312584.3	hg19	CCDS6038.1	.	.	.	.	.	.	.	.	.	.	c	5.149	0.213132	0.09757	.	.	ENSG00000173530	ENST00000312584	D	0.83755	-1.76	1.72	0.824	0.18818	.	11.086800	0.00691	U	0.000727	T	0.77592	0.4153	L	0.52573	1.65	0.09310	N	1	B	0.21381	0.055	B	0.18263	0.021	T	0.53954	-0.8365	10	0.30078	T	0.28	.	4.0905	0.09967	0.0:0.7771:0.0:0.2229	.	61	Q9UBN6	TR10D_HUMAN	H	61	ENSP00000310263:Q61H	ENSP00000310263:Q61H	Q	-	3	2	TNFRSF10D	23068405	0.000000	0.05858	0.003000	0.11579	0.004000	0.04260	-1.049000	0.03514	0.303000	0.22785	0.313000	0.20887	CAG	.	.	.	none		0.582	TNFRSF10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215135.1			A	23012460	C	A	23012460	3	1	191	1	0	0	0	0	1	0	0	0	16295	680	24	4	1009	4	TNFRSF10D	8	23012460	Missense_Mutation	SNP	C	TCGA-GL-A9DD-01A-11D-A36X-10		23012460	123351562	57	11350											
TG	7038	hgsc.bcm.edu	37	chr8	133953675	133953675	+	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	ctttctggattgtacaacccCattgtgttctcagcctcagg	7	14	8	12	0	3	0	2	0	2	0	4	1	3	1	3	2	3	2	3	2	2	5	rs142766592		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr8:133953675C>A	ENST00000220616.4	+	26	5161	c.5121C>A	c.(5119-5121)ccC>ccA	p.P1707P	TG_ENST00000377869.1_Silent_p.P1650P|TG_ENST00000542445.1_Intron	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1707					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)		TGTACAACCCCATTGTGTTCT	0.502																																					p.P1707P		Atlas-SNP	.											.	TG	416	.	0			c.C5121A						PASS	.						171	144	153					8																	133953675		2203	4300	6503	SO:0001819	synonymous_variant	7038	exon26			CAACCCCATTGTG	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.5121C>A	chr8.hg19:g.133953675C>A		113.0	0.0	.		111.0	23.0	.	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	hg19	CCDS34944.1																																																																																			.	C|1.000;T|0.000	.	alt		0.502	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		A	133953675	C	A	133953675	2	1	191	1	0	0	0	0	0	0	0	1	15825	581	21	4		4	TG	8	133953675	Silent	SNP	C	TCGA-GL-A9DD-01A-11D-A36X-10	110941215	133953675	12410347	58	11351											
PLEC	5339	hgsc.bcm.edu	37	chr8	144999275	144999275	+	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	tgcccgccgctcagcctcctCccgcagctgtgccacagcca	5	6	9	21	3	1	0	1	0	0	0	3	0	3	0	7	0	5	3	7	0	0	0			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr8:144999275C>T	ENST00000322810.4	-	31	5402	c.5233G>A	c.(5233-5235)Gag>Aag	p.E1745K	PLEC_ENST00000354589.3_Missense_Mutation_p.E1608K|PLEC_ENST00000527096.1_Missense_Mutation_p.E1631K|PLEC_ENST00000356346.3_Missense_Mutation_p.E1594K|PLEC_ENST00000357649.2_Missense_Mutation_p.E1612K|PLEC_ENST00000345136.3_Missense_Mutation_p.E1608K|PLEC_ENST00000436759.2_Missense_Mutation_p.E1635K|PLEC_ENST00000354958.2_Missense_Mutation_p.E1586K|PLEC_ENST00000398774.2_Missense_Mutation_p.E1576K	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	1745	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						TCAGCCTCCTCCCGCAGCTGT	0.711																																					p.E1745K		Atlas-SNP	.											.	PLEC	1144	.	0			c.G5233A						PASS	.						3	3	3					8																	144999275		1885	3799	5684	SO:0001583	missense	5339	exon31			CCTCCTCCCGCAG	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.5233G>A	chr8.hg19:g.144999275C>T	ENSP00000323856:p.Glu1745Lys	204.0	0.0	.		197.0	42.0	.	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	hg19	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.946650	0.73672	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.77877	-1.09;-1.08;-1.13;-1.13;-1.07;-1.09;-1.08;-1.09;-1.08	4.71	4.71	0.59529	.	0.187621	0.31010	U	0.008426	D	0.86389	0.5921	M	0.72894	2.215	0.48288	D	0.999622	P;P;P;P;P;P;D;P	0.71674	0.908;0.908;0.908;0.851;0.908;0.908;0.998;0.908	P;P;P;B;P;P;D;P	0.67900	0.492;0.492;0.492;0.297;0.492;0.492;0.954;0.492	D	0.86228	0.1635	10	0.39692	T	0.17	.	17.273	0.87107	0.0:1.0:0.0:0.0	.	1635;1594;1586;1745;1576;1608;1612;1608	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	K	1608;1612;1608;1576;1745;1586;1594;1635;1631	ENSP00000344848:E1608K;ENSP00000350277:E1612K;ENSP00000346602:E1608K;ENSP00000381756:E1576K;ENSP00000323856:E1745K;ENSP00000347044:E1586K;ENSP00000348702:E1594K;ENSP00000388180:E1635K;ENSP00000434583:E1631K	ENSP00000323856:E1745K	E	-	1	0	PLEC	145071263	0.980000	0.34600	0.989000	0.46669	0.959000	0.62525	3.143000	0.50608	2.166000	0.68216	0.542000	0.68232	GAG	.	.	.	none		0.711	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		T	144999275	C	T	144999275	3	4	191	1	0	0	0	0	1	0	0	0	12059	864	30	2	8829	2	PLEC	8	144999275	Missense_Mutation	SNP	C	TCGA-GL-A9DD-01A-11D-A36X-10	11045600	144999275	1364747	59	11352											
PTPRD	5789	hgsc.bcm.edu	37	chr9	8341183	8341183	+	Missense_Mutation	SNP	A	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	ttgtggattcatatggcataAtattaacaaggcgatttttg	12	16	9	4	1	1	0	1	0	0	0	1	2	1	1	0	3	1	1	0	3	5	8			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr9:8341183A>C	ENST00000381196.4	-	38	5576	c.5033T>G	c.(5032-5034)aTt>aGt	p.I1678S	PTPRD_ENST00000397617.3_Missense_Mutation_p.I1271S|PTPRD_ENST00000358503.5_Missense_Mutation_p.I1656S|PTPRD_ENST00000397611.3_Missense_Mutation_p.I1268S|PTPRD_ENST00000537002.1_Missense_Mutation_p.I1268S|PTPRD_ENST00000540109.1_Missense_Mutation_p.I1678S|PTPRD_ENST00000397606.3_Missense_Mutation_p.I1271S|PTPRD_ENST00000355233.5_Missense_Mutation_p.I1272S|PTPRD_ENST00000356435.5_Missense_Mutation_p.I1678S|PTPRD_ENST00000360074.4_Missense_Mutation_p.I1665S|PTPRD_ENST00000486161.1_Missense_Mutation_p.I1271S	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1678	Tyrosine-protein phosphatase 2. {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)		ATATGGCATAATATTAACAAG	0.398										TSP Lung(15;0.13)																											p.I1678S		Atlas-SNP	.											.	PTPRD	1348	.	0			c.T5033G						PASS	.						195	206	202					9																	8341183		2203	4300	6503	SO:0001583	missense	5789	exon41			GGCATAATATTAA	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.5033T>G	chr9.hg19:g.8341183A>C	ENSP00000370593:p.Ile1678Ser	152.0	0.0	.		141.0	30.0	.	NM_002839	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	hg19	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.030464	0.75504	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606	D;D;D;D;D;D;D;D;D;D;D	0.85629	-2.01;-2.01;-2.01;-2.01;-2.01;-2.01;-2.01;-2.01;-2.01;-2.01;-2.01	6.07	6.07	0.98685	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.049513	0.85682	D	0.000000	D	0.95417	0.8512	H	0.97365	3.99	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	0.994;0.994;0.994;0.994;1.0;0.992;1.0;0.996;0.999	D;D;D;D;D;D;D;D;D	0.97110	0.988;0.988;0.988;0.988;1.0;0.979;0.999;0.994;0.999	D	0.96950	0.9694	9	.	.	.	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	1271;1262;1271;1272;1268;1268;1665;1678;1678	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	S	1678;1678;1665;1656;1272;1271;1268;1268;1149;1678;1271;1271	ENSP00000370593:I1678S;ENSP00000348812:I1678S;ENSP00000353187:I1665S;ENSP00000351293:I1656S;ENSP00000347373:I1272S;ENSP00000380741:I1271S;ENSP00000380735:I1268S;ENSP00000440515:I1268S;ENSP00000438164:I1678S;ENSP00000417093:I1271S;ENSP00000380731:I1271S	.	I	-	2	0	PTPRD	8331183	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.287000	0.95975	2.326000	0.78906	0.533000	0.62120	ATT	.	.	.	none		0.398	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			C	8341183	A	C	8341183	3	2	191	1	0	0	0	0	1	0	0	0	12812	101	4	5	729	5	PTPRD	9	8341183	Missense_Mutation	SNP	A	TCGA-GL-A9DD-01A-11D-A36X-10		8341183	132872248	60	11353											
PSIP1	11168	hgsc.bcm.edu	37	chr9	15472713	15472713	+	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	cctttcagcatattccttctGtgagcagtctgaaagttcct	8	15	7	11	0	3	2	1	2	2	0	5	2	5	2	3	0	2	3	3	0	2	5			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr9:15472713G>T	ENST00000380733.4	-	10	1237	c.894C>A	c.(892-894)caC>caA	p.H298Q	PSIP1_ENST00000380716.4_Missense_Mutation_p.H298Q|PSIP1_ENST00000380715.1_Missense_Mutation_p.H298Q|PSIP1_ENST00000397519.2_Missense_Mutation_p.H298Q|PSIP1_ENST00000380738.4_Missense_Mutation_p.H298Q			O75475	PSIP1_HUMAN	PC4 and SFRS1 interacting protein 1	298					establishment of integrated proviral latency (GO:0075713)|mRNA 5'-splice site recognition (GO:0000395)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to heat (GO:0009408)|response to oxidative stress (GO:0006979)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear heterochromatin (GO:0005720)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription coactivator activity (GO:0001105)|supercoiled DNA binding (GO:0097100)			breast(2)|endometrium(2)|kidney(1)|lung(3)|prostate(1)	9				GBM - Glioblastoma multiforme(50;2.38e-06)		TATTCCTTCTGTGAGCAGTCT	0.368																																					p.H298Q		Atlas-SNP	.											.	PSIP1	93	.	0			c.C894A						PASS	.						185	163	170					9																	15472713		2203	4300	6503	SO:0001583	missense	11168	exon9			CCTTCTGTGAGCA	AF098482	CCDS6479.1, CCDS6480.1	9p22.2	2008-02-05	2004-02-24		ENSG00000164985	ENSG00000164985			9527	protein-coding gene	gene with protein product		603620	"PC4 and SFRS1 interacting protein 2"	PSIP2		9822615, 9885563	Standard	NM_033222		Approved	p52, LEDGF, p75	uc003zlw.4	O75475	OTTHUMG00000021021	ENST00000380733.4:c.894C>A	chr9.hg19:g.15472713G>T	ENSP00000370109:p.His298Gln	70.0	0.0	.		64.0	6.0	.	NM_021144	D3DRI9|O00256|O95368|Q6P391|Q86YB9|Q9NZI3|Q9UER6	Missense_Mutation	SNP	ENST00000380733.4	hg19	CCDS6479.1	.	.	.	.	.	.	.	.	.	.	G	16.21	3.058992	0.55325	.	.	ENSG00000164985	ENST00000380733;ENST00000380738;ENST00000380715;ENST00000380716;ENST00000397519	T;T;T;T;T	0.42131	1.0;1.0;0.99;0.98;0.98	6.07	0.269	0.15631	.	0.271857	0.42420	N	0.000704	T	0.26774	0.0655	L	0.35723	1.085	0.28008	N	0.935038	B;B	0.12013	0.005;0.003	B;B	0.10450	0.005;0.001	T	0.16394	-1.0404	10	0.23302	T	0.38	.	7.352	0.26697	0.3068:0.1518:0.5415:0.0	.	298;298	O75475-2;O75475	.;PSIP1_HUMAN	Q	298	ENSP00000370109:H298Q;ENSP00000370114:H298Q;ENSP00000370091:H298Q;ENSP00000370092:H298Q;ENSP00000380653:H298Q	ENSP00000370091:H298Q	H	-	3	2	PSIP1	15462713	1.000000	0.71417	0.990000	0.47175	0.971000	0.66376	1.086000	0.30853	-0.146000	0.11274	0.585000	0.79938	CAC	.	.	.	none		0.368	PSIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055445.1	NM_033222		T	15472713	G	T	15472713	3	4	191	1	0	0	0	0	1	0	0	0	12673	1368	48	4	755	4	PSIP1	9	15472713	Missense_Mutation	SNP	G	TCGA-GL-A9DD-01A-11D-A36X-10	7131530	15472713	125740718	61	11354											
MAPKAP1	79109	hgsc.bcm.edu	37	chr9	128347834	128347834	+	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	ccaaaaagagaatggattacTtgagcttcggctcccgtcct	11	10	9	11	2	0	2	0	1	0	1	3	4	2	3	3	2	2	2	3	2	4	3			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr9:128347834T>C	ENST00000373498.1	-	4	739	c.671A>G	c.(670-672)aAt>aGt	p.N224S	MAPKAP1_ENST00000394063.1_Splice_Site_p.N32S|MAPKAP1_ENST00000373503.3_Splice_Site_p.N32S|MAPKAP1_ENST00000265960.3_Splice_Site_p.N224S|MAPKAP1_ENST00000350766.3_Splice_Site_p.N224S|MAPKAP1_ENST00000373497.5_Splice_Site_p.K32R|MAPKAP1_ENST00000373511.2_Splice_Site_p.N224S|MAPKAP1_ENST00000394060.3_Splice_Site_p.N224S			Q9BPZ7	SIN1_HUMAN	mitogen-activated protein kinase associated protein 1	224	Interaction with NBN.				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						AATGGATTACTTGAGCTTCGG	0.537																																					p.N224S		Atlas-SNP	.											.	MAPKAP1	68	.	0			c.A671G						PASS	.						108	94	98					9																	128347834		2203	4300	6503	SO:0001630	splice_region_variant	79109	exon5			GATTACTTGAGCT	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.671+1A>G	chr9.hg19:g.128347834T>C		74.0	0.0	.		55.0	11.0	.	NM_001006618	A8K1Z5|B1AMA4|B7Z309|Q00426|Q5JSV5|Q5JSV6|Q5JSV9|Q658R0|Q699U1|Q699U2|Q699U3|Q699U4|Q6GVJ0|Q6GVJ1|Q6GVJ2	Missense_Mutation	SNP	ENST00000373498.1	hg19	CCDS35140.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.98|16.98	3.270351|3.270351	0.59540|0.59540	.|.	.|.	ENSG00000119487|ENSG00000119487	ENST00000373497|ENST00000373511;ENST00000350766;ENST00000373503;ENST00000373498;ENST00000265960;ENST00000394063;ENST00000420643;ENST00000394060;ENST00000427078;ENST00000468896	.|.	.|.	.|.	5.86|5.86	5.86|5.86	0.93980|0.93980	.|.	.|0.040219	.|0.85682	.|D	.|0.000000	T|T	0.43809|0.43809	0.1264|0.1264	L|L	0.48362|0.48362	1.52|1.52	0.26792|0.26792	N|N	0.969376|0.969376	P|B;B;B;B;B	0.38711|0.28933	0.643|0.228;0.228;0.034;0.169;0.074	B|B;B;B;B;B	0.36567|0.30855	0.228|0.121;0.085;0.062;0.115;0.08	T|T	0.35699|0.35699	-0.9778|-0.9778	7|8	.|.	.|.	.|.	-7.1874|-7.1874	15.448|15.448	0.75248|0.75248	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	32|224;224;224;224;224	B7Z5E5|Q9BPZ7-6;Q9BPZ7-5;Q9BPZ7-3;Q9BPZ7-2;Q9BPZ7	.|.;.;.;.;SIN1_HUMAN	R|S	32|224;224;32;224;224;32;32;224;32;125	.|.	.|.	K|N	-|-	2|2	0|0	MAPKAP1|MAPKAP1	127387655|127387655	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.966000|0.966000	0.64601|0.64601	4.118000|4.118000	0.57884|0.57884	2.240000|2.240000	0.73641|0.73641	0.533000|0.533000	0.62120|0.62120	AAA|AAT	.	.	.	none		0.537	MAPKAP1-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054092.1		Missense_Mutation	C	128347834	T	C	128347834	5	2	191	1	0	0	0	0	0	0	1	0	9295	1623	56	3	947	3	MAPKAP1	9	128347834	Splice_Site	SNP	T	TCGA-GL-A9DD-01A-11D-A36X-10	112875121	128347834	12865597	62	11355											
POMT1	10585	hgsc.bcm.edu	37	chr9	134394275	134394276	+	Frame_Shift_Del	DEL	GG	GG	-																															atcggcaactggagatcgtcGgggagaagctgtcccggggc																								rs376882399		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr9:134394275_134394276delGG	ENST00000372228.3	+	15	1662_1663	c.1483_1484delGG	c.(1483-1485)gggfs	p.G495fs	POMT1_ENST00000485278.1_3'UTR|POMT1_ENST00000423007.1_Frame_Shift_Del_p.G473fs|POMT1_ENST00000541219.1_Frame_Shift_Del_p.G251fs|POMT1_ENST00000354713.4_Frame_Shift_Del_p.G443fs|POMT1_ENST00000341012.7_Frame_Shift_Del_p.G419fs|POMT1_ENST00000404875.2_Frame_Shift_Del_p.G356fs|POMT1_ENST00000402686.3_Frame_Shift_Del_p.G473fs|POMT1_ENST00000419118.2_Frame_Shift_Del_p.G321fs|RP11-334J6.6_ENST00000415423.1_RNA	NM_007171.3	NP_009102	Q9Y6A1	POMT1_HUMAN	protein-O-mannosyltransferase 1	495	MIR 3. {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)		GGAGATCGTCGGGGAGAAGCTG	0.673																																					p.494_495del		Atlas-Indel,Pindel	.											.	POMT1	59	.	0			c.1482_1483del						PASS	.																																			SO:0001589	frameshift_variant	10585	exon15			.	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.1483_1484delGG	chr9.hg19:g.134394277_134394278delGG	ENSP00000361302:p.Gly495fs	124.0	0.0	0		110.0	17.0	0.154545	NM_007171	B3KQG0|B4DIF0|Q5JT01|Q5JT06|Q5JT08|Q8NC91|Q8TCA9|Q9NX32|Q9NX82|Q9UNT2	Frame_Shift_Del	DEL	ENST00000372228.3	hg19	CCDS6943.1																																																																																			.	.	.	none		0.673	POMT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054737.1	NM_007171		-	134394276	GG	-	134394275	7	5	191	1	0	1	0	1	0	0	0	0	12252	1116	39	0	1537	0	POMT1	9	134394275	Frame_Shift_Del	DEL	GG	TCGA-GL-A9DD-01A-11D-A36X-10	6046441	134394275	6819156	63	11356											
RPL7A	6130	hgsc.bcm.edu	37	chr9	136215842	136215842	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgtcgtgaagaagcaggaGgctaagaaagtggtgaatcc	13	7	15	6	1	0	4	0	2	0	2	2	5	1	5	1	3	1	3	1	3	5	1			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr9:136215842G>A	ENST00000323345.6	+	2	99	c.69G>A	c.(67-69)gaG>gaA	p.E23E	MED22_ENST00000344469.5_5'Flank|SURF1_ENST00000495952.1_5'Flank|RPL7A_ENST00000463740.1_3'UTR|RPL7A_ENST00000315731.4_5'UTR|SNORD36B_ENST00000363961.1_RNA|MED22_ENST00000343730.5_5'Flank|MED22_ENST00000371999.1_5'Flank|SNORD24_ENST00000383884.1_RNA|MED22_ENST00000471524.1_5'Flank|SNORD36C_ENST00000516733.1_RNA|MED22_ENST00000476080.1_5'Flank|MED22_ENST00000491289.1_5'Flank|SNORD36A_ENST00000362874.1_RNA	NM_000972.2	NP_000963.1	P62424	RL7A_HUMAN	ribosomal protein L7a	23					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosome biogenesis (GO:0042254)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(1)|kidney(1)|lung(3)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(145;4.93e-07)|Epithelial(140;4.09e-06)|all cancers(34;3.78e-05)		AGAAGCAGGAGGCTAAGAAAG	0.483																																					p.E23E		Atlas-SNP	.											.	RPL7A	9	.	0			c.G69A						PASS	.						51	55	54					9																	136215842		2203	4296	6499	SO:0001819	synonymous_variant	6130	exon2			GCAGGAGGCTAAG	BC005128	CCDS6965.1	9q34	2011-04-06			ENSG00000148303	ENSG00000148303		"L ribosomal proteins"	10364	protein-coding gene	gene with protein product	"surfeit 3", "PLA-X polypeptide", "surfeit locus protein 3", "60S ribosomal protein L7a", ";", "thyroid hormone receptor uncoupling protein"	185640				2403926, 2966065	Standard	NM_000972		Approved	SURF3, TRUP, L7A	uc004cde.1	P62424	OTTHUMG00000020864	ENST00000323345.6:c.69G>A	chr9.hg19:g.136215842G>A		54.0	0.0	.		50.0	9.0	.	NM_000972	P11518|Q5T8U4	Silent	SNP	ENST00000323345.6	hg19	CCDS6965.1																																																																																			.	.	.	none		0.483	RPL7A-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054869.1	NM_000972		A	136215842	G	A	136215842	2	1	191	1	0	0	0	0	0	0	0	1	13613	991	35	2		2	RPL7A	9	136215842	Silent	SNP	G	TCGA-GL-A9DD-01A-11D-A36X-10	1821567	136215842	4997589	64	11357											
SNAPC4	6621	hgsc.bcm.edu	37	chr9	139292750	139292751	+	Splice_Site	DNP	CC	CC	AA																															ggctaggtacaaggggcttaCctgcttcagaatctgactcg																								rs7031489	byFrequency	TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr9:139292750_139292751CC>AA	ENST00000298532.2	-	1	498_499	c.130_131GG>TT	c.(130-132)GGt>TTt	p.G44F		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)		AAGGGGCTTACCTGCTTCAGAA	0.554																																					.|p.D44Y		Atlas-SNP	.											SNAPC4,NS,malignant_melanoma,0,1|.	SNAPC4	82	.	0			c.130+1G>T|c.G130T						PASS	.																																			SO:0001630	splice_region_variant	6621	exon2|exon1			GGCTTACCTGCTT|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_131delinsAA	chr9.hg19:g.139292750_139292751delinsAA		74.0|73.0	0.0	.		55.0|59.0	14.0	.	NM_003086		Splice_Site|Missense_Mutation	SNP	ENST00000298532.2	hg19	CCDS6998.1																																																																																			.	.|C|0.991;T|0.009	.	none|alt		0.554	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	Missense_Mutation	AA	139292751	CC	AA	139292750	5	1	191	1	0	0	0	0	0	0	1	0	14850	521	18	4	4366	4	SNAPC4	9	139292750	Splice_Site	DNP	CC	TCGA-GL-A9DD-01A-11D-A36X-10	3076908	139292750	1920681	65	11358											
PIP4K2A	5305	hgsc.bcm.edu	37	chr10	22862322	22862322	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catatatttcaactccatcaAcattaagccggtacatgccc	13	11	4	13	1	2	0	2	0	0	0	3	0	3	0	3	1	5	1	3	1	6	5			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr10:22862322A>G	ENST00000376573.4	-	5	785	c.557T>C	c.(556-558)gTt>gCt	p.V186A	PIP4K2A_ENST00000545335.1_Missense_Mutation_p.V127A|PIP4K2A_ENST00000323883.7_Missense_Mutation_p.V32A|PIP4K2A_ENST00000422321.1_5'UTR	NM_005028.4	NP_005019.2	P48426	PI42A_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	186	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						AACTCCATCAACATTAAGCCG	0.388																																					p.V186A		Atlas-SNP	.											.	PIP4K2A	59	.	0			c.T557C						PASS	.						116	99	105					10																	22862322		2203	4300	6503	SO:0001583	missense	5305	exon5			CCATCAACATTAA	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.557T>C	chr10.hg19:g.22862322A>G	ENSP00000365757:p.Val186Ala	122.0	0.0	.		128.0	19.0	.	NM_005028	B0YJ66|B4DGX2|D3DRV1|P53807|Q5VUX3	Missense_Mutation	SNP	ENST00000376573.4	hg19	CCDS7141.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.723888	0.89298	.	.	ENSG00000150867	ENST00000376573;ENST00000323883;ENST00000545335;ENST00000422321;ENST00000376565	T;T;T	0.31510	1.49;1.49;1.49	5.5	5.5	0.81552	Phosphatidylinositol-4-phosphate 5-kinase, core (2);Phosphatidylinositol-4-phosphate 5-kinase, core, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.52125	0.1715	M	0.72479	2.2	0.80722	D	1	B;P	0.45240	0.261;0.854	B;P	0.59012	0.42;0.85	T	0.47971	-0.9075	10	0.39692	T	0.17	-29.164	15.9002	0.79369	1.0:0.0:0.0:0.0	.	32;186	B4DH09;P48426	.;PI42A_HUMAN	A	186;32;127;138;145	ENSP00000365757:V186A;ENSP00000326294:V32A;ENSP00000442098:V127A	ENSP00000326294:V32A	V	-	2	0	PIP4K2A	22902328	1.000000	0.71417	0.928000	0.36995	0.962000	0.63368	8.865000	0.92300	2.219000	0.72066	0.533000	0.62120	GTT	.	.	.	none		0.388	PIP4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047193.1	NM_005028		G	22862322	A	G	22862322	3	3	191	1	0	0	0	0	1	0	0	0	11943	43	2	3	687	3	PIP4K2A	10	22862322	Missense_Mutation	SNP	A	TCGA-GL-A9DD-01A-11D-A36X-10		22862322	112672425	66	11359											
JMJD1C	221037	hgsc.bcm.edu	37	chr10	64976992	64976992	+	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	cattcataacgatcatggtgCgggtgaagagatcatgatga	13	10	12	6	2	3	4	3	3	0	1	3	6	3	4	0	2	2	0	0	2	2	2			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr10:64976992C>T	ENST00000399262.2	-	5	871	c.653G>A	c.(652-654)cGc>cAc	p.R218H	JMJD1C_ENST00000489372.2_5'UTR|JMJD1C_ENST00000542921.1_Missense_Mutation_p.R36H|JMJD1C_ENST00000402544.1_5'UTR|JMJD1C_ENST00000399251.1_5'UTR	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	218					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)					GATCATGGTGCGGGTGAAGAG	0.373																																					p.R218H		Atlas-SNP	.											.	JMJD1C	347	.	0			c.G653A						PASS	.						113	109	110					10																	64976992		1848	4104	5952	SO:0001583	missense	221037	exon5			ATGGTGCGGGTGA	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.653G>A	chr10.hg19:g.64976992C>T	ENSP00000382204:p.Arg218His	65.0	0.0	.		72.0	10.0	.	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	hg19	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	C	18.19	3.569375	0.65765	.	.	ENSG00000171988	ENST00000399262;ENST00000542921	T;T	0.13657	2.57;2.57	5.74	4.83	0.62350	.	0.255682	0.32578	U	0.005909	T	0.14013	0.0339	L	0.44542	1.39	0.80722	D	1	B	0.22541	0.071	B	0.14578	0.011	T	0.02519	-1.1147	10	0.49607	T	0.09	-5.1461	15.0302	0.71701	0.0:0.9309:0.0:0.0691	.	218	Q15652	JHD2C_HUMAN	H	218;36	ENSP00000382204:R218H;ENSP00000444682:R36H	ENSP00000382204:R218H	R	-	2	0	JMJD1C	64646998	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.696000	0.61774	2.707000	0.92482	0.557000	0.71058	CGC	.	.	.	none		0.373	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		T	64976992	C	T	64976992	3	4	191	1	0	0	0	0	1	0	0	0	7957	768	27	1	7057	1	JMJD1C	10	64976992	Missense_Mutation	SNP	C	TCGA-GL-A9DD-01A-11D-A36X-10	42114670	64976992	70557755	67	11360											
DDX21	9188	hgsc.bcm.edu	37	chr10	70734488	70734488	+	Missense_Mutation	SNP	A	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	ataataaaagcttccagcaaAgatgccatcaggtatgttcc	15	10	7	9	0	1	1	1	0	0	1	3	1	3	1	3	1	3	4	3	1	5	5			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr10:70734488A>C	ENST00000354185.4	+	11	1829	c.1731A>C	c.(1729-1731)aaA>aaC	p.K577N		NM_001256910.1|NM_004728.3	NP_001243839.1|NP_004719.2	Q9NR30	DDX21_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 21	577					ATP catabolic process (GO:0006200)|osteoblast differentiation (GO:0001649)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	20						CTTCCAGCAAAGATGCCATCA	0.368																																					p.K577N		Atlas-SNP	.											.	DDX21	57	.	0			c.A1731C						PASS	.						86	80	82					10																	70734488		2203	4300	6503	SO:0001583	missense	9188	exon11			CAGCAAAGATGCC	U41387	CCDS31211.1, CCDS73144.1	10q21	2013-05-13	2012-02-23		ENSG00000165732	ENSG00000165732		"DEAD-boxes"	2744	protein-coding gene	gene with protein product		606357	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 21", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 21"			8614622, 18180292	Standard	NM_004728		Approved	RH-II/GU, GURDB	uc001jov.2	Q9NR30	OTTHUMG00000018366	ENST00000354185.4:c.1731A>C	chr10.hg19:g.70734488A>C	ENSP00000346120:p.Lys577Asn	91.0	0.0	.		101.0	24.0	.	NM_004728	B2RDL0|Q13436|Q5VX41|Q68D35	Missense_Mutation	SNP	ENST00000354185.4	hg19	CCDS31211.1	.	.	.	.	.	.	.	.	.	.	A	11.31	1.600031	0.28534	.	.	ENSG00000165732	ENST00000354185	T	0.18502	2.21	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.12860	0.0312	L	0.33293	1	0.48511	D	0.999665	B	0.24823	0.112	B	0.15870	0.014	T	0.09185	-1.0686	10	0.33141	T	0.24	-11.3454	10.2563	0.43399	0.7547:0.0:0.0:0.2453	.	577	Q9NR30	DDX21_HUMAN	N	577	ENSP00000346120:K577N	ENSP00000346120:K577N	K	+	3	2	DDX21	70404494	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.750000	0.38329	2.171000	0.68590	0.533000	0.62120	AAA	.	.	.	none		0.368	DDX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048374.1	NM_004728		C	70734488	A	C	70734488	3	2	191	1	0	0	0	0	1	0	0	0	4351	69	3	5	1773	5	DDX21	10	70734488	Missense_Mutation	SNP	A	TCGA-GL-A9DD-01A-11D-A36X-10	5757496	70734488	64800259	68	11361											
DNAJB12	54788	hgsc.bcm.edu	37	chr10	74114543	74114543	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgcgaactcgcggcgtcggaTacagccgctgtgccttctcc	5	8	12	16	7	1	0	0	0	1	0	4	2	1	1	3	2	4	1	3	2	2	2			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr10:74114543T>C	ENST00000444643.2	-	1	445	c.113A>G	c.(112-114)tAt>tGt	p.Y38C	DNAJB12_ENST00000461919.1_5'Flank|DNAJB12_ENST00000338820.3_Missense_Mutation_p.Y72C|DNAJB12_ENST00000394903.2_Missense_Mutation_p.Y72C			Q9NXW2	DJB12_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 12	38						integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|skin(1)	4						CGGCGTCGGATACAGCCGCTG	0.632																																					p.Y72C		Atlas-SNP	.											.	DNAJB12	22	.	0			c.A215G						PASS	.						34	36	35					10																	74114543		2203	4300	6503	SO:0001583	missense	54788	exon1			GTCGGATACAGCC	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.113A>G	chr10.hg19:g.74114543T>C	ENSP00000403313:p.Tyr38Cys	44.0	0.0	.		38.0	9.0	.	NM_017626	B7Z7I3|Q9H6H0	Missense_Mutation	SNP	ENST00000444643.2	hg19		.	.	.	.	.	.	.	.	.	.	T	23.4	4.405711	0.83230	.	.	ENSG00000148719	ENST00000338820;ENST00000394903;ENST00000444643	T;T;T	0.19394	2.15;2.15;2.15	5.58	5.58	0.84498	.	0.058186	0.64402	D	0.000002	T	0.40473	0.1118	M	0.77103	2.36	0.43777	D	0.9963	D;D	0.60575	0.988;0.98	P;P	0.57548	0.823;0.671	T	0.35822	-0.9773	10	0.62326	D	0.03	-30.1516	10.6161	0.45451	0.1435:0.0:0.0:0.8565	.	38;38	Q9NXW2-2;Q9NXW2	.;DJB12_HUMAN	C	72;72;38	ENSP00000345575:Y72C;ENSP00000378363:Y72C;ENSP00000403313:Y38C	ENSP00000345575:Y72C	Y	-	2	0	DNAJB12	73784549	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	3.330000	0.52068	2.111000	0.64477	0.459000	0.35465	TAT	.	.	.	none		0.632	DNAJB12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048581.2			C	74114543	T	C	74114543	3	2	191	1	0	0	0	0	1	0	0	0	4619	1406	49	3	1046	3	DNAJB12	10	74114543	Missense_Mutation	SNP	T	TCGA-GL-A9DD-01A-11D-A36X-10	3380055	74114543	61420204	69	11362											
CPN1	1369	hgsc.bcm.edu	37	chr10	101802229	101802229	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcatctccatttctttcttTctggcttggggctgcacttt	3	19	7	12	0	5	0	1	0	4	0	6	0	5	0	1	3	1	3	1	3	0	5			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr10:101802229T>C	ENST00000370418.3	-	9	1583	c.1332A>G	c.(1330-1332)agA>agG	p.R444R		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	444					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)		TTTCTTTCTTTCTGGCTTGGG	0.542																																					p.R444R		Atlas-SNP	.											.	CPN1	62	.	0			c.A1332G						PASS	.						96	84	88					10																	101802229		2203	4300	6503	SO:0001819	synonymous_variant	1369	exon9			TTTCTTTCTGGCT	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.1332A>G	chr10.hg19:g.101802229T>C		59.0	0.0	.		61.0	7.0	.	NM_001308	B1AP59	Silent	SNP	ENST00000370418.3	hg19	CCDS7486.1																																																																																			.	.	.	none		0.542	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308		C	101802229	T	C	101802229	2	2	191	1	0	0	0	0	0	0	0	1	3811	1780	62	3		3	CPN1	10	101802229	Silent	SNP	T	TCGA-GL-A9DD-01A-11D-A36X-10	27687686	101802229	33732518	70	11363											
GPAM	57678	hgsc.bcm.edu	37	chr10	113924282	113924282	+	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	aaacaattctacaaattttaCcttgaaggaagtatagctgg	16	12	7	6	0	1	1	0	1	1	0	1	2	1	2	1	2	4	2	1	2	9	7			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr10:113924282C>A	ENST00000348367.4	-	13	1505		c.e13+1		GPAM_ENST00000423155.1_Splice_Site|GPAM_ENST00000369425.1_Splice_Site			Q9HCL2	GPAT1_HUMAN	glycerol-3-phosphate acyltransferase, mitochondrial						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)		ACAAATTTTACCTTGAAGGAA	0.348																																					.	Ovarian(161;1017 2606 18293 52943)	Atlas-SNP	.											.	GPAM	68	.	0			c.1307+1G>T						PASS	.						56	57	57					10																	113924282		2203	4300	6503	SO:0001630	splice_region_variant	57678	exon14			ATTTTACCTTGAA	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.1307+1G>T	chr10.hg19:g.113924282C>A		82.0	0.0	.		90.0	22.0	.	NM_020918	Q5VW51|Q86TA3	Splice_Site	SNP	ENST00000348367.4	hg19	CCDS7570.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.025850	0.75390	.	.	ENSG00000119927	ENST00000348367;ENST00000423155;ENST00000369425	.	.	.	5.25	5.25	0.73442	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.0238	0.86440	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GPAM	113914272	1.000000	0.71417	0.989000	0.46669	0.866000	0.49608	5.794000	0.69067	2.432000	0.82394	0.643000	0.83706	.	.	.	.	none		0.348	GPAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050377.1	NM_020918	Intron	A	113924282	C	A	113924282	5	1	191	1	0	0	0	0	0	0	1	0	6595	521	18	4	1218	4	GPAM	10	113924282	Splice_Site	SNP	C	TCGA-GL-A9DD-01A-11D-A36X-10	12122053	113924282	21610465	71	11364											
PIK3C2A	5286	hgsc.bcm.edu	37	chr11	17113603	17113603	+	Missense_Mutation	SNP	A	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	taaagggtggaagaaagtacAaacaagatcacactaagaat	21	6	9	5	0	1	3	1	0	0	3	1	4	1	4	0	2	2	1	0	2	9	3			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr11:17113603A>C	ENST00000265970.7	-	29	4581	c.4582T>G	c.(4582-4584)Tgt>Ggt	p.C1528G	PIK3C2A_ENST00000531428.1_5'UTR|PIK3C2A_ENST00000540361.1_Missense_Mutation_p.C1148G	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	1528	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				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						AAGAAAGTACAAACAAGATCA	0.318																																					p.C1528G		Atlas-SNP	.											.	PIK3C2A	148	.	0			c.T4582G						PASS	.						90	93	92					11																	17113603		2200	4294	6494	SO:0001583	missense	5286	exon29			AAGTACAAACAAG	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.4582T>G	chr11.hg19:g.17113603A>C	ENSP00000265970:p.Cys1528Gly	173.0	0.0	.		139.0	20.0	.	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	hg19	CCDS7824.1	.	.	.	.	.	.	.	.	.	.	A	18.03	3.532468	0.64972	.	.	ENSG00000011405	ENST00000265970;ENST00000540361	T;T	0.38722	1.12;1.12	5.85	5.85	0.93711	Phox homologous domain (5);	0.048833	0.85682	D	0.000000	T	0.30230	0.0758	N	0.08118	0	0.44890	D	0.9979	B;P	0.42584	0.214;0.784	B;B	0.42522	0.253;0.39	T	0.27872	-1.0061	10	0.59425	D	0.04	-5.6727	16.2473	0.82450	1.0:0.0:0.0:0.0	.	1148;1528	F5H2B0;O00443	.;P3C2A_HUMAN	G	1528;1148	ENSP00000265970:C1528G;ENSP00000438687:C1148G	ENSP00000265970:C1528G	C	-	1	0	PIK3C2A	17070179	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.854000	0.92228	2.238000	0.73509	0.533000	0.62120	TGT	.	.	.	none		0.318	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		C	17113603	A	C	17113603	3	2	191	1	0	0	0	0	1	0	0	0	11916	130	5	5	494	5	PIK3C2A	11	17113603	Missense_Mutation	SNP	A	TCGA-GL-A9DD-01A-11D-A36X-10		17113603	117892913	72	11365											
FNBP4	23360	hgsc.bcm.edu	37	chr11	47745677	47745677	+	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	atttctgtagctttcctcttTattcctttagtggaagaaga	9	18	7	7	0	2	2	0	0	2	2	4	3	4	3	2	1	1	2	2	1	5	8			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr11:47745677T>G	ENST00000263773.5	-	14	2379	c.2367A>C	c.(2365-2367)atA>atC	p.I789I	Y_RNA_ENST00000363220.1_RNA	NM_015308.2	NP_056123.2	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	789						nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	44						CTTTCCTCTTTATTCCTTTAG	0.428																																					p.I789I		Atlas-SNP	.											.	FNBP4	99	.	0			c.A2367C						PASS	.						126	126	126					11																	47745677		1874	4119	5993	SO:0001819	synonymous_variant	23360	exon14			CCTCTTTATTCCT	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.2367A>C	chr11.hg19:g.47745677T>G		72.0	0.0	.		79.0	15.0	.	NM_015308	Q9H985|Q9NT81|Q9Y2L7	Silent	SNP	ENST00000263773.5	hg19	CCDS41644.1																																																																																			.	.	.	none		0.428	FNBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390237.3			G	47745677	T	G	47745677	2	3	191	1	0	0	0	0	0	0	0	1	5974	1744	61	5		5	FNBP4	11	47745677	Silent	SNP	T	TCGA-GL-A9DD-01A-11D-A36X-10	30632074	47745677	87260839	73	11366											
WNK1	65125	hgsc.bcm.edu	37	chr12	1017829	1017829	+	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	ggcgctcaatggagtgggacGggtggcccagcaccacagcc	8	4	16	13	2	1	0	1	0	0	0	1	2	1	2	3	5	2	2	3	5	1	0			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr12:1017829G>C	ENST00000315939.6	+	28	7663	c.7020G>C	c.(7018-7020)acG>acC	p.T2340T	WNK1_ENST00000537687.1_Silent_p.T2600T|WNK1_ENST00000535572.1_Silent_p.T2092T|WNK1_ENST00000530271.2_Silent_p.T2838T|WNK1_ENST00000340908.4_Silent_p.T1933T	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	2340					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)			GGAGTGGGACGGGTGGCCCAG	0.542																																					p.T2600T	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.G7800C						PASS	.						68	64	65					12																	1017829		2203	4300	6503	SO:0001819	synonymous_variant	65125	exon28			TGGGACGGGTGGC	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.7020G>C	chr12.hg19:g.1017829G>C		107.0	0.0	.		110.0	19.0	.	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Silent	SNP	ENST00000315939.6	hg19	CCDS8506.1																																																																																			.	.	.	none		0.542	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		C	1017829	G	C	1017829	2	2	191	1	0	0	0	0	0	0	0	1	17389	1103	39	4		4	WNK1	12	1017829	Silent	SNP	G	TCGA-GL-A9DD-01A-11D-A36X-10		1017829	132834066	74	11367											
ADCY6	112	hgsc.bcm.edu	37	chr12	49171962	49171964	+	In_Frame_Del	DEL	GCT	GCT	-																															ggtctcctgaaaggcctggcGctgagacacctctgctggat																										TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	GCT	GCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr12:49171962_49171964delGCT	ENST00000307885.4	-	2	1635_1637	c.941_943delAGC	c.(940-945)cagcgc>cgc	p.Q314del	ADCY6_ENST00000552090.1_5'Flank|ADCY6_ENST00000357869.3_In_Frame_Del_p.Q314del|ADCY6_ENST00000550422.1_In_Frame_Del_p.Q314del	NM_015270.3	NP_056085.1	O43306	ADCY6_HUMAN	adenylate cyclase 6	314					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						AAGGCCTGGCGCTGAGACACCTC	0.631																																					p.314_315del		Atlas-Indel,Pindel	.											.	ADCY6	81	.	0			c.942_944del						PASS	.																																			SO:0001651	inframe_deletion	112	exon2			.		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.941_943delAGC	chr12.hg19:g.49171962_49171964delGCT	ENSP00000311405:p.Gln314del	137.0	0.0	0		159.0	61.0	0.383648	NM_015270	Q9NR75|Q9UDB0	In_Frame_Del	DEL	ENST00000307885.4	hg19	CCDS8767.1																																																																																			.	.	.	none		0.631	ADCY6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408863.1	NM_020983		-	49171964	GCT	-	49171962	7	5	191	1	0	1	0	1	0	0	0	0	298	1087	38	0	2643	0	ADCY6	12	49171962	In_Frame_Del	DEL	GCT	TCGA-GL-A9DD-01A-11D-A36X-10	48154133	49171962	84679933	75	11368											
CS	1431	hgsc.bcm.edu	37	chr12	56669848	56669848	+	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	gtatagcctaacatgttggtGaaattgtgagaccagtccag	12	11	11	7	0	0	2	0	2	0	1	1	3	1	2	3	1	2	2	3	1	4	5			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr12:56669848G>T	ENST00000351328.3	-	7	910	c.720C>A	c.(718-720)ttC>ttA	p.F240L	CS_ENST00000548567.1_Missense_Mutation_p.F174L|CS_ENST00000542324.2_Missense_Mutation_p.F227L	NM_004077.2	NP_004068.2	O75390	CISY_HUMAN	citrate synthase	240					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)		ACATGTTGGTGAAATTGTGAG	0.498																																					p.F240L		Atlas-SNP	.											.	CS	44	.	0			c.C720A						PASS	.						161	133	143					12																	56669848		2203	4300	6503	SO:0001583	missense	1431	exon7			GTTGGTGAAATTG		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.720C>A	chr12.hg19:g.56669848G>T	ENSP00000342056:p.Phe240Leu	105.0	0.0	.		146.0	28.0	.	NM_004077	Q71UT9|Q7KZH0|Q96FZ8|Q9BWN8	Missense_Mutation	SNP	ENST00000351328.3	hg19	CCDS8913.1	.	.	.	.	.	.	.	.	.	.	G	19.75	3.886371	0.72410	.	.	ENSG00000062485	ENST00000548567;ENST00000351328;ENST00000542324	.	.	.	5.41	3.56	0.40772	Citrate synthase-like, large alpha subdomain (1);Citrate synthase-like, core (1);	0.000000	0.85682	D	0.000000	T	0.41236	0.1150	L	0.41573	1.285	0.58432	D	0.999999	P;B;B;B	0.36144	0.539;0.034;0.058;0.034	B;B;B;B	0.37508	0.252;0.074;0.106;0.06	T	0.14587	-1.0467	9	0.30854	T	0.27	-16.2635	8.3037	0.32029	0.2519:0.0:0.7481:0.0	.	174;227;195;240	B7Z1E1;B4DJV2;B3KTN4;O75390	.;.;.;CISY_HUMAN	L	174;240;227	.	ENSP00000342056:F240L	F	-	3	2	CS	54956115	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.240000	0.51368	0.753000	0.32945	0.555000	0.69702	TTC	.	.	.	none		0.498	CS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408588.2	NM_004077		T	56669848	G	T	56669848	3	4	191	1	0	0	0	0	1	0	0	0	3926	1281	45	4	700	4	CS	12	56669848	Missense_Mutation	SNP	G	TCGA-GL-A9DD-01A-11D-A36X-10	7497886	56669848	77182047	76	11369											
TMTC2	160335	hgsc.bcm.edu	37	chr12	83251151	83251151	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggggccagtctcttctttcTcctctccttgctctgctaca	3	15	7	16	1	5	0	0	0	5	0	8	0	5	0	3	2	3	2	3	2	1	4			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr12:83251151T>C	ENST00000321196.3	+	2	1153	c.446T>C	c.(445-447)cTc>cCc	p.L149P	TMTC2_ENST00000549919.1_Missense_Mutation_p.L143P|TMTC2_ENST00000548305.1_Missense_Mutation_p.L149P	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2	149					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						CTCTTCTTTCTCCTCTCCTTG	0.557																																					p.L149P		Atlas-SNP	.											.	TMTC2	100	.	0			c.T446C						PASS	.						123	99	107					12																	83251151		2203	4300	6503	SO:0001583	missense	160335	exon2			TCTTTCTCCTCTC	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.446T>C	chr12.hg19:g.83251151T>C	ENSP00000322300:p.Leu149Pro	59.0	0.0	.		95.0	16.0	.	NM_152588	B2RCU7|Q8N2K8	Missense_Mutation	SNP	ENST00000321196.3	hg19	CCDS9025.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.008826	0.75046	.	.	ENSG00000179104	ENST00000321196;ENST00000548305;ENST00000549919	T;T;T	0.71698	0.03;-0.59;-0.05	5.6	5.6	0.85130	.	0.000000	0.64402	D	0.000001	D	0.88603	0.6481	H	0.95260	3.645	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	D	0.91786	0.5439	10	0.87932	D	0	-14.0917	14.6569	0.68838	0.0:0.0:0.0:1.0	.	149;149	Q8N394;F8VSH2	TMTC2_HUMAN;.	P	149;149;143	ENSP00000322300:L149P;ENSP00000448292:L149P;ENSP00000447609:L143P	ENSP00000322300:L149P	L	+	2	0	TMTC2	81775282	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.456000	0.80751	2.251000	0.74343	0.528000	0.53228	CTC	.	.	.	none		0.557	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405663.1	NM_152588		C	83251151	T	C	83251151	3	2	191	1	0	0	0	0	1	0	0	0	16273	1551	54	3	452	3	TMTC2	12	83251151	Missense_Mutation	SNP	T	TCGA-GL-A9DD-01A-11D-A36X-10	26581303	83251151	50600744	77	11370											
TBC1D4	9882	hgsc.bcm.edu	37	chr13	75898483	75898483	+	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	aaggaagtgtgaagacttggAagactggaggaagaattact	16	8	14	3	0	0	4	0	1	0	3	0	8	0	8	0	4	1	0	0	4	7	2			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr13:75898483A>T	ENST00000377636.3	-	11	2434	c.2088T>A	c.(2086-2088)ctT>ctA	p.L696L	TBC1D4_ENST00000425511.1_5'UTR|TBC1D4_ENST00000377625.2_Intron|TBC1D4_ENST00000431480.2_Silent_p.L696L	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	696	Ser-rich.				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)		GAAGACTTGGAAGACTGGAGG	0.418																																					p.L696L		Atlas-SNP	.											.	TBC1D4	142	.	0			c.T2088A						PASS	.						129	136	134					13																	75898483		1900	4112	6012	SO:0001819	synonymous_variant	9882	exon11			ACTTGGAAGACTG	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.2088T>A	chr13.hg19:g.75898483A>T		133.0	0.0	.		135.0	26.0	.	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Silent	SNP	ENST00000377636.3	hg19	CCDS41901.1																																																																																			.	.	.	none		0.418	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832		T	75898483	A	T	75898483	2	4	191	1	0	0	0	0	0	0	0	1	15634	233	9	5		5	TBC1D4	13	75898483	Silent	SNP	A	TCGA-GL-A9DD-01A-11D-A36X-10		75898483	39271395	78	11371											
IRS2	8660	hgsc.bcm.edu	37	chr13	110437628	110437628	+	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	tgacggccgagcggcccaccTcgatgaagaagaagctgtcc	10	5	13	13	4	0	4	0	2	0	2	2	6	1	4	4	2	2	1	4	2	3	0			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr13:110437628T>A	ENST00000375856.3	-	1	1287	c.773A>T	c.(772-774)gAg>gTg	p.E258V		NM_003749.2	NP_003740.2	Q9Y4H2	IRS2_HUMAN	insulin receptor substrate 2	258	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.				brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular response to glucose stimulus (GO:0071333)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid homeostasis (GO:0055088)|mammary gland development (GO:0030879)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of kinase activity (GO:0033673)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mesenchymal cell proliferation (GO:0002053)|regulation of lipid metabolic process (GO:0019216)|response to glucose (GO:0009749)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	19	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)			GCGGCCCACCTCGATGAAGAA	0.652																																					p.E258V	Melanoma(100;613 2409 40847)	Atlas-SNP	.											.	IRS2	44	.	0			c.A773T						PASS	.						11	12	12					13																	110437628		2186	4283	6469	SO:0001583	missense	8660	exon1			CCCACCTCGATGA	AB000732	CCDS9510.1	13q34	2013-01-10			ENSG00000185950	ENSG00000185950		"Pleckstrin homology (PH) domain containing"	6126	protein-coding gene	gene with protein product		600797				9312143	Standard	NM_003749		Approved		uc001vqv.3	Q9Y4H2	OTTHUMG00000017338	ENST00000375856.3:c.773A>T	chr13.hg19:g.110437628T>A	ENSP00000365016:p.Glu258Val	72.0	0.0	.		68.0	14.0	.	NM_003749	Q96RR2|Q9BZG0|Q9Y6I5	Missense_Mutation	SNP	ENST00000375856.3	hg19	CCDS9510.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.270350	0.80469	.	.	ENSG00000185950	ENST00000375856	T	0.71579	-0.58	3.61	3.61	0.41365	Pleckstrin homology-type (1);Insulin receptor substrate-1, PTB (4);	0.064380	0.64402	U	0.000013	D	0.82742	0.5103	M	0.81341	2.54	0.54753	D	0.999988	D	0.89917	1.0	D	0.91635	0.999	D	0.84437	0.0580	10	0.62326	D	0.03	-13.1799	11.3514	0.49589	0.0:0.0:0.0:1.0	.	258	Q9Y4H2	IRS2_HUMAN	V	258	ENSP00000365016:E258V	ENSP00000365016:E258V	E	-	2	0	IRS2	109235629	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	6.999000	0.76283	1.527000	0.49086	0.408000	0.27601	GAG	.	.	.	none		0.652	IRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045755.1	NM_003749		A	110437628	T	A	110437628	3	1	191	1	0	0	0	0	1	0	0	0	7848	1551	54	5	3251	5	IRS2	13	110437628	Missense_Mutation	SNP	T	TCGA-GL-A9DD-01A-11D-A36X-10	34539145	110437628	4732250	79	11372											
METTL3	56339	hgsc.bcm.edu	37	chr14	21969115	21969115	+	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	acactctgtgtaagagcaagCtcctggcttggcgtgtggtc	7	11	13	10	1	1	1	0	0	1	1	3	1	2	1	1	3	2	4	1	3	2	2			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr14:21969115C>G	ENST00000298717.4	-	5	1207	c.1056G>C	c.(1054-1056)gaG>gaC	p.E352D		NM_019852.3	NP_062826.2	Q86U44	MTA70_HUMAN	methyltransferase like 3	352					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)		TAAGAGCAAGCTCCTGGCTTG	0.507																																					p.E352D		Atlas-SNP	.											.	METTL3	48	.	0			c.G1056C						PASS	.						67	61	63					14																	21969115		2203	4300	6503	SO:0001583	missense	56339	exon5			AGCAAGCTCCTGG	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.1056G>C	chr14.hg19:g.21969115C>G	ENSP00000298717:p.Glu352Asp	130.0	0.0	.		126.0	30.0	.	NM_019852	O14736|Q86V05|Q9HB32	Missense_Mutation	SNP	ENST00000298717.4	hg19	CCDS32044.1	.	.	.	.	.	.	.	.	.	.	C	12.20	1.867899	0.32977	.	.	ENSG00000165819	ENST00000298717	.	.	.	5.5	0.761	0.18448	.	0.047580	0.85682	D	0.000000	T	0.27419	0.0673	N	0.17082	0.46	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.03761	-1.1006	9	0.16896	T	0.51	-19.8692	4.8131	0.13353	0.0:0.3033:0.1686:0.5281	.	352	Q86U44	MTA70_HUMAN	D	352	.	ENSP00000298717:E352D	E	-	3	2	METTL3	21038955	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	0.640000	0.24705	0.251000	0.21505	0.655000	0.94253	GAG	.	.	.	none		0.507	METTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401227.1	NM_019852		G	21969115	C	G	21969115	3	3	191	1	0	0	0	0	1	0	0	0	9508	796	28	4	714	4	METTL3	14	21969115	Missense_Mutation	SNP	C	TCGA-GL-A9DD-01A-11D-A36X-10		21969115	85380425	80	11373											
SGPP1	81537	hgsc.bcm.edu	37	chr14	64194241	64194241	+	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	agaacaggatgtagaagagtTcgttgcccagctccgtgccg	10	8	13	10	3	0	3	0	0	0	3	2	4	1	4	3	1	4	4	3	1	3	3			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr14:64194241T>A	ENST00000247225.6	-	1	516	c.422A>T	c.(421-423)gAa>gTa	p.E141V		NM_030791.2	NP_110418.1	Q9BX95	SGPP1_HUMAN	sphingosine-1-phosphate phosphatase 1	141					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)		GTAGAAGAGTTCGTTGCCCAG	0.642																																					p.E141V		Atlas-SNP	.											.	SGPP1	29	.	0			c.A422T						PASS	.						55	63	60					14																	64194241		2203	4300	6503	SO:0001583	missense	81537	exon1			AAGAGTTCGTTGC	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.422A>T	chr14.hg19:g.64194241T>A	ENSP00000247225:p.Glu141Val	60.0	0.0	.		51.0	9.0	.	NM_030791	B2RAH0|Q9H189	Missense_Mutation	SNP	ENST00000247225.6	hg19	CCDS9760.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.637752	0.87760	.	.	ENSG00000126821	ENST00000247225	T	0.39056	1.1	4.67	3.49	0.39957	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.60011	0.2236	M	0.75447	2.3	0.80722	D	1	D	0.89917	1.0	D	0.71414	0.973	T	0.57481	-0.7804	10	0.36615	T	0.2	4.0704	11.2511	0.49026	0.0:0.0:0.1538:0.8462	.	141	Q9BX95	SGPP1_HUMAN	V	141	ENSP00000247225:E141V	ENSP00000247225:E141V	E	-	2	0	SGPP1	63263994	1.000000	0.71417	0.972000	0.41901	0.986000	0.74619	7.914000	0.87478	0.601000	0.29879	0.379000	0.24179	GAA	.	.	.	none		0.642	SGPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072626.3	NM_030791		A	64194241	T	A	64194241	3	1	191	1	0	0	0	0	1	0	0	0	14232	1783	62	5	915	5	SGPP1	14	64194241	Missense_Mutation	SNP	T	TCGA-GL-A9DD-01A-11D-A36X-10	42225126	64194241	43155299	81	11374											
PCNX	22990	hgsc.bcm.edu	37	chr14	71518644	71518644	+	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	ctgctgtctcggccttcttcTctactccactgaaccccttt	4	15	5	17	1	3	1	0	1	3	0	6	1	4	1	4	1	3	1	4	1	2	4			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr14:71518644T>A	ENST00000304743.2	+	24	4938	c.4492T>A	c.(4492-4494)Tct>Act	p.S1498T	PCNX_ENST00000439984.3_Missense_Mutation_p.S1387T|PCNX_ENST00000238570.5_Missense_Mutation_p.S1498T	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1498						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)		GGCCTTCTTCTCTACTCCACT	0.428																																					p.S1498T		Atlas-SNP	.											.	PCNX	198	.	0			c.T4492A						PASS	.						198	188	191					14																	71518644		2203	4300	6503	SO:0001583	missense	22990	exon24			TTCTTCTCTACTC	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.4492T>A	chr14.hg19:g.71518644T>A	ENSP00000304192:p.Ser1498Thr	74.0	0.0	.		77.0	19.0	.	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	hg19	CCDS9806.1	.	.	.	.	.	.	.	.	.	.	T	17.92	3.507607	0.64410	.	.	ENSG00000100731	ENST00000304743;ENST00000238570;ENST00000439984	T;T;T	0.13420	2.96;2.72;2.59	5.84	4.66	0.58398	.	0.049858	0.85682	D	0.000000	T	0.32376	0.0827	M	0.89095	3.005	0.58432	D	0.999999	P;D;P	0.62365	0.675;0.991;0.546	B;P;B	0.58331	0.13;0.837;0.097	T	0.52786	-0.8529	10	0.02654	T	1	.	13.0601	0.59002	0.0:0.0:0.1343:0.8657	.	1498;1387;1498	Q96RV3-3;B2RTR6;Q96RV3	.;.;PCX1_HUMAN	T	1498;1498;1387	ENSP00000304192:S1498T;ENSP00000238570:S1498T;ENSP00000396617:S1387T	ENSP00000238570:S1498T	S	+	1	0	PCNX	70588397	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.907000	0.69908	0.993000	0.38866	0.455000	0.32223	TCT	.	.	.	none		0.428	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		A	71518644	T	A	71518644	3	1	191	1	0	0	0	0	1	0	0	0	11598	1551	54	5	4586	5	PCNX	14	71518644	Missense_Mutation	SNP	T	TCGA-GL-A9DD-01A-11D-A36X-10	7324403	71518644	35830896	82	11375											
TRIP11	9321	hgsc.bcm.edu	37	chr14	92469868	92469876	+	In_Frame_Del	DEL	CTCTTGTAA	CTCTTGTAA	-																															atagaaaacttcatgttagtCtcttgtaacgcttgatattc																								rs528054481		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	CTCTTGTAA	CTCTTGTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr14:92469868_92469876delCTCTTGTAA	ENST00000267622.4	-	11	4817_4825	c.4444_4452delTTACAAGAG	c.(4444-4452)ttacaagagdel	p.LQE1482del		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	1482					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)		TCATGTTAGTCTCTTGTAACGCTTGATAT	0.368			T	PDGFRB	AML																																p.1482_1485del	Ovarian(84;609 1888 9852 42686)	Atlas-Indel,Pindel	.		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	.	TRIP11	184	.	0			c.4445_4453del						PASS	.																																			SO:0001651	inframe_deletion	9321	exon11			.	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.4444_4452delTTACAAGAG	chr14.hg19:g.92469868_92469876delCTCTTGTAA	ENSP00000267622:p.Leu1482_Glu1484del	83.0	0.0	0		99.0	13.0	0.131313	NM_004239	B2RUT2|O14689|O15154|O95949	In_Frame_Del	DEL	ENST00000267622.4	hg19	CCDS9899.1																																																																																			.	.	.	none		0.368	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1			-	92469876	CTCTTGTAA	-	92469868	7	5	191	1	0	1	0	1	0	0	0	0	16567	912	32	0	1531	0	TRIP11	14	92469868	In_Frame_Del	DEL	CTCTTGTAA	TCGA-GL-A9DD-01A-11D-A36X-10	20951224	92469868	14879672	83	11376											
DDX24	57062	hgsc.bcm.edu	37	chr14	94527306	94527306	+	Missense_Mutation	SNP	T	T	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	taatgcttttctttaattaaTtcccacagccggcctggagt	9	15	7	10	1	1	0	0	0	1	0	2	1	2	1	3	2	2	1	3	2	3	7			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr14:94527306T>G	ENST00000330836.5	-	4	1481	c.1350A>C	c.(1348-1350)gaA>gaC	p.E450D	DDX24_ENST00000544005.1_Missense_Mutation_p.E200D|DDX24_ENST00000555054.1_Missense_Mutation_p.E407D	NM_020414.3	NP_065147.1	Q9GZR7	DDX24_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 24	450	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)		CTTTAATTAATTCCCACAGCC	0.468																																					p.E450D		Atlas-SNP	.											.	DDX24	82	.	0			c.A1350C						PASS	.						95	94	94					14																	94527306		2203	4300	6503	SO:0001583	missense	57062	exon4			AATTAATTCCCAC	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.1350A>C	chr14.hg19:g.94527306T>G	ENSP00000328690:p.Glu450Asp	115.0	0.0	.		118.0	19.0	.	NM_020414	E7EMJ4|Q4V9L5	Missense_Mutation	SNP	ENST00000330836.5	hg19	CCDS9918.1	.	.	.	.	.	.	.	.	.	.	T	13.13	2.144094	0.37825	.	.	ENSG00000089737	ENST00000330836;ENST00000544005;ENST00000440370;ENST00000543787;ENST00000555054;ENST00000542247	T;T;T	0.03801	3.8;3.8;3.8	5.03	0.632	0.17705	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.049652	0.85682	D	0.000000	T	0.02649	0.0080	N	0.03084	-0.415	0.40889	D	0.984059	B	0.27264	0.173	B	0.35688	0.208	T	0.54609	-0.8268	10	0.29301	T	0.29	-2.3005	9.5849	0.39510	0.0:0.7044:0.0:0.2956	.	450	Q9GZR7	DDX24_HUMAN	D	450;200;395;76;407;407	ENSP00000328690:E450D;ENSP00000440623:E200D;ENSP00000452145:E407D	ENSP00000328690:E450D	E	-	3	2	DDX24	93597059	0.874000	0.30092	0.800000	0.32199	0.273000	0.26683	0.054000	0.14205	0.170000	0.19704	-0.993000	0.02533	GAA	.	.	.	none		0.468	DDX24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412861.1	NM_020414		G	94527306	T	G	94527306	3	3	191	1	0	0	0	0	1	0	0	0	4353	1490	52	5	1253	5	DDX24	14	94527306	Missense_Mutation	SNP	T	TCGA-GL-A9DD-01A-11D-A36X-10	2057438	94527306	12822234	84	11377											
ADCY7	113	hgsc.bcm.edu	37	chr16	50325746	50325746	+	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	ccgtctccactgcctcccacCtcctggtgctcggttctttg	2	13	8	18	2	2	0	0	0	2	0	6	0	4	0	6	2	2	2	6	2	0	2			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr16:50325746C>T	ENST00000394697.2	+	4	815	c.475C>T	c.(475-477)Ctc>Ttc	p.L159F	ADCY7_ENST00000564044.1_Intron|ADCY7_ENST00000537579.1_Missense_Mutation_p.L159F|ADCY7_ENST00000566433.2_Missense_Mutation_p.L159F|ADCY7_ENST00000538642.1_Missense_Mutation_p.L159F|ADCY7_ENST00000254235.3_Missense_Mutation_p.L159F			P51828	ADCY7_HUMAN	adenylate cyclase 7	159					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)		TGCCTCCCACCTCCTGGTGCT	0.622																																					p.L159F		Atlas-SNP	.											.	ADCY7	90	.	0			c.C475T						PASS	.						86	78	81					16																	50325746		2198	4300	6498	SO:0001583	missense	113	exon3			TCCCACCTCCTGG	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.475C>T	chr16.hg19:g.50325746C>T	ENSP00000378187:p.Leu159Phe	52.0	0.0	.		44.0	11.0	.	NM_001114	A0AVA6	Missense_Mutation	SNP	ENST00000394697.2	hg19	CCDS10741.1	.	.	.	.	.	.	.	.	.	.	C	18.48	3.632511	0.67015	.	.	ENSG00000121281	ENST00000538642;ENST00000394697;ENST00000537579;ENST00000254235	T;D;T;D	0.83591	-1.23;-1.74;-1.23;-1.74	4.03	4.03	0.46877	.	0.221259	0.22600	U	0.057965	T	0.79233	0.4411	L	0.54323	1.7	0.37366	D	0.911421	B;B	0.23058	0.005;0.079	B;B	0.29176	0.009;0.099	T	0.80013	-0.1560	10	0.52906	T	0.07	.	10.0746	0.42353	0.3531:0.6469:0.0:0.0	.	159;159	P51828;F5H4D1	ADCY7_HUMAN;.	F	159	ENSP00000445046:L159F;ENSP00000378187:L159F;ENSP00000437788:L159F;ENSP00000254235:L159F	ENSP00000254235:L159F	L	+	1	0	ADCY7	48883247	0.989000	0.36119	1.000000	0.80357	0.648000	0.38561	3.071000	0.50041	2.231000	0.72958	0.561000	0.74099	CTC	.	.	.	none		0.622	ADCY7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256877.3			T	50325746	C	T	50325746	3	4	191	1	0	0	0	0	1	0	0	0	299	681	24	2	485	2	ADCY7	16	50325746	Missense_Mutation	SNP	C	TCGA-GL-A9DD-01A-11D-A36X-10		50325746	40029007	85	11378											
TSR1	55720	hgsc.bcm.edu	37	chr17	2238104	2238110	+	Frame_Shift_Del	DEL	AGCGCTT	AGCGCTT	-																															gaggagtttgtcatgcggaaAgcgcttctccactgctttac																								rs139020440|rs140750763		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	AGCGCTT	AGCGCTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr17:2238104_2238110delAGCGCTT	ENST00000301364.5	-	5	1716_1722	c.637_643delAAGCGCT	c.(637-645)aagcgctttfs	p.KRF213fs	SGSM2_ENST00000268989.3_5'Flank|TSR1_ENST00000576112.2_Frame_Shift_Del_p.KRF197fs|SGSM2_ENST00000426855.2_5'Flank|SGSM2_ENST00000574563.1_5'Flank	NM_018128.4	NP_060598.3	Q2NL82	TSR1_HUMAN	TSR1, 20S rRNA accumulation, homolog (S. cerevisiae)	213	Bms1-type G.				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						TCATGCGGAAAGCGCTTCTCCACTGCT	0.478																																					p.213_215del		Atlas-Indel,Pindel	.											.	TSR1	57	.	0			c.638_644del						PASS	.																																			SO:0001589	frameshift_variant	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.637_643delAAGCGCT	chr17.hg19:g.2238104_2238110delAGCGCTT	ENSP00000301364:p.Lys213fs	86.0	0.0	0		92.0	23.0	0.25	NM_018128	Q8WUY5|Q9NVT0|Q9P2E6	Frame_Shift_Del	DEL	ENST00000301364.5	hg19	CCDS32525.1																																																																																			.	.	.	none		0.478	TSR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438180.2	NM_018128		-	2238110	AGCGCTT	-	2238104	7	5	191	1	0	1	0	1	0	0	0	0	16676	72	3	0	1815	0	TSR1	17	2238104	Frame_Shift_Del	DEL	AGCGCTT	TCGA-GL-A9DD-01A-11D-A36X-10		2238104	78957106	86	11379											
ASGR2	433	hgsc.bcm.edu	37	chr17	7011820	7011820	+	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	gacctccgtcagggtgctcgAggagaagttgctgaaagctt	9	9	14	9	2	1	2	1	1	0	1	3	5	2	2	2	2	3	4	2	2	2	2			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr17:7011820A>T	ENST00000380952.2	-	4	577	c.313T>A	c.(313-315)Tcg>Acg	p.S105T	ASGR2_ENST00000446679.2_Missense_Mutation_p.S86T|ASGR2_ENST00000254850.7_Missense_Mutation_p.S81T|ASGR2_ENST00000355035.5_Missense_Mutation_p.S105T	NM_001181.4|NM_001201352.1|NM_080912.3	NP_001172|NP_001188281.1|NP_550434	P07307	ASGR2_HUMAN	asialoglycoprotein receptor 2	105					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)	AGGGTGCTCGAGGAGAAGTTG	0.622																																					p.S105T		Atlas-SNP	.											.	ASGR2	38	.	0			c.T313A						PASS	.						68	56	60					17																	7011820		2203	4300	6503	SO:0001583	missense	433	exon4			TGCTCGAGGAGAA	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.313T>A	chr17.hg19:g.7011820A>T	ENSP00000370339:p.Ser105Thr	63.0	0.0	.		64.0	9.0	.	NM_080912	A6NLV8|A8MT12|D3DTM9|D3DTN0|O00448|Q03969	Missense_Mutation	SNP	ENST00000380952.2	hg19	CCDS32544.1	.	.	.	.	.	.	.	.	.	.	A	12.58	1.979766	0.34942	.	.	ENSG00000161944	ENST00000355035;ENST00000254850;ENST00000380952;ENST00000446679;ENST00000450034	T;T;T;T	0.22134	1.97;1.97;1.97;1.97	2.9	-1.2	0.09554	Hepatic lectin, N-terminal (1);	1.161450	0.06753	N	0.780358	T	0.15955	0.0384	L	0.32530	0.975	0.09310	N	1	P;B;P;B;B;P	0.35307	0.476;0.041;0.494;0.314;0.439;0.494	B;B;B;B;B;B	0.39935	0.145;0.011;0.314;0.248;0.209;0.314	T	0.33828	-0.9853	10	0.25106	T	0.35	.	4.3131	0.10979	0.3967:0.4057:0.0:0.1976	.	81;81;105;100;86;105	B4E1D2;P07307-3;P07307;Q7Z4G9;P07307-2;D3DTN0	.;.;ASGR2_HUMAN;.;.;.	T	105;81;105;86;81	ENSP00000347140:S105T;ENSP00000254850:S81T;ENSP00000370339:S105T;ENSP00000405844:S86T	ENSP00000254850:S81T	S	-	1	0	ASGR2	6952544	0.003000	0.15002	0.065000	0.19835	0.437000	0.31866	-0.242000	0.08928	-0.275000	0.09219	0.438000	0.28831	TCG	.	.	.	none		0.622	ASGR2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000220003.1	NM_080914		T	7011820	A	T	7011820	3	4	191	1	0	0	0	0	1	0	0	0	1040	304	11	5	646	5	ASGR2	17	7011820	Missense_Mutation	SNP	A	TCGA-GL-A9DD-01A-11D-A36X-10	4773716	7011820	74183390	87	11380											
KSR1	8844	hgsc.bcm.edu	37	chr17	25919630	25919630	+	Frame_Shift_Del	DEL	T	T	-																															cgaaccccattttggaacccTccccaaagcactgacaaaga																										TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr17:25919630delT	ENST00000319524.6	+	9	1277	c.1277delT	c.(1276-1278)ctcfs	p.L426fs	KSR1_ENST00000581975.1_3'UTR|KSR1_ENST00000398988.3_Frame_Shift_Del_p.L289fs|KSR1_ENST00000268763.6_Frame_Shift_Del_p.L289fs|KSR1_ENST00000509603.2_Frame_Shift_Del_p.L426fs			Q8IVT5	KSR1_HUMAN	kinase suppressor of ras 1	426					Ras protein signal transduction (GO:0007265)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(12)|prostate(2)|urinary_tract(1)	28	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		TTTGGAACCCTCCCCAAAGCA	0.562																																					p.L289fs	Esophageal Squamous(88;1120 1336 6324 10502 16832)	Atlas-Indel,Pindel	.											.	KSR1	151	.	0			c.865delC						PASS	.						69	69	69					17																	25919630		1911	4122	6033	SO:0001589	frameshift_variant	8844	exon9			.	U43586	CCDS58532.1	17q11.2	2012-05-23	2005-12-14	2005-12-14	ENSG00000141068	ENSG00000141068			6465	protein-coding gene	gene with protein product		601132	"kinase suppressor of ras"	KSR		8521512	Standard	XM_006722151		Approved	RSU2	uc031qzj.1	Q8IVT5	OTTHUMG00000132051	ENST00000319524.6:c.1277delT	chr17.hg19:g.25919630delT	ENSP00000323178:p.Leu426fs	50.0	0.0	0		78.0	20.0	0.25641	NM_014238	F8WEA9|H7BYU0|Q13476	Frame_Shift_Del	DEL	ENST00000319524.6	hg19																																																																																				.	.	.	none		0.562	KSR1-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_014238		-	25919630	T	-	25919630	7	5	191	1	0	1	0	1	0	0	0	0	8588	1551	54	0	888	0	KSR1	17	25919630	Frame_Shift_Del	DEL	T	TCGA-GL-A9DD-01A-11D-A36X-10	18907810	25919630	55275580	88	11381											
TMEM97	27346	hgsc.bcm.edu	37	chr17	26646334	26646334	+	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	tacttcctcagccacatcccCatcaccctgttcatggacct	8	11	4	18	0	3	0	3	0	0	0	5	1	5	1	6	1	2	1	6	1	1	3	rs369813368		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr17:26646334C>A	ENST00000226230.6	+	1	214	c.69C>A	c.(67-69)ccC>ccA	p.P23P	TMEM97_ENST00000582113.1_Silent_p.P23P|TMEM97_ENST00000336687.6_5'Flank|TMEM97_ENST00000583381.1_Intron	NM_014573.2	NP_055388.2	Q5BJF2	TMM97_HUMAN	transmembrane protein 97	23					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)		GCCACATCCCCATCACCCTGT	0.677																																					p.P23P		Atlas-SNP	.											.	TMEM97	27	.	0			c.C69A						PASS	.						27	34	31					17																	26646334		2045	4160	6205	SO:0001819	synonymous_variant	27346	exon1			CATCCCCATCACC	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.69C>A	chr17.hg19:g.26646334C>A		109.0	0.0	.		130.0	22.0	.	NM_014573	B4DS02|Q07823	Silent	SNP	ENST00000226230.6	hg19	CCDS11226.2																																																																																			.	.	.	alt		0.677	TMEM97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255675.2	NM_014573		A	26646334	C	A	26646334	2	1	191	1	0	0	0	0	0	0	0	1	16236	581	21	4		4	TMEM97	17	26646334	Silent	SNP	C	TCGA-GL-A9DD-01A-11D-A36X-10	726704	26646334	54548876	89	11382											
EXOC7	23265	hgsc.bcm.edu	37	chr17	74090635	74090635	+	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	agcggtccagctggctggagCgtatctggtagtagacgttc	7	10	15	9	3	1	1	0	0	1	1	3	2	2	2	1	4	3	6	1	4	3	4			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr17:74090635C>T	ENST00000335146.7	-	6	721	c.668G>A	c.(667-669)cGc>cAc	p.R223H	EXOC7_ENST00000405575.4_Missense_Mutation_p.R223H|EXOC7_ENST00000607838.1_Missense_Mutation_p.R223H|EXOC7_ENST00000589210.1_Missense_Mutation_p.R223H|EXOC7_ENST00000411744.2_Missense_Mutation_p.R223H|EXOC7_ENST00000467929.2_Missense_Mutation_p.R182H|EXOC7_ENST00000332065.5_Missense_Mutation_p.R223H			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	223					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)			CTGGCTGGAGCGTATCTGGTA	0.547																																					p.R223H		Atlas-SNP	.											.	EXOC7	47	.	0			c.G668A						PASS	.						125	120	121					17																	74090635		2203	4300	6503	SO:0001583	missense	23265	exon6			CTGGAGCGTATCT	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.668G>A	chr17.hg19:g.74090635C>T	ENSP00000334100:p.Arg223His	92.0	0.0	.		119.0	7.0	.	NM_001145298	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Missense_Mutation	SNP	ENST00000335146.7	hg19	CCDS45782.1	.	.	.	.	.	.	.	.	.	.	C	35	5.431701	0.96150	.	.	ENSG00000182473	ENST00000332065;ENST00000351709;ENST00000405575;ENST00000335146;ENST00000357231;ENST00000425372;ENST00000411744;ENST00000405068;ENST00000420116	.	.	.	4.84	4.84	0.62591	Cullin repeat-like-containing domain (1);	0.054405	0.64402	D	0.000001	T	0.68035	0.2957	L	0.36672	1.1	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	0.999;1.0;0.993;0.998;1.0;0.999;1.0;1.0	T	0.71424	-0.4597	9	0.87932	D	0	-17.4317	16.2936	0.82761	0.0:1.0:0.0:0.0	.	223;223;182;182;223;223;223;223	Q9UPT5-5;Q9UPT5-6;B4DJ07;F5H1P1;Q9UPT5-4;Q9UPT5;Q9UPT5-2;Q9UPT5-1	.;.;.;.;.;EXOC7_HUMAN;.;.	H	223;143;223;223;223;182;223;223;108	.	ENSP00000333806:R223H	R	-	2	0	EXOC7	71602230	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.284000	0.78650	2.508000	0.84585	0.557000	0.71058	CGC	.	.	.	none		0.547	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219		T	74090635	C	T	74090635	3	4	191	1	0	0	0	0	1	0	0	0	5312	768	27	1	1599	1	EXOC7	17	74090635	Missense_Mutation	SNP	C	TCGA-GL-A9DD-01A-11D-A36X-10	47444301	74090635	7104575	90	11383											
FOXJ1	2302	hgsc.bcm.edu	37	chr17	74136299	74136299	+	Frame_Shift_Del	DEL	G	G	-																															tggcacctggtggtagccgtGggggtcggtgccccccgggg																										TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr17:74136299delG	ENST00000322957.6	-	2	532	c.178delC	c.(178-180)cacfs	p.H60fs	RNF157_ENST00000589912.1_5'Flank|RNF157-AS1_ENST00000586627.1_RNA|RNF157-AS1_ENST00000585542.1_RNA|RNF157-AS1_ENST00000590137.1_RNA	NM_001454.3	NP_001445.2	Q92949	FOXJ1_HUMAN	forkhead box J1	60					actin cytoskeleton organization (GO:0030036)|activation of Rho GTPase activity (GO:0032862)|brain development (GO:0007420)|central tolerance induction (GO:0002508)|cilium assembly (GO:0042384)|epithelium development (GO:0060429)|establishment of apical/basal cell polarity (GO:0035089)|glomerular parietal epithelial cell development (GO:0072016)|humoral immune response (GO:0006959)|left/right pattern formation (GO:0060972)|leukocyte migration (GO:0050900)|lung epithelium development (GO:0060428)|metanephric part of ureteric bud development (GO:0035502)|negative regulation of B cell activation (GO:0050869)|negative regulation of germinal center formation (GO:0002635)|negative regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002924)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell differentiation in thymus (GO:0033085)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pattern specification process (GO:0007389)|positive regulation of central B cell tolerance induction (GO:0002897)|positive regulation of lung ciliated cell differentiation (GO:1901248)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			large_intestine(1)|liver(1)|pancreas(1)|skin(1)	4			LUSC - Lung squamous cell carcinoma(166;0.187)			TGGTAGCCGTGGGGGTCGGTG	0.736																																					p.H60fs		Atlas-Indel,Pindel	.											.	FOXJ1	11	.	0			c.179delA						PASS	.						3	5	4					17																	74136299		1712	3354	5066	SO:0001589	frameshift_variant	2302	exon2			.	X99349	CCDS32739.1	17q25.1	2008-05-14				ENSG00000129654		"Forkhead boxes"	3816	protein-coding gene	gene with protein product		602291		FKHL13		9073514, 16518568	Standard	NM_001454		Approved	HFH-4, HFH4	uc002jqx.3	Q92949		ENST00000322957.6:c.178delC	chr17.hg19:g.74136299delG	ENSP00000323880:p.His60fs	60.0	0.0	0		45.0	18.0	0.4	NM_001454	O00630	Frame_Shift_Del	DEL	ENST00000322957.6	hg19	CCDS32739.1																																																																																			.	.	.	none		0.736	FOXJ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449856.1	NM_001454		-	74136299	G	-	74136299	7	5	191	1	0	1	0	1	0	0	0	0	6018	1348	47	0	1095	0	FOXJ1	17	74136299	Frame_Shift_Del	DEL	G	TCGA-GL-A9DD-01A-11D-A36X-10	45664	74136299	7058911	91	11384											
AFG3L2	10939	hgsc.bcm.edu	37	chr18	12329586	12329586	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agttggcaactttctcacccGggggctcctctttctccttt	4	15	8	14	1	3	0	1	0	3	0	6	0	4	0	3	3	1	3	3	3	1	4	rs372136184		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr18:12329586G>A	ENST00000269143.3	-	17	2603	c.2372C>T	c.(2371-2373)cCg>cTg	p.P791L	TUBB6_ENST00000590967.1_Intron|TUBB6_ENST00000591909.1_3'UTR	NM_006796.2	NP_006787.2	Q9Y4W6	AFG32_HUMAN	AFG3-like AAA ATPase 2	791					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)	TTTCTCACCCGGGGGCTCCTC	0.532																																					p.P791L		Atlas-SNP	.											.	AFG3L2	60	.	0			c.C2372T						PASS	.	G	LEU/PRO	0,4406		0,0,2203	73	83	80		2372	1.8	0	18		80	1,8599	1.2+/-3.3	0,1,4299	no	missense	AFG3L2	NM_006796.2	98	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	791/798	12329586	1,13005	2203	4300	6503	SO:0001583	missense	10939	exon17			TCACCCGGGGGCT	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.2372C>T	chr18.hg19:g.12329586G>A	ENSP00000269143:p.Pro791Leu	108.0	0.0	.		98.0	17.0	.	NM_006796	Q6P1L0	Missense_Mutation	SNP	ENST00000269143.3	hg19	CCDS11859.1	.	.	.	.	.	.	.	.	.	.	G	16.62	3.172684	0.57584	0.0	1.16E-4	ENSG00000141385	ENST00000269143;ENST00000537174	D	0.92595	-3.07	5.56	1.75	0.24633	.	2.193060	0.01444	N	0.015203	D	0.87442	0.6178	L	0.34521	1.04	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.71537	-0.4563	10	0.44086	T	0.13	1.1635	4.8492	0.13528	0.1341:0.1195:0.6226:0.1238	.	791	Q9Y4W6	AFG32_HUMAN	L	791;806	ENSP00000269143:P791L	ENSP00000269143:P791L	P	-	2	0	AFG3L2	12319586	0.000000	0.05858	0.000000	0.03702	0.924000	0.55760	0.652000	0.24888	0.100000	0.17581	0.655000	0.94253	CCG	.	.	.	weak		0.532	AFG3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254603.2	NM_006796		A	12329586	G	A	12329586	3	1	191	1	0	0	0	0	1	0	0	0	360	1116	39	1	25	1	AFG3L2	18	12329586	Missense_Mutation	SNP	G	TCGA-GL-A9DD-01A-11D-A36X-10		12329586	65747662	92	11385											
ZNF627	199692	hgsc.bcm.edu	37	chr19	11728063	11728063	+	Frame_Shift_Del	DEL	A	A	-																															aaaggactcacactggagatAaaccctatgaatgcaagcag																										TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr19:11728063delA	ENST00000361113.5	+	4	953	c.745delA	c.(745-747)aaafs	p.K249fs	ZNF627_ENST00000588174.1_3'UTR	NM_145295.3	NP_660338.1	Q7L945	ZN627_HUMAN	zinc finger protein 627	249					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14						CACTGGAGATAAACCCTATGA	0.418																																					p.D248fs	Melanoma(112;173 1614 10731 17751 23322)	Atlas-Indel,Pindel	.											.	ZNF627	43	.	0			c.744delT						PASS	.						56	59	58					19																	11728063		2203	4299	6502	SO:0001589	frameshift_variant	199692	exon4			.	AK074846	CCDS42502.1	19p13.2	2013-01-08				ENSG00000198551		"Zinc fingers, C2H2-type", "-"	30570	protein-coding gene	gene with protein product		612248				12477932	Standard	NM_145295		Approved	FLJ90365	uc002msk.2	Q7L945		ENST00000361113.5:c.745delA	chr19.hg19:g.11728063delA	ENSP00000354414:p.Lys249fs	138.0	0.0	0		132.0	21.0	0.159091	NM_145295	O14846|Q4KMP9|Q6NT81|Q9BRG4	Frame_Shift_Del	DEL	ENST00000361113.5	hg19	CCDS42502.1																																																																																			.	.	.	none		0.418	ZNF627-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458875.1	NM_145295		-	11728063	A	-	11728063	7	5	191	1	0	1	0	1	0	0	0	0	18063	363	13	0	759	0	ZNF627	19	11728063	Frame_Shift_Del	DEL	A	TCGA-GL-A9DD-01A-11D-A36X-10		11728063	47400920	93	11386											
ILVBL	10994	hgsc.bcm.edu	37	chr19	15226999	15226999	+	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	cagggggccgcggggctgtaCcagatgggcagcagtgccca	7	4	18	12	2	0	1	0	0	0	1	0	1	0	1	3	5	3	4	3	5	1	1			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr19:15226999C>G	ENST00000263383.3	-	12	1574	c.1435G>C	c.(1435-1437)Gta>Cta	p.V479L	ILVBL_ENST00000534378.1_Missense_Mutation_p.V372L	NM_006844.3	NP_006835.2	A1L0T0	ILVBL_HUMAN	ilvB (bacterial acetolactate synthase)-like	479	Thiamine pyrophosphate binding. {ECO:0000250}.					integral component of membrane (GO:0016021)|membrane (GO:0016020)	magnesium ion binding (GO:0000287)|thiamine pyrophosphate binding (GO:0030976)|transferase activity (GO:0016740)			NS(3)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)	26						CGGGGCTGTACCAGATGGGCA	0.652																																					p.V479L		Atlas-SNP	.											.	ILVBL	54	.	0			c.G1435C						PASS	.						81	71	74					19																	15226999		2203	4300	6503	SO:0001583	missense	10994	exon12			GCTGTACCAGATG	U61263	CCDS12325.1	19p13.1	2008-07-16			ENSG00000105135	ENSG00000105135			6041	protein-coding gene	gene with protein product	"acetolactate synthase homolog"	605770				8954801	Standard	NM_006844		Approved	209L8, AHAS, ILV2H, MGC1269, FLJ39061, MGC19535	uc002nam.3	A1L0T0	OTTHUMG00000165630	ENST00000263383.3:c.1435G>C	chr19.hg19:g.15226999C>G	ENSP00000263383:p.Val479Leu	51.0	0.0	.		59.0	11.0	.	NM_006844	O43341|Q96F08|Q99651|Q9BWN5|Q9UEB2	Missense_Mutation	SNP	ENST00000263383.3	hg19	CCDS12325.1	.	.	.	.	.	.	.	.	.	.	C	3.360	-0.130703	0.06753	.	.	ENSG00000105135	ENST00000263383	T	0.36340	1.26	5.22	4.19	0.49359	Thiamine pyrophosphate enzyme, C-terminal TPP-binding (1);	0.252402	0.42294	D	0.000726	T	0.20007	0.0481	N	0.12422	0.21	0.40211	D	0.977625	B	0.20671	0.047	B	0.26094	0.066	T	0.07290	-1.0780	10	0.16896	T	0.51	-17.1147	9.8081	0.40805	0.0:0.9045:0.0:0.0955	.	479	A1L0T0	ILVBL_HUMAN	L	479	ENSP00000263383:V479L	ENSP00000263383:V479L	V	-	1	0	ILVBL	15087999	1.000000	0.71417	0.998000	0.56505	0.072000	0.16883	1.307000	0.33516	1.209000	0.43321	-0.258000	0.10820	GTA	.	.	.	none		0.652	ILVBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385439.1	NM_006844		G	15226999	C	G	15226999	3	3	191	1	0	0	0	0	1	0	0	0	7722	507	18	4	483	4	ILVBL	19	15226999	Missense_Mutation	SNP	C	TCGA-GL-A9DD-01A-11D-A36X-10	3498936	15226999	43901984	94	11387											
PGLYRP2	114770	hgsc.bcm.edu	37	chr19	15587251	15587251	+	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	agggatccaactctgtagcaTtgaggctccatgcccccagc	9	8	10	14	0	1	1	0	1	1	0	3	2	3	2	4	2	4	3	4	2	2	2			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr19:15587251T>A	ENST00000340880.4	-	2	710	c.230A>T	c.(229-231)aAt>aTt	p.N77I	PGLYRP2_ENST00000292609.4_Missense_Mutation_p.N77I	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	77					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						CTCTGTAGCATTGAGGCTCCA	0.582																																					p.N77I		Atlas-SNP	.											.	PGLYRP2	116	.	0			c.A230T						PASS	.						108	78	89					19																	15587251		2203	4300	6503	SO:0001583	missense	114770	exon2			GTAGCATTGAGGC	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.230A>T	chr19.hg19:g.15587251T>A	ENSP00000345968:p.Asn77Ile	91.0	0.0	.		81.0	14.0	.	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Missense_Mutation	SNP	ENST00000340880.4	hg19	CCDS12330.2	.	.	.	.	.	.	.	.	.	.	T	11.16	1.555531	0.27739	.	.	ENSG00000161031	ENST00000340880;ENST00000292609	T;T	0.05081	3.53;3.5	5.27	0.412	0.16397	.	3.618340	0.00864	N	0.001941	T	0.06234	0.0161	L	0.44542	1.39	0.09310	N	1	P;B	0.44946	0.846;0.412	B;B	0.37888	0.26;0.053	T	0.26052	-1.0114	10	0.66056	D	0.02	-8.1911	0.6612	0.00843	0.1668:0.1881:0.1728:0.4723	.	77;77	Q96PD5-2;Q96PD5	.;PGRP2_HUMAN	I	77	ENSP00000345968:N77I;ENSP00000292609:N77I	ENSP00000292609:N77I	N	-	2	0	PGLYRP2	15448251	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.187000	0.16998	0.006000	0.14734	-0.376000	0.06991	AAT	.	.	.	none		0.582	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890		A	15587251	T	A	15587251	3	1	191	1	0	0	0	0	1	0	0	0	11801	1493	52	5	1516	5	PGLYRP2	19	15587251	Missense_Mutation	SNP	T	TCGA-GL-A9DD-01A-11D-A36X-10	360252	15587251	43541732	95	11388											
NR2F6	2063	hgsc.bcm.edu	37	chr19	17343235	17343235	+	Missense_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	tctgatcagtgtctcaatggGcgtcttccccaccaggcgca	7	10	10	14	2	4	1	2	1	3	0	6	1	5	1	3	2	0	1	3	2	1	1			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr19:17343235G>A	ENST00000291442.3	-	4	1860	c.1141C>T	c.(1141-1143)Ccc>Tcc	p.P381S		NM_005234.3	NP_005225.2	P10588	NR2F6_HUMAN	nuclear receptor subfamily 2, group F, member 6	381	Important for dimerization. {ECO:0000250}.|Ligand-binding. {ECO:0000250}.				detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|entrainment of circadian clock by photoperiod (GO:0043153)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron development (GO:0048666)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(1)	5						GTCTCAATGGGCGTCTTCCCC	0.667																																					p.P381S		Atlas-SNP	.											.	NR2F6	18	.	0			c.C1141T						PASS	.						70	62	65					19																	17343235		2203	4300	6503	SO:0001583	missense	2063	exon4			CAATGGGCGTCTT	X12794	CCDS12352.1	19p13.11	2013-09-20			ENSG00000160113	ENSG00000160113		"Nuclear hormone receptors"	7977	protein-coding gene	gene with protein product		132880		ERBAL2		2905047	Standard	NM_005234		Approved	EAR-2	uc002nfq.3	P10588	OTTHUMG00000182728	ENST00000291442.3:c.1141C>T	chr19.hg19:g.17343235G>A	ENSP00000291442:p.Pro381Ser	108.0	0.0	.		102.0	18.0	.	NM_005234	B2RC68|Q5XGA0|Q6P586|Q9BUE8	Missense_Mutation	SNP	ENST00000291442.3	hg19	CCDS12352.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.536811	0.85812	.	.	ENSG00000160113	ENST00000291442;ENST00000536940	T	0.52983	0.64	4.71	4.71	0.59529	Nuclear hormone receptor, ligand-binding (2);	0.000000	0.85682	D	0.000000	T	0.64136	0.2571	L	0.55213	1.73	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.67845	-0.5565	10	0.87932	D	0	.	15.175	0.72903	0.0:0.0:1.0:0.0	.	381	P10588	NR2F6_HUMAN	S	381;354	ENSP00000291442:P381S	ENSP00000291442:P381S	P	-	1	0	NR2F6	17204235	1.000000	0.71417	0.999000	0.59377	0.865000	0.49528	9.658000	0.98594	2.168000	0.68352	0.555000	0.69702	CCC	.	.	.	none		0.667	NR2F6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463325.1			A	17343235	G	A	17343235	3	1	191	1	0	0	0	0	1	0	0	0	10636	1203	42	2	77	2	NR2F6	19	17343235	Missense_Mutation	SNP	G	TCGA-GL-A9DD-01A-11D-A36X-10	1755984	17343235	41785748	96	11389											
ZNF91	7644	hgsc.bcm.edu	37	chr19	23544826	23544826	+	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	ttcacatttgtagggtttctCtccagtatgaattctcttat	8	19	6	8	0	3	1	1	1	2	0	6	1	4	1	1	1	0	3	1	1	4	7			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr19:23544826C>G	ENST00000300619.7	-	4	1160	c.955G>C	c.(955-957)Gag>Cag	p.E319Q	ZNF91_ENST00000397082.2_Missense_Mutation_p.E287Q|ZNF91_ENST00000599743.1_Intron	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	319					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)				TAGGGTTTCTCTCCAGTATGA	0.398																																					p.E319Q		Atlas-SNP	.											.	ZNF91	349	.	0			c.G955C						PASS	.						66	70	69					19																	23544826		2141	4273	6414	SO:0001583	missense	7644	exon4			GTTTCTCTCCAGT	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.955G>C	chr19.hg19:g.23544826C>G	ENSP00000300619:p.Glu319Gln	79.0	0.0	.		77.0	15.0	.	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	hg19	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	C	14.48	2.548805	0.45383	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.25912	1.77;1.77	1.97	0.778	0.18543	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.25121	0.0610	L	0.49571	1.57	0.26282	N	0.978262	P;P	0.47409	0.895;0.589	B;B	0.43536	0.423;0.419	T	0.12502	-1.0545	9	0.72032	D	0.01	.	9.033	0.36271	0.0:0.7693:0.2307:0.0	.	287;319	Q05481-2;Q05481	.;ZNF91_HUMAN	Q	319;287	ENSP00000300619:E319Q;ENSP00000380272:E287Q	ENSP00000300619:E319Q	E	-	1	0	ZNF91	23336666	0.003000	0.15002	0.001000	0.08648	0.024000	0.10985	0.998000	0.29744	0.126000	0.18424	0.162000	0.16502	GAG	.	.	.	none		0.398	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		G	23544826	C	G	23544826	3	3	191	1	0	0	0	0	1	0	0	0	18212	922	32	4	2624	4	ZNF91	19	23544826	Missense_Mutation	SNP	C	TCGA-GL-A9DD-01A-11D-A36X-10	6201591	23544826	35584157	97	11390											
SFRS16	11129	hgsc.bcm.edu	37	chr19	45555367	45555367	+	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	ttcctgcaggtacatggccgAgcttgcaaggtgcacctgga	8	9	13	11	1	0	0	0	0	0	0	1	2	1	1	3	4	5	5	3	4	2	3			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr19:45555367A>C	ENST00000221455.3	+	3	236	c.138A>C	c.(136-138)cgA>cgC	p.R46R	CLASRP_ENST00000544944.2_Silent_p.R46R|CLASRP_ENST00000391953.4_Intron	NM_007056.2	NP_008987	Q8N2M8	CLASR_HUMAN	CLK4-associating serine/arginine rich protein	46					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						TACATGGCCGAGCTTGCAAGG	0.572																																					p.R46R		Atlas-SNP	.											.	CLASRP	44	.	0			c.A138C						PASS	.						99	91	94					19																	45555367		2203	4300	6503	SO:0001819	synonymous_variant	11129	exon3			TGGCCGAGCTTGC	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.138A>C	chr19.hg19:g.45555367A>C		30.0	0.0	.		41.0	10.0	.	NM_007056	B4DDT8|F8WAG9|O96026|Q6UW71|Q96DX2	Silent	SNP	ENST00000221455.3	hg19	CCDS12652.2																																																																																			.	.	.	none		0.572	CLASRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316749.1	NM_007056		C	45555367	A	C	45555367	2	2	191	1	0	0	0	0	0	0	0	1	14185	291	11	5		5	SFRS16	19	45555367	Silent	SNP	A	TCGA-GL-A9DD-01A-11D-A36X-10	22010541	45555367	13573616	98	11391											
FTL	2512	hgsc.bcm.edu	37	chr19	49469662	49469662	+	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	ttctgcccgcacggacccccAtgtacgtacccgctgcatcc	6	8	8	19	4	1	0	0	0	1	0	2	1	2	1	5	1	4	5	5	1	2	3	rs17856437		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr19:49469662A>G	ENST00000331825.6	+	3	581	c.374A>G	c.(373-375)cAt>cGt	p.H125R	CTD-2639E6.9_ENST00000599784.1_lincRNA	NM_000146.3	NP_000137.2	P02792	FRIL_HUMAN	ferritin, light polypeptide	125	Ferritin-like diiron. {ECO:0000255|PROSITE-ProRule:PRU00085}.				cell death (GO:0008219)|cellular iron ion homeostasis (GO:0006879)|iron ion homeostasis (GO:0055072)|iron ion transport (GO:0006826)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular ferritin complex (GO:0008043)|membrane (GO:0016020)	ferric iron binding (GO:0008199)|identical protein binding (GO:0042802)|iron ion binding (GO:0005506)			cervix(1)|kidney(3)|lung(5)	9		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000152)|all cancers(93;0.000435)|GBM - Glioblastoma multiforme(486;0.0171)|Epithelial(262;0.0267)	Iron Dextran(DB00893)	ACGGACCCCCATGTACGTACC	0.557																																					p.H125R		Atlas-SNP	.											.	FTL	19	.	0			c.A374G						PASS	.						46	46	46					19																	49469662		2203	4300	6503	SO:0001630	splice_region_variant	2512	exon3			ACCCCCATGTACG	AY207005	CCDS33070.1	19q13.33	2014-05-19			ENSG00000087086	ENSG00000087086			3999	protein-coding gene	gene with protein product	"ferritin light polypeptide-like 3", "L apoferritin", "ferritin L subunit", "ferritin light chain", "ferritin L-chain", "neurodegeneration with brain iron accumulation 3"	134790				3000916, 9526618	Standard	NM_000146		Approved	MGC71996, NBIA3	uc002plo.3	P02792		ENST00000331825.6:c.375+1A>G	chr19.hg19:g.49469662A>G		85.0	0.0	.		119.0	8.0	.	NM_000146	B2R4B9|Q6IBT7|Q7Z2W1|Q86WI9|Q8WU07|Q96AU9|Q96CU0|Q9BTZ8	Missense_Mutation	SNP	ENST00000331825.6	hg19	CCDS33070.1	.	.	.	.	.	.	.	.	.	.	A	17.57	3.422947	0.62733	.	.	ENSG00000087086	ENST00000331825;ENST00000397259	T	0.64803	-0.12	4.46	4.46	0.54185	Ferritin/ribonucleotide reductase-like (1);Ferritin, conserved site (1);Ferritin-related (1);Ferritin/DPS protein domain (1);Ferritin-like (1);	0.000000	0.85682	D	0.000000	T	0.70561	0.3238	M	0.65498	2.005	0.45183	D	0.998191	P	0.44380	0.834	P	0.53401	0.725	T	0.74334	-0.3699	10	0.72032	D	0.01	.	12.021	0.53344	1.0:0.0:0.0:0.0	rs17856437	125	P02792	FRIL_HUMAN	R	125	ENSP00000366525:H125R	ENSP00000366525:H125R	H	+	2	0	FTL	54161474	1.000000	0.71417	1.000000	0.80357	0.311000	0.27955	8.334000	0.90028	2.011000	0.59026	0.460000	0.39030	CAT	.	.	.	weak		0.557	FTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466233.1	NM_000146	Missense_Mutation	G	49469662	A	G	49469662	5	3	191	1	0	0	0	0	0	0	1	0	6091	231	8	3	384	3	FTL	19	49469662	Splice_Site	SNP	A	TCGA-GL-A9DD-01A-11D-A36X-10	3914295	49469662	9659321	99	11392											
ZNF628	89887	hgsc.bcm.edu	37	chr19	55992958	55992958	+	Frame_Shift_Del	DEL	C	C	-																															cctggccttcaagtggtcgtCccactaccagtaccacttaa																										TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr19:55992958delC	ENST00000598519.1	+	3	951	c.398delC	c.(397-399)tccfs	p.S133fs	ZNF628_ENST00000391718.2_Frame_Shift_Del_p.S129fs			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	133					transcription, DNA-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)		AAGTGGTCGTCCCACTACCAG	0.662																																					p.S133fs		Atlas-INDEL	.											.	ZNF628	75	.	0			c.397delT						PASS	.						40	40	40					19																	55992958		2203	4299	6502	SO:0001589	frameshift_variant	89887	exon3			.	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.398delC	chr19.hg19:g.55992958delC	ENSP00000469591:p.Ser133fs	98.0	0.0	0		90.0	15.0	0.166667	NM_033113	Q86X34	Frame_Shift_Del	DEL	ENST00000598519.1	hg19	CCDS33116.3																																																																																			.	.	.	none		0.662	ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317934.2	XM_058964		-	55992958	C	-	55992958	7	5	191	1	0	1	0	1	0	0	0	0	18064	855	30	0	388	0	ZNF628	19	55992958	Frame_Shift_Del	DEL	C	TCGA-GL-A9DD-01A-11D-A36X-10	6523296	55992958	3136025	100	11393	108	3									
ZNF628	89887	hgsc.bcm.edu	37	chr19	55992960	55992961	+	Frame_Shift_Del	DEL	CA	CA	-																															tggccttcaagtggtcgtccCactaccagtaccacttaagg																										TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr19:55992960_55992961delCA	ENST00000598519.1	+	3	953_954	c.400_401delCA	c.(400-402)cacfs	p.H134fs	ZNF628_ENST00000391718.2_Frame_Shift_Del_p.H130fs			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	134					transcription, DNA-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)		GTGGTCGTCCCACTACCAGTAC	0.663																																					p.133_134del		Pindel	.											.	ZNF628	75	.	0			c.399_400del						PASS	.																																			SO:0001589	frameshift_variant	89887	exon3			.	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.400_401delCA	chr19.hg19:g.55992960_55992961delCA	ENSP00000469591:p.His134fs	100.0	0.0	.		93.0	12.0	0.129	NM_033113	Q86X34	Frame_Shift_Del	DEL	ENST00000598519.1	hg19	CCDS33116.3																																																																																			.	.	.	none		0.663	ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317934.2	XM_058964		-	55992961	CA	-	55992960	7	5	191	1	0	1	0	1	0	0	0	0	18064	594	21	0	390	0	ZNF628	19	55992960	Frame_Shift_Del	DEL	CA	TCGA-GL-A9DD-01A-11D-A36X-10	2	55992960	3136023	101	11394	108	3									
ZNF628	89887	hgsc.bcm.edu	37	chr19	55992961	55992961	+	Missense_Mutation	SNP	A	A	T																															ggccttcaagtggtcgtcccActaccagtaccacttaaggc																										TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr19:55992961A>T	ENST00000598519.1	+	3	954	c.401A>T	c.(400-402)cAc>cTc	p.H134L	ZNF628_ENST00000391718.2_Missense_Mutation_p.H130L			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	134					transcription, DNA-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)		TGGTCGTCCCACTACCAGTAC	0.662																																					p.H134L		Atlas-SNP	.											.	ZNF628	75	.	0			c.A401T						PASS	.						40	40	40					19																	55992961		2203	4299	6502	SO:0001583	missense	89887	exon3			CGTCCCACTACCA	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.401A>T	chr19.hg19:g.55992961A>T	ENSP00000469591:p.His134Leu	101.0	0.0	.		93.0	15.0	.	NM_033113	Q86X34	Missense_Mutation	SNP	ENST00000598519.1	hg19	CCDS33116.3	.	.	.	.	.	.	.	.	.	.	.	15.79	2.936377	0.52972	.	.	ENSG00000197483	ENST00000391718	T	0.13089	2.62	3.62	3.62	0.41486	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.48767	U	0.000162	T	0.14614	0.0353	N	0.16130	0.375	0.44531	D	0.997482	D	0.76494	0.999	D	0.68353	0.957	T	0.07385	-1.0775	10	0.06625	T	0.88	-16.2924	10.5074	0.44842	1.0:0.0:0.0:0.0	.	130	Q5EBL2	ZN628_HUMAN	L	130	ENSP00000375598:H130L	ENSP00000375598:H130L	H	+	2	0	ZNF628	60684773	0.714000	0.27936	0.971000	0.41717	0.613000	0.37349	2.323000	0.43823	1.654000	0.50703	0.397000	0.26171	CAC	.	.	.	none		0.662	ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317934.2	XM_058964		T	55992961	A	T	55992961	3	4	191	1	0	0	0	0	1	0	0	0	18064	159	6	5	391	5	ZNF628	19	55992961	Missense_Mutation	SNP	A	TCGA-GL-A9DD-01A-11D-A36X-10	1	55992961	3136022	102	11395	108	3									
DIDO1	11083	hgsc.bcm.edu	37	chr20	61527694	61527695	+	Frame_Shift_Ins	INS	-	-	T																															cttctcaatatggagggcaaINStttttcctacttcgttttct																										TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr20:61527694_61527695insT	ENST00000266070.4	-	8	2429_2430	c.2104_2105insA	c.(2104-2106)attfs	p.I702fs	DIDO1_ENST00000395340.1_Frame_Shift_Ins_p.I702fs|DIDO1_ENST00000395343.1_Frame_Shift_Ins_p.I702fs|DIDO1_ENST00000395335.2_Frame_Shift_Ins_p.I702fs	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	702	TFIIS central. {ECO:0000255|PROSITE- ProRule:PRU00651}.				apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.I702V(1)		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)					ATGGAGGGCAATTTTTCCTACT	0.356																																					p.I702fs	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-Indel,Pindel	.											.	DIDO1	321	.	1	Substitution - Missense(1)	lung(1)	c.2105_2106insA						PASS	.																																			SO:0001589	frameshift_variant	11083	exon8			.	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.2105dupA	chr20.hg19:g.61527699_61527699dupT	ENSP00000266070:p.Ile702fs	128.0	0.0	0		118.0	30.0	0.254237	NM_080797	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Frame_Shift_Ins	INS	ENST00000266070.4	hg19	CCDS33506.1																																																																																			.	.	.	none		0.356	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		T	61527695	-	T	61527694	7	5	191	1	0	1	1	0	0	0	0	0	4524	101	4	0	4682	0	DIDO1	20	61527694	Frame_Shift_Ins	INS	-	TCGA-GL-A9DD-01A-11D-A36X-10		61527694	1497826	103	11396											
CCDC116	164592	hgsc.bcm.edu	37	chr22	21990901	21990901	+	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	aggacctcagtaagcagctgGgcttcttctccttccccatc	7	11	8	15	0	3	0	1	0	2	0	6	1	4	1	4	2	2	4	4	2	1	4			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr22:21990901G>C	ENST00000292779.3	+	5	1545	c.1384G>C	c.(1384-1386)Ggc>Cgc	p.G462R		NM_152612.2	NP_689825.2	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	462										endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(5)	22	Colorectal(54;0.105)					TAAGCAGCTGGGCTTCTTCTC	0.582																																					p.G462R		Atlas-SNP	.											CCDC116,lower_third,carcinoma,0,1	CCDC116	56	.	0			c.G1384C						PASS	.						97	78	84					22																	21990901		2203	4300	6503	SO:0001583	missense	164592	exon5			CAGCTGGGCTTCT	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.1384G>C	chr22.hg19:g.21990901G>C	ENSP00000292779:p.Gly462Arg	74.0	0.0	.		76.0	13.0	.	NM_152612	Q8N9Y9	Missense_Mutation	SNP	ENST00000292779.3	hg19	CCDS13791.1	.	.	.	.	.	.	.	.	.	.	G	18.04	3.534618	0.64972	.	.	ENSG00000161180	ENST00000292779	T	0.33216	1.42	4.78	4.78	0.61160	.	0.000000	0.45361	D	0.000368	T	0.45875	0.1364	L	0.39898	1.24	0.33807	D	0.627382	D	0.89917	1.0	D	0.97110	1.0	T	0.57653	-0.7774	10	0.87932	D	0	-29.332	13.5001	0.61449	0.0:0.0:1.0:0.0	.	462	Q8IYX3-2	.	R	462	ENSP00000292779:G462R	ENSP00000292779:G462R	G	+	1	0	CCDC116	20320901	1.000000	0.71417	0.998000	0.56505	0.460000	0.32559	4.725000	0.61979	2.655000	0.90218	0.585000	0.79938	GGC	.	.	.	none		0.582	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612		C	21990901	G	C	21990901	3	2	191	1	0	0	0	0	1	0	0	0	2755	1232	43	4	1398	4	CCDC116	22	21990901	Missense_Mutation	SNP	G	TCGA-GL-A9DD-01A-11D-A36X-10		21990901	29313665	104	11397											
MN1	4330	hgsc.bcm.edu	37	chr22	28194894	28194894	+	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	ttttggcgctgctgctgctgCtgctgttgctgttgctgttg	0	18	14	9	1	0	0	0	0	0	0	0	0	0	0	0	1	7	11	0	1	0	5	rs202212250		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr22:28194894C>T	ENST00000302326.4	-	1	2592	c.1638G>A	c.(1636-1638)caG>caA	p.Q546Q		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	546	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						gctgctgctgctgctgttgct	0.642			T	ETV6	"AML, meningioma"																																p.Q546Q		Atlas-SNP	.		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"L, O"	.	MN1	122	.	0			c.G1638A						PASS	.						4	5	5					22																	28194894		1986	4018	6004	SO:0001819	synonymous_variant	4330	exon1			CTGCTGCTGCTGT	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.1638G>A	chr22.hg19:g.28194894C>T		62.0	0.0	.		53.0	6.0	.	NM_002430	A9Z1V9	Silent	SNP	ENST00000302326.4	hg19	CCDS42998.1																																																																																			.	.	.	none		0.642	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430		T	28194894	C	T	28194894	2	4	191	1	0	0	0	0	0	0	0	1	9680	796	28	2		2	MN1	22	28194894	Silent	SNP	C	TCGA-GL-A9DD-01A-11D-A36X-10	6203993	28194894	23109672	105	11398											
MAP3K15	389840	hgsc.bcm.edu	37	chrX	19389154	19389154	+	Missense_Mutation	SNP	A	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	cgaacatccagtggggcctaAttaagtggttcctcaaaatt	12	11	9	9	1	1	0	1	0	0	0	3	1	3	0	3	3	1	1	3	3	5	4			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chrX:19389154A>C	ENST00000338883.4	-	24	3322	c.3323T>G	c.(3322-3324)aTt>aGt	p.I1108S	MAP3K15_ENST00000518578.1_5'UTR|MAP3K15_ENST00000469203.2_Missense_Mutation_p.I940S|MAP3K15_ENST00000359173.3_Missense_Mutation_p.I543S	NM_001001671.3	NP_001001671.3	Q6ZN16	M3K15_HUMAN	mitogen-activated protein kinase kinase kinase 15	1108							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)					GTGGGGCCTAATTAAGTGGTT	0.433																																					p.I1108S		Atlas-SNP	.											.	MAP3K15	108	.	0			c.T3323G						PASS	.						44	44	44					X																	19389154		2203	4300	6503	SO:0001583	missense	389840	exon24			GGCCTAATTAAGT	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.3323T>G	chrX.hg19:g.19389154A>C	ENSP00000345629:p.Ile1108Ser	202.0	0.0	.		191.0	78.0	.	NM_001001671	A2AI49|A2AI50|A6NJ61|Q5JPR4|Q6ZMV3	Missense_Mutation	SNP	ENST00000338883.4	hg19		.	.	.	.	.	.	.	.	.	.	A	16.69	3.192878	0.58017	.	.	ENSG00000180815	ENST00000338883;ENST00000359173;ENST00000469203	D;D;D	0.82893	-1.63;-1.66;-1.59	5.25	4.05	0.47172	.	0.045663	0.85682	D	0.000000	D	0.89230	0.6656	M	0.87180	2.865	0.80722	D	1	D;P	0.56035	0.974;0.736	P;B	0.55871	0.786;0.221	D	0.89322	0.3641	10	0.87932	D	0	.	10.8165	0.46580	0.8561:0.0:0.0:0.1439	.	583;1108	Q6ZN16-3;Q6ZN16	.;M3K15_HUMAN	S	1108;543;940	ENSP00000345629:I1108S;ENSP00000352093:I543S;ENSP00000428356:I940S	ENSP00000345629:I1108S	I	-	2	0	MAP3K15	19299075	1.000000	0.71417	0.987000	0.45799	0.992000	0.81027	6.988000	0.76212	0.705000	0.31890	0.451000	0.29950	ATT	.	.	.	none		0.433	MAP3K15-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001001671		C	19389154	A	C	19389154	3	2	191	1	0	0	0	0	1	0	0	0	9256	101	4	5	642	5	MAP3K15	23	19389154	Missense_Mutation	SNP	A	TCGA-GL-A9DD-01A-11D-A36X-10		19389154	135881406	106	11399											
KAZ	23254	hgsc.bcm.edu	37	chr1	15428105	15428105	+	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	tggctgaatgacattggcctGtcccagtactcccaggcctt	7	11	10	13	0	0	2	0	2	0	0	2	2	2	2	4	3	1	2	4	3	2	3			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:15428105G>A	ENST00000376030.2	+	11	1908	c.1614G>A	c.(1612-1614)ctG>ctA	p.L538L		NM_201628.2	NP_963922.2	Q674X7	KAZRN_HUMAN	kazrin, periplakin interacting protein	538	SAM 2. {ECO:0000255|PROSITE- ProRule:PRU00184}.				keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(1)|prostate(2)	25						ACATTGGCCTGTCCCAGTACT	0.577																																					p.L538L		Atlas-SNP	.											.	KAZN	57	.	0			c.G1614A						PASS	.						46	38	40					1																	15428105		2197	4282	6479	SO:0001819	synonymous_variant	23254	exon11			TGGCCTGTCCCAG	AY505119	CCDS30604.1, CCDS41267.1, CCDS152.2, CCDS41268.1	1p36.21	2014-02-12	2011-01-31		ENSG00000189337	ENSG00000189337		"Sterile alpha motif (SAM) domain containing"	29173	protein-coding gene	gene with protein product						15337775, 18840647	Standard	NM_015209		Approved	KIAA1026, KAZRIN, FLJ43806	uc001avm.4	Q674X7	OTTHUMG00000002042	ENST00000376030.2:c.1614G>A	chr1.hg19:g.15428105G>A		87.0	0.0	.		73.0	28.0	.	NM_201628	B0QYQ0|B1AK78|Q5TGF1|Q674X4|Q674X6|Q6ZUD1|Q8IYN7|Q8N409|Q9UIL2|Q9UPX4	Silent	SNP	ENST00000376030.2	hg19	CCDS152.2																																																																																			.	.	.	none		0.577	KAZN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005690.2	NM_001017999		A	15428105	G	A	15428105	2	1	192	1	0	0	0	0	0	0	0	1	7995	1364	48	2		2	KAZ	1	15428105	Silent	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10		15428105	233822516	1	11400											
SFRS4	6429	hgsc.bcm.edu	37	chr1	29475201	29475201	+	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	cgggatggagatctggactgGgagcggtcagtgtcttcctt	6	11	16	8	2	3	1	1	0	2	1	4	5	4	4	1	5	1	0	1	5	0	2			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:29475201G>C	ENST00000373795.4	-	6	1440	c.1206C>G	c.(1204-1206)tcC>tcG	p.S402S	SRSF4_ENST00000466448.1_5'UTR|RP11-242O24.3_ENST00000413004.1_lincRNA|SRSF4_ENST00000546138.1_3'UTR	NM_005626.4	NP_005617.2	Q08170	SRSF4_HUMAN	serine/arginine-rich splicing factor 4	402	Arg/Ser-rich (RS domain).				gene expression (GO:0010467)|hematopoietic progenitor cell differentiation (GO:0002244)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(1)	27						ATCTGGACTGGGAGCGGTCAG	0.582																																					p.S402S		Atlas-SNP	.											.	SRSF4	44	.	0			c.C1206G						PASS	.						141	145	144					1																	29475201		2203	4300	6503	SO:0001819	synonymous_variant	6429	exon6			GGACTGGGAGCGG	BC002781	CCDS333.1	1p35.3	2013-02-12	2010-06-22	2010-06-22	ENSG00000116350	ENSG00000116350		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10786	protein-coding gene	gene with protein product	"SR splicing factor 4"	601940	"splicing factor, arginine/serine-rich 4"	SFRS4		8321209, 20516191	Standard	NM_005626		Approved	SRP75	uc001bro.3	Q08170	OTTHUMG00000003663	ENST00000373795.4:c.1206C>G	chr1.hg19:g.29475201G>C		74.0	0.0	.		71.0	24.0	.	NM_005626	Q5VXP1|Q9BUA4|Q9UEB5	Silent	SNP	ENST00000373795.4	hg19	CCDS333.1																																																																																			.	.	.	none		0.582	SRSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010392.1	NM_005626		C	29475201	G	C	29475201	2	2	192	1	0	0	0	0	0	0	0	1	14192	1219	43	4		4	SFRS4	1	29475201	Silent	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10	14047096	29475201	219775420	2	11401											
IPP	3652	hgsc.bcm.edu	37	chr1	46206791	46206792	+	Frame_Shift_Ins	INS	-	-	CC																															gaactcttctccactatgaaINScctccaagaaatggacatga																										TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:46206791_46206792insCC	ENST00000396478.3	-	3	607_608	c.505_506insGG	c.(505-507)gttfs	p.V169fs		NM_005897.2	NP_005888.1	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	169						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	actin binding (GO:0003779)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|stomach(2)	20	Acute lymphoblastic leukemia(166;0.155)					TCCACTATGAACCTCCAAGAAA	0.406																																					p.V169fs		Atlas-Indel,Pindel	.											.	IPP	66	.	0			c.506_507insGG						PASS	.																																			SO:0001589	frameshift_variant	3652	exon3			.	BC032544	CCDS30702.1, CCDS44132.1	1p34-p32	2013-01-30			ENSG00000197429	ENSG00000197429		"Kelch-like", "BTB/POZ domain containing"	6108	protein-coding gene	gene with protein product	"kelch-like family member 27"	147485				1905535, 8432546	Standard	NM_005897		Approved	KLHL27	uc001cou.3	Q9Y573	OTTHUMG00000008004	ENST00000396478.3:c.504_505dupGG	chr1.hg19:g.46206792_46206793dupCC	ENSP00000379739:p.Val169fs	105.0	0.0	0		133.0	56.0	0.421053	NM_001145349	A2A6V4|D3DQ11|Q8N5C3	Frame_Shift_Ins	INS	ENST00000396478.3	hg19	CCDS30702.1																																																																																			.	.	.	none		0.406	IPP-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021974.3	NM_005897		CC	46206792	-	CC	46206791	7	5	192	1	0	1	1	0	0	0	0	0	7807	43	2	0	1378	0	IPP	1	46206791	Frame_Shift_Ins	INS	-	TCGA-GL-A9DE-01A-11D-A36X-10	16731590	46206791	203043830	3	11402											
KIAA0494	9813	hgsc.bcm.edu	37	chr1	47144277	47144277	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcagcttcccatccacgtcCtggccagtcttgcggaataa	8	10	9	14	2	2	0	1	0	1	0	5	1	5	1	4	2	2	1	4	2	2	3			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:47144277C>T	ENST00000371933.3	-	11	2320	c.1344G>A	c.(1342-1344)caG>caA	p.Q448Q	EFCAB14-AS1_ENST00000418985.1_RNA|EFCAB14_ENST00000544071.1_Intron|EFCAB14-AS1_ENST00000442839.1_RNA	NM_014774.2	NP_055589.1	O75071	EFC14_HUMAN	EF-hand calcium binding domain 14	448	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)										CATCCACGTCCTGGCCAGTCT	0.423																																					p.Q448Q		Atlas-SNP	.											.	.	.	.	0			c.G1344A						PASS	.						84	85	84					1																	47144277		2203	4300	6503	SO:0001819	synonymous_variant	9813	exon11			CACGTCCTGGCCA	AB007963	CCDS30706.1	1p33	2013-01-10	2012-11-29	2012-11-29	ENSG00000159658	ENSG00000159658		"EF-hand domain containing"	29051	protein-coding gene	gene with protein product			"KIAA0494"	KIAA0494		9455484	Standard	NM_014774		Approved		uc001cqk.4	O75071	OTTHUMG00000007992	ENST00000371933.3:c.1344G>A	chr1.hg19:g.47144277C>T		130.0	0.0	.		124.0	57.0	.	NM_014774	D3DQ23|Q5SXB8	Silent	SNP	ENST00000371933.3	hg19	CCDS30706.1																																																																																			.	.	.	none		0.423	EFCAB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021931.1	NM_014774		T	47144277	C	T	47144277	2	4	192	1	0	0	0	0	0	0	0	1	8186	680	24	2		2	KIAA0494	1	47144277	Silent	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10	937486	47144277	202106344	4	11403											
SPATA6	54558	hgsc.bcm.edu	37	chr1	48865170	48865170	+	Missense_Mutation	SNP	A	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	ggagagtgtgattttgaagaAattgtaggctgttcgtagtt	10	15	14	2	1	0	4	0	2	0	2	1	5	0	4	0	2	0	5	0	2	4	7			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:48865170A>C	ENST00000371847.3	-	7	797	c.633T>G	c.(631-633)atT>atG	p.I211M	SPATA6_ENST00000371843.3_Missense_Mutation_p.I211M|SPATA6_ENST00000463938.1_5'UTR|SPATA6_ENST00000396199.3_Missense_Mutation_p.I139M	NM_019073.2	NP_061946.1	Q9NWH7	SPAT6_HUMAN	spermatogenesis associated 6	211					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						ATTTTGAAGAAATTGTAGGCT	0.418																																					p.I211M		Atlas-SNP	.											.	SPATA6	45	.	0			c.T633G						PASS	.						267	271	270					1																	48865170		2203	4300	6503	SO:0001583	missense	54558	exon7			TGAAGAAATTGTA	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.633T>G	chr1.hg19:g.48865170A>C	ENSP00000360913:p.Ile211Met	123.0	0.0	.		152.0	58.0	.	NM_019073	Q5T3N7|Q8WUE6	Missense_Mutation	SNP	ENST00000371847.3	hg19	CCDS551.1	.	.	.	.	.	.	.	.	.	.	A	16.85	3.236288	0.58886	.	.	ENSG00000132122	ENST00000371847;ENST00000371843;ENST00000396199;ENST00000371841	T;T;T;T	0.54675	2.59;2.57;2.58;0.56	5.57	0.164	0.14990	.	0.205873	0.41938	D	0.000789	T	0.53449	0.1797	L	0.43152	1.355	0.35753	D	0.819568	D;D;D;D	0.76494	0.998;0.999;0.998;0.998	D;D;D;D	0.76575	0.967;0.988;0.983;0.983	T	0.59878	-0.7371	10	0.87932	D	0	.	0.4593	0.00513	0.4101:0.1327:0.1989:0.2582	.	139;139;211;211	B4DX17;A8MU33;Q9NWH7-2;Q9NWH7	.;.;.;SPAT6_HUMAN	M	211;211;139;52	ENSP00000360913:I211M;ENSP00000360909:I211M;ENSP00000379502:I139M;ENSP00000360907:I52M	ENSP00000360907:I52M	I	-	3	3	SPATA6	48637757	0.814000	0.29104	1.000000	0.80357	0.991000	0.79684	-0.141000	0.10327	0.356000	0.24157	-0.421000	0.06004	ATT	.	.	.	none		0.418	SPATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021347.1	NM_019073		C	48865170	A	C	48865170	3	2	192	1	0	0	0	0	1	0	0	0	15025	10	1	5	861	5	SPATA6	1	48865170	Missense_Mutation	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10	1720893	48865170	200385451	5	11404											
CACHD1	57685	hgsc.bcm.edu	37	chr1	65107535	65107535	+	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	tcatcatttacctgtcagctGgcattacatcaaaggactct	11	13	6	11	0	5	0	4	0	1	0	5	1	5	1	1	2	3	2	1	2	3	3			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:65107535G>T	ENST00000371073.2	+	8	1039	c.1039G>T	c.(1039-1041)Ggc>Tgc	p.G347C	CACHD1_ENST00000290039.5_Missense_Mutation_p.G296C|CACHD1_ENST00000495994.1_3'UTR			Q5VU97	CAHD1_HUMAN	cache domain containing 1	347	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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						CCTGTCAGCTGGCATTACATC	0.383																																					p.G296C		Atlas-SNP	.											.	CACHD1	125	.	0			c.G886T						PASS	.						131	124	127					1																	65107535		2203	4300	6503	SO:0001583	missense	57685	exon8			TCAGCTGGCATTA	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.1039G>T	chr1.hg19:g.65107535G>T	ENSP00000360113:p.Gly347Cys	134.0	0.0	.		174.0	27.0	.	NM_020925	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Missense_Mutation	SNP	ENST00000371073.2	hg19		.	.	.	.	.	.	.	.	.	.	G	29.1	4.979116	0.92982	.	.	ENSG00000158966	ENST00000371073;ENST00000290039	T;T	0.49139	0.79;0.79	5.77	5.77	0.91146	von Willebrand factor, type A (2);	0.000000	0.85682	D	0.000000	T	0.52517	0.1739	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.57705	-0.7765	10	0.87932	D	0	-35.1798	19.9906	0.97362	0.0:0.0:1.0:0.0	.	347	Q5VU97	CAHD1_HUMAN	C	347;296	ENSP00000360113:G347C;ENSP00000290039:G296C	ENSP00000290039:G296C	G	+	1	0	CACHD1	64880123	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	9.468000	0.97676	2.729000	0.93468	0.609000	0.83330	GGC	.	.	.	none		0.383	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925		T	65107535	G	T	65107535	3	4	192	1	0	0	0	0	1	0	0	0	2539	1348	47	4	916	4	CACHD1	1	65107535	Missense_Mutation	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10	16242365	65107535	184143086	6	11405											
FAM40A	85369	hgsc.bcm.edu	37	chr1	110577332	110577364	+	In_Frame_Del	DEL	CCGCCGGCAGCCGCACAGCCACCACCCGGGGCA	CCGCCGGCAGCCGCACAGCCACCACCCGGGGCA	-																															cccagcccccgccacctccgCcgccggcagccgcacagcca																										TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	CCGCCGGCAGCCGCACAGCCACCACCCGGGGCA	CCGCCGGCAGCCGCACAGCCACCACCCGGGGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:110577332_110577364delCCGCCGGCAGCCGCACAGCCACCACCCGGGGCA	ENST00000369795.3	+	1	95_127	c.73_105delCCGCCGGCAGCCGCACAGCCACCACCCGGGGCA	c.(73-105)ccgccggcagccgcacagccaccacccggggcadel	p.PPAAAQPPPGA25del	STRIP1_ENST00000369796.1_Intron|STRIP1_ENST00000369794.2_In_Frame_Del_p.PPAAAQPPPGA25del	NM_033088.3	NP_149079.2	Q5VSL9	STRP1_HUMAN	striatin interacting protein 1	25	Pro-rich.				cortical actin cytoskeleton organization (GO:0030866)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)											GCCACCTCCGCCGCCGGCAGCCGCACAGCCACCAcccggggcaccgcgggccg	0.712																																					p.24_35del		Pindel	.											.	STRIP1	1	.	0			c.72_104del						PASS	.																																			SO:0001651	inframe_deletion	85369	exon1			.	AK027649	CCDS30798.1, CCDS59197.1	1p13.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000143093	ENSG00000143093			25916	protein-coding gene	gene with protein product	"FAR11 factor arrest 11 homolog A (yeast)"		"family with sequence similarity 40, member A"	FAM40A		11214970, 12588993, 22782902, 22298706, 18782753	Standard	NM_033088		Approved	FLJ14743, KIAA1761, FAR11A	uc001dza.2	Q5VSL9	OTTHUMG00000170607	ENST00000369795.3:c.73_105delCCGCCGGCAGCCGCACAGCCACCACCCGGGGCA	chr1.hg19:g.110577332_110577364delCCGCCGGCAGCCGCACAGCCACCACCCGGGGCA	ENSP00000358810:p.Pro25_Ala35del	208.0	0.0	.		229.0	12.0	0.052	NM_033088	Q0V925|Q5VSL8|Q658K2|Q6ZV31|Q8N598|Q96SN2|Q9C0A2	In_Frame_Del	DEL	ENST00000369795.3	hg19	CCDS30798.1																																																																																			.	.	.	none		0.712	STRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032213.1	NM_033088		-	110577364	CCGCCGGCAGCCGCACAGCCACCACCCGGGGCA	-	110577332	7	5	192	1	0	1	0	1	0	0	0	0	5567	739	26	0	75	0	FAM40A	1	110577332	In_Frame_Del	DEL	CCGCCGGCAGCCGCACAGCCACCACCCGGGGCA	TCGA-GL-A9DE-01A-11D-A36X-10	45469797	110577332	138673289	7	11406											
IGSF3	3321	hgsc.bcm.edu	37	chr1	117122158	117122158	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcctgcagcactgtgagccGgtagagcaccggggagagcc	8	5	16	12	2	0	3	0	1	0	2	0	4	0	3	4	3	6	4	4	3	1	1			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:117122158G>A	ENST00000369486.3	-	10	3955	c.3190C>T	c.(3190-3192)Cgg>Tgg	p.R1064W	IGSF3_ENST00000369483.1_Missense_Mutation_p.R1084W|IGSF3_ENST00000318837.6_Missense_Mutation_p.R1084W	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	1064	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)		ACTGTGAGCCGGTAGAGCACC	0.637																																					p.R1084W		Atlas-SNP	.											.	IGSF3	294	.	0			c.C3250T						PASS	.						48	50	49					1																	117122158		2203	4300	6503	SO:0001583	missense	3321	exon11			TGAGCCGGTAGAG	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.3190C>T	chr1.hg19:g.117122158G>A	ENSP00000358498:p.Arg1064Trp	68.0	0.0	.		90.0	13.0	.	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	hg19	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	G	16.98	3.271626	0.59649	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.22945	1.93;1.93;1.93	4.67	2.66	0.31614	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.124838	0.53938	D	0.000043	T	0.27313	0.0670	L	0.48642	1.525	0.38363	D	0.944664	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.984	T	0.06698	-1.0812	10	0.87932	D	0	-49.5391	7.5572	0.27831	0.0:0.1593:0.5132:0.3275	.	1064;1084	O75054;A6NJZ6	IGSF3_HUMAN;.	W	1064;1084;1084	ENSP00000358498:R1064W;ENSP00000358495:R1084W;ENSP00000321184:R1084W	ENSP00000321184:R1084W	R	-	1	2	IGSF3	116923681	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	2.081000	0.41596	1.154000	0.42482	0.462000	0.41574	CGG	.	.	.	none		0.637	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		A	117122158	G	A	117122158	3	1	192	1	0	0	0	0	1	0	0	0	7608	1115	39	1	402	1	IGSF3	1	117122158	Missense_Mutation	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10	6544826	117122158	132128463	8	11407											
POLR3GL	84265	hgsc.bcm.edu	37	chr1	145457964	145457964	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aatcgatggcattgtcaatcGgacctgacatctgatatttg	11	13	9	8	2	2	2	1	2	1	0	4	4	2	3	1	2	0	1	1	2	3	3			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:145457964G>A	ENST00000369314.1	-	4	402	c.296C>T	c.(295-297)cCg>cTg	p.P99L	POLR3GL_ENST00000369313.3_Intron	NM_032305.1	NP_115681.1	Q9BT43	RPC7L_HUMAN	polymerase (RNA) III (DNA directed) polypeptide G (32kD)-like	99					gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)				endometrium(2)|large_intestine(1)|lung(1)	4	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					ATTGTCAATCGGACCTGACAT	0.483																																					p.P99L		Atlas-SNP	.											.	POLR3GL	21	.	0			c.C296T						PASS	.						175	140	152					1																	145457964		2203	4300	6503	SO:0001583	missense	84265	exon4			TCAATCGGACCTG	BC004355	CCDS72875.1	1q21.1	2008-02-05	2006-12-14		ENSG00000121851	ENSG00000121851			28466	protein-coding gene	gene with protein product			"polymerase (RNA) III (DNA directed) polypeptide G (32kD) like"			12477932	Standard	NM_032305		Approved	flj32422, MGC3200	uc001enp.1	Q9BT43	OTTHUMG00000013739	ENST00000369314.1:c.296C>T	chr1.hg19:g.145457964G>A	ENSP00000358320:p.Pro99Leu	67.0	0.0	.		88.0	34.0	.	NM_032305	B1MVG5	Missense_Mutation	SNP	ENST00000369314.1	hg19	CCDS914.1	.	.	.	.	.	.	.	.	.	.	G	19.56	3.850236	0.71719	.	.	ENSG00000121851	ENST00000369314	.	.	.	5.32	4.4	0.53042	.	0.212727	0.38436	N	0.001698	T	0.56934	0.2019	M	0.77820	2.39	0.80722	D	1	D	0.69078	0.997	P	0.54026	0.74	T	0.59161	-0.7506	9	0.30078	T	0.28	-14.425	11.9585	0.52995	0.0836:0.0:0.9164:0.0	.	99	Q9BT43	RPC7L_HUMAN	L	99	.	ENSP00000358320:P99L	P	-	2	0	POLR3GL	144169321	1.000000	0.71417	0.834000	0.33040	0.955000	0.61496	4.357000	0.59436	1.471000	0.48121	0.655000	0.94253	CCG	.	.	.	none		0.483	POLR3GL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038510.1	NM_032305		A	145457964	G	A	145457964	3	1	192	1	0	0	0	0	1	0	0	0	12242	1116	39	1	380	1	POLR3GL	1	145457964	Missense_Mutation	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10	28335806	145457964	103792657	9	11408											
CTSK	1513	hgsc.bcm.edu	37	chr1	150778422	150778422	+	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	cccattctgggatataaaggGtgtcattactgcgggaatga	11	11	12	7	1	2	1	1	1	1	0	2	3	2	3	1	3	2	0	1	3	5	4			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:150778422G>C	ENST00000271651.3	-	4	424	c.314C>G	c.(313-315)aCc>aGc	p.T105S	CTSK_ENST00000480670.1_5'UTR	NM_000396.3	NP_000387.1	P43235	CATK_HUMAN	cathepsin K	105					bone resorption (GO:0045453)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|intramembranous ossification (GO:0001957)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|fibronectin binding (GO:0001968)|proteoglycan binding (GO:0043394)			cervix(1)|endometrium(1)|lung(4)|skin(1)	7	all_cancers(9;2.32e-51)|all_epithelial(9;3.89e-42)|all_lung(15;4.59e-35)|Lung NSC(24;1.7e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Colorectal(459;0.171)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0485)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)			GATATAAAGGGTGTCATTACT	0.458																																					p.T105S		Atlas-SNP	.											.	CTSK	27	.	0			c.C314G						PASS	.						121	116	118					1																	150778422		2203	4300	6503	SO:0001583	missense	1513	exon4			TAAAGGGTGTCAT	BC016058	CCDS969.1	1q21	2008-02-05	2006-12-05		ENSG00000143387	ENSG00000143387		"Cathepsins"	2536	protein-coding gene	gene with protein product		601105	"cathepsin K (pycnodysostosis)"	CTSO2, CTSO, PYCD		7818555	Standard	NM_000396		Approved	PKND	uc001evp.2	P43235	OTTHUMG00000035008	ENST00000271651.3:c.314C>G	chr1.hg19:g.150778422G>C	ENSP00000271651:p.Thr105Ser	99.0	0.0	.		115.0	47.0	.	NM_000396	Q6FHS6	Missense_Mutation	SNP	ENST00000271651.3	hg19	CCDS969.1	.	.	.	.	.	.	.	.	.	.	G	2.425	-0.332121	0.05314	.	.	ENSG00000143387	ENST00000271651;ENST00000443913	D;D	0.97553	-4.43;-4.43	5.38	5.38	0.77491	.	0.289753	0.38492	N	0.001665	D	0.86234	0.5884	L	0.31120	0.905	0.38859	D	0.956449	P	0.42993	0.797	B	0.32980	0.156	D	0.87916	0.2700	10	0.02654	T	1	.	12.0088	0.53276	0.0:0.0:0.8273:0.1727	.	105	P43235	CATK_HUMAN	S	105;164	ENSP00000271651:T105S;ENSP00000405083:T164S	ENSP00000271651:T105S	T	-	2	0	CTSK	149045046	1.000000	0.71417	0.996000	0.52242	0.431000	0.31685	3.309000	0.51903	2.683000	0.91414	0.561000	0.74099	ACC	.	.	.	none		0.458	CTSK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084732.1	NM_000396		C	150778422	G	C	150778422	3	2	192	1	0	0	0	0	1	0	0	0	4039	1261	44	4	695	4	CTSK	1	150778422	Missense_Mutation	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10	5320458	150778422	98472199	10	11409											
TCHH	7062	hgsc.bcm.edu	37	chr1	152081020	152081020	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgcagctgttcctcctcgCggaattttctgtcacggtcc	4	12	11	14	4	2	0	1	0	1	0	6	1	5	1	3	3	1	3	3	3	1	3			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:152081020C>T	ENST00000368804.1	-	2	4672	c.4673G>A	c.(4672-4674)cGc>cAc	p.R1558H		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1558	23 X 26 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TTCCTCCTCGCGGAATTTTCT	0.612																																					p.R1558H		Atlas-SNP	.											.	TCHH	275	.	0			c.G4673A						PASS	.						59	60	60					1																	152081020		1888	4101	5989	SO:0001583	missense	7062	exon3			TCCTCGCGGAATT	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.4673G>A	chr1.hg19:g.152081020C>T	ENSP00000357794:p.Arg1558His	82.0	0.0	.		79.0	23.0	.	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	-	8.616	0.890198	0.17613	.	.	ENSG00000159450	ENST00000368804	T	0.05925	3.37	3.3	1.34	0.21922	.	.	.	.	.	T	0.05135	0.0137	L	0.46157	1.445	0.09310	N	1	D	0.89917	1.0	D	0.63192	0.912	T	0.29150	-1.0021	9	0.44086	T	0.13	-1.3601	4.0858	0.09947	0.4099:0.4715:0.0:0.1186	.	1558	Q07283	TRHY_HUMAN	H	1558	ENSP00000357794:R1558H	ENSP00000357794:R1558H	R	-	2	0	TCHH	150347644	0.000000	0.05858	0.007000	0.13788	0.032000	0.12392	-0.112000	0.10791	0.211000	0.20683	0.460000	0.39030	CGC	.	.	.	none		0.612	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		T	152081020	C	T	152081020	3	4	192	1	0	0	0	0	1	0	0	0	15712	768	27	1	1162	1	TCHH	1	152081020	Missense_Mutation	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10	1302598	152081020	97169601	11	11410											
LYST	1130	hgsc.bcm.edu	37	chr1	235969849	235969849	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgaggagaatctgaataagCttgctgatgatgaaaagaag	16	9	12	4	0	1	7	0	5	1	2	1	8	1	7	0	1	2	2	0	1	6	2			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:235969849C>T	ENST00000389794.3	-	6	2761	c.2587G>A	c.(2587-2589)Gct>Act	p.A863T	LYST_ENST00000536965.1_Missense_Mutation_p.A863T|LYST_ENST00000389793.2_Missense_Mutation_p.A863T			Q99698	LYST_HUMAN	lysosomal trafficking regulator	863					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)			TCTGAATAAGCTTGCTGATGA	0.408																																					p.A863T		Atlas-SNP	.											.	LYST	370	.	0			c.G2587A						PASS	.						164	164	164					1																	235969849		2203	4300	6503	SO:0001583	missense	1130	exon6			AATAAGCTTGCTG	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.2587G>A	chr1.hg19:g.235969849C>T	ENSP00000374444:p.Ala863Thr	116.0	0.0	.		149.0	57.0	.	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	hg19	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	C	11.63	1.696527	0.30142	.	.	ENSG00000143669	ENST00000389794;ENST00000389793;ENST00000536965	T;T;T	0.62364	0.03;0.03;1.18	5.48	3.56	0.40772	.	1.082300	0.07038	N	0.829561	T	0.52041	0.1710	L	0.34521	1.04	0.09310	N	1	P;B	0.40660	0.726;0.005	B;B	0.39217	0.294;0.004	T	0.39440	-0.9614	10	0.45353	T	0.12	.	7.6404	0.28290	0.2933:0.6315:0.0:0.0753	.	863;863	Q99698-3;Q99698	.;LYST_HUMAN	T	863	ENSP00000374444:A863T;ENSP00000374443:A863T;ENSP00000438315:A863T	ENSP00000374443:A863T	A	-	1	0	LYST	234036472	0.000000	0.05858	0.579000	0.28588	0.710000	0.40934	0.322000	0.19576	0.648000	0.30732	0.655000	0.94253	GCT	.	.	.	none		0.408	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			T	235969849	C	T	235969849	3	4	192	1	0	0	0	0	1	0	0	0	9135	797	28	2	9010	2	LYST	1	235969849	Missense_Mutation	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10	83888829	235969849	13280772	12	11411											
ZNF695	57116	hgsc.bcm.edu	37	chr1	247150413	247150414	+	Missense_Mutation	DNP	TT	TT	AA																															tggccaaaggctttgccacaTtcttcacatttgtagggttt																										TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr1:247150413_247150414TT>AA	ENST00000339986.7	-	4	1550_1551	c.1403_1404AA>TT	c.(1402-1404)gAA>gTT	p.E468V	ZNF695_ENST00000498046.2_Intron|ZNF695_ENST00000487338.2_Intron	NM_020394.4	NP_065127	Q8IW36	ZN695_HUMAN	zinc finger protein 695	468					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)			CTTTGCCACATTCTTCACATTT	0.386																																					p.E468D|p.E468V		Atlas-SNP	.											.	ZNF695	55	.	0			c.A1404T|c.A1403T						PASS	.																																			SO:0001583	missense	57116	exon4			GCCACATTCTTCA|CCACATTCTTCAC		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.1403_1404delinsAA	chr1.hg19:g.247150413_247150414delinsAA	ENSP00000341236:p.Glu468Val	69.0|68.0	0.0	.		99.0	48.0	.	NM_020394	Q5T0N9|Q5T0P1|Q5T0P3|Q7Z2W8|Q7Z648	Missense_Mutation	SNP	ENST00000339986.7	hg19	CCDS44344.1																																																																																			.	.	.	none		0.386	ZNF695-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097823.5	NM_020394		AA	247150414	TT	AA	247150413	3	1	192	1	0	0	0	0	1	0	0	0	18110	1490	52	5	147	5	ZNF695	1	247150413	Missense_Mutation	DNP	TT	TCGA-GL-A9DE-01A-11D-A36X-10	11180564	247150413	2100208	13	11412											
LTBP1	4052	hgsc.bcm.edu	37	chr2	33525581	33525581	+	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	gtgcaaaaataccgagggctCcttcaggtgcacctgtggac	10	8	12	11	1	1	0	1	0	0	0	2	2	2	1	3	3	3	3	3	3	3	2			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr2:33525581C>A	ENST00000404816.2	+	21	3652	c.3299C>A	c.(3298-3300)tCc>tAc	p.S1100Y	LTBP1_ENST00000272273.5_Missense_Mutation_p.S40Y|LTBP1_ENST00000418533.2_Missense_Mutation_p.S774Y|LTBP1_ENST00000498013.1_3'UTR|LTBP1_ENST00000404525.1_Missense_Mutation_p.S721Y|LTBP1_ENST00000402934.1_Missense_Mutation_p.S721Y|LTBP1_ENST00000354476.3_Missense_Mutation_p.S1101Y|LTBP1_ENST00000390003.4_Missense_Mutation_p.S775Y|LTBP1_ENST00000407925.1_Missense_Mutation_p.S774Y			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1100	EGF-like 9; 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)				ACCGAGGGCTCCTTCAGGTGC	0.453																																					p.S1100Y		Atlas-SNP	.											.	LTBP1	317	.	0			c.C3299A						PASS	.						96	96	96					2																	33525581		2203	4300	6503	SO:0001583	missense	4052	exon21			AGGGCTCCTTCAG		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.3299C>A	chr2.hg19:g.33525581C>A	ENSP00000386043:p.Ser1100Tyr	81.0	0.0	.		99.0	36.0	.	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	hg19	CCDS33177.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.1|24.1	4.488575|4.488575	0.84854|0.84854	.|.	.|.	ENSG00000049323|ENSG00000049323	ENST00000415140|ENST00000404816;ENST00000354476;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925;ENST00000272273	.|D;D;D;D;D;D;D;D	.|0.95412	.|-3.7;-3.7;-3.7;-3.7;-3.7;-3.7;-3.7;-3.7	5.39|5.39	5.39|5.39	0.77823|0.77823	.|EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.|.	.|.	.|.	.|.	D|D	0.98226|0.98226	0.9413|0.9413	M|M	0.90870|0.90870	3.155|3.155	0.58432|0.58432	D|D	0.999995|0.999995	.|P;D;D;D;D;D;D	.|0.89917	.|0.879;0.999;1.0;1.0;1.0;1.0;0.999	.|P;D;D;D;D;D;D	.|0.91635	.|0.766;0.995;0.998;0.998;0.991;0.999;0.991	D|D	0.99257|0.99257	1.0889|1.0889	5|9	.|0.87932	.|D	.|0	.|.	17.9453|17.9453	0.89036|0.89036	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|40;1100;774;721;774;775;1101	.|E7EUU6;Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4	.|.;LTBP1_HUMAN;.;.;.;.;.	T|Y	62|1100;1101;775;774;721;721;774;40	.|ENSP00000386043:S1100Y;ENSP00000346467:S1101Y;ENSP00000374653:S775Y;ENSP00000393057:S774Y;ENSP00000384373:S721Y;ENSP00000385359:S721Y;ENSP00000384091:S774Y;ENSP00000272273:S40Y	.|ENSP00000272273:S40Y	P|S	+|+	1|2	0|0	LTBP1|LTBP1	33379085|33379085	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	6.468000|6.468000	0.73551|0.73551	2.532000|2.532000	0.85374|0.85374	0.555000|0.555000	0.69702|0.69702	CCT|TCC	.	.	.	none		0.453	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		A	33525581	C	A	33525581	3	1	192	1	0	0	0	0	1	0	0	0	9080	855	30	4	3436	4	LTBP1	2	33525581	Missense_Mutation	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10		33525581	209673792	14	11413											
ALMS1	7840	hgsc.bcm.edu	37	chr2	73613036	73613037	+	Missense_Mutation	DNP	GA	GA	CT																															catggccgggcgagctggagGaggaggaggaggaggaggag																								rs61156725|rs72319667|rs3074417	byFrequency	TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr2:73613036_73613037GA>CT	ENST00000264448.6	+	1	151_152	c.40_41GA>CT	c.(40-42)GAg>CTg	p.E14L	ALMS1_ENST00000409009.1_Missense_Mutation_p.E14L|ALMS1_ENST00000377715.1_Missense_Mutation_p.E14L	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	14	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CGAGCTggaggaggaggaggag	0.693																																					p.E14Q|p.E14V		Atlas-SNP	.											.	ALMS1	384	.	1	Deletion - In frame(1)	ovary(1)	c.G40C|c.A41T						PASS	.																																			SO:0001583	missense	7840	exon1			CTGGAGGAGGAGG|TGGAGGAGGAGGA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	Exception_encountered	chr2.hg19:g.73613036_73613037delinsCT	ENSP00000264448:p.Glu14Leu	184.0|187.0	0.0	.		314.0|321.0	26.0|32.0	.	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.	.	none		0.693	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		CT	73613037	GA	CT	73613036	3	2	192	1	0	0	0	0	1	0	0	0	535	1175	41	4	42	4	ALMS1	2	73613036	Missense_Mutation	DNP	GA	TCGA-GL-A9DE-01A-11D-A36X-10	40087455	73613036	169586337	15	11414											
PRPF40A	55660	hgsc.bcm.edu	37	chr2	153551067	153551069	+	In_Frame_Del	DEL	GCT	GCT	-																															catgattaccggtaaggcagGctgcatggaagcctgagaca																										TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	GCT	GCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr2:153551067_153551069delGCT	ENST00000410080.1	-	3	825_827	c.284_286delAGC	c.(283-288)cagcct>cct	p.Q95del		NM_017892.3	NP_060362.3	O75400	PR40A_HUMAN	PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae)	122					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						GGTAAGGCAGGCTGCATGGAAGC	0.325																																					p.95_96del		Atlas-Indel,Pindel	.											.	PRPF40A	149	.	0			c.285_287del						PASS	.																																			SO:0001651	inframe_deletion	55660	exon3			.	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.284_286delAGC	chr2.hg19:g.153551067_153551069delGCT	ENSP00000386458:p.Gln95del	448.0	0.0	0		446.0	45.0	0.100897	NM_017892	O43856|O75404|Q8TBQ1|Q9H782|Q9NWU9|Q9P0Q2|Q9Y5A8	In_Frame_Del	DEL	ENST00000410080.1	hg19	CCDS46430.1																																																																																			.	.	.	none		0.325	PRPF40A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333559.2	XM_371575		-	153551069	GCT	-	153551067	7	5	192	1	0	1	0	1	0	0	0	0	12581	1203	42	0	2602	0	PRPF40A	2	153551067	In_Frame_Del	DEL	GCT	TCGA-GL-A9DE-01A-11D-A36X-10	79938031	153551067	89648306	16	11415											
DHRS9	10170	hgsc.bcm.edu	37	chr2	169939934	169939934	+	Missense_Mutation	SNP	A	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	acagagaacctattgaagtgAacctgtttggactcatcagt	13	11	9	8	0	2	3	2	2	0	1	2	5	2	4	2	1	2	1	2	1	4	3			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr2:169939934A>C	ENST00000327239.4	+	6	1913	c.409A>C	c.(409-411)Aac>Cac	p.N137H	DHRS9_ENST00000421653.1_5'UTR|DHRS9_ENST00000357546.2_Missense_Mutation_p.N137H|DHRS9_ENST00000436483.2_Missense_Mutation_p.N137H|DHRS9_ENST00000602501.1_Missense_Mutation_p.N137H|DHRS9_ENST00000432060.2_Missense_Mutation_p.N197H|DHRS9_ENST00000428522.1_Missense_Mutation_p.N137H|DHRS9_ENST00000412271.1_Missense_Mutation_p.N137H	NM_005771.4	NP_005762.2	Q9BPW9	DHRS9_HUMAN	dehydrogenase/reductase (SDR family) member 9	137					9-cis-retinoic acid biosynthetic process (GO:0042904)|androgen metabolic process (GO:0008209)|epithelial cell differentiation (GO:0030855)|progesterone metabolic process (GO:0042448)|retinol metabolic process (GO:0042572)	integral component of endoplasmic reticulum membrane (GO:0030176)	alcohol dehydrogenase (NAD) activity (GO:0004022)|racemase and epimerase activity (GO:0016854)|retinol dehydrogenase activity (GO:0004745)|testosterone dehydrogenase (NAD+) activity (GO:0047035)			breast(1)|endometrium(3)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	13						TATTGAAGTGAACCTGTTTGG	0.488																																					p.N137H		Atlas-SNP	.											.	DHRS9	29	.	0			c.A409C						PASS	.						148	136	140					2																	169939934		2203	4300	6503	SO:0001583	missense	10170	exon6			GAAGTGAACCTGT	AF067174	CCDS2231.1, CCDS74600.1	2q31.1	2011-09-14			ENSG00000073737	ENSG00000073737		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	16888	protein-coding gene	gene with protein product	"NADP-dependent retinol dehydrogenase/reductase", "3-alpha hydroxysteroid dehydrogenase", "retinol dehydrogenase homolog", "short chain dehydrogenase/reductase family 9C, member 4"	612131				11304534, 11294878, 19027726	Standard	NM_001142270		Approved	RDHL, 3alpha-HSD, RETSDR8, RDH15, SDR9C4	uc010zde.2	Q9BPW9	OTTHUMG00000132180	ENST00000327239.4:c.409A>C	chr2.hg19:g.169939934A>C	ENSP00000316670:p.Asn137His	93.0	0.0	.		96.0	12.0	.	NM_005771	B7Z416|D3DPC1|Q5RKX1|Q9NRA9|Q9NRB0	Missense_Mutation	SNP	ENST00000327239.4	hg19	CCDS2231.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.804239	0.90623	.	.	ENSG00000073737	ENST00000327239;ENST00000357546;ENST00000432060;ENST00000428522;ENST00000436483;ENST00000412271	D;D;D;D;D;D	0.94497	-3.44;-3.44;-3.44;-3.44;-3.44;-3.44	5.93	5.93	0.95920	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.98359	0.9455	H	0.97491	4.015	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.99701	1.1004	10	0.87932	D	0	.	16.0558	0.80805	1.0:0.0:0.0:0.0	.	197;137	B7Z416;Q9BPW9	.;DHRS9_HUMAN	H	137;137;197;137;137;137	ENSP00000316670:N137H;ENSP00000350154:N137H;ENSP00000389241:N197H;ENSP00000388564:N137H;ENSP00000407167:N137H;ENSP00000407747:N137H	ENSP00000316670:N137H	N	+	1	0	DHRS9	169648180	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	9.047000	0.93823	2.281000	0.76405	0.533000	0.62120	AAC	.	.	.	none		0.488	DHRS9-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333612.3	NM_005771		C	169939934	A	C	169939934	3	2	192	1	0	0	0	0	1	0	0	0	4500	246	9	5	415	5	DHRS9	2	169939934	Missense_Mutation	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10	16388867	169939934	73259439	17	11416											
MRPL44	65080	hgsc.bcm.edu	37	chr2	224824598	224824598	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctagaaacttggctgtggAgcagttaacactgagtgaag	12	9	14	6	0	0	3	0	2	0	1	0	4	0	4	0	3	3	4	0	3	4	3			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr2:224824598A>G	ENST00000258383.3	+	2	596	c.527A>G	c.(526-528)gAg>gGg	p.E176G		NM_022915.3	NP_075066.1	Q9H9J2	RM44_HUMAN	mitochondrial ribosomal protein L44	176	RNase III.				mitochondrial translational elongation (GO:0070125)|RNA processing (GO:0006396)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		all_lung(227;0.00679)|Lung NSC(271;0.00855)|Renal(207;0.0112)|all_hematologic(139;0.189)		Epithelial(121;2.51e-10)|all cancers(144;7.89e-08)|Lung(261;0.00705)|LUSC - Lung squamous cell carcinoma(224;0.008)		TTGGCTGTGGAGCAGTTAACA	0.493																																					p.E176G		Atlas-SNP	.											.	MRPL44	31	.	0			c.A527G						PASS	.						116	114	114					2																	224824598		2203	4300	6503	SO:0001583	missense	65080	exon2			CTGTGGAGCAGTT	AK022763	CCDS2459.1	2p24.3-p24.1	2012-09-13			ENSG00000135900	ENSG00000135900		"Mitochondrial ribosomal proteins / large subunits"	16650	protein-coding gene	gene with protein product	"39S ribosomal protein L44, mitochondrial"	611849					Standard	NM_022915		Approved	FLJ12701, FLJ13990	uc002vnr.4	Q9H9J2	OTTHUMG00000133164	ENST00000258383.3:c.527A>G	chr2.hg19:g.224824598A>G	ENSP00000258383:p.Glu176Gly	106.0	0.0	.		98.0	33.0	.	NM_022915	Q53S16|Q6IA62|Q9H821	Missense_Mutation	SNP	ENST00000258383.3	hg19	CCDS2459.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.684531	0.88639	.	.	ENSG00000135900	ENST00000258383	T	0.41400	1.0	5.68	5.68	0.88126	Ribonuclease III (3);	0.157358	0.56097	D	0.000036	T	0.42899	0.1223	M	0.75447	2.3	0.58432	D	0.999996	B	0.27140	0.169	B	0.24848	0.056	T	0.33085	-0.9882	10	0.16420	T	0.52	-0.8659	13.8891	0.63726	1.0:0.0:0.0:0.0	.	176	Q9H9J2	RM44_HUMAN	G	176	ENSP00000258383:E176G	ENSP00000258383:E176G	E	+	2	0	MRPL44	224532842	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.938000	0.75904	2.160000	0.67779	0.519000	0.50382	GAG	.	.	.	none		0.493	MRPL44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256866.2	NM_022915		G	224824598	A	G	224824598	3	3	192	1	0	0	0	0	1	0	0	0	9815	304	11	3	533	3	MRPL44	2	224824598	Missense_Mutation	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10	54884664	224824598	18374775	18	11417											
ASB18	401036	hgsc.bcm.edu	37	chr2	237103670	237103670	+	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	gcgtggggtgagggccaaggCaaagagggactggtagaacg	11	4	20	6	2	0	3	0	1	0	2	0	4	0	4	1	6	1	2	1	6	4	1			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr2:237103670C>G	ENST00000409749.3	-	6	1245	c.1246G>C	c.(1246-1248)Gcc>Ccc	p.A416P	ASB18_ENST00000330842.6_Missense_Mutation_p.A387P|AC079135.1_ENST00000415226.1_RNA|AC079135.1_ENST00000483218.1_RNA	NM_212556.2	NP_997721.2	Q6ZVZ8	ASB18_HUMAN	ankyrin repeat and SOCS box containing 18	416	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					large_intestine(1)|lung(3)|ovary(1)|prostate(1)	6		all_hematologic(139;0.00615)|Renal(207;0.00963)|Breast(86;0.0126)|Acute lymphoblastic leukemia(138;0.0815)		Epithelial(121;2.04e-26)|OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(100;2.88e-05)|Lung(119;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00644)|GBM - Glioblastoma multiforme(43;0.244)		AGGGCCAAGGCAAAGAGGGAC	0.537																																					p.A416P		Atlas-SNP	.											ASB18_ENST00000409749,NS,carcinoma,0,1	ASB18	34	.	0			c.G1246C						PASS	.						63	78	73					2																	237103670		2115	4243	6358	SO:0001583	missense	401036	exon6			CCAAGGCAAAGAG	AK123854	CCDS46548.1	2q37.2	2013-01-10	2011-01-25		ENSG00000182177	ENSG00000182177		"Ankyrin repeat domain containing"	19770	protein-coding gene	gene with protein product			"ankyrin repeat and SOCS box-containing 18"			12076535	Standard	NM_212556		Approved		uc010znh.2	Q6ZVZ8	OTTHUMG00000153086	ENST00000409749.3:c.1246G>C	chr2.hg19:g.237103670C>G	ENSP00000386532:p.Ala416Pro	169.0	0.0	.		133.0	58.0	.	NM_212556	B6ZDL7	Missense_Mutation	SNP	ENST00000409749.3	hg19	CCDS46548.1	.	.	.	.	.	.	.	.	.	.	C	14.68	2.606949	0.46527	.	.	ENSG00000182177	ENST00000330842;ENST00000409749	T;T	0.39592	1.07;1.14	4.65	2.62	0.31277	SOCS protein, C-terminal (1);	.	.	.	.	T	0.52853	0.1760	M	0.68593	2.085	0.09310	N	1	D	0.71674	0.998	D	0.64321	0.924	T	0.36114	-0.9761	9	0.42905	T	0.14	.	4.0084	0.09611	0.1654:0.5748:0.1613:0.0985	.	416	Q6ZVZ8	ASB18_HUMAN	P	387;416	ENSP00000329970:A387P;ENSP00000386532:A416P	ENSP00000329970:A387P	A	-	1	0	ASB18	236768409	0.017000	0.18338	0.127000	0.21898	0.760000	0.43138	0.042000	0.13949	1.127000	0.42034	0.561000	0.74099	GCC	.	.	.	none		0.537	ASB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329436.1	NM_212556		G	237103670	C	G	237103670	3	3	192	1	0	0	0	0	1	0	0	0	1022	710	25	4	157	4	ASB18	2	237103670	Missense_Mutation	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10	12279072	237103670	6095703	19	11418											
IQCA1	79781	hgsc.bcm.edu	37	chr2	237240213	237240213	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cactggtgaggactcctccaTtgcgttcaatgatttgcttc	7	14	9	11	1	1	2	1	2	0	0	4	3	3	3	2	2	2	2	2	2	1	4			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr2:237240213T>C	ENST00000409907.3	-	18	2436	c.2162A>G	c.(2161-2163)aAt>aGt	p.N721S	IQCA1_ENST00000309507.5_Missense_Mutation_p.N718S|IQCA1_ENST00000431676.2_Missense_Mutation_p.N680S	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	721							ATP binding (GO:0005524)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						GACTCCTCCATTGCGTTCAAT	0.498																																					p.N729S		Atlas-SNP	.											.	IQCA1	170	.	0			c.A2186G						PASS	.						60	59	59					2																	237240213		2009	4175	6184	SO:0001583	missense	79781	exon18			CCTCCATTGCGTT	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.2162A>G	chr2.hg19:g.237240213T>C	ENSP00000387347:p.Asn721Ser	74.0	0.0	.		73.0	11.0	.	NM_001270585	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	Missense_Mutation	SNP	ENST00000409907.3	hg19	CCDS46549.1	.	.	.	.	.	.	.	.	.	.	T	0.008	-1.878792	0.00537	.	.	ENSG00000132321	ENST00000409907;ENST00000457693;ENST00000309507;ENST00000431676	D;D;D	0.87887	-2.31;-2.31;-2.31	5.23	1.1	0.20463	.	1.245700	0.05677	N	0.589728	D	0.84074	0.5392	M	0.67953	2.075	0.09310	N	1	B;B;B	0.23128	0.017;0.044;0.08	B;B;B	0.23275	0.028;0.045;0.045	T	0.64993	-0.6276	10	0.30854	T	0.27	.	4.8923	0.13733	0.1115:0.0725:0.1289:0.6871	.	680;729;721	E7EWQ0;E9PH78;Q86XH1	.;.;IQCA1_HUMAN	S	721;729;718;680	ENSP00000387347:N721S;ENSP00000311951:N718S;ENSP00000407213:N680S	ENSP00000311951:N718S	N	-	2	0	IQCA1	236904952	0.059000	0.20769	0.000000	0.03702	0.153000	0.21895	1.431000	0.34925	0.289000	0.22422	0.533000	0.62120	AAT	.	.	.	none		0.498	IQCA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329266.1	NM_024726		C	237240213	T	C	237240213	3	2	192	1	0	0	0	0	1	0	0	0	7809	1493	52	3	314	3	IQCA1	2	237240213	Missense_Mutation	SNP	T	TCGA-GL-A9DE-01A-11D-A36X-10	136543	237240213	5959160	20	11419											
SETD2	29072	hgsc.bcm.edu	37	chr3	47058730	47058730	+	Frame_Shift_Del	DEL	A	A	-																															tacttcagctccttattcatAacaccgtgagtcagctgtcc																										TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr3:47058730delA	ENST00000409792.3	-	21	7590	c.7548delT	c.(7546-7548)gttfs	p.V2516fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2516	Interaction with POLR2A.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CCTTATTCATAACACCGTGAG	0.473			"N, F, S, Mis"		clear cell renal carcinoma																																p.M2517X		Atlas-INDEL	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.7549delA						PASS	.						135	122	126					3																	47058730		2203	4300	6503	SO:0001589	frameshift_variant	29072	exon21			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.7548delT	chr3.hg19:g.47058730delA	ENSP00000386759:p.Val2516fs	46.0	0.0	0		71.0	65.0	0.915493	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Del	DEL	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.	.	none		0.473	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		-	47058730	A	-	47058730	7	5	192	1	0	1	0	1	0	0	0	0	14144	349	13	0	150	0	SETD2	3	47058730	Frame_Shift_Del	DEL	A	TCGA-GL-A9DE-01A-11D-A36X-10		47058730	150963700	21	11420	109	3									
SETD2	29072	hgsc.bcm.edu	37	chr3	47058731	47058732	+	Frame_Shift_Del	DEL	AC	AC	-																															acttcagctccttattcataAcaccgtgagtcagctgtcca																										TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr3:47058731_47058732delAC	ENST00000409792.3	-	21	7588_7589	c.7546_7547delGT	c.(7546-7548)gttfs	p.V2516fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2516	Interaction with POLR2A.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CTTATTCATAACACCGTGAGTC	0.48			"N, F, S, Mis"		clear cell renal carcinoma																																p.2516_2516del		Pindel	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.7547_7548del						PASS	.																																			SO:0001589	frameshift_variant	29072	exon21			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.7546_7547delGT	chr3.hg19:g.47058733_47058734delAC	ENSP00000386759:p.Val2516fs	46.0	0.0	.		72.0	43.0	0.597	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Del	DEL	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.	.	none		0.48	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		-	47058732	AC	-	47058731	7	5	192	1	0	1	0	1	0	0	0	0	14144	43	2	0	151	0	SETD2	3	47058731	Frame_Shift_Del	DEL	AC	TCGA-GL-A9DE-01A-11D-A36X-10	1	47058731	150963699	22	11421	109	3									
SETD2	29072	hgsc.bcm.edu	37	chr3	47058732	47058732	+	Missense_Mutation	SNP	C	C	T																															cttcagctccttattcataaCaccgtgagtcagctgtccag																										TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr3:47058732C>T	ENST00000409792.3	-	21	7588	c.7546G>A	c.(7546-7548)Gtt>Att	p.V2516I		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2516	Interaction with POLR2A.				angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TTATTCATAACACCGTGAGTC	0.478			"N, F, S, Mis"		clear cell renal carcinoma																																p.V2516I		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.G7546A						PASS	.						132	119	124					3																	47058732		2203	4300	6503	SO:0001583	missense	29072	exon21			TCATAACACCGTG	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.7546G>A	chr3.hg19:g.47058732C>T	ENSP00000386759:p.Val2516Ile	47.0	0.0	.		72.0	67.0	.	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Missense_Mutation	SNP	ENST00000409792.3	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	C	25.9	4.684790	0.88639	.	.	ENSG00000181555	ENST00000451092;ENST00000409792	D	0.91631	-2.88	5.14	5.14	0.70334	SRI, Set2 Rpb1 interacting (1);	0.000000	0.48286	D	0.000195	D	0.93413	0.7899	N	0.21448	0.665	0.80722	D	1	B;P	0.38863	0.037;0.65	B;D	0.64687	0.438;0.928	D	0.92291	0.5841	10	0.36615	T	0.2	.	18.7829	0.91941	0.0:1.0:0.0:0.0	.	2516;2516	F2Z317;Q9BYW2	.;SETD2_HUMAN	I	2516	ENSP00000386759:V2516I	ENSP00000386759:V2516I	V	-	1	0	SETD2	47033736	1.000000	0.71417	0.908000	0.35775	0.994000	0.84299	7.562000	0.82300	2.668000	0.90789	0.655000	0.94253	GTT	.	.	.	none		0.478	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		T	47058732	C	T	47058732	3	4	192	1	0	0	0	0	1	0	0	0	14144	478	17	2	152	2	SETD2	3	47058732	Missense_Mutation	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10	1	47058732	150963698	23	11422	109	3									
PBRM1	55193	hgsc.bcm.edu	37	chr3	52678783	52678784	+	Frame_Shift_Ins	INS	-	-	T																															agcctttttcatataaaataINStttttttaattgaatttgca																								rs369874660		TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr3:52678783_52678784insT	ENST00000296302.7	-	8	836_837	c.835_836insA	c.(835-837)atafs	p.I279fs	PBRM1_ENST00000410007.1_Frame_Shift_Ins_p.I279fs|PBRM1_ENST00000409057.1_Frame_Shift_Ins_p.I279fs|PBRM1_ENST00000356770.4_Frame_Shift_Ins_p.I279fs|PBRM1_ENST00000409114.3_Frame_Shift_Ins_p.I279fs|PBRM1_ENST00000394830.3_Frame_Shift_Ins_p.I279fs|PBRM1_ENST00000337303.4_Frame_Shift_Ins_p.I279fs|PBRM1_ENST00000409767.1_Frame_Shift_Ins_p.I279fs			Q86U86	PB1_HUMAN	polybromo 1	279					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)	p.I279fs*4(7)		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)		Catataaaatatttttttaatt	0.361			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.I279fs		Pindel	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	7	Deletion - Frameshift(7)	kidney(7)	c.836_837insA						PASS	.																																			SO:0001589	frameshift_variant	55193	exon9			.	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.836dupA	chr3.hg19:g.52678790_52678790dupT	ENSP00000296302:p.Ile279fs	44.0	0.0	.		40.0	25.0	0.625	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Frame_Shift_Ins	INS	ENST00000296302.7	hg19																																																																																				.	.	.	none		0.361	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		T	52678784	-	T	52678783	7	5	192	1	0	1	1	0	0	0	0	0	11498	449	16	0	4156	0	PBRM1	3	52678783	Frame_Shift_Ins	INS	-	TCGA-GL-A9DE-01A-11D-A36X-10	5620051	52678783	145343647	24	11423											
LRIG1	26018	hgsc.bcm.edu	37	chr3	66431274	66431274	+	Frame_Shift_Del	DEL	G	G	-																															gcagtcactgcatacgacccGgccaccgtgttctgaaggac																								rs375884681		TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr3:66431274delG	ENST00000273261.3	-	18	3306	c.2782delC	c.(2782-2784)cggfs	p.R928fs	LRIG1_ENST00000496559.2_5'UTR|SLC25A26_ENST00000536651.1_3'UTR|LRIG1_ENST00000383703.3_Frame_Shift_Del_p.R905fs	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	928					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)		CATACGACCCGGCCACCGTGT	0.597																																					p.R928fs		Atlas-Indel,Pindel	.											.	LRIG1	138	.	0			c.2783delG						PASS	.						51	54	53					3																	66431274		2203	4300	6503	SO:0001589	frameshift_variant	26018	exon18			.	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.2782delC	chr3.hg19:g.66431274delG	ENSP00000273261:p.Arg928fs	49.0	0.0	0		59.0	21.0	0.355932	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Frame_Shift_Del	DEL	ENST00000273261.3	hg19	CCDS33783.1																																																																																			.	.	.	none		0.597	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541		-	66431274	G	-	66431274	7	5	192	1	0	1	0	1	0	0	0	0	8951	1115	39	0	507	0	LRIG1	3	66431274	Frame_Shift_Del	DEL	G	TCGA-GL-A9DE-01A-11D-A36X-10	13752491	66431274	131591156	25	11424											
DNAJB8	165721	hgsc.bcm.edu	37	chr3	128181520	128181520	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggtggtgaccttgtggccaTtgatcatctcggtggacgac	6	12	14	9	2	2	2	1	2	1	0	3	4	2	3	2	5	0	0	2	5	0	2			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr3:128181520T>C	ENST00000469083.1	-	2	3126	c.569A>G	c.(568-570)aAt>aGt	p.N190S	DNAJB8_ENST00000319153.3_Missense_Mutation_p.N190S|DNAJB8-AS1_ENST00000471626.1_RNA			Q8NHS0	DNJB8_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 8	190					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)		CTTGTGGCCATTGATCATCTC	0.622																																					p.N190S		Atlas-SNP	.											.	DNAJB8	34	.	0			c.A569G						PASS	.						139	116	124					3																	128181520		2203	4300	6503	SO:0001583	missense	165721	exon3			TGGCCATTGATCA		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.569A>G	chr3.hg19:g.128181520T>C	ENSP00000417418:p.Asn190Ser	76.0	0.0	.		87.0	73.0	.	NM_153330	B3KWV7	Missense_Mutation	SNP	ENST00000469083.1	hg19	CCDS3048.1	.	.	.	.	.	.	.	.	.	.	T	15.57	2.872026	0.51695	.	.	ENSG00000179407	ENST00000469083;ENST00000319153	T;T	0.41400	1.0;1.0	4.75	4.75	0.60458	.	0.000000	0.85682	D	0.000000	T	0.64713	0.2623	M	0.91140	3.18	0.58432	D	0.999995	D	0.61080	0.989	P	0.55391	0.775	T	0.74281	-0.3716	10	0.72032	D	0.01	.	12.8323	0.57752	0.0:0.0:0.0:1.0	.	190	Q8NHS0	DNJB8_HUMAN	S	190	ENSP00000417418:N190S;ENSP00000316053:N190S	ENSP00000316053:N190S	N	-	2	0	DNAJB8	129664210	1.000000	0.71417	0.531000	0.27976	0.053000	0.15095	4.000000	0.57039	1.772000	0.52199	0.459000	0.35465	AAT	.	.	.	none		0.622	DNAJB8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356933.1	NM_153330		C	128181520	T	C	128181520	3	2	192	1	0	0	0	0	1	0	0	0	4628	1493	52	3	133	3	DNAJB8	3	128181520	Missense_Mutation	SNP	T	TCGA-GL-A9DE-01A-11D-A36X-10	61750246	128181520	69840910	26	11425											
TMCC1	23023	hgsc.bcm.edu	37	chr3	129390024	129390024	+	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	gggtctggtgttccatccacAgagtctgtgtggatgctgcc	5	12	14	10	0	2	1	0	0	2	1	4	2	4	2	3	3	2	2	3	3	0	1			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr3:129390024A>T	ENST00000393238.3	-	4	1000	c.660T>A	c.(658-660)tcT>tcA	p.S220S	TMCC1_ENST00000432054.2_5'UTR|TMCC1_ENST00000329333.5_Silent_p.S41S|TMCC1_ENST00000426664.2_Silent_p.S106S	NM_001017395.3	NP_001017395.2	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	220						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)			PLXND1/TMCC1(4)	breast(1)|endometrium(3)|large_intestine(8)|lung(12)|skin(1)	25						TTCCATCCACAGAGTCTGTGT	0.507																																					p.S220S		Atlas-SNP	.											.	TMCC1	105	.	0			c.T660A						PASS	.						112	108	109					3																	129390024		2203	4300	6503	SO:0001819	synonymous_variant	23023	exon4			ATCCACAGAGTCT	AB018322	CCDS33855.1	3q21.3	2010-04-19	2005-07-13		ENSG00000172765	ENSG00000172765		"Transmembrane and coiled-coil domain containing"	29116	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 1"			9872452	Standard	NR_033361		Approved	KIAA0779	uc021xdy.1	O94876	OTTHUMG00000159579	ENST00000393238.3:c.660T>A	chr3.hg19:g.129390024A>T		53.0	0.0	.		73.0	5.0	.	NM_001017395	A8K5Y3|B4DE04|Q68E06|Q8IXM8	Silent	SNP	ENST00000393238.3	hg19	CCDS33855.1																																																																																			.	.	.	none		0.507	TMCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356418.2	NM_015008		T	129390024	A	T	129390024	2	4	192	1	0	0	0	0	0	0	0	1	16004	175	7	5		5	TMCC1	3	129390024	Silent	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10	1208504	129390024	68632406	27	11426											
EVC	2121	hgsc.bcm.edu	37	chr4	5812077	5812077	+	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	cctctacagagaagcccctaAggactaaaaggaagaagccc	16	4	9	12	0	1	2	0	0	1	2	1	5	1	4	4	2	3	0	4	2	7	3			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr4:5812077A>C	ENST00000264956.6	+	20	2978	c.2794A>C	c.(2794-2796)Agg>Cgg	p.R932R	EVC_ENST00000382674.2_Silent_p.R932R	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	932					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)				GAAGCCCCTAAGGACTAAAAG	0.562																																					p.R932R		Atlas-SNP	.											.	EVC	90	.	0			c.A2794C						PASS	.						41	45	44					4																	5812077		2203	4299	6502	SO:0001819	synonymous_variant	2121	exon20			CCCCTAAGGACTA	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.2794A>C	chr4.hg19:g.5812077A>C		230.0	0.0	.		226.0	96.0	.	NM_153717		Silent	SNP	ENST00000264956.6	hg19	CCDS3383.1																																																																																			.	.	.	none		0.562	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1			C	5812077	A	C	5812077	2	2	192	1	0	0	0	0	0	0	0	1	5287	63	3	5		5	EVC	4	5812077	Silent	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10		5812077	185342199	28	11427											
CCNI	10983	hgsc.bcm.edu	37	chr4	77969741	77969741	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagacataaacggaattcagAggcagggaagactgcagagt	16	6	13	6	1	1	4	1	0	0	4	1	6	1	6	0	3	2	2	0	3	5	3			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr4:77969741A>G	ENST00000237654.4	-	7	1341	c.765T>C	c.(763-765)ccT>ccC	p.P255P	CCNI_ENST00000537948.1_Silent_p.P241P	NM_006835.2	NP_006826.1	Q14094	CCNI_HUMAN	cyclin I	255					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						CGGAATTCAGAGGCAGGGAAG	0.517																																					p.P255P		Atlas-SNP	.											.	CCNI	22	.	0			c.T765C						PASS	.						84	77	79					4																	77969741		2203	4300	6503	SO:0001819	synonymous_variant	10983	exon7			ATTCAGAGGCAGG	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.765T>C	chr4.hg19:g.77969741A>G		70.0	0.0	.		103.0	40.0	.	NM_006835	B2R6M0|B7Z6X4	Silent	SNP	ENST00000237654.4	hg19	CCDS3580.1	.	.	.	.	.	.	.	.	.	.	A	7.455	0.643541	0.14451	.	.	ENSG00000118816	ENST00000515468	.	.	.	5.9	5.9	0.94986	.	.	.	.	.	T	0.48409	0.1498	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53337	-0.8453	4	.	.	.	-12.2282	3.2125	0.06687	0.6383:0.1553:0.0749:0.1315	.	.	.	.	P	55	.	.	S	-	1	0	CCNI	78188765	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.896000	0.28377	2.251000	0.74343	0.528000	0.53228	TCT	.	.	.	none		0.517	CCNI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252412.2	NM_006835		G	77969741	A	G	77969741	2	3	192	1	0	0	0	0	0	0	0	1	2928	291	11	3		3	CCNI	4	77969741	Silent	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10	72157664	77969741	113184535	29	11428											
PTPN13	5783	hgsc.bcm.edu	37	chr4	87671752	87671752	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgctgttcgacctttatcagTtcaagctgagattctgaaga	10	14	9	8	1	3	3	2	2	1	2	4	5	3	3	1	0	2	4	1	0	3	5			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr4:87671752T>C	ENST00000411767.2	+	18	2843	c.2780T>C	c.(2779-2781)gTt>gCt	p.V927A	PTPN13_ENST00000511467.1_Missense_Mutation_p.V927A|PTPN13_ENST00000427191.2_Missense_Mutation_p.V927A|PTPN13_ENST00000436978.1_Missense_Mutation_p.V927A|PTPN13_ENST00000316707.6_Intron			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	927					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)		CCTTTATCAGTTCAAGCTGAG	0.468																																					p.V927A		Atlas-SNP	.											.	PTPN13	203	.	0			c.T2780C						PASS	.						80	80	80					4																	87671752		1971	4165	6136	SO:0001583	missense	5783	exon18			TATCAGTTCAAGC		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.2780T>C	chr4.hg19:g.87671752T>C	ENSP00000407249:p.Val927Ala	247.0	1.0	.		296.0	127.0	.	NM_006264	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	hg19	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	T	13.05	2.120999	0.37436	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T	0.54071	0.59;0.63;0.6;0.63	6.16	3.78	0.43462	.	0.291309	0.24089	N	0.041646	T	0.47857	0.1468	L	0.57536	1.79	0.23101	N	0.99829	B;B;B	0.16166	0.016;0.016;0.012	B;B;B	0.15870	0.014;0.004;0.009	T	0.45920	-0.9228	10	0.62326	D	0.03	.	10.2207	0.43194	0.0:0.1317:0.0:0.8683	.	927;927;927	Q12923-3;Q12923;Q12923-4	.;PTN13_HUMAN;.	A	927;927;927;927;895	ENSP00000408368:V927A;ENSP00000394794:V927A;ENSP00000407249:V927A;ENSP00000426626:V927A	ENSP00000349909:V895A	V	+	2	0	PTPN13	87890776	0.771000	0.28555	0.936000	0.37596	0.976000	0.68499	2.231000	0.43009	0.584000	0.29591	0.528000	0.53228	GTT	.	.	.	none		0.468	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			C	87671752	T	C	87671752	3	2	192	1	0	0	0	0	1	0	0	0	12793	1725	60	3	2846	3	PTPN13	4	87671752	Missense_Mutation	SNP	T	TCGA-GL-A9DE-01A-11D-A36X-10	9702011	87671752	103482524	30	11429											
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123226024	123226024	+	Missense_Mutation	SNP	A	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	actggattgattgaactggaActttctaaccgacttcaaac	13	12	7	9	1	2	2	1	2	1	0	2	5	2	4	1	2	4	0	1	2	4	5			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr4:123226024A>C	ENST00000264501.4	+	56	9931	c.9558A>C	c.(9556-9558)gaA>gaC	p.E3186D	KIAA1109_ENST00000455637.1_Missense_Mutation_p.E3186D|KIAA1109_ENST00000388738.3_Missense_Mutation_p.E3186D			Q2LD37	K1109_HUMAN	KIAA1109	3186					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						TTGAACTGGAACTTTCTAACC	0.398																																					p.E3186D		Atlas-SNP	.											.	KIAA1109	424	.	0			c.A9558C						PASS	.						106	98	101					4																	123226024		1837	4090	5927	SO:0001583	missense	84162	exon54			ACTGGAACTTTCT	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.9558A>C	chr4.hg19:g.123226024A>C	ENSP00000264501:p.Glu3186Asp	121.0	0.0	.		115.0	49.0	.	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.3|21.3	4.131217|4.131217	0.77549|0.77549	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637|ENST00000419325	T;T;T|.	0.32272|.	1.46;1.46;1.46|.	5.81|5.81	0.65|0.65	0.17812|0.17812	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.53546|0.53546	0.1803|0.1803	L|L	0.55481|0.55481	1.735|1.735	0.31761|0.31761	N|N	0.63333|0.63333	P;D|.	0.67145|.	0.949;0.996|.	P;P|.	0.54499|.	0.717;0.754|.	T|T	0.59026|0.59026	-0.7531|-0.7531	10|5	0.62326|.	D|.	0.03|.	.|.	11.3914|11.3914	0.49817|0.49817	0.6293:0.0:0.3707:0.0|0.6293:0.0:0.3707:0.0	.|.	3186;3186|.	Q2LD37-6;Q2LD37|.	.;K1109_HUMAN|.	D|P	3186|1144	ENSP00000264501:E3186D;ENSP00000373390:E3186D;ENSP00000389925:E3186D|.	ENSP00000264501:E3186D|.	E|T	+|+	3|1	2|0	KIAA1109|KIAA1109	123445474|123445474	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.040000|1.040000	0.30278|0.30278	0.146000|0.146000	0.19002|0.19002	0.454000|0.454000	0.30748|0.30748	GAA|ACT	.	.	.	none		0.398	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		C	123226024	A	C	123226024	3	2	192	1	0	0	0	0	1	0	0	0	8215	40	2	5	9772	5	KIAA1109	4	123226024	Missense_Mutation	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10	35554272	123226024	67928252	31	11430											
ANXA10	11199	hgsc.bcm.edu	37	chr4	169099042	169099042	+	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	ctgctggctaatgttccaggTcctatgggaagcctgtcagc	7	11	12	11	0	1	0	1	0	0	0	3	1	3	1	3	3	3	3	3	3	3	3			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr4:169099042T>C	ENST00000359299.3	+	8	722	c.536T>C	c.(535-537)gTc>gCc	p.V179A		NM_007193.4	NP_009124.2	Q9UJ72	ANX10_HUMAN	annexin A10	179						mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)			endometrium(1)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(2)	16		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0325)		ATGTTCCAGGTCCTATGGGAA	0.498																																					p.V179A		Atlas-SNP	.											.	ANXA10	44	.	0			c.T536C						PASS	.						125	119	121					4																	169099042		2203	4300	6503	SO:0001630	splice_region_variant	11199	exon8			TCCAGGTCCTATG	AJ238979	CCDS34096.1	4q32.3	2008-02-05			ENSG00000109511	ENSG00000109511		"Annexins"	534	protein-coding gene	gene with protein product		608008				10458909	Standard	NM_007193		Approved	ANX14	uc003irm.3	Q9UJ72	OTTHUMG00000161275	ENST00000359299.3:c.535-1T>C	chr4.hg19:g.169099042T>C		83.0	0.0	.		124.0	21.0	.	NM_007193	Q96IQ5|Q9UJV4	Missense_Mutation	SNP	ENST00000359299.3	hg19	CCDS34096.1	.	.	.	.	.	.	.	.	.	.	T	9.052	0.992269	0.18966	.	.	ENSG00000109511	ENST00000359299;ENST00000393751	T	0.10382	2.88	5.66	5.66	0.87406	.	0.093082	0.47093	D	0.000246	T	0.06325	0.0163	N	0.01800	-0.715	0.58432	D	0.999996	P;P	0.45634	0.863;0.656	P;B	0.48227	0.571;0.253	T	0.45804	-0.9236	10	0.07030	T	0.85	.	15.8919	0.79305	0.0:0.0:0.0:1.0	.	51;179	Q6ITU8;Q9UJ72	.;ANX10_HUMAN	A	179	ENSP00000352248:V179A	ENSP00000352248:V179A	V	+	2	0	ANXA10	169335617	1.000000	0.71417	1.000000	0.80357	0.613000	0.37349	5.611000	0.67674	2.168000	0.68352	0.533000	0.62120	GTC	.	.	.	none		0.498	ANXA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364348.2	NM_007193	Missense_Mutation	C	169099042	T	C	169099042	5	2	192	1	0	0	0	0	0	0	1	0	715	1681	58	3	566	3	ANXA10	4	169099042	Splice_Site	SNP	T	TCGA-GL-A9DE-01A-11D-A36X-10	45873018	169099042	22055234	32	11431											
MCC	4163	hgsc.bcm.edu	37	chr5	112399744	112399744	+	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	tgcagccggccacggcaaagGctcccccacagctgccgtcc	7	4	11	19	3	0	0	0	0	0	0	2	0	2	0	6	3	4	4	6	3	1	0	rs147869500		TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr5:112399744G>C	ENST00000302475.4	-	12	2143	c.1580C>G	c.(1579-1581)gCc>gGc	p.A527G	MCC_ENST00000514701.3_5'UTR|MCC_ENST00000408903.3_Missense_Mutation_p.A717G|MCC_ENST00000515367.2_Missense_Mutation_p.A464G	NM_002387.2	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers	527					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)		CACGGCAAAGGCTCCCCCACA	0.617																																					p.A717G		Atlas-SNP	.											.	MCC	234	.	0			c.C2150G						PASS	.						59	57	58					5																	112399744		2202	4300	6502	SO:0001583	missense	4163	exon14			GCAAAGGCTCCCC		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.1580C>G	chr5.hg19:g.112399744G>C	ENSP00000305617:p.Ala527Gly	150.0	0.0	.		150.0	67.0	.	NM_001085377	D3DT05|Q6ZR04	Missense_Mutation	SNP	ENST00000302475.4	hg19	CCDS4111.1	.	.	.	.	.	.	.	.	.	.	G	18.54	3.646288	0.67358	.	.	ENSG00000171444	ENST00000302475;ENST00000515367;ENST00000408903	T;T;T	0.35789	2.46;2.46;1.29	5.61	5.61	0.85477	.	0.056778	0.64402	D	0.000002	T	0.29783	0.0744	N	0.19112	0.55	0.80722	D	1	B;B;B	0.31817	0.231;0.341;0.231	B;B;B	0.35971	0.107;0.215;0.074	T	0.05131	-1.0904	10	0.20046	T	0.44	-12.5962	19.638	0.95744	0.0:0.0:1.0:0.0	.	527;717;527	B7Z6G0;P23508-2;P23508	.;.;CRCM_HUMAN	G	527;464;717	ENSP00000305617:A527G;ENSP00000421615:A464G;ENSP00000386227:A717G	ENSP00000305617:A527G	A	-	2	0	MCC	112427643	1.000000	0.71417	0.744000	0.31058	0.703000	0.40648	7.743000	0.85020	2.626000	0.88956	0.655000	0.94253	GCC	.	G|1.000;A|0.000	.	alt		0.617	MCC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250736.3	NM_001085377		C	112399744	G	C	112399744	3	2	192	1	0	0	0	0	1	0	0	0	9380	1203	42	4	933	4	MCC	5	112399744	Missense_Mutation	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10		112399744	68515516	33	11432											
SNCAIP	9627	hgsc.bcm.edu	37	chr5	121786598	121786598	+	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	acacagactccaacaactctGaggaccccaagactacccca	15	4	5	17	0	1	3	0	1	1	2	2	4	2	4	5	1	3	0	5	1	4	1			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr5:121786598G>T	ENST00000261368.8	+	10	2318	c.2056G>T	c.(2056-2058)Gag>Tag	p.E686*	CTC-210G5.1_ENST00000506053.1_RNA|SNCAIP_ENST00000261367.7_Nonsense_Mutation_p.E733*|SNCAIP_ENST00000542191.1_Nonsense_Mutation_p.E244*|CTC-210G5.1_ENST00000503529.1_RNA|SNCAIP_ENST00000504884.2_3'UTR|CTC-210G5.1_ENST00000505546.1_RNA|SNCAIP_ENST00000414317.2_Nonsense_Mutation_p.E288*|CTC-210G5.1_ENST00000510972.1_RNA|SNCAIP_ENST00000379533.2_Nonsense_Mutation_p.E733*|SNCAIP_ENST00000379536.2_Nonsense_Mutation_p.E626*|SNCAIP_ENST00000379538.3_Nonsense_Mutation_p.E320*|CTC-210G5.1_ENST00000509993.1_RNA|SNCAIP_ENST00000503116.2_3'UTR	NM_005460.2	NP_005451.2	Q9Y6H5	SNCAP_HUMAN	synuclein, alpha interacting protein	686					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)		CAACAACTCTGAGGACCCCAA	0.537																																					p.E686X		Atlas-SNP	.											.	SNCAIP	308	.	0			c.G2056T						PASS	.						53	54	54					5																	121786598		2203	4300	6503	SO:0001587	stop_gained	9627	exon10			AACTCTGAGGACC	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.2056G>T	chr5.hg19:g.121786598G>T	ENSP00000261368:p.Glu686*	83.0	0.0	.		83.0	37.0	.	NM_005460	D3DSZ1|Q05BS1|Q1PSC2|Q49AC6|Q504U9|Q6L984|Q6L985|Q6L986|Q9HC59	Nonsense_Mutation	SNP	ENST00000261368.8	hg19	CCDS4131.1	.	.	.	.	.	.	.	.	.	.	G	40	8.438364	0.98810	.	.	ENSG00000064692	ENST00000542191;ENST00000509154;ENST00000261368;ENST00000379533;ENST00000379536;ENST00000379538;ENST00000261367;ENST00000414317;ENST00000447854	.	.	.	6.06	6.06	0.98353	.	0.049549	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-32.5971	20.6208	0.99490	0.0:0.0:1.0:0.0	.	.	.	.	X	244;626;686;733;626;320;733;288;326	.	ENSP00000261367:E733X	E	+	1	0	SNCAIP	121814497	1.000000	0.71417	0.979000	0.43373	0.934000	0.57294	9.194000	0.94962	2.882000	0.98803	0.655000	0.94253	GAG	.	.	.	none		0.537	SNCAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250888.1			T	121786598	G	T	121786598	4	4	192	1	0	0	0	0	0	1	0	0	14854	1291	45	4	2090	4	SNCAIP	5	121786598	Nonsense_Mutation	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10	9386854	121786598	59128662	34	11433											
RNF14	9604	hgsc.bcm.edu	37	chr5	141354465	141354465	+	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	tgaactgccaccagattatcCatcctcttccccaccttcat	9	12	3	17	0	2	2	1	1	1	1	5	2	5	2	7	0	2	0	7	0	2	3			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr5:141354465C>A	ENST00000394520.2	+	4	560	c.251C>A	c.(250-252)cCa>cAa	p.P84Q	RNF14_ENST00000502341.1_Intron|RNF14_ENST00000394514.2_Intron|RNF14_ENST00000394515.3_Missense_Mutation_p.P84Q|RNF14_ENST00000356143.1_Missense_Mutation_p.P84Q|RNF14_ENST00000347642.3_Missense_Mutation_p.P84Q|RNF14_ENST00000540015.1_Intron|RNF14_ENST00000394519.1_Missense_Mutation_p.P84Q|AC005740.5_ENST00000520882.1_RNA	NM_001201365.1|NM_004290.4	NP_001188294.1|NP_004281.1	Q9UBS8	RNF14_HUMAN	ring finger protein 14	84	RWD. {ECO:0000255|PROSITE- ProRule:PRU00179}.				androgen receptor signaling pathway (GO:0030521)|positive regulation of transcription, DNA-templated (GO:0045893)|protein ubiquitination (GO:0016567)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|small conjugating protein ligase activity (GO:0019787)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15		all_hematologic(541;0.0536)|Ovarian(839;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)		CCAGATTATCCATCCTCTTCC	0.408																																					p.P84Q		Atlas-SNP	.											.	RNF14	30	.	0			c.C251A						PASS	.						178	160	166					5																	141354465		2203	4300	6503	SO:0001583	missense	9604	exon4			ATTATCCATCCTC	AF060544	CCDS4270.1, CCDS4271.1	5q23.3-q31.1	2008-02-05			ENSG00000013561	ENSG00000013561		"RING-type (C3HC4) zinc fingers"	10058	protein-coding gene	gene with protein product		605675				10085091, 10320776	Standard	NM_183399		Approved	ARA54, HFB30, TRIAD2	uc003lmc.3	Q9UBS8	OTTHUMG00000129660	ENST00000394520.2:c.251C>A	chr5.hg19:g.141354465C>A	ENSP00000378028:p.Pro84Gln	89.0	0.0	.		102.0	57.0	.	NM_001201365	A0AV26|A6NMR2|A8MTW5|B3KN72|B7ZLV2|D3DQE4|O94793|Q6IBV0	Missense_Mutation	SNP	ENST00000394520.2	hg19	CCDS4270.1	.	.	.	.	.	.	.	.	.	.	C	32	5.149590	0.94645	.	.	ENSG00000013561	ENST00000511961;ENST00000506822;ENST00000513019;ENST00000356143;ENST00000394520;ENST00000347642;ENST00000506938;ENST00000394515;ENST00000507163;ENST00000394519	D;D;D;D;D;D;D;D;D;D	0.93763	-3.28;-3.28;-3.28;-3.28;-3.28;-3.28;-3.28;-3.28;-3.28;-3.28	5.87	5.87	0.94306	Ubiquitin-conjugating enzyme/RWD-like (2);RWD domain (3);	0.000000	0.85682	D	0.000000	D	0.98055	0.9359	H	0.95917	3.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98607	1.0661	10	0.87932	D	0	.	20.2084	0.98285	0.0:1.0:0.0:0.0	.	84;84	B7Z229;Q9UBS8	.;RNF14_HUMAN	Q	84	ENSP00000423420:P84Q;ENSP00000423273:P84Q;ENSP00000421780:P84Q;ENSP00000348462:P84Q;ENSP00000378028:P84Q;ENSP00000324956:P84Q;ENSP00000420837:P84Q;ENSP00000378023:P84Q;ENSP00000422527:P84Q;ENSP00000378027:P84Q	ENSP00000324956:P84Q	P	+	2	0	RNF14	141334649	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.762000	0.85270	2.774000	0.95407	0.650000	0.86243	CCA	.	.	.	none		0.408	RNF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251860.2	NM_004290		A	141354465	C	A	141354465	3	1	192	1	0	0	0	0	1	0	0	0	13456	594	21	4	257	4	RNF14	5	141354465	Missense_Mutation	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10	19567867	141354465	39560795	35	11434											
KIF4B	285643	hgsc.bcm.edu	37	chr5	154395330	154395330	+	Frame_Shift_Del	DEL	C	C	-																															cgtactgtctccaagctgaaCcaagagatatggatgatgaa																										TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr5:154395330delC	ENST00000435029.4	+	1	2071	c.1911delC	c.(1909-1911)aacfs	p.N637fs		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	637					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)			CCAAGCTGAACCAAGAGATAT	0.418																																					p.N637fs		Atlas-Indel,Pindel	.											.	KIF4B	307	.	0			c.1910delA						PASS	.						154	150	151					5																	154395330		2203	4300	6503	SO:0001589	frameshift_variant	285643	exon1			.	AF241316	CCDS47324.1	5q33.2	2010-06-22			ENSG00000226650	ENSG00000226650		"Kinesins"	6322	protein-coding gene	gene with protein product		609184					Standard	NM_001099293		Approved		uc010jih.1	Q2VIQ3	OTTHUMG00000164143	ENST00000435029.4:c.1911delC	chr5.hg19:g.154395330delC	ENSP00000387875:p.Asn637fs	321.0	0.0	0		413.0	173.0	0.418886	NM_001099293		Frame_Shift_Del	DEL	ENST00000435029.4	hg19	CCDS47324.1																																																																																			.	.	.	none		0.418	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1			-	154395330	C	-	154395330	7	5	192	1	0	1	0	1	0	0	0	0	8311	506	18	0	1913	0	KIF4B	5	154395330	Frame_Shift_Del	DEL	C	TCGA-GL-A9DE-01A-11D-A36X-10	13040865	154395330	26519930	36	11435											
FOXQ1	94234	hgsc.bcm.edu	37	chr6	1313368	1313368	+	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	ggcgggcgcttgacgctggcGgagatcaacgagtacctcat	8	7	15	11	5	2	2	2	1	0	1	2	4	2	2	1	4	2	3	1	4	2	2			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr6:1313368G>T	ENST00000296839.2	+	1	694	c.429G>T	c.(427-429)gcG>gcT	p.A143A		NM_033260.3	NP_150285.3	Q9C009	FOXQ1_HUMAN	forkhead box Q1	143					hair follicle morphogenesis (GO:0031069)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(1)|urinary_tract(1)	2	Ovarian(93;0.0733)	Breast(5;0.052)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.0954)|BRCA - Breast invasive adenocarcinoma(62;0.18)		TGACGCTGGCGGAGATCAACG	0.647																																					p.A143A		Atlas-SNP	.											.	FOXQ1	8	.	0			c.G429T						PASS	.																																			SO:0001819	synonymous_variant	94234	exon1			GCTGGCGGAGATC	AF153341	CCDS4471.1	6p25	2008-02-05			ENSG00000164379	ENSG00000164379		"Forkhead boxes"	20951	protein-coding gene	gene with protein product		612788				11747606, 12011061	Standard	NM_033260		Approved	HFH1	uc003mtl.4	Q9C009	OTTHUMG00000016160	ENST00000296839.2:c.429G>T	chr6.hg19:g.1313368G>T		82.0	0.0	.		110.0	43.0	.	NM_033260	Q9NS06	Silent	SNP	ENST00000296839.2	hg19	CCDS4471.1																																																																																			.	.	.	none		0.647	FOXQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043410.1	NM_033260		T	1313368	G	T	1313368	2	4	192	1	0	0	0	0	0	0	0	1	6037	1103	39	4		4	FOXQ1	6	1313368	Silent	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10		1313368	169801699	37	11436											
RIOK1	83732	hgsc.bcm.edu	37	chr6	7395375	7395375	+	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	tttgagaataaaattaatttAggtgagtttacaaaatacat	18	15	6	2	0	0	2	0	2	0	1	0	3	0	2	0	1	2	1	0	1	9	8			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr6:7395375A>G	ENST00000379834.2	+	3	873	c.366A>G	c.(364-366)ttA>ttG	p.L122L		NM_031480.2|NM_153005.1	NP_113668.2|NP_694550.1	Q9BRS2	RIOK1_HUMAN	RIO kinase 1	122							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19	Ovarian(93;0.0418)					AAATTAATTTAGGTGAGTTTA	0.388																																					p.L122L		Atlas-SNP	.											.	RIOK1	36	.	0			c.A366G						PASS	.						35	33	33					6																	7395375		2203	4300	6503	SO:0001630	splice_region_variant	83732	exon3			TAATTTAGGTGAG	BC006104	CCDS4500.1	6p24.3	2012-12-10	2012-12-10		ENSG00000124784	ENSG00000124784			18656	protein-coding gene	gene with protein product			"RIO kinase 1 (yeast)"				Standard	NM_031480		Approved	AD034, FLJ30006, bA288G3.1, RRP10	uc003mxn.3	Q9BRS2	OTTHUMG00000014207	ENST00000379834.2:c.367+1A>G	chr6.hg19:g.7395375A>G		193.0	0.0	.		240.0	90.0	.	NM_031480	B2RB28|Q8NDC8|Q96NV9	Silent	SNP	ENST00000379834.2	hg19	CCDS4500.1																																																																																			.	.	.	none		0.388	RIOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039780.2	NM_031480	Silent	G	7395375	A	G	7395375	5	3	192	1	0	0	0	0	0	0	1	0	13390	434	15	3	376	3	RIOK1	6	7395375	Splice_Site	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10	6082007	7395375	163719692	38	11437											
KIAA0408	9729	hgsc.bcm.edu	37	chr6	127767703	127767703	+	Missense_Mutation	SNP	A	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	tcagaattacatttggtccaAttatcctggaagcacttaga	13	13	7	8	0	1	2	1	0	0	2	3	3	3	3	2	2	2	1	2	2	6	4			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr6:127767703A>C	ENST00000483725.3	-	5	2097	c.1761T>G	c.(1759-1761)aaT>aaG	p.N587K	SOGA3_ENST00000481848.2_3'UTR|SOGA3_ENST00000556132.1_3'UTR	NM_014702.4	NP_055517.3	Q6ZU52	K0408_HUMAN	KIAA0408	587										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)		ATTTGGTCCAATTATCCTGGA	0.413																																					p.N587K		Atlas-SNP	.											.	KIAA0408	61	.	0			c.T1761G						PASS	.						133	122	126					6																	127767703		2203	4300	6503	SO:0001583	missense	9729	exon5			GGTCCAATTATCC	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.1761T>G	chr6.hg19:g.127767703A>C	ENSP00000435150:p.Asn587Lys	52.0	0.0	.		73.0	30.0	.	NM_014702	B3KRE5|E1P573|O43158|Q5TF20|Q7L2M2	Missense_Mutation	SNP	ENST00000483725.3	hg19	CCDS34531.1	.	.	.	.	.	.	.	.	.	.	A	0.008	-1.932558	0.00488	.	.	ENSG00000189367	ENST00000483725	T	0.22743	1.94	5.08	-6.14	0.02111	.	0.584041	0.13305	N	0.397945	T	0.01558	0.0050	N	0.19112	0.55	0.19300	N	0.999973	B	0.11235	0.004	B	0.08055	0.003	T	0.41840	-0.9486	10	0.02654	T	1	-2.2349	0.2684	0.00228	0.3125:0.2598:0.1825:0.2452	.	587	Q6ZU52	K0408_HUMAN	K	587	ENSP00000435150:N587K	ENSP00000435150:N587K	N	-	3	2	KIAA0408	127809396	0.518000	0.26234	0.068000	0.19968	0.016000	0.09150	-0.308000	0.08156	-0.860000	0.04099	-1.139000	0.01908	AAT	.	.	.	none		0.413	KIAA0408-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042145.3	NM_014702		C	127767703	A	C	127767703	3	2	192	1	0	0	0	0	1	0	0	0	8181	98	4	5	331	5	KIAA0408	6	127767703	Missense_Mutation	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10	120372328	127767703	43347364	39	11438											
GPNMB	10457	hgsc.bcm.edu	37	chr7	23300201	23300201	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcctagccacttcctcaattAttctaccattaactacaagt	12	14	2	13	0	2	0	1	0	1	0	4	0	4	0	4	0	4	0	4	0	7	7			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr7:23300201A>G	ENST00000381990.2	+	6	988	c.827A>G	c.(826-828)tAt>tGt	p.Y276C	GPNMB_ENST00000453162.2_Missense_Mutation_p.Y218C|GPNMB_ENST00000258733.4_Missense_Mutation_p.Y276C|GPNMB_ENST00000539136.1_Missense_Mutation_p.Y177C	NM_001005340.1|NM_002510.2	NP_001005340.1|NP_002501.1	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb	276	PKD. {ECO:0000255|PROSITE- ProRule:PRU00151}.				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)			TTCCTCAATTATTCTACCATT	0.423																																					p.Y276C		Atlas-SNP	.											.	GPNMB	88	.	0			c.A827G						PASS	.						177	169	171					7																	23300201		2203	4300	6503	SO:0001583	missense	10457	exon6			TCAATTATTCTAC	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.827A>G	chr7.hg19:g.23300201A>G	ENSP00000371420:p.Tyr276Cys	91.0	0.0	.		94.0	40.0	.	NM_002510	A4D155|Q6UVX1|Q8N1A1	Missense_Mutation	SNP	ENST00000381990.2	hg19	CCDS34610.1	.	.	.	.	.	.	.	.	.	.	A	15.34	2.803374	0.50315	.	.	ENSG00000136235	ENST00000258733;ENST00000435486;ENST00000381990;ENST00000425903;ENST00000539136;ENST00000453162	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	5.31	2.72	0.32119	PKD/Chitinase domain (1);PKD domain (2);	1.009820	0.07941	N	0.979323	T	0.43612	0.1255	N	0.22421	0.69	0.09310	N	1	D;P;D;D	0.63046	0.959;0.93;0.984;0.992	P;P;P;P	0.57152	0.62;0.632;0.814;0.634	T	0.32161	-0.9917	10	0.56958	D	0.05	-2.1972	8.3455	0.32270	0.6125:0.315:0.0725:0.0	.	177;218;276;276	F6SKP1;F5GY20;Q14956;Q14956-2	.;.;GPNMB_HUMAN;.	C	276;311;276;159;177;218	ENSP00000258733:Y276C;ENSP00000371420:Y276C;ENSP00000445266:Y177C;ENSP00000405586:Y218C	ENSP00000258733:Y276C	Y	+	2	0	GPNMB	23266726	0.439000	0.25610	0.635000	0.29338	0.863000	0.49368	1.693000	0.37742	0.933000	0.37291	0.533000	0.62120	TAT	.	.	.	none		0.423	GPNMB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327152.1	NM_001005340		G	23300201	A	G	23300201	3	3	192	1	0	0	0	0	1	0	0	0	6627	449	16	3	849	3	GPNMB	7	23300201	Missense_Mutation	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10		23300201	135838462	40	11439											
BAZ1B	9031	hgsc.bcm.edu	37	chr7	72883924	72883924	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcggtagtcaatgctgtcaTgtacccagcctttttcaatg	9	14	8	10	1	3	0	3	0	0	0	4	0	3	0	2	1	3	3	2	1	4	4			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr7:72883924T>C	ENST00000339594.4	-	9	3127	c.2789A>G	c.(2788-2790)cAt>cGt	p.H930R	BAZ1B_ENST00000404251.1_Missense_Mutation_p.H930R	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	930					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)				AATGCTGTCATGTACCCAGCC	0.408																																					p.H930R	Esophageal Squamous(112;1167 1561 21085 43672 48228)	Atlas-SNP	.											.	BAZ1B	147	.	0			c.A2789G						PASS	.						219	182	194					7																	72883924		2203	4300	6503	SO:0001583	missense	9031	exon9			CTGTCATGTACCC	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.2789A>G	chr7.hg19:g.72883924T>C	ENSP00000342434:p.His930Arg	78.0	0.0	.		84.0	30.0	.	NM_032408	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Missense_Mutation	SNP	ENST00000339594.4	hg19	CCDS5549.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.497148	0.85069	.	.	ENSG00000009954	ENST00000339594;ENST00000404251	T;T	0.58940	0.3;0.3	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.64627	0.2615	L	0.34521	1.04	0.58432	D	0.999999	D	0.76494	0.999	D	0.78314	0.991	T	0.59408	-0.7460	10	0.18276	T	0.48	-22.8212	15.2154	0.73261	0.0:0.0:0.0:1.0	.	930	Q9UIG0	BAZ1B_HUMAN	R	930	ENSP00000342434:H930R;ENSP00000385442:H930R	ENSP00000342434:H930R	H	-	2	0	BAZ1B	72521860	1.000000	0.71417	0.997000	0.53966	0.974000	0.67602	7.620000	0.83070	2.198000	0.70561	0.533000	0.62120	CAT	.	.	.	none		0.408	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408		C	72883924	T	C	72883924	3	2	192	1	0	0	0	0	1	0	0	0	1330	1464	51	3	1706	3	BAZ1B	7	72883924	Missense_Mutation	SNP	T	TCGA-GL-A9DE-01A-11D-A36X-10	49583723	72883924	86254739	41	11440											
PCLO	27445	hgsc.bcm.edu	37	chr7	82544242	82544242	+	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	ttcttcagaattctgggccaCaattggtattcttcctctac	8	16	6	11	0	5	1	1	0	4	1	6	1	6	1	2	2	1	1	2	2	4	8			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr7:82544242C>A	ENST00000333891.9	-	7	13397	c.13060G>T	c.(13060-13062)Gtg>Ttg	p.V4354L	PCLO_ENST00000423517.2_Missense_Mutation_p.V4354L|PCLO_ENST00000437081.1_Missense_Mutation_p.V1074L	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						TTCTGGGCCACAATTGGTATT	0.502																																					p.V4354L		Atlas-SNP	.											.	PCLO	1506	.	0			c.G13060T						PASS	.						106	103	104					7																	82544242		1883	4123	6006	SO:0001583	missense	27445	exon7			GGGCCACAATTGG	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.13060G>T	chr7.hg19:g.82544242C>A	ENSP00000334319:p.Val4354Leu	89.0	0.0	.		95.0	40.0	.	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	14.70	2.612259	0.46631	.	.	ENSG00000186472	ENST00000333891;ENST00000423517;ENST00000437081	T;T	0.18657	2.2;2.2	5.61	5.61	0.85477	.	.	.	.	.	T	0.40619	0.1124	L	0.52759	1.655	0.58432	D	0.999997	D;D;D	0.61697	0.959;0.99;0.99	P;P;P	0.60173	0.631;0.87;0.87	T	0.11966	-1.0566	9	0.87932	D	0	.	19.6481	0.95790	0.0:1.0:0.0:0.0	.	4285;4354;4354	Q9Y6V0;Q9Y6V0-5;Q9Y6V0-6	PCLO_HUMAN;.;.	L	4354;4354;1074	ENSP00000334319:V4354L;ENSP00000388393:V4354L	ENSP00000334319:V4354L	V	-	1	0	PCLO	82382178	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.074000	0.71253	2.651000	0.90000	0.557000	0.71058	GTG	.	.	.	none		0.502	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82544242	C	A	82544242	3	1	192	1	0	0	0	0	1	0	0	0	11590	478	17	4	2461	4	PCLO	7	82544242	Missense_Mutation	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10	9660318	82544242	76594421	42	11441											
TMEM176A	55365	hgsc.bcm.edu	37	chr7	150499366	150499366	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatttttctacatccgcgacTacaccctcctcgtcacctcg	7	12	5	17	4	2	0	1	0	1	0	6	2	4	0	4	0	2	0	4	0	2	4			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr7:150499366T>C	ENST00000484928.1	+	3	819	c.238T>C	c.(238-240)Tac>Cac	p.Y80H	TMEM176A_ENST00000004103.3_Missense_Mutation_p.Y80H|TMEM176B_ENST00000447204.2_5'Flank|TMEM176B_ENST00000492607.1_5'Flank|TMEM176B_ENST00000326442.5_5'Flank|TMEM176B_ENST00000450753.2_5'Flank|TMEM176A_ENST00000461345.1_Missense_Mutation_p.Y21H|TMEM176B_ENST00000434545.1_5'Flank			Q96HP8	T176A_HUMAN	transmembrane protein 176A	80					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)		CATCCGCGACTACACCCTCCT	0.572																																					p.Y80H		Atlas-SNP	.											.	TMEM176A	35	.	0			c.T238C						PASS	.						130	106	114					7																	150499366		2203	4300	6503	SO:0001583	missense	55365	exon3			CGCGACTACACCC	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.238T>C	chr7.hg19:g.150499366T>C	ENSP00000417626:p.Tyr80His	36.0	0.0	.		49.0	21.0	.	NM_018487	D3DX00|Q9NYC7	Missense_Mutation	SNP	ENST00000484928.1	hg19	CCDS5909.1	.	.	.	.	.	.	.	.	.	.	T	10.93	1.489966	0.26686	.	.	ENSG00000002933	ENST00000484928;ENST00000004103;ENST00000461345;ENST00000475536;ENST00000468689	T;T;T;T;T	0.02301	4.35;4.35;4.35;4.35;4.35	4.6	-4.75	0.03239	.	1.935430	0.01942	N	0.042003	T	0.02688	0.0081	L	0.50333	1.59	0.09310	N	1	P	0.44309	0.832	B	0.42386	0.386	T	0.35549	-0.9784	10	0.41790	T	0.15	-0.0945	0.4154	0.00448	0.2867:0.2834:0.147:0.2828	.	80	Q96HP8	T176A_HUMAN	H	80;80;21;32;21	ENSP00000417626:Y80H;ENSP00000004103:Y80H;ENSP00000420818:Y21H;ENSP00000417834:Y32H;ENSP00000420081:Y21H	ENSP00000004103:Y80H	Y	+	1	0	TMEM176A	150130299	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.623000	0.05546	-0.960000	0.03613	0.459000	0.35465	TAC	.	.	.	none		0.572	TMEM176A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350222.1	NM_018487		C	150499366	T	C	150499366	3	2	192	1	0	0	0	0	1	0	0	0	16104	1522	53	3	244	3	TMEM176A	7	150499366	Missense_Mutation	SNP	T	TCGA-GL-A9DE-01A-11D-A36X-10	67955124	150499366	8639297	43	11442											
ZNF596	169270	hgsc.bcm.edu	37	chr8	195728	195728	+	Frame_Shift_Del	DEL	T	T	-																															cttcactcattgctctgaccTtagaaaacatgagagaactc																										TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr8:195728delT	ENST00000398612.1	+	6	1264	c.881delT	c.(880-882)cttfs	p.L294fs	ZNF596_ENST00000308811.4_Frame_Shift_Del_p.L294fs|ZNF596_ENST00000320552.2_Frame_Shift_Del_p.L224fs	NM_001042415.1|NM_001042416.1	NP_001035880.1|NP_001035881.1	Q8TC21	ZN596_HUMAN	zinc finger protein 596	294					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			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)		TGCTCTGACCTTAGAAAACAT	0.388																																					p.L294fs		Atlas-Indel,Pindel	.											.	ZNF596	34	.	0			c.880delC						PASS	.						62	58	60					8																	195728		2203	4300	6503	SO:0001589	frameshift_variant	169270	exon6			.	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.881delT	chr8.hg19:g.195728delT	ENSP00000381613:p.Leu294fs	113.0	0.0	0		138.0	58.0	0.42029	NM_001042415	B2R8P4|O95015|Q8N9X0	Frame_Shift_Del	DEL	ENST00000398612.1	hg19	CCDS5951.2																																																																																			.	.	.	none		0.388	ZNF596-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195858.4	NM_173539		-	195728	T	-	195728	7	5	192	1	0	1	0	1	0	0	0	0	18038	1609	56	0	899	0	ZNF596	8	195728	Frame_Shift_Del	DEL	T	TCGA-GL-A9DE-01A-11D-A36X-10		195728	146168294	44	11443											
CCDC25	55246	hgsc.bcm.edu	37	chr8	27605752	27605752	+	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	actttggtcttttctaatcgGttcaggatctcatttacttt	7	20	6	8	1	4	0	2	0	3	0	6	1	4	1	0	3	1	1	0	3	2	8			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr8:27605752G>C	ENST00000356537.4	-	7	486	c.393C>G	c.(391-393)aaC>aaG	p.N131K	RP11-16P20.3_ENST00000521510.1_RNA|CCDC25_ENST00000539095.1_Missense_Mutation_p.N63K|CCDC25_ENST00000522915.1_Missense_Mutation_p.N63K	NM_018246.2	NP_060716.2	Q86WR0	CCD25_HUMAN	coiled-coil domain containing 25	131						extracellular vesicular exosome (GO:0070062)				endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	7		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0223)|KIRC - Kidney renal clear cell carcinoma(542;0.11)|Kidney(114;0.131)|Colorectal(74;0.154)		TTTCTAATCGGTTCAGGATCT	0.398																																					p.N131K		Atlas-SNP	.											.	CCDC25	14	.	0			c.C393G						PASS	.						118	113	115					8																	27605752		2203	4300	6503	SO:0001583	missense	55246	exon7			TAATCGGTTCAGG	AK001715	CCDS6062.2	8p21.1	2006-09-20			ENSG00000147419	ENSG00000147419			25591	protein-coding gene	gene with protein product						12477932	Standard	NM_018246		Approved	FLJ10853	uc003xgc.3	Q86WR0	OTTHUMG00000132173	ENST00000356537.4:c.393C>G	chr8.hg19:g.27605752G>C	ENSP00000348933:p.Asn131Lys	82.0	0.0	.		83.0	4.0	.	NM_018246	Q0P663|Q96SI2|Q9NV98	Missense_Mutation	SNP	ENST00000356537.4	hg19	CCDS6062.2	.	.	.	.	.	.	.	.	.	.	G	15.06	2.721188	0.48728	.	.	ENSG00000147419	ENST00000356537;ENST00000539095;ENST00000522915	.	.	.	5.61	2.78	0.32641	.	0.000000	0.85682	D	0.000000	T	0.47266	0.1436	M	0.68593	2.085	0.58432	D	0.999999	P	0.42456	0.78	B	0.38106	0.265	T	0.41805	-0.9488	9	0.54805	T	0.06	-24.9936	8.8923	0.35441	0.2473:0.0:0.7527:0.0	.	131	Q86WR0	CCD25_HUMAN	K	131;63;63	.	ENSP00000348933:N131K	N	-	3	2	CCDC25	27661671	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.658000	0.54482	0.285000	0.22329	0.655000	0.94253	AAC	.	.	.	none		0.398	CCDC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255224.1	NM_018246		C	27605752	G	C	27605752	3	2	192	1	0	0	0	0	1	0	0	0	2802	1252	44	4	245	4	CCDC25	8	27605752	Missense_Mutation	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10	27410024	27605752	118758270	45	11444											
ATP6V1H	51606	hgsc.bcm.edu	37	chr8	54628574	54628574	+	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	ctcggactggagctgcttgcCaaggtattccctgaaaaaaa	12	9	10	10	1	0	1	0	1	0	0	2	3	1	3	2	3	3	3	2	3	5	3			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr8:54628574C>G	ENST00000359530.2	-	14	1665	c.1402G>C	c.(1402-1404)Ggc>Cgc	p.G468R	ATP6V1H_ENST00000523899.1_5'UTR|ATP6V1H_ENST00000520188.1_Missense_Mutation_p.G428R|ATP6V1H_ENST00000355221.3_Missense_Mutation_p.G450R|ATP6V1H_ENST00000396774.2_Missense_Mutation_p.G468R	NM_015941.3	NP_057025.2	Q9UI12	VATH_HUMAN	ATPase, H+ transporting, lysosomal 50/57kDa, V1 subunit H	468					ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|endocytosis (GO:0006897)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|regulation of catalytic activity (GO:0050790)|regulation of defense response to virus by virus (GO:0050690)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|vacuolar acidification (GO:0007035)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V1 domain (GO:0000221)	enzyme regulator activity (GO:0030234)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|urinary_tract(1)	18		all_epithelial(80;0.0487)|Lung NSC(129;0.109)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;2.79e-06)|Epithelial(17;0.000629)|all cancers(17;0.00359)			AGCTGCTTGCCAAGGTATTCC	0.483																																					p.G468R		Atlas-SNP	.											.	ATP6V1H	66	.	0			c.G1402C						PASS	.						42	46	45					8																	54628574		2203	4298	6501	SO:0001583	missense	51606	exon14			GCTTGCCAAGGTA	AF132945	CCDS6153.1, CCDS6154.1	8q11.2	2011-05-24	2002-08-29		ENSG00000047249	ENSG00000047249		"ATPases / V-type"	18303	protein-coding gene	gene with protein product	"vacuolar ATP synthase subunit H"	608861	"ATPase, H+ transporting, lysosomal 50/57kD, V1 subunit H"			9620685, 10810093	Standard	NM_015941		Approved	CGI-11, SFD, VMA13, SFDalpha, SFDbeta	uc003xrm.4	Q9UI12	OTTHUMG00000164231	ENST00000359530.2:c.1402G>C	chr8.hg19:g.54628574C>G	ENSP00000352522:p.Gly468Arg	191.0	0.0	.		162.0	57.0	.	NM_015941	B3KMR0|Q6PK44|Q9H3E3|Q9Y300	Missense_Mutation	SNP	ENST00000359530.2	hg19	CCDS6153.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.268497	0.80469	.	.	ENSG00000047249	ENST00000355221;ENST00000520188;ENST00000359530;ENST00000396774	.	.	.	5.73	5.73	0.89815	.	0.205114	0.52532	D	0.000070	T	0.77452	0.4132	M	0.62723	1.935	0.80722	D	1	D;D	0.71674	0.998;0.992	D;D	0.77557	0.99;0.972	T	0.78288	-0.2262	9	0.87932	D	0	-19.1942	17.1743	0.86837	0.0:1.0:0.0:0.0	.	450;468	Q9UI12-2;Q9UI12	.;VATH_HUMAN	R	450;428;468;468	.	ENSP00000347359:G450R	G	-	1	0	ATP6V1H	54791127	1.000000	0.71417	0.999000	0.59377	0.866000	0.49608	4.271000	0.58902	2.861000	0.98227	0.655000	0.94253	GGC	.	.	.	none		0.483	ATP6V1H-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377865.1	NM_015941		G	54628574	C	G	54628574	3	3	192	1	0	0	0	0	1	0	0	0	1189	594	21	4	53	4	ATP6V1H	8	54628574	Missense_Mutation	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10	27022822	54628574	91735448	46	11445											
SNX16	64089	hgsc.bcm.edu	37	chr8	82751914	82751914	+	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	gtgtagatggtctatcttccCaattcactgtttccggattt	7	17	8	9	1	3	1	1	0	2	1	5	2	5	2	2	2	0	2	2	2	3	6			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr8:82751914C>G	ENST00000345957.4	-	2	586	c.308G>C	c.(307-309)tGg>tCg	p.W103S	SNX16_ENST00000396330.2_Missense_Mutation_p.W103S|SNX16_ENST00000353788.4_Missense_Mutation_p.W103S	NM_152836.2	NP_690049.1	P57768	SNX16_HUMAN	sorting nexin 16	103					early endosome to late endosome transport (GO:0045022)|endosome to lysosome transport (GO:0008333)|protein targeting to lysosome (GO:0006622)	early endosome (GO:0005769)|extrinsic component of endosome membrane (GO:0031313)|late endosome (GO:0005770)|lysosome (GO:0005764)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			large_intestine(1)|ovary(1)|pancreas(1)|skin(2)	5						TCTATCTTCCCAATTCACTGT	0.378																																					p.W103S		Atlas-SNP	.											.	SNX16	21	.	0			c.G308C						PASS	.						152	142	146					8																	82751914		2203	4300	6503	SO:0001583	missense	64089	exon2			TCTTCCCAATTCA	AF305779	CCDS6234.1, CCDS6235.1	8q21.13	2011-05-03			ENSG00000104497	ENSG00000104497		"Sorting nexins"	14980	protein-coding gene	gene with protein product		614903				12461558, 12813048	Standard	NM_152837		Approved		uc003ycn.3	P57768	OTTHUMG00000164727	ENST00000345957.4:c.308G>C	chr8.hg19:g.82751914C>G	ENSP00000322652:p.Trp103Ser	85.0	0.0	.		78.0	33.0	.	NM_152836	A8K4D8|Q658L0|Q8N4U3	Missense_Mutation	SNP	ENST00000345957.4	hg19	CCDS6234.1	.	.	.	.	.	.	.	.	.	.	C	9.277	1.047069	0.19827	.	.	ENSG00000104497	ENST00000353788;ENST00000396330;ENST00000345957;ENST00000520618;ENST00000523757;ENST00000521810	T;T;T;T;T;T	0.36157	1.27;1.27;1.27;1.27;1.66;1.27	5.42	2.43	0.29744	Phox homologous domain (2);	0.782608	0.12355	N	0.476157	T	0.33000	0.0848	L	0.57536	1.79	0.47094	D	0.999312	B;B	0.30511	0.282;0.006	B;B	0.25884	0.064;0.005	T	0.08659	-1.0711	10	0.11182	T	0.66	-13.4645	15.1417	0.72615	0.4023:0.5977:0.0:0.0	.	103;103	Q658L0;P57768	.;SNX16_HUMAN	S	103;103;103;103;74;103	ENSP00000322631:W103S;ENSP00000379621:W103S;ENSP00000322652:W103S;ENSP00000428699:W103S;ENSP00000430038:W74S;ENSP00000428734:W103S	ENSP00000322652:W103S	W	-	2	0	SNX16	82914469	0.999000	0.42202	0.213000	0.23690	0.565000	0.35776	1.105000	0.31086	0.168000	0.19655	0.561000	0.74099	TGG	.	.	.	none		0.378	SNX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379929.1	NM_022133		G	82751914	C	G	82751914	3	3	192	1	0	0	0	0	1	0	0	0	14900	595	21	4	754	4	SNX16	8	82751914	Missense_Mutation	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10	28123340	82751914	63612108	47	11446											
ZNF251	90987	hgsc.bcm.edu	37	chr8	145947779	145947779	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctgtgtgaatccttacgtgTtcagtaagatgagagttaaa	12	13	10	6	1	1	3	1	2	0	2	2	4	2	3	2	0	1	3	2	0	5	4			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr8:145947779T>C	ENST00000292562.7	-	5	1541	c.1266A>G	c.(1264-1266)gaA>gaG	p.E422E	ZNF251_ENST00000524394.1_Intron	NM_138367.1	NP_612376.1	Q9BRH9	ZN251_HUMAN	zinc finger protein 251	422					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|kidney(1)|large_intestine(5)|lung(9)|stomach(1)	17	all_cancers(97;3.54e-11)|all_epithelial(106;2.65e-10)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.75e-39)|Epithelial(56;7.54e-38)|all cancers(56;6.19e-33)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.11)	GBM - Glioblastoma multiforme(99;0.198)		TCCTTACGTGTTCAGTAAGAT	0.448																																					p.E422E		Atlas-SNP	.											.	ZNF251	80	.	0			c.A1266G						PASS	.						96	108	104					8																	145947779		2128	4254	6382	SO:0001819	synonymous_variant	90987	exon5			TACGTGTTCAGTA	AK000435	CCDS47944.1	8q24.3	2013-01-08			ENSG00000198169	ENSG00000198169		"Zinc fingers, C2H2-type", "-"	13045	protein-coding gene	gene with protein product							Standard	NM_138367		Approved		uc003zdv.4	Q9BRH9	OTTHUMG00000165189	ENST00000292562.7:c.1266A>G	chr8.hg19:g.145947779T>C		74.0	0.0	.		89.0	18.0	.	NM_138367	Q2M219	Silent	SNP	ENST00000292562.7	hg19	CCDS47944.1																																																																																			.	.	.	none		0.448	ZNF251-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382541.1	NM_138367		C	145947779	T	C	145947779	2	2	192	1	0	0	0	0	0	0	0	1	17808	1722	60	3		3	ZNF251	8	145947779	Silent	SNP	T	TCGA-GL-A9DE-01A-11D-A36X-10	63195865	145947779	416243	48	11447											
RPL35	11224	hgsc.bcm.edu	37	chr9	127622502	127622502	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttctttctgagtctggttaAtaactgtgagaacacgggca	10	14	10	7	1	3	2	0	2	3	1	3	3	3	2	0	2	2	2	0	2	3	4			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr9:127622502A>G	ENST00000348462.3	-	3	230	c.182T>C	c.(181-183)aTt>aCt	p.I61T	ARPC5L_ENST00000353214.2_5'Flank|RPL35_ENST00000373570.4_Missense_Mutation_p.I61T	NM_007209.3	NP_009140.1	P42766	RL35_HUMAN	ribosomal protein L35	61					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)|nucleolus (GO:0005730)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|large_intestine(1)|lung(1)|ovary(1)	4				GBM - Glioblastoma multiforme(294;0.182)		AGTCTGGTTAATAACTGTGAG	0.498																																					p.I61T		Atlas-SNP	.											.	RPL35	11	.	0			c.T182C						PASS	.						89	86	87					9																	127622502		2203	4300	6503	SO:0001583	missense	11224	exon3			TGGTTAATAACTG	U12465	CCDS6858.1	9q34.1	2011-04-06			ENSG00000136942	ENSG00000136942		"L ribosomal proteins"	10344	protein-coding gene	gene with protein product	"60S ribosomal protein L35"					11401437	Standard	NM_007209		Approved	L35	uc004boy.1	P42766	OTTHUMG00000020659	ENST00000348462.3:c.182T>C	chr9.hg19:g.127622502A>G	ENSP00000259469:p.Ile61Thr	66.0	0.0	.		92.0	37.0	.	NM_007209	A8K4V7|Q4VBY5|Q5JTN5|Q6IBC7|Q96QJ7|Q9BYF4	Missense_Mutation	SNP	ENST00000348462.3	hg19	CCDS6858.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.547839	0.86022	.	.	ENSG00000136942	ENST00000348462	.	.	.	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.76154	0.3948	M	0.90309	3.105	0.80722	D	1	P	0.45011	0.848	P	0.49085	0.6	T	0.81824	-0.0755	9	0.66056	D	0.02	.	14.7041	0.69176	1.0:0.0:0.0:0.0	.	61	P42766	RL35_HUMAN	T	61	.	ENSP00000259469:I61T	I	-	2	0	RPL35	126662323	1.000000	0.71417	0.999000	0.59377	0.861000	0.49209	8.770000	0.91746	2.125000	0.65367	0.459000	0.35465	ATT	.	.	.	none		0.498	RPL35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054035.1	NM_007209		G	127622502	A	G	127622502	3	3	192	1	0	0	0	0	1	0	0	0	13597	101	4	3	197	3	RPL35	9	127622502	Missense_Mutation	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10		127622502	13590929	49	11448											
LAMC3	10319	hgsc.bcm.edu	37	chr9	133901739	133901739	+	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	cgccctgagagctttgccatCtacaagcgcagccgcgccga	8	6	11	16	5	1	1	0	1	1	1	1	3	1	1	4	0	5	2	4	0	2	2			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr9:133901739C>A	ENST00000361069.4	+	2	574	c.441C>A	c.(439-441)atC>atA	p.I147I	LAMC3_ENST00000480883.1_3'UTR	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	147	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		GCTTTGCCATCTACAAGCGCA	0.617																																					p.I147I		Atlas-SNP	.											.	LAMC3	167	.	0			c.C441A						PASS	.						42	46	45					9																	133901739		2203	4300	6503	SO:0001819	synonymous_variant	10319	exon2			TGCCATCTACAAG	AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"Laminins"	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.441C>A	chr9.hg19:g.133901739C>A		146.0	0.0	.		137.0	53.0	.	NM_006059	B1APX9|B1APY0|Q59H72	Silent	SNP	ENST00000361069.4	hg19	CCDS6938.1																																																																																			.	.	.	none		0.617	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059		A	133901739	C	A	133901739	2	1	192	1	0	0	0	0	0	0	0	1	8623	903	32	4		4	LAMC3	9	133901739	Silent	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10	6279237	133901739	7311692	50	11449											
DIP2C	22982	hgsc.bcm.edu	37	chr10	327182	327182	+	Missense_Mutation	SNP	A	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	ctctgatgaccgaggtctcaAtgtcgattgggtggtaccgc	7	11	13	10	3	2	2	1	2	2	0	4	4	2	2	2	3	1	1	2	3	2	2			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr10:327182A>C	ENST00000280886.6	-	36	4463	c.4376T>G	c.(4375-4377)aTt>aGt	p.I1459S	RNA5SP298_ENST00000364991.1_RNA	NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1459						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)		CGAGGTCTCAATGTCGATTGG	0.542																																					p.I1459S		Atlas-SNP	.											.	DIP2C	195	.	0			c.T4376G						PASS	.						179	144	156					10																	327182		2203	4300	6503	SO:0001583	missense	22982	exon36			GTCTCAATGTCGA	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.4376T>G	chr10.hg19:g.327182A>C	ENSP00000280886:p.Ile1459Ser	74.0	0.0	.		84.0	39.0	.	NM_014974	B4DPI5|Q5SS78	Missense_Mutation	SNP	ENST00000280886.6	hg19	CCDS7054.1	.	.	.	.	.	.	.	.	.	.	A	29.4	5.004268	0.93287	.	.	ENSG00000151240	ENST00000280886;ENST00000535541	T	0.19806	2.12	5.89	5.89	0.94794	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.52273	0.1724	M	0.85945	2.785	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.59327	-0.7475	10	0.87932	D	0	-38.0194	16.3123	0.82883	1.0:0.0:0.0:0.0	.	1459	Q9Y2E4	DIP2C_HUMAN	S	1459;384	ENSP00000280886:I1459S	ENSP00000280886:I1459S	I	-	2	0	DIP2C	317182	1.000000	0.71417	0.999000	0.59377	0.916000	0.54674	9.339000	0.96797	2.254000	0.74563	0.459000	0.35465	ATT	.	.	.	none		0.542	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974		C	327182	A	C	327182	3	2	192	1	0	0	0	0	1	0	0	0	4531	101	4	5	302	5	DIP2C	10	327182	Missense_Mutation	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10		327182	135207565	51	11450											
C10orf67	256815	hgsc.bcm.edu	37	chr10	23622020	23622020	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttttgcgtagatgaactcaAttcttttactgacagtattt	10	18	6	7	1	2	3	1	2	1	1	2	3	2	3	0	0	3	2	0	0	5	8			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr10:23622020A>G	ENST00000323327.4	-	2	368	c.301T>C	c.(301-303)Ttg>Ctg	p.L101L		NM_153714.2	NP_714925.2	Q8IYJ2	CJ067_HUMAN	chromosome 10 open reading frame 67	101								p.L101M(1)		central_nervous_system(1)|endometrium(1)|lung(2)|pancreas(1)	5						GATGAACTCAATTCTTTTACT	0.343																																					p.L101L		Atlas-SNP	.											C10orf67,NS,carcinoma,0,1	C10orf67	21	.	1	Substitution - Missense(1)	lung(1)	c.T301C						PASS	.						119	112	114					10																	23622020		1838	4082	5920	SO:0001819	synonymous_variant	256815	exon2			AACTCAATTCTTT	BC035732	CCDS44365.1	10p12.31	2012-05-31			ENSG00000179133	ENSG00000179133			28716	protein-coding gene	gene with protein product						12477932	Standard	NM_153714		Approved	MGC46732	uc010qcx.2	Q8IYJ2	OTTHUMG00000017818	ENST00000323327.4:c.301T>C	chr10.hg19:g.23622020A>G		115.0	0.0	.		136.0	61.0	.	NM_153714	A8MUP9|Q5SWD4	Silent	SNP	ENST00000323327.4	hg19	CCDS44365.1																																																																																			.	.	.	none		0.343	C10orf67-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047213.1	NM_153714		G	23622020	A	G	23622020	2	3	192	1	0	0	0	0	0	0	0	1	1614	98	4	3		3	C10orf67	10	23622020	Silent	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10	23294838	23622020	111912727	52	11451											
WAC	51322	hgsc.bcm.edu	37	chr10	28906628	28906628	+	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	cgcataacatgggaactattCacatgtccgaaatttgtact	13	12	7	9	2	1	0	1	0	0	0	2	2	2	1	1	1	3	2	1	1	5	5			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr10:28906628C>G	ENST00000354911.4	+	13	1950	c.1789C>G	c.(1789-1791)Cac>Gac	p.H597D	WAC_ENST00000375664.4_Missense_Mutation_p.H552D|WAC_ENST00000375646.1_Missense_Mutation_p.H445D|WAC_ENST00000347934.4_Missense_Mutation_p.H494D	NM_016628.4	NP_057712.2	Q9BTA9	WAC_HUMAN	WW domain containing adaptor with coiled-coil	597					cellular response to DNA damage stimulus (GO:0006974)|G1 DNA damage checkpoint (GO:0044783)|histone H2B conserved C-terminal lysine ubiquitination (GO:0071894)|histone monoubiquitination (GO:0010390)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	chromatin binding (GO:0003682)|RNA polymerase II core binding (GO:0000993)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|urinary_tract(1)	32						GGGAACTATTCACATGTCCGA	0.313																																					p.H597D		Atlas-SNP	.											.	WAC	77	.	0			c.C1789G						PASS	.						38	41	40					10																	28906628		2203	4300	6503	SO:0001583	missense	51322	exon13			ACTATTCACATGT	AK055852	CCDS7159.1, CCDS7160.1, CCDS7161.1	10p12.1	2007-05-17	2003-03-19		ENSG00000095787	ENSG00000095787			17327	protein-coding gene	gene with protein product		615049	"WW domain-containing adaptor with coiled coil"			11827461	Standard	NR_024557		Approved	Wwp4, FLJ31290, PRO1741, BM-016, MGC10753	uc001iuf.3	Q9BTA9	OTTHUMG00000017872	ENST00000354911.4:c.1789C>G	chr10.hg19:g.28906628C>G	ENSP00000346986:p.His597Asp	264.0	0.0	.		240.0	105.0	.	NM_016628	A8K2A9|C9JBT9|D3DRW5|D3DRW6|D3DRW7|Q53EN9|Q5JU75|Q5JU77|Q5VXK0|Q5VXK2|Q8TCK1|Q96DP3|Q96FW6|Q96JI3	Missense_Mutation	SNP	ENST00000354911.4	hg19	CCDS7159.1	.	.	.	.	.	.	.	.	.	.	C	18.03	3.531433	0.64972	.	.	ENSG00000095787	ENST00000375664;ENST00000375646;ENST00000347934;ENST00000354911	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	5.57	5.57	0.84162	.	0.093685	0.85682	D	0.000000	T	0.35393	0.0930	L	0.34521	1.04	0.80722	D	1	P;P;P	0.42620	0.764;0.785;0.652	B;B;B	0.36418	0.224;0.182;0.112	T	0.24119	-1.0169	10	0.54805	T	0.06	-10.4861	19.5403	0.95271	0.0:1.0:0.0:0.0	.	552;494;597	Q9BTA9-2;Q9BTA9-5;Q9BTA9	.;.;WAC_HUMAN	D	552;445;494;597	ENSP00000364816:H552D;ENSP00000364797:H445D;ENSP00000311106:H494D;ENSP00000346986:H597D	ENSP00000311106:H494D	H	+	1	0	WAC	28946634	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.667000	0.68067	2.619000	0.88677	0.655000	0.94253	CAC	.	.	.	none		0.313	WAC-017	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000047371.1	NM_100264		G	28906628	C	G	28906628	3	3	192	1	0	0	0	0	1	0	0	0	17259	826	29	4	1839	4	WAC	10	28906628	Missense_Mutation	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10	5284608	28906628	106628119	53	11452											
CUEDC2	79004	hgsc.bcm.edu	37	chr10	104184908	104184908	+	Missense_Mutation	SNP	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	ggaggtgtgtctggacaaagGcaaggagggctgcactgacg	10	6	18	7	1	1	1	0	1	1	0	1	4	1	4	0	6	1	3	0	6	2	0			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr10:104184908G>A	ENST00000369937.4	-	2	183	c.38C>T	c.(37-39)gCc>gTc	p.A13V	CUEDC2_ENST00000465409.1_5'Flank	NM_024040.2	NP_076945.2	Q9H467	CUED2_HUMAN	CUE domain containing 2	13						cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(1)|stomach(1)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.122)		Epithelial(162;9.17e-09)|all cancers(201;2.16e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		CTGGACAAAGGCAAGGAGGGC	0.622																																					p.A13V		Atlas-SNP	.											.	CUEDC2	22	.	0			c.C38T						PASS	.						63	67	65					10																	104184908		2085	4206	6291	SO:0001583	missense	79004	exon2			ACAAAGGCAAGGA	BC000262	CCDS41566.1	10q24.32	2008-10-23	2004-03-04	2004-03-05	ENSG00000107874	ENSG00000107874			28352	protein-coding gene	gene with protein product		614142	"chromosome 10 open reading frame 66"	C10orf66		12477932	Standard	NM_024040		Approved	MGC2491	uc001kvn.2	Q9H467	OTTHUMG00000018958	ENST00000369937.4:c.38C>T	chr10.hg19:g.104184908G>A	ENSP00000358953:p.Ala13Val	16.0	0.0	.		35.0	13.0	.	NM_024040	D3DR88|Q9BWG8	Missense_Mutation	SNP	ENST00000369937.4	hg19	CCDS41566.1	.	.	.	.	.	.	.	.	.	.	G	13.07	2.126576	0.37533	.	.	ENSG00000107874	ENST00000369937	D	0.89485	-2.52	5.3	0.711	0.18162	.	0.533792	0.20404	N	0.092995	T	0.77170	0.4091	N	0.12182	0.205	0.09310	N	0.99999	B	0.20887	0.049	B	0.16722	0.016	T	0.68569	-0.5374	10	0.52906	T	0.07	-2.1406	10.7668	0.46299	0.0:0.4683:0.4178:0.1139	.	13	Q9H467	CUED2_HUMAN	V	13	ENSP00000358953:A13V	ENSP00000358953:A13V	A	-	2	0	CUEDC2	104174898	0.958000	0.32768	0.710000	0.30468	0.970000	0.65996	1.729000	0.38115	0.568000	0.29311	0.555000	0.69702	GCC	.	.	.	none		0.622	CUEDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050060.1	NM_024040		A	104184908	G	A	104184908	3	1	192	1	0	0	0	0	1	0	0	0	4055	1203	42	2	857	2	CUEDC2	10	104184908	Missense_Mutation	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10	75278280	104184908	31349839	54	11453											
COL17A1	1308	hgsc.bcm.edu	37	chr10	105793812	105793812	+	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	tacatgccgccttctgctgcTgccccatagcctccgcctgg	4	10	9	18	2	1	0	0	0	1	0	2	0	2	0	7	1	6	2	7	1	2	3			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr10:105793812T>A	ENST00000353479.5	-	52	4337	c.4047A>T	c.(4045-4047)gcA>gcT	p.A1349A	COL17A1_ENST00000369733.3_Silent_p.A1267A	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	1349	Triple-helical region.				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|hemidesmosome (GO:0030056)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				NS(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|liver(1)|lung(22)|ovary(5)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	62		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		CTTCTGCTGCTGCCCCATAGC	0.602																																					p.A1349A		Atlas-SNP	.											.	COL17A1	149	.	0			c.A4047T						PASS	.						83	79	80					10																	105793812		2203	4300	6503	SO:0001819	synonymous_variant	1308	exon52			TGCTGCTGCCCCA	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.4047A>T	chr10.hg19:g.105793812T>A		212.0	0.0	.		258.0	98.0	.	NM_000494	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Silent	SNP	ENST00000353479.5	hg19	CCDS7554.1																																																																																			.	.	.	none		0.602	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494		A	105793812	T	A	105793812	2	1	192	1	0	0	0	0	0	0	0	1	3676	1567	55	5		5	COL17A1	10	105793812	Silent	SNP	T	TCGA-GL-A9DE-01A-11D-A36X-10	1608904	105793812	29740935	55	11454											
RRM1	6240	hgsc.bcm.edu	37	chr11	4144483	4144483	+	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	ggtatgccatcattgagtctCagacggaaacaggcaccccg	11	7	11	12	2	2	2	2	1	1	1	3	3	2	3	3	3	2	2	3	3	2	2			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr11:4144483C>T	ENST00000300738.5	+	12	1393	c.1189C>T	c.(1189-1191)Cag>Tag	p.Q397*	RRM1_ENST00000534285.1_Nonsense_Mutation_p.Q175*|RRM1_ENST00000423050.2_Nonsense_Mutation_p.Q300*|RRM1_ENST00000537197.1_Nonsense_Mutation_p.Q59*|RRM1_ENST00000528470.1_3'UTR	NM_001033.3	NP_001024.1	P23921	RIR1_HUMAN	ribonucleotide reductase M1	397					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)	CATTGAGTCTCAGACGGAAAC	0.433																																					p.Q397X	NSCLC(45;1345 1376 6258 22925)|Ovarian(34;894 1053 6175 12768)	Atlas-SNP	.											.	RRM1	31	.	0			c.C1189T						PASS	.						100	99	99					11																	4144483		2201	4298	6499	SO:0001587	stop_gained	6240	exon12			GAGTCTCAGACGG	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.1189C>T	chr11.hg19:g.4144483C>T	ENSP00000300738:p.Gln397*	169.0	0.0	.		217.0	98.0	.	NM_001033	Q9UNN2	Nonsense_Mutation	SNP	ENST00000300738.5	hg19	CCDS7750.1	.	.	.	.	.	.	.	.	.	.	C	38	6.853298	0.97885	.	.	ENSG00000167325	ENST00000300738;ENST00000423050;ENST00000536894;ENST00000534285;ENST00000543838;ENST00000537197	.	.	.	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-10.9476	18.8429	0.92192	0.0:1.0:0.0:0.0	.	.	.	.	X	397;300;310;175;175;59	.	ENSP00000300738:Q397X	Q	+	1	0	RRM1	4101059	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	7.487000	0.81328	2.706000	0.92434	0.563000	0.77884	CAG	.	.	.	none		0.433	RRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257197.1	NM_001033		T	4144483	C	T	4144483	4	4	192	1	0	0	0	0	0	1	0	0	13694	827	29	2	1235	2	RRM1	11	4144483	Nonsense_Mutation	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10		4144483	130862033	56	11455											
TRIM3	10612	hgsc.bcm.edu	37	chr11	6470304	6470304	+	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	agcagtggttgccagcatcaGccaccaccacatggccatcc	10	6	9	16	0	1	0	1	0	0	0	2	0	2	0	6	2	4	3	6	2	0	1			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr11:6470304G>T	ENST00000525074.1	-	12	2583	c.2189C>A	c.(2188-2190)gCt>gAt	p.A730D	TRIM3_ENST00000359518.3_Missense_Mutation_p.A730D|TRIM3_ENST00000536344.1_Missense_Mutation_p.A611D|TRIM3_ENST00000537602.1_Missense_Mutation_p.A652D|TRIM3_ENST00000345851.3_Missense_Mutation_p.A730D	NM_001248006.1	NP_001234935.1	O75382	TRIM3_HUMAN	tripartite motif containing 3	730					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)		GCCAGCATCAGCCACCACCAC	0.562																																					p.A730D	Melanoma(6;5 510 1540 25169 29084)	Atlas-SNP	.											.	TRIM3	67	.	0			c.C2189A						PASS	.						88	74	79					11																	6470304		2201	4296	6497	SO:0001583	missense	10612	exon12			GCATCAGCCACCA	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.2189C>A	chr11.hg19:g.6470304G>T	ENSP00000433102:p.Ala730Asp	63.0	0.0	.		95.0	5.0	.	NM_001248006	B7Z5E6|F5H2Q8|Q4V9L4|Q9C038|Q9C039	Missense_Mutation	SNP	ENST00000525074.1	hg19	CCDS7764.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.461615	0.84425	.	.	ENSG00000110171	ENST00000525074;ENST00000345851;ENST00000336043;ENST00000537602;ENST00000359518;ENST00000536344	T;T;T;T;T	0.79352	-1.26;-1.26;-1.26;-1.26;-1.26	4.8	4.8	0.61643	Six-bladed beta-propeller, TolB-like (1);	0.066417	0.64402	D	0.000011	D	0.90665	0.7072	M	0.92122	3.275	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.92909	0.6346	10	0.87932	D	0	-11.2897	16.6192	0.84925	0.0:0.0:1.0:0.0	.	611;730	F5H2Q8;O75382	.;TRIM3_HUMAN	D	730;730;719;652;730;611	ENSP00000433102:A730D;ENSP00000340797:A730D;ENSP00000441091:A652D;ENSP00000352508:A730D;ENSP00000445460:A611D	ENSP00000337094:A719D	A	-	2	0	TRIM3	6426880	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.591000	0.98241	2.492000	0.84095	0.563000	0.77884	GCT	.	.	.	none		0.562	TRIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384224.2	NM_006458		T	6470304	G	T	6470304	3	4	192	1	0	0	0	0	1	0	0	0	16516	971	34	4	49	4	TRIM3	11	6470304	Missense_Mutation	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10	2325821	6470304	128536212	57	11456											
HPS5	11234	hgsc.bcm.edu	37	chr11	18333543	18333543	+	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	ctgaactgcccaaagccaacCatttccgagacacagctatg	13	7	7	14	1	0	2	0	1	0	1	1	3	1	2	4	0	5	1	4	0	4	2			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr11:18333543C>A	ENST00000349215.3	-	3	414	c.137G>T	c.(136-138)tGg>tTg	p.W46L	HPS5_ENST00000396253.3_5'UTR|HPS5_ENST00000531848.1_5'UTR|HPS5_ENST00000438420.2_5'UTR	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	46					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						CAAAGCCAACCATTTCCGAGA	0.433									Hermansky-Pudlak syndrome																												p.W46L		Atlas-SNP	.											.	HPS5	70	.	0			c.G137T						PASS	.						112	117	115					11																	18333543		2199	4293	6492	SO:0001583	missense	11234	exon3	Familial Cancer Database	HPS, HPS1-8	GCCAACCATTTCC	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.137G>T	chr11.hg19:g.18333543C>A	ENSP00000265967:p.Trp46Leu	86.0	0.0	.		82.0	35.0	.	NM_181507	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Missense_Mutation	SNP	ENST00000349215.3	hg19	CCDS7836.1	.	.	.	.	.	.	.	.	.	.	C	32	5.109237	0.94292	.	.	ENSG00000110756	ENST00000349215	T	0.59906	0.23	5.4	5.4	0.78164	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.67961	0.2949	L	0.29908	0.895	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.68618	-0.5361	10	0.51188	T	0.08	.	19.5422	0.95278	0.0:1.0:0.0:0.0	.	62;46	Q8IZE8;Q9UPZ3	.;HPS5_HUMAN	L	46	ENSP00000265967:W46L	ENSP00000265967:W46L	W	-	2	0	HPS5	18290119	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.403000	0.79983	2.695000	0.91970	0.561000	0.74099	TGG	.	.	.	none		0.433	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507		A	18333543	C	A	18333543	3	1	192	1	0	0	0	0	1	0	0	0	7349	595	21	4	3336	4	HPS5	11	18333543	Missense_Mutation	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10	11863239	18333543	116672973	58	11457											
SLC3A2	6520	hgsc.bcm.edu	37	chr11	62652107	62652108	+	Missense_Mutation	DNP	GC	GC	AT																															tgcttttttctttctaggatGcatcctcattcttggctgag																										TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr11:62652107_62652108GC>AT	ENST00000377890.2	+	8	1234_1235	c.1066_1067GC>AT	c.(1066-1068)GCa>ATa	p.A356I	SLC3A2_ENST00000536981.1_5'UTR|SLC3A2_ENST00000377889.2_Missense_Mutation_p.A294I|SLC3A2_ENST00000377891.2_Missense_Mutation_p.A357I|SLC3A2_ENST00000538682.1_3'UTR|SLC3A2_ENST00000338663.7_Missense_Mutation_p.A255I|SLC3A2_ENST00000377892.1_Missense_Mutation_p.A387I|SLC3A2_ENST00000535296.1_Missense_Mutation_p.A325I	NM_002394.5	NP_002385.3	P08195	4F2_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 2	356					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						TTTCTAGGATGCATCCTCATTC	0.485											OREG0021032	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A357T|p.A357V		Atlas-SNP	.											.	SLC3A2	55	.	0			c.G1069A|c.C1070T						PASS	.																																			SO:0001583	missense	6520	exon8			TAGGATGCATCCT|AGGATGCATCCTC		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	Exception_encountered	chr11.hg19:g.62652107_62652108delinsAT	ENSP00000367122:p.Ala356Ile	85.0|83.0	0.0	.	1062	67.0|69.0	25.0	.	NM_001012662	Q13543	Missense_Mutation	SNP	ENST00000377890.2	hg19	CCDS8039.2																																																																																			.	.	.	none		0.485	SLC3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157306.1	NM_001012661		AT	62652108	GC	AT	62652107	3	1	192	1	0	0	0	0	1	0	0	0	14640	1319	46	2	1196	2	SLC3A2	11	62652107	Missense_Mutation	DNP	GC	TCGA-GL-A9DE-01A-11D-A36X-10	44318564	62652107	72354409	59	11458											
NUMA1	4926	hgsc.bcm.edu	37	chr11	71720100	71720100	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcccagcctgctgtagctcAtggcccagccgttcagcttc	6	9	10	16	1	2	0	2	0	0	0	3	0	2	0	4	1	6	5	4	1	1	3			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr11:71720100A>G	ENST00000393695.3	-	19	5302	c.4971T>C	c.(4969-4971)caT>caC	p.H1657H	NUMA1_ENST00000358965.6_Silent_p.H1643H|NUMA1_ENST00000351960.6_Silent_p.H521H	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						GCTGTAGCTCATGGCCCAGCC	0.597			T	RARA	APL																																p.H1657H		Atlas-SNP	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.T4971C						PASS	.						53	50	51					11																	71720100		2200	4293	6493	SO:0001819	synonymous_variant	4926	exon19			TAGCTCATGGCCC	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.4971T>C	chr11.hg19:g.71720100A>G		49.0	0.0	.		59.0	27.0	.	NM_006185		Silent	SNP	ENST00000393695.3	hg19	CCDS31633.1	.	.	.	.	.	.	.	.	.	.	A	8.322	0.824515	0.16678	.	.	ENSG00000137497	ENST00000541584	.	.	.	5.56	-7.2	0.01495	.	.	.	.	.	T	0.47377	0.1442	.	.	.	0.45777	D	0.998668	.	.	.	.	.	.	T	0.51140	-0.8743	4	.	.	.	.	7.7891	0.29110	0.5762:0.1983:0.0:0.2256	.	.	.	.	T	488	.	.	M	-	2	0	NUMA1	71397748	0.006000	0.16342	0.638000	0.29380	0.961000	0.63080	-0.491000	0.06474	-1.624000	0.01556	0.459000	0.35465	ATG	.	.	.	none		0.597	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1			G	71720100	A	G	71720100	2	3	192	1	0	0	0	0	0	0	0	1	10757	214	8	3		3	NUMA1	11	71720100	Silent	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10	9067993	71720100	63286416	60	11459											
INPPL1	3636	hgsc.bcm.edu	37	chr11	71942228	71942228	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcttacggatctggattacCgcccggtgagggggggtcat	7	9	16	9	3	2	1	1	1	1	0	2	3	2	3	2	6	3	1	2	6	2	2			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr11:71942228C>T	ENST00000298229.2	+	12	1696	c.1492C>T	c.(1492-1494)Cgc>Tgc	p.R498C	INPPL1_ENST00000541756.1_Missense_Mutation_p.R256C|INPPL1_ENST00000538751.1_Missense_Mutation_p.R256C	NM_001567.3	NP_001558.3	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	498					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)	p.R498S(1)		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						TCTGGATTACCGCCCGGTGAG	0.597																																					p.R498C		Atlas-SNP	.											.	INPPL1	120	.	1	Substitution - Missense(1)	lung(1)	c.C1492T						PASS	.						71	81	78					11																	71942228		2199	4290	6489	SO:0001583	missense	3636	exon12			GATTACCGCCCGG	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.1492C>T	chr11.hg19:g.71942228C>T	ENSP00000298229:p.Arg498Cys	31.0	0.0	.		36.0	16.0	.	NM_001567	B2RTX5|Q13577|Q13578	Missense_Mutation	SNP	ENST00000298229.2	hg19	CCDS8213.1	.	.	.	.	.	.	.	.	.	.	c	23.4	4.416629	0.83449	.	.	ENSG00000165458	ENST00000298229;ENST00000541756;ENST00000538751	T;T;T	0.80824	-1.42;-1.42;-1.42	5.81	5.81	0.92471	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.123775	0.56097	D	0.000033	D	0.82884	0.5134	N	0.17764	0.52	0.52099	D	0.999943	D	0.76494	0.999	D	0.65573	0.936	D	0.84613	0.0679	10	0.59425	D	0.04	.	18.6606	0.91470	0.0:1.0:0.0:0.0	.	498	O15357	SHIP2_HUMAN	C	498;256;256	ENSP00000298229:R498C;ENSP00000446360:R256C;ENSP00000444619:R256C	ENSP00000298229:R498C	R	+	1	0	INPPL1	71619876	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.557000	0.67313	2.746000	0.94184	0.655000	0.94253	CGC	.	.	.	none		0.597	INPPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396789.1	NM_001567		T	71942228	C	T	71942228	3	4	192	1	0	0	0	0	1	0	0	0	7768	652	23	1	1538	1	INPPL1	11	71942228	Missense_Mutation	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10	222128	71942228	63064288	61	11460											
RAB6A	5870	hgsc.bcm.edu	37	chr11	73471628	73471628	+	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	caccgctttgctcccccaggAacaccagcttgaatttcctc	8	10	6	17	1	0	1	0	1	0	0	3	2	2	2	5	1	3	3	5	1	2	3			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr11:73471628A>T	ENST00000336083.3	-	1	508	c.53T>A	c.(52-54)tTc>tAc	p.F18Y	RAB6A_ENST00000310653.6_Missense_Mutation_p.F18Y|RAB6A_ENST00000541588.1_Missense_Mutation_p.F18Y|RP11-707G14.1_ENST00000540547.1_RNA|RAB6A_ENST00000536566.1_5'Flank	NM_198896.1	NP_942599.1	P20340	RAB6A_HUMAN	RAB6A, member RAS oncogene family	18					antigen processing and presentation (GO:0019882)|early endosome to Golgi transport (GO:0034498)|GTP catabolic process (GO:0006184)|minus-end-directed organelle transport along microtubule (GO:0072385)|peptidyl-cysteine methylation (GO:0018125)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)|protein domain specific binding (GO:0019904)			large_intestine(2)|lung(2)	4						CTCCCCCAGGAACACCAGCTT	0.682																																					p.F18Y		Atlas-SNP	.											.	RAB6A	17	.	0			c.T53A						PASS	.						35	31	32					11																	73471628		2200	4292	6492	SO:0001583	missense	5870	exon1			CCCAGGAACACCA	AF130986	CCDS8223.1, CCDS8224.1, CCDS58155.1, CCDS58156.1	11q13.3	2008-08-08			ENSG00000175582	ENSG00000175582		"RAB, member RAS oncogene"	9786	protein-coding gene	gene with protein product		179513		RAB6			Standard	NM_001243718		Approved		uc001ouf.3	P20340	OTTHUMG00000134308	ENST00000336083.3:c.53T>A	chr11.hg19:g.73471628A>T	ENSP00000336850:p.Phe18Tyr	226.0	0.0	.		248.0	99.0	.	NM_002869	A8K133|B7Z772|F5H668|Q1W5D8|Q5U0A8|Q9UBE4	Missense_Mutation	SNP	ENST00000336083.3	hg19	CCDS8224.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	28.2|28.2	4.895232|4.895232	0.91962|0.91962	.|.	.|.	ENSG00000175582|ENSG00000175582	ENST00000310653;ENST00000336083;ENST00000393571;ENST00000541588;ENST00000540771;ENST00000539750;ENST00000535748;ENST00000542366|ENST00000400470	T;T;T;T|.	0.80123|.	-1.34;-1.34;-1.34;-0.49|.	4.89|4.89	4.89|4.89	0.63831|0.63831	Small GTP-binding protein domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.80701|0.80701	0.4673|0.4673	M|M	0.91663|0.91663	3.23|3.23	0.80722|0.80722	D|D	1|1	P;D;B;B|.	0.67145|.	0.786;0.996;0.184;0.153|.	P;D;B;B|.	0.76071|.	0.733;0.987;0.239;0.199|.	D|D	0.84953|0.84953	0.0872|0.0872	10|5	0.87932|.	D|.	0|.	.|.	12.527|12.527	0.56091|0.56091	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	18;18;18;18|.	Q1W5D8;F5H3K7;P20340;P20340-2|.	.;.;RAB6A_HUMAN;.|.	Y|T	18|10	ENSP00000311449:F18Y;ENSP00000336850:F18Y;ENSP00000445350:F18Y;ENSP00000438842:F18Y|.	ENSP00000311449:F18Y|.	F|S	-|-	2|1	0|0	RAB6A|RAB6A	73149276|73149276	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	6.895000|6.895000	0.75660|0.75660	2.051000|2.051000	0.60960|0.60960	0.528000|0.528000	0.53228|0.53228	TTC|TCC	.	.	.	none		0.682	RAB6A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259241.2			T	73471628	A	T	73471628	3	4	192	1	0	0	0	0	1	0	0	0	12964	246	9	5	715	5	RAB6A	11	73471628	Missense_Mutation	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10	1529400	73471628	61534888	62	11461											
C2CD3	26005	hgsc.bcm.edu	37	chr11	73850650	73850650	+	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	gtattaggtatggtaattacCtcggagtggttgatctactg	9	15	12	5	1	1	1	0	1	1	0	2	2	1	2	1	4	2	4	1	4	6	7			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr11:73850650C>G	ENST00000334126.7	-	4	933	c.707G>C	c.(706-708)aGg>aCg	p.R236T	C2CD3_ENST00000539061.1_Splice_Site_p.R236T|C2CD3_ENST00000313663.7_Splice_Site_p.R236T			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	236					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)					TGGTAATTACCTCGGAGTGGT	0.408																																					p.R236T		Atlas-SNP	.											.	C2CD3	288	.	0			c.G707C						PASS	.						294	291	292					11																	73850650		2200	4293	6493	SO:0001630	splice_region_variant	26005	exon4			AATTACCTCGGAG	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.707+1G>C	chr11.hg19:g.73850650C>G		91.0	0.0	.		84.0	23.0	.	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	hg19		.	.	.	.	.	.	.	.	.	.	C	13.04	2.117645	0.37339	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681;ENST00000289350;ENST00000539061	T;T	0.11385	2.78;2.81	5.02	4.11	0.48088	.	0.236148	0.42548	D	0.000694	T	0.28067	0.0692	M	0.73598	2.24	0.34355	D	0.690345	D;D	0.71674	0.995;0.998	P;D	0.68621	0.841;0.959	T	0.40117	-0.9580	9	.	.	.	.	9.0399	0.36311	0.0:0.9009:0.0:0.0991	.	236;236	Q4AC94;Q4AC94-1	C2CD3_HUMAN;.	T	236	ENSP00000334379:R236T;ENSP00000323339:R236T	.	R	-	2	0	C2CD3	73528298	1.000000	0.71417	1.000000	0.80357	0.454000	0.32378	2.454000	0.44979	1.355000	0.45865	0.644000	0.83932	AGG	.	.	.	none		0.408	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	Missense_Mutation	G	73850650	C	G	73850650	5	3	192	1	0	0	0	0	0	0	1	0	2156	695	24	4	5296	4	C2CD3	11	73850650	Splice_Site	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10	379022	73850650	61155866	63	11462											
FUT4	2526	hgsc.bcm.edu	37	chr11	94277973	94277973	+	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	cggctgccgcctgctcaccgAccgcgcgtcctacggagagg	5	5	14	17	7	1	1	1	0	0	1	2	3	2	1	5	3	3	2	5	3	1	1			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr11:94277973A>T	ENST00000358752.2	+	1	957	c.674A>T	c.(673-675)gAc>gTc	p.D225V	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)	225					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)				CTGCTCACCGACCGCGCGTCC	0.736																																					p.D225V		Atlas-SNP	.											.	FUT4	17	.	0			c.A674T						PASS	.						6	7	6					11																	94277973		1699	3465	5164	SO:0001583	missense	2526	exon1			TCACCGACCGCGC		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.674A>T	chr11.hg19:g.94277973A>T	ENSP00000351602:p.Asp225Val	53.0	0.0	.		32.0	14.0	.	NM_002033	B2RMS0	Missense_Mutation	SNP	ENST00000358752.2	hg19	CCDS8301.1	.	.	.	.	.	.	.	.	.	.	a	20.8	4.052660	0.75960	.	.	ENSG00000196371	ENST00000358752	T	0.29917	1.55	4.4	3.17	0.36434	.	0.122950	0.52532	D	0.000062	T	0.57740	0.2074	M	0.88906	2.99	0.58432	D	0.999999	D	0.89917	1.0	D	0.79784	0.993	T	0.65504	-0.6152	10	0.87932	D	0	.	10.5091	0.44851	0.8375:0.1625:0.0:0.0	.	225	P22083	FUT4_HUMAN	V	225	ENSP00000351602:D225V	ENSP00000351602:D225V	D	+	2	0	FUT4	93917621	0.998000	0.40836	0.773000	0.31616	0.629000	0.37895	3.825000	0.55730	1.739000	0.51704	0.363000	0.22086	GAC	.	.	.	none		0.736	FUT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396327.2	NM_002033		T	94277973	A	T	94277973	3	4	192	1	0	0	0	0	1	0	0	0	6113	275	10	5	676	5	FUT4	11	94277973	Missense_Mutation	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10	20427323	94277973	40728543	64	11463											
MLL	4297	hgsc.bcm.edu	37	chr11	118390700	118390700	+	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	catttgacatgtttaacttcCtggcttctaaacatcgtcag	10	15	6	10	1	2	1	1	1	1	0	4	1	3	1	1	1	2	2	1	1	3	6			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr11:118390700C>G	ENST00000389506.5	+	33	11341	c.11341C>G	c.(11341-11343)Ctg>Gtg	p.L3781V	KMT2A_ENST00000354520.4_Missense_Mutation_p.L3743V|RP11-770J1.3_ENST00000556583.1_RNA|RP11-770J1.3_ENST00000554407.1_RNA|RP11-770J1.3_ENST00000532597.1_RNA|RP11-770J1.3_ENST00000525992.2_RNA|KMT2A_ENST00000534358.1_Missense_Mutation_p.L3784V|RP11-770J1.3_ENST00000528578.1_RNA			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	3781					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)										GTTTAACTTCCTGGCTTCTAA	0.418																																					p.L3784V		Atlas-SNP	.											.	MLL	548	.	0			c.C11350G						PASS	.						93	90	91					11																	118390700		2200	4295	6495	SO:0001583	missense	4297	exon33			AACTTCCTGGCTT	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.11341C>G	chr11.hg19:g.118390700C>G	ENSP00000374157:p.Leu3781Val	42.0	0.0	.		66.0	38.0	.	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	hg19	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	C	14.63	2.593068	0.46214	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	D;D;D	0.84442	-1.85;-1.85;-1.81	5.9	4.02	0.46733	.	0.000000	0.64402	D	0.000002	D	0.91690	0.7373	M	0.86953	2.85	0.48975	D	0.999731	D;D	0.69078	0.997;0.997	D;D	0.78314	0.991;0.991	D	0.91550	0.5256	10	0.87932	D	0	.	8.9014	0.35497	0.0:0.7699:0.0:0.2301	.	3784;3781	E9PQG7;Q03164	.;MLL1_HUMAN	V	3784;3781;3743;2691	ENSP00000436786:L3784V;ENSP00000374157:L3781V;ENSP00000346516:L3743V	ENSP00000346516:L3743V	L	+	1	2	MLL	117895910	0.990000	0.36364	1.000000	0.80357	0.967000	0.64934	0.319000	0.19522	2.786000	0.95864	0.563000	0.77884	CTG	.	.	.	none		0.418	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		G	118390700	C	G	118390700	3	3	192	1	0	0	0	0	1	0	0	0	9627	680	24	4	11471	4	MLL	11	118390700	Missense_Mutation	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10	24112727	118390700	16615816	65	11464											
CLEC4C	170482	hgsc.bcm.edu	37	chr12	7890038	7890038	+	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	aacatacctgttcttccctgGtgttgatcaccaccagatca	10	12	6	13	0	3	2	2	1	1	1	4	2	4	2	4	1	2	2	4	1	2	4			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr12:7890038G>C	ENST00000542353.1	-	5	858	c.368C>G	c.(367-369)aCc>aGc	p.T123S	CLEC4C_ENST00000354629.5_Missense_Mutation_p.T92S|CLEC4C_ENST00000360345.3_Missense_Mutation_p.T123S|CLEC4C_ENST00000540085.1_Missense_Mutation_p.T92S	NM_130441.2	NP_569708.1	Q8WTT0	CLC4C_HUMAN	C-type lectin domain family 4, member C	123	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)		TTCTTCCCTGGTGTTGATCAC	0.408																																					p.T123S		Atlas-SNP	.											.	CLEC4C	44	.	0			c.C368G						PASS	.						128	126	127					12																	7890038		2203	4300	6503	SO:0001583	missense	170482	exon5			TCCCTGGTGTTGA	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.368C>G	chr12.hg19:g.7890038G>C	ENSP00000440428:p.Thr123Ser	53.0	0.0	.		53.0	19.0	.	NM_130441	D3DUU3|Q3T1C3|Q6UXS8|Q8WXX8	Missense_Mutation	SNP	ENST00000542353.1	hg19	CCDS8583.1	.	.	.	.	.	.	.	.	.	.	G	6.168	0.399249	0.11696	.	.	ENSG00000198178	ENST00000542353;ENST00000354629;ENST00000540085;ENST00000360345;ENST00000537530;ENST00000543765	T;T;T;T;T;T	0.12569	2.67;2.67;2.67;2.67;2.67;2.67	2.62	0.51	0.16983	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	.	.	.	.	T	0.11110	0.0271	N	0.13327	0.33	0.09310	N	1	P;D	0.54047	0.518;0.964	B;P	0.57152	0.103;0.814	T	0.05321	-1.0892	9	0.02654	T	1	.	8.1294	0.31018	0.0:0.4976:0.5024:0.0	.	92;123	Q8WTT0-2;Q8WTT0	.;CLC4C_HUMAN	S	123;92;92;123;45;83	ENSP00000440428:T123S;ENSP00000346648:T92S;ENSP00000445338:T92S;ENSP00000353500:T123S;ENSP00000438649:T45S;ENSP00000442457:T83S	ENSP00000346648:T92S	T	-	2	0	CLEC4C	7781305	0.403000	0.25319	0.038000	0.18304	0.029000	0.11900	0.490000	0.22403	0.123000	0.18342	0.603000	0.83216	ACC	.	.	.	none		0.408	CLEC4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399750.1	NM_203503		C	7890038	G	C	7890038	3	2	192	1	0	0	0	0	1	0	0	0	3515	1261	44	4	285	4	CLEC4C	12	7890038	Missense_Mutation	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10		7890038	125961857	66	11465											
FMNL3	91010	hgsc.bcm.edu	37	chr12	50047553	50047554	+	Frame_Shift_Ins	INS	-	-	TT																															ccaccttctccagggctacaINSttcttggtctcagcatcctc																										TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr12:50047553_50047554insTT	ENST00000293590.5	-	12	1408_1409	c.1175_1176insAA	c.(1174-1176)aatfs	p.N392fs	FMNL3_ENST00000550488.1_Frame_Shift_Ins_p.N392fs|FMNL3_ENST00000335154.5_Frame_Shift_Ins_p.N392fs|FMNL3_ENST00000352151.5_Frame_Shift_Ins_p.N341fs			Q8IVF7	FMNL3_HUMAN	formin-like 3	392	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)|cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)	GTPase activating protein binding (GO:0032794)			breast(4)|endometrium(7)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|stomach(1)	39						CCAGGGCTACATTCTTGGTCTC	0.53																																					p.N392fs		Atlas-Indel,Pindel	.											FMNL3_ENST00000335154,colon,carcinoma,0,2	FMNL3	137	.	0			c.1176_1177insAA						PASS	.																																			SO:0001589	frameshift_variant	91010	exon12			.	AK128195	CCDS41780.1, CCDS44874.1	12q13.12	2006-04-10							23698	protein-coding gene	gene with protein product						12684686	Standard	NM_198900		Approved	DKFZp762B245, MGC45819, WBP3	uc001ruv.1	Q8IVF7	OTTHUMG00000169651	ENST00000293590.5:c.1174_1175dupAA	chr12.hg19:g.50047554_50047555dupTT	ENSP00000293590:p.Asn392fs	91.0	0.0	0		83.0	30.0	0.361446	NM_175736	B0JZA7|Q6ZRJ1	Frame_Shift_Ins	INS	ENST00000293590.5	hg19																																																																																				.	.	.	none		0.53	FMNL3-201	KNOWN	basic	protein_coding	protein_coding		NM_175736		TT	50047554	-	TT	50047553	7	5	192	1	0	1	1	0	0	0	0	0	5960	214	8	0	1967	0	FMNL3	12	50047553	Frame_Shift_Ins	INS	-	TCGA-GL-A9DE-01A-11D-A36X-10	42157515	50047553	83804342	67	11466											
RASSF3	283349	hgsc.bcm.edu	37	chr12	65078565	65078565	+	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	acatgtcttgtttttcttctAggatgttgagaaagagaagg	11	15	11	4	0	3	2	0	1	3	2	3	5	3	3	0	2	0	2	0	2	3	6			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr12:65078565A>C	ENST00000542104.1	+	2	231		c.e2-1		RASSF3_ENST00000336061.2_Splice_Site	NM_178169.3	NP_835463.1	Q86WH2	RASF3_HUMAN	Ras association (RalGDS/AF-6) domain family member 3						signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			Lung(2;0.00133)|LUAD - Lung adenocarcinoma(6;0.0665)|LUSC - Lung squamous cell carcinoma(43;0.132)	GBM - Glioblastoma multiforme(28;0.0611)		TTTTTCTTCTAGGATGTTGAG	0.443																																					.		Atlas-SNP	.											.	RASSF3	18	.	0			c.112-2A>C						PASS	.						93	88	90					12																	65078565		2203	4300	6503	SO:0001630	splice_region_variant	283349	exon2			TCTTCTAGGATGT		CCDS8969.1	12q14.2	2008-02-22	2008-02-22		ENSG00000153179	ENSG00000153179			14271	protein-coding gene	gene with protein product		607019					Standard	NM_178169		Approved		uc001ssd.3	Q86WH2	OTTHUMG00000168812	ENST00000542104.1:c.112-1A>C	chr12.hg19:g.65078565A>C		71.0	0.0	.		65.0	30.0	.	NM_178169	Q86WH1	Splice_Site	SNP	ENST00000542104.1	hg19	CCDS8969.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.241139	0.79912	.	.	ENSG00000153179	ENST00000542104;ENST00000336061	.	.	.	5.01	5.01	0.66863	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0409	0.71791	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RASSF3	63364832	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.594000	0.82698	2.014000	0.59158	0.459000	0.35465	.	.	.	.	none		0.443	RASSF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401161.1		Intron	C	65078565	A	C	65078565	5	2	192	1	0	0	0	0	0	0	1	0	13100	434	15	5	116	5	RASSF3	12	65078565	Splice_Site	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10	15031012	65078565	68773330	68	11467											
RAB21	23011	hgsc.bcm.edu	37	chr12	72176413	72176413	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaacagaacaaaggaattgaGgaactctttcttgacctttg	15	11	8	7	0	2	3	0	2	2	1	2	5	2	5	1	2	3	0	1	2	5	4			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr12:72176413G>A	ENST00000261263.3	+	6	766	c.510G>A	c.(508-510)gaG>gaA	p.E170E		NM_014999.2	NP_055814.1	Q9UL25	RAB21_HUMAN	RAB21, member RAS oncogene family	170					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						AAGGAATTGAGGAACTCTTTC	0.284																																					p.E170E		Atlas-SNP	.											.	RAB21	17	.	0			c.G510A						PASS	.						105	109	107					12																	72176413		2203	4298	6501	SO:0001819	synonymous_variant	23011	exon6			AATTGAGGAACTC	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.510G>A	chr12.hg19:g.72176413G>A		174.0	0.0	.		201.0	88.0	.	NM_014999	Q14466|Q569H3	Silent	SNP	ENST00000261263.3	hg19	CCDS9003.1																																																																																			.	.	.	none		0.284	RAB21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404855.1			A	72176413	G	A	72176413	2	1	192	1	0	0	0	0	0	0	0	1	12921	991	35	2		2	RAB21	12	72176413	Silent	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10	7097848	72176413	61675482	69	11468											
GALNT4	8693	hgsc.bcm.edu	37	chr12	89917333	89917333	+	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	gttttcacctccccacacttCcattcctgtgtcatacgttc	6	15	4	16	1	2	0	2	0	0	0	6	0	5	0	5	0	1	2	5	0	1	6			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr12:89917333C>T	ENST00000529983.2	-	1	1250	c.994G>A	c.(994-996)Gaa>Aaa	p.E332K	POC1B_ENST00000313546.3_Intron|POC1B_ENST00000541909.1_Intron|POC1B_ENST00000549035.1_Intron|RP11-734K2.4_ENST00000605233.1_RNA|GALNT4_ENST00000413530.1_Missense_Mutation_p.E160K|POC1B-GALNT4_ENST00000547474.1_3'UTR|POC1B_ENST00000549504.1_Intron|POC1B_ENST00000393179.4_Intron|POC1B-GALNT4_ENST00000548729.1_Missense_Mutation_p.E329K	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	332	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						CCCCACACTTCCATTCCTGTG	0.498																																					p.E332K		Atlas-SNP	.											.	GALNT4	38	.	0			c.G994A						PASS	.						183	185	184					12																	89917333		2024	4193	6217	SO:0001583	missense	8693	exon1			ACACTTCCATTCC	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.994G>A	chr12.hg19:g.89917333C>T	ENSP00000436604:p.Glu332Lys	106.0	0.0	.		101.0	37.0	.	NM_003774	B2R775|B4DMX6|O00208	Missense_Mutation	SNP	ENST00000529983.2	hg19	CCDS53817.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.871294	0.91587	.	.	ENSG00000259075;ENSG00000259075;ENSG00000257594	ENST00000548729;ENST00000413530;ENST00000529983	T;D;T	0.82711	-0.23;-1.64;-0.23	5.85	5.85	0.93711	.	.	.	.	.	D	0.90133	0.6917	M	0.64260	1.97	0.80722	D	1	D;D	0.71674	0.998;0.997	D;P	0.70016	0.967;0.896	D	0.90223	0.4273	9	0.72032	D	0.01	.	19.1613	0.93533	0.0:1.0:0.0:0.0	.	329;332	F8VUJ3;Q8N4A0	.;GALT4_HUMAN	K	329;160;332	ENSP00000447852:E329K;ENSP00000389686:E160K;ENSP00000436604:E332K	ENSP00000436604:E332K	E	-	1	0	GALNT4;RP11-1109F11.4	88441464	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.760000	0.85248	2.768000	0.95171	0.655000	0.94253	GAA	.	.	.	none		0.498	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2	NM_003774		T	89917333	C	T	89917333	3	4	192	1	0	0	0	0	1	0	0	0	6222	864	30	2	746	2	GALNT4	12	89917333	Missense_Mutation	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10	17740920	89917333	43934562	70	11469											
MYBPC1	4604	hgsc.bcm.edu	37	chr12	102043137	102043137	+	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	atcatagagggagcaacaaaGgctgatgctgcagaatattc	15	8	11	7	0	1	3	1	1	0	2	2	4	1	4	0	2	4	4	0	2	5	3			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr12:102043137G>C	ENST00000550270.1	+	13	1221	c.1221G>C	c.(1219-1221)aaG>aaC	p.K407N	MYBPC1_ENST00000550501.1_Intron|MYBPC1_ENST00000536007.1_Missense_Mutation_p.K388N|RP11-755O11.2_ENST00000552081.1_RNA|MYBPC1_ENST00000551300.1_Missense_Mutation_p.K308N|MYBPC1_ENST00000441232.1_Missense_Mutation_p.K407N|MYBPC1_ENST00000549145.1_Missense_Mutation_p.K420N|MYBPC1_ENST00000547405.1_Missense_Mutation_p.K381N|MYBPC1_ENST00000360610.2_Missense_Mutation_p.K407N|MYBPC1_ENST00000361685.2_Missense_Mutation_p.K432N|RP11-755O11.2_ENST00000547027.1_RNA|MYBPC1_ENST00000361466.2_Missense_Mutation_p.K432N|MYBPC1_ENST00000553190.1_Missense_Mutation_p.K407N|MYBPC1_ENST00000392934.3_Missense_Mutation_p.K394N|MYBPC1_ENST00000547509.1_Missense_Mutation_p.K393N|MYBPC1_ENST00000541119.1_Missense_Mutation_p.K395N|MYBPC1_ENST00000452455.2_Missense_Mutation_p.K407N|MYBPC1_ENST00000545503.2_Missense_Mutation_p.K407N			Q00872	MYPC1_HUMAN	myosin binding protein C, slow type	407	Ig-like C2-type 3.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myofibril (GO:0030016)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	57						GAGCAACAAAGGCTGATGCTG	0.393																																					p.K432N		Atlas-SNP	.											.	MYBPC1	235	.	0			c.G1296C						PASS	.						186	169	175					12																	102043137		2203	4300	6503	SO:0001583	missense	4604	exon15			AACAAAGGCTGAT		CCDS9083.1, CCDS9084.1, CCDS9085.1, CCDS55877.1, CCDS58268.1, CCDS58269.1, CCDS58270.1, CCDS58271.1, CCDS58272.1, CCDS58273.1	12q23.2	2013-02-11	2001-11-28		ENSG00000196091	ENSG00000196091		"Myosin binding proteins", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7549	protein-coding gene	gene with protein product		160794	"myosin-binding protein C, slow-type"			8375400, 16918501	Standard	NM_002465		Approved		uc010svs.2	Q00872	OTTHUMG00000170274	ENST00000550270.1:c.1221G>C	chr12.hg19:g.102043137G>C	ENSP00000449702:p.Lys407Asn	83.0	0.0	.		100.0	41.0	.	NM_206819	B4DKR5|B7Z8G8|B7ZL02|B7ZL09|B7ZL10|E7ESM5|E7EWS6|G3XAE8|Q15497|Q17RR7|Q569K7|Q86T48|Q86TC8|Q8N3L2	Missense_Mutation	SNP	ENST00000550270.1	hg19	CCDS9085.1	.	.	.	.	.	.	.	.	.	.	G	11.43	1.637917	0.29157	.	.	ENSG00000196091	ENST00000547405;ENST00000452455;ENST00000441232;ENST00000360610;ENST00000392934;ENST00000547509;ENST00000361685;ENST00000549145;ENST00000553190;ENST00000540770;ENST00000545503;ENST00000536007;ENST00000541119;ENST00000361466;ENST00000551300;ENST00000550270	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93	5.98	2.17	0.27698	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.52532	D	0.000063	T	0.50769	0.1635	L	0.53249	1.67	0.43971	D	0.996657	P;D;P;D;D;P;P;D;P;P;P	0.53885	0.924;0.963;0.578;0.963;0.963;0.924;0.954;0.963;0.794;0.954;0.954	P;P;P;P;P;P;P;P;P;P;P	0.60886	0.875;0.848;0.648;0.848;0.88;0.875;0.81;0.88;0.637;0.81;0.81	T	0.39354	-0.9618	10	0.45353	T	0.12	.	8.746	0.34587	0.4881:0.0:0.5119:0.0	.	388;395;407;407;394;381;407;407;432;432;420	B7ZL02;B7ZL10;E7EWS6;B7ZL09;E7ESM5;Q17RR7;Q00872-3;Q00872;G3XAE8;Q00872-2;F8VZY0	.;.;.;.;.;.;.;MYPC1_HUMAN;.;.;.	N	381;407;407;407;394;393;432;420;407;432;407;388;395;432;308;407	ENSP00000448175:K381N;ENSP00000400908:K407N;ENSP00000388989:K407N;ENSP00000353822:K407N;ENSP00000376665:K394N;ENSP00000447362:K393N;ENSP00000354845:K432N;ENSP00000447660:K420N;ENSP00000447900:K407N;ENSP00000440034:K407N;ENSP00000446128:K388N;ENSP00000442847:K395N;ENSP00000354849:K432N;ENSP00000447116:K308N;ENSP00000449702:K407N	ENSP00000353822:K407N	K	+	3	2	MYBPC1	100567268	1.000000	0.71417	0.973000	0.42090	0.037000	0.13140	1.952000	0.40343	0.138000	0.18790	-0.469000	0.05056	AAG	.	.	.	none		0.393	MYBPC1-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000408806.1			C	102043137	G	C	102043137	3	2	192	1	0	0	0	0	1	0	0	0	10018	991	35	4	1354	4	MYBPC1	12	102043137	Missense_Mutation	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10	12125804	102043137	31808758	71	11470											
FAM123A	219287	hgsc.bcm.edu	37	chr13	25744451	25744451	+	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	gcatgtcccagaactcctgtAgataggtgtcgtccacctcg	8	10	10	13	2	0	2	0	0	0	2	5	2	3	2	4	1	1	2	4	1	3	2			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr13:25744451A>T	ENST00000515384.1	-	1	1974	c.1307T>A	c.(1306-1308)cTa>cAa	p.L436Q	AMER2-AS1_ENST00000413501.1_lincRNA|AMER2_ENST00000381853.3_Missense_Mutation_p.L317Q|AMER2_ENST00000357816.2_Missense_Mutation_p.L317Q			Q8N7J2	AMER2_HUMAN	APC membrane recruitment protein 2	436					ectoderm development (GO:0007398)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)										GAACTCCTGTAGATAGGTGTC	0.647																																					p.L436Q		Atlas-SNP	.											.	.	.	.	0			c.T1307A						PASS	.						33	27	29					13																	25744451		2203	4300	6503	SO:0001583	missense	219287	exon1			TCCTGTAGATAGG	AK055049	CCDS9312.1, CCDS53859.1	13q12.13	2013-10-11	2012-12-03	2012-12-03	ENSG00000165566	ENSG00000165566		"-"	26360	protein-coding gene	gene with protein product		614659	"family with sequence similarity 123A"	FAM123A		20843316	Standard	XM_005266279		Approved	FLJ25477	uc001uqb.3	Q8N7J2	OTTHUMG00000016602	ENST00000515384.1:c.1307T>A	chr13.hg19:g.25744451A>T	ENSP00000426528:p.Leu436Gln	48.0	0.0	.		65.0	36.0	.	NM_152704	Q5RL80|Q5VX56|Q8N593|Q96NN5	Missense_Mutation	SNP	ENST00000515384.1	hg19	CCDS53859.1	.	.	.	.	.	.	.	.	.	.	A	18.88	3.717353	0.68844	.	.	ENSG00000165566	ENST00000357816;ENST00000381853;ENST00000515384	T;T;T	0.19938	2.11;2.11;2.11	4.42	4.42	0.53409	.	0.139225	0.50627	D	0.000113	T	0.43389	0.1245	M	0.66939	2.045	0.47476	D	0.999435	D;D	0.76494	0.999;0.999	D;D	0.77004	0.989;0.98	T	0.42327	-0.9458	10	0.87932	D	0	-31.152	12.9998	0.58667	1.0:0.0:0.0:0.0	.	436;317	Q8N7J2;Q8N7J2-2	F123A_HUMAN;.	Q	317;317;436	ENSP00000350469:L317Q;ENSP00000371277:L317Q;ENSP00000426528:L436Q	ENSP00000350469:L317Q	L	-	2	0	FAM123A	24642451	1.000000	0.71417	0.446000	0.26920	0.834000	0.47266	7.158000	0.77470	1.849000	0.53698	0.459000	0.35465	CTA	.	.	.	none		0.647	AMER2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370229.1	NM_152704		T	25744451	A	T	25744451	3	4	192	1	0	0	0	0	1	0	0	0	5426	420	15	5	712	5	FAM123A	13	25744451	Missense_Mutation	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10		25744451	89425427	72	11471											
FRY	10129	hgsc.bcm.edu	37	chr13	32705963	32705963	+	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	tggaggattttgaggcctctCttcagtttatgcaggtaatg	8	15	12	6	0	2	1	1	1	1	0	3	3	2	3	1	4	1	3	1	4	2	6			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr13:32705963C>T	ENST00000380250.3	+	8	1367	c.871C>T	c.(871-873)Ctt>Ttt	p.L291F		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	291						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)		TGAGGCCTCTCTTCAGTTTAT	0.418																																					p.L291F		Atlas-SNP	.											.	FRY	312	.	0			c.C871T						PASS	.						130	117	121					13																	32705963		1876	4115	5991	SO:0001583	missense	10129	exon8			GCCTCTCTTCAGT	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.871C>T	chr13.hg19:g.32705963C>T	ENSP00000369600:p.Leu291Phe	110.0	0.0	.		139.0	55.0	.	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	hg19	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	C	6.462	0.453397	0.12283	.	.	ENSG00000073910	ENST00000380250;ENST00000267067	T	0.20463	2.07	5.8	5.8	0.92144	.	0.059737	0.64402	D	0.000001	T	0.06005	0.0156	N	0.00054	-2.38	0.80722	D	1	B	0.06786	0.001	B	0.11329	0.006	T	0.50693	-0.8798	10	0.87932	D	0	.	20.0586	0.97663	0.0:1.0:0.0:0.0	.	291	Q5TBA9	FRY_HUMAN	F	291;219	ENSP00000369600:L291F	ENSP00000267067:L219F	L	+	1	0	FRY	31603963	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.745000	0.68672	2.741000	0.93983	0.650000	0.86243	CTT	.	.	.	none		0.418	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		T	32705963	C	T	32705963	3	4	192	1	0	0	0	0	1	0	0	0	6070	913	32	2	901	2	FRY	13	32705963	Missense_Mutation	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10	6961512	32705963	82463915	73	11472											
SCFD1	23256	hgsc.bcm.edu	37	chr14	31142532	31142533	+	Frame_Shift_Ins	INS	-	-	AA																															gagcacaggaagatgaggtcINSaaacgacttaaaagcattat																										TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr14:31142532_31142533insAA	ENST00000458591.2	+	12	1292_1293	c.1065_1066insAA	c.(1066-1068)aaafs	p.K356fs	SCFD1_ENST00000396629.2_Frame_Shift_Ins_p.K264fs|SCFD1_ENST00000544052.2_Frame_Shift_Ins_p.K289fs|SCFD1_ENST00000541123.1_Frame_Shift_Ins_p.K171fs|SCFD1_ENST00000421551.3_Frame_Shift_Ins_p.K297fs	NM_016106.3	NP_057190.2	Q8WVM8	SCFD1_HUMAN	sec1 family domain containing 1	356					post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|regulation of ER to Golgi vesicle-mediated transport (GO:0060628)|response to hypoxia (GO:0001666)|response to toxic substance (GO:0009636)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle docking involved in exocytosis (GO:0006904)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|Golgi transport complex (GO:0017119)|Golgi-associated vesicle (GO:0005798)|plasma membrane (GO:0005886)	syntaxin binding (GO:0019905)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)	13	Hepatocellular(127;0.0877)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)	GBM - Glioblastoma multiforme(265;0.0181)		AAGATGAGGTCAAACGACTTAA	0.356																																					p.V355fs		Atlas-Indel,Pindel	.											.	SCFD1	43	.	0			c.1065_1066insAA						PASS	.																																			SO:0001589	frameshift_variant	23256	exon12			.	AF110646	CCDS9639.1, CCDS45092.1, CCDS58308.1	14q12	2006-04-04	2004-01-15	2004-01-16	ENSG00000092108	ENSG00000092108			20726	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 163"	C14orf163			Standard	NM_016106		Approved	RA410, KIAA0917, STXBP1L2, SLY1	uc001wqm.2	Q8WVM8	OTTHUMG00000029420	ENST00000458591.2:c.1066_1067dupAA	chr14.hg19:g.31142533_31142534dupAA	ENSP00000390783:p.Lys356fs	251.0	0.0	0		289.0	112.0	0.387543	NM_016106	A8K2Z5|B7Z4U7|B7Z594|O60754|O94990|Q7Z529|Q9BZI3|Q9UNL3|Q9Y6A8	Frame_Shift_Ins	INS	ENST00000458591.2	hg19	CCDS9639.1																																																																																			.	.	.	none		0.356	SCFD1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276612.3	NM_182835		AA	31142533	-	AA	31142532	7	5	192	1	0	1	1	0	0	0	0	0	13902	813	29	0	1111	0	SCFD1	14	31142532	Frame_Shift_Ins	INS	-	TCGA-GL-A9DE-01A-11D-A36X-10		31142532	76207008	74	11473											
RTN1	6252	hgsc.bcm.edu	37	chr14	60074162	60074162	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcagcagcaggaaactcccaAacacgatgcccgtctgcttg	11	6	10	14	2	1	0	0	0	1	0	2	2	2	1	2	1	6	4	2	1	2	1			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr14:60074162A>G	ENST00000267484.5	-	4	2149	c.1814T>C	c.(1813-1815)tTt>tCt	p.F605S	RTN1_ENST00000342503.4_Missense_Mutation_p.F37S|RTN1_ENST00000395090.1_Missense_Mutation_p.F22S|RTN1_ENST00000557422.1_5'UTR	NM_021136.2	NP_066959.1	Q16799	RTN1_HUMAN	reticulon 1	605	Reticulon. {ECO:0000255|PROSITE- ProRule:PRU00170}.				neuron differentiation (GO:0030182)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)				central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(30)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		GAAACTCCCAAACACGATGCC	0.597																																					p.F605S		Atlas-SNP	.											.	RTN1	139	.	0			c.T1814C						PASS	.						56	52	53					14																	60074162		2203	4300	6503	SO:0001583	missense	6252	exon4			CTCCCAAACACGA	L10333	CCDS9740.1, CCDS9741.1	14q21-q22	2008-08-29			ENSG00000139970	ENSG00000139970			10467	protein-coding gene	gene with protein product		600865	"neuroendocrine-specific protein"	NSP		8275708	Standard	NM_206852		Approved		uc001xen.1	Q16799	OTTHUMG00000028947	ENST00000267484.5:c.1814T>C	chr14.hg19:g.60074162A>G	ENSP00000267484:p.Phe605Ser	78.0	0.0	.		81.0	40.0	.	NM_021136	Q16800|Q16801|Q5BKZ4|Q9BQ59	Missense_Mutation	SNP	ENST00000267484.5	hg19	CCDS9740.1	.	.	.	.	.	.	.	.	.	.	A	32	5.148436	0.94603	.	.	ENSG00000139970	ENST00000432103;ENST00000267484;ENST00000395090;ENST00000342503;ENST00000433623	T;T;T	0.54071	0.59;0.59;0.59	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	T	0.78375	0.4273	M	0.89840	3.065	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.997;1.0;0.994	T	0.83082	-0.0137	10	0.87932	D	0	.	16.4943	0.84223	1.0:0.0:0.0:0.0	.	22;605;37	A8MT72;Q16799;Q16799-3	.;RTN1_HUMAN;.	S	185;605;22;37;531	ENSP00000267484:F605S;ENSP00000378525:F22S;ENSP00000340716:F37S	ENSP00000267484:F605S	F	-	2	0	RTN1	59143915	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	9.339000	0.96797	2.291000	0.77112	0.533000	0.62120	TTT	.	.	.	none		0.597	RTN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000072278.2			G	60074162	A	G	60074162	3	3	192	1	0	0	0	0	1	0	0	0	13738	14	1	3	540	3	RTN1	14	60074162	Missense_Mutation	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10	28931630	60074162	47275378	75	11474											
ZFP36L1	677	hgsc.bcm.edu	37	chr14	69256832	69256832	+	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	ttggggtggcgggtcaggctGcggagctcgtggatgccgtg	3	9	21	8	4	1	0	1	0	0	0	2	2	1	2	1	7	3	2	1	7	0	1			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr14:69256832G>T	ENST00000439696.2	-	2	736	c.435C>A	c.(433-435)cgC>cgA	p.R145R	ZFP36L1_ENST00000555997.1_3'UTR|ZFP36L1_ENST00000336440.3_Silent_p.R145R	NM_001244701.1|NM_004926.3	NP_001231630.1|NP_004917.2	Q07352	TISB_HUMAN	ZFP36 ring finger protein-like 1	145					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)		GGGTCAGGCTGCGGAGCTCGT	0.632											OREG0022753	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R214R		Atlas-SNP	.											.	ZFP36L1	47	.	0			c.C642A						PASS	.						80	78	79					14																	69256832		2203	4300	6503	SO:0001819	synonymous_variant	677	exon3			CAGGCTGCGGAGC	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.435C>A	chr14.hg19:g.69256832G>T		68.0	0.0	.	1113	94.0	38.0	.	NM_001244701	Q13851	Silent	SNP	ENST00000439696.2	hg19	CCDS9791.1																																																																																			.	.	.	none		0.632	ZFP36L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413227.1			T	69256832	G	T	69256832	2	4	192	1	0	0	0	0	0	0	0	1	17658	1306	46	4		4	ZFP36L1	14	69256832	Silent	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10	9182670	69256832	38092708	76	11475											
NPC2	10577	hgsc.bcm.edu	37	chr14	74953056	74953057	+	Frame_Shift_Del	DEL	TG	TG	-																															ggtgaaggtgacattgacgcTgtaagactgtcctttgctca																										TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr14:74953056_74953057delTG	ENST00000555619.1	-	2	402_403	c.165_166delCA	c.(163-168)tacagcfs	p.YS55fs	NPC2_ENST00000541064.1_Frame_Shift_Del_p.YS55fs|NPC2_ENST00000557510.1_Frame_Shift_Del_p.YS55fs|NPC2_ENST00000238633.2_Frame_Shift_Del_p.YS55fs|NPC2_ENST00000434013.2_Frame_Shift_Del_p.YS55fs	NM_006432.3	NP_006423.1	P61916	NPC2_HUMAN	Niemann-Pick disease, type C2	55					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)		ACATTGACGCTGTAAGACTGTC	0.441																																					p.56_56del	Pancreas(93;260 1497 8575 30964 48133)	Atlas-Indel,Pindel	.											.	NPC2	9	.	0			c.166_167del	GRCh37	CM057462	NPC2	M		PASS	.																																			SO:0001589	frameshift_variant	10577	exon2			.	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.165_166delCA	chr14.hg19:g.74953056_74953057delTG	ENSP00000451112:p.Tyr55fs	54.0	0.0	0		62.0	29.0	0.467742	NM_006432	B4DQV7|Q15668|Q29413	Frame_Shift_Del	DEL	ENST00000555619.1	hg19	CCDS32121.1																																																																																			.	.	.	none		0.441	NPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412346.1	NM_006432		-	74953057	TG	-	74953056	7	5	192	1	0	1	0	1	0	0	0	0	10579	1580	55	0	305	0	NPC2	14	74953056	Frame_Shift_Del	DEL	TG	TCGA-GL-A9DE-01A-11D-A36X-10	5696224	74953056	32396484	77	11476											
SERPINA4	5267	hgsc.bcm.edu	37	chr14	95030170	95030170	+	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	gagctgtctgagtccgatgtCcataggggcttccagcacct	7	10	12	12	1	1	1	0	1	1	0	4	3	4	1	4	2	2	3	4	2	1	2			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr14:95030170C>A	ENST00000557004.1	+	2	772	c.351C>A	c.(349-351)gtC>gtA	p.V117V	SERPINA5_ENST00000553780.1_Intron|SERPINA4_ENST00000298841.5_Silent_p.V117V|SERPINA4_ENST00000555095.1_Silent_p.V117V			P29622	KAIN_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4	117					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(1)|kidney(1)|large_intestine(9)|lung(28)|ovary(3)|skin(1)|urinary_tract(1)	46				COAD - Colon adenocarcinoma(157;0.211)		AGTCCGATGTCCATAGGGGCT	0.627																																					p.V117V		Atlas-SNP	.											.	SERPINA4	81	.	0			c.C351A						PASS	.						68	67	67					14																	95030170		2203	4300	6503	SO:0001819	synonymous_variant	5267	exon2			CGATGTCCATAGG	L19684	CCDS9927.1	14q32.13	2014-02-18	2005-08-18		ENSG00000100665	ENSG00000100665		"Serine (or cysteine) peptidase inhibitors"	8948	protein-coding gene	gene with protein product		147935	"serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4"	PI4		8227002, 24172014	Standard	NM_001289032		Approved	KST, KAL, KLST, kallistatin	uc001ydk.3	P29622	OTTHUMG00000170859	ENST00000557004.1:c.351C>A	chr14.hg19:g.95030170C>A		26.0	0.0	.		50.0	23.0	.	NM_006215	Q53XB5|Q86TR9|Q96BZ5	Silent	SNP	ENST00000557004.1	hg19	CCDS9927.1																																																																																			.	.	.	none		0.627	SERPINA4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410718.1	NM_006215		A	95030170	C	A	95030170	2	1	192	1	0	0	0	0	0	0	0	1	14104	842	30	4		4	SERPINA4	14	95030170	Silent	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10	20077114	95030170	12319370	78	11477											
HERC2	8924	hgsc.bcm.edu	37	chr15	28459417	28459417	+	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	ctgcgccgcctcagcgtggaCtctgaggaggaaaccagggg	8	5	16	12	3	2	1	1	1	1	0	2	4	2	4	3	5	3	0	3	5	1	0			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr15:28459417C>G	ENST00000261609.7	-	41	6468	c.6360G>C	c.(6358-6360)gaG>gaC	p.E2120D		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)		TCAGCGTGGACTCTGAGGAGG	0.677																																					p.E2120D		Atlas-SNP	.											.	HERC2	501	.	0			c.G6360C						PASS	.						17	18	18					15																	28459417		2190	4275	6465	SO:0001630	splice_region_variant	8924	exon41			CGTGGACTCTGAG	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.6359-1G>C	chr15.hg19:g.28459417C>G		72.0	0.0	.		98.0	47.0	.	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	C	5.854	0.341694	0.11069	.	.	ENSG00000128731	ENST00000261609	T	0.39056	1.1	4.75	-4.8	0.03190	.	0.205916	0.40064	N	0.001188	T	0.25005	0.0607	L	0.44542	1.39	0.80722	D	1	B	0.17667	0.023	B	0.12156	0.007	T	0.13150	-1.0520	10	0.15066	T	0.55	.	8.6363	0.33950	0.0:0.2967:0.1043:0.599	.	2120	O95714	HERC2_HUMAN	D	2120	ENSP00000261609:E2120D	ENSP00000261609:E2120D	E	-	3	2	HERC2	26133012	0.743000	0.28239	0.501000	0.27601	0.127000	0.20565	-0.241000	0.08940	-0.791000	0.04486	0.484000	0.47621	GAG	.	.	.	none		0.677	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	Missense_Mutation	G	28459417	C	G	28459417	5	3	192	1	0	0	0	0	0	0	1	0	7065	579	20	4	8356	4	HERC2	15	28459417	Splice_Site	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10		28459417	74071975	79	11478											
DMXL2	23312	hgsc.bcm.edu	37	chr15	51792075	51792075	+	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	tgtttgttctaaaacccactCtgatcctcctgtagattcac	9	15	5	12	0	3	2	1	1	2	1	5	2	5	2	3	0	1	3	3	0	3	5			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr15:51792075C>T	ENST00000251076.5	-	18	3633	c.3346G>A	c.(3346-3348)Gag>Aag	p.E1116K	RP11-707P17.1_ENST00000561007.1_RNA|DMXL2_ENST00000543779.2_Missense_Mutation_p.E1116K|DMXL2_ENST00000449909.3_Intron	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	1116						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		AAAACCCACTCTGATCCTCCT	0.378																																					p.E1116K		Atlas-SNP	.											.	DMXL2	262	.	0			c.G3346A						PASS	.						73	66	68					15																	51792075		2194	4293	6487	SO:0001583	missense	23312	exon18			CCCACTCTGATCC	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.3346G>A	chr15.hg19:g.51792075C>T	ENSP00000251076:p.Glu1116Lys	95.0	0.0	.		128.0	53.0	.	NM_001174116	B2RTR3|B7ZMH3|F5GWF1|O94938	Missense_Mutation	SNP	ENST00000251076.5	hg19	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	C	16.88	3.243914	0.58995	.	.	ENSG00000104093	ENST00000251076;ENST00000543779	T;T	0.29397	1.57;1.57	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.37571	0.1008	M	0.75615	2.305	0.80722	D	1	B;P	0.35745	0.067;0.518	B;B	0.33846	0.076;0.171	T	0.23583	-1.0184	10	0.32370	T	0.25	.	19.0754	0.93159	0.0:1.0:0.0:0.0	.	1116;1116	F5GWF1;Q8TDJ6	.;DMXL2_HUMAN	K	1116	ENSP00000251076:E1116K;ENSP00000441858:E1116K	ENSP00000251076:E1116K	E	-	1	0	DMXL2	49579367	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.461000	0.80834	2.497000	0.84241	0.591000	0.81541	GAG	.	.	.	none		0.378	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		T	51792075	C	T	51792075	3	4	192	1	0	0	0	0	1	0	0	0	4597	922	32	2	5871	2	DMXL2	15	51792075	Missense_Mutation	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10	23332658	51792075	50739317	80	11479											
CELF6	60677	hgsc.bcm.edu	37	chr15	72581548	72581548	+	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	gccattggtctggggggtcaGagggccgaatccattgaccc	7	8	15	11	1	2	2	1	1	1	1	3	3	3	2	4	5	0	0	4	5	1	2			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr15:72581548G>C	ENST00000569547.1	-	8	1032	c.961C>G	c.(961-963)Ctg>Gtg	p.L321V	CELF6_ENST00000543764.2_Missense_Mutation_p.L205V|CELF6_ENST00000395258.2_Missense_Mutation_p.L208V|CELF6_ENST00000567083.1_Missense_Mutation_p.L321V|CELF6_ENST00000569311.1_5'Flank|CELF6_ENST00000539635.1_Missense_Mutation_p.L182V|RP11-106M3.2_ENST00000379915.4_RNA|RP11-106M3.3_ENST00000570175.1_RNA|CELF6_ENST00000287202.5_Missense_Mutation_p.L321V			Q96J87	CELF6_HUMAN	CUGBP, Elav-like family member 6	321					mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(2)	13						TGGGGGGTCAGAGGGCCGAAT	0.682																																					p.L321V		Atlas-SNP	.											.	CELF6	30	.	0			c.C961G						PASS	.						14	19	18					15																	72581548		2190	4274	6464	SO:0001583	missense	60677	exon8			GGGTCAGAGGGCC	AF425606	CCDS10242.1, CCDS53955.1, CCDS53956.1	15q24	2013-02-12	2010-02-19	2010-02-19	ENSG00000140488	ENSG00000140488		"RNA binding motif (RRM) containing"	14059	protein-coding gene	gene with protein product		612681	"Bruno (Drosophila) -like 6, RNA binding protein", "bruno-like 6, RNA binding protein (Drosophila)"	BRUNOL6		10893231	Standard	NM_052840		Approved		uc002auh.2	Q96J87	OTTHUMG00000133444	ENST00000569547.1:c.961C>G	chr15.hg19:g.72581548G>C	ENSP00000454749:p.Leu321Val	47.0	0.0	.		65.0	30.0	.	NM_001172684	B4DG28|B4DJB6|Q6PII4|Q6ZNJ7|Q8N607	Missense_Mutation	SNP	ENST00000569547.1	hg19	CCDS10242.1	.	.	.	.	.	.	.	.	.	.	G	10.09	1.255375	0.22965	.	.	ENSG00000140488	ENST00000287202;ENST00000437872;ENST00000543764;ENST00000379915;ENST00000395258;ENST00000539635	T;T;T;T	0.21191	2.02;2.26;2.27;3.74	5.02	2.07	0.26955	.	0.555812	0.15029	U	0.284567	T	0.16041	0.0386	L	0.39147	1.195	0.40996	D	0.984894	B;B;B;B;B	0.33103	0.096;0.096;0.357;0.397;0.096	B;B;B;B;B	0.38683	0.021;0.021;0.279;0.085;0.021	T	0.11743	-1.0575	10	0.16420	T	0.52	-6.9448	4.6841	0.12750	0.2282:0.0:0.6166:0.1551	.	321;205;208;182;321	B4DJB6;B4DG28;Q96J87-2;B3KWE6;Q96J87	.;.;.;.;CELF6_HUMAN	V	321;321;205;172;208;182	ENSP00000287202:L321V;ENSP00000439956:L205V;ENSP00000378677:L208V;ENSP00000443162:L182V	ENSP00000287202:L321V	L	-	1	2	CELF6	70368602	0.358000	0.24947	0.999000	0.59377	0.664000	0.39144	0.682000	0.25335	0.147000	0.19030	0.491000	0.48974	CTG	.	.	.	none		0.682	CELF6-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000420180.1	NM_052840		C	72581548	G	C	72581548	3	2	192	1	0	0	0	0	1	0	0	0	3222	933	33	4	504	4	CELF6	15	72581548	Missense_Mutation	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10	20789473	72581548	29949844	81	11480											
ANPEP	290	hgsc.bcm.edu	37	chr15	90349809	90349809	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttggaaatatagaagcccttGgccatggtgatggtggggag	10	10	16	5	0	0	2	0	1	0	1	0	4	0	4	2	6	1	0	2	6	4	4			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr15:90349809G>A	ENST00000300060.6	-	2	319	c.6C>T	c.(4-6)gcC>gcT	p.A2A		NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	2					angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	AGAAGCCCTTGGCCATGGTGA	0.632																																					p.A2A	NSCLC(30;827 977 2459 19669 26125)	Atlas-SNP	.											.	ANPEP	124	.	0			c.C6T						PASS	.						27	27	27					15																	90349809		2199	4295	6494	SO:0001819	synonymous_variant	290	exon2			GCCCTTGGCCATG	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"CD molecules"	500	protein-coding gene	gene with protein product	"aminopeptidase N", "aminopeptidase M", "microsomal aminopeptidase"	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.6C>T	chr15.hg19:g.90349809G>A		63.0	0.0	.		58.0	7.0	.	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Silent	SNP	ENST00000300060.6	hg19	CCDS10356.1																																																																																			.	.	.	none		0.632	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1			A	90349809	G	A	90349809	2	1	192	1	0	0	0	0	0	0	0	1	710	1335	47	2		2	ANPEP	15	90349809	Silent	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10	17768261	90349809	12181583	82	11481											
CHTF18	63922	hgsc.bcm.edu	37	chr16	842327	842327	+	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	ccaactgcctggtcatcgatGagatcgacggggcccccgtg	7	7	13	14	4	1	1	1	1	0	1	3	4	1	1	4	3	2	0	4	3	1	0			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr16:842327G>A	ENST00000262315.9	+	10	1369	c.1306G>A	c.(1306-1308)Gag>Aag	p.E436K	CHTF18_ENST00000317063.6_Missense_Mutation_p.E631K|CHTF18_ENST00000455171.2_Missense_Mutation_p.E464K	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	436					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)				GGTCATCGATGAGATCGACGG	0.692																																					p.E436K		Atlas-SNP	.											.	CHTF18	52	.	0			c.G1306A						PASS	.						23	31	28					16																	842327		1939	4039	5978	SO:0001583	missense	63922	exon10			ATCGATGAGATCG	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.1306G>A	chr16.hg19:g.842327G>A	ENSP00000262315:p.Glu436Lys	172.0	0.0	.		166.0	24.0	.	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Missense_Mutation	SNP	ENST00000262315.9	hg19	CCDS45371.1	.	.	.	.	.	.	.	.	.	.	g	36	5.735393	0.96865	.	.	ENSG00000127586	ENST00000317063;ENST00000455171;ENST00000262315	D;D;D	0.97870	-4.58;-4.58;-4.58	5.19	5.19	0.71726	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.99351	0.9772	H	0.99104	4.43	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98516	1.0621	10	0.49607	T	0.09	-36.8096	17.2796	0.87124	0.0:0.0:1.0:0.0	.	464;436	Q8WVB6-2;Q8WVB6	.;CTF18_HUMAN	K	631;464;436	ENSP00000313029:E631K;ENSP00000406252:E464K;ENSP00000262315:E436K	ENSP00000262315:E436K	E	+	1	0	CHTF18	782328	1.000000	0.71417	0.993000	0.49108	0.880000	0.50808	9.500000	0.97977	2.416000	0.81992	0.457000	0.33378	GAG	.	.	.	none		0.692	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092		A	842327	G	A	842327	3	1	192	1	0	0	0	0	1	0	0	0	3416	1291	45	2	1344	2	CHTF18	16	842327	Missense_Mutation	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10		842327	89512426	83	11482											
C16orf72	29035	hgsc.bcm.edu	37	chr16	9210571	9210571	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcgtgcgttcgagtaccccAggctctcctacacatgtaag	9	9	10	13	3	1	0	0	0	1	0	3	1	1	0	3	1	4	4	3	1	3	4			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr16:9210571A>G	ENST00000327827.7	+	4	1027	c.630A>G	c.(628-630)ccA>ccG	p.P210P		NM_014117.2	NP_054836.2	Q14CZ0	CP072_HUMAN	chromosome 16 open reading frame 72	210										endometrium(4)|large_intestine(2)|lung(2)	8						CGAGTACCCCAGGCTCTCCTA	0.423																																					p.P210P		Atlas-SNP	.											.	C16orf72	26	.	0			c.A630G						PASS	.						192	182	185					16																	9210571		2197	4300	6497	SO:0001819	synonymous_variant	29035	exon4			TACCCCAGGCTCT	AK123266	CCDS10538.1	16p13.2	2012-11-19			ENSG00000182831	ENSG00000182831			30103	protein-coding gene	gene with protein product						8889548	Standard	NM_014117		Approved	FLJ41272, PRO0149	uc002czm.3	Q14CZ0	OTTHUMG00000178147	ENST00000327827.7:c.630A>G	chr16.hg19:g.9210571A>G		108.0	0.0	.		106.0	47.0	.	NM_014117		Silent	SNP	ENST00000327827.7	hg19	CCDS10538.1																																																																																			.	.	.	none		0.423	C16orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440760.2	NM_014117		G	9210571	A	G	9210571	2	3	192	1	0	0	0	0	0	0	0	1	1833	175	7	3		3	C16orf72	16	9210571	Silent	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10	8368244	9210571	81144182	84	11483											
CNGB1	1258	hgsc.bcm.edu	37	chr16	57957180	57957180	+	Missense_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	ccccagaggggtctcactcaGtgtccttcggggtggtgggg	4	9	17	11	1	2	1	2	0	1	1	5	1	3	1	3	7	0	0	3	7	0	1			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr16:57957180G>A	ENST00000251102.8	-	18	1700	c.1640C>T	c.(1639-1641)aCt>aTt	p.T547I	CNGB1_ENST00000564448.1_Missense_Mutation_p.T541I	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	547					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						GTCTCACTCAGTGTCCTTCGG	0.582																																					p.T547I	Colon(156;1293 1853 16336 28962 38659)	Atlas-SNP	.											.	CNGB1	105	.	0			c.C1640T						PASS	.						49	51	50					16																	57957180		1885	4109	5994	SO:0001583	missense	1258	exon18			CACTCAGTGTCCT	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.1640C>T	chr16.hg19:g.57957180G>A	ENSP00000251102:p.Thr547Ile	30.0	0.0	.		36.0	16.0	.	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Missense_Mutation	SNP	ENST00000251102.8	hg19	CCDS42169.1	.	.	.	.	.	.	.	.	.	.	G	14.85	2.659448	0.47467	.	.	ENSG00000070729	ENST00000251102	T	0.29142	1.58	4.97	1.69	0.24217	.	0.655524	0.13615	N	0.374836	T	0.25754	0.0627	L	0.46157	1.445	0.09310	N	0.999999	P	0.50710	0.938	P	0.45195	0.473	T	0.10520	-1.0626	10	0.42905	T	0.14	.	3.9819	0.09498	0.1996:0.0:0.6032:0.1972	.	547	Q14028	CNGB1_HUMAN	I	547	ENSP00000251102:T547I	ENSP00000251102:T547I	T	-	2	0	CNGB1	56514681	0.012000	0.17670	0.616000	0.29078	0.522000	0.34438	1.527000	0.35975	0.681000	0.31386	0.655000	0.94253	ACT	.	.	.	none		0.582	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297		A	57957180	G	A	57957180	3	1	192	1	0	0	0	0	1	0	0	0	3602	1029	36	2	2179	2	CNGB1	16	57957180	Missense_Mutation	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10	48746609	57957180	32397573	85	11484											
GUCY2D	3000	hgsc.bcm.edu	37	chr17	7907255	7907255	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagaggagctgggcctgacCgatggctccctggtcttcct	5	9	14	13	1	1	2	0	1	1	1	3	4	3	3	4	4	1	3	4	4	0	1			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr17:7907255C>T	ENST00000254854.4	+	3	957	c.807C>T	c.(805-807)acC>acT	p.T269T		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	269					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)				TGGGCCTGACCGATGGCTCCC	0.662																																					p.T269T		Atlas-SNP	.											.	GUCY2D	82	.	0			c.C807T						PASS	.						94	88	90					17																	7907255		2203	4300	6503	SO:0001819	synonymous_variant	3000	exon3			CCTGACCGATGGC	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.807C>T	chr17.hg19:g.7907255C>T		106.0	0.0	.		106.0	20.0	.	NM_000180	Q6LEA7	Silent	SNP	ENST00000254854.4	hg19	CCDS11127.1																																																																																			.	.	.	none		0.662	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2			T	7907255	C	T	7907255	2	4	192	1	0	0	0	0	0	0	0	1	6904	639	23	1		1	GUCY2D	17	7907255	Silent	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10		7907255	73287955	86	11485											
TMIGD1	388364	hgsc.bcm.edu	37	chr17	28656425	28656425	+	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	atccactctcccctcctctcGgtaccagagcagttcttcct	6	12	5	18	1	3	1	0	0	3	1	8	1	6	1	6	1	2	3	6	1	1	3			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr17:28656425G>A	ENST00000328886.4	-	3	277	c.205C>T	c.(205-207)Cga>Tga	p.R69*	TMIGD1_ENST00000538566.2_Nonsense_Mutation_p.R69*	NM_206832.1	NP_996663.1	Q6UXZ0	TMIG1_HUMAN	transmembrane and immunoglobulin domain containing 1	69	Ig-like C2-type 1.					integral component of membrane (GO:0016021)				breast(1)|kidney(3)|large_intestine(1)|lung(5)|skin(2)	12						CCCTCCTCTCGGTACCAGAGC	0.443																																					p.R69X		Atlas-SNP	.											.	TMIGD1	38	.	0			c.C205T						PASS	.						123	111	115					17																	28656425		2203	4300	6503	SO:0001587	stop_gained	388364	exon3			CCTCTCGGTACCA	AY358153	CCDS32605.1	17q11.2	2013-01-29	2006-07-05	2006-07-05		ENSG00000182271		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	32431	protein-coding gene	gene with protein product				TMIGD		12975309	Standard	NM_206832		Approved	UNQ9372	uc002hfa.1	Q6UXZ0		ENST00000328886.4:c.205C>T	chr17.hg19:g.28656425G>A	ENSP00000332404:p.Arg69*	73.0	0.0	.		91.0	5.0	.	NM_206832	A8K2K1|Q6ZMC6	Nonsense_Mutation	SNP	ENST00000328886.4	hg19	CCDS32605.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.947315	0.92593	.	.	ENSG00000182271	ENST00000328886;ENST00000538566	.	.	.	5.52	2.21	0.28008	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.1084	14.2699	0.66145	0.0:0.0:0.5014:0.4986	.	.	.	.	X	69	.	ENSP00000332404:R69X	R	-	1	2	TMIGD1	25680551	1.000000	0.71417	0.988000	0.46212	0.980000	0.70556	1.621000	0.36986	0.196000	0.20367	0.579000	0.79373	CGA	.	.	.	none		0.443	TMIGD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447955.1	NM_206832		A	28656425	G	A	28656425	4	1	192	1	0	0	0	0	0	1	0	0	16242	1124	39	1	603	1	TMIGD1	17	28656425	Nonsense_Mutation	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10	20749170	28656425	52538785	87	11486											
NF1	4763	hgsc.bcm.edu	37	chr17	29483033	29483033	+	Missense_Mutation	SNP	T	T	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	acaggacagcagaacacacaTaccaaagtcagtactgagca	18	4	8	11	0	1	2	1	1	0	1	1	3	1	3	1	1	5	3	1	1	4	2			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr17:29483033T>G	ENST00000358273.4	+	2	476	c.93T>G	c.(91-93)caT>caG	p.H31Q	NF1_ENST00000356175.3_Missense_Mutation_p.H31Q|NF1_ENST00000431387.4_Missense_Mutation_p.H31Q	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	31			H -> R (in NF1; dbSNP:rs199474725). {ECO:0000269|PubMed:15060124}.		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)		AGAACACACATACCAAAGTCA	0.318			"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.H31Q		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)|central_nervous_system(2)	c.T93G						PASS	.						89	81	84					17																	29483033		2203	4300	6503	SO:0001583	missense	4763	exon2	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	CACACATACCAAA		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.93T>G	chr17.hg19:g.29483033T>G	ENSP00000351015:p.His31Gln	141.0	0.0	.		201.0	84.0	.	NM_001128147	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	hg19	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	T	11.32	1.605044	0.28623	.	.	ENSG00000196712	ENST00000431387;ENST00000358273;ENST00000356175	T;T;T	0.08720	3.06;3.32;3.47	4.95	2.37	0.29283	.	0.000000	0.85682	D	0.000000	T	0.11324	0.0276	L	0.38692	1.165	0.80722	D	1	D;B;D;D	0.69078	0.96;0.179;0.997;0.96	D;B;D;D	0.78314	0.962;0.039;0.991;0.962	T	0.44877	-0.9299	10	0.02654	T	1	.	4.7551	0.13080	0.0:0.4884:0.0:0.5116	.	31;31;31;31	P21359-2;P21359;Q14931;P21359-3	.;NF1_HUMAN;.;.	Q	31	ENSP00000412921:H31Q;ENSP00000351015:H31Q;ENSP00000348498:H31Q	ENSP00000348498:H31Q	H	+	3	2	NF1	26507159	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.637000	0.61346	0.836000	0.34901	-0.376000	0.06991	CAT	.	.	.	none		0.318	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		G	29483033	T	G	29483033	3	3	192	1	0	0	0	0	1	0	0	0	10363	1403	49	5	99	5	NF1	17	29483033	Missense_Mutation	SNP	T	TCGA-GL-A9DE-01A-11D-A36X-10	826608	29483033	51712177	88	11487											
PEX12	5193	hgsc.bcm.edu	37	chr17	33904058	33904058	+	Splice_Site	DEL	T	T	-																															ggaaatgttaaggccttaccTcctggctggttgctgcatca																										TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr17:33904058delT	ENST00000225873.4	-	2	1286	c.679delA	c.(679-681)agt>gt	p.S227fs	RP11-1094M14.11_ENST00000592381.1_lincRNA	NM_000286.2	NP_000277.1	O00623	PEX12_HUMAN	peroxisomal biogenesis factor 12	227					peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	integral component of peroxisomal membrane (GO:0005779)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(8)	18				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		AGGCCTTACCTCCTGGCTGGT	0.448																																					p.S227fs		Atlas-INDEL	.											.	PEX12	36	.	0			c.680delG						PASS	.						98	90	92					17																	33904058		2203	4300	6503	SO:0001630	splice_region_variant	5193	exon2			.	U91521	CCDS11296.1	17q21.1	2011-02-10			ENSG00000108733	ENSG00000108733			8854	protein-coding gene	gene with protein product		601758				9090384	Standard	NM_000286		Approved		uc002hjp.3	O00623	OTTHUMG00000132951	ENST00000225873.4:c.680+1A>-	chr17.hg19:g.33904058delT		29.0	0.0	0		48.0	19.0	0.395833	NM_000286	B2R6M2	Frame_Shift_Del	DEL	ENST00000225873.4	hg19	CCDS11296.1																																																																																			.	.	.	none		0.448	PEX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256489.2	NM_000286	Frame_Shift_Del	-	33904058	T	-	33904058	8	5	192	1	0	1	0	1	0	0	1	0	11747	1565	54	0	408	0	PEX12	17	33904058	Splice_Site	DEL	T	TCGA-GL-A9DE-01A-11D-A36X-10	4421025	33904058	47291152	89	11488	110	2									
PEX12	5193	hgsc.bcm.edu	37	chr17	33904061	33904062	+	Missense_Mutation	DNP	TG	TG	CA																															aatgttaaggccttacctccTggctggttgctgcatcatgc																										TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr17:33904061_33904062TG>CA	ENST00000225873.4	-	2	1282_1283	c.675_676CA>TG	c.(673-678)gcCAgg>gcTGgg	p.R226G	RP11-1094M14.11_ENST00000592381.1_lincRNA	NM_000286.2	NP_000277.1	O00623	PEX12_HUMAN	peroxisomal biogenesis factor 12	226					peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	integral component of peroxisomal membrane (GO:0005779)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(8)	18				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CCTTACCTCCTGGCTGGTTGCT	0.45																																					p.R226G|p.A225A		Atlas-SNP	.											.	PEX12	36	.	0			c.A676G|c.C675T						PASS	.																																			SO:0001583	missense	5193	exon2			ACCTCCTGGCTGG|CCTCCTGGCTGGT	U91521	CCDS11296.1	17q21.1	2011-02-10			ENSG00000108733	ENSG00000108733			8854	protein-coding gene	gene with protein product		601758				9090384	Standard	NM_000286		Approved		uc002hjp.3	O00623	OTTHUMG00000132951	ENST00000225873.4:c.675_676delinsCA	chr17.hg19:g.33904061_33904062delinsCA	ENSP00000225873:p.Arg226Gly	28.0|29.0	0.0	.		50.0	20.0	.	NM_000286	B2R6M2	Missense_Mutation|Silent	SNP	ENST00000225873.4	hg19	CCDS11296.1																																																																																			.	.	.	none		0.45	PEX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256489.2	NM_000286		CA	33904062	TG	CA	33904061	3	2	192	1	0	0	0	0	1	0	0	0	11747	1579	55	3	411	3	PEX12	17	33904061	Missense_Mutation	DNP	TG	TCGA-GL-A9DE-01A-11D-A36X-10	3	33904061	47291149	90	11489	110	2									
KRTAP17-1	83902	hgsc.bcm.edu	37	chr17	39471747	39471747	+	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	ccacagcaagacgatccgcaGcagctgcccccgcagccaga	11	2	10	18	3	0	2	0	0	0	2	1	3	1	2	5	0	5	5	5	0	1	0			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr17:39471747G>A	ENST00000334202.3	-	1	200	c.156C>T	c.(154-156)tgC>tgT	p.C52C		NM_031964.1	NP_114170.1	Q9BYP8	KR171_HUMAN	keratin associated protein 17-1	52						intermediate filament (GO:0005882)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			acgatccgcagcagctgcccc	0.687																																					p.C52C		Atlas-SNP	.											.	KRTAP17-1	14	.	0			c.C156T						PASS	.						15	20	19					17																	39471747		2181	4269	6450	SO:0001819	synonymous_variant	83902	exon1			TCCGCAGCAGCTG	AJ406952	CCDS11387.1	17q21.2	2013-06-20			ENSG00000186860	ENSG00000186860		"Keratin associated proteins"	18917	protein-coding gene	gene with protein product							Standard	NM_031964		Approved	KAP17.1	uc002hwj.3	Q9BYP8	OTTHUMG00000133433	ENST00000334202.3:c.156C>T	chr17.hg19:g.39471747G>A		72.0	0.0	.		59.0	28.0	.	NM_031964		Silent	SNP	ENST00000334202.3	hg19	CCDS11387.1																																																																																			.	.	.	none		0.687	KRTAP17-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257296.1			A	39471747	G	A	39471747	2	1	192	1	0	0	0	0	0	0	0	1	8534	963	34	2		2	KRTAP17-1	17	39471747	Silent	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10	5567686	39471747	41723463	91	11490											
KIF18B	146909	hgsc.bcm.edu	37	chr17	43003847	43003847	+	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	ggaggcgggcgatgcggctgCggccatgggagactgaggaa	8	4	21	8	4	0	2	0	1	0	1	0	6	0	4	1	7	2	1	1	7	1	0			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr17:43003847C>T	ENST00000593135.1	-	15	2484	c.2387G>A	c.(2386-2388)cGc>cAc	p.R796H	KIF18B_ENST00000339151.4_Missense_Mutation_p.R799H|KIF18B_ENST00000590129.1_Missense_Mutation_p.R817H|KIF18B_ENST00000438933.2_Missense_Mutation_p.R808H|KIF18B_ENST00000587309.1_Missense_Mutation_p.R808H	NM_001265577.1	NP_001252506.1	Q86Y91	KI18B_HUMAN	kinesin family member 18B	808					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|regulation of cell division (GO:0051302)	astral microtubule (GO:0000235)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule plus-end (GO:0035371)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	21		Prostate(33;0.155)				GATGCGGCTGCGGCCATGGGA	0.607																																					p.R808H		Atlas-SNP	.											.	KIF18B	63	.	0			c.G2423A						PASS	.						30	37	35					17																	43003847		2020	4182	6202	SO:0001583	missense	146909	exon15			CGGCTGCGGCCAT		CCDS45709.1, CCDS58555.1, CCDS45709.2	17q21.31	2014-09-04			ENSG00000186185			"Kinesins"	27102	protein-coding gene	gene with protein product		614570				16084724	Standard	NM_001264573		Approved		uc010wjh.3	Q86Y91	OTTHUMG00000179867	ENST00000593135.1:c.2387G>A	chr17.hg19:g.43003847C>T	ENSP00000465992:p.Arg796His	66.0	0.0	.		56.0	16.0	.	NM_001264573	A6NJI2|B7ZM49|B9EGM8|D5L6I1	Missense_Mutation	SNP	ENST00000593135.1	hg19	CCDS45709.2	.	.	.	.	.	.	.	.	.	.	C	13.25	2.179701	0.38511	.	.	ENSG00000186185	ENST00000438933;ENST00000339151;ENST00000376982	T;T	0.76709	-1.02;-1.04	5.18	-2.42	0.06542	.	.	.	.	.	T	0.69396	0.3106	M	0.65975	2.015	0.09310	N	1	B;B;B	0.28439	0.036;0.212;0.212	B;B;B	0.22880	0.007;0.042;0.042	T	0.53358	-0.8450	9	0.22109	T	0.4	.	9.4947	0.38982	0.0:0.4552:0.0:0.5448	.	808;805;817	Q86Y91;Q86Y91-3;Q86Y91-2	KI18B_HUMAN;.;.	H	808;799;808	ENSP00000412798:R808H;ENSP00000341466:R799H	ENSP00000341466:R799H	R	-	2	0	KIF18B	40359373	0.002000	0.14202	0.103000	0.21229	0.889000	0.51656	-0.800000	0.04555	-0.501000	0.06605	-0.345000	0.07892	CGC	.	.	.	none		0.607	KIF18B-001	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000448724.1	NM_001080443		T	43003847	C	T	43003847	3	4	192	1	0	0	0	0	1	0	0	0	8288	768	27	1	178	1	KIF18B	17	43003847	Missense_Mutation	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10	3532100	43003847	38191363	92	11491											
FASN	2194	hgsc.bcm.edu	37	chr17	80047168	80047168	+	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	gggggtgcgatggcctccatGaagtaggagtggaaggccat	9	7	18	7	1	0	1	0	1	0	0	1	4	1	3	3	6	1	1	3	6	3	1			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr17:80047168G>A	ENST00000306749.2	-	13	2276	c.2058C>T	c.(2056-2058)ttC>ttT	p.F686F		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	686	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)	TGGCCTCCATGAAGTAGGAGT	0.637																																					p.F686F	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.C2058T						PASS	.						52	49	50					17																	80047168		2200	4300	6500	SO:0001819	synonymous_variant	2194	exon13			CTCCATGAAGTAG	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.2058C>T	chr17.hg19:g.80047168G>A		98.0	0.0	.		93.0	51.0	.	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000306749.2	hg19	CCDS11801.1																																																																																			.	.	.	none		0.637	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		A	80047168	G	A	80047168	2	1	192	1	0	0	0	0	0	0	0	1	5690	1281	45	2		2	FASN	17	80047168	Silent	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10	37043321	80047168	1148042	93	11492											
RALBP1	10928	hgsc.bcm.edu	37	chr18	9535920	9535920	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcgcccagcagggataggaaGgagacgtccatctgagcagc	11	5	14	11	2	1	2	0	1	1	1	3	5	2	4	2	3	3	2	2	3	2	1			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr18:9535920G>A	ENST00000019317.4	+	10	2176	c.1953G>A	c.(1951-1953)aaG>aaA	p.K651K	RALBP1_ENST00000383432.3_Silent_p.K651K			Q15311	RBP1_HUMAN	ralA binding protein 1	651					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)	GGGATAGGAAGGAGACGTCCA	0.627																																					p.K651K		Atlas-SNP	.											.	RALBP1	48	.	0			c.G1953A						PASS	.						20	23	22					18																	9535920		2199	4291	6490	SO:0001819	synonymous_variant	10928	exon10			TAGGAAGGAGACG	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.1953G>A	chr18.hg19:g.9535920G>A		192.0	0.0	.		174.0	65.0	.	NM_006788	D3DUI0	Silent	SNP	ENST00000019317.4	hg19	CCDS11845.1																																																																																			.	.	.	none		0.627	RALBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254479.1	NM_006788		A	9535920	G	A	9535920	2	1	192	1	0	0	0	0	0	0	0	1	13025	991	35	2		2	RALBP1	18	9535920	Silent	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10		9535920	68541328	94	11493											
PPP4R1	9989	hgsc.bcm.edu	37	chr18	9570630	9570630	+	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	ctaacactgagatctgaaggAgtatcctctggcctgacttg	10	11	10	10	0	2	3	0	3	2	1	3	5	3	4	2	2	1	1	2	2	3	3			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr18:9570630A>T	ENST00000400556.3	-	11	1171	c.1098T>A	c.(1096-1098)acT>acA	p.T366T	PPP4R1_ENST00000400555.3_Silent_p.T349T	NM_001042388.2	NP_001035847.1	Q8TF05	PP4R1_HUMAN	protein phosphatase 4, regulatory subunit 1	366					dephosphorylation (GO:0016311)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase 4 complex (GO:0030289)	protein phosphatase type 4 regulator activity (GO:0030362)			large_intestine(1)|skin(2)	3						GATCTGAAGGAGTATCCTCTG	0.423																																					p.T366T	Melanoma(188;1232 2082 5061 11948 35994)	Atlas-SNP	.											.	PPP4R1	63	.	0			c.T1098A						PASS	.						89	87	88					18																	9570630		1898	4108	6006	SO:0001819	synonymous_variant	9989	exon11			TGAAGGAGTATCC	AF111106	CCDS42412.1, CCDS42413.1	18p11.22	2010-06-18			ENSG00000154845	ENSG00000154845		"Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"	9320	protein-coding gene	gene with protein product		604908				10026142	Standard	NM_001042388		Approved	PP4R1	uc002koe.2	Q8TF05	OTTHUMG00000137466	ENST00000400556.3:c.1098T>A	chr18.hg19:g.9570630A>T		43.0	0.0	.		59.0	33.0	.	NM_001042388	Q99774|Q9UNQ7	Silent	SNP	ENST00000400556.3	hg19	CCDS42412.1																																																																																			.	.	.	none		0.423	PPP4R1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268571.1	NM_005134		T	9570630	A	T	9570630	2	4	192	1	0	0	0	0	0	0	0	1	12413	291	11	5		5	PPP4R1	18	9570630	Silent	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10	34710	9570630	68506618	95	11494											
BSG	682	hgsc.bcm.edu	37	chr19	581506	581506	+	Frame_Shift_Del	DEL	C	C	-																															ctggccgccctctggcccttCctgggcatcgtggctgaggt																										TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr19:581506delC	ENST00000333511.3	+	6	1054	c.984delC	c.(982-984)ttcfs	p.F328fs	BSG_ENST00000346916.4_Frame_Shift_Del_p.F148fs|BSG_ENST00000353555.4_Frame_Shift_Del_p.F212fs|BSG_ENST00000545507.2_Frame_Shift_Del_p.F119fs	NM_001728.3	NP_001719.2	P35613	BASI_HUMAN	basigin (Ok blood group)	328				F -> L (in Ref. 2; BAC76828). {ECO:0000305}.	blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cellular metabolic process (GO:0044237)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis of dentin-containing tooth (GO:0042475)|protein targeting to plasma membrane (GO:0072661)|pyruvate metabolic process (GO:0006090)|response to cAMP (GO:0051591)|response to mercury ion (GO:0046689)|response to peptide hormone (GO:0043434)|small molecule metabolic process (GO:0044281)	acrosomal membrane (GO:0002080)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	mannose binding (GO:0005537)			central_nervous_system(1)|endometrium(3)|lung(1)	5		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCTGGCCCTTCCTGGGCATCG	0.672																																					p.F328fs		Atlas-Indel,Pindel	.											.	BSG	48	.	0			c.983delT						PASS	.						28	27	27					19																	581506		2185	4293	6478	SO:0001589	frameshift_variant	682	exon6			.	L10240	CCDS12032.1, CCDS12033.1, CCDS12034.1, CCDS58635.1	19p13.3	2014-07-19	2014-01-02		ENSG00000172270	ENSG00000172270		"CD molecules", "Blood group antigens", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1116	protein-coding gene	gene with protein product	"Ok blood group"	109480	"basigin"	OK		8404035, 7812975	Standard	NM_198591		Approved	EMMPRIN, CD147	uc002loz.4	P35613		ENST00000333511.3:c.984delC	chr19.hg19:g.581506delC	ENSP00000333769:p.Phe328fs	77.0	0.0	0		77.0	31.0	0.402597	NM_001728	A6NJW1|D3YLG5|Q7Z796|Q8IZL7	Frame_Shift_Del	DEL	ENST00000333511.3	hg19	CCDS12033.1																																																																																			.	.	.	none		0.672	BSG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438630.2	NM_001728		-	581506	C	-	581506	7	5	192	1	0	1	0	1	0	0	0	0	1531	854	30	0	1042	0	BSG	19	581506	Frame_Shift_Del	DEL	C	TCGA-GL-A9DE-01A-11D-A36X-10		581506	58547477	96	11495											
DOT1L	84444	hgsc.bcm.edu	37	chr19	2210838	2210838	+	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	cagaccgtgtctcagacggcGgcctcctcaccccagggtga	7	6	12	16	3	2	3	2	1	1	2	4	3	3	3	5	3	0	0	5	3	0	0	rs563972624		TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr19:2210838G>T	ENST00000398665.3	+	14	1371	c.1335G>T	c.(1333-1335)gcG>gcT	p.A445A	AC004490.1_ENST00000585593.1_RNA	NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	445					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)		CTCAGACGGCGGCCTCCTCAC	0.687																																					p.A445A		Atlas-SNP	.											.	DOT1L	205	.	0			c.G1335T						PASS	.						21	27	25					19																	2210838		1979	4136	6115	SO:0001819	synonymous_variant	84444	exon14			GACGGCGGCCTCC	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.1335G>T	chr19.hg19:g.2210838G>T		126.0	0.0	.		119.0	55.0	.	NM_032482	O60379|Q96JL1	Silent	SNP	ENST00000398665.3	hg19	CCDS42460.1	.	.	.	.	.	.	.	.	.	.	G	6.432	0.447875	0.12223	.	.	ENSG00000104885	ENST00000440640	.	.	.	4.84	-9.68	0.00528	.	.	.	.	.	T	0.16128	0.0388	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.09552	-1.0669	4	.	.	.	-12.4482	3.2203	0.06713	0.4213:0.2469:0.2445:0.0872	.	.	.	.	L	232	.	.	R	+	2	0	DOT1L	2161838	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-2.301000	0.01137	-2.984000	0.00282	-1.134000	0.01955	CGG	.	.	.	none		0.687	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482		T	2210838	G	T	2210838	2	4	192	1	0	0	0	0	0	0	0	1	4711	1103	39	4		4	DOT1L	19	2210838	Silent	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10	1629332	2210838	56918145	97	11496											
MUC16	94025	hgsc.bcm.edu	37	chr19	9011358	9011358	+	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	gttcctgtccagggtgtaggGgcccagctctttgatgccat	5	12	13	11	0	1	1	0	1	1	0	3	1	3	1	4	3	2	3	4	3	1	3			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr19:9011358G>T	ENST00000397910.4	-	36	39078	c.38875C>A	c.(38875-38877)Ccc>Acc	p.P12959T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12961	SEA 6. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGGGTGTAGGGGCCCAGCTCT	0.547																																					p.P12959T		Atlas-SNP	.											.	MUC16	4315	.	0			c.C38875A						PASS	.						228	200	209					19																	9011358		1988	4172	6160	SO:0001583	missense	94025	exon36			TGTAGGGGCCCAG	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.38875C>A	chr19.hg19:g.9011358G>T	ENSP00000381008:p.Pro12959Thr	87.0	0.0	.		96.0	23.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	8.336	0.827704	0.16749	.	.	ENSG00000181143	ENST00000397910;ENST00000441155	T	0.24151	1.87	2.76	-0.411	0.12370	.	.	.	.	.	T	0.30634	0.0771	L	0.51914	1.62	.	.	.	P	0.44659	0.84	P	0.51999	0.687	T	0.40059	-0.9583	8	0.87932	D	0	-4.8865	5.7224	0.17995	0.3682:0.0:0.6318:0.0	.	12959	B5ME49	.	T	12959;112	ENSP00000381008:P12959T	ENSP00000381008:P12959T	P	-	1	0	MUC16	8872358	0.000000	0.05858	0.441000	0.26858	0.242000	0.25591	-0.041000	0.12084	-0.157000	0.11059	0.305000	0.20034	CCC	.	.	.	none		0.547	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9011358	G	T	9011358	3	4	192	1	0	0	0	0	1	0	0	0	9980	1232	43	4	4844	4	MUC16	19	9011358	Missense_Mutation	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10	6800520	9011358	50117625	98	11497											
ZNF490	57474	hgsc.bcm.edu	37	chr19	12691823	12691824	+	Frame_Shift_Del	DEL	GG	GG	-																															ataaggttgaactccggtgtGggttttcacgtgttttcgaa																										TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr19:12691823_12691824delGG	ENST00000311437.6	-	5	1187_1188	c.1065_1066delCC	c.(1063-1068)acccacfs	p.H356fs	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	356					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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						ACTCCGGTGTGGGTTTTCACGT	0.431																																					p.356_356del		Atlas-Indel,Pindel	.											.	ZNF490	42	.	0			c.1066_1067del						PASS	.																																			SO:0001589	frameshift_variant	57474	exon5			.	AB033024	CCDS12272.1	19p13.2	2013-01-08			ENSG00000188033	ENSG00000188033		"Zinc fingers, C2H2-type", "-"	23705	protein-coding gene	gene with protein product							Standard	NM_020714		Approved	KIAA1198	uc002mtz.2	Q9ULM2	OTTHUMG00000156398	ENST00000311437.6:c.1065_1066delCC	chr19.hg19:g.12691823_12691824delGG	ENSP00000311521:p.His356fs	78.0	0.0	0		84.0	40.0	0.47619	NM_020714		Frame_Shift_Del	DEL	ENST00000311437.6	hg19	CCDS12272.1																																																																																			.	.	.	none		0.431	ZNF490-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344073.1	NM_020714		-	12691824	GG	-	12691823	7	5	192	1	0	1	0	1	0	0	0	0	17953	1348	47	0	527	0	ZNF490	19	12691823	Frame_Shift_Del	DEL	GG	TCGA-GL-A9DE-01A-11D-A36X-10	3680465	12691823	46437160	99	11498											
HOOK2	29911	hgsc.bcm.edu	37	chr19	12878236	12878236	+	Missense_Mutation	SNP	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	ccgcaggcaggatctctgcgGctaagttatccacgggtgtg	7	9	14	11	3	1	0	0	0	1	0	3	1	2	1	2	4	1	4	2	4	2	2			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr19:12878236G>A	ENST00000397668.3	-	14	1419	c.1346C>T	c.(1345-1347)gCc>gTc	p.A449V	HOOK2_ENST00000589965.1_Intron|HOOK2_ENST00000264827.5_Missense_Mutation_p.A449V	NM_013312.2	NP_037444.2	Q96ED9	HOOK2_HUMAN	hook microtubule-tethering protein 2	449	Sufficient for interaction with microtubules.				early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	centrosome (GO:0005813)|FHF complex (GO:0070695)|microtubule (GO:0005874)	identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(5)|skin(1)	20						GATCTCTGCGGCTAAGTTATC	0.627																																					p.A449V		Atlas-SNP	.											.	HOOK2	73	.	0			c.C1346T						PASS	.						53	58	57					19																	12878236		1880	4105	5985	SO:0001583	missense	29911	exon14			TCTGCGGCTAAGT	AF044924	CCDS42507.1, CCDS42508.1	19p13.2	2013-08-21	2013-08-21						19885	protein-coding gene	gene with protein product		607824	"hook homolog 2 (Drosophila)"			9927460	Standard	NM_013312		Approved	HK2	uc002muy.2	Q96ED9		ENST00000397668.3:c.1346C>T	chr19.hg19:g.12878236G>A	ENSP00000380785:p.Ala449Val	67.0	0.0	.		75.0	29.0	.	NM_001100176	O60562	Missense_Mutation	SNP	ENST00000397668.3	hg19	CCDS42508.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.939222	0.92526	.	.	ENSG00000095066	ENST00000397668;ENST00000264827	T;T	0.25085	1.82;1.82	5.51	5.51	0.81932	.	0.109656	0.64402	D	0.000010	T	0.52565	0.1742	M	0.80982	2.52	0.46749	D	0.99918	D;D	0.60160	0.984;0.987	P;D	0.63488	0.861;0.915	T	0.56300	-0.8002	10	0.66056	D	0.02	-3.622	16.9614	0.86273	0.0:0.0:1.0:0.0	.	449;449	Q96ED9-2;Q96ED9	.;HOOK2_HUMAN	V	449	ENSP00000380785:A449V;ENSP00000264827:A449V	ENSP00000264827:A449V	A	-	2	0	HOOK2	12739236	1.000000	0.71417	0.995000	0.50966	0.836000	0.47400	6.624000	0.74243	2.607000	0.88179	0.650000	0.86243	GCC	.	.	.	none		0.627	HOOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451008.1	NM_013312		A	12878236	G	A	12878236	3	1	192	1	0	0	0	0	1	0	0	0	7290	1203	42	2	853	2	HOOK2	19	12878236	Missense_Mutation	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10	186413	12878236	46250747	100	11499											
MYO9B	4650	hgsc.bcm.edu	37	chr19	17270210	17270210	+	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	ttgacctccaaacaggtgaaGcgagaaatcttggtggaggt	12	9	13	7	1	1	3	0	2	1	1	2	5	2	4	2	4	2	0	2	4	3	2			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr19:17270210G>A	ENST00000594824.1	+	8	1482	c.1335G>A	c.(1333-1335)aaG>aaA	p.K445K	MYO9B_ENST00000397274.2_Silent_p.K445K|CTD-3032J10.2_ENST00000599360.1_RNA|MYO9B_ENST00000595618.1_Silent_p.K445K|CTD-3032J10.2_ENST00000597216.1_RNA			Q13459	MYO9B_HUMAN	myosin IXB	445	Myosin motor.				actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						AACAGGTGAAGCGAGAAATCT	0.542																																					p.K445K		Atlas-SNP	.											.	MYO9B	264	.	0			c.G1335A						PASS	.						77	77	77					19																	17270210		1958	4148	6106	SO:0001819	synonymous_variant	4650	exon8			GGTGAAGCGAGAA		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.1335G>A	chr19.hg19:g.17270210G>A		78.0	0.0	.		86.0	36.0	.	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Silent	SNP	ENST00000594824.1	hg19																																																																																				.	.	.	none		0.542	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1			A	17270210	G	A	17270210	2	1	192	1	0	0	0	0	0	0	0	1	10092	962	34	2		2	MYO9B	19	17270210	Silent	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10	4391974	17270210	41858773	101	11500											
ZNF574	64763	hgsc.bcm.edu	37	chr19	42583233	42583233	+	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	cacccaccaaggctcctgccCctgttgtcctggggtcccca	5	8	9	19	0	0	0	0	0	0	0	3	0	3	0	8	3	1	2	8	3	1	1			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr19:42583233C>T	ENST00000600245.1	+	2	1130	c.475C>T	c.(475-477)Cct>Tct	p.P159S	ZNF574_ENST00000222339.7_Missense_Mutation_p.P249S|CTB-59C6.3_ENST00000594531.1_RNA|ZNF574_ENST00000359044.4_Missense_Mutation_p.P159S			Q6ZN55	ZN574_HUMAN	zinc finger protein 574	159					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			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)				GGCTCCTGCCCCTGTTGTCCT	0.637																																					p.P159S		Atlas-SNP	.											.	ZNF574	57	.	0			c.C475T						PASS	.						49	57	54					19																	42583233		2203	4300	6503	SO:0001583	missense	64763	exon2			CCTGCCCCTGTTG	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.475C>T	chr19.hg19:g.42583233C>T	ENSP00000469029:p.Pro159Ser	100.0	0.0	.		90.0	33.0	.	NM_022752	Q6IPE0|Q6ZN10|Q7L5Z5|Q8NCE3|Q9H6N0	Missense_Mutation	SNP	ENST00000600245.1	hg19	CCDS12596.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.151603	0.57151	.	.	ENSG00000105732	ENST00000222339;ENST00000359044	T;T	0.06849	3.25;3.29	4.23	3.12	0.35913	.	0.240652	0.33813	N	0.004523	T	0.04861	0.0131	N	0.08118	0	0.26252	N	0.978701	B;P	0.40180	0.202;0.705	B;B	0.38327	0.099;0.271	T	0.38329	-0.9666	10	0.42905	T	0.14	-10.3235	13.0485	0.58942	0.0:0.8377:0.1623:0.0	.	159;248	Q6ZN55;Q6ZN55-2	ZN574_HUMAN;.	S	249;159	ENSP00000222339:P249S;ENSP00000351939:P159S	ENSP00000222339:P249S	P	+	1	0	ZNF574	47275073	0.001000	0.12720	0.701000	0.30321	0.747000	0.42532	0.256000	0.18351	2.186000	0.69663	0.591000	0.81541	CCT	.	.	.	none		0.637	ZNF574-002	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463458.1	NM_022752		T	42583233	C	T	42583233	3	4	192	1	0	0	0	0	1	0	0	0	18018	623	22	2	477	2	ZNF574	19	42583233	Missense_Mutation	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10	25313023	42583233	16545750	102	11501											
GLTSCR1	29998	hgsc.bcm.edu	37	chr19	48197404	48197404	+	Frame_Shift_Del	DEL	C	C	-																															gctccgctgaagggcccaggCccctcttcgtccccgtcact																										TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr19:48197404delC	ENST00000396720.3	+	8	2510	c.2316delC	c.(2314-2316)ggcfs	p.G772fs	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	772										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)		AGGGCCCAGGCCCCTCTTCGT	0.726																																					p.G772fs		Atlas-Indel,Pindel	.											.	GLTSCR1	79	.	0			c.2315delG						PASS	.						1	1	1					19																	48197404		834	1989	2823	SO:0001589	frameshift_variant	29998	exon8			.	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.2316delC	chr19.hg19:g.48197404delC	ENSP00000379946:p.Gly772fs	91.0	0.0	0		82.0	24.0	0.292683	NM_015711	A8MW01	Frame_Shift_Del	DEL	ENST00000396720.3	hg19	CCDS46134.1																																																																																			.	.	.	none		0.726	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711		-	48197404	C	-	48197404	7	5	192	1	0	1	0	1	0	0	0	0	6481	726	26	0	2338	0	GLTSCR1	19	48197404	Frame_Shift_Del	DEL	C	TCGA-GL-A9DE-01A-11D-A36X-10	5614171	48197404	10931579	103	11502											
PTPRH	5794	hgsc.bcm.edu	37	chr19	55718205	55718205	+	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	tctgttgtgccgccgtctccAgtacactgaacccagtagtt	7	12	9	13	2	2	1	0	1	2	0	3	1	2	1	4	0	3	4	4	0	3	4			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr19:55718205A>C	ENST00000376350.3	-	3	226	c.204T>G	c.(202-204)acT>acG	p.T68T	PTPRH_ENST00000588559.1_5'UTR|PTPRH_ENST00000263434.5_Silent_p.T68T	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	68	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		CGCCGTCTCCAGTACACTGAA	0.572																																					p.T68T		Atlas-SNP	.											.	PTPRH	139	.	0			c.T204G						PASS	.						147	122	130					19																	55718205		2203	4300	6503	SO:0001819	synonymous_variant	5794	exon3			GTCTCCAGTACAC		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.204T>G	chr19.hg19:g.55718205A>C		136.0	0.0	.		180.0	65.0	.	NM_001161440	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Silent	SNP	ENST00000376350.3	hg19	CCDS33110.1																																																																																			.	.	.	none		0.572	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1			C	55718205	A	C	55718205	2	2	192	1	0	0	0	0	0	0	0	1	12816	175	7	5		5	PTPRH	19	55718205	Silent	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10	7520801	55718205	3410778	104	11503											
DUXA	503835	hgsc.bcm.edu	37	chr19	57665813	57665813	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctccagagaaatgagagtcActagtgaagttggtgccatt	12	10	12	7	0	1	3	1	2	0	2	2	5	2	3	2	1	1	2	2	1	3	3			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr19:57665813A>G	ENST00000554048.2	-	6	581	c.582T>C	c.(580-582)agT>agC	p.S194S		NM_001012729.1	NP_001012747.1	A6NLW8	DUXA_HUMAN	double homeobox A	194					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)		AATGAGAGTCACTAGTGAAGT	0.418																																					p.S194S		Atlas-SNP	.											.	DUXA	46	.	0			c.T582C						PASS	.						135	116	123					19																	57665813		2203	4300	6503	SO:0001819	synonymous_variant	503835	exon6			AGAGTCACTAGTG		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.582T>C	chr19.hg19:g.57665813A>G		101.0	0.0	.		98.0	39.0	.	NM_001012729		Silent	SNP	ENST00000554048.2	hg19	CCDS33126.1																																																																																			.	.	.	none		0.418	DUXA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410075.3	NM_001012729		G	57665813	A	G	57665813	2	3	192	1	0	0	0	0	0	0	0	1	4836	156	6	3		3	DUXA	19	57665813	Silent	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10	1947608	57665813	1463170	105	11504											
TMC2	117532	hgsc.bcm.edu	37	chr20	2618130	2618130	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttcctgcagctccgtgaagTtgagaagagtcacaaatctg	11	11	10	9	1	2	3	1	2	1	2	4	4	4	3	2	0	2	3	2	0	3	2			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr20:2618130T>C	ENST00000358864.1	+	19	2411	c.2396T>C	c.(2395-2397)gTt>gCt	p.V799A		NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	799					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						CTCCGTGAAGTTGAGAAGAGT	0.458																																					p.V799A		Atlas-SNP	.											.	TMC2	121	.	0			c.T2396C						PASS	.						90	88	89					20																	2618130		2203	4300	6503	SO:0001583	missense	117532	exon19			GTGAAGTTGAGAA	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.2396T>C	chr20.hg19:g.2618130T>C	ENSP00000351732:p.Val799Ala	66.0	0.0	.		75.0	8.0	.	NM_080751	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Missense_Mutation	SNP	ENST00000358864.1	hg19	CCDS13029.2	.	.	.	.	.	.	.	.	.	.	T	7.729	0.698802	0.15106	.	.	ENSG00000149488	ENST00000358864	T	0.62105	0.05	5.04	3.93	0.45458	.	0.185575	0.43416	D	0.000570	T	0.51550	0.1681	L	0.45581	1.43	0.22762	N	0.998764	B	0.02656	0.0	B	0.06405	0.002	T	0.43523	-0.9386	10	0.39692	T	0.17	-3.1255	8.6117	0.33806	0.1709:0.0:0.0:0.8291	.	799	Q8TDI7	TMC2_HUMAN	A	799	ENSP00000351732:V799A	ENSP00000351732:V799A	V	+	2	0	TMC2	2566130	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	1.282000	0.33226	1.007000	0.39238	-0.336000	0.08194	GTT	.	.	.	none		0.458	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2			C	2618130	T	C	2618130	3	2	192	1	0	0	0	0	1	0	0	0	15997	1725	60	3	2470	3	TMC2	20	2618130	Missense_Mutation	SNP	T	TCGA-GL-A9DE-01A-11D-A36X-10		2618130	60407390	106	11505											
PARD6B	84612	hgsc.bcm.edu	37	chr20	49354458	49354458	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggaaaatttgaggagttttAtggattactacaacatgttc	13	15	9	4	0	0	1	0	1	0	0	1	4	0	4	0	3	3	2	0	3	6	6			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr20:49354458A>G	ENST00000371610.2	+	2	374	c.131A>G	c.(130-132)tAt>tGt	p.Y44C	PARD6B_ENST00000396039.1_Missense_Mutation_p.Y44C	NM_032521.2	NP_115910.1	Q9BYG5	PAR6B_HUMAN	par-6 family cell polarity regulator beta	44	OPR.				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						GAGGAGTTTTATGGATTACTA	0.333																																					p.Y44C		Atlas-SNP	.											.	PARD6B	31	.	0			c.A131G						PASS	.						80	79	79					20																	49354458		2203	4300	6503	SO:0001583	missense	84612	exon2			AGTTTTATGGATT	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.131A>G	chr20.hg19:g.49354458A>G	ENSP00000360672:p.Tyr44Cys	104.0	0.0	.		132.0	50.0	.	NM_032521	A2A2A7|Q9Y510	Missense_Mutation	SNP	ENST00000371610.2	hg19	CCDS33485.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.151060	0.78001	.	.	ENSG00000124171	ENST00000371610;ENST00000396039	T;T	0.21734	1.99;1.99	5.92	5.92	0.95590	Phox/Bem1p (2);	0.000000	0.85682	D	0.000000	T	0.36663	0.0975	M	0.64567	1.98	0.80722	D	1	B	0.33583	0.418	P	0.46510	0.519	T	0.08764	-1.0706	10	0.49607	T	0.09	-29.6811	15.5593	0.76229	1.0:0.0:0.0:0.0	.	44	Q9BYG5	PAR6B_HUMAN	C	44	ENSP00000360672:Y44C;ENSP00000379354:Y44C	ENSP00000360672:Y44C	Y	+	2	0	PARD6B	48787865	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	8.920000	0.92779	2.277000	0.76020	0.528000	0.53228	TAT	.	.	.	none		0.333	PARD6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079697.2	NM_032521		G	49354458	A	G	49354458	3	3	192	1	0	0	0	0	1	0	0	0	11453	449	16	3	137	3	PARD6B	20	49354458	Missense_Mutation	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10	46736328	49354458	13671062	107	11506											
ATP9A	10079	hgsc.bcm.edu	37	chr20	50217801	50217801	+	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	gagaaccgtcttcgcaggtaCttgaggacatagagggggag	11	7	16	7	2	1	3	0	1	1	2	2	6	1	5	1	4	2	2	1	4	3	4			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr20:50217801C>T	ENST00000338821.5	-	28	3357	c.3093G>A	c.(3091-3093)aaG>aaA	p.K1031K	ATP9A_ENST00000402822.1_Silent_p.K910K|ATP9A_ENST00000311637.5_Silent_p.K895K	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	1031					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						TTCGCAGGTACTTGAGGACAT	0.567																																					p.K1031K		Atlas-SNP	.											.	ATP9A	135	.	0			c.G3093A						PASS	.						89	64	73					20																	50217801		2203	4300	6503	SO:0001819	synonymous_variant	10079	exon28			CAGGTACTTGAGG	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.3093G>A	chr20.hg19:g.50217801C>T		113.0	0.0	.		148.0	8.0	.	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Silent	SNP	ENST00000338821.5	hg19	CCDS33489.1																																																																																			.	.	.	none		0.567	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045		T	50217801	C	T	50217801	2	4	192	1	0	0	0	0	0	0	0	1	1198	564	20	2		2	ATP9A	20	50217801	Silent	SNP	C	TCGA-GL-A9DE-01A-11D-A36X-10	863343	50217801	12807719	108	11507											
SLC7A4	6545	hgsc.bcm.edu	37	chr22	21385638	21385638	+	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	cctgccaagaacccacgtggGtctcagtgaagttgcggatg	9	8	13	11	2	1	2	1	1	1	1	2	3	1	3	3	2	3	1	3	2	3	1			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr22:21385638G>C	ENST00000382932.2	-	2	531	c.464C>G	c.(463-465)aCc>aGc	p.T155S	AC002472.11_ENST00000450652.1_RNA|MIR649_ENST00000384843.1_RNA|SLC7A4_ENST00000403586.1_Missense_Mutation_p.T155S	NM_004173.2	NP_004164.2	O43246	CTR4_HUMAN	solute carrier family 7, member 4	155				THVGSWQVPLLGHYPDFLAAGIILLASAFVSCGARVSS -> DPRGFLAGAPPGPLPGLPGCWHHPPWPLPLSPVEPACPP (in Ref. 1; CAA04263). {ECO:0000305}.	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)	ACCCACGTGGGTCTCAGTGAA	0.622																																					p.T155S		Atlas-SNP	.											.	SLC7A4	50	.	0			c.C464G						PASS	.						34	36	35					22																	21385638		2203	4300	6503	SO:0001583	missense	6545	exon2			ACGTGGGTCTCAG	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.464C>G	chr22.hg19:g.21385638G>C	ENSP00000372390:p.Thr155Ser	30.0	0.0	.		34.0	11.0	.	NM_004173	Q0P5U2|Q3KNQ6|Q4VC45|Q6IBY8|Q96H88	Missense_Mutation	SNP	ENST00000382932.2	hg19	CCDS33608.1	.	.	.	.	.	.	.	.	.	.	G	4.566	0.105214	0.08731	.	.	ENSG00000099960	ENST00000403586;ENST00000382932	D;D	0.90004	-2.6;-2.6	5.28	4.26	0.50523	Amino acid permease domain (1);	0.304735	0.34025	N	0.004331	T	0.78710	0.4326	N	0.20766	0.605	0.26027	N	0.981795	B	0.02656	0.0	B	0.06405	0.002	T	0.60337	-0.7283	10	0.12103	T	0.63	.	11.768	0.51941	0.0862:0.0:0.9138:0.0	.	155	O43246	CTR4_HUMAN	S	155	ENSP00000384278:T155S;ENSP00000372390:T155S	ENSP00000372390:T155S	T	-	2	0	SLC7A4	19715638	1.000000	0.71417	0.071000	0.20095	0.025000	0.11179	2.808000	0.47963	1.351000	0.45789	0.561000	0.74099	ACC	.	.	.	none		0.622	SLC7A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320467.1	NM_004173		C	21385638	G	C	21385638	3	2	192	1	0	0	0	0	1	0	0	0	14712	1261	44	4	1459	4	SLC7A4	22	21385638	Missense_Mutation	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10		21385638	29918928	109	11508											
MN1	4330	hgsc.bcm.edu	37	chr22	28194900	28194900	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgctgctgctgctgctgctgTtgctgttgctgttgctgctg	0	16	14	11	1	0	0	0	0	0	0	0	0	0	0	0	0	9	13	0	0	0	3	rs202212250|rs530519178	byFrequency	TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr22:28194900T>C	ENST00000302326.4	-	1	2586	c.1632A>G	c.(1630-1632)caA>caG	p.Q544Q		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	544	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						gctgctgctgttgctgttgct	0.647			T	ETV6	"AML, meningioma"								C|||	5	0.000998403	0.0023	0	5008	,	,		12597	0		0	False		,,,				2504	0.002				p.Q544Q		Atlas-SNP	.		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"L, O"	.	MN1	122	.	0			c.A1632G						PASS	.																																			SO:0001819	synonymous_variant	4330	exon1			CTGCTGTTGCTGT	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.1632A>G	chr22.hg19:g.28194900T>C		39.0	0.0	.		63.0	7.0	.	NM_002430	A9Z1V9	Silent	SNP	ENST00000302326.4	hg19	CCDS42998.1																																																																																			.	.	.	none		0.647	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430		C	28194900	T	C	28194900	2	2	192	1	0	0	0	0	0	0	0	1	9680	1722	60	3		3	MN1	22	28194900	Silent	SNP	T	TCGA-GL-A9DE-01A-11D-A36X-10	6809262	28194900	23109666	110	11509											
PLXNB2	23654	hgsc.bcm.edu	37	chr22	50722099	50722099	+	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	gccacagagatcctctggatGtcccctgcttggacgcccaa	8	8	10	15	1	1	1	0	0	1	1	3	4	3	3	5	2	1	1	5	2	1	1			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chr22:50722099G>A	ENST00000449103.1	-	15	2642	c.2502C>T	c.(2500-2502)gaC>gaT	p.D834D	PLXNB2_ENST00000359337.4_Silent_p.D834D|PLXNB2_ENST00000496720.1_5'UTR			O15031	PLXB2_HUMAN	plexin B2	834	IPT/TIG 1.				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)		TCCTCTGGATGTCCCCTGCTT	0.647																																					p.D834D		Atlas-SNP	.											.	PLXNB2	172	.	0			c.C2502T						PASS	.						31	37	35					22																	50722099		1973	4137	6110	SO:0001819	synonymous_variant	23654	exon15			CTGGATGTCCCCT		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.2502C>T	chr22.hg19:g.50722099G>A		76.0	0.0	.		70.0	32.0	.	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Silent	SNP	ENST00000449103.1	hg19	CCDS43035.1																																																																																			.	.	.	none		0.647	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401		A	50722099	G	A	50722099	2	1	192	1	0	0	0	0	0	0	0	1	12131	1368	48	2		2	PLXNB2	22	50722099	Silent	SNP	G	TCGA-GL-A9DE-01A-11D-A36X-10	22527199	50722099	582467	111	11510											
ZBED1	9189	hgsc.bcm.edu	37	chrX	2407032	2407032	+	Missense_Mutation	SNP	A	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	gaggccaagcaccttctgggActtgaagttgctcagctcct	8	10	11	12	0	2	1	1	1	1	0	3	3	3	2	3	2	3	4	3	2	2	3			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chrX:2407032A>C	ENST00000381223.4	-	2	1932	c.1729T>G	c.(1729-1731)Tcc>Gcc	p.S577A	DHRSX_ENST00000334651.5_Intron|ZBED1_ENST00000381222.2_Missense_Mutation_p.S577A|ZBED1_ENST00000515319.1_5'Flank|ZBED1_ENST00000381218.3_Missense_Mutation_p.S577A	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	577					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)				ACCTTCTGGGACTTGAAGTTG	0.607																																					p.S577A		Atlas-SNP	.											.	ZBED1	64	.	0			c.T1729G						PASS	.						120	106	111					X																	2407032		2203	4296	6499	SO:0001583	missense	9189	exon2			TCTGGGACTTGAA	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.1729T>G	chrX.hg19:g.2407032A>C	ENSP00000370621:p.Ser577Ala	95.0	0.0	.		72.0	46.0	.	NM_001171135	Q96BY4	Missense_Mutation	SNP	ENST00000381223.4	hg19	CCDS14118.1	.	.	.	.	.	.	.	.	.	.	A	9.895	1.205342	0.22205	.	.	ENSG00000214717	ENST00000381223;ENST00000381222;ENST00000381218	T;T;T	0.22539	1.95;1.95;1.95	2.97	1.67	0.24075	HAT dimerisation (1);Ribonuclease H-like (1);	0.126167	0.34750	U	0.003715	T	0.11110	0.0271	.	.	.	0.09310	N	1	B	0.18013	0.025	B	0.20577	0.03	T	0.36335	-0.9752	9	0.15066	T	0.55	.	8.2493	0.31708	0.7999:0.2001:0.0:0.0	.	577	O96006	ZBED1_HUMAN	A	577	ENSP00000370621:S577A;ENSP00000370620:S577A;ENSP00000370616:S577A	ENSP00000370616:S577A	S	-	1	0	ZBED1	2417032	1.000000	0.71417	0.572000	0.28498	0.482000	0.33219	4.352000	0.59404	0.015000	0.14971	0.373000	0.22412	TCC	.	.	.	none		0.607	ZBED1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144310.3	NM_004729		C	2407032	A	C	2407032	3	2	192	1	0	0	0	0	1	0	0	0	17529	275	10	5	359	5	ZBED1	23	2407032	Missense_Mutation	SNP	A	TCGA-GL-A9DE-01A-11D-A36X-10		2407032	152863528	112	11511											
GPR34	2857	hgsc.bcm.edu	37	chrX	41555847	41555847	+	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	ttctctcatctttcaatagtTgcttagatccagtcatgtat	9	18	5	9	0	5	1	3	0	2	1	7	1	6	1	1	0	1	3	1	0	4	6			TCGA-GL-A9DE-01A-11D-A36X-10	TCGA-GL-A9DE-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	be0270c7-7799-4045-9a8c-3878512a73ef	bfa8f265-7a77-40f4-89f4-2102820fcdee	g.chrX:41555847T>A	ENST00000378142.4	+	3	1245	c.961T>A	c.(961-963)Tgc>Agc	p.C321S	CASK_ENST00000442742.2_Intron|GPR34_ENST00000378138.5_Missense_Mutation_p.C321S|CASK_ENST00000378154.1_Intron|CASK_ENST00000378163.1_Intron|CASK_ENST00000421587.2_Intron|CASK_ENST00000378166.4_Intron|CASK_ENST00000361962.4_Intron|CASK_ENST00000318588.9_Intron|CASK_ENST00000378158.1_Intron	NM_001097579.1|NM_005300.3	NP_001091048.1|NP_005291.1	Q9UPC5	GPR34_HUMAN	G protein-coupled receptor 34	321					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						TTTCAATAGTTGCTTAGATCC	0.368																																					p.C321S		Atlas-SNP	.											.	GPR34	42	.	0			c.T961A						PASS	.						124	102	110					X																	41555847		2202	4300	6502	SO:0001583	missense	2857	exon3			AATAGTTGCTTAG	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.961T>A	chrX.hg19:g.41555847T>A	ENSP00000367384:p.Cys321Ser	117.0	0.0	.		131.0	99.0	.	NM_001097579	O95853	Missense_Mutation	SNP	ENST00000378142.4	hg19	CCDS14258.1	.	.	.	.	.	.	.	.	.	.	T	18.02	3.529560	0.64860	.	.	ENSG00000171659	ENST00000378142;ENST00000378138;ENST00000535368	T;T	0.61510	0.1;0.1	5.73	5.73	0.89815	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.80465	0.4628	M	0.89840	3.065	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84706	0.0731	10	0.72032	D	0.01	-13.9692	14.9871	0.71356	0.0:0.0:0.0:1.0	.	321	Q9UPC5	GPR34_HUMAN	S	321;321;274	ENSP00000367384:C321S;ENSP00000367378:C321S	ENSP00000367378:C321S	C	+	1	0	GPR34	41440791	1.000000	0.71417	0.961000	0.40146	0.777000	0.43975	7.694000	0.84235	1.922000	0.55676	0.481000	0.45027	TGC	.	.	.	none		0.368	GPR34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056264.1	NM_005300		A	41555847	T	A	41555847	3	1	192	1	0	0	0	0	1	0	0	0	6696	1812	63	5	963	5	GPR34	23	41555847	Missense_Mutation	SNP	T	TCGA-GL-A9DE-01A-11D-A36X-10	39148815	41555847	113714713	113	11512											
DDI2	84301	hgsc.bcm.edu	37	chr1	15956850	15956850	+	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	aatagatttcagtagtatagCtgtgcctggcacatcaagtc	12	12	9	8	0	2	1	2	0	0	1	3	1	2	1	1	1	2	4	1	1	6	5			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr1:15956850C>A	ENST00000480945.1	+	3	470	c.299C>A	c.(298-300)gCt>gAt	p.A100D		NM_032341.4	NP_115717.3	Q5TDH0	DDI2_HUMAN	DNA-damage inducible 1 homolog 2 (S. cerevisiae)	100							aspartic-type endopeptidase activity (GO:0004190)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|stomach(1)	17		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00327)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.03e-07)|COAD - Colon adenocarcinoma(227;4.48e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)		AGTAGTATAGCTGTGCCTGGC	0.473																																					p.A100D		Atlas-SNP	.											.	DDI2	38	.	0			c.C299A						PASS	.						86	88	87					1																	15956850		2203	4300	6503	SO:0001583	missense	84301	exon3			GTATAGCTGTGCC		CCDS30607.1	1p36.13	2010-05-04	2010-05-04		ENSG00000197312	ENSG00000197312			24578	protein-coding gene	gene with protein product			"DDI1, DNA-damage inducible 1, homolog 2 (S. cerevisiae)"				Standard	NM_032341		Approved	MGC14844	uc001awx.2	Q5TDH0	OTTHUMG00000002381	ENST00000480945.1:c.299C>A	chr1.hg19:g.15956850C>A	ENSP00000417748:p.Ala100Asp	131.0	0.0	.		112.0	24.0	.	NM_032341	A8KAE1|Q7RTZ0|Q9BRT1	Missense_Mutation	SNP	ENST00000480945.1	hg19	CCDS30607.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.182624	0.78677	.	.	ENSG00000197312	ENST00000480945	T	0.23552	1.9	5.9	5.9	0.94986	.	0.130770	0.51477	U	0.000091	T	0.34774	0.0909	M	0.71036	2.16	0.80722	D	1	P	0.44946	0.846	B	0.40101	0.319	T	0.19321	-1.0309	10	0.56958	D	0.05	-28.9484	19.873	0.96856	0.0:1.0:0.0:0.0	.	100	Q5TDH0	DDI2_HUMAN	D	100	ENSP00000417748:A100D	ENSP00000417748:A100D	A	+	2	0	DDI2	15829437	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.971000	0.76105	2.802000	0.96397	0.650000	0.86243	GCT	.	.	.	none		0.473	DDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006826.1	NM_032341		A	15956850	C	A	15956850	3	1	193	1	0	0	0	0	1	0	0	0	4331	797	28	4	309	4	DDI2	1	15956850	Missense_Mutation	SNP	C	TCGA-HE-7128-01A-11D-1961-08		15956850	233293771	1	11513											
ST3GAL3	6487	hgsc.bcm.edu	37	chr1	44290408	44290408	+	Intron	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	attcccactttgcagctcacCgaggactctctgcacggtgg	7	10	10	14	2	2	0	1	0	1	0	4	2	3	1	2	3	3	3	2	3	0	2			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr1:44290408C>A	ENST00000361392.4	+	4	386				ST3GAL3_ENST00000531993.1_Intron|ST3GAL3_ENST00000461375.1_Intron|ST3GAL3_ENST00000372372.2_Missense_Mutation_p.P56Q|ST3GAL3_ENST00000528371.1_Intron|ST3GAL3_ENST00000545417.1_Intron|ST3GAL3_ENST00000335430.6_Intron|ST3GAL3_ENST00000372375.2_Missense_Mutation_p.P72Q|ST3GAL3_ENST00000372367.1_Intron|ST3GAL3_ENST00000372368.2_Missense_Mutation_p.P72Q|ST3GAL3_ENST00000372377.4_Intron|ST3GAL3_ENST00000372362.2_Intron|ST3GAL3_ENST00000262915.3_Missense_Mutation_p.P87Q|ST3GAL3_ENST00000332628.6_Intron|ST3GAL3_ENST00000372366.1_Intron|ST3GAL3_ENST00000372374.2_Intron|ST3GAL3_ENST00000351035.3_Missense_Mutation_p.P56Q|ST3GAL3_ENST00000533933.1_Intron|ST3GAL3_ENST00000361746.4_Missense_Mutation_p.P87Q|ST3GAL3_ENST00000361400.4_Intron|ST3GAL3_ENST00000531451.1_Intron|ST3GAL3_ENST00000330208.2_Intron|ST3GAL3_ENST00000372369.1_Intron|ST3GAL3_ENST00000347631.2_Intron|ST3GAL3_ENST00000353126.3_Intron|ST3GAL3_ENST00000531816.1_Intron|ST3GAL3_ENST00000361812.4_Intron|ST3GAL3_ENST00000372365.1_Intron	NM_001270459.1|NM_006279.3|NM_174964.2	NP_001257388.1|NP_006270.1|NP_777624.1	Q11203	SIAT6_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 3						carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836)|N-acetyllactosaminide alpha-2,3-sialyltransferase activity (GO:0008118)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(3)|skin(1)	19	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0518)				TGCAGCTCACCGAGGACTCTC	0.453																																					p.P87Q		Atlas-SNP	.											.	ST3GAL3	56	.	0			c.C260A						PASS	.						98	103	102					1																	44290408		2203	4300	6503	SO:0001627	intron_variant	6487	exon5			GCTCACCGAGGAC	L23768	CCDS492.1, CCDS493.1, CCDS494.1, CCDS495.1, CCDS496.1, CCDS497.1, CCDS498.1, CCDS499.1, CCDS500.1, CCDS53310.1, CCDS57988.1, CCDS57989.1, CCDS57990.1, CCDS57991.1, CCDS57992.1, CCDS57993.1, CCDS57994.1	1p34.1	2014-01-31	2005-02-07	2005-02-07	ENSG00000126091	ENSG00000126091	2.4.99.6	"Sialyltransferases"	10866	protein-coding gene	gene with protein product	"ST3Gal III"	606494	"sialyltransferase 6 (N-acetyllacosaminide alpha 2,3-sialyltransferase)", "mental retardation, non-syndromic, autosomal recessive, 12"	SIAT6, MRT12		8333853, 21907012	Standard	NM_174963		Approved		uc001cjz.4	Q11203	OTTHUMG00000007561	ENST00000361392.4:c.209+9803C>A	chr1.hg19:g.44290408C>A		179.0	0.0	.		141.0	8.0	.	NM_174963	A9Z1W2|D3DPX8|Q5T4W9|Q5T4X0|Q5T4X7|Q5T4X8|Q5T4X9|Q5T4Y0|Q5T4Y2|Q5T4Y3|Q5T4Y4|Q86UR6|Q86UR7|Q86UR8|Q86UR9|Q86US0|Q86US1|Q86US2|Q8IX41|Q8IX42|Q8IX43|Q8IX44|Q8IX45|Q8IX46|Q8IX47|Q8IX48|Q8IX49|Q8IX50|Q8IX51|Q8IX52|Q8IX53|Q8IX54|Q8IX55|Q8IX56|Q8IX57|Q8IX58	Missense_Mutation	SNP	ENST00000361392.4	hg19	CCDS492.1	.	.	.	.	.	.	.	.	.	.	C	4.533	0.098911	0.08681	.	.	ENSG00000126091	ENST00000262915;ENST00000372375;ENST00000351035;ENST00000361746;ENST00000372368;ENST00000372372	T;T;T;T;T;T	0.56611	0.55;0.54;0.45;0.55;0.54;0.45	2.47	1.54	0.23209	.	.	.	.	.	T	0.44603	0.1301	.	.	.	0.09310	N	1	B;B;B	0.24768	0.111;0.111;0.111	B;B;B	0.36504	0.054;0.054;0.226	T	0.44757	-0.9307	8	0.34782	T	0.22	.	7.2175	0.25967	0.0:0.7224:0.2776:0.0	.	56;72;87	Q11203-19;Q11203-13;Q11203-4	.;.;.	Q	87;72;56;87;72;56	ENSP00000262915:P87Q;ENSP00000361450:P72Q;ENSP00000316999:P56Q;ENSP00000354657:P87Q;ENSP00000361443:P72Q;ENSP00000361447:P56Q	ENSP00000262915:P87Q	P	+	2	0	ST3GAL3	44062995	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.185000	0.09684	0.583000	0.29574	-0.226000	0.12346	CCG	.	.	.	none		0.453	ST3GAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019964.1	NM_174963		A	44290408	C	A	44290408	1	1	193	0	1	0	0	0	0	0	0	0	15228	652	23	4		4	ST3GAL3	1	44290408	Intron	SNP	C	TCGA-HE-7128-01A-11D-1961-08	28333558	44290408	204960213	2	11514											
FAM151A	338094	hgsc.bcm.edu	37	chr1	55077353	55077353	+	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	ggtggacagcagtgttatccCggacgtagagcagatcttcc	9	9	13	10	2	1	2	0	0	1	2	3	4	3	4	2	3	2	4	2	3	2	3			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr1:55077353C>A	ENST00000302250.2	-	6	1026	c.866G>T	c.(865-867)cGg>cTg	p.R289L	FAM151A_ENST00000371304.2_Missense_Mutation_p.R289L|ACOT11_ENST00000371316.3_Intron	NM_176782.2	NP_788954.2	Q8WW52	F151A_HUMAN	family with sequence similarity 151, member A	289						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						AGTGTTATCCCGGACGTAGAG	0.577																																					p.R289L		Atlas-SNP	.											FAM151A,right_upper_lobe,carcinoma,-1,1	FAM151A	58	.	0			c.G866T						PASS	.						151	130	137					1																	55077353		2203	4300	6503	SO:0001583	missense	338094	exon6			TTATCCCGGACGT	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.866G>T	chr1.hg19:g.55077353C>A	ENSP00000306888:p.Arg289Leu	172.0	0.0	.		134.0	6.0	.	NM_176782	Q5VUG5|Q6DKH5|Q6UWV0|Q8NAX9|Q96KY5	Missense_Mutation	SNP	ENST00000302250.2	hg19	CCDS594.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.835893	0.91117	.	.	ENSG00000162391	ENST00000302250;ENST00000371304;ENST00000294370	T;T	0.14022	2.54;2.54	4.59	4.59	0.56863	.	0.078649	0.48767	D	0.000169	T	0.33411	0.0862	M	0.83953	2.67	0.80722	D	1	P	0.52577	0.954	P	0.53035	0.716	T	0.21008	-1.0258	10	0.54805	T	0.06	-29.9435	16.6818	0.85294	0.0:1.0:0.0:0.0	.	289	Q8WW52	F151A_HUMAN	L	289	ENSP00000306888:R289L;ENSP00000360353:R289L	ENSP00000294370:R289L	R	-	2	0	FAM151A	54849941	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	6.179000	0.71974	2.520000	0.84964	0.655000	0.94253	CGG	.	.	.	none		0.577	FAM151A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027342.1	NM_176782		A	55077353	C	A	55077353	3	1	193	1	0	0	0	0	1	0	0	0	5462	652	23	4	903	4	FAM151A	1	55077353	Missense_Mutation	SNP	C	TCGA-HE-7128-01A-11D-1961-08	10786945	55077353	194173268	3	11515											
CCDC88A	55704	hgsc.bcm.edu	37	chr2	55523606	55523606	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcatggtcatgaagcaggcTaaattctccactgctgtggc	9	11	10	11	0	3	1	2	1	1	0	4	1	3	1	1	3	2	3	1	3	3	2			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr2:55523606T>C	ENST00000436346.1	-	30	5720	c.4879A>G	c.(4879-4881)Agc>Ggc	p.S1627G	CCDC88A_ENST00000413716.2_Missense_Mutation_p.S1626G|CCDC88A_ENST00000336838.6_Missense_Mutation_p.S1626G|CCDC88A_ENST00000422883.2_Missense_Mutation_p.S128G|CCDC88A_ENST00000263630.8_Missense_Mutation_p.S1599G	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	1627					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						TGAAGCAGGCTAAATTCTCCA	0.453																																					p.S1626G		Atlas-SNP	.											.	CCDC88A	336	.	0			c.A4876G						PASS	.						119	105	110					2																	55523606		2203	4300	6503	SO:0001583	missense	55704	exon30			GCAGGCTAAATTC	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.4879A>G	chr2.hg19:g.55523606T>C	ENSP00000410608:p.Ser1627Gly	104.0	0.0	.		68.0	19.0	.	NM_001254943	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Missense_Mutation	SNP	ENST00000436346.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.68|14.68	2.606920|2.606920	0.46527|0.46527	.|.	.|.	ENSG00000115355|ENSG00000115355	ENST00000336838;ENST00000263630;ENST00000436346;ENST00000422883;ENST00000412148;ENST00000413716;ENST00000426576|ENST00000456975	T;T;T;T;T;T|.	0.52295|.	2.4;2.38;2.62;0.67;2.4;1.32|.	5.39|5.39	5.39|5.39	0.77823|0.77823	.|.	0.000000|.	0.56097|.	U|.	0.000024|.	T|.	0.69024|.	0.3065|.	L|L	0.54323|0.54323	1.7|1.7	0.58432|0.58432	D|D	0.999998|0.999998	B;D;D;D;B;D;D|.	0.63046|.	0.005;0.99;0.982;0.982;0.05;0.992;0.99|.	B;D;D;D;B;D;D|.	0.74674|.	0.012;0.979;0.952;0.961;0.019;0.984;0.979|.	T|.	0.67436|.	-0.5671|.	10|.	0.27082|.	T|.	0.32|.	-9.3716|-9.3716	15.4218|15.4218	0.75018|0.75018	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1626;1599;1544;128;1627;1626;1598|.	B7ZM78;Q3V6T2-2;D6W5D1;B3KW94;Q3V6T2;Q3V6T2-3;Q3V6T2-4|.	.;.;.;.;GRDN_HUMAN;.;.|.	G|W	1626;1599;1627;128;644;1626;802|579	ENSP00000338728:S1626G;ENSP00000263630:S1599G;ENSP00000410608:S1627G;ENSP00000390012:S644G;ENSP00000404431:S1626G;ENSP00000405080:S802G|.	ENSP00000263630:S1599G|.	S|X	-|-	1|2	0|0	CCDC88A|CCDC88A	55377110|55377110	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.274000|7.274000	0.78538|0.78538	2.051000|2.051000	0.60960|0.60960	0.383000|0.383000	0.25322|0.25322	AGC|TAG	.	.	.	none		0.453	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding		NM_017571		C	55523606	T	C	55523606	3	2	193	1	0	0	0	0	1	0	0	0	2865	1522	53	3	748	3	CCDC88A	2	55523606	Missense_Mutation	SNP	T	TCGA-HE-7128-01A-11D-1961-08		55523606	187675767	4	11516											
FAM161A	84140	hgsc.bcm.edu	37	chr2	62067675	62067675	+	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	caggctctgaaaatgatgtcAttaatgagacagggtgatag	14	10	12	5	0	2	4	1	4	1	1	2	5	2	4	0	2	0	1	0	2	4	2			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr2:62067675A>T	ENST00000405894.3	-	3	565	c.464T>A	c.(463-465)aTg>aAg	p.M155K	FAM161A_ENST00000404929.1_Missense_Mutation_p.M155K	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	155					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						AAATGATGTCATTAATGAGAC	0.363																																					p.M155K		Atlas-SNP	.											.	FAM161A	200	.	0			c.T464A						PASS	.						104	91	95					2																	62067675		1846	4096	5942	SO:0001583	missense	84140	exon3			GATGTCATTAATG		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.464T>A	chr2.hg19:g.62067675A>T	ENSP00000385893:p.Met155Lys	90.0	0.0	.		67.0	8.0	.	NM_032180	B4DJV7|Q9H8R2	Missense_Mutation	SNP	ENST00000405894.3	hg19	CCDS42687.2	.	.	.	.	.	.	.	.	.	.	A	12.65	2.002006	0.35320	.	.	ENSG00000170264	ENST00000404929;ENST00000405894	T;T	0.20598	2.87;2.06	5.3	-0.661	0.11417	.	1.199220	0.05573	N	0.571416	T	0.17323	0.0416	L	0.51422	1.61	0.09310	N	1	B;B	0.28233	0.204;0.018	B;B	0.21708	0.036;0.013	T	0.29119	-1.0022	9	.	.	.	-6.764	4.6748	0.12706	0.4925:0.0:0.1664:0.3411	.	155;155	Q3B820;Q3B820-3	F161A_HUMAN;.	K	155	ENSP00000385158:M155K;ENSP00000385893:M155K	.	M	-	2	0	FAM161A	61921179	0.001000	0.12720	0.000000	0.03702	0.743000	0.42351	0.901000	0.28445	-0.003000	0.14444	-0.490000	0.04691	ATG	.	.	.	none		0.363	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180		T	62067675	A	T	62067675	3	4	193	1	0	0	0	0	1	0	0	0	5476	217	8	5	1534	5	FAM161A	2	62067675	Missense_Mutation	SNP	A	TCGA-HE-7128-01A-11D-1961-08	6544069	62067675	181131698	5	11517											
MAT2A	4144	hgsc.bcm.edu	37	chr2	85770091	85770091	+	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	ccattatggtacctctcagaAgagtgagagagagctattag	13	10	11	7	0	1	4	1	1	1	4	2	6	1	4	2	1	2	2	2	1	5	4			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr2:85770091A>T	ENST00000306434.3	+	8	1142	c.1019A>T	c.(1018-1020)aAg>aTg	p.K340M	MAT2A_ENST00000409017.1_Missense_Mutation_p.K277M	NM_005911.5	NP_005902.1	P31153	METK2_HUMAN	methionine adenosyltransferase II, alpha	340					cellular nitrogen compound metabolic process (GO:0034641)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|methionine adenosyltransferase complex (GO:0048269)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methionine adenosyltransferase activity (GO:0004478)			breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	9					L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	ACCTCTCAGAAGAGTGAGAGA	0.398																																					p.K340M		Atlas-SNP	.											.	MAT2A	23	.	0			c.A1019T						PASS	.						153	156	155					2																	85770091		2203	4300	6503	SO:0001583	missense	4144	exon8			CTCAGAAGAGTGA		CCDS1977.1	2p11.2	2008-06-03			ENSG00000168906	ENSG00000168906			6904	protein-coding gene	gene with protein product		601468				1426236, 9703951	Standard	NM_005911		Approved	SAMS2, MATA2, MATII	uc002spr.3	P31153	OTTHUMG00000130174	ENST00000306434.3:c.1019A>T	chr2.hg19:g.85770091A>T	ENSP00000303147:p.Lys340Met	172.0	0.0	.		143.0	28.0	.	NM_005911	A8K511|B4DN45|D6W5L1|Q53SP5	Missense_Mutation	SNP	ENST00000306434.3	hg19	CCDS1977.1	.	.	.	.	.	.	.	.	.	.	A	13.85	2.358960	0.41801	.	.	ENSG00000168906	ENST00000306434;ENST00000424323;ENST00000409017	D;D	0.97688	-4.49;-4.49	5.8	5.8	0.92144	S-adenosylmethionine synthetase, C-terminal (1);S-adenosylmethionine synthetase superfamily (1);	0.000000	0.85682	D	0.000000	D	0.95230	0.8453	L	0.39692	1.235	0.58432	D	0.999993	B;B	0.16802	0.019;0.019	B;B	0.18263	0.021;0.021	D	0.92657	0.6138	10	0.31617	T	0.26	-9.6104	14.0949	0.65013	1.0:0.0:0.0:0.0	.	340;340	B4DEX8;P31153	.;METK2_HUMAN	M	340;121;277	ENSP00000303147:K340M;ENSP00000386353:K277M	ENSP00000303147:K340M	K	+	2	0	MAT2A	85623602	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.899000	0.69846	2.209000	0.71365	0.460000	0.39030	AAG	.	.	.	none		0.398	MAT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252491.2	NM_005911		T	85770091	A	T	85770091	3	4	193	1	0	0	0	0	1	0	0	0	9337	72	3	5	1049	5	MAT2A	2	85770091	Missense_Mutation	SNP	A	TCGA-HE-7128-01A-11D-1961-08	23702416	85770091	157429282	6	11518											
PHOSPHO2	493911	hgsc.bcm.edu	37	chr2	170557930	170557930	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgcaatagatgcccaaagaAtctttgcaaaaaggtagttt	15	12	8	6	0	1	2	0	0	1	2	1	2	1	2	1	1	3	4	1	1	7	5			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr2:170557930A>G	ENST00000359744.3	+	4	837	c.449A>G	c.(448-450)aAt>aGt	p.N150S	KLHL23_ENST00000272797.4_Intron|KLHL23_ENST00000602521.1_Intron	NM_001008489.3|NM_001199285.1|NM_001199286.1|NM_001199288.1	NP_001008489.1|NP_001186214.1|NP_001186215.1|NP_001186217.1	Q8TCD6	PHOP2_HUMAN	phosphatase, orphan 2	150							metal ion binding (GO:0046872)|pyridoxal phosphatase activity (GO:0033883)			breast(1)|large_intestine(1)|lung(6)|skin(2)	10						TGCCCAAAGAATCTTTGCAAA	0.308																																					p.N150S		Atlas-SNP	.											.	PHOSPHO2	27	.	0			c.A449G						PASS	.						64	65	64					2																	170557930		2203	4299	6502	SO:0001583	missense	493911	exon4			CAAAGAATCTTTG	BC022324	CCDS33319.1	2q31.1	2008-02-05			ENSG00000144362	ENSG00000144362			28316	protein-coding gene	gene with protein product						16054448	Standard	NM_001199285		Approved	MGC22679	uc021vsh.1	Q8TCD6	OTTHUMG00000153981	ENST00000359744.3:c.449A>G	chr2.hg19:g.170557930A>G	ENSP00000352782:p.Asn150Ser	90.0	0.0	.		75.0	13.0	.	NM_001199286	B2RC30|D3DPC7	Missense_Mutation	SNP	ENST00000359744.3	hg19	CCDS33319.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.082674	0.76528	.	.	ENSG00000144362	ENST00000359744	T	0.61980	0.06	5.96	5.96	0.96718	HAD-like domain (2);	0.000000	0.85682	U	0.000000	D	0.82508	0.5052	M	0.89353	3.025	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.84925	0.0856	10	0.52906	T	0.07	.	16.4219	0.83766	1.0:0.0:0.0:0.0	.	150	Q8TCD6	PHOP2_HUMAN	S	150	ENSP00000352782:N150S	ENSP00000352782:N150S	N	+	2	0	PHOSPHO2	170266176	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.155000	0.89643	2.282000	0.76494	0.533000	0.62120	AAT	.	.	.	none		0.308	PHOSPHO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333304.1	NM_001008489		G	170557930	A	G	170557930	3	3	193	1	0	0	0	0	1	0	0	0	11864	101	4	3	451	3	PHOSPHO2	2	170557930	Missense_Mutation	SNP	A	TCGA-HE-7128-01A-11D-1961-08	84787839	170557930	72641443	7	11519											
PSMD1	5707	hgsc.bcm.edu	37	chr2	231943417	231943417	+	Frame_Shift_Del	DEL	A	A	-																															catactgcaaccgttatagcAaactcttttatgcactgtgg																										TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr2:231943417delA	ENST00000308696.6	+	10	1278	c.1116delA	c.(1114-1116)gcafs	p.A372fs	PSMD1_ENST00000409643.1_Frame_Shift_Del_p.A372fs|PSMD1_ENST00000373635.4_Frame_Shift_Del_p.A372fs	NM_002807.3	NP_002798.2	Q99460	PSMD1_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 1	372					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)	31		Ovarian(221;0.000626)|Medulloblastoma(418;0.0109)|Renal(207;0.0112)|Lung NSC(271;0.0538)|all_lung(227;0.0713)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;4e-26)|LUSC - Lung squamous cell carcinoma(224;0.0138)|Lung(119;0.0168)	Bortezomib(DB00188)	CCGTTATAGCAAACTCTTTTA	0.343																																					p.A372fs		Atlas-INDEL	.											.	PSMD1	77	.	0			c.1115delC						PASS	.						126	120	122					2																	231943417		2203	4300	6503	SO:0001589	frameshift_variant	5707	exon10			.	D44466	CCDS2482.1, CCDS54436.1	2q37.1	2008-05-22			ENSG00000173692	ENSG00000173692		"Proteasome (prosome, macropain) subunits"	9554	protein-coding gene	gene with protein product						8816993	Standard	NM_002807		Approved	S1, P112, Rpn2	uc002vrn.2	Q99460	OTTHUMG00000133223	ENST00000308696.6:c.1116delA	chr2.hg19:g.231943417delA	ENSP00000309474:p.Ala372fs	92.0	0.0	0		85.0	12.0	0.141176	NM_001191037	B8ZZH9|Q24JU0|Q53TI2|Q6GMU5|Q6P2P4|Q6PJM7|Q6PKG9|Q86VU1|Q8IV79	Frame_Shift_Del	DEL	ENST00000308696.6	hg19	CCDS2482.1																																																																																			.	.	.	none		0.343	PSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256958.2			-	231943417	A	-	231943417	7	5	193	1	0	1	0	1	0	0	0	0	12702	117	5	0	1154	0	PSMD1	2	231943417	Frame_Shift_Del	DEL	A	TCGA-HE-7128-01A-11D-1961-08	61385487	231943417	11255956	8	11520											
OR6B2	389090	hgsc.bcm.edu	37	chr2	240969643	240969643	+	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	gacacgtaccagatctccagGaaagacatggagctcagaaa	16	5	10	10	1	2	3	1	0	1	3	3	6	2	5	2	2	2	2	2	2	3	1			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr2:240969643G>C	ENST00000402971.2	-	1	263	c.204C>G	c.(202-204)ttC>ttG	p.F68L		NM_001005853.1	NP_001005853.1	Q6IFH4	OR6B2_HUMAN	olfactory receptor, family 6, subfamily B, member 2	68						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(4)|lung(9)|prostate(1)	15		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;3.4e-29)|all cancers(36;2.08e-27)|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)		AGATCTCCAGGAAAGACATGG	0.557																																					p.F68L		Atlas-SNP	.											.	OR6B2	30	.	0			c.C204G						PASS	.						117	127	124					2																	240969643		2117	4242	6359	SO:0001583	missense	389090	exon1			CTCCAGGAAAGAC		CCDS46559.1	2q37.3	2012-08-09	2004-10-07	2004-10-07	ENSG00000182083	ENSG00000182083		"GPCR / Class A : Olfactory receptors"	15041	protein-coding gene	gene with protein product			"olfactory receptor, family 6, subfamily B, member 2 pseudogene"	OR6B2P			Standard	XM_005247004		Approved		uc010zoc.2	Q6IFH4	OTTHUMG00000152400	ENST00000402971.2:c.204C>G	chr2.hg19:g.240969643G>C	ENSP00000384563:p.Phe68Leu	242.0	0.0	.		168.0	20.0	.	NM_001005853	B2RPR3|Q8NGW0	Missense_Mutation	SNP	ENST00000402971.2	hg19	CCDS46559.1	.	.	.	.	.	.	.	.	.	.	N	4.356	0.065626	0.08388	.	.	ENSG00000182083	ENST00000402971	T	0.00966	5.49	4.35	0.501	0.16925	GPCR, rhodopsin-like superfamily (1);	0.813827	0.10478	N	0.669897	T	0.00967	0.0032	L	0.29908	0.895	0.09310	N	1	B	0.19583	0.037	B	0.22601	0.04	T	0.45818	-0.9235	10	0.38643	T	0.18	.	8.2409	0.31660	0.3395:0.0:0.6605:0.0	.	68	Q6IFH4	OR6B2_HUMAN	L	68	ENSP00000384563:F68L	ENSP00000384563:F68L	F	-	3	2	OR6B2	240618316	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.228000	0.09114	-0.029000	0.13827	-0.237000	0.12165	TTC	.	.	.	none		0.557	OR6B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326079.1	NM_001005853		C	240969643	G	C	240969643	3	2	193	1	0	0	0	0	1	0	0	0	11195	1165	41	4	736	4	OR6B2	2	240969643	Missense_Mutation	SNP	G	TCGA-HE-7128-01A-11D-1961-08	9026226	240969643	2229730	9	11521											
ERC2	26059	hgsc.bcm.edu	37	chr3	56026194	56026194	+	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	ggccttgccacactcgtcgcGgtagtaagacgcctctttat	7	11	10	13	4	1	1	0	0	1	1	3	1	1	1	3	2	1	2	3	2	3	5			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr3:56026194G>T	ENST00000288221.6	-	11	2401	c.2146C>A	c.(2146-2148)Cgc>Agc	p.R716S		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	716						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)		CACTCGTCGCGGTAGTAAGAC	0.473																																					p.R716S		Atlas-SNP	.											ERC2_ENST00000288221,caecum,carcinoma,0,2	ERC2	221	.	0			c.C2146A						PASS	.						192	187	189					3																	56026194		1911	4126	6037	SO:0001583	missense	26059	exon11			CGTCGCGGTAGTA	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.2146C>A	chr3.hg19:g.56026194G>T	ENSP00000288221:p.Arg716Ser	308.0	1.0	.		317.0	14.0	.	NM_015576	Q2T9F6|Q86TK4	Missense_Mutation	SNP	ENST00000288221.6	hg19	CCDS46851.1	.	.	.	.	.	.	.	.	.	.	G	14.99	2.699414	0.48307	.	.	ENSG00000187672	ENST00000288221	T	0.43688	0.94	5.69	5.69	0.88448	.	0.049024	0.85682	D	0.000000	T	0.42404	0.1201	M	0.70275	2.135	0.40723	D	0.982676	P	0.34815	0.47	B	0.30646	0.118	T	0.48625	-0.9019	10	0.66056	D	0.02	-8.2645	12.8431	0.57815	0.0:0.0:0.7287:0.2713	.	716	O15083	ERC2_HUMAN	S	716	ENSP00000288221:R716S	ENSP00000288221:R716S	R	-	1	0	ERC2	56001234	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	4.782000	0.62396	2.699000	0.92147	0.591000	0.81541	CGC	.	.	.	none		0.473	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576		T	56026194	G	T	56026194	3	4	193	1	0	0	0	0	1	0	0	0	5213	1116	39	4	745	4	ERC2	3	56026194	Missense_Mutation	SNP	G	TCGA-HE-7128-01A-11D-1961-08		56026194	141996236	10	11522											
DZIP3	9666	hgsc.bcm.edu	37	chr3	108324275	108324275	+	Frame_Shift_Del	DEL	T	T	-																															tggattctctaccagatgaaTtttttgtgaggtaaggccac																										TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr3:108324275delT	ENST00000361582.3	+	2	252	c.22delT	c.(22-24)tttfs	p.F9fs	DZIP3_ENST00000463306.1_Frame_Shift_Del_p.F9fs	NM_014648.3	NP_055463.1	Q86Y13	DZIP3_HUMAN	DAZ interacting zinc finger protein 3	9					protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(21)|ovary(1)|pancreas(1)|prostate(5)|skin(1)	45						ACCAGATGAATTTTTTGTGAG	0.443																																					p.E7fs		Atlas-INDEL	.											.	DZIP3	111	.	0			c.21delA						PASS	.						111	116	114					3																	108324275		2203	4300	6503	SO:0001589	frameshift_variant	9666	exon2			.	AF279370	CCDS2952.1	3q13.13	2013-05-22	2013-05-22		ENSG00000198919	ENSG00000198919		"RING-type (C3HC4) zinc fingers", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	30938	protein-coding gene	gene with protein product	"human RNA-binding ubiquitin ligase of 138 kDa", "protein phosphatase 1, regulatory subunit 66"	608672	"DAZ interacting protein 3, zinc finger"			9734811, 12538761	Standard	NM_014648		Approved	hRUL138, PPP1R66	uc003dxd.3	Q86Y13	OTTHUMG00000159232	ENST00000361582.3:c.22delT	chr3.hg19:g.108324275delT	ENSP00000355028:p.Phe9fs	94.0	0.0	0		96.0	20.0	0.208333	NM_014648	B3KN01|O75162|Q6P3R9|Q6PH82|Q86Y14|Q86Y15|Q86Y16|Q8IWI0|Q96RS9	Frame_Shift_Del	DEL	ENST00000361582.3	hg19	CCDS2952.1																																																																																			.	.	.	none		0.443	DZIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353968.1	NM_014648		-	108324275	T	-	108324275	7	5	193	1	0	1	0	1	0	0	0	0	4867	1493	52	0	24	0	DZIP3	3	108324275	Frame_Shift_Del	DEL	T	TCGA-HE-7128-01A-11D-1961-08	52298081	108324275	89698155	11	11523											
LIPH	200879	hgsc.bcm.edu	37	chr3	185241864	185241865	+	Frame_Shift_Del	DEL	AA	AA	-																															aatataaaggcttacctcccAatattgttttggggcagcca																										TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr3:185241864_185241865delAA	ENST00000296252.4	-	5	853_854	c.712_713delTT	c.(712-714)ttgfs	p.L238fs	LIPH_ENST00000424591.2_Frame_Shift_Del_p.L204fs	NM_139248.2	NP_640341.1	Q8WWY8	LIPH_HUMAN	lipase, member H	238					lipid catabolic process (GO:0016042)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(2)	20	all_cancers(143;8.87e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			CTTACCTCCCAATATTGTTTTG	0.436																																					p.238_238del		Atlas-INDEL	.											.	LIPH	56	.	0			c.713_714del						PASS	.																																			SO:0001589	frameshift_variant	200879	exon5			.	AY093498	CCDS3272.1	3q27	2012-07-31			ENSG00000163898	ENSG00000163898			18483	protein-coding gene	gene with protein product		607365				12213196, 12063250	Standard	XM_006713529		Approved	mPA-PLA1, PLA1B, mPA-PLA1alpha, LPDLR	uc003fpm.3	Q8WWY8	OTTHUMG00000156657	ENST00000296252.4:c.712_713delTT	chr3.hg19:g.185241864_185241865delAA	ENSP00000296252:p.Leu238fs	60.0	0.0	0		63.0	24.0	0.380952	NM_139248	A2IBA7|Q8TEC7	Frame_Shift_Del	DEL	ENST00000296252.4	hg19	CCDS3272.1																																																																																			.	.	.	none		0.436	LIPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345153.1			-	185241865	AA	-	185241864	7	5	193	1	0	1	0	1	0	0	0	0	8831	131	5	0	666	0	LIPH	3	185241864	Frame_Shift_Del	DEL	AA	TCGA-HE-7128-01A-11D-1961-08	76917589	185241864	12780566	12	11524											
THAP9	79725	hgsc.bcm.edu	37	chr4	83839493	83839493	+	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	aggcattactagacctgtcaGatcataggcgaaatctcatc	13	10	8	10	1	3	2	3	0	1	2	5	3	3	2	1	2	1	1	1	2	4	3			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr4:83839493G>A	ENST00000302236.5	+	5	2179	c.2128G>A	c.(2128-2130)Gat>Aat	p.D710N	LIN54_ENST00000505905.1_Intron	NM_024672.4	NP_078948.3	Q9H5L6	THAP9_HUMAN	THAP domain containing 9	710					DNA integration (GO:0015074)|DNA recombination (GO:0006310)|transposition, DNA-mediated (GO:0006313)		metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transferase activity (GO:0016740)|transposase activity (GO:0004803)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(13)|lung(5)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(3)	33		Hepatocellular(203;0.114)				AGACCTGTCAGATCATAGGCG	0.423																																					p.D710N		Atlas-SNP	.											.	THAP9	65	.	0			c.G2128A						PASS	.						117	101	106					4																	83839493		2203	4300	6503	SO:0001583	missense	79725	exon5			CTGTCAGATCATA	AK091412	CCDS3598.1	4q21.3	2013-01-25			ENSG00000168152	ENSG00000168152		"THAP (C2CH-type zinc finger) domain containing"	23192	protein-coding gene	gene with protein product		612537				12575992	Standard	NM_024672		Approved	FLJ34093	uc003hnt.2	Q9H5L6	OTTHUMG00000130291	ENST00000302236.5:c.2128G>A	chr4.hg19:g.83839493G>A	ENSP00000305533:p.Asp710Asn	101.0	0.0	.		107.0	26.0	.	NM_024672	B3KRE2|Q59AC9	Missense_Mutation	SNP	ENST00000302236.5	hg19	CCDS3598.1	.	.	.	.	.	.	.	.	.	.	G	3.185	-0.167102	0.06461	.	.	ENSG00000168152	ENST00000302236;ENST00000536314	D	0.90069	-2.61	3.87	3.02	0.34903	.	0.462748	0.18401	N	0.142355	T	0.77805	0.4185	N	0.22421	0.69	0.09310	N	0.999994	B	0.23058	0.079	B	0.21546	0.035	T	0.62124	-0.6920	10	0.22706	T	0.39	-12.7397	5.7567	0.18176	0.1093:0.218:0.6727:0.0	.	710	Q9H5L6	THAP9_HUMAN	N	710	ENSP00000305533:D710N	ENSP00000305533:D710N	D	+	1	0	THAP9	84058517	0.016000	0.18221	0.085000	0.20634	0.025000	0.11179	1.445000	0.35079	1.203000	0.43233	0.655000	0.94253	GAT	.	.	.	none		0.423	THAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252633.1	NM_024672		A	83839493	G	A	83839493	3	1	193	1	0	0	0	0	1	0	0	0	15863	942	33	2	2146	2	THAP9	4	83839493	Missense_Mutation	SNP	G	TCGA-HE-7128-01A-11D-1961-08		83839493	107314783	13	11525											
NR3C2	4306	hgsc.bcm.edu	37	chr4	149075914	149075914	+	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	gaaccagtgctgtgttgaccGagggttcttttgcaggagcg	7	11	15	8	2	1	1	0	1	1	0	1	4	1	2	2	2	4	4	2	2	1	4			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr4:149075914G>C	ENST00000358102.3	-	5	2515	c.2153C>G	c.(2152-2154)tCg>tGg	p.S718W	NR3C2_ENST00000355292.3_Missense_Mutation_p.S722W|NR3C2_ENST00000503313.1_5'UTR|NR3C2_ENST00000512865.1_Intron|NR3C2_ENST00000511528.1_Missense_Mutation_p.S722W|NR3C2_ENST00000344721.4_Missense_Mutation_p.S718W|RP11-76G10.1_ENST00000514843.1_RNA	NM_000901.4|NM_001166104.1	NP_000892.2|NP_001159576.1	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	718	Hinge.				gene expression (GO:0010467)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|receptor complex (GO:0043235)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.S718L(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)	TGTGTTGACCGAGGGTTCTTT	0.567																																					p.S718W	Melanoma(27;428 957 40335 51025 51111)	Atlas-SNP	.											NR3C2,colon,carcinoma,0,1	NR3C2	94	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2153G						PASS	.						192	172	179					4																	149075914		2203	4300	6503	SO:0001583	missense	4306	exon5			TTGACCGAGGGTT	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.2153C>G	chr4.hg19:g.149075914G>C	ENSP00000350815:p.Ser718Trp	289.0	0.0	.		177.0	30.0	.	NM_000901	B0ZBF5|B0ZBF7|Q2NKL1|Q96KQ8|Q96KQ9	Missense_Mutation	SNP	ENST00000358102.3	hg19	CCDS3772.1	.	.	.	.	.	.	.	.	.	.	G	15.76	2.928892	0.52759	.	.	ENSG00000151623	ENST00000344721;ENST00000355292;ENST00000358102;ENST00000511528	D;D;D;D	0.90676	-2.71;-2.71;-2.71;-2.71	5.57	5.57	0.84162	.	0.406531	0.27932	N	0.017264	D	0.94318	0.8174	M	0.77313	2.365	0.52501	D	0.99995	D	0.63880	0.993	P	0.56514	0.8	D	0.93801	0.7101	9	.	.	.	.	19.5581	0.95361	0.0:0.0:1.0:0.0	.	718	B0ZBF6	.	W	718;722;718;722	ENSP00000341390:S718W;ENSP00000347441:S722W;ENSP00000350815:S718W;ENSP00000421481:S722W	.	S	-	2	0	NR3C2	149295364	0.985000	0.35326	0.611000	0.29010	0.430000	0.31655	3.814000	0.55643	2.614000	0.88457	0.655000	0.94253	TCG	.	.	.	none		0.567	NR3C2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364986.1			C	149075914	G	C	149075914	3	2	193	1	0	0	0	0	1	0	0	0	10638	1059	37	4	821	4	NR3C2	4	149075914	Missense_Mutation	SNP	G	TCGA-HE-7128-01A-11D-1961-08	65236421	149075914	42078362	14	11526											
SFRS12	140890	hgsc.bcm.edu	37	chr5	65466769	65466769	+	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	atcgcgaagatctcgtagttCcagcaggtttgataatgctt	10	13	10	8	3	1	2	0	1	1	1	4	3	2	2	1	1	2	5	1	1	3	5			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr5:65466769C>T	ENST00000380918.3	+	10	1790	c.1130C>T	c.(1129-1131)tCc>tTc	p.S377F	SREK1_ENST00000284041.3_3'UTR|SREK1_ENST00000334121.6_Missense_Mutation_p.S493F	NM_139168.3	NP_631907.1	Q8WXA9	SREK1_HUMAN	splicing regulatory glutamine/lysine-rich protein 1	377	Arg/Glu/Lys/Ser-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|kidney(3)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)	9						TCTCGTAGTTCCAGCAGGTTT	0.368																																					p.S493F	GBM(10;31 347 27684 38976 41583)	Atlas-SNP	.											.	SREK1	58	.	0			c.C1478T						PASS	.						60	66	64					5																	65466769		2200	4297	6497	SO:0001583	missense	140890	exon9			GTAGTTCCAGCAG	AF459094	CCDS3991.1, CCDS43323.1, CCDS75253.1	5q11.2-q12.1	2013-02-12	2010-09-08	2010-09-08	ENSG00000153914	ENSG00000153914		"RNA binding motif (RRM) containing"	17882	protein-coding gene	gene with protein product	"serine-arginine-rich splicing regulatory protein 508"	609268	"splicing factor, arginine/serine-rich 12"	SFRS12		12043562	Standard	NM_001077199		Approved	DKFZp564B176, SRrp86, SRrp508	uc003jun.4	Q8WXA9	OTTHUMG00000097809	ENST00000380918.3:c.1130C>T	chr5.hg19:g.65466769C>T	ENSP00000370305:p.Ser377Phe	63.0	0.0	.		69.0	17.0	.	NM_001077199	A4FTW3|Q2M1J0|Q86X37	Missense_Mutation	SNP	ENST00000380918.3	hg19	CCDS3991.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.67|16.67	3.186680|3.186680	0.57909|0.57909	.|.	.|.	ENSG00000153914|ENSG00000153914	ENST00000537482|ENST00000334121;ENST00000380918	.|T;T	.|0.11821	.|2.74;2.74	5.15|5.15	5.15|5.15	0.70609|0.70609	.|.	.|0.330683	.|0.31167	.|N	.|0.008136	T|T	0.11580|0.11580	0.0282|0.0282	N|N	0.19112|0.19112	0.55|0.55	0.31022|0.31022	N|N	0.718059|0.718059	.|P;P	.|0.40794	.|0.61;0.729	.|B;B	.|0.38056	.|0.135;0.264	T|T	0.02269|0.02269	-1.1185|-1.1185	6|10	0.44086|0.56958	T|D	0.13|0.05	.|.	18.2481|18.2481	0.89993|0.89993	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|377;493	.|Q8WXA9;Q8WXA9-2	.|SREK1_HUMAN;.	S|F	493|493;377	.|ENSP00000334538:S493F;ENSP00000370305:S377F	ENSP00000445557:P493S|ENSP00000334538:S493F	P|S	+|+	1|2	0|0	SREK1|SREK1	65502525|65502525	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	4.322000|4.322000	0.59215|0.59215	2.409000|2.409000	0.81822|0.81822	0.650000|0.650000	0.86243|0.86243	CCA|TCC	.	.	.	none		0.368	SREK1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381118.1	NM_001077199		T	65466769	C	T	65466769	3	4	193	1	0	0	0	0	1	0	0	0	14180	855	30	2	1512	2	SFRS12	5	65466769	Missense_Mutation	SNP	C	TCGA-HE-7128-01A-11D-1961-08		65466769	115448491	15	11527											
STK32A	202374	hgsc.bcm.edu	37	chr5	146752790	146752790	+	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	atctgatgtccagaacttccCgtatatgaatgatataaact	14	13	6	8	1	1	4	0	3	1	1	3	4	3	4	2	0	2	1	2	0	7	5			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr5:146752790C>A	ENST00000397936.3	+	10	1169	c.836C>A	c.(835-837)cCg>cAg	p.P279Q	STK32A_ENST00000398523.3_Missense_Mutation_p.P279Q	NM_001112724.1	NP_001106195.1	Q8WU08	ST32A_HUMAN	serine/threonine kinase 32A	279	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.P279Q(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|prostate(1)|skin(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGAACTTCCCGTATATGAAT	0.398																																					p.P279Q		Atlas-SNP	.											.	STK32A	54	.	1	Substitution - Missense(1)	lung(1)	c.C836A						PASS	.						166	154	158					5																	146752790		1568	3582	5150	SO:0001583	missense	202374	exon10			ACTTCCCGTATAT		CCDS47299.1, CCDS75351.1	5q32	2008-02-05			ENSG00000169302	ENSG00000169302			28317	protein-coding gene	gene with protein product						12477932	Standard	NM_001112724		Approved	MGC22688, YANK1	uc010jgn.1	Q8WU08	OTTHUMG00000163411	ENST00000397936.3:c.836C>A	chr5.hg19:g.146752790C>A	ENSP00000381030:p.Pro279Gln	268.0	0.0	.		242.0	10.0	.	NM_001112724	B3KSY0	Missense_Mutation	SNP	ENST00000397936.3	hg19	CCDS47299.1	.	.	.	.	.	.	.	.	.	.	C	18.57	3.653447	0.67472	.	.	ENSG00000169302	ENST00000397936;ENST00000398523	T;T	0.31247	1.5;1.5	5.68	5.68	0.88126	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.170944	0.28187	N	0.016272	T	0.55924	0.1951	M	0.77313	2.365	0.80722	D	1	D;D;P	0.58620	0.983;0.961;0.861	P;P;P	0.60117	0.869;0.593;0.533	T	0.58803	-0.7572	10	0.72032	D	0.01	.	18.5479	0.91054	0.0:1.0:0.0:0.0	.	279;279;279	B7Z9H7;Q8WU08;Q8WU08-3	.;ST32A_HUMAN;.	Q	279	ENSP00000381030:P279Q;ENSP00000381535:P279Q	ENSP00000381030:P279Q	P	+	2	0	STK32A	146732983	1.000000	0.71417	0.960000	0.40013	0.482000	0.33219	5.407000	0.66363	2.676000	0.91093	0.591000	0.81541	CCG	.	.	.	none		0.398	STK32A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373306.1	NM_145001		A	146752790	C	A	146752790	3	1	193	1	0	0	0	0	1	0	0	0	15309	652	23	4	903	4	STK32A	5	146752790	Missense_Mutation	SNP	C	TCGA-HE-7128-01A-11D-1961-08	81286021	146752790	34162470	16	11528											
SCUBE3	222663	hgsc.bcm.edu	37	chr6	35213840	35213840	+	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	caagcgaggccaacagcgccCgtggcttccagattccctat	9	7	10	15	3	0	1	0	0	0	1	2	2	2	1	4	2	3	1	4	2	3	3	rs142335824	byFrequency	TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr6:35213840C>A	ENST00000274938.7	+	20	2719	c.2719C>A	c.(2719-2721)Cgt>Agt	p.R907S	SCUBE3_ENST00000394681.1_Missense_Mutation_p.R923S	NM_152753.2	NP_689966.2			signal peptide, CUB domain, EGF-like 3											breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	37						CAACAGCGCCCGTGGCTTCCA	0.542																																					p.R907S		Atlas-SNP	.											.	SCUBE3	99	.	0			c.C2719A						PASS	.						144	148	147					6																	35213840		2203	4300	6503	SO:0001583	missense	222663	exon20			AGCGCCCGTGGCT	AF452494.1	CCDS4800.1	6p21.3	2008-02-05	2004-05-19	2004-05-21		ENSG00000146197			13655	protein-coding gene	gene with protein product		614708	"CUB domain and EGF-like repeat containing 3"	CEGF3		12270931	Standard	NM_152753		Approved	FLJ34743	uc003okf.1	Q8IX30		ENST00000274938.7:c.2719C>A	chr6.hg19:g.35213840C>A	ENSP00000274938:p.Arg907Ser	278.0	0.0	.		186.0	8.0	.	NM_152753		Missense_Mutation	SNP	ENST00000274938.7	hg19	CCDS4800.1	.	.	.	.	.	.	.	.	.	.	C	19.30	3.800654	0.70567	.	.	ENSG00000146197	ENST00000394681;ENST00000274938	T;T	0.17691	2.26;2.26	5.63	4.68	0.58851	CUB (5);	0.000000	0.85682	D	0.000000	T	0.21145	0.0509	L	0.28054	0.825	0.47659	D	0.999488	D;D	0.76494	0.998;0.999	D;D	0.85130	0.994;0.997	T	0.02437	-1.1159	10	0.87932	D	0	.	15.5773	0.76400	0.2218:0.7782:0.0:0.0	.	923;907	Q8IX30-2;Q8IX30	.;SCUB3_HUMAN	S	923;907	ENSP00000378174:R923S;ENSP00000274938:R907S	ENSP00000274938:R907S	R	+	1	0	SCUBE3	35321818	0.995000	0.38212	1.000000	0.80357	0.979000	0.70002	1.636000	0.37144	2.659000	0.90383	0.650000	0.86243	CGT	.	C|1.000;T|0.000	.	alt		0.542	SCUBE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040275.1	NM_152753		A	35213840	C	A	35213840	3	1	193	1	0	0	0	0	1	0	0	0	13959	652	23	4	2797	4	SCUBE3	6	35213840	Missense_Mutation	SNP	C	TCGA-HE-7128-01A-11D-1961-08		35213840	135901227	17	11529											
SGK1	6446	hgsc.bcm.edu	37	chr6	134495704	134495704	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aataaagtcgttcagacccaTcctcctctgcttcatgaaag	12	11	6	12	1	3	2	2	1	1	1	6	2	5	2	3	0	1	2	3	0	4	3			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr6:134495704T>C	ENST00000237305.7	-	2	185	c.97A>G	c.(97-99)Atg>Gtg	p.M33V	SGK1_ENST00000413996.3_Missense_Mutation_p.M47V|SGK1_ENST00000367858.5_Missense_Mutation_p.M128V|SGK1_ENST00000489458.2_5'Flank|SGK1_ENST00000528577.1_Missense_Mutation_p.M61V|SGK1_ENST00000475719.2_Missense_Mutation_p.M33V|SGK1_ENST00000367857.5_Missense_Mutation_p.M23V	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	33	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)		TTCAGACCCATCCTCCTCTGC	0.423											OREG0017675	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.M128V		Atlas-SNP	.											.	SGK1	387	.	0			c.A382G						PASS	.						81	81	81					6																	134495704		2203	4300	6503	SO:0001583	missense	6446	exon4			GACCCATCCTCCT	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.97A>G	chr6.hg19:g.134495704T>C	ENSP00000237305:p.Met33Val	70.0	0.0	.	1611	51.0	7.0	.	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	hg19	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	T	16.43	3.121060	0.56613	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T;T	0.38401	1.66;1.66;1.66;1.66;1.66;1.66;1.14	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.47488	0.1448	M	0.62723	1.935	0.80722	D	1	B;P;B;B;B;B	0.48911	0.01;0.917;0.004;0.001;0.019;0.002	B;D;B;B;B;B	0.63488	0.018;0.915;0.008;0.01;0.032;0.008	T	0.38628	-0.9652	10	0.41790	T	0.15	.	16.3127	0.82898	0.0:0.0:0.0:1.0	.	61;47;33;23;128;33	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	V	128;47;33;23;61;33;97	ENSP00000356832:M128V;ENSP00000396242:M47V;ENSP00000237305:M33V;ENSP00000356831:M23V;ENSP00000434450:M61V;ENSP00000434302:M33V;ENSP00000435577:M97V	ENSP00000237305:M33V	M	-	1	0	SGK1	134537397	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.040000	0.89188	2.246000	0.74042	0.533000	0.62120	ATG	.	.	.	none		0.423	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			C	134495704	T	C	134495704	3	2	193	1	0	0	0	0	1	0	0	0	14220	1435	50	3	1242	3	SGK1	6	134495704	Missense_Mutation	SNP	T	TCGA-HE-7128-01A-11D-1961-08	99281864	134495704	36619363	18	11530											
MLL5	55904	hgsc.bcm.edu	37	chr7	104748161	104748161	+	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	agtgaactccaacttgagggAcctgacaccctcgcatcagt	11	8	9	13	1	1	3	1	3	0	0	3	4	2	4	3	1	2	1	3	1	2	1			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr7:104748161A>T	ENST00000311117.3	+	22	3802	c.3257A>T	c.(3256-3258)gAc>gTc	p.D1086V	KMT2E_ENST00000257745.4_Missense_Mutation_p.D1086V|KMT2E_ENST00000334914.7_Missense_Mutation_p.D141V|SRPK2_ENST00000493638.1_5'Flank|CTB-152G17.6_ENST00000607968.1_RNA|KMT2E_ENST00000334877.4_Missense_Mutation_p.D1086V	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	1086					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										AACTTGAGGGACCTGACACCC	0.498																																					p.D1086V		Atlas-SNP	.											.	MLL5	173	.	0			c.A3257T						PASS	.						83	82	82					7																	104748161		2203	4300	6503	SO:0001583	missense	55904	exon21			TGAGGGACCTGAC	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.3257A>T	chr7.hg19:g.104748161A>T	ENSP00000312379:p.Asp1086Val	54.0	0.0	.		65.0	22.0	.	NM_018682	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	hg19	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.704341	0.88924	.	.	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745;ENST00000334914	D;D;D;T	0.96136	-3.92;-3.2;-3.92;-0.21	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	D	0.96222	0.8768	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97101	0.9797	10	0.87932	D	0	.	16.5655	0.84588	1.0:0.0:0.0:0.0	.	1086	Q8IZD2	MLL5_HUMAN	V	1086;1086;1086;1006;1086;141	ENSP00000312379:D1086V;ENSP00000335599:D1086V;ENSP00000257745:D1086V;ENSP00000333986:D141V	ENSP00000257745:D1086V	D	+	2	0	MLL5	104535397	1.000000	0.71417	0.995000	0.50966	0.997000	0.91878	8.690000	0.91272	2.302000	0.77476	0.533000	0.62120	GAC	.	.	.	none		0.498	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			T	104748161	A	T	104748161	3	4	193	1	0	0	0	0	1	0	0	0	9631	275	10	5	3335	5	MLL5	7	104748161	Missense_Mutation	SNP	A	TCGA-HE-7128-01A-11D-1961-08		104748161	54390502	19	11531											
TTC26	79989	hgsc.bcm.edu	37	chr7	138822639	138822639	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaggatactaatttgtggaTtggatattgtgcctttcacc	10	15	10	6	0	1	1	1	0	0	1	1	4	1	4	2	3	2	0	2	3	3	7			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr7:138822639T>C	ENST00000464848.1	+	3	268	c.188T>C	c.(187-189)aTt>aCt	p.I63T	TTC26_ENST00000343187.4_Intron|TTC26_ENST00000474035.2_Missense_Mutation_p.I63T|TTC26_ENST00000430935.1_Missense_Mutation_p.I63T|TTC26_ENST00000495038.1_Missense_Mutation_p.I63T|TTC26_ENST00000481482.1_3'UTR|TTC26_ENST00000478836.2_Missense_Mutation_p.I63T			A0AVF1	TTC26_HUMAN	tetratricopeptide repeat domain 26	63					cilium assembly (GO:0042384)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle B (GO:0030992)|primary cilium (GO:0072372)				breast(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	24						AATTTGTGGATTGGATATTGT	0.323																																					p.I63T		Atlas-SNP	.											.	TTC26	50	.	0			c.T188C						PASS	.						154	153	153					7																	138822639		2203	4300	6503	SO:0001583	missense	79989	exon3			TGTGGATTGGATA	AK022633	CCDS5852.1, CCDS55172.1, CCDS55173.1, CCDS75665.1	7q34	2013-01-11			ENSG00000105948	ENSG00000105948		"Intraflagellar transport homologs", "Tetratricopeptide (TTC) repeat domain containing"	21882	protein-coding gene	gene with protein product							Standard	NM_001144920		Approved	FLJ12571, dyf-13, DYF13	uc003vus.2	A0AVF1	OTTHUMG00000157472	ENST00000464848.1:c.188T>C	chr7.hg19:g.138822639T>C	ENSP00000419279:p.Ile63Thr	82.0	0.0	.		110.0	7.0	.	NM_001144920	A4D1S3|B7Z5M0|C9J2N7|F8W724|Q9H9S8|Q9NTC0	Missense_Mutation	SNP	ENST00000464848.1	hg19	CCDS5852.1	.	.	.	.	.	.	.	.	.	.	T	15.05	2.717383	0.48622	.	.	ENSG00000105948	ENST00000430935;ENST00000495038;ENST00000474035;ENST00000478836;ENST00000464848	T;T;T;T;T	0.77229	-1.08;1.52;-1.08;1.15;-1.08	6.05	6.05	0.98169	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.287285	0.37761	N	0.001947	T	0.76550	0.4003	L	0.39245	1.2	0.58432	D	0.999996	P;B;P;B;B	0.41188	0.605;0.012;0.741;0.004;0.137	P;B;P;B;B	0.45660	0.489;0.018;0.489;0.012;0.062	T	0.77720	-0.2482	10	0.52906	T	0.07	.	15.5826	0.76455	0.0:0.0:0.0:1.0	.	63;63;63;63;63	B7Z2T3;C9J2N7;B7Z6R6;A0AVF1;Q96CU4	.;.;.;TTC26_HUMAN;.	T	63	ENSP00000410655:I63T;ENSP00000418788:I63T;ENSP00000443253:I63T;ENSP00000419178:I63T;ENSP00000419279:I63T	ENSP00000410655:I63T	I	+	2	0	TTC26	138473179	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.353000	0.59411	2.323000	0.78572	0.533000	0.62120	ATT	.	.	.	none		0.323	TTC26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348919.2	NM_024926		C	138822639	T	C	138822639	3	2	193	1	0	0	0	0	1	0	0	0	16706	1493	52	3	198	3	TTC26	7	138822639	Missense_Mutation	SNP	T	TCGA-HE-7128-01A-11D-1961-08	34074478	138822639	20316024	20	11532											
AGPAT6	137964	hgsc.bcm.edu	37	chr8	41467379	41467379	+	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	gagtcctggaacctgctgagCagaaccaattataacttcca	13	9	8	11	0	0	2	0	1	0	1	2	4	2	3	4	1	5	2	4	1	5	3			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr8:41467379C>T	ENST00000396987.3	+	4	1368	c.441C>T	c.(439-441)agC>agT	p.S147S	RP11-360L9.8_ENST00000581909.1_RNA	NM_178819.3	NP_848934.1	Q86UL3	GPAT4_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 6	147					acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|diacylglycerol metabolic process (GO:0046339)|fatty acid metabolic process (GO:0006631)|glandular epithelial cell maturation (GO:0002071)|glycerophospholipid biosynthetic process (GO:0046474)|lactation (GO:0007595)|lipid biosynthetic process (GO:0008610)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			endometrium(3)|kidney(2)|large_intestine(3)|lung(6)	14	Ovarian(28;0.00769)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	OV - Ovarian serous cystadenocarcinoma(14;0.00126)|Colorectal(10;0.0014)|Lung(22;0.00177)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0147)			ACCTGCTGAGCAGAACCAATT	0.493																																					p.S147S		Atlas-SNP	.											AGPAT6,caecum,carcinoma,0,1	AGPAT6	32	.	0			c.C441T						PASS	.						98	96	97					8																	41467379		2203	4300	6503	SO:0001819	synonymous_variant	137964	exon4			GCTGAGCAGAACC	AF406612	CCDS6117.1	8p11.21	2013-02-05	2013-02-05			ENSG00000158669	2.3.1.15	"1-acylglycerol-3-phosphate O-acyltransferases"	20880	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, zeta"	608143	"1-acylglycerol-3-phosphate O-acyltransferase 6 (lysophosphatidic acid acyltransferase, zeta)"			12938015	Standard	NM_178819		Approved	DKFZp586M1819, LPAAT-zeta	uc003xnz.2	Q86UL3		ENST00000396987.3:c.441C>T	chr8.hg19:g.41467379C>T		150.0	0.0	.		124.0	30.0	.	NM_178819	Q86V89	Silent	SNP	ENST00000396987.3	hg19	CCDS6117.1																																																																																			.	.	.	none		0.493	AGPAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377158.1	NM_178819		T	41467379	C	T	41467379	2	4	193	1	0	0	0	0	0	0	0	1	391	709	25	2		2	AGPAT6	8	41467379	Silent	SNP	C	TCGA-HE-7128-01A-11D-1961-08		41467379	104896643	21	11533											
CDC37L1	55664	hgsc.bcm.edu	37	chr9	4706079	4706079	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aactcggtggtacataaagaAgatgatgaacccaaaatgat	18	8	9	6	1	0	5	0	3	0	2	1	5	0	5	1	2	3	1	1	2	8	2	rs200977934		TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr9:4706079A>G	ENST00000381854.3	+	7	1183	c.981A>G	c.(979-981)gaA>gaG	p.E327E		NM_017913.2	NP_060383.2	Q7L3B6	CD37L_HUMAN	cell division cycle 37-like 1	327	Interaction with Hsp70.|Required for interaction with STIP1.					cytoplasm (GO:0005737)				breast(1)|kidney(1)|lung(2)	4	all_hematologic(13;0.137)	Breast(48;0.238)		GBM - Glioblastoma multiforme(50;0.0318)		TACATAAAGAAGATGATGAAC	0.393																																					p.E327E		Atlas-SNP	.											.	CDC37L1	19	.	0			c.A981G						PASS	.						130	112	118					9																	4706079		2203	4300	6503	SO:0001819	synonymous_variant	55664	exon7			TAAAGAAGATGAT	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.981A>G	chr9.hg19:g.4706079A>G		50.0	0.0	.		46.0	6.0	.	NM_017913	B1AL70|Q9NWS3|Q9NX16	Silent	SNP	ENST00000381854.3	hg19	CCDS6454.1																																																																																			.	.	.	alt		0.393	CDC37L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051564.1	NM_017913		G	4706079	A	G	4706079	2	3	193	1	0	0	0	0	0	0	0	1	3071	69	3	3		3	CDC37L1	9	4706079	Silent	SNP	A	TCGA-HE-7128-01A-11D-1961-08		4706079	136507352	22	11534											
OGN	4969	hgsc.bcm.edu	37	chr9	95148550	95148550	+	Frame_Shift_Del	DEL	A	A	-																															attccagggcattatggtccAagtagaggaaggtgaggtta																										TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr9:95148550delA	ENST00000262551.4	-	6	1079	c.659delT	c.(658-660)ttgfs	p.L220fs	OGN_ENST00000375561.5_Frame_Shift_Del_p.L220fs|CENPP_ENST00000375587.3_Intron	NM_033014.2	NP_148935.1	P20774	MIME_HUMAN	osteoglycin	220					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|negative regulation of smooth muscle cell proliferation (GO:0048662)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	13						ATTATGGTCCAAGTAGAGGAA	0.368																																					p.L220fs		Atlas-INDEL	.											.	OGN	26	.	0			c.660delG						PASS	.						195	188	190					9																	95148550		2203	4300	6503	SO:0001589	frameshift_variant	4969	exon6			.	AI424992	CCDS6695.1	9q22	2008-02-05	2007-02-16		ENSG00000106809	ENSG00000106809		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	8126	protein-coding gene	gene with protein product	"mimecan proteoglycan"	602383	"osteoglycin (osteoinductive factor)"			2372374	Standard	NM_033014		Approved	mimecan, OIF, SLRR3A	uc004asa.3	P20774	OTTHUMG00000020224	ENST00000262551.4:c.659delT	chr9.hg19:g.95148550delA	ENSP00000262551:p.Leu220fs	55.0	0.0	0		50.0	16.0	0.32	NM_033014	Q6FIB0|Q9UF90|Q9UNK5	Frame_Shift_Del	DEL	ENST00000262551.4	hg19	CCDS6695.1																																																																																			.	.	.	none		0.368	OGN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053087.1	NM_024416		-	95148550	A	-	95148550	7	5	193	1	0	1	0	1	0	0	0	0	10853	131	5	0	245	0	OGN	9	95148550	Frame_Shift_Del	DEL	A	TCGA-HE-7128-01A-11D-1961-08	90442471	95148550	46064881	23	11535											
C9orf7	11094	hgsc.bcm.edu	37	chr9	136333115	136333115	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aacgccatcgcctttgctacGggggtgctgtacggactctc	6	10	12	13	4	1	0	0	0	1	0	3	1	1	1	2	3	5	3	2	3	3	3	rs150411088		TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr9:136333115G>A	ENST00000316948.4	+	4	473	c.393G>A	c.(391-393)acG>acA	p.T131T	CACFD1_ENST00000540581.1_Silent_p.T131T|CACFD1_ENST00000542192.1_Silent_p.T89T|CACFD1_ENST00000291722.7_Silent_p.T89T	NM_017586.3	NP_060056.1	Q9UGQ2	FLOWR_HUMAN	calcium channel flower domain containing 1	131					synaptic vesicle endocytosis (GO:0048488)	integral component of synaptic vesicle membrane (GO:0030285)	calcium channel activity (GO:0005262)										CCTTTGCTACGGGGGTGCTGT	0.657																																					p.T131T		Atlas-SNP	.											.	CACFD1	1	.	0			c.G393A						PASS	.	G	,,,	1,4405	2.1+/-5.4	0,1,2202	76	68	70		267,393,267,393	-10.8	0.2	9	dbSNP_134	70	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C9orf7	NM_001135775.2,NM_001242369.1,NM_001242370.1,NM_017586.3	,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,	89/131,131/234,89/192,131/173	136333115	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	11094	exon4			TGCTACGGGGGTG		CCDS6974.1, CCDS48051.1, CCDS56591.1, CCDS56592.1	9q34	2012-03-06	2012-03-06	2012-03-06	ENSG00000160325	ENSG00000160325			1365	protein-coding gene	gene with protein product		613104	"chromosome 9 open reading frame 7"	C9orf7		19737521	Standard	NM_001242370		Approved	D9S2135, flower	uc011mdh.1	Q9UGQ2	OTTHUMG00000020875	ENST00000316948.4:c.393G>A	chr9.hg19:g.136333115G>A		68.0	0.0	.		59.0	16.0	.	NM_017586	B7Z3T8|B7Z5E1|F5GXX4|Q5SXD4|Q8NBM6	Silent	SNP	ENST00000316948.4	hg19	CCDS6974.1																																																																																			.	G|1.000;A|0.000	0.000	weak		0.657	CACFD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054915.1	NM_017586		A	136333115	G	A	136333115	2	1	193	1	0	0	0	0	0	0	0	1	2495	1103	39	1		1	C9orf7	9	136333115	Silent	SNP	G	TCGA-HE-7128-01A-11D-1961-08	41184565	136333115	4880316	24	11536											
ARHGAP19	84986	hgsc.bcm.edu	37	chr10	98995038	98995038	+	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	cctgggaagtagaaggttctCgccctggtgtctgggtcaat	7	11	14	9	1	3	1	1	0	2	1	4	2	3	2	2	4	0	2	2	4	4	2	rs368950765		TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr10:98995038C>A	ENST00000358531.4	-	9	1248	c.1220G>T	c.(1219-1221)cGa>cTa	p.R407L	ARHGAP19_ENST00000487035.1_5'UTR|ARHGAP19_ENST00000355366.5_Missense_Mutation_p.R398L|ARHGAP19-SLIT1_ENST00000358308.3_Missense_Mutation_p.R378L|ARHGAP19-SLIT1_ENST00000453547.2_Missense_Mutation_p.R407L|ARHGAP19-SLIT1_ENST00000316676.8_Missense_Mutation_p.R407L|ARHGAP19_ENST00000371027.1_Missense_Mutation_p.R398L	NM_001204300.1|NM_032900.5	NP_001191229.1|NP_116289.4	Q14CB8	RHG19_HUMAN	Rho GTPase activating protein 19	407					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(2)|urinary_tract(1)	13		Colorectal(252;0.0854)		Epithelial(162;7.65e-09)|all cancers(201;4.49e-07)		AGAAGGTTCTCGCCCTGGTGT	0.433																																					p.R407L		Atlas-SNP	.											.	ARHGAP19	72	.	0			c.G1220T						PASS	.						143	143	143					10																	98995038		2203	4300	6503	SO:0001583	missense	84986	exon9			GGTTCTCGCCCTG	AK074122	CCDS7454.2, CCDS58092.1, CCDS73175.1	10q24.2	2011-06-29			ENSG00000213390	ENSG00000213390		"Rho GTPase activating proteins"	23724	protein-coding gene	gene with protein product		611587					Standard	NM_032900		Approved	FLJ00194, MGC14258	uc001knb.3	Q14CB8	OTTHUMG00000018845	ENST00000358531.4:c.1220G>T	chr10.hg19:g.98995038C>A	ENSP00000351333:p.Arg407Leu	217.0	0.0	.		198.0	8.0	.	NM_032900	A1XCP1|B4DZR1|Q14CF2|Q5J8M2|Q5T460|Q5T462|Q68DG6|Q8N9X1|Q8NF34|Q8TEK1	Missense_Mutation	SNP	ENST00000358531.4	hg19	CCDS7454.2	.	.	.	.	.	.	.	.	.	.	C	12.07	1.828677	0.32329	.	.	ENSG00000213390	ENST00000453547;ENST00000316676;ENST00000355366;ENST00000358531;ENST00000371027;ENST00000393817;ENST00000358308	T;T;T;T;T;T	0.09817	3.09;3.11;3.11;3.11;3.11;2.94	5.44	2.43	0.29744	.	1.149010	0.06642	U	0.761313	T	0.09774	0.0240	L	0.36672	1.1	0.09310	N	1	B;B;B	0.25486	0.117;0.078;0.127	B;B;B	0.28011	0.056;0.039;0.085	T	0.35126	-0.9801	10	0.49607	T	0.09	-6.5763	3.8056	0.08776	0.1369:0.5215:0.2498:0.0918	.	378;407;398	Q14CB8-6;Q14CB8;Q14CB8-3	.;RHG19_HUMAN;.	L	407;407;398;407;398;226;378	ENSP00000414774:R407L;ENSP00000324468:R407L;ENSP00000347526:R398L;ENSP00000351333:R407L;ENSP00000360066:R398L;ENSP00000351058:R378L	ENSP00000324468:R407L	R	-	2	0	ARHGAP19	98985028	0.000000	0.05858	0.952000	0.39060	0.704000	0.40688	0.227000	0.17795	1.428000	0.47296	0.655000	0.94253	CGA	.	.	.	none		0.433	ARHGAP19-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049647.2	NM_032900		A	98995038	C	A	98995038	3	1	193	1	0	0	0	0	1	0	0	0	869	884	31	4	280	4	ARHGAP19	10	98995038	Missense_Mutation	SNP	C	TCGA-HE-7128-01A-11D-1961-08		98995038	36539709	25	11537											
OR51A7	119687	hgsc.bcm.edu	37	chr11	4928976	4928976	+	Frame_Shift_Del	DEL	T	T	-																															tttggaccgctttcttgccaTtcacaatcccttaagataca																										TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr11:4928976delT	ENST00000359350.4	+	1	377	c.377delT	c.(376-378)attfs	p.I126fs	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004749.1	NP_001004749.1	Q8NH64	O51A7_HUMAN	olfactory receptor, family 51, subfamily A, member 7	126						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(7)|lung(13)|ovary(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		TTTCTTGCCATTCACAATCCC	0.393																																					p.I126fs		Atlas-INDEL	.											.	OR51A7	86	.	0			c.376delA						PASS	.						102	98	99					11																	4928976		2201	4298	6499	SO:0001589	frameshift_variant	119687	exon1			.	AB065525	CCDS31364.1	11p15.4	2012-08-09			ENSG00000176895	ENSG00000176895		"GPCR / Class A : Olfactory receptors"	15188	protein-coding gene	gene with protein product							Standard	NM_001004749		Approved		uc010qyq.2	Q8NH64	OTTHUMG00000066502	ENST00000359350.4:c.377delT	chr11.hg19:g.4928976delT	ENSP00000352305:p.Ile126fs	147.0	0.0	0		117.0	15.0	0.128205	NM_001004749	Q6IFH8	Frame_Shift_Del	DEL	ENST00000359350.4	hg19	CCDS31364.1																																																																																			.	.	.	none		0.393	OR51A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142175.1	NM_001004749		-	4928976	T	-	4928976	7	5	193	1	0	1	0	1	0	0	0	0	11095	1493	52	0	379	0	OR51A7	11	4928976	Frame_Shift_Del	DEL	T	TCGA-HE-7128-01A-11D-1961-08		4928976	130077540	26	11538											
NDUFS3	4722	hgsc.bcm.edu	37	chr11	47604000	47604000	+	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	atcctttccggaaagactttCctctatctggctatgttgag	8	15	8	10	1	2	2	0	1	2	1	5	3	5	3	3	2	0	2	3	2	3	5			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr11:47604000C>T	ENST00000263774.4	+	6	689	c.607C>T	c.(607-609)Cct>Tct	p.P203S	NDUFS3_ENST00000533507.1_3'UTR	NM_004551.2	NP_004542.1	O75489	NDUS3_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 3, 30kDa (NADH-coenzyme Q reductase)	203					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|negative regulation of cell growth (GO:0030308)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)	9					Doxorubicin(DB00997)	GAAAGACTTTCCTCTATCTGG	0.512																																					p.P203S	Pancreas(15;551 601 22438 23457 52512)	Atlas-SNP	.											.	NDUFS3	19	.	0			c.C607T						PASS	.						261	270	267					11																	47604000		2201	4298	6499	SO:0001583	missense	4722	exon6			GACTTTCCTCTAT	AF067139	CCDS7941.1	11p11.11	2011-08-03	2002-08-29		ENSG00000213619	ENSG00000213619	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7710	protein-coding gene	gene with protein product	"complex I 30kDa subunit", "NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial"	603846	"NADH dehydrogenase (ubiquinone) Fe-S protein 3 (30kD) (NADH-coenzyme Q reductase)"			9763677	Standard	NM_004551		Approved	CI-30	uc001nga.2	O75489	OTTHUMG00000166893	ENST00000263774.4:c.607C>T	chr11.hg19:g.47604000C>T	ENSP00000263774:p.Pro203Ser	512.0	1.0	.		378.0	86.0	.	NM_004551	B2R9J1|B4DFM8|Q9UNQ8	Missense_Mutation	SNP	ENST00000263774.4	hg19	CCDS7941.1	.	.	.	.	.	.	.	.	.	.	C	33	5.261674	0.95368	.	.	ENSG00000213619	ENST00000263774	D	0.88124	-2.34	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	D	0.95544	0.8552	M	0.93507	3.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.72982	0.972;0.979	D	0.95909	0.8921	10	0.87932	D	0	-17.4651	20.206	0.98277	0.0:1.0:0.0:0.0	.	203;129	O75489;Q9UF24	NDUS3_HUMAN;.	S	203	ENSP00000263774:P203S	ENSP00000263774:P203S	P	+	1	0	NDUFS3	47560576	1.000000	0.71417	0.999000	0.59377	0.932000	0.56968	7.474000	0.81024	2.785000	0.95823	0.655000	0.94253	CCT	.	.	.	none		0.512	NDUFS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391749.1	NM_004551		T	47604000	C	T	47604000	3	4	193	1	0	0	0	0	1	0	0	0	10300	855	30	2	629	2	NDUFS3	11	47604000	Missense_Mutation	SNP	C	TCGA-HE-7128-01A-11D-1961-08	42675024	47604000	87402516	27	11539											
ARHGEF17	9828	hgsc.bcm.edu	37	chr11	73020521	73020521	+	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	actcctcgggcagtgacgacGaccgagacggtgagggcggc	8	4	17	12	6	0	3	0	2	0	1	2	6	1	3	2	4	0	1	2	4	0	0			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr11:73020521G>T	ENST00000263674.3	+	1	1188	c.838G>T	c.(838-840)Gac>Tac	p.D280Y	RP11-800A3.7_ENST00000546324.1_RNA	NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	280					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						CAGTGACGACGACCGAGACGG	0.697																																					p.D280Y		Atlas-SNP	.											.	ARHGEF17	117	.	0			c.G838T						PASS	.						16	21	20					11																	73020521		2151	4242	6393	SO:0001583	missense	9828	exon1			GACGACGACCGAG	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.838G>T	chr11.hg19:g.73020521G>T	ENSP00000263674:p.Asp280Tyr	82.0	0.0	.		50.0	13.0	.	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Missense_Mutation	SNP	ENST00000263674.3	hg19	CCDS8221.1	.	.	.	.	.	.	.	.	.	.	G	14.91	2.677629	0.47886	.	.	ENSG00000110237	ENST00000263674	T	0.68181	-0.31	4.72	4.72	0.59763	.	0.000000	0.40554	N	0.001072	T	0.60495	0.2273	L	0.27053	0.805	0.09310	N	0.999994	P	0.49447	0.924	P	0.46419	0.516	T	0.60239	-0.7302	10	0.87932	D	0	-17.9023	15.1972	0.73100	0.0:0.0:1.0:0.0	.	280	Q96PE2	ARHGH_HUMAN	Y	280	ENSP00000263674:D280Y	ENSP00000263674:D280Y	D	+	1	0	ARHGEF17	72698169	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	4.087000	0.57671	2.179000	0.69175	0.313000	0.20887	GAC	.	.	.	none		0.697	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		T	73020521	G	T	73020521	3	4	193	1	0	0	0	0	1	0	0	0	900	1058	37	4	840	4	ARHGEF17	11	73020521	Missense_Mutation	SNP	G	TCGA-HE-7128-01A-11D-1961-08	25416521	73020521	61985995	28	11540											
KCTD14	65987	hgsc.bcm.edu	37	chr11	77727916	77727916	+	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	acacaagcacgctggacttcCgtgctgttatggcttctgca	8	11	10	12	2	1	0	0	0	1	0	2	1	2	1	1	2	3	6	1	2	2	3	rs372373172	byFrequency	TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr11:77727916C>A	ENST00000353172.5	-	2	535	c.491G>T	c.(490-492)cGg>cTg	p.R164L	RP11-7I15.3_ENST00000533697.1_RNA|KCTD14_ENST00000533144.1_Missense_Mutation_p.R134L	NM_001203260.1|NM_001203262.1|NM_001282406.1|NM_023930.3	NP_001190189.1|NP_001190191.1|NP_001269335.1|NP_076419.2	Q9BQ13	KCD14_HUMAN	potassium channel tetramerization domain containing 14	164					protein homooligomerization (GO:0051260)					endometrium(2)|kidney(1)|large_intestine(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	15	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1e-24)			GCTGGACTTCCGTGCTGTTAT	0.532																																					p.R164L	NSCLC(86;414 1416 18100 32729 49271)|Esophageal Squamous(156;1132 1858 11406 36132 46748)	Atlas-SNP	.											.	KCTD14	32	.	0			c.G491T						PASS	.						116	110	112					11																	77727916		2200	4292	6492	SO:0001583	missense	65987	exon2			GACTTCCGTGCTG	BC001062	CCDS8255.2, CCDS60908.1	11q13.4	2013-06-20	2013-06-20		ENSG00000151364	ENSG00000151364			23295	protein-coding gene	gene with protein product			"potassium channel tetramerisation domain containing 14"			12477932	Standard	NM_023930		Approved	MGC2376	uc001oyw.4	Q9BQ13	OTTHUMG00000150224	ENST00000353172.5:c.491G>T	chr11.hg19:g.77727916C>A	ENSP00000316482:p.Arg164Leu	227.0	0.0	.		195.0	8.0	.	NM_023930	B2R9R8	Missense_Mutation	SNP	ENST00000353172.5	hg19	CCDS8255.2	.	.	.	.	.	.	.	.	.	.	C	20.7	4.030615	0.75504	.	.	ENSG00000151364	ENST00000353172;ENST00000533144	T;T	0.71341	-0.56;-0.49	4.52	4.52	0.55395	.	0.059470	0.64402	D	0.000001	D	0.84515	0.5489	M	0.81802	2.56	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.87008	0.2121	10	0.72032	D	0.01	.	16.4381	0.83884	0.0:1.0:0.0:0.0	.	164	Q9BQ13	KCD14_HUMAN	L	164;134	ENSP00000316482:R164L;ENSP00000431155:R134L	ENSP00000316482:R164L	R	-	2	0	KCTD14	77405564	0.999000	0.42202	0.061000	0.19648	0.015000	0.08874	4.182000	0.58310	2.356000	0.79943	0.561000	0.74099	CGG	.	.	.	alt		0.532	KCTD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316888.1	NM_023930		A	77727916	C	A	77727916	3	1	193	1	0	0	0	0	1	0	0	0	8108	652	23	4	280	4	KCTD14	11	77727916	Missense_Mutation	SNP	C	TCGA-HE-7128-01A-11D-1961-08	4707395	77727916	57278600	29	11541											
MLL2	8085	hgsc.bcm.edu	37	chr12	49446075	49446075	+	Missense_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	gtggtggtgacaggcgtgatGcctcaggtggtggggacgtg	5	9	21	6	2	1	2	1	2	0	0	1	3	1	3	1	7	1	0	1	7	0	0			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr12:49446075G>A	ENST00000301067.7	-	10	1390	c.1391C>T	c.(1390-1392)gCa>gTa	p.A464V		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	464	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)										CAGGCGTGATGCCTCAGGTGG	0.657																																					p.A464V		Atlas-SNP	.											.	MLL2	1173	.	0			c.C1391T						PASS	.						88	98	94					12																	49446075		2162	4235	6397	SO:0001583	missense	8085	exon10			CGTGATGCCTCAG	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.1391C>T	chr12.hg19:g.49446075G>A	ENSP00000301067:p.Ala464Val	166.0	0.0	.		180.0	48.0	.	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	7.479	0.648310	0.14516	.	.	ENSG00000167548	ENST00000301067	T	0.80393	-1.37	3.73	2.82	0.32997	.	.	.	.	.	T	0.58807	0.2148	N	0.08118	0	0.21841	N	0.999512	P	0.38395	0.629	B	0.29440	0.102	T	0.53844	-0.8381	9	0.87932	D	0	.	8.8235	0.35041	0.0:0.0:0.5915:0.4085	.	464	O14686	MLL2_HUMAN	V	464	ENSP00000301067:A464V	ENSP00000301067:A464V	A	-	2	0	MLL2	47732342	0.989000	0.36119	0.999000	0.59377	0.673000	0.39480	0.945000	0.29056	1.130000	0.42092	0.313000	0.20887	GCA	.	.	.	none		0.657	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49446075	G	A	49446075	3	1	193	1	0	0	0	0	1	0	0	0	9628	1319	46	2	15402	2	MLL2	12	49446075	Missense_Mutation	SNP	G	TCGA-HE-7128-01A-11D-1961-08		49446075	84405820	30	11542											
HSPB8	26353	hgsc.bcm.edu	37	chr12	119617182	119617182	+	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	cctgcgccgagaccccttccGggactctcccctctcctctc	3	9	7	22	3	3	1	0	0	3	1	7	3	4	2	8	1	1	0	8	1	0	1			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr12:119617182G>T	ENST00000281938.2	+	1	736	c.65G>T	c.(64-66)cGg>cTg	p.R22L	RP11-64B16.3_ENST00000538405.1_RNA|RP11-64B16.4_ENST00000535921.1_RNA	NM_014365.2	NP_055180.1	Q9UJY1	HSPB8_HUMAN	heat shock 22kDa protein 8	22					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)					GACCCCTTCCGGGACTCTCCC	0.632																																					p.R22L		Atlas-SNP	.											.	HSPB8	45	.	0			c.G65T						PASS	.						98	114	109					12																	119617182		2203	4300	6503	SO:0001583	missense	26353	exon1			CCTTCCGGGACTC	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.65G>T	chr12.hg19:g.119617182G>T	ENSP00000281938:p.Arg22Leu	315.0	0.0	.		271.0	14.0	.	NM_014365	B2R6A6|Q6FIH3|Q9UKS3	Missense_Mutation	SNP	ENST00000281938.2	hg19	CCDS9189.1	.	.	.	.	.	.	.	.	.	.	G	34	5.327752	0.95733	.	.	ENSG00000152137	ENST00000281938	D	0.88277	-2.36	4.42	4.42	0.53409	.	0.059974	0.64402	D	0.000003	D	0.92515	0.7623	M	0.72894	2.215	0.58432	D	0.999999	D	0.63880	0.993	P	0.58013	0.831	D	0.92579	0.6073	9	.	.	.	.	17.2157	0.86943	0.0:0.0:1.0:0.0	.	22	Q9UJY1	HSPB8_HUMAN	L	22	ENSP00000281938:R22L	.	R	+	2	0	HSPB8	118101565	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.646000	0.91053	2.294000	0.77228	0.563000	0.77884	CGG	.	.	.	none		0.632	HSPB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401647.1	NM_014365		T	119617182	G	T	119617182	3	4	193	1	0	0	0	0	1	0	0	0	7430	1116	39	4	67	4	HSPB8	12	119617182	Missense_Mutation	SNP	G	TCGA-HE-7128-01A-11D-1961-08	70171107	119617182	14234713	31	11543											
OGFOD2	79676	hgsc.bcm.edu	37	chr12	123463804	123463804	+	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	gcctctgtcccatgtgctgcCgtgagcccgacctggtggac	4	9	13	15	2	1	1	0	1	1	0	2	3	2	2	5	2	3	1	5	2	0	0			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr12:123463804C>G	ENST00000228922.7	+	7	996	c.964C>G	c.(964-966)Cgt>Ggt	p.R322G	OGFOD2_ENST00000454694.2_Missense_Mutation_p.R158G|ARL6IP4_ENST00000543566.1_5'Flank|RP11-197N18.2_ENST00000540866.2_RNA|OGFOD2_ENST00000397389.2_Missense_Mutation_p.R262G|ARL6IP4_ENST00000357866.4_5'Flank|ARL6IP4_ENST00000439686.2_5'Flank|OGFOD2_ENST00000536150.1_Missense_Mutation_p.R158G|OGFOD2_ENST00000538628.1_Missense_Mutation_p.R158G|ARL6IP4_ENST00000315580.5_5'Flank|ARL6IP4_ENST00000412505.2_5'Flank|OGFOD2_ENST00000545612.1_Missense_Mutation_p.R158G|ABCB9_ENST00000542678.1_5'UTR|OGFOD2_ENST00000545317.1_Missense_Mutation_p.R158G|ARL6IP4_ENST00000453766.2_5'Flank|OGFOD2_ENST00000538755.1_Missense_Mutation_p.R158G|ARL6IP4_ENST00000454885.2_5'Flank|ARL6IP4_ENST00000426960.2_5'Flank|ARL6IP4_ENST00000392435.2_5'Flank			Q6N063	OGFD2_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 2	322							iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)			breast(1)|endometrium(2)|lung(4)|pancreas(1)	8	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.11e-05)|Epithelial(86;0.000127)|BRCA - Breast invasive adenocarcinoma(302;0.107)	Vitamin C(DB00126)	CATGTGCTGCCGTGAGCCCGA	0.647																																					p.R262G		Atlas-SNP	.											.	OGFOD2	18	.	0			c.C784G						PASS	.						42	49	47					12																	123463804		2166	4249	6415	SO:0001583	missense	79676	exon8			TGCTGCCGTGAGC	AK094820	CCDS41855.1	12q24.31	2010-11-23			ENSG00000111325	ENSG00000111325			25823	protein-coding gene	gene with protein product						12477932	Standard	NM_024623		Approved	FLJ13491, FLJ37501	uc001udz.1	Q6N063		ENST00000228922.7:c.964C>G	chr12.hg19:g.123463804C>G	ENSP00000228922:p.Arg322Gly	86.0	0.0	.		70.0	13.0	.	NM_024623	B3KT24|Q4KN13|Q6N023|Q9H8K6	Missense_Mutation	SNP	ENST00000228922.7	hg19		.	.	.	.	.	.	.	.	.	.	C	2.311	-0.357912	0.05138	.	.	ENSG00000111325	ENST00000397389;ENST00000538755;ENST00000536150;ENST00000545056;ENST00000545612;ENST00000538628;ENST00000545317;ENST00000454694;ENST00000228922;ENST00000536439	D;D	0.86432	-2.12;-2.12	5.07	2.15	0.27550	.	0.765042	0.12924	N	0.427954	D	0.83691	0.5309	M	0.62723	1.935	0.09310	N	1	B;B	0.13594	0.008;0.003	B;B	0.10450	0.005;0.005	T	0.74976	-0.3480	10	0.62326	D	0.03	-12.262	8.1428	0.31093	0.2533:0.6406:0.0:0.1061	.	322;262	Q6N063;Q6N063-2	OGFD2_HUMAN;.	G	262;158;158;158;158;158;158;158;322;158	ENSP00000380544:R262G;ENSP00000228922:R322G	ENSP00000228922:R322G	R	+	1	0	OGFOD2	122029757	0.007000	0.16637	0.378000	0.26068	0.008000	0.06430	0.512000	0.22755	0.560000	0.29169	-0.954000	0.02651	CGT	.	.	.	none		0.647	OGFOD2-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000400984.1	NM_024623		G	123463804	C	G	123463804	3	3	193	1	0	0	0	0	1	0	0	0	10849	652	23	4	806	4	OGFOD2	12	123463804	Missense_Mutation	SNP	C	TCGA-HE-7128-01A-11D-1961-08	3846622	123463804	10388091	32	11544											
BTBD7	55727	hgsc.bcm.edu	37	chr14	93730186	93730186	+	Missense_Mutation	SNP	A	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	ggtctttgctgagttcataaAaaacatccgaagtcatgacc	13	11	8	9	1	3	2	2	2	1	0	4	3	4	2	2	1	2	2	2	1	4	3			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr14:93730186A>C	ENST00000334746.5	-	4	1623	c.1316T>G	c.(1315-1317)tTt>tGt	p.F439C	BTBD7_ENST00000393170.2_Intron|BTBD7_ENST00000554565.1_Missense_Mutation_p.F88C	NM_001002860.2	NP_001002860.2	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7	439	BACK.				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)		GAGTTCATAAAAAACATCCGA	0.428																																					p.F439C		Atlas-SNP	.											.	BTBD7	112	.	0			c.T1316G						PASS	.						121	113	116					14																	93730186		2203	4300	6503	SO:0001583	missense	55727	exon4			TCATAAAAAACAT	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.1316T>G	chr14.hg19:g.93730186A>C	ENSP00000335615:p.Phe439Cys	89.0	0.0	.		75.0	16.0	.	NM_001002860	A8K5V7|Q69Z05|Q7Z308|Q86TS0|Q9HAA4|Q9NVM0	Missense_Mutation	SNP	ENST00000334746.5	hg19	CCDS32146.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.453818	0.84209	.	.	ENSG00000011114	ENST00000334746;ENST00000554565	D;D	0.82526	-1.62;-1.62	4.99	4.99	0.66335	BTB/Kelch-associated (2);	0.049285	0.85682	D	0.000000	D	0.90758	0.7099	M	0.82823	2.61	0.80722	D	1	D;D	0.76494	0.999;0.992	D;P	0.65443	0.935;0.819	D	0.92297	0.5846	10	0.87932	D	0	.	14.7279	0.69357	1.0:0.0:0.0:0.0	.	88;439	Q9P203-5;Q9P203	.;BTBD7_HUMAN	C	439;88	ENSP00000335615:F439C;ENSP00000451010:F88C	ENSP00000335615:F439C	F	-	2	0	BTBD7	92799939	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	1.904000	0.55121	0.456000	0.33151	TTT	.	.	.	none		0.428	BTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412701.1	NM_001002860		C	93730186	A	C	93730186	3	2	193	1	0	0	0	0	1	0	0	0	1548	14	1	5	2114	5	BTBD7	14	93730186	Missense_Mutation	SNP	A	TCGA-HE-7128-01A-11D-1961-08		93730186	13619354	33	11545											
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43440155	43440155	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctggcaggctgctgttaaaAggggcagcaccaccagccca	10	6	12	13	0	1	0	0	0	1	0	1	0	1	0	3	4	3	6	3	4	2	1			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr18:43440155A>G	ENST00000282041.5	-	40	6957	c.6923T>C	c.(6922-6924)cTt>cCt	p.L2308P	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	2308					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						TGCTGTTAAAAGGGGCAGCAC	0.537																																					p.L2308P		Atlas-SNP	.											.	EPG5	199	.	0			c.T6923C						PASS	.						76	79	78					18																	43440155		1977	4156	6133	SO:0001583	missense	57724	exon40			GTTAAAAGGGGCA	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.6923T>C	chr18.hg19:g.43440155A>G	ENSP00000282041:p.Leu2308Pro	145.0	0.0	.		90.0	18.0	.	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	hg19	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	A	16.85	3.237609	0.58886	.	.	ENSG00000152223	ENST00000282041;ENST00000540322;ENST00000308403	T	0.12672	2.66	5.59	5.59	0.84812	.	.	.	.	.	T	0.36082	0.0954	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.08106	-1.0738	9	0.87932	D	0	-10.9784	15.7665	0.78131	1.0:0.0:0.0:0.0	.	2308	Q9HCE0	EPG5_HUMAN	P	2308;236;1183	ENSP00000282041:L2308P	ENSP00000282041:L2308P	L	-	2	0	EPG5	41694153	1.000000	0.71417	0.897000	0.35233	0.053000	0.15095	9.225000	0.95219	2.108000	0.64289	0.533000	0.62120	CTT	.	.	.	none		0.537	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		G	43440155	A	G	43440155	3	3	193	1	0	0	0	0	1	0	0	0	8256	72	3	3	836	3	KIAA1632	18	43440155	Missense_Mutation	SNP	A	TCGA-HE-7128-01A-11D-1961-08		43440155	34637093	34	11546											
MIDN	90007	hgsc.bcm.edu	37	chr19	1257046	1257048	+	In_Frame_Del	DEL	GCT	GCT	-																															acgcgctgcaaggtggaacgGctgcagctgcttctgcagca																										TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	GCT	GCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr19:1257046_1257048delGCT	ENST00000591446.2	+	7	1591_1593	c.1182_1184delGCT	c.(1180-1185)cggctg>cgg	p.L395del	MIDN_ENST00000300952.2_In_Frame_Del_p.L395del|CIRBP_ENST00000588030.1_5'Flank			Q504T8	MIDN_HUMAN	midnolin	395						cytosol (GO:0005829)|nucleolus (GO:0005730)				NS(1)|endometrium(3)|kidney(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGGTGGAACGGCTGCAGCTGCTT	0.67																																					p.394_395del		Atlas-INDEL	.											.	MIDN	34	.	0			c.1181_1183del						PASS	.																																			SO:0001651	inframe_deletion	90007	exon8			.	AC004221	CCDS32864.1	19p13.3	2013-09-20			ENSG00000167470	ENSG00000167470			16298	protein-coding gene	gene with protein product		606700				10974535	Standard	XM_005259671		Approved		uc002lrp.3	Q504T8	OTTHUMG00000180144	ENST00000591446.2:c.1182_1184delGCT	chr19.hg19:g.1257046_1257048delGCT	ENSP00000467679:p.Leu395del	70.0	0.0	0		40.0	10.0	0.25	NM_177401	Q96BW8	In_Frame_Del	DEL	ENST00000591446.2	hg19	CCDS32864.1																																																																																			.	.	.	none		0.67	MIDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449965.2			-	1257048	GCT	-	1257046	7	5	193	1	0	1	0	1	0	0	0	0	9586	1190	42	0	1208	0	MIDN	19	1257046	In_Frame_Del	DEL	GCT	TCGA-HE-7128-01A-11D-1961-08		1257046	57871937	35	11547											
LPHN1	22859	hgsc.bcm.edu	37	chr19	14263148	14263148	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgaagacagggggcgaggAgggattgaagcccactgact	11	6	17	7	1	0	4	0	3	0	1	0	7	0	6	1	4	1	1	1	4	2	2			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr19:14263148A>G	ENST00000340736.6	-	22	3934	c.3637T>C	c.(3637-3639)Tcc>Ccc	p.S1213P	CTB-55O6.12_ENST00000588658.1_RNA|LPHN1_ENST00000361434.3_Missense_Mutation_p.S1208P|CTB-55O6.12_ENST00000592086.1_RNA|CTB-55O6.12_ENST00000588387.1_RNA	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	1213					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						GGGGGCGAGGAGGGATTGAAG	0.617																																					p.S1213P		Atlas-SNP	.											.	LPHN1	107	.	0			c.T3637C						PASS	.						96	103	101					19																	14263148		2203	4300	6503	SO:0001583	missense	22859	exon22			GCGAGGAGGGATT	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.3637T>C	chr19.hg19:g.14263148A>G	ENSP00000340688:p.Ser1213Pro	110.0	0.0	.		69.0	7.0	.	NM_001008701	Q96IE7|Q9BU07|Q9HAR3	Missense_Mutation	SNP	ENST00000340736.6	hg19	CCDS32928.1	.	.	.	.	.	.	.	.	.	.	A	5.267	0.234643	0.09969	.	.	ENSG00000072071	ENST00000340736;ENST00000361434	T;T	0.66099	-0.19;-0.19	4.99	4.99	0.66335	GPCR, family 2, latrophilin, C-terminal (1);	0.061997	0.64402	D	0.000003	T	0.28797	0.0714	N	0.01235	-0.94	0.45747	D	0.998642	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.36672	-0.9738	10	0.02654	T	1	.	12.6626	0.56822	1.0:0.0:0.0:0.0	.	1208;1213	O94910-2;O94910	.;LPHN1_HUMAN	P	1213;1208	ENSP00000340688:S1213P;ENSP00000355328:S1208P	ENSP00000340688:S1213P	S	-	1	0	LPHN1	14124148	0.998000	0.40836	1.000000	0.80357	0.928000	0.56348	0.694000	0.25512	1.881000	0.54492	0.459000	0.35465	TCC	.	.	.	none		0.617	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921		G	14263148	A	G	14263148	3	3	193	1	0	0	0	0	1	0	0	0	8922	304	11	3	799	3	LPHN1	19	14263148	Missense_Mutation	SNP	A	TCGA-HE-7128-01A-11D-1961-08	13006102	14263148	44865835	36	11548											
CYP4F2	8529	hgsc.bcm.edu	37	chr19	16003152	16003153	+	Frame_Shift_Ins	INS	-	-	ATAT																															cactctcattgaaaatcttcINSatatagggcttcaggatgtt																										TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr19:16003152_16003153insATAT	ENST00000221700.6	-	5	586_587	c.491_492insATAT	c.(490-492)atgfs	p.M164fs	CYP4F2_ENST00000011989.7_Frame_Shift_Ins_p.M15fs	NM_001082.3	NP_001073.3			cytochrome P450, family 4, subfamily F, polypeptide 2											NS(2)|breast(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						TGAAAATCTTCATATAGGGCTT	0.52																																					p.M164fs		Atlas-INDEL	.											.	CYP4F2	97	.	0			c.492_493insATAT						PASS	.																																			SO:0001589	frameshift_variant	8529	exon5			.	U02388	CCDS12336.1	19p13.12	2013-11-11	2003-01-14		ENSG00000186115	ENSG00000186115		"Cytochrome P450s"	2645	protein-coding gene	gene with protein product		604426	"cytochrome P450, subfamily IVF, polypeptide 2"			8424651, 8026587	Standard	NM_001082		Approved		uc002nbs.1	P78329	OTTHUMG00000185995	ENST00000221700.6:c.488_491dupATAT	chr19.hg19:g.16003153_16003156dupATAT	ENSP00000221700:p.Met164fs	286.0	0.0	0		194.0	22.0	0.113402	NM_001082		Frame_Shift_Ins	INS	ENST00000221700.6	hg19	CCDS12336.1																																																																																			.	.	.	none		0.52	CYP4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460372.3	NM_001082		ATAT	16003153	-	ATAT	16003152	7	5	193	1	0	1	1	0	0	0	0	0	4190	826	29	0	1106	0	CYP4F2	19	16003152	Frame_Shift_Ins	INS	-	TCGA-HE-7128-01A-11D-1961-08	1740004	16003152	43125831	37	11549											
KCNQ2	3785	hgsc.bcm.edu	37	chr20	62070959	62070959	+	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	agctggacttactgcaggcaGcgcgaagaaggagacaccga	13	4	14	10	3	0	2	0	0	0	2	0	6	0	3	1	3	4	3	1	3	3	1			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr20:62070959G>A	ENST00000359125.2	-	6	1093	c.919C>T	c.(919-921)Ctg>Ttg	p.L307L	KCNQ2_ENST00000354587.3_Silent_p.L307L|KCNQ2_ENST00000344425.5_Silent_p.L307L|KCNQ2_ENST00000370224.1_Silent_p.L307L|KCNQ2_ENST00000357249.2_Silent_p.L307L|KCNQ2_ENST00000359689.1_Silent_p.L307L|KCNQ2_ENST00000344462.4_Silent_p.L307L|KCNQ2_ENST00000360480.3_Silent_p.L307L	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	307					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)	ACTGCAGGCAGCGCGAAGAAG	0.637																																					p.L307L		Atlas-SNP	.											.	KCNQ2	201	.	0			c.C919T						PASS	.						152	116	128					20																	62070959		2203	4300	6503	SO:0001819	synonymous_variant	3785	exon6			CAGGCAGCGCGAA	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.919C>T	chr20.hg19:g.62070959G>A		89.0	0.0	.		75.0	28.0	.	NM_172106	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Silent	SNP	ENST00000359125.2	hg19	CCDS13520.1																																																																																			.	.	.	none		0.637	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109		A	62070959	G	A	62070959	2	1	193	1	0	0	0	0	0	0	0	1	8090	962	34	2		2	KCNQ2	20	62070959	Silent	SNP	G	TCGA-HE-7128-01A-11D-1961-08		62070959	954561	38	11550											
L3MBTL2	83746	hgsc.bcm.edu	37	chr22	41621916	41621916	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccggccaccttctgtcagaAgaatgacattgagctcacac	11	8	8	14	1	3	4	2	2	1	2	3	4	3	4	3	1	1	1	3	1	2	2			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chr22:41621916A>G	ENST00000216237.5	+	12	1633	c.1475A>G	c.(1474-1476)aAg>aGg	p.K492R		NM_031488.4	NP_113676.2	Q969R5	LMBL2_HUMAN	l(3)mbt-like 2 (Drosophila)	492					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						TTCTGTCAGAAGAATGACATT	0.592																																					p.K492R		Atlas-SNP	.											.	L3MBTL2	61	.	0			c.A1475G						PASS	.						94	69	78					22																	41621916		2203	4300	6503	SO:0001583	missense	83746	exon12			GTCAGAAGAATGA	AJ305226	CCDS14011.1	22q13.31-q13.33	2008-06-11			ENSG00000100395	ENSG00000100395			18594	protein-coding gene	gene with protein product		611865				11682070	Standard	NM_031488		Approved	H-l(3)mbt-l, DKFZP761I141, dJ756G23.3	uc003azo.3	Q969R5	OTTHUMG00000150942	ENST00000216237.5:c.1475A>G	chr22.hg19:g.41621916A>G	ENSP00000216237:p.Lys492Arg	97.0	0.0	.		70.0	6.0	.	NM_031488	Q8TEN1|Q96SC4|Q9BQI2|Q9UGS4	Missense_Mutation	SNP	ENST00000216237.5	hg19	CCDS14011.1	.	.	.	.	.	.	.	.	.	.	A	11.68	1.711335	0.30322	.	.	ENSG00000100395	ENST00000216237	T	0.31769	1.48	5.23	4.17	0.49024	.	0.233465	0.50627	D	0.000106	T	0.27663	0.0680	L	0.54965	1.715	0.35928	D	0.832306	B;B	0.14438	0.004;0.01	B;B	0.21151	0.003;0.033	T	0.19484	-1.0304	10	0.46703	T	0.11	.	7.1971	0.25860	0.7961:0.0:0.0731:0.1308	.	492;492	Q969R5-3;Q969R5	.;LMBL2_HUMAN	R	492	ENSP00000216237:K492R	ENSP00000216237:K492R	K	+	2	0	L3MBTL2	39951862	1.000000	0.71417	0.987000	0.45799	0.906000	0.53458	2.599000	0.46231	0.792000	0.33850	0.459000	0.35465	AAG	.	.	.	none		0.592	L3MBTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320613.1	NM_031488		G	41621916	A	G	41621916	3	3	193	1	0	0	0	0	1	0	0	0	8599	72	3	3	1521	3	L3MBTL2	22	41621916	Missense_Mutation	SNP	A	TCGA-HE-7128-01A-11D-1961-08		41621916	9682650	39	11551											
DMD	1756	hgsc.bcm.edu	37	chrX	31152282	31152282	+	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	ctctaaccctgtgcttgtgtCctggggaggactgagaagat	8	11	13	9	0	1	2	0	1	1	2	2	5	2	4	2	3	2	1	2	3	2	2			TCGA-HE-7128-01A-11D-1961-08	TCGA-HE-7128-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a290bf48-c383-4a28-aed8-3d24910c3576	b9aafe9d-7537-47f4-9296-4e2581cfa7c3	g.chrX:31152282C>G	ENST00000357033.4	-	77	11157	c.10951G>C	c.(10951-10953)Gac>Cac	p.D3651H	DMD_ENST00000474231.1_Missense_Mutation_p.D1191H|DMD_ENST00000378707.3_Missense_Mutation_p.D1191H|DMD_ENST00000359836.1_Missense_Mutation_p.D1178H|DMD_ENST00000378723.3_Missense_Mutation_p.D583H|DMD_ENST00000361471.4_Missense_Mutation_p.D570H|DMD_ENST00000378702.4_Missense_Mutation_p.D583H|DMD_ENST00000378677.2_Missense_Mutation_p.D3647H|DMD_ENST00000378680.2_Missense_Mutation_p.D473H|DMD_ENST00000343523.2_Missense_Mutation_p.D1081H|DMD_ENST00000541735.1_Missense_Mutation_p.D1081H	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	3651					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)				GTGCTTGTGTCCTGGGGAGGA	0.408																																					p.D3651H		Atlas-SNP	.											.	DMD	2127	.	0			c.G10951C						PASS	.						189	119	143					X																	31152282		2202	4300	6502	SO:0001583	missense	1756	exon77			TTGTGTCCTGGGG	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.10951G>C	chrX.hg19:g.31152282C>G	ENSP00000354923:p.Asp3651His	59.0	0.0	.		39.0	13.0	.	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.4|21.4	4.136863|4.136863	0.77662|0.77662	.|.	.|.	ENSG00000198947|ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378723;ENST00000358062;ENST00000378677;ENST00000357033;ENST00000359836;ENST00000343523;ENST00000542849;ENST00000535280;ENST00000378707;ENST00000541735;ENST00000378702;ENST00000474231;ENST00000361471;ENST00000378680|ENST00000465285	T;T;T;T;T;T;T;T;T;T;T;T|.	0.65178|.	2.06;3.8;-0.14;-0.14;3.72;3.74;3.68;3.48;2.04;3.74;2.08;2.1|.	5.04|5.04	5.04|5.04	0.67666|0.67666	.|.	0.000000|.	0.36740|.	U|.	0.002431|.	T|T	0.73992|0.73992	0.3658|0.3658	M|M	0.68317|0.68317	2.08|2.08	0.45621|0.45621	D|D	0.998554|0.998554	D;D;D;D;D;D;B;B;B;D;D;P;P;B;B;B|.	0.89917|.	0.996;0.996;0.999;0.999;0.999;0.996;0.098;0.059;0.059;0.999;1.0;0.86;0.729;0.003;0.001;0.38|.	D;D;D;D;D;D;B;B;B;D;D;P;P;B;B;B|.	0.83275|.	0.926;0.955;0.974;0.995;0.945;0.926;0.077;0.035;0.052;0.99;0.996;0.661;0.526;0.003;0.005;0.326|.	T|T	0.73379|0.73379	-0.4001|-0.4001	10|5	0.52906|.	T|.	0.07|.	.|.	17.7643|17.7643	0.88473|0.88473	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	473;3643;3651;3647;2310;2307;1178;1191;1191;1081;1081;3528;570;583;570;583|.	B4DSV7;P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6;F8VX32;E7ESB2;E7EQS5;E7EQR9;F5GZY3;F5GZT3;P11532-5;Q8N754;Q6NSJ9;E9PDN1|.	.;.;DMD_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.|.	H|A	3643;2310;2307;583;1334;3647;3651;1178;1081;3651;3528;1191;1081;583;1191;570;473|1379	ENSP00000367997:D583H;ENSP00000350765:D1334H;ENSP00000367948:D3647H;ENSP00000354923:D3651H;ENSP00000352894:D1178H;ENSP00000340057:D1081H;ENSP00000367979:D1191H;ENSP00000444119:D1081H;ENSP00000367974:D583H;ENSP00000417123:D1191H;ENSP00000354464:D570H;ENSP00000367951:D473H|.	ENSP00000340057:D1081H|.	D|G	-|-	1|2	0|0	DMD|DMD	31062203|31062203	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.966000|0.966000	0.64601|0.64601	6.271000|6.271000	0.72569|0.72569	2.470000|2.470000	0.83445|0.83445	0.600000|0.600000	0.82982|0.82982	GAC|GGA	.	.	.	none		0.408	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		G	31152282	C	G	31152282	3	3	193	1	0	0	0	0	1	0	0	0	4582	855	30	4	204	4	DMD	23	31152282	Missense_Mutation	SNP	C	TCGA-HE-7128-01A-11D-1961-08		31152282	124118278	40	11552											
PRDM2	7799	hgsc.bcm.edu	37	chr1	14068533	14068533	+	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	atttgggatggatgtgcattGatgccactgatccagagaag	11	11	13	6	0	0	3	0	2	0	1	1	6	1	5	2	2	2	1	2	2	1	2			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr1:14068533G>T	ENST00000235372.7	+	5	1121	c.265G>T	c.(265-267)Gat>Tat	p.D89Y	PRDM2_ENST00000502727.1_3'UTR|PRDM2_ENST00000311066.5_Missense_Mutation_p.D89Y|PRDM2_ENST00000376048.5_Missense_Mutation_p.D89Y	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	89	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		GATGTGCATTGATGCCACTGA	0.383																																					p.D89Y		Atlas-SNP	.											.	PRDM2	147	.	0			c.G265T						PASS	.						78	72	74					1																	14068533		2203	4300	6503	SO:0001583	missense	7799	exon5			TGCATTGATGCCA	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.265G>T	chr1.hg19:g.14068533G>T	ENSP00000235372:p.Asp89Tyr	76.0	0.0	.		65.0	35.0	.	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Missense_Mutation	SNP	ENST00000235372.7	hg19	CCDS150.1	.	.	.	.	.	.	.	.	.	.	G	16.57	3.160930	0.57368	.	.	ENSG00000116731	ENST00000484063;ENST00000376048;ENST00000235372;ENST00000311066;ENST00000400800	D;D;D;D	0.94330	-3.4;-3.4;-3.4;-3.4	5.95	5.95	0.96441	SET domain (2);	0.000000	0.85682	D	0.000000	D	0.97826	0.9286	H	0.94620	3.56	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	0.98389	1.0562	10	0.87932	D	0	.	18.957	0.92662	0.0:0.0:1.0:0.0	.	89;89;89	Q13029;Q13029-2;B1AJZ4	PRDM2_HUMAN;.;.	Y	80;89;89;89;89	ENSP00000423010:D80Y;ENSP00000365216:D89Y;ENSP00000235372:D89Y;ENSP00000312352:D89Y	ENSP00000235372:D89Y	D	+	1	0	PRDM2	13941120	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.957000	0.93082	2.824000	0.97209	0.655000	0.94253	GAT	.	.	.	none		0.383	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231		T	14068533	G	T	14068533	3	4	194	1	0	0	0	0	1	0	0	0	12468	1290	45	4	279	4	PRDM2	1	14068533	Missense_Mutation	SNP	G	TCGA-HE-7129-01A-11D-1961-08		14068533	235182088	1	11553											
CAPN13	92291	hgsc.bcm.edu	37	chr2	30966306	30966306	+	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	agaactccgctgattttctcCgtgtctgtgcaaccacaaca	10	11	7	13	2	2	2	0	1	2	1	4	2	3	2	3	0	4	2	3	0	3	2	rs372490936	byFrequency	TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr2:30966306C>A	ENST00000295055.8	-	13	1564	c.1388G>T	c.(1387-1389)cGg>cTg	p.R463L	CAPN13_ENST00000534090.2_Missense_Mutation_p.R463L	NM_144575.2	NP_653176.2	Q6MZZ7	CAN13_HUMAN	calpain 13	463					proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	30	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					TGATTTTCTCCGTGTCTGTGC	0.438																																					p.R463L		Atlas-SNP	.											.	CAPN13	70	.	0			c.G1388T						PASS	.						256	247	250					2																	30966306		1893	4135	6028	SO:0001583	missense	92291	exon13			TTTCTCCGTGTCT		CCDS46252.1	2p22-p21	2008-02-05			ENSG00000162949	ENSG00000162949			16663	protein-coding gene	gene with protein product		610228				11675017	Standard	NM_144575		Approved	FLJ23523	uc021vfm.1	Q6MZZ7	OTTHUMG00000152053	ENST00000295055.8:c.1388G>T	chr2.hg19:g.30966306C>A	ENSP00000295055:p.Arg463Leu	446.0	0.0	.		458.0	21.0	.	NM_144575	Q17RF0|Q580X1|Q8TE80	Missense_Mutation	SNP	ENST00000295055.8	hg19	CCDS46252.1	.	.	.	.	.	.	.	.	.	.	C	9.805	1.181471	0.21787	.	.	ENSG00000162949	ENST00000295055;ENST00000534090	D;D	0.88741	-2.42;-2.42	5.52	-11.0	0.00169	Peptidase C2, calpain, large subunit, domain III (2);	30.332300	0.00166	N	0.000005	T	0.76730	0.4028	N	0.08118	0	0.09310	N	1	B;B	0.33448	0.412;0.412	B;B	0.36030	0.216;0.216	T	0.69855	-0.5032	10	0.38643	T	0.18	.	11.994	0.53191	0.0:0.0951:0.2979:0.607	.	463;463	A8K2N3;Q6MZZ7	.;CAN13_HUMAN	L	463	ENSP00000295055:R463L;ENSP00000431298:R463L	ENSP00000295055:R463L	R	-	2	0	CAPN13	30819810	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.578000	0.02125	-2.242000	0.00708	-1.069000	0.02264	CGG	.	.	.	alt		0.438	CAPN13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325101.2	NM_144575		A	30966306	C	A	30966306	3	1	194	1	0	0	0	0	1	0	0	0	2628	652	23	4	661	4	CAPN13	2	30966306	Missense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08		30966306	212233067	2	11554											
SFRS7	6432	hgsc.bcm.edu	37	chr2	38978383	38978384	+	Missense_Mutation	DNP	GC	GC	AA																															cttcttacctcctccgtaccGcccgtaacgcgacatgatga																										TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr2:38978383_38978384GC>AA	ENST00000313117.6	-	1	252_253	c.15_16GC>TT	c.(13-18)ggGCgg>ggTTgg	p.R6W	GEMIN6_ENST00000409011.1_5'Flank|SRSF7_ENST00000409276.1_Missense_Mutation_p.R6W|SRSF7_ENST00000446327.2_Missense_Mutation_p.R6W	NM_001031684.2|NM_001195446.1	NP_001026854.1|NP_001182375.1	Q16629	SRSF7_HUMAN	serine/arginine-rich splicing factor 7	6					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						CCTCCGTACCGCCCGTAACGCG	0.624																																					p.R6W|p.G5G		Atlas-SNP	.											.	SRSF7	29	.	0			c.C16T|c.G15T						PASS	.																																			SO:0001583	missense	6432	exon1			CGTACCGCCCGTA|GTACCGCCCGTAA	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.15_16delinsAA	chr2.hg19:g.38978383_38978384delinsAA	ENSP00000325905:p.Arg6Trp	128.0	0.0	.		88.0|87.0	34.0|32.0	.	NM_001195446	B4DLU6|G5E9M3|Q564D3	Missense_Mutation|Silent	SNP	ENST00000313117.6	hg19	CCDS33183.1																																																																																			.	.	.	none		0.624	SRSF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219889.2	NM_001031684		AA	38978384	GC	AA	38978383	3	1	194	1	0	0	0	0	1	0	0	0	14195	1086	38	1	732	1	SFRS7	2	38978383	Missense_Mutation	DNP	GC	TCGA-HE-7129-01A-11D-1961-08	8012077	38978383	204220990	3	11555											
C2orf55	343990	hgsc.bcm.edu	37	chr2	99413866	99413867	+	Frame_Shift_Del	DEL	GT	GT	-																															tggttcagacttcagggtccGtgccccaggcttgtcttcct																								rs201196594		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	GT	GT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr2:99413866_99413867delGT	ENST00000397899.2	-	8	2881_2882	c.2550_2551delAC	c.(2548-2553)gcacggfs	p.R851fs		NM_207362.2	NP_997245.2	Q6NV74	K121L_HUMAN	KIAA1211-like	851																	TTCAGGGTCCGTGCCCCAGGCT	0.619																																					p.851_851del		Atlas-INDEL	.											.	.	.	.	0			c.2551_2552del						PASS	.																																			SO:0001589	frameshift_variant	343990	exon8			.	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.2550_2551delAC	chr2.hg19:g.99413866_99413867delGT	ENSP00000380996:p.Arg851fs	181.0	0.0	0		102.0	42.0	0.411765	NM_207362		Frame_Shift_Del	DEL	ENST00000397899.2	hg19	CCDS42720.1																																																																																			.	.	.	none		0.619	KIAA1211L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329933.1	NM_207362		-	99413867	GT	-	99413866	7	5	194	1	0	1	0	1	0	0	0	0	2178	1144	40	0	349	0	C2orf55	2	99413866	Frame_Shift_Del	DEL	GT	TCGA-HE-7129-01A-11D-1961-08	60435483	99413866	143785507	4	11556											
ANKZF1	55139	hgsc.bcm.edu	37	chr2	220099828	220099828	+	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	cctggtcagccagagctctgGaatgcactgcttgctgcttg	6	11	12	12	0	2	1	1	0	1	1	2	2	2	2	2	2	6	5	2	2	1	2			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr2:220099828G>T	ENST00000323348.5	+	10	1659	c.1485G>T	c.(1483-1485)tgG>tgT	p.W495C	GLB1L_ENST00000497855.1_5'Flank|ANKZF1_ENST00000409849.1_Missense_Mutation_p.W285C|ANKZF1_ENST00000410034.3_Missense_Mutation_p.W495C	NM_018089.2	NP_060559.2	Q9H8Y5	ANKZ1_HUMAN	ankyrin repeat and zinc finger domain containing 1	495						membrane (GO:0016020)	metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	23		Renal(207;0.0474)		Epithelial(149;1.2e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CAGAGCTCTGGAATGCACTGC	0.587																																					p.W495C		Atlas-SNP	.											.	ANKZF1	45	.	0			c.G1485T						PASS	.						51	55	53					2																	220099828		2017	4171	6188	SO:0001583	missense	55139	exon10			GCTCTGGAATGCA	AF364318	CCDS42821.1, CCDS63129.1	2q35	2013-01-10			ENSG00000163516	ENSG00000163516		"Zinc fingers, C2H2-type", "Ankyrin repeat domain containing"	25527	protein-coding gene	gene with protein product						12477932	Standard	NM_018089		Approved	FLJ10415, ZNF744	uc002vkg.3	Q9H8Y5	OTTHUMG00000154533	ENST00000323348.5:c.1485G>T	chr2.hg19:g.220099828G>T	ENSP00000321617:p.Trp495Cys	68.0	0.0	.		57.0	22.0	.	NM_001042410	Q9NVZ4	Missense_Mutation	SNP	ENST00000323348.5	hg19	CCDS42821.1	.	.	.	.	.	.	.	.	.	.	G	11.67	1.709332	0.30322	.	.	ENSG00000163516	ENST00000323348;ENST00000409849;ENST00000410034	T;T;T	0.52983	0.64;0.64;0.64	5.41	4.51	0.55191	Ankyrin repeat-containing domain (2);	0.253027	0.37955	N	0.001878	T	0.43942	0.1270	M	0.65975	2.015	0.53005	D	0.999964	B	0.15141	0.012	B	0.17722	0.019	T	0.38265	-0.9669	10	0.37606	T	0.19	-6.7572	8.4061	0.32616	0.0:0.1513:0.5358:0.313	.	495	Q9H8Y5	ANKZ1_HUMAN	C	495;285;495	ENSP00000321617:W495C;ENSP00000386815:W285C;ENSP00000386337:W495C	ENSP00000321617:W495C	W	+	3	0	ANKZF1	219808072	1.000000	0.71417	0.983000	0.44433	0.353000	0.29299	1.765000	0.38481	1.473000	0.48159	0.591000	0.81541	TGG	.	.	.	none		0.587	ANKZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335790.1	NM_018089		T	220099828	G	T	220099828	3	4	194	1	0	0	0	0	1	0	0	0	693	1183	41	4	1519	4	ANKZF1	2	220099828	Missense_Mutation	SNP	G	TCGA-HE-7129-01A-11D-1961-08	120685962	220099828	23099545	5	11557											
ZBTB11	27107	hgsc.bcm.edu	37	chr3	101390912	101390912	+	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	aagttgctcaggtcatcttcCgattcattactttcttctcc	7	17	5	12	1	6	0	3	0	3	0	8	1	7	0	2	1	2	2	2	1	2	6			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr3:101390912C>A	ENST00000312938.4	-	2	1036	c.456G>T	c.(454-456)tcG>tcT	p.S152S	ZBTB11_ENST00000461821.1_Silent_p.S152S	NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	152					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S152S(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						GGTCATCTTCCGATTCATTAC	0.413																																					p.S152S		Atlas-SNP	.											.	ZBTB11	77	.	1	Substitution - coding silent(1)	lung(1)	c.G456T						PASS	.						170	167	168					3																	101390912		2203	4300	6503	SO:0001819	synonymous_variant	27107	exon2			ATCTTCCGATTCA	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.456G>T	chr3.hg19:g.101390912C>A		107.0	0.0	.		186.0	11.0	.	NM_014415	Q2NKP9	Silent	SNP	ENST00000312938.4	hg19	CCDS2943.1																																																																																			.	.	.	none		0.413	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415		A	101390912	C	A	101390912	2	1	194	1	0	0	0	0	0	0	0	1	17536	639	23	4		4	ZBTB11	3	101390912	Silent	SNP	C	TCGA-HE-7129-01A-11D-1961-08		101390912	96631518	6	11558											
KY	339855	hgsc.bcm.edu	37	chr3	134323200	134323200	+	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	catggttggagggtacacctCcaacttcatcccattcttcc	8	12	7	14	0	2	0	1	0	1	0	5	1	5	1	4	3	2	2	4	3	2	5			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr3:134323200C>A	ENST00000423778.2	-	11	1268	c.1207G>T	c.(1207-1209)Gag>Tag	p.E403*	KY_ENST00000503669.1_3'UTR|KY_ENST00000508956.1_Nonsense_Mutation_p.E382*	NM_178554.4	NP_848649.3	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	403					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						GGGTACACCTCCAACTTCATC	0.542																																					p.E403X		Atlas-SNP	.											.	KY	92	.	0			c.G1207T						PASS	.						87	86	86					3																	134323200		2128	4244	6372	SO:0001587	stop_gained	339855	exon11			ACACCTCCAACTT	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.1207G>T	chr3.hg19:g.134323200C>A	ENSP00000397598:p.Glu403*	111.0	0.0	.		143.0	104.0	.	NM_178554	B7Z1S4|Q6ZT15	Nonsense_Mutation	SNP	ENST00000423778.2	hg19	CCDS46920.1	.	.	.	.	.	.	.	.	.	.	C	36	5.846292	0.97016	.	.	ENSG00000174611	ENST00000508956;ENST00000423778;ENST00000310263	.	.	.	5.48	5.48	0.80851	.	0.368781	0.27393	N	0.019579	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-14.9747	19.3474	0.94370	0.0:1.0:0.0:0.0	.	.	.	.	X	382;403;403	.	ENSP00000309520:E403X	E	-	1	0	KY	135805890	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.042000	0.57347	2.578000	0.87016	0.561000	0.74099	GAG	.	.	.	none		0.542	KY-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357320.1	NM_178554		A	134323200	C	A	134323200	4	1	194	1	0	0	0	0	0	1	0	0	8593	864	30	4	782	4	KY	3	134323200	Nonsense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08	32932288	134323200	63699230	7	11559											
PPAT	5471	hgsc.bcm.edu	37	chr4	57272675	57272675	+	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	acgtacctttttccttaatcGagcagcatttaccaattcgc	10	14	5	12	3	0	0	0	0	0	0	3	1	1	0	3	0	4	3	3	0	4	7			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr4:57272675G>C	ENST00000264220.2	-	3	525	c.388C>G	c.(388-390)Cga>Gga	p.R130G	PPAT_ENST00000507648.1_5'UTR	NM_002703.4	NP_002694.3	Q06203	PUR1_HUMAN	phosphoribosyl pyrophosphate amidotransferase	130	Glutamine amidotransferase type-2. {ECO:0000255|PROSITE-ProRule:PRU00609}.				'de novo' IMP biosynthetic process (GO:0006189)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|G1/S transition of mitotic cell cycle (GO:0000082)|glutamine catabolic process (GO:0006543)|kidney development (GO:0001822)|lactation (GO:0007595)|maternal process involved in female pregnancy (GO:0060135)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|protein homotetramerization (GO:0051289)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|amidophosphoribosyltransferase activity (GO:0004044)|metal ion binding (GO:0046872)			cervix(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	20	Glioma(25;0.08)|all_neural(26;0.101)				Fluorouracil(DB00544)|L-Glutamine(DB00130)|Mercaptopurine(DB01033)	TTCCTTAATCGAGCAGCATTT	0.378																																					p.R130G		Atlas-SNP	.											.	PPAT	41	.	0			c.C388G						PASS	.						142	123	129					4																	57272675		2203	4300	6503	SO:0001583	missense	5471	exon3			TTAATCGAGCAGC		CCDS3505.1	4q12	2012-10-02			ENSG00000128059	ENSG00000128059	2.4.2.14		9238	protein-coding gene	gene with protein product		172450					Standard	NM_002703		Approved	GPAT, PRAT	uc003hbr.3	Q06203	OTTHUMG00000128842	ENST00000264220.2:c.388C>G	chr4.hg19:g.57272675G>C	ENSP00000264220:p.Arg130Gly	88.0	0.0	.		118.0	5.0	.	NM_002703		Missense_Mutation	SNP	ENST00000264220.2	hg19	CCDS3505.1	.	.	.	.	.	.	.	.	.	.	G	13.58	2.281110	0.40394	.	.	ENSG00000128059	ENST00000264220	T	0.76316	-1.01	5.62	4.77	0.60923	Glutamine amidotransferase, type II (1);Glutamine amidotransferase, class-II (1);	0.411032	0.27031	N	0.021280	T	0.72471	0.3464	L	0.35854	1.095	0.18873	N	0.999989	B	0.20368	0.044	B	0.27500	0.08	T	0.64550	-0.6381	10	0.51188	T	0.08	-1.2675	16.5121	0.84288	0.0:0.131:0.869:0.0	.	130	Q06203	PUR1_HUMAN	G	130	ENSP00000264220:R130G	ENSP00000264220:R130G	R	-	1	2	PPAT	56967432	0.694000	0.27738	0.732000	0.30844	0.986000	0.74619	5.006000	0.63978	1.352000	0.45808	0.585000	0.79938	CGA	.	.	.	none		0.378	PPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250781.2	NM_002703		C	57272675	G	C	57272675	3	2	194	1	0	0	0	0	1	0	0	0	12309	1066	37	4	1201	4	PPAT	4	57272675	Missense_Mutation	SNP	G	TCGA-HE-7129-01A-11D-1961-08		57272675	133881601	8	11560											
HNRNPAB	85007	hgsc.bcm.edu	37	chr5	177632984	177632984	+	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	agagggtttgggtttatcctGttcaaagatgcagccagtgt	9	13	13	6	0	1	2	1	0	0	2	2	2	2	2	2	2	2	4	2	2	2	4	rs201431713		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr5:177632984G>A	ENST00000308158.5	-	0	2038				PHYKPL_ENST00000481811.1_5'Flank|HNRNPAB_ENST00000506339.1_Silent_p.L117L|HNRNPAB_ENST00000514633.1_Silent_p.L117L|HNRNPAB_ENST00000355836.5_Silent_p.L117L|HNRNPAB_ENST00000506259.1_Silent_p.L117L|HNRNPAB_ENST00000515193.1_Silent_p.L117L|HNRNPAB_ENST00000358344.3_Silent_p.L117L|HNRNPAB_ENST00000504898.1_Silent_p.L117L	NM_153373.2	NP_699204.1	Q8IUZ5	AT2L2_HUMAN	5-phosphohydroxy-L-lysine phospho-lyase							mitochondrion (GO:0005739)	lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)									L-Alanine(DB00160)	GGTTTATCCTGTTCAAAGATG	0.408																																					p.L117L		Atlas-SNP	.											.	HNRNPAB	24	.	0			c.G351A						PASS	.						129	126	127					5																	177632984		2203	4300	6503	SO:0001628	intergenic_variant	3182	exon3			TATCCTGTTCAAA	BC037567	CCDS4434.1	5q35.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000175309	ENSG00000175309	4.2.3.134		28249	protein-coding gene	gene with protein product	"5-phosphonooxy-L-lysine phospho-lyase"	614683	"alanine-glyoxylate aminotransferase 2-like 2"	AGXT2L2		22241472	Standard	NM_153373		Approved	MGC15875	uc003miz.3	Q8IUZ5	OTTHUMG00000130892		chr5.hg19:g.177632984G>A		193.0	0.0	.		198.0	104.0	.	NM_031266	A8K7P6|B3KN36|D3DWP9|Q8WYS6|Q96HW8	Silent	SNP	ENST00000308158.5	hg19	CCDS4434.1																																																																																			.	G|0.999;C|0.001	.	alt		0.408	PHYKPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253477.1	NM_032921		A	177632984	G	A	177632984	1	1	194	0	1	0	0	0	0	0	0	0	7268	1364	48	2		2	HNRNPAB	5	177632984	IGR	SNP	G	TCGA-HE-7129-01A-11D-1961-08		177632984	3282276	9	11561											
ICK	22858	hgsc.bcm.edu	37	chr6	52878690	52878690	+	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	aggtgggcctgccttttccaGgatgcctttctgtggttttt	3	17	12	9	0	1	0	0	0	1	0	2	1	2	1	4	4	2	1	4	4	0	5			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr6:52878690G>C	ENST00000350082.5	-	9	1268	c.922C>G	c.(922-924)Ctg>Gtg	p.L308V	ICK_ENST00000356971.3_Missense_Mutation_p.L308V	NM_014920.3	NP_055735.1	Q9UPZ9	ICK_HUMAN	intestinal cell (MAK-like) kinase	308					intracellular signal transduction (GO:0035556)|multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(3)|stomach(1)	31	Lung NSC(77;0.103)					GCCTTTTCCAGGATGCCTTTC	0.512																																					p.L308V		Atlas-SNP	.											.	ICK	62	.	0			c.C922G						PASS	.						137	113	121					6																	52878690		2203	4300	6503	SO:0001583	missense	22858	exon10			TTTCCAGGATGCC	AB023153	CCDS4949.1	6p12.3-p11.2	2008-02-05			ENSG00000112144	ENSG00000112144			21219	protein-coding gene	gene with protein product		612325				12103360	Standard	NM_014920		Approved	MRK, LCK2, KIAA0936, MGC46090	uc003pbi.2	Q9UPZ9	OTTHUMG00000014870	ENST00000350082.5:c.922C>G	chr6.hg19:g.52878690G>C	ENSP00000263043:p.Leu308Val	49.0	0.0	.		48.0	23.0	.	NM_016513	A7MD41|O75985|Q5THL2|Q8IYH8|Q9BX17|Q9NYX3	Missense_Mutation	SNP	ENST00000350082.5	hg19	CCDS4949.1	.	.	.	.	.	.	.	.	.	.	G	3.787	-0.044509	0.07452	.	.	ENSG00000112144	ENST00000350082;ENST00000356971	T;T	0.72282	-0.64;-0.64	6.06	5.18	0.71444	Protein kinase-like domain (1);	1.200720	0.05905	N	0.630645	T	0.33498	0.0865	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.26677	-1.0096	10	0.15499	T	0.54	5.3033	15.6578	0.77155	0.0661:0.0:0.9339:0.0	.	308	Q9UPZ9	ICK_HUMAN	V	308	ENSP00000263043:L308V;ENSP00000349458:L308V	ENSP00000263043:L308V	L	-	1	2	ICK	52986649	0.844000	0.29557	0.232000	0.24009	0.396000	0.30629	3.921000	0.56454	1.551000	0.49450	0.655000	0.94253	CTG	.	.	.	none		0.512	ICK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040952.1	NM_016513		C	52878690	G	C	52878690	3	2	194	1	0	0	0	0	1	0	0	0	7491	991	35	4	1000	4	ICK	6	52878690	Missense_Mutation	SNP	G	TCGA-HE-7129-01A-11D-1961-08		52878690	118236377	10	11562											
CCM2	83605	hgsc.bcm.edu	37	chr7	45112359	45112359	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagtggacattaaggagacCtacgaggtggaagccagcac	15	5	13	8	1	0	1	0	0	0	1	0	5	0	3	2	4	3	1	2	4	4	2			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr7:45112359C>T	ENST00000258781.6	+	7	929	c.780C>T	c.(778-780)acC>acT	p.T260T	CCM2_ENST00000541586.1_Silent_p.T202T|CCM2_ENST00000381112.3_Silent_p.T281T|CCM2_ENST00000461377.1_3'UTR|CCM2_ENST00000474617.1_Silent_p.T163T|CCM2_ENST00000475551.1_Silent_p.T254T|CCM2_ENST00000544363.1_Silent_p.T169T	NM_031443.3	NP_113631.1	Q9BSQ5	CCM2_HUMAN	cerebral cavernous malformation 2	260					blood vessel endothelial cell differentiation (GO:0060837)|cell-cell junction organization (GO:0045216)|endothelial cell development (GO:0001885)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|inner ear development (GO:0048839)|integrin-mediated signaling pathway (GO:0007229)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|stress-activated MAPK cascade (GO:0051403)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)	cytoplasm (GO:0005737)|protein complex (GO:0043234)				NS(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						TTAAGGAGACCTACGAGGTGG	0.507																																					p.T281T		Atlas-SNP	.											.	CCM2	42	.	0			c.C843T						PASS	.						102	87	92					7																	45112359		2203	4300	6503	SO:0001819	synonymous_variant	83605	exon7			GGAGACCTACGAG	BC004903	CCDS5500.1, CCDS34630.1, CCDS55108.1, CCDS55109.1	7p13	2014-09-17	2004-02-13	2004-02-18	ENSG00000136280	ENSG00000136280			21708	protein-coding gene	gene with protein product	"malcavernin"	607929	"chromosome 7 open reading frame 22"	C7orf22		9811928	Standard	NM_001029835		Approved	MGC4607	uc003tms.3	Q9BSQ5	OTTHUMG00000129246	ENST00000258781.6:c.780C>T	chr7.hg19:g.45112359C>T		93.0	0.0	.		174.0	41.0	.	NM_001029835	A4D2L4|B3KUV0|D3DVL4|E9PDJ3|F5H0E1|F5H551|Q71RE5|Q8TAT4	Silent	SNP	ENST00000258781.6	hg19	CCDS5500.1	.	.	.	.	.	.	.	.	.	.	C	7.888	0.731770	0.15507	.	.	ENSG00000136280	ENST00000480382	.	.	.	5.55	-2.66	0.06077	.	.	.	.	.	T	0.41328	0.1154	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.28235	-1.0050	4	.	.	.	-0.5904	2.9764	0.05939	0.3625:0.1562:0.3533:0.128	.	.	.	.	L	127	.	.	P	+	2	0	CCM2	45078884	0.004000	0.15560	0.000000	0.03702	0.904000	0.53231	-0.395000	0.07287	-0.809000	0.04381	-0.165000	0.13383	CCT	.	.	.	none		0.507	CCM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251348.1	NM_031443		T	45112359	C	T	45112359	2	4	194	1	0	0	0	0	0	0	0	1	2910	668	24	2		2	CCM2	7	45112359	Silent	SNP	C	TCGA-HE-7129-01A-11D-1961-08		45112359	114026304	11	11563											
TBRG4	9238	hgsc.bcm.edu	37	chr7	45145054	45145054	+	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	cagtaccttgtcttccaggcGgttcattagtggctccgaga	7	12	11	11	2	2	1	1	0	1	1	4	2	4	1	3	3	1	3	3	3	2	5			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr7:45145054G>T	ENST00000258770.3	-	3	842	c.721C>A	c.(721-723)Cgc>Agc	p.R241S	SNORA5B_ENST00000363786.1_RNA|TBRG4_ENST00000494076.1_Missense_Mutation_p.R241S|SNORA5C_ENST00000364902.1_RNA|SNORA5A_ENST00000384111.1_RNA|TBRG4_ENST00000395655.4_Missense_Mutation_p.R241S|TBRG4_ENST00000471142.1_5'Flank|TBRG4_ENST00000361278.3_Missense_Mutation_p.R241S	NM_004749.3	NP_004740.2	Q969Z0	TBRG4_HUMAN	transforming growth factor beta regulator 4	241					cell cycle arrest (GO:0007050)|cellular respiration (GO:0045333)|positive regulation of cell proliferation (GO:0008284)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			cervix(1)|endometrium(3)|large_intestine(2)|lung(8)|skin(1)|stomach(2)	17						TCTTCCAGGCGGTTCATTAGT	0.557																																					p.R252S		Atlas-SNP	.											.	TBRG4	52	.	0			c.C754A						PASS	.						89	88	88					7																	45145054		2203	4300	6503	SO:0001583	missense	9238	exon3			CCAGGCGGTTCAT	AB023165	CCDS5501.1, CCDS5502.1	7p13	2006-07-07			ENSG00000136270	ENSG00000136270			17443	protein-coding gene	gene with protein product	"FAST kinase domains 4", "cell cycle progression 2 protein"	611325				9383053	Standard	NM_004749		Approved	Cpr2, KIAA0948, H_TD2522F11.8, FASTKD4	uc011kcd.3	Q969Z0	OTTHUMG00000129247	ENST00000258770.3:c.721C>A	chr7.hg19:g.45145054G>T	ENSP00000258770:p.Arg241Ser	195.0	0.0	.		294.0	12.0	.	NM_001261834	A4D2L2|A4D2L3|D3DVL5|D3DVL6|O14710|Q53GI8|Q8NDM4|Q9BUC6|Q9Y2F6	Missense_Mutation	SNP	ENST00000258770.3	hg19	CCDS5501.1	.	.	.	.	.	.	.	.	.	.	G	12.96	2.095624	0.36952	.	.	ENSG00000136270	ENST00000258770;ENST00000361278;ENST00000395655;ENST00000494076;ENST00000478532;ENST00000461363	T;T;T;T;T;T	0.34859	2.95;1.98;1.98;2.95;1.34;1.34	5.75	4.87	0.63330	.	0.223036	0.46145	D	0.000310	T	0.40247	0.1109	M	0.63843	1.955	0.33015	D	0.528002	P;P;P	0.45240	0.854;0.628;0.605	P;B;B	0.45610	0.487;0.203;0.336	T	0.54529	-0.8280	10	0.28530	T	0.3	.	11.7854	0.52039	0.0815:0.0:0.9185:0.0	.	252;241;241	B4DU42;Q969Z0-2;Q969Z0	.;.;TBRG4_HUMAN	S	241;241;241;241;206;187	ENSP00000258770:R241S;ENSP00000354992:R241S;ENSP00000379016:R241S;ENSP00000420597:R241S;ENSP00000418631:R206S;ENSP00000417743:R187S	ENSP00000258770:R241S	R	-	1	0	TBRG4	45111579	1.000000	0.71417	0.988000	0.46212	0.823000	0.46562	3.043000	0.49823	1.432000	0.47375	-0.136000	0.14681	CGC	.	.	.	none		0.557	TBRG4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251351.1	NM_030900		T	45145054	G	T	45145054	3	4	194	1	0	0	0	0	1	0	0	0	15661	1116	39	4	1210	4	TBRG4	7	45145054	Missense_Mutation	SNP	G	TCGA-HE-7129-01A-11D-1961-08	32695	45145054	113993609	12	11564											
PTPN12	5782	hgsc.bcm.edu	37	chr7	77267951	77267951	+	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	tgctacttagatcatccagcGggaggtattcactatgaaat	12	12	9	8	1	2	2	2	1	0	1	3	3	3	3	1	2	3	2	1	2	5	5			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr7:77267951G>T	ENST00000248594.6	+	17	2456	c.2184G>T	c.(2182-2184)gcG>gcT	p.A728A	PTPN12_ENST00000435495.2_Silent_p.A598A|PTPN12_ENST00000415482.2_Silent_p.A609A	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	728					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						ATCATCCAGCGGGAGGTATTC	0.353																																					p.A728A		Atlas-SNP	.											.	PTPN12	83	.	0			c.G2184T						PASS	.						106	108	107					7																	77267951		2203	4300	6503	SO:0001819	synonymous_variant	5782	exon17			TCCAGCGGGAGGT		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.2184G>T	chr7.hg19:g.77267951G>T		178.0	0.0	.		328.0	14.0	.	NM_002835	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	Silent	SNP	ENST00000248594.6	hg19	CCDS5592.1																																																																																			.	.	.	none		0.353	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3			T	77267951	G	T	77267951	2	4	194	1	0	0	0	0	0	0	0	1	12792	1103	39	4		4	PTPN12	7	77267951	Silent	SNP	G	TCGA-HE-7129-01A-11D-1961-08	32122897	77267951	81870712	13	11565											
PDK4	5166	hgsc.bcm.edu	37	chr7	95221864	95221872	+	In_Frame_Del	DEL	CCAATGTGG	CCAATGTGG	-																															cacagttaggatcaatgcttCcaatgtggcttgggtttcct																								rs138077797		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	CCAATGTGG	CCAATGTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr7:95221864_95221872delCCAATGTGG	ENST00000005178.5	-	5	764_772	c.567_575delCCACATTGG	c.(565-576)agccacattgga>aga	p.189_192SHIG>R		NM_002612.3	NP_002603.1	Q16654	PDK4_HUMAN	pyruvate dehydrogenase kinase, isozyme 4	189	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.				cellular metabolic process (GO:0044237)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|negative regulation of anoikis (GO:2000811)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|reactive oxygen species metabolic process (GO:0072593)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of bone resorption (GO:0045124)|regulation of cellular ketone metabolic process (GO:0010565)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose metabolic process (GO:0010906)|regulation of pH (GO:0006885)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	15	all_cancers(62;1.06e-10)|all_epithelial(64;1.04e-09)|Lung NSC(181;0.128)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0151)			ATCAATGCTTCCAATGTGGCTTGGGTTTC	0.321																																					p.190_192del		Atlas-INDEL	.											.	PDK4	42	.	0			c.568_576del						PASS	.																																			SO:0001651	inframe_deletion	5166	exon5			.	U54617	CCDS5643.1	7q21.3-q22.1	2008-07-18	2005-11-16		ENSG00000004799	ENSG00000004799			8812	protein-coding gene	gene with protein product		602527	"pyruvate dehydrogenase kinase, isoenzyme 4"			7499431	Standard	NM_002612		Approved		uc003uoa.3	Q16654	OTTHUMG00000153977	ENST00000005178.5:c.567_575delCCACATTGG	chr7.hg19:g.95221864_95221872delCCAATGTGG	ENSP00000005178:p.Ser189_Gly192delinsArg	170.0	0.0	0		204.0	78.0	0.382353	NM_002612		In_Frame_Del	DEL	ENST00000005178.5	hg19	CCDS5643.1																																																																																			.	.	.	none		0.321	PDK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333298.1	NM_002612		-	95221872	CCAATGTGG	-	95221864	7	5	194	1	0	1	0	1	0	0	0	0	11685	855	30	0	688	0	PDK4	7	95221864	In_Frame_Del	DEL	CCAATGTGG	TCGA-HE-7129-01A-11D-1961-08	17953913	95221864	63916799	14	11566											
ZKSCAN1	7586	hgsc.bcm.edu	37	chr7	99621201	99621201	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caggagaaggatggtatcgtAatagtgaaggtggaagagga	15	7	17	2	1	0	3	0	1	0	2	1	7	0	6	0	6	0	2	0	6	6	3			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr7:99621201A>G	ENST00000324306.6	+	2	306	c.72A>G	c.(70-72)gtA>gtG	p.V24V	ZKSCAN1_ENST00000426572.1_5'UTR|ZKSCAN1_ENST00000535170.1_Intron	NM_003439.1	NP_003430.1	P17029	ZKSC1_HUMAN	zinc finger with KRAB and SCAN domains 1	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)|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)			ATGGTATCGTAATAGTGAAGG	0.542																																					p.V24V		Atlas-SNP	.											.	ZKSCAN1	59	.	0			c.A72G						PASS	.						94	83	87					7																	99621201		2203	4300	6503	SO:0001819	synonymous_variant	7586	exon2			TATCGTAATAGTG	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.72A>G	chr7.hg19:g.99621201A>G		121.0	0.0	.		191.0	48.0	.	NM_003439	A4D294|P52745|Q2M1U1|Q8TBW5|Q8TEK7	Silent	SNP	ENST00000324306.6	hg19	CCDS34698.1																																																																																			.	.	.	none		0.542	ZKSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344550.2	NM_003439		G	99621201	A	G	99621201	2	3	194	1	0	0	0	0	0	0	0	1	17698	349	13	3		3	ZKSCAN1	7	99621201	Silent	SNP	A	TCGA-HE-7129-01A-11D-1961-08	4399337	99621201	59517462	15	11567											
CNTNAP2	26047	hgsc.bcm.edu	37	chr7	147336337	147336337	+	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	agtgccatcactgacagtgcCgagtactgcgagcagtatgt	10	9	12	10	2	1	1	1	1	0	0	1	3	1	1	2	0	5	3	2	0	2	2	rs539741829		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr7:147336337C>A	ENST00000361727.3	+	13	2553	c.2037C>A	c.(2035-2037)gcC>gcA	p.A679A		NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	679	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				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)			CTGACAGTGCCGAGTACTGCG	0.478										HNSCC(39;0.1)																											p.A679A		Atlas-SNP	.											.	CNTNAP2	392	.	0			c.C2037A						PASS	.						136	109	118					7																	147336337		2203	4300	6503	SO:0001819	synonymous_variant	26047	exon13			CAGTGCCGAGTAC	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.2037C>A	chr7.hg19:g.147336337C>A		84.0	0.0	.		154.0	8.0	.	NM_014141	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Silent	SNP	ENST00000361727.3	hg19	CCDS5889.1																																																																																			.	.	.	none		0.478	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1			A	147336337	C	A	147336337	2	1	194	1	0	0	0	0	0	0	0	1	3649	639	23	4		4	CNTNAP2	7	147336337	Silent	SNP	C	TCGA-HE-7129-01A-11D-1961-08	47715136	147336337	11802326	16	11568											
C7orf29	113763	hgsc.bcm.edu	37	chr7	150027695	150027695	+	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	agctcaacaagctcttctacCgcgaggagtttgtgctggcc	8	10	11	12	2	3	0	1	0	2	0	3	2	3	1	2	2	5	4	2	2	3	3			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr7:150027695C>A	ENST00000343855.4	+	1	758	c.202C>A	c.(202-204)Cgc>Agc	p.R68S	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	68																	GCTCTTCTACCGCGAGGAGTT	0.622																																					p.R68S		Atlas-SNP	.											.	C7orf29	18	.	0			c.C202A						PASS	.						93	93	93					7																	150027695		2203	4300	6503	SO:0001583	missense	113763	exon1			TTCTACCGCGAGG	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.202C>A	chr7.hg19:g.150027695C>A	ENSP00000343242:p.Arg68Ser	185.0	0.0	.		239.0	11.0	.	NM_138434		Missense_Mutation	SNP	ENST00000343855.4	hg19	CCDS5900.1	.	.	.	.	.	.	.	.	.	.	C	9.992	1.230972	0.22542	.	.	ENSG00000188707	ENST00000343855	.	.	.	3.75	3.75	0.43078	.	4.453540	0.01642	N	0.024125	T	0.18130	0.0435	N	0.11560	0.145	0.09310	N	0.999999	P	0.41748	0.761	B	0.38954	0.286	T	0.20042	-1.0287	9	0.06757	T	0.87	.	9.3723	0.38261	0.2139:0.7861:0.0:0.0	.	68	Q96FA7	CG029_HUMAN	S	68	.	ENSP00000343242:R68S	R	+	1	0	C7orf29	149658628	0.413000	0.25400	0.588000	0.28705	0.633000	0.38033	1.687000	0.37680	2.057000	0.61298	0.558000	0.71614	CGC	.	.	.	none		0.622	ZBED6CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350702.1	NM_138434		A	150027695	C	A	150027695	3	1	194	1	0	0	0	0	1	0	0	0	2387	652	23	4	204	4	C7orf29	7	150027695	Missense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08	2691358	150027695	9110968	17	11569											
ASB10	136371	hgsc.bcm.edu	37	chr7	150878302	150878302	+	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	gctgaaagcagcaagctgcaCagctgcaggcagcgggcggt	10	4	16	11	2	0	1	0	1	0	0	0	1	0	1	0	3	7	8	0	3	2	0			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr7:150878302C>G	ENST00000420175.2	-	3	852	c.828G>C	c.(826-828)ctG>ctC	p.L276L	ASB10_ENST00000422024.1_Silent_p.L321L|ASB10_ENST00000377867.3_Silent_p.L261L|ASB10_ENST00000275838.1_Silent_p.L276L|ASB10_ENST00000434669.1_Silent_p.L321L			Q8WXI3	ASB10_HUMAN	ankyrin repeat and SOCS box containing 10	276					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|lung(7)|skin(2)	12			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GCAAGCTGCACAGCTGCAGGC	0.682																																					p.L276L		Atlas-SNP	.											.	ASB10	99	.	0			c.G828C						PASS	.						29	31	30					7																	150878302		2202	4297	6499	SO:0001819	synonymous_variant	136371	exon3			GCTGCACAGCTGC	AK055536	CCDS5921.2, CCDS47749.1, CCDS47750.1, CCDS47749.2, CCDS47750.2	7q35	2014-02-04	2011-01-25		ENSG00000146926	ENSG00000146926		"Ankyrin repeat domain containing"	17185	protein-coding gene	gene with protein product		615054	"ankyrin repeat and SOCS box-containing 10", "glaucoma 1, open angle, F (adult-onset)"	GLC1F		22156576	Standard	NM_080871		Approved		uc003wjm.1	Q8WXI3	OTTHUMG00000157013	ENST00000420175.2:c.828G>C	chr7.hg19:g.150878302C>G		45.0	0.0	.		64.0	17.0	.	NM_001142459	A0AVH0|Q6ZUL6	Silent	SNP	ENST00000420175.2	hg19	CCDS47750.2																																																																																			.	.	.	none		0.682	ASB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347096.3	NM_080871		G	150878302	C	G	150878302	2	3	194	1	0	0	0	0	0	0	0	1	1014	465	17	4		4	ASB10	7	150878302	Silent	SNP	C	TCGA-HE-7129-01A-11D-1961-08	850607	150878302	8260361	18	11570											
ST18	9705	hgsc.bcm.edu	37	chr8	53077711	53077711	+	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	ttacctcctgtgggtgttgcGgttgctgttcacatgacccc	4	14	11	12	1	1	1	1	1	0	0	2	1	2	1	4	2	3	4	4	2	1	4			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr8:53077711G>T	ENST00000276480.7	-	12	1962	c.1279C>A	c.(1279-1281)Cgc>Agc	p.R427S		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	427					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				TGGGTGTTGCGGTTGCTGTTC	0.413																																					p.R427S		Atlas-SNP	.											.	ST18	212	.	0			c.C1279A						PASS	.						202	192	195					8																	53077711		2203	4300	6503	SO:0001583	missense	9705	exon12			TGTTGCGGTTGCT	AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"Zinc fingers, C2HC-type containing"	18695	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 3"		"zinc finger protein 387", "suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.1279C>A	chr8.hg19:g.53077711G>T	ENSP00000276480:p.Arg427Ser	339.0	0.0	.		320.0	15.0	.	NM_014682	Q17RY1	Missense_Mutation	SNP	ENST00000276480.7	hg19	CCDS6149.1	.	.	.	.	.	.	.	.	.	.	G	33	5.273288	0.95429	.	.	ENSG00000147488	ENST00000276480;ENST00000517580	T;T	0.63096	-0.02;0.6	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.79458	0.4449	M	0.68593	2.085	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.78344	-0.2240	10	0.54805	T	0.06	-19.9477	20.3081	0.98638	0.0:0.0:1.0:0.0	.	427;427	E5RHS3;O60284	.;ST18_HUMAN	S	427	ENSP00000276480:R427S;ENSP00000428521:R427S	ENSP00000276480:R427S	R	-	1	0	ST18	53240264	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.832000	0.86757	2.795000	0.96236	0.655000	0.94253	CGC	.	.	.	none		0.413	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1			T	53077711	G	T	53077711	3	4	194	1	0	0	0	0	1	0	0	0	15224	1116	39	4	1924	4	ST18	8	53077711	Missense_Mutation	SNP	G	TCGA-HE-7129-01A-11D-1961-08		53077711	93286311	19	11571											
WISP1	8840	hgsc.bcm.edu	37	chr8	134225321	134225321	+	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	ggaggctgccatctgtgaccCccaccggggcctctactgtg	5	8	13	15	1	2	1	0	1	2	0	2	2	2	2	5	4	2	1	5	4	1	1			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr8:134225321C>T	ENST00000250160.6	+	2	390	c.284C>T	c.(283-285)cCc>cTc	p.P95L	WISP1_ENST00000377863.2_Intron|WISP1_ENST00000519433.1_Intron|WISP1_ENST00000220856.6_Missense_Mutation_p.P95L|WISP1_ENST00000517423.1_Missense_Mutation_p.P95L	NM_003882.3	NP_003873.1	O95388	WISP1_HUMAN	WNT1 inducible signaling pathway protein 1	95	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)			ATCTGTGACCCCCACCGGGGC	0.612																																					p.P95L		Atlas-SNP	.											.	WISP1	64	.	0			c.C284T						PASS	.						57	59	58					8																	134225321		2203	4300	6503	SO:0001583	missense	8840	exon2			GTGACCCCCACCG	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.284C>T	chr8.hg19:g.134225321C>T	ENSP00000250160:p.Pro95Leu	141.0	0.0	.		82.0	41.0	.	NM_003882	A8KAG6|E7EMM5|Q5JBS6|Q5JBS7|Q5JBS8|Q9HCS3	Missense_Mutation	SNP	ENST00000250160.6	hg19	CCDS6371.1	.	.	.	.	.	.	.	.	.	.	C	15.65	2.895808	0.52121	.	.	ENSG00000104415	ENST00000250160;ENST00000517423;ENST00000220856	T;T;T	0.64618	-0.11;-0.11;-0.11	5.27	4.33	0.51752	Insulin-like growth factor-binding protein, IGFBP (3);	0.467062	0.24962	N	0.034202	T	0.57961	0.2089	M	0.63843	1.955	0.80722	D	1	P;P;B	0.45176	0.852;0.458;0.27	B;B;B	0.42462	0.388;0.137;0.089	T	0.62315	-0.6880	10	0.56958	D	0.05	-27.7812	7.9781	0.30166	0.0:0.7412:0.1659:0.0928	.	95;95;95	E7EMM5;O95388-2;O95388	.;.;WISP1_HUMAN	L	95	ENSP00000250160:P95L;ENSP00000427744:P95L;ENSP00000220856:P95L	ENSP00000220856:P95L	P	+	2	0	WISP1	134294503	0.959000	0.32827	1.000000	0.80357	0.965000	0.64279	1.247000	0.32815	2.460000	0.83146	0.542000	0.68232	CCC	.	.	.	none		0.612	WISP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378794.2	NM_003882		T	134225321	C	T	134225321	3	4	194	1	0	0	0	0	1	0	0	0	17384	623	22	2	290	2	WISP1	8	134225321	Missense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08	81147610	134225321	12138701	20	11572											
SLC35D2	11046	hgsc.bcm.edu	37	chr9	99106263	99106263	+	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	ggcattgtagaaaagtactcCgtatttccctagctcctgca	10	12	8	11	1	0	1	0	0	0	1	3	1	3	1	3	1	3	6	3	1	6	6			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr9:99106263C>A	ENST00000253270.7	-	8	669	c.607G>T	c.(607-609)Gga>Tga	p.G203*	SLC35D2_ENST00000375259.4_Intron	NM_007001.2	NP_008932.2	Q76EJ3	S35D2_HUMAN	solute carrier family 35 (UDP-GlcNAc/UDP-glucose transporter), member D2	203					carbohydrate derivative transport (GO:1901264)|carbohydrate metabolic process (GO:0005975)|carbohydrate transport (GO:0008643)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|nucleotide transmembrane transport (GO:1901679)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	nucleotide-sugar transmembrane transporter activity (GO:0005338)	p.G203R(1)		endometrium(3)|large_intestine(3)|lung(4)|skin(2)	12		Acute lymphoblastic leukemia(62;0.0167)				AAAAGTACTCCGTATTTCCCT	0.403																																					p.G203X		Atlas-SNP	.											SLC35D2,rectum,carcinoma,0,1	SLC35D2	20	.	1	Substitution - Missense(1)	large_intestine(1)	c.G607T						PASS	.						121	128	126					9																	99106263		2203	4300	6503	SO:0001587	stop_gained	11046	exon8			GTACTCCGTATTT	AB122077	CCDS6717.1, CCDS69625.1	9q22.33	2013-07-17	2013-07-17		ENSG00000130958	ENSG00000130958		"Solute carriers"	20799	protein-coding gene	gene with protein product		609182	"solute carrier family 35, member D2"			15607426	Standard	NM_007001		Approved	UGTrel8, SQV7L	uc004awc.3	Q76EJ3	OTTHUMG00000020293	ENST00000253270.7:c.607G>T	chr9.hg19:g.99106263C>A	ENSP00000253270:p.Gly203*	187.0	0.0	.		225.0	9.0	.	NM_007001	O95454|Q498C1|Q75W21|Q7Z5X5	Nonsense_Mutation	SNP	ENST00000253270.7	hg19	CCDS6717.1	.	.	.	.	.	.	.	.	.	.	C	36	5.661516	0.96734	.	.	ENSG00000130958	ENST00000253270	.	.	.	4.94	4.94	0.65067	.	0.055372	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	.	17.4527	0.87596	0.0:1.0:0.0:0.0	.	.	.	.	X	203	.	ENSP00000253270:G203X	G	-	1	0	SLC35D2	98146084	1.000000	0.71417	0.954000	0.39281	0.868000	0.49771	6.190000	0.72057	2.734000	0.93682	0.650000	0.86243	GGA	.	.	.	none		0.403	SLC35D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053261.1			A	99106263	C	A	99106263	4	1	194	1	0	0	0	0	0	1	0	0	14595	661	23	4	426	4	SLC35D2	9	99106263	Nonsense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08		99106263	42107168	21	11573											
COL27A1	85301	hgsc.bcm.edu	37	chr9	117047026	117047026	+	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	acacaaaggcattgtgggacCccttggacctcctggaccaa	11	7	10	13	0	0	0	0	0	0	0	1	3	1	3	5	4	0	1	5	4	2	2			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr9:117047026C>G	ENST00000356083.3	+	41	4347	c.3956C>G	c.(3955-3957)cCc>cGc	p.P1319R		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1319	Collagen-like 12.|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						ATTGTGGGACCCCTTGGACCT	0.557																																					p.P1319R		Atlas-SNP	.											COL27A1,NS,carcinoma,0,1	COL27A1	200	.	0			c.C3956G						PASS	.						142	119	127					9																	117047026		2203	4300	6503	SO:0001583	missense	85301	exon41			TGGGACCCCTTGG	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.3956C>G	chr9.hg19:g.117047026C>G	ENSP00000348385:p.Pro1319Arg	138.0	0.0	.		98.0	35.0	.	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	hg19	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	c	12.60	1.986411	0.35036	.	.	ENSG00000196739	ENST00000356083;ENST00000357257	D	0.93366	-3.21	4.71	3.82	0.43975	.	.	.	.	.	D	0.93779	0.8011	L	0.55017	1.72	0.38600	D	0.950644	P	0.52577	0.954	P	0.60012	0.867	D	0.91884	0.5518	9	0.22706	T	0.39	.	10.6899	0.45864	0.0:0.9065:0.0:0.0935	.	1319	Q8IZC6	CORA1_HUMAN	R	1319	ENSP00000348385:P1319R	ENSP00000348385:P1319R	P	+	2	0	COL27A1	116086847	1.000000	0.71417	1.000000	0.80357	0.672000	0.39443	5.396000	0.66297	1.205000	0.43262	-0.265000	0.10407	CCC	.	.	.	none		0.557	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888		G	117047026	C	G	117047026	3	3	194	1	0	0	0	0	1	0	0	0	3687	623	22	4	4118	4	COL27A1	9	117047026	Missense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08	17940763	117047026	24166405	22	11574											
AP3M1	26985	hgsc.bcm.edu	37	chr10	75898090	75898090	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acgctcttccagtgcttctcTagaaatatgtcaccggaaca	11	11	7	12	2	3	1	1	0	2	1	5	2	4	2	2	1	2	2	2	1	4	4	rs147488745		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr10:75898090T>C	ENST00000355264.4	-	2	359	c.48A>G	c.(46-48)ctA>ctG	p.L16L	AP3M1_ENST00000487653.1_5'UTR|AP3M1_ENST00000372745.1_Silent_p.L16L	NM_012095.4	NP_036227.1	Q9Y2T2	AP3M1_HUMAN	adaptor-related protein complex 3, mu 1 subunit	16					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)					AGTGCTTCTCTAGAAATATGT	0.358																																					p.L16L		Atlas-SNP	.											.	AP3M1	28	.	0			c.A48G						PASS	.						76	76	76					10																	75898090		2203	4300	6503	SO:0001819	synonymous_variant	26985	exon3			CTTCTCTAGAAAT	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.48A>G	chr10.hg19:g.75898090T>C		71.0	0.0	.		93.0	50.0	.	NM_207012	Q5JQ12|Q9H5L2	Silent	SNP	ENST00000355264.4	hg19	CCDS7342.1																																																																																			.	T|1.000;G|0.000	.	alt		0.358	AP3M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048747.1			C	75898090	T	C	75898090	2	2	194	1	0	0	0	0	0	0	0	1	747	1509	53	3		3	AP3M1	10	75898090	Silent	SNP	T	TCGA-HE-7129-01A-11D-1961-08		75898090	59636657	23	11575											
PDE6C	5146	hgsc.bcm.edu	37	chr10	95380726	95380726	+	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	acatgtacaatattgaatccCgaagaagccaggtaaaagga	18	7	9	7	1	0	2	0	1	0	1	1	4	1	3	2	2	2	2	2	2	8	4			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr10:95380726C>A	ENST00000371447.3	+	3	850	c.712C>A	c.(712-714)Cga>Aga	p.R238R		NM_006204.3	NP_006195.3	P51160	PDE6C_HUMAN	phosphodiesterase 6C, cGMP-specific, cone, alpha prime	238					phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|visual perception (GO:0007601)	plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.123)			Caffeine(DB00201)	TATTGAATCCCGAAGAAGCCA	0.443																																					p.R238R		Atlas-SNP	.											.	PDE6C	97	.	0			c.C712A						PASS	.						261	255	257					10																	95380726		2203	4300	6503	SO:0001819	synonymous_variant	5146	exon3			GAATCCCGAAGAA	U31973	CCDS7429.1	10q24	2013-01-23			ENSG00000095464	ENSG00000095464	3.1.4.17	"Phosphodiesterases"	8787	protein-coding gene	gene with protein product		600827					Standard	NM_006204		Approved	PDEA2, ACHM5, COD4	uc001kiu.4	P51160	OTTHUMG00000018775	ENST00000371447.3:c.712C>A	chr10.hg19:g.95380726C>A		465.0	0.0	.		408.0	17.0	.	NM_006204	A6NCR6|Q5VY29	Silent	SNP	ENST00000371447.3	hg19	CCDS7429.1																																																																																			.	.	.	none		0.443	PDE6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049437.1	NM_006204		A	95380726	C	A	95380726	2	1	194	1	0	0	0	0	0	0	0	1	11654	644	23	4		4	PDE6C	10	95380726	Silent	SNP	C	TCGA-HE-7129-01A-11D-1961-08	19482636	95380726	40154021	24	11576											
OR8I2	120586	hgsc.bcm.edu	37	chr11	55861472	55861472	+	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	catcctgaggatccagtcagCagcaggcaggcagaaggcct	11	5	13	12	0	1	2	1	1	0	1	3	3	3	3	3	4	2	4	3	4	1	0			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr11:55861472C>G	ENST00000302124.2	+	1	720	c.689C>G	c.(688-690)gCa>gGa	p.A230G		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	230						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A230E(1)		NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					ATCCAGTCAGCAGCAGGCAGG	0.468																																					p.A230G		Atlas-SNP	.											OR8I2,NS,carcinoma,0,1	OR8I2	119	.	1	Substitution - Missense(1)	lung(1)	c.C689G						PASS	.						148	133	138					11																	55861472		2201	4296	6497	SO:0001583	missense	120586	exon1			AGTCAGCAGCAGG	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.689C>G	chr11.hg19:g.55861472C>G	ENSP00000303864:p.Ala230Gly	101.0	0.0	.		91.0	26.0	.	NM_001003750	B2RNN4|Q6IFC0|Q96RC5	Missense_Mutation	SNP	ENST00000302124.2	hg19	CCDS31517.1	.	.	.	.	.	.	.	.	.	.	C	7.367	0.625989	0.14257	.	.	ENSG00000172154	ENST00000302124	T	0.00207	8.55	4.33	3.41	0.39046	GPCR, rhodopsin-like superfamily (1);	0.410674	0.17770	U	0.162617	T	0.00241	0.0007	L	0.60904	1.88	0.09310	N	1	B	0.19935	0.04	B	0.25614	0.062	T	0.31613	-0.9937	10	0.62326	D	0.03	-0.4958	11.6945	0.51536	0.0:0.9111:0.0:0.0889	.	230	Q8N0Y5	OR8I2_HUMAN	G	230	ENSP00000303864:A230G	ENSP00000303864:A230G	A	+	2	0	OR8I2	55618048	0.000000	0.05858	0.014000	0.15608	0.555000	0.35460	0.408000	0.21065	0.934000	0.37316	0.440000	0.28878	GCA	.	.	.	none		0.468	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750		G	55861472	C	G	55861472	3	3	194	1	0	0	0	0	1	0	0	0	11247	710	25	4	691	4	OR8I2	11	55861472	Missense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08		55861472	79145044	25	11577											
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117375681	117375681	+	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	cttgggtggggggtagccgtCcaccgagcagttgagcacac	7	7	16	11	2	0	1	0	1	0	0	1	2	1	1	3	4	3	4	3	4	1	3			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr11:117375681C>T	ENST00000321322.6	-	10	2321	c.2320G>A	c.(2320-2322)Gac>Aac	p.D774N	DSCAML1_ENST00000527706.1_Missense_Mutation_p.D504N	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	714	Ig-like C2-type 8.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		GGGTAGCCGTCCACCGAGCAG	0.602																																					p.D774N		Atlas-SNP	.											.	DSCAML1	286	.	0			c.G2320A						PASS	.						88	77	81					11																	117375681		2201	4296	6497	SO:0001583	missense	57453	exon10			AGCCGTCCACCGA		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.2320G>A	chr11.hg19:g.117375681C>T	ENSP00000315465:p.Asp774Asn	102.0	0.0	.		67.0	27.0	.	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	hg19	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	C	19.37	3.813851	0.70912	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.66995	-0.24;-0.24	4.32	4.32	0.51571	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.54727	0.1876	N	0.21097	0.63	0.58432	D	0.999999	B	0.18013	0.025	B	0.21360	0.034	T	0.52358	-0.8586	9	0.38643	T	0.18	.	16.5931	0.84781	0.0:1.0:0.0:0.0	.	714	Q8TD84	DSCL1_HUMAN	N	504;774;481	ENSP00000434335:D504N;ENSP00000315465:D774N	ENSP00000315465:D774N	D	-	1	0	DSCAML1	116880891	1.000000	0.71417	0.939000	0.37840	0.852000	0.48524	7.559000	0.82265	2.222000	0.72286	0.313000	0.20887	GAC	.	.	.	none		0.602	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		T	117375681	C	T	117375681	3	4	194	1	0	0	0	0	1	0	0	0	4771	855	30	2	4117	2	DSCAML1	11	117375681	Missense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08	61514209	117375681	17630835	26	11578											
LIMA1	51474	hgsc.bcm.edu	37	chr12	50571511	50571511	+	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	ccaaggcacttcctgaacttCcaagttcagtggggggtggc	8	9	13	11	0	1	1	1	1	0	0	3	1	3	1	3	5	1	2	3	5	3	3			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr12:50571511C>G	ENST00000341247.4	-	11	1765	c.1616G>C	c.(1615-1617)gGa>gCa	p.G539A	LIMA1_ENST00000552823.1_Missense_Mutation_p.G379A|LIMA1_ENST00000394943.3_Missense_Mutation_p.G540A|LIMA1_ENST00000552783.1_Missense_Mutation_p.G380A|LIMA1_ENST00000552909.1_Missense_Mutation_p.G378A|LIMA1_ENST00000547825.1_Missense_Mutation_p.G237A|LIMA1_ENST00000552491.1_Missense_Mutation_p.G236A	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	539					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						TCCTGAACTTCCAAGTTCAGT	0.532																																					p.G540A		Atlas-SNP	.											.	LIMA1	67	.	0			c.G1619C						PASS	.						113	118	116					12																	50571511		2203	4300	6503	SO:0001583	missense	51474	exon11			GAACTTCCAAGTT	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.1616G>C	chr12.hg19:g.50571511C>G	ENSP00000340184:p.Gly539Ala	213.0	0.0	.		193.0	89.0	.	NM_001113546	B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Missense_Mutation	SNP	ENST00000341247.4	hg19	CCDS8802.1	.	.	.	.	.	.	.	.	.	.	C	17.76	3.467708	0.63625	.	.	ENSG00000050405	ENST00000552491;ENST00000547825;ENST00000552823;ENST00000394943;ENST00000341247;ENST00000552783;ENST00000552909;ENST00000420992	T;T;T;D;T;T;T	0.84800	-1.15;-1.15;-1.49;-1.9;-1.16;-1.49;-1.49	5.73	4.83	0.62350	.	0.635701	0.18245	N	0.147130	D	0.82779	0.5111	L	0.44542	1.39	0.30474	N	0.773064	B;B;P	0.38129	0.072;0.293;0.619	B;B;B	0.39339	0.067;0.078;0.297	T	0.81895	-0.0723	10	0.49607	T	0.09	.	17.0525	0.86523	0.0:0.8729:0.1271:0.0	.	549;539;378	Q59FE8;Q9UHB6;F8VQE1	.;LIMA1_HUMAN;.	A	236;237;379;540;539;380;378;458	ENSP00000448463:G236A;ENSP00000448706:G237A;ENSP00000450266:G379A;ENSP00000378400:G540A;ENSP00000340184:G539A;ENSP00000448779:G380A;ENSP00000450087:G378A	ENSP00000340184:G539A	G	-	2	0	LIMA1	48857778	0.928000	0.31464	0.969000	0.41365	0.973000	0.67179	4.892000	0.63193	1.530000	0.49136	0.655000	0.94253	GGA	.	.	.	none		0.532	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357		G	50571511	C	G	50571511	3	3	194	1	0	0	0	0	1	0	0	0	8803	855	30	4	667	4	LIMA1	12	50571511	Missense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08		50571511	83280384	27	11579											
LAMP1	3916	hgsc.bcm.edu	37	chr13	113964011	113964011	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggtgctcaaccgcagctcCtgtggaaaagagaacacttc	11	8	11	11	1	1	1	1	0	0	1	3	3	2	2	2	2	4	3	2	2	4	1			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr13:113964011C>T	ENST00000332556.4	+	3	431	c.237C>T	c.(235-237)tcC>tcT	p.S79S	LAMP1_ENST00000397181.3_Silent_p.S79S	NM_005561.3	NP_005552.3	P11279	LAMP1_HUMAN	lysosomal-associated membrane protein 1	79	First lumenal domain.				autophagic cell death (GO:0048102)|autophagy (GO:0006914)|establishment of protein localization to organelle (GO:0072594)|Golgi to lysosome transport (GO:0090160)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|protein stabilization (GO:0050821)|regulation of organelle transport along microtubule (GO:1902513)	alveolar lamellar body (GO:0097208)|cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|phagolysosome membrane (GO:0061474)|sarcolemma (GO:0042383)	enzyme binding (GO:0019899)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|skin(1)|stomach(2)	16	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)			ACCGCAGCTCCTGTGGAAAAG	0.448																																					p.S79S		Atlas-SNP	.											.	LAMP1	41	.	0			c.C237T						PASS	.						110	114	113					13																	113964011		1968	4157	6125	SO:0001819	synonymous_variant	3916	exon3			CAGCTCCTGTGGA	J03263	CCDS41909.1	13q34	2011-11-24			ENSG00000185896	ENSG00000185896		"CD molecules"	6499	protein-coding gene	gene with protein product		153330					Standard	NM_005561		Approved	CD107a	uc001vtm.1	P11279	OTTHUMG00000017380	ENST00000332556.4:c.237C>T	chr13.hg19:g.113964011C>T		116.0	0.0	.		117.0	64.0	.	NM_005561	B4DWL3|Q8WU33|Q96I40|Q9BRD2|Q9NP13	Silent	SNP	ENST00000332556.4	hg19	CCDS41909.1																																																																																			.	.	.	none		0.448	LAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045876.2			T	113964011	C	T	113964011	2	4	194	1	0	0	0	0	0	0	0	1	8624	668	24	2		2	LAMP1	13	113964011	Silent	SNP	C	TCGA-HE-7129-01A-11D-1961-08		113964011	1205867	28	11580											
BAZ1A	11177	hgsc.bcm.edu	37	chr14	35242930	35242930	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctccagatatgtcgatctgtAacctgtaacaaaattcaaac	15	11	5	10	1	2	1	1	0	1	1	4	2	3	1	2	0	3	2	2	0	6	4			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr14:35242930A>G	ENST00000382422.2	-	19	3327	c.3000T>C	c.(2998-3000)gtT>gtC	p.V1000V	BAZ1A_ENST00000358716.4_Silent_p.V968V|BAZ1A_ENST00000360310.1_Silent_p.V1000V			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	1000					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)		GTCGATCTGTAACCTGTAACA	0.323																																					p.V1000V		Atlas-SNP	.											.	BAZ1A	128	.	0			c.T3000C						PASS	.						87	78	81					14																	35242930		2203	4300	6503	SO:0001819	synonymous_variant	11177	exon20			ATCTGTAACCTGT	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.3000T>C	chr14.hg19:g.35242930A>G		43.0	0.0	.		46.0	26.0	.	NM_013448	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Silent	SNP	ENST00000382422.2	hg19	CCDS9651.1																																																																																			.	.	.	none		0.323	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1			G	35242930	A	G	35242930	2	3	194	1	0	0	0	0	0	0	0	1	1329	349	13	3		3	BAZ1A	14	35242930	Silent	SNP	A	TCGA-HE-7129-01A-11D-1961-08		35242930	72106610	29	11581											
FANCM	57697	hgsc.bcm.edu	37	chr14	45636324	45636324	+	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	atgaaccagagaagccttctCggaacttgcagcgaaagtca	14	7	10	10	2	2	2	1	1	1	1	3	5	2	3	2	1	5	1	2	1	4	2	rs112784867	byFrequency	TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr14:45636324C>A	ENST00000267430.5	+	11	2045	c.1960C>A	c.(1960-1962)Cgg>Agg	p.R654R	FANCM_ENST00000556036.1_Silent_p.R654R|FANCM_ENST00000542564.2_Silent_p.R628R	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	654					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						GAAGCCTTCTCGGAACTTGCA	0.393								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.R654R		Atlas-SNP	.											.	FANCM	225	.	0			c.C1960A						PASS	.						98	102	101					14																	45636324		2203	4300	6503	SO:0001819	synonymous_variant	57697	exon11	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CCTTCTCGGAACT	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.1960C>A	chr14.hg19:g.45636324C>A		118.0	0.0	.		127.0	10.0	.	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Silent	SNP	ENST00000267430.5	hg19	CCDS32070.1																																																																																			.	C|0.999;T|0.001	.	alt		0.393	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		A	45636324	C	A	45636324	2	1	194	1	0	0	0	0	0	0	0	1	5678	875	31	4		4	FANCM	14	45636324	Silent	SNP	C	TCGA-HE-7129-01A-11D-1961-08	10393394	45636324	61713216	30	11582											
ARID4A	5926	hgsc.bcm.edu	37	chr14	58827698	58827698	+	Frame_Shift_Del	DEL	C	C	-																															gggacgacctcctttaaaatCaaccctctcatcaaacatgc																										TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr14:58827698delC	ENST00000355431.3	+	19	2391	c.2018delC	c.(2017-2019)tcafs	p.S673fs	ARID4A_ENST00000348476.3_Frame_Shift_Del_p.S673fs|ARID4A_ENST00000431317.2_Frame_Shift_Del_p.S673fs|ARID4A_ENST00000395168.3_Frame_Shift_Del_p.S673fs	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	673					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						CCTTTAAAATCAACCCTCTCA	0.433																																					p.S673fs		Atlas-INDEL	.											.	ARID4A	222	.	0			c.2017delT						PASS	.						169	155	159					14																	58827698		2203	4300	6503	SO:0001589	frameshift_variant	5926	exon19			.	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.2018delC	chr14.hg19:g.58827698delC	ENSP00000347602:p.Ser673fs	85.0	0.0	0		132.0	59.0	0.44697	NM_002892	Q15991|Q15992|Q15993	Frame_Shift_Del	DEL	ENST00000355431.3	hg19	CCDS9732.1																																																																																			.	.	.	none		0.433	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001		-	58827698	C	-	58827698	7	5	194	1	0	1	0	1	0	0	0	0	919	838	29	0	2088	0	ARID4A	14	58827698	Frame_Shift_Del	DEL	C	TCGA-HE-7129-01A-11D-1961-08	13191374	58827698	48521842	31	11583											
ESR2	2100	hgsc.bcm.edu	37	chr14	64746749	64746749	+	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	atccttcacacgaccagactCcatagtgatatcccgatgcg	11	9	7	14	3	1	2	1	1	0	1	4	4	4	2	4	0	1	0	4	0	2	3			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr14:64746749C>G	ENST00000341099.4	-	3	902	c.485G>C	c.(484-486)gGa>gCa	p.G162A	ESR2_ENST00000353772.3_Missense_Mutation_p.G162A|ESR2_ENST00000542956.1_Missense_Mutation_p.G162A|ESR2_ENST00000555483.1_Intron|ESR2_ENST00000358599.5_Missense_Mutation_p.G162A|ESR2_ENST00000553796.1_Missense_Mutation_p.G162A|ESR2_ENST00000357782.2_Missense_Mutation_p.G162A|ESR2_ENST00000554572.1_Missense_Mutation_p.G162A|ESR2_ENST00000555278.1_Missense_Mutation_p.G162A|ESR2_ENST00000557772.1_Missense_Mutation_p.G162A|ESR2_ENST00000267525.6_Missense_Mutation_p.G162A	NM_001437.2	NP_001428.1	Q92731	ESR2_HUMAN	estrogen receptor 2 (ER beta)	162					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)	CGACCAGACTCCATAGTGATA	0.453																																					p.G162A		Atlas-SNP	.											.	ESR2	82	.	0			c.G485C						PASS	.						236	229	232					14																	64746749		2203	4300	6503	SO:0001583	missense	2100	exon2			CAGACTCCATAGT	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.485G>C	chr14.hg19:g.64746749C>G	ENSP00000343925:p.Gly162Ala	426.0	1.0	.		345.0	152.0	.	NM_001214902	A8K8K5|G3V5M5|O60608|O60685|O60702|O60703|O75583|O75584|Q0MWT5|Q0MWT6|Q86Z31|Q9UEV6|Q9UHD3|Q9UQK9	Missense_Mutation	SNP	ENST00000341099.4	hg19	CCDS9762.1	.	.	.	.	.	.	.	.	.	.	C	32	5.148027	0.94603	.	.	ENSG00000140009	ENST00000556275;ENST00000542956;ENST00000554572;ENST00000353772;ENST00000358599;ENST00000555278;ENST00000553796;ENST00000357782;ENST00000557772;ENST00000341099;ENST00000267525	D;D;D;D;D;D;D;D;D;D;D	0.97575	-4.44;-4.44;-4.44;-4.44;-4.44;-4.44;-4.44;-4.44;-4.44;-4.44;-4.44	5.56	5.56	0.83823	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (5);	0.000000	0.85682	D	0.000000	D	0.99312	0.9759	H	0.99425	4.56	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	0.98376	1.0556	10	0.87932	D	0	.	19.5206	0.95183	0.0:1.0:0.0:0.0	.	162;162;162;162;162	Q92731-7;Q92731;Q92731-6;Q92731-5;F1D8N3	.;ESR2_HUMAN;.;.;.	A	162	ENSP00000452485:G162A;ENSP00000441792:G162A;ENSP00000450699:G162A;ENSP00000335551:G162A;ENSP00000351412:G162A;ENSP00000450488:G162A;ENSP00000452426:G162A;ENSP00000350427:G162A;ENSP00000451582:G162A;ENSP00000343925:G162A;ENSP00000267525:G162A	ENSP00000267525:G162A	G	-	2	0	ESR2	63816502	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.647000	0.83462	2.623000	0.88846	0.557000	0.71058	GGA	.	.	.	none		0.453	ESR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280621.1			G	64746749	C	G	64746749	3	3	194	1	0	0	0	0	1	0	0	0	5259	855	30	4	1221	4	ESR2	14	64746749	Missense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08	5919051	64746749	42602791	32	11584											
CYP46A1	10858	hgsc.bcm.edu	37	chr14	100165848	100165848	+	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	acaaggactccaagatgtacCgtgcgctccagactgtgttt	10	10	10	11	2	0	2	0	0	0	2	2	3	2	3	3	1	2	3	3	1	3	2			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr14:100165848C>A	ENST00000261835.3	+	4	432	c.328C>A	c.(328-330)Cgt>Agt	p.R110S	CYP46A1_ENST00000423126.2_Missense_Mutation_p.R13S	NM_006668.1	NP_006659.1	Q9Y6A2	CP46A_HUMAN	cytochrome P450, family 46, subfamily A, polypeptide 1	110					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|nervous system development (GO:0007399)|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)	cholesterol 24-hydroxylase activity (GO:0033781)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)	p.R110S(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|prostate(1)|skin(1)	25		Melanoma(154;0.0866)|all_epithelial(191;0.179)				CAAGATGTACCGTGCGCTCCA	0.532																																					p.R110S		Atlas-SNP	.											.	CYP46A1	62	.	1	Substitution - Missense(1)	lung(1)	c.C328A						PASS	.						275	262	267					14																	100165848		2203	4300	6503	SO:0001583	missense	10858	exon4			ATGTACCGTGCGC	AF094480	CCDS9954.1	14q32.2	2013-05-03	2003-02-14	2003-02-28	ENSG00000036530	ENSG00000036530		"Cytochrome P450s"	2641	protein-coding gene	gene with protein product		604087	"cytochrome P450, subfamily 46 (cholesterol 24-hydroxylase)"	CYP46		10377398	Standard	NM_006668		Approved		uc001ygo.3	Q9Y6A2	OTTHUMG00000171510	ENST00000261835.3:c.328C>A	chr14.hg19:g.100165848C>A	ENSP00000261835:p.Arg110Ser	404.0	0.0	.		299.0	12.0	.	NM_006668	B4DHP8|E7EQG9|Q8N2B0	Missense_Mutation	SNP	ENST00000261835.3	hg19	CCDS9954.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.951|7.951	0.744820|0.744820	0.15710|0.15710	.|.	.|.	ENSG00000036530|ENSG00000036530	ENST00000380228|ENST00000261835;ENST00000423126	.|T;D	.|0.82433	.|-0.31;-1.61	5.5|5.5	0.356|0.356	0.16074|0.16074	.|.	.|0.633707	.|0.15897	.|N	.|0.239263	T|T	0.62048|0.62048	0.2396|0.2396	N|N	0.16368|0.16368	0.405|0.405	0.27263|0.27263	N|N	0.958571|0.958571	.|B;B	.|0.14012	.|0.004;0.009	.|B;B	.|0.20384	.|0.029;0.01	T|T	0.45425|0.45425	-0.9262|-0.9262	5|10	.|0.08179	.|T	.|0.78	.|.	4.1573|4.1573	0.10266|0.10266	0.0:0.4696:0.1663:0.364|0.0:0.4696:0.1663:0.364	.|.	.|110;81	.|Q9Y6A2;Q59ER2	.|CP46A_HUMAN;.	Q|S	96|110;13	.|ENSP00000261835:R110S;ENSP00000405779:R13S	.|ENSP00000261835:R110S	P|R	+|+	2|1	0|0	CYP46A1|CYP46A1	99235601|99235601	0.968000|0.968000	0.33430|0.33430	0.978000|0.978000	0.43139|0.43139	0.933000|0.933000	0.57130|0.57130	0.329000|0.329000	0.19698|0.19698	0.398000|0.398000	0.25338|0.25338	-0.148000|-0.148000	0.13756|0.13756	CCG|CGT	.	.	.	none		0.532	CYP46A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413814.1			A	100165848	C	A	100165848	3	1	194	1	0	0	0	0	1	0	0	0	4184	652	23	4	342	4	CYP46A1	14	100165848	Missense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08	35419099	100165848	7183692	33	11585											
CP110	9738	hgsc.bcm.edu	37	chr16	19548870	19548870	+	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	gataccctaagggatctggcTtcgttaacaagaataaaatg	15	10	9	7	1	1	1	0	0	1	1	2	3	1	2	1	2	2	2	1	2	7	5			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr16:19548870T>A	ENST00000381396.5	+	4	2126	c.1879T>A	c.(1879-1881)Ttc>Atc	p.F627I	CCP110_ENST00000396212.2_Missense_Mutation_p.F627I|CCP110_ENST00000396208.2_Missense_Mutation_p.F627I	NM_001199022.1	NP_001185951	O43303	CP110_HUMAN	centriolar coiled coil protein 110kDa	627					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						GGGATCTGGCTTCGTTAACAA	0.348																																					p.F627I		Atlas-SNP	.											.	CCP110	57	.	0			c.T1879A						PASS	.						40	42	42					16																	19548870		2197	4300	6497	SO:0001583	missense	9738	exon4			TCTGGCTTCGTTA	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.1879T>A	chr16.hg19:g.19548870T>A	ENSP00000370803:p.Phe627Ile	51.0	0.0	.		62.0	25.0	.	NM_001199022	B7WP23|O43335|Q68DV9|Q8NE13	Missense_Mutation	SNP	ENST00000381396.5	hg19	CCDS55992.1	.	.	.	.	.	.	.	.	.	.	T	12.32	1.901950	0.33535	.	.	ENSG00000103540	ENST00000396212;ENST00000381396;ENST00000396208	T;T;T	0.13307	2.6;2.6;2.6	5.39	1.56	0.23342	.	0.876000	0.09983	N	0.730791	T	0.05318	0.0141	N	0.03608	-0.345	0.22213	N	0.999282	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.39251	-0.9623	10	0.37606	T	0.19	-0.0461	3.164	0.06529	0.1377:0.0766:0.1437:0.642	.	627;627	O43303;O43303-2	CP110_HUMAN;.	I	627	ENSP00000379515:F627I;ENSP00000370803:F627I;ENSP00000379511:F627I	ENSP00000370803:F627I	F	+	1	0	CCP110	19456371	0.389000	0.25205	0.861000	0.33841	0.927000	0.56198	0.910000	0.28571	0.291000	0.22468	0.460000	0.39030	TTC	.	.	.	none		0.348	CCP110-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254284.2	NM_014711		A	19548870	T	A	19548870	3	1	194	1	0	0	0	0	1	0	0	0	3790	1609	56	5	1889	5	CP110	16	19548870	Missense_Mutation	SNP	T	TCGA-HE-7129-01A-11D-1961-08		19548870	70805883	34	11586											
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24826534	24826534	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctatgactttatgaacagcaGtacttcaccagccagtcctc	11	11	6	13	0	1	2	1	2	0	0	3	2	2	2	3	0	4	2	3	0	4	5			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr16:24826534G>A	ENST00000395799.3	+	19	4868	c.4739G>A	c.(4738-4740)aGt>aAt	p.S1580N	TNRC6A_ENST00000432286.2_Missense_Mutation_p.S58N|TNRC6A_ENST00000315183.7_Missense_Mutation_p.S1531N|CTD-2515A14.1_ENST00000568895.1_RNA	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1580					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)		ATGAACAGCAGTACTTCACCA	0.458																																					p.S1580N		Atlas-SNP	.											.	TNRC6A	171	.	0			c.G4739A						PASS	.						89	87	88					16																	24826534		2197	4300	6497	SO:0001583	missense	27327	exon19			ACAGCAGTACTTC	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.4739G>A	chr16.hg19:g.24826534G>A	ENSP00000379144:p.Ser1580Asn	93.0	0.0	.		136.0	36.0	.	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	hg19	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	G	24.7	4.561278	0.86335	.	.	ENSG00000090905	ENST00000315183;ENST00000395799;ENST00000432286	T;T	0.14022	2.58;2.54	5.92	5.92	0.95590	.	0.042755	0.85682	D	0.000000	T	0.29458	0.0734	L	0.59436	1.845	0.58432	D	0.999998	P;B;B;D	0.63880	0.718;0.427;0.392;0.993	B;B;B;P	0.54629	0.366;0.254;0.315;0.757	T	0.00097	-1.2072	10	0.33141	T	0.24	-13.8994	20.3206	0.98668	0.0:0.0:1.0:0.0	.	247;719;1531;1580	B3KSX2;C9JA83;Q8NDV7-6;Q8NDV7	.;.;.;TNR6A_HUMAN	N	1531;1580;58	ENSP00000326900:S1531N;ENSP00000379144:S1580N	ENSP00000326900:S1531N	S	+	2	0	TNRC6A	24734035	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.423000	0.90264	2.809000	0.96659	0.655000	0.94253	AGT	.	.	.	none		0.458	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		A	24826534	G	A	24826534	3	1	194	1	0	0	0	0	1	0	0	0	16352	1029	36	2	4813	2	TNRC6A	16	24826534	Missense_Mutation	SNP	G	TCGA-HE-7129-01A-11D-1961-08	5277664	24826534	65528219	35	11587											
CNOT1	23019	hgsc.bcm.edu	37	chr16	58585134	58585134	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aattctctcagtttgatctgTggccacaagcaacgtatcta	11	13	7	10	1	4	1	1	1	3	0	5	1	4	1	1	1	2	3	1	1	5	4			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr16:58585134T>C	ENST00000317147.5	-	24	3576	c.3244A>G	c.(3244-3246)Aca>Gca	p.T1082A	CNOT1_ENST00000569240.1_Missense_Mutation_p.T1077A|CNOT1_ENST00000245138.4_5'UTR|CNOT1_ENST00000569732.1_5'Flank|CNOT1_ENST00000441024.2_Missense_Mutation_p.T1082A|SNORA46_ENST00000384762.1_RNA	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1082					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)		GTTTGATCTGTGGCCACAAGC	0.323																																					p.T1082A		Atlas-SNP	.											.	CNOT1	359	.	0			c.A3244G						PASS	.						106	124	118					16																	58585134		2197	4300	6497	SO:0001583	missense	23019	exon24			GATCTGTGGCCAC	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.3244A>G	chr16.hg19:g.58585134T>C	ENSP00000320949:p.Thr1082Ala	226.0	0.0	.		464.0	292.0	.	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	hg19	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.669566	0.88348	.	.	ENSG00000125107	ENST00000317147;ENST00000422872;ENST00000394200;ENST00000441024	T;T	0.45668	0.93;0.89	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.51449	0.1675	L	0.37561	1.115	0.80722	D	1	D;P;P	0.56035	0.974;0.851;0.939	D;B;P	0.70487	0.969;0.253;0.625	T	0.39522	-0.9610	10	0.13470	T	0.59	.	15.4218	0.75018	0.0:0.0:0.0:1.0	.	1082;1082;1077	A5YKK6-4;A5YKK6;A5YKK6-2	.;CNOT1_HUMAN;.	A	1082;511;1077;1082	ENSP00000320949:T1082A;ENSP00000413113:T1082A	ENSP00000320949:T1082A	T	-	1	0	CNOT1	57142635	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.040000	0.89188	2.051000	0.60960	0.383000	0.25322	ACA	.	.	.	none		0.323	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		C	58585134	T	C	58585134	3	2	194	1	0	0	0	0	1	0	0	0	3619	1696	59	3	4212	3	CNOT1	16	58585134	Missense_Mutation	SNP	T	TCGA-HE-7129-01A-11D-1961-08	33758600	58585134	31769619	36	11588											
SLC6A4	6532	hgsc.bcm.edu	37	chr17	28525539	28525565	+	Splice_Site	DEL	TAATAATACGCTATTGGGAAGAAAATA	TAATAATACGCTATTGGGAAGAAAATA	-																															tgtttctggggtaatactttTaataatacgctattgggaag																								rs202181933|rs201520429|rs200015551		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	TAATAATACGCTATTGGGAAGAAAATA	TAATAATACGCTATTGGGAAGAAAATA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:28525539_28525565delTAATAATACGCTATTGGGAAGAAAATA	ENST00000401766.2	-	14	2331_2340	c.1819_1828delTATTTTCTTCCCAATAGCGTATTATTA	c.(1819-1830)tattttcttccc>cc	p.YFLP607del	SLC6A4_ENST00000261707.3_Splice_Site_p.YFLP607del			P31645	SC6A4_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 4	607					brain morphogenesis (GO:0048854)|cellular response to cGMP (GO:0071321)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|memory (GO:0007613)|monoamine transport (GO:0015844)|negative regulation of cerebellar granule cell precursor proliferation (GO:0021941)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of organ growth (GO:0046621)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein homooligomerization (GO:0051260)|protein oligomerization (GO:0051259)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to toxic substance (GO:0009636)|serotonin transport (GO:0006837)|serotonin uptake (GO:0051610)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|thalamus development (GO:0021794)|vasoconstriction (GO:0042310)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|cocaine binding (GO:0019811)|monoamine transmembrane transporter activity (GO:0008504)|Rab GTPase binding (GO:0017137)|serotonin transmembrane transporter activity (GO:0015222)|serotonin:sodium symporter activity (GO:0005335)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(4)	25					Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexfenfluramine(DB01191)|Dexmethylphenidate(DB06701)|Dextromethorphan(DB00514)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fluoxetine(DB00472)|Fluvoxamine(DB00176)|Imipramine(DB00458)|Levomilnacipran(DB08918)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Pethidine(DB00454)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)	GTAATACTTTTAATAATACGCTATTGGGAAGAAAATACAATGTTATA	0.335																																					p.607_610del		Atlas-INDEL	.											.	SLC6A4	60	.	0			c.1819_1829del						PASS	.																																			SO:0001630	splice_region_variant	6532	exon15			.	L05568	CCDS11256.1	17q11.2	2014-01-30	2013-07-19		ENSG00000108576	ENSG00000108576		"Solute carriers"	11050	protein-coding gene	gene with protein product	"serotonin transporter 1"	182138	"solute carrier family 6 (neurotransmitter transporter, serotonin), member 4", "5-hydroxytryptamine (serotonin) transporter", "obsessive-compulsive disorder 1"	HTT, OCD1		7681602, 19806148	Standard	NM_001045		Approved	5-HTT, SERT1	uc002hey.5	P31645	OTTHUMG00000132751	ENST00000401766.2:c.1819-1TATTTTCTTCCCAATAGCGTATTATTA>-	chr17.hg19:g.28525539_28525565delTAATAATACGCTATTGGGAAGAAAATA		81.0	0.0	0		89.0	18.0	0.202247	NM_001045	Q5EE02	Frame_Shift_Del	DEL	ENST00000401766.2	hg19	CCDS11256.1																																																																																			.	.	.	none		0.335	SLC6A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256115.3	NM_001045	In_Frame_Del	-	28525565	TAATAATACGCTATTGGGAAGAAAATA	-	28525539	8	5	194	1	0	1	0	1	0	0	1	0	14699	1763	61	0	68	0	SLC6A4	17	28525539	Splice_Site	DEL	TAATAATACGCTATTGGGAAGAAAATA	TCGA-HE-7129-01A-11D-1961-08		28525539	52669671	37	11589											
LASP1	3927	hgsc.bcm.edu	37	chr17	37074921	37074921	+	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	acgaggtctccttccaggacGgggacaccatcgtcaacgtg	9	7	12	13	4	2	0	1	0	1	0	5	3	3	2	3	4	1	0	3	4	1	1			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:37074921G>T	ENST00000318008.6	+	7	1007	c.676G>T	c.(676-678)Ggg>Tgg	p.G226W	RP1-56K13.3_ENST00000580121.1_RNA|LASP1_ENST00000435347.3_Missense_Mutation_p.G226W|LASP1_ENST00000433206.2_Missense_Mutation_p.G170W	NM_006148.2	NP_006139.1	Q14847	LASP1_HUMAN	LIM and SH3 protein 1	226	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				ion transport (GO:0006811)|positive regulation of signal transduction (GO:0009967)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	ion transmembrane transporter activity (GO:0015075)|SH3/SH2 adaptor activity (GO:0005070)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(2)|lung(4)|urinary_tract(2)	9						CTTCCAGGACGGGGACACCAT	0.657			T	MLL	AML																																p.G226W		Atlas-SNP	.		Dom	yes		17	17q11-q21.3	3927	LIM and SH3 protein 1		L	.	LASP1	24	.	0			c.G676T						PASS	.						121	105	111					17																	37074921		2203	4300	6503	SO:0001583	missense	3927	exon7			CAGGACGGGGACA		CCDS11331.1, CCDS62164.1	17q11-q21.3	2008-07-18			ENSG00000002834	ENSG00000002834			6513	protein-coding gene	gene with protein product		602920				7490069	Standard	NM_006148		Approved	MLN50, Lasp-1	uc010cvq.3	Q14847	OTTHUMG00000133182	ENST00000318008.6:c.676G>T	chr17.hg19:g.37074921G>T	ENSP00000325240:p.Gly226Trp	182.0	0.0	.		205.0	9.0	.	NM_006148	B4DGQ0|Q96ED2|Q96IG0	Missense_Mutation	SNP	ENST00000318008.6	hg19	CCDS11331.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.839198	0.91117	.	.	ENSG00000002834	ENST00000318008;ENST00000433206;ENST00000435347	T;T;T	0.70045	-0.45;-0.45;-0.45	5.39	5.39	0.77823	Src homology-3 domain (5);	0.476548	0.23146	N	0.051403	D	0.90045	0.6891	H	0.99211	4.47	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94064	0.7329	10	0.87932	D	0	.	17.7153	0.88335	0.0:0.0:1.0:0.0	.	170;226	B4DGQ0;Q14847	.;LASP1_HUMAN	W	226;170;226	ENSP00000325240:G226W;ENSP00000401048:G170W;ENSP00000392853:G226W	ENSP00000325240:G226W	G	+	1	0	LASP1	34328447	1.000000	0.71417	0.961000	0.40146	0.684000	0.39900	9.779000	0.99018	2.540000	0.85666	0.462000	0.41574	GGG	.	.	.	none		0.657	LASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256890.3	NM_006148		T	37074921	G	T	37074921	3	4	194	1	0	0	0	0	1	0	0	0	8644	1116	39	4	702	4	LASP1	17	37074921	Missense_Mutation	SNP	G	TCGA-HE-7129-01A-11D-1961-08	8549382	37074921	44120289	38	11590											
MED24	9862	hgsc.bcm.edu	37	chr17	38182477	38182477	+	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	agctggcggatcatctgcagCgacttctcacgctcatccag	8	9	10	14	3	4	0	3	0	2	0	6	2	5	1	1	2	3	3	1	2	0	1	rs572516214		TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:38182477C>T	ENST00000394128.2	-	19	1998	c.1917G>A	c.(1915-1917)tcG>tcA	p.S639S	MED24_ENST00000501516.3_Silent_p.S658S|SNORD124_ENST00000459577.1_RNA|MED24_ENST00000394126.1_Silent_p.S664S|MED24_ENST00000394127.2_Silent_p.S626S|MED24_ENST00000356271.3_Silent_p.S626S	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	639					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)					TCATCTGCAGCGACTTCTCAC	0.567																																					p.S639S		Atlas-SNP	.											.	MED24	89	.	0			c.G1917A						PASS	.						143	129	134					17																	38182477		2203	4300	6503	SO:0001819	synonymous_variant	9862	exon19			CTGCAGCGACTTC	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.1917G>A	chr17.hg19:g.38182477C>T		203.0	0.0	.		200.0	45.0	.	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Silent	SNP	ENST00000394128.2	hg19	CCDS11359.1																																																																																			.	.	.	none		0.567	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815		T	38182477	C	T	38182477	2	4	194	1	0	0	0	0	0	0	0	1	9449	755	27	1		1	MED24	17	38182477	Silent	SNP	C	TCGA-HE-7129-01A-11D-1961-08	1107556	38182477	43012733	39	11591											
STAT5A	6776	hgsc.bcm.edu	37	chr17	40459443	40459443	+	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	aacttgccgggctggaactaCaccttctggcagtggtttga	8	11	12	10	1	1	1	0	1	1	0	1	2	1	2	2	4	4	3	2	4	3	4			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:40459443C>A	ENST00000345506.4	+	15	2346	c.1704C>A	c.(1702-1704)taC>taA	p.Y568*	STAT5A_ENST00000452307.2_Nonsense_Mutation_p.Y568*|STAT5A_ENST00000546010.2_Nonsense_Mutation_p.Y538*|STAT5A_ENST00000587646.1_Nonsense_Mutation_p.Y56*|STAT5A_ENST00000588868.1_Nonsense_Mutation_p.Y537*|STAT5A_ENST00000590949.1_Nonsense_Mutation_p.Y568*	NM_003152.3	NP_003143.2	P42229	STA5A_HUMAN	signal transducer and activator of transcription 5A	568					2-oxoglutarate metabolic process (GO:0006103)|allantoin metabolic process (GO:0000255)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|citrate metabolic process (GO:0006101)|creatine metabolic process (GO:0006600)|creatinine metabolic process (GO:0046449)|development of secondary female sexual characteristics (GO:0046543)|development of secondary male sexual characteristics (GO:0046544)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|fatty acid metabolic process (GO:0006631)|female pregnancy (GO:0007565)|isoleucine metabolic process (GO:0006549)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|lipid storage (GO:0019915)|luteinization (GO:0001553)|mammary gland epithelium development (GO:0061180)|natural killer cell differentiation (GO:0001779)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of mast cell apoptotic process (GO:0033026)|oxaloacetate metabolic process (GO:0006107)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch development (GO:0048541)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mast cell differentiation (GO:0060376)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prolactin signaling pathway (GO:0038161)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of cell adhesion (GO:0030155)|regulation of epithelial cell differentiation (GO:0030856)|regulation of multicellular organism growth (GO:0040014)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|succinate metabolic process (GO:0006105)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|taurine metabolic process (GO:0019530)|transcription, DNA-templated (GO:0006351)|valine metabolic process (GO:0006573)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	calcium ion binding (GO:0005509)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	14		all_cancers(22;1.56e-06)|all_epithelial(22;3.17e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.128)		GCTGGAACTACACCTTCTGGC	0.632																																					p.Y568X		Atlas-SNP	.											.	STAT5A	49	.	0			c.C1704A						PASS	.						83	76	79					17																	40459443		2203	4300	6503	SO:0001587	stop_gained	6776	exon15			GAACTACACCTTC	U43185	CCDS11424.1, CCDS74066.1, CCDS74067.1	17q11.2	2013-02-14			ENSG00000126561	ENSG00000126561		"SH2 domain containing"	11366	protein-coding gene	gene with protein product		601511		STAT5		7719937, 8631883	Standard	NM_003152		Approved	MGF	uc002hzj.2	P42229	OTTHUMG00000150725	ENST00000345506.4:c.1704C>A	chr17.hg19:g.40459443C>A	ENSP00000341208:p.Tyr568*	40.0	0.0	.		46.0	7.0	.	NM_003152	Q1KLZ6	Nonsense_Mutation	SNP	ENST00000345506.4	hg19	CCDS11424.1	.	.	.	.	.	.	.	.	.	.	C	37	6.584660	0.97684	.	.	ENSG00000126561	ENST00000345506;ENST00000546010;ENST00000540577;ENST00000452307	.	.	.	4.79	1.62	0.23740	.	0.060457	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	-36.8444	10.4319	0.44413	0.0:0.7815:0.0:0.2185	.	.	.	.	X	568;538;539;568	.	ENSP00000341208:Y568X	Y	+	3	2	STAT5A	37712969	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	1.202000	0.32271	0.171000	0.19730	0.491000	0.48974	TAC	.	.	.	none		0.632	STAT5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319804.1	NM_003152		A	40459443	C	A	40459443	4	1	194	1	0	0	0	0	0	1	0	0	15280	489	17	4	1754	4	STAT5A	17	40459443	Nonsense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08	2276966	40459443	40735767	40	11592											
RND2	8153	hgsc.bcm.edu	37	chr17	41180503	41180503	+	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	cctatgttgagtgctcctccCggtcctctgagcgcagcgtc	4	11	11	15	3	1	2	0	2	1	0	5	2	4	2	4	1	3	3	4	1	1	2	rs535296435	byFrequency	TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:41180503C>A	ENST00000587250.2	+	5	597	c.490C>A	c.(490-492)Cgg>Agg	p.R164R	RND2_ENST00000544533.1_Silent_p.R165R|CTD-3199J23.4_ENST00000225973.5_lincRNA			P52198	RND2_HUMAN	Rho family GTPase 2	164					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)		GTGCTCCTCCCGGTCCTCTGA	0.607																																					p.R164R		Atlas-SNP	.											.	RND2	10	.	0			c.C490A						PASS	.						80	75	77					17																	41180503		2203	4300	6503	SO:0001819	synonymous_variant	8153	exon5			TCCTCCCGGTCCT	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	ENST00000587250.2:c.490C>A	chr17.hg19:g.41180503C>A		136.0	0.0	.		170.0	12.0	.	NM_005440	A8K2D4|O00690|O00734|Q5U0P6|Q99535	Silent	SNP	ENST00000587250.2	hg19	CCDS11452.1																																																																																			.	.	.	none		0.607	RND2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453111.2	NM_005440		A	41180503	C	A	41180503	2	1	194	1	0	0	0	0	0	0	0	1	13433	643	23	4		4	RND2	17	41180503	Silent	SNP	C	TCGA-HE-7129-01A-11D-1961-08	721060	41180503	40014707	41	11593											
ITGB3	3690	hgsc.bcm.edu	37	chr17	45369560	45369560	+	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	tccccaggagaaggagaagtCctttaccataaagcccgtgg	12	7	11	11	1	0	2	0	0	0	2	2	4	2	2	5	3	2	0	5	3	5	3			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:45369560C>T	ENST00000559488.1	+	10	1332	c.1316C>T	c.(1315-1317)tCc>tTc	p.S439F	ITGB3_ENST00000435993.2_Missense_Mutation_p.S392F|ITGB3_ENST00000560629.1_Silent_p.V427V	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	439					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)	AAGGAGAAGTCCTTTACCATA	0.522																																					p.S439F		Atlas-SNP	.											.	ITGB3	157	.	0			c.C1316T						PASS	.						94	78	84					17																	45369560		2203	4300	6503	SO:0001583	missense	3690	exon10			AGAAGTCCTTTAC		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.1316C>T	chr17.hg19:g.45369560C>T	ENSP00000452786:p.Ser439Phe	108.0	0.0	.		104.0	67.0	.	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Missense_Mutation	SNP	ENST00000559488.1	hg19	CCDS11511.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.558922	0.86231	.	.	ENSG00000178852	ENST00000262017;ENST00000435993	T	0.67171	-0.25	5.4	5.4	0.78164	Integrin beta subunit, N-terminal (2);	0.153255	0.56097	D	0.000025	T	0.78960	0.4366	L	0.60455	1.87	0.51233	D	0.99991	D	0.64830	0.994	D	0.65573	0.936	T	0.80324	-0.1430	10	0.66056	D	0.02	.	17.9137	0.88942	0.0:1.0:0.0:0.0	.	439	P05106	ITB3_HUMAN	F	439;392	ENSP00000407801:S392F	ENSP00000262017:S439F	S	+	2	0	C17orf57	42724559	0.998000	0.40836	1.000000	0.80357	0.953000	0.61014	3.315000	0.51951	2.531000	0.85337	0.462000	0.41574	TCC	.	.	.	none		0.522	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212		T	45369560	C	T	45369560	3	4	194	1	0	0	0	0	1	0	0	0	7902	855	30	2	1354	2	ITGB3	17	45369560	Missense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08	4189057	45369560	35825650	42	11594											
HSF5	124535	hgsc.bcm.edu	37	chr17	56540550	56540550	+	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	ggaggaatgcaactcatcaaCtatctgaaagacagcctcta	15	8	8	10	0	4	2	2	1	2	1	4	4	4	4	1	2	4	1	1	2	6	2			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:56540550C>G	ENST00000323777.3	-	4	1244	c.1135G>C	c.(1135-1137)Gtt>Ctt	p.V379L		NM_001080439.1	NP_001073908.1	Q4G112	HSF5_HUMAN	heat shock transcription factor family member 5	379					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)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(3)|skin(1)	16	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AACTCATCAACTATCTGAAAG	0.438																																					p.V379L		Atlas-SNP	.											.	HSF5	51	.	0			c.G1135C						PASS	.						101	97	98					17																	56540550		2203	4300	6503	SO:0001583	missense	124535	exon4			CATCAACTATCTG	BC033020	CCDS32690.1	17q23.2	2006-04-25				ENSG00000176160			26862	protein-coding gene	gene with protein product							Standard	NM_001080439		Approved	FLJ40311	uc002iwi.1	Q4G112		ENST00000323777.3:c.1135G>C	chr17.hg19:g.56540550C>G	ENSP00000313243:p.Val379Leu	144.0	0.0	.		227.0	69.0	.	NM_001080439	Q08EH7|Q8N7V2	Missense_Mutation	SNP	ENST00000323777.3	hg19	CCDS32690.1	.	.	.	.	.	.	.	.	.	.	C	13.97	2.396051	0.42512	.	.	ENSG00000176160	ENST00000412540;ENST00000323777	T	0.43294	0.95	5.47	4.49	0.54785	.	0.247257	0.28754	N	0.014249	T	0.30448	0.0765	L	0.27053	0.805	0.38062	D	0.936116	B	0.06786	0.001	B	0.08055	0.003	T	0.11372	-1.0590	10	0.34782	T	0.22	.	12.6737	0.56882	0.1654:0.8346:0.0:0.0	.	379	Q4G112	HSF5_HUMAN	L	279;379	ENSP00000313243:V379L	ENSP00000313243:V379L	V	-	1	0	HSF5	53895549	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.377000	0.44300	1.273000	0.44346	0.650000	0.86243	GTT	.	.	.	none		0.438	HSF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444719.1	XM_064190		G	56540550	C	G	56540550	3	3	194	1	0	0	0	0	1	0	0	0	7406	565	20	4	667	4	HSF5	17	56540550	Missense_Mutation	SNP	C	TCGA-HE-7129-01A-11D-1961-08	11170990	56540550	24654660	43	11595											
METTL2A	339175	hgsc.bcm.edu	37	chr17	60501296	60501296	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taccctgaaggtgcacctgcAgtcctcgccgataagaggca	10	7	11	13	2	0	2	0	1	0	1	2	3	1	2	4	2	3	3	4	2	3	2			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:60501296A>G	ENST00000311506.5	+	1	69	c.33A>G	c.(31-33)gcA>gcG	p.A11A		NM_181725.3	NP_859076.3	Q96IZ6	MET2A_HUMAN	methyltransferase like 2A	11					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)			GTGCACCTGCAGTCCTCGCCG	0.597											OREG0024635	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A11A		Atlas-SNP	.											.	METTL2A	31	.	0			c.A33G						PASS	.						57	67	64					17																	60501296		692	1591	2283	SO:0001819	synonymous_variant	339175	exon1			ACCTGCAGTCCTC	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.33A>G	chr17.hg19:g.60501296A>G		51.0	0.0	.	1046	73.0	24.0	.	NM_181725	A6NNC4|Q9H9G9|Q9NUI8|Q9P0B5	Silent	SNP	ENST00000311506.5	hg19	CCDS45752.1																																																																																			.	.	.	none		0.597	METTL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445130.1	NM_181725		G	60501296	A	G	60501296	2	3	194	1	0	0	0	0	0	0	0	1	9506	175	7	3		3	METTL2A	17	60501296	Silent	SNP	A	TCGA-HE-7129-01A-11D-1961-08	3960746	60501296	20693914	44	11596											
CYB561	1534	hgsc.bcm.edu	37	chr17	61511913	61511913	+	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	gccagcagcaggcccagcacGttggccaggacaccctcggg	8	3	14	16	2	0	0	0	0	0	0	1	1	0	1	4	4	3	4	4	4	0	1			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:61511913G>A	ENST00000392976.1	-	6	905	c.606C>T	c.(604-606)aaC>aaT	p.N202N	CYB561_ENST00000582997.1_Silent_p.N209N|CYB561_ENST00000542042.1_Silent_p.N269N|CYB561_ENST00000582297.1_Intron|CYB561_ENST00000581163.1_5'UTR|CYB561_ENST00000448884.2_3'UTR|RP11-269G24.4_ENST00000584608.1_lincRNA|CYB561_ENST00000582034.1_Silent_p.N173N|CYB561_ENST00000360793.3_Silent_p.N202N|CYB561_ENST00000392975.2_Silent_p.N202N|CYB561_ENST00000584031.1_3'UTR|CYB561_ENST00000581573.1_Silent_p.N202N	NM_001017916.1	NP_001017916.1	P49447	CY561_HUMAN	cytochrome b561	202	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)		GGCCCAGCACGTTGGCCAGGA	0.642																																					p.N202N		Atlas-SNP	.											.	CYB561	15	.	0			c.C606T						PASS	.						48	48	48					17																	61511913		2203	4300	6503	SO:0001819	synonymous_variant	1534	exon6			CAGCACGTTGGCC		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.606C>T	chr17.hg19:g.61511913G>A		44.0	0.0	.		50.0	33.0	.	NM_001915	B2RE96|B7Z775|D3DU11|Q5BJG9|Q9BU05|Q9BWR9	Silent	SNP	ENST00000392976.1	hg19	CCDS11636.1																																																																																			.	.	.	none		0.642	CYB561-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444843.1	NM_001915		A	61511913	G	A	61511913	2	1	194	1	0	0	0	0	0	0	0	1	4121	1136	40	1		1	CYB561	17	61511913	Silent	SNP	G	TCGA-HE-7129-01A-11D-1961-08	1010617	61511913	19683297	45	11597											
ABCA5	23461	hgsc.bcm.edu	37	chr17	67303077	67303077	+	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	tgactccagctccttccaaaGagaaacattggtcttcaact	12	11	6	12	0	2	2	1	1	1	1	5	3	5	2	3	1	3	1	3	1	3	3			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr17:67303077G>A	ENST00000392676.3	-	6	641	c.577C>T	c.(577-579)Ctt>Ttt	p.L193F	ABCA5_ENST00000392677.2_Missense_Mutation_p.L193F|ABCA5_ENST00000588877.1_Missense_Mutation_p.L193F			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	193					cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	TCCTTCCAAAGAGAAACATTG	0.348																																					p.L193F		Atlas-SNP	.											.	ABCA5	162	.	0			c.C577T						PASS	.						56	60	59					17																	67303077		2198	4294	6492	SO:0001583	missense	23461	exon5			TCCAAAGAGAAAC	U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"ATP binding cassette transporters / subfamily A"	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.577C>T	chr17.hg19:g.67303077G>A	ENSP00000376443:p.Leu193Phe	63.0	0.0	.		113.0	39.0	.	NM_018672	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Missense_Mutation	SNP	ENST00000392676.3	hg19	CCDS11685.1	.	.	.	.	.	.	.	.	.	.	G	15.45	2.836993	0.50951	.	.	ENSG00000154265	ENST00000392677;ENST00000392676	D;D	0.87966	-2.32;-2.32	5.22	-9.14	0.00701	.	1.842040	0.03300	N	0.188828	T	0.60625	0.2283	N	0.01352	-0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.001;0.003	T	0.57452	-0.7809	9	.	.	.	.	6.752	0.23491	0.1697:0.5331:0.2205:0.0768	.	193;193	Q8WWZ7-2;Q8WWZ7	.;ABCA5_HUMAN	F	193	ENSP00000376444:L193F;ENSP00000376443:L193F	.	L	-	1	0	ABCA5	64814672	0.090000	0.21635	0.839000	0.33178	0.999000	0.98932	0.440000	0.21592	-1.239000	0.02532	0.650000	0.86243	CTT	.	.	.	none		0.348	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672		A	67303077	G	A	67303077	3	1	194	1	0	0	0	0	1	0	0	0	35	942	33	2	4487	2	ABCA5	17	67303077	Missense_Mutation	SNP	G	TCGA-HE-7129-01A-11D-1961-08	5791164	67303077	13892133	46	11598											
RIN2	54453	hgsc.bcm.edu	37	chr20	19955386	19955386	+	Silent	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	gacggtgtctgtcctgcctcCctgcgtcagctctgccttat	3	13	10	15	2	3	0	1	0	2	0	5	1	5	0	4	1	4	1	4	1	1	1			TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chr20:19955386C>T	ENST00000255006.6	+	8	1013	c.864C>T	c.(862-864)tcC>tcT	p.S288S	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	239					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						GTCCTGCCTCCCTGCGTCAGC	0.547																																					p.S288S		Atlas-SNP	.											.	RIN2	126	.	0			c.C864T						PASS	.						73	77	75					20																	19955386		1935	4144	6079	SO:0001819	synonymous_variant	54453	exon8			TGCCTCCCTGCGT	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.864C>T	chr20.hg19:g.19955386C>T		105.0	0.0	.		68.0	33.0	.	NM_001242581	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000255006.6	hg19	CCDS56182.1																																																																																			.	.	.	none		0.547	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1			T	19955386	C	T	19955386	2	4	194	1	0	0	0	0	0	0	0	1	13385	610	22	2		2	RIN2	20	19955386	Silent	SNP	C	TCGA-HE-7129-01A-11D-1961-08		19955386	43070134	47	11599											
KDM6A	7403	hgsc.bcm.edu	37	chrX	44920581	44920581	+	Frame_Shift_Del	DEL	A	A	-																															ttcctcagaatacttctgacAattggagtggtggacatgct																										TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chrX:44920581delA	ENST00000377967.4	+	14	1383	c.1342delA	c.(1342-1344)aatfs	p.N448fs	KDM6A_ENST00000536777.1_Frame_Shift_Del_p.N403fs|KDM6A_ENST00000543216.1_Frame_Shift_Del_p.N403fs|KDM6A_ENST00000382899.4_Frame_Shift_Del_p.N455fs	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	448	Interaction with SUPT6H. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0?(6)|p.0(2)		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						TACTTCTGACAATTGGAGTGG	0.348			"D, N, F, S"		"renal, oesophageal SCC, MM"																																p.D447fs	Colon(129;1273 1667 15230 27352 52914)	Atlas-INDEL	.		Rec	yes		X	Xp11.2	7403	"lysine (K)-specific demethylase 6A, UTX"		"E, L"	.	KDM6A	274	.	8	Whole gene deletion(6)|No detectable mRNA/protein(2)	haematopoietic_and_lymphoid_tissue(2)|oesophagus(2)|breast(2)|pancreas(2)	c.1341delC						PASS	.						58	47	51					X																	44920581		2203	4300	6503	SO:0001589	frameshift_variant	7403	exon14			.	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.1342delA	chrX.hg19:g.44920581delA	ENSP00000367203:p.Asn448fs	11.0	0.0	0		15.0	14.0	0.933333	NM_021140	Q52LL9|Q5JVQ7	Frame_Shift_Del	DEL	ENST00000377967.4	hg19	CCDS14265.1																																																																																			.	.	.	none		0.348	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140		-	44920581	A	-	44920581	7	5	194	1	0	1	0	1	0	0	0	0	8144	130	5	0	1396	0	KDM6A	23	44920581	Frame_Shift_Del	DEL	A	TCGA-HE-7129-01A-11D-1961-08		44920581	110349979	48	11600											
EMD	2010	hgsc.bcm.edu	37	chrX	153609241	153609241	+	Splice_Site	DEL	G	G	-																															tgctcccctcttttgcctcaGggaacgccccatgtacggcc																										TCGA-HE-7129-01A-11D-1961-08	TCGA-HE-7129-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c56f3efb-5a25-4967-b817-44b1eb9f440a	3c6e3907-3f31-4a91-825b-87070d603395	g.chrX:153609241delG	ENST00000369842.4	+	6	737		c.e6-1		EMD_ENST00000492448.1_Splice_Site|EMD_ENST00000369835.3_Splice_Site	NM_000117.2	NP_000108.1	P50402	EMD_HUMAN	emerin						cellular response to growth factor stimulus (GO:0071363)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of fibroblast proliferation (GO:0048147)|positive regulation of protein export from nucleus (GO:0046827)|regulation of canonical Wnt signaling pathway (GO:0060828)|skeletal muscle cell differentiation (GO:0035914)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule (GO:0005874)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|nuclear outer membrane (GO:0005640)	actin binding (GO:0003779)|beta-tubulin binding (GO:0048487)			lung(5)	5	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TTTTGCCTCAGGGAACGCCCC	0.622																																					.		Atlas-INDEL	.											.	EMD	25	.	0			c.450-2G>-						PASS	.						77	67	71					X																	153609241		2203	4300	6503	SO:0001630	splice_region_variant	2010	exon6			.	X82434	CCDS14745.1	Xq27.3-q28	2014-09-17	2008-07-29		ENSG00000102119	ENSG00000102119			3331	protein-coding gene	gene with protein product	"LEM domain containing 5"	300384	"Emery-Dreifuss muscular dystrophy"				Standard	NM_000117		Approved	STA, LEMD5	uc004fkl.3	P50402	OTTHUMG00000033186	ENST00000369842.4:c.450-1G>-	chrX.hg19:g.153609241delG		70.0	0.0	0		45.0	40.0	0.888889	NM_000117	Q6FI02	Splice_Site	DEL	ENST00000369842.4	hg19	CCDS14745.1																																																																																			.	.	.	none		0.622	EMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080921.1		Intron	-	153609241	G	-	153609241	8	5	194	1	0	1	0	1	0	0	1	0	5089	1014	35	0	471	0	EMD	23	153609241	Splice_Site	DEL	G	TCGA-HE-7129-01A-11D-1961-08	108688660	153609241	1661319	49	11601											
PEX10	5192	hgsc.bcm.edu	37	chr1	2341814	2341814	+	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	ccgtgggagcttctacctgcAagtgtggtgaggccaaagta	9	9	14	9	1	1	1	0	1	1	0	1	2	1	2	3	3	3	3	3	3	4	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:2341814A>C	ENST00000447513.2	-	2	257	c.189T>G	c.(187-189)ctT>ctG	p.L63L	PEX10_ENST00000288774.3_Silent_p.L63L|PEX10_ENST00000515760.1_5'Flank|PEX10_ENST00000507596.1_Silent_p.L63L	NM_002617.3	NP_002608.1	O60683	PEX10_HUMAN	peroxisomal biogenesis factor 10	63					peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)	integral component of peroxisomal membrane (GO:0005779)|intracellular (GO:0005622)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(2)	7	all_cancers(77;0.000247)|all_epithelial(69;9.96e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;5.35e-20)|all_lung(118;2.78e-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)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.1e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.02e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00102)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0169)|Lung(427;0.199)		TTCTACCTGCAAGTGTGGTGA	0.597																																					p.L63L	GBM(12;9 508 1649 13619)	Atlas-SNP	.											.	PEX10	18	.	0			c.T189G						PASS	.						99	86	91					1																	2341814		2203	4300	6503	SO:0001819	synonymous_variant	5192	exon2			ACCTGCAAGTGTG	AF060502	CCDS41.1, CCDS44045.1	1p36.32	2013-01-09	2008-08-26		ENSG00000157911	ENSG00000157911		"RING-type (C3HC4) zinc fingers"	8851	protein-coding gene	gene with protein product		602859	"peroxisome biogenesis factor 10"			9683594	Standard	NM_002617		Approved	RNF69	uc001ajg.3	O60683	OTTHUMG00000001637	ENST00000447513.2:c.189T>G	chr1.hg19:g.2341814A>C		47.0	0.0	.		61.0	25.0	.	NM_002617	B3KWD8|Q5T095|Q9BW90	Silent	SNP	ENST00000447513.2	hg19	CCDS44045.1																																																																																			.	.	.	none		0.597	PEX10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367454.1	NM_153818		C	2341814	A	C	2341814	2	2	195	1	0	0	0	0	0	0	0	1	11743	117	5	5		5	PEX10	1	2341814	Silent	SNP	A	TCGA-HE-7130-01A-11D-1961-08		2341814	246908807	1	11602											
KIF1B	23095	hgsc.bcm.edu	37	chr1	10431203	10431203	+	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	ttcggtttgcttccagttgtCtgatatctctccaattggac	6	17	8	10	1	2	1	0	1	2	0	6	2	4	2	2	2	1	3	2	2	2	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:10431203C>T	ENST00000377086.1	+	45	5031	c.4829C>T	c.(4828-4830)tCt>tTt	p.S1610F	KIF1B_ENST00000377081.1_Missense_Mutation_p.S1610F|KIF1B_ENST00000263934.6_Missense_Mutation_p.S1564F			O60333	KIF1B_HUMAN	kinesin family member 1B	1610					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)		TTCCAGTTGTCTGATATCTCT	0.488																																					p.S1564F		Atlas-SNP	.											.	KIF1B	242	.	0			c.C4691T						PASS	.						139	121	127					1																	10431203		2203	4300	6503	SO:0001583	missense	23095	exon43			AGTTGTCTGATAT	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.4829C>T	chr1.hg19:g.10431203C>T	ENSP00000366290:p.Ser1610Phe	101.0	0.0	.		180.0	45.0	.	NM_015074	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	hg19		.	.	.	.	.	.	.	.	.	.	C	26.3	4.719966	0.89205	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377086;ENST00000377081	T;T;T	0.11712	2.75;2.75;2.75	5.53	5.53	0.82687	.	0.060274	0.64402	D	0.000002	T	0.22126	0.0533	N	0.19112	0.55	0.80722	D	1	D;P;D;D;P;D	0.76494	0.966;0.744;0.999;0.972;0.952;0.994	P;B;D;P;B;D	0.74348	0.641;0.289;0.959;0.845;0.288;0.983	T	0.02868	-1.1100	10	0.72032	D	0.01	.	19.8228	0.96604	0.0:1.0:0.0:0.0	.	1596;1570;1610;1584;1610;1564	Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2	.;.;.;.;KIF1B_HUMAN;.	F	1610;1564;1610;1610	ENSP00000263934:S1564F;ENSP00000366290:S1610F;ENSP00000366284:S1610F	ENSP00000263934:S1564F	S	+	2	0	KIF1B	10353790	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	7.445000	0.80570	2.759000	0.94783	0.650000	0.86243	TCT	.	.	.	none		0.488	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1			T	10431203	C	T	10431203	3	4	195	1	0	0	0	0	1	0	0	0	8291	913	32	2	6346	2	KIF1B	1	10431203	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	8089389	10431203	238819418	2	11603											
C1orf187	374946	hgsc.bcm.edu	37	chr1	11775243	11775243	+	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	ggcctcaacaacaaatgcttCgatgactgcatgtgtgtgga	11	10	11	9	1	1	1	1	1	0	0	2	3	1	2	1	2	4	2	1	2	3	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:11775243C>T	ENST00000294485.5	+	6	1050	c.915C>T	c.(913-915)ttC>ttT	p.F305F		NM_198545.3	NP_940947.3			dorsal inhibitory axon guidance protein																		ACAAATGCTTCGATGACTGCA	0.582																																					p.F305F		Atlas-SNP	.											.	.	.	.	0			c.C915T						PASS	.						180	135	150					1																	11775243		2203	4300	6503	SO:0001819	synonymous_variant	374946	exon6			ATGCTTCGATGAC	AY358750	CCDS135.1	1p36.22	2012-08-20	2012-08-14	2012-08-14	ENSG00000162490	ENSG00000162490			25054	protein-coding gene	gene with protein product	"dorsal repulsive axon guidance protein", "neural tissue-specific cysteine-rich protein"	612682	"chromosome 1 open reading frame 187"	C1orf187		19150847	Standard	NM_198545		Approved	FLJ34999, Draxin, Neucrin	uc001asr.1	Q8NBI3	OTTHUMG00000002227	ENST00000294485.5:c.915C>T	chr1.hg19:g.11775243C>T		126.0	0.0	.		171.0	29.0	.	NM_198545		Silent	SNP	ENST00000294485.5	hg19	CCDS135.1																																																																																			.	.	.	none		0.582	DRAXIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006325.1	NM_198545		T	11775243	C	T	11775243	2	4	195	1	0	0	0	0	0	0	0	1	2023	883	31	1		1	C1orf187	1	11775243	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	1344040	11775243	237475378	3	11604											
CASP9	842	hgsc.bcm.edu	37	chr1	15844625	15844625	+	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	cgacatcaccaaatcctccaGaaccaatgtccactggtctg	12	8	6	15	1	2	1	1	0	1	1	5	2	5	1	5	1	1	0	5	1	3	0			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:15844625G>A	ENST00000333868.5	-	2	492	c.398C>T	c.(397-399)tCt>tTt	p.S133F	CASP9_ENST00000546424.1_Missense_Mutation_p.S133F|CASP9_ENST00000375890.4_Missense_Mutation_p.S50F|CASP9_ENST00000469637.1_5'Flank|CASP9_ENST00000348549.5_Missense_Mutation_p.S133F	NM_001229.3	NP_001220.2	P55211	CASP9_HUMAN	caspase 9, apoptosis-related cysteine peptidase	133					activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|aging (GO:0007568)|apoptotic process (GO:0006915)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell apoptotic process (GO:0034349)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of apoptotic process (GO:0042981)|regulation of response to DNA damage stimulus (GO:2001020)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|signal transduction in response to DNA damage (GO:0042770)	apoptosome (GO:0043293)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|enzyme activator activity (GO:0008047)|peptidase activity (GO:0008233)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|stomach(1)	18		Breast(348;0.000207)|all_lung(284;0.000211)|Colorectal(325;0.000259)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;8.49e-07)|COAD - Colon adenocarcinoma(227;4.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00013)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00763)|READ - Rectum adenocarcinoma(331;0.0655)		AAATCCTCCAGAACCAATGTC	0.517																																					p.S133F		Atlas-SNP	.											.	CASP9	40	.	0			c.C398T						PASS	.						114	100	105					1																	15844625		2203	4300	6503	SO:0001583	missense	842	exon2			CCTCCAGAACCAA	U60521	CCDS158.1, CCDS159.1, CCDS159.2, CCDS59995.1	1p36.21	2012-04-17	2005-08-17		ENSG00000132906	ENSG00000132906		"Caspases", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1511	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 56"	602234	"caspase 9, apoptosis-related cysteine protease"			8663294, 9390557	Standard	NM_001229		Approved	MCH6, ICE-LAP6, APAF-3, PPP1R56	uc001awn.4	P55211	OTTHUMG00000002256	ENST00000333868.5:c.398C>T	chr1.hg19:g.15844625G>A	ENSP00000330237:p.Ser133Phe	128.0	0.0	.		203.0	36.0	.	NM_001229	B4E1A3|O95348|Q53Y70|Q5JRU9|Q5UGI1|Q92852|Q9BQ62|Q9UEQ3|Q9UIJ8	Missense_Mutation	SNP	ENST00000333868.5	hg19	CCDS158.1	.	.	.	.	.	.	.	.	.	.	G	8.539	0.872713	0.17322	.	.	ENSG00000132906	ENST00000546424;ENST00000333868;ENST00000348549;ENST00000375890;ENST00000447522;ENST00000440484	T;T;T;T;T;T	0.09445	4.56;4.58;2.98;4.47;3.81;3.51	4.77	3.83	0.44106	.	1.470630	0.03659	N	0.242280	T	0.24586	0.0596	L	0.50333	1.59	0.09310	N	1	D;P;B	0.54207	0.965;0.695;0.137	P;B;B	0.54312	0.748;0.231;0.087	T	0.20042	-1.0287	10	0.66056	D	0.02	.	10.9008	0.47051	0.0:0.1903:0.8097:0.0	.	133;133;133	P55211-2;P55211;F8VVS7	.;CASP9_HUMAN;.	F	133;133;133;50;50;133	ENSP00000449584:S133F;ENSP00000330237:S133F;ENSP00000255256:S133F;ENSP00000365051:S50F;ENSP00000396540:S50F;ENSP00000411304:S133F	ENSP00000330237:S133F	S	-	2	0	CASP9	15717212	0.022000	0.18835	0.150000	0.22450	0.099000	0.18886	1.320000	0.33666	1.330000	0.45394	0.563000	0.77884	TCT	.	.	.	none		0.517	CASP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006438.1	NM_032996		A	15844625	G	A	15844625	3	1	195	1	0	0	0	0	1	0	0	0	2681	942	33	2	884	2	CASP9	1	15844625	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	4069382	15844625	233405996	4	11605											
EIF4G3	8672	hgsc.bcm.edu	37	chr1	21188793	21188793	+	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	tttctttctttcacaattttCtccatctgattaaagtactg	9	20	3	9	0	5	1	1	1	4	0	6	1	5	1	1	0	1	1	1	0	4	7			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:21188793C>G	ENST00000264211.8	-	17	3065	c.2871G>C	c.(2869-2871)gaG>gaC	p.E957D	EIF4G3_ENST00000602326.1_Missense_Mutation_p.E963D|EIF4G3_ENST00000374937.3_Missense_Mutation_p.E963D|EIF4G3_ENST00000400422.1_Missense_Mutation_p.E957D|EIF4G3_ENST00000537738.1_Missense_Mutation_p.E447D|EIF4G3_ENST00000374935.3_Missense_Mutation_p.E677D|EIF4G3_ENST00000536266.1_Missense_Mutation_p.E561D	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	957	MIF4G. {ECO:0000255|PROSITE- ProRule:PRU00698}.|eIF3/EIF4A-binding. {ECO:0000250}.				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)		TCACAATTTTCTCCATCTGAT	0.353																																					p.E993D		Atlas-SNP	.											EIF4G3_ENST00000374937,NS,carcinoma,0,2	EIF4G3	300	.	0			c.G2979C						PASS	.						123	119	121					1																	21188793		2203	4300	6503	SO:0001583	missense	8672	exon21			AATTTTCTCCATC	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.2871G>C	chr1.hg19:g.21188793C>G	ENSP00000264211:p.Glu957Asp	82.0	0.0	.		83.0	6.0	.	NM_001198801	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Missense_Mutation	SNP	ENST00000264211.8	hg19	CCDS214.1	.	.	.	.	.	.	.	.	.	.	C	16.86	3.240150	0.58995	.	.	ENSG00000075151	ENST00000264211;ENST00000400415;ENST00000400422;ENST00000374935;ENST00000537738;ENST00000374937;ENST00000536266	T;T;T;T;T;T	0.25250	1.81;1.81;1.81;1.81;1.81;1.81	5.56	1.54	0.23209	MIF4G-like, type 3 (2);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.122140	0.56097	D	0.000022	T	0.34454	0.0898	L	0.37561	1.115	0.80722	D	1	D;B;B;D;B	0.89917	1.0;0.035;0.0;0.999;0.392	D;B;B;D;B	0.85130	0.997;0.05;0.011;0.994;0.173	T	0.01484	-1.1343	10	0.27785	T	0.31	-16.9367	9.6933	0.40143	0.0:0.7145:0.0:0.2855	.	1152;677;561;963;957	Q59GJ0;Q504Z1;F5H564;B9EGQ7;O43432	.;.;.;.;IF4G3_HUMAN	D	957;1153;957;677;447;963;561	ENSP00000264211:E957D;ENSP00000383274:E957D;ENSP00000364071:E677D;ENSP00000442010:E447D;ENSP00000364073:E963D;ENSP00000444693:E561D	ENSP00000264211:E957D	E	-	3	2	EIF4G3	21061380	0.678000	0.27586	0.998000	0.56505	0.983000	0.72400	-0.070000	0.11523	0.025000	0.15241	-0.808000	0.03180	GAG	.	.	.	none		0.353	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760		G	21188793	C	G	21188793	3	3	195	1	0	0	0	0	1	0	0	0	5040	912	32	4	1946	4	EIF4G3	1	21188793	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	5344168	21188793	228061828	5	11606											
EIF4G3	8672	hgsc.bcm.edu	37	chr1	21226427	21226427	+	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	gtcaatggaaagctcctcttCagctttaagctaaataataa	15	12	6	8	0	3	0	2	0	1	0	4	1	4	1	1	1	3	3	1	1	7	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:21226427C>T	ENST00000264211.8	-	10	1788	c.1594G>A	c.(1594-1596)Gaa>Aaa	p.E532K	EIF4G3_ENST00000602326.1_Missense_Mutation_p.E538K|EIF4G3_ENST00000374937.3_Missense_Mutation_p.E538K|EIF4G3_ENST00000400422.1_Missense_Mutation_p.E532K|EIF4G3_ENST00000537738.1_5'Flank|EIF4G3_ENST00000544689.1_Missense_Mutation_p.E75K|EIF4G3_ENST00000374935.3_Missense_Mutation_p.E252K|EIF4G3_ENST00000536266.1_Missense_Mutation_p.E136K|EIF4G3_ENST00000374933.3_5'UTR	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	532					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)		AGCTCCTCTTCAGCTTTAAGC	0.358																																					p.E538K		Atlas-SNP	.											.	EIF4G3	300	.	0			c.G1612A						PASS	.						95	103	100					1																	21226427		2202	4300	6502	SO:0001583	missense	8672	exon14			CCTCTTCAGCTTT	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.1594G>A	chr1.hg19:g.21226427C>T	ENSP00000264211:p.Glu532Lys	206.0	0.0	.		164.0	38.0	.	NM_001198802	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Missense_Mutation	SNP	ENST00000264211.8	hg19	CCDS214.1	.	.	.	.	.	.	.	.	.	.	C	15.51	2.854237	0.51270	.	.	ENSG00000075151	ENST00000264211;ENST00000400415;ENST00000400422;ENST00000374935;ENST00000374937;ENST00000536266;ENST00000374933;ENST00000544689	T;T;T;T;T;D	0.87412	2.05;2.05;1.94;2.05;2.05;-2.25	4.98	4.06	0.47325	.	0.426295	0.27143	N	0.020740	T	0.74809	0.3765	N	0.08118	0	0.80722	D	1	P;P;B;P;B	0.47762	0.9;0.651;0.007;0.546;0.376	B;B;B;B;B	0.40285	0.325;0.115;0.006;0.049;0.099	T	0.78458	-0.2196	10	0.52906	T	0.07	-18.3664	13.2326	0.59951	0.0:0.9233:0.0:0.0767	.	727;252;136;538;532	Q59GJ0;Q504Z1;F5H564;B9EGQ7;O43432	.;.;.;.;IF4G3_HUMAN	K	532;728;532;252;538;136;75;75	ENSP00000264211:E532K;ENSP00000383274:E532K;ENSP00000364071:E252K;ENSP00000364073:E538K;ENSP00000444693:E136K;ENSP00000444401:E75K	ENSP00000264211:E532K	E	-	1	0	EIF4G3	21099014	0.999000	0.42202	0.967000	0.41034	0.284000	0.27059	5.276000	0.65580	1.325000	0.45301	0.644000	0.83932	GAA	.	.	.	none		0.358	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760		T	21226427	C	T	21226427	3	4	195	1	0	0	0	0	1	0	0	0	5040	835	29	2	3251	2	EIF4G3	1	21226427	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	37634	21226427	228024194	6	11607											
CDC42	998	hgsc.bcm.edu	37	chr1	22413230	22413230	+	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	gttgggactcaaattgatctCagagatgacccctctactat	11	12	8	10	0	3	3	2	2	2	1	4	5	3	4	2	1	1	1	2	1	3	4	rs143448220		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:22413230C>G	ENST00000344548.3	+	6	608	c.357C>G	c.(355-357)ctC>ctG	p.L119L	CDC42_ENST00000400259.1_Silent_p.L119L|CDC42_ENST00000498236.1_3'UTR|CDC42_ENST00000315554.8_Silent_p.L119L|CDC42_ENST00000421089.2_Silent_p.L161L	NM_001039802.1	NP_001034891.1	P60953	CDC42_HUMAN	cell division cycle 42	119					actin cytoskeleton organization (GO:0030036)|actin filament branching (GO:0090135)|actin filament bundle assembly (GO:0051017)|adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway (GO:0060070)|cardiac conduction system development (GO:0003161)|cellular protein localization (GO:0034613)|dendritic cell migration (GO:0036336)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell-cell adhesion (GO:0090136)|epithelial-mesenchymal cell signaling (GO:0060684)|establishment of Golgi localization (GO:0051683)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|filopodium assembly (GO:0046847)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|heart contraction (GO:0060047)|innate immune response (GO:0045087)|keratinization (GO:0031424)|keratinocyte development (GO:0003334)|macrophage differentiation (GO:0030225)|multicellular organism growth (GO:0035264)|muscle cell differentiation (GO:0042692)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of gene expression (GO:0010629)|negative regulation of protein complex assembly (GO:0031333)|neuron fate determination (GO:0048664)|nuclear migration (GO:0007097)|nucleus localization (GO:0051647)|organelle transport along microtubule (GO:0072384)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of hair follicle cell proliferation (GO:0071338)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of JNK cascade (GO:0046330)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of synapse structural plasticity (GO:0051835)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of filopodium assembly (GO:0051489)|regulation of mitosis (GO:0007088)|regulation of protein catabolic process (GO:0042176)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein kinase activity (GO:0045859)|regulation of protein stability (GO:0031647)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|sprouting angiogenesis (GO:0002040)|submandibular salivary gland formation (GO:0060661)|substantia nigra development (GO:0021762)|T cell costimulation (GO:0031295)	apical part of cell (GO:0045177)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|leading edge membrane (GO:0031256)|membrane (GO:0016020)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|spindle midzone (GO:0051233)	apolipoprotein A-I receptor binding (GO:0034191)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|thioesterase binding (GO:0031996)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(4)	12		Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)|Prostate(1639;0.0792)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0452)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.35e-07)|COAD - Colon adenocarcinoma(152;7.73e-06)|GBM - Glioblastoma multiforme(114;8.62e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000649)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00767)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.207)		AAATTGATCTCAGAGATGACC	0.438																																					p.L119L		Atlas-SNP	.											.	CDC42	26	.	0			c.C357G						PASS	.						167	181	177					1																	22413230		2203	4300	6503	SO:0001819	synonymous_variant	998	exon6			TGATCTCAGAGAT	BC018266	CCDS221.1, CCDS222.1	1p36.1	2013-01-17	2013-01-17		ENSG00000070831	ENSG00000070831			1736	protein-coding gene	gene with protein product	"GTP binding protein, 25kDa"	116952	"cell division cycle 42 (GTP-binding protein, 25kD)", "cell division cycle 42 (GTP binding protein, 25kDa)"			2124704, 2122236	Standard	NM_001039802		Approved	G25K, CDC42Hs	uc001bfr.3	P60953	OTTHUMG00000002753	ENST00000344548.3:c.357C>G	chr1.hg19:g.22413230C>G		383.0	0.0	.		285.0	72.0	.	NM_001039802	P21181|P25763|Q7L8R5|Q9UDI2	Silent	SNP	ENST00000344548.3	hg19	CCDS221.1																																																																																			.	C|1.000;T|0.000	.	alt		0.438	CDC42-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007787.1	NM_001791		G	22413230	C	G	22413230	2	3	195	1	0	0	0	0	0	0	0	1	3073	813	29	4		4	CDC42	1	22413230	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	1186803	22413230	226837391	7	11608											
CDC42	998	hgsc.bcm.edu	37	chr1	22413329	22413329	+	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	gcccgtgacctgaaggctgtCaagtatgtggagtgttctgc	7	11	14	9	1	2	2	1	2	1	0	2	3	2	3	2	2	1	3	2	2	3	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:22413329C>G	ENST00000344548.3	+	6	707	c.456C>G	c.(454-456)gtC>gtG	p.V152V	CDC42_ENST00000400259.1_Silent_p.V152V|CDC42_ENST00000498236.1_3'UTR|CDC42_ENST00000315554.8_Silent_p.V152V|CDC42_ENST00000421089.2_Silent_p.V194V	NM_001039802.1	NP_001034891.1	P60953	CDC42_HUMAN	cell division cycle 42	152					actin cytoskeleton organization (GO:0030036)|actin filament branching (GO:0090135)|actin filament bundle assembly (GO:0051017)|adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway (GO:0060070)|cardiac conduction system development (GO:0003161)|cellular protein localization (GO:0034613)|dendritic cell migration (GO:0036336)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell-cell adhesion (GO:0090136)|epithelial-mesenchymal cell signaling (GO:0060684)|establishment of Golgi localization (GO:0051683)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|filopodium assembly (GO:0046847)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|heart contraction (GO:0060047)|innate immune response (GO:0045087)|keratinization (GO:0031424)|keratinocyte development (GO:0003334)|macrophage differentiation (GO:0030225)|multicellular organism growth (GO:0035264)|muscle cell differentiation (GO:0042692)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of gene expression (GO:0010629)|negative regulation of protein complex assembly (GO:0031333)|neuron fate determination (GO:0048664)|nuclear migration (GO:0007097)|nucleus localization (GO:0051647)|organelle transport along microtubule (GO:0072384)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of hair follicle cell proliferation (GO:0071338)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of JNK cascade (GO:0046330)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of synapse structural plasticity (GO:0051835)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of filopodium assembly (GO:0051489)|regulation of mitosis (GO:0007088)|regulation of protein catabolic process (GO:0042176)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein kinase activity (GO:0045859)|regulation of protein stability (GO:0031647)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|sprouting angiogenesis (GO:0002040)|submandibular salivary gland formation (GO:0060661)|substantia nigra development (GO:0021762)|T cell costimulation (GO:0031295)	apical part of cell (GO:0045177)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|leading edge membrane (GO:0031256)|membrane (GO:0016020)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|spindle midzone (GO:0051233)	apolipoprotein A-I receptor binding (GO:0034191)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|thioesterase binding (GO:0031996)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(4)	12		Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)|Prostate(1639;0.0792)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0452)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.35e-07)|COAD - Colon adenocarcinoma(152;7.73e-06)|GBM - Glioblastoma multiforme(114;8.62e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000649)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00767)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.207)		TGAAGGCTGTCAAGTATGTGG	0.448																																					p.V152V		Atlas-SNP	.											.	CDC42	26	.	0			c.C456G						PASS	.						148	150	149					1																	22413329		2203	4300	6503	SO:0001819	synonymous_variant	998	exon6			GGCTGTCAAGTAT	BC018266	CCDS221.1, CCDS222.1	1p36.1	2013-01-17	2013-01-17		ENSG00000070831	ENSG00000070831			1736	protein-coding gene	gene with protein product	"GTP binding protein, 25kDa"	116952	"cell division cycle 42 (GTP-binding protein, 25kD)", "cell division cycle 42 (GTP binding protein, 25kDa)"			2124704, 2122236	Standard	NM_001039802		Approved	G25K, CDC42Hs	uc001bfr.3	P60953	OTTHUMG00000002753	ENST00000344548.3:c.456C>G	chr1.hg19:g.22413329C>G		306.0	0.0	.		245.0	62.0	.	NM_001039802	P21181|P25763|Q7L8R5|Q9UDI2	Silent	SNP	ENST00000344548.3	hg19	CCDS221.1																																																																																			.	.	.	none		0.448	CDC42-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007787.1	NM_001791		G	22413329	C	G	22413329	2	3	195	1	0	0	0	0	0	0	0	1	3073	813	29	4		4	CDC42	1	22413329	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	99	22413329	226837292	8	11609											
INPP5B	3633	hgsc.bcm.edu	37	chr1	38328025	38328025	+	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	gaactggtgaataaattcttGagccttcttcttctctgtca	9	16	7	9	0	5	2	1	2	4	0	6	3	5	2	1	1	2	0	1	1	4	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:38328025G>C	ENST00000373026.1	-	23	2944	c.2944C>G	c.(2944-2946)Caa>Gaa	p.Q982E	INPP5B_ENST00000373023.2_Missense_Mutation_p.Q982E|INPP5B_ENST00000373024.3_Missense_Mutation_p.Q902E|MTF1_ENST00000373036.4_5'Flank|INPP5B_ENST00000373027.1_Missense_Mutation_p.Q738E|RP11-109P14.10_ENST00000419993.1_RNA			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	982	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				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)				ATAAATTCTTGAGCCTTCTTC	0.453																																					p.Q902E		Atlas-SNP	.											.	INPP5B	76	.	0			c.C2704G						PASS	.						121	118	119					1																	38328025		1860	4104	5964	SO:0001583	missense	3633	exon24			ATTCTTGAGCCTT	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.2944C>G	chr1.hg19:g.38328025G>C	ENSP00000362117:p.Gln982Glu	134.0	0.0	.		131.0	19.0	.	NM_005540	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	Missense_Mutation	SNP	ENST00000373026.1	hg19		.	.	.	.	.	.	.	.	.	.	G	14.26	2.482316	0.44147	.	.	ENSG00000204084	ENST00000373027;ENST00000373023;ENST00000373026;ENST00000373024	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.45637	0.1352	L	0.56769	1.78	0.80722	D	1	P	0.44241	0.829	B	0.43274	0.414	T	0.23368	-1.0190	10	0.17832	T	0.49	.	20.054	0.97641	0.0:0.0:1.0:0.0	.	902	P32019-2	.	E	738;982;982;902	ENSP00000362118:Q738E;ENSP00000362114:Q982E;ENSP00000362117:Q982E;ENSP00000362115:Q902E	ENSP00000362114:Q982E	Q	-	1	0	INPP5B	38100612	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	8.101000	0.89546	2.808000	0.96608	0.655000	0.94253	CAA	.	.	.	none		0.453	INPP5B-003	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000012968.1	NM_005540		C	38328025	G	C	38328025	3	2	195	1	0	0	0	0	1	0	0	0	7762	1299	45	4	41	4	INPP5B	1	38328025	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	15914696	38328025	210922596	9	11610											
INPP5B	3633	hgsc.bcm.edu	37	chr1	38338748	38338748	+	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	cctgtccaagtgcagaaccaGaatgtcctcaattttgtctt	10	13	7	11	0	2	2	1	0	1	2	4	2	4	2	4	0	2	1	4	0	4	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:38338748G>A	ENST00000373026.1	-	18	2281	c.2281C>T	c.(2281-2283)Ctg>Ttg	p.L761L	INPP5B_ENST00000373023.2_Silent_p.L761L|INPP5B_ENST00000373024.3_Silent_p.L681L|INPP5B_ENST00000373027.1_Silent_p.L517L			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	761	ASH. {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)				TGCAGAACCAGAATGTCCTCA	0.438																																					p.L681L		Atlas-SNP	.											.	INPP5B	76	.	0			c.C2041T						PASS	.						207	193	198					1																	38338748		1876	4120	5996	SO:0001819	synonymous_variant	3633	exon19			GAACCAGAATGTC	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.2281C>T	chr1.hg19:g.38338748G>A		207.0	0.0	.		188.0	31.0	.	NM_005540	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	Silent	SNP	ENST00000373026.1	hg19																																																																																				.	.	.	none		0.438	INPP5B-003	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000012968.1	NM_005540		A	38338748	G	A	38338748	2	1	195	1	0	0	0	0	0	0	0	1	7762	933	33	2		2	INPP5B	1	38338748	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	10723	38338748	210911873	10	11611											
BMP8A	353500	hgsc.bcm.edu	37	chr1	39991443	39991443	+	Frame_Shift_Del	DEL	G	G	-																															ctgcgcaagcaccgcaacatGgtggtcaaggcctgcggctg																										TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:39991443delG	ENST00000331593.5	+	7	1528	c.1182delG	c.(1180-1182)atgfs	p.M394fs	RP11-69E11.4_ENST00000458207.1_RNA|RP11-69E11.4_ENST00000440190.1_RNA|RP11-69E11.4_ENST00000450157.1_RNA|RP11-69E11.4_ENST00000441741.1_RNA|RP11-69E11.4_ENST00000431553.1_RNA|RP11-69E11.4_ENST00000417869.1_RNA|RP11-69E11.4_ENST00000331856.2_RNA	NM_181809.3	NP_861525.2	Q7Z5Y6	BMP8A_HUMAN	bone morphogenetic protein 8a	394					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)			ACCGCAACATGGTGGTCAAGG	0.612																																					p.M394fs		Atlas-INDEL	.											.	BMP8A	24	.	0			c.1181delT						PASS	.						135	111	119					1																	39991443		2203	4300	6503	SO:0001589	frameshift_variant	353500	exon7			.	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.1182delG	chr1.hg19:g.39991443delG	ENSP00000327440:p.Met394fs	220.0	0.0	0		171.0	35.0	0.204678	NM_181809	Q5T3A5	Frame_Shift_Del	DEL	ENST00000331593.5	hg19	CCDS437.1																																																																																			.	.	.	none		0.612	BMP8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023079.1	NM_181809		-	39991443	G	-	39991443	7	5	195	1	0	1	0	1	0	0	0	0	1466	1348	47	0	1208	0	BMP8A	1	39991443	Frame_Shift_Del	DEL	G	TCGA-HE-7130-01A-11D-1961-08	1652695	39991443	209259178	11	11612											
PTPRF	5792	hgsc.bcm.edu	37	chr1	44063522	44063522	+	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	gacagccgcaacggcgttatCacccagtactccgtggccta	9	7	10	15	4	1	0	1	0	0	0	2	1	2	0	4	2	3	3	4	2	4	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:44063522C>T	ENST00000359947.4	+	12	2257	c.1917C>T	c.(1915-1917)atC>atT	p.I639I	PTPRF_ENST00000422171.2_Intron|PTPRF_ENST00000372413.3_Silent_p.I639I|PTPRF_ENST00000372414.3_Silent_p.I639I|PTPRF_ENST00000438120.1_Silent_p.I639I	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	639	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				ACGGCGTTATCACCCAGTACT	0.682																																					p.I639I		Atlas-SNP	.											.	PTPRF	172	.	0			c.C1917T						PASS	.						36	35	35					1																	44063522		2203	4299	6502	SO:0001819	synonymous_variant	5792	exon12			CGTTATCACCCAG	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.1917C>T	chr1.hg19:g.44063522C>T		27.0	0.0	.		30.0	17.0	.	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	hg19	CCDS489.2	.	.	.	.	.	.	.	.	.	.	C	6.416	0.444943	0.12164	.	.	ENSG00000142949	ENST00000429895	.	.	.	3.36	2.39	0.29439	.	.	.	.	.	T	0.53965	0.1829	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50101	-0.8867	4	.	.	.	.	6.7821	0.23652	0.1746:0.725:0.0:0.1004	.	.	.	.	L	296	.	.	S	+	2	0	PTPRF	43836109	0.931000	0.31567	0.996000	0.52242	0.537000	0.34900	0.201000	0.17276	1.613000	0.50231	0.313000	0.20887	TCA	.	.	.	none		0.682	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1			T	44063522	C	T	44063522	2	4	195	1	0	0	0	0	0	0	0	1	12814	816	29	2		2	PTPRF	1	44063522	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	4072079	44063522	205187099	12	11613											
CCDC18	343099	hgsc.bcm.edu	37	chr1	93705376	93705376	+	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	ttaagacaactccaggaattGagagatgtactacagaaggc	16	8	10	7	0	0	4	0	1	0	3	1	6	1	5	1	2	3	1	1	2	6	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:93705376G>C	ENST00000343253.7	+	21	3403	c.2901G>C	c.(2899-2901)ttG>ttC	p.L967F	CCDC18_ENST00000334652.5_Missense_Mutation_p.E261Q|CCDC18_ENST00000338949.4_Missense_Mutation_p.L723F|CCDC18_ENST00000401026.3_Missense_Mutation_p.L968F|CCDC18_ENST00000557479.1_Missense_Mutation_p.L1086F			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	967										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)		TCCAGGAATTGAGAGATGTAC	0.343																																					p.L968F		Atlas-SNP	.											.	CCDC18	93	.	0			c.G2904C						PASS	.						100	91	94					1																	93705376		1815	4083	5898	SO:0001583	missense	343099	exon21			GGAATTGAGAGAT			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.2901G>C	chr1.hg19:g.93705376G>C	ENSP00000343377:p.Leu967Phe	62.0	0.0	.		53.0	8.0	.	NM_206886	Q6ZU17	Missense_Mutation	SNP	ENST00000343253.7	hg19		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	17.75|17.75|17.75	3.466942|3.466942|3.466942	0.63625|0.63625|0.63625	.|.|.	.|.|.	ENSG00000122483|ENSG00000122483|ENSG00000122483	ENST00000334652|ENST00000343253;ENST00000401026;ENST00000557479;ENST00000338949;ENST00000455267|ENST00000370276	.|T;T|.	.|0.78707|.	.|-1.2;-1.2|.	5.83|5.83|5.83	5.83|5.83|5.83	0.93111|0.93111|0.93111	.|.|.	.|0.000000|.	.|0.64402|.	.|D|.	.|0.000002|.	T|T|.	0.41534|0.41534|.	0.1163|0.1163|.	L|L|L	0.58101|0.58101|0.58101	1.795|1.795|1.795	0.22066|0.22066|0.22066	N|N|N	0.999385|0.999385|0.999385	.|D;D|.	.|0.89917|.	.|1.0;1.0|.	.|D;D|.	.|0.91635|.	.|0.999;0.999|.	T|T|.	0.36986|0.36986|.	-0.9725|-0.9725|.	6|10|.	0.87932|0.62326|.	D|D|.	0|0.03|.	.|.|.	13.3361|13.3361|13.3361	0.60518|0.60518|0.60518	0.0719:0.0:0.9281:0.0|0.0719:0.0:0.9281:0.0|0.0719:0.0:0.9281:0.0	.|.|.	.|967;1086|.	.|Q5T9S5;G3V388|.	.|CCD18_HUMAN;.|.	Q|F|S	261|967;968;1086;723;643|1021	.|ENSP00000383808:L968F;ENSP00000451099:L1086F|.	ENSP00000334084:E261Q|ENSP00000344380:L723F|.	E|L|X	+|+|+	1|3|2	0|2|2	CCDC18|CCDC18|CCDC18	93477964|93477964|93477964	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	1.479000|1.479000|1.479000	0.35453|0.35453|0.35453	2.749000|2.749000|2.749000	0.94314|0.94314|0.94314	0.650000|0.650000|0.650000	0.86243|0.86243|0.86243	GAG|TTG|TGA	.	.	.	none		0.343	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886		C	93705376	G	C	93705376	3	2	195	1	0	0	0	0	1	0	0	0	2796	1281	45	4	3340	4	CCDC18	1	93705376	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	49641854	93705376	155545245	13	11614											
DDX20	11218	hgsc.bcm.edu	37	chr1	112309171	112309171	+	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	gaagtgacacccccaatccaGagaaatatcaagaatcacct	17	6	6	12	0	2	3	2	1	0	2	3	5	3	3	4	0	0	0	4	0	6	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:112309171G>A	ENST00000369702.4	+	11	2745	c.2125G>A	c.(2125-2127)Gag>Aag	p.E709K	DDX20_ENST00000475700.1_Missense_Mutation_p.E317K	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	709					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)		CCCCAATCCAGAGAAATATCA	0.478																																					p.E709K		Atlas-SNP	.											.	DDX20	50	.	0			c.G2125A						PASS	.						68	71	70					1																	112309171		2203	4299	6502	SO:0001583	missense	11218	exon11			AATCCAGAGAAAT	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.2125G>A	chr1.hg19:g.112309171G>A	ENSP00000358716:p.Glu709Lys	85.0	0.0	.		123.0	38.0	.	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Missense_Mutation	SNP	ENST00000369702.4	hg19	CCDS842.1	.	.	.	.	.	.	.	.	.	.	G	4.428	0.079164	0.08533	.	.	ENSG00000064703	ENST00000369702;ENST00000475700	T;T	0.35048	1.33;1.89	5.71	5.71	0.89125	.	1.938660	0.01863	N	0.036737	T	0.13457	0.0326	N	0.19112	0.55	0.23893	N	0.996542	B;B	0.30973	0.302;0.09	B;B	0.33620	0.167;0.016	T	0.19289	-1.0310	9	.	.	.	0.764	8.6694	0.34140	0.0762:0.0:0.7714:0.1524	.	317;709	E9PJ60;Q9UHI6	.;DDX20_HUMAN	K	709;317	ENSP00000358716:E709K;ENSP00000435660:E317K	.	E	+	1	0	DDX20	112110694	0.080000	0.21391	0.034000	0.17996	0.052000	0.14988	2.490000	0.45294	2.703000	0.92315	0.655000	0.94253	GAG	.	.	.	none		0.478	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204		A	112309171	G	A	112309171	3	1	195	1	0	0	0	0	1	0	0	0	4350	943	33	2	2167	2	DDX20	1	112309171	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	18603795	112309171	136941450	14	11615											
TXNIP	10628	hgsc.bcm.edu	37	chr1	145440057	145440059	+	In_Frame_Del	DEL	AAG	AAG	-																															ggcacctgtgtctgctaaaaAagaaaagaaagtttcctgca																										TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:145440057_145440059delAAG	ENST00000369317.4	+	4	825_827	c.491_493delAAG	c.(490-495)aaagaa>aaa	p.E165del	TXNIP_ENST00000475171.1_Intron	NM_006472.3	NP_006463.3	Q9H3M7	TXNIP_HUMAN	thioredoxin interacting protein	165					cell cycle (GO:0007049)|cellular response to tumor cell (GO:0071228)|innate immune response (GO:0045087)|keratinocyte differentiation (GO:0030216)|negative regulation of cell division (GO:0051782)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|protein import into nucleus (GO:0006606)|regulation of cell proliferation (GO:0042127)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucose (GO:0009749)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)	enzyme inhibitor activity (GO:0004857)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(1)|lung(5)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	21	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TCTGCTAAAAAAGAAAAGAAAGT	0.414																																					p.164_164del		Atlas-INDEL	.											.	TXNIP	51	.	0			c.490_492del						PASS	.																																			SO:0001651	inframe_deletion	10628	exon4			.	S73591	CCDS72876.1	1q11	2008-07-18			ENSG00000117289	ENSG00000265972			16952	protein-coding gene	gene with protein product	"upregulated by 1,25-dihydroxyvitamin D-3", "thioredoxin binding protein 2"	606599				8086474	Standard	NM_006472		Approved	VDUP1, EST01027, HHCPA78, THIF	uc001enn.4	Q9H3M7	OTTHUMG00000013755	ENST00000369317.4:c.491_493delAAG	chr1.hg19:g.145440057_145440059delAAG	ENSP00000358323:p.Glu165del	453.0	0.0	0		684.0	383.0	0.559942	NM_006472	B4E3D3|Q16226|Q6PML0|Q9BXG9	In_Frame_Del	DEL	ENST00000369317.4	hg19	CCDS913.1																																																																																			.	.	.	none		0.414	TXNIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038547.1	NM_006472		-	145440059	AAG	-	145440057	7	5	195	1	0	1	0	1	0	0	0	0	16815	14	1	0	505	0	TXNIP	1	145440057	In_Frame_Del	DEL	AAG	TCGA-HE-7130-01A-11D-1961-08	33130886	145440057	103810564	15	11616											
POGZ	23126	hgsc.bcm.edu	37	chr1	151377387	151377387	+	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	caggctcaattgtctcttcaGgagatgatctgggtcgtgga	8	12	13	8	1	4	2	2	1	2	1	6	4	4	3	0	4	0	1	0	4	1	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:151377387G>A	ENST00000271715.2	-	19	4438	c.4124C>T	c.(4123-4125)cCt>cTt	p.P1375L	POGZ_ENST00000368863.2_Missense_Mutation_p.P1280L|POGZ_ENST00000409503.1_Missense_Mutation_p.P1366L|POGZ_ENST00000491586.1_Missense_Mutation_p.P1331L|POGZ_ENST00000540984.1_Missense_Mutation_p.P737L|POGZ_ENST00000531094.1_Missense_Mutation_p.P1313L|POGZ_ENST00000361398.3_Missense_Mutation_p.P1322L|POGZ_ENST00000392723.1_Missense_Mutation_p.P1322L	NM_001194937.1|NM_015100.3	NP_001181866.1|NP_055915.2	Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain	1375					kinetochore assembly (GO:0051382)|mitotic sister chromatid cohesion (GO:0007064)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(10)|kidney(3)|large_intestine(10)|liver(2)|lung(11)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	47	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TGTCTCTTCAGGAGATGATCT	0.488											OREG0003905	type=REGULATORY REGION|Gene=POGZ|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.P1375L		Atlas-SNP	.											.	POGZ	211	.	0			c.C4124T						PASS	.						101	96	98					1																	151377387		2203	4300	6503	SO:0001583	missense	23126	exon19			TCTTCAGGAGATG	AB007930	CCDS997.1, CCDS998.1, CCDS44222.1, CCDS44222.2, CCDS53365.1, CCDS53366.1	1q21.1	2013-07-22			ENSG00000143442	ENSG00000143442			18801	protein-coding gene	gene with protein product	"zinc finger protein 280E", "putative protein product of Nbla00003"	614787				10976766	Standard	NM_015100		Approved	KIAA0461, ZNF635m, ZNF280E	uc001eyd.2	Q7Z3K3	OTTHUMG00000012499	ENST00000271715.2:c.4124C>T	chr1.hg19:g.151377387G>A	ENSP00000271715:p.Pro1375Leu	144.0	0.0	.	1739	190.0	44.0	.	NM_015100	B4DTP8|B4DYL9|B7ZBY5|E9PM80|O75049|Q3LIC4|Q5SZS1|Q5SZS2|Q5SZS3|Q5SZS4|Q8TDZ7|Q9Y4X7	Missense_Mutation	SNP	ENST00000271715.2	hg19	CCDS997.1	.	.	.	.	.	.	.	.	.	.	G	14.68	2.607106	0.46527	.	.	ENSG00000143442	ENST00000392723;ENST00000271715;ENST00000361398;ENST00000368863;ENST00000409503;ENST00000531094;ENST00000540984;ENST00000491586	T;T;T;T;T;T;T;T	0.24908	5.79;5.82;5.79;5.76;5.8;5.8;1.83;5.28	5.05	5.05	0.67936	.	0.000000	0.64402	D	0.000003	T	0.20007	0.0481	N	0.19112	0.55	0.58432	D	0.999999	B;D;P;P;B;B	0.58268	0.164;0.982;0.763;0.465;0.253;0.267	B;P;B;B;B;B	0.53006	0.04;0.715;0.173;0.124;0.087;0.058	T	0.02098	-1.1214	10	0.66056	D	0.02	-14.1248	17.4919	0.87707	0.0:0.0:1.0:0.0	.	1313;1366;1280;1331;1322;1375	E9PM80;B7ZBY5;Q7Z3K3-5;Q7Z3K3-3;Q7Z3K3-2;Q7Z3K3	.;.;.;.;.;POGZ_HUMAN	L	1322;1375;1322;1280;1366;1313;737;1331	ENSP00000376484:P1322L;ENSP00000271715:P1375L;ENSP00000354467:P1322L;ENSP00000357856:P1280L;ENSP00000386836:P1366L;ENSP00000431259:P1313L;ENSP00000443547:P737L;ENSP00000418408:P1331L	ENSP00000271715:P1375L	P	-	2	0	POGZ	149644011	1.000000	0.71417	0.999000	0.59377	0.935000	0.57460	6.397000	0.73239	2.780000	0.95670	0.655000	0.94253	CCT	.	.	.	none		0.488	POGZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034915.2	NM_207171		A	151377387	G	A	151377387	3	1	195	1	0	0	0	0	1	0	0	0	12193	1000	35	2	112	2	POGZ	1	151377387	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	5937330	151377387	97873234	16	11617											
FLG	2312	hgsc.bcm.edu	37	chr1	152281276	152281276	+	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	gtccactgtctctgactgcaGatgaagcttgtccatgccca	8	11	9	13	0	1	3	0	2	1	1	4	3	3	3	3	0	3	2	3	0	1	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:152281276G>C	ENST00000368799.1	-	3	6121	c.6086C>G	c.(6085-6087)tCt>tGt	p.S2029C	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2029	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)			TCTGACTGCAGATGAAGCTTG	0.542									Ichthyosis																												p.S2029C		Atlas-SNP	.											.	FLG	900	.	0			c.C6086G						PASS	.						601	507	539					1																	152281276		2203	4298	6501	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	ACTGCAGATGAAG	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.6086C>G	chr1.hg19:g.152281276G>C	ENSP00000357789:p.Ser2029Cys	1055.0	0.0	.		1229.0	541.0	.	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	g	5.168	0.216596	0.09810	.	.	ENSG00000143631	ENST00000368799	T	0.04083	3.71	3.44	2.51	0.30379	.	.	.	.	.	T	0.07052	0.0179	M	0.61703	1.905	0.09310	N	1	D	0.76494	0.999	D	0.65684	0.937	T	0.17440	-1.0369	9	0.56958	D	0.05	.	8.6711	0.34152	0.0:0.2608:0.7392:0.0	.	2029	P20930	FILA_HUMAN	C	2029	ENSP00000357789:S2029C	ENSP00000357789:S2029C	S	-	2	0	FLG	150547900	0.000000	0.05858	0.001000	0.08648	0.017000	0.09413	-0.118000	0.10692	0.748000	0.32831	0.485000	0.47835	TCT	.	.	.	none		0.542	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		C	152281276	G	C	152281276	3	2	195	1	0	0	0	0	1	0	0	0	5929	942	33	4	6103	4	FLG	1	152281276	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	903889	152281276	96969345	17	11618											
CHRNB2	1141	hgsc.bcm.edu	37	chr1	154544111	154544111	+	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	gaagatgacgttgtgcatctCagtgctgctggcgctcacgg	7	10	14	10	3	2	2	2	1	1	1	3	3	2	2	0	2	3	5	0	2	1	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:154544111C>A	ENST00000368476.3	+	5	1076	c.812C>A	c.(811-813)tCa>tAa	p.S271*		NM_000748.2	NP_000739.1	P17787	ACHB2_HUMAN	cholinergic receptor, nicotinic, beta 2 (neuronal)	271					action potential (GO:0001508)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|central nervous system projection neuron axonogenesis (GO:0021952)|cognition (GO:0050890)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|lateral geniculate nucleus development (GO:0021771)|learning (GO:0007612)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|neurological system process (GO:0050877)|optic nerve morphogenesis (GO:0021631)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|protein heterooligomerization (GO:0051291)|regulation of circadian sleep/wake cycle, non-REM sleep (GO:0045188)|regulation of circadian sleep/wake cycle, REM sleep (GO:0042320)|regulation of dendrite morphogenesis (GO:0048814)|regulation of dopamine metabolic process (GO:0042053)|regulation of dopamine secretion (GO:0014059)|regulation of synapse assembly (GO:0051963)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|sensory perception of pain (GO:0019233)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)|vestibulocochlear nerve development (GO:0021562)|visual learning (GO:0008542)|visual perception (GO:0007601)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)|ligand-gated ion channel activity (GO:0015276)	p.S271*(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|skin(1)|urinary_tract(3)	28	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)		Dextromethorphan(DB00514)|Galantamine(DB00674)|Nicotine(DB00184)	TTGTGCATCTCAGTGCTGCTG	0.577																																					p.S271X		Atlas-SNP	.											CHRNB2,NS,carcinoma,0,1	CHRNB2	74	.	1	Substitution - Nonsense(1)	lung(1)	c.C812A						PASS	.						280	208	233					1																	154544111		2203	4300	6503	SO:0001587	stop_gained	1141	exon5			GCATCTCAGTGCT	U62437	CCDS1070.1	1q21.3	2012-02-11	2006-02-01		ENSG00000160716	ENSG00000160716		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1962	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 2 (neuronal)"	118507	"cholinergic receptor, nicotinic, beta polypeptide 2 (neuronal)"			1505988	Standard	NM_000748		Approved		uc001ffg.3	P17787	OTTHUMG00000037262	ENST00000368476.3:c.812C>A	chr1.hg19:g.154544111C>A	ENSP00000357461:p.Ser271*	225.0	1.0	.		281.0	167.0	.	NM_000748	Q9UEH9	Nonsense_Mutation	SNP	ENST00000368476.3	hg19	CCDS1070.1	.	.	.	.	.	.	.	.	.	.	C	39	7.470747	0.98306	.	.	ENSG00000160716	ENST00000368476	.	.	.	4.1	4.1	0.47936	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.1089	0.81244	0.0:1.0:0.0:0.0	.	.	.	.	X	271	.	ENSP00000357461:S271X	S	+	2	0	CHRNB2	152810735	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	7.608000	0.82898	2.095000	0.63458	0.467000	0.42956	TCA	.	.	.	none		0.577	CHRNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090697.1	NM_000748		A	154544111	C	A	154544111	4	1	195	1	0	0	0	0	0	1	0	0	3393	838	29	4	830	4	CHRNB2	1	154544111	Nonsense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	2262835	154544111	94706510	18	11619											
GON4L	54856	hgsc.bcm.edu	37	chr1	155723194	155723194	+	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	tccttgctcttgtaggatttGctgtcacagacctgcaggga	7	13	11	10	0	2	1	1	0	1	1	3	3	3	3	2	2	3	4	2	2	1	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:155723194G>C	ENST00000368331.1	-	29	5691	c.5643C>G	c.(5641-5643)agC>agG	p.S1881R	GON4L_ENST00000437809.1_Missense_Mutation_p.S1881R|GON4L_ENST00000271883.5_Missense_Mutation_p.S1881R	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	1881					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					TGTAGGATTTGCTGTCACAGA	0.582																																					p.S1881R		Atlas-SNP	.											.	GON4L	392	.	0			c.C5643G						PASS	.						107	105	106					1																	155723194		1950	4137	6087	SO:0001583	missense	54856	exon29			GGATTTGCTGTCA	AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"gon-4 homolog (C.elegans)"	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.5643C>G	chr1.hg19:g.155723194G>C	ENSP00000357315:p.Ser1881Arg	244.0	0.0	.		270.0	13.0	.	NM_001037533	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Missense_Mutation	SNP	ENST00000368331.1	hg19		.	.	.	.	.	.	.	.	.	.	G	15.41	2.824139	0.50739	.	.	ENSG00000116580	ENST00000437809;ENST00000368331;ENST00000271883	T;T;T	0.10668	2.85;2.85;2.85	5.15	4.23	0.50019	.	0.195098	0.45867	D	0.000333	T	0.04770	0.0129	L	0.44542	1.39	0.34449	D	0.70051	P;P	0.38048	0.481;0.616	B;B	0.35312	0.098;0.2	T	0.23655	-1.0182	10	0.45353	T	0.12	.	13.8128	0.63273	0.0753:0.0:0.9247:0.0	.	1881;1881	Q3T8J9;Q3T8J9-3	GON4L_HUMAN;.	R	1881	ENSP00000396117:S1881R;ENSP00000357315:S1881R;ENSP00000271883:S1881R	ENSP00000271883:S1881R	S	-	3	2	GON4L	153989818	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	4.844000	0.62846	1.377000	0.46286	0.455000	0.32223	AGC	.	.	.	none		0.582	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292		C	155723194	G	C	155723194	3	2	195	1	0	0	0	0	1	0	0	0	6579	1310	46	4	1095	4	GON4L	1	155723194	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	1179083	155723194	93527427	19	11620											
OR10Z1	128368	hgsc.bcm.edu	37	chr1	158576303	158576303	+	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	agttctggggagttgcagctCcttctctttgccttgttcct	3	17	10	11	0	2	0	0	0	2	0	5	1	4	1	3	2	3	5	3	2	0	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:158576303C>T	ENST00000361284.1	+	1	75	c.75C>T	c.(73-75)ctC>ctT	p.L25L		NM_001004478.1	NP_001004478.1	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z, 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)			endometrium(2)|large_intestine(6)|lung(21)|pancreas(1)|prostate(3)|skin(4)	37	all_hematologic(112;0.0378)					AGTTGCAGCTCCTTCTCTTTG	0.498																																					p.L25L		Atlas-SNP	.											.	OR10Z1	99	.	0			c.C75T						PASS	.						179	173	175					1																	158576303		2203	4300	6503	SO:0001819	synonymous_variant	128368	exon1			GCAGCTCCTTCTC	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.75C>T	chr1.hg19:g.158576303C>T		171.0	0.0	.		239.0	34.0	.	NM_001004478	Q5VYL0|Q6IFR7	Silent	SNP	ENST00000361284.1	hg19	CCDS30901.1																																																																																			.	.	.	none		0.498	OR10Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051853.1	NM_001004478		T	158576303	C	T	158576303	2	4	195	1	0	0	0	0	0	0	0	1	10930	842	30	2		2	OR10Z1	1	158576303	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	2853109	158576303	90674318	20	11621											
OR6N1	128372	hgsc.bcm.edu	37	chr1	158735810	158735810	+	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	attctgagcactgtgcagatGatctgcacataggagcagag	12	9	12	8	0	2	4	0	2	2	2	2	5	2	5	0	1	4	4	0	1	1	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:158735810G>A	ENST00000335094.2	-	1	682	c.663C>T	c.(661-663)atC>atT	p.I221I		NM_001005185.1	NP_001005185.1	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N, member 1	221						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)					CTGTGCAGATGATCTGCACAT	0.488																																					p.I221I		Atlas-SNP	.											.	OR6N1	96	.	0			c.C663T						PASS	.						125	124	125					1																	158735810		2203	4300	6503	SO:0001819	synonymous_variant	128372	exon1			GCAGATGATCTGC	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.663C>T	chr1.hg19:g.158735810G>A		185.0	0.0	.		231.0	119.0	.	NM_001005185	Q5VUU8|Q96R35	Silent	SNP	ENST00000335094.2	hg19	CCDS30905.1																																																																																			.	.	.	none		0.488	OR6N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059067.1	NM_001005185		A	158735810	G	A	158735810	2	1	195	1	0	0	0	0	0	0	0	1	11213	1280	45	2		2	OR6N1	1	158735810	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	159507	158735810	90514811	21	11622											
PYHIN1	149628	hgsc.bcm.edu	37	chr1	158943473	158943473	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caggagcacagtcatcgcctGcaaactttagaatcacctca	13	8	7	13	1	3	1	3	0	0	1	4	2	3	2	2	1	3	2	2	1	3	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:158943473G>A	ENST00000368140.1	+	8	1641	c.1396G>A	c.(1396-1398)Gca>Aca	p.A466T	PYHIN1_ENST00000368138.3_Missense_Mutation_p.A457T|PYHIN1_ENST00000392254.2_Intron|PYHIN1_ENST00000392252.3_Intron	NM_152501.4|NM_198928.4|NM_198929.4	NP_689714.2|NP_945146.1|NP_945147.1	Q6K0P9	IFIX_HUMAN	pyrin and HIN domain family, member 1	466					cell cycle (GO:0007049)	nucleus (GO:0005634)				breast(2)|endometrium(3)|large_intestine(10)|lung(32)|ovary(3)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_hematologic(112;0.0378)					GTCATCGCCTGCAAACTTTAG	0.448																																					p.A466T		Atlas-SNP	.											PYHIN1,NS,carcinoma,0,1	PYHIN1	208	.	0			c.G1396A						PASS	.						162	144	150					1																	158943473		2203	4300	6503	SO:0001583	missense	149628	exon8			TCGCCTGCAAACT	AY185344	CCDS1178.1, CCDS1179.1, CCDS30907.1, CCDS30908.1	1q23.1	2008-02-05			ENSG00000163564	ENSG00000163564			28894	protein-coding gene	gene with protein product		612677				15122330	Standard	NM_152501		Approved	IFIX, MGC23885	uc001ftb.3	Q6K0P9	OTTHUMG00000037109	ENST00000368140.1:c.1396G>A	chr1.hg19:g.158943473G>A	ENSP00000357122:p.Ala466Thr	67.0	0.0	.		105.0	54.0	.	NM_152501	Q5T3W6|Q6K0P6|Q6K0P7|Q6K0P8|Q8WW65	Missense_Mutation	SNP	ENST00000368140.1	hg19	CCDS1178.1	.	.	.	.	.	.	.	.	.	.	G	1.474	-0.558987	0.03967	.	.	ENSG00000163564	ENST00000368140;ENST00000368138	T;T	0.06294	3.33;3.32	1.95	-2.27	0.06846	.	.	.	.	.	T	0.00724	0.0024	N	0.08118	0	0.09310	N	1	B;B	0.22604	0.072;0.043	B;B	0.16289	0.015;0.007	T	0.46512	-0.9186	9	0.16420	T	0.52	.	6.2156	0.20653	0.668:0.0:0.332:0.0	.	457;466	Q6K0P9-2;Q6K0P9	.;IFIX_HUMAN	T	466;457	ENSP00000357122:A466T;ENSP00000357120:A457T	ENSP00000357120:A457T	A	+	1	0	PYHIN1	157210097	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.349000	0.02627	-0.729000	0.04875	-0.143000	0.13931	GCA	.	.	.	none		0.448	PYHIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090110.1	NM_152501		A	158943473	G	A	158943473	3	1	195	1	0	0	0	0	1	0	0	0	12878	1319	46	2	1422	2	PYHIN1	1	158943473	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	207663	158943473	90307148	22	11623											
POGK	57645	hgsc.bcm.edu	37	chr1	166818273	166818273	+	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	actttgacagctttggcctcCgtctgcctcgggatatcaca	7	12	9	13	2	2	1	1	1	1	0	4	2	3	2	3	2	2	1	3	2	1	3	rs202168363		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:166818273C>A	ENST00000367875.1	+	5	817	c.457C>A	c.(457-459)Cgt>Agt	p.R153S	POGK_ENST00000537173.1_Missense_Mutation_p.R35S|POGK_ENST00000367876.4_Missense_Mutation_p.R153S|POGK_ENST00000536514.1_Missense_Mutation_p.R68S			Q9P215	POGK_HUMAN	pogo transposable element with KRAB domain	153					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						CTTTGGCCTCCGTCTGCCTCG	0.542																																					p.R153S	GBM(76;192 1530 30153 48742)	Atlas-SNP	.											.	POGK	54	.	0			c.C457A						PASS	.						110	107	108					1																	166818273		2203	4300	6503	SO:0001583	missense	57645	exon5			GGCCTCCGTCTGC	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.457C>A	chr1.hg19:g.166818273C>A	ENSP00000356849:p.Arg153Ser	131.0	0.0	.		174.0	7.0	.	NM_017542	Q5TIJ1|Q8TE07	Missense_Mutation	SNP	ENST00000367875.1	hg19	CCDS1254.1	.	.	.	.	.	.	.	.	.	.	C	12.30	1.895562	0.33442	.	.	ENSG00000143157	ENST00000537173;ENST00000536514;ENST00000449930;ENST00000367876;ENST00000367875	T;T;T;T;T	0.34472	1.38;1.36;4.67;4.6;4.6	5.3	4.37	0.52481	.	0.137019	0.33959	N	0.004396	T	0.10981	0.0268	N	0.24115	0.695	0.31455	N	0.670285	B;B;B	0.23185	0.081;0.049;0.049	B;B;B	0.20577	0.03;0.022;0.022	T	0.08827	-1.0703	9	0.30078	T	0.28	-3.0623	11.0801	0.48055	0.1848:0.8152:0.0:0.0	.	35;68;153	G3V1P0;B4DS22;Q9P215	.;.;POGK_HUMAN	S	35;68;153;153;153	ENSP00000442763:R35S;ENSP00000441187:R68S;ENSP00000404402:R153S;ENSP00000356850:R153S;ENSP00000356849:R153S	ENSP00000356849:R153S	R	+	1	0	POGK	165084897	0.996000	0.38824	0.740000	0.30986	0.861000	0.49209	3.195000	0.51013	1.442000	0.47568	0.655000	0.94253	CGT	.	.	.	alt		0.542	POGK-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082888.1	NM_017542		A	166818273	C	A	166818273	3	1	195	1	0	0	0	0	1	0	0	0	12192	652	23	4	471	4	POGK	1	166818273	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	7874800	166818273	82432348	23	11624											
FASLG	356	hgsc.bcm.edu	37	chr1	172634825	172634825	+	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	ctatggaattgtcctgctttCtggagtgaagtataagaagg	11	13	12	5	0	1	2	0	1	1	1	2	4	2	4	1	3	1	2	1	3	6	5	rs80358236		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:172634825C>T	ENST00000367721.2	+	4	699	c.515C>T	c.(514-516)tCt>tTt	p.S172F	FASLG_ENST00000340030.3_3'UTR	NM_000639.1	NP_000630.1	P48023	TNFL6_HUMAN	Fas ligand (TNF superfamily, member 6)	172					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						GTCCTGCTTTCTGGAGTGAAG	0.433																																					p.S172F	Ovarian(28;486 876 30334 44033)	Atlas-SNP	.											.	FASLG	44	.	0			c.C515T						PASS	.						136	120	126					1																	172634825		2203	4300	6503	SO:0001583	missense	356	exon4			TGCTTTCTGGAGT	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.515C>T	chr1.hg19:g.172634825C>T	ENSP00000356694:p.Ser172Phe	81.0	0.0	.		139.0	11.0	.	NM_000639	Q9BZP9	Missense_Mutation	SNP	ENST00000367721.2	hg19	CCDS1304.1	.	.	.	.	.	.	.	.	.	.	C	17.38	3.374699	0.61735	.	.	ENSG00000117560	ENST00000367721	T	0.65732	-0.17	5.24	5.24	0.73138	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	0.277042	0.34046	N	0.004302	T	0.74496	0.3724	M	0.78456	2.415	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.78064	-0.2350	10	0.72032	D	0.01	-19.152	13.9766	0.64277	0.0:0.8471:0.1529:0.0	.	172	P48023	TNFL6_HUMAN	F	172	ENSP00000356694:S172F	ENSP00000356694:S172F	S	+	2	0	FASLG	170901448	0.930000	0.31532	0.910000	0.35882	0.880000	0.50808	2.041000	0.41213	2.455000	0.83008	0.650000	0.86243	TCT	.	.	.	none		0.433	FASLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084276.1			T	172634825	C	T	172634825	3	4	195	1	0	0	0	0	1	0	0	0	5689	913	32	2	529	2	FASLG	1	172634825	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	5816552	172634825	76615796	24	11625											
OR2L8	391190	hgsc.bcm.edu	37	chr1	248112585	248112585	+	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	agcaaaagagtgtgtgtgctGatgataacagggtcttggat	12	11	14	4	0	1	3	0	2	1	1	1	4	1	4	0	2	3	2	0	2	3	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr1:248112585G>A	ENST00000357191.3	+	1	426	c.426G>A	c.(424-426)ctG>ctA	p.L142L	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	142						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)			TGTGTGTGCTGATGATAACAG	0.438																																					p.L142L		Atlas-SNP	.											.	OR2L8	92	.	0			c.G426A						PASS	.						295	240	258					1																	248112585		2203	4300	6503	SO:0001819	synonymous_variant	391190	exon1			TGTGCTGATGATA	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.426G>A	chr1.hg19:g.248112585G>A		253.0	0.0	.		270.0	24.0	.	NM_001001963	Q6IF03	Silent	SNP	ENST00000357191.3	hg19	CCDS31101.1																																																																																			.	.	.	none		0.438	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2			A	248112585	G	A	248112585	2	1	195	1	0	0	0	0	0	0	0	1	11016	1277	45	2		2	OR2L8	1	248112585	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	75477760	248112585	1138036	25	11626											
BIRC6	57448	hgsc.bcm.edu	37	chr2	32626579	32626579	+	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	atgatccagcaattgtacaaCagcttattctatcaggagac	14	11	7	9	0	2	2	1	1	1	1	3	3	3	2	1	1	4	3	1	1	5	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr2:32626579C>T	ENST00000421745.2	+	8	1440	c.1306C>T	c.(1306-1308)Cag>Tag	p.Q436*		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	436					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)					AATTGTACAACAGCTTATTCT	0.378																																					p.Q436X	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.C1306T						PASS	.						105	107	106					2																	32626579		2203	4300	6503	SO:0001587	stop_gained	57448	exon8			GTACAACAGCTTA	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.1306C>T	chr2.hg19:g.32626579C>T	ENSP00000393596:p.Gln436*	111.0	0.0	.		106.0	38.0	.	NM_016252	Q9ULD1	Nonsense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	C	36	5.679441	0.96774	.	.	ENSG00000115760	ENST00000421745	.	.	.	5.92	5.92	0.95590	.	0.157867	0.40908	D	0.000998	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08599	T	0.76	.	13.5098	0.61504	0.0:0.929:0.0:0.071	.	.	.	.	X	436	.	ENSP00000393596:Q436X	Q	+	1	0	BIRC6	32480083	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.615000	0.61190	2.813000	0.96785	0.561000	0.74099	CAG	.	.	.	none		0.378	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		T	32626579	C	T	32626579	4	4	195	1	0	0	0	0	0	1	0	0	1438	479	17	2	1336	2	BIRC6	2	32626579	Nonsense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08		32626579	210572794	26	11627											
SOS1	6654	hgsc.bcm.edu	37	chr2	39281894	39281894	+	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	aagtttgttctcctgaggtgGaaggctcttcgtcagttaaa	9	14	11	7	1	3	1	1	1	2	0	5	2	3	2	1	3	0	4	1	3	4	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr2:39281894G>A	ENST00000426016.1	-	6	667	c.581C>T	c.(580-582)tCc>tTc	p.S194F	SOS1_ENST00000402219.2_Missense_Mutation_p.S194F|SOS1_ENST00000395038.2_Missense_Mutation_p.S194F|SOS1_ENST00000428721.2_Missense_Mutation_p.S137F			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	194					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				TCCTGAGGTGGAAGGCTCTTC	0.284									Noonan syndrome																												p.S194F		Atlas-SNP	.											.	SOS1	134	.	0			c.C581T						PASS	.						86	99	94					2																	39281894		2203	4297	6500	SO:0001583	missense	6654	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	GAGGTGGAAGGCT	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	11187	protein-coding gene	gene with protein product		182530	"gingival fibromatosis, hereditary, 1"	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.581C>T	chr2.hg19:g.39281894G>A	ENSP00000387784:p.Ser194Phe	213.0	0.0	.		166.0	68.0	.	NM_005633	A8K2G3|B4DXG2	Missense_Mutation	SNP	ENST00000426016.1	hg19	CCDS1802.1	.	.	.	.	.	.	.	.	.	.	G	15.74	2.921771	0.52653	.	.	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000395038;ENST00000263879;ENST00000428721	T;T;T;D	0.96334	-1.08;-1.08;-1.21;-3.98	5.88	5.88	0.94601	.	0.063359	0.64402	D	0.000004	D	0.93575	0.7949	L	0.27053	0.805	0.58432	D	0.999995	B	0.12013	0.005	B	0.15484	0.013	D	0.88675	0.3198	10	0.59425	D	0.04	.	20.2187	0.98312	0.0:0.0:1.0:0.0	.	194	Q07889	SOS1_HUMAN	F	194;194;194;194;137	ENSP00000387784:S194F;ENSP00000384675:S194F;ENSP00000378479:S194F;ENSP00000399992:S137F	ENSP00000263879:S194F	S	-	2	0	SOS1	39135398	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.200000	0.51051	2.780000	0.95670	0.655000	0.94253	TCC	.	.	.	none		0.284	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633		A	39281894	G	A	39281894	3	1	195	1	0	0	0	0	1	0	0	0	14949	1174	41	2	3496	2	SOS1	2	39281894	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	6655315	39281894	203917479	27	11628											
ACTR2	10097	hgsc.bcm.edu	37	chr2	65492181	65492181	+	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	cattgtgcctttctagatctGaattctacaaacacattgtg	11	15	6	9	0	3	2	0	1	3	1	3	2	3	2	1	0	3	0	1	0	4	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr2:65492181G>A	ENST00000260641.5	+	8	1043	c.886G>A	c.(886-888)Gaa>Aaa	p.E296K	ACTR2_ENST00000542850.1_Missense_Mutation_p.E241K|ACTR2_ENST00000377982.4_Missense_Mutation_p.E301K	NM_005722.3	NP_005713.1	P61160	ARP2_HUMAN	ARP2 actin-related protein 2 homolog (yeast)	296					Arp2/3 complex-mediated actin nucleation (GO:0034314)|asymmetric cell division (GO:0008356)|cellular component movement (GO:0006928)|cilium assembly (GO:0042384)|cytoplasmic transport (GO:0016482)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|meiotic chromosome movement towards spindle pole (GO:0016344)|meiotic cytokinesis (GO:0033206)|spindle localization (GO:0051653)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(1)|prostate(1)	12						TTCTAGATCTGAATTCTACAA	0.428																																					p.E301K		Atlas-SNP	.											.	ACTR2	30	.	0			c.G901A						PASS	.						179	168	171					2																	65492181		2203	4300	6503	SO:0001583	missense	10097	exon9			AGATCTGAATTCT	AF006082	CCDS1881.1, CCDS46307.1	2p14	2008-05-20	2001-11-28		ENSG00000138071	ENSG00000138071			169	protein-coding gene	gene with protein product		604221	"ARP2 (actin-related protein 2, yeast) homolog"			9230079	Standard	NM_001005386		Approved	ARP2	uc002sdp.3	P61160	OTTHUMG00000129540	ENST00000260641.5:c.886G>A	chr2.hg19:g.65492181G>A	ENSP00000260641:p.Glu296Lys	169.0	0.0	.		176.0	70.0	.	NM_001005386	B2RCP5|D6W5F4|E9PF41|O15142|Q96C82	Missense_Mutation	SNP	ENST00000260641.5	hg19	CCDS1881.1	.	.	.	.	.	.	.	.	.	.	G	18.95	3.731091	0.69189	.	.	ENSG00000138071	ENST00000260641;ENST00000542850;ENST00000377982;ENST00000535303	D;D;D	0.94576	-3.46;-3.46;-3.46	5.98	5.1	0.69264	.	0.120167	0.53938	U	0.000057	D	0.93841	0.8030	M	0.70275	2.135	0.58432	D	0.999999	B;B;B	0.13594	0.005;0.008;0.004	B;B;B	0.13407	0.009;0.007;0.007	D	0.91169	0.4967	10	0.62326	D	0.03	-23.7201	17.2991	0.87177	0.0:0.1254:0.8746:0.0	.	241;296;301	F5H6T1;P61160;E9PF41	.;ARP2_HUMAN;.	K	296;241;301;241	ENSP00000260641:E296K;ENSP00000437383:E241K;ENSP00000367220:E301K	ENSP00000260641:E296K	E	+	1	0	ACTR2	65345685	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	9.476000	0.97823	1.525000	0.49052	0.591000	0.81541	GAA	.	.	.	none		0.428	ACTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251730.1	NM_001005386		A	65492181	G	A	65492181	3	1	195	1	0	0	0	0	1	0	0	0	211	1291	45	2	935	2	ACTR2	2	65492181	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	26210287	65492181	177707192	28	11629											
CNGA3	1261	hgsc.bcm.edu	37	chr2	99012521	99012522	+	Frame_Shift_Ins	INS	-	-	GT																															gcacagagacaaggaccaacINStaccccaatatgttcaggat																										TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr2:99012521_99012522insGT	ENST00000272602.2	+	7	927_928	c.888_889insGT	c.(889-891)tacfs	p.Y297fs	CNGA3_ENST00000436404.2_Frame_Shift_Ins_p.Y279fs|CNGA3_ENST00000393504.1_Frame_Shift_Ins_p.Y297fs|CNGA3_ENST00000409937.1_Frame_Shift_Ins_p.Y301fs			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	297					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						CAAGGACCAACTACCCCAATAT	0.45																																					p.N296fs		Atlas-INDEL	.											.	CNGA3	118	.	0			c.888_889insGT						PASS	.																																			SO:0001589	frameshift_variant	1261	exon8			.	S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	Exception_encountered	chr2.hg19:g.99012521_99012522insGT	ENSP00000272602:p.Tyr297fs	99.0	0.0	0		92.0	20.0	0.217391	NM_001298	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Frame_Shift_Ins	INS	ENST00000272602.2	hg19	CCDS2034.1																																																																																			.	.	.	none		0.45	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298		GT	99012522	-	GT	99012521	7	5	195	1	0	1	1	0	0	0	0	0	3600	564	20	0	914	0	CNGA3	2	99012521	Frame_Shift_Ins	INS	-	TCGA-HE-7130-01A-11D-1961-08	33520340	99012521	144186852	29	11630											
FSIP2	401024	hgsc.bcm.edu	37	chr2	186678413	186678413	+	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	aagtgtatttggaaaattacAtaaaagaggaacgagattct	18	11	9	3	1	1	2	0	0	1	2	1	5	1	4	0	2	2	1	0	2	8	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr2:186678413A>T	ENST00000424728.1	+	18	19969	c.19969A>T	c.(19969-19971)Ata>Tta	p.I6657L	FSIP2_ENST00000343098.5_Missense_Mutation_p.I6746L			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	6657										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						GGAAAATTACATAAAAGAGGA	0.308																																					p.I6746L		Atlas-SNP	.											FSIP2_ENST00000343098,NS,carcinoma,0,2	FSIP2	251	.	0			c.A20236T						PASS	.						60	58	59					2																	186678413		1815	4082	5897	SO:0001583	missense	401024	exon18			AATTACATAAAAG	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.19969A>T	chr2.hg19:g.186678413A>T	ENSP00000401306:p.Ile6657Leu	41.0	0.0	.		40.0	11.0	.	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Missense_Mutation	SNP	ENST00000424728.1	hg19		.	.	.	.	.	.	.	.	.	.	A	8.432	0.848829	0.17034	.	.	ENSG00000188738	ENST00000343098;ENST00000424728	T;T	0.39787	1.06;1.07	4.74	-6.09	0.02145	.	2.291920	0.01415	N	0.014178	T	0.16557	0.0398	N	0.03608	-0.345	0.09310	N	1	.	.	.	.	.	.	T	0.11567	-1.0582	8	0.17369	T	0.5	.	5.0483	0.14496	0.3028:0.0:0.4212:0.2761	.	.	.	.	L	6746;6657	ENSP00000344403:I6746L;ENSP00000401306:I6657L	ENSP00000344403:I6746L	I	+	1	0	FSIP2	186386658	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.003000	0.13083	-1.474000	0.01879	-1.412000	0.01120	ATA	.	.	.	none		0.308	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		T	186678413	A	T	186678413	3	4	195	1	0	0	0	0	1	0	0	0	6082	217	8	5	20306	5	FSIP2	2	186678413	Missense_Mutation	SNP	A	TCGA-HE-7130-01A-11D-1961-08	87665892	186678413	56520960	30	11631											
MSTN	2660	hgsc.bcm.edu	37	chr2	190922196	190922196	+	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	ctctccagagcagtaattggCcttatatcttttaggagcga	10	13	9	9	1	2	1	0	0	2	1	3	3	2	2	2	2	2	2	2	2	4	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr2:190922196C>T	ENST00000260950.4	-	3	1048	c.916G>A	c.(916-918)Gcc>Acc	p.A306T	C2orf88_ENST00000478197.1_Intron	NM_005259.2	NP_005250.1	O14793	GDF8_HUMAN	myostatin	306					cellular response to dexamethasone stimulus (GO:0071549)|muscle organ development (GO:0007517)|negative regulation of muscle hypertrophy (GO:0014741)|negative regulation of skeletal muscle tissue growth (GO:0048632)|ovulation cycle process (GO:0022602)|positive regulation of transcription, DNA-templated (GO:0045893)|response to electrical stimulus (GO:0051602)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gravity (GO:0009629)|response to heat (GO:0009408)|response to muscle activity (GO:0014850)|response to testosterone (GO:0033574)|skeletal muscle atrophy (GO:0014732)|skeletal muscle tissue regeneration (GO:0043403)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|skin(1)	12			OV - Ovarian serous cystadenocarcinoma(117;0.000742)|Epithelial(96;0.0121)|all cancers(119;0.0395)			CAGTAATTGGCCTTATATCTT	0.423																																					p.A306T		Atlas-SNP	.											.	MSTN	46	.	0			c.G916A						PASS	.						85	83	84					2																	190922196		2203	4300	6503	SO:0001583	missense	2660	exon3			AATTGGCCTTATA	AF019627	CCDS2303.1	2q32.1	2014-09-17	2007-06-21	2007-06-21	ENSG00000138379	ENSG00000138379			4223	protein-coding gene	gene with protein product		601788	"growth differentiation factor 8"	GDF8		9288100, 10610713, 17003236	Standard	NM_005259		Approved		uc002urp.3	O14793	OTTHUMG00000132663	ENST00000260950.4:c.916G>A	chr2.hg19:g.190922196C>T	ENSP00000260950:p.Ala306Thr	60.0	0.0	.		69.0	34.0	.	NM_005259	A1C2J7|A1C2K0|Q6B0H2	Missense_Mutation	SNP	ENST00000260950.4	hg19	CCDS2303.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.497799	0.85069	.	.	ENSG00000138379	ENST00000260950	D	0.86497	-2.13	5.79	5.79	0.91817	Transforming growth factor beta, conserved site (1);Transforming growth factor-beta, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.95604	0.8571	H	0.94886	3.595	0.80722	D	1	P	0.48089	0.905	D	0.65140	0.932	D	0.96037	0.9021	10	0.87932	D	0	-9.1744	20.0308	0.97536	0.0:1.0:0.0:0.0	.	306	O14793	GDF8_HUMAN	T	306	ENSP00000260950:A306T	ENSP00000260950:A306T	A	-	1	0	MSTN	190630441	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.818000	0.86416	2.732000	0.93576	0.585000	0.79938	GCC	.	.	.	none		0.423	MSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255917.2	NM_005259		T	190922196	C	T	190922196	3	4	195	1	0	0	0	0	1	0	0	0	9900	739	26	2	215	2	MSTN	2	190922196	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	4243783	190922196	52277177	31	11632											
KIF1A	547	hgsc.bcm.edu	37	chr2	241661280	241661280	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgtactctctgttgaatgTgtgcgtgagcaggcgcaagc	7	12	14	8	2	1	2	0	2	1	0	2	2	1	2	0	1	4	4	0	1	3	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr2:241661280T>C	ENST00000320389.7	-	42	4542	c.4384A>G	c.(4384-4386)Aca>Gca	p.T1462A	KIF1A_ENST00000498729.2_Missense_Mutation_p.T1563A	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	1462					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)		CTGTTGAATGTGTGCGTGAGC	0.657																																					p.T1563A		Atlas-SNP	.											.	KIF1A	152	.	0			c.A4687G						PASS	.						75	81	79					2																	241661280		2148	4248	6396	SO:0001583	missense	547	exon44			TGAATGTGTGCGT	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.4384A>G	chr2.hg19:g.241661280T>C	ENSP00000322791:p.Thr1462Ala	32.0	0.0	.		11.0	8.0	.	NM_001244008	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Missense_Mutation	SNP	ENST00000320389.7	hg19	CCDS46561.1	.	.	.	.	.	.	.	.	.	.	T	14.75	2.630002	0.46944	.	.	ENSG00000130294	ENST00000320389;ENST00000498729;ENST00000373308	T;T	0.72167	-0.55;-0.63	4.33	3.14	0.36123	.	0.120608	0.53938	U	0.000050	T	0.64483	0.2602	L	0.46157	1.445	0.41290	D	0.986977	P;B	0.39737	0.685;0.032	P;B	0.46299	0.511;0.014	T	0.57159	-0.7859	10	0.08599	T	0.76	.	9.5613	0.39371	0.165:0.0:0.0:0.835	.	1563;1462	F5H045;Q12756	.;KIF1A_HUMAN	A	1462;1563;1571	ENSP00000322791:T1462A;ENSP00000438388:T1563A	ENSP00000322791:T1462A	T	-	1	0	KIF1A	241309953	1.000000	0.71417	0.997000	0.53966	0.980000	0.70556	1.446000	0.35090	0.517000	0.28361	0.528000	0.53228	ACA	.	.	.	none		0.657	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483		C	241661280	T	C	241661280	3	2	195	1	0	0	0	0	1	0	0	0	8290	1696	59	3	712	3	KIF1A	2	241661280	Missense_Mutation	SNP	T	TCGA-HE-7130-01A-11D-1961-08	50739084	241661280	1538093	32	11633											
OXSM	54995	hgsc.bcm.edu	37	chr3	25833175	25833175	+	Frame_Shift_Del	DEL	T	T	-																															ctgtgggagactcatttagaTttatagcccatggtgatgct																										TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr3:25833175delT	ENST00000280701.3	+	2	763	c.664delT	c.(664-666)tttfs	p.F222fs	OXSM_ENST00000449808.1_Intron|NGLY1_ENST00000417874.2_5'Flank|OXSM_ENST00000420173.2_Frame_Shift_Del_p.F222fs	NM_017897.2	NP_060367.1	Q9NWU1	OXSM_HUMAN	3-oxoacyl-ACP synthase, mitochondrial	222					acyl-CoA metabolic process (GO:0006637)|medium-chain fatty acid biosynthetic process (GO:0051792)|short-chain fatty acid biosynthetic process (GO:0051790)	mitochondrion (GO:0005739)	3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	25						CTCATTTAGATTTATAGCCCA	0.498																																					p.R221fs		Atlas-INDEL	.											.	OXSM	54	.	0			c.663delA						PASS	.						121	119	120					3																	25833175		2203	4300	6503	SO:0001589	frameshift_variant	54995	exon2			.	BC008202	CCDS2643.1, CCDS46780.1	3p24.2	2010-03-19			ENSG00000151093	ENSG00000151093	2.3.1.41		26063	protein-coding gene	gene with protein product	"beta-ketoacyl synthase"	610324				12477932	Standard	NM_017897		Approved	KS, FLJ20604, FASN2D	uc003cdn.3	Q9NWU1	OTTHUMG00000130477	ENST00000280701.3:c.664delT	chr3.hg19:g.25833175delT	ENSP00000280701:p.Phe222fs	176.0	0.0	0		178.0	86.0	0.483146	NM_001145391		Frame_Shift_Del	DEL	ENST00000280701.3	hg19	CCDS2643.1																																																																																			.	.	.	none		0.498	OXSM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252876.2	NM_017897		-	25833175	T	-	25833175	7	5	195	1	0	1	0	1	0	0	0	0	11342	1493	52	0	666	0	OXSM	3	25833175	Frame_Shift_Del	DEL	T	TCGA-HE-7130-01A-11D-1961-08		25833175	172189255	33	11634											
SEMA3F	6405	hgsc.bcm.edu	37	chr3	50220896	50220896	+	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	tgtgtgtctactccatggctGatattcgcatggtcttcaac	7	15	9	10	1	3	1	1	1	2	0	5	1	4	1	1	2	2	2	1	2	3	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr3:50220896G>C	ENST00000002829.3	+	12	1616	c.1132G>C	c.(1132-1134)Gat>Cat	p.D378H	SEMA3F_ENST00000413852.1_Missense_Mutation_p.D279H|SEMA3F_ENST00000434342.1_Missense_Mutation_p.D347H	NM_004186.3	NP_004177.3	Q13275	SEM3F_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F	378	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|negative regulation of axon extension involved in axon guidance (GO:0048843)|nerve development (GO:0021675)|neural crest cell migration (GO:0001755)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	extracellular space (GO:0005615)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|receptor activity (GO:0004872)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	17				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)		CTCCATGGCTGATATTCGCAT	0.632																																					p.D378H		Atlas-SNP	.											.	SEMA3F	62	.	0			c.G1132C						PASS	.						86	74	78					3																	50220896		2203	4300	6503	SO:0001583	missense	6405	exon12			ATGGCTGATATTC	U33920	CCDS2811.1	3p21.3	2013-01-11			ENSG00000001617	ENSG00000001617		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10728	protein-coding gene	gene with protein product	"sema IV"	601124				8786119, 8649831	Standard	NM_004186		Approved	SEMAK, Sema4	uc003cyj.3	Q13275	OTTHUMG00000156806	ENST00000002829.3:c.1132G>C	chr3.hg19:g.50220896G>C	ENSP00000002829:p.Asp378His	85.0	0.0	.		71.0	7.0	.	NM_004186	C9JQ85|Q13274|Q13372|Q15704|Q6GTR4	Missense_Mutation	SNP	ENST00000002829.3	hg19	CCDS2811.1	.	.	.	.	.	.	.	.	.	.	G	32	5.151596	0.94645	.	.	ENSG00000001617	ENST00000450338;ENST00000413852;ENST00000002829;ENST00000434342	T;T;T;T	0.27720	1.65;1.65;1.65;1.65	5.45	5.45	0.79879	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.67590	0.2909	M	0.93720	3.45	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.81914	0.995;0.981	T	0.77096	-0.2714	10	0.87932	D	0	.	18.8886	0.92389	0.0:0.0:1.0:0.0	.	347;378	C9JQ85;Q13275	.;SEM3F_HUMAN	H	347;279;378;347	ENSP00000398399:D347H;ENSP00000388931:D279H;ENSP00000002829:D378H;ENSP00000409859:D347H	ENSP00000002829:D378H	D	+	1	0	SEMA3F	50195900	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	9.651000	0.98493	2.542000	0.85734	0.511000	0.50034	GAT	.	.	.	none		0.632	SEMA3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345929.1	NM_004186		C	50220896	G	C	50220896	3	2	195	1	0	0	0	0	1	0	0	0	14042	1290	45	4	1174	4	SEMA3F	3	50220896	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	24387721	50220896	147801534	34	11635											
CACNA2D3	55799	hgsc.bcm.edu	37	chr3	54930840	54930840	+	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	accatttccctctctggtacCgaagagccgctgagcagatt	9	10	9	13	2	1	3	0	1	1	2	3	4	2	3	4	1	3	3	4	1	2	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr3:54930840C>A	ENST00000474759.1	+	26	2359	c.2311C>A	c.(2311-2313)Cga>Aga	p.R771R	CACNA2D3_ENST00000415676.2_Silent_p.R771R|CACNA2D3_ENST00000490478.1_Silent_p.R677R|CACNA2D3-AS1_ENST00000471265.1_RNA|CACNA2D3_ENST00000288197.5_Silent_p.R771R	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	771						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)	TCTCTGGTACCGAAGAGCCGC	0.527																																					p.R771R		Atlas-SNP	.											.	CACNA2D3	159	.	0			c.C2311A						PASS	.						120	121	120					3																	54930840		1968	4153	6121	SO:0001819	synonymous_variant	55799	exon26			TGGTACCGAAGAG	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.2311C>A	chr3.hg19:g.54930840C>A		200.0	0.0	.		180.0	8.0	.	NM_018398	B2RPL6|Q9NY16|Q9NY18	Silent	SNP	ENST00000474759.1	hg19	CCDS54598.1																																																																																			.	.	.	none		0.527	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1			A	54930840	C	A	54930840	2	1	195	1	0	0	0	0	0	0	0	1	2552	644	23	4		4	CACNA2D3	3	54930840	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	4709944	54930840	143091590	35	11636											
CCDC80	151887	hgsc.bcm.edu	37	chr3	112324296	112324296	+	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	tccatggtgataactctcatGatgacggtagtcatcctggt	9	13	10	9	1	2	3	2	3	1	0	5	3	4	3	2	3	1	1	2	3	2	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr3:112324296G>A	ENST00000206423.3	-	8	3774	c.2821C>T	c.(2821-2823)Cat>Tat	p.H941Y	CCDC80_ENST00000439685.2_Missense_Mutation_p.H941Y	NM_199511.1|NM_199512.1	NP_955805.1|NP_955806.1	Q76M96	CCD80_HUMAN	coiled-coil domain containing 80	941					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						TAACTCTCATGATGACGGTAG	0.483																																					p.H941Y		Atlas-SNP	.											.	CCDC80	100	.	0			c.C2821T						PASS	.						97	89	92					3																	112324296		2203	4300	6503	SO:0001583	missense	151887	exon8			TCTCATGATGACG	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.2821C>T	chr3.hg19:g.112324296G>A	ENSP00000206423:p.His941Tyr	100.0	0.0	.		99.0	27.0	.	NM_199511	D3DN67|Q5PR20|Q6GPG9|Q8IVT6|Q8NBV1|Q8NHY8	Missense_Mutation	SNP	ENST00000206423.3	hg19	CCDS2968.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.211797	0.79240	.	.	ENSG00000091986	ENST00000206423;ENST00000439685;ENST00000444594	T;T	0.52754	0.65;0.65	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.37571	0.1008	N	0.19112	0.55	0.46317	D	0.998989	B;B	0.31931	0.347;0.236	B;B	0.26416	0.069;0.031	T	0.29058	-1.0024	10	0.87932	D	0	-20.2625	20.4324	0.99085	0.0:0.0:1.0:0.0	.	952;941	Q76M96-2;Q76M96	.;CCD80_HUMAN	Y	941;941;542	ENSP00000206423:H941Y;ENSP00000411814:H941Y	ENSP00000206423:H941Y	H	-	1	0	CCDC80	113806986	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.764000	0.74960	2.833000	0.97629	0.585000	0.79938	CAT	.	.	.	none		0.483	CCDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354219.1	NM_199511		A	112324296	G	A	112324296	3	1	195	1	0	0	0	0	1	0	0	0	2856	1290	45	2	35	2	CCDC80	3	112324296	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	57393456	112324296	85698134	36	11637											
KALRN	8997	hgsc.bcm.edu	37	chr3	124103778	124103778	+	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	gaccccgaggagatctacaaGgcagctcgacacctggaggt	11	5	13	12	2	1	1	0	0	1	1	2	6	1	2	3	4	2	2	3	4	2	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr3:124103778G>C	ENST00000240874.3	+	11	2008	c.1851G>C	c.(1849-1851)aaG>aaC	p.K617N	KALRN_ENST00000460856.1_Missense_Mutation_p.K617N|KALRN_ENST00000360013.3_Missense_Mutation_p.K617N	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	617					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						AGATCTACAAGGCAGCTCGAC	0.567																																					p.K617N		Atlas-SNP	.											.	KALRN	556	.	0			c.G1851C						PASS	.						108	88	95					3																	124103778		2203	4300	6503	SO:0001583	missense	8997	exon11			CTACAAGGCAGCT	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.1851G>C	chr3.hg19:g.124103778G>C	ENSP00000240874:p.Lys617Asn	96.0	0.0	.		84.0	38.0	.	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Missense_Mutation	SNP	ENST00000240874.3	hg19	CCDS3027.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.01|15.01	2.706440|2.706440	0.48412|0.48412	.|.	.|.	ENSG00000160145|ENSG00000160145	ENST00000460856;ENST00000240874;ENST00000360013;ENST00000439170|ENST00000354186	T;T;T;T|.	0.41758|.	0.99;0.99;0.99;0.99|.	5.0|5.0	4.09|4.09	0.47781|0.47781	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.38214|0.38214	0.1032|0.1032	N|N	0.21373|0.21373	0.66|0.66	0.80722|0.80722	D|D	1|1	P;P;P|.	0.48089|.	0.542;0.905;0.486|.	B;P;B|.	0.50314|.	0.388;0.637;0.268|.	T|T	0.15065|0.15065	-1.0450|-1.0450	10|5	0.18276|.	T|.	0.48|.	.|.	5.048|5.048	0.14494|0.14494	0.4066:0.0:0.5934:0.0|0.4066:0.0:0.5934:0.0	.|.	617;617;617|.	C9IZQ6;O60229;O60229-2|.	.;KALRN_HUMAN;.|.	N|T	617;617;617;93|595	ENSP00000418611:K617N;ENSP00000240874:K617N;ENSP00000353109:K617N;ENSP00000402950:K93N|.	ENSP00000240874:K617N|.	K|R	+|+	3|2	2|0	KALRN|KALRN	125586468|125586468	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.890000|1.890000	0.39728|0.39728	1.232000|1.232000	0.43678|0.43678	0.563000|0.563000	0.77884|0.77884	AAG|AGG	.	.	.	none		0.567	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		C	124103778	G	C	124103778	3	2	195	1	0	0	0	0	1	0	0	0	7982	991	35	4	1893	4	KALRN	3	124103778	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	11779482	124103778	73918652	37	11638											
MME	4311	hgsc.bcm.edu	37	chr3	154860114	154860114	+	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	aggagtccagaaatgctttcCgcaaggtgaagaaaaaatct	16	8	10	7	1	1	3	0	1	1	2	3	4	3	4	2	2	1	2	2	2	6	1	rs201459271		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr3:154860114C>A	ENST00000460393.1	+	12	1303	c.1183C>A	c.(1183-1185)Cgc>Agc	p.R395S	MME_ENST00000360490.2_Missense_Mutation_p.R395S|MME_ENST00000462745.1_Missense_Mutation_p.R395S|MME_ENST00000492661.1_Missense_Mutation_p.R395S|MME_ENST00000493237.1_Missense_Mutation_p.R395S	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	395					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)	AAATGCTTTCCGCAAGGTGAA	0.378																																					p.R395S		Atlas-SNP	.											.	MME	133	.	0			c.C1183A						PASS	.						61	64	63					3																	154860114		2203	4300	6503	SO:0001583	missense	4311	exon12			GCTTTCCGCAAGG		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.1183C>A	chr3.hg19:g.154860114C>A	ENSP00000418525:p.Arg395Ser	76.0	0.0	.		102.0	9.0	.	NM_007287	A8K6U6|D3DNJ9|Q3MIX4	Missense_Mutation	SNP	ENST00000460393.1	hg19	CCDS3172.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.067486	0.76301	.	.	ENSG00000196549	ENST00000492661;ENST00000460393;ENST00000462745;ENST00000493237;ENST00000360490	T;T;T;T;T	0.73363	-0.74;-0.74;-0.74;-0.74;-0.74	5.93	5.93	0.95920	Peptidase M13 (1);Metallopeptidase, catalytic domain (1);	0.053836	0.64402	D	0.000001	T	0.81851	0.4910	L	0.43152	1.355	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.82356	-0.0498	10	0.66056	D	0.02	-16.1723	15.1001	0.72269	0.1416:0.8584:0.0:0.0	.	395	P08473	NEP_HUMAN	S	395	ENSP00000420389:R395S;ENSP00000418525:R395S;ENSP00000419653:R395S;ENSP00000417079:R395S;ENSP00000353679:R395S	ENSP00000353679:R395S	R	+	1	0	MME	156342808	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.296000	0.72751	2.803000	0.96430	0.585000	0.79938	CGC	.	.	.	alt		0.378	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902		A	154860114	C	A	154860114	3	1	195	1	0	0	0	0	1	0	0	0	9652	652	23	4	1225	4	MME	3	154860114	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	30756336	154860114	43162316	38	11639											
TTC14	151613	hgsc.bcm.edu	37	chr3	180324303	180324303	+	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	gaagtttgaacaaagcaataGaagattttgagcttgcatta	16	12	9	4	0	0	4	0	2	0	2	0	5	0	4	0	0	4	4	0	0	7	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr3:180324303G>C	ENST00000296015.4	+	9	1216	c.1084G>C	c.(1084-1086)Gaa>Caa	p.E362Q	TTC14_ENST00000412756.2_Missense_Mutation_p.E362Q|TTC14_ENST00000382584.4_Missense_Mutation_p.E362Q	NM_133462.3	NP_597719.1	Q96N46	TTC14_HUMAN	tetratricopeptide repeat domain 14	362							RNA binding (GO:0003723)			endometrium(3)|kidney(5)|large_intestine(9)|lung(24)|ovary(2)|pancreas(1)|skin(1)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			CAAAGCAATAGAAGATTTTGA	0.383																																					p.E362Q		Atlas-SNP	.											.	TTC14	112	.	0			c.G1084C						PASS	.						117	124	121					3																	180324303		2203	4300	6503	SO:0001583	missense	151613	exon9			GCAATAGAAGATT	AB075860	CCDS3237.1, CCDS46963.1, CCDS75055.1	3q27.2	2013-01-10			ENSG00000163728	ENSG00000163728		"Tetratricopeptide (TTC) repeat domain containing"	24697	protein-coding gene	gene with protein product						11853319	Standard	NM_001042601		Approved	FLJ00166, KIAA1980	uc003fkk.3	Q96N46	OTTHUMG00000157859	ENST00000296015.4:c.1084G>C	chr3.hg19:g.180324303G>C	ENSP00000296015:p.Glu362Gln	111.0	0.0	.		214.0	119.0	.	NM_001042601	G5E9X0|Q6UWJ7|Q8TF22	Missense_Mutation	SNP	ENST00000296015.4	hg19	CCDS3237.1	.	.	.	.	.	.	.	.	.	.	G	17.46	3.396059	0.62177	.	.	ENSG00000163728	ENST00000296015;ENST00000412756;ENST00000382584	T;T;T	0.62232	0.04;0.04;0.04	5.93	5.93	0.95920	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.482695	0.24828	N	0.035263	T	0.64778	0.2629	L	0.42529	1.33	0.33985	D	0.648465	D;P;P	0.71674	0.998;0.787;0.912	P;B;P	0.55615	0.78;0.419;0.575	T	0.70063	-0.4975	10	0.30854	T	0.27	-20.8298	11.6377	0.51213	0.1367:0.0:0.8633:0.0	.	362;362;362	Q96N46-2;G5E9X0;Q96N46	.;.;TTC14_HUMAN	Q	362	ENSP00000296015:E362Q;ENSP00000413743:E362Q;ENSP00000372027:E362Q	ENSP00000296015:E362Q	E	+	1	0	TTC14	181806997	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.915000	0.48805	2.798000	0.96311	0.655000	0.94253	GAA	.	.	.	none		0.383	TTC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349786.1	NM_133462		C	180324303	G	C	180324303	3	2	195	1	0	0	0	0	1	0	0	0	16693	943	33	4	1118	4	TTC14	3	180324303	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	25464189	180324303	17698127	39	11640											
CCDC39	339829	hgsc.bcm.edu	37	chr3	180337752	180337752	+	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	ttgaagttcttctttttcttGagcagcctatgaagtacaga	10	16	8	7	0	3	4	0	3	3	1	3	4	3	4	1	0	3	3	1	0	4	8			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr3:180337752G>C	ENST00000442201.2	-	15	2124	c.2005C>G	c.(2005-2007)Caa>Gaa	p.Q669E	CCDC39_ENST00000273654.4_Intron	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	669					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)			TCTTTTTCTTGAGCAGCCTAT	0.383																																					p.Q669E		Atlas-SNP	.											.	CCDC39	242	.	0			c.C2005G						PASS	.						64	53	57					3																	180337752		1829	4079	5908	SO:0001583	missense	339829	exon15			TTTCTTGAGCAGC	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.2005C>G	chr3.hg19:g.180337752G>C	ENSP00000405708:p.Gln669Glu	22.0	0.0	.		55.0	9.0	.	NM_181426	B4E2H1	Missense_Mutation	SNP	ENST00000442201.2	hg19	CCDS46964.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.263405	0.80358	.	.	ENSG00000145075	ENST00000442201	T	0.77620	-1.11	5.25	5.25	0.73442	.	.	.	.	.	D	0.87446	0.6179	M	0.83953	2.67	0.80722	D	1	D	0.71674	0.998	D	0.66602	0.945	D	0.84150	0.0422	9	0.13108	T	0.6	.	19.205	0.93726	0.0:0.0:1.0:0.0	.	669	Q9UFE4	CCD39_HUMAN	E	669	ENSP00000405708:Q669E	ENSP00000405708:Q669E	Q	-	1	0	CCDC39	181820446	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.762000	0.91711	2.596000	0.87737	0.563000	0.77884	CAA	.	.	.	none		0.383	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028		C	180337752	G	C	180337752	3	2	195	1	0	0	0	0	1	0	0	0	2813	1299	45	4	844	4	CCDC39	3	180337752	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	13449	180337752	17684678	40	11641											
FGFR3	2261	hgsc.bcm.edu	37	chr4	1806099	1806099	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgacgaggcgggcagtgtgtAtgcaggcatcctcagctacg	8	8	15	10	3	1	1	1	1	0	0	2	2	2	1	1	3	3	5	1	3	2	2	rs121913485		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr4:1806099A>G	ENST00000260795.2	+	8	1220	c.1118A>G	c.(1117-1119)tAt>tGt	p.Y373C	FGFR3_ENST00000481110.2_Missense_Mutation_p.Y373C|FGFR3_ENST00000440486.2_Missense_Mutation_p.Y373C|FGFR3_ENST00000352904.1_Intron|FGFR3_ENST00000412135.2_Intron|FGFR3_ENST00000340107.4_Missense_Mutation_p.Y375C			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	373			Y -> C (in KERSEB and TD1; disulfide- linked dimer with constitutive kinase activation). {ECO:0000269|PubMed:10360402, ECO:0000269|PubMed:15772091, ECO:0000269|PubMed:8845844, ECO:0000269|PubMed:9207791}.		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)	p.Y373C(395)		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)	GGCAGTGTGTATGCAGGCATC	0.682	Y373C(KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	1	"Mis, T"	"IGH@, ETV6"	"bladder, MM, T-cell lymphoma"		"Hypochondroplasia, Thanatophoric dysplasia"		Saethre-Chotzen syndrome;Muenke syndrome																												p.Y375C		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"L, E"	FGFR3_ENST00000340107,bladder,carcinoma,0,407	FGFR3	3320	.	395	Substitution - Missense(395)	urinary_tract(371)|skin(16)|haematopoietic_and_lymphoid_tissue(8)	c.A1124G	GRCh37	CM960657	FGFR3	M	rs121913485	PASS	.						141	134	137					4																	1806099		2203	4300	6503	SO:0001583	missense	2261	exon9	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	GTGTGTATGCAGG	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.1118A>G	chr4.hg19:g.1806099A>G	ENSP00000260795:p.Tyr373Cys	304.0	1.0	.		201.0	172.0	.	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Missense_Mutation	SNP	ENST00000260795.2	hg19	CCDS3353.1	.	.	.	.	.	.	.	.	.	.	a	12.61	1.990190	0.35131	.	.	ENSG00000068078	ENST00000481110;ENST00000340107;ENST00000440486;ENST00000260795	D;D;D;D	0.88201	-2.35;-2.35;-2.35;-2.35	4.68	1.93	0.25924	.	0.343855	0.31061	N	0.008340	D	0.93148	0.7818	M	0.82517	2.595	0.80722	A	1	D;D;D	0.76494	0.992;0.994;0.999	D;P;D	0.72625	0.94;0.896;0.978	D	0.94049	0.7316	9	0.72032	D	0.01	.	8.9873	0.36001	0.7079:0.0:0.0:0.2921	.	375;373;373	P22607-2;P22607;F8W9L4	.;FGFR3_HUMAN;.	C	373;375;373;373	ENSP00000420533:Y373C;ENSP00000339824:Y375C;ENSP00000414914:Y373C;ENSP00000260795:Y373C	ENSP00000260795:Y373C	Y	+	2	0	FGFR3	1775897	0.999000	0.42202	0.495000	0.27527	0.084000	0.17831	4.274000	0.58921	0.715000	0.32103	0.379000	0.24179	TAT	.	.	.	weak		0.682	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142		G	1806099	A	G	1806099	3	3	195	1	0	0	0	0	1	0	0	0	5874	449	16	3	1303	3	FGFR3	4	1806099	Missense_Mutation	SNP	A	TCGA-HE-7130-01A-11D-1961-08		1806099	189348177	41	11642											
FGFR3	2261	hgsc.bcm.edu	37	chr4	1807891	1807891	+	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	aacctcgactactacaagaaGacgaccaacgtgagcccggc	14	4	9	14	4	0	3	0	1	0	2	1	5	0	3	3	1	5	0	3	1	6	2	rs28928868		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr4:1807891G>C	ENST00000260795.2	+	13	2052	c.1950G>C	c.(1948-1950)aaG>aaC	p.K650N	FGFR3_ENST00000481110.2_Missense_Mutation_p.K651N|FGFR3_ENST00000440486.2_Missense_Mutation_p.K650N|FGFR3_ENST00000352904.1_Missense_Mutation_p.K538N|FGFR3_ENST00000412135.2_Missense_Mutation_p.K538N|FGFR3_ENST00000340107.4_Missense_Mutation_p.K652N			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	650	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		K -> E (in KERSEB, TD2, TGCT and bladder cancer samples; bladder transitional cell carcinoma; somatic mutation; constitutively activated kinase with impaired internalization and degradation, resulting in prolonged FGFR3 signaling). {ECO:0000269|PubMed:10471491, ECO:0000269|PubMed:15772091, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:19855393, ECO:0000269|PubMed:7773297, ECO:0000269|PubMed:9207791}.|K -> M (in KERSEB, ACH and TD1; constitutively activated kinase with impaired internalization and degradation, resulting in prolonged FGFR3 signaling). {ECO:0000269|PubMed:10671061, ECO:0000269|PubMed:15772091, ECO:0000269|PubMed:9207791}.|K -> Q (in hypochondroplasia and bladder cancer; in hypochondroplasia the form is milder than that seen in individuals with the K-540 or M-650 mutations; constitutively activated kinase). {ECO:0000269|PubMed:11055896, ECO:0000269|PubMed:11314002}.		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)	ACTACAAGAAGACGACCAACG	0.662		1	"Mis, T"	"IGH@, ETV6"	"bladder, MM, T-cell lymphoma"		"Hypochondroplasia, Thanatophoric dysplasia"		Saethre-Chotzen syndrome;Muenke syndrome																												p.K652N		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"L, E"	FGFR3_ENST00000340107,colon,carcinoma,0,2	FGFR3	3320	.	0			c.G1956C	GRCh37	CM002965|CM002966	FGFR3	M	rs28928868	PASS	.						31	32	31					4																	1807891		2203	4299	6502	SO:0001583	missense	2261	exon14	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	CAAGAAGACGACC	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.1950G>C	chr4.hg19:g.1807891G>C	ENSP00000260795:p.Lys650Asn	50.0	1.0	.		18.0	16.0	.	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Missense_Mutation	SNP	ENST00000260795.2	hg19	CCDS3353.1	.	.	.	.	.	.	.	.	.	.	g	13.74	2.328521	0.41197	.	.	ENSG00000068078	ENST00000481110;ENST00000340107;ENST00000440486;ENST00000412135;ENST00000260795;ENST00000352904	D;D;D;D;D;D	0.83506	-1.73;-1.73;-1.73;-1.73;-1.73;-1.73	4.35	3.48	0.39840	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	0.86100	0.5852	L	0.53671	1.685	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.97110	1.0;0.98;1.0;1.0	D	0.85665	0.1291	10	0.87932	D	0	.	5.6966	0.17859	0.3256:0.0:0.6744:0.0	.	652;538;650;651	P22607-2;P22607-3;P22607;F8W9L4	.;.;FGFR3_HUMAN;.	N	651;652;650;538;650;538	ENSP00000420533:K651N;ENSP00000339824:K652N;ENSP00000414914:K650N;ENSP00000412903:K538N;ENSP00000260795:K650N;ENSP00000231803:K538N	ENSP00000260795:K650N	K	+	3	2	FGFR3	1777689	1.000000	0.71417	1.000000	0.80357	0.396000	0.30629	2.106000	0.41835	2.127000	0.65507	0.448000	0.29417	AAG	.	.	.	weak		0.662	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142		C	1807891	G	C	1807891	3	2	195	1	0	0	0	0	1	0	0	0	5874	933	33	4	2155	4	FGFR3	4	1807891	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	1792	1807891	189346385	42	11643											
HOPX	84525	hgsc.bcm.edu	37	chr4	57514941	57514941	+	Missense_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	cttctgagcgccgccactttGccaggcgctgcttaaaccat	7	10	9	15	3	1	1	0	1	1	0	1	1	1	1	4	1	4	2	4	1	2	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr4:57514941G>A	ENST00000337881.7	-	3	823	c.167C>T	c.(166-168)gCa>gTa	p.A56V	HOPX_ENST00000556614.2_Missense_Mutation_p.A56V|HOPX_ENST00000555760.2_Missense_Mutation_p.A56V|HOPX_ENST00000381260.3_3'UTR|HOPX_ENST00000553379.2_Missense_Mutation_p.A56V|HOPX_ENST00000556376.2_Missense_Mutation_p.A56V|HOPX_ENST00000381255.3_Missense_Mutation_p.A56V|HOPX_ENST00000420433.1_Missense_Mutation_p.A74V|HOPX_ENST00000554144.1_3'UTR|HOPX_ENST00000317745.7_Missense_Mutation_p.A56V|HOPX_ENST00000508121.1_Missense_Mutation_p.A74V|HOPX_ENST00000503639.3_Missense_Mutation_p.A56V	NM_139212.3	NP_631958.1	Q9BPY8	HOP_HUMAN	HOP homeobox	56					heart development (GO:0007507)|histone deacetylation (GO:0016575)|lung alveolus development (GO:0048286)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of skeletal muscle tissue regeneration (GO:0043415)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of heart contraction (GO:0008016)|regulation of protein binding (GO:0043393)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(2)|lung(5)|skin(1)	8	Glioma(25;0.08)|all_neural(26;0.101)					CCGCCACTTTGCCAGGCGCTG	0.478																																					p.A74V		Atlas-SNP	.											.	HOPX	28	.	0			c.C221T						PASS	.						78	77	77					4																	57514941		2203	4300	6503	SO:0001583	missense	84525	exon4			CACTTTGCCAGGC		CCDS3507.1, CCDS47062.1, CCDS54767.1	4q12	2011-06-20			ENSG00000171476	ENSG00000171476		"Homeoboxes / PRD class"	24961	protein-coding gene	gene with protein product	"homeobox only domain"	607275				12297045	Standard	NM_032495		Approved	LAGY, HOP, OB1, NECC1, SMAP31	uc003hbz.2	Q9BPY8	OTTHUMG00000128768	ENST00000337881.7:c.167C>T	chr4.hg19:g.57514941G>A	ENSP00000337330:p.Ala56Val	172.0	0.0	.		145.0	61.0	.	NM_032495	A8K0Z2|E9PB55|G3V294|Q8N0V6|Q96CI1	Missense_Mutation	SNP	ENST00000337881.7	hg19	CCDS3507.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.103343	0.76983	.	.	ENSG00000171476	ENST00000420433;ENST00000508121;ENST00000556376;ENST00000553379;ENST00000381255;ENST00000317745;ENST00000503639;ENST00000337881;ENST00000555760;ENST00000556614;ENST00000514890;ENST00000506661	D;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;-4.27	5.93	5.93	0.95920	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	.	.	.	.	D	0.98298	0.9436	.	.	.	0.80722	D	1	D;D	0.76494	0.999;0.995	D;D	0.69824	0.966;0.927	D	0.98808	1.0742	8	0.87932	D	0	.	15.8335	0.78778	0.0:0.0:1.0:0.0	.	74;56	E9PB55;Q9BPY8	.;HOP_HUMAN	V	74;74;56;56;56;56;56;56;56;56;56;56	ENSP00000396275:A74V;ENSP00000422175:A74V;ENSP00000451794:A56V;ENSP00000452340:A56V;ENSP00000370654:A56V;ENSP00000315198:A56V;ENSP00000424101:A56V;ENSP00000337330:A56V;ENSP00000452098:A56V;ENSP00000452003:A56V	ENSP00000315198:A56V	A	-	2	0	HOPX	57209698	1.000000	0.71417	0.996000	0.52242	0.528000	0.34623	5.302000	0.65733	2.818000	0.97014	0.591000	0.81541	GCA	.	.	.	none		0.478	HOPX-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250689.4			A	57514941	G	A	57514941	3	1	195	1	0	0	0	0	1	0	0	0	7292	1319	46	2	58	2	HOPX	4	57514941	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	55707050	57514941	133639335	43	11644											
PLK4	10733	hgsc.bcm.edu	37	chr4	128813651	128813651	+	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	attctcctggtgctgattttGaggtttggttttatgatggt	5	20	12	4	0	1	3	0	3	1	0	2	3	1	3	1	4	1	3	1	4	1	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr4:128813651G>C	ENST00000270861.5	+	10	2444	c.2170G>C	c.(2170-2172)Gag>Cag	p.E724Q	PLK4_ENST00000507249.1_Missense_Mutation_p.E663Q|PLK4_ENST00000513090.1_Missense_Mutation_p.E692Q|PLK4_ENST00000515069.1_Missense_Mutation_p.E646Q|RNU6-583P_ENST00000516012.1_RNA|PLK4_ENST00000514379.1_Missense_Mutation_p.E683Q	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	724					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						TGCTGATTTTGAGGTTTGGTT	0.318																																					p.E724Q	Colon(135;508 1718 19061 31832 42879)	Atlas-SNP	.											.	PLK4	65	.	0			c.G2170C						PASS	.						145	132	137					4																	128813651		2202	4300	6502	SO:0001583	missense	10733	exon10			GATTTTGAGGTTT	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.2170G>C	chr4.hg19:g.128813651G>C	ENSP00000270861:p.Glu724Gln	94.0	0.0	.		53.0	7.0	.	NM_014264	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Missense_Mutation	SNP	ENST00000270861.5	hg19	CCDS3735.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.561758	0.86335	.	.	ENSG00000142731	ENST00000270861;ENST00000515069;ENST00000513090;ENST00000507249;ENST00000514379	T;T;T;T;T	0.37058	1.22;1.22;1.22;1.22;1.22	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.66723	0.2818	M	0.86178	2.8	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.72239	-0.4351	10	0.87932	D	0	-7.7549	19.2043	0.93723	0.0:0.0:1.0:0.0	.	692;724	O00444-2;O00444	.;PLK4_HUMAN	Q	724;646;692;663;683	ENSP00000270861:E724Q;ENSP00000421774:E646Q;ENSP00000427554:E692Q;ENSP00000423412:E663Q;ENSP00000423582:E683Q	ENSP00000270861:E724Q	E	+	1	0	PLK4	129033101	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	9.502000	0.97981	2.536000	0.85505	0.313000	0.20887	GAG	.	.	.	none		0.318	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3			C	128813651	G	C	128813651	3	2	195	1	0	0	0	0	1	0	0	0	12105	1291	45	4	2208	4	PLK4	4	128813651	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	71298710	128813651	62340625	44	11645											
SLC6A19	340024	hgsc.bcm.edu	37	chr5	1216926	1216926	+	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	acatcctgaccctcatcaacGggttcgacctgcctgaaggc	9	8	9	15	2	2	2	2	2	0	0	4	3	3	2	4	2	2	1	4	2	2	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr5:1216926G>T	ENST00000304460.10	+	8	1095	c.1039G>T	c.(1039-1041)Ggg>Tgg	p.G347W		NM_001003841.2	NP_001003841.1	Q695T7	S6A19_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 19	347					amino acid transport (GO:0006865)|ion transport (GO:0006811)|response to nutrient (GO:0007584)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|neutral amino acid transmembrane transporter activity (GO:0015175)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(25)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			CCTCATCAACGGGTTCGACCT	0.652																																					p.G347W		Atlas-SNP	.											.	SLC6A19	99	.	0			c.G1039T						PASS	.						130	115	120					5																	1216926		2203	4300	6503	SO:0001583	missense	340024	exon8			ATCAACGGGTTCG	AK096054	CCDS34130.1	5p15	2013-07-19			ENSG00000174358	ENSG00000174358		"Solute carriers"	27960	protein-coding gene	gene with protein product	"Hartnup disease"	608893					Standard	NM_001003841		Approved		uc003jbw.4	Q695T7	OTTHUMG00000161636	ENST00000304460.10:c.1039G>T	chr5.hg19:g.1216926G>T	ENSP00000305302:p.Gly347Trp	217.0	0.0	.		249.0	10.0	.	NM_001003841	A8K446	Missense_Mutation	SNP	ENST00000304460.10	hg19	CCDS34130.1	.	.	.	.	.	.	.	.	.	.	G	10.26	1.301225	0.23650	.	.	ENSG00000174358	ENST00000304460	T	0.74421	-0.84	4.85	4.85	0.62838	.	0.546335	0.20606	N	0.089063	T	0.75376	0.3841	N	0.19112	0.55	0.09310	N	1	D	0.62365	0.991	P	0.62813	0.907	T	0.68637	-0.5356	10	0.38643	T	0.18	.	16.1221	0.81365	0.0:0.0:1.0:0.0	.	347	Q695T7	S6A19_HUMAN	W	347	ENSP00000305302:G347W	ENSP00000305302:G347W	G	+	1	0	SLC6A19	1269926	0.250000	0.23951	0.020000	0.16555	0.075000	0.17131	3.150000	0.50662	2.241000	0.73720	0.491000	0.48974	GGG	.	.	.	none		0.652	SLC6A19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365557.1	XM_291120		T	1216926	G	T	1216926	3	4	195	1	0	0	0	0	1	0	0	0	14695	1116	39	4	1069	4	SLC6A19	5	1216926	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08		1216926	179698334	45	11646											
CMYA5	202333	hgsc.bcm.edu	37	chr5	79027353	79027353	+	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	ggaagaaattgtccatagatCtctaaatctaaaaggtgcat	16	11	8	6	0	2	2	0	0	2	2	4	3	3	3	1	2	1	1	1	2	7	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr5:79027353C>T	ENST00000446378.2	+	2	2796	c.2765C>T	c.(2764-2766)tCt>tTt	p.S922F		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	922					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)		GTCCATAGATCTCTAAATCTA	0.413																																					p.S922F		Atlas-SNP	.											.	CMYA5	643	.	0			c.C2765T						PASS	.						103	100	101					5																	79027353		1924	4135	6059	SO:0001583	missense	202333	exon2			ATAGATCTCTAAA	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.2765C>T	chr5.hg19:g.79027353C>T	ENSP00000394770:p.Ser922Phe	114.0	0.0	.		94.0	51.0	.	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	hg19	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	C	7.587	0.669858	0.14776	.	.	ENSG00000164309	ENST00000446378	T	0.59502	0.26	5.54	2.7	0.31948	.	1.759930	0.02782	N	0.121104	T	0.67239	0.2872	M	0.78456	2.415	0.09310	N	1	D	0.56035	0.974	P	0.49752	0.621	T	0.40813	-0.9543	10	0.72032	D	0.01	.	4.9024	0.13781	0.178:0.5938:0.0:0.2282	.	922	Q8N3K9	CMYA5_HUMAN	F	922	ENSP00000394770:S922F	ENSP00000394770:S922F	S	+	2	0	CMYA5	79063109	0.035000	0.19736	0.003000	0.11579	0.048000	0.14542	0.437000	0.21543	0.358000	0.24211	-0.302000	0.09304	TCT	.	.	.	none		0.413	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		T	79027353	C	T	79027353	3	4	195	1	0	0	0	0	1	0	0	0	3592	913	32	2	2771	2	CMYA5	5	79027353	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	77810427	79027353	101887907	46	11647			1	24		4	4	5227	N	G_C	2.160406e-06
CMYA5	202333	hgsc.bcm.edu	37	chr5	79031337	79031337	+	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	taaaactgctgatgaacccaGaggtactttagtaaaatctg	15	11	8	7	0	1	3	0	2	1	1	1	3	1	3	1	1	4	3	1	1	7	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr5:79031337G>A	ENST00000446378.2	+	2	6780	c.6749G>A	c.(6748-6750)aGa>aAa	p.R2250K		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2250					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)		GATGAACCCAGAGGTACTTTA	0.343																																					p.R2250K		Atlas-SNP	.											.	CMYA5	643	.	0			c.G6749A						PASS	.						84	86	85					5																	79031337		1802	4075	5877	SO:0001583	missense	202333	exon2			AACCCAGAGGTAC	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.6749G>A	chr5.hg19:g.79031337G>A	ENSP00000394770:p.Arg2250Lys	176.0	0.0	.		140.0	75.0	.	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	hg19	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	G	4.593	0.110236	0.08780	.	.	ENSG00000164309	ENST00000446378	T	0.15718	2.4	5.74	-0.131	0.13494	.	1.286200	0.05079	N	0.483194	T	0.15046	0.0363	L	0.48362	1.52	0.09310	N	1	B	0.14805	0.011	B	0.10450	0.005	T	0.33599	-0.9862	10	0.33940	T	0.23	.	4.6556	0.12615	0.2976:0.3196:0.3827:0.0	.	2250	Q8N3K9	CMYA5_HUMAN	K	2250	ENSP00000394770:R2250K	ENSP00000394770:R2250K	R	+	2	0	CMYA5	79067093	0.000000	0.05858	0.001000	0.08648	0.014000	0.08584	-0.363000	0.07593	0.328000	0.23435	0.650000	0.86243	AGA	.	.	.	none		0.343	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		A	79031337	G	A	79031337	3	1	195	1	0	0	0	0	1	0	0	0	3592	942	33	2	6755	2	CMYA5	5	79031337	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	3984	79031337	101883923	47	11648			1	24		4	4	5227	N	G_C	2.160406e-06
CMYA5	202333	hgsc.bcm.edu	37	chr5	79031882	79031882	+	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	gtgaagacagactcaagaaaGaaatgcaaaatcctacttcc	18	7	7	9	0	1	5	1	1	0	4	3	5	3	5	2	0	2	1	2	0	7	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr5:79031882G>C	ENST00000446378.2	+	2	7325	c.7294G>C	c.(7294-7296)Gaa>Caa	p.E2432Q		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2432					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)		ACTCAAGAAAGAAATGCAAAA	0.333																																					p.E2432Q		Atlas-SNP	.											CMYA5_ENST00000446378,NS,carcinoma,0,2	CMYA5	643	.	0			c.G7294C						PASS	.						38	38	38					5																	79031882		1818	4082	5900	SO:0001583	missense	202333	exon2			AAGAAAGAAATGC	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.7294G>C	chr5.hg19:g.79031882G>C	ENSP00000394770:p.Glu2432Gln	66.0	0.0	.		58.0	24.0	.	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	hg19	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	G	17.82	3.484254	0.63962	.	.	ENSG00000164309	ENST00000446378	T	0.24723	1.84	5.87	4.09	0.47781	.	0.121012	0.37483	N	0.002068	T	0.37100	0.0991	M	0.71581	2.175	0.28279	N	0.924047	D	0.59767	0.986	P	0.53954	0.738	T	0.32877	-0.9890	10	0.66056	D	0.02	.	6.9428	0.24502	0.2444:0.0:0.7556:0.0	.	2432	Q8N3K9	CMYA5_HUMAN	Q	2432	ENSP00000394770:E2432Q	ENSP00000394770:E2432Q	E	+	1	0	CMYA5	79067638	0.992000	0.36948	0.963000	0.40424	0.963000	0.63663	1.287000	0.33284	1.493000	0.48517	0.655000	0.94253	GAA	.	.	.	none		0.333	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		C	79031882	G	C	79031882	3	2	195	1	0	0	0	0	1	0	0	0	3592	943	33	4	7300	4	CMYA5	5	79031882	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	545	79031882	101883378	48	11649			1	24		4	4	5227	N	G_C	2.160406e-06
CMYA5	202333	hgsc.bcm.edu	37	chr5	79032579	79032579	+	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	agtattagaaaagtcaagcaGagatatgccagatcacagtg	17	8	10	6	0	2	3	2	0	0	3	2	4	2	3	1	0	2	2	1	0	6	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr5:79032579G>A	ENST00000446378.2	+	2	8022	c.7991G>A	c.(7990-7992)aGa>aAa	p.R2664K		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2664					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)		AAGTCAAGCAGAGATATGCCA	0.403																																					p.R2664K		Atlas-SNP	.											.	CMYA5	643	.	0			c.G7991A						PASS	.						49	49	49					5																	79032579		1848	4092	5940	SO:0001583	missense	202333	exon2			CAAGCAGAGATAT	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.7991G>A	chr5.hg19:g.79032579G>A	ENSP00000394770:p.Arg2664Lys	68.0	0.0	.		50.0	25.0	.	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	hg19	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	G	10.79	1.448897	0.26074	.	.	ENSG00000164309	ENST00000446378	T	0.36340	1.26	3.85	2.95	0.34219	.	.	.	.	.	T	0.25419	0.0618	L	0.34521	1.04	0.09310	N	1	B	0.26483	0.15	B	0.23419	0.046	T	0.17349	-1.0372	9	0.39692	T	0.17	.	6.834	0.23925	0.1396:0.0:0.8604:0.0	.	2664	Q8N3K9	CMYA5_HUMAN	K	2664	ENSP00000394770:R2664K	ENSP00000394770:R2664K	R	+	2	0	CMYA5	79068335	0.000000	0.05858	0.016000	0.15963	0.089000	0.18198	0.577000	0.23758	0.699000	0.31761	0.393000	0.25936	AGA	.	.	.	none		0.403	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		A	79032579	G	A	79032579	3	1	195	1	0	0	0	0	1	0	0	0	3592	942	33	2	7997	2	CMYA5	5	79032579	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	697	79032579	101882681	49	11650			1	24		4	4	5227	N	G_C	2.160406e-06
VCAN	1462	hgsc.bcm.edu	37	chr5	82817031	82817031	+	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	gcctactacttatgtagactCttcccataccattcctcttt	8	16	3	14	0	2	1	0	0	2	1	4	1	4	1	4	0	3	1	4	0	5	8			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr5:82817031C>G	ENST00000265077.3	+	7	3471	c.2906C>G	c.(2905-2907)tCt>tGt	p.S969C	VCAN_ENST00000512590.2_Missense_Mutation_p.S921C|VCAN_ENST00000343200.5_Intron|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Missense_Mutation_p.S969C	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	969	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)	TATGTAGACTCTTCCCATACC	0.433																																					p.S969C		Atlas-SNP	.											.	VCAN	498	.	0			c.C2906G						PASS	.						113	112	112					5																	82817031		2203	4300	6503	SO:0001583	missense	1462	exon7			TAGACTCTTCCCA	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.2906C>G	chr5.hg19:g.82817031C>G	ENSP00000265077:p.Ser969Cys	116.0	0.0	.		105.0	9.0	.	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	hg19	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	C	10.39	1.337475	0.24253	.	.	ENSG00000038427	ENST00000265077;ENST00000342785;ENST00000512590	T;T;T	0.20332	2.08;2.08;2.08	5.26	-0.324	0.12706	.	1.069220	0.07230	N	0.862281	T	0.21718	0.0523	L	0.44542	1.39	0.09310	N	1	P;P	0.51653	0.904;0.947	P;P	0.47981	0.563;0.453	T	0.19257	-1.0311	10	0.62326	D	0.03	.	4.5464	0.12083	0.0:0.4105:0.2996:0.29	.	969;969	P13611-3;P13611	.;CSPG2_HUMAN	C	969;969;921	ENSP00000265077:S969C;ENSP00000342768:S969C;ENSP00000425959:S921C	ENSP00000265077:S969C	S	+	2	0	VCAN	82852787	0.000000	0.05858	0.022000	0.16811	0.689000	0.40095	-0.838000	0.04372	-0.249000	0.09569	0.591000	0.81541	TCT	.	.	.	none		0.433	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		G	82817031	C	G	82817031	3	3	195	1	0	0	0	0	1	0	0	0	17150	913	32	4	2928	4	VCAN	5	82817031	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	3784452	82817031	98098229	50	11651											
GRIA1	2890	hgsc.bcm.edu	37	chr5	153078520	153078520	+	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	tagagctggcggcagagattGccaagcacgtgggctactcc	9	7	14	11	2	0	2	0	0	0	2	1	3	1	2	2	3	4	4	2	3	3	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr5:153078520G>C	ENST00000285900.5	+	10	1682	c.1339G>C	c.(1339-1341)Gcc>Ccc	p.A447P	GRIA1_ENST00000448073.4_Missense_Mutation_p.A457P|GRIA1_ENST00000518783.1_Missense_Mutation_p.A457P|GRIA1_ENST00000518142.1_Missense_Mutation_p.A367P|GRIA1_ENST00000340592.5_Missense_Mutation_p.A447P|GRIA1_ENST00000521843.2_Missense_Mutation_p.A378P	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	447					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)	GGCAGAGATTGCCAAGCACGT	0.537																																					p.A457P		Atlas-SNP	.											.	GRIA1	321	.	0			c.G1369C						PASS	.						115	102	106					5																	153078520		2203	4300	6503	SO:0001583	missense	2890	exon10			GAGATTGCCAAGC		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.1339G>C	chr5.hg19:g.153078520G>C	ENSP00000285900:p.Ala447Pro	135.0	0.0	.		82.0	19.0	.	NM_001258021	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Missense_Mutation	SNP	ENST00000285900.5	hg19	CCDS4322.1	.	.	.	.	.	.	.	.	.	.	G	34	5.344853	0.95807	.	.	ENSG00000155511	ENST00000285900;ENST00000544403;ENST00000518142;ENST00000537037;ENST00000340592;ENST00000521843;ENST00000544794;ENST00000518783;ENST00000448073	T;T;D;T;T;T;D	0.81821	1.03;1.03;-1.54;1.03;1.03;1.03;-1.54	5.44	5.44	0.79542	Glutamate receptor, L-glutamate/glycine-binding (2);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	D	0.93514	0.7930	H	0.96996	3.92	0.80722	D	1	D;D;D;D;D;D	0.71674	0.987;0.987;0.998;0.987;0.984;0.998	D;D;D;D;P;D	0.91635	0.931;0.931;0.999;0.931;0.887;0.984	D	0.95457	0.8539	10	0.87932	D	0	.	18.2393	0.89961	0.0:0.0:1.0:0.0	.	457;457;367;457;447;447	E7ESV8;B7Z9G9;B7Z3F6;B7Z2W8;P42261-2;P42261	.;.;.;.;.;GRIA1_HUMAN	P	447;447;367;401;447;378;378;457;457	ENSP00000285900:A447P;ENSP00000427920:A367P;ENSP00000339343:A447P;ENSP00000427864:A378P;ENSP00000442108:A378P;ENSP00000428994:A457P;ENSP00000415569:A457P	ENSP00000285900:A447P	A	+	1	0	GRIA1	153058713	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.640000	0.98453	2.548000	0.85928	0.655000	0.94253	GCC	.	.	.	none		0.537	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3			C	153078520	G	C	153078520	3	2	195	1	0	0	0	0	1	0	0	0	6774	1319	46	4	1377	4	GRIA1	5	153078520	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	70261489	153078520	27836740	51	11652											
SGCD	6444	hgsc.bcm.edu	37	chr5	156186311	156186311	+	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	ggaacgaggcagaaggtcttCgagatctgcgtctgcgccaa	10	7	14	10	4	3	2	0	0	3	2	4	5	3	3	1	3	3	1	1	3	3	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr5:156186311C>T	ENST00000435422.3	+	8	1267	c.780C>T	c.(778-780)ttC>ttT	p.F260F	SGCD_ENST00000337851.4_Silent_p.F261F	NM_001128209.1	NP_001121681.1	Q92629	SGCD_HUMAN	sarcoglycan, delta (35kDa dystrophin-associated glycoprotein)	260					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)		p.F261L(1)		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)			AGAAGGTCTTCGAGATCTGCG	0.488																																					p.F261F		Atlas-SNP	.											SGCD,NS,carcinoma,0,1	SGCD	52	.	1	Substitution - Missense(1)	lung(1)	c.C783T						PASS	.						130	125	127					5																	156186311		1968	4175	6143	SO:0001819	synonymous_variant	6444	exon9			GGTCTTCGAGATC	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.780C>T	chr5.hg19:g.156186311C>T		171.0	1.0	.		131.0	44.0	.	NM_000337	A8K9S9|Q53XA5|Q99644	Silent	SNP	ENST00000435422.3	hg19	CCDS47327.1																																																																																			.	.	.	none		0.488	SGCD-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000373469.3			T	156186311	C	T	156186311	2	4	195	1	0	0	0	0	0	0	0	1	14214	883	31	1		1	SGCD	5	156186311	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	3107791	156186311	24728949	52	11653											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152557320	152557320	+	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	tgttacttagccagcactctCcaagttgatttagttggctt	8	16	8	9	0	1	1	0	1	1	0	2	1	1	1	2	1	3	5	2	1	4	7			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr6:152557320C>T	ENST00000367255.5	-	110	20919	c.20318G>A	c.(20317-20319)gGa>gAa	p.G6773E	SYNE1_ENST00000341594.5_Missense_Mutation_p.G6385E|SYNE1_ENST00000356820.4_Missense_Mutation_p.G1297E|SYNE1_ENST00000265368.4_Missense_Mutation_p.G6773E|SYNE1_ENST00000423061.1_Missense_Mutation_p.G6702E|SYNE1_ENST00000448038.1_Missense_Mutation_p.G6702E	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6773					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)		CCAGCACTCTCCAAGTTGATT	0.373										HNSCC(10;0.0054)																											p.G6773E		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G20318A						PASS	.						170	166	167					6																	152557320		2203	4300	6503	SO:0001583	missense	23345	exon110			CACTCTCCAAGTT	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.20318G>A	chr6.hg19:g.152557320C>T	ENSP00000356224:p.Gly6773Glu	159.0	0.0	.		81.0	58.0	.	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	12.94	2.087720	0.36855	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820	T;T;T;T;T;T	0.50548	0.83;0.81;0.74;0.82;0.92;2.82	5.56	5.56	0.83823	.	0.000000	0.56097	D	0.000029	T	0.53498	0.1800	L	0.33710	1.025	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	0.55147	-0.8186	10	0.54805	T	0.06	.	19.5353	0.95251	0.0:1.0:0.0:0.0	.	6773;6773;6702	Q8NF91;E7EQI5;Q8NF91-4	SYNE1_HUMAN;.;.	E	6773;6702;6773;6702;6385;1297	ENSP00000356224:G6773E;ENSP00000396024:G6702E;ENSP00000265368:G6773E;ENSP00000390975:G6702E;ENSP00000341887:G6385E;ENSP00000349276:G1297E	ENSP00000265368:G6773E	G	-	2	0	SYNE1	152599013	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	6.073000	0.71245	2.607000	0.88179	0.655000	0.94253	GGA	.	.	.	none		0.373	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152557320	C	T	152557320	3	4	195	1	0	0	0	0	1	0	0	0	15457	855	30	2	6296	2	SYNE1	6	152557320	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08		152557320	18557747	53	11654											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152560730	152560730	+	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	tttcagtacagcagaagcctGagccatcagctctgtatgga	11	10	10	10	0	3	2	2	1	1	1	3	3	3	3	2	1	5	4	2	1	3	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr6:152560730G>C	ENST00000367255.5	-	108	20606	c.20005C>G	c.(20005-20007)Cag>Gag	p.Q6669E	SYNE1_ENST00000341594.5_Missense_Mutation_p.Q6281E|SYNE1_ENST00000356820.4_Missense_Mutation_p.Q1193E|SYNE1_ENST00000265368.4_Missense_Mutation_p.Q6669E|SYNE1_ENST00000423061.1_Missense_Mutation_p.Q6598E|SYNE1_ENST00000448038.1_Missense_Mutation_p.Q6598E	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6669					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)		GCAGAAGCCTGAGCCATCAGC	0.468										HNSCC(10;0.0054)																											p.Q6669E		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C20005G						PASS	.						136	112	120					6																	152560730		2203	4300	6503	SO:0001583	missense	23345	exon108			AAGCCTGAGCCAT	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.20005C>G	chr6.hg19:g.152560730G>C	ENSP00000356224:p.Gln6669Glu	101.0	0.0	.		61.0	47.0	.	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	2.493	-0.316916	0.05386	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820	T;T;T;T;T;T	0.34859	1.34;1.34;1.34;1.34;1.34;1.34	5.7	4.81	0.61882	.	0.210406	0.33438	N	0.004910	T	0.14787	0.0357	L	0.36672	1.1	0.30220	N	0.796918	B;B;B	0.26876	0.101;0.101;0.162	B;B;B	0.22386	0.017;0.017;0.039	T	0.10428	-1.0630	10	0.66056	D	0.02	.	12.7363	0.57225	0.0:0.1256:0.7439:0.1305	.	6669;6669;6598	Q8NF91;E7EQI5;Q8NF91-4	SYNE1_HUMAN;.;.	E	6669;6598;6669;6598;6281;1193	ENSP00000356224:Q6669E;ENSP00000396024:Q6598E;ENSP00000265368:Q6669E;ENSP00000390975:Q6598E;ENSP00000341887:Q6281E;ENSP00000349276:Q1193E	ENSP00000265368:Q6669E	Q	-	1	0	SYNE1	152602423	0.999000	0.42202	0.997000	0.53966	0.994000	0.84299	2.850000	0.48294	1.368000	0.46115	0.655000	0.94253	CAG	.	.	.	none		0.468	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		C	152560730	G	C	152560730	3	2	195	1	0	0	0	0	1	0	0	0	15457	1299	45	4	6617	4	SYNE1	6	152560730	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	3410	152560730	18554337	54	11655											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152730280	152730280	+	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	actgtgaattttcttcagctCagataacaagtgttttcctt	10	17	6	8	0	3	2	2	1	1	1	4	2	4	2	1	0	2	2	1	0	3	7			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr6:152730280C>T	ENST00000367255.5	-	44	7064	c.6463G>A	c.(6463-6465)Gag>Aag	p.E2155K	SYNE1_ENST00000341594.5_Missense_Mutation_p.E2192K|SYNE1_ENST00000265368.4_Missense_Mutation_p.E2155K|SYNE1_ENST00000423061.1_Missense_Mutation_p.E2162K|SYNE1_ENST00000448038.1_Missense_Mutation_p.E2162K|RNA5SP223_ENST00000365174.1_RNA	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2155					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)		TTCTTCAGCTCAGATAACAAG	0.383										HNSCC(10;0.0054)																											p.E2162K		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G6484A						PASS	.						147	142	143					6																	152730280		2203	4300	6503	SO:0001583	missense	23345	exon44			TCAGCTCAGATAA	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.6463G>A	chr6.hg19:g.152730280C>T	ENSP00000356224:p.Glu2155Lys	99.0	0.0	.		55.0	45.0	.	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	18.72	3.684114	0.68157	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.52295	1.38;1.38;1.38;1.38;0.67	5.57	5.57	0.84162	.	0.000000	0.64402	D	0.000013	T	0.49115	0.1538	M	0.61703	1.905	0.80722	D	1	D;D;D;D	0.58620	0.982;0.983;0.983;0.978	P;P;P;P	0.59424	0.791;0.678;0.678;0.857	T	0.46582	-0.9181	10	0.06891	T	0.86	.	19.5527	0.95328	0.0:1.0:0.0:0.0	.	2138;2155;2155;2162	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	K	2155;2162;2155;2162;2192	ENSP00000356224:E2155K;ENSP00000396024:E2162K;ENSP00000265368:E2155K;ENSP00000390975:E2162K;ENSP00000341887:E2192K	ENSP00000265368:E2155K	E	-	1	0	SYNE1	152771973	1.000000	0.71417	0.991000	0.47740	0.194000	0.23727	7.794000	0.85869	2.630000	0.89119	0.655000	0.94253	GAG	.	.	.	none		0.383	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152730280	C	T	152730280	3	4	195	1	0	0	0	0	1	0	0	0	15457	835	29	2	20415	2	SYNE1	6	152730280	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	169550	152730280	18384787	55	11656											
MLLT4	4301	hgsc.bcm.edu	37	chr6	168347543	168347543	+	Missense_Mutation	SNP	A	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	tggtgatgacagactgatgaAaaatagagctgatcaccgtt	14	10	11	6	1	1	7	1	5	0	2	1	7	1	7	1	1	1	2	1	1	3	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr6:168347543A>C	ENST00000447894.2	+	26	3494	c.3494A>C	c.(3493-3495)aAa>aCa	p.K1165T	MLLT4_ENST00000392112.1_Missense_Mutation_p.K1148T|MLLT4_ENST00000507679.1_3'UTR|MLLT4_ENST00000351017.4_Missense_Mutation_p.K1172T|MLLT4_ENST00000366806.2_Missense_Mutation_p.K1165T|MLLT4_ENST00000344191.4_Missense_Mutation_p.K1165T|MLLT4_ENST00000400822.3_Missense_Mutation_p.K1164T|MLLT4_ENST00000392108.3_Missense_Mutation_p.K1165T			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	1165					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)		AGACTGATGAAAAATAGAGCT	0.433			T	MLL	AL																																p.K1165T		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.A3494C						PASS	.						115	116	116					6																	168347543		2203	4300	6503	SO:0001583	missense	4301	exon26			TGATGAAAAATAG	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.3494A>C	chr6.hg19:g.168347543A>C	ENSP00000404595:p.Lys1165Thr	160.0	0.0	.		77.0	60.0	.	NM_001040000	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Missense_Mutation	SNP	ENST00000447894.2	hg19		.	.	.	.	.	.	.	.	.	.	A	22.4	4.286695	0.80803	.	.	ENSG00000130396	ENST00000344191;ENST00000351017;ENST00000392108;ENST00000366806;ENST00000392112;ENST00000341575;ENST00000400822;ENST00000447894	T;T;T;T;T;T;T	0.04970	3.73;3.62;3.72;3.71;3.52;3.62;3.62	5.36	4.19	0.49359	.	0.000000	0.85682	D	0.000000	T	0.12347	0.0300	M	0.73962	2.25	0.52501	D	0.999956	P;D;P;P	0.67145	0.586;0.996;0.817;0.843	B;D;B;P	0.63703	0.263;0.917;0.345;0.63	T	0.00800	-1.1561	10	0.59425	D	0.04	-31.0185	11.4921	0.50387	0.929:0.0:0.071:0.0	.	1165;1164;1165;1149	P55196;P55196-5;P55196-6;P55196-2	AFAD_HUMAN;.;.;.	T	1165;1172;1165;1165;1148;1165;1164;1165	ENSP00000341118:K1165T;ENSP00000252692:K1172T;ENSP00000375956:K1165T;ENSP00000355771:K1165T;ENSP00000375960:K1148T;ENSP00000383623:K1164T;ENSP00000404595:K1165T	ENSP00000345834:K1165T	K	+	2	0	MLLT4	168090392	1.000000	0.71417	0.812000	0.32479	0.904000	0.53231	8.548000	0.90669	0.965000	0.38133	0.533000	0.62120	AAA	.	.	.	none		0.433	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936		C	168347543	A	C	168347543	3	2	195	1	0	0	0	0	1	0	0	0	9636	14	1	5	3596	5	MLLT4	6	168347543	Missense_Mutation	SNP	A	TCGA-HE-7130-01A-11D-1961-08	15617263	168347543	2767524	56	11657											
SBDS	51119	hgsc.bcm.edu	37	chr7	66456129	66456129	+	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	atatttgactcttacgatttCtaactgttggccataatctt	10	18	5	8	1	3	1	0	1	3	0	3	2	3	1	1	1	2	1	1	1	4	8			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr7:66456129C>G	ENST00000246868.2	-	4	802	c.619G>C	c.(619-621)Gaa>Caa	p.E207Q		NM_016038.2	NP_057122.2	Q9Y3A5	SBDS_HUMAN	Shwachman-Bodian-Diamond syndrome	207					bone marrow development (GO:0048539)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|inner cell mass cell proliferation (GO:0001833)|leukocyte chemotaxis (GO:0030595)|mature ribosome assembly (GO:0042256)|mitotic spindle stabilization (GO:0043148)|ribosomal large subunit biogenesis (GO:0042273)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|rRNA binding (GO:0019843)			cervix(1)|endometrium(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	7						CTTACGATTTCTAACTGTTGG	0.353			Gene Conversion			"AML, MDS"			Shwachman-Diamond syndrome																												p.E207Q		Atlas-SNP	.	yes	Rec		Schwachman-Diamond syndrome	7	7q11	51119	Shwachman-Bodian-Diamond syndrome protein		L	.	SBDS	20	.	0			c.G619C						PASS	.						150	125	133					7																	66456129		2203	4300	6503	SO:0001583	missense	51119	exon4	Familial Cancer Database	Shwachman syndrome, Shwachman-Bodian syndrome, Congenital Lipomatosis of the Pancreas	CGATTTCTAACTG	AF151855	CCDS5537.1	7q11.22	2014-09-17			ENSG00000126524	ENSG00000126524			19440	protein-coding gene	gene with protein product		607444				12496757	Standard	NM_016038		Approved	CGI-97, FLJ10917, SDS, SWDS	uc003tvm.1	Q9Y3A5	OTTHUMG00000023165	ENST00000246868.2:c.619G>C	chr7.hg19:g.66456129C>G	ENSP00000246868:p.Glu207Gln	65.0	0.0	.		84.0	33.0	.	NM_016038	A8K0P4|Q96FX0|Q9NV53	Missense_Mutation	SNP	ENST00000246868.2	hg19	CCDS5537.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.189067	0.78789	.	.	ENSG00000126524	ENST00000246868	D	0.96745	-4.11	5.04	5.04	0.67666	Ribosome maturation protein SBDS, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.96929	0.8997	M	0.87381	2.88	0.80722	D	1	P	0.37594	0.601	P	0.44394	0.448	D	0.96222	0.9161	10	0.30854	T	0.27	-19.3899	15.9306	0.79656	0.0:1.0:0.0:0.0	.	207	Q9Y3A5	SBDS_HUMAN	Q	207	ENSP00000246868:E207Q	ENSP00000246868:E207Q	E	-	1	0	SBDS	66093564	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	6.965000	0.76067	2.641000	0.89580	0.555000	0.69702	GAA	.	.	.	none		0.353	SBDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251746.2	NM_016038		G	66456129	C	G	66456129	3	3	195	1	0	0	0	0	1	0	0	0	13870	922	32	4	141	4	SBDS	7	66456129	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08		66456129	92682534	57	11658											
COL1A2	1278	hgsc.bcm.edu	37	chr7	94035021	94035021	+	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	ctggaactcctggacttcctGgcttcaaaggcattagggtg	8	11	12	10	0	1	0	1	0	0	0	3	2	3	2	2	5	1	2	2	5	3	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr7:94035021G>A	ENST00000297268.6	+	11	994	c.523G>A	c.(523-525)Ggc>Agc	p.G175S		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	175					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)	TGGACTTCCTGGCTTCAAAGG	0.373										HNSCC(75;0.22)																											p.G175S		Atlas-SNP	.											.	COL1A2	240	.	0			c.G523A						PASS	.						158	155	156					7																	94035021		2203	4299	6502	SO:0001583	missense	1278	exon11			CTTCCTGGCTTCA	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.523G>A	chr7.hg19:g.94035021G>A	ENSP00000297268:p.Gly175Ser	204.0	0.0	.		264.0	56.0	.	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	hg19	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.343237	0.82022	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.93659	-3.26	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	D	0.98330	0.9446	H	0.98833	4.345	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99501	1.0953	10	0.87932	D	0	.	19.1584	0.93520	0.0:0.0:1.0:0.0	.	175	P08123	CO1A2_HUMAN	S	175;176	ENSP00000297268:G175S	ENSP00000297268:G175S	G	+	1	0	COL1A2	93872957	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	9.420000	0.97426	2.697000	0.92050	0.591000	0.81541	GGC	.	.	.	none		0.373	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		A	94035021	G	A	94035021	3	1	195	1	0	0	0	0	1	0	0	0	3680	1348	47	2	565	2	COL1A2	7	94035021	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	27578892	94035021	65103642	58	11659											
PCM1	5108	hgsc.bcm.edu	37	chr8	17885162	17885162	+	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	tcagaaacggtgggagcccaGagtatatgagatgtcttcag	12	9	13	7	1	3	3	2	1	1	3	3	5	3	4	1	2	2	1	1	2	3	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr8:17885162G>C	ENST00000519253.1	+	39	6293	c.6042G>C	c.(6040-6042)caG>caC	p.Q2014H	PCM1_ENST00000524226.1_Missense_Mutation_p.Q1858H|PCM1_ENST00000325083.8_Missense_Mutation_p.Q2022H|PCM1_ENST00000327578.8_Missense_Mutation_p.Q721H			Q15154	PCM1_HUMAN	pericentriolar material 1	2022	Interaction with BBS4.				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)		TGGGAGCCCAGAGTATATGAG	0.303			T	"RET, JAK2"	"papillary thyroid, CML, MPD"																																p.Q2022H		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"E, L"	.	PCM1	120	.	0			c.G6066C						PASS	.						52	51	51					8																	17885162		1794	4062	5856	SO:0001583	missense	5108	exon39			AGCCCAGAGTATA		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.6042G>C	chr8.hg19:g.17885162G>C	ENSP00000431099:p.Gln2014His	63.0	0.0	.		62.0	10.0	.	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.24|10.24	1.296731|1.296731	0.23650|0.23650	.|.	.|.	ENSG00000078674|ENSG00000078674	ENST00000325083;ENST00000519253;ENST00000524226;ENST00000327578|ENST00000522275	T;T;T;T|.	0.22945|.	3.3;3.3;3.0;1.93|.	5.51|5.51	-6.77|-6.77	0.01727|0.01727	.|.	0.261946|.	0.40302|.	N|.	0.001133|.	T|T	0.25195|0.25195	0.0612|0.0612	N|N	0.20986|0.20986	0.625|0.625	0.29276|0.29276	N|N	0.870346|0.870346	B;B;B;B;B;B;B|.	0.06786|.	0.001;0.001;0.001;0.001;0.001;0.001;0.001|.	B;B;B;B;B;B;B|.	0.08055|.	0.003;0.003;0.003;0.003;0.003;0.003;0.003|.	T|T	0.35101|0.35101	-0.9802|-0.9802	10|5	0.87932|.	D|.	0|.	-2.5298|-2.5298	8.8371|8.8371	0.35119|0.35119	0.2748:0.2274:0.4978:0.0|0.2748:0.2274:0.4978:0.0	.|.	2014;2022;821;2014;1967;1858;2022|.	B9EIS5;D3DSQ0;B4DJ00;E7ETA6;Q15154-2;E7EV56;Q15154|.	.;.;.;.;.;.;PCM1_HUMAN|.	H|T	2022;2014;1858;721|762	ENSP00000327077:Q2022H;ENSP00000431099:Q2014H;ENSP00000430521:Q1858H;ENSP00000328332:Q721H|.	ENSP00000327077:Q2022H|.	Q|R	+|+	3|2	2|0	PCM1|PCM1	17929442|17929442	0.944000|0.944000	0.32072|0.32072	0.012000|0.012000	0.15200|0.15200	0.629000|0.629000	0.37895|0.37895	-0.012000|-0.012000	0.12699|0.12699	-1.249000|-1.249000	0.02500|0.02500	-0.302000|-0.302000	0.09304|0.09304	CAG|AGA	.	.	.	none		0.303	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197		C	17885162	G	C	17885162	3	2	195	1	0	0	0	0	1	0	0	0	11591	933	33	4	6212	4	PCM1	8	17885162	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08		17885162	128478860	59	11660											
EBF2	64641	hgsc.bcm.edu	37	chr8	25890622	25890622	+	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	tgtcaattatgactgggtccGatggagtctcatttcggttt	7	16	11	7	2	2	1	2	1	1	0	5	3	3	2	1	3	0	1	1	3	2	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr8:25890622G>C	ENST00000520164.1	-	6	1067	c.530C>G	c.(529-531)tCg>tGg	p.S177W	EBF2_ENST00000408929.3_Missense_Mutation_p.S29W	NM_022659.3	NP_073150.2	Q9HAK2	COE2_HUMAN	early B-cell factor 2	177					adipose tissue development (GO:0060612)|brown fat cell differentiation (GO:0050873)|cell fate determination (GO:0001709)|positive regulation of chromatin binding (GO:0035563)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(3)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)		GACTGGGTCCGATGGAGTCTC	0.388																																					p.S177W	Esophageal Squamous(166;1018 1046 3854 8328 13429 13634 14071 26624 32918)	Atlas-SNP	.											EBF2_ENST00000520164,NS,neuroblastoma,0,2	EBF2	138	.	0			c.C530G						PASS	.						139	138	138					8																	25890622		1949	4188	6137	SO:0001583	missense	64641	exon6			GGGTCCGATGGAG	AK021562, AK001144	CCDS43726.1	8p21.1	2007-07-26			ENSG00000221818	ENSG00000221818			19090	protein-coding gene	gene with protein product		609934				9151732	Standard	NM_022659		Approved	FLJ11500, COE2	uc003xes.2	Q9HAK2	OTTHUMG00000163838	ENST00000520164.1:c.530C>G	chr8.hg19:g.25890622G>C	ENSP00000430241:p.Ser177Trp	144.0	0.0	.		155.0	20.0	.	NM_022659	A0PJM4|A6NMF7|F5H645|Q66VZ3|Q6DK36|Q6IS86|Q6ISA4	Missense_Mutation	SNP	ENST00000520164.1	hg19	CCDS43726.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.281973	0.80692	.	.	ENSG00000221818	ENST00000520164;ENST00000408929	T;T	0.57273	0.47;0.41	6.17	5.27	0.74061	.	0.000000	0.64402	U	0.000001	T	0.76234	0.3959	M	0.84948	2.725	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79232	-0.1888	10	0.87932	D	0	-4.121	17.6654	0.88201	0.0:0.1224:0.8776:0.0	.	177	Q9HAK2	COE2_HUMAN	W	177;29	ENSP00000430241:S177W;ENSP00000386178:S29W	ENSP00000386178:S29W	S	-	2	0	EBF2	25946539	1.000000	0.71417	0.917000	0.36280	0.772000	0.43724	7.624000	0.83124	2.941000	0.99782	0.655000	0.94253	TCG	.	.	.	none		0.388	EBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375886.2	NM_022659		C	25890622	G	C	25890622	3	2	195	1	0	0	0	0	1	0	0	0	4883	1059	37	4	1241	4	EBF2	8	25890622	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	8005460	25890622	120473400	60	11661											
MATN2	4147	hgsc.bcm.edu	37	chr8	99019720	99019720	+	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	tttgcaggggtggattactgCctgctgagtgaccatggttg	6	13	15	7	0	0	2	0	2	0	0	0	3	0	3	2	4	4	3	2	4	1	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr8:99019720C>T	ENST00000520016.1	+	9	1588	c.1464C>T	c.(1462-1464)tgC>tgT	p.C488C	MATN2_ENST00000522025.2_Silent_p.C204C|MATN2_ENST00000521689.1_Silent_p.C488C|MATN2_ENST00000254898.5_Silent_p.C488C|MATN2_ENST00000524308.1_Silent_p.C447C			O00339	MATN2_HUMAN	matrilin 2	488	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)			TGGATTACTGCCTGCTGAGTG	0.547																																					p.C488C		Atlas-SNP	.											.	MATN2	165	.	0			c.C1464T						PASS	.						131	130	131					8																	99019720		2069	4211	6280	SO:0001819	synonymous_variant	4147	exon10			TTACTGCCTGCTG	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.1464C>T	chr8.hg19:g.99019720C>T		85.0	0.0	.		72.0	30.0	.	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Silent	SNP	ENST00000520016.1	hg19	CCDS55264.1	.	.	.	.	.	.	.	.	.	.	C	9.120	1.008646	0.19199	.	.	ENSG00000132561	ENST00000518154	.	.	.	5.65	4.77	0.60923	.	.	.	.	.	T	0.63827	0.2544	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62407	-0.6861	4	.	.	.	-23.2752	12.1976	0.54307	0.0:0.9189:0.0:0.0811	.	.	.	.	S	271	.	.	P	+	1	0	MATN2	99088896	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	1.602000	0.36783	1.393000	0.46605	0.655000	0.94253	CCT	.	.	.	none		0.547	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1			T	99019720	C	T	99019720	2	4	195	1	0	0	0	0	0	0	0	1	9341	747	26	2		2	MATN2	8	99019720	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	73129098	99019720	47344302	61	11662											
TG	7038	hgsc.bcm.edu	37	chr8	133945814	133945814	+	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	tggtgcttgcagattgcacaGaggacgaggcctgcagcttc	8	9	14	10	1	0	2	0	0	0	2	1	4	0	3	1	3	5	5	1	3	0	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr8:133945814G>A	ENST00000220616.4	+	24	4865	c.4825G>A	c.(4825-4827)Gag>Aag	p.E1609K	TG_ENST00000377869.1_Missense_Mutation_p.E1552K|TG_ENST00000542445.1_Missense_Mutation_p.E43K	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1609					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)		AGATTGCACAGAGGACGAGGC	0.582																																					p.E1609K		Atlas-SNP	.											.	TG	416	.	0			c.G4825A						PASS	.						237	176	197					8																	133945814		2203	4300	6503	SO:0001583	missense	7038	exon24			TGCACAGAGGACG	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.4825G>A	chr8.hg19:g.133945814G>A	ENSP00000220616:p.Glu1609Lys	138.0	0.0	.		113.0	12.0	.	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	hg19	CCDS34944.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.015|0.015	-1.564449|-1.564449	0.00903|0.00903	.|.	.|.	ENSG00000042832|ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445|ENST00000519178	T;T;T|.	0.63417|.	-0.04;-0.04;-0.04|.	5.3|5.3	-6.81|-6.81	0.01704|0.01704	.|.	2.263600|.	0.01555|.	N|.	0.019854|.	T|T	0.14056|0.14056	0.0340|0.0340	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	B;B|.	0.06786|.	0.001;0.001|.	B;B|.	0.04013|.	0.001;0.001|.	T|T	0.24764|0.24764	-1.0151|-1.0151	10|5	0.06099|.	T|.	0.92|.	.|.	1.784|1.784	0.03038|0.03038	0.3015:0.2787:0.305:0.1148|0.3015:0.2787:0.305:0.1148	.|.	43;1609|.	F5GWW5;P01266|.	.;THYG_HUMAN|.	K|K	1552;415;1609;43|128	ENSP00000367100:E1552K;ENSP00000220616:E1609K;ENSP00000441693:E43K|.	ENSP00000220616:E1609K|.	E|R	+|+	1|2	0|0	TG|TG	134014996|134014996	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	-0.841000|-0.841000	0.04359|0.04359	-0.900000|-0.900000	0.03896|0.03896	-0.154000|-0.154000	0.13518|0.13518	GAG|AGA	.	.	.	none		0.582	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		A	133945814	G	A	133945814	3	1	195	1	0	0	0	0	1	0	0	0	15825	943	33	2	4919	2	TG	8	133945814	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	34926094	133945814	12418208	62	11663											
BAI1	575	hgsc.bcm.edu	37	chr8	143603450	143603450	+	Missense_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	cctccggaaccgcctcatccGcaagcgcttcctctgcctgg	5	8	9	19	4	2	0	1	0	1	0	5	1	5	1	7	2	3	2	7	2	2	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr8:143603450G>A	ENST00000517894.1	+	21	4043	c.3149G>A	c.(3148-3150)cGc>cAc	p.R1050H	BAI1_ENST00000323289.5_Missense_Mutation_p.R1050H			O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	1050					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)					CGCCTCATCCGCAAGCGCTTC	0.652																																					p.R1050H		Atlas-SNP	.											.	BAI1	146	.	0			c.G3149A						PASS	.						30	40	37					8																	143603450		2200	4299	6499	SO:0001583	missense	575	exon20			TCATCCGCAAGCG	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.3149G>A	chr8.hg19:g.143603450G>A	ENSP00000430945:p.Arg1050His	54.0	0.0	.		78.0	30.0	.	NM_001702		Missense_Mutation	SNP	ENST00000517894.1	hg19		.	.	.	.	.	.	.	.	.	.	G	28.6	4.933063	0.92458	.	.	ENSG00000181790	ENST00000517894;ENST00000323289	T;T	0.39787	1.06;1.06	3.78	3.78	0.43462	.	0.156800	0.43110	U	0.000612	T	0.51024	0.1650	L	0.46947	1.48	0.58432	D	0.999997	D	0.60160	0.987	P	0.56648	0.803	T	0.57493	-0.7802	10	0.87932	D	0	.	14.6053	0.68475	0.0:0.0:1.0:0.0	.	1050	E9PBK0	.	H	1050	ENSP00000430945:R1050H;ENSP00000313046:R1050H	ENSP00000313046:R1050H	R	+	2	0	BAI1	143600452	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	7.618000	0.83043	1.641000	0.50575	0.305000	0.20034	CGC	.	.	.	none		0.652	BAI1-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379963.3	NM_001702		A	143603450	G	A	143603450	3	1	195	1	0	0	0	0	1	0	0	0	1298	1087	38	1	3227	1	BAI1	8	143603450	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	9657636	143603450	2760572	63	11664											
C5	727	hgsc.bcm.edu	37	chr9	123783919	123783919	+	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	acatcaattgtttgtgcattCagtgttactgggactcctcc	8	15	8	10	0	2	0	2	0	0	0	4	1	4	1	2	1	2	3	2	1	2	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr9:123783919C>G	ENST00000223642.1	-	11	1199	c.1170G>C	c.(1168-1170)ctG>ctC	p.L390L		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	390					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)	TTTGTGCATTCAGTGTTACTG	0.403																																					p.L390L		Atlas-SNP	.											.	C5	124	.	0			c.G1170C						PASS	.						201	182	188					9																	123783919		2203	4300	6503	SO:0001819	synonymous_variant	727	exon11			TGCATTCAGTGTT	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.1170G>C	chr9.hg19:g.123783919C>G		141.0	0.0	.		61.0	6.0	.	NM_001735	Q14CJ0|Q27I61	Silent	SNP	ENST00000223642.1	hg19	CCDS6826.1																																																																																			.	.	.	none		0.403	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735		G	123783919	C	G	123783919	2	3	195	1	0	0	0	0	0	0	0	1	2282	813	29	4		4	C5	9	123783919	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08		123783919	17429512	64	11665											
KCNT1	402381	hgsc.bcm.edu	37	chr9	138594186	138594186	+	5'Flank	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	gctacaccaaccggaccttcGagtttgacgacggccaatgc	10	7	10	14	4	0	1	0	1	0	0	1	4	0	2	4	2	3	2	4	2	3	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr9:138594186G>C	ENST00000298466.5	-	0	0				KCNT1_ENST00000371757.2_Missense_Mutation_p.E28Q|KCNT1_ENST00000298480.5_Missense_Mutation_p.E28Q|KCNT1_ENST00000487664.1_Missense_Mutation_p.E28Q|SOHLH1_ENST00000425225.1_5'Flank	NM_001012415.2	NP_001012415	Q5JUK2	SOLH1_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 1						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)		CCGGACCTTCGAGTTTGACGA	0.726																																					p.E28Q		Atlas-SNP	.											.	KCNT1	139	.	0			c.G82C						PASS	.						22	27	25					9																	138594186		2200	4297	6497	SO:0001631	upstream_gene_variant	57582	exon1			ACCTTCGAGTTTG	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		chr9.hg19:g.138594186G>C	Exception_encountered	61.0	0.0	.		19.0	9.0	.	NM_001272003	C9JG81|Q5EE14|Q5EGC2|Q8NEE3	Missense_Mutation	SNP	ENST00000298466.5	hg19	CCDS35174.1	.	.	.	.	.	.	.	.	.	.	G	10.15	1.270987	0.23221	.	.	ENSG00000107147	ENST00000487664;ENST00000298480;ENST00000371757	T;T;T	0.22336	1.98;1.96;1.96	2.17	2.17	0.27698	.	.	.	.	.	T	0.08582	0.0213	N	0.08118	0	0.80722	D	1	B;P	0.34757	0.315;0.467	B;B	0.26517	0.049;0.07	T	0.21861	-1.0233	9	0.41790	T	0.15	.	7.9137	0.29806	0.0:0.0:1.0:0.0	.	28;28	B9EGP2;G5E9V0	.;.	Q	28	ENSP00000417851:E28Q;ENSP00000298480:E28Q;ENSP00000360822:E28Q	ENSP00000298480:E28Q	E	+	1	0	KCNT1	137734007	0.552000	0.26505	0.891000	0.34965	0.007000	0.05969	1.839000	0.39220	1.514000	0.48869	0.650000	0.86243	GAG	.	.	.	none		0.726	SOHLH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055018.2	NM_001012415		C	138594186	G	C	138594186	1	2	195	0	1	0	0	0	0	0	0	0	8098	1059	37	4		4	KCNT1	9	138594186	5'Flank	SNP	G	TCGA-HE-7130-01A-11D-1961-08	14810267	138594186	2619245	65	11666											
FAM171A1	221061	hgsc.bcm.edu	37	chr10	15256140	15256140	+	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	gtaactacccctgtagtcatCattgcccgaggactcgtagc	9	10	9	13	2	2	0	2	0	0	0	3	2	2	1	3	1	4	3	3	1	4	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr10:15256140C>T	ENST00000378116.4	-	8	1453	c.1447G>A	c.(1447-1449)Gat>Aat	p.D483N	FAM171A1_ENST00000477161.1_5'Flank	NM_001010924.1	NP_001010924.1	Q5VUB5	F1711_HUMAN	family with sequence similarity 171, member A1	483						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						CTGTAGTCATCATTGCCCGAG	0.483																																					p.D483N		Atlas-SNP	.											FAM171A1_ENST00000378116,right_upper_lobe,carcinoma,0,2	FAM171A1	252	.	0			c.G1447A						PASS	.						126	107	113					10																	15256140		2203	4300	6503	SO:0001583	missense	221061	exon8			AGTCATCATTGCC	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.1447G>A	chr10.hg19:g.15256140C>T	ENSP00000367356:p.Asp483Asn	177.0	0.0	.		244.0	27.0	.	NM_001010924	D3DRT9|Q32M49|Q8N4I0	Missense_Mutation	SNP	ENST00000378116.4	hg19	CCDS31154.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	1.660|1.660	-0.511725|-0.511725	0.04200|0.04200	.|.	.|.	ENSG00000148468|ENSG00000148468	ENST00000378116|ENST00000396781	T|.	0.33438|.	1.41|.	5.25|5.25	2.22|2.22	0.28083|0.28083	.|.	0.813268|.	0.11427|.	N|.	0.565243|.	T|T	0.38161|0.38161	0.1030|0.1030	L|L	0.54323|0.54323	1.7|1.7	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.06405|.	0.002|.	T|T	0.26467|0.26467	-1.0102|-1.0102	10|6	0.32370|0.18276	T|T	0.25|0.48	-0.8277|-0.8277	7.3007|7.3007	0.26418|0.26418	0.0:0.692:0.0:0.308|0.0:0.692:0.0:0.308	.|.	483|.	Q5VUB5|.	F1711_HUMAN|.	N|I	483|482	ENSP00000367356:D483N|.	ENSP00000367356:D483N|ENSP00000380001:M482I	D|M	-|-	1|3	0|0	FAM171A1|FAM171A1	15296146|15296146	0.000000|0.000000	0.05858|0.05858	0.006000|0.006000	0.13384|0.13384	0.058000|0.058000	0.15608|0.15608	-0.109000|-0.109000	0.10840|0.10840	0.272000|0.272000	0.22027|0.22027	0.563000|0.563000	0.77884|0.77884	GAT|ATG	.	.	.	none		0.483	FAM171A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046984.1	XM_167709		T	15256140	C	T	15256140	3	4	195	1	0	0	0	0	1	0	0	0	5494	826	29	2	1229	2	FAM171A1	10	15256140	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08		15256140	120278607	66	11667											
MYO3A	53904	hgsc.bcm.edu	37	chr10	26446363	26446363	+	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	gaaagttctgctacagcttcGgtacacaggaattctggaaa	13	10	10	8	1	2	0	0	0	2	0	3	3	2	2	0	3	4	4	0	3	5	5	rs142974032		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr10:26446363G>T	ENST00000265944.5	+	26	3084	c.2918G>T	c.(2917-2919)cGg>cTg	p.R973L	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	973	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						CTACAGCTTCGGTACACAGGA	0.408																																					p.R973L		Atlas-SNP	.											.	MYO3A	371	.	0			c.G2918T						PASS	.						127	121	123					10																	26446363		2203	4300	6503	SO:0001583	missense	53904	exon26			AGCTTCGGTACAC	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.2918G>T	chr10.hg19:g.26446363G>T	ENSP00000265944:p.Arg973Leu	97.0	0.0	.		181.0	9.0	.	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	hg19	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.984956	0.93044	.	.	ENSG00000095777	ENST00000265944	D	0.88586	-2.4	5.07	5.07	0.68467	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.96116	0.8734	M	0.93462	3.42	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97081	0.9784	10	0.87932	D	0	.	18.8211	0.92097	0.0:0.0:1.0:0.0	.	973	Q8NEV4	MYO3A_HUMAN	L	973	ENSP00000265944:R973L	ENSP00000265944:R973L	R	+	2	0	MYO3A	26486369	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	7.966000	0.87956	2.524000	0.85096	0.655000	0.94253	CGG	.	G|1.000;A|0.000	.	alt		0.408	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		T	26446363	G	T	26446363	3	4	195	1	0	0	0	0	1	0	0	0	10083	1116	39	4	3012	4	MYO3A	10	26446363	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	11190223	26446363	109088384	67	11668											
C10orf10	11067	hgsc.bcm.edu	37	chr10	45472882	45472882	+	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	aggtgcgagtagagtgttctGaggacactgctggggcgggg	7	8	20	6	2	1	2	0	1	1	1	1	4	1	3	0	6	2	3	0	6	1	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr10:45472882G>A	ENST00000298295.3	-	2	814	c.597C>T	c.(595-597)ctC>ctT	p.L199L	RASSF4_ENST00000472561.1_Intron|RASSF4_ENST00000340258.5_Intron|RASSF4_ENST00000374417.2_Intron|RASSF4_ENST00000334940.6_Intron|C10orf10_ENST00000496638.1_Intron	NM_007021.3	NP_008952.1	Q9NTK1	DEPP_HUMAN	chromosome 10 open reading frame 10	199						mitochondrion (GO:0005739)				lung(1)	1						AGAGTGTTCTGAGGACACTGC	0.607																																					p.L199L		Atlas-SNP	.											.	C10orf10	6	.	0			c.C597T						PASS	.						59	71	67					10																	45472882		2197	4298	6495	SO:0001819	synonymous_variant	11067	exon2			TGTTCTGAGGACA	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.597C>T	chr10.hg19:g.45472882G>A		153.0	0.0	.		100.0	24.0	.	NM_007021	B2R6A1|O94997|Q5T735|Q76MX8	Silent	SNP	ENST00000298295.3	hg19	CCDS7210.1																																																																																			.	.	.	none		0.607	C10orf10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047758.1	NM_007021		A	45472882	G	A	45472882	2	1	195	1	0	0	0	0	0	0	0	1	1582	1277	45	2		2	C10orf10	10	45472882	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	19026519	45472882	90061865	68	11669											
ANK3	288	hgsc.bcm.edu	37	chr10	61830133	61830133	+	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	tgtctgccttccagtgtgaaGaactgggcccctgacttctg	6	12	11	12	0	2	3	0	2	2	1	3	3	3	3	4	1	2	0	4	1	2	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr10:61830133G>A	ENST00000280772.2	-	37	10697	c.10506C>T	c.(10504-10506)ttC>ttT	p.F3502F	ANK3_ENST00000355288.2_Intron|ANK3_ENST00000373827.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3502					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						CCAGTGTGAAGAACTGGGCCC	0.438																																					p.F3502F		Atlas-SNP	.											.	ANK3	703	.	0			c.C10506T						PASS	.						85	84	84					10																	61830133		2203	4300	6503	SO:0001819	synonymous_variant	288	exon37			TGTGAAGAACTGG	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.10506C>T	chr10.hg19:g.61830133G>A		97.0	0.0	.		65.0	16.0	.	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	hg19	CCDS7258.1																																																																																			.	.	.	none		0.438	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		A	61830133	G	A	61830133	2	1	195	1	0	0	0	0	0	0	0	1	622	933	33	2		2	ANK3	10	61830133	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	16357251	61830133	73704614	69	11670											
ANK3	288	hgsc.bcm.edu	37	chr10	61830689	61830689	+	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	aaatagattcgtcatcgcttGaatcactgacgtctgccccg	10	11	8	12	4	3	3	2	2	1	1	5	3	3	3	2	0	1	1	2	0	3	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr10:61830689G>C	ENST00000280772.2	-	37	10141	c.9950C>G	c.(9949-9951)tCa>tGa	p.S3317*	ANK3_ENST00000355288.2_Intron|ANK3_ENST00000373827.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3317					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						GTCATCGCTTGAATCACTGAC	0.443																																					p.S3317X		Atlas-SNP	.											.	ANK3	703	.	0			c.C9950G						PASS	.						130	132	131					10																	61830689		2203	4300	6503	SO:0001587	stop_gained	288	exon37			TCGCTTGAATCAC	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.9950C>G	chr10.hg19:g.61830689G>C	ENSP00000280772:p.Ser3317*	193.0	0.0	.		157.0	41.0	.	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Nonsense_Mutation	SNP	ENST00000280772.2	hg19	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	G	51	17.357246	0.99884	.	.	ENSG00000151150	ENST00000280772	.	.	.	5.48	5.48	0.80851	.	0.000000	0.38326	N	0.001738	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.359	0.94428	0.0:0.0:1.0:0.0	.	.	.	.	X	3317	.	ENSP00000280772:S3317X	S	-	2	0	ANK3	61500695	1.000000	0.71417	0.256000	0.24389	0.293000	0.27360	7.876000	0.87215	2.584000	0.87258	0.561000	0.74099	TCA	.	.	.	none		0.443	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		C	61830689	G	C	61830689	4	2	195	1	0	0	0	0	0	1	0	0	622	1294	45	4	3524	4	ANK3	10	61830689	Nonsense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	556	61830689	73704058	70	11671											
CHST3	9469	hgsc.bcm.edu	37	chr10	73765714	73765714	+	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	gtgatagtttttgtcttcatCgaaaaggaaaataaaatcat	16	14	7	4	1	3	1	2	1	1	0	4	3	3	2	0	1	0	1	0	1	7	5	rs374590185		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr10:73765714C>G	ENST00000373115.4	+	2	551	c.114C>G	c.(112-114)atC>atG	p.I38M		NM_004273.4	NP_004264.2	Q7LGC8	CHST3_HUMAN	carbohydrate (chondroitin 6) sulfotransferase 3	38					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)|T cell homeostasis (GO:0043029)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 6-sulfotransferase activity (GO:0008459)|proteoglycan sulfotransferase activity (GO:0050698)|sulfotransferase activity (GO:0008146)			endometrium(1)|lung(5)	6						TTGTCTTCATCGAAAAGGAAA	0.478																																					p.I38M		Atlas-SNP	.											CHST3,NS,carcinoma,0,1	CHST3	36	.	0			c.C114G						PASS	.						182	168	173					10																	73765714		2203	4300	6503	SO:0001583	missense	9469	exon2			CTTCATCGAAAAG	AB017915	CCDS7312.1	10q22.1	2007-03-14			ENSG00000122863	ENSG00000122863		"Sulfotransferases, membrane-bound"	1971	protein-coding gene	gene with protein product		603799				9883891, 9714738	Standard	NM_004273		Approved	C6ST, C6ST1	uc001jsn.3	Q7LGC8	OTTHUMG00000018431	ENST00000373115.4:c.114C>G	chr10.hg19:g.73765714C>G	ENSP00000362207:p.Ile38Met	175.0	0.0	.		147.0	9.0	.	NM_004273	O75099|Q52M30	Missense_Mutation	SNP	ENST00000373115.4	hg19	CCDS7312.1	.	.	.	.	.	.	.	.	.	.	C	16.26	3.072133	0.55646	.	.	ENSG00000122863	ENST00000373115	D	0.98044	-4.68	5.66	0.325	0.15903	.	0.000000	0.85682	D	0.000000	D	0.97445	0.9164	L	0.59436	1.845	0.47214	D	0.999359	D	0.89917	1.0	D	0.87578	0.998	D	0.95229	0.8341	10	0.87932	D	0	-10.7332	5.8588	0.18734	0.1406:0.4405:0.0:0.4189	.	38	Q7LGC8	CHST3_HUMAN	M	38	ENSP00000362207:I38M	ENSP00000362207:I38M	I	+	3	3	CHST3	73435720	0.992000	0.36948	0.997000	0.53966	0.982000	0.71751	0.179000	0.16840	-0.128000	0.11641	-1.202000	0.01658	ATC	.	.	.	none		0.478	CHST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048563.1	NM_004273		G	73765714	C	G	73765714	3	3	195	1	0	0	0	0	1	0	0	0	3407	874	31	4	116	4	CHST3	10	73765714	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	11935025	73765714	61769033	71	11672											
CDHR1	92211	hgsc.bcm.edu	37	chr10	85956359	85956359	+	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	ctagaagcgtcttttctgttGaccccacttttggaaacatc	9	14	7	11	1	2	2	0	1	2	1	3	3	2	3	2	1	2	1	2	1	3	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr10:85956359G>A	ENST00000372117.3	+	3	353	c.250G>A	c.(250-252)Gac>Aac	p.D84N	CDHR1_ENST00000332904.3_Missense_Mutation_p.D84N	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	84	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						CTTTTCTGTTGACCCCACTTT	0.562																																					p.D84N		Atlas-SNP	.											.	CDHR1	122	.	0			c.G250A						PASS	.						138	124	129					10																	85956359		2203	4300	6503	SO:0001583	missense	92211	exon3			TCTGTTGACCCCA	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.250G>A	chr10.hg19:g.85956359G>A	ENSP00000361189:p.Asp84Asn	155.0	0.0	.		109.0	66.0	.	NM_001171971	Q69YZ8|Q8IXY5	Missense_Mutation	SNP	ENST00000372117.3	hg19	CCDS7372.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.237685	0.79800	.	.	ENSG00000148600	ENST00000332904;ENST00000372117	T;T	0.62788	-0.0;-0.0	5.57	5.57	0.84162	Cadherin (5);Cadherin-like (1);	0.095350	0.64402	D	0.000001	T	0.54191	0.1843	L	0.37630	1.12	0.80722	D	1	B;B	0.30542	0.284;0.148	B;B	0.34722	0.188;0.186	T	0.53215	-0.8470	10	0.39692	T	0.17	-36.6578	12.4369	0.55604	0.0811:0.0:0.9189:0.0	.	84;84	Q96JP9-2;Q96JP9	.;CDHR1_HUMAN	N	84	ENSP00000331063:D84N;ENSP00000361189:D84N	ENSP00000331063:D84N	D	+	1	0	CDHR1	85946339	1.000000	0.71417	0.770000	0.31555	0.782000	0.44232	5.695000	0.68279	2.630000	0.89119	0.561000	0.74099	GAC	.	.	.	none		0.562	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100		A	85956359	G	A	85956359	3	1	195	1	0	0	0	0	1	0	0	0	3120	1290	45	2	260	2	CDHR1	10	85956359	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	12190645	85956359	49578388	72	11673											
TRUB1	142940	hgsc.bcm.edu	37	chr10	116734920	116734920	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgtgctagagctgacccgaAccaaacagggaccatttacg	13	7	10	11	2	0	2	0	1	0	1	0	4	0	3	3	1	5	2	3	1	4	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr10:116734920A>G	ENST00000298746.3	+	8	893	c.832A>G	c.(832-834)Acc>Gcc	p.T278A		NM_139169.4	NP_631908.1	Q8WWH5	TRUB1_HUMAN	TruB pseudouridine (psi) synthase family member 1	278					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			breast(2)|kidney(2)|large_intestine(1)|lung(5)|urinary_tract(2)	12		Colorectal(252;0.09)|Breast(234;0.174)|Lung NSC(174;0.245)		Epithelial(162;0.00879)|all cancers(201;0.0243)		GCTGACCCGAACCAAACAGGG	0.408																																					p.T278A		Atlas-SNP	.											.	TRUB1	30	.	0			c.A832G						PASS	.						157	145	149					10																	116734920		2203	4300	6503	SO:0001583	missense	142940	exon8			ACCCGAACCAAAC	AF448144	CCDS7591.1	10q25.3	2013-09-02	2013-09-02		ENSG00000165832	ENSG00000165832			16060	protein-coding gene	gene with protein product		610726	"TruB pseudouridine (psi) synthase homolog 1 (E. coli)"			12736709	Standard	NM_139169		Approved	PUS4	uc001lcd.3	Q8WWH5	OTTHUMG00000019094	ENST00000298746.3:c.832A>G	chr10.hg19:g.116734920A>G	ENSP00000298746:p.Thr278Ala	120.0	0.0	.		112.0	24.0	.	NM_139169	B2R716|Q53ES2	Missense_Mutation	SNP	ENST00000298746.3	hg19	CCDS7591.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.696609	0.88830	.	.	ENSG00000165832	ENST00000298746	T	0.16196	2.36	5.7	5.7	0.88788	Pseudouridine synthase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.49558	0.1564	M	0.93062	3.375	0.80722	D	1	D	0.55605	0.972	P	0.62740	0.906	T	0.61048	-0.7141	10	0.66056	D	0.02	-16.4514	14.82	0.70065	1.0:0.0:0.0:0.0	.	278	Q8WWH5	TRUB1_HUMAN	A	278	ENSP00000298746:T278A	ENSP00000298746:T278A	T	+	1	0	TRUB1	116724910	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.785000	0.85724	2.287000	0.76781	0.533000	0.62120	ACC	.	.	.	none		0.408	TRUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050504.1	NM_139169		G	116734920	A	G	116734920	3	3	195	1	0	0	0	0	1	0	0	0	16614	43	2	3	862	3	TRUB1	10	116734920	Missense_Mutation	SNP	A	TCGA-HE-7130-01A-11D-1961-08	30778561	116734920	18799827	73	11674											
MKI67	4288	hgsc.bcm.edu	37	chr10	129910532	129910532	+	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	ccctcctctcttaggaacctCtgtctgagatttgctgctgg	5	14	9	13	0	3	1	0	1	3	1	5	3	4	2	3	2	3	2	3	2	2	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr10:129910532C>T	ENST00000368654.3	-	9	2209	c.1834G>A	c.(1834-1836)Gag>Aag	p.E612K	MKI67_ENST00000368653.3_Missense_Mutation_p.E252K|MKI67_ENST00000484853.1_5'UTR	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	612					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)				TTAGGAACCTCTGTCTGAGAT	0.488																																					p.E612K		Atlas-SNP	.											.	MKI67	363	.	0			c.G1834A						PASS	.						111	102	105					10																	129910532		2203	4300	6503	SO:0001583	missense	4288	exon9			GAACCTCTGTCTG	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.1834G>A	chr10.hg19:g.129910532C>T	ENSP00000357643:p.Glu612Lys	159.0	0.0	.		84.0	11.0	.	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	hg19	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	C	13.04	2.117442	0.37339	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609;ENST00000368652	T;T	0.01335	5.04;5.0	3.15	2.24	0.28232	.	0.534998	0.18473	N	0.140147	T	0.01592	0.0051	N	0.22421	0.69	0.09310	N	1	P;P;P	0.50528	0.73;0.936;0.61	B;P;B	0.47673	0.205;0.554;0.101	T	0.55276	-0.8166	10	0.33141	T	0.24	.	8.3147	0.32093	0.0:0.8808:0.0:0.1192	.	612;252;612	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	K	612;252;612;187	ENSP00000357643:E612K;ENSP00000357642:E252K	ENSP00000357641:E187K	E	-	1	0	MKI67	129800522	0.000000	0.05858	0.031000	0.17742	0.069000	0.16628	0.316000	0.19469	0.889000	0.36185	0.655000	0.94253	GAG	.	.	.	none		0.488	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		T	129910532	C	T	129910532	3	4	195	1	0	0	0	0	1	0	0	0	9605	922	32	2	7964	2	MKI67	10	129910532	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	13175612	129910532	5624215	74	11675											
IPO7	10527	hgsc.bcm.edu	37	chr11	9451343	9451343	+	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	tgatctgtgaatatagtgaaGaagttactcctattgcagta	13	14	9	5	0	1	4	0	3	1	1	2	4	2	4	1	0	2	3	1	0	8	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:9451343G>A	ENST00000379719.3	+	15	1856	c.1714G>A	c.(1714-1716)Gaa>Aaa	p.E572K	CTD-2371O3.2_ENST00000531111.1_RNA|SNORA23_ENST00000365128.1_RNA	NM_006391.2	NP_006382.1	O95373	IPO7_HUMAN	importin 7	572					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)		ATATAGTGAAGAAGTTACTCC	0.353																																					p.E572K		Atlas-SNP	.											.	IPO7	72	.	0			c.G1714A						PASS	.						71	61	65					11																	9451343		2201	4294	6495	SO:0001583	missense	10527	exon15			AGTGAAGAAGTTA	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.1714G>A	chr11.hg19:g.9451343G>A	ENSP00000369042:p.Glu572Lys	51.0	0.0	.		26.0	12.0	.	NM_006391	A6NNM5|B2R786|Q1RMF7|Q9H177|Q9NTE3	Missense_Mutation	SNP	ENST00000379719.3	hg19	CCDS31425.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.743031	0.89663	.	.	ENSG00000205339	ENST00000379719	T	0.44881	0.91	5.86	5.86	0.93980	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.53948	0.1828	M	0.80183	2.485	0.80722	D	1	B	0.31989	0.35	B	0.36335	0.222	T	0.55049	-0.8201	10	0.51188	T	0.08	.	20.1772	0.98182	0.0:0.0:1.0:0.0	.	572	O95373	IPO7_HUMAN	K	572	ENSP00000369042:E572K	ENSP00000369042:E572K	E	+	1	0	IPO7	9407919	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.778000	0.95560	0.655000	0.94253	GAA	.	.	.	none		0.353	IPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386022.1	NM_006391		A	9451343	G	A	9451343	3	1	195	1	0	0	0	0	1	0	0	0	7804	943	33	2	1772	2	IPO7	11	9451343	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08		9451343	125555173	75	11676											
COPB1	1315	hgsc.bcm.edu	37	chr11	14501121	14501121	+	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	tattttaaacctacttgacaGatttaatagcatgaaagact	16	14	5	6	0	0	4	0	2	0	2	0	4	0	4	1	0	3	1	1	0	7	8			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:14501121G>C	ENST00000249923.3	-	11	1652	c.1352C>G	c.(1351-1353)tCt>tGt	p.S451C	RNU7-49P_ENST00000516182.1_RNA|COPB1_ENST00000439561.2_Missense_Mutation_p.S451C	NM_016451.4	NP_057535.1	P53618	COPB_HUMAN	coatomer protein complex, subunit beta 1	451					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						CTACTTGACAGATTTAATAGC	0.343																																					p.S451C		Atlas-SNP	.											.	COPB1	81	.	0			c.C1352G						PASS	.						76	78	77					11																	14501121		2200	4293	6493	SO:0001583	missense	1315	exon11			TTGACAGATTTAA	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.1352C>G	chr11.hg19:g.14501121G>C	ENSP00000249923:p.Ser451Cys	134.0	0.0	.		100.0	73.0	.	NM_001144062	D3DQX0|Q6GTT7|Q9NTK2|Q9UNW7	Missense_Mutation	SNP	ENST00000249923.3	hg19	CCDS7815.1	.	.	.	.	.	.	.	.	.	.	G	31	5.070302	0.93950	.	.	ENSG00000129083	ENST00000249923;ENST00000439561;ENST00000534234	T;T;T	0.14893	2.47;2.47;2.47	5.83	5.83	0.93111	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.049398	0.85682	D	0.000000	T	0.48589	0.1508	M	0.87971	2.92	0.80722	D	1	P	0.45768	0.866	P	0.60117	0.869	T	0.47302	-0.9128	10	0.56958	D	0.05	-0.5739	20.127	0.97984	0.0:0.0:1.0:0.0	.	451	P53618	COPB_HUMAN	C	451	ENSP00000249923:S451C;ENSP00000397873:S451C;ENSP00000436383:S451C	ENSP00000249923:S451C	S	-	2	0	COPB1	14457697	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.869000	0.99810	2.775000	0.95449	0.585000	0.79938	TCT	.	.	.	none		0.343	COPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386410.1	NM_016451		C	14501121	G	C	14501121	3	2	195	1	0	0	0	0	1	0	0	0	3730	942	33	4	1557	4	COPB1	11	14501121	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	5049778	14501121	120505395	76	11677											
RAG2	5897	hgsc.bcm.edu	37	chr11	36614896	36614896	+	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	attttcaagctgatagccacCaacaataacaaattcatcat	17	11	3	10	0	3	1	3	1	0	0	3	1	3	1	2	0	4	1	2	0	6	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:36614896C>T	ENST00000311485.3	-	2	984	c.823G>A	c.(823-825)Ggt>Agt	p.G275S	C11orf74_ENST00000334307.5_5'Flank|RAG2_ENST00000528428.1_5'Flank|C11orf74_ENST00000534635.1_5'Flank|C11orf74_ENST00000347206.4_5'Flank|C11orf74_ENST00000446510.2_5'Flank	NM_000536.3|NM_001243785.1|NM_001243786.1	NP_000527.2|NP_001230714.1|NP_001230715.1	P55895	RAG2_HUMAN	recombination activating gene 2	275					B cell differentiation (GO:0030183)|chromatin modification (GO:0016568)|pre-B cell allelic exclusion (GO:0002331)|T cell differentiation in thymus (GO:0033077)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	32	all_lung(20;0.226)	all_hematologic(20;0.00756)				TGATAGCCACCAACAATAACA	0.428									Familial Hemophagocytic Lymphohistiocytosis																												p.G275S		Atlas-SNP	.											.	RAG2	92	.	0			c.G823A						PASS	.						86	87	86					11																	36614896		2202	4298	6500	SO:0001583	missense	5897	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	AGCCACCAACAAT	AF080577	CCDS7903.1	11p13	2014-09-17				ENSG00000175097			9832	protein-coding gene	gene with protein product		179616				1283330	Standard	NM_000536		Approved		uc001mwv.4	P55895		ENST00000311485.3:c.823G>A	chr11.hg19:g.36614896C>T	ENSP00000308620:p.Gly275Ser	98.0	0.0	.		44.0	22.0	.	NM_001243785	A8K9E9|Q8TBL4	Missense_Mutation	SNP	ENST00000311485.3	hg19	CCDS7903.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.473990	0.84640	.	.	ENSG00000175097	ENST00000311485	D	0.93906	-3.31	5.69	5.69	0.88448	Galactose oxidase/kelch, beta-propeller (1);	0.000000	0.85682	D	0.000000	D	0.98027	0.9350	H	0.96048	3.76	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98794	1.0737	10	0.87932	D	0	-12.4322	19.8052	0.96529	0.0:1.0:0.0:0.0	.	275	P55895	RAG2_HUMAN	S	275	ENSP00000308620:G275S	ENSP00000308620:G275S	G	-	1	0	RAG2	36571472	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.487000	0.81328	2.692000	0.91855	0.650000	0.86243	GGT	.	.	.	none		0.428	RAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389536.1	NM_000536		T	36614896	C	T	36614896	3	4	195	1	0	0	0	0	1	0	0	0	13018	594	21	2	764	2	RAG2	11	36614896	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	22113775	36614896	98391620	77	11678											
OR9G1	390174	hgsc.bcm.edu	37	chr11	56468116	56468116	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaagatcctagtgacctgcAtctctgaagacaaaagcatc	15	8	7	11	0	1	4	0	2	1	2	4	4	2	4	2	0	2	2	2	0	5	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:56468116A>G	ENST00000312153.1	+	1	253	c.253A>G	c.(253-255)Atc>Gtc	p.I85V		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	85						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						AGTGACCTGCATCTCTGAAGA	0.507																																					p.I85V		Atlas-SNP	.											.	.	.	.	0			c.A253G						PASS	.						127	124	125					11																	56468116		2201	4293	6494	SO:0001583	missense	504191	exon1			ACCTGCATCTCTG	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.253A>G	chr11.hg19:g.56468116A>G	ENSP00000309012:p.Ile85Val	191.0	0.0	.		174.0	22.0	.	NM_001013358	Q6IEU9|Q8NGQ0	Missense_Mutation	SNP	ENST00000312153.1	hg19	CCDS31536.1	.	.	.	.	.	.	.	.	.	.	A	0.852	-0.738253	0.03111	.	.	ENSG00000174914	ENST00000312153	T	0.02236	4.38	4.54	4.54	0.55810	GPCR, rhodopsin-like superfamily (1);	0.251802	0.29178	N	0.012920	T	0.01661	0.0053	N	0.15975	0.35	0.24579	N	0.993886	B	0.06786	0.001	B	0.10450	0.005	T	0.48592	-0.9022	10	0.19590	T	0.45	-19.0486	10.2627	0.43436	0.721:0.279:0.0:0.0	.	85	Q8NH87	OR9G1_HUMAN	V	85	ENSP00000309012:I85V	ENSP00000309012:I85V	I	+	1	0	OR9G1	56224692	0.000000	0.05858	0.995000	0.50966	0.171000	0.22731	-0.467000	0.06664	2.013000	0.59113	0.477000	0.44152	ATC	.	.	.	none		0.507	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213		G	56468116	A	G	56468116	3	3	195	1	0	0	0	0	1	0	0	0	11257	217	8	3	255	3	OR9G1	11	56468116	Missense_Mutation	SNP	A	TCGA-HE-7130-01A-11D-1961-08	19853220	56468116	78538400	78	11679											
OR4D11	219986	hgsc.bcm.edu	37	chr11	59271133	59271133	+	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	accagagtttggtcttgtttCtttttttatgtcttgtgtac	5	22	8	6	0	3	1	0	0	3	1	3	1	3	1	1	1	1	3	1	1	2	9			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:59271133C>G	ENST00000313253.1	+	1	85	c.85C>G	c.(85-87)Ctt>Gtt	p.L29V		NM_001004706.1	NP_001004706.1	Q8NGI4	OR4DB_HUMAN	olfactory receptor, family 4, subfamily D, member 11	29						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(3)|liver(2)|lung(17)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29						GGTCTTGTTTCTTTTTTTATG	0.433																																					p.L29V		Atlas-SNP	.											.	OR4D11	62	.	0			c.C85G						PASS	.						103	96	98					11																	59271133		2201	4295	6496	SO:0001583	missense	219986	exon1			TTGTTTCTTTTTT	AB065810	CCDS31563.1	11q12.1	2012-08-09		2004-03-10	ENSG00000176200	ENSG00000176200		"GPCR / Class A : Olfactory receptors"	15174	protein-coding gene	gene with protein product				OR4D11P			Standard	NM_001004706		Approved		uc001noa.1	Q8NGI4	OTTHUMG00000167342	ENST00000313253.1:c.85C>G	chr11.hg19:g.59271133C>G	ENSP00000320077:p.Leu29Val	181.0	0.0	.		99.0	5.0	.	NM_001004706		Missense_Mutation	SNP	ENST00000313253.1	hg19	CCDS31563.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.816889	0.00072	.	.	ENSG00000176200	ENST00000313253	T	0.00418	7.49	5.45	-1.74	0.08056	.	0.332667	0.21503	N	0.073498	T	0.00144	0.0004	N	0.16233	0.39	0.20638	N	0.999875	B	0.02656	0.0	B	0.06405	0.002	T	0.46176	-0.9210	10	0.02654	T	1	-9.7981	2.6212	0.04917	0.2091:0.3651:0.287:0.1389	.	29	Q8NGI4	OR4DB_HUMAN	V	29	ENSP00000320077:L29V	ENSP00000320077:L29V	L	+	1	0	OR4D11	59027709	0.000000	0.05858	0.184000	0.23157	0.091000	0.18340	-1.215000	0.02985	-0.006000	0.14370	-0.311000	0.09066	CTT	.	.	.	none		0.433	OR4D11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394236.1	NM_001004706		G	59271133	C	G	59271133	3	3	195	1	0	0	0	0	1	0	0	0	11062	913	32	4	87	4	OR4D11	11	59271133	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	2803017	59271133	75735383	79	11680											
NARS2	79731	hgsc.bcm.edu	37	chr11	78154732	78154732	+	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	taagcgctcctctaagaaatGgtatcgttcttctctgaggc	9	13	9	10	2	3	2	0	1	3	1	6	2	4	2	1	2	1	3	1	2	4	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:78154732G>C	ENST00000281038.5	-	12	1612	c.1237C>G	c.(1237-1239)Cat>Gat	p.H413D	NARS2_ENST00000528850.1_Missense_Mutation_p.H186D|RP11-452H21.1_ENST00000534168.1_RNA	NM_001243251.1|NM_024678.5	NP_001230180.1|NP_078954.4	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial (putative)	413					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)	TCTAAGAAATGGTATCGTTCT	0.423																																					p.H413D		Atlas-SNP	.											.	NARS2	62	.	0			c.C1237G						PASS	.						96	91	93					11																	78154732		2200	4292	6492	SO:0001583	missense	79731	exon12			AGAAATGGTATCG	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.1237C>G	chr11.hg19:g.78154732G>C	ENSP00000281038:p.His413Asp	81.0	0.0	.		73.0	4.0	.	NM_024678	G3V178	Missense_Mutation	SNP	ENST00000281038.5	hg19	CCDS8261.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.65|15.65	2.895206|2.895206	0.52121|0.52121	.|.	.|.	ENSG00000137513|ENSG00000137513	ENST00000281038;ENST00000528850|ENST00000529771	T;T|.	0.77229|.	-1.08;-1.08|.	4.96|4.96	4.96|4.96	0.65561|0.65561	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (D/K/N) (1);|.	0.189082|.	0.56097|.	D|.	0.000031|.	T|T	0.10551|0.10551	0.0258|0.0258	N|N	0.00106|0.00106	-2.12|-2.12	0.35491|0.35491	D|D	0.798978|0.798978	B|.	0.06786|.	0.001|.	B|.	0.10450|.	0.005|.	T|T	0.29579|0.29579	-1.0007|-1.0007	10|5	0.02654|.	T|.	1|.	-6.0659|-6.0659	15.1595|15.1595	0.72771|0.72771	0.0:0.1415:0.8585:0.0|0.0:0.1415:0.8585:0.0	.|.	413|.	Q96I59|.	SYNM_HUMAN|.	D|R	413;186|25	ENSP00000281038:H413D;ENSP00000432635:H186D|.	ENSP00000281038:H413D|.	H|P	-|-	1|2	0|0	NARS2|NARS2	77832380|77832380	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.992000|0.992000	0.81027|0.81027	2.432000|2.432000	0.44784|0.44784	2.734000|2.734000	0.93682|0.93682	0.591000|0.591000	0.81541|0.81541	CAT|CCA	.	.	.	none		0.423	NARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391138.2	NM_024678		C	78154732	G	C	78154732	3	2	195	1	0	0	0	0	1	0	0	0	10178	1348	47	4	208	4	NARS2	11	78154732	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	18883599	78154732	56851784	80	11681											
CREBZF	58487	hgsc.bcm.edu	37	chr11	85375684	85375684	+	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	cctcctccatctcctcggggGagggcgcgcgcacggccacg	4	5	14	18	6	1	0	0	0	1	0	5	1	3	1	5	4	0	1	5	4	0	0			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:85375684G>A	ENST00000527447.1	-	1	462	c.236C>T	c.(235-237)tCc>tTc	p.S79F	CREBZF_ENST00000531515.1_Intron|CREBZF_ENST00000398294.2_5'UTR|CREBZF_ENST00000534224.1_Intron	NM_001039618.2	NP_001034707.1	Q9NS37	ZHANG_HUMAN	CREB/ATF bZIP transcription factor	79					negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)				CTCCTCGGGGGAGGGCGCGCG	0.701																																					p.S79F	NSCLC(172;674 2044 9050 18334 41735)	Atlas-SNP	.											.	CREBZF	26	.	0			c.C236T						PASS	.						35	42	40					11																	85375684		1861	4083	5944	SO:0001583	missense	58487	exon1			TCGGGGGAGGGCG	AF039942	CCDS41697.1	11q14.1	2013-01-10			ENSG00000137504	ENSG00000137504		"basic leucine zipper proteins"	24905	protein-coding gene	gene with protein product	"Zhangfei"	606444				10871379	Standard	NM_001039618		Approved	ZF	uc001pas.2	Q9NS37	OTTHUMG00000133648	ENST00000527447.1:c.236C>T	chr11.hg19:g.85375684G>A	ENSP00000433459:p.Ser79Phe	151.0	0.0	.		78.0	41.0	.	NM_001039618	B2R8Q9|Q0P5U9|Q52LT3	Missense_Mutation	SNP	ENST00000527447.1	hg19	CCDS41697.1	.	.	.	.	.	.	.	.	.	.	G	14.77	2.635626	0.47049	.	.	ENSG00000137504	ENST00000527447	.	.	.	3.72	3.72	0.42706	.	0.000000	0.33217	U	0.005143	T	0.29749	0.0743	N	0.08118	0	0.80722	D	1	B	0.31910	0.346	B	0.35550	0.205	T	0.09443	-1.0674	8	.	.	.	-19.421	8.7689	0.34719	0.0:0.0:0.7748:0.2252	.	79	Q9NS37	ZHANG_HUMAN	F	79	.	.	S	-	2	0	CREBZF	85053332	0.998000	0.40836	0.998000	0.56505	0.982000	0.71751	2.082000	0.41605	2.068000	0.61886	0.561000	0.74099	TCC	.	.	.	none		0.701	CREBZF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390191.2	NM_001039618		A	85375684	G	A	85375684	3	1	195	1	0	0	0	0	1	0	0	0	3865	1174	41	2	832	2	CREBZF	11	85375684	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	7220952	85375684	49630832	81	11682											
YAP1	10413	hgsc.bcm.edu	37	chr11	102080284	102080284	+	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	atcccagcacagcaaattctCcaaaatgtcaggtaggctct	13	9	7	12	0	3	0	1	0	2	0	5	0	4	0	2	2	2	4	2	2	4	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:102080284C>G	ENST00000282441.5	+	6	1409	c.1021C>G	c.(1021-1023)Cca>Gca	p.P341A	YAP1_ENST00000537274.1_Intron|YAP1_ENST00000531439.1_Intron|YAP1_ENST00000524575.1_Missense_Mutation_p.P163A|YAP1_ENST00000526343.1_Intron|YAP1_ENST00000345877.2_Intron	NM_001130145.2|NM_001282101.1	NP_001123617.1|NP_001269030.1	P46937	YAP1_HUMAN	Yes-associated protein 1	341	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)		AGCAAATTCTCCAAAATGTCA	0.368																																					p.P341A	Colon(50;247 1103 7861 28956)	Atlas-SNP	.											.	YAP1	45	.	0			c.C1021G						PASS	.						142	126	131					11																	102080284		1568	3581	5149	SO:0001583	missense	10413	exon6			AATTCTCCAAAAT		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.1021C>G	chr11.hg19:g.102080284C>G	ENSP00000282441:p.Pro341Ala	139.0	0.0	.		114.0	62.0	.	NM_001130145	B4DTY1|B7ZA01|E3WEB5|E3WEB6|E9PRV2|F5H202|K0KQ18|K0KYZ8|K0L195|K0L1G3|Q7Z574|Q8IUY9	Missense_Mutation	SNP	ENST00000282441.5	hg19	CCDS44716.1	.	.	.	.	.	.	.	.	.	.	C	16.49	3.138326	0.56936	.	.	ENSG00000137693	ENST00000282441;ENST00000445250;ENST00000524575	T	0.39592	1.07	6.17	6.17	0.99709	.	0.226095	0.38720	N	0.001598	T	0.46386	0.1390	N	0.08118	0	0.80722	D	1	D;D;D	0.69078	0.993;0.996;0.997	D;D;D	0.73708	0.956;0.981;0.98	T	0.49399	-0.8944	10	0.35671	T	0.21	.	19.0599	0.93085	0.0:1.0:0.0:0.0	.	163;258;341	B4DTY1;F5GWC5;P46937	.;.;YAP1_HUMAN	A	341;258;163	ENSP00000435602:P163A	ENSP00000282441:P341A	P	+	1	0	YAP1	101585494	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.770000	0.62309	2.941000	0.99782	0.655000	0.94253	CCA	.	.	.	none		0.368	YAP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394151.1	NM_006106		G	102080284	C	G	102080284	3	3	195	1	0	0	0	0	1	0	0	0	17478	855	30	4	1055	4	YAP1	11	102080284	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	16704600	102080284	32926232	82	11683											
YAP1	10413	hgsc.bcm.edu	37	chr11	102098224	102098224	+	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	acctatcactctcgagatgaGagtacagacagtggactaag	14	8	10	9	1	2	3	1	1	1	3	3	6	2	4	1	1	1	1	1	1	3	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:102098224G>C	ENST00000282441.5	+	8	1576	c.1188G>C	c.(1186-1188)gaG>gaC	p.E396D	YAP1_ENST00000537274.1_Missense_Mutation_p.E384D|YAP1_ENST00000531439.1_Missense_Mutation_p.E380D|RP11-864G5.3_ENST00000526310.1_RNA|YAP1_ENST00000524575.1_Missense_Mutation_p.E218D|YAP1_ENST00000528834.1_3'UTR|YAP1_ENST00000526343.1_Missense_Mutation_p.E342D|YAP1_ENST00000345877.2_Missense_Mutation_p.E346D	NM_001130145.2|NM_001282101.1	NP_001123617.1|NP_001269030.1	P46937	YAP1_HUMAN	Yes-associated protein 1	396	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)		CTCGAGATGAGAGTACAGACA	0.408																																					p.E396D	Colon(50;247 1103 7861 28956)	Atlas-SNP	.											.	YAP1	45	.	0			c.G1188C						PASS	.						155	119	131					11																	102098224		2203	4299	6502	SO:0001583	missense	10413	exon8			AGATGAGAGTACA		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.1188G>C	chr11.hg19:g.102098224G>C	ENSP00000282441:p.Glu396Asp	60.0	0.0	.		50.0	12.0	.	NM_001130145	B4DTY1|B7ZA01|E3WEB5|E3WEB6|E9PRV2|F5H202|K0KQ18|K0KYZ8|K0L195|K0L1G3|Q7Z574|Q8IUY9	Missense_Mutation	SNP	ENST00000282441.5	hg19	CCDS44716.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.43|19.43	3.825846|3.825846	0.71143|0.71143	.|.	.|.	ENSG00000137693|ENSG00000137693	ENST00000526343;ENST00000282441;ENST00000537274;ENST00000345877;ENST00000445250;ENST00000531439;ENST00000524575|ENST00000529029	T;T;T|.	0.56103|.	0.48;0.5;0.6|.	5.28|5.28	1.34|1.34	0.21922|0.21922	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.61527|0.61527	0.2354|0.2354	M|M	0.65975|0.65975	2.015|2.015	0.48632|0.48632	D|D	0.999686|0.999686	P;D;D;D;D;D|.	0.71674|.	0.956;0.998;0.991;0.97;0.991;0.998|.	D;D;P;P;P;P|.	0.68353|.	0.931;0.957;0.82;0.774;0.82;0.875|.	T|T	0.55354|0.55354	-0.8154|-0.8154	10|5	0.32370|.	T|.	0.25|.	.|.	9.06|9.06	0.36429|0.36429	0.4715:0.0:0.5285:0.0|0.4715:0.0:0.5285:0.0	.|.	218;313;342;380;396;346|.	B4DTY1;F5GWC5;E9PRV2;P46937-2;P46937;P46937-3|.	.;.;.;.;YAP1_HUMAN;.|.	D|T	342;396;384;346;313;380;218|150	ENSP00000434134:E342D;ENSP00000331023:E346D;ENSP00000435602:E218D|.	ENSP00000282441:E396D|.	E|R	+|+	3|2	2|0	YAP1|YAP1	101603434|101603434	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.980000|0.980000	0.70556|0.70556	2.046000|2.046000	0.41260|0.41260	-0.001000|-0.001000	0.14495|0.14495	0.650000|0.650000	0.86243|0.86243	GAG|AGA	.	.	.	none		0.408	YAP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394151.1	NM_006106		C	102098224	G	C	102098224	3	2	195	1	0	0	0	0	1	0	0	0	17478	933	33	4	1230	4	YAP1	11	102098224	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	17940	102098224	32908292	83	11684											
HTR3A	3359	hgsc.bcm.edu	37	chr11	113856896	113856896	+	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	ctatgcagaaatgaagttctAtgtgagtgggagtgaatgtg	12	12	14	3	0	1	4	0	3	1	1	1	5	1	5	0	1	1	2	0	1	5	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr11:113856896A>G	ENST00000504030.2	+	6	1149	c.704A>G	c.(703-705)tAt>tGt	p.Y235C	HTR3A_ENST00000375498.2_Splice_Site_p.Y241C|HTR3A_ENST00000355556.2_Splice_Site_p.Y241C|HTR3A_ENST00000535865.1_Intron|HTR3A_ENST00000506841.2_Splice_Site_p.Y235C|HTR3A_ENST00000299961.5_Splice_Site_p.Y220C			P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A, ionotropic	235					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)	ATGAAGTTCTATGTGAGTGGG	0.463																																					p.Y241C		Atlas-SNP	.											.	HTR3A	93	.	0			c.A722G						PASS	.						127	129	128					11																	113856896		2201	4296	6497	SO:0001630	splice_region_variant	3359	exon6			AGTTCTATGTGAG	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.705+1A>G	chr11.hg19:g.113856896A>G		217.0	1.0	.		132.0	82.0	.	NM_000869	B4DSY6|G5E986|O60854|Q7KZM7|Q99918|Q9BSZ9	Missense_Mutation	SNP	ENST00000504030.2	hg19		.	.	.	.	.	.	.	.	.	.	A	14.92	2.678107	0.47886	.	.	ENSG00000166736	ENST00000504030;ENST00000355556;ENST00000375498;ENST00000506841;ENST00000299961	T;T;T;T;T	0.80033	-1.33;-1.33;-1.33;-1.33;-1.33	5.19	5.19	0.71726	.	0.238980	0.43579	D	0.000549	D	0.87390	0.6165	M	0.73598	2.24	0.80722	D	1	D;D;D	0.71674	0.996;0.998;0.998	P;P;D	0.66351	0.905;0.887;0.943	D	0.87931	0.2710	10	0.54805	T	0.06	-11.3278	11.1542	0.48478	0.8621:0.0:0.0:0.1379	.	220;241;241	B4DSY6;G5E986;Q7KZM7	.;.;.	C	235;241;241;235;220	ENSP00000424189:Y235C;ENSP00000347754:Y241C;ENSP00000364648:Y241C;ENSP00000424776:Y235C;ENSP00000299961:Y220C	ENSP00000299961:Y220C	Y	+	2	0	HTR3A	113362106	1.000000	0.71417	0.987000	0.45799	0.454000	0.32378	4.949000	0.63596	2.079000	0.62486	0.533000	0.62120	TAT	.	.	.	none		0.463	HTR3A-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000360822.2	NM_000869	Missense_Mutation	G	113856896	A	G	113856896	5	3	195	1	0	0	0	0	0	0	1	0	7451	463	16	3	770	3	HTR3A	11	113856896	Splice_Site	SNP	A	TCGA-HE-7130-01A-11D-1961-08	11758672	113856896	21149620	84	11685											
VWF	7450	hgsc.bcm.edu	37	chr12	6167128	6167128	+	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	cccggggctccgccagcccaGagggggtaaggaagtcgtcg	7	4	17	13	4	0	1	0	0	0	1	3	2	1	2	4	5	1	2	4	5	2	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr12:6167128G>C	ENST00000261405.5	-	14	1870	c.1616C>G	c.(1615-1617)tCt>tGt	p.S539C		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	539	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)	CGCCAGCCCAGAGGGGGTAAG	0.662																																					p.S539C		Atlas-SNP	.											.	VWF	338	.	0			c.C1616G						PASS	.						56	59	58					12																	6167128		2203	4299	6502	SO:0001583	missense	7450	exon14			AGCCCAGAGGGGG		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.1616C>G	chr12.hg19:g.6167128G>C	ENSP00000261405:p.Ser539Cys	176.0	0.0	.		105.0	31.0	.	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	hg19	CCDS8539.1	.	.	.	.	.	.	.	.	.	.	G	12.35	1.911404	0.33721	.	.	ENSG00000110799	ENST00000261405	T	0.62498	0.02	4.94	4.03	0.46877	von Willebrand factor, type D domain (3);	0.650601	0.12694	N	0.446915	T	0.80889	0.4710	M	0.87617	2.895	0.47214	D	0.999357	D;P	0.64830	0.994;0.794	D;P	0.64687	0.928;0.694	T	0.82458	-0.0447	10	0.87932	D	0	.	14.3887	0.66963	0.0:0.1485:0.8515:0.0	.	539;539	B4DNX0;P04275	.;VWF_HUMAN	C	539	ENSP00000261405:S539C	ENSP00000261405:S539C	S	-	2	0	VWF	6037389	0.891000	0.30450	0.007000	0.13788	0.010000	0.07245	4.866000	0.63005	1.267000	0.44247	0.491000	0.48974	TCT	.	.	.	none		0.662	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		C	6167128	G	C	6167128	3	2	195	1	0	0	0	0	1	0	0	0	17258	942	33	4	6981	4	VWF	12	6167128	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08		6167128	127684767	85	11686											
CAPRIN2	65981	hgsc.bcm.edu	37	chr12	30906661	30906661	+	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	cttttccacagaagtgagctCgaaacccaatgatgcttgag	12	10	9	10	1	0	4	0	3	0	1	2	5	1	4	2	0	3	2	2	0	3	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr12:30906661C>G	ENST00000395805.2	-	1	584	c.37G>C	c.(37-39)Gag>Cag	p.E13Q	CAPRIN2_ENST00000308433.5_5'UTR|RP11-77I22.2_ENST00000500076.2_lincRNA|CAPRIN2_ENST00000417045.1_Missense_Mutation_p.E13Q|CAPRIN2_ENST00000251071.5_Missense_Mutation_p.E13Q|CAPRIN2_ENST00000298892.5_Missense_Mutation_p.E13Q	NM_001206856.1	NP_001193785.1			caprin family member 2									p.E13K(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)					GAAGTGAGCTCGAAACCCAAT	0.408											OREG0021723	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E13Q		Atlas-SNP	.											CAPRIN2,rectum,carcinoma,0,2	CAPRIN2	109	.	2	Substitution - Missense(2)	large_intestine(2)	c.G37C						PASS	.						103	104	104					12																	30906661		2202	4299	6501	SO:0001583	missense	65981	exon1			TGAGCTCGAAACC	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.37G>C	chr12.hg19:g.30906661C>G	ENSP00000379150:p.Glu13Gln	179.0	0.0	.	820	169.0	15.0	.	NM_023925		Missense_Mutation	SNP	ENST00000395805.2	hg19	CCDS55816.1	.	.	.	.	.	.	.	.	.	.	C	16.59	3.165966	0.57476	.	.	ENSG00000110888	ENST00000298892;ENST00000395805;ENST00000251071;ENST00000417045	T;T;T;T	0.73363	-0.74;2.74;-0.69;2.74	3.72	2.83	0.33086	.	.	.	.	.	T	0.48978	0.1530	N	0.08118	0	0.19575	N	0.999963	B;P;B;B	0.35226	0.358;0.491;0.218;0.325	B;B;B;B	0.32805	0.073;0.153;0.03;0.067	T	0.31833	-0.9929	8	.	.	.	0.5218	5.7801	0.18301	0.0:0.7584:0.0:0.2416	.	13;13;13;13	Q149P6;Q6IMN6-3;Q6IMN6;Q6IMN6-2	.;.;CAPR2_HUMAN;.	Q	13	ENSP00000298892:E13Q;ENSP00000379150:E13Q;ENSP00000251071:E13Q;ENSP00000391479:E13Q	.	E	-	1	0	CAPRIN2	30797928	0.001000	0.12720	0.056000	0.19401	0.500000	0.33767	0.235000	0.17948	0.783000	0.33636	0.563000	0.77884	GAG	.	.	.	none		0.408	CAPRIN2-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403322.2	NM_023925		G	30906661	C	G	30906661	3	3	195	1	0	0	0	0	1	0	0	0	2638	893	31	4	3418	4	CAPRIN2	12	30906661	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	24739533	30906661	102945234	86	11687											
SLC2A13	114134	hgsc.bcm.edu	37	chr12	40422219	40422219	+	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	tacgggccttctgagtctgtCctttctgaataagccatcga	8	13	9	11	2	3	2	0	2	3	0	5	3	4	2	3	1	2	0	3	1	3	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr12:40422219C>T	ENST00000280871.4	-	3	859	c.809G>A	c.(808-810)gGa>gAa	p.G270E	SLC2A13_ENST00000380858.1_Missense_Mutation_p.G270E	NM_052885.3	NP_443117.3	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 13	270					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	29		Lung NSC(34;0.105)|all_lung(34;0.123)				CTGAGTCTGTCCTTTCTGAAT	0.438										HNSCC(50;0.14)																											p.G270E		Atlas-SNP	.											.	SLC2A13	91	.	0			c.G809A						PASS	.						101	106	104					12																	40422219		2203	4300	6503	SO:0001583	missense	114134	exon3			GTCTGTCCTTTCT	AJ315644	CCDS8736.2	12q12	2013-05-22			ENSG00000151229	ENSG00000151229		"Solute carriers"	15956	protein-coding gene	gene with protein product	"H(+)-myo-inositol symporter"	611036				11500374	Standard	NM_052885		Approved	HMIT	uc010skm.2	Q96QE2	OTTHUMG00000059743	ENST00000280871.4:c.809G>A	chr12.hg19:g.40422219C>T	ENSP00000280871:p.Gly270Glu	166.0	0.0	.		184.0	39.0	.	NM_052885	Q17S07	Missense_Mutation	SNP	ENST00000280871.4	hg19	CCDS8736.2	.	.	.	.	.	.	.	.	.	.	C	26.9	4.781378	0.90282	.	.	ENSG00000151229	ENST00000280871;ENST00000380858	T;T	0.76839	-1.05;-1.05	5.54	5.54	0.83059	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.099482	0.64402	D	0.000001	D	0.88403	0.6427	M	0.82323	2.585	0.80722	D	1	P;D	0.60575	0.933;0.988	P;P	0.61722	0.838;0.893	D	0.88848	0.3317	10	0.59425	D	0.04	-17.57	19.8499	0.96734	0.0:1.0:0.0:0.0	.	270;270	Q96QE2;E9PE47	MYCT_HUMAN;.	E	270	ENSP00000280871:G270E;ENSP00000370239:G270E	ENSP00000280871:G270E	G	-	2	0	SLC2A13	38708486	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.290000	0.78711	2.779000	0.95612	0.591000	0.81541	GGA	.	.	.	none		0.438	SLC2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132849.2			T	40422219	C	T	40422219	3	4	195	1	0	0	0	0	1	0	0	0	14555	855	30	2	1169	2	SLC2A13	12	40422219	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	9515558	40422219	93429676	87	11688											
DDX23	9416	hgsc.bcm.edu	37	chr12	49231830	49231830	+	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	ctgccgtcgctttagagcttCagcctctcgttctgctttag	4	15	9	13	3	3	1	1	0	2	1	5	1	3	1	2	0	4	4	2	0	2	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr12:49231830C>T	ENST00000308025.3	-	6	593	c.514G>A	c.(514-516)Gaa>Aaa	p.E172K	DDX23_ENST00000553182.1_5'UTR	NM_004818.2	NP_004809.2	Q9BUQ8	DDX23_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23	172	Glu-rich.				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						TTTAGAGCTTCAGCCTCTCGT	0.498																																					p.E172K		Atlas-SNP	.											.	DDX23	82	.	0			c.G514A						PASS	.						149	140	143					12																	49231830		2203	4300	6503	SO:0001583	missense	9416	exon6			GAGCTTCAGCCTC	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.514G>A	chr12.hg19:g.49231830C>T	ENSP00000310723:p.Glu172Lys	241.0	0.0	.		232.0	92.0	.	NM_004818	B2R600|B4DH15|O43188	Missense_Mutation	SNP	ENST00000308025.3	hg19	CCDS8770.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.450245	0.84101	.	.	ENSG00000174243	ENST00000550834;ENST00000308025;ENST00000552512	T	0.22945	1.93	5.15	5.15	0.70609	.	0.055638	0.64402	D	0.000001	T	0.20333	0.0489	L	0.36672	1.1	0.58432	D	0.999999	P	0.39480	0.675	B	0.34093	0.175	T	0.03231	-1.1058	10	0.21014	T	0.42	-10.372	17.5534	0.87884	0.0:1.0:0.0:0.0	.	172	Q9BUQ8	DDX23_HUMAN	K	16;172;172	ENSP00000310723:E172K	ENSP00000310723:E172K	E	-	1	0	DDX23	47518097	1.000000	0.71417	0.999000	0.59377	0.954000	0.61252	7.411000	0.80078	2.676000	0.91093	0.563000	0.77884	GAA	.	.	.	none		0.498	DDX23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408897.2	NM_004818		T	49231830	C	T	49231830	3	4	195	1	0	0	0	0	1	0	0	0	4352	835	29	2	1996	2	DDX23	12	49231830	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	8809611	49231830	84620065	88	11689											
SPATS2	65244	hgsc.bcm.edu	37	chr12	49916614	49916614	+	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	gatgtagagaccctaaagaaGagcattgattcatttggaca	15	10	10	6	0	1	4	1	1	0	3	1	7	1	5	1	1	1	2	1	1	4	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr12:49916614G>C	ENST00000553127.1	+	13	1602	c.1089G>C	c.(1087-1089)aaG>aaC	p.K363N	SPATS2_ENST00000321898.6_Missense_Mutation_p.K363N|SPATS2_ENST00000552918.1_Missense_Mutation_p.K363N			Q86XZ4	SPAS2_HUMAN	spermatogenesis associated, serine-rich 2	363						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(1)|prostate(1)|urinary_tract(4)	21						CCCTAAAGAAGAGCATTGATT	0.448																																					p.K363N		Atlas-SNP	.											.	SPATS2	43	.	0			c.G1089C						PASS	.						145	125	132					12																	49916614		2203	4300	6503	SO:0001583	missense	65244	exon12			AAAGAAGAGCATT	AK023179	CCDS31794.1	12q13.12	2009-06-12							18650	protein-coding gene	gene with protein product		611667				11944913, 17989879	Standard	NM_023071		Approved	SPATA10, SCR59, FLJ13117	uc001rud.2	Q86XZ4		ENST00000553127.1:c.1089G>C	chr12.hg19:g.49916614G>C	ENSP00000448228:p.Lys363Asn	65.0	0.0	.		80.0	37.0	.	NM_023071	A8K8G9|Q9H7D4|Q9H8Y7|Q9H8Z8	Missense_Mutation	SNP	ENST00000553127.1	hg19	CCDS31794.1	.	.	.	.	.	.	.	.	.	.	G	18.92	3.725778	0.69074	.	.	ENSG00000123352	ENST00000553127;ENST00000321898;ENST00000552918;ENST00000395063	.	.	.	5.84	5.84	0.93424	.	0.215681	0.51477	D	0.000085	T	0.62097	0.2400	L	0.56769	1.78	0.80722	D	1	P	0.42161	0.772	P	0.49528	0.614	T	0.59139	-0.7510	9	0.38643	T	0.18	-13.4976	11.3109	0.49364	0.0822:0.0:0.9178:0.0	.	363	Q86XZ4	SPAS2_HUMAN	N	363	.	ENSP00000326841:K363N	K	+	3	2	SPATS2	48202881	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.162000	0.42367	2.937000	0.99478	0.650000	0.86243	AAG	.	.	.	none		0.448	SPATS2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404023.1	NM_023071		C	49916614	G	C	49916614	3	2	195	1	0	0	0	0	1	0	0	0	15031	933	33	4	1127	4	SPATS2	12	49916614	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	684784	49916614	83935281	89	11690											
DIP2B	57609	hgsc.bcm.edu	37	chr12	51019819	51019819	+	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	actcctatctccttacagccCgcagacacaaggtaggcaat	12	8	7	14	1	1	1	0	0	1	1	3	1	2	1	3	2	2	3	3	2	5	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr12:51019819C>A	ENST00000301180.5	+	2	195	c.161C>A	c.(160-162)cCg>cAg	p.P54Q		NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	54	DMAP-interaction.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.P54Q(1)		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						CCTTACAGCCCGCAGACACAA	0.378																																					p.P54Q		Atlas-SNP	.											DIP2B,NS,carcinoma,0,1	DIP2B	167	.	1	Substitution - Missense(1)	lung(1)	c.C161A						PASS	.						107	105	105					12																	51019819		2203	4300	6503	SO:0001583	missense	57609	exon2			ACAGCCCGCAGAC	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.161C>A	chr12.hg19:g.51019819C>A	ENSP00000301180:p.Pro54Gln	137.0	0.0	.		142.0	8.0	.	NM_173602	Q6B011|Q8N1L5|Q8NB38	Missense_Mutation	SNP	ENST00000301180.5	hg19	CCDS31799.1	.	.	.	.	.	.	.	.	.	.	c	14.24	2.476710	0.44044	.	.	ENSG00000066084	ENST00000455310;ENST00000301180	T	0.46819	0.86	4.75	3.87	0.44632	DMAP1-binding (1);	0.212294	0.49916	D	0.000135	T	0.46756	0.1409	L	0.49350	1.555	0.37755	D	0.926104	B;B	0.32800	0.385;0.182	B;B	0.41723	0.365;0.147	T	0.54430	-0.8295	10	0.56958	D	0.05	-5.0148	9.2742	0.37690	0.0:0.9016:0.0:0.0984	.	54;54	Q9P265;E9PHD6	DIP2B_HUMAN;.	Q	54	ENSP00000301180:P54Q	ENSP00000301180:P54Q	P	+	2	0	DIP2B	49306086	0.994000	0.37717	0.994000	0.49952	0.851000	0.48451	3.511000	0.53400	1.369000	0.46134	-0.213000	0.12676	CCG	.	.	.	none		0.378	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602		A	51019819	C	A	51019819	3	1	195	1	0	0	0	0	1	0	0	0	4530	652	23	4	167	4	DIP2B	12	51019819	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	1103205	51019819	82832076	90	11691											
RARG	5916	hgsc.bcm.edu	37	chr12	53607847	53607847	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagggcctaacttaccaggAtatctaggcaggcagctttg	11	9	11	10	0	1	0	0	0	1	0	1	1	1	1	2	4	3	3	2	4	4	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr12:53607847A>G	ENST00000425354.2	-	7	1296	c.809T>C	c.(808-810)aTc>aCc	p.I270T	RARG_ENST00000543726.1_Missense_Mutation_p.I248T|RARG_ENST00000543762.1_5'UTR|RARG_ENST00000327550.3_Missense_Mutation_p.I198T|RARG_ENST00000394426.1_Missense_Mutation_p.I270T|RARG_ENST00000338561.5_Missense_Mutation_p.I259T	NM_000966.5	NP_000957.1	P13631	RARG_HUMAN	retinoic acid receptor, gamma	270	Ligand-binding.				anterior/posterior pattern specification (GO:0009952)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|embryonic camera-type eye development (GO:0031076)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|face development (GO:0060324)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage chondrocyte growth (GO:0003430)|Harderian gland development (GO:0070384)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of programmed cell death (GO:0043068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of cell size (GO:0008361)|regulation of myelination (GO:0031641)|response to retinoic acid (GO:0032526)|retinal pigment epithelium development (GO:0003406)|retinoic acid receptor signaling pathway (GO:0048384)|trachea cartilage development (GO:0060534)|transcription initiation from RNA polymerase II promoter (GO:0006367)	integral component of membrane (GO:0016021)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|retinoic acid receptor activity (GO:0003708)|retinoid X receptor binding (GO:0046965)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tazarotene(DB00799)|Tretinoin(DB00755)	ACTTACCAGGATATCTAGGCA	0.532											OREG0021862	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I270T		Atlas-SNP	.											.	RARG	53	.	0			c.T809C						PASS	.						185	185	185					12																	53607847		2203	4300	6503	SO:0001583	missense	5916	exon7			ACCAGGATATCTA	M57707	CCDS8850.1, CCDS41790.1, CCDS58236.1, CCDS58237.1	12q13	2013-01-16			ENSG00000172819	ENSG00000172819		"Nuclear hormone receptors"	9866	protein-coding gene	gene with protein product		180190				1849262	Standard	NM_001042728		Approved	RARC, NR1B3	uc001scf.3	P13631	OTTHUMG00000048077	ENST00000425354.2:c.809T>C	chr12.hg19:g.53607847A>G	ENSP00000388510:p.Ile270Thr	412.0	0.0	.	993	365.0	139.0	.	NM_000966	B7Z492|B7Z4F1|B7ZAE4|J3KNP6|P22932|Q15281|Q52LZ8|Q9BYX8|Q9H1I3|Q9UJ38	Missense_Mutation	SNP	ENST00000425354.2	hg19	CCDS8850.1	.	.	.	.	.	.	.	.	.	.	A	19.87	3.906612	0.72868	.	.	ENSG00000172819	ENST00000425354;ENST00000394426;ENST00000538479;ENST00000327550;ENST00000338561;ENST00000543726;ENST00000550265	T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98	5.37	5.37	0.77165	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	T	0.65657	0.2712	M	0.79258	2.445	0.80722	D	1	D;D;D;D	0.89917	1.0;0.996;1.0;1.0	D;D;D;D	0.97110	1.0;0.993;1.0;0.999	T	0.70447	-0.4869	10	0.87932	D	0	.	14.6593	0.68858	1.0:0.0:0.0:0.0	.	307;248;270;259	F8VR45;B7Z4F1;P13631;F1D8P1	.;.;RARG_HUMAN;.	T	270;270;32;198;259;248;307	ENSP00000388510:I270T;ENSP00000377947:I270T;ENSP00000332695:I198T;ENSP00000343698:I259T;ENSP00000444335:I248T	ENSP00000332695:I198T	I	-	2	0	RARG	51894114	1.000000	0.71417	1.000000	0.80357	0.827000	0.46813	9.034000	0.93747	2.171000	0.68590	0.460000	0.39030	ATC	.	.	.	none		0.532	RARG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109404.2	NM_000966		G	53607847	A	G	53607847	3	3	195	1	0	0	0	0	1	0	0	0	13067	333	12	3	571	3	RARG	12	53607847	Missense_Mutation	SNP	A	TCGA-HE-7130-01A-11D-1961-08	2588028	53607847	80244048	91	11692											
DPY19L2	283417	hgsc.bcm.edu	37	chr12	64061939	64061939	+	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	gacgaactggaaggggccgaGaagaaaggtcttggccacca	13	4	15	9	2	1	2	0	0	1	2	1	6	1	3	3	5	1	0	3	5	4	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr12:64061939G>A	ENST00000324472.4	-	1	418	c.235C>T	c.(235-237)Ctc>Ttc	p.L79F	RP11-415I12.3_ENST00000509615.2_RNA	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	79					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)			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)		AAGGGGCCGAGAAGAAAGGTC	0.602																																					p.L79F		Atlas-SNP	.											.	DPY19L2	97	.	0			c.C235T						PASS	.						74	80	78					12																	64061939		2203	4300	6503	SO:0001583	missense	283417	exon1			GGCCGAGAAGAAA		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.235C>T	chr12.hg19:g.64061939G>A	ENSP00000315988:p.Leu79Phe	167.0	0.0	.		133.0	22.0	.	NM_173812	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Missense_Mutation	SNP	ENST00000324472.4	hg19	CCDS31851.1	.	.	.	.	.	.	.	.	.	.	G	3.843	-0.033397	0.07543	.	.	ENSG00000177990	ENST00000324472;ENST00000542209	T;T	0.45668	0.95;0.89	1.61	0.631	0.17699	.	.	.	.	.	T	0.26231	0.0640	L	0.32530	0.975	0.09310	N	0.999999	B	0.32653	0.379	B	0.30029	0.11	T	0.14643	-1.0465	8	.	.	.	.	5.6322	0.17516	0.0:0.3487:0.6513:0.0	.	79	Q6NUT2	D19L2_HUMAN	F	79	ENSP00000315988:L79F;ENSP00000444932:L79F	.	L	-	1	0	DPY19L2	62348206	0.000000	0.05858	0.010000	0.14722	0.121000	0.20230	0.247000	0.18179	0.202000	0.20498	0.195000	0.17529	CTC	.	.	.	none		0.602	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812		A	64061939	G	A	64061939	3	1	195	1	0	0	0	0	1	0	0	0	4743	942	33	2	2129	2	DPY19L2	12	64061939	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	10454092	64061939	69789956	92	11693											
LLPH	84298	hgsc.bcm.edu	37	chr12	66522754	66522754	+	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	caccacagttgctatctcttGaacatctttcattaaaacat	13	14	3	11	0	3	1	1	1	2	0	4	1	3	1	1	0	3	2	1	0	4	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr12:66522754G>A	ENST00000266604.2	-	2	203	c.133C>T	c.(133-135)Caa>Taa	p.Q45*	TMBIM4_ENST00000556010.1_3'UTR|TMBIM4_ENST00000539652.1_3'UTR|RP11-745O10.2_ENST00000510317.2_RNA|LLPH_ENST00000446587.2_Nonsense_Mutation_p.Q45*	NM_032338.3	NP_115714.1	Q9BRT6	LLPH_HUMAN	LLP homolog, long-term synaptic facilitation (Aplysia)	45	Lys-rich.						poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(1)|skin(1)	5						GCTATCTCTTGAACATCTTTC	0.403																																					p.Q45X		Atlas-SNP	.											.	LLPH	25	.	0			c.C133T						PASS	.						122	112	115					12																	66522754		2203	4297	6500	SO:0001587	stop_gained	84298	exon2			TCTCTTGAACATC	AK057947	CCDS8974.1	12q14.3	2014-05-09	2008-10-02	2008-10-02	ENSG00000139233	ENSG00000139233			28229	protein-coding gene	gene with protein product	"human LAPS18-like protein"		"chromosome 12 open reading frame 31"	C12orf31		12477932	Standard	NM_032338		Approved	MGC14817, hLLP	uc010ssw.2	Q9BRT6	OTTHUMG00000168959	ENST00000266604.2:c.133C>T	chr12.hg19:g.66522754G>A	ENSP00000266604:p.Gln45*	175.0	0.0	.		228.0	34.0	.	NM_032338	Q3B766	Nonsense_Mutation	SNP	ENST00000266604.2	hg19	CCDS8974.1	.	.	.	.	.	.	.	.	.	.	G	32	5.127434	0.94473	.	.	ENSG00000139233	ENST00000266604;ENST00000446587	.	.	.	4.13	-0.482	0.12078	.	0.626869	0.17801	N	0.161575	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-5.9384	6.7866	0.23677	0.0:0.1983:0.3284:0.4734	.	.	.	.	X	45	.	.	Q	-	1	0	LLPH	64809021	0.974000	0.33945	0.987000	0.45799	0.865000	0.49528	0.701000	0.25616	0.090000	0.17273	0.467000	0.42956	CAA	.	.	.	none		0.403	LLPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401752.1	NM_032338		A	66522754	G	A	66522754	4	1	195	1	0	0	0	0	0	1	0	0	8842	1299	45	2	264	2	LLPH	12	66522754	Nonsense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	2460815	66522754	67329141	93	11694											
AMDHD1	144193	hgsc.bcm.edu	37	chr12	96354342	96354342	+	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	ggattcttcaacgtggaaaaGatatagggttacagattaac	15	11	10	5	1	2	2	1	0	1	2	2	4	2	4	0	3	3	1	0	3	7	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr12:96354342G>C	ENST00000266736.2	+	5	860	c.754G>C	c.(754-756)Gat>Cat	p.D252H		NM_152435.2	NP_689648.2	Q96NU7	HUTI_HUMAN	amidohydrolase domain containing 1	252					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	imidazolonepropionase activity (GO:0050480)|metal ion binding (GO:0046872)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|skin(1)	22						ACGTGGAAAAGATATAGGGTT	0.428																																					p.D252H		Atlas-SNP	.											AMDHD1,NS,carcinoma,0,1	AMDHD1	56	.	0			c.G754C						PASS	.						122	117	118					12																	96354342		2203	4300	6503	SO:0001583	missense	144193	exon5			GGAAAAGATATAG	AB075878	CCDS9057.1	12q23.1	2006-02-02				ENSG00000139344			28577	protein-coding gene	gene with protein product							Standard	NM_152435		Approved	MGC35366	uc001tel.2	Q96NU7	OTTHUMG00000170353	ENST00000266736.2:c.754G>C	chr12.hg19:g.96354342G>C	ENSP00000266736:p.Asp252His	157.0	0.0	.		178.0	65.0	.	NM_152435	A8K463|Q68CI8	Missense_Mutation	SNP	ENST00000266736.2	hg19	CCDS9057.1	.	.	.	.	.	.	.	.	.	.	G	14.46	2.540809	0.45280	.	.	ENSG00000139344	ENST00000266736	T	0.46063	0.88	5.55	4.65	0.58169	Metal-dependent hydrolase, composite domain (1);	0.384940	0.33235	N	0.005136	T	0.49660	0.1570	L	0.60957	1.885	0.34446	D	0.700188	P	0.40107	0.703	P	0.47528	0.549	T	0.65340	-0.6192	10	0.54805	T	0.06	-0.0155	13.7543	0.62926	0.0749:0.0:0.9251:0.0	.	252	Q96NU7	HUTI_HUMAN	H	252	ENSP00000266736:D252H	ENSP00000266736:D252H	D	+	1	0	AMDHD1	94878473	1.000000	0.71417	0.605000	0.28930	0.004000	0.04260	4.953000	0.63624	1.447000	0.47661	0.655000	0.94253	GAT	.	.	.	none		0.428	AMDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408640.1	NM_152435		C	96354342	G	C	96354342	3	2	195	1	0	0	0	0	1	0	0	0	567	942	33	4	772	4	AMDHD1	12	96354342	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	29831588	96354342	37497553	94	11695											
UTP14C	9724	hgsc.bcm.edu	37	chr13	52603705	52603705	+	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	aaaaagtatcacaaagtcgtGaagaaaggaaaggccaagaa	22	4	10	5	1	1	3	1	1	0	2	2	4	1	4	1	2	0	1	1	2	9	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr13:52603705G>C	ENST00000521776.2	+	2	1498	c.765G>C	c.(763-765)gtG>gtC	p.V255V	ALG11_ENST00000521508.1_3'UTR|ALG11_ENST00000523764.1_3'UTR	NM_021645.5	NP_067677.4	Q5TAP6	UT14C_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog C (yeast)	255					cell differentiation (GO:0030154)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|rRNA processing (GO:0006364)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)				breast(4)|cervix(1)|endometrium(1)|large_intestine(10)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	32		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;2.3e-08)		ACAAAGTCGTGAAGAAAGGAA	0.433																																					p.V255V		Atlas-SNP	.											.	UTP14C	67	.	0			c.G765C						PASS	.						89	88	88					13																	52603705		2203	4300	6503	SO:0001819	synonymous_variant	9724	exon2			AGTCGTGAAGAAA	D87455	CCDS31978.1	13q12.2-q13.3	2010-11-23	2004-06-15	2004-06-16	ENSG00000253797	ENSG00000253797			20321	protein-coding gene	gene with protein product		608969	"KIAA0266"	KIAA0266		9039502, 16354793	Standard	NM_021645		Approved	2700066J21Rik	uc021rjw.1	Q5TAP6	OTTHUMG00000164353	ENST00000521776.2:c.765G>C	chr13.hg19:g.52603705G>C		77.0	0.0	.		83.0	5.0	.	NM_021645	Q5FWG3|Q92555	Silent	SNP	ENST00000521776.2	hg19	CCDS31978.1																																																																																			.	.	.	none		0.433	UTP14C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045049.2	NM_021645		C	52603705	G	C	52603705	2	2	195	1	0	0	0	0	0	0	0	1	17108	1277	45	4		4	UTP14C	13	52603705	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08		52603705	62566173	95	11696											
OLFM4	10562	hgsc.bcm.edu	37	chr13	53624805	53624805	+	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	tgcataagatgcaggaaaaaGtgcagagcattaactataac	18	8	9	6	0	0	2	0	0	0	2	0	3	0	3	0	1	6	4	0	1	6	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr13:53624805G>C	ENST00000219022.2	+	5	1510	c.1432G>C	c.(1432-1434)Gtg>Ctg	p.V478L		NM_006418.4	NP_006409.3	Q6UX06	OLFM4_HUMAN	olfactomedin 4	478	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				cell adhesion (GO:0007155)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|protein homooligomerization (GO:0051260)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|specific granule (GO:0042581)	cadherin binding (GO:0045296)|catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(4)|kidney(4)|large_intestine(5)|lung(20)|skin(3)|urinary_tract(1)	39		Breast(56;0.000776)|Lung NSC(96;0.000814)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.13e-08)		GCAGGAAAAAGTGCAGAGCAT	0.368																																					p.V478L		Atlas-SNP	.											.	OLFM4	94	.	0			c.G1432C						PASS	.						108	108	108					13																	53624805		2203	4300	6503	SO:0001583	missense	10562	exon5			GAAAAAGTGCAGA	AY358567	CCDS9440.1	13q14	2004-06-25			ENSG00000102837	ENSG00000102837			17190	protein-coding gene	gene with protein product		614061					Standard	NM_006418		Approved	OlfD, GW112, GC1	uc001vhl.3	Q6UX06	OTTHUMG00000016981	ENST00000219022.2:c.1432G>C	chr13.hg19:g.53624805G>C	ENSP00000219022:p.Val478Leu	84.0	0.0	.		129.0	18.0	.	NM_006418	O95362|Q5VWG0|Q86T22	Missense_Mutation	SNP	ENST00000219022.2	hg19	CCDS9440.1	.	.	.	.	.	.	.	.	.	.	G	10.48	1.362917	0.24684	.	.	ENSG00000102837	ENST00000219022	T	0.14022	2.54	5.64	-2.23	0.06930	Olfactomedin-like (3);	0.818724	0.11361	N	0.571904	T	0.03959	0.0111	N	0.03268	-0.37	0.18873	N	0.999988	B	0.06786	0.001	B	0.15484	0.013	T	0.43426	-0.9392	10	0.15499	T	0.54	.	2.2285	0.03991	0.2383:0.3579:0.2837:0.1201	.	478	Q6UX06	OLFM4_HUMAN	L	478	ENSP00000219022:V478L	ENSP00000219022:V478L	V	+	1	0	OLFM4	52522806	0.000000	0.05858	0.030000	0.17652	0.978000	0.69477	-0.374000	0.07484	-0.094000	0.12374	0.585000	0.79938	GTG	.	.	.	none		0.368	OLFM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045112.2	NM_006418		C	53624805	G	C	53624805	3	2	195	1	0	0	0	0	1	0	0	0	10862	1029	36	4	1450	4	OLFM4	13	53624805	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	1021100	53624805	61545073	96	11697											
PCDH20	64881	hgsc.bcm.edu	37	chr13	61986466	61986467	+	Missense_Mutation	DNP	CC	CC	TT																															gagtagaaactgtcagaattCctgtgacactgtctaaggaa																										TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr13:61986466_61986467CC>TT	ENST00000409186.1	-	5	3870_3871	c.1765_1766GG>AA	c.(1765-1767)GGa>AAa	p.G589K	PCDH20_ENST00000409204.4_Missense_Mutation_p.G589K			Q8N6Y1	PCD20_HUMAN	protocadherin 20	589	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)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(14)|liver(1)|lung(23)|ovary(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	58		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		TGTCAGAATTCCTGTGACACTG	0.455																																					p.G589E|p.G589R		Atlas-SNP	.											.	PCDH20	265	.	0			c.G1766A|c.G1765A						PASS	.																																			SO:0001583	missense	64881	exon2			AGAATTCCTGTGA|GAATTCCTGTGAC	AF169693	CCDS9442.2	13q21	2010-01-26			ENSG00000197991	ENSG00000197991		"Cadherins / Protocadherins : Non-clustered"	14257	protein-coding gene	gene with protein product		614449					Standard	NM_022843		Approved	PCDH13, FLJ22218	uc001vid.4	Q8N6Y1	OTTHUMG00000017012	ENST00000409186.1:c.1765_1766delinsTT	chr13.hg19:g.61986466_61986467delinsTT	ENSP00000386653:p.Gly589Lys	128.0	0.0	.		121.0	24.0|25.0	.	NM_022843	A8K1K9|B1AQU2|Q8NDN4|Q9NRT9	Missense_Mutation	SNP	ENST00000409186.1	hg19	CCDS9442.2																																																																																			.	.	.	none		0.455	PCDH20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333054.2	NM_022843		TT	61986467	CC	TT	61986466	3	4	195	1	0	0	0	0	1	0	0	0	11522	855	30	2	1093	2	PCDH20	13	61986466	Missense_Mutation	DNP	CC	TCGA-HE-7130-01A-11D-1961-08	8361661	61986466	53183412	97	11698											
CIDEB	27141	hgsc.bcm.edu	37	chr14	24775203	24775203	+	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	aagtcacaactcatagagtaGagcccgtagaatgtggcttt	13	10	10	8	1	2	3	2	0	0	3	2	3	2	3	1	1	2	3	1	1	6	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr14:24775203G>C	ENST00000336557.5	-	7	1779	c.477C>G	c.(475-477)ctC>ctG	p.L159L	NOP9_ENST00000267425.3_3'UTR|CIDEB_ENST00000258807.5_Silent_p.L159L|LTB4R2_ENST00000528054.1_5'Flank|CIDEB_ENST00000554411.1_Silent_p.L159L			Q9UHD4	CIDEB_HUMAN	cell death-inducing DFFA-like effector b	159					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)		TCATAGAGTAGAGCCCGTAGA	0.488																																					p.L159L		Atlas-SNP	.											.	CIDEB	17	.	0			c.C477G						PASS	.						141	134	136					14																	24775203		2203	4300	6503	SO:0001819	synonymous_variant	27141	exon6			AGAGTAGAGCCCG	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.477C>G	chr14.hg19:g.24775203G>C		127.0	0.0	.		104.0	24.0	.	NM_014430	D3DS73|Q546V8|Q9NNW9	Silent	SNP	ENST00000336557.5	hg19	CCDS32056.1																																																																																			.	.	.	none		0.488	CIDEB-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414120.1			C	24775203	G	C	24775203	2	2	195	1	0	0	0	0	0	0	0	1	3428	929	33	4		4	CIDEB	14	24775203	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08		24775203	82574337	98	11699											
FANCM	57697	hgsc.bcm.edu	37	chr14	45642339	45642339	+	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	atcatcctttgcctacacatCaagttgatcactcagatcga	12	12	5	12	1	4	2	4	1	0	1	6	3	5	2	2	0	2	1	2	0	2	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr14:45642339C>G	ENST00000267430.5	+	13	2327	c.2242C>G	c.(2242-2244)Caa>Gaa	p.Q748E	FANCM_ENST00000542564.2_Missense_Mutation_p.Q722E	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	748					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						GCCTACACATCAAGTTGATCA	0.398								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.Q748E		Atlas-SNP	.											.	FANCM	225	.	0			c.C2242G						PASS	.						160	144	150					14																	45642339		2203	4300	6503	SO:0001583	missense	57697	exon13	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	ACACATCAAGTTG	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.2242C>G	chr14.hg19:g.45642339C>G	ENSP00000267430:p.Gln748Glu	108.0	0.0	.		88.0	55.0	.	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	hg19	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	C	2.703	-0.270591	0.05716	.	.	ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250	T;T;T	0.18338	2.83;2.83;2.22	5.79	5.79	0.91817	.	1.031910	0.07642	N	0.930388	T	0.18841	0.0452	L	0.60455	1.87	0.09310	N	1	B;B	0.28233	0.204;0.204	B;B	0.21708	0.036;0.033	T	0.21999	-1.0229	10	0.23302	T	0.38	.	9.037	0.36293	0.1484:0.7768:0.0:0.0748	.	722;748	B2RTQ9;Q8IYD8	.;FANCM_HUMAN	E	748;722;264	ENSP00000267430:Q748E;ENSP00000442493:Q722E;ENSP00000452033:Q264E	ENSP00000267430:Q748E	Q	+	1	0	FANCM	44712089	0.001000	0.12720	0.103000	0.21229	0.402000	0.30811	1.154000	0.31688	2.746000	0.94184	0.561000	0.74099	CAA	.	.	.	none		0.398	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		G	45642339	C	G	45642339	3	3	195	1	0	0	0	0	1	0	0	0	5678	827	29	4	2292	4	FANCM	14	45642339	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	20867136	45642339	61707201	99	11700											
EML5	161436	hgsc.bcm.edu	37	chr14	89161727	89161727	+	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	tgctattgaaagtttctctcCtttcttccagtcccagagca	8	15	6	12	0	2	2	0	1	2	1	6	2	5	2	3	0	2	3	3	0	2	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr14:89161727C>T	ENST00000380664.5	-	16	2415	c.2416G>A	c.(2416-2418)Gga>Aga	p.G806R	EML5_ENST00000352093.5_Missense_Mutation_p.G806R|EML5_ENST00000554922.1_Missense_Mutation_p.G806R			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	806						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						AGTTTCTCTCCTTTCTTCCAG	0.338																																					p.G806R		Atlas-SNP	.											.	EML5	141	.	0			c.G2416A						PASS	.						88	79	82					14																	89161727		1843	4083	5926	SO:0001583	missense	161436	exon16			TCTCTCCTTTCTT	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.2416G>A	chr14.hg19:g.89161727C>T	ENSP00000370039:p.Gly806Arg	44.0	0.0	.		77.0	17.0	.	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	hg19	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.718501	0.89205	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.65916	-0.18;1.86;-0.18	4.86	4.86	0.63082	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	0.80391	0.4614	M	0.81239	2.535	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81899	-0.0721	10	0.51188	T	0.08	-15.3073	17.7789	0.88517	0.0:1.0:0.0:0.0	.	806	Q05BV3	EMAL5_HUMAN	R	806	ENSP00000451998:G806R;ENSP00000298315:G806R;ENSP00000370039:G806R	ENSP00000298315:G806R	G	-	1	0	EML5	88231480	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	7.320000	0.79064	2.526000	0.85167	0.467000	0.42956	GGA	.	.	.	none		0.338	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			T	89161727	C	T	89161727	3	4	195	1	0	0	0	0	1	0	0	0	5102	690	24	2	3629	2	EML5	14	89161727	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	43519388	89161727	18187813	100	11701											
MARK3	4140	hgsc.bcm.edu	37	chr14	103932113	103932113	+	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	tcagtggctcacttccctttGatgggcaaaacctaaaggta	11	11	9	10	0	2	1	2	1	0	0	3	1	3	1	2	3	1	3	2	3	5	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr14:103932113G>C	ENST00000429436.2	+	8	1270	c.760G>C	c.(760-762)Gat>Cat	p.D254H	MARK3_ENST00000561071.1_Intron|MARK3_ENST00000416682.2_Missense_Mutation_p.D277H|MARK3_ENST00000216288.7_Missense_Mutation_p.D254H|MARK3_ENST00000303622.9_Missense_Mutation_p.D254H|MARK3_ENST00000335102.5_Missense_Mutation_p.D277H|MARK3_ENST00000553942.1_Missense_Mutation_p.D254H|MARK3_ENST00000440884.3_Intron	NM_001128918.1|NM_001128919.1	NP_001122390.1|NP_001122391.1	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	254	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					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)			ACTTCCCTTTGATGGGCAAAA	0.403																																					p.D254H		Atlas-SNP	.											.	MARK3	86	.	0			c.G760C						PASS	.						64	65	65					14																	103932113		1975	4183	6158	SO:0001583	missense	4140	exon8			CCCTTTGATGGGC	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.760G>C	chr14.hg19:g.103932113G>C	ENSP00000411397:p.Asp254His	94.0	0.0	.		56.0	9.0	.	NM_001128919	O60219|Q86TT8|Q8TB41|Q8WX83|Q96RG1|Q9UMY9|Q9UN34	Missense_Mutation	SNP	ENST00000429436.2	hg19	CCDS45165.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.1|26.1	4.702752|4.702752	0.88924|0.88924	.|.	.|.	ENSG00000075413|ENSG00000075413	ENST00000335102;ENST00000416682;ENST00000429436;ENST00000303622;ENST00000216288;ENST00000553942|ENST00000554627	T;T;T;T;T;T|.	0.66280|.	-0.2;-0.2;-0.2;-0.2;-0.2;-0.2|.	5.84|5.84	5.84|5.84	0.93424|0.93424	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|T	0.61185|0.61185	0.2327|0.2327	L|L	0.33189|0.33189	0.99|0.99	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D|.	0.97110|.	0.997;0.996;0.999;0.998;1.0;0.995|.	T|T	0.53208|0.53208	-0.8471|-0.8471	10|5	0.87932|.	D|.	0|.	.|.	20.1454|20.1454	0.98074|0.98074	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	277;277;254;254;254;254|.	P27448-7;P27448-2;P27448-6;P27448;P27448-4;P27448-3|.	.;.;.;MARK3_HUMAN;.;.|.	H|F	277;277;254;254;254;254|21	ENSP00000335347:D277H;ENSP00000408092:D277H;ENSP00000411397:D254H;ENSP00000303698:D254H;ENSP00000216288:D254H;ENSP00000450772:D254H|.	ENSP00000216288:D254H|.	D|L	+|+	1|3	0|2	MARK3|MARK3	103001866|103001866	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.996000|0.996000	0.88848|0.88848	9.807000|9.807000	0.99171|0.99171	2.748000|2.748000	0.94277|0.94277	0.650000|0.650000	0.86243|0.86243	GAT|TTG	.	.	.	none		0.403	MARK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415144.1	NM_001128918		C	103932113	G	C	103932113	3	2	195	1	0	0	0	0	1	0	0	0	9321	1290	45	4	790	4	MARK3	14	103932113	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	14770386	103932113	3417427	101	11702											
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105409722	105409722	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcctggacctccaggtcagcGgaagggggctgaacgctgag	8	5	17	11	2	1	2	1	2	0	0	2	4	2	4	3	5	2	2	3	5	2	0	rs372712364	byFrequency	TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr14:105409722G>A	ENST00000333244.5	-	7	12185	c.12066C>T	c.(12064-12066)tcC>tcT	p.S4022S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4022						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CCAGGTCAGCGGAAGGGGGCT	0.657													.|||	2	0.000399361	8e-04	0.0014	5008	,	,		17513	0		0	False		,,,				2504	0				p.S4022S		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	.	0			c.C12066T						PASS	.						109	115	113					14																	105409722		1954	4133	6087	SO:0001819	synonymous_variant	113146	exon7			GTCAGCGGAAGGG	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"chromosome 14 open reading frame 78"	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.12066C>T	chr14.hg19:g.105409722G>A		333.0	0.0	.		126.0	88.0	.	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	hg19	CCDS45177.1																																																																																			.	.	.	alt		0.657	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105409722	G	A	105409722	2	1	195	1	0	0	0	0	0	0	0	1	415	1103	39	1		1	AHNAK2	14	105409722	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	1477609	105409722	1939818	102	11703											
ZFYVE19	84936	hgsc.bcm.edu	37	chr15	41099974	41099974	+	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	gcccaggacttggccggcgtGatctcagctctgcagaccct	6	8	12	15	2	2	2	1	1	2	1	3	3	2	3	3	3	2	2	3	3	0	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr15:41099974G>A	ENST00000355341.4	+	1	688	c.187G>A	c.(187-189)Gat>Aat	p.D63N	DNAJC17_ENST00000220496.4_5'Flank|ZFYVE19_ENST00000570108.1_Intron|ZFYVE19_ENST00000564258.1_Intron|ZFYVE19_ENST00000299173.10_Missense_Mutation_p.D63N|ZFYVE19_ENST00000336455.5_Intron|ZFYVE19_ENST00000563530.1_3'UTR	NM_001077268.1	NP_001070736.1	Q96K21	ANCHR_HUMAN	zinc finger, FYVE domain containing 19	63					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)		TGGCCGGCGTGATCTCAGCTC	0.672																																					p.D63N		Atlas-SNP	.											.	ZFYVE19	31	.	0			c.G187A						PASS	.						36	46	42					15																	41099974		2053	4206	6259	SO:0001583	missense	84936	exon1			CGGCGTGATCTCA	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.187G>A	chr15.hg19:g.41099974G>A	ENSP00000347498:p.Asp63Asn	43.0	0.0	.		30.0	18.0	.	NM_001077268	B3KVB2|C9JNF4|H3BUF9|Q86WC2|Q8WU96	Missense_Mutation	SNP	ENST00000355341.4	hg19	CCDS42025.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.756051	0.49362	.	.	ENSG00000166140	ENST00000355341;ENST00000299173	T;T	0.37058	1.23;1.22	4.57	1.69	0.24217	.	1.328960	0.05087	N	0.484506	T	0.25680	0.0625	N	0.19112	0.55	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.29610	-1.0006	10	0.72032	D	0.01	1.3232	6.5318	0.22332	0.2972:0.0:0.7028:0.0	.	63;63	Q96K21-3;Q96K21	.;ZFY19_HUMAN	N	63	ENSP00000347498:D63N;ENSP00000299173:D63N	ENSP00000299173:D63N	D	+	1	0	ZFYVE19	38887266	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	1.012000	0.29924	0.425000	0.26087	0.603000	0.83216	GAT	.	.	.	none		0.672	ZFYVE19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418996.1	NM_032850		A	41099974	G	A	41099974	3	1	195	1	0	0	0	0	1	0	0	0	17677	1290	45	2	189	2	ZFYVE19	15	41099974	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08		41099974	61431418	103	11704											
INO80	54617	hgsc.bcm.edu	37	chr15	41384347	41384347	+	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	atcgtcttcactctgagaatCagcctcgctggattcatcac	9	12	7	13	2	6	1	4	1	2	1	8	3	6	2	1	1	1	1	1	1	1	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr15:41384347C>A	ENST00000361937.3	-	5	839	c.415G>T	c.(415-417)Gat>Tat	p.D139Y	INO80_ENST00000401393.3_Missense_Mutation_p.D139Y			Q9ULG1	INO80_HUMAN	INO80 complex subunit	139	Assembles INO80 complex module with putative regulatory components INO80E, INO80F, UCHL5, NFRKB, MCRS1 and IN80D.				ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						CTCTGAGAATCAGCCTCGCTG	0.378																																					p.D139Y		Atlas-SNP	.											.	INO80	122	.	0			c.G415T						PASS	.						123	114	117					15																	41384347		2203	4300	6503	SO:0001583	missense	54617	exon5			GAGAATCAGCCTC	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.415G>T	chr15.hg19:g.41384347C>A	ENSP00000355205:p.Asp139Tyr	65.0	0.0	.		42.0	19.0	.	NM_017553	A6H8X4|Q9NTG6	Missense_Mutation	SNP	ENST00000361937.3	hg19	CCDS10071.1	.	.	.	.	.	.	.	.	.	.	C	16.39	3.111190	0.56398	.	.	ENSG00000128908	ENST00000361937;ENST00000401393	D;D	0.92752	-3.1;-3.1	5.37	5.37	0.77165	.	0.099076	0.64402	D	0.000002	D	0.92612	0.7653	L	0.59436	1.845	0.80722	D	1	P	0.51791	0.948	P	0.47626	0.552	D	0.93222	0.6609	10	0.72032	D	0.01	.	19.3098	0.94182	0.0:1.0:0.0:0.0	.	139	Q9ULG1	INO80_HUMAN	Y	139	ENSP00000355205:D139Y;ENSP00000384686:D139Y	ENSP00000355205:D139Y	D	-	1	0	INO80	39171639	1.000000	0.71417	1.000000	0.80357	0.070000	0.16714	6.847000	0.75404	2.800000	0.96347	0.455000	0.32223	GAT	.	.	.	none		0.378	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252527.2	NM_017553		A	41384347	C	A	41384347	3	1	195	1	0	0	0	0	1	0	0	0	7753	826	29	4	4383	4	INO80	15	41384347	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	284373	41384347	61147045	104	11705											
AKAP13	11214	hgsc.bcm.edu	37	chr15	86269660	86269660	+	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	gaggttcaagcagttcttctCactgacattttagttttcct	8	17	7	9	0	3	1	2	1	2	0	5	2	4	1	1	1	1	4	1	1	2	7			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr15:86269660C>G	ENST00000394518.2	+	27	6860	c.6765C>G	c.(6763-6765)ctC>ctG	p.L2255L	RP11-158M2.2_ENST00000561417.1_RNA|AKAP13_ENST00000361243.2_Silent_p.L2259L|AKAP13_ENST00000560579.1_3'UTR|AKAP13_ENST00000394510.2_Silent_p.L500L	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	2255	Interaction with ESR1.|PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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						CAGTTCTTCTCACTGACATTT	0.338																																					p.L2259L	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.C6777G						PASS	.						184	186	186					15																	86269660		2202	4298	6500	SO:0001819	synonymous_variant	11214	exon27			TCTTCTCACTGAC	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.6765C>G	chr15.hg19:g.86269660C>G		143.0	0.0	.		130.0	31.0	.	NM_006738	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Silent	SNP	ENST00000394518.2	hg19	CCDS32319.1																																																																																			.	.	.	none		0.338	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		G	86269660	C	G	86269660	2	3	195	1	0	0	0	0	0	0	0	1	449	813	29	4		4	AKAP13	15	86269660	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	44885313	86269660	16261732	105	11706											
ABAT	18	hgsc.bcm.edu	37	chr16	8844348	8844348	+	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	attacctggttgatgtggacGgcaaccgaatgctggatctt	9	12	12	8	2	1	1	0	1	1	0	1	4	1	3	2	4	3	3	2	4	3	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr16:8844348G>T	ENST00000396600.2	+	5	1206	c.268G>T	c.(268-270)Ggc>Tgc	p.G90C	ABAT_ENST00000425191.2_Missense_Mutation_p.G90C|ABAT_ENST00000268251.8_Missense_Mutation_p.G90C|ABAT_ENST00000567812.1_Missense_Mutation_p.G105C|ABAT_ENST00000569156.1_Missense_Mutation_p.G90C	NM_000663.4	NP_000654.2	P80404	GABT_HUMAN	4-aminobutyrate aminotransferase	90					behavioral response to cocaine (GO:0048148)|copulation (GO:0007620)|gamma-aminobutyric acid catabolic process (GO:0009450)|locomotory behavior (GO:0007626)|negative regulation of blood pressure (GO:0045776)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|synaptic transmission (GO:0007268)	4-aminobutyrate transaminase complex (GO:0032144)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	(S)-3-amino-2-methylpropionate transaminase activity (GO:0047298)|4-aminobutyrate transaminase activity (GO:0003867)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|succinate-semialdehyde dehydrogenase binding (GO:0032145)			breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|skin(3)|upper_aerodigestive_tract(2)	26					L-Alanine(DB00160)|Phenelzine(DB00780)|Pyruvic acid(DB00119)|Valproic Acid(DB00313)|Vigabatrin(DB01080)	TGATGTGGACGGCAACCGAAT	0.463																																					p.G90C		Atlas-SNP	.											.	ABAT	46	.	0			c.G268T						PASS	.						200	180	187					16																	8844348		2197	4300	6497	SO:0001583	missense	18	exon5			GTGGACGGCAACC	L32961	CCDS10534.1	16p13.2	2011-01-10			ENSG00000183044	ENSG00000183044	2.6.1.19		23	protein-coding gene	gene with protein product	"4-aminobutyrate transaminase"	137150				7721088	Standard	NM_020686		Approved	GABAT	uc002czc.4	P80404	OTTHUMG00000048201	ENST00000396600.2:c.268G>T	chr16.hg19:g.8844348G>T	ENSP00000379845:p.Gly90Cys	219.0	0.0	.		134.0	7.0	.	NM_001127448	A8K386|Q16260|Q8N5W2|Q96BG2|Q99800	Missense_Mutation	SNP	ENST00000396600.2	hg19	CCDS10534.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.614365	0.87359	.	.	ENSG00000183044	ENST00000268251;ENST00000396600;ENST00000425191	D;D;D	0.91464	-2.85;-2.85;-2.85	5.93	5.93	0.95920	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.103605	0.64402	D	0.000004	D	0.97353	0.9134	H	0.97635	4.045	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98221	1.0478	10	0.87932	D	0	-11.4658	18.8949	0.92419	0.0:0.0:1.0:0.0	.	90	P80404	GABT_HUMAN	C	90	ENSP00000268251:G90C;ENSP00000379845:G90C;ENSP00000411916:G90C	ENSP00000268251:G90C	G	+	1	0	ABAT	8751849	1.000000	0.71417	0.997000	0.53966	0.881000	0.50899	7.497000	0.81536	2.803000	0.96430	0.650000	0.86243	GGC	.	.	.	none		0.463	ABAT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433620.2	NM_020686		T	8844348	G	T	8844348	3	4	195	1	0	0	0	0	1	0	0	0	27	1116	39	4	282	4	ABAT	16	8844348	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08		8844348	81510405	106	11707											
ZNF689	115509	hgsc.bcm.edu	37	chr16	30616559	30616559	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccacagtctgggcaagggtAaggcttttttagattctggg	8	12	13	8	0	2	1	0	0	2	1	2	1	2	1	1	4	0	3	1	4	3	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr16:30616559A>G	ENST00000287461.3	-	3	866	c.529T>C	c.(529-531)Tac>Cac	p.Y177H	RP11-146F11.5_ENST00000563540.1_RNA|ZNF689_ENST00000566673.1_5'UTR	NM_138447.1	NP_612456.1	Q96CS4	ZN689_HUMAN	zinc finger protein 689	177					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)			GGGCAAGGGTAAGGCTTTTTT	0.617																																					p.Y177H		Atlas-SNP	.											.	ZNF689	48	.	0			c.T529C						PASS	.						73	78	77					16																	30616559		2197	4300	6497	SO:0001583	missense	115509	exon3			AAGGGTAAGGCTT	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.529T>C	chr16.hg19:g.30616559A>G	ENSP00000287461:p.Tyr177His	153.0	0.0	.		70.0	19.0	.	NM_138447	Q658J5	Missense_Mutation	SNP	ENST00000287461.3	hg19	CCDS10686.1	.	.	.	.	.	.	.	.	.	.	a	10.15	1.270760	0.23221	.	.	ENSG00000156853	ENST00000287461;ENST00000443190	T	0.60040	0.22	4.94	3.8	0.43715	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35495	N	0.003162	T	0.43567	0.1253	N	0.25332	0.735	0.32189	N	0.579329	B	0.18166	0.026	B	0.25614	0.062	T	0.54227	-0.8325	10	0.62326	D	0.03	-23.399	9.3707	0.38252	0.8409:0.0:0.0:0.159	.	177	Q96CS4	ZN689_HUMAN	H	177	ENSP00000287461:Y177H	ENSP00000287461:Y177H	Y	-	1	0	ZNF689	30524060	0.355000	0.24921	0.997000	0.53966	0.194000	0.23727	2.424000	0.44714	2.074000	0.62210	0.455000	0.32223	TAC	.	.	.	none		0.617	ZNF689-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255552.1	NM_138447		G	30616559	A	G	30616559	3	3	195	1	0	0	0	0	1	0	0	0	18106	362	13	3	977	3	ZNF689	16	30616559	Missense_Mutation	SNP	A	TCGA-HE-7130-01A-11D-1961-08	21772211	30616559	59738194	107	11708											
SRCAP	10847	hgsc.bcm.edu	37	chr16	30749163	30749163	+	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	tgtgtcagagaagaacctttCtctcaccccttctgcaccca	9	11	6	15	0	4	2	2	0	2	2	5	3	4	2	4	0	2	1	4	0	2	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr16:30749163C>G	ENST00000262518.4	+	34	8187	c.7802C>G	c.(7801-7803)tCt>tGt	p.S2601C	RP11-2C24.4_ENST00000483578.1_lincRNA|SRCAP_ENST00000344771.4_Missense_Mutation_p.S2443C|SRCAP_ENST00000395059.2_Missense_Mutation_p.S2539C	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	2601	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)			AAGAACCTTTCTCTCACCCCT	0.552																																					p.S2601C		Atlas-SNP	.											.	SRCAP	298	.	0			c.C7802G						PASS	.						79	68	72					16																	30749163		2197	4300	6497	SO:0001583	missense	10847	exon34			ACCTTTCTCTCAC	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.7802C>G	chr16.hg19:g.30749163C>G	ENSP00000262518:p.Ser2601Cys	136.0	0.0	.		84.0	24.0	.	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	hg19	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	C	7.548	0.662079	0.14645	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.91792	-2.9;-2.91;-2.91	4.88	3.85	0.44370	.	0.294453	0.24843	N	0.035160	D	0.83594	0.5288	N	0.08118	0	0.22728	N	0.9988	P;P	0.50156	0.932;0.758	P;B	0.46479	0.518;0.319	T	0.76427	-0.2963	10	0.62326	D	0.03	-9.0E-4	7.2792	0.26302	0.0:0.8786:0.0:0.1214	.	2539;2601	Q6ZRS2-2;Q6ZRS2	.;SRCAP_HUMAN	C	2601;2539;2443	ENSP00000262518:S2601C;ENSP00000378499:S2539C;ENSP00000343042:S2443C	ENSP00000262518:S2601C	S	+	2	0	SRCAP	30656664	0.483000	0.25956	0.998000	0.56505	0.666000	0.39218	0.172000	0.16704	2.543000	0.85770	0.467000	0.42956	TCT	.	.	.	none		0.552	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		G	30749163	C	G	30749163	3	3	195	1	0	0	0	0	1	0	0	0	15147	913	32	4	7928	4	SRCAP	16	30749163	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	132604	30749163	59605590	108	11709											
CMTM2	146225	hgsc.bcm.edu	37	chr16	66614056	66614056	+	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	gtacagctttgccattcataGatacatacccttcatcctgt	10	14	5	12	0	2	1	2	0	0	1	3	1	3	1	3	0	5	2	3	0	4	7			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr16:66614056G>C	ENST00000268595.2	+	2	564	c.413G>C	c.(412-414)aGa>aCa	p.R138T	CMTM2_ENST00000379486.2_Intron|RP11-403P17.2_ENST00000568430.1_RNA	NM_144673.2	NP_653274.1	Q8TAZ6	CKLF2_HUMAN	CKLF-like MARVEL transmembrane domain containing 2	138	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				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)		GCCATTCATAGATACATACCC	0.483																																					p.R138T		Atlas-SNP	.											.	CMTM2	33	.	0			c.G413C						PASS	.						258	204	223					16																	66614056		2201	4300	6501	SO:0001583	missense	146225	exon2			TTCATAGATACAT	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.413G>C	chr16.hg19:g.66614056G>C	ENSP00000268595:p.Arg138Thr	164.0	0.0	.		114.0	8.0	.	NM_144673	Q5I2A4|Q8N7E5	Missense_Mutation	SNP	ENST00000268595.2	hg19	CCDS10814.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.416443	0.83449	.	.	ENSG00000140932	ENST00000268595	T	0.35605	1.3	4.51	4.51	0.55191	Marvel (1);	0.000000	0.56097	D	0.000029	T	0.52661	0.1748	L	0.54323	1.7	0.35958	D	0.834422	D	0.89917	1.0	D	0.87578	0.998	T	0.57219	-0.7849	10	0.40728	T	0.16	20.5482	13.0353	0.58867	0.0:0.0:1.0:0.0	.	138	Q8TAZ6	CKLF2_HUMAN	T	138	ENSP00000268595:R138T	ENSP00000268595:R138T	R	+	2	0	CMTM2	65171557	1.000000	0.71417	0.997000	0.53966	0.404000	0.30871	2.341000	0.43983	2.786000	0.95864	0.561000	0.74099	AGA	.	.	.	none		0.483	CMTM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268808.1			C	66614056	G	C	66614056	3	2	195	1	0	0	0	0	1	0	0	0	3585	942	33	4	419	4	CMTM2	16	66614056	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	35864893	66614056	23740697	109	11710											
AARS	16	hgsc.bcm.edu	37	chr16	70316659	70316659	+	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	tttcacttgctgttagagtaGagtccatcttgaaagtcacc	10	14	8	9	0	3	3	2	1	1	2	4	3	4	3	2	0	1	3	2	0	3	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr16:70316659G>C	ENST00000261772.8	-	2	151	c.8C>G	c.(7-9)tCt>tGt	p.S3C		NM_001605.2	NP_001596.2			alanyl-tRNA synthetase											breast(3)|cervix(2)|endometrium(5)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)		TGTTAGAGTAGAGTCCATCTT	0.388																																					p.S3C		Atlas-SNP	.											.	AARS	62	.	0			c.C8G						PASS	.						119	117	118					16																	70316659		2198	4300	6498	SO:0001583	missense	16	exon2			AGAGTAGAGTCCA	D32050	CCDS32474.1	16q22.1	2014-09-17			ENSG00000090861	ENSG00000090861	6.1.1.7	"Aminoacyl tRNA synthetases / Class II"	20	protein-coding gene	gene with protein product	"alanine tRNA ligase 1, cytoplasmic"	601065				8595897	Standard	NM_001605		Approved		uc002eyn.1	P49588	OTTHUMG00000177042	ENST00000261772.8:c.8C>G	chr16.hg19:g.70316659G>C	ENSP00000261772:p.Ser3Cys	202.0	0.0	.		141.0	76.0	.	NM_001605		Missense_Mutation	SNP	ENST00000261772.8	hg19	CCDS32474.1	.	.	.	.	.	.	.	.	.	.	G	16.98	3.270776	0.59540	.	.	ENSG00000090861	ENST00000261772	T	0.64991	-0.13	5.56	1.06	0.20224	.	0.309320	0.37012	N	0.002288	T	0.54334	0.1852	L	0.39898	1.24	0.30179	N	0.800544	B	0.29085	0.232	B	0.38921	0.285	T	0.57353	-0.7826	10	0.66056	D	0.02	0.0292	8.518	0.33257	0.3543:0.0:0.6457:0.0	.	3	P49588	SYAC_HUMAN	C	3	ENSP00000261772:S3C	ENSP00000261772:S3C	S	-	2	0	AARS	68874160	0.401000	0.25303	0.169000	0.22859	0.874000	0.50279	3.302000	0.51849	0.212000	0.20703	0.591000	0.81541	TCT	.	.	.	none		0.388	AARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435021.2	NM_001605		C	70316659	G	C	70316659	3	2	195	1	0	0	0	0	1	0	0	0	19	942	33	4	2978	4	AARS	16	70316659	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	3702603	70316659	20038094	110	11711											
PRPF8	10594	hgsc.bcm.edu	37	chr17	1586885	1586885	+	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	ggtcatgtctccatggtctcGaatgatcttcctgacatgtt	7	15	9	10	1	4	2	1	2	3	0	7	3	5	2	2	2	0	1	2	2	1	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr17:1586885G>C	ENST00000572621.1	-	2	476	c.211C>G	c.(211-213)Cga>Gga	p.R71G	PRPF8_ENST00000304992.6_Missense_Mutation_p.R71G			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	71					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		CCATGGTCTCGAATGATCTTC	0.478																																					p.R71G		Atlas-SNP	.											.	PRPF8	169	.	0			c.C211G						PASS	.						210	180	190					17																	1586885		2203	4300	6503	SO:0001583	missense	10594	exon3			GGTCTCGAATGAT	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"PRP8 pre-mRNA processing factor 8 homolog (yeast)", "PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.211C>G	chr17.hg19:g.1586885G>C	ENSP00000460348:p.Arg71Gly	138.0	0.0	.		79.0	5.0	.	NM_006445	O14547|O75965	Missense_Mutation	SNP	ENST00000572621.1	hg19	CCDS11010.1	.	.	.	.	.	.	.	.	.	.	G	19.91	3.914983	0.72983	.	.	ENSG00000174231	ENST00000304992	T	0.44881	0.91	5.41	4.42	0.53409	Pre-mRNA-processing-splicing factor 8 (2);	0.000000	0.85682	D	0.000000	T	0.48295	0.1492	L	0.61218	1.895	0.80722	D	1	P	0.44241	0.829	P	0.45310	0.476	T	0.54510	-0.8283	10	0.72032	D	0.01	.	15.2921	0.73872	0.0:0.0:0.8586:0.1413	.	71	Q6P2Q9	PRP8_HUMAN	G	71	ENSP00000304350:R71G	ENSP00000304350:R71G	R	-	1	2	PRPF8	1533635	1.000000	0.71417	0.998000	0.56505	0.954000	0.61252	4.592000	0.61027	1.237000	0.43756	0.467000	0.42956	CGA	.	.	.	none		0.478	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2			C	1586885	G	C	1586885	3	2	195	1	0	0	0	0	1	0	0	0	12585	1066	37	4	6960	4	PRPF8	17	1586885	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08		1586885	79608325	111	11712											
ZZEF1	23140	hgsc.bcm.edu	37	chr17	3926086	3926086	+	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	caacttcagcaaatcggtctGaaggaaagtagcacggatct	14	8	10	9	2	3	1	1	1	2	0	4	3	3	3	0	3	3	3	0	3	5	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr17:3926086G>C	ENST00000381638.2	-	44	7253	c.7129C>G	c.(7129-7131)Cag>Gag	p.Q2377E		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	2377							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						AAATCGGTCTGAAGGAAAGTA	0.498																																					p.Q2377E		Atlas-SNP	.											.	ZZEF1	195	.	0			c.C7129G						PASS	.						95	85	88					17																	3926086		2203	4300	6503	SO:0001583	missense	23140	exon44			CGGTCTGAAGGAA	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.7129C>G	chr17.hg19:g.3926086G>C	ENSP00000371051:p.Gln2377Glu	79.0	0.0	.		40.0	12.0	.	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Missense_Mutation	SNP	ENST00000381638.2	hg19	CCDS11043.1	.	.	.	.	.	.	.	.	.	.	G	7.212	0.595598	0.13875	.	.	ENSG00000074755	ENST00000381638	T	0.19938	2.11	5.96	4.94	0.65067	.	0.473334	0.24301	N	0.039721	T	0.09598	0.0236	N	0.08118	0	0.27680	N	0.946471	B	0.02656	0.0	B	0.01281	0.0	T	0.15896	-1.0421	10	0.02654	T	1	-4.1226	13.6249	0.62159	0.0:0.1251:0.7598:0.1151	.	2377	O43149	ZZEF1_HUMAN	E	2377	ENSP00000371051:Q2377E	ENSP00000371051:Q2377E	Q	-	1	0	ZZEF1	3872835	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.220000	0.51207	2.832000	0.97577	0.655000	0.94253	CAG	.	.	.	none		0.498	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		C	3926086	G	C	3926086	3	2	195	1	0	0	0	0	1	0	0	0	18267	1299	45	4	1804	4	ZZEF1	17	3926086	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	2339201	3926086	77269124	112	11713											
MPRIP	23164	hgsc.bcm.edu	37	chr17	17046031	17046031	+	Frame_Shift_Del	DEL	C	C	-																															gtggggccctcaccatccagCgacacacgccagggccgcag																								rs146439071		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr17:17046031delC	ENST00000341712.4	+	8	987	c.987delC	c.(985-987)agcfs	p.S329fs	MPRIP_ENST00000395811.5_Frame_Shift_Del_p.S329fs|MPRIP_ENST00000444976.1_Frame_Shift_Del_p.S329fs|MPRIP_ENST00000395804.3_Frame_Shift_Del_p.S329fs			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	329	Interaction with F-actin. {ECO:0000250}.					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						CACCATCCAGCGACACACGCC	0.632																																					p.S329fs		Atlas-INDEL	.											.	MPRIP	87	.	0			c.986delG						PASS	.						85	77	80					17																	17046031		2203	4300	6503	SO:0001589	frameshift_variant	23164	exon8			.	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.987delC	chr17.hg19:g.17046031delC	ENSP00000342379:p.Ser329fs	106.0	0.0	0		55.0	16.0	0.290909	NM_015134	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Frame_Shift_Del	DEL	ENST00000341712.4	hg19	CCDS32578.1																																																																																			.	.	.	none		0.632	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134		-	17046031	C	-	17046031	7	5	195	1	0	1	0	1	0	0	0	0	9750	767	27	0	1017	0	MPRIP	17	17046031	Frame_Shift_Del	DEL	C	TCGA-HE-7130-01A-11D-1961-08	13119945	17046031	64149179	113	11714											
IKZF3	22806	hgsc.bcm.edu	37	chr17	37949078	37949078	+	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	tttcatattcattatattctCttgaatagctgtaagggatt	11	19	6	5	0	3	1	2	1	1	0	4	2	3	2	0	1	1	2	0	1	6	10			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr17:37949078C>T	ENST00000346872.3	-	4	333	c.272G>A	c.(271-273)aGa>aAa	p.R91K	IKZF3_ENST00000535189.1_Missense_Mutation_p.R57K|IKZF3_ENST00000377952.2_Intron|IKZF3_ENST00000377945.3_Missense_Mutation_p.R91K|IKZF3_ENST00000439016.2_Missense_Mutation_p.R91K|IKZF3_ENST00000394189.2_Intron|IKZF3_ENST00000439167.2_Missense_Mutation_p.R57K|IKZF3_ENST00000346243.3_Missense_Mutation_p.R91K|IKZF3_ENST00000377944.3_Intron|IKZF3_ENST00000467757.1_Missense_Mutation_p.R91K|IKZF3_ENST00000351680.3_Missense_Mutation_p.R91K|IKZF3_ENST00000350532.3_Missense_Mutation_p.R91K|IKZF3_ENST00000377958.2_Intron	NM_012481.4	NP_036613.2	Q9UKT9	IKZF3_HUMAN	IKAROS family zinc finger 3 (Aiolos)	91					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)	p.E92fs*29(1)		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)			ATTATATTCTCTTGAATAGCT	0.383																																					p.R91K		Atlas-SNP	.											.	IKZF3	79	.	1	Insertion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(1)	c.G272A						PASS	.						127	118	121					17																	37949078		2203	4300	6503	SO:0001583	missense	22806	exon4			TATTCTCTTGAAT	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.272G>A	chr17.hg19:g.37949078C>T	ENSP00000344544:p.Arg91Lys	86.0	0.0	.		88.0	12.0	.	NM_012481	B4DVV5|Q69BL6|Q69BL7|Q69BL8|Q69BL9|Q69BM0|Q69BM1|Q69BM2|Q69BM3|Q69BM5|Q8N574|Q8WWQ9|Q8WWR0|Q8WWR1|Q8WWR2|Q8WWR3	Missense_Mutation	SNP	ENST00000346872.3	hg19	CCDS11346.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.24|18.24	3.579420|3.579420	0.65878|0.65878	.|.	.|.	ENSG00000161405|ENSG00000161405	ENST00000439167;ENST00000439016|ENST00000488188;ENST00000346872;ENST00000377945;ENST00000535189;ENST00000351680;ENST00000346243;ENST00000350532;ENST00000467757	.|T;T;T;T;T;T;T	.|0.05855	.|3.45;3.52;3.43;3.48;3.52;3.38;4.4	5.96|5.96	5.96|5.96	0.96718|0.96718	.|.	.|0.000000	.|0.64402	.|D	.|0.000004	T|T	0.10594|0.10594	0.0259|0.0259	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	0.999992|0.999992	.|P;B;P;D;P;P;P;P;P	.|0.59357	.|0.794;0.317;0.864;0.985;0.57;0.93;0.864;0.798;0.786	.|B;B;P;D;B;P;P;B;B	.|0.70716	.|0.31;0.228;0.523;0.97;0.341;0.798;0.523;0.384;0.323	T|T	0.22661|0.22661	-1.0210|-1.0210	5|10	.|0.02654	.|T	.|1	-18.7806|-18.7806	10.1431|10.1431	0.42747|0.42747	0.0:0.7917:0.1376:0.0707|0.0:0.7917:0.1376:0.0707	.|.	.|91;57;91;91;91;91;91;57;91	.|Q9UKT9-13;Q9UKT9-7;Q9UKT9-6;Q9UKT9-5;Q9UKT9-4;Q9UKT9-2;Q9UKT9-3;Q9UKT9-8;Q9UKT9	.|.;.;.;.;.;.;.;.;IKZF3_HUMAN	K|K	45|91;91;91;57;91;91;91;91	.|ENSP00000344544:R91K;ENSP00000367180:R91K;ENSP00000438972:R57K;ENSP00000345622:R91K;ENSP00000341977:R91K;ENSP00000344471:R91K;ENSP00000420463:R91K	.|ENSP00000341977:R91K	E|R	-|-	1|2	0|0	IKZF3|IKZF3	35202604|35202604	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	1.918000|1.918000	0.40006|0.40006	2.832000|2.832000	0.97577|0.97577	0.655000|0.655000	0.94253|0.94253	GAG|AGA	.	.	.	none		0.383	IKZF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257004.2	NM_012481		T	37949078	C	T	37949078	3	4	195	1	0	0	0	0	1	0	0	0	7623	913	32	2	1277	2	IKZF3	17	37949078	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	20903047	37949078	43246132	114	11715											
HAP1	9001	hgsc.bcm.edu	37	chr17	39887800	39887800	+	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	tcctcatcctcaagagtgtcGagttgagaggcctggaggga	9	9	14	9	1	2	2	2	1	0	2	5	6	4	4	3	3	0	1	3	3	1	1			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr17:39887800G>A	ENST00000310778.5	-	6	1023	c.1014C>T	c.(1012-1014)ctC>ctT	p.L338L	JUP_ENST00000540235.1_Intron|HAP1_ENST00000347901.4_Silent_p.L338L|HAP1_ENST00000393939.2_Silent_p.L338L|RN7SL399P_ENST00000471648.2_RNA|HAP1_ENST00000341193.5_Silent_p.L346L			P54257	HAP1_HUMAN	huntingtin-associated protein 1	338	Glu-rich.|HAP1 N-terminal.				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)			CAAGAGTGTCGAGTTGAGAGG	0.557																																					p.L346L		Atlas-SNP	.											.	HAP1	48	.	0			c.C1038T						PASS	.						142	116	125					17																	39887800		2203	4300	6503	SO:0001819	synonymous_variant	9001	exon6			AGTGTCGAGTTGA	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.1014C>T	chr17.hg19:g.39887800G>A		151.0	0.0	.		103.0	66.0	.	NM_001079870	A8MQB5|O75358|Q59GK4|Q9H4G3|Q9HA98|Q9NY90	Silent	SNP	ENST00000310778.5	hg19																																																																																				.	.	.	none		0.557	HAP1-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000389619.1	NM_003949		A	39887800	G	A	39887800	2	1	195	1	0	0	0	0	0	0	0	1	6960	1045	37	1		1	HAP1	17	39887800	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	1938722	39887800	41307410	115	11716											
KIAA1267	284058	hgsc.bcm.edu	37	chr17	44248974	44248974	+	Frame_Shift_Del	DEL	C	C	-																															atgaagtgagagcccgttttCccccattgagggaagtggaa																										TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr17:44248974delC	ENST00000262419.6	-	2	1006	c.536delG	c.(535-537)ggafs	p.G179fs	KANSL1_ENST00000393476.3_5'UTR|KANSL1_ENST00000574590.1_Frame_Shift_Del_p.G179fs|KANSL1_ENST00000575318.1_Frame_Shift_Del_p.G179fs|KANSL1_ENST00000572904.1_Frame_Shift_Del_p.G179fs|KANSL1_ENST00000576248.1_5'Flank|KANSL1_ENST00000432791.1_Frame_Shift_Del_p.G179fs	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	179					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)											AGCCCGTTTTCCCCCATTGAG	0.473																																					p.G179fs		Atlas-INDEL	.											.	.	.	.	0			c.537delA						PASS	.						104	138	127					17																	44248974		2203	4300	6503	SO:0001589	frameshift_variant	284058	exon2			.	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.536delG	chr17.hg19:g.44248974delC	ENSP00000262419:p.Gly179fs	304.0	0.0	0		277.0	119.0	0.429603	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Frame_Shift_Del	DEL	ENST00000262419.6	hg19	CCDS11503.1																																																																																			.	.	.	none		0.473	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443		-	44248974	C	-	44248974	7	5	195	1	0	1	0	1	0	0	0	0	8226	855	30	0	2837	0	KIAA1267	17	44248974	Frame_Shift_Del	DEL	C	TCGA-HE-7130-01A-11D-1961-08	4361174	44248974	36946236	116	11717											
SKAP1	8631	hgsc.bcm.edu	37	chr17	46239837	46239837	+	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	ctttctgtccttaccttgctCagaatacggatgaggtcacc	8	13	8	12	1	3	2	2	1	1	1	4	3	4	3	3	2	3	1	3	2	3	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr17:46239837C>G	ENST00000336915.6	-	11	1041	c.972G>C	c.(970-972)ctG>ctC	p.L324L	SKAP1_ENST00000584924.1_Silent_p.L324L	NM_001075099.1|NM_003726.3	NP_001068567.1|NP_003717.3	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1	324	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				positive regulation of signal transduction (GO:0009967)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|SH2 domain binding (GO:0042169)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)	p.L324L(1)		large_intestine(1)|lung(10)|prostate(2)|skin(4)|urinary_tract(1)	18						TTACCTTGCTCAGAATACGGA	0.433																																					p.L324L		Atlas-SNP	.											SKAP1,bladder,carcinoma,0,1	SKAP1	41	.	1	Substitution - coding silent(1)	urinary_tract(1)	c.G972C						PASS	.						93	79	84					17																	46239837		2203	4300	6503	SO:0001819	synonymous_variant	8631	exon11			CTTGCTCAGAATA	Y11215	CCDS32674.1	17q21.32	2013-01-10	2006-09-28	2006-09-28		ENSG00000141293		"Pleckstrin homology (PH) domain containing"	15605	protein-coding gene	gene with protein product		604969	"src family associated phosphoprotein 1"	SCAP1		9195899	Standard	NM_003726		Approved	SKAP55	uc002ini.1	Q86WV1		ENST00000336915.6:c.972G>C	chr17.hg19:g.46239837C>G		58.0	0.0	.		70.0	6.0	.	NM_003726	D3DTV1|O15268	Silent	SNP	ENST00000336915.6	hg19	CCDS32674.1																																																																																			.	.	.	none		0.433	SKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443432.1	NM_003726		G	46239837	C	G	46239837	2	3	195	1	0	0	0	0	0	0	0	1	14368	813	29	4		4	SKAP1	17	46239837	Silent	SNP	C	TCGA-HE-7130-01A-11D-1961-08	1990863	46239837	34955373	117	11718											
KIF19	124602	hgsc.bcm.edu	37	chr17	72338804	72338804	+	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	gccaccaccaagagcctcatCgagggcgtcatctcaggcta	10	6	10	15	2	3	1	3	0	1	1	5	2	3	1	4	2	1	1	4	2	2	1	rs368432623		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr17:72338804C>G	ENST00000389916.4	+	4	405	c.267C>G	c.(265-267)atC>atG	p.I89M		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	89	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						AGAGCCTCATCGAGGGCGTCA	0.622																																					p.I89M		Atlas-SNP	.											.	KIF19	102	.	0			c.C267G						PASS	.						140	112	121					17																	72338804		2203	4300	6503	SO:0001583	missense	124602	exon4			CCTCATCGAGGGC	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.267C>G	chr17.hg19:g.72338804C>G	ENSP00000374566:p.Ile89Met	113.0	0.0	.		81.0	41.0	.	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Missense_Mutation	SNP	ENST00000389916.4	hg19	CCDS32718.2	.	.	.	.	.	.	.	.	.	.	C	18.38	3.611793	0.66558	.	.	ENSG00000196169	ENST00000551294;ENST00000389916	T;T	0.75821	-0.97;-0.97	5.5	-11.0	0.00169	Kinesin, motor domain (4);	.	.	.	.	T	0.77916	0.4202	M	0.79805	2.47	0.28548	N	0.91179	D;D;P;D	0.64830	0.99;0.981;0.93;0.994	D;D;P;D	0.67382	0.932;0.916;0.803;0.951	T	0.72581	-0.4250	9	0.87932	D	0	.	2.1205	0.03724	0.1636:0.208:0.163:0.4655	.	89;89;89;89	Q2TAC6;F8VW50;Q2TAC6-3;Q2TAC6-2	KIF19_HUMAN;.;.;.	M	89	ENSP00000449134:I89M;ENSP00000374566:I89M	ENSP00000374566:I89M	I	+	3	3	KIF19	69850399	0.000000	0.05858	0.008000	0.14137	0.981000	0.71138	-2.329000	0.01111	-1.540000	0.01730	0.456000	0.33151	ATC	.	.	.	alt		0.622	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209		G	72338804	C	G	72338804	3	3	195	1	0	0	0	0	1	0	0	0	8289	874	31	4	281	4	KIF19	17	72338804	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	26098967	72338804	8856406	118	11719											
AZI1	22994	hgsc.bcm.edu	37	chr17	79165116	79165116	+	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	cttccctcagctcctgttccCggttcagcagccacgcctcc	4	10	7	20	2	2	0	2	0	0	0	6	0	6	0	6	1	3	4	6	1	0	3	rs138682079		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr17:79165116C>A	ENST00000269392.4	-	22	2898	c.2651G>T	c.(2650-2652)cGg>cTg	p.R884L	AZI1_ENST00000374782.3_Missense_Mutation_p.R845L|AZI1_ENST00000450824.2_Missense_Mutation_p.R881L|AZI1_ENST00000575907.1_Missense_Mutation_p.R848L	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		884					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)			CTCCTGTTCCCGGTTCAGCAG	0.697																																					p.R881L		Atlas-SNP	.											.	AZI1	145	.	0			c.G2642T						PASS	.						68	66	67					17																	79165116		2203	4300	6503	SO:0001583	missense	22994	exon22			TGTTCCCGGTTCA																												ENST00000269392.4:c.2651G>T	chr17.hg19:g.79165116C>A	ENSP00000269392:p.Arg884Leu	205.0	0.0	.		130.0	8.0	.	NM_014984	A6NHI8|B2RN11|Q96F50	Missense_Mutation	SNP	ENST00000269392.4	hg19		.	.	.	.	.	.	.	.	.	.	C	35	5.440072	0.96168	.	.	ENSG00000141577	ENST00000450824;ENST00000374782;ENST00000269392	T;T;T	0.18338	2.22;2.26;2.23	4.22	4.22	0.49857	.	0.000000	0.64402	D	0.000001	T	0.40222	0.1108	M	0.64997	1.995	0.80722	D	1	D;D;D;D	0.89917	0.98;0.965;1.0;1.0	P;P;D;D	0.91635	0.814;0.814;0.999;0.999	T	0.36383	-0.9750	10	0.72032	D	0.01	-35.9331	16.7808	0.85563	0.0:1.0:0.0:0.0	.	881;884;845;881	B2RN10;Q9UPN4;Q9UPN4-3;Q9UPN4-2	.;AZI1_HUMAN;.;.	L	881;845;884	ENSP00000393583:R881L;ENSP00000363914:R845L;ENSP00000269392:R884L	ENSP00000269392:R884L	R	-	2	0	AZI1	76779711	1.000000	0.71417	0.999000	0.59377	0.984000	0.73092	3.686000	0.54685	2.190000	0.69967	0.491000	0.48974	CGG	.	C|1.000;T|0.000	.	alt		0.697	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1			A	79165116	C	A	79165116	3	1	195	1	0	0	0	0	1	0	0	0	1240	652	23	4	620	4	AZI1	17	79165116	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	6826312	79165116	2030094	119	11720											
TAF4B	6875	hgsc.bcm.edu	37	chr18	23866009	23866009	+	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	ctcaagccagtctgaaaagtCaattattgtttctggagcaa	13	12	8	8	0	4	1	2	1	2	0	4	2	4	2	1	1	2	2	1	1	6	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr18:23866009C>T	ENST00000269142.5	+	7	2134	c.1136C>T	c.(1135-1137)tCa>tTa	p.S379L	TAF4B_ENST00000400466.2_Missense_Mutation_p.S379L|TAF4B_ENST00000578121.1_Missense_Mutation_p.S379L	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	379					gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			TCTGAAAAGTCAATTATTGTT	0.463																																					p.S379L		Atlas-SNP	.											.	TAF4B	71	.	0			c.C1136T						PASS	.						100	97	98					18																	23866009		1925	4142	6067	SO:0001583	missense	6875	exon7			AAAAGTCAATTAT	Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"TATA box binding protein (TBP)-associated factor 4B"	601689	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.1136C>T	chr18.hg19:g.23866009C>T	ENSP00000269142:p.Ser379Leu	146.0	0.0	.		82.0	64.0	.	NM_005640	Q29YA4|Q29YA5	Missense_Mutation	SNP	ENST00000269142.5	hg19	CCDS42421.1	.	.	.	.	.	.	.	.	.	.	c	2.722	-0.266371	0.05754	.	.	ENSG00000141384	ENST00000418698;ENST00000269142;ENST00000400466	T;T;T	0.22945	1.93;1.93;1.93	5.35	4.47	0.54385	.	1.607940	0.03022	N	0.150849	T	0.16685	0.0401	N	0.08118	0	0.09310	N	1	B;B	0.13594	0.001;0.008	B;B	0.14578	0.001;0.011	T	0.23797	-1.0178	10	0.20519	T	0.43	0.3248	9.9174	0.41444	0.1569:0.6917:0.1514:0.0	.	379;379	Q92750;A4PBF7	TAF4B_HUMAN;.	L	379	ENSP00000389365:S379L;ENSP00000269142:S379L;ENSP00000383314:S379L	ENSP00000269142:S379L	S	+	2	0	TAF4B	22120007	0.028000	0.19301	0.092000	0.20876	0.014000	0.08584	2.845000	0.48254	1.228000	0.43614	0.558000	0.71614	TCA	.	.	.	none		0.463	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640		T	23866009	C	T	23866009	3	4	195	1	0	0	0	0	1	0	0	0	15539	838	29	2	1162	2	TAF4B	18	23866009	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08		23866009	54211239	120	11721											
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-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr19:879943G>C	ENST00000589119.1	-	7	1346	c.1347C>G	c.(1345-1347)caC>caG	p.H449Q	MED16_ENST00000395808.3_Missense_Mutation_p.H449Q|MED16_ENST00000269814.4_Missense_Mutation_p.H449Q|MED16_ENST00000325464.1_Missense_Mutation_p.H449Q|MED16_ENST00000312090.6_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	.	0			c.C1347G						PASS	.						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	chr19.hg19:g.879943G>C	ENSP00000464810:p.His449Gln	36.0	1.0	.		25.0	3.0	.	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Missense_Mutation	SNP	ENST00000589119.1	hg19	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	195	1	0	0	0	0	1	0	0	0	9441	1136	40	4	1322	4	MED16	19	879943	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08		879943	58249040	121	11722											
NCCRP1	342897	hgsc.bcm.edu	37	chr19	39691364	39691364	+	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	tgcggcggacacgggtgaccGactcctccgtgtctgtgcag	5	8	15	13	5	1	1	0	1	1	0	3	3	3	2	3	3	2	1	3	3	0	0			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr19:39691364G>A	ENST00000339852.4	+	6	818	c.796G>A	c.(796-798)Gac>Aac	p.D266N		NM_001001414.1	NP_001001414.1	Q6ZVX7	FBX50_HUMAN	non-specific cytotoxic cell receptor protein 1 homolog (zebrafish)	266	FBA. {ECO:0000255|PROSITE- ProRule:PRU00482}.				positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				kidney(1)|large_intestine(2)|liver(1)|lung(4)|ovary(1)|urinary_tract(1)	10						ACGGGTGACCGACTCCTCCGT	0.617																																					p.D266N	Melanoma(107;1207 1556 14956 29427 52130)	Atlas-SNP	.											.	NCCRP1	25	.	0			c.G796A						PASS	.						152	148	149					19																	39691364		2203	4300	6503	SO:0001583	missense	342897	exon6			GTGACCGACTCCT	AK123941, BC067874	CCDS12529.1	19q13.2	2013-07-31	2008-11-19		ENSG00000188505	ENSG00000188505			33739	protein-coding gene	gene with protein product		615901					Standard	NM_001001414		Approved	LOC342897, NCCRP-1, FBXO50	uc002okq.1	Q6ZVX7		ENST00000339852.4:c.796G>A	chr19.hg19:g.39691364G>A	ENSP00000342137:p.Asp266Asn	385.0	0.0	.		303.0	60.0	.	NM_001001414	Q6NVV5	Missense_Mutation	SNP	ENST00000339852.4	hg19	CCDS12529.1	.	.	.	.	.	.	.	.	.	.	G	9.500	1.103019	0.20632	.	.	ENSG00000188505	ENST00000339852	T	0.24350	1.86	4.96	4.96	0.65561	Galactose-binding domain-like (1);F-box associated (FBA) domain (2);	0.050217	0.85682	D	0.000000	T	0.22898	0.0553	N	0.11201	0.11	0.50313	D	0.999862	D	0.61697	0.99	P	0.57057	0.812	T	0.02728	-1.1118	10	0.07030	T	0.85	-30.2767	15.693	0.77469	0.0:0.0:1.0:0.0	.	266	Q6ZVX7	NCRP1_HUMAN	N	266	ENSP00000342137:D266N	ENSP00000342137:D266N	D	+	1	0	NCCRP1	44383204	1.000000	0.71417	0.955000	0.39395	0.144000	0.21451	4.099000	0.57755	2.319000	0.78375	0.484000	0.47621	GAC	.	.	.	none		0.617	NCCRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463829.1	NM_001001414		A	39691364	G	A	39691364	3	1	195	1	0	0	0	0	1	0	0	0	10220	1058	37	1	818	1	NCCRP1	19	39691364	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	38811421	39691364	19437619	122	11723											
C19orf47	126526	hgsc.bcm.edu	37	chr19	40832303	40832303	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgtggtgcctttgggcatgTtgatgacgtacttcccctcc	4	14	12	11	1	0	2	0	2	0	0	2	2	2	2	4	2	2	3	4	2	1	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr19:40832303T>C	ENST00000582783.1	-	7	653	c.641A>G	c.(640-642)aAc>aGc	p.N214S	C19orf47_ENST00000392035.2_Missense_Mutation_p.N147S	NM_001256440.1	NP_001243369.1	Q8N9M1	CS047_HUMAN	chromosome 19 open reading frame 47	214						nucleus (GO:0005634)				endometrium(5)|kidney(2)|lung(7)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	20			Lung(22;0.000636)			TTTGGGCATGTTGATGACGTA	0.662																																					p.N214S		Atlas-SNP	.											.	C19orf47	61	.	0			c.A641G						PASS	.						132	102	112					19																	40832303		2203	4300	6503	SO:0001583	missense	126526	exon7			GGCATGTTGATGA	AL834131	CCDS58662.1	19q13.2	2012-07-20			ENSG00000160392	ENSG00000160392			26723	protein-coding gene	gene with protein product						12477932	Standard	NM_001256440		Approved	FLJ36888	uc002oni.5	Q8N9M1	OTTHUMG00000179028	ENST00000582783.1:c.641A>G	chr19.hg19:g.40832303T>C	ENSP00000463159:p.Asn214Ser	84.0	0.0	.		55.0	26.0	.	NM_001256440	Q8IZ33|Q8N0V9	Missense_Mutation	SNP	ENST00000582783.1	hg19	CCDS58662.1	.	.	.	.	.	.	.	.	.	.	T	17.31	3.356248	0.61293	.	.	ENSG00000160392	ENST00000357884;ENST00000392035	.	.	.	5.54	4.44	0.53790	.	0.086607	0.85682	D	0.000000	T	0.51329	0.1668	L	0.59436	1.845	0.50632	D	0.999884	B	0.32753	0.383	B	0.33521	0.165	T	0.46803	-0.9165	9	0.14656	T	0.56	1.1855	13.0399	0.58893	0.0:0.0:0.1429:0.8571	.	214	Q8N9M1	CS047_HUMAN	S	214;147	.	ENSP00000350556:N214S	N	-	2	0	C19orf47	45524143	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.596000	0.54024	2.115000	0.64714	0.379000	0.24179	AAC	.	.	.	none		0.662	C19orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444488.1	NM_178830		C	40832303	T	C	40832303	3	2	195	1	0	0	0	0	1	0	0	0	1932	1725	60	3	639	3	C19orf47	19	40832303	Missense_Mutation	SNP	T	TCGA-HE-7130-01A-11D-1961-08	1140939	40832303	18296680	123	11724											
KLK10	5655	hgsc.bcm.edu	37	chr19	51518766	51518766	+	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	tcacactctttagggctcagGatagtgatgctggagcaggt	9	11	13	8	0	3	1	2	1	1	0	3	3	3	3	0	4	2	3	0	4	2	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr19:51518766G>T	ENST00000309958.3	-	5	803	c.585C>A	c.(583-585)atC>atA	p.I195I	KLK10_ENST00000391805.1_Silent_p.I195I|KLK10_ENST00000358789.3_Silent_p.I195I|CTC-518B2.12_ENST00000596286.1_RNA	NM_002776.4	NP_002767.2	O43240	KLK10_HUMAN	kallikrein-related peptidase 10	195	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cell cycle (GO:0007049)	extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	13		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00885)		TAGGGCTCAGGATAGTGATGC	0.567																																					p.I195I		Atlas-SNP	.											.	KLK10	32	.	0			c.C585A						PASS	.						273	256	262					19																	51518766		2203	4300	6503	SO:0001819	synonymous_variant	5655	exon5			GCTCAGGATAGTG	AF024605	CCDS12817.1	19q13	2011-03-07	2006-10-27			ENSG00000129451		"Kallikreins"	6358	protein-coding gene	gene with protein product		602673	"kallikrein 10"	PRSSL1		8764136, 9533035, 16800724, 16800723, 10675891	Standard	NM_145888		Approved	NES1	uc002pva.3	O43240		ENST00000309958.3:c.585C>A	chr19.hg19:g.51518766G>T		468.0	0.0	.		385.0	66.0	.	NM_145888	A6NC12|Q53YL3|Q99920|Q9GZW9	Silent	SNP	ENST00000309958.3	hg19	CCDS12817.1																																																																																			.	.	.	none		0.567	KLK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464337.2	NM_002776		T	51518766	G	T	51518766	2	4	195	1	0	0	0	0	0	0	0	1	8405	1164	41	4		4	KLK10	19	51518766	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	10686463	51518766	7610217	124	11725											
ZNF347	84671	hgsc.bcm.edu	37	chr19	53643875	53643875	+	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	acactcattgcatttgtaagGtttttttccagtatggattg	9	18	8	6	0	1	0	1	0	0	0	2	1	2	1	1	2	1	4	1	2	2	8			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr19:53643875G>T	ENST00000334197.7	-	5	2274	c.2206C>A	c.(2206-2208)Cct>Act	p.P736T	ZNF347_ENST00000601804.1_Intron|ZNF347_ENST00000601469.2_Missense_Mutation_p.P737T|ZNF347_ENST00000452676.2_Missense_Mutation_p.P737T	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	736					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		CATTTGTAAGGTTTTTTTCCA	0.423																																					p.P737T	Melanoma(64;205 1597 17324 45721)	Atlas-SNP	.											.	ZNF347	87	.	0			c.C2209A						PASS	.						167	155	159					19																	53643875		2203	4300	6503	SO:0001583	missense	84671	exon5			TGTAAGGTTTTTT	AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"Zinc fingers, C2H2-type", "-"	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.2206C>A	chr19.hg19:g.53643875G>T	ENSP00000334146:p.Pro736Thr	232.0	0.0	.		172.0	28.0	.	NM_001172675	B3KU77|B9EG59|G5E9N4|Q8TCN1	Missense_Mutation	SNP	ENST00000334197.7	hg19	CCDS33097.1	.	.	.	.	.	.	.	.	.	.	G	14.27	2.486058	0.44147	.	.	ENSG00000197937	ENST00000334197;ENST00000452676	T;T	0.16897	2.31;2.31	2.64	-0.0406	0.13871	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36054	0.0953	M	0.76574	2.34	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.981	T	0.11036	-1.0604	9	0.87932	D	0	.	6.5531	0.22446	0.3119:0.0:0.6881:0.0	.	737;736	G5E9N4;Q96SE7	.;ZN347_HUMAN	T	736;737	ENSP00000334146:P736T;ENSP00000405218:P737T	ENSP00000334146:P736T	P	-	1	0	ZNF347	58335687	0.348000	0.24861	0.000000	0.03702	0.251000	0.25915	1.732000	0.38146	-0.074000	0.12820	0.655000	0.94253	CCT	.	.	.	none		0.423	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		T	53643875	G	T	53643875	3	4	195	1	0	0	0	0	1	0	0	0	17873	1261	44	4	317	4	ZNF347	19	53643875	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	2125109	53643875	5485108	125	11726											
GALP	85569	hgsc.bcm.edu	37	chr19	56694579	56694579	+	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	gtttgccaaaccagagattgGaggtaaagccaggaaacaca	16	6	11	8	0	0	1	0	0	0	1	0	4	0	3	3	3	4	2	3	3	4	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr19:56694579G>C	ENST00000357330.2	+	5	375	c.293G>C	c.(292-294)gGa>gCa	p.G98A	GALP_ENST00000440823.1_3'UTR	NM_033106.3	NP_149097.1	Q9UBC7	GALP_HUMAN	galanin-like peptide	98					behavioral response to starvation (GO:0042595)|defense response to bacterium (GO:0042742)|neuropeptide signaling pathway (GO:0007218)|regulation of appetite (GO:0032098)|response to insulin (GO:0032868)	extracellular region (GO:0005576)				lung(4)	4		Colorectal(82;0.000147)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0507)		CCAGAGATTGGAGGTAAAGCC	0.507																																					p.G98A		Atlas-SNP	.											.	GALP	13	.	0			c.G293C						PASS	.						94	88	90					19																	56694579		2203	4300	6503	SO:0001583	missense	85569	exon5			AGATTGGAGGTAA	AF188493	CCDS12940.1, CCDS46202.1	19q13.42	2013-02-26	2007-08-24			ENSG00000197487		"Endogenous ligands"	24840	protein-coding gene	gene with protein product		611178				10601261	Standard	NM_033106		Approved		uc002qmo.1	Q9UBC7		ENST00000357330.2:c.293G>C	chr19.hg19:g.56694579G>C	ENSP00000349884:p.Gly98Ala	130.0	0.0	.		96.0	32.0	.	NM_033106	A1KXL3	Missense_Mutation	SNP	ENST00000357330.2	hg19	CCDS12940.1	.	.	.	.	.	.	.	.	.	.	G	11.60	1.687848	0.29962	.	.	ENSG00000197487	ENST00000357330	T	0.60797	0.16	2.07	0.986	0.19784	.	.	.	.	.	T	0.35508	0.0934	L	0.32530	0.975	0.80722	D	1	B	0.33266	0.404	B	0.18561	0.022	T	0.07597	-1.0764	9	0.25106	T	0.35	-6.1554	6.4753	0.22033	0.0:0.3481:0.6519:0.0	.	98	Q9UBC7	GALP_HUMAN	A	98	ENSP00000349884:G98A	ENSP00000349884:G98A	G	+	2	0	GALP	61386391	0.945000	0.32115	0.166000	0.22797	0.024000	0.10985	0.450000	0.21762	0.410000	0.25675	0.591000	0.81541	GGA	.	.	.	none		0.507	GALP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457832.1	NM_033106		C	56694579	G	C	56694579	3	2	195	1	0	0	0	0	1	0	0	0	6233	1174	41	4	307	4	GALP	19	56694579	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	3050704	56694579	2434404	126	11727											
USP29	57663	hgsc.bcm.edu	37	chr19	57641187	57641187	+	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	agtttttaggtcagtgtttaGaccagctgaaagaagacatg	13	12	11	5	0	1	4	1	1	0	3	1	4	1	4	1	1	1	3	1	1	4	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr19:57641187G>C	ENST00000254181.4	+	4	1598	c.1144G>C	c.(1144-1146)Gac>Cac	p.D382H	USP29_ENST00000598197.1_Missense_Mutation_p.D382H	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	382	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)		TCAGTGTTTAGACCAGCTGAA	0.368																																					p.D382H		Atlas-SNP	.											.	USP29	186	.	0			c.G1144C						PASS	.						58	58	58					19																	57641187		2203	4298	6501	SO:0001583	missense	57663	exon4			TGTTTAGACCAGC		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.1144G>C	chr19.hg19:g.57641187G>C	ENSP00000254181:p.Asp382His	102.0	0.0	.		106.0	42.0	.	NM_020903		Missense_Mutation	SNP	ENST00000254181.4	hg19	CCDS33124.1	.	.	.	.	.	.	.	.	.	.	G	14.62	2.588551	0.46110	.	.	ENSG00000131864	ENST00000254181	T	0.78595	-1.19	2.44	2.44	0.29823	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.617223	0.13416	U	0.389500	D	0.87688	0.6240	M	0.85630	2.765	0.29467	N	0.857365	D	0.89917	1.0	D	0.76575	0.988	T	0.80843	-0.1201	10	0.87932	D	0	-5.0112	11.0121	0.47669	0.0:0.0:1.0:0.0	.	382	Q9HBJ7	UBP29_HUMAN	H	382	ENSP00000254181:D382H	ENSP00000254181:D382H	D	+	1	0	USP29	62332999	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.330000	0.52068	1.646000	0.50622	0.591000	0.81541	GAC	.	.	.	none		0.368	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1			C	57641187	G	C	57641187	3	2	195	1	0	0	0	0	1	0	0	0	17071	942	33	4	1146	4	USP29	19	57641187	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	946608	57641187	1487796	127	11728											
CHD6	84181	hgsc.bcm.edu	37	chr20	40033767	40033767	+	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	gtggttgccatgggtggactGaggagtcccccaacaccaaa	10	7	13	11	0	0	1	0	1	0	0	1	3	1	3	4	4	2	1	4	4	2	1	rs559201396		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr20:40033767G>A	ENST00000373233.3	-	37	7791	c.7614C>T	c.(7612-7614)ctC>ctT	p.L2538L	CHD6_ENST00000480022.1_5'UTR	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	2538					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)				TGGGTGGACTGAGGAGTCCCC	0.557																																					p.L2538L		Atlas-SNP	.											.	CHD6	312	.	0			c.C7614T						PASS	.						90	83	85					20																	40033767		2203	4300	6503	SO:0001819	synonymous_variant	84181	exon37			TGGACTGAGGAGT	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.7614C>T	chr20.hg19:g.40033767G>A		170.0	0.0	.		156.0	23.0	.	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Silent	SNP	ENST00000373233.3	hg19	CCDS13317.1																																																																																			.	.	.	none		0.557	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			A	40033767	G	A	40033767	2	1	195	1	0	0	0	0	0	0	0	1	3331	1277	45	2		2	CHD6	20	40033767	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08		40033767	22991753	128	11729											
PTPN1	5770	hgsc.bcm.edu	37	chr20	49195155	49195155	+	Missense_Mutation	SNP	T	T	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	ccttctgtctggctgataccTgcctcttgctggtaaggagg	5	13	12	11	0	3	1	0	1	3	0	3	2	3	2	3	4	3	3	3	4	2	4			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr20:49195155T>G	ENST00000371621.3	+	6	865	c.691T>G	c.(691-693)Tgc>Ggc	p.C231G	PTPN1_ENST00000541713.1_Missense_Mutation_p.C158G|RP4-530I15.9_ENST00000431019.1_RNA	NM_001278618.1|NM_002827.2	NP_001265547.1|NP_002818.1	P18031	PTN1_HUMAN	protein tyrosine phosphatase, non-receptor type 1	231	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)	GGCTGATACCTGCCTCTTGCT	0.597																																					p.C231G		Atlas-SNP	.											.	PTPN1	36	.	0			c.T691G						PASS	.						47	48	48					20																	49195155		2203	4300	6503	SO:0001583	missense	5770	exon6			GATACCTGCCTCT		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.691T>G	chr20.hg19:g.49195155T>G	ENSP00000360683:p.Cys231Gly	77.0	0.0	.		56.0	18.0	.	NM_002827	Q5TGD8|Q9BQV9|Q9NQQ4	Missense_Mutation	SNP	ENST00000371621.3	hg19	CCDS13430.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.457273	0.84317	.	.	ENSG00000196396	ENST00000371621;ENST00000541713	D;D	0.83250	-1.7;-1.7	5.24	5.24	0.73138	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.85682	D	0.000000	D	0.91408	0.7289	M	0.84082	2.675	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.92757	0.6221	10	0.87932	D	0	.	15.139	0.72595	0.0:0.0:0.0:1.0	.	231	P18031	PTN1_HUMAN	G	231;158	ENSP00000360683:C231G;ENSP00000437732:C158G	ENSP00000360683:C231G	C	+	1	0	PTPN1	48628562	1.000000	0.71417	0.997000	0.53966	0.975000	0.68041	7.977000	0.88081	1.979000	0.57680	0.379000	0.24179	TGC	.	.	.	none		0.597	PTPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079694.2			G	49195155	T	G	49195155	3	3	195	1	0	0	0	0	1	0	0	0	12790	1580	55	5	713	5	PTPN1	20	49195155	Missense_Mutation	SNP	T	TCGA-HE-7130-01A-11D-1961-08	9161388	49195155	13830365	129	11730											
SERPIND1	3053	hgsc.bcm.edu	37	chr22	21140297	21140297	+	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	tccttttctgtctagaactcGagaagtgcttctgccgaaat	9	14	8	10	2	3	2	0	0	3	2	5	4	4	2	2	0	3	1	2	0	4	4	rs368023291		TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr22:21140297G>A	ENST00000215727.5	+	4	1452	c.1169G>A	c.(1168-1170)cGa>cAa	p.R390Q	PI4KA_ENST00000255882.6_Intron|SERPIND1_ENST00000406799.1_Missense_Mutation_p.R390Q|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	390					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)	TCTAGAACTCGAGAAGTGCTT	0.423																																					p.R390Q		Atlas-SNP	.											.	SERPIND1	92	.	0			c.G1169A						PASS	.	G	GLN/ARG,	0,4406		0,0,2203	130	134	132		1169,	5.3	1	22		132	1,8599	1.2+/-3.3	0,1,4299	no	missense,intron	SERPIND1,PI4KA	NM_000185.3,NM_058004.3	43,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,	390/500,	21140297	1,13005	2203	4300	6503	SO:0001583	missense	3053	exon4			GAACTCGAGAAGT	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.1169G>A	chr22.hg19:g.21140297G>A	ENSP00000215727:p.Arg390Gln	249.0	0.0	.		187.0	20.0	.	NM_000185	B2RAI1|D3DX34|Q6IBZ5	Missense_Mutation	SNP	ENST00000215727.5	hg19	CCDS13783.1	.	.	.	.	.	.	.	.	.	.	G	32	5.164332	0.94727	0.0	1.16E-4	ENSG00000099937	ENST00000215727;ENST00000406799	D;D	0.87650	-2.28;-2.28	5.28	5.28	0.74379	Serpin domain (3);	0.000000	0.85682	D	0.000000	D	0.93032	0.7782	M	0.73962	2.25	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.66979	0.948;0.948	D	0.92954	0.6383	10	0.56958	D	0.05	.	19.0957	0.93249	0.0:0.0:1.0:0.0	.	390;390	Q8IVC0;P05546	.;HEP2_HUMAN	Q	390	ENSP00000215727:R390Q;ENSP00000384050:R390Q	ENSP00000215727:R390Q	R	+	2	0	SERPIND1	19470297	1.000000	0.71417	0.988000	0.46212	0.855000	0.48748	8.835000	0.92100	2.755000	0.94549	0.655000	0.94253	CGA	.	.	.	weak		0.423	SERPIND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319961.1	NM_000185		A	21140297	G	A	21140297	3	1	195	1	0	0	0	0	1	0	0	0	14123	1058	37	1	1179	1	SERPIND1	22	21140297	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08		21140297	30164269	130	11731											
SERPIND1	3053	hgsc.bcm.edu	37	chr22	21140328	21140328	+	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	ctgccgaaattcaagctggaGaagaactacaatctagtgga	15	8	10	8	1	2	2	1	0	1	2	2	5	2	3	1	2	4	1	1	2	7	3			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr22:21140328G>A	ENST00000215727.5	+	4	1483	c.1200G>A	c.(1198-1200)gaG>gaA	p.E400E	PI4KA_ENST00000255882.6_Intron|SERPIND1_ENST00000406799.1_Silent_p.E400E|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	400					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)	TCAAGCTGGAGAAGAACTACA	0.448																																					p.E400E		Atlas-SNP	.											.	SERPIND1	92	.	0			c.G1200A						PASS	.						171	164	166					22																	21140328		2203	4300	6503	SO:0001819	synonymous_variant	3053	exon4			GCTGGAGAAGAAC	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.1200G>A	chr22.hg19:g.21140328G>A		254.0	0.0	.		199.0	24.0	.	NM_000185	B2RAI1|D3DX34|Q6IBZ5	Silent	SNP	ENST00000215727.5	hg19	CCDS13783.1																																																																																			.	.	.	none		0.448	SERPIND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319961.1	NM_000185		A	21140328	G	A	21140328	2	1	195	1	0	0	0	0	0	0	0	1	14123	933	33	2		2	SERPIND1	22	21140328	Silent	SNP	G	TCGA-HE-7130-01A-11D-1961-08	31	21140328	30164238	131	11732											
MCM5	4174	hgsc.bcm.edu	37	chr22	35806777	35806777	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccctgggaacagggttaccAtcatgggcatctactccatc	9	10	9	13	0	2	0	1	0	1	0	5	1	4	1	3	3	3	2	3	3	3	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr22:35806777A>G	ENST00000216122.4	+	7	947	c.793A>G	c.(793-795)Atc>Gtc	p.I265V	MCM5_ENST00000382011.5_Missense_Mutation_p.I222V	NM_006739.3	NP_006730.2	P33992	MCM5_HUMAN	minichromosome maintenance complex component 5	265					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29						CAGGGTTACCATCATGGGCAT	0.557																																					p.I265V		Atlas-SNP	.											.	MCM5	54	.	0			c.A793G						PASS	.						166	144	151					22																	35806777		2203	4300	6503	SO:0001583	missense	4174	exon7			GTTACCATCATGG		CCDS13915.1	22q13.1-q13.2	2007-04-04	2007-04-04		ENSG00000100297	ENSG00000100297			6948	protein-coding gene	gene with protein product		602696	"minichromosome maintenance deficient (S. cerevisiae) 5 (cell division cycle 46)", "MCM5 minichromosome maintenance deficient 5, cell division cycle 46 (S. cerevisiae)"	CDC46		8751386, 10591208	Standard	NM_006739		Approved		uc003anu.4	P33992	OTTHUMG00000150961	ENST00000216122.4:c.793A>G	chr22.hg19:g.35806777A>G	ENSP00000216122:p.Ile265Val	209.0	0.0	.		176.0	54.0	.	NM_006739	O60785|Q14578|Q9BTJ4|Q9BWL8	Missense_Mutation	SNP	ENST00000216122.4	hg19	CCDS13915.1	.	.	.	.	.	.	.	.	.	.	A	7.703	0.693600	0.15039	.	.	ENSG00000100297	ENST00000216122;ENST00000382011;ENST00000444582;ENST00000444778	T;T;T	0.03413	3.94;3.94;3.94	5.32	5.32	0.75619	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);	0.046124	0.85682	D	0.000000	T	0.02727	0.0082	N	0.11789	0.175	0.58432	D	0.999999	B;B;B;B	0.11235	0.004;0.004;0.004;0.004	B;B;B;B	0.17979	0.009;0.009;0.02;0.009	T	0.48115	-0.9063	10	0.08837	T	0.75	-32.0355	15.5601	0.76237	1.0:0.0:0.0:0.0	.	265;265;222;265	B1AHB0;Q53FG5;B1AHB1;P33992	.;.;.;MCM5_HUMAN	V	265;222;174;122	ENSP00000216122:I265V;ENSP00000371441:I222V;ENSP00000408705:I122V	ENSP00000216122:I265V	I	+	1	0	MCM5	34136777	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.001000	0.57046	2.142000	0.66516	0.459000	0.35465	ATC	.	.	.	none		0.557	MCM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320661.3			G	35806777	A	G	35806777	3	3	195	1	0	0	0	0	1	0	0	0	9397	217	8	3	815	3	MCM5	22	35806777	Missense_Mutation	SNP	A	TCGA-HE-7130-01A-11D-1961-08	14666449	35806777	15497789	132	11733											
MYH9	4627	hgsc.bcm.edu	37	chr22	36696256	36696256	+	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	cgcctcggtggtcaccttctCcagctgcagcttctgccggg	3	10	12	16	3	3	0	1	0	2	0	5	0	3	0	4	3	4	3	4	3	0	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chr22:36696256C>G	ENST00000216181.5	-	23	3123	c.2893G>C	c.(2893-2895)Gag>Cag	p.E965Q		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	965					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						GTCACCTTCTCCAGCTGCAGC	0.632			T	ALK	ALCL		"Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"		Hereditary Macrothrombocytopenia, MYH9-associated																												p.E965Q		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"myosin, heavy polypeptide 9, non-muscle"	yes	L	.	MYH9	225	.	0			c.G2893C						PASS	.						76	71	73					22																	36696256		2203	4300	6503	SO:0001583	missense	4627	exon23	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	CCTTCTCCAGCTG		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.2893G>C	chr22.hg19:g.36696256C>G	ENSP00000216181:p.Glu965Gln	131.0	0.0	.		113.0	50.0	.	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Missense_Mutation	SNP	ENST00000216181.5	hg19	CCDS13927.1	.	.	.	.	.	.	.	.	.	.	C	35	5.458931	0.96240	.	.	ENSG00000100345	ENST00000337818;ENST00000216181	D	0.92911	-3.13	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	D	0.97517	0.9187	H	0.96889	3.9	0.80722	D	1	D	0.62365	0.991	D	0.65773	0.938	D	0.98548	1.0635	10	0.87932	D	0	.	19.3857	0.94555	0.0:1.0:0.0:0.0	.	965	P35579	MYH9_HUMAN	Q	829;965	ENSP00000216181:E965Q	ENSP00000216181:E965Q	E	-	1	0	MYH9	35026202	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.781000	0.85668	2.665000	0.90641	0.655000	0.94253	GAG	.	.	.	none		0.632	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473		G	36696256	C	G	36696256	3	3	195	1	0	0	0	0	1	0	0	0	10049	864	30	4	3065	4	MYH9	22	36696256	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	889479	36696256	14608310	133	11734											
MAOB	4129	hgsc.bcm.edu	37	chrX	43655117	43655117	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcactcacttgaccagatcCgcccacaaatttcctctcct	9	11	3	18	1	3	2	2	1	1	1	6	2	5	2	5	0	0	0	5	0	1	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chrX:43655117C>T	ENST00000378069.4	-	7	784	c.637G>A	c.(637-639)Gga>Aga	p.G213R	MAOB_ENST00000487544.1_5'Flank|MAOB_ENST00000538942.1_Missense_Mutation_p.G197R|MAOB_ENST00000536181.1_Missense_Mutation_p.G197R	NM_000898.4	NP_000889.3	P27338	AOFB_HUMAN	monoamine oxidase B	213					negative regulation of serotonin secretion (GO:0014063)|positive regulation of dopamine metabolic process (GO:0045964)|response to aluminum ion (GO:0010044)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|primary amine oxidase activity (GO:0008131)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(2)|skin(5)	21					Amantadine(DB00915)|Amphetamine(DB00182)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Procaine(DB00721)|Rasagiline(DB01367)|Selegiline(DB01037)|Sertraline(DB01104)|Tranylcypromine(DB00752)|Zonisamide(DB00909)	TGACCAGATCCGCCCACAAAT	0.458																																					p.G213R		Atlas-SNP	.											.	MAOB	52	.	0			c.G637A						PASS	.						82	69	74					X																	43655117		2203	4300	6503	SO:0001583	missense	4129	exon7			CAGATCCGCCCAC		CCDS14261.1	Xp11.4-p11.3	2008-02-05			ENSG00000069535	ENSG00000069535	1.4.3.4		6834	protein-coding gene	gene with protein product		309860					Standard	NM_000898		Approved		uc004dfz.4	P27338	OTTHUMG00000021388	ENST00000378069.4:c.637G>A	chrX.hg19:g.43655117C>T	ENSP00000367309:p.Gly213Arg	138.0	0.0	.		125.0	46.0	.	NM_000898	B2R6R3|B7Z5H3|D3DWC3|Q7Z6S2	Missense_Mutation	SNP	ENST00000378069.4	hg19	CCDS14261.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.778441	0.90195	.	.	ENSG00000069535	ENST00000378069;ENST00000536181;ENST00000538942	T;T;T	0.25085	1.82;1.82;1.82	5.42	5.42	0.78866	Amine oxidase (1);	0.000000	0.85682	D	0.000000	T	0.67306	0.2879	H	0.96861	3.895	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.80054	-0.1543	10	0.87932	D	0	-15.4168	18.5254	0.90969	0.0:1.0:0.0:0.0	.	197;213	B7Z5H3;P27338	.;AOFB_HUMAN	R	213;197;197	ENSP00000367309:G213R;ENSP00000441613:G197R;ENSP00000442240:G197R	ENSP00000367309:G213R	G	-	1	0	MAOB	43540061	1.000000	0.71417	0.991000	0.47740	0.950000	0.60333	7.104000	0.77024	2.404000	0.81709	0.600000	0.82982	GGA	.	.	.	none		0.458	MAOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056303.1	NM_000898		T	43655117	C	T	43655117	3	4	195	1	0	0	0	0	1	0	0	0	9233	661	23	1	961	1	MAOB	23	43655117	Missense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08		43655117	111615443	134	11735											
KDM6A	7403	hgsc.bcm.edu	37	chrX	44870205	44870205	+	Splice_Site	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	tctttttcccttcctttacaGaatgctgcctttttatatgg	6	20	5	10	0	1	1	0	0	1	1	3	1	3	1	3	1	3	1	3	1	4	9			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chrX:44870205G>C	ENST00000377967.4	+	5	425		c.e5-1		KDM6A_ENST00000536777.1_Splice_Site|KDM6A_ENST00000382899.4_Splice_Site|KDM6A_ENST00000543216.1_Splice_Site	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A						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(10)|p.0?(6)|p.?(1)		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						TTCCTTTACAGAATGCTGCCT	0.299			"D, N, F, S"		"renal, oesophageal SCC, MM"																																.	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	.	17	No detectable mRNA/protein(10)|Whole gene deletion(6)|Unknown(1)	haematopoietic_and_lymphoid_tissue(11)|oesophagus(2)|breast(2)|pancreas(2)	c.385-1G>C						PASS	.						121	102	108					X																	44870205		2203	4299	6502	SO:0001630	splice_region_variant	7403	exon5			TTTACAGAATGCT	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.385-1G>C	chrX.hg19:g.44870205G>C		60.0	0.0	.		67.0	30.0	.	NM_021140	Q52LL9|Q5JVQ7	Splice_Site	SNP	ENST00000377967.4	hg19	CCDS14265.1	.	.	.	.	.	.	.	.	.	.	G	12.63	1.994801	0.35226	.	.	ENSG00000147050	ENST00000377967;ENST00000536777;ENST00000382899;ENST00000543216;ENST00000542299	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.2912	0.90131	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KDM6A	44755149	1.000000	0.71417	0.995000	0.50966	0.078000	0.17371	9.225000	0.95219	2.258000	0.74832	0.506000	0.49869	.	.	.	.	none		0.299	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140	Intron	C	44870205	G	C	44870205	5	2	195	1	0	0	0	0	0	0	1	0	8144	956	33	4	402	4	KDM6A	23	44870205	Splice_Site	SNP	G	TCGA-HE-7130-01A-11D-1961-08	1215088	44870205	110400355	135	11736											
KDM6A	7403	hgsc.bcm.edu	37	chrX	44969446	44969447	+	Frame_Shift_Del	DEL	AC	AC	-																															gaaaactttgtggtgctagaAcagtacaaaatggaggacct																										TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chrX:44969446_44969447delAC	ENST00000377967.4	+	28	4169_4170	c.4128_4129delAC	c.(4126-4131)gaacagfs	p.Q1377fs	KDM6A_ENST00000536777.1_Frame_Shift_Del_p.Q1332fs|KDM6A_ENST00000479423.1_3'UTR|KDM6A_ENST00000382899.4_Frame_Shift_Del_p.Q1384fs|KDM6A_ENST00000543216.1_Frame_Shift_Del_p.Q1298fs	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	1377					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)|p.Q1377*(1)		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						TGGTGCTAGAACAGTACAAAAT	0.386			"D, N, F, S"		"renal, oesophageal SCC, MM"																																p.1376_1376del	Colon(129;1273 1667 15230 27352 52914)	Atlas-INDEL	.		Rec	yes		X	Xp11.2	7403	"lysine (K)-specific demethylase 6A, UTX"		"E, L"	.	KDM6A	274	.	7	Whole gene deletion(6)|Substitution - Nonsense(1)	oesophagus(2)|breast(2)|pancreas(2)|urinary_tract(1)	c.4127_4128del						PASS	.																																			SO:0001589	frameshift_variant	7403	exon28			.	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.4128_4129delAC	chrX.hg19:g.44969446_44969447delAC	ENSP00000367203:p.Gln1377fs	79.0	0.0	0		106.0	36.0	0.339623	NM_021140	Q52LL9|Q5JVQ7	Frame_Shift_Del	DEL	ENST00000377967.4	hg19	CCDS14265.1																																																																																			.	.	.	none		0.386	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140		-	44969447	AC	-	44969446	7	5	195	1	0	1	0	1	0	0	0	0	8144	40	2	0	4238	0	KDM6A	23	44969446	Frame_Shift_Del	DEL	AC	TCGA-HE-7130-01A-11D-1961-08	99241	44969446	110301114	136	11737											
ERCC6L	54821	hgsc.bcm.edu	37	chrX	71426809	71426809	+	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	cagtagtttgtcttattaatGagtccttgaaaacctgtctt	10	17	7	7	0	2	2	0	2	2	0	3	2	3	2	2	0	1	2	2	0	5	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chrX:71426809G>C	ENST00000334463.3	-	2	1943	c.1808C>G	c.(1807-1809)tCa>tGa	p.S603*	PIN4_ENST00000423432.2_Intron|ERCC6L_ENST00000373657.1_Nonsense_Mutation_p.S480*	NM_017669.2	NP_060139.2	Q2NKX8	ERC6L_HUMAN	excision repair cross-complementation group 6-like	603	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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)					TCTTATTAATGAGTCCTTGAA	0.348																																					p.S603X		Atlas-SNP	.											.	ERCC6L	98	.	0			c.C1808G						PASS	.						101	99	99					X																	71426809		2203	4300	6503	SO:0001587	stop_gained	54821	exon2			ATTAATGAGTCCT	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.1808C>G	chrX.hg19:g.71426809G>C	ENSP00000334675:p.Ser603*	122.0	0.0	.		175.0	12.0	.	NM_017669	Q8NCI1|Q96H93|Q9NXQ8	Nonsense_Mutation	SNP	ENST00000334463.3	hg19	CCDS35329.1	.	.	.	.	.	.	.	.	.	.	G	42	9.316536	0.99135	.	.	ENSG00000186871	ENST00000373657;ENST00000334463	.	.	.	5.46	5.46	0.80206	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	-9.103	15.597	0.76590	0.0:0.0:1.0:0.0	.	.	.	.	X	480;603	.	ENSP00000334675:S603X	S	-	2	0	ERCC6L	71343534	1.000000	0.71417	0.937000	0.37676	0.994000	0.84299	7.739000	0.84976	2.279000	0.76181	0.594000	0.82650	TCA	.	.	.	none		0.348	ERCC6L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057174.2	NM_017669		C	71426809	G	C	71426809	4	2	195	1	0	0	0	0	0	1	0	0	5220	1294	45	4	1948	4	ERCC6L	23	71426809	Nonsense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	26457363	71426809	83843751	137	11738											
PHKA1	5255	hgsc.bcm.edu	37	chrX	71886083	71886083	+	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	aggcagggaaggaaaccactGagagtagactagcatcaacc	16	4	12	9	0	1	2	1	1	0	2	1	5	1	4	2	3	3	3	2	3	5	2			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chrX:71886083G>A	ENST00000373542.4	-	8	941	c.782C>T	c.(781-783)tCa>tTa	p.S261L	PHKA1_ENST00000339490.3_Missense_Mutation_p.S261L|PHKA1_ENST00000373539.3_Missense_Mutation_p.S261L|PHKA1_ENST00000541944.1_Missense_Mutation_p.S261L|PHKA1_ENST00000373545.3_Missense_Mutation_p.S261L	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	261					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)					GGAAACCACTGAGAGTAGACT	0.423																																					p.S261L		Atlas-SNP	.											.	PHKA1	129	.	0			c.C782T						PASS	.						109	91	97					X																	71886083		2203	4300	6503	SO:0001583	missense	5255	exon8			ACCACTGAGAGTA		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.782C>T	chrX.hg19:g.71886083G>A	ENSP00000362643:p.Ser261Leu	60.0	0.0	.		92.0	48.0	.	NM_001172436	B7ZL05|B7ZL07|Q2M3D7	Missense_Mutation	SNP	ENST00000373542.4	hg19	CCDS14421.1	.	.	.	.	.	.	.	.	.	.	G	35	5.514712	0.96402	.	.	ENSG00000067177	ENST00000373545;ENST00000373542;ENST00000541944;ENST00000339490;ENST00000373539	D;D;D;D;D	0.93811	-3.29;-3.29;-3.29;-3.29;-3.29	5.78	5.78	0.91487	Six-hairpin glycosidase (1);Six-hairpin glycosidase-like (1);Glycoside hydrolase 15-related (1);	0.059029	0.64402	D	0.000002	D	0.96349	0.8809	M	0.80746	2.51	0.58432	D	0.999999	P;D;D	0.67145	0.916;0.989;0.996	P;P;D	0.65773	0.515;0.897;0.938	D	0.95897	0.8912	10	0.42905	T	0.14	-12.5655	16.1536	0.81640	0.0:0.0:1.0:0.0	.	261;261;261	B7ZL07;P46020-2;P46020	.;.;KPB1_HUMAN	L	261	ENSP00000362646:S261L;ENSP00000362643:S261L;ENSP00000441251:S261L;ENSP00000342469:S261L;ENSP00000362640:S261L	ENSP00000342469:S261L	S	-	2	0	PHKA1	71802808	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.296000	0.96104	2.417000	0.82017	0.600000	0.82982	TCA	.	.	.	none		0.423	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1			A	71886083	G	A	71886083	3	1	195	1	0	0	0	0	1	0	0	0	11850	1294	45	2	2989	2	PHKA1	23	71886083	Missense_Mutation	SNP	G	TCGA-HE-7130-01A-11D-1961-08	459274	71886083	83384477	138	11739											
STAG2	10735	hgsc.bcm.edu	37	chrX	123202456	123202456	+	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	aacaaatgagagtattttgtCagatatgtcaacattacctg	15	13	7	6	0	2	2	2	1	0	2	2	3	2	2	1	0	3	1	1	0	6	5			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chrX:123202456C>T	ENST00000371160.1	+	24	2598	c.2308C>T	c.(2308-2310)Cag>Tag	p.Q770*	STAG2_ENST00000371145.3_Nonsense_Mutation_p.Q770*|STAG2_ENST00000354548.5_Nonsense_Mutation_p.Q701*|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Nonsense_Mutation_p.Q770*|STAG2_ENST00000371157.3_Nonsense_Mutation_p.Q770*|STAG2_ENST00000371144.3_Nonsense_Mutation_p.Q770*	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	770					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						AGTATTTTGTCAGATATGTCA	0.284																																					p.Q770X		Atlas-SNP	.											.	STAG2	309	.	0			c.C2308T						PASS	.						75	70	72					X																	123202456		2203	4285	6488	SO:0001587	stop_gained	10735	exon24			TTTTGTCAGATAT	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.2308C>T	chrX.hg19:g.123202456C>T	ENSP00000360202:p.Gln770*	122.0	0.0	.		183.0	57.0	.	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Nonsense_Mutation	SNP	ENST00000371160.1	hg19	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	C	41	8.670079	0.98908	.	.	ENSG00000101972	ENST00000218089;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	.	.	.	5.19	5.19	0.71726	.	0.185733	0.49305	D	0.000159	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	-2.5759	18.1116	0.89538	0.0:1.0:0.0:0.0	.	.	.	.	X	770;701;770;770;770;770	.	ENSP00000218089:Q770X	Q	+	1	0	STAG2	123030137	1.000000	0.71417	1.000000	0.80357	0.671000	0.39405	3.356000	0.52269	2.301000	0.77427	0.534000	0.68092	CAG	.	.	.	none		0.284	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		T	123202456	C	T	123202456	4	4	195	1	0	0	0	0	0	1	0	0	15255	827	29	2	2394	2	STAG2	23	123202456	Nonsense_Mutation	SNP	C	TCGA-HE-7130-01A-11D-1961-08	51316373	123202456	32068104	139	11740											
ODZ1	10178	hgsc.bcm.edu	37	chrX	123680889	123680889	+	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	cctggcagagaggacttataTaacagttgctttgttgacaa	12	12	10	7	0	0	2	0	1	0	1	0	4	0	3	1	2	2	4	1	2	4	6			TCGA-HE-7130-01A-11D-1961-08	TCGA-HE-7130-10A-01D-1962-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0f6da78c-86f4-41ec-b368-485fe4865ddb	e08a90e3-a3ba-48a4-9d47-d6d40602f0e1	g.chrX:123680889T>A	ENST00000371130.3	-	15	2549	c.2486A>T	c.(2485-2487)tAt>tTt	p.Y829F	TENM1_ENST00000422452.2_Missense_Mutation_p.Y829F	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	829					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)										AGGACTTATATAACAGTTGCT	0.403																																					p.Y829F		Atlas-SNP	.											.	.	.	.	0			c.A2486T						PASS	.						119	102	108					X																	123680889		2203	4300	6503	SO:0001583	missense	10178	exon15			CTTATATAACAGT	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.2486A>T	chrX.hg19:g.123680889T>A	ENSP00000360171:p.Tyr829Phe	132.0	0.0	.		201.0	112.0	.	NM_001163278	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	hg19	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	T	11.45	1.641329	0.29157	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	T;T	0.11169	2.8;2.8	5.32	5.32	0.75619	.	0.304797	0.31772	N	0.007082	T	0.05090	0.0136	N	0.08118	0	0.32290	N	0.566467	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.08055	0.003;0.001;0.002	T	0.23332	-1.0191	10	0.10902	T	0.67	.	9.7127	0.40256	0.1566:0.0:0.0:0.8434	.	828;829;829	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	F	829	ENSP00000360171:Y829F;ENSP00000403954:Y829F	ENSP00000360171:Y829F	Y	-	2	0	ODZ1	123508570	1.000000	0.71417	0.954000	0.39281	0.787000	0.44495	3.654000	0.54453	1.955000	0.56771	0.481000	0.45027	TAT	.	.	.	none		0.403	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		A	123680889	T	A	123680889	3	1	195	1	0	0	0	0	1	0	0	0	10841	1406	49	5	5784	5	ODZ1	23	123680889	Missense_Mutation	SNP	T	TCGA-HE-7130-01A-11D-1961-08	478433	123680889	31589671	140	11741											
AGRN	375790	hgsc.bcm.edu	37	chr1	957703	957703	+	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	atctgtgacaaccaggtgtcCactggggacaccaggatctt	10	9	11	11	0	2	1	0	1	2	0	3	3	3	3	3	4	1	0	3	4	1	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr1:957703C>A	ENST00000379370.2	+	2	374	c.324C>A	c.(322-324)tcC>tcA	p.S108S		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	108	NtA. {ECO:0000255|PROSITE- ProRule:PRU00443}.				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)		ACCAGGTGTCCACTGGGGACA	0.602																																					p.S108S		Atlas-SNP	.											.	AGRN	110	.	0			c.C324A						PASS	.						131	137	135					1																	957703		2203	4300	6503	SO:0001819	synonymous_variant	375790	exon2			GGTGTCCACTGGG	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.324C>A	chr1.hg19:g.957703C>A		160.0	0.0	.		216.0	38.0	.	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Silent	SNP	ENST00000379370.2	hg19	CCDS30551.1																																																																																			.	.	.	none		0.602	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576		A	957703	C	A	957703	2	1	196	1	0	0	0	0	0	0	0	1	397	581	21	4		4	AGRN	1	957703	Silent	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10		957703	248292918	1	11742											
OTUD3	23252	hgsc.bcm.edu	37	chr1	20233031	20233031	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttggaaatcagggcttaaaTgaaggcaggaccgaaaacaa	17	7	11	6	1	1	1	1	1	0	0	1	4	1	3	1	4	1	2	1	4	7	2			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr1:20233031T>C	ENST00000375120.3	+	7	943	c.942T>C	c.(940-942)aaT>aaC	p.N314N		NM_015207.1	NP_056022.1	Q5T2D3	OTUD3_HUMAN	OTU deubiquitinase 3	314					protein K11-linked deubiquitination (GO:0035871)|protein K6-linked deubiquitination (GO:0044313)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|kidney(2)|large_intestine(4)|lung(1)|skin(1)	9		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000276)|Lung NSC(340;0.000338)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.12e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000142)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.000408)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		AGGGCTTAAATGAAGGCAGGA	0.488																																					p.N314N		Atlas-SNP	.											.	OTUD3	25	.	0			c.T942C						PASS	.						107	112	110					1																	20233031		1980	4166	6146	SO:0001819	synonymous_variant	23252	exon7			CTTAAATGAAGGC	AB007928	CCDS41279.1	1p36.13	2014-02-24	2014-02-24		ENSG00000169914	ENSG00000169914		"OTU domain containing"	29038	protein-coding gene	gene with protein product		611758	"OTU domain containing 3"			9455484, 23827681	Standard	NM_015207		Approved	KIAA0459, DUBA4	uc001bcs.4	Q5T2D3	OTTHUMG00000002696	ENST00000375120.3:c.942T>C	chr1.hg19:g.20233031T>C		136.0	0.0	.		138.0	23.0	.	NM_015207	O75047	Silent	SNP	ENST00000375120.3	hg19	CCDS41279.1																																																																																			.	.	.	none		0.488	OTUD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007655.1			C	20233031	T	C	20233031	2	2	196	1	0	0	0	0	0	0	0	1	11320	1461	51	3		3	OTUD3	1	20233031	Silent	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10	19275328	20233031	229017590	2	11743											
KANK4	163782	hgsc.bcm.edu	37	chr1	62739262	62739262	+	Missense_Mutation	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	ggcctccttcctgttcagtgCctgcttcttcaatcctgagt	4	15	8	14	0	3	1	2	1	1	0	6	1	6	1	5	1	2	2	5	1	1	4			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr1:62739262C>T	ENST00000371153.4	-	3	1892	c.1514G>A	c.(1513-1515)gGc>gAc	p.G505D	KANK4_ENST00000354381.3_Intron|KANK4_ENST00000371150.1_5'Flank	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	505						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						CTGTTCAGTGCCTGCTTCTTC	0.602																																					p.G505D		Atlas-SNP	.											.	KANK4	135	.	0			c.G1514A						PASS	.						74	76	75					1																	62739262		2203	4300	6503	SO:0001583	missense	163782	exon3			TCAGTGCCTGCTT	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.1514G>A	chr1.hg19:g.62739262C>T	ENSP00000360195:p.Gly505Asp	96.0	0.0	.		133.0	18.0	.	NM_181712	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Missense_Mutation	SNP	ENST00000371153.4	hg19	CCDS620.1	.	.	.	.	.	.	.	.	.	.	C	6.119	0.390267	0.11581	.	.	ENSG00000132854	ENST00000371153	T	0.45668	0.89	5.0	-4.67	0.03319	.	0.629621	0.13219	N	0.404541	T	0.18173	0.0436	N	0.20685	0.6	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24333	-1.0163	10	0.14656	T	0.56	-0.895	4.4402	0.11570	0.4045:0.2134:0.0:0.382	.	505	Q5T7N3	KANK4_HUMAN	D	505	ENSP00000360195:G505D	ENSP00000360195:G505D	G	-	2	0	KANK4	62511850	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.315000	0.08081	-0.487000	0.06735	-0.880000	0.02959	GGC	.	.	.	none		0.602	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712		T	62739262	C	T	62739262	3	4	196	1	0	0	0	0	1	0	0	0	7986	739	26	2	1505	2	KANK4	1	62739262	Missense_Mutation	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10	42506231	62739262	186511359	3	11744											
SYDE2	84144	hgsc.bcm.edu	37	chr1	85648463	85648463	+	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	caggtgagtctccatcactaAggtaaccacctttgcaggaa	12	9	9	11	0	2	1	1	1	1	0	3	2	2	2	3	3	2	2	3	3	3	3			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr1:85648463A>T	ENST00000341460.5	-	3	1911	c.1862T>A	c.(1861-1863)cTt>cAt	p.L621H		NM_032184.1	NP_115560.1	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	621					activation of Rho GTPase activity (GO:0032862)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	20				all cancers(265;0.0126)|Epithelial(280;0.0336)		TCCATCACTAAGGTAACCACC	0.378																																					p.L621H		Atlas-SNP	.											.	SYDE2	135	.	0			c.T1862A						PASS	.						86	80	82					1																	85648463		1853	4086	5939	SO:0001583	missense	84144	exon3			TCACTAAGGTAAC	AL834286	CCDS44169.1	1p22.3	2008-02-05		2005-08-09	ENSG00000097096	ENSG00000097096			25841	protein-coding gene	gene with protein product							Standard	NM_032184		Approved	FLJ13815	uc009wcm.3	Q5VT97	OTTHUMG00000009956	ENST00000341460.5:c.1862T>A	chr1.hg19:g.85648463A>T	ENSP00000340594:p.Leu621His	85.0	0.0	.		84.0	13.0	.	NM_032184	Q5VT96|Q8NDB8|Q9H8A6	Missense_Mutation	SNP	ENST00000341460.5	hg19	CCDS44169.1	.	.	.	.	.	.	.	.	.	.	A	18.98	3.737544	0.69304	.	.	ENSG00000097096	ENST00000341460	T	0.25749	1.78	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.46502	0.1396	M	0.81942	2.565	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.54125	-0.8340	10	0.87932	D	0	.	15.6946	0.77484	1.0:0.0:0.0:0.0	.	621;621	Q5VT97;Q5VT97-2	SYDE2_HUMAN;.	H	621	ENSP00000340594:L621H	ENSP00000340594:L621H	L	-	2	0	SYDE2	85421051	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.923000	0.92808	2.116000	0.64780	0.454000	0.30748	CTT	.	.	.	none		0.378	SYDE2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127989.2			T	85648463	A	T	85648463	3	4	196	1	0	0	0	0	1	0	0	0	15448	72	3	5	1742	5	SYDE2	1	85648463	Missense_Mutation	SNP	A	TCGA-HE-A5NF-01A-11D-A26P-10	22909201	85648463	163602158	4	11745											
NTRK1	4914	hgsc.bcm.edu	37	chr1	156851384	156851384	+	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	tcaaggatgtgcacgcccggCtgcaagccctggcccaggca	8	5	13	15	2	1	0	1	0	0	0	1	1	1	1	3	4	3	4	3	4	2	0			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr1:156851384C>T	ENST00000524377.1	+	17	2382	c.2341C>T	c.(2341-2343)Ctg>Ttg	p.L781L	NTRK1_ENST00000368196.3_Silent_p.L775L|NTRK1_ENST00000392302.2_Silent_p.L745L|NTRK1_ENST00000358660.3_Silent_p.L778L|NTRK1_ENST00000531606.1_3'UTR	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	781	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|axon guidance (GO:0007411)|axonogenesis involved in innervation (GO:0060385)|B cell differentiation (GO:0030183)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to nicotine (GO:0071316)|circadian rhythm (GO:0007623)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|developmental programmed cell death (GO:0010623)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory nerve development (GO:0021553)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to hydrostatic pressure (GO:0051599)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|Sertoli cell development (GO:0060009)|small GTPase mediated signal transduction (GO:0007264)|sympathetic nervous system development (GO:0048485)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	74	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Amitriptyline(DB00321)|Imatinib(DB00619)|Regorafenib(DB08896)	GCACGCCCGGCTGCAAGCCCT	0.697			T	"TPM3, TPR, TFG"	papillary thyroid					TSP Lung(10;0.080)																											p.L781L		Atlas-SNP	.		Dom	yes		1	1q21-q22	4914	"neurotrophic tyrosine kinase, receptor, type 1"		E	.	NTRK1	287	.	0			c.C2341T						PASS	.						23	24	24					1																	156851384		2202	4297	6499	SO:0001819	synonymous_variant	4914	exon17			GCCCGGCTGCAAG	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.2341C>T	chr1.hg19:g.156851384C>T		18.0	0.0	.		19.0	4.0	.	NM_002529	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Silent	SNP	ENST00000524377.1	hg19	CCDS1161.1																																																																																			.	.	.	none		0.697	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1	NM_002529		T	156851384	C	T	156851384	2	4	196	1	0	0	0	0	0	0	0	1	10713	796	28	2		2	NTRK1	1	156851384	Silent	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10	71202921	156851384	92399237	5	11746											
ARHGEF4	50649	hgsc.bcm.edu	37	chr2	131801154	131801154	+	Frame_Shift_Del	DEL	A	A	-																															accagctcatctactgtaagAaggtaccagagctgctctgc																										TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr2:131801154delA	ENST00000326016.5	+	11	2116	c.1597delA	c.(1597-1599)aagfs	p.K533fs	ARHGEF4_ENST00000392953.3_Frame_Shift_Del_p.K533fs|ARHGEF4_ENST00000525839.1_Frame_Shift_Del_p.K533fs|ARHGEF4_ENST00000409303.1_Frame_Shift_Del_p.K473fs|ARHGEF4_ENST00000355771.3_Frame_Shift_Del_p.K462fs|ARHGEF4_ENST00000428230.2_Intron	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	533	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein domain specific binding (GO:0019904)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(4)	29		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		CTACTGTAAGAAGGTACCAGA	0.572																																					p.K532fs		Atlas-Indel,Pindel	.											.	ARHGEF4	89	.	0			c.1596delG						PASS	.						97	87	90					2																	131801154		2203	4300	6503	SO:0001589	frameshift_variant	50649	exon11			.	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.1597delA	chr2.hg19:g.131801154delA	ENSP00000316845:p.Lys533fs	126.0	0.0	0		202.0	54.0	0.267327	NM_032995	Q9HDC6|Q9UPP0	Frame_Shift_Del	DEL	ENST00000326016.5	hg19	CCDS2165.1																																																																																			.	.	.	none		0.572	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254554.4			-	131801154	A	-	131801154	7	5	196	1	0	1	0	1	0	0	0	0	908	247	9	0	1631	0	ARHGEF4	2	131801154	Frame_Shift_Del	DEL	A	TCGA-HE-A5NF-01A-11D-A26P-10		131801154	111398219	6	11747											
ERMN	57471	hgsc.bcm.edu	37	chr2	158178038	158178038	+	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	ttaaattctatcactcgaacTtcatcttcatcattattgca	12	17	2	10	1	6	0	4	0	2	0	7	1	6	0	0	0	2	1	0	0	5	7			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr2:158178038T>A	ENST00000410096.1	-	3	891	c.600A>T	c.(598-600)gaA>gaT	p.E200D	ERMN_ENST00000397283.2_Missense_Mutation_p.E213D|ERMN_ENST00000420719.2_Missense_Mutation_p.E180D|ERMN_ENST00000535935.1_Missense_Mutation_p.E94D	NM_020711.1	NP_065762.1	Q8TAM6	ERMIN_HUMAN	ermin, ERM-like protein	200					actin filament organization (GO:0007015)|morphogenesis of a branching structure (GO:0001763)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|internode region of axon (GO:0033269)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|paranode region of axon (GO:0033270)				endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12						TCACTCGAACTtcatcttcat	0.383																																					p.E213D		Atlas-SNP	.											.	ERMN	31	.	0			c.A639T						PASS	.						122	118	119					2																	158178038		1908	4131	6039	SO:0001583	missense	57471	exon4			TCGAACTTCATCT	AB033015	CCDS42764.1, CCDS46431.1	2q24	2008-02-05	2008-01-15	2008-01-15	ENSG00000136541	ENSG00000136541			29208	protein-coding gene	gene with protein product	"juxtanodin", "ermin"	610072	"KIAA1189"	KIAA1189		16051705, 16421295	Standard	NM_020711		Approved	JN, ERMIN	uc002tzi.3	Q8TAM6	OTTHUMG00000153843	ENST00000410096.1:c.600A>T	chr2.hg19:g.158178038T>A	ENSP00000387047:p.Glu200Asp	61.0	0.0	.		73.0	12.0	.	NM_001009959	B4DKA6|Q9ULN1	Missense_Mutation	SNP	ENST00000410096.1	hg19	CCDS46431.1	.	.	.	.	.	.	.	.	.	.	T	13.62	2.290199	0.40494	.	.	ENSG00000136541	ENST00000410096;ENST00000397283;ENST00000535935;ENST00000420719	.	.	.	5.81	4.66	0.58398	.	0.162184	0.43416	D	0.000573	T	0.48021	0.1477	L	0.36672	1.1	0.28039	N	0.933847	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.66602	0.945;0.945;0.945	T	0.37549	-0.9701	9	0.38643	T	0.18	.	8.1808	0.31309	0.0:0.1976:0.0:0.8024	.	180;213;200	B4DIZ1;Q8TAM6-2;Q8TAM6	.;.;ERMIN_HUMAN	D	200;213;94;180	.	ENSP00000380453:E213D	E	-	3	2	ERMN	157886284	0.998000	0.40836	1.000000	0.80357	0.979000	0.70002	0.434000	0.21494	1.031000	0.39867	0.533000	0.62120	GAA	.	.	.	none		0.383	ERMN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332659.1	NM_001009959		A	158178038	T	A	158178038	3	1	196	1	0	0	0	0	1	0	0	0	5237	1606	56	5	258	5	ERMN	2	158178038	Missense_Mutation	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10	26376884	158178038	85021335	7	11748											
UBR3	130507	hgsc.bcm.edu	37	chr2	170762609	170762609	+	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	ctcagacctactatgctgccTttgctgctgaacttgaggcc	7	12	9	13	0	1	3	1	2	0	1	1	3	1	3	3	1	6	3	3	1	3	4			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr2:170762609T>A	ENST00000272793.5	+	10	1764	c.1714T>A	c.(1714-1716)Ttt>Att	p.F572I	UBR3_ENST00000418381.1_Missense_Mutation_p.F572I			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	572					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						CTATGCTGCCTTTGCTGCTGA	0.388																																					p.F572I		Atlas-SNP	.											.	UBR3	182	.	0			c.T1714A						PASS	.						116	103	107					2																	170762609		692	1591	2283	SO:0001583	missense	130507	exon10			GCTGCCTTTGCTG	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.1714T>A	chr2.hg19:g.170762609T>A	ENSP00000272793:p.Phe572Ile	73.0	0.0	.		101.0	29.0	.	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Missense_Mutation	SNP	ENST00000272793.5	hg19		.	.	.	.	.	.	.	.	.	.	T	34	5.361453	0.95877	.	.	ENSG00000144357	ENST00000272793;ENST00000442603;ENST00000418381	T;T	0.58060	0.36;0.36	5.58	5.58	0.84498	.	.	.	.	.	T	0.64316	0.2587	L	0.43923	1.385	0.80722	D	1	D	0.57899	0.981	D	0.69824	0.966	T	0.60835	-0.7184	9	0.30854	T	0.27	.	15.7431	0.77918	0.0:0.0:0.0:1.0	.	572	Q6ZT12	UBR3_HUMAN	I	572	ENSP00000272793:F572I;ENSP00000396068:F572I	ENSP00000272793:F572I	F	+	1	0	UBR3	170470855	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.040000	0.89188	2.116000	0.64780	0.482000	0.46254	TTT	.	.	.	none		0.388	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070		A	170762609	T	A	170762609	3	1	196	1	0	0	0	0	1	0	0	0	16915	1609	56	5	1752	5	UBR3	2	170762609	Missense_Mutation	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10	12584571	170762609	72436764	8	11749											
OBSL1	23363	hgsc.bcm.edu	37	chr2	220416332	220416332	+	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	gtcctcaggtcgaacgtcatGgatgaccaggctgtgggtgg	7	9	16	9	2	2	1	2	1	0	0	4	3	3	2	2	5	1	1	2	5	1	0			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr2:220416332G>T	ENST00000404537.1	-	20	5658	c.5602C>A	c.(5602-5604)Cat>Aat	p.H1868N	OBSL1_ENST00000265318.4_3'UTR|OBSL1_ENST00000373876.1_Missense_Mutation_p.H1776N|MIR3132_ENST00000581997.1_RNA	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	1868	Ig-like 14.				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)		CGAACGTCATGGATGACCAGG	0.657																																					p.H1868N		Atlas-SNP	.											.	OBSL1	120	.	0			c.C5602A						PASS	.						32	37	36					2																	220416332		2086	4208	6294	SO:0001583	missense	23363	exon20			CGTCATGGATGAC	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.5602C>A	chr2.hg19:g.220416332G>T	ENSP00000385636:p.His1868Asn	151.0	0.0	.		209.0	53.0	.	NM_015311	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Missense_Mutation	SNP	ENST00000404537.1	hg19	CCDS46520.1	.	.	.	.	.	.	.	.	.	.	G	13.23	2.174528	0.38413	.	.	ENSG00000124006	ENST00000404537;ENST00000373876	T;T	0.65916	-0.18;-0.18	5.32	3.38	0.38709	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.53449	0.1797	L	0.28344	0.845	0.80722	D	1	B	0.27192	0.171	B	0.41691	0.364	T	0.43798	-0.9369	9	0.21540	T	0.41	.	9.4425	0.38677	0.0:0.1395:0.5724:0.2881	.	1868	O75147	OBSL1_HUMAN	N	1868;1776	ENSP00000385636:H1868N;ENSP00000362983:H1776N	ENSP00000362983:H1776N	H	-	1	0	OBSL1	220124576	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.056000	0.57448	1.220000	0.43490	0.655000	0.94253	CAT	.	.	.	none		0.657	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1			T	220416332	G	T	220416332	3	4	196	1	0	0	0	0	1	0	0	0	10820	1348	47	4	96	4	OBSL1	2	220416332	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	49653723	220416332	22783041	9	11750											
SNED1	25992	hgsc.bcm.edu	37	chr2	242026825	242026825	+	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	aggtataaaagagtctaccgAgttcaccaagacatctgctt	14	10	8	9	1	3	2	1	0	2	2	3	3	3	2	2	1	2	3	2	1	5	5			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr2:242026825A>T	ENST00000310397.8	+	30	4140	c.4140A>T	c.(4138-4140)cgA>cgT	p.R1380R	SNED1_ENST00000342631.6_Silent_p.R1347R|SNED1_ENST00000405547.3_Intron|MTERFD2_ENST00000464344.2_Intron	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	1380					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)		GAGTCTACCGAGTTCACCAAG	0.488																																					p.R1380R		Atlas-SNP	.											.	SNED1	76	.	0			c.A4140T						PASS	.						50	46	47					2																	242026825		1886	4111	5997	SO:0001819	synonymous_variant	25992	exon30			CTACCGAGTTCAC	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.4140A>T	chr2.hg19:g.242026825A>T		151.0	0.0	.		196.0	70.0	.	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Silent	SNP	ENST00000310397.8	hg19	CCDS46562.1																																																																																			.	.	.	none		0.488	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482		T	242026825	A	T	242026825	2	4	196	1	0	0	0	0	0	0	0	1	14858	291	11	5		5	SNED1	2	242026825	Silent	SNP	A	TCGA-HE-A5NF-01A-11D-A26P-10	21610493	242026825	1172548	10	11751											
SRGAP3	9901	hgsc.bcm.edu	37	chr3	9100033	9100033	+	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	cttgtcacttcgggaatccaGgttgtccactgcattctcaa	8	13	8	12	1	2	0	2	0	1	0	6	1	4	1	2	2	1	2	2	2	2	4			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr3:9100033G>T	ENST00000383836.3	-	7	1352	c.925C>A	c.(925-927)Ctg>Atg	p.L309M	SRGAP3_ENST00000433332.3_5'UTR|SRGAP3_ENST00000360413.3_Missense_Mutation_p.L309M	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	309	F-BAR domain.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)		SRGAP3/RAF1(6)	breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		CGGGAATCCAGGTTGTCCACT	0.552			T	RAF1	pilocytic astrocytoma																																p.L309M		Atlas-SNP	.		Dom	yes		3	3p25.3	9901	SLIT-ROBO Rho GTPase activating protein 3		M	.	SRGAP3	146	.	0			c.C925A						PASS	.						246	203	218					3																	9100033		2203	4300	6503	SO:0001583	missense	9901	exon7			AATCCAGGTTGTC	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.925C>A	chr3.hg19:g.9100033G>T	ENSP00000373347:p.Leu309Met	173.0	0.0	.		178.0	29.0	.	NM_014850	Q8IX13|Q8IZV8	Missense_Mutation	SNP	ENST00000383836.3	hg19	CCDS2572.1	.	.	.	.	.	.	.	.	.	.	G	15.76	2.927507	0.52759	.	.	ENSG00000196220	ENST00000383836;ENST00000360413;ENST00000544908	T;T	0.14893	2.47;2.47	5.54	4.66	0.58398	.	0.000000	0.64402	D	0.000001	T	0.18800	0.0451	M	0.67397	2.05	0.58432	D	0.999993	B;B;B	0.30937	0.074;0.301;0.2	B;B;B	0.27796	0.083;0.083;0.038	T	0.01956	-1.1240	10	0.45353	T	0.12	.	10.889	0.46984	0.1445:0.0:0.8555:0.0	.	178;309;309	Q9ULR4;O43295-2;O43295	.;.;SRGP2_HUMAN	M	309;309;189	ENSP00000373347:L309M;ENSP00000353587:L309M	ENSP00000353587:L309M	L	-	1	2	SRGAP3	9075033	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.275000	0.43399	2.606000	0.88127	0.655000	0.94253	CTG	.	.	.	none		0.552	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3			T	9100033	G	T	9100033	3	4	196	1	0	0	0	0	1	0	0	0	15159	991	35	4	2473	4	SRGAP3	3	9100033	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10		9100033	188922397	11	11752											
TBC1D5	9779	hgsc.bcm.edu	37	chr3	17550057	17550057	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctagtttcagataaggaatgAtacattgtgggaactggaca	14	11	11	5	0	1	2	1	1	0	1	1	5	1	5	0	3	2	1	0	3	5	5			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr3:17550057A>G	ENST00000253692.7	-	3	1670	c.6T>C	c.(4-6)taT>taC	p.Y2Y	TBC1D5_ENST00000414318.2_Intron|TBC1D5_ENST00000429383.4_Silent_p.Y2Y|TBC1D5_ENST00000446818.2_Silent_p.Y2Y	NM_014744.2	NP_055559.1	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5	2						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						ATAAGGAATGATACATTGTGG	0.403																																					p.Y2Y		Atlas-SNP	.											.	TBC1D5	69	.	0			c.T6C						PASS	.						142	122	129					3																	17550057		2203	4300	6503	SO:0001819	synonymous_variant	9779	exon3			GGAATGATACATT	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.6T>C	chr3.hg19:g.17550057A>G		106.0	0.0	.		109.0	32.0	.	NM_014744	A6NP25|C9JP52	Silent	SNP	ENST00000253692.7	hg19	CCDS33714.1																																																																																			.	.	.	none		0.403	TBC1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340301.3	NM_014744		G	17550057	A	G	17550057	2	3	196	1	0	0	0	0	0	0	0	1	15635	340	12	3		3	TBC1D5	3	17550057	Silent	SNP	A	TCGA-HE-A5NF-01A-11D-A26P-10	8450024	17550057	180472373	12	11753											
STAG1	10274	hgsc.bcm.edu	37	chr3	136060303	136060303	+	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	acagcatgcctcactccagtTctcactttcatgtagttcat	9	14	5	13	0	4	0	4	0	1	0	6	0	5	0	2	0	2	4	2	0	1	4			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr3:136060303T>A	ENST00000383202.2	-	31	3793	c.3537A>T	c.(3535-3537)agA>agT	p.R1179S	STAG1_ENST00000536929.1_Missense_Mutation_p.R763S|STAG1_ENST00000434713.2_Missense_Mutation_p.R919S|STAG1_ENST00000236698.5_Intron	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	1179					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						TCACTCCAGTTCTCACTTTCA	0.423																																					p.R1179S		Atlas-SNP	.											.	STAG1	135	.	0			c.A3537T						PASS	.						273	206	228					3																	136060303		2203	4300	6503	SO:0001583	missense	10274	exon31			TCCAGTTCTCACT	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.3537A>T	chr3.hg19:g.136060303T>A	ENSP00000372689:p.Arg1179Ser	77.0	0.0	.		115.0	31.0	.	NM_005862	O00539|Q6P275	Missense_Mutation	SNP	ENST00000383202.2	hg19	CCDS3090.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.970648	0.74246	.	.	ENSG00000118007	ENST00000383202;ENST00000434713;ENST00000536929	T;T;T	0.50277	1.31;0.75;0.97	5.91	3.52	0.40303	.	0.100808	0.64402	D	0.000003	T	0.50633	0.1627	M	0.63843	1.955	0.54753	D	0.999983	D	0.60160	0.987	P	0.54174	0.744	T	0.47724	-0.9095	10	0.13108	T	0.6	.	8.6846	0.34229	0.0:0.2062:0.0:0.7938	.	1179	Q8WVM7	STAG1_HUMAN	S	1179;919;763	ENSP00000372689:R1179S;ENSP00000404396:R919S;ENSP00000445787:R763S	ENSP00000372689:R1179S	R	-	3	2	STAG1	137542993	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.775000	0.26689	0.483000	0.27608	0.528000	0.53228	AGA	.	.	.	none		0.423	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862		A	136060303	T	A	136060303	3	1	196	1	0	0	0	0	1	0	0	0	15254	1780	62	5	255	5	STAG1	3	136060303	Missense_Mutation	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10	118510246	136060303	61962127	13	11754											
UBE2K	3093	hgsc.bcm.edu	37	chr4	39757353	39757353	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtttggatatcctgaaagAtcaatggtaagagattttga	13	15	10	3	0	1	4	1	2	0	2	2	6	2	5	1	2	0	2	1	2	4	6			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr4:39757353A>G	ENST00000261427.5	+	4	577	c.293A>G	c.(292-294)gAt>gGt	p.D98G	UBE2K_ENST00000438068.2_3'UTR|UBE2K_ENST00000503368.1_Missense_Mutation_p.D47G|UBE2K_ENST00000295963.6_Intron|UBE2K_ENST00000445950.2_Missense_Mutation_p.D98G	NM_001111112.1|NM_005339.4	NP_001104582.1|NP_005330.1	P61086	UBE2K_HUMAN	ubiquitin-conjugating enzyme E2K	98					intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|protein K48-linked ubiquitination (GO:0070936)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)			large_intestine(1)|lung(1)|ovary(2)	4						ATCCTGAAAGATCAATGGTAA	0.343																																					p.D98G	NSCLC(101;689 1592 16105 29682 31745)	Atlas-SNP	.											.	UBE2K	16	.	0			c.A293G						PASS	.						152	150	151					4																	39757353		2203	4300	6503	SO:0001583	missense	3093	exon4			TGAAAGATCAATG	U58522	CCDS33976.1, CCDS47043.1, CCDS47044.1	4p14	2011-05-19	2011-05-19	2007-12-04	ENSG00000078140	ENSG00000078140		"Ubiquitin-conjugating enzymes E2"	4914	protein-coding gene	gene with protein product		602846	"huntingtin interacting protein 2", "ubiquitin-conjugating enzyme E2K (UBC1 homolog, yeast)"	HIP2		8702625, 17873885	Standard	NM_005339		Approved	HYPG, UBC1	uc003guu.4	P61086	OTTHUMG00000160543	ENST00000261427.5:c.293A>G	chr4.hg19:g.39757353A>G	ENSP00000261427:p.Asp98Gly	43.0	0.0	.		57.0	8.0	.	NM_005339	A6NJC1|A8K5Y9|B2RDF8|C9JGP1|O54806|P27924|Q16721|Q9CVV9|Q9Y2D3	Missense_Mutation	SNP	ENST00000261427.5	hg19	CCDS33976.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.885370	0.91814	.	.	ENSG00000078140	ENST00000261427;ENST00000503368;ENST00000445950	T;T;T	0.72835	-0.69;-0.69;-0.69	5.98	5.98	0.97165	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.85682	D	0.000000	D	0.82935	0.5145	M	0.74467	2.265	0.80722	D	1	D;D;B	0.61697	0.97;0.99;0.034	D;D;B	0.66497	0.925;0.944;0.131	D	0.84525	0.0630	10	0.62326	D	0.03	-22.3267	15.4553	0.75308	1.0:0.0:0.0:0.0	.	98;47;98	P61086;P61086-2;C9JGP1	UBE2K_HUMAN;.;.	G	98;47;98	ENSP00000261427:D98G;ENSP00000421203:D47G;ENSP00000390483:D98G	ENSP00000261427:D98G	D	+	2	0	UBE2K	39433748	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.872000	0.92352	2.296000	0.77279	0.482000	0.46254	GAT	.	.	.	none		0.343	UBE2K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361061.1	NM_005339		G	39757353	A	G	39757353	3	3	196	1	0	0	0	0	1	0	0	0	16874	333	12	3	307	3	UBE2K	4	39757353	Missense_Mutation	SNP	A	TCGA-HE-A5NF-01A-11D-A26P-10		39757353	151396923	14	11755											
OCIAD2	132299	hgsc.bcm.edu	37	chr4	48887522	48887522	+	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	taggaagctgaaggctgagaGtctcccttctcacttaatcc	10	11	9	11	0	2	2	1	2	2	1	5	4	3	3	2	2	1	2	2	2	4	3			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr4:48887522G>T	ENST00000508632.1	-	7	676	c.444C>A	c.(442-444)gaC>gaA	p.D148E	OCIAD2_ENST00000273860.4_3'UTR|OCIAD2_ENST00000508069.2_5'UTR	NM_001014446.1	NP_001014446.1	Q56VL3	OCAD2_HUMAN	OCIA domain containing 2	148						endosome (GO:0005768)|mitochondrial inner membrane (GO:0005743)				kidney(1)|lung(3)|skin(1)|urinary_tract(1)	6						AAGGCTGAGAGTCTCCCTTCT	0.368																																					p.D148E		Atlas-SNP	.											.	OCIAD2	16	.	0			c.C444A						PASS	.						185	180	182					4																	48887522		2203	4300	6503	SO:0001583	missense	132299	exon7			CTGAGAGTCTCCC	BC032808	CCDS3485.1, CCDS33981.1	4p12	2013-10-11			ENSG00000145247	ENSG00000145247			28685	protein-coding gene	gene with protein product						17054434	Standard	NM_001286774		Approved	MGC45416	uc003gyt.3	Q56VL3	OTTHUMG00000128626	ENST00000508632.1:c.444C>A	chr4.hg19:g.48887522G>T	ENSP00000423014:p.Asp148Glu	158.0	0.0	.		195.0	42.0	.	NM_001014446	B4DPE7|Q8N544	Missense_Mutation	SNP	ENST00000508632.1	hg19	CCDS33981.1	.	.	.	.	.	.	.	.	.	.	G	5.308	0.242112	0.10077	.	.	ENSG00000145247	ENST00000508632	T	0.41758	0.99	5.25	-4.51	0.03483	.	0.562361	0.17338	N	0.177837	T	0.15349	0.0370	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18178	-1.0345	9	.	.	.	1.3177	6.0446	0.19752	0.3698:0.2579:0.3723:0.0	.	148	Q56VL3	OCAD2_HUMAN	E	148	ENSP00000423014:D148E	.	D	-	3	2	OCIAD2	48582279	0.006000	0.16342	0.000000	0.03702	0.004000	0.04260	-0.089000	0.11180	-1.031000	0.03308	-0.302000	0.09304	GAC	.	.	.	none		0.368	OCIAD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361984.5	NM_152398		T	48887522	G	T	48887522	3	4	196	1	0	0	0	0	1	0	0	0	10825	1020	36	4	24	4	OCIAD2	4	48887522	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	9130169	48887522	142266754	15	11756											
ADH1B	125	hgsc.bcm.edu	37	chr4	100231924	100231924	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aactaacttaaaatctacctTttcccagagtgaagcaggtc	14	11	6	10	0	1	2	0	1	1	1	3	2	2	2	2	1	4	1	2	1	6	5			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr4:100231924T>C	ENST00000305046.8	-	8	1168	c.1101A>G	c.(1099-1101)aaA>aaG	p.K367K	ADH1B_ENST00000394887.3_Silent_p.K327K			P00325	ADH1B_HUMAN	alcohol dehydrogenase 1B (class I), beta polypeptide	367					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)	AAATCTACCTTTTCCCAGAGT	0.333																																					p.K367K		Atlas-SNP	.											.	ADH1B	68	.	0			c.A1101G						PASS	.						72	72	72					4																	100231924		2202	4300	6502	SO:0001819	synonymous_variant	125	exon8			CTACCTTTTCCCA	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.1101A>G	chr4.hg19:g.100231924T>C		100.0	0.0	.		90.0	13.0	.	NM_000668	A8MYN5|B4DRS9|B4DVC3|Q13711|Q4ZGI9|Q96KI7	Silent	SNP	ENST00000305046.8	hg19	CCDS34033.1																																																																																			.	.	.	none		0.333	ADH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364853.1	NM_000668		C	100231924	T	C	100231924	2	2	196	1	0	0	0	0	0	0	0	1	308	1838	64	3		3	ADH1B	4	100231924	Silent	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10	51344402	100231924	90922352	16	11757											
FAT4	79633	hgsc.bcm.edu	37	chr4	126408614	126408614	+	Frame_Shift_Del	DEL	A	A	-																															ggcacacttttctaattgggAaaaatggaacagcaacagta																										TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr4:126408614delA	ENST00000394329.3	+	16	12944	c.12931delA	c.(12931-12933)aaafs	p.K4311fs	FAT4_ENST00000335110.5_Frame_Shift_Del_p.K2552fs	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4311	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						TCTAATTGGGAAAAATGGAAC	0.403																																					p.G4310fs		Atlas-Indel,Pindel	.											FAT4_ENST00000394329,right_upper_lobe,carcinoma,0,2	FAT4	1752	.	0			c.12930delG						PASS	.						82	83	83					4																	126408614		2203	4300	6503	SO:0001589	frameshift_variant	79633	exon16			.	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.12931delA	chr4.hg19:g.126408614delA	ENSP00000377862:p.Lys4311fs	54.0	0.0	0		65.0	15.0	0.230769	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Frame_Shift_Del	DEL	ENST00000394329.3	hg19	CCDS3732.3																																																																																			.	.	.	none		0.403	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		-	126408614	A	-	126408614	7	5	196	1	0	1	0	1	0	0	0	0	5699	247	9	0	12993	0	FAT4	4	126408614	Frame_Shift_Del	DEL	A	TCGA-HE-A5NF-01A-11D-A26P-10	26176690	126408614	64745662	17	11758											
SLC6A3	6531	hgsc.bcm.edu	37	chr5	1394869	1394869	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctacaccttgagccagtggCggagctggaaagaaaacagg	13	6	13	9	1	1	2	0	1	1	1	1	4	1	4	2	4	4	1	2	4	4	2			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr5:1394869C>T	ENST00000270349.9	-	15	1971	c.1844G>A	c.(1843-1845)cGc>cAc	p.R615H	SLC6A3_ENST00000453492.2_Missense_Mutation_p.R615H	NM_001044.4	NP_001035.1	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 3	615					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)	p.R615P(1)		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)	GAGCCAGTGGCGGAGCTGGAA	0.522																																					p.R615H		Atlas-SNP	.											SLC6A3,NS,carcinoma,0,1	SLC6A3	102	.	1	Substitution - Missense(1)	lung(1)	c.G1844A						PASS	.						101	100	100					5																	1394869		2203	4300	6503	SO:0001583	missense	6531	exon15			CAGTGGCGGAGCT		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.1844G>A	chr5.hg19:g.1394869C>T	ENSP00000270349:p.Arg615His	66.0	0.0	.		83.0	5.0	.	NM_001044	A2RUN4|Q14996	Missense_Mutation	SNP	ENST00000270349.9	hg19	CCDS3863.1	.	.	.	.	.	.	.	.	.	.	C	11.40	1.627534	0.28978	.	.	ENSG00000142319	ENST00000270349;ENST00000453492	T;T	0.74632	-0.86;-0.86	4.79	2.97	0.34412	.	0.585459	0.14305	N	0.328004	T	0.53834	0.1821	N	0.12182	0.205	0.32012	N	0.60198	B	0.16802	0.019	B	0.13407	0.009	T	0.56643	-0.7945	10	0.49607	T	0.09	.	6.8118	0.23809	0.0:0.7896:0.0:0.2104	.	615	Q01959	SC6A3_HUMAN	H	615	ENSP00000270349:R615H;ENSP00000399806:R615H	ENSP00000270349:R615H	R	-	2	0	SLC6A3	1447869	1.000000	0.71417	0.999000	0.59377	0.917000	0.54804	0.574000	0.23714	1.139000	0.42245	0.655000	0.94253	CGC	.	.	.	none		0.522	SLC6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253650.3	NM_001044		T	1394869	C	T	1394869	3	4	196	1	0	0	0	0	1	0	0	0	14698	768	27	1	22	1	SLC6A3	5	1394869	Missense_Mutation	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10		1394869	179520391	18	11759											
MEGF10	84466	hgsc.bcm.edu	37	chr5	126790286	126790286	+	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	ggacttgacagaagctatatGggaaaatccttaaaaggtat	16	10	10	5	0	0	2	0	1	0	1	1	4	1	4	1	3	1	2	1	3	8	5			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr5:126790286G>T	ENST00000274473.6	+	24	3276	c.3009G>T	c.(3007-3009)atG>atT	p.M1003I	MEGF10_ENST00000510828.1_3'UTR|MEGF10_ENST00000503335.2_Missense_Mutation_p.M1003I	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10	1003	Necessary for formation of large intracellular vacuoles.				homotypic cell-cell adhesion (GO:0034109)|muscle cell development (GO:0055001)|recognition of apoptotic cell (GO:0043654)|regulation of muscle cell differentiation (GO:0051147)|regulation of skeletal muscle tissue development (GO:0048641)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell differentiation (GO:0014816)|skeletal muscle satellite cell proliferation (GO:0014841)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				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)		GAAGCTATATGGGAAAATCCT	0.328																																					p.M1003I		Atlas-SNP	.											.	MEGF10	152	.	0			c.G3009T						PASS	.						71	73	72					5																	126790286		2203	4300	6503	SO:0001583	missense	84466	exon24			CTATATGGGAAAA	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.3009G>T	chr5.hg19:g.126790286G>T	ENSP00000274473:p.Met1003Ile	18.0	0.0	.		26.0	4.0	.	NM_032446	Q68DE5|Q8WUL3	Missense_Mutation	SNP	ENST00000274473.6	hg19	CCDS4142.1	.	.	.	.	.	.	.	.	.	.	G	13.08	2.130925	0.37630	.	.	ENSG00000145794	ENST00000503335;ENST00000274473	T;T	0.79940	-1.32;-1.32	6.03	5.16	0.70880	.	0.346611	0.28847	N	0.013959	T	0.62925	0.2468	N	0.08118	0	0.37163	D	0.902706	B	0.02656	0.0	B	0.04013	0.001	T	0.61461	-0.7058	10	0.24483	T	0.36	-5.9793	12.4451	0.55647	0.1344:0.0:0.8656:0.0	.	1003	Q96KG7	MEG10_HUMAN	I	1003	ENSP00000423354:M1003I;ENSP00000274473:M1003I	ENSP00000274473:M1003I	M	+	3	0	MEGF10	126818185	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.346000	0.52190	1.558000	0.49541	0.655000	0.94253	ATG	.	.	.	none		0.328	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446		T	126790286	G	T	126790286	3	4	196	1	0	0	0	0	1	0	0	0	9467	1348	47	4	3095	4	MEGF10	5	126790286	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	125395417	126790286	54124974	19	11760											
CTNNA1	1495	hgsc.bcm.edu	37	chr5	138118896	138118897	+	Frame_Shift_Del	DEL	GG	GG	-																															ttgtaaacaccaatagtaaaGggccctctaataagaagaga																										TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr5:138118896_138118897delGG	ENST00000302763.7	+	3	226_227	c.136_137delGG	c.(136-138)gggfs	p.G46fs	CTNNA1_ENST00000355078.5_Intron|CTNNA1_ENST00000518825.1_Frame_Shift_Del_p.G46fs	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	46	Involved in homodimerization.				adherens junction organization (GO:0034332)|aging (GO:0007568)|apical junction assembly (GO:0043297)|axon regeneration (GO:0031103)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular protein localization (GO:0034613)|cellular response to indole-3-methanol (GO:0071681)|epithelial cell-cell adhesion (GO:0090136)|establishment or maintenance of cell polarity (GO:0007163)|gap junction assembly (GO:0016264)|male gonad development (GO:0008584)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell motility (GO:2000146)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|negative regulation of neuroblast proliferation (GO:0007406)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of smoothened signaling pathway (GO:0045880)|protein heterooligomerization (GO:0051291)|response to estrogen (GO:0043627)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|catenin complex (GO:0016342)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|gamma-catenin binding (GO:0045295)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|vinculin binding (GO:0017166)			NS(1)|breast(7)|cervix(2)|endometrium(4)|kidney(6)|large_intestine(16)|lung(9)|oesophagus(2)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	52			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CAATAGTAAAGGGCCCTCTAAT	0.356																																					p.45_46del		Atlas-Indel,Pindel	.											.	CTNNA1	114	.	0			c.135_136del						PASS	.																																			SO:0001589	frameshift_variant	1495	exon3			.	D13866	CCDS34243.1, CCDS75315.1	5q31.2	2008-02-05	2002-08-29			ENSG00000044115			2509	protein-coding gene	gene with protein product		116805	"catenin (cadherin-associated protein), alpha 1 (102kD)"			1924379	Standard	XM_005271898		Approved	CAP102	uc003ldh.3	P35221		ENST00000302763.7:c.136_137delGG	chr5.hg19:g.138118896_138118897delGG	ENSP00000304669:p.Gly46fs	72.0	0.0	0		104.0	18.0	0.173077	NM_001903	Q12795|Q8N1C0	Frame_Shift_Del	DEL	ENST00000302763.7	hg19	CCDS34243.1																																																																																			.	.	.	none		0.356	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903		-	138118897	GG	-	138118896	7	5	196	1	0	1	0	1	0	0	0	0	4014	1000	35	0	142	0	CTNNA1	5	138118896	Frame_Shift_Del	DEL	GG	TCGA-HE-A5NF-01A-11D-A26P-10	11328610	138118896	42796364	20	11761											
ADAM19	8728	hgsc.bcm.edu	37	chr5	156908922	156908922	+	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	actgggtttgccgggagtgcCttctggggcggccgaggcct	3	9	18	11	3	1	0	0	0	1	0	1	2	1	1	4	6	2	1	4	6	0	2			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr5:156908922C>A	ENST00000517905.1	-	22	2624	c.2580G>T	c.(2578-2580)aaG>aaT	p.K860N	ADAM19_ENST00000394020.1_Missense_Mutation_p.K862N|ADAM19_ENST00000430702.2_Intron|ADAM19_ENST00000257527.4_Missense_Mutation_p.K860N			Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19	860					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)			CCGGGAGTGCCTTCTGGGGCG	0.622																																					p.K860N		Atlas-SNP	.											.	ADAM19	216	.	0			c.G2580T						PASS	.						12	15	14					5																	156908922		2201	4297	6498	SO:0001583	missense	8728	exon22			GAGTGCCTTCTGG	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.2580G>T	chr5.hg19:g.156908922C>A	ENSP00000428654:p.Lys860Asn	71.0	0.0	.		64.0	16.0	.	NM_033274	Q9BZL5|Q9UHP2	Missense_Mutation	SNP	ENST00000517905.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.8|20.8	4.047583|4.047583	0.75846|0.75846	.|.	.|.	ENSG00000135074|ENSG00000135074	ENST00000257527;ENST00000394020;ENST00000517905|ENST00000517374	T;T;T|.	0.01854|.	4.61;4.62;4.6|.	5.51|5.51	1.19|1.19	0.21007|0.21007	.|.	0.184073|.	0.37809|.	N|.	0.001925|.	T|T	0.50205|0.50205	0.1602|0.1602	L|L	0.50333|0.50333	1.59|1.59	0.35227|0.35227	D|D	0.776606|0.776606	D;D|.	0.76494|.	0.999;0.997|.	D;P|.	0.69479|.	0.964;0.888|.	T|T	0.54827|0.54827	-0.8235|-0.8235	10|5	0.87932|.	D|.	0|.	.|.	7.8|7.8	0.29168|0.29168	0.0:0.5227:0.0:0.4773|0.0:0.5227:0.0:0.4773	.|.	860;860|.	Q9H013-2;Q9H013|.	.;ADA19_HUMAN|.	N|M	860;862;860|431	ENSP00000257527:K860N;ENSP00000377588:K862N;ENSP00000428654:K860N|.	ENSP00000257527:K860N|.	K|R	-|-	3|2	2|0	ADAM19|ADAM19	156841500|156841500	0.995000|0.995000	0.38212|0.38212	0.997000|0.997000	0.53966|0.53966	0.977000|0.977000	0.68977|0.68977	0.140000|0.140000	0.16056|0.16056	0.304000|0.304000	0.22809|0.22809	0.561000|0.561000	0.74099|0.74099	AAG|AGG	.	.	.	none		0.622	ADAM19-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000373918.1	NM_033274		A	156908922	C	A	156908922	3	1	196	1	0	0	0	0	1	0	0	0	240	680	24	4	184	4	ADAM19	5	156908922	Missense_Mutation	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10	18790026	156908922	24006338	21	11762											
UNC5CL	222643	hgsc.bcm.edu	37	chr6	41000635	41000635	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccctcaccctctgagatgtAcgtgagcttcaggcactggt	7	11	10	13	1	3	2	2	2	1	1	4	3	4	2	2	2	2	3	2	2	1	2			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr6:41000635A>G	ENST00000373164.1	-	3	997	c.937T>C	c.(937-939)Tac>Cac	p.Y313H	UNC5CL_ENST00000244565.3_Missense_Mutation_p.Y313H|UNC5CL_ENST00000470102.1_5'UTR			Q8IV45	UN5CL_HUMAN	unc-5 homolog C (C. elegans)-like	313	Interaction with RELA and NFKB1.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|proteolysis (GO:0006508)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	peptidase activity (GO:0008233)			endometrium(1)|kidney(3)|large_intestine(3)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	13	Ovarian(28;0.0418)|Colorectal(47;0.196)					TCTGAGATGTACGTGAGCTTC	0.632																																					p.Y313H		Atlas-SNP	.											.	UNC5CL	52	.	0			c.T937C						PASS	.						19	21	20					6																	41000635		2201	4299	6500	SO:0001583	missense	222643	exon4			AGATGTACGTGAG	BC035284	CCDS4847.1	6p21.1	2013-10-15			ENSG00000124602	ENSG00000124602			21203	protein-coding gene	gene with protein product	"ZU5 and death domain containing"					14769797	Standard	NM_173561		Approved	MGC34763, ZUD	uc003opi.3	Q8IV45	OTTHUMG00000014665	ENST00000373164.1:c.937T>C	chr6.hg19:g.41000635A>G	ENSP00000362258:p.Tyr313His	77.0	0.0	.		77.0	10.0	.	NM_173561	Q5TGU1	Missense_Mutation	SNP	ENST00000373164.1	hg19	CCDS4847.1	.	.	.	.	.	.	.	.	.	.	A	7.812	0.716007	0.15306	.	.	ENSG00000124602	ENST00000244565;ENST00000373164	T;T	0.52526	0.66;0.66	5.43	5.43	0.79202	.	0.000000	0.40554	N	0.001066	T	0.16342	0.0393	N	0.24115	0.695	0.33409	D	0.578337	B	0.14438	0.01	B	0.12156	0.007	T	0.08785	-1.0705	10	0.19590	T	0.45	-29.4271	11.8914	0.52630	1.0:0.0:0.0:0.0	.	313	Q8IV45	UN5CL_HUMAN	H	313	ENSP00000244565:Y313H;ENSP00000362258:Y313H	ENSP00000244565:Y313H	Y	-	1	0	UNC5CL	41108613	1.000000	0.71417	1.000000	0.80357	0.566000	0.35808	4.569000	0.60865	2.042000	0.60477	0.533000	0.62120	TAC	.	.	.	none		0.632	UNC5CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040491.1	NM_173561		G	41000635	A	G	41000635	3	3	196	1	0	0	0	0	1	0	0	0	17006	391	14	3	643	3	UNC5CL	6	41000635	Missense_Mutation	SNP	A	TCGA-HE-A5NF-01A-11D-A26P-10		41000635	130114432	22	11763											
DEFB110	245913	hgsc.bcm.edu	37	chr6	49986835	49986835	+	Missense_Mutation	SNP	T	T	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	catactcaggatatttctttTtggctgtaagaagggaagaa	13	13	10	5	0	2	2	1	0	1	2	2	4	2	4	0	3	1	2	0	3	6	6			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr6:49986835T>G	ENST00000371148.2	-	2	104	c.59A>C	c.(58-60)aAa>aCa	p.K20T	DEFB110_ENST00000393660.2_Intron	NM_001037497.1	NP_001032586.1	Q30KQ9	DB110_HUMAN	defensin, beta 110 locus	20					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(1)|lung(1)|ovary(1)	3	Lung NSC(77;0.042)					ATATTTCTTTTTGGCTGTAAG	0.353																																					p.K20T		Atlas-SNP	.											.	DEFB110	5	.	0			c.A59C						PASS	.						129	126	127					6																	49986835		2203	4300	6503	SO:0001583	missense	245913	exon2			TTCTTTTTGGCTG	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.59A>C	chr6.hg19:g.49986835T>G	ENSP00000360190:p.Lys20Thr	70.0	0.0	.		102.0	6.0	.	NM_001037497	Q30KR0	Missense_Mutation	SNP	ENST00000371148.2	hg19	CCDS34475.1	.	.	.	.	.	.	.	.	.	.	T	11.38	1.622246	0.28889	.	.	ENSG00000203970	ENST00000371148	.	.	.	4.77	-6.13	0.02118	.	0.904575	0.09377	N	0.810521	T	0.07954	0.0199	.	.	.	0.23882	N	0.996572	B	0.12630	0.006	B	0.12837	0.008	T	0.34700	-0.9818	7	.	.	.	-4.2088	9.1953	0.37224	0.0:0.6424:0.1253:0.2323	.	20	Q30KQ9	DB110_HUMAN	T	20	.	.	K	-	2	0	DEFB110	50094794	0.245000	0.23899	0.575000	0.28536	0.857000	0.48899	-1.073000	0.03430	-1.040000	0.03271	-0.408000	0.06270	AAA	.	.	.	none		0.353	DEFB110-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359664.1	NM_001037728		G	49986835	T	G	49986835	3	3	196	1	0	0	0	0	1	0	0	0	4402	1841	64	5	284	5	DEFB110	6	49986835	Missense_Mutation	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10	8986200	49986835	121128232	23	11764											
SERINC1	57515	hgsc.bcm.edu	37	chr6	122766258	122766258	+	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	acatacagcacgatgccaatCcaactggaagagattttcac	15	8	7	11	1	1	1	1	0	0	1	2	4	2	2	2	1	4	1	2	1	4	3			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr6:122766258C>G	ENST00000339697.4	-	10	1377	c.1293G>C	c.(1291-1293)tgG>tgC	p.W431C		NM_020755.2	NP_065806.1	Q9NRX5	SERC1_HUMAN	serine incorporator 1	431					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)		CGATGCCAATCCAACTGGAAG	0.428																																					p.W431C		Atlas-SNP	.											.	SERINC1	39	.	0			c.G1293C						PASS	.						107	96	99					6																	122766258		2203	4300	6503	SO:0001583	missense	57515	exon10			GCCAATCCAACTG	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.1293G>C	chr6.hg19:g.122766258C>G	ENSP00000342962:p.Trp431Cys	68.0	0.0	.		92.0	19.0	.	NM_020755	B3KY69|E1P565|O75655|Q7Z2F5|Q8TAG1|Q9NTH8|Q9ULG7	Missense_Mutation	SNP	ENST00000339697.4	hg19	CCDS5125.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.569369	0.86439	.	.	ENSG00000111897	ENST00000339697;ENST00000368454	T;T	0.25579	1.79;1.79	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.62405	0.2425	H	0.96269	3.795	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75502	-0.3295	10	0.87932	D	0	-7.4299	19.5937	0.95526	0.0:1.0:0.0:0.0	.	431	Q9NRX5	SERC1_HUMAN	C	431	ENSP00000342962:W431C;ENSP00000357439:W431C	ENSP00000342962:W431C	W	-	3	0	SERINC1	122807957	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.798000	0.85924	2.629000	0.89072	0.655000	0.94253	TGG	.	.	.	none		0.428	SERINC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042031.2	NM_020755		G	122766258	C	G	122766258	3	3	196	1	0	0	0	0	1	0	0	0	14092	856	30	4	72	4	SERINC1	6	122766258	Missense_Mutation	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10	72779423	122766258	48348809	24	11765											
AEBP1	165	hgsc.bcm.edu	37	chr7	44150535	44150535	+	Frame_Shift_Del	DEL	G	G	-																															tttcatgggaacgtggacaaGgacacacccgtgctgagtga																										TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr7:44150535delG	ENST00000223357.3	+	13	1814	c.1509delG	c.(1507-1509)aagfs	p.K503fs	MIR4649_ENST00000582839.1_RNA|AEBP1_ENST00000450684.2_Frame_Shift_Del_p.K46fs	NM_001129.3	NP_001120.3	Q8IUX7	AEBP1_HUMAN	AE binding protein 1	503	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.|Interaction with MAPK1 and MAPK3. {ECO:0000250}.|Required for DNA-binding and interaction with NFKBIA. {ECO:0000250}.				cell adhesion (GO:0007155)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(13)|upper_aerodigestive_tract(2)	33						ACGTGGACAAGGACACACCCG	0.627																																					p.K503fs		Atlas-Indel,Pindel	.											.	AEBP1	102	.	0			c.1508delA						PASS	.						88	81	83					7																	44150535		2203	4300	6503	SO:0001589	frameshift_variant	165	exon13			.	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.1509delG	chr7.hg19:g.44150535delG	ENSP00000223357:p.Lys503fs	73.0	0.0	0		105.0	30.0	0.285714	NM_001129	Q14113|Q59ER7|Q6ZSC7|Q7KZ79	Frame_Shift_Del	DEL	ENST00000223357.3	hg19	CCDS5476.1																																																																																			.	.	.	none		0.627	AEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250993.2	NM_001129		-	44150535	G	-	44150535	7	5	196	1	0	1	0	1	0	0	0	0	349	991	35	0	1559	0	AEBP1	7	44150535	Frame_Shift_Del	DEL	G	TCGA-HE-A5NF-01A-11D-A26P-10		44150535	114988128	25	11766											
DUSP26	78986	hgsc.bcm.edu	37	chr8	33454873	33454873	+	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	ggttacaggctgtcttgcctGtgtagaggagccgctccaac	7	10	13	11	1	1	1	0	0	1	1	2	2	2	2	3	3	4	4	3	3	3	3			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr8:33454873G>T	ENST00000256261.4	-	2	678	c.161C>A	c.(160-162)aCa>aAa	p.T54K	DUSP26_ENST00000523956.1_Missense_Mutation_p.T54K	NM_024025.1	NP_076930.1	Q9BV47	DUS26_HUMAN	dual specificity phosphatase 26 (putative)	54					negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of cell adhesion (GO:0045785)|positive regulation of peptidyl-serine dephosphorylation (GO:1902310)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	p53 binding (GO:0002039)|phosphoprotein phosphatase activity (GO:0004721)|phosphoserine phosphatase activity (GO:0004647)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|RNA polymerase II activating transcription factor binding (GO:0001102)			NS(1)|breast(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)	15				KIRC - Kidney renal clear cell carcinoma(67;0.0918)|Kidney(114;0.111)		TGTCTTGCCTGTGTAGAGGAG	0.572																																					p.T54K		Atlas-SNP	.											.	DUSP26	42	.	0			c.C161A						PASS	.						69	52	58					8																	33454873		2203	4300	6503	SO:0001583	missense	78986	exon2			TTGCCTGTGTAGA	AY902194	CCDS6092.1	8p12	2014-09-09			ENSG00000133878	ENSG00000133878		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	28161	protein-coding gene	gene with protein product							Standard	NM_024025		Approved	MGC1136, DUSP24	uc003xjp.3	Q9BV47	OTTHUMG00000163961	ENST00000256261.4:c.161C>A	chr8.hg19:g.33454873G>T	ENSP00000256261:p.Thr54Lys	94.0	0.0	.		93.0	16.0	.	NM_024025	D3DSV8|Q9BTW0	Missense_Mutation	SNP	ENST00000256261.4	hg19	CCDS6092.1	.	.	.	.	.	.	.	.	.	.	G	14.78	2.638232	0.47153	.	.	ENSG00000133878	ENST00000256261;ENST00000523956;ENST00000522982	T;T;T	0.60040	0.22;0.22;0.22	5.5	5.5	0.81552	.	0.146976	0.64402	D	0.000010	T	0.43765	0.1262	L	0.27053	0.805	0.54753	D	0.999983	B	0.21520	0.057	B	0.20955	0.032	T	0.40776	-0.9545	10	0.05436	T	0.98	-14.8884	18.9825	0.92760	0.0:0.0:1.0:0.0	.	54	Q9BV47	DUS26_HUMAN	K	54	ENSP00000256261:T54K;ENSP00000429176:T54K;ENSP00000430922:T54K	ENSP00000256261:T54K	T	-	2	0	DUSP26	33574415	1.000000	0.71417	0.962000	0.40283	0.975000	0.68041	7.744000	0.85034	2.590000	0.87494	0.561000	0.74099	ACA	.	.	.	none		0.572	DUSP26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376564.1	NM_024025		T	33454873	G	T	33454873	3	4	196	1	0	0	0	0	1	0	0	0	4825	1377	48	4	486	4	DUSP26	8	33454873	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10		33454873	112909149	26	11767											
CA13	377677	hgsc.bcm.edu	37	chr8	86162972	86162972	+	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	ggtcctatatatttaaggtcCtattcactggaaggaatttt	11	16	8	6	0	1	0	1	0	0	0	3	2	3	2	2	4	0	0	2	4	7	9			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr8:86162972C>T	ENST00000321764.3	+	2	343	c.41C>T	c.(40-42)cCt>cTt	p.P14L	CA13_ENST00000517298.1_3'UTR|RP11-219B4.6_ENST00000551479.1_5'Flank	NM_198584.2	NP_940986.1	Q8N1Q1	CAH13_HUMAN	carbonic anhydrase XIII	14					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)	ATTTAAGGTCCTATTCACTGG	0.338																																					p.P14L		Atlas-SNP	.											.	CA13	26	.	0			c.C41T						PASS	.						62	64	63					8																	86162972		2203	4300	6503	SO:0001583	missense	377677	exon2			AAGGTCCTATTCA	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.41C>T	chr8.hg19:g.86162972C>T	ENSP00000318912:p.Pro14Leu	105.0	0.0	.		91.0	11.0	.	NM_198584		Missense_Mutation	SNP	ENST00000321764.3	hg19	CCDS6236.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.887731	0.91814	.	.	ENSG00000185015	ENST00000321764	T	0.68624	-0.34	5.48	5.48	0.80851	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.000000	0.85682	D	0.000000	D	0.89361	0.6693	H	0.98133	4.155	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93109	0.6515	10	0.87932	D	0	-23.2453	19.3527	0.94395	0.0:1.0:0.0:0.0	.	14	Q8N1Q1	CAH13_HUMAN	L	14	ENSP00000318912:P14L	ENSP00000318912:P14L	P	+	2	0	CA13	86350224	1.000000	0.71417	0.973000	0.42090	0.987000	0.75469	7.044000	0.76578	2.567000	0.86603	0.563000	0.77884	CCT	.	.	.	none		0.338	CA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381066.1	NM_198584		T	86162972	C	T	86162972	3	4	196	1	0	0	0	0	1	0	0	0	2516	681	24	2	47	2	CA13	8	86162972	Missense_Mutation	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10	52708099	86162972	60201050	27	11768											
ADCY8	114	hgsc.bcm.edu	37	chr8	132002781	132002781	+	Missense_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	acatgaatagcactgcctggGccacaacctaaaataaacac	17	6	6	12	0	0	1	0	1	0	0	0	1	0	1	3	1	4	1	3	1	7	3			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr8:132002781G>A	ENST00000286355.5	-	2	3060	c.968C>T	c.(967-969)gCc>gTc	p.A323V	ADCY8_ENST00000377928.3_Missense_Mutation_p.A323V	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	323					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			CACTGCCTGGGCCACAACCTA	0.428										HNSCC(32;0.087)																											p.A323V		Atlas-SNP	.											.	ADCY8	291	.	0			c.C968T						PASS	.						96	106	103					8																	132002781		2203	4300	6503	SO:0001583	missense	114	exon2			GCCTGGGCCACAA	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.968C>T	chr8.hg19:g.132002781G>A	ENSP00000286355:p.Ala323Val	70.0	0.0	.		91.0	8.0	.	NM_001115		Missense_Mutation	SNP	ENST00000286355.5	hg19	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.767301	0.90020	.	.	ENSG00000155897	ENST00000286355;ENST00000377928	T;T	0.81163	-1.46;-1.45	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.89326	0.6683	M	0.76002	2.32	0.58432	D	0.999991	D;P	0.63880	0.993;0.455	D;B	0.70227	0.968;0.214	D	0.88311	0.2956	10	0.44086	T	0.13	.	18.7877	0.91961	0.0:0.0:1.0:0.0	.	323;323	E7EVL1;P40145	.;ADCY8_HUMAN	V	323	ENSP00000286355:A323V;ENSP00000367161:A323V	ENSP00000286355:A323V	A	-	2	0	ADCY8	132071963	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.792000	0.99085	2.751000	0.94390	0.650000	0.86243	GCC	.	.	.	none		0.428	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			A	132002781	G	A	132002781	3	1	196	1	0	0	0	0	1	0	0	0	300	1203	42	2	2855	2	ADCY8	8	132002781	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	45839809	132002781	14361241	28	11769											
TG	7038	hgsc.bcm.edu	37	chr8	133899726	133899727	+	Frame_Shift_Ins	INS	-	-	TA																															agtgcttcaactcagagtgcINStactgtgttgatgctgaggg																										TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr8:133899726_133899727insTA	ENST00000220616.4	+	9	2149_2150	c.2109_2110insTA	c.(2110-2112)tacfs	p.Y704fs	TG_ENST00000377869.1_Frame_Shift_Ins_p.Y704fs	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	704	Thyroglobulin type-1 6. {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)		ACTCAGAGTGCTACTGTGTTGA	0.515																																					p.C703fs		Atlas-Indel,Pindel	.											.	TG	416	.	0			c.2109_2110insTA						PASS	.																																			SO:0001589	frameshift_variant	7038	exon9			.	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.2110_2111dupTA	chr8.hg19:g.133899727_133899728dupTA	ENSP00000220616:p.Tyr704fs	416.0	0.0	0		497.0	91.0	0.183099	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Frame_Shift_Ins	INS	ENST00000220616.4	hg19	CCDS34944.1																																																																																			.	.	.	none		0.515	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		TA	133899727	-	TA	133899726	7	5	196	1	0	1	1	0	0	0	0	0	15825	805	28	0	2143	0	TG	8	133899726	Frame_Shift_Ins	INS	-	TCGA-HE-A5NF-01A-11D-A26P-10	1896945	133899726	12464296	29	11770											
RMI1	80010	hgsc.bcm.edu	37	chr9	86617525	86617525	+	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	ctgatggtactgcatatctaGatgtagactttgtggatgaa	11	14	11	5	0	1	4	0	2	1	2	1	5	1	5	0	2	2	3	0	2	5	5			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr9:86617525G>T	ENST00000325875.3	+	3	1956	c.1624G>T	c.(1624-1626)Gat>Tat	p.D542Y		NM_024945.2	NP_079221.2	Q9H9A7	RMI1_HUMAN	RecQ mediated genome instability 1	542					DNA replication (GO:0006260)|glucose homeostasis (GO:0042593)|multicellular organism growth (GO:0035264)|reduction of food intake in response to dietary excess (GO:0002023)|response to glucose (GO:0009749)	nucleus (GO:0005634)				biliary_tract(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18						TGCATATCTAGATGTAGACTT	0.368																																					p.D542Y		Atlas-SNP	.											.	RMI1	50	.	0			c.G1624T						PASS	.						197	193	194					9																	86617525		2203	4300	6503	SO:0001583	missense	80010	exon3			TATCTAGATGTAG	AK022950	CCDS6669.1	9q22.1	2013-06-10	2013-06-10	2006-06-12	ENSG00000178966	ENSG00000178966			25764	protein-coding gene	gene with protein product	"BLM-Associated Polypeptide, 75 kDa"	610404	"chromosome 9 open reading frame 76", "RMI1, RecQ mediated genome instability 1, homolog (S. cerevisiae)"	C9orf76		15775963, 20826341	Standard	NM_024945		Approved	FLJ12888, BLAP75	uc004anq.4	Q9H9A7	OTTHUMG00000020113	ENST00000325875.3:c.1624G>T	chr9.hg19:g.86617525G>T	ENSP00000317039:p.Asp542Tyr	110.0	0.0	.		97.0	19.0	.	NM_024945	Q05BX1|Q05CW3|Q5SQG8|Q5SQG9|Q6P1Q4|Q6PI89|Q7Z6L6	Missense_Mutation	SNP	ENST00000325875.3	hg19	CCDS6669.1	.	.	.	.	.	.	.	.	.	.	G	15.78	2.935730	0.52972	.	.	ENSG00000178966	ENST00000325875	T	0.47177	0.85	5.29	5.29	0.74685	.	0.104013	0.64402	D	0.000005	T	0.61198	0.2328	L	0.55481	1.735	0.47659	D	0.999484	D	0.89917	1.0	D	0.70487	0.969	T	0.58702	-0.7590	9	.	.	.	-9.5894	12.6452	0.56731	0.0762:0.0:0.9238:0.0	.	542	Q9H9A7	RMI1_HUMAN	Y	542	ENSP00000317039:D542Y	.	D	+	1	0	RMI1	85807345	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	6.827000	0.75303	2.620000	0.88729	0.563000	0.77884	GAT	.	.	.	none		0.368	RMI1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052870.1	NM_024945		T	86617525	G	T	86617525	3	4	196	1	0	0	0	0	1	0	0	0	13408	942	33	4	1626	4	RMI1	9	86617525	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10		86617525	54595906	30	11771											
LPAR1	1902	hgsc.bcm.edu	37	chr9	113704022	113704022	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacccgccggttgctcatccGtgtgtggagctgcatgcgga	5	10	14	12	4	1	0	1	0	0	0	2	2	2	2	3	3	5	4	3	3	1	2			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr9:113704022G>A	ENST00000374431.3	-	4	855	c.472C>T	c.(472-474)Cgg>Tgg	p.R158W	LPAR1_ENST00000374430.2_Missense_Mutation_p.R158W|LPAR1_ENST00000541779.1_Missense_Mutation_p.R159W|LPAR1_ENST00000538760.1_Missense_Mutation_p.R159W|LPAR1_ENST00000358883.4_Missense_Mutation_p.R158W	NM_057159.2	NP_476500.1	Q92633	LPAR1_HUMAN	lysophosphatidic acid receptor 1	158					activation of MAPK activity (GO:0000187)|activation of phospholipase C activity (GO:0007202)|bleb assembly (GO:0032060)|cellular response to oxygen levels (GO:0071453)|G-protein coupled receptor signaling pathway (GO:0007186)|myelination (GO:0042552)|negative regulation of neuron projection development (GO:0010977)|positive regulation of apoptotic process (GO:0043065)|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 dendritic spine development (GO:0060999)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle cell chemotaxis (GO:0071673)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lysophosphatidic acid receptor activity (GO:0070915)|phospholipid binding (GO:0005543)	p.R158W(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(1)|ovary(2)|prostate(6)|skin(1)	21						TTGCTCATCCGTGTGTGGAGC	0.542																																					p.R158W	NSCLC(115;661 2323 9836 34256)	Atlas-SNP	.											LPAR1,colon,carcinoma,0,1	LPAR1	48	.	1	Substitution - Missense(1)	large_intestine(1)	c.C472T						PASS	.						117	104	109					9																	113704022		2203	4300	6503	SO:0001583	missense	1902	exon3			TCATCCGTGTGTG	U80811	CCDS6777.1	9q	2012-08-08	2008-04-11	2008-04-11	ENSG00000198121	ENSG00000198121		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	3166	protein-coding gene	gene with protein product		602282	"endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 2"	EDG2		8922387, 9070858	Standard	NM_001401		Approved	edg-2, rec.1.3, vzg-1, Gpcr26, Mrec1.3, LPA1, GPR26	uc004bfc.3	Q92633	OTTHUMG00000020486	ENST00000374431.3:c.472C>T	chr9.hg19:g.113704022G>A	ENSP00000363553:p.Arg158Trp	154.0	0.0	.		180.0	28.0	.	NM_001401	B4DK36|O00656|O00722|P78351	Missense_Mutation	SNP	ENST00000374431.3	hg19	CCDS6777.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.017060	0.75161	.	.	ENSG00000198121	ENST00000374431;ENST00000541779;ENST00000374430;ENST00000358883;ENST00000449490;ENST00000538760;ENST00000441240	T;T;T;T;T;T	0.39592	1.07;1.07;1.07;1.07;1.07;1.07	5.53	4.64	0.57946	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.60301	0.2258	M	0.76328	2.33	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74348	0.983;0.983;0.983	T	0.63189	-0.6693	10	0.72032	D	0.01	.	8.4744	0.33005	0.0771:0.0:0.7707:0.1522	.	159;159;158	B4DQ18;B4DK36;Q92633	.;.;LPAR1_HUMAN	W	158;159;158;158;140;159;158	ENSP00000363553:R158W;ENSP00000445697:R159W;ENSP00000363552:R158W;ENSP00000351755:R158W;ENSP00000440201:R159W;ENSP00000401810:R158W	ENSP00000351755:R158W	R	-	1	2	LPAR1	112743843	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.528000	0.73807	1.357000	0.45904	0.655000	0.94253	CGG	.	.	.	none		0.542	LPAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053631.1	NM_057159		A	113704022	G	A	113704022	3	1	196	1	0	0	0	0	1	0	0	0	8911	1144	40	1	630	1	LPAR1	9	113704022	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	27086497	113704022	27509409	31	11772											
SPTAN1	6709	hgsc.bcm.edu	37	chr9	131362363	131362363	+	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	ctctttctttgaataggatgAaactgattccaagacagcct	12	13	7	9	0	2	4	0	3	2	1	3	5	3	5	2	1	2	0	2	1	4	4			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr9:131362363A>T	ENST00000372731.4	+	27	3658	c.3548A>T	c.(3547-3549)gAa>gTa	p.E1183V	SPTAN1_ENST00000372739.3_Missense_Mutation_p.E1183V|SPTAN1_ENST00000358161.5_Missense_Mutation_p.E1183V	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1183					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						GAATAGGATGAAACTGATTCC	0.433																																					p.E1183V	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.A3548T						PASS	.						125	114	118					9																	131362363		2203	4300	6503	SO:0001583	missense	6709	exon27			AGGATGAAACTGA	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.3548A>T	chr9.hg19:g.131362363A>T	ENSP00000361816:p.Glu1183Val	108.0	0.0	.		94.0	9.0	.	NM_003127	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Missense_Mutation	SNP	ENST00000372731.4	hg19	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	A	17.11	3.305120	0.60305	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	T;T;T	0.51574	0.7;0.72;0.7	6.08	6.08	0.98989	.	0.142496	0.64402	D	0.000006	T	0.40398	0.1115	N	0.19112	0.55	0.80722	D	1	P;B;B;B	0.36733	0.567;0.384;0.384;0.265	B;B;B;B	0.39840	0.18;0.311;0.311;0.165	T	0.42103	-0.9471	10	0.87932	D	0	.	16.6438	0.85155	1.0:0.0:0.0:0.0	.	1183;1163;1183;1183	A6NG51;Q13813-3;Q13813-2;Q13813	.;.;.;SPTA2_HUMAN	V	1183;1183;1183;1163	ENSP00000350882:E1183V;ENSP00000361816:E1183V;ENSP00000361824:E1183V	ENSP00000350882:E1183V	E	+	2	0	SPTAN1	130402184	1.000000	0.71417	0.945000	0.38365	0.557000	0.35523	8.593000	0.90832	2.333000	0.79357	0.533000	0.62120	GAA	.	.	.	none		0.433	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		T	131362363	A	T	131362363	3	4	196	1	0	0	0	0	1	0	0	0	15129	246	9	5	3650	5	SPTAN1	9	131362363	Missense_Mutation	SNP	A	TCGA-HE-A5NF-01A-11D-A26P-10	17658341	131362363	9851068	32	11773											
LCN10	414332	hgsc.bcm.edu	37	chr9	139633991	139633991	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggctctcatggcaggatggTgtgtgtacgggacgctgtgg	5	11	18	7	2	1	0	1	0	1	0	2	2	1	2	0	6	1	4	0	6	1	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr9:139633991T>C	ENST00000474369.1	-	5	549	c.550A>G	c.(550-552)Acc>Gcc	p.T184A	LCN10_ENST00000497771.1_Missense_Mutation_p.T197A|LCN10_ENST00000527229.1_Missense_Mutation_p.T161A|LCN6_ENST00000480584.1_5'Flank|LCN6_ENST00000435202.1_3'UTR			Q6JVE6	LCN10_HUMAN	lipocalin 10	184					transport (GO:0006810)	extracellular region (GO:0005576)				breast(2)|cervix(1)|large_intestine(1)	4	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.32e-06)|Epithelial(140;7.83e-05)		GGCAGGATGGTGTGTGTACGG	0.617																																					p.T197A		Atlas-SNP	.											.	LCN10	21	.	0			c.A589G						PASS	.						92	76	81					9																	139633991		2199	4295	6494	SO:0001583	missense	414332	exon6			GGATGGTGTGTGT	AY301271	CCDS35182.2	9q34.3	2011-10-24			ENSG00000187922	ENSG00000187922		"Lipocalins"	20892	protein-coding gene	gene with protein product		612904				15363845	Standard	NM_001001712		Approved		uc004civ.3	Q6JVE6	OTTHUMG00000150428	ENST00000474369.1:c.550A>G	chr9.hg19:g.139633991T>C	ENSP00000420564:p.Thr184Ala	140.0	0.0	.		196.0	24.0	.	NM_001001712	A2RUU3|B0QZ79	Missense_Mutation	SNP	ENST00000474369.1	hg19	CCDS35182.2	.	.	.	.	.	.	.	.	.	.	T	13.52	2.260996	0.39995	.	.	ENSG00000187922	ENST00000527229;ENST00000497771;ENST00000474369	T;T	0.33865	1.39;1.41	3.17	2.04	0.26737	.	0.000000	0.36002	U	0.002855	T	0.39655	0.1086	.	.	.	0.27101	N	0.962612	D;D;D	0.71674	0.998;0.998;0.998	D;D;D	0.63957	0.92;0.92;0.92	T	0.17410	-1.0370	9	0.19147	T	0.46	-7.4152	4.3041	0.10938	0.0:0.1588:0.0:0.8412	.	161;184;197	E9PK15;Q6JVE6;Q6JVE6-2	.;LCN10_HUMAN;.	A	161;197;184	ENSP00000418491:T197A;ENSP00000420564:T184A	ENSP00000420564:T184A	T	-	1	0	LCN10	138753812	0.530000	0.26330	1.000000	0.80357	0.718000	0.41266	1.557000	0.36299	1.410000	0.46936	0.451000	0.29950	ACC	.	.	.	none		0.617	LCN10-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318062.2	NM_001001712		C	139633991	T	C	139633991	3	2	196	1	0	0	0	0	1	0	0	0	8688	1696	59	3	17	3	LCN10	9	139633991	Missense_Mutation	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10	8271628	139633991	1579440	33	11774											
CUBN	8029	hgsc.bcm.edu	37	chr10	16941145	16941145	+	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	tgaggccagtgaggggatctGattgtaccattatcagaatg	11	11	13	6	0	2	4	1	3	1	1	2	5	2	5	2	3	1	1	2	3	3	3			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr10:16941145G>C	ENST00000377833.4	-	54	8513	c.8448C>G	c.(8446-8448)atC>atG	p.I2816M		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2816	CUB 21. {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)	GAGGGGATCTGATTGTACCAT	0.403																																					p.I2816M		Atlas-SNP	.											.	CUBN	515	.	0			c.C8448G						PASS	.						118	112	114					10																	16941145		2203	4300	6503	SO:0001583	missense	8029	exon54			GGATCTGATTGTA	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.8448C>G	chr10.hg19:g.16941145G>C	ENSP00000367064:p.Ile2816Met	92.0	0.0	.		100.0	4.0	.	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	G	9.641	1.139005	0.21123	.	.	ENSG00000107611	ENST00000377833	T	0.40476	1.03	5.63	0.557	0.17260	CUB (5);	0.137522	0.33057	N	0.005332	T	0.64494	0.2603	M	0.93150	3.385	0.80722	D	1	D	0.60160	0.987	P	0.62298	0.9	T	0.64782	-0.6326	10	0.66056	D	0.02	.	7.5405	0.27735	0.1201:0.0:0.4925:0.3874	.	2816	O60494	CUBN_HUMAN	M	2816	ENSP00000367064:I2816M	ENSP00000367064:I2816M	I	-	3	3	CUBN	16981151	1.000000	0.71417	0.001000	0.08648	0.014000	0.08584	3.071000	0.50041	-0.070000	0.12908	-0.940000	0.02684	ATC	.	.	.	none		0.403	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		C	16941145	G	C	16941145	3	2	196	1	0	0	0	0	1	0	0	0	4053	1280	45	4	2479	4	CUBN	10	16941145	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10		16941145	118593602	34	11775											
NUDT13	25961	hgsc.bcm.edu	37	chr10	74879794	74879794	+	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	aggtatttatttgaactgaaGgaagatgatgatgcatgtaa	15	13	11	2	0	0	5	0	4	0	1	0	6	0	6	0	2	2	3	0	2	6	5			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr10:74879794G>T	ENST00000357321.4	+	3	220	c.102G>T	c.(100-102)aaG>aaT	p.K34N	NUDT13_ENST00000372997.3_Missense_Mutation_p.K34N|NUDT13_ENST00000488223.1_3'UTR|NUDT13_ENST00000544879.1_5'UTR|NUDT13_ENST00000537969.1_5'UTR|NUDT13_ENST00000349051.5_Missense_Mutation_p.K34N	NM_001283016.1|NM_015901.4	NP_001269945.1|NP_056985.3			nudix (nucleoside diphosphate linked moiety X)-type motif 13											large_intestine(2)|lung(5)	7	Prostate(51;0.0119)					TTGAACTGAAGGAAGATGATG	0.403																																					p.K34N		Atlas-SNP	.											.	NUDT13	16	.	0			c.G102T						PASS	.						134	144	141					10																	74879794		2203	4300	6503	SO:0001583	missense	25961	exon3			ACTGAAGGAAGAT	AL050114	CCDS31220.1, CCDS60551.1, CCDS60552.1, CCDS60553.1, CCDS73148.1	10q22.3	2014-04-24			ENSG00000166321	ENSG00000166321		"Nudix motif containing"	18827	protein-coding gene	gene with protein product		609233				15164054	Standard	NM_001283019		Approved	DKFZp586P2219	uc001jtj.3	Q86X67	OTTHUMG00000018453	ENST00000357321.4:c.102G>T	chr10.hg19:g.74879794G>T	ENSP00000349874:p.Lys34Asn	51.0	0.0	.		43.0	15.0	.	NM_015901		Missense_Mutation	SNP	ENST00000357321.4	hg19	CCDS31220.1	.	.	.	.	.	.	.	.	.	.	G	18.98	3.736917	0.69304	.	.	ENSG00000166321	ENST00000357321;ENST00000349051;ENST00000372997	T;T;T	0.58797	1.36;0.36;0.31	5.18	-2.34	0.06704	.	0.000000	0.85682	D	0.000000	T	0.60932	0.2307	L	0.32530	0.975	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.992;0.993	T	0.59862	-0.7374	10	0.72032	D	0.01	-2.5729	12.2089	0.54369	0.6313:0.0:0.3687:0.0	.	34;34;34	Q86X67-2;Q5SQM6;Q86X67	.;.;NUD13_HUMAN	N	34	ENSP00000349874:K34N;ENSP00000335326:K34N;ENSP00000362088:K34N	ENSP00000335326:K34N	K	+	3	2	NUDT13	74549800	0.999000	0.42202	0.977000	0.42913	0.998000	0.95712	0.456000	0.21859	-0.547000	0.06207	0.655000	0.94253	AAG	.	.	.	none		0.403	NUDT13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048614.1	NM_015901		T	74879794	G	T	74879794	3	4	196	1	0	0	0	0	1	0	0	0	10736	991	35	4	108	4	NUDT13	10	74879794	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	57938649	74879794	60654953	35	11776											
LZTS2	84445	hgsc.bcm.edu	37	chr10	102763858	102763858	+	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	tcctggaaggaaagctccgaGaccgggaggcagagcttcag	11	5	15	10	2	1	2	1	0	0	2	3	6	3	5	3	4	2	3	3	4	2	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr10:102763858G>C	ENST00000370220.1	+	2	4066	c.1003G>C	c.(1003-1005)Gac>Cac	p.D335H	LZTS2_ENST00000370223.3_Missense_Mutation_p.D335H					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)		AAAGCTCCGAGACCGGGAGGC	0.637																																					p.D335H	Esophageal Squamous(8;38 437 13604 19902 37640)	Atlas-SNP	.											.	LZTS2	57	.	0			c.G1003C						PASS	.						43	47	46					10																	102763858		2202	4297	6499	SO:0001583	missense	84445	exon3			CTCCGAGACCGGG	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.1003G>C	chr10.hg19:g.102763858G>C	ENSP00000359240:p.Asp335His	122.0	0.0	.		156.0	33.0	.	NM_032429		Missense_Mutation	SNP	ENST00000370220.1	hg19	CCDS7507.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.123472	0.56613	.	.	ENSG00000107816	ENST00000370223;ENST00000315797;ENST00000370220	T;T	0.41065	1.01;1.01	5.12	4.19	0.49359	.	0.157325	0.56097	D	0.000028	T	0.42494	0.1205	L	0.39898	1.24	0.43222	D	0.995102	P	0.40398	0.716	P	0.45946	0.498	T	0.20405	-1.0276	9	.	.	.	-23.6803	15.3201	0.74115	0.0:0.1408:0.8592:0.0	.	335	Q9BRK4	LZTS2_HUMAN	H	335	ENSP00000359243:D335H;ENSP00000359240:D335H	.	D	+	1	0	LZTS2	102753848	1.000000	0.71417	0.732000	0.30844	0.655000	0.38815	7.542000	0.82095	1.243000	0.43853	0.561000	0.74099	GAC	.	.	.	none		0.637	LZTS2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049872.1	XM_046743		C	102763858	G	C	102763858	3	2	196	1	0	0	0	0	1	0	0	0	9146	942	33	4	1009	4	LZTS2	10	102763858	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	27884064	102763858	32770889	36	11777											
TIAL1	7073	hgsc.bcm.edu	37	chr10	121338280	121338280	+	Missense_Mutation	SNP	A	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	aggtggtttacgagtggcccAattggttcggatttgacgac	8	12	14	7	3	0	1	0	1	0	0	1	4	0	2	1	5	1	2	1	5	2	5			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr10:121338280A>C	ENST00000436547.2	-	7	558	c.514T>G	c.(514-516)Tgg>Ggg	p.W172G	TIAL1_ENST00000369092.4_Missense_Mutation_p.W49G|TIAL1_ENST00000463089.2_5'Flank|TIAL1_ENST00000369093.2_Missense_Mutation_p.W189G	NM_003252.3	NP_003243.1	Q01085	TIAR_HUMAN	TIA1 cytotoxic granule-associated RNA binding protein-like 1	172	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				apoptotic process (GO:0006915)|defense response (GO:0006952)|germ cell development (GO:0007281)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell division (GO:0017145)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(3)|ovary(1)	13		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00239)|BRCA - Breast invasive adenocarcinoma(275;0.0932)		CGAGTGGCCCAATTGGTTCGG	0.398																																					p.W189G		Atlas-SNP	.											.	TIAL1	47	.	0			c.T565G						PASS	.						160	141	147					10																	121338280		2203	4300	6503	SO:0001583	missense	7073	exon7			TGGCCCAATTGGT	AL833106	CCDS7613.1, CCDS31295.1	10q	2013-02-12	2001-11-28		ENSG00000151923	ENSG00000151923		"RNA binding motif (RRM) containing"	11804	protein-coding gene	gene with protein product		603413	"TIA1 cytotoxic granule-associated RNA-binding protein-like 1"			1326761	Standard	XM_005270108		Approved	TIAR	uc001lej.1	Q01085	OTTHUMG00000019156	ENST00000436547.2:c.514T>G	chr10.hg19:g.121338280A>C	ENSP00000394902:p.Trp172Gly	173.0	0.0	.		183.0	39.0	.	NM_001033925	A8K3T0|A8K4L9	Missense_Mutation	SNP	ENST00000436547.2	hg19	CCDS7613.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.385753	0.82792	.	.	ENSG00000151923	ENST00000369093;ENST00000369092;ENST00000436547	T;T;T	0.75367	3.33;-0.93;-0.93	5.61	5.61	0.85477	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.000000	0.85682	D	0.000000	D	0.85008	0.5599	M	0.65975	2.015	0.80722	D	1	D;D;D;D	0.89917	0.993;1.0;1.0;0.999	D;D;D;D	0.91635	0.968;0.999;0.994;0.966	D	0.86674	0.1912	10	0.87932	D	0	-1.9553	15.8113	0.78568	1.0:0.0:0.0:0.0	.	49;49;189;172	B4DHS3;Q49AS9;A8K4L9;Q01085	.;.;.;TIAR_HUMAN	G	189;49;172	ENSP00000358089:W189G;ENSP00000358088:W49G;ENSP00000394902:W172G	ENSP00000358088:W49G	W	-	1	0	TIAL1	121328270	1.000000	0.71417	0.993000	0.49108	0.863000	0.49368	9.125000	0.94402	2.137000	0.66172	0.482000	0.46254	TGG	.	.	.	none		0.398	TIAL1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050672.2	NM_022333, NM_003252		C	121338280	A	C	121338280	3	2	196	1	0	0	0	0	1	0	0	0	15901	130	5	5	637	5	TIAL1	10	121338280	Missense_Mutation	SNP	A	TCGA-HE-A5NF-01A-11D-A26P-10	18574422	121338280	14196467	37	11778											
WDR11	55717	hgsc.bcm.edu	37	chr10	122664157	122664157	+	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	aaaaaccgtttctcttactaGacagacagagctgtgcagtt	13	11	8	9	1	1	3	0	0	1	3	2	3	1	3	1	0	4	4	1	0	4	4			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr10:122664157G>A	ENST00000263461.6	+	25	3273		c.e25-1		WDR11_ENST00000604509.1_Intron	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11						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						TCTCTTACTAGACAGACAGAG	0.358																																					.		Atlas-SNP	.											.	WDR11	95	.	0			c.3028-1G>A						PASS	.						93	89	90					10																	122664157		2203	4300	6503	SO:0001630	splice_region_variant	55717	exon25			TTACTAGACAGAC	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.3028-1G>A	chr10.hg19:g.122664157G>A		93.0	0.0	.		98.0	15.0	.	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Splice_Site	SNP	ENST00000263461.6	hg19	CCDS7619.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.566439	0.86439	.	.	ENSG00000120008	ENST00000263461	.	.	.	5.97	5.97	0.96955	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.4387	0.99107	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	WDR11	122654147	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	9.434000	0.97515	2.836000	0.97738	0.655000	0.94253	.	.	.	.	none		0.358	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		Intron	A	122664157	G	A	122664157	5	1	196	1	0	0	0	0	0	0	1	0	17285	956	33	2	3125	2	WDR11	10	122664157	Splice_Site	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	1325877	122664157	12870590	38	11779											
C11orf40	143501	hgsc.bcm.edu	37	chr11	4592781	4592781	+	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	aagtgttttgtaatcagtgcGgtccaattcaatggcccagt	10	13	10	8	1	2	0	2	0	0	0	3	0	3	0	2	2	1	2	2	2	4	4	rs573632085	byFrequency	TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr11:4592781G>C	ENST00000307616.1	-	4	525	c.526C>G	c.(526-528)Cgc>Ggc	p.R176G		NM_144663.1	NP_653264.1	Q8WZ69	CK040_HUMAN	chromosome 11 open reading frame 40	176										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)		taatcagtgcggtccaattca	0.433																																					p.R176G		Atlas-SNP	.											.	C11orf40	37	.	0			c.C526G						PASS	.						81	73	76					11																	4592781		2201	4298	6499	SO:0001583	missense	143501	exon4			CAGTGCGGTCCAA		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.526C>G	chr11.hg19:g.4592781G>C	ENSP00000302918:p.Arg176Gly	67.0	0.0	.		86.0	14.0	.	NM_144663		Missense_Mutation	SNP	ENST00000307616.1	hg19	CCDS31354.1	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.039801	0.00402	.	.	ENSG00000171987	ENST00000307616	T	0.55930	0.49	0.832	-1.66	0.08265	.	.	.	.	.	T	0.26774	0.0655	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.08743	-1.0707	9	0.87932	D	0	.	3.0485	0.06161	0.2412:0.0:0.4837:0.275	.	176	Q8WZ69	CK040_HUMAN	G	176	ENSP00000302918:R176G	ENSP00000302918:R176G	R	-	1	0	C11orf40	4549357	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.923000	0.04000	-1.894000	0.01105	-1.561000	0.00884	CGC	.	.	.	none		0.433	C11orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383529.1	NM_144663		C	4592781	G	C	4592781	3	2	196	1	0	0	0	0	1	0	0	0	1641	1116	39	4	130	4	C11orf40	11	4592781	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10		4592781	130413735	39	11780											
DCHS1	8642	hgsc.bcm.edu	37	chr11	6646473	6646473	+	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	aggtgcattgtcattgacatCctccacaagcactgtgaggt	10	11	10	10	0	1	2	1	2	0	0	3	2	3	2	2	2	2	2	2	2	1	2			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr11:6646473C>G	ENST00000299441.3	-	19	7513	c.7102G>C	c.(7102-7104)Gat>Cat	p.D2368H	RP11-732A19.5_ENST00000526456.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	2368	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)		TCATTGACATCCTCCACAAGC	0.587																																					p.D2368H		Atlas-SNP	.											.	DCHS1	277	.	0			c.G7102C						PASS	.						101	92	95					11																	6646473		2201	4296	6497	SO:0001583	missense	8642	exon19			TGACATCCTCCAC	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.7102G>C	chr11.hg19:g.6646473C>G	ENSP00000299441:p.Asp2368His	97.0	0.0	.		136.0	20.0	.	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	hg19	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	c	22.9	4.351321	0.82132	.	.	ENSG00000166341	ENST00000299441	T	0.76186	-1.0	4.94	4.94	0.65067	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.43747	D	0.000525	D	0.91202	0.7228	H	0.97682	4.055	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.94164	0.7417	10	0.87932	D	0	.	16.9335	0.86197	0.0:1.0:0.0:0.0	.	2368	Q96JQ0	PCD16_HUMAN	H	2368	ENSP00000299441:D2368H	ENSP00000299441:D2368H	D	-	1	0	DCHS1	6603049	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.632000	0.83247	2.560000	0.86352	0.651000	0.88453	GAT	.	.	.	none		0.587	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		G	6646473	C	G	6646473	3	3	196	1	0	0	0	0	1	0	0	0	4289	855	30	4	2806	4	DCHS1	11	6646473	Missense_Mutation	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10	2053692	6646473	128360043	40	11781											
LRP4	4038	hgsc.bcm.edu	37	chr11	46898795	46898795	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatggtgttcttcatggtaaTgttgattggtaccaccacat	10	15	9	7	0	2	1	1	1	1	0	2	1	2	1	2	3	1	4	2	3	3	6			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr11:46898795T>C	ENST00000378623.1	-	23	3474	c.3232A>G	c.(3232-3234)Att>Gtt	p.I1078V	LRP4-AS1_ENST00000502049.2_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1078					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)		TTCATGGTAATGTTGATTGGT	0.507																																					p.I1078V		Atlas-SNP	.											.	LRP4	160	.	0			c.A3232G						PASS	.						250	187	208					11																	46898795		2201	4299	6500	SO:0001583	missense	4038	exon23			TGGTAATGTTGAT	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.3232A>G	chr11.hg19:g.46898795T>C	ENSP00000367888:p.Ile1078Val	183.0	0.0	.		176.0	25.0	.	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	hg19	CCDS31478.1	.	.	.	.	.	.	.	.	.	.	T	12.62	1.991485	0.35131	.	.	ENSG00000134569	ENST00000378623	D	0.90955	-2.76	6.17	-1.45	0.08828	Six-bladed beta-propeller, TolB-like (1);	0.729507	0.14357	N	0.324711	T	0.70850	0.3271	N	0.00926	-1.1	0.20926	N	0.999826	B	0.02656	0.0	B	0.01281	0.0	T	0.58440	-0.7636	10	0.14656	T	0.56	.	13.3945	0.60843	0.0:0.5812:0.0:0.4188	.	1078	O75096	LRP4_HUMAN	V	1078	ENSP00000367888:I1078V	ENSP00000367888:I1078V	I	-	1	0	LRP4	46855371	1.000000	0.71417	0.959000	0.39883	0.998000	0.95712	0.814000	0.27239	-0.251000	0.09542	0.533000	0.62120	ATT	.	.	.	none		0.507	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334		C	46898795	T	C	46898795	3	2	196	1	0	0	0	0	1	0	0	0	8966	1464	51	3	2549	3	LRP4	11	46898795	Missense_Mutation	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10	40252322	46898795	88107721	41	11782											
AMOTL1	154810	hgsc.bcm.edu	37	chr11	94533391	94533391	+	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	cccgggatgctccacgagatGgtcaagccctaccctgctcc	7	7	10	17	2	1	1	1	0	0	1	3	3	3	2	5	2	4	2	5	2	2	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr11:94533391G>T	ENST00000433060.2	+	3	1176	c.1035G>T	c.(1033-1035)atG>atT	p.M345I	AMOTL1_ENST00000317837.9_Missense_Mutation_p.M345I|AMOTL1_ENST00000317829.8_Missense_Mutation_p.M295I	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	345					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)				TCCACGAGATGGTCAAGCCCT	0.562																																					p.M345I		Atlas-SNP	.											.	AMOTL1	95	.	0			c.G1035T						PASS	.						115	116	116					11																	94533391		2016	4172	6188	SO:0001583	missense	154810	exon3			CGAGATGGTCAAG	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.1035G>T	chr11.hg19:g.94533391G>T	ENSP00000387739:p.Met345Ile	121.0	0.0	.		127.0	22.0	.	NM_130847	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Missense_Mutation	SNP	ENST00000433060.2	hg19	CCDS44712.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.471025	0.43942	.	.	ENSG00000166025	ENST00000317829;ENST00000542840;ENST00000317837;ENST00000433060	T;T;T	0.13307	2.6;2.6;2.6	5.13	4.15	0.48705	.	0.155049	0.44688	D	0.000423	T	0.10380	0.0254	L	0.40543	1.245	0.30008	N	0.815444	B;B	0.16802	0.013;0.019	B;B	0.13407	0.009;0.006	T	0.06127	-1.0844	9	.	.	.	-21.0972	7.6609	0.28402	0.0937:0.2865:0.6198:0.0	.	295;345	Q8IY63-2;Q8IY63	.;AMOL1_HUMAN	I	295;351;345;345	ENSP00000320968:M295I;ENSP00000323474:M345I;ENSP00000387739:M345I	.	M	+	3	0	AMOTL1	94173039	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	0.997000	0.29731	2.395000	0.81488	0.555000	0.69702	ATG	.	.	.	none		0.562	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847		T	94533391	G	T	94533391	3	4	196	1	0	0	0	0	1	0	0	0	583	1348	47	4	1045	4	AMOTL1	11	94533391	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	47634596	94533391	40473125	42	11783											
ZW10	9183	hgsc.bcm.edu	37	chr11	113619115	113619115	+	Frame_Shift_Del	DEL	T	T	-																															ggacagtagatgttttttcaTtttccaggtcagtgtcaagt																										TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr11:113619115delT	ENST00000200135.3	-	8	1097	c.953delA	c.(952-954)aatfs	p.N318fs		NM_004724.3	NP_004715.1	O43264	ZW10_HUMAN	zw10 kinetochore protein	318					ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic metaphase plate congression (GO:0007080)|mitotic sister chromatid segregation (GO:0000070)|protein complex assembly (GO:0006461)|protein localization to kinetochore (GO:0034501)|protein transport (GO:0015031)|regulation of exit from mitosis (GO:0007096)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|nucleus (GO:0005634)|spindle pole (GO:0000922)	centromeric DNA binding (GO:0019237)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)	18		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)		TGTTTTTTCATTTTCCAGGTC	0.373																																					p.N318fs		Pindel	.											.	ZW10	49	.	0			c.954delT						PASS	.						94	87	90					11																	113619115		2201	4296	6497	SO:0001589	frameshift_variant	9183	exon8			.	U54996	CCDS8363.1	11q23	2013-01-17	2012-12-13		ENSG00000086827	ENSG00000086827			13194	protein-coding gene	gene with protein product		603954	"ZW10 (Drosophila) homolog, centromere/kinetochore protein", "ZW10, kinetochore associated, homolog (Drosophila)"			9298984	Standard	NM_004724		Approved	KNTC1AP	uc001poe.3	O43264	OTTHUMG00000168190	ENST00000200135.3:c.953delA	chr11.hg19:g.113619115delT	ENSP00000200135:p.Asn318fs	62.0	0.0	.		67.0	10.0	0.149	NM_004724	A1A528	Frame_Shift_Del	DEL	ENST00000200135.3	hg19	CCDS8363.1																																																																																			.	.	.	none		0.373	ZW10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398700.1	NM_004724		-	113619115	T	-	113619115	7	5	196	1	0	1	0	1	0	0	0	0	18259	1493	52	0	1422	0	ZW10	11	113619115	Frame_Shift_Del	DEL	T	TCGA-HE-A5NF-01A-11D-A26P-10	19085724	113619115	21387401	43	11784											
TMBIM4	51643	hgsc.bcm.edu	37	chr12	66546147	66546147	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccgagggcaaacagcaaaatTaaggcaggactgaaagacat	18	4	11	8	1	0	2	0	1	0	1	0	4	0	3	1	3	2	3	1	3	5	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr12:66546147T>C	ENST00000358230.3	-	3	336	c.216A>G	c.(214-216)ttA>ttG	p.L72L	TMBIM4_ENST00000544599.1_5'UTR|TMBIM4_ENST00000556010.1_Silent_p.L72L|TMBIM4_ENST00000286424.7_Silent_p.L119L|TMBIM4_ENST00000398033.4_Silent_p.L72L|TMBIM4_ENST00000539652.1_Silent_p.L72L|TMBIM4_ENST00000542724.1_Silent_p.L41L	NM_016056.2	NP_057140.2	Q9HC24	LFG4_HUMAN	transmembrane BAX inhibitor motif containing 4	72					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|regulation of calcium-mediated signaling (GO:0050848)	Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|ovary(1)|prostate(2)	9				GBM - Glioblastoma multiforme(28;0.0745)		ACAGCAAAATTAAGGCAGGAC	0.303																																					p.L72L		Atlas-SNP	.											.	TMBIM4	47	.	0			c.A216G						PASS	.						79	75	76					12																	66546147		1821	4077	5898	SO:0001819	synonymous_variant	51643	exon3			CAAAATTAAGGCA	AF113127	CCDS41805.1, CCDS61187.1, CCDS73493.1	12q14.3	2014-05-09			ENSG00000155957	ENSG00000155957			24257	protein-coding gene	gene with protein product						11042152, 10810093	Standard	NM_001282609		Approved	CGI-119, S1R, ZPRO, LFG4, GAAP	uc001stc.3	Q9HC24	OTTHUMG00000168973	ENST00000358230.3:c.216A>G	chr12.hg19:g.66546147T>C		114.0	0.0	.		123.0	20.0	.	NM_016056	Q542Z6|Q9UHY5|Q9Y3C2	Silent	SNP	ENST00000358230.3	hg19	CCDS41805.1																																																																																			.	.	.	none		0.303	TMBIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401832.2	NM_016056		C	66546147	T	C	66546147	2	2	196	1	0	0	0	0	0	0	0	1	15994	1751	61	3		3	TMBIM4	12	66546147	Silent	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10		66546147	67305748	44	11785											
ZNF140	7699	hgsc.bcm.edu	37	chr12	133683062	133683062	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcagccggagcttttcccTcattctacatcagagaactc	9	12	6	14	1	4	1	3	0	1	1	6	3	5	2	2	1	4	1	2	1	2	5			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr12:133683062T>C	ENST00000355557.2	+	5	2482	c.1199T>C	c.(1198-1200)cTc>cCc	p.L400P	ZNF140_ENST00000440550.2_3'UTR|ZNF140_ENST00000544426.1_Missense_Mutation_p.L297P	NM_003440.2	NP_003431.2	P52738	ZN140_HUMAN	zinc finger protein 140	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.114)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		AGCTTTTCCCTCATTCTACAT	0.448																																					p.L400P		Atlas-SNP	.											.	ZNF140	18	.	0			c.T1199C						PASS	.						90	91	91					12																	133683062		2203	4300	6503	SO:0001583	missense	7699	exon5			TTTCCCTCATTCT	U09368	CCDS9282.1, CCDS73550.1	12q24.33	2013-01-08	2006-06-13		ENSG00000196387	ENSG00000196387		"Zinc fingers, C2H2-type", "-"	12925	protein-coding gene	gene with protein product		604082	"zinc finger protein 140 (clone pHZ-39)"			7557990	Standard	XR_245353		Approved	pHZ-39	uc001ulo.3	P52738	OTTHUMG00000167942	ENST00000355557.2:c.1199T>C	chr12.hg19:g.133683062T>C	ENSP00000347755:p.Leu400Pro	21.0	0.0	.		47.0	7.0	.	NM_003440	D3DXJ3|Q05CP6|Q8IV75	Missense_Mutation	SNP	ENST00000355557.2	hg19	CCDS9282.1	.	.	.	.	.	.	.	.	.	.	T	17.08	3.296703	0.60086	.	.	ENSG00000196387	ENST00000355557;ENST00000544426;ENST00000433577	T;T	0.14266	2.52;2.52	3.85	3.85	0.44370	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.31859	N	0.006952	T	0.39627	0.1085	M	0.89715	3.055	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.36672	-0.9738	10	0.87932	D	0	.	7.0829	0.25241	0.0:0.1065:0.0:0.8935	.	400	P52738	ZN140_HUMAN	P	400;297;191	ENSP00000347755:L400P;ENSP00000445411:L297P	ENSP00000347755:L400P	L	+	2	0	ZNF140	132193135	0.996000	0.38824	0.998000	0.56505	0.958000	0.62258	5.435000	0.66532	1.736000	0.51660	0.460000	0.39030	CTC	.	.	.	none		0.448	ZNF140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397169.1	NM_003440		C	133683062	T	C	133683062	3	2	196	1	0	0	0	0	1	0	0	0	17741	1551	54	3	1213	3	ZNF140	12	133683062	Missense_Mutation	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10	67136915	133683062	168833	45	11786											
KCTD12	115207	hgsc.bcm.edu	37	chr13	77460122	77460122	+	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	cagagcagcgagtcgggcacCgacaccaccgtgcagcgccg	9	2	14	16	6	0	1	0	0	0	1	1	3	0	1	4	1	4	3	4	1	0	0	rs371800969		TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr13:77460122C>G	ENST00000377474.2	-	1	403	c.162G>C	c.(160-162)tcG>tcC	p.S54S	AC000403.1_ENST00000579275.1_RNA|KCTD12_ENST00000317765.2_Silent_p.S54S	NM_138444.3	NP_612453.1	Q96CX2	KCD12_HUMAN	potassium channel tetramerization domain containing 12	54					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(1)|lung(1)|ovary(1)	4		Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.0499)		AGTCGGGCACCGACACCACCG	0.692																																					p.S54S		Atlas-SNP	.											.	KCTD12	11	.	0			c.G162C						PASS	.	C		0,4356		0,0,2178	16	15	15		162	0.4	1	13		15	2,8550		0,2,4274	no	coding-synonymous	KCTD12	NM_138444.3		0,2,6452	GG,GC,CC		0.0234,0.0,0.0155		54/326	77460122	2,12906	2178	4276	6454	SO:0001819	synonymous_variant	115207	exon1			GGGCACCGACACC	AF359381	CCDS9455.1	13q21	2013-06-20	2013-06-20	2003-11-26	ENSG00000178695	ENSG00000178695			14678	protein-coding gene	gene with protein product	"predominantly fetal expressed T1 domain"	610521	"chromosome 13 open reading frame 2", "potassium channel tetramerisation domain containing 12"	C13orf2		15357420	Standard	NM_138444		Approved	KIAA1778, PFET1	uc010aeu.1	Q96CX2	OTTHUMG00000017096	ENST00000377474.2:c.162G>C	chr13.hg19:g.77460122C>G		2.0	0.0	.		6.0	4.0	.	NM_138444		Silent	SNP	ENST00000377474.2	hg19	CCDS9455.1																																																																																			.	.	.	weak		0.692	KCTD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045309.2	NM_138444		G	77460122	C	G	77460122	2	3	196	1	0	0	0	0	0	0	0	1	8106	639	23	4		4	KCTD12	13	77460122	Silent	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10		77460122	37709756	46	11787											
TEP1	7011	hgsc.bcm.edu	37	chr14	20845648	20845648	+	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	cctgaccctgagccccctggGaacctagagaatgagagaga	12	5	12	12	0	0	5	0	3	0	3	0	9	0	6	5	1	2	0	5	1	3	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr14:20845648G>T	ENST00000262715.5	-	41	5919	c.5879C>A	c.(5878-5880)tCc>tAc	p.S1960Y	TEP1_ENST00000545983.1_Missense_Mutation_p.S298Y|TEP1_ENST00000556935.1_Missense_Mutation_p.S1852Y	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1960					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)		AGCCCCCTGGGAACCTAGAGA	0.582																																					p.S1960Y		Atlas-SNP	.											.	TEP1	224	.	0			c.C5879A						PASS	.						53	54	54					14																	20845648		2203	4300	6503	SO:0001583	missense	7011	exon41			CCCTGGGAACCTA		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.5879C>A	chr14.hg19:g.20845648G>T	ENSP00000262715:p.Ser1960Tyr	79.0	0.0	.		76.0	17.0	.	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	hg19	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.164956	0.78339	.	.	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935;ENST00000545983	T;T;T	0.71461	0.73;-0.57;1.23	5.33	5.33	0.75918	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.606102	0.17469	N	0.173149	T	0.80639	0.4661	M	0.71036	2.16	0.38057	D	0.935966	D;D;D;D	0.59767	0.976;0.983;0.986;0.971	P;P;P;P	0.57152	0.556;0.804;0.814;0.641	D	0.83486	0.0067	10	0.59425	D	0.04	-4.4509	15.9418	0.79758	0.0:0.0:1.0:0.0	.	298;1852;1303;1960	B4E0B6;G3V5X7;G3V2A4;Q99973	.;.;.;TEP1_HUMAN	Y	1960;1960;1852;298	ENSP00000262715:S1960Y;ENSP00000452574:S1852Y;ENSP00000438849:S298Y	ENSP00000262715:S1960Y	S	-	2	0	TEP1	19915488	0.983000	0.35010	0.894000	0.35097	0.940000	0.58332	4.982000	0.63825	2.502000	0.84385	0.563000	0.77884	TCC	.	.	.	none		0.582	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		T	20845648	G	T	20845648	3	4	196	1	0	0	0	0	1	0	0	0	15771	1174	41	4	2064	4	TEP1	14	20845648	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10		20845648	86503892	47	11788											
CDH24	64403	hgsc.bcm.edu	37	chr14	23524349	23524349	+	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	gtcgttgatgtcttgcacttTgatgatgaactctgatgggg	7	15	13	6	1	2	5	0	5	2	0	3	5	2	5	0	2	2	2	0	2	1	3			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr14:23524349T>A	ENST00000267383.5	-	2	507	c.415A>T	c.(415-417)Aaa>Taa	p.K139*	CDH24_ENST00000554034.1_Nonsense_Mutation_p.K139*|CDH24_ENST00000397359.3_Nonsense_Mutation_p.K139*|CDH24_ENST00000487137.2_Nonsense_Mutation_p.K139*			Q86UP0	CAD24_HUMAN	cadherin 24, type 2	139	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|delta-catenin binding (GO:0070097)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00654)		TCTTGCACTTTGATGATGAAC	0.587											OREG0022594	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K139X		Atlas-SNP	.											.	CDH24	129	.	0			c.A415T						PASS	.						86	90	88					14																	23524349		2203	4300	6503	SO:0001587	stop_gained	64403	exon3			GCACTTTGATGAT	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.415A>T	chr14.hg19:g.23524349T>A	ENSP00000267383:p.Lys139*	118.0	0.0	.	764	138.0	23.0	.	NM_022478	D3DS44|Q86UP1|Q9NT84	Nonsense_Mutation	SNP	ENST00000267383.5	hg19	CCDS9585.1	.	.	.	.	.	.	.	.	.	.	T	36	5.772834	0.96922	.	.	ENSG00000139880	ENST00000397359;ENST00000487137;ENST00000422751;ENST00000554034;ENST00000267383	.	.	.	3.72	3.72	0.42706	.	0.061985	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.8066	0.52158	0.0:0.0:0.0:1.0	.	.	.	.	X	139	.	ENSP00000267383:K139X	K	-	1	0	CDH24	22594189	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.825000	0.86693	1.689000	0.51079	0.459000	0.35465	AAA	.	.	.	none		0.587	CDH24-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257241.2	NM_022478		A	23524349	T	A	23524349	4	1	196	1	0	0	0	0	0	1	0	0	3111	1821	63	5	2088	5	CDH24	14	23524349	Nonsense_Mutation	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10	2678701	23524349	83825191	48	11789											
NYNRIN	57523	hgsc.bcm.edu	37	chr14	24885037	24885037	+	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	cctggcagccgtggcctgcgGcctggagcgctttggccagt	3	8	16	14	3	0	0	0	0	0	0	0	1	0	1	5	5	3	2	5	5	0	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr14:24885037G>T	ENST00000382554.3	+	9	4400	c.4082G>T	c.(4081-4083)gGc>gTc	p.G1361V		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	1361					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						GTGGCCTGCGGCCTGGAGCGC	0.627																																					p.G1361V		Atlas-SNP	.											.	NYNRIN	120	.	0			c.G4082T						PASS	.						68	73	71					14																	24885037		1961	4143	6104	SO:0001583	missense	57523	exon9			CCTGCGGCCTGGA	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.4082G>T	chr14.hg19:g.24885037G>T	ENSP00000371994:p.Gly1361Val	66.0	0.0	.		85.0	27.0	.	NM_025081	Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	hg19	CCDS45090.1	.	.	.	.	.	.	.	.	.	.	G	14.65	2.597704	0.46318	.	.	ENSG00000205978	ENST00000382554	T	0.10668	2.85	4.93	4.02	0.46733	Ribonuclease H-like (1);	.	.	.	.	T	0.12603	0.0306	N	0.24115	0.695	0.49582	D	0.999804	P	0.50066	0.931	P	0.50860	0.652	T	0.03555	-1.1025	9	0.87932	D	0	.	11.5825	0.50900	0.0:0.3481:0.6519:0.0	.	1361	Q9P2P1	NYNRI_HUMAN	V	1361	ENSP00000371994:G1361V	ENSP00000371994:G1361V	G	+	2	0	NYNRIN	23954877	0.997000	0.39634	0.949000	0.38748	0.982000	0.71751	2.871000	0.48459	1.254000	0.44035	0.655000	0.94253	GGC	.	.	.	none		0.627	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1			T	24885037	G	T	24885037	3	4	196	1	0	0	0	0	1	0	0	0	10803	1203	42	4	4112	4	NYNRIN	14	24885037	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	1360688	24885037	82464503	49	11790											
MLH3	27030	hgsc.bcm.edu	37	chr14	75516201	75516205	+	Frame_Shift_Del	DEL	TGAAC	TGAAC	-																															caaatccattgtctatcactTgaacttggaaggtttccata																										TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	TGAAC	TGAAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr14:75516201_75516205delTGAAC	ENST00000556740.1	-	1	189_193	c.154_158delGTTCA	c.(154-159)gttcaafs	p.VQ52fs	MLH3_ENST00000556257.1_Frame_Shift_Del_p.VQ52fs|MLH3_ENST00000238662.7_Frame_Shift_Del_p.VQ52fs|MLH3_ENST00000380968.2_5'UTR|MLH3_ENST00000355774.2_Frame_Shift_Del_p.VQ52fs|MLH3_ENST00000555671.1_5'Flank|MLH3_ENST00000544985.1_5'Flank			Q9UHC1	MLH3_HUMAN	mutL homolog 3	52					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		GTCTATCACTTGAACTTGGAAGGTT	0.444								Mismatch excision repair (MMR)																													p.52_53del		Atlas-Indel,Pindel	.											.	MLH3	200	.	0			c.155_159del						PASS	.																																			SO:0001589	frameshift_variant	27030	exon2			.	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"mutL (E. coli) homolog 3", "mutL homolog 3 (E. coli)"			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.154_158delGTTCA	chr14.hg19:g.75516201_75516205delTGAAC	ENSP00000452316:p.Val52fs	157.0	0.0	0		172.0	22.0	0.127907	NM_014381	P49751|Q56DK9|Q9P292|Q9UHC0	Frame_Shift_Del	DEL	ENST00000556740.1	hg19	CCDS32123.1																																																																																			.	.	.	none		0.444	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381		-	75516205	TGAAC	-	75516201	7	5	196	1	0	1	0	1	0	0	0	0	9625	1812	63	0	4251	0	MLH3	14	75516201	Frame_Shift_Del	DEL	TGAAC	TCGA-HE-A5NF-01A-11D-A26P-10	50631164	75516201	31833339	50	11791											
ATXN3	4287	hgsc.bcm.edu	37	chr14	92549507	92549507	+	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	tgctaattcttctccaataaGttttggtcgatgcatctgtt	8	18	7	8	1	3	0	0	0	3	0	5	1	3	0	1	1	2	4	1	1	3	7			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr14:92549507G>C	ENST00000532032.1	-	7	580	c.571C>G	c.(571-573)Ctt>Gtt	p.L191V	ATXN3_ENST00000340660.6_Missense_Mutation_p.L136V|ATXN3_ENST00000503767.1_Missense_Mutation_p.L176V|ATXN3_ENST00000502250.1_Missense_Mutation_p.L12V|ATXN3_ENST00000429774.2_Missense_Mutation_p.L176V|ATXN3_ENST00000393287.5_Missense_Mutation_p.L191V|ATXN3_ENST00000545170.1_Missense_Mutation_p.L191V|ATXN3_ENST00000554491.1_5'UTR			P54252	ATX3_HUMAN	ataxin 3	191					actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|cellular response to misfolded protein (GO:0071218)|intermediate filament cytoskeleton organization (GO:0045104)|microtubule cytoskeleton organization (GO:0000226)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|monoubiquitinated protein deubiquitination (GO:0035520)|nervous system development (GO:0007399)|nucleotide-excision repair (GO:0006289)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of cell-substrate adhesion (GO:0010810)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATPase binding (GO:0051117)|identical protein binding (GO:0042802)|Lys48-specific deubiquitinase activity (GO:1990380)|Lys63-specific deubiquitinase activity (GO:0061578)|omega peptidase activity (GO:0008242)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)	12		all_cancers(154;0.0768)		COAD - Colon adenocarcinoma(157;0.224)		TCTCCAATAAGTTTTGGTCGA	0.368																																					p.L191V	Esophageal Squamous(190;752 2094 29897 44875 49530)	Atlas-SNP	.											.	ATXN3	46	.	0			c.C571G						PASS	.						146	138	141					14																	92549507		2203	4300	6503	SO:0001583	missense	4287	exon7			CAATAAGTTTTGG	U64820	CCDS9900.1, CCDS32143.1, CCDS45154.1, CCDS53908.1, CCDS73680.1	14q21	2014-09-17	2004-08-12	2004-08-13	ENSG00000066427	ENSG00000066427		"Ataxins"	7106	protein-coding gene	gene with protein product		607047	"Machado-Joseph disease (spinocerebellar ataxia 3, olivopontocerebellar ataxia 3, autosomal dominant, ataxin 3)"	SCA3, MJD		8358439	Standard	NM_004993		Approved	ATX3, JOS	uc001yac.4	P54252	OTTHUMG00000162212	ENST00000532032.1:c.571C>G	chr14.hg19:g.92549507G>C	ENSP00000437157:p.Leu191Val	42.0	0.0	.		47.0	7.0	.	NM_004993	A7LFZ5|D6RDL9|E9PB63|O15284|O15285|O15286|Q8N189|Q96TC3|Q96TC4|Q9H3N0	Missense_Mutation	SNP	ENST00000532032.1	hg19		.	.	.	.	.	.	.	.	.	.	G	25.0	4.587229	0.86851	.	.	ENSG00000066427	ENST00000545278;ENST00000539555;ENST00000537884;ENST00000545170;ENST00000447800;ENST00000359819;ENST00000393289;ENST00000429774;ENST00000539454;ENST00000393287;ENST00000502250;ENST00000503767;ENST00000340660;ENST00000532032;ENST00000555381;ENST00000557311;ENST00000554592;ENST00000554672;ENST00000553491;ENST00000556220;ENST00000506466	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.55760	2.13;2.17;2.16;0.72;2.16;1.82;1.81;1.42;0.5;1.85;1.41;1.39;1.38;1.45	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.71592	0.3358	M	0.65498	2.005	0.58432	D	0.999997	D;D;D;D;D	0.71674	0.974;0.993;0.97;0.998;0.996	P;P;P;D;D	0.75484	0.829;0.901;0.804;0.986;0.966	T	0.71866	-0.4463	10	0.46703	T	0.11	.	18.7593	0.91843	0.0:0.0:1.0:0.0	.	191;176;191;136;191	P54252;E9PB63;F5H096;P54252-3;P54252-2	ATX3_HUMAN;.;.;.;.	V	191;191;191;191;191;191;191;176;190;191;12;176;136;191;121;12;190;93;140;85;125	ENSP00000445618:L191V;ENSP00000389376:L176V;ENSP00000376965:L191V;ENSP00000425322:L12V;ENSP00000426697:L176V;ENSP00000339110:L136V;ENSP00000437157:L191V;ENSP00000451001:L121V;ENSP00000450642:L12V;ENSP00000451385:L190V;ENSP00000451417:L93V;ENSP00000451996:L140V;ENSP00000450641:L85V;ENSP00000435571:L125V	ENSP00000339110:L136V	L	-	1	0	ATXN3	91619260	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.235000	0.51328	2.450000	0.82876	0.478000	0.44815	CTT	.	.	.	none		0.368	ATXN3-015	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000388065.1	NM_004993		C	92549507	G	C	92549507	3	2	196	1	0	0	0	0	1	0	0	0	1213	1029	36	4	534	4	ATXN3	14	92549507	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	17033306	92549507	14800033	51	11792											
TLE3	7090	hgsc.bcm.edu	37	chr15	70368460	70368460	+	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	gtgacaggaaaggcatgatcTgtgctaaaattgtgttcagt	12	12	12	5	0	2	2	1	2	1	0	2	3	2	3	0	2	1	3	0	2	3	3			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr15:70368460T>A	ENST00000558939.1	-	5	1649	c.272A>T	c.(271-273)cAg>cTg	p.Q91L	TLE3_ENST00000560939.1_Missense_Mutation_p.Q97L|TLE3_ENST00000442299.2_Missense_Mutation_p.Q91L|TLE3_ENST00000560589.1_Missense_Mutation_p.Q35L|TLE3_ENST00000557997.1_Missense_Mutation_p.Q91L|TLE3_ENST00000539550.1_Missense_Mutation_p.Q25L|TLE3_ENST00000557907.1_Missense_Mutation_p.Q91L|TLE3_ENST00000317509.8_Missense_Mutation_p.Q91L|TLE3_ENST00000559929.1_Missense_Mutation_p.Q91L|TLE3_ENST00000440567.3_Missense_Mutation_p.Q84L|TLE3_ENST00000451782.2_Missense_Mutation_p.Q91L|TLE3_ENST00000559048.1_Missense_Mutation_p.Q97L|TLE3_ENST00000558379.1_Missense_Mutation_p.Q91L|TLE3_ENST00000559191.1_Intron|TLE3_ENST00000558201.1_Missense_Mutation_p.Q97L	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	91	Gln-rich.				Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						AGGCATGATCTGTGCTAAAAT	0.438																																					p.Q91L		Atlas-SNP	.											.	TLE3	104	.	0			c.A272T						PASS	.						170	166	167					15																	70368460		1956	4138	6094	SO:0001583	missense	7090	exon5			ATGATCTGTGCTA	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.272A>T	chr15.hg19:g.70368460T>A	ENSP00000452871:p.Gln91Leu	56.0	0.0	.		57.0	7.0	.	NM_001105192	B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Missense_Mutation	SNP	ENST00000558939.1	hg19	CCDS45293.1	.	.	.	.	.	.	.	.	.	.	T	33	5.250170	0.95305	.	.	ENSG00000140332	ENST00000442299;ENST00000451782;ENST00000317509;ENST00000440567;ENST00000539550	T;T;T;T;T	0.63913	0.26;0.29;0.34;0.26;-0.07	5.85	5.85	0.93711	Groucho/TLE, N-terminal Q-rich domain (1);	0.000000	0.85682	D	0.000000	T	0.81635	0.4864	M	0.93854	3.465	0.80722	D	1	P;P;D;P;P;P;P;P	0.54397	0.851;0.927;0.966;0.877;0.748;0.877;0.62;0.911	B;P;P;P;P;P;P;P	0.56216	0.419;0.794;0.783;0.72;0.575;0.72;0.46;0.786	D	0.86775	0.1975	10	0.87932	D	0	-17.3549	16.2303	0.82332	0.0:0.0:0.0:1.0	.	84;91;91;91;91;91;97;25	F8W964;E9PD64;Q04726-3;Q6PI57;Q04726-2;Q04726;Q04726-4;F5H7D6	.;.;.;.;.;TLE3_HUMAN;.;.	L	91;91;91;84;25	ENSP00000390007:Q91L;ENSP00000394717:Q91L;ENSP00000319233:Q91L;ENSP00000415057:Q84L;ENSP00000442594:Q25L	ENSP00000319233:Q91L	Q	-	2	0	TLE3	68155514	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.924000	0.87555	2.233000	0.73108	0.533000	0.62120	CAG	.	.	.	none		0.438	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1	NM_005078		A	70368460	T	A	70368460	3	1	196	1	0	0	0	0	1	0	0	0	15952	1580	55	5	2110	5	TLE3	15	70368460	Missense_Mutation	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10		70368460	32162932	52	11793											
UACA	55075	hgsc.bcm.edu	37	chr15	70961458	70961458	+	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	ttgttaagtgttctttaaggGcaagaaaatgggtctgcatt	11	15	11	4	0	2	1	0	0	2	1	2	1	2	1	0	2	1	4	0	2	5	6			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr15:70961458G>C	ENST00000322954.6	-	16	1750	c.1565C>G	c.(1564-1566)gCc>gGc	p.A522G	UACA_ENST00000539319.1_Missense_Mutation_p.A413G|UACA_ENST00000379983.2_Missense_Mutation_p.A509G|UACA_ENST00000560441.1_Missense_Mutation_p.A507G	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	522					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						TTCTTTAAGGGCAAGAAAATG	0.378																																					p.A522G		Atlas-SNP	.											.	UACA	235	.	0			c.C1565G						PASS	.						226	204	211					15																	70961458		2199	4297	6496	SO:0001583	missense	55075	exon16			TTAAGGGCAAGAA	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.1565C>G	chr15.hg19:g.70961458G>C	ENSP00000314556:p.Ala522Gly	92.0	0.0	.		84.0	4.0	.	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Missense_Mutation	SNP	ENST00000322954.6	hg19	CCDS10235.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.171155	0.78452	.	.	ENSG00000137831	ENST00000322954;ENST00000379983;ENST00000395362;ENST00000539319	T;T;T	0.46451	0.87;0.89;1.33	5.68	5.68	0.88126	.	0.000000	0.56097	D	0.000034	T	0.67031	0.2850	M	0.74258	2.255	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;0.998	T	0.66060	-0.6017	10	0.48119	T	0.1	-10.6478	19.7842	0.96430	0.0:0.0:1.0:0.0	.	413;522;522;509	F5H2B9;B7ZKM6;Q9BZF9;G3XAG2	.;.;UACA_HUMAN;.	G	522;509;498;413	ENSP00000314556:A522G;ENSP00000369319:A509G;ENSP00000438667:A413G	ENSP00000314556:A522G	A	-	2	0	UACA	68748512	1.000000	0.71417	0.993000	0.49108	0.473000	0.32948	6.105000	0.71505	2.676000	0.91093	0.591000	0.81541	GCC	.	.	.	none		0.378	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			C	70961458	G	C	70961458	3	2	196	1	0	0	0	0	1	0	0	0	16836	1203	42	4	2701	4	UACA	15	70961458	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	592998	70961458	31569934	53	11794											
CYP11A1	1583	hgsc.bcm.edu	37	chr15	74640247	74640247	+	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	ggcccaggactcacttcaacAggactcctatgggtctctgg	8	9	11	13	0	3	0	2	0	1	0	5	2	4	2	2	5	1	0	2	5	2	2			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr15:74640247A>T	ENST00000268053.6	-	2	573	c.419T>A	c.(418-420)cTg>cAg	p.L140Q	CYP11A1_ENST00000358632.4_5'UTR|CYP11A1_ENST00000419019.2_Intron|CYP11A1_ENST00000541301.1_Missense_Mutation_p.L140Q	NM_000781.2	NP_000772.2	P05108	CP11A_HUMAN	cytochrome P450, family 11, subfamily A, polypeptide 1	140					biphenyl metabolic process (GO:0018879)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to antibiotic (GO:0071236)|cellular response to cadmium ion (GO:0071276)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|cerebellum development (GO:0021549)|cholesterol metabolic process (GO:0008203)|dibenzo-p-dioxin metabolic process (GO:0018894)|estrogen biosynthetic process (GO:0006703)|fractalkine metabolic process (GO:0050756)|granulosa cell differentiation (GO:0060014)|hippocampus development (GO:0021766)|Leydig cell differentiation (GO:0033327)|maternal process involved in female pregnancy (GO:0060135)|mating behavior (GO:0007617)|phenol-containing compound metabolic process (GO:0018958)|phthalate metabolic process (GO:0018963)|progesterone biosynthetic process (GO:0006701)|response to alkaloid (GO:0043279)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to fungicide (GO:0060992)|response to gamma radiation (GO:0010332)|response to genistein (GO:0033595)|response to hydrogen peroxide (GO:0042542)|response to insecticide (GO:0017085)|response to L-ascorbic acid (GO:0033591)|response to salt stress (GO:0009651)|response to vitamin E (GO:0033197)|Schwann cell differentiation (GO:0014037)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|testosterone biosynthetic process (GO:0061370)|vitamin D metabolic process (GO:0042359)|xenobiotic metabolic process (GO:0006805)	mitochondrial crista (GO:0030061)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|perikaryon (GO:0043204)	cholesterol binding (GO:0015485)|cholesterol monooxygenase (side-chain-cleaving) activity (GO:0008386)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20					Aminoglutethimide(DB00357)|Cholecalciferol(DB00169)|Clomifene(DB00882)|Clotrimazole(DB00257)|Dexamethasone(DB01234)|Digitoxin(DB01396)|Digoxin(DB00390)|Dinoprostone(DB00917)|Glutethimide(DB01437)|Ketoconazole(DB01026)|Omeprazole(DB00338)|Saquinavir(DB01232)|Terbinafine(DB00857)|Testosterone(DB00624)	TCACTTCAACAGGACTCCTAT	0.622																																					p.L140Q	Esophageal Squamous(87;818 1337 4093 9268 37314)	Atlas-SNP	.											.	CYP11A1	54	.	0			c.T419A						PASS	.						45	42	43					15																	74640247		2197	4296	6493	SO:0001583	missense	1583	exon2			TTCAACAGGACTC	AK056794	CCDS32291.1, CCDS45303.1	15q23-q24	2010-05-04	2003-01-14	2003-01-17	ENSG00000140459	ENSG00000140459	1.14.15.6	"Cytochrome P450s"	2590	protein-coding gene	gene with protein product	"cholesterol monooxygenase (side-chain-cleaving)"	118485	"cytochrome P450, subfamily XIA (cholesterol side chain cleavage)"	CYP11A			Standard	NM_000781		Approved	P450SCC	uc002axt.2	P05108	OTTHUMG00000150716	ENST00000268053.6:c.419T>A	chr15.hg19:g.74640247A>T	ENSP00000268053:p.Leu140Gln	120.0	0.0	.		102.0	15.0	.	NM_000781	A8K8D5|B3KPU8|G3XAD7|Q15081|Q16805|Q8N1A7	Missense_Mutation	SNP	ENST00000268053.6	hg19	CCDS32291.1	.	.	.	.	.	.	.	.	.	.	A	16.15	3.040820	0.55003	.	.	ENSG00000140459	ENST00000268053;ENST00000541301;ENST00000450547;ENST00000433240;ENST00000416978	T;T;T	0.71222	-0.55;-0.55;-0.55	4.46	4.46	0.54185	.	0.000000	0.64402	D	0.000001	T	0.81917	0.4924	M	0.71871	2.18	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.79108	0.929;0.992;0.929	T	0.83072	-0.0142	10	0.51188	T	0.08	-0.0287	13.4211	0.60998	1.0:0.0:0.0:0.0	.	140;140;140	E7EPP8;B4DTE5;P05108	.;.;CP11A_HUMAN	Q	140;140;52;140;140	ENSP00000268053:L140Q;ENSP00000439750:L140Q;ENSP00000388018:L140Q	ENSP00000268053:L140Q	L	-	2	0	CYP11A1	72427300	1.000000	0.71417	0.556000	0.28293	0.404000	0.30871	7.439000	0.80444	1.642000	0.50584	0.523000	0.50628	CTG	.	.	.	none		0.622	CYP11A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319737.1			T	74640247	A	T	74640247	3	4	196	1	0	0	0	0	1	0	0	0	4146	188	7	5	1178	5	CYP11A1	15	74640247	Missense_Mutation	SNP	A	TCGA-HE-A5NF-01A-11D-A26P-10	3678789	74640247	27891145	54	11795											
E4F1	1877	hgsc.bcm.edu	37	chr16	2285002	2285002	+	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	acccaggagtatatcatcgaGgtgggtgtggggccctgggg	7	8	18	8	1	1	0	1	0	0	0	2	2	1	1	2	7	0	1	2	7	2	2			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr16:2285002G>T	ENST00000301727.4	+	12	1983	c.1935G>T	c.(1933-1935)gaG>gaT	p.E645D	DNASE1L2_ENST00000567494.1_5'Flank|DNASE1L2_ENST00000564065.1_5'Flank|RP11-304L19.12_ENST00000564055.1_lincRNA|E4F1_ENST00000564139.1_Intron|DNASE1L2_ENST00000382437.4_5'Flank|DNASE1L2_ENST00000320700.5_5'Flank|E4F1_ENST00000565090.1_Splice_Site_p.E468D	NM_004424.3	NP_004415.2	Q66K89	E4F1_HUMAN	E4F transcription factor 1	645					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						ATATCATCGAGGTGGGTGTGG	0.662																																					p.E645D		Atlas-SNP	.											.	E4F1	53	.	0			c.G1935T						PASS	.						18	19	19					16																	2285002		2191	4296	6487	SO:0001630	splice_region_variant	1877	exon12			CATCGAGGTGGGT	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.1935+1G>T	chr16.hg19:g.2285002G>T		98.0	0.0	.		108.0	5.0	.	NM_004424	A8K2R4|O00146	Missense_Mutation	SNP	ENST00000301727.4	hg19	CCDS32370.1	.	.	.	.	.	.	.	.	.	.	G	13.06	2.123776	0.37436	.	.	ENSG00000167967	ENST00000301727	T	0.36699	1.24	5.3	4.34	0.51931	.	0.101702	0.64402	D	0.000002	T	0.31420	0.0796	N	0.24115	0.695	0.80722	D	1	P	0.52842	0.956	P	0.47528	0.549	T	0.13522	-1.0506	10	0.87932	D	0	-29.9183	12.9793	0.58554	0.0806:0.0:0.9194:0.0	.	645	Q66K89	E4F1_HUMAN	D	645	ENSP00000301727:E645D	ENSP00000301727:E645D	E	+	3	2	E4F1	2225003	.	.	1.000000	0.80357	0.453000	0.32348	.	.	2.477000	0.83638	0.561000	0.74099	GAG	.	.	.	none		0.662	E4F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435225.1	NM_004424	Missense_Mutation	T	2285002	G	T	2285002	5	4	196	1	0	0	0	0	0	0	1	0	4876	1014	35	4	1981	4	E4F1	16	2285002	Splice_Site	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10		2285002	88069751	55	11796											
SRCAP	10847	hgsc.bcm.edu	37	chr16	30734928	30734928	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagcccccggagctgcccccTtgaccatctcttctcctctc	4	10	6	21	1	3	1	0	1	3	0	6	2	3	2	6	1	3	1	6	1	0	2			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr16:30734928T>C	ENST00000262518.4	+	25	4568	c.4183T>C	c.(4183-4185)Ttg>Ctg	p.L1395L	SRCAP_ENST00000395059.2_Silent_p.L1333L|SRCAP_ENST00000344771.4_Silent_p.L1237L	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1395	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)			AGCTGCCCCCTTGACCATCTC	0.567																																					p.L1395L		Atlas-SNP	.											.	SRCAP	298	.	0			c.T4183C						PASS	.						149	141	144					16																	30734928		2197	4300	6497	SO:0001819	synonymous_variant	10847	exon25			GCCCCCTTGACCA	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.4183T>C	chr16.hg19:g.30734928T>C		109.0	0.0	.		123.0	30.0	.	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Silent	SNP	ENST00000262518.4	hg19	CCDS10689.2																																																																																			.	.	.	none		0.567	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		C	30734928	T	C	30734928	2	2	196	1	0	0	0	0	0	0	0	1	15147	1606	56	3		3	SRCAP	16	30734928	Silent	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10	28449926	30734928	59619825	56	11797											
SLC12A3	6559	hgsc.bcm.edu	37	chr16	56919183	56919183	+	Missense_Mutation	SNP	A	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	ccttgctctcccagaggtaaAttggggctcctcggtacagg	7	10	12	12	1	1	1	0	0	1	1	4	1	2	1	3	5	2	4	3	5	3	4			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr16:56919183A>C	ENST00000563236.1	+	15	1857	c.1832A>C	c.(1831-1833)aAt>aCt	p.N611T	SLC12A3_ENST00000566786.1_Missense_Mutation_p.N610T|SLC12A3_ENST00000438926.2_Missense_Mutation_p.N611T|SLC12A3_ENST00000262502.5_Missense_Mutation_p.N610T			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3	611					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)	CCAGAGGTAAATTGGGGCTCC	0.567																																					p.N611T		Atlas-SNP	.											.	SLC12A3	99	.	0			c.A1832C	GRCh37	CM075008	SLC12A3	M		PASS	.						85	63	70					16																	56919183		2156	4234	6390	SO:0001583	missense	6559	exon15			AGGTAAATTGGGG		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.1832A>C	chr16.hg19:g.56919183A>C	ENSP00000456149:p.Asn611Thr	68.0	0.0	.		99.0	35.0	.	NM_001126108	A8MSJ2|C9JNN9	Missense_Mutation	SNP	ENST00000563236.1	hg19	CCDS58464.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.386422	0.82902	.	.	ENSG00000070915	ENST00000438926;ENST00000262502	.	.	.	5.4	5.4	0.78164	Amino acid permease domain (1);	0.088014	0.85682	D	0.000000	T	0.77478	0.4136	M	0.71296	2.17	0.80722	D	1	P;D;D	0.76494	0.735;0.999;0.999	B;D;D	0.74674	0.426;0.984;0.973	T	0.80415	-0.1392	9	0.87932	D	0	.	14.4174	0.67160	1.0:0.0:0.0:0.0	.	610;611;611	P55017-3;P55017;P55017-2	.;S12A3_HUMAN;.	T	610;611	.	ENSP00000262502:N611T	N	+	2	0	SLC12A3	55476684	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	9.060000	0.93907	2.048000	0.60808	0.533000	0.62120	AAT	.	.	.	none		0.567	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1			C	56919183	A	C	56919183	3	2	196	1	0	0	0	0	1	0	0	0	14397	101	4	5	1890	5	SLC12A3	16	56919183	Missense_Mutation	SNP	A	TCGA-HE-A5NF-01A-11D-A26P-10	26184255	56919183	33435570	57	11798											
KIAA0753	9851	hgsc.bcm.edu	37	chr17	6526336	6526336	+	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	aggaagtggatgctcccctcGgtcagtaaactgagtgacaa	12	8	12	9	1	1	2	1	2	0	0	3	4	2	4	2	3	2	2	2	3	4	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr17:6526336G>C	ENST00000361413.3	-	6	1328	c.970C>G	c.(970-972)Cga>Gga	p.R324G	KIAA0753_ENST00000589033.1_5'Flank|KIAA0753_ENST00000542606.1_Missense_Mutation_p.R25G|KIAA0753_ENST00000572370.1_Missense_Mutation_p.R25G	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	324						centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		TGCTCCCCTCGGTCAGTAAAC	0.517																																					p.R324G		Atlas-SNP	.											.	KIAA0753	63	.	0			c.C970G						PASS	.						62	60	60					17																	6526336		1915	4127	6042	SO:0001583	missense	9851	exon6			CCCCTCGGTCAGT		CCDS42247.1	17p13.1	2014-04-04			ENSG00000198920	ENSG00000198920			29110	protein-coding gene	gene with protein product						24613305	Standard	NM_014804		Approved		uc002gde.4	Q2KHM9	OTTHUMG00000177928	ENST00000361413.3:c.970C>G	chr17.hg19:g.6526336G>C	ENSP00000355250:p.Arg324Gly	178.0	0.0	.		256.0	68.0	.	NM_014804	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Missense_Mutation	SNP	ENST00000361413.3	hg19	CCDS42247.1	.	.	.	.	.	.	.	.	.	.	G	11.08	1.533928	0.27387	.	.	ENSG00000198920	ENST00000361413;ENST00000542606	D;D	0.86230	-2.09;-2.09	5.7	-0.0324	0.13905	.	0.841046	0.10770	N	0.636068	T	0.79052	0.4381	L	0.42245	1.32	0.80722	D	1	B	0.18013	0.025	B	0.17098	0.017	T	0.65903	-0.6055	10	0.30078	T	0.28	-0.3706	5.2141	0.15332	0.0698:0.1147:0.3462:0.4694	.	324	Q2KHM9	K0753_HUMAN	G	324;25	ENSP00000355250:R324G;ENSP00000444634:R25G	ENSP00000355250:R324G	R	-	1	2	KIAA0753	6467060	1.000000	0.71417	0.995000	0.50966	0.396000	0.30629	2.647000	0.46639	0.118000	0.18165	-1.035000	0.02400	CGA	.	.	.	none		0.517	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804		C	6526336	G	C	6526336	3	2	196	1	0	0	0	0	1	0	0	0	8198	1124	39	4	1989	4	KIAA0753	17	6526336	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10		6526336	74668874	58	11799											
SHBG	6462	hgsc.bcm.edu	37	chr17	7534128	7534128	+	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	ctgagatccaactgcacaatCactgggcccagcttacggtg	10	8	10	13	1	1	1	1	1	0	1	2	2	2	1	2	2	4	2	2	2	3	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr17:7534128C>G	ENST00000380450.4	+	3	365	c.334C>G	c.(334-336)Cac>Gac	p.H112D	SHBG_ENST00000340624.5_Missense_Mutation_p.H54D|SAT2_ENST00000380466.2_5'Flank|SHBG_ENST00000576478.1_Missense_Mutation_p.H54D|SHBG_ENST00000575903.1_Missense_Mutation_p.H112D|SHBG_ENST00000576728.1_Missense_Mutation_p.H54D|SHBG_ENST00000570547.1_Missense_Mutation_p.H54D|SHBG_ENST00000441599.2_Missense_Mutation_p.H112D|SHBG_ENST00000575314.1_Missense_Mutation_p.H54D|SHBG_ENST00000572262.1_Missense_Mutation_p.H54D|SHBG_ENST00000574539.1_Missense_Mutation_p.H54D|SHBG_ENST00000416273.3_Missense_Mutation_p.H112D|SAT2_ENST00000269298.5_5'Flank|SHBG_ENST00000572182.1_Missense_Mutation_p.H54D	NM_001040.3	NP_001031.2	P04278	SHBG_HUMAN	sex hormone-binding globulin	112	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				primary spermatocyte growth (GO:0007285)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	androgen binding (GO:0005497)	p.?(1)		cervix(1)|endometrium(2)|large_intestine(4)|lung(2)|skin(1)	10		all_cancers(10;0.0867)		READ - Rectum adenocarcinoma(115;0.168)	Danazol(DB01406)|Drostanolone(DB00858)|Estradiol(DB00783)|Estropipate(DB04574)|Fluoxymesterone(DB01185)|Hydrocortisone(DB00741)|Methyltestosterone(DB06710)|Mitotane(DB00648)|Norethindrone(DB00717)|Spironolactone(DB00421)|Testosterone(DB00624)|transdermal testosterone gel(DB05275)	ACTGCACAATCACTGGGCCCA	0.567																																					p.H112D		Atlas-SNP	.											.	SHBG	21	.	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.C334G						PASS	.						81	77	78					17																	7534128		2203	4300	6503	SO:0001583	missense	6462	exon3			CACAATCACTGGG		CCDS11117.1, CCDS54082.1, CCDS54083.1, CCDS58513.1, CCDS73961.1, CCDS73962.1	17p13.1	2013-09-19			ENSG00000129214	ENSG00000129214			10839	protein-coding gene	gene with protein product	"androgen binding protein"	182205				2587256	Standard	NM_001146279		Approved	ABP, TEBG, MGC126834, MGC138391	uc002gie.2	P04278	OTTHUMG00000108153	ENST00000380450.4:c.334C>G	chr17.hg19:g.7534128C>G	ENSP00000369816:p.His112Asp	143.0	0.0	.		202.0	59.0	.	NM_001040	B0FWH4|E9PGW1|F5H5Z8|I3L1N7|P14689|Q16616|Q3MIL0|Q6ISD2	Missense_Mutation	SNP	ENST00000380450.4	hg19	CCDS11117.1	.	.	.	.	.	.	.	.	.	.	C	8.055	0.766779	0.15983	.	.	ENSG00000129214	ENST00000340624;ENST00000441599;ENST00000416273;ENST00000441313;ENST00000452698;ENST00000380450	T;T;T;T	0.77620	-1.11;-1.11;-1.11;-1.11	5.04	-0.0208	0.13954	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	2.361970	0.01468	N	0.016151	T	0.71592	0.3358	L	0.47716	1.5	0.09310	N	1	B;B;B;B;B;B;B;B;B;B;B	0.25007	0.01;0.045;0.023;0.001;0.013;0.116;0.116;0.03;0.007;0.013;0.013	B;B;B;B;B;B;B;B;B;B;B	0.28011	0.011;0.03;0.044;0.001;0.042;0.085;0.085;0.045;0.038;0.031;0.013	T	0.49194	-0.8965	10	0.12103	T	0.63	2.7497	9.104	0.36687	0.0:0.6418:0.1148:0.2435	.	112;107;85;112;112;112;85;85;85;112;54	F5H5Z8;P04278-2;B0FWH6;E9PH59;E9PGW1;E9PGQ3;B0FWH7;B0FWH5;B0FWH4;P04278;B4DYU0	.;.;.;.;.;.;.;.;.;SHBG_HUMAN;.	D	54;112;112;112;112;112	ENSP00000345675:H54D;ENSP00000393426:H112D;ENSP00000388867:H112D;ENSP00000369816:H112D	ENSP00000345675:H54D	H	+	1	0	SHBG	7474853	0.001000	0.12720	0.000000	0.03702	0.014000	0.08584	-0.109000	0.10840	-0.068000	0.12953	-1.134000	0.01955	CAC	.	.	.	none		0.567	SHBG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226957.2	NM_001040		G	7534128	C	G	7534128	3	3	196	1	0	0	0	0	1	0	0	0	14282	826	29	4	344	4	SHBG	17	7534128	Missense_Mutation	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10	1007792	7534128	73661082	59	11800											
SOCS7	30837	hgsc.bcm.edu	37	chr17	36508826	36508826	+	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	tccggcggtggggatgggacCggcaagaggccttctggaga	7	6	19	9	3	1	2	0	0	1	2	2	5	2	4	3	8	0	1	3	8	1	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr17:36508826C>A	ENST00000577233.1	+	1	699	c.699C>A	c.(697-699)acC>acA	p.T233T	SOCS7_ENST00000331159.5_Silent_p.T233T	NM_014598.2	NP_055413.1	O14512	SOCS7_HUMAN	suppressor of cytokine signaling 7	233	Mediates interaction with SORBS3.				fat cell differentiation (GO:0045444)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of signal transduction (GO:0009968)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)			central_nervous_system(1)|endometrium(1)|kidney(1)|prostate(1)|skin(5)	9	Breast(7;3.47e-17)					GGGATGGGACCGGCAAGAGGC	0.667																																					p.T233T		Atlas-SNP	.											.	SOCS7	22	.	0			c.C699A						PASS	.						7	10	9					17																	36508826		2166	4235	6401	SO:0001819	synonymous_variant	30837	exon1			TGGGACCGGCAAG	AB005216	CCDS32637.1	17q12	2014-08-12			ENSG00000274211	ENSG00000274211		"Suppressors of cytokine signaling", "SH2 domain containing"	29846	protein-coding gene	gene with protein product	"Nck, Ash and phospholipase C binding protein", "NCK-associated protein 4"	608788				9344857, 12076535	Standard	XM_005257264		Approved	NAP4, NCKAP4	uc002hqa.3	O14512	OTTHUMG00000188546	ENST00000577233.1:c.699C>A	chr17.hg19:g.36508826C>A		18.0	0.0	.		47.0	10.0	.	NM_014598	A2VCU2|Q0IJ63	Silent	SNP	ENST00000577233.1	hg19	CCDS32637.1																																																																																			.	.	.	none		0.667	SOCS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440486.4	XM_371052		A	36508826	C	A	36508826	2	1	196	1	0	0	0	0	0	0	0	1	14932	639	23	4		4	SOCS7	17	36508826	Silent	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10	28974698	36508826	44686384	60	11801											
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-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	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	49	.	2	Unknown(1)|Deletion - In frame(1)	NS(2)	c.G338C						PASS	.																																			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	chr17.hg19:g.39240796G>C	ENSP00000375236:p.Ser113Thr	12.0	0.0	.		14.0	9.0	.	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	hg19	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	196	1	0	0	0	0	1	0	0	0	8562	971	34	4	340	4	KRTAP4-7	17	39240796	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	2731970	39240796	41954414	61	11802											
TOB1	10140	hgsc.bcm.edu	37	chr17	48940734	48940734	+	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	atggctttctgcttcaagagGtcattcacattcaagccgag	10	12	9	10	1	5	1	4	0	1	1	5	2	5	1	1	2	2	2	1	2	2	4			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr17:48940734G>C	ENST00000268957.3	-	3	1073	c.645C>G	c.(643-645)gaC>gaG	p.D215E	TOB1_ENST00000509385.1_5'UTR|TOB1_ENST00000499247.2_Missense_Mutation_p.D215E	NM_001243877.1	NP_001230806.1	P50616	TOB1_HUMAN	transducer of ERBB2, 1	215					negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060212)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of translation (GO:0017148)|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 signal transduction (GO:0009967)|SMAD protein import into nucleus (GO:0007184)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	receptor tyrosine kinase binding (GO:0030971)|SH3/SH2 adaptor activity (GO:0005070)|transcription corepressor activity (GO:0003714)			breast(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			GCTTCAAGAGGTCATTCACAT	0.527																																					p.D215E	NSCLC(144;643 1919 24513 29423 40686)	Atlas-SNP	.											.	TOB1	40	.	0			c.C645G						PASS	.						98	100	99					17																	48940734		2203	4300	6503	SO:0001583	missense	10140	exon2			CAAGAGGTCATTC	D38305	CCDS11576.1	17q21.33	2012-08-14			ENSG00000141232	ENSG00000141232			11979	protein-coding gene	gene with protein product		605523		TROB1		8632892, 17785442	Standard	NM_005749		Approved	TOB, TROB	uc002isw.3	P50616	OTTHUMG00000162277	ENST00000268957.3:c.645C>G	chr17.hg19:g.48940734G>C	ENSP00000268957:p.Asp215Glu	135.0	0.0	.		230.0	64.0	.	NM_005749	B2R9T0|D3DTY3|Q4KMQ0	Missense_Mutation	SNP	ENST00000268957.3	hg19	CCDS11576.1	.	.	.	.	.	.	.	.	.	.	G	6.571	0.473717	0.12521	.	.	ENSG00000141232	ENST00000499247;ENST00000268957	T;T	0.39229	1.09;1.09	6.07	6.07	0.98685	.	0.168901	0.51477	D	0.000081	T	0.21550	0.0519	N	0.02539	-0.55	0.38296	D	0.94283	B	0.16396	0.017	B	0.12156	0.007	T	0.14254	-1.0479	10	0.38643	T	0.18	.	14.7663	0.69642	0.0684:0.0:0.9316:0.0	.	215	P50616	TOB1_HUMAN	E	215	ENSP00000427695:D215E;ENSP00000268957:D215E	ENSP00000268957:D215E	D	-	3	2	TOB1	46295733	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.185000	0.32065	2.885000	0.99019	0.655000	0.94253	GAC	.	.	.	none		0.527	TOB1-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000368364.1			C	48940734	G	C	48940734	3	2	196	1	0	0	0	0	1	0	0	0	16359	1252	44	4	396	4	TOB1	17	48940734	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10	9699938	48940734	32254476	62	11803											
TOMM40	10452	hgsc.bcm.edu	37	chr19	45397281	45397281	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcggggctctgacttcacaGcagccgtcaccctggggaac	8	7	12	14	2	3	1	2	1	1	0	4	2	3	2	2	4	3	2	2	4	1	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr19:45397281G>A	ENST00000426677.2	+	5	781	c.601G>A	c.(601-603)Gca>Aca	p.A201T	TOMM40_ENST00000592434.1_Missense_Mutation_p.A201T|TOMM40_ENST00000405636.2_Missense_Mutation_p.A201T|TOMM40_ENST00000252487.5_Missense_Mutation_p.A201T	NM_001128917.1	NP_001122389.1	O96008	TOM40_HUMAN	translocase of outer mitochondrial membrane 40 homolog (yeast)	201					cellular protein metabolic process (GO:0044267)|ion transport (GO:0006811)|protein targeting to mitochondrion (GO:0006626)|protein transmembrane transport (GO:0071806)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial outer membrane translocase complex (GO:0005742)|pore complex (GO:0046930)	porin activity (GO:0015288)|protein transmembrane transporter activity (GO:0008320)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|ovary(1)	5	Lung NSC(12;0.0018)|all_lung(12;0.00481)			OV - Ovarian serous cystadenocarcinoma(262;0.0033)|Epithelial(262;0.176)		TGACTTCACAGCAGCCGTCAC	0.617																																					p.A201T		Atlas-SNP	.											.	TOMM40	13	.	0			c.G601A						PASS	.						45	44	45					19																	45397281		2203	4300	6503	SO:0001583	missense	10452	exon5			TTCACAGCAGCCG	AF043250	CCDS12646.1	19q13	2008-07-04				ENSG00000130204			18001	protein-coding gene	gene with protein product		608061				10980201, 15644312	Standard	NM_006114		Approved	PEREC1, D19S1177E, C19orf1, TOM40, PER-EC1	uc002paa.4	O96008		ENST00000426677.2:c.601G>A	chr19.hg19:g.45397281G>A	ENSP00000410339:p.Ala201Thr	75.0	0.0	.		106.0	12.0	.	NM_001128917	Q86VW4|Q8WY09|Q8WY10|Q8WY11|Q9BR95	Missense_Mutation	SNP	ENST00000426677.2	hg19	CCDS12646.1	.	.	.	.	.	.	.	.	.	.	G	16.63	3.176405	0.57692	.	.	ENSG00000130204	ENST00000426677;ENST00000405636;ENST00000252487	T;T;T	0.45668	0.89;0.89;0.89	4.76	4.76	0.60689	.	0.122142	0.53938	D	0.000046	T	0.39145	0.1067	L	0.49571	1.57	0.46701	D	0.999162	B;B	0.26975	0.165;0.037	B;B	0.28139	0.086;0.05	T	0.20306	-1.0279	10	0.28530	T	0.3	1.0773	15.2511	0.73545	0.0:0.0:1.0:0.0	.	201;201	O96008-2;O96008	.;TOM40_HUMAN	T	201	ENSP00000410339:A201T;ENSP00000385184:A201T;ENSP00000252487:A201T	ENSP00000252487:A201T	A	+	1	0	TOMM40	50089121	1.000000	0.71417	0.016000	0.15963	0.939000	0.58152	5.430000	0.66501	2.191000	0.70037	0.561000	0.74099	GCA	.	.	.	none		0.617	TOMM40-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453241.1			A	45397281	G	A	45397281	3	1	196	1	0	0	0	0	1	0	0	0	16370	971	34	2	619	2	TOMM40	19	45397281	Missense_Mutation	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10		45397281	13731702	63	11804											
NKX2-2	4821	hgsc.bcm.edu	37	chr20	21492814	21492814	+	Missense_Mutation	SNP	T	T	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	ggggcgtcacctccatacctTtctcggcccgggcgcgcttc	3	9	12	17	5	2	0	1	0	1	0	5	0	3	0	4	4	1	1	4	4	1	3			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr20:21492814T>G	ENST00000377142.4	-	2	925	c.569A>C	c.(568-570)aAa>aCa	p.K190T	NKX2-2-AS1_ENST00000549659.1_RNA	NM_002509.3	NP_002500.1	O95096	NKX22_HUMAN	NK2 homeobox 2	190					astrocyte differentiation (GO:0048708)|brain development (GO:0007420)|digestive tract development (GO:0048565)|endocrine pancreas development (GO:0031018)|negative regulation of neuron differentiation (GO:0045665)|neuron fate specification (GO:0048665)|oligodendrocyte development (GO:0014003)|optic nerve development (GO:0021554)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to glucose (GO:0009749)|response to progesterone (GO:0032570)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)|spinal cord oligodendrocyte cell fate specification (GO:0021530)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell fate commitment (GO:0003327)|ventral spinal cord interneuron fate determination (GO:0060580)	nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|core promoter proximal region DNA binding (GO:0001159)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21						CTCCATACCTTTCTCGGCCCG	0.667																																					p.K190T		Atlas-SNP	.											.	NKX2-2	49	.	0			c.A569C						PASS	.						38	40	39					20																	21492814		2202	4300	6502	SO:0001583	missense	4821	exon2			ATACCTTTCTCGG	AF019415	CCDS13145.1	20p11.22	2012-03-09	2007-07-09	2002-10-04	ENSG00000125820	ENSG00000125820		"Homeoboxes / ANTP class : NKL subclass"	7835	protein-coding gene	gene with protein product		604612	"NK-2 (Drosophila) homolog B", "NK2 transcription factor related, locus 2 (Drosophila)"	NKX2B		9703340, 1346742	Standard	NM_002509		Approved	NKX2.2	uc002wsi.3	O95096	OTTHUMG00000170524	ENST00000377142.4:c.569A>C	chr20.hg19:g.21492814T>G	ENSP00000366347:p.Lys190Thr	29.0	0.0	.		48.0	5.0	.	NM_002509		Missense_Mutation	SNP	ENST00000377142.4	hg19	CCDS13145.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.724176	0.89298	.	.	ENSG00000125820	ENST00000377142	D	0.91996	-2.95	5.35	5.35	0.76521	Homeobox (1);	0.000000	0.85682	D	0.000000	D	0.94499	0.8229	M	0.73217	2.22	0.80722	D	1	D	0.57257	0.979	P	0.57620	0.824	D	0.94718	0.7898	10	0.56958	D	0.05	.	15.3169	0.74089	0.0:0.0:0.0:1.0	.	190	O95096	NKX22_HUMAN	T	190	ENSP00000366347:K190T	ENSP00000366347:K190T	K	-	2	0	NKX2-2	21440814	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.002000	0.88514	2.014000	0.59158	0.379000	0.24179	AAA	.	.	.	none		0.667	NKX2-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078278.9			G	21492814	T	G	21492814	3	3	196	1	0	0	0	0	1	0	0	0	10457	1841	64	5	256	5	NKX2-2	20	21492814	Missense_Mutation	SNP	T	TCGA-HE-A5NF-01A-11D-A26P-10		21492814	41532706	64	11805											
SETD4	54093	hgsc.bcm.edu	37	chr21	37408418	37408418	+	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	aatgcgcttcggtgaaatcaGgtaaaagctgtttgcaaact	13	11	10	7	2	1	1	1	1	0	0	2	1	1	1	0	2	4	5	0	2	5	3			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr21:37408418G>C	ENST00000399215.1	-	10	2692	c.1320C>G	c.(1318-1320)acC>acG	p.T440T	SETD4_ENST00000481477.1_5'UTR|SETD4_ENST00000332131.4_Silent_p.T440T|AP000688.1_ENST00000600312.1_Intron|SETD4_ENST00000399212.1_Silent_p.T416T			Q9NVD3	SETD4_HUMAN	SET domain containing 4	440				EILVKYLPSTDKQMDKKISILKDHGYIENLTFGWDGPSWRL LTALKLLCLEAEKFTCWKKVLLGEVISDTNEKTSLDIAQKI CYYFIEETNAVLQKVSHMKDEKEALINQLTLVESLWTEELK ILRASAETLHSLQTAFT -> GWNQLCS (in Ref. 5; AAH02898). {ECO:0000305}.			methyltransferase activity (GO:0008168)			autonomic_ganglia(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	15						GGTGAAATCAGGTAAAAGCTG	0.433																																					p.T440T		Atlas-SNP	.											.	SETD4	37	.	0			c.C1320G						PASS	.						147	146	146					21																	37408418		2203	4300	6503	SO:0001819	synonymous_variant	54093	exon11			AAATCAGGTAAAA	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.1320C>G	chr21.hg19:g.37408418G>C		78.0	0.0	.		65.0	13.0	.	NM_017438	B4DT14|D3DSG2|D3DSG4|Q8NE19|Q9BU46	Silent	SNP	ENST00000399215.1	hg19	CCDS13640.1																																																																																			.	.	.	none		0.433	SETD4-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194456.1	NM_017438		C	37408418	G	C	37408418	2	2	196	1	0	0	0	0	0	0	0	1	14146	987	35	4		4	SETD4	21	37408418	Silent	SNP	G	TCGA-HE-A5NF-01A-11D-A26P-10		37408418	10721477	65	11806											
MCM3AP	8888	hgsc.bcm.edu	37	chr21	47664760	47664760	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	catctgcggaagctggaaccCgagcacagcctgcttcagcc	9	6	11	15	2	2	0	1	0	1	0	2	3	2	2	3	2	7	3	3	2	2	1			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr21:47664760C>T	ENST00000397708.1	-	24	5253	c.4999G>A	c.(4999-5001)Ggg>Agg	p.G1667R	MCM3AP_ENST00000467026.1_5'UTR|MCM3AP-AS1_ENST00000455567.1_RNA|MCM3AP-AS1_ENST00000421927.1_RNA|AP001469.7_ENST00000444966.1_RNA|MCM3AP-AS1_ENST00000591223.1_RNA|MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP-AS1_ENST00000414659.1_RNA|MCM3AP_ENST00000291688.1_Missense_Mutation_p.G1667R|MCM3AP-AS1_ENST00000444998.1_RNA|MCM3AP-AS1_ENST00000432735.1_RNA|MCM3AP-AS1_ENST00000588753.1_RNA			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1667	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)					AGCTGGAACCCGAGCACAGCC	0.642																																					p.G1667R		Atlas-SNP	.											.	MCM3AP	146	.	0			c.G4999A						PASS	.						38	38	38					21																	47664760		2203	4300	6503	SO:0001583	missense	8888	exon23			GGAACCCGAGCAC	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.4999G>A	chr21.hg19:g.47664760C>T	ENSP00000380820:p.Gly1667Arg	152.0	0.0	.		138.0	32.0	.	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Missense_Mutation	SNP	ENST00000397708.1	hg19	CCDS13734.1	.	.	.	.	.	.	.	.	.	.	C	13.13	2.146050	0.37923	.	.	ENSG00000160294	ENST00000397708;ENST00000291688;ENST00000539647	T;T	0.03468	3.92;3.92	5.55	2.48	0.30137	.	0.335736	0.36409	N	0.002607	T	0.05456	0.0144	L	0.47716	1.5	0.29780	N	0.834087	B;D	0.59767	0.022;0.986	B;P	0.49421	0.005;0.61	T	0.14699	-1.0463	10	0.56958	D	0.05	-13.7278	5.035	0.14430	0.3494:0.4672:0.0:0.1834	.	1667;162	O60318;B3KT88	MCM3A_HUMAN;.	R	1667;1667;162	ENSP00000380820:G1667R;ENSP00000291688:G1667R	ENSP00000291688:G1667R	G	-	1	0	MCM3AP	46489188	0.922000	0.31269	0.682000	0.30024	0.188000	0.23474	1.789000	0.38724	0.711000	0.32018	-0.136000	0.14681	GGG	.	.	.	none		0.642	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906		T	47664760	C	T	47664760	3	4	196	1	0	0	0	0	1	0	0	0	9395	652	23	1	967	1	MCM3AP	21	47664760	Missense_Mutation	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10	10256342	47664760	465135	66	11807											
PI4KA	5297	hgsc.bcm.edu	37	chr22	21119517	21119517	+	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	ccctcgtaccattcttctggCcagagtcctgcaataaagtg	9	11	8	13	1	2	1	0	0	2	1	4	1	3	1	4	1	2	2	4	1	4	4			TCGA-HE-A5NF-01A-11D-A26P-10	TCGA-HE-A5NF-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c14407ad-670e-4d1e-9417-2b76f4810fff	fcfc53c2-52b3-44d1-ae32-76375e3a0836	g.chr22:21119517C>T	ENST00000572273.1	-	21	2501	c.2271G>A	c.(2269-2271)tgG>tgA	p.W757*	PI4KA_ENST00000466162.1_5'UTR|PI4KA_ENST00000255882.6_Nonsense_Mutation_p.W815*			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	757					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)			ATTCTTCTGGCCAGAGTCCTG	0.493																																					p.W815X	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											.	PI4KA	313	.	0			c.G2445A						PASS	.						93	97	96					22																	21119517		2203	4300	6503	SO:0001587	stop_gained	5297	exon21			TTCTGGCCAGAGT	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.2271G>A	chr22.hg19:g.21119517C>T	ENSP00000458238:p.Trp757*	145.0	0.0	.		145.0	28.0	.	NM_058004	Q7Z625|Q9UPG2	Nonsense_Mutation	SNP	ENST00000572273.1	hg19		.	.	.	.	.	.	.	.	.	.	C	40	8.059858	0.98632	.	.	ENSG00000241973	ENST00000255882	.	.	.	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.5831	19.2017	0.93713	0.0:1.0:0.0:0.0	.	.	.	.	X	757	.	ENSP00000255882:W757X	W	-	3	0	PI4KA	19449517	1.000000	0.71417	1.000000	0.80357	0.579000	0.36224	7.539000	0.82063	2.770000	0.95276	0.650000	0.86243	TGG	.	.	.	none		0.493	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004		T	21119517	C	T	21119517	4	4	196	1	0	0	0	0	0	1	0	0	11880	740	26	2	4003	2	PI4KA	22	21119517	Nonsense_Mutation	SNP	C	TCGA-HE-A5NF-01A-11D-A26P-10		21119517	30185049	67	11808											
ZNF436	80818	hgsc.bcm.edu	37	chr1	23693623	23693623	+	Silent	SNP	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	agaggtctccattcttcccgGgtgagatacatggccatatc	9	11	10	11	1	2	2	0	1	2	2	5	3	3	2	3	3	1	0	3	3	2	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr1:23693623G>A	ENST00000314011.4	-	3	208	c.72C>T	c.(70-72)acC>acT	p.T24T	C1orf213_ENST00000335648.3_5'Flank|C1orf213_ENST00000454117.1_5'Flank|C1orf213_ENST00000518821.1_5'Flank|ZNF436_ENST00000374608.3_Silent_p.T24T|C1orf213_ENST00000437367.2_5'Flank	NM_001077195.1	NP_001070663.1	Q9C0F3	ZN436_HUMAN	zinc finger protein 436	24	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;5.97e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000977)|KIRC - Kidney renal clear cell carcinoma(1967;0.00336)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		ATTCTTCCCGGGTGAGATACA	0.438																																					p.T24T		Atlas-SNP	.											.	ZNF436	49	.	0			c.C72T						PASS	.						136	129	132					1																	23693623		2203	4300	6503	SO:0001819	synonymous_variant	80818	exon3			TTCCCGGGTGAGA	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.72C>T	chr1.hg19:g.23693623G>A		108.0	0.0	.		131.0	47.0	.	NM_001077195	Q658I9	Silent	SNP	ENST00000314011.4	hg19	CCDS233.1																																																																																			.	.	.	none		0.438	ZNF436-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008908.1	NM_030634		A	23693623	G	A	23693623	2	1	197	1	0	0	0	0	0	0	0	1	17921	1219	43	2		2	ZNF436	1	23693623	Silent	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10		23693623	225556998	1	11809											
KLF17	128209	hgsc.bcm.edu	37	chr1	44595405	44595405	+	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	ggtgggaatctaaggatgccCcccaatgggctgccagtctc	8	8	13	12	0	2	0	0	0	2	0	3	2	2	2	4	4	2	1	4	4	3	1			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr1:44595405C>G	ENST00000372299.3	+	2	520	c.462C>G	c.(460-462)ccC>ccG	p.P154P	KLF17_ENST00000476802.1_Intron	NM_173484.3	NP_775755.3	Q5JT82	KLF17_HUMAN	Kruppel-like factor 17	154					gamete generation (GO:0007276)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|central_nervous_system(1)|large_intestine(1)|lung(6)|ovary(3)|prostate(1)|skin(2)|stomach(1)	18	Acute lymphoblastic leukemia(166;0.155)					TAAGGATGCCCCCCAATGGGC	0.562																																					p.P154P		Atlas-SNP	.											.	KLF17	92	.	0			c.C462G						PASS	.						33	37	35					1																	44595405		2203	4300	6503	SO:0001819	synonymous_variant	128209	exon2			GATGCCCCCCAAT	BC049844	CCDS508.1	1p34.1	2011-11-15	2006-02-17	2006-02-17	ENSG00000171872	ENSG00000171872		"Zinc fingers, C2H2-type", "Kruppel-like transcription factors"	18830	protein-coding gene	gene with protein product		609602	"zinc finger protein 393"	ZNF393		16460907	Standard	NM_173484		Approved	Zfp393, FLJ40160	uc001clp.3	Q5JT82	OTTHUMG00000009664	ENST00000372299.3:c.462C>G	chr1.hg19:g.44595405C>G		35.0	0.0	.		43.0	16.0	.	NM_173484	Q86VQ7|Q8N805	Silent	SNP	ENST00000372299.3	hg19	CCDS508.1																																																																																			.	.	.	none		0.562	KLF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026646.1	NM_173484		G	44595405	C	G	44595405	2	3	197	1	0	0	0	0	0	0	0	1	8352	610	22	4		4	KLF17	1	44595405	Silent	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	20901782	44595405	204655216	2	11810											
LRRC8C	84230	hgsc.bcm.edu	37	chr1	90179946	90179946	+	Missense_Mutation	SNP	A	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	tgacctggagcgtattcctcAtgctgtgttcagcctactca	7	13	9	12	1	3	1	3	1	0	0	4	2	4	2	3	1	4	3	3	1	2	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr1:90179946A>C	ENST00000370454.4	+	3	2072	c.1817A>C	c.(1816-1818)cAt>cCt	p.H606P	RP11-302M6.4_ENST00000370453.5_Intron|LRRC8C_ENST00000479252.1_Intron	NM_032270.4	NP_115646	Q8TDW0	LRC8C_HUMAN	leucine rich repeat containing 8 family, member C	606					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)		CGTATTCCTCATGCTGTGTTC	0.448																																					p.H606P		Atlas-SNP	.											.	LRRC8C	73	.	0			c.A1817C						PASS	.						57	55	56					1																	90179946		2203	4300	6503	SO:0001583	missense	84230	exon3			TTCCTCATGCTGT		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.1817A>C	chr1.hg19:g.90179946A>C	ENSP00000359483:p.His606Pro	80.0	0.0	.		121.0	40.0	.	NM_032270	B3KXS9|Q29RV6|Q9H075	Missense_Mutation	SNP	ENST00000370454.4	hg19	CCDS725.1	.	.	.	.	.	.	.	.	.	.	A	15.17	2.754041	0.49362	.	.	ENSG00000171488	ENST00000370454	T	0.54866	0.55	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.31199	0.0789	N	0.00656	-1.285	0.80722	D	1	D	0.67145	0.996	D	0.72625	0.978	T	0.63730	-0.6571	10	0.39692	T	0.17	.	16.5441	0.84409	1.0:0.0:0.0:0.0	.	606	Q8TDW0	LRC8C_HUMAN	P	606	ENSP00000359483:H606P	ENSP00000359483:H606P	H	+	2	0	LRRC8C	89952534	1.000000	0.71417	0.397000	0.26308	0.684000	0.39900	9.284000	0.95882	2.364000	0.80123	0.524000	0.50904	CAT	.	.	.	none		0.448	LRRC8C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028435.2	NM_032270		C	90179946	A	C	90179946	3	2	197	1	0	0	0	0	1	0	0	0	9030	217	8	5	1823	5	LRRC8C	1	90179946	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10	45584541	90179946	159070675	3	11811											
EVI5	7813	hgsc.bcm.edu	37	chr1	93073196	93073196	+	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	ttaattgagtaaggagtcctTtgttctgtgcagaaagatac	12	14	10	5	0	1	3	0	1	1	2	2	4	2	4	1	1	2	3	1	1	4	6			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr1:93073196T>A	ENST00000370331.1	-	15	1877	c.1868A>T	c.(1867-1869)aAa>aTa	p.K623I	EVI5_ENST00000540033.1_Missense_Mutation_p.K623I|EVI5_ENST00000543509.1_Missense_Mutation_p.K634I|EVI5_ENST00000491940.1_5'UTR	NM_005665.4	NP_005656.4	O60447	EVI5_HUMAN	ecotropic viral integration site 5	623	Dimerization.|Interaction with AURKB and INCENP.|Targeting to the centrosomes.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|retrograde transport, endosome to Golgi (GO:0042147)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|skin(1)	38		all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203)		Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211)		AAGGAGTCCTTTGTTCTGTGC	0.358																																					p.K623I		Atlas-SNP	.											.	EVI5	94	.	0			c.A1868T						PASS	.						166	149	154					1																	93073196		2202	4299	6501	SO:0001583	missense	7813	exon15			AGTCCTTTGTTCT	AF008915	CCDS30774.1	1p22	2013-07-09			ENSG00000067208	ENSG00000067208			3501	protein-coding gene	gene with protein product	"neuroblastoma stage 4S gene"	602942				9618176	Standard	XM_005271180		Approved	NB4S	uc001dox.3	O60447	OTTHUMG00000010895	ENST00000370331.1:c.1868A>T	chr1.hg19:g.93073196T>A	ENSP00000359356:p.Lys623Ile	47.0	0.0	.		88.0	45.0	.	NM_005665	A6NKX8|B9A6J0|Q9H1Y9	Missense_Mutation	SNP	ENST00000370331.1	hg19	CCDS30774.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.656843	0.88154	.	.	ENSG00000067208	ENST00000370331;ENST00000540033;ENST00000543509	T;T;T	0.37584	1.19;1.19;1.19	5.59	4.26	0.50523	.	0.052940	0.85682	D	0.000000	T	0.44286	0.1286	M	0.79123	2.44	0.51767	D	0.999936	P;P	0.49696	0.927;0.88	P;P	0.55455	0.776;0.602	T	0.51124	-0.8745	10	0.87932	D	0	-27.0804	12.0805	0.53667	0.0:0.0783:0.0:0.9217	.	634;623	F5H4R0;O60447	.;EVI5_HUMAN	I	623;623;634	ENSP00000359356:K623I;ENSP00000440826:K623I;ENSP00000445019:K634I	ENSP00000359356:K623I	K	-	2	0	EVI5	92845784	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.949000	0.70257	2.132000	0.65825	0.533000	0.62120	AAA	.	.	.	none		0.358	EVI5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030047.1	NM_005665		A	93073196	T	A	93073196	3	1	197	1	0	0	0	0	1	0	0	0	5291	1841	64	5	580	5	EVI5	1	93073196	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	2893250	93073196	156177425	4	11812											
EDEM3	80267	hgsc.bcm.edu	37	chr1	184723718	184723718	+	Frame_Shift_Del	DEL	T	T	-																															aacgcggccgtcgccgccacTagtctccatcgcgctcgctg																										TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr1:184723718delT	ENST00000318130.8	-	1	329	c.63delA	c.(61-63)ctafs	p.L21fs	EDEM3_ENST00000367512.3_5'Flank	NM_025191.3	NP_079467.3	Q9BZQ6	EDEM3_HUMAN	ER degradation enhancer, mannosidase alpha-like 3	21					cellular protein metabolic process (GO:0044267)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TCGCCGCCACTAGTCTCCATC	0.716																																					p.V22fs		Atlas-INDEL	.											.	EDEM3	63	.	0			c.64delG						PASS	.						5	10	9					1																	184723718		667	1557	2224	SO:0001589	frameshift_variant	80267	exon1			.	AF288393	CCDS1363.2	1q25	2008-02-05	2006-03-31	2006-03-31	ENSG00000116406	ENSG00000116406			16787	protein-coding gene	gene with protein product		610214	"chromosome 1 open reading frame 22"	C1orf22		15537790, 15579471	Standard	NM_025191		Approved		uc010pok.2	Q9BZQ6	OTTHUMG00000035387	ENST00000318130.8:c.63delA	chr1.hg19:g.184723718delT	ENSP00000318147:p.Leu21fs	89.0	0.0	0		54.0	13.0	0.240741	NM_025191	B2RCH6|B7ZLZ2|Q0VGM5|Q5TEZ0|Q9HCW1|Q9UFV7	Frame_Shift_Del	DEL	ENST00000318130.8	hg19	CCDS1363.2																																																																																			.	.	.	none		0.716	EDEM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085785.3	NM_025191		-	184723718	T	-	184723718	7	5	197	1	0	1	0	1	0	0	0	0	4915	1509	53	0	2815	0	EDEM3	1	184723718	Frame_Shift_Del	DEL	T	TCGA-HE-A5NH-01A-11D-A26P-10	91650522	184723718	64526903	5	11813											
HMCN1	83872	hgsc.bcm.edu	37	chr1	186082053	186082053	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgccagcaacattgcaggaaAgactacaagagaatttattc	16	9	8	8	0	0	2	0	0	0	2	1	4	0	3	1	1	5	2	1	1	6	5			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr1:186082053A>G	ENST00000271588.4	+	72	11328	c.11099A>G	c.(11098-11100)aAg>aGg	p.K3700R	HMCN1_ENST00000367492.2_Missense_Mutation_p.K3700R	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3700	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						ATTGCAGGAAAGACTACAAGA	0.393																																					p.K3700R		Atlas-SNP	.											.	HMCN1	797	.	0			c.A11099G						PASS	.						106	101	103					1																	186082053		2203	4300	6503	SO:0001583	missense	83872	exon72			CAGGAAAGACTAC	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.11099A>G	chr1.hg19:g.186082053A>G	ENSP00000271588:p.Lys3700Arg	46.0	0.0	.		69.0	24.0	.	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	A	14.68	2.607517	0.46527	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.69561	-0.41;-0.41	4.91	3.77	0.43336	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.134451	0.64402	D	0.000003	T	0.62527	0.2435	N	0.12637	0.245	0.45747	D	0.99864	D	0.69078	0.997	D	0.80764	0.994	T	0.58278	-0.7664	10	0.21014	T	0.42	.	10.2014	0.43087	0.921:0.0:0.079:0.0	.	3700	Q96RW7	HMCN1_HUMAN	R	3700	ENSP00000271588:K3700R;ENSP00000356462:K3700R	ENSP00000271588:K3700R	K	+	2	0	HMCN1	184348676	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.263000	0.58853	1.957000	0.56846	0.533000	0.62120	AAG	.	.	.	none		0.393	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		G	186082053	A	G	186082053	3	3	197	1	0	0	0	0	1	0	0	0	7227	72	3	3	11385	3	HMCN1	1	186082053	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10	1358335	186082053	63168568	6	11814											
NBAS	51594	hgsc.bcm.edu	37	chr2	15519770	15519770	+	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	gtgaggttggtagaagaattGaagtactctctgctggcagc	10	11	14	6	0	1	4	0	2	1	2	2	4	1	4	0	3	3	5	0	3	5	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr2:15519770G>T	ENST00000281513.5	-	30	3571	c.3546C>A	c.(3544-3546)ttC>ttA	p.F1182L	NBAS_ENST00000441750.1_Missense_Mutation_p.F1062L	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	1182					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						TAGAAGAATTGAAGTACTCTC	0.443																																					p.F1182L		Atlas-SNP	.											.	NBAS	246	.	0			c.C3546A						PASS	.						115	113	114					2																	15519770		2203	4300	6503	SO:0001583	missense	51594	exon30			AGAATTGAAGTAC	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.3546C>A	chr2.hg19:g.15519770G>T	ENSP00000281513:p.Phe1182Leu	110.0	0.0	.		150.0	61.0	.	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	hg19	CCDS1685.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.8|27.8	4.863074|4.863074	0.91511|0.91511	.|.	.|.	ENSG00000151779|ENSG00000151779	ENST00000441750;ENST00000281513;ENST00000441755|ENST00000442506	T;T;T|.	0.32272|.	1.46;1.46;1.46|.	5.79|5.79	4.92|4.92	0.64577|0.64577	Secretory pathway Sec39 (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.75258|.	0.3825|.	M|M	0.78637|0.78637	2.42|2.42	0.58432|0.58432	D|D	0.999999|0.999999	D;D|.	0.89917|.	0.992;1.0|.	D;D|.	0.91635|.	0.965;0.999|.	T|.	0.76699|.	-0.2863|.	10|.	0.87932|.	D|.	0|.	.|.	14.7925|14.7925	0.69854|0.69854	0.0691:0.0:0.9309:0.0|0.0691:0.0:0.9309:0.0	.|.	1062;1182|.	A2RRP1-2;A2RRP1|.	.;NBAS_HUMAN|.	L|X	1062;1182;229|230	ENSP00000413201:F1062L;ENSP00000281513:F1182L;ENSP00000396501:F229L|.	ENSP00000281513:F1182L|.	F|S	-|-	3|2	2|0	NBAS|NBAS	15437221|15437221	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	4.815000|4.815000	0.62634|0.62634	1.461000|1.461000	0.47929|0.47929	0.563000|0.563000	0.77884|0.77884	TTC|TCA	.	.	.	none		0.443	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		T	15519770	G	T	15519770	3	4	197	1	0	0	0	0	1	0	0	0	10193	1281	45	4	3661	4	NBAS	2	15519770	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10		15519770	227679603	7	11815											
PNPT1	87178	hgsc.bcm.edu	37	chr2	55863462	55863462	+	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	ctgaccacggttgtagctggCgactgaagcacttttcgaga	9	10	12	10	3	0	3	0	2	0	1	1	5	0	3	1	2	2	4	1	2	2	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr2:55863462C>T	ENST00000447944.2	-	28	2348	c.2262G>A	c.(2260-2262)tcG>tcA	p.S754S		NM_033109.3	NP_149100.2	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	754					cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA polyadenylation (GO:0097222)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA 5'-end processing (GO:0000964)|mitochondrial RNA catabolic process (GO:0000957)|mitochondrion morphogenesis (GO:0070584)|mitotic cell cycle arrest (GO:0071850)|mRNA catabolic process (GO:0006402)|negative regulation of growth (GO:0045926)|nuclear polyadenylation-dependent mRNA catabolic process (GO:0071042)|positive regulation of miRNA catabolic process (GO:2000627)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|positive regulation of mRNA catabolic process (GO:0061014)|protein homooligomerization (GO:0051260)|protein homotrimerization (GO:0070207)|regulation of cellular respiration (GO:0043457)|regulation of cellular senescence (GO:2000772)|RNA catabolic process (GO:0006401)|RNA import into mitochondrion (GO:0035927)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA polyadenylation (GO:0043631)|rRNA import into mitochondrion (GO:0035928)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrial degradosome (GO:0045025)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	3'-5'-exoribonuclease activity (GO:0000175)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|polyribonucleotide nucleotidyltransferase activity (GO:0004654)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			TTGTAGCTGGCGACTGAAGCA	0.393																																					p.S754S		Atlas-SNP	.											.	PNPT1	68	.	0			c.G2262A						PASS	.						93	84	87					2																	55863462		2203	4300	6503	SO:0001819	synonymous_variant	87178	exon28			AGCTGGCGACTGA	BC053660	CCDS1856.1	2p15	2013-01-08			ENSG00000138035	ENSG00000138035			23166	protein-coding gene	gene with protein product	"polynucleotide phosphorylase", "3'-5' RNA exonuclease"	610316	"deafness, autosomal recessive 70"	DFNB70		12419256	Standard	NM_033109		Approved	PNPase, OLD35, old-35	uc002rzf.3	Q8TCS8	OTTHUMG00000129335	ENST00000447944.2:c.2262G>A	chr2.hg19:g.55863462C>T		95.0	0.0	.		96.0	4.0	.	NM_033109	Q53SU0|Q68CN1|Q7Z7D1|Q8IWX1|Q96T05|Q9BRU3|Q9BVX0	Silent	SNP	ENST00000447944.2	hg19	CCDS1856.1																																																																																			.	.	.	none		0.393	PNPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251481.2	NM_033109		T	55863462	C	T	55863462	2	4	197	1	0	0	0	0	0	0	0	1	12180	755	27	1		1	PNPT1	2	55863462	Silent	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	40343692	55863462	187335911	8	11816											
RIF1	55183	hgsc.bcm.edu	37	chr2	152320162	152320162	+	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	actaatactgtagaggagaaAaatgtagaaattaatttgga	19	11	9	2	0	0	3	0	0	0	3	0	5	0	4	0	2	1	2	0	2	8	6			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr2:152320162A>T	ENST00000243326.5	+	29	4611	c.4128A>T	c.(4126-4128)aaA>aaT	p.K1376N	RIF1_ENST00000428287.2_Missense_Mutation_p.K1376N|RIF1_ENST00000444746.2_Missense_Mutation_p.K1376N|RIF1_ENST00000453091.2_Missense_Mutation_p.K1376N|RIF1_ENST00000430328.2_Missense_Mutation_p.K1376N			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)		TAGAGGAGAAAAATGTAGAAA	0.348																																					p.K1376N		Atlas-SNP	.											.	RIF1	244	.	0			c.A4128T						PASS	.						72	78	76					2																	152320162		2203	4300	6503	SO:0001583	missense	55183	exon30			GGAGAAAAATGTA	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.4128A>T	chr2.hg19:g.152320162A>T	ENSP00000243326:p.Lys1376Asn	26.0	0.0	.		25.0	11.0	.	NM_018151	A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000243326.5	hg19	CCDS2194.1	.	.	.	.	.	.	.	.	.	.	A	0.921	-0.715998	0.03206	.	.	ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000430328	T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58	5.45	1.54	0.23209	.	0.844182	0.10956	N	0.615469	T	0.20210	0.0486	L	0.41710	1.295	0.09310	N	1	B;B	0.28512	0.078;0.214	B;B	0.21546	0.015;0.035	T	0.21895	-1.0232	10	0.39692	T	0.17	-9.694	3.1462	0.06472	0.5289:0.0:0.2045:0.2666	.	1376;1376	Q5UIP0;Q5UIP0-2	RIF1_HUMAN;.	N	1376	ENSP00000390181:K1376N;ENSP00000414615:K1376N;ENSP00000415691:K1376N;ENSP00000243326:K1376N;ENSP00000416123:K1376N	ENSP00000243326:K1376N	K	+	3	2	RIF1	152028408	0.003000	0.15002	0.001000	0.08648	0.192000	0.23643	0.898000	0.28404	0.384000	0.24942	0.455000	0.32223	AAA	.	.	.	none		0.348	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3			T	152320162	A	T	152320162	3	4	197	1	0	0	0	0	1	0	0	0	13372	11	1	5	4242	5	RIF1	2	152320162	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10	96456700	152320162	90879211	9	11817											
PLA2R1	22925	hgsc.bcm.edu	37	chr2	160825863	160825863	+	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	gtatatcactggtgttccatCtctccagctgtgggaagatt	8	14	10	9	0	2	1	1	0	1	1	5	2	4	2	2	2	1	3	2	2	3	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr2:160825863C>G	ENST00000283243.7	-	19	2874	c.2668G>C	c.(2668-2670)Gat>Cat	p.D890H	PLA2R1_ENST00000392771.1_Missense_Mutation_p.D890H	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	890	C-type lectin 5. {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						GGTGTTCCATCTCTCCAGCTG	0.408																																					p.D890H		Atlas-SNP	.											.	PLA2R1	153	.	0			c.G2668C						PASS	.						116	110	112					2																	160825863		2203	4300	6503	SO:0001583	missense	22925	exon19			TTCCATCTCTCCA	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.2668G>C	chr2.hg19:g.160825863C>G	ENSP00000283243:p.Asp890His	57.0	0.0	.		59.0	15.0	.	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Missense_Mutation	SNP	ENST00000283243.7	hg19	CCDS33309.1	.	.	.	.	.	.	.	.	.	.	C	19.65	3.867614	0.72065	.	.	ENSG00000153246	ENST00000283243;ENST00000392771	T;T	0.15834	2.39;2.39	5.8	4.92	0.64577	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.107665	0.64402	D	0.000009	T	0.51143	0.1657	H	0.95365	3.66	0.47994	D	0.999564	B;D;D	0.89917	0.372;1.0;0.999	B;D;D	0.71414	0.309;0.973;0.966	T	0.62604	-0.6819	10	0.51188	T	0.08	.	11.2567	0.49058	0.0:0.9128:0.0:0.0872	.	890;890;890	B7ZML4;Q13018-2;Q13018	.;.;PLA2R_HUMAN	H	890	ENSP00000283243:D890H;ENSP00000376524:D890H	ENSP00000283243:D890H	D	-	1	0	PLA2R1	160534109	0.976000	0.34144	0.999000	0.59377	0.993000	0.82548	1.512000	0.35812	1.426000	0.47256	0.650000	0.86243	GAT	.	.	.	none		0.408	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1			G	160825863	C	G	160825863	3	3	197	1	0	0	0	0	1	0	0	0	12017	913	32	4	1779	4	PLA2R1	2	160825863	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	8505701	160825863	82373510	10	11818											
TTLL4	9654	hgsc.bcm.edu	37	chr2	219611762	219611762	+	Missense_Mutation	SNP	A	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	gctcattccagattgggaggAaggaccggctatggcggaac	10	7	15	9	2	1	1	1	0	0	1	2	5	2	5	2	6	1	2	2	6	3	3			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr2:219611762A>C	ENST00000392102.1	+	9	2351	c.2011A>C	c.(2011-2013)Aag>Cag	p.K671Q	TTLL4_ENST00000442769.1_Intron|TTLL4_ENST00000457313.1_Missense_Mutation_p.K506Q|TTLL4_ENST00000258398.4_Missense_Mutation_p.K671Q	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	671	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				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)		GATTGGGAGGAAGGACCGGCT	0.537																																					p.K671Q	GBM(172;1818 2053 15407 20943 49753)	Atlas-SNP	.											.	TTLL4	96	.	0			c.A2011C						PASS	.						135	125	128					2																	219611762		2203	4300	6503	SO:0001583	missense	9654	exon9			GGGAGGAAGGACC		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.2011A>C	chr2.hg19:g.219611762A>C	ENSP00000375951:p.Lys671Gln	109.0	0.0	.		197.0	73.0	.	NM_014640	A8K6V5|Q8WW29	Missense_Mutation	SNP	ENST00000392102.1	hg19	CCDS2422.1	.	.	.	.	.	.	.	.	.	.	A	29.1	4.973585	0.92919	.	.	ENSG00000135912	ENST00000457313;ENST00000392102;ENST00000258398	T;T;T	0.09255	3.0;3.0;3.0	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.50548	0.1622	H	0.97918	4.105	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.69982	-0.4997	10	0.87932	D	0	.	15.3584	0.74448	1.0:0.0:0.0:0.0	.	506;671	E9PH58;Q14679	.;TTLL4_HUMAN	Q	506;671;671	ENSP00000393332:K506Q;ENSP00000375951:K671Q;ENSP00000258398:K671Q	ENSP00000258398:K671Q	K	+	1	0	TTLL4	219320006	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.904000	0.92590	2.217000	0.71921	0.482000	0.46254	AAG	.	.	.	none		0.537	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640		C	219611762	A	C	219611762	3	2	197	1	0	0	0	0	1	0	0	0	16741	247	9	5	2037	5	TTLL4	2	219611762	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10	58785899	219611762	23587611	11	11819											
CCDC108	255101	hgsc.bcm.edu	37	chr2	219878079	219878079	+	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	ctccggcttcactgtcacacCtatgaaatttagctggaaat	11	12	7	11	1	2	1	2	1	0	0	3	2	3	2	2	2	1	2	2	2	4	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr2:219878079C>T	ENST00000341552.5	-	24	3942	c.3859G>A	c.(3859-3861)Ggt>Agt	p.G1287S	CCDC108_ENST00000453220.1_Missense_Mutation_p.G1287S|CCDC108_ENST00000441968.1_Missense_Mutation_p.G1287S|AC097468.4_ENST00000441450.1_RNA	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	1287						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)		ACTGTCACACCTATGAAATTT	0.542																																					p.G1287S		Atlas-SNP	.											.	CCDC108	208	.	0			c.G3859A						PASS	.						96	86	89					2																	219878079		2202	4299	6501	SO:0001583	missense	255101	exon24			TCACACCTATGAA	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.3859G>A	chr2.hg19:g.219878079C>T	ENSP00000340776:p.Gly1287Ser	114.0	0.0	.		179.0	76.0	.	NM_194302	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Missense_Mutation	SNP	ENST00000341552.5	hg19	CCDS2430.2	.	.	.	.	.	.	.	.	.	.	C	31	5.066292	0.93898	.	.	ENSG00000181378	ENST00000341552;ENST00000441968;ENST00000453220	T;T;T	0.13307	2.6;2.6;2.6	5.11	5.11	0.69529	.	0.000000	0.42420	D	0.000714	T	0.40222	0.1108	M	0.75264	2.295	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.31081	-0.9956	10	0.72032	D	0.01	-14.6861	18.1538	0.89686	0.0:1.0:0.0:0.0	.	1287	Q6ZU64	CC108_HUMAN	S	1287	ENSP00000340776:G1287S;ENSP00000413377:G1287S;ENSP00000409117:G1287S	ENSP00000340776:G1287S	G	-	1	0	CCDC108	219586323	1.000000	0.71417	0.998000	0.56505	0.916000	0.54674	6.610000	0.74178	2.372000	0.80975	0.650000	0.86243	GGT	.	.	.	none		0.542	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302		T	219878079	C	T	219878079	3	4	197	1	0	0	0	0	1	0	0	0	2745	681	24	2	1966	2	CCDC108	2	219878079	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	266317	219878079	23321294	12	11820											
SPEG	10290	hgsc.bcm.edu	37	chr2	220349151	220349151	+	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	ccaggcagcagtctcagtagCagcatcgaaaacttggagtc	12	7	11	11	1	1	0	1	0	1	0	4	2	1	1	1	2	4	5	1	2	3	2			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr2:220349151C>T	ENST00000312358.7	+	30	7098	c.6966C>T	c.(6964-6966)agC>agT	p.S2322S	SPEG_ENST00000485813.1_3'UTR|AC053503.11_ENST00000429882.1_RNA	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2322					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)		GTCTCAGTAGCAGCATCGAAA	0.692																																					p.S2322S		Atlas-SNP	.											.	SPEG	272	.	0			c.C6966T						PASS	.						15	19	18					2																	220349151		1916	4034	5950	SO:0001819	synonymous_variant	10290	exon30			CAGTAGCAGCATC	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.6966C>T	chr2.hg19:g.220349151C>T		44.0	0.0	.		52.0	15.0	.	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Silent	SNP	ENST00000312358.7	hg19	CCDS42824.1																																																																																			.	.	.	none		0.692	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		T	220349151	C	T	220349151	2	4	197	1	0	0	0	0	0	0	0	1	15048	709	25	2		2	SPEG	2	220349151	Silent	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	471072	220349151	22850222	13	11821											
STK11IP	114790	hgsc.bcm.edu	37	chr2	220470428	220470428	+	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	gctctgggggtcctgatactGcgaggcaatgagcttcggag	7	9	16	9	2	1	2	0	2	1	0	3	4	2	3	1	4	3	3	1	4	2	2			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr2:220470428G>T	ENST00000456909.1	+	8	807	c.717G>T	c.(715-717)ctG>ctT	p.L239L	STK11IP_ENST00000459692.1_3'UTR|STK11IP_ENST00000295641.10_Silent_p.L250L			Q8N1F8	S11IP_HUMAN	serine/threonine kinase 11 interacting protein	250					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)		TCCTGATACTGCGAGGCAATG	0.602																																					p.L250L		Atlas-SNP	.											.	STK11IP	152	.	0			c.G750T						PASS	.						32	32	32					2																	220470428		1964	4137	6101	SO:0001819	synonymous_variant	114790	exon8			GATACTGCGAGGC	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.717G>T	chr2.hg19:g.220470428G>T		27.0	0.0	.		43.0	4.0	.	NM_052902	Q8NAW9|Q8WXE4|Q96CN3|Q96PY9	Silent	SNP	ENST00000456909.1	hg19																																																																																				.	.	.	none		0.602	STK11IP-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000131432.1	NM_052902		T	220470428	G	T	220470428	2	4	197	1	0	0	0	0	0	0	0	1	15300	1306	46	4		4	STK11IP	2	220470428	Silent	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	121277	220470428	22728945	14	11822											
IL5RA	3568	hgsc.bcm.edu	37	chr3	3139630	3139630	+	Frame_Shift_Del	DEL	A	A	-																															gagccgttaacaagcaccgcAagccagtcacgccctttgct																										TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr3:3139630delA	ENST00000446632.2	-	7	1207	c.633delT	c.(631-633)cttfs	p.L211fs	IL5RA_ENST00000256452.3_Frame_Shift_Del_p.L211fs|IL5RA_ENST00000456302.1_Frame_Shift_Del_p.L211fs|IL5RA_ENST00000438560.1_Frame_Shift_Del_p.L211fs|IL5RA_ENST00000445864.2_Intron|IL5RA_ENST00000418488.2_Frame_Shift_Del_p.L211fs|IL5RA_ENST00000383846.1_Frame_Shift_Del_p.L211fs|IL5RA_ENST00000430514.2_Frame_Shift_Del_p.L211fs|IL5RA_ENST00000311981.8_Frame_Shift_Del_p.L211fs	NM_175726.3	NP_783853.1	Q01344	IL5RA_HUMAN	interleukin 5 receptor, alpha	211					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)		CAAGCACCGCAAGCCAGTCAC	0.507																																					p.A212fs	GBM(169;430 2801 24955 28528)	Atlas-Indel,Pindel	.											.	IL5RA	55	.	0			c.634delG						PASS	.						112	97	102					3																	3139630		2203	4300	6503	SO:0001589	frameshift_variant	3568	exon7			.	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.633delT	chr3.hg19:g.3139630delA	ENSP00000412209:p.Leu211fs	168.0	0.0	0		217.0	86.0	0.396313	NM_175727	B3IU77|B4E2G0|Q14633|Q15469|Q6ISX9	Frame_Shift_Del	DEL	ENST00000446632.2	hg19	CCDS2559.1																																																																																			.	.	.	none		0.507	IL5RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337537.2			-	3139630	A	-	3139630	7	5	197	1	0	1	0	1	0	0	0	0	7707	117	5	0	679	0	IL5RA	3	3139630	Frame_Shift_Del	DEL	A	TCGA-HE-A5NH-01A-11D-A26P-10		3139630	194882800	15	11823											
IL17RC	84818	hgsc.bcm.edu	37	chr3	9971714	9971714	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctctcaccccttccagacTccctggggcctctcaaagac	7	8	7	19	0	2	2	2	0	2	2	6	2	4	2	6	2	0	0	6	2	1	1			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr3:9971714T>C	ENST00000295981.3	+	14	1590	c.1372T>C	c.(1372-1374)Tcc>Ccc	p.S458P	IL17RC_ENST00000455057.1_Missense_Mutation_p.S355P|IL17RC_ENST00000383812.4_Missense_Mutation_p.S372P|IL17RC_ENST00000416074.2_Missense_Mutation_p.S226P|IL17RC_ENST00000498214.1_Intron|IL17RC_ENST00000403601.3_Missense_Mutation_p.S387P|IL17RC_ENST00000413608.1_Missense_Mutation_p.S387P	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	458					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						CCTTCCAGACTCCCTGGGGCC	0.597																																					p.S458P		Atlas-SNP	.											.	IL17RC	55	.	0			c.T1372C						PASS	.						62	66	65					3																	9971714		2203	4300	6503	SO:0001583	missense	84818	exon14			CCAGACTCCCTGG	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.1372T>C	chr3.hg19:g.9971714T>C	ENSP00000295981:p.Ser458Pro	86.0	0.0	.		116.0	44.0	.	NM_153461	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Missense_Mutation	SNP	ENST00000295981.3	hg19	CCDS2590.1	.	.	.	.	.	.	.	.	.	.	T	18.01	3.526941	0.64860	.	.	ENSG00000163702	ENST00000383812;ENST00000295981;ENST00000436503;ENST00000403601;ENST00000416074;ENST00000455057;ENST00000413608	T;T;T;T;T;T;T	0.18174	2.23;2.23;2.23;2.23;2.23;2.23;2.23	5.84	1.78	0.24846	.	0.258488	0.27223	N	0.020354	T	0.25269	0.0614	L	0.59436	1.845	0.26156	N	0.980074	D;D;P;P;P;P;P;D;D;D	0.59357	0.98;0.967;0.93;0.93;0.883;0.883;0.944;0.958;0.966;0.985	P;P;B;P;P;P;B;P;P;P	0.56916	0.731;0.642;0.368;0.462;0.462;0.462;0.439;0.663;0.543;0.809	T	0.03148	-1.1067	10	0.72032	D	0.01	-27.1927	5.0209	0.14361	0.2862:0.0:0.2374:0.4764	.	372;226;355;370;387;387;226;372;458;387	Q8NAC3-4;F5H4Z2;E9PHG1;A8BWD5;E9PHJ6;A8BWC9;B4E008;Q8NAC3-3;Q8NAC3;Q8NAC3-2	.;.;.;.;.;.;.;.;I17RC_HUMAN;.	P	372;458;362;387;226;355;387	ENSP00000373323:S372P;ENSP00000295981:S458P;ENSP00000401128:S362P;ENSP00000384969:S387P;ENSP00000395315:S226P;ENSP00000407894:S355P;ENSP00000396064:S387P	ENSP00000295981:S458P	S	+	1	0	IL17RC	9946714	0.275000	0.24201	1.000000	0.80357	0.836000	0.47400	0.499000	0.22546	1.000000	0.39049	0.459000	0.35465	TCC	.	.	.	none		0.597	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732		C	9971714	T	C	9971714	3	2	197	1	0	0	0	0	1	0	0	0	7648	1551	54	3	1426	3	IL17RC	3	9971714	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	6832084	9971714	188050716	16	11824											
ARL13B	200894	hgsc.bcm.edu	37	chr3	93761993	93761993	+	Frame_Shift_Del	DEL	T	T	-																															aatcacaatggccaaaaaaaTaatgaatttggactagtaga																										TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr3:93761993delT	ENST00000394222.3	+	7	1208	c.933delT	c.(931-933)aatfs	p.N312fs	ARL13B_ENST00000471138.1_Frame_Shift_Del_p.N312fs|ARL13B_ENST00000535334.1_Frame_Shift_Del_p.N209fs|ARL13B_ENST00000303097.7_Frame_Shift_Del_p.N205fs|ARL13B_ENST00000539730.1_Frame_Shift_Del_p.N33fs	NM_001174150.1	NP_001167621.1	Q3SXY8	AR13B_HUMAN	ADP-ribosylation factor-like 13B	312					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						GCCAAAAAAATAATGAATTTG	0.373																																					p.N311fs		Atlas-Indel,Pindel	.											.	ARL13B	52	.	0			c.932delA						PASS	.						81	80	81					3																	93761993		2203	4300	6503	SO:0001589	frameshift_variant	200894	exon7			.	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.933delT	chr3.hg19:g.93761993delT	ENSP00000377769:p.Asn312fs	158.0	0.0	0		164.0	56.0	0.341463	NM_001174150	D3DN29|G3V1S8|Q504W8|Q8TCL5	Frame_Shift_Del	DEL	ENST00000394222.3	hg19	CCDS2925.1																																																																																			.	.	.	none		0.373	ARL13B-005	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352904.1	NM_182896		-	93761993	T	-	93761993	7	5	197	1	0	1	0	1	0	0	0	0	929	1403	49	0	959	0	ARL13B	3	93761993	Frame_Shift_Del	DEL	T	TCGA-HE-A5NH-01A-11D-A26P-10	83790279	93761993	104260437	17	11825											
DZIP1L	199221	hgsc.bcm.edu	37	chr3	137813760	137813760	+	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	ttccagctccccttgggtccActttagcttggcccgtagct	4	13	9	15	1	0	0	0	0	0	0	3	0	3	0	5	2	3	4	5	2	2	6			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr3:137813760A>T	ENST00000327532.2	-	4	1014	c.652T>A	c.(652-654)Tgg>Agg	p.W218R	DZIP1L_ENST00000488595.1_5'Flank|DZIP1L_ENST00000469243.1_Missense_Mutation_p.W218R	NM_173543.2	NP_775814.2	Q8IYY4	DZI1L_HUMAN	DAZ interacting zinc finger protein 1-like	218					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						CCTTGGGTCCACTTTAGCTTG	0.567																																					p.W218R		Atlas-SNP	.											.	DZIP1L	88	.	0			c.T652A						PASS	.						204	183	190					3																	137813760		2203	4300	6503	SO:0001583	missense	199221	exon5			GGGTCCACTTTAG	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.652T>A	chr3.hg19:g.137813760A>T	ENSP00000332148:p.Trp218Arg	103.0	0.0	.		166.0	58.0	.	NM_001170538	C9JUG5|Q96M38	Missense_Mutation	SNP	ENST00000327532.2	hg19	CCDS3096.1	.	.	.	.	.	.	.	.	.	.	A	2.056	-0.416478	0.04766	.	.	ENSG00000158163	ENST00000327532;ENST00000469243;ENST00000536706	T;T	0.58940	0.3;0.3	4.85	0.616	0.17613	.	0.838115	0.10499	N	0.667430	T	0.49287	0.1548	L	0.57536	1.79	0.24258	N	0.995292	B;B	0.16166	0.016;0.007	B;B	0.15870	0.01;0.014	T	0.44967	-0.9293	10	0.49607	T	0.09	-4.0524	5.9081	0.19012	0.3628:0.38:0.0:0.2572	.	218;218	Q8IYY4-2;Q8IYY4	.;DZI1L_HUMAN	R	218	ENSP00000332148:W218R;ENSP00000419486:W218R	ENSP00000332148:W218R	W	-	1	0	DZIP1L	139296450	0.994000	0.37717	0.993000	0.49108	0.676000	0.39594	0.188000	0.17018	0.280000	0.22209	0.460000	0.39030	TGG	.	.	.	none		0.567	DZIP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357548.1	NM_173543		T	137813760	A	T	137813760	3	4	197	1	0	0	0	0	1	0	0	0	4866	159	6	5	1712	5	DZIP1L	3	137813760	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10	44051767	137813760	60208670	18	11826											
ARAP2	116984	hgsc.bcm.edu	37	chr4	36069579	36069579	+	Missense_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	ttttggaagggttcttgaccGttgtagaaccacattaagtt	10	15	10	6	1	1	2	0	1	1	1	1	3	1	3	2	2	1	4	2	2	4	8	rs377015356		TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr4:36069579G>A	ENST00000303965.4	-	33	5554	c.5065C>T	c.(5065-5067)Cgg>Tgg	p.R1689W		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	1689					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						GTTCTTGACCGTTGTAGAACC	0.358																																					p.R1689W		Atlas-SNP	.											ARAP2,NS,carcinoma,0,1	ARAP2	210	.	0			c.C5065T						PASS	.						97	98	98					4																	36069579		2203	4300	6503	SO:0001583	missense	116984	exon33			TTGACCGTTGTAG	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.5065C>T	chr4.hg19:g.36069579G>A	ENSP00000302895:p.Arg1689Trp	76.0	0.0	.		79.0	33.0	.	NM_015230	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Missense_Mutation	SNP	ENST00000303965.4	hg19	CCDS3441.1	.	.	.	.	.	.	.	.	.	.	G	16.25	3.069954	0.55539	.	.	ENSG00000047365	ENST00000303965	T	0.10573	2.86	5.79	2.62	0.31277	.	0.081885	0.48286	D	0.000197	T	0.19327	0.0464	L	0.32530	0.975	0.26832	N	0.968552	D	0.89917	1.0	D	0.65573	0.936	T	0.02391	-1.1166	10	0.87932	D	0	.	12.1751	0.54180	0.0:0.0:0.5359:0.4641	.	1689	Q8WZ64	ARAP2_HUMAN	W	1689	ENSP00000302895:R1689W	ENSP00000302895:R1689W	R	-	1	2	ARAP2	35745974	0.543000	0.26434	0.703000	0.30354	0.768000	0.43524	1.288000	0.33296	0.691000	0.31592	0.650000	0.86243	CGG	.	.	.	weak		0.358	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230		A	36069579	G	A	36069579	3	1	197	1	0	0	0	0	1	0	0	0	839	1144	40	1	53	1	ARAP2	4	36069579	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10		36069579	155084697	19	11827											
GABRB1	2560	hgsc.bcm.edu	37	chr4	47427723	47427723	+	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	ggtaacattctcctcagcacCctggaaatccggaatgagac	12	8	9	12	1	2	1	1	1	1	1	4	4	3	3	3	3	2	2	3	3	3	2			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr4:47427723C>G	ENST00000295454.3	+	9	1405	c.1113C>G	c.(1111-1113)acC>acG	p.T371T	GABRB1_ENST00000538619.1_Silent_p.T301T	NM_000812.3	NP_000803.2	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 1	371					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)	TCCTCAGCACCCTGGAAATCC	0.547																																					p.T371T		Atlas-SNP	.											.	GABRB1	107	.	0			c.C1113G						PASS	.						77	75	76					4																	47427723		2203	4300	6503	SO:0001819	synonymous_variant	2560	exon9			CAGCACCCTGGAA		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.1113C>G	chr4.hg19:g.47427723C>G		77.0	0.0	.		128.0	50.0	.	NM_000812	B2R6U7|D6REL3|Q16166|Q8TBK3	Silent	SNP	ENST00000295454.3	hg19	CCDS3474.1																																																																																			.	.	.	none		0.547	GABRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216896.1			G	47427723	C	G	47427723	2	3	197	1	0	0	0	0	0	0	0	1	6173	610	22	4		4	GABRB1	4	47427723	Silent	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	11358144	47427723	143726553	20	11828											
MTRR	4552	hgsc.bcm.edu	37	chr5	7895903	7895903	+	Frame_Shift_Del	DEL	C	C	-																															ttaccagatgacccctcaatCcccatcataatggtgggtcc																										TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr5:7895903delC	ENST00000264668.2	+	12	1725	c.1695delC	c.(1693-1695)atcfs	p.I565fs	MTRR_ENST00000440940.2_Frame_Shift_Del_p.I538fs	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	565					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)	ACCCCTCAATCCCCATCATAA	0.403																																					p.I565fs		Atlas-Indel,Pindel	.											.	MTRR	74	.	0			c.1694delT						PASS	.						137	138	138					5																	7895903		2203	4300	6503	SO:0001589	frameshift_variant	4552	exon12			.	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.1695delC	chr5.hg19:g.7895903delC	ENSP00000264668:p.Ile565fs	84.0	0.0	0		81.0	39.0	0.481481	NM_024010	O60471|Q32MA9|Q7Z4M8	Frame_Shift_Del	DEL	ENST00000264668.2	hg19	CCDS3874.1																																																																																			.	.	.	none		0.403	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1			-	7895903	C	-	7895903	7	5	197	1	0	1	0	1	0	0	0	0	9968	845	30	0	1741	0	MTRR	5	7895903	Frame_Shift_Del	DEL	C	TCGA-HE-A5NH-01A-11D-A26P-10		7895903	173019357	21	11829											
PRR16	51334	hgsc.bcm.edu	37	chr5	120021685	120021685	+	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	acaccctgacctctgacctaCagctggaggatgagatgact	11	8	10	12	0	1	4	0	4	1	1	1	7	1	6	3	2	2	1	3	2	1	1			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr5:120021685C>A	ENST00000407149.2	+	2	405	c.196C>A	c.(196-198)Cag>Aag	p.Q66K	PRR16_ENST00000446965.1_5'UTR|PRR16_ENST00000379551.2_Missense_Mutation_p.Q43K|PRR16_ENST00000505123.1_5'UTR			Q569H4	LARGN_HUMAN	proline rich 16	66					positive regulation of cell size (GO:0045793)|positive regulation of translation (GO:0045727)					endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0464)|Prostate(80;0.00446)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)		CTCTGACCTACAGCTGGAGGA	0.463																																					p.Q43K		Atlas-SNP	.											.	PRR16	71	.	0			c.C127A						PASS	.						97	88	91					5																	120021685		2203	4300	6503	SO:0001583	missense	51334	exon3			GACCTACAGCTGG	AF242769	CCDS4127.1, CCDS75290.1	5q23.1	2006-08-22			ENSG00000184838	ENSG00000184838			29654	protein-coding gene	gene with protein product		615931				15971941	Standard	XM_005272010		Approved	DSC54	uc003ksp.3	Q569H4	OTTHUMG00000128903	ENST00000407149.2:c.196C>A	chr5.hg19:g.120021685C>A	ENSP00000385118:p.Gln66Lys	87.0	0.0	.		87.0	37.0	.	NM_016644	D3DSZ0|Q8IXY1|Q9NYI5	Missense_Mutation	SNP	ENST00000407149.2	hg19		.	.	.	.	.	.	.	.	.	.	C	22.1	4.240061	0.79912	.	.	ENSG00000184838	ENST00000407149;ENST00000379551	T;T	0.45668	0.89;0.89	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.52240	0.1722	L	0.43152	1.355	0.80722	D	1	D;D	0.67145	0.988;0.996	P;P	0.57911	0.829;0.829	T	0.44190	-0.9344	9	.	.	.	-0.1775	17.7817	0.88526	0.0:1.0:0.0:0.0	.	66;43	Q569H4;Q569H4-3	PRR16_HUMAN;.	K	66;43	ENSP00000385118:Q66K;ENSP00000368869:Q43K	.	Q	+	1	0	PRR16	120049584	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.383000	0.79741	2.568000	0.86640	0.555000	0.69702	CAG	.	.	.	none		0.463	PRR16-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000371059.1	NM_016644		A	120021685	C	A	120021685	3	1	197	1	0	0	0	0	1	0	0	0	12599	479	17	4	133	4	PRR16	5	120021685	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	112125782	120021685	60893575	22	11830											
CCNI2	645121	hgsc.bcm.edu	37	chr5	132088594	132088594	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acagctgctgcaaggaacttGtaatgcagcaactgagaagt	14	8	11	8	0	0	1	0	1	0	1	0	3	0	2	0	1	7	6	0	1	5	2			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr5:132088594G>A	ENST00000378731.1	+	6	1093	c.1042G>A	c.(1042-1044)Gta>Ata	p.V348I	SEPT8_ENST00000481030.1_Intron|SEPT8_ENST00000378719.2_Intron	NM_001039780.2	NP_001034869.1	Q6ZMN8	CCNI2_HUMAN	cyclin I family, member 2	348					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)					haematopoietic_and_lymphoid_tissue(1)|prostate(1)|urinary_tract(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CAAGGAACTTGTAATGCAGCA	0.478																																					p.V348I		Atlas-SNP	.											.	CCNI2	11	.	0			c.G1042A						PASS	.						122	105	111					5																	132088594		2203	4300	6503	SO:0001583	missense	645121	exon6			GAACTTGTAATGC	BC132837	CCDS34236.1, CCDS75297.1	5q31.1	2014-07-03			ENSG00000205089	ENSG00000205089			33869	protein-coding gene	gene with protein product						23707792	Standard	NM_001287252		Approved	FLJ16793	uc003kxq.1	Q6ZMN8	OTTHUMG00000059737	ENST00000378731.1:c.1042G>A	chr5.hg19:g.132088594G>A	ENSP00000368005:p.Val348Ile	78.0	0.0	.		98.0	38.0	.	NM_001039780	B2RNE2|B7ZMB7|B7ZMB8	Missense_Mutation	SNP	ENST00000378731.1	hg19	CCDS34236.1	.	.	.	.	.	.	.	.	.	.	g	15.24	2.775517	0.49786	.	.	ENSG00000205089	ENST00000378731	T	0.42131	0.98	5.35	2.54	0.30619	.	0.252001	0.38959	N	0.001518	T	0.43055	0.1230	M	0.66297	2.02	0.09310	N	0.999999	B;B;P	0.41710	0.261;0.261;0.76	B;B;P	0.45232	0.03;0.052;0.474	T	0.31194	-0.9952	10	0.52906	T	0.07	.	6.9365	0.24468	0.1591:0.1432:0.6976:0.0	.	349;364;348	B7ZMB7;B7ZMB8;Q6ZMN8	.;.;CCNI2_HUMAN	I	348	ENSP00000368005:V348I	ENSP00000368005:V348I	V	+	1	0	CCNI2	132116493	0.435000	0.25577	0.001000	0.08648	0.003000	0.03518	1.780000	0.38634	0.434000	0.26340	-0.144000	0.13903	GTA	.	.	.	none		0.478	CCNI2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132833.1	NM_001039780		A	132088594	G	A	132088594	3	1	197	1	0	0	0	0	1	0	0	0	2929	1377	48	2	1064	2	CCNI2	5	132088594	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	12066909	132088594	48826666	23	11831											
FAM13B	51306	hgsc.bcm.edu	37	chr5	137354741	137354741	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcatcaagtggaattccaaaTattttgttagcaagaacgga	15	12	8	6	1	2	1	2	0	0	1	3	3	3	3	1	2	2	2	1	2	7	5			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr5:137354741T>C	ENST00000033079.3	-	3	511	c.60A>G	c.(58-60)atA>atG	p.I20M	FAM13B_ENST00000425075.2_Intron|FAM13B_ENST00000420893.2_Missense_Mutation_p.I20M	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	20					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						GAATTCCAAATATTTTGTTAG	0.448																																					p.I20M		Atlas-SNP	.											.	FAM13B	46	.	0			c.A60G						PASS	.						102	99	100					5																	137354741		2203	4300	6503	SO:0001583	missense	51306	exon3			TCCAAATATTTTG	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.60A>G	chr5.hg19:g.137354741T>C	ENSP00000033079:p.Ile20Met	188.0	0.0	.		256.0	120.0	.	NM_001101800	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Missense_Mutation	SNP	ENST00000033079.3	hg19	CCDS4195.1	.	.	.	.	.	.	.	.	.	.	T	17.19	3.327093	0.60743	.	.	ENSG00000031003	ENST00000033079;ENST00000420893;ENST00000514310;ENST00000502471;ENST00000509596;ENST00000508403;ENST00000505961	T;T;T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89;0.89;0.89	5.87	5.87	0.94306	Rho GTPase-activating protein domain (1);Rho GTPase activation protein (1);	0.045544	0.85682	D	0.000000	T	0.48874	0.1524	N	0.14661	0.345	0.43394	D	0.995515	D;D	0.76494	0.999;0.998	D;D	0.74023	0.952;0.982	T	0.56986	-0.7888	10	0.87932	D	0	-9.9548	16.27	0.82612	0.0:0.0:0.0:1.0	.	20;20	Q9NYF5-2;Q9NYF5	.;FA13B_HUMAN	M	20	ENSP00000033079:I20M;ENSP00000388521:I20M;ENSP00000425326:I20M;ENSP00000424785:I20M;ENSP00000422311:I20M;ENSP00000426863:I20M;ENSP00000422673:I20M	ENSP00000033079:I20M	I	-	3	3	FAM13B	137382640	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.908000	0.56355	2.248000	0.74166	0.533000	0.62120	ATA	.	.	.	none		0.448	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1			C	137354741	T	C	137354741	3	2	197	1	0	0	0	0	1	0	0	0	5457	1396	49	3	2841	3	FAM13B	5	137354741	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	5266147	137354741	43560519	24	11832											
C6orf146	222826	hgsc.bcm.edu	37	chr6	4069042	4069042	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acactatattttgtcggtaaAgtttctttttggtcccaaag	10	17	7	7	1	1	0	0	0	1	0	3	0	2	0	1	2	0	2	1	2	5	8			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr6:4069042A>G	ENST00000274673.3	-	7	1818	c.1415T>C	c.(1414-1416)cTt>cCt	p.L472P	FAM217A_ENST00000380188.2_5'UTR	NM_173563.2	NP_775834.2	Q8IXS0	F217A_HUMAN	family with sequence similarity 217, member A	472																	TTGTCGGTAAAGTTTCTTTTT	0.403																																					p.L472P		Atlas-SNP	.											.	.	.	.	0			c.T1415C						PASS	.						87	92	90					6																	4069042		2203	4300	6503	SO:0001583	missense	222826	exon7			CGGTAAAGTTTCT	BC039349	CCDS4489.1	6p25.1	2012-02-07	2012-02-07	2012-02-07	ENSG00000145975	ENSG00000145975			21362	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 146"	C6orf146			Standard	NM_173563		Approved	MGC43581	uc003mvx.3	Q8IXS0	OTTHUMG00000014159	ENST00000274673.3:c.1415T>C	chr6.hg19:g.4069042A>G	ENSP00000274673:p.Leu472Pro	70.0	0.0	.		97.0	35.0	.	NM_173563	Q5JYK1	Missense_Mutation	SNP	ENST00000274673.3	hg19	CCDS4489.1	.	.	.	.	.	.	.	.	.	.	A	9.632	1.136613	0.21123	.	.	ENSG00000145975	ENST00000274673;ENST00000538080	T	0.19806	2.12	4.94	1.19	0.21007	.	0.439613	0.19414	N	0.114873	T	0.04724	0.0128	L	0.27053	0.805	0.38087	D	0.936832	B	0.22683	0.073	B	0.25884	0.064	T	0.21586	-1.0241	10	0.45353	T	0.12	.	3.9837	0.09506	0.6123:0.1915:0.1961:0.0	.	472	Q8IXS0	CF146_HUMAN	P	472;319	ENSP00000274673:L472P	ENSP00000274673:L472P	L	-	2	0	C6orf146	4014041	0.583000	0.26757	0.264000	0.24511	0.732000	0.41865	1.295000	0.33377	0.055000	0.16094	0.477000	0.44152	CTT	.	.	.	none		0.403	FAM217A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352577.2	NM_173563		G	4069042	A	G	4069042	3	3	197	1	0	0	0	0	1	0	0	0	2337	72	3	3	115	3	C6orf146	6	4069042	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10		4069042	167046025	25	11833											
MYLIP	29116	hgsc.bcm.edu	37	chr6	16143330	16143330	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttttgcagattgtgtcggcaAtggaaaactatggcatagaa	13	12	11	5	1	0	2	0	0	0	2	1	3	0	3	0	3	2	3	0	3	6	5			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr6:16143330A>G	ENST00000356840.3	+	4	742	c.544A>G	c.(544-546)Atg>Gtg	p.M182V	MYLIP_ENST00000349606.4_Start_Codon_SNP_p.M1V|MIR4639_ENST00000584938.1_RNA	NM_013262.3	NP_037394.2	Q8WY64	MYLIP_HUMAN	myosin regulatory light chain interacting protein	182	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cellular component movement (GO:0006928)|cholesterol homeostasis (GO:0042632)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|nervous system development (GO:0007399)|positive regulation of protein catabolic process (GO:0045732)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	cytoskeletal protein binding (GO:0008092)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28	Breast(50;0.0799)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.241)			TGTGTCGGCAATGGAAAACTA	0.473																																					p.M182V		Atlas-SNP	.											.	MYLIP	44	.	0			c.A544G						PASS	.						130	122	125					6																	16143330		2203	4300	6503	SO:0001583	missense	29116	exon4			TCGGCAATGGAAA	AF187016	CCDS4536.1	6p23-p22.3	2011-11-17			ENSG00000007944	ENSG00000007944			21155	protein-coding gene	gene with protein product	"E3 ubiquitin ligase-inducible degrader of the low density lipoprotein receptor"	610082				10593918, 11162443, 19688294	Standard	NM_013262		Approved	MIR, IDOL	uc003nbq.3	Q8WY64	OTTHUMG00000016405	ENST00000356840.3:c.544A>G	chr6.hg19:g.16143330A>G	ENSP00000349298:p.Met182Val	102.0	0.0	.		158.0	77.0	.	NM_013262	Q5TIA4|Q9BU73|Q9NRL9|Q9UHE7	Missense_Mutation	SNP	ENST00000356840.3	hg19	CCDS4536.1	.	.	.	.	.	.	.	.	.	.	A	11.61	1.689703	0.29962	.	.	ENSG00000007944	ENST00000356840;ENST00000349606	T;T	0.76839	-1.05;1.32	5.57	5.57	0.84162	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.135191	0.64402	D	0.000002	T	0.57548	0.2061	L	0.38175	1.15	0.80722	D	1	B	0.10296	0.003	B	0.11329	0.006	T	0.63125	-0.6707	10	0.87932	D	0	.	11.5381	0.50651	0.7336:0.2664:0.0:0.0	.	182	Q8WY64	MYLIP_HUMAN	V	182;1	ENSP00000349298:M182V;ENSP00000008686:M1V	ENSP00000008686:M1V	M	+	1	0	MYLIP	16251309	0.995000	0.38212	0.927000	0.36925	0.499000	0.33736	3.374000	0.52402	2.230000	0.72887	0.533000	0.62120	ATG	.	.	.	none		0.473	MYLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043864.1	NM_013262		G	16143330	A	G	16143330	3	3	197	1	0	0	0	0	1	0	0	0	10062	101	4	3	558	3	MYLIP	6	16143330	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10	12074288	16143330	154971737	26	11834											
SLC17A1	6568	hgsc.bcm.edu	37	chr6	25811999	25811999	+	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	agggaagacaagaacccattCtgaagaggaaacattattct	17	8	9	7	0	2	4	0	1	2	3	2	6	2	6	1	2	2	0	1	2	6	3			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr6:25811999C>T	ENST00000244527.4	-	9	1013		c.e9-1		SLC17A1_ENST00000468082.1_Splice_Site|SLC17A1_ENST00000427328.1_Splice_Site|SLC17A1_ENST00000476801.1_Splice_Site	NM_005074.3	NP_005065.2	Q14916	NPT1_HUMAN	solute carrier family 17 (organic anion transporter), member 1						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						AGAACCCATTCTGAAGAGGAA	0.403																																					.		Atlas-SNP	.											.	SLC17A1	71	.	0			c.898-1G>A						PASS	.						87	79	82					6																	25811999		2203	4300	6503	SO:0001630	splice_region_variant	6568	exon10			CCCATTCTGAAGA		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.898-1G>A	chr6.hg19:g.25811999C>T		61.0	0.0	.		73.0	26.0	.	NM_005074	A8K418|O60761|Q13783|Q3MIP5|Q5MJP8|Q5TB83|Q96KL8	Splice_Site	SNP	ENST00000244527.4	hg19	CCDS4565.1	.	.	.	.	.	.	.	.	.	.	C	7.361	0.624846	0.14193	.	.	ENSG00000124568	ENST00000244527;ENST00000427328;ENST00000476801;ENST00000468082	.	.	.	3.38	3.38	0.38709	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.5584	0.45131	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC17A1	25919978	1.000000	0.71417	0.946000	0.38457	0.079000	0.17450	4.214000	0.58527	2.191000	0.70037	0.650000	0.86243	.	.	.	.	none		0.403	SLC17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043647.2		Intron	T	25811999	C	T	25811999	5	4	197	1	0	0	0	0	0	0	1	0	14429	927	32	2	522	2	SLC17A1	6	25811999	Splice_Site	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	9668669	25811999	145303068	27	11835											
GCLC	2729	hgsc.bcm.edu	37	chr6	53370243	53370243	+	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	ggaaaggatcactctggtgaGcagtaccacaaacaccacat	15	6	9	11	0	2	1	1	1	1	0	2	3	2	3	2	3	3	2	2	3	3	1			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr6:53370243G>C	ENST00000229416.6	-	12	1825	c.1342C>G	c.(1342-1344)Ctc>Gtc	p.L448V	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	448					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)	ACTCTGGTGAGCAGTACCACA	0.403																																					p.L448V		Atlas-SNP	.											.	GCLC	58	.	0			c.C1342G						PASS	.						98	90	93					6																	53370243		2203	4300	6503	SO:0001583	missense	2729	exon12			TGGTGAGCAGTAC	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.1342C>G	chr6.hg19:g.53370243G>C	ENSP00000229416:p.Leu448Val	137.0	0.0	.		178.0	72.0	.	NM_001498	Q14399	Missense_Mutation	SNP	ENST00000229416.6	hg19	CCDS4952.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.15|17.15	3.315237|3.315237	0.60524|0.60524	.|.	.|.	ENSG00000001084|ENSG00000001084	ENST00000514373|ENST00000229416	.|T	.|0.77358	.|-1.09	5.94|5.94	5.94|5.94	0.96194|0.96194	.|.	.|0.055897	.|0.85682	.|D	.|0.000000	T|T	0.71787|0.71787	0.3381|0.3381	M|M	0.66297|0.66297	2.02|2.02	0.80722|0.80722	D|D	1|1	.|B	.|0.18968	.|0.032	.|B	.|0.22152	.|0.038	T|T	0.66779|0.66779	-0.5837|-0.5837	5|10	.|0.42905	.|T	.|0.14	.|.	20.3594|20.3594	0.98849|0.98849	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|448	.|P48506	.|GSH1_HUMAN	W|V	49|448	.|ENSP00000229416:L448V	.|ENSP00000229416:L448V	C|L	-|-	3|1	2|0	GCLC|GCLC	53478202|53478202	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.830000|0.830000	0.47004|0.47004	8.018000|8.018000	0.88722|0.88722	2.816000|2.816000	0.96949|0.96949	0.563000|0.563000	0.77884|0.77884	TGC|CTC	.	.	.	none		0.403	GCLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359710.2			C	53370243	G	C	53370243	3	2	197	1	0	0	0	0	1	0	0	0	6302	971	34	4	591	4	GCLC	6	53370243	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	27558244	53370243	117744824	28	11836											
C6orf162	57150	hgsc.bcm.edu	37	chr6	88046811	88046811	+	Missense_Mutation	SNP	A	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	acccaaagagaaagagtttcAaagcccagggctcagagggg	15	4	13	9	0	2	3	2	0	0	3	2	4	2	3	2	3	1	2	2	3	3	1			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr6:88046811A>C	ENST00000392863.1	+	3	151	c.62A>C	c.(61-63)cAa>cCa	p.Q21P	SMIM8_ENST00000608353.1_Missense_Mutation_p.Q21P|SMIM8_ENST00000608868.1_Missense_Mutation_p.Q21P|SMIM8_ENST00000608525.1_Missense_Mutation_p.Q21P|RP1-102H19.8_ENST00000448282.2_Missense_Mutation_p.Q21P|SMIM8_ENST00000229570.5_Missense_Mutation_p.Q21P	NM_001042493.1	NP_001035958.1	Q96KF7	SMIM8_HUMAN	small integral membrane protein 8	21						integral component of membrane (GO:0016021)											AAAGAGTTTCAAAGCCCAGGG	0.398																																					p.Q21P		Atlas-SNP	.											.	.	.	.	0			c.A62C						PASS	.						89	91	90					6																	88046811		2203	4300	6503	SO:0001583	missense	57150	exon3			AGTTTCAAAGCCC	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.62A>C	chr6.hg19:g.88046811A>C	ENSP00000376603:p.Gln21Pro	41.0	0.0	.		64.0	31.0	.	NM_001042493	B2R4V6|E1P505|Q5TEZ3|Q6NSD2|Q8IZ10	Missense_Mutation	SNP	ENST00000392863.1	hg19	CCDS34496.1	.	.	.	.	.	.	.	.	.	.	A	12.70	2.015538	0.35511	.	.	ENSG00000111850	ENST00000392863;ENST00000229570	.	.	.	5.69	-0.263	0.12954	.	0.368122	0.29501	N	0.011965	T	0.08044	0.0201	.	.	.	0.25064	N	0.991047	B	0.02656	0.0	B	0.04013	0.001	T	0.35475	-0.9787	8	0.25106	T	0.35	0.3915	5.1987	0.15252	0.2411:0.3105:0.4483:0.0	.	21	Q96KF7	CF162_HUMAN	P	21	.	ENSP00000229570:Q21P	Q	+	2	0	C6orf162	88103530	0.489000	0.26004	0.812000	0.32479	0.823000	0.46562	0.679000	0.25291	-0.373000	0.07979	0.533000	0.62120	CAA	.	.	.	none		0.398	SMIM8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472479.2	NM_020425		C	88046811	A	C	88046811	3	2	197	1	0	0	0	0	1	0	0	0	2342	130	5	5	64	5	C6orf162	6	88046811	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10	34676568	88046811	83068256	29	11837											
MET	4233	hgsc.bcm.edu	37	chr7	116411633	116411634	+	In_Frame_Ins	INS	-	-	TTGTCTCAATATCAACAGCACTGTTATTACTACTTGGGT																															cacaggattgattgctggtgINSttgtctcaatatcaacagca																										TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr7:116411633_116411634insTTGTCTCAATATCAACAGCACTGTTATTACTACTTGGGT	ENST00000318493.6	+	13	3053_3054	c.2866_2867insTTGTCTCAATATCAACAGCACTGTTATTACTACTTGGGT	c.(2866-2868)gtt>gTTGTCTCAATATCAACAGCACTGTTATTACTACTTGGGTtt	p.969_970insVSISTALLLLLGF	MET_ENST00000397752.3_In_Frame_Ins_p.951_952insVSISTALLLLLGF			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)			GATTGCTGGTGTTGTCTCAATA	0.347			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.V956delinsVVSISTALLLLLGF		Pindel	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.2866_2867insTTGTCTCAATATCAACAGCACTGTTATTACTACTTGGGT						PASS	.																																			SO:0001652	inframe_insertion	4233	exon13	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	.	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.2867_2905dupTTGTCTCAATATCAACAGCACTGTTATTACTACTTGGGT	chr7.hg19:g.116411633_116411634insTTGTCTCAATATCAACAGCACTGTTATTACTACTTGGGT	ENSP00000317272:p.Val957_Phe969dup	68.0	0.0	.		110.0	20.0	0.182	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	In_Frame_Ins	INS	ENST00000318493.6	hg19	CCDS47689.1																																																																																			.	.	.	none		0.347	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			TTGTCTCAATATCAACAGCACTGTTATTACTACTTGGGT	116411634	-	TTGTCTCAATATCAACAGCACTGTTATTACTACTTGGGT	116411633	7	5	197	1	0	1	1	0	0	0	0	0	9492	1377	48	0	2912	0	MET	7	116411633	In_Frame_Ins	INS	-	TCGA-HE-A5NH-01A-11D-A26P-10		116411633	42727030	30	11838											
MET	4233	hgsc.bcm.edu	37	chr7	116411675	116411675	+	Missense_Mutation	SNP	T	T	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	tgttattactacttgggtttTtcctgtggctgaaaaagaga	10	16	10	5	0	0	2	0	1	0	1	1	3	1	2	1	2	2	3	1	2	5	6			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr7:116411675T>G	ENST00000318493.6	+	13	3095	c.2908T>G	c.(2908-2910)Ttc>Gtc	p.F970V	MET_ENST00000397752.3_Missense_Mutation_p.F952V			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)			ACTTGGGTTTTTCCTGTGGCT	0.348			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.F970V		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.T2908G						PASS	.						117	110	112					7																	116411675		1845	4085	5930	SO:0001583	missense	4233	exon13	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	GGGTTTTTCCTGT	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.2908T>G	chr7.hg19:g.116411675T>G	ENSP00000317272:p.Phe970Val	52.0	0.0	.		97.0	15.0	.	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	T	13.91	2.377141	0.42105	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000454623	T;T	0.72167	-0.63;-0.63	5.76	5.76	0.90799	.	0.096961	0.64402	D	0.000001	T	0.67420	0.2891	M	0.73598	2.24	0.80722	D	1	P;B	0.38129	0.619;0.349	B;B	0.35510	0.204;0.185	T	0.67428	-0.5673	10	0.31617	T	0.26	.	10.6767	0.45789	0.0:0.0713:0.0:0.9287	.	970;952	P08581-2;P08581	.;MET_HUMAN	V	952;970;84	ENSP00000380860:F952V;ENSP00000317272:F970V	ENSP00000317272:F970V	F	+	1	0	MET	116198911	1.000000	0.71417	0.999000	0.59377	0.905000	0.53344	2.954000	0.49113	2.324000	0.78689	0.533000	0.62120	TTC	.	.	.	none		0.348	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			G	116411675	T	G	116411675	3	3	197	1	0	0	0	0	1	0	0	0	9492	1841	64	5	2954	5	MET	7	116411675	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	42	116411675	42726988	31	11839											
PLXNA4	91584	hgsc.bcm.edu	37	chr7	131859582	131859583	+	Frame_Shift_Ins	INS	-	-	AA																															cttcaattcctgggaacagcINSacccgcatggtgtaagttct																										TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr7:131859582_131859583insAA	ENST00000359827.3	-	21	4933_4934	c.3971_3972insTT	c.(3970-3972)gtgfs	p.V1324fs	PLXNA4_ENST00000321063.4_Frame_Shift_Ins_p.V1324fs			Q9HCM2	PLXA4_HUMAN	plexin A4	1324					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						CTGGGAACAGCACCCGCATGGT	0.569																																					p.V1324fs		Pindel	.											.	PLXNA4	873	.	0			c.3972_3973insTT						PASS	.																																			SO:0001589	frameshift_variant	91584	exon21			.	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.3971_3972insTT	chr7.hg19:g.131859582_131859583insAA	ENSP00000352882:p.Val1324fs	120.0	0.0	.		172.0	55.0	0.320	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Frame_Shift_Ins	INS	ENST00000359827.3	hg19	CCDS43646.1																																																																																			.	.	.	none		0.569	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		AA	131859583	-	AA	131859582	7	5	197	1	0	1	1	0	0	0	0	0	12129	697	25	0	1760	0	PLXNA4	7	131859582	Frame_Shift_Ins	INS	-	TCGA-HE-A5NH-01A-11D-A26P-10	15447907	131859582	27279081	32	11840											
FAM86B2	653333	hgsc.bcm.edu	37	chr8	12291589	12291590	+	Frame_Shift_Ins	INS	-	-	A																															aatatcccgcagcagctcagINSaatctgatgagtctcttaac																										TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr8:12291589_12291590insA	ENST00000262365.4	-	2	129_130	c.130_131insT	c.(130-132)tctfs	p.S44fs	FAM86B2_ENST00000309608.5_Frame_Shift_Ins_p.S44fs|FAM86B2_ENST00000351291.4_Frame_Shift_Ins_p.S44fs|FAM86B2_ENST00000393715.3_Intron	NM_001137610.1	NP_001131082.1	P0C5J1	F86B2_HUMAN	family with sequence similarity 86, member B2	44										endometrium(1)|kidney(2)	3						CAGCAGCTCAGAATCTGATGAG	0.48																																					p.S44fs		Atlas-INDEL	.											.	FAM86B2	19	.	0			c.131_132insT						PASS	.																																			SO:0001589	frameshift_variant	653333	exon2			.		CCDS59092.1	8p23.1	2011-07-01			ENSG00000145002	ENSG00000145002			32222	protein-coding gene	gene with protein product							Standard	NM_001137610		Approved		uc003wvt.4	P0C5J1	OTTHUMG00000165462	ENST00000262365.4:c.131dupT	chr8.hg19:g.12291591_12291591dupA	ENSP00000262365:p.Ser44fs	64.0	0.0	0		93.0	13.0	0.139785	NM_001137610		Frame_Shift_Ins	INS	ENST00000262365.4	hg19	CCDS59092.1																																																																																			.	.	.	none		0.48	FAM86B2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_928336		A	12291590	-	A	12291589	7	5	197	1	0	1	1	0	0	0	0	0	5652	942	33	0	889	0	FAM86B2	8	12291589	Frame_Shift_Ins	INS	-	TCGA-HE-A5NH-01A-11D-A26P-10		12291589	134072433	33	11841											
MTUS1	57509	hgsc.bcm.edu	37	chr8	17579357	17579357	+	Intron	SNP	T	T	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	agtgtagaattgataaagatTtttgaagaaatatcagtttc	16	15	8	2	0	1	5	1	2	0	3	2	5	1	5	0	0	0	2	0	0	7	7			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr8:17579357T>A	ENST00000262102.6	-	4	2674				MTUS1_ENST00000519263.1_Intron|MTUS1_ENST00000381861.3_Missense_Mutation_p.K18N|MTUS1_ENST00000381869.3_Intron|MTUS1_ENST00000544260.1_Intron	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1						cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		TGATAAAGATTTTTGAAGAAA	0.428																																					p.K18N		Atlas-SNP	.											.	MTUS1	144	.	0			c.A54T						PASS	.						86	86	86					8																	17579357		1840	4094	5934	SO:0001627	intron_variant	57509	exon1			AAAGATTTTTGAA	AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"AT2 receptor-interacting protein", "AT2R binding protein", "mitochondrial tumor suppressor gene 1"	609589	"mitochondrial tumor suppressor 1"			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.2449+1823A>T	chr8.hg19:g.17579357T>A		57.0	0.0	.		74.0	35.0	.	NM_001001931	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	hg19	CCDS43717.1	.	.	.	.	.	.	.	.	.	.	T	13.03	2.116072	0.37339	.	.	ENSG00000129422	ENST00000381861	T	0.15487	2.42	5.48	1.4	0.22301	.	.	.	.	.	T	0.07234	0.0183	.	.	.	0.23602	N	0.997312	B	0.09022	0.002	B	0.11329	0.006	T	0.39860	-0.9593	8	0.16896	T	0.51	.	0.4383	0.00482	0.2369:0.2954:0.15:0.3178	.	18	Q9ULD2-6	.	N	18	ENSP00000371285:K18N	ENSP00000371285:K18N	K	-	3	2	MTUS1	17623637	0.479000	0.25925	0.804000	0.32291	0.992000	0.81027	0.640000	0.24705	0.443000	0.26582	0.533000	0.62120	AAA	.	.	.	none		0.428	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		A	17579357	T	A	17579357	1	1	197	0	1	0	0	0	0	0	0	0	9972	1838	64	5		5	MTUS1	8	17579357	Intron	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	5287768	17579357	128784665	34	11842											
LPL	4023	hgsc.bcm.edu	37	chr8	19811710	19811710	+	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	gatgatgcagattttgtagaCgtcttacacacattcaccag	12	12	8	9	1	2	3	1	1	1	2	2	4	2	3	1	0	2	2	1	0	2	5	rs118204076		TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr8:19811710C>T	ENST00000311322.8	+	5	1091	c.621C>T	c.(619-621)gaC>gaT	p.D207D		NM_000237.2	NP_000228.1	P06858	LIPL_HUMAN	lipoprotein lipase	207			D -> E (in LPL deficiency). {ECO:0000269|PubMed:8288243}.		chylomicron remodeling (GO:0034371)|fatty acid biosynthetic process (GO:0006633)|lipoprotein metabolic process (GO:0042157)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of sequestering of triglyceride (GO:0010890)|response to cold (GO:0009409)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|triglyceride metabolic process (GO:0006641)|very-low-density lipoprotein particle remodeling (GO:0034372)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|lipoprotein lipase activity (GO:0004465)|phospholipase activity (GO:0004620)|receptor binding (GO:0005102)|triglyceride binding (GO:0017129)|triglyceride lipase activity (GO:0004806)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	36				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	AST-120(DB05269)|Tyloxapol(DB06439)	ATTTTGTAGACGTCTTACACA	0.483																																					p.D207D		Atlas-SNP	.											.	LPL	78	.	0			c.C621T	GRCh37	CM930483	LPL	M	rs118204076	PASS	.						139	134	135					8																	19811710		2203	4300	6503	SO:0001819	synonymous_variant	4023	exon5			TGTAGACGTCTTA		CCDS6012.1	8p22	2012-10-02			ENSG00000175445	ENSG00000175445	3.1.1.34		6677	protein-coding gene	gene with protein product		609708		LIPD			Standard	NM_000237		Approved		uc003wzk.4	P06858	OTTHUMG00000036645	ENST00000311322.8:c.621C>T	chr8.hg19:g.19811710C>T		109.0	0.0	.		155.0	73.0	.	NM_000237	B2R5T9|Q16282|Q16283|Q96FC4	Silent	SNP	ENST00000311322.8	hg19	CCDS6012.1																																																																																			.	.	.	alt		0.483	LPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089113.3			T	19811710	C	T	19811710	2	4	197	1	0	0	0	0	0	0	0	1	8928	535	19	1		1	LPL	8	19811710	Silent	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	2232353	19811710	126552312	35	11843											
PPP2R2A	5520	hgsc.bcm.edu	37	chr8	26211991	26211991	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttttcattttagaacaaaaTccagtctcatagcagaggag	14	12	8	7	0	2	2	2	0	1	2	4	3	3	3	1	1	2	2	1	1	5	5	rs373174942		TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr8:26211991T>C	ENST00000380737.3	+	4	517	c.188T>C	c.(187-189)aTc>aCc	p.I63T	PPP2R2A_ENST00000315985.7_Missense_Mutation_p.I73T	NM_002717.3	NP_002708.1	P63151	2ABA_HUMAN	protein phosphatase 2, regulatory subunit B, alpha	63					G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|response to morphine (GO:0043278)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			kidney(1)|large_intestine(2)|ovary(1)	4		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		TAGAACAAAATCCAGTCTCAT	0.318																																					p.I73T		Atlas-SNP	.											.	PPP2R2A	44	.	0			c.T218C						PASS	.	T	THR/ILE,THR/ILE	0,4406		0,0,2203	70	73	72		218,188	4.8	1	8		72	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense	PPP2R2A	NM_001177591.1,NM_002717.3	89,89	0,1,6501	CC,CT,TT		0.0116,0.0,0.0077	,	73/458,63/448	26211991	1,13003	2203	4299	6502	SO:0001583	missense	5520	exon4			ACAAAATCCAGTC	M64929	CCDS34867.1, CCDS55213.1	8p21.2	2013-01-10	2010-04-14		ENSG00000221914	ENSG00000221914	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "WD repeat domain containing"	9304	protein-coding gene	gene with protein product	"PP2A subunit B isoform alpha"	604941	"protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), alpha isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B, alpha isoform"			1849734	Standard	NM_001177591		Approved	PR52A, PR55A, B55A		P63151	OTTHUMG00000163850	ENST00000380737.3:c.188T>C	chr8.hg19:g.26211991T>C	ENSP00000370113:p.Ile63Thr	35.0	0.0	.		38.0	12.0	.	NM_001177591	B2RBU8|B4E1T7|P50409|Q00007	Missense_Mutation	SNP	ENST00000380737.3	hg19	CCDS34867.1	.	.	.	.	.	.	.	.	.	.	T	6.035	0.374882	0.11409	0.0	1.16E-4	ENSG00000221914	ENST00000380737;ENST00000315985	T;T	0.29142	1.59;1.58	5.97	4.84	0.62591	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.287722	0.32204	U	0.006432	T	0.08358	0.0208	N	0.01576	-0.805	0.37304	D	0.908831	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.28522	-1.0041	10	0.09843	T	0.71	-14.6536	2.6676	0.05057	0.0:0.1705:0.291:0.5384	.	73;63	B4E1T7;P63151	.;2ABA_HUMAN	T	63;73	ENSP00000370113:I63T;ENSP00000325074:I73T	ENSP00000325074:I73T	I	+	2	0	PPP2R2A	26267908	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.834000	0.39171	2.285000	0.76669	0.528000	0.53228	ATC	.	.	.	weak		0.318	PPP2R2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375954.2	NM_002717		C	26211991	T	C	26211991	3	2	197	1	0	0	0	0	1	0	0	0	12394	1435	50	3	243	3	PPP2R2A	8	26211991	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	6400281	26211991	120152031	36	11844											
ASPH	444	hgsc.bcm.edu	37	chr8	62460750	62460750	+	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	tgtcctctcttgtgcccaagCtcataccacttatatgcctg	7	14	6	14	0	2	0	1	0	1	0	4	0	3	0	4	0	4	1	4	0	4	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr8:62460750C>T	ENST00000379454.4	-	21	1831	c.1644G>A	c.(1642-1644)gaG>gaA	p.E548E	ASPH_ENST00000541428.1_Silent_p.E519E	NM_004318.3	NP_004309.2	Q12797	ASPH_HUMAN	aspartate beta-hydroxylase	548					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)	p.E548E(1)		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)	TGTGCCCAAGCTCATACCACT	0.403																																					p.E548E		Atlas-SNP	.											ASPH,NS,carcinoma,0,2	ASPH	87	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1644A						PASS	.						119	102	108					8																	62460750		2203	4300	6503	SO:0001819	synonymous_variant	444	exon21			CCCAAGCTCATAC	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.1644G>A	chr8.hg19:g.62460750C>T		102.0	0.0	.		134.0	54.0	.	NM_004318	A6NDF4|A6NHI2|B4DIC9|B4E2K4|B7ZM95|E5RGP5|F5H667|Q6NXR7|Q8TB28|Q9H291|Q9H2C4|Q9NRI0|Q9NRI1|Q9Y4J0	Silent	SNP	ENST00000379454.4	hg19	CCDS34898.1																																																																																			.	.	.	none		0.403	ASPH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378510.3	NM_004318		T	62460750	C	T	62460750	2	4	197	1	0	0	0	0	0	0	0	1	1053	796	28	2		2	ASPH	8	62460750	Silent	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	36248759	62460750	83903272	37	11845											
WWP1	11059	hgsc.bcm.edu	37	chr8	87460401	87460401	+	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	tatttcatggaaagtttatcGatactggtttctctttacca	10	18	6	7	1	2	0	1	0	1	0	4	2	2	1	1	2	2	2	1	2	5	8			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr8:87460401G>T	ENST00000517970.1	+	19	2330	c.2023G>T	c.(2023-2025)Gat>Tat	p.D675Y	WWP1_ENST00000349423.2_Missense_Mutation_p.D457Y|WWP1_ENST00000265428.4_Missense_Mutation_p.D675Y|WWP1_ENST00000341922.2_Missense_Mutation_p.D545Y	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	675	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						AAAGTTTATCGATACTGGTTT	0.254																																					p.D675Y		Atlas-SNP	.											WWP1,NS,carcinoma,0,1	WWP1	97	.	0			c.G2023T						PASS	.						44	45	45					8																	87460401		2198	4275	6473	SO:0001583	missense	11059	exon19			TTTATCGATACTG	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.2023G>T	chr8.hg19:g.87460401G>T	ENSP00000427793:p.Asp675Tyr	24.0	0.0	.		36.0	3.0	.	NM_007013	O00307|Q5YLC1|Q96BP4	Missense_Mutation	SNP	ENST00000517970.1	hg19	CCDS6242.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.3|20.3	3.975526|3.975526	0.74360|0.74360	.|.	.|.	ENSG00000123124|ENSG00000123124	ENST00000517970;ENST00000265428;ENST00000341922;ENST00000349423|ENST00000520453	T;T;T;T|.	0.53206|.	0.63;0.63;0.63;0.63|.	5.05|5.05	5.05|5.05	0.67936|0.67936	HECT (4);|.	0.098860|.	0.64402|.	D|.	0.000002|.	T|T	0.75664|0.75664	0.3880|0.3880	M|M	0.71871|0.71871	2.18|2.18	0.80722|0.80722	D|D	1|1	P;D|.	0.89917|.	0.861;1.0|.	P;D|.	0.85130|.	0.489;0.997|.	T|T	0.75230|0.75230	-0.3391|-0.3391	10|5	0.36615|.	T|.	0.2|.	.|.	18.7714|18.7714	0.91893|0.91893	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	457;675|.	Q9H0M0-6;Q9H0M0|.	.;WWP1_HUMAN|.	Y|L	675;675;545;457|175	ENSP00000427793:D675Y;ENSP00000265428:D675Y;ENSP00000340564:D545Y;ENSP00000342665:D457Y|.	ENSP00000265428:D675Y|.	D|R	+|+	1|2	0|0	WWP1|WWP1	87529517|87529517	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	9.813000|9.813000	0.99286|0.99286	2.510000|2.510000	0.84645|0.84645	0.655000|0.655000	0.94253|0.94253	GAT|CGA	.	.	.	none		0.254	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013		T	87460401	G	T	87460401	3	4	197	1	0	0	0	0	1	0	0	0	17427	1058	37	4	2089	4	WWP1	8	87460401	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	24999651	87460401	58903621	38	11846											
FOXD4L3	286380	hgsc.bcm.edu	37	chr9	70919081	70919082	+	Frame_Shift_Del	DEL	GG	GG	-																															tgcgctcccaccaagggcgcGgtgctgggcgggcacctgtc																										TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr9:70919081_70919082delGG	ENST00000342833.2	+	1	1806_1807	c.1214_1215delGG	c.(1213-1215)cggfs	p.R405fs		NM_199135.4	NP_954586.4	Q6VB84	FX4L3_HUMAN	forkhead box D4-like 3	405						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)		CCAAGGGCGCGGTGCTGGGCGG	0.668																																					p.405_405del		Atlas-INDEL	.											.	FOXD4L3	7	.	0			c.1213_1214del						PASS	.																																			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.1214_1215delGG	chr9.hg19:g.70919081_70919082delGG	ENSP00000341961:p.Arg405fs	186.0	0.0	0		144.0	27.0	0.1875	NM_199135	Q5JTX9	Frame_Shift_Del	DEL	ENST00000342833.2	hg19	CCDS43833.1																																																																																			.	.	.	none		0.668	FOXD4L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052539.2	NM_199358		-	70919082	GG	-	70919081	7	5	197	1	0	1	0	1	0	0	0	0	6008	1116	39	0	1216	0	FOXD4L3	9	70919081	Frame_Shift_Del	DEL	GG	TCGA-HE-A5NH-01A-11D-A26P-10		70919081	70294350	39	11847											
ODF2	4957	hgsc.bcm.edu	37	chr9	131256869	131256869	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcacggaggcgaagctggcTgagtgccaagaccaactgca	12	5	13	11	2	1	2	1	1	0	1	1	4	1	3	2	3	4	3	2	3	3	0			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr9:131256869T>C	ENST00000434106.3	+	17	2196	c.1833T>C	c.(1831-1833)gcT>gcC	p.A611A	ODF2_ENST00000372814.3_Silent_p.A655A|ODF2_ENST00000372791.3_Silent_p.A592A|ODF2_ENST00000393527.3_Silent_p.A587A|ODF2_ENST00000372807.5_Silent_p.A606A|ODF2_ENST00000448249.3_Silent_p.A530A|ODF2_ENST00000604420.1_Silent_p.A611A|ODF2_ENST00000444119.2_Silent_p.A587A|ODF2_ENST00000393533.2_Silent_p.A611A|ODF2_ENST00000546203.1_Silent_p.A592A|ODF2_ENST00000351030.3_Silent_p.A606A	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	611					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)			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						CGAAGCTGGCTGAGTGCCAAG	0.572																																					p.A675A		Atlas-SNP	.											ODF2_ENST00000372814,NS,carcinoma,+1,3	ODF2	227	.	0			c.T2025C						PASS	.						74	64	68					9																	131256869		2203	4300	6503	SO:0001819	synonymous_variant	4957	exon17			GCTGGCTGAGTGC	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.1833T>C	chr9.hg19:g.131256869T>C		194.0	1.0	.		228.0	88.0	.	NM_153435	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Silent	SNP	ENST00000434106.3	hg19	CCDS56588.1																																																																																			.	.	.	none		0.572	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3			C	131256869	T	C	131256869	2	2	197	1	0	0	0	0	0	0	0	1	10834	1567	55	3		3	ODF2	9	131256869	Silent	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	60337788	131256869	9956562	40	11848											
CUBN	8029	hgsc.bcm.edu	37	chr10	16941145	16941145	+	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	tgaggccagtgaggggatctGattgtaccattatcagaatg	11	11	13	6	0	2	4	1	3	1	1	2	5	2	5	2	3	1	1	2	3	3	3			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr10:16941145G>C	ENST00000377833.4	-	54	8513	c.8448C>G	c.(8446-8448)atC>atG	p.I2816M		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2816	CUB 21. {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)	GAGGGGATCTGATTGTACCAT	0.403																																					p.I2816M		Atlas-SNP	.											.	CUBN	515	.	0			c.C8448G						PASS	.						118	112	114					10																	16941145		2203	4300	6503	SO:0001583	missense	8029	exon54			GGATCTGATTGTA	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.8448C>G	chr10.hg19:g.16941145G>C	ENSP00000367064:p.Ile2816Met	89.0	0.0	.		88.0	38.0	.	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	G	9.641	1.139005	0.21123	.	.	ENSG00000107611	ENST00000377833	T	0.40476	1.03	5.63	0.557	0.17260	CUB (5);	0.137522	0.33057	N	0.005332	T	0.64494	0.2603	M	0.93150	3.385	0.80722	D	1	D	0.60160	0.987	P	0.62298	0.9	T	0.64782	-0.6326	10	0.66056	D	0.02	.	7.5405	0.27735	0.1201:0.0:0.4925:0.3874	.	2816	O60494	CUBN_HUMAN	M	2816	ENSP00000367064:I2816M	ENSP00000367064:I2816M	I	-	3	3	CUBN	16981151	1.000000	0.71417	0.001000	0.08648	0.014000	0.08584	3.071000	0.50041	-0.070000	0.12908	-0.940000	0.02684	ATC	.	.	.	none		0.403	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		C	16941145	G	C	16941145	3	2	197	1	0	0	0	0	1	0	0	0	4053	1280	45	4	2479	4	CUBN	10	16941145	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10		16941145	118593602	41	11849											
JMJD1C	221037	hgsc.bcm.edu	37	chr10	64974605	64974605	+	Missense_Mutation	SNP	T	T	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	tctctgcttcttcatgttttTtatcttcctgtatttgatcc	4	23	4	10	0	4	1	1	1	3	0	7	1	6	1	2	0	1	3	2	0	2	8			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr10:64974605T>G	ENST00000399262.2	-	8	1540	c.1322A>C	c.(1321-1323)aAa>aCa	p.K441T	JMJD1C_ENST00000489372.2_5'Flank|JMJD1C_ENST00000402544.1_Missense_Mutation_p.K222T|JMJD1C_ENST00000399251.1_Missense_Mutation_p.K222T|JMJD1C_ENST00000542921.1_Missense_Mutation_p.K259T	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	441					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)					TTCATGTTTTTTATCTTCCTG	0.388																																					p.K441T		Atlas-SNP	.											.	JMJD1C	347	.	0			c.A1322C						PASS	.						148	131	136					10																	64974605		1826	4079	5905	SO:0001583	missense	221037	exon8			TGTTTTTTATCTT	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.1322A>C	chr10.hg19:g.64974605T>G	ENSP00000382204:p.Lys441Thr	30.0	0.0	.		53.0	16.0	.	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	hg19	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	T	17.31	3.356618	0.61293	.	.	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000399251;ENST00000542921	T;T;T;T	0.55930	0.84;0.49;2.4;0.84	5.85	4.71	0.59529	.	0.256048	0.33290	U	0.005078	T	0.44159	0.1280	L	0.51422	1.61	0.44012	D	0.99672	P;P	0.39282	0.666;0.666	B;B	0.33339	0.162;0.115	T	0.51631	-0.8681	10	0.62326	D	0.03	-15.2085	12.0787	0.53659	0.0:0.0679:0.0:0.9321	.	441;259	Q15652;A0T124	JHD2C_HUMAN;.	T	441;222;222;259	ENSP00000382204:K441T;ENSP00000384990:K222T;ENSP00000382195:K222T;ENSP00000444682:K259T	ENSP00000382195:K222T	K	-	2	0	JMJD1C	64644611	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	2.933000	0.48948	2.237000	0.73441	0.459000	0.35465	AAA	.	.	.	none		0.388	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		G	64974605	T	G	64974605	3	3	197	1	0	0	0	0	1	0	0	0	7957	1841	64	5	6376	5	JMJD1C	10	64974605	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	48033460	64974605	70560142	42	11850											
LDB1	8861	hgsc.bcm.edu	37	chr10	103871028	103871028	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttacccaatccctggctccAggtatgtaggcggatacatg	9	10	10	12	1	0	0	0	0	0	0	2	1	2	1	3	4	2	3	3	4	5	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr10:103871028A>G	ENST00000425280.1	-	3	500	c.158T>C	c.(157-159)cTg>cCg	p.L53P	LDB1_ENST00000490751.1_5'UTR|LDB1_ENST00000361198.5_Missense_Mutation_p.L17P	NM_001113407.1	NP_001106878.1	Q86U70	LDB1_HUMAN	LIM domain binding 1	53					anterior/posterior axis specification (GO:0009948)|cellular component assembly (GO:0022607)|cerebellar Purkinje cell differentiation (GO:0021702)|epithelial structure maintenance (GO:0010669)|gastrulation with mouth forming second (GO:0001702)|hair follicle development (GO:0001942)|head development (GO:0060322)|histone H3-K4 acetylation (GO:0043973)|multicellular organismal development (GO:0007275)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|positive regulation of cell adhesion (GO:0045785)|positive regulation of hemoglobin biosynthetic process (GO:0046985)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell maintenance (GO:0035019)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery (GO:0000972)|Wnt signaling pathway (GO:0016055)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|enzyme binding (GO:0019899)|LIM domain binding (GO:0030274)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(1)	21		Colorectal(252;0.122)		Epithelial(162;1.11e-07)|all cancers(201;1.82e-06)		CCCTGGCTCCAGGTATGTAGG	0.577																																					p.L53P		Atlas-SNP	.											.	LDB1	61	.	0			c.T158C						PASS	.						98	98	98					10																	103871028		2203	4300	6503	SO:0001583	missense	8861	exon3			GGCTCCAGGTATG	AF068652	CCDS7528.1, CCDS44472.1	10q24-q25	2008-08-01			ENSG00000198728	ENSG00000198728			6532	protein-coding gene	gene with protein product	"carboxy terminal LIM domain protein 2"	603451				9503020, 9799849	Standard	NM_003893		Approved	NLI, CLIM2	uc009xwz.3	Q86U70	OTTHUMG00000018950	ENST00000425280.1:c.158T>C	chr10.hg19:g.103871028A>G	ENSP00000392466:p.Leu53Pro	125.0	0.0	.		155.0	68.0	.	NM_001113407	B4DUC4|O75479|O96010|Q1EQX1|Q9UGM4	Missense_Mutation	SNP	ENST00000425280.1	hg19	CCDS44472.1	.	.	.	.	.	.	.	.	.	.	A	16.53	3.149912	0.57151	.	.	ENSG00000198728	ENST00000361198;ENST00000425280	.	.	.	5.73	5.73	0.89815	.	0.148563	0.46442	D	0.000281	T	0.39733	0.1089	N	0.19112	0.55	0.80722	D	1	P;B	0.48407	0.91;0.0	B;B	0.41135	0.348;0.001	T	0.26503	-1.0101	9	0.31617	T	0.26	-13.3126	15.6898	0.77442	1.0:0.0:0.0:0.0	.	53;17	Q86U70;Q86U70-3	LDB1_HUMAN;.	P	17;53	.	ENSP00000354616:L17P	L	-	2	0	LDB1	103861018	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.008000	0.76341	2.199000	0.70637	0.459000	0.35465	CTG	.	.	.	none		0.577	LDB1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113407		G	103871028	A	G	103871028	3	3	197	1	0	0	0	0	1	0	0	0	8702	188	7	3	1113	3	LDB1	10	103871028	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10	38896423	103871028	31663719	43	11851											
FAM53B	9679	hgsc.bcm.edu	37	chr10	126311947	126311947	+	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	cgtccagggcgcagctgtctGactcctcacaggacaggtcc	7	7	12	15	2	2	1	1	1	1	0	5	2	5	2	3	3	1	2	3	3	0	0			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr10:126311947G>A	ENST00000337318.3	-	5	1344	c.1133C>T	c.(1132-1134)tCa>tTa	p.S378L	FAM53B_ENST00000392754.3_Missense_Mutation_p.S378L|RP11-12J10.3_ENST00000494792.1_Intron	NM_014661.3	NP_055476.3	Q14153	FA53B_HUMAN	family with sequence similarity 53, member B	378										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)		GCAGCTGTCTGACTCCTCACA	0.711																																					p.S378L		Atlas-SNP	.											.	FAM53B	22	.	0			c.C1133T						PASS	.						21	22	21					10																	126311947		2200	4294	6494	SO:0001583	missense	9679	exon5			CTGTCTGACTCCT	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.1133C>T	chr10.hg19:g.126311947G>A	ENSP00000338532:p.Ser378Leu	31.0	0.0	.		38.0	23.0	.	NM_014661	D3DRF1|Q5VUW1|Q5VUW2|Q8N5S6	Missense_Mutation	SNP	ENST00000337318.3	hg19	CCDS7641.1	.	.	.	.	.	.	.	.	.	.	G	11.60	1.688447	0.29962	.	.	ENSG00000189319	ENST00000337318;ENST00000392754	.	.	.	4.78	3.86	0.44501	.	0.743799	0.11858	N	0.522697	T	0.30978	0.0782	L	0.34521	1.04	0.19945	N	0.999948	B	0.26809	0.16	B	0.31337	0.128	T	0.21793	-1.0235	9	0.06365	T	0.9	-7.9821	11.3285	0.49463	0.0:0.0:0.6724:0.3276	.	378	Q14153	FA53B_HUMAN	L	378	.	ENSP00000338532:S378L	S	-	2	0	FAM53B	126301937	0.742000	0.28228	0.299000	0.25016	0.686000	0.39977	2.551000	0.45820	1.213000	0.43380	0.655000	0.94253	TCA	.	.	.	none		0.711	FAM53B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050879.1	NM_014661		A	126311947	G	A	126311947	3	1	197	1	0	0	0	0	1	0	0	0	5587	1294	45	2	139	2	FAM53B	10	126311947	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	22440919	126311947	9222800	44	11852											
TRPM5	29850	hgsc.bcm.edu	37	chr11	2428360	2428360	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcctcacccaggtgctccCgcttgtgctcagcctccttc	3	10	9	19	2	2	0	2	0	0	0	5	0	4	0	5	2	3	3	5	2	0	2			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr11:2428360C>T	ENST00000155858.6	-	20	3115	c.3107G>A	c.(3106-3108)cGg>cAg	p.R1036Q	TRPM5_ENST00000452833.1_Missense_Mutation_p.R1038Q|AC124057.5_ENST00000433035.1_RNA|TRPM5_ENST00000528453.1_Missense_Mutation_p.R1036Q|TRPM5_ENST00000533060.1_Missense_Mutation_p.R1036Q	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)		CAGGTGCTCCCGCTTGTGCTC	0.706																																					p.R1036Q	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.G3107A						PASS	.						26	25	26					11																	2428360		2193	4288	6481	SO:0001583	missense	29850	exon20			TGCTCCCGCTTGT	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.3107G>A	chr11.hg19:g.2428360C>T	ENSP00000155858:p.Arg1036Gln	20.0	0.0	.		24.0	15.0	.	NM_014555		Missense_Mutation	SNP	ENST00000155858.6	hg19	CCDS31340.1	.	.	.	.	.	.	.	.	.	.	C	1.660	-0.511828	0.04200	.	.	ENSG00000070985	ENST00000533881;ENST00000155858;ENST00000452833;ENST00000533060;ENST00000528453	T;T;T;T;T	0.61627	0.27;0.21;0.21;0.09;0.21	3.21	1.21	0.21127	.	0.630612	0.15729	N	0.247507	T	0.33644	0.0870	N	0.15975	0.35	0.21553	N	0.999642	B;B;B	0.17465	0.022;0.022;0.006	B;B;B	0.13407	0.007;0.007;0.009	T	0.15065	-1.0450	10	0.25751	T	0.34	-7.4235	6.0447	0.19753	0.0:0.6066:0.0:0.3934	.	1036;1038;1036	E9PRW0;Q9NZQ8-2;Q9NZQ8	.;.;TRPM5_HUMAN	Q	1030;1036;1038;1036;1036	ENSP00000434383:R1030Q;ENSP00000155858:R1036Q;ENSP00000387965:R1038Q;ENSP00000434121:R1036Q;ENSP00000436809:R1036Q	ENSP00000155858:R1036Q	R	-	2	0	TRPM5	2384936	0.007000	0.16637	0.005000	0.12908	0.300000	0.27592	1.127000	0.31357	0.058000	0.16222	0.134000	0.15878	CGG	.	.	.	none		0.706	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555		T	2428360	C	T	2428360	3	4	197	1	0	0	0	0	1	0	0	0	16601	652	23	1	410	1	TRPM5	11	2428360	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10		2428360	132578156	45	11853											
CALCB	797	hgsc.bcm.edu	37	chr11	15096663	15096663	+	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	cagtaaagaggacgcgcgccTcctgctggctgcactggtgc	7	7	14	13	3	0	1	0	0	0	1	1	2	1	2	2	3	3	4	2	3	2	1			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr11:15096663T>A	ENST00000533448.1	+	3	254	c.143T>A	c.(142-144)cTc>cAc	p.L48H	CALCB_ENST00000523376.1_Missense_Mutation_p.L59H|CALCB_ENST00000324229.6_Missense_Mutation_p.L48H			P10092	CALCB_HUMAN	calcitonin-related polypeptide beta	48					cellular calcium ion homeostasis (GO:0006874)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	neuropeptide hormone activity (GO:0005184)			endometrium(1)|large_intestine(1)|lung(1)|skin(2)	5						GACGCGCGCCTCCTGCTGGCT	0.627											OREG0020793	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L48H		Atlas-SNP	.											.	CALCB	7	.	0			c.T143A						PASS	.						58	61	60					11																	15096663		2200	4294	6494	SO:0001583	missense	797	exon3			CGCGCCTCCTGCT		CCDS7820.1	11p14.2-p12	2013-02-25	2008-02-20			ENSG00000175868		"Endogenous ligands"	1438	protein-coding gene	gene with protein product		114160	"calcitonin 2"	CALC2			Standard	NM_000728		Approved	FLJ30166, CGRP-II	uc001mlx.1	P10092		ENST00000533448.1:c.143T>A	chr11.hg19:g.15096663T>A	ENSP00000433490:p.Leu48His	343.0	0.0	.	700	419.0	177.0	.	NM_000728	A8K573|D3DQX4|Q569I0|Q9UCN9	Missense_Mutation	SNP	ENST00000533448.1	hg19	CCDS7820.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.370035	0.82573	.	.	ENSG00000175868	ENST00000523376;ENST00000324229;ENST00000533448	T;T;T	0.24151	1.87;1.87;1.87	5.4	3.0	0.34707	.	0.000000	0.46442	D	0.000284	T	0.28267	0.0698	M	0.81239	2.535	0.27438	N	0.953794	B	0.30686	0.29	B	0.32022	0.139	T	0.17077	-1.0381	10	0.44086	T	0.13	-26.0769	6.6446	0.22929	0.1187:0.0:0.3692:0.512	.	48	P10092	CALCB_HUMAN	H	59;48;48	ENSP00000428882:L59H;ENSP00000346017:L48H;ENSP00000433490:L48H	ENSP00000346017:L48H	L	+	2	0	CALCB	15053239	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.094000	0.64523	2.176000	0.68965	0.454000	0.30748	CTC	.	.	.	none		0.627	CALCB-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387433.1	NM_000728		A	15096663	T	A	15096663	3	1	197	1	0	0	0	0	1	0	0	0	2578	1551	54	5	149	5	CALCB	11	15096663	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	12668303	15096663	119909853	46	11854											
PIK3C2A	5286	hgsc.bcm.edu	37	chr11	17150900	17150900	+	Missense_Mutation	SNP	T	T	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	cccaaagcttctggtcccttTctctgcttattagaatcagg	8	14	7	12	0	3	1	1	0	2	1	5	1	4	1	2	2	2	2	2	2	4	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr11:17150900T>G	ENST00000265970.7	-	12	2345	c.2346A>C	c.(2344-2346)agA>agC	p.R782S	PIK3C2A_ENST00000531428.1_Intron|PIK3C2A_ENST00000540361.1_Missense_Mutation_p.R402S	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	782	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00041, ECO:0000255|PROSITE- ProRule:PRU00880}.				clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)			central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						CTGGTCCCTTTCTCTGCTTAT	0.388																																					p.R782S		Atlas-SNP	.											.	PIK3C2A	148	.	0			c.A2346C						PASS	.						90	96	94					11																	17150900		2200	4293	6493	SO:0001583	missense	5286	exon12			TCCCTTTCTCTGC	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.2346A>C	chr11.hg19:g.17150900T>G	ENSP00000265970:p.Arg782Ser	96.0	0.0	.		153.0	55.0	.	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	hg19	CCDS7824.1	.	.	.	.	.	.	.	.	.	.	T	19.33	3.807327	0.70797	.	.	ENSG00000011405	ENST00000265970;ENST00000540361	T;T	0.77229	-1.08;-1.08	6.17	3.81	0.43845	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (2);	0.000000	0.85682	D	0.000000	D	0.82834	0.5123	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.79967	-0.1580	10	0.33940	T	0.23	-23.3516	5.1651	0.15081	0.1256:0.1839:0.0:0.6905	.	782	O00443	P3C2A_HUMAN	S	782;402	ENSP00000265970:R782S;ENSP00000438687:R402S	ENSP00000265970:R782S	R	-	3	2	PIK3C2A	17107476	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.962000	0.29280	1.126000	0.42016	0.533000	0.62120	AGA	.	.	.	none		0.388	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		G	17150900	T	G	17150900	3	3	197	1	0	0	0	0	1	0	0	0	11916	1780	62	5	2798	5	PIK3C2A	11	17150900	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	2054237	17150900	117855616	47	11855											
OR5AR1	219493	hgsc.bcm.edu	37	chr11	56432020	56432028	+	In_Frame_Del	DEL	CCCTTGATC	CCCTTGATC	-																															ttatcatccccatgttaaatCccttgatctacagtttgcgg																								rs139654321		TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	CCCTTGATC	CCCTTGATC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr11:56432020_56432028delCCCTTGATC	ENST00000302969.2	+	1	883_891	c.859_867delCCCTTGATC	c.(859-867)cccttgatcdel	p.PLI287del		NM_001004730.1	NP_001004730.1	Q8NGP9	O5AR1_HUMAN	olfactory receptor, family 5, subfamily AR, member 1 (gene/pseudogene)	287						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(12)|prostate(1)|skin(3)|stomach(1)	26						CATGTTAAATCCCTTGATCTACAGTTTGC	0.407																																					p.286_289del		Atlas-Indel,Pindel	.											.	OR5AR1	68	.	0			c.858_866del						PASS	.																																			SO:0001651	inframe_deletion	219493	exon1			.	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.859_867delCCCTTGATC	chr11.hg19:g.56432020_56432028delCCCTTGATC	ENSP00000302639:p.Pro287_Ile289del	147.0	0.0	0		169.0	27.0	0.159763	NM_001004730	Q6IF61	In_Frame_Del	DEL	ENST00000302969.2	hg19	CCDS31535.1																																																																																			.	.	.	none		0.407	OR5AR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334434.1	NM_001004730		-	56432028	CCCTTGATC	-	56432020	7	5	197	1	0	1	0	1	0	0	0	0	11152	855	30	0	861	0	OR5AR1	11	56432020	In_Frame_Del	DEL	CCCTTGATC	TCGA-HE-A5NH-01A-11D-A26P-10	39281120	56432020	78574496	48	11856											
MOGAT2	80168	hgsc.bcm.edu	37	chr11	75431106	75431106	+	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	gctcctcactgtcctgtatgCggcctggtggtatctggacc	4	12	12	13	1	2	0	1	0	1	0	4	1	4	1	4	4	1	3	4	4	2	2			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr11:75431106C>A	ENST00000198801.5	+	2	231	c.161C>A	c.(160-162)gCg>gAg	p.A54E	MOGAT2_ENST00000526712.1_5'UTR	NM_025098.2	NP_079374.2	Q3SYC2	MOGT2_HUMAN	monoacylglycerol O-acyltransferase 2	54					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)					GTCCTGTATGCGGCCTGGTGG	0.567																																					p.A54E		Atlas-SNP	.											MOGAT2,colon,carcinoma,0,2	MOGAT2	49	.	0			c.C161A						PASS	.						175	164	168					11																	75431106		2200	4293	6493	SO:0001583	missense	80168	exon2			TGTATGCGGCCTG	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.161C>A	chr11.hg19:g.75431106C>A	ENSP00000198801:p.Ala54Glu	81.0	0.0	.		131.0	47.0	.	NM_025098	A8K7I3|Q3SYC1|Q6ZQZ2|Q86UH6|Q9H630	Missense_Mutation	SNP	ENST00000198801.5	hg19	CCDS8240.1	.	.	.	.	.	.	.	.	.	.	C	16.83	3.230712	0.58777	.	.	ENSG00000166391	ENST00000198801	T	0.15487	2.42	5.14	3.25	0.37280	.	0.175147	0.49916	D	0.000127	T	0.40595	0.1123	M	0.87180	2.865	0.37511	D	0.917131	D;D	0.67145	0.983;0.996	P;D	0.65233	0.815;0.933	T	0.47071	-0.9145	10	0.62326	D	0.03	.	8.4411	0.32816	0.0:0.6272:0.2933:0.0795	.	54;54	Q3SYC2;Q3SYC2-3	MOGT2_HUMAN;.	E	54	ENSP00000198801:A54E	ENSP00000198801:A54E	A	+	2	0	MOGAT2	75108754	0.114000	0.22134	0.003000	0.11579	0.143000	0.21401	2.008000	0.40893	0.732000	0.32470	-0.215000	0.12644	GCG	.	.	.	none		0.567	MOGAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383520.1	NM_025098		A	75431106	C	A	75431106	3	1	197	1	0	0	0	0	1	0	0	0	9702	768	27	4	167	4	MOGAT2	11	75431106	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	18999086	75431106	59575410	49	11857											
ARCN1	372	hgsc.bcm.edu	37	chr11	118464375	118464375	+	Missense_Mutation	SNP	T	T	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	tatgagctacaagaagataaTttagaactgaatgatgtggt	16	12	10	3	0	0	6	0	3	0	3	0	6	0	6	0	1	3	1	0	1	8	5	rs546784519		TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr11:118464375T>G	ENST00000264028.4	+	8	1298	c.1203T>G	c.(1201-1203)aaT>aaG	p.N401K	ARCN1_ENST00000392859.3_Missense_Mutation_p.N313K|ARCN1_ENST00000359415.4_Missense_Mutation_p.N442K|ARCN1_ENST00000534182.2_Intron|RNU6-1157P_ENST00000384456.1_RNA	NM_001655.4	NP_001646.2	P48444	COPD_HUMAN	archain 1	401	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)		AAGAAGATAATTTAGAACTGA	0.438													T|||	1	0.000199681	0	0	5008	,	,		20456	0.001		0	False		,,,				2504	0				p.N401K		Atlas-SNP	.											.	ARCN1	33	.	0			c.T1203G						PASS	.						118	100	106					11																	118464375		2200	4295	6495	SO:0001583	missense	372	exon8			AGATAATTTAGAA	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.1203T>G	chr11.hg19:g.118464375T>G	ENSP00000264028:p.Asn401Lys	94.0	0.0	.		98.0	42.0	.	NM_001655	B4E1X2|E9PEU4|Q52M80	Missense_Mutation	SNP	ENST00000264028.4	hg19	CCDS8400.1	.	.	.	.	.	.	.	.	.	.	T	9.897	1.205804	0.22205	.	.	ENSG00000095139	ENST00000392859;ENST00000359415;ENST00000264028	T;T;T	0.17528	2.27;2.27;2.27	5.95	1.01	0.19927	Clathrin adaptor, mu subunit, C-terminal (3);	0.266986	0.47455	D	0.000229	T	0.10121	0.0248	L	0.29908	0.895	0.29104	N	0.881303	B;B;B	0.14438	0.003;0.01;0.002	B;B;B	0.17979	0.006;0.02;0.005	T	0.18085	-1.0348	10	0.30078	T	0.28	-13.078	5.5305	0.16983	0.0:0.491:0.1917:0.3174	.	313;442;401	E9PEU4;B0YIW6;P48444	.;.;COPD_HUMAN	K	313;442;401	ENSP00000376599:N313K;ENSP00000352385:N442K;ENSP00000264028:N401K	ENSP00000264028:N401K	N	+	3	2	ARCN1	117969585	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.769000	0.26604	0.173000	0.19788	0.460000	0.39030	AAT	.	.	.	none		0.438	ARCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389278.1			G	118464375	T	G	118464375	3	3	197	1	0	0	0	0	1	0	0	0	842	1490	52	5	1233	5	ARCN1	11	118464375	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	43033269	118464375	16542141	50	11858											
SORL1	6653	hgsc.bcm.edu	37	chr11	121475939	121475939	+	Missense_Mutation	SNP	T	T	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	tgcttcttgtgtatataatgTctactacaggtaggtcccat	9	16	8	8	0	2	0	0	0	2	0	3	0	3	0	1	2	3	3	1	2	6	8			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr11:121475939T>G	ENST00000260197.7	+	34	4898	c.4769T>G	c.(4768-4770)gTc>gGc	p.V1590G	SORL1_ENST00000527934.1_Missense_Mutation_p.V205G|SORL1_ENST00000532694.1_Missense_Mutation_p.V436G|SORL1_ENST00000525532.1_Missense_Mutation_p.V534G|SORL1_ENST00000534286.1_Missense_Mutation_p.V500G	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	1590	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		GTATATAATGTCTACTACAGG	0.443																																					p.V1590G		Atlas-SNP	.											.	SORL1	218	.	0			c.T4769G						PASS	.						121	119	120					11																	121475939		2203	4299	6502	SO:0001583	missense	6653	exon34			ATAATGTCTACTA	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.4769T>G	chr11.hg19:g.121475939T>G	ENSP00000260197:p.Val1590Gly	61.0	0.0	.		79.0	30.0	.	NM_003105	B2RNX7|Q92856	Missense_Mutation	SNP	ENST00000260197.7	hg19	CCDS8436.1	.	.	.	.	.	.	.	.	.	.	T	16.47	3.133710	0.56828	.	.	ENSG00000137642	ENST00000260197;ENST00000525532;ENST00000532694;ENST00000534286;ENST00000527934	T;T;T;T;T	0.69040	-0.37;-0.37;-0.37;-0.37;-0.37	5.3	4.17	0.49024	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.537145	0.18359	N	0.143626	T	0.61185	0.2327	N	0.19112	0.55	0.51012	D	0.999904	P;P	0.51933	0.942;0.949	P;P	0.52386	0.697;0.659	T	0.60984	-0.7154	10	0.52906	T	0.07	.	10.8817	0.46942	0.0:0.0749:0.0:0.9251	.	205;1590	E9PKB0;Q92673	.;SORL_HUMAN	G	1590;534;436;500;205	ENSP00000260197:V1590G;ENSP00000434634:V534G;ENSP00000432131:V436G;ENSP00000436447:V500G;ENSP00000435405:V205G	ENSP00000260197:V1590G	V	+	2	0	SORL1	120981149	0.992000	0.36948	0.699000	0.30290	0.670000	0.39368	7.698000	0.84413	0.854000	0.35336	0.533000	0.62120	GTC	.	.	.	none		0.443	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105		G	121475939	T	G	121475939	3	3	197	1	0	0	0	0	1	0	0	0	14947	1667	58	5	4903	5	SORL1	11	121475939	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	3011564	121475939	13530577	51	11859											
IGSF9B	22997	hgsc.bcm.edu	37	chr11	133789844	133789844	+	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	tcccactgcggctgctctggGagggggagcctgtggacggc	4	7	18	12	2	1	0	0	0	1	0	2	3	2	3	2	6	3	2	2	6	0	0			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr11:133789844G>A	ENST00000321016.8	-	18	4006	c.3776C>T	c.(3775-3777)tCc>tTc	p.S1259F	IGSF9B_ENST00000533871.2_Missense_Mutation_p.S1259F			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	1259	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)		GCTGCTCTGGGAGGGGGAGCC	0.687																																					p.S1259F		Atlas-SNP	.											.	IGSF9B	290	.	0			c.C3776T						PASS	.						19	25	23					11																	133789844		1888	4098	5986	SO:0001583	missense	22997	exon18			CTCTGGGAGGGGG	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.3776C>T	chr11.hg19:g.133789844G>A	ENSP00000317980:p.Ser1259Phe	32.0	0.0	.		62.0	27.0	.	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	hg19		.	.	.	.	.	.	.	.	.	.	G	10.57	1.386761	0.25031	.	.	ENSG00000080854	ENST00000321016;ENST00000533871	T;T	0.68479	-0.0;-0.33	5.29	4.38	0.52667	.	0.164446	0.29119	N	0.013091	T	0.47414	0.1444	N	0.08118	0	0.33398	D	0.577033	B	0.06786	0.001	B	0.04013	0.001	T	0.56402	-0.7985	10	0.66056	D	0.02	.	13.4086	0.60929	0.0768:0.0:0.9232:0.0	.	1259	Q9UPX0	TUTLB_HUMAN	F	1259;1101	ENSP00000317980:S1259F;ENSP00000436552:S1101F	ENSP00000317980:S1259F	S	-	2	0	IGSF9B	133295054	1.000000	0.71417	0.411000	0.26484	0.307000	0.27823	7.382000	0.79729	1.243000	0.43853	0.555000	0.69702	TCC	.	.	.	none		0.687	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		A	133789844	G	A	133789844	3	1	197	1	0	0	0	0	1	0	0	0	7613	1174	41	2	281	2	IGSF9B	11	133789844	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	12313905	133789844	1216672	52	11860											
ING4	51147	hgsc.bcm.edu	37	chr12	6760401	6760401	+	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	gggagcagcgtgggcaaaacCtgaaacagagaaggggagag	15	2	18	6	1	0	3	0	1	0	2	0	6	0	4	1	4	4	2	1	4	4	0			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr12:6760401C>T	ENST00000396807.4	-	8	749		c.e8-1		ING4_ENST00000341550.4_Splice_Site|ING4_ENST00000444704.2_Splice_Site|ING4_ENST00000423703.2_Splice_Site|ING4_ENST00000446105.2_Splice_Site|ING4_ENST00000486287.1_Splice_Site|ING4_ENST00000412586.2_Splice_Site	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						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						TGGGCAAAACCTGAAACAGAG	0.512																																					.		Atlas-SNP	.											.	ING4	31	.	0			c.563-1G>A						PASS	.						112	96	102					12																	6760401		2203	4300	6503	SO:0001630	splice_region_variant	51147	exon8			CAAAACCTGAAAC	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.711-1G>A	chr12.hg19:g.6760401C>T		162.0	0.0	.		238.0	90.0	.	NM_001127586	A4KYM4|A4KYM6|D3DUR8|Q0EF62|Q0EF63|Q4VBQ6|Q96E15|Q9H3J0	Splice_Site	SNP	ENST00000396807.4	hg19	CCDS44813.1	.	.	.	.	.	.	.	.	.	.	C	19.52	3.842434	0.71488	.	.	ENSG00000111653	ENST00000341550;ENST00000396807;ENST00000446105;ENST00000444704;ENST00000412586	.	.	.	4.63	4.63	0.57726	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5782	0.84706	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ING4	6630662	1.000000	0.71417	0.997000	0.53966	0.968000	0.65278	6.445000	0.73456	2.556000	0.86216	0.561000	0.74099	.	.	.	.	none		0.512	ING4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280467.2	NM_198287	Intron	T	6760401	C	T	6760401	5	4	197	1	0	0	0	0	0	0	1	0	7745	695	24	2	43	2	ING4	12	6760401	Splice_Site	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10		6760401	127091494	53	11861											
BHLHE41	79365	hgsc.bcm.edu	37	chr12	26276658	26276658	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attccaagactacagctttcTccagatgtcccagagtctgc	10	11	7	13	0	2	3	0	0	2	3	5	3	4	3	3	0	3	1	3	0	2	3			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr12:26276658T>C	ENST00000242728.4	-	4	598	c.251A>G	c.(250-252)gAg>gGg	p.E84G	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	84	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				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						TACAGCTTTCTCCAGATGTCC	0.408																																					p.E84G		Atlas-SNP	.											.	BHLHE41	20	.	0			c.A251G						PASS	.						93	92	92					12																	26276658		2202	4300	6502	SO:0001583	missense	79365	exon4			GCTTTCTCCAGAT	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.251A>G	chr12.hg19:g.26276658T>C	ENSP00000242728:p.Glu84Gly	44.0	0.0	.		48.0	19.0	.	NM_030762	A2I2N8	Missense_Mutation	SNP	ENST00000242728.4	hg19	CCDS8706.1	.	.	.	.	.	.	.	.	.	.	T	18.09	3.546283	0.65198	.	.	ENSG00000123095	ENST00000242728;ENST00000540731	D	0.98120	-4.73	4.15	4.15	0.48705	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	U	0.000000	D	0.98172	0.9396	M	0.67569	2.06	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98797	1.0738	10	0.87932	D	0	-16.7562	12.4813	0.55844	0.0:0.0:0.0:1.0	.	84	Q9C0J9	BHE41_HUMAN	G	84	ENSP00000242728:E84G	ENSP00000242728:E84G	E	-	2	0	BHLHE41	26167925	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.709000	0.84645	1.876000	0.54355	0.528000	0.53228	GAG	.	.	.	none		0.408	BHLHE41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402714.1	NM_030762		C	26276658	T	C	26276658	3	2	197	1	0	0	0	0	1	0	0	0	1424	1551	54	3	1205	3	BHLHE41	12	26276658	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	19516257	26276658	107575237	54	11862											
ERGIC2	51290	hgsc.bcm.edu	37	chr12	29502995	29502995	+	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	gcatgaccacgaggatgtggAattgccctgaaaggagaaaa	15	6	13	7	1	0	3	0	2	0	1	0	7	0	5	2	3	1	1	2	3	4	1			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr12:29502995A>T	ENST00000360150.4	-	9	654	c.579T>A	c.(577-579)atT>atA	p.I193I		NM_016570.2	NP_057654.2	Q96RQ1	ERGI2_HUMAN	ERGIC and golgi 2	193					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)					GAGGATGTGGAATTGCCCTGA	0.303																																					p.I193I		Atlas-SNP	.											.	ERGIC2	29	.	0			c.T579A						PASS	.						57	53	54					12																	29502995		1824	4085	5909	SO:0001819	synonymous_variant	51290	exon9			ATGTGGAATTGCC	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.579T>A	chr12.hg19:g.29502995A>T		168.0	0.0	.		214.0	77.0	.	NM_016570	A6NHH6|Q53GY2|Q8N2Q9|Q9BVV9|Q9NZA3	Silent	SNP	ENST00000360150.4	hg19	CCDS41765.1	.	.	.	.	.	.	.	.	.	.	a	11.11	1.541269	0.27563	.	.	ENSG00000087502	ENST00000548909	.	.	.	5.78	0.983	0.19767	.	.	.	.	.	T	0.55114	0.1900	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45556	-0.9253	4	.	.	.	.	8.0069	0.30329	0.655:0.0:0.345:0.0	.	.	.	.	T	3	.	.	S	-	1	0	ERGIC2	29394262	0.982000	0.34865	1.000000	0.80357	0.989000	0.77384	0.257000	0.18369	0.143000	0.18926	0.524000	0.50904	TCC	.	.	.	none		0.303	ERGIC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403489.1	NM_016570		T	29502995	A	T	29502995	2	4	197	1	0	0	0	0	0	0	0	1	5226	242	9	5		5	ERGIC2	12	29502995	Silent	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10	3226337	29502995	104348900	55	11863											
C12orf64	283310	hgsc.bcm.edu	37	chr12	80730767	80730767	+	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	ccatacataaaataattgtcAatcggttggcaagaaaggta	17	10	8	6	1	1	1	1	0	0	1	2	1	1	1	1	3	1	3	1	3	8	6			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr12:80730767A>T	ENST00000547103.1	+	41	4786	c.4780A>T	c.(4780-4782)Aat>Tat	p.N1594Y	OTOGL_ENST00000458043.2_Missense_Mutation_p.N1606Y			Q3ZCN5	OTOGL_HUMAN	otogelin-like	1594	VWFD 4. {ECO:0000255|PROSITE- ProRule:PRU00580}.				L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						AATAATTGTCAATCGGTTGGC	0.279																																					p.N1606Y		Atlas-SNP	.											.	OTOGL	235	.	0			c.A4816T						PASS	.						28	26	26					12																	80730767		1788	4046	5834	SO:0001583	missense	283310	exon41			ATTGTCAATCGGT	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.4780A>T	chr12.hg19:g.80730767A>T	ENSP00000447211:p.Asn1594Tyr	30.0	0.0	.		12.0	5.0	.	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	hg19		.	.	.	.	.	.	.	.	.	.	A	14.88	2.668809	0.47677	.	.	ENSG00000165899	ENST00000547103;ENST00000458043	T;T	0.58652	0.32;0.32	4.92	3.72	0.42706	.	.	.	.	.	T	0.65428	0.2690	M	0.72118	2.19	0.28910	N	0.892741	.	.	.	.	.	.	T	0.61888	-0.6970	7	0.59425	D	0.04	.	10.9776	0.47475	0.8598:0.0:0.0:0.1402	.	.	.	.	Y	1594;1606	ENSP00000447211:N1594Y;ENSP00000400895:N1606Y	ENSP00000400895:N1606Y	N	+	1	0	OTOGL	79254898	1.000000	0.71417	0.989000	0.46669	0.943000	0.58893	4.208000	0.58486	0.757000	0.33036	0.482000	0.46254	AAT	.	.	.	none		0.279	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591		T	80730767	A	T	80730767	3	4	197	1	0	0	0	0	1	0	0	0	1709	130	5	5	4978	5	C12orf64	12	80730767	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10	51227772	80730767	53121128	56	11864											
PPP1CC	5501	hgsc.bcm.edu	37	chr12	111168372	111168372	+	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	aaattctgttgatgctggcaCattcatggttccctctgaga	9	14	9	9	0	3	2	1	2	2	1	4	3	4	2	1	2	1	4	1	2	1	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr12:111168372C>T	ENST00000335007.5	-	3	570	c.380G>A	c.(379-381)tGt>tAt	p.C127Y	PPP1CC_ENST00000340766.5_Missense_Mutation_p.C127Y|PPP1CC_ENST00000551690.1_5'Flank|PPP1CC_ENST00000551676.1_Missense_Mutation_p.C127Y|PPP1CC_ENST00000550991.1_Missense_Mutation_p.C127Y|PPP1CC_ENST00000546933.1_Missense_Mutation_p.C136Y	NM_002710.3	NP_002701.1	P36873	PP1G_HUMAN	protein phosphatase 1, catalytic subunit, gamma isozyme	127					cell division (GO:0051301)|circadian regulation of gene expression (GO:0032922)|entrainment of circadian clock by photoperiod (GO:0043153)|glycogen metabolic process (GO:0005977)|mitotic cell cycle (GO:0000278)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron differentiation (GO:0030182)|protein dephosphorylation (GO:0006470)|regulation of circadian rhythm (GO:0042752)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)|triglyceride catabolic process (GO:0019433)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|focal adhesion (GO:0005925)|kinetochore (GO:0000776)|mitochondrion (GO:0005739)|MLL5-L complex (GO:0070688)|nucleolus (GO:0005730)|nucleus (GO:0005634)|protein complex (GO:0043234)|PTW/PP1 phosphatase complex (GO:0072357)	metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(1)|large_intestine(2)|lung(3)	6						GATGCTGGCACATTCATGGTT	0.338																																					p.C127Y		Atlas-SNP	.											.	PPP1CC	22	.	0			c.G380A						PASS	.						62	67	65					12																	111168372		2203	4300	6503	SO:0001583	missense	5501	exon3			CTGGCACATTCAT		CCDS9150.1, CCDS58279.1	12q24.1-q24.2	2013-01-17	2010-03-05		ENSG00000186298	ENSG00000186298	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9283	protein-coding gene	gene with protein product		176914	"protein phosphatase 1, catalytic subunit, gamma isoform"				Standard	NM_002710		Approved	PP1C, PP1gamma	uc021rdx.1	P36873	OTTHUMG00000169531	ENST00000335007.5:c.380G>A	chr12.hg19:g.111168372C>T	ENSP00000335084:p.Cys127Tyr	13.0	0.0	.		19.0	7.0	.	NM_002710		Missense_Mutation	SNP	ENST00000335007.5	hg19	CCDS9150.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.520313	0.85495	.	.	ENSG00000186298	ENST00000335007;ENST00000340766;ENST00000546933;ENST00000550991;ENST00000551676	D;D;D;D;D	0.84589	-1.87;-1.87;-1.87;-1.87;-1.87	5.61	5.61	0.85477	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (2);Metallophosphoesterase domain (1);	0.039374	0.85682	D	0.000000	D	0.93015	0.7777	H	0.95611	3.695	0.80722	D	1	P	0.51240	0.943	P	0.50231	0.635	D	0.94583	0.7781	10	0.87932	D	0	-4.8814	19.998	0.97395	0.0:1.0:0.0:0.0	.	127	P36873	PP1G_HUMAN	Y	127;127;136;127;127	ENSP00000335084:C127Y;ENSP00000341779:C127Y;ENSP00000447122:C136Y;ENSP00000448981:C127Y;ENSP00000448437:C127Y	ENSP00000335084:C127Y	C	-	2	0	PPP1CC	109652755	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.692000	0.84203	2.804000	0.96469	0.462000	0.41574	TGT	.	.	.	none		0.338	PPP1CC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404659.1			T	111168372	C	T	111168372	3	4	197	1	0	0	0	0	1	0	0	0	12361	478	17	2	611	2	PPP1CC	12	111168372	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	30437605	111168372	22683523	57	11865											
SSTR1	6751	hgsc.bcm.edu	37	chr14	38678806	38678806	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctactccgtggtgtgcctggTggggctgtgtgggaactcta	4	12	16	9	1	1	0	0	0	1	0	2	1	2	1	2	5	3	1	2	5	3	2			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr14:38678806T>C	ENST00000267377.2	+	3	829	c.212T>C	c.(211-213)gTg>gCg	p.V71A		NM_001049.2	NP_001040.1	P30872	SSR1_HUMAN	somatostatin receptor 1	71					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)	GTGTGCCTGGTGGGGCTGTGT	0.562																																					p.V71A		Atlas-SNP	.											.	SSTR1	66	.	0			c.T212C						PASS	.						144	130	135					14																	38678806		2203	4300	6503	SO:0001583	missense	6751	exon3			GCCTGGTGGGGCT		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.212T>C	chr14.hg19:g.38678806T>C	ENSP00000267377:p.Val71Ala	122.0	0.0	.		133.0	48.0	.	NM_001049		Missense_Mutation	SNP	ENST00000267377.2	hg19	CCDS9666.1	.	.	.	.	.	.	.	.	.	.	T	14.87	2.664028	0.47572	.	.	ENSG00000139874	ENST00000267377	T	0.20598	2.06	4.74	3.58	0.41010	.	0.000000	0.48767	D	0.000167	T	0.16685	0.0401	L	0.32530	0.975	0.49687	D	0.99981	B	0.31581	0.329	B	0.32090	0.14	T	0.04427	-1.0952	10	0.52906	T	0.07	.	10.861	0.46827	0.0:0.0:0.1584:0.8416	.	71	P30872	SSR1_HUMAN	A	71	ENSP00000267377:V71A	ENSP00000267377:V71A	V	+	2	0	SSTR1	37748557	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.841000	0.86834	0.828000	0.34709	0.533000	0.62120	GTG	.	.	.	none		0.562	SSTR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409930.2			C	38678806	T	C	38678806	3	2	197	1	0	0	0	0	1	0	0	0	15209	1696	59	3	214	3	SSTR1	14	38678806	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10		38678806	68670734	58	11866											
ZBTB1	22890	hgsc.bcm.edu	37	chr14	64988346	64988346	+	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	ttcaagcacacaaggcagttCtagctgcctgtagctcctat	10	11	8	12	0	2	0	1	0	1	0	3	0	3	0	2	1	4	6	2	1	5	5			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr14:64988346C>G	ENST00000554015.1	+	4	555	c.124C>G	c.(124-126)Cta>Gta	p.L42V	ZBTB1_ENST00000358738.3_Missense_Mutation_p.L42V|ZBTB1_ENST00000394712.2_Missense_Mutation_p.L42V|RP11-973N13.4_ENST00000554918.1_RNA			Q9Y2K1	ZBTB1_HUMAN	zinc finger and BTB domain containing 1	42	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				B cell differentiation (GO:0030183)|innate immune response (GO:0045087)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of pro-T cell differentiation (GO:2000176)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated immunity (GO:0002711)|protein homooligomerization (GO:0051260)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	13		all_lung(585;0.000567)|Myeloproliferative disorder(585;0.0255)|all_neural(303;0.0294)		UCEC - Uterine corpus endometrioid carcinoma (185;0.0182)|all cancers(60;3.78e-43)|OV - Ovarian serous cystadenocarcinoma(108;1.22e-20)|BRCA - Breast invasive adenocarcinoma(234;6.75e-06)|KIRC - Kidney renal clear cell carcinoma(182;0.00269)|STAD - Stomach adenocarcinoma(64;0.012)		CAAGGCAGTTCTAGCTGCCTG	0.393																																					p.L42V		Atlas-SNP	.											.	ZBTB1	93	.	0			c.C124G						PASS	.						106	98	101					14																	64988346		2203	4300	6503	SO:0001583	missense	22890	exon2			GCAGTTCTAGCTG	AB023214	CCDS32097.1, CCDS45126.1	14q23.3	2013-01-09			ENSG00000126804	ENSG00000126804		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	20259	protein-coding gene	gene with protein product						10231032	Standard	NM_014950		Approved	KIAA0997, ZNF909	uc010aqg.3	Q9Y2K1		ENST00000554015.1:c.124C>G	chr14.hg19:g.64988346C>G	ENSP00000451000:p.Leu42Val	63.0	0.0	.		87.0	27.0	.	NM_014950	A8K6S8|Q86SW8	Missense_Mutation	SNP	ENST00000554015.1	hg19	CCDS45126.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.937405	0.73557	.	.	ENSG00000126804	ENST00000553583;ENST00000556965;ENST00000554015;ENST00000358738;ENST00000394712	D;D;D;D;D	0.89485	-2.52;-2.52;-2.52;-2.52;-2.52	6.16	2.42	0.29668	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.250565	0.28219	N	0.016157	D	0.95385	0.8502	H	0.95043	3.615	0.46203	D	0.998929	D;D	0.76494	0.999;0.997	D;D	0.85130	0.994;0.997	D	0.94162	0.7415	10	0.87932	D	0	-10.7701	9.9144	0.41425	0.0:0.6811:0.0:0.3189	.	42;42	Q9Y2K1-2;Q9Y2K1	.;ZBTB1_HUMAN	V	42	ENSP00000451584:L42V;ENSP00000450689:L42V;ENSP00000451000:L42V;ENSP00000351587:L42V;ENSP00000378201:L42V	ENSP00000351587:L42V	L	+	1	2	ZBTB1	64058099	0.970000	0.33590	0.892000	0.35008	0.997000	0.91878	1.715000	0.37971	0.195000	0.20347	0.650000	0.86243	CTA	.	.	.	none		0.393	ZBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411912.1			G	64988346	C	G	64988346	3	3	197	1	0	0	0	0	1	0	0	0	17534	912	32	4	126	4	ZBTB1	14	64988346	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	26309540	64988346	42361194	59	11867											
WDR20	91833	hgsc.bcm.edu	37	chr14	102674963	102674964	+	Frame_Shift_Ins	INS	-	-	A																															taatagacaagtcacgagttINSacctgtgtcaaatgggttcc																										TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr14:102674963_102674964insA	ENST00000342702.3	+	3	487_488	c.456_457insA	c.(457-459)accfs	p.T153fs	WDR20_ENST00000499851.2_Intron|WDR20_ENST00000322340.5_Intron|WDR20_ENST00000335263.5_Frame_Shift_Ins_p.T153fs|WDR20_ENST00000545563.1_5'UTR|WDR20_ENST00000424963.2_Frame_Shift_Ins_p.T29fs|WDR20_ENST00000454394.2_Frame_Shift_Ins_p.T184fs|WDR20_ENST00000299135.6_3'UTR|WDR20_ENST00000556807.1_Frame_Shift_Ins_p.T92fs|WDR20_ENST00000556511.2_Frame_Shift_Ins_p.T92fs	NM_001242418.1|NM_144574.3	NP_001229347.1|NP_653175.2	Q8TBZ3	WDR20_HUMAN	WD repeat domain 20	153										breast(1)|large_intestine(2)|lung(4)|prostate(1)	8						AGTCACGAGTTACCTGTGTCAA	0.45																																					p.V183fs		Atlas-Indel,Pindel	.											.	WDR20	35	.	0			c.549_550insA						PASS	.																																			SO:0001589	frameshift_variant	91833	exon4			.	BC028387	CCDS9968.1, CCDS9969.1, CCDS9970.1, CCDS55942.1, CCDS55943.1, CCDS55944.1, CCDS55945.1	14q32.31	2013-01-09				ENSG00000140153		"WD repeat domain containing"	19667	protein-coding gene	gene with protein product							Standard	NM_181291		Approved	DMR, MGC33177, FLJ33659	uc010txu.2	Q8TBZ3		ENST00000342702.3:c.457dupA	chr14.hg19:g.102674964_102674964dupA	ENSP00000341037:p.Thr153fs	50.0	0.0	0		60.0	14.0	0.233333	NM_001242417	B4DN18|E7EUY8|F8W9S4|G3V2F8|G3V5R0|H0YJJ1|Q86TU2|Q8NCN7|Q8WXX2|Q9UF86	Frame_Shift_Ins	INS	ENST00000342702.3	hg19	CCDS9969.1																																																																																			.	.	.	none		0.45	WDR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414963.1	NM_181291		A	102674964	-	A	102674963	7	5	197	1	0	1	1	0	0	0	0	0	17292	1741	61	0	483	0	WDR20	14	102674963	Frame_Shift_Ins	INS	-	TCGA-HE-A5NH-01A-11D-A26P-10	37686617	102674963	4674577	60	11868											
C15orf2	23742	hgsc.bcm.edu	37	chr15	24921405	24921405	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctcctgctgccttcaccaCgtgagccggcggtcaaggcc	5	8	11	17	3	3	1	2	1	1	0	4	1	3	1	5	3	3	1	5	3	1	1			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr15:24921405C>T	ENST00000329468.2	+	1	865	c.391C>T	c.(391-393)Cgt>Tgt	p.R131C		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	131					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)		p.R131C(1)									GCCTTCACCACGTGAGCCGGC	0.627																																					p.R131C		Atlas-SNP	.											C15orf2,NS,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	endometrium(1)	c.C391T						PASS	.						51	43	46					15																	24921405		2203	4300	6503	SO:0001583	missense	23742	exon1			TCACCACGTGAGC	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.391C>T	chr15.hg19:g.24921405C>T	ENSP00000333735:p.Arg131Cys	51.0	0.0	.		75.0	26.0	.	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	hg19	CCDS10015.1	.	.	.	.	.	.	.	.	.	.	.	7.490	0.650540	0.14516	.	.	ENSG00000185823	ENST00000329468	T	0.06294	3.32	2.27	1.33	0.21861	.	4.968620	0.00575	N	0.000313	T	0.05410	0.0143	N	0.14661	0.345	0.09310	N	1	P	0.43094	0.799	B	0.37780	0.258	T	0.39643	-0.9604	10	0.56958	D	0.05	.	8.6687	0.34137	0.2269:0.7731:0.0:0.0	.	131	Q9NZP6	CO002_HUMAN	C	131	ENSP00000333735:R131C	ENSP00000333735:R131C	R	+	1	0	C15orf2	22472498	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.028000	0.13644	0.082000	0.17018	-2.175000	0.00321	CGT	.	.	.	none		0.627	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		T	24921405	C	T	24921405	3	4	197	1	0	0	0	0	1	0	0	0	1786	536	19	1	393	1	C15orf2	15	24921405	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10		24921405	77609987	61	11869											
UNC13C	440279	hgsc.bcm.edu	37	chr15	54557623	54557623	+	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	ccatatgttacagttcaagtTggaaagaacaaaagaagaac	19	8	8	6	0	1	3	1	0	0	3	1	4	1	4	1	1	3	3	1	1	9	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr15:54557623T>A	ENST00000260323.11	+	9	3747	c.3747T>A	c.(3745-3747)gtT>gtA	p.V1249V	UNC13C_ENST00000537900.1_Silent_p.V1247V|UNC13C_ENST00000545554.1_Silent_p.V1249V	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1249	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		CAGTTCAAGTTGGAAAGAACA	0.318																																					p.V1249V		Atlas-SNP	.											.	UNC13C	674	.	0			c.T3747A						PASS	.						54	50	51					15																	54557623		1800	4067	5867	SO:0001819	synonymous_variant	440279	exon8			TCAAGTTGGAAAG	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.3747T>A	chr15.hg19:g.54557623T>A		118.0	0.0	.		174.0	70.0	.	NM_001080534	Q0P613|Q8ND48|Q96NP3	Silent	SNP	ENST00000260323.11	hg19	CCDS45264.1																																																																																			.	.	.	none		0.318	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		A	54557623	T	A	54557623	2	1	197	1	0	0	0	0	0	0	0	1	16998	1799	63	5		5	UNC13C	15	54557623	Silent	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	29636218	54557623	47973769	62	11870											
SNX1	6642	hgsc.bcm.edu	37	chr15	64424017	64424017	+	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	aaattgagcagctccaccagGaacaggccaacaatgacttc	15	6	8	12	0	0	2	0	2	0	0	2	3	1	3	3	2	4	2	3	2	4	2			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr15:64424017G>C	ENST00000559844.1	+	11	1161	c.1147G>C	c.(1147-1149)Gaa>Caa	p.E383Q	SNX1_ENST00000353874.4_Missense_Mutation_p.E383Q|SNX1_ENST00000560829.1_Missense_Mutation_p.E165Q|SNX1_ENST00000561026.1_Missense_Mutation_p.E318Q|SNX1_ENST00000261889.5_Missense_Mutation_p.E383Q			Q13596	SNX1_HUMAN	sorting nexin 1	383	BAR.				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						GCTCCACCAGGAACAGGCCAA	0.537																																					p.E383Q		Atlas-SNP	.											.	SNX1	36	.	0			c.G1147C						PASS	.						125	118	120					15																	64424017		2203	4300	6503	SO:0001583	missense	6642	exon11			CACCAGGAACAGG	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.1147G>C	chr15.hg19:g.64424017G>C	ENSP00000453785:p.Glu383Gln	127.0	0.0	.		174.0	69.0	.	NM_003099	A6NM19|A8K6T7|H0Y2M5|O60750|O60751|Q6ZRJ8	Missense_Mutation	SNP	ENST00000559844.1	hg19	CCDS32266.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.180341	0.78677	.	.	ENSG00000028528	ENST00000380285;ENST00000353874;ENST00000261889	T	0.32023	1.47	5.2	5.2	0.72013	Vps5 C-terminal (1);	0.092925	0.64402	D	0.000001	T	0.38532	0.1044	L	0.45137	1.4	0.80722	D	1	P;B;P;P;B;P;P	0.47106	0.89;0.167;0.74;0.74;0.365;0.475;0.571	P;B;P;P;B;B;B	0.48952	0.596;0.34;0.513;0.457;0.142;0.411;0.378	T	0.09885	-1.0654	10	0.52906	T	0.07	-19.057	17.8936	0.88879	0.0:0.0:1.0:0.0	.	383;293;383;383;318;383;383	Q6ZRJ8;Q59GU6;Q53HL9;Q53GY8;Q13596-2;A6NKH4;Q13596	.;.;.;.;.;.;SNX1_HUMAN	Q	383;383;318	ENSP00000326668:E383Q	ENSP00000261889:E318Q	E	+	1	0	SNX1	62211070	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.657000	0.98554	2.693000	0.91896	0.561000	0.74099	GAA	.	.	.	none		0.537	SNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418559.1	NM_003099		C	64424017	G	C	64424017	3	2	197	1	0	0	0	0	1	0	0	0	14893	1175	41	4	1189	4	SNX1	15	64424017	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	9866394	64424017	38107375	63	11871											
ALPK3	57538	hgsc.bcm.edu	37	chr15	85411510	85411510	+	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	aagagtccatctgctggcagGaaaggctcccagctgagtcc	10	7	12	12	0	1	2	0	1	1	1	4	3	4	3	3	3	2	4	3	3	2	0			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr15:85411510G>C	ENST00000258888.5	+	14	5714	c.5547G>C	c.(5545-5547)agG>agC	p.R1849S		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1849					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)			CTGCTGGCAGGAAAGGCTCCC	0.627																																					p.R1849S		Atlas-SNP	.											.	ALPK3	289	.	0			c.G5547C						PASS	.						56	65	62					15																	85411510		2203	4299	6502	SO:0001583	missense	57538	exon14			TGGCAGGAAAGGC	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.5547G>C	chr15.hg19:g.85411510G>C	ENSP00000258888:p.Arg1849Ser	65.0	0.0	.		92.0	41.0	.	NM_020778	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	hg19	CCDS10333.1	.	.	.	.	.	.	.	.	.	.	G	18.38	3.610641	0.66558	.	.	ENSG00000136383	ENST00000258888	T	0.68903	-0.36	3.93	1.99	0.26369	.	0.271361	0.27778	N	0.017892	T	0.76307	0.3969	M	0.74258	2.255	0.37283	D	0.907916	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.996	T	0.75625	-0.3253	10	0.54805	T	0.06	-23.6009	5.715	0.17954	0.3613:0.0:0.6387:0.0	.	150;1849	B4DU37;Q96L96	.;ALPK3_HUMAN	S	1849	ENSP00000258888:R1849S	ENSP00000258888:R1849S	R	+	3	2	ALPK3	83212514	1.000000	0.71417	0.996000	0.52242	0.906000	0.53458	0.646000	0.24797	0.408000	0.25621	0.313000	0.20887	AGG	.	.	.	none		0.627	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778		C	85411510	G	C	85411510	3	2	197	1	0	0	0	0	1	0	0	0	546	1165	41	4	5601	4	ALPK3	15	85411510	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	20987493	85411510	17119882	64	11872											
BTBD12	84464	hgsc.bcm.edu	37	chr16	3645657	3645657	+	Frame_Shift_Del	DEL	C	C	-																															tcctgcgatggcaccacaaaCccagtcagaggaaggccgcc																										TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr16:3645657delC	ENST00000294008.3	-	9	2602	c.1962delG	c.(1960-1962)gggfs	p.G654fs		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	654	Interaction with SLX4IP, ERCC4 and MSH2.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						GCACCACAAACCCAGTCAGAG	0.627								Direct reversal of damage																													p.F655fs		Atlas-Indel,Pindel	.											.	SLX4	173	.	0			c.1963delT						PASS	.						63	65	64					16																	3645657		2197	4300	6497	SO:0001589	frameshift_variant	84464	exon9			.	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.1962delG	chr16.hg19:g.3645657delC	ENSP00000294008:p.Gly654fs	75.0	0.0	0		103.0	41.0	0.398058	NM_032444	Q69YT8|Q8TF15|Q96JP1	Frame_Shift_Del	DEL	ENST00000294008.3	hg19	CCDS10506.2																																																																																			.	.	.	none		0.627	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444		-	3645657	C	-	3645657	7	5	197	1	0	1	0	1	0	0	0	0	1542	494	18	0	3570	0	BTBD12	16	3645657	Frame_Shift_Del	DEL	C	TCGA-HE-A5NH-01A-11D-A26P-10		3645657	86709096	65	11873											
SSH2	85464	hgsc.bcm.edu	37	chr17	27959441	27959441	+	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	aagaatcattctttgaattcTtacgagtggacaatgaggta	14	13	9	5	1	3	3	1	2	2	1	3	5	3	4	0	2	1	1	0	2	6	5			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr17:27959441T>A	ENST00000269033.3	-	15	2841	c.2690A>T	c.(2689-2691)aAg>aTg	p.K897M	RP11-68I3.2_ENST00000581474.1_RNA|SSH2_ENST00000540801.1_Missense_Mutation_p.K924M	NM_001282129.1|NM_033389.2	NP_001269058.1|NP_203747.2	Q76I76	SSH2_HUMAN	slingshot protein phosphatase 2	897					actin cytoskeleton organization (GO:0030036)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)		SSH2/SUZ12(2)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CTTTGAATTCTTACGAGTGGA	0.502																																					p.K897M		Atlas-SNP	.											.	SSH2	107	.	0			c.A2690T						PASS	.						184	192	189					17																	27959441		2203	4300	6503	SO:0001583	missense	85464	exon15			GAATTCTTACGAG	AB072359	CCDS11253.1, CCDS74024.1	17q11.2	2013-03-05	2013-03-05		ENSG00000141298	ENSG00000141298		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"	30580	protein-coding gene	gene with protein product		606779	"slingshot homolog 2 (Drosophila)"			11832213, 11214970	Standard	XM_005258059		Approved	KIAA1725	uc002heo.1	Q76I76	OTTHUMG00000132752	ENST00000269033.3:c.2690A>T	chr17.hg19:g.27959441T>A	ENSP00000269033:p.Lys897Met	97.0	0.0	.		189.0	106.0	.	NM_033389	Q8TDB5|Q8WYL1|Q8WYL2|Q96F40|Q96H36|Q9C0D8	Missense_Mutation	SNP	ENST00000269033.3	hg19	CCDS11253.1	.	.	.	.	.	.	.	.	.	.	T	18.26	3.585604	0.66105	.	.	ENSG00000141298	ENST00000269033;ENST00000540801	T;T	0.19806	2.14;2.12	5.97	4.89	0.63831	.	0.456816	0.25546	N	0.029933	T	0.43809	0.1264	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.36407	-0.9749	10	0.87932	D	0	-19.645	11.9775	0.53100	0.0:0.0675:0.0:0.9325	.	924;897	F5H527;Q76I76	.;SSH2_HUMAN	M	897;924	ENSP00000269033:K897M;ENSP00000444743:K924M	ENSP00000269033:K897M	K	-	2	0	SSH2	24983567	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.807000	0.69157	1.089000	0.41292	0.472000	0.43445	AAG	.	.	.	none		0.502	SSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256116.1	NM_033389		A	27959441	T	A	27959441	3	1	197	1	0	0	0	0	1	0	0	0	15197	1609	56	5	1585	5	SSH2	17	27959441	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10		27959441	53235769	66	11874											
TGIF1	7050	hgsc.bcm.edu	37	chr18	3452341	3452341	+	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	ccccatcccagggcgcacagGgtccagctcctcggcgccga	6	4	12	19	4	0	0	0	0	0	0	4	1	3	0	6	3	1	2	6	3	0	0			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr18:3452341G>C	ENST00000330513.5	+	1	667	c.364G>C	c.(364-366)Ggt>Cgt	p.G122R	TGIF1_ENST00000577543.1_Intron|TGIF1_ENST00000405385.3_Intron|TGIF1_ENST00000551402.1_Intron|TGIF1_ENST00000407501.2_Intron|TGIF1_ENST00000548489.2_Intron|TGIF1_ENST00000343820.5_Intron|TGIF1_ENST00000345133.5_Intron|TGIF1_ENST00000551541.1_Intron|TGIF1_ENST00000400167.2_5'Flank|TGIF1_ENST00000401449.1_Intron	NM_170695.2	NP_733796.2	Q15583	TGIF1_HUMAN	TGFB-induced factor homeobox 1	122					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)				GGGCGCACAGGGTCCAGCTCC	0.687																																					p.G122R		Atlas-SNP	.											.	TGIF1	41	.	0			c.G364C						PASS	.						14	16	15					18																	3452341		2171	4257	6428	SO:0001583	missense	7050	exon1			GCACAGGGTCCAG	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.364G>C	chr18.hg19:g.3452341G>C	ENSP00000327959:p.Gly122Arg	98.0	0.0	.		99.0	50.0	.	NM_170695	A6NE42|A6NLU7|F8VZB6|Q6ICR0|Q8N5X9|Q9NRS0	Missense_Mutation	SNP	ENST00000330513.5	hg19	CCDS11834.1	.	.	.	.	.	.	.	.	.	.	G	16.14	3.037731	0.54896	.	.	ENSG00000177426	ENST00000330513	T	0.52295	0.67	3.89	3.01	0.34805	.	.	.	.	.	T	0.37348	0.1000	L	0.38175	1.15	0.21473	N	0.999675	P	0.44877	0.845	B	0.41813	0.367	T	0.15235	-1.0444	9	0.52906	T	0.07	3.9769	7.1745	0.25736	0.1232:0.0:0.8768:0.0	.	122	Q15583	TGIF1_HUMAN	R	122	ENSP00000327959:G122R	ENSP00000327959:G122R	G	+	1	0	TGIF1	3442341	0.004000	0.15560	0.040000	0.18447	0.018000	0.09664	1.238000	0.32707	0.855000	0.35359	0.655000	0.94253	GGT	.	.	.	none		0.687	TGIF1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254368.4	NM_170695		C	3452341	G	C	3452341	3	2	197	1	0	0	0	0	1	0	0	0	15837	1232	43	4	448	4	TGIF1	18	3452341	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10		3452341	74624907	67	11875											
PTPRM	5797	hgsc.bcm.edu	37	chr18	8378412	8378412	+	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	cagattaaagaggaattccgGgtaagtgatgcctaagggag	14	8	14	5	1	0	3	0	1	0	2	1	5	1	5	2	3	1	1	2	3	5	4	rs374669816		TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr18:8378412G>T	ENST00000332175.8	+	25	4610	c.3573G>T	c.(3571-3573)cgG>cgT	p.R1191R	PTPRM_ENST00000400053.4_Splice_Site_p.R1129R|PTPRM_ENST00000444013.1_Splice_Site_p.R978R|PTPRM_ENST00000400060.4_Splice_Site_p.R1205R|PTPRM_ENST00000580170.1_Splice_Site_p.R1204R	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	1191	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				AGGAATTCCGGGTAAGTGATG	0.493																																					p.R1204R		Atlas-SNP	.											.	PTPRM	185	.	0			c.G3612T						PASS	.						116	97	103					18																	8378412		2203	4300	6503	SO:0001630	splice_region_variant	5797	exon27			ATTCCGGGTAAGT	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.3573+1G>T	chr18.hg19:g.8378412G>T		82.0	0.0	.		150.0	57.0	.	NM_001105244	A7MBN1|D3DUH8|J3QL11	Silent	SNP	ENST00000332175.8	hg19	CCDS11840.1																																																																																			.	.	.	alt		0.493	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1		Silent	T	8378412	G	T	8378412	5	4	197	1	0	0	0	0	0	0	1	0	12819	1246	43	4	3718	4	PTPRM	18	8378412	Splice_Site	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	4926071	8378412	69698836	68	11876											
FUT6	2528	hgsc.bcm.edu	37	chr19	5832530	5832530	+	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	ctgaaacagcagcgtggtcaGacagcagcgccacgaccact	12	4	11	14	3	1	2	1	1	0	1	1	3	1	2	2	1	5	2	2	1	1	0			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr19:5832530G>T	ENST00000318336.4	-	3	1243	c.49C>A	c.(49-51)Ctg>Atg	p.L17M	FUT6_ENST00000527106.1_Missense_Mutation_p.L17M|FUT6_ENST00000286955.5_Missense_Mutation_p.L17M|FUT6_ENST00000524754.1_Missense_Mutation_p.L17M|FUT6_ENST00000592563.1_Missense_Mutation_p.L17M	NM_000150.2	NP_000141.1	P51993	FUT6_HUMAN	fucosyltransferase 6 (alpha (1,3) fucosyltransferase)	17					fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)	6						AGCGTGGTCAGACAGCAGCGC	0.572																																					p.L17M		Atlas-SNP	.											.	FUT6	30	.	0			c.C49A						PASS	.						35	30	32					19																	5832530		2203	4300	6503	SO:0001583	missense	2528	exon3			TGGTCAGACAGCA		CCDS12152.1	19p13.3	2013-02-26			ENSG00000156413	ENSG00000156413	2.4.1.65	"Fucosyltransferases"	4017	protein-coding gene	gene with protein product	"alpha-(1,3)-fucosyltransferase", "galactoside 3-L-fucosyltransferase"	136836				1520296, 7782074	Standard	NM_001040701		Approved	FT1A, FCT3A, FucT-VI, FLJ40754	uc002mdh.1	P51993	OTTHUMG00000167335	ENST00000318336.4:c.49C>A	chr19.hg19:g.5832530G>T	ENSP00000313398:p.Leu17Met	113.0	0.0	.		139.0	61.0	.	NM_000150	A6NEX0|D6W637|Q9UND8	Missense_Mutation	SNP	ENST00000318336.4	hg19	CCDS12152.1	.	.	.	.	.	.	.	.	.	.	G	10.54	1.377927	0.24944	.	.	ENSG00000156413	ENST00000524754;ENST00000527106;ENST00000318336;ENST00000286955;ENST00000341530;ENST00000529165;ENST00000531085;ENST00000531199;ENST00000532464;ENST00000528505	T;T;T;T;T;T;T;T;T	0.61859	1.81;1.81;1.81;1.81;1.81;0.81;0.24;0.07;0.19	3.7	1.52	0.23074	.	0.960505	0.08559	U	0.927769	T	0.72803	0.3506	M	0.77616	2.38	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.995;0.997	T	0.55068	-0.8198	10	0.54805	T	0.06	.	6.2965	0.21089	0.1124:0.195:0.6925:0.0	.	17;17	C9J8A2;P51993	.;FUT6_HUMAN	M	17	ENSP00000431708:L17M;ENSP00000432954:L17M;ENSP00000313398:L17M;ENSP00000286955:L17M;ENSP00000436547:L17M;ENSP00000432161:L17M;ENSP00000436413:L17M;ENSP00000431880:L17M;ENSP00000433811:L17M	ENSP00000286955:L17M	L	-	1	2	FUT6	5783530	0.017000	0.18338	0.005000	0.12908	0.033000	0.12548	1.348000	0.33987	0.849000	0.35215	0.436000	0.28706	CTG	.	.	.	none		0.572	FUT6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394218.2	NM_000150		T	5832530	G	T	5832530	3	4	197	1	0	0	0	0	1	0	0	0	6115	933	33	4	1034	4	FUT6	19	5832530	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10		5832530	53296453	69	11877											
ZNF844	284391	hgsc.bcm.edu	37	chr19	12187226	12187226	+	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	gtgtagtaaagccttcatttCttccacttcctttcgatatc	8	17	5	11	1	2	0	1	0	1	0	6	1	4	0	3	0	1	2	3	0	4	8			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr19:12187226C>T	ENST00000439326.3	+	4	1466	c.1291C>T	c.(1291-1293)Ctt>Ttt	p.L431F	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	431					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						GCCTTCATTTCTTCCACTTCC	0.433																																					p.L431F		Atlas-SNP	.											ZNF844,NS,carcinoma,0,2	ZNF844	69	.	0			c.C1291T						PASS	.						61	61	61					19																	12187226		692	1591	2283	SO:0001583	missense	284391	exon4			TCATTTCTTCCAC	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.1291C>T	chr19.hg19:g.12187226C>T	ENSP00000392024:p.Leu431Phe	38.0	0.0	.		64.0	3.0	.	NM_001136501	Q5JPI8	Missense_Mutation	SNP	ENST00000439326.3	hg19	CCDS45985.1	.	.	.	.	.	.	.	.	.	.	C	12.36	1.915954	0.33815	.	.	ENSG00000223547	ENST00000439326;ENST00000541708	T	0.08008	3.14	2.74	-5.49	0.02584	.	.	.	.	.	T	0.03520	0.0101	N	0.21097	0.63	0.09310	N	0.999999	P	0.49961	0.93	B	0.37550	0.253	T	0.33752	-0.9856	9	0.10111	T	0.7	.	7.4624	0.27302	0.2498:0.309:0.4413:0.0	.	431	Q08AG5	ZN844_HUMAN	F	431	ENSP00000392024:L431F	ENSP00000392024:L431F	L	+	1	0	ZNF844	12048226	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.229000	0.09098	-1.610000	0.01583	0.407000	0.27541	CTT	.	.	.	none		0.433	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2			T	12187226	C	T	12187226	3	4	197	1	0	0	0	0	1	0	0	0	18202	913	32	2	1305	2	ZNF844	19	12187226	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	6354696	12187226	46941757	70	11878											
IL28B	282617	hgsc.bcm.edu	37	chr19	39735444	39735444	+	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	tcactaaggcatctttggccCtcttaaaggcctgcagctcc	8	11	8	14	0	3	0	1	0	2	0	4	0	4	0	3	3	2	3	3	3	3	3	rs201018323	byFrequency	TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr19:39735444C>T	ENST00000413851.2	-	1	202	c.164G>A	c.(163-165)aGg>aAg	p.R55K	IFNL4_ENST00000606380.1_RNA	NM_172139.2	NP_742151.2	Q8IZI9	IFNL3_HUMAN	interferon, lambda 3	55					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)											ATCTTTGGCCCTCTTAAAGGC	0.622													C|||	3	0.000599042	8e-04	0	5008	,	,		19948	0		0.001	False		,,,				2504	0.001				p.R55K		Atlas-SNP	.											.	.	.	.	0			c.G164A						PASS	.						21	24	23					19																	39735444		2203	4292	6495	SO:0001583	missense	282617	exon1			TTGGCCCTCTTAA	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.164G>A	chr19.hg19:g.39735444C>T	ENSP00000409000:p.Arg55Lys	266.0	0.0	.		347.0	107.0	.	NM_172139	A2BDE1|Q6VN56|Q7Z4J3|Q8IWL6	Missense_Mutation	SNP	ENST00000413851.2	hg19	CCDS12530.1	.	.	.	.	.	.	.	.	.	.	C	0.482	-0.879400	0.02550	.	.	ENSG00000197110	ENST00000413851	T	0.26223	1.75	2.97	-4.43	0.03568	.	0.765632	0.12009	N	0.508070	T	0.03739	0.0106	N	0.00521	-1.4	0.18873	N	0.999982	B	0.06786	0.001	B	0.04013	0.001	T	0.37197	-0.9716	10	0.06757	T	0.87	2.9441	0.3638	0.00368	0.1912:0.2524:0.1896:0.3668	.	55	Q8IZI9	IL28B_HUMAN	K	55	ENSP00000409000:R55K	ENSP00000409000:R55K	R	-	2	0	IL28B	44427284	0.000000	0.05858	0.388000	0.26195	0.653000	0.38743	-1.727000	0.01860	-0.398000	0.07679	0.194000	0.17425	AGG	.	.	.	weak		0.622	IFNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463832.1	NM_172139		T	39735444	C	T	39735444	3	4	197	1	0	0	0	0	1	0	0	0	7690	681	24	2	445	2	IL28B	19	39735444	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	27548218	39735444	19393539	71	11879											
CCDC9	26093	hgsc.bcm.edu	37	chr19	47767895	47767895	+	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	cgcaggcagaacattgagaaGatgaatgaggagatggagaa	17	5	15	4	1	0	7	0	3	0	5	0	10	0	7	0	3	1	2	0	3	4	1			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr19:47767895G>T	ENST00000221922.6	+	6	720	c.498G>T	c.(496-498)aaG>aaT	p.K166N		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	166							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)		ACATTGAGAAGATGAATGAGG	0.617																																					p.K166N		Atlas-SNP	.											.	CCDC9	37	.	0			c.G498T						PASS	.						80	63	69					19																	47767895		2202	4299	6501	SO:0001583	missense	26093	exon6			TGAGAAGATGAAT	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.498G>T	chr19.hg19:g.47767895G>T	ENSP00000221922:p.Lys166Asn	36.0	0.0	.		52.0	17.0	.	NM_015603		Missense_Mutation	SNP	ENST00000221922.6	hg19	CCDS12698.1	.	.	.	.	.	.	.	.	.	.	g	16.68	3.191307	0.58017	.	.	ENSG00000105321	ENST00000221922;ENST00000504556	T	0.27890	1.64	4.63	4.63	0.57726	.	0.356482	0.30667	N	0.009121	T	0.53769	0.1817	M	0.67953	2.075	0.44694	D	0.997682	D	0.89917	1.0	D	0.77004	0.989	T	0.55477	-0.8135	10	0.52906	T	0.07	-46.2641	16.3937	0.83548	0.0:0.0:1.0:0.0	.	166	Q9Y3X0	CCDC9_HUMAN	N	166;148	ENSP00000221922:K166N	ENSP00000221922:K166N	K	+	3	2	CCDC9	52459735	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.672000	0.54583	2.416000	0.81992	0.561000	0.74099	AAG	.	.	.	none		0.617	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603		T	47767895	G	T	47767895	3	4	197	1	0	0	0	0	1	0	0	0	2869	933	33	4	516	4	CCDC9	19	47767895	Missense_Mutation	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	8032451	47767895	11361088	72	11880											
ZNF600	162966	hgsc.bcm.edu	37	chr19	53269420	53269420	+	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	gactgaaggtcttgctgcacTcattacacttgtaaggtttc	9	14	9	9	0	2	1	1	1	1	0	3	2	2	1	0	2	3	4	0	2	3	5			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr19:53269420T>A	ENST00000338230.3	-	3	1856	c.1589A>T	c.(1588-1590)gAg>gTg	p.E530V		NM_198457.2	NP_940859	Q6ZNG1	ZN600_HUMAN	zinc finger protein 600	530					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(2)|kidney(4)|large_intestine(9)|liver(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(262;0.0241)|GBM - Glioblastoma multiforme(134;0.0404)		CTTGCTGCACTCATTACACTT	0.458																																					p.E530V	Esophageal Squamous(196;1235 2112 2375 33339 34207)	Atlas-SNP	.											.	ZNF600	75	.	0			c.A1589T						PASS	.						220	195	204					19																	53269420		2203	4300	6503	SO:0001583	missense	162966	exon3			CTGCACTCATTAC	U52096	CCDS12856.1	19q13.42	2013-01-08				ENSG00000189190		"Zinc fingers, C2H2-type"	30951	protein-coding gene	gene with protein product						12576331	Standard	NM_198457		Approved	KR-ZNF1, DKFZp686F06123	uc002qab.4	Q6ZNG1		ENST00000338230.3:c.1589A>T	chr19.hg19:g.53269420T>A	ENSP00000344791:p.Glu530Val	67.0	0.0	.		109.0	37.0	.	NM_198457	Q6MZR0	Missense_Mutation	SNP	ENST00000338230.3	hg19	CCDS12856.1	.	.	.	.	.	.	.	.	.	.	.	12.82	2.052449	0.36181	.	.	ENSG00000189190	ENST00000338230	T	0.17528	2.27	1.51	0.278	0.15673	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.18593	0.0446	N	0.11789	0.175	0.09310	N	1	D	0.55172	0.97	D	0.74348	0.983	T	0.16928	-1.0386	9	0.45353	T	0.12	.	5.4227	0.16409	0.251:0.0:0.0:0.749	.	530	Q6ZNG1	ZN600_HUMAN	V	530	ENSP00000344791:E530V	ENSP00000344791:E530V	E	-	2	0	ZNF600	57961232	0.000000	0.05858	0.001000	0.08648	0.042000	0.13812	0.274000	0.18680	-0.139000	0.11414	0.163000	0.16589	GAG	.	.	.	none		0.458	ZNF600-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463093.1	NM_198457		A	53269420	T	A	53269420	3	1	197	1	0	0	0	0	1	0	0	0	18042	1551	54	5	583	5	ZNF600	19	53269420	Missense_Mutation	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	5501525	53269420	5859563	73	11881											
ZNF761	388561	hgsc.bcm.edu	37	chr19	53959526	53959526	+	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	atagtgacaaagcttacagtTtcaaatcaaaccttgaaata	18	11	5	7	0	2	2	2	2	0	0	2	2	2	2	1	0	3	2	1	0	7	5			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr19:53959526T>G	ENST00000454407.1	+	0	2218							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		AGCTTACAGTTTCAAATCAAA	0.403																																					p.F589V		Atlas-SNP	.											.	ZNF761	104	.	0			c.T1765G						PASS	.						98	102	101					19																	53959526		2203	4299	6502			388561	exon7			TACAGTTTCAAAT	AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"Zinc fingers, C2H2-type"	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		chr19.hg19:g.53959526T>G		83.0	0.0	.		103.0	47.0	.	NM_001008401	Q6ZNB9	Missense_Mutation	SNP	ENST00000454407.1	hg19																																																																																				.	.	.	none		0.403	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401		G	53959526	T	G	53959526	1	3	197	0	1	0	0	0	0	0	0	0	18148	1841	64	5		5	ZNF761	19	53959526	RNA	SNP	T	TCGA-HE-A5NH-01A-11D-A26P-10	690106	53959526	5169457	74	11882											
CRNKL1	51340	hgsc.bcm.edu	37	chr20	20026023	20026023	+	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	catatgttcatctccaaagaAttccacagctctctcataca	13	12	3	13	0	4	1	2	0	2	1	7	1	5	1	2	0	2	2	2	0	4	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr20:20026023A>T	ENST00000377340.2	-	7	1244	c.1213T>A	c.(1213-1215)Ttc>Atc	p.F405I	CRNKL1_ENST00000536226.1_Missense_Mutation_p.F244I|CRNKL1_ENST00000377327.4_Missense_Mutation_p.F393I	NM_001278628.1|NM_016652.4	NP_001265557.1|NP_057736.4	Q9BZJ0	CRNL1_HUMAN	crooked neck pre-mRNA splicing factor 1	405					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						TCTCCAAAGAATTCCACAGCT	0.398																																					p.F405I		Atlas-SNP	.											.	CRNKL1	101	.	0			c.T1213A						PASS	.						175	173	173					20																	20026023		2203	4300	6503	SO:0001583	missense	51340	exon7			CAAAGAATTCCAC	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.1213T>A	chr20.hg19:g.20026023A>T	ENSP00000366557:p.Phe405Ile	110.0	0.0	.		153.0	54.0	.	NM_016652	A8K9T4|Q5JY64|Q8WYI5|Q9BZI9|Q9BZJ1|Q9BZJ2|Q9GZW7|Q9H8F8|Q9NQH5|Q9NYD8	Missense_Mutation	SNP	ENST00000377340.2	hg19	CCDS33446.1	.	.	.	.	.	.	.	.	.	.	A	19.11	3.764213	0.69878	.	.	ENSG00000101343	ENST00000377327;ENST00000377340;ENST00000536226	T;T;T	0.08984	3.03;3.03;3.03	5.8	5.8	0.92144	Tetratricopeptide-like helical (1);	0.091092	0.85682	D	0.000000	T	0.13114	0.0318	M	0.70787	2.145	0.80722	D	1	B	0.29716	0.255	B	0.26517	0.07	T	0.02301	-1.1180	10	0.33141	T	0.24	-21.9403	16.1384	0.81506	1.0:0.0:0.0:0.0	.	405	Q9BZJ0	CRNL1_HUMAN	I	393;405;244	ENSP00000366544:F393I;ENSP00000366557:F405I;ENSP00000440733:F244I	ENSP00000366544:F393I	F	-	1	0	CRNKL1	19974023	1.000000	0.71417	0.976000	0.42696	0.987000	0.75469	9.339000	0.96797	2.203000	0.70933	0.460000	0.39030	TTC	.	.	.	none		0.398	CRNKL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000127787.1			T	20026023	A	T	20026023	3	4	197	1	0	0	0	0	1	0	0	0	3893	101	4	5	1369	5	CRNKL1	20	20026023	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10		20026023	42999497	75	11883											
KIAA1755	85449	hgsc.bcm.edu	37	chr20	36841970	36841970	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcctggcccaggcctgccCggctcagggaggccacctgc	4	5	14	18	1	1	0	1	0	0	0	2	1	2	1	6	5	2	2	6	5	0	0			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr20:36841970C>T	ENST00000279024.4	-	14	3348	c.3077G>A	c.(3076-3078)cGg>cAg	p.R1026Q		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	1026										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)				CAGGCCTGCCCGGCTCAGGGA	0.677																																					p.R1026Q		Atlas-SNP	.											.	KIAA1755	145	.	0			c.G3077A						PASS	.						25	25	25					20																	36841970		2200	4297	6497	SO:0001583	missense	85449	exon14			CCTGCCCGGCTCA	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.3077G>A	chr20.hg19:g.36841970C>T	ENSP00000279024:p.Arg1026Gln	47.0	0.0	.		51.0	23.0	.	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	hg19	CCDS33467.1	.	.	.	.	.	.	.	.	.	.	C	10.69	1.421251	0.25639	.	.	ENSG00000149633	ENST00000279024	T	0.05717	3.4	5.29	-4.25	0.03766	.	0.891096	0.09443	N	0.801481	T	0.03011	0.0089	N	0.11064	0.09	0.09310	N	1	B	0.17667	0.023	B	0.08055	0.003	T	0.48692	-0.9013	10	0.10902	T	0.67	.	11.6604	0.51343	0.0:0.3634:0.0:0.6366	.	1026	Q5JYT7	K1755_HUMAN	Q	1026	ENSP00000279024:R1026Q	ENSP00000279024:R1026Q	R	-	2	0	KIAA1755	36275384	0.000000	0.05858	0.002000	0.10522	0.669000	0.39330	-2.684000	0.00835	-1.072000	0.03141	-0.224000	0.12420	CGG	.	.	.	none		0.677	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864		T	36841970	C	T	36841970	3	4	197	1	0	0	0	0	1	0	0	0	8264	652	23	1	529	1	KIAA1755	20	36841970	Missense_Mutation	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	16815947	36841970	26183550	76	11884											
CABLES2	81928	hgsc.bcm.edu	37	chr20	60967982	60967982	+	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	gagagggcactcaccatgtaCgacgcaaagatgaggacacg	14	4	13	10	3	1	3	1	1	0	2	1	6	1	4	1	2	1	3	1	2	2	1			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr20:60967982C>G	ENST00000279101.5	-	7	986	c.978G>C	c.(976-978)tcG>tcC	p.S326S		NM_031215.2	NP_112492.2	Q9BTV7	CABL2_HUMAN	Cdk5 and Abl enzyme substrate 2	326					cell cycle (GO:0007049)|cell division (GO:0051301)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)		cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			endometrium(2)|kidney(1)|lung(6)|pancreas(1)|skin(1)	11	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			TCACCATGTACGACGCAAAGA	0.657																																					p.S326S		Atlas-SNP	.											.	CABLES2	30	.	0			c.G978C						PASS	.						140	122	128					20																	60967982		2203	4300	6503	SO:0001819	synonymous_variant	81928	exon7			CATGTACGACGCA	BC003122	CCDS33503.1	20q13.33	2004-01-09	2004-01-09	2004-01-09	ENSG00000149679	ENSG00000149679			16143	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 150"	C20orf150		12477932	Standard	NM_031215		Approved	dJ908M14.2, ik3-2	uc002ycv.2	Q9BTV7	OTTHUMG00000032912	ENST00000279101.5:c.978G>C	chr20.hg19:g.60967982C>G		118.0	0.0	.		147.0	52.0	.	NM_031215	Q5JWL0|Q9BYK0	Silent	SNP	ENST00000279101.5	hg19	CCDS33503.1	.	.	.	.	.	.	.	.	.	.	C	0.070	-1.204574	0.01568	.	.	ENSG00000149679	ENST00000453274	.	.	.	5.05	-10.1	0.00402	.	.	.	.	.	T	0.30448	0.0765	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39742	-0.9599	4	.	.	.	-34.41	0.1912	0.00134	0.2752:0.1684:0.22:0.3364	.	.	.	.	P	120	.	.	R	-	2	0	CABLES2	60401377	0.000000	0.05858	0.020000	0.16555	0.052000	0.14988	-2.225000	0.01212	-2.475000	0.00527	-1.774000	0.00658	CGT	.	.	.	none		0.657	CABLES2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080027.2	XM_037265		G	60967982	C	G	60967982	2	3	197	1	0	0	0	0	0	0	0	1	2532	523	19	4		4	CABLES2	20	60967982	Silent	SNP	C	TCGA-HE-A5NH-01A-11D-A26P-10	24126012	60967982	2057538	77	11885											
DGCR8	54487	hgsc.bcm.edu	37	chr22	20077782	20077782	+	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	gtgcaaagatgaatccgttgGtgagtttttgaaggactctt	10	14	12	5	1	1	4	0	3	1	1	2	5	2	5	1	2	1	3	1	2	3	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr22:20077782G>C	ENST00000351989.3	+	5	1735		c.e5+1		DGCR8_ENST00000407755.1_Splice_Site|DGCR8_ENST00000383024.2_Splice_Site	NM_022720.6	NP_073557.3	Q8WYQ5	DGCR8_HUMAN	DGCR8 microprocessor complex subunit						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)					GAATCCGTTGGTGAGTTTTTG	0.532																																					.		Atlas-SNP	.											.	DGCR8	53	.	0			c.1306+1G>C						PASS	.						34	41	38					22																	20077782		2198	4297	6495	SO:0001630	splice_region_variant	54487	exon5			CCGTTGGTGAGTT	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.1306+1G>C	chr22.hg19:g.20077782G>C		36.0	0.0	.		57.0	25.0	.	NM_001190326	B2R8G1|Q6DCB2|Q6MZE9|Q6Y2L0|Q96G39|Q96GP8|Q9H6L8|Q9H6T7|Q9NRW2	Splice_Site	SNP	ENST00000351989.3	hg19	CCDS13773.1	.	.	.	.	.	.	.	.	.	.	G	12.65	2.002878	0.35320	.	.	ENSG00000128191	ENST00000351989;ENST00000383024;ENST00000407755	.	.	.	4.75	4.75	0.60458	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.878	0.88830	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DGCR8	18457782	1.000000	0.71417	1.000000	0.80357	0.214000	0.24535	9.225000	0.95219	2.618000	0.88619	0.467000	0.42956	.	.	.	.	none		0.532	DGCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318654.1		Intron	C	20077782	G	C	20077782	5	2	197	1	0	0	0	0	0	0	1	0	4466	1275	44	4	1321	4	DGCR8	22	20077782	Splice_Site	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10		20077782	31226784	78	11886											
CELSR1	9620	hgsc.bcm.edu	37	chr22	46931730	46931730	+	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	ttctcgtcctccacctcgatGtacacggtggccgtggcact	5	11	10	15	4	1	0	0	0	1	0	5	1	3	0	4	3	1	2	4	3	1	2			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chr22:46931730G>A	ENST00000262738.3	-	1	1337	c.1338C>T	c.(1336-1338)taC>taT	p.Y446Y	CELSR1_ENST00000395964.1_Silent_p.Y446Y|CELSR1_ENST00000497509.1_5'Flank	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	446	Cadherin 2. {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)		CCACCTCGATGTACACGGTGG	0.672																																					p.Y446Y		Atlas-SNP	.											.	CELSR1	242	.	0			c.C1338T						PASS	.						64	39	47					22																	46931730		2198	4295	6493	SO:0001819	synonymous_variant	9620	exon1			CTCGATGTACACG	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.1338C>T	chr22.hg19:g.46931730G>A		29.0	0.0	.		28.0	9.0	.	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	hg19	CCDS14076.1																																																																																			.	.	.	none		0.672	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		A	46931730	G	A	46931730	2	1	197	1	0	0	0	0	0	0	0	1	3223	1372	48	2		2	CELSR1	22	46931730	Silent	SNP	G	TCGA-HE-A5NH-01A-11D-A26P-10	26853948	46931730	4372836	79	11887											
ATP11C	286410	hgsc.bcm.edu	37	chrX	138880882	138880882	+	Missense_Mutation	SNP	A	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	gcgtagctcctttcagcaagAgattttcaggtcccaaagac	11	10	9	11	1	2	2	2	0	0	2	4	3	4	2	2	1	2	3	2	1	3	4			TCGA-HE-A5NH-01A-11D-A26P-10	TCGA-HE-A5NH-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	33b7e799-ad10-498f-9948-8ce433311539	10fb6a4b-3cb8-484e-abfd-0987cdecb32e	g.chrX:138880882A>C	ENST00000327569.3	-	9	838	c.740T>G	c.(739-741)cTc>cGc	p.L247R	ATP11C_ENST00000460773.1_5'Flank|ATP11C_ENST00000359686.2_Missense_Mutation_p.L247R|ATP11C_ENST00000370557.1_Missense_Mutation_p.L244R|ATP11C_ENST00000370543.1_Missense_Mutation_p.L247R|ATP11C_ENST00000361648.2_Missense_Mutation_p.L247R	NM_173694.4	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C	247					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|positive regulation of B cell differentiation (GO:0045579)|pre-B cell differentiation (GO:0002329)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(31)|ovary(5)|prostate(1)|skin(3)	75	Acute lymphoblastic leukemia(192;0.000127)					TTTCAGCAAGAGATTTTCAGG	0.368																																					p.L247R		Atlas-SNP	.											.	ATP11C	319	.	0			c.T740G						PASS	.						61	56	58					X																	138880882		2203	4300	6503	SO:0001583	missense	286410	exon9			AGCAAGAGATTTT	AJ580094	CCDS14668.1, CCDS35410.1	Xq27.1	2011-06-09	2007-09-19		ENSG00000101974	ENSG00000101974		"ATPases / P-type"	13554	protein-coding gene	gene with protein product		300516	"ATPase, Class VI, type 11C"			11015572	Standard	NM_173694		Approved	ATPIG, ATPIQ	uc004faz.3	Q8NB49	OTTHUMG00000022538	ENST00000327569.3:c.740T>G	chrX.hg19:g.138880882A>C	ENSP00000332756:p.Leu247Arg	56.0	0.0	.		59.0	49.0	.	NM_001010986	Q5JT69|Q5JT70|Q5JT71|Q5JT72|Q5JT73|Q6ZND5|Q6ZU50|Q6ZUP7|Q70IJ9|Q70IK0|Q8WX24	Missense_Mutation	SNP	ENST00000327569.3	hg19	CCDS14668.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.355898	0.82243	.	.	ENSG00000101974	ENST00000370557;ENST00000361648;ENST00000327569;ENST00000370543;ENST00000359686	D;D;D;D;D	0.90900	-2.75;-2.75;-2.75;-2.75;-2.75	5.62	5.62	0.85841	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	D	0.96911	0.8991	H	0.96748	3.875	0.54753	D	0.999986	D;D	0.89917	1.0;1.0	D;D	0.85130	0.994;0.997	D	0.98001	1.0360	10	0.87932	D	0	.	13.8743	0.63643	1.0:0.0:0.0:0.0	.	247;247	Q8NB49-3;Q8NB49	.;AT11C_HUMAN	R	244;247;247;247;247	ENSP00000359588:L244R;ENSP00000355165:L247R;ENSP00000332756:L247R;ENSP00000359574:L247R;ENSP00000352715:L247R	ENSP00000332756:L247R	L	-	2	0	ATP11C	138708548	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	1.873000	0.54277	0.481000	0.45027	CTC	.	.	.	none		0.368	ATP11C-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354945.1	NM_173694		C	138880882	A	C	138880882	3	2	197	1	0	0	0	0	1	0	0	0	1121	304	11	5	2809	5	ATP11C	23	138880882	Missense_Mutation	SNP	A	TCGA-HE-A5NH-01A-11D-A26P-10		138880882	16389678	80	11888											
RERE	473	hgsc.bcm.edu	37	chr1	8422784	8422784	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctgctttactgtcattgcTggaggtactggcagcgctgg	5	13	13	10	1	2	0	1	0	1	0	2	1	2	1	0	4	5	5	0	4	2	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr1:8422784T>C	ENST00000337907.3	-	17	2495	c.1861A>G	c.(1861-1863)Agc>Ggc	p.S621G	RERE_ENST00000476556.1_Missense_Mutation_p.S67G|RERE_ENST00000400907.2_Intron|RERE_ENST00000400908.2_Missense_Mutation_p.S621G|RERE_ENST00000377464.1_Missense_Mutation_p.S353G	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	621					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)		CTGTCATTGCTGGAGGTACTG	0.577																																					p.S621G		Atlas-SNP	.											.	RERE	129	.	0			c.A1861G						PASS	.						137	114	122					1																	8422784		2203	4300	6503	SO:0001583	missense	473	exon17			CATTGCTGGAGGT	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.1861A>G	chr1.hg19:g.8422784T>C	ENSP00000338629:p.Ser621Gly	233.0	0.0	.		201.0	70.0	.	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Missense_Mutation	SNP	ENST00000337907.3	hg19	CCDS95.1	.	.	.	.	.	.	.	.	.	.	T	27.5	4.838657	0.91117	.	.	ENSG00000142599	ENST00000337907;ENST00000377464;ENST00000476556;ENST00000400908;ENST00000505225	T;T;T;T	0.64260	-0.09;3.35;1.89;-0.09	5.7	5.7	0.88788	.	.	.	.	.	T	0.77226	0.4099	M	0.67953	2.075	0.80722	D	1	D;D	0.63046	0.992;0.979	D;D	0.76071	0.987;0.982	T	0.78347	-0.2239	9	0.52906	T	0.07	-23.6318	15.138	0.72583	0.0:0.0:0.0:1.0	.	353;621	B1AKN3;Q9P2R6	.;RERE_HUMAN	G	621;353;67;621;41	ENSP00000338629:S621G;ENSP00000366684:S353G;ENSP00000422246:S67G;ENSP00000383700:S621G	ENSP00000338629:S621G	S	-	1	0	RERE	8345371	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.644000	0.83416	2.158000	0.67659	0.460000	0.39030	AGC	.	.	.	none		0.577	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1			C	8422784	T	C	8422784	3	2	198	1	0	0	0	0	1	0	0	0	13244	1580	55	3	2871	3	RERE	1	8422784	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10		8422784	240827837	1	11889											
MFN2	9927	hgsc.bcm.edu	37	chr1	12052666	12052667	+	Frame_Shift_Del	DEL	AC	AC	-																															cacagaagaacaggttctggAcgtcaaaggttacctatcca																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr1:12052666_12052667delAC	ENST00000235329.5	+	4	552_553	c.230_231delAC	c.(229-231)gacfs	p.D77fs	MFN2_ENST00000444836.1_Frame_Shift_Del_p.D77fs|MFN2_ENST00000497302.1_3'UTR	NM_014874.3	NP_055689.1	O95140	MFN2_HUMAN	mitofusin 2	77					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)		CAGGTTCTGGACGTCAAAGGTT	0.525																																					p.77_77del		Atlas-Indel,Pindel	.											.	MFN2	83	.	0			c.229_230del						PASS	.																																			SO:0001589	frameshift_variant	9927	exon4			.	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.230_231delAC	chr1.hg19:g.12052666_12052667delAC	ENSP00000235329:p.Asp77fs	472.0	0.0	0		347.0	129.0	0.371758	NM_014874	A8K1B3|O95572|Q5JXC3|Q5JXC4|Q9H131|Q9NSX8	Frame_Shift_Del	DEL	ENST00000235329.5	hg19	CCDS30587.1																																																																																			.	.	.	none		0.525	MFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006859.2	NM_014874		-	12052667	AC	-	12052666	7	5	198	1	0	1	0	1	0	0	0	0	9531	275	10	0	236	0	MFN2	1	12052666	Frame_Shift_Del	DEL	AC	TCGA-HE-A5NI-01A-11D-A26P-10	3629882	12052666	237197955	2	11890											
SPEN	23013	hgsc.bcm.edu	37	chr1	16260463	16260463	+	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	gaggccccgcccccgccagtTgactctaaaaagcctttaga	10	7	9	15	2	1	2	0	1	1	1	1	3	1	2	6	1	1	1	6	1	4	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr1:16260463T>G	ENST00000375759.3	+	11	7932	c.7728T>G	c.(7726-7728)gtT>gtG	p.V2576V		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	2576	RID.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			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)		CCCCGCCAGTTGACTCTAAAA	0.527																																					p.V2576V		Atlas-SNP	.											.	SPEN	374	.	0			c.T7728G						PASS	.						72	83	79					1																	16260463		2203	4300	6503	SO:0001819	synonymous_variant	23013	exon11			GCCAGTTGACTCT		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.7728T>G	chr1.hg19:g.16260463T>G		42.0	0.0	.		25.0	10.0	.	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Silent	SNP	ENST00000375759.3	hg19	CCDS164.1																																																																																			.	.	.	none		0.527	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		G	16260463	T	G	16260463	2	3	198	1	0	0	0	0	0	0	0	1	15050	1799	63	5		5	SPEN	1	16260463	Silent	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	4207797	16260463	232990158	3	11891											
AKR7A3	22977	hgsc.bcm.edu	37	chr1	19611546	19611546	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggcatagaacctcagtccAaagtgcctgaggcaggggaa	14	5	13	9	0	1	2	1	1	0	1	2	3	2	3	3	4	2	2	3	4	5	1			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr1:19611546A>G	ENST00000361640.4	-	4	1110	c.570T>C	c.(568-570)ttT>ttC	p.F190F		NM_012067.2	NP_036199.2	O95154	ARK73_HUMAN	aldo-keto reductase family 7, member A3 (aflatoxin aldehyde reductase)	190					cellular aldehyde metabolic process (GO:0006081)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldo-keto reductase (NADP) activity (GO:0004033)|electron carrier activity (GO:0009055)			NS(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|ovary(1)|stomach(2)	13		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;1.78e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00276)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		ACCTCAGTCCAAAGTGCCTGA	0.612																																					p.F190F		Atlas-SNP	.											.	AKR7A3	30	.	0			c.T570C						PASS	.						94	96	95					1																	19611546		2199	4300	6499	SO:0001819	synonymous_variant	22977	exon4			CAGTCCAAAGTGC	AF040639	CCDS193.1	1p36.13	2008-05-14			ENSG00000162482	ENSG00000162482		"Aldo-keto reductases"	390	protein-coding gene	gene with protein product		608477				10383892	Standard	NM_012067		Approved		uc001bbv.1	O95154	OTTHUMG00000002523	ENST00000361640.4:c.570T>C	chr1.hg19:g.19611546A>G		338.0	0.0	.		296.0	116.0	.	NM_012067	Q86SR4|Q8IVN6|Q8N5V6|Q8TAX1|Q9NUC3	Silent	SNP	ENST00000361640.4	hg19	CCDS193.1																																																																																			.	.	.	none		0.612	AKR7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007166.1	NM_012067		G	19611546	A	G	19611546	2	3	198	1	0	0	0	0	0	0	0	1	476	127	5	3		3	AKR7A3	1	19611546	Silent	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10	3351083	19611546	229639075	4	11892											
ZMYM1	79830	hgsc.bcm.edu	37	chr1	35569920	35569920	+	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	attttaaatccaaaggatgtGattagtgtccagctggaaga	14	12	10	5	0	0	2	0	1	0	1	2	4	2	4	2	2	1	1	2	2	5	3			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr1:35569920G>C	ENST00000373330.1	+	6	618	c.444G>C	c.(442-444)gtG>gtC	p.V148V	ZMYM1_ENST00000359858.4_Silent_p.V148V|ZMYM1_ENST00000373329.1_3'UTR			Q5SVZ6	ZMYM1_HUMAN	zinc finger, MYM-type 1	148						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(8)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				CAAAGGATGTGATTAGTGTCC	0.308																																					p.V148V		Atlas-SNP	.											.	ZMYM1	86	.	0			c.G444C						PASS	.						41	40	41					1																	35569920		1830	4087	5917	SO:0001819	synonymous_variant	79830	exon5			GGATGTGATTAGT	AK096206	CCDS41302.1	1p34.3	2008-05-02	2005-09-12		ENSG00000197056	ENSG00000197056		"Zinc fingers, MYM type"	26253	protein-coding gene	gene with protein product			"zinc finger, MYM domain containing 1"			12477932	Standard	XM_005271216		Approved	FLJ23151, MYM	uc001bym.3	Q5SVZ6	OTTHUMG00000004374	ENST00000373330.1:c.444G>C	chr1.hg19:g.35569920G>C		96.0	0.0	.		78.0	31.0	.	NM_024772	D3DPR7|Q7Z3Q4	Silent	SNP	ENST00000373330.1	hg19	CCDS41302.1																																																																																			.	.	.	none		0.308	ZMYM1-001	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012705.1	NM_024772		C	35569920	G	C	35569920	2	2	198	1	0	0	0	0	0	0	0	1	17711	1277	45	4		4	ZMYM1	1	35569920	Silent	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	15958374	35569920	213680701	5	11893											
FAM46C	54855	hgsc.bcm.edu	37	chr1	118165851	118165851	+	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	gttcccttctgaacttcctgCcagagggtgtgaacaagctc	8	11	10	12	0	1	3	0	2	1	1	4	3	3	3	3	1	4	2	3	1	3	3			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr1:118165851C>G	ENST00000369448.3	+	2	608	c.361C>G	c.(361-363)Cca>Gca	p.P121A		NM_017709.3	NP_060179.2	Q5VWP2	FA46C_HUMAN	family with sequence similarity 46, member C	121										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)		GAACTTCCTGCCAGAGGGTGT	0.502			"Mis, F, O"		MM					Multiple Myeloma(3;1.13e-06)																											p.P121A		Atlas-SNP	.		Rec	yes		1	1p12	54855	"family with sequence similarity 46, member C"		L	.	FAM46C	25	.	0			c.C361G						PASS	.						104	106	105					1																	118165851		2203	4300	6503	SO:0001583	missense	54855	exon2			TTCCTGCCAGAGG	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.361C>G	chr1.hg19:g.118165851C>G	ENSP00000358458:p.Pro121Ala	173.0	0.0	.		146.0	64.0	.	NM_017709	A3KMG2|Q8NE25|Q9NXK0	Missense_Mutation	SNP	ENST00000369448.3	hg19	CCDS896.1	.	.	.	.	.	.	.	.	.	.	C	19.71	3.877619	0.72294	.	.	ENSG00000183508	ENST00000369448	T	0.46819	0.86	5.75	5.75	0.90469	Domain of unknown function DUF1693 (1);	0.000000	0.64402	D	0.000002	T	0.70456	0.3226	M	0.87971	2.92	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.74850	-0.3524	10	0.72032	D	0.01	-31.2719	18.9258	0.92544	0.0:1.0:0.0:0.0	.	121	Q5VWP2	FA46C_HUMAN	A	121	ENSP00000358458:P121A	ENSP00000358458:P121A	P	+	1	0	FAM46C	117967374	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	7.818000	0.86416	2.711000	0.92665	0.655000	0.94253	CCA	.	.	.	none		0.502	FAM46C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038424.1	NM_017709		G	118165851	C	G	118165851	3	3	198	1	0	0	0	0	1	0	0	0	5574	739	26	4	363	4	FAM46C	1	118165851	Missense_Mutation	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	82595931	118165851	131084770	6	11894											
ZC3H11A	9877	hgsc.bcm.edu	37	chr1	203819761	203819761	+	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	attgccgctgtgaagccactCagctccagcagtgtcctaca	9	9	9	14	1	1	1	1	1	0	0	3	1	3	1	4	0	5	3	4	0	2	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr1:203819761C>T	ENST00000545588.1	+	15	5885	c.2058C>T	c.(2056-2058)ctC>ctT	p.L686L	ZC3H11A_ENST00000332127.4_Silent_p.L686L|ZC3H11A_ENST00000367214.1_Silent_p.L686L|ZC3H11A_ENST00000367210.1_Silent_p.L686L|ZC3H11A_ENST00000367212.3_Silent_p.L686L	NM_001271675.1	NP_001258604.1	O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A	686					poly(A)+ mRNA export from nucleus (GO:0016973)		metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)			TGAAGCCACTCAGCTCCAGCA	0.502																																					p.L686L		Atlas-SNP	.											.	ZC3H11A	71	.	0			c.C2058T						PASS	.						80	80	80					1																	203819761		2203	4300	6503	SO:0001819	synonymous_variant	9877	exon18			GCCACTCAGCTCC		CCDS30978.1	1q32.1	2012-07-05	2005-06-02	2005-06-02	ENSG00000058673	ENSG00000058673		"Zinc fingers, CCCH-type domain containing"	29093	protein-coding gene	gene with protein product		613513	"zinc finger CCCH-type domain containing 11A"	ZC3HDC11A		9734811	Standard	NM_014827		Approved	KIAA0663	uc001hac.3	O75152	OTTHUMG00000035909	ENST00000545588.1:c.2058C>T	chr1.hg19:g.203819761C>T		184.0	0.0	.		142.0	62.0	.	NM_014827	Q6AHY4|Q6AHY9|Q6AW79|Q6AWA1|Q6PJK4|Q86XZ7	Silent	SNP	ENST00000545588.1	hg19	CCDS30978.1																																																																																			.	.	.	none		0.502	ZC3H11A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087471.3	NM_014827		T	203819761	C	T	203819761	2	4	198	1	0	0	0	0	0	0	0	1	17572	813	29	2		2	ZC3H11A	1	203819761	Silent	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	85653910	203819761	45430860	7	11895											
NUAK2	81788	hgsc.bcm.edu	37	chr1	205272646	205272646	+	Frame_Shift_Del	DEL	G	G	-																															cacctcctggcagtctgtcaGggaaaagcagctgtccccca																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr1:205272646delG	ENST00000367157.3	-	7	1945	c.1819delC	c.(1819-1821)ctgfs	p.L607fs		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)			CAGTCTGTCAGGGAAAAGCAG	0.642																																					p.L607fs		Atlas-Indel,Pindel	.											.	NUAK2	107	.	0			c.1820delT						PASS	.						55	53	54					1																	205272646		2203	4300	6503	SO:0001589	frameshift_variant	81788	exon7			.	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.1819delC	chr1.hg19:g.205272646delG	ENSP00000356125:p.Leu607fs	106.0	0.0	0		85.0	32.0	0.376471	NM_030952		Frame_Shift_Del	DEL	ENST00000367157.3	hg19	CCDS1453.1																																																																																			.	.	.	none		0.642	NUAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090390.1	NM_030952		-	205272646	G	-	205272646	7	5	198	1	0	1	0	1	0	0	0	0	10720	991	35	0	71	0	NUAK2	1	205272646	Frame_Shift_Del	DEL	G	TCGA-HE-A5NI-01A-11D-A26P-10	1452885	205272646	43977975	8	11896											
PLXNA2	5362	hgsc.bcm.edu	37	chr1	208213052	208213052	+	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	cgtgatggcatcaatggggcCcttctccatctgctgcttga	6	12	11	12	1	3	2	1	2	2	0	4	2	3	2	2	3	2	3	2	3	1	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr1:208213052C>T	ENST00000367033.3	-	24	5171	c.4414G>A	c.(4414-4416)Ggc>Agc	p.G1472S		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	1472					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)		TCAATGGGGCCCTTCTCCATC	0.622																																					p.G1472S		Atlas-SNP	.											.	PLXNA2	178	.	0			c.G4414A						PASS	.						96	88	91					1																	208213052		2203	4300	6503	SO:0001583	missense	5362	exon24			TGGGGCCCTTCTC	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.4414G>A	chr1.hg19:g.208213052C>T	ENSP00000356000:p.Gly1472Ser	140.0	0.0	.		111.0	31.0	.	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	hg19	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	C	36	5.938808	0.97122	.	.	ENSG00000076356	ENST00000367033	T	0.35789	1.29	5.51	5.51	0.81932	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.71745	0.3376	M	0.93678	3.445	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79752	-0.1671	10	0.87932	D	0	.	19.4545	0.94882	0.0:1.0:0.0:0.0	.	1472	O75051	PLXA2_HUMAN	S	1472	ENSP00000356000:G1472S	ENSP00000356000:G1472S	G	-	1	0	PLXNA2	206279675	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.538000	0.82048	2.590000	0.87494	0.650000	0.86243	GGC	.	.	.	none		0.622	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		T	208213052	C	T	208213052	3	4	198	1	0	0	0	0	1	0	0	0	12127	623	22	2	1306	2	PLXNA2	1	208213052	Missense_Mutation	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	2940406	208213052	41037569	9	11897											
CAPN2	824	hgsc.bcm.edu	37	chr1	223900487	223900487	+	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	ccgggacgctcttccaggacCcgtccttcccggccatcccc	4	7	9	21	4	1	0	0	0	1	0	5	2	5	2	8	3	0	1	8	3	0	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr1:223900487C>A	ENST00000295006.5	+	1	454	c.145C>A	c.(145-147)Ccg>Acg	p.P49T	CAPN2_ENST00000433674.2_Intron	NM_001748.4	NP_001739	P17655	CAN2_HUMAN	calpain 2, (m/II) large subunit	49	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				blastocyst development (GO:0001824)|cellular response to amino acid stimulus (GO:0071230)|myoblast fusion (GO:0007520)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of cytoskeleton organization (GO:0051493)|response to hypoxia (GO:0001666)	chromatin (GO:0000785)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|cytoskeletal protein binding (GO:0008092)			breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|stomach(3)	29				GBM - Glioblastoma multiforme(131;0.109)		CTTCCAGGACCCGTCCTTCCC	0.672																																					p.P49T		Atlas-SNP	.											.	CAPN2	69	.	0			c.C145A						PASS	.						24	24	24					1																	223900487		2201	4297	6498	SO:0001583	missense	824	exon1			CAGGACCCGTCCT	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.145C>A	chr1.hg19:g.223900487C>A	ENSP00000295006:p.Pro49Thr	132.0	0.0	.		71.0	30.0	.	NM_001748	A6NDG7|B7ZA96|E7ES58|Q16738|Q6PJT3|Q8WU26|Q9HBB1	Missense_Mutation	SNP	ENST00000295006.5	hg19	CCDS31035.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.935915	0.52972	.	.	ENSG00000162909	ENST00000295006;ENST00000366869	T	0.49432	0.78	3.88	3.88	0.44766	Peptidase C2, calpain, catalytic domain (3);	0.526246	0.19489	U	0.113025	T	0.54046	0.1834	M	0.81112	2.525	0.24034	N	0.996105	B	0.34214	0.442	B	0.39094	0.29	T	0.54556	-0.8276	10	0.54805	T	0.06	.	12.5002	0.55952	0.0:0.6877:0.3123:0.0	.	49	P17655	CAN2_HUMAN	T	49;78	ENSP00000295006:P49T	ENSP00000295006:P49T	P	+	1	0	CAPN2	221967110	0.000000	0.05858	0.913000	0.36048	0.489000	0.33432	0.484000	0.22308	1.862000	0.54008	0.491000	0.48974	CCG	.	.	.	none		0.672	CAPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090973.1	NM_001748		A	223900487	C	A	223900487	3	1	198	1	0	0	0	0	1	0	0	0	2629	623	22	4	154	4	CAPN2	1	223900487	Missense_Mutation	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	15687435	223900487	25350134	10	11898											
ASXL2	55252	hgsc.bcm.edu	37	chr2	25972919	25972919	+	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	gctgtggtgagatggttcttCtcagattcctgttcagcaga	7	14	12	8	0	3	3	2	1	2	3	5	4	4	3	1	2	1	4	1	2	0	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr2:25972919C>T	ENST00000435504.4	-	12	1799	c.1506G>A	c.(1504-1506)gaG>gaA	p.E502E	ASXL2_ENST00000336112.4_Silent_p.E474E|ASXL2_ENST00000404843.1_Silent_p.E242E|ASXL2_ENST00000272341.4_Silent_p.E242E			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	502					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)					GATGGTTCTTCTCAGATTCCT	0.443																																					p.E502E		Atlas-SNP	.											.	ASXL2	217	.	0			c.G1506A						PASS	.						148	136	140					2																	25972919		1903	4132	6035	SO:0001819	synonymous_variant	55252	exon11			GTTCTTCTCAGAT			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.1506G>A	chr2.hg19:g.25972919C>T		44.0	0.0	.		57.0	29.0	.	NM_018263	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Silent	SNP	ENST00000435504.4	hg19																																																																																				.	.	.	none		0.443	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263		T	25972919	C	T	25972919	2	4	198	1	0	0	0	0	0	0	0	1	1067	912	32	2		2	ASXL2	2	25972919	Silent	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10		25972919	217226454	11	11899											
HADHA	3030	hgsc.bcm.edu	37	chr2	26427053	26427053	+	Missense_Mutation	SNP	A	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	cccatcagccctgcaccaagAatagccagatgcctgcaagg	12	5	9	15	0	1	2	1	0	0	2	1	2	1	2	5	1	5	2	5	1	4	1			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr2:26427053A>C	ENST00000380649.3	-	12	1227	c.1098T>G	c.(1096-1098)atT>atG	p.I366M		NM_000182.4	NP_000173.2	P40939	ECHA_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit	366					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acetyltransferase activity (GO:0003985)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)			autonomic_ganglia(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(4)|skin(1)	30	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTGCACCAAGAATAGCCAGAT	0.468																																					p.I366M		Atlas-SNP	.											.	HADHA	87	.	0			c.T1098G						PASS	.						223	216	219					2																	26427053		2203	4300	6503	SO:0001583	missense	3030	exon12			ACCAAGAATAGCC	D16480	CCDS1721.1	2p23	2014-09-17	2010-04-30		ENSG00000084754	ENSG00000084754	1.1.1.211, 4.2.1.17		4801	protein-coding gene	gene with protein product	"gastrin-binding protein", "long-chain-3-hydroxyacyl-CoA dehydrogenase", "long-chain 2-enoyl-CoA hydratase", "mitochondrial trifunctional protein, alpha subunit"	600890	"hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit"			9605857, 7918661	Standard	NM_000182		Approved	GBP, LCEH, LCHAD, MTPA	uc002rgy.3	P40939	OTTHUMG00000096979	ENST00000380649.3:c.1098T>G	chr2.hg19:g.26427053A>C	ENSP00000370023:p.Ile366Met	125.0	0.0	.		131.0	36.0	.	NM_000182	B2R7L4|B4DYP2|Q16679|Q53T69|Q53TA2|Q96GT7|Q9UQC5	Missense_Mutation	SNP	ENST00000380649.3	hg19	CCDS1721.1	.	.	.	.	.	.	.	.	.	.	A	17.98	3.521115	0.64747	.	.	ENSG00000084754	ENST00000380649	T	0.81163	-1.46	5.0	3.85	0.44370	3-hydroxyacyl-CoA dehydrogenase, NAD binding (1);NAD(P)-binding domain (1);	0.398782	0.28834	N	0.013995	D	0.83454	0.5258	M	0.65677	2.01	0.80722	D	1	P;P	0.40731	0.728;0.728	P;P	0.57057	0.812;0.812	T	0.81743	-0.0793	10	0.66056	D	0.02	-14.6089	1.9477	0.03360	0.5809:0.166:0.0927:0.1603	.	366;366	E9KL44;P40939	.;ECHA_HUMAN	M	366	ENSP00000370023:I366M	ENSP00000370023:I366M	I	-	3	3	HADHA	26280557	0.998000	0.40836	0.972000	0.41901	0.988000	0.76386	0.641000	0.24720	0.867000	0.35654	0.533000	0.62120	ATT	.	.	.	none		0.468	HADHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214051.1	NM_000182		C	26427053	A	C	26427053	3	2	198	1	0	0	0	0	1	0	0	0	6950	242	9	5	1229	5	HADHA	2	26427053	Missense_Mutation	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10	454134	26427053	216772320	12	11900											
TET3	200424	hgsc.bcm.edu	37	chr2	74320721	74320721	+	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	gaaggacggcccttcgcgggGgtcacggcctgcatggactt	6	7	16	12	4	1	0	1	0	0	0	2	3	1	2	2	6	1	1	2	6	1	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr2:74320721G>T	ENST00000409262.3	+	7	2790	c.2790G>T	c.(2788-2790)ggG>ggT	p.G930G		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3	930					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						CCTTCGCGGGGGTCACGGCCT	0.597																																					p.G930G		Atlas-SNP	.											.	TET3	101	.	0			c.G2790T						PASS	.						71	76	74					2																	74320721		2052	4226	6278	SO:0001819	synonymous_variant	200424	exon7			CGCGGGGGTCACG		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.2790G>T	chr2.hg19:g.74320721G>T		159.0	0.0	.		152.0	46.0	.	NM_144993	A6NEI3|Q86Z24|Q8TBM9	Silent	SNP	ENST00000409262.3	hg19	CCDS46339.1																																																																																			.	.	.	none		0.597	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328141.4			T	74320721	G	T	74320721	2	4	198	1	0	0	0	0	0	0	0	1	15783	1219	43	4		4	TET3	2	74320721	Silent	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	47893668	74320721	168878652	13	11901											
MAP4K4	9448	hgsc.bcm.edu	37	chr2	102493592	102493592	+	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	gtacttgagggcttgaatgtCttggtgacaatatctggtga	9	14	13	5	0	2	4	0	4	2	0	2	4	2	4	0	3	1	2	0	3	4	5	rs575144210		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr2:102493592C>G	ENST00000347699.4	+	24	2934	c.2934C>G	c.(2932-2934)gtC>gtG	p.V978V	MAP4K4_ENST00000324219.4_Silent_p.V1059V|MAP4K4_ENST00000350878.4_Silent_p.V1018V|MAP4K4_ENST00000302217.5_Silent_p.V781V|MAP4K4_ENST00000413150.2_Silent_p.V893V|MAP4K4_ENST00000456652.1_Silent_p.V777V|MAP4K4_ENST00000350198.4_Silent_p.V897V|MAP4K4_ENST00000425019.1_Silent_p.V1011V	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4	978	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.|Mediates interaction with RAP2A.				intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of JNK cascade (GO:0046328)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						GCTTGAATGTCTTGGTGACAA	0.418													C|||	1	0.000199681	0	0	5008	,	,		22716	0.001		0	False		,,,				2504	0				p.V1012V		Atlas-SNP	.											.	MAP4K4	111	.	0			c.C3036G						PASS	.						180	173	175					2																	102493592		1970	4164	6134	SO:0001819	synonymous_variant	9448	exon25			GAATGTCTTGGTG	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.2934C>G	chr2.hg19:g.102493592C>G		311.0	0.0	.		420.0	124.0	.	NM_145686	O75172|Q9NST7	Silent	SNP	ENST00000347699.4	hg19	CCDS56130.1	.	.	.	.	.	.	.	.	.	.	C	8.328	0.825853	0.16749	.	.	ENSG00000071054	ENST00000421882	.	.	.	5.48	1.44	0.22558	.	.	.	.	.	T	0.53965	0.1829	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43972	-0.9358	4	.	.	.	.	6.5872	0.22626	0.1267:0.6675:0.0:0.2057	.	.	.	.	V	795	.	.	L	+	1	0	MAP4K4	101860024	1.000000	0.71417	0.986000	0.45419	0.981000	0.71138	1.591000	0.36665	0.368000	0.24481	-0.136000	0.14681	CTT	.	.	.	none		0.418	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834		G	102493592	C	G	102493592	2	3	198	1	0	0	0	0	0	0	0	1	9269	900	32	4		4	MAP4K4	2	102493592	Silent	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	28172871	102493592	140705781	14	11902											
CCDC74B	91409	hgsc.bcm.edu	37	chr2	130899739	130899739	+	Missense_Mutation	SNP	T	T	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	ggacttgacagactggaagcTtgacgtggagaggctgtctg	9	9	16	7	1	1	4	0	2	1	2	1	7	1	6	0	4	1	2	0	4	1	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr2:130899739T>G	ENST00000310463.6	-	3	648	c.511A>C	c.(511-513)Agc>Cgc	p.S171R	CCDC74B_ENST00000409943.3_Missense_Mutation_p.S105R|CCDC74B_ENST00000392984.3_Missense_Mutation_p.S273R|MED15P9_ENST00000427638.1_RNA|CCDC74B_ENST00000409128.1_Missense_Mutation_p.S147R	NM_207310.2	NP_997193.1	Q96LY2	CC74B_HUMAN	coiled-coil domain containing 74B	171										endometrium(2)|large_intestine(1)|lung(3)	6	Colorectal(110;0.1)					GACTGGAAGCTTGACGTGGAG	0.647																																					p.S171R		Atlas-SNP	.											.	CCDC74B	27	.	0			c.A511C						PASS	.						98	73	81					2																	130899739		2201	4298	6499	SO:0001583	missense	91409	exon3			GGAAGCTTGACGT		CCDS2155.1, CCDS58726.1	2q21.1	2006-11-29		2006-02-16	ENSG00000152076	ENSG00000152076			25267	protein-coding gene	gene with protein product							Standard	NM_001258307		Approved	DKFZp434E2321	uc002tqn.2	Q96LY2	OTTHUMG00000131629	ENST00000310463.6:c.511A>C	chr2.hg19:g.130899739T>G	ENSP00000308873:p.Ser171Arg	383.0	1.0	.		433.0	205.0	.	NM_207310	Q6NW18	Missense_Mutation	SNP	ENST00000310463.6	hg19	CCDS2155.1	.	.	.	.	.	.	.	.	.	.	.	13.91	2.377052	0.42105	.	.	ENSG00000152076	ENST00000409943;ENST00000310463;ENST00000392984;ENST00000409488;ENST00000409128	T;T;T;T	0.57273	1.77;1.86;1.79;0.41	2.21	2.21	0.28008	.	0.538074	0.15538	U	0.257135	T	0.62134	0.2403	M	0.69823	2.125	0.09310	N	1	D;D;D	0.71674	0.995;0.998;0.991	P;P;P	0.61070	0.763;0.862;0.883	T	0.48822	-0.9001	10	0.42905	T	0.14	-14.6217	6.277	0.20987	0.0:0.0:0.0:1.0	.	273;105;171	E7ESC5;Q96LY2-2;Q96LY2	.;.;CC74B_HUMAN	R	105;171;273;105;147	ENSP00000386294:S105R;ENSP00000308873:S171R;ENSP00000376710:S273R;ENSP00000386644:S147R	ENSP00000308873:S171R	S	-	1	0	CCDC74B	130616209	0.427000	0.25514	0.007000	0.13788	0.018000	0.09664	2.792000	0.47837	1.010000	0.39314	0.248000	0.18094	AGC	.	.	.	none		0.647	CCDC74B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254522.3	NM_207310		G	130899739	T	G	130899739	3	3	198	1	0	0	0	0	1	0	0	0	2850	1609	56	5	655	5	CCDC74B	2	130899739	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	28406147	130899739	112299634	15	11903											
C2orf69	205327	hgsc.bcm.edu	37	chr2	200790075	200790075	+	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	ttatcaaagaaaagtttgaaTgtttggaataaggactccat	16	13	8	4	0	1	2	1	1	0	1	2	4	2	4	1	2	0	2	1	2	7	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr2:200790075T>A	ENST00000319974.5	+	2	807	c.624T>A	c.(622-624)aaT>aaA	p.N208K	C2orf69_ENST00000491721.1_Intron	NM_153689.5	NP_710156.3	Q8N8R5	CB069_HUMAN	chromosome 2 open reading frame 69	208						extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(2)|stomach(1)|urinary_tract(1)	11						AAAGTTTGAATGTTTGGAATA	0.348																																					p.N208K		Atlas-SNP	.											.	C2orf69	17	.	0			c.T624A						PASS	.						52	52	52					2																	200790075		1819	4078	5897	SO:0001583	missense	205327	exon2			TTTGAATGTTTGG		CCDS46482.1	2q33.1	2008-08-08			ENSG00000178074	ENSG00000178074			26799	protein-coding gene	gene with protein product	"hypothetical protein FLJ38973"					12477932	Standard	NM_153689		Approved	FLJ38973	uc010zhb.2	Q8N8R5	OTTHUMG00000154480	ENST00000319974.5:c.624T>A	chr2.hg19:g.200790075T>A	ENSP00000312770:p.Asn208Lys	54.0	0.0	.		46.0	12.0	.	NM_153689	Q8NE30	Missense_Mutation	SNP	ENST00000319974.5	hg19	CCDS46482.1	.	.	.	.	.	.	.	.	.	.	T	0.008	-1.923247	0.00498	.	.	ENSG00000178074	ENST00000319974	.	.	.	5.5	-1.14	0.09741	.	0.634163	0.16276	N	0.221571	T	0.06050	0.0157	N	0.01048	-1.04	0.09310	N	0.999996	B	0.06786	0.001	B	0.08055	0.003	T	0.29518	-1.0009	9	0.05620	T	0.96	-2.3723	1.9048	0.03275	0.1333:0.2218:0.111:0.5339	.	208	Q8N8R5	CB069_HUMAN	K	208	.	ENSP00000312770:N208K	N	+	3	2	C2orf69	200498320	0.999000	0.42202	0.155000	0.22561	0.064000	0.16182	0.773000	0.26661	-0.325000	0.08577	-0.250000	0.11733	AAT	.	.	.	none		0.348	C2orf69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335446.1	NM_153689		A	200790075	T	A	200790075	3	1	198	1	0	0	0	0	1	0	0	0	2190	1461	51	5	630	5	C2orf69	2	200790075	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	69890336	200790075	42409298	16	11904											
CLK1	1195	hgsc.bcm.edu	37	chr2	201721517	201721517	+	Frame_Shift_Del	DEL	G	G	-																															ttaatatctggatttattaaGgtgcgttcatcacgtttctg																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr2:201721517delG	ENST00000321356.4	-	9	1080	c.945delC	c.(943-945)accfs	p.T315fs	CLK1_ENST00000434813.2_Frame_Shift_Del_p.T357fs|CLK1_ENST00000409769.2_Frame_Shift_Del_p.T138fs	NM_004071.3	NP_004062.2	P49759	CLK1_HUMAN	CDC-like kinase 1	315	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						GATTTATTAAGGTGCGTTCAT	0.328																																					p.L358X		Atlas-Indel,Pindel	.											.	CLK1	103	.	0			c.1072delT						PASS	.						163	159	161					2																	201721517		2202	4300	6502	SO:0001589	frameshift_variant	1195	exon9			.	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.945delC	chr2.hg19:g.201721517delG	ENSP00000326830:p.Thr315fs	153.0	0.0	0		164.0	98.0	0.597561	NM_001162407	B4DFW7|Q0P694|Q8N5V8	Frame_Shift_Del	DEL	ENST00000321356.4	hg19	CCDS2331.1																																																																																			.	.	.	none		0.328	CLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256192.2			-	201721517	G	-	201721517	7	5	198	1	0	1	0	1	0	0	0	0	3538	987	35	0	529	0	CLK1	2	201721517	Frame_Shift_Del	DEL	G	TCGA-HE-A5NI-01A-11D-A26P-10	931442	201721517	41477856	17	11905											
ORC2L	4999	hgsc.bcm.edu	37	chr2	201778083	201778083	+	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	ggcccggagtgtcagatcacTattgacgaggaatgcctccc	9	8	12	12	2	2	2	2	1	0	1	3	5	3	4	3	3	1	0	3	3	2	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr2:201778083T>A	ENST00000234296.2	-	17	1831	c.1582A>T	c.(1582-1584)Agt>Tgt	p.S528C		NM_006190.4	NP_006181.1	Q13416	ORC2_HUMAN	origin recognition complex, subunit 2	528					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	condensed chromosome inner kinetochore (GO:0000939)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)|plasma membrane (GO:0005886)	DNA replication origin binding (GO:0003688)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	20						GTCAGATCACTATTGACGAGG	0.428																																					p.S528C		Atlas-SNP	.											.	ORC2	48	.	0			c.A1582T						PASS	.						101	95	97					2																	201778083		2203	4300	6503	SO:0001583	missense	4999	exon17			GATCACTATTGAC		CCDS2334.1	2q33	2010-10-12	2010-10-12	2010-10-12	ENSG00000115942	ENSG00000115942			8488	protein-coding gene	gene with protein product		601182	"origin recognition complex, subunit 2 (yeast homolog)-like", "origin recognition complex, subunit 2-like (yeast)", "origin recognition complex, subunit 2 homolog (yeast)"	ORC2L		8808289	Standard	NM_006190		Approved		uc002uwr.3	Q13416	OTTHUMG00000132783	ENST00000234296.2:c.1582A>T	chr2.hg19:g.201778083T>A	ENSP00000234296:p.Ser528Cys	86.0	0.0	.		76.0	42.0	.	NM_006190	Q13204|Q53TX5	Missense_Mutation	SNP	ENST00000234296.2	hg19	CCDS2334.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.506382	0.85282	.	.	ENSG00000115942	ENST00000234296	T	0.52057	0.68	5.6	5.6	0.85130	.	0.091390	0.85682	D	0.000000	T	0.76190	0.3953	M	0.92219	3.285	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82835	-0.0261	10	0.87932	D	0	-13.9094	15.7889	0.78338	0.0:0.0:0.0:1.0	.	528	Q13416	ORC2_HUMAN	C	528	ENSP00000234296:S528C	ENSP00000234296:S528C	S	-	1	0	ORC2	201486328	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	6.057000	0.71119	2.116000	0.64780	0.482000	0.46254	AGT	.	.	.	none		0.428	ORC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256191.2	NM_006190		A	201778083	T	A	201778083	3	1	198	1	0	0	0	0	1	0	0	0	11269	1522	53	5	159	5	ORC2L	2	201778083	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	56566	201778083	41421290	18	11906											
FN1	2335	hgsc.bcm.edu	37	chr2	216271073	216271073	+	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	gtgacttctgcaaaggtgttCctgctgatgggcagcctctg	6	12	13	10	0	2	2	0	2	2	0	3	2	3	2	2	2	3	4	2	2	1	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr2:216271073C>T	ENST00000359671.1	-	19	3139	c.2874G>A	c.(2872-2874)agG>agA	p.R958R	FN1_ENST00000421182.1_Silent_p.R958R|FN1_ENST00000345488.5_Silent_p.R958R|FN1_ENST00000357867.4_Silent_p.R958R|FN1_ENST00000446046.1_Silent_p.R958R|FN1_ENST00000443816.1_Silent_p.R958R|FN1_ENST00000356005.4_Silent_p.R958R|FN1_ENST00000354785.4_Silent_p.R958R|FN1_ENST00000323926.6_Silent_p.R958R|FN1_ENST00000336916.4_Silent_p.R958R|FN1_ENST00000432072.2_Silent_p.R958R|FN1_ENST00000346544.3_Silent_p.R958R|FN1_ENST00000357009.2_Silent_p.R958R			P02751	FINC_HUMAN	fibronectin 1	958	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316, ECO:0000255|PROSITE-ProRule:PRU00478, ECO:0000255|PROSITE-ProRule:PRU00479}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	CAAAGGTGTTCCTGCTGATGG	0.597																																					p.R958R		Atlas-SNP	.											.	FN1	521	.	0			c.G2874A						PASS	.						63	62	63					2																	216271073		2203	4300	6503	SO:0001819	synonymous_variant	2335	exon19			GGTGTTCCTGCTG		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.2874G>A	chr2.hg19:g.216271073C>T		137.0	0.0	.		144.0	24.0	.	NM_212476	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Silent	SNP	ENST00000359671.1	hg19																																																																																				.	.	.	none		0.597	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		T	216271073	C	T	216271073	2	4	198	1	0	0	0	0	0	0	0	1	5969	854	30	2		2	FN1	2	216271073	Silent	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	14492990	216271073	26928300	19	11907											
TRNT1	51095	hgsc.bcm.edu	37	chr3	3182301	3182309	+	In_Frame_Del	DEL	CAGAGATCT	CAGAGATCT	-																															tggcagaaagatgcggaacgCagagatctcactataaattc																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	CAGAGATCT	CAGAGATCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:3182301_3182309delCAGAGATCT	ENST00000251607.6	+	4	552_560	c.450_458delCAGAGATCT	c.(448-459)cgcagagatctc>cgc	p.RDL151del	TRNT1_ENST00000280591.6_In_Frame_Del_p.RDL151del	NM_182916.2	NP_886552	Q96Q11	TRNT1_HUMAN	tRNA nucleotidyl transferase, CCA-adding, 1	151					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)		ATGCGGAACGCAGAGATCTCACTATAAAT	0.354																																					p.150_153del		Atlas-Indel,Pindel	.											.	TRNT1	34	.	0			c.449_457del						PASS	.																																			SO:0001651	inframe_deletion	51095	exon4			.	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.450_458delCAGAGATCT	chr3.hg19:g.3182301_3182309delCAGAGATCT	ENSP00000251607:p.Arg151_Leu153del	151.0	0.0	0		104.0	24.0	0.230769	NM_182916	A8K2Z6|B7WP13|C9JKA2|Q8ND57|Q9BS97|Q9Y362	In_Frame_Del	DEL	ENST00000251607.6	hg19	CCDS2561.2																																																																																			.	.	.	none		0.354	TRNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337616.1			-	3182309	CAGAGATCT	-	3182301	7	5	198	1	0	1	0	1	0	0	0	0	16585	697	25	0	460	0	TRNT1	3	3182301	In_Frame_Del	DEL	CAGAGATCT	TCGA-HE-A5NI-01A-11D-A26P-10		3182301	194840129	20	11908											
OSBPL10	114884	hgsc.bcm.edu	37	chr3	31705657	31705657	+	Missense_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	ttgcttctcctccaggtgccGcttctgctcggtggctgcgt	1	14	12	14	3	2	0	0	0	2	0	5	0	3	0	3	3	4	4	3	3	0	3	rs375455808		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:31705657G>A	ENST00000396556.2	-	11	2286	c.2164C>T	c.(2164-2166)Cgg>Tgg	p.R722W	OSBPL10_ENST00000438237.2_Missense_Mutation_p.R658W	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	722					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)		TCCAGGTGCCGCTTCTGCTCG	0.607																																					p.R722W		Atlas-SNP	.											.	OSBPL10	160	.	0			c.C2164T						PASS	.	G	TRP/ARG,TRP/ARG	0,4406		0,0,2203	110	100	103		1972,2164	5.2	1	3		103	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	OSBPL10	NM_001174060.1,NM_017784.4	101,101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	658/701,722/765	31705657	1,13005	2203	4300	6503	SO:0001583	missense	114884	exon11			GGTGCCGCTTCTG	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.2164C>T	chr3.hg19:g.31705657G>A	ENSP00000379804:p.Arg722Trp	133.0	0.0	.		183.0	58.0	.	NM_017784	B4E212|Q9BTU5	Missense_Mutation	SNP	ENST00000396556.2	hg19	CCDS2651.1	.	.	.	.	.	.	.	.	.	.	G	34	5.329303	0.95733	0.0	1.16E-4	ENSG00000144645	ENST00000396556;ENST00000438237	T;T	0.31247	1.5;1.5	5.25	5.25	0.73442	.	0.051590	0.85682	D	0.000000	T	0.57989	0.2091	M	0.77103	2.36	0.48696	D	0.999691	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.70935	0.971;0.93;0.969	T	0.57412	-0.7816	10	0.42905	T	0.14	-24.6464	19.2246	0.93814	0.0:0.0:1.0:0.0	.	658;722;490	B4E212;Q9BXB5;Q59ED9	.;OSB10_HUMAN;.	W	722;658	ENSP00000379804:R722W;ENSP00000406124:R658W	ENSP00000379804:R722W	R	-	1	2	OSBPL10	31680661	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.694000	0.74587	2.635000	0.89317	0.655000	0.94253	CGG	.	.	.	weak		0.607	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2			A	31705657	G	A	31705657	3	1	198	1	0	0	0	0	1	0	0	0	11282	1086	38	1	138	1	OSBPL10	3	31705657	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	28523356	31705657	166316773	21	11909											
PRKCD	5580	hgsc.bcm.edu	37	chr3	53220041	53220041	+	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	tgggcaaaggcagcttcgggAaggtgagggctgtgagccgg	8	6	20	7	2	0	2	0	2	0	0	1	3	0	3	1	6	2	4	1	6	2	1			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:53220041A>T	ENST00000394729.2	+	11	1412	c.1084A>T	c.(1084-1086)Aag>Tag	p.K362*	PRKCD_ENST00000330452.3_Nonsense_Mutation_p.K362*	NM_212539.1	NP_997704.1	Q05655	KPCD_HUMAN	protein kinase C, delta	362	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)	CAGCTTCGGGAAGGTGAGGGC	0.602																																					p.K362X		Atlas-SNP	.											.	PRKCD	124	.	0			c.A1084T						PASS	.						72	66	68					3																	53220041		2203	4300	6503	SO:0001587	stop_gained	5580	exon11			TTCGGGAAGGTGA		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.1084A>T	chr3.hg19:g.53220041A>T	ENSP00000378217:p.Lys362*	371.0	0.0	.		450.0	235.0	.	NM_212539	B0KZ81|B2R834|Q15144|Q86XJ6	Nonsense_Mutation	SNP	ENST00000394729.2	hg19	CCDS2870.1	.	.	.	.	.	.	.	.	.	.	A	41	8.637830	0.98895	.	.	ENSG00000163932	ENST00000394729;ENST00000330452	.	.	.	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.9599	0.64172	1.0:0.0:0.0:0.0	.	.	.	.	X	362	.	ENSP00000331602:K362X	K	+	1	0	PRKCD	53195081	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	9.283000	0.95860	1.990000	0.58119	0.482000	0.46254	AAG	.	.	.	none		0.602	PRKCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257818.1			T	53220041	A	T	53220041	4	4	198	1	0	0	0	0	0	1	0	0	12519	247	9	5	1122	5	PRKCD	3	53220041	Nonsense_Mutation	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10	21514384	53220041	144802389	22	11910											
C3orf63	23272	hgsc.bcm.edu	37	chr3	56667344	56667344	+	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	ttgaggctggttcatttctaCttcagttaaagccgaagtgg	9	14	11	7	1	3	1	2	1	1	0	3	2	3	1	1	3	2	3	1	3	4	6			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:56667344C>G	ENST00000493960.2	-	18	3485	c.3475G>C	c.(3475-3477)Gta>Cta	p.V1159L	FAM208A_ENST00000431842.2_Missense_Mutation_p.V722L|FAM208A_ENST00000355628.5_Missense_Mutation_p.V1098L	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	1159							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						TTCATTTCTACTTCAGTTAAA	0.423																																					p.V1159L		Atlas-SNP	.											.	FAM208A	113	.	0			c.G3475C						PASS	.						161	153	156					3																	56667344		2203	4300	6503	SO:0001583	missense	23272	exon18			TTTCTACTTCAGT	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.3475G>C	chr3.hg19:g.56667344C>G	ENSP00000417509:p.Val1159Leu	255.0	1.0	.		282.0	153.0	.	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Missense_Mutation	SNP	ENST00000493960.2	hg19	CCDS46853.1	.	.	.	.	.	.	.	.	.	.	C	10.01	1.233960	0.22626	.	.	ENSG00000163946	ENST00000431842;ENST00000493960;ENST00000355628	T;T;T	0.11930	2.73;2.92;2.92	5.71	2.97	0.34412	.	0.560812	0.17265	N	0.180629	T	0.14141	0.0342	L	0.59436	1.845	0.33043	D	0.531757	B;B;B;B	0.29481	0.052;0.082;0.046;0.245	B;B;B;B	0.26202	0.067;0.053;0.045;0.049	T	0.07731	-1.0757	10	0.49607	T	0.09	0.2694	9.0639	0.36451	0.0:0.7733:0.0:0.2267	.	1159;1098;722;1159	Q9UK61-3;Q9UK61-4;Q9UK61-2;Q9UK61	.;.;.;F208A_HUMAN	L	722;1159;1098	ENSP00000399410:V722L;ENSP00000417509:V1159L;ENSP00000347845:V1098L	ENSP00000347845:V1098L	V	-	1	0	C3orf63	56642384	0.810000	0.29049	0.970000	0.41538	0.807000	0.45602	0.627000	0.24506	0.444000	0.26612	-0.145000	0.13849	GTA	.	.	.	none		0.423	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224		G	56667344	C	G	56667344	3	3	198	1	0	0	0	0	1	0	0	0	2241	565	20	4	1625	4	C3orf63	3	56667344	Missense_Mutation	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	3447303	56667344	141355086	23	11911											
FRMD4B	23150	hgsc.bcm.edu	37	chr3	69247894	69247894	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caaattttttctcacggaaaTataagttctccagctgtttc	11	16	5	9	1	2	0	1	0	2	0	5	1	2	1	1	1	1	3	1	1	4	7			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:69247894T>C	ENST00000398540.3	-	12	991	c.908A>G	c.(907-909)tAt>tGt	p.Y303C	FRMD4B_ENST00000478263.1_De_novo_Start_OutOfFrame|FRMD4B_ENST00000542259.1_Missense_Mutation_p.Y249C	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	303	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		CTCACGGAAATATAAGTTCTC	0.333																																					p.Y303C		Atlas-SNP	.											FRMD4B_ENST00000398540,NS,carcinoma,0,2	FRMD4B	90	.	0			c.A908G						PASS	.						49	44	45					3																	69247894		1798	4063	5861	SO:0001583	missense	23150	exon12			CGGAAATATAAGT	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.908A>G	chr3.hg19:g.69247894T>C	ENSP00000381549:p.Tyr303Cys	80.0	1.0	.		98.0	57.0	.	NM_015123	Q8TAI3	Missense_Mutation	SNP	ENST00000398540.3	hg19	CCDS46863.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.628228	0.87560	.	.	ENSG00000114541	ENST00000398540;ENST00000542259;ENST00000462512	D;D;D	0.87334	-2.24;-2.24;-2.24	5.73	5.73	0.89815	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	D	0.93360	0.7883	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;0.973	D;D	0.97110	1.0;0.934	D	0.94028	0.7298	10	0.72032	D	0.01	-14.0669	16.026	0.80545	0.0:0.0:0.0:1.0	.	147;303	B4DHD5;Q9Y2L6	.;FRM4B_HUMAN	C	303;249;14	ENSP00000381549:Y303C;ENSP00000437658:Y249C;ENSP00000419869:Y14C	ENSP00000381549:Y303C	Y	-	2	0	FRMD4B	69330584	1.000000	0.71417	0.999000	0.59377	0.953000	0.61014	8.040000	0.89188	2.191000	0.70037	0.533000	0.62120	TAT	.	.	.	none		0.333	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1			C	69247894	T	C	69247894	3	2	198	1	0	0	0	0	1	0	0	0	6059	1406	49	3	2244	3	FRMD4B	3	69247894	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	12580550	69247894	128774536	24	11912											
CEP97	79598	hgsc.bcm.edu	37	chr3	101450739	101450739	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tagaatggcacctgcttaccTacccagaagtcttgctatac	11	11	7	12	0	1	2	0	0	1	2	1	2	1	2	3	1	5	3	3	1	7	6			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:101450739T>C	ENST00000341893.3	+	5	1255	c.503T>C	c.(502-504)cTa>cCa	p.L168P	CEP97_ENST00000327230.4_Missense_Mutation_p.L168P|CEP97_ENST00000494050.1_Missense_Mutation_p.L168P			Q8IW35	CEP97_HUMAN	centrosomal protein 97kDa	168					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						CCTGCTTACCTACCCAGAAGT	0.358																																					p.L168P		Atlas-SNP	.											.	CEP97	122	.	0			c.T503C						PASS	.						175	171	172					3																	101450739		2203	4300	6503	SO:0001583	missense	79598	exon5			CTTACCTACCCAG	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.503T>C	chr3.hg19:g.101450739T>C	ENSP00000342510:p.Leu168Pro	77.0	0.0	.		72.0	15.0	.	NM_024548	B5MDY8|Q8NA71|Q9H5T9	Missense_Mutation	SNP	ENST00000341893.3	hg19	CCDS2944.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.711642	0.89112	.	.	ENSG00000182504	ENST00000341893;ENST00000327230;ENST00000494050	T;T;T	0.54866	0.55;0.55;0.55	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.78220	0.4249	M	0.90542	3.125	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	T	0.83115	-0.0121	10	0.87932	D	0	-9.0356	16.2507	0.82485	0.0:0.0:0.0:1.0	.	168;168;168	E9PG22;Q8IW35-2;Q8IW35	.;.;CEP97_HUMAN	P	168	ENSP00000342510:L168P;ENSP00000325881:L168P;ENSP00000418185:L168P	ENSP00000325881:L168P	L	+	2	0	CEP97	102933429	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.867000	0.87062	2.237000	0.73441	0.528000	0.53228	CTA	.	.	.	none		0.358	CEP97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353597.2	NM_024548		C	101450739	T	C	101450739	3	2	198	1	0	0	0	0	1	0	0	0	3265	1522	53	3	521	3	CEP97	3	101450739	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	32202845	101450739	96571691	25	11913											
ITGB5	3693	hgsc.bcm.edu	37	chr3	124536482	124536482	+	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	acttacattgtatgcattaaTaatcagttgaataatatttt	15	18	4	4	0	1	1	1	1	0	0	1	1	1	1	0	0	2	3	0	0	7	10			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:124536482T>A	ENST00000296181.4	-	8	1410	c.1114A>T	c.(1114-1116)Att>Ttt	p.I372F		NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	372	VWFA.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|epithelial cell-cell adhesion (GO:0090136)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alphav-beta5 complex (GO:0034684)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	30				GBM - Glioblastoma multiforme(114;0.163)		TATGCATTAATAATCAGTTGA	0.463																																					p.I372F		Atlas-SNP	.											.	ITGB5	66	.	0			c.A1114T						PASS	.						90	93	92					3																	124536482		2203	4300	6503	SO:0001583	missense	3693	exon8			CATTAATAATCAG	J05633	CCDS3030.1	3q21.2	2010-03-23			ENSG00000082781	ENSG00000082781		"Integrins"	6160	protein-coding gene	gene with protein product		147561				2211615	Standard	NM_002213		Approved		uc003eho.3	P18084	OTTHUMG00000159432	ENST00000296181.4:c.1114A>T	chr3.hg19:g.124536482T>A	ENSP00000296181:p.Ile372Phe	61.0	0.0	.		60.0	33.0	.	NM_002213	B0LPF8|B2RD70	Missense_Mutation	SNP	ENST00000296181.4	hg19	CCDS3030.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.39|10.39	1.336008|1.336008	0.24253|0.24253	.|.	.|.	ENSG00000082781|ENSG00000082781	ENST00000296181|ENST00000481591	D|.	0.97731|.	-4.51|.	5.91|5.91	3.56|3.56	0.40772|0.40772	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);|.	0.258920|.	0.37761|.	N|.	0.001959|.	T|T	0.58177|0.58177	0.2104|0.2104	M|M	0.62723|0.62723	1.935|1.935	0.48087|0.48087	D|D	0.99958|0.99958	D|.	0.53745|.	0.962|.	P|.	0.54401|.	0.751|.	T|T	0.55829|0.55829	-0.8079|-0.8079	10|5	0.87932|.	D|.	0|.	.|.	4.6147|4.6147	0.12420|0.12420	0.0:0.4306:0.0:0.5694|0.0:0.4306:0.0:0.5694	.|.	372|.	P18084|.	ITB5_HUMAN|.	F|F	372|106	ENSP00000296181:I372F|.	ENSP00000296181:I372F|.	I|L	-|-	1|3	0|2	ITGB5|ITGB5	126019172|126019172	0.989000|0.989000	0.36119|0.36119	0.981000|0.981000	0.43875|0.43875	0.079000|0.079000	0.17450|0.17450	2.520000|2.520000	0.45554|0.45554	1.062000|1.062000	0.40625|0.40625	-0.290000|-0.290000	0.09829|0.09829	ATT|TTA	.	.	.	none		0.463	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3	NM_002213		A	124536482	T	A	124536482	3	1	198	1	0	0	0	0	1	0	0	0	7905	1406	49	5	1317	5	ITGB5	3	124536482	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	23085743	124536482	73485948	26	11914											
IFT122	55764	hgsc.bcm.edu	37	chr3	129200472	129200472	+	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	gtgcctcccgtaagaagctgGccgtggtagatgaaaatgac	11	8	13	9	2	0	4	0	2	0	2	1	4	1	4	3	2	2	3	3	2	5	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:129200472G>C	ENST00000348417.2	+	14	1665	c.1588G>C	c.(1588-1590)Gcc>Ccc	p.A530P	IFT122_ENST00000349441.2_Missense_Mutation_p.A419P|IFT122_ENST00000507564.1_Missense_Mutation_p.A522P|IFT122_ENST00000440957.2_Missense_Mutation_p.A321P|IFT122_ENST00000504021.1_Missense_Mutation_p.A424P|IFT122_ENST00000347300.2_Missense_Mutation_p.A471P|IFT122_ENST00000296266.3_Missense_Mutation_p.A581P|IFT122_ENST00000431818.2_Missense_Mutation_p.A380P	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	530					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						TAAGAAGCTGGCCGTGGTAGA	0.537																																					p.A581P		Atlas-SNP	.											.	IFT122	117	.	0			c.G1741C						PASS	.						36	37	36					3																	129200472		2202	4280	6482	SO:0001583	missense	55764	exon15			AAGCTGGCCGTGG	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.1588G>C	chr3.hg19:g.129200472G>C	ENSP00000324005:p.Ala530Pro	829.0	2.0	.		1002.0	371.0	.	NM_052985	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Missense_Mutation	SNP	ENST00000348417.2	hg19	CCDS3061.1	.	.	.	.	.	.	.	.	.	.	G	31	5.058399	0.93846	.	.	ENSG00000163913	ENST00000347300;ENST00000296266;ENST00000507564;ENST00000454840;ENST00000431818;ENST00000504021;ENST00000349441;ENST00000348417;ENST00000446384;ENST00000440957;ENST00000509522	T;T;T;D;T;T;T;D;T	0.91237	2.88;0.84;0.84;-2.81;1.18;1.18;0.84;-2.81;0.28	5.5	5.5	0.81552	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.052903	0.85682	D	0.000000	D	0.96676	0.8915	M	0.92507	3.315	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0;1.0;0.999;1.0	D;D;D;D;D;D;D;D	0.97110	0.998;0.991;1.0;1.0;0.999;1.0;0.996;0.998	D	0.97335	0.9953	10	0.87932	D	0	-22.9133	19.3987	0.94619	0.0:0.0:1.0:0.0	.	321;522;424;370;419;471;530;581	E9PDG2;E7EQF4;B4DEY9;B4DPW7;Q9BTY4;Q9HBG6-3;Q9HBG6;G3XAB1	.;.;.;.;.;.;IF122_HUMAN;.	P	471;581;522;471;380;424;419;530;370;321;45	ENSP00000323973:A471P;ENSP00000296266:A581P;ENSP00000425536:A522P;ENSP00000410946:A380P;ENSP00000422179:A424P;ENSP00000324165:A419P;ENSP00000324005:A530P;ENSP00000401569:A321P;ENSP00000424727:A45P	ENSP00000296266:A581P	A	+	1	0	IFT122	130683162	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.113000	0.94321	2.553000	0.86117	0.585000	0.79938	GCC	.	.	.	none		0.537	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262		C	129200472	G	C	129200472	3	2	198	1	0	0	0	0	1	0	0	0	7562	1203	42	4	1799	4	IFT122	3	129200472	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	4663990	129200472	68821958	27	11915											
DZIP1L	199221	hgsc.bcm.edu	37	chr3	137790541	137790541	+	Missense_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	cattctcctgtctctccttcGctctgctggtgacttccttg	2	17	7	15	1	3	1	0	1	3	0	8	1	5	1	3	1	1	2	3	1	0	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:137790541G>A	ENST00000327532.2	-	12	1921	c.1559C>T	c.(1558-1560)gCg>gTg	p.A520V	DZIP1L_ENST00000469243.1_Missense_Mutation_p.A520V|DZIP1L_ENST00000488595.1_Intron	NM_173543.2	NP_775814.2	Q8IYY4	DZI1L_HUMAN	DAZ interacting zinc finger protein 1-like	520					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						TCTCTCCTTCGCTCTGCTGGT	0.582																																					p.A520V		Atlas-SNP	.											.	DZIP1L	88	.	0			c.C1559T						PASS	.						90	92	91					3																	137790541		2203	4300	6503	SO:0001583	missense	199221	exon13			TCCTTCGCTCTGC	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.1559C>T	chr3.hg19:g.137790541G>A	ENSP00000332148:p.Ala520Val	104.0	0.0	.		112.0	65.0	.	NM_001170538	C9JUG5|Q96M38	Missense_Mutation	SNP	ENST00000327532.2	hg19	CCDS3096.1	.	.	.	.	.	.	.	.	.	.	G	4.821	0.152566	0.09185	.	.	ENSG00000158163	ENST00000327532;ENST00000469243;ENST00000536706	T;T	0.38240	1.15;1.55	4.86	-3.99	0.04069	.	0.809238	0.10642	N	0.650958	T	0.12263	0.0298	N	0.03324	-0.35	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.001	T	0.38351	-0.9665	10	0.02654	T	1	-4.7251	11.046	0.47859	0.5108:0.0:0.4892:0.0	.	520;520	Q8IYY4-2;Q8IYY4	.;DZI1L_HUMAN	V	520	ENSP00000332148:A520V;ENSP00000419486:A520V	ENSP00000332148:A520V	A	-	2	0	DZIP1L	139273231	0.009000	0.17119	0.025000	0.17156	0.009000	0.06853	0.410000	0.21098	-0.777000	0.04572	-1.004000	0.02495	GCG	.	.	.	none		0.582	DZIP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357548.1	NM_173543		A	137790541	G	A	137790541	3	1	198	1	0	0	0	0	1	0	0	0	4866	1087	38	1	773	1	DZIP1L	3	137790541	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	8590069	137790541	60231889	28	11916											
KNG1	3827	hgsc.bcm.edu	37	chr3	186445075	186445075	+	Missense_Mutation	SNP	A	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	ctactcaattgtgcaaacgaAttgttccaaagagaattttc	14	13	6	8	1	1	1	1	0	0	1	3	3	2	1	1	0	3	2	1	0	6	6			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:186445075A>C	ENST00000265023.4	+	5	826	c.614A>C	c.(613-615)aAt>aCt	p.N205T	RP11-573D15.8_ENST00000599314.1_RNA|KNG1_ENST00000287611.2_Missense_Mutation_p.N205T|KNG1_ENST00000447445.1_Intron	NM_001102416.2	NP_001095886.1	P01042	KNG1_HUMAN	kininogen 1	205	Cystatin kininogen-type 2. {ECO:0000255|PROSITE-ProRule:PRU00979}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|inflammatory response (GO:0006954)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|smooth muscle contraction (GO:0006939)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			endometrium(1)|lung(15)|prostate(1)|skin(2)|stomach(2)	21	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)		GTGCAAACGAATTGTTCCAAA	0.348																																					p.N205T		Atlas-SNP	.											.	KNG1	129	.	0			c.A614C						PASS	.						105	109	108					3																	186445075		2203	4300	6503	SO:0001583	missense	3827	exon5			AAACGAATTGTTC		CCDS3281.1, CCDS43183.1, CCDS54695.1	3q27.3	2014-05-15	2004-05-21	2004-05-26	ENSG00000113889	ENSG00000113889		"Endogenous ligands"	6383	protein-coding gene	gene with protein product	"alpha-2-thiol proteinase inhibitor", "bradykinin"	612358	"kininogen"	KNG, BDK		1733668	Standard	NM_000893		Approved	BK	uc011bsa.2	P01042	OTTHUMG00000150348	ENST00000265023.4:c.614A>C	chr3.hg19:g.186445075A>C	ENSP00000265023:p.Asn205Thr	101.0	0.0	.		77.0	27.0	.	NM_000893	A8K474|B2RCR2|C9JEX1|P01043|Q53EQ0|Q6PAU9|Q7M4P1	Missense_Mutation	SNP	ENST00000265023.4	hg19	CCDS43183.1	.	.	.	.	.	.	.	.	.	.	A	17.29	3.353296	0.61293	.	.	ENSG00000113889	ENST00000287611;ENST00000265023;ENST00000432028	T;T	0.26067	1.76;1.76	4.98	3.82	0.43975	Proteinase inhibitor I25, cystatin (2);	0.085672	0.49916	D	0.000134	T	0.40473	0.1118	L	0.52011	1.625	0.80722	D	1	D;D	0.89917	0.974;1.0	D;D	0.85130	0.961;0.997	T	0.15263	-1.0443	10	0.54805	T	0.06	-28.4834	7.9142	0.29808	0.9039:0.0:0.0961:0.0	.	205;205	P01042;P01042-2	KNG1_HUMAN;.	T	205;205;193	ENSP00000287611:N205T;ENSP00000265023:N205T	ENSP00000265023:N205T	N	+	2	0	KNG1	187927769	0.996000	0.38824	0.989000	0.46669	0.901000	0.52897	4.757000	0.62213	0.998000	0.38996	0.528000	0.53228	AAT	.	.	.	none		0.348	KNG1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317738.1	NM_001102416		C	186445075	A	C	186445075	3	2	198	1	0	0	0	0	1	0	0	0	8434	101	4	5	632	5	KNG1	3	186445075	Missense_Mutation	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10	48654534	186445075	11577355	29	11917											
RNF168	165918	hgsc.bcm.edu	37	chr3	196214285	196214286	+	Frame_Shift_Ins	INS	-	-	T																															ttacaatatcaatgcttagcINStttcttgccagttcctcatc																								rs375146769		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr3:196214285_196214286insT	ENST00000318037.3	-	3	1136_1137	c.542_543insA	c.(541-543)aagfs	p.K181fs		NM_152617.3	NP_689830.2	Q8IYW5	RN168_HUMAN	ring finger protein 168, E3 ubiquitin protein ligase	181					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone H2A K63-linked ubiquitination (GO:0070535)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K13 ubiquitination (GO:0036351)|histone H2A-K15 ubiquitination (GO:0036352)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|negative regulation of translational elongation (GO:0045900)|positive regulation of DNA repair (GO:0045739)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)	20	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)		CAATGCTTAGCTTTCTTGCCAG	0.47																																					p.K181fs		Atlas-Indel,Pindel	.											.	RNF168	49	.	0			c.543_544insA						PASS	.																																			SO:0001589	frameshift_variant	165918	exon3			.	AK054732	CCDS3317.1	3q29	2014-09-17	2012-02-23		ENSG00000163961	ENSG00000163961		"RING-type (C3HC4) zinc fingers"	26661	protein-coding gene	gene with protein product		612688	"ring finger protein 168"			12477932	Standard	NM_152617		Approved	FLJ35794	uc003fwq.3	Q8IYW5	OTTHUMG00000155582	ENST00000318037.3:c.543dupA	chr3.hg19:g.196214288_196214288dupT	ENSP00000320898:p.Lys181fs	155.0	0.0	0		180.0	89.0	0.494444	NM_152617	Q8NA67|Q96NS4	Frame_Shift_Ins	INS	ENST00000318037.3	hg19	CCDS3317.1																																																																																			.	.	.	none		0.47	RNF168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340778.1	NM_152617		T	196214286	-	T	196214285	7	5	198	1	0	1	1	0	0	0	0	0	13472	796	28	0	1188	0	RNF168	3	196214285	Frame_Shift_Ins	INS	-	TCGA-HE-A5NI-01A-11D-A26P-10	9769210	196214285	1808145	30	11918											
TIGD4	201798	hgsc.bcm.edu	37	chr4	153690653	153690653	+	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	agagttaataaaattttcaaGgtctgctaaagaattttgaa	17	14	7	3	0	2	3	1	1	1	2	2	3	2	3	0	1	1	2	0	1	8	7			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr4:153690653G>C	ENST00000304337.2	-	2	2324	c.1504C>G	c.(1504-1506)Ctt>Gtt	p.L502V		NM_145720.3	NP_663772.1	Q8IY51	TIGD4_HUMAN	tigger transposable element derived 4	502						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.093)					AAATTTTCAAGGTCTGCTAAA	0.284																																					p.L502V		Atlas-SNP	.											.	TIGD4	53	.	0			c.C1504G						PASS	.						34	39	38					4																	153690653		2202	4299	6501	SO:0001583	missense	201798	exon2			TTTCAAGGTCTGC	AK058054	CCDS34079.1	4q31.23	2008-02-05							18335	protein-coding gene	gene with protein product							Standard	NM_145720		Approved		uc003imy.3	Q8IY51		ENST00000304337.2:c.1504C>G	chr4.hg19:g.153690653G>C	ENSP00000355162:p.Leu502Val	68.0	0.0	.		51.0	13.0	.	NM_145720	Q96LP5	Missense_Mutation	SNP	ENST00000304337.2	hg19	CCDS34079.1	.	.	.	.	.	.	.	.	.	.	G	4.593	0.110214	0.08780	.	.	ENSG00000169989	ENST00000304337	T	0.17854	2.25	6.08	2.33	0.28932	Centromere protein Cenp-B, dimerisation domain (1);	0.493860	0.17134	N	0.185704	T	0.10981	0.0268	L	0.29908	0.895	0.26016	N	0.981923	B	0.06786	0.001	B	0.06405	0.002	T	0.24048	-1.0171	10	0.56958	D	0.05	-8.793	4.401	0.11386	0.0666:0.2372:0.3299:0.3663	.	502	Q8IY51	TIGD4_HUMAN	V	502	ENSP00000355162:L502V	ENSP00000355162:L502V	L	-	1	0	TIGD4	153910103	0.997000	0.39634	0.991000	0.47740	0.706000	0.40770	0.275000	0.18698	0.118000	0.18165	-0.293000	0.09583	CTT	.	.	.	none		0.284	TIGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365028.1	NM_145720		C	153690653	G	C	153690653	3	2	198	1	0	0	0	0	1	0	0	0	15910	1000	35	4	38	4	TIGD4	4	153690653	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10		153690653	37463623	31	11919											
MFAP3L	9848	hgsc.bcm.edu	37	chr4	170913188	170913189	+	Frame_Shift_Ins	INS	-	-	A																															ttctctgcaccttcggtcctINSaaagaactcattgatggcct																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr4:170913188_170913189insA	ENST00000361618.3	-	3	877_878	c.570_571insT	c.(568-573)tttaggfs	p.R191fs	RP11-6E9.4_ENST00000508955.1_RNA|MFAP3L_ENST00000393704.3_Frame_Shift_Ins_p.R88fs	NM_021647.6	NP_067679.6	O75121	MFA3L_HUMAN	microfibrillar-associated protein 3-like	191						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)		CCTTCGGTCCTAAAGAACTCAT	0.525																																					p.R191_T192delinsX		Atlas-Indel,Pindel	.											.	MFAP3L	59	.	0			c.571_572insT						PASS	.																																			SO:0001589	frameshift_variant	9848	exon3			.	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.571dupT	chr4.hg19:g.170913191_170913191dupA	ENSP00000354583:p.Arg191fs	186.0	0.0	0		162.0	52.0	0.320988	NM_021647	A8K1X6|D3DP35|Q4W5N7|Q4W5N9|Q6TNA8|Q9BVE1|Q9BXK0	Frame_Shift_Ins	INS	ENST00000361618.3	hg19	CCDS34103.1																																																																																			.	.	.	none		0.525	MFAP3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363043.2	NM_021647		A	170913189	-	A	170913188	7	5	198	1	0	1	1	0	0	0	0	0	9523	1521	53	0	662	0	MFAP3L	4	170913188	Frame_Shift_Ins	INS	-	TCGA-HE-A5NI-01A-11D-A26P-10	17222535	170913188	20241088	32	11920											
CARD6	84674	hgsc.bcm.edu	37	chr5	40852818	40852818	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctcttttgtgcgtctaggaTactgtagcttctctaagtcc	6	17	8	10	1	3	0	0	0	3	0	6	1	4	1	1	1	3	2	1	1	4	7			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr5:40852818T>C	ENST00000254691.5	+	3	1583	c.1384T>C	c.(1384-1386)Tac>Cac	p.Y462H	CARD6_ENST00000381677.3_Intron	NM_032587.3	NP_115976.2	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	462					apoptotic process (GO:0006915)|regulation of apoptotic process (GO:0042981)					NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(2)|lung(29)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	62						GCGTCTAGGATACTGTAGCTT	0.433																																					p.Y462H		Atlas-SNP	.											.	CARD6	141	.	0			c.T1384C						PASS	.						87	91	89					5																	40852818		2203	4300	6503	SO:0001583	missense	84674	exon3			CTAGGATACTGTA	AF356193	CCDS3935.1	5p13.1	2008-05-23			ENSG00000132357	ENSG00000132357			16394	protein-coding gene	gene with protein product		609986				12775719	Standard	NM_032587		Approved	CINCIN1	uc003jmg.3	Q9BX69	OTTHUMG00000094775	ENST00000254691.5:c.1384T>C	chr5.hg19:g.40852818T>C	ENSP00000254691:p.Tyr462His	115.0	0.0	.		145.0	64.0	.	NM_032587	Q52LR2	Missense_Mutation	SNP	ENST00000254691.5	hg19	CCDS3935.1	.	.	.	.	.	.	.	.	.	.	T	4.601	0.111736	0.08831	.	.	ENSG00000132357	ENST00000254691	T	0.11169	2.8	5.48	-5.23	0.02798	.	1.493650	0.03820	N	0.267293	T	0.04724	0.0128	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.34950	-0.9808	10	0.35671	T	0.21	3.1866	3.3078	0.07006	0.209:0.5204:0.1052:0.1655	.	462	Q9BX69	CARD6_HUMAN	H	462	ENSP00000254691:Y462H	ENSP00000254691:Y462H	Y	+	1	0	CARD6	40888575	0.000000	0.05858	0.002000	0.10522	0.968000	0.65278	-0.582000	0.05814	-1.244000	0.02516	-0.248000	0.11899	TAC	.	.	.	none		0.433	CARD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211584.3			C	40852818	T	C	40852818	3	2	198	1	0	0	0	0	1	0	0	0	2652	1406	49	3	1394	3	CARD6	5	40852818	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10		40852818	140062442	33	11921											
MSH3	4437	hgsc.bcm.edu	37	chr5	80037368	80037368	+	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	tggaaatcctacagaatcagGtcaggcaaatacaagggcta	16	7	10	8	0	2	1	2	0	0	1	3	2	3	2	1	4	2	2	1	4	7	3	rs550626088		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr5:80037368G>C	ENST00000265081.6	+	11	1733		c.e11+1		MSH3_ENST00000512258.1_Splice_Site	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3						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)		ACAGAATCAGGTCAGGCAAAT	0.333								Mismatch excision repair (MMR)																													.	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											.	MSH3	129	.	0			c.1653+1G>C						PASS	.						53	58	57					5																	80037368		2203	4297	6500	SO:0001630	splice_region_variant	4437	exon11			AATCAGGTCAGGC	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.1653+1G>C	chr5.hg19:g.80037368G>C		166.0	0.0	.		103.0	34.0	.	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Splice_Site	SNP	ENST00000265081.6	hg19	CCDS34195.1	.	.	.	.	.	.	.	.	.	.	G	19.14	3.770243	0.69992	.	.	ENSG00000113318	ENST00000265081;ENST00000535995	.	.	.	4.79	4.79	0.61399	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.9659	0.86285	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MSH3	80073124	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	6.767000	0.74975	2.369000	0.80426	0.650000	0.86243	.	.	.	.	none		0.333	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439	Intron	C	80037368	G	C	80037368	5	2	198	1	0	0	0	0	0	0	1	0	9878	1275	44	4	1696	4	MSH3	5	80037368	Splice_Site	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	39184550	80037368	100877892	34	11922											
PAM	5066	hgsc.bcm.edu	37	chr5	102203042	102203042	+	Frame_Shift_Del	DEL	T	T	-																															caccagacccgtagttcctaTtgattcatcagattttgcat																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr5:102203042delT	ENST00000438793.3	+	2	625	c.155delT	c.(154-156)attfs	p.I52fs	PAM_ENST00000348126.2_Frame_Shift_Del_p.I52fs|PAM_ENST00000513648.1_3'UTR|PAM_ENST00000274392.9_De_novo_Start_OutOfFrame|PAM_ENST00000379787.4_De_novo_Start_InFrame|PAM_ENST00000346918.2_Frame_Shift_Del_p.I52fs|PAM_ENST00000304400.7_Frame_Shift_Del_p.I52fs|PAM_ENST00000455264.2_Frame_Shift_Del_p.I52fs	NM_000919.3|NM_001177306.1|NM_138766.2	NP_000910.2|NP_001170777.1|NP_620121.1	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	52	Peptidylglycine alpha-hydroxylating monooxygenase. {ECO:0000250}.				central nervous system development (GO:0007417)|heart development (GO:0007507)|lactation (GO:0007595)|limb development (GO:0060173)|long-chain fatty acid metabolic process (GO:0001676)|maternal process involved in female pregnancy (GO:0060135)|odontogenesis (GO:0042476)|ovulation cycle process (GO:0022602)|peptide amidation (GO:0001519)|protein amidation (GO:0018032)|protein homooligomerization (GO:0051260)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of protein secretion (GO:0050708)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to pH (GO:0009268)|toxin metabolic process (GO:0009404)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|L-ascorbic acid binding (GO:0031418)|peptidylamidoglycolate lyase activity (GO:0004598)|peptidylglycine monooxygenase activity (GO:0004504)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	25		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	GTAGTTCCTATTGATTCATCA	0.373																																					p.I52fs		Atlas-INDEL	.											.	PAM	180	.	0			c.154delA						PASS	.						168	148	155					5																	102203042		2203	4300	6503	SO:0001589	frameshift_variant	5066	exon2			.	AB095007	CCDS4092.1, CCDS4093.1, CCDS4094.1, CCDS43348.1, CCDS54885.1	5q	2008-02-05			ENSG00000145730	ENSG00000145730	1.14.17.3		8596	protein-coding gene	gene with protein product	"peptidyl-alpha-hydroxyglycine alpha-amidating lyase", "peptidylglycine alpha-hydroxylating monooxygenase"	170270				2357221	Standard	NM_000919		Approved	PAL, PHM	uc003knt.3	P19021	OTTHUMG00000128729	ENST00000438793.3:c.155delT	chr5.hg19:g.102203042delT	ENSP00000396493:p.Ile52fs	104.0	0.0	0		79.0	21.0	0.265823	NM_138821	A6NMR0|A8K293|O43211|O95080|Q16252|Q16253|Q54A45|Q86U53|Q8WVC7|Q9UCG0	Frame_Shift_Del	DEL	ENST00000438793.3	hg19	CCDS54885.1																																																																																			.	.	.	none		0.373	PAM-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250640.2	NM_000919		-	102203042	T	-	102203042	7	5	198	1	0	1	0	1	0	0	0	0	11419	1493	52	0	161	0	PAM	5	102203042	Frame_Shift_Del	DEL	T	TCGA-HE-A5NI-01A-11D-A26P-10	22165674	102203042	78712218	35	11923	111	3									
PAM	5066	hgsc.bcm.edu	37	chr5	102203043	102203044	+	Frame_Shift_Del	DEL	TG	TG	-																															accagacccgtagttcctatTgattcatcagattttgcatt																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr5:102203043_102203044delTG	ENST00000438793.3	+	2	626_627	c.156_157delTG	c.(154-159)attgatfs	p.D53fs	PAM_ENST00000348126.2_Frame_Shift_Del_p.D53fs|PAM_ENST00000513648.1_3'UTR|PAM_ENST00000274392.9_5'UTR|PAM_ENST00000379787.4_5'UTR|PAM_ENST00000346918.2_Frame_Shift_Del_p.D53fs|PAM_ENST00000304400.7_Frame_Shift_Del_p.D53fs|PAM_ENST00000455264.2_Frame_Shift_Del_p.D53fs	NM_000919.3|NM_001177306.1|NM_138766.2	NP_000910.2|NP_001170777.1|NP_620121.1	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	53	Peptidylglycine alpha-hydroxylating monooxygenase. {ECO:0000250}.				central nervous system development (GO:0007417)|heart development (GO:0007507)|lactation (GO:0007595)|limb development (GO:0060173)|long-chain fatty acid metabolic process (GO:0001676)|maternal process involved in female pregnancy (GO:0060135)|odontogenesis (GO:0042476)|ovulation cycle process (GO:0022602)|peptide amidation (GO:0001519)|protein amidation (GO:0018032)|protein homooligomerization (GO:0051260)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of protein secretion (GO:0050708)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to pH (GO:0009268)|toxin metabolic process (GO:0009404)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|L-ascorbic acid binding (GO:0031418)|peptidylamidoglycolate lyase activity (GO:0004598)|peptidylglycine monooxygenase activity (GO:0004504)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	25		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	TAGTTCCTATTGATTCATCAGA	0.376																																					p.52_52del		Pindel	.											.	PAM	180	.	0			c.155_156del						PASS	.																																			SO:0001589	frameshift_variant	5066	exon2			.	AB095007	CCDS4092.1, CCDS4093.1, CCDS4094.1, CCDS43348.1, CCDS54885.1	5q	2008-02-05			ENSG00000145730	ENSG00000145730	1.14.17.3		8596	protein-coding gene	gene with protein product	"peptidyl-alpha-hydroxyglycine alpha-amidating lyase", "peptidylglycine alpha-hydroxylating monooxygenase"	170270				2357221	Standard	NM_000919		Approved	PAL, PHM	uc003knt.3	P19021	OTTHUMG00000128729	ENST00000438793.3:c.156_157delTG	chr5.hg19:g.102203043_102203044delTG	ENSP00000396493:p.Asp53fs	107.0	0.0	.		80.0	17.0	0.213	NM_138821	A6NMR0|A8K293|O43211|O95080|Q16252|Q16253|Q54A45|Q86U53|Q8WVC7|Q9UCG0	Frame_Shift_Del	DEL	ENST00000438793.3	hg19	CCDS54885.1																																																																																			.	.	.	none		0.376	PAM-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250640.2	NM_000919		-	102203044	TG	-	102203043	7	5	198	1	0	1	0	1	0	0	0	0	11419	1800	63	0	162	0	PAM	5	102203043	Frame_Shift_Del	DEL	TG	TCGA-HE-A5NI-01A-11D-A26P-10	1	102203043	78712217	36	11924	111	3									
PAM	5066	hgsc.bcm.edu	37	chr5	102203044	102203044	+	Missense_Mutation	SNP	G	G	A																															ccagacccgtagttcctattGattcatcagattttgcattg																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr5:102203044G>A	ENST00000438793.3	+	2	627	c.157G>A	c.(157-159)Gat>Aat	p.D53N	PAM_ENST00000348126.2_Missense_Mutation_p.D53N|PAM_ENST00000513648.1_3'UTR|PAM_ENST00000274392.9_5'UTR|PAM_ENST00000379787.4_5'UTR|PAM_ENST00000346918.2_Missense_Mutation_p.D53N|PAM_ENST00000304400.7_Missense_Mutation_p.D53N|PAM_ENST00000455264.2_Missense_Mutation_p.D53N	NM_000919.3|NM_001177306.1|NM_138766.2	NP_000910.2|NP_001170777.1|NP_620121.1	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	53	Peptidylglycine alpha-hydroxylating monooxygenase. {ECO:0000250}.				central nervous system development (GO:0007417)|heart development (GO:0007507)|lactation (GO:0007595)|limb development (GO:0060173)|long-chain fatty acid metabolic process (GO:0001676)|maternal process involved in female pregnancy (GO:0060135)|odontogenesis (GO:0042476)|ovulation cycle process (GO:0022602)|peptide amidation (GO:0001519)|protein amidation (GO:0018032)|protein homooligomerization (GO:0051260)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of protein secretion (GO:0050708)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to pH (GO:0009268)|toxin metabolic process (GO:0009404)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|L-ascorbic acid binding (GO:0031418)|peptidylamidoglycolate lyase activity (GO:0004598)|peptidylglycine monooxygenase activity (GO:0004504)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	25		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	AGTTCCTATTGATTCATCAGA	0.373																																					p.D53N		Atlas-SNP	.											.	PAM	180	.	0			c.G157A						PASS	.						166	147	153					5																	102203044		2203	4300	6503	SO:0001583	missense	5066	exon2			CCTATTGATTCAT	AB095007	CCDS4092.1, CCDS4093.1, CCDS4094.1, CCDS43348.1, CCDS54885.1	5q	2008-02-05			ENSG00000145730	ENSG00000145730	1.14.17.3		8596	protein-coding gene	gene with protein product	"peptidyl-alpha-hydroxyglycine alpha-amidating lyase", "peptidylglycine alpha-hydroxylating monooxygenase"	170270				2357221	Standard	NM_000919		Approved	PAL, PHM	uc003knt.3	P19021	OTTHUMG00000128729	ENST00000438793.3:c.157G>A	chr5.hg19:g.102203044G>A	ENSP00000396493:p.Asp53Asn	108.0	0.0	.		80.0	22.0	.	NM_138822	A6NMR0|A8K293|O43211|O95080|Q16252|Q16253|Q54A45|Q86U53|Q8WVC7|Q9UCG0	Missense_Mutation	SNP	ENST00000438793.3	hg19	CCDS54885.1	.	.	.	.	.	.	.	.	.	.	G	13.81	2.347969	0.41599	.	.	ENSG00000145730	ENST00000511839;ENST00000509832;ENST00000438793;ENST00000346918;ENST00000348126;ENST00000304400;ENST00000455264	T;T;T;T;T;T;T	0.64085	0.66;-0.08;1.36;1.36;1.36;1.36;1.36	5.68	5.68	0.88126	Copper type II, ascorbate-dependent monooxygenase, N-terminal (1);PHM/PNGase F domain (1);	0.264128	0.41396	D	0.000899	T	0.54481	0.1861	L	0.29908	0.895	0.80722	D	1	B;B;B;B;B	0.12630	0.004;0.006;0.006;0.006;0.006	B;B;B;B;B	0.12156	0.003;0.006;0.006;0.006;0.007	T	0.45760	-0.9239	10	0.39692	T	0.17	.	19.791	0.96456	0.0:0.0:1.0:0.0	.	53;53;53;53;53	P19021;P19021-4;P19021-3;P19021-5;P19021-2	AMD_HUMAN;.;.;.;.	N	53	ENSP00000426448:D53N;ENSP00000423763:D53N;ENSP00000396493:D53N;ENSP00000282992:D53N;ENSP00000314638:D53N;ENSP00000306100:D53N;ENSP00000403461:D53N	ENSP00000306100:D53N	D	+	1	0	PAM	102230943	1.000000	0.71417	0.985000	0.45067	0.013000	0.08279	5.413000	0.66399	2.677000	0.91161	0.491000	0.48974	GAT	.	.	.	none		0.373	PAM-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250640.2	NM_000919		A	102203044	G	A	102203044	3	1	198	1	0	0	0	0	1	0	0	0	11419	1290	45	2	163	2	PAM	5	102203044	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	1	102203044	78712216	37	11925	111	3									
SYCP2L	221711	hgsc.bcm.edu	37	chr6	10931696	10931696	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgccagttttccctcccagtAgtggcagtggccatgagaaa	9	10	11	11	0	0	1	0	1	0	1	2	2	2	1	4	2	1	3	4	2	2	3			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr6:10931696A>G	ENST00000283141.6	+	20	1953	c.1657A>G	c.(1657-1659)Agt>Ggt	p.S553G		NM_001040274.2	NP_001035364.2	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like	553						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)			CCCTCCCAGTAGTGGCAGTGG	0.398																																					p.S553G		Atlas-SNP	.											.	SYCP2L	101	.	0			c.A1657G						PASS	.						162	153	156					6																	10931696		1894	4121	6015	SO:0001583	missense	221711	exon20			CCCAGTAGTGGCA	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.1657A>G	chr6.hg19:g.10931696A>G	ENSP00000283141:p.Ser553Gly	99.0	0.0	.		104.0	37.0	.	NM_001040274	A6NDS5|Q08GK5|Q6ZRM2|Q96EJ2	Missense_Mutation	SNP	ENST00000283141.6	hg19	CCDS43423.1	.	.	.	.	.	.	.	.	.	.	A	12.52	1.964123	0.34659	.	.	ENSG00000153157	ENST00000283141	T	0.31247	1.5	4.54	3.37	0.38596	.	0.357110	0.31648	N	0.007296	T	0.19327	0.0464	L	0.52011	1.625	0.24843	N	0.992458	D	0.60160	0.987	P	0.50270	0.636	T	0.03325	-1.1048	10	0.59425	D	0.04	.	8.5559	0.33480	0.7752:0.2248:0.0:0.0	.	553	Q5T4T6	SYC2L_HUMAN	G	553	ENSP00000283141:S553G	ENSP00000283141:S553G	S	+	1	0	SYCP2L	11039682	0.004000	0.15560	0.006000	0.13384	0.043000	0.13939	0.576000	0.23744	0.822000	0.34565	0.460000	0.39030	AGT	.	.	.	none		0.398	SYCP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039845.3	NM_194299		G	10931696	A	G	10931696	3	3	198	1	0	0	0	0	1	0	0	0	15445	420	15	3	1735	3	SYCP2L	6	10931696	Missense_Mutation	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10		10931696	160183371	38	11926											
GPLD1	2822	hgsc.bcm.edu	37	chr6	24450018	24450018	+	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	tatccagcagcagccttactTtgtaggtgagctgctcggag	8	11	12	10	1	0	1	0	1	0	0	2	2	1	2	2	2	6	5	2	2	3	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr6:24450018T>C	ENST00000230036.1	-	15	1555	c.1445A>G	c.(1444-1446)aAa>aGa	p.K482R		NM_001503.3	NP_001494.2	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific phospholipase D1	482					cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to calcium ion (GO:0071277)|cellular response to cholesterol (GO:0071397)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|cellular response to pH (GO:0071467)|cellular response to triglyceride (GO:0071401)|chondrocyte differentiation (GO:0002062)|complement receptor mediated signaling pathway (GO:0002430)|GPI anchor release (GO:0006507)|hematopoietic stem cell migration (GO:0035701)|hematopoietic stem cell migration to bone marrow (GO:0097241)|insulin receptor signaling pathway (GO:0008286)|negative regulation of cell proliferation (GO:0008285)|negative regulation of triglyceride catabolic process (GO:0010897)|ossification (GO:0001503)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of secretion (GO:0051047)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cellular response to insulin stimulus (GO:1900076)|response to glucose (GO:0009749)|transepithelial transport (GO:0070633)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|proteinaceous extracellular matrix (GO:0005578)	glycosylphosphatidylinositol phospholipase D activity (GO:0004621)|phospholipase D activity (GO:0004630)|sodium channel regulator activity (GO:0017080)			breast(3)|endometrium(5)|kidney(1)|large_intestine(11)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	32						CAGCCTTACTTTGTAGGTGAG	0.632																																					p.K482R		Atlas-SNP	.											.	GPLD1	91	.	0			c.A1445G						PASS	.						67	71	69					6																	24450018		2203	4300	6503	SO:0001630	splice_region_variant	2822	exon15			CTTACTTTGTAGG	L11701	CCDS4553.1	6p22.1	2008-02-05			ENSG00000112293	ENSG00000112293			4459	protein-coding gene	gene with protein product		602515				11072085	Standard	NM_001503		Approved		uc003ned.2	P80108	OTTHUMG00000016104	ENST00000230036.1:c.1446+1A>G	chr6.hg19:g.24450018T>C		90.0	0.0	.		69.0	32.0	.	NM_001503	Q15127|Q15128|Q2M2F2|Q5T3Y0|Q7Z6T8|Q8TCV0|Q8WW82|Q96ID6|Q9H167|Q9H4M1|Q9UJC9	Missense_Mutation	SNP	ENST00000230036.1	hg19	CCDS4553.1	.	.	.	.	.	.	.	.	.	.	T	9.926	1.213638	0.22289	.	.	ENSG00000112293	ENST00000230036	T	0.66995	-0.24	5.5	-3.95	0.04118	.	0.800408	0.11589	N	0.548920	T	0.20455	0.0492	N	0.12527	0.23	0.53005	D	0.999964	B	0.09022	0.002	B	0.14578	0.011	T	0.12142	-1.0559	10	0.12766	T	0.61	-0.5038	9.3674	0.38232	0.0:0.1973:0.5455:0.2572	.	482	P80108	PHLD_HUMAN	R	482	ENSP00000230036:K482R	ENSP00000230036:K482R	K	-	2	0	GPLD1	24557997	0.006000	0.16342	0.147000	0.22382	0.634000	0.38068	-0.438000	0.06905	-0.534000	0.06315	0.482000	0.46254	AAA	.	.	.	none		0.632	GPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043315.1	NM_001503	Missense_Mutation	C	24450018	T	C	24450018	5	2	198	1	0	0	0	0	0	0	1	0	6621	1855	64	3	1121	3	GPLD1	6	24450018	Splice_Site	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	13518322	24450018	146665049	39	11927											
NOTCH4	4855	hgsc.bcm.edu	37	chr6	32169043	32169043	+	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	tccctgccatcacgatccttCcttacccagagtcctaccct	7	11	4	19	1	1	1	1	0	0	1	5	2	5	1	7	0	3	0	7	0	2	3			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr6:32169043C>T	ENST00000375023.3	-	22	4128	c.3990G>A	c.(3988-3990)agG>agA	p.R1330R		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1330					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						CACGATCCTTCCTTACCCAGA	0.622																																					p.R1330R		Atlas-SNP	.											.	NOTCH4	201	.	0			c.G3990A						PASS	.						59	65	63					6																	32169043		1511	2709	4220	SO:0001819	synonymous_variant	4855	exon22			ATCCTTCCTTACC		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.3990G>A	chr6.hg19:g.32169043C>T		229.0	0.0	.		142.0	53.0	.	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	hg19	CCDS34420.1																																																																																			.	.	.	none		0.622	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			T	32169043	C	T	32169043	2	4	198	1	0	0	0	0	0	0	0	1	10558	854	30	2		2	NOTCH4	6	32169043	Silent	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	7719025	32169043	138946024	40	11928											
C6orf106	64771	hgsc.bcm.edu	37	chr6	34664262	34664262	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaaggcgcaaccggcaggaTtgagctggaagccgagcagc	12	3	16	10	3	0	2	0	1	0	1	0	5	0	4	2	4	5	4	2	4	3	1	rs369638409		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr6:34664262T>C	ENST00000374023.3	-	1	362	c.119A>G	c.(118-120)aAt>aGt	p.N40S	RP11-140K17.3_ENST00000606496.1_RNA|C6orf106_ENST00000374026.3_Missense_Mutation_p.N40S|RP11-140K17.3_ENST00000606971.1_RNA	NM_024294.2	NP_077270.1	Q9H6K1	CF106_HUMAN	chromosome 6 open reading frame 106	40										endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)	10						ACCGGCAGGATTGAGCTGGAA	0.662																																					p.N40S		Atlas-SNP	.											.	C6orf106	29	.	0			c.A119G						PASS	.	T	SER/ASN,SER/ASN	0,4406		0,0,2203	62	43	49		119,119	1.8	1	6		49	1,8599		0,1,4299	no	missense,missense	C6orf106	NM_022758.4,NM_024294.2	46,46	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	40/233,40/299	34664262	1,13005	2203	4300	6503	SO:0001583	missense	64771	exon1			GCAGGATTGAGCT	AF052106	CCDS4795.1, CCDS4796.1	6p21.31	2012-01-27			ENSG00000196821	ENSG00000196821			21215	protein-coding gene	gene with protein product		612217					Standard	XM_005249298		Approved	FLJ22195, dJ391O22.4	uc003ojr.2	Q9H6K1	OTTHUMG00000014553	ENST00000374023.3:c.119A>G	chr6.hg19:g.34664262T>C	ENSP00000363135:p.Asn40Ser	38.0	0.0	.		50.0	7.0	.	NM_024294	B2R8K7|Q5VV77|Q96MG5|Q9BUR9	Missense_Mutation	SNP	ENST00000374023.3	hg19	CCDS4796.1	.	.	.	.	.	.	.	.	.	.	T	10.61	1.399579	0.25291	0.0	1.16E-4	ENSG00000196821	ENST00000374023;ENST00000374026	.	.	.	2.99	1.78	0.24846	UBA-like (1);	0.185370	0.46442	D	0.000288	T	0.21186	0.0510	L	0.46670	1.46	0.80722	D	1	B;P	0.46142	0.207;0.873	B;B	0.44163	0.219;0.443	T	0.04178	-1.0971	9	0.33940	T	0.23	-7.2216	2.9531	0.05868	0.2121:0.1602:0.0:0.6277	.	40;40	Q9H6K1-2;Q9H6K1	.;CF106_HUMAN	S	40	.	ENSP00000363135:N40S	N	-	2	0	C6orf106	34772240	1.000000	0.71417	1.000000	0.80357	0.515000	0.34225	3.873000	0.56093	0.535000	0.28714	-0.669000	0.03829	AAT	.	.	.	weak		0.662	C6orf106-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040251.1	NM_022758		C	34664262	T	C	34664262	3	2	198	1	0	0	0	0	1	0	0	0	2321	1493	52	3	797	3	C6orf106	6	34664262	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	2495219	34664262	136450805	41	11929											
DST	667	hgsc.bcm.edu	37	chr6	56501422	56501422	+	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	agagctgtaagatccagctcCactgcgtctgcattgccgct	8	10	10	13	2	1	2	0	0	1	2	3	2	3	2	3	0	5	5	3	0	1	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr6:56501422C>T	ENST00000361203.3	-	19	2367	c.2360G>A	c.(2359-2361)tGg>tAg	p.W787*	DST_ENST00000244364.6_Nonsense_Mutation_p.W461*|DST_ENST00000312431.6_Nonsense_Mutation_p.W787*|DST_ENST00000421834.2_Nonsense_Mutation_p.W787*|DST_ENST00000370788.2_Nonsense_Mutation_p.W787*|DST_ENST00000370765.6_Nonsense_Mutation_p.W461*|DST_ENST00000446842.2_Nonsense_Mutation_p.W461*|DST_ENST00000370754.5_Nonsense_Mutation_p.W965*|DST_ENST00000518935.1_Nonsense_Mutation_p.W461*|DST_ENST00000370769.4_Nonsense_Mutation_p.W787*			Q03001	DYST_HUMAN	dystonin	787					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)			GATCCAGCTCCACTGCGTCTG	0.453																																					p.W461X		Atlas-SNP	.											.	DST	1427	.	0			c.G1382A						PASS	.						171	142	152					6																	56501422		2203	4300	6503	SO:0001587	stop_gained	667	exon9			CAGCTCCACTGCG	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.2360G>A	chr6.hg19:g.56501422C>T	ENSP00000354508:p.Trp787*	55.0	0.0	.		40.0	23.0	.	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Nonsense_Mutation	SNP	ENST00000361203.3	hg19		.	.	.	.	.	.	.	.	.	.	C	38	6.731382	0.97796	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203;ENST00000439203;ENST00000520645;ENST00000370765;ENST00000518935	.	.	.	5.25	5.25	0.73442	.	0.000000	0.46145	D	0.000304	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.029	0.92948	0.0:1.0:0.0:0.0	.	.	.	.	X	461;965;787;787;461;787;787;787;461;827;461;461	.	ENSP00000244364:W461X	W	-	2	0	DST	56609381	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	7.644000	0.83416	2.726000	0.93360	0.579000	0.79373	TGG	.	.	.	none		0.453	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		T	56501422	C	T	56501422	4	4	198	1	0	0	0	0	0	1	0	0	4785	595	21	2	19077	2	DST	6	56501422	Nonsense_Mutation	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	21837160	56501422	114613645	42	11930											
KIAA1009	22832	hgsc.bcm.edu	37	chr6	84872967	84872967	+	Missense_Mutation	SNP	T	T	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	gtttcagtcttttgatgtctTccaataaactgtctttttct	7	21	5	8	0	5	1	1	1	4	0	6	1	6	1	1	0	1	1	1	0	3	7			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr6:84872967T>G	ENST00000403245.3	-	19	2522	c.2408A>C	c.(2407-2409)gAa>gCa	p.E803A	KIAA1009_ENST00000461137.1_5'UTR|KIAA1009_ENST00000257766.4_Missense_Mutation_p.E727A	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)		TTTGATGTCTTCCAATAAACT	0.318																																					p.E803A		Atlas-SNP	.											.	KIAA1009	119	.	0			c.A2408C						PASS	.						180	165	170					6																	84872967		2203	4300	6503	SO:0001583	missense	22832	exon19			ATGTCTTCCAATA																												ENST00000403245.3:c.2408A>C	chr6.hg19:g.84872967T>G	ENSP00000385215:p.Glu803Ala	57.0	0.0	.		31.0	11.0	.	NM_014895		Missense_Mutation	SNP	ENST00000403245.3	hg19	CCDS34494.2	.	.	.	.	.	.	.	.	.	.	T	18.77	3.694256	0.68386	.	.	ENSG00000135315	ENST00000257766;ENST00000403245	T;T	0.33216	1.42;1.42	4.82	4.82	0.62117	.	0.000000	0.64402	D	0.000005	T	0.43523	0.1251	M	0.66506	2.035	0.46437	D	0.999046	D	0.71674	0.998	D	0.81914	0.995	T	0.37686	-0.9695	10	0.44086	T	0.13	-22.1089	14.6743	0.68967	0.0:0.0:0.0:1.0	.	803	Q5TB80	QN1_HUMAN	A	727;803	ENSP00000257766:E727A;ENSP00000385215:E803A	ENSP00000257766:E727A	E	-	2	0	KIAA1009	84929686	1.000000	0.71417	0.998000	0.56505	0.910000	0.53928	6.642000	0.74329	1.912000	0.55364	0.460000	0.39030	GAA	.	.	.	none		0.318	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1			G	84872967	T	G	84872967	3	3	198	1	0	0	0	0	1	0	0	0	8210	1783	62	5	1839	5	KIAA1009	6	84872967	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	28371545	84872967	86242100	43	11931											
ZNF292	23036	hgsc.bcm.edu	37	chr6	87943085	87943085	+	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	gggtcccatcttgttggataTgagaattaaacatctaatca	13	13	8	7	0	3	1	1	1	2	1	4	3	4	2	1	2	1	1	1	2	5	5			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr6:87943085T>A	ENST00000369577.3	+	5	624	c.581T>A	c.(580-582)aTg>aAg	p.M194K	ZNF292_ENST00000339907.4_Missense_Mutation_p.M189K	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	194						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		TTGTTGGATATGAGAATTAAA	0.313																																					p.M194K		Atlas-SNP	.											.	ZNF292	479	.	0			c.T581A						PASS	.						81	77	78					6																	87943085		1825	4076	5901	SO:0001583	missense	23036	exon5			TGGATATGAGAAT	AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.581T>A	chr6.hg19:g.87943085T>A	ENSP00000358590:p.Met194Lys	88.0	0.0	.		85.0	24.0	.	NM_015021	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	hg19	CCDS47457.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.376146	0.82682	.	.	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.10860	2.83;2.85	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.24198	0.0586	M	0.72894	2.215	0.58432	D	0.999993	D	0.76494	0.999	D	0.79784	0.993	T	0.01524	-1.1333	10	0.87932	D	0	.	15.658	0.77158	0.0:0.0:0.0:1.0	.	194	O60281	ZN292_HUMAN	K	194;189	ENSP00000358590:M194K;ENSP00000342847:M189K	ENSP00000342847:M189K	M	+	2	0	ZNF292	87999804	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.183000	0.77697	2.158000	0.67659	0.460000	0.39030	ATG	.	.	.	none		0.313	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		A	87943085	T	A	87943085	3	1	198	1	0	0	0	0	1	0	0	0	17838	1464	51	5	599	5	ZNF292	6	87943085	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	3070118	87943085	83171982	44	11932											
PNRC1	10957	hgsc.bcm.edu	37	chr6	89793801	89793801	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttagtgatccaccttctccTagtgttcttccaaagcctcc	7	15	5	14	0	2	1	0	1	2	0	6	1	5	1	6	0	1	1	6	0	3	6			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr6:89793801T>C	ENST00000336032.3	+	2	987	c.870T>C	c.(868-870)ccT>ccC	p.P290P	PNRC1_ENST00000369472.1_Silent_p.P105P|PNRC1_ENST00000354922.3_Silent_p.P105P	NM_006813.2	NP_006804.1	Q12796	PNRC1_HUMAN	proline-rich nuclear receptor coactivator 1	290					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(1)|large_intestine(2)|lung(3)	6		all_cancers(76;3.64e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.102)		CACCTTCTCCTAGTGTTCTTC	0.413										Multiple Myeloma(7;0.094)																											p.P290P		Atlas-SNP	.											.	PNRC1	17	.	0			c.T870C						PASS	.						81	83	83					6																	89793801		2203	4300	6503	SO:0001819	synonymous_variant	10957	exon2			TTCTCCTAGTGTT	U03105	CCDS5018.1	6q16.1	2008-02-05	2003-09-25	2003-09-26	ENSG00000146278	ENSG00000146278			17278	protein-coding gene	gene with protein product		606714	"proline rich 2"	PROL2		7578250	Standard	NM_006813		Approved	B4-2, PRR2	uc003pmv.3	Q12796	OTTHUMG00000015191	ENST00000336032.3:c.870T>C	chr6.hg19:g.89793801T>C		124.0	0.0	.		105.0	43.0	.	NM_006813	B2R6Q0|E1P515|Q5T7J6|Q7Z5N0	Silent	SNP	ENST00000336032.3	hg19	CCDS5018.1																																																																																			.	.	.	none		0.413	PNRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041471.1	NM_006813		C	89793801	T	C	89793801	2	2	198	1	0	0	0	0	0	0	0	1	12181	1509	53	3		3	PNRC1	6	89793801	Silent	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	1850716	89793801	81321266	45	11933											
MCM9	254394	hgsc.bcm.edu	37	chr6	119245294	119245294	+	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	tcaggacagacaggcaaaccTgatggagaaaacaaaaaaac	21	3	9	8	0	1	3	1	1	0	2	1	5	1	4	1	3	3	1	1	3	6	0			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr6:119245294T>C	ENST00000316316.6	-	3	591		c.e3-2		MCM9_ENST00000316068.3_Splice_Site	NM_017696.2	NP_060166.2	Q9NXL9	MCM9_HUMAN	minichromosome maintenance complex component 9						cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)	MCM8-MCM9 complex (GO:0097362)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		all_cancers(87;0.122)|all_epithelial(87;0.179)		GBM - Glioblastoma multiforme(226;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.194)		CAGGCAAACCTGATGGAGAAA	0.393																																					.		Atlas-SNP	.											.	MCM9	73	.	0			c.305-2A>G						PASS	.						118	126	124					6																	119245294		2201	4300	6501	SO:0001630	splice_region_variant	254394	exon3			CAAACCTGATGGA	BC031658	CCDS5121.1, CCDS56447.1	6q22.31	2009-11-16	2007-04-04	2007-04-04	ENSG00000111877	ENSG00000111877			21484	protein-coding gene	gene with protein product		610098	"minichromosome maintenance deficient domain containing 1", "chromosome 6 open reading frame 61"	MCMDC1, C6orf61		16226853, 15850810, 16495042	Standard	NM_153255		Approved	MGC35304, dJ329L24.3, FLJ20170	uc021zeh.1	Q9NXL9	OTTHUMG00000015468	ENST00000316316.6:c.305-2A>G	chr6.hg19:g.119245294T>C		49.0	0.0	.		54.0	21.0	.	NM_017696	B4DR30|B9DI77|Q2KHJ0|Q8N5S5|Q9HCV5	Splice_Site	SNP	ENST00000316316.6	hg19	CCDS56447.1	.	.	.	.	.	.	.	.	.	.	T	16.26	3.073982	0.55646	.	.	ENSG00000111877	ENST00000316316;ENST00000316068;ENST00000425154	.	.	.	5.48	5.48	0.80851	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5716	0.76341	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	MCM9	119286993	1.000000	0.71417	0.963000	0.40424	0.735000	0.41995	7.499000	0.81566	2.072000	0.62099	0.460000	0.39030	.	.	.	.	none		0.393	MCM9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042005.4	NM_153255	Intron	C	119245294	T	C	119245294	5	2	198	1	0	0	0	0	0	0	1	0	9401	1594	55	3	892	3	MCM9	6	119245294	Splice_Site	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	29451493	119245294	51869773	46	11934											
FGFR1OP	11116	hgsc.bcm.edu	37	chr6	167435950	167435950	+	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	agtgtctccttgtcagaaccCaagagcaaaagcagccttca	13	8	8	12	0	3	2	2	0	1	2	4	2	3	2	3	0	4	2	3	0	4	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr6:167435950C>A	ENST00000366847.4	+	8	864	c.633C>A	c.(631-633)ccC>ccA	p.P211P	FGFR1OP_ENST00000349556.4_Silent_p.P191P|RP11-517H2.6_ENST00000609590.1_RNA	NM_007045.2	NP_008976.1	O95684	FR1OP_HUMAN	FGFR1 oncogene partner	211					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|mitotic cell cycle (GO:0000278)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein tyrosine kinase activity (GO:0061099)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|protein tyrosine kinase inhibitor activity (GO:0030292)			large_intestine(2)|ovary(1)|stomach(1)	4		Breast(66;1.48e-05)|Ovarian(120;0.0607)		OV - Ovarian serous cystadenocarcinoma(33;1.73e-19)|BRCA - Breast invasive adenocarcinoma(81;5.1e-06)|GBM - Glioblastoma multiforme(31;0.00231)		TGTCAGAACCCAAGAGCAAAA	0.428			T	FGFR1	"MPD, NHL"																																p.P211P		Atlas-SNP	.		Dom	yes		6	6q27	11116	FGFR1 oncogene partner (FOP)		L	.	FGFR1OP	24	.	0			c.C633A						PASS	.						96	92	93					6																	167435950		2203	4300	6503	SO:0001819	synonymous_variant	11116	exon8			AGAACCCAAGAGC	Y18046	CCDS5296.1, CCDS5297.1, CCDS75550.1	6q27	2008-02-05			ENSG00000213066	ENSG00000213066			17012	protein-coding gene	gene with protein product		605392				9949182, 10373756	Standard	NM_007045		Approved	FOP	uc003qvj.3	O95684	OTTHUMG00000016011	ENST00000366847.4:c.633C>A	chr6.hg19:g.167435950C>A		61.0	0.0	.		38.0	11.0	.	NM_007045	A8K1D1|B2R705|Q49AI0|Q5R3F6|Q96EW1	Silent	SNP	ENST00000366847.4	hg19	CCDS5296.1																																																																																			.	.	.	none		0.428	FGFR1OP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043099.2	NM_007045		A	167435950	C	A	167435950	2	1	198	1	0	0	0	0	0	0	0	1	5871	581	21	4		4	FGFR1OP	6	167435950	Silent	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	48190656	167435950	3679117	47	11935											
WBSCR27	155368	hgsc.bcm.edu	37	chr7	73249148	73249148	+	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	gatgaagccatccttggcagAgatgccggataccacctcca	11	7	10	13	1	0	2	0	1	0	1	2	5	2	3	6	2	3	1	6	2	2	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr7:73249148A>C	ENST00000297873.4	-	6	712	c.663T>G	c.(661-663)tcT>tcG	p.S221S		NM_152559.2	NP_689772.2	Q8N6F8	WBS27_HUMAN	Williams Beuren syndrome chromosome region 27	221										NS(1)|central_nervous_system(1)|lung(2)|prostate(1)	5		Lung NSC(55;0.159)				TCCTTGGCAGAGATGCCGGAT	0.637																																					p.S221S		Atlas-SNP	.											.	WBSCR27	21	.	0			c.T663G						PASS	.						68	61	63					7																	73249148		2203	4300	6503	SO:0001819	synonymous_variant	155368	exon6			TGGCAGAGATGCC	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.663T>G	chr7.hg19:g.73249148A>C		100.0	0.0	.		117.0	42.0	.	NM_152559		Silent	SNP	ENST00000297873.4	hg19	CCDS5561.1																																																																																			.	.	.	none		0.637	WBSCR27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252312.1	NM_152559		C	73249148	A	C	73249148	2	2	198	1	0	0	0	0	0	0	0	1	17278	291	11	5		5	WBSCR27	7	73249148	Silent	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10		73249148	85889515	48	11936											
GDAP1	54332	hgsc.bcm.edu	37	chr8	75274164	75274164	+	Frame_Shift_Del	DEL	A	A	-																															gctgaagaaacttgctgaagAaaacccagatttacaagaag																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr8:75274164delA	ENST00000220822.7	+	4	610	c.530delA	c.(529-531)gaafs	p.E177fs	GDAP1_ENST00000521096.1_3'UTR|GDAP1_ENST00000434412.2_Frame_Shift_Del_p.E109fs	NM_001040875.2|NM_018972.2	NP_001035808.1|NP_061845.2	Q8TB36	GDAP1_HUMAN	ganglioside induced differentiation associated protein 1	177	GST C-terminal.				cell death (GO:0008219)|mitochondrial fission (GO:0000266)|protein targeting to mitochondrion (GO:0006626)|response to retinoic acid (GO:0032526)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	Breast(64;0.00769)	Myeloproliferative disorder(644;0.0122)	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.104)|all cancers(69;0.234)			CTTGCTGAAGAAAACCCAGAT	0.373																																					p.E177fs		Atlas-Indel,Pindel	.											.	GDAP1	36	.	0			c.529delG						PASS	.						118	110	113					8																	75274164		2203	4300	6503	SO:0001589	frameshift_variant	54332	exon4			.		CCDS34911.1, CCDS47877.1	8q13.3	2014-09-17	2012-02-09						15968	protein-coding gene	gene with protein product		606598	"Charcot-Marie-Tooth neuropathy 4A"	CMT4A		8268915, 11743579	Standard	NM_018972		Approved	CMT4	uc003yah.3	Q8TB36		ENST00000220822.7:c.530delA	chr8.hg19:g.75274164delA	ENSP00000220822:p.Glu177fs	31.0	0.0	0		31.0	16.0	0.516129	NM_018972	A8K957|E7FJF3|E7FJF4	Frame_Shift_Del	DEL	ENST00000220822.7	hg19	CCDS34911.1																																																																																			.	.	.	none		0.373	GDAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379061.1	NM_018972		-	75274164	A	-	75274164	7	5	198	1	0	1	0	1	0	0	0	0	6314	246	9	0	544	0	GDAP1	8	75274164	Frame_Shift_Del	DEL	A	TCGA-HE-A5NI-01A-11D-A26P-10		75274164	71089858	49	11937											
ACER2	340485	hgsc.bcm.edu	37	chr9	19435060	19435060	+	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	tgggagttccttgcactgcaCtgctcatcgcagagctaaag	9	10	11	11	1	1	1	1	0	0	1	3	2	2	2	1	1	4	6	1	1	2	3			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr9:19435060C>T	ENST00000340967.2	+	4	507	c.481C>T	c.(481-483)Ctg>Ttg	p.L161L	ACER2_ENST00000380376.1_Silent_p.L112L	NM_001010887.2	NP_001010887.2	Q5QJU3	ACER2_HUMAN	alkaline ceramidase 2	161					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						TTGCACTGCACTGCTCATCGC	0.557																																					p.L161L		Atlas-SNP	.											.	ACER2	24	.	0			c.C481T						PASS	.						219	164	182					9																	19435060		2203	4300	6503	SO:0001819	synonymous_variant	340485	exon4			ACTGCACTGCTCA	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.481C>T	chr9.hg19:g.19435060C>T		243.0	0.0	.		212.0	50.0	.	NM_001010887	A2A3R8|Q569G5|Q5VZR7|Q71RD2	Silent	SNP	ENST00000340967.2	hg19	CCDS34992.1																																																																																			.	.	.	none		0.557	ACER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051864.1	XM_294540		T	19435060	C	T	19435060	2	4	198	1	0	0	0	0	0	0	0	1	139	564	20	2		2	ACER2	9	19435060	Silent	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10		19435060	121778371	50	11938											
GPR21	2844	hgsc.bcm.edu	37	chr9	125797664	125797664	+	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	ccatatatcatctacttcttGttggaaagctccactggcca	10	13	6	12	0	3	0	1	0	2	0	4	1	4	1	3	2	2	2	3	2	4	6			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr9:125797664G>T	ENST00000373642.1	+	1	859	c.819G>T	c.(817-819)ttG>ttT	p.L273F	RABGAP1_ENST00000373647.4_Intron|RABGAP1_ENST00000493854.1_Intron|RABGAP1_ENST00000373643.5_Intron	NM_005294.1	NP_005285.1	Q99679	GPR21_HUMAN	G protein-coupled receptor 21	273					G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|negative regulation of insulin receptor signaling pathway (GO:0046627)|positive regulation of multicellular organism growth (GO:0040018)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	15						TCTACTTCTTGTTGGAAAGCT	0.458																																					p.L273F		Atlas-SNP	.											.	GPR21	29	.	0			c.G819T						PASS	.						148	128	135					9																	125797664		2203	4300	6503	SO:0001583	missense	2844	exon2			CTTCTTGTTGGAA	BC066885	CCDS6849.1	9q33	2012-08-21			ENSG00000188394	ENSG00000188394		"GPCR / Class A : Orphans"	4476	protein-coding gene	gene with protein product		601909					Standard	NM_005294		Approved		uc011lzk.3	Q99679	OTTHUMG00000020631	ENST00000373642.1:c.819G>T	chr9.hg19:g.125797664G>T	ENSP00000362746:p.Leu273Phe	136.0	0.0	.		129.0	49.0	.	NM_005294	B2R8W9|Q6NXU2	Missense_Mutation	SNP	ENST00000373642.1	hg19	CCDS6849.1	.	.	.	.	.	.	.	.	.	.	G	10.49	1.365299	0.24684	.	.	ENSG00000188394	ENST00000373642	T	0.41758	0.99	5.93	1.91	0.25777	GPCR, rhodopsin-like superfamily (1);	0.281802	0.23228	U	0.050493	T	0.33352	0.0860	M	0.64630	1.985	0.80722	D	1	P	0.41232	0.743	B	0.36244	0.22	T	0.05099	-1.0906	10	0.44086	T	0.13	-6.8862	5.7514	0.18148	0.2774:0.2257:0.4969:0.0	.	273	Q99679	GPR21_HUMAN	F	273	ENSP00000362746:L273F	ENSP00000362746:L273F	L	+	3	2	GPR21	124837485	0.993000	0.37304	0.989000	0.46669	0.976000	0.68499	0.535000	0.23114	0.080000	0.16959	-0.218000	0.12543	TTG	.	.	.	none		0.458	GPR21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053965.1	NM_005294		T	125797664	G	T	125797664	3	4	198	1	0	0	0	0	1	0	0	0	6688	1368	48	4	821	4	GPR21	9	125797664	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	106362604	125797664	15415767	51	11939											
SPTAN1	6709	hgsc.bcm.edu	37	chr9	131386741	131386741	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttccttcagttcaactggaaGgcggacgtggtggagtcctg	7	11	14	9	2	2	0	2	0	0	0	4	3	4	3	2	5	1	1	2	5	2	3			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr9:131386741G>A	ENST00000372731.4	+	45	6062	c.5952G>A	c.(5950-5952)aaG>aaA	p.K1984K	SPTAN1_ENST00000372739.3_Silent_p.K1989K|SPTAN1_ENST00000358161.5_Silent_p.K1989K	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1984					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						TCAACTGGAAGGCGGACGTGG	0.562																																					p.K1989K	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.G5967A						PASS	.						64	53	57					9																	131386741		2203	4300	6503	SO:0001819	synonymous_variant	6709	exon46			CTGGAAGGCGGAC	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.5952G>A	chr9.hg19:g.131386741G>A		165.0	0.0	.		159.0	68.0	.	NM_001130438	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Silent	SNP	ENST00000372731.4	hg19	CCDS6905.1																																																																																			.	.	.	none		0.562	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		A	131386741	G	A	131386741	2	1	198	1	0	0	0	0	0	0	0	1	15129	991	35	2		2	SPTAN1	9	131386741	Silent	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	5589077	131386741	9826690	52	11940											
KIF5B	3799	hgsc.bcm.edu	37	chr10	32320043	32320043	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctaagcaattcatattccttAgttttgtcttcaacttcctg	9	18	4	10	0	3	0	2	0	1	0	5	0	5	0	2	0	2	2	2	0	5	9			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr10:32320043A>G	ENST00000302418.4	-	14	1996	c.1539T>C	c.(1537-1539)acT>acC	p.T513T		NM_004521.2	NP_004512.1	P33176	KINH_HUMAN	kinesin family member 5B	513					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cellular protein metabolic process (GO:0044267)|cytoplasm organization (GO:0007028)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane potential (GO:0042391)|stress granule disassembly (GO:0035617)|vesicle transport along microtubule (GO:0047496)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)		KIF5B/ALK(8)|KIF5B/RET(79)	NS(2)|breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)	35		Prostate(175;0.0137)				CATATTCCTTAGTTTTGTCTT	0.313			T	"RET, ALK"	NSCLC																																p.T513T		Atlas-SNP	.		Dom	yes		10	10p11.22	3799	kinesin family member 5B		E	.	KIF5B	81	.	0			c.T1539C						PASS	.						103	101	102					10																	32320043		2203	4300	6503	SO:0001819	synonymous_variant	3799	exon14			TTCCTTAGTTTTG	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.1539T>C	chr10.hg19:g.32320043A>G		48.0	0.0	.		37.0	10.0	.	NM_004521	A0AVB2|Q5VZ85	Silent	SNP	ENST00000302418.4	hg19	CCDS7171.1																																																																																			.	.	.	none		0.313	KIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047467.1	NM_004521		G	32320043	A	G	32320043	2	3	198	1	0	0	0	0	0	0	0	1	8313	407	15	3		3	KIF5B	10	32320043	Silent	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10		32320043	103214704	53	11941											
CYP26A1	1592	hgsc.bcm.edu	37	chr10	94834101	94834101	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agatgaagcgcaggaaatacGgcttcatctacaagacgcat	15	7	10	9	3	2	3	1	1	1	2	2	4	2	4	0	2	3	3	0	2	5	3			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr10:94834101G>A	ENST00000224356.4	+	2	271	c.226G>A	c.(226-228)Ggc>Agc	p.G76S	CYP26A1_ENST00000371531.1_Missense_Mutation_p.G7S|CYP26A1_ENST00000394139.1_Missense_Mutation_p.G7S	NM_000783.3	NP_000774.2	O43174	CP26A_HUMAN	cytochrome P450, family 26, subfamily A, polypeptide 1	76					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)	CAGGAAATACGGCTTCATCTA	0.657																																					p.G76S		Atlas-SNP	.											.	CYP26A1	59	.	0			c.G226A						PASS	.						53	56	55					10																	94834101		2203	4300	6503	SO:0001583	missense	1592	exon2			AAATACGGCTTCA	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.226G>A	chr10.hg19:g.94834101G>A	ENSP00000224356:p.Gly76Ser	70.0	0.0	.		51.0	17.0	.	NM_000783	B3KNI4|Q5VXH9|Q5VXI0	Missense_Mutation	SNP	ENST00000224356.4	hg19	CCDS7426.1	.	.	.	.	.	.	.	.	.	.	G	34	5.324133	0.95708	.	.	ENSG00000095596	ENST00000371531;ENST00000224356;ENST00000394139	T;T;T	0.78003	-1.14;-1.14;-1.14	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	D	0.85504	0.5712	L	0.52759	1.655	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84672	0.0712	10	0.45353	T	0.12	-21.1018	18.8725	0.92320	0.0:0.0:1.0:0.0	.	76	O43174	CP26A_HUMAN	S	7;76;7	ENSP00000360586:G7S;ENSP00000224356:G76S;ENSP00000377695:G7S	ENSP00000224356:G76S	G	+	1	0	CYP26A1	94824091	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.187000	0.94912	2.711000	0.92665	0.561000	0.74099	GGC	.	.	.	none		0.657	CYP26A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049408.3			A	94834101	G	A	94834101	3	1	198	1	0	0	0	0	1	0	0	0	4157	1116	39	1	232	1	CYP26A1	10	94834101	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	62514058	94834101	40700646	54	11942											
LGI1	9211	hgsc.bcm.edu	37	chr10	95549895	95549895	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctccagacactcccaaaagaTattttcaaaggcctggattc	13	10	6	12	0	1	2	1	0	0	2	4	3	3	3	3	2	0	0	3	2	4	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr10:95549895T>C	ENST00000371418.4	+	5	731	c.471T>C	c.(469-471)gaT>gaC	p.D157D	LGI1_ENST00000371413.3_Silent_p.D157D|LGI1_ENST00000542308.1_Silent_p.D109D	NM_005097.2	NP_005088.1	O95970	LGI1_HUMAN	leucine-rich, glioma inactivated 1	157					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|nervous system development (GO:0007399)|neuron projection development (GO:0031175)|positive regulation of cell growth (GO:0030307)|positive regulation of synaptic transmission (GO:0050806)|protein homooligomerization (GO:0051260)	cell junction (GO:0030054)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|synapse (GO:0045202)	receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(18)|ovary(2)|skin(1)	29		Colorectal(252;0.124)				TCCCAAAAGATATTTTCAAAG	0.328																																					p.D157D		Atlas-SNP	.											.	LGI1	69	.	0			c.T471C						PASS	.						54	57	56					10																	95549895		2203	4299	6502	SO:0001819	synonymous_variant	9211	exon5			AAAAGATATTTTC	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.471T>C	chr10.hg19:g.95549895T>C		5.0	0.0	.		10.0	5.0	.	NM_005097	A8K0Z1|B4E1S0|Q5W001|Q5W002|Q8NI23|Q96LF5	Silent	SNP	ENST00000371418.4	hg19	CCDS7431.1																																																																																			.	.	.	none		0.328	LGI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049445.1	NM_005097		C	95549895	T	C	95549895	2	2	198	1	0	0	0	0	0	0	0	1	8758	1403	49	3		3	LGI1	10	95549895	Silent	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	715794	95549895	39984852	55	11943											
SEMA4G	57715	hgsc.bcm.edu	37	chr10	102738660	102738660	+	Missense_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	gagcaaggccagtgcagtggGtgatgatgacaaggtgtact	11	8	16	6	0	0	3	0	3	0	0	0	4	0	3	1	3	3	3	1	3	3	1			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr10:102738660G>A	ENST00000370250.4	+	7	1071	c.698G>A	c.(697-699)gGt>gAt	p.G233D	MRPL43_ENST00000370241.3_3'UTR|SEMA4G_ENST00000519756.1_Intron|RP11-108L7.4_ENST00000447344.1_RNA|SEMA4G_ENST00000517724.1_Missense_Mutation_p.G233D|MRPL43_ENST00000318325.2_3'UTR|SEMA4G_ENST00000210633.3_Missense_Mutation_p.G233D	NM_017893.3	NP_060363.2	Q9NTN9	SEM4G_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G	233	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Colorectal(252;0.234)		Epithelial(162;3.71e-09)|all cancers(201;2.1e-07)		AGTGCAGTGGGTGATGATGAC	0.587																																					p.G233D		Atlas-SNP	.											.	SEMA4G	55	.	0			c.G698A						PASS	.						84	65	71					10																	102738660		2203	4300	6503	SO:0001583	missense	57715	exon7			CAGTGGGTGATGA	AB046839	CCDS7501.1, CCDS55724.1	10q24.31	2013-01-11			ENSG00000095539	ENSG00000095539		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10735	protein-coding gene	gene with protein product							Standard	NM_017893		Approved	FLJ20590, KIAA1619	uc001krw.2	Q9NTN9	OTTHUMG00000018922	ENST00000370250.4:c.698G>A	chr10.hg19:g.102738660G>A	ENSP00000359270:p.Gly233Asp	370.0	0.0	.		288.0	106.0	.	NM_001203244	A1A5C6|A6NJY8|Q58EY1|Q9HCF3	Missense_Mutation	SNP	ENST00000370250.4	hg19		.	.	.	.	.	.	.	.	.	.	G	23.0	4.363918	0.82353	.	.	ENSG00000095539	ENST00000519649;ENST00000457585;ENST00000370250;ENST00000517724;ENST00000210633	T;T;T;T	0.29917	1.55;1.55;1.55;1.55	5.74	4.84	0.62591	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.050938	0.85682	D	0.000000	T	0.52805	0.1757	M	0.68952	2.095	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.984	D;D;P	0.97110	1.0;1.0;0.907	T	0.53049	-0.8493	10	0.45353	T	0.12	.	13.9543	0.64137	0.0731:0.0:0.9269:0.0	.	233;233;233	Q9NTN9;A1A5C6;Q9NTN9-2	SEM4G_HUMAN;.;.	D	233	ENSP00000428896:G233D;ENSP00000359270:G233D;ENSP00000430175:G233D;ENSP00000210633:G233D	ENSP00000210633:G233D	G	+	2	0	SEMA4G	102728650	1.000000	0.71417	0.959000	0.39883	0.876000	0.50452	7.636000	0.83301	1.433000	0.47394	0.484000	0.47621	GGT	.	.	.	none		0.587	SEMA4G-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049920.2			A	102738660	G	A	102738660	3	1	198	1	0	0	0	0	1	0	0	0	14049	1261	44	2	724	2	SEMA4G	10	102738660	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	7188765	102738660	32796087	56	11944											
C2CD3	26005	hgsc.bcm.edu	37	chr11	73748552	73748561	+	Frame_Shift_Del	DEL	AGGTTACTGG	AGGTTACTGG	-																															aggagctgacttgcaacaccAggttactggatttctccagg																								rs146977583		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	AGGTTACTGG	AGGTTACTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr11:73748552_73748561delAGGTTACTGG	ENST00000334126.7	-	30	6069_6078	c.5843_5852delCCAGTAACCT	c.(5842-5853)tccagtaacctgfs	p.SSNL1948fs	C2CD3_ENST00000313663.7_Frame_Shift_Del_p.SSNL1948fs			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1948					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)					TTGCAACACCAGGTTACTGGATTTCTCCAG	0.49																																					p.1948_1951del		Atlas-Indel,Pindel	.											.	C2CD3	288	.	0			c.5844_5853del						PASS	.																																			SO:0001589	frameshift_variant	26005	exon30			.	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.5843_5852delCCAGTAACCT	chr11.hg19:g.73748552_73748561delAGGTTACTGG	ENSP00000334379:p.Ser1948fs	141.0	0.0	0		98.0	29.0	0.295918	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Frame_Shift_Del	DEL	ENST00000334126.7	hg19																																																																																				.	.	.	none		0.49	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		-	73748561	AGGTTACTGG	-	73748552	7	5	198	1	0	1	0	1	0	0	0	0	2156	188	7	0	47	0	C2CD3	11	73748552	Frame_Shift_Del	DEL	AGGTTACTGG	TCGA-HE-A5NI-01A-11D-A26P-10		73748552	61257964	57	11945											
NAALAD2	10003	hgsc.bcm.edu	37	chr11	89896525	89896525	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggactcctgggtatttggaGctattgacccaaccagtggg	8	10	14	9	0	0	1	0	1	0	0	1	3	1	3	3	4	2	2	3	4	3	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr11:89896525G>A	ENST00000534061.1	+	10	1353	c.1123G>A	c.(1123-1125)Gct>Act	p.A375T	NAALAD2_ENST00000375944.3_Intron|NAALAD2_ENST00000321955.4_Missense_Mutation_p.A342T|NAALAD2_ENST00000525171.1_Missense_Mutation_p.A282T	NM_005467.3	NP_005458.1	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	375	NAALADase.				neurotransmitter catabolic process (GO:0042135)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|N-formylglutamate deformylase activity (GO:0050129)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(32)|pancreas(1)|prostate(3)|skin(5)|stomach(2)	59		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				GGTATTTGGAGCTATTGACCC	0.403																																					p.A375T		Atlas-SNP	.											.	NAALAD2	113	.	0			c.G1123A						PASS	.						122	129	126					11																	89896525		2201	4299	6500	SO:0001583	missense	10003	exon10			TTTGGAGCTATTG	AJ012370	CCDS8288.1, CCDS73364.1	11q14.3-q21	2011-08-16			ENSG00000077616	ENSG00000077616	3.4.17.21		14526	protein-coding gene	gene with protein product	"glutamate carboxypeptidase III"	611636				10085079	Standard	NM_005467		Approved	NAALADASE2, NAADALASE2, GPCIII	uc001pdf.4	Q9Y3Q0	OTTHUMG00000166368	ENST00000534061.1:c.1123G>A	chr11.hg19:g.89896525G>A	ENSP00000432481:p.Ala375Thr	80.0	0.0	.		59.0	19.0	.	NM_005467	B3KQR4|Q4KKV4|Q4VAM9	Missense_Mutation	SNP	ENST00000534061.1	hg19	CCDS8288.1	.	.	.	.	.	.	.	.	.	.	G	18.74	3.688939	0.68271	.	.	ENSG00000077616	ENST00000534061;ENST00000321955;ENST00000525171	T;T;T	0.65364	-0.15;-0.15;-0.15	5.51	4.61	0.57282	Peptidase M28 (1);	0.502085	0.19690	N	0.108285	T	0.69975	0.3171	M	0.83012	2.62	0.80722	D	1	P;B	0.45283	0.855;0.001	P;B	0.45753	0.492;0.004	T	0.73726	-0.3892	9	.	.	.	-1.5086	14.2116	0.65769	0.0725:0.0:0.9275:0.0	.	375;282	Q9Y3Q0;E9PKX5	NALD2_HUMAN;.	T	375;342;282	ENSP00000432481:A375T;ENSP00000320083:A342T;ENSP00000435249:A282T	.	A	+	1	0	NAALAD2	89536173	1.000000	0.71417	0.972000	0.41901	0.993000	0.82548	7.040000	0.76551	1.467000	0.48044	-0.218000	0.12543	GCT	.	.	.	none		0.403	NAALAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389424.2	NM_005467		A	89896525	G	A	89896525	3	1	198	1	0	0	0	0	1	0	0	0	10135	971	34	2	1161	2	NAALAD2	11	89896525	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	16147973	89896525	45109991	58	11946											
GPRC5D	55507	hgsc.bcm.edu	37	chr12	13102558	13102558	+	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	cagggacgatgtacagcagcAggaaaacccatgcgttggtg	12	6	14	9	2	0	0	0	0	0	0	0	3	0	2	1	3	5	4	1	3	3	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr12:13102558A>T	ENST00000228887.1	-	1	760	c.761T>A	c.(760-762)cTg>cAg	p.L254Q	RP11-392P7.6_ENST00000394742.3_RNA|RP11-392P7.6_ENST00000545914.1_RNA|RP11-392P7.6_ENST00000543515.2_RNA|RP11-392P7.6_ENST00000538231.1_RNA|RP11-392P7.6_ENST00000542078.1_RNA|RP11-392P7.6_ENST00000536029.1_RNA|GPRC5D_ENST00000396333.3_Missense_Mutation_p.L254Q|RP11-392P7.6_ENST00000540198.1_RNA	NM_018654.1	NP_061124.1	Q9NZD1	GPC5D_HUMAN	G protein-coupled receptor, class C, group 5, member D	254						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)		GTACAGCAGCAGGAAAACCCA	0.577																																					p.L254Q		Atlas-SNP	.											.	GPRC5D	23	.	0			c.T761A						PASS	.						144	132	136					12																	13102558		2203	4300	6503	SO:0001583	missense	55507	exon1			AGCAGCAGGAAAA	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.761T>A	chr12.hg19:g.13102558A>T	ENSP00000228887:p.Leu254Gln	194.0	0.0	.		245.0	129.0	.	NM_018654	Q3KNV3|Q7Z5J9|Q8TDS6	Missense_Mutation	SNP	ENST00000228887.1	hg19	CCDS8658.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.684961	0.88639	.	.	ENSG00000111291	ENST00000228887;ENST00000396333	D;D	0.94793	-3.52;-3.52	6.03	6.03	0.97812	GPCR, family 3, C-terminal (1);	0.000000	0.56097	D	0.000037	D	0.97269	0.9107	M	0.80183	2.485	0.51767	D	0.999936	D	0.89917	1.0	D	0.97110	1.0	D	0.97842	1.0269	10	0.87932	D	0	.	16.5655	0.84588	1.0:0.0:0.0:0.0	.	254	Q9NZD1	GPC5D_HUMAN	Q	254	ENSP00000228887:L254Q;ENSP00000379624:L254Q	ENSP00000228887:L254Q	L	-	2	0	GPRC5D	12993825	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.300000	0.96151	2.302000	0.77476	0.533000	0.62120	CTG	.	.	.	none		0.577	GPRC5D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400687.1			T	13102558	A	T	13102558	3	4	198	1	0	0	0	0	1	0	0	0	6734	188	7	5	286	5	GPRC5D	12	13102558	Missense_Mutation	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10		13102558	120749337	59	11947											
PDZRN4	29951	hgsc.bcm.edu	37	chr12	41966603	41966603	+	Frame_Shift_Del	DEL	A	A	-																															ttgcttaatgaagaactgagAaacattgagcttgagtgtca																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr12:41966603delA	ENST00000402685.2	+	10	2030	c.2022delA	c.(2020-2022)agafs	p.R674fs	PDZRN4_ENST00000539469.2_Frame_Shift_Del_p.R416fs|PDZRN4_ENST00000298919.7_Frame_Shift_Del_p.R414fs	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	674							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)				AAGAACTGAGAAACATTGAGC	0.458																																					p.R674fs		Atlas-Indel,Pindel	.											.	PDZRN4	346	.	0			c.2021delG						PASS	.						112	100	104					12																	41966603		2203	4300	6503	SO:0001589	frameshift_variant	29951	exon10			.	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.2022delA	chr12.hg19:g.41966603delA	ENSP00000384197:p.Arg674fs	155.0	0.0	0		212.0	64.0	0.301887	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Frame_Shift_Del	DEL	ENST00000402685.2	hg19	CCDS53777.1																																																																																			.	.	.	none		0.458	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377		-	41966603	A	-	41966603	7	5	198	1	0	1	0	1	0	0	0	0	11717	243	9	0	2133	0	PDZRN4	12	41966603	Frame_Shift_Del	DEL	A	TCGA-HE-A5NI-01A-11D-A26P-10	28864045	41966603	91885292	60	11948											
GALNT6	11226	hgsc.bcm.edu	37	chr12	51751976	51751982	+	Frame_Shift_Del	DEL	ACCAGGA	ACCAGGA	-																															tgggtagacattgtgcaggtAccaggaaaagttgtgacagt																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	ACCAGGA	ACCAGGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr12:51751976_51751982delACCAGGA	ENST00000543196.2	-	8	1637_1643	c.1432_1438delTCCTGGT	c.(1432-1440)tcctggtacfs	p.SWY478fs	GALNT6_ENST00000356317.3_Frame_Shift_Del_p.SWY478fs			Q8NCL4	GALT6_HUMAN	polypeptide N-acetylgalactosaminyltransferase 6	478					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(2)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						TTGTGCAGGTACCAGGAAAAGTTGTGA	0.517																																					p.478_480del		Atlas-Indel,Pindel	.											.	GALNT6	63	.	0			c.1433_1439del						PASS	.																																			SO:0001589	frameshift_variant	11226	exon9			.	Y08565	CCDS8813.1	12q13	2014-03-13	2014-03-13		ENSG00000139629	ENSG00000139629		"Glycosyltransferase family 2 domain containing"	4128	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 6"	605148	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6)"			10464263	Standard	NM_007210		Approved	GalNAc-T6	uc001ryl.1	Q8NCL4		ENST00000543196.2:c.1432_1438delTCCTGGT	chr12.hg19:g.51751976_51751982delACCAGGA	ENSP00000444171:p.Ser478fs	194.0	0.0	0		242.0	33.0	0.136364	NM_007210	Q8IYH4|Q9H6G2|Q9UIV5	Frame_Shift_Del	DEL	ENST00000543196.2	hg19	CCDS8813.1																																																																																			.	.	.	none		0.517	GALNT6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469735.1	NM_007210		-	51751982	ACCAGGA	-	51751976	7	5	198	1	0	1	0	1	0	0	0	0	6224	391	14	0	446	0	GALNT6	12	51751976	Frame_Shift_Del	DEL	ACCAGGA	TCGA-HE-A5NI-01A-11D-A26P-10	9785373	51751976	82099919	61	11949											
KRT2	3849	hgsc.bcm.edu	37	chr12	53045635	53045636	+	In_Frame_Ins	INS	-	-	TCCAAAGCCGCTGCCGCC																															cctccaaagctgctgccgccINStccaaaaccacctcctctgc																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr12:53045635_53045636insTCCAAAGCCGCTGCCGCC	ENST00000309680.3	-	1	312_313	c.291_292insGGCGGCAGCGGCTTTGGA	c.(289-294)ggaggc>ggaGGCGGCAGCGGCTTTGGAggc	p.97_98GG>GGGSGFGG		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	97	Head.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		ctgctgccgcctccaaaaccac	0.624																																					p.G98delinsGGSGFGG		Atlas-INDEL	.											.	KRT2	94	.	0			c.292_293insGGCGGCAGCGGCTTTGGA						PASS	.																																			SO:0001652	inframe_insertion	3849	exon1			.		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"-", "Intermediate filaments type II, keratins (basic)"	6439	protein-coding gene	gene with protein product	"epidermal ichthyosis bullosa of Siemens"	600194	"keratin 2A (epidermal ichthyosis bullosa of Siemens)"	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.291_292insGGCGGCAGCGGCTTTGGA	chr12.hg19:g.53045635_53045636insTCCAAAGCCGCTGCCGCC	ENSP00000310861:p.Gly97_Gly98insGlyGlySerGlyPheGly	209.0	0.0	0		225.0	20.0	0.0888889	NM_000423	Q4VAQ2	In_Frame_Ins	INS	ENST00000309680.3	hg19	CCDS8835.1																																																																																			.	.	.	none		0.624	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423		TCCAAAGCCGCTGCCGCC	53045636	-	TCCAAAGCCGCTGCCGCC	53045635	7	5	198	1	0	1	1	0	0	0	0	0	8464	681	24	0	1663	0	KRT2	12	53045635	In_Frame_Ins	INS	-	TCGA-HE-A5NI-01A-11D-A26P-10	1293659	53045635	80806260	62	11950											
SP7	121340	hgsc.bcm.edu	37	chr12	53722359	53722359	+	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	cagctgtggatgggcttcttCcgcagcccagccgctgctgc	4	9	13	15	2	1	0	0	0	1	0	2	1	2	1	3	2	5	5	3	2	0	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr12:53722359C>T	ENST00000536324.2	-	3	1150	c.867G>A	c.(865-867)cgG>cgA	p.R289R	SP7_ENST00000303846.3_Silent_p.R289R|SP7_ENST00000537210.2_Silent_p.R271R	NM_001173467.1	NP_001166938.1	Q8TDD2	SP7_HUMAN	Sp7 transcription factor	289					hematopoietic stem cell differentiation (GO:0060218)|osteoblast differentiation (GO:0001649)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DEAD/H-box RNA helicase binding (GO:0017151)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(2)|large_intestine(3)|lung(7)|skin(1)|urinary_tract(1)	14						TGGGCTTCTTCCGCAGCCCAG	0.657																																					p.R289R		Atlas-SNP	.											.	SP7	30	.	0			c.G867A						PASS	.						17	22	20					12																	53722359		2187	4292	6479	SO:0001819	synonymous_variant	121340	exon2			CTTCTTCCGCAGC	AF477981	CCDS44897.1, CCDS73475.1	12q13.13	2013-01-08				ENSG00000170374		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	17321	protein-coding gene	gene with protein product		606633				11792318	Standard	NM_152860		Approved	osterix, OSX	uc001sct.3	Q8TDD2		ENST00000536324.2:c.867G>A	chr12.hg19:g.53722359C>T		54.0	0.0	.		43.0	17.0	.	NM_152860	B3KY26|Q3MJ72|Q7Z718	Silent	SNP	ENST00000536324.2	hg19	CCDS44897.1																																																																																			.	.	.	none		0.657	SP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406917.1			T	53722359	C	T	53722359	2	4	198	1	0	0	0	0	0	0	0	1	14982	842	30	2		2	SP7	12	53722359	Silent	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	676724	53722359	80129536	63	11951											
DNAJC14	85406	hgsc.bcm.edu	37	chr12	56216194	56216194	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcctggaatccgagaaccaaAtgagatgtgataggggactc	13	7	13	8	1	0	3	0	2	0	2	2	7	1	5	3	3	1	0	3	3	4	1			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr12:56216194A>G	ENST00000357606.3	-	7	2150	c.1861T>C	c.(1861-1863)Ttt>Ctt	p.F621L	RP11-762I7.5_ENST00000546837.1_Missense_Mutation_p.I250T|RP11-762I7.5_ENST00000552719.1_5'UTR|DNAJC14_ENST00000317269.3_Missense_Mutation_p.F621L|DNAJC14_ENST00000317287.5_Missense_Mutation_p.F621L			Q6Y2X3	DJC14_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 14	621					protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(2)|kidney(1)|large_intestine(8)|lung(7)|ovary(3)|prostate(1)|skin(1)	23						CGAGAACCAAATGAGATGTGA	0.463											OREG0021910	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F621L		Atlas-SNP	.											.	DNAJC14	52	.	0			c.T1861C						PASS	.						107	112	110					12																	56216194		2203	4300	6503	SO:0001583	missense	85406	exon6			AACCAAATGAGAT	AF141342	CCDS8894.1	12q12	2011-09-02				ENSG00000135392		"Heat shock proteins / DNAJ (HSP40)"	24581	protein-coding gene	gene with protein product		606092				11331877, 11984006	Standard	NM_032364		Approved	DNAJ, DRIP78, HDJ3, LIP6, FLJ32792	uc001shu.2	Q6Y2X3		ENST00000357606.3:c.1861T>C	chr12.hg19:g.56216194A>G	ENSP00000350223:p.Phe621Leu	104.0	0.0	.	1013	120.0	62.0	.	NM_032364	A5YM67|Q17RY2|Q66K17|Q96N59|Q96T63	Missense_Mutation	SNP	ENST00000357606.3	hg19	CCDS8894.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	23.5|23.5	4.424150|4.424150	0.83667|0.83667	.|.	.|.	ENSG00000135392|ENSG00000257390	ENST00000357606;ENST00000317269;ENST00000537962;ENST00000317287;ENST00000540330|ENST00000546837	T;T;T|.	0.33216|.	1.42;1.42;1.42|.	5.73|5.73	5.73|5.73	0.89815|0.89815	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.53481|0.53481	0.1799|0.1799	L|L	0.28014|0.28014	0.82|0.82	0.58432|0.58432	D|D	0.999997|0.999997	D;D|.	0.71674|.	0.998;0.998|.	D;D|.	0.72625|.	0.978;0.978|.	T|T	0.50285|0.50285	-0.8846|-0.8846	10|5	0.29301|.	T|.	0.29|.	-12.4258|-12.4258	14.2815|14.2815	0.66216|0.66216	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	621;621|.	Q6Y2X3;A8K5A7|.	DJC14_HUMAN;.|.	L|T	621;621;331;621;117|250	ENSP00000350223:F621L;ENSP00000316240:F621L;ENSP00000317500:F621L|.	ENSP00000316240:F621L|.	F|I	-|-	1|2	0|0	DNAJC14|RP11-762I7.5	54502461|54502461	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	8.512000|8.512000	0.90538|0.90538	2.324000|2.324000	0.78689|0.78689	0.533000|0.533000	0.62120|0.62120	TTT|ATT	.	.	.	none		0.463	DNAJC14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409095.1	NM_032364		G	56216194	A	G	56216194	3	3	198	1	0	0	0	0	1	0	0	0	4635	101	4	3	255	3	DNAJC14	12	56216194	Missense_Mutation	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10	2493835	56216194	77635701	64	11952											
DPY19L2	283417	hgsc.bcm.edu	37	chr12	63991615	63991615	+	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	ttccatgaagtcaaattcggGagcacaggtatatattaaag	15	11	9	6	1	1	1	1	1	0	0	3	2	2	2	1	2	1	2	1	2	7	6			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr12:63991615G>A	ENST00000324472.4	-	14	1618	c.1435C>T	c.(1435-1437)Ccc>Tcc	p.P479S		NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	479					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)			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)		TCAAATTCGGGAGCACAGGTA	0.323																																					p.P479S		Atlas-SNP	.											.	DPY19L2	97	.	0			c.C1435T						PASS	.						53	58	56					12																	63991615		2202	4287	6489	SO:0001583	missense	283417	exon14			ATTCGGGAGCACA		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.1435C>T	chr12.hg19:g.63991615G>A	ENSP00000315988:p.Pro479Ser	132.0	0.0	.		129.0	29.0	.	NM_173812	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Missense_Mutation	SNP	ENST00000324472.4	hg19	CCDS31851.1	.	.	.	.	.	.	.	.	.	.	G	15.22	2.769090	0.49680	.	.	ENSG00000177990	ENST00000324472	T	0.54071	0.59	3.15	2.22	0.28083	.	0.062767	0.64402	U	0.000008	T	0.51991	0.1707	M	0.71581	2.175	0.58432	D	0.999999	B	0.25272	0.122	B	0.36186	0.219	T	0.44050	-0.9353	9	.	.	.	.	8.3442	0.32263	0.0:0.2427:0.7573:0.0	.	479	Q6NUT2	D19L2_HUMAN	S	479	ENSP00000315988:P479S	.	P	-	1	0	DPY19L2	62277882	1.000000	0.71417	0.698000	0.30274	0.953000	0.61014	2.632000	0.46511	0.619000	0.30197	0.586000	0.80456	CCC	.	.	.	none		0.323	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812		A	63991615	G	A	63991615	3	1	198	1	0	0	0	0	1	0	0	0	4743	1174	41	2	877	2	DPY19L2	12	63991615	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	7775421	63991615	69860280	65	11953											
TMPO	7112	hgsc.bcm.edu	37	chr12	98925573	98925573	+	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	tcagcagaaaatacaaggcaGaatggaagtaatgattctga	18	8	10	5	0	2	4	1	2	1	2	2	5	2	5	0	2	2	3	0	2	7	3			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr12:98925573G>C	ENST00000556029.1	+	3	878	c.522G>C	c.(520-522)caG>caC	p.Q174H	TMPO_ENST00000266732.4_Missense_Mutation_p.Q174H|TMPO_ENST00000393053.2_Missense_Mutation_p.Q174H|TMPO_ENST00000343315.5_Missense_Mutation_p.Q174H|TMPO_ENST00000261210.5_Missense_Mutation_p.Q174H	NM_001032283.2	NP_001027454.1	P42167	LAP2B_HUMAN	thymopoietin	174	NAKAP95-binding N.|Nucleoplasmic. {ECO:0000255}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)|lamin binding (GO:0005521)			breast(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						ATACAAGGCAGAATGGAAGTA	0.323																																					p.Q174H		Atlas-SNP	.											.	TMPO	111	.	0			c.G522C						PASS	.						70	70	70					12																	98925573		2203	4300	6503	SO:0001583	missense	7112	exon3			AAGGCAGAATGGA		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.522G>C	chr12.hg19:g.98925573G>C	ENSP00000450627:p.Gln174His	135.0	0.0	.		160.0	36.0	.	NM_003276	A2T926|Q14861	Missense_Mutation	SNP	ENST00000556029.1	hg19	CCDS31879.1	.	.	.	.	.	.	.	.	.	.	G	18.16	3.562332	0.65538	.	.	ENSG00000120802	ENST00000556029;ENST00000343315;ENST00000266732;ENST00000393053;ENST00000261210;ENST00000556678	T;T;T;T;T;T	0.74421	0.18;0.22;1.55;-0.23;-0.84;-0.8	5.4	2.51	0.30379	.	0.053524	0.85682	D	0.000000	T	0.78046	0.4222	L	0.46157	1.445	0.49687	D	0.999819	D;P;D;D	0.71674	0.997;0.604;0.998;0.997	D;B;D;D	0.79784	0.991;0.204;0.993;0.99	T	0.75611	-0.3258	10	0.59425	D	0.04	.	6.5002	0.22164	0.2145:0.1293:0.6561:0.0	.	207;174;174;174	Q59G12;P42167;A2T926;P42166	.;LAP2B_HUMAN;.;LAP2A_HUMAN	H	174;174;174;174;174;81	ENSP00000450627:Q174H;ENSP00000340251:Q174H;ENSP00000266732:Q174H;ENSP00000376773:Q174H;ENSP00000261210:Q174H;ENSP00000451552:Q81H	ENSP00000261210:Q174H	Q	+	3	2	TMPO	97449704	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.511000	0.45476	0.634000	0.30469	0.655000	0.94253	CAG	.	.	.	none		0.323	TMPO-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407973.2	NM_003276		C	98925573	G	C	98925573	3	2	198	1	0	0	0	0	1	0	0	0	16249	933	33	4	532	4	TMPO	12	98925573	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	34933958	98925573	34926322	66	11954											
RNF34	80196	hgsc.bcm.edu	37	chr12	121855373	121855374	+	Frame_Shift_Del	DEL	AG	AG	-																															tcttacaagaaaatctccgtAgatgttctacttgtcactta																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr12:121855373_121855374delAG	ENST00000392464.2	+	3	361_362	c.292_293delAG	c.(292-294)agafs	p.R98fs	RNF34_ENST00000392465.3_Frame_Shift_Del_p.R99fs|RNF34_ENST00000555076.1_Intron|RNF34_ENST00000361234.5_Frame_Shift_Del_p.R98fs					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)		AAATCTCCGTAGATGTTCTACT	0.416																																					p.98_99del		Atlas-Indel,Pindel	.											.	RNF34	54	.	0			c.294_295del						PASS	.																																			SO:0001589	frameshift_variant	80196	exon4			.	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.292_293delAG	chr12.hg19:g.121855373_121855374delAG	ENSP00000376257:p.Arg98fs	68.0	0.0	0		82.0	44.0	0.536585	NM_194271		Frame_Shift_Del	DEL	ENST00000392464.2	hg19																																																																																				.	.	.	none		0.416	RNF34-005	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000413892.1	NM_194271		-	121855374	AG	-	121855373	7	5	198	1	0	1	0	1	0	0	0	0	13502	412	15	0	315	0	RNF34	12	121855373	Frame_Shift_Del	DEL	AG	TCGA-HE-A5NI-01A-11D-A26P-10	22929800	121855373	11996522	67	11955											
SACS	26278	hgsc.bcm.edu	37	chr13	23906370	23906371	+	Frame_Shift_Ins	INS	-	-	A																															tagactcctgaacagaccagINSaaactactctcttaactgta																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr13:23906370_23906371insA	ENST00000382292.3	-	9	11917_11918	c.11644_11645insT	c.(11644-11646)tctfs	p.S3882fs	SACS_ENST00000382298.3_Frame_Shift_Ins_p.S3882fs|SACS_ENST00000402364.1_Frame_Shift_Ins_p.S3132fs			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3882					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)		GAACAGACCAGAAACTACTCTC	0.416																																					p.S3882fs		Atlas-Indel,Pindel	.											.	SACS	871	.	0			c.11645_11646insT						PASS	.																																			SO:0001589	frameshift_variant	26278	exon10			.	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.11645dupT	chr13.hg19:g.23906373_23906373dupA	ENSP00000371729:p.Ser3882fs	58.0	0.0	0		46.0	14.0	0.304348	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Frame_Shift_Ins	INS	ENST00000382292.3	hg19	CCDS9300.2																																																																																			.	.	.	none		0.416	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		A	23906371	-	A	23906370	7	5	198	1	0	1	1	0	0	0	0	0	13817	942	33	0	2098	0	SACS	13	23906370	Frame_Shift_Ins	INS	-	TCGA-HE-A5NI-01A-11D-A26P-10		23906370	91263508	68	11956											
IPO4	79711	hgsc.bcm.edu	37	chr14	24654679	24654679	+	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	gttcacctgtaggttttctgAgaactggcccagggcaaaca	10	10	11	10	0	2	1	1	1	1	1	2	2	2	1	2	3	2	4	2	3	3	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr14:24654679A>T	ENST00000354464.6	-	13	1440	c.1264T>A	c.(1264-1266)Tca>Aca	p.S422T	RP11-468E2.2_ENST00000561419.1_3'UTR	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4	422					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)		AGGTTTTCTGAGAACTGGCCC	0.562																																					p.S422T		Atlas-SNP	.											.	IPO4	74	.	0			c.T1264A						PASS	.						85	91	89					14																	24654679		2042	4182	6224	SO:0001583	missense	79711	exon13			TTTCTGAGAACTG	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.1264T>A	chr14.hg19:g.24654679A>T	ENSP00000346453:p.Ser422Thr	133.0	0.0	.		141.0	60.0	.	NM_024658	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Missense_Mutation	SNP	ENST00000354464.6	hg19	CCDS9616.1	.	.	.	.	.	.	.	.	.	.	A	29.5	5.007813	0.93287	.	.	ENSG00000196497	ENST00000354464;ENST00000399536	T	0.05513	3.43	5.44	5.44	0.79542	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.21962	0.0529	M	0.69185	2.1	0.80722	D	1	D	0.65815	0.995	D	0.70016	0.967	T	0.00138	-1.2003	10	0.72032	D	0.01	-9.0334	13.1234	0.59340	1.0:0.0:0.0:0.0	.	422	Q8TEX9	IPO4_HUMAN	T	422;98	ENSP00000346453:S422T	ENSP00000346453:S422T	S	-	1	0	IPO4	23724519	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.283000	0.65621	2.288000	0.76882	0.533000	0.62120	TCA	.	.	.	none		0.562	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658		T	24654679	A	T	24654679	3	4	198	1	0	0	0	0	1	0	0	0	7802	304	11	5	2053	5	IPO4	14	24654679	Missense_Mutation	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10		24654679	82694861	69	11957											
BRMS1L	84312	hgsc.bcm.edu	37	chr14	36300676	36300676	+	Frame_Shift_Del	DEL	T	T	-																															tttggatgaaatgtccaatcTtgaaaaacagtttaccgatc																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr14:36300676delT	ENST00000216807.7	+	2	402	c.203delT	c.(202-204)cttfs	p.L68fs	BRMS1L_ENST00000543183.1_Frame_Shift_Del_p.L20fs	NM_032352.3	NP_115728.2	Q5PSV4	BRM1L_HUMAN	breast cancer metastasis-suppressor 1-like	68					regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9	Breast(36;0.137)|Hepatocellular(127;0.158)		Lung(8;1.7e-07)|LUAD - Lung adenocarcinoma(9;3e-07)|Epithelial(34;0.00467)|all cancers(34;0.0157)|BRCA - Breast invasive adenocarcinoma(188;0.158)	GBM - Glioblastoma multiforme(112;0.0333)		ATGTCCAATCTTGAAAAACAG	0.333																																					p.L68fs		Atlas-Indel,Pindel	.											.	BRMS1L	26	.	0			c.202delC						PASS	.						116	117	116					14																	36300676		2203	4300	6503	SO:0001589	frameshift_variant	84312	exon2			.	AK096496	CCDS32066.1	14q13.1	2005-09-22	2003-12-02	2003-12-03		ENSG00000100916			20512	protein-coding gene	gene with protein product			"breast cancer metastasis-suppressor 1"	BRMS1			Standard	XM_005268128		Approved	MGC11296, FLJ39177	uc001wtl.3	Q5PSV4		ENST00000216807.7:c.203delT	chr14.hg19:g.36300676delT	ENSP00000216807:p.Leu68fs	242.0	0.0	0		203.0	80.0	0.394089	NM_032352	A6NFW5|A6NH45|B2RD65|Q9BRI4	Frame_Shift_Del	DEL	ENST00000216807.7	hg19	CCDS32066.1																																																																																			.	.	.	none		0.333	BRMS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409601.2	NM_032352		-	36300676	T	-	36300676	7	5	198	1	0	1	0	1	0	0	0	0	1519	1609	56	0	209	0	BRMS1L	14	36300676	Frame_Shift_Del	DEL	T	TCGA-HE-A5NI-01A-11D-A26P-10	11645997	36300676	71048864	70	11958											
NIN	51199	hgsc.bcm.edu	37	chr14	51223359	51223359	+	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	tccttcaacttcctagtcagCtcctgtaactttgttttctc	6	18	4	13	0	3	0	2	0	1	0	7	0	6	0	3	0	3	3	3	0	3	7			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr14:51223359C>G	ENST00000382041.3	-	18	4579	c.4389G>C	c.(4387-4389)gaG>gaC	p.E1463D	NIN_ENST00000389868.3_Intron|NIN_ENST00000324330.9_Missense_Mutation_p.E1463D|NIN_ENST00000245441.5_Missense_Mutation_p.E1463D|NIN_ENST00000382043.4_Intron|NIN_ENST00000530997.2_Missense_Mutation_p.E1463D|NIN_ENST00000453196.1_Missense_Mutation_p.E1463D	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	1463					centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					tcctagtcagctcctgtaact	0.418			T	PDGFRB	MPD																																p.E1463D		Atlas-SNP	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN	475	.	0			c.G4389C						PASS	.						113	88	96					14																	51223359		2194	4286	6480	SO:0001583	missense	51199	exon18			AGTCAGCTCCTGT	AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"EF-hand domain containing"	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.4389G>C	chr14.hg19:g.51223359C>G	ENSP00000371472:p.Glu1463Asp	125.0	0.0	.		81.0	27.0	.	NM_020921	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Missense_Mutation	SNP	ENST00000382041.3	hg19	CCDS32079.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.37|16.37	3.103971|3.103971	0.56291|0.56291	.|.	.|.	ENSG00000100503|ENSG00000100503	ENST00000530997;ENST00000389869;ENST00000530853|ENST00000245441;ENST00000311149;ENST00000324292;ENST00000382041;ENST00000324330;ENST00000453196	.|T;T;T;T	.|0.10192	.|3.17;2.91;2.9;2.91	5.59|5.59	4.7|4.7	0.59300|0.59300	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.20170|0.20170	0.0485|0.0485	M|M	0.62723|0.62723	1.935|1.935	0.31457|0.31457	N|N	0.670061|0.670061	.|P;D;P;P	.|0.59767	.|0.873;0.986;0.852;0.8	.|B;P;B;B	.|0.53224	.|0.291;0.721;0.275;0.416	T|T	0.11842|0.11842	-1.0571|-1.0571	5|10	.|0.48119	.|T	.|0.1	-1.0688|-1.0688	10.3959|10.3959	0.44201|0.44201	0.0:0.9099:0.0:0.0901|0.0:0.9099:0.0:0.0901	.|.	.|1469;1463;1463;1463	.|Q8N4C6-5;C9J066;Q8N4C6;Q8N4C6-7	.|.;.;NIN_HUMAN;.	P|D	954|1463;1446;1469;1463;1463;1463	.|ENSP00000245441:E1463D;ENSP00000371472:E1463D;ENSP00000324210:E1463D;ENSP00000412391:E1463D	.|ENSP00000245441:E1463D	A|E	-|-	1|3	0|2	NIN|NIN	50293109|50293109	0.999000|0.999000	0.42202|0.42202	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	0.415000|0.415000	0.21181|0.21181	1.366000|1.366000	0.46076|0.46076	0.655000|0.655000	0.94253|0.94253	GCT|GAG	.	.	.	none		0.418	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946		G	51223359	C	G	51223359	3	3	198	1	0	0	0	0	1	0	0	0	10424	796	28	4	2216	4	NIN	14	51223359	Missense_Mutation	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	14922683	51223359	56126181	71	11959											
CHGA	1113	hgsc.bcm.edu	37	chr14	93397675	93397675	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagaaaagtggtgaagccAcagacggagccaggccccag	14	2	14	11	1	0	3	0	1	0	2	0	5	0	4	4	3	2	0	4	3	3	0			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr14:93397675A>G	ENST00000216492.5	+	6	716	c.436A>G	c.(436-438)Aca>Gca	p.T146A	CHGA_ENST00000334654.4_Intron|CHGA_ENST00000553866.1_3'UTR	NM_001275.3	NP_001266.1	P10645	CMGA_HUMAN	chromogranin A (parathyroid secretory protein 1)	146					regulation of blood pressure (GO:0008217)	extracellular region (GO:0005576)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|secretory granule (GO:0030141)				cervix(1)|large_intestine(1)|lung(3)|skin(3)	8		all_cancers(154;0.0843)		Epithelial(152;0.102)|COAD - Colon adenocarcinoma(157;0.208)|all cancers(159;0.224)		TGGTGAAGCCACAGACGGAGC	0.597																																					p.T146A	Colon(31;154 822 45066 49155)|NSCLC(28;804 1157 13734 25204)	Atlas-SNP	.											.	CHGA	32	.	0			c.A436G						PASS	.						33	40	37					14																	93397675		2203	4300	6503	SO:0001583	missense	1113	exon6			GAAGCCACAGACG		CCDS9906.1	14q32	2012-10-02			ENSG00000100604	ENSG00000100604			1929	protein-coding gene	gene with protein product	"vasostatin", "pancreastatin", "parastatin"	118910				3403545	Standard	NM_001275		Approved		uc001ybc.4	P10645		ENST00000216492.5:c.436A>G	chr14.hg19:g.93397675A>G	ENSP00000216492:p.Thr146Ala	147.0	0.0	.		118.0	43.0	.	NM_001275	B2R9E9|Q53FA8|Q6NR84|Q96E84|Q96GL7|Q9BQB5	Missense_Mutation	SNP	ENST00000216492.5	hg19	CCDS9906.1	.	.	.	.	.	.	.	.	.	.	A	5.459	0.269804	0.10349	.	.	ENSG00000100604	ENST00000216492	T	0.01647	4.71	4.7	-9.4	0.00616	.	2.536240	0.01191	N	0.007328	T	0.01061	0.0035	N	0.16656	0.425	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45862	-0.9232	10	0.11182	T	0.66	6.9295	4.398	0.11372	0.216:0.2247:0.4493:0.11	.	146	P10645	CMGA_HUMAN	A	146	ENSP00000216492:T146A	ENSP00000216492:T146A	T	+	1	0	CHGA	92467428	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.711000	0.05019	-2.936000	0.00299	-0.441000	0.05720	ACA	.	.	.	none		0.597	CHGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412411.1	NM_001275		G	93397675	A	G	93397675	3	3	198	1	0	0	0	0	1	0	0	0	3340	159	6	3	458	3	CHGA	14	93397675	Missense_Mutation	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10	42174316	93397675	13951865	72	11960											
GCNT3	9245	hgsc.bcm.edu	37	chr15	59911000	59911000	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgcttcccaaatgtcttcaTagccagtaagctggttcggg	8	13	10	10	1	2	0	1	0	1	0	4	0	3	0	2	2	3	4	2	2	3	6			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr15:59911000T>C	ENST00000396065.1	+	3	1011	c.563T>C	c.(562-564)aTa>aCa	p.I188T	GCNT3_ENST00000560585.1_Missense_Mutation_p.I188T	NM_004751.2	NP_004742.1	O95395	GCNT3_HUMAN	glucosaminyl (N-acetyl) transferase 3, mucin type	188					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|immunoglobulin production in mucosal tissue (GO:0002426)|intestinal absorption (GO:0050892)|kidney morphogenesis (GO:0060993)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|tissue morphogenesis (GO:0048729)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0047225)|beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						AATGTCTTCATAGCCAGTAAG	0.498																																					p.I188T		Atlas-SNP	.											.	GCNT3	42	.	0			c.T563C						PASS	.						117	110	112					15																	59911000		2190	4290	6480	SO:0001583	missense	9245	exon3			TCTTCATAGCCAG	AF102542	CCDS10172.1	15q22	2013-02-25			ENSG00000140297	ENSG00000140297	2.4.1.102, 2.4.1.150	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	4205	protein-coding gene	gene with protein product		606836				9915862, 9988682	Standard	NM_004751		Approved	C2GnT-M, C2/4GnT, C2GnT2	uc002age.3	O95395	OTTHUMG00000132726	ENST00000396065.1:c.563T>C	chr15.hg19:g.59911000T>C	ENSP00000379377:p.Ile188Thr	76.0	0.0	.		72.0	31.0	.	NM_004751		Missense_Mutation	SNP	ENST00000396065.1	hg19	CCDS10172.1	.	.	.	.	.	.	.	.	.	.	T	17.13	3.311833	0.60414	.	.	ENSG00000140297	ENST00000396065	T	0.11712	2.75	6.13	6.13	0.99165	.	0.536118	0.20374	N	0.093586	T	0.20210	0.0486	M	0.80183	2.485	0.45035	D	0.998058	P	0.36354	0.549	B	0.35182	0.197	T	0.01249	-1.1406	10	0.87932	D	0	.	16.8061	0.85666	0.0:0.0:0.0:1.0	.	188	O95395	GCNT3_HUMAN	T	188	ENSP00000379377:I188T	ENSP00000379377:I188T	I	+	2	0	GCNT3	57698292	1.000000	0.71417	0.948000	0.38648	0.868000	0.49771	7.955000	0.87856	2.367000	0.80283	0.529000	0.55759	ATA	.	.	.	none		0.498	GCNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256068.1	NM_004751		C	59911000	T	C	59911000	3	2	198	1	0	0	0	0	1	0	0	0	6309	1406	49	3	565	3	GCNT3	15	59911000	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10		59911000	42620392	73	11961											
DENND4A	10260	hgsc.bcm.edu	37	chr15	65956990	65956991	+	Frame_Shift_Ins	INS	-	-	T																															ttttaatgctttttaccataINScttttcaacagttcctggtt																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr15:65956990_65956991insT	ENST00000431932.2	-	30	5505_5506	c.5297_5298insA	c.(5296-5298)agtfs	p.S1766fs	DENND4A_ENST00000443035.3_Frame_Shift_Ins_p.S1809fs	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	1766					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						TTTTTACCATACTTTTCAACAG	0.337																																					p.S1809fs		Atlas-Indel,Pindel	.											.	DENND4A	217	.	0			c.5427_5428insA						PASS	.																																			SO:0001589	frameshift_variant	10260	exon31			.	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.5297_5298insA	chr15.hg19:g.65956990_65956991insT	ENSP00000396830:p.Ser1766fs	84.0	0.0	0		53.0	15.0	0.283019	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Frame_Shift_Ins	INS	ENST00000431932.2	hg19	CCDS45285.1																																																																																			.	.	.	none		0.337	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		T	65956991	-	T	65956990	7	5	198	1	0	1	1	0	0	0	0	0	4435	388	14	0	305	0	DENND4A	15	65956990	Frame_Shift_Ins	INS	-	TCGA-HE-A5NI-01A-11D-A26P-10	6045990	65956990	36574402	74	11962											
UACA	55075	hgsc.bcm.edu	37	chr15	70991969	70991969	+	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	ttctgctgctttcatcaatcGgtcatcatatttattccaat	9	18	4	10	1	5	0	4	0	1	0	7	0	6	0	1	1	2	2	1	1	4	6			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr15:70991969G>A	ENST00000322954.6	-	2	294	c.109C>T	c.(109-111)Cga>Tga	p.R37*	UACA_ENST00000560441.1_Nonsense_Mutation_p.R24*|UACA_ENST00000539319.1_Nonsense_Mutation_p.R37*|UACA_ENST00000379983.2_Nonsense_Mutation_p.R24*	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	37					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						TTCATCAATCGGTCATCATAT	0.363																																					p.R37X		Atlas-SNP	.											.	UACA	235	.	0			c.C109T						PASS	.						145	125	132					15																	70991969		2199	4297	6496	SO:0001587	stop_gained	55075	exon2			TCAATCGGTCATC	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.109C>T	chr15.hg19:g.70991969G>A	ENSP00000314556:p.Arg37*	61.0	0.0	.		58.0	20.0	.	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Nonsense_Mutation	SNP	ENST00000322954.6	hg19	CCDS10235.1	.	.	.	.	.	.	.	.	.	.	G	37	6.366924	0.97511	.	.	ENSG00000137831	ENST00000322954;ENST00000379983;ENST00000395362;ENST00000539319	.	.	.	5.28	3.23	0.37069	.	0.000000	0.48286	D	0.000192	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.7105	14.3737	0.66860	0.0:0.0:0.6557:0.3443	.	.	.	.	X	37;24;24;37	.	ENSP00000314556:R37X	R	-	1	2	UACA	68779023	1.000000	0.71417	0.999000	0.59377	0.956000	0.61745	4.021000	0.57196	1.312000	0.45043	0.491000	0.48974	CGA	.	.	.	none		0.363	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			A	70991969	G	A	70991969	4	1	198	1	0	0	0	0	0	1	0	0	16836	1124	39	1	4213	1	UACA	15	70991969	Nonsense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	5034979	70991969	31539423	75	11963											
ST8SIA2	8128	hgsc.bcm.edu	37	chr15	92973323	92973323	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagatcagctgtgaacagctTacatagcaaatctaataggt	15	10	8	8	0	2	2	1	1	1	1	2	2	2	2	0	1	5	3	0	1	6	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr15:92973323T>C	ENST00000268164.3	+	2	380	c.143T>C	c.(142-144)tTa>tCa	p.L48S	ST8SIA2_ENST00000539113.1_Intron	NM_006011.3	NP_006002.1	Q92186	SIA8B_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	48					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|ganglioside biosynthetic process (GO:0001574)|N-glycan processing (GO:0006491)|nervous system development (GO:0007399)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	early endosome (GO:0005769)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|recycling endosome (GO:0055037)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			endometrium(2)|large_intestine(6)|lung(9)|skin(2)|urinary_tract(1)	20	Lung NSC(78;0.0893)|all_lung(78;0.125)		BRCA - Breast invasive adenocarcinoma(143;0.0355)|OV - Ovarian serous cystadenocarcinoma(32;0.203)			GTGAACAGCTTACATAGCAAA	0.393																																					p.L48S		Atlas-SNP	.											.	ST8SIA2	41	.	0			c.T143C						PASS	.						143	133	136					15																	92973323		2198	4298	6496	SO:0001583	missense	8128	exon2			ACAGCTTACATAG	U33551	CCDS10372.1	15q26	2013-03-01	2003-01-14	2005-02-07	ENSG00000140557	ENSG00000140557		"Sialyltransferases"	10870	protein-coding gene	gene with protein product		602546	"sialyltransferase 8 (alpha-2, 8-sialytransferase) B"	SIAT8B		7559389	Standard	NM_006011		Approved	STX, ST8SIA-II, HsT19690	uc002bra.3	Q92186	OTTHUMG00000149843	ENST00000268164.3:c.143T>C	chr15.hg19:g.92973323T>C	ENSP00000268164:p.Leu48Ser	74.0	0.0	.		82.0	30.0	.	NM_006011	Q4VAZ0|Q92470|Q92746	Missense_Mutation	SNP	ENST00000268164.3	hg19	CCDS10372.1	.	.	.	.	.	.	.	.	.	.	T	10.03	1.239532	0.22711	.	.	ENSG00000140557	ENST00000268164;ENST00000555434	T;T	0.27720	1.95;1.65	5.55	5.55	0.83447	.	0.179000	0.35436	N	0.003205	T	0.23054	0.0557	L	0.27053	0.805	0.80722	D	1	B	0.12630	0.006	B	0.09377	0.004	T	0.05053	-1.0909	10	0.20046	T	0.44	0.2846	15.71	0.77620	0.0:0.0:0.0:1.0	.	48	Q92186	SIA8B_HUMAN	S	48	ENSP00000268164:L48S;ENSP00000450851:L48S	ENSP00000268164:L48S	L	+	2	0	ST8SIA2	90774327	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.306000	0.65756	2.105000	0.64084	0.533000	0.62120	TTA	.	.	.	none		0.393	ST8SIA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313526.1	NM_006011		C	92973323	T	C	92973323	3	2	198	1	0	0	0	0	1	0	0	0	15244	1764	61	3	149	3	ST8SIA2	15	92973323	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	21981354	92973323	9558069	76	11964											
SRCAP	10847	hgsc.bcm.edu	37	chr16	30733555	30733555	+	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	cagggcaacaagctgactttGactggtgcccaggtgcgcca	9	7	13	12	1	0	2	0	2	0	0	0	2	0	2	2	3	4	2	2	3	2	1			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr16:30733555G>C	ENST00000262518.4	+	22	4039	c.3654G>C	c.(3652-3654)ttG>ttC	p.L1218F	SRCAP_ENST00000344771.4_Missense_Mutation_p.L1122F|SRCAP_ENST00000395059.2_Missense_Mutation_p.L1218F	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1218	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)			AGCTGACTTTGACTGGTGCCC	0.587																																					p.L1218F		Atlas-SNP	.											.	SRCAP	298	.	0			c.G3654C						PASS	.						113	96	102					16																	30733555		2197	4300	6497	SO:0001583	missense	10847	exon22			GACTTTGACTGGT	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.3654G>C	chr16.hg19:g.30733555G>C	ENSP00000262518:p.Leu1218Phe	233.0	0.0	.		267.0	72.0	.	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	hg19	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	G	14.90	2.673750	0.47781	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.96913	-4.07;-4.17;-3.98	4.68	4.68	0.58851	.	0.000000	0.40064	N	0.001186	D	0.96522	0.8865	L	0.29908	0.895	0.27411	N	0.954569	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.997	D	0.92402	0.5930	10	0.72032	D	0.01	-5.1815	16.5291	0.84353	0.0:0.0:1.0:0.0	.	1122;1218;1218	Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2	.;.;SRCAP_HUMAN	F	1218;1218;1122	ENSP00000262518:L1218F;ENSP00000378499:L1218F;ENSP00000343042:L1122F	ENSP00000262518:L1218F	L	+	3	2	SRCAP	30641056	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	2.423000	0.44705	2.414000	0.81942	0.462000	0.41574	TTG	.	.	.	none		0.587	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		C	30733555	G	C	30733555	3	2	198	1	0	0	0	0	1	0	0	0	15147	1281	45	4	3732	4	SRCAP	16	30733555	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10		30733555	59621198	77	11965											
ITGAX	3687	hgsc.bcm.edu	37	chr16	31371302	31371302	+	Missense_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	cactttcgaggaattcaggcGcagctcaaaccccctcagcc	10	7	8	16	2	3	0	3	0	0	0	4	2	3	1	3	2	3	2	3	2	2	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr16:31371302G>A	ENST00000268296.4	+	7	744	c.623G>A	c.(622-624)cGc>cAc	p.R208H	ITGAX_ENST00000562522.1_Missense_Mutation_p.R208H	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	208	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						GAATTCAGGCGCAGCTCAAAC	0.517																																					p.R208H		Atlas-SNP	.											ITGAX,NS,carcinoma,0,1	ITGAX	198	.	0			c.G623A						PASS	.						101	103	102					16																	31371302		2197	4300	6497	SO:0001583	missense	3687	exon7			TCAGGCGCAGCTC	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.623G>A	chr16.hg19:g.31371302G>A	ENSP00000268296:p.Arg208His	57.0	0.0	.		71.0	43.0	.	NM_000887	Q8IVA6	Missense_Mutation	SNP	ENST00000268296.4	hg19	CCDS10711.1	.	.	.	.	.	.	.	.	.	.	G	11.36	1.616950	0.28801	.	.	ENSG00000140678	ENST00000268296	T	0.78246	-1.16	4.88	-5.48	0.02592	von Willebrand factor, type A (3);	.	.	.	.	T	0.64800	0.2631	L	0.41492	1.28	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.54002	-0.8358	9	0.56958	D	0.05	.	8.8842	0.35394	0.176:0.46:0.364:0.0	.	208	P20702	ITAX_HUMAN	H	208	ENSP00000268296:R208H	ENSP00000268296:R208H	R	+	2	0	ITGAX	31278803	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.940000	0.01543	-0.882000	0.03987	-0.670000	0.03821	CGC	.	.	.	none		0.517	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887		A	31371302	G	A	31371302	3	1	198	1	0	0	0	0	1	0	0	0	7896	1087	38	1	649	1	ITGAX	16	31371302	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	637747	31371302	58983451	78	11966											
ZNF319	57567	hgsc.bcm.edu	37	chr16	58031774	58031774	+	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	atcttgcagaccccacagacGaagggcttctgctcagcctg	9	8	10	14	1	3	2	1	0	2	2	3	3	3	2	3	1	3	3	3	1	1	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr16:58031774G>A	ENST00000299237.2	-	2	1018	c.396C>T	c.(394-396)ttC>ttT	p.F132F	USB1_ENST00000561743.1_5'Flank	NM_020807.1	NP_065858.1	Q9P2F9	ZN319_HUMAN	zinc finger protein 319	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)			large_intestine(2)|lung(4)|ovary(1)|urinary_tract(1)	8						CCCCACAGACGAAGGGCTTCT	0.572																																					p.F132F		Atlas-SNP	.											.	ZNF319	42	.	0			c.C396T						PASS	.						59	57	57					16																	58031774		2198	4300	6498	SO:0001819	synonymous_variant	57567	exon2			ACAGACGAAGGGC	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.396C>T	chr16.hg19:g.58031774G>A		69.0	0.0	.		98.0	46.0	.	NM_020807	Q52LH8	Silent	SNP	ENST00000299237.2	hg19	CCDS32462.1																																																																																			.	.	.	none		0.572	ZNF319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430317.1			A	58031774	G	A	58031774	2	1	198	1	0	0	0	0	0	0	0	1	17849	1049	37	1		1	ZNF319	16	58031774	Silent	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	26660472	58031774	32322979	79	11967											
AP1G1	164	hgsc.bcm.edu	37	chr16	71772895	71772895	+	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	cgtcatatctagctctgtgcTgttggaggcctgtatcgtta	6	15	11	9	2	3	0	1	0	2	0	4	1	3	1	1	2	2	5	1	2	4	5			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr16:71772895T>A	ENST00000299980.4	-	21	2659	c.2218A>T	c.(2218-2220)Agc>Tgc	p.S740C	AP1G1_ENST00000564155.1_Missense_Mutation_p.S165C|AP1G1_ENST00000433195.2_Missense_Mutation_p.S763C|AP1G1_ENST00000423132.2_Missense_Mutation_p.S743C|AP1G1_ENST00000393512.3_Missense_Mutation_p.S743C|AP1G1_ENST00000569748.1_Missense_Mutation_p.S740C	NM_001128.5	NP_001119.3	O43747	AP1G1_HUMAN	adaptor-related protein complex 1, gamma 1 subunit	740	GAE. {ECO:0000255|PROSITE- ProRule:PRU00093}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|Golgi to lysosome transport (GO:0090160)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network membrane (GO:0032588)	GTP-dependent protein binding (GO:0030742)|kinesin binding (GO:0019894)|protein transporter activity (GO:0008565)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)			breast(1)|endometrium(8)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|urinary_tract(1)	28		Ovarian(137;0.125)				AGCTCTGTGCTGTTGGAGGCC	0.418																																					p.S743C		Atlas-SNP	.											.	AP1G1	83	.	0			c.A2227T						PASS	.						208	183	191					16																	71772895		2198	4300	6498	SO:0001583	missense	164	exon22			CTGTGCTGTTGGA	Y12226	CCDS32480.1, CCDS45522.1	16q23	2009-08-03				ENSG00000166747			555	protein-coding gene	gene with protein product	"gamma1-adaptin"	603533		CLAPG1, ADTG		9653655, 9733768	Standard	NM_001128		Approved		uc010cgg.3	O43747		ENST00000299980.4:c.2218A>T	chr16.hg19:g.71772895T>A	ENSP00000299980:p.Ser740Cys	252.0	0.0	.		348.0	94.0	.	NM_001030007	O75709|O75842|Q9UG09|Q9Y3U4	Missense_Mutation	SNP	ENST00000299980.4	hg19	CCDS32480.1	.	.	.	.	.	.	.	.	.	.	T	13.67	2.307011	0.40795	.	.	ENSG00000166747	ENST00000299980;ENST00000393512;ENST00000423132;ENST00000433195	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.29	5.29	0.74685	Coatomer/clathrin adaptor appendage, Ig-like subdomain (1);Clathrin adaptor, gamma-adaptin, appendage (2);Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain (2);	0.135369	0.64402	D	0.000002	T	0.38878	0.1057	L	0.52905	1.665	0.49687	D	0.999819	B;B;B	0.12013	0.005;0.002;0.002	B;B;B	0.19666	0.026;0.017;0.023	T	0.26608	-1.0098	10	0.48119	T	0.1	-8.7323	10.4684	0.44622	0.1451:0.0:0.0:0.8549	.	740;763;743	O43747;B3KXW5;O43747-2	AP1G1_HUMAN;.;.	C	740;743;743;763	ENSP00000299980:S740C;ENSP00000377148:S743C;ENSP00000409153:S743C;ENSP00000403259:S763C	ENSP00000299980:S740C	S	-	1	0	AP1G1	70330396	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	3.020000	0.49643	1.996000	0.58369	0.528000	0.53228	AGC	.	.	.	none		0.418	AP1G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434147.1			A	71772895	T	A	71772895	3	1	198	1	0	0	0	0	1	0	0	0	732	1580	55	5	262	5	AP1G1	16	71772895	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	13741121	71772895	18581858	80	11968											
PRPF8	10594	hgsc.bcm.edu	37	chr17	1585300	1585301	+	Frame_Shift_Ins	INS	-	-	T																															cttgaaatgcctcctatctcINSttttttctcggcgcatcata																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr17:1585300_1585301insT	ENST00000572621.1	-	4	731_732	c.466_467insA	c.(466-468)agafs	p.R156fs	PRPF8_ENST00000304992.6_Frame_Shift_Ins_p.R156fs			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	156					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		CCTCCTATCTCTTTTTTCTCGG	0.51																																					p.R156fs		Atlas-INDEL	.											.	PRPF8	169	.	0			c.467_468insA						PASS	.																																			SO:0001589	frameshift_variant	10594	exon5			.	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"PRP8 pre-mRNA processing factor 8 homolog (yeast)", "PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.467dupA	chr17.hg19:g.1585306_1585306dupT	ENSP00000460348:p.Arg156fs	110.0	0.0	0		123.0	10.0	0.0813008	NM_006445	O14547|O75965	Frame_Shift_Ins	INS	ENST00000572621.1	hg19	CCDS11010.1																																																																																			.	.	.	none		0.51	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2			T	1585301	-	T	1585300	7	5	198	1	0	1	1	0	0	0	0	0	12585	913	32	0	6696	0	PRPF8	17	1585300	Frame_Shift_Ins	INS	-	TCGA-HE-A5NI-01A-11D-A26P-10		1585300	79609910	81	11969											
ACACA	31	hgsc.bcm.edu	37	chr17	35615281	35615281	+	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	tccttgattctatatagaggAatccccatggcaatctgaaa	13	12	7	9	0	2	3	0	2	2	1	4	4	4	4	3	2	0	1	3	2	6	5			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr17:35615281A>T	ENST00000394406.2	-	13	1594	c.1404T>A	c.(1402-1404)atT>atA	p.I468I	ACACA_ENST00000353139.5_Silent_p.I505I|ACACA_ENST00000335166.5_Silent_p.I390I|ACACA_ENST00000360679.3_Silent_p.I410I	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	468	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)	TATATAGAGGAATCCCCATGG	0.368																																					p.I505I	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-SNP	.											.	ACACA	395	.	0			c.T1515A						PASS	.						67	66	66					17																	35615281		2203	4300	6503	SO:0001819	synonymous_variant	31	exon13			TAGAGGAATCCCC	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.1404T>A	chr17.hg19:g.35615281A>T		104.0	0.0	.		108.0	61.0	.	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Silent	SNP	ENST00000394406.2	hg19	CCDS11317.1																																																																																			.	.	.	none		0.368	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		T	35615281	A	T	35615281	2	4	198	1	0	0	0	0	0	0	0	1	106	242	9	5		5	ACACA	17	35615281	Silent	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10	34029981	35615281	45579929	82	11970											
KRT23	25984	hgsc.bcm.edu	37	chr17	39092459	39092459	+	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	cagggtcacccagcatcttaCctgctcctgcaggtgtgtga	7	10	11	13	0	2	1	1	1	1	0	3	1	3	1	3	2	4	3	3	2	1	1			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr17:39092459C>G	ENST00000209718.3	-	2	821		c.e2+1		AC004231.2_ENST00000418393.1_RNA|KRT23_ENST00000436344.3_Intron|KRT23_ENST00000582283.1_5'Flank	NM_015515.3	NP_056330.3	Q9C075	K1C23_HUMAN	keratin 23 (histone deacetylase inducible)							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)				CAGCATCTTACCTGCTCCTGC	0.517																																					.		Atlas-SNP	.											.	KRT23	59	.	0			c.396+1G>C						PASS	.						55	57	56					17																	39092459		2203	4300	6503	SO:0001630	splice_region_variant	25984	exon3			ATCTTACCTGCTC	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.396+1G>C	chr17.hg19:g.39092459C>G		45.0	0.0	.		63.0	32.0	.	NM_015515	A8K084|B7Z7J2|I3L3Q6|Q9NUR6	Splice_Site	SNP	ENST00000209718.3	hg19	CCDS11380.1	.	.	.	.	.	.	.	.	.	.	C	13.33	2.205300	0.39003	.	.	ENSG00000108244	ENST00000209718	.	.	.	5.73	5.73	0.89815	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8915	0.96931	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KRT23	36345985	1.000000	0.71417	1.000000	0.80357	0.197000	0.23852	7.797000	0.85911	2.707000	0.92482	0.557000	0.71058	.	.	.	.	none		0.517	KRT23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257223.1		Intron	G	39092459	C	G	39092459	5	3	198	1	0	0	0	0	0	0	1	0	8467	521	18	4	903	4	KRT23	17	39092459	Splice_Site	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	3477178	39092459	42102751	83	11971											
PSMD12	5718	hgsc.bcm.edu	37	chr17	65362549	65362549	+	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	ttggctagcttcgcacactcGggtaggcgctgatccaccgt	6	10	12	13	4	0	1	0	1	0	0	3	1	1	1	2	3	1	5	2	3	2	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr17:65362549G>C	ENST00000356126.3	-	1	194	c.87C>G	c.(85-87)ccC>ccG	p.P29P	PSMD12_ENST00000357146.4_Silent_p.P29P|PSMD12_ENST00000581618.1_5'UTR	NM_002816.3	NP_002807.1	O00232	PSD12_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	29					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				breast(1)|large_intestine(4)|lung(6)|pancreas(1)|urinary_tract(1)	13	all_cancers(12;2.38e-11)|all_epithelial(3;8.27e-13)					TCGCACACTCGGGTAGGCGCT	0.706																																					p.P29P		Atlas-SNP	.											.	PSMD12	32	.	0			c.C87G						PASS	.						40	31	34					17																	65362549		2203	4299	6502	SO:0001819	synonymous_variant	5718	exon1			ACACTCGGGTAGG	AB003103	CCDS11669.1, CCDS11670.1	17q24.3	2008-05-22			ENSG00000197170	ENSG00000197170		"Proteasome (prosome, macropain) subunits"	9557	protein-coding gene	gene with protein product		604450				9426256	Standard	NM_002816		Approved	p55, Rpn5	uc002jfy.3	O00232	OTTHUMG00000140376	ENST00000356126.3:c.87C>G	chr17.hg19:g.65362549G>C		31.0	0.0	.		34.0	14.0	.	NM_174871	A6NP15|Q53HA2|Q6P053	Silent	SNP	ENST00000356126.3	hg19	CCDS11669.1																																																																																			.	.	.	none		0.706	PSMD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277103.1	NM_002816, NM_174871		C	65362549	G	C	65362549	2	2	198	1	0	0	0	0	0	0	0	1	12705	1103	39	4		4	PSMD12	17	65362549	Silent	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	26270090	65362549	15832661	84	11972											
TRIM47	91107	hgsc.bcm.edu	37	chr17	73872839	73872839	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcctggactgtgcaatgccaGcacccagctcgtccatgcgg	7	7	12	15	2	0	0	0	0	0	0	2	1	1	1	4	2	5	3	4	2	1	0	rs377764139		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr17:73872839G>A	ENST00000254816.2	-	2	757	c.731C>T	c.(730-732)gCt>gTt	p.A244V	TRIM47_ENST00000587339.1_Missense_Mutation_p.A6V|RP11-552F3.9_ENST00000586076.1_RNA	NM_033452.2	NP_258411.2	Q96LD4	TRI47_HUMAN	tripartite motif containing 47	244						cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	22			Epithelial(20;4.23e-06)|all cancers(21;5.24e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			TGCAATGCCAGCACCCAGCTC	0.587																																					p.A244V		Atlas-SNP	.											.	TRIM47	40	.	0			c.C731T						PASS	.						170	119	136					17																	73872839		2203	4300	6503	SO:0001583	missense	91107	exon2			ATGCCAGCACCCA	AY026763	CCDS32737.1	17q25	2013-01-09	2011-01-25			ENSG00000132481		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19020	protein-coding gene	gene with protein product		611041	"tripartite motif-containing 47"				Standard	NM_033452		Approved	GOA, RNF100	uc002jpw.3	Q96LD4		ENST00000254816.2:c.731C>T	chr17.hg19:g.73872839G>A	ENSP00000254816:p.Ala244Val	133.0	0.0	.		167.0	106.0	.	NM_033452	Q96AD0|Q96GU5|Q9BRN7	Missense_Mutation	SNP	ENST00000254816.2	hg19	CCDS32737.1	.	.	.	.	.	.	.	.	.	.	G	14.00	2.404309	0.42613	.	.	ENSG00000132481	ENST00000254816	T	0.45276	0.9	4.91	4.91	0.64330	.	0.105328	0.42682	D	0.000664	T	0.27524	0.0676	N	0.24115	0.695	0.37335	D	0.910149	B	0.02656	0.0	B	0.06405	0.002	T	0.14783	-1.0460	10	0.39692	T	0.17	.	9.121	0.36786	0.097:0.0:0.903:0.0	.	244	Q96LD4	TRI47_HUMAN	V	244	ENSP00000254816:A244V	ENSP00000254816:A244V	A	-	2	0	TRIM47	71384434	0.747000	0.28283	0.927000	0.36925	0.785000	0.44390	3.752000	0.55172	2.560000	0.86352	0.511000	0.50034	GCT	.	.	.	alt		0.587	TRIM47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448934.1			A	73872839	G	A	73872839	3	1	198	1	0	0	0	0	1	0	0	0	16534	971	34	2	1205	2	TRIM47	17	73872839	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	8510290	73872839	7322371	85	11973											
MADCAM1	8174	hgsc.bcm.edu	37	chr19	504882	504883	+	Missense_Mutation	DNP	CC	CC	AT																															ctgaggacgacacccacccaCcagcttctctgaggcttctg																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr19:504882_504883CC>AT	ENST00000215637.3	+	5	1112_1113	c.1066_1067CC>AT	c.(1066-1068)CCa>ATa	p.P356I	MADCAM1_ENST00000382683.4_Missense_Mutation_p.P174I|MADCAM1_ENST00000346144.4_Missense_Mutation_p.P269I|TPGS1_ENST00000359315.5_5'Flank|AC005775.2_ENST00000592413.1_RNA|MADCAM1_ENST00000587541.1_Missense_Mutation_p.P137I	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	356					aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CACCCACCCACCAGCTTCTCTG	0.673																																					p.P356T|p.P356L		Atlas-SNP	.											.	MADCAM1	29	.	0			c.C1066A|c.C1067T						PASS	.																																			SO:0001583	missense	8174	exon5			CACCCACCAGCTT|ACCCACCAGCTTC	U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6765	protein-coding gene	gene with protein product	"mucosal addressin cell adhesion molecule-1"	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	Exception_encountered	chr19.hg19:g.504882_504883delinsAT	ENSP00000215637:p.Pro356Ile	158.0|159.0	0.0	.		66.0	22.0	.	NM_130760	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Missense_Mutation	SNP	ENST00000215637.3	hg19	CCDS12028.1																																																																																			.	.	.	none		0.673	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1	NM_130760		AT	504883	CC	AT	504882	3	1	198	1	0	0	0	0	1	0	0	0	9158	507	18	4	1084	4	MADCAM1	19	504882	Missense_Mutation	DNP	CC	TCGA-HE-A5NI-01A-11D-A26P-10		504882	58624101	86	11974											
PLIN4	729359	hgsc.bcm.edu	37	chr19	4511773	4511773	+	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	gcaccggtcaccccactgcaGacggtgtccttggtaccagt	7	8	11	15	2	1	1	1	0	0	1	2	1	2	1	5	3	2	3	5	3	1	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr19:4511773G>A	ENST00000301286.3	-	3	2156	c.2157C>T	c.(2155-2157)gtC>gtT	p.V719V		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	719	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						CCCCACTGCAGACGGTGTCCT	0.572																																					p.V719V		Atlas-SNP	.											.	PLIN4	191	.	0			c.C2157T						PASS	.						210	212	211					19																	4511773		2098	4206	6304	SO:0001819	synonymous_variant	729359	exon3			ACTGCAGACGGTG	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.2157C>T	chr19.hg19:g.4511773G>A		293.0	0.0	.		234.0	37.0	.	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	hg19	CCDS45927.1																																																																																			.	.	.	none		0.572	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901		A	4511773	G	A	4511773	2	1	198	1	0	0	0	0	0	0	0	1	12099	929	33	2		2	PLIN4	19	4511773	Silent	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	4006891	4511773	54617210	87	11975											
PLIN3	10226	hgsc.bcm.edu	37	chr19	4839279	4839279	+	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	agccacgtgacaggtgtgttCtgggccacatattccaccat	9	10	10	12	1	1	1	0	1	1	0	2	1	2	1	4	2	1	1	4	2	1	3			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr19:4839279C>G	ENST00000221957.4	-	8	1406	c.1230G>C	c.(1228-1230)caG>caC	p.Q410H	PLIN3_ENST00000585479.1_Missense_Mutation_p.Q409H|CTC-518P12.6_ENST00000591657.1_RNA|PLIN3_ENST00000592528.1_Missense_Mutation_p.Q398H	NM_001164189.1|NM_001164194.1|NM_005817.4	NP_001157661.1|NP_001157666.1|NP_005808.3	O60664	PLIN3_HUMAN	perilipin 3	410					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)	CAGGTGTGTTCTGGGCCACAT	0.632																																					p.Q410H		Atlas-SNP	.											.	PLIN3	36	.	0			c.G1230C						PASS	.						66	70	69					19																	4839279		2203	4300	6503	SO:0001583	missense	10226	exon8			TGTGTTCTGGGCC	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.1230G>C	chr19.hg19:g.4839279C>G	ENSP00000221957:p.Gln410His	122.0	0.0	.		80.0	7.0	.	NM_005817	A8K4Y9|K7EQF4|Q53G77|Q9BS03|Q9UBD7|Q9UP92	Missense_Mutation	SNP	ENST00000221957.4	hg19	CCDS12137.1	.	.	.	.	.	.	.	.	.	.	C	7.106	0.575129	0.13623	.	.	ENSG00000105355	ENST00000221957	T	0.18960	2.18	4.97	2.65	0.31530	.	0.938934	0.08920	N	0.874576	T	0.19287	0.0463	L	0.28192	0.835	0.34333	D	0.68787	B;B;B	0.23249	0.027;0.082;0.033	B;B;B	0.25140	0.022;0.058;0.038	T	0.21690	-1.0238	10	0.37606	T	0.19	-13.9129	16.1339	0.81465	0.0:0.4858:0.5141:0.0	.	409;227;410	O60664-3;O60664-2;O60664	.;.;PLIN3_HUMAN	H	410	ENSP00000221957:Q410H	ENSP00000221957:Q410H	Q	-	3	2	PLIN3	4790279	1.000000	0.71417	0.992000	0.48379	0.108000	0.19459	0.655000	0.24933	1.042000	0.40150	0.561000	0.74099	CAG	.	.	.	none		0.632	PLIN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450436.1	NM_005817		G	4839279	C	G	4839279	3	3	198	1	0	0	0	0	1	0	0	0	12098	912	32	4	78	4	PLIN3	19	4839279	Missense_Mutation	SNP	C	TCGA-HE-A5NI-01A-11D-A26P-10	327506	4839279	54289704	88	11976											
PLIN3	10226	hgsc.bcm.edu	37	chr19	4839466	4839466	+	Missense_Mutation	SNP	A	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	cattggtggggaggccctgaAtgctggaccccagggaggta	8	7	17	9	0	0	1	0	1	0	0	0	4	0	4	3	7	1	2	3	7	2	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr19:4839466A>C	ENST00000221957.4	-	8	1219	c.1043T>G	c.(1042-1044)aTt>aGt	p.I348S	PLIN3_ENST00000585479.1_Missense_Mutation_p.I347S|CTC-518P12.6_ENST00000591657.1_RNA|PLIN3_ENST00000592528.1_Missense_Mutation_p.I336S	NM_001164189.1|NM_001164194.1|NM_005817.4	NP_001157661.1|NP_001157666.1|NP_005808.3	O60664	PLIN3_HUMAN	perilipin 3	348					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)	GAGGCCCTGAATGCTGGACCC	0.647																																					p.I348S		Atlas-SNP	.											.	PLIN3	36	.	0			c.T1043G						PASS	.						37	31	33					19																	4839466		2203	4300	6503	SO:0001583	missense	10226	exon8			CCCTGAATGCTGG	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.1043T>G	chr19.hg19:g.4839466A>C	ENSP00000221957:p.Ile348Ser	135.0	0.0	.		89.0	27.0	.	NM_005817	A8K4Y9|K7EQF4|Q53G77|Q9BS03|Q9UBD7|Q9UP92	Missense_Mutation	SNP	ENST00000221957.4	hg19	CCDS12137.1	.	.	.	.	.	.	.	.	.	.	A	14.10	2.433232	0.43224	.	.	ENSG00000105355	ENST00000221957	T	0.20332	2.08	4.85	4.85	0.62838	.	422.645000	0.01670	U	0.025543	T	0.50120	0.1597	M	0.78637	2.42	0.27909	N	0.93868	D;P;D	0.56746	0.971;0.937;0.977	P;P;D	0.64506	0.879;0.698;0.926	T	0.06881	-1.0802	10	0.87932	D	0	-13.3555	9.052	0.36383	0.9163:0.0:0.0837:0.0	.	347;165;348	O60664-3;O60664-2;O60664	.;.;PLIN3_HUMAN	S	348	ENSP00000221957:I348S	ENSP00000221957:I348S	I	-	2	0	PLIN3	4790466	0.801000	0.28930	0.975000	0.42487	0.034000	0.12701	3.474000	0.53129	1.817000	0.53016	0.454000	0.30748	ATT	.	.	.	none		0.647	PLIN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450436.1	NM_005817		C	4839466	A	C	4839466	3	2	198	1	0	0	0	0	1	0	0	0	12098	101	4	5	265	5	PLIN3	19	4839466	Missense_Mutation	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10	187	4839466	54289517	89	11977											
DCAF15	90379	hgsc.bcm.edu	37	chr19	14070072	14070072	+	Missense_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	tcttccgccgggccaaagagGccaagggcggggtccctgag	7	5	16	13	3	1	2	0	1	1	1	3	2	3	2	5	5	0	0	5	5	2	1			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr19:14070072G>A	ENST00000254337.6	+	7	1021	c.1000G>A	c.(1000-1002)Gcc>Acc	p.A334T		NM_138353.2	NP_612362.2	Q66K64	DCA15_HUMAN	DDB1 and CUL4 associated factor 15	334					protein ubiquitination (GO:0016567)					breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)	11						GGCCAAAGAGGCCAAGGGCGG	0.682																																					p.A334T		Atlas-SNP	.											.	DCAF15	30	.	0			c.G1000A						PASS	.						27	35	32					19																	14070072		2203	4300	6503	SO:0001583	missense	90379	exon7			AAAGAGGCCAAGG	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.1000G>A	chr19.hg19:g.14070072G>A	ENSP00000254337:p.Ala334Thr	14.0	0.0	.		12.0	6.0	.	NM_138353	B3KS86|Q96DW0|Q9BU31	Missense_Mutation	SNP	ENST00000254337.6	hg19	CCDS32926.1	.	.	.	.	.	.	.	.	.	.	g	32	5.112699	0.94339	.	.	ENSG00000132017	ENST00000254337	.	.	.	4.46	4.46	0.54185	.	0.085620	0.44097	D	0.000488	T	0.60470	0.2271	L	0.29908	0.895	0.41151	D	0.986027	D	0.54207	0.965	P	0.55871	0.786	T	0.65998	-0.6032	9	0.62326	D	0.03	-24.0048	15.8605	0.79017	0.0:0.0:1.0:0.0	.	334	Q66K64	DCA15_HUMAN	T	334	.	ENSP00000254337:A334T	A	+	1	0	DCAF15	13931072	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.504000	0.66968	2.043000	0.60533	0.491000	0.48974	GCC	.	.	.	none		0.682	DCAF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458099.1	NM_138353		A	14070072	G	A	14070072	3	1	198	1	0	0	0	0	1	0	0	0	4269	1203	42	2	1026	2	DCAF15	19	14070072	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	9230606	14070072	45058911	90	11978											
TECR	9524	hgsc.bcm.edu	37	chr19	14674655	14674657	+	In_Frame_Del	DEL	CGT	CGT	-																															gatgttctgcagaagctgccCgtgggcaccacggccacact																								rs367952165|rs201634024		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	CGT	CGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr19:14674655_14674657delCGT	ENST00000215567.5	+	5	344_346	c.207_209delCGT	c.(205-210)cccgtg>ccg	p.V70del	TECR_ENST00000596164.1_3'UTR|TECR_ENST00000436007.2_In_Frame_Del_p.V85del|TECR_ENST00000600083.1_5'UTR|TECR_ENST00000596073.1_5'UTR	NM_138501.5	NP_612510.1	Q9NZ01	TECR_HUMAN	trans-2,3-enoyl-CoA reductase	70					cellular lipid metabolic process (GO:0044255)|fatty acid elongation (GO:0030497)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|nucleus (GO:0005634)	oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)			endometrium(1)|large_intestine(1)|ovary(1)	3						AGAAGCTGCCCGTGGGCACCACG	0.66																																					p.69_70del		Atlas-Indel,Pindel	.											.	TECR	22	.	0			c.206_208del						PASS	.																																			SO:0001651	inframe_deletion	9524	exon5			.	AK001416	CCDS12313.1	19p13.12	2014-05-27	2009-07-21	2009-07-21	ENSG00000099797	ENSG00000099797			4551	protein-coding gene	gene with protein product		610057	"glycoprotein, synaptic 2"	SC2, GPSN2		9653160, 12482854	Standard	NM_138501		Approved	TER, MRT14	uc002mza.3	Q9NZ01		ENST00000215567.5:c.207_209delCGT	chr19.hg19:g.14674655_14674657delCGT	ENSP00000215567:p.Val70del	116.0	0.0	0		87.0	35.0	0.402299	NM_138501	B2RD55|O75350|Q6IBB2|Q9BWK3|Q9Y6P0	In_Frame_Del	DEL	ENST00000215567.5	hg19	CCDS12313.1																																																																																			.	.	.	none		0.66	TECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466000.1	NM_138501		-	14674657	CGT	-	14674655	7	5	198	1	0	1	0	1	0	0	0	0	15757	639	23	0	225	0	TECR	19	14674655	In_Frame_Del	DEL	CGT	TCGA-HE-A5NI-01A-11D-A26P-10	604583	14674655	44454328	91	11979											
NAPA	8775	hgsc.bcm.edu	37	chr19	47996229	47996229	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtccccacctgttcgtagaTgtcaatggccttctgatact	7	14	8	12	1	2	2	1	1	1	1	4	2	3	2	4	1	1	2	4	1	3	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr19:47996229T>C	ENST00000263354.3	-	7	849	c.550A>G	c.(550-552)Atc>Gtc	p.I184V	NAPA-AS1_ENST00000594367.1_RNA|NAPA_ENST00000595227.1_Missense_Mutation_p.I145V|NAPA-AS1_ENST00000593284.1_RNA|NAPA_ENST00000593785.1_5'Flank	NM_003827.3	NP_003818.2	P54920	SNAA_HUMAN	N-ethylmaleimide-sensitive factor attachment protein, alpha	184					apical protein localization (GO:0045176)|brain development (GO:0007420)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|membrane organization (GO:0061024)|neuron differentiation (GO:0030182)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of synaptic vesicle priming (GO:0010807)|SNARE complex disassembly (GO:0035494)|synaptic transmission, glutamatergic (GO:0035249)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)	11		all_cancers(25;1.55e-10)|all_epithelial(76;3.4e-08)|all_lung(116;1.73e-07)|Lung NSC(112;3.95e-07)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		OV - Ovarian serous cystadenocarcinoma(262;0.000466)|all cancers(93;0.000739)|Epithelial(262;0.0168)|GBM - Glioblastoma multiforme(486;0.049)		TGTTCGTAGATGTCAATGGCC	0.607																																					p.I184V	Ovarian(185;1135 2042 27703 31345 42493)	Atlas-SNP	.											.	NAPA	34	.	0			c.A550G						PASS	.						113	101	105					19																	47996229		2203	4300	6503	SO:0001583	missense	8775	exon7			CGTAGATGTCAAT	U39412	CCDS12702.1	19q13.33	2012-08-16			ENSG00000105402	ENSG00000105402			7641	protein-coding gene	gene with protein product	"alpha SNAP"	603215				9269766	Standard	NM_003827		Approved		uc002pha.2	P54920		ENST00000263354.3:c.550A>G	chr19.hg19:g.47996229T>C	ENSP00000263354:p.Ile184Val	146.0	0.0	.		186.0	74.0	.	NM_003827	A8K879|Q96IK3|Q9BVJ3	Missense_Mutation	SNP	ENST00000263354.3	hg19	CCDS12702.1	.	.	.	.	.	.	.	.	.	.	T	13.73	2.323538	0.41096	.	.	ENSG00000105402	ENST00000263354	T	0.76448	-1.02	5.16	5.16	0.70880	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.77605	0.4155	M	0.76170	2.325	0.80722	D	1	B	0.16603	0.018	B	0.20577	0.03	T	0.75190	-0.3405	10	0.45353	T	0.12	-33.228	14.1002	0.65049	0.0:0.0:0.0:1.0	.	184	P54920	SNAA_HUMAN	V	184	ENSP00000263354:I184V	ENSP00000263354:I184V	I	-	1	0	NAPA	52688041	1.000000	0.71417	1.000000	0.80357	0.456000	0.32438	7.585000	0.82584	2.168000	0.68352	0.496000	0.49642	ATC	.	.	.	none		0.607	NAPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466048.2	NM_003827		C	47996229	T	C	47996229	3	2	198	1	0	0	0	0	1	0	0	0	10168	1464	51	3	357	3	NAPA	19	47996229	Missense_Mutation	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10	33321574	47996229	11132754	92	11980											
ZNF836	162962	hgsc.bcm.edu	37	chr19	52658860	52658860	+	Frame_Shift_Del	DEL	T	T	-																															aactcattacaattgtaaggTttctctccagtatgaattat																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr19:52658860delT	ENST00000322146.8	-	5	2597	c.2076delA	c.(2074-2076)aaafs	p.K692fs	CTC-471J1.8_ENST00000594362.1_RNA|ZNF836_ENST00000597252.1_Frame_Shift_Del_p.K692fs	NM_001102657.1	NP_001096127.1	Q6ZNA1	ZN836_HUMAN	zinc finger protein 836	692					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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						AATTGTAAGGTTTCTCTCCAG	0.393																																					p.P693fs		Atlas-INDEL	.											.	ZNF836	158	.	0			c.2077delC						PASS	.						71	76	74					19																	52658860		2071	4245	6316	SO:0001589	frameshift_variant	162962	exon5			.	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.2076delA	chr19.hg19:g.52658860delT	ENSP00000325038:p.Lys692fs	55.0	0.0	0		36.0	20.0	0.555556	NM_001102657		Frame_Shift_Del	DEL	ENST00000322146.8	hg19	CCDS46162.1																																																																																			.	.	.	none		0.393	ZNF836-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462456.1	NM_001102657		-	52658860	T	-	52658860	7	5	198	1	0	1	0	1	0	0	0	0	18199	1722	60	0	736	0	ZNF836	19	52658860	Frame_Shift_Del	DEL	T	TCGA-HE-A5NI-01A-11D-A26P-10	4662631	52658860	6470123	93	11981											
MZF1	7593	hgsc.bcm.edu	37	chr19	59082640	59082640	+	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	cgcaggcgtgcagcttcaggGcctgggtcccataaggcagc	7	6	15	13	2	1	0	1	0	0	0	2	0	2	0	2	4	3	4	2	4	1	2			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr19:59082640G>A	ENST00000215057.2	-	2	677	c.117C>T	c.(115-117)ggC>ggT	p.G39G	MZF1_ENST00000599369.1_Silent_p.G39G|MZF1_ENST00000594108.1_Silent_p.G39G|MZF1_ENST00000594234.1_Silent_p.G39G|AC016629.8_ENST00000593642.1_RNA|AC016629.8_ENST00000600726.1_RNA|AC016629.8_ENST00000600534.1_RNA	NM_001267033.1|NM_198055.1	NP_001253962.1|NP_932172.1	P28698	MZF1_HUMAN	myeloid zinc finger 1	39					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0443)|all cancers(4;7.92e-14)|Epithelial(4;5.57e-11)|OV - Ovarian serous cystadenocarcinoma(4;1.13e-09)|GBM - Glioblastoma multiforme(193;0.0108)|Lung(386;0.182)		CAGCTTCAGGGCCTGGGTCCC	0.657																																					p.G39G		Atlas-SNP	.											.	MZF1	37	.	0			c.C117T						PASS	.						26	29	28					19																	59082640		2203	4300	6503	SO:0001819	synonymous_variant	7593	exon2			TTCAGGGCCTGGG	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.117C>T	chr19.hg19:g.59082640G>A		91.0	0.0	.		50.0	16.0	.	NM_198055	M0QXU0|Q7Z729|Q96I71|Q9NRY0|Q9UBW2	Silent	SNP	ENST00000215057.2	hg19	CCDS12988.1																																																																																			.	.	.	none		0.657	MZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467112.1	NM_198055		A	59082640	G	A	59082640	2	1	198	1	0	0	0	0	0	0	0	1	10115	1190	42	2		2	MZF1	19	59082640	Silent	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	6423780	59082640	46343	94	11982											
PLCB1	23236	hgsc.bcm.edu	37	chr20	8608961	8608961	+	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	gaccccaaattacgtgaactTttggatgtggggaacatcgg	11	10	12	8	2	0	1	0	1	0	0	1	4	0	3	2	4	3	0	2	4	4	3			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr20:8608961T>G	ENST00000338037.6	+	4	294	c.267T>G	c.(265-267)ctT>ctG	p.L89L	PLCB1_ENST00000378637.2_Silent_p.L89L|PLCB1_ENST00000378641.3_Silent_p.L89L	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	89					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						TACGTGAACTTTTGGATGTGG	0.443																																					p.N89K		Atlas-SNP	.											.	PLCB1	394	.	0			c.C267G						PASS	.						78	78	78					20																	8608961		2203	4300	6503	SO:0001819	synonymous_variant	23236	exon4			TGAACTTTTGGAT	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.267T>G	chr20.hg19:g.8608961T>G		102.0	0.0	.		116.0	34.0	.	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Missense_Mutation	SNP	ENST00000338037.6	hg19	CCDS13102.1																																																																																			.	.	.	none		0.443	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3			G	8608961	T	G	8608961	2	3	198	1	0	0	0	0	0	0	0	1	12034	1828	64	5		5	PLCB1	20	8608961	Silent	SNP	T	TCGA-HE-A5NI-01A-11D-A26P-10		8608961	54416559	95	11983											
ASIP	434	hgsc.bcm.edu	37	chr20	32856797	32856797	+	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	ccccggcgtttcccacgcagAaggaggcttcgatgaagaaa	11	6	12	12	4	0	3	0	1	0	2	2	5	1	4	3	3	0	3	3	3	3	2	rs538816237		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr20:32856797A>G	ENST00000568305.1	+	4	425	c.223A>G	c.(223-225)Aag>Gag	p.K75E	RP4-785G19.5_ENST00000512005.1_RNA|ASIP_ENST00000374954.3_Splice_Site_p.K75E			P42127	ASIP_HUMAN	agouti signaling protein	75	Arg/Lys-rich (basic).				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						TCCCACGCAGAAGGAGGCTTC	0.697													A|||	1	0.000199681	0	0	5008	,	,		12806	0.001		0	False		,,,				2504	0				p.K75E		Atlas-SNP	.											.	ASIP	6	.	0			c.A223G						PASS	.						8	11	10					20																	32856797		2188	4282	6470	SO:0001630	splice_region_variant	434	exon3			ACGCAGAAGGAGG		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.223-1A>G	chr20.hg19:g.32856797A>G		89.0	0.0	.		67.0	33.0	.	NM_001672	Q3SXL2	Missense_Mutation	SNP	ENST00000568305.1	hg19	CCDS13232.1	.	.	.	.	.	.	.	.	.	.	A	15.14	2.744523	0.49151	.	.	ENSG00000101440	ENST00000374954	T	0.31769	1.48	4.61	4.61	0.57282	.	0.063957	0.64402	D	0.000013	T	0.48660	0.1512	M	0.82323	2.585	0.40299	D	0.978584	P	0.51240	0.943	P	0.54346	0.749	T	0.54970	-0.8213	9	.	.	.	.	10.3603	0.43989	1.0:0.0:0.0:0.0	.	75	P42127	ASIP_HUMAN	E	75	ENSP00000364092:K75E	.	K	+	1	0	ASIP	32320458	1.000000	0.71417	1.000000	0.80357	0.127000	0.20565	3.560000	0.53763	1.942000	0.56320	0.397000	0.26171	AAG	.	.	.	none		0.697	ASIP-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430541.1		Missense_Mutation	G	32856797	A	G	32856797	5	3	198	1	0	0	0	0	0	0	1	0	1043	260	9	3	233	3	ASIP	20	32856797	Splice_Site	SNP	A	TCGA-HE-A5NI-01A-11D-A26P-10	24247836	32856797	30168723	96	11984											
SALL4	57167	hgsc.bcm.edu	37	chr20	50401006	50401006	+	Frame_Shift_Del	DEL	A	A	-																															ccccactctggatcacagagAtctcattggtcttcacggcc																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr20:50401006delA	ENST00000217086.4	-	4	3071	c.2960delT	c.(2959-2961)atcfs	p.I987fs	SALL4_ENST00000371539.3_Frame_Shift_Del_p.I210fs|SALL4_ENST00000395997.3_Frame_Shift_Del_p.I550fs	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	987					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						GATCACAGAGATCTCATTGGT	0.572																																					p.I987fs		Pindel	.											.	SALL4	168	.	0			c.2961delC						PASS	.						85	78	80					20																	50401006		2203	4300	6503	SO:0001589	frameshift_variant	57167	exon4			.	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.2960delT	chr20.hg19:g.50401006delA	ENSP00000217086:p.Ile987fs	193.0	0.0	.		211.0	66.0	0.313	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Frame_Shift_Del	DEL	ENST00000217086.4	hg19	CCDS13438.1																																																																																			.	.	.	none		0.572	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			-	50401006	A	-	50401006	7	5	198	1	0	1	0	1	0	0	0	0	13826	333	12	0	205	0	SALL4	20	50401006	Frame_Shift_Del	DEL	A	TCGA-HE-A5NI-01A-11D-A26P-10	17544209	50401006	12624514	97	11985											
ARVCF	421	hgsc.bcm.edu	37	chr22	19967432	19967432	+	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	cgcacctcagcccgcgggtgGtccagcagtgccacaagcag	8	4	13	16	3	1	0	1	0	0	0	2	0	2	0	4	2	4	3	4	2	1	0			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr22:19967432G>T	ENST00000263207.3	-	6	1521	c.1230C>A	c.(1228-1230)gaC>gaA	p.D410E	ARVCF_ENST00000406259.1_Missense_Mutation_p.D410E|ARVCF_ENST00000344269.3_Missense_Mutation_p.D347E|ARVCF_ENST00000487793.1_5'Flank|ARVCF_ENST00000401994.1_Missense_Mutation_p.D347E|ARVCF_ENST00000406522.1_Missense_Mutation_p.D347E	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	410					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)					CCCGCGGGTGGTCCAGCAGTG	0.682																																					p.D410E		Atlas-SNP	.											.	ARVCF	54	.	0			c.C1230A						PASS	.						19	19	19					22																	19967432		2178	4274	6452	SO:0001583	missense	421	exon6			CGGGTGGTCCAGC		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.1230C>A	chr22.hg19:g.19967432G>T	ENSP00000263207:p.Asp410Glu	9.0	0.0	.		8.0	4.0	.	NM_001670	B7WNV2	Missense_Mutation	SNP	ENST00000263207.3	hg19	CCDS13771.1	.	.	.	.	.	.	.	.	.	.	G	16.60	3.167282	0.57476	.	.	ENSG00000099889	ENST00000263207;ENST00000344269;ENST00000401994;ENST00000406522;ENST00000406259	T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81	4.51	-0.0128	0.13987	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.42040	0.1185	L	0.28115	0.83	0.50171	D	0.999858	P	0.39601	0.68	P	0.51742	0.678	T	0.11966	-1.0566	9	.	.	.	-21.2014	9.1754	0.37109	0.4923:0.0:0.5077:0.0	.	410	O00192	ARVC_HUMAN	E	410;347;347;347;410	ENSP00000263207:D410E;ENSP00000342042:D347E;ENSP00000384341:D347E;ENSP00000384732:D347E;ENSP00000385444:D410E	.	D	-	3	2	ARVCF	18347432	0.997000	0.39634	0.997000	0.53966	0.684000	0.39900	0.345000	0.19979	0.012000	0.14892	-0.131000	0.14894	GAC	.	.	.	none		0.682	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670		T	19967432	G	T	19967432	3	4	198	1	0	0	0	0	1	0	0	0	1003	1252	44	4	1714	4	ARVCF	22	19967432	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10		19967432	31337134	98	11986											
LARGE	9215	hgsc.bcm.edu	37	chr22	33679190	33679190	+	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	gcagctagagccactcacctGaatgtgaagagggtccccat	11	7	11	12	0	1	4	1	2	0	2	2	4	2	4	4	1	2	2	4	1	3	1			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chr22:33679190G>A	ENST00000354992.2	-	14	2446	c.1875C>T	c.(1873-1875)ttC>ttT	p.F625F	LARGE_ENST00000337431.2_Silent_p.F573F|LARGE_ENST00000437602.2_Intron|LARGE_ENST00000452586.2_Silent_p.F424F|LARGE_ENST00000397394.2_Silent_p.F625F|LARGE_ENST00000402320.1_Silent_p.F573F	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	625					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)				CCACTCACCTGAATGTGAAGA	0.552																																					p.F625F	Colon(70;397 1175 4573 19089 45288)	Atlas-SNP	.											.	LARGE	98	.	0			c.C1875T						PASS	.						140	124	129					22																	33679190		2203	4300	6503	SO:0001819	synonymous_variant	9215	exon14			TCACCTGAATGTG	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.1875C>T	chr22.hg19:g.33679190G>A		224.0	0.0	.		187.0	61.0	.	NM_004737	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	Silent	SNP	ENST00000354992.2	hg19	CCDS13912.1																																																																																			.	.	.	none		0.552	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320515.2	NM_133642		A	33679190	G	A	33679190	2	1	198	1	0	0	0	0	0	0	0	1	8634	1281	45	2		2	LARGE	22	33679190	Silent	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	13711758	33679190	17625376	99	11987											
SFRS17A	8227	hgsc.bcm.edu	37	chrX	1714403	1714403	+	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	gcagagagaaggaagcggagGagaggcagcgagcggaggaa	15	0	21	5	3	0	3	0	0	0	3	0	10	0	7	0	6	3	2	0	6	3	0			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chrX:1714403G>A	ENST00000313871.3	+	3	1085	c.889G>A	c.(889-891)Gag>Aag	p.E297K	AKAP17A_ENST00000381261.3_Missense_Mutation_p.E297K	NM_005088.2	NP_005079.2	Q02040	AK17A_HUMAN	A kinase (PRKA) anchor protein 17A	297					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						GGAAGCGGAGGAGAGGCAGCG	0.607																																					p.E297K		Atlas-SNP	.											.	AKAP17A	46	.	0			c.G889A						PASS	.						253	268	263					X																	1714403		2203	4296	6499	SO:0001583	missense	8227	exon3			GCGGAGGAGAGGC	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.889G>A	chrX.hg19:g.1714403G>A	ENSP00000324827:p.Glu297Lys	152.0	1.0	.		89.0	73.0	.	NM_005088	Q02832|Q2TB98|Q5JQ74|Q5JQ76|Q8N6U9	Missense_Mutation	SNP	ENST00000313871.3	hg19	CCDS14116.1	.	.	.	.	.	.	.	.	.	.	g	6.684	0.494845	0.12702	.	.	ENSG00000197976	ENST00000313871;ENST00000381261	T;T	0.41400	1.59;1.0	2.29	2.29	0.28610	.	0.000000	0.64402	U	0.000001	T	0.57373	0.2049	.	.	.	0.09310	N	0.999995	D;P	0.60575	0.988;0.823	D;P	0.73708	0.981;0.805	T	0.50162	-0.8860	9	0.36615	T	0.2	.	13.0471	0.58933	0.0:0.0:1.0:0.0	.	297;297	Q02040-3;Q02040	.;AK17A_HUMAN	K	297	ENSP00000324827:E297K;ENSP00000370660:E297K	ENSP00000324827:E297K	E	+	1	0	AKAP17A	1674403	1.000000	0.71417	0.362000	0.25862	0.418000	0.31294	3.642000	0.54367	0.973000	0.38340	0.100000	0.15512	GAG	.	.	.	none		0.607	AKAP17A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055609.2	NM_005088		A	1714403	G	A	1714403	3	1	198	1	0	0	0	0	1	0	0	0	14186	1175	41	2	895	2	SFRS17A	23	1714403	Missense_Mutation	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10		1714403	153556157	100	11988											
BCOR	54880	hgsc.bcm.edu	37	chrX	39923132	39923132	+	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	tcaatgcacaccttcaggttGgtcagctcactataatgtgg	10	12	9	10	0	4	0	4	0	0	0	4	0	4	0	1	3	2	3	1	3	3	4			TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chrX:39923132G>T	ENST00000378444.4	-	8	3804	c.3576C>A	c.(3574-3576)acC>acA	p.T1192T	BCOR_ENST00000378455.4_Intron|BCOR_ENST00000342274.4_Intron|BCOR_ENST00000378463.1_Intron|BCOR_ENST00000397354.3_Intron	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	1192					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						CCTTCAGGTTGGTCAGCTCAC	0.453			"F, N, S, T"	RARA	"retinoblastoma, AML, APL(translocation)"		oculo-facio-cardio-dental genetic																														p.T1192T		Atlas-SNP	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	0			c.C3576A						PASS	.						57	55	55					X																	39923132		2202	4300	6502	SO:0001819	synonymous_variant	54880	exon8			CAGGTTGGTCAGC	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.3576C>A	chrX.hg19:g.39923132G>T		88.0	0.0	.		56.0	4.0	.	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Silent	SNP	ENST00000378444.4	hg19	CCDS48093.1																																																																																			.	.	.	none		0.453	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		T	39923132	G	T	39923132	2	4	198	1	0	0	0	0	0	0	0	1	1386	1335	47	4		4	BCOR	23	39923132	Silent	SNP	G	TCGA-HE-A5NI-01A-11D-A26P-10	38208729	39923132	115347428	101	11989											
GATA1	2623	hgsc.bcm.edu	37	chrX	48650855	48650855	+	Frame_Shift_Del	DEL	A	A	-																															atgggcagaacaggcccctcAtccggcccaagaagcgcctg																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chrX:48650855delA	ENST00000376670.3	+	4	835	c.724delA	c.(724-726)atcfs	p.I242fs	GATA1_ENST00000376665.3_Frame_Shift_Del_p.I242fs	NM_002049.3	NP_002040.1	P15976	GATA1_HUMAN	GATA binding protein 1 (globin transcription factor 1)	242					basophil differentiation (GO:0030221)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cellular response to thyroid hormone stimulus (GO:0097067)|dendritic cell differentiation (GO:0097028)|embryonic hemopoiesis (GO:0035162)|eosinophil differentiation (GO:0030222)|eosinophil fate commitment (GO:0035854)|erythrocyte development (GO:0048821)|erythrocyte differentiation (GO:0030218)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|megakaryocyte differentiation (GO:0030219)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of definitive erythrocyte differentiation (GO:0010724)|regulation of glycoprotein biosynthetic process (GO:0010559)|transcription from RNA polymerase II promoter (GO:0006366)|transcriptional activation by promoter-enhancer looping (GO:0071733)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	C2H2 zinc finger domain binding (GO:0070742)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(259)|large_intestine(8)|lung(9)|prostate(1)	283						CAGGCCCCTCATCCGGCCCAA	0.562			"Mis, F"		megakaryoblastic leukemia of Downs Syndrome																																p.L241fs	Pancreas(9;429 505 11287 29617)	Atlas-Indel,Pindel	.		Dom	yes		X	Xp11.23	2623	GATA binding protein 1 (globin transcription factor 1)		L	.	GATA1	342	.	0			c.723delC						PASS	.						62	58	59					X																	48650855		2203	4300	6503	SO:0001589	frameshift_variant	2623	exon4			.	X17254	CCDS14305.1	Xp11.23	2014-09-17	2001-11-28		ENSG00000102145	ENSG00000102145		"GATA zinc finger domain containing"	4170	protein-coding gene	gene with protein product	"nuclear factor, erythroid 1"	305371	"GATA-binding protein 1 (globin transcription factor 1)"	GF1		1999341	Standard	NM_002049		Approved	ERYF1, NFE1, GATA-1, NF-E1	uc004dkq.4	P15976	OTTHUMG00000021504	ENST00000376670.3:c.724delA	chrX.hg19:g.48650855delA	ENSP00000365858:p.Ile242fs	148.0	0.0	0		132.0	99.0	0.75	NM_002049	Q96GB8	Frame_Shift_Del	DEL	ENST00000376670.3	hg19	CCDS14305.1																																																																																			.	.	.	none		0.562	GATA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056517.1	NM_002049		-	48650855	A	-	48650855	7	5	198	1	0	1	0	1	0	0	0	0	6260	217	8	0	734	0	GATA1	23	48650855	Frame_Shift_Del	DEL	A	TCGA-HE-A5NI-01A-11D-A26P-10	8727723	48650855	106619705	102	11990											
PRRG3	79057	hgsc.bcm.edu	37	chrX	150869380	150869380	+	Frame_Shift_Del	DEL	C	C	-																															gactgtccagcaccacccctCccccctcctacgaggaggtg																										TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	g.chrX:150869380delC	ENST00000370353.3	+	4	961	c.571delC	c.(571-573)cccfs	p.P192fs	PRRG3_ENST00000538575.1_Frame_Shift_Del_p.P192fs			Q9BZD7	TMG3_HUMAN	proline rich Gla (G-carboxyglutamic acid) 3 (transmembrane)	192						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(3)|prostate(2)|skin(3)	24	Acute lymphoblastic leukemia(192;6.56e-05)					CACCACCCCTCCCCCCTCCTA	0.647																																					p.P190fs		Atlas-Indel,Pindel	.											.	PRRG3	74	.	0			c.570delT						PASS	.						55	44	48					X																	150869380		2203	4300	6503	SO:0001589	frameshift_variant	79057	exon4			.	AK074574	CCDS14699.1	Xq28	2008-02-05			ENSG00000130032	ENSG00000130032			30798	protein-coding gene	gene with protein product		300685				11171957	Standard	NM_024082		Approved	TMG3	uc022cgt.1	Q9BZD7	OTTHUMG00000024170	ENST00000370353.3:c.571delC	chrX.hg19:g.150869380delC	ENSP00000359378:p.Pro192fs	149.0	0.0	0		154.0	102.0	0.662338	NM_024082	A1A523|A1A575|Q8N2N6	Frame_Shift_Del	DEL	ENST00000370353.3	hg19	CCDS14699.1																																																																																			.	.	.	none		0.647	PRRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060880.1	NM_024082		-	150869380	C	-	150869380	7	5	198	1	0	1	0	1	0	0	0	0	12617	855	30	0	581	0	PRRG3	23	150869380	Frame_Shift_Del	DEL	C	TCGA-HE-A5NI-01A-11D-A26P-10	102218525	150869380	4401180	103	11991											
ARID1A	8289	hgsc.bcm.edu	37	chr1	27106015	27106015	+	Frame_Shift_Del	DEL	C	C	-																															ggcctcacgcaccctgcccaCcagcccctcggaagcatgtg																										TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr1:27106015delC	ENST00000324856.7	+	20	5997	c.5626delC	c.(5626-5628)ccafs	p.P1876fs	ARID1A_ENST00000374152.2_Frame_Shift_Del_p.P1493fs|ARID1A_ENST00000457599.2_Frame_Shift_Del_p.P1659fs|ARID1A_ENST00000540690.1_Frame_Shift_Del_p.P204fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1876					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)		ACCCTGCCCACCAGCCCCTCG	0.622			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.P1875fs		Atlas-Indel,Pindel	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.5625delA						PASS	.						64	70	68					1																	27106015		2203	4300	6503	SO:0001589	frameshift_variant	8289	exon20			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.5626delC	chr1.hg19:g.27106015delC	ENSP00000320485:p.Pro1876fs	118.0	0.0	0		122.0	49.0	0.401639	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Del	DEL	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.	.	none		0.622	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		-	27106015	C	-	27106015	7	5	199	1	0	1	0	1	0	0	0	0	913	507	18	0	5704	0	ARID1A	1	27106015	Frame_Shift_Del	DEL	C	TCGA-HE-A5NJ-01A-11D-A26P-10		27106015	222144606	1	11992											
FAM46B	115572	hgsc.bcm.edu	37	chr1	27332779	27332779	+	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	ctccaccaggtctggaaagtCgatgaagaagcgggagcaca	13	5	13	10	2	1	2	0	1	1	1	3	5	2	4	2	3	2	1	2	3	3	0			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr1:27332779C>T	ENST00000289166.5	-	2	1099	c.934G>A	c.(934-936)Gac>Aac	p.D312N		NM_052943.3	NP_443175.2	Q96A09	FA46B_HUMAN	family with sequence similarity 46, member B	312										breast(1)|central_nervous_system(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;7.71e-51)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|STAD - Stomach adenocarcinoma(196;0.00114)|READ - Rectum adenocarcinoma(331;0.0419)		TCTGGAAAGTCGATGAAGAAG	0.677																																					p.D312N		Atlas-SNP	.											.	FAM46B	44	.	0			c.G934A						PASS	.						20	23	22					1																	27332779		2199	4296	6495	SO:0001583	missense	115572	exon2			GAAAGTCGATGAA	AK122816	CCDS294.2	1p35.3	2008-02-05			ENSG00000158246	ENSG00000158246			28273	protein-coding gene	gene with protein product						12477932	Standard	NM_052943		Approved	MGC16491	uc010ofj.2	Q96A09	OTTHUMG00000004278	ENST00000289166.5:c.934G>A	chr1.hg19:g.27332779C>T	ENSP00000289166:p.Asp312Asn	34.0	0.0	.		91.0	4.0	.	NM_052943		Missense_Mutation	SNP	ENST00000289166.5	hg19	CCDS294.2	.	.	.	.	.	.	.	.	.	.	C	34	5.352046	0.95830	.	.	ENSG00000158246	ENST00000289166	T	0.39406	1.08	5.31	5.31	0.75309	Domain of unknown function DUF1693 (1);	0.178869	0.64402	D	0.000014	T	0.73329	0.3573	M	0.90870	3.155	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79398	-0.1820	10	0.87932	D	0	-6.0156	19.1626	0.93539	0.0:1.0:0.0:0.0	.	312	Q96A09	FA46B_HUMAN	N	312	ENSP00000289166:D312N	ENSP00000289166:D312N	D	-	1	0	FAM46B	27205366	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	7.651000	0.83577	2.768000	0.95171	0.561000	0.74099	GAC	.	.	.	none		0.677	FAM46B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012347.2	NM_052943		T	27332779	C	T	27332779	3	4	199	1	0	0	0	0	1	0	0	0	5573	884	31	1	347	1	FAM46B	1	27332779	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	226764	27332779	221917842	2	11993											
TMEM125	128218	hgsc.bcm.edu	37	chr1	43739036	43739036	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcacgagaccacatccagcAttgccagcctcatctgacgg	10	7	9	15	2	3	2	2	1	1	1	4	3	4	2	4	1	3	1	4	1	0	1			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr1:43739036A>G	ENST00000432792.2	+	4	1213	c.643A>G	c.(643-645)Att>Gtt	p.I215V	TMEM125_ENST00000439858.1_Missense_Mutation_p.I215V			Q96AQ2	TM125_HUMAN	transmembrane protein 125	215						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)				CACATCCAGCATTGCCAGCCT	0.627																																					p.I215V		Atlas-SNP	.											.	TMEM125	18	.	0			c.A643G						PASS	.						35	29	31					1																	43739036		2203	4300	6503	SO:0001583	missense	128218	exon4			TCCAGCATTGCCA	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.643A>G	chr1.hg19:g.43739036A>G	ENSP00000429275:p.Ile215Val	205.0	0.0	.		150.0	80.0	.	NM_144626	D3DPX1	Missense_Mutation	SNP	ENST00000432792.2	hg19	CCDS480.1	.	.	.	.	.	.	.	.	.	.	A	13.78	2.340390	0.41498	.	.	ENSG00000179178	ENST00000439858;ENST00000432792	T;T	0.44482	0.92;0.92	4.91	4.91	0.64330	.	0.123297	0.53938	D	0.000057	T	0.28599	0.0708	N	0.19112	0.55	0.29819	N	0.830963	P	0.34462	0.454	B	0.31337	0.128	T	0.19844	-1.0293	10	0.36615	T	0.2	.	14.5656	0.68173	1.0:0.0:0.0:0.0	.	215	Q96AQ2	TM125_HUMAN	V	215	ENSP00000429775:I215V;ENSP00000429275:I215V	ENSP00000429275:I215V	I	+	1	0	TMEM125	43511623	1.000000	0.71417	0.997000	0.53966	0.784000	0.44337	2.906000	0.48735	1.842000	0.53543	0.460000	0.39030	ATT	.	.	.	none		0.627	TMEM125-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019032.2	NM_144626		G	43739036	A	G	43739036	3	3	199	1	0	0	0	0	1	0	0	0	16049	217	8	3	645	3	TMEM125	1	43739036	Missense_Mutation	SNP	A	TCGA-HE-A5NJ-01A-11D-A26P-10	16406257	43739036	205511585	3	11994											
RPTN	126638	hgsc.bcm.edu	37	chr1	152127305	152127305	+	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	cttcatgggtttgcctgtctCgtctctgatggctctgctca	3	16	10	12	1	5	1	2	1	3	0	7	1	5	1	1	2	2	3	1	2	0	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr1:152127305C>T	ENST00000316073.3	-	3	2334	c.2270G>A	c.(2269-2271)cGa>cAa	p.R757Q		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	757	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						TTGCCTGTCTCGTCTCTGATG	0.512																																					p.R757Q		Atlas-SNP	.											.	RPTN	123	.	0			c.G2270A						PASS	.						835	660	713					1																	152127305		1568	3582	5150	SO:0001583	missense	126638	exon3			CTGTCTCGTCTCT	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.2270G>A	chr1.hg19:g.152127305C>T	ENSP00000317895:p.Arg757Gln	367.0	1.0	.		399.0	158.0	.	NM_001122965	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	hg19	CCDS41397.1	.	.	.	.	.	.	.	.	.	.	C	4.873	0.162231	0.09287	.	.	ENSG00000215853	ENST00000316073;ENST00000541545	T	0.12569	2.67	5.46	-6.92	0.01644	.	1.609200	0.05690	N	0.591997	T	0.02688	0.0081	N	0.25286	0.73	0.09310	N	1	B	0.13145	0.007	B	0.06405	0.002	T	0.25187	-1.0139	10	0.29301	T	0.29	0.289	14.9735	0.71251	0.0:0.6643:0.0:0.3357	.	757	Q6XPR3	RPTN_HUMAN	Q	757;412	ENSP00000317895:R757Q	ENSP00000317895:R757Q	R	-	2	0	RPTN	150393929	0.000000	0.05858	0.000000	0.03702	0.087000	0.18053	-1.478000	0.02329	-2.128000	0.00818	-1.183000	0.01708	CGA	.	.	.	none		0.512	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312		T	152127305	C	T	152127305	3	4	199	1	0	0	0	0	1	0	0	0	13677	884	31	1	88	1	RPTN	1	152127305	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	108388269	152127305	97123316	4	11995											
NUP210L	91181	hgsc.bcm.edu	37	chr1	154108401	154108401	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agacccgttaagtgcaactcTatggtcttgcaattccagta	11	12	8	10	1	2	1	0	0	2	1	3	1	3	1	2	1	3	4	2	1	5	5			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr1:154108401T>C	ENST00000368559.3	-	7	969	c.898A>G	c.(898-900)Aga>Gga	p.R300G	NUP210L_ENST00000271854.3_Missense_Mutation_p.R300G	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	300					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)			AGTGCAACTCTATGGTCTTGC	0.418																																					p.R300G		Atlas-SNP	.											.	NUP210L	181	.	0			c.A898G						PASS	.						108	99	102					1																	154108401		1876	4103	5979	SO:0001583	missense	91181	exon7			CAACTCTATGGTC	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.898A>G	chr1.hg19:g.154108401T>C	ENSP00000357547:p.Arg300Gly	90.0	0.0	.		94.0	29.0	.	NM_001159484	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Missense_Mutation	SNP	ENST00000368559.3	hg19	CCDS41399.1	.	.	.	.	.	.	.	.	.	.	T	10.65	1.410097	0.25465	.	.	ENSG00000143552	ENST00000368559;ENST00000271854	T;T	0.05447	3.44;3.44	5.0	2.53	0.30540	.	0.593551	0.16379	N	0.216995	T	0.01387	0.0045	L	0.44542	1.39	0.09310	N	1	B;B	0.31125	0.201;0.309	B;B	0.21917	0.037;0.037	T	0.48714	-0.9011	10	0.23302	T	0.38	-11.1939	4.5019	0.11869	0.0:0.1237:0.3878:0.4885	.	300;300	E7EP56;Q5VU65	.;P210L_HUMAN	G	300	ENSP00000357547:R300G;ENSP00000271854:R300G	ENSP00000271854:R300G	R	-	1	2	NUP210L	152375025	0.003000	0.15002	0.002000	0.10522	0.896000	0.52359	1.475000	0.35409	0.321000	0.23259	0.533000	0.62120	AGA	.	.	.	none		0.418	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308		C	154108401	T	C	154108401	3	2	199	1	0	0	0	0	1	0	0	0	10768	1530	53	3	4904	3	NUP210L	1	154108401	Missense_Mutation	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10	1981096	154108401	95142220	5	11996											
TMEM9	252839	hgsc.bcm.edu	37	chr1	201123024	201123024	+	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	gggcaccagcaaacacccgaCcacagccaccaaagataaga	17	1	8	15	1	0	2	0	0	0	2	0	3	0	2	5	1	3	2	5	1	3	1			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr1:201123024C>T	ENST00000367330.1	-	1	544	c.28G>A	c.(28-30)Gtc>Atc	p.V10I	TMEM9_ENST00000367334.5_Missense_Mutation_p.V10I|TMEM9_ENST00000367332.1_Missense_Mutation_p.V10I|TMEM9_ENST00000485839.2_Missense_Mutation_p.V10I|TMEM9_ENST00000367333.2_Missense_Mutation_p.V10I			Q9P0T7	TMEM9_HUMAN	transmembrane protein 9	10					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)				AAACACCCGACCACAGCCACC	0.582																																					p.V10I		Atlas-SNP	.											.	TMEM9	12	.	0			c.G28A						PASS	.						70	66	67					1																	201123024		2203	4300	6503	SO:0001583	missense	252839	exon2			ACCCGACCACAGC		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.28G>A	chr1.hg19:g.201123024C>T	ENSP00000356299:p.Val10Ile	275.0	0.0	.		251.0	89.0	.	NM_016456	B1ALM6|Q96NQ9|Q9BQF5	Missense_Mutation	SNP	ENST00000367330.1	hg19	CCDS1408.1	.	.	.	.	.	.	.	.	.	.	C	16.71	3.198740	0.58126	.	.	ENSG00000116857	ENST00000367334;ENST00000367332;ENST00000367330;ENST00000367329;ENST00000367333;ENST00000455367;ENST00000435310;ENST00000414605	.	.	.	4.66	3.75	0.43078	.	0.790844	0.10935	N	0.617956	T	0.20210	0.0486	N	0.19112	0.55	0.19300	N	0.999979	B;B;B;B	0.31581	0.329;0.049;0.008;0.003	B;B;B;B	0.25987	0.065;0.039;0.003;0.004	T	0.11641	-1.0579	9	0.08599	T	0.76	-18.4909	9.8146	0.40844	0.0:0.9026:0.0:0.0974	.	10;10;10;10	B4DJZ4;B4E1H4;B1ALM5;Q9P0T7	.;.;.;TMEM9_HUMAN	I	10	.	ENSP00000356298:V10I	V	-	1	0	TMEM9	199389647	0.000000	0.05858	0.772000	0.31596	0.991000	0.79684	0.133000	0.15912	1.175000	0.42826	0.557000	0.71058	GTC	.	.	.	none		0.582	TMEM9-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000087160.1	NM_016456		T	201123024	C	T	201123024	3	4	199	1	0	0	0	0	1	0	0	0	16229	507	18	2	543	2	TMEM9	1	201123024	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	47014623	201123024	48127597	6	11997											
GPN1	11321	hgsc.bcm.edu	37	chr2	27858007	27858007	+	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	tgatttttttgtggctttagGcatcctcatttccaacagtt	7	19	7	8	0	1	1	1	1	0	0	3	1	3	1	2	2	1	3	2	2	2	7			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr2:27858007G>A	ENST00000610189.1	+	7	437	c.430G>A	c.(430-432)Gca>Aca	p.A144T	RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000556601.1_3'UTR|GPN1_ENST00000264718.3_Splice_Site_p.A158T|GPN1_ENST00000458167.2_Splice_Site_p.A49T|GPN1_ENST00000461249.1_3'UTR|GPN1_ENST00000503738.1_Splice_Site_p.A49T|GPN1_ENST00000407583.3_Splice_Site_p.A132T|GPN1_ENST00000515877.1_Splice_Site_p.A65T|GPN1_ENST00000424214.1_Splice_Site_p.A65T	NM_007266.3	NP_009197.2			GPN-loop GTPase 1											endometrium(1)|large_intestine(1)|lung(12)	14						GTGGCTTTAGGCATCCTCATT	0.443																																					p.A158T		Atlas-SNP	.											.	GPN1	28	.	0			c.G472A						PASS	.						209	190	196					2																	27858007		2203	4300	6503	SO:0001630	splice_region_variant	11321	exon7			CTTTAGGCATCCT	AB044661	CCDS1760.2, CCDS46248.1, CCDS46249.1, CCDS46250.1	2p23.3	2011-11-04	2008-04-30	2008-04-30	ENSG00000198522	ENSG00000198522		"GPN-loop GTPases"	17030	protein-coding gene	gene with protein product	"RNA polymerase II associated protein 4"	611479	"XPA binding protein 1", "XPA binding protein 1, GTPase"	XAB1		11058119, 11124703	Standard	NM_007266		Approved	NTPBP, MBDIN, ATPBD1A, RPAP4	uc010ymc.2	Q9HCN4	OTTHUMG00000097784	ENST00000610189.1:c.430-1G>A	chr2.hg19:g.27858007G>A		209.0	0.0	.		189.0	73.0	.	NM_007266		Missense_Mutation	SNP	ENST00000610189.1	hg19		.	.	.	.	.	.	.	.	.	.	G	36	5.660616	0.96734	.	.	ENSG00000198522	ENST00000515877;ENST00000503738;ENST00000458167;ENST00000424214;ENST00000407583;ENST00000264718	T;T;T;T;T;T	0.23552	1.9;1.9;1.9;1.9;1.9;1.9	5.96	5.96	0.96718	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.53449	0.1797	M	0.77616	2.38	0.80722	D	1	P;D;D;D	0.89917	0.792;1.0;0.98;0.992	P;D;P;D	0.81914	0.9;0.995;0.876;0.92	T	0.50039	-0.8874	9	.	.	.	-8.5718	17.1122	0.86679	0.0:0.0:1.0:0.0	.	144;158;49;132	Q9HCN4;B4DQM4;B4DXU4;B5MBZ5	GPN1_HUMAN;.;.;.	T	65;49;49;65;132;158	ENSP00000424678:A65T;ENSP00000427269:A49T;ENSP00000412170:A49T;ENSP00000398115:A65T;ENSP00000384255:A132T;ENSP00000264718:A158T	.	A	+	1	0	GPN1	27711511	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	8.896000	0.92521	2.820000	0.97059	0.655000	0.94253	GCA	.	.	.	none		0.443	GPN1-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000473126.1	NM_007266	Missense_Mutation	A	27858007	G	A	27858007	5	1	199	1	0	0	0	0	0	0	1	0	6624	1217	42	2	581	2	GPN1	2	27858007	Splice_Site	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10		27858007	215341366	7	11998											
ALMS1	7840	hgsc.bcm.edu	37	chr2	73836707	73836707	+	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	ttctacagagagtgaccaatCaacttctggggagaaaagtt	14	10	10	7	0	3	3	1	1	2	2	3	5	3	3	1	2	2	1	1	2	5	4			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr2:73836707C>T	ENST00000264448.6	+	23	12583	c.12472C>T	c.(12472-12474)Caa>Taa	p.Q4158*	ALMS1_ENST00000409009.1_Nonsense_Mutation_p.Q4116*	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	4158	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						AGTGACCAATCAACTTCTGGG	0.433																																					p.Q4158X		Atlas-SNP	.											.	ALMS1	384	.	0			c.C12472T						PASS	.						117	116	116					2																	73836707		1850	4083	5933	SO:0001587	stop_gained	7840	exon23			ACCAATCAACTTC	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.12472C>T	chr2.hg19:g.73836707C>T	ENSP00000264448:p.Gln4158*	54.0	0.0	.		53.0	15.0	.	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Nonsense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	C	53	21.012144	0.99936	.	.	ENSG00000116127	ENST00000409009;ENST00000264448	.	.	.	5.34	5.34	0.76211	.	0.658065	0.14442	N	0.319301	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	.	14.4071	0.67090	0.0:1.0:0.0:0.0	.	.	.	.	X	4116;4158	.	ENSP00000264448:Q4158X	Q	+	1	0	ALMS1	73690215	0.984000	0.35163	0.996000	0.52242	0.780000	0.44128	2.387000	0.44389	2.779000	0.95612	0.591000	0.81541	CAA	.	.	.	none		0.433	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		T	73836707	C	T	73836707	4	4	199	1	0	0	0	0	0	1	0	0	535	827	29	2	12562	2	ALMS1	2	73836707	Nonsense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	45978700	73836707	169362666	8	11999											
ACVR2A	92	hgsc.bcm.edu	37	chr2	148676153	148676153	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatggccacaaacctgccatAtctcacaggtagactaaatt	14	9	7	11	0	1	1	1	0	1	1	2	2	1	1	3	2	2	1	3	2	5	4			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr2:148676153A>G	ENST00000241416.7	+	7	1590	c.954A>G	c.(952-954)atA>atG	p.I318M	ACVR2A_ENST00000535787.1_Missense_Mutation_p.I210M|ACVR2A_ENST00000404590.1_Missense_Mutation_p.I318M	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	318	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		AACCTGCCATATCTCACAGGT	0.348																																					p.I318M		Atlas-SNP	.											.	ACVR2A	125	.	0			c.A954G						PASS	.						42	44	43					2																	148676153		2202	4300	6502	SO:0001583	missense	92	exon7			TGCCATATCTCAC		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.954A>G	chr2.hg19:g.148676153A>G	ENSP00000241416:p.Ile318Met	28.0	0.0	.		56.0	22.0	.	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Missense_Mutation	SNP	ENST00000241416.7	hg19	CCDS33301.1	.	.	.	.	.	.	.	.	.	.	A	17.99	3.524183	0.64747	.	.	ENSG00000121989	ENST00000241416;ENST00000535787;ENST00000404590	T;T;T	0.73789	-0.78;-0.78;-0.78	5.63	0.102	0.14522	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.050216	0.85682	D	0.000000	D	0.84465	0.5478	M	0.86178	2.8	0.54753	D	0.999987	P	0.42827	0.791	P	0.56514	0.8	D	0.85693	0.1308	10	0.59425	D	0.04	.	15.9363	0.79712	0.3896:0.6104:0.0:0.0	.	318	P27037	AVR2A_HUMAN	M	318;210;318	ENSP00000241416:I318M;ENSP00000439988:I210M;ENSP00000384338:I318M	ENSP00000241416:I318M	I	+	3	3	ACVR2A	148392623	0.981000	0.34729	0.995000	0.50966	0.986000	0.74619	0.307000	0.19296	-0.207000	0.10187	0.460000	0.39030	ATA	.	.	.	none		0.348	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616		G	148676153	A	G	148676153	3	3	199	1	0	0	0	0	1	0	0	0	223	439	16	3	980	3	ACVR2A	2	148676153	Missense_Mutation	SNP	A	TCGA-HE-A5NJ-01A-11D-A26P-10	74839446	148676153	94523220	9	12000											
SH3BP4	23677	hgsc.bcm.edu	37	chr2	235949726	235949726	+	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	ccaccgaaatgggctacatcCcctcctcctatgtgcagccc	8	8	7	18	1	0	0	0	0	0	0	3	1	3	0	7	1	3	2	7	1	3	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr2:235949726C>G	ENST00000409212.1	+	4	820	c.313C>G	c.(313-315)Ccc>Gcc	p.P105A	SH3BP4_ENST00000392011.2_Missense_Mutation_p.P105A|SH3BP4_ENST00000344528.4_Missense_Mutation_p.P105A			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	105	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		GGGCTACATCCCCTCCTCCTA	0.537																																					p.P105A		Atlas-SNP	.											.	SH3BP4	109	.	0			c.C313G						PASS	.						171	144	153					2																	235949726		2203	4300	6503	SO:0001583	missense	23677	exon4			TACATCCCCTCCT	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.313C>G	chr2.hg19:g.235949726C>G	ENSP00000386862:p.Pro105Ala	321.0	0.0	.		320.0	127.0	.	NM_014521	O95082|Q309A3|Q53QD0|Q53TD1	Missense_Mutation	SNP	ENST00000409212.1	hg19	CCDS2513.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.895268	0.91962	.	.	ENSG00000130147	ENST00000392011;ENST00000420127;ENST00000416021;ENST00000409212;ENST00000344528;ENST00000446904	D;D;D;D;D	0.99454	-5.92;-5.92;-5.92;-5.92;-5.92	5.24	5.24	0.73138	Src homology-3 domain (4);	0.000000	0.85682	D	0.000000	D	0.99635	0.9866	M	0.93062	3.375	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97817	1.0254	10	0.72032	D	0.01	-9.9278	17.3901	0.87427	0.0:1.0:0.0:0.0	.	105;105	A8K594;Q9P0V3	.;SH3B4_HUMAN	A	105	ENSP00000375867:P105A;ENSP00000403251:P105A;ENSP00000386862:P105A;ENSP00000340237:P105A;ENSP00000415391:P105A	ENSP00000340237:P105A	P	+	1	0	SH3BP4	235614465	1.000000	0.71417	0.996000	0.52242	0.940000	0.58332	7.571000	0.82399	2.442000	0.82660	0.655000	0.94253	CCC	.	.	.	none		0.537	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1			G	235949726	C	G	235949726	3	3	199	1	0	0	0	0	1	0	0	0	14259	623	22	4	319	4	SH3BP4	2	235949726	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	87273573	235949726	7249647	10	12001											
ITPR1	3708	hgsc.bcm.edu	37	chr3	4859771	4859771	+	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	ttgtctcatttttaggcttgGaaagagacaagtttgacaac	12	14	9	6	0	1	2	1	1	1	1	2	4	1	3	0	2	1	2	0	2	4	6			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr3:4859771G>A	ENST00000443694.2	+	57	7828	c.7828G>A	c.(7828-7830)Gaa>Aaa	p.E2610K	AC018816.3_ENST00000489771.1_Intron|ITPR1_ENST00000544951.1_Missense_Mutation_p.E588K|AC018816.3_ENST00000441894.1_Intron|ITPR1_ENST00000302640.8_Missense_Mutation_p.E2610K|ITPR1_ENST00000357086.4_Missense_Mutation_p.E2577K|ITPR1_ENST00000456211.2_Missense_Mutation_p.E2562K|ITPR1_ENST00000463980.1_3'UTR|AC018816.3_ENST00000449914.1_Intron|ITPR1_ENST00000423119.2_Missense_Mutation_p.E2577K|ITPR1_ENST00000354582.6_Missense_Mutation_p.E2610K			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	2625					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)	TTTAGGCTTGGAAAGAGACAA	0.448																																					p.E2610K		Atlas-SNP	.											.	ITPR1	659	.	0			c.G7828A						PASS	.						52	48	49					3																	4859771		1897	4121	6018	SO:0001583	missense	3708	exon59			GGCTTGGAAAGAG	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.7828G>A	chr3.hg19:g.4859771G>A	ENSP00000401671:p.Glu2610Lys	101.0	0.0	.		126.0	45.0	.	NM_001168272	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	hg19	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	g	32	5.120856	0.94385	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000426160;ENST00000357086;ENST00000456211;ENST00000544951;ENST00000443694	T;T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97;0.97	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.58581	0.2132	L	0.57536	1.79	0.80722	D	1	D;B;B	0.62365	0.991;0.102;0.226	P;B;B	0.61201	0.885;0.07;0.425	T	0.56147	-0.8027	10	0.35671	T	0.21	.	18.3362	0.90288	0.0:0.0:1.0:0.0	.	588;2625;2577	B7ZMI3;Q14643;G5E9P1	.;ITPR1_HUMAN;.	K	2625;2610;2610;2577;1071;2577;2562;588;2610	ENSP00000306253:E2610K;ENSP00000346595:E2610K;ENSP00000405934:E2577K;ENSP00000349597:E2577K;ENSP00000397885:E2562K;ENSP00000440564:E588K;ENSP00000401671:E2610K	ENSP00000306253:E2610K	E	+	1	0	ITPR1	4834771	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	9.709000	0.98729	2.311000	0.77944	0.461000	0.40582	GAA	.	.	.	none		0.448	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		A	4859771	G	A	4859771	3	1	199	1	0	0	0	0	1	0	0	0	7927	1175	41	2	8103	2	ITPR1	3	4859771	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10		4859771	193162659	11	12002											
THUMPD3	25917	hgsc.bcm.edu	37	chr3	9406849	9406849	+	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	cagaaagtgacctcggaagtGaatctgagcttctagtcact	12	10	10	9	1	3	4	1	3	2	1	4	5	3	5	1	1	1	1	1	1	4	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr3:9406849G>A	ENST00000345094.3	+	2	431	c.97G>A	c.(97-99)Gaa>Aaa	p.E33K	RP11-380O24.1_ENST00000517687.1_RNA|SETD5-AS1_ENST00000468186.1_RNA|THUMPD3_ENST00000452837.2_Missense_Mutation_p.E33K|RP11-380O24.1_ENST00000466431.2_RNA|THUMPD3_ENST00000515662.2_Missense_Mutation_p.E33K|RP11-380O24.1_ENST00000491930.2_RNA|RP11-380O24.1_ENST00000517846.1_RNA|RP11-380O24.1_ENST00000518331.1_RNA	NM_001114092.1|NM_015453.2	NP_001107564.1|NP_056268.2	Q9BV44	THUM3_HUMAN	THUMP domain containing 3	33						cytoplasm (GO:0005737)|nucleolus (GO:0005730)	methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	19	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.101)		CCTCGGAAGTGAATCTGAGCT	0.443																																					p.E33K		Atlas-SNP	.											.	THUMPD3	46	.	0			c.G97A						PASS	.						94	95	94					3																	9406849		2203	4300	6503	SO:0001583	missense	25917	exon2			GGAAGTGAATCTG	AL117483	CCDS2573.1	3p25.3	2004-06-04			ENSG00000134077	ENSG00000134077			24493	protein-coding gene	gene with protein product						12477932	Standard	NM_015453		Approved	DKFZP434F091	uc003brn.4	Q9BV44	OTTHUMG00000097031	ENST00000345094.3:c.97G>A	chr3.hg19:g.9406849G>A	ENSP00000339532:p.Glu33Lys	133.0	0.0	.		128.0	51.0	.	NM_001114092	Q9H8V6|Q9NVC1|Q9UFS3	Missense_Mutation	SNP	ENST00000345094.3	hg19	CCDS2573.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.044109	0.75732	.	.	ENSG00000134077	ENST00000452837;ENST00000417036;ENST00000419437;ENST00000345094;ENST00000515662	T;T;T	0.44083	0.93;0.93;0.93	5.57	4.47	0.54385	.	0.949351	0.08920	N	0.874534	T	0.35595	0.0937	L	0.51422	1.61	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	T	0.11494	-1.0585	10	0.40728	T	0.16	.	5.2477	0.15506	0.1312:0.2026:0.6662:0.0	.	33	Q9BV44	THUM3_HUMAN	K	33	ENSP00000395893:E33K;ENSP00000339532:E33K;ENSP00000424064:E33K	ENSP00000339532:E33K	E	+	1	0	THUMPD3	9381849	0.049000	0.20398	0.085000	0.20634	0.888000	0.51559	2.198000	0.42705	2.785000	0.95823	0.655000	0.94253	GAA	.	.	.	none		0.443	THUMPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214127.1	NM_015453		A	9406849	G	A	9406849	3	1	199	1	0	0	0	0	1	0	0	0	15896	1291	45	2	99	2	THUMPD3	3	9406849	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	4547078	9406849	188615581	12	12003											
COL7A1	1294	hgsc.bcm.edu	37	chr3	48610131	48610131	+	Frame_Shift_Del	DEL	T	T	-																															ggggcccccgtggggccaggTtctcctttaggtccgacagg																										TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr3:48610131delT	ENST00000328333.8	-	87	6980	c.6873delA	c.(6871-6873)gaafs	p.E2291fs	COL7A1_ENST00000454817.1_Frame_Shift_Del_p.E2259fs	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2291	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		TGGGGCCAGGTTCTCCTTTAG	0.632																																					p.P2292fs		Pindel	.											.	COL7A1	320	.	0			c.6874delC						PASS	.						24	30	28					3																	48610131		2200	4297	6497	SO:0001589	frameshift_variant	1294	exon87			.	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.6873delA	chr3.hg19:g.48610131delT	ENSP00000332371:p.Glu2291fs	136.0	0.0	.		114.0	31.0	0.272	NM_000094	Q14054|Q16507	Frame_Shift_Del	DEL	ENST00000328333.8	hg19	CCDS2773.1																																																																																			.	.	.	none		0.632	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		-	48610131	T	-	48610131	7	5	199	1	0	1	0	1	0	0	0	0	3706	1722	60	0	2089	0	COL7A1	3	48610131	Frame_Shift_Del	DEL	T	TCGA-HE-A5NJ-01A-11D-A26P-10	39203282	48610131	149412299	13	12004											
IL17RD	54756	hgsc.bcm.edu	37	chr3	57144293	57144293	+	Frame_Shift_Del	DEL	C	C	-																															tggcactgtcttccctccgaCttcagctcctccagtattac																										TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr3:57144293delC	ENST00000296318.7	-	4	445	c.357delG	c.(355-357)aagfs	p.K119fs	IL17RD_ENST00000320057.5_5'UTR|IL17RD_ENST00000463523.1_5'UTR|IL17RD_ENST00000427856.2_Frame_Shift_Del_p.K95fs	NM_017563.3	NP_060033.3	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D	119					signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)	16				KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204)		TTCCCTCCGACTTCAGCTCCT	0.438																																					p.S120fs		Pindel	.											.	IL17RD	93	.	0			c.358delT						PASS	.						121	109	113					3																	57144293		1911	4137	6048	SO:0001589	frameshift_variant	54756	exon4			.	AF494208	CCDS2880.2	3p21.1	2008-02-05			ENSG00000144730	ENSG00000144730		"Interleukins and interleukin receptors"	17616	protein-coding gene	gene with protein product		606807				11802164, 12604616	Standard	NM_017563		Approved	SEF, IL17RLM, FLJ35755, IL-17RD	uc003dil.3	Q8NFM7	OTTHUMG00000150171	ENST00000296318.7:c.357delG	chr3.hg19:g.57144293delC	ENSP00000296318:p.Lys119fs	123.0	0.0	.		90.0	27.0	0.300	NM_017563	Q2NKP7|Q58EZ7|Q6RVF4|Q6UWI5|Q8N113|Q8NFS0|Q9UFA0	Frame_Shift_Del	DEL	ENST00000296318.7	hg19	CCDS2880.2																																																																																			.	.	.	none		0.438	IL17RD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316680.1	NM_017563		-	57144293	C	-	57144293	7	5	199	1	0	1	0	1	0	0	0	0	7649	564	20	0	1902	0	IL17RD	3	57144293	Frame_Shift_Del	DEL	C	TCGA-HE-A5NJ-01A-11D-A26P-10	8534162	57144293	140878137	14	12005											
IGSF10	285313	hgsc.bcm.edu	37	chr3	151155196	151155196	+	Missense_Mutation	SNP	T	T	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	tgctatcagatactgataacTttgtggtccattggaaaatc	12	14	8	7	0	1	2	1	1	0	1	3	3	2	3	1	2	3	1	1	2	5	5			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr3:151155196T>G	ENST00000282466.3	-	6	7152	c.7153A>C	c.(7153-7155)Agt>Cgt	p.S2385R	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	2385	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)			TACTGATAACTTTGTGGTCCA	0.408																																					p.S2385R		Atlas-SNP	.											.	IGSF10	279	.	0			c.A7153C						PASS	.						125	125	125					3																	151155196		2203	4300	6503	SO:0001583	missense	285313	exon6			GATAACTTTGTGG	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.7153A>C	chr3.hg19:g.151155196T>G	ENSP00000282466:p.Ser2385Arg	79.0	0.0	.		77.0	41.0	.	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	hg19	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	T	4.176	0.031261	0.08101	.	.	ENSG00000152580	ENST00000282466	T	0.63580	-0.05	5.59	0.331	0.15933	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.945401	0.08716	N	0.904233	T	0.42607	0.1210	L	0.28115	0.83	0.09310	N	1	P;B	0.41080	0.737;0.141	B;B	0.36845	0.234;0.066	T	0.18681	-1.0329	10	0.22706	T	0.39	.	6.415	0.21712	0.0:0.1304:0.2469:0.6227	.	2385;412	Q6WRI0;Q6WRI0-2	IGS10_HUMAN;.	R	2385	ENSP00000282466:S2385R	ENSP00000282466:S2385R	S	-	1	0	IGSF10	152637886	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	1.061000	0.30542	-0.160000	0.11002	-0.316000	0.08728	AGT	.	.	.	none		0.408	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		G	151155196	T	G	151155196	3	3	199	1	0	0	0	0	1	0	0	0	7604	1609	56	5	722	5	IGSF10	3	151155196	Missense_Mutation	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10	94010903	151155196	46867234	15	12006											
ENPEP	2028	hgsc.bcm.edu	37	chr4	111397929	111397929	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacctacacgggcaccgtgaGcatctccatcaacctgagcg	10	6	9	16	3	2	2	1	2	1	0	3	2	2	2	4	1	4	2	4	1	2	1			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr4:111397929G>A	ENST00000265162.5	+	1	701	c.359G>A	c.(358-360)aGc>aAc	p.S120N		NM_001977.3	NP_001968.3	Q07075	AMPE_HUMAN	glutamyl aminopeptidase (aminopeptidase A)	120					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)		GGCACCGTGAGCATCTCCATC	0.627																																					p.S120N		Atlas-SNP	.											.	ENPEP	149	.	0			c.G359A						PASS	.						96	100	99					4																	111397929		2203	4300	6503	SO:0001583	missense	2028	exon1			CCGTGAGCATCTC	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.359G>A	chr4.hg19:g.111397929G>A	ENSP00000265162:p.Ser120Asn	132.0	0.0	.		143.0	38.0	.	NM_001977	Q504U2	Missense_Mutation	SNP	ENST00000265162.5	hg19	CCDS3691.1	.	.	.	.	.	.	.	.	.	.	G	4.521	0.096620	0.08681	.	.	ENSG00000138792	ENST00000265162	T	0.02709	4.19	5.83	-6.19	0.02078	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	1.193580	0.05705	N	0.594848	T	0.02342	0.0072	N	0.12443	0.215	0.20489	N	0.999897	B	0.09022	0.002	B	0.14023	0.01	T	0.41270	-0.9518	10	0.17832	T	0.49	.	18.7095	0.91651	0.2671:0.1216:0.6113:0.0	.	120	Q07075	AMPE_HUMAN	N	120	ENSP00000265162:S120N	ENSP00000265162:S120N	S	+	2	0	ENPEP	111617378	0.004000	0.15560	0.072000	0.20136	0.026000	0.11368	-0.722000	0.04958	-1.974000	0.00998	-0.305000	0.09177	AGC	.	.	.	none		0.627	ENPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255747.2			A	111397929	G	A	111397929	3	1	199	1	0	0	0	0	1	0	0	0	5130	971	34	2	361	2	ENPEP	4	111397929	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10		111397929	79756347	16	12007											
CCT5	22948	hgsc.bcm.edu	37	chr5	10263419	10263419	+	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	atcgactgtttgcacaagggGacaaatggtgaggagctgtc	11	9	14	7	1	0	1	0	1	0	0	2	4	0	3	0	4	2	3	0	4	2	1			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr5:10263419G>A	ENST00000280326.4	+	10	1911	c.1491G>A	c.(1489-1491)ggG>ggA	p.G497G	CCT5_ENST00000515676.1_Silent_p.G459G|CCT5_ENST00000503026.1_Silent_p.G476G|CTD-2256P15.4_ENST00000606194.1_RNA|CCT5_ENST00000506600.1_Silent_p.G404G|CCT5_ENST00000515390.1_Silent_p.G442G	NM_012073.3	NP_036205.1	P48643	TCPE_HUMAN	chaperonin containing TCP1, subunit 5 (epsilon)	497					'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						TGCACAAGGGGACAAATGGTG	0.512																																					p.G497G		Atlas-SNP	.											.	CCT5	49	.	0			c.G1491A						PASS	.						59	55	56					5																	10263419		2203	4300	6503	SO:0001819	synonymous_variant	22948	exon10			CAAGGGGACAAAT	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.1491G>A	chr5.hg19:g.10263419G>A		97.0	0.0	.		111.0	50.0	.	NM_012073	A8JZY8|A8K2X8|B4DYD8	Silent	SNP	ENST00000280326.4	hg19	CCDS3877.1																																																																																			.	.	.	none		0.512	CCT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253688.2			A	10263419	G	A	10263419	2	1	199	1	0	0	0	0	0	0	0	1	2958	1161	41	2		2	CCT5	5	10263419	Silent	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10		10263419	170651841	17	12008											
ZNF366	167465	hgsc.bcm.edu	37	chr5	71739709	71739709	+	Silent	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	cgccgggtactctgaaaagcCctgagactgagacactcatc	11	7	10	13	2	2	3	1	3	1	2	3	5	2	3	2	1	2	1	2	1	3	1			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr5:71739709C>T	ENST00000318442.5	-	5	2599	c.2109G>A	c.(2107-2109)agG>agA	p.R703R	RP11-389C8.2_ENST00000564956.1_RNA	NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	703	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)		TCTGAAAAGCCCTGAGACTGA	0.517																																					p.R703R		Atlas-SNP	.											.	ZNF366	108	.	0			c.G2109A						PASS	.						102	107	105					5																	71739709		2203	4300	6503	SO:0001819	synonymous_variant	167465	exon5			AAAAGCCCTGAGA	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.2109G>A	chr5.hg19:g.71739709C>T		36.0	0.0	.		42.0	13.0	.	NM_152625	Q5HYI9|Q7RTV4	Silent	SNP	ENST00000318442.5	hg19	CCDS4015.1																																																																																			.	.	.	none		0.517	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3			T	71739709	C	T	71739709	2	4	199	1	0	0	0	0	0	0	0	1	17882	622	22	2		2	ZNF366	5	71739709	Silent	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	61476290	71739709	109175551	18	12009											
SLC12A2	6558	hgsc.bcm.edu	37	chr5	127477532	127477532	+	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	tgtgctttaggttcttgtgtTgttcgagatgccactggaaa	7	16	12	6	1	1	1	0	0	1	1	2	3	1	2	1	2	2	4	1	2	2	6			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr5:127477532T>A	ENST00000262461.2	+	10	1821	c.1632T>A	c.(1630-1632)gtT>gtA	p.V544V	SLC12A2_ENST00000343225.4_Silent_p.V544V	NM_001046.2	NP_001037.1	P55011	S12A2_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 2	544					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|branching involved in mammary gland duct morphogenesis (GO:0060444)|chloride transmembrane transport (GO:1902476)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|gamma-aminobutyric acid signaling pathway (GO:0007214)|hyperosmotic response (GO:0006972)|ion transport (GO:0006811)|mammary duct terminal end bud growth (GO:0060763)|multicellular organism growth (GO:0035264)|positive regulation of cell volume (GO:0045795)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transepithelial ammonium transport (GO:0070634)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ammonium transmembrane transporter activity (GO:0008519)|sodium:potassium:chloride symporter activity (GO:0008511)			breast(3)|endometrium(5)|kidney(5)|large_intestine(12)|lung(16)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)|Quinethazone(DB01325)	GTTCTTGTGTTGTTCGAGATG	0.308																																					p.V544V		Atlas-SNP	.											.	SLC12A2	119	.	0			c.T1632A						PASS	.						171	162	165					5																	127477532		2203	4300	6503	SO:0001819	synonymous_variant	6558	exon10			TTGTGTTGTTCGA		CCDS4144.1, CCDS58965.1	5q23.3	2014-06-13	2013-07-18		ENSG00000064651	ENSG00000064651		"Solute carriers"	10911	protein-coding gene	gene with protein product	"bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1", "basolateral Na-K-Cl symporter", "protein phosphatase 1, regulatory subunit 141"	600840				7629105	Standard	NM_001256461		Approved	NKCC1, BSC, BSC2, PPP1R141	uc003kus.3	P55011	OTTHUMG00000128983	ENST00000262461.2:c.1632T>A	chr5.hg19:g.127477532T>A		100.0	0.0	.		74.0	25.0	.	NM_001046	Q8N713|Q8WWH7	Silent	SNP	ENST00000262461.2	hg19	CCDS4144.1																																																																																			.	.	.	none		0.308	SLC12A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250972.1	NM_001046		A	127477532	T	A	127477532	2	1	199	1	0	0	0	0	0	0	0	1	14396	1799	63	5		5	SLC12A2	5	127477532	Silent	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10	55737823	127477532	53437728	19	12010											
SLC26A2	1836	hgsc.bcm.edu	37	chr5	149361289	149361289	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaaaccttctcttctatagTgtgtatgaagcgatggcttt	10	15	9	7	1	2	1	0	1	2	0	3	3	2	1	1	1	2	2	1	1	6	6			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr5:149361289T>C	ENST00000286298.4	+	3	2401	c.2133T>C	c.(2131-2133)agT>agC	p.S711S		NM_000112.3	NP_000103.2	P50443	S26A2_HUMAN	solute carrier family 26 (anion exchanger), member 2	711	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|ossification (GO:0001503)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(1)|prostate(2)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			TCTTCTATAGTGTGTATGAAG	0.413																																					p.S711S		Atlas-SNP	.											.	SLC26A2	48	.	0			c.T2133C						PASS	.						57	63	61					5																	149361289		2203	4299	6502	SO:0001819	synonymous_variant	1836	exon3			CTATAGTGTGTAT	U14528	CCDS4300.1	5q31-q34	2014-09-17	2013-07-18		ENSG00000155850	ENSG00000155850		"Solute carriers"	10994	protein-coding gene	gene with protein product		606718	"solute carrier family 26 (sulfate transporter), member 2"	DTD		7923357	Standard	NM_000112		Approved	DTDST	uc003lrh.3	P50443	OTTHUMG00000130054	ENST00000286298.4:c.2133T>C	chr5.hg19:g.149361289T>C		42.0	0.0	.		41.0	17.0	.	NM_000112	A8K2U3|B2R6J1|Q6N051	Silent	SNP	ENST00000286298.4	hg19	CCDS4300.1																																																																																			.	.	.	none		0.413	SLC26A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252333.2	NM_000112		C	149361289	T	C	149361289	2	2	199	1	0	0	0	0	0	0	0	1	14530	1693	59	3		3	SLC26A2	5	149361289	Silent	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10	21883757	149361289	31553971	20	12011											
C6orf108	23113	hgsc.bcm.edu	37	chr6	43193768	43193768	+	IGR	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	ggagggaggcttggggtgctCaccgcggccagactgcgggc	5	5	20	11	3	1	1	1	0	0	1	1	3	1	3	2	7	2	2	2	7	0	1			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr6:43193768C>A	ENST00000252050.4	+	0	7780				DNPH1_ENST00000230431.6_Intron|DNPH1_ENST00000393987.2_Nonsense_Mutation_p.E127*|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						TTGGGGTGCTCACCGCGGCCA	0.647																																					p.E127X		Atlas-SNP	.											.	.	.	.	0			c.G379T						PASS	.						27	26	26					6																	43193768		2203	4298	6501	SO:0001628	intergenic_variant	10591	exon3			GGTGCTCACCGCG	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		chr6.hg19:g.43193768C>A		76.0	0.0	.		72.0	25.0	.	NM_199184	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Nonsense_Mutation	SNP	ENST00000252050.4	hg19	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	C	11.10	1.539836	0.27563	.	.	ENSG00000112667	ENST00000393987	.	.	.	4.24	2.38	0.29361	.	.	.	.	.	.	.	.	.	.	.	0.53688	D	0.999974	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	.	6.7563	0.23516	0.0:0.7731:0.0:0.2269	.	.	.	.	X	127	.	ENSP00000377556:E127X	E	-	1	0	C6orf108	43301746	0.036000	0.19791	0.992000	0.48379	0.353000	0.29299	0.002000	0.13061	0.989000	0.38761	0.462000	0.41574	GAG	.	.	.	none		0.647	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		A	43193768	C	A	43193768	1	1	199	0	1	0	0	0	0	0	0	0	2322	835	29	4		4	C6orf108	6	43193768	IGR	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10		43193768	127921299	21	12012											
IGF2R	3482	hgsc.bcm.edu	37	chr6	160467594	160467594	+	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	tataaagttgagacaaagaaGtatgacttttatataaatgt	18	14	7	2	0	0	3	0	2	0	2	0	4	0	3	0	0	0	2	0	0	10	8			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr6:160467594G>C	ENST00000356956.1	+	15	2116	c.1968G>C	c.(1966-1968)aaG>aaC	p.K656N		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	656					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)	AGACAAAGAAGTATGACTTTT	0.413																																					p.K656N		Atlas-SNP	.											.	IGF2R	251	.	0			c.G1968C						PASS	.						81	88	86					6																	160467594		2203	4300	6503	SO:0001583	missense	3482	exon15			AAAGAAGTATGAC	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.1968G>C	chr6.hg19:g.160467594G>C	ENSP00000349437:p.Lys656Asn	22.0	0.0	.		32.0	9.0	.	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	hg19	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	G	10.21	1.287371	0.23478	.	.	ENSG00000197081	ENST00000356956	T	0.11277	2.79	5.07	3.25	0.37280	Mannose-6-phosphate receptor, binding (1);	0.269818	0.41500	D	0.000876	T	0.04770	0.0129	L	0.58354	1.805	0.45995	D	0.998804	P	0.45396	0.857	P	0.45377	0.478	T	0.37798	-0.9690	10	0.19147	T	0.46	-5.8683	3.1762	0.06569	0.2087:0.1255:0.5372:0.1286	.	656	P11717	MPRI_HUMAN	N	656	ENSP00000349437:K656N	ENSP00000349437:K656N	K	+	3	2	IGF2R	160387584	0.158000	0.22850	0.965000	0.40720	0.840000	0.47671	-0.185000	0.09684	1.262000	0.44165	0.655000	0.94253	AAG	.	.	.	none		0.413	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		C	160467594	G	C	160467594	3	2	199	1	0	0	0	0	1	0	0	0	7583	1020	36	4	2026	4	IGF2R	6	160467594	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	117273826	160467594	10647473	22	12013											
ISPD	729920	hgsc.bcm.edu	37	chr7	16255771	16255771	+	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	aaattctctaatctgcattaGgttttccattttctgactgg	9	18	6	8	0	3	1	0	1	3	0	5	1	4	1	1	2	1	2	1	2	3	7			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr7:16255771G>C	ENST00000407010.2	-	9	1170	c.1171C>G	c.(1171-1173)Cta>Gta	p.L391V	ISPD-AS1_ENST00000579293.1_RNA|ISPD-AS1_ENST00000582683.1_RNA|ISPD_ENST00000399310.3_Missense_Mutation_p.L341V|ISPD-AS1_ENST00000438573.1_RNA|ISPD-AS1_ENST00000457112.1_RNA	NM_001101426.3	NP_001094896.1	A4D126	ISPD_HUMAN	isoprenoid synthase domain containing	391					axon guidance (GO:0007411)|isoprenoid biosynthetic process (GO:0008299)|protein O-linked mannosylation (GO:0035269)		nucleotidyltransferase activity (GO:0016779)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)	9						ATCTGCATTAGGTTTTCCATT	0.303										Multiple Myeloma(15;0.18)																											p.L391V		Atlas-SNP	.											.	ISPD	63	.	0			c.C1171G						PASS	.						64	60	61					7																	16255771		1786	4057	5843	SO:0001583	missense	729920	exon9			GCATTAGGTTTTC	AK124805		7p21.2	2010-03-19			ENSG00000214960	ENSG00000214960			37276	protein-coding gene	gene with protein product	"notch1-induced protein", "4-diphosphocytidyl-2C-methyl-D-erythritol synthase homolog (Arabidopsis)"	614631				11181995	Standard	NM_001101417		Approved	hCG_1745121, IspD, Nip	uc010ktx.2	A4D126	OTTHUMG00000152447	ENST00000407010.2:c.1171C>G	chr7.hg19:g.16255771G>C	ENSP00000385478:p.Leu391Val	23.0	0.0	.		50.0	28.0	.	NM_001101426	A8MU35|H9KVB2	Missense_Mutation	SNP	ENST00000407010.2	hg19		.	.	.	.	.	.	.	.	.	.	G	5.747	0.322274	0.10900	.	.	ENSG00000214960	ENST00000407010;ENST00000399310	D;D	0.87729	-2.23;-2.29	5.22	3.4	0.38934	.	.	.	.	.	T	0.77711	0.4171	N	0.24115	0.695	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.65857	-0.6066	9	0.48119	T	0.1	-18.4993	7.3675	0.26781	0.0916:0.1697:0.7388:0.0	.	391	A4D126	ISPD_HUMAN	V	391;341	ENSP00000385478:L391V;ENSP00000382249:L341V	ENSP00000382249:L341V	L	-	1	2	ISPD	16222296	0.250000	0.23951	0.038000	0.18304	0.431000	0.31685	0.794000	0.26958	0.685000	0.31468	0.591000	0.81541	CTA	.	.	.	none		0.303	ISPD-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000326252.4	NM_001101426		C	16255771	G	C	16255771	3	2	199	1	0	0	0	0	1	0	0	0	7871	991	35	4	192	4	ISPD	7	16255771	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10		16255771	142882892	23	12014											
HIP1	3092	hgsc.bcm.edu	37	chr7	75183809	75183809	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctggaaatggatgtgacCgtggagaggaggtgatctgt	10	9	17	5	1	1	3	0	2	1	1	1	7	1	6	1	5	1	1	1	5	1	0			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr7:75183809C>T	ENST00000336926.6	-	20	2006	c.1980G>A	c.(1978-1980)acG>acA	p.T660T	HIP1_ENST00000434438.2_Silent_p.T660T	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	660					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						TGGATGTGACCGTGGAGAGGA	0.527			T	PDGFRB	CMML																																p.T660T		Atlas-SNP	.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	.	HIP1	91	.	0			c.G1980A						PASS	.						98	90	92					7																	75183809		2203	4300	6503	SO:0001819	synonymous_variant	3092	exon20			TGTGACCGTGGAG	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.1980G>A	chr7.hg19:g.75183809C>T		105.0	0.0	.		105.0	63.0	.	NM_005338	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Silent	SNP	ENST00000336926.6	hg19	CCDS34669.1																																																																																			.	.	.	none		0.527	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338		T	75183809	C	T	75183809	2	4	199	1	0	0	0	0	0	0	0	1	7121	639	23	1		1	HIP1	7	75183809	Silent	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	58928038	75183809	83954854	24	12015											
PAXIP1	22976	hgsc.bcm.edu	37	chr7	154767474	154767474	+	Missense_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	agtaatattcctcagtgtccGtacagctggactccaggtag	10	11	10	10	1	1	0	1	0	0	0	4	1	4	1	3	2	2	4	3	2	4	5	rs540417697		TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr7:154767474G>A	ENST00000404141.1	-	6	1160	c.1006C>T	c.(1006-1008)Cgg>Tgg	p.R336W	PAXIP1_ENST00000473219.1_5'UTR|PAXIP1_ENST00000397192.1_Missense_Mutation_p.R336W			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	336					adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		CTCAGTGTCCGTACAGCTGGA	0.433																																					p.R336W		Atlas-SNP	.											.	PAXIP1	150	.	0			c.C1006T						PASS	.						45	44	44					7																	154767474		1947	4167	6114	SO:0001583	missense	22976	exon6			GTGTCCGTACAGC	U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"PAX transcription activation domain interacting protein 1 like"	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.1006C>T	chr7.hg19:g.154767474G>A	ENSP00000384048:p.Arg336Trp	101.0	0.0	.		202.0	86.0	.	NM_007349	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Missense_Mutation	SNP	ENST00000404141.1	hg19	CCDS47753.1	.	.	.	.	.	.	.	.	.	.	G	17.83	3.486598	0.63962	.	.	ENSG00000157212	ENST00000404141;ENST00000397192;ENST00000357094;ENST00000323199	T;T	0.48836	0.8;0.8	5.04	4.16	0.48862	.	0.000000	0.50627	U	0.000119	T	0.63141	0.2486	M	0.68952	2.095	0.40826	D	0.983548	B;D;B;D	0.89917	0.225;1.0;0.333;1.0	B;D;B;D	0.91635	0.028;0.999;0.061;0.998	T	0.66040	-0.6022	10	0.72032	D	0.01	-63.4587	8.8578	0.35238	0.0761:0.0:0.7761:0.1478	.	289;245;302;336	B4DEQ6;Q6ZW49-3;Q6ZW49-1;Q6ZW49	.;.;.;PAXI1_HUMAN	W	336;336;284;289	ENSP00000384048:R336W;ENSP00000380376:R336W	ENSP00000319149:R289W	R	-	1	2	PAXIP1	154398407	1.000000	0.71417	0.985000	0.45067	0.878000	0.50629	3.274000	0.51631	1.250000	0.43966	0.305000	0.20034	CGG	.	.	.	none		0.433	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349		A	154767474	G	A	154767474	3	1	199	1	0	0	0	0	1	0	0	0	11494	1144	40	1	2267	1	PAXIP1	7	154767474	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	79583665	154767474	4371189	25	12016											
SGK223	157285	hgsc.bcm.edu	37	chr8	8235300	8235300	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcagccagtttctggcggaAgctctcctgggtggagggcc	5	8	17	11	1	2	0	0	0	2	0	3	2	2	2	3	6	2	3	3	6	1	1			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr8:8235300A>G	ENST00000520004.1	-	3	883	c.619T>C	c.(619-621)Ttc>Ctc	p.F207L	SGK223_ENST00000330777.4_Missense_Mutation_p.F207L			Q86YV5	SG223_HUMAN		207							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										TTCTGGCGGAAGCTCTCCTGG	0.602																																					p.F207L	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.T619C						PASS	.						88	97	94					8																	8235300		1951	4139	6090	SO:0001583	missense	0	exon2			GGCGGAAGCTCTC																												ENST00000520004.1:c.619T>C	chr8.hg19:g.8235300A>G	ENSP00000428054:p.Phe207Leu	111.0	0.0	.		94.0	43.0	.	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	hg19	CCDS43706.1	.	.	.	.	.	.	.	.	.	.	A	10.85	1.466943	0.26335	.	.	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.56103	0.48;0.48	5.2	5.2	0.72013	.	0.099877	0.41605	D	0.000844	T	0.38188	0.1031	L	0.32530	0.975	0.30179	N	0.800576	B	0.27351	0.176	B	0.25884	0.064	T	0.37150	-0.9718	10	0.37606	T	0.19	.	7.5573	0.27831	0.8992:0.0:0.1008:0.0	.	207	Q86YV5	SG223_HUMAN	L	207	ENSP00000330930:F207L;ENSP00000428054:F207L	ENSP00000330930:F207L	F	-	1	0	AC068353.1	8272710	0.988000	0.35896	1.000000	0.80357	0.426000	0.31534	1.270000	0.33086	2.089000	0.63090	0.533000	0.62120	TTC	.	.	.	none		0.602	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1			G	8235300	A	G	8235300	3	3	199	1	0	0	0	0	1	0	0	0	14223	72	3	3	3605	3	SGK223	8	8235300	Missense_Mutation	SNP	A	TCGA-HE-A5NJ-01A-11D-A26P-10		8235300	138128722	26	12017											
PXDNL	137902	hgsc.bcm.edu	37	chr8	52359698	52359698	+	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	cagaggagagaactgtatgcTggccttccacagggagctgc	10	7	14	10	0	0	2	0	0	0	2	1	5	1	4	2	3	4	3	2	3	2	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr8:52359698T>A	ENST00000356297.4	-	12	1491	c.1391A>T	c.(1390-1392)cAg>cTg	p.Q464L	PXDNL_ENST00000543296.1_Missense_Mutation_p.Q464L	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	464	Ig-like C2-type 3.				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)				AACTGTATGCTGGCCTTCCAC	0.512																																					p.Q464L		Atlas-SNP	.											.	PXDNL	414	.	0			c.A1391T						PASS	.						109	107	108					8																	52359698		2028	4190	6218	SO:0001583	missense	137902	exon12			GTATGCTGGCCTT		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.1391A>T	chr8.hg19:g.52359698T>A	ENSP00000348645:p.Gln464Leu	100.0	0.0	.		108.0	44.0	.	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	hg19	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	T	5.421	0.262910	0.10294	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	D;D	0.81659	-1.52;-1.52	4.02	-7.16	0.01516	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.65450	0.2692	L	0.43701	1.375	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.49523	-0.8931	9	0.36615	T	0.2	.	4.0424	0.09758	0.3721:0.1572:0.0:0.4707	.	464	A1KZ92	PXDNL_HUMAN	L	464	ENSP00000348645:Q464L;ENSP00000444865:Q464L	ENSP00000348645:Q464L	Q	-	2	0	PXDNL	52522251	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	0.100000	0.15231	-1.355000	0.02186	-0.375000	0.07067	CAG	.	.	.	none		0.512	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		A	52359698	T	A	52359698	3	1	199	1	0	0	0	0	1	0	0	0	12861	1580	55	5	3048	5	PXDNL	8	52359698	Missense_Mutation	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10	44124398	52359698	94004324	27	12018											
RB1CC1	9821	hgsc.bcm.edu	37	chr8	53555097	53555097	+	Missense_Mutation	SNP	T	T	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	tactgacttcttcttcaagcTttttcttttcctcaagcaaa	9	18	3	11	0	5	1	2	1	3	0	6	1	6	1	1	0	3	2	1	0	4	8			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr8:53555097T>G	ENST00000025008.5	-	18	4674	c.4151A>C	c.(4150-4152)aAg>aCg	p.K1384T	RB1CC1_ENST00000435644.2_Missense_Mutation_p.K1384T|RB1CC1_ENST00000521611.1_Intron|RB1CC1_ENST00000539297.1_Missense_Mutation_p.K1384T	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	1384					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)				TTCTTCAAGCTTTTTCTTTTC	0.383																																					p.K1384T	GBM(180;1701 2102 13475 42023 52570)	Atlas-SNP	.											.	RB1CC1	163	.	0			c.A4151C						PASS	.						96	91	93					8																	53555097		2203	4300	6503	SO:0001583	missense	9821	exon18			TCAAGCTTTTTCT	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.4151A>C	chr8.hg19:g.53555097T>G	ENSP00000025008:p.Lys1384Thr	85.0	0.0	.		93.0	39.0	.	NM_001083617	Q86YR4|Q8WVU9|Q92601	Missense_Mutation	SNP	ENST00000025008.5	hg19	CCDS34892.1	.	.	.	.	.	.	.	.	.	.	T	16.15	3.040807	0.55003	.	.	ENSG00000023287	ENST00000025008;ENST00000435644;ENST00000539297	T;T;T	0.18338	2.22;2.22;2.22	5.61	4.46	0.54185	.	0.235291	0.44097	D	0.000482	T	0.12561	0.0305	L	0.27053	0.805	0.34041	D	0.654965	B;B	0.30361	0.277;0.181	B;B	0.33042	0.157;0.075	T	0.22941	-1.0202	10	0.26408	T	0.33	-15.3958	10.1369	0.42712	0.0:0.0806:0.0:0.9194	.	1384;1384	Q8TDY2-2;Q8TDY2	.;RBCC1_HUMAN	T	1384	ENSP00000025008:K1384T;ENSP00000396067:K1384T;ENSP00000445960:K1384T	ENSP00000025008:K1384T	K	-	2	0	RB1CC1	53717650	0.999000	0.42202	0.825000	0.32803	0.998000	0.95712	3.259000	0.51515	0.950000	0.37743	0.533000	0.62120	AAG	.	.	.	none		0.383	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781		G	53555097	T	G	53555097	3	3	199	1	0	0	0	0	1	0	0	0	13112	1609	56	5	661	5	RB1CC1	8	53555097	Missense_Mutation	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10	1195399	53555097	92808925	28	12019											
UTP23	84294	hgsc.bcm.edu	37	chr8	117782585	117782585	+	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	ttgaagagggaaatcctcatCattattttgtggcaacacag	13	12	9	7	0	2	2	2	1	0	1	3	3	3	3	1	2	1	1	1	2	4	4			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr8:117782585C>T	ENST00000309822.2	+	2	444	c.343C>T	c.(343-345)Cat>Tat	p.H115Y	UTP23_ENST00000517820.1_Intron|UTP23_ENST00000357148.3_Missense_Mutation_p.H115Y|UTP23_ENST00000520733.1_Missense_Mutation_p.H9Y	NM_032334.2	NP_115710.2	Q9BRU9	UTP23_HUMAN	UTP23, small subunit (SSU) processome component, homolog (yeast)	115					rRNA processing (GO:0006364)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	12						AAATCCTCATCATTATTTTGT	0.353																																					p.H115Y		Atlas-SNP	.											.	UTP23	38	.	0			c.C343T						PASS	.						112	105	107					8																	117782585		2203	4300	6503	SO:0001583	missense	84294	exon2			CCTCATCATTATT		CCDS6320.1	8q24.11	2008-06-12	2008-06-12	2008-06-12		ENSG00000147679			28224	protein-coding gene	gene with protein product			"chromosome 8 open reading frame 53"	C8orf53		16769905	Standard	NM_032334		Approved	MGC14595	uc003yoc.3	Q9BRU9		ENST00000309822.2:c.343C>T	chr8.hg19:g.117782585C>T	ENSP00000308332:p.His115Tyr	58.0	0.0	.		87.0	30.0	.	NM_032334	B2RE25|Q96NJ8	Missense_Mutation	SNP	ENST00000309822.2	hg19	CCDS6320.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.351801	0.82132	.	.	ENSG00000147679	ENST00000309822;ENST00000357148;ENST00000517814;ENST00000520733	T	0.24151	1.87	5.9	5.9	0.94986	.	0.093959	0.64402	D	0.000001	T	0.54935	0.1889	M	0.79011	2.435	0.58432	D	0.999998	D	0.71674	0.998	D	0.69142	0.962	T	0.54662	-0.8260	10	0.62326	D	0.03	-17.3326	20.2789	0.98501	0.0:1.0:0.0:0.0	.	115	Q9BRU9	UTP23_HUMAN	Y	115;115;115;9	ENSP00000308332:H115Y	ENSP00000308332:H115Y	H	+	1	0	UTP23	117851766	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.525000	0.67110	2.788000	0.95919	0.650000	0.86243	CAT	.	.	.	none		0.353	UTP23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381173.1	NM_032334		T	117782585	C	T	117782585	3	4	199	1	0	0	0	0	1	0	0	0	17112	826	29	2	349	2	UTP23	8	117782585	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	64227488	117782585	28581437	29	12020											
NFKBIL2	4796	hgsc.bcm.edu	37	chr8	145668588	145668588	+	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	tgtgcctgcagcaaagcatcCctcgactggcagtggtcata	9	9	11	12	1	1	0	1	0	0	0	3	1	2	0	2	2	4	4	2	2	2	1			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr8:145668588C>G	ENST00000409379.3	-	4	410	c.381G>C	c.(379-381)agG>agC	p.R127S		NM_013432.4	NP_038460.4	Q96HA7	TONSL_HUMAN	tonsoku-like, DNA repair protein	127					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						GCAAAGCATCCCTCGACTGGC	0.622																																					p.R127S		Atlas-SNP	.											.	TONSL	128	.	0			c.G381C						PASS	.						78	80	79					8																	145668588		692	1591	2283	SO:0001583	missense	4796	exon4			AGCATCCCTCGAC		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.381G>C	chr8.hg19:g.145668588C>G	ENSP00000386239:p.Arg127Ser	169.0	0.0	.		160.0	50.0	.	NM_013432	B5MDP0|C9JKB1|C9JNV8|Q13006|Q9UGJ2	Missense_Mutation	SNP	ENST00000409379.3	hg19	CCDS34968.2	.	.	.	.	.	.	.	.	.	.	C	3.081	-0.189045	0.06299	.	.	ENSG00000160949	ENST00000409379;ENST00000422691	T	0.75367	-0.93	4.66	2.56	0.30785	Tetratricopeptide-like helical (1);	.	.	.	.	T	0.56630	0.1998	L	0.36672	1.1	0.09310	N	0.999996	B	0.29716	0.255	B	0.19148	0.024	T	0.36040	-0.9764	9	0.10111	T	0.7	.	7.8666	0.29541	0.1718:0.7237:0.0:0.1045	.	127	Q96HA7	TONSL_HUMAN	S	127	ENSP00000386239:R127S	ENSP00000386239:R127S	R	-	3	2	TONSL	145639396	0.079000	0.21365	0.105000	0.21289	0.613000	0.37349	0.816000	0.27267	0.930000	0.37217	0.462000	0.41574	AGG	.	.	.	none		0.622	TONSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329668.2	NM_013432		G	145668588	C	G	145668588	3	3	199	1	0	0	0	0	1	0	0	0	10389	622	22	4	3847	4	NFKBIL2	8	145668588	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	27886003	145668588	695434	30	12021											
KIAA1529	100499483	hgsc.bcm.edu	37	chr9	100128909	100128909	+	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	tgtgacacctttgaccagtgCgccgagaacattagcaaaaa	14	8	9	10	2	0	3	0	2	0	1	0	4	0	3	3	0	3	1	3	0	4	2	rs575555258		TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr9:100128909C>T	ENST00000357054.1	+	43	5018	c.4083C>T	c.(4081-4083)tgC>tgT	p.C1361C	CCDC180_ENST00000395220.1_3'UTR|MIR1302-8_ENST00000408342.1_RNA|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000529487.1_Silent_p.C1416C|CCDC180_ENST00000375202.2_Silent_p.C1416C			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	1361						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.C1361C(1)									TTGACCAGTGCGCCGAGAACA	0.532													C|||	1	0.000199681	0	0	5008	,	,		20527	0		0	False		,,,				2504	0.001				p.C1416C		Atlas-SNP	.											KIAA1529,colon,carcinoma,0,1	.	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4248T						PASS	.						108	90	96					9																	100128909		2203	4300	6503	SO:0001819	synonymous_variant	0	exon31			CCAGTGCGCCGAG	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.4083C>T	chr9.hg19:g.100128909C>T		300.0	2.0	.		336.0	119.0	.	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Silent	SNP	ENST00000357054.1	hg19																																																																																				.	.	.	none		0.532	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893		T	100128909	C	T	100128909	2	4	199	1	0	0	0	0	0	0	0	1	8247	776	27	1		1	KIAA1529	9	100128909	Silent	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10		100128909	41084522	31	12022											
IDI2	91734	hgsc.bcm.edu	37	chr10	1066741	1066741	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcccagctctgcttgcagaCgcctctgggctgccctcctc	3	11	9	18	1	2	1	0	0	2	1	5	1	4	1	4	1	4	4	4	1	0	2	rs368608756		TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr10:1066741C>T	ENST00000277517.1	-	4	396	c.332G>A	c.(331-333)cGt>cAt	p.R111H	IDI2-AS1_ENST00000434470.1_RNA|IDI2-AS1_ENST00000420381.1_RNA|IDI2-AS1_ENST00000437374.1_RNA|IDI2-AS1_ENST00000536039.1_RNA|IDI2-AS1_ENST00000428780.2_RNA	NM_033261.2	NP_150286.1	Q9BXS1	IDI2_HUMAN	isopentenyl-diphosphate delta isomerase 2	111	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				cholesterol biosynthetic process (GO:0006695)|dimethylallyl diphosphate biosynthetic process (GO:0050992)|isopentenyl diphosphate metabolic process (GO:0046490)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisome (GO:0005777)	hydrolase activity (GO:0016787)|isopentenyl-diphosphate delta-isomerase activity (GO:0004452)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	9		Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.143)	Epithelial(11;0.067)|OV - Ovarian serous cystadenocarcinoma(14;0.169)|all cancers(11;0.192)		TGCTTGCAGACGCCTCTGGGC	0.572													C|||	1	0.000199681	0	0.0014	5008	,	,		16338	0		0	False		,,,				2504	0				p.R111H		Atlas-SNP	.											IDI2,caecum,carcinoma,0,1	IDI2	20	.	0			c.G332A						PASS	.						100	86	91					10																	1066741		2203	4300	6503	SO:0001583	missense	91734	exon4			TGCAGACGCCTCT	AF271725	CCDS7055.1	10p15.3	2003-11-19			ENSG00000148377	ENSG00000148377			23487	protein-coding gene	gene with protein product		615389				12477932	Standard	NM_033261		Approved	IPPI2	uc001ifv.1	Q9BXS1	OTTHUMG00000017537	ENST00000277517.1:c.332G>A	chr10.hg19:g.1066741C>T	ENSP00000277517:p.Arg111His	92.0	0.0	.		90.0	4.0	.	NM_033261		Missense_Mutation	SNP	ENST00000277517.1	hg19	CCDS7055.1	.	.	.	.	.	.	.	.	.	.	C	14.90	2.673904	0.47781	.	.	ENSG00000148377	ENST00000277517	T	0.08193	3.12	4.09	-1.8	0.07907	NUDIX hydrolase domain (3);NUDIX hydrolase domain-like (1);	0.116280	0.53938	U	0.000051	T	0.25568	0.0622	M	0.88979	2.995	0.20403	N	0.999907	D	0.71674	0.998	D	0.65573	0.936	T	0.05354	-1.0890	10	0.87932	D	0	-4.7047	8.2637	0.31801	0.0:0.6495:0.1046:0.246	.	111	Q9BXS1	IDI2_HUMAN	H	111	ENSP00000277517:R111H	ENSP00000277517:R111H	R	-	2	0	IDI2	1056741	0.103000	0.21917	0.000000	0.03702	0.001000	0.01503	2.002000	0.40835	-1.050000	0.03230	-2.005000	0.00442	CGT	.	.	.	none		0.572	IDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046411.1	NM_033261		T	1066741	C	T	1066741	3	4	199	1	0	0	0	0	1	0	0	0	7507	536	19	1	359	1	IDI2	10	1066741	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10		1066741	134468006	32	12023											
MYPN	84665	hgsc.bcm.edu	37	chr10	69959137	69959137	+	Missense_Mutation	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	tttattaggtgagtggtttaCcgcccccggagctgacatgg	7	12	13	9	2	0	2	0	2	0	0	0	3	0	3	3	4	2	2	3	4	3	5			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr10:69959137C>T	ENST00000358913.5	+	17	3786	c.3298C>T	c.(3298-3300)Ccg>Tcg	p.P1100S	MYPN_ENST00000540630.1_Missense_Mutation_p.P1100S|MYPN_ENST00000354393.2_Missense_Mutation_p.P825S	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	1100	Ig-like 4.|Interaction with ACTN.				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						GAGTGGTTTACCGCCCCCGGA	0.507																																					p.P1100S		Atlas-SNP	.											.	MYPN	189	.	0			c.C3298T						PASS	.						56	48	50					10																	69959137		2203	4300	6503	SO:0001583	missense	84665	exon17			GGTTTACCGCCCC	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.3298C>T	chr10.hg19:g.69959137C>T	ENSP00000351790:p.Pro1100Ser	124.0	0.0	.		129.0	47.0	.	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	hg19	CCDS7275.1	.	.	.	.	.	.	.	.	.	.	C	30	5.053409	0.93793	.	.	ENSG00000138347	ENST00000354393;ENST00000542332;ENST00000358913;ENST00000540630	T;T;T	0.80393	-1.37;-1.37;-1.37	5.38	5.38	0.77491	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.94072	0.8100	H	0.97806	4.08	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;0.999;1.0	D	0.95767	0.8805	9	.	.	.	.	19.3311	0.94288	0.0:1.0:0.0:0.0	.	1100;825;1100	F5GWA6;Q86TC9-2;Q86TC9	.;.;MYPN_HUMAN	S	825;825;1100;1100	ENSP00000346369:P825S;ENSP00000351790:P1100S;ENSP00000441668:P1100S	.	P	+	1	0	MYPN	69629143	1.000000	0.71417	0.999000	0.59377	0.978000	0.69477	7.595000	0.82710	2.813000	0.96785	0.655000	0.94253	CCG	.	.	.	none		0.507	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578		T	69959137	C	T	69959137	3	4	199	1	0	0	0	0	1	0	0	0	10105	507	18	2	3360	2	MYPN	10	69959137	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	68892396	69959137	65575610	33	12024											
TRIM8	81603	hgsc.bcm.edu	37	chr10	104416093	104416093	+	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	cacctgaactccaagctcttCctgaacgaagtggccaagaa	13	7	8	13	1	1	3	0	2	1	1	3	4	3	3	4	1	3	1	4	1	6	1			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr10:104416093C>A	ENST00000302424.7	+	5	1121	c.999C>A	c.(997-999)ttC>ttA	p.F333L	TRIM8_ENST00000487927.1_3'UTR	NM_030912.2	NP_112174.2	Q9BZR9	TRIM8_HUMAN	tripartite motif containing 8	333					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|PML body (GO:0016605)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		CCAAGCTCTTCCTGAACGAAG	0.607																																					p.F333L		Atlas-SNP	.											.	TRIM8	35	.	0			c.C999A						PASS	.						59	46	50					10																	104416093		2203	4300	6503	SO:0001583	missense	81603	exon5			GCTCTTCCTGAAC	AF281046	CCDS31274.1	10q24.3	2013-01-09	2011-01-25	2002-06-14	ENSG00000171206	ENSG00000171206		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	15579	protein-coding gene	gene with protein product	"glioblastoma expressed ring finger protein"	606125	"ring finger protein 27", "tripartite motif-containing 8"	RNF27		11118312, 12163497	Standard	NM_030912		Approved	GERP	uc001kvz.2	Q9BZR9	OTTHUMG00000018964	ENST00000302424.7:c.999C>A	chr10.hg19:g.104416093C>A	ENSP00000302120:p.Phe333Leu	170.0	0.0	.		200.0	86.0	.	NM_030912	A6NI31|Q9C028	Missense_Mutation	SNP	ENST00000302424.7	hg19	CCDS31274.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.940287	0.52972	.	.	ENSG00000171206	ENST00000302424;ENST00000369896	T	0.77489	-1.1	5.67	3.82	0.43975	.	0.000000	0.85682	D	0.000000	T	0.76205	0.3955	L	0.29908	0.895	0.58432	D	0.99999	P	0.52842	0.956	P	0.62184	0.899	T	0.69525	-0.5122	10	0.08837	T	0.75	.	12.1033	0.53796	0.0:0.8608:0.0:0.1392	.	333	Q9BZR9	TRIM8_HUMAN	L	333;332	ENSP00000302120:F333L	ENSP00000302120:F333L	F	+	3	2	TRIM8	104406083	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.588000	0.36633	0.753000	0.32945	0.555000	0.69702	TTC	.	.	.	none		0.607	TRIM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050084.3	NM_030912		A	104416093	C	A	104416093	3	1	199	1	0	0	0	0	1	0	0	0	16560	854	30	4	1017	4	TRIM8	10	104416093	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	34456956	104416093	31118654	34	12025											
GPR83	10888	hgsc.bcm.edu	37	chr11	94113422	94113422	+	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	gggagccctctggccatcatTcttctctgtccaggccaccc	5	10	9	17	0	4	0	1	0	3	0	6	1	5	1	5	3	1	0	5	3	0	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr11:94113422T>A	ENST00000243673.2	-	4	1336	c.1165A>T	c.(1165-1167)Aat>Tat	p.N389Y	GPR83_ENST00000539203.2_Missense_Mutation_p.N347Y	NM_016540.3	NP_057624.3	Q9NYM4	GPR83_HUMAN	G protein-coupled receptor 83	389					response to glucocorticoid (GO:0051384)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)			NS(1)|breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)	19		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TGGCCATCATTCTTCTCTGTC	0.562																																					p.N389Y		Atlas-SNP	.											.	GPR83	47	.	0			c.A1165T						PASS	.						83	82	82					11																	94113422		2201	4298	6499	SO:0001583	missense	10888	exon4			CATCATTCTTCTC	AF236081	CCDS8297.1	11q21	2012-08-21	2003-07-30	2003-08-01	ENSG00000123901	ENSG00000123901		"GPCR / Class A : Orphans"	4523	protein-coding gene	gene with protein product		605569	"G protein-coupled receptor 72"	GPR72		10760605, 11060465	Standard	NM_016540		Approved		uc001pet.2	Q9NYM4	OTTHUMG00000167779	ENST00000243673.2:c.1165A>T	chr11.hg19:g.94113422T>A	ENSP00000243673:p.Asn389Tyr	152.0	0.0	.		175.0	76.0	.	NM_016540	B0M0K5|Q6NWR4|Q9P1Y8	Missense_Mutation	SNP	ENST00000243673.2	hg19	CCDS8297.1	.	.	.	.	.	.	.	.	.	.	T	0	-2.689837	0.00100	.	.	ENSG00000123901	ENST00000243673;ENST00000539203	T;T	0.61392	0.11;0.22	5.75	0.538	0.17150	.	0.659318	0.17607	N	0.168232	T	0.31544	0.0800	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.17319	-1.0373	10	0.21014	T	0.42	.	9.6421	0.39846	0.0:0.4117:0.0:0.5883	.	389	Q9NYM4	GPR83_HUMAN	Y	389;347	ENSP00000243673:N389Y;ENSP00000441550:N347Y	ENSP00000243673:N389Y	N	-	1	0	GPR83	93753070	0.772000	0.28567	0.077000	0.20336	0.003000	0.03518	0.384000	0.20668	0.096000	0.17463	-0.250000	0.11733	AAT	.	.	.	none		0.562	GPR83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396232.1	NM_016540		A	94113422	T	A	94113422	3	1	199	1	0	0	0	0	1	0	0	0	6720	1783	62	5	110	5	GPR83	11	94113422	Missense_Mutation	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10		94113422	40893094	35	12026											
PIWIL4	143689	hgsc.bcm.edu	37	chr11	94340737	94340737	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aacagggcatgatgatgagtAtcgccaccaagatcgctatg	13	8	11	9	2	0	4	0	3	0	1	2	4	0	4	2	1	1	3	2	1	4	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr11:94340737A>G	ENST00000299001.6	+	14	1982	c.1771A>G	c.(1771-1773)Atc>Gtc	p.I591V	RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	591	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				GATGATGAGTATCGCCACCAA	0.453																																					p.I591V		Atlas-SNP	.											.	PIWIL4	70	.	0			c.A1771G						PASS	.						89	82	84					11																	94340737		2201	4298	6499	SO:0001583	missense	143689	exon14			ATGAGTATCGCCA	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.1771A>G	chr11.hg19:g.94340737A>G	ENSP00000299001:p.Ile591Val	74.0	0.0	.		95.0	37.0	.	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Missense_Mutation	SNP	ENST00000299001.6	hg19	CCDS31656.1	.	.	.	.	.	.	.	.	.	.	A	0.557	-0.846779	0.02671	.	.	ENSG00000134627	ENST00000299001	T	0.30448	1.53	4.75	-9.49	0.00587	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	1.548280	0.03817	N	0.266847	T	0.10337	0.0253	N	0.03881	-0.34	0.40307	D	0.978677	B	0.14438	0.01	B	0.21546	0.035	T	0.24621	-1.0155	10	0.06099	T	0.92	0.1986	8.5103	0.33213	0.4048:0.3269:0.2683:0.0	.	591	Q7Z3Z4	PIWL4_HUMAN	V	591	ENSP00000299001:I591V	ENSP00000299001:I591V	I	+	1	0	PIWIL4	93980385	0.000000	0.05858	0.000000	0.03702	0.135000	0.20990	-0.634000	0.05477	-2.120000	0.00826	-0.472000	0.04984	ATC	.	.	.	none		0.453	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431		G	94340737	A	G	94340737	3	3	199	1	0	0	0	0	1	0	0	0	11967	449	16	3	1825	3	PIWIL4	11	94340737	Missense_Mutation	SNP	A	TCGA-HE-A5NJ-01A-11D-A26P-10	227315	94340737	40665779	36	12027											
CD9	928	hgsc.bcm.edu	37	chr12	6309731	6309731	+	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	ggatttaacttcatcttctgGgtgagtgagcgcgactgccg	7	12	13	9	3	3	2	1	2	2	0	3	4	3	3	1	2	3	0	1	2	1	4			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr12:6309731G>A	ENST00000382518.1	+	2	502	c.66G>A	c.(64-66)tgG>tgA	p.W22*	CD9_ENST00000382515.2_5'Flank|CD9_ENST00000009180.4_Splice_Site_p.W22*			P21926	CD9_HUMAN	CD9 molecule	22					blood coagulation (GO:0007596)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|negative regulation of cell proliferation (GO:0008285)|oligodendrocyte development (GO:0014003)|paranodal junction assembly (GO:0030913)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|response to water deprivation (GO:0009414)|single fertilization (GO:0007338)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|vesicle (GO:0031982)				endometrium(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|stomach(1)	8						TCATCTTCTGGGTGAGTGAGC	0.652																																					p.W22X		Atlas-SNP	.											.	CD9	24	.	0			c.G66A						PASS	.						84	75	78					12																	6309731		2203	4300	6503	SO:0001630	splice_region_variant	928	exon1			CTTCTGGGTGAGT	M38690	CCDS8540.1	12p13	2013-02-14	2006-03-28		ENSG00000010278	ENSG00000010278		"CD molecules", "Tetraspanins"	1709	protein-coding gene	gene with protein product	"motility related protein-1"	143030	"CD9 antigen (p24)"	MIC3		6198179	Standard	NM_001769		Approved	BA2, P24, TSPAN29, MRP-1	uc001qnq.2	P21926	OTTHUMG00000044400	ENST00000382518.1:c.66+1G>A	chr12.hg19:g.6309731G>A		58.0	0.0	.		97.0	4.0	.	NM_001769	D3DUQ9|Q5J7W6|Q96ES4	Nonsense_Mutation	SNP	ENST00000382518.1	hg19	CCDS8540.1	.	.	.	.	.	.	.	.	.	.	G	38	6.691846	0.97768	.	.	ENSG00000010278	ENST00000382518;ENST00000536586;ENST00000382519;ENST00000425469;ENST00000009180	.	.	.	4.21	4.21	0.49690	.	0.298550	0.40302	N	0.001139	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.934	0.52864	0.0:0.0:1.0:0.0	.	.	.	.	X	22	.	ENSP00000009180:W22X	W	+	3	0	CD9	6179992	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.636000	0.67848	2.176000	0.68965	0.544000	0.68410	TGG	.	.	.	none		0.652	CD9-004	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103348.1		Nonsense_Mutation	A	6309731	G	A	6309731	5	1	199	1	0	0	0	0	0	0	1	0	3048	1246	43	2	68	2	CD9	12	6309731	Splice_Site	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10		6309731	127542164	37	12028											
XPOT	11260	hgsc.bcm.edu	37	chr12	64827226	64827226	+	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	ccgtttttacaacagatgttCatgcccctgcttcatgcaat	9	14	6	12	1	2	1	2	0	0	1	2	1	2	1	3	0	5	4	3	0	3	5			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr12:64827226C>A	ENST00000332707.5	+	19	2824	c.2295C>A	c.(2293-2295)ttC>ttA	p.F765L		NM_007235.4	NP_009166.2	O43592	XPOT_HUMAN	exportin, tRNA	765	Necessary for tRNA-binding, cytoplasmic localization and nuclear export.				intracellular protein transport (GO:0006886)|tRNA export from nucleus (GO:0006409)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(7)|lung(12)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				GBM - Glioblastoma multiforme(28;0.0404)		AACAGATGTTCATGCCCCTGC	0.383																																					p.F765L		Atlas-SNP	.											.	XPOT	105	.	0			c.C2295A						PASS	.						142	139	140					12																	64827226		2203	4300	6503	SO:0001583	missense	11260	exon19			GATGTTCATGCCC	AF039022	CCDS31852.1	12q14.1	2012-10-17	2012-10-17		ENSG00000184575	ENSG00000184575		"Exportins"	12826	protein-coding gene	gene with protein product		603180	"exportin, tRNA (nuclear export receptor for tRNAs)"			9660920, 9512417	Standard	NM_007235		Approved	XPO3	uc001ssb.3	O43592	OTTHUMG00000168794	ENST00000332707.5:c.2295C>A	chr12.hg19:g.64827226C>A	ENSP00000327821:p.Phe765Leu	122.0	0.0	.		126.0	74.0	.	NM_007235	A6NLH1|O43784|Q8WUG2|Q9BVS7	Missense_Mutation	SNP	ENST00000332707.5	hg19	CCDS31852.1	.	.	.	.	.	.	.	.	.	.	C	9.351	1.065624	0.20067	.	.	ENSG00000184575	ENST00000332707	T	0.35048	1.33	4.99	1.1	0.20463	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.25121	0.0610	L	0.43923	1.385	0.58432	D	0.999994	B	0.26483	0.15	B	0.19946	0.027	T	0.05632	-1.0873	9	.	.	.	.	8.7565	0.34648	0.0:0.4567:0.0:0.5433	.	765	O43592	XPOT_HUMAN	L	765	ENSP00000327821:F765L	.	F	+	3	2	XPOT	63113493	1.000000	0.71417	0.998000	0.56505	0.566000	0.35808	0.960000	0.29253	-0.000000	0.14550	0.650000	0.86243	TTC	.	.	.	none		0.383	XPOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401122.1	NM_007235		A	64827226	C	A	64827226	3	1	199	1	0	0	0	0	1	0	0	0	17462	825	29	4	2365	4	XPOT	12	64827226	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	58517495	64827226	69024669	38	12029											
SLC35E3	55508	hgsc.bcm.edu	37	chr12	69158530	69158530	+	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	tctgcattactttattcggaGgatatgttttatttaaggat	10	19	8	4	1	1	0	0	0	1	0	2	3	1	3	0	3	2	2	0	3	5	9			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr12:69158530G>T	ENST00000398004.2	+	5	1074	c.802G>T	c.(802-804)Gga>Tga	p.G268*	SLC35E3_ENST00000538043.1_Intron	NM_018656.2	NP_061126.2	Q7Z769	S35E3_HUMAN	solute carrier family 35, member E3	268						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)			TTTATTCGGAGGATATGTTTT	0.348																																					p.G268X		Atlas-SNP	.											.	SLC35E3	23	.	0			c.G802T						PASS	.						193	176	181					12																	69158530		1870	4096	5966	SO:0001587	stop_gained	55508	exon5			TTCGGAGGATATG	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.802G>T	chr12.hg19:g.69158530G>T	ENSP00000381089:p.Gly268*	72.0	0.0	.		94.0	4.0	.	NM_018656	A8K0T0|Q0P5Y5|Q9P0V1	Nonsense_Mutation	SNP	ENST00000398004.2	hg19	CCDS41808.1	.	.	.	.	.	.	.	.	.	.	G	38	6.908915	0.97928	.	.	ENSG00000175782	ENST00000398004	.	.	.	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-2.3112	19.4381	0.94806	0.0:0.0:1.0:0.0	.	.	.	.	X	268	.	.	G	+	1	0	SLC35E3	67444797	1.000000	0.71417	0.999000	0.59377	0.697000	0.40408	8.902000	0.92568	2.676000	0.91093	0.561000	0.74099	GGA	.	.	.	none		0.348	SLC35E3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403241.1	NM_018656		T	69158530	G	T	69158530	4	4	199	1	0	0	0	0	0	1	0	0	14599	1001	35	4	820	4	SLC35E3	12	69158530	Nonsense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	4331304	69158530	64693365	39	12030											
UHRF1BP1L	23074	hgsc.bcm.edu	37	chr12	100453199	100453199	+	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	aagcttctaggtcagaatgtCgacagtttggacagtgcctt	10	12	11	8	1	2	1	1	0	1	1	3	3	2	2	1	2	2	2	1	2	3	4	rs374748413		TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr12:100453199C>G	ENST00000279907.7	-	14	2068	c.1856G>C	c.(1855-1857)cGa>cCa	p.R619P	UHRF1BP1L_ENST00000545232.2_Missense_Mutation_p.R269P	NM_015054.1	NP_055869.1	A0JNW5	UH1BL_HUMAN	UHRF1 binding protein 1-like	619								p.R619Q(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(21)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	50						GTCAGAATGTCGACAGTTTGG	0.353																																					p.R619P		Atlas-SNP	.											UHRF1BP1L,colon,carcinoma,0,1	UHRF1BP1L	144	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1856C						PASS	.						47	50	49					12																	100453199		2203	4300	6503	SO:0001583	missense	23074	exon14			GAATGTCGACAGT		CCDS31882.1, CCDS31883.1	12q23.1	2011-04-15	2008-08-15		ENSG00000111647	ENSG00000111647			29102	protein-coding gene	gene with protein product							Standard	XM_005268737		Approved	KIAA0701	uc001tgq.3	A0JNW5	OTTHUMG00000170195	ENST00000279907.7:c.1856G>C	chr12.hg19:g.100453199C>G	ENSP00000279907:p.Arg619Pro	83.0	0.0	.		103.0	22.0	.	NM_015054	A0PJE5|O75183|Q8NDL1|Q96C30|Q9BTS5|Q9H0F1	Missense_Mutation	SNP	ENST00000279907.7	hg19	CCDS31882.1	.	.	.	.	.	.	.	.	.	.	C	16.39	3.110310	0.56398	.	.	ENSG00000111647	ENST00000279907;ENST00000545232	T;T	0.10960	2.83;2.82	5.56	5.56	0.83823	.	0.071690	0.56097	D	0.000028	T	0.26159	0.0638	L	0.51422	1.61	0.80722	D	1	D	0.63046	0.992	P	0.59115	0.852	T	0.00102	-1.2063	10	0.48119	T	0.1	-7.7813	19.5255	0.95203	0.0:1.0:0.0:0.0	.	619	A0JNW5	UH1BL_HUMAN	P	619;269	ENSP00000279907:R619P;ENSP00000444824:R269P	ENSP00000279907:R619P	R	-	2	0	UHRF1BP1L	98977330	1.000000	0.71417	0.996000	0.52242	0.984000	0.73092	4.740000	0.62087	2.624000	0.88883	0.650000	0.86243	CGA	.	.	.	alt		0.353	UHRF1BP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407875.1	NM_001006947		G	100453199	C	G	100453199	3	3	199	1	0	0	0	0	1	0	0	0	16981	884	31	4	2570	4	UHRF1BP1L	12	100453199	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	31294669	100453199	33398696	40	12031											
SCYL2	55681	hgsc.bcm.edu	37	chr12	100707272	100707272	+	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	aacatgtaaagctactgttaAatgtaactccgactgtaaga	16	11	7	7	1	0	1	0	0	0	1	1	2	1	1	1	0	4	5	1	0	8	5			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr12:100707272A>T	ENST00000360820.2	+	7	1362	c.925A>T	c.(925-927)Aat>Tat	p.N309Y		NM_017988.4	NP_060458.3	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 (S. cerevisiae)	309	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						GCTACTGTTAAATGTAACTCC	0.363																																					p.N309Y		Atlas-SNP	.											.	SCYL2	99	.	0			c.A925T						PASS	.						94	84	87					12																	100707272		2203	4300	6503	SO:0001583	missense	55681	exon7			CTGTTAAATGTAA	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.925A>T	chr12.hg19:g.100707272A>T	ENSP00000354061:p.Asn309Tyr	54.0	0.0	.		102.0	27.0	.	NM_017988	A8KAB5|Q96EF4|Q96ST4|Q9H7V5|Q9NVH3|Q9P2I7	Missense_Mutation	SNP	ENST00000360820.2	hg19	CCDS9076.1	.	.	.	.	.	.	.	.	.	.	A	29.9	5.046858	0.93740	.	.	ENSG00000136021	ENST00000549687;ENST00000258506;ENST00000360820	T;T	0.66815	-0.23;-0.23	5.87	5.87	0.94306	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.039673	0.85682	D	0.000000	T	0.78349	0.4269	M	0.68952	2.095	0.80722	D	1	P	0.45240	0.854	P	0.57009	0.811	T	0.79680	-0.1702	10	0.62326	D	0.03	.	16.2736	0.82632	1.0:0.0:0.0:0.0	.	309	Q6P3W7	SCYL2_HUMAN	Y	309;136;309	ENSP00000448366:N309Y;ENSP00000354061:N309Y	ENSP00000258506:N136Y	N	+	1	0	SCYL2	99231403	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	8.769000	0.91742	2.247000	0.74100	0.477000	0.44152	AAT	.	.	.	none		0.363	SCYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408493.2	NM_017988		T	100707272	A	T	100707272	3	4	199	1	0	0	0	0	1	0	0	0	13961	14	1	5	947	5	SCYL2	12	100707272	Missense_Mutation	SNP	A	TCGA-HE-A5NJ-01A-11D-A26P-10	254073	100707272	33144623	41	12032											
IFT81	28981	hgsc.bcm.edu	37	chr12	110565896	110565896	+	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	tgccagagcagacagccaaaCgaatgttgagccttcttggt	11	9	11	10	1	1	3	0	1	1	2	1	4	1	3	3	1	5	2	3	1	2	3	rs372027811		TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr12:110565896C>T	ENST00000242591.5	+	3	696	c.190C>T	c.(190-192)Cga>Tga	p.R64*	IFT81_ENST00000552912.1_Nonsense_Mutation_p.R64*|IFT81_ENST00000361948.4_Nonsense_Mutation_p.R64*	NM_014055.3	NP_054774.2	Q8WYA0	IFT81_HUMAN	intraflagellar transport 81	64	CH (calponin-homology)-like region.				cilium assembly (GO:0042384)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|spermatogenesis (GO:0007283)	centrosome (GO:0005813)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)	tubulin binding (GO:0015631)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)	10						GACAGCCAAACGAATGTTGAG	0.343																																					p.R64X		Atlas-SNP	.											.	IFT81	86	.	0			c.C190T						PASS	.	C	stop/ARG,stop/ARG,stop/ARG	2,4404	4.2+/-10.8	0,2,2201	125	120	122		190,190,190	2.9	1	12		122	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained,stop-gained,stop-gained	IFT81	NM_001143779.1,NM_014055.3,NM_031473.3	,,	0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231	,,	64/677,64/677,64/432	110565896	3,13003	2203	4300	6503	SO:0001587	stop_gained	28981	exon3			GCCAAACGAATGT	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.190C>T	chr12.hg19:g.110565896C>T	ENSP00000242591:p.Arg64*	71.0	0.0	.		119.0	36.0	.	NM_014055	Q2YDY1|Q8NB51|Q9BSV2|Q9UNY8	Nonsense_Mutation	SNP	ENST00000242591.5	hg19	CCDS41831.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.830743	0.91036	4.54E-4	1.16E-4	ENSG00000122970	ENST00000361948;ENST00000552912;ENST00000242591;ENST00000546374	.	.	.	5.96	2.88	0.33553	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.6056	16.1793	0.81889	0.5747:0.4253:0.0:0.0	.	.	.	.	X	64	.	ENSP00000242591:R64X	R	+	1	2	IFT81	109050279	0.998000	0.40836	0.997000	0.53966	0.972000	0.66771	1.423000	0.34837	0.248000	0.21435	0.655000	0.94253	CGA	.	.	.	weak		0.343	IFT81-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403529.1	NM_014055		T	110565896	C	T	110565896	4	4	199	1	0	0	0	0	0	1	0	0	7572	528	19	1	196	1	IFT81	12	110565896	Nonsense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	9858624	110565896	23285999	42	12033											
OLFM4	10562	hgsc.bcm.edu	37	chr13	53624827	53624827	+	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	gcagagcattaactataaccCttttgaccagaaactttatg	14	12	6	9	0	0	3	0	1	0	2	0	3	0	3	2	0	4	2	2	0	5	7			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr13:53624827C>A	ENST00000219022.2	+	5	1532	c.1454C>A	c.(1453-1455)cCt>cAt	p.P485H		NM_006418.4	NP_006409.3	Q6UX06	OLFM4_HUMAN	olfactomedin 4	485	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				cell adhesion (GO:0007155)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|protein homooligomerization (GO:0051260)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|specific granule (GO:0042581)	cadherin binding (GO:0045296)|catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(4)|kidney(4)|large_intestine(5)|lung(20)|skin(3)|urinary_tract(1)	39		Breast(56;0.000776)|Lung NSC(96;0.000814)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.13e-08)		AACTATAACCCTTTTGACCAG	0.378																																					p.P485H		Atlas-SNP	.											.	OLFM4	94	.	0			c.C1454A						PASS	.						99	100	100					13																	53624827		2203	4300	6503	SO:0001583	missense	10562	exon5			ATAACCCTTTTGA	AY358567	CCDS9440.1	13q14	2004-06-25			ENSG00000102837	ENSG00000102837			17190	protein-coding gene	gene with protein product		614061					Standard	NM_006418		Approved	OlfD, GW112, GC1	uc001vhl.3	Q6UX06	OTTHUMG00000016981	ENST00000219022.2:c.1454C>A	chr13.hg19:g.53624827C>A	ENSP00000219022:p.Pro485His	63.0	0.0	.		72.0	43.0	.	NM_006418	O95362|Q5VWG0|Q86T22	Missense_Mutation	SNP	ENST00000219022.2	hg19	CCDS9440.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.816222	0.90790	.	.	ENSG00000102837	ENST00000219022	T	0.19669	2.13	5.64	5.64	0.86602	Olfactomedin-like (3);	0.049423	0.85682	D	0.000000	T	0.58409	0.2120	M	0.90922	3.16	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.67465	-0.5664	10	0.87932	D	0	.	19.7082	0.96082	0.0:1.0:0.0:0.0	.	485	Q6UX06	OLFM4_HUMAN	H	485	ENSP00000219022:P485H	ENSP00000219022:P485H	P	+	2	0	OLFM4	52522828	1.000000	0.71417	0.882000	0.34594	0.914000	0.54420	6.095000	0.71439	2.651000	0.90000	0.585000	0.79938	CCT	.	.	.	none		0.378	OLFM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045112.2	NM_006418		A	53624827	C	A	53624827	3	1	199	1	0	0	0	0	1	0	0	0	10862	681	24	4	1472	4	OLFM4	13	53624827	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10		53624827	61545051	43	12034											
C14orf105	55195	hgsc.bcm.edu	37	chr14	57960296	57960296	+	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	tggtcctgcagtcttgccagTgaatatgaagtcttttcttc	7	16	9	9	0	3	2	0	2	3	0	5	2	4	2	2	1	2	1	2	1	3	5			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr14:57960296T>A	ENST00000216445.3	-	1	274	c.138A>T	c.(136-138)tcA>tcT	p.S46S	C14orf105_ENST00000534126.1_Silent_p.S46S|C14orf105_ENST00000422976.2_Silent_p.S46S|C14orf105_ENST00000526336.1_Silent_p.S46S	NM_001283057.1|NM_018168.2	NP_001269986.1|NP_060638.2	Q9NVL8	CN105_HUMAN	chromosome 14 open reading frame 105	46										breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)	11						GTCTTGCCAGTGAATATGAAG	0.438																																					p.S46S		Atlas-SNP	.											.	C14orf105	26	.	0			c.A138T						PASS	.						126	127	127					14																	57960296		2203	4300	6503	SO:0001819	synonymous_variant	55195	exon1			TGCCAGTGAATAT	AK001512	CCDS9730.1, CCDS61458.1, CCDS61459.1	14q22.2	2012-09-25			ENSG00000100557	ENSG00000100557			20189	protein-coding gene	gene with protein product							Standard	XM_005267806		Approved	FLJ10650	uc001xcy.2	Q9NVL8	OTTHUMG00000140317	ENST00000216445.3:c.138A>T	chr14.hg19:g.57960296T>A		67.0	0.0	.		75.0	35.0	.	NM_018168	Q53G04	Silent	SNP	ENST00000216445.3	hg19	CCDS9730.1																																																																																			.	.	.	none		0.438	C14orf105-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276921.2	NM_018168		A	57960296	T	A	57960296	2	1	199	1	0	0	0	0	0	0	0	1	1739	1683	59	5		5	C14orf105	14	57960296	Silent	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10		57960296	49389244	44	12035											
PAPLN	89932	hgsc.bcm.edu	37	chr14	73712877	73712877	+	Missense_Mutation	SNP	T	T	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	ggtatcggtggctgccctacTacagcggtgagcgcggccgg	5	7	17	12	5	0	1	0	1	0	0	1	1	0	1	2	6	5	2	2	6	3	3			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr14:73712877T>G	ENST00000554301.1	+	4	491	c.328T>G	c.(328-330)Tac>Gac	p.Y110D	RNU6-419P_ENST00000517030.1_RNA|PAPLN_ENST00000555445.1_Missense_Mutation_p.Y110D|PAPLN_ENST00000381166.3_Missense_Mutation_p.Y110D|PAPLN_ENST00000340738.5_Missense_Mutation_p.Y110D|RP4-647C14.2_ENST00000554614.1_RNA|PAPLN_ENST00000427855.1_Missense_Mutation_p.Y110D			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	110						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)		GCTGCCCTACTACAGCGGTGA	0.642																																					p.Y110D		Atlas-SNP	.											.	PAPLN	180	.	0			c.T328G						PASS	.						8	10	10					14																	73712877		2163	4255	6418	SO:0001583	missense	89932	exon5			CCCTACTACAGCG	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.328T>G	chr14.hg19:g.73712877T>G	ENSP00000451803:p.Tyr110Asp	28.0	0.0	.		60.0	20.0	.	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Missense_Mutation	SNP	ENST00000554301.1	hg19		.	.	.	.	.	.	.	.	.	.	T	23.3	4.398999	0.83120	.	.	ENSG00000100767	ENST00000340738;ENST00000427855;ENST00000381166;ENST00000394134;ENST00000554301;ENST00000555445	T;T;T;T;T	0.03441	3.93;3.93;3.93;3.93;3.93	4.26	4.26	0.50523	.	.	.	.	.	T	0.17662	0.0424	M	0.82132	2.575	0.47698	D	0.999491	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.72625	0.978;0.951;0.975	T	0.00593	-1.1654	9	0.62326	D	0.03	.	13.222	0.59894	0.0:0.0:0.0:1.0	.	110;110;110	O95428-5;O95428;O95428-6	.;PPN_HUMAN;.	D	110	ENSP00000345395:Y110D;ENSP00000403403:Y110D;ENSP00000370558:Y110D;ENSP00000451803:Y110D;ENSP00000451729:Y110D	ENSP00000216658:Y110D	Y	+	1	0	PAPLN	72782630	1.000000	0.71417	0.997000	0.53966	0.671000	0.39405	4.002000	0.57053	1.789000	0.52484	0.379000	0.24179	TAC	.	.	.	none		0.642	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462		G	73712877	T	G	73712877	3	3	199	1	0	0	0	0	1	0	0	0	11435	1522	53	5	342	5	PAPLN	14	73712877	Missense_Mutation	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10	15752581	73712877	33636663	45	12036											
C14orf43	91748	hgsc.bcm.edu	37	chr14	74186137	74186137	+	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	tcccttcccttggcttctccGaggcctggccaccggcagac	4	9	10	18	2	1	1	0	0	1	1	4	2	3	1	6	4	0	2	6	4	0	3			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr14:74186137G>A	ENST00000286523.5	-	12	3787	c.3005C>T	c.(3004-3006)tCg>tTg	p.S1002L	ELMSAN1_ENST00000394071.2_Missense_Mutation_p.S1002L	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	1002					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										TGGCTTCTCCGAGGCCTGGCC	0.527																																					p.S1002L		Atlas-SNP	.											.	.	.	.	0			c.C3005T						PASS	.						66	57	60					14																	74186137		2203	4300	6503	SO:0001583	missense	91748	exon12			TTCTCCGAGGCCT	BF971739	CCDS9819.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000156030	ENSG00000156030			19853	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 117", "chromosome 14 open reading frame 43"	C14orf117, C14orf43			Standard	NM_194278		Approved	LSR68	uc001xou.3	Q6PJG2	OTTHUMG00000150359	ENST00000286523.5:c.3005C>T	chr14.hg19:g.74186137G>A	ENSP00000286523:p.Ser1002Leu	123.0	0.0	.		115.0	5.0	.	NM_194278	Q6PK13|Q6PK59|Q6ZS23	Missense_Mutation	SNP	ENST00000286523.5	hg19	CCDS9819.1	.	.	.	.	.	.	.	.	.	.	G	10.03	1.238379	0.22711	.	.	ENSG00000156030	ENST00000394071;ENST00000286523;ENST00000423556;ENST00000435371	T;T;T;T	0.16597	2.33;2.33;2.33;2.34	5.78	3.01	0.34805	.	0.864589	0.10001	N	0.728430	T	0.10723	0.0262	N	0.14661	0.345	0.09310	N	1	B;B	0.11235	0.004;0.002	B;B	0.06405	0.002;0.001	T	0.31336	-0.9947	10	0.54805	T	0.06	-0.0033	7.6864	0.28542	0.2049:0.1262:0.6689:0.0	.	1002;1002	A0PJD3;Q6PJG2	.;CN043_HUMAN	L	1002	ENSP00000377634:S1002L;ENSP00000286523:S1002L;ENSP00000407767:S1002L;ENSP00000402380:S1002L	ENSP00000286523:S1002L	S	-	2	0	C14orf43	73255890	0.009000	0.17119	0.019000	0.16419	0.097000	0.18754	0.897000	0.28390	0.389000	0.25086	-0.258000	0.10820	TCG	.	.	.	none		0.527	ELMSAN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317793.1	NM_194278		A	74186137	G	A	74186137	3	1	199	1	0	0	0	0	1	0	0	0	1776	1059	37	1	136	1	C14orf43	14	74186137	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	473260	74186137	33163403	46	12037											
NUSAP1	51203	hgsc.bcm.edu	37	chr15	41669495	41669495	+	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	cttacaaacaaccccatctcCagacaaagtaagtacataat	18	8	3	12	0	1	1	0	0	1	1	2	1	1	1	3	0	4	2	3	0	7	4			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr15:41669495C>T	ENST00000559596.1	+	10	1312	c.1225C>T	c.(1225-1227)Cag>Tag	p.Q409*	NUSAP1_ENST00000450592.2_Nonsense_Mutation_p.Q346*|NUSAP1_ENST00000560747.1_Nonsense_Mutation_p.Q407*|NUSAP1_ENST00000558123.1_3'UTR|NUSAP1_ENST00000260359.6_Nonsense_Mutation_p.Q394*|NUSAP1_ENST00000414849.2_Nonsense_Mutation_p.Q408*|NUSAP1_ENST00000450318.1_Nonsense_Mutation_p.Q370*|NUSAP1_ENST00000560177.1_Nonsense_Mutation_p.Q408*			Q9BXS6	NUSAP_HUMAN	nucleolar and spindle associated protein 1	409					establishment of mitotic spindle localization (GO:0040001)|mitotic chromosome condensation (GO:0007076)|mitotic cytokinesis (GO:0000281)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of mitosis (GO:0045840)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(3)|ovary(1)|prostate(2)|urinary_tract(2)	13		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;9.63e-17)|GBM - Glioblastoma multiforme(113;1.59e-06)|BRCA - Breast invasive adenocarcinoma(123;0.168)		ACCCCATCTCCAGACAAAGTA	0.333																																					p.Q409X		Atlas-SNP	.											.	NUSAP1	32	.	0			c.C1225T						PASS	.						16	14	15					15																	41669495		1771	4000	5771	SO:0001587	stop_gained	51203	exon10			CATCTCCAGACAA	AF290612	CCDS45234.1, CCDS45236.1, CCDS58356.1, CCDS58357.1, CCDS58358.1, CCDS73708.1	15q14	2008-02-05				ENSG00000137804			18538	protein-coding gene	gene with protein product		612818				12963707	Standard	NM_016359		Approved	FLJ13421, LNP, ANKT, NuSAP1, SAPL, BM037, PRO0310p1, Q0310	uc001zns.4	Q9BXS6		ENST00000559596.1:c.1225C>T	chr15.hg19:g.41669495C>T	ENSP00000453403:p.Gln409*	40.0	0.0	.		56.0	20.0	.	NM_016359	B4DDF1|E7ERR5|J3KN21|Q53GW2|Q8TBT4|Q96E58|Q96FJ1|Q9GZM9|Q9NZ85|Q9UI70	Nonsense_Mutation	SNP	ENST00000559596.1	hg19	CCDS45234.1	.	.	.	.	.	.	.	.	.	.	C	15.20	2.761477	0.49468	.	.	ENSG00000137804	ENST00000260359;ENST00000414849;ENST00000450318;ENST00000450592	.	.	.	5.65	4.71	0.59529	.	0.367085	0.31922	N	0.006860	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	12.8916	0.58073	0.1626:0.8374:0.0:0.0	.	.	.	.	X	409;408;370;346	.	ENSP00000260359:Q409X	Q	+	1	0	NUSAP1	39456787	1.000000	0.71417	0.756000	0.31282	0.567000	0.35839	2.988000	0.49386	1.561000	0.49584	0.655000	0.94253	CAG	.	.	.	none		0.333	NUSAP1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000419427.1	NM_016359		T	41669495	C	T	41669495	4	4	199	1	0	0	0	0	0	1	0	0	10785	595	21	2	1263	2	NUSAP1	15	41669495	Nonsense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10		41669495	60861897	47	12038											
SHF	90525	hgsc.bcm.edu	37	chr15	45491143	45491143	+	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	cggcgtgagcatccaggaatGgggctgggcggaactcagac	9	5	17	10	3	1	2	1	1	0	1	2	4	2	4	1	6	2	2	1	6	2	0			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr15:45491143G>T	ENST00000290894.8	-	2	624	c.130C>A	c.(130-132)Cat>Aat	p.H44N	SHF_ENST00000318390.6_Missense_Mutation_p.H101N|RP11-519G16.2_ENST00000560034.1_RNA|CTD-2651B20.7_ENST00000568314.1_RNA|CTD-2651B20.6_ENST00000563103.1_RNA	NM_138356.2	NP_612365			Src homology 2 domain containing F											endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(2)	12		all_cancers(109;8.13e-11)|all_epithelial(112;6.29e-09)|Lung NSC(122;3.57e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.1e-16)|GBM - Glioblastoma multiforme(94;5.98e-06)		ATCCAGGAATGGGGCTGGGCG	0.632											OREG0023105	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H44N		Atlas-SNP	.											.	SHF	27	.	0			c.C130A						PASS	.						50	54	53					15																	45491143		1969	4159	6128	SO:0001583	missense	90525	exon2			AGGAATGGGGCTG	BC007586	CCDS10120.2, CCDS73721.1	15q21.1	2013-02-14			ENSG00000138606	ENSG00000138606		"SH2 domain containing"	25116	protein-coding gene	gene with protein product						11095946	Standard	NM_138356		Approved		uc001zuy.3	Q7M4L6	OTTHUMG00000131353	ENST00000290894.8:c.130C>A	chr15.hg19:g.45491143G>T	ENSP00000290894:p.His44Asn	123.0	0.0	.	932	137.0	68.0	.	NM_138356		Missense_Mutation	SNP	ENST00000290894.8	hg19	CCDS10120.2	.	.	.	.	.	.	.	.	.	.	G	11.94	1.788761	0.31685	.	.	ENSG00000138606	ENST00000290894;ENST00000361989;ENST00000318390	T;T	0.38240	1.57;1.15	3.04	-6.08	0.02151	.	7739.210000	0.00166	N	0.000000	T	0.23886	0.0578	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15578	-1.0432	10	0.37606	T	0.19	3.8664	8.6801	0.34203	0.0:0.4794:0.1588:0.3618	.	44	Q7M4L6	SHF_HUMAN	N	44;44;101	ENSP00000290894:H44N;ENSP00000315978:H101N	ENSP00000290894:H44N	H	-	1	0	SHF	43278435	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-1.536000	0.02208	-1.992000	0.00975	0.655000	0.94253	CAT	.	.	.	none		0.632	SHF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254141.2	NM_138356		T	45491143	G	T	45491143	3	4	199	1	0	0	0	0	1	0	0	0	14290	1348	47	4	1169	4	SHF	15	45491143	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	3821648	45491143	57040249	48	12039											
C15orf39	56905	hgsc.bcm.edu	37	chr15	75499667	75499667	+	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	ttgccagcgagccagccctgCtcagagcctgtgaggcctgc	6	7	13	15	1	1	2	1	1	0	1	1	3	1	2	5	1	7	1	5	1	0	1			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr15:75499667C>T	ENST00000360639.2	+	2	1598	c.1278C>T	c.(1276-1278)tgC>tgT	p.C426C	C15orf39_ENST00000567617.1_Silent_p.C426C|C15orf39_ENST00000394987.4_Silent_p.C426C			Q6ZRI6	CO039_HUMAN	chromosome 15 open reading frame 39	426						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16						GCCAGCCCTGCTCAGAGCCTG	0.642																																					p.C426C		Atlas-SNP	.											.	C15orf39	64	.	0			c.C1278T						PASS	.						37	42	40					15																	75499667		2197	4295	6492	SO:0001819	synonymous_variant	56905	exon2			GCCCTGCTCAGAG	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.1278C>T	chr15.hg19:g.75499667C>T		119.0	0.0	.		150.0	64.0	.	NM_015492	B3KWI3|C9J888|Q71JB1|Q7L3S0|Q8N3F2|Q96FB6|Q9NTU5	Silent	SNP	ENST00000360639.2	hg19	CCDS10276.1																																																																																			.	.	.	none		0.642	C15orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286410.1	NM_015492		T	75499667	C	T	75499667	2	4	199	1	0	0	0	0	0	0	0	1	1795	805	28	2		2	C15orf39	15	75499667	Silent	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	30008524	75499667	27031725	49	12040											
CREBBP	1387	hgsc.bcm.edu	37	chr16	3901001	3901001	+	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	cattttccaagtcaaacaatGatccaaaatctagaaattaa	19	11	3	8	0	2	2	1	1	1	1	4	2	4	2	2	0	1	0	2	0	8	4			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr16:3901001G>A	ENST00000262367.5	-	2	904	c.95C>T	c.(94-96)tCa>tTa	p.S32L	CREBBP_ENST00000382070.3_Missense_Mutation_p.S32L	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	32					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)		GTCAAACAATGATCCAAAATC	0.403			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.S32L		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.C95T						PASS	.						55	54	55					16																	3901001		2195	4291	6486	SO:0001583	missense	1387	exon2			AACAATGATCCAA	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.95C>T	chr16.hg19:g.3901001G>A	ENSP00000262367:p.Ser32Leu	49.0	0.0	.		78.0	22.0	.	NM_001079846	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	hg19	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.054063	0.75960	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	D;D	0.86562	-2.14;-2.12	5.92	5.92	0.95590	.	0.086452	0.49916	D	0.000127	D	0.92172	0.7518	M	0.72894	2.215	0.80722	D	1	P;D	0.58620	0.949;0.983	P;P	0.57101	0.719;0.813	D	0.92259	0.5815	10	0.87932	D	0	-4.3311	20.3206	0.98668	0.0:0.0:1.0:0.0	.	100;32	Q4LE28;Q92793	.;CBP_HUMAN	L	32;100;32	ENSP00000262367:S32L;ENSP00000371502:S32L	ENSP00000262367:S32L	S	-	2	0	CREBBP	3841002	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.390000	0.79816	2.809000	0.96659	0.655000	0.94253	TCA	.	.	.	none		0.403	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		A	3901001	G	A	3901001	3	1	199	1	0	0	0	0	1	0	0	0	3863	1294	45	2	7353	2	CREBBP	16	3901001	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10		3901001	86453752	50	12041											
UBN1	29855	hgsc.bcm.edu	37	chr16	4908004	4908004	+	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	tttacagaagaaagatctgtCagatcctttcaatgacgaag	15	11	8	7	1	3	5	2	1	1	4	4	6	4	5	1	0	1	0	1	0	5	3			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr16:4908004C>T	ENST00000396658.4	+	2	966	c.263C>T	c.(262-264)tCa>tTa	p.S88L	UBN1_ENST00000590769.1_Missense_Mutation_p.S88L|UBN1_ENST00000545171.1_Missense_Mutation_p.S88L|UBN1_ENST00000262376.6_Missense_Mutation_p.S88L	NM_016936.3	NP_058632.2	Q9NPG3	UBN1_HUMAN	ubinuclein 1	88	Sufficient for interaction with HIRA.				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						AAAGATCTGTCAGATCCTTTC	0.338																																					p.S88L		Atlas-SNP	.											.	UBN1	88	.	0			c.C263T						PASS	.						70	77	75					16																	4908004		2197	4300	6497	SO:0001583	missense	29855	exon3			ATCTGTCAGATCC	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.263C>T	chr16.hg19:g.4908004C>T	ENSP00000379894:p.Ser88Leu	12.0	0.0	.		32.0	9.0	.	NM_001079514	B7Z6D3|D3DUE8|Q13079|Q9P1P7	Missense_Mutation	SNP	ENST00000396658.4	hg19	CCDS10525.1	.	.	.	.	.	.	.	.	.	.	C	10.11	1.260216	0.23051	.	.	ENSG00000118900	ENST00000262376;ENST00000545171;ENST00000396658	T;T;T	0.44083	1.51;0.93;1.51	5.37	-2.3	0.06785	.	1.211730	0.05673	N	0.589051	T	0.27313	0.0670	N	0.16266	0.395	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.26258	-1.0108	10	0.27785	T	0.31	1.4387	11.8692	0.52511	0.0:0.4651:0.0:0.5349	.	88;88	Q9NPG3-2;Q9NPG3	.;UBN1_HUMAN	L	88	ENSP00000262376:S88L;ENSP00000442379:S88L;ENSP00000379894:S88L	ENSP00000262376:S88L	S	+	2	0	UBN1	4848005	0.000000	0.05858	0.017000	0.16124	0.976000	0.68499	-1.157000	0.03157	-0.259000	0.09432	0.655000	0.94253	TCA	.	.	.	none		0.338	UBN1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251719.1	NM_016936		T	4908004	C	T	4908004	3	4	199	1	0	0	0	0	1	0	0	0	16904	838	29	2	269	2	UBN1	16	4908004	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	1007003	4908004	85446749	51	12042											
DNAH3	55567	hgsc.bcm.edu	37	chr16	21051260	21051260	+	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	atcatggccactgtccggaaCaaggcctggaaaagaaacaa	16	5	10	10	1	1	1	1	0	0	1	2	3	2	3	3	4	2	0	3	4	6	0			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr16:21051260C>A	ENST00000261383.3	-	33	4643	c.4644G>T	c.(4642-4644)ttG>ttT	p.L1548F	DNAH3_ENST00000415178.1_Missense_Mutation_p.L1548F	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1548	AAA 1. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		CTGTCCGGAACAAGGCCTGGA	0.488																																					p.L1548F		Atlas-SNP	.											.	DNAH3	1142	.	0			c.G4644T						PASS	.						114	103	107					16																	21051260		2201	4300	6501	SO:0001583	missense	55567	exon33			CCGGAACAAGGCC	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.4644G>T	chr16.hg19:g.21051260C>A	ENSP00000261383:p.Leu1548Phe	177.0	0.0	.		236.0	59.0	.	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	hg19	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	c	19.21	3.783406	0.70222	.	.	ENSG00000158486	ENST00000261383;ENST00000415178	T;T	0.40756	1.02;1.02	5.48	-3.63	0.04529	ATPase, AAA+ type, core (1);	0.000000	0.64402	D	0.000008	T	0.71787	0.3381	H	0.98048	4.135	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.76408	-0.2970	10	0.87932	D	0	.	11.9329	0.52857	0.0:0.4256:0.0:0.5744	.	1548	Q8TD57	DYH3_HUMAN	F	1548	ENSP00000261383:L1548F;ENSP00000394245:L1548F	ENSP00000261383:L1548F	L	-	3	2	DNAH3	20958761	0.014000	0.17966	0.915000	0.36163	0.963000	0.63663	-0.900000	0.04097	-0.896000	0.03915	-0.753000	0.03488	TTG	.	.	.	none		0.488	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		A	21051260	C	A	21051260	3	1	199	1	0	0	0	0	1	0	0	0	4605	477	17	4	7825	4	DNAH3	16	21051260	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	16143256	21051260	69303493	52	12043											
MBTPS1	8720	hgsc.bcm.edu	37	chr16	84094306	84094306	+	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	ccttccatcctctctggagtGactgagcctgctccactggg	5	11	10	15	0	1	2	0	2	1	0	5	3	4	3	5	2	2	1	5	2	0	1			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr16:84094306G>C	ENST00000343411.3	-	20	3180	c.2685C>G	c.(2683-2685)gtC>gtG	p.V895V		NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	895					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						TCTCTGGAGTGACTGAGCCTG	0.592																																					p.V895V		Atlas-SNP	.											.	MBTPS1	85	.	0			c.C2685G						PASS	.						65	53	57					16																	84094306		2200	4300	6500	SO:0001819	synonymous_variant	8720	exon20			TGGAGTGACTGAG	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.2685C>G	chr16.hg19:g.84094306G>C		110.0	0.0	.		126.0	55.0	.	NM_003791	A8K6V8|Q24JQ2|Q9UF67	Silent	SNP	ENST00000343411.3	hg19	CCDS10941.1																																																																																			.	.	.	none		0.592	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269080.2	NM_003791		C	84094306	G	C	84094306	2	2	199	1	0	0	0	0	0	0	0	1	9368	1277	45	4		4	MBTPS1	16	84094306	Silent	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	63043046	84094306	6260447	53	12044											
ZCCHC14	23174	hgsc.bcm.edu	37	chr16	87445209	87445209	+	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	gtaacaagataggttcccgcTctttttgtgactggaaccat	10	13	9	9	1	1	2	0	1	1	1	2	3	2	3	2	2	2	3	2	2	4	5			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr16:87445209T>A	ENST00000268616.4	-	12	2924	c.2707A>T	c.(2707-2709)Agc>Tgc	p.S903C		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	903							nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		AGGTTCCCGCTCTTTTTGTGA	0.597																																					p.S903C		Atlas-SNP	.											.	ZCCHC14	87	.	0			c.A2707T						PASS	.						85	74	78					16																	87445209		2198	4300	6498	SO:0001583	missense	23174	exon12			TCCCGCTCTTTTT	AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"Zinc fingers, CCHC domain containing", "Sterile alpha motif (SAM) domain containing"	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.2707A>T	chr16.hg19:g.87445209T>A	ENSP00000268616:p.Ser903Cys	136.0	0.0	.		165.0	56.0	.	NM_015144	D3DUN1|O60324|Q3MJD8|Q9UFP0	Missense_Mutation	SNP	ENST00000268616.4	hg19	CCDS10961.1	.	.	.	.	.	.	.	.	.	.	T	14.84	2.654553	0.47467	.	.	ENSG00000140948	ENST00000268616	T	0.76968	-1.06	5.55	5.55	0.83447	.	0.169858	0.53938	D	0.000059	T	0.79375	0.4435	L	0.27053	0.805	0.33555	D	0.596683	D;D	0.67145	0.996;0.993	P;P	0.59288	0.855;0.72	D	0.85907	0.1438	10	0.87932	D	0	-19.183	15.975	0.80057	0.0:0.0:0.0:1.0	.	903;903	Q8WYQ9-2;Q8WYQ9	.;ZCH14_HUMAN	C	903	ENSP00000268616:S903C	ENSP00000268616:S903C	S	-	1	0	ZCCHC14	86002710	0.998000	0.40836	0.998000	0.56505	0.927000	0.56198	1.668000	0.37481	2.223000	0.72356	0.533000	0.62120	AGC	.	.	.	none		0.597	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269107.1	NM_015144		A	87445209	T	A	87445209	3	1	199	1	0	0	0	0	1	0	0	0	17595	1551	54	5	150	5	ZCCHC14	16	87445209	Missense_Mutation	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10	3350903	87445209	2909544	54	12045											
FXR2	9513	hgsc.bcm.edu	37	chr17	7497319	7497319	+	Missense_Mutation	SNP	T	T	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	aacaaaaatgaagggaaccaTtccctagagaacagagagca	20	4	9	8	0	0	3	0	1	0	2	1	6	1	4	2	1	4	1	2	1	7	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr17:7497319T>G	ENST00000250113.7	-	11	1358	c.1024A>C	c.(1024-1026)Atg>Ctg	p.M342L	FXR2_ENST00000573057.1_5'Flank	NM_004860.3	NP_004851.2	P51116	FXR2_HUMAN	fragile X mental retardation, autosomal homolog 2	342						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)		AAGGGAACCATTCCCTAGAGA	0.532																																					p.M342L		Atlas-SNP	.											.	FXR2	44	.	0			c.A1024C						PASS	.						60	59	59					17																	7497319		1905	4126	6031	SO:0001583	missense	9513	exon11			GAACCATTCCCTA	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.1024A>C	chr17.hg19:g.7497319T>G	ENSP00000250113:p.Met342Leu	46.0	0.0	.		63.0	18.0	.	NM_004860	B2R9M2|D3DTQ1|Q86V09|Q8WUM2	Missense_Mutation	SNP	ENST00000250113.7	hg19	CCDS45604.1	.	.	.	.	.	.	.	.	.	.	T	9.196	1.027335	0.19512	.	.	ENSG00000129245	ENST00000250113	T	0.27720	1.65	5.52	5.52	0.82312	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.122387	0.64402	D	0.000001	T	0.18299	0.0439	N	0.12746	0.255	0.42425	D	0.992651	B	0.06786	0.001	B	0.09377	0.004	T	0.08932	-1.0698	10	0.22706	T	0.39	1.2613	13.6401	0.62246	0.0:0.0:0.0:1.0	.	342	P51116	FXR2_HUMAN	L	342	ENSP00000250113:M342L	ENSP00000250113:M342L	M	-	1	0	FXR2	7438044	1.000000	0.71417	1.000000	0.80357	0.081000	0.17604	5.842000	0.69417	2.317000	0.78254	0.460000	0.39030	ATG	.	.	.	none		0.532	FXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441084.1			G	7497319	T	G	7497319	3	3	199	1	0	0	0	0	1	0	0	0	6123	1493	52	5	925	5	FXR2	17	7497319	Missense_Mutation	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10		7497319	73697891	55	12046											
MYH4	4622	hgsc.bcm.edu	37	chr17	10366950	10366950	+	Missense_Mutation	SNP	T	T	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	tagcactgatgatttgatctTcaagggtccccttaagagaa	12	12	9	8	0	2	4	1	3	1	1	3	5	3	4	2	1	1	1	2	1	4	4			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr17:10366950T>G	ENST00000255381.2	-	8	769	c.659A>C	c.(658-660)gAa>gCa	p.E220A	RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	220	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						GATTTGATCTTCAAGGGTCCC	0.448																																					p.E220A		Atlas-SNP	.											.	MYH4	349	.	0			c.A659C						PASS	.						73	73	73					17																	10366950		2203	4300	6503	SO:0001583	missense	4622	exon8			TGATCTTCAAGGG		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.659A>C	chr17.hg19:g.10366950T>G	ENSP00000255381:p.Glu220Ala	58.0	0.0	.		72.0	55.0	.	NM_017533		Missense_Mutation	SNP	ENST00000255381.2	hg19	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.567354	0.86439	.	.	ENSG00000141048	ENST00000255381	D	0.89050	-2.46	5.14	5.14	0.70334	Myosin head, motor domain (2);	0.000000	0.38005	U	0.001849	D	0.96503	0.8859	H	0.97707	4.06	0.80722	D	1	D	0.63880	0.993	D	0.77557	0.99	D	0.97990	1.0354	10	0.87932	D	0	.	15.2278	0.73364	0.0:0.0:0.0:1.0	.	220	Q9Y623	MYH4_HUMAN	A	220	ENSP00000255381:E220A	ENSP00000255381:E220A	E	-	2	0	MYH4	10307675	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.966000	0.87956	2.052000	0.61016	0.455000	0.32223	GAA	.	.	.	none		0.448	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		G	10366950	T	G	10366950	3	3	199	1	0	0	0	0	1	0	0	0	10044	1783	62	5	5292	5	MYH4	17	10366950	Missense_Mutation	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10	2869631	10366950	70828260	56	12047											
STAC2	342667	hgsc.bcm.edu	37	chr17	37373422	37373422	+	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	catcgcaagccctgtttggaGtttcctaggaagaatttggg	9	12	12	8	1	0	1	0	0	0	1	2	3	1	3	2	3	1	3	2	3	4	4			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr17:37373422G>A	ENST00000333461.5	-	3	771	c.402C>T	c.(400-402)aaC>aaT	p.N134N		NM_198993.3	NP_945344.1	Q6ZMT1	STAC2_HUMAN	SH3 and cysteine rich domain 2	134					intracellular signal transduction (GO:0035556)		metal ion binding (GO:0046872)			NS(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|pancreas(1)|prostate(1)|skin(2)	17						CCTGTTTGGAGTTTCCTAGGA	0.562																																					p.N134N		Atlas-SNP	.											.	STAC2	47	.	0			c.C402T						PASS	.						59	56	57					17																	37373422		2203	4300	6503	SO:0001819	synonymous_variant	342667	exon3			TTTGGAGTTTCCT	AJ608762	CCDS11335.1	17q21.2	2012-11-19			ENSG00000141750	ENSG00000141750			23990	protein-coding gene	gene with protein product							Standard	NM_198993		Approved	24b2	uc002hrs.3	Q6ZMT1	OTTHUMG00000179039	ENST00000333461.5:c.402C>T	chr17.hg19:g.37373422G>A		83.0	0.0	.		115.0	60.0	.	NM_198993	Q32MA3	Silent	SNP	ENST00000333461.5	hg19	CCDS11335.1																																																																																			.	.	.	none		0.562	STAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444533.2	NM_198993		A	37373422	G	A	37373422	2	1	199	1	0	0	0	0	0	0	0	1	15252	1020	36	2		2	STAC2	17	37373422	Silent	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	27006472	37373422	43821788	57	12048											
PPM1E	22843	hgsc.bcm.edu	37	chr17	56833454	56833454	+	Silent	SNP	G	G	A																															tgcggcggcggcgagccggaGccggaacccgaacccgaacc																								rs77856248		TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	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	.	0			c.G96A						PASS	.						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	chr17.hg19:g.56833454G>A		31.0	0.0	.		79.0	11.0	.	NM_014906	Q8N8J9|Q96DB8	Silent	SNP	ENST00000308249.2	hg19	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	199	1	0	0	0	0	0	0	0	1	12348	962	34	2		2	PPM1E	17	56833454	Silent	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	19460032	56833454	24361756	58	12049	112	2									
PPM1E	22843	hgsc.bcm.edu	37	chr17	56833457	56833457	+	Silent	SNP	G	G	C																															ggcggcggcgagccggagccGgaacccgaacccgaacccga																								rs3834568|rs201186780|rs74256772	byFrequency	TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	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	.	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	chr17.hg19:g.56833457G>C		28.0	1.0	.		72.0	12.0	.	NM_014906	Q8N8J9|Q96DB8	Silent	SNP	ENST00000308249.2	hg19	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	199	1	0	0	0	0	0	0	0	1	12348	1103	39	4		4	PPM1E	17	56833457	Silent	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	3	56833457	24361753	59	12050	112	2									
NEDD4L	23327	hgsc.bcm.edu	37	chr18	56033337	56033337	+	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	accagatgtcctaaaagctaGactgtggattgagtttgaat	13	12	10	6	0	0	4	0	2	0	2	1	5	1	5	2	1	1	2	2	1	4	4			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr18:56033337G>C	ENST00000400345.3	+	21	2223	c.1940G>C	c.(1939-1941)aGa>aCa	p.R647T	NEDD4L_ENST00000256832.7_Missense_Mutation_p.R507T|NEDD4L_ENST00000356462.6_Missense_Mutation_p.R583T|NEDD4L_ENST00000456986.1_Missense_Mutation_p.R526T|NEDD4L_ENST00000256830.9_Missense_Mutation_p.R543T|NEDD4L_ENST00000431212.2_Missense_Mutation_p.R526T|NEDD4L_ENST00000586263.1_Missense_Mutation_p.R619T|NEDD4L_ENST00000357895.5_Missense_Mutation_p.R639T|NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000382850.4_Missense_Mutation_p.R627T|NEDD4L_ENST00000435432.2_Missense_Mutation_p.R506T|NEDD4L_ENST00000456173.2_Missense_Mutation_p.R506T	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	647	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						CTAAAAGCTAGACTGTGGATT	0.408																																					p.R647T		Atlas-SNP	.											.	NEDD4L	126	.	0			c.G1940C						PASS	.						122	114	117					18																	56033337		1867	4102	5969	SO:0001583	missense	23327	exon21			AAGCTAGACTGTG	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.1940G>C	chr18.hg19:g.56033337G>C	ENSP00000383199:p.Arg647Thr	93.0	0.0	.		132.0	9.0	.	NM_001144967	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Missense_Mutation	SNP	ENST00000400345.3	hg19	CCDS45872.1	.	.	.	.	.	.	.	.	.	.	G	30	5.052900	0.93793	.	.	ENSG00000049759	ENST00000400345;ENST00000382850;ENST00000356462;ENST00000256830;ENST00000256832;ENST00000456986;ENST00000357895;ENST00000435432;ENST00000456173;ENST00000431212	T;T;T;T;T;T;T;T;T;T	0.75938	0.97;0.97;0.97;0.97;-0.98;-0.98;0.97;-0.98;-0.98;-0.98	5.54	5.54	0.83059	HECT (3);	0.000000	0.85682	D	0.000000	D	0.86727	0.6002	M	0.76574	2.34	0.80722	D	1	D;D;D;D;D;D	0.76494	0.999;0.999;0.966;0.985;0.999;0.999	D;D;P;D;D;D	0.77004	0.989;0.985;0.574;0.955;0.977;0.985	D	0.87407	0.2373	10	0.87932	D	0	.	19.8487	0.96730	0.0:0.0:1.0:0.0	.	619;639;506;583;647;627	Q96PU5-6;Q96PU5-7;Q3LSM7;Q96PU5-2;Q96PU5;Q96PU5-5	.;.;.;.;NED4L_HUMAN;.	T	647;627;583;543;507;526;639;506;506;526	ENSP00000383199:R647T;ENSP00000372301:R627T;ENSP00000348847:R583T;ENSP00000256830:R543T;ENSP00000256832:R507T;ENSP00000411947:R526T;ENSP00000350569:R639T;ENSP00000393395:R506T;ENSP00000405440:R506T;ENSP00000389406:R526T	ENSP00000256830:R543T	R	+	2	0	NEDD4L	54184317	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.813000	0.99286	2.748000	0.94277	0.650000	0.86243	AGA	.	.	.	none		0.408	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1			C	56033337	G	C	56033337	3	2	199	1	0	0	0	0	1	0	0	0	10318	942	33	4	2050	4	NEDD4L	18	56033337	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10		56033337	22043911	60	12051											
LPPR3	79948	hgsc.bcm.edu	37	chr19	815207	815207	+	Missense_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	cacaaaccgcaccgtacgccGcaggaaggagttgaagttgc	12	5	12	12	4	0	1	0	1	0	0	0	3	0	3	3	2	3	5	3	2	4	3			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr19:815207G>A	ENST00000520876.3	-	4	460	c.382C>T	c.(382-384)Cgg>Tgg	p.R128W	MIR3187_ENST00000583431.1_RNA|LPPR3_ENST00000359894.2_Missense_Mutation_p.R128W	NM_001270366.1	NP_001257295.1	Q6T4P5	LPPR3_HUMAN		128						integral component of membrane (GO:0016021)	phosphatidate phosphatase activity (GO:0008195)										ACCGTACGCCGCAGGAAGGAG	0.716																																					p.R128W		Atlas-SNP	.											.	.	.	.	0			c.C382T						PASS	.						23	28	26					19																	815207		2181	4286	6467	SO:0001583	missense	0	exon4			TACGCCGCAGGAA																												ENST00000520876.3:c.382C>T	chr19.hg19:g.815207G>A	ENSP00000430297:p.Arg128Trp	0.0	0.0	.		4.0	4.0	.	NM_001270366	Q86XQ4|Q96EH1|Q9BQF9|Q9HAJ4	Missense_Mutation	SNP	ENST00000520876.3	hg19	CCDS58636.1	.	.	.	.	.	.	.	.	.	.	G	19.24	3.790052	0.70337	.	.	ENSG00000129951	ENST00000300947;ENST00000359894;ENST00000520876;ENST00000521445	T;T	0.52526	0.66;0.66	4.33	3.27	0.37495	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.000000	0.85682	U	0.000000	T	0.68339	0.2990	M	0.82517	2.595	0.52501	D	0.999955	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.71712	-0.4510	10	0.87932	D	0	-9.9087	11.2342	0.48931	0.0:0.0:0.8149:0.1851	.	128;128;128	Q6T4P5-2;Q6T4P5;Q6T4P5-3	.;LPPR3_HUMAN;.	W	128	ENSP00000352962:R128W;ENSP00000430297:R128W	ENSP00000300947:R128W	R	-	1	2	AC006273.1	766207	0.599000	0.26891	0.997000	0.53966	0.459000	0.32528	0.345000	0.19979	0.788000	0.33755	0.462000	0.41574	CGG	.	.	.	none		0.716	LPPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379096.3			A	815207	G	A	815207	3	1	199	1	0	0	0	0	1	0	0	0	8933	1086	38	1	1874	1	LPPR3	19	815207	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10		815207	58313776	61	12052											
ZNF57	126295	hgsc.bcm.edu	37	chr19	2915555	2915555	+	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	gaggatgtggctgtggacttCaccctggaggagtgggcttt	6	11	17	7	0	1	0	1	0	0	0	1	5	1	4	1	6	0	2	1	6	0	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr19:2915555C>T	ENST00000306908.5	+	2	187	c.39C>T	c.(37-39)ttC>ttT	p.F13F	AC006277.2_ENST00000520090.2_RNA|ZNF57_ENST00000523428.1_5'UTR	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	13	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)|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)		CTGTGGACTTCACCCTGGAGG	0.542																																					p.F13F	NSCLC(150;910 1964 4303 10464 26498)	Atlas-SNP	.											.	ZNF57	57	.	0			c.C39T						PASS	.						160	141	147					19																	2915555		2203	4300	6503	SO:0001819	synonymous_variant	126295	exon2			GGACTTCACCCTG	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.39C>T	chr19.hg19:g.2915555C>T		174.0	0.0	.		170.0	76.0	.	NM_173480	Q8N6R9	Silent	SNP	ENST00000306908.5	hg19	CCDS12098.1																																																																																			.	.	.	none		0.542	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480		T	2915555	C	T	2915555	2	4	199	1	0	0	0	0	0	0	0	1	18013	825	29	2		2	ZNF57	19	2915555	Silent	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	2100348	2915555	56213428	62	12053											
ZFR2	23217	hgsc.bcm.edu	37	chr19	3808936	3808936	+	Missense_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	tgcatccccggggcccagggGcccagccgcactgctcacag	6	4	13	18	2	1	0	1	0	0	0	2	0	2	0	5	4	3	3	5	4	0	0			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr19:3808936G>A	ENST00000262961.4	-	17	2489	c.2479C>T	c.(2479-2481)Ccc>Tcc	p.P827S		NM_015174.1	NP_055989.1	Q9UPR6	ZFR2_HUMAN	zinc finger RNA binding protein 2	827	DZF. {ECO:0000255|PROSITE- ProRule:PRU01040}.						nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00514)|STAD - Stomach adenocarcinoma(1328;0.19)		GGGCCCAGGGGCCCAGCCGCA	0.697																																					p.P827S		Atlas-SNP	.											.	ZFR2	63	.	0			c.C2479T						PASS	.						10	15	14					19																	3808936		2017	4182	6199	SO:0001583	missense	23217	exon17			CCAGGGGCCCAGC	AB029009	CCDS45921.1, CCDS45922.1	19p13.3	2012-10-05	2008-03-25	2008-03-25	ENSG00000105278	ENSG00000105278			29189	protein-coding gene	gene with protein product			"KIAA1086"	KIAA1086		10470851	Standard	NM_015174		Approved		uc002lyw.2	Q9UPR6	OTTHUMG00000180918	ENST00000262961.4:c.2479C>T	chr19.hg19:g.3808936G>A	ENSP00000262961:p.Pro827Ser	16.0	0.0	.		33.0	15.0	.	NM_015174		Missense_Mutation	SNP	ENST00000262961.4	hg19	CCDS45921.1	.	.	.	.	.	.	.	.	.	.	G	14.62	2.588474	0.46110	.	.	ENSG00000105278	ENST00000262961	T	0.42131	0.98	3.97	3.97	0.46021	DZF (2);	0.084158	0.48767	U	0.000179	T	0.62962	0.2471	M	0.81112	2.525	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.65668	-0.6112	10	0.48119	T	0.1	-16.1842	11.3964	0.49845	0.0:0.0:1.0:0.0	.	827	Q9UPR6	ZFR2_HUMAN	S	827	ENSP00000262961:P827S	ENSP00000262961:P827S	P	-	1	0	ZFR2	3759936	1.000000	0.71417	0.677000	0.29947	0.009000	0.06853	5.975000	0.70475	2.053000	0.61076	0.484000	0.47621	CCC	.	.	.	none		0.697	ZFR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453648.2	NM_015174		A	3808936	G	A	3808936	3	1	199	1	0	0	0	0	1	0	0	0	17672	1203	42	2	352	2	ZFR2	19	3808936	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	893381	3808936	55320047	63	12054											
IL27RA	9466	hgsc.bcm.edu	37	chr19	14150421	14150421	+	Missense_Mutation	SNP	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	tgacaaactccttgtctgggGcactaaggcaggccagcctc	9	8	11	13	0	1	1	0	1	1	0	3	1	2	1	3	4	2	2	3	4	2	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr19:14150421G>A	ENST00000263379.2	+	3	445	c.320G>A	c.(319-321)gGc>gAc	p.G107D		NM_004843.3	NP_004834.1	Q6UWB1	I27RA_HUMAN	interleukin 27 receptor, alpha	107					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						CTTGTCTGGGGCACTAAGGCA	0.612																																					p.G107D	Colon(164;1849 1896 4443 37792 47834)	Atlas-SNP	.											.	IL27RA	56	.	0			c.G320A						PASS	.						66	61	63					19																	14150421		2203	4300	6503	SO:0001583	missense	9466	exon3			TCTGGGGCACTAA	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.320G>A	chr19.hg19:g.14150421G>A	ENSP00000263379:p.Gly107Asp	170.0	0.0	.		190.0	61.0	.	NM_004843	A0N0L1|O60624	Missense_Mutation	SNP	ENST00000263379.2	hg19	CCDS12303.1	.	.	.	.	.	.	.	.	.	.	G	13.70	2.314782	0.40996	.	.	ENSG00000104998	ENST00000263379	T	0.61627	0.09	4.54	-2.12	0.07165	.	0.705821	0.12338	N	0.477779	T	0.46073	0.1374	L	0.32530	0.975	0.09310	N	0.999991	P	0.52316	0.952	P	0.49140	0.601	T	0.43718	-0.9374	10	0.23891	T	0.37	-20.1299	7.3547	0.26713	0.0:0.2745:0.2642:0.4613	.	107	Q6UWB1	I27RA_HUMAN	D	107	ENSP00000263379:G107D	ENSP00000263379:G107D	G	+	2	0	IL27RA	14011421	0.006000	0.16342	0.097000	0.21041	0.288000	0.27193	-0.354000	0.07681	-0.030000	0.13804	0.555000	0.69702	GGC	.	.	.	none		0.612	IL27RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458539.1	NM_004843		A	14150421	G	A	14150421	3	1	199	1	0	0	0	0	1	0	0	0	7688	1203	42	2	330	2	IL27RA	19	14150421	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	10341485	14150421	44978562	64	12055											
MYO9B	4650	hgsc.bcm.edu	37	chr19	17322846	17322846	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggacccccatcatgcccacGgccaacatcaagctcccacc	10	4	6	21	2	2	0	2	0	0	0	3	1	3	1	6	2	3	1	6	2	2	0			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr19:17322846G>A	ENST00000594824.1	+	40	6348	c.6201G>A	c.(6199-6201)acG>acA	p.T2067T	MYO9B_ENST00000397274.2_3'UTR|MYO9B_ENST00000595618.1_3'UTR			Q13459	MYO9B_HUMAN	myosin IXB	2067	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						TCATGCCCACGGCCAACATCA	0.736																																					p.T2067T		Atlas-SNP	.											.	MYO9B	264	.	0			c.G6201A						PASS	.						9	11	10					19																	17322846		1808	4035	5843	SO:0001819	synonymous_variant	4650	exon40			GCCCACGGCCAAC		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.6201G>A	chr19.hg19:g.17322846G>A		32.0	0.0	.		59.0	36.0	.	NM_004145	O75314|Q9NUJ2|Q9UHN0	Silent	SNP	ENST00000594824.1	hg19																																																																																				.	.	.	none		0.736	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1			A	17322846	G	A	17322846	2	1	199	1	0	0	0	0	0	0	0	1	10092	1103	39	1		1	MYO9B	19	17322846	Silent	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	3172425	17322846	41806137	65	12056											
USF2	7392	hgsc.bcm.edu	37	chr19	35761401	35761402	+	In_Frame_Ins	INS	-	-	TCAGCGGGGAGGCACGATTTGCCT																															cagtccggcggccgaggctgINStcagcggggaggcacgattt																										TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr19:35761401_35761402insTCAGCGGGGAGGCACGATTTGCCT	ENST00000222305.3	+	5	518_519	c.481_482insTCAGCGGGGAGGCACGATTTGCCT	c.(481-483)gtc>gTCAGCGGGGAGGCACGATTTGCCTtc	p.161_162insSGEARFAF	USF2_ENST00000595068.1_In_Frame_Ins_p.161_162insSGEARFAF|USF2_ENST00000343550.5_In_Frame_Ins_p.94_95insSGEARFAF|USF2_ENST00000594064.1_In_Frame_Ins_p.159_160insSGEARFAF|USF2_ENST00000379134.3_Intron	NM_003367.2	NP_003358.1	Q15853	USF2_HUMAN	upstream transcription factor 2, c-fos interacting	161					lactation (GO:0007595)|late viral transcription (GO:0019086)|lipid homeostasis (GO:0055088)|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 by glucose (GO:0000430)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|double-stranded DNA binding (GO:0003690)|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 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)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|urinary_tract(1)	13	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)		Epithelial(14;7.4e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.47e-19)|all cancers(14;4.17e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			GGCCGAGGCTGTCAGCGGGGAG	0.589																																					p.V161delinsVSGEARFAF	NSCLC(103;173 2832 8890)	Pindel	.											.	USF2	26	.	0			c.481_482insTCAGCGGGGAGGCACGATTTGCCT						PASS	.																																			SO:0001652	inframe_insertion	7392	exon5			.	AY007087	CCDS12452.1, CCDS12453.1	19q13	2013-05-21				ENSG00000105698		"Basic helix-loop-helix proteins"	12594	protein-coding gene	gene with protein product		600390				8954795	Standard	NM_003367		Approved	FIP, bHLHb12	uc002nyq.1	Q15853		ENST00000222305.3:c.482_505dupTCAGCGGGGAGGCACGATTTGCCT	chr19.hg19:g.35761401_35761402insTCAGCGGGGAGGCACGATTTGCCT	ENSP00000222305:p.Val161_Ser162insSerGlyGluAlaArgPheAlaPhe	287.0	0.0	.		225.0	32.0	0.142	NM_003367	O00671|O00709|Q05750|Q07952|Q15851|Q15852|Q6FI33|Q6YI47	In_Frame_Ins	INS	ENST00000222305.3	hg19	CCDS12452.1																																																																																			.	.	.	none		0.589	USF2-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466056.1	NM_003367		TCAGCGGGGAGGCACGATTTGCCT	35761402	-	TCAGCGGGGAGGCACGATTTGCCT	35761401	7	5	199	1	0	1	1	0	0	0	0	0	17045	1377	48	0	499	0	USF2	19	35761401	In_Frame_Ins	INS	-	TCGA-HE-A5NJ-01A-11D-A26P-10	18438555	35761401	23367582	66	12057											
MAP3K10	4294	hgsc.bcm.edu	37	chr19	40698281	40698281	+	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	gctttggcaaggtctatcggGccctgtggcgtggcgaggag	5	9	18	9	3	1	0	0	0	1	0	2	2	1	1	1	6	0	2	1	6	2	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr19:40698281G>T	ENST00000253055.3	+	1	631	c.343G>T	c.(343-345)Gcc>Tcc	p.A115S	MAP3K10_ENST00000593906.1_3'UTR	NM_002446.3	NP_002437.2	Q02779	M3K10_HUMAN	mitogen-activated protein kinase kinase kinase 10	115	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|JNK cascade (GO:0007254)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of apoptotic process (GO:0043065)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|bHLH transcription factor binding (GO:0043425)|JUN kinase kinase kinase activity (GO:0004706)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription corepressor activity (GO:0003714)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						GGTCTATCGGGCCCTGTGGCG	0.687																																					p.A115S		Atlas-SNP	.											.	MAP3K10	70	.	0			c.G343T						PASS	.						33	38	36					19																	40698281		2202	4298	6500	SO:0001583	missense	4294	exon1			TATCGGGCCCTGT	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.343G>T	chr19.hg19:g.40698281G>T	ENSP00000253055:p.Ala115Ser	9.0	0.0	.		28.0	4.0	.	NM_002446	Q12761|Q14871	Missense_Mutation	SNP	ENST00000253055.3	hg19	CCDS12549.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.976122	0.92982	.	.	ENSG00000130758	ENST00000253055	D	0.84944	-1.92	4.3	4.3	0.51218	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.207947	0.38897	N	0.001532	D	0.89223	0.6654	M	0.63428	1.95	0.39678	D	0.970865	P	0.51933	0.949	P	0.58660	0.843	D	0.91138	0.4943	10	0.87932	D	0	.	14.3128	0.66426	0.0:0.0:1.0:0.0	.	115	Q02779	M3K10_HUMAN	S	115	ENSP00000253055:A115S	ENSP00000253055:A115S	A	+	1	0	MAP3K10	45390121	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.646000	0.98474	2.232000	0.73038	0.655000	0.94253	GCC	.	.	.	none		0.687	MAP3K10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462552.1	NM_002446		T	40698281	G	T	40698281	3	4	199	1	0	0	0	0	1	0	0	0	9251	1203	42	4	345	4	MAP3K10	19	40698281	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	4936880	40698281	18430702	67	12058											
ZNF221	7638	hgsc.bcm.edu	37	chr19	44471195	44471195	+	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	atgtgaagagtgtggaaagaGatttactcagagttcacaac	15	10	11	5	0	2	4	2	1	0	3	2	6	2	5	0	1	2	1	0	1	4	3			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr19:44471195G>C	ENST00000251269.5	+	6	1869	c.1541G>C	c.(1540-1542)aGa>aCa	p.R514T	ZNF221_ENST00000587682.1_Missense_Mutation_p.R514T|ZNF221_ENST00000592350.1_Missense_Mutation_p.R514T	NM_013359.2	NP_037491	Q9UK13	ZN221_HUMAN	zinc finger protein 221	514					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(11)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	30		Prostate(69;0.0352)				TGTGGAAAGAGATTTACTCAG	0.428																																					p.R514T		Atlas-SNP	.											ZNF221,colon,carcinoma,0,1	ZNF221	59	.	0			c.G1541C						PASS	.						94	89	91					19																	44471195		2203	4300	6503	SO:0001583	missense	7638	exon6			GAAAGAGATTTAC	AF187987	CCDS12633.1	19q13.31	2013-01-08				ENSG00000159905		"Zinc fingers, C2H2-type", "-"	13014	protein-coding gene	gene with protein product							Standard	NM_013359		Approved		uc002oxx.2	Q9UK13		ENST00000251269.5:c.1541G>C	chr19.hg19:g.44471195G>C	ENSP00000251269:p.Arg514Thr	51.0	0.0	.		51.0	15.0	.	NM_013359	B2RAI6|Q2M2H2|Q9P1U8	Missense_Mutation	SNP	ENST00000251269.5	hg19	CCDS12633.1	.	.	.	.	.	.	.	.	.	.	g	12.16	1.853235	0.32699	.	.	ENSG00000159905	ENST00000251269	T	0.16597	2.33	2.63	-1.52	0.08637	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10895	0.0266	N	0.11870	0.19	0.09310	N	1	P	0.51240	0.943	P	0.48873	0.593	T	0.25152	-1.0140	9	0.38643	T	0.18	.	5.5077	0.16864	0.1145:0.0:0.5338:0.3517	.	514	Q9UK13	ZN221_HUMAN	T	514	ENSP00000251269:R514T	ENSP00000251269:R514T	R	+	2	0	ZNF221	49163035	0.000000	0.05858	0.000000	0.03702	0.888000	0.51559	0.114000	0.15520	-0.005000	0.14395	0.313000	0.20887	AGA	.	.	.	none		0.428	ZNF221-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460068.1			C	44471195	G	C	44471195	3	2	199	1	0	0	0	0	1	0	0	0	17787	942	33	4	1555	4	ZNF221	19	44471195	Missense_Mutation	SNP	G	TCGA-HE-A5NJ-01A-11D-A26P-10	3772914	44471195	14657788	68	12059											
SEPT5	5413	hgsc.bcm.edu	37	chr22	19709430	19709430	+	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	gacctcaaggacgtgacgtgCgacgtgcactacgagaacta	12	6	12	11	5	1	2	1	1	0	1	1	6	1	3	1	1	4	1	1	1	4	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr22:19709430C>T	ENST00000455784.2	+	10	1025	c.900C>T	c.(898-900)tgC>tgT	p.C300C	SEPT5_ENST00000438754.2_Nonsense_Mutation_p.R306*|GP1BB_ENST00000366425.3_5'Flank|SEPT5_ENST00000383045.3_Silent_p.C309C|SEPT5_ENST00000406395.1_Nonsense_Mutation_p.R297*	NM_002688.5	NP_002679.2	Q99719	SEPT5_HUMAN	septin 5	300	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)					ACGTGACGTGCGACGTGCACT	0.662																																					p.R306X		Atlas-SNP	.											SEPT5_ENST00000455784,caecum,carcinoma,0,1	SEPT5	32	.	0			c.C916T						PASS	.						58	52	54					22																	19709430		2203	4299	6502	SO:0001819	synonymous_variant	5413	exon9			GACGTGCGACGTG	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.900C>T	chr22.hg19:g.19709430C>T		67.0	0.0	.		119.0	43.0	.	NM_001009939	O15251|Q96MY5	Nonsense_Mutation	SNP	ENST00000455784.2	hg19	CCDS13764.1	.	.	.	.	.	.	.	.	.	.	C	35	5.483869	0.96307	.	.	ENSG00000184702	ENST00000406395;ENST00000438754	.	.	.	3.66	-2.26	0.06867	.	.	.	.	.	.	.	.	.	.	.	0.58432	A	0.999992	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	.	5.9818	0.19411	0.0:0.3259:0.1386:0.5355	.	.	.	.	X	297;306	.	ENSP00000384535:R297X	R	+	1	2	SEPT5	18089430	0.020000	0.18652	0.802000	0.32245	0.983000	0.72400	-0.876000	0.04201	-0.201000	0.10284	0.297000	0.19635	CGA	.	.	.	none		0.662	SEPT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317937.1	NM_002688		T	19709430	C	T	19709430	2	4	199	1	0	0	0	0	0	0	0	1	14080	776	27	1		1	SEPT5	22	19709430	Silent	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10		19709430	31595136	69	12060											
MTMR3	8897	hgsc.bcm.edu	37	chr22	30416249	30416249	+	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	caaggtcatcatagatcttgCcttgtaaatagtggcaagga	13	11	10	7	0	3	1	2	0	1	1	3	2	3	2	1	3	1	2	1	3	6	5			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chr22:30416249C>T	ENST00000401950.2	+	17	2943	c.2601C>T	c.(2599-2601)tgC>tgT	p.C867C	MTMR3_ENST00000351488.3_Silent_p.C867C|MTMR3_ENST00000406629.1_Silent_p.C867C|MTMR3_ENST00000323630.5_Silent_p.C731C|CTA-85E5.10_ENST00000429350.1_RNA|CTA-85E5.10_ENST00000453743.2_RNA|MTMR3_ENST00000333027.3_Silent_p.C867C	NM_021090.3	NP_066576.1	Q13615	MTMR3_HUMAN	myotubularin related protein 3	867					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)			ATAGATCTTGCCTTGTAAATA	0.512																																					p.C867C		Atlas-SNP	.											.	MTMR3	106	.	0			c.C2601T						PASS	.						69	65	66					22																	30416249		2203	4300	6503	SO:0001819	synonymous_variant	8897	exon17			ATCTTGCCTTGTA	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.2601C>T	chr22.hg19:g.30416249C>T		139.0	0.0	.		145.0	60.0	.	NM_153050	A5PL26|A7MD32|Q9NYN5|Q9NYN6|Q9UDX6|Q9UEG3	Silent	SNP	ENST00000401950.2	hg19	CCDS13870.1																																																																																			.	.	.	none		0.512	MTMR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322066.1	NM_021090		T	30416249	C	T	30416249	2	4	199	1	0	0	0	0	0	0	0	1	9952	747	26	2		2	MTMR3	22	30416249	Silent	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	10706819	30416249	20888317	70	12061											
POLA1	5422	hgsc.bcm.edu	37	chrX	24750526	24750526	+	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	tggtccatcacagttttgcaTtggataaagcagccccaaag	12	10	9	10	0	1	0	1	0	0	0	2	1	2	1	3	2	3	3	3	2	3	4			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chrX:24750526T>A	ENST00000379059.3	+	16	1723	c.1708T>A	c.(1708-1710)Ttg>Atg	p.L570M	POLA1_ENST00000493342.1_3'UTR|POLA1_ENST00000379068.3_Missense_Mutation_p.L576M	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	570					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)	CAGTTTTGCATTGGATAAAGC	0.398																																					p.L570M		Atlas-SNP	.											.	POLA1	117	.	0			c.T1708A						PASS	.						189	158	168					X																	24750526		2203	4300	6503	SO:0001583	missense	5422	exon16			TTTGCATTGGATA		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.1708T>A	chrX.hg19:g.24750526T>A	ENSP00000368349:p.Leu570Met	43.0	0.0	.		26.0	23.0	.	NM_016937	Q86UQ7	Missense_Mutation	SNP	ENST00000379059.3	hg19	CCDS14214.1	.	.	.	.	.	.	.	.	.	.	T	14.44	2.534808	0.45073	.	.	ENSG00000101868	ENST00000379068;ENST00000379059	T;T	0.45276	0.9;0.9	5.42	0.376	0.16193	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.268948	0.37483	N	0.002076	T	0.45357	0.1338	M	0.82323	2.585	0.33032	D	0.530339	B	0.32283	0.362	B	0.36244	0.22	T	0.54675	-0.8258	10	0.54805	T	0.06	-6.8741	9.4781	0.38884	0.0:0.4038:0.0:0.5962	.	570	P09884	DPOLA_HUMAN	M	576;570	ENSP00000368358:L576M;ENSP00000368349:L570M	ENSP00000368349:L570M	L	+	1	2	POLA1	24660447	0.321000	0.24625	0.054000	0.19295	0.938000	0.57974	0.682000	0.25335	-0.193000	0.10415	0.417000	0.27973	TTG	.	.	.	none		0.398	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937		A	24750526	T	A	24750526	3	1	199	1	0	0	0	0	1	0	0	0	12194	1490	52	5	1770	5	POLA1	23	24750526	Missense_Mutation	SNP	T	TCGA-HE-A5NJ-01A-11D-A26P-10		24750526	130520034	71	12062											
GATA1	2623	hgsc.bcm.edu	37	chrX	48652221	48652221	+	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	tgaaccggccactgaccatgCggaaggatggtattcagact	11	8	12	10	2	1	3	1	2	0	1	1	5	1	5	3	4	2	1	3	4	3	2			TCGA-HE-A5NJ-01A-11D-A26P-10	TCGA-HE-A5NJ-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a9dbd55c-5dcc-48db-8785-6baef3fdd7db	de0653ad-a848-4f4b-b675-6cb625cb5167	g.chrX:48652221C>T	ENST00000376670.3	+	6	1003	c.892C>T	c.(892-894)Cgg>Tgg	p.R298W	GATA1_ENST00000376665.3_Intron	NM_002049.3	NP_002040.1	P15976	GATA1_HUMAN	GATA binding protein 1 (globin transcription factor 1)	298					basophil differentiation (GO:0030221)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cellular response to thyroid hormone stimulus (GO:0097067)|dendritic cell differentiation (GO:0097028)|embryonic hemopoiesis (GO:0035162)|eosinophil differentiation (GO:0030222)|eosinophil fate commitment (GO:0035854)|erythrocyte development (GO:0048821)|erythrocyte differentiation (GO:0030218)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|megakaryocyte differentiation (GO:0030219)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of definitive erythrocyte differentiation (GO:0010724)|regulation of glycoprotein biosynthetic process (GO:0010559)|transcription from RNA polymerase II promoter (GO:0006366)|transcriptional activation by promoter-enhancer looping (GO:0071733)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	C2H2 zinc finger domain binding (GO:0070742)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(259)|large_intestine(8)|lung(9)|prostate(1)	283						ACTGACCATGCGGAAGGATGG	0.582			"Mis, F"		megakaryoblastic leukemia of Downs Syndrome																																p.R298W	Pancreas(9;429 505 11287 29617)	Atlas-SNP	.		Dom	yes		X	Xp11.23	2623	GATA binding protein 1 (globin transcription factor 1)		L	.	GATA1	342	.	0			c.C892T						PASS	.						21	20	21					X																	48652221		2203	4299	6502	SO:0001583	missense	2623	exon6			ACCATGCGGAAGG	X17254	CCDS14305.1	Xp11.23	2014-09-17	2001-11-28		ENSG00000102145	ENSG00000102145		"GATA zinc finger domain containing"	4170	protein-coding gene	gene with protein product	"nuclear factor, erythroid 1"	305371	"GATA-binding protein 1 (globin transcription factor 1)"	GF1		1999341	Standard	NM_002049		Approved	ERYF1, NFE1, GATA-1, NF-E1	uc004dkq.4	P15976	OTTHUMG00000021504	ENST00000376670.3:c.892C>T	chrX.hg19:g.48652221C>T	ENSP00000365858:p.Arg298Trp	73.0	0.0	.		75.0	4.0	.	NM_002049	Q96GB8	Missense_Mutation	SNP	ENST00000376670.3	hg19	CCDS14305.1	.	.	.	.	.	.	.	.	.	.	c	18.07	3.540683	0.65085	.	.	ENSG00000102145	ENST00000376670	D	0.99667	-6.34	4.21	-2.43	0.06522	Zinc finger, NHR/GATA-type (1);Zinc finger, GATA-type (2);	0.068357	0.56097	U	0.000034	D	0.99007	0.9661	L	0.28694	0.88	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.96825	0.9607	10	0.87932	D	0	-11.8489	14.9001	0.70672	0.8239:0.1761:0.0:0.0	.	298	P15976	GATA1_HUMAN	W	298	ENSP00000365858:R298W	ENSP00000365858:R298W	R	+	1	2	GATA1	48537165	0.693000	0.27728	0.976000	0.42696	0.976000	0.68499	-0.187000	0.09656	-1.041000	0.03266	0.365000	0.22127	CGG	.	.	.	none		0.582	GATA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056517.1	NM_002049		T	48652221	C	T	48652221	3	4	199	1	0	0	0	0	1	0	0	0	6260	759	27	1	910	1	GATA1	23	48652221	Missense_Mutation	SNP	C	TCGA-HE-A5NJ-01A-11D-A26P-10	23901695	48652221	106618339	72	12063											
FAM46B	115572	hgsc.bcm.edu	37	chr1	27332755	27332755	+	Missense_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	gtagcgctctagggtgcgccGctgctccaccaggtctggaa	6	8	14	13	3	2	0	0	0	2	0	3	1	3	1	3	3	3	4	3	3	3	2			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr1:27332755G>A	ENST00000289166.5	-	2	1123	c.958C>T	c.(958-960)Cgg>Tgg	p.R320W		NM_052943.3	NP_443175.2	Q96A09	FA46B_HUMAN	family with sequence similarity 46, member B	320										breast(1)|central_nervous_system(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;7.71e-51)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|STAD - Stomach adenocarcinoma(196;0.00114)|READ - Rectum adenocarcinoma(331;0.0419)		AGGGTGCGCCGCTGCTCCACC	0.682																																					p.R320W		Atlas-SNP	.											.	FAM46B	44	.	0			c.C958T						PASS	.						20	22	21					1																	27332755		2201	4298	6499	SO:0001583	missense	115572	exon2			TGCGCCGCTGCTC	AK122816	CCDS294.2	1p35.3	2008-02-05			ENSG00000158246	ENSG00000158246			28273	protein-coding gene	gene with protein product						12477932	Standard	NM_052943		Approved	MGC16491	uc010ofj.2	Q96A09	OTTHUMG00000004278	ENST00000289166.5:c.958C>T	chr1.hg19:g.27332755G>A	ENSP00000289166:p.Arg320Trp	89.0	0.0	.		89.0	4.0	.	NM_052943		Missense_Mutation	SNP	ENST00000289166.5	hg19	CCDS294.2	.	.	.	.	.	.	.	.	.	.	G	16.33	3.094188	0.56075	.	.	ENSG00000158246	ENST00000289166	T	0.25085	1.82	5.31	3.24	0.37175	Domain of unknown function DUF1693 (1);	0.379713	0.30584	N	0.009309	T	0.42131	0.1189	L	0.54323	1.7	0.37467	D	0.915445	D	0.57899	0.981	P	0.61070	0.883	T	0.53330	-0.8454	10	0.59425	D	0.04	-5.9287	15.2423	0.73480	0.0:0.0:0.7268:0.2732	.	320	Q96A09	FA46B_HUMAN	W	320	ENSP00000289166:R320W	ENSP00000289166:R320W	R	-	1	2	FAM46B	27205342	1.000000	0.71417	1.000000	0.80357	0.580000	0.36256	4.588000	0.60999	1.415000	0.47037	0.561000	0.74099	CGG	.	.	.	none		0.682	FAM46B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012347.2	NM_052943		A	27332755	G	A	27332755	3	1	200	1	0	0	0	0	1	0	0	0	5573	1086	38	1	323	1	FAM46B	1	27332755	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10		27332755	221917866	1	12064											
FUBP1	8880	hgsc.bcm.edu	37	chr1	78414969	78414969	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggaggagccccagtcggAgcaggaactgcctgaccttt	8	7	13	13	1	0	1	0	1	0	0	1	5	0	5	5	4	4	1	5	4	1	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr1:78414969A>G	ENST00000370768.2	-	19	1878	c.1797T>C	c.(1795-1797)gcT>gcC	p.A599A	FUBP1_ENST00000370767.1_Silent_p.A599A|FUBP1_ENST00000436586.2_Silent_p.A620A|FUBP1_ENST00000489495.1_5'Flank	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1	599					positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						CCCCAGTCGGAGCAGGAACTG	0.448			"F, N"		oligodendroglioma																																p.A599A		Atlas-SNP	.		Rec	yes		1	1p13.1	8880	far upstream element (FUSE) binding protein 1		O	.	FUBP1	112	.	0			c.T1797C						PASS	.						64	69	67					1																	78414969		2203	4300	6503	SO:0001819	synonymous_variant	8880	exon19			AGTCGGAGCAGGA	U05040	CCDS683.1	1p31.1	2008-02-05			ENSG00000162613	ENSG00000162613			4004	protein-coding gene	gene with protein product		603444		FUBP		8125259	Standard	XM_005271309		Approved	FBP	uc001dii.3	Q96AE4	OTTHUMG00000040799	ENST00000370768.2:c.1797T>C	chr1.hg19:g.78414969A>G		64.0	0.0	.		69.0	14.0	.	NM_003902	Q12828	Silent	SNP	ENST00000370768.2	hg19	CCDS683.1																																																																																			.	.	.	none		0.448	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902		G	78414969	A	G	78414969	2	3	200	1	0	0	0	0	0	0	0	1	6099	291	11	3		3	FUBP1	1	78414969	Silent	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	51082214	78414969	170835652	2	12065											
RBMXL1	494115	hgsc.bcm.edu	37	chr1	89449426	89449426	+	Frame_Shift_Del	DEL	A	A	-																															actattcgtccatatttgccAaatactgtttcaagagcttt																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr1:89449426delA	ENST00000321792.5	-	2	511	c.84delT	c.(82-84)tttfs	p.F28fs	CCBL2_ENST00000446900.2_Intron|RBMXL1_ENST00000413769.1_5'UTR|CCBL2_ENST00000370485.2_Intron|CCBL2_ENST00000260508.4_Intron|RBMXL1_ENST00000399794.2_Frame_Shift_Del_p.F28fs|CCBL2_ENST00000370491.3_Intron	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	28	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										CATATTTGCCAAATACTGTTT	0.413											OREG0013593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G29fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.85delG						PASS	.						191	187	188					1																	89449426		2203	4300	6503	SO:0001589	frameshift_variant	494115	exon2			.	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.84delT	chr1.hg19:g.89449426delA	ENSP00000318415:p.Phe28fs	522.0	0.0	0	1267	503.0	53.0	0.105368	NM_019610		Frame_Shift_Del	DEL	ENST00000321792.5	hg19	CCDS716.1																																																																																			.	.	.	none		0.413	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610		-	89449426	A	-	89449426	7	5	200	1	0	1	0	1	0	0	0	0	13166	127	5	0	1092	0	RBMXL1	1	89449426	Frame_Shift_Del	DEL	A	TCGA-HE-A5NK-01A-11D-A26P-10	11034457	89449426	159801195	3	12066											
LRRC8C	84230	hgsc.bcm.edu	37	chr1	90179188	90179188	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggaatattcctttgagtaTgtccgtcaggagactggaat	10	12	12	7	2	1	2	1	1	0	1	3	5	3	4	2	3	0	1	2	3	4	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr1:90179188T>C	ENST00000370454.4	+	3	1314	c.1059T>C	c.(1057-1059)taT>taC	p.Y353Y	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	353					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)		CCTTTGAGTATGTCCGTCAGG	0.388																																					p.Y353Y		Atlas-SNP	.											.	LRRC8C	73	.	0			c.T1059C						PASS	.						54	50	51					1																	90179188		2203	4299	6502	SO:0001819	synonymous_variant	84230	exon3			TGAGTATGTCCGT		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.1059T>C	chr1.hg19:g.90179188T>C		142.0	0.0	.		146.0	36.0	.	NM_032270	B3KXS9|Q29RV6|Q9H075	Silent	SNP	ENST00000370454.4	hg19	CCDS725.1																																																																																			.	.	.	none		0.388	LRRC8C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028435.2	NM_032270		C	90179188	T	C	90179188	2	2	200	1	0	0	0	0	0	0	0	1	9030	1471	51	3		3	LRRC8C	1	90179188	Silent	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	729762	90179188	159071433	4	12067											
IQGAP3	128239	hgsc.bcm.edu	37	chr1	156517916	156517917	+	Frame_Shift_Del	DEL	AG	AG	-																															ctcagaaagtgggaatgctcAgcaaacttctgccgaactag																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr1:156517916_156517917delAG	ENST00000361170.2	-	19	2262_2263	c.2252_2253delCT	c.(2251-2253)gctfs	p.A751fs		NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	751	IQ 1. {ECO:0000255|PROSITE- ProRule:PRU00116}.				activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GGGAATGCTCAGCAAACTTCTG	0.579																																					p.751_752del		Atlas-Indel,Pindel	.											.	IQGAP3	146	.	0			c.2253_2254del						PASS	.																																			SO:0001589	frameshift_variant	128239	exon19			.	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.2252_2253delCT	chr1.hg19:g.156517916_156517917delAG	ENSP00000354451:p.Ala751fs	101.0	0.0	0		131.0	33.0	0.251908	NM_178229	Q5T3H8	Frame_Shift_Del	DEL	ENST00000361170.2	hg19	CCDS1144.1																																																																																			.	.	.	none		0.579	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229		-	156517917	AG	-	156517916	7	5	200	1	0	1	0	1	0	0	0	0	7823	175	7	0	2722	0	IQGAP3	1	156517916	Frame_Shift_Del	DEL	AG	TCGA-HE-A5NK-01A-11D-A26P-10	66338728	156517916	92732705	5	12068											
SLC19A2	10560	hgsc.bcm.edu	37	chr1	169446750	169446750	+	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	actttctggtacatgcccagGtccaccacactgtagatata	11	11	7	12	0	1	1	0	0	1	1	2	1	2	1	3	2	2	2	3	2	4	5			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr1:169446750G>A	ENST00000236137.5	-	2	686	c.450C>T	c.(448-450)gaC>gaT	p.D150D	SLC19A2_ENST00000367804.4_Intron	NM_006996.2	NP_008927.1	O60779	S19A2_HUMAN	solute carrier family 19 (thiamine transporter), member 2	150					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)	ACATGCCCAGGTCCACCACAC	0.478																																					p.D150D		Atlas-SNP	.											.	SLC19A2	35	.	0			c.C450T						PASS	.						93	96	95					1																	169446750		2203	4300	6503	SO:0001819	synonymous_variant	10560	exon2			GCCCAGGTCCACC	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.450C>T	chr1.hg19:g.169446750G>A		179.0	0.0	.		176.0	52.0	.	NM_006996	B2R9H0|B4E1X4|Q8WV87|Q9UBL7|Q9UKJ2|Q9UN31|Q9UN43	Silent	SNP	ENST00000236137.5	hg19	CCDS1280.1																																																																																			.	.	.	none		0.478	SLC19A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086106.1	NM_006996		A	169446750	G	A	169446750	2	1	200	1	0	0	0	0	0	0	0	1	14442	1252	44	2		2	SLC19A2	1	169446750	Silent	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	12928834	169446750	79803871	6	12069											
CACNA1E	777	hgsc.bcm.edu	37	chr1	181701628	181701628	+	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	gccctcaacagagaggaggcGccgaccatgaacccgctcaa	12	3	11	15	3	2	2	2	1	0	1	2	5	2	3	4	2	2	1	4	2	3	0			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr1:181701628G>A	ENST00000367573.2	+	20	2406	c.2406G>A	c.(2404-2406)gcG>gcA	p.A802A	CACNA1E_ENST00000367570.1_Silent_p.A802A|CACNA1E_ENST00000367567.4_Silent_p.A409A|CACNA1E_ENST00000357570.5_Silent_p.A753A|CACNA1E_ENST00000526775.1_Silent_p.A783A|CACNA1E_ENST00000360108.3_Silent_p.A783A|CACNA1E_ENST00000358338.5_Silent_p.A734A	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	802					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						GAGAGGAGGCGCCGACCATGa	0.657																																					p.A802A		Atlas-SNP	.											.	CACNA1E	778	.	0			c.G2406A						PASS	.						39	57	51					1																	181701628		1759	3301	5060	SO:0001819	synonymous_variant	777	exon20			GGAGGCGCCGACC	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.2406G>A	chr1.hg19:g.181701628G>A		328.0	0.0	.		380.0	44.0	.	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	ENST00000367573.2	hg19	CCDS55664.1																																																																																			.	.	.	none		0.657	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		A	181701628	G	A	181701628	2	1	200	1	0	0	0	0	0	0	0	1	2544	1074	38	1		1	CACNA1E	1	181701628	Silent	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	12254878	181701628	67548993	7	12070											
CABC1	56997	hgsc.bcm.edu	37	chr1	227172964	227172964	+	Missense_Mutation	SNP	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	cctctccccagatcatcaggGctgctgccgacagggacagg	8	6	12	15	1	3	1	2	0	1	1	4	3	3	2	4	3	2	2	4	3	0	0			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr1:227172964G>A	ENST00000366779.1	+	19	4353	c.1582G>A	c.(1582-1584)Gct>Act	p.A528T	ADCK3_ENST00000366777.3_Missense_Mutation_p.A528T|ADCK3_ENST00000458507.2_Missense_Mutation_p.A249T|ADCK3_ENST00000433743.2_Missense_Mutation_p.A202T|ADCK3_ENST00000478406.1_3'UTR|ADCK3_ENST00000366778.1_Missense_Mutation_p.A476T			Q8NI60	ADCK3_HUMAN	aarF domain containing kinase 3	528					cell death (GO:0008219)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|kidney(2)|large_intestine(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	9						GATCATCAGGGCTGCTGCCGA	0.632																																					p.A528T		Atlas-SNP	.											.	ADCK3	77	.	0			c.G1582A						PASS	.						119	116	117					1																	227172964		2203	4300	6503	SO:0001583	missense	56997	exon14			ATCAGGGCTGCTG	AJ278126	CCDS1557.1	1q42.11	2011-05-03	2010-10-01	2010-10-01	ENSG00000163050	ENSG00000163050			16812	protein-coding gene	gene with protein product	"coenzyme Q8 homolog (yeast)"	606980	"chaperone-ABC1 (activity of bc1 complex, S.pombe)-like", "chaperone, ABC1 activity of bc1 complex like (S. pombe)", "chaperone, ABC1 activity of bc1 complex homolog (S. pombe)"	CABC1			Standard	NM_020247		Approved	COQ8, SCAR9	uc001hqn.1	Q8NI60	OTTHUMG00000037621	ENST00000366779.1:c.1582G>A	chr1.hg19:g.227172964G>A	ENSP00000355741:p.Ala528Thr	62.0	0.0	.		62.0	17.0	.	NM_020247	Q5T7A5|Q63HK0|Q8NCJ6|Q9HBQ1|Q9NQ67	Missense_Mutation	SNP	ENST00000366779.1	hg19	CCDS1557.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.998025	0.93227	.	.	ENSG00000163050	ENST00000366779;ENST00000366778;ENST00000366777;ENST00000366776;ENST00000458507;ENST00000366775;ENST00000405743;ENST00000433743	T;T;T;T;T;T;T	0.61510	0.1;0.1;0.1;0.1;0.1;0.1;0.1	5.69	5.69	0.88448	.	0.105243	0.64402	D	0.000005	D	0.82554	0.5062	H	0.94847	3.59	0.58432	D	0.999995	D;D	0.64830	0.982;0.994	P;D	0.63033	0.796;0.91	D	0.87070	0.2159	10	0.87932	D	0	-11.9896	19.815	0.96564	0.0:0.0:1.0:0.0	.	202;528	E7EVZ8;Q8NI60	.;ADCK3_HUMAN	T	528;476;528;453;249;373;479;202	ENSP00000355741:A528T;ENSP00000355740:A476T;ENSP00000355739:A528T;ENSP00000355738:A453T;ENSP00000403704:A249T;ENSP00000355737:A373T;ENSP00000404550:A202T	ENSP00000355737:A373T	A	+	1	0	ADCK3	225239587	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	3.953000	0.56699	2.681000	0.91329	0.561000	0.74099	GCT	.	.	.	none		0.632	ADCK3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091712.1	NM_020247		A	227172964	G	A	227172964	3	1	200	1	0	0	0	0	1	0	0	0	2529	1203	42	2	1632	2	CABC1	1	227172964	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	45471336	227172964	22077657	8	12071											
FMN2	56776	hgsc.bcm.edu	37	chr1	240370577	240370577	+	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	ccttctgtggtctgctgggcAaggacagcctgggtcacagc	6	9	14	12	0	3	0	1	0	2	0	3	1	3	1	2	4	3	2	2	4	1	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr1:240370577A>T	ENST00000319653.9	+	5	2695	c.2465A>T	c.(2464-2466)cAa>cTa	p.Q822L		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	822	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)			TCTGCTGGGCAAGGACAGCCT	0.537																																					p.Q822L		Atlas-SNP	.											.	FMN2	451	.	0			c.A2465T						PASS	.						74	71	72					1																	240370577		2203	4300	6503	SO:0001583	missense	56776	exon5			CTGGGCAAGGACA	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.2465A>T	chr1.hg19:g.240370577A>T	ENSP00000318884:p.Gln822Leu	128.0	0.0	.		121.0	32.0	.	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	hg19	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	A	7.760	0.705185	0.15172	.	.	ENSG00000155816	ENST00000319653	T	0.31510	1.49	4.09	4.09	0.47781	Actin-binding FH2/DRF autoregulatory (1);	0.425372	0.19864	N	0.104352	T	0.30823	0.0777	L	0.57536	1.79	0.80722	D	1	B	0.30482	0.281	B	0.32533	0.147	T	0.07849	-1.0751	9	.	.	.	.	12.1017	0.53788	1.0:0.0:0.0:0.0	.	822	Q9NZ56	FMN2_HUMAN	L	822	ENSP00000318884:Q822L	.	Q	+	2	0	FMN2	238437200	0.247000	0.23920	0.447000	0.26932	0.071000	0.16799	1.728000	0.38105	1.842000	0.53543	0.454000	0.30748	CAA	.	.	.	none		0.537	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		T	240370577	A	T	240370577	3	4	200	1	0	0	0	0	1	0	0	0	5957	130	5	5	2483	5	FMN2	1	240370577	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	13197613	240370577	8880044	9	12072											
ABCB6	10058	hgsc.bcm.edu	37	chr2	220075010	220075010	+	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	gatctggtcagcattgaccaCagttgagagcctgagaagtc	11	9	12	9	0	2	3	1	3	1	2	3	6	2	3	2	1	2	2	2	1	1	2			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr2:220075010C>A	ENST00000265316.3	-	18	2678	c.2362G>T	c.(2362-2364)Gtg>Ttg	p.V788L	ABCB6_ENST00000439002.2_Missense_Mutation_p.V742L	NM_005689.2	NP_005680.1	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 6 (Langereis blood group)	788	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				brain development (GO:0007420)|cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|porphyrin-containing compound biosynthetic process (GO:0006779)|skin development (GO:0043588)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial envelope (GO:0005740)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|efflux transmembrane transporter activity (GO:0015562)|heme binding (GO:0020037)|heme transporter activity (GO:0015232)|heme-transporting ATPase activity (GO:0015439)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	34		Renal(207;0.0474)		Epithelial(149;1.22e-06)|all cancers(144;0.000201)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCATTGACCACAGTTGAGAGC	0.547																																					p.V788L		Atlas-SNP	.											.	ABCB6	76	.	0			c.G2362T						PASS	.						96	92	93					2																	220075010		2203	4300	6503	SO:0001583	missense	10058	exon18			TGACCACAGTTGA	AF070598	CCDS2436.1	2q36	2014-08-27	2014-08-27		ENSG00000115657	ENSG00000115657		"ATP binding cassette transporters / subfamily B"	47	protein-coding gene	gene with protein product	"ATP-binding cassette half-transporter"	605452	"ATP-binding cassette, sub-family B (MDR/TAP), member 6"			8894702, 9110174	Standard	NM_005689		Approved	EST45597, umat, MTABC3	uc002vkc.2	Q9NP58	OTTHUMG00000133131	ENST00000265316.3:c.2362G>T	chr2.hg19:g.220075010C>A	ENSP00000265316:p.Val788Leu	122.0	0.0	.		175.0	28.0	.	NM_005689	O75542|Q49A66|Q59GQ5|Q6ZME6|Q96ME8|Q9HAQ6|Q9HAQ7	Missense_Mutation	SNP	ENST00000265316.3	hg19	CCDS2436.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.954783	0.73902	.	.	ENSG00000115657	ENST00000265316;ENST00000439002	D;D	0.85088	-1.94;-1.94	4.83	4.83	0.62350	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.060728	0.64402	D	0.000004	T	0.76054	0.3934	N	0.04805	-0.155	0.80722	D	1	P;P	0.43431	0.807;0.707	B;B	0.43575	0.424;0.204	T	0.82082	-0.0633	10	0.72032	D	0.01	-19.1858	18.0957	0.89489	0.0:1.0:0.0:0.0	.	742;788	Q9NP58-4;Q9NP58	.;ABCB6_HUMAN	L	788;742	ENSP00000265316:V788L;ENSP00000394333:V742L	ENSP00000265316:V788L	V	-	1	0	ABCB6	219783254	1.000000	0.71417	0.976000	0.42696	0.995000	0.86356	2.882000	0.48546	2.673000	0.90976	0.650000	0.86243	GTG	.	.	.	none		0.547	ABCB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256820.2	NM_005689		A	220075010	C	A	220075010	3	1	200	1	0	0	0	0	1	0	0	0	45	478	17	4	174	4	ABCB6	2	220075010	Missense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10		220075010	23124363	10	12073											
TMEM43	79188	hgsc.bcm.edu	37	chr3	14183165	14183165	+	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	tgccttctgtgtggccacctCgctgaccctgctgaccgtgg	3	11	12	15	2	1	2	0	2	1	0	2	2	1	2	5	2	2	2	5	2	0	1	rs63750743		TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr3:14183165C>T	ENST00000306077.4	+	12	1327	c.1073C>T	c.(1072-1074)tCg>tTg	p.S358L	RP11-434D12.1_ENST00000601399.1_Intron|RP11-434D12.1_ENST00000608606.1_Intron	NM_024334.2	NP_077310.1	Q9BTV4	TMM43_HUMAN	transmembrane protein 43	358			S -> L (in ARVD5). {ECO:0000269|PubMed:18313022}.		nuclear membrane organization (GO:0071763)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|cervix(3)|endometrium(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(2)	19						GTGGCCACCTCGCTGACCCTG	0.602																																					p.S358L		Atlas-SNP	.											.	TMEM43	33	.	0			c.C1073T	GRCh37	CM081452	TMEM43	M	rs63750743	PASS	.						135	110	119					3																	14183165		2203	4300	6503	SO:0001583	missense	79188	exon12			CCACCTCGCTGAC	BC008054	CCDS2618.1	3p25.1	2014-09-17			ENSG00000170876	ENSG00000170876			28472	protein-coding gene	gene with protein product		612048	"arrhythmogenic right ventricular dysplasia 5"	ARVD5		11230166, 18313022	Standard	NM_024334		Approved	MGC3222, DKFZp586G1919, LUMA	uc003byk.2	Q9BTV4	OTTHUMG00000129802	ENST00000306077.4:c.1073C>T	chr3.hg19:g.14183165C>T	ENSP00000303992:p.Ser358Leu	135.0	0.0	.		155.0	14.0	.	NM_024334	Q7L4N5|Q8NC30|Q96A63|Q96F19|Q96JX0|Q9H076	Missense_Mutation	SNP	ENST00000306077.4	hg19	CCDS2618.1	.	.	.	.	.	.	.	.	.	.	C	35	5.493272	0.96339	.	.	ENSG00000170876	ENST00000306077	T	0.35973	1.28	5.71	5.71	0.89125	.	0.066812	0.64402	D	0.000008	T	0.58293	0.2112	L	0.57536	1.79	0.80722	A	1	D	0.89917	1.0	D	0.69142	0.962	T	0.55711	-0.8098	9	0.52906	T	0.07	-15.2636	19.8516	0.96743	0.0:1.0:0.0:0.0	rs63750743	358	Q9BTV4	TMM43_HUMAN	L	358	ENSP00000303992:S358L	ENSP00000303992:S358L	S	+	2	0	TMEM43	14158166	1.000000	0.71417	0.940000	0.37924	0.911000	0.54048	7.205000	0.77881	2.685000	0.91497	0.585000	0.79938	TCG	.	.	.	weak		0.602	TMEM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252030.2	NM_024334		T	14183165	C	T	14183165	3	4	200	1	0	0	0	0	1	0	0	0	16179	893	31	1	1119	1	TMEM43	3	14183165	Missense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10		14183165	183839265	11	12074											
SMARCC1	6599	hgsc.bcm.edu	37	chr3	47718172	47718172	+	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	agagggggtatcagctaataCattaaaatgaggagtaggag	16	8	14	3	0	1	2	1	1	0	1	1	4	1	4	0	4	2	3	0	4	6	5			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr3:47718172C>A	ENST00000254480.5	-	17	1791	c.1672G>T	c.(1672-1674)Gta>Tta	p.V558L	SMARCC1_ENST00000425518.1_5'UTR	NM_003074.3	NP_003065.3	Q92922	SMRC1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	558					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|insulin receptor signaling pathway (GO:0008286)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(15)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)		TCAGCTAATACATTAAAATGA	0.463																																					p.V558L		Atlas-SNP	.											.	SMARCC1	85	.	0			c.G1672T						PASS	.						73	70	71					3																	47718172		2203	4300	6503	SO:0001583	missense	6599	exon17			CTAATACATTAAA	U66615	CCDS2758.1	3p21.31	2008-05-15			ENSG00000173473	ENSG00000173473			11104	protein-coding gene	gene with protein product		601732				8804307	Standard	NM_003074		Approved	BAF155, SRG3, Rsc8, CRACC1	uc003crq.2	Q92922	OTTHUMG00000133519	ENST00000254480.5:c.1672G>T	chr3.hg19:g.47718172C>A	ENSP00000254480:p.Val558Leu	112.0	0.0	.		131.0	19.0	.	NM_003074	Q17RS0|Q6P172|Q8IWH2	Missense_Mutation	SNP	ENST00000254480.5	hg19	CCDS2758.1	.	.	.	.	.	.	.	.	.	.	C	35	5.457122	0.96223	.	.	ENSG00000173473	ENST00000254480	T	0.55760	0.5	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.77294	0.4109	M	0.85099	2.735	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.78959	-0.1998	10	0.87932	D	0	-21.3909	19.4236	0.94732	0.0:1.0:0.0:0.0	.	558	Q92922	SMRC1_HUMAN	L	558	ENSP00000254480:V558L	ENSP00000254480:V558L	V	-	1	0	SMARCC1	47693176	1.000000	0.71417	0.995000	0.50966	0.958000	0.62258	7.580000	0.82523	2.937000	0.99478	0.650000	0.86243	GTA	.	.	.	none		0.463	SMARCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257491.1			A	47718172	C	A	47718172	3	1	200	1	0	0	0	0	1	0	0	0	14788	478	17	4	1693	4	SMARCC1	3	47718172	Missense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	33535007	47718172	150304258	12	12075											
APEH	327	hgsc.bcm.edu	37	chr3	49718019	49718019	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcacaattgaccaggaccTcatggtggcacagttttcca	10	10	9	12	0	2	1	2	1	0	0	3	2	3	2	3	3	0	3	3	3	1	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr3:49718019T>C	ENST00000296456.5	+	14	1656	c.1256T>C	c.(1255-1257)cTc>cCc	p.L419P	APEH_ENST00000438011.1_Missense_Mutation_p.L419P	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase	419					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)		GACCAGGACCTCATGGTGGCA	0.572																																					p.L419P		Atlas-SNP	.											.	APEH	45	.	0			c.T1256C						PASS	.						136	107	117					3																	49718019		2203	4300	6503	SO:0001583	missense	327	exon14			AGGACCTCATGGT	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.1256T>C	chr3.hg19:g.49718019T>C	ENSP00000296456:p.Leu419Pro	175.0	0.0	.		269.0	67.0	.	NM_001640	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	hg19	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.573571	0.86542	.	.	ENSG00000164062	ENST00000296456;ENST00000438011	T;T	0.39787	1.06;1.06	5.44	5.44	0.79542	Peptidase S9A/B/C, oligopeptidase, N-terminal beta-propeller (1);	0.000000	0.85682	D	0.000000	T	0.59074	0.2167	M	0.66939	2.045	0.80722	D	1	D;D	0.64830	0.994;0.994	P;P	0.61201	0.885;0.885	T	0.58228	-0.7673	10	0.36615	T	0.2	-28.7761	15.1365	0.72572	0.0:0.0:0.0:1.0	.	419;419	C9JIF9;P13798	.;ACPH_HUMAN	P	419	ENSP00000296456:L419P;ENSP00000415862:L419P	ENSP00000296456:L419P	L	+	2	0	APEH	49693023	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.147000	0.77382	2.056000	0.61249	0.459000	0.35465	CTC	.	.	.	none		0.572	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			C	49718019	T	C	49718019	3	2	200	1	0	0	0	0	1	0	0	0	768	1551	54	3	1310	3	APEH	3	49718019	Missense_Mutation	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	1999847	49718019	148304411	13	12076											
CACNA1D	776	hgsc.bcm.edu	37	chr3	53844325	53844325	+	Splice_Site	DEL	A	A	-																															gcggacagcttggtggaggcAgtgagtacggttcttggccg																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr3:53844325delA	ENST00000350061.5	+	47	6703	c.6192delA	c.(6190-6192)gca>gc	p.A2064fs	CACNA1D_ENST00000288139.4_Splice_Site_p.A2084fs|CACNA1D_ENST00000544977.1_3'UTR|CACNA1D_ENST00000422281.2_Splice_Site_p.A2040fs	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	2064					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)			breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TGGTGGAGGCAGTGAGTACGG	0.612																																					p.A2084fs		Atlas-Indel,Pindel	.											.	CACNA1D	324	.	0			c.6251delC						PASS	.						53	60	57					3																	53844325		2203	4300	6503	SO:0001630	splice_region_variant	776	exon48			.	AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"Calcium channel subunits", "Voltage-gated ion channels / Calcium channels"	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.6192+1A>-	chr3.hg19:g.53844325delA		376.0	0.0	0		472.0	86.0	0.182203	NM_000720	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Frame_Shift_Del	DEL	ENST00000350061.5	hg19	CCDS46848.1																																																																																			.	.	.	none		0.612	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720	Frame_Shift_Del	-	53844325	A	-	53844325	8	5	200	1	0	1	0	1	0	0	1	0	2543	202	7	0	6550	0	CACNA1D	3	53844325	Splice_Site	DEL	A	TCGA-HE-A5NK-01A-11D-A26P-10	4126306	53844325	144178105	14	12077											
SLC15A2	6565	hgsc.bcm.edu	37	chr3	121649781	121649781	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atggtgtgtctgcttatagaActgtgcaaagaggagagtaa	13	11	13	4	0	1	3	0	0	1	3	1	4	1	3	0	2	3	3	0	2	5	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr3:121649781A>G	ENST00000489711.1	+	18	2036	c.1648A>G	c.(1648-1650)Act>Gct	p.T550A	SLC15A2_ENST00000465060.1_3'UTR|SLC15A2_ENST00000295605.2_Missense_Mutation_p.T519A	NM_021082.3	NP_066568.3	Q16348	S15A2_HUMAN	solute carrier family 15 (oligopeptide transporter), member 2	550					drug transport (GO:0015893)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|dipeptide transporter activity (GO:0042936)|high-affinity oligopeptide transporter activity (GO:0015334)|peptide:proton symporter activity (GO:0015333)			NS(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(17)|skin(6)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(114;0.0967)	Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Fosinopril(DB00492)|Glyburide(DB01016)|Moexipril(DB00691)|Nateglinide(DB00731)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Tranexamic Acid(DB00302)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	TGCTTATAGAACTGTGCAAAG	0.388																																					p.T550A		Atlas-SNP	.											.	SLC15A2	92	.	0			c.A1648G						PASS	.						196	183	187					3																	121649781		2203	4300	6503	SO:0001583	missense	6565	exon18			TATAGAACTGTGC	BC044572	CCDS3007.1, CCDS54631.1	3q21.1	2013-07-18	2013-07-18		ENSG00000163406	ENSG00000163406		"Solute carriers"	10921	protein-coding gene	gene with protein product		602339	"solute carrier family 15 (H+/peptide transporter), member 2"			7756356	Standard	NM_021082		Approved	PEPT2	uc003eep.2	Q16348	OTTHUMG00000159423	ENST00000489711.1:c.1648A>G	chr3.hg19:g.121649781A>G	ENSP00000417085:p.Thr550Ala	157.0	0.0	.		199.0	31.0	.	NM_021082	A8K1A5|B4E2A7	Missense_Mutation	SNP	ENST00000489711.1	hg19	CCDS3007.1	.	.	.	.	.	.	.	.	.	.	A	0.388	-0.925105	0.02377	.	.	ENSG00000163406	ENST00000489711;ENST00000542599;ENST00000295605	T;T	0.02656	4.5;4.21	5.42	1.6	0.23607	.	0.546824	0.20900	N	0.083650	T	0.02156	0.0067	L	0.45228	1.405	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.49051	-0.8979	10	0.08599	T	0.76	-1.3387	3.1896	0.06613	0.5309:0.0:0.1062:0.3628	.	519;550	B4E2A7;Q16348	.;S15A2_HUMAN	A	550;512;519	ENSP00000417085:T550A;ENSP00000295605:T519A	ENSP00000295605:T519A	T	+	1	0	SLC15A2	123132471	0.000000	0.05858	0.036000	0.18154	0.509000	0.34042	0.828000	0.27435	0.109000	0.17891	0.528000	0.53228	ACT	.	.	.	none		0.388	SLC15A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355239.1	NM_021082		G	121649781	A	G	121649781	3	3	200	1	0	0	0	0	1	0	0	0	14412	43	2	3	1718	3	SLC15A2	3	121649781	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	67805456	121649781	76372649	15	12078											
HEG1	57493	hgsc.bcm.edu	37	chr3	124748131	124748131	+	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	ttgttctacttgaagagccgCtccttcctctagcatctgct	6	15	7	13	1	3	2	0	1	3	1	5	2	5	2	3	0	4	4	3	0	3	6			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr3:124748131C>T	ENST00000311127.4	-	2	585	c.518G>A	c.(517-519)aGc>aAc	p.S173N		NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	173					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						TGAAGAGCCGCTCCTTCCTCT	0.512																																					p.S173N		Atlas-SNP	.											.	HEG1	109	.	0			c.G518A						PASS	.						92	89	90					3																	124748131		1958	4173	6131	SO:0001583	missense	57493	exon2			GAGCCGCTCCTTC	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.518G>A	chr3.hg19:g.124748131C>T	ENSP00000311502:p.Ser173Asn	195.0	0.0	.		241.0	56.0	.	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	hg19	CCDS46898.1	.	.	.	.	.	.	.	.	.	.	C	0.917	-0.717219	0.03182	.	.	ENSG00000173706	ENST00000311127	T	0.44482	0.92	5.38	-10.8	0.00216	.	.	.	.	.	T	0.09158	0.0226	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	0.13361	-1.0512	9	0.02654	T	1	.	5.997	0.19499	0.0926:0.2061:0.5365:0.1648	.	173;173	Q9ULI3-2;Q9ULI3	.;HEG1_HUMAN	N	173	ENSP00000311502:S173N	ENSP00000311502:S173N	S	-	2	0	HEG1	126230821	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.000000	0.03693	-1.869000	0.01141	-1.298000	0.01336	AGC	.	.	.	none		0.512	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386		T	124748131	C	T	124748131	3	4	200	1	0	0	0	0	1	0	0	0	7051	797	28	2	3691	2	HEG1	3	124748131	Missense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	3098350	124748131	73274299	16	12079											
COL6A5	256076	hgsc.bcm.edu	37	chr3	130095526	130095526	+	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	tctccgtgggggtgcagaaaGcttctgaggaaaatctgaag	11	9	14	7	1	3	3	0	2	3	1	4	4	3	4	1	3	2	2	1	3	4	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr3:130095526G>T	ENST00000432398.2	+	3	1008	c.514G>T	c.(514-516)Gct>Tct	p.A172S	COL6A5_ENST00000265379.6_Missense_Mutation_p.A172S	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	172	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						GGTGCAGAAAGCTTCTGAGGA	0.502																																					p.A172S		Atlas-SNP	.											.	COL6A5	205	.	0			c.G514T						PASS	.						81	81	81					3																	130095526		692	1591	2283	SO:0001583	missense	256076	exon3			CAGAAAGCTTCTG	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.514G>T	chr3.hg19:g.130095526G>T	ENSP00000390895:p.Ala172Ser	108.0	0.0	.		155.0	20.0	.	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	hg19		.	.	.	.	.	.	.	.	.	.	G	6.971	0.549091	0.13312	.	.	ENSG00000172752	ENST00000432398;ENST00000265379	T;T	0.80214	-1.35;-1.35	5.14	3.34	0.38264	.	.	.	.	.	T	0.80989	0.4730	M	0.72479	2.2	0.09310	N	0.99999	P	0.38582	0.638	P	0.45577	0.486	T	0.69379	-0.5161	9	0.38643	T	0.18	.	6.3024	0.21119	0.1591:0.0:0.6941:0.1469	.	172	A8TX70-2	.	S	172	ENSP00000390895:A172S;ENSP00000265379:A172S	ENSP00000265379:A172S	A	+	1	0	COL6A5	131578216	0.445000	0.25657	0.010000	0.14722	0.017000	0.09413	2.715000	0.47210	0.671000	0.31185	-0.259000	0.10710	GCT	.	.	.	none		0.502	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		T	130095526	G	T	130095526	3	4	200	1	0	0	0	0	1	0	0	0	3704	971	34	4	520	4	COL6A5	3	130095526	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	5347395	130095526	67926904	17	12080											
KLHL24	54800	hgsc.bcm.edu	37	chr3	183381404	183381404	+	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	atcagagtatgcagtctgtgCtctaaggaatgacattcttg	11	13	10	7	0	4	2	1	1	3	1	4	3	4	3	0	1	2	3	0	1	3	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr3:183381404C>A	ENST00000454652.2	+	5	1465	c.1079C>A	c.(1078-1080)gCt>gAt	p.A360D	KLHL24_ENST00000476808.1_Missense_Mutation_p.A360D|KLHL24_ENST00000242810.6_Missense_Mutation_p.A360D	NM_017644.3	NP_060114.2	Q6TFL4	KLH24_HUMAN	kelch-like family member 24	360						cell projection (GO:0042995)|cytoplasm (GO:0005737)				NS(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(10)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;2.88e-10)|Ovarian(172;0.0303)		all cancers(12;1.43e-42)|Epithelial(37;1.73e-36)|OV - Ovarian serous cystadenocarcinoma(80;8.75e-22)			GCAGTCTGTGCTCTAAGGAAT	0.353																																					p.A360D		Atlas-SNP	.											.	KLHL24	56	.	0			c.C1079A						PASS	.						104	99	101					3																	183381404		2203	4300	6503	SO:0001583	missense	54800	exon4			TCTGTGCTCTAAG		CCDS3246.1	3q27.1	2013-02-22	2013-02-22		ENSG00000114796	ENSG00000114796		"Kelch-like", "BTB/POZ domain containing"	25947	protein-coding gene	gene with protein product		611295	"kelch-like 24 (Drosophila)"				Standard	XM_005247552		Approved	DRE1, FLJ20059	uc003flv.3	Q6TFL4	OTTHUMG00000156911	ENST00000454652.2:c.1079C>A	chr3.hg19:g.183381404C>A	ENSP00000395012:p.Ala360Asp	84.0	0.0	.		107.0	11.0	.	NM_017644	A5PLN8|Q9H620|Q9NXT9	Missense_Mutation	SNP	ENST00000454652.2	hg19	CCDS3246.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.086083	0.76642	.	.	ENSG00000114796	ENST00000242810;ENST00000454652;ENST00000476808	T;T;T	0.79352	-1.26;-1.26;-1.26	5.34	5.34	0.76211	Galactose oxidase, beta-propeller (1);	0.047926	0.85682	D	0.000000	D	0.85048	0.5608	M	0.80847	2.515	0.80722	D	1	B;B	0.30146	0.131;0.27	B;B	0.42593	0.04;0.392	D	0.84947	0.0869	10	0.66056	D	0.02	.	19.4149	0.94690	0.0:1.0:0.0:0.0	.	360;360	Q6TFL4-2;Q6TFL4	.;KLH24_HUMAN	D	360	ENSP00000242810:A360D;ENSP00000395012:A360D;ENSP00000419010:A360D	ENSP00000242810:A360D	A	+	2	0	KLHL24	184864098	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	7.445000	0.80570	2.675000	0.91044	0.462000	0.41574	GCT	.	.	.	none		0.353	KLHL24-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346586.2	NM_017644		A	183381404	C	A	183381404	3	1	200	1	0	0	0	0	1	0	0	0	8386	797	28	4	1085	4	KLHL24	3	183381404	Missense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	53285878	183381404	14641026	18	12081											
YEATS2	55689	hgsc.bcm.edu	37	chr3	183476664	183476664	+	Frame_Shift_Del	DEL	A	A	-																															tatcaggaagtcctacaaacAagatctccacggcttctcag																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr3:183476664delA	ENST00000305135.5	+	13	1762	c.1567delA	c.(1567-1569)aagfs	p.K523fs		NM_018023.4	NP_060493.3	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	523					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686)	TBP-class protein binding (GO:0017025)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			TCCTACAAACAAGATCTCCAC	0.373																																					p.N522fs		Atlas-Indel,Pindel	.											.	YEATS2	111	.	0			c.1566delC						PASS	.						138	126	129					3																	183476664		1834	4080	5914	SO:0001589	frameshift_variant	55689	exon13			.	AB033023	CCDS43175.1	3q27.3	2004-08-18			ENSG00000163872	ENSG00000163872			25489	protein-coding gene	gene with protein product		613373				10574462	Standard	NM_018023		Approved	FLJ10201, FLJ12841, FLJ13308, KIAA1197	uc003fly.2	Q9ULM3	OTTHUMG00000156898	ENST00000305135.5:c.1567delA	chr3.hg19:g.183476664delA	ENSP00000306983:p.Lys523fs	339.0	0.0	0		383.0	55.0	0.143603	NM_018023	A7E2B9|D3DNS9|Q641P6|Q9NW96	Frame_Shift_Del	DEL	ENST00000305135.5	hg19	CCDS43175.1																																																																																			.	.	.	none		0.373	YEATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346507.2	NM_018023		-	183476664	A	-	183476664	7	5	200	1	0	1	0	1	0	0	0	0	17484	131	5	0	1613	0	YEATS2	3	183476664	Frame_Shift_Del	DEL	A	TCGA-HE-A5NK-01A-11D-A26P-10	95260	183476664	14545766	19	12082											
CNGA1	1259	hgsc.bcm.edu	37	chr4	47938977	47938977	+	Frame_Shift_Del	DEL	T	T	-																															aatgtacatctctcgtccgaTatcccctttcttgcaaatat																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr4:47938977delT	ENST00000514170.1	-	11	1853	c.1534delA	c.(1534-1536)atcfs	p.I512fs	CNGA1_ENST00000544810.1_Frame_Shift_Del_p.I512fs|CNGA1_ENST00000402813.3_Frame_Shift_Del_p.I581fs|CNGA1_ENST00000358519.4_Frame_Shift_Del_p.I512fs|CNGA1_ENST00000420489.2_Frame_Shift_Del_p.I512fs			P29973	CNGA1_HUMAN	cyclic nucleotide gated channel alpha 1	512					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|urinary_tract(1)	28						TCTCGTCCGATATCCCCTTTC	0.463																																					p.I581fs		Atlas-Indel,Pindel	.											.	CNGA1	74	.	0			c.1742delT						PASS	.						111	112	111					4																	47938977		2138	4277	6415	SO:0001589	frameshift_variant	1259	exon10			.	M84741	CCDS43226.1, CCDS47050.1	4p12	2013-02-14				ENSG00000198515		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	2148	protein-coding gene	gene with protein product		123825		CNCG1, CNCG		7683629, 16382102	Standard	NM_000087		Approved	RCNC1, RCNCa, CNG1, RP49	uc003gxu.3	P29973		ENST00000514170.1:c.1534delA	chr4.hg19:g.47938977delT	ENSP00000426862:p.Ile512fs	189.0	0.0	0		176.0	29.0	0.164773	NM_001142564	A8K7K6|J3KPZ2|Q16279|Q16485|Q4W5E3	Frame_Shift_Del	DEL	ENST00000514170.1	hg19	CCDS43226.1																																																																																			.	.	.	none		0.463	CNGA1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372070.2	NM_000087		-	47938977	T	-	47938977	7	5	200	1	0	1	0	1	0	0	0	0	3598	1406	49	0	542	0	CNGA1	4	47938977	Frame_Shift_Del	DEL	T	TCGA-HE-A5NK-01A-11D-A26P-10		47938977	143215299	20	12083											
WDFY3	23001	hgsc.bcm.edu	37	chr4	85716095	85716095	+	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	tgtgacggtattatttgtagGagcattatgaggggccaaac	11	12	13	5	1	0	2	0	2	0	0	0	3	0	3	1	4	2	3	1	4	5	5			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr4:85716095G>T	ENST00000295888.4	-	20	3612	c.3205C>A	c.(3205-3207)Cct>Act	p.P1069T	WDFY3_ENST00000322366.6_Missense_Mutation_p.P1069T	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	1069					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)		TTATTTGTAGGAGCATTATGA	0.378																																					p.P1069T		Atlas-SNP	.											.	WDFY3	314	.	0			c.C3205A						PASS	.						72	69	70					4																	85716095		2203	4300	6503	SO:0001583	missense	23001	exon20			TTGTAGGAGCATT	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.3205C>A	chr4.hg19:g.85716095G>T	ENSP00000295888:p.Pro1069Thr	357.0	0.0	.		404.0	105.0	.	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	hg19	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	G	3.505	-0.100986	0.06967	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.40476	1.03;1.03	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.30417	0.0764	N	0.24115	0.695	0.80722	D	1	B	0.12013	0.005	B	0.11329	0.006	T	0.14643	-1.0465	10	0.07325	T	0.83	.	19.6264	0.95679	0.0:0.0:1.0:0.0	.	1069	Q8IZQ1	WDFY3_HUMAN	T	1069	ENSP00000318466:P1069T;ENSP00000295888:P1069T	ENSP00000295888:P1069T	P	-	1	0	WDFY3	85935119	1.000000	0.71417	0.996000	0.52242	0.219000	0.24729	7.424000	0.80242	2.717000	0.92951	0.655000	0.94253	CCT	.	.	.	none		0.378	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		T	85716095	G	T	85716095	3	4	200	1	0	0	0	0	1	0	0	0	17282	1174	41	4	7571	4	WDFY3	4	85716095	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	37777118	85716095	105438181	21	12084											
C4orf37	285555	hgsc.bcm.edu	37	chr4	98893529	98893529	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgcacttttcttctgtttctTtgagcagatatttctaacac	8	19	5	9	0	4	2	0	1	4	1	4	2	4	2	0	0	3	3	0	0	2	8			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr4:98893529T>C	ENST00000295268.3	-	7	924	c.835A>G	c.(835-837)Aag>Gag	p.K279E		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	279			K -> R (in dbSNP:rs7654193).														TTCTGTTTCTTTGAGCAGATA	0.358																																					p.K279E		Atlas-SNP	.											.	.	.	.	0			c.A835G						PASS	.						71	71	71					4																	98893529		2203	4300	6503	SO:0001583	missense	285555	exon7			GTTTCTTTGAGCA	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.835A>G	chr4.hg19:g.98893529T>C	ENSP00000295268:p.Lys279Glu	248.0	0.0	.		220.0	41.0	.	NM_174952		Missense_Mutation	SNP	ENST00000295268.3	hg19	CCDS3645.1	.	.	.	.	.	.	.	.	.	.	T	0.011	-1.723977	0.00694	.	.	ENSG00000163116	ENST00000295268	T	0.11604	2.76	5.45	1.74	0.24563	.	0.432965	0.22937	N	0.053831	T	0.06005	0.0156	L	0.27053	0.805	0.09310	N	1	B	0.11235	0.004	B	0.16289	0.015	T	0.34800	-0.9814	9	.	.	.	-8.5472	4.1354	0.10169	0.0:0.3996:0.2191:0.3813	.	279	Q8N412	CD037_HUMAN	E	279	ENSP00000295268:K279E	.	K	-	1	0	C4orf37	99112552	0.115000	0.22152	0.080000	0.20451	0.292000	0.27327	0.392000	0.20801	0.901000	0.36495	0.455000	0.32223	AAG	.	.	.	none		0.358	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952		C	98893529	T	C	98893529	3	2	200	1	0	0	0	0	1	0	0	0	2269	1850	64	3	564	3	C4orf37	4	98893529	Missense_Mutation	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	13177434	98893529	92260747	22	12085											
NR3C2	4306	hgsc.bcm.edu	37	chr4	149356416	149356416	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agccgatcgtgataaagataTtgtaccttgagcaccaatcc	13	10	8	10	2	0	3	0	2	0	1	2	4	1	3	4	0	3	2	4	0	5	5			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr4:149356416T>C	ENST00000358102.3	-	2	1959	c.1597A>G	c.(1597-1599)Ata>Gta	p.I533V	NR3C2_ENST00000344721.4_Missense_Mutation_p.I533V|NR3C2_ENST00000512865.1_Missense_Mutation_p.I533V|NR3C2_ENST00000511528.1_Missense_Mutation_p.I533V|NR3C2_ENST00000355292.3_Missense_Mutation_p.I533V	NM_000901.4|NM_001166104.1	NP_000892.2|NP_001159576.1	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	533	Modulating.				gene expression (GO:0010467)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|receptor complex (GO:0043235)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Drospirenone(DB01395)|Eplerenone(DB00700)|Felodipine(DB01023)|Fludrocortisone(DB00687)|Fluticasone Propionate(DB00588)|Nimodipine(DB00393)|Progesterone(DB00396)|Spironolactone(DB00421)	GATAAAGATATTGTACCTTGA	0.483																																					p.I533V	Melanoma(27;428 957 40335 51025 51111)	Atlas-SNP	.											.	NR3C2	94	.	0			c.A1597G						PASS	.						121	112	115					4																	149356416		2203	4300	6503	SO:0001583	missense	4306	exon2			AAGATATTGTACC	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.1597A>G	chr4.hg19:g.149356416T>C	ENSP00000350815:p.Ile533Val	200.0	0.0	.		216.0	54.0	.	NM_001166104	B0ZBF5|B0ZBF7|Q2NKL1|Q96KQ8|Q96KQ9	Missense_Mutation	SNP	ENST00000358102.3	hg19	CCDS3772.1	.	.	.	.	.	.	.	.	.	.	T	13.43	2.234464	0.39498	.	.	ENSG00000151623	ENST00000344721;ENST00000355292;ENST00000358102;ENST00000512865;ENST00000544252;ENST00000342437;ENST00000511528	D;D;D;D;D;D	0.90069	-2.6;-2.61;-2.6;-2.17;-2.18;-2.61	5.51	5.51	0.81932	.	0.037872	0.85682	D	0.000000	T	0.80839	0.4700	N	0.24115	0.695	0.45806	D	0.998684	B;P	0.41524	0.144;0.753	B;B	0.35550	0.035;0.205	T	0.80576	-0.1321	9	.	.	.	.	15.9104	0.79470	0.0:0.0:0.0:1.0	.	533;533	B0ZBF5;B0ZBF6	.;.	V	533	ENSP00000341390:I533V;ENSP00000347441:I533V;ENSP00000350815:I533V;ENSP00000423510:I533V;ENSP00000343907:I533V;ENSP00000421481:I533V	.	I	-	1	0	NR3C2	149575866	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.615000	0.83006	2.210000	0.71456	0.533000	0.62120	ATA	.	.	.	none		0.483	NR3C2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364986.1			C	149356416	T	C	149356416	3	2	200	1	0	0	0	0	1	0	0	0	10638	1493	52	3	1389	3	NR3C2	4	149356416	Missense_Mutation	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	50462887	149356416	41797860	23	12086											
C5orf42	65250	hgsc.bcm.edu	37	chr5	37121780	37121780	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agggctgggtttgttaggcaAtggtttctgtggtagagttg	6	15	17	3	0	1	1	0	0	1	1	1	1	1	1	0	5	0	7	0	5	3	5			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr5:37121780A>G	ENST00000508244.1	-	47	9055	c.8962T>C	c.(8962-8964)Ttg>Ctg	p.L2988L	C5orf42_ENST00000425232.2_Silent_p.L2988L|C5orf42_ENST00000274258.7_Silent_p.L1886L|C5orf42_ENST00000512288.1_5'UTR			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2988						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)			TTGTTAGGCAATGGTTTCTGT	0.463																																					p.L2988L		Atlas-SNP	.											.	C5orf42	422	.	0			c.T8962C						PASS	.						308	265	280					5																	37121780		2203	4300	6503	SO:0001819	synonymous_variant	65250	exon48			TAGGCAATGGTTT		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.8962T>C	chr5.hg19:g.37121780A>G		445.0	1.0	.		701.0	235.0	.	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Silent	SNP	ENST00000508244.1	hg19	CCDS34146.2																																																																																			.	.	.	none		0.463	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		G	37121780	A	G	37121780	2	3	200	1	0	0	0	0	0	0	0	1	2303	98	4	3		3	C5orf42	5	37121780	Silent	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10		37121780	143793480	24	12087											
ADAMTS6	11174	hgsc.bcm.edu	37	chr5	64587271	64587271	+	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	1	0	0	0	0	0	0	agtcacgcttgggaggctcaTtatcaaggcaagtaccacgg	11	8	12	10	2	3	0	3	0	0	0	3	1	3	1	1	4	1	4	1	4	4	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr5:64587271T>A								ADAMTS6 (92679 upstream) : ADAMTS6 (5763 downstream)																							GGGAGGCTCATTATCAAGGCA	0.458																																					p.N466I		Atlas-SNP	.											.	ADAMTS6	174	.	0			c.A1397T						PASS	.						107	97	101					5																	64587271		2203	4300	6503	SO:0001628	intergenic_variant	11174	exon11			GGCTCATTATCAA																													chr5.hg19:g.64587271T>A		171.0	0.0	.		326.0	50.0	.	NM_197941		Missense_Mutation	SNP		hg19		.	.	.	.	.	.	.	.	.	.	T	18.48	3.633123	0.67015	.	.	ENSG00000049192	ENST00000381055;ENST00000464680	D;D	0.90004	-2.6;-2.6	5.26	5.26	0.73747	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.85682	D	0.000000	D	0.92854	0.7727	L	0.53249	1.67	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.85130	0.987;0.997	D	0.93648	0.6970	10	0.87932	D	0	.	15.4604	0.75353	0.0:0.0:0.0:1.0	.	466;466	D6R9L6;Q9UKP5	.;ATS6_HUMAN	I	466	ENSP00000370443:N466I;ENSP00000423551:N466I	ENSP00000370443:N466I	N	-	2	0	ADAMTS6	64623027	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.578000	0.82498	2.117000	0.64856	0.533000	0.62120	AAT	.	.	.	none	0	0.458									A	64587271	T	A	64587271	1	1	200	0	1	0	0	0	0	0	0	0	270	1493	52	5		5	ADAMTS6	5	64587271	IGR	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	27465491	64587271	116327989	25	12088											
UTP15	84135	hgsc.bcm.edu	37	chr5	72864379	72864379	+	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	gaagatggtggagttcaactTtttgatataagtgggagggc	11	12	15	3	0	1	2	1	1	0	1	1	5	1	4	0	4	1	1	0	4	4	5			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr5:72864379T>A	ENST00000296792.4	+	4	573	c.318T>A	c.(316-318)ctT>ctA	p.L106L	UTP15_ENST00000543251.1_5'UTR|UTP15_ENST00000508491.1_Silent_p.L87L|ANKRA2_ENST00000296785.3_5'Flank	NM_001284431.1|NM_032175.2	NP_001271360.1|NP_115551.2	Q8TED0	UTP15_HUMAN	UTP15, U3 small nucleolar ribonucleoprotein, homolog (S. cerevisiae)	106					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	15		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)		GAGTTCAACTTTTTGATATAA	0.413																																					p.L106L		Atlas-SNP	.											.	UTP15	30	.	0			c.T318A						PASS	.						101	103	102					5																	72864379		2203	4300	6503	SO:0001819	synonymous_variant	84135	exon4			TCAACTTTTTGAT	AL831972	CCDS34186.1, CCDS68893.1, CCDS68894.1	5q13.2	2013-01-10	2006-04-20		ENSG00000164338	ENSG00000164338		"WD repeat domain containing"	25758	protein-coding gene	gene with protein product			"UTP15, U3 small nucleolar ribonucleoprotein, homolog (yeast)"			12477932	Standard	NM_032175		Approved	FLJ12787, NET21, FLJ23637	uc003kcw.1	Q8TED0	OTTHUMG00000162453	ENST00000296792.4:c.318T>A	chr5.hg19:g.72864379T>A		115.0	0.0	.		187.0	33.0	.	NM_032175	B4DU75|B4DXK8|Q6IA60|Q96E08|Q9H9F8	Silent	SNP	ENST00000296792.4	hg19	CCDS34186.1	.	.	.	.	.	.	.	.	.	.	T	10.81	1.454530	0.26161	.	.	ENSG00000164338	ENST00000509005	.	.	.	5.55	-2.87	0.05700	.	.	.	.	.	T	0.51500	0.1678	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49735	-0.8908	4	.	.	.	.	7.9204	0.29843	0.0:0.4287:0.3982:0.1731	.	.	.	.	Y	133	.	.	F	+	2	0	UTP15	72900135	0.042000	0.20092	0.996000	0.52242	0.996000	0.88848	-1.057000	0.03486	-0.143000	0.11334	0.533000	0.62120	TTT	.	.	.	none		0.413	UTP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368965.1	NM_032175		A	72864379	T	A	72864379	2	1	200	1	0	0	0	0	0	0	0	1	17109	1828	64	5		5	UTP15	5	72864379	Silent	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	8277108	72864379	108050881	26	12089											
CCDC112	153733	hgsc.bcm.edu	37	chr5	114603580	114603581	+	Frame_Shift_Ins	INS	-	-	TT																															aatttgattatctcatactcINSttctctgtattccttgtctc																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr5:114603580_114603581insTT	ENST00000512261.1	-	11	1749_1750	c.1333_1334insAA	c.(1333-1335)agafs	p.R445fs	CCDC112_ENST00000379611.5_Frame_Shift_Ins_p.R528fs|CCDC112_ENST00000506442.1_Frame_Shift_Ins_p.R413fs|CCDC112_ENST00000395557.4_Frame_Shift_Ins_p.R445fs			Q8NEF3	CC112_HUMAN	coiled-coil domain containing 112	445										endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|skin(1)	20		all_cancers(142;0.000523)|all_epithelial(76;6.44e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;4.09e-08)|Epithelial(69;5.28e-08)|all cancers(49;7.06e-06)		ATCTCATACTCTTCTCTGTATT	0.327																																					p.R528fs		Atlas-Indel,Pindel	.											.	CCDC112	55	.	0			c.1583_1584insAA						PASS	.																																			SO:0001589	frameshift_variant	153733	exon10			.	BC031242	CCDS4117.1, CCDS34213.1	5q22.3	2009-04-17			ENSG00000164221	ENSG00000164221			28599	protein-coding gene	gene with protein product						12477932	Standard	NM_001040440		Approved	MGC39633	uc003kqz.2	Q8NEF3	OTTHUMG00000128894	ENST00000512261.1:c.1332_1333dupAA	chr5.hg19:g.114603581_114603582dupTT	ENSP00000423712:p.Arg445fs	238.0	0.0	0		238.0	31.0	0.130252	NM_001040440	Q6A334	Frame_Shift_Ins	INS	ENST00000512261.1	hg19	CCDS4117.1																																																																																			.	.	.	none		0.327	CCDC112-003	PUTATIVE	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000370999.1	NM_152549		TT	114603581	-	TT	114603580	7	5	200	1	0	1	1	0	0	0	0	0	2751	913	32	0	10	0	CCDC112	5	114603580	Frame_Shift_Ins	INS	-	TCGA-HE-A5NK-01A-11D-A26P-10	41739201	114603580	66311680	27	12090											
RAPGEF6	51735	hgsc.bcm.edu	37	chr5	130767032	130767032	+	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	cttgattagagatggcttcaAgagtgtccacctaaaattgg	12	12	10	7	0	1	3	1	1	0	2	2	4	2	3	2	2	0	1	2	2	4	5			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr5:130767032A>T	ENST00000509018.1	-	26	4190	c.3985T>A	c.(3985-3987)Ttg>Atg	p.L1329M	RAPGEF6_ENST00000307984.5_Missense_Mutation_p.L1342M|RAPGEF6_ENST00000296859.6_Missense_Mutation_p.L1337M|RAPGEF6_ENST00000507093.1_Missense_Mutation_p.L1337M|CTC-432M15.3_ENST00000514667.1_Missense_Mutation_p.L1379M	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	1329	Ser-rich.				positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		GATGGCTTCAAGAGTGTCCAC	0.393																																					p.L1342M	Melanoma(168;435 1955 13113 13877 23213)	Atlas-SNP	.											.	RAPGEF6	361	.	0			c.T4024A						PASS	.						72	72	72					5																	130767032		2197	4299	6496	SO:0001583	missense	51735	exon28			GCTTCAAGAGTGT	AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"PDZ domain containing guanine nucleotide exchange factor (GEF) 2"	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.3985T>A	chr5.hg19:g.130767032A>T	ENSP00000421684:p.Leu1329Met	59.0	0.0	.		89.0	4.0	.	NM_001164387	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Missense_Mutation	SNP	ENST00000509018.1	hg19	CCDS34225.1	.	.	.	.	.	.	.	.	.	.	A	4.759	0.141223	0.09083	.	.	ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000217128	ENST00000509018;ENST00000307984;ENST00000507093;ENST00000296859;ENST00000358714;ENST00000514667	T;T;T;T;T	0.24908	1.92;1.83;1.83;1.92;2.01	5.11	2.68	0.31781	.	0.495083	0.22765	N	0.055912	T	0.10423	0.0255	N	0.08118	0	0.21933	N	0.999463	B;B;B;B;B	0.22983	0.01;0.078;0.01;0.017;0.01	B;B;B;B;B	0.27170	0.007;0.077;0.007;0.017;0.007	T	0.14476	-1.0471	10	0.33940	T	0.23	.	1.1646	0.01813	0.486:0.1362:0.2288:0.1489	.	1337;1337;1379;1342;1329	A3KN82;B7ZML2;E9PCH4;Q8TEU7-3;Q8TEU7	.;.;.;.;RPGF6_HUMAN	M	1329;1342;1337;1337;1342;1379	ENSP00000421684:L1329M;ENSP00000309298:L1342M;ENSP00000426081:L1337M;ENSP00000296859:L1337M;ENSP00000426948:L1379M	ENSP00000426948:L1379M	L	-	1	2	RAPGEF6;FNIP1	130794931	0.923000	0.31300	0.787000	0.31911	0.394000	0.30568	0.496000	0.22499	0.899000	0.36444	0.533000	0.62120	TTG	.	.	.	none		0.393	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340		T	130767032	A	T	130767032	3	4	200	1	0	0	0	0	1	0	0	0	13061	69	3	5	832	5	RAPGEF6	5	130767032	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	16163452	130767032	50148228	28	12091											
DEFB113	245927	hgsc.bcm.edu	37	chr6	49936558	49936558	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctctttttctctctgcaacTtctcttgtttttttctgtgg	2	24	5	10	0	5	0	0	0	5	0	8	0	5	0	0	1	2	2	0	1	1	7			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr6:49936558T>C	ENST00000398718.1	-	2	80	c.81A>G	c.(79-81)gaA>gaG	p.E27E		NM_001037729.1	NP_001032818.1	Q30KQ7	DB113_HUMAN	defensin, beta 113	27					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)	7	Lung NSC(77;0.042)					TCTCTGCAACTTCTCTTGTTT	0.363																																					p.E27E		Atlas-SNP	.											.	DEFB113	18	.	0			c.A81G						PASS	.						95	92	93					6																	49936558		1859	4093	5952	SO:0001819	synonymous_variant	245927	exon2			TGCAACTTCTCTT	DQ012017	CCDS43472.1	6p12.3	2010-03-30			ENSG00000214642	ENSG00000214642		"Defensins, beta"	18094	protein-coding gene	gene with protein product						11854508, 16033865	Standard	NM_001037729		Approved	DEFB-13	uc011dwq.2	Q30KQ7	OTTHUMG00000160210	ENST00000398718.1:c.81A>G	chr6.hg19:g.49936558T>C		57.0	0.0	.		85.0	15.0	.	NM_001037729		Silent	SNP	ENST00000398718.1	hg19	CCDS43472.1																																																																																			.	.	.	none		0.363	DEFB113-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359666.1			C	49936558	T	C	49936558	2	2	200	1	0	0	0	0	0	0	0	1	4404	1606	56	3		3	DEFB113	6	49936558	Silent	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10		49936558	121178509	29	12092											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51750667	51750667	+	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	aacaacaaaaaagcttacctGggcaccacctgcactttccc	14	7	5	15	0	0	0	0	0	0	0	1	0	1	0	4	1	5	3	4	1	6	2			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr6:51750667G>T	ENST00000371117.3	-	45	7488	c.7213C>A	c.(7213-7215)Cag>Aag	p.Q2405K	PKHD1_ENST00000340994.4_Missense_Mutation_p.Q2405K	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2405					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)					AAGCTTACCTGGGCACCACCT	0.383																																					p.Q2405K		Atlas-SNP	.											.	PKHD1	927	.	0			c.C7213A						PASS	.						43	41	42					6																	51750667		2203	4300	6503	SO:0001583	missense	5314	exon45			TTACCTGGGCACC	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.7213C>A	chr6.hg19:g.51750667G>T	ENSP00000360158:p.Gln2405Lys	136.0	0.0	.		130.0	29.0	.	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	G	15.47	2.841905	0.51057	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	T;T	0.79653	-1.29;-1.29	5.81	5.81	0.92471	Pectin lyase fold/virulence factor (1);Pectin lyase fold (1);	0.147468	0.48286	D	0.000193	T	0.69797	0.3151	M	0.67953	2.075	0.34697	D	0.726304	P;B;P	0.40000	0.698;0.313;0.698	B;B;B	0.35353	0.201;0.104;0.167	T	0.72704	-0.4213	10	0.27082	T	0.32	.	17.2257	0.86970	0.0:0.0:1.0:0.0	.	2405;2405;2405	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	K	2405	ENSP00000360158:Q2405K;ENSP00000341097:Q2405K	ENSP00000341097:Q2405K	Q	-	1	0	PKHD1	51858626	0.998000	0.40836	0.941000	0.38009	0.505000	0.33919	3.052000	0.49893	2.756000	0.94617	0.650000	0.86243	CAG	.	.	.	none		0.383	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		T	51750667	G	T	51750667	3	4	200	1	0	0	0	0	1	0	0	0	11978	1357	47	4	5142	4	PKHD1	6	51750667	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	1814109	51750667	119364400	30	12093											
ALDH8A1	64577	hgsc.bcm.edu	37	chr6	135260502	135260502	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgcagccatcgctggagctAtcttccaggtcagcaagtag	9	9	11	12	1	2	0	1	0	1	0	4	1	3	1	2	2	4	5	2	2	3	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr6:135260502A>G	ENST00000265605.2	-	4	562	c.494T>C	c.(493-495)aTa>aCa	p.I165T	ALDH8A1_ENST00000367847.2_Intron|RP11-349J5.2_ENST00000416448.2_RNA|ALDH8A1_ENST00000367845.2_Missense_Mutation_p.I165T	NM_022568.3	NP_072090.1	Q9H2A2	AL8A1_HUMAN	aldehyde dehydrogenase 8 family, member A1	165					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)		CGCTGGAGCTATCTTCCAGGT	0.542																																					p.I165T		Atlas-SNP	.											.	ALDH8A1	68	.	0			c.T494C						PASS	.						100	87	91					6																	135260502		2203	4300	6503	SO:0001583	missense	64577	exon4			GGAGCTATCTTCC	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.494T>C	chr6.hg19:g.135260502A>G	ENSP00000265605:p.Ile165Thr	106.0	0.0	.		128.0	17.0	.	NM_022568	B7Z521|O60793|Q24JS9|Q53GT3|Q5TI80	Missense_Mutation	SNP	ENST00000265605.2	hg19	CCDS5171.1	.	.	.	.	.	.	.	.	.	.	A	18.58	3.654610	0.67472	.	.	ENSG00000118514	ENST00000265605;ENST00000367845	T;T	0.78364	-1.17;-1.17	5.45	4.29	0.51040	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.097324	0.64402	D	0.000001	T	0.79805	0.4509	M	0.72118	2.19	0.80722	D	1	D;D	0.54397	0.958;0.966	P;D	0.64687	0.881;0.928	T	0.78919	-0.2014	10	0.35671	T	0.21	.	11.1526	0.48469	0.9277:0.0:0.0723:0.0	.	165;165	Q9H2A2-2;Q9H2A2	.;AL8A1_HUMAN	T	165	ENSP00000265605:I165T;ENSP00000356819:I165T	ENSP00000265605:I165T	I	-	2	0	ALDH8A1	135302195	1.000000	0.71417	0.338000	0.25549	0.733000	0.41908	7.522000	0.81844	0.909000	0.36697	0.460000	0.39030	ATA	.	.	.	none		0.542	ALDH8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042334.2			G	135260502	A	G	135260502	3	3	200	1	0	0	0	0	1	0	0	0	505	449	16	3	985	3	ALDH8A1	6	135260502	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	83509835	135260502	35854565	31	12094											
RBM16	22828	hgsc.bcm.edu	37	chr6	155154048	155154048	+	Missense_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	ggttctaccggtctatggtgGtccaaaaggcttacatgaag	10	11	12	8	1	2	1	0	1	2	0	3	1	3	1	2	5	2	2	2	5	6	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr6:155154048G>A	ENST00000367178.3	+	20	3911	c.3335G>A	c.(3334-3336)gGt>gAt	p.G1112D	SCAF8_ENST00000417268.1_Missense_Mutation_p.G1112D|TIAM2_ENST00000461783.3_5'UTR|SCAF8_ENST00000367186.4_Missense_Mutation_p.G1178D	NM_014892.3	NP_055707.3	Q9UPN6	SCAF8_HUMAN	SR-related CTD-associated factor 8	1112					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						GTCTATGGTGGTCCAAAAGGC	0.468																																					p.G1112D		Atlas-SNP	.											.	SCAF8	122	.	0			c.G3335A						PASS	.						66	72	70					6																	155154048		2203	4300	6503	SO:0001583	missense	22828	exon20			ATGGTGGTCCAAA	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.3335G>A	chr6.hg19:g.155154048G>A	ENSP00000356146:p.Gly1112Asp	199.0	0.0	.		216.0	40.0	.	NM_014892	B7Z888|Q5TBU6|Q6NSK3|Q9BQN8|Q9BX43	Missense_Mutation	SNP	ENST00000367178.3	hg19	CCDS5247.1	.	.	.	.	.	.	.	.	.	.	G	19.22	3.784709	0.70222	.	.	ENSG00000213079;ENSG00000213079;ENSG00000213079;ENSG00000146426	ENST00000367178;ENST00000417268;ENST00000367186;ENST00000528928	T;T;T	0.61274	0.18;0.18;0.12	5.97	5.97	0.96955	.	0.000000	0.64402	U	0.000001	T	0.63534	0.2519	L	0.29908	0.895	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.66388	-0.5936	10	0.87932	D	0	.	20.4238	0.99064	0.0:0.0:1.0:0.0	.	1157;1178;1112	B7Z876;B7Z888;Q9UPN6	.;.;SCAF8_HUMAN	D	1112;1112;1178;73	ENSP00000356146:G1112D;ENSP00000413098:G1112D;ENSP00000356154:G1178D	ENSP00000356146:G1112D	G	+	2	0	TIAM2;SCAF8	155195740	1.000000	0.71417	0.999000	0.59377	0.976000	0.68499	5.774000	0.68906	2.828000	0.97474	0.655000	0.94253	GGT	.	.	.	none		0.468	SCAF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042798.1	NM_014892		A	155154048	G	A	155154048	3	1	200	1	0	0	0	0	1	0	0	0	13131	1261	44	2	3413	2	RBM16	6	155154048	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	19893546	155154048	15961019	32	12095											
LPA	4018	hgsc.bcm.edu	37	chr6	161071523	161071523	+	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	ggaccacatggctttgctcaGgtgctgctaaaattaaaaca	13	10	9	9	0	1	0	1	0	0	0	1	1	1	1	1	3	4	4	1	3	4	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr6:161071523G>T	ENST00000316300.5	-	2	100	c.56C>A	c.(55-57)cCt>cAt	p.P19H	LPA_ENST00000447678.1_Missense_Mutation_p.P19H			P08519	APOA_HUMAN	lipoprotein, Lp(a)	2527					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)	GCTTTGCTCAGGTGCTGCTAA	0.433																																					p.P19H		Atlas-SNP	.											.	LPA	237	.	0			c.C56A						PASS	.						129	134	132					6																	161071523		2186	4297	6483	SO:0001583	missense	4018	exon3			TGCTCAGGTGCTG	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.56C>A	chr6.hg19:g.161071523G>T	ENSP00000321334:p.Pro19His	95.0	0.0	.		109.0	16.0	.	NM_005577	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	hg19	CCDS43523.1	.	.	.	.	.	.	.	.	.	.	g	7.332	0.619100	0.14129	.	.	ENSG00000198670	ENST00000316300;ENST00000447678	T;T	0.61627	0.09;0.09	2.71	2.71	0.32032	.	.	.	.	.	T	0.32164	0.0820	L	0.43152	1.355	0.09310	N	1	.	.	.	.	.	.	T	0.16719	-1.0393	7	0.20519	T	0.43	.	9.0216	0.36204	0.0:0.0:1.0:0.0	.	.	.	.	H	19	ENSP00000321334:P19H;ENSP00000395608:P19H	ENSP00000321334:P19H	P	-	2	0	LPA	160991513	0.652000	0.27349	0.137000	0.22149	0.005000	0.04900	4.568000	0.60857	1.519000	0.48950	0.499000	0.49734	CCT	.	.	.	none		0.433	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		T	161071523	G	T	161071523	3	4	200	1	0	0	0	0	1	0	0	0	8910	1000	35	4	6218	4	LPA	6	161071523	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	5917475	161071523	10043544	33	12096											
NPTX2	4885	hgsc.bcm.edu	37	chr7	98257767	98257767	+	Frame_Shift_Del	DEL	C	C	-																															gcatttgtcggggagctcagCcagttcaacatatgggaccg																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr7:98257767delC	ENST00000265634.3	+	5	1287	c.1122delC	c.(1120-1122)agcfs	p.S374fs		NM_002523.2	NP_002514.1	P47972	NPTX2_HUMAN	neuronal pentraxin II	374	Pentaxin.				synaptic transmission (GO:0007268)	extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18	all_cancers(62;2.28e-09)|all_epithelial(64;4.86e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0128)|all_lung(186;0.0142)		STAD - Stomach adenocarcinoma(171;0.215)			GGGAGCTCAGCCAGTTCAACA	0.567																																					p.S374fs		Pindel	.											.	NPTX2	45	.	0			c.1121delG						PASS	.						89	70	76					7																	98257767		2203	4300	6503	SO:0001589	frameshift_variant	4885	exon5			.		CCDS5657.1	7q21.3-q22.1	2008-04-30			ENSG00000106236	ENSG00000106236			7953	protein-coding gene	gene with protein product	"apexin"	600750				8530029	Standard	NM_002523		Approved		uc003upl.2	P47972	OTTHUMG00000154369	ENST00000265634.3:c.1122delC	chr7.hg19:g.98257767delC	ENSP00000265634:p.Ser374fs	170.0	0.0	.		250.0	30.0	0.120	NM_002523	A4D267|Q86XV7|Q96G70	Frame_Shift_Del	DEL	ENST00000265634.3	hg19	CCDS5657.1																																																																																			.	.	.	none		0.567	NPTX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334982.1	NM_002523		-	98257767	C	-	98257767	7	5	200	1	0	1	0	1	0	0	0	0	10610	738	26	0	1140	0	NPTX2	7	98257767	Frame_Shift_Del	DEL	C	TCGA-HE-A5NK-01A-11D-A26P-10		98257767	60880896	34	12097											
METTL2B	55798	hgsc.bcm.edu	37	chr7	128119287	128119287	+	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	aaatgggtttttcaaggataGacattggctttttaccgaat	12	15	9	5	1	1	1	1	0	0	1	1	3	1	2	1	3	1	2	1	3	5	7			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr7:128119287G>T	ENST00000262432.8	+	3	315	c.278G>T	c.(277-279)aGa>aTa	p.R93I	RP11-212P7.3_ENST00000462662.1_RNA|METTL2B_ENST00000480046.1_Missense_Mutation_p.R28I	NM_018396.2	NP_060866.2	Q6P1Q9	MET2B_HUMAN	methyltransferase like 2B	93					tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)			breast(1)|cervix(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						TTCAAGGATAGACATTGGCTT	0.348																																					p.R93I		Atlas-SNP	.											.	METTL2B	34	.	0			c.G278T						PASS	.						46	48	47					7																	128119287		2202	4296	6498	SO:0001583	missense	55798	exon3			AGGATAGACATTG	AK002212	CCDS5803.2	7q32.2	2012-06-12	2006-02-09	2006-02-09	ENSG00000165055	ENSG00000165055			18272	protein-coding gene	gene with protein product		607846	"methyltransferase like 2"	METTL2		11738826	Standard	NM_018396		Approved	METL, FLJ11350	uc003vnf.3	Q6P1Q9	OTTHUMG00000143738	ENST00000262432.8:c.278G>T	chr7.hg19:g.128119287G>T	ENSP00000262432:p.Arg93Ile	390.0	0.0	.		481.0	67.0	.	NM_018396	B4DZ68|Q0IJ54|Q3B7J1	Missense_Mutation	SNP	ENST00000262432.8	hg19	CCDS5803.2	.	.	.	.	.	.	.	.	.	.	G	15.00	2.704511	0.48412	.	.	ENSG00000165055	ENST00000462662;ENST00000262432;ENST00000480046	T;T;T	0.04654	3.58;3.58;3.58	2.86	1.97	0.26223	.	0.000000	0.85682	D	0.000000	T	0.24624	0.0597	M	0.94021	3.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.01583	-1.1319	10	0.87932	D	0	-0.8843	7.7593	0.28942	0.1338:0.0:0.8662:0.0	.	28;93	Q6P1Q9-2;Q6P1Q9	.;MTL2B_HUMAN	I	87;93;28	ENSP00000418634:R87I;ENSP00000262432:R93I;ENSP00000418402:R28I	ENSP00000262432:R93I	R	+	2	0	METTL2B	127906523	1.000000	0.71417	0.984000	0.44739	0.344000	0.29017	9.445000	0.97587	0.540000	0.28808	-0.491000	0.04670	AGA	.	.	.	none		0.348	METTL2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289817.1	NM_018396		T	128119287	G	T	128119287	3	4	200	1	0	0	0	0	1	0	0	0	9507	942	33	4	288	4	METTL2B	7	128119287	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	29861520	128119287	31019376	35	12098											
TAS2R39	259285	hgsc.bcm.edu	37	chr7	142880641	142880641	+	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	ttttagcagttttacttgctGaatacctcattggtatcatt	9	19	6	7	0	2	1	2	1	0	0	2	1	2	1	1	1	4	4	1	1	5	9			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr7:142880641G>A	ENST00000446620.1	+	1	130	c.130G>A	c.(130-132)Gaa>Aaa	p.E44K		NM_176881.2	NP_795362.2	P59534	T2R39_HUMAN	taste receptor, type 2, member 39	44					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)					TTTACTTGCTGAATACCTCAT	0.413																																					p.E44K		Atlas-SNP	.											.	TAS2R39	42	.	0			c.G130A						PASS	.						145	132	136					7																	142880641		1939	4149	6088	SO:0001583	missense	259285	exon1			CTTGCTGAATACC	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.130G>A	chr7.hg19:g.142880641G>A	ENSP00000405095:p.Glu44Lys	106.0	0.0	.		188.0	13.0	.	NM_176881	A4FUI7|Q3ZCN6|Q645W4	Missense_Mutation	SNP	ENST00000446620.1	hg19	CCDS47729.1	.	.	.	.	.	.	.	.	.	.	G	15.58	2.876777	0.51801	.	.	ENSG00000236398	ENST00000446620	T	0.37411	1.2	4.66	4.66	0.58398	.	.	.	.	.	T	0.65196	0.2668	M	0.89478	3.035	0.29517	N	0.853797	D	0.71674	0.998	D	0.68765	0.96	T	0.65676	-0.6110	9	0.72032	D	0.01	.	14.7561	0.69567	0.0:0.0:1.0:0.0	.	44	P59534	T2R39_HUMAN	K	44	ENSP00000405095:E44K	ENSP00000405095:E44K	E	+	1	0	TAS2R39	142590763	0.321000	0.24625	0.437000	0.26809	0.026000	0.11368	1.677000	0.37576	2.583000	0.87209	0.557000	0.71058	GAA	.	.	.	none		0.413	TAS2R39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327090.2	NM_176881		A	142880641	G	A	142880641	3	1	200	1	0	0	0	0	1	0	0	0	15588	1291	45	2	132	2	TAS2R39	7	142880641	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	14761354	142880641	16258022	36	12099											
REPIN1	29803	hgsc.bcm.edu	37	chr7	150069172	150069172	+	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	caataagccctatctgacttCgcaccggcgcatccacaccg	10	7	7	17	4	1	1	0	1	1	0	3	1	2	1	4	1	1	2	4	1	3	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr7:150069172C>A	ENST00000425389.2	+	1	920	c.842C>A	c.(841-843)tCg>tAg	p.S281*	REPIN1_ENST00000444957.1_Nonsense_Mutation_p.S281*|REPIN1_ENST00000540729.1_Nonsense_Mutation_p.S281*|REPIN1_ENST00000479668.1_3'UTR|REPIN1_ENST00000489432.2_Nonsense_Mutation_p.S338*|REPIN1_ENST00000466559.1_3'UTR|REPIN1_ENST00000397281.2_Nonsense_Mutation_p.S281*|RP4-584D14.5_ENST00000488310.1_RNA	NM_014374.3	NP_055189.2	Q9BWE0	REPI1_HUMAN	replication initiator 1	281					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)			TATCTGACTTCGCACCGGCGC	0.637																																					p.S338X		Atlas-SNP	.											.	REPIN1	74	.	0			c.C1013A						PASS	.						18	23	22					7																	150069172		2160	4279	6439	SO:0001587	stop_gained	29803	exon3			TGACTTCGCACCG	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.842C>A	chr7.hg19:g.150069172C>A	ENSP00000388287:p.Ser281*	35.0	0.0	.		52.0	9.0	.	NM_001099695	C9J3L7|D3DWZ1|Q7LE03|Q9BUZ6|Q9NZH2|Q9UMP5	Nonsense_Mutation	SNP	ENST00000425389.2	hg19	CCDS43677.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.090002	0.76756	.	.	ENSG00000214022	ENST00000540729;ENST00000397281;ENST00000444957;ENST00000489432;ENST00000475514;ENST00000488943;ENST00000425389	.	.	.	4.91	4.91	0.64330	.	.	.	.	.	.	.	.	.	.	.	0.22017	N	0.999416	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	-5.8606	11.3408	0.49531	0.0:0.8167:0.1833:0.0	.	.	.	.	X	281;281;281;338;340;341;281	.	ENSP00000380451:S281X	S	+	2	0	REPIN1	149700105	0.000000	0.05858	0.985000	0.45067	0.853000	0.48598	-1.414000	0.02471	2.550000	0.86006	0.462000	0.41574	TCG	.	.	.	none		0.637	REPIN1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376940.1	NM_014374		A	150069172	C	A	150069172	4	1	200	1	0	0	0	0	0	1	0	0	13240	893	31	4	1019	4	REPIN1	7	150069172	Nonsense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	7188531	150069172	9069491	37	12100											
MTUS1	57509	hgsc.bcm.edu	37	chr8	17612803	17612803	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatggcatgatgtgatataaAggtgcagttaactttatcca	13	13	10	5	0	0	2	0	2	0	0	1	3	1	2	1	2	2	3	1	2	5	5	rs374892928		TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr8:17612803A>G	ENST00000262102.6	-	2	738	c.514T>C	c.(514-516)Ttt>Ctt	p.F172L	MTUS1_ENST00000381869.3_Missense_Mutation_p.F172L|MTUS1_ENST00000381862.3_Missense_Mutation_p.F172L|MTUS1_ENST00000519263.1_Missense_Mutation_p.F172L	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	172					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)		TGTGATATAAAGGTGCAGTTA	0.438																																					p.F172L		Atlas-SNP	.											.	MTUS1	144	.	0			c.T514C						PASS	.						146	132	136					8																	17612803		1963	4150	6113	SO:0001583	missense	57509	exon2			ATATAAAGGTGCA	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.514T>C	chr8.hg19:g.17612803A>G	ENSP00000262102:p.Phe172Leu	191.0	0.0	.		224.0	34.0	.	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	hg19	CCDS43717.1	.	.	.	.	.	.	.	.	.	.	A	13.70	2.316888	0.40996	.	.	ENSG00000129422	ENST00000381869;ENST00000262102;ENST00000519263;ENST00000381862	T;T;T;T	0.30182	2.43;2.5;2.43;1.54	4.09	2.91	0.33838	.	0.407817	0.21445	N	0.074440	T	0.21921	0.0528	L	0.32530	0.975	0.09310	N	0.999999	B;B;P	0.44139	0.356;0.206;0.827	B;B;B	0.43331	0.104;0.052;0.416	T	0.05886	-1.0858	9	.	.	.	-5.1088	5.1218	0.14863	0.5864:0.2499:0.0:0.1636	.	172;172;172	Q9ULD2-5;Q9ULD2-2;Q9ULD2	.;.;MTUS1_HUMAN	L	172	ENSP00000371293:F172L;ENSP00000262102:F172L;ENSP00000430167:F172L;ENSP00000371286:F172L	.	F	-	1	0	MTUS1	17657083	0.265000	0.24102	0.123000	0.21794	0.013000	0.08279	1.311000	0.33562	0.883000	0.36040	-0.490000	0.04691	TTT	.	.	.	alt		0.438	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		G	17612803	A	G	17612803	3	3	200	1	0	0	0	0	1	0	0	0	9972	72	3	3	3673	3	MTUS1	8	17612803	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10		17612803	128751219	38	12101											
MYST3	7994	hgsc.bcm.edu	37	chr8	41794945	41794945	+	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	gatctcaaacgtgggttctaAtcttggcattggcctctcgg	7	13	11	10	2	4	0	1	0	4	0	6	1	4	0	1	4	1	2	1	4	2	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr8:41794945A>T	ENST00000396930.3	-	17	3724	c.3181T>A	c.(3181-3183)Tta>Ata	p.L1061I	KAT6A_ENST00000265713.2_Missense_Mutation_p.L1061I|KAT6A_ENST00000406337.1_Missense_Mutation_p.L1061I	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1061					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)										GTGGGTTCTAATCTTGGCATT	0.428																																					p.L1061I		Atlas-SNP	.											.	.	.	.	0			c.T3181A						PASS	.						120	115	117					8																	41794945		2203	4300	6503	SO:0001583	missense	7994	exon17			GTTCTAATCTTGG	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.3181T>A	chr8.hg19:g.41794945A>T	ENSP00000380136:p.Leu1061Ile	215.0	0.0	.		281.0	58.0	.	NM_001099412	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	hg19	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	A	13.75	2.330228	0.41297	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930;ENST00000418721	T;T;T	0.66099	-0.19;-0.19;-0.19	5.63	3.27	0.37495	.	0.000000	0.53938	D	0.000041	T	0.73853	0.3640	M	0.69823	2.125	0.42293	D	0.992149	D	0.69078	0.997	D	0.78314	0.991	T	0.72571	-0.4253	10	0.62326	D	0.03	-9.4799	7.9093	0.29780	0.6901:0.0:0.3099:0.0	.	1061	Q92794	KAT6A_HUMAN	I	1061;1061;1061;641	ENSP00000265713:L1061I;ENSP00000385888:L1061I;ENSP00000380136:L1061I	ENSP00000265713:L1061I	L	-	1	2	KAT6A	41914102	0.999000	0.42202	0.996000	0.52242	0.990000	0.78478	3.600000	0.54052	0.436000	0.26393	0.528000	0.53228	TTA	.	.	.	none		0.428	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		T	41794945	A	T	41794945	3	4	200	1	0	0	0	0	1	0	0	0	10111	98	4	5	2841	5	MYST3	8	41794945	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	24182142	41794945	104569077	39	12102											
WWP1	11059	hgsc.bcm.edu	37	chr8	87423961	87423961	+	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	gtgcagaattggaatctgaaGctagaagtatattagagcct	14	11	11	5	0	1	4	0	1	1	3	1	5	1	5	1	1	3	3	1	1	8	5			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr8:87423961G>C	ENST00000517970.1	+	9	1226	c.919G>C	c.(919-921)Gct>Cct	p.A307P	WWP1_ENST00000341922.2_Missense_Mutation_p.A177P|WWP1_ENST00000265428.4_Missense_Mutation_p.A307P|WWP1_ENST00000349423.2_Missense_Mutation_p.A89P	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	307					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						GGAATCTGAAGCTAGAAGTAT	0.408																																					p.A307P		Atlas-SNP	.											.	WWP1	97	.	0			c.G919C						PASS	.						78	76	77					8																	87423961		2203	4300	6503	SO:0001583	missense	11059	exon9			TCTGAAGCTAGAA	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.919G>C	chr8.hg19:g.87423961G>C	ENSP00000427793:p.Ala307Pro	109.0	0.0	.		111.0	18.0	.	NM_007013	O00307|Q5YLC1|Q96BP4	Missense_Mutation	SNP	ENST00000517970.1	hg19	CCDS6242.1	.	.	.	.	.	.	.	.	.	.	G	5.203	0.222924	0.09863	.	.	ENSG00000123124	ENST00000517970;ENST00000265428;ENST00000341922;ENST00000349423	T;T;T;T	0.46451	0.89;0.89;0.87;0.89	5.69	4.81	0.61882	.	0.669254	0.14402	N	0.321845	T	0.21962	0.0529	N	0.08118	0	0.39335	D	0.965486	B;B	0.06786	0.0;0.001	B;B	0.09377	0.004;0.003	T	0.08513	-1.0718	10	0.30078	T	0.28	.	7.2873	0.26346	0.1504:0.1403:0.7094:0.0	.	89;307	Q9H0M0-6;Q9H0M0	.;WWP1_HUMAN	P	307;307;177;89	ENSP00000427793:A307P;ENSP00000265428:A307P;ENSP00000340564:A177P;ENSP00000342665:A89P	ENSP00000265428:A307P	A	+	1	0	WWP1	87493077	0.557000	0.26546	0.093000	0.20910	0.015000	0.08874	0.271000	0.18626	1.410000	0.46936	0.650000	0.86243	GCT	.	.	.	none		0.408	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013		C	87423961	G	C	87423961	3	2	200	1	0	0	0	0	1	0	0	0	17427	971	34	4	945	4	WWP1	8	87423961	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	45629016	87423961	58940061	40	12103											
PLIN2	123	hgsc.bcm.edu	37	chr9	19126158	19126158	+	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	ggcagagcactggtcatggcCacggaggtgatggtcttcac	8	8	15	10	1	3	2	2	1	1	1	3	3	3	3	1	6	1	2	1	6	0	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr9:19126158C>A	ENST00000276914.2	-	3	359	c.180G>T	c.(178-180)gtG>gtT	p.V60V	PLIN2_ENST00000380464.3_Silent_p.V60V|PLIN2_ENST00000380465.3_Silent_p.V60V|PLIN2_ENST00000411567.1_Silent_p.V60V	NM_001122.3	NP_001113.2	Q99541	PLIN2_HUMAN	perilipin 2	60					cellular lipid metabolic process (GO:0044255)|lipid storage (GO:0019915)|long-chain fatty acid transport (GO:0015909)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|lipid particle (GO:0005811)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	19						TGGTCATGGCCACGGAGGTGA	0.527																																					p.V60V		Atlas-SNP	.											.	PLIN2	41	.	0			c.G180T						PASS	.						160	124	136					9																	19126158		2203	4300	6503	SO:0001819	synonymous_variant	123	exon3			CATGGCCACGGAG	X97324	CCDS6490.1	9p22.1	2009-08-12	2009-08-12	2009-08-12	ENSG00000147872	ENSG00000147872		"Perilipins"	248	protein-coding gene	gene with protein product	"adipophilin"	103195	"adipose differentiation-related protein"	ADFP		9003395, 19638644	Standard	NM_001122		Approved	ADRP	uc003zno.3	Q99541	OTTHUMG00000019624	ENST00000276914.2:c.180G>T	chr9.hg19:g.19126158C>A		207.0	0.0	.		263.0	49.0	.	NM_001122	Q9BSC3	Silent	SNP	ENST00000276914.2	hg19	CCDS6490.1																																																																																			.	.	.	none		0.527	PLIN2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051835.1	NM_001122		A	19126158	C	A	19126158	2	1	200	1	0	0	0	0	0	0	0	1	12097	581	21	4		4	PLIN2	9	19126158	Silent	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10		19126158	122087273	41	12104											
AGTPBP1	23287	hgsc.bcm.edu	37	chr9	88233969	88233969	+	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	aagcaacacctggtcgcattCcactgacttcaaagtaaaac	15	8	6	12	1	1	1	1	1	0	0	3	1	2	1	2	1	3	3	2	1	5	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr9:88233969C>G	ENST00000357081.3	-	17	2408	c.2264G>C	c.(2263-2265)gGa>gCa	p.G755A	AGTPBP1_ENST00000376109.3_Missense_Mutation_p.G767A|AGTPBP1_ENST00000432218.1_Missense_Mutation_p.G593A|AGTPBP1_ENST00000376083.3_Missense_Mutation_p.G715A|AGTPBP1_ENST00000337006.4_3'UTR			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	755					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						TGGTCGCATTCCACTGACTTC	0.328																																					p.G715A		Atlas-SNP	.											.	AGTPBP1	128	.	0			c.G2144C						PASS	.						92	93	92					9																	88233969		2203	4300	6503	SO:0001583	missense	23287	exon17			CGCATTCCACTGA	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.2264G>C	chr9.hg19:g.88233969C>G	ENSP00000349592:p.Gly755Ala	136.0	0.0	.		130.0	27.0	.	NM_015239	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Missense_Mutation	SNP	ENST00000357081.3	hg19		.	.	.	.	.	.	.	.	.	.	C	16.55	3.154898	0.57259	.	.	ENSG00000135049	ENST00000357081;ENST00000376083;ENST00000376109;ENST00000432218	T;T;T;T	0.31510	1.49;1.49;1.49;1.49	5.38	5.38	0.77491	.	0.097920	0.64402	D	0.000001	T	0.55593	0.1930	M	0.67517	2.055	0.80722	D	1	B;D;D;P	0.76494	0.34;0.992;0.999;0.729	B;P;D;B	0.73708	0.257;0.872;0.981;0.439	T	0.54057	-0.8350	10	0.48119	T	0.1	-15.9497	19.1333	0.93415	0.0:1.0:0.0:0.0	.	767;755;593;715	Q9UPW5-3;Q9UPW5;B4DHX2;Q9UPW5-2	.;CBPC1_HUMAN;.;.	A	755;715;767;593	ENSP00000349592:G755A;ENSP00000365251:G715A;ENSP00000365277:G767A;ENSP00000402804:G593A	ENSP00000349592:G755A	G	-	2	0	AGTPBP1	87423789	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.890000	0.69774	2.532000	0.85374	0.650000	0.86243	GGA	.	.	.	none		0.328	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239		G	88233969	C	G	88233969	3	3	200	1	0	0	0	0	1	0	0	0	400	855	30	4	1456	4	AGTPBP1	9	88233969	Missense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	69107811	88233969	52979462	42	12105											
PHPT1	29085	hgsc.bcm.edu	37	chr9	139744582	139744582	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaagattcacgtgtacggctAttccatggtgagccgcagcc	9	9	12	11	3	1	2	1	1	0	1	2	3	2	2	3	2	3	3	3	2	3	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr9:139744582A>G	ENST00000247665.10	+	2	615	c.278A>G	c.(277-279)tAt>tGt	p.Y93C	PHPT1_ENST00000371661.1_Missense_Mutation_p.Y93C|MAMDC4_ENST00000445819.1_5'Flank|PHPT1_ENST00000492540.1_3'UTR|PHPT1_ENST00000545326.1_Missense_Mutation_p.Y93C|MAMDC4_ENST00000317446.2_5'Flank	NM_014172.4	NP_054891.2	Q9NRX4	PHP14_HUMAN	phosphohistidine phosphatase 1	93					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)		GTGTACGGCTATTCCATGGTG	0.662																																					p.Y93C		Atlas-SNP	.											.	PHPT1	14	.	0			c.A278G						PASS	.						93	86	88					9																	139744582		2202	4300	6502	SO:0001583	missense	29085	exon2			ACGGCTATTCCAT	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.278A>G	chr9.hg19:g.139744582A>G	ENSP00000247665:p.Tyr93Cys	120.0	0.0	.		179.0	30.0	.	NM_001135861	B1AMX0|B1AMX1|Q9H0Y3	Missense_Mutation	SNP	ENST00000247665.10	hg19	CCDS7009.1	.	.	.	.	.	.	.	.	.	.	.	22.3	4.267724	0.80469	.	.	ENSG00000054148	ENST00000371661;ENST00000545326;ENST00000247665	.	.	.	4.61	4.61	0.57282	.	.	.	.	.	T	0.80979	0.4728	M	0.88450	2.955	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.83346	-0.0005	8	0.46703	T	0.11	-0.3441	13.1692	0.59589	1.0:0.0:0.0:0.0	.	93;93	Q9NRX4-2;Q9NRX4	.;PHP14_HUMAN	C	93	.	ENSP00000247665:Y93C	Y	+	2	0	PHPT1	138864403	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	5.655000	0.67981	1.703000	0.51240	0.374000	0.22700	TAT	.	.	.	none		0.662	PHPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055150.1	NM_014172		G	139744582	A	G	139744582	3	3	200	1	0	0	0	0	1	0	0	0	11867	449	16	3	284	3	PHPT1	9	139744582	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	51510613	139744582	1468849	43	12106											
NOLC1	9221	hgsc.bcm.edu	37	chr10	103917872	103917872	+	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	aggccaagagctctgattctGattctgactcaagctccgag	10	10	10	11	1	4	4	1	3	3	1	5	5	5	4	2	1	2	2	2	1	2	2			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr10:103917872G>A	ENST00000605788.1	+	5	743	c.508G>A	c.(508-510)Gat>Aat	p.D170N	NOLC1_ENST00000405356.1_Missense_Mutation_p.D170N|NOLC1_ENST00000603742.1_5'UTR|NOLC1_ENST00000488254.2_Missense_Mutation_p.D171N	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	170	11 X 12 AA approximate repeats of an acidic serine cluster.				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)		CTCTGATTCTGATTCTGACTC	0.488																																					p.D170N		Atlas-SNP	.											.	NOLC1	61	.	0			c.G508A						PASS	.						88	90	89					10																	103917872		2203	4300	6503	SO:0001583	missense	9221	exon5			GATTCTGATTCTG	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.508G>A	chr10.hg19:g.103917872G>A	ENSP00000474710:p.Asp170Asn	162.0	0.0	.		193.0	35.0	.	NM_004741	Q15030|Q5VV70|Q9BUV3	Missense_Mutation	SNP	ENST00000605788.1	hg19	CCDS7530.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.948000	0.73787	.	.	ENSG00000166197	ENST00000405356;ENST00000370007	T	0.52057	0.68	5.72	5.72	0.89469	.	0.256859	0.33834	N	0.004509	T	0.68796	0.3040	M	0.77313	2.365	0.80722	D	1	D;D;D	0.63046	0.992;0.992;0.986	P;P;P	0.61592	0.891;0.891;0.78	T	0.71341	-0.4622	10	0.66056	D	0.02	-7.6697	18.8652	0.92289	0.0:0.0:1.0:0.0	.	171;170;170	Q14978-3;Q14978-2;Q14978	.;.;NOLC1_HUMAN	N	170	ENSP00000385410:D170N	ENSP00000359024:D170N	D	+	1	0	NOLC1	103907862	1.000000	0.71417	0.959000	0.39883	0.796000	0.44982	6.775000	0.75018	2.709000	0.92574	0.561000	0.74099	GAT	.	.	.	none		0.488	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741		A	103917872	G	A	103917872	3	1	200	1	0	0	0	0	1	0	0	0	10536	1290	45	2	526	2	NOLC1	10	103917872	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10		103917872	31616875	44	12107											
DNHD1	144132	hgsc.bcm.edu	37	chr11	6561201	6561201	+	Frame_Shift_Del	DEL	C	C	-																															cagctgcgcctgctcaacttCatcctgcatgtaccctacga																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr11:6561201delC	ENST00000527990.2	+	16	3516	c.3516delC	c.(3514-3516)ttcfs	p.F1172fs	DNHD1_ENST00000254579.6_Frame_Shift_Del_p.F1172fs			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	1172					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)		TGCTCAACTTCATCCTGCATG	0.582																																					p.F1172fs		Atlas-Indel,Pindel	.											.	DNHD1	198	.	0			c.3515delT						PASS	.						62	66	65					11																	6561201		692	1591	2283	SO:0001589	frameshift_variant	144132	exon18			.	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.3516delC	chr11.hg19:g.6561201delC	ENSP00000436180:p.Phe1172fs	170.0	0.0	0		219.0	19.0	0.086758	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Frame_Shift_Del	DEL	ENST00000527990.2	hg19	CCDS44532.1																																																																																			.	.	.	none		0.582	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		-	6561201	C	-	6561201	7	5	200	1	0	1	0	1	0	0	0	0	4670	825	29	0	3587	0	DNHD1	11	6561201	Frame_Shift_Del	DEL	C	TCGA-HE-A5NK-01A-11D-A26P-10		6561201	128445315	45	12108											
OR2AG2	338755	hgsc.bcm.edu	37	chr11	6789370	6789370	+	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	attgtgtagaaaacagagatGatgttgtcttgtttggggct	10	15	13	3	0	1	3	0	1	1	2	1	4	1	3	0	2	1	4	0	2	3	5			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr11:6789370G>T	ENST00000338569.2	-	1	916	c.819C>A	c.(817-819)atC>atA	p.I273I		NM_001004490.1	NP_001004490.1	A6NM03	O2AG2_HUMAN	olfactory receptor, family 2, subfamily AG, member 2	273						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)		AAACAGAGATGATGTTGTCTT	0.512																																					p.I273I		Atlas-SNP	.											OR2AG2,caecum,carcinoma,0,1	OR2AG2	55	.	0			c.C819A						PASS	.						151	138	142					11																	6789370		2201	4296	6497	SO:0001819	synonymous_variant	338755	exon1			AGAGATGATGTTG	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.819C>A	chr11.hg19:g.6789370G>T		332.0	0.0	.		456.0	86.0	.	NM_001004490		Silent	SNP	ENST00000338569.2	hg19	CCDS31413.1																																																																																			.	.	.	none		0.512	OR2AG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386775.1	NM_001004490		T	6789370	G	T	6789370	2	4	200	1	0	0	0	0	0	0	0	1	10992	1280	45	4		4	OR2AG2	11	6789370	Silent	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	228169	6789370	128217146	46	12109											
RBM14	10432	hgsc.bcm.edu	37	chr11	66384484	66384484	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagccaggaactgcgcagccTcttcgagcgccgcggacgcg	7	4	15	15	7	1	0	0	0	1	0	2	4	1	2	3	2	5	1	3	2	1	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr11:66384484T>C	ENST00000310137.4	+	1	432	c.293T>C	c.(292-294)cTc>cCc	p.L98P	RBM14_ENST00000443702.1_Missense_Mutation_p.L98P|RBM14_ENST00000409372.1_Missense_Mutation_p.L98P|RBM14-RBM4_ENST00000511114.1_3'UTR|RBM14-RBM4_ENST00000500635.2_Missense_Mutation_p.L98P|RBM4_ENST00000514361.3_Missense_Mutation_p.L98P|RBM4_ENST00000503028.2_5'UTR|RBM14_ENST00000409738.4_Missense_Mutation_p.L98P|RNU4-39P_ENST00000362455.1_RNA|RBM14-RBM4_ENST00000412278.2_Missense_Mutation_p.L98P|RBM14_ENST00000393979.3_Missense_Mutation_p.L98P	NM_006328.3	NP_006319.1	Q96PK6	RBM14_HUMAN	RNA binding motif protein 14	98	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|glucocorticoid receptor signaling pathway (GO:0042921)|histone deacetylation (GO:0016575)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to hormone (GO:0009725)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)		RBM14/PACS1(2)	breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						CTGCGCAGCCTCTTCGAGCGC	0.647																																					p.L98P		Atlas-SNP	.											.	RBM14	59	.	0			c.T293C						PASS	.						52	62	59					11																	66384484		2141	4173	6314	SO:0001583	missense	10432	exon1			GCAGCCTCTTCGA	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.293T>C	chr11.hg19:g.66384484T>C	ENSP00000311747:p.Leu98Pro	63.0	0.0	.		67.0	8.0	.	NM_001198837	B0LM41|B3KMN4|D6RGD8|O75932|Q2PYN1|Q53GV1|Q68DQ9|Q96PK5	Missense_Mutation	SNP	ENST00000310137.4	hg19	CCDS8147.1	.	.	.	.	.	.	.	.	.	.	T	19.10	3.761857	0.69763	.	.	ENSG00000239306;ENSG00000239306;ENSG00000239306;ENSG00000239306;ENSG00000239306;ENSG00000248643;ENSG00000248643	ENST00000310137;ENST00000393979;ENST00000409372;ENST00000443702;ENST00000409738;ENST00000412278;ENST00000500635	T;T;T;T;T;T;T	0.23754	1.89;1.89;1.89;1.89;1.89;1.89;1.89	5.19	4.01	0.46588	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.257070	0.27811	N	0.017747	T	0.58977	0.2160	H	0.94808	3.585	0.80722	D	1	D;D;D;B	0.89917	1.0;0.999;0.995;0.213	D;D;D;B	0.87578	0.998;0.964;0.974;0.398	T	0.68002	-0.5524	10	0.59425	D	0.04	-4.9687	10.4857	0.44719	0.0:0.0:0.1621:0.8379	.	98;98;98;98	B0LM41;Q96PK6-2;Q2PYN1;Q96PK6	.;.;.;RBM14_HUMAN	P	98	ENSP00000311747:L98P;ENSP00000377548:L98P;ENSP00000386518:L98P;ENSP00000414650:L98P;ENSP00000386995:L98P;ENSP00000388552:L98P;ENSP00000421279:L98P	ENSP00000311747:L98P	L	+	2	0	RBM14;RBM14-RBM4	66141060	0.914000	0.31030	1.000000	0.80357	0.966000	0.64601	1.791000	0.38744	1.971000	0.57363	0.459000	0.35465	CTC	.	.	.	none		0.647	RBM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277128.1	NM_006328		C	66384484	T	C	66384484	3	2	200	1	0	0	0	0	1	0	0	0	13128	1551	54	3	295	3	RBM14	11	66384484	Missense_Mutation	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	59595114	66384484	68622032	47	12110											
MAML2	84441	hgsc.bcm.edu	37	chr11	95712439	95712440	+	Frame_Shift_Ins	INS	-	-	T																															ttagctgattgggtctgagaINSttcagacccctgaggggacc																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr11:95712439_95712440insT	ENST00000524717.1	-	5	4427_4428	c.3143_3144insA	c.(3142-3144)aatfs	p.N1048fs		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	1048					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)				TGGGTCTGAGATTCAGACCCCT	0.5			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.N1048fs		Atlas-Indel,Pindel	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2	94	.	0			c.3144_3145insA						PASS	.																																			SO:0001589	frameshift_variant	84441	exon5			.	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"mastermind (Drosophila)-like 2"			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.3144dupA	chr11.hg19:g.95712441_95712441dupT	ENSP00000434552:p.Asn1048fs	154.0	0.0	0		214.0	49.0	0.228972	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Frame_Shift_Ins	INS	ENST00000524717.1	hg19	CCDS44714.1																																																																																			.	.	.	none		0.5	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95712440	-	T	95712439	7	5	200	1	0	1	1	0	0	0	0	0	9213	330	12	0	330	0	MAML2	11	95712439	Frame_Shift_Ins	INS	-	TCGA-HE-A5NK-01A-11D-A26P-10	29327955	95712439	39294077	48	12111											
KIAA1377	57562	hgsc.bcm.edu	37	chr11	101832493	101832493	+	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	aatttggtgatgaagttaatCagataaccaattctgaaacc	16	12	7	6	0	2	4	1	3	1	1	2	4	2	4	2	1	2	1	2	1	6	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr11:101832493C>G	ENST00000263468.8	+	6	997	c.727C>G	c.(727-729)Cag>Gag	p.Q243E	KIAA1377_ENST00000537689.1_Missense_Mutation_p.Q44E	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	243										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)		TGAAGTTAATCAGATAACCAA	0.313																																					p.Q243E		Atlas-SNP	.											.	KIAA1377	111	.	0			c.C727G						PASS	.						39	42	41					11																	101832493		2199	4295	6494	SO:0001583	missense	57562	exon6			GTTAATCAGATAA	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.727C>G	chr11.hg19:g.101832493C>G	ENSP00000263468:p.Gln243Glu	57.0	0.0	.		73.0	14.0	.	NM_020802	Q4G0U6	Missense_Mutation	SNP	ENST00000263468.8	hg19	CCDS31658.1	.	.	.	.	.	.	.	.	.	.	C	10.77	1.444976	0.25987	.	.	ENSG00000110318	ENST00000263468;ENST00000537689	T;T	0.07908	3.15;3.15	5.51	5.51	0.81932	.	0.475599	0.20115	N	0.098938	T	0.12860	0.0312	M	0.70595	2.14	0.22684	N	0.998852	B	0.24823	0.112	B	0.26094	0.066	T	0.07597	-1.0764	10	0.48119	T	0.1	0.0806	11.3463	0.49563	0.1257:0.6801:0.1941:0.0	.	243	Q9P2H0	K1377_HUMAN	E	243;44	ENSP00000263468:Q243E;ENSP00000443184:Q44E	ENSP00000263468:Q243E	Q	+	1	0	KIAA1377	101337703	0.999000	0.42202	0.995000	0.50966	0.907000	0.53573	1.559000	0.36320	2.595000	0.87683	0.561000	0.74099	CAG	.	.	.	none		0.313	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802		G	101832493	C	G	101832493	3	3	200	1	0	0	0	0	1	0	0	0	8234	827	29	4	749	4	KIAA1377	11	101832493	Missense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	6120054	101832493	33174023	49	12112											
CACNA1C	775	hgsc.bcm.edu	37	chr12	2763057	2763057	+	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	ttcttcatctacgcggtgatCgggatgcaggtagggaggct	7	11	15	8	3	3	1	1	1	2	0	4	3	3	3	0	5	2	3	0	5	2	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr12:2763057C>T	ENST00000347598.4	+	35	4275	c.4275C>T	c.(4273-4275)atC>atT	p.I1425I	CACNA1C_ENST00000335762.5_Silent_p.I1402I|CACNA1C_ENST00000399617.1_Silent_p.I1377I|CACNA1C_ENST00000399649.1_Silent_p.I1364I|CACNA1C_ENST00000399655.1_Silent_p.I1377I|CACNA1C_ENST00000399606.1_Silent_p.I1397I|CACNA1C_ENST00000327702.7_Silent_p.I1377I|CACNA1C_ENST00000399621.1_Silent_p.I1377I|CACNA1C_ENST00000399591.1_Silent_p.I1366I|CACNA1C_ENST00000399601.1_Silent_p.I1377I|CACNA1C_ENST00000399634.1_Silent_p.I1377I|CACNA1C_ENST00000399644.1_Silent_p.I1377I|CACNA1C_ENST00000399629.1_Silent_p.I1394I|CACNA1C_ENST00000402845.3_Silent_p.I1377I|CACNA1C_ENST00000399641.1_Silent_p.I1377I|CACNA1C_ENST00000399637.1_Silent_p.I1377I|CACNA1C_ENST00000344100.3_Silent_p.I1399I|CACNA1C_ENST00000399595.1_Silent_p.I1366I|CACNA1C_ENST00000399603.1_Silent_p.I1377I|CACNA1C_ENST00000399638.1_Silent_p.I1405I|CACNA1C_ENST00000399597.1_Silent_p.I1377I|CACNA1C_ENST00000406454.3_Silent_p.I1377I	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1425					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)	ACGCGGTGATCGGGATGCAGG	0.627																																					p.I1425I		Atlas-SNP	.											Q6YL47_HUMAN,right_upper_lobe,carcinoma,0,5	CACNA1C	1023	.	0			c.C4275T						PASS	.						75	78	77					12																	2763057		2028	4203	6231	SO:0001819	synonymous_variant	775	exon35			GGTGATCGGGATG	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.4275C>T	chr12.hg19:g.2763057C>T		69.0	0.0	.		109.0	27.0	.	NM_199460	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Silent	SNP	ENST00000347598.4	hg19	CCDS44788.1																																																																																			.	.	.	none		0.627	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		T	2763057	C	T	2763057	2	4	200	1	0	0	0	0	0	0	0	1	2542	874	31	1		1	CACNA1C	12	2763057	Silent	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10		2763057	131088838	50	12113											
A2M	2	hgsc.bcm.edu	37	chr12	9242617	9242617	+	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	gctcacagtgaaattcacatTtcctgaaaaaaaaggccagt	16	9	7	9	0	2	2	2	2	0	0	3	2	3	2	2	1	0	1	2	1	5	2			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr12:9242617T>A	ENST00000318602.7	-	21	2906	c.2599A>T	c.(2599-2601)Aat>Tat	p.N867Y		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	867					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)	AAATTCACATTTCCTGAAAAA	0.438																																					p.N867Y		Atlas-SNP	.											.	A2M	180	.	0			c.A2599T						PASS	.						119	118	118					12																	9242617		1893	4112	6005	SO:0001583	missense	2	exon21			TCACATTTCCTGA	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.2599A>T	chr12.hg19:g.9242617T>A	ENSP00000323929:p.Asn867Tyr	144.0	0.0	.		171.0	35.0	.	NM_000014	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Missense_Mutation	SNP	ENST00000318602.7	hg19	CCDS44827.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.24|11.24	1.580426|1.580426	0.28180|0.28180	.|.	.|.	ENSG00000175899|ENSG00000175899	ENST00000543436|ENST00000318602;ENST00000540099	.|T	.|0.17054	.|2.3	5.68|5.68	3.33|3.33	0.38152|0.38152	.|.	.|0.737822	.|0.13068	.|N	.|0.416350	T|T	0.19327|0.19327	0.0464|0.0464	M|M	0.80028|0.80028	2.48|2.48	0.09310|0.09310	N|N	1|1	.|B	.|0.17465	.|0.022	.|B	.|0.15870	.|0.014	T|T	0.41998|0.41998	-0.9477|-0.9477	5|10	.|0.66056	.|D	.|0.02	.|.	0.9957|0.9957	0.01466|0.01466	0.1621:0.1524:0.1695:0.516|0.1621:0.1524:0.1695:0.516	.|.	.|867	.|P01023	.|A2MG_HUMAN	D|Y	114|867;882	.|ENSP00000323929:N867Y	.|ENSP00000323929:N867Y	E|N	-|-	3|1	2|0	A2M|A2M	9133884|9133884	0.000000|0.000000	0.05858|0.05858	0.405000|0.405000	0.26409|0.26409	0.850000|0.850000	0.48378|0.48378	0.257000|0.257000	0.18369|0.18369	0.955000|0.955000	0.37878|0.37878	-0.336000|-0.336000	0.08194|0.08194	GAA|AAT	.	.	.	none		0.438	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014		A	9242617	T	A	9242617	3	1	200	1	0	0	0	0	1	0	0	0	4	1841	64	5	1889	5	A2M	12	9242617	Missense_Mutation	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	6479560	9242617	124609278	51	12114											
PTPRB	5787	hgsc.bcm.edu	37	chr12	71002988	71002988	+	Silent	SNP	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	gggcacaacgcggcccccagGgtgtcactgctatagatgag	9	6	14	12	2	1	2	1	1	0	1	1	2	1	2	2	3	2	2	2	3	3	2			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr12:71002988G>A	ENST00000261266.5	-	2	215	c.186C>T	c.(184-186)acC>acT	p.T62T	PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000538708.1_Silent_p.T62T|PTPRB_ENST00000551525.1_Silent_p.T279T|PTPRB_ENST00000451516.2_Silent_p.T62T|PTPRB_ENST00000334414.6_Silent_p.T280T|PTPRB_ENST00000550857.1_Silent_p.T62T|PTPRB_ENST00000550358.1_Silent_p.T280T	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	62	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			CGGCCCCCAGGGTGTCACTGC	0.498																																					p.T280T		Atlas-SNP	.											.	PTPRB	676	.	0			c.C840T						PASS	.						86	90	88					12																	71002988		1923	4116	6039	SO:0001819	synonymous_variant	5787	exon4			CCCCAGGGTGTCA	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.186C>T	chr12.hg19:g.71002988G>A		275.0	0.0	.		372.0	77.0	.	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Silent	SNP	ENST00000261266.5	hg19	CCDS44944.1	.	.	.	.	.	.	.	.	.	.	G	0.050	-1.252789	0.01469	.	.	ENSG00000127329	ENST00000547715	.	.	.	4.75	-4.0	0.04057	.	.	.	.	.	T	0.17023	0.0409	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.21930	-1.0231	4	.	.	.	.	0.6526	0.00829	0.3902:0.1252:0.1784:0.3062	.	.	.	.	S	54	.	.	P	-	1	0	PTPRB	69289255	0.707000	0.27866	0.000000	0.03702	0.051000	0.14879	-0.453000	0.06778	-1.290000	0.02372	-0.194000	0.12790	CCT	.	.	.	none		0.498	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			A	71002988	G	A	71002988	2	1	200	1	0	0	0	0	0	0	0	1	12809	1219	43	2		2	PTPRB	12	71002988	Silent	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	61760371	71002988	62848907	52	12115											
PGAM5	192111	hgsc.bcm.edu	37	chr12	133294130	133294130	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccatagagaccaccgataTcatcagccggcacctgccag	11	5	9	16	3	2	1	2	0	0	1	2	3	2	1	6	1	2	1	6	1	2	2			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr12:133294130T>C	ENST00000498926.2	+	3	534	c.476T>C	c.(475-477)aTc>aCc	p.I159T	PGAM5_ENST00000543955.1_Missense_Mutation_p.I10T|PGAM5_ENST00000454808.2_Missense_Mutation_p.I10T|PXMP2_ENST00000545677.1_3'UTR|PGAM5_ENST00000317555.2_Missense_Mutation_p.I159T	NM_001170543.1|NM_001170544.1	NP_001164014.1|NP_001164015.1	Q96HS1	PGAM5_HUMAN	phosphoglycerate mutase family member 5	159					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)		ACCACCGATATCATCAGCCGG	0.632																																					p.I159T		Atlas-SNP	.											.	PGAM5	18	.	0			c.T476C						PASS	.						49	55	53					12																	133294130		2203	4298	6501	SO:0001583	missense	192111	exon3			CCGATATCATCAG	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.476T>C	chr12.hg19:g.133294130T>C	ENSP00000438465:p.Ile159Thr	29.0	0.0	.		43.0	4.0	.	NM_138575	A9LN06|C9IZY7|Q96JB0	Missense_Mutation	SNP	ENST00000498926.2	hg19	CCDS53845.1	.	.	.	.	.	.	.	.	.	.	T	19.44	3.827390	0.71143	.	.	ENSG00000247077	ENST00000317555;ENST00000498926;ENST00000543955;ENST00000454808	T;T	0.73681	1.36;-0.77	5.6	5.6	0.85130	Histidine phosphatase superfamily, clade-1 (2);	0.000000	0.85682	D	0.000000	D	0.86577	0.5966	M	0.79693	2.465	0.80722	D	1	D;D	0.76494	0.999;0.988	D;D	0.81914	0.995;0.962	D	0.88249	0.2915	10	0.66056	D	0.02	-3.8102	15.8035	0.78473	0.0:0.0:0.0:1.0	.	159;159	Q96HS1;Q96HS1-2	PGAM5_HUMAN;.	T	159;159;10;10	ENSP00000321503:I159T;ENSP00000438465:I159T	ENSP00000321503:I159T	I	+	2	0	PGAM5	131804203	1.000000	0.71417	1.000000	0.80357	0.267000	0.26476	7.459000	0.80802	2.130000	0.65690	0.482000	0.46254	ATC	.	.	.	none		0.632	PGAM5-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397562.1	NM_138575		C	133294130	T	C	133294130	3	2	200	1	0	0	0	0	1	0	0	0	11783	1435	50	3	486	3	PGAM5	12	133294130	Missense_Mutation	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	62291142	133294130	557765	53	12116											
MTRF1	9617	hgsc.bcm.edu	37	chr13	41791352	41791352	+	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	ctgatccaggcccttcccacCacataaaaattcctggtaaa	13	9	5	14	0	0	1	0	1	0	0	3	1	3	1	5	2	0	1	5	2	5	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr13:41791352C>T	ENST00000379480.4	-	10	1337	c.1237G>A	c.(1237-1239)Ggt>Agt	p.G413S	MTRF1_ENST00000379477.1_Missense_Mutation_p.G413S|MTRF1_ENST00000430347.2_Silent_p.V461V	NM_004294.2	NP_004285.2	O75570	RF1M_HUMAN	mitochondrial translational release factor 1	413					regulation of translational termination (GO:0006449)	mitochondrion (GO:0005739)	translation release factor activity (GO:0003747)|translation release factor activity, codon specific (GO:0016149)			breast(1)|endometrium(4)|large_intestine(3)|lung(6)	14		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)|Ovarian(182;0.125)		OV - Ovarian serous cystadenocarcinoma(117;4.24e-10)|all cancers(112;2.05e-09)|Epithelial(112;2.48e-09)|GBM - Glioblastoma multiforme(144;0.00115)|BRCA - Breast invasive adenocarcinoma(63;0.0721)|KIRC - Kidney renal clear cell carcinoma(186;0.248)		CCCTTCCCACCACATAAAAAT	0.348																																					p.G413S		Atlas-SNP	.											.	MTRF1	24	.	0			c.G1237A						PASS	.						56	61	59					13																	41791352		2203	4300	6503	SO:0001583	missense	9617	exon10			TCCCACCACATAA	AF072934	CCDS9378.1	13q14.1-q14.3	2008-07-18			ENSG00000120662	ENSG00000120662			7469	protein-coding gene	gene with protein product	"mitochontrial peptide chain release factor 1"	604601				9838146, 10773675	Standard	NM_004294		Approved	RF1, MTTRF1, MGC47721	uc001uxy.3	O75570	OTTHUMG00000016790	ENST00000379480.4:c.1237G>A	chr13.hg19:g.41791352C>T	ENSP00000368793:p.Gly413Ser	131.0	0.0	.		181.0	38.0	.	NM_004294	B4DG01|Q5T6Y5|Q8IUQ6	Missense_Mutation	SNP	ENST00000379480.4	hg19	CCDS9378.1	.	.	.	.	.	.	.	.	.	.	C	17.91	3.505562	0.64410	.	.	ENSG00000120662	ENST00000379480;ENST00000379477	T;T	0.58210	0.35;0.35	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.72334	0.3447	M	0.71036	2.16	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.75068	-0.3448	10	0.87932	D	0	-9.2822	16.8351	0.85955	0.0:1.0:0.0:0.0	.	413	O75570	RF1M_HUMAN	S	413	ENSP00000368793:G413S;ENSP00000368790:G413S	ENSP00000368790:G413S	G	-	1	0	MTRF1	40689352	1.000000	0.71417	1.000000	0.80357	0.228000	0.25075	4.053000	0.57427	2.583000	0.87209	0.655000	0.94253	GGT	.	.	.	none		0.348	MTRF1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044666.3	NM_004294		T	41791352	C	T	41791352	3	4	200	1	0	0	0	0	1	0	0	0	9966	594	21	2	104	2	MTRF1	13	41791352	Missense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10		41791352	73378526	54	12117											
BCL2L2	599	hgsc.bcm.edu	37	chr14	23776985	23776985	+	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	atagccgcccggatggcgacCccagcctcggccccagacac	8	3	11	19	4	0	1	0	0	0	1	1	3	0	2	7	3	2	0	7	3	1	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr14:23776985C>A	ENST00000250405.5	+	3	238	c.9C>A	c.(7-9)acC>acA	p.T3T	BCL2L2-PABPN1_ENST00000557008.1_Silent_p.T3T|BCL2L2-PABPN1_ENST00000553781.1_Silent_p.T3T	NM_001199839.1|NM_004050.4	NP_001186768.1|NP_004041	Q92843	B2CL2_HUMAN	BCL2-like 2	3					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)|Sertoli cell proliferation (GO:0060011)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial outer membrane (GO:0005741)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|lung(4)|prostate(1)	6	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00654)		GGATGGCGACCCCAGCCTCGG	0.562																																					p.T3T		Atlas-SNP	.											.	.	.	.	0			c.C9A						PASS	.						53	63	60					14																	23776985		2203	4298	6501	SO:0001819	synonymous_variant	100529063	exon3			GGCGACCCCAGCC	D87461	CCDS9591.1	14q11.2-q12	2014-03-07			ENSG00000129473	ENSG00000129473		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	995	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 51"	601931				8761287	Standard	NM_001199839		Approved	KIAA0271, BCL-W, PPP1R51		Q92843	OTTHUMG00000028738	ENST00000250405.5:c.9C>A	chr14.hg19:g.23776985C>A		80.0	0.0	.		83.0	26.0	.	NM_001199864	A8K0F4|Q2M3U0|Q5U0H4	Silent	SNP	ENST00000250405.5	hg19	CCDS9591.1																																																																																			.	.	.	none		0.562	BCL2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071763.3	NM_004050		A	23776985	C	A	23776985	2	1	200	1	0	0	0	0	0	0	0	1	1374	610	22	4		4	BCL2L2	14	23776985	Silent	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10		23776985	83572555	55	12118											
SAV1	60485	hgsc.bcm.edu	37	chr14	51132105	51132106	+	Frame_Shift_Del	DEL	CT	CT	-																															aatgactgagaagaaccataCtctctagggacatctgctag																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr14:51132105_51132106delCT	ENST00000324679.4	-	2	689_690	c.326_327delAG	c.(325-327)gagfs	p.E109fs	RP11-248J18.2_ENST00000602954.1_RNA	NM_021818.3	NP_068590.1	Q9H4B6	SAV1_HUMAN	salvador family WW domain containing protein 1	109					hair follicle development (GO:0001942)|hippo signaling (GO:0035329)|intestinal epithelial cell differentiation (GO:0060575)|keratinocyte differentiation (GO:0030216)|lung epithelial cell differentiation (GO:0060487)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of epithelial cell proliferation (GO:0050680)|positive regulation of apoptotic process (GO:0043065)|regulation of stem cell maintenance (GO:2000036)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)				breast(1)|kidney(2)|lung(2)|prostate(1)	6	all_epithelial(31;0.000611)|Breast(41;0.0333)					AAGAACCATACTCTCTAGGGAC	0.376																																					p.109_110del		Atlas-Indel,Pindel	.											.	SAV1	18	.	0			c.327_328del						PASS	.																																			SO:0001589	frameshift_variant	60485	exon2			.	AK023071	CCDS9701.1	14q13-q23	2014-04-14	2014-04-14		ENSG00000151748	ENSG00000151748			17795	protein-coding gene	gene with protein product	"WW domain-containing adaptor 45"	607203	"salvador homolog 1 (Drosophila)"			12202036, 11027580	Standard	NM_021818		Approved	WW45, WWP4, salvador	uc001wyh.2	Q9H4B6	OTTHUMG00000140293	ENST00000324679.4:c.326_327delAG	chr14.hg19:g.51132109_51132110delCT	ENSP00000324729:p.Glu109fs	725.0	0.0	0		757.0	161.0	0.212682	NM_021818	A8K4B8|D3DSB6|Q6IA58|Q9H949|Q9HAK9	Frame_Shift_Del	DEL	ENST00000324679.4	hg19	CCDS9701.1																																																																																			.	.	.	none		0.376	SAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276879.1			-	51132106	CT	-	51132105	7	5	200	1	0	1	0	1	0	0	0	0	13869	564	20	0	840	0	SAV1	14	51132105	Frame_Shift_Del	DEL	CT	TCGA-HE-A5NK-01A-11D-A26P-10	27355120	51132105	56217435	56	12119											
MAP1A	4130	hgsc.bcm.edu	37	chr15	43817788	43817788	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttttacagcagaaagacaaaActctggagcacaaggaggtg	16	7	11	7	0	1	2	0	0	1	2	1	4	1	4	0	3	4	2	0	3	5	2			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr15:43817788A>G	ENST00000300231.5	+	4	4567	c.4117A>G	c.(4117-4119)Act>Gct	p.T1373A	MAP1A_ENST00000399453.1_Missense_Mutation_p.T1373A|MAP1A_ENST00000382031.1_Missense_Mutation_p.T1611A			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1373					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)	GAAAGACAAAACTCTGGAGCA	0.443																																					p.T1373A		Atlas-SNP	.											.	MAP1A	189	.	0			c.A4117G						PASS	.						99	96	97					15																	43817788		1906	4125	6031	SO:0001583	missense	4130	exon4			GACAAAACTCTGG	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.4117A>G	chr15.hg19:g.43817788A>G	ENSP00000300231:p.Thr1373Ala	151.0	0.0	.		171.0	52.0	.	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	hg19	CCDS42031.1	.	.	.	.	.	.	.	.	.	.	A	9.136	1.012745	0.19277	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.02280	4.36;4.36;4.36	4.47	1.97	0.26223	.	.	.	.	.	T	0.02807	0.0084	M	0.63428	1.95	0.09310	N	0.999998	B	0.33549	0.417	B	0.30495	0.116	T	0.41431	-0.9509	9	0.27785	T	0.31	0.3065	5.6758	0.17747	0.7318:0.171:0.0972:0.0	.	1373	P78559	MAP1A_HUMAN	A	1611;1373;1373	ENSP00000371462:T1611A;ENSP00000382380:T1373A;ENSP00000300231:T1373A	ENSP00000300231:T1373A	T	+	1	0	MAP1A	41605080	0.004000	0.15560	0.999000	0.59377	0.716000	0.41182	1.917000	0.39996	0.866000	0.35629	0.460000	0.39030	ACT	.	.	.	none		0.443	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373		G	43817788	A	G	43817788	3	3	200	1	0	0	0	0	1	0	0	0	9234	43	2	3	4119	3	MAP1A	15	43817788	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10		43817788	58713604	57	12120											
NUBP2	3483	hgsc.bcm.edu	37	chr16	1837738	1837738	+	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	gctggactacctggtggtggAcacgcccccggggacctccg	5	6	15	15	3	0	0	0	0	0	0	1	3	1	3	5	6	1	1	5	6	1	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr16:1837738A>G	ENST00000215539.3	-	0	2116				NUBP2_ENST00000568706.1_5'UTR|NUBP2_ENST00000262302.9_Missense_Mutation_p.D132G|NUBP2_ENST00000543305.1_5'UTR|NUBP2_ENST00000565134.1_Missense_Mutation_p.D132G|NUBP2_ENST00000565987.1_Missense_Mutation_p.D72G			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						CTGGTGGTGGACACGCCCCCG	0.682																																					p.D132G		Atlas-SNP	.											.	NUBP2	25	.	0			c.A395G						PASS	.						66	67	66					16																	1837738		2199	4300	6499	SO:0001628	intergenic_variant	10101	exon4			TGGTGGACACGCC	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		chr16.hg19:g.1837738A>G		97.0	0.0	.		141.0	6.0	.	NM_012225	B4DZY8|E9PGU3	Missense_Mutation	SNP	ENST00000215539.3	hg19	CCDS10446.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.307453	0.81247	.	.	ENSG00000095906	ENST00000262302	D	0.81821	-1.54	4.92	4.92	0.64577	Mrp, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.94555	0.8246	H	0.99867	4.865	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96490	0.9363	10	0.87932	D	0	-9.7752	13.4012	0.60883	1.0:0.0:0.0:0.0	.	132	Q9Y5Y2	NUBP2_HUMAN	G	132	ENSP00000262302:D132G	ENSP00000262302:D132G	D	+	2	0	NUBP2	1777739	1.000000	0.71417	1.000000	0.80357	0.817000	0.46193	7.008000	0.76341	1.854000	0.53819	0.459000	0.35465	GAC	.	.	.	none		0.682	IGFALS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250509.2			G	1837738	A	G	1837738	1	3	200	0	1	0	0	0	0	0	0	0	10723	275	10	3		3	NUBP2	16	1837738	IGR	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10		1837738	88517015	58	12121											
CP110	9738	hgsc.bcm.edu	37	chr16	19548820	19548820	+	Missense_Mutation	SNP	A	A	T																															cataacaagtggaataactgAacaagaaaggcaacatttgc																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr16:19548820A>T	ENST00000381396.5	+	4	2076	c.1829A>T	c.(1828-1830)gAa>gTa	p.E610V	CCP110_ENST00000396212.2_Missense_Mutation_p.E610V|CCP110_ENST00000396208.2_Missense_Mutation_p.E610V	NM_001199022.1	NP_001185951	O43303	CP110_HUMAN	centriolar coiled coil protein 110kDa	610					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						GGAATAACTGAACAAGAAAGG	0.348																																					p.E610V		Atlas-SNP	.											.	CCP110	57	.	0			c.A1829T						PASS	.						67	72	70					16																	19548820		2197	4300	6497	SO:0001583	missense	9738	exon4			TAACTGAACAAGA	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.1829A>T	chr16.hg19:g.19548820A>T	ENSP00000370803:p.Glu610Val	184.0	0.0	.		235.0	40.0	.	NM_001199022	B7WP23|O43335|Q68DV9|Q8NE13	Missense_Mutation	SNP	ENST00000381396.5	hg19	CCDS55992.1	.	.	.	.	.	.	.	.	.	.	A	14.41	2.527464	0.44969	.	.	ENSG00000103540	ENST00000396212;ENST00000381396;ENST00000396208	T;T;T	0.16897	2.31;2.31;2.31	5.17	5.17	0.71159	.	0.139138	0.46145	D	0.000310	T	0.16557	0.0398	L	0.58101	1.795	0.30579	N	0.762718	P;P	0.45715	0.865;0.865	B;B	0.42555	0.391;0.391	T	0.30090	-0.9990	10	0.48119	T	0.1	-1.1381	3.1962	0.06634	0.6412:0.1436:0.0771:0.1382	.	610;610	O43303;O43303-2	CP110_HUMAN;.	V	610	ENSP00000379515:E610V;ENSP00000370803:E610V;ENSP00000379511:E610V	ENSP00000370803:E610V	E	+	2	0	CCP110	19456321	1.000000	0.71417	0.981000	0.43875	0.972000	0.66771	2.685000	0.46959	1.933000	0.56026	0.460000	0.39030	GAA	.	.	.	none		0.348	CCP110-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254284.2	NM_014711		T	19548820	A	T	19548820	3	4	200	1	0	0	0	0	1	0	0	0	3790	246	9	5	1839	5	CP110	16	19548820	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	17711082	19548820	70805933	59	12122	113	2									
CP110	9738	hgsc.bcm.edu	37	chr16	19548822	19548822	+	Missense_Mutation	SNP	C	C	A																															taacaagtggaataactgaaCaagaaaggcaacatttgcca																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr16:19548822C>A	ENST00000381396.5	+	4	2078	c.1831C>A	c.(1831-1833)Caa>Aaa	p.Q611K	CCP110_ENST00000396212.2_Missense_Mutation_p.Q611K|CCP110_ENST00000396208.2_Missense_Mutation_p.Q611K	NM_001199022.1	NP_001185951	O43303	CP110_HUMAN	centriolar coiled coil protein 110kDa	611					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						AATAACTGAACAAGAAAGGCA	0.348																																					p.Q611K		Atlas-SNP	.											.	CCP110	57	.	0			c.C1831A						PASS	.						66	71	69					16																	19548822		2197	4300	6497	SO:0001583	missense	9738	exon4			ACTGAACAAGAAA	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.1831C>A	chr16.hg19:g.19548822C>A	ENSP00000370803:p.Gln611Lys	181.0	0.0	.		234.0	40.0	.	NM_001199022	B7WP23|O43335|Q68DV9|Q8NE13	Missense_Mutation	SNP	ENST00000381396.5	hg19	CCDS55992.1	.	.	.	.	.	.	.	.	.	.	C	14.97	2.694577	0.48202	.	.	ENSG00000103540	ENST00000396212;ENST00000381396;ENST00000396208	T;T;T	0.19105	2.17;2.17;2.17	5.17	5.17	0.71159	.	0.260422	0.33127	N	0.005246	T	0.25005	0.0607	L	0.58101	1.795	0.35963	D	0.834752	P;P	0.41978	0.767;0.767	B;B	0.41510	0.359;0.359	T	0.33904	-0.9850	10	0.72032	D	0.01	-0.143	12.0805	0.53667	0.0:0.9211:0.0:0.0789	.	611;611	O43303;O43303-2	CP110_HUMAN;.	K	611	ENSP00000379515:Q611K;ENSP00000370803:Q611K;ENSP00000379511:Q611K	ENSP00000370803:Q611K	Q	+	1	0	CCP110	19456323	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	3.793000	0.55484	2.385000	0.81259	0.563000	0.77884	CAA	.	.	.	none		0.348	CCP110-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254284.2	NM_014711		A	19548822	C	A	19548822	3	1	200	1	0	0	0	0	1	0	0	0	3790	479	17	4	1841	4	CP110	16	19548822	Missense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	2	19548822	70805931	60	12123	113	2									
PRR14	78994	hgsc.bcm.edu	37	chr16	30666137	30666137	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccgtcccccccaatgaagctGgagttgaagatcgccatctc	9	8	9	15	2	1	3	0	2	1	1	4	4	2	4	5	1	1	2	5	1	3	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr16:30666137G>A	ENST00000542965.2	+	7	1302	c.846G>A	c.(844-846)ctG>ctA	p.L282L	PRR14_ENST00000300835.4_Silent_p.L282L			Q9BWN1	PRR14_HUMAN	proline rich 14	282	Pro-rich.									breast(3)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	18			Colorectal(24;0.103)			CAATGAAGCTGGAGTTGAAGA	0.637																																					p.L282L		Atlas-SNP	.											.	PRR14	45	.	0			c.G846A						PASS	.						19	23	21					16																	30666137		2192	4295	6487	SO:0001819	synonymous_variant	78994	exon8			GAAGCTGGAGTTG	AK074783	CCDS10687.1	16p11.2	2008-02-05			ENSG00000156858	ENSG00000156858			28458	protein-coding gene	gene with protein product						12477932	Standard	NM_024031		Approved	MGC3121	uc002dyy.3	Q9BWN1	OTTHUMG00000132414	ENST00000542965.2:c.846G>A	chr16.hg19:g.30666137G>A		37.0	0.0	.		37.0	6.0	.	NM_024031	Q8WTX2	Silent	SNP	ENST00000542965.2	hg19	CCDS10687.1																																																																																			.	.	.	none		0.637	PRR14-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434433.1	NM_024031		A	30666137	G	A	30666137	2	1	200	1	0	0	0	0	0	0	0	1	12596	1335	47	2		2	PRR14	16	30666137	Silent	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	11117315	30666137	59688616	61	12124											
FBXL19	54620	hgsc.bcm.edu	37	chr16	30958111	30958111	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgcgtctggcaggtttggAgctgacagatgcctccctgc	6	10	13	12	1	1	2	0	1	1	1	2	3	2	3	2	3	4	3	2	3	0	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr16:30958111A>G	ENST00000380310.2	+	10	1906	c.1748A>G	c.(1747-1749)gAg>gGg	p.E583G	AC135048.13_ENST00000566056.1_RNA|ORAI3_ENST00000566237.1_5'Flank|FBXL19_ENST00000562319.1_Missense_Mutation_p.E563G|ORAI3_ENST00000318663.4_5'Flank|FBXL19_ENST00000565690.1_Missense_Mutation_p.E447G|ORAI3_ENST00000562699.1_5'Flank|FBXL19_ENST00000471231.2_Missense_Mutation_p.E271G|FBXL19_ENST00000338343.4_Missense_Mutation_p.E563G	NM_001099784.2	NP_001093254.2	Q6PCT2	FXL19_HUMAN	F-box and leucine-rich repeat protein 19	583					proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)	SCF ubiquitin ligase complex (GO:0019005)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|lung(5)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16						GCAGGTTTGGAGCTGACAGAT	0.667																																					p.E583G		Atlas-SNP	.											.	FBXL19	74	.	0			c.A1748G						PASS	.						33	40	38					16																	30958111		2140	4240	6380	SO:0001583	missense	54620	exon10			GTTTGGAGCTGAC	AK127701	CCDS45465.1, CCDS73873.1	16p11.2	2014-02-20			ENSG00000099364	ENSG00000099364		"F-boxes / Leucine-rich repeats"	25300	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1C"	609085					Standard	NM_001099784		Approved	DKFZp434K0410, Fbl19, JHDM1C, CXXC11	uc002eab.2	Q6PCT2	OTTHUMG00000132403	ENST00000380310.2:c.1748A>G	chr16.hg19:g.30958111A>G	ENSP00000369666:p.Glu583Gly	102.0	0.0	.		100.0	4.0	.	NM_001099784	A8MT10|Q8N789|Q9NT14	Missense_Mutation	SNP	ENST00000380310.2	hg19	CCDS45465.1	.	.	.	.	.	.	.	.	.	.	A	14.02	2.411339	0.42817	.	.	ENSG00000099364	ENST00000338343;ENST00000380310	T;T	0.35421	1.31;1.31	4.76	4.76	0.60689	.	0.135420	0.48286	D	0.000188	T	0.26882	0.0658	N	0.25031	0.7	0.48762	D	0.999706	B;B	0.25390	0.125;0.005	B;B	0.24006	0.05;0.005	T	0.08827	-1.0703	10	0.62326	D	0.03	-16.01	13.2832	0.60228	1.0:0.0:0.0:0.0	.	583;540	Q6PCT2;Q6PCT2-2	FXL19_HUMAN;.	G	563;583	ENSP00000339712:E563G;ENSP00000369666:E583G	ENSP00000339712:E563G	E	+	2	0	FBXL19	30865612	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.381000	0.79718	1.789000	0.52484	0.459000	0.35465	GAG	.	.	.	none		0.667	FBXL19-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_019085		G	30958111	A	G	30958111	3	3	200	1	0	0	0	0	1	0	0	0	5722	304	11	3	1786	3	FBXL19	16	30958111	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	291974	30958111	59396642	62	12125											
ITGAX	3687	hgsc.bcm.edu	37	chr16	31374006	31374006	+	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	ccccccgctaccagcacaccGggaaggctgtcatcttcacc	8	6	8	19	2	3	0	2	0	1	0	3	1	3	1	6	2	2	3	6	2	2	2	rs554674355		TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr16:31374006G>C	ENST00000268296.4	+	12	1412	c.1291G>C	c.(1291-1293)Ggg>Cgg	p.G431R	ITGAX_ENST00000562522.1_Missense_Mutation_p.G431R	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	431					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						CCAGCACACCGGGAAGGCTGT	0.647																																					p.G431R		Atlas-SNP	.											.	ITGAX	198	.	0			c.G1291C						PASS	.						34	33	33					16																	31374006		2197	4300	6497	SO:0001583	missense	3687	exon12			CACACCGGGAAGG	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.1291G>C	chr16.hg19:g.31374006G>C	ENSP00000268296:p.Gly431Arg	371.0	0.0	.		523.0	116.0	.	NM_000887	Q8IVA6	Missense_Mutation	SNP	ENST00000268296.4	hg19	CCDS10711.1	.	.	.	.	.	.	.	.	.	.	g	18.79	3.698354	0.68386	.	.	ENSG00000140678	ENST00000268296	T	0.54479	0.57	3.76	2.69	0.31865	.	.	.	.	.	T	0.80979	0.4728	H	0.98559	4.265	0.33798	D	0.62635	D	0.89917	1.0	D	0.87578	0.998	D	0.87513	0.2441	9	0.87932	D	0	.	10.1899	0.43019	0.0:0.2038:0.7962:0.0	.	431	P20702	ITAX_HUMAN	R	431	ENSP00000268296:G431R	ENSP00000268296:G431R	G	+	1	0	ITGAX	31281507	0.999000	0.42202	0.997000	0.53966	0.899000	0.52679	3.647000	0.54403	1.829000	0.53265	0.448000	0.29417	GGG	.	.	.	none		0.647	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887		C	31374006	G	C	31374006	3	2	200	1	0	0	0	0	1	0	0	0	7896	1116	39	4	1337	4	ITGAX	16	31374006	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	415895	31374006	58980747	63	12126											
GHDC	84514	hgsc.bcm.edu	37	chr17	40344519	40344519	+	Frame_Shift_Del	DEL	A	A	-																															catcagtctccaggcccaagAaaacatccagaagttcgaca																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr17:40344519delA	ENST00000301671.8	-	4	1070	c.629delT	c.(628-630)ttcfs	p.F210fs	GHDC_ENST00000414034.3_Frame_Shift_Del_p.F210fs|GHDC_ENST00000428494.2_Frame_Shift_Del_p.F171fs|GHDC_ENST00000436923.2_Frame_Shift_Del_p.F210fs|GHDC_ENST00000593209.1_Frame_Shift_Del_p.F210fs|GHDC_ENST00000590520.1_5'Flank|GHDC_ENST00000587427.1_Frame_Shift_Del_p.F210fs			Q8N2G8	GHDC_HUMAN	GH3 domain containing	210						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		all_cancers(22;0.000229)|Breast(137;0.00104)|all_epithelial(22;0.00304)		BRCA - Breast invasive adenocarcinoma(366;0.124)		CAGGCCCAAGAAAACATCCAG	0.652																																					p.F210fs		Atlas-Indel,Pindel	.											.	GHDC	63	.	0			c.630delC						PASS	.						82	94	89					17																	40344519		2202	4298	6500	SO:0001589	frameshift_variant	84514	exon5			.	AF316997, BC011056	CCDS11422.1, CCDS45682.1	17q21.2	2006-08-02				ENSG00000167925			24438	protein-coding gene	gene with protein product		608587				11161808, 11735219	Standard	NR_024573		Approved	LGP1	uc002hzf.4	Q8N2G8		ENST00000301671.8:c.629delT	chr17.hg19:g.40344519delA	ENSP00000301671:p.Phe210fs	132.0	0.0	0		194.0	19.0	0.0979381	NM_032484	B4DQS4|E9PDB5|Q9BXM6	Frame_Shift_Del	DEL	ENST00000301671.8	hg19	CCDS11422.1																																																																																			.	.	.	none		0.652	GHDC-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449794.1	NM_032484		-	40344519	A	-	40344519	7	5	200	1	0	1	0	1	0	0	0	0	6376	246	9	0	1076	0	GHDC	17	40344519	Frame_Shift_Del	DEL	A	TCGA-HE-A5NK-01A-11D-A26P-10		40344519	40850691	64	12127											
MMD	23531	hgsc.bcm.edu	37	chr17	53485137	53485138	+	Frame_Shift_Ins	INS	-	-	AG																															agaagcagcaatgaagaaatINSagataaccattctatcacac																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr17:53485137_53485138insAG	ENST00000262065.3	-	4	609_610	c.313_314insCT	c.(313-315)tatfs	p.Y105fs		NM_012329.2	NP_036461.2	Q15546	PAQRB_HUMAN	monocyte to macrophage differentiation-associated	105					cytolysis (GO:0019835)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|large_intestine(1)|lung(4)|prostate(1)	7						AATGAAGAAATAGATAACCATT	0.386																																					p.Y105fs		Atlas-Indel,Pindel	.											.	MMD	26	.	0			c.314_315insCT						PASS	.																																			SO:0001589	frameshift_variant	23531	exon4			.	X85750	CCDS11586.1	17q	2008-05-02				ENSG00000108960			7153	protein-coding gene	gene with protein product		604467				7503749, 16044242	Standard	NM_012329		Approved	MMA, PAQR11	uc002iui.3	Q15546		ENST00000262065.3:c.312_313dupCT	chr17.hg19:g.53485138_53485139dupAG	ENSP00000262065:p.Tyr105fs	114.0	0.0	0		115.0	31.0	0.269565	NM_012329	B2R6X9|D3DTY6|Q8TAN7	Frame_Shift_Ins	INS	ENST00000262065.3	hg19	CCDS11586.1																																																																																			.	.	.	none		0.386	MMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439214.1			AG	53485138	-	AG	53485137	7	5	200	1	0	1	1	0	0	0	0	0	9650	1406	49	0	418	0	MMD	17	53485137	Frame_Shift_Ins	INS	-	TCGA-HE-A5NK-01A-11D-A26P-10	13140618	53485137	27710073	65	12128											
PPM1E	22843	hgsc.bcm.edu	37	chr17	56833454	56833454	+	Silent	SNP	G	G	A																															tgcggcggcggcgagccggaGccggaacccgaacccgaacc																								rs77856248		TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	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	.	0			c.G96A						PASS	.						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	chr17.hg19:g.56833454G>A		54.0	0.0	.		78.0	14.0	.	NM_014906	Q8N8J9|Q96DB8	Silent	SNP	ENST00000308249.2	hg19	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	200	1	0	0	0	0	0	0	0	1	12348	962	34	2		2	PPM1E	17	56833454	Silent	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	3348317	56833454	24361756	66	12129	114	2	1	25		3	2	37	N	G	9.535435e-05
PPM1E	22843	hgsc.bcm.edu	37	chr17	56833457	56833457	+	Silent	SNP	G	G	C																															ggcggcggcgagccggagccGgaacccgaacccgaacccga																								rs3834568|rs201186780|rs74256772	byFrequency	TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	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	.	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	chr17.hg19:g.56833457G>C		50.0	0.0	.		76.0	17.0	.	NM_014906	Q8N8J9|Q96DB8	Silent	SNP	ENST00000308249.2	hg19	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	200	1	0	0	0	0	0	0	0	1	12348	1103	39	4		4	PPM1E	17	56833457	Silent	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	3	56833457	24361753	67	12130	114	2	1	25		3	2	37	N	G	9.535435e-05
PPM1E	22843	hgsc.bcm.edu	37	chr17	56833490	56833490	+	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	gaacccgaacccgaacccgaGtccgagcccgagcccgaacc	11	1	10	19	6	0	0	0	0	0	0	1	7	1	0	7	0	6	0	7	0	4	0	rs59676153		TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	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	.	0			c.G132A						PASS	.																																			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	chr17.hg19:g.56833490G>A		65.0	0.0	.		97.0	9.0	.	NM_014906	Q8N8J9|Q96DB8	Silent	SNP	ENST00000308249.2	hg19	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	200	1	0	0	0	0	0	0	0	1	12348	1020	36	2		2	PPM1E	17	56833490	Silent	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	33	56833490	24361720	68	12131			1	25		3	2	37	N	G	9.535435e-05
RNF213	57674	hgsc.bcm.edu	37	chr17	78350139	78350141	+	In_Frame_Del	DEL	GAT	GAT	-																															aaattcattggcgaatgcaaGatcctttcacctcctgatat																										TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	GAT	GAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr17:78350139_78350141delGAT	ENST00000582970.1	+	52	13367_13369	c.13224_13226delGAT	c.(13222-13227)aagatc>aac	p.4408_4409KI>N	RNF213_ENST00000508628.2_In_Frame_Del_p.4457_4458KI>N|CTD-2047H16.4_ENST00000575034.1_RNA|CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000336301.6_In_Frame_Del_p.2481_2482KI>N	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	4408					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)			GCGAATGCAAGATCCTTTCACCT	0.433																																					p.4408_4409del		Atlas-Indel,Pindel	.											.	RNF213	766	.	0			c.13223_13225del						PASS	.																																			SO:0001651	inframe_deletion	57674	exon52			.	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.13224_13226delGAT	chr17.hg19:g.78350139_78350141delGAT	ENSP00000464087:p.Lys4408_Ile4409delinsAsn	159.0	0.0	0		253.0	32.0	0.126482	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	In_Frame_Del	DEL	ENST00000582970.1	hg19	CCDS58606.1																																																																																			.	.	.	none		0.433	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		-	78350141	GAT	-	78350139	7	5	200	1	0	1	0	1	0	0	0	0	13490	933	33	0	13745	0	RNF213	17	78350139	In_Frame_Del	DEL	GAT	TCGA-HE-A5NK-01A-11D-A26P-10	21516649	78350139	2845071	69	12132											
ZNF236	7776	hgsc.bcm.edu	37	chr18	74680294	74680294	+	Nonstop_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	ggccctcacccacgtcttctGatgcgagttggaagtacacc	8	9	10	14	2	3	1	1	1	2	0	3	3	3	2	3	2	2	2	3	2	2	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr18:74680294G>T	ENST00000253159.8	+	31	5735	c.5537G>T	c.(5536-5538)tGa>tTa	p.*1846L	ZNF236_ENST00000320610.9_Nonstop_Mutation_p.*1848L	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	0					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)		CACGTCTTCTGATGCGAGTTG	0.542																																					p.X1846L		Atlas-SNP	.											.	ZNF236	325	.	0			c.G5537T						PASS	.						65	76	72					18																	74680294		1938	4135	6073	SO:0001578	stop_lost	7776	exon31			TCTTCTGATGCGA	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.5537G>T	chr18.hg19:g.74680294G>T	ENSP00000253159:p.*1846Leuext*8	56.0	0.0	.		72.0	4.0	.	NM_007345	B2RTX9|Q9UL37	Missense_Mutation	SNP	ENST00000253159.8	hg19	CCDS42447.1	.	.	.	.	.	.	.	.	.	.	G	8.724	0.914980	0.17907	.	.	ENSG00000130856	ENST00000253159	.	.	.	4.91	4.04	0.47022	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5206	0.61566	0.0765:0.0:0.9235:0.0	.	.	.	.	L	1846	.	.	X	+	2	2	ZNF236	72809282	1.000000	0.71417	0.888000	0.34837	0.039000	0.13416	5.969000	0.70422	1.207000	0.43291	0.557000	0.71058	TGA	.	.	.	none		0.542	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1			T	74680294	G	T	74680294	4	4	200	1	0	0	0	0	0	0	0	0	17801	1285	45	4	5659	4	ZNF236	18	74680294	Nonstop_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10		74680294	3396954	70	12133											
DOT1L	84444	hgsc.bcm.edu	37	chr19	2210830	2210830	+	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	tgcacgctcagaccgtgtctCagacggcggcctcctcaccc	6	7	10	18	4	3	2	3	0	1	2	5	2	4	2	4	2	1	2	4	2	0	0			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr19:2210830C>T	ENST00000398665.3	+	14	1363	c.1327C>T	c.(1327-1329)Cag>Tag	p.Q443*	AC004490.1_ENST00000585593.1_RNA	NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	443					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)		GACCGTGTCTCAGACGGCGGC	0.692																																					p.Q443X		Atlas-SNP	.											.	DOT1L	205	.	0			c.C1327T						PASS	.						26	34	31					19																	2210830		1991	4142	6133	SO:0001587	stop_gained	84444	exon14			GTGTCTCAGACGG	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.1327C>T	chr19.hg19:g.2210830C>T	ENSP00000381657:p.Gln443*	98.0	0.0	.		151.0	35.0	.	NM_032482	O60379|Q96JL1	Nonsense_Mutation	SNP	ENST00000398665.3	hg19	CCDS42460.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.878112	0.91664	.	.	ENSG00000104885	ENST00000398665;ENST00000221482	.	.	.	4.84	4.84	0.62591	.	0.625695	0.16263	N	0.222122	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-7.1526	16.9353	0.86202	0.0:1.0:0.0:0.0	.	.	.	.	X	443	.	ENSP00000221482:Q443X	Q	+	1	0	DOT1L	2161830	0.963000	0.33076	0.020000	0.16555	0.076000	0.17211	4.755000	0.62198	2.222000	0.72286	0.561000	0.74099	CAG	.	.	.	none		0.692	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482		T	2210830	C	T	2210830	4	4	200	1	0	0	0	0	0	1	0	0	4711	827	29	2	1381	2	DOT1L	19	2210830	Nonsense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10		2210830	56918153	71	12134											
HAPLN4	404037	hgsc.bcm.edu	37	chr19	19371725	19371725	+	Silent	SNP	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	gtgacgttgcggaggaccagGgaggcatccccaggcccgtc	7	5	16	13	3	0	1	0	1	0	0	2	4	1	4	4	5	1	2	4	5	0	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr19:19371725G>A	ENST00000291481.7	-	3	444	c.381C>T	c.(379-381)tcC>tcT	p.S127S	AC138430.4_ENST00000586064.2_RNA	NM_023002.2	NP_075378.1	Q86UW8	HPLN4_HUMAN	hyaluronan and proteoglycan link protein 4	127	Ig-like C2-type.				cell adhesion (GO:0007155)	proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(1)	16			Epithelial(12;0.00575)		Hyaluronan(DB08818)	GGAGGACCAGGGAGGCATCCC	0.652																																					p.S127S		Atlas-SNP	.											.	HAPLN4	44	.	0			c.C381T						PASS	.						66	61	63					19																	19371725		2203	4300	6503	SO:0001819	synonymous_variant	404037	exon3			GACCAGGGAGGCA	AB107883	CCDS12398.1	19p13.1	2013-01-11						"Immunoglobulin superfamily / V-set domain containing"	31357	protein-coding gene	gene with protein product	"brain link protein 2"					12663660	Standard	NM_023002		Approved	BRAL2, KIAA1926	uc002nmb.3	Q86UW8		ENST00000291481.7:c.381C>T	chr19.hg19:g.19371725G>A		64.0	0.0	.		50.0	12.0	.	NM_023002	A5PKW5|Q96PW2	Silent	SNP	ENST00000291481.7	hg19	CCDS12398.1																																																																																			.	.	.	none		0.652	HAPLN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460117.2	NM_023002		A	19371725	G	A	19371725	2	1	200	1	0	0	0	0	0	0	0	1	6964	1219	43	2		2	HAPLN4	19	19371725	Silent	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	17160895	19371725	39757258	72	12135											
GRAMD1A	57655	hgsc.bcm.edu	37	chr19	35500151	35500151	+	Missense_Mutation	SNP	A	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	catggtggagaagggatcagAtagctcctcagagaagggtg	12	7	16	6	0	2	3	2	0	0	3	3	6	3	4	1	4	1	1	1	4	3	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr19:35500151A>C	ENST00000317991.5	+	2	329	c.137A>C	c.(136-138)gAt>gCt	p.D46A	GRAMD1A_ENST00000424536.2_Missense_Mutation_p.D46A|GRAMD1A_ENST00000411896.2_Missense_Mutation_p.D46A|GRAMD1A_ENST00000599564.1_Missense_Mutation_p.D133A|GRAMD1A_ENST00000504615.2_5'UTR|GRAMD1A_ENST00000598073.1_3'UTR	NM_020895.3	NP_065946.2	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A	46						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)			AAGGGATCAGATAGCTCCTCA	0.647																																					p.D46A		Atlas-SNP	.											.	GRAMD1A	39	.	0			c.A137C						PASS	.						38	45	43					19																	35500151		1939	4128	6067	SO:0001583	missense	57655	exon2			GATCAGATAGCTC	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.137A>C	chr19.hg19:g.35500151A>C	ENSP00000441032:p.Asp46Ala	72.0	0.0	.		138.0	22.0	.	NM_020895	A6NKY7|Q8NC77|Q9P1Z5	Missense_Mutation	SNP	ENST00000317991.5	hg19	CCDS42546.1	.	.	.	.	.	.	.	.	.	.	A	18.24	3.579681	0.65992	.	.	ENSG00000089351	ENST00000453966;ENST00000317991;ENST00000411896	T;T	0.25250	1.81;1.83	4.67	4.67	0.58626	.	0.081214	0.49916	D	0.000124	T	0.30665	0.0772	N	0.19112	0.55	0.80722	D	1	D;D;D;D	0.60160	0.987;0.978;0.987;0.987	P;P;P;P	0.61477	0.889;0.698;0.841;0.889	T	0.05402	-1.0887	10	0.45353	T	0.12	.	12.1081	0.53823	1.0:0.0:0.0:0.0	.	46;46;46;133	Q96CP6-3;Q96CP6;Q96CP6-2;F5GZ02	.;GRM1A_HUMAN;.;.	A	133;46;46	ENSP00000441032:D46A;ENSP00000439267:D46A	ENSP00000441032:D46A	D	+	2	0	GRAMD1A	40191991	1.000000	0.71417	0.569000	0.28460	0.688000	0.40055	4.842000	0.62831	1.965000	0.57142	0.459000	0.35465	GAT	.	.	.	none		0.647	GRAMD1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461557.1	NM_020895		C	35500151	A	C	35500151	3	2	200	1	0	0	0	0	1	0	0	0	6754	333	12	5	143	5	GRAMD1A	19	35500151	Missense_Mutation	SNP	A	TCGA-HE-A5NK-01A-11D-A26P-10	16128426	35500151	23628832	73	12136											
ZNF749	388567	hgsc.bcm.edu	37	chr19	57956504	57956504	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tattcatcagagagttcataCtggagaaaagccttatgaat	15	12	8	6	0	3	3	3	1	0	2	3	5	3	3	1	1	2	1	1	1	6	5			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr19:57956504C>T	ENST00000334181.4	+	3	2238	c.1988C>T	c.(1987-1989)aCt>aTt	p.T663I	AC004076.9_ENST00000596831.1_Intron	NM_001023561.2	NP_001018855.2	O43361	ZN749_HUMAN	zinc finger protein 749	663					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)|lung(3)|prostate(1)	13		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;0.0264)|Lung(386;0.177)		AGAGTTCATACTGGAGAAAAG	0.383																																					p.T663I		Atlas-SNP	.											.	ZNF749	75	.	0			c.C1988T						PASS	.						42	44	43					19																	57956504		2203	4300	6503	SO:0001583	missense	388567	exon3			TTCATACTGGAGA	AK122740	CCDS33132.2	19q13.43	2013-01-08			ENSG00000186230	ENSG00000186230		"Zinc fingers, C2H2-type", "-"	32783	protein-coding gene	gene with protein product							Standard	NM_001023561		Approved	FLJ16360	uc002qoq.2	O43361	OTTHUMG00000150372	ENST00000334181.4:c.1988C>T	chr19.hg19:g.57956504C>T	ENSP00000333980:p.Thr663Ile	82.0	0.0	.		86.0	4.0	.	NM_001023561		Missense_Mutation	SNP	ENST00000334181.4	hg19	CCDS33132.2	.	.	.	.	.	.	.	.	.	.	C	11.60	1.686234	0.29962	.	.	ENSG00000186230	ENST00000334181	T	0.25749	1.78	2.05	-3.04	0.05412	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17746	0.0426	L	0.46819	1.47	0.22835	N	0.998678	P	0.35959	0.53	B	0.34180	0.177	T	0.15809	-1.0424	9	0.87932	D	0	.	3.6737	0.08284	0.1878:0.558:0.0:0.2541	.	663	O43361	ZN749_HUMAN	I	663	ENSP00000333980:T663I	ENSP00000333980:T663I	T	+	2	0	ZNF749	62648316	0.000000	0.05858	0.000000	0.03702	0.188000	0.23474	-0.145000	0.10265	-0.817000	0.04335	0.313000	0.20887	ACT	.	.	.	none		0.383	ZNF749-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317879.1	NM_001023561		T	57956504	C	T	57956504	3	4	200	1	0	0	0	0	1	0	0	0	18143	565	20	2	1998	2	ZNF749	19	57956504	Missense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	22456353	57956504	1172479	74	12137											
ZNF418	147686	hgsc.bcm.edu	37	chr19	58438722	58438722	+	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	tcccagtgtgaactcgctgaTgctgaacaaggctgccctta	9	10	10	12	1	0	3	0	3	0	0	2	3	1	3	2	1	4	3	2	1	4	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr19:58438722T>A	ENST00000396147.1	-	4	1118	c.827A>T	c.(826-828)cAt>cTt	p.H276L	ZNF418_ENST00000599086.1_5'Flank|ZNF418_ENST00000599852.1_Missense_Mutation_p.H191L|ZNF418_ENST00000595830.1_Missense_Mutation_p.H276L|ZNF418_ENST00000425570.3_Missense_Mutation_p.H297L|ZNF418_ENST00000600989.1_Intron	NM_133460.1	NP_597717.1	Q8TF45	ZN418_HUMAN	zinc finger protein 418	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)			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)		AACTCGCTGATGCTGAACAAG	0.433																																					p.H276L		Atlas-SNP	.											.	ZNF418	76	.	0			c.A827T						PASS	.						90	92	91					19																	58438722		2189	4296	6485	SO:0001583	missense	147686	exon4			CGCTGATGCTGAA	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.827A>T	chr19.hg19:g.58438722T>A	ENSP00000379451:p.His276Leu	142.0	0.0	.		172.0	34.0	.	NM_133460	Q2M1S2|Q670L5|Q96N18	Missense_Mutation	SNP	ENST00000396147.1	hg19	CCDS42642.1	.	.	.	.	.	.	.	.	.	.	.	11.49	1.655252	0.29425	.	.	ENSG00000196724	ENST00000396147;ENST00000425570;ENST00000545403	D;D	0.86865	-2.18;-2.18	2.26	1.15	0.20763	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.90147	0.6921	H	0.98295	4.195	0.09310	N	0.999995	P	0.38110	0.618	B	0.33254	0.16	D	0.83866	0.0271	9	0.87932	D	0	.	6.5871	0.22626	0.2146:0.0:0.0:0.7854	.	276	Q8TF45	ZN418_HUMAN	L	276;297;242	ENSP00000379451:H276L;ENSP00000407039:H297L	ENSP00000379451:H276L	H	-	2	0	ZNF418	63130534	.	.	0.001000	0.08648	0.109000	0.19521	.	.	0.129000	0.18514	0.240000	0.17902	CAT	.	.	.	none		0.433	ZNF418-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466693.1	NM_133460		A	58438722	T	A	58438722	3	1	200	1	0	0	0	0	1	0	0	0	17907	1464	51	5	1207	5	ZNF418	19	58438722	Missense_Mutation	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	482218	58438722	690261	75	12138											
CST9L	128821	hgsc.bcm.edu	37	chr20	23546696	23546696	+	Missense_Mutation	SNP	T	T	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	tagttctccccagcagtagcTccattgagaatacagtcttg	10	12	8	11	0	2	1	0	1	2	1	4	2	3	1	3	0	3	4	3	0	4	6			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr20:23546696T>G	ENST00000376979.3	-	2	567	c.269A>C	c.(268-270)gAg>gCg	p.E90A		NM_080610.2	NP_542177.1	Q9H4G1	CST9L_HUMAN	cystatin 9-like	90						extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	8	Colorectal(13;0.0431)|Lung NSC(19;0.235)					CAGCAGTAGCTCCATTGAGAA	0.468																																					p.E90A		Atlas-SNP	.											.	CST9L	25	.	0			c.A269C						PASS	.						205	177	187					20																	23546696		2203	4300	6503	SO:0001583	missense	128821	exon2			AGTAGCTCCATTG		CCDS13157.1	20p11.21	2012-08-14	2008-03-06		ENSG00000101435	ENSG00000101435			16233	protein-coding gene	gene with protein product			"cystatin 9 (mouse)-like"			20565543	Standard	NM_080610		Approved	bA218C14.1, CTES7B	uc002wtk.4	Q9H4G1	OTTHUMG00000032073	ENST00000376979.3:c.269A>C	chr20.hg19:g.23546696T>G	ENSP00000366178:p.Glu90Ala	244.0	0.0	.		338.0	67.0	.	NM_080610	B2R5A1	Missense_Mutation	SNP	ENST00000376979.3	hg19	CCDS13157.1	.	.	.	.	.	.	.	.	.	.	T	12.87	2.067516	0.36470	.	.	ENSG00000101435	ENST00000376979	T	0.28666	1.6	1.92	1.92	0.25849	Proteinase inhibitor I25, cystatin (2);	0.919888	0.08938	N	0.872000	T	0.44265	0.1285	M	0.75264	2.295	0.09310	N	1	D	0.58970	0.984	P	0.55749	0.783	T	0.23619	-1.0183	10	0.37606	T	0.19	.	5.8418	0.18637	0.0:0.0:0.0:1.0	.	90	Q9H4G1	CST9L_HUMAN	A	90	ENSP00000366178:E90A	ENSP00000366178:E90A	E	-	2	0	CST9L	23494696	0.004000	0.15560	0.108000	0.21378	0.004000	0.04260	0.143000	0.16115	1.118000	0.41863	0.402000	0.26972	GAG	.	.	.	none		0.468	CST9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078338.1	NM_080610		G	23546696	T	G	23546696	3	3	200	1	0	0	0	0	1	0	0	0	3982	1551	54	5	182	5	CST9L	20	23546696	Missense_Mutation	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10		23546696	39478824	76	12139											
DHX35	60625	hgsc.bcm.edu	37	chr20	37653978	37653978	+	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	aaaagcttcttgtcaagtttCaagtgcccaggaagtctagt	12	12	9	8	0	4	0	2	0	2	0	4	1	4	1	1	1	2	2	1	1	6	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr20:37653978C>T	ENST00000252011.3	+	18	1810	c.1777C>T	c.(1777-1779)Caa>Taa	p.Q593*	DHX35_ENST00000373323.4_Nonsense_Mutation_p.Q562*|DHX35_ENST00000373325.2_Nonsense_Mutation_p.Q593*	NM_021931.3	NP_068750.2	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35	593					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	40		Myeloproliferative disorder(115;0.00878)				TGTCAAGTTTCAAGTGCCCAG	0.443																																					p.Q593X		Atlas-SNP	.											.	DHX35	82	.	0			c.C1777T						PASS	.						176	185	182					20																	37653978		2203	4300	6503	SO:0001587	stop_gained	60625	exon18			AAGTTTCAAGTGC	AK026412	CCDS13310.1, CCDS54463.1	20q11.22-q12	2003-06-13	2003-06-13	2003-06-13	ENSG00000101452	ENSG00000101452		"DEAH-boxes"	15861	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 35"	C20orf15, DDX35			Standard	NM_001190809		Approved	FLJ22759, KAIA0875	uc002xjh.3	Q9H5Z1	OTTHUMG00000032463	ENST00000252011.3:c.1777C>T	chr20.hg19:g.37653978C>T	ENSP00000252011:p.Gln593*	186.0	0.0	.		222.0	42.0	.	NM_021931	A2RTX3|B4E0J0|F5GXM6|Q5THR0|Q9H4H7|Q9H6T6	Nonsense_Mutation	SNP	ENST00000252011.3	hg19	CCDS13310.1	.	.	.	.	.	.	.	.	.	.	C	38	6.967926	0.97971	.	.	ENSG00000101452	ENST00000373325;ENST00000252011;ENST00000373323;ENST00000373321;ENST00000449559	.	.	.	5.41	4.4	0.53042	.	0.097447	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.4304	0.44405	0.3784:0.6216:0.0:0.0	.	.	.	.	X	593;593;562;73;57	.	ENSP00000252011:Q593X	Q	+	1	0	DHX35	37087392	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.037000	0.64170	2.530000	0.85305	0.655000	0.94253	CAA	.	.	.	none		0.443	DHX35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079212.2	NM_021931		T	37653978	C	T	37653978	4	4	200	1	0	0	0	0	0	1	0	0	4510	827	29	2	1847	2	DHX35	20	37653978	Nonsense_Mutation	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10	14107282	37653978	25371542	77	12140											
SLC9A8	23315	hgsc.bcm.edu	37	chr20	48431566	48431566	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggttccccaatacaactcaTgagggtttcaatgtcaccct	11	11	7	12	0	3	1	3	1	0	0	4	1	4	1	3	2	2	2	3	2	4	3	rs536021956		TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr20:48431566T>C	ENST00000361573.2	+	2	90	c.48T>C	c.(46-48)caT>caC	p.H16H	SLC9A8_ENST00000417961.1_Silent_p.H16H|SLC9A8_ENST00000539601.1_5'UTR|SLC9A8_ENST00000541138.1_5'UTR			Q9Y2E8	SL9A8_HUMAN	solute carrier family 9, subfamily A (NHE8, cation proton antiporter 8), member 8	16					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)			ATACAACTCATGAGGGTTTCA	0.522																																					p.H16H		Atlas-SNP	.											.	SLC9A8	63	.	0			c.T48C						PASS	.						90	78	82					20																	48431566		2203	4300	6503	SO:0001819	synonymous_variant	23315	exon2			AACTCATGAGGGT	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.48T>C	chr20.hg19:g.48431566T>C		127.0	0.0	.		184.0	45.0	.	NM_001260491	B4DTQ8|Q2M1U9|Q68CZ8|Q9BX15|Q9Y507	Silent	SNP	ENST00000361573.2	hg19	CCDS13421.1																																																																																			.	.	.	none		0.522	SLC9A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106483.3	XM_030524		C	48431566	T	C	48431566	2	2	200	1	0	0	0	0	0	0	0	1	14733	1461	51	3		3	SLC9A8	20	48431566	Silent	SNP	T	TCGA-HE-A5NK-01A-11D-A26P-10	10777588	48431566	14593954	78	12141											
MYO18B	84700	hgsc.bcm.edu	37	chr22	26422672	26422672	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtcgagggaaaagctgccCagtccttcagcggccctctc	7	8	11	15	2	2	0	1	0	1	0	5	2	3	1	3	2	3	1	3	2	2	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr22:26422672C>T	ENST00000407587.2	+	43	6904	c.6735C>T	c.(6733-6735)ccC>ccT	p.P2245P	MYO18B_ENST00000335473.7_Silent_p.P2244P|MYO18B_ENST00000536101.1_Silent_p.P2244P			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2244						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						AAAAGCTGCCCAGTCCTTCAG	0.607																																					p.P2244P		Atlas-SNP	.											.	MYO18B	322	.	0			c.C6732T						PASS	.						24	25	25					22																	26422672		1910	4104	6014	SO:0001819	synonymous_variant	84700	exon43			GCTGCCCAGTCCT	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.6735C>T	chr22.hg19:g.26422672C>T		128.0	0.0	.		159.0	30.0	.	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	hg19		.	.	.	.	.	.	.	.	.	.	C	10.77	1.444427	0.25987	.	.	ENSG00000133454	ENST00000543971	T	0.55234	0.53	4.94	-4.84	0.03151	.	0.116110	0.34002	N	0.004359	T	0.50394	0.1613	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53315	-0.8456	7	0.72032	D	0.01	.	5.3684	0.16127	0.2432:0.2637:0.4198:0.0733	.	.	.	.	L	194	ENSP00000444262:P194L	ENSP00000444262:P194L	P	+	2	0	MYO18B	24752672	0.013000	0.17824	0.962000	0.40283	0.992000	0.81027	-1.785000	0.01767	-0.418000	0.07450	0.491000	0.48974	CCA	.	.	.	none		0.607	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		T	26422672	C	T	26422672	2	4	200	1	0	0	0	0	0	0	0	1	10073	581	21	2		2	MYO18B	22	26422672	Silent	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10		26422672	24881894	79	12142											
BAIAP2L2	80115	hgsc.bcm.edu	37	chr22	38483172	38483172	+	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	gggttcatgggtgtcatgggGgacatggaggtcatggaggt	7	10	20	4	0	3	0	3	0	0	0	3	3	3	3	0	8	0	1	0	8	0	1	rs539447143	byFrequency	TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr22:38483172G>T	ENST00000381669.3	-	11	1362	c.1218C>A	c.(1216-1218)tcC>tcA	p.S406S	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)			large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	8	Melanoma(58;0.045)					gtgtcatgggggacatggagg	0.662													G|||	30	0.00599042	0.0068	0.0014	5008	,	,		13061	0		0.004	False		,,,				2504	0.0164				p.S406S		Atlas-SNP	.											.	BAIAP2L2	39	.	0			c.C1218A						PASS	.						31	37	35					22																	38483172		1925	4122	6047	SO:0001819	synonymous_variant	80115	exon11			CATGGGGGACATG	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.1218C>A	chr22.hg19:g.38483172G>T		103.0	0.0	.		146.0	17.0	.	NM_025045	B0QYE2|Q96BG7	Silent	SNP	ENST00000381669.3	hg19	CCDS43018.1																																																																																			.	.	.	none		0.662	BAIAP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321727.1	NM_025045		T	38483172	G	T	38483172	2	4	200	1	0	0	0	0	0	0	0	1	1303	1219	43	4		4	BAIAP2L2	22	38483172	Silent	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	12060500	38483172	12821394	80	12143											
SMC1B	27127	hgsc.bcm.edu	37	chr22	45785629	45785629	+	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	cgaggaatgtctcaggttcaGctctttcctccttcagaaat	9	13	8	11	1	4	1	3	0	2	1	7	3	6	2	2	2	1	2	2	2	2	3			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr22:45785629G>C	ENST00000357450.4	-	10	1693	c.1694C>G	c.(1693-1695)gCt>gGt	p.A565G	SMC1B_ENST00000404354.3_Missense_Mutation_p.A565G	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	565	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)		CTCAGGTTCAGCTCTTTCCTC	0.383																																					p.A565G		Atlas-SNP	.											.	SMC1B	215	.	0			c.C1694G						PASS	.						150	138	141					22																	45785629		1873	4115	5988	SO:0001583	missense	27127	exon10			GGTTCAGCTCTTT	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.1694C>G	chr22.hg19:g.45785629G>C	ENSP00000350036:p.Ala565Gly	155.0	0.0	.		169.0	36.0	.	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Missense_Mutation	SNP	ENST00000357450.4	hg19	CCDS43027.1	.	.	.	.	.	.	.	.	.	.	G	11.78	1.742185	0.30865	.	.	ENSG00000077935	ENST00000357450;ENST00000404354	D;D	0.86297	-2.1;-2.1	5.49	5.49	0.81192	SMCs flexible hinge (3);RecF/RecN/SMC (1);	0.108364	0.40728	N	0.001024	D	0.86674	0.5989	L	0.52759	1.655	0.58432	D	0.999991	B;B;B	0.24533	0.105;0.04;0.04	B;B;B	0.32289	0.143;0.037;0.037	T	0.82969	-0.0193	10	0.44086	T	0.13	.	19.3758	0.94508	0.0:0.0:1.0:0.0	.	565;565;565	Q8NDV3;Q8NDV3-2;Q8NDV3-3	SMC1B_HUMAN;.;.	G	565	ENSP00000350036:A565G;ENSP00000385902:A565G	ENSP00000350036:A565G	A	-	2	0	SMC1B	44164293	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.695000	0.61767	2.577000	0.86979	0.655000	0.94253	GCT	.	.	.	none		0.383	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674		C	45785629	G	C	45785629	3	2	200	1	0	0	0	0	1	0	0	0	14795	971	34	4	2077	4	SMC1B	22	45785629	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	7302457	45785629	5518937	81	12144											
SHANK3	85358	hgsc.bcm.edu	37	chr22	51159826	51159826	+	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	gggaggagcggaagtcacccGaggacaagaagtccatgatc	13	4	15	9	2	1	2	1	1	0	1	3	7	2	6	2	4	1	0	2	4	3	0			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chr22:51159826G>A	ENST00000414786.2	+	21	3750	c.3523G>A	c.(3523-3525)Gag>Aag	p.E1175K	SHANK3_ENST00000262795.3_Missense_Mutation_p.E1205K|SHANK3_ENST00000445220.2_Missense_Mutation_p.E1191K			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	1189					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)		GAAGTCACCCGAGGACAAGAA	0.662																																					p.E1175K		Atlas-SNP	.											.	SHANK3	96	.	0			c.G3523A						PASS	.						39	48	45					22																	51159826		2100	4200	6300	SO:0001583	missense	85358	exon21			TCACCCGAGGACA	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.3523G>A	chr22.hg19:g.51159826G>A	ENSP00000464552:p.Glu1175Lys	177.0	0.0	.		213.0	39.0	.	NM_033517	D7UT47|Q8TET3	Missense_Mutation	SNP	ENST00000414786.2	hg19		.	.	.	.	.	.	.	.	.	.	G	15.47	2.843265	0.51057	.	.	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.26373	1.74;1.74	4.58	4.58	0.56647	.	0.163605	0.51477	D	0.000081	T	0.25827	0.0629	M	0.70275	2.135	0.29353	N	0.865219	D;P;P	0.53462	0.96;0.492;0.921	B;B;B	0.34489	0.184;0.024;0.163	T	0.43556	-0.9384	10	0.56958	D	0.05	.	14.8583	0.70359	0.0:0.0:1.0:0.0	.	1189;1190;1205	D7UT47;Q9BYB0;F2Z3L0	.;SHAN3_HUMAN;.	K	1205;1191	ENSP00000442518:E1205K;ENSP00000446078:E1191K	ENSP00000442518:E1205K	E	+	1	0	SHANK3	49506692	1.000000	0.71417	0.875000	0.34327	0.943000	0.58893	8.323000	0.90002	2.093000	0.63338	0.462000	0.41574	GAG	.	.	.	none		0.662	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420		A	51159826	G	A	51159826	3	1	200	1	0	0	0	0	1	0	0	0	14279	1059	37	1	3699	1	SHANK3	22	51159826	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	5374197	51159826	144740	82	12145											
BMP15	9210	hgsc.bcm.edu	37	chrX	50658965	50658965	+	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	aaaccttccctgatgtctaaCgcttggaaagagatggatat	13	11	9	8	1	1	2	0	1	1	1	2	5	2	4	2	2	2	1	2	2	4	4			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chrX:50658965C>T	ENST00000252677.3	+	2	537	c.537C>T	c.(535-537)aaC>aaT	p.N179N		NM_005448.2	NP_005439.2	O95972	BMP15_HUMAN	bone morphogenetic protein 15	179					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)					TGATGTCTAACGCTTGGAAAG	0.473																																					p.N179N		Atlas-SNP	.											.	BMP15	62	.	0			c.C537T						PASS	.						116	94	101					X																	50658965		2203	4299	6502	SO:0001819	synonymous_variant	9210	exon2			GTCTAACGCTTGG	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.537C>T	chrX.hg19:g.50658965C>T		184.0	0.0	.		217.0	78.0	.	NM_005448	Q17RM6|Q5JST1|Q9UMS1	Silent	SNP	ENST00000252677.3	hg19	CCDS14334.1																																																																																			.	.	.	none		0.473	BMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056572.1	NM_005448		T	50658965	C	T	50658965	2	4	200	1	0	0	0	0	0	0	0	1	1458	535	19	1		1	BMP15	23	50658965	Silent	SNP	C	TCGA-HE-A5NK-01A-11D-A26P-10		50658965	104611595	83	12146											
ZCCHC5	203430	hgsc.bcm.edu	37	chrX	77913359	77913359	+	Missense_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	ctccagaggctcctggggagGtggaagctcaaggaactcta	10	7	14	10	0	2	1	1	0	1	1	4	4	4	4	2	6	2	2	2	6	4	1			TCGA-HE-A5NK-01A-11D-A26P-10	TCGA-HE-A5NK-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	73f57b92-a6e6-4472-940b-579c22d208bf	254baf21-7011-4eb9-84cf-45364c96ccb7	g.chrX:77913359G>A	ENST00000321110.1	-	2	854	c.559C>T	c.(559-561)Cct>Tct	p.P187S		NM_152694.2	NP_689907.1	Q8N8U3	ZCHC5_HUMAN	zinc finger, CCHC domain containing 5	187	Pro-rich.						nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)|prostate(1)|skin(1)	37						TCCTGGGGAGGTGGAAGCTCA	0.537																																					p.P187S		Atlas-SNP	.											.	ZCCHC5	101	.	0			c.C559T						PASS	.						41	41	41					X																	77913359		2203	4300	6503	SO:0001583	missense	203430	exon2			GGGGAGGTGGAAG	AK096184	CCDS14440.1	Xq13.3	2008-02-05			ENSG00000179300	ENSG00000179300		"Zinc fingers, CCHC domain containing"	22997	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_152694		Approved	FLJ38865, Mar3, Mart3, ZHC5	uc004edc.1	Q8N8U3	OTTHUMG00000021892	ENST00000321110.1:c.559C>T	chrX.hg19:g.77913359G>A	ENSP00000316794:p.Pro187Ser	15.0	0.0	.		47.0	18.0	.	NM_152694	B2RMZ0|Q5JQE9	Missense_Mutation	SNP	ENST00000321110.1	hg19	CCDS14440.1	.	.	.	.	.	.	.	.	.	.	G	0.020	-1.432832	0.01108	.	.	ENSG00000179300	ENST00000321110	T	0.17691	2.26	3.46	-5.74	0.02391	.	.	.	.	.	T	0.05547	0.0146	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40289	-0.9571	9	0.07175	T	0.84	.	1.35	0.02171	0.2436:0.2501:0.329:0.1772	.	187	Q8N8U3	ZCHC5_HUMAN	S	187	ENSP00000316794:P187S	ENSP00000316794:P187S	P	-	1	0	ZCCHC5	77800015	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.423000	0.01030	-1.795000	0.01255	-3.016000	0.00074	CCT	.	.	.	none		0.537	ZCCHC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057319.1	NM_152694		A	77913359	G	A	77913359	3	1	200	1	0	0	0	0	1	0	0	0	17603	1261	44	2	872	2	ZCCHC5	23	77913359	Missense_Mutation	SNP	G	TCGA-HE-A5NK-01A-11D-A26P-10	27254394	77913359	77357201	84	12147											
PRAMEF12	390999	hgsc.bcm.edu	37	chr1	12837407	12837407	+	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	gcgccatcctgcctgccctgAgccgctgctcccagctcagc	4	7	10	20	2	1	1	1	1	0	0	3	1	3	1	6	0	6	3	6	0	0	0			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr1:12837407A>T	ENST00000357726.4	+	3	1144	c.1117A>T	c.(1117-1119)Agc>Tgc	p.S373C		NM_001080830.1	NP_001074299.1	O95522	PRA12_HUMAN	PRAME family member 12	373					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					NS(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(9)|ovary(3)|skin(1)|urinary_tract(1)	23	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00818)|Colorectal(212;5.04e-06)|Kidney(185;4.99e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000198)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GCCTGCCCTGAGCCGCTGCTC	0.627																																					p.S373C		Atlas-SNP	.											.	PRAMEF12	69	.	0			c.A1117T						PASS	.						99	101	100					1																	12837407		2203	4300	6503	SO:0001583	missense	390999	exon3			GCCCTGAGCCGCT		CCDS41254.1	1p36.21	2013-01-17			ENSG00000116726	ENSG00000116726		"-"	22125	protein-coding gene	gene with protein product							Standard	NM_001080830		Approved	OTTHUMG00000001927	uc001aui.3	O95522	OTTHUMG00000001927	ENST00000357726.4:c.1117A>T	chr1.hg19:g.12837407A>T	ENSP00000350358:p.Ser373Cys	505.0	0.0	.		737.0	215.0	.	NM_001080830		Missense_Mutation	SNP	ENST00000357726.4	hg19	CCDS41254.1	.	.	.	.	.	.	.	.	.	.	.	15.97	2.990792	0.54041	.	.	ENSG00000116726	ENST00000357726	T	0.12672	2.66	2.72	1.59	0.23543	.	0.618526	0.16899	N	0.194981	T	0.32102	0.0818	M	0.83384	2.64	0.27627	N	0.948171	D	0.89917	1.0	D	0.85130	0.997	T	0.10451	-1.0629	10	0.56958	D	0.05	.	3.0429	0.06143	0.6004:0.2557:0.1439:0.0	.	373	O95522	PRA12_HUMAN	C	373	ENSP00000350358:S373C	ENSP00000350358:S373C	S	+	1	0	PRAMEF12	12759994	0.357000	0.24938	0.906000	0.35671	0.303000	0.27691	-0.407000	0.07178	0.455000	0.26910	0.164000	0.16699	AGC	.	.	.	none		0.627	PRAMEF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005457.1	XM_372760		T	12837407	A	T	12837407	3	4	201	1	0	0	0	0	1	0	0	0	12438	304	11	5	1127	5	PRAMEF12	1	12837407	Missense_Mutation	SNP	A	TCGA-HE-A5NL-01A-11D-A26P-10		12837407	236413214	1	12148											
SPEN	23013	hgsc.bcm.edu	37	chr1	16257911	16257911	+	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	ttgaggaaggttcatcaggtGaccagccgccttatctggat	9	11	12	9	1	3	2	2	2	1	0	3	4	3	4	3	4	1	1	3	4	2	3			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr1:16257911G>A	ENST00000375759.3	+	11	5380	c.5176G>A	c.(5176-5178)Gac>Aac	p.D1726N		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1726					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)		TTCATCAGGTGACCAGCCGCC	0.587																																					p.D1726N		Atlas-SNP	.											.	SPEN	374	.	0			c.G5176A						PASS	.						136	148	144					1																	16257911		2203	4300	6503	SO:0001583	missense	23013	exon11			TCAGGTGACCAGC		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.5176G>A	chr1.hg19:g.16257911G>A	ENSP00000364912:p.Asp1726Asn	149.0	0.0	.		152.0	16.0	.	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	hg19	CCDS164.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.032932	0.54790	.	.	ENSG00000065526	ENST00000375759	T	0.09163	3.01	5.16	4.25	0.50352	.	.	.	.	.	T	0.08891	0.0220	N	0.24115	0.695	0.09310	N	1	B	0.32245	0.361	B	0.30646	0.118	T	0.24548	-1.0157	9	0.40728	T	0.16	-3.0207	13.4332	0.61068	0.0759:0.0:0.9241:0.0	.	1726	Q96T58	MINT_HUMAN	N	1726	ENSP00000364912:D1726N	ENSP00000364912:D1726N	D	+	1	0	SPEN	16130498	0.999000	0.42202	0.001000	0.08648	0.749000	0.42624	6.058000	0.71126	1.152000	0.42452	0.467000	0.42956	GAC	.	.	.	none		0.587	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		A	16257911	G	A	16257911	3	1	201	1	0	0	0	0	1	0	0	0	15050	1290	45	2	5218	2	SPEN	1	16257911	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	3420504	16257911	232992710	2	12149											
CADM3	57863	hgsc.bcm.edu	37	chr1	159170698	159170698	+	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	caggaggggacgacaagaagGaatatttcatctagaggcgc	14	6	14	7	2	2	2	1	0	1	2	2	6	2	5	0	5	0	0	0	5	5	3			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr1:159170698G>T	ENST00000368125.4	+	9	1340	c.1183G>T	c.(1183-1185)Gaa>Taa	p.E395*	CTA-134P22.2_ENST00000415675.2_RNA|CTA-134P22.2_ENST00000609696.1_RNA|CADM3_ENST00000368124.4_Nonsense_Mutation_p.E429*|CADM3_ENST00000497636.1_3'UTR|DARC_ENST00000537147.1_5'Flank	NM_001127173.1	NP_001120645.1	Q8N126	CADM3_HUMAN	cell adhesion molecule 3	395					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)					CGACAAGAAGGAATATTTCAT	0.617																																					p.E429X		Atlas-SNP	.											CADM3,NS,malignant_melanoma,0,1	CADM3	118	.	0			c.G1285T						PASS	.						78	76	77					1																	159170698		2203	4300	6503	SO:0001587	stop_gained	57863	exon10			AAGAAGGAATATT	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.1183G>T	chr1.hg19:g.159170698G>T	ENSP00000357107:p.Glu395*	183.0	0.0	.		239.0	25.0	.	NM_021189	Q8IZQ9|Q9NVJ5|Q9UJP1	Nonsense_Mutation	SNP	ENST00000368125.4	hg19	CCDS44251.1	.	.	.	.	.	.	.	.	.	.	G	38	6.895315	0.97916	.	.	ENSG00000162706	ENST00000368124;ENST00000368125	.	.	.	3.81	3.81	0.43845	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.48571	D	0.999671	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.2211	0.59887	0.0:0.0:1.0:0.0	.	.	.	.	X	429;395	.	ENSP00000357106:E429X	E	+	1	0	CADM3	157437322	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.966000	0.93397	1.965000	0.57142	0.591000	0.81541	GAA	.	.	.	none		0.617	CADM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090330.1	NM_021189		T	159170698	G	T	159170698	4	4	201	1	0	0	0	0	0	1	0	0	2570	1175	41	4	1323	4	CADM3	1	159170698	Nonsense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	142912787	159170698	90079923	3	12150											
C1orf129	80133	hgsc.bcm.edu	37	chr1	170965712	170965712	+	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	tgcaacaggtggatattactCtaatgaaggagaatttctgg	13	12	11	5	0	2	2	0	1	2	1	2	4	2	3	0	4	3	1	0	4	6	4			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr1:170965712C>G	ENST00000367758.3	+	14	1501	c.1402C>G	c.(1402-1404)Cta>Gta	p.L468V	MROH9_ENST00000367759.4_Missense_Mutation_p.L468V	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	468																	GGATATTACTCTAATGAAGGA	0.443																																					p.L468V		Atlas-SNP	.											.	.	.	.	0			c.C1402G						PASS	.						181	172	175					1																	170965712		1873	4113	5986	SO:0001583	missense	80133	exon14			ATTACTCTAATGA	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.1402C>G	chr1.hg19:g.170965712C>G	ENSP00000356732:p.Leu468Val	128.0	0.0	.		138.0	32.0	.	NM_025063	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Missense_Mutation	SNP	ENST00000367758.3	hg19	CCDS41436.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.85|17.85	3.489337|3.489337	0.64074|0.64074	.|.	.|.	ENSG00000117501|ENSG00000117501	ENST00000367759;ENST00000367758|ENST00000426136	T;T|.	0.67698|.	-0.28;1.49|.	5.75|5.75	5.75|5.75	0.90469|0.90469	Armadillo-like helical (1);|.	0.127327|.	0.36101|.	N|.	0.002798|.	T|T	0.49626|0.49626	0.1568|0.1568	M|M	0.69823|0.69823	2.125|2.125	0.29405|0.29405	N|N	0.86168|0.86168	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.85130|.	0.997;0.997|.	T|T	0.49390|0.49390	-0.8945|-0.8945	10|5	0.72032|.	D|.	0.01|.	-13.2876|-13.2876	15.4599|15.4599	0.75346|0.75346	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	468;468|.	F5GWX6;Q5TGP6|.	.;CA129_HUMAN|.	V|C	468|74	ENSP00000356733:L468V;ENSP00000356732:L468V|.	ENSP00000356732:L468V|.	L|S	+|+	1|2	2|0	C1orf129|C1orf129	169232336|169232336	0.790000|0.790000	0.28787|0.28787	0.271000|0.271000	0.24616|0.24616	0.008000|0.008000	0.06430|0.06430	3.549000|3.549000	0.53681|0.53681	2.716000|2.716000	0.92895|0.92895	0.655000|0.655000	0.94253|0.94253	CTA|TCT	.	.	.	none		0.443	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063		G	170965712	C	G	170965712	3	3	201	1	0	0	0	0	1	0	0	0	1998	912	32	4	1452	4	C1orf129	1	170965712	Missense_Mutation	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	11795014	170965712	78284909	4	12151											
LYST	1130	hgsc.bcm.edu	37	chr1	235872510	235872510	+	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	gtcagactctagagcctgccGatggatgaggataaaaagac	14	7	12	8	1	2	4	1	1	1	3	2	7	2	6	2	2	2	0	2	2	4	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr1:235872510G>A	ENST00000389794.3	-	44	10198	c.10024C>T	c.(10024-10026)Cgg>Tgg	p.R3342W	LYST_ENST00000473037.1_5'UTR|LYST_ENST00000389793.2_Missense_Mutation_p.R3342W			Q99698	LYST_HUMAN	lysosomal trafficking regulator	3342	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.				blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			AGAGCCTGCCGATGGATGAGG	0.483																																					p.R3342W		Atlas-SNP	.											.	LYST	370	.	0			c.C10024T						PASS	.						97	95	96					1																	235872510		2203	4300	6503	SO:0001583	missense	1130	exon44			CCTGCCGATGGAT	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.10024C>T	chr1.hg19:g.235872510G>A	ENSP00000374444:p.Arg3342Trp	275.0	0.0	.		291.0	82.0	.	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	hg19	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.601748	0.87055	.	.	ENSG00000143669	ENST00000389794;ENST00000389793	T;T	0.74209	-0.82;-0.82	5.39	4.47	0.54385	BEACH domain (4);	0.000000	0.85682	D	0.000000	D	0.91345	0.7270	H	0.98005	4.125	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94675	0.7860	10	0.87932	D	0	.	15.9845	0.80142	0.0:0.0:0.8645:0.1355	.	3342	Q99698	LYST_HUMAN	W	3342	ENSP00000374444:R3342W;ENSP00000374443:R3342W	ENSP00000374443:R3342W	R	-	1	2	LYST	233939133	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.049000	0.71053	1.391000	0.46566	0.655000	0.94253	CGG	.	.	.	none		0.483	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			A	235872510	G	A	235872510	3	1	201	1	0	0	0	0	1	0	0	0	9135	1057	37	1	1421	1	LYST	1	235872510	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	64906798	235872510	13378111	5	12152											
NCOA1	8648	hgsc.bcm.edu	37	chr2	24929447	24929447	+	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	ttccccctagggagcacagtGggctttctcctcaagatgac	8	10	10	13	0	2	2	1	1	1	1	4	3	3	3	3	2	1	2	3	2	2	3			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr2:24929447G>A	ENST00000406961.1	+	13	1760	c.1108G>A	c.(1108-1110)Ggg>Agg	p.G370R	NCOA1_ENST00000407230.1_Missense_Mutation_p.G219R|NCOA1_ENST00000395856.3_Missense_Mutation_p.G370R|NCOA1_ENST00000538539.1_Missense_Mutation_p.G370R|NCOA1_ENST00000405141.1_Missense_Mutation_p.G370R|NCOA1_ENST00000348332.3_Missense_Mutation_p.G370R|NCOA1_ENST00000288599.5_Missense_Mutation_p.G370R			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	370	Interaction with STAT3.				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)					GGAGCACAGTGGGCTTTCTCC	0.383			T	PAX3	alveolar rhadomyosarcoma																																p.G370R		Atlas-SNP	.		Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	NCOA1	210	.	0			c.G1108A						PASS	.						65	66	66					2																	24929447		2203	4300	6503	SO:0001583	missense	8648	exon11			CACAGTGGGCTTT	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.1108G>A	chr2.hg19:g.24929447G>A	ENSP00000385216:p.Gly370Arg	71.0	0.0	.		70.0	24.0	.	NM_147223	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Missense_Mutation	SNP	ENST00000406961.1	hg19	CCDS1712.1	.	.	.	.	.	.	.	.	.	.	G	7.212	0.595682	0.13875	.	.	ENSG00000084676	ENST00000406961;ENST00000405141;ENST00000407230;ENST00000538539;ENST00000348332;ENST00000288599;ENST00000395856	T;T;T;T;T;T;T	0.02158	4.54;4.54;4.42;4.54;4.54;4.54;4.54	5.02	5.02	0.67125	.	0.298923	0.37483	N	0.002071	T	0.01940	0.0061	L	0.34521	1.04	0.29230	N	0.873364	B;B;B;B	0.31790	0.34;0.28;0.014;0.203	B;B;B;B	0.33392	0.101;0.163;0.049;0.127	T	0.38156	-0.9674	10	0.20046	T	0.44	.	4.5462	0.12081	0.083:0.1533:0.6049:0.1588	.	370;370;370;219	Q15788-3;Q15788;Q15788-2;B5MCN7	.;NCOA1_HUMAN;.;.	R	370;370;219;370;370;370;370	ENSP00000385216:G370R;ENSP00000385097:G370R;ENSP00000385195:G219R;ENSP00000444039:G370R;ENSP00000320940:G370R;ENSP00000288599:G370R;ENSP00000379197:G370R	ENSP00000288599:G370R	G	+	1	0	NCOA1	24782951	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.987000	0.49378	2.485000	0.83878	0.655000	0.94253	GGG	.	.	.	none		0.383	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223		A	24929447	G	A	24929447	3	1	201	1	0	0	0	0	1	0	0	0	10235	1348	47	2	1142	2	NCOA1	2	24929447	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10		24929447	218269926	6	12153											
TTL	150465	hgsc.bcm.edu	37	chr2	113260589	113260589	+	Frame_Shift_Del	DEL	A	A	-																															atgttgataatttccaagacAaaacctgccatttgaccaat																										TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr2:113260589delA	ENST00000233336.6	+	5	897	c.706delA	c.(706-708)aaafs	p.K236fs		NM_153712.4	NP_714923.1	Q8NG68	TTL_HUMAN	tubulin tyrosine ligase	236	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)|microtubule cytoskeleton organization (GO:0000226)|regulation of axon extension (GO:0030516)		ATP binding (GO:0005524)|tubulin-tyrosine ligase activity (GO:0004835)			breast(1)|large_intestine(2)|ovary(1)	4		Ovarian(717;0.024)		BRCA - Breast invasive adenocarcinoma(221;6.17e-07)|STAD - Stomach adenocarcinoma(1183;0.00644)		TTTCCAAGACAAAACCTGCCA	0.388			T	ETV6	ALL																																p.D235fs		Atlas-Indel,Pindel	.		Dom	yes		2	2q13	150465	tubulin tyrosine ligase		L	.	TTL	27	.	0			c.705delC						PASS	.						126	124	125					2																	113260589		2203	4300	6503	SO:0001589	frameshift_variant	150465	exon5			.		CCDS2096.1	2q13	2010-04-21			ENSG00000114999	ENSG00000114999	6.3.2.25		21586	protein-coding gene	gene with protein product		608291				11431336	Standard	NM_153712		Approved	MGC46235	uc002thu.3	Q8NG68	OTTHUMG00000131316	ENST00000233336.6:c.706delA	chr2.hg19:g.113260589delA	ENSP00000233336:p.Lys236fs	130.0	0.0	0		126.0	31.0	0.246032	NM_153712	Q585T3|Q7Z302|Q8N426	Frame_Shift_Del	DEL	ENST00000233336.6	hg19	CCDS2096.1																																																																																			.	.	.	none		0.388	TTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254085.2	NM_153712		-	113260589	A	-	113260589	7	5	201	1	0	1	0	1	0	0	0	0	16733	131	5	0	724	0	TTL	2	113260589	Frame_Shift_Del	DEL	A	TCGA-HE-A5NL-01A-11D-A26P-10	88331142	113260589	129938784	7	12154											
GAD1	2571	hgsc.bcm.edu	37	chr2	171705820	171705820	+	Frame_Shift_Del	DEL	A	A	-																															cctggggaggtgggctgctcAtgtccaggaagcaccgccat																										TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr2:171705820delA	ENST00000358196.3	+	12	1694	c.1144delA	c.(1144-1146)atgfs	p.M382fs		NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	382					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						TGGGCTGCTCATGTCCAGGAA	0.537																																					p.L381fs		Atlas-Indel,Pindel	.											.	GAD1	79	.	0			c.1143delC						PASS	.						76	67	70					2																	171705820		2203	4300	6503	SO:0001589	frameshift_variant	2571	exon12			.		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.1144delA	chr2.hg19:g.171705820delA	ENSP00000350928:p.Met382fs	128.0	0.0	0		138.0	50.0	0.362319	NM_000817	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Frame_Shift_Del	DEL	ENST00000358196.3	hg19	CCDS2239.1																																																																																			.	.	.	none		0.537	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2			-	171705820	A	-	171705820	7	5	201	1	0	1	0	1	0	0	0	0	6186	217	8	0	1227	0	GAD1	2	171705820	Frame_Shift_Del	DEL	A	TCGA-HE-A5NL-01A-11D-A26P-10	58445231	171705820	71493553	8	12155											
FN1	2335	hgsc.bcm.edu	37	chr2	216274676	216274676	+	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	ctggtcacaggtgtgctggtGctggtggtggtgaagtcaaa	7	11	17	6	0	2	1	2	1	0	0	2	1	2	1	0	6	2	2	0	6	2	0			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr2:216274676G>T	ENST00000359671.1	-	14	2368	c.2103C>A	c.(2101-2103)agC>agA	p.S701R	FN1_ENST00000446046.1_Missense_Mutation_p.S701R|FN1_ENST00000356005.4_Missense_Mutation_p.S701R|FN1_ENST00000443816.1_Missense_Mutation_p.S701R|FN1_ENST00000345488.5_Missense_Mutation_p.S701R|FN1_ENST00000357867.4_Missense_Mutation_p.S701R|FN1_ENST00000323926.6_Missense_Mutation_p.S701R|FN1_ENST00000354785.4_Missense_Mutation_p.S701R|FN1_ENST00000421182.1_Missense_Mutation_p.S701R|FN1_ENST00000336916.4_Missense_Mutation_p.S701R|FN1_ENST00000432072.2_Missense_Mutation_p.S701R|FN1_ENST00000346544.3_Missense_Mutation_p.S701R|FN1_ENST00000357009.2_Missense_Mutation_p.S701R			P02751	FINC_HUMAN	fibronectin 1	701	Fibronectin type-III 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)	GTGTGCTGGTGCTGGTGGTGG	0.557																																					p.S701R		Atlas-SNP	.											.	FN1	521	.	0			c.C2103A						PASS	.						370	375	373					2																	216274676		2203	4300	6503	SO:0001583	missense	2335	exon14			GCTGGTGCTGGTG		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.2103C>A	chr2.hg19:g.216274676G>T	ENSP00000352696:p.Ser701Arg	398.0	0.0	.		506.0	121.0	.	NM_212476	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	hg19		.	.	.	.	.	.	.	.	.	.	G	11.17	1.559369	0.27827	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005	T;T;T;T;T;T;T;T;T;T;T;T;T	0.47869	0.83;2.19;2.35;0.92;2.42;2.05;2.4;2.07;2.37;2.08;1.58;0.9;1.49	5.65	3.84	0.44239	.	0.360826	0.30464	N	0.009573	T	0.56077	0.1961	L	0.44542	1.39	0.42852	D	0.994085	D;B;B;B;B;P;D;B;B;D	0.89917	1.0;0.353;0.17;0.17;0.106;0.533;0.998;0.17;0.17;0.987	D;P;B;B;B;B;P;B;B;P	0.87578	0.998;0.522;0.079;0.127;0.036;0.326;0.865;0.127;0.127;0.904	T	0.54549	-0.8277	10	0.40728	T	0.16	.	8.8981	0.35476	0.2229:0.0:0.7771:0.0	.	701;701;701;701;701;701;701;701;701;701	P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.	R	701	ENSP00000394423:S701R;ENSP00000323534:S701R;ENSP00000338200:S701R;ENSP00000350534:S701R;ENSP00000346839:S701R;ENSP00000352696:S701R;ENSP00000265312:S701R;ENSP00000273049:S701R;ENSP00000349509:S701R;ENSP00000410422:S701R;ENSP00000415018:S701R;ENSP00000399538:S701R;ENSP00000348285:S701R	ENSP00000265313:S701R	S	-	3	2	FN1	215982921	1.000000	0.71417	0.896000	0.35187	0.102000	0.19082	1.257000	0.32932	1.531000	0.49152	-0.140000	0.14226	AGC	.	.	.	none		0.557	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		T	216274676	G	T	216274676	3	4	201	1	0	0	0	0	1	0	0	0	5969	1310	46	4	5462	4	FN1	2	216274676	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	44568856	216274676	26924697	9	12156											
PDCD6IP	10015	hgsc.bcm.edu	37	chr3	33840351	33840351	+	Missense_Mutation	SNP	A	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	ccagtactgccgcgcggcggAggagctcagcaagctgcgcc	7	4	15	15	5	1	0	1	0	0	0	1	2	1	2	3	3	6	4	3	3	2	1			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr3:33840351A>C	ENST00000307296.3	+	1	508	c.131A>C	c.(130-132)gAg>gCg	p.E44A	RP11-10C24.1_ENST00000605513.1_lincRNA|PDCD6IP_ENST00000457054.2_Missense_Mutation_p.E44A|RP11-10C24.3_ENST00000604982.1_lincRNA			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	44	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						CGCGCGGCGGAGGAGCTCAGC	0.692																																					p.E44A		Atlas-SNP	.											.	PDCD6IP	62	.	0			c.A131C						PASS	.						10	11	11					3																	33840351		2139	4155	6294	SO:0001583	missense	10015	exon1			CGGCGGAGGAGCT	BC020066	CCDS2660.1, CCDS54561.1	3p22.3	2012-08-30	2001-11-29		ENSG00000170248	ENSG00000170248			8766	protein-coding gene	gene with protein product	"ALG-2 interacting protein X"	608074	"programmed cell death 6-interacting protein"			9880530	Standard	NM_001162429		Approved	Alix, AIP1, Hp95	uc003cfy.4	Q8WUM4	OTTHUMG00000130751	ENST00000307296.3:c.131A>C	chr3.hg19:g.33840351A>C	ENSP00000307387:p.Glu44Ala	61.0	0.0	.		111.0	28.0	.	NM_013374	C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Missense_Mutation	SNP	ENST00000307296.3	hg19	CCDS2660.1	.	.	.	.	.	.	.	.	.	.	A	15.41	2.824727	0.50739	.	.	ENSG00000170248	ENST00000307296;ENST00000457054;ENST00000413073	T;T;T	0.16324	2.35;2.35;2.35	5.03	5.03	0.67393	BRO1 domain (3);	0.048074	0.85682	D	0.000000	T	0.09202	0.0227	N	0.13299	0.325	0.80722	D	1	B;B;B	0.09022	0.002;0.002;0.001	B;B;B	0.11329	0.006;0.006;0.002	T	0.14364	-1.0475	10	0.08381	T	0.77	-21.2451	11.3154	0.49388	0.8641:0.0:0.0:0.1359	.	44;44;44	C5MQH7;E9PFU1;Q8WUM4	.;.;PDC6I_HUMAN	A	44	ENSP00000307387:E44A;ENSP00000411825:E44A;ENSP00000406693:E44A	ENSP00000307387:E44A	E	+	2	0	PDCD6IP	33815355	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.731000	0.74785	2.108000	0.64289	0.482000	0.46254	GAG	.	.	.	none		0.692	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2			C	33840351	A	C	33840351	3	2	201	1	0	0	0	0	1	0	0	0	11631	304	11	5	133	5	PDCD6IP	3	33840351	Missense_Mutation	SNP	A	TCGA-HE-A5NL-01A-11D-A26P-10		33840351	164182079	10	12157											
ARHGEF3	50650	hgsc.bcm.edu	37	chr3	56766301	56766301	+	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	tgaatgcccctcgcagggagCcacccagcctcacttctcca	8	7	8	18	1	2	1	1	1	1	0	4	2	2	2	6	1	3	1	6	1	1	1			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr3:56766301C>A	ENST00000296315.3	-	9	1361	c.1193G>T	c.(1192-1194)gGc>gTc	p.G398V	ARHGEF3_ENST00000413728.2_Missense_Mutation_p.G404V|ARHGEF3_ENST00000497267.1_Missense_Mutation_p.G369V|ARHGEF3_ENST00000496106.1_Missense_Mutation_p.G404V|ARHGEF3_ENST00000495373.1_Missense_Mutation_p.G398V|ARHGEF3_ENST00000338458.4_Missense_Mutation_p.G430V	NM_019555.2	NP_062455.1	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor (GEF) 3	398	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)		TCGCAGGGAGCCACCCAGCCT	0.552																																					p.G430V		Atlas-SNP	.											.	ARHGEF3	128	.	0			c.G1289T						PASS	.						116	102	106					3																	56766301		2203	4300	6503	SO:0001583	missense	50650	exon12			AGGGAGCCACCCA	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.1193G>T	chr3.hg19:g.56766301C>A	ENSP00000296315:p.Gly398Val	133.0	0.0	.		202.0	46.0	.	NM_001128615	A8K5U7|Q4FZB6|Q4QQI5|Q4QQQ0|Q59F00|Q6NUN3|Q7Z4U2|Q7Z5T2|Q9H7T4	Missense_Mutation	SNP	ENST00000296315.3	hg19	CCDS2878.1	.	.	.	.	.	.	.	.	.	.	C	32	5.120131	0.94385	.	.	ENSG00000163947	ENST00000296315;ENST00000338458;ENST00000413728;ENST00000496106;ENST00000497267;ENST00000495373	T;T;T;T;T;T	0.28666	1.88;1.79;1.8;1.8;1.82;1.6	5.83	5.83	0.93111	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	T	0.55016	0.1894	M	0.73962	2.25	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;0.998;0.999;1.0;0.999;0.998;0.999	D;D;D;D;D;D;D	0.79108	0.982;0.97;0.982;0.982;0.982;0.97;0.992	T	0.46871	-0.9160	10	0.09590	T	0.72	-7.7666	20.1218	0.97964	0.0:1.0:0.0:0.0	.	404;369;196;398;430;398;404	E9PG37;E7EU49;Q9NR81-4;C9J586;Q9NR81-2;Q9NR81;Q9NR81-3	.;.;.;.;.;ARHG3_HUMAN;.	V	398;430;404;404;369;398	ENSP00000296315:G398V;ENSP00000341071:G430V;ENSP00000410922:G404V;ENSP00000420420:G404V;ENSP00000418826:G369V;ENSP00000417986:G398V	ENSP00000296315:G398V	G	-	2	0	ARHGEF3	56741341	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.818000	0.86416	2.763000	0.94921	0.561000	0.74099	GGC	.	.	.	none		0.552	ARHGEF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352431.2	NM_019555		A	56766301	C	A	56766301	3	1	201	1	0	0	0	0	1	0	0	0	904	739	26	4	395	4	ARHGEF3	3	56766301	Missense_Mutation	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	22925950	56766301	141256129	11	12158											
SPON2	10417	hgsc.bcm.edu	37	chr4	1164263	1164263	+	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	gggatgaaggccctggggctCtgtcgcagccgcaccagtgt	6	7	16	12	2	1	1	0	1	1	0	2	2	1	2	3	4	1	3	3	4	1	0			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr4:1164263C>A	ENST00000290902.5	-	5	1070	c.738G>T	c.(736-738)caG>caT	p.Q246H	SPON2_ENST00000431380.1_Missense_Mutation_p.Q246H|RP11-20I20.4_ENST00000609548.1_RNA	NM_012445.3	NP_036577	Q9BUD6	SPON2_HUMAN	spondin 2, extracellular matrix protein	246					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|pancreas(1)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(23;0.00805)	UCEC - Uterine corpus endometrioid carcinoma (64;0.139)|Colorectal(103;0.19)		CCCTGGGGCTCTGTCGCAGCC	0.637																																					p.Q246H		Atlas-SNP	.											.	SPON2	22	.	0			c.G738T						PASS	.						104	102	103					4																	1164263		2203	4300	6503	SO:0001583	missense	10417	exon5			GGGGCTCTGTCGC	AB027466	CCDS3347.1	4p16.3	2008-07-29			ENSG00000159674	ENSG00000159674			11253	protein-coding gene	gene with protein product	"Mindin", "M-spondin"	605918				10512675, 15094111	Standard	NM_012445		Approved	DIL1	uc003gco.4	Q9BUD6	OTTHUMG00000089002	ENST00000290902.5:c.738G>T	chr4.hg19:g.1164263C>A	ENSP00000290902:p.Gln246His	58.0	0.0	.		124.0	46.0	.	NM_012445	D3DVN9|Q4W5N4|Q9ULW1	Missense_Mutation	SNP	ENST00000290902.5	hg19	CCDS3347.1	.	.	.	.	.	.	.	.	.	.	C	4.701	0.130282	0.08981	.	.	ENSG00000159674	ENST00000290902;ENST00000431380	T;T	0.10005	2.92;2.92	4.73	0.866	0.19079	.	0.275166	0.40640	N	0.001054	T	0.10465	0.0256	M	0.62723	1.935	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.20773	-1.0265	10	0.48119	T	0.1	.	5.9277	0.19122	0.0:0.4937:0.254:0.2523	.	246;246	D3DVN9;Q9BUD6	.;SPON2_HUMAN	H	246	ENSP00000290902:Q246H;ENSP00000394832:Q246H	ENSP00000290902:Q246H	Q	-	3	2	SPON2	1154263	0.003000	0.15002	0.455000	0.27031	0.047000	0.14425	-0.195000	0.09546	0.077000	0.16863	0.603000	0.83216	CAG	.	.	.	none		0.637	SPON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202080.2			A	1164263	C	A	1164263	3	1	201	1	0	0	0	0	1	0	0	0	15095	912	32	4	265	4	SPON2	4	1164263	Missense_Mutation	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10		1164263	189990013	12	12159											
SEL1L3	23231	hgsc.bcm.edu	37	chr4	25819805	25819806	+	Frame_Shift_Ins	INS	-	-	T																															gcctggaacaagctggggtgINStttgtctttcagctccttct																										TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr4:25819805_25819806insT	ENST00000399878.3	-	9	1640_1641	c.1518_1519insA	c.(1516-1521)aaacacfs	p.H507fs	SEL1L3_ENST00000502949.1_Frame_Shift_Ins_p.H354fs|SEL1L3_ENST00000264868.5_Frame_Shift_Ins_p.H472fs	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	507						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						AAGCTGGGGTGTTTGTCTTTCA	0.55																																					p.H507fs		Atlas-Indel,Pindel	.											.	SEL1L3	62	.	0			c.1519_1520insA						PASS	.																																			SO:0001589	frameshift_variant	23231	exon9			.	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.1519dupA	chr4.hg19:g.25819808_25819808dupT	ENSP00000382767:p.His507fs	175.0	0.0	0		198.0	49.0	0.247475	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Frame_Shift_Ins	INS	ENST00000399878.3	hg19	CCDS47037.1																																																																																			.	.	.	none		0.55	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187		T	25819806	-	T	25819805	7	5	201	1	0	1	1	0	0	0	0	0	14025	1377	48	0	1943	0	SEL1L3	4	25819805	Frame_Shift_Ins	INS	-	TCGA-HE-A5NL-01A-11D-A26P-10	24655542	25819805	165334471	13	12160											
KLB	152831	hgsc.bcm.edu	37	chr4	39435931	39435931	+	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	cattggatcgagccaaaccgGtcggaaaacacgatggatat	14	7	11	9	4	0	0	0	0	0	0	2	5	0	3	2	4	3	0	2	4	4	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr4:39435931G>T	ENST00000257408.4	+	2	1024	c.927G>T	c.(925-927)cgG>cgT	p.R309R		NM_175737.3	NP_783864.1	Q86Z14	KLOTB_HUMAN	klotho beta	309	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						AGCCAAACCGGTCGGAAAACA	0.473																																					p.R309R		Atlas-SNP	.											.	KLB	95	.	0			c.G927T						PASS	.						118	101	107					4																	39435931		2203	4300	6503	SO:0001819	synonymous_variant	152831	exon2			AAACCGGTCGGAA	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.927G>T	chr4.hg19:g.39435931G>T		307.0	0.0	.		373.0	119.0	.	NM_175737	Q2M3K8	Silent	SNP	ENST00000257408.4	hg19	CCDS3451.1																																																																																			.	.	.	none		0.473	KLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250429.1	NM_175737		T	39435931	G	T	39435931	2	4	201	1	0	0	0	0	0	0	0	1	8339	1248	44	4		4	KLB	4	39435931	Silent	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	13616126	39435931	151718345	14	12161											
GABRG1	2565	hgsc.bcm.edu	37	chr4	46043272	46043272	+	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	ggatggagaccaggagtcatCtgagcacaataataaatgaa	17	7	11	6	0	2	3	1	2	1	1	2	6	2	5	1	3	1	1	1	3	5	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr4:46043272C>T	ENST00000295452.4	-	9	1299		c.e9-1			NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1						gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CAGGAGTCATCTGAGCACAAT	0.388																																					.		Atlas-SNP	.											.	GABRG1	172	.	0			c.1132-1G>A						PASS	.						44	46	45					4																	46043272		2203	4297	6500	SO:0001630	splice_region_variant	2565	exon10			AGTCATCTGAGCA	BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4086	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma"	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.1132-1G>A	chr4.hg19:g.46043272C>T		66.0	0.0	.		70.0	17.0	.	NM_173536	Q5H9T8	Splice_Site	SNP	ENST00000295452.4	hg19	CCDS3470.1	.	.	.	.	.	.	.	.	.	.	C	10.91	1.483181	0.26598	.	.	ENSG00000163285	ENST00000295452;ENST00000540030	.	.	.	5.22	5.22	0.72569	.	.	.	.	.	.	.	.	.	.	.	0.36548	D	0.871662	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.8364	0.40971	0.0:0.9066:0.0:0.0934	.	.	.	.	.	-1	.	.	.	-	.	.	GABRG1	45738029	0.279000	0.24239	0.267000	0.24556	0.006000	0.05464	1.471000	0.35365	2.436000	0.82500	0.585000	0.79938	.	.	.	.	none		0.388	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536	Intron	T	46043272	C	T	46043272	5	4	201	1	0	0	0	0	0	0	1	0	6178	927	32	2	270	2	GABRG1	4	46043272	Splice_Site	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	6607341	46043272	145111004	15	12162											
FAT4	79633	hgsc.bcm.edu	37	chr4	126239108	126239108	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctaatctgcgttacagcatTgtctctggcaatggactggg	8	12	12	9	1	2	0	0	0	2	0	3	1	2	1	0	3	3	4	0	3	3	3			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr4:126239108T>C	ENST00000394329.3	+	1	1555	c.1542T>C	c.(1540-1542)atT>atC	p.I514I		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	514	Cadherin 5. {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						GTTACAGCATTGTCTCTGGCA	0.562											OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I514I		Atlas-SNP	.											.	FAT4	1752	.	0			c.T1542C						PASS	.						63	65	65					4																	126239108		2203	4300	6503	SO:0001819	synonymous_variant	79633	exon1			CAGCATTGTCTCT	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.1542T>C	chr4.hg19:g.126239108T>C		150.0	0.0	.	1548	147.0	55.0	.	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	hg19	CCDS3732.3																																																																																			.	.	.	none		0.562	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		C	126239108	T	C	126239108	2	2	201	1	0	0	0	0	0	0	0	1	5699	1800	63	3		3	FAT4	4	126239108	Silent	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10	80195836	126239108	64915168	16	12163											
HAND2	9464	hgsc.bcm.edu	37	chr4	174450317	174450317	+	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	gatgagccagccatggaagtAggggttctcctcatggctgc	8	9	14	10	0	2	1	1	1	1	0	3	3	2	2	3	4	3	3	3	4	2	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr4:174450317A>T	ENST00000359562.4	-	1	1063	c.124T>A	c.(124-126)Tac>Aac	p.Y42N	HAND2-AS1_ENST00000507636.1_RNA|HAND2-AS1_ENST00000507571.1_RNA|HAND2-AS1_ENST00000507062.1_RNA|HAND2-AS1_ENST00000504740.1_RNA|HAND2-AS1_ENST00000512099.1_RNA|HAND2-AS1_ENST00000505817.1_RNA|HAND2-AS1_ENST00000515310.1_RNA|HAND2-AS1_ENST00000511196.1_RNA|HAND2-AS1_ENST00000512929.1_RNA|HAND2-AS1_ENST00000514431.1_RNA|HAND2-AS1_ENST00000509866.1_RNA|HAND2-AS1_ENST00000511728.1_RNA|HAND2-AS1_ENST00000514673.1_RNA|HAND2-AS1_ENST00000515345.1_RNA|HAND2-AS1_ENST00000508887.1_RNA|HAND2-AS1_ENST00000505621.1_RNA|HAND2-AS1_ENST00000512246.1_RNA|HAND2-AS1_ENST00000502334.1_RNA|HAND2-AS1_ENST00000510268.1_RNA|HAND2-AS1_ENST00000515376.1_RNA|HAND2-AS1_ENST00000515350.1_RNA|HAND2-AS1_ENST00000503198.1_RNA|HAND2-AS1_ENST00000503474.1_RNA|HAND2-AS1_ENST00000508534.1_RNA|HAND2-AS1_ENST00000507322.1_RNA|HAND2-AS1_ENST00000510339.1_RNA|HAND2-AS1_ENST00000509640.1_RNA|HAND2-AS1_ENST00000515741.1_RNA|HAND2-AS1_ENST00000505032.1_RNA|HAND2-AS1_ENST00000502896.1_RNA|HAND2-AS1_ENST00000504429.1_RNA|HAND2-AS1_ENST00000503309.1_RNA|HAND2-AS1_ENST00000512943.1_RNA|HAND2_ENST00000505300.1_5'UTR|HAND2-AS1_ENST00000512209.2_RNA|HAND2-AS1_ENST00000510221.1_RNA|HAND2-AS1_ENST00000502941.1_RNA	NM_021973.2	NP_068808.1	P61296	HAND2_HUMAN	heart and neural crest derivatives expressed 2	42					adult heart development (GO:0007512)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic process involved in heart morphogenesis (GO:0003278)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac neural crest cell migration involved in outflow tract morphogenesis (GO:0003253)|cardiac right ventricle formation (GO:0003219)|cartilage morphogenesis (GO:0060536)|cell proliferation involved in outflow tract morphogenesis (GO:0061325)|coronary artery morphogenesis (GO:0060982)|embryonic digit morphogenesis (GO:0042733)|heart development (GO:0007507)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mesenchymal cell proliferation (GO:0010463)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of DNA binding (GO:0043392)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|neural crest cell development (GO:0014032)|noradrenergic neuron differentiation (GO:0003357)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peripheral nervous system neuron development (GO:0048935)|positive regulation of semaphorin-plexin signaling pathway involved in outflow tract morphogenesis (GO:2000764)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in norepinephrine biosynthetic process (GO:2000763)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|sympathetic nervous system development (GO:0048485)|thymus development (GO:0048538)|tongue development (GO:0043586)|visceral serous pericardium development (GO:0061032)	nuclear chromatin (GO:0000790)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|AT DNA binding (GO:0003680)|E-box binding (GO:0070888)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			endometrium(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	13		Prostate(90;0.00601)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_neural(102;0.0837)|all_hematologic(60;0.107)		all cancers(43;1.37e-18)|Epithelial(43;5.5e-17)|OV - Ovarian serous cystadenocarcinoma(60;3.3e-10)|STAD - Stomach adenocarcinoma(60;0.00273)|GBM - Glioblastoma multiforme(59;0.0064)|LUSC - Lung squamous cell carcinoma(193;0.0903)|Kidney(143;0.249)		CCATGGAAGTAGGGGTTCTCC	0.726																																					p.Y42N		Atlas-SNP	.											.	HAND2	25	.	0			c.T124A						PASS	.						5	6	6					4																	174450317		1939	3897	5836	SO:0001583	missense	9464	exon1			GGAAGTAGGGGTT	AF087941	CCDS3819.1	4q34.1	2014-08-12			ENSG00000164107	ENSG00000164107		"Basic helix-loop-helix proteins"	4808	protein-coding gene	gene with protein product		602407				9878849	Standard	NM_021973		Approved	dHand, Thing2, Hed, bHLHa26	uc003ith.1	P61296	OTTHUMG00000160775	ENST00000359562.4:c.124T>A	chr4.hg19:g.174450317A>T	ENSP00000352565:p.Tyr42Asn	17.0	0.0	.		29.0	7.0	.	NM_021973	B6ECG9|O95300|O95301|P97833|Q494T1	Missense_Mutation	SNP	ENST00000359562.4	hg19	CCDS3819.1	.	.	.	.	.	.	.	.	.	.	A	18.74	3.688940	0.68271	.	.	ENSG00000164107	ENST00000359562;ENST00000393686	D	0.97066	-4.23	3.57	3.57	0.40892	.	0.281047	0.34178	N	0.004194	D	0.96078	0.8722	L	0.38175	1.15	0.58432	D	0.999995	D;D;D	0.63046	0.992;0.992;0.986	P;P;P	0.57204	0.815;0.815;0.701	D	0.94998	0.8140	10	0.39692	T	0.17	-0.0407	12.291	0.54819	1.0:0.0:0.0:0.0	.	42;42;42	B6ECG9;P61296;E9PCP7	.;HAND2_HUMAN;.	N	42	ENSP00000352565:Y42N	ENSP00000352565:Y42N	Y	-	1	0	HAND2	174686892	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.391000	0.66266	1.491000	0.48482	0.379000	0.24179	TAC	.	.	.	none		0.726	HAND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362241.3			T	174450317	A	T	174450317	3	4	201	1	0	0	0	0	1	0	0	0	6957	420	15	5	537	5	HAND2	4	174450317	Missense_Mutation	SNP	A	TCGA-HE-A5NL-01A-11D-A26P-10	48211209	174450317	16703959	17	12164											
WDR17	116966	hgsc.bcm.edu	37	chr4	177056301	177056301	+	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	actgcaaattcaaacctgacGatcctaatcttttagcaaca	15	11	4	11	1	2	1	1	1	1	0	3	2	3	1	2	0	4	2	2	0	5	4	rs140987021		TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr4:177056301G>A	ENST00000280190.4	+	9	1369	c.1213G>A	c.(1213-1215)Gat>Aat	p.D405N	WDR17_ENST00000393643.2_Missense_Mutation_p.D381N|WDR17_ENST00000508596.1_Missense_Mutation_p.D381N|WDR17_ENST00000507824.2_Missense_Mutation_p.D388N			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	405										breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		CAAACCTGACGATCCTAATCT	0.353																																					p.D405N		Atlas-SNP	.											.	WDR17	198	.	0			c.G1213A						PASS	.	G	ASN/ASP,ASN/ASP	0,4406		0,0,2203	121	122	122		1213,1141	2.4	1	4	dbSNP_134	122	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	WDR17	NM_170710.4,NM_181265.3	23,23	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	405/1323,381/1284	177056301	1,13005	2203	4300	6503	SO:0001583	missense	116966	exon9			CCTGACGATCCTA	AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"WD repeat domain containing"	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.1213G>A	chr4.hg19:g.177056301G>A	ENSP00000280190:p.Asp405Asn	213.0	0.0	.		190.0	62.0	.	NM_170710	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	hg19	CCDS3825.1	.	.	.	.	.	.	.	.	.	.	G	10.35	1.326502	0.24080	0.0	1.16E-4	ENSG00000150627	ENST00000508596;ENST00000393643;ENST00000280190;ENST00000507824	T;T;T	0.58652	0.35;3.58;0.32	5.5	2.42	0.29668	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (2);WD40-repeat-containing domain (1);	0.265065	0.38164	N	0.001790	T	0.30324	0.0761	N	0.13198	0.31	0.48571	D	0.999678	B;B	0.19445	0.036;0.036	B;B	0.18871	0.023;0.023	T	0.15150	-1.0447	10	0.05525	T	0.97	-17.5458	6.7154	0.23300	0.433:0.0:0.567:0.0	.	381;405	E7EQX0;Q8IZU2	.;WDR17_HUMAN	N	381;381;405;388	ENSP00000422763:D381N;ENSP00000377258:D381N;ENSP00000280190:D405N	ENSP00000280190:D405N	D	+	1	0	WDR17	177293295	1.000000	0.71417	0.998000	0.56505	0.740000	0.42216	3.339000	0.52135	0.703000	0.31848	0.650000	0.86243	GAT	.	G|1.000;A|0.000	0.000	weak		0.353	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2			A	177056301	G	A	177056301	3	1	201	1	0	0	0	0	1	0	0	0	17289	1058	37	1	1243	1	WDR17	4	177056301	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	2605984	177056301	14097975	18	12165											
RGMB	285704	hgsc.bcm.edu	37	chr5	98115590	98115591	+	Frame_Shift_Del	DEL	GG	GG	-																															tcacagccacgctggagccaGggaacacaggagaggggacc																										TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr5:98115590_98115591delGG	ENST00000513185.1	+	2	879_880	c.443_444delGG	c.(442-444)aggfs	p.R148fs	RGMB_ENST00000308234.7_Frame_Shift_Del_p.R189fs|RGMB_ENST00000504776.1_3'UTR			Q6NW40	RGMB_HUMAN	repulsive guidance molecule family member b	148					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|cell adhesion (GO:0007155)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	anchored component of plasma membrane (GO:0046658)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)	identical protein binding (GO:0042802)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	10		all_cancers(142;2.76e-08)|all_epithelial(76;2.98e-11)|all_lung(232;0.000485)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0587)		GCTGGAGCCAGGGAACACAGGA	0.51																																					p.189_189del		Atlas-Indel,Pindel	.											.	RGMB	29	.	0			c.565_566del						PASS	.																																			SO:0001589	frameshift_variant	285704	exon4			.	AK074887	CCDS47251.1	5q21.1	2013-11-06	2013-11-06		ENSG00000174136	ENSG00000174136			26896	protein-coding gene	gene with protein product		612687	"RGM domain family, member B"			19324014	Standard	NM_001012761		Approved	FLJ90406, DRAGON	uc003knc.3	Q6NW40	OTTHUMG00000162745	ENST00000513185.1:c.443_444delGG	chr5.hg19:g.98115590_98115591delGG	ENSP00000423256:p.Arg148fs	174.0	0.0	0		204.0	65.0	0.318627	NM_001012761	D6R9A0|Q8NC92	Frame_Shift_Del	DEL	ENST00000513185.1	hg19																																																																																				.	.	.	none		0.51	RGMB-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000370308.1	NM_173670		-	98115591	GG	-	98115590	7	5	201	1	0	1	0	1	0	0	0	0	13294	1000	35	0	576	0	RGMB	5	98115590	Frame_Shift_Del	DEL	GG	TCGA-HE-A5NL-01A-11D-A26P-10		98115590	82799670	19	12166											
ANKHD1	54882	hgsc.bcm.edu	37	chr5	139876316	139876316	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aacaaagataagatagaagaActtaaaaagaacagagaaga	26	4	8	3	0	0	7	0	0	0	7	0	8	0	7	0	0	3	0	0	0	11	3			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr5:139876316A>G	ENST00000360839.2	+	15	2611	c.2457A>G	c.(2455-2457)gaA>gaG	p.E819E	ANKHD1_ENST00000462121.1_3'UTR|ANKHD1-EIF4EBP3_ENST00000532219.1_Silent_p.E819E|ANKHD1_ENST00000297183.6_Silent_p.E819E	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	819						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)			AGATAGAAGAACTTAAAAAGA	0.368																																					p.E819E		Atlas-SNP	.											.	ANKHD1	233	.	0			c.A2457G						PASS	.						69	73	71					5																	139876316		2203	4300	6503	SO:0001819	synonymous_variant	54882	exon15			AGAAGAACTTAAA	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.2457A>G	chr5.hg19:g.139876316A>G		80.0	0.0	.		61.0	29.0	.	NM_017747	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Silent	SNP	ENST00000360839.2	hg19	CCDS4225.1																																																																																			.	.	.	none		0.368	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		G	139876316	A	G	139876316	2	3	201	1	0	0	0	0	0	0	0	1	628	40	2	3		3	ANKHD1	5	139876316	Silent	SNP	A	TCGA-HE-A5NL-01A-11D-A26P-10	41760726	139876316	41038944	20	12167											
FAT2	2196	hgsc.bcm.edu	37	chr5	150921871	150921871	+	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	atgtagcaggtgacctgcctGttctgctcagaaatgtcagc	9	11	11	10	0	3	2	2	1	1	1	3	2	3	2	2	1	4	4	2	1	2	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr5:150921871G>T	ENST00000261800.5	-	9	8829	c.8817C>A	c.(8815-8817)aaC>aaA	p.N2939K		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2939	Cadherin 26. {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)			TGACCTGCCTGTTCTGCTCAG	0.502																																					p.N2939K		Atlas-SNP	.											.	FAT2	465	.	0			c.C8817A						PASS	.						127	121	123					5																	150921871		2203	4300	6503	SO:0001583	missense	2196	exon9			CTGCCTGTTCTGC	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.8817C>A	chr5.hg19:g.150921871G>T	ENSP00000261800:p.Asn2939Lys	91.0	0.0	.		104.0	30.0	.	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	hg19	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	19.95	3.921781	0.73213	.	.	ENSG00000086570	ENST00000261800	T	0.59906	0.23	6.05	1.26	0.21427	Cadherin (4);Cadherin-like (1);	0.000000	0.64402	D	0.000002	T	0.76807	0.4039	M	0.89601	3.045	0.47511	D	0.999445	D	0.89917	1.0	D	0.97110	1.0	T	0.77199	-0.2675	10	0.56958	D	0.05	.	10.6765	0.45789	0.4552:0.0:0.5448:0.0	.	2939	Q9NYQ8	FAT2_HUMAN	K	2939	ENSP00000261800:N2939K	ENSP00000261800:N2939K	N	-	3	2	FAT2	150902064	1.000000	0.71417	0.999000	0.59377	0.984000	0.73092	1.206000	0.32321	0.147000	0.19030	0.650000	0.86243	AAC	.	.	.	none		0.502	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		T	150921871	G	T	150921871	3	4	201	1	0	0	0	0	1	0	0	0	5697	1368	48	4	4292	4	FAT2	5	150921871	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	11045555	150921871	29993389	21	12168											
KIF4B	285643	hgsc.bcm.edu	37	chr5	154395501	154395501	+	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	aaacttgaaagaaacttccaGaaacaatccagtgtgctcag	17	8	7	9	0	1	3	1	1	0	2	3	3	3	3	2	0	4	1	2	0	5	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr5:154395501G>A	ENST00000435029.4	+	1	2242	c.2082G>A	c.(2080-2082)caG>caA	p.Q694Q		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	694	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)			GAAACTTCCAGAAACAATCCA	0.438																																					p.Q694Q		Atlas-SNP	.											.	KIF4B	307	.	0			c.G2082A						PASS	.						103	107	106					5																	154395501		2203	4300	6503	SO:0001819	synonymous_variant	285643	exon1			CTTCCAGAAACAA	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.2082G>A	chr5.hg19:g.154395501G>A		302.0	0.0	.		320.0	79.0	.	NM_001099293		Silent	SNP	ENST00000435029.4	hg19	CCDS47324.1																																																																																			.	.	.	none		0.438	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1			A	154395501	G	A	154395501	2	1	201	1	0	0	0	0	0	0	0	1	8311	933	33	2		2	KIF4B	5	154395501	Silent	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	3473630	154395501	26519759	22	12169											
CASP8AP2	9994	hgsc.bcm.edu	37	chr6	90577520	90577520	+	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	ggagtctgataattcaagcaGtaaatcaagttgttcttctt	12	15	8	6	0	5	1	2	1	3	0	5	2	5	2	0	1	1	4	0	1	5	7			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr6:90577520G>T	ENST00000551025.1	+	0	5948									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)		AATTCAAGCAGTAAATCAAGT	0.423																																					p.S1504I	Colon(187;1656 2025 17045 31481 39901)	Atlas-SNP	.											.	CASP8AP2	108	.	0			c.G4511T						PASS	.						84	80	82					6																	90577520		1902	4115	6017			9994	exon8			CAAGCAGTAAATC	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"FLICE-associated huge protein"	606880	"CASP8 associated protein 2"			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		chr6.hg19:g.90577520G>T		142.0	0.0	.		156.0	44.0	.	NM_001137667		Missense_Mutation	SNP	ENST00000551025.1	hg19																																																																																				.	.	.	none		0.423	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667		T	90577520	G	T	90577520	1	4	201	0	1	0	0	0	0	0	0	0	2680	1029	36	4		4	CASP8AP2	6	90577520	RNA	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10		90577520	80537547	23	12170											
FBXO30	84085	hgsc.bcm.edu	37	chr6	146126628	146126628	+	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	agttactttgttttgaatcaCcatgtaaattctgattctgg	10	18	7	6	0	3	2	1	2	2	0	3	2	3	2	1	1	1	3	1	1	4	7			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr6:146126628C>T	ENST00000237281.4	-	2	1080	c.914G>A	c.(913-915)gGt>gAt	p.G305D		NM_032145.4	NP_115521.3	Q8TB52	FBX30_HUMAN	F-box protein 30	305							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.G305D(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26		Ovarian(120;0.0776)		OV - Ovarian serous cystadenocarcinoma(155;1.95e-07)|GBM - Glioblastoma multiforme(68;0.0149)		TTTTGAATCACCATGTAAATT	0.403																																					p.G305D		Atlas-SNP	.											FBXO30,NS,carcinoma,0,1	FBXO30	56	.	1	Substitution - Missense(1)	lung(1)	c.G914A						PASS	.						125	119	121					6																	146126628		2203	4300	6503	SO:0001583	missense	84085	exon2			GAATCACCATGTA	AF248640	CCDS5208.1	6q24	2008-02-05	2004-06-15		ENSG00000118496	ENSG00000118496		"F-boxes /  "other""	15600	protein-coding gene	gene with protein product		609101	"F-box only protein, helicase, 18"				Standard	XM_005267159		Approved	MGC21674, Fbx30	uc003qla.3	Q8TB52	OTTHUMG00000015749	ENST00000237281.4:c.914G>A	chr6.hg19:g.146126628C>T	ENSP00000237281:p.Gly305Asp	77.0	0.0	.		84.0	16.0	.	NM_032145	Q9BXZ7	Missense_Mutation	SNP	ENST00000237281.4	hg19	CCDS5208.1	.	.	.	.	.	.	.	.	.	.	C	0.042	-1.281092	0.01398	.	.	ENSG00000118496	ENST00000237281	T	0.17691	2.26	5.29	0.298	0.15766	.	1.121610	0.06334	N	0.706654	T	0.02767	0.0083	L	0.36672	1.1	0.22127	N	0.999344	B	0.02656	0.0	B	0.01281	0.0	T	0.40905	-0.9538	10	0.08381	T	0.77	-3.4918	2.8503	0.05555	0.1103:0.4508:0.2365:0.2024	.	305	Q8TB52	FBX30_HUMAN	D	305	ENSP00000237281:G305D	ENSP00000237281:G305D	G	-	2	0	FBXO30	146168321	0.000000	0.05858	0.946000	0.38457	0.946000	0.59487	0.028000	0.13644	0.046000	0.15833	0.655000	0.94253	GGT	.	.	.	none		0.403	FBXO30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042570.2			T	146126628	C	T	146126628	3	4	201	1	0	0	0	0	1	0	0	0	5747	507	18	2	1331	2	FBXO30	6	146126628	Missense_Mutation	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	55549108	146126628	24988439	24	12171											
ABCB4	5244	hgsc.bcm.edu	37	chr7	87037472	87037472	+	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	cttcacctccaggctcagccCctgaagcactggcacgtttg	7	9	9	16	1	2	1	2	1	0	0	3	1	3	1	4	2	2	4	4	2	1	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr7:87037472C>T	ENST00000265723.4	-	25	3271	c.3160G>A	c.(3160-3162)Ggg>Agg	p.G1054R	ABCB4_ENST00000358400.3_Missense_Mutation_p.G1007R|ABCB4_ENST00000359206.3_Missense_Mutation_p.G1054R|ABCB4_ENST00000545634.1_Missense_Mutation_p.G1054R|ABCB4_ENST00000453593.1_Missense_Mutation_p.G1007R	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	1054	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	AGGCTCAGCCCCTGAAGCACT	0.498																																					p.G1054R		Atlas-SNP	.											.	ABCB4	177	.	0			c.G3160A						PASS	.						82	80	81					7																	87037472		2203	4300	6503	SO:0001583	missense	5244	exon25			TCAGCCCCTGAAG	M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"ATP binding cassette transporters / subfamily B"	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.3160G>A	chr7.hg19:g.87037472C>T	ENSP00000265723:p.Gly1054Arg	93.0	0.0	.		150.0	30.0	.	NM_018849	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Missense_Mutation	SNP	ENST00000265723.4	hg19	CCDS5606.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.390489	0.82902	.	.	ENSG00000005471	ENST00000359206;ENST00000358400;ENST00000265723;ENST00000453593;ENST00000545634	D;D;D;D;D	0.91011	-2.77;-2.77;-2.77;-2.77;-2.77	5.19	3.18	0.36537	ABC transporter-like (1);	0.158975	0.56097	N	0.000029	D	0.92632	0.7659	L	0.51914	1.62	0.80722	D	1	P;D;P	0.54047	0.947;0.964;0.939	P;D;D	0.68943	0.789;0.961;0.914	D	0.91904	0.5534	10	0.87932	D	0	-4.0274	11.256	0.49054	0.0:0.8415:0.0:0.1585	.	1007;1054;1054	A4D1D5;P21439-2;P21439	.;.;MDR3_HUMAN	R	1054;1007;1054;1007;1054	ENSP00000352135:G1054R;ENSP00000351172:G1007R;ENSP00000265723:G1054R;ENSP00000392983:G1007R;ENSP00000437465:G1054R	ENSP00000265723:G1054R	G	-	1	0	ABCB4	86875408	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.034000	0.57289	0.565000	0.29255	0.655000	0.94253	GGG	.	.	.	none		0.498	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443		T	87037472	C	T	87037472	3	4	201	1	0	0	0	0	1	0	0	0	43	623	22	2	716	2	ABCB4	7	87037472	Missense_Mutation	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10		87037472	72101191	25	12172											
SLC25A40	55972	hgsc.bcm.edu	37	chr7	87466048	87466048	+	Frame_Shift_Del	DEL	A	A	-																															aaagcaagtatttttacctgAaaataatccggaaaatccat																										TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr7:87466048delA	ENST00000341119.5	-	11	1247	c.901delT	c.(901-903)tcafs	p.S301fs		NM_018843.3	NP_061331.2	Q8TBP6	S2540_HUMAN	solute carrier family 25, member 40	301					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)					TTTTTACCTGAAAATAATCCG	0.264																																					p.S301X		Atlas-Indel,Pindel	.											.	SLC25A40	32	.	0			c.902delC						PASS	.						25	27	26					7																	87466048		2182	4244	6426	SO:0001589	frameshift_variant	55972	exon11			.	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.901delT	chr7.hg19:g.87466048delA	ENSP00000344831:p.Ser301fs	103.0	0.0	0		112.0	21.0	0.1875	NM_018843	A8K483|D6W5P6|Q53GB1|Q9UHR1	Frame_Shift_Del	DEL	ENST00000341119.5	hg19	CCDS5610.1																																																																																			.	.	.	none		0.264	SLC25A40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253677.5	NM_018843		-	87466048	A	-	87466048	7	5	201	1	0	1	0	1	0	0	0	0	14518	246	9	0	123	0	SLC25A40	7	87466048	Frame_Shift_Del	DEL	A	TCGA-HE-A5NL-01A-11D-A26P-10	428576	87466048	71672615	26	12173											
TECPR1	25851	hgsc.bcm.edu	37	chr7	97847037	97847037	+	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	tcccagccgtggcccttgggCtcgtgaggctgcacgccggt	3	8	15	15	4	0	1	0	1	0	0	2	1	1	1	4	4	2	3	4	4	0	1			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr7:97847037C>T	ENST00000447648.2	-	25	3650	c.3351G>A	c.(3349-3351)gaG>gaA	p.E1117E	TECPR1_ENST00000379795.3_Silent_p.E1119E			Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	1117					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						GGCCCTTGGGCTCGTGAGGCT	0.667																																					p.E1117E		Atlas-SNP	.											.	TECPR1	77	.	0			c.G3351A						PASS	.						12	16	15					7																	97847037		2009	3915	5924	SO:0001819	synonymous_variant	25851	exon25			CTTGGGCTCGTGA		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.3351G>A	chr7.hg19:g.97847037C>T		15.0	0.0	.		68.0	20.0	.	NM_015395	A8KAD1|B3KPZ1|C9J024|F5GX57|Q96EB0|Q9P2I9|Q9UFR6	Silent	SNP	ENST00000447648.2	hg19	CCDS47648.1																																																																																			.	.	.	none		0.667	TECPR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334661.1	NM_015395		T	97847037	C	T	97847037	2	4	201	1	0	0	0	0	0	0	0	1	15755	796	28	2		2	TECPR1	7	97847037	Silent	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	10380989	97847037	61291626	27	12174											
MEPCE	56257	hgsc.bcm.edu	37	chr7	100030705	100030705	+	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	gcacctacgccctgggggcaTcctggtcctagagccccaac	7	6	11	17	1	0	1	0	0	0	1	2	1	2	1	6	3	3	2	6	3	3	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr7:100030705T>A	ENST00000310512.2	+	2	2223	c.1835T>A	c.(1834-1836)aTc>aAc	p.I612N	PPP1R35_ENST00000476185.1_5'Flank|RP11-758P17.2_ENST00000492523.1_RNA|MEPCE_ENST00000414441.1_Missense_Mutation_p.I143N	NM_019606.5	NP_062552.2	Q7L2J0	MEPCE_HUMAN	methylphosphate capping enzyme	612	Bin3-type SAM. {ECO:0000255|PROSITE- ProRule:PRU00848}.				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)					CCTGGGGGCATCCTGGTCCTA	0.577																																					p.I612N		Atlas-SNP	.											.	MEPCE	52	.	0			c.T1835A						PASS	.						72	69	70					7																	100030705		2203	4300	6503	SO:0001583	missense	56257	exon2			GGGGCATCCTGGT	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.1835T>A	chr7.hg19:g.100030705T>A	ENSP00000308546:p.Ile612Asn	219.0	0.0	.		367.0	83.0	.	NM_019606	B3KP86|D6W5V7|Q9NPD4	Missense_Mutation	SNP	ENST00000310512.2	hg19	CCDS5693.1	.	.	.	.	.	.	.	.	.	.	T	19.74	3.883852	0.72410	.	.	ENSG00000146834	ENST00000414441;ENST00000425355;ENST00000310512	T;T	0.46819	0.86;0.86	5.37	5.37	0.77165	Bin3-type S-adenosyl-L-methionine binding domain (1);Bicoid-interacting 3 (1);	0.077394	0.52532	D	0.000064	T	0.50837	0.1639	L	0.45352	1.415	0.45066	D	0.998087	D	0.59357	0.985	P	0.58013	0.831	T	0.46470	-0.9189	10	0.29301	T	0.29	-24.0822	8.2283	0.31582	0.0:0.0895:0.0:0.9105	.	612	Q7L2J0	MEPCE_HUMAN	N	143;143;612	ENSP00000400875:I143N;ENSP00000308546:I612N	ENSP00000308546:I612N	I	+	2	0	MEPCE	99868641	1.000000	0.71417	1.000000	0.80357	0.751000	0.42716	5.644000	0.67902	2.156000	0.67533	0.379000	0.24179	ATC	.	.	.	none		0.577	MEPCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339135.1			A	100030705	T	A	100030705	3	1	201	1	0	0	0	0	1	0	0	0	9484	1435	50	5	1841	5	MEPCE	7	100030705	Missense_Mutation	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10	2183668	100030705	59107958	28	12175											
ELP3	55140	hgsc.bcm.edu	37	chr8	28047190	28047190	+	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	cggcaccaggaattattataGaaagatcggctacagattac	15	9	9	8	2	0	3	0	0	0	3	1	4	0	4	1	3	2	2	1	3	7	5			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr8:28047190G>C	ENST00000256398.8	+	15	1969	c.1592G>C	c.(1591-1593)aGa>aCa	p.R531T	ELP3_ENST00000537665.1_Missense_Mutation_p.R412T|ELP3_ENST00000542181.1_Missense_Mutation_p.R402T|ELP3_ENST00000521015.1_Missense_Mutation_p.R517T|ELP3_ENST00000524103.1_Missense_Mutation_p.R459T|ELP3_ENST00000380353.4_Missense_Mutation_p.R439T	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	531	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	histone acetyltransferase activity (GO:0004402)|iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|phosphorylase kinase regulator activity (GO:0008607)			kidney(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.151)|Colorectal(74;0.183)		AATTATTATAGAAAGATCGGC	0.468																																					p.R531T		Atlas-SNP	.											.	ELP3	36	.	0			c.G1592C						PASS	.						127	132	130					8																	28047190		2203	4300	6503	SO:0001583	missense	55140	exon15			ATTATAGAAAGAT		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.1592G>C	chr8.hg19:g.28047190G>C	ENSP00000256398:p.Arg531Thr	78.0	0.0	.		82.0	28.0	.	NM_018091	B4DE19|B4DIG1|E2QRI5|Q53G84|Q6AWB0|Q9BVF7|Q9NVZ1	Missense_Mutation	SNP	ENST00000256398.8	hg19	CCDS6065.1	.	.	.	.	.	.	.	.	.	.	G	17.08	3.297498	0.60086	.	.	ENSG00000134014	ENST00000521015;ENST00000256398;ENST00000542181;ENST00000524103;ENST00000537665;ENST00000380353	T;T;T;T;T;T	0.22743	1.94;1.94;1.94;1.94;1.94;1.94	5.13	5.13	0.70059	GCN5-related N-acetyltransferase (GNAT) domain (2);Acyl-CoA N-acyltransferase (2);	0.000000	0.85682	D	0.000000	T	0.44371	0.1290	H	0.96604	3.85	0.58432	D	0.999995	B;B	0.24576	0.106;0.062	B;B	0.31337	0.128;0.128	T	0.56238	-0.8012	10	0.72032	D	0.01	-17.8026	13.9575	0.64160	0.0:0.0:1.0:0.0	.	412;531	B4DE19;Q9H9T3	.;ELP3_HUMAN	T	517;531;402;459;412;439	ENSP00000428449:R517T;ENSP00000256398:R531T;ENSP00000439242:R402T;ENSP00000429180:R459T;ENSP00000445558:R412T;ENSP00000369711:R439T	ENSP00000256398:R531T	R	+	2	0	ELP3	28103109	1.000000	0.71417	0.978000	0.43139	0.982000	0.71751	4.723000	0.61965	2.669000	0.90835	0.655000	0.94253	AGA	.	.	.	none		0.468	ELP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219963.2	NM_018091		C	28047190	G	C	28047190	3	2	201	1	0	0	0	0	1	0	0	0	5083	942	33	4	1650	4	ELP3	8	28047190	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10		28047190	118316832	29	12176											
TRIM55	84675	hgsc.bcm.edu	37	chr8	67064722	67064722	+	Frame_Shift_Del	DEL	T	T	-																															tagaaaatgttcaaacagagTttccaggagaagatgaaaac																										TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr8:67064722delT	ENST00000315962.4	+	8	1469	c.1096delT	c.(1096-1098)tttfs	p.F366fs	TRIM55_ENST00000276573.7_Frame_Shift_Del_p.F366fs|TRIM55_ENST00000353317.5_Frame_Shift_Del_p.F366fs|TRIM55_ENST00000350034.4_Intron	NM_184085.1	NP_908973.1	Q9BYV6	TRI55_HUMAN	tripartite motif containing 55	366					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)			TCAAACAGAGTTTCCAGGAGA	0.498																																					p.E365fs		Atlas-Indel,Pindel	.											.	TRIM55	91	.	0			c.1095delG						PASS	.						70	70	70					8																	67064722		2203	4300	6503	SO:0001589	frameshift_variant	84675	exon8			.	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.1096delT	chr8.hg19:g.67064722delT	ENSP00000323913:p.Phe366fs	55.0	0.0	0		44.0	17.0	0.386364	NM_033058	B3KRC0|B3KRJ3|Q53XX3|Q8IUD9|Q8IUE4|Q96DV2|Q96DV3|Q9BYV5	Frame_Shift_Del	DEL	ENST00000315962.4	hg19	CCDS6184.1																																																																																			.	.	.	none		0.498	TRIM55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378921.1	NM_184085		-	67064722	T	-	67064722	7	5	201	1	0	1	0	1	0	0	0	0	16541	1725	60	0	1126	0	TRIM55	8	67064722	Frame_Shift_Del	DEL	T	TCGA-HE-A5NL-01A-11D-A26P-10	39017532	67064722	79299300	30	12177											
CSMD3	114788	hgsc.bcm.edu	37	chr8	113516202	113516202	+	Missense_Mutation	SNP	T	T	C																															gtcatagtttggttctatgcTaaaactgaaaaaaaaaagga																										TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr8:113516202T>C	ENST00000297405.5	-	30	5144	c.4900A>G	c.(4900-4902)Agc>Ggc	p.S1634G	CSMD3_ENST00000352409.3_Missense_Mutation_p.S1634G|CSMD3_ENST00000343508.3_Missense_Mutation_p.S1594G|CSMD3_ENST00000455883.2_Missense_Mutation_p.S1530G	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1634	CUB 9. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GGTTCTATGCTAAAACTgaaa	0.308										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.S1634G		Atlas-SNP	.											.	CSMD3	2325	.	0			c.A4900G						PASS	.						69	67	68					8																	113516202		2203	4300	6503	SO:0001583	missense	114788	exon30			CTATGCTAAAACT	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.4900A>G	chr8.hg19:g.113516202T>C	ENSP00000297405:p.Ser1634Gly	51.0	0.0	.		32.0	10.0	.	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	T	19.81	3.897390	0.72639	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.18174	2.23;2.23;2.23;2.23;2.23	4.96	4.96	0.65561	CUB (5);	0.056809	0.64402	D	0.000002	T	0.31104	0.0786	L	0.55990	1.75	0.33482	D	0.587596	B;B;P	0.49635	0.007;0.008;0.926	B;B;P	0.58454	0.026;0.044;0.839	T	0.33266	-0.9875	10	0.22706	T	0.39	.	14.7774	0.69740	0.0:0.0:0.0:1.0	.	1530;1634;1594	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	G	1594;1634;974;1530;1634	ENSP00000345799:S1594G;ENSP00000297405:S1634G;ENSP00000341558:S974G;ENSP00000412263:S1530G;ENSP00000343124:S1634G	ENSP00000297405:S1634G	S	-	1	0	CSMD3	113585378	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.657000	0.83745	2.069000	0.61940	0.455000	0.32223	AGC	.	.	.	none		0.308	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		C	113516202	T	C	113516202	3	2	201	1	0	0	0	0	1	0	0	0	3948	1522	53	3	6391	3	CSMD3	8	113516202	Missense_Mutation	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10	46451480	113516202	32847820	31	12178	115	2									
CSMD3	114788	hgsc.bcm.edu	37	chr8	113516207	113516207	+	Splice_Site	SNP	C	C	G																															agtttggttctatgctaaaaCtgaaaaaaaaaaggaaagaa																								rs76670724		TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr8:113516207C>G	ENST00000297405.5	-	30	5140		c.e30-1		CSMD3_ENST00000352409.3_Splice_Site|CSMD3_ENST00000343508.3_Splice_Site|CSMD3_ENST00000455883.2_Splice_Site	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TATGCTAAAACTgaaaaaaaa	0.318										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											.		Atlas-SNP	.											.	CSMD3	2325	.	0			c.4584-1G>C						PASS	.						61	60	60					8																	113516207		2203	4299	6502	SO:0001630	splice_region_variant	114788	exon30			CTAAAACTGAAAA	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.4896-1G>C	chr8.hg19:g.113516207C>G		42.0	0.0	.		25.0	9.0	.	NM_052900	Q96PZ3	Splice_Site	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	18.97	3.736213	0.69189	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	.	.	.	4.96	4.96	0.65561	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.378	0.90441	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CSMD3	113585383	1.000000	0.71417	1.000000	0.80357	0.757000	0.42996	7.446000	0.80609	2.560000	0.86352	0.557000	0.71058	.	.	.	.	alt		0.318	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	Intron	G	113516207	C	G	113516207	5	3	201	1	0	0	0	0	0	0	1	0	3948	579	20	4	6396	4	CSMD3	8	113516207	Splice_Site	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	5	113516207	32847815	32	12179	115	2									
ZNF79	7633	hgsc.bcm.edu	37	chr9	130206739	130206739	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccttacaagtgcagtgaaTgtggaagagccttcagccag	12	8	12	9	0	1	2	1	1	0	1	1	3	1	3	3	1	5	1	3	1	4	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr9:130206739T>C	ENST00000342483.5	+	5	1166	c.760T>C	c.(760-762)Tgt>Cgt	p.C254R	ZNF79_ENST00000543471.1_Missense_Mutation_p.C230R	NM_007135.2	NP_009066.2	Q15937	ZNF79_HUMAN	zinc finger protein 79	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)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|stomach(2)	28						GTGCAGTGAATGTGGAAGAGC	0.532																																					p.C254R		Atlas-SNP	.											.	ZNF79	47	.	0			c.T760C						PASS	.						101	92	95					9																	130206739		2203	4300	6503	SO:0001583	missense	7633	exon5			AGTGAATGTGGAA	X65232	CCDS6871.1, CCDS69664.1, CCDS75904.1	9q34	2013-01-08	2006-05-12		ENSG00000196152	ENSG00000196152		"Zinc fingers, C2H2-type"	13153	protein-coding gene	gene with protein product		194552	"zinc finger protein 79 (pT7)"			8478004	Standard	NM_007135		Approved	pT7	uc004bqw.4	Q15937	OTTHUMG00000020703	ENST00000342483.5:c.760T>C	chr9.hg19:g.130206739T>C	ENSP00000362446:p.Cys254Arg	93.0	0.0	.		129.0	35.0	.	NM_007135	Q5VVW1|Q96NV1	Missense_Mutation	SNP	ENST00000342483.5	hg19	CCDS6871.1	.	.	.	.	.	.	.	.	.	.	T	16.12	3.034463	0.54896	.	.	ENSG00000196152	ENST00000342483;ENST00000543471	D;D	0.85955	-2.05;-2.05	3.53	2.38	0.29361	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.92404	0.7589	H	0.98682	4.3	0.80722	D	1	D	0.53745	0.962	P	0.53313	0.723	D	0.90977	0.4824	9	0.87932	D	0	.	6.7985	0.23738	0.0:0.1169:0.0:0.8831	.	254	Q15937	ZNF79_HUMAN	R	254;230	ENSP00000362446:C254R;ENSP00000438418:C230R	ENSP00000362446:C254R	C	+	1	0	ZNF79	129246560	1.000000	0.71417	0.659000	0.29680	0.986000	0.74619	5.308000	0.65768	0.555000	0.29079	0.533000	0.62120	TGT	.	.	.	none		0.532	ZNF79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054188.1	NM_007135		C	130206739	T	C	130206739	3	2	201	1	0	0	0	0	1	0	0	0	18173	1464	51	3	778	3	ZNF79	9	130206739	Missense_Mutation	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10		130206739	11006692	33	12180											
ACBD5	91452	hgsc.bcm.edu	37	chr10	27529275	27529275	+	Missense_Mutation	SNP	T	T	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	cggcaaactctggatcacctTcacggccgcctcaaacctag	10	7	8	16	3	4	0	3	0	1	0	4	1	4	1	4	3	2	1	4	3	3	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr10:27529275T>G	ENST00000375888.1	-	1	212	c.148A>C	c.(148-150)Aag>Cag	p.K50Q	ACBD5_ENST00000375901.1_5'UTR|ACBD5_ENST00000375905.4_Missense_Mutation_p.K17Q|ACBD5_ENST00000396271.3_Missense_Mutation_p.K52Q|ACBD5_ENST00000476758.1_5'UTR|RP11-85G18.6_ENST00000574842.1_lincRNA|ACBD5_ENST00000375897.3_5'UTR			Q5T8D3	ACBD5_HUMAN	acyl-CoA binding domain containing 5	50	ACB. {ECO:0000255|PROSITE- ProRule:PRU00573}.				peroxisome degradation (GO:0030242)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisome (GO:0005777)	fatty-acyl-CoA binding (GO:0000062)|lipid binding (GO:0008289)			breast(1)|endometrium(1)|large_intestine(3)|lung(7)|prostate(1)	13						TGGATCACCTTCACGGCCGCC	0.617																																					p.K52Q		Atlas-SNP	.											.	ACBD5	75	.	0			c.A154C						PASS	.						101	91	94					10																	27529275		2203	4300	6503	SO:0001583	missense	91452	exon2			TCACCTTCACGGC	AF505653	CCDS7154.1, CCDS44368.1, CCDS73079.1	10p12.1	2010-04-30	2010-04-30		ENSG00000107897	ENSG00000107897			23338	protein-coding gene	gene with protein product			"acyl-Coenzyme A binding domain containing 5"			12056414	Standard	NR_024150		Approved	DKFZp434A2417, KIAA1996	uc010qdp.2	Q5T8D3	OTTHUMG00000017854	ENST00000375888.1:c.148A>C	chr10.hg19:g.27529275T>G	ENSP00000365049:p.Lys50Gln	127.0	0.0	.		136.0	39.0	.	NM_145698	B3KQ56|D3DRW0|Q5T8D4|Q5T8E1|Q5T8E2|Q86UV1|Q8N6E3|Q9UFB5	Missense_Mutation	SNP	ENST00000375888.1	hg19		.	.	.	.	.	.	.	.	.	.	T	24.0	4.487454	0.84854	.	.	ENSG00000107897	ENST00000375889;ENST00000396271;ENST00000375905;ENST00000375888;ENST00000426079;ENST00000412279	T;T;T;T;T	0.23754	1.89;1.89;1.89;1.89;1.89	4.87	4.87	0.63330	.	0.087964	0.85682	D	0.000000	T	0.42921	0.1224	L	0.45352	1.415	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.99	T	0.25082	-1.0142	10	0.46703	T	0.11	-20.8054	14.7721	0.69688	0.0:0.0:0.0:1.0	.	52;50	Q5T8D3-3;B7Z2R7	.;.	Q	47;52;17;50;59;17	ENSP00000379568:K52Q;ENSP00000365070:K17Q;ENSP00000365049:K50Q;ENSP00000401591:K59Q;ENSP00000393398:K17Q	ENSP00000365049:K50Q	K	-	1	0	ACBD5	27569281	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	4.285000	0.58989	1.945000	0.56424	0.383000	0.25322	AAG	.	.	.	none		0.617	ACBD5-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000047314.1	NM_145698		G	27529275	T	G	27529275	3	3	201	1	0	0	0	0	1	0	0	0	125	1792	62	5	1471	5	ACBD5	10	27529275	Missense_Mutation	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10		27529275	108005472	34	12181											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1264092	1264092	+	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	ctgggcaccacctggacccgCctatcacagaccaccacacc	10	4	7	20	1	1	1	1	0	0	1	1	2	1	2	7	2	0	1	7	2	1	1			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr11:1264092C>T	ENST00000529681.1	+	31	6040	c.5982C>T	c.(5980-5982)cgC>cgT	p.R1994R	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Silent_p.R1997R	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1994	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)		CCTGGACCCGCCTATCACAGA	0.637																																					p.R1994R		Atlas-SNP	.											.	MUC5B	473	.	0			c.C5982T						PASS	.						118	172	154					11																	1264092		2117	4210	6327	SO:0001819	synonymous_variant	727897	exon31			GACCCGCCTATCA	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.5982C>T	chr11.hg19:g.1264092C>T		785.0	0.0	.		1304.0	383.0	.	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	hg19	CCDS44515.2																																																																																			.	.	.	none		0.637	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		T	1264092	C	T	1264092	2	4	201	1	0	0	0	0	0	0	0	1	9986	726	26	2		2	MUC5B	11	1264092	Silent	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10		1264092	133742424	35	12182											
NAV2	89797	hgsc.bcm.edu	37	chr11	19890497	19890497	+	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	aacatagatgcctgcttgaaTttcctggcagctaagggaat	12	11	10	8	0	0	2	0	1	0	1	1	3	1	3	2	2	4	3	2	2	5	4			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr11:19890497T>A	ENST00000396087.3	+	4	564	c.465T>A	c.(463-465)aaT>aaA	p.N155K	NAV2_ENST00000360655.4_Missense_Mutation_p.N91K|NAV2_ENST00000396085.1_Missense_Mutation_p.N155K|NAV2_ENST00000527559.2_Missense_Mutation_p.N84K|NAV2_ENST00000534229.1_3'UTR|NAV2_ENST00000540292.1_Missense_Mutation_p.N86K|NAV2_ENST00000349880.4_Missense_Mutation_p.N155K	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	155	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				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						CCTGCTTGAATTTCCTGGCAG	0.438																																					p.N155K		Atlas-SNP	.											.	NAV2	255	.	0			c.T465A						PASS	.						70	71	70					11																	19890497		2199	4293	6492	SO:0001583	missense	89797	exon4			CTTGAATTTCCTG	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.465T>A	chr11.hg19:g.19890497T>A	ENSP00000379396:p.Asn155Lys	59.0	0.0	.		53.0	16.0	.	NM_145117	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Missense_Mutation	SNP	ENST00000396087.3	hg19	CCDS58126.1	.	.	.	.	.	.	.	.	.	.	T	16.47	3.133723	0.56828	.	.	ENSG00000166833	ENST00000360655;ENST00000396085;ENST00000349880;ENST00000396087;ENST00000527559;ENST00000540292	T;T;T;T;T;T	0.56444	0.46;0.46;0.46;0.46;0.46;0.46	5.87	5.87	0.94306	.	0.090463	0.47852	D	0.000201	T	0.36166	0.0957	N	0.05177	-0.1	0.80722	D	1	B;B	0.20052	0.002;0.041	B;B	0.34722	0.034;0.188	T	0.29610	-1.0006	9	.	.	.	.	13.7906	0.63138	0.0:0.0:0.0:1.0	.	155;91	Q8IVL1-3;Q8IVL1-4	.;.	K	91;155;155;155;84;86	ENSP00000353871:N91K;ENSP00000379394:N155K;ENSP00000309577:N155K;ENSP00000379396:N155K;ENSP00000435395:N84K;ENSP00000443489:N86K	.	N	+	3	2	NAV2	19847073	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.897000	0.39799	2.242000	0.73789	0.533000	0.62120	AAT	.	.	.	none		0.438	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		A	19890497	T	A	19890497	3	1	201	1	0	0	0	0	1	0	0	0	10191	1490	52	5	558	5	NAV2	11	19890497	Missense_Mutation	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10	18626405	19890497	115116019	36	12183											
GAS2	2620	hgsc.bcm.edu	37	chr11	22759307	22759307	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgctagagcttggccggattGcagccaggtaggtcaaacca	10	8	13	10	1	1	1	1	0	0	1	1	2	1	2	3	4	5	4	3	4	3	4			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr11:22759307G>A	ENST00000454584.2	+	5	771	c.466G>A	c.(466-468)Gca>Aca	p.A156T	GAS2_ENST00000433790.1_Missense_Mutation_p.A156T|GAS2_ENST00000278187.3_Missense_Mutation_p.A156T	NM_001143830.1	NP_001137302.1	O43903	GAS2_HUMAN	growth arrest-specific 2	156	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				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						TGGCCGGATTGCAGCCAGGTA	0.458																																					p.A156T		Atlas-SNP	.											.	GAS2	46	.	0			c.G466A						PASS	.						145	122	130					11																	22759307		2203	4300	6503	SO:0001583	missense	2620	exon5			CGGATTGCAGCCA	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.466G>A	chr11.hg19:g.22759307G>A	ENSP00000401145:p.Ala156Thr	143.0	0.0	.		210.0	60.0	.	NM_177553	B2R9C8|D3DQZ0|Q6ICV8|Q7Z3X8	Missense_Mutation	SNP	ENST00000454584.2	hg19	CCDS7858.1	.	.	.	.	.	.	.	.	.	.	G	34	5.368653	0.95900	.	.	ENSG00000148935	ENST00000528582;ENST00000454584;ENST00000278187;ENST00000532398;ENST00000433790	T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83	5.64	5.64	0.86602	Calponin homology domain (3);	0.051266	0.85682	D	0.000000	T	0.70605	0.3243	M	0.82923	2.615	0.52501	D	0.999956	P	0.52316	0.952	P	0.62885	0.908	T	0.74256	-0.3724	10	0.72032	D	0.01	-13.9779	17.5008	0.87731	0.0:0.0:1.0:0.0	.	156	O43903	GAS2_HUMAN	T	156	ENSP00000432584:A156T;ENSP00000401145:A156T;ENSP00000278187:A156T;ENSP00000435946:A156T;ENSP00000396708:A156T	ENSP00000278187:A156T	A	+	1	0	GAS2	22715883	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.950000	0.75977	2.664000	0.90586	0.650000	0.86243	GCA	.	.	.	none		0.458	GAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387717.1	NM_177553		A	22759307	G	A	22759307	3	1	201	1	0	0	0	0	1	0	0	0	6252	1319	46	2	480	2	GAS2	11	22759307	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	2868810	22759307	112247209	37	12184											
SLC43A3	29015	hgsc.bcm.edu	37	chr11	57182446	57182446	+	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	gccatgttggtcagcaaggaGttgagagtgccaatgaagag	12	8	15	6	0	1	3	1	2	0	2	1	5	1	4	2	2	2	3	2	2	3	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr11:57182446G>C	ENST00000395123.2	-	10	1207	c.903C>G	c.(901-903)aaC>aaG	p.N301K	SLC43A3_ENST00000529554.1_Missense_Mutation_p.N301K|SLC43A3_ENST00000352187.1_Missense_Mutation_p.N301K|SLC43A3_ENST00000528098.1_5'Flank|SLC43A3_ENST00000533524.1_Missense_Mutation_p.N314K|SLC43A3_ENST00000395124.1_Missense_Mutation_p.N301K	NM_001278201.1|NM_014096.2	NP_001265130.1|NP_054815.2	Q8NBI5	S43A3_HUMAN	solute carrier family 43, member 3	301					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	27						TCAGCAAGGAGTTGAGAGTGC	0.582																																					p.N301K		Atlas-SNP	.											.	SLC43A3	54	.	0			c.C903G						PASS	.						129	110	117					11																	57182446		2201	4296	6497	SO:0001583	missense	29015	exon10			CAAGGAGTTGAGA	AL157431	CCDS7956.1, CCDS60784.1	11q11	2013-05-22			ENSG00000134802	ENSG00000134802		"Solute carriers"	17466	protein-coding gene	gene with protein product	"likely ortholog of mouse embryonic epithelial gene 1"					7531438, 11704567	Standard	NM_017611		Approved	SEEEG-1, Eeg1, DKFZp762A227, FOAP-13, PRO1659	uc001nki.3	Q8NBI5	OTTHUMG00000167113	ENST00000395123.2:c.903C>G	chr11.hg19:g.57182446G>C	ENSP00000378555:p.Asn301Lys	55.0	0.0	.		69.0	21.0	.	NM_017611	B4DNR8|E7EQD2|Q9NSS4	Missense_Mutation	SNP	ENST00000395123.2	hg19	CCDS7956.1	.	.	.	.	.	.	.	.	.	.	G	17.62	3.434719	0.62955	.	.	ENSG00000134802	ENST00000395123;ENST00000395124;ENST00000352187;ENST00000529554;ENST00000533524;ENST00000530005	T;T;T;T;T;T	0.58652	0.37;0.37;0.37;0.37;0.37;0.32	5.05	4.13	0.48395	Major facilitator superfamily domain, general substrate transporter (1);	0.094270	0.64402	D	0.000001	T	0.58395	0.2119	M	0.71296	2.17	0.43924	D	0.99657	P;B;B	0.37548	0.599;0.186;0.343	B;B;B	0.44278	0.445;0.158;0.314	T	0.56019	-0.8048	10	0.06625	T	0.88	-17.6813	12.7477	0.57289	0.0:0.1658:0.8342:0.0	.	314;301;301	E7EQD2;Q8NBI5;A8K2X6	.;S43A3_HUMAN;.	K	301;301;301;301;314;301	ENSP00000378555:N301K;ENSP00000378556:N301K;ENSP00000337561:N301K;ENSP00000436254:N301K;ENSP00000434515:N314K;ENSP00000435893:N301K	ENSP00000337561:N301K	N	-	3	2	SLC43A3	56939022	1.000000	0.71417	0.996000	0.52242	0.418000	0.31294	6.596000	0.74113	1.117000	0.41842	0.563000	0.77884	AAC	.	.	.	none		0.582	SLC43A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393057.1	NM_017611		C	57182446	G	C	57182446	3	2	201	1	0	0	0	0	1	0	0	0	14647	1020	36	4	592	4	SLC43A3	11	57182446	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	34423139	57182446	77824070	38	12185											
TUT1	64852	hgsc.bcm.edu	37	chr11	62343357	62343370	+	Frame_Shift_Del	DEL	GTAAAGGGATCGGC	GTAAAGGGATCGGC	-																															ctgggtgaagggtgcaagggGtaaagggatcggcgtagcag																								rs149885942|rs371469091		TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	GTAAAGGGATCGGC	GTAAAGGGATCGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr11:62343357_62343370delGTAAAGGGATCGGC	ENST00000476907.1	-	9	2512_2525	c.1821_1834delGCCGATCCCTTTAC	c.(1819-1836)acgccgatccctttacccfs	p.PIPLP608fs	EEF1G_ENST00000378019.3_5'Flank|EEF1G_ENST00000532986.1_5'Flank|EEF1G_ENST00000329251.4_5'Flank|MIR3654_ENST00000496634.2_Intron|TUT1_ENST00000308436.7_Frame_Shift_Del_p.PIPLP646fs			Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6 snRNA-specific	608					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						GGTGCAAGGGGTAAAGGGATCGGCGTAGCAGAGA	0.636																																					p.646_650del		Atlas-Indel,Pindel	.											.	TUT1	122	.	0			c.1936_1949del						PASS	.																																			SO:0001589	frameshift_variant	64852	exon9			.	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.1821_1834delGCCGATCCCTTTAC	chr11.hg19:g.62343357_62343370delGTAAAGGGATCGGC	ENSP00000419607:p.Pro608fs	145.0	0.0	0		130.0	27.0	0.207692	NM_022830	A1A527|A8K995|Q2NL65|Q7L583|Q9H6H7	Frame_Shift_Del	DEL	ENST00000476907.1	hg19																																																																																				.	.	.	none		0.636	TUT1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000351319.2	NM_022830		-	62343370	GTAAAGGGATCGGC	-	62343357	7	5	201	1	0	1	0	1	0	0	0	0	16792	1261	44	0	794	0	TUT1	11	62343357	Frame_Shift_Del	DEL	GTAAAGGGATCGGC	TCGA-HE-A5NL-01A-11D-A26P-10	5160911	62343357	72663159	39	12186											
KBTBD3	143879	hgsc.bcm.edu	37	chr11	105925034	105925034	+	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	aacttgaagaaatgatgacaActggaagaacatttccacat	18	9	7	7	0	0	5	0	3	0	2	1	6	1	6	1	1	3	0	1	1	6	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr11:105925034A>T	ENST00000526793.1	-	3	541	c.382T>A	c.(382-384)Ttg>Atg	p.L128M	KBTBD3_ENST00000531837.1_Missense_Mutation_p.L128M|KBTBD3_ENST00000534815.1_Missense_Mutation_p.L49M	NM_152433.3	NP_689646.2	Q8NAB2	KBTB3_HUMAN	kelch repeat and BTB (POZ) domain containing 3	124										NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|prostate(1)	25		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.43e-05)|Epithelial(105;0.00418)|all cancers(92;0.0299)		AATGATGACAACTGGAAGAAC	0.308																																					p.L128M		Atlas-SNP	.											.	KBTBD3	59	.	0			c.T382A						PASS	.						82	88	86					11																	105925034		2201	4298	6499	SO:0001583	missense	143879	exon3			ATGACAACTGGAA	AK055247	CCDS8334.1	11q22.3	2013-01-08	2003-12-12	2003-12-17		ENSG00000182359		"BTB/POZ domain containing"	22934	protein-coding gene	gene with protein product			"BTB and kelch domain containing 3"	BKLHD3			Standard	NM_198439		Approved		uc001pjb.3	Q8NAB2		ENST00000526793.1:c.382T>A	chr11.hg19:g.105925034A>T	ENSP00000436262:p.Leu128Met	95.0	0.0	.		107.0	34.0	.	NM_152433	Q6N066|Q86X38|Q96NK5	Missense_Mutation	SNP	ENST00000526793.1	hg19	CCDS8334.1	.	.	.	.	.	.	.	.	.	.	A	7.067	0.567452	0.13560	.	.	ENSG00000182359	ENST00000534815;ENST00000526793;ENST00000531837	T;T;T	0.72835	-0.69;-0.69;-0.69	5.22	1.55	0.23275	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.271361	0.35936	N	0.002898	T	0.47451	0.1446	N	0.21545	0.675	0.32074	N	0.594092	B;B	0.23377	0.052;0.084	B;B	0.23018	0.043;0.029	T	0.33650	-0.9860	10	0.33940	T	0.23	.	1.1059	0.01693	0.4145:0.1523:0.286:0.1472	.	128;124	A8K1K0;Q8NAB2	.;KBTB3_HUMAN	M	49;128;128	ENSP00000431910:L49M;ENSP00000436262:L128M;ENSP00000432163:L128M	ENSP00000436262:L128M	L	-	1	2	KBTBD3	105430244	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	1.122000	0.31295	0.006000	0.14734	-0.421000	0.06004	TTG	.	.	.	none		0.308	KBTBD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388705.2	NM_152433		T	105925034	A	T	105925034	3	4	201	1	0	0	0	0	1	0	0	0	8001	40	2	5	1460	5	KBTBD3	11	105925034	Missense_Mutation	SNP	A	TCGA-HE-A5NL-01A-11D-A26P-10	43581677	105925034	29081482	40	12187											
ESAM	90952	hgsc.bcm.edu	37	chr11	124623587	124623587	+	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	tgggcaggcaccatcacaggCacagcacccatgcggctcaa	11	4	11	15	1	2	0	2	0	0	0	2	0	2	0	2	4	2	5	2	4	1	0			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr11:124623587C>T	ENST00000278927.5	-	7	1257	c.1128G>A	c.(1126-1128)gtG>gtA	p.V376V	ESAM_ENST00000442070.2_Intron|VSIG2_ENST00000403470.1_5'Flank|VSIG2_ENST00000326621.5_5'Flank	NM_138961.2	NP_620411.2	Q96AP7	ESAM_HUMAN	endothelial cell adhesion molecule	376					blood coagulation (GO:0007596)|homophilic cell adhesion (GO:0007156)|leukocyte migration (GO:0050900)|single organismal cell-cell adhesion (GO:0016337)	adherens junction (GO:0005912)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.022)		CCATCACAGGCACAGCACCCA	0.577																																					p.V376V		Atlas-SNP	.											.	ESAM	31	.	0			c.G1128A						PASS	.						56	58	57					11																	124623587		2201	4299	6500	SO:0001819	synonymous_variant	90952	exon7			CACAGGCACAGCA	AK075396	CCDS8453.1	11q24.2	2013-01-29			ENSG00000149564	ENSG00000149564		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17474	protein-coding gene	gene with protein product		614281				11279107, 11906820	Standard	NM_138961		Approved	W117m	uc001qav.4	Q96AP7	OTTHUMG00000151986	ENST00000278927.5:c.1128G>A	chr11.hg19:g.124623587C>T		55.0	0.0	.		84.0	7.0	.	NM_138961	B4DVN8|Q96T50	Silent	SNP	ENST00000278927.5	hg19	CCDS8453.1																																																																																			.	.	.	none		0.577	ESAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324686.1	NM_138961		T	124623587	C	T	124623587	2	4	201	1	0	0	0	0	0	0	0	1	5249	697	25	2		2	ESAM	11	124623587	Silent	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	18698553	124623587	10382929	41	12188											
NTM	50863	hgsc.bcm.edu	37	chr11	132180102	132180102	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagtcccctcagcagaatTccagtggtacaaggatgaca	13	7	10	11	0	1	2	1	1	0	1	3	3	3	3	3	2	3	3	3	2	3	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr11:132180102T>C	ENST00000374786.1	+	5	1237	c.758T>C	c.(757-759)tTc>tCc	p.F253S	NTM_ENST00000425719.2_Missense_Mutation_p.F253S|NTM_ENST00000374784.1_Missense_Mutation_p.F253S|NTM_ENST00000427481.2_Missense_Mutation_p.F244S|NTM_ENST00000474900.1_3'UTR|NTM_ENST00000374791.3_Missense_Mutation_p.F253S|NTM_ENST00000539799.1_Missense_Mutation_p.F253S	NM_001144058.1|NM_016522.2	NP_001137530.1|NP_057606.1	Q9P121	NTRI_HUMAN	neurotrimin	253	Ig-like C2-type 3.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(9)|lung(30)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	56						TCAGCAGAATTCCAGTGGTAC	0.517																																					p.F253S		Atlas-SNP	.											.	NTM	253	.	0			c.T758C						PASS	.						165	162	163					11																	132180102		2201	4297	6498	SO:0001583	missense	50863	exon5			CAGAATTCCAGTG	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.758T>C	chr11.hg19:g.132180102T>C	ENSP00000363918:p.Phe253Ser	229.0	0.0	.		307.0	91.0	.	NM_001144059	A0MTT2|Q6UXJ3|Q86VJ9	Missense_Mutation	SNP	ENST00000374786.1	hg19	CCDS8491.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	27.9|27.9	4.869133|4.869133	0.91587|0.91587	.|.	.|.	ENSG00000182667|ENSG00000182667	ENST00000374791;ENST00000539799;ENST00000427481;ENST00000374786;ENST00000425719;ENST00000374784|ENST00000457381	T;T;T;T;T;T|.	0.67523|.	-0.27;-0.27;-0.27;-0.27;-0.27;-0.27|.	6.07|6.07	6.07|6.07	0.98685|0.98685	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.78886|0.78886	0.4354|0.4354	M|M	0.82323|0.82323	2.585|2.585	0.80722|0.80722	D|D	1|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|.	0.998;0.999;0.996;0.999;0.997;0.997|.	T|T	0.80251|0.80251	-0.1460|-0.1460	10|5	0.13853|.	T|.	0.58|.	-27.0916|-27.0916	16.6288|16.6288	0.85011|0.85011	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	253;244;253;253;253;253|.	B7Z1Z5;B7Z1I4;Q9P121-4;Q9P121;Q9P121-3;Q9P121-2|.	.;.;.;NTRI_HUMAN;.;.|.	S|P	253;253;244;253;253;253|5	ENSP00000363923:F253S;ENSP00000437668:F253S;ENSP00000416320:F244S;ENSP00000363918:F253S;ENSP00000396722:F253S;ENSP00000363916:F253S|.	ENSP00000363916:F253S|.	F|S	+|+	2|1	0|0	NTM|NTM	131685312|131685312	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.864000|5.864000	0.69575|0.69575	2.326000|2.326000	0.78906|0.78906	0.533000|0.533000	0.62120|0.62120	TTC|TCC	.	.	.	none		0.517	NTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141937.1	NM_016522		C	132180102	T	C	132180102	3	2	201	1	0	0	0	0	1	0	0	0	10706	1783	62	3	862	3	NTM	11	132180102	Missense_Mutation	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10	7556515	132180102	2826414	42	12189											
EXOSC8	11340	hgsc.bcm.edu	37	chr13	37583387	37583387	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagttacaagacacaaagAagttaaaaaactgatggatg	20	7	9	5	0	0	3	0	1	0	2	0	4	0	4	0	1	3	3	0	1	7	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr13:37583387A>G	ENST00000389704.3	+	11	1047	c.782A>G	c.(781-783)gAa>gGa	p.E261G		NM_181503.2	NP_852480.1	Q96B26	EXOS8_HUMAN	exosome component 8	261					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)		AGACACAAAGAAGTTAAAAAA	0.338																																					p.E261G		Atlas-SNP	.											.	EXOSC8	16	.	0			c.A782G						PASS	.						57	56	56					13																	37583387		2203	4300	6503	SO:0001583	missense	11340	exon11			ACAAAGAAGTTAA	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.782A>G	chr13.hg19:g.37583387A>G	ENSP00000374354:p.Glu261Gly	146.0	0.0	.		138.0	29.0	.	NM_181503	O43480|Q5TBA5	Missense_Mutation	SNP	ENST00000389704.3	hg19	CCDS31958.1	.	.	.	.	.	.	.	.	.	.	A	19.62	3.862459	0.71949	.	.	ENSG00000120699	ENST00000389704;ENST00000379809;ENST00000481013	T	0.52754	0.65	5.92	5.92	0.95590	Exoribonuclease, phosphorolytic domain 2 (1);	0.000000	0.85682	D	0.000000	T	0.69088	0.3072	M	0.77820	2.39	0.80722	D	1	P;D	0.76494	0.944;0.999	P;D	0.69654	0.56;0.965	T	0.71052	-0.4704	10	0.49607	T	0.09	-29.8227	16.3593	0.83251	1.0:0.0:0.0:0.0	.	233;261	Q5JXM0;Q96B26	.;EXOS8_HUMAN	G	261;233;54	ENSP00000374354:E261G	ENSP00000369137:E233G	E	+	2	0	EXOSC8	36481387	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.372000	0.90127	2.267000	0.75376	0.383000	0.25322	GAA	.	.	.	none		0.338	EXOSC8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044535.2	NM_181503		G	37583387	A	G	37583387	3	3	201	1	0	0	0	0	1	0	0	0	5322	246	9	3	824	3	EXOSC8	13	37583387	Missense_Mutation	SNP	A	TCGA-HE-A5NL-01A-11D-A26P-10		37583387	77586491	43	12190											
KIAA0564	23078	hgsc.bcm.edu	37	chr13	42293875	42293875	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggagagaccttcagtcggaaAtttctgtattaaaaaaaaat	17	11	8	5	1	2	1	1	0	1	1	3	4	2	3	1	2	0	1	1	2	7	4			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr13:42293875A>G	ENST00000379310.3	-	26	3036	c.2968T>C	c.(2968-2970)Ttt>Ctt	p.F990L	VWA8_ENST00000281496.6_Missense_Mutation_p.F990L	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	990						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										TCAGTCGGAAATTTCTGTATT	0.294																																					p.F990L		Atlas-SNP	.											KIAA0564,rectum,carcinoma,+2,1	.	.	.	0			c.T2968C						PASS	.						68	64	65					13																	42293875		2203	4300	6503	SO:0001583	missense	23078	exon26			TCGGAAATTTCTG	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"KIAA0564"	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.2968T>C	chr13.hg19:g.42293875A>G	ENSP00000368612:p.Phe990Leu	62.0	0.0	.		62.0	30.0	.	NM_015058	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Missense_Mutation	SNP	ENST00000379310.3	hg19	CCDS41881.1	.	.	.	.	.	.	.	.	.	.	A	29.6	5.023069	0.93462	.	.	ENSG00000102763	ENST00000251030;ENST00000379310;ENST00000281496	T;T	0.26810	1.71;1.71	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.52240	0.1722	M	0.87456	2.885	0.80722	D	1	D	0.59357	0.985	P	0.57720	0.826	T	0.61133	-0.7124	10	0.62326	D	0.03	.	15.7306	0.77800	1.0:0.0:0.0:0.0	.	990	A3KMH1	K0564_HUMAN	L	894;990;990	ENSP00000368612:F990L;ENSP00000281496:F990L	ENSP00000251030:F894L	F	-	1	0	KIAA0564	41191875	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.248000	0.95456	2.175000	0.68902	0.477000	0.44152	TTT	.	.	.	none		0.294	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058		G	42293875	A	G	42293875	3	3	201	1	0	0	0	0	1	0	0	0	8192	101	4	3	2833	3	KIAA0564	13	42293875	Missense_Mutation	SNP	A	TCGA-HE-A5NL-01A-11D-A26P-10	4710488	42293875	72876003	44	12191											
TIMM9	26520	hgsc.bcm.edu	37	chr14	58878635	58878635	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aataccttacctgttttatcTgatcagattctggtatttgt	9	19	6	7	0	3	2	1	1	2	1	3	2	3	2	2	1	2	2	2	1	5	7			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr14:58878635T>C	ENST00000395159.2	-	4	554	c.29A>G	c.(28-30)cAg>cGg	p.Q10R	TIMM9_ENST00000556007.2_Missense_Mutation_p.Q10R|TIMM9_ENST00000555404.1_Missense_Mutation_p.Q10R|TIMM9_ENST00000216463.4_Intron|TIMM9_ENST00000555593.1_Missense_Mutation_p.Q10R|RP11-517O13.1_ENST00000556734.1_RNA|TIMM9_ENST00000555061.1_Missense_Mutation_p.Q10R	NM_012460.2	NP_036592.1	Q9Y5J7	TIM9_HUMAN	translocase of inner mitochondrial membrane 9 homolog (yeast)	10					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein transport (GO:0072321)|protein import into mitochondrial inner membrane (GO:0045039)|protein targeting to mitochondrion (GO:0006626)|sensory perception of sound (GO:0007605)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial intermembrane space protein transporter complex (GO:0042719)|mitochondrion (GO:0005739)	chaperone binding (GO:0051087)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			kidney(2)|skin(1)	3						CTGTTTTATCTGATCAGATTC	0.353																																					p.Q10R		Atlas-SNP	.											.	TIMM9	7	.	0			c.A29G						PASS	.						113	110	111					14																	58878635		2203	4300	6503	SO:0001583	missense	26520	exon4			TTTATCTGATCAG	AF150100	CCDS9735.1	14q22.3-q24	2008-07-04	2001-11-28		ENSG00000100575	ENSG00000100575			11819	protein-coding gene	gene with protein product		607384	"translocase of inner mitochondrial membrane 9 (yeast) homolog"			10552927, 14726512	Standard	NM_012460		Approved	TIM9A	uc001xds.3	Q9Y5J7	OTTHUMG00000140322	ENST00000395159.2:c.29A>G	chr14.hg19:g.58878635T>C	ENSP00000378588:p.Gln10Arg	121.0	0.0	.		75.0	35.0	.	NM_012460	B2R584	Missense_Mutation	SNP	ENST00000395159.2	hg19	CCDS9735.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.480758	0.84747	.	.	ENSG00000100575	ENST00000395159;ENST00000555593;ENST00000556007;ENST00000555061;ENST00000555404;ENST00000555097;ENST00000553450	T;T;T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28;-0.28;-0.28	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.81302	0.4794	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	D	0.84141	0.0417	9	0.87932	D	0	-16.1458	14.6598	0.68861	0.0:0.0:0.0:1.0	.	10	Q9Y5J7	TIM9_HUMAN	R	10	ENSP00000378588:Q10R;ENSP00000451006:Q10R;ENSP00000452091:Q10R;ENSP00000450638:Q10R;ENSP00000451198:Q10R;ENSP00000450624:Q10R	ENSP00000216463:Q10R	Q	-	2	0	TIMM9	57948388	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.606000	0.82863	2.130000	0.65690	0.528000	0.53228	CAG	.	.	.	none		0.353	TIMM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276936.2			C	58878635	T	C	58878635	3	2	201	1	0	0	0	0	1	0	0	0	15928	1580	55	3	252	3	TIMM9	14	58878635	Missense_Mutation	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10		58878635	48470905	45	12192											
WDR72	256764	hgsc.bcm.edu	37	chr15	53815462	53815462	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctgtcaggcatgtcctccAcgtcttggaagtttgccgag	7	12	11	11	2	3	0	1	0	2	0	5	2	5	1	3	2	1	2	3	2	1	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr15:53815462A>G	ENST00000396328.1	-	19	3445	c.3206T>C	c.(3205-3207)gTg>gCg	p.V1069A	WDR72_ENST00000559418.1_Missense_Mutation_p.V1079A|WDR72_ENST00000557913.1_Missense_Mutation_p.V1066A|WDR72_ENST00000360509.5_Missense_Mutation_p.V1069A|WDR72_ENST00000567224.1_5'UTR	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	1069										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)		CATGTCCTCCACGTCTTGGAA	0.443																																					p.V1069A		Atlas-SNP	.											.	WDR72	177	.	0			c.T3206C						PASS	.						190	181	184					15																	53815462		2194	4293	6487	SO:0001583	missense	256764	exon19			TCCTCCACGTCTT	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.3206T>C	chr15.hg19:g.53815462A>G	ENSP00000379619:p.Val1069Ala	57.0	0.0	.		70.0	14.0	.	NM_182758	Q7Z3I3|Q8N8X2	Missense_Mutation	SNP	ENST00000396328.1	hg19	CCDS10151.1	.	.	.	.	.	.	.	.	.	.	A	0.124	-1.121308	0.01785	.	.	ENSG00000166415	ENST00000396328;ENST00000360509	T;T	0.33216	1.42;1.42	6.17	1.97	0.26223	.	1.192530	0.05923	N	0.633818	T	0.09949	0.0244	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31308	-0.9948	10	0.10636	T	0.68	.	1.0072	0.01489	0.2223:0.1286:0.3848:0.2643	.	1069	Q3MJ13	WDR72_HUMAN	A	1069	ENSP00000379619:V1069A;ENSP00000353699:V1069A	ENSP00000353699:V1069A	V	-	2	0	WDR72	51602754	0.018000	0.18449	0.000000	0.03702	0.436000	0.31835	0.638000	0.24674	0.137000	0.18759	-0.177000	0.13119	GTG	.	.	.	none		0.443	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758		G	53815462	A	G	53815462	3	3	201	1	0	0	0	0	1	0	0	0	17334	159	6	3	110	3	WDR72	15	53815462	Missense_Mutation	SNP	A	TCGA-HE-A5NL-01A-11D-A26P-10		53815462	48715930	46	12193											
TLN2	83660	hgsc.bcm.edu	37	chr15	63097959	63097959	+	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	caacctgagccggaaagccgTgtcagatatgttgacggctt	10	9	12	10	3	1	3	1	2	0	1	1	4	1	4	3	2	3	2	3	2	3	3			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr15:63097959T>A	ENST00000561311.1	+	50	6868	c.6638T>A	c.(6637-6639)gTg>gAg	p.V2213E	TLN2_ENST00000306829.6_Missense_Mutation_p.V2213E			Q9Y4G6	TLN2_HUMAN	talin 2	2213					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						CGGAAAGCCGTGTCAGATATG	0.512																																					p.V2213E		Atlas-SNP	.											.	TLN2	253	.	0			c.T6638A						PASS	.						77	68	71					15																	63097959		2203	4300	6503	SO:0001583	missense	83660	exon48			AAGCCGTGTCAGA	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.6638T>A	chr15.hg19:g.63097959T>A	ENSP00000453508:p.Val2213Glu	154.0	0.0	.		196.0	56.0	.	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	hg19	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	T	32	5.119444	0.94385	.	.	ENSG00000171914	ENST00000306829	T	0.77098	-1.07	5.83	5.83	0.93111	.	0.055071	0.64402	D	0.000001	T	0.79724	0.4495	M	0.62723	1.935	0.80722	D	1	P	0.40398	0.716	B	0.43478	0.421	T	0.82133	-0.0608	10	0.87932	D	0	-21.9765	16.2009	0.82078	0.0:0.0:0.0:1.0	.	2213	Q9Y4G6	TLN2_HUMAN	E	2213	ENSP00000303476:V2213E	ENSP00000303476:V2213E	V	+	2	0	TLN2	60885012	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.997000	0.88414	2.235000	0.73313	0.533000	0.62120	GTG	.	.	.	none		0.512	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			A	63097959	T	A	63097959	3	1	201	1	0	0	0	0	1	0	0	0	15960	1696	59	5	6828	5	TLN2	15	63097959	Missense_Mutation	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10	9282497	63097959	39433433	47	12194											
MEGF11	84465	hgsc.bcm.edu	37	chr15	66190397	66190397	+	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	ctggatatagctggagttatGaccgcaaccttcttggacca	10	11	10	10	1	1	1	0	1	1	0	1	4	1	4	3	3	2	3	3	3	4	5			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr15:66190397G>A	ENST00000409699.2	-	23	3182	c.3010C>T	c.(3010-3012)Cat>Tat	p.H1004Y	MEGF11_ENST00000422354.1_Missense_Mutation_p.H1004Y|MEGF11_ENST00000478721.1_5'Flank|MEGF11_ENST00000360698.4_3'UTR|MEGF11_ENST00000395625.2_Missense_Mutation_p.H929Y|MEGF11_ENST00000288745.3_Missense_Mutation_p.H929Y			A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11	1004					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						CTGGAGTTATGACCGCAACCT	0.463																																					p.H1004Y		Atlas-SNP	.											.	MEGF11	70	.	0			c.C3010T						PASS	.						124	107	113					15																	66190397		2201	4299	6500	SO:0001583	missense	84465	exon23			AGTTATGACCGCA	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.3010C>T	chr15.hg19:g.66190397G>A	ENSP00000386908:p.His1004Tyr	142.0	0.0	.		139.0	34.0	.	NM_032445	Q17R86|Q6UXS5|Q8ND91|Q96KG6	Missense_Mutation	SNP	ENST00000409699.2	hg19	CCDS10213.2	.	.	.	.	.	.	.	.	.	.	G	0.007	-1.943794	0.00479	.	.	ENSG00000157890	ENST00000409699;ENST00000288745;ENST00000422354;ENST00000395625	D;D;D;D	0.86694	-2.16;-2.05;-2.16;-2.05	5.03	4.11	0.48088	.	0.766593	0.10702	U	0.643968	T	0.77191	0.4094	N	0.22421	0.69	0.18873	N	0.999982	B;B	0.22746	0.015;0.074	B;B	0.24269	0.008;0.052	T	0.56619	-0.7949	10	0.02654	T	1	.	12.3211	0.54985	0.0833:0.0:0.9167:0.0	.	1004;929	A6BM72;A6BM72-2	MEG11_HUMAN;.	Y	1004;929;1004;929	ENSP00000386908:H1004Y;ENSP00000288745:H929Y;ENSP00000414475:H1004Y;ENSP00000378987:H929Y	ENSP00000288745:H929Y	H	-	1	0	MEGF11	63977451	0.017000	0.18338	0.046000	0.18839	0.418000	0.31294	1.820000	0.39032	1.300000	0.44818	0.655000	0.94253	CAT	.	.	.	none		0.463	MEGF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329307.2	NM_032445		A	66190397	G	A	66190397	3	1	201	1	0	0	0	0	1	0	0	0	9468	1290	45	2	128	2	MEGF11	15	66190397	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	3092438	66190397	36340995	48	12195											
IL21R	50615	hgsc.bcm.edu	37	chr16	27459983	27459983	+	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	gccaagaggctgcagctcacGgagctacaagaaccagcaga	14	3	12	12	1	1	3	1	0	0	3	1	4	1	4	2	2	6	5	2	2	4	1			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr16:27459983G>T	ENST00000337929.3	+	9	1469	c.996G>T	c.(994-996)acG>acT	p.T332T	IL21R_ENST00000564089.1_Silent_p.T332T|IL21R_ENST00000395754.4_Silent_p.T332T|IL21R-AS1_ENST00000563191.1_RNA|IL21R_ENST00000564583.1_3'UTR|IL21R_ENST00000395755.1_Silent_p.T332T	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	332					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						TGCAGCTCACGGAGCTACAAG	0.662			T	BCL6	NHL																																p.T354T		Atlas-SNP	.		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	IL21R_ENST00000395754,NS,carcinoma,0,1	IL21R	95	.	0			c.G1062T						PASS	.						27	29	28					16																	27459983		2196	4297	6493	SO:0001819	synonymous_variant	50615	exon10			GCTCACGGAGCTA	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.996G>T	chr16.hg19:g.27459983G>T		94.0	1.0	.		259.0	65.0	.	NM_181079	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Silent	SNP	ENST00000337929.3	hg19	CCDS10630.1																																																																																			.	.	.	none		0.662	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078		T	27459983	G	T	27459983	2	4	201	1	0	0	0	0	0	0	0	1	7678	1103	39	4		4	IL21R	16	27459983	Silent	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10		27459983	62894770	49	12196											
POLR2C	5432	hgsc.bcm.edu	37	chr16	57503976	57503976	+	Silent	SNP	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	aagtggaaccctactgcaggGgtggcttttgaatacgatcc	10	10	12	9	1	0	1	0	1	0	0	1	3	1	2	2	4	4	2	2	4	5	4			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr16:57503976G>A	ENST00000219252.5	+	7	881	c.543G>A	c.(541-543)ggG>ggA	p.G181G	POLR2C_ENST00000564651.1_3'UTR	NM_032940.2	NP_116558.1	P19387	RPB3_HUMAN	polymerase (RNA) II (DNA directed) polypeptide C, 33kDa	181					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)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, core complex (GO:0005665)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(2)|upper_aerodigestive_tract(1)	10						CTACTGCAGGGGTGGCTTTTG	0.537																																					p.G181G		Atlas-SNP	.											.	POLR2C	24	.	0			c.G543A						PASS	.						67	63	64					16																	57503976		2198	4300	6498	SO:0001819	synonymous_variant	5432	exon7			TGCAGGGGTGGCT		CCDS10782.1	16q13-q21	2013-01-21	2002-08-29		ENSG00000102978	ENSG00000102978		"RNA polymerase subunits"	9189	protein-coding gene	gene with protein product	"RNA polymerase II subunit 3"	180663	"polymerase (RNA) II (DNA directed) polypeptide C (33kD)"			8034326	Standard	NM_032940		Approved	RPB3	uc002elt.1	P19387	OTTHUMG00000133464	ENST00000219252.5:c.543G>A	chr16.hg19:g.57503976G>A		185.0	0.0	.		337.0	182.0	.	NM_032940	O15161	Silent	SNP	ENST00000219252.5	hg19	CCDS10782.1																																																																																			.	.	.	none		0.537	POLR2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257340.3	NM_032940		A	57503976	G	A	57503976	2	1	201	1	0	0	0	0	0	0	0	1	12223	1219	43	2		2	POLR2C	16	57503976	Silent	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	30043993	57503976	32850777	50	12197											
KLHDC4	54758	hgsc.bcm.edu	37	chr16	87760467	87760467	+	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	ggccccgtccctgacggggaCagcttgctccatgtgaaggt	6	8	14	13	2	0	2	0	2	0	0	2	3	2	3	4	4	2	2	4	4	1	1	rs548850415		TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr16:87760467C>T	ENST00000270583.5	-	7	721	c.663G>A	c.(661-663)ctG>ctA	p.L221L	KLHDC4_ENST00000566349.1_5'UTR|KLHDC4_ENST00000353170.5_Silent_p.L164L|KLHDC4_ENST00000347925.5_Silent_p.L190L	NM_017566.3	NP_060036.2	Q8TBB5	KLDC4_HUMAN	kelch domain containing 4	221										breast(2)|endometrium(3)|lung(10)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	21				BRCA - Breast invasive adenocarcinoma(80;0.0283)		CTGACGGGGACAGCTTGCTCC	0.557																																					p.L221L		Atlas-SNP	.											.	KLHDC4	45	.	0			c.G663A						PASS	.						91	90	90					16																	87760467		2198	4300	6498	SO:0001819	synonymous_variant	54758	exon7			CGGGGACAGCTTG	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.663G>A	chr16.hg19:g.87760467C>T		102.0	0.0	.		269.0	142.0	.	NM_017566	D3DUN3|D3DUN4|D3DUN5|Q96F29|Q9BVN3	Silent	SNP	ENST00000270583.5	hg19	CCDS10963.1																																																																																			.	.	.	none		0.557	KLHDC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269109.2	NM_017566		T	87760467	C	T	87760467	2	4	201	1	0	0	0	0	0	0	0	1	8365	465	17	2		2	KLHDC4	16	87760467	Silent	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	30256491	87760467	2594286	51	12198											
WDR81	124997	hgsc.bcm.edu	37	chr17	1630178	1630178	+	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	gccagttttagaggccactcCctgtgaggctagctggacca	8	9	12	12	0	0	2	0	1	0	1	1	3	1	3	4	3	1	3	4	3	2	3			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr17:1630178C>G	ENST00000409644.1	+	1	1925	c.1925C>G	c.(1924-1926)cCc>cGc	p.P642R	RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000437219.2_Intron|WDR81_ENST00000419248.1_Intron|WDR81_ENST00000446363.1_Intron|WDR81_ENST00000309182.5_Intron	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	642					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)		GAGGCCACTCCCTGTGAGGCT	0.587																																					p.P642R		Atlas-SNP	.											.	WDR81	180	.	0			c.C1925G						PASS	.						7	9	9					17																	1630178		690	1579	2269	SO:0001583	missense	124997	exon1			CCACTCCCTGTGA	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.1925C>G	chr17.hg19:g.1630178C>G	ENSP00000386609:p.Pro642Arg	61.0	0.0	.		99.0	42.0	.	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Missense_Mutation	SNP	ENST00000409644.1	hg19	CCDS54062.1	.	.	.	.	.	.	.	.	.	.	C	4.713	0.132661	0.09032	.	.	ENSG00000167716	ENST00000409644	T	0.56275	0.47	5.59	4.62	0.57501	.	.	.	.	.	T	0.55433	0.1920	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52646	-0.8548	6	0.33940	T	0.23	.	9.7471	0.40453	0.0:0.8428:0.0:0.1572	.	.	.	.	R	642	ENSP00000386609:P642R	ENSP00000386609:P642R	P	+	2	0	WDR81	1576928	0.940000	0.31905	0.835000	0.33067	0.224000	0.24922	3.300000	0.51834	1.349000	0.45751	0.462000	0.41574	CCC	.	.	.	none		0.587	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348		G	1630178	C	G	1630178	3	3	201	1	0	0	0	0	1	0	0	0	17342	623	22	4	1989	4	WDR81	17	1630178	Missense_Mutation	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10		1630178	79565032	52	12199											
NUP88	4927	hgsc.bcm.edu	37	chr17	5312151	5312152	+	Frame_Shift_Ins	INS	-	-	A																															ctttgccgttttgtccaaatINSagagtctttgggactgctgc																										TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr17:5312151_5312152insA	ENST00000573584.1	-	5	1267_1268	c.758_759insT	c.(757-759)ctafs	p.L253fs		NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	253					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						TTTGTCCAAATAGAGTCTTTGG	0.436																																					p.L253fs		Atlas-Indel,Pindel	.											.	NUP88	47	.	0			c.759_760insT						PASS	.																																			SO:0001589	frameshift_variant	4927	exon5			.	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.759dupT	chr17.hg19:g.5312152_5312152dupA	ENSP00000458954:p.Leu253fs	162.0	0.0	0		254.0	61.0	0.240157	NM_002532	D3DTM2|Q9BWE5	Frame_Shift_Ins	INS	ENST00000573584.1	hg19	CCDS11070.1																																																																																			.	.	.	none		0.436	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532		A	5312152	-	A	5312151	7	5	201	1	0	1	1	0	0	0	0	0	10778	1393	49	0	1518	0	NUP88	17	5312151	Frame_Shift_Ins	INS	-	TCGA-HE-A5NL-01A-11D-A26P-10	3681973	5312151	75883059	53	12200											
C17orf104	284071	hgsc.bcm.edu	37	chr17	42744034	42744034	+	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	taactgtcacaatattcagaCaaatgatacagctaagacaa	19	9	5	8	0	2	3	2	1	0	2	2	3	2	3	0	0	3	1	0	0	7	5			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr17:42744034C>T	ENST00000409122.2	+	5	897	c.755C>T	c.(754-756)aCa>aTa	p.T252I	C17orf104_ENST00000409464.1_Missense_Mutation_p.T86I|C17orf104_ENST00000359945.3_Missense_Mutation_p.T252I	NM_001145080.2	NP_001138552.2	A2RUB1	CQ104_HUMAN	chromosome 17 open reading frame 104	252										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						AATATTCAGACAAATGATACA	0.353																																					p.T252I		Atlas-SNP	.											.	C17orf104	75	.	0			c.C755T						PASS	.						72	63	66					17																	42744034		2203	4300	6503	SO:0001583	missense	284071	exon5			TTCAGACAAATGA		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.755C>T	chr17.hg19:g.42744034C>T	ENSP00000386452:p.Thr252Ile	112.0	0.0	.		190.0	12.0	.	NM_001145080	B4DXJ2|B5MD93|B9EGQ6|C4AM97|Q4G0Y1|Q8IVZ7|Q8NA45	Missense_Mutation	SNP	ENST00000409122.2	hg19	CCDS45703.2	.	.	.	.	.	.	.	.	.	.	C	10.68	1.418212	0.25552	.	.	ENSG00000180336	ENST00000359945;ENST00000409122;ENST00000432494;ENST00000456912;ENST00000409464	T;T;T;T;T	0.35048	1.33;1.33;1.63;1.63;1.34	5.54	4.58	0.56647	.	0.518815	0.20253	N	0.096034	T	0.24547	0.0595	N	0.14661	0.345	0.24157	N	0.995676	B;B;B	0.10296	0.003;0.003;0.003	B;B;B	0.14023	0.01;0.006;0.006	T	0.15350	-1.0440	10	0.39692	T	0.17	-10.3947	14.6777	0.68993	0.0:0.9298:0.0:0.0702	.	252;252;86	A2RUB1-5;A2RUB1;A2RUB1-1	.;CQ104_HUMAN;.	I	252;252;86;86;86	ENSP00000353028:T252I;ENSP00000386452:T252I;ENSP00000399809:T86I;ENSP00000397957:T86I;ENSP00000386586:T86I	ENSP00000353028:T252I	T	+	2	0	C17orf104	40099560	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.331000	0.52075	1.468000	0.48064	0.591000	0.81541	ACA	.	.	.	none		0.353	C17orf104-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329171.2	NM_001145080		T	42744034	C	T	42744034	3	4	201	1	0	0	0	0	1	0	0	0	1853	478	17	2	773	2	C17orf104	17	42744034	Missense_Mutation	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	37431883	42744034	38451176	54	12201											
PPM1E	22843	hgsc.bcm.edu	37	chr17	56833454	56833454	+	Silent	SNP	G	G	A																															tgcggcggcggcgagccggaGccggaacccgaacccgaacc																								rs77856248		TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	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	.	0			c.G96A						PASS	.						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	chr17.hg19:g.56833454G>A		17.0	0.0	.		39.0	9.0	.	NM_014906	Q8N8J9|Q96DB8	Silent	SNP	ENST00000308249.2	hg19	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	201	1	0	0	0	0	0	0	0	1	12348	962	34	2		2	PPM1E	17	56833454	Silent	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	14089420	56833454	24361756	55	12202	116	2									
PPM1E	22843	hgsc.bcm.edu	37	chr17	56833457	56833457	+	Silent	SNP	G	G	C																															ggcggcggcgagccggagccGgaacccgaacccgaacccga																								rs3834568|rs201186780|rs74256772	byFrequency	TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	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	.	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	chr17.hg19:g.56833457G>C		17.0	0.0	.		44.0	16.0	.	NM_014906	Q8N8J9|Q96DB8	Silent	SNP	ENST00000308249.2	hg19	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	201	1	0	0	0	0	0	0	0	1	12348	1103	39	4		4	PPM1E	17	56833457	Silent	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	3	56833457	24361753	56	12203	116	2									
RNF152	220441	hgsc.bcm.edu	37	chr18	59483369	59483369	+	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	gtctccgggcagcagcgcacGctccttggagatgggcaggg	6	6	17	12	3	1	1	0	0	1	1	3	2	2	1	2	4	2	5	2	4	0	1			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr18:59483369G>C	ENST00000312828.3	-	2	1427	c.328C>G	c.(328-330)Cgt>Ggt	p.R110G		NM_173557.2	NP_775828.1	Q8N8N0	RN152_HUMAN	ring finger protein 152	110					apoptotic process (GO:0006915)|protein K48-linked ubiquitination (GO:0070936)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(10)|skin(1)	17		Colorectal(73;0.186)				AGCAGCGCACGCTCCTTGGAG	0.627																																					p.R110G		Atlas-SNP	.											.	RNF152	37	.	0			c.C328G						PASS	.						68	74	72					18																	59483369		2203	4300	6503	SO:0001583	missense	220441	exon2			GCGCACGCTCCTT	AK096495	CCDS11978.1	18q21.33	2013-01-09			ENSG00000176641	ENSG00000176641		"RING-type (C3HC4) zinc fingers"	26811	protein-coding gene	gene with protein product							Standard	XM_005266650		Approved	FLJ39176	uc002lih.1	Q8N8N0	OTTHUMG00000132774	ENST00000312828.3:c.328C>G	chr18.hg19:g.59483369G>C	ENSP00000316628:p.Arg110Gly	28.0	0.0	.		78.0	26.0	.	NM_173557	B3KV99|Q52LA4	Missense_Mutation	SNP	ENST00000312828.3	hg19	CCDS11978.1	.	.	.	.	.	.	.	.	.	.	G	5.884	0.347185	0.11126	.	.	ENSG00000176641	ENST00000312828	D	0.83335	-1.71	4.97	4.97	0.65823	.	0.139197	0.44902	D	0.000405	T	0.69424	0.3109	N	0.17082	0.46	0.45621	D	0.998557	B	0.06786	0.001	B	0.06405	0.002	T	0.63501	-0.6623	10	0.18710	T	0.47	-3.5749	13.096	0.59192	0.0:0.0:0.7221:0.2779	.	110	Q8N8N0	RN152_HUMAN	G	110	ENSP00000316628:R110G	ENSP00000316628:R110G	R	-	1	0	RNF152	57634349	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	3.456000	0.53000	2.600000	0.87896	0.655000	0.94253	CGT	.	.	.	none		0.627	RNF152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256180.1	NM_173557		C	59483369	G	C	59483369	3	2	201	1	0	0	0	0	1	0	0	0	13466	1087	38	4	287	4	RNF152	18	59483369	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10		59483369	18593879	57	12204											
ATP13A1	57130	hgsc.bcm.edu	37	chr19	19762514	19762515	+	Frame_Shift_Ins	INS	-	-	TGCAGGA																															cacctttctcggagggaggcINStgcaggatcagcgtgtgggc																										TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr19:19762514_19762515insTGCAGGA	ENST00000357324.6	-	17	2344_2345	c.2318_2319insTCCTGCA	c.(2317-2319)cagfs	p.Q773fs	ATP13A1_ENST00000291503.5_Frame_Shift_Ins_p.Q655fs|ATP13A1_ENST00000496082.1_5'Flank	NM_020410.2	NP_065143.2	Q9HD20	AT131_HUMAN	ATPase type 13A1	773						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						CGGAGGGAGGCTGCAGGATCAG	0.609																																					p.Q773fs	Esophageal Squamous(142;920 1789 9047 14684 24777)	Atlas-Indel,Pindel	.											ATP13A1,NS,carcinoma,0,1	ATP13A1	82	.	0			c.2319_2320insTCCTGCA						PASS	.																																			SO:0001589	frameshift_variant	57130	exon17			.	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.2312_2318dupTCCTGCA	chr19.hg19:g.19762515_19762521dupTGCAGGA	ENSP00000349877:p.Gln773fs	169.0	0.0	0		241.0	36.0	0.149378	NM_020410	B3KPJ2|B3KTA7|Q6NT90|Q6ZMG7|Q9H6C6	Frame_Shift_Ins	INS	ENST00000357324.6	hg19	CCDS32970.2																																																																																			.	.	.	none		0.609	ATP13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329005.1	NM_020410		TGCAGGA	19762515	-	TGCAGGA	19762514	7	5	201	1	0	1	1	0	0	0	0	0	1123	796	28	0	1335	0	ATP13A1	19	19762514	Frame_Shift_Ins	INS	-	TCGA-HE-A5NL-01A-11D-A26P-10		19762514	39366469	58	12205											
PSG11	5680	hgsc.bcm.edu	37	chr19	43519496	43519496	+	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	atagtaagaggtgactgaagGgaaaattctggggaggtctg	13	9	16	3	0	2	3	0	2	2	1	2	5	2	5	0	5	0	1	0	5	5	3			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr19:43519496G>T	ENST00000401740.1	-	4	839	c.736C>A	c.(736-738)Cct>Act	p.P246T	PSG11_ENST00000403486.1_Missense_Mutation_p.P124T|PSG11_ENST00000320078.7_Missense_Mutation_p.P246T|PSG11_ENST00000306322.7_Missense_Mutation_p.P124T|PSG11_ENST00000595312.1_5'Flank			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11	244	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)				GTGACTGAAGGGAAAATTCTG	0.468																																					p.P246T		Atlas-SNP	.											.	PSG11	57	.	0			c.C736A						PASS	.						112	125	120					19																	43519496		2199	4298	6497	SO:0001583	missense	5680	exon4			CTGAAGGGAAAAT	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.736C>A	chr19.hg19:g.43519496G>T	ENSP00000384995:p.Pro246Thr	102.0	0.0	.		102.0	46.0	.	NM_002785	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000401740.1	hg19	CCDS12614.2	.	.	.	.	.	.	.	.	.	.	g	7.213	0.595792	0.13875	.	.	ENSG00000243130	ENST00000320078;ENST00000403486;ENST00000306322;ENST00000401740	T;T;T;T	0.74842	-0.88;-0.88;-0.88;-0.88	0.961	-0.805	0.10879	Immunoglobulin-like (1);	.	.	.	.	T	0.80154	0.4571	M	0.84683	2.71	0.09310	N	1	B;B	0.28636	0.085;0.218	B;P	0.45037	0.078;0.467	T	0.75110	-0.3433	9	0.87932	D	0	.	4.7032	0.12837	0.2746:0.0:0.7254:0.0	.	124;246	Q9UQ72-2;Q9UQ72	.;PSG11_HUMAN	T	246;124;124;246	ENSP00000319140:P246T;ENSP00000385427:P124T;ENSP00000304913:P124T;ENSP00000384995:P246T	ENSP00000304913:P124T	P	-	1	0	PSG11	48211336	0.001000	0.12720	0.001000	0.08648	0.002000	0.02628	0.167000	0.16602	-1.109000	0.02996	-1.109000	0.02080	CCT	.	.	.	none		0.468	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	NM_002785		T	43519496	G	T	43519496	3	4	201	1	0	0	0	0	1	0	0	0	12664	1232	43	4	279	4	PSG11	19	43519496	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	23756982	43519496	15609487	59	12206											
ZNF415	55786	hgsc.bcm.edu	37	chr19	53612760	53612760	+	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	tttgatggtagaagaaattaTttggggtggtgaaactgagg	12	13	15	1	0	0	5	0	3	0	2	0	5	0	5	0	5	1	1	0	5	5	4			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr19:53612760T>A	ENST00000500065.4	-	4	871	c.538A>T	c.(538-540)Ata>Tta	p.I180L	ZNF415_ENST00000243643.4_Missense_Mutation_p.I180L|ZNF415_ENST00000455735.2_Missense_Mutation_p.I228L|ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000601493.1_5'UTR|ZNF415_ENST00000448501.1_Missense_Mutation_p.I228L|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000440291.1_Missense_Mutation_p.I167L|ZNF415_ENST00000595193.1_3'UTR|ZNF415_ENST00000421033.1_Missense_Mutation_p.I192L	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	228					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		GAAGAAATTATTTGGGGTGGT	0.383																																					p.I180L		Atlas-SNP	.											.	ZNF415	68	.	0			c.A538T						PASS	.						103	100	101					19																	53612760		2203	4300	6503	SO:0001583	missense	55786	exon4			AAATTATTTGGGG	AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"Zinc fingers, C2H2-type", "-"	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.538A>T	chr19.hg19:g.53612760T>A	ENSP00000439435:p.Ile180Leu	87.0	0.0	.		80.0	29.0	.	NM_018355	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Missense_Mutation	SNP	ENST00000500065.4	hg19	CCDS54313.1	.	.	.	.	.	.	.	.	.	.	T	11.10	1.538587	0.27475	.	.	ENSG00000170954	ENST00000243643;ENST00000500065;ENST00000448501;ENST00000421033;ENST00000455735;ENST00000440291	T;T;T;T;T;T	0.07908	3.15;3.15;3.15;3.15;3.15;3.15	2.74	-0.82	0.10826	.	.	.	.	.	T	0.07007	0.0178	L	0.31578	0.945	0.09310	N	1	B;B;B;B;B;B	0.29085	0.033;0.041;0.038;0.11;0.033;0.232	B;B;B;B;B;B	0.34138	0.015;0.028;0.017;0.033;0.02;0.176	T	0.39440	-0.9614	9	0.59425	D	0.04	.	6.2583	0.20885	0.0:0.3858:0.0:0.6142	.	180;228;228;180;167;192	F5H287;B3KTG1;Q09FC8;Q09FC8-5;Q09FC8-4;Q09FC8-2	.;.;ZN415_HUMAN;.;.;.	L	180;180;228;192;228;167	ENSP00000243643:I180L;ENSP00000439435:I180L;ENSP00000396492:I228L;ENSP00000395055:I192L;ENSP00000388787:I228L;ENSP00000414601:I167L	ENSP00000243643:I180L	I	-	1	0	ZNF415	58304572	0.000000	0.05858	0.000000	0.03702	0.086000	0.17979	-0.921000	0.04008	-0.410000	0.07542	0.260000	0.18958	ATA	.	.	.	none		0.383	ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464043.1	NM_018355		A	53612760	T	A	53612760	3	1	201	1	0	0	0	0	1	0	0	0	17904	1493	52	5	1133	5	ZNF415	19	53612760	Missense_Mutation	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10	10093264	53612760	5516223	60	12207											
SEL1L2	80343	hgsc.bcm.edu	37	chr20	13868446	13868446	+	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	actttcttgtaataacttagGgcaacttcacaattctgtag	12	15	6	8	0	3	0	1	0	2	0	3	0	3	0	0	1	2	3	0	1	6	8			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr20:13868446G>T	ENST00000284951.5	-	8	788	c.714C>A	c.(712-714)gcC>gcA	p.A238A	SEL1L2_ENST00000378072.5_Silent_p.A238A|SEL1L2_ENST00000486903.1_5'UTR			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	238						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						AATAACTTAGGGCAACTTCAC	0.299																																					p.A238A		Atlas-SNP	.											.	SEL1L2	103	.	0			c.C714A						PASS	.						129	123	125					20																	13868446		1817	4072	5889	SO:0001819	synonymous_variant	80343	exon8			ACTTAGGGCAACT	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.714C>A	chr20.hg19:g.13868446G>T		98.0	0.0	.		83.0	21.0	.	NM_001271539	B4DXX5	Silent	SNP	ENST00000284951.5	hg19																																																																																				.	.	.	none		0.299	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229		T	13868446	G	T	13868446	2	4	201	1	0	0	0	0	0	0	0	1	14024	1219	43	4		4	SEL1L2	20	13868446	Silent	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10		13868446	49157074	61	12208											
TRPC4AP	26133	hgsc.bcm.edu	37	chr20	33623074	33623074	+	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	tttcgagtcgccagtttgcaAagccgctcaacaaagccagg	11	8	10	12	3	1	0	1	0	0	0	3	1	1	0	3	1	4	3	3	1	3	2			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr20:33623074A>C	ENST00000252015.2	-	8	992	c.903T>G	c.(901-903)ctT>ctG	p.L301L	TRPC4AP_ENST00000432634.2_Silent_p.L262L|TRPC4AP_ENST00000451813.2_Silent_p.L301L|TRPC4AP_ENST00000539834.1_5'UTR			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein	301	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)			CCAGTTTGCAAAGCCGCTCAA	0.507																																					p.L301L		Atlas-SNP	.											.	TRPC4AP	64	.	0			c.T903G						PASS	.						87	78	81					20																	33623074		2203	4300	6503	SO:0001819	synonymous_variant	26133	exon8			TTTGCAAAGCCGC	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.903T>G	chr20.hg19:g.33623074A>C		115.0	0.0	.		90.0	26.0	.	NM_199368	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Silent	SNP	ENST00000252015.2	hg19	CCDS13246.1																																																																																			.	.	.	none		0.507	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638		C	33623074	A	C	33623074	2	2	201	1	0	0	0	0	0	0	0	1	16593	1	1	5		5	TRPC4AP	20	33623074	Silent	SNP	A	TCGA-HE-A5NL-01A-11D-A26P-10	19754628	33623074	29402446	62	12209			1	26		2	2	26	N	C_A	5.329876e-05
TRPC4AP	26133	hgsc.bcm.edu	37	chr20	33623099	33623099	+	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	gctcaacaaagccaggaatgCtgagaagggccgctgccagg	12	4	14	11	1	1	1	1	1	0	1	1	3	1	2	3	3	4	3	3	3	4	0			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr20:33623099C>A	ENST00000252015.2	-	8	967	c.878G>T	c.(877-879)aGc>aTc	p.S293I	TRPC4AP_ENST00000432634.2_Missense_Mutation_p.S254I|TRPC4AP_ENST00000451813.2_Missense_Mutation_p.S293I|TRPC4AP_ENST00000539834.1_5'Flank			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein	293	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)			GCCAGGAATGCTGAGAAGGGC	0.498																																					p.S293I		Atlas-SNP	.											.	TRPC4AP	64	.	0			c.G878T						PASS	.						61	57	58					20																	33623099		2203	4300	6503	SO:0001583	missense	26133	exon8			GGAATGCTGAGAA	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.878G>T	chr20.hg19:g.33623099C>A	ENSP00000252015:p.Ser293Ile	93.0	0.0	.		75.0	20.0	.	NM_199368	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Missense_Mutation	SNP	ENST00000252015.2	hg19	CCDS13246.1	.	.	.	.	.	.	.	.	.	.	C	15.76	2.929049	0.52759	.	.	ENSG00000100991	ENST00000252015;ENST00000451813;ENST00000432634;ENST00000541994	T;T;T	0.27720	1.65;1.65;1.65	5.49	4.45	0.53987	.	0.085031	0.85682	D	0.000000	T	0.13329	0.0323	N	0.14661	0.345	0.80722	D	1	B;P;P	0.38335	0.396;0.475;0.627	B;B;B	0.31614	0.044;0.133;0.133	T	0.03524	-1.1028	10	0.54805	T	0.06	.	3.5606	0.07881	0.0:0.6443:0.0:0.3557	.	254;293;293	B4E0Q1;E1P5Q0;Q8TEL6	.;.;TP4AP_HUMAN	I	293;293;254;278	ENSP00000252015:S293I;ENSP00000400614:S293I;ENSP00000400497:S254I	ENSP00000252015:S293I	S	-	2	0	TRPC4AP	33086760	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	3.786000	0.55431	2.587000	0.87381	0.557000	0.71058	AGC	.	.	.	none		0.498	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638		A	33623099	C	A	33623099	3	1	201	1	0	0	0	0	1	0	0	0	16593	797	28	4	1563	4	TRPC4AP	20	33623099	Missense_Mutation	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	25	33623099	29402421	63	12210			1	26		2	2	26	N	C_A	5.329876e-05
PCK1	5105	hgsc.bcm.edu	37	chr20	56140806	56140806	+	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	caagtcaatgccgacctcccCtgtgaaatcgagagagagat	13	7	10	11	2	1	3	1	1	0	2	3	7	2	3	4	0	1	0	4	0	3	0			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr20:56140806C>A	ENST00000319441.4	+	10	1979	c.1815C>A	c.(1813-1815)ccC>ccA	p.P605P	PCK1_ENST00000543666.1_Silent_p.P288P	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	605					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			CCGACCTCCCCTGTGAAATCG	0.463																																					p.P605P		Atlas-SNP	.											.	PCK1	95	.	0			c.C1815A						PASS	.						54	50	51					20																	56140806		2203	4300	6503	SO:0001819	synonymous_variant	5105	exon10			CCTCCCCTGTGAA		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.1815C>A	chr20.hg19:g.56140806C>A		114.0	0.0	.		151.0	50.0	.	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Silent	SNP	ENST00000319441.4	hg19	CCDS13460.1																																																																																			.	.	.	none		0.463	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2			A	56140806	C	A	56140806	2	1	201	1	0	0	0	0	0	0	0	1	11588	668	24	4		4	PCK1	20	56140806	Silent	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	22517707	56140806	6884714	64	12211											
ZGPAT	84619	hgsc.bcm.edu	37	chr20	62366740	62366740	+	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	aagctgcaaggtcaggctccTggggccctagaagccggggc	8	5	16	12	1	1	1	1	0	0	1	2	1	2	1	3	6	3	3	3	6	4	1			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr20:62366740T>A	ENST00000328969.5	+	6	1408	c.1281T>A	c.(1279-1281)ccT>ccA	p.P427P	ZGPAT_ENST00000355969.6_Silent_p.P407P|ZGPAT_ENST00000369967.3_Silent_p.P407P|ZGPAT_ENST00000448100.2_Silent_p.P407P|RP4-583P15.15_ENST00000490623.2_Missense_Mutation_p.L313Q|ZGPAT_ENST00000357119.4_Silent_p.P398P|LIME1_ENST00000309546.3_5'Flank|RP4-583P15.14_ENST00000467211.1_5'Flank	NM_032527.4	NP_115916.3	Q8N5A5	ZGPAT_HUMAN	zinc finger, CCCH-type with G patch domain	427					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)					GTCAGGCTCCTGGGGCCCTAG	0.672																																					p.P427P		Atlas-SNP	.											.	ZGPAT	57	.	0			c.T1281A						PASS	.						20	23	22					20																	62366740		2183	4294	6477	SO:0001819	synonymous_variant	84619	exon6			GGCTCCTGGGGCC	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.1281T>A	chr20.hg19:g.62366740T>A		58.0	0.0	.		61.0	20.0	.	NM_032527	E1P5K1|Q4VXN9|Q5JWI9|Q5JWJ0|Q8NC55|Q8WUV4|Q96JI0|Q96JU4|Q9H401	Silent	SNP	ENST00000328969.5	hg19	CCDS13534.1																																																																																			.	.	.	none		0.672	ZGPAT-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080214.1	NM_181484		A	62366740	T	A	62366740	2	1	201	1	0	0	0	0	0	0	0	1	17686	1567	55	5		5	ZGPAT	20	62366740	Silent	SNP	T	TCGA-HE-A5NL-01A-11D-A26P-10	6225934	62366740	658780	65	12212											
NEFH	4744	hgsc.bcm.edu	37	chr22	29885400	29885417	+	In_Frame_Del	DEL	GAGGCAAAGTCACCGGCT	GAGGCAAAGTCACCGGCT	-																															ccaagtccccagcaaaggaaGaggcaaagtcaccggctgag																								rs6006165|rs1061372	byFrequency	TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	GAGGCAAAGTCACCGGCT	GAGGCAAAGTCACCGGCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr22:29885400_29885417delGAGGCAAAGTCACCGGCT	ENST00000310624.6	+	4	1804_1821	c.1771_1788delGAGGCAAAGTCACCGGCT	c.(1771-1788)gaggcaaagtcaccggctdel	p.EAKSPA591del		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	591	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AGCAAAGGAAGAGGCAAAGTCACCGGCTGAGGCCAAGT	0.569																																					p.590_596del		Atlas-INDEL	.											.	NEFH	178	.	0			c.1770_1787del						PASS	.																																			SO:0001651	inframe_deletion	4744	exon4			.		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1771_1788delGAGGCAAAGTCACCGGCT	chr22.hg19:g.29885400_29885417delGAGGCAAAGTCACCGGCT	ENSP00000311997:p.Glu591_Ala596del	182.0	0.0	0		264.0	22.0	0.0833333	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Del	DEL	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.	.	none		0.569	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		-	29885417	GAGGCAAAGTCACCGGCT	-	29885400	7	5	201	1	0	1	0	1	0	0	0	0	10321	943	33	0	1785	0	NEFH	22	29885400	In_Frame_Del	DEL	GAGGCAAAGTCACCGGCT	TCGA-HE-A5NL-01A-11D-A26P-10		29885400	21419166	66	12213											
LGALS2	3957	hgsc.bcm.edu	37	chr22	37966307	37966307	+	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	aagaggacatgttgaacccgCcccttacgctcaggtagctc	10	8	10	13	2	1	2	1	1	0	1	2	3	1	3	3	2	3	4	3	2	4	3			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr22:37966307C>T	ENST00000215886.4	-	4	536	c.362G>A	c.(361-363)gGc>gAc	p.G121D		NM_006498.2	NP_006489.1	P05162	LEG2_HUMAN	lectin, galactoside-binding, soluble, 2	121	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.						carbohydrate binding (GO:0030246)|galactoside binding (GO:0016936)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|stomach(1)	11	Melanoma(58;0.0574)					GTTGAACCCGCCCCTTACGCT	0.498																																					p.G121D	GBM(193;1840 2185 13711 20676 24505)	Atlas-SNP	.											.	LGALS2	16	.	0			c.G362A						PASS	.						90	94	93					22																	37966307		2203	4300	6503	SO:0001583	missense	3957	exon4			AACCCGCCCCTTA		CCDS13950.1	22q13.1	2011-08-04	2007-02-01		ENSG00000100079	ENSG00000100079		"Lectins, galactoside-binding"	6562	protein-coding gene	gene with protein product	"galectin 2"	150571				1988031, 15356130	Standard	NM_006498		Approved	HL14	uc003ata.3	P05162	OTTHUMG00000150590	ENST00000215886.4:c.362G>A	chr22.hg19:g.37966307C>T	ENSP00000215886:p.Gly121Asp	138.0	0.0	.		174.0	10.0	.	NM_006498	Q6FGY4	Missense_Mutation	SNP	ENST00000215886.4	hg19	CCDS13950.1	.	.	.	.	.	.	.	.	.	.	C	15.41	2.824838	0.50739	.	.	ENSG00000100079	ENST00000215886	T	0.68181	-0.31	5.65	1.17	0.20885	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.292084	0.42821	D	0.000648	T	0.64983	0.2648	M	0.82056	2.57	0.09310	N	0.999994	B	0.30870	0.298	B	0.30943	0.122	T	0.59958	-0.7356	10	0.62326	D	0.03	0.0582	10.2071	0.43120	0.0:0.7317:0.0:0.2683	.	121	P05162	LEG2_HUMAN	D	121	ENSP00000215886:G121D	ENSP00000215886:G121D	G	-	2	0	LGALS2	36296253	0.010000	0.17322	0.000000	0.03702	0.000000	0.00434	1.026000	0.30103	0.056000	0.16144	-0.291000	0.09656	GGC	.	.	.	none		0.498	LGALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318991.1	NM_006498		T	37966307	C	T	37966307	3	4	201	1	0	0	0	0	1	0	0	0	8749	739	26	2	40	2	LGALS2	22	37966307	Missense_Mutation	SNP	C	TCGA-HE-A5NL-01A-11D-A26P-10	8080907	37966307	13338259	67	12214											
PNPLA3	80339	hgsc.bcm.edu	37	chr22	44333050	44333050	+	Missense_Mutation	SNP	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	ccccggagtcggctgccttgGctgtgaggctggagggagat	5	8	18	10	2	0	2	0	1	0	1	1	5	0	4	3	6	1	3	3	6	0	1			TCGA-HE-A5NL-01A-11D-A26P-10	TCGA-HE-A5NL-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a441697c-4ca0-4eab-9b01-b9cb50223ce2	49cd5084-c2b5-47d4-b921-2f2316afe33a	g.chr22:44333050G>A	ENST00000216180.3	+	6	1050	c.877G>A	c.(877-879)Gct>Act	p.A293T	PNPLA3_ENST00000423180.2_Missense_Mutation_p.A289T	NM_025225.2	NP_079501.2	Q9NST1	PLPL3_HUMAN	patatin-like phospholipase domain containing 3	293					acylglycerol acyl-chain remodeling (GO:0036155)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	diolein transacylation activity (GO:0051265)|mono-olein transacylation activity (GO:0051264)|phospholipase A2 activity (GO:0004623)|triglyceride lipase activity (GO:0004806)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|prostate(1)|skin(1)|stomach(2)	19		Ovarian(80;0.024)|all_neural(38;0.0416)				GGCTGCCTTGGCTGTGAGGCT	0.617																																					p.A293T		Atlas-SNP	.											.	PNPLA3	53	.	0			c.G877A						PASS	.						105	84	91					22																	44333050		2203	4300	6503	SO:0001583	missense	80339	exon6			GCCTTGGCTGTGA		CCDS14054.1	22q13.31	2014-03-14	2006-05-26	2006-05-26	ENSG00000100344	ENSG00000100344	3.1.1.3	"Patatin-like phospholipase domain containing"	18590	protein-coding gene	gene with protein product		609567	"chromosome 22 open reading frame 20", "adiponutrin"	C22orf20, ADPN		16799181, 19029121	Standard	NM_025225		Approved	dJ796I17.1, FLJ22012, adiponutrin, iPLA2epsilon	uc003bei.1	Q9NST1	OTTHUMG00000150555	ENST00000216180.3:c.877G>A	chr22.hg19:g.44333050G>A	ENSP00000216180:p.Ala293Thr	106.0	0.0	.		133.0	44.0	.	NM_025225	B0QYI0|B2RCL3|B3KW00|Q6P1A1|Q96CB4	Missense_Mutation	SNP	ENST00000216180.3	hg19	CCDS14054.1	.	.	.	.	.	.	.	.	.	.	G	8.597	0.885868	0.17540	.	.	ENSG00000100344	ENST00000216180;ENST00000423180	T;T	0.28895	1.59;1.59	3.7	-1.2	0.09554	.	.	.	.	.	T	0.13670	0.0331	N	0.22421	0.69	0.09310	N	1	B	0.30326	0.276	B	0.25614	0.062	T	0.25363	-1.0134	9	0.18276	T	0.48	-0.1582	1.9895	0.03443	0.1065:0.1711:0.3719:0.3504	.	293	Q9NST1	PLPL3_HUMAN	T	293;289	ENSP00000216180:A293T;ENSP00000397987:A289T	ENSP00000216180:A293T	A	+	1	0	PNPLA3	42664383	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.317000	0.08060	-0.232000	0.09811	0.462000	0.41574	GCT	.	.	.	none		0.617	PNPLA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318891.1	NM_025225		A	44333050	G	A	44333050	3	1	201	1	0	0	0	0	1	0	0	0	12173	1203	42	2	899	2	PNPLA3	22	44333050	Missense_Mutation	SNP	G	TCGA-HE-A5NL-01A-11D-A26P-10	6366743	44333050	6971516	68	12215											
BAI2	576	hgsc.bcm.edu	37	chr1	32205741	32205741	+	Missense_Mutation	SNP	T	T	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	tcgtcccacttctccttgttTtccgcatccaccatgaagct	6	14	5	16	2	1	1	0	1	1	0	6	1	4	1	5	0	1	3	5	0	1	4			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr1:32205741T>G	ENST00000373658.3	-	13	2369	c.2028A>C	c.(2026-2028)gaA>gaC	p.E676D	BAI2_ENST00000398556.3_Missense_Mutation_p.E624D|BAI2_ENST00000527361.1_Missense_Mutation_p.E676D|BAI2_ENST00000257070.4_Missense_Mutation_p.E676D|BAI2_ENST00000398542.1_Missense_Mutation_p.E609D|BAI2_ENST00000398538.1_Missense_Mutation_p.E664D|BAI2_ENST00000373655.2_Missense_Mutation_p.E676D|BAI2_ENST00000398547.1_Missense_Mutation_p.E609D|BAI2_ENST00000440175.2_Missense_Mutation_p.E318D	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	676					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)		TCTCCTTGTTTTCCGCATCCA	0.612																																					p.E676D		Atlas-SNP	.											.	BAI2	128	.	0			c.A2028C						PASS	.						125	110	115					1																	32205741		2203	4300	6503	SO:0001583	missense	576	exon13			CTTGTTTTCCGCA	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.2028A>C	chr1.hg19:g.32205741T>G	ENSP00000362762:p.Glu676Asp	214.0	0.0	.		148.0	50.0	.	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Missense_Mutation	SNP	ENST00000373658.3	hg19	CCDS346.2	.	.	.	.	.	.	.	.	.	.	T	18.09	3.546810	0.65198	.	.	ENSG00000121753	ENST00000398556;ENST00000398547;ENST00000373658;ENST00000373655;ENST00000398542;ENST00000257070;ENST00000527361;ENST00000440175;ENST00000398538;ENST00000420125	T;T;T;T;T;T;T;T;T;T	0.10288	2.89;2.89;2.89;2.89;2.89;2.89;2.89;2.89;2.89;2.89	4.62	1.63	0.23807	Domain of unknown function DUF3497 (1);	0.192067	0.26106	N	0.026319	T	0.16385	0.0394	L	0.54323	1.7	0.32584	N	0.528032	P;D;B;P;P;P	0.52996	0.804;0.957;0.307;0.815;0.804;0.815	P;P;P;P;P;P	0.53313	0.526;0.723;0.534;0.631;0.526;0.631	T	0.12268	-1.0554	10	0.46703	T	0.11	.	7.784	0.29080	0.0:0.6153:0.0:0.3847	.	676;664;318;609;676;676	O60241-4;O60241-3;B4DKC3;A2A3C1;O60241-2;O60241	.;.;.;.;.;BAI2_HUMAN	D	624;609;676;676;609;676;676;318;664;614	ENSP00000381564:E624D;ENSP00000381555:E609D;ENSP00000362762:E676D;ENSP00000362759:E676D;ENSP00000381550:E609D;ENSP00000257070:E676D;ENSP00000435397:E676D;ENSP00000391071:E318D;ENSP00000381548:E664D;ENSP00000410921:E614D	ENSP00000257070:E676D	E	-	3	2	BAI2	31978328	1.000000	0.71417	0.975000	0.42487	0.765000	0.43378	0.796000	0.26986	0.124000	0.18369	-0.474000	0.04947	GAA	.	.	.	none		0.612	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703		G	32205741	T	G	32205741	3	3	202	1	0	0	0	0	1	0	0	0	1299	1838	64	5	2813	5	BAI2	1	32205741	Missense_Mutation	SNP	T	TCGA-IA-A40U-01A-11D-A25F-10		32205741	217044880	1	12216											
PMF1	632	hgsc.bcm.edu	37	chr1	156209392	156209392	+	5'Flank	SNP	A	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	gtgctgagggagcctgagtgAggagaccgccagccccagaa	10	4	16	11	1	0	5	0	3	0	2	0	7	0	6	5	2	3	1	5	2	1	0			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr1:156209392A>C	ENST00000368272.4	+	0	0				PMF1_ENST00000368273.4_Nonstop_Mutation_p.*208C|PMF1_ENST00000368277.3_Nonstop_Mutation_p.*206C|PMF1-BGLAP_ENST00000320139.5_Intron|PMF1_ENST00000565805.1_Intron|PMF1-BGLAP_ENST00000490491.1_Intron|PMF1_ENST00000567140.1_Intron|PMF1-BGLAP_ENST00000368276.4_Intron|PMF1_ENST00000368279.3_3'UTR	NM_199173.4	NP_954642.1	P02818	OSTCN_HUMAN	bone gamma-carboxyglutamate (gla) protein						bone development (GO:0060348)|bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|cell aging (GO:0007569)|cellular response to growth factor stimulus (GO:0071363)|cellular response to vitamin D (GO:0071305)|odontogenesis (GO:0042476)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|regulation of bone mineralization (GO:0030500)|regulation of bone resorption (GO:0045124)|regulation of osteoclast differentiation (GO:0045670)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to gravity (GO:0009629)|response to hydroxyisoflavone (GO:0033594)|response to mechanical stimulus (GO:0009612)|response to testosterone (GO:0033574)|response to vitamin D (GO:0033280)|response to vitamin K (GO:0032571)|response to zinc ion (GO:0010043)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|perikaryon (GO:0043204)|rough endoplasmic reticulum (GO:0005791)	calcium ion binding (GO:0005509)|hydroxyapatite binding (GO:0046848)|structural constituent of bone (GO:0008147)|structural molecule activity (GO:0005198)			large_intestine(3)|lung(1)|urinary_tract(1)	5	Hepatocellular(266;0.158)				Gallium nitrate(DB05260)|Menadione(DB00170)|Phylloquinone(DB01022)	AGCCTGAGTGAGGAGACCGCC	0.572																																					p.X208C		Atlas-SNP	.											.	PMF1	12	.	0			c.A624C						PASS	.						81	85	84					1																	156209392		2203	4300	6503	SO:0001631	upstream_gene_variant	11243	exon5			TGAGTGAGGAGAC	X04143	CCDS1134.1	1q22	2014-05-13	2008-08-01		ENSG00000242252	ENSG00000242252			1043	protein-coding gene	gene with protein product	"osteocalcin"	112260				2785029, 2394711	Standard	NM_199173		Approved	OCN	uc001fnt.3	P02818	OTTHUMG00000014819		chr1.hg19:g.156209392A>C	Exception_encountered	169.0	0.0	.		121.0	42.0	.	NM_001199654	Q5TCK6	Missense_Mutation	SNP	ENST00000368272.4	hg19	CCDS1134.1	.	.	.	.	.	.	.	.	.	.	a	16.96	3.267332	0.59540	.	.	ENSG00000160783	ENST00000368273;ENST00000368277	.	.	.	5.07	3.95	0.45737	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.4393	0.27174	0.9034:0.0:0.0966:0.0	.	.	.	.	C	208;206	.	.	X	+	3	0	PMF1	154476016	0.998000	0.40836	0.883000	0.34634	0.969000	0.65631	2.898000	0.48672	1.073000	0.40885	0.529000	0.55759	TGA	.	.	.	none		0.572	BGLAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040867.2	NM_199173		C	156209392	A	C	156209392	1	2	202	0	1	0	0	0	0	0	0	0	12140	317	11	5		5	PMF1	1	156209392	5'Flank	SNP	A	TCGA-IA-A40U-01A-11D-A25F-10	124003651	156209392	93041229	2	12217											
OR2T3	343173	hgsc.bcm.edu	37	chr1	248637175	248637175	+	Missense_Mutation	SNP	A	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	catgagcttccccttttgccAgtctaggaaaatcctgagtt	9	13	8	11	0	1	2	0	2	1	0	3	3	3	3	4	1	2	2	4	1	3	5			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr1:248637175A>C	ENST00000359594.2	+	1	549	c.524A>C	c.(523-525)cAg>cCg	p.Q175P		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	175						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)			CCCTTTTGCCAGTCTAGGAAA	0.527																																					p.Q175P		Atlas-SNP	.											.	OR2T3	79	.	0			c.A524C						PASS	.						42	39	40					1																	248637175		2162	4256	6418	SO:0001583	missense	343173	exon1			TTTGCCAGTCTAG		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.524A>C	chr1.hg19:g.248637175A>C	ENSP00000352604:p.Gln175Pro	467.0	1.0	.		430.0	119.0	.	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	hg19	CCDS31117.1	.	.	.	.	.	.	.	.	.	.	a	10.12	1.262159	0.23051	.	.	ENSG00000196539	ENST00000359594	T	0.37235	1.21	2.37	-2.34	0.06704	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.27629	0.0679	N	0.20807	0.61	0.09310	N	1	B	0.29909	0.261	B	0.40602	0.334	T	0.45396	-0.9264	9	0.66056	D	0.02	.	8.3181	0.32113	0.2131:0.0:0.7869:0.0	.	175	Q8NH03	OR2T3_HUMAN	P	175	ENSP00000352604:Q175P	ENSP00000352604:Q175P	Q	+	2	0	OR2T3	246703798	0.000000	0.05858	0.000000	0.03702	0.062000	0.15995	-0.077000	0.11394	-1.019000	0.03358	0.156000	0.16432	CAG	.	.	.	none		0.527	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495		C	248637175	A	C	248637175	3	2	202	1	0	0	0	0	1	0	0	0	11030	188	7	5	526	5	OR2T3	1	248637175	Missense_Mutation	SNP	A	TCGA-IA-A40U-01A-11D-A25F-10	92427783	248637175	613446	3	12218											
ERBB4	2066	hgsc.bcm.edu	37	chr2	212248449	212248449	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgccacaataggccggatcCgcccattctgtttataaaaa	12	10	7	12	2	1	0	0	0	1	0	2	1	2	1	4	2	1	1	4	2	6	5			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr2:212248449C>T	ENST00000342788.4	-	28	4128	c.3818G>A	c.(3817-3819)cGg>cAg	p.R1273Q	ERBB4_ENST00000436443.1_Missense_Mutation_p.R1257Q|ERBB4_ENST00000402597.1_Missense_Mutation_p.R1263Q	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	1273					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)	AGGCCGGATCCGCCCATTCTG	0.532										TSP Lung(8;0.080)																											p.R1273Q		Atlas-SNP	.											.	ERBB4	480	.	0			c.G3818A						PASS	.						89	91	91					2																	212248449		2203	4300	6503	SO:0001583	missense	2066	exon28			CGGATCCGCCCAT	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.3818G>A	chr2.hg19:g.212248449C>T	ENSP00000342235:p.Arg1273Gln	178.0	1.0	.		197.0	111.0	.	NM_005235	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	hg19	CCDS2394.1	.	.	.	.	.	.	.	.	.	.	C	17.20	3.328293	0.60743	.	.	ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597	T;T;T	0.75367	-0.92;-0.93;-0.92	5.41	5.41	0.78517	.	0.000000	0.64402	D	0.000001	T	0.72518	0.3470	L	0.44542	1.39	0.52501	D	0.999958	P;P;P;P	0.50710	0.938;0.873;0.938;0.897	P;P;P;B	0.44860	0.462;0.462;0.462;0.273	T	0.73151	-0.4073	10	0.42905	T	0.14	.	19.39	0.94576	0.0:1.0:0.0:0.0	.	1247;1263;1257;1273	Q15303-4;Q15303-2;Q15303-3;Q15303	.;.;.;ERBB4_HUMAN	Q	1273;1257;1263	ENSP00000342235:R1273Q;ENSP00000403204:R1257Q;ENSP00000385565:R1263Q	ENSP00000342235:R1273Q	R	-	2	0	ERBB4	211956694	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.584000	0.67490	2.812000	0.96745	0.557000	0.71058	CGG	.	.	.	none		0.532	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		T	212248449	C	T	212248449	3	4	202	1	0	0	0	0	1	0	0	0	5211	652	23	1	112	1	ERBB4	2	212248449	Missense_Mutation	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10		212248449	30950924	4	12219											
CCDC66	285331	hgsc.bcm.edu	37	chr3	56627039	56627039	+	Missense_Mutation	SNP	A	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	cctttcagtgctgtgaaacaAgaactgcaaagaaaatggat	16	9	9	7	0	1	3	1	1	0	2	1	4	1	4	1	1	4	2	1	1	6	1			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr3:56627039A>C	ENST00000394672.3	+	8	1048	c.978A>C	c.(976-978)caA>caC	p.Q326H	CCDC66_ENST00000436465.2_Missense_Mutation_p.Q326H|CCDC66_ENST00000326595.7_Missense_Mutation_p.Q292H	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	326					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)		CTGTGAAACAAGAACTGCAAA	0.333																																					p.Q326H		Atlas-SNP	.											.	CCDC66	145	.	0			c.A978C						PASS	.						100	108	106					3																	56627039		2203	4300	6503	SO:0001583	missense	285331	exon8			GAAACAAGAACTG	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.978A>C	chr3.hg19:g.56627039A>C	ENSP00000378167:p.Gln326His	123.0	0.0	.		69.0	30.0	.	NM_001141947	B3KWL8|Q4VC34|Q8N949	Missense_Mutation	SNP	ENST00000394672.3	hg19	CCDS46852.1	.	.	.	.	.	.	.	.	.	.	A	17.71	3.456082	0.63401	.	.	ENSG00000180376	ENST00000394672;ENST00000326595;ENST00000436465	T;T;T	0.23950	1.88;1.88;1.88	5.6	0.516	0.17019	.	0.359209	0.26542	N	0.023798	T	0.19005	0.0456	L	0.55103	1.725	0.80722	D	1	B	0.17038	0.02	B	0.19391	0.025	T	0.06661	-1.0814	10	0.38643	T	0.18	-3.3314	2.9391	0.05824	0.4431:0.0:0.258:0.2989	.	326	A2RUB6	CCD66_HUMAN	H	326;292;326	ENSP00000378167:Q326H;ENSP00000326050:Q292H;ENSP00000404320:Q326H	ENSP00000326050:Q292H	Q	+	3	2	CCDC66	56602079	0.989000	0.36119	0.920000	0.36463	0.969000	0.65631	0.062000	0.14389	-0.134000	0.11516	0.533000	0.62120	CAA	.	.	.	none		0.333	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506		C	56627039	A	C	56627039	3	2	202	1	0	0	0	0	1	0	0	0	2840	69	3	5	1008	5	CCDC66	3	56627039	Missense_Mutation	SNP	A	TCGA-IA-A40U-01A-11D-A25F-10		56627039	141395391	5	12220											
TRIM42	287015	hgsc.bcm.edu	37	chr3	140401754	140401754	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgtgcaacgactgcctcaaGgccttccactcggatgtggc	7	9	11	14	2	1	0	1	0	0	0	3	2	2	1	3	3	3	1	3	3	2	1			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr3:140401754G>A	ENST00000286349.3	+	2	983	c.792G>A	c.(790-792)aaG>aaA	p.K264K		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	264						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						ACTGCCTCAAGGCCTTCCACT	0.617																																					p.K264K		Atlas-SNP	.											.	TRIM42	143	.	0			c.G792A						PASS	.						115	102	106					3																	140401754		2203	4300	6503	SO:0001819	synonymous_variant	287015	exon2			CCTCAAGGCCTTC	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.792G>A	chr3.hg19:g.140401754G>A		277.0	0.0	.		248.0	102.0	.	NM_152616	A1L4B4|Q8N832|Q8NDL3	Silent	SNP	ENST00000286349.3	hg19	CCDS3113.1																																																																																			.	.	.	none		0.617	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616		A	140401754	G	A	140401754	2	1	202	1	0	0	0	0	0	0	0	1	16529	991	35	2		2	TRIM42	3	140401754	Silent	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10	83774715	140401754	57620676	6	12221											
PRKCI	5584	hgsc.bcm.edu	37	chr3	170013708	170013708	+	Frame_Shift_Del	DEL	A	A	-																															tatctttctagttattttggAaaaacaaattcgcataccac																										TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr3:170013708delA	ENST00000295797.4	+	15	1732	c.1427delA	c.(1426-1428)gaafs	p.E476fs		NM_002740.5	NP_002731.4	P41743	KPCI_HUMAN	protein kinase C, iota	476	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament organization (GO:0007015)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell junction organization (GO:0045216)|cellular response to insulin stimulus (GO:0032869)|cytoskeleton organization (GO:0007010)|establishment of apical/basal cell polarity (GO:0035089)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|eye photoreceptor cell development (GO:0042462)|Golgi vesicle budding (GO:0048194)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of glucose import (GO:0046326)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein phosphorylation (GO:0006468)|protein targeting to membrane (GO:0006612)|response to interleukin-1 (GO:0070555)|secretion (GO:0046903)|tight junction assembly (GO:0070830)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Schmidt-Lanterman incisure (GO:0043220)	ATP binding (GO:0005524)|phospholipid binding (GO:0005543)|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)|endometrium(5)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	36	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|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;0.197)		Tamoxifen(DB00675)	GTTATTTTGGAAAAACAAATT	0.289																																					p.E476fs		Atlas-Indel,Pindel	.											.	PRKCI	82	.	0			c.1426delG						PASS	.						51	55	54					3																	170013708		2202	4298	6500	SO:0001589	frameshift_variant	5584	exon15			.		CCDS3212.2	3q26.3	2008-07-18			ENSG00000163558	ENSG00000163558	2.7.11.13		9404	protein-coding gene	gene with protein product		600539		DXS1179E		7607695, 11978974	Standard	NM_002740		Approved	PKCI	uc003fgs.2	P41743	OTTHUMG00000150214	ENST00000295797.4:c.1427delA	chr3.hg19:g.170013708delA	ENSP00000295797:p.Glu476fs	118.0	0.0	0		85.0	42.0	0.494118	NM_002740	D3DNQ4|Q8WW06	Frame_Shift_Del	DEL	ENST00000295797.4	hg19	CCDS3212.2																																																																																			.	.	.	none		0.289	PRKCI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316866.3	NM_002740		-	170013708	A	-	170013708	7	5	202	1	0	1	0	1	0	0	0	0	12524	246	9	0	1485	0	PRKCI	3	170013708	Frame_Shift_Del	DEL	A	TCGA-IA-A40U-01A-11D-A25F-10	29611954	170013708	28008722	7	12222											
CDKL2	8999	hgsc.bcm.edu	37	chr4	76532433	76532433	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcgggttgccacataatcaGtataaacctccccaggagct	12	9	8	12	1	1	0	1	0	0	0	3	1	2	1	4	2	3	3	4	2	4	4			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr4:76532433G>A	ENST00000429927.2	-	4	1179	c.476C>T	c.(475-477)aCt>aTt	p.T159I	CDKL2_ENST00000307465.4_Missense_Mutation_p.T159I	NM_003948.3	NP_003939.1	Q92772	CDKL2_HUMAN	cyclin-dependent kinase-like 2 (CDC2-related kinase)	159	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				sex differentiation (GO:0007548)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)			breast(3)|endometrium(1)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(2)|stomach(2)	22			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			CACATAATCAGTATAAACCTC	0.443																																					p.T159I		Atlas-SNP	.											.	CDKL2	58	.	0			c.C476T						PASS	.						90	86	87					4																	76532433		2203	4300	6503	SO:0001583	missense	8999	exon4			TAATCAGTATAAA	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.476C>T	chr4.hg19:g.76532433G>A	ENSP00000412365:p.Thr159Ile	201.0	0.0	.		125.0	41.0	.	NM_003948	B2R695	Missense_Mutation	SNP	ENST00000429927.2	hg19	CCDS3570.1	.	.	.	.	.	.	.	.	.	.	g	23.8	4.454370	0.84209	.	.	ENSG00000138769	ENST00000429927;ENST00000307465	T;T	0.68025	-0.3;-0.3	4.72	4.72	0.59763	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.81945	0.4930	M	0.78344	2.41	0.50813	D	0.999894	D;D	0.89917	1.0;1.0	D;D	0.81914	0.988;0.995	D	0.84486	0.0608	9	0.87932	D	0	-11.7169	16.9749	0.86310	0.0:0.0:1.0:0.0	.	159;159	B4DH08;Q92772	.;CDKL2_HUMAN	I	159	ENSP00000412365:T159I;ENSP00000306340:T159I	ENSP00000306340:T159I	T	-	2	0	CDKL2	76751457	1.000000	0.71417	0.946000	0.38457	0.908000	0.53690	8.407000	0.90218	2.605000	0.88082	0.639000	0.83563	ACT	.	.	.	none		0.443	CDKL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252409.2	NM_003948		A	76532433	G	A	76532433	3	1	202	1	0	0	0	0	1	0	0	0	3156	1029	36	2	1037	2	CDKL2	4	76532433	Missense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10		76532433	114621843	8	12223											
SYNPO2	171024	hgsc.bcm.edu	37	chr4	119947961	119947961	+	Missense_Mutation	SNP	A	A	C																															agttcccctagctgagaaccAaagaagtggtcccgactgtg																								rs70944826	byFrequency	TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr4:119947961A>C	ENST00000429713.2	+	3	619	c.437A>C	c.(436-438)cAa>cCa	p.Q146P	SYNPO2_ENST00000434046.2_Missense_Mutation_p.Q146P|SYNPO2_ENST00000307142.4_Missense_Mutation_p.Q146P|SYNPO2_ENST00000448416.2_Intron	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	146						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						GCTGAGAACCAAAGAAGTGGT	0.557																																					p.Q146P		Atlas-SNP	.											.	SYNPO2	353	.	0			c.A437C						PASS	.						43	45	44					4																	119947961		2203	4300	6503	SO:0001583	missense	171024	exon3			AGAACCAAAGAAG	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.437A>C	chr4.hg19:g.119947961A>C	ENSP00000395143:p.Gln146Pro	172.0	0.0	.		162.0	48.0	.	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	hg19	CCDS47129.1	.	.	.	.	.	.	.	.	.	.	A	8.210	0.800113	0.16397	.	.	ENSG00000172403	ENST00000307142;ENST00000429713;ENST00000434046	T;T;T	0.08896	3.04;3.04;3.04	5.51	2.93	0.34026	.	0.395951	0.21221	N	0.078143	T	0.07999	0.0200	M	0.62723	1.935	0.09310	N	1	B;P;B;B	0.34757	0.165;0.467;0.165;0.165	B;B;B;B	0.28139	0.043;0.086;0.069;0.043	T	0.28459	-1.0043	10	0.59425	D	0.04	-2.8964	4.6069	0.12382	0.561:0.1597:0.2792:0.0	.	146;146;146;146	B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6	.;.;.;SYNP2_HUMAN	P	146	ENSP00000306015:Q146P;ENSP00000395143:Q146P;ENSP00000390965:Q146P	ENSP00000306015:Q146P	Q	+	2	0	SYNPO2	120167409	0.019000	0.18553	0.400000	0.26346	0.322000	0.28314	1.517000	0.35867	0.792000	0.33850	0.455000	0.32223	CAA	.	.	.	none		0.557	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1			C	119947961	A	C	119947961	3	2	202	1	0	0	0	0	1	0	0	0	15469	130	5	5	447	5	SYNPO2	4	119947961	Missense_Mutation	SNP	A	TCGA-IA-A40U-01A-11D-A25F-10	43415528	119947961	71206315	9	12224	117	2									
SYNPO2	171024	hgsc.bcm.edu	37	chr4	119947965	119947967	+	In_Frame_Del	DEL	AAG	AAG	-																															cccctagctgagaaccaaagAagtggtcccgactgtgcagg																										TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr4:119947965_119947967delAAG	ENST00000429713.2	+	3	623_625	c.441_443delAAG	c.(439-444)agaagt>agt	p.R147del	SYNPO2_ENST00000434046.2_In_Frame_Del_p.R147del|SYNPO2_ENST00000307142.4_In_Frame_Del_p.R147del|SYNPO2_ENST00000448416.2_Intron	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	147				Missing (in Ref. 3; AL832031). {ECO:0000305}.		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						AGAACCAAAGAAGTGGTCCCGAC	0.552																																					p.147_148del		Pindel	.											.	SYNPO2	353	.	0			c.440_442del						PASS	.																																			SO:0001651	inframe_deletion	171024	exon3			.	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.441_443delAAG	chr4.hg19:g.119947965_119947967delAAG	ENSP00000395143:p.Arg147del	171.0	0.0	.		165.0	32.0	0.194	NM_001128933	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	In_Frame_Del	DEL	ENST00000429713.2	hg19	CCDS47129.1																																																																																			.	.	.	none		0.552	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1			-	119947967	AAG	-	119947965	7	5	202	1	0	1	0	1	0	0	0	0	15469	243	9	0	451	0	SYNPO2	4	119947965	In_Frame_Del	DEL	AAG	TCGA-IA-A40U-01A-11D-A25F-10	4	119947965	71206311	10	12225	117	2									
FAT4	79633	hgsc.bcm.edu	37	chr4	126240999	126240999	+	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	cttttgaaatggtgcagccaGattttgagttgcatgccatc	9	14	10	8	0	0	3	0	2	0	1	1	3	0	3	2	1	4	3	2	1	1	5			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr4:126240999G>A	ENST00000394329.3	+	1	3446	c.3433G>A	c.(3433-3435)Gat>Aat	p.D1145N		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1145	Cadherin 11. {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						GGTGCAGCCAGATTTTGAGTT	0.453																																					p.D1145N		Atlas-SNP	.											.	FAT4	1752	.	0			c.G3433A						PASS	.						160	162	162					4																	126240999		1913	4132	6045	SO:0001583	missense	79633	exon1			CAGCCAGATTTTG	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.3433G>A	chr4.hg19:g.126240999G>A	ENSP00000377862:p.Asp1145Asn	114.0	0.0	.		96.0	30.0	.	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	11.28	1.592284	0.28357	.	.	ENSG00000196159	ENST00000394329	T	0.49432	0.78	4.99	4.14	0.48551	Cadherin (4);Cadherin-like (1);	0.223514	0.21270	N	0.077330	T	0.36580	0.0972	L	0.37507	1.11	0.80722	D	1	B	0.11235	0.004	B	0.10450	0.005	T	0.12400	-1.0549	10	0.13108	T	0.6	.	13.9069	0.63841	0.0744:0.0:0.9256:0.0	.	1145	Q6V0I7	FAT4_HUMAN	N	1145	ENSP00000377862:D1145N	ENSP00000377862:D1145N	D	+	1	0	FAT4	126460449	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.076000	0.71267	1.299000	0.44798	0.561000	0.74099	GAT	.	.	.	none		0.453	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126240999	G	A	126240999	3	1	202	1	0	0	0	0	1	0	0	0	5699	942	33	2	3435	2	FAT4	4	126240999	Missense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10	6293034	126240999	64913277	11	12226											
ADCY2	108	hgsc.bcm.edu	37	chr5	7816984	7816984	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgtttgttctcaggagccCgagcggcagtacatgcacat	8	11	12	10	2	1	0	1	0	1	0	2	2	1	1	1	2	4	5	1	2	1	3			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr5:7816984C>T	ENST00000338316.4	+	23	2978	c.2889C>T	c.(2887-2889)ccC>ccT	p.P963P	ADCY2_ENST00000537121.1_Silent_p.P783P	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	963					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						CTCAGGAGCCCGAGCGGCAGT	0.502											OREG0016499	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P963P		Atlas-SNP	.											.	ADCY2	337	.	0			c.C2889T						PASS	.						148	124	132					5																	7816984		2203	4300	6503	SO:0001819	synonymous_variant	108	exon23			GGAGCCCGAGCGG	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.2889C>T	chr5.hg19:g.7816984C>T		234.0	0.0	.	644	181.0	17.0	.	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Silent	SNP	ENST00000338316.4	hg19	CCDS3872.2																																																																																			.	.	.	none		0.502	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		T	7816984	C	T	7816984	2	4	202	1	0	0	0	0	0	0	0	1	294	639	23	1		1	ADCY2	5	7816984	Silent	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10		7816984	173098276	12	12227											
NUP155	9631	hgsc.bcm.edu	37	chr5	37307409	37307409	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggaatgcacctttcttggaAggcctgaagtccaactatgt	10	12	10	9	0	1	1	0	1	1	0	2	3	2	3	3	3	2	1	3	3	5	3			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr5:37307409A>G	ENST00000231498.3	-	25	3096	c.2893T>C	c.(2893-2895)Ttc>Ctc	p.F965L	NUP155_ENST00000502533.1_5'UTR|NUP155_ENST00000513532.1_Missense_Mutation_p.F901L|NUP155_ENST00000381843.2_Missense_Mutation_p.F906L	NM_153485.1	NP_705618.1	O75694	NU155_HUMAN	nucleoporin 155kDa	965					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)			CTTTCTTGGAAGGCCTGAAGT	0.358																																					p.F965L		Atlas-SNP	.											.	NUP155	116	.	0			c.T2893C						PASS	.						112	104	106					5																	37307409		2203	4300	6503	SO:0001583	missense	9631	exon25			CTTGGAAGGCCTG	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.2893T>C	chr5.hg19:g.37307409A>G	ENSP00000231498:p.Phe965Leu	138.0	0.0	.		165.0	67.0	.	NM_153485	Q9UBE9|Q9UFL5	Missense_Mutation	SNP	ENST00000231498.3	hg19	CCDS3921.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.964993	0.74131	.	.	ENSG00000113569	ENST00000231498;ENST00000381843;ENST00000434056;ENST00000513532	T;T;T	0.77750	-1.11;-1.1;-1.12	5.3	5.3	0.74995	Nucleoporin, Nup133/Nup155-like, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.77778	0.4181	L	0.56124	1.755	0.58432	D	0.999999	P;P	0.45827	0.867;0.568	P;P	0.48063	0.565;0.534	T	0.74734	-0.3565	10	0.20046	T	0.44	-2.0962	15.2661	0.73663	1.0:0.0:0.0:0.0	.	901;965	E9PF10;O75694	.;NU155_HUMAN	L	965;906;927;901	ENSP00000231498:F965L;ENSP00000371265:F906L;ENSP00000422019:F901L	ENSP00000231498:F965L	F	-	1	0	NUP155	37343166	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	8.959000	0.93110	2.016000	0.59253	0.533000	0.62120	TTC	.	.	.	none		0.358	NUP155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207593.2	NM_153485, NM_004298		G	37307409	A	G	37307409	3	3	202	1	0	0	0	0	1	0	0	0	10763	72	3	3	1326	3	NUP155	5	37307409	Missense_Mutation	SNP	A	TCGA-IA-A40U-01A-11D-A25F-10	29490425	37307409	143607851	13	12228											
PAM	5066	hgsc.bcm.edu	37	chr5	102237063	102237063	+	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	aatcttttttttaatagtccGatacatacttctgcatgtct	10	19	4	8	1	3	0	0	0	3	0	4	1	4	0	1	0	3	1	1	0	5	8			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr5:102237063G>A	ENST00000438793.3	+	3	684	c.214G>A	c.(214-216)Gat>Aat	p.D72N	PAM_ENST00000346918.2_Missense_Mutation_p.D72N|PAM_ENST00000379787.4_5'UTR|PAM_ENST00000455264.2_Missense_Mutation_p.D72N|PAM_ENST00000304400.7_Missense_Mutation_p.D72N|PAM_ENST00000348126.2_Missense_Mutation_p.D72N|PAM_ENST00000274392.9_Intron	NM_000919.3|NM_001177306.1|NM_138766.2	NP_000910.2|NP_001170777.1|NP_620121.1	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	72	Peptidylglycine alpha-hydroxylating monooxygenase. {ECO:0000250}.				central nervous system development (GO:0007417)|heart development (GO:0007507)|lactation (GO:0007595)|limb development (GO:0060173)|long-chain fatty acid metabolic process (GO:0001676)|maternal process involved in female pregnancy (GO:0060135)|odontogenesis (GO:0042476)|ovulation cycle process (GO:0022602)|peptide amidation (GO:0001519)|protein amidation (GO:0018032)|protein homooligomerization (GO:0051260)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of protein secretion (GO:0050708)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to pH (GO:0009268)|toxin metabolic process (GO:0009404)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|L-ascorbic acid binding (GO:0031418)|peptidylamidoglycolate lyase activity (GO:0004598)|peptidylglycine monooxygenase activity (GO:0004504)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	25		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	TTAATAGTCCGATACATACTT	0.353																																					p.D72N		Atlas-SNP	.											.	PAM	180	.	0			c.G214A						PASS	.						106	107	107					5																	102237063		2203	4300	6503	SO:0001583	missense	5066	exon3			TAGTCCGATACAT	AB095007	CCDS4092.1, CCDS4093.1, CCDS4094.1, CCDS43348.1, CCDS54885.1	5q	2008-02-05			ENSG00000145730	ENSG00000145730	1.14.17.3		8596	protein-coding gene	gene with protein product	"peptidyl-alpha-hydroxyglycine alpha-amidating lyase", "peptidylglycine alpha-hydroxylating monooxygenase"	170270				2357221	Standard	NM_000919		Approved	PAL, PHM	uc003knt.3	P19021	OTTHUMG00000128729	ENST00000438793.3:c.214G>A	chr5.hg19:g.102237063G>A	ENSP00000396493:p.Asp72Asn	98.0	0.0	.		63.0	4.0	.	NM_138822	A6NMR0|A8K293|O43211|O95080|Q16252|Q16253|Q54A45|Q86U53|Q8WVC7|Q9UCG0	Missense_Mutation	SNP	ENST00000438793.3	hg19	CCDS54885.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.396904	0.83120	.	.	ENSG00000145730	ENST00000438793;ENST00000346918;ENST00000348126;ENST00000304400;ENST00000455264	T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01	5.39	5.39	0.77823	Copper type II, ascorbate-dependent monooxygenase, N-terminal (2);PHM/PNGase F domain (1);	0.092891	0.64402	D	0.000001	T	0.69205	0.3085	M	0.86651	2.83	0.80722	D	1	D;D;P;D;D	0.76494	0.993;0.997;0.798;0.991;0.999	P;P;B;P;D	0.64237	0.824;0.826;0.236;0.73;0.923	T	0.74494	-0.3647	10	0.66056	D	0.02	.	19.5261	0.95208	0.0:0.0:1.0:0.0	.	72;72;72;72;72	P19021;P19021-4;P19021-3;P19021-5;P19021-2	AMD_HUMAN;.;.;.;.	N	72	ENSP00000396493:D72N;ENSP00000282992:D72N;ENSP00000314638:D72N;ENSP00000306100:D72N;ENSP00000403461:D72N	ENSP00000306100:D72N	D	+	1	0	PAM	102264962	1.000000	0.71417	1.000000	0.80357	0.742000	0.42306	6.709000	0.74665	2.668000	0.90789	0.650000	0.86243	GAT	.	.	.	none		0.353	PAM-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250640.2	NM_000919		A	102237063	G	A	102237063	3	1	202	1	0	0	0	0	1	0	0	0	11419	1058	37	1	224	1	PAM	5	102237063	Missense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10	64929654	102237063	78678197	14	12229											
RNF14	9604	hgsc.bcm.edu	37	chr5	141357939	141357939	+	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	agcgtggtcctgtttgcctgGatgcaatttcttaaggaaga	9	13	12	7	1	1	1	0	0	1	1	2	3	2	3	2	3	3	2	2	3	3	3			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr5:141357939G>T	ENST00000394520.2	+	5	687	c.378G>T	c.(376-378)tgG>tgT	p.W126C	RNF14_ENST00000394519.1_Missense_Mutation_p.W126C|RNF14_ENST00000394515.3_Intron|RNF14_ENST00000356143.1_Missense_Mutation_p.W126C|RNF14_ENST00000347642.3_Missense_Mutation_p.W126C|RNF14_ENST00000540015.1_Intron|RNF14_ENST00000502341.1_3'UTR|AC005740.5_ENST00000520882.1_RNA|RNF14_ENST00000394514.2_5'UTR	NM_001201365.1|NM_004290.4	NP_001188294.1|NP_004281.1	Q9UBS8	RNF14_HUMAN	ring finger protein 14	126	RWD. {ECO:0000255|PROSITE- ProRule:PRU00179}.				androgen receptor signaling pathway (GO:0030521)|positive regulation of transcription, DNA-templated (GO:0045893)|protein ubiquitination (GO:0016567)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|small conjugating protein ligase activity (GO:0019787)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15		all_hematologic(541;0.0536)|Ovarian(839;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)		TGTTTGCCTGGATGCAATTTC	0.448																																					p.W126C		Atlas-SNP	.											.	RNF14	30	.	0			c.G378T						PASS	.						126	113	117					5																	141357939		2203	4300	6503	SO:0001583	missense	9604	exon5			TGCCTGGATGCAA	AF060544	CCDS4270.1, CCDS4271.1	5q23.3-q31.1	2008-02-05			ENSG00000013561	ENSG00000013561		"RING-type (C3HC4) zinc fingers"	10058	protein-coding gene	gene with protein product		605675				10085091, 10320776	Standard	NM_183399		Approved	ARA54, HFB30, TRIAD2	uc003lmc.3	Q9UBS8	OTTHUMG00000129660	ENST00000394520.2:c.378G>T	chr5.hg19:g.141357939G>T	ENSP00000378028:p.Trp126Cys	306.0	0.0	.		248.0	70.0	.	NM_001201365	A0AV26|A6NMR2|A8MTW5|B3KN72|B7ZLV2|D3DQE4|O94793|Q6IBV0	Missense_Mutation	SNP	ENST00000394520.2	hg19	CCDS4270.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.419220	0.83559	.	.	ENSG00000013561	ENST00000511961;ENST00000506822;ENST00000356143;ENST00000394520;ENST00000347642;ENST00000506938;ENST00000507163;ENST00000394519	T;T;T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92	5.67	5.67	0.87782	Ubiquitin-conjugating enzyme/RWD-like (2);RWD domain (3);	0.000000	0.85682	D	0.000000	T	0.72645	0.3486	M	0.90922	3.16	0.80722	D	1	D	0.59767	0.986	D	0.72338	0.977	T	0.74490	-0.3648	10	0.37606	T	0.19	.	19.8351	0.96655	0.0:0.0:1.0:0.0	.	126	Q9UBS8	RNF14_HUMAN	C	126	ENSP00000423420:W126C;ENSP00000423273:W126C;ENSP00000348462:W126C;ENSP00000378028:W126C;ENSP00000324956:W126C;ENSP00000420837:W126C;ENSP00000422527:W126C;ENSP00000378027:W126C	ENSP00000324956:W126C	W	+	3	0	RNF14	141338123	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.513000	0.98010	2.702000	0.92279	0.558000	0.71614	TGG	.	.	.	none		0.448	RNF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251860.2	NM_004290		T	141357939	G	T	141357939	3	4	202	1	0	0	0	0	1	0	0	0	13456	1183	41	4	388	4	RNF14	5	141357939	Missense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10	39120876	141357939	39557321	15	12230											
GEMIN5	25929	hgsc.bcm.edu	37	chr5	154278113	154278113	+	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	agacaactcatcctctcctaCgatggcagccaactctgcag	11	8	7	15	1	3	1	1	0	2	1	5	2	4	1	3	1	5	2	3	1	3	1	rs144363013	byFrequency	TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr5:154278113C>T	ENST00000285873.7	-	23	3307	c.3232G>A	c.(3232-3234)Gta>Ata	p.V1078I		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5	1078					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|protein complex assembly (GO:0006461)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)|snRNA binding (GO:0017069)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TCCTCTCCTACGATGGCAGCC	0.552													C|||	2	0.000399361	8e-04	0	5008	,	,		18001	0		0.001	False		,,,				2504	0				p.V1078I		Atlas-SNP	.											.	GEMIN5	120	.	0			c.G3232A						PASS	.	C	ILE/VAL	3,4403	6.2+/-15.9	0,3,2200	95	86	89		3232	2.2	0	5	dbSNP_134	89	6,8594	5.0+/-18.6	0,6,4294	yes	missense	GEMIN5	NM_015465.3	29	0,9,6494	TT,TC,CC		0.0698,0.0681,0.0692	benign	1078/1509	154278113	9,12997	2203	4300	6503	SO:0001583	missense	25929	exon23			CTCCTACGATGGC	AK022748	CCDS4330.1	5q34	2013-01-10			ENSG00000082516	ENSG00000082516		"WD repeat domain containing"	20043	protein-coding gene	gene with protein product		607005				11714716	Standard	NM_015465		Approved		uc003lvx.3	Q8TEQ6	OTTHUMG00000130189	ENST00000285873.7:c.3232G>A	chr5.hg19:g.154278113C>T	ENSP00000285873:p.Val1078Ile	301.0	0.0	.		244.0	85.0	.	NM_015465	Q14CV0|Q8WWV4|Q969W4|Q9H9K3|Q9UFI5	Missense_Mutation	SNP	ENST00000285873.7	hg19	CCDS4330.1	.	.	.	.	.	.	.	.	.	.	C	7.692	0.691317	0.15039	6.81E-4	6.98E-4	ENSG00000082516	ENST00000285873	T	0.69806	-0.43	5.91	2.19	0.27852	.	0.811288	0.11495	N	0.558347	T	0.47097	0.1427	L	0.36672	1.1	0.09310	N	1	P;P	0.36768	0.569;0.569	B;B	0.22152	0.038;0.038	T	0.13098	-1.0522	10	0.20519	T	0.43	-0.487	8.1531	0.31152	0.1114:0.6337:0.0:0.2549	.	1077;1078	B7ZLC9;Q8TEQ6	.;GEMI5_HUMAN	I	1078	ENSP00000285873:V1078I	ENSP00000285873:V1078I	V	-	1	0	GEMIN5	154258306	0.247000	0.23920	0.000000	0.03702	0.428000	0.31595	0.291000	0.18994	0.135000	0.18707	-0.797000	0.03246	GTA	.	C|1.000;T|0.000	0.000	weak		0.552	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1			T	154278113	C	T	154278113	3	4	202	1	0	0	0	0	1	0	0	0	6338	536	19	1	1318	1	GEMIN5	5	154278113	Missense_Mutation	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10	12920174	154278113	26637147	16	12231											
TULP1	7287	hgsc.bcm.edu	37	chr6	35471606	35471606	+	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	gttgtcaaagaccgtgaagcGgttccccaggaggttggacc	9	8	14	10	2	1	2	1	1	0	1	2	4	2	4	4	4	1	3	4	4	2	3			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr6:35471606G>C	ENST00000229771.6	-	12	1211	c.1132C>G	c.(1132-1134)Cgc>Ggc	p.R378G	TULP1_ENST00000322263.4_Missense_Mutation_p.R325G	NM_003322.3	NP_003313.3	O00294	TULP1_HUMAN	tubby like protein 1	378			R -> H (in RP14).		dendrite development (GO:0016358)|detection of light stimulus involved in visual perception (GO:0050908)|eye photoreceptor cell development (GO:0042462)|phagocytosis (GO:0006909)|photoreceptor cell maintenance (GO:0045494)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|retina development in camera-type eye (GO:0060041)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|synapse (GO:0045202)	actin filament binding (GO:0051015)|G-protein coupled photoreceptor activity (GO:0008020)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	19						ACCGTGAAGCGGTTCCCCAGG	0.607																																					p.R378G	GBM(55;1027 1091 11115 23439)	Atlas-SNP	.											.	TULP1	51	.	0			c.C1132G						PASS	.						44	39	41					6																	35471606		2203	4300	6503	SO:0001583	missense	7287	exon12			TGAAGCGGTTCCC	U82468	CCDS4807.1, CCDS75436.1	6p21.3	2014-01-28			ENSG00000112041	ENSG00000112041			12423	protein-coding gene	gene with protein product		602280		RP14		9096357, 9521870	Standard	NM_003322		Approved	TUBL1, LCA15	uc003okv.4	O00294	OTTHUMG00000014575	ENST00000229771.6:c.1132C>G	chr6.hg19:g.35471606G>C	ENSP00000229771:p.Arg378Gly	36.0	0.0	.		44.0	20.0	.	NM_003322	O43536|Q5TGM5|Q8N571	Missense_Mutation	SNP	ENST00000229771.6	hg19	CCDS4807.1	.	.	.	.	.	.	.	.	.	.	G	17.47	3.398726	0.62177	.	.	ENSG00000112041	ENST00000229771;ENST00000322263	D;D	0.85861	-2.04;-2.04	4.95	4.08	0.47627	Tubby, C-terminal (4);	0.060704	0.64402	D	0.000009	D	0.82976	0.5154	L	0.60455	1.87	0.33292	D	0.563614	D;P	0.56035	0.974;0.913	P;P	0.58577	0.841;0.584	D	0.83863	0.0269	10	0.87932	D	0	-13.8748	7.85	0.29448	0.0803:0.0:0.6548:0.2649	.	325;378	O00294-2;O00294	.;TULP1_HUMAN	G	378;325	ENSP00000229771:R378G;ENSP00000319414:R325G	ENSP00000229771:R378G	R	-	1	0	TULP1	35579584	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	5.638000	0.67861	1.075000	0.40932	0.491000	0.48974	CGC	.	.	.	none		0.607	TULP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040307.2			C	35471606	G	C	35471606	3	2	202	1	0	0	0	0	1	0	0	0	16785	1116	39	4	512	4	TULP1	6	35471606	Missense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10		35471606	135643461	17	12232											
CNKSR3	154043	hgsc.bcm.edu	37	chr6	154732110	154732110	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catttttgtgggcagaatgtTggtttccaccgagtacccag	8	13	11	9	1	0	1	0	0	0	1	1	2	1	1	3	2	1	4	3	2	2	5			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr6:154732110T>C	ENST00000607772.1	-	11	1781	c.1237A>G	c.(1237-1239)Aac>Gac	p.N413D	CNKSR3_ENST00000479339.1_Missense_Mutation_p.N333D|CNKSR3_ENST00000433165.2_Missense_Mutation_p.N238D	NM_173515.2	NP_775786.2	Q6P9H4	CNKR3_HUMAN	CNKSR family member 3	413	DUF1170.				negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)	cytoplasm (GO:0005737)|membrane (GO:0016020)				breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	15		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;5.03e-11)|BRCA - Breast invasive adenocarcinoma(81;0.00627)		GGCAGAATGTTGGTTTCCACC	0.502																																					p.N413D		Atlas-SNP	.											.	CNKSR3	56	.	0			c.A1237G						PASS	.						186	176	179					6																	154732110		2203	4300	6503	SO:0001583	missense	154043	exon11			GAATGTTGGTTTC	AK055911	CCDS5246.1	6q25.2	2013-01-10	2005-04-11	2005-04-11	ENSG00000153721	ENSG00000153721		"Sterile alpha motif (SAM) domain containing"	23034	protein-coding gene	gene with protein product			"membrane associated guanylate kinase interacting protein-like 1"	MAGI1			Standard	NM_173515		Approved	FLJ31349		Q6P9H4	OTTHUMG00000015873	ENST00000607772.1:c.1237A>G	chr6.hg19:g.154732110T>C	ENSP00000475915:p.Asn413Asp	180.0	0.0	.		163.0	60.0	.	NM_173515	Q5SGD5|Q96N65	Missense_Mutation	SNP	ENST00000607772.1	hg19	CCDS5246.1	.	.	.	.	.	.	.	.	.	.	T	14.04	2.416814	0.42918	.	.	ENSG00000153721	ENST00000367209;ENST00000367213;ENST00000433165;ENST00000479339;ENST00000424998	T;T;T	0.46063	1.48;0.88;0.89	5.82	5.82	0.92795	Connector enhancer of kinase suppressor of ras 2 (1);	0.275495	0.38326	N	0.001731	T	0.26846	0.0657	L	0.59436	1.845	0.20764	N	0.999854	B	0.27625	0.183	B	0.31495	0.131	T	0.17349	-1.0372	10	0.59425	D	0.04	.	12.6716	0.56870	0.0:0.0:0.1375:0.8625	.	413	Q6P9H4	CNKR3_HUMAN	D	188;413;238;333;175	ENSP00000356182:N413D;ENSP00000414185:N238D;ENSP00000418975:N333D	ENSP00000356178:N188D	N	-	1	0	CNKSR3	154773802	0.999000	0.42202	0.966000	0.40874	0.822000	0.46500	3.065000	0.49994	2.222000	0.72286	0.533000	0.62120	AAC	.	.	.	none		0.502	CNKSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042792.2	NM_173515		C	154732110	T	C	154732110	3	2	202	1	0	0	0	0	1	0	0	0	3610	1812	63	3	442	3	CNKSR3	6	154732110	Missense_Mutation	SNP	T	TCGA-IA-A40U-01A-11D-A25F-10	119260504	154732110	16382957	18	12233											
MET	4233	hgsc.bcm.edu	37	chr7	116397543	116397543	+	Missense_Mutation	SNP	A	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	agcatttcaatatgtccataAttatttcaaatggccacggg	13	13	7	8	1	2	0	2	0	0	0	3	0	3	0	2	2	1	1	2	2	5	5			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr7:116397543A>C	ENST00000318493.6	+	7	2102	c.1915A>C	c.(1915-1917)Att>Ctt	p.I639L	MET_ENST00000436117.2_Missense_Mutation_p.I639L|MET_ENST00000397752.3_Missense_Mutation_p.I639L			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)			TATGTCCATAATTATTTCAAA	0.323			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.I639L		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.A1915C						PASS	.						88	86	86					7																	116397543		1844	4100	5944	SO:0001583	missense	4233	exon7	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	TCCATAATTATTT	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.1915A>C	chr7.hg19:g.116397543A>C	ENSP00000317272:p.Ile639Leu	92.0	0.0	.		86.0	40.0	.	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	A	12.37	1.917098	0.33815	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000436117	T;T;T	0.58652	0.32;0.32;0.32	5.4	-0.479	0.12089	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.634640	0.17750	N	0.163272	T	0.36991	0.0987	L	0.33485	1.01	0.58432	D	0.999999	B;B;B;B;B;B;B;B	0.06786	0.0;0.0;0.001;0.0;0.001;0.0;0.0;0.0	B;B;B;B;B;B;B;B	0.10450	0.001;0.002;0.004;0.005;0.004;0.004;0.001;0.004	T	0.07731	-1.0757	10	0.33141	T	0.24	.	2.8283	0.05491	0.6225:0.12:0.1419:0.1157	.	639;639;639;639;611;639;639;639	B5A929;E7EQ94;B5A930;B5A934;B5A936;B5A937;P08581-2;P08581	.;.;.;.;.;.;.;MET_HUMAN	L	639	ENSP00000380860:I639L;ENSP00000317272:I639L;ENSP00000410980:I639L	ENSP00000317272:I639L	I	+	1	0	MET	116184779	0.099000	0.21834	0.845000	0.33349	0.858000	0.48976	0.480000	0.22244	0.057000	0.16193	-0.334000	0.08254	ATT	.	.	.	none		0.323	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			C	116397543	A	C	116397543	3	2	202	1	0	0	0	0	1	0	0	0	9492	101	4	5	1937	5	MET	7	116397543	Missense_Mutation	SNP	A	TCGA-IA-A40U-01A-11D-A25F-10		116397543	42741120	19	12234											
MFHAS1	9258	hgsc.bcm.edu	37	chr8	8643536	8643536	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccacagccacaaacgtcacTggtttctgtgcttttcacca	9	12	6	14	1	3	0	2	0	1	0	4	0	4	0	3	1	3	2	3	1	1	3			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr8:8643536T>C	ENST00000276282.6	-	3	3741	c.3155A>G	c.(3154-3156)cAg>cGg	p.Q1052R	MFHAS1_ENST00000520091.1_5'UTR	NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	1052										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)		CAAACGTCACTGGTTTCTGTG	0.473																																					p.Q1052R	Melanoma(103;1201 2045 17515 28966)	Atlas-SNP	.											.	MFHAS1	58	.	0			c.A3155G						PASS	.						192	159	170					8																	8643536		2203	4300	6503	SO:0001583	missense	9258	exon3			CGTCACTGGTTTC	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.3155A>G	chr8.hg19:g.8643536T>C	ENSP00000276282:p.Gln1052Arg	165.0	0.0	.		135.0	13.0	.	NM_004225	Q96CI0	Missense_Mutation	SNP	ENST00000276282.6	hg19	CCDS34844.1	.	.	.	.	.	.	.	.	.	.	T	18.70	3.679279	0.68042	.	.	ENSG00000147324	ENST00000276282	T	0.35236	1.32	5.61	5.61	0.85477	.	0.000000	0.42420	D	0.000702	T	0.36580	0.0972	N	0.08118	0	0.31388	N	0.678181	D	0.54601	0.967	P	0.62382	0.901	T	0.47749	-0.9093	10	0.87932	D	0	.	12.4865	0.55877	0.0:0.0:0.0:1.0	.	1052	Q9Y4C4	MFHA1_HUMAN	R	1052	ENSP00000276282:Q1052R	ENSP00000276282:Q1052R	Q	-	2	0	MFHAS1	8680946	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	2.564000	0.45931	2.266000	0.75297	0.533000	0.62120	CAG	.	.	.	none		0.473	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225		C	8643536	T	C	8643536	3	2	202	1	0	0	0	0	1	0	0	0	9528	1580	55	3	7	3	MFHAS1	8	8643536	Missense_Mutation	SNP	T	TCGA-IA-A40U-01A-11D-A25F-10		8643536	137720486	20	12235											
C9orf89	84270	hgsc.bcm.edu	37	chr9	95874554	95874555	+	Missense_Mutation	DNP	TG	TG	GT																															tgtgggactggccctgctccTgtactgctatccgccaggtg																										TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr9:95874554_95874555TG>GT	ENST00000375464.2	+	5	547_548	c.419_420TG>GT	c.(418-420)cTG>cGT	p.L140R	C9orf89_ENST00000488630.1_3'UTR	NM_032310.3	NP_115686.3	Q96LW7	BINCA_HUMAN	chromosome 9 open reading frame 89	145					negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	CARD domain binding (GO:0050700)			endometrium(1)|kidney(1)|lung(3)|ovary(1)|skin(1)	7						GCCCTGCTCCTGTACTGCTATC	0.668																																					p.L140R|p.L140L		Atlas-SNP	.											.	C9orf89	12	.	0			c.T419G|c.G420T						PASS	.																																			SO:0001583	missense	84270	exon5			TGCTCCTGTACTG|GCTCCTGTACTGC	AK057716	CCDS6702.2	9q22.32	2012-03-16			ENSG00000165233	ENSG00000165233			28148	protein-coding gene	gene with protein product	"Bcl10-interacting protein with CARD"					12477932	Standard	XM_005252273		Approved	MGC11115, bA370F5.1, BinCARD	uc004atd.3	Q96LW7	OTTHUMG00000020243	Exception_encountered	chr9.hg19:g.95874554_95874555delinsGT	ENSP00000364613:p.Leu140Arg	70.0	0.0	.		57.0|56.0	23.0	.	NM_032310	Q5BJH8|Q9BSY2	Missense_Mutation|Silent	SNP	ENST00000375464.2	hg19	CCDS6702.2																																																																																			.	.	.	none		0.668	C9orf89-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053128.1	NM_032310		GT	95874555	TG	GT	95874554	3	3	202	1	0	0	0	0	1	0	0	0	2505	1580	55	5	437	5	C9orf89	9	95874554	Missense_Mutation	DNP	TG	TCGA-IA-A40U-01A-11D-A25F-10		95874554	45338877	21	12236											
CCDC3	83643	hgsc.bcm.edu	37	chr10	13043327	13043327	+	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	gccccacgcctggtcgcacaGcatctcgacctcggccgagt	6	6	11	18	5	1	0	0	0	1	0	4	2	1	0	5	2	1	2	5	2	0	0			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr10:13043327G>T	ENST00000378825.3	-	1	370	c.244C>A	c.(244-246)Ctg>Atg	p.L82M	CCDC3_ENST00000378839.1_Intron	NM_031455.3	NP_113643.1	Q9BQI4	CCDC3_HUMAN	coiled-coil domain containing 3	82						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)			TGGTCGCACAGCATCTCGACC	0.706																																					p.L82M		Atlas-SNP	.											.	CCDC3	27	.	0			c.C244A						PASS	.						14	16	15					10																	13043327		2194	4293	6487	SO:0001583	missense	83643	exon1			CGCACAGCATCTC	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.244C>A	chr10.hg19:g.13043327G>T	ENSP00000368102:p.Leu82Met	70.0	0.0	.		70.0	27.0	.	NM_031455	Q5VYV8|Q5VYV9	Missense_Mutation	SNP	ENST00000378825.3	hg19	CCDS7093.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.029083	0.75504	.	.	ENSG00000151468	ENST00000378825	.	.	.	4.55	3.65	0.41850	.	0.000000	0.64402	D	0.000001	T	0.75788	0.3897	M	0.74258	2.255	0.50813	D	0.999899	D	0.76494	0.999	D	0.71656	0.974	T	0.76623	-0.2891	9	0.54805	T	0.06	-8.5593	11.5639	0.50794	0.0889:0.0:0.9111:0.0	.	82	Q9BQI4	CCDC3_HUMAN	M	82	.	ENSP00000368102:L82M	L	-	1	2	CCDC3	13083333	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.135000	0.71696	0.905000	0.36596	-0.224000	0.12420	CTG	.	.	.	none		0.706	CCDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046829.1	NM_031455		T	13043327	G	T	13043327	3	4	202	1	0	0	0	0	1	0	0	0	2806	962	34	4	580	4	CCDC3	10	13043327	Missense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10		13043327	122491420	22	12237											
C10orf72	196740	hgsc.bcm.edu	37	chr10	50311832	50311835	+	Intron	DEL	GGGC	GGGC	-																															atggttaagtctgcggtgaaGggcaaagagtgaggtagtat																										TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	GGGC	GGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr10:50311832_50311835delGGGC	ENST00000332853.4	-	2	481				VSTM4_ENST00000298454.3_Frame_Shift_Del_p.LP176fs	NM_001031746.3	NP_001026916.2	Q8IW00	VSTM4_HUMAN	V-set and transmembrane domain containing 4							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|skin(2)	31						CTGCGGTGAAGGGCAAAGAGTGAG	0.49																																					p.177_178del		Atlas-Indel,Pindel	.											.	VSTM4	83	.	0			c.529_532del						PASS	.																																			SO:0001627	intron_variant	196740	exon3			.	BC041414	CCDS7228.1, CCDS31198.1	10q11.23	2013-01-11	2011-07-01	2011-07-01	ENSG00000165633	ENSG00000165633		"Immunoglobulin superfamily / V-set domain containing"	26470	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 72"	C10orf72			Standard	XR_246075		Approved	FLJ31737	uc001jhf.2	Q8IW00	OTTHUMG00000018184	ENST00000332853.4:c.457+3803GCCC>-	chr10.hg19:g.50311832_50311835delGGGC		201.0	0.0	0		130.0	34.0	0.261538	NM_144984	B4DNI6|Q96MX7	Frame_Shift_Del	DEL	ENST00000332853.4	hg19	CCDS31198.1																																																																																			.	.	.	none		0.49	VSTM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047966.2	NM_144984		-	50311835	GGGC	-	50311832	6	5	202	0	1	1	0	1	0	0	0	0	1617	987	35	0		0	C10orf72	10	50311832	Intron	DEL	GGGC	TCGA-IA-A40U-01A-11D-A25F-10	37268505	50311832	85222915	23	12238											
C10orf76	79591	hgsc.bcm.edu	37	chr10	103789497	103789497	+	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	actcctcgaatgagtgcgcaCagggtctgcagaaatgagag	12	7	13	9	2	1	3	0	2	1	2	3	5	2	3	1	1	2	2	1	1	2	0			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr10:103789497C>T	ENST00000370033.4	-	5	431	c.312G>A	c.(310-312)ctG>ctA	p.L104L	C10orf76_ENST00000311122.5_Silent_p.L104L	NM_024541.2	NP_078817.2	Q5T2E6	CJ076_HUMAN	chromosome 10 open reading frame 76	104						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|prostate(2)|upper_aerodigestive_tract(2)	24		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)		TGAGTGCGCACAGGGTCTGCA	0.473																																					p.L104L		Atlas-SNP	.											.	C10orf76	48	.	0			c.G312A						PASS	.						112	104	107					10																	103789497		1928	4137	6065	SO:0001819	synonymous_variant	79591	exon5			TGCGCACAGGGTC	AK023176	CCDS41563.1	10q24.32	2008-10-21			ENSG00000120029	ENSG00000120029			25788	protein-coding gene	gene with protein product						14702039	Standard	NM_024541		Approved	FLJ13114	uc009xwy.1	Q5T2E6	OTTHUMG00000018943	ENST00000370033.4:c.312G>A	chr10.hg19:g.103789497C>T		48.0	0.0	.		46.0	10.0	.	NM_024541	Q2TB87|Q9H8Z9	Silent	SNP	ENST00000370033.4	hg19	CCDS41563.1																																																																																			.	.	.	none		0.473	C10orf76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050007.1	NM_024541		T	103789497	C	T	103789497	2	4	202	1	0	0	0	0	0	0	0	1	1618	465	17	2		2	C10orf76	10	103789497	Silent	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10	53477665	103789497	31745250	24	12239											
PSD	5662	hgsc.bcm.edu	37	chr10	104173630	104173630	+	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	ctggcctctgcctcctcctcCtcccctctctgtgtccaagg	2	12	7	20	0	2	0	0	0	2	0	8	0	7	0	8	2	1	0	8	2	1	0			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr10:104173630C>A	ENST00000020673.5	-	5	1975	c.1449G>T	c.(1447-1449)gaG>gaT	p.E483D	PSD_ENST00000406432.1_Missense_Mutation_p.E483D|PSD_ENST00000492902.2_5'Flank	NM_001270966.1|NM_002779.4	NP_001257895.1|NP_002770.3	A5PKW4	PSD1_HUMAN	pleckstrin and Sec7 domain containing	483	Poly-Glu.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)		CCTCCTCCTCCTCCCCTCTCT	0.677																																					p.E483D		Atlas-SNP	.											.	PSD	164	.	0			c.G1449T						PASS	.						30	34	33					10																	104173630		2203	4300	6503	SO:0001583	missense	5662	exon6			CTCCTCCTCCCCT	X99688	CCDS31272.1, CCDS73187.1	10q24	2013-01-10	2004-04-28		ENSG00000059915	ENSG00000059915		"Pleckstrin homology (PH) domain containing"	9507	protein-coding gene	gene with protein product		602327	"pleckstrin and Sec7 domain protein"			9417912	Standard	NM_002779		Approved	KIAA2011, TYL, PSD1	uc009xxd.2	A5PKW4	OTTHUMG00000018954	ENST00000020673.5:c.1449G>T	chr10.hg19:g.104173630C>A	ENSP00000020673:p.Glu483Asp	209.0	0.0	.		147.0	50.0	.	NM_001270965	B1AKX7|D3DR87|Q15673|Q8IVG0	Missense_Mutation	SNP	ENST00000020673.5	hg19	CCDS31272.1	.	.	.	.	.	.	.	.	.	.	C	13.92	2.379979	0.42207	.	.	ENSG00000059915	ENST00000020673;ENST00000541902;ENST00000406432	T;T	0.19806	2.12;2.12	4.65	0.0368	0.14193	.	0.480088	0.20167	N	0.097814	T	0.11067	0.0270	N	0.24115	0.695	0.20638	N	0.999877	B	0.16396	0.017	B	0.09377	0.004	T	0.35895	-0.9770	10	0.13853	T	0.58	.	9.4906	0.38958	0.0:0.5847:0.0:0.4153	.	483	A5PKW4	PSD1_HUMAN	D	483;386;483	ENSP00000020673:E483D;ENSP00000384830:E483D	ENSP00000020673:E483D	E	-	3	2	PSD	104163620	0.473000	0.25878	0.998000	0.56505	0.989000	0.77384	-0.538000	0.06120	0.064000	0.16427	0.456000	0.33151	GAG	.	.	.	none		0.677	PSD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050041.2			A	104173630	C	A	104173630	3	1	202	1	0	0	0	0	1	0	0	0	12656	680	24	4	1677	4	PSD	10	104173630	Missense_Mutation	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10	384133	104173630	31361117	25	12240											
INPPL1	3636	hgsc.bcm.edu	37	chr11	71944164	71944164	+	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	cacctaccgctatgagcgggGttcccgggacacatatgcct	8	8	11	14	3	0	1	0	1	0	0	1	2	1	2	4	3	3	2	4	3	3	4			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr11:71944164G>T	ENST00000298229.2	+	17	2201	c.1997G>T	c.(1996-1998)gGt>gTt	p.G666V	INPPL1_ENST00000541756.1_Missense_Mutation_p.G424V|INPPL1_ENST00000538751.1_Missense_Mutation_p.G424V	NM_001567.3	NP_001558.3	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	666					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						TATGAGCGGGGTTCCCGGGAC	0.602																																					p.G666V		Atlas-SNP	.											.	INPPL1	120	.	0			c.G1997T						PASS	.						49	48	48					11																	71944164		2200	4293	6493	SO:0001583	missense	3636	exon17			AGCGGGGTTCCCG	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.1997G>T	chr11.hg19:g.71944164G>T	ENSP00000298229:p.Gly666Val	219.0	0.0	.		158.0	66.0	.	NM_001567	B2RTX5|Q13577|Q13578	Missense_Mutation	SNP	ENST00000298229.2	hg19	CCDS8213.1	.	.	.	.	.	.	.	.	.	.	g	18.33	3.599890	0.66332	.	.	ENSG00000165458	ENST00000298229;ENST00000541756;ENST00000538751	D;D;D	0.95656	-3.77;-3.77;-3.77	5.66	5.66	0.87406	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.230735	0.44688	D	0.000437	D	0.98457	0.9486	H	0.97051	3.93	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	D	0.98338	1.0537	10	0.27082	T	0.32	.	17.588	0.87988	0.0:0.0:1.0:0.0	.	666	O15357	SHIP2_HUMAN	V	666;424;424	ENSP00000298229:G666V;ENSP00000446360:G424V;ENSP00000444619:G424V	ENSP00000298229:G666V	G	+	2	0	INPPL1	71621812	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.393000	0.97256	2.830000	0.97506	0.655000	0.94253	GGT	.	.	.	none		0.602	INPPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396789.1	NM_001567		T	71944164	G	T	71944164	3	4	202	1	0	0	0	0	1	0	0	0	7768	1261	44	4	2063	4	INPPL1	11	71944164	Missense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10		71944164	63062352	26	12241											
MMP27	64066	hgsc.bcm.edu	37	chr11	102563689	102563689	+	Missense_Mutation	SNP	T	T	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	ctttgtactggaaagcagcaTcaacacggatactgattcca	13	10	8	10	1	1	1	1	1	0	0	2	3	2	3	1	2	5	3	1	2	4	4			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr11:102563689T>G	ENST00000260229.4	-	9	1368	c.1277A>C	c.(1276-1278)gAt>gCt	p.D426A		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	426					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)	GAAAGCAGCATCAACACGGAT	0.413																																					p.D426A		Atlas-SNP	.											.	MMP27	84	.	0			c.A1277C						PASS	.						215	201	206					11																	102563689		2203	4299	6502	SO:0001583	missense	64066	exon9			GCAGCATCAACAC	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.1277A>C	chr11.hg19:g.102563689T>G	ENSP00000260229:p.Asp426Ala	178.0	0.0	.		157.0	48.0	.	NM_022122	Q6UWK6	Missense_Mutation	SNP	ENST00000260229.4	hg19	CCDS8319.1	.	.	.	.	.	.	.	.	.	.	T	15.18	2.756835	0.49362	.	.	ENSG00000137675	ENST00000260229	T	0.20598	2.06	5.67	4.55	0.56014	Hemopexin/matrixin (2);	0.204141	0.33813	N	0.004526	T	0.50497	0.1619	M	0.90483	3.12	0.53688	D	0.999973	D	0.76494	0.999	D	0.67900	0.954	T	0.58578	-0.7612	10	0.72032	D	0.01	.	11.5591	0.50766	0.0:0.0698:0.0:0.9302	.	426	Q9H306	MMP27_HUMAN	A	426	ENSP00000260229:D426A	ENSP00000260229:D426A	D	-	2	0	MMP27	102068899	0.445000	0.25657	0.431000	0.26735	0.430000	0.31655	2.306000	0.43673	0.996000	0.38943	0.529000	0.55759	GAT	.	.	.	none		0.413	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122		G	102563689	T	G	102563689	3	3	202	1	0	0	0	0	1	0	0	0	9671	1435	50	5	272	5	MMP27	11	102563689	Missense_Mutation	SNP	T	TCGA-IA-A40U-01A-11D-A25F-10	30619525	102563689	32442827	27	12242											
PAFAH1B2	5049	hgsc.bcm.edu	37	chr11	117038364	117038364	+	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	aaacccctgcatgaactgatCatgcagttgttggaggaaac	13	9	10	9	0	1	2	1	2	0	0	1	4	1	4	2	2	5	4	2	2	3	2	rs569223304		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr11:117038364C>G	ENST00000527958.1	+	6	798	c.639C>G	c.(637-639)atC>atG	p.I213M	PAFAH1B2_ENST00000530272.1_Intron|PAFAH1B2_ENST00000526888.1_Intron|PAFAH1B2_ENST00000419197.2_Intron|PAFAH1B2_ENST00000529887.2_Intron	NM_002572.3	NP_002563.1	P68402	PA1B2_HUMAN	platelet-activating factor acetylhydrolase 1b, catalytic subunit 2 (30kDa)	213					brain development (GO:0007420)|lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|positive regulation of macroautophagy (GO:0016239)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)			kidney(1)	1	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;1.68e-05)|Epithelial(105;0.000162)|all cancers(92;0.00111)		ATGAACTGATCATGCAGTTGT	0.488			T	IGH@	MLCLS																																p.I213M		Atlas-SNP	.		Dom	yes		11	11q23	5049	"platelet-activating factor acetylhydrolase, isoform Ib, beta subunit 30kDa"		L	.	PAFAH1B2	19	.	0			c.C639G						PASS	.						82	68	73					11																	117038364		2201	4296	6497	SO:0001583	missense	5049	exon6			ACTGATCATGCAG	D63390	CCDS8380.1, CCDS53713.1, CCDS53714.1, CCDS53715.1	11q23	2011-10-24	2010-02-10			ENSG00000168092			8575	protein-coding gene	gene with protein product	"PAF-AH1b alpha 2 subunit"	602508	"platelet-activating factor acetylhydrolase, isoform Ib, beta subunit 30kDa", "platelet-activating factor acetylhydrolase, isoform Ib, subunit 2 (30kDa)"			9144386, 9693049	Standard	NM_002572		Approved		uc001pqe.2	P68402		ENST00000527958.1:c.639C>G	chr11.hg19:g.117038364C>G	ENSP00000435289:p.Ile213Met	340.0	0.0	.		330.0	137.0	.	NM_002572	A8DPS5|A8DPS6|A8DPS7|E9PEJ5|E9PLP3|O00687|Q29459|Q6IBR6	Missense_Mutation	SNP	ENST00000527958.1	hg19	CCDS8380.1	.	.	.	.	.	.	.	.	.	.	C	17.72	3.458076	0.63401	.	.	ENSG00000168092	ENST00000527958;ENST00000304808	T;T	0.56776	0.62;0.44	5.49	5.49	0.81192	Esterase, SGNH hydrolase-type (1);Esterase, SGNH hydrolase-type, subgroup (1);	0.053461	0.85682	D	0.000000	T	0.64360	0.2591	L	0.54323	1.7	0.80722	D	1	P	0.40931	0.733	P	0.51193	0.662	T	0.65685	-0.6108	10	0.72032	D	0.01	-9.1136	19.3671	0.94468	0.0:1.0:0.0:0.0	.	213	P68402	PA1B2_HUMAN	M	213;159	ENSP00000435289:I213M;ENSP00000304006:I159M	ENSP00000304006:I159M	I	+	3	3	PAFAH1B2	116543574	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.100000	0.50275	2.593000	0.87608	0.563000	0.77884	ATC	.	.	.	none		0.488	PAFAH1B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392826.1	NM_002572		G	117038364	C	G	117038364	3	3	202	1	0	0	0	0	1	0	0	0	11392	816	29	4	657	4	PAFAH1B2	11	117038364	Missense_Mutation	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10	14474675	117038364	17968152	28	12243											
RECQL	5965	hgsc.bcm.edu	37	chr12	21623145	21623145	+	Missense_Mutation	SNP	T	T	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	atatcaggcatcatcgatttTtcttttcttagctcctgtat	8	19	5	9	1	4	0	2	0	2	0	6	1	5	0	1	1	1	3	1	1	3	7			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr12:21623145T>G	ENST00000444129.2	-	15	2401	c.1933A>C	c.(1933-1935)Aaa>Caa	p.K645Q	PYROXD1_ENST00000240651.9_3'UTR|RECQL_ENST00000421138.2_Missense_Mutation_p.K645Q|PYROXD1_ENST00000538582.1_3'UTR	NM_002907.3|NM_032941.2	NP_002898.2|NP_116559.1	P46063	RECQ1_HUMAN	RecQ helicase-like	645					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						TCATCGATTTTTCTTTTCTTA	0.313								Other identified genes with known or suspected DNA repair function																													p.K645Q		Atlas-SNP	.											.	RECQL	45	.	0			c.A1933C						PASS	.						79	81	80					12																	21623145		2202	4297	6499	SO:0001583	missense	5965	exon16			CGATTTTTCTTTT	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.1933A>C	chr12.hg19:g.21623145T>G	ENSP00000416739:p.Lys645Gln	243.0	0.0	.		427.0	263.0	.	NM_032941	A8K6G2	Missense_Mutation	SNP	ENST00000444129.2	hg19	CCDS31756.1	.	.	.	.	.	.	.	.	.	.	T	17.60	3.429403	0.62844	.	.	ENSG00000004700	ENST00000444129;ENST00000421138	T;T	0.57907	0.37;0.37	4.56	4.56	0.56223	.	0.597468	0.16648	N	0.205325	T	0.48926	0.1527	L	0.32530	0.975	0.33037	D	0.530956	P	0.52316	0.952	P	0.49140	0.601	T	0.62553	-0.6830	10	0.66056	D	0.02	-7.7317	10.4656	0.44604	0.0:0.0:0.0:1.0	.	645	P46063	RECQ1_HUMAN	Q	645	ENSP00000416739:K645Q;ENSP00000395449:K645Q	ENSP00000395449:K645Q	K	-	1	0	RECQL	21514412	1.000000	0.71417	0.988000	0.46212	0.886000	0.51366	3.310000	0.51911	2.036000	0.60181	0.528000	0.53228	AAA	.	.	.	none		0.313	RECQL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402371.1	NM_002907		G	21623145	T	G	21623145	3	3	202	1	0	0	0	0	1	0	0	0	13214	1850	64	5	20	5	RECQL	12	21623145	Missense_Mutation	SNP	T	TCGA-IA-A40U-01A-11D-A25F-10		21623145	112228750	29	12244											
LRIG3	121227	hgsc.bcm.edu	37	chr12	59308047	59308047	+	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	caaaataacgaagactcacaCttctcgaaggctttgaaggt	15	9	8	9	2	2	2	1	1	1	1	3	4	2	2	0	2	1	1	0	2	6	3	rs373824765		TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr12:59308047C>T	ENST00000320743.3	-	2	593	c.307G>A	c.(307-309)Gtg>Atg	p.V103M	LRIG3_ENST00000379141.4_Splice_Site_p.V43M	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	103					otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)			LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			AAGACTCACACTTCTCGAAGG	0.323			T	ROS1	NSCLC																																p.V103M		Atlas-SNP	.		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	.	LRIG3	120	.	0			c.G307A						PASS	.	C	MET/VAL,MET/VAL	0,4406		0,0,2203	97	104	101		127,307	4	1	12		101	1,8599	1.2+/-3.3	0,1,4299	no	missense-near-splice,missense-near-splice	LRIG3	NM_001136051.1,NM_153377.3	21,21	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	43/1060,103/1120	59308047	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	121227	exon2			CTCACACTTCTCG	AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"Immunoglobulin superfamily / I-set domain containing"	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.308+1G>A	chr12.hg19:g.59308047C>T		61.0	0.0	.		88.0	13.0	.	NM_153377	Q6UXL7|Q8NC72	Missense_Mutation	SNP	ENST00000320743.3	hg19	CCDS8960.1	.	.	.	.	.	.	.	.	.	.	C	13.83	2.352857	0.41700	0.0	1.16E-4	ENSG00000139263	ENST00000379141;ENST00000320743;ENST00000552267	T;T;T	0.55052	1.74;1.53;0.54	5.86	3.99	0.46301	.	0.234157	0.21955	N	0.066677	T	0.44850	0.1313	M	0.63428	1.95	0.41104	D	0.985693	B;B	0.24823	0.112;0.02	B;B	0.24541	0.054;0.006	T	0.31696	-0.9934	9	.	.	.	.	5.4651	0.16637	0.0:0.5541:0.1389:0.307	.	43;103	Q6UXM1-2;Q6UXM1	.;LRIG3_HUMAN	M	43;103;10	ENSP00000368436:V43M;ENSP00000326759:V103M;ENSP00000449109:V10M	.	V	-	1	0	LRIG3	57594314	0.999000	0.42202	1.000000	0.80357	0.987000	0.75469	0.426000	0.21363	0.753000	0.32945	0.655000	0.94253	GTG	.	.	.	weak		0.323	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377	Missense_Mutation	T	59308047	C	T	59308047	5	4	202	1	0	0	0	0	0	0	1	0	8953	579	20	2	3124	2	LRIG3	12	59308047	Splice_Site	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10	37684902	59308047	74543848	30	12245											
CLMN	79789	hgsc.bcm.edu	37	chr14	95670380	95670380	+	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	caggttcttactgcagaaagGatccttgtaggtgtcagcct	9	12	11	9	0	2	1	1	0	1	1	3	2	3	2	2	3	3	3	2	3	3	4			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr14:95670380G>A	ENST00000298912.4	-	9	1419	c.1306C>T	c.(1306-1308)Cct>Tct	p.P436S		NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	436					negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		CTGCAGAAAGGATCCTTGTAG	0.478																																					p.P436S		Atlas-SNP	.											.	CLMN	103	.	0			c.C1306T						PASS	.						115	110	112					14																	95670380		2203	4300	6503	SO:0001583	missense	79789	exon9			AGAAAGGATCCTT	AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.1306C>T	chr14.hg19:g.95670380G>A	ENSP00000298912:p.Pro436Ser	221.0	0.0	.		113.0	68.0	.	NM_024734	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Missense_Mutation	SNP	ENST00000298912.4	hg19	CCDS9933.1	.	.	.	.	.	.	.	.	.	.	G	5.446	0.267351	0.10294	.	.	ENSG00000165959	ENST00000298912	D	0.91894	-2.93	5.91	3.07	0.35406	.	0.178386	0.27311	N	0.019959	T	0.81555	0.4847	N	0.08118	0	0.09310	N	0.999997	B	0.16802	0.019	B	0.14023	0.01	T	0.71755	-0.4497	10	0.62326	D	0.03	.	8.3135	0.32086	0.0:0.6159:0.3036:0.0805	.	436	Q96JQ2	CLMN_HUMAN	S	436	ENSP00000298912:P436S	ENSP00000298912:P436S	P	-	1	0	CLMN	94740133	0.051000	0.20477	0.007000	0.13788	0.002000	0.02628	0.554000	0.23407	0.388000	0.25054	-0.839000	0.03059	CCT	.	.	.	none		0.478	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2			A	95670380	G	A	95670380	3	1	202	1	0	0	0	0	1	0	0	0	3544	1174	41	2	1722	2	CLMN	14	95670380	Missense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10		95670380	11679160	31	12246											
CSPG4	1464	hgsc.bcm.edu	37	chr15	75968209	75968209	+	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	ctgaacatgttggcctcaagGaagctcaggaagcctccctt	10	9	10	12	0	2	1	2	1	0	0	3	3	3	3	3	3	3	2	3	3	4	2			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr15:75968209G>C	ENST00000308508.5	-	10	6743	c.6651C>G	c.(6649-6651)ttC>ttG	p.F2217L	AC105020.1_ENST00000435356.1_5'Flank|CTD-2026K11.1_ENST00000569467.1_RNA	NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	2217	Cysteine-containing.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						TGGCCTCAAGGAAGCTCAGGA	0.622																																					p.F2217L		Atlas-SNP	.											.	CSPG4	175	.	0			c.C6651G						PASS	.						80	78	79					15																	75968209		2197	4294	6491	SO:0001583	missense	1464	exon10			CTCAAGGAAGCTC	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.6651C>G	chr15.hg19:g.75968209G>C	ENSP00000312506:p.Phe2217Leu	73.0	0.0	.		56.0	21.0	.	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	hg19	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	G	12.42	1.931673	0.34096	.	.	ENSG00000173546	ENST00000308508;ENST00000537176	T	0.18657	2.2	5.33	2.43	0.29744	.	0.080794	0.52532	N	0.000076	T	0.15609	0.0376	L	0.50333	1.59	0.24930	N	0.991921	B	0.10296	0.003	B	0.08055	0.003	T	0.36261	-0.9755	10	0.09843	T	0.71	.	8.3535	0.32316	0.3053:0.0:0.6947:0.0	.	2217	Q6UVK1	CSPG4_HUMAN	L	2217;249	ENSP00000312506:F2217L	ENSP00000312506:F2217L	F	-	3	2	CSPG4	73755264	1.000000	0.71417	0.865000	0.33974	0.938000	0.57974	0.970000	0.29383	0.251000	0.21505	0.561000	0.74099	TTC	.	.	.	none		0.622	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		C	75968209	G	C	75968209	3	2	202	1	0	0	0	0	1	0	0	0	3962	1165	41	4	321	4	CSPG4	15	75968209	Missense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10		75968209	26563183	32	12247											
RHCG	51458	hgsc.bcm.edu	37	chr15	90030138	90030138	+	Missense_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	acaggaagttgaagcccacgGcgctgaagccgtagcgctgc	10	5	14	12	4	0	2	0	2	0	0	0	3	0	3	2	2	4	4	2	2	4	2			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr15:90030138G>A	ENST00000268122.4	-	2	331	c.263C>T	c.(262-264)gCc>gTc	p.A88V	RHCG_ENST00000544600.1_Missense_Mutation_p.A88V	NM_016321.1	NP_057405.1	Q9UBD6	RHCG_HUMAN	Rh family, C glycoprotein	88					amine transport (GO:0015837)|ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|cellular ion homeostasis (GO:0006873)|epithelial cell differentiation (GO:0030855)|homeostatic process (GO:0042592)|regulation of pH (GO:0006885)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Lung NSC(78;0.0237)|all_lung(78;0.0478)					GAAGCCCACGGCGCTGAAGCC	0.622																																					p.A88V		Atlas-SNP	.											.	RHCG	49	.	0			c.C263T						PASS	.						65	56	59					15																	90030138		2200	4299	6499	SO:0001583	missense	51458	exon2			CCCACGGCGCTGA	AF081497	CCDS10351.1	15q25	2013-05-22	2006-02-23		ENSG00000140519	ENSG00000140519		"Solute carriers"	18140	protein-coding gene	gene with protein product		605381	"chromosome 15 open reading frame 6", "Rhesus blood group, C glycoprotein"	C15orf6		10852913	Standard	NM_016321		Approved	RHGK, PDRC2, SLC42A3	uc002bnz.2	Q9UBD6	OTTHUMG00000149647	ENST00000268122.4:c.263C>T	chr15.hg19:g.90030138G>A	ENSP00000268122:p.Ala88Val	379.0	0.0	.		357.0	159.0	.	NM_016321	A8K4D4|Q6X3Y4	Missense_Mutation	SNP	ENST00000268122.4	hg19	CCDS10351.1	.	.	.	.	.	.	.	.	.	.	g	17.75	3.466191	0.63625	.	.	ENSG00000140519	ENST00000544600;ENST00000268122;ENST00000536247	T;T	0.23552	1.9;1.9	4.76	2.79	0.32731	Ammonium transporter AmtB-like (3);	0.658388	0.16053	N	0.231841	T	0.49592	0.1566	M	0.88310	2.945	0.21386	N	0.99971	P	0.49358	0.923	P	0.53760	0.734	T	0.50021	-0.8876	9	.	.	.	-2.9237	14.3657	0.66805	0.0:0.4295:0.5705:0.0	.	88	Q9UBD6	RHCG_HUMAN	V	88;88;79	ENSP00000438123:A88V;ENSP00000268122:A88V	.	A	-	2	0	RHCG	87831142	0.691000	0.27709	0.099000	0.21106	0.817000	0.46193	2.392000	0.44433	0.397000	0.25310	0.479000	0.44913	GCC	.	.	.	none		0.622	RHCG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000312855.2	NM_016321		A	90030138	G	A	90030138	3	1	202	1	0	0	0	0	1	0	0	0	13339	1203	42	2	1212	2	RHCG	15	90030138	Missense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10	14061929	90030138	12501254	33	12248											
STUB1	339123	hgsc.bcm.edu	37	chr16	732019	732019	+	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	0	0	0	0	0	0	0	0	0	acagcactcaactcttcacaGgacaagtacatggcggacat	14	7	8	12	1	3	0	2	0	1	0	3	2	3	2	0	3	3	2	0	3	3	2			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr16:732019G>T	ENST00000293882.4	-	0	1779				STUB1_ENST00000219548.4_Splice_Site|STUB1_ENST00000564370.1_Splice_Site|LA16c-313D11.9_ENST00000571933.1_RNA|STUB1_ENST00000565677.1_Splice_Site|JMJD8_ENST00000454700.1_3'UTR|JMJD8_ENST00000609261.1_3'UTR|JMJD8_ENST00000412368.2_3'UTR|STUB1_ENST00000566181.2_Splice_Site|LA16c-313D11.9_ENST00000567091.1_RNA			Q96S16	JMJD8_HUMAN	jumonji domain containing 8							extracellular vesicular exosome (GO:0070062)				breast(1)	1						ACTCTTCACAGGACAAGTACA	0.592																																					.		Atlas-SNP	.											STUB1,colon,carcinoma,0,1	STUB1	26	.	0			c.613-1G>T						PASS	.						196	177	184					16																	732019		2201	4300	6501	SO:0001624	3_prime_UTR_variant	10273	exon5			TTCACAGGACAAG		CCDS45369.1	16p13.3	2008-07-28	2008-07-28	2008-07-28		ENSG00000161999			14148	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 20"	C16orf20			Standard	NM_001005920		Approved		uc002ciw.1	Q96S16		ENST00000293882.4:c.*775C>A	chr16.hg19:g.732019G>T		220.0	0.0	.		276.0	156.0	.	NM_005861	B2RNS7|D3DU58|Q4PKE3|Q4VBY1|Q6GMW5|Q71RB8	Splice_Site	SNP	ENST00000293882.4	hg19		.	.	.	.	.	.	.	.	.	.	G	13.81	2.348521	0.41599	.	.	ENSG00000103266	ENST00000219548	.	.	.	4.81	4.81	0.61882	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.8172	0.85737	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	STUB1	672020	1.000000	0.71417	0.999000	0.59377	0.292000	0.27327	8.863000	0.92288	2.366000	0.80165	0.555000	0.69702	.	.	.	.	none		0.592	JMJD8-201	KNOWN	basic	protein_coding	protein_coding		NM_001005920		T	732019	G	T	732019	1	4	202	0	1	0	0	0	0	0	0	0	15347	1014	35	4		4	STUB1	16	732019	3'UTR	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10		732019	89622734	34	12249											
GLG1	2734	hgsc.bcm.edu	37	chr16	74505165	74505165	+	Missense_Mutation	SNP	A	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	ccatcaggtccccagagtctAtctggttatctgccacatcc	8	11	7	15	0	4	1	1	0	3	1	6	1	6	1	5	2	1	1	5	2	2	2			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr16:74505165A>C	ENST00000422840.2	-	15	2134	c.2135T>G	c.(2134-2136)aTa>aGa	p.I712R	GLG1_ENST00000205061.5_Missense_Mutation_p.I712R|GLG1_ENST00000447066.2_Missense_Mutation_p.I701R	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	712					blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						CCCAGAGTCTATCTGGTTATC	0.458																																					p.I712R		Atlas-SNP	.											.	GLG1	106	.	0			c.T2135G						PASS	.						251	213	226					16																	74505165		2198	4300	6498	SO:0001583	missense	2734	exon15			GAGTCTATCTGGT		CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"golgi apparatus protein 1"			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.2135T>G	chr16.hg19:g.74505165A>C	ENSP00000405984:p.Ile712Arg	191.0	0.0	.		227.0	60.0	.	NM_001145667	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Missense_Mutation	SNP	ENST00000422840.2	hg19	CCDS45527.1	.	.	.	.	.	.	.	.	.	.	A	13.05	2.122299	0.37436	.	.	ENSG00000090863	ENST00000205061;ENST00000447066;ENST00000422840	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.68559	0.3014	L	0.49350	1.555	0.80722	D	1	D;D;D	0.65815	0.984;0.995;0.97	D;P;P	0.65684	0.937;0.901;0.905	T	0.62595	-0.6821	9	0.16896	T	0.51	-0.9347	16.8222	0.85835	1.0:0.0:0.0:0.0	.	712;712;701	Q92896;Q92896-2;B7Z8Y4	GSLG1_HUMAN;.;.	R	712;701;712	.	ENSP00000205061:I712R	I	-	2	0	GLG1	73062666	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.923000	0.70045	2.371000	0.80710	0.533000	0.62120	ATA	.	.	.	none		0.458	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201		C	74505165	A	C	74505165	3	2	202	1	0	0	0	0	1	0	0	0	6443	449	16	5	1532	5	GLG1	16	74505165	Missense_Mutation	SNP	A	TCGA-IA-A40U-01A-11D-A25F-10	73773146	74505165	15849588	35	12250											
C16orf46	123775	hgsc.bcm.edu	37	chr16	81094972	81094972	+	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	gctttgcactccccgtttctGcagaagctgcaaggcagcaa	9	9	10	13	1	1	1	0	0	1	1	2	1	2	1	2	1	5	8	2	1	3	2			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr16:81094972G>A	ENST00000299578.5	-	4	1217	c.982C>T	c.(982-984)Cag>Tag	p.Q328*	RP11-303E16.8_ENST00000564536.1_RNA|C16orf46_ENST00000378611.4_Nonsense_Mutation_p.Q328*|C16orf46_ENST00000444657.3_5'Flank	NM_152337.2	NP_689550.2	Q6P387	CP046_HUMAN	chromosome 16 open reading frame 46	328						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|large_intestine(3)|lung(9)|prostate(1)|stomach(1)|urinary_tract(1)	18						CCCCGTTTCTGCAGAAGCTGC	0.552																																					p.Q328X		Atlas-SNP	.											.	C16orf46	57	.	0			c.C982T						PASS	.						103	101	102					16																	81094972		2202	4300	6502	SO:0001587	stop_gained	123775	exon3			GTTTCTGCAGAAG	BC064143	CCDS10932.1, CCDS42201.1	16q23.2	2012-10-09			ENSG00000166455	ENSG00000166455			26525	protein-coding gene	gene with protein product							Standard	NM_152337		Approved	FLJ32702	uc002fgc.4	Q6P387	OTTHUMG00000137629	ENST00000299578.5:c.982C>T	chr16.hg19:g.81094972G>A	ENSP00000299578:p.Gln328*	250.0	0.0	.		316.0	83.0	.	NM_001100873	Q96MA7	Nonsense_Mutation	SNP	ENST00000299578.5	hg19	CCDS10932.1	.	.	.	.	.	.	.	.	.	.	G	14.52	2.561321	0.45590	.	.	ENSG00000166455	ENST00000378611;ENST00000444657;ENST00000299578	.	.	.	5.23	1.87	0.25490	.	0.466272	0.20153	N	0.098118	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	.	14.4868	0.67622	0.0:0.414:0.5859:0.0	.	.	.	.	X	328;55;328	.	ENSP00000299578:Q328X	Q	-	1	0	C16orf46	79652473	1.000000	0.71417	0.998000	0.56505	0.073000	0.16967	1.093000	0.30939	0.653000	0.30826	0.563000	0.77884	CAG	.	.	.	none		0.552	C16orf46-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269054.2	NM_152337		A	81094972	G	A	81094972	4	1	202	1	0	0	0	0	0	1	0	0	1817	1328	46	2	237	2	C16orf46	16	81094972	Nonsense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10	6589807	81094972	9259781	36	12251											
TRPV1	7442	hgsc.bcm.edu	37	chr17	3480482	3480482	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacggcacaggtctctcaggAtcatctgcaggagacagcag	12	6	12	11	1	4	1	2	0	2	1	5	3	4	2	0	4	3	3	0	4	1	0			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr17:3480482A>G	ENST00000571088.1	-	12	1931	c.1718T>C	c.(1717-1719)aTc>aCc	p.I573T	TRPV1_ENST00000310522.5_Missense_Mutation_p.I513T|RP11-235E17.3_ENST00000573568.1_RNA|TRPV1_ENST00000399756.4_Missense_Mutation_p.I573T|TRPV1_ENST00000174621.6_Missense_Mutation_p.I571T|TRPV1_ENST00000425167.2_Missense_Mutation_p.I584T|TRPV1_ENST00000576351.1_Missense_Mutation_p.I563T|TRPV1_ENST00000399759.3_Missense_Mutation_p.I573T|SHPK_ENST00000572705.1_Missense_Mutation_p.I573T	NM_018727.5	NP_061197.4	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel, subfamily V, member 1	573					calcium ion transmembrane transport (GO:0070588)|cell surface receptor signaling pathway (GO:0007166)|cellular response to alkaloid (GO:0071312)|cellular response to ATP (GO:0071318)|chemosensory behavior (GO:0007635)|ion transmembrane transport (GO:0034220)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|calcium-release channel activity (GO:0015278)|excitatory extracellular ligand-gated ion channel activity (GO:0005231)|phosphoprotein binding (GO:0051219)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	17				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	GTCTCTCAGGATCATCTGCAG	0.602																																					p.I573T	Melanoma(38;962 1762 15789)	Atlas-SNP	.											.	TRPV1	99	.	0			c.T1718C						PASS	.						34	34	34					17																	3480482		2044	4170	6214	SO:0001583	missense	7442	exon12			CTCAGGATCATCT	AJ272063	CCDS45576.1	17p13.2	2014-08-12	2002-01-29	2002-02-01	ENSG00000196689	ENSG00000262304		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	12716	protein-coding gene	gene with protein product		602076	"vanilloid receptor subtype 1"	VR1		9349813, 11549313, 16382100	Standard	NM_018727		Approved		uc010vrt.2	Q8NER1	OTTHUMG00000177649	ENST00000571088.1:c.1718T>C	chr17.hg19:g.3480482A>G	ENSP00000461007:p.Ile573Thr	213.0	0.0	.		257.0	125.0	.	NM_018727	A2RUA9|Q3LU47|Q9H0G9|Q9H303|Q9H304|Q9NQ74|Q9NY22	Missense_Mutation	SNP	ENST00000571088.1	hg19	CCDS45576.1	.	.	.	.	.	.	.	.	.	.	A	19.04	3.749434	0.69533	.	.	ENSG00000196689	ENST00000399759;ENST00000399756;ENST00000174621;ENST00000425167;ENST00000310522	D;D;D;D;D	0.90504	-2.68;-2.68;-2.68;-2.68;-2.68	5.15	5.15	0.70609	Ion transport (1);	0.045746	0.85682	D	0.000000	D	0.95007	0.8384	M	0.88842	2.985	0.58432	D	0.999999	P;D;D;P	0.63046	0.764;0.975;0.992;0.77	B;P;P;B	0.58660	0.394;0.717;0.843;0.282	D	0.95830	0.8857	10	0.87932	D	0	-0.9535	14.4569	0.67423	1.0:0.0:0.0:0.0	.	573;571;513;584	Q8NER1;E7EQ80;E7ESJ2;E7EQ78	TRPV1_HUMAN;.;.;.	T	573;573;571;584;513	ENSP00000382661:I573T;ENSP00000382659:I573T;ENSP00000174621:I571T;ENSP00000409627:I584T;ENSP00000311692:I513T	ENSP00000174621:I571T	I	-	2	0	TRPV1	3427231	1.000000	0.71417	1.000000	0.80357	0.693000	0.40251	6.734000	0.74801	2.072000	0.62099	0.460000	0.39030	ATC	.	.	.	none		0.602	TRPV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438254.1	NM_018727		G	3480482	A	G	3480482	3	3	202	1	0	0	0	0	1	0	0	0	16607	333	12	3	494	3	TRPV1	17	3480482	Missense_Mutation	SNP	A	TCGA-IA-A40U-01A-11D-A25F-10		3480482	77714728	37	12252											
NCOR1	9611	hgsc.bcm.edu	37	chr17	15968952	15968952	+	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	cattgcgtaaagctgatactGacttgggtaacctggagttg	10	12	12	7	1	0	2	0	2	0	0	0	3	0	3	1	2	4	4	1	2	4	6			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr17:15968952G>T	ENST00000268712.3	-	33	5055	c.4798C>A	c.(4798-4800)Cag>Aag	p.Q1600K	NCOR1_ENST00000395851.1_Missense_Mutation_p.Q1616K|NCOR1_ENST00000395857.3_Missense_Mutation_p.Q184K	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1600	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)		AGCTGATACTGACTTGGGTAA	0.453																																					p.Q1616K		Atlas-SNP	.											.	NCOR1	240	.	0			c.C4846A						PASS	.						154	137	143					17																	15968952		2203	4300	6503	SO:0001583	missense	9611	exon32			GATACTGACTTGG	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.4798C>A	chr17.hg19:g.15968952G>T	ENSP00000268712:p.Gln1600Lys	222.0	0.0	.		279.0	72.0	.	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	hg19	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.087095	0.76642	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849;ENST00000395857	T;T;T	0.47528	0.84;0.84;0.84	5.58	5.58	0.84498	.	0.104733	0.64402	D	0.000003	T	0.65964	0.2742	L	0.57536	1.79	0.40995	D	0.984889	D;D;P;P;P	0.59767	0.986;0.962;0.9;0.94;0.856	D;P;B;P;P	0.72338	0.977;0.53;0.366;0.57;0.501	T	0.63611	-0.6598	10	0.39692	T	0.17	-9.3223	18.5647	0.91113	0.0:0.0:1.0:0.0	.	410;1504;1600;1616;120	B4DZ48;E7EVK1;O75376;O75376-2;Q86YY1	.;.;NCOR1_HUMAN;.;.	K	1600;1616;1504;184	ENSP00000268712:Q1600K;ENSP00000379192:Q1616K;ENSP00000379198:Q184K	ENSP00000268712:Q1600K	Q	-	1	0	NCOR1	15909677	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.984000	0.76186	2.625000	0.88918	0.557000	0.71058	CAG	.	.	.	none		0.453	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		T	15968952	G	T	15968952	3	4	202	1	0	0	0	0	1	0	0	0	10242	1299	45	4	2580	4	NCOR1	17	15968952	Missense_Mutation	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10	12488470	15968952	65226258	38	12253											
KCNJ12	3768	hgsc.bcm.edu	37	chr17	21318895	21318895	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgtgtggacatccgctggCggtacatgctgctcatcttc	5	12	11	13	2	2	0	1	0	1	0	4	1	3	1	2	3	3	4	2	3	1	2			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr17:21318895C>T	ENST00000583088.1	+	3	1136	c.241C>T	c.(241-243)Cgg>Tgg	p.R81W	KCNJ12_ENST00000331718.5_Missense_Mutation_p.R81W	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	81					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)	p.R81G(1)		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)	CATCCGCTGGCGGTACATGCT	0.577										Prostate(3;0.18)																											p.R81W		Atlas-SNP	.											KCNJ12,NS,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	lung(1)	c.C241T						PASS	.						205	126	153					17																	21318895		2203	4300	6503	SO:0001583	missense	100134444	exon3			CGCTGGCGGTACA	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.241C>T	chr17.hg19:g.21318895C>T	ENSP00000463778:p.Arg81Trp	300.0	2.0	.		373.0	50.0	.	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	hg19	CCDS11219.1	.	.	.	.	.	.	.	.	.	.	C	19.52	3.843005	0.71488	.	.	ENSG00000184185	ENST00000331718	D	0.96011	-3.88	5.33	4.31	0.51392	Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);	0.000000	0.85682	D	0.000000	D	0.98128	0.9382	H	0.95043	3.615	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.98223	1.0479	10	0.87932	D	0	.	10.7711	0.46323	0.4271:0.5729:0.0:0.0	.	81	Q14500	IRK12_HUMAN	W	81	ENSP00000328150:R81W	ENSP00000328150:R81W	R	+	1	2	KCNJ12	21259488	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.669000	0.46825	2.506000	0.84524	0.591000	0.81541	CGG	.	.	.	none		0.577	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012		T	21318895	C	T	21318895	3	4	202	1	0	0	0	0	1	0	0	0	8053	759	27	1	243	1	KCNJ12	17	21318895	Missense_Mutation	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10	5349943	21318895	59876315	39	12254											
PPM1E	22843	hgsc.bcm.edu	37	chr17	56833457	56833457	+	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	ggcggcggcgagccggagccGgaacccgaacccgaacccga	9	0	16	16	8	0	0	0	0	0	0	0	6	0	2	5	5	5	0	5	5	3	0	rs3834568|rs201186780|rs74256772	byFrequency	TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	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	.	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	chr17.hg19:g.56833457G>C		65.0	0.0	.		83.0	5.0	.	NM_014906	Q8N8J9|Q96DB8	Silent	SNP	ENST00000308249.2	hg19	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	202	1	0	0	0	0	0	0	0	1	12348	1103	39	4		4	PPM1E	17	56833457	Silent	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10	35514562	56833457	24361753	40	12255											
DNAH17	8632	hgsc.bcm.edu	37	chr17	76449535	76449535	+	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	tccgagatggcctgctcgatGacatccaggtagctgcgggc	7	8	14	12	3	0	2	0	1	0	1	3	4	2	2	3	3	3	3	3	3	1	1			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr17:76449535G>T	ENST00000585328.1	-	65	10528	c.10404C>A	c.(10402-10404)gtC>gtA	p.V3468V	DNAH17_ENST00000586052.1_5'UTR|DNAH17_ENST00000389840.5_Silent_p.V3459V	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	3459	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)			CCTGCTCGATGACATCCAGGT	0.617																																					p.V3473V		Atlas-SNP	.											.	DNAH17	347	.	0			c.C10419A						PASS	.						112	76	88					17																	76449535		2203	4300	6503	SO:0001819	synonymous_variant	8632	exon65			CTCGATGACATCC	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.10404C>A	chr17.hg19:g.76449535G>T		203.0	0.0	.		238.0	118.0	.	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	hg19																																																																																				.	.	.	none		0.617	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		T	76449535	G	T	76449535	2	4	202	1	0	0	0	0	0	0	0	1	4603	1277	45	4		4	DNAH17	17	76449535	Silent	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10	19616078	76449535	4745675	41	12256											
PTPRM	5797	hgsc.bcm.edu	37	chr18	8314790	8314790	+	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	cctttgcagacgatcattccCgagtgaggctgcagacaata	11	9	10	11	2	1	3	1	1	0	2	2	5	2	3	2	1	2	3	2	1	2	3			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr18:8314790C>T	ENST00000332175.8	+	19	3852	c.2815C>T	c.(2815-2817)Cga>Tga	p.R939*	PTPRM_ENST00000444013.1_Nonsense_Mutation_p.R726*|PTPRM_ENST00000400060.4_Nonsense_Mutation_p.R953*|PTPRM_ENST00000580170.1_Nonsense_Mutation_p.R952*|PTPRM_ENST00000400053.4_Nonsense_Mutation_p.R877*	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	939	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)				CGATCATTCCCGAGTGAGGCT	0.353																																					p.R952X		Atlas-SNP	.											.	PTPRM	185	.	0			c.C2854T						PASS	.						149	142	145					18																	8314790		2203	4300	6503	SO:0001587	stop_gained	5797	exon21			CATTCCCGAGTGA	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.2815C>T	chr18.hg19:g.8314790C>T	ENSP00000331418:p.Arg939*	100.0	0.0	.		72.0	4.0	.	NM_001105244	A7MBN1|D3DUH8|J3QL11	Nonsense_Mutation	SNP	ENST00000332175.8	hg19	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	C	50	17.034461	0.99877	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	.	.	.	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.1802	0.98196	0.0:1.0:0.0:0.0	.	.	.	.	X	939;953;877;726	.	ENSP00000331418:R939X	R	+	1	2	PTPRM	8304790	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.775000	0.55349	2.777000	0.95525	0.655000	0.94253	CGA	.	.	.	none		0.353	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			T	8314790	C	T	8314790	4	4	202	1	0	0	0	0	0	1	0	0	12819	644	23	1	2936	1	PTPRM	18	8314790	Nonsense_Mutation	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10		8314790	69762458	42	12257											
MAP4K1	11184	hgsc.bcm.edu	37	chr19	39101749	39101755	+	Frame_Shift_Del	DEL	ATGAAGT	ATGAAGT	-																															tcttagtcagagtgactttgAtgaagttgtggaaggcagcc																										TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	ATGAAGT	ATGAAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr19:39101749_39101755delATGAAGT	ENST00000591517.1	-	11	774_780	c.746_752delACTTCAT	c.(745-753)aacttcatcfs	p.NFI249fs	MAP4K1_ENST00000423454.2_Intron|MAP4K1_ENST00000589130.1_Frame_Shift_Del_p.NFI245fs|MAP4K1_ENST00000589002.1_Intron|MAP4K1_ENST00000396857.2_Frame_Shift_Del_p.NFI249fs|MAP4K1_ENST00000586296.1_Frame_Shift_Del_p.NFI249fs	NM_007181.4	NP_009112.1	Q92918	M4K1_HUMAN	mitogen-activated protein kinase kinase kinase kinase 1	249	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)			AGTGACTTTGATGAAGTTGTGGAAGGC	0.575																																					p.249_251del		Atlas-Indel,Pindel	.											.	MAP4K1	165	.	0			c.747_753del						PASS	.																																			SO:0001589	frameshift_variant	11184	exon11			.	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.746_752delACTTCAT	chr19.hg19:g.39101749_39101755delATGAAGT	ENSP00000465039:p.Asn249fs	190.0	0.0	0		141.0	29.0	0.205674	NM_007181		Frame_Shift_Del	DEL	ENST00000591517.1	hg19	CCDS59385.1																																																																																			.	.	.	none		0.575	MAP4K1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000453390.1	NM_001042600		-	39101755	ATGAAGT	-	39101749	7	5	202	1	0	1	0	1	0	0	0	0	9266	333	12	0	1899	0	MAP4K1	19	39101749	Frame_Shift_Del	DEL	ATGAAGT	TCGA-IA-A40U-01A-11D-A25F-10		39101749	20027234	43	12258											
MZF1	7593	hgsc.bcm.edu	37	chr19	59082699	59082699	+	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	gtcctctagcttcaccatgaCaggcccctcatcttctgggg	6	11	9	15	0	5	1	2	1	3	0	6	1	6	1	4	3	1	1	4	3	1	3			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr19:59082699C>T	ENST00000215057.2	-	2	618	c.58G>A	c.(58-60)Gtc>Atc	p.V20I	MZF1_ENST00000594108.1_Missense_Mutation_p.V20I|MZF1_ENST00000599369.1_Missense_Mutation_p.V20I|MZF1_ENST00000594234.1_Missense_Mutation_p.V20I|AC016629.8_ENST00000593642.1_RNA|AC016629.8_ENST00000600726.1_RNA|AC016629.8_ENST00000600534.1_RNA	NM_001267033.1|NM_198055.1	NP_001253962.1|NP_932172.1	P28698	MZF1_HUMAN	myeloid zinc finger 1	20					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0443)|all cancers(4;7.92e-14)|Epithelial(4;5.57e-11)|OV - Ovarian serous cystadenocarcinoma(4;1.13e-09)|GBM - Glioblastoma multiforme(193;0.0108)|Lung(386;0.182)		TTCACCATGACAGGCCCCTCA	0.627																																					p.V20I		Atlas-SNP	.											.	MZF1	37	.	0			c.G58A						PASS	.						32	37	35					19																	59082699		2200	4300	6500	SO:0001583	missense	7593	exon2			CCATGACAGGCCC	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.58G>A	chr19.hg19:g.59082699C>T	ENSP00000215057:p.Val20Ile	127.0	0.0	.		117.0	39.0	.	NM_198055	M0QXU0|Q7Z729|Q96I71|Q9NRY0|Q9UBW2	Missense_Mutation	SNP	ENST00000215057.2	hg19	CCDS12988.1	.	.	.	.	.	.	.	.	.	.	.	9.755	1.168475	0.21621	.	.	ENSG00000099326	ENST00000215057	T	0.06768	3.26	4.06	-3.61	0.04556	.	0.426572	0.17300	N	0.179278	T	0.02848	0.0085	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.001	T	0.42032	-0.9475	9	.	.	.	-14.6825	5.3908	0.16244	0.0:0.4053:0.1456:0.4491	.	20;20	Q7Z729;P28698	.;MZF1_HUMAN	I	20	ENSP00000215057:V20I	.	V	-	1	0	MZF1	63774511	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.161000	0.10026	-0.559000	0.06110	-0.878000	0.02970	GTC	.	.	.	none		0.627	MZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467112.1	NM_198055		T	59082699	C	T	59082699	3	4	202	1	0	0	0	0	1	0	0	0	10115	478	17	2	2166	2	MZF1	19	59082699	Missense_Mutation	SNP	C	TCGA-IA-A40U-01A-11D-A25F-10	19980950	59082699	46284	44	12259											
TAB1	10454	hgsc.bcm.edu	37	chr22	39814795	39814795	+	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	gggttgcaggtgacacagctGaacgtggaccacaccacaga	12	5	13	11	1	0	3	0	2	0	1	0	4	0	4	2	3	3	3	2	3	1	1			TCGA-IA-A40U-01A-11D-A25F-10	TCGA-IA-A40U-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dd80d4b5-7825-4f99-b2e2-2559763b8661	384b9f8f-9231-4ab8-b556-8083ee51d965	g.chr22:39814795G>A	ENST00000216160.6	+	6	671	c.609G>A	c.(607-609)ctG>ctA	p.L203L	TAB1_ENST00000331454.3_Silent_p.L203L	NM_006116.2	NP_006107.1	Q15750	TAB1_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 1	203	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						TGACACAGCTGAACGTGGACC	0.537																																					p.L203L		Atlas-SNP	.											.	TAB1	36	.	0			c.G609A						PASS	.						164	122	136					22																	39814795		2203	4300	6503	SO:0001819	synonymous_variant	10454	exon6			ACAGCTGAACGTG	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.609G>A	chr22.hg19:g.39814795G>A		206.0	0.0	.		179.0	68.0	.	NM_153497	Q2PP09|Q8IZW2	Silent	SNP	ENST00000216160.6	hg19	CCDS13993.1																																																																																			.	.	.	none		0.537	TAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321313.1	NM_153497		A	39814795	G	A	39814795	2	1	202	1	0	0	0	0	0	0	0	1	15507	1277	45	2		2	TAB1	22	39814795	Silent	SNP	G	TCGA-IA-A40U-01A-11D-A25F-10		39814795	11489771	45	12260											
LRRC8B	23507	hgsc.bcm.edu	37	chr1	90048545	90048545	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatgccgtctgttacgagaaAcagctccattggtttgcaaa	11	11	10	9	2	1	1	0	0	1	1	2	3	2	1	2	1	5	4	2	1	3	3			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr1:90048545A>G	ENST00000330947.2	+	5	696	c.336A>G	c.(334-336)aaA>aaG	p.K112K	LRRC8B_ENST00000439853.1_Silent_p.K112K|LRRC8B_ENST00000358200.4_Silent_p.K112K|RP5-1007M22.2_ENST00000443562.1_RNA	NM_001134476.1	NP_001127948.1	Q6P9F7	LRC8B_HUMAN	leucine rich repeat containing 8 family, member B	112					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)		GTTACGAGAAACAGCTCCATT	0.512																																					p.K112K		Atlas-SNP	.											.	LRRC8B	49	.	0			c.A336G						PASS	.						158	154	155					1																	90048545		2203	4300	6503	SO:0001819	synonymous_variant	23507	exon5			CGAGAAACAGCTC	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.336A>G	chr1.hg19:g.90048545A>G		152.0	0.0	.		174.0	61.0	.	NM_015350	D3DT28|Q6UY21|Q8N106|Q92627	Silent	SNP	ENST00000330947.2	hg19	CCDS724.1																																																																																			.	.	.	none		0.512	LRRC8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028008.1	NM_015350		G	90048545	A	G	90048545	2	3	203	1	0	0	0	0	0	0	0	1	9029	40	2	3		3	LRRC8B	1	90048545	Silent	SNP	A	TCGA-IA-A40X-01A-11D-A25F-10		90048545	159202076	1	12261											
OTX1	5013	hgsc.bcm.edu	37	chr2	63282730	63282730	+	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	caagaagaagtcctctccagTgcgggagagctcgggctccg	9	6	14	12	3	1	3	0	0	1	3	5	4	3	3	3	2	2	2	3	2	3	0			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr2:63282730T>A	ENST00000282549.2	+	5	620	c.344T>A	c.(343-345)gTg>gAg	p.V115E	OTX1_ENST00000366671.3_Missense_Mutation_p.V115E	NM_014562.3	NP_055377.1	P32242	OTX1_HUMAN	orthodenticle homeobox 1	115					anterior/posterior pattern specification (GO:0009952)|diencephalon morphogenesis (GO:0048852)|inner ear morphogenesis (GO:0042472)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Lung NSC(7;0.121)|all_lung(7;0.211)					TCCTCTCCAGTGCGGGAGAGC	0.647																																					p.V115E		Atlas-SNP	.											.	OTX1	49	.	0			c.T344A						PASS	.						37	38	38					2																	63282730		2203	4300	6503	SO:0001583	missense	5013	exon5			CTCCAGTGCGGGA		CCDS1873.1	2p15	2011-06-20	2007-02-15		ENSG00000115507	ENSG00000115507		"Homeoboxes / PRD class"	8521	protein-coding gene	gene with protein product		600036	"orthodenticle (Drosophila) homolog 1", "orthodenticle homolog 1 (Drosophila)"			7959790	Standard	NM_001199770		Approved		uc002scd.3	P32242	OTTHUMG00000129454	ENST00000282549.2:c.344T>A	chr2.hg19:g.63282730T>A	ENSP00000282549:p.Val115Glu	149.0	0.0	.		239.0	86.0	.	NM_014562	A6NHA2|B3KTJ4|Q53TG6	Missense_Mutation	SNP	ENST00000282549.2	hg19	CCDS1873.1	.	.	.	.	.	.	.	.	.	.	T	17.88	3.497563	0.64186	.	.	ENSG00000115507	ENST00000366671;ENST00000282549	D;D	0.90385	-2.66;-2.66	3.69	2.55	0.30701	.	0.158837	0.42053	D	0.000765	T	0.79411	0.4441	N	0.19112	0.55	0.41015	D	0.985031	P	0.45531	0.86	P	0.45232	0.474	T	0.76572	-0.2910	10	0.06757	T	0.87	.	3.9166	0.09225	0.0:0.3229:0.0:0.6771	.	115	P32242	OTX1_HUMAN	E	115	ENSP00000355631:V115E;ENSP00000282549:V115E	ENSP00000282549:V115E	V	+	2	0	OTX1	63136234	0.998000	0.40836	1.000000	0.80357	0.945000	0.59286	3.890000	0.56220	1.676000	0.50930	0.460000	0.39030	GTG	.	.	.	none		0.647	OTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251617.1			A	63282730	T	A	63282730	3	1	203	1	0	0	0	0	1	0	0	0	11327	1696	59	5	354	5	OTX1	2	63282730	Missense_Mutation	SNP	T	TCGA-IA-A40X-01A-11D-A25F-10		63282730	179916643	2	12262											
KCNJ3	3760	hgsc.bcm.edu	37	chr2	155555531	155555531	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtggacctcaagtggcgcTggaacctcttcatcttcatt	7	13	10	11	1	5	0	3	0	2	0	5	2	5	2	2	4	1	1	2	4	2	3			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr2:155555531T>C	ENST00000295101.2	+	1	721	c.244T>C	c.(244-246)Tgg>Cgg	p.W82R	AC061961.2_ENST00000443901.1_RNA|KCNJ3_ENST00000544049.1_Missense_Mutation_p.W82R	NM_001260509.1|NM_002239.3	NP_001247438.1|NP_002230.1	P48549	KCNJ3_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 3	82					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)	CAAGTGGCGCTGGAACCTCTT	0.592																																					p.W82R		Atlas-SNP	.											.	KCNJ3	126	.	0			c.T244C						PASS	.						147	139	142					2																	155555531		2203	4300	6503	SO:0001583	missense	3760	exon1			TGGCGCTGGAACC	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.244T>C	chr2.hg19:g.155555531T>C	ENSP00000295101:p.Trp82Arg	352.0	0.0	.		467.0	30.0	.	NM_001260509	B4DEW7|Q8TBI0	Missense_Mutation	SNP	ENST00000295101.2	hg19	CCDS2200.1	.	.	.	.	.	.	.	.	.	.	T	18.26	3.585481	0.66105	.	.	ENSG00000162989	ENST00000295101;ENST00000544049	D;D	0.94184	-3.37;-3.37	5.16	5.16	0.70880	Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);	0.063086	0.64402	D	0.000001	D	0.95717	0.8607	M	0.73430	2.235	0.80722	D	1	D;D	0.54207	0.965;0.965	P;P	0.60886	0.88;0.879	D	0.96140	0.9099	10	0.87932	D	0	.	13.8034	0.63216	0.0:0.0:0.0:1.0	.	82;82	B4DEW7;P48549	.;IRK3_HUMAN	R	82	ENSP00000295101:W82R;ENSP00000438410:W82R	ENSP00000295101:W82R	W	+	1	0	KCNJ3	155263777	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.981000	0.88123	1.946000	0.56461	0.454000	0.30748	TGG	.	.	.	none		0.592	KCNJ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254890.2	NM_002239		C	155555531	T	C	155555531	3	2	203	1	0	0	0	0	1	0	0	0	8059	1580	55	3	246	3	KCNJ3	2	155555531	Missense_Mutation	SNP	T	TCGA-IA-A40X-01A-11D-A25F-10	92272801	155555531	87643842	3	12263											
TTN	7273	hgsc.bcm.edu	37	chr2	179615958	179615958	+	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	cttgagcttatttcagaagaCgtatctaaaagagataattt	15	14	7	5	1	2	4	1	1	1	3	2	5	2	4	0	0	1	2	0	0	6	7	rs145004106	byFrequency	TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr2:179615958C>T	ENST00000591111.1	-	45	10585				TTN_ENST00000342992.6_Intron|TTN_ENST00000589042.1_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000360870.5_Silent_p.T3723T|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000359218.5_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)			TTTCAGAAGACGTATCTAAAA	0.358													C|||	2	0.000399361	8e-04	0	5008	,	,		20087	0.001		0	False		,,,				2504	0				p.T3723T		Atlas-SNP	.											.	TTN	18412	.	0			c.G11169A						PASS	.	C	,,,,	1,4403	2.1+/-5.4	0,1,2201	61	60	60		,,11169,,	-1.5	0	2	dbSNP_134	60	1,8593	1.2+/-3.3	0,1,4296	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	0,2,6497	TT,TC,CC		0.0116,0.0227,0.0154	,,,,	,,3723/5605,,	179615958	2,12996	2202	4297	6499	SO:0001627	intron_variant	7273	exon46			AGAAGACGTATCT	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+1892G>A	chr2.hg19:g.179615958C>T		133.0	0.0	.		121.0	36.0	.	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	C|1.000;T|0.000	0.000	weak		0.358	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179615958	C	T	179615958	1	4	203	0	1	0	0	0	0	0	0	0	16747	523	19	1		1	TTN	2	179615958	Intron	SNP	C	TCGA-IA-A40X-01A-11D-A25F-10	24060427	179615958	63583415	4	12264											
CRBN	51185	hgsc.bcm.edu	37	chr3	3209472	3209472	+	Missense_Mutation	SNP	T	T	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	gaatttgcactttagcttgcTggattctaaaataaagagaa	15	13	8	5	0	1	1	0	0	1	1	1	4	1	2	0	1	3	3	0	1	7	7			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr3:3209472T>G	ENST00000231948.4	-	5	555	c.533A>C	c.(532-534)cAg>cCg	p.Q178P	CRBN_ENST00000432408.2_Missense_Mutation_p.Q177P	NM_016302.3	NP_057386.2	Q96SW2	CRBN_HUMAN	cereblon	178	Lon.				negative regulation of ion transmembrane transport (GO:0034766)|negative regulation of protein homooligomerization (GO:0032463)|positive regulation of protein homodimerization activity (GO:0090073)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP-dependent peptidase activity (GO:0004176)			endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	11				Epithelial(13;0.00244)|OV - Ovarian serous cystadenocarcinoma(96;0.00617)|all cancers(10;0.0079)	Lenalidomide(DB00480)|Pomalidomide(DB08910)|Thalidomide(DB01041)	TTTAGCTTGCTGGATTCTAAA	0.333																																					p.Q178P		Atlas-SNP	.											.	CRBN	29	.	0			c.A533C						PASS	.						90	89	89					3																	3209472		2203	4300	6503	SO:0001583	missense	51185	exon5			GCTTGCTGGATTC	BC017419	CCDS2562.1, CCDS54547.1	3p26.3	2014-05-27			ENSG00000113851	ENSG00000113851			30185	protein-coding gene	gene with protein product		609262	"mental retardation, non-syndromic, autosomal recessive, 2A"	MRT2A		15557513	Standard	NM_016302		Approved	MRT2	uc003bpq.3	Q96SW2	OTTHUMG00000090261	ENST00000231948.4:c.533A>C	chr3.hg19:g.3209472T>G	ENSP00000231948:p.Gln178Pro	50.0	0.0	.		52.0	19.0	.	NM_016302	B2R6H4|C9IZA9|C9JAH6|Q6AI62|Q6NVZ0|Q9UHW4	Missense_Mutation	SNP	ENST00000231948.4	hg19	CCDS2562.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.59|13.59	2.282820|2.282820	0.40394|0.40394	.|.	.|.	ENSG00000113851|ENSG00000113851	ENST00000231948;ENST00000432408;ENST00000546075|ENST00000424814;ENST00000450014	T;T|.	0.40225|.	1.04;1.04|.	5.1|5.1	5.1|5.1	0.69264|0.69264	Peptidase S16, lon N-terminal (2);PUA-like domain (1);|.	0.056186|.	0.64402|.	D|.	0.000001|.	T|T	0.38931|0.38931	0.1059|0.1059	N|N	0.08118|0.08118	0|0	0.54753|0.54753	D|D	0.999981|0.999981	B;B;B|.	0.06786|.	0.001;0.0;0.001|.	B;B;B|.	0.08055|.	0.003;0.002;0.003|.	T|T	0.31779|0.31779	-0.9931|-0.9931	10|5	0.29301|.	T|.	0.29|.	-13.9919|-13.9919	15.19|15.19	0.73035|0.73035	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	115;177;178|.	F5H3U1;Q96SW2-2;Q96SW2|.	.;.;CRBN_HUMAN|.	P|R	178;177;115|174	ENSP00000231948:Q178P;ENSP00000412499:Q177P|.	ENSP00000231948:Q178P|.	Q|S	-|-	2|1	0|0	CRBN|CRBN	3184472|3184472	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.567000|3.567000	0.53813|0.53813	2.045000|2.045000	0.60652|0.60652	0.533000|0.533000	0.62120|0.62120	CAG|AGC	.	.	.	none		0.333	CRBN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206579.3	NM_016302		G	3209472	T	G	3209472	3	3	203	1	0	0	0	0	1	0	0	0	3853	1580	55	5	823	5	CRBN	3	3209472	Missense_Mutation	SNP	T	TCGA-IA-A40X-01A-11D-A25F-10		3209472	194812958	5	12265											
KLHDC8B	200942	hgsc.bcm.edu	37	chr3	49212303	49212303	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgccatggctgaaggcagcGtctttagcctgggtggcctg	5	9	16	11	2	1	1	0	1	1	0	1	1	1	1	3	4	2	2	3	4	2	2			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr3:49212303G>A	ENST00000332780.2	+	4	879	c.670G>A	c.(670-672)Gtc>Atc	p.V224I	KLHDC8B_ENST00000476495.2_3'UTR|C3orf84_ENST00000443990.1_5'Flank	NM_173546.2	NP_775817.1	Q8IXV7	KLD8B_HUMAN	kelch domain containing 8B	224						cytoplasm (GO:0005737)				endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|stomach(1)	7				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		TGAAGGCAGCGTCTTTAGCCT	0.592																																					p.V224I		Atlas-SNP	.											.	KLHDC8B	28	.	0			c.G670A						PASS	.						50	51	51					3																	49212303		2203	4300	6503	SO:0001583	missense	200942	exon4			GGCAGCGTCTTTA		CCDS2791.1	3p21.31	2008-02-05			ENSG00000185909	ENSG00000185909			28557	protein-coding gene	gene with protein product		613169					Standard	NM_173546		Approved	MGC35097	uc003cwh.3	Q8IXV7	OTTHUMG00000156814	ENST00000332780.2:c.670G>A	chr3.hg19:g.49212303G>A	ENSP00000327468:p.Val224Ile	63.0	0.0	.		58.0	31.0	.	NM_173546		Missense_Mutation	SNP	ENST00000332780.2	hg19	CCDS2791.1	.	.	.	.	.	.	.	.	.	.	G	10.82	1.459584	0.26248	.	.	ENSG00000185909	ENST00000332780	T	0.71222	-0.55	5.97	2.98	0.34508	Kelch-type beta propeller (1);	0.187468	0.46145	N	0.000320	T	0.44498	0.1296	N	0.12182	0.205	0.32968	D	0.521921	B;B	0.25272	0.103;0.122	B;B	0.16289	0.009;0.015	T	0.44590	-0.9318	10	0.14252	T	0.57	-25.1154	6.9162	0.24361	0.1603:0.0:0.608:0.2317	.	178;224	B4DFM2;Q8IXV7	.;KLD8B_HUMAN	I	224	ENSP00000327468:V224I	ENSP00000327468:V224I	V	+	1	0	KLHDC8B	49187307	0.897000	0.30589	0.786000	0.31890	0.987000	0.75469	1.471000	0.35365	0.874000	0.35823	0.655000	0.94253	GTC	.	.	.	none		0.592	KLHDC8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345974.1	NM_173546		A	49212303	G	A	49212303	3	1	203	1	0	0	0	0	1	0	0	0	8370	1145	40	1	680	1	KLHDC8B	3	49212303	Missense_Mutation	SNP	G	TCGA-IA-A40X-01A-11D-A25F-10	46002831	49212303	148810127	6	12266											
MAML3	55534	hgsc.bcm.edu	37	chr4	140811102	140811102	+	Silent	SNP	C	C	T																															tgctgctgctgctgctgctgCtgctgctgctgctgctgctg																										TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr4:140811102C>T	ENST00000509479.2	-	2	2344	c.1488G>A	c.(1486-1488)caG>caA	p.Q496Q	MAML3_ENST00000327122.5_Silent_p.Q340Q|MAML3_ENST00000398940.1_Silent_p.Q35Q	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					gctgctgctgctgctgctgct	0.542																																					p.Q496Q		Atlas-SNP	.											.	MAML3	192	.	0			c.G1488A						PASS	.						13	19	17					4																	140811102		2124	4242	6366	SO:0001819	synonymous_variant	55534	exon2			CTGCTGCTGCTGC	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"mastermind (drosophila)-like 3"	608991	"trinucleotide repeat containing 3"	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1488G>A	chr4.hg19:g.140811102C>T		77.0	0.0	.		92.0	12.0	.	NM_018717		Silent	SNP	ENST00000509479.2	hg19	CCDS54805.1																																																																																			.	.	.	none		0.542	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			T	140811102	C	T	140811102	2	4	203	1	0	0	0	0	0	0	0	1	9214	796	28	2		2	MAML3	4	140811102	Silent	SNP	C	TCGA-IA-A40X-01A-11D-A25F-10		140811102	50343174	7	12267	118	2									
MAML3	55534	hgsc.bcm.edu	37	chr4	140811104	140811104	+	Missense_Mutation	SNP	G	G	T																															ctgctgctgctgctgctgctGctgctgctgctgctgctgtt																										TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr4:140811104G>T	ENST00000509479.2	-	2	2342	c.1486C>A	c.(1486-1488)Cag>Aag	p.Q496K	MAML3_ENST00000327122.5_Missense_Mutation_p.Q340K|MAML3_ENST00000398940.1_Missense_Mutation_p.Q35K	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					tgctgctgctgctgctgctgc	0.542																																					p.Q496K		Atlas-SNP	.											.	MAML3	192	.	0			c.C1486A						PASS	.						13	18	17					4																	140811104		2145	4254	6399	SO:0001583	missense	55534	exon2			GCTGCTGCTGCTG	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"mastermind (drosophila)-like 3"	608991	"trinucleotide repeat containing 3"	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1486C>A	chr4.hg19:g.140811104G>T	ENSP00000421180:p.Gln496Lys	79.0	0.0	.		93.0	10.0	.	NM_018717		Missense_Mutation	SNP	ENST00000509479.2	hg19	CCDS54805.1	.	.	.	.	.	.	.	.	.	.	g	6.502	0.460780	0.12342	.	.	ENSG00000196782	ENST00000509479;ENST00000327122;ENST00000398940	T;T	0.64260	0.89;-0.09	4.53	4.53	0.55603	.	0.116387	0.37577	N	0.002035	T	0.39937	0.1097	N	0.08118	0	0.32507	N	0.538137	B	0.22276	0.067	B	0.19391	0.025	T	0.35025	-0.9805	10	0.06494	T	0.89	.	17.2683	0.87093	0.0:0.0:1.0:0.0	.	496	Q96JK9	MAML3_HUMAN	K	496;340;35	ENSP00000421180:Q496K;ENSP00000313316:Q340K	ENSP00000313316:Q340K	Q	-	1	0	MAML3	141030554	0.998000	0.40836	0.988000	0.46212	0.665000	0.39181	0.180000	0.16860	2.038000	0.60285	0.455000	0.32223	CAG	.	.	.	none		0.542	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			T	140811104	G	T	140811104	3	4	203	1	0	0	0	0	1	0	0	0	9214	1328	46	4	1938	4	MAML3	4	140811104	Missense_Mutation	SNP	G	TCGA-IA-A40X-01A-11D-A25F-10	2	140811104	50343172	8	12268	118	2									
SLC6A19	340024	hgsc.bcm.edu	37	chr5	1219218	1219218	+	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	aagtggcccaaggaggtgctCacaggtacgtgtgcagtcgg	9	7	16	9	2	1	0	1	0	0	0	2	1	1	1	1	5	3	3	1	5	3	1			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr5:1219218C>T	ENST00000304460.10	+	9	1430	c.1374C>T	c.(1372-1374)ctC>ctT	p.L458L		NM_001003841.2	NP_001003841.1	Q695T7	S6A19_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 19	458					amino acid transport (GO:0006865)|ion transport (GO:0006811)|response to nutrient (GO:0007584)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|neutral amino acid transmembrane transporter activity (GO:0015175)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(25)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			AGGAGGTGCTCACAGGTACGT	0.642																																					p.L458L		Atlas-SNP	.											.	SLC6A19	99	.	0			c.C1374T						PASS	.						117	100	106					5																	1219218		2201	4298	6499	SO:0001819	synonymous_variant	340024	exon9			GGTGCTCACAGGT	AK096054	CCDS34130.1	5p15	2013-07-19			ENSG00000174358	ENSG00000174358		"Solute carriers"	27960	protein-coding gene	gene with protein product	"Hartnup disease"	608893					Standard	NM_001003841		Approved		uc003jbw.4	Q695T7	OTTHUMG00000161636	ENST00000304460.10:c.1374C>T	chr5.hg19:g.1219218C>T		79.0	0.0	.		106.0	41.0	.	NM_001003841	A8K446	Silent	SNP	ENST00000304460.10	hg19	CCDS34130.1																																																																																			.	.	.	none		0.642	SLC6A19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365557.1	XM_291120		T	1219218	C	T	1219218	2	4	203	1	0	0	0	0	0	0	0	1	14695	813	29	2		2	SLC6A19	5	1219218	Silent	SNP	C	TCGA-IA-A40X-01A-11D-A25F-10		1219218	179696042	9	12269											
LYRM4	57128	hgsc.bcm.edu	37	chr6	5260906	5260906	+	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	attgtaggcgctgaaacgctTgctctctctcagcatcgccc	7	11	9	14	3	2	1	1	1	2	0	5	1	2	1	1	1	3	5	1	1	2	3			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr6:5260906T>A	ENST00000330636.4	-	1	266	c.61A>T	c.(61-63)Aag>Tag	p.K21*	LYRM4_ENST00000500576.2_Nonsense_Mutation_p.K21*|LYRM4_ENST00000480566.1_Nonsense_Mutation_p.K21*|LYRM4_ENST00000468929.1_Nonsense_Mutation_p.K21*|FARS2_ENST00000274680.4_5'Flank|LYRM4_ENST00000464010.1_Nonsense_Mutation_p.K21*|FARS2_ENST00000324331.6_5'Flank	NM_020408.4	NP_065141.3	Q9HD34	LYRM4_HUMAN	LYR motif containing 4	21					small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)				endometrium(1)	1	Ovarian(93;0.11)	all_hematologic(90;0.0901)				CTGAAACGCTTGCTCTCTCTC	0.627																																					p.K21X	NSCLC(130;1006 2426 17608 36797)	Atlas-SNP	.											.	LYRM4	5	.	0			c.A61T						PASS	.						25	24	24					6																	5260906		2161	4232	6393	SO:0001587	stop_gained	57128	exon1			AACGCTTGCTCTC	AF258559	CCDS4493.1, CCDS54961.1	6p25.1	2008-02-05	2006-09-19	2006-09-19	ENSG00000214113	ENSG00000214113		"LYR motif containing"	21365	protein-coding gene	gene with protein product		613311	"chromosome 6 open reading frame 149"	C6orf149			Standard	XM_005249239		Approved	CGI-203, ISD11	uc021ykw.1	Q9HD34	OTTHUMG00000014173	ENST00000330636.4:c.61A>T	chr6.hg19:g.5260906T>A	ENSP00000418787:p.Lys21*	6.0	0.0	.		13.0	9.0	.	NM_020408	A8K543|Q5XKP1	Nonsense_Mutation	SNP	ENST00000330636.4	hg19	CCDS4493.1	.	.	.	.	.	.	.	.	.	.	T	40	8.023762	0.98616	.	.	ENSG00000214113	ENST00000468929;ENST00000330636;ENST00000464010;ENST00000480566;ENST00000500576	.	.	.	5.04	1.08	0.20341	.	0.185374	0.32753	U	0.005684	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05351	T	0.99	-6.0522	1.2294	0.01940	0.1825:0.1031:0.1903:0.5241	.	.	.	.	X	21	.	ENSP00000418787:K21X	K	-	1	0	LYRM4	5205905	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	0.725000	0.25970	1.898000	0.54952	0.533000	0.62120	AAG	.	.	.	none		0.627	LYRM4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353461.3	NM_020408		A	5260906	T	A	5260906	4	1	203	1	0	0	0	0	0	1	0	0	9128	1821	63	5	504	5	LYRM4	6	5260906	Nonsense_Mutation	SNP	T	TCGA-IA-A40X-01A-11D-A25F-10		5260906	165854161	10	12270											
C7orf31	136895	hgsc.bcm.edu	37	chr7	25182389	25182389	+	Missense_Mutation	SNP	T	T	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	ggagcgaaggttttaggaggTtttgggtagaatactggctt	9	13	16	3	1	0	1	0	0	0	1	0	4	0	3	0	6	2	4	0	6	5	7			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr7:25182389T>G	ENST00000409280.1	-	8	1037	c.729A>C	c.(727-729)aaA>aaC	p.K243N	C7orf31_ENST00000283905.3_Missense_Mutation_p.K243N			Q8N865	CG031_HUMAN	chromosome 7 open reading frame 31	243										autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|skin(2)|stomach(1)	14						TTTTAGGAGGTTTTGGGTAGA	0.378																																					p.K243N		Atlas-SNP	.											.	C7orf31	53	.	0			c.A729C						PASS	.						91	98	95					7																	25182389		2203	4300	6503	SO:0001583	missense	136895	exon8			AGGAGGTTTTGGG	AK097248	CCDS5394.1	7p15.2	2011-11-24			ENSG00000153790	ENSG00000153790			21722	protein-coding gene	gene with protein product							Standard	NM_138811		Approved		uc003sxn.1	Q8N865	OTTHUMG00000128497	ENST00000409280.1:c.729A>C	chr7.hg19:g.25182389T>G	ENSP00000386604:p.Lys243Asn	81.0	0.0	.		89.0	38.0	.	NM_138811	A4D165|Q6MZV8|Q6P989|Q7LE28|Q86XK1|Q8N1H5|Q96BN4	Missense_Mutation	SNP	ENST00000409280.1	hg19	CCDS5394.1	.	.	.	.	.	.	.	.	.	.	T	16.47	3.131855	0.56828	.	.	ENSG00000153790	ENST00000409280;ENST00000283905	T;T	0.08720	3.06;3.06	5.51	3.06	0.35304	.	0.133847	0.47093	D	0.000247	T	0.21267	0.0512	M	0.65975	2.015	0.30063	N	0.810728	D	0.76494	0.999	D	0.74674	0.984	T	0.03597	-1.1021	10	0.40728	T	0.16	-1.5455	7.6462	0.28321	0.0:0.3231:0.0:0.6769	.	243	Q8N865	CG031_HUMAN	N	243	ENSP00000386604:K243N;ENSP00000283905:K243N	ENSP00000283905:K243N	K	-	3	2	C7orf31	25148914	0.998000	0.40836	1.000000	0.80357	0.986000	0.74619	0.178000	0.16820	0.357000	0.24183	0.397000	0.26171	AAA	.	.	.	none		0.378	C7orf31-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326929.1	NM_138811		G	25182389	T	G	25182389	3	3	203	1	0	0	0	0	1	0	0	0	2389	1722	60	5	1055	5	C7orf31	7	25182389	Missense_Mutation	SNP	T	TCGA-IA-A40X-01A-11D-A25F-10		25182389	133956274	11	12271											
C9orf153	389766	hgsc.bcm.edu	37	chr9	88844472	88844472	+	Missense_Mutation	SNP	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	ctgaacattgaggaagggtgGcttctctattgtcctcagct	8	13	11	9	0	2	2	1	2	1	0	4	3	3	3	1	3	2	2	1	3	3	4			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr9:88844472G>A	ENST00000376001.3	-	2	127	c.47C>T	c.(46-48)gCc>gTc	p.A16V	C9orf153_ENST00000339137.3_Missense_Mutation_p.A16V|C9orf153_ENST00000469914.1_5'UTR	NM_001276366.1	NP_001263295.1	Q5TBE3	CI153_HUMAN	chromosome 9 open reading frame 153	16										breast(1)|lung(1)	2						AGGAAGGGTGGCTTCTCTATT	0.393																																					p.A16V		Atlas-SNP	.											.	C9orf153	10	.	0			c.C47T						PASS	.						173	130	144					9																	88844472		2203	4300	6503	SO:0001583	missense	389766	exon3			AGGGTGGCTTCTC		CCDS35055.1, CCDS35055.2	9q22.1	2012-04-03			ENSG00000187753	ENSG00000187753			31456	protein-coding gene	gene with protein product							Standard	NM_001276366		Approved	bA507D14.1	uc031teh.1	Q5TBE3	OTTHUMG00000020134	ENST00000376001.3:c.47C>T	chr9.hg19:g.88844472G>A	ENSP00000365169:p.Ala16Val	105.0	0.0	.		103.0	37.0	.	NM_001276368	Q5TBE4	Missense_Mutation	SNP	ENST00000376001.3	hg19	CCDS35055.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.166595	0.38217	.	.	ENSG00000187753	ENST00000339137;ENST00000376001	T;T	0.43294	0.95;0.95	3.33	-2.4	0.06583	.	1.675050	0.04061	N	0.306344	T	0.22704	0.0548	N	0.24115	0.695	0.09310	N	1	P;P	0.42584	0.784;0.642	B;B	0.33690	0.168;0.089	T	0.15093	-1.0449	10	0.52906	T	0.07	.	2.4955	0.04621	0.1061:0.1403:0.2414:0.5123	.	16;16	Q5TBE3;Q5TBE3-2	CI153_HUMAN;.	V	16	ENSP00000344865:A16V;ENSP00000365169:A16V	ENSP00000344865:A16V	A	-	2	0	C9orf153	88034292	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.853000	0.04303	-0.543000	0.06240	0.655000	0.94253	GCC	.	.	.	none		0.393	C9orf153-003	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052913.1	NM_001010907		A	88844472	G	A	88844472	3	1	203	1	0	0	0	0	1	0	0	0	2466	1203	42	2	270	2	C9orf153	9	88844472	Missense_Mutation	SNP	G	TCGA-IA-A40X-01A-11D-A25F-10		88844472	52368959	12	12272											
CTNNA3	29119	hgsc.bcm.edu	37	chr10	67726425	67726425	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tctcagctttaacttgactgCagattttcagttggtgggag	8	15	11	7	0	2	2	2	1	1	1	3	3	2	3	0	2	3	3	0	2	1	6			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr10:67726425C>T	ENST00000433211.2	-	17	2519	c.2345G>A	c.(2344-2346)tGc>tAc	p.C782Y	CTNNA3_ENST00000373744.4_Missense_Mutation_p.C782Y|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						AACTTGACTGCAGATTTTCAG	0.438																																					p.C782Y		Atlas-SNP	.											.	CTNNA3	401	.	0			c.G2345A						PASS	.						114	109	111					10																	67726425		2203	4300	6503	SO:0001583	missense	29119	exon17			TGACTGCAGATTT	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.2345G>A	chr10.hg19:g.67726425C>T	ENSP00000389714:p.Cys782Tyr	124.0	0.0	.		131.0	53.0	.	NM_013266		Missense_Mutation	SNP	ENST00000433211.2	hg19	CCDS7269.1	.	.	.	.	.	.	.	.	.	.	C	19.15	3.771295	0.69992	.	.	ENSG00000183230	ENST00000433211;ENST00000373744;ENST00000373735	T;T;T	0.37915	1.17;1.17;1.17	5.41	3.56	0.40772	.	0.000000	0.64402	D	0.000004	T	0.39911	0.1096	M	0.75447	2.3	0.80722	D	1	P	0.37500	0.597	B	0.38562	0.276	T	0.36383	-0.9750	10	0.72032	D	0.01	-1.9994	10.42	0.44344	0.0:0.8383:0.0:0.1617	.	782	Q9UI47	CTNA3_HUMAN	Y	782;782;121	ENSP00000389714:C782Y;ENSP00000362849:C782Y;ENSP00000362840:C121Y	ENSP00000362840:C121Y	C	-	2	0	CTNNA3	67396431	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.776000	0.85560	0.771000	0.33359	0.650000	0.86243	TGC	.	.	.	none		0.438	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048282.2	NM_013266		T	67726425	C	T	67726425	3	4	203	1	0	0	0	0	1	0	0	0	4016	710	25	2	350	2	CTNNA3	10	67726425	Missense_Mutation	SNP	C	TCGA-IA-A40X-01A-11D-A25F-10		67726425	67808322	13	12273											
NUP98	4928	hgsc.bcm.edu	37	chr11	3744474	3744474	+	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	aaaagacgtttcttcactgcTtccttccagcccatttcgca	9	13	5	14	2	2	1	1	0	1	1	5	1	4	1	3	0	2	3	3	0	2	5			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr11:3744474T>A	ENST00000324932.7	-	16	2479	c.2059A>T	c.(2059-2061)Agc>Tgc	p.S687C	NUP98_ENST00000397004.4_Missense_Mutation_p.S687C|NUP98_ENST00000355260.3_Missense_Mutation_p.S687C|NUP98_ENST00000359171.4_Missense_Mutation_p.S687C|NUP98_ENST00000397007.4_Missense_Mutation_p.S704C	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	704					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		TCTTCACTGCTTCCTTCCAGC	0.433			T	"HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"	AML																																p.S704C		Atlas-SNP	.		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	NUP98	149	.	0			c.A2110T						PASS	.						181	154	163					11																	3744474		2201	4298	6499	SO:0001583	missense	4928	exon16			CACTGCTTCCTTC	AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"nucleoporin 98kD"			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.2059A>T	chr11.hg19:g.3744474T>A	ENSP00000316032:p.Ser687Cys	205.0	0.0	.		251.0	93.0	.	NM_005387	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Missense_Mutation	SNP	ENST00000324932.7	hg19	CCDS7746.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.985170	0.74474	.	.	ENSG00000110713	ENST00000324932;ENST00000359171;ENST00000355260;ENST00000397004;ENST00000397007	.	.	.	4.73	4.73	0.59995	.	0.000000	0.85682	D	0.000000	T	0.77046	0.4073	M	0.70275	2.135	0.53005	D	0.999969	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.85130	0.98;0.951;0.997;0.997	T	0.79546	-0.1759	9	0.62326	D	0.03	.	13.3986	0.60870	0.0:0.0:0.0:1.0	.	704;687;687;687	P52948-3;P52948-4;P52948-2;P52948-5	.;.;.;.	C	687;687;687;687;704	.	ENSP00000316032:S687C	S	-	1	0	NUP98	3701050	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.800000	0.62524	1.773000	0.52216	0.477000	0.44152	AGC	.	.	.	none		0.433	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320		A	3744474	T	A	3744474	3	1	203	1	0	0	0	0	1	0	0	0	10780	1609	56	5	3436	5	NUP98	11	3744474	Missense_Mutation	SNP	T	TCGA-IA-A40X-01A-11D-A25F-10		3744474	131262042	14	12274											
EFCAB4B	84766	hgsc.bcm.edu	37	chr12	3765545	3765545	+	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	cagtttctgctccagctcttGactgcgggcttgaaacctct	6	13	9	13	1	3	2	0	2	3	0	4	2	4	2	2	1	4	4	2	1	1	3			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr12:3765545G>T	ENST00000252322.1	-	9	1258	c.790C>A	c.(790-792)Caa>Aaa	p.Q264K	EFCAB4B_ENST00000440314.2_Missense_Mutation_p.Q264K|EFCAB4B_ENST00000444507.1_Missense_Mutation_p.Q264K	NM_032680.3	NP_116069.1	Q9BSW2	EFC4B_HUMAN		264					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)			TCCAGCTCTTGACTGCGGGCT	0.517																																					p.Q264K		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.C790A						PASS	.						117	98	105					12																	3765545		2203	4300	6503	SO:0001583	missense	84766	exon9			GCTCTTGACTGCG																												ENST00000252322.1:c.790C>A	chr12.hg19:g.3765545G>T	ENSP00000252322:p.Gln264Lys	85.0	0.0	.		109.0	37.0	.	NM_001144958	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000252322.1	hg19	CCDS8522.1	.	.	.	.	.	.	.	.	.	.	g	8.882	0.951842	0.18431	.	.	ENSG00000130038	ENST00000440314;ENST00000444507;ENST00000252322	T;T;T	0.21031	2.03;2.62;2.62	4.87	4.87	0.63330	.	0.650048	0.16394	N	0.216346	T	0.15003	0.0362	L	0.31294	0.92	0.27366	N	0.955823	B;B;B	0.22346	0.068;0.037;0.022	B;B;B	0.15484	0.006;0.013;0.006	T	0.10154	-1.0642	10	0.23302	T	0.38	-9.002	11.0361	0.47802	0.0:0.0:0.8142:0.1858	.	264;264;264	D7UEQ6;Q9BSW2-2;Q9BSW2	.;.;EFC4B_HUMAN	K	264	ENSP00000409382:Q264K;ENSP00000412496:Q264K;ENSP00000252322:Q264K	ENSP00000252322:Q264K	Q	-	1	0	EFCAB4B	3635806	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	3.957000	0.56730	2.385000	0.81259	0.556000	0.70494	CAA	.	.	.	none		0.517	EFCAB4B-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398673.1			T	3765545	G	T	3765545	3	4	203	1	0	0	0	0	1	0	0	0	4939	1299	45	4	1645	4	EFCAB4B	12	3765545	Missense_Mutation	SNP	G	TCGA-IA-A40X-01A-11D-A25F-10		3765545	130086350	15	12275											
IL21R	50615	hgsc.bcm.edu	37	chr16	27445763	27445763	+	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	tccaccccagcacgctcaccCttacctggtaagtagccggg	8	7	9	17	2	1	0	1	0	0	0	2	0	2	0	6	2	3	4	6	2	3	3			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr16:27445763C>G	ENST00000337929.3	+	3	618	c.145C>G	c.(145-147)Ctt>Gtt	p.L49V	IL21R_ENST00000395754.4_Missense_Mutation_p.L49V|IL21R_ENST00000564089.1_Missense_Mutation_p.L49V|IL21R_ENST00000395755.1_Missense_Mutation_p.L49V	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	49	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)			breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						CACGCTCACCCTTACCTGGTA	0.612			T	BCL6	NHL																																p.L71V		Atlas-SNP	.		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	.	IL21R	95	.	0			c.C211G						PASS	.						92	67	75					16																	27445763		2197	4300	6497	SO:0001583	missense	50615	exon4			CTCACCCTTACCT	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.145C>G	chr16.hg19:g.27445763C>G	ENSP00000338010:p.Leu49Val	64.0	0.0	.		89.0	42.0	.	NM_181079	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Missense_Mutation	SNP	ENST00000337929.3	hg19	CCDS10630.1	.	.	.	.	.	.	.	.	.	.	c	3.641	-0.073506	0.07184	.	.	ENSG00000103522	ENST00000337929;ENST00000395755;ENST00000395754	D;D;D	0.97994	-4.65;-4.65;-4.65	4.39	0.877	0.19145	Fibronectin, type III (1);	55.521400	0.00166	N	0.000000	D	0.96272	0.8784	M	0.67953	2.075	0.80722	D	1	B	0.21225	0.053	B	0.17722	0.019	D	0.85799	0.1372	10	0.34782	T	0.22	-22.7421	6.3283	0.21257	0.3777:0.4383:0.184:0.0	.	49	Q9HBE5	IL21R_HUMAN	V	49	ENSP00000338010:L49V;ENSP00000379104:L49V;ENSP00000379103:L49V	ENSP00000338010:L49V	L	+	1	0	IL21R	27353264	0.011000	0.17503	0.032000	0.17829	0.011000	0.07611	0.263000	0.18478	0.530000	0.28619	0.555000	0.69702	CTT	.	.	.	none		0.612	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078		G	27445763	C	G	27445763	3	3	203	1	0	0	0	0	1	0	0	0	7678	681	24	4	151	4	IL21R	16	27445763	Missense_Mutation	SNP	C	TCGA-IA-A40X-01A-11D-A25F-10		27445763	62908990	16	12276											
IL21R	50615	hgsc.bcm.edu	37	chr16	27459874	27459874	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaatgggtgggtgcaccctTcactggctccagcctggagc	7	8	14	12	0	1	0	1	0	0	0	2	2	2	1	3	4	3	2	3	4	1	1			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr16:27459874T>C	ENST00000337929.3	+	9	1360	c.887T>C	c.(886-888)tTc>tCc	p.F296S	IL21R_ENST00000395754.4_Missense_Mutation_p.F296S|IL21R_ENST00000564583.1_3'UTR|IL21R-AS1_ENST00000563191.1_RNA|IL21R_ENST00000564089.1_Missense_Mutation_p.F296S|IL21R_ENST00000395755.1_Missense_Mutation_p.F296S	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	296					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						GGTGCACCCTTCACTGGCTCC	0.547			T	BCL6	NHL																																p.F318S		Atlas-SNP	.		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	.	IL21R	95	.	0			c.T953C						PASS	.						16	19	18					16																	27459874		2177	4255	6432	SO:0001583	missense	50615	exon10			CACCCTTCACTGG	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.887T>C	chr16.hg19:g.27459874T>C	ENSP00000338010:p.Phe296Ser	148.0	0.0	.		172.0	62.0	.	NM_181079	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Missense_Mutation	SNP	ENST00000337929.3	hg19	CCDS10630.1	.	.	.	.	.	.	.	.	.	.	T	10.95	1.495777	0.26774	.	.	ENSG00000103522	ENST00000337929;ENST00000395755;ENST00000395754	T;T;T	0.37411	1.2;1.2;1.2	5.24	2.9	0.33743	.	0.718376	0.13350	N	0.394470	T	0.26810	0.0656	M	0.64997	1.995	0.09310	N	1	P	0.41265	0.744	B	0.38327	0.271	T	0.17776	-1.0358	10	0.06365	T	0.9	-23.6851	4.7668	0.13135	0.1986:0.0:0.1808:0.6206	.	296	Q9HBE5	IL21R_HUMAN	S	296	ENSP00000338010:F296S;ENSP00000379104:F296S;ENSP00000379103:F296S	ENSP00000338010:F296S	F	+	2	0	IL21R	27367375	0.006000	0.16342	0.739000	0.30968	0.006000	0.05464	1.501000	0.35693	1.980000	0.57719	0.459000	0.35465	TTC	.	.	.	none		0.547	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078		C	27459874	T	C	27459874	3	2	203	1	0	0	0	0	1	0	0	0	7678	1783	62	3	917	3	IL21R	16	27459874	Missense_Mutation	SNP	T	TCGA-IA-A40X-01A-11D-A25F-10	14111	27459874	62894879	17	12277											
GSDMA	284110	hgsc.bcm.edu	37	chr17	38121980	38121980	+	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	tcacccgggccctggccagaCagctaaaccctcgaggggac	9	4	12	16	2	1	1	1	0	0	1	2	3	1	2	4	4	2	1	4	4	2	1			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr17:38121980C>T	ENST00000301659.4	+	2	158	c.40C>T	c.(40-42)Cag>Tag	p.Q14*		NM_178171.4	NP_835465.2	Q96QA5	GSDMA_HUMAN	gasdermin A	14					apoptotic process (GO:0006915)	perinuclear region of cytoplasm (GO:0048471)				NS(1)|endometrium(2)|large_intestine(3)|lung(1)	7						CCTGGCCAGACAGCTAAACCC	0.577																																					p.Q14X		Atlas-SNP	.											.	GSDMA	26	.	0			c.C40T						PASS	.						54	59	57					17																	38121980		1971	4144	6115	SO:0001587	stop_gained	284110	exon2			GCCAGACAGCTAA	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.40C>T	chr17.hg19:g.38121980C>T	ENSP00000301659:p.Gln14*	72.0	0.0	.		107.0	5.0	.	NM_178171	Q32MC5|Q86VE7|Q8N1M6	Nonsense_Mutation	SNP	ENST00000301659.4	hg19	CCDS45669.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.360594	0.82353	.	.	ENSG00000167914	ENST00000301659	.	.	.	5.36	4.38	0.52667	.	0.211121	0.33346	N	0.005003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-11.3738	12.1468	0.54028	0.0:0.8276:0.1724:0.0	.	.	.	.	X	14	.	ENSP00000301659:Q14X	Q	+	1	0	GSDMA	35375506	1.000000	0.71417	0.998000	0.56505	0.663000	0.39108	2.821000	0.48065	1.254000	0.44035	0.462000	0.41574	CAG	.	.	.	none		0.577	GSDMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446847.1	NM_178171		T	38121980	C	T	38121980	4	4	203	1	0	0	0	0	0	1	0	0	6823	479	17	2	42	2	GSDMA	17	38121980	Nonsense_Mutation	SNP	C	TCGA-IA-A40X-01A-11D-A25F-10		38121980	43073230	18	12278											
TRIM37	4591	hgsc.bcm.edu	37	chr17	57134407	57134407	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtgaaccatctctacacgaTattcatatctaaaattgaaa	16	12	5	8	1	3	2	1	2	2	0	4	3	3	2	1	1	2	0	1	1	7	6			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr17:57134407T>C	ENST00000262294.7	-	13	1287	c.1028A>G	c.(1027-1029)tAt>tGt	p.Y343C	TRIM37_ENST00000393065.2_Missense_Mutation_p.Y309C|TRIM37_ENST00000376149.3_Missense_Mutation_p.Y221C|RN7SL716P_ENST00000580539.1_RNA|TRIM37_ENST00000393066.3_Missense_Mutation_p.Y343C	NM_015294.3	NP_056109.1	O94972	TRI37_HUMAN	tripartite motif containing 37	343	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				aggresome assembly (GO:0070842)|negative regulation of centriole replication (GO:0046600)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autoubiquitination (GO:0051865)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisome (GO:0005777)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(13)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					CTCTACACGATATTCATATCT	0.318									Mulibrey Nanism																												p.Y343C		Atlas-SNP	.											.	TRIM37	105	.	0			c.A1028G						PASS	.						63	61	62					17																	57134407		2203	4300	6503	SO:0001583	missense	4591	exon13	Familial Cancer Database	Perheentupa syndrome	ACACGATATTCAT	AB020705	CCDS32694.1, CCDS45746.1	17q	2014-02-17	2011-01-25	2001-11-30		ENSG00000108395		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	7523	protein-coding gene	gene with protein product	"RING-B-box-coiled-coil protein"	605073	"tripartite motif-containing 37"	MUL		9106536, 10888877	Standard	NM_015294		Approved	KIAA0898, POB1, TEF3	uc002iwy.4	O94972		ENST00000262294.7:c.1028A>G	chr17.hg19:g.57134407T>C	ENSP00000262294:p.Tyr343Cys	46.0	0.0	.		36.0	21.0	.	NM_015294	Q7Z3E6|Q8IYF7|Q8WYF7	Missense_Mutation	SNP	ENST00000262294.7	hg19	CCDS32694.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.164224	0.78339	.	.	ENSG00000108395	ENST00000393066;ENST00000262294;ENST00000376149;ENST00000393065	T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16	5.43	5.43	0.79202	TRAF-type (1);TRAF-like (1);MATH (3);	0.000000	0.85682	D	0.000000	T	0.81635	0.4864	M	0.86420	2.815	0.80722	D	1	D;D;P	0.89917	1.0;1.0;0.943	D;D;P	0.87578	0.998;0.998;0.896	D	0.84579	0.0660	10	0.56958	D	0.05	-9.1299	15.4842	0.75551	0.0:0.0:0.0:1.0	.	309;221;343	F8WEE6;O94972-2;O94972	.;.;TRI37_HUMAN	C	343;343;221;309	ENSP00000376785:Y343C;ENSP00000262294:Y343C;ENSP00000365319:Y221C;ENSP00000376784:Y309C	ENSP00000262294:Y343C	Y	-	2	0	TRIM37	54489189	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.036000	0.88901	2.048000	0.60808	0.482000	0.46254	TAT	.	.	.	none		0.318	TRIM37-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445930.1	NM_015294		C	57134407	T	C	57134407	3	2	203	1	0	0	0	0	1	0	0	0	16523	1406	49	3	1922	3	TRIM37	17	57134407	Missense_Mutation	SNP	T	TCGA-IA-A40X-01A-11D-A25F-10	19012427	57134407	24060803	19	12279											
ZNF536	9745	hgsc.bcm.edu	37	chr19	30936011	30936011	+	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	gcggctgccaaggctgcggaGatggaccccgtgaacagcta	9	5	15	12	3	0	2	0	1	0	1	0	4	0	3	3	4	4	3	3	4	3	1			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr19:30936011G>C	ENST00000355537.3	+	2	1689	c.1542G>C	c.(1540-1542)gaG>gaC	p.E514D		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	514					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)					AGGCTGCGGAGATGGACCCCG	0.632																																					p.E514D		Atlas-SNP	.											.	ZNF536	424	.	0			c.G1542C						PASS	.						38	43	42					19																	30936011		2202	4299	6501	SO:0001583	missense	9745	exon2			TGCGGAGATGGAC		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.1542G>C	chr19.hg19:g.30936011G>C	ENSP00000347730:p.Glu514Asp	31.0	0.0	.		44.0	21.0	.	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	hg19	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	G	15.44	2.833785	0.50951	.	.	ENSG00000198597	ENST00000355537	T	0.16743	2.32	5.53	2.25	0.28309	.	0.000000	0.85682	D	0.000000	T	0.33962	0.0881	M	0.64404	1.975	0.41871	D	0.99027	D;D	0.69078	0.997;0.997	D;D	0.72625	0.978;0.978	T	0.02020	-1.1228	10	0.51188	T	0.08	-39.7837	9.9979	0.41911	0.2217:0.0:0.7783:0.0	.	514;514	A7E228;O15090	.;ZN536_HUMAN	D	514	ENSP00000347730:E514D	ENSP00000347730:E514D	E	+	3	2	ZNF536	35627851	1.000000	0.71417	0.993000	0.49108	0.967000	0.64934	1.738000	0.38207	0.276000	0.22118	0.655000	0.94253	GAG	.	.	.	none		0.632	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		C	30936011	G	C	30936011	3	2	203	1	0	0	0	0	1	0	0	0	17986	933	33	4	1544	4	ZNF536	19	30936011	Missense_Mutation	SNP	G	TCGA-IA-A40X-01A-11D-A25F-10		30936011	28192972	20	12280											
KCNN4	3783	hgsc.bcm.edu	37	chr19	44278354	44278354	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaccctcacctctcggccaCggacagcacccaggcggtgg	7	5	11	18	3	3	0	2	0	1	0	4	1	3	1	4	5	1	1	4	5	0	0			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr19:44278354C>T	ENST00000262888.3	-	3	1068	c.673G>A	c.(673-675)Gtg>Atg	p.V225M		NM_002250.2	NP_002241.1	O15554	KCNN4_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	225					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)	CTCTCGGCCACGGACAGCACC	0.677											OREG0025535	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V225M		Atlas-SNP	.											.	KCNN4	37	.	0			c.G673A						PASS	.						17	19	18					19																	44278354		2196	4295	6491	SO:0001583	missense	3783	exon3			CGGCCACGGACAG	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.673G>A	chr19.hg19:g.44278354C>T	ENSP00000262888:p.Val225Met	41.0	0.0	.	922	89.0	48.0	.	NM_002250	Q53XR4	Missense_Mutation	SNP	ENST00000262888.3	hg19	CCDS12630.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.961648	0.74016	.	.	ENSG00000104783	ENST00000262888;ENST00000407385	T	0.24538	1.85	4.31	4.31	0.51392	Ion transport 2 (1);	0.149552	0.43416	D	0.000563	T	0.41834	0.1176	L	0.42245	1.32	0.40618	D	0.981731	D;D	0.76494	0.999;0.999	D;D	0.70487	0.969;0.961	T	0.36529	-0.9744	10	0.56958	D	0.05	-28.677	14.7241	0.69329	0.0:1.0:0.0:0.0	.	119;225	D1MQ10;O15554	.;KCNN4_HUMAN	M	225;93	ENSP00000262888:V225M	ENSP00000262888:V225M	V	-	1	0	KCNN4	48970194	0.982000	0.34865	0.985000	0.45067	0.977000	0.68977	2.272000	0.43373	2.104000	0.64026	0.478000	0.44815	GTG	.	.	.	none		0.677	KCNN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463598.1	NM_002250		T	44278354	C	T	44278354	3	4	203	1	0	0	0	0	1	0	0	0	8088	536	19	1	634	1	KCNN4	19	44278354	Missense_Mutation	SNP	C	TCGA-IA-A40X-01A-11D-A25F-10	13342343	44278354	14850629	21	12281											
C20orf185	359710	hgsc.bcm.edu	37	chr20	31660577	31660577	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcttaatatcaatttttccaAttcagttctggagatcgtag	11	17	6	7	1	4	1	2	0	2	1	6	2	5	1	1	1	0	2	1	1	5	7			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr20:31660577A>G	ENST00000375494.3	+	14	1379	c.1379A>G	c.(1378-1380)aAt>aGt	p.N460S		NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	460					innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										AATTTTTCCAATTCAGTTCTG	0.473																																					p.N460S		Atlas-SNP	.											.	.	.	.	0			c.A1379G						PASS	.						156	143	148					20																	31660577		2203	4300	6503	SO:0001583	missense	359710	exon14			TTTCCAATTCAGT	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.1379A>G	chr20.hg19:g.31660577A>G	ENSP00000364643:p.Asn460Ser	191.0	0.0	.		163.0	62.0	.	NM_182658	Q5TDX7	Missense_Mutation	SNP	ENST00000375494.3	hg19	CCDS13212.1	.	.	.	.	.	.	.	.	.	.	A	1.299	-0.605319	0.03717	.	.	ENSG00000186190	ENST00000375494	T	0.09255	3.0	4.64	-3.29	0.05017	.	0.321650	0.26258	N	0.025402	T	0.07638	0.0192	L	0.53561	1.675	0.24245	N	0.995343	B	0.02656	0.0	B	0.08055	0.003	T	0.41413	-0.9510	10	0.15499	T	0.54	0.023	6.6155	0.22774	0.4895:0.4045:0.106:0.0	.	460	P59826	BPIB3_HUMAN	S	460	ENSP00000364643:N460S	ENSP00000364643:N460S	N	+	2	0	BPIFB3	31124238	0.983000	0.35010	0.689000	0.30133	0.014000	0.08584	-0.057000	0.11768	-0.887000	0.03961	-1.064000	0.02280	AAT	.	.	.	none		0.473	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658		G	31660577	A	G	31660577	3	3	203	1	0	0	0	0	1	0	0	0	2099	101	4	3	1433	3	C20orf185	20	31660577	Missense_Mutation	SNP	A	TCGA-IA-A40X-01A-11D-A25F-10		31660577	31364943	22	12282											
FAM83C	128876	hgsc.bcm.edu	37	chr20	33874582	33874582	+	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	ttagccgtttctcatccccaGacccagctccagccgtgcga	7	9	8	17	3	1	1	1	0	1	1	4	2	3	1	6	0	4	2	6	0	1	2			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr20:33874582G>C	ENST00000374408.3	-	4	2096	c.2000C>G	c.(1999-2001)tCt>tGt	p.S667C	EIF6_ENST00000462894.1_5'Flank|EIF6_ENST00000374443.3_5'Flank|EIF6_ENST00000374436.3_5'Flank|FAM83C-AS1_ENST00000429167.1_RNA|EIF6_ENST00000374450.3_5'Flank	NM_178468.5	NP_848563.1	Q9BQN1	FA83C_HUMAN	family with sequence similarity 83, member C	667										central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(18;0.00252)			CTCATCCCCAGACCCAGCTCC	0.617																																					p.S667C		Atlas-SNP	.											.	FAM83C	80	.	0			c.C2000G						PASS	.						54	48	50					20																	33874582		2203	4300	6503	SO:0001583	missense	128876	exon4			TCCCCAGACCCAG	AL121753	CCDS13251.1	20q11.22	2011-04-01	2006-03-23	2006-03-23	ENSG00000125998	ENSG00000125998			16121	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 128"	C20orf128			Standard	NM_178468		Approved	dJ614O4.7	uc021wck.1	Q9BQN1	OTTHUMG00000032332	ENST00000374408.3:c.2000C>G	chr20.hg19:g.33874582G>C	ENSP00000363529:p.Ser667Cys	173.0	0.0	.		236.0	101.0	.	NM_178468	Q14D67|Q5JWN6|Q8N276	Missense_Mutation	SNP	ENST00000374408.3	hg19	CCDS13251.1	.	.	.	.	.	.	.	.	.	.	G	9.533	1.111448	0.20714	.	.	ENSG00000125998	ENST00000374408	T	0.11385	2.78	4.93	3.99	0.46301	.	1.069840	0.07374	N	0.886296	T	0.15392	0.0371	L	0.59436	1.845	0.09310	N	1	P	0.50369	0.934	B	0.43916	0.436	T	0.23691	-1.0181	10	0.87932	D	0	-20.9594	6.8394	0.23955	0.0917:0.0:0.7235:0.1848	.	667	Q9BQN1	FA83C_HUMAN	C	667	ENSP00000363529:S667C	ENSP00000363529:S667C	S	-	2	0	FAM83C	33337996	0.485000	0.25972	0.025000	0.17156	0.218000	0.24690	2.726000	0.47302	1.235000	0.43724	0.462000	0.41574	TCT	.	.	.	none		0.617	FAM83C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078854.3			C	33874582	G	C	33874582	3	2	203	1	0	0	0	0	1	0	0	0	5642	942	33	4	247	4	FAM83C	20	33874582	Missense_Mutation	SNP	G	TCGA-IA-A40X-01A-11D-A25F-10	2214005	33874582	29150938	23	12283											
TMPRSS3	64699	hgsc.bcm.edu	37	chr21	43802332	43802332	+	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	cctggatggtccatgacttgGggaggtacaagctgaaatga	11	9	14	7	0	0	3	0	3	0	0	1	5	1	5	2	5	2	2	2	5	3	2			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr21:43802332G>C	ENST00000291532.3	-	9	1749	c.794C>G	c.(793-795)cCc>cGc	p.P265R	TMPRSS3_ENST00000380399.1_Missense_Mutation_p.P349R|TMPRSS3_ENST00000398397.3_Missense_Mutation_p.P265R|TMPRSS3_ENST00000433957.2_Missense_Mutation_p.P265R|TMPRSS3_ENST00000398405.1_Missense_Mutation_p.P263R|TMPRSS3_ENST00000474596.1_5'UTR	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3	265	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular sodium ion homeostasis (GO:0006883)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						CCATGACTTGGGGAGGTACAA	0.493																																					p.P265R		Atlas-SNP	.											.	TMPRSS3	40	.	0			c.C794G						PASS	.						68	51	57					21																	43802332		2203	4300	6503	SO:0001583	missense	64699	exon9			GACTTGGGGAGGT	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.794C>G	chr21.hg19:g.43802332G>C	ENSP00000291532:p.Pro265Arg	67.0	0.0	.		70.0	27.0	.	NM_001256317	D3DSJ6|Q5USC7|Q6ZMC3	Missense_Mutation	SNP	ENST00000291532.3	hg19	CCDS13686.1	.	.	.	.	.	.	.	.	.	.	G	19.58	3.853752	0.71719	.	.	ENSG00000160183	ENST00000291532;ENST00000433957;ENST00000398405;ENST00000380399;ENST00000398397	D;D;D;D;D	0.88586	-2.4;-2.4;-2.4;-2.4;-2.4	4.8	4.8	0.61643	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.64402	D	0.000001	D	0.92984	0.7767	L	0.58428	1.81	0.53688	D	0.999975	D;D;P;D	0.76494	0.998;0.999;0.949;0.999	D;D;P;D	0.74348	0.977;0.983;0.803;0.982	D	0.92525	0.6028	9	.	.	.	.	17.8827	0.88845	0.0:0.0:1.0:0.0	.	265;265;265;263	P57727-3;P57727-5;P57727;B7WPR2	.;.;TMPS3_HUMAN;.	R	265;265;263;349;265	ENSP00000291532:P265R;ENSP00000411013:P265R;ENSP00000381442:P263R;ENSP00000369762:P349R;ENSP00000381434:P265R	.	P	-	2	0	TMPRSS3	42675401	1.000000	0.71417	1.000000	0.80357	0.757000	0.42996	7.925000	0.87563	2.213000	0.71641	0.655000	0.94253	CCC	.	.	.	none		0.493	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1			C	43802332	G	C	43802332	3	2	203	1	0	0	0	0	1	0	0	0	16260	1232	43	4	673	4	TMPRSS3	21	43802332	Missense_Mutation	SNP	G	TCGA-IA-A40X-01A-11D-A25F-10		43802332	4327563	24	12284											
MMP11	4320	hgsc.bcm.edu	37	chr22	24125618	24125618	+	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	gctatgcctacttcctgcgcGgccgcctctactggaagttt	5	12	10	14	3	1	0	0	0	1	0	2	1	2	1	4	2	4	2	4	2	4	5			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chr22:24125618G>T	ENST00000215743.3	+	8	1406	c.1354G>T	c.(1354-1356)Ggc>Tgc	p.G452C	AP000349.1_ENST00000598975.1_Silent_p.A176A	NM_005940.3	NP_005931.2	P24347	MMP11_HUMAN	matrix metallopeptidase 11 (stromelysin 3)	452					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)	CTTCCTGCGCGGCCGCCTCTA	0.622																																					p.G452C		Atlas-SNP	.											.	MMP11	53	.	0			c.G1354T						PASS	.						102	82	89					22																	24125618		2203	4300	6503	SO:0001583	missense	4320	exon8			CTGCGCGGCCGCC		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.1354G>T	chr22.hg19:g.24125618G>T	ENSP00000215743:p.Gly452Cys	116.0	0.0	.		166.0	21.0	.	NM_005940	Q5FX24|Q6PEZ6|Q9UC26	Missense_Mutation	SNP	ENST00000215743.3	hg19	CCDS13816.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.383170	0.82792	.	.	ENSG00000099953	ENST00000215743	T	0.10382	2.88	4.73	4.73	0.59995	Hemopexin/matrixin (2);	0.049339	0.85682	D	0.000000	T	0.45915	0.1366	H	0.95004	3.61	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.61549	-0.7040	10	0.87932	D	0	.	17.3138	0.87217	0.0:0.0:1.0:0.0	.	452	P24347	MMP11_HUMAN	C	452	ENSP00000215743:G452C	ENSP00000215743:G452C	G	+	1	0	MMP11	22455618	1.000000	0.71417	0.971000	0.41717	0.995000	0.86356	7.028000	0.76470	2.649000	0.89929	0.650000	0.86243	GGC	.	.	.	none		0.622	MMP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319891.2	NM_005940		T	24125618	G	T	24125618	3	4	203	1	0	0	0	0	1	0	0	0	9657	1116	39	4	1384	4	MMP11	22	24125618	Missense_Mutation	SNP	G	TCGA-IA-A40X-01A-11D-A25F-10		24125618	27178948	25	12285											
VCX	26609	hgsc.bcm.edu	37	chrX	7811790	7811790	+	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	gaaccactgagtcaggagagCgaggtggaagaaccactgag	14	4	15	8	1	1	4	1	2	0	2	1	8	1	5	2	3	3	0	2	3	3	0	rs200229312		TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chrX:7811790C>T	ENST00000381059.3	+	3	573	c.354C>T	c.(352-354)agC>agT	p.S118S	VCX_ENST00000341408.4_Silent_p.S118S	NM_013452.2	NP_038480.2	Q9H320	VCX1_HUMAN	variable charge, X-linked	118	10 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.|Glu-rich.				chromatin organization (GO:0006325)|ribosome assembly (GO:0042255)|spermatogenesis (GO:0007283)	nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.S118S(1)		NS(1)|endometrium(4)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	10		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				GTCAGGAGAGCGAGGTGGAAG	0.637																																					p.S118S		Atlas-SNP	.											.	VCX	28	.	1	Substitution - coding silent(1)	endometrium(1)	c.C354T						PASS	.						54	67	62					X																	7811790		2129	4090	6219	SO:0001819	synonymous_variant	26609	exon3			GGAGAGCGAGGTG	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.354C>T	chrX.hg19:g.7811790C>T		269.0	0.0	.		308.0	103.0	.	NM_013452	A0JNS5|Q4V774|Q9P0H3	Silent	SNP	ENST00000381059.3	hg19	CCDS14128.1																																																																																			.	.	.	weak		0.637	VCX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071474.1	NM_013452		T	7811790	C	T	7811790	2	4	203	1	0	0	0	0	0	0	0	1	17154	767	27	1		1	VCX	23	7811790	Silent	SNP	C	TCGA-IA-A40X-01A-11D-A25F-10		7811790	147458770	26	12286											
VCX2	51480	hgsc.bcm.edu	37	chrX	8138172	8138173	+	In_Frame_Ins	INS	-	-	TCCTGACTCAGTGGTTCCTCCAGCTCGGCC																															gtggttcttccacctcgctcINStcctgactcagggggtcgtg																										TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chrX:8138172_8138173insTCCTGACTCAGTGGTTCCTCCAGCTCGGCC	ENST00000317103.4	-	3	626_627	c.320_321insGGCCGAGCTGGAGGAACCACTGAGTCAGGA	c.(319-321)gag>gaGGCCGAGCTGGAGGAACCACTGAGTCAGGAg	p.107_107E>EAELEEPLSQE		NM_016378.2	NP_057462.2	Q9H322	VCX2_HUMAN	variable charge, X-linked 2	107	2 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.									endometrium(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				CCACCTCGCTCTCCTGACTCAG	0.653																																					p.E107delinsEAELEEPLSQE		Pindel	.											.	VCX2	16	.	0			c.321_322insGGCCGAGCTGGAGGAACCACTGAGTCAGGA						PASS	.																																			SO:0001652	inframe_insertion	51480	exon3			.	AF159127	CCDS35200.1	Xp22.32	2008-02-05			ENSG00000177504	ENSG00000177504			18158	protein-coding gene	gene with protein product		300532				10607842	Standard	NM_016378		Approved	VCX-2r, VCX-2R	uc004csb.3	Q9H322	OTTHUMG00000021105	ENST00000317103.4:c.320_321insGGCCGAGCTGGAGGAACCACTGAGTCAGGA	chrX.hg19:g.8138172_8138173insTCCTGACTCAGTGGTTCCTCCAGCTCGGCC	Exception_encountered	127.0	0.0	.		182.0	11.0	0.060	NM_016378	A3KPB6|Q4V9T2|Q9P0H5	In_Frame_Ins	INS	ENST00000317103.4	hg19	CCDS35200.1																																																																																			.	.	.	none		0.653	VCX2-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055690.1	NM_016378		TCCTGACTCAGTGGTTCCTCCAGCTCGGCC	8138173	-	TCCTGACTCAGTGGTTCCTCCAGCTCGGCC	8138172	7	5	203	1	0	1	1	0	0	0	0	0	17155	912	32	0	102	0	VCX2	23	8138172	In_Frame_Ins	INS	-	TCGA-IA-A40X-01A-11D-A25F-10	326382	8138172	147132388	27	12287											
FAM48B1	100130302	hgsc.bcm.edu	37	chrX	24382384	24382385	+	IGR	DNP	GC	GC	AT																															ctgctgctattgctgctgctGctgctgctgctgctgctgct																										TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chrX:24382384_24382385GC>AT								AC004552.1 (15361 upstream) : PDK3 (100952 downstream)																							tgctgctgctgctgctgctgct	0.579																																					p.A503T|p.A503V		Atlas-SNP	.											.	.	.	.	0			c.G1507A|c.C1508T						PASS	.																																			SO:0001628	intergenic_variant	100130302	exon1			GCTGCTGCTGCTG|CTGCTGCTGCTGC																													chrX.hg19:g.24382384_24382385delinsAT		249.0|244.0	0.0	.		330.0|324.0	22.0|25.0	.	NM_001136234		Missense_Mutation	SNP		hg19																																																																																				.	.	.	none	0	0.579									AT	24382385	GC	AT	24382384	1	1	203	0	1	0	0	0	0	0	0	0	5580	1319	46	2		2	FAM48B1	23	24382384	IGR	DNP	GC	TCGA-IA-A40X-01A-11D-A25F-10	16244212	24382384	130888176	28	12288											
GAB3	139716	hgsc.bcm.edu	37	chrX	153908429	153908429	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctgcatgggggctggtgAtgctgaattgaagtccaggg	7	10	17	7	0	0	3	0	3	0	0	1	3	1	3	1	4	3	4	1	4	2	1			TCGA-IA-A40X-01A-11D-A25F-10	TCGA-IA-A40X-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e1217ebe-1826-41a9-b6c4-702100a66f5e	611a2445-8df1-4abd-bb6b-4954ee1dc47d	g.chrX:153908429A>G	ENST00000369575.3	-	9	1655	c.1624T>C	c.(1624-1626)Tca>Cca	p.S542P	GAB3_ENST00000424127.2_Missense_Mutation_p.S543P|GAB3_ENST00000496390.1_5'UTR	NM_001081573.1|NM_080612.2	NP_001075042.1|NP_542179.1	Q8WWW8	GAB3_HUMAN	GRB2-associated binding protein 3	542					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)					GGGGCTGGTGATGCTGAATTG	0.488																																					p.S543P		Atlas-SNP	.											.	GAB3	73	.	0			c.T1627C						PASS	.						205	201	202					X																	153908429		2203	4300	6503	SO:0001583	missense	139716	exon9			CTGGTGATGCTGA	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.1624T>C	chrX.hg19:g.153908429A>G	ENSP00000358588:p.Ser542Pro	145.0	0.0	.		149.0	57.0	.	NM_001081573	A6NHF8|E9PB44	Missense_Mutation	SNP	ENST00000369575.3	hg19	CCDS14760.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.60|17.60	3.430652|3.430652	0.62844|0.62844	.|.	.|.	ENSG00000160219|ENSG00000160219	ENST00000454973|ENST00000369575;ENST00000424127	.|T;T	.|0.28895	.|1.59;1.91	5.36|5.36	4.2|4.2	0.49525|0.49525	.|.	.|0.063412	.|0.64402	.|D	.|0.000004	T|T	0.54775|0.54775	0.1879|0.1879	M|M	0.84219|0.84219	2.685|2.685	0.52099|0.52099	D|D	0.999946|0.999946	.|D;D	.|0.76494	.|0.999;0.999	.|D;D	.|0.83275	.|0.996;0.996	T|T	0.55829|0.55829	-0.8079|-0.8079	5|10	.|0.72032	.|D	.|0.01	-5.3879|-5.3879	8.3095|8.3095	0.32062|0.32062	0.9048:0.0:0.0952:0.0|0.9048:0.0:0.0952:0.0	.|.	.|543;542	.|E9PB44;Q8WWW8	.|.;GAB3_HUMAN	T|P	23|542;543	.|ENSP00000358588:S542P;ENSP00000399588:S543P	.|ENSP00000358588:S542P	I|S	-|-	2|1	0|0	GAB3|GAB3	153561623|153561623	0.998000|0.998000	0.40836|0.40836	0.338000|0.338000	0.25549|0.25549	0.747000|0.747000	0.42532|0.42532	3.865000|3.865000	0.56033|0.56033	0.695000|0.695000	0.31675|0.31675	0.412000|0.412000	0.27726|0.27726	ATC|TCA	.	.	.	none		0.488	GAB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061192.2	NM_001081573		G	153908429	A	G	153908429	3	3	203	1	0	0	0	0	1	0	0	0	6157	333	12	3	144	3	GAB3	23	153908429	Missense_Mutation	SNP	A	TCGA-IA-A40X-01A-11D-A25F-10	129526045	153908429	1362131	29	12289											
VCAM1	7412	hgsc.bcm.edu	37	chr1	101198018	101198018	+	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	tggtcagcccttcctccatcCtggaggaaggcagttctgtg	6	11	12	12	0	2	0	1	0	1	0	5	2	5	2	4	4	1	2	4	4	1	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr1:101198018C>G	ENST00000294728.2	+	7	1671	c.1570C>G	c.(1570-1572)Ctg>Gtg	p.L524V	VCAM1_ENST00000347652.2_Missense_Mutation_p.L432V|VCAM1_ENST00000370119.4_Missense_Mutation_p.L462V|VCAM1_ENST00000370115.1_Missense_Mutation_p.L325V	NM_001078.3	NP_001069.1	P19320	VCAM1_HUMAN	vascular cell adhesion molecule 1	524	Ig-like C2-type 6.				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)	TTCCTCCATCCTGGAGGAAGG	0.537																																					p.L524V		Atlas-SNP	.											.	VCAM1	111	.	0			c.C1570G						PASS	.						66	70	69					1																	101198018		2203	4300	6503	SO:0001583	missense	7412	exon7			TCCATCCTGGAGG	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.1570C>G	chr1.hg19:g.101198018C>G	ENSP00000294728:p.Leu524Val	63.0	0.0	.		27.0	9.0	.	NM_001078	A8K6R7|B4DKS4|E9PDD1|Q6NUP8	Missense_Mutation	SNP	ENST00000294728.2	hg19	CCDS773.1	.	.	.	.	.	.	.	.	.	.	C	2.960	-0.214840	0.06101	.	.	ENSG00000162692	ENST00000370119;ENST00000347652;ENST00000294728;ENST00000370115	T;T;T;T	0.11712	2.75;2.75;2.75;2.75	5.57	-3.82	0.04281	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.317042	0.32884	N	0.005531	T	0.00524	0.0017	N	0.01048	-1.04	0.09310	N	1	B;B;B	0.19706	0.001;0.038;0.0	B;B;B	0.23150	0.007;0.044;0.008	T	0.33675	-0.9859	10	0.02654	T	1	-0.0111	4.6967	0.12808	0.1001:0.1771:0.5014:0.2214	.	462;432;524	E9PDD1;P19320-2;P19320	.;.;VCAM1_HUMAN	V	462;432;524;325	ENSP00000359137:L462V;ENSP00000304611:L432V;ENSP00000294728:L524V;ENSP00000359133:L325V	ENSP00000294728:L524V	L	+	1	2	VCAM1	100970606	0.000000	0.05858	0.002000	0.10522	0.771000	0.43674	-1.681000	0.01937	-0.367000	0.08052	-0.140000	0.14226	CTG	.	.	.	none		0.537	VCAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030213.1	NM_001078		G	101198018	C	G	101198018	3	3	204	1	0	0	0	0	1	0	0	0	17149	680	24	4	1596	4	VCAM1	1	101198018	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10		101198018	148052603	1	12290											
TTC24	164118	hgsc.bcm.edu	37	chr1	156552861	156552861	+	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	ggggcagcggtgggagcaggGccggagctttggcagcctgg	5	5	22	9	2	0	0	0	0	0	0	0	2	0	2	2	8	4	4	2	8	0	1			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr1:156552861G>C	ENST00000368237.3	+	3	938	c.938G>C	c.(937-939)gGc>gCc	p.G313A	TTC24_ENST00000478081.1_Intron|TTC24_ENST00000368236.3_Missense_Mutation_p.G313A			A2A3L6	TTC24_HUMAN	tetratricopeptide repeat domain 24	313										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)					TGGGAGCAGGGCCGGAGCTTT	0.657																																					p.G313A		Atlas-SNP	.											.	TTC24	46	.	0			c.G938C						PASS	.						33	39	37					1																	156552861		2031	4169	6200	SO:0001583	missense	164118	exon4			AGCAGGGCCGGAG		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.938G>C	chr1.hg19:g.156552861G>C	ENSP00000357220:p.Gly313Ala	190.0	0.0	.		183.0	38.0	.	NM_001105669	Q5T3H7	Missense_Mutation	SNP	ENST00000368237.3	hg19	CCDS53379.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.276|7.276	0.608179|0.608179	0.14002|0.14002	.|.	.|.	ENSG00000187862|ENSG00000187862	ENST00000340086;ENST00000413282|ENST00000368236;ENST00000368237	.|T;T	.|0.70869	.|-0.52;-0.52	4.72|4.72	4.72|4.72	0.59763|0.59763	.|Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	.|0.000000	.|0.48767	.|D	.|0.000175	T|T	0.56761|0.56761	0.2007|0.2007	L|L	0.33245|0.33245	0.995|0.995	0.37041|0.37041	D|D	0.897135|0.897135	.|D	.|0.62365	.|0.991	.|P	.|0.60541	.|0.876	T|T	0.59402|0.59402	-0.7461|-0.7461	5|10	.|0.02654	.|T	.|1	-14.4059|-14.4059	13.0458|13.0458	0.58925|0.58925	0.0:0.163:0.8369:0.0|0.0:0.163:0.8369:0.0	.|.	.|313	.|A2A3L6	.|TTC24_HUMAN	P|A	86;78|313	.|ENSP00000357219:G313A;ENSP00000357220:G313A	.|ENSP00000357219:G313A	A|G	+|+	1|2	0|0	TTC24|TTC24	154819485|154819485	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.445000|4.445000	0.60007|0.60007	2.474000|2.474000	0.83562|0.83562	0.455000|0.455000	0.32223|0.32223	GCC|GGC	.	.	.	none		0.657	TTC24-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158547.1	XM_089384		C	156552861	G	C	156552861	3	2	204	1	0	0	0	0	1	0	0	0	16704	1203	42	4	948	4	TTC24	1	156552861	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	55354843	156552861	92697760	2	12291											
SPTA1	6708	hgsc.bcm.edu	37	chr1	158596772	158596772	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctatcttggaagaaatctctTtgttctgactttcctcctgc	7	17	6	11	0	3	2	0	1	3	1	6	3	5	3	2	1	1	1	2	1	3	5			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr1:158596772T>C	ENST00000368147.4	-	41	5870	c.5690A>G	c.(5689-5691)aAa>aGa	p.K1897R		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1897					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)					AGAAATCTCTTTGTTCTGACT	0.413																																					p.K1897R		Atlas-SNP	.											.	SPTA1	720	.	0			c.A5690G						PASS	.						127	125	126					1																	158596772		1849	4090	5939	SO:0001583	missense	6708	exon41			ATCTCTTTGTTCT	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.5690A>G	chr1.hg19:g.158596772T>C	ENSP00000357129:p.Lys1897Arg	97.0	0.0	.		127.0	19.0	.	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	T	12.07	1.827369	0.32329	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.53640	0.61;0.61	4.87	3.73	0.42828	.	.	.	.	.	T	0.15435	0.0372	N	0.21448	0.665	0.29575	N	0.849575	B	0.02656	0.0	B	0.12837	0.008	T	0.14643	-1.0465	9	0.46703	T	0.11	.	8.4299	0.32750	0.3124:0.0:0.0:0.6876	.	1897	P02549	SPTA1_HUMAN	R	1897;1894	ENSP00000357130:K1897R;ENSP00000357129:K1894R	ENSP00000357129:K1894R	K	-	2	0	SPTA1	156863396	0.976000	0.34144	0.910000	0.35882	0.968000	0.65278	0.874000	0.28065	0.864000	0.35578	0.460000	0.39030	AAA	.	.	.	none		0.413	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		C	158596772	T	C	158596772	3	2	204	1	0	0	0	0	1	0	0	0	15128	1841	64	3	1617	3	SPTA1	1	158596772	Missense_Mutation	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10	2043911	158596772	90653849	3	12292											
OLFML2B	25903	hgsc.bcm.edu	37	chr1	161989778	161989778	+	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	ccctcgcagggattgagggcCgatgggggtgctacacaggc	7	6	17	11	2	0	1	0	1	0	0	1	3	0	2	2	5	2	2	2	5	1	2	rs138821383		TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr1:161989778C>G	ENST00000294794.3	-	2	792	c.369G>C	c.(367-369)tcG>tcC	p.S123S	OLFML2B_ENST00000367940.2_Silent_p.S123S	NM_015441.1	NP_056256.1	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B	123					extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)			GATTGAGGGCCGATGGGGGTG	0.592																																					p.S123S		Atlas-SNP	.											.	OLFML2B	114	.	0			c.G369C						PASS	.						69	68	68					1																	161989778		2203	4300	6503	SO:0001819	synonymous_variant	25903	exon2			GAGGGCCGATGGG	BX648975	CCDS1236.1, CCDS72966.1	1q23.1	2008-02-05			ENSG00000162745	ENSG00000162745			24558	protein-coding gene	gene with protein product							Standard	XM_005245075		Approved	DKFZP586L151	uc001gbu.3	Q68BL8	OTTHUMG00000024047	ENST00000294794.3:c.369G>C	chr1.hg19:g.161989778C>G		149.0	0.0	.		190.0	8.0	.	NM_015441	B7ZA39|Q5VU96|Q6NX46|Q86X11|Q9Y3X6	Silent	SNP	ENST00000294794.3	hg19	CCDS1236.1																																																																																			.	C|1.000;T|0.000	.	alt		0.592	OLFML2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060552.2	NM_015441		G	161989778	C	G	161989778	2	3	204	1	0	0	0	0	0	0	0	1	10865	639	23	4		4	OLFML2B	1	161989778	Silent	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	3393006	161989778	87260843	4	12293											
HHIPL2	79802	hgsc.bcm.edu	37	chr1	222715413	222715413	+	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	gcctgtcccccgtccccagtGaatatgtacatatagccatc	9	10	7	15	1	0	1	0	1	0	0	3	1	2	1	6	0	2	1	6	0	5	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr1:222715413G>A	ENST00000343410.6	-	3	1117	c.1059C>T	c.(1057-1059)ttC>ttT	p.F353F		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	353					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)	p.F353F(1)		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)		CGTCCCCAGTGAATATGTACA	0.507																																					p.F353F		Atlas-SNP	.											HHIPL2,NS,carcinoma,0,1	HHIPL2	122	.	1	Substitution - coding silent(1)	stomach(1)	c.C1059T						PASS	.						69	66	67					1																	222715413		2203	4300	6503	SO:0001819	synonymous_variant	79802	exon3			CCCAGTGAATATG	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.1059C>T	chr1.hg19:g.222715413G>A		165.0	0.0	.		207.0	10.0	.	NM_024746	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Silent	SNP	ENST00000343410.6	hg19	CCDS1530.2																																																																																			.	.	.	none		0.507	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746		A	222715413	G	A	222715413	2	1	204	1	0	0	0	0	0	0	0	1	7101	1281	45	2		2	HHIPL2	1	222715413	Silent	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	60725635	222715413	26535208	5	12294											
RYR2	6262	hgsc.bcm.edu	37	chr1	237993878	237993878	+	Missense_Mutation	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	atgattacttcgacacagtgCcacatggctttgaaacccac	12	10	7	12	1	0	2	0	2	0	0	1	3	0	2	2	1	3	1	2	1	2	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr1:237993878C>T	ENST00000366574.2	+	103	15021	c.14704C>T	c.(14704-14706)Cca>Tca	p.P4902S	RYR2_ENST00000542537.1_Missense_Mutation_p.P4886S|RYR2_ENST00000360064.6_Missense_Mutation_p.P4908S	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4902			P -> L (in CPVT1). {ECO:0000269|PubMed:14571276}.		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)			CGACACAGTGCCACATGGCTT	0.433																																					p.P4902S		Atlas-SNP	.											RYR2,NS,carcinoma,0,1	RYR2	1273	.	0			c.C14704T						PASS	.						213	200	204					1																	237993878		1968	4170	6138	SO:0001583	missense	6262	exon103			ACAGTGCCACATG	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.14704C>T	chr1.hg19:g.237993878C>T	ENSP00000355533:p.Pro4902Ser	132.0	0.0	.		212.0	74.0	.	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	C	34	5.362728	0.95877	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.96774	-4.12;-4.08;-4.11	5.39	5.39	0.77823	.	0.000000	0.64402	D	0.000007	D	0.97539	0.9194	L	0.56280	1.765	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.98376	1.0556	10	0.87932	D	0	-8.5845	19.143	0.93452	0.0:1.0:0.0:0.0	.	4902	Q92736	RYR2_HUMAN	S	4902;4908;4886	ENSP00000355533:P4902S;ENSP00000353174:P4908S;ENSP00000443798:P4886S	ENSP00000353174:P4908S	P	+	1	0	RYR2	236060501	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.773000	0.85462	2.509000	0.84616	0.561000	0.74099	CCA	.	.	.	none		0.433	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237993878	C	T	237993878	3	4	204	1	0	0	0	0	1	0	0	0	13782	739	26	2	15114	2	RYR2	1	237993878	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	15278465	237993878	11256743	6	12295											
CHRM3	1131	hgsc.bcm.edu	37	chr1	240072456	240072456	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgtgacaaaaaaaagaggCgcaagcagcagtaccagcag	18	3	12	8	1	0	2	0	1	0	1	0	2	0	2	1	1	4	5	1	1	6	1			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr1:240072456C>T	ENST00000255380.4	+	5	2484	c.1705C>T	c.(1705-1707)Cgc>Tgc	p.R569C		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	569					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)	AAAAAAGAGGCGCAAGCAGCA	0.498																																					p.R569C		Atlas-SNP	.											.	CHRM3	118	.	0			c.C1705T						PASS	.						49	49	49					1																	240072456		2203	4300	6503	SO:0001583	missense	1131	exon5			AAGAGGCGCAAGC	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.1705C>T	chr1.hg19:g.240072456C>T	ENSP00000255380:p.Arg569Cys	161.0	0.0	.		210.0	18.0	.	NM_000740	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Missense_Mutation	SNP	ENST00000255380.4	hg19	CCDS1616.1	.	.	.	.	.	.	.	.	.	.	C	18.30	3.593426	0.66219	.	.	ENSG00000133019	ENST00000255380	T	0.38887	1.11	5.58	5.58	0.84498	.	0.120714	0.51477	D	0.000092	T	0.58637	0.2136	L	0.58101	1.795	0.80722	D	1	D	0.89917	1.0	P	0.57324	0.818	T	0.60459	-0.7259	10	0.72032	D	0.01	-16.0194	19.5758	0.95444	0.0:1.0:0.0:0.0	.	569	P20309	ACM3_HUMAN	C	569	ENSP00000255380:R569C	ENSP00000255380:R569C	R	+	1	0	CHRM3	238139079	0.996000	0.38824	0.992000	0.48379	0.986000	0.74619	3.339000	0.52135	2.632000	0.89209	0.655000	0.94253	CGC	.	.	.	none		0.498	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740		T	240072456	C	T	240072456	3	4	204	1	0	0	0	0	1	0	0	0	3380	768	27	1	1707	1	CHRM3	1	240072456	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	2078578	240072456	9178165	7	12296											
RAD51AP2	729475	hgsc.bcm.edu	37	chr2	17699184	17699184	+	Missense_Mutation	SNP	T	T	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	ctcatttctaattccatgtaTatcgtgtatagaggtgctgg	9	16	9	7	1	2	1	1	0	1	1	4	1	3	1	1	2	1	3	1	2	5	7			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr2:17699184T>G	ENST00000399080.2	-	1	522	c.499A>C	c.(499-501)Ata>Cta	p.I167L		NM_001099218.2	NP_001092688.1	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	167										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)					ATTCCATGTATATCGTGTATA	0.423																																					p.I167L		Atlas-SNP	.											.	RAD51AP2	134	.	0			c.A499C						PASS	.						64	62	63					2																	17699184		1913	4131	6044	SO:0001583	missense	729475	exon1			CATGTATATCGTG	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.499A>C	chr2.hg19:g.17699184T>G	ENSP00000382030:p.Ile167Leu	72.0	0.0	.		125.0	27.0	.	NM_001099218		Missense_Mutation	SNP	ENST00000399080.2	hg19	CCDS42656.1	.	.	.	.	.	.	.	.	.	.	T	10.22	1.291283	0.23564	.	.	ENSG00000214842	ENST00000399080	T	0.30182	1.54	3.6	-4.94	0.03057	.	.	.	.	.	T	0.18509	0.0444	N	0.19112	0.55	0.09310	N	1	B	0.16396	0.017	B	0.16289	0.015	T	0.21690	-1.0238	9	0.48119	T	0.1	.	12.4465	0.55653	0.0:0.7287:0.0:0.2713	.	167	Q09MP3	R51A2_HUMAN	L	167	ENSP00000382030:I167L	ENSP00000382030:I167L	I	-	1	0	RAD51AP2	17562665	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.991000	0.00657	-1.048000	0.03238	-0.290000	0.09829	ATA	.	.	.	none		0.423	RAD51AP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323801.3	NM_001099218		G	17699184	T	G	17699184	3	3	204	1	0	0	0	0	1	0	0	0	13000	1406	49	5	2992	5	RAD51AP2	2	17699184	Missense_Mutation	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10		17699184	225500189	8	12297											
DNMT3A	1788	hgsc.bcm.edu	37	chr2	25458669	25458669	+	Missense_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	gctttatggagtttgacctcGtagtaatggtcctcactttg	7	16	10	8	1	1	1	1	1	0	0	3	2	2	2	2	2	0	4	2	2	3	6			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr2:25458669G>A	ENST00000264709.3	-	22	2841	c.2504C>T	c.(2503-2505)aCg>aTg	p.T835M	DNMT3A_ENST00000321117.5_Missense_Mutation_p.T835M|DNMT3A_ENST00000474887.1_5'UTR|DNMT3A_ENST00000402667.1_Missense_Mutation_p.T612M|DNMT3A_ENST00000380746.4_Missense_Mutation_p.T646M	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	835	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTTTGACCTCGTAGTAATGGT	0.438			"Mis, F, N, S"		AML																																p.T835M		Atlas-SNP	.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	DNMT3A,rectum,carcinoma,+1,1	DNMT3A	1807	.	0			c.C2504T						PASS	.						171	155	160					2																	25458669		2203	4300	6503	SO:0001583	missense	1788	exon22			GACCTCGTAGTAA		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.2504C>T	chr2.hg19:g.25458669G>A	ENSP00000264709:p.Thr835Met	146.0	1.0	.		271.0	88.0	.	NM_175629	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Missense_Mutation	SNP	ENST00000264709.3	hg19	CCDS33157.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.953779	0.92660	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	D;D;D;D	0.97089	-4.24;-4.24;-4.24;-4.24	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	D	0.98617	0.9537	M	0.87827	2.91	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.991;0.997	D	0.99453	1.0941	10	0.72032	D	0.01	-6.841	18.1492	0.89669	0.0:0.0:1.0:0.0	.	835;646	Q9Y6K1;E9PEB8	DNM3A_HUMAN;.	M	646;835;835;612	ENSP00000370122:T646M;ENSP00000324375:T835M;ENSP00000264709:T835M;ENSP00000384237:T612M	ENSP00000264709:T835M	T	-	2	0	DNMT3A	25312173	1.000000	0.71417	0.993000	0.49108	0.988000	0.76386	9.697000	0.98697	2.717000	0.92951	0.650000	0.86243	ACG	.	.	.	none		0.438	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552		A	25458669	G	A	25458669	3	1	204	1	0	0	0	0	1	0	0	0	4678	1145	40	1	242	1	DNMT3A	2	25458669	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	7759485	25458669	217740704	9	12298											
CEBPZ	10153	hgsc.bcm.edu	37	chr2	37430124	37430124	+	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	atacaaataggctggaatcaTttaagtttcttttctttttt	11	20	5	5	0	3	0	1	0	2	0	3	1	3	1	0	2	1	2	0	2	5	10			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr2:37430124T>A	ENST00000234170.5	-	14	3057	c.2912A>T	c.(2911-2913)aAt>aTt	p.N971I	AC007390.5_ENST00000402297.1_3'UTR|AC007390.5_ENST00000406711.1_Intron|AC007390.5_ENST00000392061.2_Intron|AC007390.5_ENST00000397064.2_Intron	NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	971					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)				GCTGGAATCATTTAAGTTTCT	0.264																																					p.N971I		Atlas-SNP	.											.	CEBPZ	68	.	0			c.A2912T						PASS	.						54	58	57					2																	37430124		2200	4294	6494	SO:0001583	missense	10153	exon14			GAATCATTTAAGT	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.2912A>T	chr2.hg19:g.37430124T>A	ENSP00000234170:p.Asn971Ile	150.0	0.0	.		216.0	75.0	.	NM_005760	Q8NE75	Missense_Mutation	SNP	ENST00000234170.5	hg19	CCDS1787.1	.	.	.	.	.	.	.	.	.	.	T	6.448	0.450836	0.12223	.	.	ENSG00000115816	ENST00000234170;ENST00000545744	T	0.14144	2.53	5.53	-1.96	0.07525	.	0.448282	0.25529	N	0.030057	T	0.11367	0.0277	L	0.44542	1.39	0.09310	N	1	B	0.26744	0.158	B	0.26517	0.07	T	0.16897	-1.0387	10	0.72032	D	0.01	.	11.4206	0.49978	0.0:0.2571:0.0:0.7429	.	971	Q03701	CEBPZ_HUMAN	I	971	ENSP00000234170:N971I	ENSP00000234170:N971I	N	-	2	0	CEBPZ	37283628	0.000000	0.05858	0.014000	0.15608	0.199000	0.23934	-0.102000	0.10956	-0.622000	0.05626	-0.400000	0.06385	AAT	.	.	.	none		0.264	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760		A	37430124	T	A	37430124	3	1	204	1	0	0	0	0	1	0	0	0	3206	1493	52	5	264	5	CEBPZ	2	37430124	Missense_Mutation	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10	11971455	37430124	205769249	10	12299											
PREPL	9581	hgsc.bcm.edu	37	chr2	44566372	44566372	+	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	gtaaaggaccccatgtattcGcttctggataagtactggtg	10	12	11	8	1	1	0	0	0	1	0	2	2	1	2	2	3	1	4	2	3	5	6	rs145356495		TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr2:44566372G>A	ENST00000409936.1	-	7	1320	c.883C>T	c.(883-885)Cga>Tga	p.R295*	PREPL_ENST00000378511.3_Nonsense_Mutation_p.R295*|PREPL_ENST00000409411.1_Nonsense_Mutation_p.R206*|PREPL_ENST00000410081.1_Nonsense_Mutation_p.R295*|PREPL_ENST00000409957.1_Nonsense_Mutation_p.R206*|PREPL_ENST00000409272.1_Nonsense_Mutation_p.R295*|PREPL_ENST00000541738.1_Nonsense_Mutation_p.R206*|PREPL_ENST00000260648.6_Nonsense_Mutation_p.R295*|PREPL_ENST00000378520.3_Nonsense_Mutation_p.R295*	NM_001171606.1	NP_001165077.1	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like	295						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)				CCATGTATTCGCTTCTGGATA	0.413																																					p.R295X		Atlas-SNP	.											.	PREPL	69	.	0			c.C883T						PASS	.	G	stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG	0,4406		0,0,2203	113	109	110		883,883,883,883,616,616,883	3.4	1	2	dbSNP_134	110	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained,stop-gained,stop-gained,stop-gained,stop-gained,stop-gained,stop-gained	PREPL	NM_001042385.2,NM_001042386.2,NM_001171603.1,NM_001171606.1,NM_001171613.1,NM_001171617.1,NM_006036.4	,,,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,,,	295/666,295/662,295/728,295/728,206/639,206/639,295/728	44566372	1,13005	2203	4300	6503	SO:0001587	stop_gained	9581	exon7			GTATTCGCTTCTG	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.883C>T	chr2.hg19:g.44566372G>A	ENSP00000386543:p.Arg295*	161.0	0.0	.		182.0	14.0	.	NM_001171603	A7E2X6|D6W5A3|O43163|Q4J6C3|Q4J6C4|Q4ZG39|Q6ZMW7|Q96DW7	Nonsense_Mutation	SNP	ENST00000409936.1	hg19	CCDS33190.1	.	.	.	.	.	.	.	.	.	.	G	36	5.741979	0.96873	0.0	1.16E-4	ENSG00000138078	ENST00000541738;ENST00000409411;ENST00000409957;ENST00000409936;ENST00000260648;ENST00000409272;ENST00000410081;ENST00000378520;ENST00000378511	.	.	.	5.46	3.39	0.38822	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.5424	14.6218	0.68592	0.0:0.0:0.6226:0.3774	.	.	.	.	X	206;206;206;295;295;295;295;295;295	.	ENSP00000260648:R295X	R	-	1	2	PREPL	44419876	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.377000	0.34317	1.221000	0.43506	0.650000	0.86243	CGA	.	G|1.000;A|0.000	0.000	weak		0.413	PREPL-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327900.1	NM_006036		A	44566372	G	A	44566372	4	1	204	1	0	0	0	0	0	1	0	0	12485	1095	38	1	1336	1	PREPL	2	44566372	Nonsense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	7136248	44566372	198633001	11	12300											
PREPL	9581	hgsc.bcm.edu	37	chr2	44566451	44566451	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaagtagtcttgttcataatAtttatggtgaggaaacgact	13	14	10	4	1	2	1	1	1	1	0	2	4	2	2	0	2	1	2	0	2	6	7			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr2:44566451A>G	ENST00000409936.1	-	7	1241	c.804T>C	c.(802-804)aaT>aaC	p.N268N	PREPL_ENST00000378511.3_Silent_p.N268N|PREPL_ENST00000409411.1_Silent_p.N179N|PREPL_ENST00000410081.1_Silent_p.N268N|PREPL_ENST00000409957.1_Silent_p.N179N|PREPL_ENST00000409272.1_Silent_p.N268N|PREPL_ENST00000541738.1_Silent_p.N179N|PREPL_ENST00000260648.6_Silent_p.N268N|PREPL_ENST00000378520.3_Silent_p.N268N	NM_001171606.1	NP_001165077.1	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like	268						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)				TGTTCATAATATTTATGGTGA	0.413																																					p.N268N		Atlas-SNP	.											.	PREPL	69	.	0			c.T804C						PASS	.						84	79	81					2																	44566451		2203	4300	6503	SO:0001819	synonymous_variant	9581	exon7			CATAATATTTATG	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.804T>C	chr2.hg19:g.44566451A>G		143.0	0.0	.		142.0	16.0	.	NM_001171603	A7E2X6|D6W5A3|O43163|Q4J6C3|Q4J6C4|Q4ZG39|Q6ZMW7|Q96DW7	Silent	SNP	ENST00000409936.1	hg19	CCDS33190.1																																																																																			.	.	.	none		0.413	PREPL-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327900.1	NM_006036		G	44566451	A	G	44566451	2	3	204	1	0	0	0	0	0	0	0	1	12485	446	16	3		3	PREPL	2	44566451	Silent	SNP	A	TCGA-IA-A40Y-01A-11D-A25F-10	79	44566451	198632922	12	12301											
CCDC88A	55704	hgsc.bcm.edu	37	chr2	55561724	55561724	+	Missense_Mutation	SNP	T	T	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	tgttttcttgaaagatgcttTcaggagctccaaacccttct	9	15	7	10	0	3	2	1	1	2	1	4	3	4	3	2	1	3	3	2	1	2	5			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr2:55561724T>G	ENST00000436346.1	-	15	3074	c.2233A>C	c.(2233-2235)Aaa>Caa	p.K745Q	CCDC88A_ENST00000413716.2_Missense_Mutation_p.K745Q|CCDC88A_ENST00000336838.6_Missense_Mutation_p.K745Q|AC012358.8_ENST00000594078.1_RNA|CCDC88A_ENST00000263630.8_Missense_Mutation_p.K745Q|AC012358.8_ENST00000600219.1_RNA|AC012358.8_ENST00000599352.1_RNA|AC012358.8_ENST00000608103.1_RNA|AC012358.8_ENST00000599475.1_RNA	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	745					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						AAAGATGCTTTCAGGAGCTCC	0.363																																					p.K745Q		Atlas-SNP	.											.	CCDC88A	336	.	0			c.A2233C						PASS	.						91	93	92					2																	55561724		2202	4299	6501	SO:0001583	missense	55704	exon15			ATGCTTTCAGGAG	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.2233A>C	chr2.hg19:g.55561724T>G	ENSP00000410608:p.Lys745Gln	36.0	0.0	.		74.0	14.0	.	NM_018084	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Missense_Mutation	SNP	ENST00000436346.1	hg19		.	.	.	.	.	.	.	.	.	.	T	14.75	2.628283	0.46944	.	.	ENSG00000115355	ENST00000336838;ENST00000263630;ENST00000436346;ENST00000413716	T;T;T;T	0.17213	2.29;2.51;2.48;2.3	4.86	4.86	0.63082	.	0.126339	0.34725	U	0.003726	T	0.17238	0.0414	L	0.46885	1.475	0.80722	D	1	B;P;B;B;B	0.44478	0.061;0.836;0.018;0.009;0.031	B;B;B;B;B	0.40101	0.145;0.319;0.092;0.028;0.028	T	0.03130	-1.1069	10	0.29301	T	0.29	-11.7377	14.7941	0.69865	0.0:0.0:0.0:1.0	.	745;745;745;745;745	B7ZM78;Q3V6T2-2;Q3V6T2;Q3V6T2-3;Q3V6T2-4	.;.;GRDN_HUMAN;.;.	Q	745	ENSP00000338728:K745Q;ENSP00000263630:K745Q;ENSP00000410608:K745Q;ENSP00000404431:K745Q	ENSP00000263630:K745Q	K	-	1	0	CCDC88A	55415228	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	5.647000	0.67923	1.956000	0.56807	0.374000	0.22700	AAA	.	.	.	none		0.363	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding		NM_017571		G	55561724	T	G	55561724	3	3	204	1	0	0	0	0	1	0	0	0	2865	1792	62	5	3454	5	CCDC88A	2	55561724	Missense_Mutation	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10	10995273	55561724	187637649	13	12302											
MBD5	55777	hgsc.bcm.edu	37	chr2	149247732	149247732	+	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	gaactatgatgagttttaagGagagactagagaacactgtg	15	10	12	4	0	0	4	0	2	0	2	0	8	0	5	0	1	2	1	0	1	5	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr2:149247732G>A	ENST00000407073.1	+	12	4829	c.3832G>A	c.(3832-3834)Gag>Aag	p.E1278K	MBD5_ENST00000404807.1_Missense_Mutation_p.E1511K	NM_018328.4	NP_060798.2	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	1278					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)		GAGTTTTAAGGAGAGACTAGA	0.413																																					p.E1278K		Atlas-SNP	.											.	MBD5	164	.	0			c.G3832A						PASS	.						61	62	61					2																	149247732		2203	4300	6503	SO:0001583	missense	55777	exon12			TTTAAGGAGAGAC	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.3832G>A	chr2.hg19:g.149247732G>A	ENSP00000386049:p.Glu1278Lys	73.0	0.0	.		64.0	6.0	.	NM_018328	A5HMQ4|A7E2B1|Q53SR1|Q9NUV6	Missense_Mutation	SNP	ENST00000407073.1	hg19	CCDS33302.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.493136	0.84962	.	.	ENSG00000204406	ENST00000407073;ENST00000404807	T;T	0.63913	0.15;-0.07	5.89	5.89	0.94794	.	0.093845	0.46442	D	0.000287	T	0.68366	0.2993	N	0.24115	0.695	0.58432	D	0.999999	B;D	0.64830	0.302;0.994	B;P	0.61397	0.182;0.888	T	0.71421	-0.4598	10	0.87932	D	0	-2.9361	20.2363	0.98357	0.0:0.0:1.0:0.0	.	1511;1278	E9PHH0;Q9P267	.;MBD5_HUMAN	K	1278;1511	ENSP00000386049:E1278K;ENSP00000384672:E1511K	ENSP00000384672:E1511K	E	+	1	0	MBD5	148964202	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.039000	0.93777	2.789000	0.95967	0.655000	0.94253	GAG	.	.	.	none		0.413	MBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318111.2			A	149247732	G	A	149247732	3	1	204	1	0	0	0	0	1	0	0	0	9354	1175	41	2	3858	2	MBD5	2	149247732	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	93686008	149247732	93951641	14	12303											
C2orf77	129881	hgsc.bcm.edu	37	chr2	170506849	170506849	+	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	aattgtttaccacaatggctCgatattctgcaattgttttt	10	18	6	7	1	1	0	0	0	1	0	2	1	1	0	1	1	2	4	1	1	5	8			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr2:170506849C>T	ENST00000447353.1	-	7	1247	c.1142G>A	c.(1141-1143)cGa>cAa	p.R381Q		NM_001085447.1	NP_001078916.1	Q0VFZ6	CC173_HUMAN	coiled-coil domain containing 173	381																	CACAATGGCTCGATATTCTGC	0.338																																					p.R381Q		Atlas-SNP	.											.	.	.	.	0			c.G1142A						PASS	.						86	76	79					2																	170506849		1811	4068	5879	SO:0001583	missense	129881	exon7			ATGGCTCGATATT	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.1142G>A	chr2.hg19:g.170506849C>T	ENSP00000391504:p.Arg381Gln	51.0	0.0	.		64.0	4.0	.	NM_001085447	Q6PJF6	Missense_Mutation	SNP	ENST00000447353.1	hg19	CCDS46445.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.543115	0.86022	.	.	ENSG00000154479	ENST00000447353	T	0.15256	2.44	5.42	5.42	0.78866	.	.	.	.	.	T	0.41096	0.1144	M	0.71581	2.175	0.45946	D	0.998779	D	0.89917	1.0	D	0.87578	0.998	T	0.06267	-1.0836	9	0.30854	T	0.27	.	16.2096	0.82148	0.0:1.0:0.0:0.0	.	381	Q0VFZ6	CB077_HUMAN	Q	381	ENSP00000391504:R381Q	ENSP00000391504:R381Q	R	-	2	0	C2orf77	170215095	1.000000	0.71417	0.986000	0.45419	0.965000	0.64279	4.503000	0.60407	2.565000	0.86533	0.558000	0.71614	CGA	.	.	.	none		0.338	CCDC173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333954.2	NM_001085447		T	170506849	C	T	170506849	3	4	204	1	0	0	0	0	1	0	0	0	2196	884	31	1	528	1	C2orf77	2	170506849	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	21259117	170506849	72692524	15	12304											
SF3B1	23451	hgsc.bcm.edu	37	chr2	198265617	198265617	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caatcctggatataatttctGctgcacctactttgtttgcc	8	16	6	11	0	1	0	0	0	1	0	2	1	2	1	3	1	4	3	3	1	4	6			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr2:198265617G>A	ENST00000335508.6	-	18	2631	c.2540C>T	c.(2539-2541)gCa>gTa	p.A847V	SF3B1_ENST00000462613.1_5'Flank	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	847					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)			TATAATTTCTGCTGCACCTAC	0.358			Mis		myelodysplastic syndrome																																p.A847V		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1	1038	.	0			c.C2540T						PASS	.						99	97	98					2																	198265617		2203	4300	6503	SO:0001583	missense	23451	exon18			ATTTCTGCTGCAC	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.2540C>T	chr2.hg19:g.198265617G>A	ENSP00000335321:p.Ala847Val	91.0	0.0	.		78.0	11.0	.	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	hg19	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	G	19.47	3.833082	0.71258	.	.	ENSG00000115524	ENST00000335508	T	0.65549	-0.16	5.77	5.77	0.91146	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.59622	0.2207	L	0.41961	1.31	0.80722	D	1	B	0.14438	0.01	B	0.18561	0.022	T	0.52917	-0.8511	10	0.48119	T	0.1	.	20.3626	0.98863	0.0:0.0:1.0:0.0	.	847	O75533	SF3B1_HUMAN	V	847	ENSP00000335321:A847V	ENSP00000335321:A847V	A	-	2	0	SF3B1	197973862	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.737000	0.98831	2.885000	0.99019	0.655000	0.94253	GCA	.	.	.	none		0.358	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			A	198265617	G	A	198265617	3	1	204	1	0	0	0	0	1	0	0	0	14162	1319	46	2	1406	2	SF3B1	2	198265617	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	27758768	198265617	44933756	16	12305											
PLEKHM3	389072	hgsc.bcm.edu	37	chr2	208725904	208725904	+	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	cacagatgaaccccttctggCtacaaagactgcagctgtac	12	8	8	13	0	1	3	0	1	1	2	1	3	1	3	2	1	5	4	2	1	4	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr2:208725904C>G	ENST00000427836.2	-	7	2522	c.2033G>C	c.(2032-2034)aGc>aCc	p.S678T	PLEKHM3_ENST00000389247.4_Missense_Mutation_p.S678T	NM_001080475.2	NP_001073944.1	Q6ZWE6	PKHM3_HUMAN	pleckstrin homology domain containing, family M, member 3	678					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						CCCCTTCTGGCTACAAAGACT	0.418																																					p.S678T		Atlas-SNP	.											.	PLEKHM3	101	.	0			c.G2033C						PASS	.						148	142	144					2																	208725904		1924	4136	6060	SO:0001583	missense	389072	exon7			TTCTGGCTACAAA	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.2033G>C	chr2.hg19:g.208725904C>G	ENSP00000417003:p.Ser678Thr	119.0	0.0	.		133.0	7.0	.	NM_001080475	B9EKV2|Q8WW68	Missense_Mutation	SNP	ENST00000427836.2	hg19	CCDS42808.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.28|15.28	2.787482|2.787482	0.49997|0.49997	.|.	.|.	ENSG00000178385|ENSG00000178385	ENST00000427836;ENST00000389247|ENST00000447645	D;D|.	0.83163|.	-1.68;-1.69|.	5.06|5.06	5.06|5.06	0.68205|0.68205	Protein kinase C-like, phorbol ester/diacylglycerol binding (1);|.	0.045109|.	0.85682|.	D|.	0.000000|.	T|.	0.55321|.	0.1913|.	N|N	0.21194|0.21194	0.64|0.64	0.52501|0.52501	D|D	0.999957|0.999957	P|.	0.39060|.	0.657|.	P|.	0.46585|.	0.521|.	T|.	0.48875|.	-0.8996|.	10|.	0.09084|.	T|.	0.74|.	.|.	18.9822|18.9822	0.92758|0.92758	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	678|.	Q6ZWE6|.	PKHM3_HUMAN|.	T|Y	678|429	ENSP00000417003:S678T;ENSP00000373899:S678T|.	ENSP00000373899:S678T|.	S|X	-|-	2|3	0|2	PLEKHM3|PLEKHM3	208434149|208434149	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	5.870000|5.870000	0.69620|0.69620	2.763000|2.763000	0.94921|0.94921	0.655000|0.655000	0.94253|0.94253	AGC|TAG	.	.	.	none		0.418	PLEKHM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337036.1	NM_001080475		G	208725904	C	G	208725904	3	3	204	1	0	0	0	0	1	0	0	0	12089	797	28	4	260	4	PLEKHM3	2	208725904	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	10460287	208725904	34473469	17	12306											
DGKD	8527	hgsc.bcm.edu	37	chr2	234368474	234368474	+	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	gtggacggagaggcctgggtCcagccgccagggtacattcg	7	6	17	11	3	0	1	0	0	0	1	2	3	1	2	4	5	2	1	4	5	1	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr2:234368474C>T	ENST00000264057.2	+	23	2778	c.2766C>T	c.(2764-2766)gtC>gtT	p.V922V	DGKD_ENST00000409813.3_Silent_p.V878V	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	922					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)	AGGCCTGGGTCCAGCCGCCAG	0.602																																					p.V922V		Atlas-SNP	.											.	DGKD	106	.	0			c.C2766T						PASS	.						76	66	69					2																	234368474		2203	4300	6503	SO:0001819	synonymous_variant	8527	exon23			CTGGGTCCAGCCG	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.2766C>T	chr2.hg19:g.234368474C>T		131.0	0.0	.		134.0	8.0	.	NM_152879	Q14158|Q6PK55|Q8NG53	Silent	SNP	ENST00000264057.2	hg19	CCDS2504.1																																																																																			.	.	.	none		0.602	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648		T	234368474	C	T	234368474	2	4	204	1	0	0	0	0	0	0	0	1	4469	842	30	2		2	DGKD	2	234368474	Silent	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	25642570	234368474	8830899	18	12307											
FANCD2	2177	hgsc.bcm.edu	37	chr3	10089633	10089633	+	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	atgtgttcatccattctgtcGctggctcagagtttgcttca	6	16	9	10	1	4	1	3	0	1	1	6	1	5	1	1	1	1	5	1	1	0	4	rs564577177		TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr3:10089633G>A	ENST00000419585.1	+	16	1472	c.1311G>A	c.(1309-1311)tcG>tcA	p.S437S	FANCD2_ENST00000383806.1_Silent_p.S437S|FANCD2_ENST00000383807.1_Silent_p.S437S|FANCD2_ENST00000287647.3_Silent_p.S437S			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	437					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)		CCATTCTGTCGCTGGCTCAGA	0.408			"D, Mis, N, F"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.S437S		Atlas-SNP	.	yes	Rec		Fanconi anaemia D2	3	3p26	2177	"Fanconi anemia, complementation group D2"		L	.	FANCD2	253	.	0			c.G1311A						PASS	.						171	174	173					3																	10089633		2203	4300	6503	SO:0001819	synonymous_variant	2177	exon16	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TCTGTCGCTGGCT	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.1311G>A	chr3.hg19:g.10089633G>A		137.0	0.0	.		107.0	8.0	.	NM_001018115	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Silent	SNP	ENST00000419585.1	hg19	CCDS33696.1																																																																																			.	.	.	none		0.408	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1			A	10089633	G	A	10089633	2	1	204	1	0	0	0	0	0	0	0	1	5672	1074	38	1		1	FANCD2	3	10089633	Silent	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10		10089633	187932797	19	12308											
SCN11A	11280	hgsc.bcm.edu	37	chr3	38962716	38962716	+	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	tgaccagcttcttcacagagCgtagcaaggcccccacgatg	10	7	10	14	2	2	2	1	1	1	1	2	3	2	2	3	1	3	3	3	1	2	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr3:38962716C>T	ENST00000302328.3	-	6	941	c.743G>A	c.(742-744)cGc>cAc	p.R248H	SCN11A_ENST00000456224.3_Missense_Mutation_p.R248H|SCN11A_ENST00000444237.2_Missense_Mutation_p.R248H|SCN11A_ENST00000450244.1_Missense_Mutation_p.R248H	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	248					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)	CTTCACAGAGCGTAGCAAGGC	0.542																																					p.R248H		Atlas-SNP	.											.	SCN11A	296	.	0			c.G743A						PASS	.						115	111	112					3																	38962716		2203	4300	6503	SO:0001583	missense	11280	exon6			ACAGAGCGTAGCA	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.743G>A	chr3.hg19:g.38962716C>T	ENSP00000307599:p.Arg248His	149.0	1.0	.		138.0	106.0	.	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Missense_Mutation	SNP	ENST00000302328.3	hg19	CCDS33737.1	.	.	.	.	.	.	.	.	.	.	C	12.93	2.085095	0.36758	.	.	ENSG00000168356	ENST00000302328;ENST00000450244;ENST00000456224;ENST00000444237	D;D;D;D	0.98701	-5.08;-5.08;-5.08;-5.08	4.67	3.79	0.43588	Ion transport (1);	0.217778	0.42964	D	0.000631	D	0.94729	0.8299	N	0.25332	0.735	0.32489	N	0.540524	B	0.26081	0.141	B	0.22880	0.042	D	0.92393	0.5923	10	0.16896	T	0.51	.	7.3286	0.26569	0.0:0.7983:0.0:0.2017	.	248	Q9UI33	SCNBA_HUMAN	H	248	ENSP00000307599:R248H;ENSP00000400945:R248H;ENSP00000416757:R248H;ENSP00000408028:R248H	ENSP00000307599:R248H	R	-	2	0	SCN11A	38937720	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	4.635000	0.61332	0.966000	0.38159	0.585000	0.79938	CGC	.	.	.	none		0.542	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		T	38962716	C	T	38962716	3	4	204	1	0	0	0	0	1	0	0	0	13926	768	27	1	4716	1	SCN11A	3	38962716	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	28873083	38962716	159059714	20	12309											
AADACL2	344752	hgsc.bcm.edu	37	chr3	151475280	151475280	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcatgaacatattgaggaTggaattcatggagctttatc	12	14	10	5	0	2	2	2	2	0	0	3	5	2	5	0	3	2	2	0	3	4	6			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr3:151475280T>C	ENST00000356517.3	+	5	1213	c.1104T>C	c.(1102-1104)gaT>gaC	p.D368D	RP11-454C18.2_ENST00000475855.1_RNA|RP11-454C18.2_ENST00000483843.2_RNA	NM_207365.3	NP_997248.2	Q6P093	ADCL2_HUMAN	arylacetamide deacetylase-like 2	368						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			NS(1)|breast(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(13)|skin(2)	24			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			ATATTGAGGATGGAATTCATG	0.338																																					p.D368D		Atlas-SNP	.											.	AADACL2	102	.	0			c.T1104C						PASS	.						97	95	96					3																	151475280		2203	4299	6502	SO:0001819	synonymous_variant	344752	exon5			TGAGGATGGAATT	BC065724	CCDS3161.2	3q25.1	2010-12-14			ENSG00000197953	ENSG00000197953			24427	protein-coding gene	gene with protein product							Standard	NM_207365		Approved	MGC72001	uc003ezc.3	Q6P093	OTTHUMG00000155914	ENST00000356517.3:c.1104T>C	chr3.hg19:g.151475280T>C		137.0	0.0	.		191.0	15.0	.	NM_207365	Q5HYJ4	Silent	SNP	ENST00000356517.3	hg19	CCDS3161.2																																																																																			.	.	.	none		0.338	AADACL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342288.3	NM_207365		C	151475280	T	C	151475280	2	2	204	1	0	0	0	0	0	0	0	1	11	1461	51	3		3	AADACL2	3	151475280	Silent	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10	112512564	151475280	46547150	21	12310											
SI	6476	hgsc.bcm.edu	37	chr3	164767590	164767590	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaattttaccaggagtaaacGgtggataattcaatttgttt	14	15	8	4	1	1	0	1	0	0	0	1	2	1	2	1	3	2	2	1	3	6	7			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr3:164767590G>A	ENST00000264382.3	-	14	1648	c.1586C>T	c.(1585-1587)cCg>cTg	p.P529L		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	529	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)	AGGAGTAAACGGTGGATAATT	0.279										HNSCC(35;0.089)																											p.P529L		Atlas-SNP	.											.	SI	500	.	0			c.C1586T						PASS	.						90	100	97					3																	164767590		2203	4289	6492	SO:0001583	missense	6476	exon14			GTAAACGGTGGAT	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.1586C>T	chr3.hg19:g.164767590G>A	ENSP00000264382:p.Pro529Leu	95.0	0.0	.		131.0	9.0	.	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	hg19	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	G	19.18	3.778691	0.70107	.	.	ENSG00000090402	ENST00000264382	D	0.91686	-2.89	5.58	5.58	0.84498	Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.97188	0.9081	M	0.93375	3.41	0.80722	D	1	D	0.89917	1.0	D	0.72625	0.978	D	0.97952	1.0332	10	0.87932	D	0	.	18.5615	0.91101	0.0:0.0:1.0:0.0	.	529	P14410	SUIS_HUMAN	L	529	ENSP00000264382:P529L	ENSP00000264382:P529L	P	-	2	0	SI	166250284	1.000000	0.71417	1.000000	0.80357	0.394000	0.30568	9.114000	0.94329	2.622000	0.88805	0.585000	0.79938	CCG	.	.	.	none		0.279	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		A	164767590	G	A	164767590	3	1	204	1	0	0	0	0	1	0	0	0	14310	1116	39	1	4037	1	SI	3	164767590	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	13292310	164767590	33254840	22	12311											
KLB	152831	hgsc.bcm.edu	37	chr4	39439409	39439409	+	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	ggtctctcctggatggctttGaatggcaggatgcttacacc	7	12	12	10	0	1	1	0	1	1	0	3	3	2	3	2	5	2	3	2	5	2	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr4:39439409G>C	ENST00000257408.4	+	3	1496	c.1399G>C	c.(1399-1401)Gaa>Caa	p.E467Q		NM_175737.3	NP_783864.1	Q86Z14	KLOTB_HUMAN	klotho beta	467	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						GGATGGCTTTGAATGGCAGGA	0.428																																					p.E467Q		Atlas-SNP	.											.	KLB	95	.	0			c.G1399C						PASS	.						189	178	182					4																	39439409		2203	4300	6503	SO:0001583	missense	152831	exon3			GGCTTTGAATGGC	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.1399G>C	chr4.hg19:g.39439409G>C	ENSP00000257408:p.Glu467Gln	178.0	0.0	.		112.0	15.0	.	NM_175737	Q2M3K8	Missense_Mutation	SNP	ENST00000257408.4	hg19	CCDS3451.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.956339	0.92726	.	.	ENSG00000134962	ENST00000257408	T	0.41065	1.01	6.03	5.19	0.71726	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.095361	0.64402	D	0.000001	T	0.77239	0.4101	H	0.98446	4.235	0.51767	D	0.999938	D;D	0.76494	0.999;0.999	D;D	0.66716	0.946;0.946	D	0.86716	0.1939	10	0.87932	D	0	-28.1831	15.0523	0.71885	0.0674:0.0:0.9326:0.0	.	467;467	B7ZL50;Q86Z14	.;KLOTB_HUMAN	Q	467	ENSP00000257408:E467Q	ENSP00000257408:E467Q	E	+	1	0	KLB	39115804	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.869000	0.99810	1.562000	0.49601	0.655000	0.94253	GAA	.	.	.	none		0.428	KLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250429.1	NM_175737		C	39439409	G	C	39439409	3	2	204	1	0	0	0	0	1	0	0	0	8339	1291	45	4	1409	4	KLB	4	39439409	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10		39439409	151714867	23	12312											
POLR2B	5431	hgsc.bcm.edu	37	chr4	57889646	57889646	+	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	caccaatagacgctataccaAgagagactgtagcacttttc	14	9	7	11	1	0	3	0	0	0	3	1	4	0	3	2	0	2	3	2	0	6	6			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr4:57889646A>T	ENST00000381227.1	+	20	3079	c.2666A>T	c.(2665-2667)aAg>aTg	p.K889M	POLR2B_ENST00000431623.2_Missense_Mutation_p.K814M|POLR2B_ENST00000314595.5_Missense_Mutation_p.K889M|POLR2B_ENST00000441246.2_Missense_Mutation_p.K882M			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	889					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					CGCTATACCAAGAGAGACTGT	0.413																																					p.K889M		Atlas-SNP	.											.	POLR2B	108	.	0			c.A2666T						PASS	.						108	104	105					4																	57889646		2203	4300	6503	SO:0001583	missense	5431	exon19			ATACCAAGAGAGA		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.2666A>T	chr4.hg19:g.57889646A>T	ENSP00000370625:p.Lys889Met	167.0	0.0	.		92.0	7.0	.	NM_000938	A8K1A8|Q8IZ61	Missense_Mutation	SNP	ENST00000381227.1	hg19	CCDS3511.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.834179	0.91036	.	.	ENSG00000047315	ENST00000381227;ENST00000431623;ENST00000441246;ENST00000314595	T;T;T;T	0.71817	-0.6;-0.6;-0.6;-0.6	6.04	6.04	0.98038	RNA polymerase Rpb2, OB-fold (1);DNA-directed RNA polymerase, subunit 2, domain 6 (1);	0.000000	0.85682	D	0.000000	D	0.88066	0.6337	M	0.93062	3.375	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90731	0.4642	10	0.87932	D	0	.	16.5885	0.84745	1.0:0.0:0.0:0.0	.	814;889	C9J4M6;P30876	.;RPB2_HUMAN	M	889;814;882;889	ENSP00000370625:K889M;ENSP00000391096:K814M;ENSP00000391452:K882M;ENSP00000312735:K889M	ENSP00000312735:K889M	K	+	2	0	POLR2B	57584403	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.317000	0.78254	0.460000	0.39030	AAG	.	.	.	none		0.413	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938		T	57889646	A	T	57889646	3	4	204	1	0	0	0	0	1	0	0	0	12222	72	3	5	2740	5	POLR2B	4	57889646	Missense_Mutation	SNP	A	TCGA-IA-A40Y-01A-11D-A25F-10	18450237	57889646	133264630	24	12313											
GUCY1B3	2983	hgsc.bcm.edu	37	chr4	156724870	156724870	+	Missense_Mutation	SNP	T	T	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	ctgccacctggccttggacaTgatggaaattgctggccagg	8	9	13	11	0	0	1	0	1	0	0	0	3	0	3	4	5	2	1	4	5	1	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr4:156724870T>G	ENST00000264424.8	+	11	1590	c.1508T>G	c.(1507-1509)aTg>aGg	p.M503R	GUCY1B3_ENST00000507146.1_Missense_Mutation_p.M478R|GUCY1B3_ENST00000505154.1_Missense_Mutation_p.M435R|GUCY1B3_ENST00000513437.1_Missense_Mutation_p.M435R|GUCY1B3_ENST00000502959.1_Missense_Mutation_p.M525R|GUCY1B3_ENST00000505764.1_Missense_Mutation_p.M483R|GUCY1B3_ENST00000503520.1_Missense_Mutation_p.M470R	NM_000857.2	NP_000848.1	Q02153	GCYB1_HUMAN	guanylate cyclase 1, soluble, beta 3	503	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)	cytoplasm (GO:0005737)|guanylate cyclase complex, soluble (GO:0008074)|intracellular membrane-bounded organelle (GO:0043231)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.148)		GCCTTGGACATGATGGAAATT	0.423																																					p.M503R		Atlas-SNP	.											.	GUCY1B3	65	.	0			c.T1508G						PASS	.						76	79	78					4																	156724870		1960	4160	6120	SO:0001583	missense	2983	exon11			TGGACATGATGGA	AF020340	CCDS47154.1, CCDS75203.1	4q31.3-q33	2008-03-18			ENSG00000061918	ENSG00000061918	4.6.1.2		4687	protein-coding gene	gene with protein product		139397		GUC1B3		1352257	Standard	XM_005262959		Approved	GC-SB3, GC-S-beta-1	uc003ipc.3	Q02153	OTTHUMG00000161698	ENST00000264424.8:c.1508T>G	chr4.hg19:g.156724870T>G	ENSP00000264424:p.Met503Arg	82.0	0.0	.		39.0	4.0	.	NM_000857	B7Z426|Q86WY5	Missense_Mutation	SNP	ENST00000264424.8	hg19	CCDS47154.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.327658	0.81690	.	.	ENSG00000061918	ENST00000505154;ENST00000502959;ENST00000505764;ENST00000507146;ENST00000264424;ENST00000503520;ENST00000513437	D;D;D;D;D;D;D	0.83335	-1.71;-1.71;-1.71;-1.71;-1.71;-1.71;-1.71	5.61	5.61	0.85477	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.85682	D	0.000000	D	0.93848	0.8032	H	0.96576	3.845	0.80722	D	1	P;P;D;P;P	0.58970	0.94;0.941;0.984;0.875;0.867	P;P;D;P;P	0.65010	0.735;0.86;0.931;0.517;0.735	D	0.95757	0.8797	10	0.87932	D	0	.	16.1025	0.81194	0.0:0.0:0.0:1.0	.	483;525;478;470;503	B7Z426;E9PCN2;D6RC99;Q02153-2;Q02153	.;.;.;.;GCYB1_HUMAN	R	435;525;483;478;503;470;435	ENSP00000427226:M435R;ENSP00000426786:M525R;ENSP00000426319:M483R;ENSP00000422313:M478R;ENSP00000264424:M503R;ENSP00000420842:M470R;ENSP00000425065:M435R	ENSP00000264424:M503R	M	+	2	0	GUCY1B3	156944320	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.990000	0.88215	2.254000	0.74563	0.533000	0.62120	ATG	.	.	.	none		0.423	GUCY1B3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365770.2			G	156724870	T	G	156724870	3	3	204	1	0	0	0	0	1	0	0	0	6902	1464	51	5	1550	5	GUCY1B3	4	156724870	Missense_Mutation	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10	98835224	156724870	34429406	25	12314											
DNAH5	1767	hgsc.bcm.edu	37	chr5	13771076	13771076	+	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	tcaatatcataggaagtgagGaagtgttcagacactagaga	16	9	11	5	0	3	3	3	1	0	2	3	6	3	5	0	2	0	1	0	2	6	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr5:13771076G>T	ENST00000265104.4	-	56	9491	c.9387C>A	c.(9385-9387)ttC>ttA	p.F3129L	DNAH5_ENST00000504001.3_5'UTR	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3129	AAA 4. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					AGGAAGTGAGGAAGTGTTCAG	0.388									Kartagener syndrome																												p.F3129L		Atlas-SNP	.											.	DNAH5	868	.	0			c.C9387A						PASS	.						63	60	61					5																	13771076		2203	4300	6503	SO:0001583	missense	1767	exon56	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AGTGAGGAAGTGT	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.9387C>A	chr5.hg19:g.13771076G>T	ENSP00000265104:p.Phe3129Leu	70.0	0.0	.		104.0	7.0	.	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	hg19	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	G	14.39	2.521574	0.44866	.	.	ENSG00000039139	ENST00000265104	T	0.54071	0.59	5.71	2.58	0.30949	Dynein heavy chain, P-loop containing D4 domain (1);	0.000000	0.85682	D	0.000000	T	0.67268	0.2875	M	0.89601	3.045	0.80722	D	1	B	0.31989	0.35	P	0.46585	0.521	T	0.68792	-0.5315	10	0.72032	D	0.01	.	7.8099	0.29226	0.1782:0.0:0.6883:0.1335	.	3129	Q8TE73	DYH5_HUMAN	L	3129	ENSP00000265104:F3129L	ENSP00000265104:F3129L	F	-	3	2	DNAH5	13824076	1.000000	0.71417	1.000000	0.80357	0.201000	0.24016	2.368000	0.44222	0.759000	0.33084	-0.152000	0.13540	TTC	.	.	.	none		0.388	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		T	13771076	G	T	13771076	3	4	204	1	0	0	0	0	1	0	0	0	4606	1165	41	4	4583	4	DNAH5	5	13771076	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10		13771076	167144184	26	12315											
DDX4	54514	hgsc.bcm.edu	37	chr5	55110902	55110902	+	Missense_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	atatgttcatcgaattgggcGtactggtcgttgtgggaata	9	14	13	5	3	1	0	1	0	0	0	3	2	1	1	0	3	1	3	0	3	5	6			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr5:55110902G>A	ENST00000505374.1	+	20	1981	c.1889G>A	c.(1888-1890)cGt>cAt	p.R630H	DDX4_ENST00000354991.5_Missense_Mutation_p.R596H|DDX4_ENST00000353507.5_Missense_Mutation_p.R596H|DDX4_ENST00000514278.2_Missense_Mutation_p.R610H|DDX4_ENST00000511853.1_Missense_Mutation_p.R481H	NM_024415.2	NP_077726.1	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	630	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				male meiosis I (GO:0007141)|multicellular organismal development (GO:0007275)|regulation of protein localization (GO:0032880)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pi-body (GO:0071546)|piP-body (GO:0071547)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	24		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				CGAATTGGGCGTACTGGTCGT	0.393																																					p.R630H		Atlas-SNP	.											.	DDX4	194	.	0			c.G1889A						PASS	.						183	179	180					5																	55110902		2203	4300	6503	SO:0001583	missense	54514	exon20			TTGGGCGTACTGG	AF262962	CCDS3969.1, CCDS47208.1, CCDS54854.1, CCDS54855.1	5p15.2-p13.1	2008-02-05	2003-06-13		ENSG00000152670	ENSG00000152670		"DEAD-boxes"	18700	protein-coding gene	gene with protein product		605281	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 4"			10920202, 11850529	Standard	NM_001142549		Approved	VASA	uc003jqg.4	Q9NQI0	OTTHUMG00000097044	ENST00000505374.1:c.1889G>A	chr5.hg19:g.55110902G>A	ENSP00000424838:p.Arg630His	244.0	0.0	.		287.0	16.0	.	NM_024415	A8K8Q2|B3KSF4|D6RDK4|E9PCD8|Q5M7Z3|Q86VX0|Q9NT92|Q9NYB1	Missense_Mutation	SNP	ENST00000505374.1	hg19	CCDS3969.1	.	.	.	.	.	.	.	.	.	.	G	16.38	3.106807	0.56291	.	.	ENSG00000152670	ENST00000353507;ENST00000514278;ENST00000505374;ENST00000354991;ENST00000511853	D;D;D;D;D	0.99143	-5.48;-5.48;-5.48;-5.48;-5.48	5.69	3.83	0.44106	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.99576	0.9847	H	0.99042	4.41	0.47737	D	0.999505	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	0.97744	1.0210	10	0.87932	D	0	-18.9385	12.9225	0.58241	0.0:0.1242:0.7465:0.1293	.	610;481;596;630	D6RDK4;E9PCD8;Q9NQI0-2;Q9NQI0	.;.;.;DDX4_HUMAN	H	596;610;630;596;481	ENSP00000334167:R596H;ENSP00000425359:R610H;ENSP00000424838:R630H;ENSP00000347087:R596H;ENSP00000423123:R481H	ENSP00000334167:R596H	R	+	2	0	DDX4	55146659	1.000000	0.71417	0.997000	0.53966	0.125000	0.20455	7.630000	0.83225	1.390000	0.46547	-0.305000	0.09177	CGT	.	.	.	none		0.393	DDX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214147.2	NM_024415		A	55110902	G	A	55110902	3	1	204	1	0	0	0	0	1	0	0	0	4362	1145	40	1	2004	1	DDX4	5	55110902	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	41339826	55110902	125804358	27	12316											
PCDHGA1	56114	hgsc.bcm.edu	37	chr5	140711698	140711698	+	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	cccacgacttggacagcaatGagaatgcacaaatcacttac	15	7	7	12	1	1	1	1	1	0	1	1	4	1	2	1	1	3	2	1	1	4	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr5:140711698G>A	ENST00000517417.1	+	1	1447	c.1447G>A	c.(1447-1449)Gag>Aag	p.E483K	AC005618.6_ENST00000606901.1_lincRNA|PCDHGA1_ENST00000378105.3_Missense_Mutation_p.E483K	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	483	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)			GGACAGCAATGAGAATGCACA	0.537																																					p.E483K		Atlas-SNP	.											PCDHGA1_ENST00000517417,bladder,carcinoma,0,2	PCDHGA1	397	.	0			c.G1447A						PASS	.						113	121	119					5																	140711698		2203	4300	6503	SO:0001583	missense	56114	exon1			AGCAATGAGAATG	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.1447G>A	chr5.hg19:g.140711698G>A	ENSP00000431083:p.Glu483Lys	74.0	0.0	.		75.0	15.0	.	NM_018912	Q2M273|Q9Y5D6	Missense_Mutation	SNP	ENST00000517417.1	hg19	CCDS54922.1	.	.	.	.	.	.	.	.	.	.	G	6.770	0.511030	0.12883	.	.	ENSG00000204956	ENST00000517417;ENST00000378105	T;T	0.51574	4.68;0.7	3.82	2.91	0.33838	Cadherin (4);Cadherin-like (1);	0.321295	0.22123	N	0.064320	T	0.43523	0.1251	L	0.52266	1.64	0.09310	N	0.999999	B;B	0.14805	0.011;0.009	B;B	0.24701	0.049;0.055	T	0.42430	-0.9452	10	0.46703	T	0.11	.	12.8583	0.57899	0.0:0.3118:0.6881:0.0	.	483;483	Q9Y5H4-2;Q9Y5H4	.;PCDG1_HUMAN	K	483	ENSP00000431083:E483K;ENSP00000367345:E483K	ENSP00000367345:E483K	E	+	1	0	PCDHGA1	140691882	0.000000	0.05858	0.121000	0.21740	0.494000	0.33585	0.184000	0.16939	0.905000	0.36596	0.557000	0.71058	GAG	.	.	.	none		0.537	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		A	140711698	G	A	140711698	3	1	204	1	0	0	0	0	1	0	0	0	11557	1291	45	2	1449	2	PCDHGA1	5	140711698	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	85600796	140711698	40203562	28	12317											
FLT4	2324	hgsc.bcm.edu	37	chr5	180050943	180050943	+	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	gctggcctgtaccttattctTtccctccacaaactcggtcc	6	13	6	16	1	1	0	0	0	1	0	5	0	4	0	5	2	2	2	5	2	3	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr5:180050943T>A	ENST00000261937.6	-	11	1618	c.1540A>T	c.(1540-1542)Aag>Tag	p.K514*	FLT4_ENST00000393347.3_Nonsense_Mutation_p.K514*|FLT4_ENST00000424276.2_5'UTR|FLT4_ENST00000502649.1_Nonsense_Mutation_p.K514*	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	514	Ig-like C2-type 5.				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)	ACCTTATTCTTTCCCTCCACA	0.602																																					p.K514X	Colon(97;1075 1466 27033 27547 35871)	Atlas-SNP	.											.	FLT4	356	.	0			c.A1540T						PASS	.						95	82	87					5																	180050943		2203	4300	6503	SO:0001587	stop_gained	2324	exon11			TATTCTTTCCCTC	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.1540A>T	chr5.hg19:g.180050943T>A	ENSP00000261937:p.Lys514*	203.0	0.0	.		197.0	21.0	.	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Nonsense_Mutation	SNP	ENST00000261937.6	hg19	CCDS4457.1	.	.	.	.	.	.	.	.	.	.	T	39	7.440611	0.98286	.	.	ENSG00000037280	ENST00000261937;ENST00000393347;ENST00000502649;ENST00000376868	.	.	.	4.72	4.72	0.59763	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.8621	0.46833	0.0:0.0:0.2833:0.7166	.	.	.	.	X	514;514;514;324	.	ENSP00000261937:K514X	K	-	1	0	FLT4	179983549	1.000000	0.71417	0.996000	0.52242	0.985000	0.73830	3.078000	0.50096	1.906000	0.55180	0.459000	0.35465	AAG	.	.	.	none		0.602	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4			A	180050943	T	A	180050943	4	1	204	1	0	0	0	0	0	1	0	0	5951	1850	64	5	2639	5	FLT4	5	180050943	Nonsense_Mutation	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10	39339245	180050943	864317	29	12318											
HIST1H2AE	3012	hgsc.bcm.edu	37	chr6	26217223	26217223	+	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	atgtctggacgtggaaagcaAggcggcaaagctcgggcaaa	13	5	15	8	3	1	0	0	0	1	0	2	2	1	2	0	5	2	4	0	5	4	0			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr6:26217223A>T	ENST00000303910.2	+	1	59	c.21A>T	c.(19-21)caA>caT	p.Q7H	HIST1H2BG_ENST00000244601.3_5'Flank	NM_021052.2	NP_066390.1	P04908	H2A1B_HUMAN	histone cluster 1, H2ae	7						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)				GTGGAAAGCAAGGCGGCAAAG	0.502																																					p.Q7H		Atlas-SNP	.											.	HIST1H2AE	25	.	0			c.A21T						PASS	.						62	55	57					6																	26217223		2203	4300	6503	SO:0001583	missense	3012	exon1			AAAGCAAGGCGGC	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.21A>T	chr6.hg19:g.26217223A>T	ENSP00000303373:p.Gln7His	193.0	0.0	.		131.0	68.0	.	NM_021052	P28001|Q76P63	Missense_Mutation	SNP	ENST00000303910.2	hg19	CCDS4595.1	.	.	.	.	.	.	.	.	.	.	.	11.14	1.551016	0.27739	.	.	ENSG00000168274	ENST00000303910	T	0.42900	0.96	4.08	-4.32	0.03688	.	0.000000	0.32640	U	0.005837	T	0.14830	0.0358	N	0.17474	0.49	0.34285	D	0.682566	.	.	.	.	.	.	T	0.14811	-1.0459	8	0.66056	D	0.02	.	10.9427	0.47283	0.6741:0.0:0.3259:0.0	.	.	.	.	H	7	ENSP00000303373:Q7H	ENSP00000303373:Q7H	Q	+	3	2	HIST1H2AE	26325202	0.014000	0.17966	0.774000	0.31636	0.857000	0.48899	-1.328000	0.02680	-1.206000	0.02641	0.533000	0.62120	CAA	.	.	.	none		0.502	HIST1H2AE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040103.1	NM_021052		T	26217223	A	T	26217223	3	4	204	1	0	0	0	0	1	0	0	0	7139	69	3	5	23	5	HIST1H2AE	6	26217223	Missense_Mutation	SNP	A	TCGA-IA-A40Y-01A-11D-A25F-10		26217223	144897844	30	12319											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51889790	51889790	+	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	caggtctgctggtcaatataGactgacgtggtgttctgtcc	7	13	12	9	1	3	2	1	1	2	1	4	2	4	2	1	3	1	2	1	3	3	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr6:51889790G>A	ENST00000371117.3	-	32	5093	c.4818C>T	c.(4816-4818)gtC>gtT	p.V1606V	PKHD1_ENST00000340994.4_Silent_p.V1606V	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1606	IPT/TIG 11.				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)					GGTCAATATAGACTGACGTGG	0.507																																					p.V1606V		Atlas-SNP	.											PKHD1_ENST00000340994,lower_third,carcinoma,0,2	PKHD1	927	.	0			c.C4818T						PASS	.						148	133	138					6																	51889790		2203	4300	6503	SO:0001819	synonymous_variant	5314	exon32			AATATAGACTGAC	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.4818C>T	chr6.hg19:g.51889790G>A		209.0	0.0	.		209.0	9.0	.	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	hg19	CCDS4935.1																																																																																			.	.	.	none		0.507	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51889790	G	A	51889790	2	1	204	1	0	0	0	0	0	0	0	1	11978	929	33	2		2	PKHD1	6	51889790	Silent	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	25672567	51889790	119225277	31	12320											
PM20D2	135293	hgsc.bcm.edu	37	chr6	89859124	89859124	+	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	gcttatctaccagatatggcTgaacatgagtgagtaatcaa	14	11	9	7	0	2	4	1	3	1	1	2	4	2	4	1	1	2	3	1	1	6	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr6:89859124T>A	ENST00000275072.4	+	2	701	c.606T>A	c.(604-606)gcT>gcA	p.A202A		NM_001010853.1	NP_001010853.1	Q8IYS1	P20D2_HUMAN	peptidase M20 domain containing 2	202						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(2)|skin(1)	12		all_cancers(76;9.47e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00813)		CAGATATGGCTGAACATGAGT	0.373																																					p.A202A		Atlas-SNP	.											.	PM20D2	30	.	0			c.T606A						PASS	.						135	136	135					6																	89859124		2203	4300	6503	SO:0001819	synonymous_variant	135293	exon2			TATGGCTGAACAT	BC035036	CCDS34499.1	6q15	2014-07-14	2007-11-14	2007-11-14	ENSG00000146281	ENSG00000146281			21408	protein-coding gene	gene with protein product	"&#946;-alanyl-lysine dipeptidase"	615913	"aminoacylase 1-like 2"	ACY1L2		24891507	Standard	NM_001010853		Approved	bA63L7.3	uc003pmz.4	Q8IYS1	OTTHUMG00000015193	ENST00000275072.4:c.606T>A	chr6.hg19:g.89859124T>A		98.0	0.0	.		79.0	6.0	.	NM_001010853	B4DYJ2|Q5T7J9|Q6MZV2|Q86XD9	Silent	SNP	ENST00000275072.4	hg19	CCDS34499.1																																																																																			.	.	.	none		0.373	PM20D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041477.1	NM_001010853		A	89859124	T	A	89859124	2	1	204	1	0	0	0	0	0	0	0	1	12136	1567	55	5		5	PM20D2	6	89859124	Silent	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10	37969334	89859124	81255943	32	12321											
HDDC2	51020	hgsc.bcm.edu	37	chr6	125619919	125619919	+	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	tgctggtgctatgtccccaaCgatgcattctgccatatcat	8	13	8	12	1	2	0	1	0	1	0	3	1	3	0	3	1	5	3	3	1	3	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr6:125619919C>T	ENST00000398153.2	-	3	292	c.250G>A	c.(250-252)Gtt>Att	p.V84I	HDDC2_ENST00000608284.1_Missense_Mutation_p.V84I|HDDC2_ENST00000368377.4_Intron|HDDC2_ENST00000608295.1_Missense_Mutation_p.V84I	NM_016063.2	NP_057147.2	Q7Z4H3	HDDC2_HUMAN	HD domain containing 2	84	HD.					extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|lung(4)	6			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0186)		ATGTCCCCAACGATGCATTCT	0.413																																					p.V84I		Atlas-SNP	.											.	HDDC2	21	.	0			c.G250A						PASS	.						190	168	175					6																	125619919		1925	4164	6089	SO:0001583	missense	51020	exon3			CCCCAACGATGCA	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.250G>A	chr6.hg19:g.125619919C>T	ENSP00000381220:p.Val84Ile	179.0	0.0	.		185.0	85.0	.	NM_016063	Q5TDQ4|Q6NZ49|Q9BTT2|Q9BV31|Q9Y3D1	Missense_Mutation	SNP	ENST00000398153.2	hg19	CCDS43503.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.039411	0.93630	.	.	ENSG00000111906	ENST00000398153	T	0.43688	0.94	5.62	4.76	0.60689	Metal-dependent phosphohydrolase, HD domain (1);Metal-dependent phosphohydrolase, HD subdomain (1);HD domain (1);	0.000000	0.64402	U	0.000001	T	0.35770	0.0943	L	0.48877	1.53	0.80722	D	1	D	0.60575	0.988	P	0.51895	0.683	T	0.28004	-1.0057	10	0.59425	D	0.04	.	13.6517	0.62314	0.0:0.9242:0.0:0.0758	.	84	Q7Z4H3	HDDC2_HUMAN	I	84	ENSP00000381220:V84I	ENSP00000381220:V84I	V	-	1	0	HDDC2	125661618	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.426000	0.80270	1.527000	0.49086	0.655000	0.94253	GTT	.	.	.	none		0.413	HDDC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472493.1	NM_016063		T	125619919	C	T	125619919	3	4	204	1	0	0	0	0	1	0	0	0	7023	536	19	1	380	1	HDDC2	6	125619919	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	35760795	125619919	45495148	33	12322											
SNX10	29887	hgsc.bcm.edu	37	chr7	26404687	26404687	+	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	acaactgccagaacttccatCtaaaaacctgtttttcaaca	15	11	3	12	0	2	1	1	0	1	1	3	1	3	1	3	0	5	1	3	0	6	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr7:26404687C>G	ENST00000338523.4	+	5	420	c.233C>G	c.(232-234)tCt>tGt	p.S78C	SNX10_ENST00000409838.1_5'UTR|SNX10_ENST00000396376.1_Missense_Mutation_p.S78C|SNX10_ENST00000409367.1_Missense_Mutation_p.S38C|SNX10_ENST00000446848.2_Missense_Mutation_p.S104C	NM_001199835.1|NM_013322.2	NP_001186764.1|NP_037454.2	Q9Y5X0	SNX10_HUMAN	sorting nexin 10	78	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.|Required for the interaction with ATP6V1D.				cilium assembly (GO:0042384)|endosome organization (GO:0007032)|intracellular protein transport (GO:0006886)|osteoclast differentiation (GO:0030316)|protein localization to centrosome (GO:0071539)|protein localization to cilium (GO:0061512)	cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extrinsic component of endosome membrane (GO:0031313)|nucleus (GO:0005634)	1-phosphatidylinositol binding (GO:0005545)|ATPase binding (GO:0051117)			endometrium(1)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	6						GAACTTCCATCTAAAAACCTG	0.408											OREG0017908	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S78C		Atlas-SNP	.											.	SNX10	19	.	0			c.C233G						PASS	.						58	61	60					7																	26404687		2203	4300	6503	SO:0001583	missense	29887	exon5			TTCCATCTAAAAA	AF121860	CCDS5399.1, CCDS56470.1	7p15.2	2008-05-22			ENSG00000086300	ENSG00000086300		"Sorting nexins"	14974	protein-coding gene	gene with protein product		614780				17012226	Standard	NM_013322		Approved		uc010kuu.3	Q9Y5X0	OTTHUMG00000023650	ENST00000338523.4:c.233C>G	chr7.hg19:g.26404687C>G	ENSP00000343709:p.Ser78Cys	81.0	0.0	.	786	109.0	6.0	.	NM_001199835	E9PFH5|Q8IYT5	Missense_Mutation	SNP	ENST00000338523.4	hg19	CCDS5399.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.333040	0.81801	.	.	ENSG00000086300	ENST00000416246;ENST00000338523;ENST00000446848;ENST00000396376;ENST00000409367	T;T;T;T;T	0.37752	1.18;1.18;1.18;1.18;1.18	6.17	6.17	0.99709	Phox homologous domain (5);	0.052852	0.85682	D	0.000000	T	0.61540	0.2355	M	0.68952	2.095	0.47659	D	0.999481	D;D	0.76494	0.999;0.999	D;D	0.70487	0.969;0.917	T	0.57711	-0.7764	10	0.56958	D	0.05	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	104;78	B4DJM0;Q9Y5X0	.;SNX10_HUMAN	C	104;78;104;78;38	ENSP00000408164:S104C;ENSP00000343709:S78C;ENSP00000395474:S104C;ENSP00000379661:S78C;ENSP00000387274:S38C	ENSP00000343709:S78C	S	+	2	0	SNX10	26371212	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	6.525000	0.73795	2.941000	0.99782	0.655000	0.94253	TCT	.	.	.	none		0.408	SNX10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214120.1			G	26404687	C	G	26404687	3	3	204	1	0	0	0	0	1	0	0	0	14894	913	32	4	247	4	SNX10	7	26404687	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10		26404687	132733976	34	12323											
CCDC129	223075	hgsc.bcm.edu	37	chr7	31609394	31609394	+	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	tctttgtatgaacaagggatGgttcaaatgactgtgaaaga	14	12	11	4	0	2	4	1	3	1	1	2	5	2	5	0	2	1	2	0	2	5	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr7:31609394G>T	ENST00000407970.3	+	5	317	c.279G>T	c.(277-279)atG>atT	p.M93I	CCDC129_ENST00000319386.3_Missense_Mutation_p.M93I|CCDC129_ENST00000409210.1_Start_Codon_SNP_p.M1I|CCDC129_ENST00000451887.2_Missense_Mutation_p.M119I|CCDC129_ENST00000482748.1_3'UTR	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	93										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						AACAAGGGATGGTTCAAATGA	0.373																																					p.M119I		Atlas-SNP	.											.	CCDC129	127	.	0			c.G357T						PASS	.						119	101	107					7																	31609394		2203	4300	6503	SO:0001583	missense	223075	exon5			AGGGATGGTTCAA	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.279G>T	chr7.hg19:g.31609394G>T	ENSP00000384416:p.Met93Ile	140.0	0.0	.		147.0	24.0	.	NM_001257968	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Missense_Mutation	SNP	ENST00000407970.3	hg19	CCDS5435.2	.	.	.	.	.	.	.	.	.	.	G	13.03	2.116871	0.37339	.	.	ENSG00000180347	ENST00000409717;ENST00000456011;ENST00000319386;ENST00000407970;ENST00000454513;ENST00000451887;ENST00000538406;ENST00000409210	T;T;T;T;T;T;T	0.39997	1.05;1.07;2.39;2.66;1.06;2.63;2.3	5.49	0.437	0.16555	.	0.576671	0.16859	N	0.196589	T	0.20373	0.0490	N	0.21448	0.665	0.20563	N	0.999888	B;B;B;B	0.20887	0.049;0.049;0.049;0.049	B;B;B;B	0.17433	0.008;0.018;0.018;0.018	T	0.18777	-1.0326	10	0.12766	T	0.61	-0.3883	3.0709	0.06230	0.1436:0.2578:0.4642:0.1344	.	119;103;93;93	F5H3V5;F5H2J8;Q6ZRS4;Q6ZRS4-2	.;.;CC129_HUMAN;.	I	93;93;93;93;93;119;103;1	ENSP00000387220:M93I;ENSP00000390544:M93I;ENSP00000313062:M93I;ENSP00000384416:M93I;ENSP00000413233:M93I;ENSP00000395835:M119I;ENSP00000387214:M1I	ENSP00000313062:M93I	M	+	3	0	CCDC129	31575919	0.999000	0.42202	0.971000	0.41717	0.937000	0.57800	0.316000	0.19469	-0.088000	0.12506	0.655000	0.94253	ATG	.	.	.	none		0.373	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300		T	31609394	G	T	31609394	3	4	204	1	0	0	0	0	1	0	0	0	2766	1348	47	4	293	4	CCDC129	7	31609394	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	5204707	31609394	127529269	35	12324											
CFTR	1080	hgsc.bcm.edu	37	chr7	117267708	117267708	+	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	agaattcacacgtgaagaaaGatgacatctggccctcaggg	14	7	11	9	1	3	5	2	2	1	3	3	5	3	5	1	2	0	0	1	2	3	1			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr7:117267708G>T	ENST00000003084.6	+	22	3733	c.3601G>T	c.(3601-3603)Gat>Tat	p.D1201Y	AC000111.6_ENST00000456270.1_RNA|CFTR_ENST00000454343.1_Missense_Mutation_p.D1140Y	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	1201					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)	CGTGAAGAAAGATGACATCTG	0.413									Cystic Fibrosis																												p.D1201Y		Atlas-SNP	.											.	CFTR	171	.	0			c.G3601T						PASS	.						86	78	81					7																	117267708		2203	4300	6503	SO:0001583	missense	1080	exon22	Familial Cancer Database	CF	AAGAAAGATGACA	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.3601G>T	chr7.hg19:g.117267708G>T	ENSP00000003084:p.Asp1201Tyr	91.0	0.0	.		103.0	24.0	.	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Missense_Mutation	SNP	ENST00000003084.6	hg19	CCDS5773.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.99|13.99	2.402264|2.402264	0.42613|0.42613	.|.	.|.	ENSG00000001626|ENSG00000001626	ENST00000003084;ENST00000454343;ENST00000426809|ENST00000468795	D;D;D|D	0.93366|0.93366	-3.15;-2.96;-3.21|-3.21	5.86|5.86	2.07|2.07	0.26955|0.26955	.|.	0.549977|.	0.20348|.	N|.	0.094112|.	D|D	0.91140|0.91140	0.7210|0.7210	L|L	0.45581|0.45581	1.43|1.43	0.34472|0.34472	D|D	0.702874|0.702874	P|.	0.47409|.	0.895|.	B|.	0.43536|.	0.423|.	D|D	0.89511|0.89511	0.3771|0.3771	10|7	0.72032|0.66056	D|D	0.01|0.02	-3.7623|-3.7623	5.6055|5.6055	0.17377|0.17377	0.261:0.0:0.6124:0.1266|0.261:0.0:0.6124:0.1266	.|.	1201|.	P13569|.	CFTR_HUMAN|.	Y|N	1201;1140;1171|142	ENSP00000003084:D1201Y;ENSP00000403677:D1140Y;ENSP00000389119:D1171Y|ENSP00000419254:K142N	ENSP00000003084:D1201Y|ENSP00000419254:K142N	D|K	+|+	1|3	0|2	CFTR|CFTR	117054944|117054944	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.591000|0.591000	0.36615|0.36615	2.668000|2.668000	0.46816|0.46816	0.177000|0.177000	0.19895|0.19895	-0.142000|-0.142000	0.14014|0.14014	GAT|AAG	.	.	.	none		0.413	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492		T	117267708	G	T	117267708	3	4	204	1	0	0	0	0	1	0	0	0	3296	942	33	4	3687	4	CFTR	7	117267708	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	85658314	117267708	41870955	36	12325											
CCNE2	9134	hgsc.bcm.edu	37	chr8	95906316	95906316	+	Missense_Mutation	SNP	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	gggggattccgtctggctggGctggggctgctgcttagctt	2	12	18	9	1	1	0	0	0	1	0	2	1	2	1	1	6	3	6	1	6	1	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr8:95906316G>A	ENST00000520509.1	-	3	298	c.46C>T	c.(46-48)Ccc>Tcc	p.P16S	CCNE2_ENST00000396133.3_Missense_Mutation_p.P16S|NDUFAF6_ENST00000396113.1_5'Flank|CCNE2_ENST00000523476.1_5'Flank|CCNE2_ENST00000308108.4_Missense_Mutation_p.P16S			O96020	CCNE2_HUMAN	cyclin E2	16					cell cycle checkpoint (GO:0000075)|cell division (GO:0051301)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			cervix(1)|endometrium(2)|large_intestine(3)|lung(4)|prostate(1)	11	Breast(36;8.75e-07)					GTCTGGCTGGGCTGGGGCTGC	0.443																																					p.P16S		Atlas-SNP	.											.	CCNE2	29	.	0			c.C46T						PASS	.						141	161	154					8																	95906316		2203	4300	6503	SO:0001583	missense	9134	exon3			GGCTGGGCTGGGG	AF091433	CCDS6264.1	8q22.1	2005-10-18			ENSG00000175305	ENSG00000175305			1590	protein-coding gene	gene with protein product		603775				9840927, 9840943	Standard	NM_057749		Approved	CYCE2	uc003yhc.3	O96020	OTTHUMG00000164696	ENST00000520509.1:c.46C>T	chr8.hg19:g.95906316G>A	ENSP00000429089:p.Pro16Ser	71.0	0.0	.		89.0	19.0	.	NM_057749	O95439	Missense_Mutation	SNP	ENST00000520509.1	hg19	CCDS6264.1	.	.	.	.	.	.	.	.	.	.	G	12.89	2.072843	0.36566	.	.	ENSG00000175305	ENST00000520509;ENST00000308108;ENST00000396133	T;T;T	0.30981	1.94;1.94;1.51	5.29	2.11	0.27256	.	0.268590	0.33980	N	0.004370	T	0.24470	0.0593	L	0.50333	1.59	0.30643	N	0.7563	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.001	T	0.24977	-1.0145	10	0.13853	T	0.58	.	11.6218	0.51121	0.0:0.1897:0.6789:0.1315	.	16;16	Q8WUE3;O96020	.;CCNE2_HUMAN	S	16	ENSP00000429089:P16S;ENSP00000309181:P16S;ENSP00000379437:P16S	ENSP00000309181:P16S	P	-	1	0	CCNE2	95975492	0.949000	0.32298	1.000000	0.80357	0.956000	0.61745	0.420000	0.21263	0.601000	0.29879	0.561000	0.74099	CCC	.	.	.	none		0.443	CCNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379808.1	NM_057749, NM_004702		A	95906316	G	A	95906316	3	1	204	1	0	0	0	0	1	0	0	0	2923	1203	42	2	1208	2	CCNE2	8	95906316	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10		95906316	50457706	37	12326											
IFT74	80173	hgsc.bcm.edu	37	chr9	26962063	26962075	+	Frame_Shift_Del	DEL	GAAATATTCGAGT	GAAATATTCGAGT	-																															tgggatacgacccctatcagGaaatattcgagtggcaactg																								rs200556379|rs542289534		TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	GAAATATTCGAGT	GAAATATTCGAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr9:26962063_26962075delGAAATATTCGAGT	ENST00000443698.1	+	2	269_281	c.98_110delGAAATATTCGAGT	c.(97-111)ggaaatattcgagtgfs	p.GNIRV33fs	IFT74_ENST00000433700.1_Frame_Shift_Del_p.GNIRV33fs|IFT74_ENST00000380062.5_Frame_Shift_Del_p.GNIRV33fs|IFT74_ENST00000429045.2_Frame_Shift_Del_p.GNIRV33fs	NM_001099222.1	NP_001092692.1	Q96LB3	IFT74_HUMAN	intraflagellar transport 74	33	Basic region.				cilium assembly (GO:0042384)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|keratinocyte development (GO:0003334)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|nucleus (GO:0005634)	beta-tubulin binding (GO:0048487)|chromatin binding (GO:0003682)			endometrium(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	6		all_neural(11;2.36e-10)		Lung(218;1.4e-05)|LUSC - Lung squamous cell carcinoma(38;0.000114)		CCCCTATCAGGAAATATTCGAGTGGCAACTGCA	0.493																																					p.33_37del		Pindel	.											.	IFT74	46	.	0			c.97_109del						PASS	.																																			SO:0001589	frameshift_variant	80173	exon2			.	AK023707	CCDS43793.1, CCDS47955.1	9p21.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000096872	ENSG00000096872		"Intraflagellar transport homologs"	21424	protein-coding gene	gene with protein product	"capillary morphogenesis protein 1"	608040	"coiled-coil domain containing 2", "intraflagellar transport 74 homolog (Chlamydomonas)"	CCDC2		11683410	Standard	NM_001099223		Approved	CMG1, CMG-1, FLJ22621	uc003zqg.4	Q96LB3	OTTHUMG00000021028	ENST00000443698.1:c.98_110delGAAATATTCGAGT	chr9.hg19:g.26962063_26962075delGAAATATTCGAGT	ENSP00000404122:p.Gly33fs	84.0	0.0	.		27.0	10.0	0.370	NM_001099222	Q3B789|Q5VY34|Q6PGQ8|Q9H643|Q9H8G7	Frame_Shift_Del	DEL	ENST00000443698.1	hg19	CCDS43793.1																																																																																			.	.	.	none		0.493	IFT74-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055476.2	NM_025103		-	26962075	GAAATATTCGAGT	-	26962063	7	5	204	1	0	1	0	1	0	0	0	0	7570	1174	41	0	100	0	IFT74	9	26962063	Frame_Shift_Del	DEL	GAAATATTCGAGT	TCGA-IA-A40Y-01A-11D-A25F-10		26962063	114251368	38	12327											
ALAD	210	hgsc.bcm.edu	37	chr9	116153879	116153879	+	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	tccaccaagggcctcagcatCtcttccagccgcttcacacc	8	8	6	19	1	3	0	2	0	1	0	6	0	5	0	6	1	2	2	6	1	1	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr9:116153879C>T	ENST00000409155.3	-	4	385	c.189G>A	c.(187-189)gaG>gaA	p.E63E	ALAD_ENST00000482001.1_5'UTR|ALAD_ENST00000277315.5_Silent_p.E46E	NM_000031.5	NP_000022.3	P13716	HEM2_HUMAN	aminolevulinate dehydratase	63					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)	GCCTCAGCATCTCTTCCAGCC	0.577																																					p.E63E		Atlas-SNP	.											.	ALAD	36	.	0			c.G189A						PASS	.						82	75	77					9																	116153879		2203	4300	6503	SO:0001819	synonymous_variant	210	exon4			CAGCATCTCTTCC	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.189G>A	chr9.hg19:g.116153879C>T		189.0	0.0	.		116.0	5.0	.	NM_000031	A8K375|B2R6F2|Q16870|Q16871|Q9BVQ9	Silent	SNP	ENST00000409155.3	hg19	CCDS6794.2																																																																																			.	.	.	none		0.577	ALAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053724.3	NM_001003945		T	116153879	C	T	116153879	2	4	204	1	0	0	0	0	0	0	0	1	483	912	32	2		2	ALAD	9	116153879	Silent	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	89191816	116153879	25059552	39	12328											
PHF19	26147	hgsc.bcm.edu	37	chr9	123620475	123620475	+	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	cactgctgtccgaggggcagCgtccatccagctcagctgcc	6	7	12	16	2	1	0	1	0	0	0	4	1	4	0	4	2	5	4	4	2	0	0	rs144405933		TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr9:123620475C>T	ENST00000373896.3	-	15	1742	c.1490G>A	c.(1489-1491)cGc>cAc	p.R497H	PHF19_ENST00000419155.1_Missense_Mutation_p.R288H|PHF19_ENST00000487555.1_5'UTR	NM_015651.1	NP_056466.1	Q5T6S3	PHF19_HUMAN	PHD finger protein 19	497					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						CGAGGGGCAGCGTCCATCCAG	0.597																																					p.R497H		Atlas-SNP	.											.	PHF19	47	.	0			c.G1490A						PASS	.	C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	79	71	74		1490	3	0.6	9	dbSNP_134	74	0,8600		0,0,4300	no	missense	PHF19	NM_015651.1	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	497/581	123620475	1,13005	2203	4300	6503	SO:0001583	missense	26147	exon15			GGGCAGCGTCCAT	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.1490G>A	chr9.hg19:g.123620475C>T	ENSP00000363003:p.Arg497His	80.0	0.0	.		45.0	21.0	.	NM_015651	Q32NF2|Q5T6S4|Q6N038|Q8TBL6|Q9UFS9	Missense_Mutation	SNP	ENST00000373896.3	hg19	CCDS35116.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.059942	0.76074	2.27E-4	0.0	ENSG00000119403	ENST00000544082;ENST00000373896;ENST00000419155	T;T	0.49432	1.79;0.78	4.97	3.03	0.35002	.	0.659654	0.15009	N	0.285669	T	0.39627	0.1085	N	0.24115	0.695	0.36632	D	0.876372	D	0.67145	0.996	P	0.49502	0.613	T	0.36841	-0.9731	10	0.45353	T	0.12	-8.0699	9.2722	0.37679	0.0:0.8127:0.0:0.1873	.	497	Q5T6S3	PHF19_HUMAN	H	497;497;288	ENSP00000363003:R497H;ENSP00000407433:R288H	ENSP00000363003:R497H	R	-	2	0	PHF19	122660296	0.728000	0.28080	0.574000	0.28523	0.897000	0.52465	0.193000	0.17116	0.449000	0.26747	-0.367000	0.07326	CGC	.	C|1.000;T|0.000	0.000	weak		0.597	PHF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053838.3	XM_045308		T	123620475	C	T	123620475	3	4	204	1	0	0	0	0	1	0	0	0	11836	768	27	1	256	1	PHF19	9	123620475	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	7466596	123620475	17592956	40	12329											
FUBP3	8939	hgsc.bcm.edu	37	chr9	133501892	133501892	+	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	gtggcctcgtcataggcaaaGgtaagaggcagctggggttt	9	9	16	7	1	1	1	1	0	0	1	2	1	1	1	1	6	1	5	1	6	3	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr9:133501892G>A	ENST00000319725.9	+	12	1192	c.1117G>A	c.(1117-1119)Ggg>Agg	p.G373R		NM_003934.1	NP_003925.1	Q96I24	FUBP3_HUMAN	far upstream element (FUSE) binding protein 3	373	KH 4. {ECO:0000255|PROSITE- ProRule:PRU00117}.				positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(10)|ovary(2)|urinary_tract(2)	21				OV - Ovarian serous cystadenocarcinoma(145;0.000279)		CATAGGCAAAGGTAAGAGGCA	0.607											OREG0019546	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G373R		Atlas-SNP	.											.	FUBP3	44	.	0			c.G1117A						PASS	.						65	74	71					9																	133501892		2024	4189	6213	SO:0001630	splice_region_variant	8939	exon12			GGCAAAGGTAAGA	U69127	CCDS43893.1	9q34.11	2008-02-05			ENSG00000107164	ENSG00000107164			4005	protein-coding gene	gene with protein product		603536		FBP3		8940189	Standard	NM_003934		Approved		uc004bzr.1	Q96I24	OTTHUMG00000020809	ENST00000319725.9:c.1117+1G>A	chr9.hg19:g.133501892G>A		132.0	0.0	.	1603	83.0	4.0	.	NM_003934	A3KFK8|A3KFL0|Q92946|Q9BVB6	Missense_Mutation	SNP	ENST00000319725.9	hg19	CCDS43893.1	.	.	.	.	.	.	.	.	.	.	G	34	5.383763	0.95967	.	.	ENSG00000107164	ENST00000319725	T	0.39592	1.07	5.52	5.52	0.82312	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.70587	0.3241	M	0.87381	2.88	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.74688	-0.3581	10	0.56958	D	0.05	-18.5882	18.4484	0.90695	0.0:0.0:1.0:0.0	.	373;373	A3KFK8;Q96I24	.;FUBP3_HUMAN	R	373	ENSP00000318177:G373R	ENSP00000318177:G373R	G	+	1	0	FUBP3	132491713	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.869000	0.99810	2.590000	0.87494	0.655000	0.94253	GGG	.	.	.	none		0.607	FUBP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054666.1		Missense_Mutation	A	133501892	G	A	133501892	5	1	204	1	0	0	0	0	0	0	1	0	6100	1014	35	2	1163	2	FUBP3	9	133501892	Splice_Site	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	9881417	133501892	7711539	41	12330											
CUBN	8029	hgsc.bcm.edu	37	chr10	16955917	16955917	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gattctccactcgcagatccGgccatgaggatttgggttcg	7	11	12	11	3	1	2	0	1	1	1	5	4	2	3	3	3	0	2	3	3	0	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr10:16955917G>A	ENST00000377833.4	-	48	7491	c.7426C>T	c.(7426-7428)Cgg>Tgg	p.R2476W		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2476	CUB 18. {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)	TCGCAGATCCGGCCATGAGGA	0.532																																					p.R2476W		Atlas-SNP	.											CUBN,NS,carcinoma,0,1	CUBN	515	.	0			c.C7426T						PASS	.						113	107	109					10																	16955917		2203	4300	6503	SO:0001583	missense	8029	exon48			AGATCCGGCCATG	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.7426C>T	chr10.hg19:g.16955917G>A	ENSP00000367064:p.Arg2476Trp	68.0	0.0	.		42.0	14.0	.	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.165155	0.38217	.	.	ENSG00000107611	ENST00000377833	T	0.28895	1.59	5.42	2.44	0.29823	CUB (5);	0.173875	0.27686	N	0.018262	T	0.32585	0.0834	M	0.76838	2.35	0.80722	D	1	B	0.20988	0.05	B	0.18561	0.022	T	0.11060	-1.0603	10	0.59425	D	0.04	.	8.2013	0.31426	0.0727:0.0:0.5311:0.3961	.	2476	O60494	CUBN_HUMAN	W	2476	ENSP00000367064:R2476W	ENSP00000367064:R2476W	R	-	1	2	CUBN	16995923	1.000000	0.71417	0.175000	0.22980	0.703000	0.40648	1.663000	0.37429	0.219000	0.20840	0.591000	0.81541	CGG	.	.	.	none		0.532	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		A	16955917	G	A	16955917	3	1	204	1	0	0	0	0	1	0	0	0	4053	1115	39	1	3525	1	CUBN	10	16955917	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10		16955917	118578830	42	12331											
BMI1	648	hgsc.bcm.edu	37	chr10	22618246	22618246	+	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	gctggagaactggaaagtgaCtctgggagtgacaaggccaa	13	6	15	7	0	1	3	0	2	1	1	1	6	1	5	1	4	1	1	1	4	4	0			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr10:22618246C>G	ENST00000376663.3	+	10	1261	c.756C>G	c.(754-756)gaC>gaG	p.D252E	COMMD3-BMI1_ENST00000602390.1_Missense_Mutation_p.D395E	NM_005180.8	NP_005171.4	P35226	BMI1_HUMAN	BMI1 proto-oncogene, polycomb ring finger	252	Pro/Ser-rich.				chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|regulation of gene expression (GO:0010468)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|ubiquitin ligase complex (GO:0000151)	RING-like zinc finger domain binding (GO:0071535)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|urinary_tract(1)	12						TGGAAAGTGACTCTGGGAGTG	0.493																																					p.D395E		Atlas-SNP	.											.	.	.	.	0			c.C1185G						PASS	.						92	86	88					10																	22618246		2203	4300	6503	SO:0001583	missense	0	exon14			AAGTGACTCTGGG	BC011652	CCDS7138.1	10p13	2014-06-26	2014-06-26	2006-04-26	ENSG00000168283	ENSG00000168283		"RING-type (C3HC4) zinc fingers", "Polycomb group ring fingers"	1066	protein-coding gene	gene with protein product		164831	"polycomb group ring finger 4", "B lymphoma Mo-MLV insertion region 1 homolog (mouse)"	PCGF4		8268912	Standard	NM_005180		Approved	RNF51		P35226	OTTHUMG00000017807	ENST00000376663.3:c.756C>G	chr10.hg19:g.22618246C>G	ENSP00000365851:p.Asp252Glu	74.0	0.0	.		65.0	22.0	.	NM_001204062	Q16030|Q5T8Z3|Q96F37	Missense_Mutation	SNP	ENST00000376663.3	hg19	CCDS7138.1	.	.	.	.	.	.	.	.	.	.	C	2.210	-0.380859	0.05000	.	.	ENSG00000168283	ENST00000376691;ENST00000376663;ENST00000443519	T;T	0.46063	1.61;0.88	5.58	5.58	0.84498	.	0.045306	0.85682	D	0.000000	T	0.28532	0.0706	N	0.20328	0.56	0.49483	D	0.99979	B;B	0.26547	0.152;0.091	B;B	0.23275	0.03;0.045	T	0.11542	-1.0583	10	0.06891	T	0.86	-6.5673	19.1861	0.93644	0.0:1.0:0.0:0.0	.	252;252	Q5U0M5;P35226	.;BMI1_HUMAN	E	164;252;157	ENSP00000365851:D252E;ENSP00000390768:D157E	ENSP00000365851:D252E	D	+	3	2	BMI1	22658252	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.602000	0.61098	2.638000	0.89438	0.650000	0.86243	GAC	.	.	.	none		0.493	BMI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047176.1	NM_005180		G	22618246	C	G	22618246	3	3	204	1	0	0	0	0	1	0	0	0	1455	564	20	4	790	4	BMI1	10	22618246	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	5662329	22618246	112916501	43	12332											
ABCC2	1244	hgsc.bcm.edu	37	chr10	101578919	101578919	+	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	tgtagttctggggaatggaaCaattgtagagaaaggatcct	13	11	13	4	0	1	1	0	0	1	1	2	5	2	4	1	4	1	3	1	4	6	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr10:101578919C>A	ENST00000370449.4	+	19	2626	c.2513C>A	c.(2512-2514)aCa>aAa	p.T838K		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	838	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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)	GGGAATGGAACAATTGTAGAG	0.403																																					p.T838K		Atlas-SNP	.											.	ABCC2	160	.	0			c.C2513A						PASS	.						111	111	111					10																	101578919		2203	4300	6503	SO:0001583	missense	1244	exon19			ATGGAACAATTGT	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.2513C>A	chr10.hg19:g.101578919C>A	ENSP00000359478:p.Thr838Lys	88.0	0.0	.		105.0	21.0	.	NM_000392	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Missense_Mutation	SNP	ENST00000370449.4	hg19	CCDS7484.1	.	.	.	.	.	.	.	.	.	.	C	0.012	-1.655317	0.00779	.	.	ENSG00000023839	ENST00000370449	T	0.75050	-0.9	5.6	2.69	0.31865	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.560580	0.20863	N	0.084313	T	0.43033	0.1229	N	0.04355	-0.22	0.09310	N	0.999999	B	0.11235	0.004	B	0.10450	0.005	T	0.25847	-1.0120	10	0.07813	T	0.8	-14.5155	3.6997	0.08378	0.1227:0.5036:0.2384:0.1353	.	838	Q92887	MRP2_HUMAN	K	838	ENSP00000359478:T838K	ENSP00000359478:T838K	T	+	2	0	ABCC2	101568909	0.000000	0.05858	0.950000	0.38849	0.198000	0.23893	-0.155000	0.10115	0.699000	0.31761	0.561000	0.74099	ACA	.	.	.	none		0.403	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392		A	101578919	C	A	101578919	3	1	204	1	0	0	0	0	1	0	0	0	53	478	17	4	2587	4	ABCC2	10	101578919	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	78960673	101578919	33955828	44	12333											
OR6A2	8590	hgsc.bcm.edu	37	chr11	6816105	6816105	+	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	gacagcatacagtacagagaCcaacttgttggtgtcaaaag	15	8	10	8	0	1	1	1	0	0	1	1	3	1	1	1	1	4	3	1	1	5	4	rs369095527		TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr11:6816105C>A	ENST00000332601.3	-	1	1023	c.835G>T	c.(835-837)Gtc>Ttc	p.V279F		NM_003696.2	NP_003687.2	O95222	OR6A2_HUMAN	olfactory receptor, family 6, subfamily A, member 2	279					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)		AGTACAGAGACCAACTTGTTG	0.468																																					p.V279F		Atlas-SNP	.											.	OR6A2	68	.	0			c.G835T						PASS	.	C	PHE/VAL	0,4402		0,0,2201	139	130	133		835	4.1	0.9	11		133	1,8591	1.2+/-3.3	0,1,4295	no	missense	OR6A2	NM_003696.2	50	0,1,6496	AA,AC,CC		0.0116,0.0,0.0077	probably-damaging	279/328	6816105	1,12993	2201	4296	6497	SO:0001583	missense	8590	exon1			CAGAGACCAACTT	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.835G>T	chr11.hg19:g.6816105C>A	ENSP00000330384:p.Val279Phe	192.0	0.0	.		152.0	18.0	.	NM_003696	Q3MJC7|Q6IF35|Q9H206	Missense_Mutation	SNP	ENST00000332601.3	hg19	CCDS7772.1	.	.	.	.	.	.	.	.	.	.	C	12.13	1.845132	0.32606	0.0	1.16E-4	ENSG00000184933	ENST00000332601	T	0.38722	1.12	5.04	4.13	0.48395	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49916	D	0.000122	T	0.51719	0.1691	L	0.42632	1.34	0.33539	D	0.594625	D	0.89917	1.0	D	0.97110	1.0	T	0.63959	-0.6519	10	0.87932	D	0	.	7.3142	0.26491	0.0:0.7407:0.1697:0.0896	.	279	O95222	OR6A2_HUMAN	F	279	ENSP00000330384:V279F	ENSP00000330384:V279F	V	-	1	0	OR6A2	6772681	0.000000	0.05858	0.883000	0.34634	0.059000	0.15707	-0.095000	0.11077	1.508000	0.48769	0.655000	0.94253	GTC	.	.	.	weak		0.468	OR6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385981.1	NM_003696		A	6816105	C	A	6816105	3	1	204	1	0	0	0	0	1	0	0	0	11193	507	18	4	152	4	OR6A2	11	6816105	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10		6816105	128190411	45	12334											
IGSF22	283284	hgsc.bcm.edu	37	chr11	18738381	18738381	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaagcgtgtgcgtcagaccAtcttcggacaccgtgatttc	8	12	10	11	4	2	2	1	1	1	1	4	3	2	3	2	1	2	0	2	1	1	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr11:18738381A>G	ENST00000513874.1	-	10	1279	c.1140T>C	c.(1138-1140)gaT>gaC	p.D380D	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	380										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						GCGTCAGACCATCTTCGGACA	0.522																																					p.D380D		Atlas-SNP	.											.	IGSF22	211	.	0			c.T1140C						PASS	.						242	237	238					11																	18738381		2077	4197	6274	SO:0001819	synonymous_variant	283284	exon10			CAGACCATCTTCG	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.1140T>C	chr11.hg19:g.18738381A>G		443.0	0.0	.		370.0	109.0	.	NM_173588	A6NNA0|D6RGV7	Silent	SNP	ENST00000513874.1	hg19	CCDS41625.2																																																																																			.	.	.	none		0.522	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588		G	18738381	A	G	18738381	2	3	204	1	0	0	0	0	0	0	0	1	7607	214	8	3		3	IGSF22	11	18738381	Silent	SNP	A	TCGA-IA-A40Y-01A-11D-A25F-10	11922276	18738381	116268135	46	12335											
OR4S1	256148	hgsc.bcm.edu	37	chr11	48328626	48328626	+	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	cctttgctgaaccctttgatCtatacactaaggaacaacga	13	11	6	11	1	1	2	0	2	1	0	1	4	1	3	2	1	5	1	2	1	6	5			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr11:48328626C>G	ENST00000319988.1	+	1	852	c.852C>G	c.(850-852)atC>atG	p.I284M		NM_001004725.1	NP_001004725.1	Q8NGB4	OR4S1_HUMAN	olfactory receptor, family 4, subfamily S, member 1	284						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|skin(3)	21						ACCCTTTGATCTATACACTAA	0.458																																					p.I284M		Atlas-SNP	.											OR4S1,colon,carcinoma,0,1	OR4S1	52	.	0			c.C852G						PASS	.						116	103	108					11																	48328626		2201	4298	6499	SO:0001583	missense	256148	exon1			TTTGATCTATACA	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.852C>G	chr11.hg19:g.48328626C>G	ENSP00000321447:p.Ile284Met	254.0	0.0	.		170.0	8.0	.	NM_001004725	Q6IFB4	Missense_Mutation	SNP	ENST00000319988.1	hg19	CCDS31488.1	.	.	.	.	.	.	.	.	.	.	C	12.07	1.826742	0.32329	.	.	ENSG00000176555	ENST00000319988	T	0.57273	0.41	5.02	-0.74	0.11115	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.72415	0.3457	M	0.91612	3.225	0.29229	N	0.87339	D	0.89917	1.0	D	0.91635	0.999	T	0.63633	-0.6593	9	0.87932	D	0	.	5.8325	0.18588	0.1251:0.5577:0.0:0.3173	.	284	Q8NGB4	OR4S1_HUMAN	M	284	ENSP00000321447:I284M	ENSP00000321447:I284M	I	+	3	3	OR4S1	48285202	0.001000	0.12720	0.255000	0.24374	0.385000	0.30292	-1.467000	0.02352	-0.015000	0.14150	0.655000	0.94253	ATC	.	.	.	none		0.458	OR4S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390556.1	NM_001004725		G	48328626	C	G	48328626	3	3	204	1	0	0	0	0	1	0	0	0	11089	903	32	4	854	4	OR4S1	11	48328626	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	29590245	48328626	86677890	47	12336											
OR4D9	390199	hgsc.bcm.edu	37	chr11	59282746	59282746	+	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	ctctctctgtgatggcgtttGaccgctatatagccatctcc	6	14	8	13	2	3	2	0	2	3	0	5	2	3	2	3	1	1	2	3	1	3	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr11:59282746G>C	ENST00000329328.3	+	1	361	c.361G>C	c.(361-363)Gac>Cac	p.D121H		NM_001004711.1	NP_001004711.1	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D, member 9	121						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						GATGGCGTTTGACCGCTATAT	0.522																																					p.D121H		Atlas-SNP	.											.	OR4D9	47	.	0			c.G361C						PASS	.						83	80	81					11																	59282746		2201	4295	6496	SO:0001583	missense	390199	exon1			GCGTTTGACCGCT	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.361G>C	chr11.hg19:g.59282746G>C	ENSP00000328563:p.Asp121His	115.0	0.0	.		72.0	6.0	.	NM_001004711	Q6IFF3	Missense_Mutation	SNP	ENST00000329328.3	hg19	CCDS31564.1	.	.	.	.	.	.	.	.	.	.	G	14.71	2.617776	0.46736	.	.	ENSG00000172742	ENST00000329328	T	0.55234	0.53	4.16	4.16	0.48862	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42821	U	0.000643	T	0.80053	0.4553	H	0.95437	3.67	0.40769	D	0.983072	D	0.89917	1.0	D	0.81914	0.995	D	0.87427	0.2386	10	0.87932	D	0	-6.8922	15.3691	0.74548	0.0:0.0:1.0:0.0	.	121	Q8NGE8	OR4D9_HUMAN	H	121	ENSP00000328563:D121H	ENSP00000328563:D121H	D	+	1	0	OR4D9	59039322	1.000000	0.71417	0.849000	0.33467	0.015000	0.08874	9.723000	0.98772	2.002000	0.58637	0.563000	0.77884	GAC	.	.	.	none		0.522	OR4D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394237.1	NM_001004711		C	59282746	G	C	59282746	3	2	204	1	0	0	0	0	1	0	0	0	11066	1290	45	4	363	4	OR4D9	11	59282746	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	10954120	59282746	75723770	48	12337											
SLCO2B1	11309	hgsc.bcm.edu	37	chr11	74875111	74875111	+	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	gaagcgcttcggcctctccaGccagacgtcggggctgctgg	5	7	15	14	4	1	1	0	0	1	1	4	2	1	1	3	4	3	3	3	4	1	1			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr11:74875111G>T	ENST00000289575.5	+	3	646	c.251G>T	c.(250-252)aGc>aTc	p.S84I	SLCO2B1_ENST00000454962.2_Intron|SLCO2B1_ENST00000531756.1_Intron|SLCO2B1_ENST00000341411.4_5'UTR|SLCO2B1_ENST00000525650.1_Intron|SLCO2B1_ENST00000526660.1_Intron|SLCO2B1_ENST00000428359.2_Missense_Mutation_p.S62I|SLCO2B1_ENST00000532236.1_Intron	NM_007256.4	NP_009187	O94956	SO2B1_HUMAN	solute carrier organic anion transporter family, member 2B1	84					liver development (GO:0001889)|sodium-independent icosanoid transport (GO:0071718)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid transmembrane transporter activity (GO:0015125)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(2)|endometrium(1)|large_intestine(7)|lung(20)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	39					Acetic acid(DB03166)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Digoxin(DB00390)|Dinoprostone(DB00917)|Ergoloid mesylate(DB01049)|Estradiol(DB00783)|Estrone(DB00655)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Glyburide(DB01016)|Ibuprofen(DB01050)|Iloprost(DB01088)|Latanoprost(DB00654)|Montelukast(DB00471)|Niacin(DB00627)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Tolbutamide(DB01124)	GGCCTCTCCAGCCAGACGTCG	0.637																																					p.S84I		Atlas-SNP	.											.	SLCO2B1	84	.	0			c.G251T						PASS	.						26	22	23					11																	74875111		2200	4293	6493	SO:0001583	missense	11309	exon3			TCTCCAGCCAGAC	AB026256	CCDS8235.1, CCDS44683.1, CCDS53679.1	11q13	2013-05-22	2003-11-25	2003-11-26				"Solute carriers"	10962	protein-coding gene	gene with protein product		604988	"solute carrier family 21 (organic anion transporter), member 9"	SLC21A9			Standard	NM_007256		Approved	OATP-B, OATP2B1	uc001owb.3	O94956		ENST00000289575.5:c.251G>T	chr11.hg19:g.74875111G>T	ENSP00000289575:p.Ser84Ile	150.0	0.0	.		99.0	9.0	.	NM_007256	A8K2G9|B4DGA9|B4DTB0|E7ERN5|E9PPU8|Q9H2Z0|Q9UFU1	Missense_Mutation	SNP	ENST00000289575.5	hg19	CCDS8235.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.547002	0.86022	.	.	ENSG00000137491	ENST00000531713;ENST00000289575;ENST00000527180;ENST00000534186;ENST00000428359	T;T;T;T;T	0.58060	0.36;0.36;0.36;0.36;0.36	4.82	4.82	0.62117	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	T	0.80303	0.4598	H	0.95328	3.655	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.86661	0.1904	10	0.87932	D	0	.	15.3904	0.74739	0.0:0.0:1.0:0.0	.	84	O94956	SO2B1_HUMAN	I	62;84;62;62;62	ENSP00000432889:S62I;ENSP00000289575:S84I;ENSP00000436513:S62I;ENSP00000433872:S62I;ENSP00000388912:S62I	ENSP00000289575:S84I	S	+	2	0	SLCO2B1	74552759	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	9.180000	0.94867	2.240000	0.73641	0.591000	0.81541	AGC	.	.	.	none		0.637	SLCO2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383933.1	NM_007256		T	74875111	G	T	74875111	3	4	204	1	0	0	0	0	1	0	0	0	14740	971	34	4	261	4	SLCO2B1	11	74875111	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	15592365	74875111	60131405	49	12338											
ODZ4	26011	hgsc.bcm.edu	37	chr11	78413254	78413254	+	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	acagccaaagcggtggctgaCtccagggttgcgtggatggc	8	7	16	10	2	0	1	0	1	0	0	1	2	1	2	2	5	3	2	2	5	1	1			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr11:78413254C>A	ENST00000278550.7	-	28	4866	c.4404G>T	c.(4402-4404)gaG>gaT	p.E1468D		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1468					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)										CGGTGGCTGACTCCAGGGTTG	0.567																																					p.E1468D		Atlas-SNP	.											.	.	.	.	0			c.G4404T						PASS	.						59	60	60					11																	78413254		2071	4210	6281	SO:0001583	missense	26011	exon28			GGCTGACTCCAGG	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.4404G>T	chr11.hg19:g.78413254C>A	ENSP00000278550:p.Glu1468Asp	102.0	0.0	.		58.0	30.0	.	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	hg19	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	C	17.59	3.428265	0.62844	.	.	ENSG00000149256	ENST00000278550	D	0.90004	-2.6	5.53	5.53	0.82687	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.89636	0.6772	L	0.35593	1.075	0.50467	D	0.999876	D	0.64830	0.994	D	0.70716	0.97	D	0.87315	0.2314	9	.	.	.	.	10.0702	0.42328	0.0:0.8536:0.0:0.1464	.	1468	Q6N022	TEN4_HUMAN	D	1468	ENSP00000278550:E1468D	.	E	-	3	2	ODZ4	78090902	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	0.803000	0.27083	2.882000	0.98803	0.655000	0.94253	GAG	.	.	.	none		0.567	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			A	78413254	C	A	78413254	3	1	204	1	0	0	0	0	1	0	0	0	10844	564	20	4	3933	4	ODZ4	11	78413254	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	3538143	78413254	56593262	50	12339											
A2M	2	hgsc.bcm.edu	37	chr12	9251341	9251341	+	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	agactttgtgatgggctgaaGctcaaatccacctgtgaaat	12	11	10	8	0	1	4	1	3	0	1	2	4	2	4	2	1	1	2	2	1	3	1			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr12:9251341G>C	ENST00000318602.7	-	15	2020	c.1713C>G	c.(1711-1713)agC>agG	p.S571R		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	571					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)	ATGGGCTGAAGCTCAAATCCA	0.527																																					p.S571R		Atlas-SNP	.											.	A2M	180	.	0			c.C1713G						PASS	.						45	46	46					12																	9251341		2203	4300	6503	SO:0001583	missense	2	exon15			GCTGAAGCTCAAA	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.1713C>G	chr12.hg19:g.9251341G>C	ENSP00000323929:p.Ser571Arg	73.0	0.0	.		88.0	15.0	.	NM_000014	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Missense_Mutation	SNP	ENST00000318602.7	hg19	CCDS44827.1	.	.	.	.	.	.	.	.	.	.	G	11.71	1.720504	0.30503	.	.	ENSG00000175899	ENST00000318602;ENST00000540099	T	0.62232	0.04	5.55	3.61	0.41365	Alpha-2-macroglobulin, N-terminal 2 (1);	0.741044	0.13685	N	0.369887	T	0.55924	0.1951	L	0.60455	1.87	0.33904	D	0.638822	B	0.24092	0.097	B	0.30316	0.114	T	0.61574	-0.7035	10	0.36615	T	0.2	.	5.8923	0.18919	0.0783:0.135:0.6479:0.1387	.	571	P01023	A2MG_HUMAN	R	571;586	ENSP00000323929:S571R	ENSP00000323929:S571R	S	-	3	2	A2M	9142608	0.512000	0.26186	0.998000	0.56505	0.376000	0.30014	0.897000	0.28390	1.484000	0.48361	0.655000	0.94253	AGC	.	.	.	none		0.527	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014		C	9251341	G	C	9251341	3	2	204	1	0	0	0	0	1	0	0	0	4	962	34	4	2799	4	A2M	12	9251341	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10		9251341	124600554	51	12340											
ABCD2	225	hgsc.bcm.edu	37	chr12	39973352	39973352	+	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	cttacttatgataaaacataCgagccatgcccattctttgc	12	13	5	11	1	1	1	0	1	1	0	1	2	1	1	2	0	6	0	2	0	5	6			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr12:39973352C>T	ENST00000308666.3	-	8	1997	c.1862G>A	c.(1861-1863)cGt>cAt	p.R621H		NM_005164.3	NP_005155.1	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D (ALD), member 2	621	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				fatty acid beta-oxidation (GO:0006635)|positive regulation of fatty acid beta-oxidation (GO:0032000)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)	p.R621L(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(24)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	52						ATAAAACATACGAGCCATGCC	0.358																																					p.R621H		Atlas-SNP	.											ABCD2,NS,malignant_melanoma,-1,1	ABCD2	127	.	1	Substitution - Missense(1)	lung(1)	c.G1862A						PASS	.						141	136	138					12																	39973352		2203	4300	6503	SO:0001583	missense	225	exon8			AACATACGAGCCA	U28150	CCDS8734.1	12q12	2012-05-16			ENSG00000173208	ENSG00000173208		"ATP binding cassette transporters / subfamily D"	66	protein-coding gene	gene with protein product		601081		ALDL1		8577752	Standard	NM_005164		Approved	ALDR, ALDRP	uc001rmb.2	Q9UBJ2	OTTHUMG00000169337	ENST00000308666.3:c.1862G>A	chr12.hg19:g.39973352C>T	ENSP00000310688:p.Arg621His	60.0	0.0	.		72.0	13.0	.	NM_005164	B2RAM3|Q13210|Q2M3H9	Missense_Mutation	SNP	ENST00000308666.3	hg19	CCDS8734.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.589233	0.86851	.	.	ENSG00000173208	ENST00000308666	D	0.99893	-7.57	5.08	5.08	0.68730	ABC transporter, conserved site (1);ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.069130	0.56097	D	0.000022	D	0.99932	0.9969	H	0.98542	4.26	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.95891	0.8907	9	.	.	.	-16.2697	18.5246	0.90967	0.0:1.0:0.0:0.0	.	621	Q9UBJ2	ABCD2_HUMAN	H	621	ENSP00000310688:R621H	.	R	-	2	0	ABCD2	38259619	1.000000	0.71417	0.983000	0.44433	0.666000	0.39218	7.520000	0.81821	2.381000	0.81170	0.579000	0.79373	CGT	.	.	.	none		0.358	ABCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403591.1	NM_005164		T	39973352	C	T	39973352	3	4	204	1	0	0	0	0	1	0	0	0	61	536	19	1	372	1	ABCD2	12	39973352	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	30722011	39973352	93878543	52	12341											
MLL2	8085	hgsc.bcm.edu	37	chr12	49431988	49431988	+	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	cagctcaggatcagtatatgCcagcaggtcaaactcgtctc	11	9	9	12	1	4	0	3	0	1	0	6	1	4	1	1	2	4	3	1	2	3	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr12:49431988C>G	ENST00000301067.7	-	34	9150	c.9151G>C	c.(9151-9153)Gca>Cca	p.A3051P	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3051					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)										TCAGTATATGCCAGCAGGTCA	0.517																																					p.A3051P		Atlas-SNP	.											.	MLL2	1173	.	0			c.G9151C						PASS	.						97	95	95					12																	49431988		2015	4202	6217	SO:0001583	missense	8085	exon34			TATATGCCAGCAG	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.9151G>C	chr12.hg19:g.49431988C>G	ENSP00000301067:p.Ala3051Pro	235.0	0.0	.		256.0	59.0	.	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	13.32	2.202944	0.38905	.	.	ENSG00000167548	ENST00000301067	D	0.94457	-3.43	5.11	5.11	0.69529	.	0.000000	0.38272	N	0.001746	D	0.96284	0.8788	L	0.49126	1.545	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	D	0.96801	0.9589	10	0.87932	D	0	.	17.698	0.88286	0.0:1.0:0.0:0.0	.	3051	O14686	MLL2_HUMAN	P	3051	ENSP00000301067:A3051P	ENSP00000301067:A3051P	A	-	1	0	MLL2	47718255	1.000000	0.71417	0.972000	0.41901	0.971000	0.66376	7.707000	0.84623	2.549000	0.85964	0.655000	0.94253	GCA	.	.	.	none		0.517	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			G	49431988	C	G	49431988	3	3	204	1	0	0	0	0	1	0	0	0	9628	739	26	4	7546	4	MLL2	12	49431988	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	9458636	49431988	84419907	53	12342											
SHMT2	6472	hgsc.bcm.edu	37	chr12	57625677	57625677	+	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	acgaccggatcatggggctgGacctgcccgatgggggccag	7	5	17	12	3	1	0	1	0	0	0	1	4	1	2	4	6	1	1	4	6	0	0			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr12:57625677G>C	ENST00000328923.3	+	4	945	c.493G>C	c.(493-495)Gac>Cac	p.D165H	SHMT2_ENST00000393827.4_Missense_Mutation_p.W59C|SHMT2_ENST00000557487.1_Missense_Mutation_p.D165H|SHMT2_ENST00000449049.3_Missense_Mutation_p.D144H|SHMT2_ENST00000554600.1_3'UTR|SHMT2_ENST00000553474.1_Missense_Mutation_p.D144H|SHMT2_ENST00000414700.3_Missense_Mutation_p.D144H	NM_001166356.1|NM_005412.5	NP_001159828.1|NP_005403.2	P34897	GLYM_HUMAN	serine hydroxymethyltransferase 2 (mitochondrial)	165					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)	CATGGGGCTGGACCTGCCCGA	0.587																																					p.D165H	Esophageal Squamous(150;1369 2416 49071 49364)	Atlas-SNP	.											.	SHMT2	40	.	0			c.G493C						PASS	.						30	27	28					12																	57625677		2203	4300	6503	SO:0001583	missense	6472	exon4			GGGCTGGACCTGC	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.493G>C	chr12.hg19:g.57625677G>C	ENSP00000333667:p.Asp165His	64.0	0.0	.		75.0	15.0	.	NM_005412	B7Z9F1|E7EQ19|E7EU43|O00740|Q8N1A5	Missense_Mutation	SNP	ENST00000328923.3	hg19	CCDS8934.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.6|24.6	4.546641|4.546641	0.86022|0.86022	.|.	.|.	ENSG00000182199|ENSG00000182199	ENST00000328923;ENST00000557487;ENST00000555634;ENST00000556689;ENST00000414700;ENST00000553529;ENST00000554310;ENST00000557427;ENST00000553474;ENST00000555773;ENST00000554975;ENST00000449049;ENST00000556737|ENST00000393827	T;T;T;T;T;T;T;T;T;T;T;T;T|T	0.50001|0.31510	1.39;0.76;0.76;0.76;1.39;1.39;1.39;1.39;1.39;1.39;1.39;1.39;1.39|1.49	4.53|4.53	4.53|4.53	0.55603|0.55603	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.57110|0.57110	0.2031|0.2031	M|M	0.89163|0.89163	3.01|3.01	0.58432|0.58432	D|D	0.999999|0.999999	D;D;D|D	0.71674|0.67145	0.998;0.993;0.997|0.996	D;D;P|P	0.66497|0.57371	0.944;0.925;0.815|0.819	T|T	0.68228|0.68228	-0.5464|-0.5464	10|9	0.87932|0.87932	D|D	0|0	-5.8122|-5.8122	16.58|16.58	0.84712|0.84712	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	174;165;165|59	B4DWA7;Q8N1A5;P34897|B4DLV4	.;.;GLYM_HUMAN|.	H|C	165;165;4;165;144;144;144;144;144;144;144;144;144|59	ENSP00000333667:D165H;ENSP00000452315:D165H;ENSP00000450930:D4H;ENSP00000452035:D165H;ENSP00000406881:D144H;ENSP00000452161:D144H;ENSP00000450893:D144H;ENSP00000452045:D144H;ENSP00000452419:D144H;ENSP00000451968:D144H;ENSP00000452404:D144H;ENSP00000413770:D144H;ENSP00000451495:D144H|ENSP00000377413:W59C	ENSP00000333667:D165H|ENSP00000377413:W59C	D|W	+|+	1|3	0|0	SHMT2|SHMT2	55911944|55911944	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	9.657000|9.657000	0.98554|0.98554	2.517000|2.517000	0.84864|0.84864	0.561000|0.561000	0.74099|0.74099	GAC|TGG	.	.	.	none		0.587	SHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412525.2	NM_005412		C	57625677	G	C	57625677	3	2	204	1	0	0	0	0	1	0	0	0	14299	1174	41	4	507	4	SHMT2	12	57625677	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	8193689	57625677	76226218	54	12343											
CYP27B1	1594	hgsc.bcm.edu	37	chr12	58160674	58160674	+	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	cccccccttgcagaaaagttCggccagaaagctgggcgtag	10	6	12	13	2	0	2	0	0	0	2	1	2	0	2	4	2	2	4	4	2	4	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr12:58160674C>G	ENST00000228606.4	-	1	360	c.151G>C	c.(151-153)Gaa>Caa	p.E51Q	CYP27B1_ENST00000546496.1_5'Flank	NM_000785.3	NP_000776.1	O15528	CP27B_HUMAN	cytochrome P450, family 27, subfamily B, polypeptide 1	51					bone mineralization (GO:0030282)|calcitriol biosynthetic process from calciol (GO:0036378)|calcium ion homeostasis (GO:0055074)|calcium ion transport (GO:0006816)|decidualization (GO:0046697)|G1 to G0 transition (GO:0070314)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of vitamin D 24-hydroxylase activity (GO:0010980)|positive regulation of vitamin D receptor signaling pathway (GO:0070564)|regulation of bone mineralization (GO:0030500)|response to estrogen (GO:0043627)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)|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 metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	calcidiol 1-monooxygenase activity (GO:0004498)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|urinary_tract(1)	15	all_cancers(7;8.09e-80)|Lung NSC(6;2.26e-27)|all_lung(6;1.99e-25)|all_epithelial(6;3.62e-18)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;1.97e-113)|all cancers(5;1.54e-78)|BRCA - Breast invasive adenocarcinoma(9;0.0294)		Alfacalcidol(DB01436)|Calcidiol(DB00146)|Corticotropin(DB01285)|Ergocalciferol(DB00153)	CAGAAAAGTTCGGCCAGAAAG	0.632																																					p.E51Q		Atlas-SNP	.											.	CYP27B1	47	.	0			c.G151C						PASS	.						65	73	70					12																	58160674		2203	4300	6503	SO:0001583	missense	1594	exon1			AAAGTTCGGCCAG	AB006987	CCDS8954.1	12q14.1	2013-11-13	2003-01-14		ENSG00000111012	ENSG00000111012		"Cytochrome P450s"	2606	protein-coding gene	gene with protein product	"VDDR I", "1alpha(OH)ase", "25-Hydroxyvitamin D3 1alpha-hydroxylase"	609506	"cytochrome P450, subfamily XXVIIB (25-hydroxyvitamin D-1-alpha-hydroxylase), polypeptide 1"	VDD1, PDDR		9295274, 9344864	Standard	NM_000785		Approved	CYP1, P450c1	uc001spz.1	O15528	OTTHUMG00000170457	ENST00000228606.4:c.151G>C	chr12.hg19:g.58160674C>G	ENSP00000228606:p.Glu51Gln	164.0	0.0	.		203.0	9.0	.	NM_000785	B2RC61|Q548T3	Missense_Mutation	SNP	ENST00000228606.4	hg19	CCDS8954.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.516287	0.85495	.	.	ENSG00000111012	ENST00000228606	T	0.68479	-0.33	5.26	5.26	0.73747	.	0.059156	0.64402	D	0.000003	T	0.54127	0.1839	N	0.12920	0.275	0.49299	D	0.999778	B	0.30634	0.288	B	0.39094	0.29	T	0.48603	-0.9021	10	0.08837	T	0.75	.	17.7796	0.88519	0.0:1.0:0.0:0.0	.	51	O15528	CP27B_HUMAN	Q	51	ENSP00000228606:E51Q	ENSP00000228606:E51Q	E	-	1	0	CYP27B1	56446941	1.000000	0.71417	0.963000	0.40424	0.870000	0.49936	6.357000	0.73051	2.729000	0.93468	0.655000	0.94253	GAA	.	.	.	none		0.632	CYP27B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409248.1	NM_000785		G	58160674	C	G	58160674	3	3	204	1	0	0	0	0	1	0	0	0	4161	893	31	4	1411	4	CYP27B1	12	58160674	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	534997	58160674	75691221	55	12344											
TCP11L2	255394	hgsc.bcm.edu	37	chr12	106717360	106717360	+	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	attatgagtctcagaccgcaCcttcaacgccagttggtgga	10	10	10	11	2	2	2	2	1	1	1	3	3	2	3	3	2	1	2	3	2	2	3	rs138241328		TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr12:106717360C>G	ENST00000299045.3	+	6	882	c.708C>G	c.(706-708)caC>caG	p.H236Q	TCP11L2_ENST00000547153.1_Missense_Mutation_p.H236Q|TCP11L2_ENST00000546625.1_Missense_Mutation_p.H236Q|TCP11L2_ENST00000552690.1_3'UTR	NM_152772.1	NP_689985.1	Q8N4U5	T11L2_HUMAN	t-complex 11, testis-specific-like 2	236										endometrium(2)|kidney(2)|large_intestine(5)|ovary(3)|prostate(1)|urinary_tract(2)	15						TCAGACCGCACCTTCAACGCC	0.343																																					p.H236Q		Atlas-SNP	.											.	TCP11L2	59	.	0			c.C708G						PASS	.						55	60	58					12																	106717360		2203	4300	6503	SO:0001583	missense	255394	exon6			ACCGCACCTTCAA	BC033617	CCDS9104.1, CCDS66456.1	12q23.3	2014-08-12	2012-09-20		ENSG00000166046	ENSG00000166046			28627	protein-coding gene	gene with protein product			"t-complex 11 (mouse) like 2", "t-complex 11 (mouse)-like 2"				Standard	XM_005268769		Approved	MGC40368	uc001tln.3	Q8N4U5	OTTHUMG00000170087	ENST00000299045.3:c.708C>G	chr12.hg19:g.106717360C>G	ENSP00000299045:p.His236Gln	130.0	0.0	.		153.0	22.0	.	NM_152772	B2RA65|G3V1Y9	Missense_Mutation	SNP	ENST00000299045.3	hg19	CCDS9104.1	.	.	.	.	.	.	.	.	.	.	C	16.09	3.024466	0.54683	.	.	ENSG00000166046	ENST00000547153;ENST00000299045;ENST00000546625	T;T;T	0.10960	2.82;2.82;2.82	5.76	2.51	0.30379	.	0.573213	0.19030	N	0.124583	T	0.07908	0.0198	N	0.25380	0.74	0.27925	N	0.938083	P;B;B	0.34815	0.47;0.13;0.138	B;B;B	0.39465	0.3;0.039;0.022	T	0.27020	-1.0086	10	0.25751	T	0.34	-14.6909	5.8057	0.18438	0.0:0.5201:0.1733:0.3066	.	236;236;236	Q8N4U5;G3V1Y9;G3V1Z2	T11L2_HUMAN;.;.	Q	236	ENSP00000448952:H236Q;ENSP00000299045:H236Q;ENSP00000449123:H236Q	ENSP00000299045:H236Q	H	+	3	2	TCP11L2	105241490	0.044000	0.20184	0.935000	0.37517	0.949000	0.60115	-0.293000	0.08320	0.588000	0.29660	0.655000	0.94253	CAC	.	C|1.000;T|0.000	.	alt		0.343	TCP11L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407206.1	NM_152772		G	106717360	C	G	106717360	3	3	204	1	0	0	0	0	1	0	0	0	15727	506	18	4	726	4	TCP11L2	12	106717360	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	48556686	106717360	27134535	56	12345											
C12orf34	84915	hgsc.bcm.edu	37	chr12	110207030	110207030	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgggcaagggctatgagacGgtggccgtgccccggctact	6	7	16	12	3	0	1	0	1	0	1	0	2	0	1	3	5	2	3	3	5	3	2	rs138993259		TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr12:110207030G>A	ENST00000538780.1	+	3	2012	c.1296G>A	c.(1294-1296)acG>acA	p.T432T	FAM222A-AS1_ENST00000541723.1_RNA|FAM222A_ENST00000358906.3_Silent_p.T432T|FAM222A-AS1_ENST00000541460.1_RNA	NM_032829.2	NP_116218.2	Q5U5X8	F222A_HUMAN	family with sequence similarity 222, member A	432																	GCTATGAGACGGTGGCCGTGC	0.627																																					p.T432T		Atlas-SNP	.											.	.	.	.	0			c.G1296A						PASS	.	G		0,4396		0,0,2198	22	18	19		1296	-6.8	0.9	12	dbSNP_134	19	1,8569		0,1,4284	no	coding-synonymous	C12orf34	NM_032829.2		0,1,6482	AA,AG,GG		0.0117,0.0,0.0077		432/453	110207030	1,12965	2198	4285	6483	SO:0001819	synonymous_variant	84915	exon3			TGAGACGGTGGCC	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.1296G>A	chr12.hg19:g.110207030G>A		154.0	0.0	.		209.0	18.0	.	NM_032829	Q8NCD5|Q96SP6	Silent	SNP	ENST00000538780.1	hg19	CCDS9133.1																																																																																			.	G|1.000;A|0.000	0.000	weak		0.627	FAM222A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403175.1	NM_032829		A	110207030	G	A	110207030	2	1	204	1	0	0	0	0	0	0	0	1	1683	1103	39	1		1	C12orf34	12	110207030	Silent	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	3489670	110207030	23644865	57	12346											
TRPV4	59341	hgsc.bcm.edu	37	chr12	110234478	110234478	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgccgtgtgtcctcatccGtcacctcccgccggatgatg	4	10	12	15	4	2	1	2	1	0	0	5	2	5	2	6	2	1	0	6	2	0	0	rs374197231		TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr12:110234478G>A	ENST00000418703.2	-	6	1278	c.1184C>T	c.(1183-1185)aCg>aTg	p.T395M	TRPV4_ENST00000536838.1_Missense_Mutation_p.T361M|TRPV4_ENST00000346520.2_Intron|TRPV4_ENST00000541794.1_Missense_Mutation_p.T348M|TRPV4_ENST00000544971.1_Intron|TRPV4_ENST00000261740.2_Missense_Mutation_p.T395M|TRPV4_ENST00000537083.1_Intron|TRPV4_ENST00000392719.2_Missense_Mutation_p.T348M	NM_001177431.1	NP_001170902.1	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel, subfamily V, member 4	395					actin cytoskeleton reorganization (GO:0031532)|actin filament organization (GO:0007015)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cell death (GO:0008219)|cell volume homeostasis (GO:0006884)|cell-cell junction assembly (GO:0007043)|cellular calcium ion homeostasis (GO:0006874)|cellular hypotonic response (GO:0071476)|cellular response to heat (GO:0034605)|cellular response to osmotic stress (GO:0071470)|cortical microtubule organization (GO:0043622)|hyperosmotic salinity response (GO:0042538)|ion transmembrane transport (GO:0034220)|microtubule polymerization (GO:0046785)|negative regulation of neuron projection development (GO:0010977)|osmosensory signaling pathway (GO:0007231)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of microtubule depolymerization (GO:0031117)|regulation of response to osmotic stress (GO:0047484)|response to mechanical stimulus (GO:0009612)|transmembrane transport (GO:0055085)|vasopressin secretion (GO:0030103)	adherens junction (GO:0005912)|cell surface (GO:0009986)|cilium (GO:0005929)|cortical actin cytoskeleton (GO:0030864)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|beta-tubulin binding (GO:0048487)|calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)|cation channel activity (GO:0005261)|microtubule binding (GO:0008017)|osmosensor activity (GO:0005034)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(2)|skin(4)|stomach(1)	35						GTCCTCATCCGTCACCTCCCG	0.627																																					p.T395M		Atlas-SNP	.											.	TRPV4	88	.	0			c.C1184T						PASS	.	G	MET/THR,MET/THR,,MET/THR,	0,4406		0,0,2203	102	85	91		1043,1082,,1184,	3.2	0.9	12		91	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,intron,missense,intron	TRPV4	NM_001177428.1,NM_001177431.1,NM_001177433.1,NM_021625.4,NM_147204.2	81,81,,81,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,,probably-damaging,	348/825,361/838,,395/872,	110234478	1,13005	2203	4300	6503	SO:0001583	missense	59341	exon7			TCATCCGTCACCT	AF263523	CCDS9134.1, CCDS9135.1, CCDS53827.1, CCDS53828.1, CCDS53829.1	12q24.1	2014-09-17				ENSG00000111199		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	18083	protein-coding gene	gene with protein product	"osmosensitive transient receptor potential channel 4"	605427				11025659, 11081638, 16382100, 20037587	Standard	NM_147204		Approved	OTRPC4, TRP12, VROAC, VRL-2, VR-OAC, CMT2C	uc001tpk.2	Q9HBA0		ENST00000418703.2:c.1184C>T	chr12.hg19:g.110234478G>A	ENSP00000406191:p.Thr395Met	95.0	0.0	.		113.0	18.0	.	NM_021625	B7ZKQ6|Q17R79|Q2Y122|Q2Y123|Q2Y124|Q86YZ6|Q8NDY7|Q8NG64|Q96Q92|Q96RS7|Q9HBC0	Missense_Mutation	SNP	ENST00000418703.2	hg19	CCDS9134.1	.	.	.	.	.	.	.	.	.	.	G	12.77	2.037326	0.35989	0.0	1.16E-4	ENSG00000111199	ENST00000418703;ENST00000261740;ENST00000392719;ENST00000541794;ENST00000536838	D;D;D;D;D	0.89552	-2.53;-2.53;-2.31;-2.31;-2.53	5.16	3.22	0.36961	.	0.149468	0.64402	D	0.000018	T	0.81631	0.4863	L	0.31476	0.935	0.80722	D	1	D;B;B	0.54772	0.968;0.184;0.32	P;B;B	0.45276	0.475;0.103;0.103	T	0.78386	-0.2224	10	0.38643	T	0.18	-9.8296	6.9524	0.24552	0.0814:0.0:0.6258:0.2927	.	395;348;361	Q9HBA0;Q9HBA0-4;Q9HBA0-5	TRPV4_HUMAN;.;.	M	395;395;348;348;361	ENSP00000406191:T395M;ENSP00000261740:T395M;ENSP00000376480:T348M;ENSP00000442167:T348M;ENSP00000444336:T361M	ENSP00000261740:T395M	T	-	2	0	TRPV4	108718861	0.916000	0.31088	0.919000	0.36401	0.863000	0.49368	1.418000	0.34782	1.181000	0.42912	-0.251000	0.11542	ACG	.	.	.	weak		0.627	TRPV4-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403270.1	NM_021625		A	110234478	G	A	110234478	3	1	204	1	0	0	0	0	1	0	0	0	16610	1145	40	1	1471	1	TRPV4	12	110234478	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	27448	110234478	23617417	58	12347											
RCBTB1	55213	hgsc.bcm.edu	37	chr13	50134123	50134123	+	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	tccaccacttgcttgatcaaGagattggtacagacctggac	11	10	9	11	0	1	3	1	1	0	2	2	5	2	4	3	2	2	2	3	2	2	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr13:50134123G>C	ENST00000378302.2	-	5	635	c.375C>G	c.(373-375)ctC>ctG	p.L125L	RCBTB1_ENST00000258646.3_Silent_p.L125L|RCBTB1_ENST00000546015.1_Silent_p.L125L	NM_018191.3	NP_060661.3	Q8NDN9	RCBT1_HUMAN	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1	125					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(1)	16		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;4.7e-09)		GCTTGATCAAGAGATTGGTAC	0.483																																					p.L125L		Atlas-SNP	.											.	RCBTB1	34	.	0			c.C375G						PASS	.						210	203	206					13																	50134123		2203	4300	6503	SO:0001819	synonymous_variant	55213	exon5			GATCAAGAGATTG	AF334406	CCDS9418.1	13q14	2013-01-08			ENSG00000136144	ENSG00000136144		"BTB/POZ domain containing"	18243	protein-coding gene	gene with protein product		607867				11306461	Standard	XM_005266441		Approved	FLJ10716, CLLD7, CLLL7	uc001vde.1	Q8NDN9	OTTHUMG00000016915	ENST00000378302.2:c.375C>G	chr13.hg19:g.50134123G>C		224.0	0.0	.		217.0	47.0	.	NM_018191	Q8IY29|Q969U9	Silent	SNP	ENST00000378302.2	hg19	CCDS9418.1																																																																																			.	.	.	none		0.483	RCBTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044912.2	NM_018191		C	50134123	G	C	50134123	2	2	204	1	0	0	0	0	0	0	0	1	13184	929	33	4		4	RCBTB1	13	50134123	Silent	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10		50134123	65035755	59	12348											
NALCN	259232	hgsc.bcm.edu	37	chr13	101881861	101881861	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accaaactcccaagctttttTccaggaccaaatatcttgta	13	12	4	12	0	1	0	0	0	1	0	3	1	3	1	4	1	2	2	4	1	5	6			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr13:101881861T>C	ENST00000251127.6	-	13	1590	c.1509A>G	c.(1507-1509)ggA>ggG	p.G503G	NALCN_ENST00000376196.3_Silent_p.G503G|NALCN_ENST00000470333.1_5'UTR	NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	503					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					CAAGCTTTTTTCCAGGACCAA	0.398																																					p.G503G		Atlas-SNP	.											.	NALCN	431	.	0			c.A1509G						PASS	.						104	112	110					13																	101881861		2203	4300	6503	SO:0001819	synonymous_variant	259232	exon13			CTTTTTTCCAGGA	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.1509A>G	chr13.hg19:g.101881861T>C		51.0	0.0	.		18.0	7.0	.	NM_052867	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Silent	SNP	ENST00000251127.6	hg19	CCDS9498.1																																																																																			.	.	.	none		0.398	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867		C	101881861	T	C	101881861	2	2	204	1	0	0	0	0	0	0	0	1	10155	1770	62	3		3	NALCN	13	101881861	Silent	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10	51747738	101881861	13288017	60	12349											
HECTD1	25831	hgsc.bcm.edu	37	chr14	31582629	31582629	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttaaattaagaatatcactaCtttgaagagtagaaatggcc	17	12	7	5	0	1	4	1	1	0	3	1	4	1	4	1	1	1	1	1	1	9	6			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr14:31582629C>T	ENST00000399332.1	-	33	6406	c.5918G>A	c.(5917-5919)aGt>aAt	p.S1973N	HECTD1_ENST00000553700.1_Missense_Mutation_p.S1973N	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	1973					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)		AATATCACTACTTTGAAGAGT	0.388																																					p.S1973N		Atlas-SNP	.											.	HECTD1	159	.	0			c.G5918A						PASS	.						167	164	165					14																	31582629		1831	4088	5919	SO:0001583	missense	25831	exon33			TCACTACTTTGAA	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.5918G>A	chr14.hg19:g.31582629C>T	ENSP00000382269:p.Ser1973Asn	53.0	0.0	.		52.0	10.0	.	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	hg19	CCDS41939.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	1.089|1.089	-0.664515|-0.664515	0.03428|0.03428	.|.	.|.	ENSG00000092148|ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332;ENST00000553957|ENST00000554882	T;T;T|.	0.43294|.	0.95;0.95;1.2|.	5.94|5.94	2.88|2.88	0.33553|0.33553	.|.	0.115316|.	0.56097|.	U|.	0.000027|.	T|T	0.46112|0.46112	0.1376|0.1376	L|L	0.40543|0.40543	1.245|1.245	0.38847|0.38847	D|D	0.956199|0.956199	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.30679|0.30679	-0.9970|-0.9970	10|5	0.18276|.	T|.	0.48|.	-2.8194|-2.8194	6.637|6.637	0.22889|0.22889	0.0:0.4212:0.0:0.5788|0.0:0.4212:0.0:0.5788	.|.	1973;1973|.	D3DS86;Q9ULT8|.	.;HECD1_HUMAN|.	N|I	1973;1975;1973;1400|339	ENSP00000450697:S1973N;ENSP00000382269:S1973N;ENSP00000451860:S1400N|.	ENSP00000261312:S1975N|.	S|V	-|-	2|1	0|0	HECTD1|HECTD1	30652380|30652380	1.000000|1.000000	0.71417|0.71417	0.970000|0.970000	0.41538|0.41538	0.020000|0.020000	0.10135|0.10135	2.462000|2.462000	0.45049|0.45049	0.363000|0.363000	0.24346|0.24346	-0.145000|-0.145000	0.13849|0.13849	AGT|GTA	.	.	.	none		0.388	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			T	31582629	C	T	31582629	3	4	204	1	0	0	0	0	1	0	0	0	7046	565	20	2	1958	2	HECTD1	14	31582629	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10		31582629	75766911	61	12350											
HEATR5A	25938	hgsc.bcm.edu	37	chr14	31763220	31763220	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcagtttttccatgatacAggatgctaaagagtaaatgt	13	13	9	6	0	0	2	0	1	0	1	1	3	1	3	1	1	3	4	1	1	5	5			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr14:31763220A>G	ENST00000389961.3	-	34	5691	c.5692T>C	c.(5692-5694)Tgt>Cgt	p.C1898R	RP11-596D21.1_ENST00000551799.1_RNA|HEATR5A_ENST00000439727.1_Missense_Mutation_p.C1611R|HEATR5A_ENST00000439348.1_Missense_Mutation_p.C1823R|HEATR5A_ENST00000543095.2_Missense_Mutation_p.C1904R			Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	1898										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)		TCCATGATACAGGATGCTAAA	0.398																																					p.C1904R		Atlas-SNP	.											.	HEATR5A	181	.	0			c.T5710C						PASS	.						119	103	108					14																	31763220		1848	4109	5957	SO:0001583	missense	25938	exon35			TGATACAGGATGC	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.5692T>C	chr14.hg19:g.31763220A>G	ENSP00000374611:p.Cys1898Arg	186.0	0.0	.		101.0	5.0	.	NM_015473	Q68DD8|Q6P3S5|Q6P5R9|Q9H8D7|Q9NXB7|Q9P2N0|Q9UFQ3	Missense_Mutation	SNP	ENST00000389961.3	hg19		.	.	.	.	.	.	.	.	.	.	A	0.006	-2.045063	0.00398	.	.	ENSG00000129493	ENST00000389961;ENST00000439348;ENST00000439727;ENST00000543095	T;T;T;T	0.67865	-0.07;-0.29;-0.07;-0.07	5.22	1.47	0.22746	.	0.352635	0.30227	N	0.010105	T	0.20129	0.0484	N	0.00237	-1.79	0.19575	N	0.999969	B	0.02656	0.0	B	0.01281	0.0	T	0.40683	-0.9550	10	0.02654	T	1	.	4.434	0.11542	0.6479:0.0:0.2188:0.1333	.	1823	Q86XA9-2	.	R	1898;1823;1611;1904	ENSP00000374611:C1898R;ENSP00000405407:C1823R;ENSP00000408681:C1611R;ENSP00000437968:C1904R	ENSP00000374611:C1898R	C	-	1	0	HEATR5A	30832971	0.000000	0.05858	0.277000	0.24703	0.168000	0.22595	0.567000	0.23608	0.317000	0.23160	-0.509000	0.04479	TGT	.	.	.	none		0.398	HEATR5A-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015473		G	31763220	A	G	31763220	3	3	204	1	0	0	0	0	1	0	0	0	7038	188	7	3	438	3	HEATR5A	14	31763220	Missense_Mutation	SNP	A	TCGA-IA-A40Y-01A-11D-A25F-10	180591	31763220	75586320	62	12351											
SYNE2	23224	hgsc.bcm.edu	37	chr14	64519117	64519117	+	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	aactcaaagatcacagcaatTagaatttaagttggaagaaa	20	9	7	5	0	2	3	2	0	0	3	2	4	2	4	0	1	2	2	0	1	8	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr14:64519117T>G	ENST00000344113.4	+	48	8698	c.8486T>G	c.(8485-8487)tTa>tGa	p.L2829*	SYNE2_ENST00000554584.1_Nonsense_Mutation_p.L2862*|SYNE2_ENST00000358025.3_Nonsense_Mutation_p.L2829*|SYNE2_ENST00000357395.3_5'UTR	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2829					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)		TCACAGCAATTAGAATTTAAG	0.343																																					p.L2829X		Atlas-SNP	.											.	SYNE2	577	.	0			c.T8486G						PASS	.						43	41	42					14																	64519117		1811	4086	5897	SO:0001587	stop_gained	23224	exon48			AGCAATTAGAATT	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.8486T>G	chr14.hg19:g.64519117T>G	ENSP00000341781:p.Leu2829*	50.0	0.0	.		45.0	6.0	.	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Nonsense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	T	50	16.272729	0.99859	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	.	.	.	5.27	5.27	0.74061	.	0.000000	0.38720	N	0.001585	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.7819	0.63087	0.0:0.0:0.0:1.0	.	.	.	.	X	2829;2829;2862;2862	.	ENSP00000261678:L2862X	L	+	2	0	SYNE2	63588870	0.992000	0.36948	0.998000	0.56505	0.933000	0.57130	5.172000	0.65003	2.004000	0.58718	0.260000	0.18958	TTA	.	.	.	none		0.343	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		G	64519117	T	G	64519117	4	3	204	1	0	0	0	0	0	1	0	0	15458	1764	61	5	8672	5	SYNE2	14	64519117	Nonsense_Mutation	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10	32755897	64519117	42830423	63	12352											
SIPA1L1	26037	hgsc.bcm.edu	37	chr14	72171977	72171977	+	Missense_Mutation	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	cagcagtatcaaaggtactgCcagctttccgagagagcccc	11	7	10	13	1	1	1	1	0	0	1	2	3	2	1	4	1	5	4	4	1	3	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr14:72171977C>T	ENST00000555818.1	+	14	4096	c.3748C>T	c.(3748-3750)Cca>Tca	p.P1250S	SIPA1L1_ENST00000554874.1_3'UTR|SIPA1L1_ENST00000537413.1_Missense_Mutation_p.P704S|SIPA1L1_ENST00000381232.3_Missense_Mutation_p.P1229S|SIPA1L1_ENST00000358550.2_Missense_Mutation_p.P1229S	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	1250					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)		AAAGGTACTGCCAGCTTTCCG	0.468																																					p.P1250S		Atlas-SNP	.											.	SIPA1L1	219	.	0			c.C3748T						PASS	.						119	112	114					14																	72171977		2203	4300	6503	SO:0001583	missense	26037	exon14			GTACTGCCAGCTT	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.3748C>T	chr14.hg19:g.72171977C>T	ENSP00000450832:p.Pro1250Ser	115.0	0.0	.		98.0	4.0	.	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	hg19	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	C	7.356	0.623914	0.14193	.	.	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550;ENST00000537413	T;T;T;T	0.54866	0.55;0.55;0.55;0.55	6.16	6.16	0.99307	.	0.145473	0.64402	D	0.000007	T	0.52322	0.1727	N	0.11560	0.145	0.58432	D	0.999998	B;D;B;B;D	0.63880	0.012;0.993;0.004;0.066;0.972	B;D;B;B;P	0.70227	0.022;0.968;0.008;0.039;0.777	T	0.38908	-0.9639	10	0.02654	T	1	-15.1553	20.8598	0.99761	0.0:1.0:0.0:0.0	.	704;1250;704;1229;1250	F5GYF8;A6H8W6;B4DYX7;O43166-2;O43166	.;.;.;.;SI1L1_HUMAN	S	1229;1250;1229;704	ENSP00000370630:P1229S;ENSP00000450832:P1250S;ENSP00000351352:P1229S;ENSP00000440682:P704S	ENSP00000351352:P1250S	P	+	1	0	SIPA1L1	71241730	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.359000	0.66074	2.937000	0.99478	0.650000	0.86243	CCA	.	.	.	none		0.468	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		T	72171977	C	T	72171977	3	4	204	1	0	0	0	0	1	0	0	0	14342	739	26	2	3798	2	SIPA1L1	14	72171977	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	7652860	72171977	35177563	64	12353											
CKB	1152	hgsc.bcm.edu	37	chr14	103988811	103988811	+	Missense_Mutation	SNP	T	T	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	agcgcagcttcagtgcgttgTggctgttggagaagggcatg	7	10	17	7	2	1	1	1	0	0	1	1	2	1	1	0	3	3	6	0	3	1	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr14:103988811T>G	ENST00000348956.2	-	2	377	c.20A>C	c.(19-21)cAc>cCc	p.H7P	RP11-600F24.7_ENST00000568177.1_RNA	NM_001823.4	NP_001814.2	P12277	KCRB_HUMAN	creatine kinase, brain	7					cellular chloride ion homeostasis (GO:0030644)|cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)			lung(2)|prostate(1)	3		Melanoma(154;0.155)	Epithelial(46;0.14)		Creatine(DB00148)	CAGTGCGTTGTGGCTGTTGGA	0.706																																					p.H7P	Esophageal Squamous(186;2492 2823 49929 50127)	Atlas-SNP	.											.	CKB	9	.	0			c.A20C						PASS	.						49	43	45					14																	103988811		2201	4300	6501	SO:0001583	missense	1152	exon2			GCGTTGTGGCTGT		CCDS9981.1	14q32.32	2012-10-02			ENSG00000166165	ENSG00000166165	2.7.3.2		1991	protein-coding gene	gene with protein product		123280		CKBB			Standard	NM_001823		Approved		uc001ynf.2	P12277	OTTHUMG00000171786	ENST00000348956.2:c.20A>C	chr14.hg19:g.103988811T>G	ENSP00000299198:p.His7Pro	46.0	0.0	.		22.0	9.0	.	NM_001823	A8K236|B2R5R4|Q2LE07|Q6FG40|Q9UC66	Missense_Mutation	SNP	ENST00000348956.2	hg19	CCDS9981.1	.	.	.	.	.	.	.	.	.	.	T	14.98	2.696367	0.48202	.	.	ENSG00000166165	ENST00000348956;ENST00000428256;ENST00000553878	T;T	0.38240	1.82;1.15	4.17	4.17	0.49024	ATP:guanido phosphotransferase, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.56202	0.1969	M	0.82193	2.58	0.80722	D	1	P	0.48503	0.911	P	0.55112	0.769	T	0.64896	-0.6299	10	0.87932	D	0	.	13.5095	0.61504	0.0:0.0:0.0:1.0	.	7	P12277	KCRB_HUMAN	P	7	ENSP00000299198:H7P;ENSP00000451904:H7P	ENSP00000299198:H7P	H	-	2	0	CKB	103058564	1.000000	0.71417	1.000000	0.80357	0.800000	0.45204	6.860000	0.75473	1.783000	0.52377	0.246000	0.17985	CAC	.	.	.	none		0.706	CKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415111.1			G	103988811	T	G	103988811	3	3	204	1	0	0	0	0	1	0	0	0	3448	1696	59	5	1153	5	CKB	14	103988811	Missense_Mutation	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10	31816834	103988811	3360729	65	12354											
SOLH	6650	hgsc.bcm.edu	37	chr16	598994	598994	+	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	atggccgtggtctctgcagaAcaatgtgagcttcgtggatg	8	11	14	8	2	1	2	0	1	1	1	3	3	1	3	1	3	3	2	1	3	2	1			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr16:598994A>G	ENST00000219611.2	+	5	1814	c.1451A>G	c.(1450-1452)aAc>aGc	p.N484S	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	484					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)										TCTCTGCAGAACAATGTGAGC	0.662																																					p.N484S		Atlas-SNP	.											.	SOLH	47	.	0			c.A1451G						PASS	.						112	92	99					16																	598994		2198	4297	6495	SO:0001630	splice_region_variant	6650	exon5			TGCAGAACAATGT	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.1450-1A>G	chr16.hg19:g.598994A>G		85.0	0.0	.		65.0	4.0	.	NM_005632	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Missense_Mutation	SNP	ENST00000219611.2	hg19	CCDS10410.1	.	.	.	.	.	.	.	.	.	.	a	10.23	1.292148	0.23564	.	.	ENSG00000103326	ENST00000219611	T	0.40756	1.02	5.04	5.04	0.67666	Peptidase C2, calpain, catalytic domain (1);	0.090831	0.64402	D	0.000001	T	0.49372	0.1553	L	0.27053	0.805	0.58432	D	0.999994	D	0.71674	0.998	D	0.77004	0.989	T	0.43147	-0.9409	10	0.30854	T	0.27	.	13.6292	0.62186	1.0:0.0:0.0:0.0	.	484	O75808	CAN15_HUMAN	S	484	ENSP00000219611:N484S	ENSP00000219611:N484S	N	+	2	0	SOLH	538995	1.000000	0.71417	0.967000	0.41034	0.345000	0.29048	6.977000	0.76141	1.903000	0.55091	0.454000	0.30748	AAC	.	.	.	none		0.662	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1	NM_005632	Missense_Mutation	G	598994	A	G	598994	5	3	204	1	0	0	0	0	0	0	1	0	14938	57	2	3	1457	3	SOLH	16	598994	Splice_Site	SNP	A	TCGA-IA-A40Y-01A-11D-A25F-10		598994	89755759	66	12355											
MYH8	4626	hgsc.bcm.edu	37	chr17	10300168	10300168	+	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	agggctgcacaggctgcattAgacctttccacatcaagcat	11	9	9	12	0	1	1	1	0	0	1	2	1	2	1	2	2	3	5	2	2	2	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr17:10300168A>T	ENST00000403437.2	-	31	4408	c.4314T>A	c.(4312-4314)tcT>tcA	p.S1438S	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	1438					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						AGGCTGCATTAGACCTTTCCA	0.463									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																												p.S1438S		Atlas-SNP	.											.	MYH8	346	.	0			c.T4314A						PASS	.						110	100	103					17																	10300168		2203	4300	6503	SO:0001819	synonymous_variant	4626	exon31	Familial Cancer Database	Carney Complex Variant	TGCATTAGACCTT		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.4314T>A	chr17.hg19:g.10300168A>T		177.0	0.0	.		230.0	19.0	.	NM_002472	Q14910	Silent	SNP	ENST00000403437.2	hg19	CCDS11153.1																																																																																			.	.	.	none		0.463	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		T	10300168	A	T	10300168	2	4	204	1	0	0	0	0	0	0	0	1	10048	407	15	5		5	MYH8	17	10300168	Silent	SNP	A	TCGA-IA-A40Y-01A-11D-A25F-10		10300168	70895042	67	12356											
CLTC	1213	hgsc.bcm.edu	37	chr17	57728648	57728648	+	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	atgtcttctttcctccagaaGcacaaaatgattttcctgtt	10	16	5	10	0	2	2	0	1	2	1	5	2	5	2	3	0	1	2	3	0	3	5			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr17:57728648G>T	ENST00000269122.3	+	5	1040	c.766G>T	c.(766-768)Gca>Tca	p.A256S	CLTC_ENST00000393043.1_Missense_Mutation_p.A256S|CLTC_ENST00000579456.1_Intron	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	256	Globular terminal domain.|WD40-like repeat 5.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					TCCTCCAGAAGCACAAAATGA	0.353			T	"ALK, TFE3"	"ALCL, renal "																																p.A256S		Atlas-SNP	.		Dom	yes		17	17q11-qter	1213	"clathrin, heavy polypeptide (Hc)"		L	.	CLTC	124	.	0			c.G766T						PASS	.						146	149	148					17																	57728648		2203	4300	6503	SO:0001583	missense	1213	exon5			CCAGAAGCACAAA	X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"clathrin, heavy polypeptide (Hc)", "clathrin, heavy chain", "clathrin, heavy polypeptide-like 2"	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.766G>T	chr17.hg19:g.57728648G>T	ENSP00000269122:p.Ala256Ser	148.0	0.0	.		195.0	8.0	.	NM_004859	D3DU00|Q6N0A0|Q86TF2	Missense_Mutation	SNP	ENST00000269122.3	hg19	CCDS32696.1	.	.	.	.	.	.	.	.	.	.	G	35	5.556566	0.96514	.	.	ENSG00000141367	ENST00000269122;ENST00000393043	T;T	0.24350	1.86;1.86	5.62	5.62	0.85841	Clathrin, heavy chain, propeller, N-terminal (1);Clathrin, heavy chain, linker/propeller domain (1);	0.000000	0.85682	D	0.000000	T	0.63640	0.2528	M	0.93283	3.4	0.80722	D	1	D;P	0.58268	0.982;0.857	D;P	0.72338	0.977;0.876	T	0.68992	-0.5263	10	0.44086	T	0.13	.	20.0333	0.97547	0.0:0.0:1.0:0.0	.	256;256	Q00610;Q00610-2	CLH1_HUMAN;.	S	256	ENSP00000269122:A256S;ENSP00000376763:A256S	ENSP00000269122:A256S	A	+	1	0	CLTC	55083430	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.810000	0.96702	0.585000	0.79938	GCA	.	.	.	none		0.353	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859		T	57728648	G	T	57728648	3	4	204	1	0	0	0	0	1	0	0	0	3568	971	34	4	784	4	CLTC	17	57728648	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	47428480	57728648	23466562	68	12357											
BPTF	2186	hgsc.bcm.edu	37	chr17	65960510	65960510	+	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	ggggttgaagagggtgctccGttccttacaggtgagacccc	7	9	15	10	1	0	3	0	2	0	2	2	4	2	3	4	4	2	3	4	4	2	3	rs368469411		TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr17:65960510G>T	ENST00000321892.4	+	27	8883	c.8822G>T	c.(8821-8823)cGt>cTt	p.R2941L	BPTF_ENST00000335221.5_Missense_Mutation_p.R2798L|BPTF_ENST00000424123.3_Missense_Mutation_p.R2659L|BPTF_ENST00000306378.6_Missense_Mutation_p.R2815L			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2941					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)			AGGGTGCTCCGTTCCTTACAG	0.458																																					p.R2815L		Atlas-SNP	.											.	BPTF	415	.	0			c.G8444T						PASS	.						83	74	77					17																	65960510		2203	4300	6503	SO:0001583	missense	2186	exon25			TGCTCCGTTCCTT	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.8822G>T	chr17.hg19:g.65960510G>T	ENSP00000315454:p.Arg2941Leu	106.0	0.0	.		153.0	14.0	.	NM_182641	Q6NX67|Q7Z7D6|Q9UIG2	Missense_Mutation	SNP	ENST00000321892.4	hg19		.	.	.	.	.	.	.	.	.	.	G	16.21	3.057919	0.55325	.	.	ENSG00000171634	ENST00000306378;ENST00000335221;ENST00000321892;ENST00000342579	T;T;T	0.30448	1.53;1.53;1.53	5.65	5.65	0.86999	.	.	.	.	.	T	0.52435	0.1734	L	0.49455	1.56	0.80722	D	1	P;P;D;D	0.76494	0.587;0.872;0.999;0.999	B;P;D;D	0.80764	0.187;0.773;0.994;0.994	T	0.45190	-0.9278	9	0.49607	T	0.09	-6.4917	19.7202	0.96139	0.0:0.0:1.0:0.0	.	146;619;2815;2798	E9PE19;B4DJV8;Q12830-2;Q12830-4	.;.;.;.	L	2815;2798;2941;146	ENSP00000307208:R2815L;ENSP00000334351:R2798L;ENSP00000315454:R2941L	ENSP00000307208:R2815L	R	+	2	0	BPTF	63390972	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.807000	0.99171	2.660000	0.90430	0.555000	0.69702	CGT	.	.	.	alt		0.458	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		T	65960510	G	T	65960510	3	4	204	1	0	0	0	0	1	0	0	0	1497	1145	40	4	8928	4	BPTF	17	65960510	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	8231862	65960510	15234700	69	12358											
CBX4	8535	hgsc.bcm.edu	37	chr17	77807886	77807886	+	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	ttcgtcctgggcctcggctgGaggcttctccgccgtcgtgg	1	11	15	14	5	1	0	0	0	1	0	6	1	2	1	4	5	0	2	4	5	0	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr17:77807886G>C	ENST00000269397.4	-	5	1732	c.1555C>G	c.(1555-1557)Cca>Gca	p.P519A		NM_003655.2	NP_003646.2	O00257	CBX4_HUMAN	chromobox homolog 4	519	Interaction with BMI1.				chromatin modification (GO:0016568)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein sumoylation (GO:0016925)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|single-stranded RNA binding (GO:0003727)|SUMO binding (GO:0032183)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GCCTCGGCTGGAGGCTTCTCC	0.672																																					p.P519A		Atlas-SNP	.											.	CBX4	40	.	0			c.C1555G						PASS	.						36	45	42					17																	77807886		2201	4296	6497	SO:0001583	missense	8535	exon5			CGGCTGGAGGCTT	AF013956	CCDS32758.1	17q25.3	2010-07-06	2010-06-24		ENSG00000141582	ENSG00000141582			1554	protein-coding gene	gene with protein product	"NS5ATP1-binding protein 16", "Pc class 2 homolog (Drosophila)"	603079	"chromobox homolog 4 (Drosophila Pc class)"			9315667	Standard	NM_003655		Approved	hPC2, PC2, NBP16	uc002jxe.3	O00257	OTTHUMG00000150415	ENST00000269397.4:c.1555C>G	chr17.hg19:g.77807886G>C	ENSP00000269397:p.Pro519Ala	80.0	0.0	.		77.0	7.0	.	NM_003655	B1PJR7|Q6TPI8|Q96C04	Missense_Mutation	SNP	ENST00000269397.4	hg19	CCDS32758.1	.	.	.	.	.	.	.	.	.	.	g	8.387	0.838920	0.16891	.	.	ENSG00000141582	ENST00000269397;ENST00000343048	.	.	.	3.16	3.16	0.36331	.	3.167460	0.02836	N	0.127360	T	0.20251	0.0487	N	0.11560	0.145	0.19575	N	0.999969	B	0.20261	0.043	B	0.17433	0.018	T	0.25152	-1.0140	9	0.12103	T	0.63	-14.3825	5.4008	0.16295	0.1115:0.0:0.6877:0.2008	.	519	O00257	CBX4_HUMAN	A	519;249	.	ENSP00000269397:P519A	P	-	1	0	CBX4	75422481	0.931000	0.31567	0.470000	0.27216	0.496000	0.33645	2.539000	0.45718	1.796000	0.52611	0.299000	0.19835	CCA	.	.	.	none		0.672	CBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318007.1	NM_003655		C	77807886	G	C	77807886	3	2	204	1	0	0	0	0	1	0	0	0	2722	1174	41	4	131	4	CBX4	17	77807886	Missense_Mutation	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10	11847376	77807886	3387324	70	12359											
AZI1	22994	hgsc.bcm.edu	37	chr17	79165083	79165083	+	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	gctcaatctccttgtcccggCctttccggatttcttccctc	3	15	6	17	2	3	0	1	0	2	0	8	1	6	1	5	2	0	1	5	2	1	4			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr17:79165083C>A	ENST00000269392.4	-	22	2931	c.2684G>T	c.(2683-2685)gGc>gTc	p.G895V	AZI1_ENST00000374782.3_Missense_Mutation_p.G856V|AZI1_ENST00000575907.1_Missense_Mutation_p.G859V|AZI1_ENST00000450824.2_Missense_Mutation_p.G892V	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		895					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)			CTTGTCCCGGCCTTTCCGGAT	0.667																																					p.G892V		Atlas-SNP	.											.	AZI1	145	.	0			c.G2675T						PASS	.						84	79	81					17																	79165083		2203	4300	6503	SO:0001583	missense	22994	exon22			TCCCGGCCTTTCC																												ENST00000269392.4:c.2684G>T	chr17.hg19:g.79165083C>A	ENSP00000269392:p.Gly895Val	138.0	0.0	.		169.0	32.0	.	NM_014984	A6NHI8|B2RN11|Q96F50	Missense_Mutation	SNP	ENST00000269392.4	hg19		.	.	.	.	.	.	.	.	.	.	C	13.17	2.157738	0.38119	.	.	ENSG00000141577	ENST00000450824;ENST00000374782;ENST00000269392	T;T;T	0.14266	2.52;2.55;2.52	4.37	0.923	0.19413	.	0.413716	0.23832	N	0.044131	T	0.06690	0.0171	L	0.29908	0.895	0.54753	D	0.999988	B;B;P;P	0.37122	0.218;0.135;0.583;0.583	B;B;B;B	0.32090	0.081;0.055;0.14;0.14	T	0.35992	-0.9766	10	0.41790	T	0.15	-20.1739	1.6764	0.02823	0.1712:0.4525:0.148:0.2282	.	892;895;856;892	B2RN10;Q9UPN4;Q9UPN4-3;Q9UPN4-2	.;AZI1_HUMAN;.;.	V	892;856;895	ENSP00000393583:G892V;ENSP00000363914:G856V;ENSP00000269392:G895V	ENSP00000269392:G895V	G	-	2	0	AZI1	76779678	0.999000	0.42202	0.994000	0.49952	0.993000	0.82548	0.828000	0.27435	0.474000	0.27392	0.491000	0.48974	GGC	.	.	.	none		0.667	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1			A	79165083	C	A	79165083	3	1	204	1	0	0	0	0	1	0	0	0	1240	739	26	4	587	4	AZI1	17	79165083	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	1357197	79165083	2030127	71	12360											
PGLYRP2	114770	hgsc.bcm.edu	37	chr19	15587343	15587343	+	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	cacgcagaagctgtgtgtctGgtcttggcagctggcacttt	6	12	13	10	1	2	1	0	0	2	1	2	1	2	1	0	3	2	5	0	3	1	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr19:15587343G>T	ENST00000340880.4	-	2	618	c.138C>A	c.(136-138)acC>acA	p.T46T	PGLYRP2_ENST00000292609.4_Silent_p.T46T	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	46			T -> A (in dbSNP:rs3813135). {ECO:0000269|PubMed:12975309}.		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						CTGTGTGTCTGGTCTTGGCAG	0.587																																					p.T46T		Atlas-SNP	.											.	PGLYRP2	116	.	0			c.C138A						PASS	.						50	47	48					19																	15587343		2203	4300	6503	SO:0001819	synonymous_variant	114770	exon2			GTGTCTGGTCTTG	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.138C>A	chr19.hg19:g.15587343G>T		131.0	0.0	.		123.0	19.0	.	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Silent	SNP	ENST00000340880.4	hg19	CCDS12330.2																																																																																			.	.	.	none		0.587	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890		T	15587343	G	T	15587343	2	4	204	1	0	0	0	0	0	0	0	1	11801	1335	47	4		4	PGLYRP2	19	15587343	Silent	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10		15587343	43541640	72	12361											
GRAMD1A	57655	hgsc.bcm.edu	37	chr19	35512474	35512474	+	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	gtcgctcattgagaagaactCgtggagcggcattgaagact	11	9	13	8	3	1	4	1	2	0	3	3	6	1	5	0	2	2	2	0	2	3	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr19:35512474C>T	ENST00000317991.5	+	14	1736	c.1544C>T	c.(1543-1545)tCg>tTg	p.S515L	CTD-2527I21.14_ENST00000605640.1_RNA|GRAMD1A_ENST00000411896.2_Missense_Mutation_p.S508L|GRAMD1A_ENST00000599564.1_Missense_Mutation_p.S602L|GRAMD1A_ENST00000504615.2_Missense_Mutation_p.S281L	NM_020895.3	NP_065946.2	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A	515						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)			GAGAAGAACTCGTGGAGCGGC	0.582																																					p.S515L		Atlas-SNP	.											.	GRAMD1A	39	.	0			c.C1544T						PASS	.						70	73	72					19																	35512474		1948	4122	6070	SO:0001583	missense	57655	exon14			AGAACTCGTGGAG	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.1544C>T	chr19.hg19:g.35512474C>T	ENSP00000441032:p.Ser515Leu	86.0	0.0	.		95.0	24.0	.	NM_020895	A6NKY7|Q8NC77|Q9P1Z5	Missense_Mutation	SNP	ENST00000317991.5	hg19	CCDS42546.1	.	.	.	.	.	.	.	.	.	.	C	16.65	3.182600	0.57800	.	.	ENSG00000089351	ENST00000453966;ENST00000504615;ENST00000317991;ENST00000411896	T;T;T	0.22336	1.96;1.96;1.96	4.33	4.33	0.51752	.	0.086126	0.48767	D	0.000164	T	0.29458	0.0734	L	0.60455	1.87	0.42985	D	0.994471	D;P;D;D	0.62365	0.971;0.83;0.991;0.968	B;B;P;P	0.48873	0.439;0.086;0.539;0.593	T	0.07635	-1.0762	10	0.51188	T	0.08	.	14.3583	0.66752	0.0:1.0:0.0:0.0	.	515;515;281;508	Q96CP6-3;Q96CP6;B3KQF7;Q96CP6-2	.;GRM1A_HUMAN;.;.	L	601;281;515;508	ENSP00000423728:S281L;ENSP00000441032:S515L;ENSP00000439267:S508L	ENSP00000441032:S515L	S	+	2	0	GRAMD1A	40204314	0.806000	0.28996	0.955000	0.39395	0.977000	0.68977	2.268000	0.43338	2.255000	0.74692	0.491000	0.48974	TCG	.	.	.	none		0.582	GRAMD1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461557.1	NM_020895		T	35512474	C	T	35512474	3	4	204	1	0	0	0	0	1	0	0	0	6754	893	31	1	1598	1	GRAMD1A	19	35512474	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	19925131	35512474	23616509	73	12362											
ZNF585B	92285	hgsc.bcm.edu	37	chr19	37680577	37680577	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcacctgggcagctgtgaCgtggcctctcaccctgcagt	6	9	11	15	1	2	1	2	1	1	0	3	1	2	1	3	2	2	3	3	2	0	0			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr19:37680577C>T	ENST00000532828.2	-	4	529	c.278G>A	c.(277-279)cGt>cAt	p.R93H	ZNF585B_ENST00000531805.1_Missense_Mutation_p.R38H|ZNF585B_ENST00000312908.5_5'Flank|ZNF585B_ENST00000527838.1_Missense_Mutation_p.R93H|CTC-454I21.3_ENST00000585860.2_Missense_Mutation_p.R93H|ZNF585B_ENST00000586320.1_Missense_Mutation_p.R78H	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	93	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)			GCAGCTGTGACGTGGCCTCTC	0.498																																					p.R93H	Melanoma(93;882 1454 18863 28917 48427)	Atlas-SNP	.											.	ZNF585B	91	.	0			c.G278A						PASS	.						159	125	136					19																	37680577		2203	4300	6503	SO:0001583	missense	92285	exon4			CTGTGACGTGGCC	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.278G>A	chr19.hg19:g.37680577C>T	ENSP00000433773:p.Arg93His	270.0	0.0	.		186.0	8.0	.	NM_152279	Q8IZD3|Q96JW6	Missense_Mutation	SNP	ENST00000532828.2	hg19	CCDS12500.1	.	.	.	.	.	.	.	.	.	.	C	9.289	1.050057	0.19827	.	.	ENSG00000245680	ENST00000531805;ENST00000532828;ENST00000527838	T;T;T	0.09163	3.03;3.01;6.62	2.55	-1.74	0.08056	Krueppel-associated box (1);	1.911660	0.03152	N	0.168174	T	0.10937	0.0267	L	0.48218	1.51	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35076	-0.9803	10	0.33940	T	0.23	.	6.7578	0.23524	0.0:0.6143:0.0:0.3857	.	93	Q52M93	Z585B_HUMAN	H	38;93;93	ENSP00000436774:R38H;ENSP00000433773:R93H;ENSP00000435268:R93H	ENSP00000435268:R93H	R	-	2	0	ZNF585B	42372417	0.000000	0.05858	0.000000	0.03702	0.268000	0.26511	-0.529000	0.06186	-0.421000	0.07416	0.305000	0.20034	CGT	.	.	.	none		0.498	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279		T	37680577	C	T	37680577	3	4	204	1	0	0	0	0	1	0	0	0	18030	536	19	1	2039	1	ZNF585B	19	37680577	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10	2168103	37680577	21448406	74	12363											
AHCY	191	hgsc.bcm.edu	37	chr20	32873337	32873337	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctggttggtgaaggagttaCtcatcacgaagctggggtgg	8	10	16	7	1	2	1	2	1	0	0	2	3	2	2	1	6	2	3	1	6	3	2			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr20:32873337C>T	ENST00000217426.2	-	9	1153	c.1076G>A	c.(1075-1077)aGt>aAt	p.S359N	AHCY_ENST00000538132.1_Missense_Mutation_p.S331N|CTD-3216D2.5_ENST00000609218.1_RNA	NM_000687.2	NP_000678.1	P23526	SAHH_HUMAN	adenosylhomocysteinase	359					cellular nitrogen compound metabolic process (GO:0034641)|chronic inflammatory response to antigenic stimulus (GO:0002439)|circadian sleep/wake cycle (GO:0042745)|homocysteine biosynthetic process (GO:0071268)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|S-adenosylhomocysteine catabolic process (GO:0019510)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|nucleus (GO:0005634)	adenosylhomocysteinase activity (GO:0004013)|adenyl nucleotide binding (GO:0030554)|NAD binding (GO:0051287)			endometrium(6)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						GAAGGAGTTACTCATCACGAA	0.587																																					p.S359N		Atlas-SNP	.											.	AHCY	43	.	0			c.G1076A						PASS	.						91	78	82					20																	32873337		2203	4300	6503	SO:0001583	missense	191	exon9			GAGTTACTCATCA	M61832	CCDS13233.1, CCDS54457.1	20q11.22	2009-06-12	2009-06-12		ENSG00000101444	ENSG00000101444	3.3.1.1		343	protein-coding gene	gene with protein product		180960	"S-adenosylhomocysteine hydrolase"			7079734, 6580258	Standard	NM_001161766		Approved	SAHH	uc002xai.3	P23526	OTTHUMG00000140098	ENST00000217426.2:c.1076G>A	chr20.hg19:g.32873337C>T	ENSP00000217426:p.Ser359Asn	103.0	0.0	.		140.0	27.0	.	NM_000687	A8K307|B3KUN3|E1P5P2|F5H737|Q96A36	Missense_Mutation	SNP	ENST00000217426.2	hg19	CCDS13233.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.040615	0.93630	.	.	ENSG00000101444	ENST00000217426;ENST00000538132	T;T	0.79033	-1.23;-1.23	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	D	0.88952	0.6577	H	0.96777	3.88	0.80722	D	1	P	0.48589	0.912	P	0.48524	0.58	D	0.92976	0.6402	10	0.87932	D	0	.	18.522	0.90956	0.0:1.0:0.0:0.0	.	359	P23526	SAHH_HUMAN	N	359;331	ENSP00000217426:S359N;ENSP00000442820:S331N	ENSP00000217426:S359N	S	-	2	0	AHCY	32336998	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.701000	0.84566	2.457000	0.83068	0.650000	0.86243	AGT	.	.	.	none		0.587	AHCY-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078773.2	NM_000687		T	32873337	C	T	32873337	3	4	204	1	0	0	0	0	1	0	0	0	409	565	20	2	230	2	AHCY	20	32873337	Missense_Mutation	SNP	C	TCGA-IA-A40Y-01A-11D-A25F-10		32873337	30152183	75	12364											
SMTN	6525	hgsc.bcm.edu	37	chr22	31484747	31484747	+	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	gctgccatccgccgtgtacgGgctcaggagattgagggtat	7	9	15	10	3	1	2	1	1	0	1	2	3	2	2	3	3	2	4	3	3	2	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr22:31484747G>C	ENST00000347557.2	+	5	575	c.357G>C	c.(355-357)cgG>cgC	p.R119R	SMTN_ENST00000358743.1_Silent_p.R119R|SMTN_ENST00000333137.7_Silent_p.R119R	NM_001207017.1|NM_006932.4	NP_001193946.1|NP_008863.3	P53814	SMTN_HUMAN	smoothelin	119					muscle organ development (GO:0007517)|smooth muscle contraction (GO:0006939)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)			breast(2)|endometrium(2)|large_intestine(5)|lung(9)|ovary(3)|pancreas(1)|prostate(3)	25						GCCGTGTACGGGCTCAGGAGA	0.632											OREG0026472	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R175R		Atlas-SNP	.											.	SMTN	219	.	0			c.G525C						PASS	.						75	63	67					22																	31484747		2202	4300	6502	SO:0001819	synonymous_variant	6525	exon4			TGTACGGGCTCAG	AY061972	CCDS13886.1, CCDS13887.1, CCDS13888.1, CCDS74845.1, CCDS74846.1	22q12	2006-01-27			ENSG00000183963	ENSG00000183963			11126	protein-coding gene	gene with protein product		602127				9244445, 8707825	Standard	NM_006932		Approved		uc011ale.2	P53814	OTTHUMG00000151203	ENST00000347557.2:c.357G>C	chr22.hg19:g.31484747G>C		141.0	0.0	.	825	94.0	26.0	.	NM_001207018	O00569|O95769|O95937|Q8N4H8|Q8WWW1|Q8WWW2|Q9P1S8|Q9UIT1|Q9UIT2	Silent	SNP	ENST00000347557.2	hg19	CCDS13886.1	.	.	.	.	.	.	.	.	.	.	G	5.557	0.287703	0.10513	.	.	ENSG00000183963	ENST00000438223	.	.	.	4.79	1.3	0.21679	.	.	.	.	.	T	0.43055	0.1230	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.26744	-1.0094	4	.	.	.	-19.7875	1.9964	0.03457	0.2418:0.1338:0.4874:0.137	.	.	.	.	R	174	.	.	G	+	1	0	SMTN	29814747	1.000000	0.71417	0.975000	0.42487	0.527000	0.34593	0.687000	0.25407	0.543000	0.28864	0.655000	0.94253	GGC	.	.	.	none		0.632	SMTN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321766.1	NM_134270		C	31484747	G	C	31484747	2	2	204	1	0	0	0	0	0	0	0	1	14827	1219	43	4		4	SMTN	22	31484747	Silent	SNP	G	TCGA-IA-A40Y-01A-11D-A25F-10		31484747	19819819	76	12365											
RAC2	5880	hgsc.bcm.edu	37	chr22	37627391	37627391	+	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	cttggtgcccaccaggatgaTgggtgtgctggggcagtggt	5	10	18	8	0	0	1	0	1	0	0	0	2	0	2	2	6	2	2	2	6	0	1			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chr22:37627391T>A	ENST00000249071.6	-	5	449	c.328A>T	c.(328-330)Atc>Ttc	p.I110F	RAC2_ENST00000406508.1_Missense_Mutation_p.I66F|RAC2_ENST00000405484.1_Missense_Mutation_p.I103F	NM_002872.3	NP_002863.1	P15153	RAC2_HUMAN	ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2)	110					actin filament organization (GO:0007015)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|bone resorption (GO:0045453)|cell projection assembly (GO:0030031)|G-protein coupled receptor signaling pathway (GO:0007186)|lymphocyte aggregation (GO:0071593)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of neutrophil chemotaxis (GO:0090023)|regulation of cell-substrate adhesion (GO:0010810)|regulation of hydrogen peroxide metabolic process (GO:0010310)|regulation of neutrophil migration (GO:1902622)|regulation of respiratory burst (GO:0060263)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(2)|upper_aerodigestive_tract(1)	12					Dextromethorphan(DB00514)	ACCAGGATGATGGGTGTGCTG	0.632																																					p.I110F		Atlas-SNP	.											.	RAC2	22	.	0			c.A328T						PASS	.						91	78	83					22																	37627391		2203	4300	6503	SO:0001583	missense	5880	exon5			GGATGATGGGTGT	M64595	CCDS13945.1	22q13.1	2014-09-17			ENSG00000128340	ENSG00000128340		"Endogenous ligands"	9802	protein-coding gene	gene with protein product		602049				2674130	Standard	NM_002872		Approved	EN-7	uc003arc.3	P15153	OTTHUMG00000150540	ENST00000249071.6:c.328A>T	chr22.hg19:g.37627391T>A	ENSP00000249071:p.Ile110Phe	273.0	0.0	.		225.0	83.0	.	NM_002872	Q9UDJ4	Missense_Mutation	SNP	ENST00000249071.6	hg19	CCDS13945.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.992414	0.74703	.	.	ENSG00000128340	ENST00000249071;ENST00000406508;ENST00000405484;ENST00000441619	T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68	4.98	4.98	0.66077	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.68467	0.3004	L	0.47190	1.495	0.80722	D	1	B	0.22746	0.074	B	0.36030	0.216	T	0.63554	-0.6611	10	0.22109	T	0.4	.	14.9666	0.71198	0.0:0.0:0.0:1.0	.	110	P15153	RAC2_HUMAN	F	110;66;103;110	ENSP00000249071:I110F;ENSP00000385270:I66F;ENSP00000385590:I103F;ENSP00000403778:I110F	ENSP00000249071:I110F	I	-	1	0	RAC2	35957337	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.003000	0.58678	0.459000	0.35465	ATC	.	.	.	none		0.632	RAC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318812.1			A	37627391	T	A	37627391	3	1	204	1	0	0	0	0	1	0	0	0	12988	1464	51	5	258	5	RAC2	22	37627391	Missense_Mutation	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10	6142644	37627391	13677175	77	12366											
SEPT6	23157	hgsc.bcm.edu	37	chrX	118797595	118797595	+	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	gctccccttcgaatttggtgTtgaacagggtgtccatgagg	7	12	13	9	1	0	2	0	2	0	0	3	3	2	2	3	3	1	2	3	3	2	3			TCGA-IA-A40Y-01A-11D-A25F-10	TCGA-IA-A40Y-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	ad9455e9-7147-489e-9b1f-3540c457c260	aab4115c-fdfe-45ae-9a51-91ee50250623	g.chrX:118797595T>A	ENST00000343984.5	-	3	455	c.191A>T	c.(190-192)aAc>aTc	p.N64I	SEPT6_ENST00000489216.1_Missense_Mutation_p.N64I|SEPT6_ENST00000394617.2_Missense_Mutation_p.N94I|SEPT6_ENST00000360156.7_Missense_Mutation_p.N64I|SEPT6_ENST00000354416.3_Missense_Mutation_p.N64I|SEPT6_ENST00000394616.4_Missense_Mutation_p.N6I|SEPT6_ENST00000394610.1_Missense_Mutation_p.N64I|SEPT6_ENST00000354228.4_Missense_Mutation_p.N64I	NM_015129.5	NP_055944.2	Q14141	SEPT6_HUMAN	septin 6	64	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						GAATTTGGTGTTGAACAGGGT	0.502			T	MLL	AML																																p.N64I		Atlas-SNP	.		Dom	yes		X	Xq24	23157	septin 6		L	.	SEPT6	53	.	0			c.A191T						PASS	.						213	198	203					X																	118797595		2203	4300	6503	SO:0001583	missense	23157	exon3			TTGGTGTTGAACA	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.191A>T	chrX.hg19:g.118797595T>A	ENSP00000341524:p.Asn64Ile	147.0	0.0	.		87.0	9.0	.	NM_145802	Q5JTK0|Q969W5|Q96A13|Q96GR1|Q96P86|Q96P87	Missense_Mutation	SNP	ENST00000343984.5	hg19	CCDS14584.1	.	.	.	.	.	.	.	.	.	.	t	21.9	4.214865	0.79352	.	.	ENSG00000125354	ENST00000360156;ENST00000354228;ENST00000489216;ENST00000354416;ENST00000394610;ENST00000343984;ENST00000394616;ENST00000394617;ENST00000520510	T;T;T;T;T;T;D;T	0.81739	1.28;1.28;1.28;1.28;1.28;1.28;-1.53;1.28	4.47	4.47	0.54385	.	0.081767	0.85682	D	0.000000	D	0.91415	0.7291	H	0.94925	3.6	0.80722	D	1	D;P;D;D	0.60575	0.973;0.922;0.961;0.988	P;P;P;D	0.67548	0.894;0.908;0.864;0.952	D	0.93282	0.6661	10	0.72032	D	0.01	.	12.648	0.56746	0.0:0.0:0.0:1.0	.	94;6;64;64	F5H1J5;B4E049;Q14141;Q548C9	.;.;SEPT6_HUMAN;.	I	64;64;64;64;64;64;6;94;64	ENSP00000353278:N64I;ENSP00000346169:N64I;ENSP00000418715:N64I;ENSP00000346397:N64I;ENSP00000378108:N64I;ENSP00000341524:N64I;ENSP00000378114:N6I;ENSP00000378115:N94I	ENSP00000341524:N64I	N	-	2	0	SEPT6	118681623	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.649000	0.83500	1.736000	0.51660	0.483000	0.47432	AAC	.	.	.	none		0.502	SEPT6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058059.1	NM_145802		A	118797595	T	A	118797595	3	1	204	1	0	0	0	0	1	0	0	0	14081	1725	60	5	1167	5	SEPT6	23	118797595	Missense_Mutation	SNP	T	TCGA-IA-A40Y-01A-11D-A25F-10		118797595	36472965	78	12367											
PRDM16	63976	hgsc.bcm.edu	37	chr1	3322089	3322089	+	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	accccagcaaccttcagcggCacatccgctcgcagcacgtg	9	5	9	18	4	1	0	1	0	0	0	3	0	2	0	4	1	4	5	4	1	1	1			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr1:3322089C>A	ENST00000270722.5	+	8	1112	c.1063C>A	c.(1063-1065)Cac>Aac	p.H355N	PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000378391.2_Missense_Mutation_p.H355N|PRDM16_ENST00000442529.2_Missense_Mutation_p.H355N|PRDM16_ENST00000511072.1_Missense_Mutation_p.H356N|PRDM16_ENST00000514189.1_Missense_Mutation_p.H356N|PRDM16_ENST00000441472.2_Missense_Mutation_p.H355N|PRDM16_ENST00000378398.3_Missense_Mutation_p.H356N			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	355					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)		CCTTCAGCGGCACATCCGCTC	0.687			T	EVI1	"MDS, AML"																																p.H355N		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.C1063A						PASS	.						35	40	38					1																	3322089		2201	4297	6498	SO:0001583	missense	63976	exon8			CAGCGGCACATCC	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.1063C>A	chr1.hg19:g.3322089C>A	ENSP00000270722:p.His355Asn	87.0	0.0	.		75.0	19.0	.	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Missense_Mutation	SNP	ENST00000270722.5	hg19	CCDS41236.2	.	.	.	.	.	.	.	.	.	.	C	33	5.250276	0.95305	.	.	ENSG00000142611	ENST00000511072;ENST00000378398;ENST00000441472;ENST00000442529;ENST00000378391;ENST00000514189;ENST00000270722;ENST00000512462;ENST00000408992;ENST00000509860	D;D;D;D;D;D;D;D;D	0.99974	-10.2;-10.2;-10.2;-10.2;-10.2;-10.2;-10.2;-10.2;-10.2	4.56	4.56	0.56223	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49916	U	0.000138	D	0.99981	0.9994	H	0.96916	3.905	0.58432	D	0.999998	D;D;D;D	0.76494	0.997;0.992;0.997;0.999	D;P;D;D	0.73380	0.948;0.843;0.956;0.98	D	0.97889	1.0296	10	0.87932	D	0	.	17.307	0.87198	0.0:1.0:0.0:0.0	.	355;355;355;355	Q9HAZ2;Q9HAZ2-2;F8WEV3;D3YTA5	PRD16_HUMAN;.;.;.	N	356;356;355;355;355;356;355;171;171;164	ENSP00000426975:H356N;ENSP00000367651:H356N;ENSP00000407968:H355N;ENSP00000405253:H355N;ENSP00000367643:H355N;ENSP00000421400:H356N;ENSP00000270722:H355N;ENSP00000422504:H171N;ENSP00000425796:H164N	ENSP00000270722:H355N	H	+	1	0	PRDM16	3311949	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.677000	0.84024	2.066000	0.61787	0.491000	0.48974	CAC	.	.	.	none		0.687	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114		A	3322089	C	A	3322089	3	1	205	1	0	0	0	0	1	0	0	0	12467	710	25	4	1093	4	PRDM16	1	3322089	Missense_Mutation	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10		3322089	245928532	1	12368											
TNFRSF8	943	hgsc.bcm.edu	37	chr1	12169703	12169703	+	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	ccagcccagagaactgcaagGaaccctccaggtgactccct	11	5	9	16	0	0	2	0	1	0	1	2	4	2	3	5	2	4	1	5	2	3	0			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr1:12169703G>C	ENST00000263932.2	+	5	724	c.502G>C	c.(502-504)Gaa>Caa	p.E168Q	TNFRSF8_ENST00000417814.2_Missense_Mutation_p.E57Q	NM_001243.3|NM_001281430.1	NP_001234.2|NP_001268359.1	P28908	TNR8_HUMAN	tumor necrosis factor receptor superfamily, member 8	168					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)	GAACTGCAAGGAACCCTCCAG	0.647																																					p.E168Q		Atlas-SNP	.											.	TNFRSF8	70	.	0			c.G502C						PASS	.						49	51	50					1																	12169703		2203	4300	6503	SO:0001583	missense	943	exon5			TGCAAGGAACCCT	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.502G>C	chr1.hg19:g.12169703G>C	ENSP00000263932:p.Glu168Gln	74.0	0.0	.		51.0	13.0	.	NM_001243	B1AN79|B9EGD9|D3YTD8|Q6P4D9	Missense_Mutation	SNP	ENST00000263932.2	hg19	CCDS144.1	.	.	.	.	.	.	.	.	.	.	.	5.361	0.251949	0.10185	.	.	ENSG00000120949	ENST00000263932;ENST00000417814	T;T	0.06528	3.29;3.29	3.86	-4.19	0.03835	.	3.622260	0.00732	N	0.000951	T	0.02727	0.0082	N	0.08118	0	0.09310	N	1	B;B	0.13594	0.008;0.004	B;B	0.14578	0.011;0.003	T	0.35748	-0.9776	10	0.12766	T	0.61	-0.0897	1.4258	0.02323	0.4681:0.1472:0.2362:0.1485	.	57;168	D3YTD8;P28908	.;TNR8_HUMAN	Q	168;57	ENSP00000263932:E168Q;ENSP00000390650:E57Q	ENSP00000263932:E168Q	E	+	1	0	TNFRSF8	12092290	0.000000	0.05858	0.000000	0.03702	0.236000	0.25371	0.010000	0.13242	-0.870000	0.04047	-0.244000	0.11960	GAA	.	.	.	none		0.647	TNFRSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005130.1			C	12169703	G	C	12169703	3	2	205	1	0	0	0	0	1	0	0	0	16311	1175	41	4	520	4	TNFRSF8	1	12169703	Missense_Mutation	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	8847614	12169703	237080918	2	12369											
ARID1A	8289	hgsc.bcm.edu	37	chr1	27056261	27056261	+	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	caaggacatgggtacccaggGcagccatacgggtcccagac	11	4	13	13	1	0	1	0	0	0	1	1	2	1	2	3	4	3	2	3	4	3	2			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr1:27056261G>T	ENST00000324856.7	+	2	1628	c.1257G>T	c.(1255-1257)ggG>ggT	p.G419G	ARID1A_ENST00000374152.2_Silent_p.G36G|ARID1A_ENST00000457599.2_Silent_p.G419G	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	419					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)		GGTACCCAGGGCAGCCATACG	0.622			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.G419G		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.G1257T						PASS	.						57	61	59					1																	27056261		2203	4300	6503	SO:0001819	synonymous_variant	8289	exon2			CCCAGGGCAGCCA	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.1257G>T	chr1.hg19:g.27056261G>T		246.0	0.0	.		240.0	63.0	.	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Silent	SNP	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.	.	none		0.622	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		T	27056261	G	T	27056261	2	4	205	1	0	0	0	0	0	0	0	1	913	1190	42	4		4	ARID1A	1	27056261	Silent	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	14886558	27056261	222194360	3	12370											
DAB1	1600	hgsc.bcm.edu	37	chr1	57610985	57610985	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagtttcatcatggaatctTgacataacttgtctccccga	10	14	7	10	1	4	2	2	2	2	0	5	4	4	3	2	1	1	1	2	1	2	4			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr1:57610985T>C	ENST00000371231.1	-	2	219	c.185A>G	c.(184-186)cAa>cGa	p.Q62R	DAB1_ENST00000420954.2_Missense_Mutation_p.Q62R|DAB1_ENST00000371230.1_Missense_Mutation_p.Q62R|DAB1_ENST00000439789.2_Missense_Mutation_p.Q62R|DAB1_ENST00000485760.1_5'UTR|DAB1_ENST00000371236.2_Missense_Mutation_p.Q62R|DAB1_ENST00000371234.4_Missense_Mutation_p.Q62R|DAB1_ENST00000414851.2_Missense_Mutation_p.Q62R			O75553	DAB1_HUMAN	Dab, reelin signal transducer, homolog 1 (Drosophila)	62	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				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						CATGGAATCTTGACATAACTT	0.393																																					p.Q62R		Atlas-SNP	.											.	DAB1	129	.	0			c.A185G						PASS	.						146	128	134					1																	57610985		2203	4300	6503	SO:0001583	missense	1600	exon5			GAATCTTGACATA	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.185A>G	chr1.hg19:g.57610985T>C	ENSP00000360275:p.Gln62Arg	136.0	0.0	.		106.0	27.0	.	NM_021080	A4FU90|B3KTG3|Q4LE59|Q5T6M6|Q5T6M9|Q5T835|Q5T836|Q5T837|Q6NWS9|Q6NWT0|Q6NWT1|Q9NYA8	Missense_Mutation	SNP	ENST00000371231.1	hg19		.	.	.	.	.	.	.	.	.	.	T	29.1	4.976972	0.92982	.	.	ENSG00000173406	ENST00000371236;ENST00000371233;ENST00000371234;ENST00000420954;ENST00000414851;ENST00000439789;ENST00000371231;ENST00000371232;ENST00000332102;ENST00000371230	T;T;T;T;T;T;T;T;T	0.19394	2.15;2.15;2.15;2.15;2.15;2.15;2.15;2.15;2.15	5.49	5.49	0.81192	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	T	0.38825	0.1055	L	0.39514	1.22	0.46356	D	0.999002	D;D;D;P;D	0.76494	0.999;0.996;0.992;0.768;0.992	D;D;D;P;D	0.85130	0.997;0.991;0.984;0.806;0.989	T	0.15925	-1.0420	10	0.66056	D	0.02	-28.791	15.5959	0.76578	0.0:0.0:0.0:1.0	.	62;62;62;62;62	O75553-4;O75553;O75553-6;O75553-3;O75553-5	.;DAB1_HUMAN;.;.;.	R	62	ENSP00000360280:Q62R;ENSP00000360278:Q62R;ENSP00000395296:Q62R;ENSP00000387581:Q62R;ENSP00000409328:Q62R;ENSP00000360275:Q62R;ENSP00000360276:Q62R;ENSP00000329120:Q62R;ENSP00000360274:Q62R	ENSP00000329120:Q62R	Q	-	2	0	DAB1	57383573	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	8.036000	0.88901	2.079000	0.62486	0.533000	0.62120	CAA	.	.	.	none		0.393	DAB1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000027962.1	NM_021080		C	57610985	T	C	57610985	3	2	205	1	0	0	0	0	1	0	0	0	4219	1812	63	3	1530	3	DAB1	1	57610985	Missense_Mutation	SNP	T	TCGA-IA-A83S-01A-11D-A34Z-10	30554724	57610985	191639636	4	12371											
DNAJC6	9829	hgsc.bcm.edu	37	chr1	65830460	65830461	+	Frame_Shift_Del	DEL	TG	TG	-																															tcttctagagtgatacaatcTgtgaccaggtacgcacattc																										TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr1:65830460_65830461delTG	ENST00000395325.3	+	2	322_323	c.165_166delTG	c.(163-168)tctgtgfs	p.V56fs	DNAJC6_ENST00000371069.4_Frame_Shift_Del_p.V113fs|DNAJC6_ENST00000263441.7_Frame_Shift_Del_p.V43fs	NM_014787.3	NP_055602.1	O75061	AUXI_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 6	56	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				cell death (GO:0008219)|clathrin coat disassembly (GO:0072318)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of clathrin-mediated endocytosis (GO:2000369)	cytosol (GO:0005829)|synapse (GO:0045202)	protein tyrosine phosphatase activity (GO:0004725)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(22)|ovary(1)|prostate(2)|skin(1)	39						TGATACAATCTGTGACCAGGTA	0.45																																					p.112_112del		Atlas-Indel,Pindel	.											DNAJC6,NS,carcinoma,0,1	DNAJC6	104	.	0			c.335_336del						PASS	.																																			SO:0001589	frameshift_variant	9829	exon2			.	AB007942	CCDS30739.1, CCDS58004.1, CCDS58005.1	1p31.3	2011-09-02			ENSG00000116675	ENSG00000116675		"Heat shock proteins / DNAJ (HSP40)"	15469	protein-coding gene	gene with protein product	"auxilin"	608375				9455484, 11147971	Standard	NM_001256864		Approved	KIAA0473	uc001dce.2	O75061	OTTHUMG00000009066	ENST00000395325.3:c.165_166delTG	chr1.hg19:g.65830462_65830463delTG	ENSP00000378735:p.Val56fs	41.0	0.0	0		47.0	11.0	0.234043	NM_001256864	B7Z3V8|D3DQ65|D3DQ66|Q32M66|Q4G0K1|Q5T614|Q5T615	Frame_Shift_Del	DEL	ENST00000395325.3	hg19	CCDS30739.1																																																																																			.	.	.	none		0.45	DNAJC6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025134.1			-	65830461	TG	-	65830460	7	5	205	1	0	1	0	1	0	0	0	0	4655	1567	55	0	171	0	DNAJC6	1	65830460	Frame_Shift_Del	DEL	TG	TCGA-IA-A83S-01A-11D-A34Z-10	8219475	65830460	183420161	5	12372											
FUBP1	8880	hgsc.bcm.edu	37	chr1	78425867	78425892	+	Splice_Site	DEL	CTTCTACCTGGATCAGGAGGAGCCTG	CTTCTACCTGGATCAGGAGGAGCCTG	-																															acaaataataagcatcttctAcctggatcaggaggagcctg																								rs149973677		TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	CTTCTACCTGGATCAGGAGGAGCCTG	CTTCTACCTGGATCAGGAGGAGCCTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr1:78425867_78425892delCTTCTACCTGGATCAGGAGGAGCCTG	ENST00000370768.2	-	16	1634_1658	c.1553_1577delCAGGCTCCTCCTGATCCAGGTAGAAG	c.(1552-1578)ccaggctcctcctgatccaggtagaag>cg	p.PGSS*SR*K518fs	FUBP1_ENST00000370767.1_Splice_Site_p.PGSS*SR*K518fs|FUBP1_ENST00000436586.2_Splice_Site_p.PGSS*SR*K539fs	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1	518	Pro-rich.				positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)	p.Q520*(1)		central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						AGCATCTTCTACCTGGATCAGGAGGAGCCTGCTGCTGCCAGTGTGG	0.403			"F, N"		oligodendroglioma																																p.520_526del		Atlas-INDEL	.		Rec	yes		1	1p13.1	8880	far upstream element (FUSE) binding protein 1		O	.	FUBP1	112	.	1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	c.1559_1576del						PASS	.																																			SO:0001630	splice_region_variant	8880	exon16			.	U05040	CCDS683.1	1p31.1	2008-02-05			ENSG00000162613	ENSG00000162613			4004	protein-coding gene	gene with protein product		603444		FUBP		8125259	Standard	XM_005271309		Approved	FBP	uc001dii.3	Q96AE4	OTTHUMG00000040799	ENST00000370768.2:c.1576+1CAGGCTCCTCCTGATCCAGGTAGAAG>-	chr1.hg19:g.78425867_78425892delCTTCTACCTGGATCAGGAGGAGCCTG		117.0	0.0	0		89.0	11.0	0.123596	NM_003902	Q12828	In_Frame_Del	DEL	ENST00000370768.2	hg19	CCDS683.1																																																																																			.	.	.	none		0.403	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902	Frame_Shift_Del	-	78425892	CTTCTACCTGGATCAGGAGGAGCCTG	-	78425867	8	5	205	1	0	1	0	1	0	0	1	0	6099	405	14	0	376	0	FUBP1	1	78425867	Splice_Site	DEL	CTTCTACCTGGATCAGGAGGAGCCTG	TCGA-IA-A83S-01A-11D-A34Z-10	12595407	78425867	170824754	6	12373											
SYCP1	6847	hgsc.bcm.edu	37	chr1	115428830	115428830	+	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	aagaaaaagaaactcaaatgGaagaatctaataaagctaga	24	6	7	4	0	2	4	1	0	1	4	2	5	2	5	0	1	2	1	0	1	11	3			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr1:115428830G>C	ENST00000369522.3	+	14	1330	c.1090G>C	c.(1090-1092)Gaa>Caa	p.E364Q	SYCP1_ENST00000369518.1_Missense_Mutation_p.E364Q	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	364					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)		AACTCAAATGGAAGAATCTAA	0.338																																					p.E364Q		Atlas-SNP	.											SYCP1,NS,malignant_melanoma,0,2	SYCP1	149	.	0			c.G1090C						PASS	.						79	86	84					1																	115428830		2203	4300	6503	SO:0001583	missense	6847	exon14			CAAATGGAAGAAT	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.1090G>C	chr1.hg19:g.115428830G>C	ENSP00000358535:p.Glu364Gln	112.0	0.0	.		121.0	34.0	.	NM_003176	O14963|Q5VXJ6	Missense_Mutation	SNP	ENST00000369522.3	hg19	CCDS879.1	.	.	.	.	.	.	.	.	.	.	G	17.88	3.497246	0.64186	.	.	ENSG00000198765	ENST00000369522;ENST00000536734;ENST00000455987;ENST00000369518	T;T;T	0.56611	0.45;0.45;0.45	5.83	5.83	0.93111	.	0.110634	0.64402	D	0.000012	T	0.64057	0.2564	M	0.72894	2.215	0.41456	D	0.988014	D;D	0.69078	0.997;0.997	D;D	0.65323	0.934;0.934	T	0.65319	-0.6197	10	0.54805	T	0.06	-7.2709	15.6081	0.76689	0.0:0.0:1.0:0.0	.	364;364	B7ZLS9;Q15431	.;SYCP1_HUMAN	Q	364	ENSP00000358535:E364Q;ENSP00000410011:E364Q;ENSP00000358531:E364Q	ENSP00000358531:E364Q	E	+	1	0	SYCP1	115230353	1.000000	0.71417	1.000000	0.80357	0.669000	0.39330	4.056000	0.57448	2.746000	0.94184	0.561000	0.74099	GAA	.	.	.	none		0.338	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176		C	115428830	G	C	115428830	3	2	205	1	0	0	0	0	1	0	0	0	15443	1175	41	4	1140	4	SYCP1	1	115428830	Missense_Mutation	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	37002963	115428830	133821791	7	12374											
CD1C	911	hgsc.bcm.edu	37	chr1	158262079	158262080	+	Frame_Shift_Ins	INS	-	-	AA																															gcgtcacagaaacagtgtatINSaatctcataagaagcacttg																										TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr1:158262079_158262080insAA	ENST00000368170.3	+	3	813_814	c.534_535insAA	c.(535-537)aatfs	p.N179fs		NM_001765.2	NP_001756.2	P29017	CD1C_HUMAN	CD1c molecule	179					antigen processing and presentation (GO:0019882)|T cell activation involved in immune response (GO:0002286)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	endogenous lipid antigen binding (GO:0030883)|exogenous lipid antigen binding (GO:0030884)|glycolipid binding (GO:0051861)|lipopeptide binding (GO:0071723)			NS(1)|endometrium(3)|large_intestine(4)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	39	all_hematologic(112;0.0378)					AAACAGTGTATAATCTCATAAG	0.475																																					p.Y178fs		Atlas-Indel,Pindel	.											.	CD1C	100	.	0			c.534_535insAA						PASS	.																																			SO:0001589	frameshift_variant	911	exon3			.	M28827	CCDS1175.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158481	ENSG00000158481		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1636	protein-coding gene	gene with protein product		188340	"CD1C antigen, c polypeptide", "CD1c antigen"	CD1		2447586	Standard	NM_001765		Approved		uc001fru.3	P29017	OTTHUMG00000017514	ENST00000368170.3:c.535_536dupAA	chr1.hg19:g.158262080_158262081dupAA	ENSP00000357152:p.Asn179fs	74.0	0.0	0		78.0	21.0	0.269231	NM_001765	Q5TDJ7|Q6IAS4|Q9UMM0|Q9UN96	Frame_Shift_Ins	INS	ENST00000368170.3	hg19	CCDS1175.1																																																																																			.	.	.	none		0.475	CD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046351.2	NM_001765		AA	158262080	-	AA	158262079	7	5	205	1	0	1	1	0	0	0	0	0	2978	1413	49	0	544	0	CD1C	1	158262079	Frame_Shift_Ins	INS	-	TCGA-IA-A83S-01A-11D-A34Z-10	42833249	158262079	90988542	8	12375											
C1orf110	339512	hgsc.bcm.edu	37	chr1	162825494	162825494	+	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	acacgagaacatcttctggtCtcttctgaaatccattcccc	10	12	5	14	1	4	2	0	1	4	1	7	3	6	2	3	1	1	0	3	1	2	3			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr1:162825494C>G	ENST00000367910.1	-	3	362	c.242G>C	c.(241-243)aGa>aCa	p.R81T	C1orf110_ENST00000367912.2_Missense_Mutation_p.R80T|C1orf110_ENST00000367911.2_Missense_Mutation_p.R76T|C1orf110_ENST00000524691.1_5'UTR	NM_178550.4	NP_848645.3	Q86UF4	CA110_HUMAN	chromosome 1 open reading frame 110	81										endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	12						ATCTTCTGGTCTCTTCTGAAA	0.413																																					p.R81T		Atlas-SNP	.											.	C1orf110	22	.	0			c.G242C						PASS	.						121	110	114					1																	162825494		1883	4108	5991	SO:0001583	missense	339512	exon3			TCTGGTCTCTTCT	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.242G>C	chr1.hg19:g.162825494C>G	ENSP00000356886:p.Arg81Thr	224.0	0.0	.		220.0	52.0	.	NM_178550	Q5JSG1|Q6ZW57	Missense_Mutation	SNP	ENST00000367910.1	hg19	CCDS44269.1	.	.	.	.	.	.	.	.	.	.	C	15.19	2.760276	0.49468	.	.	ENSG00000185860	ENST00000367912;ENST00000367911;ENST00000367910	.	.	.	4.33	1.45	0.22620	.	0.482216	0.19466	N	0.113574	T	0.43964	0.1271	M	0.67953	2.075	0.32586	N	0.527883	D;D	0.63046	0.992;0.992	P;P	0.60541	0.876;0.876	T	0.42816	-0.9429	8	0.87932	D	0	-7.4143	5.7335	0.18053	0.0:0.6659:0.0:0.3341	.	80;81	Q86UF4-2;Q86UF4	.;CA110_HUMAN	T	80;76;81	.	ENSP00000356886:R81T	R	-	2	0	C1orf110	161092118	0.112000	0.22096	0.077000	0.20336	0.980000	0.70556	-0.042000	0.12063	0.559000	0.29153	0.655000	0.94253	AGA	.	.	.	none		0.413	C1orf110-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083211.2	NM_178550		G	162825494	C	G	162825494	3	3	205	1	0	0	0	0	1	0	0	0	1985	913	32	4	674	4	C1orf110	1	162825494	Missense_Mutation	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10	4563415	162825494	86425127	9	12376											
TROVE2	6738	hgsc.bcm.edu	37	chr1	193038376	193038376	+	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	gctgaagctttaattagattGattgaagatggcagaggatg	13	12	13	3	0	0	6	0	3	0	3	0	7	0	7	0	2	1	3	0	2	4	5			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr1:193038376G>T	ENST00000367446.3	+	2	402	c.192G>T	c.(190-192)ttG>ttT	p.L64F	TROVE2_ENST00000367444.3_Missense_Mutation_p.L64F|TROVE2_ENST00000432079.1_Intron|TROVE2_ENST00000400968.2_Missense_Mutation_p.L64F|TROVE2_ENST00000460715.2_Intron|TROVE2_ENST00000416058.2_5'UTR|TROVE2_ENST00000367445.3_Missense_Mutation_p.L64F|TROVE2_ENST00000367443.1_Missense_Mutation_p.L64F|TROVE2_ENST00000367441.1_Missense_Mutation_p.L64F	NM_004600.5	NP_004591.2	P10155	RO60_HUMAN	TROVE domain family, member 2	64	TROVE. {ECO:0000255|PROSITE- ProRule:PRU00343}.				cilium morphogenesis (GO:0060271)|immune system development (GO:0002520)|response to UV (GO:0009411)|smoothened signaling pathway (GO:0007224)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	metal ion binding (GO:0046872)|RNA binding (GO:0003723)|U2 snRNA binding (GO:0030620)	p.L64F(1)		biliary_tract(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|urinary_tract(1)	21						TAATTAGATTGATTGAAGATG	0.398																																					p.L64F		Atlas-SNP	.											TROVE2,NS,carcinoma,0,1	TROVE2	50	.	1	Substitution - Missense(1)	lung(1)	c.G192T						PASS	.						64	59	61					1																	193038376		1881	4119	6000	SO:0001583	missense	6738	exon2			TAGATTGATTGAA	BC036658	CCDS41449.1, CCDS1379.1, CCDS41450.1, CCDS41450.2, CCDS53451.1	1q31	2014-08-06	2005-06-14	2005-06-14	ENSG00000116747	ENSG00000116747			11313	protein-coding gene	gene with protein product		600063	"Sjogren syndrome antigen A2 (60kDa, ribonucleoprotein autoantigen SS-A/Ro)"	SSA2		8188321	Standard	NM_001042369		Approved	Ro60	uc001gss.3	P10155	OTTHUMG00000035675	ENST00000367446.3:c.192G>T	chr1.hg19:g.193038376G>T	ENSP00000356416:p.Leu64Phe	136.0	0.0	.		141.0	21.0	.	NM_004600	B2RBB9|Q5LJ98|Q5LJ99|Q5LJA0|Q86WL3|Q86WL4|Q92787|Q9H1W6	Missense_Mutation	SNP	ENST00000367446.3	hg19	CCDS1379.1	.	.	.	.	.	.	.	.	.	.	G	18.00	3.525859	0.64860	.	.	ENSG00000116747	ENST00000400968;ENST00000367446;ENST00000367443;ENST00000367445;ENST00000367444;ENST00000367441;ENST00000512587	T;T;T;T;T;T;T	0.17528	2.27;2.27;2.27;2.27;2.27;2.27;2.27	5.6	5.6	0.85130	TROVE (2);	0.075418	0.53938	D	0.000050	T	0.39759	0.1090	M	0.75447	2.3	0.80722	D	1	D;D;D;D	0.89917	0.978;0.992;1.0;1.0	D;D;D;D	0.77557	0.941;0.941;0.99;0.99	T	0.11792	-1.0573	10	0.51188	T	0.08	-9.6748	10.9958	0.47575	0.0:0.1392:0.7166:0.1442	.	64;64;64;64	Q5LJ99;Q5LJ98;Q5LJA0;P10155	.;.;.;RO60_HUMAN	F	64;64;64;64;64;64;5	ENSP00000383752:L64F;ENSP00000356416:L64F;ENSP00000356413:L64F;ENSP00000356415:L64F;ENSP00000356414:L64F;ENSP00000356411:L64F;ENSP00000424612:L5F	ENSP00000356411:L64F	L	+	3	2	TROVE2	191304999	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.829000	0.27449	2.648000	0.89879	0.557000	0.71058	TTG	.	.	.	none		0.398	TROVE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086688.1	NM_004600		T	193038376	G	T	193038376	3	4	205	1	0	0	0	0	1	0	0	0	16588	1281	45	4	194	4	TROVE2	1	193038376	Missense_Mutation	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	30212882	193038376	56212245	10	12377											
PYCR2	29920	hgsc.bcm.edu	37	chr1	226111423	226111423	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcgcggacaccgtgggcAggttcatttctggggagctg	6	9	17	9	3	2	1	1	1	1	0	2	3	2	3	1	5	2	3	1	5	0	2			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr1:226111423A>G	ENST00000343818.6	-	2	264	c.116T>C	c.(115-117)cTg>cCg	p.L39P	RP4-559A3.7_ENST00000432920.2_Missense_Mutation_p.L39P|PYCR2_ENST00000478402.1_5'UTR	NM_013328.2	NP_037460.2	Q96C36	P5CR2_HUMAN	pyrroline-5-carboxylate reductase family, member 2	39					L-proline biosynthetic process (GO:0055129)	cytoplasm (GO:0005737)	pyrroline-5-carboxylate reductase activity (GO:0004735)			kidney(1)|lung(3)	4	Breast(184;0.197)				L-Proline(DB00172)	CACCGTGGGCAGGTTCATTTC	0.612																																					p.L39P		Atlas-SNP	.											.	PYCR2	13	.	0			c.T116C						PASS	.						47	51	49					1																	226111423		2203	4300	6503	SO:0001583	missense	29920	exon2			GTGGGCAGGTTCA	AF151351	CCDS31043.1, CCDS73039.1	1q42.13	2008-02-05			ENSG00000143811	ENSG00000143811			30262	protein-coding gene	gene with protein product						12477932	Standard	NM_013328		Approved	P5CR2	uc001hpq.4	Q96C36	OTTHUMG00000037506	ENST00000343818.6:c.116T>C	chr1.hg19:g.226111423A>G	ENSP00000342502:p.Leu39Pro	78.0	0.0	.		87.0	20.0	.	NM_013328	A8K798|Q7Z515|Q9Y5J4	Missense_Mutation	SNP	ENST00000343818.6	hg19	CCDS31043.1	.	.	.	.	.	.	.	.	.	.	a	28.5	4.921791	0.92319	.	.	ENSG00000255835;ENSG00000143811	ENST00000432920;ENST00000343818	T;T	0.42131	0.98;0.98	4.36	4.36	0.52297	NAD(P)-binding domain (1);	0.000000	0.64402	D	0.000001	T	0.53850	0.1822	L	0.45581	1.43	0.80722	D	1	D;B	0.76494	0.999;0.004	D;B	0.72982	0.979;0.005	T	0.50996	-0.8761	9	.	.	.	-10.908	11.8145	0.52202	1.0:0.0:0.0:0.0	.	39;39	E7EUD8;Q96C36	.;P5CR2_HUMAN	P	39	ENSP00000414068:L39P;ENSP00000342502:L39P	.	L	-	2	0	PYCR2;RP4-559A3.7	224178046	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.530000	0.90606	1.963000	0.57068	0.533000	0.62120	CTG	.	.	.	none		0.612	PYCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091314.1	NM_013328		G	226111423	A	G	226111423	3	3	205	1	0	0	0	0	1	0	0	0	12869	188	7	3	870	3	PYCR2	1	226111423	Missense_Mutation	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10	33073047	226111423	23139198	11	12378											
GRHL1	29841	hgsc.bcm.edu	37	chr2	10139100	10139100	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcctcttttagatctcagAcaaatacgatgttccccatg	10	15	5	11	1	2	2	1	0	2	2	5	3	4	2	3	0	1	1	3	0	3	5			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr2:10139100A>G	ENST00000324907.9	+	15	1821	c.1685A>G	c.(1684-1686)gAc>gGc	p.D562G	GRHL1_ENST00000324883.5_Missense_Mutation_p.D373G|GRHL1_ENST00000405379.2_Missense_Mutation_p.D562G|GRHL1_ENST00000480736.1_Missense_Mutation_p.D16G	NM_198182.2	NP_937825.2	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1 (Drosophila)	562					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)		TAGATCTCAGACAAATACGAT	0.353																																					p.D562G		Atlas-SNP	.											.	GRHL1	95	.	0			c.A1685G						PASS	.						49	45	47					2																	10139100		2203	4300	6503	SO:0001583	missense	29841	exon15			TCTCAGACAAATA	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.1685A>G	chr2.hg19:g.10139100A>G	ENSP00000324693:p.Asp562Gly	160.0	0.0	.		141.0	8.0	.	NM_198182	A6NLA4|B2R7E4|B5MEC2|Q53T93|Q6NWN7|Q6NWN8|Q6NWN9|Q8NI33	Missense_Mutation	SNP	ENST00000324907.9	hg19	CCDS33144.2	.	.	.	.	.	.	.	.	.	.	A	16.90	3.248796	0.59103	.	.	ENSG00000134317	ENST00000405379;ENST00000324883;ENST00000324907;ENST00000480736	T;T;T	0.17691	2.74;2.26;2.74	5.34	5.34	0.76211	.	0.047940	0.85682	D	0.000000	T	0.17789	0.0427	L	0.40543	1.245	0.80722	D	1	B;B	0.13145	0.007;0.001	B;B	0.17098	0.017;0.005	T	0.02150	-1.1205	10	0.72032	D	0.01	-11.0287	15.269	0.73683	1.0:0.0:0.0:0.0	.	373;562	Q9NZI5-2;Q9NZI5	.;GRHL1_HUMAN	G	562;373;562;16	ENSP00000384209:D562G;ENSP00000324494:D373G;ENSP00000324693:D562G	ENSP00000324494:D373G	D	+	2	0	GRHL1	10056551	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	8.630000	0.90987	2.138000	0.66242	0.482000	0.46254	GAC	.	.	.	none		0.353	GRHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323543.2	NM_014552		G	10139100	A	G	10139100	3	3	205	1	0	0	0	0	1	0	0	0	6770	275	10	3	1743	3	GRHL1	2	10139100	Missense_Mutation	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10		10139100	233060273	12	12379											
ITSN2	50618	hgsc.bcm.edu	37	chr2	24535083	24535086	+	Frame_Shift_Del	DEL	AAAC	AAAC	-																															aaattaatacatacttaccaAaacgagcagaaattaatgga																										TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	AAAC	AAAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr2:24535083_24535086delAAAC	ENST00000355123.4	-	5	790_793	c.347_350delGTTT	c.(346-351)cgttttfs	p.RF116fs	ITSN2_ENST00000407704.1_5'UTR|ITSN2_ENST00000361999.3_Frame_Shift_Del_p.RF116fs|ITSN2_ENST00000406921.3_Frame_Shift_Del_p.RF116fs	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	116					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)					ATACTTACCAAAACGAGCAGAAAT	0.353																																					p.116_117del		Atlas-INDEL	.											.	ITSN2	224	.	0			c.348_351del						PASS	.																																			SO:0001589	frameshift_variant	50618	exon5			.	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.347_350delGTTT	chr2.hg19:g.24535083_24535086delAAAC	ENSP00000347244:p.Arg116fs	155.0	0.0	0		127.0	12.0	0.0944882	NM_147152	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Frame_Shift_Del	DEL	ENST00000355123.4	hg19	CCDS1710.2																																																																																			.	.	.	none		0.353	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277		-	24535086	AAAC	-	24535083	7	5	205	1	0	1	0	1	0	0	0	0	7934	14	1	0	4938	0	ITSN2	2	24535083	Frame_Shift_Del	DEL	AAAC	TCGA-IA-A83S-01A-11D-A34Z-10	14395983	24535083	218664290	13	12380	119	2									
ITSN2	50618	hgsc.bcm.edu	37	chr2	24535088	24535094	+	Frame_Shift_Del	DEL	AGCAGAA	AGCAGAA	-																															aatacatacttaccaaaacgAgcagaaattaatggagaaaa																										TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	AGCAGAA	AGCAGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr2:24535088_24535094delAGCAGAA	ENST00000355123.4	-	5	782_788	c.339_345delTTCTGCT	c.(337-345)atttctgctfs	p.ISA113fs	ITSN2_ENST00000407704.1_5'UTR|ITSN2_ENST00000361999.3_Frame_Shift_Del_p.ISA113fs|ITSN2_ENST00000406921.3_Frame_Shift_Del_p.ISA113fs	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	113					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)					TACCAAAACGAGCAGAAATTAATGGAG	0.357																																					p.114_116del		Atlas-INDEL	.											.	ITSN2	224	.	0			c.340_346del						PASS	.																																			SO:0001589	frameshift_variant	50618	exon5			.	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.339_345delTTCTGCT	chr2.hg19:g.24535088_24535094delAGCAGAA	ENSP00000347244:p.Ile113fs	161.0	0.0	0		129.0	12.0	0.0930233	NM_147152	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Frame_Shift_Del	DEL	ENST00000355123.4	hg19	CCDS1710.2																																																																																			.	.	.	none		0.357	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277		-	24535094	AGCAGAA	-	24535088	7	5	205	1	0	1	0	1	0	0	0	0	7934	291	11	0	4943	0	ITSN2	2	24535088	Frame_Shift_Del	DEL	AGCAGAA	TCGA-IA-A83S-01A-11D-A34Z-10	5	24535088	218664285	14	12381	119	2									
ATL2	64225	hgsc.bcm.edu	37	chr2	38527436	38527436	+	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	gaagcatggactttggatgtGgaagttcttctccttgatag	9	14	12	6	0	2	1	0	1	2	0	3	5	2	4	1	3	1	2	1	3	3	5			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr2:38527436G>C	ENST00000378954.4	-	10	1107	c.1106C>G	c.(1105-1107)cCa>cGa	p.P369R	ATL2_ENST00000406122.1_Missense_Mutation_p.P198R|ATL2_ENST00000419554.2_Missense_Mutation_p.P369R|ATL2_ENST00000539122.1_Missense_Mutation_p.P198R|ATL2_ENST00000452935.2_Missense_Mutation_p.P351R|ATL2_ENST00000546051.1_Missense_Mutation_p.P198R|ATL2_ENST00000332337.4_Missense_Mutation_p.P351R|ATL2_ENST00000402054.1_Missense_Mutation_p.P198R	NM_001135673.1|NM_022374.2	NP_001129145.1|NP_071769.2	Q8NHH9	ATLA2_HUMAN	atlastin GTPase 2	369					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						CTTTGGATGTGGAAGTTCTTC	0.373																																					p.P369R		Atlas-SNP	.											.	ATL2	49	.	0			c.C1106G						PASS	.						143	141	142					2																	38527436		2203	4300	6503	SO:0001583	missense	64225	exon10			GGATGTGGAAGTT		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.1106C>G	chr2.hg19:g.38527436G>C	ENSP00000368237:p.Pro369Arg	41.0	0.0	.		38.0	11.0	.	NM_001135673	B7Z1X2|B7Z7X8|Q4ZG30|Q7Z630|Q8NHH8|Q9H5M7	Missense_Mutation	SNP	ENST00000378954.4	hg19	CCDS46260.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.709464	0.89018	.	.	ENSG00000119787	ENST00000378954;ENST00000406122;ENST00000402054;ENST00000539122;ENST00000332337;ENST00000419554;ENST00000452935;ENST00000546051	T;T;T;T;T;T;T;T	0.20463	2.07;2.07;2.07;2.07;2.07;2.07;2.07;2.07	5.51	5.51	0.81932	Guanylate-binding protein, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.56673	0.2001	M	0.89601	3.045	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.64859	-0.6308	10	0.87932	D	0	-13.0964	18.7695	0.91885	0.0:0.0:1.0:0.0	.	198;351;351;369;369	B5MCN0;B7Z7X8;Q8NHH9-4;Q8NHH9-2;Q8NHH9	.;.;.;.;ATLA2_HUMAN	R	369;198;198;198;351;369;351;198	ENSP00000368237:P369R;ENSP00000385446:P198R;ENSP00000384062:P198R;ENSP00000446192:P198R;ENSP00000333393:P351R;ENSP00000415336:P369R;ENSP00000390743:P351R;ENSP00000438938:P198R	ENSP00000333393:P351R	P	-	2	0	ATL2	38380940	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.529000	0.98049	2.736000	0.93811	0.655000	0.94253	CCA	.	.	.	none		0.373	ATL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219886.2	NM_022374		C	38527436	G	C	38527436	3	2	205	1	0	0	0	0	1	0	0	0	1107	1348	47	4	773	4	ATL2	2	38527436	Missense_Mutation	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	13992348	38527436	204671937	15	12382											
PLEKHH2	130271	hgsc.bcm.edu	37	chr2	43937155	43937155	+	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	ctctctcctctgtggcttctGaaagtgattatgctattcct	6	17	7	11	0	3	2	0	2	3	0	6	2	5	2	2	1	1	2	2	1	3	4			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr2:43937155G>A	ENST00000282406.4	+	12	2103	c.1993G>A	c.(1993-1995)Gaa>Aaa	p.E665K		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	665	Ser-rich.				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)	p.E665K(1)		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)				TGTGGCTTCTGAAAGTGATTA	0.458																																					p.E665K		Atlas-SNP	.											PLEKHH2,NS,carcinoma,0,1	PLEKHH2	156	.	1	Substitution - Missense(1)	lung(1)	c.G1993A						PASS	.						177	170	172					2																	43937155		2203	4300	6503	SO:0001583	missense	130271	exon12			GCTTCTGAAAGTG	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.1993G>A	chr2.hg19:g.43937155G>A	ENSP00000282406:p.Glu665Lys	323.0	0.0	.		308.0	82.0	.	NM_172069	Q5JPJ6|Q6P4Q1|Q8N3Q3	Missense_Mutation	SNP	ENST00000282406.4	hg19	CCDS1812.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.194124	0.78902	.	.	ENSG00000152527	ENST00000282406	T	0.75589	-0.95	5.23	5.23	0.72850	.	0.346472	0.32533	N	0.005963	T	0.77644	0.4161	L	0.41492	1.28	0.58432	D	0.999996	P;P;D	0.55385	0.92;0.787;0.971	P;B;P	0.53401	0.694;0.254;0.725	T	0.80346	-0.1421	10	0.72032	D	0.01	-11.6976	18.7989	0.92008	0.0:0.0:1.0:0.0	.	665;102;665	Q8IVE3;Q8IVE3-2;Q8IVE3-3	PKHH2_HUMAN;.;.	K	665	ENSP00000282406:E665K	ENSP00000282406:E665K	E	+	1	0	PLEKHH2	43790659	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	9.355000	0.97087	2.423000	0.82170	0.563000	0.77884	GAA	.	.	.	none		0.458	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069		A	43937155	G	A	43937155	3	1	205	1	0	0	0	0	1	0	0	0	12084	1291	45	2	2035	2	PLEKHH2	2	43937155	Missense_Mutation	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	5409719	43937155	199262218	16	12383											
C2orf73	129852	hgsc.bcm.edu	37	chr2	54587567	54587567	+	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	ttatcagaaacagacgtcagAcaggcagccaaggcatgccc	14	5	10	12	1	2	3	2	0	0	3	2	3	2	3	2	2	3	2	2	2	3	1			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr2:54587567A>T	ENST00000398634.2	+	5	774	c.732A>T	c.(730-732)agA>agT	p.R244S	C2orf73_ENST00000491538.1_Intron|C2orf73_ENST00000405749.1_Intron	NM_001100396.1	NP_001093866.1	Q8N5S3	CB073_HUMAN	chromosome 2 open reading frame 73	244										breast(2)	2						CAGACGTCAGACAGGCAGCCA	0.498																																					p.R244S		Atlas-SNP	.											.	C2orf73	17	.	0			c.A732T						PASS	.						33	32	32					2																	54587567		1907	4131	6038	SO:0001583	missense	129852	exon5			CGTCAGACAGGCA	BC031669, AK097617	CCDS46285.1	2p16.2	2008-07-07			ENSG00000177994	ENSG00000177994			26861	protein-coding gene	gene with protein product						14702039	Standard	NM_001100396		Approved	FLJ40298	uc002rxt.1	Q8N5S3	OTTHUMG00000151826	ENST00000398634.2:c.732A>T	chr2.hg19:g.54587567A>T	ENSP00000381631:p.Arg244Ser	112.0	0.0	.		123.0	25.0	.	NM_001100396	A0AV79|A0AV81|Q8N7V4	Missense_Mutation	SNP	ENST00000398634.2	hg19	CCDS46285.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.756992	0.89843	.	.	ENSG00000177994	ENST00000398634;ENST00000447328	T;T	0.43688	0.94;0.94	5.22	-4.39	0.03611	.	0.275143	0.30989	N	0.008480	T	0.27559	0.0677	L	0.51422	1.61	0.09310	N	1	B;B	0.16396	0.017;0.017	B;B	0.14578	0.007;0.011	T	0.18085	-1.0348	9	.	.	.	-22.3764	7.55	0.27790	0.3399:0.4503:0.2098:0.0	.	186;244	B7ZM12;Q8N5S3	.;CB073_HUMAN	S	244;186	ENSP00000381631:R244S;ENSP00000389570:R186S	.	R	+	3	2	C2orf73	54441071	0.996000	0.38824	0.026000	0.17262	0.956000	0.61745	0.694000	0.25512	-0.510000	0.06523	0.455000	0.32223	AGA	.	.	.	none		0.498	C2orf73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324075.2	NM_001100396		T	54587567	A	T	54587567	3	4	205	1	0	0	0	0	1	0	0	0	2194	272	10	5	750	5	C2orf73	2	54587567	Missense_Mutation	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10	10650412	54587567	188611806	17	12384											
AFTPH	54812	hgsc.bcm.edu	37	chr2	64779245	64779245	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaagggacggaagcctcttAgcactcatagcactgagtat	13	8	10	10	1	2	1	1	1	1	0	2	3	2	3	1	2	3	3	1	2	5	3			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr2:64779245A>G	ENST00000422803.1	+	2	951	c.637A>G	c.(637-639)Agc>Ggc	p.S213G	AFTPH_ENST00000409933.1_Missense_Mutation_p.S213G|AFTPH_ENST00000238855.7_Missense_Mutation_p.S213G|AFTPH_ENST00000238856.4_Missense_Mutation_p.S213G|AFTPH_ENST00000409183.1_5'Flank			Q6ULP2	AFTIN_HUMAN	aftiphilin	213					protein transport (GO:0015031)	AP-1 adaptor complex (GO:0030121)|cytosol (GO:0005829)	clathrin binding (GO:0030276)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	35						GAAGCCTCTTAGCACTCATAG	0.408																																					p.S213G		Atlas-SNP	.											.	AFTPH	117	.	0			c.A637G						PASS	.						99	94	95					2																	64779245		2203	4300	6503	SO:0001583	missense	54812	exon2			CCTCTTAGCACTC	AB073356	CCDS1878.1, CCDS46303.1	2p14	2008-02-05			ENSG00000119844	ENSG00000119844			25951	protein-coding gene	gene with protein product						14665628, 15758025, 15811338	Standard	NM_017657		Approved	MGC33965, FLJ20080, FLJ23793, Nbla10388	uc002scz.3	Q6ULP2	OTTHUMG00000129539	ENST00000422803.1:c.637A>G	chr2.hg19:g.64779245A>G	ENSP00000397726:p.Ser213Gly	81.0	0.0	.		89.0	22.0	.	NM_017657	D6W5E9|Q6ZM66|Q86VW3|Q8TCF3|Q9H7E3|Q9HAB9|Q9NXS4	Missense_Mutation	SNP	ENST00000422803.1	hg19		.	.	.	.	.	.	.	.	.	.	A	10.69	1.421187	0.25639	.	.	ENSG00000119844	ENST00000238856;ENST00000422803;ENST00000238855;ENST00000409933	T;T;T;T	0.25414	1.8;1.8;1.8;1.8	5.11	5.11	0.69529	.	0.449420	0.26166	N	0.025958	T	0.18882	0.0453	L	0.40543	1.245	0.28041	N	0.933768	B;B;B;B	0.33171	0.4;0.4;0.4;0.4	B;B;B;B	0.31101	0.124;0.124;0.124;0.124	T	0.11966	-1.0566	10	0.20519	T	0.43	-0.0973	10.0775	0.42368	0.9237:0.0:0.0763:0.0	.	213;213;213;213	Q6ULP2;Q6ULP2-2;Q6ULP2-5;Q6ULP2-4	AFTIN_HUMAN;.;.;.	G	213	ENSP00000238856:S213G;ENSP00000397726:S213G;ENSP00000238855:S213G;ENSP00000387071:S213G	ENSP00000238855:S213G	S	+	1	0	AFTPH	64632749	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.209000	0.32357	2.243000	0.73865	0.482000	0.46254	AGC	.	.	.	none		0.408	AFTPH-202	KNOWN	basic	protein_coding	protein_coding		NM_017657		G	64779245	A	G	64779245	3	3	205	1	0	0	0	0	1	0	0	0	364	420	15	3	639	3	AFTPH	2	64779245	Missense_Mutation	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10	10191678	64779245	178420128	18	12385											
SH2D6	284948	hgsc.bcm.edu	37	chr2	85662170	85662170	+	Missense_Mutation	SNP	A	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	ccccaccccaccccagctcaAtaatctgcttcttctagaag	10	9	4	18	0	4	1	1	0	3	1	4	1	4	1	6	0	2	2	6	0	4	4			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr2:85662170A>C	ENST00000340326.2	+	1	253	c.92A>C	c.(91-93)aAt>aCt	p.N31T	SH2D6_ENST00000389938.2_Intron|SH2D6_ENST00000481426.2_Intron|Y_RNA_ENST00000384478.1_RNA	NM_198482.1	NP_940884.1	Q7Z4S9	SH2D6_HUMAN	SH2 domain containing 6	31										central_nervous_system(1)|lung(2)	3						ccccaGCTCAATAATCTGCTT	0.637																																					p.N31T		Atlas-SNP	.											.	SH2D6	15	.	0			c.A92C						PASS	.						12	13	13					2																	85662170		2197	4298	6495	SO:0001583	missense	284948	exon1			AGCTCAATAATCT	AF450483	CCDS1976.1	2p11.2	2013-02-14			ENSG00000152292	ENSG00000152292		"SH2 domain containing"	30439	protein-coding gene	gene with protein product						12477932	Standard	NM_198482		Approved	FLJ35993	uc002spq.3	Q7Z4S9	OTTHUMG00000130176	ENST00000340326.2:c.92A>C	chr2.hg19:g.85662170A>C	ENSP00000341867:p.Asn31Thr	257.0	0.0	.		194.0	46.0	.	NM_198482	A6ND14|Q6R306	Missense_Mutation	SNP	ENST00000340326.2	hg19	CCDS1976.1	.	.	.	.	.	.	.	.	.	.	A	2.895	-0.228883	0.06022	.	.	ENSG00000152292	ENST00000340326	T	0.76968	-1.06	3.25	-6.5	0.01884	.	66.330300	0.00166	N	0.000000	T	0.55097	0.1899	N	0.08118	0	0.09310	N	1	B	0.16396	0.017	B	0.10450	0.005	T	0.50224	-0.8853	10	0.20046	T	0.44	7.3091	7.7682	0.28993	0.2024:0.2909:0.5066:0.0	.	31	Q7Z4S9	SH2D6_HUMAN	T	31	ENSP00000341867:N31T	ENSP00000341867:N31T	N	+	2	0	SH2D6	85515681	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-1.051000	0.03507	-1.835000	0.01191	-0.475000	0.04921	AAT	.	.	.	none		0.637	SH2D6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252493.2	NM_198482		C	85662170	A	C	85662170	3	2	205	1	0	0	0	0	1	0	0	0	14251	101	4	5	94	5	SH2D6	2	85662170	Missense_Mutation	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10	20882925	85662170	157537203	19	12386											
ANAPC1	64682	hgsc.bcm.edu	37	chr2	112638235	112638235	+	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	tcctgaagggatcccaccaaGccagcagcaccatcagaaga	14	4	9	14	0	1	3	1	1	0	2	3	4	3	4	5	1	3	2	5	1	3	0			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr2:112638235G>T	ENST00000341068.3	-	2	940	c.168C>A	c.(166-168)ggC>ggA	p.G56G	ANAPC1_ENST00000489177.1_5'UTR	NM_022662.3	NP_073153.1	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	56					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(7)|lung(16)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	49						ATCCCACCAAGCCAGCAGCAC	0.463																																					p.G56G		Atlas-SNP	.											.	ANAPC1	116	.	0			c.C168A						PASS	.						37	37	37					2																	112638235		2203	4300	6503	SO:0001819	synonymous_variant	64682	exon2			CACCAAGCCAGCA	AJ278357	CCDS2093.1	2q12.1	2011-06-15			ENSG00000153107	ENSG00000153107		"Anaphase promoting complex subunits"	19988	protein-coding gene	gene with protein product		608473				11179667	Standard	NM_022662		Approved	MCPR, TSG24, APC1	uc002ssh.3	Q9H1A4	OTTHUMG00000131277	ENST00000341068.3:c.168C>A	chr2.hg19:g.112638235G>T		272.0	0.0	.		267.0	75.0	.	NM_022662	Q2M3H8|Q9BSE6|Q9H8D0	Silent	SNP	ENST00000341068.3	hg19	CCDS2093.1																																																																																			.	.	.	none		0.463	ANAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254045.2	NM_022662		T	112638235	G	T	112638235	2	4	205	1	0	0	0	0	0	0	0	1	598	958	34	4		4	ANAPC1	2	112638235	Silent	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	26976065	112638235	130561138	20	12387											
LY75	4065	hgsc.bcm.edu	37	chr2	160746833	160746833	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agagccgtctgagtattaaaTtggtagcaacttccaaactg	13	11	9	8	1	1	2	0	1	1	1	2	2	2	2	2	1	4	3	2	1	6	5			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr2:160746833T>C	ENST00000263636.4	-	4	720	c.693A>G	c.(691-693)caA>caG	p.Q231Q	LY75-CD302_ENST00000505052.1_Silent_p.Q231Q|LY75_ENST00000554112.1_Silent_p.Q231Q|LY75_ENST00000553424.1_Silent_p.Q231Q|LY75-CD302_ENST00000504764.1_Silent_p.Q231Q	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	231	C-type lectin 1. {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)		GAGTATTAAATTGGTAGCAAC	0.373																																					p.Q231Q		Atlas-SNP	.											.	LY75	151	.	0			c.A693G						PASS	.						94	95	95					2																	160746833		2203	4300	6503	SO:0001819	synonymous_variant	4065	exon4			ATTAAATTGGTAG	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.693A>G	chr2.hg19:g.160746833T>C		115.0	0.0	.		105.0	12.0	.	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Silent	SNP	ENST00000263636.4	hg19	CCDS2211.1																																																																																			.	.	.	none		0.373	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1			C	160746833	T	C	160746833	2	2	205	1	0	0	0	0	0	0	0	1	9106	1490	52	3		3	LY75	2	160746833	Silent	SNP	T	TCGA-IA-A83S-01A-11D-A34Z-10	48108598	160746833	82452540	21	12388											
HOXD4	3233	hgsc.bcm.edu	37	chr2	177017568	177017568	+	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	cccaacactaaaggcaggtcAtcgtcctcatcttcctcctc	9	10	5	17	1	3	0	2	0	1	0	8	0	6	0	4	2	1	1	4	2	3	2			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr2:177017568A>T	ENST00000306324.3	+	2	1078	c.666A>T	c.(664-666)tcA>tcT	p.S222S	MIR10B_ENST00000385011.1_RNA|HOXD3_ENST00000468418.3_5'UTR	NM_014621.2	NP_055436.2	P09016	HXD4_HUMAN	homeobox D4	222	Poly-Ser.				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)		AAGGCAGGTCATCGTCCTCAT	0.537																																					p.S222S		Atlas-SNP	.											.	HOXD4	32	.	0			c.A666T						PASS	.						119	121	120					2																	177017568		2203	4300	6503	SO:0001819	synonymous_variant	3233	exon2			CAGGTCATCGTCC		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.666A>T	chr2.hg19:g.177017568A>T		94.0	0.0	.		94.0	19.0	.	NM_014621	B2R9R3|Q96AU0	Silent	SNP	ENST00000306324.3	hg19	CCDS2269.1																																																																																			.	.	.	none		0.537	HOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255697.2			T	177017568	A	T	177017568	2	4	205	1	0	0	0	0	0	0	0	1	7331	204	8	5		5	HOXD4	2	177017568	Silent	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10	16270735	177017568	66181805	22	12389											
PRKRA	8575	hgsc.bcm.edu	37	chr2	179300994	179300994	+	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	agttgatcttttcaccaggaGaattcctcaaggaatgccaa	13	11	8	9	0	3	2	2	1	1	1	4	4	4	3	3	2	1	1	3	2	4	4			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr2:179300994G>A	ENST00000325748.4	-	7	862	c.662C>T	c.(661-663)tCt>tTt	p.S221F	AC009948.5_ENST00000436616.2_RNA|AC009948.5_ENST00000453026.2_RNA|PRKRA_ENST00000438687.3_Missense_Mutation_p.S108F|AC009948.5_ENST00000454488.1_RNA|PRKRA_ENST00000432031.2_Missense_Mutation_p.S210F|PRKRA_ENST00000487082.1_Missense_Mutation_p.S196F	NM_003690.4	NP_003681.1	O75569	PRKRA_HUMAN	protein kinase, interferon-inducible double stranded RNA dependent activator	221	Sufficient for self-association and interaction with TARBP2.				cellular response to oxidative stress (GO:0034599)|gene expression (GO:0010467)|immune response (GO:0006955)|middle ear morphogenesis (GO:0042474)|negative regulation of cell proliferation (GO:0008285)|outer ear morphogenesis (GO:0042473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|production of siRNA involved in RNA interference (GO:0030422)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|skeletal system morphogenesis (GO:0048705)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	enzyme activator activity (GO:0008047)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.00634)|all cancers(119;0.0265)			TTCACCAGGAGAATTCCTCAA	0.388																																					p.S221F	Melanoma(200;68 3001 23825 48764)	Atlas-SNP	.											.	PRKRA	56	.	0			c.C662T						PASS	.						154	173	167					2																	179300994		2203	4300	6503	SO:0001583	missense	8575	exon7			CCAGGAGAATTCC	AF072860	CCDS2279.1, CCDS46460.1, CCDS46461.1	2q31.2	2009-08-25			ENSG00000180228	ENSG00000180228			9438	protein-coding gene	gene with protein product	"protein activator of the interferon-induced protein kinase"	603424				9687506, 10336432	Standard	NM_003690		Approved	PACT, RAX, HSD14, DYT16	uc002umf.3	O75569	OTTHUMG00000132576	ENST00000325748.4:c.662C>T	chr2.hg19:g.179300994G>A	ENSP00000318176:p.Ser221Phe	68.0	0.0	.		77.0	14.0	.	NM_003690	A8K3I6|Q53G24|Q6X7T5|Q8NDK4	Missense_Mutation	SNP	ENST00000325748.4	hg19	CCDS2279.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.432252	0.83776	.	.	ENSG00000180228	ENST00000325748;ENST00000438687;ENST00000487082;ENST00000432031	T;T;T;T	0.76186	-0.98;-0.99;-0.98;-1.0	5.92	5.92	0.95590	.	0.065506	0.64402	D	0.000008	D	0.85695	0.5756	M	0.73217	2.22	0.48762	D	0.999701	D;D	0.89917	1.0;0.999	D;D	0.76071	0.987;0.964	D	0.86199	0.1617	10	0.72032	D	0.01	.	17.2511	0.87042	0.0:0.0:1.0:0.0	.	221;210	O75569;O75569-2	PRKRA_HUMAN;.	F	221;108;196;210	ENSP00000318176:S221F;ENSP00000398980:S108F;ENSP00000430604:S196F;ENSP00000393883:S210F	ENSP00000318176:S221F	S	-	2	0	PRKRA	179009240	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.222000	0.72249	2.822000	0.97130	0.650000	0.86243	TCT	.	.	.	none		0.388	PRKRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255782.2	NM_003690		A	179300994	G	A	179300994	3	1	205	1	0	0	0	0	1	0	0	0	12534	942	33	2	287	2	PRKRA	2	179300994	Missense_Mutation	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	2283426	179300994	63898379	23	12390											
TTN	7273	hgsc.bcm.edu	37	chr2	179455837	179455837	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtttctcaacaatataattTatcacagggcttcctccatc	11	15	4	11	0	2	0	2	0	1	0	6	0	4	0	2	1	1	2	2	1	5	6			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr2:179455837T>C	ENST00000591111.1	-	254	55916	c.55692A>G	c.(55690-55692)atA>atG	p.I18564M	TTN_ENST00000342992.6_Missense_Mutation_p.I17637M|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I11332M|TTN_ENST00000359218.5_Missense_Mutation_p.I11265M|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.I20205M|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I11140M|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589907.1_RNA			Q8WZ42	TITIN_HUMAN	titin	18564	Fibronectin type-III 34. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAATATAATTTATCACAGGGC	0.448																																					p.I20205M		Atlas-SNP	.											.	TTN	18412	.	0			c.A60615G						PASS	.						103	102	102					2																	179455837		1868	4097	5965	SO:0001583	missense	7273	exon304			ATAATTTATCACA	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.55692A>G	chr2.hg19:g.179455837T>C	ENSP00000465570:p.Ile18564Met	181.0	0.0	.		149.0	35.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	7.626	0.677919	0.14841	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57436	0.4;0.4;0.4;0.4	6.11	-1.34	0.09143	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.30135	0.0755	N	0.12746	0.255	0.28797	N	0.899017	B;B;B;B	0.25850	0.136;0.136;0.136;0.136	B;B;B;B	0.21151	0.033;0.033;0.033;0.033	T	0.27640	-1.0068	9	0.87932	D	0	.	7.5324	0.27691	0.1013:0.0615:0.5558:0.2813	.	11140;11265;11332;18564	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	M	17637;11140;11332;11265;11138	ENSP00000343764:I17637M;ENSP00000434586:I11140M;ENSP00000340554:I11332M;ENSP00000352154:I11265M	ENSP00000340554:I11332M	I	-	3	3	TTN	179164083	0.992000	0.36948	1.000000	0.80357	0.993000	0.82548	0.173000	0.16724	0.143000	0.18926	-0.331000	0.08364	ATA	.	.	.	none		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179455837	T	C	179455837	3	2	205	1	0	0	0	0	1	0	0	0	16747	1744	61	3	47600	3	TTN	2	179455837	Missense_Mutation	SNP	T	TCGA-IA-A83S-01A-11D-A34Z-10	154843	179455837	63743536	24	12391											
DLEC1	9940	hgsc.bcm.edu	37	chr3	38101345	38101345	+	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	tttcactctgcacctaaaggTaatgcttctgtgctctcaag	9	14	7	11	0	4	0	2	0	3	0	5	0	4	0	1	1	3	4	1	1	4	4			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr3:38101345T>A	ENST00000308059.6	+	3	694		c.e3+2		DLEC1_ENST00000346219.3_Splice_Site|DLEC1_ENST00000452631.2_Splice_Site					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		CACCTAAAGGTAATGCTTCTG	0.488																																					.		Atlas-SNP	.											.	DLEC1	278	.	0			c.673+2T>A						PASS	.						130	128	128					3																	38101345		1939	4141	6080	SO:0001630	splice_region_variant	9940	exon3			TAAAGGTAATGCT	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.673+2T>A	chr3.hg19:g.38101345T>A		88.0	0.0	.		79.0	12.0	.	NM_007337		Splice_Site	SNP	ENST00000308059.6	hg19	CCDS2672.2	.	.	.	.	.	.	.	.	.	.	T	16.28	3.077564	0.55753	.	.	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	.	.	.	4.99	4.99	0.66335	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.0009	0.47604	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	DLEC1	38076349	1.000000	0.71417	0.996000	0.52242	0.627000	0.37826	3.947000	0.56652	2.089000	0.63090	0.533000	0.62120	.	.	.	.	none		0.488	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	Intron	A	38101345	T	A	38101345	5	1	205	1	0	0	0	0	0	0	1	0	4554	1652	57	5	685	5	DLEC1	3	38101345	Splice_Site	SNP	T	TCGA-IA-A83S-01A-11D-A34Z-10		38101345	159921085	25	12392											
FAM19A4	151647	hgsc.bcm.edu	37	chr3	68929968	68929968	+	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	tagaaagagccagtgcgacaGcaacactgacttagcacaga	16	5	10	10	1	0	4	0	1	0	3	0	5	0	4	1	0	5	2	1	0	4	2			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr3:68929968G>T	ENST00000295569.7	-	3	535	c.43C>A	c.(43-45)Ctg>Atg	p.L15M	RNA5SP135_ENST00000517019.1_RNA	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	15						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)		CAGTGCGACAGCAACACTGAC	0.552																																					p.L15M		Atlas-SNP	.											.	FAM19A4	23	.	0			c.C43A						PASS	.						83	75	78					3																	68929968		2203	4300	6503	SO:0001583	missense	151647	exon3			GCGACAGCAACAC	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.43C>A	chr3.hg19:g.68929968G>T	ENSP00000295569:p.Leu15Met	103.0	0.0	.		141.0	8.0	.	NM_182522	A8MVT2	Missense_Mutation	SNP	ENST00000295569.7	hg19	CCDS2907.1	.	.	.	.	.	.	.	.	.	.	G	14.83	2.652658	0.47362	.	.	ENSG00000163377	ENST00000295569;ENST00000495737	.	.	.	5.18	5.18	0.71444	.	0.492735	0.18075	N	0.152484	T	0.26666	0.0652	N	0.08118	0	0.28953	N	0.890319	P	0.36438	0.553	B	0.31751	0.135	T	0.18304	-1.0341	9	0.46703	T	0.11	-7.3645	18.7219	0.91698	0.0:0.0:1.0:0.0	.	15	Q96LR4	F19A4_HUMAN	M	15	.	ENSP00000295569:L15M	L	-	1	2	FAM19A4	69012658	1.000000	0.71417	0.691000	0.30163	0.990000	0.78478	4.329000	0.59260	2.414000	0.81942	0.591000	0.81541	CTG	.	.	.	none		0.552	FAM19A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352002.1	NM_182522		T	68929968	G	T	68929968	3	4	205	1	0	0	0	0	1	0	0	0	5538	962	34	4	395	4	FAM19A4	3	68929968	Missense_Mutation	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	30828623	68929968	129092462	26	12393											
ABI3BP	25890	hgsc.bcm.edu	37	chr3	100470405	100470405	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaaaacataccttctttgaTtggtaactggtcagaagtga	14	12	9	6	0	2	4	1	2	1	2	2	4	2	4	1	2	3	1	1	2	5	5			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr3:100470405T>C	ENST00000284322.5	-	34	3212	c.3103A>G	c.(3103-3105)Atc>Gtc	p.I1035V	ABI3BP_ENST00000471714.1_Missense_Mutation_p.I1737V|ABI3BP_ENST00000383691.4_Missense_Mutation_p.I989V	NM_015429.3	NP_056244.2	Q7Z7G0	TARSH_HUMAN	ABI family, member 3 (NESH) binding protein	1035					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						CCTTCTTTGATTGGTAACTGG	0.408																																					p.I1035V		Atlas-SNP	.											.	ABI3BP	305	.	0			c.A3103G						PASS	.						59	55	56					3																	100470405		1880	4109	5989	SO:0001583	missense	25890	exon34			CTTTGATTGGTAA	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.3103A>G	chr3.hg19:g.100470405T>C	ENSP00000284322:p.Ile1035Val	94.0	0.0	.		116.0	21.0	.	NM_015429	B3KSL4|Q6ZW20|Q6ZW22|Q9C082|Q9UFI6	Missense_Mutation	SNP	ENST00000284322.5	hg19	CCDS46880.1	.	.	.	.	.	.	.	.	.	.	T	13.50	2.255157	0.39896	.	.	ENSG00000154175	ENST00000471714;ENST00000284322;ENST00000383692;ENST00000429331;ENST00000383691	T;T;T	0.44482	0.92;0.92;0.92	5.92	4.74	0.60224	.	0.502303	0.22224	N	0.062901	T	0.16981	0.0408	N	0.02011	-0.69	0.20403	N	0.999902	B;B;B;B	0.22276	0.011;0.002;0.067;0.057	B;B;B;B	0.18263	0.021;0.007;0.018;0.003	T	0.13522	-1.0506	10	0.33940	T	0.23	-0.2949	8.009	0.30342	0.0:0.0748:0.1379:0.7872	.	989;1035;1737;744	B4DSV9;Q7Z7G0;D3YTG3;D3YTD6	.;TARSH_HUMAN;.;.	V	1737;1035;744;446;989	ENSP00000420524:I1737V;ENSP00000284322:I1035V;ENSP00000373189:I989V	ENSP00000284322:I1035V	I	-	1	0	ABI3BP	101953095	0.949000	0.32298	1.000000	0.80357	0.984000	0.73092	1.044000	0.30329	1.034000	0.39945	0.533000	0.62120	ATC	.	.	.	none		0.408	ABI3BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353260.1			C	100470405	T	C	100470405	3	2	205	1	0	0	0	0	1	0	0	0	91	1493	52	3	132	3	ABI3BP	3	100470405	Missense_Mutation	SNP	T	TCGA-IA-A83S-01A-11D-A34Z-10	31540437	100470405	97552025	27	12394											
TRPC1	7220	hgsc.bcm.edu	37	chr3	142443574	142443574	+	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	cttgctggcgtgcgacaaggGtgagagttaggcccctttct	6	11	14	10	2	1	1	0	1	1	1	1	3	1	1	2	3	2	2	2	3	2	3			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr3:142443574G>A	ENST00000476941.1	+	1	658		c.e1+1		TRPC1_ENST00000273482.6_Splice_Site	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1						axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						TGCGACAAGGGTGAGAGTTAG	0.572																																					.		Atlas-SNP	.											.	TRPC1	82	.	0			c.172+1G>A						PASS	.						137	118	124					3																	142443574		2203	4300	6503	SO:0001630	splice_region_variant	7220	exon1			ACAAGGGTGAGAG	X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"Voltage-gated ion channels / Transient receptor potential cation channels"	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.172+1G>A	chr3.hg19:g.142443574G>A		45.0	0.0	.		63.0	23.0	.	NM_003304	Q14CE4	Splice_Site	SNP	ENST00000476941.1	hg19	CCDS58856.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.178518	0.78564	.	.	ENSG00000144935	ENST00000476941;ENST00000273482	.	.	.	5.02	4.14	0.48551	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5725	0.61856	0.0:0.0:0.8446:0.1554	.	.	.	.	.	-1	.	.	.	+	.	.	TRPC1	143926264	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.209000	0.72171	1.231000	0.43661	0.650000	0.86243	.	.	.	.	none		0.572	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304	Intron	A	142443574	G	A	142443574	5	1	205	1	0	0	0	0	0	0	1	0	16590	1275	44	2	175	2	TRPC1	3	142443574	Splice_Site	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	41973169	142443574	55578856	28	12395											
ETV5	2119	hgsc.bcm.edu	37	chr3	185774898	185774898	+	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	tcagcttgaactccatgcctCgacctgtccaggcaatgaag	10	9	9	13	1	1	2	1	2	0	0	4	3	3	2	4	1	3	2	4	1	3	1			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr3:185774898C>A	ENST00000306376.5	-	11	1421	c.1175G>T	c.(1174-1176)cGa>cTa	p.R392L	ETV5_ENST00000537818.1_Missense_Mutation_p.R434L|ETV5_ENST00000434744.1_Missense_Mutation_p.R392L|ETV5_ENST00000480706.1_5'UTR	NM_004454.2	NP_004445.1	P41161	ETV5_HUMAN	ets variant 5	392					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)			CTCCATGCCTCGACCTGTCCA	0.517			T	"TMPRSS2, SCL45A3"	Prostate																																p.R392L		Atlas-SNP	.		Dom	yes		3	3q28	2119	ets variant gene 5		E	ETV5_ENST00000306376,NS,carcinoma,0,2	ETV5	106	.	0			c.G1175T						PASS	.						91	89	89					3																	185774898		2203	4300	6503	SO:0001583	missense	2119	exon11			ATGCCTCGACCTG	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.1175G>T	chr3.hg19:g.185774898C>A	ENSP00000306894:p.Arg392Leu	81.0	0.0	.		94.0	33.0	.	NM_004454	A6NH46|B7Z7D7|Q6IBN5	Missense_Mutation	SNP	ENST00000306376.5	hg19	CCDS33906.1	.	.	.	.	.	.	.	.	.	.	C	33	5.288657	0.95517	.	.	ENSG00000244405	ENST00000306376;ENST00000434744;ENST00000537818	T;T;T	0.57107	0.42;0.42;0.42	5.69	5.69	0.88448	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (4);	0.000000	0.85682	D	0.000000	T	0.78323	0.4265	M	0.89214	3.015	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.81996	-0.0676	10	0.87932	D	0	.	18.5905	0.91210	0.0:1.0:0.0:0.0	.	392;434	P41161;B7Z7D7	ETV5_HUMAN;.	L	392;392;434	ENSP00000306894:R392L;ENSP00000413755:R392L;ENSP00000441737:R434L	ENSP00000306894:R392L	R	-	2	0	ETV5	187257592	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.818000	0.86416	2.691000	0.91804	0.655000	0.94253	CGA	.	.	.	none		0.517	ETV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344947.1	NM_004454		A	185774898	C	A	185774898	3	1	205	1	0	0	0	0	1	0	0	0	5284	884	31	4	369	4	ETV5	3	185774898	Missense_Mutation	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10	43331324	185774898	12247532	29	12396											
CCDC50	152137	hgsc.bcm.edu	37	chr3	191092937	191092937	+	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	gagatggaaagactgtgaagCacaagaaagagaaaccagaa	21	3	12	5	0	0	6	0	1	0	5	0	9	0	7	1	1	2	1	1	1	6	0			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr3:191092937C>T	ENST00000392455.3	+	6	1046				CCDC50_ENST00000392456.3_Missense_Mutation_p.H179Y	NM_174908.3	NP_777568.1	Q8IVM0	CCD50_HUMAN	coiled-coil domain containing 50							cytoplasm (GO:0005737)	ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|stomach(1)	23	all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000136)		GACTGTGAAGCACAAGAAAGA	0.498																																					p.H179Y		Atlas-SNP	.											.	CCDC50	39	.	0			c.C535T						PASS	.						83	78	79					3																	191092937		2203	4300	6503	SO:0001627	intron_variant	152137	exon6			GTGAAGCACAAGA	AJ416916	CCDS33912.1, CCDS33913.1	3q28	2010-12-24		2005-12-23	ENSG00000152492	ENSG00000152492			18111	protein-coding gene	gene with protein product		611051	"deafness, autosomal dominant 44"	C3orf6, DFNA44		16803894, 17503326	Standard	NM_178335		Approved	Ymer	uc003fsv.3	Q8IVM0	OTTHUMG00000156177	ENST00000392455.3:c.449-5011C>T	chr3.hg19:g.191092937C>T		84.0	0.0	.		84.0	14.0	.	NM_178335	Q86VH7	Missense_Mutation	SNP	ENST00000392455.3	hg19	CCDS33913.1	.	.	.	.	.	.	.	.	.	.	C	9.887	1.203179	0.22121	.	.	ENSG00000152492	ENST00000392456	T	0.32023	1.47	5.65	5.65	0.86999	.	0.753598	0.11889	N	0.519796	T	0.27559	0.0677	.	.	.	0.09310	N	0.999996	B	0.15930	0.015	B	0.19148	0.024	T	0.10636	-1.0621	9	0.40728	T	0.16	.	15.5749	0.76368	0.0:1.0:0.0:0.0	.	179	Q8IVM0-2	.	Y	179	ENSP00000376250:H179Y	ENSP00000376250:H179Y	H	+	1	0	CCDC50	192575631	0.294000	0.24380	0.102000	0.21198	0.129000	0.20672	1.489000	0.35562	2.821000	0.97095	0.650000	0.86243	CAC	.	.	.	none		0.498	CCDC50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343315.1	NM_174908		T	191092937	C	T	191092937	1	4	205	0	1	0	0	0	0	0	0	0	2822	710	25	2		2	CCDC50	3	191092937	Intron	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10	5318039	191092937	6929493	30	12397											
C4orf44	345222	hgsc.bcm.edu	37	chr4	3254938	3254938	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgtctctcgtttcaggaaaTtaaaatgcatgacagatagc	13	12	9	7	1	2	2	1	1	1	1	4	3	2	3	0	1	2	2	0	1	4	3			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr4:3254938T>C	ENST00000438480.2	+	2	2072	c.325T>C	c.(325-327)Tta>Cta	p.L109L	MSANTD1_ENST00000510580.1_Silent_p.L109L|MSANTD1_ENST00000507492.1_Silent_p.L96L	NM_001042690.1	NP_001036155.1	Q6ZTZ1	MSD1_HUMAN	Myb/SANT-like DNA-binding domain containing 1	109	Myb-like.									endometrium(1)|lung(2)	3						TTTCAGGAAATTAAAATGCAT	0.597																																					p.L109L		Atlas-SNP	.											.	MSANTD1	14	.	0			c.T325C						PASS	.						67	84	78					4																	3254938		2203	4300	6503	SO:0001819	synonymous_variant	345222	exon2			AGGAAATTAAAAT		CCDS47003.1	4p16.2	2012-03-02	2012-03-02	2012-03-02	ENSG00000188981	ENSG00000188981			33741	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 44"	C4orf44			Standard	NM_001042690		Approved	LOC345222	uc003ggs.3	Q6ZTZ1	OTTHUMG00000159977	ENST00000438480.2:c.325T>C	chr4.hg19:g.3254938T>C		86.0	0.0	.		70.0	12.0	.	NM_001042690	C9J6V0	Silent	SNP	ENST00000438480.2	hg19	CCDS47003.1																																																																																			.	.	.	none		0.597	MSANTD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370924.1	NM_001012982		C	3254938	T	C	3254938	2	2	205	1	0	0	0	0	0	0	0	1	2274	1490	52	3		3	C4orf44	4	3254938	Silent	SNP	T	TCGA-IA-A83S-01A-11D-A34Z-10		3254938	187899338	31	12398											
KIAA0232	9778	hgsc.bcm.edu	37	chr4	6863999	6864000	+	Frame_Shift_Ins	INS	-	-	A																															attcacacctgcttgctggcINSaatcaagagctcttttcaga																										TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr4:6863999_6864000insA	ENST00000307659.5	+	7	2345_2346	c.1890_1891insA	c.(1891-1893)aatfs	p.N631fs	KIAA0232_ENST00000425103.1_Frame_Shift_Ins_p.N631fs	NM_014743.2	NP_055558.2	Q92628	K0232_HUMAN	KIAA0232	631							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						TGCTTGCTGGCAATCAAGAGCT	0.421																																					p.G630fs		Atlas-Indel,Pindel	.											.	KIAA0232	102	.	0			c.1890_1891insA						PASS	.																																			SO:0001589	frameshift_variant	9778	exon6			.	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.1892dupA	chr4.hg19:g.6864001_6864001dupA	ENSP00000303928:p.Asn631fs	84.0	0.0	0		79.0	22.0	0.278481	NM_001100590	A7E2D2	Frame_Shift_Ins	INS	ENST00000307659.5	hg19	CCDS43209.1																																																																																			.	.	.	none		0.421	KIAA0232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359102.2	NM_014743		A	6864000	-	A	6863999	7	5	205	1	0	1	1	0	0	0	0	0	8170	697	25	0	1908	0	KIAA0232	4	6863999	Frame_Shift_Ins	INS	-	TCGA-IA-A83S-01A-11D-A34Z-10	3609061	6863999	184290277	32	12399											
CDH9	1007	hgsc.bcm.edu	37	chr5	26988254	26988254	+	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	agtacctgtgtactcttccaAtaagaagaactgattccaca	14	11	6	10	0	1	3	0	1	1	2	3	3	3	3	3	0	3	2	3	0	6	5	rs144749356		TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr5:26988254A>T	ENST00000231021.4	-	2	359	c.187T>A	c.(187-189)Ttg>Atg	p.L63M		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	63	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	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						TACTCTTCCAATAAGAAGAAC	0.383																																					p.L63M	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.T187A						PASS	.						93	88	89					5																	26988254		2203	4300	6503	SO:0001583	missense	1007	exon2			CTTCCAATAAGAA	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.187T>A	chr5.hg19:g.26988254A>T	ENSP00000231021:p.Leu63Met	147.0	0.0	.		137.0	50.0	.	NM_016279	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	hg19	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	A	19.29	3.799156	0.70567	.	.	ENSG00000113100	ENST00000231021;ENST00000513289;ENST00000511822	T;T;T	0.00571	6.5;6.5;6.5	5.64	2.02	0.26589	Cadherin-like (1);	0.080037	0.50627	D	0.000105	T	0.01523	0.0049	M	0.74467	2.265	0.41359	D	0.987417	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.991	T	0.63359	-0.6655	9	.	.	.	.	6.2494	0.20837	0.4865:0.0:0.5135:0.0	.	63;63	E7EPN0;Q9ULB4	.;CADH9_HUMAN	M	63	ENSP00000231021:L63M;ENSP00000426239:L63M;ENSP00000422538:L63M	.	L	-	1	2	CDH9	27024011	0.988000	0.35896	1.000000	0.80357	0.993000	0.82548	0.656000	0.24948	0.435000	0.26365	0.482000	0.46254	TTG	.	A|1.000;G|0.000	.	alt		0.383	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		T	26988254	A	T	26988254	3	4	205	1	0	0	0	0	1	0	0	0	3119	98	4	5	2226	5	CDH9	5	26988254	Missense_Mutation	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10		26988254	153927006	33	12400											
NIPBL	25836	hgsc.bcm.edu	37	chr5	36976168	36976169	+	Frame_Shift_Ins	INS	-	-	A																															ggaaaatagcaatgtttcagINSaaaatgatattccttttaat																										TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr5:36976168_36976169insA	ENST00000282516.8	+	9	1658_1659	c.1159_1160insA	c.(1159-1161)gaafs	p.E387fs	NIPBL_ENST00000448238.2_Frame_Shift_Ins_p.E387fs|NIPBL_ENST00000504430.1_3'UTR	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	387					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)			CAATGTTTCAGAAAATGATATT	0.391																																					p.E387fs		Atlas-Indel,Pindel	.											.	NIPBL	513	.	0			c.1159_1160insA						PASS	.																																			SO:0001589	frameshift_variant	25836	exon9			.	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.1163dupA	chr5.hg19:g.36976172_36976172dupA	ENSP00000282516:p.Glu387fs	126.0	0.0	0		122.0	32.0	0.262295	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Frame_Shift_Ins	INS	ENST00000282516.8	hg19	CCDS3920.1																																																																																			.	.	.	none		0.391	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		A	36976169	-	A	36976168	7	5	205	1	0	1	1	0	0	0	0	0	10435	943	33	0	1189	0	NIPBL	5	36976168	Frame_Shift_Ins	INS	-	TCGA-IA-A83S-01A-11D-A34Z-10	9987914	36976168	143939092	34	12401											
GABRG2	2566	hgsc.bcm.edu	37	chr5	161524860	161524860	+	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	atggtcgagtgctctacaccCtaaggtattcttttgcaaaa	11	13	8	9	1	2	0	0	0	2	0	3	1	2	0	1	2	3	3	1	2	5	6			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr5:161524860C>G	ENST00000361925.4	+	4	764	c.544C>G	c.(544-546)Cta>Gta	p.L182V	GABRG2_ENST00000414552.2_Missense_Mutation_p.L182V|GABRG2_ENST00000393933.4_Missense_Mutation_p.L87V|GABRG2_ENST00000356592.3_Missense_Mutation_p.L182V			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	182					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GCTCTACACCCTAAGGTATTC	0.368																																					p.L182V		Atlas-SNP	.											.	GABRG2	142	.	0			c.C544G						PASS	.						70	71	71					5																	161524860		2203	4300	6503	SO:0001583	missense	2566	exon4			TACACCCTAAGGT		CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4087	protein-coding gene	gene with protein product	"GABA(A) receptor, gamma 2"	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.544C>G	chr5.hg19:g.161524860C>G	ENSP00000354651:p.Leu182Val	47.0	0.0	.		65.0	7.0	.	NM_198904	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Missense_Mutation	SNP	ENST00000361925.4	hg19	CCDS4358.1	.	.	.	.	.	.	.	.	.	.	C	15.49	2.850018	0.51270	.	.	ENSG00000113327	ENST00000356592;ENST00000414552;ENST00000361925;ENST00000393933;ENST00000522053	T;T;T;T;T	0.78924	-1.22;-1.22;-1.22;-1.22;-1.22	5.82	0.467	0.16721	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	T	0.79828	0.4513	L	0.52206	1.635	0.58432	D	0.999999	D;P;P	0.56035	0.974;0.629;0.939	P;P;P	0.58660	0.843;0.531;0.615	T	0.77691	-0.2493	10	0.87932	D	0	.	10.5972	0.45345	0.0:0.4263:0.0:0.5737	.	182;182;182	F5HB82;P18507;P18507-2	.;GBRG2_HUMAN;.	V	182;182;182;87;87	ENSP00000349000:L182V;ENSP00000410732:L182V;ENSP00000354651:L182V;ENSP00000377510:L87V;ENSP00000430182:L87V	ENSP00000349000:L182V	L	+	1	2	GABRG2	161457438	0.005000	0.15991	0.636000	0.29352	0.990000	0.78478	0.140000	0.16056	-0.234000	0.09782	0.563000	0.77884	CTA	.	.	.	none		0.368	GABRG2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252706.1			G	161524860	C	G	161524860	3	3	205	1	0	0	0	0	1	0	0	0	6179	680	24	4	558	4	GABRG2	5	161524860	Missense_Mutation	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10	124548692	161524860	19390400	35	12402											
TNXB	7148	hgsc.bcm.edu	37	chr6	32014119	32014119	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtgtccctgtactggaccAcgaaggagtcaaaggggccc	9	6	13	13	2	1	0	1	0	0	0	2	3	2	2	4	4	1	1	4	4	3	1			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr6:32014119A>G	ENST00000375244.3	-	31	10640	c.10439T>C	c.(10438-10440)gTg>gCg	p.V3480A	TNXB_ENST00000451343.1_5'Flank|TNXB_ENST00000375247.2_Missense_Mutation_p.V3478A			P22105	TENX_HUMAN	tenascin XB	3525	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						GTACTGGACCACGAAGGAGTC	0.652																																					p.V3478A		Atlas-SNP	.											.	TNXB	553	.	0			c.T10433C						PASS	.						37	44	41					6																	32014119		1427	2654	4081	SO:0001583	missense	7148	exon31			TGGACCACGAAGG	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.10439T>C	chr6.hg19:g.32014119A>G	ENSP00000364393:p.Val3480Ala	57.0	0.0	.		57.0	12.0	.	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	hg19		.	.	.	.	.	.	.	.	.	.	A	14.77	2.634222	0.47049	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.56611	0.45;0.45	4.25	3.04	0.35103	.	0.175077	0.27270	N	0.020129	T	0.33990	0.0882	M	0.87328	2.875	0.23113	N	0.998276	B	0.24823	0.112	B	0.31337	0.128	T	0.45527	-0.9255	10	0.07990	T	0.79	.	9.1299	0.36839	0.9067:0.0:0.0933:0.0	.	3478	P22105-3	.	A	3480;3478	ENSP00000364393:V3480A;ENSP00000364396:V3478A	ENSP00000364393:V3480A	V	-	2	0	TNXB	32122097	0.376000	0.25098	0.997000	0.53966	0.484000	0.33280	2.793000	0.47845	1.772000	0.52199	0.260000	0.18958	GTG	.	.	.	none		0.652	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		G	32014119	A	G	32014119	3	3	205	1	0	0	0	0	1	0	0	0	16358	159	6	3	4336	3	TNXB	6	32014119	Missense_Mutation	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10		32014119	139100948	36	12403											
DNAH8	1769	hgsc.bcm.edu	37	chr6	38976613	38976613	+	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	tcagagtaacactgcttctgCtgttcttgaaacaattacca	12	13	6	10	0	3	2	1	1	2	1	3	2	3	2	1	0	5	4	1	0	4	5			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr6:38976613C>A	ENST00000359357.3	+	87	12841	c.12587C>A	c.(12586-12588)gCt>gAt	p.A4196D	DNAH8_ENST00000441566.1_Missense_Mutation_p.A4160D			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	4196					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						ACTGCTTCTGCTGTTCTTGAA	0.403																																					p.A4413D		Atlas-SNP	.											.	DNAH8	1239	.	0			c.C13238A						PASS	.						139	141	140					6																	38976613		2203	4300	6503	SO:0001583	missense	1769	exon89			CTTCTGCTGTTCT	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.12587C>A	chr6.hg19:g.38976613C>A	ENSP00000352312:p.Ala4196Asp	129.0	0.0	.		132.0	31.0	.	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	C	9.309	1.055145	0.19907	.	.	ENSG00000124721	ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.08458	3.09;3.09;3.09	5.68	0.0947	0.14482	Dynein heavy chain (1);	0.691017	0.13632	N	0.373632	T	0.00815	0.0027	N	0.02420	-0.555	0.32197	N	0.578309	B	0.02656	0.0	B	0.04013	0.001	T	0.47861	-0.9084	10	0.09843	T	0.71	.	9.2075	0.37298	0.6484:0.1727:0.1789:0.0	.	4196	Q96JB1	DYH8_HUMAN	D	4401;4196;4160	ENSP00000333363:A4401D;ENSP00000352312:A4196D;ENSP00000402294:A4160D	ENSP00000333363:A4401D	A	+	2	0	DNAH8	39084591	0.890000	0.30428	0.949000	0.38748	0.993000	0.82548	1.792000	0.38754	0.235000	0.21160	0.650000	0.86243	GCT	.	.	.	none		0.403	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		A	38976613	C	A	38976613	3	1	205	1	0	0	0	0	1	0	0	0	4609	797	28	4	12925	4	DNAH8	6	38976613	Missense_Mutation	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10	6962494	38976613	132138454	37	12404											
TTBK1	84630	hgsc.bcm.edu	37	chr6	43250879	43250879	+	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	agaggagcactgaccggagcCaggagggtgccccgtccacg	9	3	16	13	3	0	2	0	1	0	1	1	5	1	5	5	4	3	1	5	4	0	0			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr6:43250879C>T	ENST00000259750.4	+	14	2484	c.2401C>T	c.(2401-2403)Cag>Tag	p.Q801*		NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	801					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)			TGACCGGAGCCAGGAGGGTGC	0.682																																					p.Q801X		Atlas-SNP	.											.	TTBK1	124	.	0			c.C2401T						PASS	.						9	9	9					6																	43250879		2191	4284	6475	SO:0001587	stop_gained	84630	exon14			CGGAGCCAGGAGG	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.2401C>T	chr6.hg19:g.43250879C>T	ENSP00000259750:p.Gln801*	94.0	0.0	.		103.0	20.0	.	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Nonsense_Mutation	SNP	ENST00000259750.4	hg19	CCDS34455.1	.	.	.	.	.	.	.	.	.	.	C	37	6.087026	0.97271	.	.	ENSG00000146216	ENST00000259750	.	.	.	4.62	4.62	0.57501	.	0.184674	0.35179	N	0.003390	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	16.2343	0.82363	0.0:1.0:0.0:0.0	.	.	.	.	X	801	.	ENSP00000259750:Q801X	Q	+	1	0	TTBK1	43358857	1.000000	0.71417	1.000000	0.80357	0.528000	0.34623	5.728000	0.68531	2.099000	0.63709	0.561000	0.74099	CAG	.	.	.	none		0.682	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3			T	43250879	C	T	43250879	4	4	205	1	0	0	0	0	0	1	0	0	16688	595	21	2	2451	2	TTBK1	6	43250879	Nonsense_Mutation	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10	4274266	43250879	127864188	38	12405											
SCML4	256380	hgsc.bcm.edu	37	chr6	108093476	108093476	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaactgccatcttcataggcGtggagtgaagtgagggtcgg	9	9	16	7	2	2	2	1	2	1	0	3	4	2	3	1	4	2	0	1	4	3	2			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr6:108093476G>A	ENST00000369020.3	-	2	301	c.56C>T	c.(55-57)aCg>aTg	p.T19M	SCML4_ENST00000369022.2_Intron	NM_198081.3	NP_932347.2	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4 (Drosophila)	19					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)		CTTCATAGGCGTGGAGTGAAG	0.512																																					p.T19M		Atlas-SNP	.											.	SCML4	65	.	0			c.C56T						PASS	.						136	130	132					6																	108093476		692	1591	2283	SO:0001583	missense	256380	exon2			ATAGGCGTGGAGT		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.56C>T	chr6.hg19:g.108093476G>A	ENSP00000358016:p.Thr19Met	113.0	0.0	.		115.0	18.0	.	NM_198081	B0QZ10|B0QZ11|B7ZBX3|Q5JXD0|Q5T0T6|Q8IYY6	Missense_Mutation	SNP	ENST00000369020.3	hg19	CCDS5060.2	.	.	.	.	.	.	.	.	.	.	G	15.77	2.930166	0.52759	.	.	ENSG00000146285	ENST00000369020	T	0.47528	0.84	5.35	5.35	0.76521	AT hook, DNA-binding motif (1);	.	.	.	.	T	0.25865	0.0630	N	0.22421	0.69	0.42132	D	0.991477	D;P	0.67145	0.996;0.834	B;B	0.43809	0.432;0.34	T	0.08554	-1.0716	9	0.56958	D	0.05	.	13.7945	0.63162	0.0:0.0:0.8467:0.1533	.	19;19	B4E0X3;Q8N228	.;SCML4_HUMAN	M	19	ENSP00000358016:T19M	ENSP00000358016:T19M	T	-	2	0	SCML4	108200169	0.537000	0.26386	0.010000	0.14722	0.973000	0.67179	4.366000	0.59492	2.789000	0.95967	0.655000	0.94253	ACG	.	.	.	none		0.512	SCML4-005	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000041700.3	XM_171128		A	108093476	G	A	108093476	3	1	205	1	0	0	0	0	1	0	0	0	13924	1145	40	1	1216	1	SCML4	6	108093476	Missense_Mutation	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	64842597	108093476	63021591	39	12406											
BCLAF1	9774	hgsc.bcm.edu	37	chr6	136599311	136599311	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagcaagatgaactctgactAggtggtgtagcaataggtga	13	9	14	5	0	1	4	0	3	1	1	1	5	1	4	0	3	3	3	0	3	6	3			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr6:136599311A>G	ENST00000531224.1	-	4	960	c.708T>C	c.(706-708)ccT>ccC	p.P236P	BCLAF1_ENST00000392348.2_Silent_p.P234P|BCLAF1_ENST00000353331.4_Silent_p.P234P|BCLAF1_ENST00000527536.1_Silent_p.P236P|BCLAF1_ENST00000530767.1_Silent_p.P236P|BCLAF1_ENST00000527759.1_Silent_p.P234P	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	236					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)		AACTCTGACTAGGTGGTGTAG	0.448																																					p.P236P	Colon(142;1534 1789 5427 7063 28491)	Atlas-SNP	.											.	BCLAF1	203	.	0			c.T708C						PASS	.						194	183	186					6																	136599311		2203	4300	6503	SO:0001819	synonymous_variant	9774	exon4			CTGACTAGGTGGT	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.708T>C	chr6.hg19:g.136599311A>G		98.0	0.0	.		109.0	17.0	.	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Silent	SNP	ENST00000531224.1	hg19	CCDS5177.1																																																																																			.	.	.	none		0.448	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		G	136599311	A	G	136599311	2	3	205	1	0	0	0	0	0	0	0	1	1383	407	15	3		3	BCLAF1	6	136599311	Silent	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10	28505835	136599311	34515756	40	12407											
CNKSR3	154043	hgsc.bcm.edu	37	chr6	154771340	154771340	+	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	tgcagcagctgctcgccgttGatcttctctcgttcaaactt	6	14	8	13	3	3	1	1	1	2	0	6	1	3	1	1	0	5	6	1	0	1	4			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr6:154771340G>A	ENST00000607772.1	-	2	649	c.105C>T	c.(103-105)atC>atT	p.I35I	CNKSR3_ENST00000479339.1_5'UTR	NM_173515.2	NP_775786.2	Q6P9H4	CNKR3_HUMAN	CNKSR family member 3	35	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)	cytoplasm (GO:0005737)|membrane (GO:0016020)				breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	15		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;5.03e-11)|BRCA - Breast invasive adenocarcinoma(81;0.00627)		GCTCGCCGTTGATCTTCTCTC	0.507																																					p.I35I		Atlas-SNP	.											.	CNKSR3	56	.	0			c.C105T						PASS	.						120	114	116					6																	154771340		2203	4300	6503	SO:0001819	synonymous_variant	154043	exon2			GCCGTTGATCTTC	AK055911	CCDS5246.1	6q25.2	2013-01-10	2005-04-11	2005-04-11	ENSG00000153721	ENSG00000153721		"Sterile alpha motif (SAM) domain containing"	23034	protein-coding gene	gene with protein product			"membrane associated guanylate kinase interacting protein-like 1"	MAGI1			Standard	NM_173515		Approved	FLJ31349		Q6P9H4	OTTHUMG00000015873	ENST00000607772.1:c.105C>T	chr6.hg19:g.154771340G>A		87.0	0.0	.		78.0	23.0	.	NM_173515	Q5SGD5|Q96N65	Silent	SNP	ENST00000607772.1	hg19	CCDS5246.1																																																																																			.	.	.	none		0.507	CNKSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042792.2	NM_173515		A	154771340	G	A	154771340	2	1	205	1	0	0	0	0	0	0	0	1	3610	1280	45	2		2	CNKSR3	6	154771340	Silent	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	18172029	154771340	16343727	41	12408											
EIF3B	8662	hgsc.bcm.edu	37	chr7	2409282	2409282	+	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	agaagaacggagactacttgTgtgtgaaagtagataggact	15	9	13	4	1	0	5	0	1	0	4	0	7	0	6	0	2	2	1	0	2	6	4			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr7:2409282T>A	ENST00000360876.4	+	10	1635	c.1579T>A	c.(1579-1581)Tgt>Agt	p.C527S	EIF3B_ENST00000397011.2_Missense_Mutation_p.C527S	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)		AGACTACTTGTGTGTGAAAGT	0.507																																					p.C527S		Atlas-SNP	.											.	EIF3B	54	.	0			c.T1579A						PASS	.						111	101	104					7																	2409282		2203	4300	6503	SO:0001583	missense	8662	exon10			TACTTGTGTGTGA	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.1579T>A	chr7.hg19:g.2409282T>A	ENSP00000354125:p.Cys527Ser	95.0	0.0	.		95.0	19.0	.	NM_001037283		Missense_Mutation	SNP	ENST00000360876.4	hg19	CCDS5332.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.099575	0.76983	.	.	ENSG00000106263	ENST00000314800;ENST00000360876;ENST00000397011;ENST00000489558	T;T	0.05382	3.45;3.45	5.77	5.77	0.91146	Translation initiation factor 2A, beta propellor-like domain (1);Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.33614	0.0869	M	0.92923	3.36	0.80722	D	1	D	0.56287	0.975	D	0.65773	0.938	T	0.38520	-0.9657	10	0.87932	D	0	-25.5088	16.383	0.83481	0.0:0.0:0.0:1.0	.	527	P55884	EIF3B_HUMAN	S	527;527;527;451	ENSP00000354125:C527S;ENSP00000380206:C527S	ENSP00000316638:C527S	C	+	1	0	EIF3B	2375808	1.000000	0.71417	0.926000	0.36857	0.559000	0.35586	7.796000	0.85898	2.326000	0.78906	0.533000	0.62120	TGT	.	.	.	none		0.507	EIF3B-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207006.1			A	2409282	T	A	2409282	3	1	205	1	0	0	0	0	1	0	0	0	5015	1696	59	5	1617	5	EIF3B	7	2409282	Missense_Mutation	SNP	T	TCGA-IA-A83S-01A-11D-A34Z-10		2409282	156729381	42	12409											
CDK14	5218	hgsc.bcm.edu	37	chr7	90547017	90547017	+	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	cttctgatcagtgacacgggGgagttaaagctggcagattt	10	11	13	7	1	2	3	1	2	1	1	2	4	2	4	0	3	1	3	0	3	2	3			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr7:90547017G>T	ENST00000380050.3	+	8	935	c.804G>T	c.(802-804)ggG>ggT	p.G268G	CDK14_ENST00000436577.2_Silent_p.G139G|CDK14_ENST00000406263.1_Silent_p.G222G|CDK14_ENST00000265741.3_Silent_p.G250G			O94921	CDK14_HUMAN	cyclin-dependent kinase 14	268	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of cell cycle (GO:0051726)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoplasmic cyclin-dependent protein kinase holoenzyme complex (GO:0000308)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(1)|lung(12)|ovary(1)|skin(4)	32						GTGACACGGGGGAGTTAAAGC	0.438																																					p.G250G	GBM(83;1228 1256 8311 16577 31299)	Atlas-SNP	.											.	CDK14	153	.	0			c.G750T						PASS	.						118	116	117					7																	90547017		2203	4300	6503	SO:0001819	synonymous_variant	5218	exon7			CACGGGGGAGTTA		CCDS5619.1, CCDS75626.1, CCDS75627.1, CCDS75628.1	7q21-q22	2011-11-08	2009-12-16	2009-12-16	ENSG00000058091	ENSG00000058091		"Cyclin-dependent kinases"	8883	protein-coding gene	gene with protein product		610679	"PFTAIRE protein kinase 1"	PFTK1		9202329, 11313143, 19884882	Standard	XM_005250436		Approved	PFTAIRE1	uc003ukz.1	O94921	OTTHUMG00000023649	ENST00000380050.3:c.804G>T	chr7.hg19:g.90547017G>T		129.0	0.0	.		118.0	9.0	.	NM_012395	A4D1E6|A6NK51|A8WFP6|B4DHG5|B4DNM2|Q75N06|Q75N22|Q8N764|Q9H3D7|Q9UDR0	Silent	SNP	ENST00000380050.3	hg19																																																																																				.	.	.	none		0.438	CDK14-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000059970.5	NM_012395		T	90547017	G	T	90547017	2	4	205	1	0	0	0	0	0	0	0	1	3132	1219	43	4		4	CDK14	7	90547017	Silent	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	88137735	90547017	68591646	43	12410											
C8orf41	80185	hgsc.bcm.edu	37	chr8	33364813	33364813	+	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	tggtataggacctgggctctGttatactggagcaaatcagc	10	11	12	8	0	2	0	1	0	1	0	2	2	2	2	1	4	3	4	1	4	5	4			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr8:33364813G>A	ENST00000431156.2	-	4	1479	c.861C>T	c.(859-861)aaC>aaT	p.N287N	TTI2_ENST00000519356.1_5'UTR|TTI2_ENST00000360742.5_Silent_p.N287N|TTI2_ENST00000520636.1_Intron	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	287																	CCTGGGCTCTGTTATACTGGA	0.428																																					p.N287N		Atlas-SNP	.											.	.	.	.	0			c.C861T						PASS	.						142	117	125					8																	33364813		2203	4300	6503	SO:0001819	synonymous_variant	80185	exon4			GGCTCTGTTATAC	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.861C>T	chr8.hg19:g.33364813G>A		166.0	0.0	.		167.0	39.0	.	NM_001265581	D3DSV7|Q96IM2|Q9H5N4	Silent	SNP	ENST00000431156.2	hg19	CCDS6090.1																																																																																			.	.	.	none		0.428	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115		A	33364813	G	A	33364813	2	1	205	1	0	0	0	0	0	0	0	1	2429	1368	48	2		2	C8orf41	8	33364813	Silent	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10		33364813	112999209	44	12411											
SOX17	64321	hgsc.bcm.edu	37	chr8	55370847	55370847	+	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	ggtgaagggcgaggcgccggCgaacagcggagcaccggccg	8	1	20	12	7	0	1	0	1	0	0	0	4	0	2	3	6	3	1	3	6	2	0			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr8:55370847C>G	ENST00000297316.4	+	1	353	c.149C>G	c.(148-150)gCg>gGg	p.A50G		NM_022454.3	NP_071899.1	Q9H6I2	SOX17_HUMAN	SRY (sex determining region Y)-box 17	50					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)			GAGGCGCCGGCGAACAGCGGA	0.736																																					p.A50G		Atlas-SNP	.											.	SOX17	37	.	0			c.C149G						PASS	.						8	11	10					8																	55370847		2132	4192	6324	SO:0001583	missense	64321	exon1			CGCCGGCGAACAG	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.149C>G	chr8.hg19:g.55370847C>G	ENSP00000297316:p.Ala50Gly	33.0	0.0	.		41.0	9.0	.	NM_022454		Missense_Mutation	SNP	ENST00000297316.4	hg19	CCDS6159.1	.	.	.	.	.	.	.	.	.	.	C	17.00	3.275942	0.59649	.	.	ENSG00000164736	ENST00000297316	D	0.97256	-4.31	4.45	2.5	0.30297	High mobility group, superfamily (1);	0.135798	0.49305	D	0.000146	D	0.93200	0.7834	L	0.53249	1.67	0.28938	N	0.891172	B	0.12630	0.006	B	0.10450	0.005	D	0.84162	0.0429	10	0.22109	T	0.4	.	4.3996	0.11379	0.1554:0.601:0.1519:0.0917	.	50	Q9H6I2	SOX17_HUMAN	G	50	ENSP00000297316:A50G	ENSP00000297316:A50G	A	+	2	0	SOX17	55533400	0.266000	0.24112	0.987000	0.45799	0.817000	0.46193	2.262000	0.43285	1.225000	0.43566	0.561000	0.74099	GCG	.	.	.	none		0.736	SOX17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378526.2			G	55370847	C	G	55370847	3	3	205	1	0	0	0	0	1	0	0	0	14960	768	27	4	151	4	SOX17	8	55370847	Missense_Mutation	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10	22006034	55370847	90993175	45	12412											
RPS20	6224	hgsc.bcm.edu	37	chr8	56986652	56986652	+	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	ttttacgttgcggcttgttaGggtgattcgaattcggtgaa	7	16	13	5	4	0	2	0	2	0	0	2	3	0	2	0	3	2	3	0	3	4	7			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr8:56986652G>T	ENST00000521262.1	-	2	323	c.70C>A	c.(70-72)Cta>Ata	p.L24I	RPS20_ENST00000519606.1_Missense_Mutation_p.L24I|RPS20_ENST00000519807.1_Missense_Mutation_p.L24I|SNORD54_ENST00000459159.1_RNA|RPS20_ENST00000520490.1_5'UTR|RPS20_ENST00000523936.1_Missense_Mutation_p.L24I|RPS20_ENST00000524349.1_5'UTR|RPS20_ENST00000520627.1_Intron|RPS20_ENST00000518875.1_Missense_Mutation_p.L24I|RPS20_ENST00000009589.3_Missense_Mutation_p.L24I|CTA-397H3.3_ENST00000521403.1_RNA			P60866	RS20_HUMAN	ribosomal protein S20	24					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)						all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.155)	Epithelial(17;0.00117)|all cancers(17;0.00879)			CGGCTTGTTAGGGTGATTCGA	0.468																																					p.L24I		Atlas-SNP	.											.	RPS20	16	.	0			c.C70A						PASS	.						72	77	75					8																	56986652		2203	4300	6503	SO:0001583	missense	6224	exon2			TTGTTAGGGTGAT	L06498	CCDS6163.1, CCDS55231.1	8q12.1	2011-04-05				ENSG00000008988		"S ribosomal proteins"	10405	protein-coding gene	gene with protein product		603682				9582194, 8479924	Standard	NM_001023		Approved	S20	uc003xsm.2	P60866		ENST00000521262.1:c.70C>A	chr8.hg19:g.56986652G>T	ENSP00000427788:p.Leu24Ile	31.0	0.0	.		29.0	11.0	.	NM_001146227	B2R4F4|B4DW28|P17075|Q5M8S9	Missense_Mutation	SNP	ENST00000521262.1	hg19		.	.	.	.	.	.	.	.	.	.	G	15.59	2.877815	0.51801	.	.	ENSG00000008988	ENST00000519807;ENST00000009589;ENST00000521262;ENST00000523936;ENST00000519606;ENST00000518875	.	.	.	5.17	3.38	0.38709	.	0.000000	0.64402	D	0.000001	T	0.80292	0.4596	M	0.92077	3.27	0.80722	D	1	P;D	0.54772	0.824;0.968	D;P	0.72338	0.977;0.785	T	0.79288	-0.1865	9	0.72032	D	0.01	-24.3785	6.6251	0.22824	0.4059:0.0:0.5941:0.0	.	24;24	P60866;B4DW28	RS20_HUMAN;.	I	24	.	ENSP00000009589:L24I	L	-	1	2	RPS20	57149206	1.000000	0.71417	0.010000	0.14722	0.016000	0.09150	3.119000	0.50422	0.588000	0.29660	0.655000	0.94253	CTA	.	.	.	none		0.468	RPS20-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000378166.1	NM_001023		T	56986652	G	T	56986652	3	4	205	1	0	0	0	0	1	0	0	0	13645	991	35	4	401	4	RPS20	8	56986652	Missense_Mutation	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	1615805	56986652	89377370	46	12413											
CRISPLD1	83690	hgsc.bcm.edu	37	chr8	75925137	75925137	+	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	tctaatagatataggcccccGacgtttcatgtacaatcgtg	11	12	8	10	3	2	1	1	0	1	1	3	2	2	1	2	1	1	2	2	1	6	6	rs369100451		TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr8:75925137G>A	ENST00000262207.4	+	4	858	c.390G>A	c.(388-390)ccG>ccA	p.P130P	CRISPLD1_ENST00000517786.1_5'UTR|CRISPLD1_ENST00000523524.1_5'UTR	NM_031461.5	NP_113649.1	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain containing 1	130	SCP.				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)			ATAGGCCCCCGACGTTTCATG	0.378																																					p.P130P		Atlas-SNP	.											CRISPLD1,NS,carcinoma,0,1	CRISPLD1	94	.	0			c.G390A						PASS	.	G		0,4406		0,0,2203	102	96	98		390	0.2	1	8		98	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CRISPLD1	NM_031461.5		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		130/501	75925137	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	83690	exon4			GCCCCCGACGTTT	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.390G>A	chr8.hg19:g.75925137G>A		105.0	2.0	.		89.0	17.0	.	NM_031461	B2RA60|B7Z929	Silent	SNP	ENST00000262207.4	hg19	CCDS6219.1																																																																																			.	.	.	weak		0.378	CRISPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379117.1	NM_031461		A	75925137	G	A	75925137	2	1	205	1	0	0	0	0	0	0	0	1	3884	1045	37	1		1	CRISPLD1	8	75925137	Silent	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	18938485	75925137	70438885	47	12414											
PYCRL	65263	hgsc.bcm.edu	37	chr8	144687925	144687956	+	Frame_Shift_Del	DEL	GTGGCTGCTCGCAGCCCGCCCTGCTCCAGGGC	GTGGCTGCTCGCAGCCCGCCCTGCTCCAGGGC	-																															cagcctccacggcgctcatgGtggctgctcgcagcccgccc																								rs138226068|rs575409447|rs199825286|rs375748238		TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	GTGGCTGCTCGCAGCCCGCCCTGCTCCAGGGC	GTGGCTGCTCGCAGCCCGCCCTGCTCCAGGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr8:144687925_144687956delGTGGCTGCTCGCAGCCCGCCCTGCTCCAGGGC	ENST00000220966.6	-	6	804_835	c.775_806delGCCCTGGAGCAGGGCGGGCTGCGAGCAGCCAC	c.(775-807)gccctggagcagggcgggctgcgagcagccaccfs	p.ALEQGGLRAAT259fs	RP11-661A12.14_ENST00000606452.1_lincRNA|PYCRL_ENST00000495276.1_5'UTR|PYCRL_ENST00000377579.3_Frame_Shift_Del_p.ALEQGGLRAAT110fs	NM_023078.3	NP_075566.2	Q53H96	P5CR3_HUMAN	pyrroline-5-carboxylate reductase-like	247					L-proline biosynthetic process (GO:0055129)		pyrroline-5-carboxylate reductase activity (GO:0004735)	p.A255V(1)|p.L248_A256delLEQGGLRAA(1)		central_nervous_system(1)|endometrium(1)|lung(2)|ovary(1)	5	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.17e-38)|Epithelial(56;7.17e-37)|all cancers(56;2.46e-32)|Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)		L-Proline(DB00172)	GGCGCTCATGGTGGCTGCTCGCAGCCCGCCCTGCTCCAGGGCGTGGAGTCCA	0.677																																					p.259_269del		Pindel	.											.	PYCRL	14	.	2	Substitution - Missense(1)|Deletion - In frame(1)	ovary(1)|endometrium(1)	c.776_807del						PASS	.																																			SO:0001589	frameshift_variant	65263	exon6			.	AF086378	CCDS6407.2	8q24.3	2011-09-30	2011-09-30	2011-09-30	ENSG00000104524	ENSG00000104524			25846	protein-coding gene	gene with protein product							Standard	NM_023078		Approved	FLJ13852	uc003yyy.3	Q53H96	OTTHUMG00000157010	ENST00000220966.6:c.775_806delGCCCTGGAGCAGGGCGGGCTGCGAGCAGCCAC	chr8.hg19:g.144687925_144687956delGTGGCTGCTCGCAGCCCGCCCTGCTCCAGGGC	ENSP00000220966:p.Ala259fs	96.0	0.0	.		89.0	11.0	0.124	NM_023078	B3KMB5|B4DVT6|H0Y6C3|Q8N3N9|Q96HX4|Q9H896	Frame_Shift_Del	DEL	ENST00000220966.6	hg19	CCDS6407.2																																																																																			.	.	.	none		0.677	PYCRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347081.2	NM_023078		-	144687956	GTGGCTGCTCGCAGCCCGCCCTGCTCCAGGGC	-	144687925	7	5	205	1	0	1	0	1	0	0	0	0	12870	1261	44	0	58	0	PYCRL	8	144687925	Frame_Shift_Del	DEL	GTGGCTGCTCGCAGCCCGCCCTGCTCCAGGGC	TCGA-IA-A83S-01A-11D-A34Z-10	68762788	144687925	1676097	48	12415											
JAK2	3717	hgsc.bcm.edu	37	chr9	5081774	5081774	+	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	ttaccaaatatgaggataggTgccctggggttttctggtgc	8	13	13	7	0	1	1	0	1	1	0	1	2	1	2	2	5	3	1	2	5	4	5			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr9:5081774T>A	ENST00000381652.3	+	19	2978	c.2484T>A	c.(2482-2484)ggT>ggA	p.G828G	JAK2_ENST00000539801.1_Silent_p.G828G|AL161450.1_ENST00000601793.1_Intron|JAK2_ENST00000544510.1_Silent_p.G679G	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	828					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)	TGAGGATAGGTGCCCTGGGGT	0.363		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial																												p.G828G		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.T2484A						PASS	.						110	111	111					9																	5081774		2203	4300	6503	SO:0001819	synonymous_variant	3717	exon19	Familial Cancer Database		GATAGGTGCCCTG		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.2484T>A	chr9.hg19:g.5081774T>A		105.0	0.0	.		122.0	25.0	.	NM_004972	O14636|O75297	Silent	SNP	ENST00000381652.3	hg19	CCDS6457.1																																																																																			.	.	.	none		0.363	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			A	5081774	T	A	5081774	2	1	205	1	0	0	0	0	0	0	0	1	7945	1683	59	5		5	JAK2	9	5081774	Silent	SNP	T	TCGA-IA-A83S-01A-11D-A34Z-10		5081774	136131657	49	12416											
NTRK2	4915	hgsc.bcm.edu	37	chr9	87359981	87359981	+	Frame_Shift_Del	DEL	A	A	-																															tgataaaaccggtcgggaacAtctctcggtgagtggaataa																										TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr9:87359981delA	ENST00000323115.4	+	10	1642	c.1289delA	c.(1288-1290)catfs	p.H430fs	NTRK2_ENST00000376208.1_Frame_Shift_Del_p.H430fs|NTRK2_ENST00000304053.6_Frame_Shift_Del_p.H430fs|NTRK2_ENST00000359847.3_Frame_Shift_Del_p.H430fs|NTRK2_ENST00000277120.3_Frame_Shift_Del_p.H430fs|NTRK2_ENST00000376213.1_Frame_Shift_Del_p.H430fs|NTRK2_ENST00000395866.2_Frame_Shift_Del_p.H274fs|NTRK2_ENST00000376214.1_Frame_Shift_Del_p.H430fs|NTRK2_ENST00000395882.1_Frame_Shift_Del_p.H430fs			Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2	430					activation of adenylate cyclase activity (GO:0007190)|aging (GO:0007568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|circadian rhythm (GO:0007623)|feeding behavior (GO:0007631)|glutamate secretion (GO:0014047)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mechanoreceptor differentiation (GO:0042490)|negative regulation of anoikis (GO:2000811)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular junction development (GO:0007528)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system neuron development (GO:0048935)|positive regulation of axonogenesis (GO:0050772)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|regulation of dendrite development (GO:0050773)|regulation of neurotransmitter secretion (GO:0046928)|regulation of protein kinase B signaling (GO:0051896)|regulation of Rac GTPase activity (GO:0032314)|response to auditory stimulus (GO:0010996)|retinal rod cell development (GO:0046548)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasculogenesis (GO:0001570)	cell surface (GO:0009986)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endosome (GO:0005768)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|brain-derived neurotrophic factor binding (GO:0048403)|brain-derived neurotrophic factor-activated receptor activity (GO:0060175)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	46					Amitriptyline(DB00321)	GGTCGGGAACATCTCTCGGTG	0.433										TSP Lung(25;0.17)																											p.H430fs		Atlas-Indel,Pindel	.											.	NTRK2	331	.	0			c.1288delC						PASS	.						125	116	119					9																	87359981		2203	4300	6503	SO:0001589	frameshift_variant	4915	exon11			.	AF410902	CCDS6671.1, CCDS35050.1, CCDS35051.1, CCDS35052.1, CCDS35053.1	9q22.1	2013-01-11			ENSG00000148053	ENSG00000148053	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing"	8032	protein-coding gene	gene with protein product		600456				7789988	Standard	NM_001018065		Approved	TRKB	uc004anz.1	Q16620	OTTHUMG00000020120	ENST00000323115.4:c.1289delA	chr9.hg19:g.87359981delA	ENSP00000314586:p.His430fs	99.0	0.0	0		91.0	18.0	0.197802	NM_001018066	B1ANZ4|B4DFV9|Q16675|Q59GJ1|Q8WXJ5|Q8WXJ6|Q8WXJ7	Frame_Shift_Del	DEL	ENST00000323115.4	hg19	CCDS35050.1																																																																																			.	.	.	none		0.433	NTRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052882.1			-	87359981	A	-	87359981	7	5	205	1	0	1	0	1	0	0	0	0	10714	217	8	0	1327	0	NTRK2	9	87359981	Frame_Shift_Del	DEL	A	TCGA-IA-A83S-01A-11D-A34Z-10	82278207	87359981	53853450	50	12417											
DAB2IP	153090	hgsc.bcm.edu	37	chr9	124526156	124526156	+	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	tgcaagatcatcaactcctaCtggtcagtgcggtgcccagg	9	9	11	12	1	3	1	3	0	0	1	4	1	4	1	2	3	5	1	2	3	3	1			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr9:124526156C>T	ENST00000408936.3	+	8	1640	c.1458C>T	c.(1456-1458)taC>taT	p.Y486Y	DAB2IP_ENST00000309989.1_Silent_p.Y362Y|DAB2IP_ENST00000259371.2_Silent_p.Y458Y			Q5VWQ8	DAB2P_HUMAN	DAB2 interacting protein	486	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|angiogenesis (GO:0001525)|cell cycle (GO:0007049)|cell motility involved in cerebral cortex radial glia guided migration (GO:0021814)|cellular protein catabolic process (GO:0044257)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|layer formation in cerebral cortex (GO:0021819)|negative regulation of angiogenesis (GO:0016525)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of GTPase activity (GO:0034260)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase activity (GO:0043553)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuron projection morphogenesis (GO:0048812)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of dendrite development (GO:1900006)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of synapse maturation (GO:0090129)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of ARF GTPase activity (GO:0032312)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein complex assembly (GO:0043254)|response to unfolded protein (GO:0006986)|transformed cell apoptotic process (GO:0006927)|tube formation (GO:0035148)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	axon (GO:0030424)|cerebellar mossy fiber (GO:0044300)|climbing fiber (GO:0044301)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|neuronal cell body (GO:0043025)|neuronal cell body membrane (GO:0032809)|parallel fiber (GO:1990032)|plasma membrane (GO:0005886)	14-3-3 protein binding (GO:0071889)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|mitogen-activated protein kinase kinase binding (GO:0031434)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase 2A binding (GO:0051721)|Ras GTPase activator activity (GO:0005099)|SH3 domain binding (GO:0017124)|signaling adaptor activity (GO:0035591)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(8)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	27						TCAACTCCTACTGGTCAGTGC	0.622																																					p.Y458Y		Atlas-SNP	.											.	DAB2IP	150	.	0			c.C1374T						PASS	.						110	89	96					9																	124526156		2203	4300	6503	SO:0001819	synonymous_variant	153090	exon8			CTCCTACTGGTCA	AF367051	CCDS6832.1, CCDS6833.2	9q33.1-q33.3	2008-07-21			ENSG00000136848	ENSG00000136848			17294	protein-coding gene	gene with protein product	"nGAP-like protein", "DOC-2/DAB2 interactive protein", "ASK-interacting protein", "ASK1-interacting protein 1"	609205				11944990, 11812785	Standard	XM_005251721		Approved	AF9Q34, DIP1/2, KIAA1743, AIP1	uc004bln.3	Q5VWQ8	OTTHUMG00000020595	ENST00000408936.3:c.1458C>T	chr9.hg19:g.124526156C>T		80.0	0.0	.		77.0	22.0	.	NM_032552	A6H8V2|A6NHI9|B0QZB1|G3XA90|Q8TDL2|Q96SE1|Q9C0C0	Silent	SNP	ENST00000408936.3	hg19																																																																																				.	.	.	none		0.622	DAB2IP-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317857.1	NM_032552		T	124526156	C	T	124526156	2	4	205	1	0	0	0	0	0	0	0	1	4221	576	20	2		2	DAB2IP	9	124526156	Silent	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10	37166175	124526156	16687275	51	12418											
TTC16	158248	hgsc.bcm.edu	37	chr9	130485525	130485525	+	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	ccaagatgcggggatcctggCtgtgcagggcaagctgcagc	8	6	16	11	1	0	1	0	0	0	1	1	2	1	2	2	4	5	5	2	4	2	0			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr9:130485525C>A	ENST00000373289.3	+	7	865	c.785C>A	c.(784-786)gCt>gAt	p.A262D	PTRH1_ENST00000419060.1_Intron|TTC16_ENST00000489226.1_3'UTR|PTRH1_ENST00000429848.1_Intron|TTC16_ENST00000393748.4_Missense_Mutation_p.A86D	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	262										central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						GGGATCCTGGCTGTGCAGGGC	0.632																																					p.A262D		Atlas-SNP	.											.	TTC16	55	.	0			c.C785A						PASS	.						73	63	66					9																	130485525		2203	4300	6503	SO:0001583	missense	158248	exon7			TCCTGGCTGTGCA	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.785C>A	chr9.hg19:g.130485525C>A	ENSP00000362386:p.Ala262Asp	57.0	0.0	.		45.0	12.0	.	NM_144965	B4DYG4|B5ME24|Q5JU66|Q96M72	Missense_Mutation	SNP	ENST00000373289.3	hg19	CCDS6875.1	.	.	.	.	.	.	.	.	.	.	C	14.63	2.592520	0.46214	.	.	ENSG00000167094	ENST00000373289;ENST00000393748;ENST00000316259	T;T	0.63580	-0.05;0.19	5.03	5.03	0.67393	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.77096	0.4080	M	0.75615	2.305	0.37008	D	0.895586	D;D;D	0.89917	1.0;0.991;1.0	D;D;D	0.97110	1.0;0.944;1.0	T	0.79027	-0.1971	10	0.36615	T	0.2	-22.1378	13.7181	0.62710	0.0:1.0:0.0:0.0	.	249;214;262	B4DZ42;B4DH05;Q8NEE8	.;.;TTC16_HUMAN	D	262;86;207	ENSP00000362386:A262D;ENSP00000377349:A86D	ENSP00000319048:A207D	A	+	2	0	TTC16	129525346	0.984000	0.35163	0.496000	0.27539	0.082000	0.17680	3.469000	0.53093	2.623000	0.88846	0.462000	0.41574	GCT	.	.	.	none		0.632	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054224.1	NM_144965		A	130485525	C	A	130485525	3	1	205	1	0	0	0	0	1	0	0	0	16695	797	28	4	811	4	TTC16	9	130485525	Missense_Mutation	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10	5959369	130485525	10727906	52	12419											
QRFP	347148	hgsc.bcm.edu	37	chr9	133768991	133768991	+	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	tctgcagccagcatgctctcTgcccgatgtctgcagccccc	5	9	9	18	1	3	0	0	0	3	0	4	1	3	0	4	0	7	4	4	0	0	0			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr9:133768991T>A	ENST00000343079.1	-	1	234	c.235A>T	c.(235-237)Aga>Tga	p.R79*		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)		GCATGCTCTCTGCCCGATGTC	0.672																																					p.R79X		Atlas-SNP	.											.	QRFP	14	.	0			c.A235T						PASS	.						60	62	61					9																	133768991		2203	4300	6503	SO:0001587	stop_gained	347148	exon1			GCTCTCTGCCCGA	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.235A>T	chr9.hg19:g.133768991T>A	ENSP00000345487:p.Arg79*	79.0	0.0	.		84.0	20.0	.	NM_198180		Nonsense_Mutation	SNP	ENST00000343079.1	hg19	CCDS6936.1	.	.	.	.	.	.	.	.	.	.	T	17.72	3.459665	0.63401	.	.	ENSG00000188710	ENST00000343079	.	.	.	4.65	-0.931	0.10438	.	0.790949	0.10741	N	0.639422	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.0344	6.0641	0.19854	0.0:0.1555:0.4051:0.4393	.	.	.	.	X	79	.	ENSP00000345487:R79X	R	-	1	2	QRFP	132758812	0.000000	0.05858	0.000000	0.03702	0.257000	0.26127	-0.356000	0.07661	-0.361000	0.08125	0.379000	0.24179	AGA	.	.	.	none		0.672	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	133768991	T	A	133768991	4	1	205	1	0	0	0	0	0	1	0	0	12890	1588	55	5	178	5	QRFP	9	133768991	Nonsense_Mutation	SNP	T	TCGA-IA-A83S-01A-11D-A34Z-10	3283466	133768991	7444440	53	12420											
SETX	23064	hgsc.bcm.edu	37	chr9	135203246	135203246	+	Frame_Shift_Del	DEL	A	A	-																															ctgtccttttttggcatctgAatgagttttcttaggggtct																										TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr9:135203246delA	ENST00000224140.5	-	10	3921	c.3739delT	c.(3739-3741)tcafs	p.S1247fs	SETX_ENST00000393220.1_Frame_Shift_Del_p.S1247fs|SETX_ENST00000372169.2_Frame_Shift_Del_p.S1247fs	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	1247					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)		TTGGCATCTGAATGAGTTTTC	0.413																																					p.S1247X		Atlas-Indel,Pindel	.											.	SETX	234	.	0			c.3740delC						PASS	.						113	109	110					9																	135203246		2203	4300	6503	SO:0001589	frameshift_variant	23064	exon10			.	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.3739delT	chr9.hg19:g.135203246delA	ENSP00000224140:p.Ser1247fs	173.0	0.0	0		143.0	31.0	0.216783	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Frame_Shift_Del	DEL	ENST00000224140.5	hg19	CCDS6947.1																																																																																			.	.	.	none		0.413	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		-	135203246	A	-	135203246	7	5	205	1	0	1	0	1	0	0	0	0	14154	246	9	0	4362	0	SETX	9	135203246	Frame_Shift_Del	DEL	A	TCGA-IA-A83S-01A-11D-A34Z-10	1434255	135203246	6010185	54	12421											
ITIH5	80760	hgsc.bcm.edu	37	chr10	7683994	7683994	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgcaggaaaccgtagtgaaGgcataacgggaaatgatggt	14	7	14	6	2	0	2	0	2	0	0	0	4	0	4	1	4	3	3	1	4	5	2			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr10:7683994G>A	ENST00000256861.6	-	3	273	c.195C>T	c.(193-195)gcC>gcT	p.A65A	ITIH5_ENST00000446830.2_5'UTR|ITIH5_ENST00000397145.2_Silent_p.A65A|ITIH5_ENST00000397146.2_Silent_p.A65A|ITIH5_ENST00000434980.1_5'Flank	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	65	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				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						CCGTAGTGAAGGCATAACGGG	0.438																																					p.A65A		Atlas-SNP	.											.	ITIH5	343	.	0			c.C195T						PASS	.						151	135	140					10																	7683994		2203	4300	6503	SO:0001819	synonymous_variant	80760	exon3			AGTGAAGGCATAA			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.195C>T	chr10.hg19:g.7683994G>A		161.0	0.0	.		143.0	11.0	.	NM_001001851	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Silent	SNP	ENST00000256861.6	hg19																																																																																				.	.	.	none		0.438	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569		A	7683994	G	A	7683994	2	1	205	1	0	0	0	0	0	0	0	1	7914	987	35	2		2	ITIH5	10	7683994	Silent	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10		7683994	127850753	55	12422											
SLC16A9	220963	hgsc.bcm.edu	37	chr10	61424076	61424076	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtataataaaccacatccAagacctaagcatgagaagac	18	7	7	9	0	0	3	0	1	0	3	1	4	1	3	3	0	2	2	3	0	7	4			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr10:61424076A>G	ENST00000395348.3	-	4	981	c.345T>C	c.(343-345)ctT>ctC	p.L115L	SLC16A9_ENST00000395347.1_Silent_p.L115L	NM_194298.2	NP_919274.1	Q7RTY1	MOT9_HUMAN	solute carrier family 16, member 9	115					urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			kidney(3)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	23						AACCACATCCAAGACCTAAGC	0.398																																					p.L115L		Atlas-SNP	.											.	SLC16A9	58	.	0			c.T345C						PASS	.						122	114	117					10																	61424076		2203	4300	6503	SO:0001819	synonymous_variant	220963	exon4			ACATCCAAGACCT	AK125791	CCDS7256.1	10q21.3	2013-07-18	2013-07-18	2004-01-21	ENSG00000165449	ENSG00000165449		"Solute carriers"	23520	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 9"	614242	"chromosome 10 open reading frame 36", "solute carrier family 16 (monocarboxylic acid transporters), member 9", "solute carrier family 16, member 9 (monocarboxylic acid transporter 9)"	C10orf36			Standard	NM_194298		Approved	FLJ43803, MCT9	uc010qig.1	Q7RTY1	OTTHUMG00000018283	ENST00000395348.3:c.345T>C	chr10.hg19:g.61424076A>G		71.0	0.0	.		64.0	19.0	.	NM_194298	Q6ZMI2|Q9UFH8	Silent	SNP	ENST00000395348.3	hg19	CCDS7256.1																																																																																			.	.	.	none		0.398	SLC16A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048174.2	NM_194298		G	61424076	A	G	61424076	2	3	205	1	0	0	0	0	0	0	0	1	14428	117	5	3		3	SLC16A9	10	61424076	Silent	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10	53740082	61424076	74110671	56	12423											
POLR3A	11128	hgsc.bcm.edu	37	chr10	79744981	79744981	+	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	atccggggcacgcccagggtGatgttcatggaggccacacc	8	6	14	13	2	1	1	1	1	0	0	2	2	2	2	4	5	0	2	4	5	0	1			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr10:79744981G>A	ENST00000372371.3	-	24	3326	c.3189C>T	c.(3187-3189)atC>atT	p.I1063I		NM_007055.3	NP_008986.2	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa	1063					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)			CGCCCAGGGTGATGTTCATGG	0.542																																					p.I1063I		Atlas-SNP	.											.	POLR3A	104	.	0			c.C3189T						PASS	.						145	140	141					10																	79744981		2203	4300	6503	SO:0001819	synonymous_variant	11128	exon24			CAGGGTGATGTTC	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.3189C>T	chr10.hg19:g.79744981G>A		51.0	0.0	.		75.0	18.0	.	NM_007055	Q8IW34|Q8TCW5	Silent	SNP	ENST00000372371.3	hg19	CCDS7354.1																																																																																			.	.	.	none		0.542	POLR3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048923.1	NM_007055		A	79744981	G	A	79744981	2	1	205	1	0	0	0	0	0	0	0	1	12235	1280	45	2		2	POLR3A	10	79744981	Silent	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	18320905	79744981	55789766	57	12424											
C10orf76	79591	hgsc.bcm.edu	37	chr10	103769138	103769138	+	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	taatgtgaccaacctgagctAatactgtgatgaagttgcga	13	11	10	7	1	0	4	0	4	0	0	0	5	0	4	2	0	4	2	2	0	5	4			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr10:103769138A>C	ENST00000370033.4	-	13	1066	c.947T>G	c.(946-948)tTa>tGa	p.L316*		NM_024541.2	NP_078817.2	Q5T2E6	CJ076_HUMAN	chromosome 10 open reading frame 76	316						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|prostate(2)|upper_aerodigestive_tract(2)	24		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)		AACCTGAGCTAATACTGTGAT	0.348																																					p.L316X		Atlas-SNP	.											.	C10orf76	48	.	0			c.T947G						PASS	.						229	229	229					10																	103769138		1812	4082	5894	SO:0001587	stop_gained	79591	exon13			TGAGCTAATACTG	AK023176	CCDS41563.1	10q24.32	2008-10-21			ENSG00000120029	ENSG00000120029			25788	protein-coding gene	gene with protein product						14702039	Standard	NM_024541		Approved	FLJ13114	uc009xwy.1	Q5T2E6	OTTHUMG00000018943	ENST00000370033.4:c.947T>G	chr10.hg19:g.103769138A>C	ENSP00000359050:p.Leu316*	73.0	0.0	.		79.0	16.0	.	NM_024541	Q2TB87|Q9H8Z9	Nonsense_Mutation	SNP	ENST00000370033.4	hg19	CCDS41563.1	.	.	.	.	.	.	.	.	.	.	A	37	6.589992	0.97688	.	.	ENSG00000120029	ENST00000370033	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.4391	13.0603	0.59003	0.8661:0.1339:0.0:0.0	.	.	.	.	X	316	.	ENSP00000359050:L316X	L	-	2	0	C10orf76	103759128	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	8.160000	0.89653	2.326000	0.78906	0.533000	0.62120	TTA	.	.	.	none		0.348	C10orf76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050007.1	NM_024541		C	103769138	A	C	103769138	4	2	205	1	0	0	0	0	0	1	0	0	1618	372	13	5	1178	5	C10orf76	10	103769138	Nonsense_Mutation	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10	24024157	103769138	31765609	58	12425											
C10orf79	80217	hgsc.bcm.edu	37	chr10	105926263	105926263	+	Frame_Shift_Del	DEL	G	G	-																															cactttcaataatataatttGgttgattttctcttctctgg																										TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr10:105926263delG	ENST00000357060.3	-	23	3137	c.3022delC	c.(3022-3024)caafs	p.Q1008fs	WDR96_ENST00000428666.1_Frame_Shift_Del_p.Q1009fs	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						AATATAATTTGGTTGATTTTC	0.383																																					p.Q1008fs		Atlas-Indel,Pindel	.											.	WDR96	183	.	0			c.3023delA						PASS	.						72	70	71					10																	105926263		2203	4300	6503	SO:0001589	frameshift_variant	80217	exon23			.																												ENST00000357060.3:c.3022delC	chr10.hg19:g.105926263delG	ENSP00000349568:p.Gln1008fs	88.0	0.0	0		94.0	26.0	0.276596	NM_025145		Frame_Shift_Del	DEL	ENST00000357060.3	hg19	CCDS31281.1																																																																																			.	.	.	none		0.383	WDR96-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				-	105926263	G	-	105926263	7	5	205	1	0	1	0	1	0	0	0	0	1620	1357	47	0	2039	0	C10orf79	10	105926263	Frame_Shift_Del	DEL	G	TCGA-IA-A83S-01A-11D-A34Z-10	2157125	105926263	29608484	59	12426											
ATRNL1	26033	hgsc.bcm.edu	37	chr10	116919943	116919943	+	Frame_Shift_Del	DEL	T	T	-																															tgggtgattggtggatatacTtttaactacagttcttttca																										TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr10:116919943delT	ENST00000355044.3	+	6	1098	c.972delT	c.(970-972)actfs	p.T324fs	ATRNL1_ENST00000527407.1_Frame_Shift_Del_p.T324fs|ATRNL1_ENST00000529665.1_3'UTR	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	324					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)		GTGGATATACTTTTAACTACA	0.343																																					p.T324fs		Pindel	.											.	ATRNL1	219	.	0			c.971delC						PASS	.						197	205	202					10																	116919943		2203	4300	6503	SO:0001589	frameshift_variant	26033	exon6			.	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.972delT	chr10.hg19:g.116919943delT	ENSP00000347152:p.Thr324fs	134.0	0.0	.		144.0	22.0	0.153	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Frame_Shift_Del	DEL	ENST00000355044.3	hg19	CCDS7592.1																																																																																			.	.	.	none		0.343	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		-	116919943	T	-	116919943	7	5	205	1	0	1	0	1	0	0	0	0	1207	1596	56	0	994	0	ATRNL1	10	116919943	Frame_Shift_Del	DEL	T	TCGA-IA-A83S-01A-11D-A34Z-10	10993680	116919943	18614804	60	12427	120	2									
ATRNL1	26033	hgsc.bcm.edu	37	chr10	116919947	116919947	+	Frame_Shift_Del	DEL	A	A	-																															tgattggtggatatacttttAactacagttcttttcaaatg																										TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr10:116919947delA	ENST00000355044.3	+	6	1102	c.976delA	c.(976-978)aacfs	p.N326fs	ATRNL1_ENST00000527407.1_Frame_Shift_Del_p.N326fs|ATRNL1_ENST00000529665.1_3'UTR	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	326					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)		ATATACTTTTAACTACAGTTC	0.333																																					p.F325fs		Atlas-INDEL	.											.	ATRNL1	219	.	0			c.975delT						PASS	.						189	198	195					10																	116919947		2203	4300	6503	SO:0001589	frameshift_variant	26033	exon6			.	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.976delA	chr10.hg19:g.116919947delA	ENSP00000347152:p.Asn326fs	129.0	0.0	0		142.0	32.0	0.225352	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Frame_Shift_Del	DEL	ENST00000355044.3	hg19	CCDS7592.1																																																																																			.	.	.	none		0.333	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		-	116919947	A	-	116919947	7	5	205	1	0	1	0	1	0	0	0	0	1207	362	13	0	998	0	ATRNL1	10	116919947	Frame_Shift_Del	DEL	A	TCGA-IA-A83S-01A-11D-A34Z-10	4	116919947	18614800	61	12428	120	2									
SEC23IP	11196	hgsc.bcm.edu	37	chr10	121689138	121689138	+	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	ggtttctgttgcttacaactCattagattttgaaccagaga	11	15	8	7	0	2	3	1	1	1	2	2	4	2	3	1	1	4	3	1	1	4	6			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr10:121689138C>T	ENST00000369075.3	+	14	2405	c.2333C>T	c.(2332-2334)tCa>tTa	p.S778L	SEC23IP_ENST00000543134.1_Missense_Mutation_p.S567L	NM_007190.3	NP_009121.1	Q9Y6Y8	S23IP_HUMAN	SEC23 interacting protein	778					acrosome assembly (GO:0001675)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|single fertilization (GO:0007338)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear endoplasmic reticulum (GO:0097038)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	36		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		GCTTACAACTCATTAGATTTT	0.373																																					p.S778L		Atlas-SNP	.											.	SEC23IP	100	.	0			c.C2333T						PASS	.						167	171	170					10																	121689138		2203	4300	6503	SO:0001583	missense	11196	exon14			ACAACTCATTAGA	AB019435	CCDS7618.1	10q26.11-q26.12	2013-01-10			ENSG00000107651	ENSG00000107651		"Sterile alpha motif (SAM) domain containing"	17018	protein-coding gene	gene with protein product						10400679	Standard	NM_007190		Approved	p125	uc001leu.2	Q9Y6Y8	OTTHUMG00000019161	ENST00000369075.3:c.2333C>T	chr10.hg19:g.121689138C>T	ENSP00000358071:p.Ser778Leu	162.0	0.0	.		174.0	38.0	.	NM_007190	D3DRD2|Q8IXH5|Q9BUK5	Missense_Mutation	SNP	ENST00000369075.3	hg19	CCDS7618.1	.	.	.	.	.	.	.	.	.	.	C	16.55	3.153540	0.57259	.	.	ENSG00000107651	ENST00000369075;ENST00000543134	T;T	0.31247	1.5;1.5	5.62	5.62	0.85841	.	0.316794	0.35013	N	0.003513	T	0.31827	0.0809	L	0.47716	1.5	0.47862	D	0.99953	P;B	0.34977	0.478;0.399	B;B	0.33254	0.16;0.101	T	0.04333	-1.0959	10	0.41790	T	0.15	-14.0611	19.6585	0.95853	0.0:1.0:0.0:0.0	.	567;778	F5H0L8;Q9Y6Y8	.;S23IP_HUMAN	L	778;567	ENSP00000358071:S778L;ENSP00000438773:S567L	ENSP00000358071:S778L	S	+	2	0	SEC23IP	121679128	0.007000	0.16637	1.000000	0.80357	0.991000	0.79684	2.352000	0.44080	2.657000	0.90304	0.467000	0.42956	TCA	.	.	.	none		0.373	SEC23IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050688.1			T	121689138	C	T	121689138	3	4	205	1	0	0	0	0	1	0	0	0	14006	838	29	2	2387	2	SEC23IP	10	121689138	Missense_Mutation	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10	4769191	121689138	13845609	62	12429											
RIC8A	60626	hgsc.bcm.edu	37	chr11	209732	209732	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgtgtggggctgtaccgtgAgaggagcttcccccacgatg	6	8	16	11	3	0	1	0	1	0	1	1	4	1	2	3	3	2	3	3	3	1	2			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr11:209732A>G	ENST00000526104.1	+	3	1802	c.458A>G	c.(457-459)gAg>gGg	p.E153G	RIC8A_ENST00000325207.5_Missense_Mutation_p.E153G|BET1L_ENST00000486280.1_5'Flank|BET1L_ENST00000382762.3_5'Flank|BET1L_ENST00000325147.9_5'Flank|BET1L_ENST00000529614.2_5'Flank|BET1L_ENST00000410108.1_5'Flank|BET1L_ENST00000332865.6_5'Flank|RIC8A_ENST00000527696.1_Missense_Mutation_p.E147G			Q9NPQ8	RIC8A_HUMAN	RIC8 guanine nucleotide exchange factor A	153					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)		CTGTACCGTGAGAGGAGCTTC	0.617																																					p.E153G		Atlas-SNP	.											.	RIC8A	45	.	0			c.A458G						PASS	.						58	52	54					11																	209732		2203	4300	6503	SO:0001583	missense	60626	exon3			ACCGTGAGAGGAG	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.458A>G	chr11.hg19:g.209732A>G	ENSP00000432008:p.Glu153Gly	54.0	0.0	.		53.0	13.0	.	NM_021932	Q0P508|Q2T9J1|Q7Z352|Q96EZ1|Q96SZ2|Q9H064|Q9H5H3|Q9H9E7	Missense_Mutation	SNP	ENST00000526104.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.91|12.91	2.079005|2.079005	0.36662|0.36662	.|.	.|.	ENSG00000177963|ENSG00000177963	ENST00000526104;ENST00000325207;ENST00000528357;ENST00000530889;ENST00000527696;ENST00000527468|ENST00000527728	.|.	.|.	.|.	4.45|4.45	1.98|1.98	0.26296|0.26296	Armadillo-type fold (1);|.	0.388332|.	0.27618|.	N|.	0.018576|.	T|T	0.45796|0.45796	0.1360|0.1360	M|M	0.65498|0.65498	2.005|2.005	0.09310|0.09310	N|N	0.999999|0.999999	P;P;P|.	0.36837|.	0.547;0.571;0.515|.	B;B;B|.	0.37198|.	0.221;0.243;0.156|.	T|T	0.33879|0.33879	-0.9851|-0.9851	9|5	0.37606|.	T|.	0.19|.	-8.9933|-8.9933	7.3499|7.3499	0.26684|0.26684	0.7073:0.1496:0.0:0.143|0.7073:0.1496:0.0:0.143	.|.	147;153;153|.	Q9NPQ8-2;Q9NPQ8;Q9NPQ8-3|.	.;RIC8A_HUMAN;.|.	G|G	153;153;129;157;147;43|35	.|.	ENSP00000325941:E153G|.	E|R	+|+	2|1	0|2	RIC8A|RIC8A	199732|199732	0.977000|0.977000	0.34250|0.34250	0.001000|0.001000	0.08648|0.08648	0.623000|0.623000	0.37688|0.37688	2.748000|2.748000	0.47483|0.47483	0.257000|0.257000	0.21650|0.21650	-0.444000|-0.444000	0.05651|0.05651	GAG|AGA	.	.	.	none		0.617	RIC8A-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000384761.1	NM_021932		G	209732	A	G	209732	3	3	205	1	0	0	0	0	1	0	0	0	13368	304	11	3	468	3	RIC8A	11	209732	Missense_Mutation	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10		209732	134796784	63	12430											
OR10A2	341276	hgsc.bcm.edu	37	chr11	6891542	6891542	+	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	agcactctttgagatctacgCcatcgtcggaaccattctgg	9	11	9	12	3	3	1	0	1	3	1	5	3	3	2	2	2	3	1	2	2	2	3			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr11:6891542C>T	ENST00000307322.4	+	1	619	c.557C>T	c.(556-558)gCc>gTc	p.A186V		NM_001004460.1	NP_001004460.1	Q9H208	O10A2_HUMAN	olfactory receptor, family 10, subfamily A, member 2	186						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(12)|urinary_tract(1)	24		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.89e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		GAGATCTACGCCATCGTCGGA	0.507																																					p.A186V		Atlas-SNP	.											.	OR10A2	55	.	0			c.C557T						PASS	.						241	183	203					11																	6891542		2201	4296	6497	SO:0001583	missense	341276	exon1			TCTACGCCATCGT	BK004293	CCDS31415.1	11p15.4	2012-08-09		2004-03-10	ENSG00000170790	ENSG00000170790		"GPCR / Class A : Olfactory receptors"	8161	protein-coding gene	gene with protein product				OR10A2P			Standard	NM_001004460		Approved	OST363	uc001meu.1	Q9H208	OTTHUMG00000165739	ENST00000307322.4:c.557C>T	chr11.hg19:g.6891542C>T	ENSP00000303862:p.Ala186Val	158.0	0.0	.		126.0	28.0	.	NM_001004460	B2RNL9|Q6IFG9	Missense_Mutation	SNP	ENST00000307322.4	hg19	CCDS31415.1	.	.	.	.	.	.	.	.	.	.	c	2.385	-0.341102	0.05243	.	.	ENSG00000170790	ENST00000307322	T	0.00034	8.87	4.18	4.18	0.49190	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000019	T	0.00073	0.0002	N	0.00282	-1.705	0.25130	N	0.990577	D	0.76494	0.999	D	0.73708	0.981	T	0.66085	-0.6011	10	0.02654	T	1	.	9.6519	0.39904	0.2081:0.7919:0.0:0.0	.	186	Q9H208	O10A2_HUMAN	V	186	ENSP00000303862:A186V	ENSP00000303862:A186V	A	+	2	0	OR10A2	6848118	0.000000	0.05858	0.985000	0.45067	0.372000	0.29890	0.467000	0.22035	2.356000	0.79943	0.650000	0.86243	GCC	.	.	.	none		0.507	OR10A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385984.1	NM_001004460		T	6891542	C	T	6891542	3	4	205	1	0	0	0	0	1	0	0	0	10897	739	26	2	559	2	OR10A2	11	6891542	Missense_Mutation	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10	6681810	6891542	128114974	64	12431											
MICAL2	9645	hgsc.bcm.edu	37	chr11	12244191	12244191	+	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	ctctaccggctgttacctcaGacaaccccggagaacatcaa	12	7	7	15	2	3	2	2	0	1	2	3	3	3	2	4	2	4	2	4	2	5	2			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr11:12244191G>A	ENST00000256194.4	+	11	1638	c.1350G>A	c.(1348-1350)caG>caA	p.Q450Q	MICAL2_ENST00000342902.5_Silent_p.Q450Q|MICAL2_ENST00000537344.1_Silent_p.Q450Q|MICAL2_ENST00000379612.3_Silent_p.Q450Q|MICAL2_ENST00000527546.1_Silent_p.Q450Q	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	450	Monooxygenase domain. {ECO:0000250}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		TGTTACCTCAGACAACCCCGG	0.572																																					p.Q450Q		Atlas-SNP	.											.	MICAL2	114	.	0			c.G1350A						PASS	.						93	75	81					11																	12244191		2201	4294	6495	SO:0001819	synonymous_variant	9645	exon11			ACCTCAGACAACC	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.1350G>A	chr11.hg19:g.12244191G>A		34.0	0.0	.		34.0	10.0	.	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Silent	SNP	ENST00000256194.4	hg19	CCDS7809.1																																																																																			.	.	.	none		0.572	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632		A	12244191	G	A	12244191	2	1	205	1	0	0	0	0	0	0	0	1	9577	933	33	2		2	MICAL2	11	12244191	Silent	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	5352649	12244191	122762325	65	12432											
SLC1A2	6506	hgsc.bcm.edu	37	chr11	35287253	35287254	+	In_Frame_Ins	INS	-	-	CCCCCC																															ttggagaggtgatagactatINScccagccccaaaagagtcac																										TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr11:35287253_35287254insCCCCCC	ENST00000278379.3	-	10	1755_1756	c.1473_1474insGGGGGG	c.(1471-1476)gggata>gggGGGGGGata	p.490_491insGG	SLC1A2_ENST00000479543.1_5'UTR|SLC1A2_ENST00000395750.1_In_Frame_Ins_p.481_482insGG|SLC1A2_ENST00000395753.1_In_Frame_Ins_p.481_482insGG|SLC1A2_ENST00000606205.1_In_Frame_Ins_p.490_491insGG	NM_004171.3	NP_004162.2	P43004	EAA2_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 2	490					adult behavior (GO:0030534)|cellular response to extracellular stimulus (GO:0031668)|D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|positive regulation of glucose import (GO:0046326)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to wounding (GO:0009611)|synaptic transmission (GO:0007268)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)|visual behavior (GO:0007632)	axolemma (GO:0030673)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)	p.I492L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|urinary_tract(1)	24	all_lung(20;0.211)|all_epithelial(35;0.234)	all_hematologic(20;0.109)	STAD - Stomach adenocarcinoma(6;0.00731)			TGATAGACTATCCCAGCCCCAA	0.45																																					p.I492delinsGGI	NSCLC(100;1273 1575 12993 16869 47409)|Ovarian(164;45 1946 8965 30452 48454)	Atlas-Indel,Pindel	.											SLC1A2,colon,carcinoma,0,1	SLC1A2	54	.	1	Substitution - Missense(1)	large_intestine(1)	c.1474_1475insGGGGGG						PASS	.																																			SO:0001652	inframe_insertion	6506	exon10			.	AB209444	CCDS31459.1, CCDS55756.1	11p13-p12	2013-05-22			ENSG00000110436	ENSG00000110436		"Solute carriers"	10940	protein-coding gene	gene with protein product		600300				1448170	Standard	NM_004171		Approved	GLT-1, EAAT2	uc001mwd.3	P43004	OTTHUMG00000044391	ENST00000278379.3:c.1473_1474insGGGGGG	chr11.hg19:g.35287253_35287254insCCCCCC	ENSP00000278379:p.Ala490_Gly491insGlyGly	154.0	0.0	0		117.0	26.0	0.222222	NM_004171	B4DQE9|Q14417|Q541G6|U3KQQ4	In_Frame_Ins	INS	ENST00000278379.3	hg19	CCDS31459.1																																																																																			.	.	.	none		0.45	SLC1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258181.1	NM_004171		CCCCCC	35287254	-	CCCCCC	35287253	7	5	205	1	0	1	1	0	0	0	0	0	14445	1435	50	0	258	0	SLC1A2	11	35287253	In_Frame_Ins	INS	-	TCGA-IA-A83S-01A-11D-A34Z-10	23043062	35287253	99719263	66	12433											
OR5AS1	219447	hgsc.bcm.edu	37	chr11	55798423	55798423	+	Missense_Mutation	SNP	T	T	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	gctccaatatcgtcaatcatTttttctgtgatatcccacct	9	16	4	12	1	3	1	2	1	1	0	6	1	5	1	3	0	0	1	3	0	4	5			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr11:55798423T>G	ENST00000313555.1	+	1	529	c.529T>G	c.(529-531)Ttt>Gtt	p.F177V		NM_001001921.1	NP_001001921.1	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS, member 1	177						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(7)|large_intestine(7)|liver(1)|lung(22)|ovary(3)|prostate(4)|skin(3)|stomach(1)	48	Esophageal squamous(21;0.00693)					CGTCAATCATTTTTTCTGTGA	0.443																																					p.F177V		Atlas-SNP	.											.	OR5AS1	121	.	0			c.T529G						PASS	.						266	261	263					11																	55798423		2201	4296	6497	SO:0001583	missense	219447	exon1			AATCATTTTTTCT	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.529T>G	chr11.hg19:g.55798423T>G	ENSP00000324111:p.Phe177Val	240.0	0.0	.		241.0	56.0	.	NM_001001921	Q6IFB8	Missense_Mutation	SNP	ENST00000313555.1	hg19	CCDS31516.1	.	.	.	.	.	.	.	.	.	.	T	11.96	1.793640	0.31685	.	.	ENSG00000181785	ENST00000313555	T	0.00350	7.98	5.46	4.31	0.51392	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35805	U	0.002971	T	0.01092	0.0036	M	0.93150	3.385	0.09310	N	0.999993	D	0.89917	1.0	D	0.87578	0.998	T	0.20338	-1.0278	10	0.54805	T	0.06	.	11.6	0.50997	0.0:0.0:0.1495:0.8505	.	177	Q8N127	O5AS1_HUMAN	V	177	ENSP00000324111:F177V	ENSP00000324111:F177V	F	+	1	0	OR5AS1	55554999	0.995000	0.38212	0.667000	0.29798	0.142000	0.21351	2.802000	0.47916	0.882000	0.36016	0.523000	0.50628	TTT	.	.	.	none		0.443	OR5AS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391538.1	NM_001001921		G	55798423	T	G	55798423	3	3	205	1	0	0	0	0	1	0	0	0	11153	1841	64	5	531	5	OR5AS1	11	55798423	Missense_Mutation	SNP	T	TCGA-IA-A83S-01A-11D-A34Z-10	20511170	55798423	79208093	67	12434											
OR5M10	390167	hgsc.bcm.edu	37	chr11	56344355	56344355	+	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	aatgggttcagcattgggctCaaaaaagtataaaagactgc	16	9	10	6	0	2	1	2	0	0	1	2	1	2	1	0	2	2	4	0	2	7	4			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr11:56344355C>A	ENST00000526812.2	-	1	908	c.843G>T	c.(841-843)ttG>ttT	p.L281F		NM_001004741.1	NP_001004741.1	Q6IEU7	OR5MA_HUMAN	olfactory receptor, family 5, subfamily M, member 10	281						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						GCATTGGGCTCAAAAAAGTAT	0.393																																					p.L281F		Atlas-SNP	.											.	OR5M10	56	.	0			c.G843T						PASS	.						189	187	188					11																	56344355		1827	4083	5910	SO:0001583	missense	390167	exon1			TGGGCTCAAAAAA	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.843G>T	chr11.hg19:g.56344355C>A	ENSP00000436004:p.Leu281Phe	244.0	0.0	.		250.0	47.0	.	NM_001004741	B9EIL9	Missense_Mutation	SNP	ENST00000526812.2	hg19	CCDS53630.1	.	.	.	.	.	.	.	.	.	.	C	16.13	3.034578	0.54896	.	.	ENSG00000254834	ENST00000526812	T	0.00202	8.56	4.2	1.22	0.21188	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00210	0.0006	N	0.21282	0.65	0.24031	N	0.996113	D	0.53151	0.958	P	0.55455	0.776	T	0.54248	-0.8322	9	0.87932	D	0	.	5.4515	0.16568	0.0:0.5849:0.1474:0.2677	.	281	Q6IEU7	OR5MA_HUMAN	F	281	ENSP00000436004:L281F	ENSP00000436004:L281F	L	-	3	2	OR5M10	56100931	0.000000	0.05858	0.819000	0.32651	0.878000	0.50629	-1.843000	0.01680	0.149000	0.19098	0.632000	0.83419	TTG	.	.	.	none		0.393	OR5M10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391609.1	NM_001004741		A	56344355	C	A	56344355	3	1	205	1	0	0	0	0	1	0	0	0	11180	825	29	4	108	4	OR5M10	11	56344355	Missense_Mutation	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10	545932	56344355	78662161	68	12435											
FAM111B	374393	hgsc.bcm.edu	37	chr11	58893342	58893342	+	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	caagaaaatagatggttgtaCtgtgattcctctaaacgaac	15	11	8	7	1	1	3	0	1	1	2	2	4	2	3	1	1	3	2	1	1	8	5			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr11:58893342C>A	ENST00000343597.3	+	4	1963	c.1772C>A	c.(1771-1773)aCt>aAt	p.T591N	FAM111B_ENST00000529618.1_Missense_Mutation_p.T561N|FAM111B_ENST00000411426.1_Missense_Mutation_p.T561N	NM_198947.3	NP_945185.1	Q6SJ93	F111B_HUMAN	family with sequence similarity 111, member B	591							catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(12)|ovary(3)|pancreas(1)|skin(1)	40						GATGGTTGTACTGTGATTCCT	0.383																																					p.T591N		Atlas-SNP	.											.	FAM111B	84	.	0			c.C1772A						PASS	.						126	110	115					11																	58893342		2201	4295	6496	SO:0001583	missense	374393	exon4			GTTGTACTGTGAT	BC062456	CCDS7972.1, CCDS44611.1	11q12.1	2014-03-13			ENSG00000189057	ENSG00000189057			24200	protein-coding gene	gene with protein product		615584				24268661	Standard	NM_198947		Approved	CANP	uc001nnl.3	Q6SJ93	OTTHUMG00000167279	ENST00000343597.3:c.1772C>A	chr11.hg19:g.58893342C>A	ENSP00000341565:p.Thr591Asn	132.0	0.0	.		143.0	35.0	.	NM_198947	B4E2G2|Q6P661	Missense_Mutation	SNP	ENST00000343597.3	hg19	CCDS7972.1	.	.	.	.	.	.	.	.	.	.	C	11.22	1.573566	0.28092	.	.	ENSG00000189057	ENST00000411426;ENST00000529618;ENST00000343597	T;T;T	0.33438	1.41;1.41;1.41	4.62	2.75	0.32379	Peptidase cysteine/serine, trypsin-like (1);	0.662303	0.13892	N	0.355572	T	0.23249	0.0562	L	0.27053	0.805	0.09310	N	1	B	0.33413	0.411	B	0.37346	0.247	T	0.17776	-1.0358	10	0.56958	D	0.05	.	7.9224	0.29854	0.0:0.8058:0.0:0.1942	.	591	Q6SJ93	F111B_HUMAN	N	561;561;591	ENSP00000393855:T561N;ENSP00000432875:T561N;ENSP00000341565:T591N	ENSP00000341565:T591N	T	+	2	0	FAM111B	58649918	0.000000	0.05858	0.001000	0.08648	0.166000	0.22503	-0.344000	0.07780	0.571000	0.29365	0.650000	0.86243	ACT	.	.	.	none		0.383	FAM111B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393974.1	NM_198947		A	58893342	C	A	58893342	3	1	205	1	0	0	0	0	1	0	0	0	5404	565	20	4	1778	4	FAM111B	11	58893342	Missense_Mutation	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10	2548987	58893342	76113174	69	12436											
TMEM132A	54972	hgsc.bcm.edu	37	chr11	60704300	60704300	+	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	ggcaggcgaggaggacatccGctgggtgtgtgaggacatgg	8	6	20	7	2	0	1	0	1	0	0	1	5	1	4	1	7	0	2	1	7	0	0			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr11:60704300G>C	ENST00000453848.2	+	11	3151	c.2993G>C	c.(2992-2994)cGc>cCc	p.R998P	TMEM132A_ENST00000005286.4_Missense_Mutation_p.R999P			Q24JP5	T132A_HUMAN	transmembrane protein 132A	998	Confers cellular localization similar to full-length form. {ECO:0000250}.					endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|prostate(1)|skin(3)	32						GAGGACATCCGCTGGGTGTGT	0.627																																					p.R999P		Atlas-SNP	.											.	TMEM132A	135	.	0			c.G2996C						PASS	.						33	41	38					11																	60704300		2203	4299	6502	SO:0001583	missense	54972	exon11			ACATCCGCTGGGT	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.2993G>C	chr11.hg19:g.60704300G>C	ENSP00000405823:p.Arg998Pro	36.0	0.0	.		46.0	12.0	.	NM_017870	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Missense_Mutation	SNP	ENST00000453848.2	hg19	CCDS44618.1	.	.	.	.	.	.	.	.	.	.	G	15.89	2.965535	0.53507	.	.	ENSG00000006118	ENST00000444690;ENST00000453848;ENST00000005286	T;T	0.05925	3.37;3.37	4.55	3.63	0.41609	.	0.492294	0.18280	N	0.146041	T	0.13415	0.0325	L	0.47716	1.5	0.34714	D	0.728022	D;D	0.71674	0.998;0.998	P;P	0.59643	0.861;0.861	T	0.13361	-1.0512	10	0.87932	D	0	-19.0101	7.9668	0.30104	0.0827:0.0:0.7597:0.1576	.	998;999	Q24JP5;Q24JP5-2	T132A_HUMAN;.	P	749;998;999	ENSP00000405823:R998P;ENSP00000005286:R999P	ENSP00000005286:R999P	R	+	2	0	TMEM132A	60460876	0.286000	0.24305	1.000000	0.80357	0.998000	0.95712	1.948000	0.40303	1.282000	0.44496	0.655000	0.94253	CGC	.	.	.	none		0.627	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870		C	60704300	G	C	60704300	3	2	205	1	0	0	0	0	1	0	0	0	16057	1087	38	4	3038	4	TMEM132A	11	60704300	Missense_Mutation	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	1810958	60704300	74302216	70	12437											
CPT1A	1374	hgsc.bcm.edu	37	chr11	68571538	68571538	+	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	tctggaagctgtacaacatgGgttttcggcctgaaaagatc	11	11	11	8	1	1	2	0	1	1	1	3	3	1	3	1	3	3	3	1	3	5	3			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr11:68571538G>T	ENST00000265641.5	-	5	639	c.485C>A	c.(484-486)cCc>cAc	p.P162H	CPT1A_ENST00000540367.1_Missense_Mutation_p.P162H|CPT1A_ENST00000539743.1_Missense_Mutation_p.P162H|CPT1A_ENST00000376618.2_Missense_Mutation_p.P162H	NM_001876.3	NP_001867.2	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A (liver)	162					carnitine metabolic process (GO:0009437)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|eating behavior (GO:0042755)|epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|glucose metabolic process (GO:0006006)|long-chain fatty acid metabolic process (GO:0001676)|positive regulation of fatty acid beta-oxidation (GO:0032000)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		Glyburide(DB01016)|L-Carnitine(DB00583)|Perhexiline(DB01074)	GTACAACATGGGTTTTCGGCC	0.498																																					p.P162H		Atlas-SNP	.											.	CPT1A	89	.	0			c.C485A						PASS	.						97	88	91					11																	68571538		2200	4294	6494	SO:0001583	missense	1374	exon5			AACATGGGTTTTC	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.485C>A	chr11.hg19:g.68571538G>T	ENSP00000265641:p.Pro162His	62.0	0.0	.		88.0	18.0	.	NM_001876	Q8TCU0|Q9BWK0	Missense_Mutation	SNP	ENST00000265641.5	hg19	CCDS8185.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.056444	0.76074	.	.	ENSG00000110090	ENST00000540367;ENST00000376618;ENST00000265641;ENST00000538308;ENST00000539743	D;D;D;D	0.85258	-1.96;-1.96;-1.96;-1.96	5.11	4.2	0.49525	.	0.053589	0.85682	D	0.000000	D	0.92625	0.7657	M	0.87038	2.855	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.80764	0.987;0.967;0.994	D	0.93446	0.6798	10	0.72032	D	0.01	.	13.5493	0.61723	0.0755:0.0:0.9245:0.0	.	162;162;162	B2RAQ8;P50416;P50416-2	.;CPT1A_HUMAN;.	H	162	ENSP00000439084:P162H;ENSP00000365803:P162H;ENSP00000265641:P162H;ENSP00000446108:P162H	ENSP00000265641:P162H	P	-	2	0	CPT1A	68328114	1.000000	0.71417	0.590000	0.28732	0.888000	0.51559	9.426000	0.97469	1.162000	0.42619	0.591000	0.81541	CCC	.	.	.	none		0.498	CPT1A-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397457.2	NM_001876		T	68571538	G	T	68571538	3	4	205	1	0	0	0	0	1	0	0	0	3833	1232	43	4	1936	4	CPT1A	11	68571538	Missense_Mutation	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	7867238	68571538	66434978	71	12438											
PCF11	51585	hgsc.bcm.edu	37	chr11	82877674	82877674	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcattctacaaagtcaggcActgaaccaaaggagaatgta	17	7	9	8	0	2	2	1	1	1	1	2	3	2	2	1	2	3	3	1	2	6	3			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr11:82877674A>G	ENST00000298281.4	+	5	2187	c.1735A>G	c.(1735-1737)Act>Gct	p.T579A		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	579					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						AAAGTCAGGCACTGAACCAAA	0.393																																					p.T579A		Atlas-SNP	.											.	PCF11	220	.	0			c.A1735G						PASS	.						64	64	64					11																	82877674		1850	4075	5925	SO:0001583	missense	51585	exon5			TCAGGCACTGAAC	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.1735A>G	chr11.hg19:g.82877674A>G	ENSP00000298281:p.Thr579Ala	80.0	0.0	.		83.0	16.0	.	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	hg19	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	A	7.818	0.717156	0.15372	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.42131	1.99;0.98;0.99	6.07	-8.05	0.01106	.	1.378680	0.04525	N	0.385316	T	0.18130	0.0435	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	0.10337	-1.0634	9	.	.	.	.	2.4752	0.04574	0.2456:0.0806:0.1902:0.4836	.	579;579	E9PQ01;O94913	.;PCF11_HUMAN	A	579	ENSP00000298281:T579A;ENSP00000434540:T579A;ENSP00000431567:T579A	.	T	+	1	0	PCF11	82555322	0.000000	0.05858	0.178000	0.23040	0.985000	0.73830	-0.195000	0.09546	-1.112000	0.02984	0.533000	0.62120	ACT	.	.	.	none		0.393	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		G	82877674	A	G	82877674	3	3	205	1	0	0	0	0	1	0	0	0	11580	159	6	3	1753	3	PCF11	11	82877674	Missense_Mutation	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10	14306136	82877674	52128842	72	12439											
C3AR1	719	hgsc.bcm.edu	37	chr12	8212016	8212016	+	Frame_Shift_Del	DEL	A	A	-																															agcaggtttaaatacattagAatacagattttgacttgtta																										TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr12:8212016delA	ENST00000307637.4	-	2	969	c.766delT	c.(766-768)tctfs	p.S256fs		NM_004054.2	NP_004045.1	Q16581	C3AR_HUMAN	complement component 3a receptor 1	256					blood circulation (GO:0008015)|chemotaxis (GO:0006935)|complement receptor mediated signaling pathway (GO:0002430)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation vascular endothelial growth factor production (GO:0010575)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C3a anaphylatoxin receptor activity (GO:0004943)|complement component C3a receptor activity (GO:0004876)|G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)	20				Kidney(36;0.0893)		AATACATTAGAATACAGATTT	0.433																																					p.S256fs		Atlas-Indel,Pindel	.											.	C3AR1	61	.	0			c.767delC						PASS	.						64	66	66					12																	8212016		2203	4300	6503	SO:0001589	frameshift_variant	719	exon2			.	U28488	CCDS8588.1	12p13.31	2012-08-10				ENSG00000171860		"Complement system", "GPCR / Class A : Complement component receptors"	1319	protein-coding gene	gene with protein product		605246				8605247	Standard	NM_004054		Approved	C3AR, AZ3B	uc001qtv.1	Q16581		ENST00000307637.4:c.766delT	chr12.hg19:g.8212016delA	ENSP00000302079:p.Ser256fs	61.0	0.0	0		97.0	34.0	0.350515	NM_004054	O43771|Q92868	Frame_Shift_Del	DEL	ENST00000307637.4	hg19	CCDS8588.1																																																																																			.	.	.	none		0.433	C3AR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400254.1			-	8212016	A	-	8212016	7	5	205	1	0	1	0	1	0	0	0	0	2207	246	9	0	686	0	C3AR1	12	8212016	Frame_Shift_Del	DEL	A	TCGA-IA-A83S-01A-11D-A34Z-10		8212016	125639879	73	12440											
GPD1	2819	hgsc.bcm.edu	37	chr12	50500627	50500627	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggacaactcctgaaagagcTgatgcagacaccaaacttcc	14	6	9	12	0	0	4	0	2	0	2	2	5	2	5	3	1	4	2	3	1	3	1			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr12:50500627T>C	ENST00000301149.3	+	5	771	c.539T>C	c.(538-540)cTg>cCg	p.L180P	GPD1_ENST00000547190.1_3'UTR|GPD1_ENST00000548814.1_Missense_Mutation_p.L157P	NM_001257199.1|NM_005276.3	NP_001244128.1|NP_005267.2	P21695	GPDA_HUMAN	glycerol-3-phosphate dehydrogenase 1 (soluble)	180					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						CTGAAAGAGCTGATGCAGACA	0.498																																					p.L180P	NSCLC(141;1402 1905 9497 13391 44868)	Atlas-SNP	.											.	GPD1	23	.	0			c.T539C						PASS	.						64	58	60					12																	50500627		2203	4300	6503	SO:0001583	missense	2819	exon5			AAGAGCTGATGCA		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.539T>C	chr12.hg19:g.50500627T>C	ENSP00000301149:p.Leu180Pro	32.0	0.0	.		50.0	11.0	.	NM_005276	F8W1L5|Q8N1B0	Missense_Mutation	SNP	ENST00000301149.3	hg19	CCDS8799.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.604642	0.87157	.	.	ENSG00000167588	ENST00000301149;ENST00000547190;ENST00000548814	T;T	0.59364	0.27;0.27	5.39	5.39	0.77823	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.84497	0.5485	H	0.97659	4.05	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.99;1.0	D	0.90186	0.4246	10	0.87932	D	0	-14.9432	15.7152	0.77663	0.0:0.0:0.0:1.0	.	157;180	F8W1L5;P21695	.;GPDA_HUMAN	P	180;180;157	ENSP00000301149:L180P;ENSP00000446768:L157P	ENSP00000301149:L180P	L	+	2	0	GPD1	48786894	1.000000	0.71417	0.998000	0.56505	0.925000	0.55904	8.040000	0.89188	2.184000	0.69523	0.459000	0.35465	CTG	.	.	.	none		0.498	GPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406018.1			C	50500627	T	C	50500627	3	2	205	1	0	0	0	0	1	0	0	0	6611	1580	55	3	557	3	GPD1	12	50500627	Missense_Mutation	SNP	T	TCGA-IA-A83S-01A-11D-A34Z-10	42288611	50500627	83351268	74	12441											
PCBP2	5094	hgsc.bcm.edu	37	chr12	53848614	53848614	+	Missense_Mutation	SNP	A	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	ggtgtgattgaaggtggattAaatgtcactctcaccatccg	10	12	11	8	1	2	2	2	2	1	0	4	3	3	3	2	3	0	0	2	3	3	2			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr12:53848614A>C	ENST00000439930.3	+	1	52	c.30A>C	c.(28-30)ttA>ttC	p.L10F	PCBP2_ENST00000603815.1_Missense_Mutation_p.L10F|PCBP2_ENST00000546463.1_Missense_Mutation_p.L10F|PCBP2_ENST00000359462.5_Missense_Mutation_p.L10F|PCBP2_ENST00000552819.1_Missense_Mutation_p.L10F|RP11-793H13.8_ENST00000547717.1_RNA|PCBP2_ENST00000437231.1_Missense_Mutation_p.L10F|PCBP2_ENST00000359282.5_Missense_Mutation_p.L10F|PCBP2_ENST00000549863.1_Missense_Mutation_p.L10F|PCBP2_ENST00000455667.3_Missense_Mutation_p.L10F|PCBP2_ENST00000447282.1_Missense_Mutation_p.L10F|PCBP2_ENST00000552296.2_Missense_Mutation_p.L10F|PCBP2_ENST00000548933.1_Missense_Mutation_p.L10F|PCBP2_ENST00000541275.1_Missense_Mutation_p.L10F			Q15366	PCBP2_HUMAN	poly(rC) binding protein 2	10					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of defense response to virus (GO:0050687)|negative regulation of type I interferon production (GO:0032480)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(4)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	15						AAGGTGGATTAAATGTCACTC	0.517																																					p.L10F		Atlas-SNP	.											.	PCBP2	38	.	0			c.A30C						PASS	.						148	122	131					12																	53848614		2203	4300	6503	SO:0001583	missense	5094	exon2			TGGATTAAATGTC	BC035420	CCDS8859.1, CCDS44900.1, CCDS44901.1, CCDS44902.1, CCDS44903.1, CCDS44904.1, CCDS55830.1	12q13.13	2013-10-30	2001-11-28		ENSG00000197111	ENSG00000197111			8648	protein-coding gene	gene with protein product	"heterogenous nuclear ribonucleoprotein E2"	601210	"poly(rC)-binding protein 2"			8833161	Standard	NM_001098620		Approved	HNRPE2, hnRNP-E2, HNRNPE2	uc001sdc.4	Q15366	OTTHUMG00000169439	ENST00000439930.3:c.30A>C	chr12.hg19:g.53848614A>C	ENSP00000408949:p.Leu10Phe	110.0	0.0	.		109.0	26.0	.	NM_005016	A8K7X6|F8VYL7|G3V0E8|I6L8F9|Q32Q82|Q59HD4|Q68Y55|Q6IPF4|Q6PKG5	Missense_Mutation	SNP	ENST00000439930.3	hg19	CCDS44901.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.950795	0.73787	.	.	ENSG00000197111	ENST00000541275;ENST00000359282;ENST00000447282;ENST00000437231;ENST00000439930;ENST00000549863;ENST00000359462;ENST00000550927;ENST00000546463;ENST00000550192;ENST00000551104;ENST00000550520;ENST00000552296;ENST00000552083;ENST00000552819;ENST00000455667;ENST00000548933	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.50277	0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.75;0.87;0.87;0.87;0.87	5.15	5.15	0.70609	.	0.145946	0.46758	D	0.000266	T	0.65903	0.2736	M	0.77820	2.39	0.46981	D	0.999279	D;D;D;D;D;D;D;D;D	0.89917	0.998;1.0;0.999;0.999;0.981;1.0;0.999;1.0;0.999	D;D;D;D;D;D;D;D;D	0.87578	0.98;0.997;0.99;0.979;0.949;0.998;0.979;0.996;0.99	T	0.68622	-0.5360	10	0.56958	D	0.05	.	8.701	0.34325	0.9141:0.0:0.0859:0.0	.	10;10;10;10;10;10;10;10;10	B4DLC0;F8VRG9;Q15366;Q32Q82;G3V0E8;F8VYL7;Q68Y55;Q6IPF4;A8K7X6	.;.;PCBP2_HUMAN;.;.;.;.;.;.	F	10	ENSP00000446130:L10F;ENSP00000352228:L10F;ENSP00000394116:L10F;ENSP00000390304:L10F;ENSP00000408949:L10F;ENSP00000447670:L10F;ENSP00000352438:L10F;ENSP00000448762:L10F;ENSP00000448079:L10F;ENSP00000446601:L10F;ENSP00000448847:L10F;ENSP00000448927:L10F;ENSP00000449070:L10F;ENSP00000388008:L10F;ENSP00000449062:L10F	ENSP00000352228:L10F	L	+	3	2	PCBP2	52134881	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	0.763000	0.26517	2.171000	0.68590	0.454000	0.30748	TTA	.	.	.	none		0.517	PCBP2-027	NOVEL	NAGNAG_splice_site|non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000407545.2	NM_005016		C	53848614	A	C	53848614	3	2	205	1	0	0	0	0	1	0	0	0	11508	359	13	5	32	5	PCBP2	12	53848614	Missense_Mutation	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10	3347987	53848614	80003281	75	12442											
PAN2	9924	hgsc.bcm.edu	37	chr12	56720418	56720418	+	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	aacctgggagctggagcagaGttggcagcaggccaatcaga	12	5	15	9	0	1	2	1	0	0	2	1	4	1	4	2	4	4	5	2	4	2	1			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr12:56720418G>A	ENST00000425394.2	-	7	1621	c.1245C>T	c.(1243-1245)aaC>aaT	p.N415N	PAN2_ENST00000440411.3_Silent_p.N415N|PAN2_ENST00000257931.5_Silent_p.N415N|PAN2_ENST00000548043.1_Silent_p.N415N	NM_001127460.2	NP_001120932	Q9HBH5	RDH14_HUMAN	PAN2 poly(A) specific ribonuclease subunit	0					osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	41					Vitamin A(DB00162)	CTGGAGCAGAGTTGGCAGCAG	0.577																																					p.N415N		Atlas-SNP	.											.	PAN2	107	.	0			c.C1245T						PASS	.						43	38	40					12																	56720418		2203	4299	6502	SO:0001819	synonymous_variant	9924	exon7			AGCAGAGTTGGCA	AB014610	CCDS8915.1, CCDS44922.1, CCDS53802.1	12q13.2	2014-03-27	2014-03-27	2008-01-08		ENSG00000135473		"Ubiquitin-specific peptidases"	20074	protein-coding gene	gene with protein product	"PAN2 homolog, PABP1 dependent poly A specific ribonuclease subunit (S. cerevisiae)"		"ubiquitin specific protease 52", "ubiquitin specific peptidase 52", "PAN2 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"	USP52		12838346, 14583602	Standard	NM_014871		Approved	KIAA0710, hPAN2	uc001skx.3	Q504Q3	OTTHUMG00000170412	ENST00000425394.2:c.1245C>T	chr12.hg19:g.56720418G>A		70.0	0.0	.		66.0	23.0	.	NM_014871		Silent	SNP	ENST00000425394.2	hg19	CCDS44922.1																																																																																			.	.	.	none		0.577	PAN2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409024.1	NM_014871		A	56720418	G	A	56720418	2	1	205	1	0	0	0	0	0	0	0	1	11421	1020	36	2		2	PAN2	12	56720418	Silent	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	2871804	56720418	77131477	76	12443											
LRP1	4035	hgsc.bcm.edu	37	chr12	57548432	57548432	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcctatctggactatattgAagtggtggactatgagggca	10	12	13	6	0	1	2	0	2	1	0	1	4	1	4	1	4	1	1	1	4	5	5			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr12:57548432A>G	ENST00000243077.3	+	8	1641	c.1175A>G	c.(1174-1176)gAa>gGa	p.E392G	LRP1_ENST00000554174.1_Missense_Mutation_p.E392G	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	392					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)	GACTATATTGAAGTGGTGGAC	0.557																																					p.E392G		Atlas-SNP	.											.	LRP1	428	.	0			c.A1175G						PASS	.						50	43	45					12																	57548432		2203	4297	6500	SO:0001583	missense	4035	exon8			ATATTGAAGTGGT	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.1175A>G	chr12.hg19:g.57548432A>G	ENSP00000243077:p.Glu392Gly	68.0	0.0	.		62.0	18.0	.	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	A	13.71	2.319176	0.41096	.	.	ENSG00000123384	ENST00000243077;ENST00000554174	D;D	0.91124	-2.79;-2.79	4.53	4.53	0.55603	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000001	D	0.93145	0.7817	L	0.60455	1.87	0.49798	D	0.999829	D;B	0.71674	0.998;0.357	D;B	0.70227	0.968;0.108	D	0.92651	0.6133	10	0.45353	T	0.12	.	12.1491	0.54040	1.0:0.0:0.0:0.0	.	392;392	Q07954;Q6PJ72	LRP1_HUMAN;.	G	392	ENSP00000243077:E392G;ENSP00000451737:E392G	ENSP00000243077:E392G	E	+	2	0	LRP1	55834699	1.000000	0.71417	0.994000	0.49952	0.469000	0.32828	9.139000	0.94554	2.039000	0.60335	0.528000	0.53228	GAA	.	.	.	none		0.557	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		G	57548432	A	G	57548432	3	3	205	1	0	0	0	0	1	0	0	0	8958	246	9	3	1205	3	LRP1	12	57548432	Missense_Mutation	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10	828014	57548432	76303463	77	12444											
FAM19A2	338811	hgsc.bcm.edu	37	chr12	62148697	62148697	+	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	gcgtggtgcctgccacctgcCcagggaagcaggagcacttg	7	6	15	13	1	0	0	0	0	0	0	0	2	0	2	4	3	5	2	4	3	1	1			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr12:62148697C>T	ENST00000416284.3	-	3	1799	c.215G>A	c.(214-216)gGg>gAg	p.G72E	FAM19A2_ENST00000551619.1_Missense_Mutation_p.G72E|FAM19A2_ENST00000551449.1_Intron|FAM19A2_ENST00000550003.1_5'UTR	NM_178539.4	NP_848634.1	Q8N3H0	F19A2_HUMAN	family with sequence similarity 19 (chemokine (C-C motif)-like), member A2	72						cytoplasm (GO:0005737)				endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)	15			GBM - Glioblastoma multiforme(1;0.00484)	GBM - Glioblastoma multiforme(3;0.02)		TGCCACCTGCCCAGGGAAGCA	0.498																																					p.G72E		Atlas-SNP	.											.	FAM19A2	38	.	0			c.G215A						PASS	.						186	125	146					12																	62148697		2203	4300	6503	SO:0001583	missense	338811	exon3			ACCTGCCCAGGGA	AY325115	CCDS8962.1	12q14.1	2012-10-03			ENSG00000198673	ENSG00000198673			21589	protein-coding gene	gene with protein product						15028294	Standard	NM_178539		Approved	TAFA-2	uc001sqw.3	Q8N3H0	OTTHUMG00000170207	ENST00000416284.3:c.215G>A	chr12.hg19:g.62148697C>T	ENSP00000393987:p.Gly72Glu	95.0	0.0	.		128.0	54.0	.	NM_178539	B3KVV4|Q4G0R9|Q68DK0|Q6GTX6	Missense_Mutation	SNP	ENST00000416284.3	hg19	CCDS8962.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.730284	0.89390	.	.	ENSG00000198673	ENST00000416284;ENST00000551619;ENST00000552075;ENST00000549958;ENST00000548780	.	.	.	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	D	0.84120	0.5402	M	0.85542	2.76	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85714	0.1321	8	.	.	.	.	18.8508	0.92227	0.0:1.0:0.0:0.0	.	72	Q8N3H0	F19A2_HUMAN	E	72;72;73;79;73	.	.	G	-	2	0	FAM19A2	60434964	1.000000	0.71417	0.977000	0.42913	0.891000	0.51852	7.752000	0.85141	2.455000	0.83008	0.558000	0.71614	GGG	.	.	.	none		0.498	FAM19A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407967.2	NM_178539		T	62148697	C	T	62148697	3	4	205	1	0	0	0	0	1	0	0	0	5536	623	22	2	192	2	FAM19A2	12	62148697	Missense_Mutation	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10	4600265	62148697	71703198	78	12445											
TPTE2	93492	hgsc.bcm.edu	37	chr13	20048076	20048076	+	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	ttctacaaatactcgaagaaGaacatccatgagaaaaaata	21	8	5	7	1	1	3	0	1	1	3	3	5	2	3	1	0	3	0	1	0	10	4			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr13:20048076G>C	ENST00000400230.2	-	6	414	c.370C>G	c.(370-372)Ctt>Gtt	p.L124V	TPTE2_ENST00000382977.4_Missense_Mutation_p.L124V|TPTE2_ENST00000382975.4_Missense_Mutation_p.L124V|TPTE2_ENST00000457266.2_Intron|TPTE2_ENST00000382978.1_Missense_Mutation_p.L124V|TPTE2_ENST00000255310.6_Missense_Mutation_p.L87V|TPTE2_ENST00000400103.2_Intron|TPTE2_ENST00000390680.2_Missense_Mutation_p.L87V			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	124					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		ACTCGAAGAAGAACATCCATG	0.358																																					p.L124V		Atlas-SNP	.											.	TPTE2	225	.	0			c.C370G						PASS	.						36	41	39					13																	20048076		2198	4290	6488	SO:0001583	missense	93492	exon7			GAAGAAGAACATC	AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.370C>G	chr13.hg19:g.20048076G>C	ENSP00000383089:p.Leu124Val	90.0	0.0	.		112.0	31.0	.	NM_199254	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Missense_Mutation	SNP	ENST00000400230.2	hg19	CCDS45014.1	.	.	.	.	.	.	.	.	.	.	g	11.47	1.647647	0.29246	.	.	ENSG00000132958	ENST00000382978;ENST00000400230;ENST00000255310;ENST00000390680;ENST00000382977;ENST00000382975;ENST00000343548	D;D;D;D;D;D	0.98419	-4.45;-4.92;-4.45;-4.45;-4.92;-4.45	2.33	-0.47	0.12131	Ion transport (1);	0.079005	0.50627	U	0.000114	D	0.96697	0.8922	L	0.49513	1.565	0.26630	N	0.972498	P;P	0.47962	0.903;0.831	P;P	0.53722	0.487;0.733	D	0.92530	0.6032	9	.	.	.	-8.3239	4.9435	0.13978	0.5016:0.0:0.4984:0.0	.	87;124	Q6XPS3-3;Q6XPS3	.;TPTE2_HUMAN	V	124;124;87;87;124;124;124	ENSP00000372438:L124V;ENSP00000383089:L124V;ENSP00000255310:L87V;ENSP00000375098:L87V;ENSP00000372437:L124V;ENSP00000372435:L124V	.	L	-	1	0	TPTE2	18946076	0.997000	0.39634	0.042000	0.18584	0.096000	0.18686	0.842000	0.27627	-0.167000	0.10871	0.411000	0.27672	CTT	.	.	.	none		0.358	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254		C	20048076	G	C	20048076	3	2	205	1	0	0	0	0	1	0	0	0	16443	942	33	4	1258	4	TPTE2	13	20048076	Missense_Mutation	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10		20048076	95121802	79	12446											
ATP7B	540	hgsc.bcm.edu	37	chr13	52513260	52513260	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtccacacccatgctctgcAgcgtgtgcacagccagggca	8	6	11	16	2	1	0	0	0	1	0	2	0	2	0	3	1	5	4	3	1	0	0			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr13:52513260A>G	ENST00000242839.4	-	17	3782	c.3626T>C	c.(3625-3627)cTg>cCg	p.L1209P	ATP7B_ENST00000482841.1_5'Flank|ATP7B_ENST00000400370.3_Missense_Mutation_p.L779P|ATP7B_ENST00000417240.2_Missense_Mutation_p.L420P|ATP7B_ENST00000418097.2_Missense_Mutation_p.L1144P|ATP7B_ENST00000400366.3_Missense_Mutation_p.L1098P|ATP7B_ENST00000344297.5_Missense_Mutation_p.L1002P|ATP7B_ENST00000448424.2_Missense_Mutation_p.L1131P	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	1209					cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	CATGCTCTGCAGCGTGTGCAC	0.582									Wilson disease																												p.L1209P		Atlas-SNP	.											.	ATP7B	123	.	0			c.T3626C						PASS	.						79	84	82					13																	52513260		2172	4271	6443	SO:0001583	missense	540	exon17	Familial Cancer Database		CTCTGCAGCGTGT	U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"ATPases / P-type"	870	protein-coding gene	gene with protein product	"Wilson disease", "copper pump 2", "copper-transporting ATPase 2"	606882	"ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.3626T>C	chr13.hg19:g.52513260A>G	ENSP00000242839:p.Leu1209Pro	73.0	0.0	.		60.0	16.0	.	NM_000053	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Missense_Mutation	SNP	ENST00000242839.4	hg19	CCDS41892.1	.	.	.	.	.	.	.	.	.	.	A	18.39	3.613031	0.66672	.	.	ENSG00000123191	ENST00000242839;ENST00000400366;ENST00000344297;ENST00000417240;ENST00000448424;ENST00000400370;ENST00000418097	D;D;D;D;D;D;D	0.98531	-4.98;-4.98;-4.98;-4.98;-4.98;-4.98;-4.98	5.15	5.15	0.70609	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (2);	0.000000	0.85682	D	0.000000	D	0.99284	0.9750	H	0.96048	3.76	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	0.999;1.0;0.999;0.999;0.999;0.999;0.999;1.0	D	0.98821	1.0747	10	0.87932	D	0	-17.3007	15.1342	0.72549	1.0:0.0:0.0:0.0	.	1131;1161;1144;420;779;1098;1002;1209	E7ET55;B7ZLR4;F5H748;E7EQQ2;F5H562;P35670-3;P35670-2;P35670	.;.;.;.;.;.;.;ATP7B_HUMAN	P	1209;1098;1002;420;1131;779;1144	ENSP00000242839:L1209P;ENSP00000383217:L1098P;ENSP00000342559:L1002P;ENSP00000390360:L420P;ENSP00000416738:L1131P;ENSP00000383221:L779P;ENSP00000393343:L1144P	ENSP00000242839:L1209P	L	-	2	0	ATP7B	51411261	1.000000	0.71417	1.000000	0.80357	0.379000	0.30106	9.081000	0.94049	2.169000	0.68431	0.460000	0.39030	CTG	.	.	.	none		0.582	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053		G	52513260	A	G	52513260	3	3	205	1	0	0	0	0	1	0	0	0	1191	188	7	3	791	3	ATP7B	13	52513260	Missense_Mutation	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10	32465184	52513260	62656618	80	12447											
SLITRK1	114798	hgsc.bcm.edu	37	chr13	84455218	84455218	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccccgggtctatatctcgtAataaattaaaatcagcctgg	12	11	7	11	2	3	0	1	0	2	0	4	0	3	0	3	2	1	1	3	2	7	5			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr13:84455218A>G	ENST00000377084.2	-	1	1310	c.425T>C	c.(424-426)tTa>tCa	p.L142S		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	142					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)		TATATCTCGTAATAAATTAAA	0.453																																					p.L142S		Atlas-SNP	.											.	SLITRK1	196	.	0			c.T425C						PASS	.						59	64	62					13																	84455218		2203	4300	6503	SO:0001583	missense	114798	exon1			TCTCGTAATAAAT	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.425T>C	chr13.hg19:g.84455218A>G	ENSP00000366288:p.Leu142Ser	79.0	0.0	.		72.0	25.0	.	NM_052910	Q5U5I6|Q96SF9	Missense_Mutation	SNP	ENST00000377084.2	hg19	CCDS9464.1	.	.	.	.	.	.	.	.	.	.	A	15.40	2.822760	0.50739	.	.	ENSG00000178235	ENST00000377084	T	0.66815	-0.23	4.45	4.45	0.53987	.	0.000000	0.64402	D	0.000004	D	0.85483	0.5707	H	0.94385	3.53	0.52099	D	0.999942	D	0.76494	0.999	D	0.77557	0.99	D	0.89217	0.3568	10	0.87932	D	0	-3.848	12.6952	0.56999	1.0:0.0:0.0:0.0	.	142	Q96PX8	SLIK1_HUMAN	S	142	ENSP00000366288:L142S	ENSP00000366288:L142S	L	-	2	0	SLITRK1	83353219	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.139000	0.94554	1.874000	0.54306	0.459000	0.35465	TTA	.	.	.	none		0.453	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910		G	84455218	A	G	84455218	3	3	205	1	0	0	0	0	1	0	0	0	14755	372	13	3	1669	3	SLITRK1	13	84455218	Missense_Mutation	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10	31941958	84455218	30714660	81	12448											
SLC10A2	6555	hgsc.bcm.edu	37	chr13	103701721	103701721	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgacattgagctcctcaggAgtgaaggagagctgaacgat	13	7	13	8	2	1	4	1	3	0	1	2	8	2	5	1	2	3	2	1	2	2	1			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr13:103701721A>G	ENST00000245312.3	-	5	1433	c.837T>C	c.(835-837)acT>acC	p.T279T		NM_000452.2	NP_000443	Q12908	NTCP2_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 2	279					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)	bile acid:sodium symporter activity (GO:0008508)			breast(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_neural(89;0.0662)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)				Aciclovir(DB00787)|Cyclosporine(DB00091)|Ursodeoxycholic acid(DB01586)|Valaciclovir(DB00577)	GCTCCTCAGGAGTGAAGGAGA	0.478																																					p.T279T		Atlas-SNP	.											.	SLC10A2	67	.	0			c.T837C						PASS	.						183	144	157					13																	103701721		2203	4300	6503	SO:0001819	synonymous_variant	6555	exon5			CTCAGGAGTGAAG	U10417	CCDS9506.1	13q33	2013-07-18	2013-07-18		ENSG00000125255	ENSG00000125255		"Solute carriers"	10906	protein-coding gene	gene with protein product		601295		ASBT, ISBT		8661017	Standard	NM_000452		Approved		uc001vpy.4	Q12908	OTTHUMG00000017313	ENST00000245312.3:c.837T>C	chr13.hg19:g.103701721A>G		86.0	0.0	.		97.0	18.0	.	NM_000452	A1L4F4|Q13839	Silent	SNP	ENST00000245312.3	hg19	CCDS9506.1																																																																																			.	.	.	none		0.478	SLC10A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045716.1			G	103701721	A	G	103701721	2	3	205	1	0	0	0	0	0	0	0	1	14387	291	11	3		3	SLC10A2	13	103701721	Silent	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10	19246503	103701721	11468157	82	12449											
OR4K17	390436	hgsc.bcm.edu	37	chr14	20586055	20586055	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgtaagcccctacactacAtgaccatcatgaacaagaag	15	9	6	11	0	1	3	1	2	0	1	1	3	1	3	3	0	4	1	3	0	6	4			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr14:20586055A>G	ENST00000315543.4	+	1	490	c.490A>G	c.(490-492)Atg>Gtg	p.M164V		NM_001004715.1	NP_001004715.1	Q8NGC6	OR4KH_HUMAN	olfactory receptor, family 4, subfamily K, member 17	136						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)		CCTACACTACATGACCATCAT	0.443																																					p.M164V		Atlas-SNP	.											.	OR4K17	58	.	0			c.A490G						PASS	.						206	172	183					14																	20586055		2203	4300	6503	SO:0001583	missense	390436	exon1			CACTACATGACCA		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.490A>G	chr14.hg19:g.20586055A>G	ENSP00000319197:p.Met164Val	186.0	0.0	.		244.0	54.0	.	NM_001004715	Q6IF12	Missense_Mutation	SNP	ENST00000315543.4	hg19	CCDS32030.1	.	.	.	.	.	.	.	.	.	.	.	4.360	0.066302	0.08388	.	.	ENSG00000176230	ENST00000315543	T	0.19105	2.17	2.86	0.121	0.14695	GPCR, rhodopsin-like superfamily (1);	0.561138	0.13408	U	0.390079	T	0.11153	0.0272	N	0.21617	0.685	0.09310	N	0.999999	B	0.02656	0.0	B	0.06405	0.002	T	0.23976	-1.0173	10	0.38643	T	0.18	.	3.7424	0.08536	0.5547:0.1951:0.2502:0.0	.	136	Q8NGC6	OR4KH_HUMAN	V	164	ENSP00000319197:M164V	ENSP00000319197:M164V	M	+	1	0	OR4K17	19655895	0.000000	0.05858	0.834000	0.33040	0.839000	0.47603	-1.897000	0.01603	0.316000	0.23135	0.332000	0.21555	ATG	.	.	.	none		0.443	OR4K17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410346.1			G	20586055	A	G	20586055	3	3	205	1	0	0	0	0	1	0	0	0	11078	217	8	3	492	3	OR4K17	14	20586055	Missense_Mutation	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10		20586055	86763485	83	12450											
METTL3	56339	hgsc.bcm.edu	37	chr14	21967914	21967914	+	Missense_Mutation	SNP	A	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	caaccactacttacccccagAgatttagacattctctcccc	11	10	3	17	0	1	2	0	0	1	2	3	3	2	2	5	0	3	0	5	0	4	5			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr14:21967914A>C	ENST00000298717.4	-	7	1488	c.1337T>G	c.(1336-1338)cTc>cGc	p.L446R		NM_019852.3	NP_062826.2	Q86U44	MTA70_HUMAN	methyltransferase like 3	446					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)		TTACCCCCAGAGATTTAGACA	0.383																																					p.L446R		Atlas-SNP	.											.	METTL3	48	.	0			c.T1337G						PASS	.						161	149	153					14																	21967914		2203	4300	6503	SO:0001583	missense	56339	exon7			CCCCAGAGATTTA	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.1337T>G	chr14.hg19:g.21967914A>C	ENSP00000298717:p.Leu446Arg	119.0	0.0	.		126.0	42.0	.	NM_019852	O14736|Q86V05|Q9HB32	Missense_Mutation	SNP	ENST00000298717.4	hg19	CCDS32044.1	.	.	.	.	.	.	.	.	.	.	A	17.87	3.495927	0.64186	.	.	ENSG00000165819	ENST00000298717	T	0.38401	1.14	5.02	5.02	0.67125	.	0.064498	0.64402	D	0.000008	T	0.31513	0.0799	L	0.28274	0.84	0.80722	D	1	P	0.42248	0.774	B	0.44224	0.444	T	0.06534	-1.0821	10	0.40728	T	0.16	-9.7454	13.8626	0.63571	1.0:0.0:0.0:0.0	.	446	Q86U44	MTA70_HUMAN	R	446	ENSP00000298717:L446R	ENSP00000298717:L446R	L	-	2	0	METTL3	21037754	1.000000	0.71417	1.000000	0.80357	0.836000	0.47400	6.366000	0.73095	2.116000	0.64780	0.377000	0.23210	CTC	.	.	.	none		0.383	METTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401227.1	NM_019852		C	21967914	A	C	21967914	3	2	205	1	0	0	0	0	1	0	0	0	9508	304	11	5	425	5	METTL3	14	21967914	Missense_Mutation	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10	1381859	21967914	85381626	84	12451											
REM2	161253	hgsc.bcm.edu	37	chr14	23355339	23355339	+	Frame_Shift_Del	DEL	C	C	-																															tttctccaaagttccagagaCcctacttcggctccgggctg																										TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr14:23355339delC	ENST00000267396.4	+	4	749	c.626delC	c.(625-627)accfs	p.T209fs	REM2_ENST00000536884.1_Frame_Shift_Del_p.D184fs	NM_173527.2	NP_775798.2	Q8IYK8	REM2_HUMAN	RAS (RAD and GEM)-like GTP binding 2	209					small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|central_nervous_system(1)|large_intestine(2)|ovary(1)	5	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.012)		GTTCCAGAGACCCTACTTCGG	0.622																																					p.T209fs		Atlas-Indel,Pindel	.											REM2,NS,carcinoma,0,1	REM2	21	.	0			c.625delA						PASS	.						46	51	50					14																	23355339		1940	4134	6074	SO:0001589	frameshift_variant	161253	exon4			.		CCDS45082.1	14q11.2	2014-05-09	2006-12-14		ENSG00000139890	ENSG00000139890			20248	protein-coding gene	gene with protein product			"RAS (RAD and GEM) like GTP binding 2"			10727423	Standard	NM_173527		Approved	FLJ38964	uc001whf.1	Q8IYK8	OTTHUMG00000170277	ENST00000267396.4:c.626delC	chr14.hg19:g.23355339delC	ENSP00000267396:p.Thr209fs	60.0	0.0	0		69.0	20.0	0.289855	NM_173527	B7Z5P1|Q8N8R8	Frame_Shift_Del	DEL	ENST00000267396.4	hg19	CCDS45082.1																																																																																			.	.	.	none		0.622	REM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408290.1	NM_173527		-	23355339	C	-	23355339	7	5	205	1	0	1	0	1	0	0	0	0	13236	507	18	0	640	0	REM2	14	23355339	Frame_Shift_Del	DEL	C	TCGA-IA-A83S-01A-11D-A34Z-10	1387425	23355339	83994201	85	12452											
PCNX	22990	hgsc.bcm.edu	37	chr14	71524368	71524368	+	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	atccttgcctctgactatctCaatgcattagtacaccttat	10	15	4	12	0	2	1	1	1	2	0	4	1	3	1	3	0	3	2	3	0	5	5			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr14:71524368C>G	ENST00000304743.2	+	26	5225	c.4779C>G	c.(4777-4779)ctC>ctG	p.L1593L	PCNX_ENST00000439984.3_Silent_p.L1482L|PCNX_ENST00000238570.5_Intron	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1593						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)		CTGACTATCTCAATGCATTAG	0.448																																					p.L1593L		Atlas-SNP	.											.	PCNX	198	.	0			c.C4779G						PASS	.						324	325	325					14																	71524368		2203	4300	6503	SO:0001819	synonymous_variant	22990	exon26			CTATCTCAATGCA	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.4779C>G	chr14.hg19:g.71524368C>G		120.0	0.0	.		94.0	24.0	.	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Silent	SNP	ENST00000304743.2	hg19	CCDS9806.1																																																																																			.	.	.	none		0.448	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		G	71524368	C	G	71524368	2	3	205	1	0	0	0	0	0	0	0	1	11598	813	29	4		4	PCNX	14	71524368	Silent	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10	48169029	71524368	35825172	86	12453											
LTBP2	4053	hgsc.bcm.edu	37	chr14	74976904	74976904	+	Frame_Shift_Del	DEL	C	C	-																															cacagaccccgggagtcagaCactcattcacatctgtggga																										TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr14:74976904delC	ENST00000261978.4	-	20	3427	c.3041delG	c.(3040-3042)tgtfs	p.C1014fs	LTBP2_ENST00000556690.1_Frame_Shift_Del_p.C1014fs	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	1014	Cys-rich.|EGF-like 8; 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)		GGGAGTCAGACACTCATTCAC	0.577																																					p.C1014fs		Atlas-INDEL	.											.	LTBP2	158	.	0			c.3042delT						PASS	.						81	73	75					14																	74976904		2203	4300	6503	SO:0001589	frameshift_variant	4053	exon20			.		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.3041delG	chr14.hg19:g.74976904delC	ENSP00000261978:p.Cys1014fs	25.0	0.0	0		35.0	15.0	0.428571	NM_000428	Q99907|Q9NS51	Frame_Shift_Del	DEL	ENST00000261978.4	hg19	CCDS9831.1																																																																																			.	.	.	none		0.577	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428		-	74976904	C	-	74976904	7	5	205	1	0	1	0	1	0	0	0	0	9081	478	17	0	2492	0	LTBP2	14	74976904	Frame_Shift_Del	DEL	C	TCGA-IA-A83S-01A-11D-A34Z-10	3452536	74976904	32372636	87	12454	121	2									
LTBP2	4053	hgsc.bcm.edu	37	chr14	74976906	74976906	+	Frame_Shift_Del	DEL	C	C	-																															cagaccccgggagtcagacaCtcattcacatctgtgggaga																										TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr14:74976906delC	ENST00000261978.4	-	20	3425	c.3039delG	c.(3037-3039)gagfs	p.E1013fs	LTBP2_ENST00000556690.1_Frame_Shift_Del_p.E1013fs	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	1013	Cys-rich.|EGF-like 8; 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)		GAGTCAGACACTCATTCACAT	0.582																																					p.C1014fs		Atlas-INDEL	.											.	LTBP2	158	.	0			c.3040delT						PASS	.						80	72	75					14																	74976906		2203	4300	6503	SO:0001589	frameshift_variant	4053	exon20			.		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.3039delG	chr14.hg19:g.74976906delC	ENSP00000261978:p.Glu1013fs	25.0	0.0	0		35.0	15.0	0.428571	NM_000428	Q99907|Q9NS51	Frame_Shift_Del	DEL	ENST00000261978.4	hg19	CCDS9831.1																																																																																			.	.	.	none		0.582	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428		-	74976906	C	-	74976906	7	5	205	1	0	1	0	1	0	0	0	0	9081	564	20	0	2494	0	LTBP2	14	74976906	Frame_Shift_Del	DEL	C	TCGA-IA-A83S-01A-11D-A34Z-10	2	74976906	32372634	88	12455	121	2									
CPSF2	53981	hgsc.bcm.edu	37	chr14	92608527	92608527	+	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	gcaaatgtcctggaaacactTcgaggtgatggaaatgtgtt	12	11	12	6	1	0	1	0	1	0	0	2	4	1	3	1	3	1	2	1	3	3	2			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr14:92608527T>A	ENST00000298875.4	+	8	966	c.681T>A	c.(679-681)ctT>ctA	p.L227L		NM_017437.2	NP_059133.1	Q9P2I0	CPSF2_HUMAN	cleavage and polyadenylation specific factor 2, 100kDa	227					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	RNA binding (GO:0003723)			breast(2)|cervix(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	24		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)		TGGAAACACTTCGAGGTGATG	0.373																																					p.L227L	Ovarian(78;28 1788 18702 44111)	Atlas-SNP	.											.	CPSF2	63	.	0			c.T681A						PASS	.						162	148	153					14																	92608527		2203	4300	6503	SO:0001819	synonymous_variant	53981	exon8			AACACTTCGAGGT	AB037788	CCDS9902.1	14q31.1	2008-07-28	2002-08-29			ENSG00000165934			2325	protein-coding gene	gene with protein product		606028	"cleavage and polyadenylation specific factor 2, 100kD subunit"			7969155, 11124543	Standard	NM_017437		Approved	KIAA1367	uc001yah.2	Q9P2I0		ENST00000298875.4:c.681T>A	chr14.hg19:g.92608527T>A		265.0	0.0	.		237.0	64.0	.	NM_017437	B3KME1|Q6NSJ1|Q9H3W7	Silent	SNP	ENST00000298875.4	hg19	CCDS9902.1																																																																																			.	.	.	none		0.373	CPSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412123.1			A	92608527	T	A	92608527	2	1	205	1	0	0	0	0	0	0	0	1	3827	1770	62	5		5	CPSF2	14	92608527	Silent	SNP	T	TCGA-IA-A83S-01A-11D-A34Z-10	17631621	92608527	14741013	89	12456											
USP3	9960	hgsc.bcm.edu	37	chr15	63866572	63866572	+	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	gaagtaagcgctctaagaatCaagaaaatggaccagtttgt	16	9	10	6	1	2	2	1	0	1	2	2	4	2	3	1	1	1	3	1	1	7	3			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr15:63866572C>A	ENST00000380324.3	+	11	1195	c.1066C>A	c.(1066-1068)Caa>Aaa	p.Q356K	USP3_ENST00000536001.1_3'UTR|USP3-AS1_ENST00000560350.1_RNA|USP3_ENST00000559711.1_Missense_Mutation_p.Q267K|USP3_ENST00000539772.1_Missense_Mutation_p.Q107K|USP3_ENST00000540797.1_Missense_Mutation_p.Q312K|USP3-AS1_ENST00000559357.1_RNA|USP3-AS1_ENST00000559861.1_RNA|USP3_ENST00000558285.1_Missense_Mutation_p.Q339K|USP3_ENST00000268049.7_Missense_Mutation_p.Q334K	NM_006537.3	NP_006528.2	Q9Y6I4	UBP3_HUMAN	ubiquitin specific peptidase 3	356	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)		CTCTAAGAATCAAGAAAATGG	0.323																																					p.Q356K		Atlas-SNP	.											.	USP3	37	.	0			c.C1066A						PASS	.						102	100	100					15																	63866572		2203	4300	6503	SO:0001583	missense	9960	exon11			AAGAATCAAGAAA	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.1066C>A	chr15.hg19:g.63866572C>A	ENSP00000369681:p.Gln356Lys	299.0	0.0	.		278.0	61.0	.	NM_006537	B4DVU5|F5H1A6|Q8WVD0	Missense_Mutation	SNP	ENST00000380324.3	hg19	CCDS32265.1	.	.	.	.	.	.	.	.	.	.	C	18.53	3.644326	0.67244	.	.	ENSG00000140455	ENST00000540797;ENST00000380324;ENST00000268049;ENST00000539772;ENST00000536848;ENST00000538686	T;T;T;T	0.28454	2.12;2.23;2.33;1.61	5.98	5.98	0.97165	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.31734	0.0806	L	0.50333	1.59	0.58432	D	0.999999	B;B;B;B	0.26041	0.056;0.069;0.14;0.14	B;B;B;B	0.31869	0.046;0.053;0.137;0.137	T	0.16928	-1.0386	10	0.02654	T	1	.	20.452	0.99131	0.0:1.0:0.0:0.0	.	312;312;334;356	F5H1A6;B4DVU5;Q6JHV3;Q9Y6I4	.;.;.;UBP3_HUMAN	K	312;356;334;107;271;187	ENSP00000445828:Q312K;ENSP00000369681:Q356K;ENSP00000268049:Q334K;ENSP00000445642:Q107K	ENSP00000268049:Q334K	Q	+	1	0	USP3	61653625	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.838000	0.97847	0.591000	0.81541	CAA	.	.	.	none		0.323	USP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417773.1			A	63866572	C	A	63866572	3	1	205	1	0	0	0	0	1	0	0	0	17072	827	29	4	1108	4	USP3	15	63866572	Missense_Mutation	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10		63866572	38664820	90	12457											
THSD4	79875	hgsc.bcm.edu	37	chr15	72030175	72030175	+	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	acttgcgtggggaggcccctGagatgttcacctcagaatcg	8	9	13	11	2	2	2	2	1	0	2	3	4	2	3	3	3	1	1	3	3	1	2			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr15:72030175G>A	ENST00000355327.3	+	11	1869	c.1735G>A	c.(1735-1737)Gag>Aag	p.E579K	THSD4_ENST00000567838.1_3'UTR|THSD4_ENST00000357769.4_Missense_Mutation_p.E219K|THSD4_ENST00000261862.6_Missense_Mutation_p.E579K			Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4	579					elastic fiber assembly (GO:0048251)	extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						GGAGGCCCCTGAGATGTTCAC	0.582																																					p.E579K		Atlas-SNP	.											.	THSD4	75	.	0			c.G1735A						PASS	.						141	180	167					15																	72030175		2062	4187	6249	SO:0001583	missense	79875	exon10			GCCCCTGAGATGT	AK023772	CCDS10238.2, CCDS66817.1	15q23	2009-11-09			ENSG00000187720	ENSG00000187720			25835	protein-coding gene	gene with protein product		614476				19734141	Standard	NM_001286429		Approved	FVSY9334, PRO34005, FLJ13710, ADAMTSL6	uc002atb.1	Q6ZMP0	OTTHUMG00000133389	ENST00000355327.3:c.1735G>A	chr15.hg19:g.72030175G>A	ENSP00000347484:p.Glu579Lys	114.0	0.0	.		103.0	15.0	.	NM_024817	B2RTY3|B4DR13|Q6MZI3|Q6UXZ8|Q9H8E4	Missense_Mutation	SNP	ENST00000355327.3	hg19	CCDS10238.2	.	.	.	.	.	.	.	.	.	.	G	5.140	0.211483	0.09757	.	.	ENSG00000187720	ENST00000355327;ENST00000261862;ENST00000357769	T;T;T	0.61158	0.13;0.13;0.4	5.31	4.39	0.52855	.	.	.	.	.	T	0.33352	0.0860	N	0.24115	0.695	0.09310	N	1	P;B;B	0.35328	0.495;0.008;0.091	B;B;B	0.22753	0.041;0.001;0.024	T	0.14531	-1.0469	9	0.06365	T	0.9	.	9.5486	0.39295	0.0966:0.0:0.9034:0.0	.	219;219;579	B4E1J6;B4DR13;Q6ZMP0	.;.;THSD4_HUMAN	K	579;579;219	ENSP00000347484:E579K;ENSP00000261862:E579K;ENSP00000350413:E219K	ENSP00000261862:E579K	E	+	1	0	THSD4	69817229	0.989000	0.36119	0.005000	0.12908	0.004000	0.04260	2.904000	0.48719	1.230000	0.43646	0.650000	0.86243	GAG	.	.	.	none		0.582	THSD4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257253.2	NM_024817		A	72030175	G	A	72030175	3	1	205	1	0	0	0	0	1	0	0	0	15890	1291	45	2	1773	2	THSD4	15	72030175	Missense_Mutation	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	8163603	72030175	30501217	91	12458											
SCAMP2	10066	hgsc.bcm.edu	37	chr15	75146985	75146985	+	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	ttggtcagctgggtcacagaGggatcctgagaaggtgaaaa	12	8	15	6	0	2	3	2	2	0	2	3	5	3	4	1	4	1	1	1	4	3	1			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr15:75146985G>T	ENST00000268099.9	-	2	172	c.63C>A	c.(61-63)ccC>ccA	p.P21P		NM_005697.3	NP_005688.2	O15127	SCAM2_HUMAN	secretory carrier membrane protein 2	21					post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|recycling endosome membrane (GO:0055038)|trans-Golgi network membrane (GO:0032588)|transport vesicle (GO:0030133)				kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	9						GGGTCACAGAGGGATCCTGAG	0.627																																					p.P21P		Atlas-SNP	.											.	SCAMP2	18	.	0			c.C63A						PASS	.						32	41	38					15																	75146985		2197	4295	6492	SO:0001819	synonymous_variant	10066	exon2			CACAGAGGGATCC	AF005038	CCDS10271.1	15q23-q25	2013-02-21			ENSG00000140497	ENSG00000140497		"Secretory carrier membrane proteins"	10564	protein-coding gene	gene with protein product		606912				9378760	Standard	NM_005697		Approved		uc002azb.1	O15127	OTTHUMG00000142817	ENST00000268099.9:c.63C>A	chr15.hg19:g.75146985G>T		97.0	0.0	.		66.0	15.0	.	NM_005697	B2RDF0|Q9BQE8	Silent	SNP	ENST00000268099.9	hg19	CCDS10271.1																																																																																			.	.	.	none		0.627	SCAMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286403.3	NM_005697		T	75146985	G	T	75146985	2	4	205	1	0	0	0	0	0	0	0	1	13884	987	35	4		4	SCAMP2	15	75146985	Silent	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	3116810	75146985	27384407	92	12459											
ITGAM	3684	hgsc.bcm.edu	37	chr16	31341675	31341675	+	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	aatccagtgtgacatcccgtTctttggcatccaggaagaat	11	11	9	10	1	1	2	0	1	1	1	4	3	4	3	3	2	0	2	3	2	3	2			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr16:31341675T>A	ENST00000287497.8	+	27	3182	c.3107T>A	c.(3106-3108)tTc>tAc	p.F1036Y	ITGAM_ENST00000544665.3_Missense_Mutation_p.F1037Y			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	1036					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)			endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						GACATCCCGTTCTTTGGCATC	0.567																																					p.F1037Y		Atlas-SNP	.											.	ITGAM	137	.	0			c.T3110A						PASS	.						97	96	96					16																	31341675		2027	4194	6221	SO:0001583	missense	3684	exon27			TCCCGTTCTTTGG	J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"CD molecules", "Complement system", "Integrins"	6149	protein-coding gene	gene with protein product		120980	"integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.3107T>A	chr16.hg19:g.31341675T>A	ENSP00000287497:p.Phe1036Tyr	95.0	0.0	.		107.0	38.0	.	NM_001145808	Q4VAK0|Q4VAK1|Q4VAK2	Missense_Mutation	SNP	ENST00000287497.8	hg19	CCDS45470.1	.	.	.	.	.	.	.	.	.	.	T	17.56	3.419955	0.62622	.	.	ENSG00000169896	ENST00000544665;ENST00000287497	T;T	0.47869	0.83;0.83	5.51	1.04	0.20106	.	.	.	.	.	T	0.26702	0.0653	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.19031	-1.0318	9	0.56958	D	0.05	.	4.1662	0.10308	0.1547:0.5648:0.0:0.2805	.	1036;1036	Q4VAK1;P11215	.;ITAM_HUMAN	Y	1037;1036	ENSP00000441691:F1037Y;ENSP00000287497:F1036Y	ENSP00000287497:F1036Y	F	+	2	0	ITGAM	31249176	0.023000	0.18921	0.023000	0.16930	0.960000	0.62799	-0.047000	0.11963	0.216000	0.20781	0.372000	0.22366	TTC	.	.	.	none		0.567	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632		A	31341675	T	A	31341675	3	1	205	1	0	0	0	0	1	0	0	0	7894	1783	62	5	3216	5	ITGAM	16	31341675	Missense_Mutation	SNP	T	TCGA-IA-A83S-01A-11D-A34Z-10		31341675	59013078	93	12460											
ESRP2	80004	hgsc.bcm.edu	37	chr16	68267898	68267898	+	Splice_Site	DEL	T	T	-																															ttttccttcaggagcataccTtcctggaggcctcggggtgc																										TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr16:68267898delT	ENST00000565858.1	-	3	526	c.440delA	c.(439-441)aag>ag	p.K147fs	ESRP2_ENST00000473183.2_Splice_Site_p.K147fs|RP11-96D1.6_ENST00000564147.1_RNA	NM_024939.2	NP_079215.2	Q9H6T0	ESRP2_HUMAN	epithelial splicing regulatory protein 2	147					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						GGAGCATACCTTCCTGGAGGC	0.622																																					p.K147fs		Atlas-INDEL	.											.	ESRP2	118	.	0			c.441delG						PASS	.						46	46	46					16																	68267898		2198	4300	6498	SO:0001630	splice_region_variant	80004	exon3			.	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.441+1A>-	chr16.hg19:g.68267898delT		41.0	0.0	0		50.0	11.0	0.22	NM_024939	Q8N6H8|Q8WZ15|Q9H6I4	Frame_Shift_Del	DEL	ENST00000565858.1	hg19																																																																																				.	.	.	none		0.622	ESRP2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000433083.1	NM_024939	Frame_Shift_Del	-	68267898	T	-	68267898	8	5	205	1	0	1	0	1	0	0	1	0	5261	1623	56	0	1765	0	ESRP2	16	68267898	Splice_Site	DEL	T	TCGA-IA-A83S-01A-11D-A34Z-10	36926223	68267898	22086855	94	12461											
GLG1	2734	hgsc.bcm.edu	37	chr16	74487150	74487150	+	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	acaatatacagatgctcccaCtgatcacagagagaatgtag	16	8	8	9	0	1	4	1	1	0	3	2	5	2	4	1	0	2	2	1	0	5	3			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr16:74487150C>T	ENST00000422840.2	-	26	3454	c.3455G>A	c.(3454-3456)aGt>aAt	p.S1152N	GLG1_ENST00000205061.5_Missense_Mutation_p.S1152N|GLG1_ENST00000447066.2_Missense_Mutation_p.S1141N	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	1152					blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						GATGCTCCCACTGATCACAGA	0.502																																					p.S1152N		Atlas-SNP	.											.	GLG1	106	.	0			c.G3455A						PASS	.						242	202	216					16																	74487150		2198	4300	6498	SO:0001583	missense	2734	exon26			CTCCCACTGATCA		CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"golgi apparatus protein 1"			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.3455G>A	chr16.hg19:g.74487150C>T	ENSP00000405984:p.Ser1152Asn	133.0	0.0	.		142.0	52.0	.	NM_001145667	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Missense_Mutation	SNP	ENST00000422840.2	hg19	CCDS45527.1	.	.	.	.	.	.	.	.	.	.	C	9.147	1.015288	0.19355	.	.	ENSG00000090863	ENST00000205061;ENST00000447066;ENST00000422840	.	.	.	5.54	3.53	0.40419	.	0.247900	0.47093	D	0.000242	T	0.15869	0.0382	N	0.08118	0	0.22693	N	0.998846	B;B;B;B	0.21520	0.0;0.057;0.0;0.0	B;B;B;B	0.18871	0.0;0.023;0.0;0.0	T	0.12426	-1.0548	9	0.26408	T	0.33	-17.7364	5.7869	0.18338	0.1097:0.6149:0.1891:0.0863	.	282;1152;1152;1141	Q6ZMF1;Q92896;Q92896-2;B7Z8Y4	.;GSLG1_HUMAN;.;.	N	1152;1141;1152	.	ENSP00000205061:S1152N	S	-	2	0	GLG1	73044651	0.946000	0.32159	0.986000	0.45419	0.757000	0.42996	1.676000	0.37565	1.339000	0.45563	-0.346000	0.07831	AGT	.	.	.	none		0.502	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201		T	74487150	C	T	74487150	3	4	205	1	0	0	0	0	1	0	0	0	6443	565	20	2	168	2	GLG1	16	74487150	Missense_Mutation	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10	6219252	74487150	15867603	95	12462											
CENPN	55839	hgsc.bcm.edu	37	chr16	81060147	81060147	+	Missense_Mutation	SNP	T	T	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	atagtggattcaaggatcatTcatgaaaacatagtagaaaa	19	10	8	4	0	3	2	3	1	0	1	3	4	3	4	0	2	1	1	0	2	8	5			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr16:81060147T>G	ENST00000305850.5	+	9	1504	c.714T>G	c.(712-714)atT>atG	p.I238M	RP11-303E16.3_ENST00000561808.1_RNA|CENPN_ENST00000439957.3_Missense_Mutation_p.I218M|RP11-303E16.3_ENST00000566390.1_RNA|RP11-303E16.3_ENST00000562315.1_RNA|CENPN_ENST00000428963.2_Missense_Mutation_p.I204M|CENPN_ENST00000393335.3_Missense_Mutation_p.I238M	NM_001100624.2|NM_001270474.1	NP_001094094.2|NP_001257403.1	Q96H22	CENPN_HUMAN	centromere protein N	238					CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|large_intestine(5)|lung(4)	10						CAAGGATCATTCATGAAAACA	0.343																																					p.I238M		Atlas-SNP	.											CENPN_ENST00000439957,NS,lymphoid_neoplasm,0,3	CENPN	84	.	0			c.T714G						PASS	.						88	84	85					16																	81060147		1815	4073	5888	SO:0001583	missense	55839	exon9			GATCATTCATGAA	AK026313	CCDS10931.1, CCDS42199.1, CCDS42200.1, CCDS58482.1, CCDS58483.1	16q23.2	2013-11-05	2006-06-15	2006-06-15	ENSG00000166451	ENSG00000166451			30873	protein-coding gene	gene with protein product		611509	"chromosome 16 open reading frame 60"	C16orf60		16622419	Standard	NM_001100625		Approved	FLJ13607, FLJ22660, BM039	uc002ffy.4	Q96H22	OTTHUMG00000137628	ENST00000305850.5:c.714T>G	chr16.hg19:g.81060147T>G	ENSP00000305608:p.Ile238Met	252.0	0.0	.		260.0	104.0	.	NM_001100624	A8MZE6|B3KN53|B4DJD1|B4DPY7|C9JJM5|D3DUK8|E7ES30|E7ETS3|Q9NZ83	Missense_Mutation	SNP	ENST00000305850.5	hg19	CCDS42200.1	.	.	.	.	.	.	.	.	.	.	T	12.36	1.915992	0.33815	.	.	ENSG00000166451	ENST00000305850;ENST00000439957;ENST00000393335;ENST00000428963	T;T;T;T	0.22539	1.95;1.95;1.95;1.95	5.25	2.99	0.34606	.	0.607838	0.18923	N	0.127436	T	0.28333	0.0700	L	0.57536	1.79	0.22142	N	0.999337	P;P;P;P	0.51147	0.627;0.681;0.942;0.681	P;P;P;P	0.52309	0.5;0.581;0.695;0.581	T	0.08186	-1.0734	10	0.41790	T	0.15	-9.6647	7.0343	0.24985	0.1146:0.131:0.0:0.7544	.	218;204;238;238	E7ETS3;E7ES30;A8MZE6;Q96H22	.;.;.;CENPN_HUMAN	M	238;218;238;204	ENSP00000305608:I238M;ENSP00000395235:I218M;ENSP00000377007:I238M;ENSP00000393991:I204M	ENSP00000305608:I238M	I	+	3	3	CENPN	79617648	1.000000	0.71417	0.998000	0.56505	0.691000	0.40173	0.720000	0.25896	0.156000	0.19299	-1.967000	0.00467	ATT	.	.	.	none		0.343	CENPN-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269051.1	NM_018455		G	81060147	T	G	81060147	3	3	205	1	0	0	0	0	1	0	0	0	3240	1771	62	5	832	5	CENPN	16	81060147	Missense_Mutation	SNP	T	TCGA-IA-A83S-01A-11D-A34Z-10	6572997	81060147	9294606	96	12463											
SHPK	23729	hgsc.bcm.edu	37	chr17	3526658	3526658	+	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	tacgttccagctttggctctGcgtgttgaaatagccccagc	7	12	10	12	2	1	1	0	1	1	0	2	1	2	1	3	1	5	4	3	1	3	5			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr17:3526658G>A	ENST00000225519.3	-	4	724	c.622C>T	c.(622-624)Cag>Tag	p.Q208*		NM_013276.2	NP_037408	Q9UHJ6	SHPK_HUMAN	sedoheptulokinase	208					carbohydrate metabolic process (GO:0005975)|cellular response to interleukin-13 (GO:0035963)|cellular response to interleukin-4 (GO:0071353)|cellular response to lipopolysaccharide (GO:0071222)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|phosphorylation (GO:0016310)|regulation of inflammatory response (GO:0050727)|regulation of macrophage activation (GO:0043030)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|sedoheptulokinase activity (GO:0050277)			breast(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				COAD - Colon adenocarcinoma(5;0.0828)		CTTTGGCTCTGCGTGTTGAAA	0.562																																					p.Q208X		Atlas-SNP	.											.	SHPK	34	.	0			c.C622T						PASS	.						167	150	156					17																	3526658		2203	4300	6503	SO:0001587	stop_gained	23729	exon4			GGCTCTGCGTGTT	AF163573	CCDS11030.1	17p13	2008-02-08	2008-02-08	2008-02-08	ENSG00000197417	ENSG00000197417	2.7.1.14		1492	protein-coding gene	gene with protein product		605060	"carbohydrate kinase-like"	CARKL		10673275, 18186520	Standard	NM_013276		Approved	SHK	uc002fvz.1	Q9UHJ6	OTTHUMG00000090694	ENST00000225519.3:c.622C>T	chr17.hg19:g.3526658G>A	ENSP00000225519:p.Gln208*	98.0	0.0	.		86.0	23.0	.	NM_013276	B2R640|Q8WUH3	Nonsense_Mutation	SNP	ENST00000225519.3	hg19	CCDS11030.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.885948	0.91814	.	.	ENSG00000197417	ENST00000225519	.	.	.	5.15	0.667	0.17907	.	0.788742	0.11854	N	0.523030	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	-0.7028	4.2396	0.10642	0.0832:0.1092:0.4512:0.3564	.	.	.	.	X	208	.	ENSP00000225519:Q208X	Q	-	1	0	SHPK	3473407	0.281000	0.24258	0.676000	0.29932	0.912000	0.54170	1.047000	0.30367	0.656000	0.30886	0.561000	0.74099	CAG	.	.	.	none		0.562	SHPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207378.2			A	3526658	G	A	3526658	4	1	205	1	0	0	0	0	0	1	0	0	14303	1328	46	2	830	2	SHPK	17	3526658	Nonsense_Mutation	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10		3526658	77668552	97	12464											
USP6	9098	hgsc.bcm.edu	37	chr17	5071273	5071273	+	Missense_Mutation	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	gcagagtcggcgagcgcaagCcgagcccatcaacctggaca	11	3	13	14	4	1	1	1	0	0	1	2	4	1	2	3	2	4	2	3	2	2	0			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr17:5071273C>T	ENST00000574788.1	+	34	5313	c.3083C>T	c.(3082-3084)gCc>gTc	p.A1028V	USP6_ENST00000304328.5_Missense_Mutation_p.A711V|USP6_ENST00000250066.6_Missense_Mutation_p.A1028V|USP6_ENST00000332776.4_3'UTR			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	1028	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						CGAGCGCAAGCCGAGCCCATC	0.532			T	"COL1A1, CDH11, ZNF9, OMD"	aneurysmal bone cysts																																p.A1028V		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	.	USP6	213	.	0			c.C3083T						PASS	.						59	58	58					17																	5071273		2203	4300	6503	SO:0001583	missense	9098	exon26			CGCAAGCCGAGCC	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.3083C>T	chr17.hg19:g.5071273C>T	ENSP00000460380:p.Ala1028Val	116.0	0.0	.		139.0	25.0	.	NM_004505	Q15634|Q86WP6|Q8IWT4	Missense_Mutation	SNP	ENST00000574788.1	hg19	CCDS11069.2	.	.	.	.	.	.	.	.	.	.	C	14.85	2.657489	0.47467	.	.	ENSG00000129204	ENST00000250066;ENST00000304328	T;T	0.14391	2.9;2.51	2.35	2.35	0.29111	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.26412	0.0645	L	0.46741	1.465	0.48632	D	0.999683	D;D	0.71674	0.998;0.987	D;D	0.80764	0.994;0.939	T	0.01617	-1.1311	10	0.59425	D	0.04	.	10.4068	0.44266	0.0:1.0:0.0:0.0	.	711;1028	P35125-2;P35125	.;UBP6_HUMAN	V	1028;711	ENSP00000250066:A1028V;ENSP00000305473:A711V	ENSP00000250066:A1028V	A	+	2	0	USP6	5011997	1.000000	0.71417	0.998000	0.56505	0.338000	0.28826	7.512000	0.81728	1.313000	0.45069	0.184000	0.17185	GCC	.	.	.	none		0.532	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505		T	5071273	C	T	5071273	3	4	205	1	0	0	0	0	1	0	0	0	17098	739	26	2	3181	2	USP6	17	5071273	Missense_Mutation	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10	1544615	5071273	76123937	98	12465											
ALOX12	239	hgsc.bcm.edu	37	chr17	6899465	6899465	+	Frame_Shift_Del	DEL	C	C	-																															ctaccgcatccgcgtggccaCcggggcctggctcttctccg																										TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr17:6899465delC	ENST00000251535.6	+	1	82	c.29delC	c.(28-30)accfs	p.T10fs	AC027763.2_ENST00000399541.2_Intron|RP11-589P10.7_ENST00000572547.1_RNA|RP11-589P10.5_ENST00000573222.1_lincRNA	NM_000697.2	NP_000688.2	P18054	LOX12_HUMAN	arachidonate 12-lipoxygenase	10	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				aging (GO:0007568)|arachidonic acid metabolic process (GO:0019369)|cellular component movement (GO:0006928)|cellular response to lipid (GO:0071396)|establishment of skin barrier (GO:0061436)|fatty acid oxidation (GO:0019395)|hepoxilin biosynthetic process (GO:0051122)|hepoxilin metabolic process (GO:0051121)|leukotriene A4 metabolic process (GO:1901751)|linoleic acid metabolic process (GO:0043651)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxin B4 biosynthetic process (GO:2001306)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of platelet aggregation (GO:0090331)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|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 endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of gene expression (GO:0010628)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|superoxide anion generation (GO:0042554)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|sarcolemma (GO:0042383)	arachidonate 12-lipoxygenase activity (GO:0004052)|hepoxilin A3 synthase activity (GO:0051120)|hepoxilin-epoxide hydrolase activity (GO:0047977)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(3)|urinary_tract(1)	19						CGCGTGGCCACCGGGGCCTGG	0.756																																					p.T10fs		Atlas-Indel,Pindel	.											.	ALOX12	49	.	0			c.28delA						PASS	.						4	4	4					17																	6899465		1668	3237	4905	SO:0001589	frameshift_variant	239	exon1			.	M35418	CCDS11084.1	17p13.1	2010-01-14			ENSG00000108839	ENSG00000108839	1.13.11.31	"Arachidonate lipoxygenases"	429	protein-coding gene	gene with protein product	"platelet 12-LOX"	152391				1570320	Standard	NM_000697		Approved	12S-LOX	uc002gdx.4	P18054	OTTHUMG00000102088	ENST00000251535.6:c.29delC	chr17.hg19:g.6899465delC	ENSP00000251535:p.Thr10fs	161.0	0.0	0		132.0	30.0	0.227273	NM_000697	O95569|Q6ISF8|Q9UQM4	Frame_Shift_Del	DEL	ENST00000251535.6	hg19	CCDS11084.1																																																																																			.	.	.	none		0.756	ALOX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219922.2			-	6899465	C	-	6899465	7	5	205	1	0	1	0	1	0	0	0	0	536	507	18	0	31	0	ALOX12	17	6899465	Frame_Shift_Del	DEL	C	TCGA-IA-A83S-01A-11D-A34Z-10	1828192	6899465	74295745	99	12466											
DLG4	1742	hgsc.bcm.edu	37	chr17	7106870	7106870	+	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	gccgctgagtgggtcacctcGcgcacgtccacttcatttac	6	10	10	15	4	2	1	2	1	0	0	4	1	3	1	3	1	1	2	3	1	1	3			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr17:7106870G>A	ENST00000399506.2	-	6	569	c.378C>T	c.(376-378)cgC>cgT	p.R126R	DLG4_ENST00000302955.6_Silent_p.R123R|DLG4_ENST00000399510.2_Silent_p.R169R|DLG4_ENST00000485100.1_Silent_p.R123R			P78352	DLG4_HUMAN	discs, large homolog 4 (Drosophila)	126	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|axon guidance (GO:0007411)|dendritic spine morphogenesis (GO:0060997)|establishment of protein localization (GO:0045184)|learning (GO:0007612)|locomotory exploration behavior (GO:0035641)|negative regulation of receptor internalization (GO:0002091)|nervous system development (GO:0007399)|neuromuscular process controlling balance (GO:0050885)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synaptic transmission (GO:0050806)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|receptor localization to synapse (GO:0097120)|regulation of grooming behavior (GO:2000821)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|signal transduction (GO:0007165)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vocalization behavior (GO:0071625)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|juxtaparanode region of axon (GO:0044224)|neuron projection terminus (GO:0044306)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	acetylcholine receptor binding (GO:0033130)|beta-1 adrenergic receptor binding (GO:0031697)|D1 dopamine receptor binding (GO:0031748)|ionotropic glutamate receptor binding (GO:0035255)|P2Y1 nucleotide receptor binding (GO:0031812)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein phosphatase binding (GO:0019903)|scaffold protein binding (GO:0097110)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)	18					Guanidine(DB00536)	GGGTCACCTCGCGCACGTCCA	0.622																																					p.R169R		Atlas-SNP	.											DLG4_ENST00000302955,NS,carcinoma,0,2	DLG4	110	.	0			c.C507T						PASS	.						35	40	39					17																	7106870		2056	4183	6239	SO:0001819	synonymous_variant	1742	exon8			CACCTCGCGCACG	U83192	CCDS45599.1, CCDS45600.1	17p13.1	2008-12-15	2001-12-04		ENSG00000132535	ENSG00000132535			2903	protein-coding gene	gene with protein product		602887				9286702	Standard	NM_001128827		Approved	PSD-95, PSD95, SAP90, SAP-90	uc010cly.3	P78352	OTTHUMG00000134327	ENST00000399506.2:c.378C>T	chr17.hg19:g.7106870G>A		43.0	0.0	.		31.0	8.0	.	NM_001365	B7Z1S1|G5E939|Q92941|Q9UKK8	Silent	SNP	ENST00000399506.2	hg19																																																																																				.	.	.	none		0.622	DLG4-002	KNOWN	non_canonical_TEC|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000259419.2	NM_001365		A	7106870	G	A	7106870	2	1	205	1	0	0	0	0	0	0	0	1	4559	1074	38	1		1	DLG4	17	7106870	Silent	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	207405	7106870	74088340	100	12467											
RAI1	10743	hgsc.bcm.edu	37	chr17	17697241	17697241	+	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	gctactgccagccggacgcaGccgtccggaccccagagcag	8	3	13	17	4	0	1	0	0	0	1	1	3	1	3	6	2	5	3	6	2	1	1			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr17:17697241G>T	ENST00000353383.1	+	3	1448	c.979G>T	c.(979-981)Gcc>Tcc	p.A327S	RAI1_ENST00000261641.6_Missense_Mutation_p.A327S	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	327	Gln-rich.				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)		GCCGGACGCAGCCGTCCGGAC	0.642																																					p.A327S		Atlas-SNP	.											.	RAI1	121	.	0			c.G979T						PASS	.						60	75	70					17																	17697241		2203	4300	6503	SO:0001583	missense	10743	exon3			GACGCAGCCGTCC	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.979G>T	chr17.hg19:g.17697241G>T	ENSP00000323074:p.Ala327Ser	51.0	0.0	.		48.0	11.0	.	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Missense_Mutation	SNP	ENST00000353383.1	hg19	CCDS11188.1	.	.	.	.	.	.	.	.	.	.	G	4.494	0.091621	0.08632	.	.	ENSG00000108557	ENST00000353383;ENST00000395774;ENST00000395776;ENST00000355970;ENST00000261641;ENST00000315321	T;T;T	0.25414	1.8;1.8;1.8	5.55	2.35	0.29111	.	0.294557	0.33753	N	0.004581	T	0.14485	0.0350	N	0.19112	0.55	0.24098	N	0.995885	B	0.14012	0.009	B	0.14023	0.01	T	0.16928	-1.0386	10	0.51188	T	0.08	.	6.7903	0.23695	0.1908:0.3483:0.4608:0.0	.	327	Q7Z5J4	RAI1_HUMAN	S	327;327;327;327;327;304	ENSP00000323074:A327S;ENSP00000379120:A327S;ENSP00000261641:A327S	ENSP00000261641:A327S	A	+	1	0	RAI1	17637966	0.127000	0.22367	0.027000	0.17364	0.221000	0.24807	0.574000	0.23714	0.711000	0.32018	0.561000	0.74099	GCC	.	.	.	none		0.642	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665		T	17697241	G	T	17697241	3	4	205	1	0	0	0	0	1	0	0	0	13020	971	34	4	981	4	RAI1	17	17697241	Missense_Mutation	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	10590371	17697241	63497969	101	12468											
ALDH3A2	224	hgsc.bcm.edu	37	chr17	19564524	19564524	+	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	ttaagaggatactaagtttgCttgaaggacaaaagatagct	16	11	10	4	0	0	3	0	1	0	2	0	5	0	5	0	2	3	3	0	2	7	6			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr17:19564524C>A	ENST00000176643.6	+	6	1329	c.883C>A	c.(883-885)Ctt>Att	p.L295I	ALDH3A2_ENST00000581518.1_Missense_Mutation_p.L295I|ALDH3A2_ENST00000579855.1_Missense_Mutation_p.L295I|SNORA31_ENST00000516540.1_RNA|ALDH3A2_ENST00000571163.1_5'Flank|ALDH3A2_ENST00000395575.2_Missense_Mutation_p.L295I|ALDH3A2_ENST00000339618.4_Missense_Mutation_p.L295I			P51648	AL3A2_HUMAN	aldehyde dehydrogenase 3 family, member A2	295					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)					ACTAAGTTTGCTTGAAGGACA	0.368																																					p.L295I		Atlas-SNP	.											.	ALDH3A2	41	.	0			c.C883A						PASS	.						84	79	80					17																	19564524		2203	4300	6503	SO:0001583	missense	224	exon6			AGTTTGCTTGAAG	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.883C>A	chr17.hg19:g.19564524C>A	ENSP00000176643:p.Leu295Ile	88.0	0.0	.		90.0	26.0	.	NM_001031806	Q6I9T3|Q93011|Q96J37	Missense_Mutation	SNP	ENST00000176643.6	hg19	CCDS11210.1	.	.	.	.	.	.	.	.	.	.	C	12.11	1.839363	0.32513	.	.	ENSG00000072210	ENST00000176643;ENST00000395575;ENST00000339618	T;T;T	0.73681	-0.77;-0.77;-0.77	5.91	5.91	0.95273	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.044427	0.85682	D	0.000000	T	0.68320	0.2988	L	0.45051	1.395	0.80722	D	1	B;B	0.16603	0.018;0.014	B;B	0.26969	0.074;0.075	T	0.61312	-0.7088	10	0.26408	T	0.33	-23.027	14.1492	0.65370	0.1497:0.8503:0.0:0.0	.	295;295	P51648;P51648-2	AL3A2_HUMAN;.	I	295	ENSP00000176643:L295I;ENSP00000378942:L295I;ENSP00000345774:L295I	ENSP00000176643:L295I	L	+	1	0	ALDH3A2	19505116	0.959000	0.32827	1.000000	0.80357	0.978000	0.69477	0.014000	0.13333	2.803000	0.96430	0.650000	0.86243	CTT	.	.	.	none		0.368	ALDH3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132268.1			A	19564524	C	A	19564524	3	1	205	1	0	0	0	0	1	0	0	0	498	797	28	4	905	4	ALDH3A2	17	19564524	Missense_Mutation	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10	1867283	19564524	61630686	102	12469											
ATP6V0A1	535	hgsc.bcm.edu	37	chr17	40647714	40647714	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctggagtgtttggtggaccaTacccttttggcattgatcca	7	14	11	9	0	0	1	0	1	0	0	1	3	1	3	3	4	1	2	3	4	1	5			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr17:40647714T>C	ENST00000343619.4	+	14	1663	c.1540T>C	c.(1540-1542)Tac>Cac	p.Y514H	ATP6V0A1_ENST00000537728.1_Missense_Mutation_p.Y471H|ATP6V0A1_ENST00000264649.6_Missense_Mutation_p.Y521H|RP11-194N12.2_ENST00000591343.1_RNA|ATP6V0A1_ENST00000544137.1_Missense_Mutation_p.Y160H|MIR548AT_ENST00000578714.1_RNA|ATP6V0A1_ENST00000393829.2_Missense_Mutation_p.Y514H|ATP6V0A1_ENST00000546249.1_Missense_Mutation_p.Y514H|ATP6V0A1_ENST00000585525.1_Missense_Mutation_p.Y471H	NM_001130021.1	NP_001123493.1	Q93050	VPP1_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a1	514					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)		TGGTGGACCATACCCTTTTGG	0.433																																					p.Y521H		Atlas-SNP	.											.	ATP6V0A1	67	.	0			c.T1561C						PASS	.						84	66	72					17																	40647714		2203	4300	6503	SO:0001583	missense	535	exon14			GGACCATACCCTT	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.1540T>C	chr17.hg19:g.40647714T>C	ENSP00000342951:p.Tyr514His	78.0	0.0	.		67.0	17.0	.	NM_001130020	B7Z3B7|Q8N5G7|Q9NSX0	Missense_Mutation	SNP	ENST00000343619.4	hg19	CCDS45684.1	.	.	.	.	.	.	.	.	.	.	T	33	5.195566	0.94960	.	.	ENSG00000033627	ENST00000343619;ENST00000546249;ENST00000393829;ENST00000264649;ENST00000537728;ENST00000544137	D;D;D;D;D;D	0.91407	-2.84;-2.84;-2.84;-2.84;-2.84;-2.84	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.97340	0.9130	H	0.98218	4.175	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.997;0.999	D;D;D;D;D	0.91635	0.996;0.999;0.999;0.966;0.994	D	0.98763	1.0725	10	0.87932	D	0	-21.8156	16.6288	0.85011	0.0:0.0:0.0:1.0	.	471;471;521;514;514	B7Z641;B7Z2A9;B7Z3B7;Q93050;Q93050-1	.;.;.;VPP1_HUMAN;.	H	514;514;514;521;471;160	ENSP00000342951:Y514H;ENSP00000444676:Y514H;ENSP00000377415:Y514H;ENSP00000264649:Y521H;ENSP00000443991:Y471H;ENSP00000446377:Y160H	ENSP00000264649:Y521H	Y	+	1	0	ATP6V0A1	37901240	1.000000	0.71417	0.982000	0.44146	0.974000	0.67602	8.012000	0.88631	2.326000	0.78906	0.533000	0.62120	TAC	.	.	.	none		0.433	ATP6V0A1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450364.1	NM_001130020		C	40647714	T	C	40647714	3	2	205	1	0	0	0	0	1	0	0	0	1168	1406	49	3	1611	3	ATP6V0A1	17	40647714	Missense_Mutation	SNP	T	TCGA-IA-A83S-01A-11D-A34Z-10	21083190	40647714	40547496	103	12470											
NBR1	4077	hgsc.bcm.edu	37	chr17	41353793	41353793	+	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	tcagtccctgatcagatcagAggaggtaatgatcagcctaa	13	9	10	9	0	4	4	4	2	0	2	5	5	5	5	2	2	1	1	2	2	2	2			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr17:41353793A>T	ENST00000422280.1	+	18	3018	c.2559A>T	c.(2557-2559)agA>agT	p.R853S	NBR1_ENST00000389312.4_Missense_Mutation_p.R853S|NBR1_ENST00000341165.6_Missense_Mutation_p.R853S|NBR1_ENST00000589872.1_Missense_Mutation_p.R853S|NBR1_ENST00000542611.1_Missense_Mutation_p.R832S|NBR1_ENST00000590996.1_Missense_Mutation_p.R853S	NM_031858.2	NP_114064.1	Q14596	NBR1_HUMAN	neighbor of BRCA1 gene 1	853					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)		ATCAGATCAGAGGAGGTAATG	0.433																																					p.R853S		Atlas-SNP	.											.	NBR1	55	.	0			c.A2559T						PASS	.						149	118	127					17																	41353793		1568	3582	5150	SO:0001583	missense	4077	exon18			GATCAGAGGAGGT	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.2559A>T	chr17.hg19:g.41353793A>T	ENSP00000411250:p.Arg853Ser	194.0	0.0	.		160.0	31.0	.	NM_031862	Q13173|Q15026|Q5J7Q8|Q96GB6|Q9NRF7	Missense_Mutation	SNP	ENST00000422280.1	hg19	CCDS45694.1	.	.	.	.	.	.	.	.	.	.	A	13.21	2.167954	0.38315	.	.	ENSG00000188554	ENST00000422280;ENST00000542611;ENST00000537493;ENST00000341165;ENST00000389312;ENST00000389311	T;T;T;T	0.55760	1.56;0.5;1.56;1.56	5.54	5.54	0.83059	.	.	.	.	.	T	0.67429	0.2892	M	0.64997	1.995	0.46631	D	0.999136	D;B;B	0.63880	0.993;0.08;0.017	D;B;B	0.72338	0.977;0.074;0.008	T	0.67473	-0.5662	9	0.45353	T	0.12	-18.4523	11.9929	0.53186	1.0:0.0:0.0:0.0	.	832;853;853	B7Z5R6;Q14596-2;Q14596	.;.;NBR1_HUMAN	S	853;832;104;853;853;853	ENSP00000411250:R853S;ENSP00000437545:R832S;ENSP00000343479:R853S;ENSP00000373963:R853S	ENSP00000343479:R853S	R	+	3	2	NBR1	38709319	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.322000	0.59215	2.327000	0.79052	0.533000	0.62120	AGA	.	.	.	none		0.433	NBR1-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453461.1	NM_005899		T	41353793	A	T	41353793	3	4	205	1	0	0	0	0	1	0	0	0	10207	301	11	5	2625	5	NBR1	17	41353793	Missense_Mutation	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10	706079	41353793	39841417	104	12471											
NFE2L1	4779	hgsc.bcm.edu	37	chr17	46136179	46136179	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctctgaaggcagttcttccTcttcttcctcctcctcttcc	3	16	5	17	0	5	1	0	1	5	0	10	1	10	1	5	1	0	3	5	1	1	5			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr17:46136179T>C	ENST00000362042.3	+	6	2111	c.1495T>C	c.(1495-1497)Tct>Cct	p.S499P	RP5-890E16.4_ENST00000583349.1_RNA|NFE2L1_ENST00000585291.1_Missense_Mutation_p.S469P|NFE2L1_ENST00000583378.1_Missense_Mutation_p.S300P|NFE2L1_ENST00000361665.3_Missense_Mutation_p.S488P|NFE2L1_ENST00000536222.1_Missense_Mutation_p.S343P|NFE2L1_ENST00000357480.5_Missense_Mutation_p.S469P|NFE2L1_ENST00000582155.1_Missense_Mutation_p.S311P	NM_003204.2	NP_003195.1	Q14494	NF2L1_HUMAN	nuclear factor, erythroid 2-like 1	499	Poly-Ser.				anatomical structure morphogenesis (GO:0009653)|erythrocyte differentiation (GO:0030218)|heme biosynthetic process (GO:0006783)|inflammatory response (GO:0006954)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)			cervix(1)|endometrium(3)|kidney(9)|large_intestine(7)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						CAGttcttcctcttcttcctc	0.537																																					p.S499P		Atlas-SNP	.											.	NFE2L1	60	.	0			c.T1495C						PASS	.						85	84	84					17																	46136179		2203	4300	6503	SO:0001583	missense	4779	exon6			TCTTCCTCTTCTT	AK090459	CCDS11524.1	17q21.3	2013-08-23	2013-08-23			ENSG00000082641		"basic leucine zipper proteins"	7781	protein-coding gene	gene with protein product		163260	"nuclear factor (erythroid-derived 2)-like 1"	TCF11		8248256, 9501099	Standard	NM_003204		Approved	NRF1, LCR-F1, FLJ00380	uc002imz.4	Q14494		ENST00000362042.3:c.1495T>C	chr17.hg19:g.46136179T>C	ENSP00000354855:p.Ser499Pro	40.0	0.0	.		53.0	18.0	.	NM_003204	D3DTU3|D3DTU5|Q12877|Q96FN6	Missense_Mutation	SNP	ENST00000362042.3	hg19	CCDS11524.1	.	.	.	.	.	.	.	.	.	.	T	10.16	1.272865	0.23221	.	.	ENSG00000082641	ENST00000362042;ENST00000361665;ENST00000357480;ENST00000536222	T;T	0.38240	1.15;1.15	3.45	3.45	0.39498	.	0.195954	0.32785	N	0.005651	T	0.48077	0.1480	L	0.52573	1.65	0.50039	D	0.999841	P;P;P;D	0.54601	0.945;0.909;0.945;0.967	D;P;P;D	0.68621	0.959;0.665;0.82;0.939	T	0.39251	-0.9623	10	0.41790	T	0.15	-6.8658	8.8827	0.35384	0.0:0.0:0.0:1.0	.	343;311;469;499	F5H1B7;B4DYE1;Q14494-2;Q14494	.;.;.;NF2L1_HUMAN	P	518;499;469;343	ENSP00000350072:S469P;ENSP00000445811:S343P	ENSP00000350072:S469P	S	+	1	0	NFE2L1	43491178	0.998000	0.40836	0.808000	0.32385	0.295000	0.27426	2.390000	0.44416	1.545000	0.49373	0.460000	0.39030	TCT	.	.	.	none		0.537	NFE2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443019.1	NM_003204		C	46136179	T	C	46136179	3	2	205	1	0	0	0	0	1	0	0	0	10374	1551	54	3	1513	3	NFE2L1	17	46136179	Missense_Mutation	SNP	T	TCGA-IA-A83S-01A-11D-A34Z-10	4782386	46136179	35059031	105	12472											
ACE	1636	hgsc.bcm.edu	37	chr17	61573760	61573760	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcgctctgctccaggtactTtgtcagcttcatcatccagt	6	14	7	14	1	4	0	3	0	1	0	7	0	6	0	2	1	3	4	2	1	1	3			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr17:61573760T>C	ENST00000290866.4	+	23	3410	c.3386T>C	c.(3385-3387)tTt>tCt	p.F1129S	ACE_ENST00000490216.2_Missense_Mutation_p.F555S|ACE_ENST00000413513.3_Intron|ACE_ENST00000577647.1_Missense_Mutation_p.F555S|ACE_ENST00000290863.6_Missense_Mutation_p.F555S|ACE_ENST00000428043.1_Missense_Mutation_p.F1129S|ACE_ENST00000421982.2_Intron	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	1129	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)	TCCAGGTACTTTGTCAGCTTC	0.617																																					p.F1129S		Atlas-SNP	.											.	ACE	187	.	0			c.T3386C						PASS	.						101	97	98					17																	61573760		2203	4300	6503	SO:0001583	missense	1636	exon23			GGTACTTTGTCAG	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.3386T>C	chr17.hg19:g.61573760T>C	ENSP00000290866:p.Phe1129Ser	86.0	0.0	.		105.0	32.0	.	NM_000789	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Missense_Mutation	SNP	ENST00000290866.4	hg19	CCDS11637.1	.	.	.	.	.	.	.	.	.	.	T	11.78	1.740370	0.30865	.	.	ENSG00000159640	ENST00000290866;ENST00000428043;ENST00000290863	T;T;T	0.47528	0.84;0.84;0.84	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.77638	0.4160	H	0.95437	3.67	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	D	0.84953	0.0872	10	0.87932	D	0	-25.0283	14.67	0.68937	0.0:0.0:0.0:1.0	.	555;1129	P12821-3;P12821	.;ACE_HUMAN	S	1129;1129;555	ENSP00000290866:F1129S;ENSP00000397593:F1129S;ENSP00000290863:F555S	ENSP00000290863:F555S	F	+	2	0	ACE	58927492	1.000000	0.71417	0.891000	0.34965	0.277000	0.26821	6.174000	0.71943	1.938000	0.56188	0.397000	0.26171	TTT	.	.	.	none		0.617	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2			C	61573760	T	C	61573760	3	2	205	1	0	0	0	0	1	0	0	0	136	1841	64	3	3679	3	ACE	17	61573760	Missense_Mutation	SNP	T	TCGA-IA-A83S-01A-11D-A34Z-10	15437581	61573760	19621450	106	12473											
THOC1	9984	hgsc.bcm.edu	37	chr18	267995	267995	+	Frame_Shift_Del	DEL	T	T	-																															cgtccgcgcttcgggcaaacTgaagagcggcggcgtcggag																										TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr18:267995delT	ENST00000261600.6	-	1	32	c.25delA	c.(25-27)agtfs	p.S9fs	RP11-705O1.8_ENST00000581677.1_lincRNA|THOC1_ENST00000582313.1_5'UTR	NM_005131.2	NP_005122.2	Q96FV9	THOC1_HUMAN	THO complex 1	9					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)				TCGGGCAAACTGAAGAGCGGC	0.647																																					p.S9fs		Atlas-Indel,Pindel	.											.	THOC1	43	.	0			c.26delG						PASS	.						18	23	21					18																	267995		1948	4131	6079	SO:0001589	frameshift_variant	9984	exon1			.	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.25delA	chr18.hg19:g.267995delT	ENSP00000261600:p.Ser9fs	44.0	0.0	0		58.0	16.0	0.275862	NM_005131	B2RBP6|Q15219|Q64I72|Q64I73	Frame_Shift_Del	DEL	ENST00000261600.6	hg19	CCDS45820.1																																																																																			.	.	.	none		0.647	THOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440348.5	NM_005131		-	267995	T	-	267995	7	5	205	1	0	1	0	1	0	0	0	0	15876	1580	55	0	2032	0	THOC1	18	267995	Frame_Shift_Del	DEL	T	TCGA-IA-A83S-01A-11D-A34Z-10		267995	77809253	107	12474											
LPIN2	9663	hgsc.bcm.edu	37	chr18	2927795	2927795	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcatcttgtctttcacccaGgactcaactgtggcctgaaa	9	11	9	12	0	4	1	2	1	2	0	4	2	4	2	2	3	1	1	2	3	2	2			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr18:2927795G>A	ENST00000261596.4	-	12	1873	c.1635C>T	c.(1633-1635)tcC>tcT	p.S545S		NM_014646.2	NP_055461.1	Q92539	LPIN2_HUMAN	lipin 2	545					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)		CTTTCACCCAGGACTCAACTG	0.498																																					p.S545S		Atlas-SNP	.											.	LPIN2	75	.	0			c.C1635T						PASS	.						124	115	118					18																	2927795		2203	4300	6503	SO:0001819	synonymous_variant	9663	exon12			CACCCAGGACTCA	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.1635C>T	chr18.hg19:g.2927795G>A		151.0	0.0	.		134.0	24.0	.	NM_014646	A7MD25|D3DUH3	Silent	SNP	ENST00000261596.4	hg19	CCDS11829.1																																																																																			.	.	.	none		0.498	LPIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254363.2	NM_014646		A	2927795	G	A	2927795	2	1	205	1	0	0	0	0	0	0	0	1	8926	987	35	2		2	LPIN2	18	2927795	Silent	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	2659800	2927795	75149453	108	12475											
SOCS6	9306	hgsc.bcm.edu	37	chr18	67992989	67992989	+	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	aagagtttatgactcagtgcAaagtagtggtcccatggttg	11	12	12	6	0	1	2	1	1	0	1	2	2	2	2	1	2	1	4	1	2	4	4			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr18:67992989A>T	ENST00000397942.3	+	2	1401	c.1085A>T	c.(1084-1086)cAa>cTa	p.Q362L	SOCS6_ENST00000582322.1_Missense_Mutation_p.Q362L	NM_004232.3	NP_004223.2	O14544	SOCS6_HUMAN	suppressor of cytokine signaling 6	362					defense response (GO:0006952)|JAK-STAT cascade (GO:0007259)|negative regulation of signal transduction (GO:0009968)|negative regulation of T cell activation (GO:0050868)|proteasomal protein catabolic process (GO:0010498)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|immunological synapse (GO:0001772)				NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)	22		Esophageal squamous(42;0.129)|Colorectal(73;0.152)				GACTCAGTGCAAAGTAGTGGT	0.493																																					p.Q362L	Melanoma(84;1024 1361 24382 36583 42651)	Atlas-SNP	.											.	SOCS6	54	.	0			c.A1085T						PASS	.						84	81	82					18																	67992989		2203	4300	6503	SO:0001583	missense	9306	exon2			CAGTGCAAAGTAG	AB006968	CCDS11998.1	18q22	2013-02-14	2004-02-25	2004-02-27	ENSG00000170677	ENSG00000170677		"Suppressors of cytokine signaling", "SH2 domain containing"	16833	protein-coding gene	gene with protein product		605118	"suppressor of cytokine signaling 4"	SOCS4		9344848, 11042152	Standard	NM_004232		Approved	CIS4, SSI4, HSPC060, STATI4, STAI4, Cish4	uc002lkr.1	O14544	OTTHUMG00000132816	ENST00000397942.3:c.1085A>T	chr18.hg19:g.67992989A>T	ENSP00000381034:p.Gln362Leu	72.0	0.0	.		88.0	18.0	.	NM_004232	Q8WUM3	Missense_Mutation	SNP	ENST00000397942.3	hg19	CCDS11998.1	.	.	.	.	.	.	.	.	.	.	A	19.24	3.789933	0.70337	.	.	ENSG00000170677	ENST00000397942	T	0.24908	1.83	5.34	5.34	0.76211	.	0.000000	0.64402	D	0.000001	T	0.22975	0.0555	L	0.32530	0.975	0.58432	D	0.999999	P	0.35714	0.517	B	0.35550	0.205	T	0.04165	-1.0972	10	0.66056	D	0.02	-11.4417	15.3465	0.74343	1.0:0.0:0.0:0.0	.	362	O14544	SOCS6_HUMAN	L	362	ENSP00000381034:Q362L	ENSP00000381034:Q362L	Q	+	2	0	SOCS6	66143969	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	7.210000	0.77924	2.029000	0.59856	0.459000	0.35465	CAA	.	.	.	none		0.493	SOCS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256270.2			T	67992989	A	T	67992989	3	4	205	1	0	0	0	0	1	0	0	0	14931	130	5	5	1087	5	SOCS6	18	67992989	Missense_Mutation	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10	65065194	67992989	10084259	109	12476											
CIRBP	1153	hgsc.bcm.edu	37	chr19	1272031	1272031	+	Missense_Mutation	SNP	A	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	agctcgggcgggtcctacagAgacagttatgacagttacgg	10	8	14	9	3	0	2	0	1	0	1	2	3	1	2	1	3	3	3	1	3	3	3			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr19:1272031A>C	ENST00000588030.1	+	6	743	c.483A>C	c.(481-483)agA>agC	p.R161S	CIRBP_ENST00000587896.1_Missense_Mutation_p.R161S|CIRBP-AS1_ENST00000600215.1_RNA|C19orf24_ENST00000409293.4_5'Flank|CIRBP-AS1_ENST00000585832.1_RNA|CIRBP_ENST00000588090.1_Missense_Mutation_p.R161S|CIRBP_ENST00000591935.1_Missense_Mutation_p.R161S|CIRBP_ENST00000589686.1_Missense_Mutation_p.R161S|CIRBP_ENST00000589660.1_Missense_Mutation_p.R161S|CIRBP_ENST00000587323.1_Missense_Mutation_p.R161S|CIRBP_ENST00000413636.2_Missense_Mutation_p.R127S|CIRBP_ENST00000585630.1_Missense_Mutation_p.R161S|CIRBP_ENST00000588230.1_Missense_Mutation_p.R161S|CIRBP_ENST00000320936.5_Missense_Mutation_p.R161S|CIRBP_ENST00000586773.1_Missense_Mutation_p.R161S|CIRBP_ENST00000589710.1_Missense_Mutation_p.R161S|CIRBP_ENST00000589235.1_Missense_Mutation_p.R161S|CIRBP_ENST00000444172.2_Missense_Mutation_p.R108S|CIRBP_ENST00000586472.1_Missense_Mutation_p.R161S			Q14011	CIRBP_HUMAN	cold inducible RNA binding protein	161					mRNA stabilization (GO:0048255)|positive regulation of translation (GO:0045727)|response to cold (GO:0009409)|response to UV (GO:0009411)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|small ribosomal subunit rRNA binding (GO:0070181)|translation repressor activity (GO:0030371)			endometrium(1)|large_intestine(1)|lung(3)	5		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000332)|all_lung(49;0.000498)|Breast(49;0.0014)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGTCCTACAGAGACAGTTATG	0.592																																					p.R161S		Atlas-SNP	.											.	CIRBP	19	.	0			c.A483C						PASS	.						129	109	116					19																	1272031		2203	4300	6503	SO:0001583	missense	1153	exon6			CTACAGAGACAGT	D78134	CCDS12059.1, CCDS74244.1, CCDS74245.1	19p13.3	2013-02-12	2001-11-28		ENSG00000099622	ENSG00000099622		"RNA binding motif (RRM) containing"	1982	protein-coding gene	gene with protein product	"Cold-inducible RNA-binding protein", "glycine-rich RNA binding protein"	602649	"cold inducible RNA-binding protein"			9434172, 9151692	Standard	NM_001280		Approved	CIRP	uc002lrr.4	Q14011		ENST00000588030.1:c.483A>C	chr19.hg19:g.1272031A>C	ENSP00000468788:p.Arg161Ser	154.0	0.0	.		110.0	35.0	.	NM_001280	B3KT17|B4E2X2	Missense_Mutation	SNP	ENST00000588030.1	hg19	CCDS12059.1	.	.	.	.	.	.	.	.	.	.	A	13.13	2.144678	0.37825	.	.	ENSG00000099622	ENST00000320936;ENST00000413636;ENST00000444172	T;T	0.71579	0.11;-0.58	4.78	2.68	0.31781	.	0.000000	0.85682	D	0.000000	T	0.78874	0.4352	M	0.65975	2.015	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.80764	0.994;0.994;0.981	T	0.76162	-0.3060	10	0.87932	D	0	-21.1913	6.8142	0.23820	0.7263:0.0:0.2737:0.0	.	127;161;161	B4E2X2;D6W5Y5;Q14011	.;.;CIRBP_HUMAN	S	161;127;108	ENSP00000322887:R161S;ENSP00000412831:R127S	ENSP00000322887:R161S	R	+	3	2	CIRBP	1223031	1.000000	0.71417	0.999000	0.59377	0.261000	0.26267	1.005000	0.29834	0.220000	0.20860	0.260000	0.18958	AGA	.	.	.	none		0.592	CIRBP-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449969.1	NM_001280		C	1272031	A	C	1272031	3	2	205	1	0	0	0	0	1	0	0	0	3435	301	11	5	501	5	CIRBP	19	1272031	Missense_Mutation	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10		1272031	57856952	110	12477											
GTF2F1	2962	hgsc.bcm.edu	37	chr19	6387445	6387445	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcagtgagcgtgcgatgcCgggccagcggtgtgaaattg	7	7	18	9	5	0	2	0	2	0	0	0	3	0	2	2	3	4	1	2	3	1	1			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr19:6387445C>T	ENST00000394456.5	-	5	916	c.452G>A	c.(451-453)cGg>cAg	p.R151Q	GTF2F1_ENST00000429701.2_Intron|CTB-180A7.6_ENST00000599584.1_RNA	NM_002096.2	NP_002087.2	P35269	T2FA_HUMAN	general transcription factor IIF, polypeptide 1, 74kDa	151					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						CGTGCGATGCCGGGCCAGCGG	0.627																																					p.R151Q		Atlas-SNP	.											.	GTF2F1	39	.	0			c.G452A						PASS	.						127	116	120					19																	6387445		2203	4300	6503	SO:0001583	missense	2962	exon5			CGATGCCGGGCCA		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.452G>A	chr19.hg19:g.6387445C>T	ENSP00000377969:p.Arg151Gln	67.0	0.0	.		48.0	11.0	.	NM_002096	B2RCS0|Q9BWN0	Missense_Mutation	SNP	ENST00000394456.5	hg19	CCDS12165.1	.	.	.	.	.	.	.	.	.	.	C	17.17	3.320920	0.60634	.	.	ENSG00000125651	ENST00000394456;ENST00000542045	T	0.43294	0.95	5.39	3.24	0.37175	Transcription Factor IIF, Rap30/Rap74, interaction (1);	0.212725	0.39475	N	0.001358	T	0.20414	0.0491	N	0.22421	0.69	0.80722	D	1	B	0.27932	0.194	B	0.19666	0.026	T	0.11542	-1.0583	10	0.02654	T	1	-22.0428	7.1332	0.25512	0.0:0.6463:0.0:0.3537	.	151	P35269	T2FA_HUMAN	Q	151;211	ENSP00000377969:R151Q	ENSP00000377969:R151Q	R	-	2	0	GTF2F1	6338445	1.000000	0.71417	0.997000	0.53966	0.920000	0.55202	3.013000	0.49582	0.608000	0.30000	0.655000	0.94253	CGG	.	.	.	none		0.627	GTF2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398033.1	NM_002096		T	6387445	C	T	6387445	3	4	205	1	0	0	0	0	1	0	0	0	6865	652	23	1	1137	1	GTF2F1	19	6387445	Missense_Mutation	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10	5115414	6387445	52741538	111	12478											
MUC16	94025	hgsc.bcm.edu	37	chr19	9071193	9071194	+	Missense_Mutation	DNP	TG	TG	AA																															tcactgcggtgtttgtggaaTgatgcatggcggcttctgtg																										TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr19:9071193_9071194TG>AA	ENST00000397910.4	-	3	16455_16456	c.16252_16253CA>TT	c.(16252-16254)CAt>TTt	p.H5418F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5420	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						GTTTGTGGAATGATGCATGGCG	0.505																																					p.H5418L|p.H5418Y		Atlas-SNP	.											.	MUC16	4315	.	0			c.A16253T|c.C16252T						PASS	.																																			SO:0001583	missense	94025	exon3			GTGGAATGATGCA|TGGAATGATGCAT	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.16252_16253delinsAA	chr19.hg19:g.9071193_9071194delinsAA	ENSP00000381008:p.His5418Phe	159.0|162.0	0.0	.		183.0	48.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.	.	none		0.505	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		AA	9071194	TG	AA	9071193	3	1	205	1	0	0	0	0	1	0	0	0	9980	1464	51	5	27598	5	MUC16	19	9071193	Missense_Mutation	DNP	TG	TCGA-IA-A83S-01A-11D-A34Z-10	2683748	9071193	50057790	112	12479											
COL5A3	50509	hgsc.bcm.edu	37	chr19	10106262	10106262	+	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	tcttgcccactcggccagggGgtccatgaggtccctgcagg	5	8	14	14	1	1	1	0	1	1	0	4	1	3	1	4	5	2	1	4	5	0	1			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr19:10106262G>T	ENST00000264828.3	-	16	1650	c.1565C>A	c.(1564-1566)cCc>cAc	p.P522H	CTD-2553C6.1_ENST00000592332.1_RNA	NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	522	Collagen-like 2.|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)			TCGGCCAGGGGGTCCATGAGG	0.512																																					p.P522H		Atlas-SNP	.											.	COL5A3	243	.	0			c.C1565A						PASS	.						61	54	56					19																	10106262		2203	4300	6503	SO:0001583	missense	50509	exon16			CCAGGGGGTCCAT	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.1565C>A	chr19.hg19:g.10106262G>T	ENSP00000264828:p.Pro522His	40.0	0.0	.		41.0	9.0	.	NM_015719	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	hg19	CCDS12222.1	.	.	.	.	.	.	.	.	.	.	G	15.17	2.753677	0.49362	.	.	ENSG00000080573	ENST00000264828	D	0.96967	-4.19	5.06	5.06	0.68205	.	0.411439	0.21579	N	0.072270	D	0.97964	0.9330	M	0.83012	2.62	0.46901	D	0.999248	D	0.89917	1.0	D	0.77004	0.989	D	0.98171	1.0452	10	0.56958	D	0.05	.	14.2733	0.66164	0.0:0.0:1.0:0.0	.	522	P25940	CO5A3_HUMAN	H	522	ENSP00000264828:P522H	ENSP00000264828:P522H	P	-	2	0	COL5A3	9967262	0.986000	0.35501	0.986000	0.45419	0.895000	0.52256	1.924000	0.40065	2.519000	0.84933	0.655000	0.94253	CCC	.	.	.	none		0.512	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719		T	10106262	G	T	10106262	3	4	205	1	0	0	0	0	1	0	0	0	3700	1232	43	4	3880	4	COL5A3	19	10106262	Missense_Mutation	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	1035069	10106262	49022721	113	12480											
UNC13A	23025	hgsc.bcm.edu	37	chr19	17720812	17720812	+	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	tggatttggtcgcaaacttgCgtttcttgtcgctgagctgg	5	15	13	8	3	1	1	0	1	1	0	3	2	1	2	0	3	3	4	0	3	1	4			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr19:17720812C>T	ENST00000519716.2	-	43	4747	c.4748G>A	c.(4747-4749)cGc>cAc	p.R1583H	UNC13A_ENST00000551649.1_Missense_Mutation_p.R1602H|UNC13A_ENST00000252773.7_Missense_Mutation_p.R1583H|UNC13A_ENST00000552293.1_Missense_Mutation_p.R1577H|UNC13A_ENST00000550896.1_Missense_Mutation_p.R1556H|UNC13A_ENST00000428389.2_Missense_Mutation_p.R1671H	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	1583	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						CGCAAACTTGCGTTTCTTGTC	0.527																																					p.R1583H		Atlas-SNP	.											.	UNC13A	299	.	0			c.G4748A						PASS	.						145	153	150					19																	17720812		2079	4234	6313	SO:0001583	missense	23025	exon41			AACTTGCGTTTCT	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.4748G>A	chr19.hg19:g.17720812C>T	ENSP00000429562:p.Arg1583His	117.0	0.0	.		90.0	18.0	.	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	hg19	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	C	26.7	4.759588	0.89932	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	T;T;T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.38;-0.38;-0.38	4.13	4.13	0.48395	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	U	0.000000	T	0.78648	0.4316	M	0.62154	1.92	0.51767	D	0.999935	D	0.89917	1.0	D	0.97110	1.0	T	0.81099	-0.1086	10	0.66056	D	0.02	-15.6131	13.9527	0.64129	0.0:1.0:0.0:0.0	.	1583	Q9UPW8	UN13A_HUMAN	H	1583;1671;1583;1602;1577;1556	ENSP00000429562:R1583H;ENSP00000400409:R1671H;ENSP00000252773:R1583H;ENSP00000447236:R1602H;ENSP00000447572:R1577H;ENSP00000446831:R1556H	ENSP00000252773:R1583H	R	-	2	0	UNC13A	17581812	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.691000	0.84191	1.869000	0.54173	0.478000	0.44815	CGC	.	.	.	none		0.527	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		T	17720812	C	T	17720812	3	4	205	1	0	0	0	0	1	0	0	0	16996	768	27	1	371	1	UNC13A	19	17720812	Missense_Mutation	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10	7614550	17720812	41408171	114	12481											
NLRP7	199713	hgsc.bcm.edu	37	chr19	55447667	55447667	+	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	catttatgatttctgagcagGtcacacagcatcagcatcat	12	12	7	10	0	4	2	3	2	1	0	4	2	4	2	0	1	3	3	0	1	1	3			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr19:55447667G>T	ENST00000590030.1	-	5	2302	c.2262C>A	c.(2260-2262)gaC>gaA	p.D754E	NLRP7_ENST00000592784.1_Missense_Mutation_p.D754E|NLRP7_ENST00000588756.1_Missense_Mutation_p.D754E|NLRP7_ENST00000340844.2_Missense_Mutation_p.D754E|NLRP7_ENST00000446217.1_Missense_Mutation_p.D782E|NLRP7_ENST00000328092.5_Missense_Mutation_p.D726E|NLRP7_ENST00000448121.2_Missense_Mutation_p.D726E			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	754							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)		TTCTGAGCAGGTCACACAGCA	0.577																																					p.D754E		Atlas-SNP	.											.	NLRP7	411	.	0			c.C2262A						PASS	.						136	102	114					19																	55447667		2203	4300	6503	SO:0001583	missense	199713	exon6			GAGCAGGTCACAC	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.2262C>A	chr19.hg19:g.55447667G>T	ENSP00000465520:p.Asp754Glu	69.0	0.0	.		81.0	22.0	.	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	hg19	CCDS33109.1	.	.	.	.	.	.	.	.	.	.	g	0.004	-2.281893	0.00251	.	.	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217;ENST00000399724	T;T;T	0.51071	0.72;0.72;0.72	2.31	-2.58	0.06228	.	1.603560	0.04433	N	0.369540	T	0.18509	0.0444	N	0.05306	-0.075	0.09310	N	1	B;B;B;B	0.13145	0.004;0.004;0.004;0.007	B;B;B;B	0.08055	0.002;0.002;0.002;0.003	T	0.16364	-1.0405	10	0.02654	T	1	.	1.8101	0.03089	0.199:0.301:0.3702:0.1298	.	782;754;754;726	E7EPM2;Q32MH9;Q8WX94;Q8WX94-2	.;.;NALP7_HUMAN;.	E	754;726;754;782;521	ENSP00000409137:D726E;ENSP00000339491:D754E;ENSP00000414273:D782E	ENSP00000329568:D754E	D	-	3	2	NLRP7	60139479	0.021000	0.18746	0.000000	0.03702	0.001000	0.01503	-0.000000	0.12993	-0.524000	0.06400	-2.688000	0.00140	GAC	.	.	.	none		0.577	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		T	55447667	G	T	55447667	3	4	205	1	0	0	0	0	1	0	0	0	10489	1252	44	4	875	4	NLRP7	19	55447667	Missense_Mutation	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	37726855	55447667	3681316	115	12482											
ZNF551	90233	hgsc.bcm.edu	37	chr19	58199244	58199244	+	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	cacaagaccttatgagtgcaGtgaatgtggcaaatctttta	13	12	9	7	0	1	3	0	2	1	1	1	3	1	3	1	1	1	2	1	1	5	3			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr19:58199244G>T	ENST00000282296.5	+	3	1786	c.1601G>T	c.(1600-1602)aGt>aTt	p.S534I	AC003006.7_ENST00000594684.1_Intron|ZNF551_ENST00000356715.4_Missense_Mutation_p.S518I|AC003006.7_ENST00000599221.1_Intron|ZNF551_ENST00000596085.1_Intron			Q7Z340	ZN551_HUMAN	zinc finger protein 551	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)			endometrium(4)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)	15		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		TATGAGTGCAGTGAATGTGGC	0.443																																					p.S534I		Atlas-SNP	.											.	ZNF551	65	.	0			c.G1601T						PASS	.						86	81	83					19																	58199244		2203	4300	6503	SO:0001583	missense	90233	exon3			AGTGCAGTGAATG	BX538151	CCDS12959.1, CCDS12959.2	19q13.43	2013-09-20			ENSG00000204519	ENSG00000204519		"Zinc fingers, C2H2-type", "-"	25108	protein-coding gene	gene with protein product							Standard	NM_138347		Approved	DKFZp686H1038	uc002qpw.5	Q7Z340	OTTHUMG00000183470	ENST00000282296.5:c.1601G>T	chr19.hg19:g.58199244G>T	ENSP00000282296:p.Ser534Ile	82.0	0.0	.		67.0	16.0	.	NM_138347	B4DU22|P17034|Q8N246|Q9BRY1	Missense_Mutation	SNP	ENST00000282296.5	hg19	CCDS12959.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.02|12.02	1.811290|1.811290	0.32053|0.32053	.|.	.|.	ENSG00000204519|ENSG00000228006	ENST00000356715;ENST00000282296;ENST00000359821|ENST00000541705	.|.	.|.	.|.	2.31|2.31	-3.52|-3.52	0.04682|0.04682	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);|.	.|1.745300	.|0.03889	.|U	.|0.278446	T|T	0.47710|0.47710	0.1460|0.1460	M|M	0.73430|0.73430	2.235|2.235	0.09310|0.09310	N|N	1|1	D|.	0.64830|.	0.994|.	D|.	0.73708|.	0.981|.	T|T	0.31833|0.31833	-0.9929|-0.9929	7|7	.|0.17369	.|T	.|0.5	.|.	5.7017|5.7017	0.17885|0.17885	0.2834:0.4143:0.3024:0.0|0.2834:0.4143:0.3024:0.0	.|.	534|.	Q7Z340|.	ZN551_HUMAN|.	I|N	534;518;317|54	.|.	.|ENSP00000437781:T54N	S|T	+|-	2|2	0|0	ZNF551|AC004017.1	62891056|62891056	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-4.012000|-4.012000	0.00314|0.00314	-1.099000|-1.099000	0.03034|0.03034	-1.134000|-1.134000	0.01955|0.01955	AGT|ACT	.	.	.	none		0.443	ZNF551-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466803.2	NM_138347		T	58199244	G	T	58199244	3	4	205	1	0	0	0	0	1	0	0	0	17995	1029	36	4	1563	4	ZNF551	19	58199244	Missense_Mutation	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	2751577	58199244	929739	116	12483											
C20orf194	25943	hgsc.bcm.edu	37	chr20	3305593	3305593	+	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	aatctaacccagatcccagaGtttgctctgctacctccttg	9	12	6	14	0	2	2	0	0	2	2	4	2	4	2	4	0	4	3	4	0	3	4	rs190605250		TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr20:3305593G>C	ENST00000252032.9	-	14	1278	c.1211C>G	c.(1210-1212)aCt>aGt	p.T404S	C20orf194_ENST00000453730.2_Missense_Mutation_p.T142S	NM_001009984.2	NP_001009984.1	Q5TEA3	CT194_HUMAN	chromosome 20 open reading frame 194	404										NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	39						AGATCCCAGAGTTTGCTCTGC	0.418																																					p.T404S		Atlas-SNP	.											.	C20orf194	83	.	0			c.C1211G						PASS	.						100	106	104					20																	3305593		1866	4105	5971	SO:0001583	missense	25943	exon14			CCCAGAGTTTGCT	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.1211C>G	chr20.hg19:g.3305593G>C	ENSP00000252032:p.Thr404Ser	75.0	0.0	.		59.0	5.0	.	NM_001009984	Q66K86|Q6P2R9|Q9UFX9	Missense_Mutation	SNP	ENST00000252032.9	hg19	CCDS42851.1	.	.	.	.	.	.	.	.	.	.	G	14.14	2.446795	0.43429	.	.	ENSG00000088854	ENST00000252032;ENST00000453730	T;T	0.33216	2.23;1.42	5.34	4.39	0.52855	.	0.175484	0.49305	D	0.000147	T	0.31040	0.0784	L	0.60455	1.87	0.37681	D	0.9235	B;B	0.10296	0.003;0.001	B;B	0.12156	0.007;0.007	T	0.19811	-1.0294	10	0.39692	T	0.17	.	12.9761	0.58538	0.0789:0.0:0.9211:0.0	.	143;404	Q0IIP3;Q5TEA3	.;CT194_HUMAN	S	404;142	ENSP00000252032:T404S;ENSP00000407229:T142S	ENSP00000252032:T404S	T	-	2	0	C20orf194	3253593	0.758000	0.28405	0.993000	0.49108	0.986000	0.74619	1.707000	0.37888	1.479000	0.48272	0.655000	0.94253	ACT	.	G|1.000;A|0.000	.	alt		0.418	C20orf194-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077734.1	NM_001009984		C	3305593	G	C	3305593	3	2	205	1	0	0	0	0	1	0	0	0	2101	1029	36	4	2418	4	C20orf194	20	3305593	Missense_Mutation	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10		3305593	59719927	117	12484											
RALGAPB	57148	hgsc.bcm.edu	37	chr20	37159824	37159824	+	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	ttgtaggggcaatgttaaatAttgttcaagattcagcactt	12	15	9	5	0	2	1	2	0	0	1	2	1	2	1	0	2	1	5	0	2	6	8			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr20:37159824A>T	ENST00000262879.6	+	14	2349	c.2065A>T	c.(2065-2067)Att>Ttt	p.I689F	RALGAPB_ENST00000397038.1_Missense_Mutation_p.I467F|RALGAPB_ENST00000397040.1_Missense_Mutation_p.I689F|RALGAPB_ENST00000397042.3_Missense_Mutation_p.I689F			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	689					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						AATGTTAAATATTGTTCAAGA	0.313																																					p.I689F		Atlas-SNP	.											.	RALGAPB	134	.	0			c.A2065T						PASS	.						116	114	115					20																	37159824		2203	4300	6503	SO:0001583	missense	57148	exon14			TTAAATATTGTTC	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.2065A>T	chr20.hg19:g.37159824A>T	ENSP00000262879:p.Ile689Phe	127.0	0.0	.		130.0	34.0	.	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Missense_Mutation	SNP	ENST00000262879.6	hg19	CCDS13305.1	.	.	.	.	.	.	.	.	.	.	A	27.9	4.876802	0.91664	.	.	ENSG00000170471	ENST00000262879;ENST00000397042;ENST00000304939;ENST00000397038;ENST00000397040;ENST00000438490	.	.	.	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.60676	0.2287	L	0.40543	1.245	0.80722	D	1	D;D;D;D	0.57899	0.981;0.981;0.981;0.981	P;P;P;P	0.57101	0.813;0.813;0.813;0.813	T	0.54990	-0.8210	9	0.10111	T	0.7	.	15.8481	0.78907	1.0:0.0:0.0:0.0	.	517;689;689;689	A2A2F0;Q86X10-4;A2A2E9;Q86X10	.;.;.;RLGPB_HUMAN	F	689;689;689;467;689;517	.	ENSP00000262879:I689F	I	+	1	0	RALGAPB	36593238	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.574000	0.74014	2.149000	0.67028	0.397000	0.26171	ATT	.	.	.	none		0.313	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336		T	37159824	A	T	37159824	3	4	205	1	0	0	0	0	1	0	0	0	13028	449	16	5	2115	5	RALGAPB	20	37159824	Missense_Mutation	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10	33854231	37159824	25865696	118	12485											
L3MBTL	26013	hgsc.bcm.edu	37	chr20	42157990	42157990	+	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	caacacccgtccatgtacttCatcctcaccgtggctgaggt	8	10	8	15	2	2	1	2	1	0	0	4	1	4	1	4	2	2	2	4	2	2	2			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr20:42157990C>T	ENST00000427442.2	+	9	1131	c.972C>T	c.(970-972)ttC>ttT	p.F324F	L3MBTL1_ENST00000373134.1_Silent_p.F256F|L3MBTL1_ENST00000373135.3_Silent_p.F256F|L3MBTL1_ENST00000444063.1_Silent_p.F256F|L3MBTL1_ENST00000418998.1_Silent_p.F324F			Q9Y468	LMBL1_HUMAN	l(3)mbt-like 1 (Drosophila)	256					chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of mitosis (GO:0007088)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|nucleosome binding (GO:0031491)|SAM domain binding (GO:0032093)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(3)|ovary(1)|skin(2)	7						CCATGTACTTCATCCTCACCG	0.517																																					p.F324F		Atlas-SNP	.											.	L3MBTL1	105	.	0			c.C972T						PASS	.						191	121	145					20																	42157990		2203	4300	6503	SO:0001819	synonymous_variant	26013	exon9			GTACTTCATCCTC	U89358	CCDS13319.1, CCDS46602.1, CCDS46602.2	20q13.12	2013-01-10	2010-09-03	2010-09-03	ENSG00000185513	ENSG00000185513		"Zinc fingers, C2HC-type containing", "Sterile alpha motif (SAM) domain containing"	15905	protein-coding gene	gene with protein product	"lethal (3) malignant brain tumor l(3)"	608802	"l(3)mbt (Drosophila)-like", "l(3)mbt-like (Drosophila)"	L3MBTL		10445843, 17540172	Standard	NM_032107		Approved	ZC2HC3, dJ138B7.3, DKFZp586P1522, KIAA0681	uc010zwh.2	Q9Y468	OTTHUMG00000032503	ENST00000427442.2:c.972C>T	chr20.hg19:g.42157990C>T		58.0	0.0	.		71.0	26.0	.	NM_032107	B4DRC9|E1P5W7|Q5H8Y8|Q5H8Y9|Q8IUV7|Q9H1E6|Q9H1G5|Q9UG06|Q9UJB9|Q9Y4C9	Silent	SNP	ENST00000427442.2	hg19	CCDS46602.2																																																																																			.	.	.	none		0.517	L3MBTL1-007	KNOWN	upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079300.3	NM_032107		T	42157990	C	T	42157990	2	4	205	1	0	0	0	0	0	0	0	1	8598	825	29	2		2	L3MBTL	20	42157990	Silent	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10	4998166	42157990	20867530	119	12486											
CSE1L	1434	hgsc.bcm.edu	37	chr20	47686789	47686789	+	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	atggaaacttggatgaataaTtttcatactctcttaacatt	14	16	5	6	0	2	1	1	1	1	0	3	3	2	3	0	2	3	0	0	2	5	7			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr20:47686789T>A	ENST00000262982.2	+	8	846	c.723T>A	c.(721-723)aaT>aaA	p.N241K	CSE1L_ENST00000542325.1_Missense_Mutation_p.N24K|CSE1L_ENST00000396192.3_Missense_Mutation_p.N241K	NM_001256135.1|NM_001316.3	NP_001243064.1|NP_001307.2	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like (yeast)	241					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	importin-alpha export receptor activity (GO:0008262)			breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(11)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	35			BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)			GGATGAATAATTTTCATACTC	0.284																																					p.N241K		Atlas-SNP	.											.	CSE1L	83	.	0			c.T723A						PASS	.						69	80	77					20																	47686789		2198	4298	6496	SO:0001583	missense	1434	exon8			GAATAATTTTCAT	U33286	CCDS13412.1, CCDS58773.1	20q13	2013-05-01	2001-11-28		ENSG00000124207	ENSG00000124207		"Exportins"	2431	protein-coding gene	gene with protein product	"cellular apoptosis susceptibility"	601342	"chromosome segregation 1 (yeast homolog)-like"			8963895, 7479798	Standard	NM_001316		Approved	CAS, XPO2, CSE1	uc002xty.4	P55060	OTTHUMG00000033046	ENST00000262982.2:c.723T>A	chr20.hg19:g.47686789T>A	ENSP00000262982:p.Asn241Lys	87.0	0.0	.		82.0	23.0	.	NM_001256135	A3RLL6|B2R5T4|E1P5Y0|F8W904|O75432|Q32M40|Q9H5B7|Q9NTS0|Q9UP98|Q9UP99|Q9UPA0	Missense_Mutation	SNP	ENST00000262982.2	hg19	CCDS13412.1	.	.	.	.	.	.	.	.	.	.	T	14.79	2.639615	0.47153	.	.	ENSG00000124207	ENST00000417408;ENST00000262982;ENST00000542325;ENST00000396192	T;T;T	0.66280	-0.2;-0.2;-0.2	5.42	2.91	0.33838	Armadillo-like helical (1);Armadillo-type fold (1);Exportin/Importin, Cse1-like (1);	0.000000	0.85682	D	0.000000	T	0.55481	0.1923	L	0.39898	1.24	0.58432	D	0.999999	P;B;P	0.44344	0.833;0.418;0.737	P;B;P	0.49140	0.499;0.236;0.601	T	0.46076	-0.9217	10	0.11182	T	0.66	-24.0938	9.6613	0.39956	0.0:0.2852:0.0:0.7148	.	24;241;241	B4DUC5;F8W904;P55060	.;.;XPO2_HUMAN	K	7;241;24;241	ENSP00000262982:N241K;ENSP00000446477:N24K;ENSP00000379495:N241K	ENSP00000262982:N241K	N	+	3	2	CSE1L	47120196	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	0.762000	0.26503	0.354000	0.24105	0.482000	0.46254	AAT	.	.	.	none		0.284	CSE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080345.2	NM_001316		A	47686789	T	A	47686789	3	1	205	1	0	0	0	0	1	0	0	0	3932	1490	52	5	749	5	CSE1L	20	47686789	Missense_Mutation	SNP	T	TCGA-IA-A83S-01A-11D-A34Z-10	5528799	47686789	15338731	120	12487											
PCK1	5105	hgsc.bcm.edu	37	chr20	56137813	56137813	+	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	ggctcgcctctgtcaaagatCggcatcgagctgacggattc	8	9	12	12	4	2	2	1	1	1	1	6	4	2	3	1	3	1	3	1	3	1	1	rs144907840	byFrequency	TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr20:56137813C>A	ENST00000319441.4	+	4	632	c.468C>A	c.(466-468)atC>atA	p.I156I	PCK1_ENST00000543666.1_Intron|PCK1_ENST00000535860.1_Silent_p.I24I	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	156					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			TGTCAAAGATCGGCATCGAGC	0.617																																					p.I156I		Atlas-SNP	.											.	PCK1	95	.	0			c.C468A						PASS	.						68	56	60					20																	56137813		2203	4300	6503	SO:0001819	synonymous_variant	5105	exon4			AAAGATCGGCATC		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.468C>A	chr20.hg19:g.56137813C>A		75.0	0.0	.		55.0	15.0	.	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Silent	SNP	ENST00000319441.4	hg19	CCDS13460.1																																																																																			.	C|1.000;T|0.000	.	alt		0.617	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2			A	56137813	C	A	56137813	2	1	205	1	0	0	0	0	0	0	0	1	11588	874	31	4		4	PCK1	20	56137813	Silent	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10	8451024	56137813	6887707	121	12488											
RNF160	26046	hgsc.bcm.edu	37	chr21	30339388	30339388	+	Missense_Mutation	SNP	T	T	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	ttgtgagctgttttttcatcTttttccgtgtctgctttggc	2	22	9	8	1	3	1	1	1	2	0	4	1	4	1	1	1	2	3	1	1	0	7			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr21:30339388T>G	ENST00000361371.5	-	10	1504	c.1425A>C	c.(1423-1425)aaA>aaC	p.K475N	LTN1_ENST00000389194.2_Missense_Mutation_p.K521N|LTN1_ENST00000389195.2_Missense_Mutation_p.K521N			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	475					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						TTTTTTCATCTTTTTCCGTGT	0.433																																					p.K521N		Atlas-SNP	.											.	LTN1	141	.	0			c.A1563C						PASS	.						173	153	160					21																	30339388		2203	4300	6503	SO:0001583	missense	26046	exon10			TTCATCTTTTTCC	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.1425A>C	chr21.hg19:g.30339388T>G	ENSP00000354977:p.Lys475Asn	202.0	0.0	.		180.0	33.0	.	NM_015565	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Missense_Mutation	SNP	ENST00000361371.5	hg19		.	.	.	.	.	.	.	.	.	.	T	7.074	0.568893	0.13560	.	.	ENSG00000198862	ENST00000389194;ENST00000361371;ENST00000446611;ENST00000389195	T;T;T	0.23950	2.22;2.23;1.88	5.02	2.38	0.29361	Armadillo-type fold (1);	0.380490	0.31566	N	0.007428	T	0.09512	0.0234	N	0.08118	0	0.29856	N	0.828004	B	0.02656	0.0	B	0.01281	0.0	T	0.23762	-1.0179	10	0.14252	T	0.57	.	3.8422	0.08918	0.1875:0.2734:0.0:0.5391	.	475	O94822	LTN1_HUMAN	N	521;475;477;521	ENSP00000373846:K521N;ENSP00000354977:K475N;ENSP00000373847:K521N	ENSP00000354977:K475N	K	-	3	2	LTN1	29261259	0.060000	0.20803	0.102000	0.21198	0.563000	0.35712	0.127000	0.15790	0.388000	0.25054	-0.256000	0.11100	AAA	.	.	.	none		0.433	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565		G	30339388	T	G	30339388	3	3	205	1	0	0	0	0	1	0	0	0	13468	1606	56	5	3959	5	RNF160	21	30339388	Missense_Mutation	SNP	T	TCGA-IA-A83S-01A-11D-A34Z-10		30339388	17790507	122	12489											
MX2	4600	hgsc.bcm.edu	37	chr21	42775260	42775260	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaatttttcaaccttaaccAaactgttcaggtaagcaccc	13	11	5	12	1	2	0	2	0	0	0	2	1	2	0	3	1	4	3	3	1	5	5			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr21:42775260A>G	ENST00000330714.3	+	12	1824	c.1640A>G	c.(1639-1641)cAa>cGa	p.Q547R		NM_002463.1	NP_002454.1	P20592	MX2_HUMAN	MX dynamin-like GTPase 2	547					cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|defense response to virus (GO:0051607)|GTP catabolic process (GO:0006184)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of nucleocytoplasmic transport (GO:0046822)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	34		Prostate(19;1.57e-07)|all_epithelial(19;0.0222)				AACCTTAACCAAACTGTTCAG	0.398																																					p.Q547R		Atlas-SNP	.											.	MX2	84	.	0			c.A1640G						PASS	.						72	69	70					21																	42775260		2203	4300	6503	SO:0001583	missense	4600	exon12			TTAACCAAACTGT		CCDS13672.1	21q22.3	2014-07-15	2014-07-15		ENSG00000183486	ENSG00000183486			7533	protein-coding gene	gene with protein product	"interferon-regulated resistance GTP-binding protein MXB", "second interferon-induced protein p78"	147890	"myxovirus (influenza) resistance 2, homolog of murine", "myxovirus (influenza virus) resistance 2 (mouse)"			2481229, 8798556	Standard	NM_002463		Approved	MXB	uc002yzf.1	P20592	OTTHUMG00000086753	ENST00000330714.3:c.1640A>G	chr21.hg19:g.42775260A>G	ENSP00000333657:p.Gln547Arg	128.0	0.0	.		105.0	24.0	.	NM_002463	B7Z5D3|D3DSI7	Missense_Mutation	SNP	ENST00000330714.3	hg19	CCDS13672.1	.	.	.	.	.	.	.	.	.	.	A	0.015	-1.540708	0.00934	.	.	ENSG00000183486	ENST00000330714	T	0.72835	-0.69	3.63	0.0676	0.14366	Dynamin central domain (1);	0.316592	0.32687	N	0.005766	T	0.36826	0.0981	N	0.04805	-0.155	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.31194	-0.9952	10	0.02654	T	1	.	5.4593	0.16607	0.5476:0.0:0.4524:0.0	.	547	P20592	MX2_HUMAN	R	547	ENSP00000333657:Q547R	ENSP00000333657:Q547R	Q	+	2	0	MX2	41697130	0.009000	0.17119	0.000000	0.03702	0.001000	0.01503	0.513000	0.22770	0.132000	0.18615	0.533000	0.62120	CAA	.	.	.	none		0.398	MX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195147.1	NM_002463		G	42775260	A	G	42775260	3	3	205	1	0	0	0	0	1	0	0	0	10005	130	5	3	1682	3	MX2	21	42775260	Missense_Mutation	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10	12435872	42775260	5354635	123	12490											
PFKL	5211	hgsc.bcm.edu	37	chr21	45744509	45744509	+	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	ccgacgccgcctacgtcttcGaggaccctttcaacatccac	8	8	7	18	5	2	0	1	0	1	0	4	3	3	1	5	1	2	0	5	1	2	3	rs138177950		TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr21:45744509G>A	ENST00000349048.4	+	17	1841	c.1786G>A	c.(1786-1788)Gag>Aag	p.E596K	PFKL_ENST00000403390.1_Missense_Mutation_p.E643K	NM_002626.4	NP_002617.3	P17858	PFKAL_HUMAN	phosphofructokinase, liver	596	C-terminal regulatory PFK domain 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 1,6-bisphosphate metabolic process (GO:0030388)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|negative regulation of insulin secretion (GO:0046676)|protein homotetramerization (GO:0051289)|protein oligomerization (GO:0051259)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	6-phosphofructokinase complex (GO:0005945)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|fructose binding (GO:0070061)|fructose-6-phosphate binding (GO:0070095)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	23				Colorectal(79;0.0811)		CTACGTCTTCGAGGACCCTTT	0.652																																					p.E596K		Atlas-SNP	.											.	PFKL	65	.	0			c.G1786A						PASS	.	G	LYS/GLU	0,4404		0,0,2202	67	64	65		1786	4.1	1	21	dbSNP_134	65	1,8599	1.2+/-3.3	0,1,4299	no	missense	PFKL	NM_002626.4	56	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	596/781	45744509	1,13003	2202	4300	6502	SO:0001583	missense	5211	exon17			GTCTTCGAGGACC		CCDS33582.1	21q22.3	1992-12-17			ENSG00000141959	ENSG00000141959	2.7.1.11		8876	protein-coding gene	gene with protein product		171860					Standard	NR_024108		Approved		uc002zel.3	P17858	OTTHUMG00000086910	ENST00000349048.4:c.1786G>A	chr21.hg19:g.45744509G>A	ENSP00000269848:p.Glu596Lys	32.0	0.0	.		54.0	14.0	.	NM_002626	Q96A64|Q96IH4|Q9BR91	Missense_Mutation	SNP	ENST00000349048.4	hg19	CCDS33582.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.066876	0.76301	0.0	1.16E-4	ENSG00000141959	ENST00000349048;ENST00000534847;ENST00000403390	D;D	0.93076	-3.16;-3.16	4.1	4.1	0.47936	Phosphofructokinase domain (2);	0.000000	0.85682	D	0.000000	D	0.97788	0.9274	H	0.97103	3.94	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.991	D	0.99312	1.0904	10	0.87932	D	0	-38.3049	15.126	0.72483	0.0:0.0:1.0:0.0	.	596;643	P17858;P17858-2	K6PL_HUMAN;.	K	596;389;643	ENSP00000269848:E596K;ENSP00000384038:E643K	ENSP00000269848:E596K	E	+	1	0	PFKL	44568937	1.000000	0.71417	0.962000	0.40283	0.118000	0.20060	9.323000	0.96364	1.852000	0.53769	0.467000	0.42956	GAG	.	G|1.000;A|0.000	0.000	weak		0.652	PFKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195805.1			A	45744509	G	A	45744509	3	1	205	1	0	0	0	0	1	0	0	0	11771	1059	37	1	1852	1	PFKL	21	45744509	Missense_Mutation	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	2969249	45744509	2385386	124	12491											
SREBF2	6721	hgsc.bcm.edu	37	chr22	42301503	42301503	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgccatcctgctggcctgcCgccacctgcccctctccttc	2	9	7	23	2	1	0	0	0	1	0	4	0	2	0	10	1	3	1	10	1	0	1	rs372007376		TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr22:42301503C>T	ENST00000361204.4	+	19	3431	c.3265C>T	c.(3265-3267)Cgc>Tgc	p.R1089C	SREBF2_ENST00000491541.1_3'UTR	NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	1089					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						GCTGGCCTGCCGCCACCTGCC	0.692																																					p.R1089C		Atlas-SNP	.											.	SREBF2	99	.	0			c.C3265T						PASS	.						8	9	9					22																	42301503		2135	4233	6368	SO:0001583	missense	6721	exon19			GCCTGCCGCCACC	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.3265C>T	chr22.hg19:g.42301503C>T	ENSP00000354476:p.Arg1089Cys	43.0	0.0	.		39.0	8.0	.	NM_004599	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Missense_Mutation	SNP	ENST00000361204.4	hg19	CCDS14023.1	.	.	.	.	.	.	.	.	.	.	C	34	5.301054	0.95601	.	.	ENSG00000198911	ENST00000361204;ENST00000457567;ENST00000543221	T	0.08370	3.1	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.23492	0.0568	L	0.41027	1.25	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.00154	-1.1981	10	0.42905	T	0.14	-22.1429	19.9374	0.97146	0.0:1.0:0.0:0.0	.	1089	Q12772	SRBP2_HUMAN	C	1089;1089;163	ENSP00000354476:R1089C	ENSP00000354476:R1089C	R	+	1	0	SREBF2	40631449	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.772000	0.55325	2.711000	0.92665	0.655000	0.94253	CGC	.	.	.	weak		0.692	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599		T	42301503	C	T	42301503	3	4	205	1	0	0	0	0	1	0	0	0	15154	652	23	1	3339	1	SREBF2	22	42301503	Missense_Mutation	SNP	C	TCGA-IA-A83S-01A-11D-A34Z-10		42301503	9003063	125	12492											
SBF1	6305	hgsc.bcm.edu	37	chr22	50903456	50903456	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaacaggtccgtagggcggtAtgggaccccacgctctgaca	9	6	14	12	3	1	1	0	1	1	0	2	3	2	2	3	4	1	3	3	4	3	2			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chr22:50903456A>G	ENST00000390679.3	-	12	1490	c.1306T>C	c.(1306-1308)Tac>Cac	p.Y436H	SBF1_ENST00000348911.6_Missense_Mutation_p.Y437H|SBF1_ENST00000380817.3_Missense_Mutation_p.Y436H			O95248	MTMR5_HUMAN	SET binding factor 1	436					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)		GTAGGGCGGTATGGGACCCCA	0.627																																					p.Y436H		Atlas-SNP	.											.	SBF1	211	.	0			c.T1306C						PASS	.						81	87	85					22																	50903456		2161	4249	6410	SO:0001583	missense	6305	exon12			GGCGGTATGGGAC	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.1306T>C	chr22.hg19:g.50903456A>G	ENSP00000375097:p.Tyr436His	41.0	0.0	.		43.0	8.0	.	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Missense_Mutation	SNP	ENST00000390679.3	hg19		.	.	.	.	.	.	.	.	.	.	A	16.91	3.251520	0.59212	.	.	ENSG00000100241	ENST00000380817;ENST00000348911;ENST00000356279;ENST00000337034;ENST00000390679	D;D;D	0.86562	-2.14;-2.14;-2.14	3.93	3.93	0.45458	.	0.162423	0.42420	D	0.000712	D	0.91516	0.7321	M	0.65498	2.005	0.58432	D	0.999999	D;D;D	0.76494	0.999;0.998;0.999	D;D;D	0.74023	0.982;0.93;0.961	D	0.91527	0.5239	10	0.51188	T	0.08	.	12.6118	0.56556	1.0:0.0:0.0:0.0	.	436;437;436	O95248;G5E933;O95248-4	MTMR5_HUMAN;.;.	H	436;437;447;446;436	ENSP00000370196:Y436H;ENSP00000252027:Y437H;ENSP00000375097:Y436H	ENSP00000336522:Y446H	Y	-	1	0	SBF1	49250322	1.000000	0.71417	0.830000	0.32933	0.288000	0.27193	7.086000	0.76885	1.650000	0.50662	0.533000	0.62120	TAC	.	.	.	none		0.627	SBF1-201	KNOWN	basic	protein_coding	protein_coding				G	50903456	A	G	50903456	3	3	205	1	0	0	0	0	1	0	0	0	13871	449	16	3	4495	3	SBF1	22	50903456	Missense_Mutation	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10	8601953	50903456	401110	126	12493											
GK	2710	hgsc.bcm.edu	37	chrX	30671708	30671708	+	Frame_Shift_Del	DEL	G	G	-																															ttggtgggggcggtggaccaGggcaccagttcgacgcgctt																										TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chrX:30671708delG	ENST00000378941.3	+	1	54	c.54delG	c.(52-54)cagfs	p.Q18fs	GK_ENST00000378943.3_Frame_Shift_Del_p.Q18fs|GK_ENST00000378945.3_Frame_Shift_Del_p.Q18fs|GK_ENST00000378946.3_Frame_Shift_Del_p.Q18fs|GK_ENST00000427190.1_5'UTR			P32189	GLPK_HUMAN	glycerol kinase	18					cellular lipid metabolic process (GO:0044255)|glucose homeostasis (GO:0042593)|glycerol catabolic process (GO:0019563)|glycerol metabolic process (GO:0006071)|glycerol-3-phosphate biosynthetic process (GO:0046167)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride metabolic process (GO:0006641)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	ATP binding (GO:0005524)|glycerol kinase activity (GO:0004370)			central_nervous_system(1)|large_intestine(3)	4						CGGTGGACCAGGGCACCAGTT	0.657																																					p.Q18fs		Atlas-Indel,Pindel	.											.	GK	95	.	0			c.53delA						PASS	.						57	57	57					X																	30671708		2202	4300	6502	SO:0001589	frameshift_variant	2710	exon1			.	X78711	CCDS14225.1, CCDS35224.1, CCDS48090.1, CCDS75963.1	Xp21.3	2014-09-17			ENSG00000198814	ENSG00000198814	2.7.1.30	"Glycerol kinases"	4289	protein-coding gene	gene with protein product		300474				7987308	Standard	NM_203391		Approved	GK1, GKD	uc022buj.1	P32189	OTTHUMG00000021328	ENST00000378941.3:c.54delG	chrX.hg19:g.30671708delG	ENSP00000368224:p.Gln18fs	108.0	0.0	0		95.0	51.0	0.536842	NM_203391	A6NJP5|B2R833|Q6IQ27|Q8IVR5|Q9UMP0|Q9UMP1	Frame_Shift_Del	DEL	ENST00000378941.3	hg19																																																																																				.	.	.	none		0.657	GK-005	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000056171.1	NM_000167		-	30671708	G	-	30671708	7	5	205	1	0	1	0	1	0	0	0	0	6427	991	35	0	56	0	GK	23	30671708	Frame_Shift_Del	DEL	G	TCGA-IA-A83S-01A-11D-A34Z-10		30671708	124598852	127	12494											
NUDT10	170685	hgsc.bcm.edu	37	chrX	51076122	51076122	+	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	gtatgtactgactgtcacggAgctgctggaggattgggaag	9	10	16	6	1	1	1	1	1	0	0	1	5	1	5	0	4	3	4	0	4	3	3			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chrX:51076122A>T	ENST00000376006.3	+	2	525	c.305A>T	c.(304-306)gAg>gTg	p.E102V	NUDT10_ENST00000356450.2_Missense_Mutation_p.E102V	NM_153183.2	NP_694853.1	Q9BW91	NUDT9_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 10	0					ADP catabolic process (GO:0046032)|IDP catabolic process (GO:0046709)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|mitochondrial matrix (GO:0005759)	adenosine-diphosphatase activity (GO:0043262)|ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)			cervix(1)|endometrium(8)|kidney(1)|large_intestine(1)|lung(1)|prostate(3)|upper_aerodigestive_tract(1)	16	Ovarian(276;0.236)					ACTGTCACGGAGCTGCTGGAG	0.562																																					p.E102V	NSCLC(90;1817 2035 37909 38249)	Atlas-SNP	.											.	NUDT10	28	.	0			c.A305T						PASS	.						70	65	67					X																	51076122		2203	4300	6503	SO:0001583	missense	170685	exon2			TCACGGAGCTGCT	AF469196	CCDS35278.1	Xp11.22-p11.1	2014-05-20			ENSG00000122824	ENSG00000122824		"Nudix motif containing"	17621	protein-coding gene	gene with protein product		300527				12105228	Standard	NM_153183		Approved	DIPP3a, hDIPP3alpha	uc004dph.3	Q8NFP7	OTTHUMG00000021530	ENST00000376006.3:c.305A>T	chrX.hg19:g.51076122A>T	ENSP00000365174:p.Glu102Val	216.0	0.0	.		222.0	107.0	.	NM_153183	Q8NBN1|Q8NCB9|Q8NG25	Missense_Mutation	SNP	ENST00000376006.3	hg19	CCDS35278.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.151107	0.78001	.	.	ENSG00000122824	ENST00000376006;ENST00000356450	T;T	0.08370	3.1;3.1	3.14	3.14	0.36123	NUDIX hydrolase domain (3);NUDIX hydrolase domain-like (1);	0.000000	0.85682	D	0.000000	T	0.25865	0.0630	M	0.84433	2.695	0.42409	D	0.992596	D	0.61080	0.989	P	0.61874	0.895	T	0.43861	-0.9365	9	0.87932	D	0	-2.7732	8.9702	0.35901	1.0:0.0:0.0:0.0	.	102	Q8NFP7	NUD10_HUMAN	V	102	ENSP00000365174:E102V;ENSP00000348831:E102V	ENSP00000348831:E102V	E	+	2	0	NUDT10	51092862	1.000000	0.71417	0.993000	0.49108	0.989000	0.77384	6.591000	0.74090	1.295000	0.44724	0.350000	0.21858	GAG	.	.	.	none		0.562	NUDT10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056578.1	NM_153183		T	51076122	A	T	51076122	3	4	205	1	0	0	0	0	1	0	0	0	10733	304	11	5	307	5	NUDT10	23	51076122	Missense_Mutation	SNP	A	TCGA-IA-A83S-01A-11D-A34Z-10	20404414	51076122	104194438	128	12495											
NXT2	55916	hgsc.bcm.edu	37	chrX	108779141	108779141	+	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	tacagaagccactggtctcaGggagacagagaaggatacca	15	5	12	9	0	1	3	1	0	1	3	2	6	1	4	2	3	3	0	2	3	4	2			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chrX:108779141G>A	ENST00000372106.1	+	0	0				NXT2_ENST00000372107.1_5'Flank|NXT2_ENST00000218004.1_Silent_p.Q10Q|NXT2_ENST00000372103.1_5'Flank	NM_001242617.1	NP_001229546.1	Q9NPJ8	NXT2_HUMAN	nuclear transport factor 2-like export factor 2						mRNA transport (GO:0051028)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|large_intestine(1)|lung(1)|ovary(1)	6						ACTGGTCTCAGGGAGACAGAG	0.403																																					p.Q10Q		Atlas-SNP	.											.	NXT2	16	.	0			c.G30A						PASS	.						60	54	56					X																	108779141		2203	4300	6503	SO:0001631	upstream_gene_variant	55916	exon1			GTCTCAGGGAGAC	AF246127	CCDS14546.1, CCDS56605.1, CCDS56606.1	Xq22.3	2008-02-05			ENSG00000101888	ENSG00000101888			18151	protein-coding gene	gene with protein product		300320				11073998	Standard	NM_018698		Approved	P15-2	uc004eoe.2	Q9NPJ8	OTTHUMG00000022185		chrX.hg19:g.108779141G>A	Exception_encountered	179.0	0.0	.		151.0	83.0	.	NM_018698	D3DUY1|Q0VAN8|Q5JYV5|Q5JYV6|Q5JYV7|Q9H8U0|Q9NQ64|Q9NRL7|Q9Y3M4|Q9Y3M5	Silent	SNP	ENST00000372106.1	hg19	CCDS56605.1																																																																																			.	.	.	none		0.403	NXT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057886.1	NM_018698		A	108779141	G	A	108779141	1	1	205	0	1	0	0	0	0	0	0	0	10802	991	35	2		2	NXT2	23	108779141	5'Flank	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	57703019	108779141	46491419	129	12496											
F8	2157	hgsc.bcm.edu	37	chrX	154159622	154159622	+	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	cccatgtggagtaggactctGtcgcaagagcatcaacaaat	13	8	10	10	1	2	1	1	0	1	1	3	3	2	3	1	2	2	3	1	2	4	1			TCGA-IA-A83S-01A-11D-A34Z-10	TCGA-IA-A83S-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	239993db-83a2-4300-9378-31070f75b60b	2d7ce817-8f00-4d31-b073-fca46cc77009	g.chrX:154159622G>A	ENST00000360256.4	-	14	2643	c.2443C>T	c.(2443-2445)Cag>Tag	p.Q815*		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	815	B.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	GTAGGACTCTGTCGCAAGAGC	0.408																																					p.Q815X		Atlas-SNP	.											.	F8	646	.	0			c.C2443T	GRCh37	CM011329	F8	M		PASS	.						210	193	199					X																	154159622		2203	4299	6502	SO:0001587	stop_gained	2157	exon14			GACTCTGTCGCAA	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.2443C>T	chrX.hg19:g.154159622G>A	ENSP00000353393:p.Gln815*	122.0	0.0	.		122.0	52.0	.	NM_000132	Q14286|Q5HY69	Nonsense_Mutation	SNP	ENST00000360256.4	hg19	CCDS35457.1	.	.	.	.	.	.	.	.	.	.	G	37	6.182840	0.97357	.	.	ENSG00000185010	ENST00000360256	.	.	.	5.37	4.49	0.54785	.	1.017170	0.07808	N	0.957575	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	-0.2379	11.2271	0.48890	0.0:0.1799:0.8201:0.0	.	.	.	.	X	815	.	ENSP00000353393:Q815X	Q	-	1	0	F8	153812816	0.652000	0.27349	0.868000	0.34077	0.032000	0.12392	1.555000	0.36277	1.028000	0.39785	0.544000	0.68410	CAG	.	.	.	none		0.408	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4			A	154159622	G	A	154159622	4	1	205	1	0	0	0	0	0	1	0	0	5352	1386	48	2	4692	2	F8	23	154159622	Nonsense_Mutation	SNP	G	TCGA-IA-A83S-01A-11D-A34Z-10	45380481	154159622	1110938	130	12497											
PRAMEF12	390999	hgsc.bcm.edu	37	chr1	12835275	12835275	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggaggggcttgatgcactgCttgcccagaaggttcgcccc	6	9	14	12	1	0	2	0	1	0	1	1	3	0	3	3	4	3	4	3	4	1	3	rs376821629		TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr1:12835275C>T	ENST00000357726.4	+	1	292	c.265C>T	c.(265-267)Ctt>Ttt	p.L89F		NM_001080830.1	NP_001074299.1	O95522	PRA12_HUMAN	PRAME family member 12	89					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					NS(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(9)|ovary(3)|skin(1)|urinary_tract(1)	23	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00818)|Colorectal(212;5.04e-06)|Kidney(185;4.99e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000198)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TGATGCACTGCTTGCCCAGAA	0.597																																					p.L89F		Atlas-SNP	.											.	PRAMEF12	69	.	0			c.C265T						PASS	.	C	PHE/LEU	0,4396		0,0,2198	75	78	77		265	2.7	0.1	1		77	2,8598		0,2,4298	no	missense	PRAMEF12	NM_001080830.1	22	0,2,6496	TT,TC,CC		0.0233,0.0,0.0154	possibly-damaging	89/484	12835275	2,12994	2198	4300	6498	SO:0001583	missense	390999	exon1			GCACTGCTTGCCC		CCDS41254.1	1p36.21	2013-01-17			ENSG00000116726	ENSG00000116726		"-"	22125	protein-coding gene	gene with protein product							Standard	NM_001080830		Approved	OTTHUMG00000001927	uc001aui.3	O95522	OTTHUMG00000001927	ENST00000357726.4:c.265C>T	chr1.hg19:g.12835275C>T	ENSP00000350358:p.Leu89Phe	74.0	0.0	.		83.0	25.0	.	NM_001080830		Missense_Mutation	SNP	ENST00000357726.4	hg19	CCDS41254.1	.	.	.	.	.	.	.	.	.	.	.	13.29	2.193803	0.38707	0.0	2.33E-4	ENSG00000116726	ENST00000357726	T	0.06068	3.35	2.68	2.68	0.31781	.	0.378221	0.23234	N	0.050437	T	0.13884	0.0336	M	0.90369	3.11	0.09310	N	0.999999	P	0.35174	0.488	B	0.40506	0.331	T	0.09271	-1.0682	10	0.66056	D	0.02	.	5.5671	0.17177	0.0:0.8465:0.0:0.1535	.	89	O95522	PRA12_HUMAN	F	89	ENSP00000350358:L89F	ENSP00000350358:L89F	L	+	1	0	PRAMEF12	12757862	0.076000	0.21285	0.104000	0.21259	0.371000	0.29859	1.313000	0.33585	1.791000	0.52520	0.195000	0.17529	CTT	.	.	.	none		0.597	PRAMEF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005457.1	XM_372760		T	12835275	C	T	12835275	3	4	206	1	0	0	0	0	1	0	0	0	12438	797	28	2	267	2	PRAMEF12	1	12835275	Missense_Mutation	SNP	C	TCGA-IA-A83T-01A-11D-A34Z-10		12835275	236415346	1	12498											
RPE65	6121	hgsc.bcm.edu	37	chr1	68910320	68910320	+	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	agacattaacaagggcattgTcagtaacctctactcctcga	13	10	7	11	1	2	1	1	0	1	1	4	2	3	1	2	1	3	2	2	1	4	4			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr1:68910320T>A	ENST00000262340.5	-	5	442	c.389A>T	c.(388-390)gAc>gTc	p.D130V		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	130					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						AAGGGCATTGTCAGTAACCTC	0.378																																					p.D130V		Atlas-SNP	.											.	RPE65	87	.	0			c.A389T						PASS	.						71	74	73					1																	68910320		2203	4300	6503	SO:0001583	missense	6121	exon5			GCATTGTCAGTAA	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.389A>T	chr1.hg19:g.68910320T>A	ENSP00000262340:p.Asp130Val	134.0	0.0	.		126.0	28.0	.	NM_000329	A8K1L0|Q5T9U3	Missense_Mutation	SNP	ENST00000262340.5	hg19	CCDS643.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.373457	0.82573	.	.	ENSG00000116745	ENST00000262340	D	0.95412	-3.7	5.05	5.05	0.67936	.	0.124550	0.64402	D	0.000001	D	0.97813	0.9282	M	0.89534	3.04	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98674	1.0689	10	0.66056	D	0.02	-19.5298	14.9454	0.71026	0.0:0.0:0.0:1.0	.	130	Q16518	RPE65_HUMAN	V	130	ENSP00000262340:D130V	ENSP00000262340:D130V	D	-	2	0	RPE65	68682908	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.525000	0.81892	2.122000	0.65172	0.533000	0.62120	GAC	.	.	.	none		0.378	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329		A	68910320	T	A	68910320	3	1	206	1	0	0	0	0	1	0	0	0	13558	1667	58	5	1252	5	RPE65	1	68910320	Missense_Mutation	SNP	T	TCGA-IA-A83T-01A-11D-A34Z-10	56075045	68910320	180340301	2	12499			1	27		2	2	12	N	TACTCCTCGAAAG_T	2.096452e-05
RPE65	6121	hgsc.bcm.edu	37	chr1	68910331	68910343	+	Frame_Shift_Del	DEL	TACTCCTCGAAAG	TACTCCTCGAAAG	-																															agggcattgtcagtaacctcTactcctcgaaagtaagaaaa																								rs61752877		TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	TACTCCTCGAAAG	TACTCCTCGAAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr1:68910331_68910343delTACTCCTCGAAAG	ENST00000262340.5	-	5	419_431	c.366_378delCTTTCGAGGAGTA	c.(364-378)tactttcgaggagtafs	p.YFRGV122fs		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	122					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)	p.R124*(1)|p.R124L(1)		central_nervous_system(1)|kidney(3)|large_intestine(12)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	35						CAGTAACCTCTACTCCTCGAAAGTAAGAAAAAA	0.371																																					p.123_127del		Atlas-Indel,Pindel	.											.	RPE65	87	.	2	Substitution - Missense(1)|Substitution - Nonsense(1)	large_intestine(1)|lung(1)	c.367_379del	GRCh37	CM983760	RPE65	M	rs61752877	PASS	.																																			SO:0001589	frameshift_variant	6121	exon5			.	U18991	CCDS643.1	1p31	2014-05-13	2002-08-29		ENSG00000116745	ENSG00000116745	3.1.1.64		10294	protein-coding gene	gene with protein product	"retinol isomerase", "all-trans-retinyl-palmitate hydrolase", "retinoid isomerohydrolase", "BCO family, member 3"	180069	"retinal pigment epithelium-specific protein (65kD)"	RP20		8340400	Standard	XM_006710811		Approved	LCA2, rd12, BCO3	uc001dei.1	Q16518	OTTHUMG00000009208	ENST00000262340.5:c.366_378delCTTTCGAGGAGTA	chr1.hg19:g.68910331_68910343delTACTCCTCGAAAG	ENSP00000262340:p.Tyr122fs	128.0	0.0	0		116.0	24.0	0.206897	NM_000329	A8K1L0|Q5T9U3	Frame_Shift_Del	DEL	ENST00000262340.5	hg19	CCDS643.1																																																																																			.	.	.	none		0.371	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329		-	68910343	TACTCCTCGAAAG	-	68910331	7	5	206	1	0	1	0	1	0	0	0	0	13558	1509	53	0	1263	0	RPE65	1	68910331	Frame_Shift_Del	DEL	TACTCCTCGAAAG	TCGA-IA-A83T-01A-11D-A34Z-10	11	68910331	180340290	3	12500			1	27		2	2	12	N	TACTCCTCGAAAG_T	2.096452e-05
CENPF	1063	hgsc.bcm.edu	37	chr1	214802436	214802436	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaattgacggaagatttgagTtgtcagcgacaaaatgcaga	16	9	11	5	2	1	4	1	2	0	2	1	6	1	5	0	1	2	2	0	1	4	3			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr1:214802436T>C	ENST00000366955.3	+	8	1284	c.1116T>C	c.(1114-1116)agT>agC	p.S372S		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0	Interaction with SNAP25 and required for localization to the cytoplasm. {ECO:0000250}.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		AAGATTTGAGTTGTCAGCGAC	0.313																																					p.S372S	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.T1116C						PASS	.						64	69	68					1																	214802436		2203	4300	6503	SO:0001819	synonymous_variant	1063	exon8			TTTGAGTTGTCAG	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.1116T>C	chr1.hg19:g.214802436T>C		301.0	0.0	.		340.0	14.0	.	NM_016343	Q13171|Q13246|Q5VVM7	Silent	SNP	ENST00000366955.3	hg19	CCDS31023.1																																																																																			.	.	.	none		0.313	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		C	214802436	T	C	214802436	2	2	206	1	0	0	0	0	0	0	0	1	3233	1722	60	3		3	CENPF	1	214802436	Silent	SNP	T	TCGA-IA-A83T-01A-11D-A34Z-10	145892105	214802436	34448185	4	12501											
LBR	3930	hgsc.bcm.edu	37	chr1	225592163	225592163	+	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	acccaagtaattggggtggcGaacaaagccccaccatccag	13	5	10	13	1	0	0	0	0	0	0	1	1	1	0	5	3	2	1	5	3	4	2			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr1:225592163G>A	ENST00000338179.2	-	13	1755	c.1630C>T	c.(1630-1632)Cgc>Tgc	p.R544C	LBR_ENST00000272163.4_Missense_Mutation_p.R544C	NM_194442.2	NP_919424.1	Q14739	LBR_HUMAN	lamin B receptor	544					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)		TTGGGGTGGCGAACAAAGCCC	0.413																																					p.R544C		Atlas-SNP	.											.	LBR	54	.	0			c.C1630T						PASS	.						67	69	68					1																	225592163		2203	4300	6503	SO:0001583	missense	3930	exon13			GGTGGCGAACAAA	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.1630C>T	chr1.hg19:g.225592163G>A	ENSP00000339883:p.Arg544Cys	133.0	0.0	.		118.0	13.0	.	NM_194442	B2R5P3|Q14740|Q53GU7|Q59FE6	Missense_Mutation	SNP	ENST00000338179.2	hg19	CCDS1545.1	.	.	.	.	.	.	.	.	.	.	G	33	5.274431	0.95459	.	.	ENSG00000143815	ENST00000272163;ENST00000338179	D;D	0.98762	-5.12;-5.12	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.99557	0.9841	H	0.98111	4.15	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97985	1.0351	10	0.87932	D	0	-19.7542	20.3316	0.98722	0.0:0.0:1.0:0.0	.	544	Q14739	LBR_HUMAN	C	544	ENSP00000272163:R544C;ENSP00000339883:R544C	ENSP00000272163:R544C	R	-	1	0	LBR	223658786	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	9.708000	0.98727	2.871000	0.98454	0.655000	0.94253	CGC	.	.	.	none		0.413	LBR-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091398.1	NM_002296		A	225592163	G	A	225592163	3	1	206	1	0	0	0	0	1	0	0	0	8659	1058	37	1	225	1	LBR	1	225592163	Missense_Mutation	SNP	G	TCGA-IA-A83T-01A-11D-A34Z-10	10789727	225592163	23658458	5	12502											
OTOF	9381	hgsc.bcm.edu	37	chr2	26781380	26781380	+	Silent	SNP	G	G	A																															cctcggaaagtcactttggcGatccggtcgcccctgccccg																										TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr2:26781380G>A	ENST00000272371.2	-	1	186	c.60C>T	c.(58-60)atC>atT	p.I20I	OTOF_ENST00000403946.3_Silent_p.I20I	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	20					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)					TCACTTTGGCGATCCGGTCGC	0.657																																					p.I20I	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.C60T						PASS	.						58	57	58					2																	26781380		2203	4300	6503	SO:0001819	synonymous_variant	9381	exon1			TTTGGCGATCCGG	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.60C>T	chr2.hg19:g.26781380G>A		172.0	0.0	.		164.0	39.0	.	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Silent	SNP	ENST00000272371.2	hg19	CCDS1725.1																																																																																			.	.	.	none		0.657	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3			A	26781380	G	A	26781380	2	1	206	1	0	0	0	0	0	0	0	1	11310	1048	37	1		1	OTOF	2	26781380	Silent	SNP	G	TCGA-IA-A83T-01A-11D-A34Z-10		26781380	216417993	6	12503	122	2									
OTOF	9381	hgsc.bcm.edu	37	chr2	26781388	26781388	+	Missense_Mutation	SNP	C	C	A																															agtcactttggcgatccggtCgcccctgccccgcagctccg																								rs376856990		TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr2:26781388C>A	ENST00000272371.2	-	1	178	c.52G>T	c.(52-54)Gac>Tac	p.D18Y	OTOF_ENST00000403946.3_Missense_Mutation_p.D18Y	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	18					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)					GCGATCCGGTCGCCCCTGCCC	0.662																																					p.D18Y	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.G52T						PASS	.						57	56	57					2																	26781388		2203	4300	6503	SO:0001583	missense	9381	exon1			TCCGGTCGCCCCT	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.52G>T	chr2.hg19:g.26781388C>A	ENSP00000272371:p.Asp18Tyr	165.0	0.0	.		160.0	37.0	.	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	hg19	CCDS1725.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.974238	0.74246	.	.	ENSG00000115155	ENST00000272371;ENST00000403946	T;T	0.79653	-1.29;-1.29	5.67	4.79	0.61399	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.87744	0.6254	M	0.70275	2.135	0.50813	D	0.999892	D	0.71674	0.998	D	0.69479	0.964	D	0.88796	0.3281	10	0.87932	D	0	-35.1014	12.7055	0.57058	0.0:0.9196:0.0:0.0804	.	18	Q9HC10	OTOF_HUMAN	Y	18	ENSP00000272371:D18Y;ENSP00000385255:D18Y	ENSP00000272371:D18Y	D	-	1	0	OTOF	26634892	0.989000	0.36119	0.990000	0.47175	0.896000	0.52359	3.138000	0.50570	1.386000	0.46466	0.650000	0.86243	GAC	.	.	.	alt		0.662	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3			A	26781388	C	A	26781388	3	1	206	1	0	0	0	0	1	0	0	0	11310	884	31	4	6454	4	OTOF	2	26781388	Missense_Mutation	SNP	C	TCGA-IA-A83T-01A-11D-A34Z-10	8	26781388	216417985	7	12504	122	2									
DCLK3	85443	hgsc.bcm.edu	37	chr3	36779671	36779671	+	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	cccatatccagctcactggtCcccagagaaagcctctcacg	10	7	7	17	1	2	1	2	0	1	1	5	2	4	1	5	1	2	1	5	1	2	1			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr3:36779671C>T	ENST00000416516.2	-	2	970	c.480G>A	c.(478-480)ggG>ggA	p.G160G		NM_033403.1	NP_208382.1	Q9C098	DCLK3_HUMAN	doublecortin-like kinase 3	160						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						GCTCACTGGTCCCCAGAGAAA	0.547																																					p.G160G		Atlas-SNP	.											.	DCLK3	95	.	0			c.G480A						PASS	.						117	122	121					3																	36779671		1954	4150	6104	SO:0001819	synonymous_variant	85443	exon2			ACTGGTCCCCAGA	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.480G>A	chr3.hg19:g.36779671C>T		142.0	0.0	.		160.0	27.0	.	NM_033403		Silent	SNP	ENST00000416516.2	hg19	CCDS43064.1																																																																																			.	.	.	none		0.547	DCLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341727.1	XM_047355		T	36779671	C	T	36779671	2	4	206	1	0	0	0	0	0	0	0	1	4295	842	30	2		2	DCLK3	3	36779671	Silent	SNP	C	TCGA-IA-A83T-01A-11D-A34Z-10		36779671	161242759	8	12505											
SCN11A	11280	hgsc.bcm.edu	37	chr3	38908836	38908836	+	Silent	SNP	G	G	A																															ttctgctgttggttgaagttGtcaatgataacgccaatgaa																								rs371852759		TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr3:38908836G>A	ENST00000302328.3	-	23	4125	c.3927C>T	c.(3925-3927)gaC>gaT	p.D1309D	SCN11A_ENST00000450244.1_Silent_p.D1309D|SCN11A_ENST00000456224.3_Silent_p.D1271D|SCN11A_ENST00000444237.2_Silent_p.D1309D	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	1309					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)	GGTTGAAGTTGTCAATGATAA	0.368																																					p.D1309D		Atlas-SNP	.											.	SCN11A	296	.	0			c.C3927T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	150	140	144		3927	2.3	1	3		144	0,8600		0,0,4300	no	coding-synonymous	SCN11A	NM_014139.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		1309/1792	38908836	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	11280	exon23			GAAGTTGTCAATG	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.3927C>T	chr3.hg19:g.38908836G>A		92.0	0.0	.		86.0	21.0	.	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Silent	SNP	ENST00000302328.3	hg19	CCDS33737.1																																																																																			.	.	.	weak		0.368	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		A	38908836	G	A	38908836	2	1	206	1	0	0	0	0	0	0	0	1	13926	1368	48	2		2	SCN11A	3	38908836	Silent	SNP	G	TCGA-IA-A83T-01A-11D-A34Z-10	2129165	38908836	159113594	9	12506	123	2									
SCN11A	11280	hgsc.bcm.edu	37	chr3	38908838	38908838	+	Frame_Shift_Del	DEL	C	C	-																															ctgctgttggttgaagttgtCaatgataacgccaatgaaga																										TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr3:38908838delC	ENST00000302328.3	-	23	4123	c.3925delG	c.(3925-3927)gacfs	p.D1309fs	SCN11A_ENST00000450244.1_Frame_Shift_Del_p.D1309fs|SCN11A_ENST00000456224.3_Frame_Shift_Del_p.D1271fs|SCN11A_ENST00000444237.2_Frame_Shift_Del_p.D1309fs	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	1309					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)	TTGAAGTTGTCAATGATAACG	0.368																																					p.D1309fs		Atlas-INDEL	.											.	SCN11A	296	.	0			c.3926delA						PASS	.						149	141	144					3																	38908838		2203	4300	6503	SO:0001589	frameshift_variant	11280	exon23			.	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.3925delG	chr3.hg19:g.38908838delC	ENSP00000307599:p.Asp1309fs	94.0	0.0	0		87.0	21.0	0.241379	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Frame_Shift_Del	DEL	ENST00000302328.3	hg19	CCDS33737.1																																																																																			.	.	.	none		0.368	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		-	38908838	C	-	38908838	7	5	206	1	0	1	0	1	0	0	0	0	13926	826	29	0	1466	0	SCN11A	3	38908838	Frame_Shift_Del	DEL	C	TCGA-IA-A83T-01A-11D-A34Z-10	2	38908838	159113592	10	12507	123	2									
SCFD2	152579	hgsc.bcm.edu	37	chr4	54140020	54140020	+	Frame_Shift_Del	DEL	A	A	-																															aggagcctttcaaaagccagAaagttgtcccacttggcagt																										TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr4:54140020delA	ENST00000401642.3	-	4	1417	c.1284delT	c.(1282-1284)tttfs	p.F428fs	SCFD2_ENST00000388940.4_Frame_Shift_Del_p.F428fs	NM_152540.3	NP_689753.2	Q8WU76	SCFD2_HUMAN	sec1 family domain containing 2	428					protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)					breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	30			GBM - Glioblastoma multiforme(3;1.07e-26)|LUSC - Lung squamous cell carcinoma(32;0.0134)			CAAAAGCCAGAAAGTTGTCCC	0.443																																					p.L429fs		Atlas-Indel,Pindel	.											.	SCFD2	78	.	0			c.1285delC						PASS	.						101	96	98					4																	54140020		2203	4300	6503	SO:0001589	frameshift_variant	152579	exon4			.	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.1284delT	chr4.hg19:g.54140020delA	ENSP00000384182:p.Phe428fs	80.0	0.0	0		93.0	18.0	0.193548	NM_152540	Q8N5F3|Q8N8H0|Q96ED3	Frame_Shift_Del	DEL	ENST00000401642.3	hg19	CCDS33984.1																																																																																			.	.	.	none		0.443	SCFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361311.3	NM_152540		-	54140020	A	-	54140020	7	5	206	1	0	1	0	1	0	0	0	0	13903	243	9	0	794	0	SCFD2	4	54140020	Frame_Shift_Del	DEL	A	TCGA-IA-A83T-01A-11D-A34Z-10		54140020	137014256	11	12508											
C5orf42	65250	hgsc.bcm.edu	37	chr5	37185181	37185181	+	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	tcatttcctcagtctggggtCctggaaagaaaagaataaaa	15	10	9	7	0	3	2	2	0	1	2	5	3	5	3	2	3	0	0	2	3	6	2			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr5:37185181C>T	ENST00000508244.1	-	24	4283	c.4190G>A	c.(4189-4191)gGa>gAa	p.G1397E	C5orf42_ENST00000274258.7_Splice_Site_p.G278E|C5orf42_ENST00000425232.2_Splice_Site_p.G1397E			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	1397						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)			AGTCTGGGGTCCTGGAAAGAA	0.398																																					p.G1397E		Atlas-SNP	.											.	C5orf42	422	.	0			c.G4190A						PASS	.						49	49	49					5																	37185181		2203	4300	6503	SO:0001630	splice_region_variant	65250	exon25			TGGGGTCCTGGAA		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.4190-1G>A	chr5.hg19:g.37185181C>T		191.0	0.0	.		193.0	47.0	.	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	hg19	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	C	29.3	4.996523	0.93167	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16	5.98	5.98	0.97165	.	0.081462	0.45126	D	0.000390	T	0.68054	0.2959	N	0.24115	0.695	0.43480	D	0.995705	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.67768	-0.5585	10	0.45353	T	0.12	.	15.5265	0.75915	0.0:0.9324:0.0:0.0676	.	1397;278	E9PH94;Q9H799	.;CE042_HUMAN	E	1397;1397;278;445;278	ENSP00000421690:G1397E;ENSP00000389014:G1397E;ENSP00000274258:G278E;ENSP00000424223:G445E	ENSP00000274258:G278E	G	-	2	0	C5orf42	37220938	0.996000	0.38824	0.983000	0.44433	0.982000	0.71751	2.961000	0.49168	2.847000	0.97988	0.591000	0.81541	GGA	.	.	.	none		0.398	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	Missense_Mutation	T	37185181	C	T	37185181	5	4	206	1	0	0	0	0	0	0	1	0	2303	869	30	2	5515	2	C5orf42	5	37185181	Splice_Site	SNP	C	TCGA-IA-A83T-01A-11D-A34Z-10		37185181	143730079	12	12509											
CCNO	10309	hgsc.bcm.edu	37	chr5	54528321	54528321	+	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	tcgaaggagaggccgaattgGcggtgcaccgggatcagcca	10	5	16	10	4	1	1	1	0	0	1	2	5	1	2	3	5	2	1	3	5	2	1			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr5:54528321G>A	ENST00000282572.4	-	2	591	c.435C>T	c.(433-435)cgC>cgT	p.R145R	RP11-506H20.1_ENST00000506435.1_RNA	NM_021147.3	NP_066970.3	P22674	CCNO_HUMAN	cyclin O	145					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|cell cycle (GO:0007049)|cell division (GO:0051301)|cilium assembly (GO:0042384)|depyrimidination (GO:0045008)|DNA repair (GO:0006281)|embryo development (GO:0009790)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to drug (GO:0042493)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	uracil DNA N-glycosylase activity (GO:0004844)			endometrium(1)|lung(3)|skin(1)	5		Lung NSC(810;4.08e-05)|Breast(144;0.0735)|Prostate(74;0.183)	LUSC - Lung squamous cell carcinoma(15;0.142)|Lung(15;0.161)			GGCCGAATTGGCGGTGCACCG	0.667																																					p.R145R		Atlas-SNP	.											.	CCNO	17	.	0			c.C435T						PASS	.						71	60	64					5																	54528321		2203	4300	6503	SO:0001819	synonymous_variant	10309	exon2			GAATTGGCGGTGC	M87499	CCDS34157.1	5q11.2	2010-11-15	2007-07-26	2007-07-26	ENSG00000152669	ENSG00000152669			18576	protein-coding gene	gene with protein product		607752	"cyclin U"	CCNU			Standard	NR_125346		Approved	UDG2, FLJ22422, UNG2	uc003jpw.3	P22674	OTTHUMG00000162598	ENST00000282572.4:c.435C>T	chr5.hg19:g.54528321G>A		162.0	0.0	.		204.0	43.0	.	NM_021147	A8K1W5|Q0P6J2|Q9H6B0|Q9UMD5	Silent	SNP	ENST00000282572.4	hg19	CCDS34157.1																																																																																			.	.	.	none		0.667	CCNO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369707.1	NM_021147		A	54528321	G	A	54528321	2	1	206	1	0	0	0	0	0	0	0	1	2935	1190	42	2		2	CCNO	5	54528321	Silent	SNP	G	TCGA-IA-A83T-01A-11D-A34Z-10	17343140	54528321	126386939	13	12510											
MAS1L	116511	hgsc.bcm.edu	37	chr6	29455103	29455103	+	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	gccccagatgagggtgcagaCaacattagatgtgtattttg	11	11	12	7	0	0	4	0	1	0	3	0	4	0	4	2	1	2	2	2	1	3	4			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr6:29455103C>G	ENST00000377127.3	-	1	635	c.577G>C	c.(577-579)Gtc>Ctc	p.V193L		NM_052967.1	NP_443199.1	P35410	MAS1L_HUMAN	MAS1 proto-oncogene like, G protein-coupled receptor	193					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(7)|pancreas(1)|prostate(2)|skin(2)	28						AGGGTGCAGACAACATTAGAT	0.463																																					p.V193L	NSCLC(153;755 1987 3859 11251 32945)	Atlas-SNP	.											.	MAS1L	66	.	0			c.G577C						PASS	.						68	59	62					6																	29455103		2203	4300	6503	SO:0001583	missense	116511	exon1			TGCAGACAACATT	S78653	CCDS4661.1	6p22.1	2014-06-26	2014-06-26		ENSG00000204687	ENSG00000204687		"GPCR / Class A : Orphans"	13961	protein-coding gene	gene with protein product		607235	"MAS1 oncogene-like"				Standard	NM_052967		Approved	MAS-L, MRG, dJ994E9.2	uc011dlq.2	P35410	OTTHUMG00000031089	ENST00000377127.3:c.577G>C	chr6.hg19:g.29455103C>G	ENSP00000366331:p.Val193Leu	111.0	0.0	.		127.0	10.0	.	NM_052967	Q5SUN5	Missense_Mutation	SNP	ENST00000377127.3	hg19	CCDS4661.1	.	.	.	.	.	.	.	.	.	.	C	10.63	1.403256	0.25291	.	.	ENSG00000204687	ENST00000377127	T	0.34275	1.37	2.36	-1.09	0.09904	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.19208	0.0461	L	0.37800	1.135	0.09310	N	1	P	0.37500	0.597	P	0.51701	0.677	T	0.36720	-0.9736	9	0.51188	T	0.08	.	4.0133	0.09632	0.0:0.5369:0.1966:0.2665	.	193	P35410	MAS1L_HUMAN	L	193	ENSP00000366331:V193L	ENSP00000366331:V193L	V	-	1	0	MAS1L	29563082	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	0.056000	0.14256	-0.452000	0.07087	0.596000	0.82720	GTC	.	.	.	none		0.463	MAS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076126.2	NM_052967		G	29455103	C	G	29455103	3	3	206	1	0	0	0	0	1	0	0	0	9328	478	17	4	561	4	MAS1L	6	29455103	Missense_Mutation	SNP	C	TCGA-IA-A83T-01A-11D-A34Z-10		29455103	141659964	14	12511											
CASP8AP2	9994	hgsc.bcm.edu	37	chr6	90573481	90573481	+	RNA	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agacttccttcccatctcctAtggaaatacaacagacagaa	15	9	5	12	0	1	3	0	0	1	3	4	4	3	4	3	1	2	0	3	1	5	4			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr6:90573481A>G	ENST00000551025.1	+	0	3490									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)		CCCATCTCCTATGGAAATACA	0.398																																					p.M685V	Colon(187;1656 2025 17045 31481 39901)	Atlas-SNP	.											.	CASP8AP2	108	.	0			c.A2053G						PASS	.						60	54	56					6																	90573481		1899	4122	6021			9994	exon7			TCTCCTATGGAAA	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"FLICE-associated huge protein"	606880	"CASP8 associated protein 2"			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		chr6.hg19:g.90573481A>G		86.0	0.0	.		110.0	25.0	.	NM_001137667		Missense_Mutation	SNP	ENST00000551025.1	hg19																																																																																				.	.	.	none		0.398	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667		G	90573481	A	G	90573481	1	3	206	0	1	0	0	0	0	0	0	0	2680	449	16	3		3	CASP8AP2	6	90573481	RNA	SNP	A	TCGA-IA-A83T-01A-11D-A34Z-10	61118378	90573481	80541586	15	12512											
COQ3	51805	hgsc.bcm.edu	37	chr6	99817502	99817502	+	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	cttcagcttttcatgcacagCtggattggtgcaggcattag	8	13	11	9	0	2	0	2	0	0	0	2	1	2	1	0	3	4	5	0	3	1	5			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr6:99817502C>A	ENST00000254759.3	-	7	1108	c.1084G>T	c.(1084-1086)Gct>Tct	p.A362S	COQ3_ENST00000369242.1_Missense_Mutation_p.A134S|COQ3_ENST00000369240.1_Missense_Mutation_p.A134S	NM_017421.3	NP_059117.3	Q9NZJ6	COQ3_HUMAN	coenzyme Q3 methyltransferase	362					glycerol metabolic process (GO:0006071)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity (GO:0008425)|3-demethylubiquinone-9 3-O-methyltransferase activity (GO:0008689)|hexaprenyldihydroxybenzoate methyltransferase activity (GO:0004395)|O-methyltransferase activity (GO:0008171)			cervix(1)|lung(5)|upper_aerodigestive_tract(2)	8		all_cancers(76;1.24e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00716)|Colorectal(196;0.0691)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0625)		TCATGCACAGCTGGATTGGTG	0.393																																					p.A362S		Atlas-SNP	.											.	COQ3	19	.	0			c.G1084T						PASS	.						136	141	139					6																	99817502		2203	4300	6503	SO:0001583	missense	51805	exon7			GCACAGCTGGATT	AF193016	CCDS5042.1	6q21	2013-05-01	2013-05-01		ENSG00000132423	ENSG00000132423	2.1.1.114		18175	protein-coding gene	gene with protein product	"polyprenyldihydroxybenzoate methyltransferase"	605196	"coenzyme Q3 homolog, methyltransferase (yeast)", "coenzyme Q3 homolog, methyltransferase (S. cerevisiae)"			10777520	Standard	NM_017421		Approved	bA9819.1	uc003ppk.3	Q9NZJ6	OTTHUMG00000015264	ENST00000254759.3:c.1084G>T	chr6.hg19:g.99817502C>A	ENSP00000254759:p.Ala362Ser	169.0	0.0	.		181.0	41.0	.	NM_017421	B3KPX0|Q5T061|Q6P4F0|Q8IXG6|Q96BG1|Q9H0N1	Missense_Mutation	SNP	ENST00000254759.3	hg19	CCDS5042.1	.	.	.	.	.	.	.	.	.	.	C	7.031	0.560676	0.13498	.	.	ENSG00000132423	ENST00000254759;ENST00000369242;ENST00000369240	T;T;T	0.28454	2.03;1.61;1.61	4.74	1.85	0.25348	.	1.012920	0.07926	N	0.976816	T	0.03053	0.0090	N	0.02011	-0.69	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.42682	-0.9437	10	0.25751	T	0.34	-28.7078	4.1853	0.10395	0.0:0.5306:0.1727:0.2967	.	362	Q9NZJ6	COQ3_HUMAN	S	362;134;134	ENSP00000254759:A362S;ENSP00000358245:A134S;ENSP00000358243:A134S	ENSP00000254759:A362S	A	-	1	0	COQ3	99924223	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.606000	0.05654	0.132000	0.18615	0.650000	0.86243	GCT	.	.	.	none		0.393	COQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041602.1	NM_017421		A	99817502	C	A	99817502	3	1	206	1	0	0	0	0	1	0	0	0	3748	797	28	4	29	4	COQ3	6	99817502	Missense_Mutation	SNP	C	TCGA-IA-A83T-01A-11D-A34Z-10	9244021	99817502	71297565	16	12513											
TNRC18	84629	hgsc.bcm.edu	37	chr7	5414035	5414035	+	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	ccggcggtggccaggccagcCttgcccgcagcctccaggcc	4	4	14	19	3	0	0	0	0	0	0	1	0	1	0	8	5	3	1	8	5	0	1			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr7:5414035C>G	ENST00000430969.1	-	10	3228	c.2880G>C	c.(2878-2880)aaG>aaC	p.K960N	TNRC18_ENST00000399537.4_Missense_Mutation_p.K960N	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	960							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)		CCAGGCCAGCCTTGCCCGCAG	0.771																																					p.K960N		Atlas-SNP	.											.	TNRC18	311	.	0			c.G2880C						PASS	.						4	4	4					7																	5414035		1555	3371	4926	SO:0001583	missense	84629	exon10			GCCAGCCTTGCCC	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.2880G>C	chr7.hg19:g.5414035C>G	ENSP00000395538:p.Lys960Asn	28.0	0.0	.		50.0	16.0	.	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	hg19	CCDS47534.1	.	.	.	.	.	.	.	.	.	.	C	4.254	0.046072	0.08243	.	.	ENSG00000182095	ENST00000399537;ENST00000430969;ENST00000399544;ENST00000327499	T;T	0.14022	2.54;2.54	5.34	-0.488	0.12056	.	.	.	.	.	T	0.28433	0.0703	M	0.66939	2.045	0.20307	N	0.999916	D	0.89917	1.0	D	0.85130	0.997	T	0.09618	-1.0666	9	0.87932	D	0	.	4.6366	0.12527	0.1483:0.4114:0.0:0.4403	.	960	O15417	TNC18_HUMAN	N	960;960;15;15	ENSP00000382452:K960N;ENSP00000395538:K960N	ENSP00000330383:K15N	K	-	3	2	TNRC18	5380561	0.986000	0.35501	0.689000	0.30133	0.036000	0.12997	0.120000	0.15647	-0.006000	0.14370	-0.224000	0.12420	AAG	.	.	.	none		0.771	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				G	5414035	C	G	5414035	3	3	206	1	0	0	0	0	1	0	0	0	16351	680	24	4	6110	4	TNRC18	7	5414035	Missense_Mutation	SNP	C	TCGA-IA-A83T-01A-11D-A34Z-10		5414035	153724628	17	12514											
VWC2	375567	hgsc.bcm.edu	37	chr7	49815638	49815638	+	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	acccgcgctgcatccacgtcGacacgagccagtgctgcccg	7	5	11	18	6	0	0	0	0	0	0	2	2	1	0	4	0	4	3	4	0	0	0			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr7:49815638G>C	ENST00000340652.4	+	2	1163	c.607G>C	c.(607-609)Gac>Cac	p.D203H		NM_198570.3	NP_940972.2	Q2TAL6	VWC2_HUMAN	von Willebrand factor C domain containing 2	203	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.				negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of neuron differentiation (GO:0045666)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|basement membrane (GO:0005604)|cell junction (GO:0030054)|extracellular space (GO:0005615)|interstitial matrix (GO:0005614)|synapse (GO:0045202)				cervix(1)|endometrium(2)|large_intestine(1)|lung(3)|prostate(1)	8						CATCCACGTCGACACGAGCCA	0.677																																					p.D203H		Atlas-SNP	.											.	VWC2	30	.	0			c.G607C						PASS	.						13	18	16					7																	49815638		2147	4233	6380	SO:0001583	missense	375567	exon2			CACGTCGACACGA	AY358393	CCDS5508.1	7p12.3-p12.2	2007-07-19			ENSG00000188730	ENSG00000188730			30200	protein-coding gene	gene with protein product	"brorin", "brain-specific chordin-like"	611108				17400546	Standard	NM_198570		Approved	PSST739, UNQ739	uc003tot.1	Q2TAL6	OTTHUMG00000129265	ENST00000340652.4:c.607G>C	chr7.hg19:g.49815638G>C	ENSP00000341819:p.Asp203His	17.0	0.0	.		28.0	16.0	.	NM_198570	Q6UXE2	Missense_Mutation	SNP	ENST00000340652.4	hg19	CCDS5508.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.580112	0.86645	.	.	ENSG00000188730	ENST00000340652	T	0.13778	2.56	4.81	4.81	0.61882	von Willebrand factor, type C (1);	0.000000	0.85682	D	0.000000	T	0.22085	0.0532	N	0.14661	0.345	0.58432	D	0.999998	D	0.67145	0.996	D	0.70016	0.967	T	0.13629	-1.0502	10	0.41790	T	0.15	.	18.301	0.90163	0.0:0.0:1.0:0.0	.	203	Q2TAL6	VWC2_HUMAN	H	203	ENSP00000341819:D203H	ENSP00000341819:D203H	D	+	1	0	VWC2	49786184	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.595000	0.98260	2.379000	0.81126	0.555000	0.69702	GAC	.	.	.	none		0.677	VWC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251375.2	NM_198570		C	49815638	G	C	49815638	3	2	206	1	0	0	0	0	1	0	0	0	17255	1058	37	4	609	4	VWC2	7	49815638	Missense_Mutation	SNP	G	TCGA-IA-A83T-01A-11D-A34Z-10	44401603	49815638	109323025	18	12515											
FAM83A	84985	hgsc.bcm.edu	37	chr8	124206353	124206353	+	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	atccgggagaagttcatcatCtcggactggagatttgtcct	9	12	11	9	2	3	2	2	0	1	2	6	5	5	3	2	3	0	1	2	3	1	2			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr8:124206353C>T	ENST00000518448.1	+	4	2752	c.738C>T	c.(736-738)atC>atT	p.I246I	FAM83A_ENST00000546351.1_Silent_p.I190I|FAM83A_ENST00000536633.1_Silent_p.I246I|FAM83A_ENST00000318462.6_Silent_p.I246I|FAM83A_ENST00000276699.6_Silent_p.I246I|FAM83A_ENST00000522648.1_Silent_p.I190I			Q86UY5	FA83A_HUMAN	family with sequence similarity 83, member A	246										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(2)|skin(1)	17	Lung NSC(37;1.55e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			AGTTCATCATCTCGGACTGGA	0.507																																					p.I246I		Atlas-SNP	.											.	FAM83A	64	.	0			c.C738T						PASS	.						138	119	126					8																	124206353		2203	4300	6503	SO:0001819	synonymous_variant	84985	exon3			CATCATCTCGGAC	BC052300	CCDS6339.1, CCDS6340.1, CCDS75784.1	8q24.13	2014-03-13			ENSG00000147689	ENSG00000147689			28210	protein-coding gene	gene with protein product						22886303	Standard	XM_005251087		Approved	MGC14128, BJ-TSA-9	uc003ypx.3	Q86UY5	OTTHUMG00000165083	ENST00000518448.1:c.738C>T	chr8.hg19:g.124206353C>T		59.0	0.0	.		64.0	15.0	.	NM_032899	Q71HL2|Q8N7I1|Q96I47	Silent	SNP	ENST00000518448.1	hg19	CCDS6340.1																																																																																			.	.	.	none		0.507	FAM83A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381737.1	NM_032899		T	124206353	C	T	124206353	2	4	206	1	0	0	0	0	0	0	0	1	5640	903	32	2		2	FAM83A	8	124206353	Silent	SNP	C	TCGA-IA-A83T-01A-11D-A34Z-10		124206353	22157669	19	12516											
HNRNPH3	3189	hgsc.bcm.edu	37	chr10	70098907	70098907	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aattacacaggttatggaggTtttgatgactatggtggcta	11	14	12	4	0	0	2	0	2	0	0	0	3	0	3	0	5	1	3	0	5	5	6			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr10:70098907T>C	ENST00000265866.7	+	5	612	c.447T>C	c.(445-447)ggT>ggC	p.G149G	HNRNPH3_ENST00000469172.1_3'UTR|HNRNPH3_ENST00000354695.5_Silent_p.G134G|HNRNPH3_ENST00000441000.2_Silent_p.G41G	NM_012207.2|NM_021644.3	NP_036339.1|NP_067676.2	P31942	HNRH3_HUMAN	heterogeneous nuclear ribonucleoprotein H3 (2H9)	149	Gly-rich.				epithelial cell differentiation (GO:0030855)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)|ovary(2)|prostate(2)	11						GTTATGGAGGTTTTGATGACT	0.318																																					p.G149G		Atlas-SNP	.											.	HNRNPH3	33	.	0			c.T447C						PASS	.						135	145	142					10																	70098907		2203	4300	6503	SO:0001819	synonymous_variant	3189	exon5			TGGAGGTTTTGAT		CCDS7278.1, CCDS7279.1	10q22	2013-02-12		2008-04-18	ENSG00000096746	ENSG00000096746		"RNA binding motif (RRM) containing"	5043	protein-coding gene	gene with protein product		602324		HNRPH3		8999868	Standard	NM_021644		Approved	2H9	uc001jnw.4	P31942	OTTHUMG00000018349	ENST00000265866.7:c.447T>C	chr10.hg19:g.70098907T>C		123.0	0.0	.		131.0	38.0	.	NM_012207	A8K682|B3KRE1|Q9BSX1|Q9NP53|Q9NP96|Q9NPA7|Q9NPI4|Q9UFU4|Q9Y4J5	Silent	SNP	ENST00000265866.7	hg19	CCDS7278.1																																																																																			.	.	.	none		0.318	HNRNPH3-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090165.1			C	70098907	T	C	70098907	2	2	206	1	0	0	0	0	0	0	0	1	7275	1712	60	3		3	HNRNPH3	10	70098907	Silent	SNP	T	TCGA-IA-A83T-01A-11D-A34Z-10		70098907	65435840	20	12517											
PLAC9	219348	hgsc.bcm.edu	37	chr10	81901918	81901918	+	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	acatggctgtgcaacgccgtCtagatgtcatggaggaggta	10	9	14	8	2	2	1	1	0	1	1	2	3	2	3	1	4	2	3	1	4	3	2			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr10:81901918C>G	ENST00000372263.3	+	2	187	c.145C>G	c.(145-147)Cta>Gta	p.L49V	PLAC9_ENST00000372270.2_Missense_Mutation_p.L7V|PLAC9_ENST00000372267.2_Missense_Mutation_p.L49V	NM_001012973.1	NP_001012991.1	Q5JTB6	PLAC9_HUMAN	placenta-specific 9	49						extracellular region (GO:0005576)				kidney(1)|ovary(1)	2	Prostate(51;0.0095)|all_epithelial(25;0.175)		Colorectal(32;0.109)			GCAACGCCGTCTAGATGTCAT	0.537																																					p.L49V		Atlas-SNP	.											.	PLAC9	9	.	0			c.C145G						PASS	.						128	89	102					10																	81901918		2203	4300	6503	SO:0001583	missense	219348	exon2			CGCCGTCTAGATG		CCDS31232.1	10q23.2	2008-02-04			ENSG00000189129	ENSG00000189129			19255	protein-coding gene	gene with protein product		612857					Standard	NM_001012973		Approved		uc001kbp.1	Q5JTB6	OTTHUMG00000018596	ENST00000372263.3:c.145C>G	chr10.hg19:g.81901918C>G	ENSP00000361337:p.Leu49Val	28.0	0.0	.		44.0	10.0	.	NM_001012973		Missense_Mutation	SNP	ENST00000372263.3	hg19	CCDS31232.1	.	.	.	.	.	.	.	.	.	.	C	2.210	-0.380998	0.05000	.	.	ENSG00000189129	ENST00000372270;ENST00000372267;ENST00000372263	.	.	.	3.74	0.113	0.14631	.	0.000000	0.31404	N	0.007712	T	0.54822	0.1882	.	.	.	0.09310	N	1	D	0.67145	0.996	D	0.79108	0.992	T	0.43015	-0.9417	8	0.66056	D	0.02	.	5.8715	0.18807	0.0:0.4521:0.0:0.5479	.	49	Q5JTB6	PLAC9_HUMAN	V	7;49;49	.	ENSP00000361337:L49V	L	+	1	2	PLAC9	81891898	0.003000	0.15002	0.001000	0.08648	0.033000	0.12548	0.053000	0.14184	0.011000	0.14865	0.537000	0.68136	CTA	.	.	.	none		0.537	PLAC9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049019.1	NM_001012973		G	81901918	C	G	81901918	3	3	206	1	0	0	0	0	1	0	0	0	12024	912	32	4	151	4	PLAC9	10	81901918	Missense_Mutation	SNP	C	TCGA-IA-A83T-01A-11D-A34Z-10	11803011	81901918	53632829	21	12518											
SORCS1	114815	hgsc.bcm.edu	37	chr10	108427453	108427453	+	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	ctccagacacttacccagtaCtattgaggtaactctgtccc	10	11	6	14	0	1	2	0	1	1	1	3	2	3	2	3	1	3	2	3	1	4	5			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr10:108427453C>A	ENST00000263054.6	-	17	2304	c.2297G>T	c.(2296-2298)aGt>aTt	p.S766I	SORCS1_ENST00000369698.1_Missense_Mutation_p.S301I|SORCS1_ENST00000344440.6_Missense_Mutation_p.S766I	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	766					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)		TTACCCAGTACTATTGAGGTA	0.488																																					p.S766I		Atlas-SNP	.											.	SORCS1	534	.	0			c.G2297T						PASS	.						74	65	68					10																	108427453		2203	4300	6503	SO:0001583	missense	114815	exon17			CCAGTACTATTGA	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.2297G>T	chr10.hg19:g.108427453C>A	ENSP00000263054:p.Ser766Ile	52.0	0.0	.		65.0	15.0	.	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	hg19	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.240052	0.79912	.	.	ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440	T;T;T	0.27557	1.66;2.23;2.23	5.49	5.49	0.81192	VPS10 (1);	0.051681	0.85682	D	0.000000	T	0.63355	0.2504	M	0.87180	2.865	0.51233	D	0.999919	D;D;D;D;D	0.71674	0.994;0.998;0.998;0.997;0.998	D;D;D;D;D	0.76575	0.924;0.988;0.988;0.957;0.988	T	0.66952	-0.5793	9	.	.	.	-17.8618	19.7394	0.96219	0.0:1.0:0.0:0.0	.	766;766;766;766;766	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	I	301;766;766	ENSP00000358712:S301I;ENSP00000263054:S766I;ENSP00000345964:S766I	.	S	-	2	0	SORCS1	108417443	1.000000	0.71417	0.990000	0.47175	0.838000	0.47535	4.588000	0.60999	2.745000	0.94114	0.462000	0.41574	AGT	.	.	.	none		0.488	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		A	108427453	C	A	108427453	3	1	206	1	0	0	0	0	1	0	0	0	14943	565	20	4	1483	4	SORCS1	10	108427453	Missense_Mutation	SNP	C	TCGA-IA-A83T-01A-11D-A34Z-10	26525535	108427453	27107294	22	12519											
CSTF3	1479	hgsc.bcm.edu	37	chr11	33163206	33163206	+	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	taagaaaaaataaaataaaaTagtaacctctgcttcaatgt	21	11	4	5	0	2	1	1	0	1	1	2	1	2	1	1	0	2	2	1	0	11	6			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr11:33163206T>C	ENST00000323959.4	-	3	365				CSTF3_ENST00000438862.2_Missense_Mutation_p.I78V|CSTF3_ENST00000526480.1_Intron|CSTF3_ENST00000524827.1_Intron|CSTF3_ENST00000431742.2_3'UTR	NM_001326.2	NP_001317.1	Q12996	CSTF3_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 3, 77kDa						gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|prostate(1)|skin(1)|stomach(1)	19						TAAAATAAAATAGTAACCTCT	0.373																																					p.I78V		Atlas-SNP	.											.	CSTF3	59	.	0			c.A232G						PASS	.						41	40	40					11																	33163206		2202	4298	6500	SO:0001627	intron_variant	1479	exon3			ATAAAATAGTAAC	U15782	CCDS7883.1, CCDS44563.1, CCDS44564.1	11p13	2007-01-05	2002-08-29		ENSG00000176102	ENSG00000176102			2485	protein-coding gene	gene with protein product		600367	"cleavage stimulation factor, 3' pre-RNA, subunit 3, 77kD"			7984242	Standard	XM_006718154		Approved	CstF-77	uc001muh.3	Q12996	OTTHUMG00000166268	ENST00000323959.4:c.225+6A>G	chr11.hg19:g.33163206T>C		119.0	0.0	.		147.0	9.0	.	NM_001033505	A8K471|D3DR04|E9PB40|Q32P22|Q96FQ8|Q96QD6|Q96QK4	Missense_Mutation	SNP	ENST00000323959.4	hg19	CCDS7883.1	.	.	.	.	.	.	.	.	.	.	T	11.38	1.621909	0.28889	.	.	ENSG00000176102	ENST00000438862	T	0.33654	1.4	5.34	2.87	0.33458	.	.	.	.	.	T	0.20820	0.0501	.	.	.	0.80722	D	1	B	0.09022	0.002	B	0.10450	0.005	T	0.04946	-1.0916	8	0.16896	T	0.51	.	7.5882	0.28006	0.1261:0.0714:0.0:0.8025	.	78	Q96QK4	.	V	78	ENSP00000388711:I78V	ENSP00000388711:I78V	I	-	1	0	CSTF3	33119782	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.006000	0.70724	0.971000	0.38288	0.528000	0.53228	ATT	.	.	.	none		0.373	CSTF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388801.1	NM_001326		C	33163206	T	C	33163206	1	2	206	0	1	0	0	0	0	0	0	0	3988	1406	49	3		3	CSTF3	11	33163206	Intron	SNP	T	TCGA-IA-A83T-01A-11D-A34Z-10		33163206	101843310	23	12520											
C11orf94	143678	hgsc.bcm.edu	37	chr11	45928455	45928456	+	Frame_Shift_Ins	INS	-	-	G																															aagtggctgcgagagttccaINSggggggcggaaaatgcctca																										TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr11:45928455_45928456insG	ENST00000449465.1	-	2	175_176	c.139_140insC	c.(139-141)ctgfs	p.L47fs	RP11-618K13.2_ENST00000533218.1_RNA	NM_001080446.2	NP_001073915.2	C9JXX5	CK094_HUMAN	chromosome 11 open reading frame 94	47						extracellular region (GO:0005576)				NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|ovary(1)|pancreas(1)|prostate(1)	7						CGAGAGTTCCAGGGGGGCGGAA	0.619																																					p.L47fs		Atlas-Indel,Pindel	.											.	C11orf94	13	.	0			c.140_141insC						PASS	.																																			SO:0001589	frameshift_variant	143678	exon2			.		CCDS44577.1	11p11.2	2012-08-10			ENSG00000234776	ENSG00000234776			37213	protein-coding gene	gene with protein product							Standard	NM_001080446		Approved		uc001nbs.4	C9JXX5	OTTHUMG00000167004	ENST00000449465.1:c.140dupC	chr11.hg19:g.45928461_45928461dupG	ENSP00000401498:p.Leu47fs	37.0	0.0	0		57.0	12.0	0.210526	NM_001080446		Frame_Shift_Ins	INS	ENST00000449465.1	hg19	CCDS44577.1																																																																																			.	.	.	none		0.619	C11orf94-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392395.1	NM_001080446		G	45928456	-	G	45928455	7	5	206	1	0	1	1	0	0	0	0	0	1675	188	7	0	164	0	C11orf94	11	45928455	Frame_Shift_Ins	INS	-	TCGA-IA-A83T-01A-11D-A34Z-10	12765249	45928455	89078061	24	12521											
GLYATL1	92292	hgsc.bcm.edu	37	chr11	58723454	58723454	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctttgaggcctcctgtgAgtggcaccaatggacttgct	6	14	11	10	0	1	2	0	2	1	0	2	3	2	3	3	3	1	2	3	3	1	3			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr11:58723454A>G	ENST00000317391.4	+	8	1203	c.863A>G	c.(862-864)gAg>gGg	p.E288G	GLYATL1_ENST00000300079.5_Missense_Mutation_p.E319G|RP11-142C4.6_ENST00000533954.1_RNA|RP11-142C4.6_ENST00000525714.1_RNA	NM_001220494.1	NP_001207423.1	Q969I3	GLYL1_HUMAN	glycine-N-acyltransferase-like 1	288						mitochondrion (GO:0005739)	glutamine N-acyltransferase activity (GO:0047946)|glycine N-acyltransferase activity (GO:0047961)			NS(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|skin(4)|urinary_tract(1)	34					Glycine(DB00145)	GCCTCCTGTGAGTGGCACCAA	0.428																																					p.E319G		Atlas-SNP	.											.	GLYATL1	89	.	0			c.A956G						PASS	.						64	65	65					11																	58723454		2200	4295	6495	SO:0001583	missense	92292	exon7			CCTGTGAGTGGCA	AK091965	CCDS31556.1, CCDS55768.1	11q12.1	2014-08-12			ENSG00000166840	ENSG00000166840			30519	protein-coding gene	gene with protein product		614761				12477932	Standard	NM_080661		Approved	MGC15397, FLJ34646	uc001nnh.2	Q969I3	OTTHUMG00000167221	ENST00000317391.4:c.863A>G	chr11.hg19:g.58723454A>G	ENSP00000322223:p.Glu288Gly	67.0	0.0	.		108.0	23.0	.	NM_080661	A6NDT0|Q7Z510|Q8NAW8	Missense_Mutation	SNP	ENST00000317391.4	hg19	CCDS55768.1	.	.	.	.	.	.	.	.	.	.	.	0.007	-2.002586	0.00431	.	.	ENSG00000166840	ENST00000444580;ENST00000317391;ENST00000300079	T;T	0.16743	2.32;2.32	1.97	-3.94	0.04130	Acyl-CoA N-acyltransferase (1);Glycine N-acyltransferase, C-terminal (1);	1.211330	0.06583	N	0.750716	T	0.04318	0.0119	N	0.01352	-0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.34950	-0.9808	10	0.18276	T	0.48	.	2.9615	0.05894	0.5318:0.0:0.2621:0.2061	.	319;288	Q969I3-2;Q969I3	.;GLYL1_HUMAN	G	265;288;319	ENSP00000322223:E288G;ENSP00000300079:E319G	ENSP00000300079:E319G	E	+	2	0	GLYATL1	58480030	0.000000	0.05858	0.000000	0.03702	0.081000	0.17604	-1.929000	0.01558	-1.331000	0.02252	-0.526000	0.04340	GAG	.	.	.	none		0.428	GLYATL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393783.1	NM_080661		G	58723454	A	G	58723454	3	3	206	1	0	0	0	0	1	0	0	0	6487	304	11	3	982	3	GLYATL1	11	58723454	Missense_Mutation	SNP	A	TCGA-IA-A83T-01A-11D-A34Z-10	12794999	58723454	76283062	25	12522											
MS4A8B	83661	hgsc.bcm.edu	37	chr11	60470856	60470856	+	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	tggctctcctgacaggccatCcagatcatcattggcctggc	7	10	10	14	0	3	2	2	1	1	1	5	2	4	2	4	4	0	1	4	4	0	1			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr11:60470856C>A	ENST00000300226.2	+	3	428	c.225C>A	c.(223-225)atC>atA	p.I75I		NM_031457.1	NP_113645.1	Q9BY19	M4A8_HUMAN	membrane-spanning 4-domains, subfamily A, member 8	75						integral component of membrane (GO:0016021)											GACAGGCCATCCAGATCATCA	0.493																																					p.I75I		Atlas-SNP	.											.	.	.	.	0			c.C225A						PASS	.						100	92	95					11																	60470856		2203	4300	6503	SO:0001819	synonymous_variant	83661	exon3			GGCCATCCAGATC	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.225C>A	chr11.hg19:g.60470856C>A		141.0	0.0	.		160.0	17.0	.	NM_031457	Q8TCA5	Silent	SNP	ENST00000300226.2	hg19	CCDS7990.1	.	.	.	.	.	.	.	.	.	.	C	3.360	-0.130637	0.06753	.	.	ENSG00000166959	ENST00000525458	.	.	.	3.62	1.56	0.23342	.	.	.	.	.	T	0.58133	0.2101	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50533	-0.8817	4	.	.	.	-2.4498	9.6989	0.40173	0.0:0.5864:0.4136:0.0	.	.	.	.	Y	57	.	.	S	+	2	0	MS4A8B	60227432	0.962000	0.33011	0.728000	0.30774	0.348000	0.29142	0.877000	0.28106	0.123000	0.18342	0.491000	0.48974	TCC	.	.	.	none		0.493	MS4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395605.1			A	60470856	C	A	60470856	2	1	206	1	0	0	0	0	0	0	0	1	9874	845	30	4		4	MS4A8B	11	60470856	Silent	SNP	C	TCGA-IA-A83T-01A-11D-A34Z-10	1747402	60470856	74535660	26	12523											
TMEM134	80194	hgsc.bcm.edu	37	chr11	67232160	67232160	+	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	gcgcagtagatgaagatcacGtgatagactgcggggcgggg	10	6	18	7	4	1	5	1	2	0	3	1	5	1	5	0	4	1	2	0	4	3	2			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr11:67232160G>A	ENST00000308022.2	-	7	554	c.513C>T	c.(511-513)caC>caT	p.H171H	CTC-1337H24.2_ENST00000602944.1_lincRNA|TMEM134_ENST00000541059.1_5'UTR|TMEM134_ENST00000393877.3_Silent_p.H156H	NM_001078651.1|NM_025124.2	NP_001072119.1|NP_079400.1	Q9H6X4	TM134_HUMAN	transmembrane protein 134	171						integral component of membrane (GO:0016021)				endometrium(1)|lung(1)	2						TGAAGATCACGTGATAGACTG	0.697																																					p.H171H		Atlas-SNP	.											.	TMEM134	4	.	0			c.C513T						PASS	.						22	25	24					11																	67232160		2121	4143	6264	SO:0001819	synonymous_variant	80194	exon7			GATCACGTGATAG	AK025402	CCDS8167.1, CCDS41678.1	11q13.2	2006-03-09			ENSG00000172663	ENSG00000172663			26142	protein-coding gene	gene with protein product							Standard	NM_025124		Approved	FLJ21749	uc001olq.2	Q9H6X4	OTTHUMG00000168034	ENST00000308022.2:c.513C>T	chr11.hg19:g.67232160G>A		82.0	0.0	.		105.0	6.0	.	NM_025124	Q08AK4|Q6PJN3	Silent	SNP	ENST00000308022.2	hg19	CCDS8167.1																																																																																			.	.	.	none		0.697	TMEM134-020	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398994.1	NM_025124		A	67232160	G	A	67232160	2	1	206	1	0	0	0	0	0	0	0	1	16062	1136	40	1		1	TMEM134	11	67232160	Silent	SNP	G	TCGA-IA-A83T-01A-11D-A34Z-10	6761304	67232160	67774356	27	12524											
KRTAP5-7	440050	hgsc.bcm.edu	37	chr11	71238734	71238760	+	In_Frame_Del	DEL	TGCTGCTGTTCCTCAGGCTGTGGGTCA	TGCTGCTGTTCCTCAGGCTGTGGGTCA	-																															agtccagctgctgtaagcccTgctgctgttcctcaggctgt																								rs533945918|rs79842834	byFrequency	TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	TGCTGCTGTTCCTCAGGCTGTGGGTCA	TGCTGCTGTTCCTCAGGCTGTGGGTCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr11:71238734_71238760delTGCTGCTGTTCCTCAGGCTGTGGGTCA	ENST00000398536.4	+	1	422_448	c.388_414delTGCTGCTGTTCCTCAGGCTGTGGGTCA	c.(388-414)tgctgctgttcctcaggctgtgggtcadel	p.CCCSSGCGS130del		NM_001012503.1	NP_001012521.1	Q6L8G8	KRA57_HUMAN	keratin associated protein 5-7	130	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)		p.G137W(1)		breast(1)|endometrium(1)|kidney(3)|lung(6)|ovary(1)	12						ctgtaagccctgctgctgttcctcaggctgtgggtcatcctgctgcc	0.604																																					p.129_138del		Atlas-INDEL	.											.	KRTAP5-7	23	.	1	Substitution - Missense(1)	lung(1)	c.387_413del						PASS	.																																			SO:0001651	inframe_deletion	440050	exon1			.	AB126076	CCDS41682.1	11q13.4	2008-02-05			ENSG00000244411	ENSG00000244411		"Keratin associated proteins"	23602	protein-coding gene	gene with protein product						15144888	Standard	NM_001012503		Approved	KRTAP5.7, KRTAP5-3	uc001oqq.1	Q6L8G8	OTTHUMG00000057570	ENST00000398536.4:c.388_414delTGCTGCTGTTCCTCAGGCTGTGGGTCA	chr11.hg19:g.71238734_71238760delTGCTGCTGTTCCTCAGGCTGTGGGTCA	ENSP00000417330:p.Cys130_Ser138del	89.0	0.0	0		117.0	12.0	0.102564	NM_001012503	B2RNM3|Q701N5	In_Frame_Del	DEL	ENST00000398536.4	hg19	CCDS41682.1																																																																																			.	.	.	none		0.604	KRTAP5-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127953.1			-	71238760	TGCTGCTGTTCCTCAGGCTGTGGGTCA	-	71238734	7	5	206	1	0	1	0	1	0	0	0	0	8573	1580	55	0	390	0	KRTAP5-7	11	71238734	In_Frame_Del	DEL	TGCTGCTGTTCCTCAGGCTGTGGGTCA	TCGA-IA-A83T-01A-11D-A34Z-10	4006574	71238734	63767782	28	12525											
ITPR2	3709	hgsc.bcm.edu	37	chr12	26639109	26639109	+	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	ggctgcatgatggcaattgcGggactcattgttacttcctc	7	13	11	10	1	1	1	1	1	0	0	3	2	2	2	1	3	3	4	1	3	2	4			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr12:26639109G>C	ENST00000381340.3	-	41	6155	c.5739C>G	c.(5737-5739)ccC>ccG	p.P1913P		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1913					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)	p.P1913P(2)	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)	TGGCAATTGCGGGACTCATTG	0.428																																					p.P1913P		Atlas-SNP	.											.	ITPR2	270	.	2	Substitution - coding silent(2)	lung(1)|kidney(1)	c.C5739G						PASS	.						226	213	217					12																	26639109		1915	4130	6045	SO:0001819	synonymous_variant	3709	exon41			AATTGCGGGACTC	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.5739C>G	chr12.hg19:g.26639109G>C		437.0	0.0	.		577.0	32.0	.	NM_002223	O94773	Silent	SNP	ENST00000381340.3	hg19	CCDS41764.1																																																																																			.	.	.	none		0.428	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		C	26639109	G	C	26639109	2	2	206	1	0	0	0	0	0	0	0	1	7928	1103	39	4		4	ITPR2	12	26639109	Silent	SNP	G	TCGA-IA-A83T-01A-11D-A34Z-10		26639109	107212786	29	12526											
KRT72	140807	hgsc.bcm.edu	37	chr12	52981529	52981549	+	In_Frame_Del	DEL	GCCTGGTGCAGGGCGCCCTCC	GCCTGGTGCAGGGCGCCCTCC	-																															tccgtgccagctcctccttgGcctggtgcagggcgccctcc																								rs145882334	byFrequency	TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	GCCTGGTGCAGGGCGCCCTCC	GCCTGGTGCAGGGCGCCCTCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr12:52981529_52981549delGCCTGGTGCAGGGCGCCCTCC	ENST00000537672.2	-	7	1186_1206	c.1176_1196delGGAGGGCGCCCTGCACCAGGC	c.(1174-1197)ctggagggcgccctgcaccaggcc>ctc	p.EGALHQA393del	KRT72_ENST00000354310.4_In_Frame_Del_p.EGALHQA351del|KRT72_ENST00000293745.2_In_Frame_Del_p.EGALHQA393del|KRT72_ENST00000398066.3_In_Frame_Del_p.EGALHQA205del	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	393	Coil 2.|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)		CTCCTCCTTGGCCTGGTGCAGGGCGCCCTCCAGCTCATCCA	0.652																																					p.393_399del		Pindel	.											.	KRT72	70	.	0			c.1177_1197del						PASS	.																																			SO:0001651	inframe_deletion	140807	exon7			.	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.1176_1196delGGAGGGCGCCCTGCACCAGGC	chr12.hg19:g.52981529_52981549delGCCTGGTGCAGGGCGCCCTCC	ENSP00000441160:p.Glu393_Ala399del	103.0	0.0	.		128.0	12.0	0.094	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	In_Frame_Del	DEL	ENST00000537672.2	hg19	CCDS8833.1																																																																																			.	.	.	none		0.652	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747		-	52981549	GCCTGGTGCAGGGCGCCCTCC	-	52981529	7	5	206	1	0	1	0	1	0	0	0	0	8492	1203	42	0	351	0	KRT72	12	52981529	In_Frame_Del	DEL	GCCTGGTGCAGGGCGCCCTCC	TCGA-IA-A83T-01A-11D-A34Z-10	26342420	52981529	80870366	30	12527											
USP30	84749	hgsc.bcm.edu	37	chr12	109520853	109520853	+	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	ggagctgcaggatgggccggGagcccccacaccaggtgtgt	7	5	17	12	1	0	0	0	0	0	0	0	3	0	3	4	5	3	2	4	5	0	0			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr12:109520853G>A	ENST00000257548.5	+	11	1247	c.1154G>A	c.(1153-1155)gGa>gAa	p.G385E	USP30_ENST00000392784.2_Missense_Mutation_p.G354E	NM_032663.3	NP_116052.2	Q70CQ3	UBP30_HUMAN	ubiquitin specific peptidase 30	385	USP.				mitochondrial fusion (GO:0008053)|mitochondrion degradation (GO:0000422)|protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(7)|kidney(1)|large_intestine(1)|liver(2)|lung(11)|prostate(1)|skin(3)|stomach(2)	28						GATGGGCCGGGAGCCCCCACA	0.542																																					p.G385E		Atlas-SNP	.											.	USP30	48	.	0			c.G1154A						PASS	.						52	47	49					12																	109520853		2203	4300	6503	SO:0001583	missense	84749	exon11			GGCCGGGAGCCCC	BC022094	CCDS9123.2	12q23.3	2006-01-20	2005-08-08		ENSG00000135093	ENSG00000135093		"Ubiquitin-specific peptidases"	20065	protein-coding gene	gene with protein product		612492	"ubiquitin specific protease 30"			12838346	Standard	XM_005253962		Approved	MGC10702, FLJ40511	uc010sxi.2	Q70CQ3	OTTHUMG00000133613	ENST00000257548.5:c.1154G>A	chr12.hg19:g.109520853G>A	ENSP00000257548:p.Gly385Glu	59.0	0.0	.		96.0	7.0	.	NM_032663	Q8WTU7|Q96JX4|Q9BSS3	Missense_Mutation	SNP	ENST00000257548.5	hg19	CCDS9123.2	.	.	.	.	.	.	.	.	.	.	G	3.397	-0.122993	0.06795	.	.	ENSG00000135093	ENST00000392784;ENST00000257548	T;T	0.31247	1.51;1.5	4.91	4.01	0.46588	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.781706	0.12074	N	0.501919	T	0.12092	0.0294	N	0.00621	-1.32	0.09310	N	1	B;B	0.19073	0.033;0.0	B;B	0.23852	0.049;0.0	T	0.25950	-1.0117	10	0.41790	T	0.15	-0.8916	12.7132	0.57102	0.0:0.8311:0.1689:0.0	.	385;354	Q70CQ3;B3KUS5	UBP30_HUMAN;.	E	354;385	ENSP00000376535:G354E;ENSP00000257548:G385E	ENSP00000257548:G385E	G	+	2	0	USP30	108005236	0.005000	0.15991	0.003000	0.11579	0.009000	0.06853	1.864000	0.39469	1.208000	0.43306	-0.270000	0.10280	GGA	.	.	.	none		0.542	USP30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257733.2	NM_032663		A	109520853	G	A	109520853	3	1	206	1	0	0	0	0	1	0	0	0	17073	1174	41	2	1196	2	USP30	12	109520853	Missense_Mutation	SNP	G	TCGA-IA-A83T-01A-11D-A34Z-10	56539324	109520853	24331042	31	12528											
FLT3	2322	hgsc.bcm.edu	37	chr13	28624244	28624244	+	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	agtgttacctattgtgaacaGcctggtgcattccctgccca	8	12	9	12	0	0	1	0	1	0	0	1	1	1	1	4	1	5	2	4	1	3	4			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr13:28624244G>C	ENST00000241453.7	-	6	811	c.730C>G	c.(730-732)Ctg>Gtg	p.L244V	FLT3_ENST00000380982.4_Missense_Mutation_p.L244V|FLT3_ENST00000537084.1_Missense_Mutation_p.L244V	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	244					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)	ATTGTGAACAGCCTGGTGCAT	0.423			"Mis, O"		"AML, ALL"																																p.L244V		Atlas-SNP	.		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	.	FLT3	15525	.	0			c.C730G						PASS	.						170	147	155					13																	28624244		2203	4300	6503	SO:0001583	missense	2322	exon6			TGAACAGCCTGGT	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.730C>G	chr13.hg19:g.28624244G>C	ENSP00000241453:p.Leu244Val	113.0	0.0	.		137.0	35.0	.	NM_004119	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Missense_Mutation	SNP	ENST00000241453.7	hg19	CCDS31953.1	.	.	.	.	.	.	.	.	.	.	G	14.53	2.562109	0.45590	.	.	ENSG00000122025	ENST00000241453;ENST00000380982;ENST00000537084	T;T;T	0.77489	-1.03;-1.1;-0.84	5.64	5.64	0.86602	.	0.000000	0.53938	D	0.000047	T	0.74397	0.3711	L	0.29908	0.895	0.43118	D	0.994837	P;P	0.49358	0.923;0.521	P;B	0.48189	0.57;0.246	T	0.72730	-0.4205	10	0.30078	T	0.28	.	17.8943	0.88881	0.0:0.0:1.0:0.0	.	244;244	P36888-2;P36888	.;FLT3_HUMAN	V	244	ENSP00000241453:L244V;ENSP00000370369:L244V;ENSP00000438139:L244V	ENSP00000241453:L244V	L	-	1	2	FLT3	27522244	1.000000	0.71417	1.000000	0.80357	0.448000	0.32197	4.617000	0.61204	2.655000	0.90218	0.462000	0.41574	CTG	.	.	.	none		0.423	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2			C	28624244	G	C	28624244	3	2	206	1	0	0	0	0	1	0	0	0	5949	962	34	4	2327	4	FLT3	13	28624244	Missense_Mutation	SNP	G	TCGA-IA-A83T-01A-11D-A34Z-10		28624244	86545634	32	12529											
G2E3	55632	hgsc.bcm.edu	37	chr14	31061654	31061654	+	Splice_Site	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	cagtttactggcaattttgcGtgagttatttaactgttaaa	11	17	8	5	1	0	1	0	1	0	0	0	1	0	1	0	1	3	4	0	1	6	8			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr14:31061654G>C	ENST00000206595.6	+	5	516		c.e5+1		G2E3_ENST00000544007.1_Splice_Site|G2E3_ENST00000553504.1_Splice_Site|G2E3_ENST00000438909.2_Splice_Site	NM_017769.3	NP_060239.2	Q7L622	G2E3_HUMAN	G2/M-phase specific E3 ubiquitin protein ligase						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						GCAATTTTGCGTGAGTTATTT	0.333																																					.		Atlas-SNP	.											.	G2E3	82	.	0			c.362+1G>C						PASS	.						89	86	87					14																	31061654		2203	4299	6502	SO:0001630	splice_region_variant	55632	exon5			TTTTGCGTGAGTT	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.362+1G>C	chr14.hg19:g.31061654G>C		121.0	0.0	.		146.0	28.0	.	NM_017769	Q9BVR2|Q9H9E9|Q9NXC0|Q9P2L3	Splice_Site	SNP	ENST00000206595.6	hg19	CCDS9638.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.039163	0.75617	.	.	ENSG00000092140	ENST00000206595;ENST00000438909;ENST00000553504;ENST00000554714;ENST00000547532	.	.	.	5.82	5.82	0.92795	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.091	0.97817	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	G2E3	30131405	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.206000	0.89745	2.755000	0.94549	0.591000	0.81541	.	.	.	.	none		0.333	G2E3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276613.2	NM_017769	Intron	C	31061654	G	C	31061654	5	2	206	1	0	0	0	0	0	0	1	0	6147	1159	40	4	377	4	G2E3	14	31061654	Splice_Site	SNP	G	TCGA-IA-A83T-01A-11D-A34Z-10		31061654	76287886	33	12530											
C14orf145	145508	hgsc.bcm.edu	37	chr14	81297497	81297497	+	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	gcaaagtcacctctacttgtGatgccaaatgtgctttctcc	9	13	7	12	0	3	1	1	1	2	0	4	1	3	1	3	0	3	2	3	0	3	3			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr14:81297497G>T	ENST00000555265.1	-	13	1574	c.1199C>A	c.(1198-1200)tCa>tAa	p.S400*	CEP128_ENST00000281129.3_Nonsense_Mutation_p.S400*|CEP128_ENST00000216517.6_Nonsense_Mutation_p.S400*			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	400						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						CTCTACTTGTGATGCCAAATG	0.353																																					p.S400X		Atlas-SNP	.											CEP128,NS,carcinoma,0,1	CEP128	146	.	0			c.C1199A						PASS	.						218	197	204					14																	81297497		2203	4300	6503	SO:0001587	stop_gained	145508	exon12			ACTTGTGATGCCA	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.1199C>A	chr14.hg19:g.81297497G>T	ENSP00000451162:p.Ser400*	188.0	0.0	.		215.0	43.0	.	NM_152446	B9EK52|Q86X97|Q96ML4	Nonsense_Mutation	SNP	ENST00000555265.1	hg19	CCDS32130.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	38|38	7.102862|7.102862	0.98066|0.98066	.|.	.|.	ENSG00000100629|ENSG00000100629	ENST00000554827|ENST00000281129;ENST00000555265;ENST00000393619;ENST00000216517	.|.	.|.	.|.	5.63|5.63	1.13|1.13	0.20643|0.20643	.|.	.|0.827576	.|0.10699	.|N	.|0.644299	T|.	0.30262|.	0.0759|.	.|.	.|.	.|.	0.53688|0.53688	D|D	0.999978|0.999978	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.17806|.	-1.0357|.	4|.	.|0.10636	.|T	.|0.68	.|.	1.9124|1.9124	0.03290|0.03290	0.2577:0.1381:0.4636:0.1406|0.2577:0.1381:0.4636:0.1406	.|.	.|.	.|.	.|.	N|X	279|400	.|.	.|ENSP00000216517:S400X	H|S	-|-	1|2	0|0	CEP128|CEP128	80367250|80367250	0.003000|0.003000	0.15002|0.15002	0.902000|0.902000	0.35471|0.35471	0.661000|0.661000	0.39034|0.39034	0.429000|0.429000	0.21412|0.21412	0.331000|0.331000	0.23511|0.23511	-0.282000|-0.282000	0.10007|0.10007	CAC|TCA	.	.	.	none		0.353	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446		T	81297497	G	T	81297497	4	4	206	1	0	0	0	0	0	1	0	0	1751	1294	45	4	2137	4	C14orf145	14	81297497	Nonsense_Mutation	SNP	G	TCGA-IA-A83T-01A-11D-A34Z-10	50235843	81297497	26052043	34	12531											
FAM181A	90050	hgsc.bcm.edu	37	chr14	94395093	94395093	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agctaccatgtggggctggaGgggggactgggccccaggga	7	5	20	9	0	0	0	0	0	0	0	0	3	0	3	3	8	2	2	3	8	1	1			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr14:94395093G>A	ENST00000267594.5	+	3	955	c.648G>A	c.(646-648)gaG>gaA	p.E216E	FAM181A_ENST00000557000.2_Silent_p.E154E|FAM181A_ENST00000556222.1_Silent_p.E154E|FAM181A_ENST00000557719.1_Silent_p.E154E|FAM181A-AS1_ENST00000554742.1_RNA	NM_001207073.1|NM_001207074.1|NM_138344.4	NP_001194002.1|NP_001194003.1|NP_612353.3	Q8N9Y4	F181A_HUMAN	family with sequence similarity 181, member A	216										cervix(1)|endometrium(2)|large_intestine(8)|lung(4)|prostate(1)|skin(2)	18						TGGGGCTGGAGGGGGGACTGG	0.622																																					p.E216E		Atlas-SNP	.											.	FAM181A	42	.	0			c.G648A						PASS	.						25	30	28					14																	94395093		2203	4299	6502	SO:0001819	synonymous_variant	90050	exon3			GCTGGAGGGGGGA	BC009073	CCDS9914.1, CCDS55939.1	14q32.12	2011-11-30	2008-07-22	2008-07-22	ENSG00000140067	ENSG00000140067			20491	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 152"	C14orf152			Standard	NM_138344		Approved		uc021saz.1	Q8N9Y4	OTTHUMG00000171297	ENST00000267594.5:c.648G>A	chr14.hg19:g.94395093G>A		27.0	0.0	.		53.0	11.0	.	NM_138344	B2RD39|Q96GY1	Silent	SNP	ENST00000267594.5	hg19	CCDS9914.1																																																																																			.	.	.	none		0.622	FAM181A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412840.1	NM_138344		A	94395093	G	A	94395093	2	1	206	1	0	0	0	0	0	0	0	1	5512	991	35	2		2	FAM181A	14	94395093	Silent	SNP	G	TCGA-IA-A83T-01A-11D-A34Z-10	13097596	94395093	12954447	35	12532											
ZNF839	55778	hgsc.bcm.edu	37	chr14	102805492	102805492	+	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	agaagccctgtccaacgataCcactgaatctcttgctgcca	11	9	7	14	1	1	2	0	1	1	1	3	3	2	2	4	0	5	1	4	0	4	2			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr14:102805492C>A	ENST00000558850.1	+	7	1861	c.1511C>A	c.(1510-1512)aCc>aAc	p.T504N	ZNF839_ENST00000420933.2_3'UTR|ZNF839_ENST00000559185.1_Missense_Mutation_p.T504N|ZNF839_ENST00000262236.5_Missense_Mutation_p.T504N|AL137229.1_ENST00000577622.1_RNA|ZNF839_ENST00000442396.2_Missense_Mutation_p.T620N	NM_001267827.1	NP_001254756.1	A8K0R7	ZN839_HUMAN	zinc finger protein 839	504							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						TCCAACGATACCACTGAATCT	0.552																																					p.T620N		Atlas-SNP	.											.	ZNF839	41	.	0			c.C1859A						PASS	.						50	53	52					14																	102805492		1933	4137	6070	SO:0001583	missense	55778	exon7			ACGATACCACTGA	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.1511C>A	chr14.hg19:g.102805492C>A	ENSP00000453363:p.Thr504Asn	102.0	0.0	.		118.0	28.0	.	NM_018335	B3KSD2|Q53FH5|Q6GPI5|Q86TU1|Q9BQ86|Q9NUU3	Missense_Mutation	SNP	ENST00000558850.1	hg19	CCDS58336.1	.	.	.	.	.	.	.	.	.	.	C	14.71	2.618148	0.46736	.	.	ENSG00000022976	ENST00000442396;ENST00000262236;ENST00000398436;ENST00000420933	T;T	0.20200	2.09;2.09	4.29	-3.04	0.05412	.	2.167110	0.01436	N	0.014925	T	0.18676	0.0448	L	0.48642	1.525	0.09310	N	1	B;B;P;B	0.38020	0.11;0.021;0.615;0.11	B;B;B;B	0.39738	0.063;0.025;0.308;0.042	T	0.18871	-1.0323	10	0.66056	D	0.02	.	0.5543	0.00668	0.2964:0.209:0.2926:0.2019	.	620;504;383;504	A8K0R7-5;A8K0R7-2;Q9NT83;A8K0R7	.;.;.;ZN839_HUMAN	N	620;504;172;38	ENSP00000399863:T620N;ENSP00000262236:T504N	ENSP00000262236:T504N	T	+	2	0	ZNF839	101875245	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-0.397000	0.07269	-0.446000	0.07149	0.558000	0.71614	ACC	.	.	.	none		0.552	ZNF839-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415492.2	NM_018335		A	102805492	C	A	102805492	3	1	206	1	0	0	0	0	1	0	0	0	18200	507	18	4	1885	4	ZNF839	14	102805492	Missense_Mutation	SNP	C	TCGA-IA-A83T-01A-11D-A34Z-10	8410399	102805492	4544048	36	12533											
OR4M2	390538	hgsc.bcm.edu	37	chr15	22369316	22369316	+	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	acctgctattcccacattacCattgtggtgctaatgtttgg	8	15	8	10	0	0	0	0	0	0	0	1	0	1	0	3	2	3	3	3	2	3	6			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr15:22369316C>G	ENST00000332663.2	+	1	839	c.741C>G	c.(739-741)acC>acG	p.T247T	RP11-69H14.6_ENST00000558896.1_RNA	NM_001004719.2	NP_001004719.2	Q8NGB6	OR4M2_HUMAN	olfactory receptor, family 4, subfamily M, member 2	247						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(38)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	63		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		CCCACATTACCATTGTGGTGC	0.433																																					p.T247T		Atlas-SNP	.											.	OR4M2	140	.	0			c.C741G						PASS	.						265	195	218					15																	22369316		2203	4297	6500	SO:0001819	synonymous_variant	390538	exon1			CATTACCATTGTG	AC060768	CCDS32172.1	15q11.2	2013-09-23			ENSG00000182974	ENSG00000182974		"GPCR / Class A : Olfactory receptors"	15373	protein-coding gene	gene with protein product							Standard	NM_001004719		Approved		uc010tzu.2	Q8NGB6	OTTHUMG00000171738	ENST00000332663.2:c.741C>G	chr15.hg19:g.22369316C>G		336.0	0.0	.		399.0	57.0	.	NM_001004719	B9EH16|Q6IEY2	Silent	SNP	ENST00000332663.2	hg19	CCDS32172.1																																																																																			.	.	.	none		0.433	OR4M2-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414921.1			G	22369316	C	G	22369316	2	3	206	1	0	0	0	0	0	0	0	1	11083	581	21	4		4	OR4M2	15	22369316	Silent	SNP	C	TCGA-IA-A83T-01A-11D-A34Z-10		22369316	80162076	37	12534											
CEP152	22995	hgsc.bcm.edu	37	chr15	49030644	49030644	+	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	atctttcctggctccaaataCgtggtttcttctgacaggta	8	15	8	10	1	3	1	0	1	3	0	5	1	5	1	2	3	1	3	2	3	3	5			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr15:49030644C>T	ENST00000380950.2	-	27	5122	c.4935G>A	c.(4933-4935)acG>acA	p.T1645T	CEP152_ENST00000399334.3_Silent_p.T1589T	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	1645					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		GCTCCAAATACGTGGTTTCTT	0.388																																					p.T1645T		Atlas-SNP	.											CEP152,NS,carcinoma,0,1	CEP152	145	.	0			c.G4935A						PASS	.						194	187	189					15																	49030644		2010	4179	6189	SO:0001819	synonymous_variant	22995	exon27			CAAATACGTGGTT	AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"asterless"	613529	"microcephaly, primary autosomal recessive 4"	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.4935G>A	chr15.hg19:g.49030644C>T		200.0	0.0	.		215.0	40.0	.	NM_001194998	E7ER66|Q17RV1|Q6NTA0	Silent	SNP	ENST00000380950.2	hg19	CCDS58361.1																																																																																			.	.	.	none		0.388	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985		T	49030644	C	T	49030644	2	4	206	1	0	0	0	0	0	0	0	1	3250	523	19	1		1	CEP152	15	49030644	Silent	SNP	C	TCGA-IA-A83T-01A-11D-A34Z-10	26661328	49030644	53500748	38	12535											
TRPM7	54822	hgsc.bcm.edu	37	chr15	50978726	50978726	+	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	cgggcctgcgtgggtccagtAccattctcctcacggggcgg	4	8	15	14	4	2	0	1	0	1	0	4	0	3	0	4	5	2	1	4	5	1	2			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr15:50978726A>G	ENST00000313478.7	-	1	285		c.e1+1		TRPM7_ENST00000560955.1_Splice_Site|RN7SL354P_ENST00000469282.2_RNA	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7						actomyosin structure organization (GO:0031032)|calcium ion transmembrane transport (GO:0070588)|calcium-dependent cell-matrix adhesion (GO:0016340)|cellular magnesium ion homeostasis (GO:0010961)|ion transmembrane transport (GO:0034220)|necroptotic process (GO:0070266)|protein autophosphorylation (GO:0046777)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		TGGGTCCAGTACCATTCTCCT	0.667																																					.		Atlas-SNP	.											.	TRPM7	145	.	0			c.3+2T>C						PASS	.						37	43	41					15																	50978726		2011	4163	6174	SO:0001630	splice_region_variant	54822	exon2			TCCAGTACCATTC	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.3+1T>C	chr15.hg19:g.50978726A>G		44.0	0.0	.		46.0	10.0	.	NM_017672	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	Splice_Site	SNP	ENST00000313478.7	hg19	CCDS42035.1	.	.	.	.	.	.	.	.	.	.	A	17.89	3.500279	0.64298	.	.	ENSG00000092439	ENST00000313478	.	.	.	4.36	4.36	0.52297	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.1097	0.42555	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TRPM7	48766018	1.000000	0.71417	0.999000	0.59377	0.895000	0.52256	3.683000	0.54663	1.951000	0.56629	0.374000	0.22700	.	.	.	.	none		0.667	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672	Intron	G	50978726	A	G	50978726	5	3	206	1	0	0	0	0	0	0	1	0	16603	405	14	3	5748	3	TRPM7	15	50978726	Splice_Site	SNP	A	TCGA-IA-A83T-01A-11D-A34Z-10	1948082	50978726	51552666	39	12536											
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24801625	24801625	+	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	gcaactctaatgcagcctggCgtaaatggtcctatgggcac	10	9	11	11	1	1	0	0	0	1	0	2	0	2	0	2	3	3	4	2	3	5	3	rs377201148		TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr16:24801625C>G	ENST00000395799.3	+	6	1791	c.1662C>G	c.(1660-1662)ggC>ggG	p.G554G	TNRC6A_ENST00000315183.7_Silent_p.G554G	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	554	Interaction with argonaute family proteins.|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)		TGCAGCCTGGCGTAAATGGTC	0.473																																					p.G554G		Atlas-SNP	.											.	TNRC6A	171	.	0			c.C1662G						PASS	.						127	121	123					16																	24801625		2197	4300	6497	SO:0001819	synonymous_variant	27327	exon6			GCCTGGCGTAAAT	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.1662C>G	chr16.hg19:g.24801625C>G		115.0	0.0	.		124.0	29.0	.	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Silent	SNP	ENST00000395799.3	hg19	CCDS10624.2																																																																																			.	.	.	alt		0.473	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		G	24801625	C	G	24801625	2	3	206	1	0	0	0	0	0	0	0	1	16352	755	27	4		4	TNRC6A	16	24801625	Silent	SNP	C	TCGA-IA-A83T-01A-11D-A34Z-10		24801625	65553128	40	12537											
OR1E1	8387	hgsc.bcm.edu	37	chr17	3301172	3301172	+	Frame_Shift_Del	DEL	A	A	-																															gcagagcagacatatcacagAaaaagtgggggatcacattg																										TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr17:3301172delA	ENST00000322608.2	-	1	532	c.533delT	c.(532-534)ttcfs	p.F178fs		NM_003553.2	NP_003544.2	P30953	OR1E1_HUMAN	olfactory receptor, family 1, subfamily E, member 1	178				F -> L (in Ref. 6; AAA17447). {ECO:0000305}.	detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(2)|lung(5)	10						CATATCACAGAAAAAGTGGGG	0.483																																					p.F178fs		Atlas-Indel,Pindel	.											.	OR1E1	37	.	0			c.534delC						PASS	.						59	51	54					17																	3301172		2202	4300	6502	SO:0001589	frameshift_variant	8387	exon1			.	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.533delT	chr17.hg19:g.3301172delA	ENSP00000313384:p.Phe178fs	106.0	0.0	0		156.0	59.0	0.378205	NM_003553	O43884|P47882|P47885|Q6IFA9|Q6IFM5|Q9UBJ1|Q9UM60	Frame_Shift_Del	DEL	ENST00000322608.2	hg19	CCDS11024.1																																																																																			.	.	.	none		0.483	OR1E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207303.1	NM_003553		-	3301172	A	-	3301172	7	5	206	1	0	1	0	1	0	0	0	0	10961	246	9	0	415	0	OR1E1	17	3301172	Frame_Shift_Del	DEL	A	TCGA-IA-A83T-01A-11D-A34Z-10		3301172	77894038	41	12538											
SMARCE1	6605	hgsc.bcm.edu	37	chr17	38793826	38793826	+	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	tcgtgataccagaggatgccTacgaaagagttaaatacatt	15	10	9	7	2	0	3	0	1	0	2	1	5	0	4	2	1	4	1	2	1	6	5			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr17:38793826T>C	ENST00000348513.6	-	5	937		c.e5-2		SMARCE1_ENST00000377808.4_Splice_Site|SMARCE1_ENST00000431889.2_Splice_Site|SMARCE1_ENST00000400122.3_Splice_Site|KRT222_ENST00000476049.1_Intron|SMARCE1_ENST00000580419.1_Splice_Site|SMARCE1_ENST00000544009.1_Splice_Site|SMARCE1_ENST00000578044.1_Splice_Site	NM_003079.4	NP_003070.3	Q969G3	SMCE1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1						ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|metabolic process (GO:0008152)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|N-acetyltransferase activity (GO:0008080)|protein N-terminus binding (GO:0047485)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)			large_intestine(1)	1		Breast(137;0.000812)				AGAGGATGCCTACGAAAGAGT	0.433																																					.		Atlas-SNP	.											.	SMARCE1	34	.	0			c.157-2A>G						PASS	.						91	83	86					17																	38793826		2203	4299	6502	SO:0001630	splice_region_variant	6605	exon6			GATGCCTACGAAA	AF035262	CCDS11370.1	17q21.2	2006-09-20			ENSG00000073584	ENSG00000073584			11109	protein-coding gene	gene with protein product		603111				9435219	Standard	NM_003079		Approved	BAF57	uc002hux.2	Q969G3	OTTHUMG00000133367	ENST00000348513.6:c.157-2A>G	chr17.hg19:g.38793826T>C		75.0	0.0	.		118.0	49.0	.	NM_003079	B3KMC1|B4DFR4|C0IMW4|C0IMW5|C0IMW7|H7C3F6|O43539	Splice_Site	SNP	ENST00000348513.6	hg19	CCDS11370.1	.	.	.	.	.	.	.	.	.	.	T	19.49	3.837887	0.71373	.	.	ENSG00000073584	ENST00000348513;ENST00000431889;ENST00000377808	.	.	.	5.78	5.78	0.91487	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4053	0.83662	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SMARCE1	36047352	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.997000	0.88414	2.333000	0.79357	0.482000	0.46254	.	.	.	.	none		0.433	SMARCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257203.1	NM_003079	Intron	C	38793826	T	C	38793826	5	2	206	1	0	0	0	0	0	0	1	0	14793	1536	53	3	1108	3	SMARCE1	17	38793826	Splice_Site	SNP	T	TCGA-IA-A83T-01A-11D-A34Z-10	35492654	38793826	42401384	42	12539											
GPS1	2873	hgsc.bcm.edu	37	chr17	80013100	80013100	+	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	aagctcaagtgtgccgcaggTgagggcctgggtcacgccca	8	6	15	12	2	2	1	2	1	0	0	2	1	2	1	3	3	2	2	3	3	2	0			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr17:80013100T>C	ENST00000306823.6	+	6	783		c.e6+2		GPS1_ENST00000392358.2_Splice_Site|GPS1_ENST00000355130.2_Splice_Site|GPS1_ENST00000320548.4_Splice_Site|GPS1_ENST00000578552.1_Splice_Site			Q13098	CSN1_HUMAN	G protein pathway suppressor 1						cell cycle (GO:0007049)|cullin deneddylation (GO:0010388)|inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)			breast(1)|central_nervous_system(1)|endometrium(3)|liver(1)|lung(4)|prostate(1)|skin(2)	13	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0211)			GTGCCGCAGGTGAGGGCCTGG	0.637																																					.		Atlas-SNP	.											.	GPS1	30	.	0			c.760+2T>C						PASS	.						39	32	34					17																	80013100		2134	4212	6346	SO:0001630	splice_region_variant	2873	exon6			CGCAGGTGAGGGC		CCDS11800.1, CCDS32774.1	17q25.3	2013-03-14				ENSG00000169727			4549	protein-coding gene	gene with protein product	"COP9 signalosome subunit 1"	601934				9535219	Standard	NM_212492		Approved	COPS1, CSN1	uc002kdl.1	Q13098		ENST00000306823.6:c.760+2T>C	chr17.hg19:g.80013100T>C		88.0	0.0	.		114.0	18.0	.	NM_004127	Q8NA10|Q9BWL1	Splice_Site	SNP	ENST00000306823.6	hg19	CCDS32774.1	.	.	.	.	.	.	.	.	.	.	T	12.53	1.966042	0.34659	.	.	ENSG00000169727	ENST00000392358;ENST00000320548;ENST00000306823;ENST00000355130	.	.	.	4.13	4.13	0.48395	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.2976	0.60307	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	GPS1	77606389	1.000000	0.71417	0.985000	0.45067	0.355000	0.29361	5.275000	0.65575	1.743000	0.51761	0.482000	0.46254	.	.	.	.	none		0.637	GPS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442176.1	NM_212492	Intron	C	80013100	T	C	80013100	5	2	206	1	0	0	0	0	0	0	1	0	6739	1710	59	3	941	3	GPS1	17	80013100	Splice_Site	SNP	T	TCGA-IA-A83T-01A-11D-A34Z-10	41219274	80013100	1182110	43	12540											
CCDC57	284001	hgsc.bcm.edu	37	chr17	80156212	80156212	+	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	gtctctgcagagcaagctcaCcgtcgagctcctcaagtttt	8	11	9	13	2	3	1	2	0	1	1	6	2	4	1	2	0	4	5	2	0	2	2			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr17:80156212C>T	ENST00000389641.4	-	3	530	c.494G>A	c.(493-495)gGt>gAt	p.G165D	CCDC57_ENST00000392343.3_Missense_Mutation_p.G165D|CCDC57_ENST00000392347.1_Missense_Mutation_p.G165D			Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	165										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)			AGCAAGCTCACCGTCGAGCTC	0.498																																					p.G165D		Atlas-SNP	.											.	CCDC57	102	.	0			c.G494A						PASS	.						86	86	86					17																	80156212		1875	4097	5972	SO:0001583	missense	284001	exon3			AGCTCACCGTCGA	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.494G>A	chr17.hg19:g.80156212C>T	ENSP00000374292:p.Gly165Asp	130.0	0.0	.		172.0	32.0	.	NM_198082	A6NP51|A8MQC7|Q8IWG2|Q8TER3	Missense_Mutation	SNP	ENST00000389641.4	hg19		.	.	.	.	.	.	.	.	.	.	C	7.170	0.587487	0.13812	.	.	ENSG00000176155	ENST00000389641;ENST00000392347;ENST00000392343	T;T;T	0.24908	3.01;3.01;1.83	5.28	4.17	0.49024	.	0.257900	0.32444	N	0.006092	T	0.39489	0.1080	M	0.61703	1.905	0.42578	D	0.993207	D;P	0.55800	0.973;0.933	P;P	0.57283	0.817;0.659	T	0.17745	-1.0359	10	0.51188	T	0.08	-9.5475	9.5436	0.39266	0.0:0.8694:0.0:0.1306	.	165;165	Q2TAC2-2;Q2TAC2	.;CCD57_HUMAN	D	165	ENSP00000374292:G165D;ENSP00000376158:G165D;ENSP00000376154:G165D	ENSP00000374292:G165D	G	-	2	0	CCDC57	77749501	0.352000	0.24895	0.002000	0.10522	0.160000	0.22226	3.742000	0.55097	0.970000	0.38263	0.655000	0.94253	GGT	.	.	.	none		0.498	CCDC57-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000277182.3	NM_198082		T	80156212	C	T	80156212	3	4	206	1	0	0	0	0	1	0	0	0	2829	507	18	2	2313	2	CCDC57	17	80156212	Missense_Mutation	SNP	C	TCGA-IA-A83T-01A-11D-A34Z-10	143112	80156212	1038998	44	12541											
AFG3L2	10939	hgsc.bcm.edu	37	chr18	12359961	12359965	+	Frame_Shift_Del	DEL	ATTTT	ATTTT	-																															atgtagacaacaggcacccgAttttctccttctatgcccaa																										TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	ATTTT	ATTTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr18:12359961_12359965delATTTT	ENST00000269143.3	-	7	944_948	c.713_717delAAAAT	c.(712-717)gaaaatfs	p.EN238fs		NM_006796.2	NP_006787.2	Q9Y4W6	AFG32_HUMAN	AFG3-like AAA ATPase 2	238					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)	CAGGCACCCGATTTTCTCCTTCTAT	0.395																																					p.238_240del		Atlas-Indel,Pindel	.											.	AFG3L2	60	.	0			c.714_718del						PASS	.																																			SO:0001589	frameshift_variant	10939	exon7			.	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.713_717delAAAAT	chr18.hg19:g.12359961_12359965delATTTT	ENSP00000269143:p.Glu238fs	100.0	0.0	0		123.0	14.0	0.113821	NM_006796	Q6P1L0	Frame_Shift_Del	DEL	ENST00000269143.3	hg19	CCDS11859.1																																																																																			.	.	.	none		0.395	AFG3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254603.2	NM_006796		-	12359965	ATTTT	-	12359961	7	5	206	1	0	1	0	1	0	0	0	0	360	330	12	0	1720	0	AFG3L2	18	12359961	Frame_Shift_Del	DEL	ATTTT	TCGA-IA-A83T-01A-11D-A34Z-10		12359961	65717287	45	12542											
MAP2K7	5609	hgsc.bcm.edu	37	chr19	7975668	7975757	+	Splice_Site	DEL	CTGGGCAAGATGACAGTGGCGGTGAGTGACCAGGCGGGGCTTGCACTGGGCAGGATGACAGAGGCGGTGAGTGACCAGGCGGGGCGTGCA	CTGGGCAAGATGACAGTGGCGGTGAGTGACCAGGCGGGGCTTGCACTGGGCAGGATGACAGAGGCGGTGAGTGACCAGGCGGGGCGTGCA	-																															gccccatccccgagcgcattCtgggcaagatgacagtggcg																								rs373789571|rs367903083|rs12609075|rs41285782|rs537403823|rs574489981|rs554660875|rs372316207|rs191490120|rs566635337|rs550936407|rs538578150|rs551097008|rs370462728|rs181230065|rs12610278	byFrequency	TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	CTGGGCAAGATGACAGTGGCGGTGAGTGACCAGGCGGGGCTTGCACTGGGCAGGATGACAGAGGCGGTGAGTGACCAGGCGGGGCGTGCA	CTGGGCAAGATGACAGTGGCGGTGAGTGACCAGGCGGGGCTTGCACTGGGCAGGATGACAGAGGCGGTGAGTGACCAGGCGGGGCGTGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr19:7975668_7975757delCTGGGCAAGATGACAGTGGCGGTGAGTGACCAGGCGGGGCTTGCACTGGGCAGGATGACAGAGGCGGTGAGTGACCAGGCGGGGCGTGCA	ENST00000397979.3	+	6	709_729	c.655_675delCTGGGCAAGATGACAGTGGCGGTGAGTGACCAGGCGGGGCTTGCACTGGGCAGGATGACAGAGGCGGTGAGTGACCAGGCGGGGCGTGCA	c.(655-675)ctgggcaagatgacagtggcgdel	p.LGKMTVA219del	MAP2K7_ENST00000397981.3_Splice_Site_p.LGKMTVA219del|MAP2K7_ENST00000545011.1_Splice_Site_p.LGKMTVA261del|CTD-3193O13.13_ENST00000595655.1_RNA|MAP2K7_ENST00000397983.3_Splice_Site_p.LGKMTVA235del	NM_145185.2	NP_660186.1	O14733	MP2K7_HUMAN	mitogen-activated protein kinase kinase 7	219	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of neuron apoptotic process (GO:0043525)|response to heat (GO:0009408)|response to osmotic stress (GO:0006970)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|magnesium ion binding (GO:0000287)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(2)|central_nervous_system(3)|endometrium(1)|large_intestine(8)|lung(4)|ovary(1)	19						CGAGCGCATTCTGGGCAAGATGACAGTGGCGGTGAGTGACCAGGCGGGGCTTGCACTGGGCAGGATGACAGAGGCGGTGAGTGACCAGGCGGGGCGTGCACTGGGCAAGA	0.666																																					p.218_225del		Pindel	.											.	MAP2K7	66	.	0			c.654_675del						PASS	.																																			SO:0001630	splice_region_variant	5609	exon6			.	AF006689	CCDS42491.1, CCDS74277.1, CCDS74278.1	19p13.3-p13.2	2011-06-09			ENSG00000076984	ENSG00000076984	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6847	protein-coding gene	gene with protein product		603014		PRKMK7		9312068	Standard	XM_005272489		Approved	MKK7, Jnkk2	uc002mit.3	O14733	OTTHUMG00000137368	ENST00000397979.3:c.675+1CTGGGCAAGATGACAGTGGCGGTGAGTGACCAGGCGGGGCTTGCACTGGGCAGGATGACAGAGGCGGTGAGTGACCAGGCGGGGCGTGCA>-	chr19.hg19:g.7975668_7975757delCTGGGCAAGATGACAGTGGCGGTGAGTGACCAGGCGGGGCTTGCACTGGGCAGGATGACAGAGGCGGTGAGTGACCAGGCGGGGCGTGCA		65.0	0.0	.		56.0	18.0	0.321	NM_145185	B2R9S5|D6W659|O14648|O14816|O60452|O60453|Q1PG43|Q8IY10	Frame_Shift_Del	DEL	ENST00000397979.3	hg19	CCDS42491.1																																																																																			.	.	.	none		0.666	MAP2K7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000267980.1		In_Frame_Del	-	7975757	CTGGGCAAGATGACAGTGGCGGTGAGTGACCAGGCGGGGCTTGCACTGGGCAGGATGACAGAGGCGGTGAGTGACCAGGCGGGGCGTGCA	-	7975668	8	5	206	1	0	1	0	1	0	0	1	0	9249	912	32	0	677	0	MAP2K7	19	7975668	Splice_Site	DEL	CTGGGCAAGATGACAGTGGCGGTGAGTGACCAGGCGGGGCTTGCACTGGGCAGGATGACAGAGGCGGTGAGTGACCAGGCGGGGCGTGCA	TCGA-IA-A83T-01A-11D-A34Z-10		7975668	51153315	46	12543											
MUC16	94025	hgsc.bcm.edu	37	chr19	9016700	9016700	+	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	gatggagtccctgacccaagGtccactgtggaggtcccagg	8	7	14	12	0	0	1	0	1	0	0	3	4	3	3	4	5	0	0	4	5	1	0			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr19:9016700G>A	ENST00000397910.4	-	28	38240	c.38037C>T	c.(38035-38037)gaC>gaT	p.D12679D		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12681					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						CTGACCCAAGGTCCACTGTGG	0.488																																					p.D12679D		Atlas-SNP	.											.	MUC16	4315	.	0			c.C38037T						PASS	.						56	55	56					19																	9016700		1884	4123	6007	SO:0001819	synonymous_variant	94025	exon28			CCCAAGGTCCACT	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.38037C>T	chr19.hg19:g.9016700G>A		97.0	0.0	.		89.0	24.0	.	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.	.	none		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9016700	G	A	9016700	2	1	206	1	0	0	0	0	0	0	0	1	9980	1252	44	2		2	MUC16	19	9016700	Silent	SNP	G	TCGA-IA-A83T-01A-11D-A34Z-10	1041032	9016700	50112283	47	12544											
MUC16	94025	hgsc.bcm.edu	37	chr19	9075870	9075870	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgtagctcttgcctctgttGtaagagctgtctgcccttgt	5	16	10	10	0	3	1	0	0	3	1	3	1	3	1	2	0	4	5	2	0	2	5			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr19:9075870G>A	ENST00000397910.4	-	3	11779	c.11576C>T	c.(11575-11577)aCa>aTa	p.T3859I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3860	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						TGCCTCTGTTGTAAGAGCTGT	0.473																																					p.T3859I		Atlas-SNP	.											.	MUC16	4315	.	0			c.C11576T						PASS	.						148	132	137					19																	9075870		2026	4193	6219	SO:0001583	missense	94025	exon3			TCTGTTGTAAGAG	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.11576C>T	chr19.hg19:g.9075870G>A	ENSP00000381008:p.Thr3859Ile	157.0	0.0	.		167.0	43.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	5.304	0.241447	0.10077	.	.	ENSG00000181143	ENST00000397910	T	0.02472	4.28	1.52	0.439	0.16567	.	.	.	.	.	T	0.01489	0.0048	N	0.08118	0	.	.	.	B	0.30068	0.267	B	0.21708	0.036	T	0.43032	-0.9416	8	0.87932	D	0	.	3.9495	0.09363	0.2362:0.0:0.7638:0.0	.	3859	B5ME49	.	I	3859	ENSP00000381008:T3859I	ENSP00000381008:T3859I	T	-	2	0	MUC16	8936870	0.010000	0.17322	0.057000	0.19452	0.459000	0.32528	0.103000	0.15292	0.202000	0.20498	0.205000	0.17691	ACA	.	.	.	none		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9075870	G	A	9075870	3	1	206	1	0	0	0	0	1	0	0	0	9980	1377	48	2	32275	2	MUC16	19	9075870	Missense_Mutation	SNP	G	TCGA-IA-A83T-01A-11D-A34Z-10	59170	9075870	50053113	48	12545											
GCDH	2639	hgsc.bcm.edu	37	chr19	13002330	13002330	+	Missense_Mutation	SNP	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	ggagaacacagagccaactgGctaagtgtaaggacctctgg	13	6	13	9	0	1	2	0	0	1	2	1	4	1	3	2	4	3	2	2	4	4	2			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr19:13002330G>A	ENST00000222214.5	+	3	332	c.121G>A	c.(121-123)Gct>Act	p.A41T	GCDH_ENST00000457854.1_Missense_Mutation_p.A41T|GCDH_ENST00000422947.2_5'UTR|GCDH_ENST00000591470.1_Missense_Mutation_p.A41T			Q92947	GCDH_HUMAN	glutaryl-CoA dehydrogenase	41					cellular nitrogen compound metabolic process (GO:0034641)|fatty acid oxidation (GO:0019395)|fatty-acyl-CoA biosynthetic process (GO:0046949)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tryptophan metabolic process (GO:0006568)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|glutaryl-CoA dehydrogenase activity (GO:0004361)			autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)	19					Flavin adenine dinucleotide(DB03147)	GAGCCAACTGGCTAAGTGTAA	0.597																																					p.R41R	GBM(123;875 1636 7726 16444 26754)	Atlas-SNP	.											.	GCDH	76	.	0			c.A121A						PASS	.						151	137	142					19																	13002330		2203	4300	6503	SO:0001583	missense	2639	exon3			CAACTGGCTAAGT	AF012342	CCDS12286.1	19p13.2	2010-04-30	2010-04-30			ENSG00000105607	1.3.99.7		4189	protein-coding gene	gene with protein product		608801	"glutaryl-Coenzyme A dehydrogenase"			1438360, 8088809	Standard	NM_000159		Approved	ACAD5	uc002mvq.4	Q92947		ENST00000222214.5:c.121G>A	chr19.hg19:g.13002330G>A	ENSP00000222214:p.Ala41Thr	55.0	0.0	.		68.0	13.0	.	NM_013976	A8K2Z2|O14719	Silent	SNP	ENST00000222214.5	hg19	CCDS12286.1	.	.	.	.	.	.	.	.	.	.	G	13.33	2.203936	0.38905	.	.	ENSG00000105607	ENST00000457854;ENST00000222214	D;D	0.97575	-4.37;-4.44	3.74	0.44	0.16572	.	2.183690	0.01751	N	0.029922	D	0.91341	0.7269	N	0.08118	0	0.19300	N	0.999978	B;B	0.11235	0.0;0.004	B;B	0.09377	0.002;0.004	D	0.85180	0.1003	10	0.27082	T	0.32	.	5.9903	0.19456	0.3389:0.0:0.6611:0.0	.	41;41	Q92947;Q92947-2	GCDH_HUMAN;.	T	41	ENSP00000394872:A41T;ENSP00000222214:A41T	ENSP00000222214:A41T	A	+	1	0	GCDH	12863330	0.000000	0.05858	0.003000	0.11579	0.448000	0.32197	-0.354000	0.07681	0.201000	0.20466	-0.448000	0.05591	GCT	.	.	.	none		0.597	GCDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451897.1			A	13002330	G	A	13002330	3	1	206	1	0	0	0	0	1	0	0	0	6294	1203	42	2	127	2	GCDH	19	13002330	Missense_Mutation	SNP	G	TCGA-IA-A83T-01A-11D-A34Z-10	3926460	13002330	46126653	49	12546											
EPS15L1	58513	hgsc.bcm.edu	37	chr19	16545212	16545214	+	In_Frame_Del	DEL	GAG	GAG	-																															agaggcagctttgagttcatGaggactggcttgactttgtc																										TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr19:16545212_16545214delGAG	ENST00000248070.6	-	7	599_601	c.460_462delCTC	c.(460-462)ctcdel	p.L154del	EPS15L1_ENST00000594975.1_In_Frame_Del_p.L154del|EPS15L1_ENST00000597937.1_In_Frame_Del_p.L154del|EPS15L1_ENST00000602009.1_5'UTR|EPS15L1_ENST00000455140.2_In_Frame_Del_p.L154del|EPS15L1_ENST00000535753.2_In_Frame_Del_p.L154del	NM_021235.2	NP_067058.1	Q9UBC2	EP15R_HUMAN	epidermal growth factor receptor pathway substrate 15-like 1	154	EH 2. {ECO:0000255|PROSITE- ProRule:PRU00077}.|Interaction with DAB2. {ECO:0000250}.				endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	clathrin coat of coated pit (GO:0030132)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(4)|skin(2)	30						TTGAGTTCATGAGGACTGGCTTG	0.512																																					p.154_155del		Atlas-Indel,Pindel	.											.	EPS15L1	81	.	0			c.461_463del						PASS	.																																			SO:0001651	inframe_deletion	58513	exon7			.	AF110265	CCDS32944.1, CCDS58653.1, CCDS58654.1, CCDS59363.1	19p13.12	2013-01-10				ENSG00000127527		"EF-hand domain containing"	24634	protein-coding gene	gene with protein product							Standard	NM_001258374		Approved	eps15R	uc002ndx.4	Q9UBC2		ENST00000248070.6:c.460_462delCTC	chr19.hg19:g.16545212_16545214delGAG	ENSP00000248070:p.Leu154del	83.0	0.0	0		61.0	11.0	0.180328	NM_021235	A2RRF3|A5PL29|B4DKA3	In_Frame_Del	DEL	ENST00000248070.6	hg19	CCDS32944.1																																																																																			.	.	.	none		0.512	EPS15L1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461040.1	NM_021235		-	16545214	GAG	-	16545212	7	5	206	1	0	1	0	1	0	0	0	0	5195	1277	45	0	2200	0	EPS15L1	19	16545212	In_Frame_Del	DEL	GAG	TCGA-IA-A83T-01A-11D-A34Z-10	3542882	16545212	42583771	50	12547											
ZBTB32	27033	hgsc.bcm.edu	37	chr19	36206193	36206193	+	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	gagggaaaatccagggggctCtgaggaaagtctgcgcaagc	12	5	16	8	1	2	1	0	1	2	0	3	4	3	3	1	4	2	2	1	4	4	0			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr19:36206193C>T	ENST00000392197.2	+	3	983	c.665C>T	c.(664-666)tCt>tTt	p.S222F	KMT2B_ENST00000341701.1_5'Flank|KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_5'Flank|ZBTB32_ENST00000262630.3_Missense_Mutation_p.S222F|KMT2B_ENST00000222270.7_5'Flank			Q9Y2Y4	ZBT32_HUMAN	zinc finger and BTB domain containing 32	222					DNA repair (GO:0006281)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cytokine production (GO:0001817)|T cell proliferation (GO:0042098)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(1)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	14	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CCAGGGGGCTCTGAGGAAAGT	0.627																																					p.S222F		Atlas-SNP	.											.	ZBTB32	33	.	0			c.C665T						PASS	.						50	51	51					19																	36206193		2203	4300	6503	SO:0001583	missense	27033	exon2			GGGGCTCTGAGGA	AF130255	CCDS12471.1	19q13.1	2013-01-08			ENSG00000011590	ENSG00000011590		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16763	protein-coding gene	gene with protein product	"repressor of GATA"	605859				10572087	Standard	XM_005258739		Approved	TZFP, FAZF, FAXF, Rog, ZNF538	uc002oay.3	Q9Y2Y4	OTTHUMG00000048118	ENST00000392197.2:c.665C>T	chr19.hg19:g.36206193C>T	ENSP00000376035:p.Ser222Phe	20.0	0.0	.		19.0	7.0	.	NM_014383	Q8WVP2	Missense_Mutation	SNP	ENST00000392197.2	hg19	CCDS12471.1	.	.	.	.	.	.	.	.	.	.	C	16.77	3.215582	0.58452	.	.	ENSG00000011590	ENST00000262630;ENST00000392197	T;T	0.10763	2.84;2.84	5.06	5.06	0.68205	.	0.000000	0.42964	D	0.000622	T	0.21921	0.0528	L	0.32530	0.975	0.39248	D	0.963974	D	0.71674	0.998	D	0.79784	0.993	T	0.01566	-1.1323	10	0.45353	T	0.12	-11.7321	13.9419	0.64059	0.0:1.0:0.0:0.0	.	222	Q9Y2Y4	ZBT32_HUMAN	F	222	ENSP00000262630:S222F;ENSP00000376035:S222F	ENSP00000262630:S222F	S	+	2	0	ZBTB32	40898033	0.998000	0.40836	1.000000	0.80357	0.471000	0.32888	2.812000	0.47994	2.359000	0.80004	0.561000	0.74099	TCT	.	.	.	none		0.627	ZBTB32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109491.3	NM_014383		T	36206193	C	T	36206193	3	4	206	1	0	0	0	0	1	0	0	0	17547	913	32	2	667	2	ZBTB32	19	36206193	Missense_Mutation	SNP	C	TCGA-IA-A83T-01A-11D-A34Z-10	19660981	36206193	22922790	51	12548											
BAX	581	hgsc.bcm.edu	37	chr19	49459013	49459013	+	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	gccctggacccggtgcctcaGgatgcgtccaccaagaagct	8	6	12	15	2	1	1	1	0	0	1	2	3	2	3	5	3	3	1	5	3	2	0			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr19:49459013G>T	ENST00000345358.7	+	3	208	c.156G>T	c.(154-156)caG>caT	p.Q52H	BAX_ENST00000293288.8_Missense_Mutation_p.Q52H|BAX_ENST00000391871.3_Missense_Mutation_p.R35M|BAX_ENST00000539787.1_Missense_Mutation_p.Q52H|BAX_ENST00000354470.3_Intron|BAX_ENST00000415969.2_Missense_Mutation_p.Q52H	NM_138761.3|NM_138764.4	NP_620116.1|NP_620119.2	Q07812	BAX_HUMAN	BCL2-associated X protein	52					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|apoptotic process involved in patterning of blood vessels (GO:1902262)|apoptotic signaling pathway (GO:0097190)|B cell apoptotic process (GO:0001783)|B cell homeostasis (GO:0001782)|B cell homeostatic proliferation (GO:0002358)|B cell negative selection (GO:0002352)|B cell receptor apoptotic signaling pathway (GO:1990117)|blood vessel remodeling (GO:0001974)|cellular response to organic substance (GO:0071310)|cellular response to UV (GO:0034644)|cerebral cortex development (GO:0021987)|development of secondary sexual characteristics (GO:0045136)|ectopic germ cell programmed cell death (GO:0035234)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|establishment or maintenance of transmembrane electrochemical gradient (GO:0010248)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|fertilization (GO:0009566)|germ cell development (GO:0007281)|glycosphingolipid metabolic process (GO:0006687)|homeostasis of number of cells within a tissue (GO:0048873)|hypothalamus development (GO:0021854)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion morphogenesis (GO:0070584)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein binding (GO:0032091)|neuron apoptotic process (GO:0051402)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of apoptotic DNA fragmentation (GO:1902512)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of developmental pigmentation (GO:0048087)|positive regulation of endoplasmic reticulum unfolded protein response (GO:1900103)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|post-embryonic camera-type eye morphogenesis (GO:0048597)|protein homooligomerization (GO:0051260)|protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:0001844)|protein oligomerization (GO:0051259)|regulation of cell cycle (GO:0051726)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of mitochondrial membrane permeability involved in programmed necrotic cell death (GO:1902445)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of nitrogen utilization (GO:0006808)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|release of cytochrome c from mitochondria (GO:0001836)|release of matrix enzymes from mitochondria (GO:0032976)|response to axon injury (GO:0048678)|response to gamma radiation (GO:0010332)|response to salt stress (GO:0009651)|response to toxic substance (GO:0009636)|retina development in camera-type eye (GO:0060041)|retinal cell apoptotic process (GO:1990009)|retinal cell programmed cell death (GO:0046666)|Sertoli cell proliferation (GO:0060011)|spermatid differentiation (GO:0048515)|T cell homeostatic proliferation (GO:0001777)|thymocyte apoptotic process (GO:0070242)|transformed cell apoptotic process (GO:0006927)|vagina development (GO:0060068)|viral process (GO:0016032)	BAX complex (GO:0097144)|Bcl-2 family protein complex (GO:0097136)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrial permeability transition pore complex (GO:0005757)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|pore complex (GO:0046930)	BH3 domain binding (GO:0051434)|channel activity (GO:0015267)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(4)	17		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000159)|all cancers(93;0.00047)|GBM - Glioblastoma multiforme(486;0.018)|Epithelial(262;0.0279)		CGGTGCCTCAGGATGCGTCCA	0.622																																					p.Q52H		Atlas-SNP	.											.	BAX	69	.	0			c.G156T						PASS	.						54	52	53					19																	49459013		2203	4300	6503	SO:0001583	missense	581	exon3			GCCTCAGGATGCG		CCDS12742.1, CCDS12743.1, CCDS12744.1, CCDS12745.1, CCDS12745.2	19q13.3-q13.4	2014-03-07			ENSG00000087088	ENSG00000087088			959	protein-coding gene	gene with protein product		600040				8358790	Standard	NM_138761		Approved	BCL2L4	uc002plf.1	Q07812	OTTHUMG00000160476	ENST00000345358.7:c.156G>T	chr19.hg19:g.49459013G>T	ENSP00000263262:p.Gln52His	97.0	0.0	.		116.0	37.0	.	NM_004324	A8K4W1|P55269|Q07814|Q07815|Q8WZ49|Q9NR76|Q9NYG7|Q9UCZ6|Q9UCZ7|Q9UQD6	Missense_Mutation	SNP	ENST00000345358.7	hg19	CCDS12742.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.523|8.523	0.869294|0.869294	0.17322|0.17322	.|.	.|.	ENSG00000087088|ENSG00000087088	ENST00000539787;ENST00000345358;ENST00000415969;ENST00000293288|ENST00000391871	T;T;T;T|.	0.31247|.	2.61;1.5;2.85;2.81|.	4.21|4.21	0.963|0.963	0.19649|0.19649	.|.	0.765258|.	0.12506|.	N|.	0.462920|.	T|T	0.38161|0.38161	0.1030|0.1030	L|L	0.44542|0.44542	1.39|1.39	0.20563|0.20563	N|N	0.999888|0.999888	B;B;P|.	0.51653|.	0.315;0.383;0.947|.	B;B;B|.	0.40228|.	0.044;0.07;0.323|.	T|T	0.35475|0.35475	-0.9787|-0.9787	10|6	0.48119|0.87932	T|D	0.1|0	-4.6172|-4.6172	5.9709|5.9709	0.19351|0.19351	0.3253:0.0:0.6747:0.0|0.3253:0.0:0.6747:0.0	.|.	52;52;52|.	Q07812;Q07812-8;Q07812-2|.	BAX_HUMAN;.;.|.	H|M	52|35	ENSP00000441413:Q52H;ENSP00000263262:Q52H;ENSP00000389971:Q52H;ENSP00000293288:Q52H|.	ENSP00000293288:Q52H|ENSP00000375744:R35M	Q|R	+|+	3|2	2|0	BAX|BAX	54150825|54150825	1.000000|1.000000	0.71417|0.71417	0.570000|0.570000	0.28473|0.28473	0.556000|0.556000	0.35491|0.35491	2.007000|2.007000	0.40883|0.40883	0.331000|0.331000	0.23511|0.23511	-0.259000|-0.259000	0.10710|0.10710	CAG|AGG	.	.	.	none		0.622	BAX-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360767.1	NM_138763		T	49459013	G	T	49459013	3	4	206	1	0	0	0	0	1	0	0	0	1328	991	35	4	166	4	BAX	19	49459013	Missense_Mutation	SNP	G	TCGA-IA-A83T-01A-11D-A34Z-10	13252820	49459013	9669970	52	12549											
TTYH1	57348	hgsc.bcm.edu	37	chr19	54946848	54946848	+	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	gcagcctgccccgagcctggGccctcttcccacccaggtca	5	6	10	20	1	2	0	1	0	1	0	3	1	3	0	7	2	3	1	7	2	0	1			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr19:54946848G>T	ENST00000376530.3	+	11	1355	c.1252G>T	c.(1252-1254)Gcc>Tcc	p.A418S	CTD-2587H19.3_ENST00000597355.1_lincRNA|TTYH1_ENST00000376531.3_Missense_Mutation_p.A418S|TTYH1_ENST00000489425.1_3'UTR|TTYH1_ENST00000301194.4_Missense_Mutation_p.A418S|AC008746.3_ENST00000457113.1_RNA|AC008746.12_ENST00000599382.1_lincRNA|TTYH1_ENST00000391739.3_Missense_Mutation_p.G448V|CTD-2587H19.2_ENST00000596631.1_RNA	NM_001201461.1|NM_020659.3	NP_001188390.1|NP_065710.1	Q9H313	TTYH1_HUMAN	tweety family member 1	418					cell-substrate adhesion (GO:0031589)|chloride transport (GO:0006821)|filopodium assembly (GO:0046847)|ion transmembrane transport (GO:0034220)|iron ion transmembrane transport (GO:0034755)|iron ion transport (GO:0006826)|mitotic nuclear division (GO:0007067)|regulation of anion transport (GO:0044070)|single organismal cell-cell adhesion (GO:0016337)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|filopodium membrane (GO:0031527)|filopodium tip (GO:0032433)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum membrane (GO:0030868)	calcium ion binding (GO:0005509)|iron ion transmembrane transporter activity (GO:0005381)|volume-sensitive chloride channel activity (GO:0072320)			endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0767)		CCGAGCCTGGGCCCTCTTCCC	0.701																																					p.A418S		Atlas-SNP	.											.	TTYH1	78	.	0			c.G1252T						PASS	.						22	21	21					19																	54946848		2201	4295	6496	SO:0001583	missense	57348	exon11			GCCTGGGCCCTCT	AF177909	CCDS12893.1, CCDS33106.1, CCDS56102.1	19q13.4	2013-09-02	2013-09-02		ENSG00000167614	ENSG00000167614			13476	protein-coding gene	gene with protein product		605784	"tweety (Drosophila) homolog 1", "tweety homolog 1 (Drosophila)"			10950931	Standard	NM_020659		Approved		uc002qfr.3	Q9H313	OTTHUMG00000065544	ENST00000376530.3:c.1252G>T	chr19.hg19:g.54946848G>T	ENSP00000365713:p.Ala418Ser	85.0	0.0	.		108.0	38.0	.	NM_020659	B0VJY3|B0VJY4|B0VJY5|B2VAL9|Q5U682|Q68A17|Q6L750|Q6ZTE5|Q8WUU2	Missense_Mutation	SNP	ENST00000376530.3	hg19	CCDS12893.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.79|13.79	2.341380|2.341380	0.41498|0.41498	.|.	.|.	ENSG00000167614|ENSG00000167614	ENST00000301194;ENST00000376530;ENST00000376531|ENST00000391739	T;T;T|T	0.11385|0.29397	2.78;2.78;2.78|1.57	4.04|4.04	4.04|4.04	0.47022|0.47022	.|.	0.236204|.	0.37393|.	N|.	0.002102|.	T|T	0.43722|0.43722	0.1260|0.1260	L|L	0.60455|0.60455	1.87|1.87	0.47407|0.47407	D|D	0.999411|0.999411	D;D;D|D	0.69078|0.69078	0.99;0.978;0.997|0.997	P;P;D|P	0.79108|0.60789	0.744;0.738;0.992|0.879	T|T	0.40079|0.40079	-0.9582|-0.9582	10|9	0.10636|0.87932	T|D	0.68|0	-17.4112|-17.4112	8.0399|8.0399	0.30515|0.30515	0.1138:0.0:0.8862:0.0|0.1138:0.0:0.8862:0.0	.|.	418;418;418|448	Q9H313-2;Q9H313-3;Q9H313|B7Z1H9	.;.;TTYH1_HUMAN|.	S|V	418|448	ENSP00000301194:A418S;ENSP00000365713:A418S;ENSP00000365714:A418S|ENSP00000375619:G448V	ENSP00000301194:A418S|ENSP00000375619:G448V	A|G	+|+	1|2	0|0	TTYH1|TTYH1	59638660|59638660	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	2.072000|2.072000	0.41510|0.41510	1.982000|1.982000	0.57802|0.57802	0.561000|0.561000	0.74099|0.74099	GCC|GGC	.	.	.	none		0.701	TTYH1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140498.1			T	54946848	G	T	54946848	3	4	206	1	0	0	0	0	1	0	0	0	16751	1203	42	4	1294	4	TTYH1	19	54946848	Missense_Mutation	SNP	G	TCGA-IA-A83T-01A-11D-A34Z-10	5487835	54946848	4182135	53	12550											
MMP24	10893	hgsc.bcm.edu	37	chr20	33862094	33862094	+	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	gattacacctatttctacaaGggccgggactactggaagtt	11	11	10	9	1	1	0	0	0	1	0	1	3	1	2	2	3	3	1	2	3	6	6			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr20:33862094G>T	ENST00000246186.6	+	9	1705	c.1620G>T	c.(1618-1620)aaG>aaT	p.K540N	MMP24-AS1_ENST00000454184.1_RNA|MMP24-AS1_ENST00000456350.1_RNA|MMP24-AS1_ENST00000455178.1_RNA|MMP24-AS1_ENST00000438751.1_RNA|MMP24-AS1_ENST00000424358.1_RNA|MMP24-AS1_ENST00000435366.1_RNA|MMP24-AS1_ENST00000433764.1_RNA|EDEM2_ENST00000540582.1_Intron|MMP24-AS1_ENST00000566203.2_RNA|MMP24-AS1_ENST00000453892.1_RNA|RP4-614O4.11_ENST00000444717.1_RNA	NM_006690.3	NP_006681.1	Q9Y5R2	MMP24_HUMAN	matrix metallopeptidase 24 (membrane-inserted)	540					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)	ATTTCTACAAGGGCCGGGACT	0.567																																					p.K540N		Atlas-SNP	.											.	MMP24	35	.	0			c.G1620T						PASS	.						90	104	99					20																	33862094		2049	4192	6241	SO:0001583	missense	10893	exon9			CTACAAGGGCCGG	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.1620G>T	chr20.hg19:g.33862094G>T	ENSP00000246186:p.Lys540Asn	15.0	0.0	.		32.0	11.0	.	NM_006690	B7ZBG8|Q9H440	Missense_Mutation	SNP	ENST00000246186.6	hg19	CCDS46593.1	.	.	.	.	.	.	.	.	.	.	G	16.35	3.099273	0.56183	.	.	ENSG00000125966	ENST00000246186;ENST00000540655	T	0.04551	3.6	5.1	-0.206	0.13193	Hemopexin/matrixin (2);	0.215289	0.46145	D	0.000307	T	0.29914	0.0748	H	0.98027	4.13	0.58432	D	0.999997	D	0.76494	0.999	D	0.77004	0.989	T	0.30208	-0.9986	10	0.87932	D	0	.	10.0056	0.41955	0.5282:0.0:0.4718:0.0	.	540	Q9Y5R2	MMP24_HUMAN	N	540;488	ENSP00000246186:K540N	ENSP00000246186:K540N	K	+	3	2	MMP24	33325508	1.000000	0.71417	0.993000	0.49108	0.989000	0.77384	1.437000	0.34991	-0.268000	0.09312	-0.150000	0.13652	AAG	.	.	.	none		0.567	MMP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078851.4	NM_006690		T	33862094	G	T	33862094	3	4	206	1	0	0	0	0	1	0	0	0	9668	991	35	4	1404	4	MMP24	20	33862094	Missense_Mutation	SNP	G	TCGA-IA-A83T-01A-11D-A34Z-10		33862094	29163426	54	12551											
KREMEN1	83999	hgsc.bcm.edu	37	chr22	29533423	29533423	+	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	ctatgccacggggagggtctGctactggaccatccgggttc	6	9	14	12	2	1	0	0	0	1	0	3	2	2	2	3	5	3	2	3	5	2	3			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr22:29533423G>C	ENST00000407188.1	+	6	719	c.719G>C	c.(718-720)tGc>tCc	p.C240S	KREMEN1_ENST00000400335.4_Missense_Mutation_p.C242S|KREMEN1_ENST00000327813.5_Missense_Mutation_p.C242S|KREMEN1_ENST00000400338.2_Missense_Mutation_p.C242S			Q96MU8	KREM1_HUMAN	kringle containing transmembrane protein 1	240	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				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						GGGAGGGTCTGCTACTGGACC	0.612																																					p.C242S		Atlas-SNP	.											.	KREMEN1	46	.	0			c.G725C						PASS	.						76	77	77					22																	29533423		1917	4125	6042	SO:0001583	missense	83999	exon6			GGGTCTGCTACTG	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.719G>C	chr22.hg19:g.29533423G>C	ENSP00000385431:p.Cys240Ser	111.0	0.0	.		169.0	29.0	.	NM_001039570	B0QY46|B0QY47|B1AJR5|Q5TIB9|Q6P3X6|Q9BY70|Q9UGS5|Q9UGU1	Missense_Mutation	SNP	ENST00000407188.1	hg19	CCDS43000.2	.	.	.	.	.	.	.	.	.	.	G	24.9	4.579944	0.86645	.	.	ENSG00000183762	ENST00000400335;ENST00000400338;ENST00000327813;ENST00000407188	T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18	5.14	5.14	0.70334	CUB (5);	0.000000	0.64402	D	0.000002	D	0.85682	0.5753	H	0.96460	3.825	0.80722	D	1	D;D;D	0.89917	0.997;1.0;0.989	D;D;D	0.83275	0.994;0.996;0.985	D	0.90105	0.4187	10	0.87932	D	0	.	16.485	0.84182	0.0:0.0:1.0:0.0	.	240;242;242	Q96MU8;Q96MU8-2;Q96MU8-3	KREM1_HUMAN;.;.	S	242;242;242;240	ENSP00000383189:C242S;ENSP00000383192:C242S;ENSP00000331242:C242S;ENSP00000385431:C240S	ENSP00000331242:C242S	C	+	2	0	KREMEN1	27863423	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	9.476000	0.97823	2.587000	0.87381	0.591000	0.81541	TGC	.	.	.	none		0.612	KREMEN1-004	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320947.1			C	29533423	G	C	29533423	3	2	206	1	0	0	0	0	1	0	0	0	8449	1319	46	4	747	4	KREMEN1	22	29533423	Missense_Mutation	SNP	G	TCGA-IA-A83T-01A-11D-A34Z-10		29533423	21771143	55	12552											
CABP7	164633	hgsc.bcm.edu	37	chr22	30123661	30123661	+	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	ctctcctcagagatccgagaGgccttcaaggtgtttgaccg	8	10	11	12	2	3	3	2	1	1	2	5	5	4	3	4	2	0	1	4	2	1	2			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr22:30123661G>T	ENST00000216144.3	+	2	461	c.120G>T	c.(118-120)gaG>gaT	p.E40D		NM_182527.2	NP_872333.1	Q86V35	CABP7_HUMAN	calcium binding protein 7	40	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	calcium ion binding (GO:0005509)			lung(1)|skin(3)	4			OV - Ovarian serous cystadenocarcinoma(5;0.00442)|Epithelial(10;0.215)|all cancers(5;0.233)			AGATCCGAGAGGCCTTCAAGG	0.607																																					p.E40D		Atlas-SNP	.											.	CABP7	9	.	0			c.G120T						PASS	.						136	126	130					22																	30123661		2203	4300	6503	SO:0001583	missense	164633	exon2			CCGAGAGGCCTTC	BC051805	CCDS13867.1	22q12.2	2013-01-10			ENSG00000100314	ENSG00000100314		"EF-hand domain containing"	20834	protein-coding gene	gene with protein product						11785943	Standard	NM_182527		Approved	MGC57793	uc003agl.3	Q86V35	OTTHUMG00000151282	ENST00000216144.3:c.120G>T	chr22.hg19:g.30123661G>T	ENSP00000216144:p.Glu40Asp	44.0	0.0	.		56.0	9.0	.	NM_182527		Missense_Mutation	SNP	ENST00000216144.3	hg19	CCDS13867.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.981132	0.93044	.	.	ENSG00000100314	ENST00000216144	T	0.72835	-0.69	5.59	4.58	0.56647	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.77246	0.4102	L	0.41079	1.255	0.80722	D	1	D	0.76494	0.999	D	0.72625	0.978	T	0.79412	-0.1814	10	0.87932	D	0	-13.5271	12.9895	0.58610	0.0784:0.0:0.9215:0.0	.	40	Q86V35	CABP7_HUMAN	D	40	ENSP00000216144:E40D	ENSP00000216144:E40D	E	+	3	2	CABP7	28453661	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.603000	0.46266	1.366000	0.46076	0.561000	0.74099	GAG	.	.	.	none		0.607	CABP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322080.1	NM_182527		T	30123661	G	T	30123661	3	4	206	1	0	0	0	0	1	0	0	0	2537	991	35	4	126	4	CABP7	22	30123661	Missense_Mutation	SNP	G	TCGA-IA-A83T-01A-11D-A34Z-10	590238	30123661	21180905	56	12553											
TMEM184B	25829	hgsc.bcm.edu	37	chr22	38621517	38621517	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcagctcccgggtggcgAagtagaagaggaagagggcg	11	4	19	7	3	0	4	0	1	0	3	1	6	1	5	1	4	2	3	1	4	4	1			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chr22:38621517A>G	ENST00000361906.3	-	7	909	c.701T>C	c.(700-702)tTc>tCc	p.F234S	TMEM184B_ENST00000361684.4_Missense_Mutation_p.F234S|TMEM184B_ENST00000504337.1_5'Flank	NM_001195072.1|NM_012264.4	NP_001182001.1|NP_036396.2	Q9Y519	T184B_HUMAN	transmembrane protein 184B	234						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(2)|skin(2)|upper_aerodigestive_tract(1)	8	Melanoma(58;0.045)					CCGGGTGGCGAAGTAGAAGAG	0.597																																					p.F234S		Atlas-SNP	.											.	TMEM184B	19	.	0			c.T701C						PASS	.						131	116	121					22																	38621517		2203	4300	6503	SO:0001583	missense	25829	exon7			GTGGCGAAGTAGA	AL096879	CCDS13969.2	22q12	2008-02-04	2007-07-11	2007-07-11	ENSG00000198792	ENSG00000198792			1310	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 5"	C22orf5		10591208	Standard	NM_012264		Approved	HS5O6A, DKFZP586A1024, FM08	uc003avf.1	Q9Y519	OTTHUMG00000030557	ENST00000361906.3:c.701T>C	chr22.hg19:g.38621517A>G	ENSP00000355210:p.Phe234Ser	33.0	0.0	.		52.0	8.0	.	NM_001195071	A8K9D7|Q63HM8|Q7Z421|Q8NBM5|Q9UGT8|Q9UGT9|Q9UGV5	Missense_Mutation	SNP	ENST00000361906.3	hg19	CCDS13969.2	.	.	.	.	.	.	.	.	.	.	A	18.13	3.556279	0.65425	.	.	ENSG00000198792	ENST00000361906;ENST00000361684	T;T	0.40756	1.02;1.02	5.85	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.38532	0.1044	L	0.55743	1.74	0.80722	D	1	B	0.17465	0.022	B	0.18263	0.021	T	0.12578	-1.0542	10	0.32370	T	0.25	-14.3997	12.0788	0.53659	0.8709:0.0:0.0:0.1291	.	234	Q9Y519	T184B_HUMAN	S	234	ENSP00000355210:F234S;ENSP00000354441:F234S	ENSP00000354441:F234S	F	-	2	0	TMEM184B	36951463	1.000000	0.71417	0.732000	0.30844	0.884000	0.51177	9.339000	0.96797	0.982000	0.38575	0.533000	0.62120	TTC	.	.	.	none		0.597	TMEM184B-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075445.4	NM_012264		G	38621517	A	G	38621517	3	3	206	1	0	0	0	0	1	0	0	0	16117	246	9	3	534	3	TMEM184B	22	38621517	Missense_Mutation	SNP	A	TCGA-IA-A83T-01A-11D-A34Z-10	8497856	38621517	12683049	57	12554											
MXRA5	25878	hgsc.bcm.edu	37	chrX	3229194	3229194	+	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	tgaaccgccaagtaagtcttGttccggatggtggcgggcgc	7	9	15	10	4	1	1	0	1	1	0	2	2	2	2	3	4	1	2	3	4	3	3			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chrX:3229194G>T	ENST00000217939.6	-	7	7204	c.7050C>A	c.(7048-7050)aaC>aaA	p.N2350K		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	2350	Ig-like C2-type 8.					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)				AGTAAGTCTTGTTCCGGATGG	0.562																																					p.N2350K		Atlas-SNP	.											.	MXRA5	815	.	0			c.C7050A						PASS	.						152	124	133					X																	3229194		2203	4300	6503	SO:0001583	missense	25878	exon7			AGTCTTGTTCCGG	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.7050C>A	chrX.hg19:g.3229194G>T	ENSP00000217939:p.Asn2350Lys	37.0	0.0	.		38.0	4.0	.	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	hg19	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	G	11.57	1.677795	0.29783	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.62941	-0.01	4.29	1.46	0.22682	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.41294	U	0.000913	T	0.61825	0.2378	L	0.43152	1.355	0.33584	D	0.600307	D	0.59767	0.986	D	0.63381	0.914	T	0.63739	-0.6569	10	0.11182	T	0.66	.	7.8018	0.29178	0.4656:0.0:0.5344:0.0	.	2350	Q9NR99	MXRA5_HUMAN	K	2350	ENSP00000217939:N2350K	ENSP00000217939:N2350K	N	-	3	2	MXRA5	3239194	0.999000	0.42202	0.794000	0.32065	0.289000	0.27227	0.507000	0.22675	-0.097000	0.12307	0.597000	0.82753	AAC	.	.	.	none		0.562	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		T	3229194	G	T	3229194	3	4	206	1	0	0	0	0	1	0	0	0	10010	1368	48	4	1440	4	MXRA5	23	3229194	Missense_Mutation	SNP	G	TCGA-IA-A83T-01A-11D-A34Z-10		3229194	152041366	58	12555											
AR	367	hgsc.bcm.edu	37	chrX	66765167	66765167	+	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	tttgctgctgctgcagcagcAgcagcagcagcagcagcagc	9	6	13	13	0	0	0	0	0	0	0	0	0	0	0	0	0	13	12	0	0	0	1			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chrX:66765167A>T	ENST00000374690.3	+	1	703	c.179A>T	c.(178-180)cAg>cTg	p.Q60L	AR_ENST00000513847.1_3'UTR|AR_ENST00000504326.1_Missense_Mutation_p.Q60L|AR_ENST00000396044.3_Missense_Mutation_p.Q60L	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	60	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)	CTgcagcagcagcagcagcag	0.677									Androgen Insensitivity Syndrome																												p.Q60L		Atlas-SNP	.											.	AR	249	.	0			c.A179T	GRCh37	CI994028	AR	I		PASS	.						6	9	8					X																	66765167		1971	3901	5872	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	AGCAGCAGCAGCA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.179A>T	chrX.hg19:g.66765167A>T	ENSP00000363822:p.Gln60Leu	34.0	0.0	.		48.0	6.0	.	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	11.27	1.588228	0.28357	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.57436	0.4;0.4;0.4	.	.	.	.	1.241110	0.06210	N	0.684797	T	0.29288	0.0729	N	0.19112	0.55	0.09310	N	0.999999	P;P;.	0.36048	0.534;0.534;.	B;B;.	0.29862	0.08;0.108;.	T	0.11494	-1.0585	8	0.12103	T	0.63	.	.	.	.	.	60;60;58	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	L	60	ENSP00000363822:Q60L;ENSP00000421155:Q60L;ENSP00000379359:Q60L	ENSP00000363822:Q60L	Q	+	2	0	AR	66681892	0.997000	0.39634	0.860000	0.33809	0.513000	0.34164	1.220000	0.32491	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	66765167	A	T	66765167	3	4	206	1	0	0	0	0	1	0	0	0	836	188	7	5	181	5	AR	23	66765167	Missense_Mutation	SNP	A	TCGA-IA-A83T-01A-11D-A34Z-10	63535973	66765167	88505393	59	12556											
STAG2	10735	hgsc.bcm.edu	37	chrX	123229293	123229293	+	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	gatccagcttcaattatggaTgaatcagtaggtttaattta	13	15	8	5	0	2	1	2	1	0	0	3	3	3	2	1	2	1	3	1	2	6	7			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chrX:123229293T>A	ENST00000371160.1	+	33	3956	c.3666T>A	c.(3664-3666)gaT>gaA	p.D1222E	STAG2_ENST00000371144.3_Missense_Mutation_p.D1222E|STAG2_ENST00000371145.3_Missense_Mutation_p.D1259E|STAG2_ENST00000354548.5_Missense_Mutation_p.D1153E|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Missense_Mutation_p.D1259E|STAG2_ENST00000371157.3_Missense_Mutation_p.D1222E	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	1222					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						CAATTATGGATGAATCAGTAG	0.393																																					p.D1259E		Atlas-SNP	.											.	STAG2	309	.	0			c.T3777A						PASS	.						107	95	99					X																	123229293		2203	4300	6503	SO:0001583	missense	10735	exon34			TATGGATGAATCA	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.3666T>A	chrX.hg19:g.123229293T>A	ENSP00000360202:p.Asp1222Glu	142.0	0.0	.		134.0	24.0	.	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Missense_Mutation	SNP	ENST00000371160.1	hg19	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	T	18.32	3.599001	0.66332	.	.	ENSG00000101972	ENST00000218089;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	T;T;T;T;T;T	0.51817	1.46;0.76;0.69;0.69;1.46;0.69	4.94	3.77	0.43336	.	0.115346	0.56097	N	0.000023	T	0.51007	0.1649	L	0.41492	1.28	0.45403	D	0.998383	D;D	0.59767	0.984;0.986	P;P	0.60609	0.877;0.81	T	0.41378	-0.9512	10	0.36615	T	0.2	-11.9936	7.9773	0.30161	0.0:0.1694:0.0:0.8306	.	1259;1222	Q8N3U4-2;Q8N3U4	.;STAG2_HUMAN	E	1259;1153;1222;1222;1259;1222	ENSP00000218089:D1259E;ENSP00000346555:D1153E;ENSP00000360202:D1222E;ENSP00000360199:D1222E;ENSP00000360187:D1259E;ENSP00000360186:D1222E	ENSP00000218089:D1259E	D	+	3	2	STAG2	123056974	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.616000	0.36933	0.558000	0.29135	-0.438000	0.05819	GAT	.	.	.	none		0.393	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		A	123229293	T	A	123229293	3	1	206	1	0	0	0	0	1	0	0	0	15255	1461	51	5	3903	5	STAG2	23	123229293	Missense_Mutation	SNP	T	TCGA-IA-A83T-01A-11D-A34Z-10	56464126	123229293	32041267	60	12557											
MAGEA4	4103	hgsc.bcm.edu	37	chrX	151092975	151092975	+	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	gtggggtccaagggctctggCtgaaaccagctatgtgaaag	10	8	15	8	0	1	2	0	2	1	0	2	2	2	2	2	4	2	3	2	4	4	1			TCGA-IA-A83T-01A-11D-A34Z-10	TCGA-IA-A83T-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	580ff01c-dd91-46ed-a426-7b2afea92207	cfd3629b-47b9-4934-86ab-9695c9f95668	g.chrX:151092975C>T	ENST00000360243.2	+	3	1106	c.839C>T	c.(838-840)gCt>gTt	p.A280V	MAGEA4_ENST00000393920.1_Missense_Mutation_p.A280V|MAGEA4_ENST00000370337.4_Missense_Mutation_p.A280V|MAGEA4_ENST00000370335.1_Missense_Mutation_p.A280V|MAGEA4_ENST00000276344.2_Missense_Mutation_p.A280V|MAGEA4_ENST00000370340.3_Missense_Mutation_p.A280V|MAGEA4_ENST00000393921.1_Missense_Mutation_p.A280V	NM_001011550.1	NP_001011550.1	P43358	MAGA4_HUMAN	melanoma antigen family A, 4	280	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)					AGGGCTCTGGCTGAAACCAGC	0.552																																					p.A280V		Atlas-SNP	.											.	MAGEA4	68	.	0			c.C839T						PASS	.						132	130	131					X																	151092975		2203	4300	6503	SO:0001583	missense	4103	exon3			CTCTGGCTGAAAC		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.839C>T	chrX.hg19:g.151092975C>T	ENSP00000353379:p.Ala280Val	67.0	0.0	.		85.0	46.0	.	NM_001011548	Q14798	Missense_Mutation	SNP	ENST00000360243.2	hg19	CCDS14702.1	.	.	.	.	.	.	.	.	.	.	C	9.150	1.016148	0.19355	.	.	ENSG00000147381	ENST00000276344;ENST00000393921;ENST00000370337;ENST00000393920;ENST00000370340;ENST00000370335;ENST00000360243	T;T;T;T;T;T;T	0.04809	3.55;3.55;3.55;3.55;3.55;3.55;3.55	2.55	0.688	0.18027	.	0.916903	0.09375	N	0.810810	T	0.05960	0.0155	M	0.64997	1.995	0.09310	N	1	B	0.20671	0.047	B	0.17722	0.019	T	0.41680	-0.9495	9	.	.	.	.	4.6093	0.12395	0.0:0.6542:0.0:0.3458	.	280	P43358	MAGA4_HUMAN	V	280	ENSP00000276344:A280V;ENSP00000377498:A280V;ENSP00000359362:A280V;ENSP00000377497:A280V;ENSP00000359365:A280V;ENSP00000359360:A280V;ENSP00000353379:A280V	.	A	+	2	0	MAGEA4	150843631	0.001000	0.12720	0.013000	0.15412	0.030000	0.12068	0.332000	0.19751	0.058000	0.16222	0.292000	0.19580	GCT	.	.	.	none		0.552	MAGEA4-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060898.1	NM_002362		T	151092975	C	T	151092975	3	4	206	1	0	0	0	0	1	0	0	0	9175	797	28	2	841	2	MAGEA4	23	151092975	Missense_Mutation	SNP	C	TCGA-IA-A83T-01A-11D-A34Z-10	27863682	151092975	4177585	61	12558											
HSPG2	3339	hgsc.bcm.edu	37	chr1	22173002	22173002	+	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	tgacctgggcatgggcctgcCcggggaccacgcagttcaga	7	6	15	13	2	1	2	1	1	0	1	1	3	1	3	4	4	1	3	4	4	0	1			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr1:22173002C>G	ENST00000374695.3	-	63	8334	c.8255G>C	c.(8254-8256)gGg>gCg	p.G2752A	HSPG2_ENST00000430507.1_3'UTR	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2752	Ig-like C2-type 13.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	ATGGGCCTGCCCGGGGACCAC	0.637																																					p.G2752A		Atlas-SNP	.											.	HSPG2	311	.	0			c.G8255C						PASS	.						63	65	64					1																	22173002		2203	4300	6503	SO:0001583	missense	3339	exon63			GCCTGCCCGGGGA	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.8255G>C	chr1.hg19:g.22173002C>G	ENSP00000363827:p.Gly2752Ala	133.0	0.0	.		135.0	43.0	.	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.156178	0.78114	.	.	ENSG00000142798	ENST00000374695;ENST00000453796	T;T	0.79141	-1.24;-1.24	4.94	4.94	0.65067	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.40385	N	0.001115	D	0.89012	0.6594	M	0.86953	2.85	0.53688	D	0.999979	D;P	0.76494	0.999;0.861	D;P	0.73380	0.98;0.668	D	0.90625	0.4562	10	0.59425	D	0.04	.	15.683	0.77388	0.0:1.0:0.0:0.0	.	692;2752	Q59EG0;P98160	.;PGBM_HUMAN	A	2752;167	ENSP00000363827:G2752A;ENSP00000396310:G167A	ENSP00000363827:G2752A	G	-	2	0	HSPG2	22045589	0.643000	0.27269	0.987000	0.45799	0.931000	0.56810	5.418000	0.66429	2.292000	0.77174	0.561000	0.74099	GGG	.	.	.	none		0.637	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		G	22173002	C	G	22173002	3	3	207	1	0	0	0	0	1	0	0	0	7437	623	22	4	5060	4	HSPG2	1	22173002	Missense_Mutation	SNP	C	TCGA-IA-A83V-01A-11D-A34Z-10		22173002	227077619	1	12559											
LUZP1	7798	hgsc.bcm.edu	37	chr1	23418024	23418024	+	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	atgtctggcatctgagaagcCcacttctgaaggggcactat	10	10	11	10	0	3	2	0	2	3	1	3	3	3	2	1	3	1	2	1	3	3	2			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr1:23418024C>G	ENST00000302291.4	-	4	3532	c.2731G>C	c.(2731-2733)Ggc>Cgc	p.G911R	LUZP1_ENST00000418342.1_Missense_Mutation_p.G911R|LUZP1_ENST00000374623.3_Missense_Mutation_p.G911R|LUZP1_ENST00000314174.5_Missense_Mutation_p.G911R			Q86V48	LUZP1_HUMAN	leucine zipper protein 1	911					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)		TCTGAGAAGCCCACTTCTGAA	0.493																																					p.G911R		Atlas-SNP	.											.	LUZP1	83	.	0			c.G2731C						PASS	.						96	90	92					1																	23418024		2203	4300	6503	SO:0001583	missense	7798	exon4			AGAAGCCCACTTC	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.2731G>C	chr1.hg19:g.23418024C>G	ENSP00000303758:p.Gly911Arg	132.0	0.0	.		148.0	31.0	.	NM_033631	Q5TH93|Q8N4X3|Q8TEH1	Missense_Mutation	SNP	ENST00000302291.4	hg19	CCDS30628.1	.	.	.	.	.	.	.	.	.	.	C	12.52	1.962845	0.34659	.	.	ENSG00000169641	ENST00000418342;ENST00000374623;ENST00000302291;ENST00000314174	T;T;T;T	0.14266	2.74;2.74;2.74;2.52	5.28	4.37	0.52481	.	0.508271	0.16793	N	0.199305	T	0.14313	0.0346	L	0.36672	1.1	0.09310	N	1	P;P	0.46512	0.879;0.879	P;P	0.45167	0.472;0.472	T	0.07712	-1.0758	10	0.62326	D	0.03	.	9.6043	0.39624	0.0:0.8325:0.0:0.1675	.	911;911	Q86V48-2;Q86V48	.;LUZP1_HUMAN	R	911	ENSP00000393460:G911R;ENSP00000363752:G911R;ENSP00000303758:G911R;ENSP00000313705:G911R	ENSP00000303758:G911R	G	-	1	0	LUZP1	23290611	0.000000	0.05858	0.085000	0.20634	0.692000	0.40212	0.624000	0.24462	1.253000	0.44018	0.485000	0.47835	GGC	.	.	.	none		0.493	LUZP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008900.3	NM_033631		G	23418024	C	G	23418024	3	3	207	1	0	0	0	0	1	0	0	0	9093	623	22	4	507	4	LUZP1	1	23418024	Missense_Mutation	SNP	C	TCGA-IA-A83V-01A-11D-A34Z-10	1245022	23418024	225832597	2	12560											
FAF1	11124	hgsc.bcm.edu	37	chr1	51253751	51253751	+	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	aagtccagcatccgaggttgCctttctacaatctgcctgga	9	11	9	12	1	2	0	0	0	2	0	4	2	4	1	4	2	4	2	4	2	3	3			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr1:51253751C>T	ENST00000396153.2	-	4	739	c.288G>A	c.(286-288)agG>agA	p.R96R	FAF1_ENST00000371778.4_Silent_p.R96R	NM_007051.2	NP_008982.1	Q9UNN5	FAF1_HUMAN	Fas (TNFRSF6) associated factor 1	96					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?(3)		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)		TCCGAGGTTGCCTTTCTACAA	0.458																																					p.R96R		Atlas-SNP	.											.	FAF1	64	.	3	Whole gene deletion(3)	thyroid(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	c.G288A						PASS	.						120	102	108					1																	51253751		2203	4300	6503	SO:0001819	synonymous_variant	11124	exon4			AGGTTGCCTTTCT	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.288G>A	chr1.hg19:g.51253751C>T		159.0	0.0	.		158.0	38.0	.	NM_007051	Q549F0|Q9UF34|Q9UNT3|Q9Y2Z3	Silent	SNP	ENST00000396153.2	hg19	CCDS554.1																																																																																			.	.	.	none		0.458	FAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021807.1	NM_007051		T	51253751	C	T	51253751	2	4	207	1	0	0	0	0	0	0	0	1	5373	738	26	2		2	FAF1	1	51253751	Silent	SNP	C	TCGA-IA-A83V-01A-11D-A34Z-10	27835727	51253751	197996870	3	12561											
RPRD2	23248	hgsc.bcm.edu	37	chr1	150337220	150337220	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggcggcggcggaggcagcagTaaggcctcctcctcgtcggc	5	5	17	14	5	0	0	0	0	0	0	4	1	2	1	3	7	1	3	3	7	1	1			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr1:150337220T>C	ENST00000369068.4	+	1	34	c.30T>C	c.(28-30)agT>agC	p.S10S	RPRD2_ENST00000492220.1_Intron|RPRD2_ENST00000401000.4_Silent_p.S10S|RPRD2_ENST00000369067.3_Silent_p.S10S|RPRD2_ENST00000539519.1_Silent_p.S10S	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	10	Gly/Ser-rich.					DNA-directed RNA polymerase II, holoenzyme (GO:0016591)				central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						GAGGCAGCAGTAAGGCCTCCT	0.667																																					p.S10S		Atlas-SNP	.											.	RPRD2	189	.	0			c.T30C						PASS	.						35	33	33					1																	150337220		692	1591	2283	SO:0001819	synonymous_variant	23248	exon1			CAGCAGTAAGGCC	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.30T>C	chr1.hg19:g.150337220T>C		53.0	0.0	.		45.0	5.0	.	NM_015203	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Silent	SNP	ENST00000369068.4	hg19	CCDS44216.1																																																																																			.	.	.	none		0.667	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203		C	150337220	T	C	150337220	2	2	207	1	0	0	0	0	0	0	0	1	13630	1635	57	3		3	RPRD2	1	150337220	Silent	SNP	T	TCGA-IA-A83V-01A-11D-A34Z-10	99083469	150337220	98913401	4	12562											
TNFAIP8L2	79626	hgsc.bcm.edu	37	chr1	151131378	151131379	+	Missense_Mutation	DNP	AA	AA	GG																															acctgatcaaagtggccatcAaggtggctgtgctgcaccgc																										TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr1:151131378_151131379AA>GG	ENST00000368910.3	+	2	331_332	c.205_206AA>GG	c.(205-207)AAg>GGg	p.K69G		NM_024575.4	NP_078851.2	Q6P589	TP8L2_HUMAN	tumor necrosis factor, alpha-induced protein 8-like 2	69					innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of T cell activation (GO:0050868)	cytoplasm (GO:0005737)				lung(1)|skin(2)	3	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)			AGTGGCCATCAAGGTGGCTGTG	0.624																																					p.K69E|p.K69R		Atlas-SNP	.											.	TNFAIP8L2	19	.	0			c.A205G|c.A206G						PASS	.																																			SO:0001583	missense	79626	exon2			GCCATCAAGGTGG|CCATCAAGGTGGC	BC063014	CCDS985.1	1q21.2	2008-02-05			ENSG00000163154	ENSG00000163154			26277	protein-coding gene	gene with protein product		612112					Standard	NM_024575		Approved	FLJ23467	uc001ewx.2	Q6P589	OTTHUMG00000012259	Exception_encountered	chr1.hg19:g.151131378_151131379delinsGG	ENSP00000357906:p.Lys69Gly	214.0	0.0	.		165.0|166.0	28.0|29.0	.	NM_024575	Q6I9Y0|Q9H2H7|Q9H5G2	Missense_Mutation	SNP	ENST00000368910.3	hg19	CCDS985.1																																																																																			.	.	.	none		0.624	TNFAIP8L2-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034069.2	NM_024575		GG	151131379	AA	GG	151131378	3	3	207	1	0	0	0	0	1	0	0	0	16290	131	5	3	207	3	TNFAIP8L2	1	151131378	Missense_Mutation	DNP	AA	TCGA-IA-A83V-01A-11D-A34Z-10	794158	151131378	98119243	5	12563											
FMO1	2326	hgsc.bcm.edu	37	chr1	171254631	171254631	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccctttgaaagttttcttaAagtctttagctttctggctt	7	20	6	8	0	3	1	0	1	3	0	4	1	4	1	1	1	1	3	1	1	4	8			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr1:171254631A>G	ENST00000354841.4	+	8	1678	c.1547A>G	c.(1546-1548)aAa>aGa	p.K516R	FMO1_ENST00000402921.2_Missense_Mutation_p.K453R|FMO1_ENST00000367750.3_Missense_Mutation_p.K516R|FMO1_ENST00000469112.1_3'UTR	NM_001282692.1	NP_001269621.1	Q01740	FMO1_HUMAN	flavin containing monooxygenase 1	516					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)	AGTTTTCTTAAAGTCTTTAGC	0.403																																					p.K516R		Atlas-SNP	.											.	FMO1	79	.	0			c.A1547G						PASS	.						67	70	69					1																	171254631		2203	4300	6503	SO:0001583	missense	2326	exon9			TTCTTAAAGTCTT	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.1547A>G	chr1.hg19:g.171254631A>G	ENSP00000346901:p.Lys516Arg	212.0	0.0	.		227.0	55.0	.	NM_002021	A8K248|B7Z3P4|Q5QPT2|Q9UJC2	Missense_Mutation	SNP	ENST00000354841.4	hg19	CCDS1294.1	.	.	.	.	.	.	.	.	.	.	A	14.23	2.473896	0.43942	.	.	ENSG00000010932	ENST00000367750;ENST00000402921;ENST00000354841	T;T;T	0.58060	0.36;0.36;0.36	5.61	3.27	0.37495	.	0.384897	0.27185	N	0.020536	T	0.24314	0.0589	L	0.58101	1.795	0.30209	N	0.7979	B;B	0.26672	0.053;0.156	B;B	0.30105	0.078;0.111	T	0.14924	-1.0455	10	0.22706	T	0.39	-12.9555	6.2625	0.20907	0.7559:0.1615:0.0825:0.0	.	453;516	B7Z3P4;Q01740	.;FMO1_HUMAN	R	516;453;516	ENSP00000356724:K516R;ENSP00000385543:K453R;ENSP00000346901:K516R	ENSP00000346901:K516R	K	+	2	0	FMO1	169521255	0.025000	0.19082	0.815000	0.32552	0.356000	0.29392	0.808000	0.27154	0.401000	0.25424	0.455000	0.32223	AAA	.	.	.	none		0.403	FMO1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086212.1	NM_002021		G	171254631	A	G	171254631	3	3	207	1	0	0	0	0	1	0	0	0	5961	14	1	3	1577	3	FMO1	1	171254631	Missense_Mutation	SNP	A	TCGA-IA-A83V-01A-11D-A34Z-10	20123253	171254631	77995990	6	12564											
CENPF	1063	hgsc.bcm.edu	37	chr1	214832273	214832273	+	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	caactcggaccagcccccgcCtggctgcacagaagttagcg	9	5	11	16	3	0	1	0	0	0	1	1	2	0	2	4	2	4	3	4	2	3	1			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr1:214832273C>A	ENST00000366955.3	+	19	9211	c.9043C>A	c.(9043-9045)Ctg>Atg	p.L3015M		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	3111	Sufficient for centromere localization.|Sufficient for nuclear localization.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		CAGCCCCCGCCTGGCTGCACA	0.512											OREG0014250	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L3015M	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.C9043A						PASS	.						113	116	115					1																	214832273		2203	4300	6503	SO:0001583	missense	1063	exon19			CCCCGCCTGGCTG	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.9043C>A	chr1.hg19:g.214832273C>A	ENSP00000355922:p.Leu3015Met	86.0	0.0	.	2224	78.0	18.0	.	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	hg19	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.025949	0.75390	.	.	ENSG00000117724	ENST00000366955	T	0.12879	2.64	5.63	4.7	0.59300	.	0.261378	0.20300	N	0.095055	T	0.34424	0.0897	M	0.65498	2.005	0.33693	D	0.613617	D	0.76494	0.999	D	0.66716	0.946	T	0.52525	-0.8564	10	0.87932	D	0	.	14.088	0.64971	0.0:0.9273:0.0:0.0727	.	3111	P49454	CENPF_HUMAN	M	3015	ENSP00000355922:L3015M	ENSP00000355922:L3015M	L	+	1	2	CENPF	212898896	0.801000	0.28930	0.995000	0.50966	0.940000	0.58332	1.933000	0.40153	1.351000	0.45789	0.655000	0.94253	CTG	.	.	.	none		0.512	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		A	214832273	C	A	214832273	3	1	207	1	0	0	0	0	1	0	0	0	3233	680	24	4	9113	4	CENPF	1	214832273	Missense_Mutation	SNP	C	TCGA-IA-A83V-01A-11D-A34Z-10	43577642	214832273	34418348	7	12565											
CEP170	9859	hgsc.bcm.edu	37	chr1	243328302	243328302	+	Missense_Mutation	SNP	T	T	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	tttttgttttcttttccattTtttccctagcacctgaagat	6	22	4	9	0	1	2	0	1	1	1	3	2	3	2	3	0	1	2	3	0	2	10			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr1:243328302T>G	ENST00000366542.1	-	13	3011	c.2960A>C	c.(2959-2961)aAa>aCa	p.K987T	CEP170_ENST00000490813.1_5'Flank|RP11-261C10.4_ENST00000422938.1_RNA|RP11-261C10.4_ENST00000437499.1_RNA|CEP170_ENST00000366544.1_Missense_Mutation_p.K889T|CEP170_ENST00000366543.1_Missense_Mutation_p.K889T	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	987	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)			CTTTTCCATTTTTTCCCTAGC	0.408																																					p.K987T		Atlas-SNP	.											.	CEP170	153	.	0			c.A2960C						PASS	.						41	40	40					1																	243328302		1832	4062	5894	SO:0001583	missense	9859	exon13			TCCATTTTTTCCC	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.2960A>C	chr1.hg19:g.243328302T>G	ENSP00000355500:p.Lys987Thr	629.0	0.0	.		571.0	79.0	.	NM_014812	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Missense_Mutation	SNP	ENST00000366542.1	hg19	CCDS44339.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.05|16.05	3.014245|3.014245	0.54468|0.54468	.|.	.|.	ENSG00000143702|ENSG00000143702	ENST00000336415|ENST00000366542;ENST00000366544;ENST00000366543	T|T;T;T	0.48836|0.51325	0.8|0.75;0.73;0.71	4.89|4.89	4.89|4.89	0.63831|0.63831	.|.	0.048059|0.048059	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.57770|0.57770	0.2076|0.2076	L|L	0.44542|0.44542	1.39|1.39	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.76494	.|0.997;0.996;0.996;0.999	.|D;D;D;D	.|0.80764	.|0.993;0.986;0.986;0.994	T|T	0.52290|0.52290	-0.8595|-0.8595	8|10	0.25751|0.20046	T|T	0.34|0.44	-17.5403|-17.5403	13.6896|13.6896	0.62537|0.62537	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|950;889;889;987	.|B1ARM6;Q5SW79-3;Q5SW79-2;Q5SW79	.|.;.;.;CE170_HUMAN	Q|T	951|987;889;889	ENSP00000338161:K951Q|ENSP00000355500:K987T;ENSP00000355502:K889T;ENSP00000355501:K889T	ENSP00000338161:K951Q|ENSP00000355500:K987T	K|K	-|-	1|2	0|0	CEP170|CEP170	241394925|241394925	1.000000|1.000000	0.71417|0.71417	0.941000|0.941000	0.38009|0.38009	0.962000|0.962000	0.63368|0.63368	5.584000|5.584000	0.67490|0.67490	1.823000|1.823000	0.53134|0.53134	0.454000|0.454000	0.30748|0.30748	AAA|AAA	.	.	.	none		0.408	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812		G	243328302	T	G	243328302	3	3	207	1	0	0	0	0	1	0	0	0	3252	1841	64	5	1856	5	CEP170	1	243328302	Missense_Mutation	SNP	T	TCGA-IA-A83V-01A-11D-A34Z-10	28496029	243328302	5922319	8	12566											
SPDYA	55006	hgsc.bcm.edu	37	chr2	29072767	29072767	+	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	1	0	0	0	0	0	0	0	gaaaactaatttcttgaagaAagacaaatctatggagtggt	17	11	9	4	0	2	3	0	1	2	2	2	5	2	4	0	2	1	0	0	2	7	4			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr2:29072767A>G	ENST00000306108.5	-	0	1755				SPDYA_ENST00000334056.5_Missense_Mutation_p.K301R|TRMT61B_ENST00000484060.1_5'Flank|SPDYA_ENST00000379579.4_Missense_Mutation_p.K301R	NM_017910.3	NP_060380.3	Q9BVS5	TR61B_HUMAN	tRNA methyltransferase 61 homolog B (S. cerevisiae)						mitochondrial tRNA methylation (GO:0070901)|protein homooligomerization (GO:0051260)	mitochondrion (GO:0005739)|tRNA (m1A) methyltransferase complex (GO:0031515)	tRNA (adenine-N1-)-methyltransferase activity (GO:0016429)			endometrium(2)|kidney(1)|large_intestine(2)|lung(8)	13						TTCTTGAAGAAAGACAAATCT	0.299																																					p.K301R		Atlas-SNP	.											.	SPDYA	41	.	0			c.A902G						PASS	.						50	55	53					2																	29072767		2203	4297	6500	SO:0001624	3_prime_UTR_variant	245711	exon7			TGAAGAAAGACAA	BC010365	CCDS1768.1	2p23.2	2009-01-09			ENSG00000171103	ENSG00000171103			26070	protein-coding gene	gene with protein product						11230166	Standard	NM_017910		Approved	FLJ20628	uc002rmm.3	Q9BVS5	OTTHUMG00000128433	ENST00000306108.5:c.*298T>C	chr2.hg19:g.29072767A>G		180.0	0.0	.		171.0	42.0	.	NM_001142634	Q9H0Q9|Q9NWS7	Missense_Mutation	SNP	ENST00000306108.5	hg19	CCDS1768.1	.	.	.	.	.	.	.	.	.	.	A	12.94	2.087655	0.36855	.	.	ENSG00000163806	ENST00000379579;ENST00000334056	.	.	.	5.63	3.16	0.36331	.	0.231056	0.21337	U	0.076194	T	0.42966	0.1226	L	0.44542	1.39	0.80722	D	1	B	0.24823	0.112	B	0.19148	0.024	T	0.13388	-1.0511	9	0.15066	T	0.55	-0.301	8.0324	0.30472	0.7234:0.1417:0.0:0.1349	.	301	Q5MJ70	SPDYA_HUMAN	R	301	.	ENSP00000335628:K301R	K	+	2	0	SPDYA	28926271	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.333000	0.43912	0.441000	0.26529	0.533000	0.62120	AAA	.	.	.	none		0.299	TRMT61B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250224.1	NM_017910		G	29072767	A	G	29072767	1	3	207	0	1	0	0	0	0	0	0	0	15039	14	1	3		3	SPDYA	2	29072767	3'UTR	SNP	A	TCGA-IA-A83V-01A-11D-A34Z-10		29072767	214126606	9	12567											
FBXO11	80204	hgsc.bcm.edu	37	chr2	48040432	48040432	+	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	catcatggattttatttcttCttagtgtaggattactatct	9	20	6	6	0	4	0	1	0	3	0	4	2	4	2	0	2	1	1	0	2	5	8			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr2:48040432C>A	ENST00000403359.3	-	18	2240	c.2168G>T	c.(2167-2169)aGa>aTa	p.R723I	FBXO11_ENST00000434523.2_Missense_Mutation_p.R147I|FBXO11_ENST00000316377.4_Missense_Mutation_p.R639I|FBXO11_ENST00000402508.1_Missense_Mutation_p.R639I	NM_001190274.1	NP_001177203.1	Q86XK2	FBX11_HUMAN	F-box protein 11	723					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)			TTTATTTCTTCTTAGTGTAGG	0.343			"Mis, F, D"		DLBCL																																p.R723I		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.G2168T						PASS	.						120	123	122					2																	48040432		2203	4299	6502	SO:0001583	missense	80204	exon18			TTTCTTCTTAGTG	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.2168G>T	chr2.hg19:g.48040432C>A	ENSP00000384823:p.Arg723Ile	323.0	0.0	.		285.0	63.0	.	NM_001190274	A1L491|Q52ZP1|Q53EP7|Q53RT5|Q8IXG3|Q96E90|Q9H6V8|Q9H9L1|Q9NR14|Q9UFK1|Q9UHI1|Q9UKC2	Missense_Mutation	SNP	ENST00000403359.3	hg19	CCDS54357.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.234868|5.234868	0.95207|0.95207	.|.	.|.	ENSG00000138081|ENSG00000138081	ENST00000493962|ENST00000402508;ENST00000403359;ENST00000316377;ENST00000434523	.|T;T;T;T	.|0.80214	.|-1.35;-1.35;-1.35;-1.35	5.25|5.25	5.25|5.25	0.73442|0.73442	.|Pectin lyase fold/virulence factor (1);Carbohydrate-binding/sugar hydrolysis domain (1);F-box domain, Skp2-like (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.90386|0.90386	0.6991|0.6991	M|M	0.80616|0.80616	2.505|2.505	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|0.999;1.0	.|D;D	.|0.81914	.|0.987;0.995	D|D	0.91390|0.91390	0.5134|0.5134	5|10	.|0.87932	.|D	.|0	-9.8728|-9.8728	19.1978|19.1978	0.93696|0.93696	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|147;723	.|B3KUR1;Q86XK2	.|.;FBX11_HUMAN	N|I	514|639;723;639;147	.|ENSP00000385398:R639I;ENSP00000384823:R723I;ENSP00000323822:R639I;ENSP00000397359:R147I	.|ENSP00000323822:R639I	K|R	-|-	3|2	2|0	FBXO11|FBXO11	47893936|47893936	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.776000|7.776000	0.85560|0.85560	2.597000|2.597000	0.87782|0.87782	0.655000|0.655000	0.94253|0.94253	AAG|AGA	.	.	.	none		0.343	FBXO11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251181.3	NM_012167, NM_018693, NM_025133		A	48040432	C	A	48040432	3	1	207	1	0	0	0	0	1	0	0	0	5734	913	32	4	725	4	FBXO11	2	48040432	Missense_Mutation	SNP	C	TCGA-IA-A83V-01A-11D-A34Z-10	18967665	48040432	195158941	10	12568											
FER1L5	90342	hgsc.bcm.edu	37	chr2	97361397	97361397	+	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	gtctgtcctagtcctcacagTggtaagaggccccagggcag	8	8	13	12	0	2	1	1	0	1	1	4	1	4	1	4	3	0	2	4	3	2	2			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr2:97361397T>C	ENST00000457909.1	+	0	3396							A0AVI2	FR1L5_HUMAN	fer-1-like family member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(9)|large_intestine(9)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	38						GTCCTCACAGTGGTAAGAGGC	0.612																																					p.V1325A		Atlas-SNP	.											.	FER1L5	113	.	0			c.T3974C						PASS	.						25	29	28					2																	97361397		1923	4122	6045			90342	exon34			TCACAGTGGTAAG	BC126368		2q11.2	2014-06-27	2014-06-27		ENSG00000249715	ENSG00000249715			19044	protein-coding gene	gene with protein product			"fer-1-like 5 (C. elegans)"				Standard	XM_006712826		Approved	DKFZp434I0121	uc010fia.3	A0AVI2	OTTHUMG00000154929		chr2.hg19:g.97361397T>C		73.0	0.0	.		75.0	21.0	.	NM_001113382	Q17RH2|Q6ZU24	Missense_Mutation	SNP	ENST00000457909.1	hg19		.	.	.	.	.	.	.	.	.	.	T	7.763	0.705846	0.15172	.	.	ENSG00000214272	ENST00000414152;ENST00000436930;ENST00000397978	.	.	.	4.25	4.25	0.50352	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	T	0.46600	0.1401	L	0.55017	1.72	.	.	.	P;P	0.50819	0.939;0.72	P;B	0.45232	0.474;0.261	T	0.63879	-0.6537	7	0.59425	D	0.04	-6.2493	10.9692	0.47431	0.0:0.0:0.0:1.0	.	1325;43	A0AVI2;A0AVI2-2	FR1L5_HUMAN;.	A	1325;1339;43	.	ENSP00000442027:V43A	V	+	2	0	FER1L5	96725124	1.000000	0.71417	0.869000	0.34112	0.194000	0.23727	4.797000	0.62503	1.788000	0.52465	0.379000	0.24179	GTG	.	.	.	none		0.612	FER1L5-001	KNOWN	basic|exp_conf	retained_intron	pseudogene	OTTHUMT00000339030.1	NM_001077400		C	97361397	T	C	97361397	1	2	207	0	1	0	0	0	0	0	0	0	5821	1710	59	3		3	FER1L5	2	97361397	RNA	SNP	T	TCGA-IA-A83V-01A-11D-A34Z-10	49320965	97361397	145837976	11	12569											
DBR1	51163	hgsc.bcm.edu	37	chr3	137889003	137889003	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgatatatactcctgattgtAgatgaattataaggggggca	13	13	11	4	0	0	4	0	3	0	1	1	4	1	4	1	3	1	2	1	3	7	7			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr3:137889003A>G	ENST00000260803.4	-	4	588	c.435T>C	c.(433-435)tcT>tcC	p.S145S	DBR1_ENST00000505015.2_5'UTR|DBR1_ENST00000463982.2_5'Flank	NM_016216.3	NP_057300.2	Q9UK59	DBR1_HUMAN	debranching RNA lariats 1	145					mRNA splicing, via spliceosome (GO:0000398)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|RNA splicing, via transesterification reactions (GO:0000375)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA lariat debranching enzyme activity (GO:0008419)			NS(1)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	15						TCCTGATTGTAGATGAATTAT	0.294																																					p.S145S		Atlas-SNP	.											.	DBR1	45	.	0			c.T435C						PASS	.						67	77	73					3																	137889003		2203	4297	6500	SO:0001819	synonymous_variant	51163	exon4			GATTGTAGATGAA	AF180919	CCDS33863.1	3q22.3	2013-05-01	2013-05-01		ENSG00000138231	ENSG00000138231			15594	protein-coding gene	gene with protein product		607024	"debranching enzyme (S. Cerevisiae) homolog 1", "debranching enzyme homolog 1 (S. cerevisiae)"			10982890	Standard	NM_016216		Approved		uc003erv.3	Q9UK59	OTTHUMG00000159824	ENST00000260803.4:c.435T>C	chr3.hg19:g.137889003A>G		65.0	0.0	.		64.0	14.0	.	NM_016216	Q96GH0|Q9NXQ6	Silent	SNP	ENST00000260803.4	hg19	CCDS33863.1																																																																																			.	.	.	none		0.294	DBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357585.1			G	137889003	A	G	137889003	2	3	207	1	0	0	0	0	0	0	0	1	4259	407	15	3		3	DBR1	3	137889003	Silent	SNP	A	TCGA-IA-A83V-01A-11D-A34Z-10		137889003	60133427	12	12570											
MED12L	116931	hgsc.bcm.edu	37	chr3	151148131	151148131	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acccagcagcagcagcagacGgccgccttggtgcggcagct	8	4	14	15	3	0	1	0	0	0	1	0	1	0	1	3	3	6	6	3	3	0	1	rs568498781	byFrequency	TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr3:151148131G>A	ENST00000474524.1	+	42	6386	c.6348G>A	c.(6346-6348)acG>acA	p.T2116T	MED12L_ENST00000273432.4_Silent_p.T1780T	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	2116	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)			AGCAGCAGACGGCCGCCTTGG	0.527													g|||	4	0.000798722	0	0	5008	,	,		16791	0		0	False		,,,				2504	0.0041				p.T2116T		Atlas-SNP	.											.	MED12L	271	.	0			c.G6348A						PASS	.						53	54	54					3																	151148131		2203	4300	6503	SO:0001819	synonymous_variant	116931	exon42			GCAGACGGCCGCC	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.6348G>A	chr3.hg19:g.151148131G>A		106.0	0.0	.		102.0	29.0	.	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Silent	SNP	ENST00000474524.1	hg19	CCDS33876.1																																																																																			.	.	.	none		0.527	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		A	151148131	G	A	151148131	2	1	207	1	0	0	0	0	0	0	0	1	9436	1103	39	1		1	MED12L	3	151148131	Silent	SNP	G	TCGA-IA-A83V-01A-11D-A34Z-10	13259128	151148131	46874299	13	12571											
CCNL1	57018	hgsc.bcm.edu	37	chr3	156870895	156870895	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctctctgctttgataactTgatttttggtgttaatgtag	7	20	8	6	0	1	2	0	2	1	0	3	2	2	2	1	1	2	3	1	1	3	7			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr3:156870895T>C	ENST00000295926.3	-	4	657	c.539A>G	c.(538-540)cAa>cGa	p.Q180R	CCNL1_ENST00000479052.1_5'UTR|Y_RNA_ENST00000364908.1_RNA|CCNL1_ENST00000461804.1_Missense_Mutation_p.Q180R	NM_020307.2	NP_064703.1	Q9UK58	CCNL1_HUMAN	cyclin L1	180	Cyclin-like 1.				regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	nuclear speck (GO:0016607)|nucleus (GO:0005634)				NS(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|stomach(1)	18			LUSC - Lung squamous cell carcinoma(72;0.0295)|Lung(72;0.0308)			TTTGATAACTTGATTTTTGGT	0.383																																					p.Q180R		Atlas-SNP	.											.	CCNL1	53	.	0			c.A539G						PASS	.						115	102	106					3																	156870895		2203	4300	6503	SO:0001583	missense	57018	exon4			ATAACTTGATTTT	AF180920	CCDS3178.1	3q25.31	2008-02-05			ENSG00000163660	ENSG00000163660			20569	protein-coding gene	gene with protein product		613384				11980906	Standard	NM_020307		Approved	ania-6a	uc003fbf.3	Q9UK58	OTTHUMG00000158713	ENST00000295926.3:c.539A>G	chr3.hg19:g.156870895T>C	ENSP00000295926:p.Gln180Arg	144.0	0.0	.		139.0	32.0	.	NM_020307	B3KMY3|Q6NVY9|Q6UWS7|Q8NI48|Q96QT0|Q9NZF3	Missense_Mutation	SNP	ENST00000295926.3	hg19	CCDS3178.1	.	.	.	.	.	.	.	.	.	.	T	19.69	3.875402	0.72180	.	.	ENSG00000163660	ENST00000461804;ENST00000295926	T;T	0.12039	2.72;2.72	5.9	5.9	0.94986	Cyclin, N-terminal (1);Cyclin-like (3);	0.050844	0.85682	D	0.000000	T	0.22475	0.0542	L	0.37897	1.145	0.80722	D	1	B;P;P	0.36837	0.171;0.571;0.571	B;P;B	0.48738	0.124;0.588;0.386	T	0.01146	-1.1437	10	0.49607	T	0.09	-23.0591	16.3232	0.82961	0.0:0.0:0.0:1.0	.	180;180;180	Q9UK58-4;Q9UK58;C9JPL0	.;CCNL1_HUMAN;.	R	180	ENSP00000420277:Q180R;ENSP00000295926:Q180R	ENSP00000295926:Q180R	Q	-	2	0	CCNL1	158353589	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.587000	0.82613	2.254000	0.74563	0.482000	0.46254	CAA	.	.	.	none		0.383	CCNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351859.1	NM_020307		C	156870895	T	C	156870895	3	2	207	1	0	0	0	0	1	0	0	0	2933	1812	63	3	1073	3	CCNL1	3	156870895	Missense_Mutation	SNP	T	TCGA-IA-A83V-01A-11D-A34Z-10	5722764	156870895	41151535	14	12572											
NIPBL	25836	hgsc.bcm.edu	37	chr5	37020651	37020652	+	Frame_Shift_Del	DEL	TC	TC	-																															cacaaaaagatgaagaatcaTctgaaggaacacatcatgca																								rs139819353		TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr5:37020651_37020652delTC	ENST00000282516.8	+	26	5600_5601	c.5101_5102delTC	c.(5101-5103)tctfs	p.S1701fs	NIPBL_ENST00000448238.2_Frame_Shift_Del_p.S1701fs	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	1701					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)			TGAAGAATCATCTGAAGGAACA	0.361																																					p.1700_1701del		Atlas-Indel,Pindel	.											.	NIPBL	513	.	0			c.5100_5101del						PASS	.																																			SO:0001589	frameshift_variant	25836	exon26			.	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.5101_5102delTC	chr5.hg19:g.37020651_37020652delTC	ENSP00000282516:p.Ser1701fs	202.0	0.0	0		194.0	44.0	0.226804	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Frame_Shift_Del	DEL	ENST00000282516.8	hg19	CCDS3920.1																																																																																			.	.	.	none		0.361	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		-	37020652	TC	-	37020651	7	5	207	1	0	1	0	1	0	0	0	0	10435	1435	50	0	5199	0	NIPBL	5	37020651	Frame_Shift_Del	DEL	TC	TCGA-IA-A83V-01A-11D-A34Z-10		37020651	143894609	15	12573											
VCAN	1462	hgsc.bcm.edu	37	chr5	82817377	82817377	+	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	gatgaattgttgacaggttcTgagagggtcccagttttaga	10	13	13	5	0	1	4	0	3	1	2	2	6	2	4	1	2	0	3	1	2	2	5			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr5:82817377T>A	ENST00000265077.3	+	7	3817	c.3252T>A	c.(3250-3252)tcT>tcA	p.S1084S	VCAN_ENST00000342785.4_Silent_p.S1084S|VCAN_ENST00000343200.5_Intron|VCAN_ENST00000512590.2_Silent_p.S1036S|VCAN_ENST00000502527.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1084	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)	TGACAGGTTCTGAGAGGGTCC	0.453																																					p.S1084S		Atlas-SNP	.											.	VCAN	498	.	0			c.T3252A						PASS	.						84	78	80					5																	82817377		2203	4300	6503	SO:0001819	synonymous_variant	1462	exon7			AGGTTCTGAGAGG	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.3252T>A	chr5.hg19:g.82817377T>A		85.0	0.0	.		69.0	19.0	.	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	hg19	CCDS4060.1																																																																																			.	.	.	none		0.453	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		A	82817377	T	A	82817377	2	1	207	1	0	0	0	0	0	0	0	1	17150	1567	55	5		5	VCAN	5	82817377	Silent	SNP	T	TCGA-IA-A83V-01A-11D-A34Z-10	45796726	82817377	98097883	16	12574											
ERAP1	51752	hgsc.bcm.edu	37	chr5	96126038	96126038	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgacttctagagcaaaagccAtccatcccttttacaccatc	12	11	4	14	0	1	2	0	1	1	1	4	2	3	2	4	0	3	1	4	0	4	4			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr5:96126038A>G	ENST00000443439.2	-	10	1551	c.1485T>C	c.(1483-1485)gaT>gaC	p.D495D	ERAP1_ENST00000296754.3_Silent_p.D495D	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	495					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)		AGCAAAAGCCATCCATCCCTT	0.353																																					p.D495D		Atlas-SNP	.											.	ERAP1	59	.	0			c.T1485C						PASS	.						131	126	128					5																	96126038		2203	4300	6503	SO:0001819	synonymous_variant	51752	exon10			AAAGCCATCCATC	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.1485T>C	chr5.hg19:g.96126038A>G		71.0	0.0	.		69.0	16.0	.	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Silent	SNP	ENST00000443439.2	hg19	CCDS47250.1																																																																																			.	.	.	none		0.353	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442		G	96126038	A	G	96126038	2	3	207	1	0	0	0	0	0	0	0	1	5205	214	8	3		3	ERAP1	5	96126038	Silent	SNP	A	TCGA-IA-A83V-01A-11D-A34Z-10	13308661	96126038	84789222	17	12575											
AARS2	57505	hgsc.bcm.edu	37	chr6	44278164	44278164	+	Frame_Shift_Del	DEL	G	G	-																															ccgctggggcaggggctgcaGgcttccatctgcctctctgg																										TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr6:44278164delG	ENST00000244571.4	-	5	768	c.766delC	c.(766-768)ctgfs	p.L256fs	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)			AGGGGCTGCAGGCTTCCATCT	0.592																																					p.L256fs		Pindel	.											.	AARS2	77	.	0			c.767delT						PASS	.						84	71	76					6																	44278164		2203	4300	6503	SO:0001589	frameshift_variant	57505	exon5			.	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.766delC	chr6.hg19:g.44278164delG	ENSP00000244571:p.Leu256fs	53.0	0.0	.		56.0	10.0	0.179	NM_020745		Frame_Shift_Del	DEL	ENST00000244571.4	hg19	CCDS34464.1																																																																																			.	.	.	none		0.592	AARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040741.2	NM_020745		-	44278164	G	-	44278164	7	5	207	1	0	1	0	1	0	0	0	0	20	991	35	0	2263	0	AARS2	6	44278164	Frame_Shift_Del	DEL	G	TCGA-IA-A83V-01A-11D-A34Z-10		44278164	126836903	18	12576											
UBE2J1	51465	hgsc.bcm.edu	37	chr6	90047953	90047953	+	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	agtgctcttctttcctcaggAgtgtaatctagagaacctat	10	14	8	9	0	4	1	1	0	3	1	5	3	5	2	2	1	2	2	2	1	4	5			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr6:90047953A>T	ENST00000435041.2	-	5	677	c.399T>A	c.(397-399)acT>acA	p.T133T		NM_016021.2	NP_057105.2	Q9Y385	UB2J1_HUMAN	ubiquitin-conjugating enzyme E2, J1	133					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)		TTTCCTCAGGAGTGTAATCTA	0.388																																					p.T133T		Atlas-SNP	.											.	UBE2J1	28	.	0			c.T399A						PASS	.						133	134	134					6																	90047953		2203	4300	6503	SO:0001819	synonymous_variant	51465	exon5			CTCAGGAGTGTAA	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.399T>A	chr6.hg19:g.90047953A>T		170.0	0.0	.		138.0	25.0	.	NM_016021	A8K3F9|Q53F25|Q5W0N4|Q9BZ32|Q9NQL3|Q9NY66|Q9P011|Q9P0S0|Q9UF10	Silent	SNP	ENST00000435041.2	hg19	CCDS5021.1																																																																																			.	.	.	none		0.388	UBE2J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043742.2	NM_016021		T	90047953	A	T	90047953	2	4	207	1	0	0	0	0	0	0	0	1	16872	291	11	5		5	UBE2J1	6	90047953	Silent	SNP	A	TCGA-IA-A83V-01A-11D-A34Z-10	45769789	90047953	81067114	19	12577											
RANBP6	26953	hgsc.bcm.edu	37	chr9	6013047	6013047	+	Frame_Shift_Del	DEL	A	A	-																															aagtactaaataatgagtgcAaaatatctgatactttggtc																										TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr9:6013047delA	ENST00000259569.5	-	1	2571	c.2561delT	c.(2560-2562)ttgfs	p.L854fs	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	854					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)		TAATGAGTGCAAAATATCTGA	0.333																																					p.L854fs		Pindel	.											.	RANBP6	127	.	0			c.2562delG						PASS	.						63	64	63					9																	6013047		2203	4300	6503	SO:0001589	frameshift_variant	26953	exon1			.	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.2561delT	chr9.hg19:g.6013047delA	ENSP00000259569:p.Leu854fs	141.0	0.0	.		115.0	24.0	0.209	NM_012416	Q5T7X4|Q7Z3V2|Q96E78	Frame_Shift_Del	DEL	ENST00000259569.5	hg19	CCDS6467.1																																																																																			.	.	.	none		0.333	RANBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051650.1	NM_012416		-	6013047	A	-	6013047	7	5	207	1	0	1	0	1	0	0	0	0	13044	131	5	0	760	0	RANBP6	9	6013047	Frame_Shift_Del	DEL	A	TCGA-IA-A83V-01A-11D-A34Z-10		6013047	135200384	20	12578											
POMT1	10585	hgsc.bcm.edu	37	chr9	134379628	134379628	+	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	gtggggatttttgaagcgccCtgtagtggtgacggctgaca	7	11	16	7	2	0	3	0	3	0	0	0	4	0	4	1	4	1	2	1	4	2	3			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr9:134379628C>T	ENST00000372228.3	+	2	202	c.23C>T	c.(22-24)cCt>cTt	p.P8L	POMT1_ENST00000354713.4_Missense_Mutation_p.P8L|POMT1_ENST00000341012.7_Intron|POMT1_ENST00000541219.1_Intron|POMT1_ENST00000404875.2_Intron|POMT1_ENST00000423007.1_Missense_Mutation_p.P8L|POMT1_ENST00000419118.2_Intron|POMT1_ENST00000402686.3_Missense_Mutation_p.P8L	NM_007171.3	NP_009102	Q9Y6A1	POMT1_HUMAN	protein-O-mannosyltransferase 1	8					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)		TTGAAGCGCCCTGTAGTGGTG	0.597											OREG0019563	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P8L		Atlas-SNP	.											.	POMT1	59	.	0			c.C23T						PASS	.						175	148	157					9																	134379628		2203	4300	6503	SO:0001583	missense	10585	exon2			AGCGCCCTGTAGT	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.23C>T	chr9.hg19:g.134379628C>T	ENSP00000361302:p.Pro8Leu	254.0	0.0	.	1610	253.0	64.0	.	NM_001136113	B3KQG0|B4DIF0|Q5JT01|Q5JT06|Q5JT08|Q8NC91|Q8TCA9|Q9NX32|Q9NX82|Q9UNT2	Missense_Mutation	SNP	ENST00000372228.3	hg19	CCDS6943.1	.	.	.	.	.	.	.	.	.	.	C	16.18	3.051297	0.55218	.	.	ENSG00000130714	ENST00000423007;ENST00000372228;ENST00000402686;ENST00000354713;ENST00000418774	D;D;D;D;T	0.90197	-1.61;-1.6;-1.61;-2.63;-1.18	5.02	5.02	0.67125	.	0.057319	0.64402	D	0.000001	D	0.94742	0.8303	M	0.73217	2.22	0.80722	D	1	D;D;D;P	0.89917	0.957;1.0;1.0;0.956	P;D;D;P	0.87578	0.463;0.998;0.998;0.664	D	0.94435	0.7653	10	0.45353	T	0.12	-20.8968	17.3307	0.87262	0.0:1.0:0.0:0.0	.	8;8;8;8	B4DTW4;B4DWD8;Q9Y6A1;Q9Y6A1-2	.;.;POMT1_HUMAN;.	L	8	ENSP00000404119:P8L;ENSP00000361302:P8L;ENSP00000385797:P8L;ENSP00000346748:P8L;ENSP00000390737:P8L	ENSP00000346748:P8L	P	+	2	0	POMT1	133369449	1.000000	0.71417	0.336000	0.25522	0.137000	0.21094	6.556000	0.73932	2.317000	0.78254	0.655000	0.94253	CCT	.	.	.	none		0.597	POMT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054737.1	NM_007171		T	134379628	C	T	134379628	3	4	207	1	0	0	0	0	1	0	0	0	12252	681	24	2	25	2	POMT1	9	134379628	Missense_Mutation	SNP	C	TCGA-IA-A83V-01A-11D-A34Z-10	128366581	134379628	6833803	21	12579											
SFMBT2	57713	hgsc.bcm.edu	37	chr10	7423824	7423824	+	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	ttccaagggtgaagatgaagGgtcttgcatattggaagctg	11	11	14	5	0	1	3	0	2	1	1	2	4	2	4	1	3	2	2	1	3	5	4			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr10:7423824G>A	ENST00000361972.4	-	2	127	c.37C>T	c.(37-39)Cct>Tct	p.P13S	SFMBT2_ENST00000379713.3_Missense_Mutation_p.P13S|SFMBT2_ENST00000379711.2_Missense_Mutation_p.P13S|SFMBT2_ENST00000397167.1_Missense_Mutation_p.P13S|SFMBT2_ENST00000397160.3_Missense_Mutation_p.P13S	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	13					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						GAAGATGAAGGGTCTTGCATA	0.413																																					p.P13S		Atlas-SNP	.											.	SFMBT2	209	.	0			c.C37T						PASS	.						125	119	121					10																	7423824		2203	4300	6503	SO:0001583	missense	57713	exon2			ATGAAGGGTCTTG	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.37C>T	chr10.hg19:g.7423824G>A	ENSP00000355109:p.Pro13Ser	78.0	0.0	.		54.0	11.0	.	NM_001029880	A7MD09|Q9HCF5	Missense_Mutation	SNP	ENST00000361972.4	hg19	CCDS31138.1	.	.	.	.	.	.	.	.	.	.	G	7.150	0.583667	0.13749	.	.	ENSG00000198879	ENST00000361972;ENST00000397167;ENST00000379713;ENST00000379711;ENST00000397160	T;T;T;T;T	0.29917	2.62;2.62;1.95;1.55;1.55	4.82	-3.95	0.04118	.	0.531028	0.16003	N	0.234228	T	0.11110	0.0271	N	0.22421	0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.28490	-1.0042	10	0.09843	T	0.71	.	0.1011	0.00048	0.27:0.2475:0.2071:0.2754	.	13;13	Q5T981;Q5VUG0	.;SMBT2_HUMAN	S	13	ENSP00000355109:P13S;ENSP00000380353:P13S;ENSP00000369035:P13S;ENSP00000369033:P13S;ENSP00000380346:P13S	ENSP00000355109:P13S	P	-	1	0	SFMBT2	7463830	0.552000	0.26505	0.000000	0.03702	0.043000	0.13939	0.403000	0.20982	-0.397000	0.07691	-0.158000	0.13435	CCT	.	.	.	none		0.413	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880		A	7423824	G	A	7423824	3	1	207	1	0	0	0	0	1	0	0	0	14171	1232	43	2	2727	2	SFMBT2	10	7423824	Missense_Mutation	SNP	G	TCGA-IA-A83V-01A-11D-A34Z-10		7423824	128110923	22	12580											
FZD8	8325	hgsc.bcm.edu	37	chr10	35928674	35928674	+	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	cgggcagttgtgcgtggcctCccagcgcgggcggttgtgct	2	9	18	12	5	0	0	0	0	0	0	1	0	1	0	2	4	3	4	2	4	0	2			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr10:35928674C>G	ENST00000374694.1	-	1	1688	c.1684G>C	c.(1684-1686)Gag>Cag	p.E562Q	MIR4683_ENST00000579659.1_RNA	NM_031866.2	NP_114072.1	Q9H461	FZD8_HUMAN	frizzled class receptor 8	562					axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|gonad development (GO:0008406)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|T cell differentiation in thymus (GO:0033077)|vasculature development (GO:0001944)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	11						TGCGTGGCCTCCCAGCGCGGG	0.667																																					p.E562Q		Atlas-SNP	.											.	FZD8	41	.	0			c.G1684C						PASS	.						35	34	34					10																	35928674		2198	4297	6495	SO:0001583	missense	8325	exon1			TGGCCTCCCAGCG	AB043703	CCDS7192.1	10p11.2	2014-01-29	2014-01-29		ENSG00000177283	ENSG00000177283		"GPCR / Class F : Frizzled receptors"	4046	protein-coding gene	gene with protein product		606146	"frizzled (Drosophila) homolog 8", "frizzled homolog 8 (Drosophila)", "frizzled 8, seven transmembrane spanning receptor", "frizzled family receptor 8"			11295046	Standard	NM_031866		Approved		uc001iyz.1	Q9H461	OTTHUMG00000017956	ENST00000374694.1:c.1684G>C	chr10.hg19:g.35928674C>G	ENSP00000363826:p.Glu562Gln	36.0	0.0	.		37.0	6.0	.	NM_031866		Missense_Mutation	SNP	ENST00000374694.1	hg19	CCDS7192.1	.	.	.	.	.	.	.	.	.	.	C	19.62	3.861563	0.71949	.	.	ENSG00000177283	ENST00000374694	D	0.81996	-1.56	3.25	3.25	0.37280	GPCR, family 2-like (1);	0.000000	0.64402	U	0.000001	D	0.90055	0.6894	M	0.81802	2.56	0.54753	D	0.999984	D	0.69078	0.997	D	0.70227	0.968	D	0.90388	0.4393	10	0.42905	T	0.14	.	14.6096	0.68507	0.0:1.0:0.0:0.0	.	562	Q9H461	FZD8_HUMAN	Q	562	ENSP00000363826:E562Q	ENSP00000363826:E562Q	E	-	1	0	FZD8	35968680	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.179000	0.77665	1.807000	0.52817	0.289000	0.19496	GAG	.	.	.	none		0.667	FZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047575.2	NM_031866		G	35928674	C	G	35928674	3	3	207	1	0	0	0	0	1	0	0	0	6143	864	30	4	404	4	FZD8	10	35928674	Missense_Mutation	SNP	C	TCGA-IA-A83V-01A-11D-A34Z-10	28504850	35928674	99606073	23	12581											
MKI67	4288	hgsc.bcm.edu	37	chr10	129904689	129904689	+	Frame_Shift_Del	DEL	T	T	-																															aaatttcctggctggtccagTttctgcactggagttcccaa																										TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr10:129904689delT	ENST00000368654.3	-	13	5790	c.5415delA	c.(5413-5415)aaafs	p.K1805fs	MKI67_ENST00000368653.3_Frame_Shift_Del_p.K1445fs	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1805	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)				GCTGGTCCAGTTTCTGCACTG	0.493																																					p.L1806fs		Atlas-Indel,Pindel	.											.	MKI67	363	.	0			c.5416delC						PASS	.						170	163	165					10																	129904689		2203	4300	6503	SO:0001589	frameshift_variant	4288	exon13			.	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.5415delA	chr10.hg19:g.129904689delT	ENSP00000357643:p.Lys1805fs	381.0	0.0	0		349.0	81.0	0.232092	NM_002417	Q5VWH2	Frame_Shift_Del	DEL	ENST00000368654.3	hg19	CCDS7659.1																																																																																			.	.	.	none		0.493	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		-	129904689	T	-	129904689	7	5	207	1	0	1	0	1	0	0	0	0	9605	1722	60	0	4367	0	MKI67	10	129904689	Frame_Shift_Del	DEL	T	TCGA-IA-A83V-01A-11D-A34Z-10	93976015	129904689	5630058	24	12582											
CAPRIN1	4076	hgsc.bcm.edu	37	chr11	34118208	34118208	+	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	atggataccggggccctgccAatggattcagaggtaaaaaa	14	7	12	8	1	1	1	1	0	0	1	1	3	1	3	3	5	2	1	3	5	5	3			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr11:34118208A>T	ENST00000341394.4	+	16	2077	c.1888A>T	c.(1888-1890)Aat>Tat	p.N630Y	CAPRIN1_ENST00000530820.1_Missense_Mutation_p.N630Y|CAPRIN1_ENST00000533657.1_3'UTR|CAPRIN1_ENST00000532820.1_Missense_Mutation_p.N630Y|CAPRIN1_ENST00000389645.3_Missense_Mutation_p.N630Y|CAPRIN1_ENST00000529307.1_Missense_Mutation_p.N549Y	NM_005898.4	NP_005889.3	Q14444	CAPR1_HUMAN	cell cycle associated protein 1	630					negative regulation of translation (GO:0017148)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)	18		Acute lymphoblastic leukemia(5;0.00045)|all_hematologic(20;0.0016)				GGGCCCTGCCAATGGATTCAG	0.403																																					p.N630Y		Atlas-SNP	.											.	CAPRIN1	110	.	0			c.A1888T						PASS	.						53	60	58					11																	34118208		2202	4298	6500	SO:0001583	missense	4076	exon16			CCTGCCAATGGAT	BC001731	CCDS31453.1, CCDS31454.1	11p13	2010-08-03	2007-03-27	2007-03-27	ENSG00000135387	ENSG00000135387			6743	protein-coding gene	gene with protein product	"cytoplasmic activation/proliferation-associated protein-1"	601178	"membrane component, chromosome 11, surface marker 1", "GPI-anchored membrane protein 1"	M11S1, GPIAP1		7657653, 16177067, 17210633, 14764709, 15471883	Standard	NM_005898		Approved	caprin-1, RNG105	uc001mvh.1	Q14444	OTTHUMG00000166248	ENST00000341394.4:c.1888A>T	chr11.hg19:g.34118208A>T	ENSP00000340329:p.Asn630Tyr	124.0	0.0	.		118.0	31.0	.	NM_203364	A6NMY7|D3DR06|Q15074|Q6IMN4|Q6IMN7|Q9BV09	Missense_Mutation	SNP	ENST00000341394.4	hg19	CCDS31453.1	.	.	.	.	.	.	.	.	.	.	A	25.7	4.669325	0.88348	.	.	ENSG00000135387	ENST00000341394;ENST00000389645;ENST00000532820;ENST00000530820;ENST00000529307	T;T;T;T;T	0.34072	1.38;1.38;1.38;1.38;1.38	5.91	5.91	0.95273	.	0.041083	0.85682	D	0.000000	T	0.57169	0.2035	M	0.68317	2.08	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.51934	-0.8642	10	0.18276	T	0.48	-8.4317	16.3453	0.83126	1.0:0.0:0.0:0.0	.	630;630	Q14444;Q14444-2	CAPR1_HUMAN;.	Y	630;630;630;630;549	ENSP00000340329:N630Y;ENSP00000374296:N630Y;ENSP00000434150:N630Y;ENSP00000434204:N630Y;ENSP00000431581:N549Y	ENSP00000340329:N630Y	N	+	1	0	CAPRIN1	34074784	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.919000	0.92770	2.261000	0.74972	0.533000	0.62120	AAT	.	.	.	none		0.403	CAPRIN1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000388680.2	NM_005898		T	34118208	A	T	34118208	3	4	207	1	0	0	0	0	1	0	0	0	2637	130	5	5	1946	5	CAPRIN1	11	34118208	Missense_Mutation	SNP	A	TCGA-IA-A83V-01A-11D-A34Z-10		34118208	100888308	25	12583											
TM7SF2	7108	hgsc.bcm.edu	37	chr11	64882832	64882832	+	Frame_Shift_Del	DEL	T	T	-																															gcgaattcccagaaaaacacTttccgaaagaatccttctga																										TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr11:64882832delT	ENST00000279263.7	+	8	1101	c.939delT	c.(937-939)actfs	p.T313fs	TM7SF2_ENST00000540748.1_Frame_Shift_Del_p.T197fs|TM7SF2_ENST00000345348.5_Intron|AP003068.12_ENST00000527789.1_RNA	NM_003273.2	NP_003264.2	O76062	ERG24_HUMAN	transmembrane 7 superfamily member 2	313					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						AGAAAAACACTTTCCGAAAGA	0.567																																					p.T313fs		Atlas-Indel,Pindel	.											.	TM7SF2	30	.	0			c.938delC						PASS	.						128	129	129					11																	64882832		1910	4124	6034	SO:0001589	frameshift_variant	7108	exon8			.	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.939delT	chr11.hg19:g.64882832delT	ENSP00000279263:p.Thr313fs	101.0	0.0	0		89.0	23.0	0.258427	NM_003273	A8K4H0|O95982|Q8IY06|Q96E64|Q96GZ1	Frame_Shift_Del	DEL	ENST00000279263.7	hg19	CCDS41669.1																																																																																			.	.	.	none		0.567	TM7SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385234.1	NM_003273		-	64882832	T	-	64882832	7	5	207	1	0	1	0	1	0	0	0	0	15986	1596	56	0	969	0	TM7SF2	11	64882832	Frame_Shift_Del	DEL	T	TCGA-IA-A83V-01A-11D-A34Z-10	30764624	64882832	70123684	26	12584											
KRTAP5-11	440051	hgsc.bcm.edu	37	chr11	71293623	71293623	+	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	gaggagcagcagggcttacaGcagttggactgggagcagcc	10	5	17	9	0	0	0	0	0	0	0	0	4	0	3	1	4	6	6	1	4	1	2			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr11:71293623G>A	ENST00000398530.1	-	1	298	c.261C>T	c.(259-261)tgC>tgT	p.C87C	KRTAP5-11_ENST00000526239.1_Intron|AP000867.1_ENST00000343767.3_Intron	NM_001005405.2	NP_001005405.1	Q6L8G4	KR511_HUMAN	keratin associated protein 5-11	87	6 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						agGGCTTACAGCAGTTGGACT	0.627																																					p.C87C		Atlas-SNP	.											.	KRTAP5-11	36	.	0			c.C261T						PASS	.						86	111	102					11																	71293623		2200	4293	6493	SO:0001819	synonymous_variant	440051	exon1			CTTACAGCAGTTG	AB126080	CCDS41685.1	11q13.4	2008-11-06			ENSG00000204571	ENSG00000204571		"Keratin associated proteins"	23606	protein-coding gene	gene with protein product						15144888	Standard	NM_001005405		Approved	KRTAP5.11, KRTAP5-6	uc001oqu.3	Q6L8G4	OTTHUMG00000057586	ENST00000398530.1:c.261C>T	chr11.hg19:g.71293623G>A		74.0	0.0	.		73.0	18.0	.	NM_001005405		Silent	SNP	ENST00000398530.1	hg19	CCDS41685.1																																																																																			.	.	.	none		0.627	KRTAP5-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127969.1	NM_001005405		A	71293623	G	A	71293623	2	1	207	1	0	0	0	0	0	0	0	1	8567	963	34	2		2	KRTAP5-11	11	71293623	Silent	SNP	G	TCGA-IA-A83V-01A-11D-A34Z-10	6410791	71293623	63712893	27	12585											
RBP5	83758	hgsc.bcm.edu	37	chr12	7276771	7276771	+	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	gcatcccttgcagtcagttcCtggggagagaggggaagtga	9	8	16	8	0	1	2	1	1	0	1	3	5	3	4	2	4	1	3	2	4	1	2			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr12:7276771C>A	ENST00000266560.3	-	4	521		c.e4-1		C1RL-AS1_ENST00000535078.1_RNA|C1RL-AS1_ENST00000545775.1_RNA|C1RL-AS1_ENST00000541775.1_RNA	NM_031491.2	NP_113679.1	P29762	RABP1_HUMAN	retinol binding protein 5, cellular						multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)	cytosol (GO:0005829)	retinal binding (GO:0016918)|retinoic acid binding (GO:0001972)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			autonomic_ganglia(1)|endometrium(4)|large_intestine(1)|lung(3)|ovary(1)	10					Alitretinoin(DB00523)|Tretinoin(DB00755)	CAGTCAGTTCCTGGGGAGAGA	0.577																																					.		Atlas-SNP	.											.	RBP5	20	.	0			c.355-1G>T						PASS	.						64	55	58					12																	7276771		2203	4300	6503	SO:0001630	splice_region_variant	83758	exon5			CAGTTCCTGGGGA	AY007436	CCDS8574.1	12p13.31	2013-03-01	2001-11-28		ENSG00000139194	ENSG00000139194		"Fatty acid binding protein family"	15847	protein-coding gene	gene with protein product		611866	"retinol-binding protein 5, cellular"			11274389	Standard	NM_031491		Approved	CRBPIII	uc001qsq.3	P82980	OTTHUMG00000168165	ENST00000266560.3:c.355-1G>T	chr12.hg19:g.7276771C>A		52.0	0.0	.		42.0	6.0	.	NM_031491	Q6IAY7|Q8WTV5	Splice_Site	SNP	ENST00000266560.3	hg19	CCDS8574.1	.	.	.	.	.	.	.	.	.	.	C	16.41	3.115989	0.56505	.	.	ENSG00000139194	ENST00000266560	.	.	.	3.67	3.67	0.42095	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.2006	0.59765	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RBP5	7168045	1.000000	0.71417	1.000000	0.80357	0.744000	0.42396	4.017000	0.57167	2.347000	0.79759	0.462000	0.41574	.	.	.	.	none		0.577	RBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398554.1	NM_031491	Intron	A	7276771	C	A	7276771	5	1	207	1	0	0	0	0	0	0	1	0	13172	695	24	4	57	4	RBP5	12	7276771	Splice_Site	SNP	C	TCGA-IA-A83V-01A-11D-A34Z-10		7276771	126575124	28	12586											
GEFT	115557	hgsc.bcm.edu	37	chr12	58010621	58010621	+	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	ctcctccagtctctccaactCcaaaaacccctccctgccaa	10	8	2	21	0	1	0	0	0	1	0	7	0	6	0	8	0	3	0	8	0	4	0			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr12:58010621C>G	ENST00000286494.4	+	15	2147	c.1687C>G	c.(1687-1689)Cca>Gca	p.P563A	AC025165.8_ENST00000444467.1_RNA|AC025165.8_ENST00000610219.1_RNA|ARHGEF25_ENST00000477314.1_3'UTR|AC025165.8_ENST00000356672.3_RNA|ARHGEF25_ENST00000333972.7_Missense_Mutation_p.P602A|AC025165.8_ENST00000593846.1_RNA	NM_182947.3	NP_891992	Q86VW2	ARHGP_HUMAN	Rho guanine nucleotide exchange factor (GEF) 25	563						cytosol (GO:0005829)|myofibril (GO:0030016)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	28						CTCTCCAACTCCAAAAACCCC	0.527																																					p.P602A		Atlas-SNP	.											.	ARHGEF25	111	.	0			c.C1804G						PASS	.						104	117	112					12																	58010621		2203	4300	6503	SO:0001583	missense	115557	exon16			CCAACTCCAAAAA		CCDS8947.1, CCDS44931.1	12q13.3	2011-11-16			ENSG00000240771	ENSG00000240771		"Rho guanine nucleotide exchange factors"	30275	protein-coding gene	gene with protein product	"RAC/CDC42 exchange factor"	610215				12547822	Standard	NM_182947		Approved	GEFT, p63RhoGEF	uc009zpy.4	Q86VW2	OTTHUMG00000152516	ENST00000286494.4:c.1687C>G	chr12.hg19:g.58010621C>G	ENSP00000286494:p.Pro563Ala	130.0	0.0	.		127.0	32.0	.	NM_001111270	A6NJH5|A9CQZ6|F8W7Z4|Q8WV84|Q96E63	Missense_Mutation	SNP	ENST00000286494.4	hg19	CCDS8947.1	.	.	.	.	.	.	.	.	.	.	c	7.924	0.739308	0.15642	.	.	ENSG00000240771	ENST00000333972;ENST00000286494	T;T	0.38560	1.13;1.17	4.83	2.96	0.34315	.	0.955133	0.08554	N	0.928584	T	0.30070	0.0753	L	0.27053	0.805	0.09310	N	1	B;B	0.12630	0.006;0.003	B;B	0.15870	0.014;0.004	T	0.23368	-1.0190	10	0.34782	T	0.22	.	7.799	0.29164	0.0:0.7392:0.1704:0.0904	.	602;563	F8W7Z4;Q86VW2	.;ARHGP_HUMAN	A	602;563	ENSP00000335560:P602A;ENSP00000286494:P563A	ENSP00000286494:P563A	P	+	1	0	ARHGEF25	56296888	0.002000	0.14202	0.001000	0.08648	0.647000	0.38526	1.605000	0.36815	0.724000	0.32296	0.563000	0.77884	CCA	.	.	.	none		0.527	ARHGEF25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000326561.1	NM_133483		G	58010621	C	G	58010621	3	3	207	1	0	0	0	0	1	0	0	0	6335	855	30	4	1967	4	GEFT	12	58010621	Missense_Mutation	SNP	C	TCGA-IA-A83V-01A-11D-A34Z-10	50733850	58010621	75841274	29	12587											
FLT1	2321	hgsc.bcm.edu	37	chr13	28942739	28942739	+	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	gatgatgatgatgatgacgaTgatgatgatgatgacaatgg	14	11	14	2	1	0	10	0	10	0	0	0	12	0	10	0	1	0	0	0	1	1	0	rs371573097|rs558386334	byFrequency	TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr13:28942739T>C	ENST00000282397.4	-	15	2368				FLT1_ENST00000541932.1_Silent_p.S726S	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1						blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	atgatgacgatgatgatgatg	0.343																																					p.S726S		Atlas-SNP	.											.	FLT1	393	.	0			c.A2178G						PASS	.						289	303	299					13																	28942739		692	1591	2283	SO:0001627	intron_variant	2321	exon15			TGACGATGATGAT	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3763	protein-coding gene	gene with protein product	"vascular endothelial growth factor receptor 1", "vascular permeability factor receptor"	165070	"fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.2117-10917A>G	chr13.hg19:g.28942739T>C		65.0	0.0	.		75.0	4.0	.	NM_001160030	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Silent	SNP	ENST00000282397.4	hg19	CCDS9330.1																																																																																			.	.	.	none		0.343	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			C	28942739	T	C	28942739	1	2	207	0	1	0	0	0	0	0	0	0	5948	1451	51	3		3	FLT1	13	28942739	Intron	SNP	T	TCGA-IA-A83V-01A-11D-A34Z-10		28942739	86227139	30	12588											
MYH7	4625	hgsc.bcm.edu	37	chr14	23888454	23888454	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaggtgagcttgcctcgggTcagctgggagatcagtgcct	6	10	16	9	1	2	2	2	1	0	1	3	3	2	2	2	3	4	3	2	3	1	2			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr14:23888454T>C	ENST00000355349.3	-	29	4066	c.3904A>G	c.(3904-3906)Acc>Gcc	p.T1302A	MIR208B_ENST00000401172.1_RNA	NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1302					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		TTGCCTCGGGTCAGCTGGGAG	0.607																																					p.T1302A		Atlas-SNP	.											.	MYH7	349	.	0			c.A3904G						PASS	.						96	83	88					14																	23888454		2203	4300	6503	SO:0001583	missense	4625	exon29			CTCGGGTCAGCTG	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.3904A>G	chr14.hg19:g.23888454T>C	ENSP00000347507:p.Thr1302Ala	52.0	0.0	.		61.0	14.0	.	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	hg19	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	T	19.72	3.881046	0.72294	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	T	0.78364	-1.17	4.99	4.99	0.66335	Myosin tail (1);	.	.	.	.	D	0.83746	0.5321	M	0.75264	2.295	0.51233	D	0.999918	B	0.29378	0.243	P	0.46685	0.524	D	0.84607	0.0676	9	0.72032	D	0.01	.	11.2964	0.49280	0.136:0.0:0.0:0.864	.	1302	P12883	MYH7_HUMAN	A	1302;1307	ENSP00000347507:T1302A	ENSP00000347507:T1302A	T	-	1	0	MYH7	22958294	0.946000	0.32159	1.000000	0.80357	0.997000	0.91878	1.564000	0.36375	2.104000	0.64026	0.533000	0.62120	ACC	.	.	.	none		0.607	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		C	23888454	T	C	23888454	3	2	207	1	0	0	0	0	1	0	0	0	10046	1667	58	3	1951	3	MYH7	14	23888454	Missense_Mutation	SNP	T	TCGA-IA-A83V-01A-11D-A34Z-10		23888454	83461086	31	12589											
PSEN1	5663	hgsc.bcm.edu	37	chr14	73678584	73678584	+	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	tagggcctcatcgctctacaCctgagtcacgagctgctgtc	7	10	10	14	2	3	1	2	1	1	0	5	2	3	1	2	1	3	3	2	1	2	2	rs376433615		TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr14:73678584C>G	ENST00000324501.5	+	10	1335	c.1063C>G	c.(1063-1065)Cct>Gct	p.P355A	PSEN1_ENST00000357710.4_Missense_Mutation_p.P351A|PSEN1_ENST00000394164.1_Missense_Mutation_p.P351A|PSEN1_ENST00000261970.3_Intron|PSEN1_ENST00000406768.1_Missense_Mutation_p.P263A|PSEN1_ENST00000344094.3_3'UTR|PSEN1_ENST00000557511.1_Intron	NM_000021.3|NM_007318.2	NP_000012.1|NP_015557.2	P49768	PSN1_HUMAN	presenilin 1	355	Required for interaction with CTNNB1.				activation of MAPKK activity (GO:0000186)|amyloid precursor protein catabolic process (GO:0042987)|anagen (GO:0042640)|autophagic vacuole assembly (GO:0000045)|beta-amyloid formation (GO:0034205)|beta-amyloid metabolic process (GO:0050435)|blood vessel development (GO:0001568)|brain morphogenesis (GO:0048854)|Cajal-Retzius cell differentiation (GO:0021870)|calcium ion transmembrane transport (GO:0070588)|canonical Wnt signaling pathway (GO:0060070)|cell fate specification (GO:0001708)|cellular response to DNA damage stimulus (GO:0006974)|cerebral cortex cell migration (GO:0021795)|choline transport (GO:0015871)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic limb morphogenesis (GO:0030326)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|hematopoietic progenitor cell differentiation (GO:0002244)|intracellular signal transduction (GO:0035556)|L-glutamate transport (GO:0015813)|membrane protein ectodomain proteolysis (GO:0006509)|memory (GO:0007613)|mitochondrial transport (GO:0006839)|myeloid leukocyte differentiation (GO:0002573)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of axonogenesis (GO:0050771)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|neuron migration (GO:0001764)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|positive regulation of coagulation (GO:0050820)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of receptor recycling (GO:0001921)|post-embryonic development (GO:0009791)|protein glycosylation (GO:0006486)|protein processing (GO:0016485)|protein transport (GO:0015031)|regulation of phosphorylation (GO:0042325)|regulation of protein binding (GO:0043393)|regulation of resting membrane potential (GO:0060075)|regulation of synaptic plasticity (GO:0048167)|regulation of synaptic transmission, glutamatergic (GO:0051966)|response to oxidative stress (GO:0006979)|single organismal cell-cell adhesion (GO:0016337)|skeletal system morphogenesis (GO:0048705)|skin morphogenesis (GO:0043589)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|somitogenesis (GO:0001756)|synaptic vesicle targeting (GO:0016080)|T cell activation involved in immune response (GO:0002286)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cell cortex (GO:0005938)|cell surface (GO:0009986)|centrosome (GO:0005813)|ciliary rootlet (GO:0035253)|cytoplasmic vesicle (GO:0031410)|dendritic shaft (GO:0043198)|endoplasmic reticulum (GO:0005783)|gamma-secretase complex (GO:0070765)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|kinetochore (GO:0000776)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nuclear outer membrane (GO:0005640)|perinuclear region of cytoplasm (GO:0048471)|rough endoplasmic reticulum (GO:0005791)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	aspartic-type endopeptidase activity (GO:0004190)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|calcium channel activity (GO:0005262)|endopeptidase activity (GO:0004175)|PDZ domain binding (GO:0030165)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.075)		TCGCTCTACACCTGAGTCACG	0.512																																					p.P355A		Atlas-SNP	.											.	PSEN1	38	.	0			c.C1063G						PASS	.						125	106	113					14																	73678584		2203	4300	6503	SO:0001583	missense	5663	exon10			TCTACACCTGAGT	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.1063C>G	chr14.hg19:g.73678584C>G	ENSP00000326366:p.Pro355Ala	99.0	0.0	.		79.0	18.0	.	NM_000021	B2R6D3|O95465|Q14762|Q15719|Q15720|Q96P33|Q9UIF0	Missense_Mutation	SNP	ENST00000324501.5	hg19	CCDS9812.1	.	.	.	.	.	.	.	.	.	.	C	2.251	-0.371435	0.05034	.	.	ENSG00000080815	ENST00000324501;ENST00000357710;ENST00000394164;ENST00000406768	D;D;D;D	0.99507	-6.04;-6.04;-6.04;-6.04	6.07	-4.33	0.03677	.	0.587506	0.19956	N	0.102313	D	0.95227	0.8452	N	0.17082	0.46	0.09310	N	0.999998	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	D	0.93070	0.6482	10	0.09338	T	0.73	0.404	4.5188	0.11949	0.1006:0.3795:0.3539:0.166	.	351;355	P49768-2;P49768	.;PSN1_HUMAN	A	355;351;351;263	ENSP00000326366:P355A;ENSP00000350342:P351A;ENSP00000377719:P351A;ENSP00000385948:P263A	ENSP00000326366:P355A	P	+	1	0	PSEN1	72748337	0.000000	0.05858	0.000000	0.03702	0.098000	0.18820	-0.084000	0.11268	-1.337000	0.02236	-0.150000	0.13652	CCT	.	.	.	alt		0.512	PSEN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280500.2			G	73678584	C	G	73678584	3	3	207	1	0	0	0	0	1	0	0	0	12660	507	18	4	1093	4	PSEN1	14	73678584	Missense_Mutation	SNP	C	TCGA-IA-A83V-01A-11D-A34Z-10	49790130	73678584	33670956	32	12590											
ASB2	51676	hgsc.bcm.edu	37	chr14	94413717	94413717	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagttgcccttcttggaggCgatgtgcagcgggagcaagc	7	9	16	9	2	1	0	0	0	1	0	1	3	1	2	1	3	5	4	1	3	2	4			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr14:94413717C>T	ENST00000315988.4	-	5	1374	c.886G>A	c.(886-888)Gcc>Acc	p.A296T	MIR4506_ENST00000584693.1_RNA|ASB2_ENST00000555019.1_Missense_Mutation_p.A344T|ASB2_ENST00000556337.1_Intron	NM_016150.4	NP_057234.2	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box containing 2	296					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)		TTCTTGGAGGCGATGTGCAGC	0.632																																					p.A344T		Atlas-SNP	.											.	ASB2	71	.	0			c.G1030A						PASS	.						158	129	139					14																	94413717		2203	4300	6503	SO:0001583	missense	51676	exon7			TGGAGGCGATGTG	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.886G>A	chr14.hg19:g.94413717C>T	ENSP00000320675:p.Ala296Thr	96.0	0.0	.		96.0	20.0	.	NM_001202429	B2RDP9|B4E166|Q9NSU5|Q9Y567	Missense_Mutation	SNP	ENST00000315988.4	hg19	CCDS9915.1	.	.	.	.	.	.	.	.	.	.	C	35	5.593233	0.96602	.	.	ENSG00000100628	ENST00000555019;ENST00000434324;ENST00000315988;ENST00000543546;ENST00000555507	T;D;T	0.86956	-1.46;-2.19;-0.31	5.19	5.19	0.71726	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.95906	0.8667	H	0.96175	3.78	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.97286	0.9921	10	0.87932	D	0	-25.2568	18.7174	0.91680	0.0:1.0:0.0:0.0	.	312;344;296	B3KPZ6;B4E166;Q96Q27	.;.;ASB2_HUMAN	T	344;312;296;242;242	ENSP00000451575:A344T;ENSP00000320675:A296T;ENSP00000450940:A242T	ENSP00000320675:A296T	A	-	1	0	ASB2	93483470	1.000000	0.71417	0.948000	0.38648	0.953000	0.61014	7.818000	0.86416	2.417000	0.82017	0.462000	0.41574	GCC	.	.	.	none		0.632	ASB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412845.1			T	94413717	C	T	94413717	3	4	207	1	0	0	0	0	1	0	0	0	1023	768	27	1	893	1	ASB2	14	94413717	Missense_Mutation	SNP	C	TCGA-IA-A83V-01A-11D-A34Z-10	20735133	94413717	12935823	33	12591											
DNAJC17	55192	hgsc.bcm.edu	37	chr15	41066037	41066037	+	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	cattctggacagccagctccTgccaaacacagcatctagtc	11	8	7	15	0	2	0	0	0	2	0	4	1	3	1	3	1	5	2	3	1	2	2			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr15:41066037T>A	ENST00000220496.4	-	10	712		c.e10-2			NM_018163.2	NP_060633.1	Q9NVM6	DJC17_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 17						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)		AGCCAGCTCCTGCCAAACACA	0.562																																					.		Atlas-SNP	.											.	DNAJC17	18	.	0			c.682-2A>T						PASS	.						32	28	29					15																	41066037		2203	4300	6503	SO:0001630	splice_region_variant	55192	exon11			AGCTCCTGCCAAA	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.682-2A>T	chr15.hg19:g.41066037T>A		58.0	0.0	.		82.0	21.0	.	NM_018163		Splice_Site	SNP	ENST00000220496.4	hg19	CCDS10065.1	.	.	.	.	.	.	.	.	.	.	T	19.72	3.880172	0.72294	.	.	ENSG00000104129	ENST00000220496	.	.	.	5.17	5.17	0.71159	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8314	0.70151	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	DNAJC17	38853329	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	6.416000	0.73332	2.181000	0.69327	0.459000	0.35465	.	.	.	.	none		0.562	DNAJC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252356.2	NM_018163	Intron	A	41066037	T	A	41066037	5	1	207	1	0	0	0	0	0	0	1	0	4638	1594	55	5	242	5	DNAJC17	15	41066037	Splice_Site	SNP	T	TCGA-IA-A83V-01A-11D-A34Z-10		41066037	61465355	34	12592											
IMP3	55272	hgsc.bcm.edu	37	chr15	75931982	75931982	+	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	tccagatcgaagtcatcgcgCtcctcattgtactctagcac	9	11	7	14	3	3	1	2	0	1	1	7	2	5	1	2	0	2	3	2	0	3	3			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr15:75931982C>T	ENST00000314852.2	-	2	1471	c.528G>A	c.(526-528)gaG>gaA	p.E176E	IMP3_ENST00000565349.1_5'Flank|CTD-2026K11.2_ENST00000564683.1_RNA|IMP3_ENST00000403490.1_Silent_p.E176E			Q8TCT8	SPP2A_HUMAN	IMP3, U3 small nucleolar ribonucleoprotein	0					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)			large_intestine(1)	1						AGTCATCGCGCTCCTCATTGT	0.537																																					p.E176E		Atlas-SNP	.											IMP3,NS,carcinoma,0,1	IMP3	10	.	0			c.G528A						PASS	.						95	82	86					15																	75931982		2197	4294	6491	SO:0001819	synonymous_variant	55272	exon1			ATCGCGCTCCTCA	AB051628	CCDS10282.1	15q24	2014-02-19	2014-02-19	2005-07-14	ENSG00000177971	ENSG00000177971			14497	protein-coding gene	gene with protein product		612980	"mitochondrial ribosomal protein S4", "chromosome 15 open reading frame 12", "IMP3, U3 small nucleolar ribonucleoprotein, homolog (yeast)"	MRPS4, C15orf12		11543634, 12655004	Standard	NM_018285		Approved	FLJ10968, BRMS2	uc010bkl.2	Q9NV31	OTTHUMG00000142840	ENST00000314852.2:c.528G>A	chr15.hg19:g.75931982C>T		49.0	0.0	.		73.0	15.0	.	NM_018285	B2RDS0|Q8TAW1|Q96SZ8	Silent	SNP	ENST00000314852.2	hg19	CCDS10282.1																																																																																			.	.	.	none		0.537	IMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286476.1	NM_018285		T	75931982	C	T	75931982	2	4	207	1	0	0	0	0	0	0	0	1	7726	796	28	2		2	IMP3	15	75931982	Silent	SNP	C	TCGA-IA-A83V-01A-11D-A34Z-10	34865945	75931982	26599410	35	12593											
WDR24	84219	hgsc.bcm.edu	37	chr16	739631	739631	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgtggtcacacgggacaTcttctccatggctgcacagg	7	9	13	12	1	3	0	1	0	2	0	4	1	3	1	1	5	1	3	1	5	0	1			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr16:739631T>C	ENST00000248142.6	-	3	195	c.196A>G	c.(196-198)Atg>Gtg	p.M66V	WDR24_ENST00000293883.4_Missense_Mutation_p.M4V|LA16c-313D11.12_ENST00000566927.1_RNA			Q96S15	WDR24_HUMAN	WD repeat domain 24	66										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)				ACACGGGACATCTTCTCCATG	0.632																																					p.M4V		Atlas-SNP	.											.	WDR24	111	.	0			c.A10G						PASS	.						30	25	26					16																	739631		2199	4299	6498	SO:0001583	missense	84219	exon1			GGGACATCTTCTC	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.196A>G	chr16.hg19:g.739631T>C	ENSP00000248142:p.Met66Val	67.0	0.0	.		89.0	36.0	.	NM_032259	A2IDB8|D3DU59|Q96GC7|Q9H0B7	Missense_Mutation	SNP	ENST00000248142.6	hg19		.	.	.	.	.	.	.	.	.	.	t	11.89	1.772343	0.31411	.	.	ENSG00000127580	ENST00000248142;ENST00000293883	T;T	0.76578	-1.03;0.32	4.09	4.09	0.47781	.	0.000000	0.85682	D	0.000000	T	0.75459	0.3852	L	0.44542	1.39	0.40630	D	0.98184	B	0.34399	0.452	P	0.44623	0.455	T	0.72934	-0.4141	10	0.27785	T	0.31	1.7223	12.0317	0.53401	0.0:0.0:0.0:1.0	.	4	Q96S15-2	.	V	66;4	ENSP00000248142:M66V;ENSP00000293883:M4V	ENSP00000248142:M66V	M	-	1	0	WDR24	679632	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.157000	0.77461	1.715000	0.51383	0.459000	0.35465	ATG	.	.	.	none		0.632	WDR24-201	KNOWN	basic	protein_coding	protein_coding		NM_032259		C	739631	T	C	739631	3	2	207	1	0	0	0	0	1	0	0	0	17293	1435	50	3	2398	3	WDR24	16	739631	Missense_Mutation	SNP	T	TCGA-IA-A83V-01A-11D-A34Z-10		739631	89615122	36	12594											
C16orf62	57020	hgsc.bcm.edu	37	chr16	19584527	19584527	+	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	accaacaaacggggagaaatCcttgcccggtacaccactac	14	5	8	14	2	0	1	0	0	0	1	1	2	1	1	4	3	5	1	4	3	5	3			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr16:19584527C>G	ENST00000251143.5	+	4	384	c.372C>G	c.(370-372)atC>atG	p.I124M	C16orf62_ENST00000538853.1_Missense_Mutation_p.I213M|C16orf62_ENST00000542263.1_Missense_Mutation_p.I213M|C16orf62_ENST00000417362.2_Missense_Mutation_p.I124M|C16orf62_ENST00000438132.3_Missense_Mutation_p.I213M			Q7Z3J2	CP062_HUMAN	chromosome 16 open reading frame 62	124						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						GGGGAGAAATCCTTGCCCGGT	0.448																																					p.I213M		Atlas-SNP	.											.	C16orf62	164	.	0			c.C639G						PASS	.						136	135	135					16																	19584527		2197	4300	6497	SO:0001583	missense	57020	exon4			AGAAATCCTTGCC		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.372C>G	chr16.hg19:g.19584527C>G	ENSP00000251143:p.Ile124Met	67.0	0.0	.		66.0	10.0	.	NM_020314	A8K2M1|O43329|Q69YI1|Q6PDA0|Q7L371|Q86W66|Q8WXA5|Q9H0L7|Q9H7C8	Missense_Mutation	SNP	ENST00000251143.5	hg19		.	.	.	.	.	.	.	.	.	.	C	25.5	4.639579	0.87760	.	.	ENSG00000103544	ENST00000438132;ENST00000538853;ENST00000542263;ENST00000251143;ENST00000417362	T;T;T;T;T	0.64803	1.56;-0.12;1.56;1.56;1.56	5.32	4.36	0.52297	.	0.000000	0.85682	D	0.000000	T	0.79936	0.4532	M	0.86740	2.835	0.80722	D	1	D;D;D	0.89917	0.997;0.999;1.0	D;D;D	0.91635	0.994;0.996;0.999	T	0.81512	-0.0899	10	0.48119	T	0.1	-26.3365	12.4816	0.55847	0.0:0.9197:0.0:0.0803	.	213;124;213	F5H7K1;Q7Z3J2;E7EWW0	.;CP062_HUMAN;.	M	213;213;213;124;124	ENSP00000400815:I213M;ENSP00000444363:I213M;ENSP00000442468:I213M;ENSP00000251143:I124M;ENSP00000395973:I124M	ENSP00000251143:I124M	I	+	3	3	C16orf62	19492028	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.813000	0.55636	2.488000	0.83962	0.557000	0.71058	ATC	.	.	.	none		0.448	C16orf62-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_020314		G	19584527	C	G	19584527	3	3	207	1	0	0	0	0	1	0	0	0	1827	845	30	4	386	4	C16orf62	16	19584527	Missense_Mutation	SNP	C	TCGA-IA-A83V-01A-11D-A34Z-10	18844896	19584527	70770226	37	12595											
LONP2	83752	hgsc.bcm.edu	37	chr16	48296782	48296782	+	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	ccttggaacaaaagtacaacTggtaagccaaaaaataacac	20	6	6	9	0	0	0	0	0	0	0	0	1	0	1	2	2	5	2	2	2	10	4			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr16:48296782T>C	ENST00000285737.4	+	6	1074	c.981T>C	c.(979-981)acT>acC	p.T327T	LONP2_ENST00000535754.1_Splice_Site_p.T283T	NM_031490.2	NP_113678.2			lon peptidase 2, peroxisomal											breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						AAAGTACAACTGGTAAGCCAA	0.358																																					p.T327T		Atlas-SNP	.											.	LONP2	63	.	0			c.T981C						PASS	.						62	61	61					16																	48296782		2200	4299	6499	SO:0001630	splice_region_variant	83752	exon6			TACAACTGGTAAG	AJ548761	CCDS10734.1, CCDS73880.1	16q12.1	2010-04-21			ENSG00000102910	ENSG00000102910		"ATPases / AAA-type"	20598	protein-coding gene	gene with protein product						14561759	Standard	XM_005256191		Approved	MGC4840, LONP, LONPL	uc002efi.1	Q86WA8	OTTHUMG00000133144	ENST00000285737.4:c.982+1T>C	chr16.hg19:g.48296782T>C		149.0	0.0	.		155.0	48.0	.	NM_031490		Silent	SNP	ENST00000285737.4	hg19	CCDS10734.1																																																																																			.	.	.	none		0.358	LONP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256839.2	NM_031490	Silent	C	48296782	T	C	48296782	5	2	207	1	0	0	0	0	0	0	1	0	8900	1594	55	3	1003	3	LONP2	16	48296782	Splice_Site	SNP	T	TCGA-IA-A83V-01A-11D-A34Z-10	28712255	48296782	42057971	38	12596											
FA2H	79152	hgsc.bcm.edu	37	chr16	74808459	74808459	+	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	ttggccgagtgcctgtgcggCggcccgtccaggtcggcgct	2	8	17	14	6	0	0	0	0	0	0	2	1	1	0	4	5	2	1	4	5	0	1			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr16:74808459C>A	ENST00000219368.3	-	1	264	c.195G>T	c.(193-195)ccG>ccT	p.P65P	FA2H_ENST00000544337.1_5'UTR	NM_024306.4	NP_077282.3	Q7L5A8	FA2H_HUMAN	fatty acid 2-hydroxylase	65	Cytochrome b5 heme-binding. {ECO:0000255|PROSITE-ProRule:PRU00279}.				cell death (GO:0008219)|central nervous system myelin maintenance (GO:0032286)|fatty acid biosynthetic process (GO:0006633)|lipid modification (GO:0030258)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of cell proliferation (GO:0042127)|regulation of hair cycle (GO:0042634)|sebaceous gland cell differentiation (GO:0001949)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	fatty acid alpha-hydroxylase activity (GO:0080132)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			endometrium(2)|large_intestine(4)|lung(3)|skin(1)	10						GCCTGTGCGGCGGCCCGTCCA	0.751																																					p.P65P		Atlas-SNP	.											.	FA2H	21	.	0			c.G195T						PASS	.						4	4	4					16																	74808459		1728	3475	5203	SO:0001819	synonymous_variant	79152	exon1			GTGCGGCGGCCCG	BC002679	CCDS10911.1	16q23	2013-03-04	2003-10-29	2003-10-31	ENSG00000103089	ENSG00000103089		"Fatty acid hydroxylase domain containing"	21197	protein-coding gene	gene with protein product	"fatty acid hydroxylase"	611026	"fatty acid hydroxylase domain containing 1", "spastic paraplegia 35 (autosomal recessive)"	FAXDC1, SPG35		20104589	Standard	NM_024306		Approved	FAAH, FLJ25287	uc002fde.2	Q7L5A8	OTTHUMG00000137603	ENST00000219368.3:c.195G>T	chr16.hg19:g.74808459C>A		30.0	0.0	.		17.0	6.0	.	NM_024306	B7Z8T6|O75213|Q96DK1|Q9H1A5	Silent	SNP	ENST00000219368.3	hg19	CCDS10911.1																																																																																			.	.	.	none		0.751	FA2H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269015.2	NM_024306		A	74808459	C	A	74808459	2	1	207	1	0	0	0	0	0	0	0	1	5356	755	27	4		4	FA2H	16	74808459	Silent	SNP	C	TCGA-IA-A83V-01A-11D-A34Z-10	26511677	74808459	15546294	39	12597											
THRA	7067	hgsc.bcm.edu	37	chr17	38249559	38249559	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggaagacgacagcagtgAggcggactccccgagctcct	9	5	15	12	3	0	2	0	1	0	1	2	6	2	4	3	4	2	2	3	4	1	0			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr17:38249559A>G	ENST00000264637.4	+	10	1977	c.1397A>G	c.(1396-1398)gAg>gGg	p.E466G	NR1D1_ENST00000246672.3_Intron|THRA_ENST00000584985.1_Missense_Mutation_p.E427G|THRA_ENST00000394121.4_Missense_Mutation_p.E466G	NM_003250.5	NP_003241.2	P10827	THA_HUMAN	thyroid hormone receptor, alpha	466					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)	GACAGCAGTGAGGCGGACTCC	0.662																																					p.E466G		Atlas-SNP	.											.	THRA	88	.	0			c.A1397G						PASS	.						28	31	30					17																	38249559		2203	4300	6503	SO:0001583	missense	7067	exon10			GCAGTGAGGCGGA	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.1397A>G	chr17.hg19:g.38249559A>G	ENSP00000264637:p.Glu466Gly	82.0	0.0	.		102.0	44.0	.	NM_003250	A8K3B5|P21205|Q8N6A1|Q96H73	Missense_Mutation	SNP	ENST00000264637.4	hg19	CCDS11360.1	.	.	.	.	.	.	.	.	.	.	A	15.84	2.952359	0.53293	.	.	ENSG00000126351	ENST00000394121;ENST00000264637	D;D	0.94280	-3.39;-3.39	4.73	3.66	0.41972	.	0.355296	0.21196	N	0.078543	D	0.84817	0.5556	N	0.14661	0.345	0.80722	D	1	P;P	0.37330	0.59;0.455	B;B	0.35607	0.206;0.102	D	0.84397	0.0558	10	0.51188	T	0.08	.	8.2837	0.31915	0.9049:0.0:0.0951:0.0	.	427;466	P10827-3;P10827	.;THA_HUMAN	G	466	ENSP00000377679:E466G;ENSP00000264637:E466G	ENSP00000264637:E466G	E	+	2	0	THRA	35503085	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	1.912000	0.39946	2.117000	0.64856	0.460000	0.39030	GAG	.	.	.	none		0.662	THRA-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257160.2			G	38249559	A	G	38249559	3	3	207	1	0	0	0	0	1	0	0	0	15885	304	11	3	1554	3	THRA	17	38249559	Missense_Mutation	SNP	A	TCGA-IA-A83V-01A-11D-A34Z-10		38249559	42945651	40	12598											
KIAA1267	284058	hgsc.bcm.edu	37	chr17	44116537	44116537	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcccccacatcgtctaagtGctgcctgtgggtcctgtcag	5	10	12	14	1	2	0	1	0	1	0	4	0	3	0	4	2	2	1	4	2	1	1			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr17:44116537G>A	ENST00000262419.6	-	9	2718	c.2248C>T	c.(2248-2250)Cac>Tac	p.H750Y	KANSL1_ENST00000575318.1_Intron|KANSL1_ENST00000574590.1_Missense_Mutation_p.H750Y|KANSL1_ENST00000572904.1_Missense_Mutation_p.H750Y|KANSL1_ENST00000393476.3_Intron|KANSL1_ENST00000432791.1_Missense_Mutation_p.H750Y	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	750					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)											TCGTCTAAGTGCTGCCTGTGG	0.547																																					p.H750Y		Atlas-SNP	.											.	.	.	.	0			c.C2248T						PASS	.						103	94	97					17																	44116537		2203	4300	6503	SO:0001583	missense	284058	exon9			CTAAGTGCTGCCT	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.2248C>T	chr17.hg19:g.44116537G>A	ENSP00000262419:p.His750Tyr	156.0	0.0	.		199.0	34.0	.	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	hg19	CCDS11503.1	.	.	.	.	.	.	.	.	.	.	G	3.887	-0.024870	0.07589	.	.	ENSG00000120071	ENST00000262419;ENST00000432791	T;T	0.11821	2.74;2.74	5.8	4.83	0.62350	.	0.526646	0.20277	N	0.095526	T	0.05135	0.0137	N	0.08118	0	0.80722	D	1	B;P;P	0.35982	0.255;0.531;0.531	B;B;B	0.28849	0.095;0.065;0.065	T	0.25187	-1.0139	10	0.02654	T	1	-5.0476	11.2703	0.49136	0.0838:0.0:0.9162:0.0	.	81;750;750	Q7Z3B3-2;C9JHY2;Q7Z3B3	.;.;K1267_HUMAN	Y	750	ENSP00000262419:H750Y;ENSP00000387393:H750Y	ENSP00000262419:H750Y	H	-	1	0	KIAA1267	41472384	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.235000	0.51328	2.758000	0.94735	0.561000	0.74099	CAC	.	.	.	none		0.547	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443		A	44116537	G	A	44116537	3	1	207	1	0	0	0	0	1	0	0	0	8226	1319	46	2	1097	2	KIAA1267	17	44116537	Missense_Mutation	SNP	G	TCGA-IA-A83V-01A-11D-A34Z-10	5866978	44116537	37078673	41	12599											
CBX1	10951	hgsc.bcm.edu	37	chr17	46154301	46154301	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggtcgagaactttttccacCacatattcctcttcctcctc	7	14	4	16	2	1	1	0	0	1	1	7	2	5	1	5	1	1	0	5	1	2	5			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr17:46154301C>T	ENST00000393408.3	-	2	546	c.66G>A	c.(64-66)gtG>gtA	p.V22V	CBX1_ENST00000225603.4_Silent_p.V22V|CBX1_ENST00000495350.1_Silent_p.V22V	NM_006807.4	NP_006798.1	P83916	CBX1_HUMAN	chromobox homolog 1	22	Chromo 1. {ECO:0000255|PROSITE- ProRule:PRU00053}.				negative regulation of transcription, DNA-templated (GO:0045892)	chromatin (GO:0000785)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear heterochromatin (GO:0005720)|nucleoplasm (GO:0005654)|pericentric heterochromatin (GO:0005721)|spindle (GO:0005819)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone methyltransferase binding (GO:1990226)			breast(1)|central_nervous_system(1)|kidney(1)|prostate(1)	4						CTTTTTCCACCACATATTCCT	0.473																																					p.V22V	NSCLC(136;694 2497 38792 39034)	Atlas-SNP	.											.	CBX1	18	.	0			c.G66A						PASS	.						314	258	277					17																	46154301		2203	4300	6503	SO:0001819	synonymous_variant	10951	exon2			TTCCACCACATAT	U35451	CCDS11525.1	17q21.32	2010-07-06	2010-06-24		ENSG00000108468	ENSG00000108468			1551	protein-coding gene	gene with protein product	"HP1 beta homolog (Drosophila )"	604511	"chromobox homolog 1 (Drosophila HP1 beta)"			9169582	Standard	NM_001127228		Approved	HP1Hs-beta, M31, MOD1, CBX, HP1-BETA	uc002ind.4	P83916	OTTHUMG00000150417	ENST00000393408.3:c.66G>A	chr17.hg19:g.46154301C>T		269.0	0.0	.		305.0	19.0	.	NM_006807	P23197	Silent	SNP	ENST00000393408.3	hg19	CCDS11525.1																																																																																			.	.	.	none		0.473	CBX1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318016.1	NM_006807		T	46154301	C	T	46154301	2	4	207	1	0	0	0	0	0	0	0	1	2719	581	21	2		2	CBX1	17	46154301	Silent	SNP	C	TCGA-IA-A83V-01A-11D-A34Z-10	2037764	46154301	35040909	42	12600											
MRPL38	64978	hgsc.bcm.edu	37	chr17	73897871	73897871	+	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	gcgtaggccacgtgcaggggGactcggggcacaaaggtggc	8	4	19	10	3	0	0	0	0	0	0	1	1	0	1	1	7	1	3	1	7	2	1			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr17:73897871G>T	ENST00000309352.3	-	4	1050	c.513C>A	c.(511-513)gtC>gtA	p.V171V	MRPL38_ENST00000409963.3_5'UTR|MRPL38_ENST00000585475.1_5'UTR|RP11-552F3.10_ENST00000587267.1_RNA	NM_032478.3	NP_115867.2	Q96DV4	RM38_HUMAN	mitochondrial ribosomal protein L38	171						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)			CGTGCAGGGGGACTCGGGGCA	0.602																																					p.V171V		Atlas-SNP	.											.	MRPL38	26	.	0			c.C513A						PASS	.						87	66	73					17																	73897871		2203	4300	6503	SO:0001819	synonymous_variant	64978	exon4			CAGGGGGACTCGG	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.513C>A	chr17.hg19:g.73897871G>T		59.0	0.0	.		71.0	32.0	.	NM_032478	B3KN96|Q96Q66|Q9P0B9	Silent	SNP	ENST00000309352.3	hg19	CCDS11733.2																																																																																			.	.	.	none		0.602	MRPL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328829.1	NM_032478		T	73897871	G	T	73897871	2	4	207	1	0	0	0	0	0	0	0	1	9808	1161	41	4		4	MRPL38	17	73897871	Silent	SNP	G	TCGA-IA-A83V-01A-11D-A34Z-10	27743570	73897871	7297339	43	12601											
MIDN	90007	hgsc.bcm.edu	37	chr19	1255541	1255541	+	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	ctaccagggcatgcccccttCgctggcccagctccgctgcc	4	7	10	20	2	0	0	0	0	0	0	2	0	1	0	6	2	4	4	6	2	1	2			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr19:1255541C>T	ENST00000591446.2	+	6	1386	c.977C>T	c.(976-978)tCg>tTg	p.S326L	MIDN_ENST00000300952.2_Missense_Mutation_p.S326L			Q504T8	MIDN_HUMAN	midnolin	326						cytosol (GO:0005829)|nucleolus (GO:0005730)				NS(1)|endometrium(3)|kidney(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ATGCCCCCTTCGCTGGCCCAG	0.716																																					p.S326L		Atlas-SNP	.											.	MIDN	34	.	0			c.C977T						PASS	.						30	27	28					19																	1255541		2199	4296	6495	SO:0001583	missense	90007	exon7			CCCCTTCGCTGGC	AC004221	CCDS32864.1	19p13.3	2013-09-20			ENSG00000167470	ENSG00000167470			16298	protein-coding gene	gene with protein product		606700				10974535	Standard	XM_005259671		Approved		uc002lrp.3	Q504T8	OTTHUMG00000180144	ENST00000591446.2:c.977C>T	chr19.hg19:g.1255541C>T	ENSP00000467679:p.Ser326Leu	60.0	0.0	.		54.0	20.0	.	NM_177401	Q96BW8	Missense_Mutation	SNP	ENST00000591446.2	hg19	CCDS32864.1	.	.	.	.	.	.	.	.	.	.	C	16.29	3.080268	0.55753	.	.	ENSG00000167470	ENST00000300952	.	.	.	3.5	3.5	0.40072	.	0.000000	0.85682	D	0.000000	T	0.56630	0.1998	M	0.66939	2.045	0.48830	D	0.999716	B	0.23650	0.089	B	0.18871	0.023	T	0.61584	-0.7033	9	0.72032	D	0.01	-14.4784	8.6818	0.34214	0.0:0.8835:0.0:0.1165	.	326	Q504T8	MIDN_HUMAN	L	326	.	ENSP00000300952:S326L	S	+	2	0	MIDN	1206541	0.984000	0.35163	0.976000	0.42696	0.958000	0.62258	2.814000	0.48010	1.785000	0.52413	0.462000	0.41574	TCG	.	.	.	none		0.716	MIDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449965.2			T	1255541	C	T	1255541	3	4	207	1	0	0	0	0	1	0	0	0	9586	893	31	1	999	1	MIDN	19	1255541	Missense_Mutation	SNP	C	TCGA-IA-A83V-01A-11D-A34Z-10		1255541	57873442	44	12602											
LOC729991-MEF2B	100271849	hgsc.bcm.edu	37	chr19	19257425	19257425	+	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	ggtccgggagttgcagtggaGcaggggttctgcaggccact	6	8	18	9	1	1	0	0	0	1	0	2	2	2	2	2	6	3	5	2	6	0	2			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr19:19257425G>A	ENST00000602424.2	-	9	1434	c.708C>T	c.(706-708)tgC>tgT	p.C236C	MEF2BNB-MEF2B_ENST00000444486.3_Silent_p.C236C|MEF2BNB-MEF2B_ENST00000514819.3_Silent_p.C253C|MEF2B_ENST00000409224.1_Silent_p.C239C|MEF2B_ENST00000409447.2_Missense_Mutation_p.L192F|MEF2BNB-MEF2B_ENST00000602276.1_5'Flank|MEF2B_ENST00000410050.1_Silent_p.C236C|MEF2B_ENST00000162023.5_Silent_p.C236C|MEF2B_ENST00000424583.2_Silent_p.C236C	NM_005919.3	NP_005910.1	Q02080	MEF2B_HUMAN	myocyte enhancer factor 2B	236					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)			TTGCAGTGGAGCAGGGGTTCT	0.667																																					p.C236C		Atlas-SNP	.											.	MEF2BNB-MEF2B	29	.	0			c.C708T						PASS	.						28	31	30					19																	19257425		2200	4297	6497	SO:0001819	synonymous_variant	4207	exon9			AGTGGAGCAGGGG	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.708C>T	chr19.hg19:g.19257425G>A		48.0	0.0	.		40.0	12.0	.	NM_005919	A0AV80|B4DVH7|B7ZVY1|G5E9M1	Silent	SNP	ENST00000602424.2	hg19	CCDS12394.1	.	.	.	.	.	.	.	.	.	.	G	8.757	0.922660	0.18056	.	.	ENSG00000213999	ENST00000409447	.	.	.	4.49	2.35	0.29111	.	.	.	.	.	T	0.16769	0.0403	.	.	.	0.22591	N	0.998958	P	0.44578	0.838	B	0.30029	0.11	T	0.13980	-1.0489	7	0.62326	D	0.03	-6.4313	5.9893	0.19452	0.2352:0.0:0.7648:0.0	.	239	B8ZZJ5	.	F	239	.	ENSP00000386784:L239F	L	-	1	0	MEF2B	19118425	0.007000	0.16637	0.025000	0.17156	0.115000	0.19883	0.405000	0.21015	0.891000	0.36235	0.561000	0.74099	CTC	.	.	.	none		0.667	MEF2B-202	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_005919		A	19257425	G	A	19257425	2	1	207	1	0	0	0	0	0	0	0	1	8896	963	34	2		2	LOC729991-MEF2B	19	19257425	Silent	SNP	G	TCGA-IA-A83V-01A-11D-A34Z-10	18001884	19257425	39871558	45	12603											
C19orf55	126393	hgsc.bcm.edu	37	chr19	36250862	36250862	+	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	ggcctccccagcacccacccTgattgacagcggggactccg	7	5	11	18	2	0	2	0	2	0	0	2	3	2	3	6	3	2	1	6	3	0	1			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr19:36250862T>C	ENST00000592984.1	-	0	0				HSPB6_ENST00000587965.1_5'Flank|C19orf55_ENST00000536950.1_Missense_Mutation_p.L94P|C19orf55_ENST00000396908.4_Missense_Mutation_p.L94P|C19orf55_ENST00000537459.1_Missense_Mutation_p.L94P|HSPB6_ENST00000004982.3_5'Flank|C19orf55_ENST00000544099.1_Missense_Mutation_p.L94P|C19orf55_ENST00000421853.2_Intron			O14558	HSPB6_HUMAN	heat shock protein, alpha-crystallin-related, B6						regulation of muscle contraction (GO:0006937)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)|structural constituent of eye lens (GO:0005212)			lung(1)	1	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GCACCCACCCTGATTGACAGC	0.602																																					p.L94P		Atlas-SNP	.											.	C19orf55	39	.	0			c.T281C						PASS	.						25	27	26					19																	36250862		1954	4128	6082	SO:0001631	upstream_gene_variant	148137	exon3			CCACCCTGATTGA	AJ278121	CCDS12475.1	19q13.13	2014-06-12			ENSG00000004776	ENSG00000004776		"Heat shock proteins / HSPB"	26511	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 91"	610695				12820654, 14717697	Standard	NM_144617		Approved	FLJ32389, Hsp20, PPP1R91	uc002obn.2	O14558	OTTHUMG00000048122		chr19.hg19:g.36250862T>C	Exception_encountered	75.0	0.0	.		49.0	6.0	.	NM_001039887	O14551|Q6NVI3|Q96MG9	Missense_Mutation	SNP	ENST00000592984.1	hg19	CCDS12475.1	.	.	.	.	.	.	.	.	.	.	T	3.312	-0.140508	0.06669	.	.	ENSG00000167595	ENST00000444637;ENST00000396908;ENST00000301165;ENST00000537459;ENST00000545674	T;T;T;T	0.51574	0.7;0.7;0.7;0.7	3.65	1.5	0.22942	.	0.723756	0.10666	N	0.648169	T	0.38931	0.1059	L	0.55481	1.735	0.19945	N	0.999942	B;B;B	0.17667	0.008;0.023;0.023	B;B;B	0.17098	0.007;0.017;0.017	T	0.32981	-0.9886	10	0.39692	T	0.17	-2.0221	4.561	0.12160	0.0:0.324:0.0:0.676	.	94;94;94	E5RFB9;Q2NL68-3;Q2NL68-4	.;.;.	P	9;94;94;9;9	ENSP00000394231:L9P;ENSP00000380116:L94P;ENSP00000301165:L94P;ENSP00000440357:L9P	ENSP00000301165:L94P	L	+	2	0	C19orf55	40942702	0.002000	0.14202	0.003000	0.11579	0.045000	0.14185	1.163000	0.31798	0.284000	0.22305	0.383000	0.25322	CTG	.	.	.	none		0.602	HSPB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109498.3	NM_144617		C	36250862	T	C	36250862	1	2	207	0	1	0	0	0	0	0	0	0	1939	1580	55	3		3	C19orf55	19	36250862	5'Flank	SNP	T	TCGA-IA-A83V-01A-11D-A34Z-10	16993437	36250862	22878121	46	12604											
ZNF780A	284323	hgsc.bcm.edu	37	chr19	40589098	40589098	+	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	caggctgcaggcactcccacTcctcctgagagaagtcaatg	10	7	10	14	0	1	2	1	1	0	1	4	3	4	2	3	2	1	3	3	2	2	0			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr19:40589098T>A	ENST00000595687.2	-	4	265	c.56A>T	c.(55-57)gAg>gTg	p.E19V	AC005614.5_ENST00000595508.1_RNA|ZNF780A_ENST00000340963.5_Missense_Mutation_p.E19V|ZNF780A_ENST00000594395.1_Missense_Mutation_p.E19V|ZNF780A_ENST00000455521.1_Missense_Mutation_p.E19V|ZNF780A_ENST00000450241.2_5'UTR|ZNF780A_ENST00000414720.2_Missense_Mutation_p.E35V	NM_001010880.2	NP_001010880.2	O75290	Z780A_HUMAN	zinc finger protein 780A	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(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)					GCACTCCCACTCCTCCTGAGA	0.478																																					p.E35V		Atlas-SNP	.											.	ZNF780A	156	.	0			c.A104T						PASS	.						127	115	119					19																	40589098		2203	4297	6500	SO:0001583	missense	284323	exon5			TCCCACTCCTCCT	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.56A>T	chr19.hg19:g.40589098T>A	ENSP00000472189:p.Glu19Val	115.0	0.0	.		87.0	28.0	.	NM_001142579	E9PB48|Q6ZN87	Missense_Mutation	SNP	ENST00000595687.2	hg19	CCDS33026.2	.	.	.	.	.	.	.	.	.	.	T	23.4	4.410399	0.83340	.	.	ENSG00000197782	ENST00000443072;ENST00000450241;ENST00000414720;ENST00000455521;ENST00000340963	T;T;T	0.12361	2.69;2.69;2.69	1.65	1.65	0.23941	Krueppel-associated box (4);	.	.	.	.	T	0.54431	0.1858	H	0.99815	4.805	0.28205	N	0.927167	D;P;D	0.89917	0.975;0.789;1.0	D;B;D	0.91635	0.987;0.33;0.999	T	0.52290	-0.8595	9	0.87932	D	0	.	6.9604	0.24593	0.0:0.0:0.0:1.0	.	19;19;35	E9PB48;O75290;O75290-2	.;Z780A_HUMAN;.	V	19;19;35;19;19	ENSP00000416294:E35V;ENSP00000400997:E19V;ENSP00000341507:E19V	ENSP00000341507:E19V	E	-	2	0	ZNF780A	45280938	0.947000	0.32204	0.894000	0.35097	0.973000	0.67179	1.929000	0.40114	0.749000	0.32854	0.254000	0.18369	GAG	.	.	.	none		0.478	ZNF780A-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000470066.1	NM_001010880		A	40589098	T	A	40589098	3	1	207	1	0	0	0	0	1	0	0	0	18164	1551	54	5	2011	5	ZNF780A	19	40589098	Missense_Mutation	SNP	T	TCGA-IA-A83V-01A-11D-A34Z-10	4338236	40589098	18539885	47	12605											
ZNF226	7769	hgsc.bcm.edu	37	chr19	44681813	44681816	+	Frame_Shift_Del	DEL	AAAT	AAAT	-																															gagaatccacacaggaaaaaAaatctataaaatgattcttt																										TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	AAAT	AAAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr19:44681813_44681816delAAAT	ENST00000590089.1	+	7	2765_2768	c.2398_2401delAAAT	c.(2398-2403)aaatctfs	p.KS800fs	ZNF226_ENST00000454662.2_Frame_Shift_Del_p.KS800fs|ZNF226_ENST00000588883.1_3'UTR|ZNF226_ENST00000337433.5_Frame_Shift_Del_p.KS800fs			Q9NYT6	ZN226_HUMAN	zinc finger protein 226	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)						Prostate(69;0.0352)|all_neural(266;0.202)				ACAGGAAAAAAAATCTATAAAATG	0.382																																					p.799_800del	Pancreas(115;581 1665 13228 19278 50070)	Atlas-Indel,Pindel	.											ZNF234_ENST00000454662,colon,carcinoma,0,1	.	.	.	0			c.2397_2400del						PASS	.																																			SO:0001589	frameshift_variant	7769	exon6			.	AF024707	CCDS46102.1, CCDS46103.1	19q13.31	2013-01-08	2012-09-11	2012-09-11	ENSG00000167380	ENSG00000167380		"Zinc fingers, C2H2-type", "-"	13019	protein-coding gene	gene with protein product							Standard	NM_001146220		Approved		uc002oyp.3	Q9NYT6		ENST00000590089.1:c.2398_2401delAAAT	chr19.hg19:g.44681813_44681816delAAAT	ENSP00000465121:p.Lys800fs	85.0	0.0	0		77.0	13.0	0.168831	NM_001032372	Q8WWE6|Q96TE6|Q9NS44	Frame_Shift_Del	DEL	ENST00000590089.1	hg19	CCDS46102.1																																																																																			.	.	.	none		0.382	ZNF226-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460712.1			-	44681816	AAAT	-	44681813	7	5	207	1	0	1	0	1	0	0	0	0	17792	15	1	0	2466	0	ZNF226	19	44681813	Frame_Shift_Del	DEL	AAAT	TCGA-IA-A83V-01A-11D-A34Z-10	4092715	44681813	14447170	48	12606											
RUNX1	861	hgsc.bcm.edu	37	chr21	36206708	36206708	+	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	ggctccatctggtacttaccCtgcatctgactctgaggctg	6	12	10	13	0	3	2	0	2	3	0	4	2	4	2	2	3	3	4	2	3	2	2			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr21:36206708C>T	ENST00000344691.4	-	4	2300	c.723G>A	c.(721-723)caG>caA	p.Q241Q	RUNX1_ENST00000437180.1_Splice_Site_p.Q268Q|RUNX1_ENST00000399240.1_Intron|RUNX1_ENST00000358356.5_Splice_Site_p.Q241Q|RUNX1_ENST00000325074.5_Splice_Site_p.Q256Q|RUNX1_ENST00000300305.3_Splice_Site_p.Q268Q	NM_001001890.2	NP_001001890.1	Q01196	RUNX1_HUMAN	runt-related transcription factor 1	241	Pro/Ser/Thr-rich.	Breakpoint for translocation to form AML1-EAP in T-MDS and CML and to form type II MACROD1-RUNX1 fusion protein.			behavioral response to pain (GO:0048266)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system development (GO:0007417)|definitive hemopoiesis (GO:0060216)|embryonic hemopoiesis (GO:0035162)|hair follicle morphogenesis (GO:0031069)|hematopoietic stem cell proliferation (GO:0071425)|hemopoiesis (GO:0030097)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|myeloid cell differentiation (GO:0030099)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of granulocyte differentiation (GO:0030853)|peripheral nervous system neuron development (GO:0048935)|positive regulation of angiogenesis (GO:0045766)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of progesterone secretion (GO:2000872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hair follicle cell proliferation (GO:0071336)|regulation of signal transduction (GO:0009966)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(5)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(428)|large_intestine(3)|lung(6)|oesophagus(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	452						GGTACTTACCCTGCATCTGAC	0.637			T	"RPL22, MDS1, EVI1, CBFA2T3, CBFA2T1, ETV6, LAF4"	"AML, preB- ALL, T-ALL"																																p.Q268Q		Atlas-SNP	.		Dom	yes		21	21q22.3	861	runt-related transcription factor 1  (AML1)		L	.	RUNX1	687	.	0			c.G804A						PASS	.						93	90	91					21																	36206708		2203	4300	6503	SO:0001630	splice_region_variant	861	exon7			CTTACCCTGCATC	X79549	CCDS13639.1, CCDS42922.1, CCDS46646.1	21q22.3	2014-09-17	2008-07-29		ENSG00000159216	ENSG00000159216			10471	protein-coding gene	gene with protein product	"aml1 oncogene"	151385	"acute myeloid leukemia 1"	AML1, CBFA2		1427868, 7835892	Standard	NM_001001890		Approved	PEBP2A2, AMLCR1	uc010gmv.3	Q01196	OTTHUMG00000086299	ENST00000344691.4:c.724+1G>A	chr21.hg19:g.36206708C>T		42.0	0.0	.		33.0	7.0	.	NM_001754	A8MV94|B2RMS4|D3DSG1|O60472|O60473|O76047|O76089|Q13081|Q13755|Q13756|Q13757|Q13758|Q13759|Q15341|Q15343|Q16122|Q16284|Q16285|Q16286|Q16346|Q16347|Q92479	Silent	SNP	ENST00000344691.4	hg19	CCDS42922.1																																																																																			.	.	.	none		0.637	RUNX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000194230.1		Silent	T	36206708	C	T	36206708	5	4	207	1	0	0	0	0	0	0	1	0	13759	695	24	2	683	2	RUNX1	21	36206708	Splice_Site	SNP	C	TCGA-IA-A83V-01A-11D-A34Z-10		36206708	11923187	49	12607											
SEPT5	5413	hgsc.bcm.edu	37	chr22	19709805	19709805	+	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	gagagccccatcccgatcctGccgctgcccaccccggacgc	6	4	10	21	4	0	1	0	0	0	1	2	4	2	2	8	1	3	1	8	1	0	0			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chr22:19709805G>A	ENST00000455784.2	+	11	1121	c.996G>A	c.(994-996)ctG>ctA	p.L332L	SEPT5_ENST00000383045.3_Silent_p.L341L|GP1BB_ENST00000366425.3_5'Flank|SEPT5_ENST00000406395.1_Missense_Mutation_p.A329T|SEPT5_ENST00000438754.2_Missense_Mutation_p.A338T	NM_002688.5	NP_002679.2	Q99719	SEPT5_HUMAN	septin 5	332					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)					TCCCGATCCTGCCGCTGCCCA	0.711																																					p.A338T		Atlas-SNP	.											.	SEPT5	32	.	0			c.G1012A						PASS	.						14	19	18					22																	19709805		2175	4265	6440	SO:0001819	synonymous_variant	5413	exon10			GATCCTGCCGCTG	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.996G>A	chr22.hg19:g.19709805G>A		115.0	0.0	.		81.0	24.0	.	NM_001009939	O15251|Q96MY5	Missense_Mutation	SNP	ENST00000455784.2	hg19	CCDS13764.1	.	.	.	.	.	.	.	.	.	.	G	15.01	2.705363	0.48412	.	.	ENSG00000184702	ENST00000406395;ENST00000438754	T;T	0.55052	0.54;0.54	3.79	-0.381	0.12485	.	.	.	.	.	T	0.47451	0.1446	.	.	.	0.22226	N	0.999276	.	.	.	.	.	.	T	0.47328	-0.9126	6	0.87932	D	0	.	5.5224	0.16939	0.2298:0.1586:0.6116:0.0	.	.	.	.	T	329;338	ENSP00000384535:A329T;ENSP00000394541:A338T	ENSP00000384535:A329T	A	+	1	0	SEPT5	18089805	1.000000	0.71417	0.996000	0.52242	0.955000	0.61496	2.131000	0.42074	-0.176000	0.10707	0.297000	0.19635	GCC	.	.	.	none		0.711	SEPT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317937.1	NM_002688		A	19709805	G	A	19709805	2	1	207	1	0	0	0	0	0	0	0	1	14080	1306	46	2		2	SEPT5	22	19709805	Silent	SNP	G	TCGA-IA-A83V-01A-11D-A34Z-10		19709805	31594761	50	12608											
FAM48B1	100130302	hgsc.bcm.edu	37	chrX	24381466	24381466	+	IGR	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	aggaagacaagcttcagcttGagagccagctgatcttagcg	12	8	12	9	1	2	3	1	2	1	2	2	5	2	4	1	1	5	3	1	1	3	3			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chrX:24381466G>C								AC004552.1 (14443 upstream) : PDK3 (101871 downstream)																							GCTTCAGCTTGAGAGCCAGCT	0.478																																					p.E197Q		Atlas-SNP	.											.	.	.	.	0			c.G589C						PASS	.						149	126	133					X																	24381466		1568	3582	5150	SO:0001628	intergenic_variant	100130302	exon1			CAGCTTGAGAGCC																													chrX.hg19:g.24381466G>C		272.0	1.0	.		239.0	120.0	.	NM_001136234		Missense_Mutation	SNP		hg19																																																																																				.	.	.	none	0	0.478									C	24381466	G	C	24381466	1	2	207	0	1	0	0	0	0	0	0	0	5580	1291	45	4		4	FAM48B1	23	24381466	IGR	SNP	G	TCGA-IA-A83V-01A-11D-A34Z-10		24381466	130889094	51	12609											
BRCC3	79184	hgsc.bcm.edu	37	chrX	154299852	154299852	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcggttcatctcgagtctgAcgctttcctcgtttgtctca	4	15	10	12	4	4	1	2	1	3	0	8	2	5	1	1	2	0	3	1	2	0	3			TCGA-IA-A83V-01A-11D-A34Z-10	TCGA-IA-A83V-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3f9166f6-9ec6-4026-b8b0-23be6e2c7cdd	d632f44e-8673-43b1-9b56-519cdbbd3008	g.chrX:154299852A>G	ENST00000369462.1	+	1	75	c.50A>G	c.(49-51)gAc>gGc	p.D17G	BRCC3_ENST00000399042.1_Missense_Mutation_p.D17G|CMC4_ENST00000369484.3_5'Flank|MTCP1_ENST00000369476.3_5'Flank|MTCP1_ENST00000362018.2_Intron|BRCC3_ENST00000369459.2_Missense_Mutation_p.D17G|BRCC3_ENST00000330045.7_Missense_Mutation_p.D17G|BRCC3_ENST00000340647.4_Missense_Mutation_p.D17G|MTCP1_ENST00000482244.1_5'Flank	NM_024332.3	NP_077308.1	P46736	BRCC3_HUMAN	BRCA1/BRCA2-containing complex, subunit 3	17	MPN.				double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|positive regulation of DNA repair (GO:0045739)|protein K63-linked deubiquitination (GO:0070536)|regulation of catalytic activity (GO:0050790)|response to ionizing radiation (GO:0010212)|response to X-ray (GO:0010165)	BRCA1-A complex (GO:0070531)|BRISC complex (GO:0070552)|nuclear ubiquitin ligase complex (GO:0000152)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	enzyme regulator activity (GO:0030234)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|polyubiquitin binding (GO:0031593)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|pancreas(1)|skin(1)	22	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CTCGAGTCTGACGCTTTCCTC	0.597																																					p.D17G		Atlas-SNP	.											.	BRCC3	44	.	0			c.A50G						PASS	.						50	68	62					X																	154299852		2130	4207	6337	SO:0001583	missense	79184	exon1			AGTCTGACGCTTT	X64643	CCDS56610.1, CCDS56611.1, CCDS56612.1	Xq28	2013-05-29	2005-11-21	2005-11-21	ENSG00000185515	ENSG00000185515			24185	protein-coding gene	gene with protein product	"Lys-63-specific deubiquitinase"	300617	"chromosome X open reading frame 53"	CXorf53		1303175, 14636569	Standard	NM_024332		Approved	C6.1A, BRCC36	uc004fna.3	P46736	OTTHUMG00000022658	ENST00000369462.1:c.50A>G	chrX.hg19:g.154299852A>G	ENSP00000358474:p.Asp17Gly	57.0	0.0	.		43.0	25.0	.	NM_024332	A6QRF8|A6QRF9|A8MUX5|A8MWH0|A9Z1Y0|A9Z1Y5|B1B062|B4DQN7|Q16107|Q53YX5|Q9BTZ6	Missense_Mutation	SNP	ENST00000369462.1	hg19	CCDS56611.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.334459	0.81801	.	.	ENSG00000185515	ENST00000340647;ENST00000330045;ENST00000369459;ENST00000369462;ENST00000411985;ENST00000399042;ENST00000457026	T;T;T;T;T;T	0.64085	-0.08;0.4;0.4;0.4;0.4;0.4	3.96	3.96	0.45880	.	0.000000	0.85682	D	0.000000	T	0.74329	0.3702	M	0.80616	2.505	0.80722	D	1	D;D;D	0.63046	0.992;0.992;0.991	P;P;P	0.61592	0.891;0.891;0.881	T	0.76255	-0.3026	10	0.56958	D	0.05	-11.2441	8.8139	0.34985	1.0:0.0:0.0:0.0	.	17;17;17	P46736-3;P46736-2;P46736	.;.;BRCC3_HUMAN	G	17	ENSP00000344103:D17G;ENSP00000328641:D17G;ENSP00000358471:D17G;ENSP00000358474:D17G;ENSP00000413170:D17G;ENSP00000381998:D17G	ENSP00000328641:D17G	D	+	2	0	BRCC3	153953046	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	8.070000	0.89493	1.531000	0.49152	0.417000	0.27973	GAC	.	.	.	none		0.597	BRCC3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058788.4	NM_024332		G	154299852	A	G	154299852	3	3	207	1	0	0	0	0	1	0	0	0	1502	275	10	3	52	3	BRCC3	23	154299852	Missense_Mutation	SNP	A	TCGA-IA-A83V-01A-11D-A34Z-10	129918386	154299852	970708	52	12610											
VPS13D	55187	hgsc.bcm.edu	37	chr1	12567023	12567023	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cattttcctagaagtcaaatAcgatgacctctaccactgcc	12	11	5	13	1	2	2	1	1	1	1	3	3	3	2	4	0	3	0	4	0	5	5			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr1:12567023A>G	ENST00000358136.3	+	69	13041	c.12911A>G	c.(12910-12912)tAc>tGc	p.Y4304C	VPS13D_ENST00000543766.1_Missense_Mutation_p.Y302C|VPS13D_ENST00000356315.4_Missense_Mutation_p.Y4279C|VPS13D_ENST00000471923.1_5'UTR|VPS13D_ENST00000496628.1_3'UTR|VPS13D_ENST00000543710.1_Missense_Mutation_p.Y108C|SNORA59A_ENST00000459326.1_RNA	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)		GAAGTCAAATACGATGACCTC	0.498																																					p.Y4304C		Atlas-SNP	.											.	VPS13D	316	.	0			c.A12911G						PASS	.						135	127	129					1																	12567023		2203	4300	6503	SO:0001583	missense	55187	exon69			TCAAATACGATGA	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.12911A>G	chr1.hg19:g.12567023A>G	ENSP00000350854:p.Tyr4304Cys	70.0	0.0	.		85.0	18.0	.	NM_015378		Missense_Mutation	SNP	ENST00000358136.3	hg19	CCDS30588.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.479843|4.479843	0.84747|0.84747	.|.	.|.	ENSG00000048707|ENSG00000048707	ENST00000011700|ENST00000356315;ENST00000358136;ENST00000543766;ENST00000543710	.|T;T;T	.|0.77750	.|0.54;0.53;-1.12	5.88|5.88	5.88|5.88	0.94601|0.94601	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.85106|0.85106	0.5621|0.5621	L|L	0.50333|0.50333	1.59|1.59	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;0.999;0.998	.|D;D;D	.|0.74348	.|0.976;0.983;0.962	D|D	0.86187|0.86187	0.1610|0.1610	5|10	.|0.66056	.|D	.|0.02	.|.	16.2879|16.2879	0.82732|0.82732	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|302;4279;4303	.|F5GX56;Q5THJ4-2;Q5THJ4	.|.;.;VP13D_HUMAN	A|C	3126|4279;4304;302;108	.|ENSP00000348666:Y4279C;ENSP00000350854:Y4304C;ENSP00000441122:Y302C	.|ENSP00000348666:Y4279C	T|Y	+|+	1|2	0|0	VPS13D|VPS13D	12489610|12489610	1.000000|1.000000	0.71417|0.71417	0.754000|0.754000	0.31244|0.31244	0.978000|0.978000	0.69477|0.69477	8.882000|8.882000	0.92420|0.92420	2.242000|2.242000	0.73789|0.73789	0.533000|0.533000	0.62120|0.62120	ACG|TAC	.	.	.	none		0.498	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		G	12567023	A	G	12567023	3	3	208	1	0	0	0	0	1	0	0	0	17204	391	14	3	13181	3	VPS13D	1	12567023	Missense_Mutation	SNP	A	TCGA-IA-A83W-01A-11D-A34Z-10		12567023	236683598	1	12611											
COL11A1	1301	hgsc.bcm.edu	37	chr1	103471851	103471851	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcccgttggaccagggggAccctggacgcctcgagggcc	5	7	15	14	3	0	0	0	0	0	0	2	4	1	3	5	5	0	1	5	5	0	2			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr1:103471851A>G	ENST00000370096.3	-	16	2016	c.1704T>C	c.(1702-1704)ggT>ggC	p.G568G	COL11A1_ENST00000461720.1_5'UTR|COL11A1_ENST00000512756.1_Silent_p.G452G|COL11A1_ENST00000353414.4_Silent_p.G529G|COL11A1_ENST00000358392.2_Silent_p.G580G	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	568	Collagen-like 2.|Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		GACCAGGGGGACCCTGGACGC	0.378																																					p.G580G		Atlas-SNP	.											.	COL11A1	972	.	0			c.T1740C						PASS	.						47	54	52					1																	103471851		2203	4300	6503	SO:0001819	synonymous_variant	1301	exon16			AGGGGGACCCTGG	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.1704T>C	chr1.hg19:g.103471851A>G		163.0	0.0	.		174.0	7.0	.	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Silent	SNP	ENST00000370096.3	hg19	CCDS778.1																																																																																			.	.	.	none		0.378	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		G	103471851	A	G	103471851	2	3	208	1	0	0	0	0	0	0	0	1	3669	262	10	3		3	COL11A1	1	103471851	Silent	SNP	A	TCGA-IA-A83W-01A-11D-A34Z-10	90904828	103471851	145778770	2	12612											
GABPB2	126626	hgsc.bcm.edu	37	chr1	151079554	151079554	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggaaattccgttgactcaTcaatccagcaagtaatgggg	14	9	10	8	1	2	1	2	1	0	0	4	2	4	2	2	3	1	3	2	3	5	3			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr1:151079554T>C	ENST00000368918.3	+	7	1109	c.778T>C	c.(778-780)Tca>Cca	p.S260P	GABPB2_ENST00000368916.1_Missense_Mutation_p.S222P|GABPB2_ENST00000467551.1_3'UTR|GABPB2_ENST00000368917.1_Missense_Mutation_p.S222P	NM_144618.2	NP_653219.1	Q8TAK5	GABP2_HUMAN	GA binding protein transcription factor, beta subunit 2	260					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(3)|liver(2)|lung(7)	15				all cancers(107;7.17e-05)|GBM - Glioblastoma multiforme(94;0.000662)		CGTTGACTCATCAATCCAGCA	0.408																																					p.S260P		Atlas-SNP	.											.	GABPB2	41	.	0			c.T778C						PASS	.						74	74	74					1																	151079554		2203	4300	6503	SO:0001583	missense	126626	exon7			GACTCATCAATCC		CCDS983.1	1q21.2	2013-01-10			ENSG00000143458	ENSG00000143458		"Ankyrin repeat domain containing"	28441	protein-coding gene	gene with protein product						7958862	Standard	NM_144618		Approved	MGC29891	uc001ewr.2	Q8TAK5	OTTHUMG00000012193	ENST00000368918.3:c.778T>C	chr1.hg19:g.151079554T>C	ENSP00000357914:p.Ser260Pro	43.0	0.0	.		50.0	12.0	.	NM_144618	B1AVJ8|D3DV14|Q8NAR5	Missense_Mutation	SNP	ENST00000368918.3	hg19	CCDS983.1	.	.	.	.	.	.	.	.	.	.	T	18.66	3.671611	0.67928	.	.	ENSG00000143458	ENST00000368918;ENST00000368917;ENST00000368916	T;T;T	0.60548	0.18;0.24;0.24	5.41	4.27	0.50696	.	0.422547	0.26026	N	0.026794	T	0.37652	0.1011	L	0.50333	1.59	0.38047	D	0.935656	P;P;P	0.45715	0.534;0.865;0.668	B;B;B	0.43478	0.092;0.421;0.28	T	0.23833	-1.0177	10	0.28530	T	0.3	-6.6402	9.4384	0.38653	0.0:0.0:0.2761:0.7239	.	222;260;260	Q5SZG2;B2R924;Q8TAK5	.;.;GABP2_HUMAN	P	260;222;222	ENSP00000357914:S260P;ENSP00000357913:S222P;ENSP00000357912:S222P	ENSP00000357912:S222P	S	+	1	0	GABPB2	149346178	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	3.278000	0.51662	2.269000	0.75478	0.455000	0.32223	TCA	.	.	.	none		0.408	GABPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033700.2	NM_144618		C	151079554	T	C	151079554	3	2	208	1	0	0	0	0	1	0	0	0	6166	1435	50	3	800	3	GABPB2	1	151079554	Missense_Mutation	SNP	T	TCGA-IA-A83W-01A-11D-A34Z-10	47607703	151079554	98171067	3	12613											
BIRC6	57448	hgsc.bcm.edu	37	chr2	32754825	32754825	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctgactgttaaattgggaTcaagagttataacagacccc	14	11	8	8	0	2	3	1	1	1	2	2	4	2	4	2	1	1	2	2	1	5	4			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr2:32754825T>C	ENST00000421745.2	+	60	12162	c.12028T>C	c.(12028-12030)Tca>Cca	p.S4010P	MIR558_ENST00000384920.1_RNA	NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	4010					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)					TAAATTGGGATCAAGAGTTAT	0.373																																					p.S4010P	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.T12028C						PASS	.						81	78	79					2																	32754825		2203	4300	6503	SO:0001583	missense	57448	exon60			TTGGGATCAAGAG	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.12028T>C	chr2.hg19:g.32754825T>C	ENSP00000393596:p.Ser4010Pro	87.0	0.0	.		80.0	36.0	.	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	T	24.7	4.557828	0.86231	.	.	ENSG00000115760	ENST00000421745	T	0.79940	-1.32	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	T	0.81498	0.4835	N	0.19112	0.55	0.80722	D	1	D	0.54601	0.967	D	0.63033	0.91	D	0.84394	0.0556	10	0.66056	D	0.02	.	15.073	0.72053	0.0:0.0:0.0:1.0	.	4010	Q9NR09	BIRC6_HUMAN	P	4010	ENSP00000393596:S4010P	ENSP00000393596:S4010P	S	+	1	0	BIRC6	32608329	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.608000	0.82898	1.975000	0.57531	0.477000	0.44152	TCA	.	.	.	none		0.373	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		C	32754825	T	C	32754825	3	2	208	1	0	0	0	0	1	0	0	0	1438	1435	50	3	12266	3	BIRC6	2	32754825	Missense_Mutation	SNP	T	TCGA-IA-A83W-01A-11D-A34Z-10		32754825	210444548	4	12614											
ORC2L	4999	hgsc.bcm.edu	37	chr2	201814321	201814321	+	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	gttttctattctgaaaagaaTaaactttatttccaccacct	13	16	3	9	0	2	2	0	1	2	1	3	2	3	2	3	0	1	1	3	0	7	8			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr2:201814321T>A	ENST00000234296.2	-	5	533	c.284A>T	c.(283-285)tAt>tTt	p.Y95F	ORC2_ENST00000467605.1_5'UTR	NM_006190.4	NP_006181.1	Q13416	ORC2_HUMAN	origin recognition complex, subunit 2	95					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	condensed chromosome inner kinetochore (GO:0000939)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)|plasma membrane (GO:0005886)	DNA replication origin binding (GO:0003688)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	20						CTGAAAAGAATAAACTTTATT	0.284																																					p.Y95F		Atlas-SNP	.											.	ORC2	48	.	0			c.A284T						PASS	.						52	51	51					2																	201814321		2202	4290	6492	SO:0001583	missense	4999	exon5			AAAGAATAAACTT		CCDS2334.1	2q33	2010-10-12	2010-10-12	2010-10-12	ENSG00000115942	ENSG00000115942			8488	protein-coding gene	gene with protein product		601182	"origin recognition complex, subunit 2 (yeast homolog)-like", "origin recognition complex, subunit 2-like (yeast)", "origin recognition complex, subunit 2 homolog (yeast)"	ORC2L		8808289	Standard	NM_006190		Approved		uc002uwr.3	Q13416	OTTHUMG00000132783	ENST00000234296.2:c.284A>T	chr2.hg19:g.201814321T>A	ENSP00000234296:p.Tyr95Phe	200.0	0.0	.		181.0	64.0	.	NM_006190	Q13204|Q53TX5	Missense_Mutation	SNP	ENST00000234296.2	hg19	CCDS2334.1	.	.	.	.	.	.	.	.	.	.	T	13.28	2.190690	0.38707	.	.	ENSG00000115942	ENST00000234296;ENST00000410039	T;T	0.47177	1.38;0.85	5.71	4.54	0.55810	.	0.062023	0.64402	D	0.000002	T	0.31420	0.0796	L	0.35723	1.085	0.38691	D	0.952751	B;B	0.16802	0.019;0.015	B;B	0.17098	0.017;0.01	T	0.15665	-1.0429	10	0.02654	T	1	-8.9205	9.1288	0.36833	0.1624:0.0:0.0:0.8376	.	95;95	B4DYU9;Q13416	.;ORC2_HUMAN	F	95	ENSP00000234296:Y95F;ENSP00000386390:Y95F	ENSP00000234296:Y95F	Y	-	2	0	ORC2	201522566	1.000000	0.71417	0.996000	0.52242	0.952000	0.60782	4.333000	0.59285	0.966000	0.38159	0.477000	0.44152	TAT	.	.	.	none		0.284	ORC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256191.2	NM_006190		A	201814321	T	A	201814321	3	1	208	1	0	0	0	0	1	0	0	0	11269	1406	49	5	1505	5	ORC2L	2	201814321	Missense_Mutation	SNP	T	TCGA-IA-A83W-01A-11D-A34Z-10	169059496	201814321	41385052	5	12615											
IGFBP2	3485	hgsc.bcm.edu	37	chr2	217528687	217528687	+	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	agatgtctctgaacgggcagCgtggggagtgctggtgtgtg	6	10	19	6	2	1	2	0	1	1	1	2	3	1	3	0	4	3	2	0	4	1	0			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr2:217528687C>T	ENST00000233809.4	+	4	967	c.838C>T	c.(838-840)Cgt>Tgt	p.R280C	IGFBP2_ENST00000456764.1_Missense_Mutation_p.R136C	NM_000597.2	NP_000588	P18065	IBP2_HUMAN	insulin-like growth factor binding protein 2, 36kDa	280	Thyroglobulin type-1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				aging (GO:0007568)|cellular protein metabolic process (GO:0044267)|cellular response to hormone stimulus (GO:0032870)|female pregnancy (GO:0007565)|positive regulation of activated T cell proliferation (GO:0042104)|regulation of cell growth (GO:0001558)|regulation of insulin-like growth factor receptor signaling pathway (GO:0043567)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)	apical plasma membrane (GO:0016324)|cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)			endometrium(2)|large_intestine(1)|lung(2)	5		Renal(323;0.0458)		Epithelial(149;2.9e-06)|all cancers(144;0.000223)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00968)		GAACGGGCAGCGTGGGGAGTG	0.612																																					p.R280C		Atlas-SNP	.											IGFBP2,NS,carcinoma,0,1	IGFBP2	25	.	0			c.C838T						PASS	.						36	44	41					2																	217528687		2054	4192	6246	SO:0001583	missense	3485	exon4			GGGCAGCGTGGGG		CCDS42815.1	2q35	2014-09-16	2002-08-29		ENSG00000115457	ENSG00000115457			5471	protein-coding gene	gene with protein product		146731	"insulin-like growth factor binding protein 2 (36kD)"	IBP2		1697583	Standard	NM_000597		Approved		uc021vwn.1	P18065	OTTHUMG00000155341	ENST00000233809.4:c.838C>T	chr2.hg19:g.217528687C>T	ENSP00000233809:p.Arg280Cys	138.0	0.0	.		118.0	35.0	.	NM_000597	Q14619|Q9UCL3	Missense_Mutation	SNP	ENST00000233809.4	hg19	CCDS42815.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.029265	0.75504	.	.	ENSG00000115457	ENST00000233809;ENST00000456764	T;T	0.65916	-0.18;-0.18	4.78	4.78	0.61160	Thyroglobulin type-1 (6);	0.000000	0.85682	D	0.000000	D	0.83936	0.5362	M	0.92219	3.285	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87978	0.2741	10	0.87932	D	0	-0.1858	17.3391	0.87291	0.0:1.0:0.0:0.0	.	280	P18065	IBP2_HUMAN	C	280;136	ENSP00000233809:R280C;ENSP00000389646:R136C	ENSP00000233809:R280C	R	+	1	0	IGFBP2	217236932	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.656000	0.46716	2.626000	0.88956	0.561000	0.74099	CGT	.	.	.	none		0.612	IGFBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339540.1	NM_000597		T	217528687	C	T	217528687	3	4	208	1	0	0	0	0	1	0	0	0	7586	768	27	1	852	1	IGFBP2	2	217528687	Missense_Mutation	SNP	C	TCGA-IA-A83W-01A-11D-A34Z-10	15714366	217528687	25670686	6	12616											
STK11IP	114790	hgsc.bcm.edu	37	chr2	220477901	220477901	+	Missense_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	agttcatgtgccttgtggttGtgtctgaccgcaggctgtac	5	14	13	9	1	2	1	1	1	1	0	2	1	2	1	2	2	2	5	2	2	1	4			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr2:220477901G>A	ENST00000456909.1	+	20	2581	c.2491G>A	c.(2491-2493)Gtg>Atg	p.V831M	STK11IP_ENST00000295641.10_Missense_Mutation_p.V842M			Q8N1F8	S11IP_HUMAN	serine/threonine kinase 11 interacting protein	842					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)		CCTTGTGGTTGTGTCTGACCG	0.597																																					p.V842M		Atlas-SNP	.											.	STK11IP	152	.	0			c.G2524A						PASS	.						82	87	85					2																	220477901		2038	4189	6227	SO:0001583	missense	114790	exon20			GTGGTTGTGTCTG	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.2491G>A	chr2.hg19:g.220477901G>A	ENSP00000389383:p.Val831Met	58.0	0.0	.		52.0	24.0	.	NM_052902	Q8NAW9|Q8WXE4|Q96CN3|Q96PY9	Missense_Mutation	SNP	ENST00000456909.1	hg19		.	.	.	.	.	.	.	.	.	.	g	8.720	0.914062	0.17907	.	.	ENSG00000144589	ENST00000456909;ENST00000295641	T;T	0.07908	3.15;3.15	4.46	1.67	0.24075	.	0.145417	0.45126	D	0.000383	T	0.08714	0.0216	M	0.64997	1.995	0.28916	N	0.892419	B	0.21905	0.062	B	0.24848	0.056	T	0.18967	-1.0320	10	0.72032	D	0.01	-6.4198	2.8496	0.05553	0.1011:0.1965:0.5231:0.1793	.	842	Q8N1F8	S11IP_HUMAN	M	831;842	ENSP00000389383:V831M;ENSP00000295641:V842M	ENSP00000295641:V842M	V	+	1	0	STK11IP	220186145	0.885000	0.30320	0.682000	0.30024	0.431000	0.31685	1.140000	0.31516	0.160000	0.19432	-0.509000	0.04479	GTG	.	.	.	none		0.597	STK11IP-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000131432.1	NM_052902		A	220477901	G	A	220477901	3	1	208	1	0	0	0	0	1	0	0	0	15300	1377	48	2	2602	2	STK11IP	2	220477901	Missense_Mutation	SNP	G	TCGA-IA-A83W-01A-11D-A34Z-10	2949214	220477901	22721472	7	12617											
BHLHE40	8553	hgsc.bcm.edu	37	chr3	5025187	5025187	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtatcccacctcagtgccagTgctatacccaggcctcaacg	9	8	8	16	1	2	0	2	0	0	0	3	0	3	0	5	1	4	2	5	1	4	3			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr3:5025187T>C	ENST00000256495.3	+	5	1652	c.1049T>C	c.(1048-1050)gTg>gCg	p.V350A		NM_003670.2	NP_003661.1	O14503	BHE40_HUMAN	basic helix-loop-helix family, member e40	350					circadian regulation of gene expression (GO:0032922)|entrainment of circadian clock by photoperiod (GO:0043153)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|MRF binding (GO:0043426)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(2)	12						TCAGTGCCAGTGCTATACCCA	0.592																																					p.V350A		Atlas-SNP	.											.	BHLHE40	35	.	0			c.T1049C						PASS	.						169	143	152					3																	5025187		2203	4300	6503	SO:0001583	missense	8553	exon5			TGCCAGTGCTATA	AB004066	CCDS2565.1	3p26	2009-01-12	2009-01-12	2009-01-12	ENSG00000134107	ENSG00000134107		"Basic helix-loop-helix proteins"	1046	protein-coding gene	gene with protein product	"differentially expressed in chondrocytes 1", " differentiated embryo chondrocyte expressed gene 1"	604256	"basic helix-loop-helix domain containing, class B, 2"	STRA13, BHLHB2		9240428, 10449910, 18557763	Standard	NM_003670		Approved	DEC1, bHLHe40	uc003bqf.3	O14503	OTTHUMG00000119035	ENST00000256495.3:c.1049T>C	chr3.hg19:g.5025187T>C	ENSP00000256495:p.Val350Ala	65.0	0.0	.		66.0	32.0	.	NM_003670	Q96TD3	Missense_Mutation	SNP	ENST00000256495.3	hg19	CCDS2565.1	.	.	.	.	.	.	.	.	.	.	T	12.84	2.057339	0.36277	.	.	ENSG00000134107	ENST00000256495	T	0.79749	-1.3	5.51	5.51	0.81932	.	0.385391	0.23815	N	0.044282	T	0.79633	0.4479	M	0.61703	1.905	0.18873	N	0.999988	B	0.12013	0.005	B	0.17098	0.017	T	0.71810	-0.4480	10	0.62326	D	0.03	.	15.6247	0.76845	0.0:0.0:0.0:1.0	.	350	O14503	BHE40_HUMAN	A	350	ENSP00000256495:V350A	ENSP00000256495:V350A	V	+	2	0	BHLHE40	5000187	0.997000	0.39634	0.027000	0.17364	0.972000	0.66771	6.116000	0.71571	2.093000	0.63338	0.533000	0.62120	GTG	.	.	.	none		0.592	BHLHE40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239244.2	NM_003670		C	5025187	T	C	5025187	3	2	208	1	0	0	0	0	1	0	0	0	1423	1696	59	3	1067	3	BHLHE40	3	5025187	Missense_Mutation	SNP	T	TCGA-IA-A83W-01A-11D-A34Z-10		5025187	192997243	8	12618											
SLC4A7	9497	hgsc.bcm.edu	37	chr3	27442329	27442329	+	Missense_Mutation	SNP	T	T	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	ccattgtgctagagtttcatTgctggggtttggaggttcag	6	15	14	6	0	2	1	2	0	0	1	2	2	2	2	1	4	2	5	1	4	1	6			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr3:27442329T>G	ENST00000295736.5	-	16	2396	c.2326A>C	c.(2326-2328)Aat>Cat	p.N776H	SLC4A7_ENST00000455077.1_Missense_Mutation_p.N657H|SLC4A7_ENST00000446700.1_Missense_Mutation_p.N768H|SLC4A7_ENST00000454389.1_Missense_Mutation_p.N785H|SLC4A7_ENST00000428386.1_Missense_Mutation_p.N652H|SLC4A7_ENST00000437179.1_Missense_Mutation_p.N657H|SLC4A7_ENST00000435667.2_Missense_Mutation_p.N661H|SLC4A7_ENST00000388777.4_Missense_Mutation_p.N326H|SLC4A7_ENST00000440156.1_Missense_Mutation_p.N772H|SLC4A7_ENST00000425128.2_3'UTR|SLC4A7_ENST00000445684.1_Missense_Mutation_p.N772H	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	776					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)	AGAGTTTCATTGCTGGGGTTT	0.323																																					p.N776H		Atlas-SNP	.											.	SLC4A7	119	.	0			c.A2326C						PASS	.						155	152	153					3																	27442329		2203	4298	6501	SO:0001583	missense	9497	exon16			TTTCATTGCTGGG	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.2326A>C	chr3.hg19:g.27442329T>G	ENSP00000295736:p.Asn776His	100.0	0.0	.		121.0	51.0	.	NM_003615	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Missense_Mutation	SNP	ENST00000295736.5	hg19	CCDS33721.1	.	.	.	.	.	.	.	.	.	.	T	15.43	2.831012	0.50845	.	.	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	0.79454	-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27	5.42	4.24	0.50183	Bicarbonate transporter, C-terminal (1);	0.215214	0.47455	D	0.000230	D	0.87497	0.6192	M	0.82323	2.585	0.80722	D	1	D;P;P;D;D;P;P;D;D	0.64830	0.992;0.922;0.645;0.961;0.992;0.946;0.904;0.992;0.994	D;P;B;P;D;P;P;D;D	0.75020	0.969;0.906;0.411;0.905;0.985;0.843;0.847;0.969;0.93	D	0.88094	0.2815	10	0.87932	D	0	.	11.6564	0.51320	0.1331:0.0:0.0:0.8669	.	772;657;768;772;785;326;652;776;657	E9PFN4;B5M452;E9PGC1;B5M453;E9PDL9;F8W7E6;Q9Y6M7-2;Q9Y6M7;B2CI53	.;.;.;.;.;.;.;S4A7_HUMAN;.	H	327;776;652;785;772;657;768;657;772;661;326;672	ENSP00000411031:N327H;ENSP00000295736:N776H;ENSP00000416368:N652H;ENSP00000390394:N785H;ENSP00000414797:N772H;ENSP00000394252:N657H;ENSP00000406605:N768H;ENSP00000407382:N657H;ENSP00000406804:N772H;ENSP00000395336:N661H;ENSP00000373429:N326H;ENSP00000388703:N672H	ENSP00000295736:N776H	N	-	1	0	SLC4A7	27417333	1.000000	0.71417	1.000000	0.80357	0.653000	0.38743	6.272000	0.72575	0.876000	0.35872	0.377000	0.23210	AAT	.	.	.	none		0.323	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615		G	27442329	T	G	27442329	3	3	208	1	0	0	0	0	1	0	0	0	14671	1812	63	5	1358	5	SLC4A7	3	27442329	Missense_Mutation	SNP	T	TCGA-IA-A83W-01A-11D-A34Z-10	22417142	27442329	170580101	9	12619											
GOLGA4	2803	hgsc.bcm.edu	37	chr3	37365357	37365357	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaaacattgttgaaagacaaAgagattatcttccaggccca	16	9	8	8	0	1	3	0	1	1	2	2	5	2	3	2	1	1	1	2	1	4	4			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr3:37365357A>G	ENST00000361924.2	+	14	2354	c.1980A>G	c.(1978-1980)aaA>aaG	p.K660K	GOLGA4_ENST00000356847.4_Silent_p.K682K|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	660	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						TGAAAGACAAAGAGATTATCT	0.338																																					p.K682K		Atlas-SNP	.											.	GOLGA4	173	.	0			c.A2046G						PASS	.						45	48	47					3																	37365357		2203	4300	6503	SO:0001819	synonymous_variant	2803	exon15			AGACAAAGAGATT	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.1980A>G	chr3.hg19:g.37365357A>G		125.0	0.0	.		124.0	39.0	.	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Silent	SNP	ENST00000361924.2	hg19	CCDS2666.1																																																																																			.	.	.	none		0.338	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		G	37365357	A	G	37365357	2	3	208	1	0	0	0	0	0	0	0	1	6562	69	3	3		3	GOLGA4	3	37365357	Silent	SNP	A	TCGA-IA-A83W-01A-11D-A34Z-10	9923028	37365357	160657073	10	12620											
PBRM1	55193	hgsc.bcm.edu	37	chr3	52677267	52677267	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aacactctttttctcaccggTaatacttgctagtgggattt	9	16	7	9	1	2	0	1	0	2	0	3	1	2	1	1	2	3	2	1	2	4	7			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr3:52677267T>C	ENST00000296302.7	-	9	993	c.992A>G	c.(991-993)tAc>tGc	p.Y331C	PBRM1_ENST00000410007.1_Missense_Mutation_p.Y331C|PBRM1_ENST00000409057.1_Missense_Mutation_p.Y331C|PBRM1_ENST00000409114.3_Missense_Mutation_p.Y331C|PBRM1_ENST00000337303.4_Missense_Mutation_p.Y331C|PBRM1_ENST00000356770.4_Intron|PBRM1_ENST00000394830.3_Missense_Mutation_p.Y331C|PBRM1_ENST00000409767.1_Missense_Mutation_p.Y331C			Q86U86	PB1_HUMAN	polybromo 1	331					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)		TTCTCACCGGTAATACTTGCT	0.443			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.Y331C		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.A992G						PASS	.						170	161	164					3																	52677267		2203	4300	6503	SO:0001583	missense	55193	exon10			CACCGGTAATACT	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.992A>G	chr3.hg19:g.52677267T>C	ENSP00000296302:p.Tyr331Cys	142.0	0.0	.		163.0	57.0	.	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Missense_Mutation	SNP	ENST00000296302.7	hg19		.	.	.	.	.	.	.	.	.	.	T	11.29	1.595409	0.28445	.	.	ENSG00000163939	ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103	T;T;T;T;T;T;T;T;T	0.34472	1.37;1.41;1.36;1.37;1.36;1.83;1.37;1.37;1.37	5.14	5.14	0.70334	Bromodomain (1);	0.546082	0.18050	N	0.153309	T	0.21103	0.0508	N	0.08118	0	0.27045	N	0.96393	P;B;P;P;P;P;B;P	0.49447	0.456;0.282;0.456;0.456;0.924;0.456;0.0;0.456	B;B;B;B;B;B;B;B	0.43360	0.178;0.163;0.178;0.178;0.417;0.247;0.001;0.115	T	0.03957	-1.0989	10	0.38643	T	0.18	.	9.497	0.38995	0.1569:0.0:0.0:0.8431	.	331;331;331;331;331;331;331;331	Q86U86-9;Q86U86-6;Q86U86-4;Q86U86-2;Q86U86-8;Q86U86-7;Q86U86;Q86U86-5	.;.;.;.;.;.;PB1_HUMAN;.	C	331;331;331;331;331;331;331;331;275	ENSP00000378307:Y331C;ENSP00000296302:Y331C;ENSP00000338302:Y331C;ENSP00000386593:Y331C;ENSP00000386529:Y331C;ENSP00000386643:Y331C;ENSP00000386601:Y331C;ENSP00000387775:Y331C;ENSP00000397662:Y275C	ENSP00000296302:Y331C	Y	-	2	0	PBRM1	52652307	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.279000	0.43435	1.963000	0.57068	0.524000	0.50904	TAC	.	.	.	none		0.443	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		C	52677267	T	C	52677267	3	2	208	1	0	0	0	0	1	0	0	0	11498	1638	57	3	3996	3	PBRM1	3	52677267	Missense_Mutation	SNP	T	TCGA-IA-A83W-01A-11D-A34Z-10	15311910	52677267	145345163	11	12621											
ATP6V1A	523	hgsc.bcm.edu	37	chr3	113505219	113505219	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actggccagagagtccttgaTgccctttttccgtaagtttg	7	14	10	10	1	0	2	0	1	0	1	2	3	2	2	4	1	1	2	4	1	1	5			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr3:113505219T>C	ENST00000273398.3	+	6	813	c.705T>C	c.(703-705)gaT>gaC	p.D235D	ATP6V1A_ENST00000538620.1_Silent_p.D202D	NM_001690.3	NP_001681.2	P38606	VATA_HUMAN	ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A	235					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus (GO:0005902)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	ATP binding (GO:0005524)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Alendronate(DB00630)|Etidronic acid(DB01077)|Tiludronate(DB01133)	GAGTCCTTGATGCCCTTTTTC	0.433																																					p.D235D		Atlas-SNP	.											.	ATP6V1A	71	.	0			c.T705C						PASS	.						222	203	209					3																	113505219		2203	4300	6503	SO:0001819	synonymous_variant	523	exon6			CCTTGATGCCCTT	L09235	CCDS2976.1	3q13.31	2010-04-21	2002-08-29	2003-04-25	ENSG00000114573	ENSG00000114573	3.6.3.14	"ATPases / V-type"	851	protein-coding gene	gene with protein product		607027	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), alpha polypeptide, 70kD, isoform 1"	VPP2, ATP6A1, ATP6V1A1		8463241	Standard	NM_001690		Approved	Vma1, VA68	uc003eao.3	P38606	OTTHUMG00000159295	ENST00000273398.3:c.705T>C	chr3.hg19:g.113505219T>C		94.0	0.0	.		142.0	65.0	.	NM_001690	B2RBR8|B7Z1R5|D3DN75|Q53YD9|Q96DY6|Q9UHY3	Silent	SNP	ENST00000273398.3	hg19	CCDS2976.1																																																																																			.	.	.	none		0.433	ATP6V1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354457.1	NM_001690		C	113505219	T	C	113505219	2	2	208	1	0	0	0	0	0	0	0	1	1177	1461	51	3		3	ATP6V1A	3	113505219	Silent	SNP	T	TCGA-IA-A83W-01A-11D-A34Z-10	60827952	113505219	84517211	12	12622											
MSL2	55167	hgsc.bcm.edu	37	chr3	135870914	135870914	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agctgcggagtacttcctcaAcactcagtaacagagagtct	12	9	9	11	1	3	1	2	0	1	1	4	3	4	2	1	1	5	3	1	1	3	3			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr3:135870914A>G	ENST00000309993.2	-	2	1541	c.809T>C	c.(808-810)gTt>gCt	p.V270A	MSL2_ENST00000434835.2_Missense_Mutation_p.V196A	NM_018133.3	NP_060603.2	Q9HCI7	MSL2_HUMAN	male-specific lethal 2 homolog (Drosophila)	270					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						TACTTCCTCAACACTCAGTAA	0.443																																					p.V270A		Atlas-SNP	.											.	MSL2	63	.	0			c.T809C						PASS	.						62	68	66					3																	135870914		2203	4300	6503	SO:0001583	missense	55167	exon2			TCCTCAACACTCA	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.809T>C	chr3.hg19:g.135870914A>G	ENSP00000311827:p.Val270Ala	51.0	0.0	.		71.0	14.0	.	NM_018133	B4DYL4|G5E9I1|Q0D2P1|Q8NDB4|Q9NVS4	Missense_Mutation	SNP	ENST00000309993.2	hg19	CCDS33861.1	.	.	.	.	.	.	.	.	.	.	A	16.96	3.266033	0.59540	.	.	ENSG00000174579	ENST00000309993;ENST00000434835	.	.	.	6.17	6.17	0.99709	.	0.000000	0.64402	D	0.000001	T	0.59662	0.2210	L	0.34521	1.04	0.58432	D	0.99999	D	0.60160	0.987	P	0.56088	0.791	T	0.53809	-0.8386	9	0.17832	T	0.49	-9.5412	16.0034	0.80327	1.0:0.0:0.0:0.0	.	270	Q9HCI7	MSL2_HUMAN	A	270;196	.	ENSP00000311827:V270A	V	-	2	0	MSL2	137353604	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.389000	0.90172	2.371000	0.80710	0.533000	0.62120	GTT	.	.	.	none		0.443	MSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357347.1	NM_018133		G	135870914	A	G	135870914	3	3	208	1	0	0	0	0	1	0	0	0	9885	43	2	3	928	3	MSL2	3	135870914	Missense_Mutation	SNP	A	TCGA-IA-A83W-01A-11D-A34Z-10	22365695	135870914	62151516	13	12623											
IFT80	57560	hgsc.bcm.edu	37	chr3	160018773	160018773	+	Frame_Shift_Del	DEL	A	A	-																															tccaggaaattttggagatgAaataaagcgcccttcatatg																										TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr3:160018773delA	ENST00000326448.7	-	12	1645	c.1213delT	c.(1213-1215)tcafs	p.S406fs	IFT80_ENST00000496589.1_Frame_Shift_Del_p.S269fs|RP11-432B6.3_ENST00000483754.1_Frame_Shift_Del_p.S577fs|IFT80_ENST00000483465.1_Frame_Shift_Del_p.S269fs	NM_020800.2	NP_065851.1	Q9P2H3	IFT80_HUMAN	intraflagellar transport 80	406					bone morphogenesis (GO:0060349)|chondrocyte differentiation (GO:0002062)|cilium assembly (GO:0042384)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|osteoblast differentiation (GO:0001649)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)				NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(12)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			TTTGGAGATGAAATAAAGCGC	0.318																																					p.S405fs		Atlas-Indel,Pindel	.											.	IFT80	68	.	0			c.1214delC						PASS	.						50	54	53					3																	160018773		2202	4292	6494	SO:0001589	frameshift_variant	57560	exon12			.	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.1213delT	chr3.hg19:g.160018773delA	ENSP00000312778:p.Ser406fs	252.0	0.0	0		325.0	167.0	0.513846	NM_020800	B4E0K1|C9J8I0|Q3MJC4|Q86YF4|Q9UIX1	Frame_Shift_Del	DEL	ENST00000326448.7	hg19	CCDS3188.1																																																																																			.	.	.	none		0.318	IFT80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352651.2	NM_020800		-	160018773	A	-	160018773	7	5	208	1	0	1	0	1	0	0	0	0	7571	246	9	0	1156	0	IFT80	3	160018773	Frame_Shift_Del	DEL	A	TCGA-IA-A83W-01A-11D-A34Z-10	24147859	160018773	38003657	14	12624											
OPA1	4976	hgsc.bcm.edu	37	chr3	193335033	193335033	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcaccagactttgacaagaTtgttgaaagccttagcttat	13	12	8	8	0	0	4	0	2	0	2	0	4	0	4	2	0	3	3	2	0	4	5			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr3:193335033T>C	ENST00000392438.3	+	4	749	c.515T>C	c.(514-516)aTt>aCt	p.I172T	OPA1-AS1_ENST00000444085.1_RNA|OPA1_ENST00000361715.2_Intron|OPA1_ENST00000361150.2_Intron|OPA1_ENST00000361510.2_Missense_Mutation_p.I172T|OPA1-AS1_ENST00000433105.1_RNA|OPA1_ENST00000487986.1_3'UTR|OPA1_ENST00000361828.2_Missense_Mutation_p.I172T|OPA1_ENST00000361908.3_Missense_Mutation_p.I172T	NM_015560.2	NP_056375.2	O60313	OPA1_HUMAN	optic atrophy 1 (autosomal dominant)	172					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)		TTTGACAAGATTGTTGAAAGC	0.333																																					p.I172T		Atlas-SNP	.											.	OPA1	79	.	0			c.T515C						PASS	.						63	67	66					3																	193335033		2202	4296	6498	SO:0001583	missense	4976	exon4			ACAAGATTGTTGA	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.515T>C	chr3.hg19:g.193335033T>C	ENSP00000376233:p.Ile172Thr	266.0	0.0	.		313.0	36.0	.	NM_130836	D3DNW4	Missense_Mutation	SNP	ENST00000392438.3	hg19	CCDS43186.1	.	.	.	.	.	.	.	.	.	.	T	17.09	3.300951	0.60195	.	.	ENSG00000198836	ENST00000361908;ENST00000392438;ENST00000361510;ENST00000361828;ENST00000419435;ENST00000392436	D;D;D;D;T;T	0.94897	-3.25;-3.35;-3.55;-3.15;1.49;-1.36	5.86	5.86	0.93980	.	0.115123	0.64402	D	0.000016	D	0.91250	0.7242	L	0.43152	1.355	0.80722	D	1	B;B;B;B	0.28552	0.079;0.181;0.0;0.215	B;B;B;B	0.26517	0.07;0.068;0.001;0.064	D	0.88625	0.3165	10	0.23302	T	0.38	-14.9597	15.4463	0.75232	0.0:0.0:0.0:1.0	.	172;172;172;172	O60313;E5KLJ6;E5KLJ7;E5KLJ5	OPA1_HUMAN;.;.;.	T	172;172;172;172;48;172	ENSP00000354681:I172T;ENSP00000376233:I172T;ENSP00000355324:I172T;ENSP00000354429:I172T;ENSP00000399877:I48T;ENSP00000376231:I172T	ENSP00000355324:I172T	I	+	2	0	OPA1	194817727	1.000000	0.71417	0.991000	0.47740	0.997000	0.91878	6.940000	0.75917	2.241000	0.73720	0.528000	0.53228	ATT	.	.	.	none		0.333	OPA1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313812.2	NM_130837		C	193335033	T	C	193335033	3	2	208	1	0	0	0	0	1	0	0	0	10878	1493	52	3	529	3	OPA1	3	193335033	Missense_Mutation	SNP	T	TCGA-IA-A83W-01A-11D-A34Z-10	33316260	193335033	4687397	15	12625											
POU5F2	134187	hgsc.bcm.edu	37	chr5	93077053	93077053	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcagggtgctatccagccccGgaattcgtgtggcaggggac	7	7	16	11	2	0	0	0	0	0	0	2	2	1	2	3	5	2	3	3	5	2	2			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr5:93077053G>A	ENST00000510627.4	-	1	290	c.217C>T	c.(217-219)Cgg>Tgg	p.R73W	FAM172A_ENST00000509163.1_Intron|POU5F2_ENST00000606183.1_5'Flank|RP11-185E12.2_ENST00000606528.1_RNA|FAM172A_ENST00000509739.1_Intron|FAM172A_ENST00000395965.3_Intron|FAM172A_ENST00000505869.1_Intron	NM_153216.1	NP_694948.1	Q8N7G0	PO5F2_HUMAN	POU domain class 5, transcription factor 2	73					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)						all_cancers(142;3.87e-05)|all_epithelial(76;4.59e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0415)|all cancers(79;2.03e-19)		ATCCAGCCCCGGAATTCGTGT	0.692																																					p.R73W		Atlas-SNP	.											.	POU5F2	10	.	0			c.C217T						PASS	.						15	18	17					5																	93077053		1888	4105	5993	SO:0001583	missense	134187	exon1			AGCCCCGGAATTC		CCDS59489.1	5q15	2011-06-20				ENSG00000248483		"Homeoboxes / POU class"	26367	protein-coding gene	gene with protein product						7908264	Standard	NM_153216		Approved	SPRM-1, FLJ25680	uc003kkl.1	Q8N7G0		ENST00000510627.4:c.217C>T	chr5.hg19:g.93077053G>A	ENSP00000464890:p.Arg73Trp	35.0	0.0	.		50.0	18.0	.	NM_153216	Q15169|Q6MZL7|Q8N748	Missense_Mutation	SNP	ENST00000510627.4	hg19	CCDS59489.1																																																																																			.	.	.	none		0.692	POU5F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369873.5	NM_153216		A	93077053	G	A	93077053	3	1	208	1	0	0	0	0	1	0	0	0	12290	1115	39	1	773	1	POU5F2	5	93077053	Missense_Mutation	SNP	G	TCGA-IA-A83W-01A-11D-A34Z-10		93077053	87838207	16	12626											
FAM153B	202134	hgsc.bcm.edu	37	chr5	175530235	175530235	+	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	tttgtatcctcctagttctgAtcagggatgtacttcaggag	8	15	10	8	0	3	1	2	1	1	0	5	3	5	3	2	2	1	3	2	2	3	6			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr5:175530235A>T	ENST00000253490.4	+	13	727	c.670A>T	c.(670-672)Atc>Ttc	p.I224F	FAM153B_ENST00000510151.1_Missense_Mutation_p.I147F|FAM153B_ENST00000512862.1_Intron|FAM153B_ENST00000515817.1_Missense_Mutation_p.I147F			P0C7A2	F153B_HUMAN	family with sequence similarity 153, member B	224										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)		CCTAGTTCTGATCAGGGATGT	0.507																																					p.I147F		Atlas-SNP	.											.	FAM153B	28	.	0			c.A439T						PASS	.						165	174	171					5																	175530235		2203	4300	6503	SO:0001583	missense	202134	exon12			GTTCTGATCAGGG	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.670A>T	chr5.hg19:g.175530235A>T	ENSP00000253490:p.Ile224Phe	643.0	0.0	.		678.0	136.0	.	NM_001265615	A8MTI1	Missense_Mutation	SNP	ENST00000253490.4	hg19		.	.	.	.	.	.	.	.	.	.	A	9.135	1.012435	0.19277	.	.	ENSG00000182230	ENST00000515817;ENST00000253490	.	.	.	1.26	-2.53	0.06326	.	.	.	.	.	T	0.08714	0.0216	N	0.08118	0	0.09310	N	1	P	0.46020	0.871	B	0.31245	0.126	T	0.21827	-1.0234	8	0.87932	D	0	.	5.9593	0.19291	0.3919:0.6081:0.0:0.0	.	224	P0C7A2	F153B_HUMAN	F	147;224	.	ENSP00000253490:I224F	I	+	1	0	FAM153B	175462841	0.002000	0.14202	0.000000	0.03702	0.005000	0.04900	0.742000	0.26216	-0.649000	0.05430	0.145000	0.16022	ATC	.	.	.	none		0.507	FAM153B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001079529		T	175530235	A	T	175530235	3	4	208	1	0	0	0	0	1	0	0	0	5465	333	12	5	720	5	FAM153B	5	175530235	Missense_Mutation	SNP	A	TCGA-IA-A83W-01A-11D-A34Z-10	82453182	175530235	5385025	17	12627											
JARID2	3720	hgsc.bcm.edu	37	chr6	15513599	15513599	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctcgaaagtggctgcagttGgagacgtcagagaggaggtg	10	7	17	7	2	1	2	1	0	0	2	2	6	1	3	1	4	1	3	1	4	1	1			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr6:15513599G>A	ENST00000341776.2	+	16	3640	c.3396G>A	c.(3394-3396)ttG>ttA	p.L1132L	JARID2_ENST00000397311.3_Silent_p.L960L	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	1132					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)				GGCTGCAGTTGGAGACGTCAG	0.637																																					p.L1132L		Atlas-SNP	.											.	JARID2	135	.	0			c.G3396A						PASS	.						66	59	61					6																	15513599		2203	4300	6503	SO:0001819	synonymous_variant	3720	exon16			GCAGTTGGAGACG	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.3396G>A	chr6.hg19:g.15513599G>A		49.0	0.0	.		34.0	17.0	.	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Silent	SNP	ENST00000341776.2	hg19	CCDS4533.1																																																																																			.	.	.	none		0.637	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973		A	15513599	G	A	15513599	2	1	208	1	0	0	0	0	0	0	0	1	7952	1339	47	2		2	JARID2	6	15513599	Silent	SNP	G	TCGA-IA-A83W-01A-11D-A34Z-10		15513599	155601468	18	12628											
CCND3	896	hgsc.bcm.edu	37	chr6	41908179	41908179	+	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	gatggtcaggggcgtggtctCgcgcagcttggaggccagca	6	7	18	10	3	2	0	1	0	1	0	3	2	2	1	1	6	2	3	1	6	0	1			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr6:41908179C>G	ENST00000372991.4	-	2	541	c.343G>C	c.(343-345)Gag>Cag	p.E115Q	CCND3_ENST00000511686.1_Intron|CCND3_ENST00000511642.1_Missense_Mutation_p.E34Q|CCND3_ENST00000372987.4_Missense_Mutation_p.E65Q|CCND3_ENST00000372988.4_Missense_Mutation_p.E34Q|CCND3_ENST00000414200.2_Intron|CCND3_ENST00000510503.1_Missense_Mutation_p.E34Q|CCND3_ENST00000415497.2_Intron	NM_001760.3	NP_001751.1	P30281	CCND3_HUMAN	cyclin D3	115	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)			GGCGTGGTCTCGCGCAGCTTG	0.632			T	IGH@	MM																																p.E115Q		Atlas-SNP	.		Dom	yes		6	6p21	896	cyclin D3		L	CCND3,NS,carcinoma,0,1	CCND3	40	.	0			c.G343C						PASS	.						110	103	105					6																	41908179		2203	4300	6503	SO:0001583	missense	896	exon2			TGGTCTCGCGCAG		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.343G>C	chr6.hg19:g.41908179C>G	ENSP00000362082:p.Glu115Gln	49.0	0.0	.		59.0	23.0	.	NM_001760	B2RD63|B3KQ22|E9PAS4|E9PB36|Q5T8J0|Q6FG62|Q96F49	Missense_Mutation	SNP	ENST00000372991.4	hg19	CCDS4863.1	.	.	.	.	.	.	.	.	.	.	c	31	5.074437	0.94000	.	.	ENSG00000112576	ENST00000372991;ENST00000511642;ENST00000372987;ENST00000372988;ENST00000510503;ENST00000505064;ENST00000502771	T;T;T;T;T;T;T	0.20598	2.06;2.06;2.06;2.06;2.06;2.06;2.06	4.26	4.26	0.50523	Cyclin, N-terminal (1);Cyclin-like (3);	0.115517	0.37761	N	0.001951	T	0.48241	0.1489	M	0.92219	3.285	0.58432	D	0.999999	D;D;D	0.69078	0.971;0.995;0.997	P;D;D	0.69654	0.856;0.931;0.965	T	0.64214	-0.6460	10	0.87932	D	0	.	16.4266	0.83816	0.0:1.0:0.0:0.0	.	34;115;65	B4E0N5;P30281;Q5T8J1	.;CCND3_HUMAN;.	Q	115;34;65;34;34;34;34	ENSP00000362082:E115Q;ENSP00000426212:E34Q;ENSP00000362078:E65Q;ENSP00000362079:E34Q;ENSP00000425986:E34Q;ENSP00000425830:E34Q;ENSP00000425334:E34Q	ENSP00000362078:E65Q	E	-	1	0	CCND3	42016157	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	7.604000	0.82830	2.199000	0.70637	0.462000	0.41574	GAG	.	.	.	none		0.632	CCND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040540.2	NM_001760		G	41908179	C	G	41908179	3	3	208	1	0	0	0	0	1	0	0	0	2920	893	31	4	551	4	CCND3	6	41908179	Missense_Mutation	SNP	C	TCGA-IA-A83W-01A-11D-A34Z-10	26394580	41908179	129206888	19	12629											
GCM1	8521	hgsc.bcm.edu	37	chr6	52993306	52993306	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caatggaagctgctggtaaaAgggttctgaagagttttggg	11	11	15	4	0	1	2	0	1	1	1	1	3	1	3	0	4	2	5	0	4	5	4			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr6:52993306A>G	ENST00000259803.7	-	6	1220	c.1009T>C	c.(1009-1011)Ttt>Ctt	p.F337L	RP11-506E9.3_ENST00000566420.1_RNA	NM_003643.3	NP_003634.2	Q9NP62	GCM1_HUMAN	glial cells missing homolog 1 (Drosophila)	337					anatomical structure morphogenesis (GO:0009653)|astrocyte fate commitment (GO:0060018)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|cell differentiation involved in embryonic placenta development (GO:0060706)|positive regulation of syncytium formation by plasma membrane fusion (GO:0060143)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|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)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|skin(1)	24	Lung NSC(77;0.0755)					TGCTGGTAAAAGGGTTCTGAA	0.473																																					p.F337L		Atlas-SNP	.											.	GCM1	47	.	0			c.T1009C						PASS	.						67	73	71					6																	52993306		2203	4300	6503	SO:0001583	missense	8521	exon6			GGTAAAAGGGTTC	D88613	CCDS4950.1	6p21-p12	2008-08-29	2001-11-28	2002-09-27	ENSG00000137270	ENSG00000137270			4197	protein-coding gene	gene with protein product		603715	"glial cells missing (Drosophila) homolog a"	GCMA		8962155	Standard	NM_003643		Approved	hGCMa	uc003pbp.3	Q9NP62	OTTHUMG00000014871	ENST00000259803.7:c.1009T>C	chr6.hg19:g.52993306A>G	ENSP00000259803:p.Phe337Leu	54.0	0.0	.		61.0	15.0	.	NM_003643	Q4VAQ7|Q5T0X0|Q99468|Q9P1X3	Missense_Mutation	SNP	ENST00000259803.7	hg19	CCDS4950.1	.	.	.	.	.	.	.	.	.	.	A	7.813	0.716023	0.15306	.	.	ENSG00000137270	ENST00000259803	T	0.72505	-0.66	5.73	-1.06	0.10002	.	1.093520	0.06892	N	0.804337	T	0.21022	0.0506	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.07635	-1.0762	10	0.10902	T	0.67	-22.1899	2.5637	0.04778	0.2555:0.1237:0.0831:0.5377	.	337	Q9NP62	GCM1_HUMAN	L	337	ENSP00000259803:F337L	ENSP00000259803:F337L	F	-	1	0	GCM1	53101265	0.017000	0.18338	0.001000	0.08648	0.964000	0.63967	0.200000	0.17257	0.085000	0.17107	0.482000	0.46254	TTT	.	.	.	none		0.473	GCM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040953.1			G	52993306	A	G	52993306	3	3	208	1	0	0	0	0	1	0	0	0	6304	72	3	3	305	3	GCM1	6	52993306	Missense_Mutation	SNP	A	TCGA-IA-A83W-01A-11D-A34Z-10	11085127	52993306	118121761	20	12630											
KLHL31	401265	hgsc.bcm.edu	37	chr6	53516723	53516723	+	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	agcacgtccacgcgctccccGcgcggccccagctggctgcc	4	4	12	21	6	0	0	0	0	0	0	2	0	2	0	6	2	3	4	6	2	0	0			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr6:53516723G>A	ENST00000407079.1	-	2	1577	c.1578C>T	c.(1576-1578)cgC>cgT	p.R526R	KLHL31_ENST00000370905.3_Silent_p.R526R			Q9H511	KLH31_HUMAN	kelch-like family member 31	526					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(3)	20	Lung NSC(77;0.0158)					CGCGCTCCCCGCGCGGCCCCA	0.731																																					p.R526R		Atlas-SNP	.											.	KLHL31	48	.	0			c.C1578T						PASS	.						6	7	7					6																	53516723		2131	4169	6300	SO:0001819	synonymous_variant	401265	exon3			CTCCCCGCGCGGC		CCDS34478.1	6p12.1	2013-09-27	2013-02-22	2007-01-09	ENSG00000124743	ENSG00000124743		"Kelch-like", "BTB/POZ domain containing"	21353	protein-coding gene	gene with protein product		610749	"kelch repeat and BTB (POZ) domain containing 1", "kelch-like 31 (Drosophila)"	KBTBD1			Standard	NM_001003760		Approved	bA345L23.2, BKLHD6	uc003pcb.4	Q9H511	OTTHUMG00000014882	ENST00000407079.1:c.1578C>T	chr6.hg19:g.53516723G>A		22.0	0.0	.		24.0	8.0	.	NM_001003760	A6N9J2|B2RP49	Silent	SNP	ENST00000407079.1	hg19	CCDS34478.1																																																																																			.	.	.	none		0.731	KLHL31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040965.1	NM_001003760		A	53516723	G	A	53516723	2	1	208	1	0	0	0	0	0	0	0	1	8392	1074	38	1		1	KLHL31	6	53516723	Silent	SNP	G	TCGA-IA-A83W-01A-11D-A34Z-10	523417	53516723	117598344	21	12631											
GJC3	349149	hgsc.bcm.edu	37	chr7	99527002	99527002	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggtacagccaccaagatgAcctggaagacccagaaacgc	14	4	11	12	1	0	4	0	1	0	3	0	5	0	5	4	2	3	1	4	2	4	1			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr7:99527002A>G	ENST00000312891.2	-	1	241	c.242T>C	c.(241-243)gTc>gCc	p.V81A	RP4-604G5.1_ENST00000456499.1_RNA	NM_181538.2	NP_853516.1	Q8NFK1	CXG3_HUMAN	gap junction protein, gamma 3, 30.2kDa	81					cell communication (GO:0007154)|myelination (GO:0042552)|sensory perception of sound (GO:0007605)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)				breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)	9	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					CACCAAGATGACCTGGAAGAC	0.577																																					p.V81A		Atlas-SNP	.											GJC3,colon,carcinoma,0,1	GJC3	18	.	0			c.T242C						PASS	.						98	102	101					7																	99527002		2203	4300	6503	SO:0001583	missense	349149	exon1			AAGATGACCTGGA	AF503615	CCDS34697.1	7q22.1	2008-09-04	2007-11-06	2007-11-06	ENSG00000176402	ENSG00000176402		"Ion channels / Gap junction proteins (connexins)"	17495	protein-coding gene	gene with protein product	"connexin 30.2"	611925	"gap junction protein, epsilon 1, 29kDa"	GJE1			Standard	NM_181538		Approved	CX30.2	uc011kjd.2	Q8NFK1	OTTHUMG00000156649	ENST00000312891.2:c.242T>C	chr7.hg19:g.99527002A>G	ENSP00000325775:p.Val81Ala	47.0	0.0	.		48.0	23.0	.	NM_181538	A4D296|Q86XI9	Missense_Mutation	SNP	ENST00000312891.2	hg19	CCDS34697.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.143140	0.77888	.	.	ENSG00000176402	ENST00000312891	D	0.99186	-5.53	4.73	4.73	0.59995	Connexin, N-terminal (1);	0.366774	0.19830	N	0.105106	D	0.98601	0.9532	M	0.76574	2.34	0.41351	D	0.987367	D	0.56746	0.977	P	0.51453	0.67	D	0.99204	1.0874	10	0.87932	D	0	.	12.5098	0.56000	1.0:0.0:0.0:0.0	.	81	Q8NFK1	CXG3_HUMAN	A	81	ENSP00000325775:V81A	ENSP00000325775:V81A	V	-	2	0	GJC3	99364938	1.000000	0.71417	0.973000	0.42090	0.714000	0.41099	7.017000	0.76399	2.128000	0.65567	0.533000	0.62120	GTC	.	.	.	none		0.577	GJC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345052.1	NM_181538		G	99527002	A	G	99527002	3	3	208	1	0	0	0	0	1	0	0	0	6423	275	10	3	605	3	GJC3	7	99527002	Missense_Mutation	SNP	A	TCGA-IA-A83W-01A-11D-A34Z-10		99527002	59611661	22	12632											
MET	4233	hgsc.bcm.edu	37	chr7	116423474	116423474	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagctgccagtgaagtggaTggctttggaaagtctgcaaa	13	9	13	6	0	1	1	0	1	1	0	1	3	1	3	1	3	3	3	1	3	4	1	rs121913245		TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr7:116423474T>C	ENST00000318493.6	+	19	3990	c.3803T>C	c.(3802-3804)aTg>aCg	p.M1268T	MET_ENST00000539704.1_Missense_Mutation_p.M120T|MET_ENST00000397752.3_Missense_Mutation_p.M1250T			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.M1268T(4)		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)			GTGAAGTGGATGGCTTTGGAA	0.393			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.M1268T		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,rectum,carcinoma,+1,5	MET	412	.	4	Substitution - Missense(4)	kidney(4)	c.T3803C	GRCh37	CM992181	MET	M	rs121913245	PASS	.						93	92	92					7																	116423474		1872	4102	5974	SO:0001583	missense	4233	exon19	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	AGTGGATGGCTTT	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.3803T>C	chr7.hg19:g.116423474T>C	ENSP00000317272:p.Met1268Thr	79.0	0.0	.		83.0	34.0	.	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	T	18.99	3.740165	0.69304	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000539704	T;T;T	0.37752	1.18;1.18;1.18	5.68	5.68	0.88126	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	0.61714	0.2369	M	0.75264	2.295	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;1.0	T	0.65734	-0.6096	10	0.87932	D	0	.	16.2225	0.82267	0.0:0.0:0.0:1.0	.	1268;1250	P08581-2;P08581	.;MET_HUMAN	T	1250;1268;120	ENSP00000380860:M1250T;ENSP00000317272:M1268T;ENSP00000445020:M120T	ENSP00000317272:M1268T	M	+	2	0	MET	116210710	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.997000	0.88414	2.289000	0.77006	0.460000	0.39030	ATG	.	.	.	weak		0.393	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			C	116423474	T	C	116423474	3	2	208	1	0	0	0	0	1	0	0	0	9492	1464	51	3	3873	3	MET	7	116423474	Missense_Mutation	SNP	T	TCGA-IA-A83W-01A-11D-A34Z-10	16896472	116423474	42715189	23	12633											
PPP2R2A	5520	hgsc.bcm.edu	37	chr8	26220333	26220333	+	Silent	SNP	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	attcggctatgtgacatgagGgcatctgccctctgtgatag	8	12	12	9	1	2	3	0	3	2	0	3	3	2	3	1	2	1	2	1	2	2	3			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr8:26220333G>A	ENST00000380737.3	+	7	1100	c.771G>A	c.(769-771)agG>agA	p.R257R	PPP2R2A_ENST00000315985.7_Silent_p.R267R	NM_002717.3	NP_002708.1	P63151	2ABA_HUMAN	protein phosphatase 2, regulatory subunit B, alpha	257					G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|response to morphine (GO:0043278)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			kidney(1)|large_intestine(2)|ovary(1)	4		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		GTGACATGAGGGCATCTGCCC	0.373																																					p.R267R		Atlas-SNP	.											.	PPP2R2A	44	.	0			c.G801A						PASS	.						82	75	77					8																	26220333		2203	4300	6503	SO:0001819	synonymous_variant	5520	exon7			CATGAGGGCATCT	M64929	CCDS34867.1, CCDS55213.1	8p21.2	2013-01-10	2010-04-14		ENSG00000221914	ENSG00000221914	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "WD repeat domain containing"	9304	protein-coding gene	gene with protein product	"PP2A subunit B isoform alpha"	604941	"protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), alpha isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B, alpha isoform"			1849734	Standard	NM_001177591		Approved	PR52A, PR55A, B55A		P63151	OTTHUMG00000163850	ENST00000380737.3:c.771G>A	chr8.hg19:g.26220333G>A		49.0	0.0	.		76.0	25.0	.	NM_001177591	B2RBU8|B4E1T7|P50409|Q00007	Silent	SNP	ENST00000380737.3	hg19	CCDS34867.1																																																																																			.	.	.	none		0.373	PPP2R2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375954.2	NM_002717		A	26220333	G	A	26220333	2	1	208	1	0	0	0	0	0	0	0	1	12394	1223	43	2		2	PPP2R2A	8	26220333	Silent	SNP	G	TCGA-IA-A83W-01A-11D-A34Z-10		26220333	120143689	24	12634											
PRDM14	63978	hgsc.bcm.edu	37	chr8	70964477	70964477	+	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	ttaccacagtacttgcatttGaagggcttctccccggagtg	8	12	10	11	1	1	1	0	1	1	0	2	2	1	2	3	2	3	3	3	2	3	5			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr8:70964477G>T	ENST00000276594.2	-	8	1752	c.1551C>A	c.(1549-1551)ttC>ttA	p.F517L		NM_024504.3	NP_078780.1	Q9GZV8	PRD14_HUMAN	PR domain containing 14	517					cell fate specification (GO:0001708)|cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|germ cell development (GO:0007281)|germ-line stem cell maintenance (GO:0030718)|histone H3-R26 methylation (GO:0034972)|homeostasis of number of cells within a tissue (GO:0048873)|inner cell mass cell fate commitment (GO:0001827)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|regulation of DNA methylation (GO:0044030)|regulation of gene expression, epigenetic (GO:0040029)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			ACTTGCATTTGAAGGGCTTCT	0.507																																					p.F517L	NSCLC(129;99 1813 5906 40656 46114)	Atlas-SNP	.											.	PRDM14	102	.	0			c.C1551A						PASS	.						153	143	146					8																	70964477		2203	4300	6503	SO:0001583	missense	63978	exon8			GCATTTGAAGGGC	AF319458	CCDS6206.1	8q13.3	2013-01-08			ENSG00000147596	ENSG00000147596		"Zinc fingers, C2H2-type"	14001	protein-coding gene	gene with protein product		611781					Standard	NM_024504		Approved		uc003xym.3	Q9GZV8	OTTHUMG00000150495	ENST00000276594.2:c.1551C>A	chr8.hg19:g.70964477G>T	ENSP00000276594:p.Phe517Leu	117.0	0.0	.		83.0	34.0	.	NM_024504	Q86UX9	Missense_Mutation	SNP	ENST00000276594.2	hg19	CCDS6206.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.477602	0.84640	.	.	ENSG00000147596	ENST00000276594	T	0.21932	1.98	6.08	4.3	0.51218	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	0.38983	0.1061	L	0.61387	1.9	0.58432	D	0.999998	D	0.67145	0.996	D	0.65443	0.935	T	0.17776	-1.0358	10	0.56958	D	0.05	-32.8024	10.6211	0.45481	0.2001:0.0:0.7999:0.0	.	517	Q9GZV8	PRD14_HUMAN	L	517	ENSP00000276594:F517L	ENSP00000276594:F517L	F	-	3	2	PRDM14	71127031	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.692000	0.54727	1.590000	0.49995	0.655000	0.94253	TTC	.	.	.	none		0.507	PRDM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318505.1			T	70964477	G	T	70964477	3	4	208	1	0	0	0	0	1	0	0	0	12465	1281	45	4	168	4	PRDM14	8	70964477	Missense_Mutation	SNP	G	TCGA-IA-A83W-01A-11D-A34Z-10	44744144	70964477	75399545	25	12635											
KANK1	23189	hgsc.bcm.edu	37	chr9	744586	744586	+	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	aactttgcaaaagcccagtcTccggtcagtgttgtgcattt	9	13	9	10	1	2	0	1	0	1	0	3	0	2	0	2	1	4	3	2	1	3	3			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr9:744586T>G	ENST00000382303.1	+	15	4645	c.3993T>G	c.(3991-3993)tcT>tcG	p.S1331S	KANK1_ENST00000382293.3_Silent_p.S1173S|KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382297.2_Silent_p.S1331S	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	1331					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)		AAGCCCAGTCTCCGGTCAGTG	0.498																																					p.S1331S		Atlas-SNP	.											.	KANK1	231	.	0			c.T3993G						PASS	.						139	116	124					9																	744586		2203	4300	6503	SO:0001819	synonymous_variant	23189	exon15			CCAGTCTCCGGTC	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.3993T>G	chr9.hg19:g.744586T>G		68.0	0.0	.		89.0	31.0	.	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Silent	SNP	ENST00000382303.1	hg19	CCDS34976.1																																																																																			.	.	.	none		0.498	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158		G	744586	T	G	744586	2	3	208	1	0	0	0	0	0	0	0	1	7983	1538	54	5		5	KANK1	9	744586	Silent	SNP	T	TCGA-IA-A83W-01A-11D-A34Z-10		744586	140468845	26	12636											
TESK1	7016	hgsc.bcm.edu	37	chr9	35605737	35605737	+	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	gccggggccgcccctcctccTaccgggctctccgcagcgcc	2	5	12	22	5	1	0	0	0	1	0	4	0	3	0	9	3	2	2	9	3	1	1			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr9:35605737T>A	ENST00000336395.5	+	1	371	c.121T>A	c.(121-123)Tac>Aac	p.Y41N	MIR4667_ENST00000578933.1_RNA|TESK1_ENST00000498522.1_3'UTR	NM_006285.2	NP_006276.2	Q15569	TESK1_HUMAN	testis-specific kinase 1	41					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)			ccccTCCTCCTACCGGGCTCT	0.751																																					p.Y41N		Atlas-SNP	.											.	TESK1	46	.	0			c.T121A						PASS	.						6	6	6					9																	35605737		2011	4058	6069	SO:0001583	missense	7016	exon1			TCCTCCTACCGGG	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.121T>A	chr9.hg19:g.35605737T>A	ENSP00000338127:p.Tyr41Asn	19.0	0.0	.		17.0	9.0	.	NM_006285	Q8IXZ8	Missense_Mutation	SNP	ENST00000336395.5	hg19	CCDS6580.1	.	.	.	.	.	.	.	.	.	.	T	19.96	3.923903	0.73213	.	.	ENSG00000107140	ENST00000336395	T	0.76578	-1.03	4.01	2.75	0.32379	Protein kinase-like domain (1);	0.000000	0.33691	N	0.004652	T	0.71626	0.3362	N	0.08118	0	0.45704	D	0.998617	D	0.64830	0.994	D	0.66602	0.945	T	0.74630	-0.3601	10	0.87932	D	0	-8.0246	8.4095	0.32636	0.0:0.0:0.1975:0.8025	.	41	Q15569	TESK1_HUMAN	N	41	ENSP00000338127:Y41N	ENSP00000338127:Y41N	Y	+	1	0	TESK1	35595737	1.000000	0.71417	1.000000	0.80357	0.678000	0.39670	3.246000	0.51414	1.581000	0.49865	0.448000	0.29417	TAC	.	.	.	none		0.751	TESK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052314.1	NM_006285		A	35605737	T	A	35605737	3	1	208	1	0	0	0	0	1	0	0	0	15779	1522	53	5	123	5	TESK1	9	35605737	Missense_Mutation	SNP	T	TCGA-IA-A83W-01A-11D-A34Z-10	34861151	35605737	105607694	27	12637											
FAM53B	9679	hgsc.bcm.edu	37	chr10	126384767	126384767	+	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	agtgtaggtccttgactcatCttctttggcgtgtgctgaaa	7	15	11	8	1	3	2	1	2	2	0	4	2	4	2	1	2	1	2	1	2	2	4			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr10:126384767C>T	ENST00000337318.3	-	3	304	c.93G>A	c.(91-93)aaG>aaA	p.K31K	FAM53B_ENST00000280780.6_Silent_p.K31K|RP11-12J10.3_ENST00000494792.1_3'UTR|FAM53B_ENST00000392754.3_Silent_p.K31K	NM_014661.3	NP_055476.3	Q14153	FA53B_HUMAN	family with sequence similarity 53, member B	31								p.K31N(1)		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)		CTTGACTCATCTTCTTTGGCG	0.448																																					p.K31K		Atlas-SNP	.											FAM53B,NS,carcinoma,0,1	FAM53B	22	.	1	Substitution - Missense(1)	cervix(1)	c.G93A						PASS	.						224	211	215					10																	126384767		2203	4300	6503	SO:0001819	synonymous_variant	9679	exon3			ACTCATCTTCTTT	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.93G>A	chr10.hg19:g.126384767C>T		63.0	0.0	.		54.0	15.0	.	NM_014661	D3DRF1|Q5VUW1|Q5VUW2|Q8N5S6	Silent	SNP	ENST00000337318.3	hg19	CCDS7641.1																																																																																			.	.	.	none		0.448	FAM53B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050879.1	NM_014661		T	126384767	C	T	126384767	2	4	208	1	0	0	0	0	0	0	0	1	5587	912	32	2		2	FAM53B	10	126384767	Silent	SNP	C	TCGA-IA-A83W-01A-11D-A34Z-10		126384767	9149980	28	12638											
OSBPL5	114879	hgsc.bcm.edu	37	chr11	3114204	3114204	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggcccgctgccgctgtgcCtcctccagtgcaaacttctc	4	9	10	18	3	1	0	0	0	1	0	4	0	3	0	5	1	4	3	5	1	1	1			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr11:3114204C>T	ENST00000263650.7	-	18	2184	c.2025G>A	c.(2023-2025)gaG>gaA	p.E675E	OSBPL5_ENST00000348039.5_Silent_p.E607E|OSBPL5_ENST00000478260.1_Silent_p.E129E|OSBPL5_ENST00000389989.3_Silent_p.E607E|OSBPL5_ENST00000525498.1_Silent_p.E586E|OSBPL5_ENST00000542243.1_Silent_p.E306E	NM_020896.3	NP_065947.1	Q9H0X9	OSBL5_HUMAN	oxysterol binding protein-like 5	675					cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|Golgi to plasma membrane transport (GO:0006893)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|oxysterol binding (GO:0008142)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	25		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		GCCGCTGTGCCTCCTCCAGTG	0.662																																					p.E675E		Atlas-SNP	.											.	OSBPL5	78	.	0			c.G2025A						PASS	.						49	38	42					11																	3114204		2200	4293	6493	SO:0001819	synonymous_variant	114879	exon18			CTGTGCCTCCTCC	AF392453	CCDS31343.1, CCDS31344.1	11p15.4	2013-01-10			ENSG00000021762	ENSG00000021762		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16392	protein-coding gene	gene with protein product		606733					Standard	NM_145638		Approved	KIAA1534, ORP5	uc001lxk.2	Q9H0X9	OTTHUMG00000011702	ENST00000263650.7:c.2025G>A	chr11.hg19:g.3114204C>T		43.0	0.0	.		42.0	21.0	.	NM_020896	A6NDP0|A6NJS8|Q54A90|Q8N596|Q9BZB0|Q9P1Z4	Silent	SNP	ENST00000263650.7	hg19	CCDS31344.1																																																																																			.	.	.	none		0.662	OSBPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032332.2			T	3114204	C	T	3114204	2	4	208	1	0	0	0	0	0	0	0	1	11287	680	24	2		2	OSBPL5	11	3114204	Silent	SNP	C	TCGA-IA-A83W-01A-11D-A34Z-10		3114204	131892312	29	12639											
GUCY1A2	2977	hgsc.bcm.edu	37	chr11	106810476	106810476	+	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	aacttgggaggttccctgtgGaaggttcttcatgatattag	9	14	12	6	0	2	1	1	1	1	0	3	3	3	3	1	4	1	2	1	4	4	6			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr11:106810476G>A	ENST00000526355.2	-	4	1384	c.916C>T	c.(916-918)Cca>Tca	p.P306S	GUCY1A2_ENST00000347596.2_Missense_Mutation_p.P306S|GUCY1A2_ENST00000282249.2_Missense_Mutation_p.P306S	NM_000855.2	NP_000846.1	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	306					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|positive regulation of cGMP biosynthetic process (GO:0030828)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)			breast(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(18)|liver(1)|lung(32)|ovary(1)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	74		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)	Isosorbide Mononitrate(DB01020)|Nitric Oxide(DB00435)	GTTCCCTGTGGAAGGTTCTTC	0.423																																					p.P306S		Atlas-SNP	.											.	GUCY1A2	180	.	0			c.C916T						PASS	.						79	76	77					11																	106810476		2201	4298	6499	SO:0001583	missense	2977	exon4			CCTGTGGAAGGTT	X63282	CCDS8335.1, CCDS58170.1	11q21-q22	2008-03-18			ENSG00000152402	ENSG00000152402	4.6.1.2		4684	protein-coding gene	gene with protein product		601244		GUC1A2		1683630	Standard	NM_000855		Approved	GC-SA2	uc001pjg.2	P33402	OTTHUMG00000166296	ENST00000526355.2:c.916C>T	chr11.hg19:g.106810476G>A	ENSP00000431245:p.Pro306Ser	69.0	0.0	.		80.0	30.0	.	NM_000855	A1L4C4|B7ZLT5	Missense_Mutation	SNP	ENST00000526355.2	hg19	CCDS8335.1	.	.	.	.	.	.	.	.	.	.	G	4.058	0.008459	0.07912	.	.	ENSG00000152402	ENST00000526355;ENST00000282249;ENST00000347596	D;D;D	0.86627	-1.82;-2.15;-1.82	5.77	2.74	0.32292	.	0.000000	0.44902	U	0.000408	T	0.77558	0.4148	L	0.27053	0.805	0.44067	D	0.99681	B;B;B	0.30763	0.038;0.007;0.294	B;B;B	0.24974	0.009;0.016;0.057	T	0.67868	-0.5559	10	0.13853	T	0.58	.	16.0098	0.80391	0.0:0.382:0.618:0.0	.	306;306;306	B7ZLT5;P33402-2;P33402	.;.;GCYA2_HUMAN	S	306	ENSP00000431245:P306S;ENSP00000282249:P306S;ENSP00000344874:P306S	ENSP00000282249:P306S	P	-	1	0	GUCY1A2	106315686	1.000000	0.71417	0.174000	0.22961	0.028000	0.11728	2.943000	0.49026	0.300000	0.22699	-0.282000	0.10007	CCA	.	.	.	none		0.423	GUCY1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389003.2			A	106810476	G	A	106810476	3	1	208	1	0	0	0	0	1	0	0	0	6900	1174	41	2	1302	2	GUCY1A2	11	106810476	Missense_Mutation	SNP	G	TCGA-IA-A83W-01A-11D-A34Z-10	103696272	106810476	28196040	30	12640											
OR8B2	26595	hgsc.bcm.edu	37	chr11	124252506	124252516	+	Frame_Shift_Del	DEL	ACATGAGAGCT	ACATGAGAGCT	-																															aaaacagagacagagcaatgAcatgagagctacaagtactg																								rs370946771		TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	ACATGAGAGCT	ACATGAGAGCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr11:124252506_124252516delACATGAGAGCT	ENST00000375013.2	-	1	742_752	c.724_734delAGCTCTCATGT	c.(724-735)agctctcatgtcfs	p.SSHV242fs		NM_001005468.1	NP_001005468.1	Q96RD0	OR8B2_HUMAN	olfactory receptor, family 8, subfamily B, member 2	242						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			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)		CAGAGCAATGACATGAGAGCTACAAGTACTG	0.384																																					p.242_245del		Atlas-Indel,Pindel	.											.	OR8B2	42	.	0			c.725_735del						PASS	.																																			SO:0001589	frameshift_variant	26595	exon1			.	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.724_734delAGCTCTCATGT	chr11.hg19:g.124252506_124252516delACATGAGAGCT	ENSP00000364152:p.Ser242fs	196.0	0.0	0		219.0	35.0	0.159817	NM_001005468	Q8NGH2	Frame_Shift_Del	DEL	ENST00000375013.2	hg19	CCDS31708.1																																																																																			.	.	.	none		0.384	OR8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387290.1	NM_001005468		-	124252516	ACATGAGAGCT	-	124252506	7	5	208	1	0	1	0	1	0	0	0	0	11234	275	10	0	210	0	OR8B2	11	124252506	Frame_Shift_Del	DEL	ACATGAGAGCT	TCGA-IA-A83W-01A-11D-A34Z-10	17442030	124252506	10754010	31	12641											
TBRG1	84897	hgsc.bcm.edu	37	chr11	124494840	124494840	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttaaaggaaaatgctgctaTttgtgatgaaattgctcgtc	12	14	9	6	1	0	2	0	2	0	0	2	3	0	3	0	1	3	3	0	1	6	4			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr11:124494840T>C	ENST00000441174.3	+	2	368	c.164T>C	c.(163-165)aTt>aCt	p.I55T	TBRG1_ENST00000375005.4_5'UTR	NM_032811.2	NP_116200.2	Q3YBR2	TBRG1_HUMAN	transforming growth factor beta regulator 1	55					cell cycle arrest (GO:0007050)|DNA replication (GO:0006260)|negative regulation of cell proliferation (GO:0008285)|nucleolus to nucleoplasm transport (GO:0032066)|protein stabilization (GO:0050821)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)				kidney(1)|prostate(1)	2	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0218)		AATGCTGCTATTTGTGATGAA	0.313																																					p.I55T		Atlas-SNP	.											.	TBRG1	13	.	0			c.T164C						PASS	.						113	102	105					11																	124494840		692	1591	2283	SO:0001583	missense	84897	exon2			CTGCTATTTGTGA	AK074140	CCDS8448.2	11q24.2	2008-02-05			ENSG00000154144	ENSG00000154144			29551	protein-coding gene	gene with protein product	"nuclear interactor of ARF and MDM2"	610614				7654366, 17110379	Standard	NM_032811		Approved	FLJ14621, TB-5, NIAM	uc001qak.4	Q3YBR2	OTTHUMG00000153024	ENST00000441174.3:c.164T>C	chr11.hg19:g.124494840T>C	ENSP00000409016:p.Ile55Thr	204.0	0.0	.		240.0	87.0	.	NM_032811	Q53GJ5|Q66ZJ6|Q69YS7|Q8TCS4|Q8TEI4|Q96SV0	Missense_Mutation	SNP	ENST00000441174.3	hg19	CCDS8448.2	.	.	.	.	.	.	.	.	.	.	T	17.33	3.362644	0.61403	.	.	ENSG00000154144	ENST00000441174	D	0.81739	-1.53	5.46	5.46	0.80206	.	0.140838	0.48286	D	0.000187	T	0.73916	0.3648	L	0.43152	1.355	0.80722	D	1	B	0.32245	0.361	B	0.28139	0.086	T	0.75909	-0.3151	10	0.87932	D	0	-5.4942	13.5458	0.61702	0.0:0.0:0.0:1.0	.	55	Q3YBR2	TBRG1_HUMAN	T	55	ENSP00000409016:I55T	ENSP00000284290:I55T	I	+	2	0	TBRG1	124000050	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.617000	0.74210	2.291000	0.77112	0.533000	0.62120	ATT	.	.	.	none		0.313	TBRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329057.2	NM_032811		C	124494840	T	C	124494840	3	2	208	1	0	0	0	0	1	0	0	0	15660	1493	52	3	170	3	TBRG1	11	124494840	Missense_Mutation	SNP	T	TCGA-IA-A83W-01A-11D-A34Z-10	242334	124494840	10511676	32	12642											
CHD8	57680	hgsc.bcm.edu	37	chr14	21860710	21860710	+	Frame_Shift_Del	DEL	G	G	-																															cttttcatccatgcctcggcGaagtttggtgaactgggctg																										TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr14:21860710delG	ENST00000557364.1	-	34	6990	c.6727delC	c.(6727-6729)cgcfs	p.R2244fs	SNORD9_ENST00000362566.1_RNA|CHD8_ENST00000399982.2_Frame_Shift_Del_p.R2244fs|CHD8_ENST00000555962.1_5'Flank|CHD8_ENST00000430710.3_Frame_Shift_Del_p.R1965fs			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	2244					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)		ATGCCTCGGCGAAGTTTGGTG	0.522																																					p.R2243fs		Atlas-Indel,Pindel	.											.	CHD8	339	.	0			c.6728delG						PASS	.						146	150	149					14																	21860710		2091	4228	6319	SO:0001589	frameshift_variant	57680	exon33			.	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.6727delC	chr14.hg19:g.21860710delG	ENSP00000451601:p.Arg2244fs	82.0	0.0	0		80.0	22.0	0.275	NM_001170629	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Frame_Shift_Del	DEL	ENST00000557364.1	hg19	CCDS53885.1																																																																																			.	.	.	none		0.522	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920		-	21860710	G	-	21860710	7	5	208	1	0	1	0	1	0	0	0	0	3333	1058	37	0	1038	0	CHD8	14	21860710	Frame_Shift_Del	DEL	G	TCGA-IA-A83W-01A-11D-A34Z-10		21860710	85488830	33	12643											
MAPKBP1	23005	hgsc.bcm.edu	37	chr15	42111022	42111022	+	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	ctgtgtggctttaccccagcTgcatatttgtgtggcgcctg	4	14	12	11	1	0	0	0	0	0	0	0	0	0	0	3	2	3	3	3	2	2	4			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr15:42111022T>C	ENST00000456763.2	+	21	2372	c.2176T>C	c.(2176-2178)Tgc>Cgc	p.C726R	MAPKBP1_ENST00000457542.2_Splice_Site_p.C720R|MAPKBP1_ENST00000221214.6_Splice_Site_p.C603R|MAPKBP1_ENST00000260357.7_Splice_Site_p.C559R|MAPKBP1_ENST00000514566.1_Splice_Site_p.C720R	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	726										breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		TTACCCCAGCTGCATATTTGT	0.602																																					p.C726R		Atlas-SNP	.											.	MAPKBP1	120	.	0			c.T2176C						PASS	.						51	44	46					15																	42111022		2203	4300	6503	SO:0001630	splice_region_variant	23005	exon21			CCCAGCTGCATAT	AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"WD repeat domain containing"	29536	protein-coding gene	gene with protein product			"mitogen activated protein kinase binding protein 1"			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.2175-1T>C	chr15.hg19:g.42111022T>C		77.0	0.0	.		76.0	22.0	.	NM_001128608	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Missense_Mutation	SNP	ENST00000456763.2	hg19	CCDS45239.1	.	.	.	.	.	.	.	.	.	.	t	25.7	4.667026	0.88251	.	.	ENSG00000137802	ENST00000457542;ENST00000221214;ENST00000260357;ENST00000456763;ENST00000514566	T;T;T;T;T	0.59502	0.26;0.26;0.26;0.26;0.26	5.67	5.67	0.87782	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.040834	0.85682	D	0.000000	T	0.64057	0.2564	N	0.20685	0.6	0.80722	D	1	D;D;P;D;D	0.89917	1.0;0.962;0.947;1.0;1.0	D;D;P;D;D	0.97110	0.999;0.953;0.58;1.0;0.999	T	0.69555	-0.5114	10	0.87932	D	0	-17.5168	15.5731	0.76354	0.0:0.0:0.0:1.0	.	559;603;720;726;720	F8WC21;O60336-3;O60336-2;O60336;O60336-6	.;.;.;MABP1_HUMAN;.	R	720;603;559;726;720	ENSP00000397570:C720R;ENSP00000221214:C603R;ENSP00000260357:C559R;ENSP00000393099:C726R;ENSP00000426154:C720R	ENSP00000221214:C603R	C	+	1	0	MAPKBP1	39898314	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	7.855000	0.86950	2.160000	0.67779	0.454000	0.30748	TGC	.	.	.	none		0.602	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359745.1	NM_014994	Missense_Mutation	C	42111022	T	C	42111022	5	2	208	1	0	0	0	0	0	0	1	0	9299	1594	55	3	2254	3	MAPKBP1	15	42111022	Splice_Site	SNP	T	TCGA-IA-A83W-01A-11D-A34Z-10		42111022	60420370	34	12644											
MEX3B	84206	hgsc.bcm.edu	37	chr15	82337942	82337942	+	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	gagagctggtcgagcgcgagCtgcagggctctttggtcatc	6	9	16	10	3	2	1	1	0	1	1	4	4	2	1	0	3	4	4	0	3	0	1			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr15:82337942C>T	ENST00000329713.4	-	1	540	c.105G>A	c.(103-105)caG>caA	p.Q35Q	MEX3B_ENST00000558133.1_Silent_p.Q35Q|AC026956.1_ENST00000410589.1_RNA	NM_032246.4	NP_115622.2	Q6ZN04	MEX3B_HUMAN	mex-3 RNA binding family member B	35					protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|upper_aerodigestive_tract(1)	19						CGAGCGCGAGCTGCAGGGCTC	0.687																																					p.Q35Q		Atlas-SNP	.											.	MEX3B	50	.	0			c.G105A						PASS	.						23	18	20					15																	82337942		2200	4299	6499	SO:0001819	synonymous_variant	84206	exon1			CGCGAGCTGCAGG	AK131424	CCDS10319.1	15q25.1	2013-08-21	2013-08-21	2007-07-18	ENSG00000183496	ENSG00000183496		"RING-type (C3HC4) zinc fingers", "Mex-3 homologs"	25297	protein-coding gene	gene with protein product		611008	"ring finger and KH domain containing 3", "mex-3 homolog B (C. elegans)"	RKHD3		11230166, 17267406	Standard	NM_032246		Approved	DKFZp434J0617, RNF195	uc002bgq.2	Q6ZN04	OTTHUMG00000147356	ENST00000329713.4:c.105G>A	chr15.hg19:g.82337942C>T		25.0	0.0	.		31.0	12.0	.	NM_032246	Q4G0W1|Q8IVG2|Q9H0J0	Silent	SNP	ENST00000329713.4	hg19	CCDS10319.1																																																																																			.	.	.	none		0.687	MEX3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304000.1	XM_290645		T	82337942	C	T	82337942	2	4	208	1	0	0	0	0	0	0	0	1	9517	796	28	2		2	MEX3B	15	82337942	Silent	SNP	C	TCGA-IA-A83W-01A-11D-A34Z-10	40226920	82337942	20193450	35	12645											
IL32	9235	hgsc.bcm.edu	37	chr16	3119039	3119039	+	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	gagatggattacggtgccgaGgcaacagatcccctgtcccg	9	7	13	12	3	0	2	0	0	0	2	2	5	2	3	4	3	3	1	4	3	2	1			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr16:3119039G>A	ENST00000534507.1	+	6	599	c.388G>A	c.(388-390)Ggc>Agc	p.G130S	IL32_ENST00000548476.1_Missense_Mutation_p.G130S|IL32_ENST00000396887.3_Missense_Mutation_p.G84S|IL32_ENST00000549213.1_Missense_Mutation_p.G84S|IL32_ENST00000529699.1_Missense_Mutation_p.G64S|IL32_ENST00000530890.1_Missense_Mutation_p.G64S|IL32_ENST00000528163.2_Missense_Mutation_p.G84S|IL32_ENST00000530538.2_Missense_Mutation_p.G84S|IL32_ENST00000444393.3_Missense_Mutation_p.G84S|IL32_ENST00000396890.2_Missense_Mutation_p.G130S|IL32_ENST00000008180.9_Missense_Mutation_p.G64S|IL32_ENST00000325568.5_Missense_Mutation_p.G84S|IL32_ENST00000440815.3_Missense_Mutation_p.G84S|IL32_ENST00000548652.1_Missense_Mutation_p.G75S|IL32_ENST00000551122.1_Missense_Mutation_p.G84S|IL32_ENST00000548246.1_Missense_Mutation_p.G44S|IL32_ENST00000552936.1_Missense_Mutation_p.G108S|RNU1-125P_ENST00000516752.1_RNA|IL32_ENST00000552664.1_Missense_Mutation_p.G84S|IL32_ENST00000531965.1_Missense_Mutation_p.G74S|IL32_ENST00000529550.1_Missense_Mutation_p.G84S|IL32_ENST00000382213.3_Missense_Mutation_p.G75S|IL32_ENST00000526464.2_Missense_Mutation_p.G84S|IL32_ENST00000525643.2_Missense_Mutation_p.G84S|IL32_ENST00000533097.2_Missense_Mutation_p.G84S|IL32_ENST00000551513.1_Missense_Mutation_p.G121S|IL32_ENST00000552356.1_Missense_Mutation_p.G64S			P24001	IL32_HUMAN	interleukin 32	130					cell adhesion (GO:0007155)|defense response (GO:0006952)|immune response (GO:0006955)	extracellular space (GO:0005615)|membrane (GO:0016020)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	15						ACGGTGCCGAGGCAACAGATC	0.562																																					p.G84S		Atlas-SNP	.											IL32,colon,carcinoma,-1,1	IL32	32	.	0			c.G250A						PASS	.						8	11	10					16																	3119039		2078	4205	6283	SO:0001583	missense	9235	exon7			TGCCGAGGCAACA	M59807	CCDS32377.1, CCDS32378.1, CCDS32379.1, CCDS45394.1	16p13.3	2011-07-21			ENSG00000008517	ENSG00000008517		"Interleukins and interleukin receptors"	16830	protein-coding gene	gene with protein product	"natural killer cell transcript 4"	606001				1729377, 9653642	Standard	XM_005255686		Approved	NK4, TAIF, TAIFb, TAIFd	uc002ctn.3	P24001	OTTHUMG00000167498	ENST00000534507.1:c.388G>A	chr16.hg19:g.3119039G>A	ENSP00000431775:p.Gly130Ser	187.0	1.0	.		193.0	25.0	.	NM_004221	A6NNM0|A8MPX0|B4DJM1|B8Q191|D3DUB0|D3DUB2|Q5VFH7|Q5VFH8|Q8WV38|Q96GK9	Missense_Mutation	SNP	ENST00000534507.1	hg19		.	.	.	.	.	.	.	.	.	.	G	10.98	1.503057	0.26949	.	.	ENSG00000008517	ENST00000325568;ENST00000534507;ENST00000531965;ENST00000396887;ENST00000529699;ENST00000526464;ENST00000440815;ENST00000529550;ENST00000551122;ENST00000525643;ENST00000548807;ENST00000528163;ENST00000530890;ENST00000444393;ENST00000533097;ENST00000008180;ENST00000396890;ENST00000525228;ENST00000548652;ENST00000530538;ENST00000549213;ENST00000552936;ENST00000548476;ENST00000552664;ENST00000552356;ENST00000551513;ENST00000382213;ENST00000548246	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	0.74002	0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;0.9;-0.8;-0.8;0.9;0.9;0.9;0.9;0.9;0.9;0.9;-0.8;0.9	1.63	-0.842	0.10748	.	.	.	.	.	T	0.67411	0.2890	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B;B;D	0.76494	0.311;0.311;0.311;0.311;0.311;0.311;0.999	B;B;B;B;B;B;D	0.70716	0.036;0.048;0.048;0.048;0.048;0.048;0.97	T	0.55522	-0.8128	9	0.40728	T	0.16	.	2.5712	0.04795	0.236:0.313:0.451:0.0	.	44;64;75;64;130;84;84	B8Q191;C6GKH1;A6NNM0;A8MPX0;P24001;P24001-2;P24001-4	.;.;.;.;IL32_HUMAN;.;.	S	84;130;74;84;64;84;84;84;84;84;130;84;64;84;84;64;130;55;75;84;84;108;130;84;64;121;75;44	ENSP00000324742:G84S;ENSP00000431775:G130S;ENSP00000433177:G74S;ENSP00000380096:G84S;ENSP00000436937:G64S;ENSP00000450364:G84S;ENSP00000405063:G84S;ENSP00000437020:G84S;ENSP00000447496:G84S;ENSP00000432218:G84S;ENSP00000448354:G130S;ENSP00000432850:G84S;ENSP00000433747:G64S;ENSP00000411958:G84S;ENSP00000432917:G84S;ENSP00000008180:G64S;ENSP00000380099:G130S;ENSP00000431740:G55S;ENSP00000446624:G75S;ENSP00000436929:G84S;ENSP00000447812:G84S;ENSP00000447033:G108S;ENSP00000449483:G130S;ENSP00000448683:G84S;ENSP00000446978:G64S;ENSP00000449147:G121S;ENSP00000371648:G75S;ENSP00000447979:G44S	ENSP00000008180:G64S	G	+	1	0	IL32	3059040	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.184000	0.01254	-0.162000	0.10964	0.543000	0.68304	GGC	.	.	.	none		0.562	IL32-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000394812.2	NM_004221		A	3119039	G	A	3119039	3	1	208	1	0	0	0	0	1	0	0	0	7699	1000	35	2	272	2	IL32	16	3119039	Missense_Mutation	SNP	G	TCGA-IA-A83W-01A-11D-A34Z-10		3119039	87235714	36	12646											
CNTNAP4	85445	hgsc.bcm.edu	37	chr16	76574667	76574667	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attcagtgcagtcaaatctcTggtattgggcaggattttag	10	14	11	6	0	3	0	2	0	1	0	4	1	3	1	0	3	1	3	0	3	3	5			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr16:76574667T>C	ENST00000476707.1	+	20	3570	c.3431T>C	c.(3430-3432)cTg>cCg	p.L1144P	CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000377504.4_Missense_Mutation_p.L1092P|CNTNAP4_ENST00000478060.1_Missense_Mutation_p.L1068P|CNTNAP4_ENST00000307431.8_Missense_Mutation_p.L1140P			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	1141	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)				breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						GTCAAATCTCTGGTATTGGGC	0.368																																					p.L1068P		Atlas-SNP	.											.	CNTNAP4	600	.	0			c.T3203C						PASS	.						76	70	72					16																	76574667		1895	4124	6019	SO:0001583	missense	85445	exon20			AATCTCTGGTATT	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.3431T>C	chr16.hg19:g.76574667T>C	ENSP00000417628:p.Leu1144Pro	68.0	0.0	.		91.0	30.0	.	NM_138994	E9PFZ6|Q86YZ7	Missense_Mutation	SNP	ENST00000476707.1	hg19		.	.	.	.	.	.	.	.	.	.	T	23.1	4.370884	0.82573	.	.	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04	5.65	5.65	0.86999	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.35495	N	0.003164	D	0.92519	0.7624	.	.	.	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	0.93393	0.6753	9	0.87932	D	0	.	16.0399	0.80667	0.0:0.0:0.0:1.0	.	1068;1144;1141	E9PFZ6;E9PDN6;Q9C0A0	.;.;CNTP4_HUMAN	P	1140;1092;1068;1144	ENSP00000306893:L1140P;ENSP00000439733:L1092P;ENSP00000418741:L1068P;ENSP00000417628:L1144P	ENSP00000306893:L1140P	L	+	2	0	CNTNAP4	75132168	1.000000	0.71417	0.893000	0.35052	0.988000	0.76386	7.293000	0.78740	2.371000	0.80710	0.533000	0.62120	CTG	.	.	.	none		0.368	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401		C	76574667	T	C	76574667	3	2	208	1	0	0	0	0	1	0	0	0	3651	1580	55	3	3517	3	CNTNAP4	16	76574667	Missense_Mutation	SNP	T	TCGA-IA-A83W-01A-11D-A34Z-10	73455628	76574667	13780086	37	12647											
KIAA1609	57707	hgsc.bcm.edu	37	chr16	84529314	84529314	+	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	ggacttctctggccttcacgGgaccttctgtggcagaaatc	7	11	11	12	1	3	1	1	0	2	1	5	3	3	3	2	4	0	1	2	4	1	3			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr16:84529314G>A	ENST00000343629.6	-	3	541	c.359C>T	c.(358-360)cCc>cTc	p.P120L	TLDC1_ENST00000561807.1_5'UTR|RP11-517C16.4_ENST00000568771.1_RNA|TLDC1_ENST00000535580.1_Missense_Mutation_p.P93L	NM_020947.3	NP_065998.3	Q6P9B6	TLDC1_HUMAN	TBC/LysM-associated domain containing 1	120						lysosomal membrane (GO:0005765)											GGCCTTCACGGGACCTTCTGT	0.537																																					p.P120L		Atlas-SNP	.											.	KIAA1609	39	.	0			c.C359T						PASS	.						105	99	101					16																	84529314		2200	4300	6500	SO:0001583	missense	57707	exon3			TTCACGGGACCTT	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.359C>T	chr16.hg19:g.84529314G>A	ENSP00000343635:p.Pro120Leu	105.0	0.0	.		92.0	6.0	.	NM_020947	Q8IZ64|Q9HCG3|Q9NTE8	Missense_Mutation	SNP	ENST00000343629.6	hg19	CCDS32498.1	.	.	.	.	.	.	.	.	.	.	G	8.563	0.878146	0.17395	.	.	ENSG00000140950	ENST00000343629;ENST00000535580	T;T	0.13901	2.55;2.55	4.46	4.46	0.54185	.	0.708586	0.14302	N	0.328228	T	0.19087	0.0458	M	0.66939	2.045	0.21697	N	0.999581	B;B	0.26258	0.145;0.121	B;B	0.23852	0.049;0.031	T	0.06588	-1.0818	10	0.49607	T	0.09	-9.2031	15.1519	0.72706	0.0:0.0:1.0:0.0	.	93;120	F5GWS3;Q6P9B6	.;K1609_HUMAN	L	120;93	ENSP00000343635:P120L;ENSP00000441997:P93L	ENSP00000343635:P120L	P	-	2	0	KIAA1609	83086815	0.964000	0.33143	0.005000	0.12908	0.086000	0.17979	5.657000	0.67996	2.402000	0.81655	0.563000	0.77884	CCC	.	.	.	none		0.537	TLDC1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433421.1	NM_020947		A	84529314	G	A	84529314	3	1	208	1	0	0	0	0	1	0	0	0	8254	1232	43	2	1035	2	KIAA1609	16	84529314	Missense_Mutation	SNP	G	TCGA-IA-A83W-01A-11D-A34Z-10	7954647	84529314	5825439	38	12648											
FBXO31	79791	hgsc.bcm.edu	37	chr16	87367551	87367551	+	Frame_Shift_Del	DEL	G	G	-																															ctcacgcccacgggcagcacGaacggctgcccctgcccaca																								rs139174683	byFrequency	TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr16:87367551delG	ENST00000311635.7	-	8	1350	c.1338delC	c.(1336-1338)ttcfs	p.F446fs	RP11-178L8.4_ENST00000568879.1_Frame_Shift_Del_p.S110fs	NM_001282683.1|NM_024735.3	NP_001269612.1|NP_079011.3	Q5XUX0	FBX31_HUMAN	F-box protein 31	446					cellular response to DNA damage stimulus (GO:0006974)|cyclin catabolic process (GO:0008054)|mitotic G1 DNA damage checkpoint (GO:0031571)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	17				BRCA - Breast invasive adenocarcinoma(80;0.0272)		CGGGCAGCACGAACGGCTGCC	0.677																																					p.V447fs		Atlas-Indel,Pindel	.											.	FBXO31	82	.	0			c.1339delG						PASS	.						32	39	37					16																	87367551		2196	4296	6492	SO:0001589	frameshift_variant	79791	exon8			.	BC002985	CCDS32501.1, CCDS73922.1	16q24	2008-12-18	2004-05-27			ENSG00000103264		"F-boxes /  "other""	16510	protein-coding gene	gene with protein product		609102	"F-box only protein 31"				Standard	NM_024735		Approved	FBX14, FBXO14, Fbx31, MGC15419	uc002fjw.3	Q5XUX0		ENST00000311635.7:c.1338delC	chr16.hg19:g.87367551delG	ENSP00000310841:p.Phe446fs	54.0	0.0	0		60.0	22.0	0.366667	NM_024735	Q5K680|Q8WYV1|Q96D73|Q9UFV4	Frame_Shift_Del	DEL	ENST00000311635.7	hg19	CCDS32501.1																																																																																			.	.	.	none		0.677	FBXO31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430799.2	NM_024735		-	87367551	G	-	87367551	7	5	208	1	0	1	0	1	0	0	0	0	5748	1049	37	0	289	0	FBXO31	16	87367551	Frame_Shift_Del	DEL	G	TCGA-IA-A83W-01A-11D-A34Z-10	2838237	87367551	2987202	39	12649											
SMYD4	114826	hgsc.bcm.edu	37	chr17	1704144	1704148	+	Frame_Shift_Del	DEL	CATCT	CATCT	-																															ctgcagagtctgagggaggaCatctgctagggctggtgtgg																								rs139571127|rs372624455	byFrequency	TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	CATCT	CATCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr17:1704144_1704148delCATCT	ENST00000305513.7	-	5	707_711	c.540_544delAGATG	c.(538-546)gcagatgtcfs	p.DV181fs		NM_052928.2	NP_443160.2	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	181							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						TGAGGGAGGACATCTGCTAGGGCTG	0.517																																					p.181_182del		Pindel	.											.	SMYD4	50	.	0			c.541_545del						PASS	.																																			SO:0001589	frameshift_variant	114826	exon5			.	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.540_544delAGATG	chr17.hg19:g.1704144_1704148delCATCT	ENSP00000304360:p.Asp181fs	121.0	0.0	.		109.0	31.0	0.284	NM_052928	Q8N1P2|Q8NAT0|Q96LV4|Q96PV2	Frame_Shift_Del	DEL	ENST00000305513.7	hg19	CCDS11013.1																																																																																			.	.	.	none		0.517	SMYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207108.4	XM_056082		-	1704148	CATCT	-	1704144	7	5	208	1	0	1	0	1	0	0	0	0	14837	478	17	0	1898	0	SMYD4	17	1704144	Frame_Shift_Del	DEL	CATCT	TCGA-IA-A83W-01A-11D-A34Z-10		1704144	79491066	40	12650											
MYH10	4628	hgsc.bcm.edu	37	chr17	8404148	8404148	+	Missense_Mutation	SNP	T	T	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	gcagggcctcccttacccgcTtggcctgttccagctgctct	3	11	10	17	1	1	0	0	0	1	0	3	0	3	0	5	2	3	5	5	2	1	3			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr17:8404148T>G	ENST00000269243.4	-	27	3785	c.3647A>C	c.(3646-3648)aAg>aCg	p.K1216T	MYH10_ENST00000360416.3_Missense_Mutation_p.K1247T|MYH10_ENST00000396239.1_Missense_Mutation_p.K1237T|MYH10_ENST00000379980.4_Missense_Mutation_p.K1232T	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	1216					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						CCTTACCCGCTTGGCCTGTTC	0.542																																					p.K1247T		Atlas-SNP	.											.	MYH10	148	.	0			c.A3740C						PASS	.						144	128	134					17																	8404148		2203	4300	6503	SO:0001583	missense	4628	exon29			ACCCGCTTGGCCT	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.3647A>C	chr17.hg19:g.8404148T>G	ENSP00000269243:p.Lys1216Thr	61.0	0.0	.		49.0	17.0	.	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Missense_Mutation	SNP	ENST00000269243.4	hg19	CCDS11144.1	.	.	.	.	.	.	.	.	.	.	T	18.75	3.689612	0.68271	.	.	ENSG00000133026	ENST00000269243;ENST00000360416;ENST00000396239;ENST00000379980	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	4.71	4.71	0.59529	Myosin tail (1);	0.100830	0.64402	D	0.000003	D	0.86826	0.6026	M	0.78456	2.415	0.80722	D	1	D;D;D	0.55605	0.972;0.965;0.972	D;P;D	0.64410	0.925;0.877;0.925	D	0.88793	0.3279	10	0.87932	D	0	.	14.3623	0.66782	0.0:0.0:0.0:1.0	.	1225;1247;1216	B2RWP9;F8VTL3;P35580	.;.;MYH10_HUMAN	T	1216;1247;1237;1232	ENSP00000269243:K1216T;ENSP00000353590:K1247T;ENSP00000379539:K1237T;ENSP00000369315:K1232T	ENSP00000269243:K1216T	K	-	2	0	MYH10	8344873	1.000000	0.71417	0.132000	0.22025	0.733000	0.41908	4.643000	0.61390	1.954000	0.56735	0.533000	0.62120	AAG	.	.	.	none		0.542	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			G	8404148	T	G	8404148	3	3	208	1	0	0	0	0	1	0	0	0	10037	1609	56	5	2343	5	MYH10	17	8404148	Missense_Mutation	SNP	T	TCGA-IA-A83W-01A-11D-A34Z-10	6700004	8404148	72791062	41	12651											
DNAH9	1770	hgsc.bcm.edu	37	chr17	11696924	11696924	+	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	cgggataagatggtagaagaAaaggactttgatctttttga	14	12	12	3	1	1	5	0	2	1	3	1	7	1	7	0	3	0	1	0	3	5	5			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr17:11696924A>T	ENST00000262442.4	+	42	8234	c.8166A>T	c.(8164-8166)gaA>gaT	p.E2722D	DNAH9_ENST00000454412.2_Missense_Mutation_p.E2722D	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2722					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)		TGGTAGAAGAAAAGGACTTTG	0.348																																					p.E2722D		Atlas-SNP	.											.	DNAH9	695	.	0			c.A8166T						PASS	.						118	120	119					17																	11696924		2203	4300	6503	SO:0001583	missense	1770	exon42			AGAAGAAAAGGAC	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.8166A>T	chr17.hg19:g.11696924A>T	ENSP00000262442:p.Glu2722Asp	137.0	0.0	.		160.0	55.0	.	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	A	7.177	0.588782	0.13812	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.39997	1.05;1.05	5.76	2.04	0.26737	.	0.172799	0.50627	D	0.000109	T	0.24547	0.0595	L	0.31065	0.9	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.06127	-1.0844	10	0.13470	T	0.59	.	7.0036	0.24823	0.7388:0.1231:0.1382:0.0	.	2722	Q9NYC9	DYH9_HUMAN	D	2722;2722;1304	ENSP00000262442:E2722D;ENSP00000414874:E2722D	ENSP00000262442:E2722D	E	+	3	2	DNAH9	11637649	1.000000	0.71417	1.000000	0.80357	0.408000	0.30992	0.979000	0.29500	0.394000	0.25230	-0.264000	0.10439	GAA	.	.	.	none		0.348	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11696924	A	T	11696924	3	4	208	1	0	0	0	0	1	0	0	0	4610	11	1	5	8332	5	DNAH9	17	11696924	Missense_Mutation	SNP	A	TCGA-IA-A83W-01A-11D-A34Z-10	3292776	11696924	69498286	42	12652											
PCGF2	7703	hgsc.bcm.edu	37	chr17	36891741	36891741	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagccttgtcgctgactgacTcacactcggacgccccgctg	6	8	11	16	4	1	2	1	2	0	0	3	4	1	3	3	1	1	2	3	1	0	1			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr17:36891741T>C	ENST00000580830.1	-	12	1471	c.770A>G	c.(769-771)gAg>gGg	p.E257G	PCGF2_ENST00000360797.2_Missense_Mutation_p.E257G|PCGF2_ENST00000579882.1_Nonstop_Mutation_p.*258W|PCGF2_ENST00000585100.1_Nonstop_Mutation_p.*258W|PCGF2_ENST00000581345.1_Missense_Mutation_p.E257G|PCGF2_ENST00000578109.1_Nonstop_Mutation_p.*204W			P35227	PCGF2_HUMAN	polycomb group ring finger 2	257	Pro/Ser-rich.				anterior/posterior pattern specification (GO:0009952)|cellular response to hydrogen peroxide (GO:0070301)|embryonic skeletal system morphogenesis (GO:0048704)|histone acetylation (GO:0016573)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	10	Breast(7;9.07e-22)					GCTGACTGACTCACACTCGGA	0.687											OREG0024367	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E257G		Atlas-SNP	.											.	PCGF2	24	.	0			c.A770G						PASS	.						20	18	18					17																	36891741		2193	4292	6485	SO:0001583	missense	7703	exon11			ACTGACTCACACT	D13969	CCDS32638.1	17q12	2013-01-09	2005-01-17	2005-01-19		ENSG00000277258		"RING-type (C3HC4) zinc fingers", "Polycomb group ring fingers"	12929	protein-coding gene	gene with protein product		600346	"ring finger protein 110"	ZNF144, RNF110		8325509	Standard	NM_007144		Approved	MEL-18	uc002hqp.1	P35227		ENST00000580830.1:c.770A>G	chr17.hg19:g.36891741T>C	ENSP00000461961:p.Glu257Gly	51.0	0.0	.	866	50.0	25.0	.	NM_007144	A6NGD8	Missense_Mutation	SNP	ENST00000580830.1	hg19	CCDS32638.1	.	.	.	.	.	.	.	.	.	.	T	16.51	3.144822	0.57044	.	.	ENSG00000056661	ENST00000360797	T	0.33654	1.4	4.82	4.82	0.62117	.	0.057727	0.64402	D	0.000002	T	0.33644	0.0870	L	0.29908	0.895	0.49483	D	0.999793	D	0.55605	0.972	P	0.47673	0.554	T	0.12477	-1.0546	10	0.54805	T	0.06	-25.0052	13.3514	0.60603	0.0:0.0:0.0:1.0	.	257	P35227	PCGF2_HUMAN	G	257	ENSP00000354033:E257G	ENSP00000354033:E257G	E	-	2	0	PCGF2	34145267	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.130000	0.77235	2.035000	0.60131	0.459000	0.35465	GAG	.	.	.	none		0.687	PCGF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442246.2	NM_007144		C	36891741	T	C	36891741	3	2	208	1	0	0	0	0	1	0	0	0	11582	1551	54	3	268	3	PCGF2	17	36891741	Missense_Mutation	SNP	T	TCGA-IA-A83W-01A-11D-A34Z-10	25194817	36891741	44303469	43	12653											
NAGLU	4669	hgsc.bcm.edu	37	chr17	40695970	40695970	+	Frame_Shift_Del	DEL	G	G	-																															ccgctaccagctgaccttgtGggggccagaaggcaacatcc																								rs527236038		TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr17:40695970delG	ENST00000225927.2	+	6	2047	c.1946delG	c.(1945-1947)tggfs	p.W649fs	RP11-400F19.8_ENST00000585572.1_RNA	NM_000263.3	NP_000254.2	P54802	ANAG_HUMAN	N-acetylglucosaminidase, alpha	649			W -> C (in MPS3B; no enzyme activity; synthesizes a polypeptide with a molecular size similar to that of the wild-type). {ECO:0000269|PubMed:11153910}.		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)	CTGACCTTGTGGGGGCCAGAA	0.627																																					p.W649fs		Atlas-Indel,Pindel	.											.	NAGLU	36	.	0			c.1945delT						PASS	.						31	25	27					17																	40695970		2202	4300	6502	SO:0001589	frameshift_variant	4669	exon6			.		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.1946delG	chr17.hg19:g.40695970delG	ENSP00000225927:p.Trp649fs	29.0	0.0	0		33.0	16.0	0.484848	NM_000263		Frame_Shift_Del	DEL	ENST00000225927.2	hg19	CCDS11427.1																																																																																			.	.	.	none		0.627	NAGLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450385.1	NM_000263		-	40695970	G	-	40695970	7	5	208	1	0	1	0	1	0	0	0	0	10150	1357	47	0	1968	0	NAGLU	17	40695970	Frame_Shift_Del	DEL	G	TCGA-IA-A83W-01A-11D-A34Z-10	3804229	40695970	40499240	44	12654											
ACSF2	80221	hgsc.bcm.edu	37	chr17	48541192	48541192	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatacagaggcaccttcctgTatggtacccccacgatgttc	9	11	8	13	1	0	1	0	0	0	1	2	2	1	1	4	2	2	4	4	2	4	6			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr17:48541192T>C	ENST00000300441.4	+	9	1164	c.1060T>C	c.(1060-1062)Tat>Cat	p.Y354H	ACSF2_ENST00000427954.2_Missense_Mutation_p.Y379H|ACSF2_ENST00000502667.1_Missense_Mutation_p.Y341H|ACSF2_ENST00000504392.1_Missense_Mutation_p.Y311H|ACSF2_ENST00000541920.1_Missense_Mutation_p.Y194H	NM_025149.4	NP_079425.3	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2	354					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ligase activity (GO:0016874)			endometrium(7)|kidney(3)|large_intestine(1)|lung(1)|stomach(1)	13	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			CACCTTCCTGTATGGTACCCC	0.552																																					p.Y354H		Atlas-SNP	.											.	ACSF2	46	.	0			c.T1060C						PASS	.						140	135	137					17																	48541192		2203	4300	6503	SO:0001583	missense	80221	exon9			TTCCTGTATGGTA	AK024573, BC012053	CCDS11567.1, CCDS74103.1, CCDS74104.1, CCDS74105.1	17q21.33	2007-10-17			ENSG00000167107	ENSG00000167107		"Acyl-CoA synthetase family"	26101	protein-coding gene	gene with protein product		610465				17762044	Standard	NM_001288968		Approved	FLJ20920, ACSMW	uc002iqu.2	Q96CM8	OTTHUMG00000162128	ENST00000300441.4:c.1060T>C	chr17.hg19:g.48541192T>C	ENSP00000300441:p.Tyr354His	59.0	0.0	.		70.0	17.0	.	NM_025149	B4DFQ6|B4DHT5|B4DUF5|Q9H7G2	Missense_Mutation	SNP	ENST00000300441.4	hg19	CCDS11567.1	.	.	.	.	.	.	.	.	.	.	T	10.66	1.413740	0.25465	.	.	ENSG00000167107	ENST00000300441;ENST00000541920;ENST00000504392;ENST00000427954;ENST00000502667	T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76	4.8	4.8	0.61643	AMP-dependent synthetase/ligase (1);	0.125162	0.56097	D	0.000030	T	0.41073	0.1143	L	0.28274	0.84	0.47698	D	0.999499	P;P;P;P	0.42357	0.632;0.777;0.632;0.632	P;P;P;P	0.53266	0.582;0.722;0.582;0.582	T	0.31752	-0.9932	10	0.07813	T	0.8	-5.2894	7.5258	0.27653	0.0:0.1322:0.0:0.8678	.	341;379;311;354	B4DHT5;B4DFQ6;E9PF16;Q96CM8	.;.;.;ACSF2_HUMAN	H	354;194;311;379;341	ENSP00000300441:Y354H;ENSP00000437987:Y194H;ENSP00000425964:Y311H;ENSP00000401831:Y379H;ENSP00000421884:Y341H	ENSP00000300441:Y354H	Y	+	1	0	ACSF2	45896191	0.981000	0.34729	0.997000	0.53966	0.768000	0.43524	3.223000	0.51231	2.016000	0.59253	0.533000	0.62120	TAT	.	.	.	none		0.552	ACSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367423.3	NM_025149		C	48541192	T	C	48541192	3	2	208	1	0	0	0	0	1	0	0	0	175	1638	57	3	1094	3	ACSF2	17	48541192	Missense_Mutation	SNP	T	TCGA-IA-A83W-01A-11D-A34Z-10	7845222	48541192	32654018	45	12655											
MIB1	57534	hgsc.bcm.edu	37	chr18	19438539	19438539	+	Frame_Shift_Del	DEL	A	A	-																															ttccagtattacaaaaggacAaggataataccaatgtcaat																										TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr18:19438539delA	ENST00000261537.6	+	20	3076	c.2812delA	c.(2812-2814)aagfs	p.K938fs	MIB1_ENST00000578646.1_3'UTR	NM_020774.2	NP_065825.1	Q86YT6	MIB1_HUMAN	mindbomb E3 ubiquitin protein ligase 1	938					blood vessel development (GO:0001568)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|negative regulation of neuron differentiation (GO:0045665)|neural tube formation (GO:0001841)|Notch signaling pathway (GO:0007219)|positive regulation of endocytosis (GO:0045807)|somitogenesis (GO:0001756)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|ovary(5)	27			STAD - Stomach adenocarcinoma(5;0.212)			ACAAAAGGACAAGGATAATAC	0.299																																					p.D937fs		Atlas-Indel,Pindel	.											MIB1,NS,carcinoma,0,1	MIB1	87	.	0			c.2811delC						PASS	.						110	115	114					18																	19438539		2203	4299	6502	SO:0001589	frameshift_variant	57534	exon20			.	AB037744	CCDS11871.1	18q11.2	2014-09-17	2012-02-23		ENSG00000101752	ENSG00000101752		"Zinc fingers, ZZ-type", "Ankyrin repeat domain containing"	21086	protein-coding gene	gene with protein product		608677	"mindbomb homolog 1 (Drosophila)"				Standard	NM_020774		Approved	DIP-1, MIB, KIAA1323, ZZANK2, ZZZ6	uc002ktq.3	Q86YT6	OTTHUMG00000131753	ENST00000261537.6:c.2812delA	chr18.hg19:g.19438539delA	ENSP00000261537:p.Lys938fs	241.0	0.0	0		238.0	80.0	0.336134	NM_020774	B0YJ38|Q2TB37|Q68D01|Q6YI51|Q8NBY0|Q8TCB5|Q8TCL7|Q9P2M3	Frame_Shift_Del	DEL	ENST00000261537.6	hg19	CCDS11871.1																																																																																			.	.	.	none		0.299	MIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254675.1	NM_020774		-	19438539	A	-	19438539	7	5	208	1	0	1	0	1	0	0	0	0	9573	131	5	0	2890	0	MIB1	18	19438539	Frame_Shift_Del	DEL	A	TCGA-IA-A83W-01A-11D-A34Z-10		19438539	58638709	46	12656											
ALPK2	115701	hgsc.bcm.edu	37	chr18	56246675	56246675	+	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	gagtttatatctcccctgttCtgtcactgaagacgttccat	8	15	7	11	1	3	2	1	1	2	1	5	3	4	2	3	0	0	3	3	0	3	5			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr18:56246675C>T	ENST00000361673.3	-	4	1546	c.1333G>A	c.(1333-1335)Gaa>Aaa	p.E445K	ALPK2_ENST00000587399.1_5'Flank	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	445						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						CTCCCCTGTTCTGTCACTGAA	0.522											OREG0025011	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E445K		Atlas-SNP	.											.	ALPK2	487	.	0			c.G1333A						PASS	.						119	119	119					18																	56246675		2203	4300	6503	SO:0001583	missense	115701	exon4			CCTGTTCTGTCAC	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.1333G>A	chr18.hg19:g.56246675C>T	ENSP00000354991:p.Glu445Lys	111.0	0.0	.	1014	90.0	36.0	.	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	hg19	CCDS11966.2	.	.	.	.	.	.	.	.	.	.	C	11.79	1.742506	0.30865	.	.	ENSG00000198796	ENST00000361673	T	0.51817	0.69	5.39	5.39	0.77823	.	1.454940	0.04982	N	0.465878	T	0.41696	0.1170	L	0.34521	1.04	0.09310	N	1	P	0.38922	0.651	B	0.33521	0.165	T	0.41395	-0.9511	10	0.87932	D	0	-2.3006	12.1567	0.54081	0.0:0.9211:0.0:0.0789	.	445	Q86TB3	ALPK2_HUMAN	K	445	ENSP00000354991:E445K	ENSP00000354991:E445K	E	-	1	0	ALPK2	54397655	0.869000	0.29996	0.009000	0.14445	0.219000	0.24729	1.808000	0.38912	2.542000	0.85734	0.561000	0.74099	GAA	.	.	.	none		0.522	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		T	56246675	C	T	56246675	3	4	208	1	0	0	0	0	1	0	0	0	545	922	32	2	5219	2	ALPK2	18	56246675	Missense_Mutation	SNP	C	TCGA-IA-A83W-01A-11D-A34Z-10	36808136	56246675	21830573	47	12657											
MUC16	94025	hgsc.bcm.edu	37	chr19	8993026	8993026	+	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	ctgctggtggtgggtacagaGctccgatgggtgaaacctgc	7	9	16	9	1	0	2	0	1	0	1	1	3	1	2	2	4	5	3	2	4	2	1			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr19:8993026G>A	ENST00000397910.4	-	67	41936	c.41733C>T	c.(41731-41733)agC>agT	p.S13911S	MUC16_ENST00000380951.5_Silent_p.S552S	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13936				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						TGGGTACAGAGCTCCGATGGG	0.537																																					p.S13911S		Atlas-SNP	.											.	MUC16	4315	.	0			c.C41733T						PASS	.						129	118	121					19																	8993026		1912	4130	6042	SO:0001819	synonymous_variant	94025	exon67			TACAGAGCTCCGA	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.41733C>T	chr19.hg19:g.8993026G>A		59.0	0.0	.		72.0	20.0	.	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	G	3.206	-0.162630	0.06502	.	.	ENSG00000181143	ENST00000542240	.	.	.	2.64	-1.81	0.07882	.	.	.	.	.	T	0.25680	0.0625	.	.	.	.	.	.	.	.	.	.	.	.	T	0.30119	-0.9989	3	.	.	.	.	2.8138	0.05450	0.2886:0.0:0.496:0.2154	.	.	.	.	V	751	.	.	A	-	2	0	MUC16	8854026	0.000000	0.05858	0.000000	0.03702	0.111000	0.19643	-0.235000	0.09016	-0.398000	0.07679	0.400000	0.26472	GCT	.	.	.	none		0.537	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	8993026	G	A	8993026	2	1	208	1	0	0	0	0	0	0	0	1	9980	962	34	2		2	MUC16	19	8993026	Silent	SNP	G	TCGA-IA-A83W-01A-11D-A34Z-10		8993026	50135957	48	12658											
BRD4	23476	hgsc.bcm.edu	37	chr19	15349622	15349622	+	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	ctgctggtccagcatggactGgggctgggagctctgggcct	4	9	17	11	0	1	0	0	0	1	0	2	2	2	2	2	6	3	4	2	6	0	0			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr19:15349622G>A	ENST00000263377.2	-	19	4173	c.3952C>T	c.(3952-3954)Cag>Tag	p.Q1318*	AC004257.3_ENST00000602793.1_lincRNA	NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	1318	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)			AGCATGGACTGGGGCTGGGAG	0.697			T	C15orf55	lethal midline carcinoma of young people																																p.Q1318X		Atlas-SNP	.		Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	.	BRD4	172	.	0			c.C3952T						PASS	.						10	13	12					19																	15349622		2197	4292	6489	SO:0001587	stop_gained	23476	exon19			TGGACTGGGGCTG	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.3952C>T	chr19.hg19:g.15349622G>A	ENSP00000263377:p.Gln1318*	70.0	0.0	.		82.0	35.0	.	NM_058243	O60433|Q4G0X8|Q86YS8|Q96PD3	Nonsense_Mutation	SNP	ENST00000263377.2	hg19	CCDS12328.1	.	.	.	.	.	.	.	.	.	.	g	44	11.038961	0.99507	.	.	ENSG00000141867	ENST00000263377	.	.	.	5.16	5.16	0.70880	.	0.000000	0.47455	D	0.000226	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	-17.7226	15.5799	0.76425	0.0:0.0:1.0:0.0	.	.	.	.	X	1318	.	ENSP00000263377:Q1318X	Q	-	1	0	BRD4	15210622	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.219000	0.89770	2.396000	0.81511	0.645000	0.84053	CAG	.	.	.	none		0.697	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243		A	15349622	G	A	15349622	4	1	208	1	0	0	0	0	0	1	0	0	1506	1357	47	2	144	2	BRD4	19	15349622	Nonsense_Mutation	SNP	G	TCGA-IA-A83W-01A-11D-A34Z-10	6356596	15349622	43779361	49	12659											
RPL18A	6142	hgsc.bcm.edu	37	chr19	17974057	17974058	+	Frame_Shift_Ins	INS	-	-	A																															gcttcaccaccaagaggcccINSaacaccttcttctaggtgca																										TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr19:17974057_17974058insA	ENST00000222247.5	+	5	597_598	c.516_517insA	c.(517-519)aacfs	p.N173fs	SNORA68_ENST00000384437.1_RNA|RPL18A_ENST00000599870.1_Frame_Shift_Ins_p.N144fs|RPL18A_ENST00000599898.1_Frame_Shift_Ins_p.N134fs|RPL18A_ENST00000600147.1_Frame_Shift_Ins_p.N151fs	NM_000980.3	NP_000971.1	Q02543	RL18A_HUMAN	ribosomal protein L18a	173					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|upper_aerodigestive_tract(1)	5						CCAAGAGGCCCAACACCTTCTT	0.609																																					p.P172fs		Atlas-INDEL	.											.	RPL18A	15	.	0			c.516_517insA						PASS	.																																			SO:0001589	frameshift_variant	6142	exon5			.	AB007175	CCDS12367.1	19p13.11	2011-04-06			ENSG00000105640	ENSG00000105640		"L ribosomal proteins"	10311	protein-coding gene	gene with protein product	"60S ribosomal protein L18a", "ribosomal protein L18a-like protein"	604178				9582194	Standard	NM_000980		Approved	L18A	uc002nhp.3	Q02543		ENST00000222247.5:c.518dupA	chr19.hg19:g.17974059_17974059dupA	ENSP00000222247:p.Asn173fs	44.0	0.0	0		50.0	13.0	0.26	NM_000980		Frame_Shift_Ins	INS	ENST00000222247.5	hg19	CCDS12367.1																																																																																			.	.	.	none		0.609	RPL18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466679.1	NM_000980		A	17974058	-	A	17974057	7	5	208	1	0	1	1	0	0	0	0	0	13578	581	21	0	534	0	RPL18A	19	17974057	Frame_Shift_Ins	INS	-	TCGA-IA-A83W-01A-11D-A34Z-10	2624435	17974057	41154926	50	12660											
ACTN4	81	hgsc.bcm.edu	37	chr19	39214666	39214666	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aacaactggatggagagcgcCatggaggacctccaggacat	13	5	13	10	1	0	1	0	0	0	1	1	6	1	5	3	5	3	0	3	5	2	0			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr19:39214666C>T	ENST00000252699.2	+	14	1717	c.1641C>T	c.(1639-1641)gcC>gcT	p.A547A	ACTN4_ENST00000390009.3_Silent_p.A328A|ACTN4_ENST00000424234.2_Silent_p.A157A	NM_004924.4	NP_004915.2	O43707	ACTN4_HUMAN	actinin, alpha 4	547					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)			TGGAGAGCGCCATGGAGGACC	0.607																																					p.A547A	Colon(168;199 1940 10254 46213 46384)	Atlas-SNP	.											.	ACTN4	69	.	0			c.C1641T						PASS	.						57	59	59					19																	39214666		2203	4300	6503	SO:0001819	synonymous_variant	81	exon14			GAGCGCCATGGAG	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.1641C>T	chr19.hg19:g.39214666C>T		40.0	0.0	.		43.0	14.0	.	NM_004924	A4K467|D6PXK4|O76048	Silent	SNP	ENST00000252699.2	hg19	CCDS12518.1																																																																																			.	.	.	none		0.607	ACTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268091.1			T	39214666	C	T	39214666	2	4	208	1	0	0	0	0	0	0	0	1	207	581	21	2		2	ACTN4	19	39214666	Silent	SNP	C	TCGA-IA-A83W-01A-11D-A34Z-10	21240609	39214666	19914317	51	12661											
APCDD1L	164284	hgsc.bcm.edu	37	chr20	57035951	57035951	+	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	ttctgcagcgatggcctgtgCtgcggtggcctggagaagtc	5	10	16	10	2	1	1	0	0	1	1	2	3	1	1	2	4	4	2	2	4	1	1			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr20:57035951C>A	ENST00000371149.3	-	4	1631	c.1401G>T	c.(1399-1401)caG>caT	p.Q467H	APCDD1L_ENST00000491015.1_5'Flank|APCDD1L_ENST00000439429.1_Missense_Mutation_p.Q478H	NM_153360.1	NP_699191.1	Q8NCL9	APCDL_HUMAN	adenomatosis polyposis coli down-regulated 1-like	467						integral component of membrane (GO:0016021)				large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(1)	18	Lung NSC(12;0.000856)|all_lung(29;0.0025)		BRCA - Breast invasive adenocarcinoma(13;5.6e-11)|Epithelial(14;1.67e-07)|all cancers(14;1.48e-06)			ATGGCCTGTGCTGCGGTGGCC	0.632																																					p.Q467H		Atlas-SNP	.											.	APCDD1L	48	.	0			c.G1401T						PASS	.						62	60	60					20																	57035951		2203	4300	6503	SO:0001583	missense	164284	exon4			CCTGTGCTGCGGT	AK074647	CCDS13467.1	20q13.32	2006-07-07			ENSG00000198768	ENSG00000198768			26892	protein-coding gene	gene with protein product							Standard	NM_153360		Approved	FLJ90166	uc002xze.1	Q8NCL9	OTTHUMG00000032845	ENST00000371149.3:c.1401G>T	chr20.hg19:g.57035951C>A	ENSP00000360191:p.Gln467His	43.0	0.0	.		45.0	14.0	.	NM_153360		Missense_Mutation	SNP	ENST00000371149.3	hg19	CCDS13467.1	.	.	.	.	.	.	.	.	.	.	C	7.052	0.564739	0.13498	.	.	ENSG00000198768	ENST00000371149;ENST00000439429	T;T	0.14516	2.51;2.5	3.68	-4.72	0.03269	.	1.125310	0.06733	U	0.777012	T	0.06917	0.0176	N	0.24115	0.695	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37663	-0.9696	10	0.41790	T	0.15	.	0.9016	0.01275	0.4548:0.1971:0.1255:0.2226	.	478;467	F5H6V6;Q8NCL9	.;APCDL_HUMAN	H	467;478	ENSP00000360191:Q467H;ENSP00000413261:Q478H	ENSP00000360191:Q467H	Q	-	3	2	APCDD1L	56469357	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.983000	0.03759	-1.079000	0.03113	-0.657000	0.03884	CAG	.	.	.	none		0.632	APCDD1L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000079881.2	NM_153360		A	57035951	C	A	57035951	3	1	208	1	0	0	0	0	1	0	0	0	766	796	28	4	108	4	APCDD1L	20	57035951	Missense_Mutation	SNP	C	TCGA-IA-A83W-01A-11D-A34Z-10		57035951	5989569	52	12662											
N6AMT1	29104	hgsc.bcm.edu	37	chr21	30257571	30257571	+	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	cgctgcctccagcgcgttcaAaagcagaaacgtgtcctccg	9	7	10	15	5	1	1	1	0	0	1	4	1	4	1	4	0	4	3	4	0	3	1			TCGA-IA-A83W-01A-11D-A34Z-10	TCGA-IA-A83W-11A-11D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b5bc3d4-904a-4ece-a4fb-4263014e4b39	da2fe768-0f46-492c-99cc-6b417fd4a40c	g.chr21:30257571A>T	ENST00000303775.5	-	1	122	c.97T>A	c.(97-99)Ttg>Atg	p.L33M	N6AMT1_ENST00000351429.3_Missense_Mutation_p.L33M	NM_013240.4	NP_037372	Q9Y5N5	HEMK2_HUMAN	N-6 adenine-specific DNA methyltransferase 1 (putative)	33					positive regulation of cell growth (GO:0030307)|protein methylation (GO:0006479)	protein complex (GO:0043234)	nucleic acid binding (GO:0003676)|protein methyltransferase activity (GO:0008276)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)	12						AGCGCGTTCAAAAGCAGAAAC	0.657																																					p.L33M		Atlas-SNP	.											.	N6AMT1	31	.	0			c.T97A						PASS	.						53	63	60					21																	30257571		2202	4296	6498	SO:0001583	missense	29104	exon1			CGTTCAAAAGCAG	AF139682	CCDS33525.1, CCDS33526.1	21q21.3	2006-12-14	2006-12-14	2006-12-14	ENSG00000156239	ENSG00000156239	2.1.1.72		16021	protein-coding gene	gene with protein product		614553	"chromosome 21 open reading frame 127", "HemK methyltransferase family member 2"	C21orf127, HEMK2			Standard	NM_013240		Approved	PRED28, N6AMT, MTQ2	uc002ymo.2	Q9Y5N5	OTTHUMG00000078750	ENST00000303775.5:c.97T>A	chr21.hg19:g.30257571A>T	ENSP00000303584:p.Leu33Met	68.0	0.0	.		95.0	43.0	.	NM_182749	Q96F73	Missense_Mutation	SNP	ENST00000303775.5	hg19	CCDS33526.1	.	.	.	.	.	.	.	.	.	.	A	10.81	1.454935	0.26161	.	.	ENSG00000156239	ENST00000303775;ENST00000351429	T;T	0.19806	2.37;2.12	5.18	0.254	0.15557	Methyltransferase small (1);	0.142986	0.49305	D	0.000141	T	0.15652	0.0377	L	0.39020	1.185	0.35178	D	0.772183	B;P	0.35944	0.295;0.529	B;B	0.38921	0.101;0.285	T	0.16012	-1.0417	10	0.46703	T	0.11	-9.2302	7.7917	0.29125	0.4453:0.0:0.5547:0.0	.	33;33	Q9Y5N5-2;Q9Y5N5	.;HEMK2_HUMAN	M	33	ENSP00000303584:L33M;ENSP00000286764:L33M	ENSP00000303584:L33M	L	-	1	2	N6AMT1	29179442	0.997000	0.39634	0.967000	0.41034	0.171000	0.22731	1.076000	0.30729	0.096000	0.17463	-1.013000	0.02462	TTG	.	.	.	none		0.657	N6AMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171738.1	NM_013240		T	30257571	A	T	30257571	3	4	208	1	0	0	0	0	1	0	0	0	10121	11	1	5	571	5	N6AMT1	21	30257571	Missense_Mutation	SNP	A	TCGA-IA-A83W-01A-11D-A34Z-10		30257571	17872324	53	12663											
KIAA1614	57710	hgsc.bcm.edu	37	chr1	180885553	180885553	+	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	acagggagtgagtccctgctCtgcttcccaagagtggtcat	8	10	12	11	0	2	2	1	1	1	1	4	3	4	3	2	2	2	2	2	2	1	1			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr1:180885553C>T	ENST00000367588.4	+	2	369	c.314C>T	c.(313-315)tCt>tTt	p.S105F		NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	105										NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						AGTCCCTGCTCTGCTTCCCAA	0.587																																					p.S105F		Atlas-SNP	.											.	KIAA1614	75	.	0			c.C314T						PASS	.						80	89	86					1																	180885553		2038	4181	6219	SO:0001583	missense	57710	exon2			CCTGCTCTGCTTC	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.314C>T	chr1.hg19:g.180885553C>T	ENSP00000356560:p.Ser105Phe	162.0	0.0	.		108.0	44.0	.	NM_020950	Q5VZ45|Q9HCF8	Missense_Mutation	SNP	ENST00000367588.4	hg19	CCDS41442.1	.	.	.	.	.	.	.	.	.	.	C	9.289	1.050241	0.19827	.	.	ENSG00000135835	ENST00000367588	T	0.05580	3.42	4.87	1.69	0.24217	.	1.482150	0.04336	N	0.353230	T	0.03695	0.0105	N	0.08118	0	0.29690	N	0.841037	B	0.23735	0.09	B	0.20955	0.032	T	0.40905	-0.9538	9	0.37606	T	0.19	-0.5476	3.0596	0.06195	0.2088:0.5355:0.0:0.2557	.	105	Q5VZ46	K1614_HUMAN	F	105	ENSP00000356560:S105F	ENSP00000356560:S105F	S	+	2	0	KIAA1614	179152176	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.043000	0.13971	0.143000	0.18926	0.655000	0.94253	TCT	.	.	.	none		0.587	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531		T	180885553	C	T	180885553	3	4	209	1	0	0	0	0	1	0	0	0	8255	913	32	2	320	2	KIAA1614	1	180885553	Missense_Mutation	SNP	C	TCGA-IZ-8195-01A-31D-2396-08		180885553	68365068	1	12664											
C1orf25	81627	hgsc.bcm.edu	37	chr1	185094118	185094118	+	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	tgcatgaattgaaaactgacTttgaggcgtacactctgatt	12	13	9	7	1	1	5	0	5	1	0	1	5	1	5	0	1	3	2	0	1	4	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr1:185094118T>A	ENST00000367506.5	-	12	1985	c.1717A>T	c.(1717-1719)Agt>Tgt	p.S573C	TRMT1L_ENST00000367504.3_3'UTR	NM_001202423.1|NM_030934.4	NP_001189352.1|NP_112196.3	Q7Z2T5	TRM1L_HUMAN	tRNA methyltransferase 1 homolog (S. cerevisiae)-like	573	Trm1 methyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00958}.				adult locomotory behavior (GO:0008344)		metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA (guanine-N2-)-methyltransferase activity (GO:0004809)|tRNA binding (GO:0000049)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	21						GAAAACTGACTTTGAGGCGTA	0.358																																					p.S573C		Atlas-SNP	.											.	TRMT1L	50	.	0			c.A1717T						PASS	.						143	134	137					1																	185094118		2203	4300	6503	SO:0001583	missense	81627	exon12			ACTGACTTTGAGG	AF288399	CCDS1366.1	1q25.2	2012-06-29	2012-06-29	2011-01-24	ENSG00000121486	ENSG00000121486			16782	protein-coding gene	gene with protein product	"TRM1-like"	611673	"chromosome 1 open reading frame 25", "TRM1 tRNA methyltransferase 1-like"	C1orf25		11318611, 17198746	Standard	NM_030934		Approved		uc001grf.4	Q7Z2T5	OTTHUMG00000035389	ENST00000367506.5:c.1717A>T	chr1.hg19:g.185094118T>A	ENSP00000356476:p.Ser573Cys	125.0	0.0	.		112.0	42.0	.	NM_030934	Q5TEN0|Q6ZMX0|Q8IWH5|Q8NC68|Q9BZQ1	Missense_Mutation	SNP	ENST00000367506.5	hg19	CCDS1366.1	.	.	.	.	.	.	.	.	.	.	T	18.22	3.575763	0.65878	.	.	ENSG00000121486	ENST00000367506;ENST00000458395	.	.	.	4.79	4.79	0.61399	.	0.178960	0.64402	D	0.000016	T	0.44829	0.1312	N	0.08118	0	0.80722	D	1	D	0.56287	0.975	P	0.53689	0.732	T	0.49818	-0.8899	9	0.38643	T	0.18	-18.1595	14.6174	0.68558	0.0:0.0:0.0:1.0	.	573	Q7Z2T5	TRM1L_HUMAN	C	573;197	.	ENSP00000356476:S573C	S	-	1	0	TRMT1L	183360741	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	6.348000	0.73009	1.935000	0.56089	0.477000	0.44152	AGT	.	.	.	none		0.358	TRMT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085787.1	NM_030934		A	185094118	T	A	185094118	3	1	209	1	0	0	0	0	1	0	0	0	2036	1609	56	5	500	5	C1orf25	1	185094118	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08	4208565	185094118	64156503	2	12665											
C1orf150	148823	hgsc.bcm.edu	37	chr1	247737622	247737622	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatatgcccttcttaggactTctgttagtaggccttgttcc	7	16	8	10	0	2	0	0	0	2	0	3	1	3	1	3	2	1	3	3	2	5	8			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr1:247737622T>C	ENST00000366488.4	+	5	450	c.346T>C	c.(346-348)Tct>Cct	p.S116P	RP11-978I15.10_ENST00000446347.1_RNA|GCSAML_ENST00000536561.1_Missense_Mutation_p.S96P|GCSAML_ENST00000366491.2_Missense_Mutation_p.S96P|GCSAML_ENST00000527541.1_Missense_Mutation_p.S84P|RP11-978I15.10_ENST00000435333.1_RNA|GCSAML_ENST00000527084.1_Missense_Mutation_p.S84P|GCSAML_ENST00000463359.1_Missense_Mutation_p.S84P|GCSAML_ENST00000366489.1_Missense_Mutation_p.S96P	NM_001281836.1|NM_001281837.1|NM_001281853.1|NM_145278.3	NP_001268765.1|NP_001268766.1|NP_001268782.1|NP_660321.1	Q5JQS6	GSAML_HUMAN	germinal center-associated, signaling and motility-like	116																	TCTTAGGACTTCTGTTAGTAG	0.433																																					p.S116P		Atlas-SNP	.											.	.	.	.	0			c.T346C						PASS	.						154	129	137					1																	247737622		2203	4300	6503	SO:0001583	missense	148823	exon5			AGGACTTCTGTTA	AK126682	CCDS1635.1, CCDS60470.1, CCDS73058.1	1q44	2012-08-23	2012-08-23	2012-08-23	ENSG00000169224	ENSG00000169224			29583	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 150"	C1orf150			Standard	NM_001281834		Approved	FLJ44728	uc001idf.3	Q5JQS6	OTTHUMG00000040648	ENST00000366488.4:c.346T>C	chr1.hg19:g.247737622T>C	ENSP00000355444:p.Ser116Pro	107.0	0.0	.		89.0	36.0	.	NM_145278	B2R4Y5|B3KX46|Q5JQT3	Missense_Mutation	SNP	ENST00000366488.4	hg19	CCDS1635.1	.	.	.	.	.	.	.	.	.	.	T	10.44	1.350166	0.24512	.	.	ENSG00000169224	ENST00000527084;ENST00000527541;ENST00000366491;ENST00000366489;ENST00000463359;ENST00000366488;ENST00000536561	.	.	.	3.91	2.73	0.32206	.	1.484660	0.04639	N	0.405118	T	0.28830	0.0715	L	0.34521	1.04	0.09310	N	1	P	0.47677	0.899	P	0.45099	0.469	T	0.12091	-1.0561	9	0.02654	T	1	-1.0246	7.2357	0.26067	0.0:0.0:0.2272:0.7728	.	116	Q5JQS6	CA150_HUMAN	P	84;84;96;96;84;116;96	.	ENSP00000355444:S116P	S	+	1	0	C1orf150	245804245	0.001000	0.12720	0.001000	0.08648	0.338000	0.28826	0.818000	0.27295	0.638000	0.30545	0.482000	0.46254	TCT	.	.	.	none		0.433	GCSAML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097745.4	NM_145278		C	247737622	T	C	247737622	3	2	209	1	0	0	0	0	1	0	0	0	2006	1783	62	3	364	3	C1orf150	1	247737622	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08	62643504	247737622	1512999	3	12666											
OR2M2	391194	hgsc.bcm.edu	37	chr1	248344277	248344277	+	Frame_Shift_Del	DEL	A	A	-																															gctaaattcttctttctaatAtccatctttttctatgatgt																										TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr1:248344277delA	ENST00000359682.2	+	1	990	c.990delA	c.(988-990)atafs	p.I330fs		NM_001004688.1	NP_001004688.1	Q96R28	OR2M2_HUMAN	olfactory receptor, family 2, subfamily M, member 2	330						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)			TCTTTCTAATATCCATCTTTT	0.318																																					p.I330fs		Atlas-INDEL	.											.	OR2M2	149	.	0			c.989delT						PASS	.						164	175	171					1																	248344277		2203	4300	6503	SO:0001589	frameshift_variant	391194	exon1			.	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.990delA	chr1.hg19:g.248344277delA	ENSP00000352710:p.Ile330fs	201.0	0.0	0		166.0	49.0	0.295181	NM_001004688	A3KFT4	Frame_Shift_Del	DEL	ENST00000359682.2	hg19	CCDS31106.1																																																																																			.	.	.	none		0.318	OR2M2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097356.2	NM_001004688		-	248344277	A	-	248344277	7	5	209	1	0	1	0	1	0	0	0	0	11017	439	16	0	992	0	OR2M2	1	248344277	Frame_Shift_Del	DEL	A	TCGA-IZ-8195-01A-31D-2396-08	606655	248344277	906344	4	12667											
ASAP2	8853	hgsc.bcm.edu	37	chr2	9528579	9528579	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcatcttgcagaatgagactTacggagccctcctgagtggc	9	9	12	11	1	1	3	0	2	1	2	2	5	2	4	2	2	3	2	2	2	2	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr2:9528579T>C	ENST00000281419.3	+	22	2627	c.2287T>C	c.(2287-2289)Tac>Cac	p.Y763H	ASAP2_ENST00000491413.1_3'UTR|ASAP2_ENST00000315273.4_Missense_Mutation_p.Y763H	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	763					positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						GAATGAGACTTACGGAGCCCT	0.597																																					p.Y763H		Atlas-SNP	.											.	ASAP2	91	.	0			c.T2287C						PASS	.						45	50	48					2																	9528579		2203	4300	6503	SO:0001583	missense	8853	exon22			GAGACTTACGGAG	AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2721	protein-coding gene	gene with protein product	"centaurin, beta 3"	603817	"development and differentiation enhancing factor 2"	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.2287T>C	chr2.hg19:g.9528579T>C	ENSP00000281419:p.Tyr763His	92.0	0.0	.		49.0	22.0	.	NM_001135191	D6W4Y8	Missense_Mutation	SNP	ENST00000281419.3	hg19	CCDS1661.1	.	.	.	.	.	.	.	.	.	.	T	19.33	3.806023	0.70682	.	.	ENSG00000151693	ENST00000281419;ENST00000315273	T;T	0.57436	0.41;0.4	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.66137	0.2759	L	0.49778	1.585	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.85130	0.997;0.915	T	0.61724	-0.7004	10	0.23891	T	0.37	.	15.7424	0.77910	0.0:0.0:0.0:1.0	.	763;763	O43150-2;O43150	.;ASAP2_HUMAN	H	763	ENSP00000281419:Y763H;ENSP00000316404:Y763H	ENSP00000281419:Y763H	Y	+	1	0	ASAP2	9446030	1.000000	0.71417	0.081000	0.20488	0.971000	0.66376	7.614000	0.82996	2.118000	0.64928	0.459000	0.35465	TAC	.	.	.	none		0.597	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887		C	9528579	T	C	9528579	3	2	209	1	0	0	0	0	1	0	0	0	1011	1754	61	3	2373	3	ASAP2	2	9528579	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08		9528579	233670794	5	12668											
SLC4A1AP	22950	hgsc.bcm.edu	37	chr2	27888159	27888159	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agatgggttgcacctggggaAtgggtaagaaattaaaattg	14	10	14	3	0	0	2	0	0	0	2	0	3	0	3	1	4	1	3	1	4	5	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr2:27888159A>G	ENST00000326019.6	+	2	1300	c.1018A>G	c.(1018-1020)Atg>Gtg	p.M340V	SUPT7L_ENST00000337768.5_5'Flank|SUPT7L_ENST00000405491.1_5'Flank|SUPT7L_ENST00000406540.1_5'Flank|SUPT7L_ENST00000404798.2_5'Flank|SUPT7L_ENST00000464789.2_5'Flank	NM_018158.2	NP_060628.2	Q9BWU0	NADAP_HUMAN	solute carrier family 4 (anion exchanger), member 1, adaptor protein	340						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)					CACCTGGGGAATGGGTAAGAA	0.388																																					p.M340V		Atlas-SNP	.											.	SLC4A1AP	63	.	0			c.A1018G						PASS	.						133	138	136					2																	27888159		2203	4300	6503	SO:0001583	missense	22950	exon2			TGGGGAATGGGTA		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.1018A>G	chr2.hg19:g.27888159A>G	ENSP00000323837:p.Met340Val	147.0	0.0	.		120.0	56.0	.	NM_018158	A6NJ39|Q4KMT1|Q4KMX0|Q7Z5Q9|Q9NVN2	Missense_Mutation	SNP	ENST00000326019.6	hg19	CCDS33166.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.135945	0.77662	.	.	ENSG00000163798	ENST00000326019	T	0.51574	0.7	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.58921	0.2156	M	0.84948	2.725	0.80722	D	1	P	0.42010	0.768	B	0.43386	0.418	T	0.67821	-0.5571	10	0.72032	D	0.01	-17.2495	15.2303	0.73383	1.0:0.0:0.0:0.0	.	340	Q9BWU0	NADAP_HUMAN	V	340	ENSP00000323837:M340V	ENSP00000323837:M340V	M	+	1	0	SLC4A1AP	27741663	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.617000	0.74210	1.995000	0.58328	0.379000	0.24179	ATG	.	.	.	none		0.388	SLC4A1AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324550.1	NM_018158		G	27888159	A	G	27888159	3	3	209	1	0	0	0	0	1	0	0	0	14666	101	4	3	1024	3	SLC4A1AP	2	27888159	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	18359580	27888159	215311214	6	12669											
GPR75	10936	hgsc.bcm.edu	37	chr2	54080607	54080607	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttggagataacatgtaggcAgagtttgtttcatgatggga	11	14	13	3	0	1	3	1	1	0	2	1	5	1	4	0	3	1	4	0	3	2	5			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr2:54080607A>G	ENST00000394705.2	-	2	1557	c.1287T>C	c.(1285-1287)tcT>tcC	p.S429S	ASB3_ENST00000498475.2_Intron|ASB3_ENST00000406625.2_Intron|GPR75-ASB3_ENST00000352846.3_Intron	NM_006794.3	NP_006785.1	O95800	GPR75_HUMAN	G protein-coupled receptor 75	429					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)			ACATGTAGGCAGAGTTTGTTT	0.448																																					p.S429S		Atlas-SNP	.											.	GPR75	55	.	0			c.T1287C						PASS	.						122	122	122					2																	54080607		2203	4300	6503	SO:0001819	synonymous_variant	10936	exon2			GTAGGCAGAGTTT	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.1287T>C	chr2.hg19:g.54080607A>G		303.0	0.0	.		190.0	49.0	.	NM_006794	B2RC02|Q6NWR2	Silent	SNP	ENST00000394705.2	hg19	CCDS1849.1																																																																																			.	.	.	none		0.448	GPR75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251403.2			G	54080607	A	G	54080607	2	3	209	1	0	0	0	0	0	0	0	1	6715	175	7	3		3	GPR75	2	54080607	Silent	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	26192448	54080607	189118766	7	12670											
USP39	10713	hgsc.bcm.edu	37	chr2	85875075	85875075	+	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	gacaggcaaatggtatgaatTacaagacctccaggtgactg	14	8	11	8	0	0	3	0	2	0	1	1	4	1	3	2	3	1	2	2	3	5	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr2:85875075T>G	ENST00000323701.6	+	12	1596	c.1586T>G	c.(1585-1587)tTa>tGa	p.L529*	USP39_ENST00000409766.3_Missense_Mutation_p.Y484D|USP39_ENST00000450066.2_Nonsense_Mutation_p.L426*|USP39_ENST00000409470.1_Nonsense_Mutation_p.L529*|USP39_ENST00000459775.1_3'UTR|USP39_ENST00000409025.1_Intron	NM_006590.3	NP_006581.2	Q53GS9	SNUT2_HUMAN	ubiquitin specific peptidase 39	529	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						TGGTATGAATTACAAGACCTC	0.478																																					p.L529X		Atlas-SNP	.											.	USP39	33	.	0			c.T1586G						PASS	.						98	91	93					2																	85875075		2203	4300	6503	SO:0001587	stop_gained	10713	exon12			ATGAATTACAAGA	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.1586T>G	chr2.hg19:g.85875075T>G	ENSP00000312981:p.Leu529*	100.0	0.0	.		102.0	44.0	.	NM_001256725	A8K086|B3KM40|B4DHT4|D6W5L4|G5E9H0|Q6NX47|Q96RK9|Q9BV89|Q9H381|Q9P050|Q9Y310	Nonsense_Mutation	SNP	ENST00000323701.6	hg19	CCDS33234.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	37|37	6.533352|6.533352	0.97641|0.97641	.|.	.|.	ENSG00000168883|ENSG00000168883	ENST00000450066;ENST00000409268;ENST00000409470;ENST00000323701|ENST00000409766	.|T	.|0.19105	.|2.17	5.93|5.93	5.93|5.93	0.95920|0.95920	.|.	0.065227|.	0.56097|.	D|.	0.000040|.	.|T	.|0.21145	.|0.0509	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|B	.|0.21905	.|0.062	.|B	.|0.21360	.|0.034	.|T	.|0.16129	.|-1.0413	.|7	0.14252|0.87932	T|D	0.57|0	-7.4979|-7.4979	14.3391|14.3391	0.66614|0.66614	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|484	.|G5E9H0	.|.	X|D	426;466;529;529|484	.|ENSP00000386803:Y484D	ENSP00000312981:L529X|ENSP00000386803:Y484D	L|Y	+|+	2|1	0|0	USP39|USP39	85728586|85728586	1.000000|1.000000	0.71417|0.71417	0.977000|0.977000	0.42913|0.42913	0.995000|0.995000	0.86356|0.86356	7.252000|7.252000	0.78309|0.78309	2.265000|2.265000	0.75225|0.75225	0.533000|0.533000	0.62120|0.62120	TTA|TAC	.	.	.	none		0.478	USP39-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329892.1	NM_006590		G	85875075	T	G	85875075	4	3	209	1	0	0	0	0	0	1	0	0	17082	1764	61	5	1632	5	USP39	2	85875075	Nonsense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08	31794468	85875075	157324298	8	12671											
MBD5	55777	hgsc.bcm.edu	37	chr2	149248040	149248040	+	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	gaattgatacattatagaccAaggacgttcaatgttggcga	14	11	10	6	2	1	2	1	1	0	1	1	5	1	3	1	2	1	2	1	2	6	6			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr2:149248040A>C	ENST00000407073.1	+	12	5137	c.4140A>C	c.(4138-4140)ccA>ccC	p.P1380P	MBD5_ENST00000404807.1_Silent_p.P1613P	NM_018328.4	NP_060798.2	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	1380					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)		ATTATAGACCAAGGACGTTCA	0.453																																					p.P1380P		Atlas-SNP	.											.	MBD5	164	.	0			c.A4140C						PASS	.						77	78	78					2																	149248040		2203	4300	6503	SO:0001819	synonymous_variant	55777	exon12			TAGACCAAGGACG	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.4140A>C	chr2.hg19:g.149248040A>C		150.0	0.0	.		109.0	51.0	.	NM_018328	A5HMQ4|A7E2B1|Q53SR1|Q9NUV6	Silent	SNP	ENST00000407073.1	hg19	CCDS33302.1																																																																																			.	.	.	none		0.453	MBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318111.2			C	149248040	A	C	149248040	2	2	209	1	0	0	0	0	0	0	0	1	9354	117	5	5		5	MBD5	2	149248040	Silent	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	63372965	149248040	93951333	9	12672											
PAX3	5077	hgsc.bcm.edu	37	chr2	223066673	223066673	+	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	caaggcttactttgtccataCtgcccatattggtagcctgt	8	14	8	11	0	0	0	0	0	0	0	1	0	1	0	3	2	4	2	3	2	5	6			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr2:223066673C>T	ENST00000350526.4	-	8	1546	c.1410G>A	c.(1408-1410)caG>caA	p.Q470Q	PAX3_ENST00000392069.2_Silent_p.Q470Q|PAX3_ENST00000464706.1_5'Flank|PAX3_ENST00000344493.4_Intron|PAX3_ENST00000336840.6_Intron|PAX3_ENST00000409551.3_Silent_p.Q469Q|PAX3_ENST00000392070.2_Silent_p.Q470Q	NM_181457.3	NP_852122.1	P23760	PAX3_HUMAN	paired box 3	470					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|mammary gland specification (GO:0060594)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of somitogenesis (GO:0014807)|sensory perception of sound (GO:0007605)|spinal cord association neuron differentiation (GO:0021527)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)		PAX3/NCOA2(4)|PAX3/NCOA1(8)|PAX3/FOXO1(749)	NS(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(13)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	38		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TTTGTCCATACTGCCCATATT	0.468			T	"FOXO1A, NCOA1"	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome																														p.Q470Q		Atlas-SNP	.		Dom	yes		2	2q35	5077	paired box gene 3	yes	M	.	PAX3	106	.	0			c.G1410A						PASS	.						99	93	95					2																	223066673		2203	4300	6503	SO:0001819	synonymous_variant	5077	exon8			TCCATACTGCCCA		CCDS2449.1, CCDS2450.1, CCDS2451.1, CCDS42825.1, CCDS2448.1, CCDS42826.1, CCDS46522.1, CCDS46523.1	2q36.1	2011-06-20	2007-07-12		ENSG00000135903	ENSG00000135903		"Paired boxes", "Homeoboxes / PRD class"	8617	protein-coding gene	gene with protein product		606597	"Waardenburg syndrome 1", "paired box gene 3 (Waardenburg syndrome 1)"	WS1		1347149	Standard	NM_181461		Approved	HUP2	uc002vmt.2	P23760	OTTHUMG00000133157	ENST00000350526.4:c.1410G>A	chr2.hg19:g.223066673C>T		123.0	0.0	.		82.0	8.0	.	NM_181457	G5E9C1|Q16448|Q494Z3|Q494Z4|Q53T90|Q6GSJ9|Q86UQ2|Q86UQ3	Silent	SNP	ENST00000350526.4	hg19	CCDS42826.1																																																																																			.	.	.	none		0.468	PAX3-006	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328670.1			T	223066673	C	T	223066673	2	4	209	1	0	0	0	0	0	0	0	1	11487	564	20	2		2	PAX3	2	223066673	Silent	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	73818633	223066673	20132700	10	12673											
CELSR3	1951	hgsc.bcm.edu	37	chr3	48690562	48690562	+	Missense_Mutation	SNP	A	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	cagtcacctggtccagaaggAgatgggaagcacggcccgag	11	4	15	11	2	1	2	1	0	0	2	2	5	2	3	3	4	1	1	3	4	2	0			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr3:48690562A>C	ENST00000164024.4	-	10	5787	c.5507T>G	c.(5506-5508)cTc>cGc	p.L1836R	CELSR3_ENST00000544264.1_Missense_Mutation_p.L1836R	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	1836	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GTCCAGAAGGAGATGGGAAGC	0.622																																					p.L1836R		Atlas-SNP	.											.	CELSR3	237	.	0			c.T5507G						PASS	.						69	59	62					3																	48690562		2203	4300	6503	SO:0001583	missense	1951	exon10			AGAAGGAGATGGG	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.5507T>G	chr3.hg19:g.48690562A>C	ENSP00000164024:p.Leu1836Arg	153.0	0.0	.		65.0	28.0	.	NM_001407	O75092	Missense_Mutation	SNP	ENST00000164024.4	hg19	CCDS2775.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.699442	0.88830	.	.	ENSG00000008300	ENST00000164024;ENST00000544264	D;D	0.81821	-1.54;-1.54	5.33	5.33	0.75918	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	D	0.88584	0.6476	M	0.70275	2.135	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.97110	0.988;1.0	D	0.88600	0.3149	9	0.45353	T	0.12	.	15.3149	0.74065	1.0:0.0:0.0:0.0	.	1836;1906	Q9NYQ7;Q5Y190	CELR3_HUMAN;.	R	1836	ENSP00000164024:L1836R;ENSP00000445694:L1836R	ENSP00000164024:L1836R	L	-	2	0	CELSR3	48665566	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	8.549000	0.90672	2.026000	0.59711	0.460000	0.39030	CTC	.	.	.	none		0.622	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		C	48690562	A	C	48690562	3	2	209	1	0	0	0	0	1	0	0	0	3225	304	11	5	4535	5	CELSR3	3	48690562	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08		48690562	149331868	11	12674											
COL6A6	131873	hgsc.bcm.edu	37	chr3	130292932	130292932	+	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	tgatgtcagcctcaacagagTgcgaataggagcggcccagt	11	7	13	10	2	2	2	2	1	0	1	2	4	2	3	2	2	4	0	2	2	3	1			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr3:130292932T>A	ENST00000358511.6	+	7	3141	c.3110T>A	c.(3109-3111)gTg>gAg	p.V1037E	COL6A6_ENST00000453409.2_Missense_Mutation_p.V1037E	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1037	Nonhelical region.|VWFA 6. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular 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						CTCAACAGAGTGCGAATAGGA	0.418																																					p.V1037E		Atlas-SNP	.											.	COL6A6	497	.	0			c.T3110A						PASS	.						67	62	64					3																	130292932		1868	4100	5968	SO:0001583	missense	131873	exon7			ACAGAGTGCGAAT	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.3110T>A	chr3.hg19:g.130292932T>A	ENSP00000351310:p.Val1037Glu	65.0	0.0	.		41.0	20.0	.	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	hg19	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	T	15.98	2.993314	0.54041	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	D;D	0.85171	-1.95;-1.95	5.15	3.99	0.46301	von Willebrand factor, type A (3);	0.000000	0.52532	D	0.000074	D	0.92596	0.7648	M	0.92784	3.345	0.38839	D	0.956029	D	0.58268	0.982	P	0.62740	0.906	D	0.93390	0.6751	10	0.66056	D	0.02	.	10.6799	0.45809	0.0:0.0762:0.0:0.9238	.	1037	A6NMZ7	CO6A6_HUMAN	E	1037	ENSP00000351310:V1037E;ENSP00000399236:V1037E	ENSP00000351310:V1037E	V	+	2	0	COL6A6	131775622	0.928000	0.31464	0.677000	0.29947	0.260000	0.26232	3.286000	0.51724	0.919000	0.36945	0.459000	0.35465	GTG	.	.	.	none		0.418	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		A	130292932	T	A	130292932	3	1	209	1	0	0	0	0	1	0	0	0	3705	1696	59	5	3136	5	COL6A6	3	130292932	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08	81602370	130292932	67729498	12	12675											
LRPAP1	4043	hgsc.bcm.edu	37	chr4	3519768	3519768	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgggcactcaccagcctcAgtgctgtagccctggtggct	5	8	14	14	1	2	0	2	0	0	0	2	0	2	0	3	4	3	4	3	4	1	1			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr4:3519768A>G	ENST00000500728.2	-	5	890	c.744T>C	c.(742-744)acT>acC	p.T248T	LRPAP1_ENST00000296325.5_5'UTR	NM_002337.3	NP_002328.1	P30533	AMRP_HUMAN	low density lipoprotein receptor-related protein associated protein 1	248	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)		CACCAGCCTCAGTGCTGTAGC	0.657																																					p.T248T		Atlas-SNP	.											.	LRPAP1	29	.	0			c.T744C						PASS	.						40	37	38					4																	3519768		2203	4300	6503	SO:0001819	synonymous_variant	4043	exon5			AGCCTCAGTGCTG		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.744T>C	chr4.hg19:g.3519768A>G		66.0	0.0	.		41.0	13.0	.	NM_002337	D3DVR9|Q2M310|Q53HQ3|Q53HS6	Silent	SNP	ENST00000500728.2	hg19	CCDS3371.1																																																																																			.	.	.	none		0.657	LRPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206659.4			G	3519768	A	G	3519768	2	3	209	1	0	0	0	0	0	0	0	1	8971	175	7	3		3	LRPAP1	4	3519768	Silent	SNP	A	TCGA-IZ-8195-01A-31D-2396-08		3519768	187634508	13	12676											
TBC1D19	55296	hgsc.bcm.edu	37	chr4	26737100	26737100	+	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	ttatcccttttcatggatttTcaatgtatggtaagttgggc	8	18	9	6	0	2	0	2	0	0	0	3	1	3	1	1	3	0	3	1	3	4	8			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr4:26737100T>A	ENST00000264866.4	+	16	1386	c.1108T>A	c.(1108-1110)Tca>Aca	p.S370T	TBC1D19_ENST00000511789.1_Missense_Mutation_p.S305T	NM_018317.2	NP_060787.2	Q8N5T2	TBC19_HUMAN	TBC1 domain family, member 19	370	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			breast(4)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	17		Breast(46;0.0503)				TCATGGATTTTCAATGTATGG	0.264																																					p.S370T		Atlas-SNP	.											.	TBC1D19	53	.	0			c.T1108A						PASS	.						40	36	38					4																	26737100		2186	4257	6443	SO:0001583	missense	55296	exon16			GGATTTTCAATGT	AK001944	CCDS3439.1, CCDS75115.1	4p15.2	2008-02-05			ENSG00000109680	ENSG00000109680			25624	protein-coding gene	gene with protein product							Standard	XM_006713967		Approved	FLJ11082	uc003gsf.4	Q8N5T2	OTTHUMG00000097797	ENST00000264866.4:c.1108T>A	chr4.hg19:g.26737100T>A	ENSP00000264866:p.Ser370Thr	15.0	0.0	.		22.0	7.0	.	NM_018317	B9A6M0|Q9NUX1	Missense_Mutation	SNP	ENST00000264866.4	hg19	CCDS3439.1	.	.	.	.	.	.	.	.	.	.	T	7.982	0.751339	0.15778	.	.	ENSG00000109680	ENST00000264866;ENST00000511789	T;T	0.12361	2.69;2.69	5.7	5.7	0.88788	Rab-GAP/TBC domain (3);	0.000000	0.85682	D	0.000000	T	0.21801	0.0525	L	0.31065	0.9	0.80722	D	1	B;D;D	0.53885	0.013;0.963;0.963	B;D;D	0.69824	0.02;0.966;0.966	T	0.01879	-1.1255	10	0.02654	T	1	-10.0854	15.9517	0.79843	0.0:0.0:0.0:1.0	.	305;370;370	B9A6M0;A8K0R6;Q8N5T2	.;.;TBC19_HUMAN	T	370;305	ENSP00000264866:S370T;ENSP00000425569:S305T	ENSP00000264866:S370T	S	+	1	0	TBC1D19	26346198	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.742000	0.74843	2.172000	0.68678	0.519000	0.50382	TCA	.	.	.	none		0.264	TBC1D19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215052.2	NM_018317		A	26737100	T	A	26737100	3	1	209	1	0	0	0	0	1	0	0	0	15619	1783	62	5	1170	5	TBC1D19	4	26737100	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08	23217332	26737100	164417176	14	12677											
AFF1	4299	hgsc.bcm.edu	37	chr4	88029381	88029381	+	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	cagagtcagaaagcaccagtGactcagacagttcctcagac	14	6	9	12	0	3	5	3	1	0	4	4	5	4	5	2	0	1	2	2	0	1	1			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr4:88029381G>T	ENST00000307808.6	+	10	1846	c.1426G>T	c.(1426-1428)Gac>Tac	p.D476Y	AFF1_ENST00000395146.4_Missense_Mutation_p.D483Y|AFF1_ENST00000544085.1_Missense_Mutation_p.D114Y	NM_005935.2	NP_005926.1	P51825	AFF1_HUMAN	AF4/FMR2 family, member 1	476					positive regulation of transcription, DNA-templated (GO:0045893)	transcription elongation factor complex (GO:0008023)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(2)	3		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		AAGCACCAGTGACTCAGACAG	0.512																																					p.D483Y		Atlas-SNP	.											.	AFF1	102	.	0			c.G1447T						PASS	.						114	104	108					4																	88029381		2203	4300	6503	SO:0001583	missense	4299	exon11			ACCAGTGACTCAG	L22179	CCDS3616.1, CCDS54775.1	4q21.3	2009-08-04	2005-06-27	2005-06-27	ENSG00000172493	ENSG00000172493			7135	protein-coding gene	gene with protein product		159557	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 2", "pre-B-cell monocytic leukemia partner 1"	PBM1, MLLT2		7689231, 1423625, 8353274	Standard	NM_005935		Approved	AF-4, AF4	uc011ccz.2	P51825	OTTHUMG00000130603	ENST00000307808.6:c.1426G>T	chr4.hg19:g.88029381G>T	ENSP00000305689:p.Asp476Tyr	94.0	0.0	.		64.0	24.0	.	NM_001166693	B4DTU1|E9PBM3	Missense_Mutation	SNP	ENST00000307808.6	hg19	CCDS3616.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.164359	0.78339	.	.	ENSG00000172493	ENST00000395146;ENST00000307808;ENST00000511722;ENST00000544085;ENST00000514970	T;T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22;-0.22	5.5	5.5	0.81552	.	0.131246	0.52532	D	0.000065	T	0.80319	0.4601	L	0.59436	1.845	0.54753	D	0.999987	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.72338	0.977;0.977;0.977	T	0.80761	-0.1238	10	0.66056	D	0.02	-14.424	19.7664	0.96346	0.0:0.0:1.0:0.0	.	483;476;476	E9PBM3;Q14C88;P51825	.;.;AFF1_HUMAN	Y	483;476;114;114;167	ENSP00000378578:D483Y;ENSP00000305689:D476Y;ENSP00000424766:D114Y;ENSP00000440843:D114Y;ENSP00000424881:D167Y	ENSP00000305689:D476Y	D	+	1	0	AFF1	88248405	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.723000	0.91458	2.735000	0.93741	0.655000	0.94253	GAC	.	.	.	none		0.512	AFF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253053.3	NM_005935		T	88029381	G	T	88029381	3	4	209	1	0	0	0	0	1	0	0	0	356	1290	45	4	1506	4	AFF1	4	88029381	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	61292281	88029381	103124895	15	12678											
SEC24B	10427	hgsc.bcm.edu	37	chr4	110415933	110415933	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccaacacttcagcctggttAtcagaatgctacagcaccac	12	9	6	14	0	2	1	2	0	0	1	3	1	3	1	3	1	5	3	3	1	4	3			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr4:110415933A>G	ENST00000265175.5	+	6	1464	c.1409A>G	c.(1408-1410)tAt>tGt	p.Y470C	SEC24B_ENST00000504968.2_Missense_Mutation_p.Y501C|SEC24B_ENST00000399100.2_Missense_Mutation_p.Y435C	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B	470					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)		CAGCCTGGTTATCAGAATGCT	0.473																																					p.Y470C		Atlas-SNP	.											.	SEC24B	186	.	0			c.A1409G						PASS	.						116	117	117					4																	110415933		2080	4262	6342	SO:0001583	missense	10427	exon6			CTGGTTATCAGAA	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.1409A>G	chr4.hg19:g.110415933A>G	ENSP00000265175:p.Tyr470Cys	188.0	0.0	.		144.0	59.0	.	NM_006323	B7ZKM8|B7ZKN4|Q0VG08	Missense_Mutation	SNP	ENST00000265175.5	hg19	CCDS47124.1	.	.	.	.	.	.	.	.	.	.	A	19.06	3.754236	0.69648	.	.	ENSG00000138802	ENST00000504968;ENST00000399100;ENST00000265175	T;T;T	0.23754	1.89;1.89;1.89	5.47	5.47	0.80525	.	.	.	.	.	T	0.48943	0.1528	M	0.65975	2.015	0.54753	D	0.999987	D;P;D;D;D	0.89917	0.997;0.951;1.0;0.998;1.0	D;P;D;D;D	0.81914	0.926;0.759;0.995;0.947;0.995	T	0.50849	-0.8779	9	0.72032	D	0.01	2.3658	13.7816	0.63085	1.0:0.0:0.0:0.0	.	385;69;501;435;470	B4DTM6;B4E2E1;B7ZKM8;O95487-2;O95487	.;.;.;.;SC24B_HUMAN	C	501;435;470	ENSP00000428564:Y501C;ENSP00000382051:Y435C;ENSP00000265175:Y470C	ENSP00000265175:Y470C	Y	+	2	0	SEC24B	110635382	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	6.401000	0.73256	2.064000	0.61679	0.533000	0.62120	TAT	.	.	.	none		0.473	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364693.2			G	110415933	A	G	110415933	3	3	209	1	0	0	0	0	1	0	0	0	14008	449	16	3	1431	3	SEC24B	4	110415933	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	22386552	110415933	80738343	16	12679											
TRIM2	23321	hgsc.bcm.edu	37	chr4	154215496	154215496	+	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	gctcttcagttcatctctgaAatcattcatcagttaaccaa	12	14	4	11	0	7	1	5	1	2	0	8	1	7	1	1	0	1	3	1	0	3	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr4:154215496A>T	ENST00000437508.2	+	5	765	c.564A>T	c.(562-564)gaA>gaT	p.E188D	TRIM2_ENST00000494872.1_3'UTR|TRIM2_ENST00000338700.5_Missense_Mutation_p.E215D	NM_001130067.1	NP_001123539.1	Q9C040	TRIM2_HUMAN	tripartite motif containing 2	188					cell death (GO:0008219)|regulation of neuron apoptotic process (GO:0043523)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)	19	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)		TCATCTCTGAAATCATTCATC	0.413																																					p.E215D		Atlas-SNP	.											.	TRIM2	105	.	0			c.A645T						PASS	.						108	103	104					4																	154215496		2203	4300	6503	SO:0001583	missense	23321	exon5			CTCTGAAATCATT	AF220018	CCDS3781.2, CCDS47147.1	4q31.3	2013-01-09	2011-01-25		ENSG00000109654	ENSG00000109654		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	15974	protein-coding gene	gene with protein product		614141	"tripartite motif-containing 2"			9628581, 11331580	Standard	NM_015271		Approved	KIAA0517, RNF86	uc003inh.2	Q9C040	OTTHUMG00000155991	ENST00000437508.2:c.564A>T	chr4.hg19:g.154215496A>T	ENSP00000415812:p.Glu188Asp	113.0	0.0	.		83.0	33.0	.	NM_015271	D3DP09|O60272|Q9BSI9|Q9UFZ1	Missense_Mutation	SNP	ENST00000437508.2	hg19	CCDS47147.1	.	.	.	.	.	.	.	.	.	.	A	14.02	2.411858	0.42817	.	.	ENSG00000109654	ENST00000437508;ENST00000338700;ENST00000433687	T;T;T	0.71222	-0.54;-0.55;-0.23	6.17	5.0	0.66597	B-box, C-terminal (1);	0.041315	0.85682	D	0.000000	T	0.57829	0.2080	L	0.34521	1.04	0.54753	D	0.999982	B;B	0.12013	0.005;0.005	B;B	0.10450	0.005;0.005	T	0.50693	-0.8798	10	0.17369	T	0.5	-3.329	12.1877	0.54250	0.9342:0.0:0.0658:0.0	.	215;188	D3DP09;Q9C040	.;TRIM2_HUMAN	D	188;215;102	ENSP00000415812:E188D;ENSP00000339659:E215D;ENSP00000400375:E102D	ENSP00000339659:E215D	E	+	3	2	TRIM2	154434946	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	3.959000	0.56744	1.166000	0.42689	0.533000	0.62120	GAA	.	.	.	none		0.413	TRIM2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342652.1			T	154215496	A	T	154215496	3	4	209	1	0	0	0	0	1	0	0	0	16506	11	1	5	663	5	TRIM2	4	154215496	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	43799563	154215496	36938780	17	12680											
DCHS2	54798	hgsc.bcm.edu	37	chr4	155225827	155225827	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaaacaaacttaccaattaTgtgatattcaacagctctgt	16	12	4	9	0	2	1	1	1	1	0	2	1	2	1	1	0	5	1	1	0	7	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr4:155225827T>C	ENST00000357232.4	-	17	4233	c.4234A>G	c.(4234-4236)Ata>Gta	p.I1412V		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1412	Cadherin 12. {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)		TTACCAATTATGTGATATTCA	0.418																																					p.I1412V		Atlas-SNP	.											.	DCHS2	594	.	0			c.A4234G						PASS	.						59	58	59					4																	155225827		2203	4300	6503	SO:0001583	missense	54798	exon17			CAATTATGTGATA	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.4234A>G	chr4.hg19:g.155225827T>C	ENSP00000349768:p.Ile1412Val	55.0	0.0	.		48.0	23.0	.	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	hg19	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	T	7.389	0.630312	0.14257	.	.	ENSG00000197410	ENST00000357232	T	0.58797	0.31	5.09	3.91	0.45181	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.69160	0.3080	M	0.74258	2.255	0.80722	D	1	D	0.57899	0.981	P	0.58077	0.832	T	0.70784	-0.4778	10	0.56958	D	0.05	.	10.979	0.47483	0.0:0.074:0.0:0.926	.	1412	Q6V1P9	PCD23_HUMAN	V	1412	ENSP00000349768:I1412V	ENSP00000349768:I1412V	I	-	1	0	DCHS2	155445277	0.984000	0.35163	0.546000	0.28166	0.036000	0.12997	2.011000	0.40922	0.883000	0.36040	0.460000	0.39030	ATA	.	.	.	none		0.418	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		C	155225827	T	C	155225827	3	2	209	1	0	0	0	0	1	0	0	0	4290	1464	51	3	4552	3	DCHS2	4	155225827	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08	1010331	155225827	35928449	18	12681											
FAT1	2195	hgsc.bcm.edu	37	chr4	187539116	187539116	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtctctcttttcatggtcaAgttcctttaaagttgtaatc	8	19	6	8	0	4	0	2	0	2	0	7	0	5	0	1	1	0	3	1	1	4	7			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr4:187539116A>G	ENST00000441802.2	-	10	8833	c.8624T>C	c.(8623-8625)cTt>cCt	p.L2875P		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2875	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						TTCATGGTCAAGTTCCTTTAA	0.418										HNSCC(5;0.00058)																											p.L2875P	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T8624C						PASS	.						175	154	161					4																	187539116		1930	4152	6082	SO:0001583	missense	2195	exon10			TGGTCAAGTTCCT	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.8624T>C	chr4.hg19:g.187539116A>G	ENSP00000406229:p.Leu2875Pro	100.0	0.0	.		67.0	26.0	.	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	hg19	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	A	18.14	3.557734	0.65425	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.75154	-0.91	4.86	4.86	0.63082	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.90256	0.6953	H	0.96269	3.795	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.93285	0.6663	10	0.87932	D	0	.	14.9179	0.70812	1.0:0.0:0.0:0.0	.	2875	Q14517	FAT1_HUMAN	P	2875;2877	ENSP00000406229:L2875P	ENSP00000260147:L2877P	L	-	2	0	FAT1	187776110	1.000000	0.71417	0.993000	0.49108	0.998000	0.95712	9.139000	0.94554	2.167000	0.68274	0.528000	0.53228	CTT	.	.	.	none		0.418	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		G	187539116	A	G	187539116	3	3	209	1	0	0	0	0	1	0	0	0	5696	72	3	3	5214	3	FAT1	4	187539116	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	32313289	187539116	3615160	19	12682											
SLC6A19	340024	hgsc.bcm.edu	37	chr5	1219640	1219640	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcctcatctgcctggggacaTtcctcattggcttcatcttc	5	14	8	14	0	5	0	3	0	2	0	7	1	6	1	3	3	1	1	3	3	0	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr5:1219640T>C	ENST00000304460.10	+	10	1455	c.1399T>C	c.(1399-1401)Ttc>Ctc	p.F467L		NM_001003841.2	NP_001003841.1	Q695T7	S6A19_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 19	467					amino acid transport (GO:0006865)|ion transport (GO:0006811)|response to nutrient (GO:0007584)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|neutral amino acid transmembrane transporter activity (GO:0015175)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(25)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			CCTGGGGACATTCCTCATTGG	0.627																																					p.F467L		Atlas-SNP	.											.	SLC6A19	99	.	0			c.T1399C						PASS	.						140	118	125					5																	1219640		2203	4300	6503	SO:0001583	missense	340024	exon10			GGGACATTCCTCA	AK096054	CCDS34130.1	5p15	2013-07-19			ENSG00000174358	ENSG00000174358		"Solute carriers"	27960	protein-coding gene	gene with protein product	"Hartnup disease"	608893					Standard	NM_001003841		Approved		uc003jbw.4	Q695T7	OTTHUMG00000161636	ENST00000304460.10:c.1399T>C	chr5.hg19:g.1219640T>C	ENSP00000305302:p.Phe467Leu	81.0	0.0	.		51.0	20.0	.	NM_001003841	A8K446	Missense_Mutation	SNP	ENST00000304460.10	hg19	CCDS34130.1	.	.	.	.	.	.	.	.	.	.	T	8.371	0.835267	0.16820	.	.	ENSG00000174358	ENST00000304460	T	0.76316	-1.01	4.83	4.83	0.62350	.	0.341281	0.33691	N	0.004644	T	0.79311	0.4424	M	0.83603	2.65	0.09310	N	1	B	0.12630	0.006	B	0.17722	0.019	T	0.70128	-0.4957	10	0.41790	T	0.15	.	14.3784	0.66895	0.0:0.0:0.0:1.0	.	467	Q695T7	S6A19_HUMAN	L	467	ENSP00000305302:F467L	ENSP00000305302:F467L	F	+	1	0	SLC6A19	1272640	0.950000	0.32346	0.052000	0.19188	0.038000	0.13279	3.934000	0.56553	1.801000	0.52704	0.391000	0.25812	TTC	.	.	.	none		0.627	SLC6A19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365557.1	XM_291120		C	1219640	T	C	1219640	3	2	209	1	0	0	0	0	1	0	0	0	14695	1493	52	3	1437	3	SLC6A19	5	1219640	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08		1219640	179695620	20	12683											
TRIO	7204	hgsc.bcm.edu	37	chr5	14497016	14497016	+	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	catcttggcacacagcactcCgtttaaggaaaaaatctgag	14	9	8	10	1	2	1	0	1	2	0	3	2	3	2	1	2	1	3	1	2	4	3			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr5:14497016C>A	ENST00000344204.4	+	50	7933	c.7909C>A	c.(7909-7911)Cgt>Agt	p.R2637S	TRIO_ENST00000537187.1_Missense_Mutation_p.R2461S|TRIO_ENST00000344135.5_Missense_Mutation_p.R136S	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	2637					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)					CACAGCACTCCGTTTAAGGAA	0.448																																					p.R2637S		Atlas-SNP	.											.	TRIO	305	.	0			c.C7909A						PASS	.						121	112	115					5																	14497016		2203	4300	6503	SO:0001583	missense	7204	exon50			GCACTCCGTTTAA	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.7909C>A	chr5.hg19:g.14497016C>A	ENSP00000339299:p.Arg2637Ser	100.0	0.0	.		80.0	35.0	.	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	hg19	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.915239	0.92178	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000513206;ENST00000344135	T;T;T	0.71341	-0.56;-0.36;-0.53	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	D	0.82282	0.5003	M	0.65498	2.005	0.36519	D	0.87004	D	0.89917	1.0	D	0.79784	0.993	D	0.84372	0.0544	10	0.37606	T	0.19	.	16.8938	0.86094	0.0:1.0:0.0:0.0	.	2637	O75962	TRIO_HUMAN	S	2637;2461;2324;136	ENSP00000339299:R2637S;ENSP00000446348:R2461S;ENSP00000339291:R136S	ENSP00000339291:R136S	R	+	1	0	TRIO	14550016	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.596000	0.67570	2.414000	0.81942	0.655000	0.94253	CGT	.	.	.	none		0.448	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		A	14497016	C	A	14497016	3	1	209	1	0	0	0	0	1	0	0	0	16564	652	23	4	8107	4	TRIO	5	14497016	Missense_Mutation	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	13277376	14497016	166418244	21	12684											
POLK	51426	hgsc.bcm.edu	37	chr5	74892358	74892358	+	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	atgagaatttggaaatatcaGagaattcagatgactgtcag	16	11	10	4	0	3	4	3	2	0	3	3	7	3	5	0	1	0	0	0	1	4	3			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr5:74892358G>C	ENST00000241436.4	+	13	2012	c.1840G>C	c.(1840-1842)Gag>Cag	p.E614Q	POLK_ENST00000352007.5_Missense_Mutation_p.E416Q|POLK_ENST00000506928.1_3'UTR|POLK_ENST00000380481.3_Missense_Mutation_p.E524Q|POLK_ENST00000504026.1_Intron|CTC-366B18.2_ENST00000511329.1_RNA|POLK_ENST00000508526.1_Missense_Mutation_p.E416Q	NM_016218.2	NP_057302.1	Q9UBT6	POLK_HUMAN	polymerase (DNA directed) kappa	614					DNA repair (GO:0006281)|nucleotide-excision repair, DNA gap filling (GO:0006297)	nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)			endometrium(1)|kidney(4)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	27		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;2.9e-54)|all cancers(79;1.27e-42)		GGAAATATCAGAGAATTCAGA	0.368								DNA polymerases (catalytic subunits)																													p.E614Q		Atlas-SNP	.											.	POLK	123	.	0			c.G1840C						PASS	.						106	108	107					5																	74892358		2203	4300	6503	SO:0001583	missense	51426	exon13			ATATCAGAGAATT	AB027564	CCDS4030.1	5q13	2012-05-18			ENSG00000122008	ENSG00000122008		"DNA polymerases"	9183	protein-coding gene	gene with protein product	"polymerase (DNA-directed) kappa", "DINB protein", "DNA polymerase kappa"	605650		DINB1		10887153, 10518552	Standard	NM_016218		Approved	POLQ, DINP	uc003kdw.3	Q9UBT6	OTTHUMG00000102107	ENST00000241436.4:c.1840G>C	chr5.hg19:g.74892358G>C	ENSP00000241436:p.Glu614Gln	215.0	0.0	.		171.0	76.0	.	NM_016218	B2RBD2|Q5Q9G5|Q5Q9G6|Q5Q9G7|Q5Q9G8|Q86VJ8|Q8IZY0|Q8IZY1|Q8NB30|Q96L01|Q96Q86|Q96Q87|Q9UHC5	Missense_Mutation	SNP	ENST00000241436.4	hg19	CCDS4030.1	.	.	.	.	.	.	.	.	.	.	G	16.10	3.027552	0.54683	.	.	ENSG00000122008	ENST00000241436;ENST00000352007;ENST00000508526;ENST00000380481	T;T;T;T	0.58358	1.15;0.34;0.34;1.13	5.15	4.28	0.50868	.	0.893154	0.09986	N	0.730347	T	0.50480	0.1618	M	0.65498	2.005	0.22888	N	0.998601	B;B	0.28419	0.211;0.098	B;B	0.23275	0.045;0.021	T	0.43909	-0.9362	10	0.48119	T	0.1	-2.8619	9.5091	0.39065	0.0815:0.1534:0.7651:0.0	.	416;614	Q9UBT6-3;Q9UBT6	.;POLK_HUMAN	Q	614;416;416;524	ENSP00000241436:E614Q;ENSP00000342256:E416Q;ENSP00000426853:E416Q;ENSP00000369848:E524Q	ENSP00000241436:E614Q	E	+	1	0	POLK	74928114	0.025000	0.19082	0.097000	0.21041	0.978000	0.69477	0.423000	0.21313	1.148000	0.42385	0.655000	0.94253	GAG	.	.	.	none		0.368	POLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219945.3	NM_016218		C	74892358	G	C	74892358	3	2	209	1	0	0	0	0	1	0	0	0	12211	943	33	4	1886	4	POLK	5	74892358	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	60395342	74892358	106022902	22	12685											
MSH3	4437	hgsc.bcm.edu	37	chr5	80040402	80040402	+	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	tttgggagacggaagttaaaGaagtgggtgacccagccact	12	8	14	7	1	0	3	0	1	0	2	0	5	0	4	2	3	1	1	2	3	4	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr5:80040402G>A	ENST00000265081.6	+	12	1811	c.1731G>A	c.(1729-1731)aaG>aaA	p.K577K	MSH3_ENST00000512258.1_3'UTR	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	577					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)		GGAAGTTAAAGAAGTGGGTGA	0.338								Mismatch excision repair (MMR)																													p.K577K	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											.	MSH3	129	.	0			c.G1731A						PASS	.						22	25	24					5																	80040402		2200	4295	6495	SO:0001819	synonymous_variant	4437	exon12			GTTAAAGAAGTGG	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.1731G>A	chr5.hg19:g.80040402G>A		53.0	0.0	.		52.0	20.0	.	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Silent	SNP	ENST00000265081.6	hg19	CCDS34195.1																																																																																			.	.	.	none		0.338	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		A	80040402	G	A	80040402	2	1	209	1	0	0	0	0	0	0	0	1	9878	933	33	2		2	MSH3	5	80040402	Silent	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	5148044	80040402	100874858	23	12686											
DMXL1	1657	hgsc.bcm.edu	37	chr5	118500212	118500213	+	Frame_Shift_Ins	INS	-	-	AGTCATTT																															tttcttcaggcctgtctacaINSagtcattttgcttgggcatt																										TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr5:118500212_118500213insAGTCATTT	ENST00000311085.8	+	20	4793_4794	c.4713_4714insAGTCATTT	c.(4714-4716)agtfs	p.-1572fs	DMXL1_ENST00000539542.1_Frame_Shift_Ins_p.-1572fs	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1											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)		GCCTGTCTACAAGTCATTTTGC	0.342																																					p.T1571fs		Atlas-INDEL	.											.	DMXL1	268	.	0			c.4713_4714insAGTCATTT						PASS	.																																			SO:0001589	frameshift_variant	1657	exon20			.	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.4714_4721dupAGTCATTT	chr5.hg19:g.118500213_118500220dupAGTCATTT	ENSP00000309690:p.Ser1572fs	107.0	0.0	0		62.0	20.0	0.322581	NM_005509		Frame_Shift_Ins	INS	ENST00000311085.8	hg19	CCDS4125.1																																																																																			.	.	.	none		0.342	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		AGTCATTT	118500213	-	AGTCATTT	118500212	7	5	209	1	0	1	1	0	0	0	0	0	4596	117	5	0	4791	0	DMXL1	5	118500212	Frame_Shift_Ins	INS	-	TCGA-IZ-8195-01A-31D-2396-08	38459810	118500212	62415048	24	12687											
SOX30	11063	hgsc.bcm.edu	37	chr5	157075894	157075894	+	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	ctgtccttactgaagggagtAtctggtatgcctacatgaca	10	12	10	9	0	1	2	0	2	1	0	2	3	2	3	2	2	3	2	2	2	5	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr5:157075894A>T	ENST00000265007.6	-	2	1319	c.978T>A	c.(976-978)gaT>gaA	p.D326E	SOX30_ENST00000519442.1_Missense_Mutation_p.D21E|SOX30_ENST00000311371.5_Missense_Mutation_p.D326E	NM_178424.1	NP_848511.1	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30	326					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)			TGAAGGGAGTATCTGGTATGC	0.428																																					p.D326E	Esophageal Squamous(31;525 799 19355 21125 41744)	Atlas-SNP	.											.	SOX30	67	.	0			c.T978A						PASS	.						126	111	116					5																	157075894		2203	4300	6503	SO:0001583	missense	11063	exon2			GGGAGTATCTGGT	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.978T>A	chr5.hg19:g.157075894A>T	ENSP00000265007:p.Asp326Glu	126.0	0.0	.		106.0	41.0	.	NM_178424	O94995|Q8IYX6	Missense_Mutation	SNP	ENST00000265007.6	hg19	CCDS4339.1	.	.	.	.	.	.	.	.	.	.	A	18.28	3.588194	0.66105	.	.	ENSG00000039600	ENST00000311371;ENST00000265007;ENST00000519442	D;D;D	0.97976	-4.64;-4.3;-4.57	5.72	-2.31	0.06765	High mobility group, superfamily (1);	0.152930	0.45867	D	0.000328	D	0.95793	0.8631	N	0.08118	0	0.30089	N	0.808462	D;D;D	0.76494	0.999;0.99;0.983	D;D;P	0.78314	0.991;0.933;0.858	D	0.92745	0.6211	10	0.66056	D	0.02	.	14.1885	0.65623	0.5913:0.0:0.4087:0.0	.	21;326;326	B4DXW7;O94993-2;O94993	.;.;SOX30_HUMAN	E	326;326;21	ENSP00000309343:D326E;ENSP00000265007:D326E;ENSP00000427984:D21E	ENSP00000265007:D326E	D	-	3	2	SOX30	157008472	0.992000	0.36948	0.971000	0.41717	0.971000	0.66376	0.280000	0.18790	-0.732000	0.04856	-1.477000	0.00996	GAT	.	.	.	none		0.428	SOX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252571.2	NM_007017		T	157075894	A	T	157075894	3	4	209	1	0	0	0	0	1	0	0	0	14965	446	16	5	1299	5	SOX30	5	157075894	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	38575682	157075894	23839366	25	12688											
MAML1	9794	hgsc.bcm.edu	37	chr5	179193185	179193185	+	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	agggcccaggaggggcctcaGagctgtcctctgcccaccag	7	5	14	15	0	2	1	1	0	1	1	3	2	3	2	5	4	2	1	5	4	0	0			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr5:179193185G>T	ENST00000292599.3	+	2	1437	c.1174G>T	c.(1174-1176)Gag>Tag	p.E392*	MAML1_ENST00000503050.1_3'UTR	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)											central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGGGGCCTCAGAGCTGTCCTC	0.657																																					p.E392X		Atlas-SNP	.											.	MAML1	118	.	0			c.G1174T						PASS	.						42	46	45					5																	179193185		2203	4300	6503	SO:0001587	stop_gained	9794	exon2			GCCTCAGAGCTGT	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.1174G>T	chr5.hg19:g.179193185G>T	ENSP00000292599:p.Glu392*	153.0	0.0	.		104.0	28.0	.	NM_014757		Nonsense_Mutation	SNP	ENST00000292599.3	hg19	CCDS34315.1	.	.	.	.	.	.	.	.	.	.	G	39	7.386389	0.98252	.	.	ENSG00000161021	ENST00000292599;ENST00000376951	.	.	.	4.88	4.88	0.63580	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	-25.6288	18.0213	0.89255	0.0:0.0:1.0:0.0	.	.	.	.	X	392;429	.	ENSP00000292599:E392X	E	+	1	0	MAML1	179125791	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	9.169000	0.94788	2.250000	0.74265	0.305000	0.20034	GAG	.	.	.	none		0.657	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757		T	179193185	G	T	179193185	4	4	209	1	0	0	0	0	0	1	0	0	9212	943	33	4	1180	4	MAML1	5	179193185	Nonsense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	22117291	179193185	1722075	26	12689											
TBC1D9B	23061	hgsc.bcm.edu	37	chr5	179320371	179320371	+	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	ggaacatggagaagaagagcTcctggtcgcgggtgtccaca	11	6	15	9	2	0	3	0	0	0	3	3	5	2	4	2	4	2	1	2	4	3	0			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr5:179320371T>A	ENST00000356834.3	-	5	711	c.674A>T	c.(673-675)gAg>gTg	p.E225V	TBC1D9B_ENST00000355235.3_Missense_Mutation_p.E225V	NM_198868.2	NP_942568.2	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	225						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)			GAAGAAGAGCTCCTGGTCGCG	0.607																																					p.E225V		Atlas-SNP	.											.	TBC1D9B	157	.	0			c.A674T						PASS	.						86	76	79					5																	179320371		2203	4300	6503	SO:0001583	missense	23061	exon5			AAGAGCTCCTGGT	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.674A>T	chr5.hg19:g.179320371T>A	ENSP00000349291:p.Glu225Val	106.0	0.0	.		69.0	24.0	.	NM_198868	D3DWQ5|D3DWQ6|O75163|Q53EY0|Q6MZI2|Q96H49	Missense_Mutation	SNP	ENST00000356834.3	hg19	CCDS43408.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.196607	0.79015	.	.	ENSG00000197226	ENST00000356834;ENST00000355235	T;T	0.11712	2.75;2.84	4.57	4.57	0.56435	.	0.000000	0.85682	D	0.000000	T	0.26304	0.0642	L	0.58810	1.83	0.80722	D	1	D;D;P	0.69078	0.997;0.995;0.79	P;P;B	0.62649	0.87;0.905;0.441	T	0.01087	-1.1456	10	0.59425	D	0.04	-27.504	14.075	0.64885	0.0:0.0:0.0:1.0	.	225;225;225	A1L3A9;Q66K14-2;Q66K14	.;.;TBC9B_HUMAN	V	225	ENSP00000349291:E225V;ENSP00000347375:E225V	ENSP00000347375:E225V	E	-	2	0	TBC1D9B	179252977	1.000000	0.71417	1.000000	0.80357	0.716000	0.41182	7.791000	0.85805	1.929000	0.55896	0.260000	0.18958	GAG	.	.	.	none		0.607	TBC1D9B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253501.3	NM_015043		A	179320371	T	A	179320371	3	1	209	1	0	0	0	0	1	0	0	0	15640	1551	54	5	3150	5	TBC1D9B	5	179320371	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08	127186	179320371	1594889	27	12690											
TBC1D7	51256	hgsc.bcm.edu	37	chr6	13307966	13307966	+	Missense_Mutation	SNP	A	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	tccagattcaagtattgttcAaacgcttttggctaaagatt	12	15	7	7	1	2	2	2	0	0	2	3	2	3	2	1	1	1	4	1	1	5	8			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr6:13307966A>C	ENST00000379300.3	-	6	774	c.531T>G	c.(529-531)ttT>ttG	p.F177L	TBC1D7_ENST00000379307.2_Missense_Mutation_p.F150L|TBC1D7_ENST00000356436.4_Missense_Mutation_p.F177L|TBC1D7_ENST00000607658.1_Missense_Mutation_p.F150L|TBC1D7_ENST00000607532.1_5'UTR|TBC1D7_ENST00000343141.4_Missense_Mutation_p.F131L	NM_001143964.2|NM_016495.4	NP_001137436.1|NP_057579.1	Q9P0N9	TBCD7_HUMAN	TBC1 domain family, member 7	177	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				activation of Rho GTPase activity (GO:0032862)|negative regulation of cilium assembly (GO:1902018)|negative regulation of TOR signaling (GO:0032007)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of Rab GTPase activity (GO:0032851)|response to growth factor (GO:0070848)	ciliary basal body (GO:0036064)|cytoplasmic vesicle (GO:0031410)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(1)|large_intestine(4)|lung(14)|ovary(1)|stomach(1)	22	Breast(50;0.0296)|Ovarian(93;0.0339)	all_hematologic(90;0.135)	Epithelial(50;0.0784)|BRCA - Breast invasive adenocarcinoma(129;0.13)|all cancers(50;0.21)			AGTATTGTTCAAACGCTTTTG	0.398																																					p.F177L		Atlas-SNP	.											.	TBC1D7	34	.	0			c.T531G						PASS	.						74	70	71					6																	13307966		2203	4300	6503	SO:0001583	missense	51256	exon6			TTGTTCAAACGCT	AF151073	CCDS4523.1, CCDS47376.1, CCDS58995.1	6p23	2013-07-10			ENSG00000145979	ENSG00000145979			21066	protein-coding gene	gene with protein product		612655				11042152, 17646400	Standard	XM_005249163		Approved	dJ257A7.3, FLJ32666	uc003nan.3	Q9P0N9	OTTHUMG00000014272	ENST00000379300.3:c.531T>G	chr6.hg19:g.13307966A>C	ENSP00000368602:p.Phe177Leu	116.0	0.0	.		85.0	26.0	.	NM_001143965	E7EV96|Q2TU37|Q53F44|Q5SZL7|Q86VM8|Q96MB8	Missense_Mutation	SNP	ENST00000379300.3	hg19	CCDS4523.1	.	.	.	.	.	.	.	.	.	.	A	6.453	0.451648	0.12223	.	.	ENSG00000145979	ENST00000334971;ENST00000356436;ENST00000379300;ENST00000379307;ENST00000343141;ENST00000452989;ENST00000450347;ENST00000422136;ENST00000446018;ENST00000420456	T;T;T;T;T;T;T;T;T	0.26660	2.42;2.42;2.42;2.42;2.42;2.42;2.42;2.42;1.72	6.17	1.03	0.20045	Rab-GAP/TBC domain (3);	0.105355	0.64402	D	0.000003	T	0.02970	0.0088	N	0.11154	0.105	0.48236	D	0.999617	B;B;B;B	0.09022	0.0;0.0;0.0;0.002	B;B;B;B	0.08055	0.0;0.003;0.001;0.002	T	0.35450	-0.9788	10	0.08837	T	0.75	-16.1625	5.7639	0.18215	0.5313:0.2616:0.2071:0.0	.	131;150;150;177	Q2TU37;Q5SZL5;Q9P0N9-2;Q9P0N9	.;.;.;TBCD7_HUMAN	L	118;177;177;150;131;150;150;177;150;150	ENSP00000348813:F177L;ENSP00000368602:F177L;ENSP00000368609:F150L;ENSP00000343100:F131L;ENSP00000414292:F150L;ENSP00000404680:F150L;ENSP00000394425:F177L;ENSP00000417005:F150L;ENSP00000412102:F150L	ENSP00000334212:F118L	F	-	3	2	TBC1D7	13415945	0.997000	0.39634	1.000000	0.80357	0.901000	0.52897	0.600000	0.24104	0.165000	0.19558	0.533000	0.62120	TTT	.	.	.	none		0.398	TBC1D7-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039896.2	NM_016495		C	13307966	A	C	13307966	3	2	209	1	0	0	0	0	1	0	0	0	15636	127	5	5	362	5	TBC1D7	6	13307966	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08		13307966	157807101	28	12691											
AIM1	202	hgsc.bcm.edu	37	chr6	106968989	106968991	+	In_Frame_Del	DEL	TCT	TCT	-																															ttgaacaaagaacagtcaaaTcttctgcccgacaactcctt																										TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr6:106968989_106968991delTCT	ENST00000369066.3	+	2	3169_3171	c.2682_2684delTCT	c.(2680-2685)aatctt>aat	p.L896del		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)		AACAGTCAAATCTTCTGCCCGAC	0.463																																					p.894_895del		Atlas-INDEL	.											.	AIM1	161	.	0			c.2681_2683del						PASS	.																																			SO:0001651	inframe_deletion	202	exon2			.	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"suppression of tumorigenicity 4", "beta-gamma crystallin domain containing 1"	601797	"suppression of tumorigenicity 4 (malignant melanoma)"	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.2682_2684delTCT	chr6.hg19:g.106968992_106968994delTCT	ENSP00000358062:p.Leu896del	196.0	0.0	0		148.0	55.0	0.371622	NM_001624	Q6P2P0|Q9BTM3	In_Frame_Del	DEL	ENST00000369066.3	hg19	CCDS34506.1																																																																																			.	.	.	none		0.463	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			-	106968991	TCT	-	106968989	7	5	209	1	0	1	0	1	0	0	0	0	430	1432	50	0	2688	0	AIM1	6	106968989	In_Frame_Del	DEL	TCT	TCGA-IZ-8195-01A-31D-2396-08	93661023	106968989	64146078	29	12692											
AHI1	54806	hgsc.bcm.edu	37	chr6	135644423	135644423	+	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	tccgcgatggatggttagttCatctgatcgattcgctgtgt	6	15	12	8	4	2	1	1	1	1	0	5	4	3	2	1	2	0	3	1	2	1	3			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr6:135644423C>A	ENST00000367800.4	-	23	3421	c.3205G>T	c.(3205-3207)Gaa>Taa	p.E1069*	AHI1_ENST00000457866.2_Nonsense_Mutation_p.E1069*|AHI1_ENST00000417892.2_Nonsense_Mutation_p.E423*	NM_001134830.1	NP_001128302.1	Q8N157	AHI1_HUMAN	Abelson helper integration site 1	1069	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cellular protein localization (GO:0034613)|central nervous system development (GO:0007417)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|cloaca development (GO:0035844)|heart looping (GO:0001947)|hindbrain development (GO:0030902)|Kupffer's vesicle development (GO:0070121)|left/right axis specification (GO:0070986)|morphogenesis of a polarized epithelium (GO:0001738)|negative regulation of apoptotic process (GO:0043066)|otic vesicle development (GO:0071599)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of polarized epithelial cell differentiation (GO:0030862)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pronephric duct morphogenesis (GO:0039023)|pronephric nephron tubule morphogenesis (GO:0039008)|protein localization to organelle (GO:0033365)|regulation of behavior (GO:0050795)|retina layer formation (GO:0010842)|specification of axis polarity (GO:0065001)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vesicle targeting (GO:0006903)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|nonmotile primary cilium (GO:0031513)|photoreceptor outer segment (GO:0001750)|primary cilium (GO:0072372)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)	37	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		ATGGTTAGTTCATCTGATCGA	0.438																																					p.E1069X		Atlas-SNP	.											.	AHI1	81	.	0			c.G3205T						PASS	.						99	91	93					6																	135644423		1940	4132	6072	SO:0001587	stop_gained	54806	exon24			TTAGTTCATCTGA	AJ459824	CCDS47483.1, CCDS47484.1	6q23.2	2013-01-10	2005-11-29		ENSG00000135541	ENSG00000135541		"WD repeat domain containing"	21575	protein-coding gene	gene with protein product	"Jouberin"	608894	"Abelson helper integration site"			15060101, 16240161	Standard	NM_017651		Approved	FLJ20069, ORF1, JBTS3	uc003qgj.3	Q8N157	OTTHUMG00000015631	ENST00000367800.4:c.3205G>T	chr6.hg19:g.135644423C>A	ENSP00000356774:p.Glu1069*	45.0	0.0	.		27.0	13.0	.	NM_017651	E1P584|Q4FD35|Q504T3|Q5TCP9|Q6P098|Q6PIT6|Q8NDX0|Q9H0H2	Nonsense_Mutation	SNP	ENST00000367800.4	hg19	CCDS47483.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	39|39	7.418512|7.418512	0.98272|0.98272	.|.	.|.	ENSG00000135541|ENSG00000135541	ENST00000367800;ENST00000457866;ENST00000417892;ENST00000265602|ENST00000367799	.|.	.|.	.|.	6.06|6.06	6.06|6.06	0.98353|0.98353	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.72606	.|0.3481	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.68503	.|-0.5391	.|4	0.52906|.	T|.	0.07|.	-28.0524|-28.0524	20.6208|20.6208	0.99490|0.99490	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|I	1069;1069;423;1069|568	.|.	ENSP00000265602:E1069X|.	E|M	-|-	1|3	0|0	AHI1|AHI1	135686116|135686116	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.487000|7.487000	0.81328|0.81328	2.882000|2.882000	0.98803|0.98803	0.655000|0.655000	0.94253|0.94253	GAA|ATG	.	.	.	none		0.438	AHI1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391948.1	NM_017651		A	135644423	C	A	135644423	4	1	209	1	0	0	0	0	0	1	0	0	413	835	29	4	405	4	AHI1	6	135644423	Nonsense_Mutation	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	28675434	135644423	35470644	30	12693											
REPS1	85021	hgsc.bcm.edu	37	chr6	139251190	139251190	+	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	acttgcttggaggagcttcaGcaggagagcctgaataacct	11	9	12	9	0	1	2	1	1	0	1	1	5	1	4	2	3	5	3	2	3	2	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr6:139251190G>C	ENST00000450536.2	-	9	1755	c.1181C>G	c.(1180-1182)gCt>gGt	p.A394G	REPS1_ENST00000409812.2_Missense_Mutation_p.A394G|REPS1_ENST00000258062.5_Missense_Mutation_p.A394G|REPS1_ENST00000415951.2_Missense_Mutation_p.A394G|REPS1_ENST00000367663.4_Missense_Mutation_p.A394G			Q96D71	REPS1_HUMAN	RALBP1 associated Eps domain containing 1	394					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)		AGGAGCTTCAGCAGGAGAGCC	0.418																																					p.A394G		Atlas-SNP	.											.	REPS1	58	.	0			c.C1181G						PASS	.						146	123	131					6																	139251190		2203	4300	6503	SO:0001583	missense	85021	exon9			GCTTCAGCAGGAG		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.1181C>G	chr6.hg19:g.139251190G>C	ENSP00000392065:p.Ala394Gly	120.0	0.0	.		107.0	49.0	.	NM_001128617	B7ZBZ8|B7ZBZ9|B7ZC00|J3KP76|Q5JWJ5|Q5JWJ6|Q5JWJ7|Q8NDR7|Q8WU62|Q9BXY9	Missense_Mutation	SNP	ENST00000450536.2	hg19		.	.	.	.	.	.	.	.	.	.	G	14.17	2.454329	0.43634	.	.	ENSG00000135597	ENST00000450536;ENST00000367663;ENST00000529597;ENST00000409812;ENST00000258062;ENST00000415951;ENST00000367668	T;T;T;T;T;T	0.34667	1.37;1.35;1.37;1.37;1.37;1.36	5.72	5.72	0.89469	.	0.168464	0.53938	D	0.000060	T	0.17534	0.0421	L	0.36672	1.1	0.46749	D	0.999188	B;B;P;B;B	0.38504	0.005;0.007;0.634;0.002;0.361	B;B;B;B;B	0.33620	0.009;0.006;0.167;0.002;0.081	T	0.02691	-1.1123	10	0.24483	T	0.36	-10.4052	18.069	0.89399	0.0:0.0:1.0:0.0	.	394;342;394;394;394	Q96D71-3;B2R7D3;Q96D71-2;Q96D71;E9PMG1	.;.;.;REPS1_HUMAN;.	G	394;394;380;394;394;394;342	ENSP00000392065:A394G;ENSP00000356635:A394G;ENSP00000434251:A380G;ENSP00000386699:A394G;ENSP00000258062:A394G;ENSP00000397941:A394G	ENSP00000258062:A394G	A	-	2	0	REPS1	139292883	1.000000	0.71417	0.986000	0.45419	0.985000	0.73830	7.353000	0.79414	2.700000	0.92200	0.563000	0.77884	GCT	.	.	.	none		0.418	REPS1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000042447.3			C	139251190	G	C	139251190	3	2	209	1	0	0	0	0	1	0	0	0	13241	971	34	4	1257	4	REPS1	6	139251190	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	3606767	139251190	31863877	31	12694											
HOXA3	3200	hgsc.bcm.edu	37	chr7	27147884	27147884	+	Missense_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	cgcccctgccgccgtgtagcGcttctgtgggggtggcgggg	1	8	19	13	5	1	0	0	0	1	0	1	0	1	0	4	5	2	2	4	5	1	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr7:27147884G>A	ENST00000396352.4	-	3	1181	c.982C>T	c.(982-984)Cgc>Tgc	p.R328C	HOXA3_ENST00000317201.2_Missense_Mutation_p.R328C|HOXA-AS2_ENST00000518088.1_RNA|HOXA3_ENST00000521401.1_5'Flank	NM_030661.4	NP_109377.1	O43365	HXA3_HUMAN	homeobox A3	328					angiogenesis (GO:0001525)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|lung(18)|skin(1)	29						GCCGTGTAGCGCTTCTGTGGG	0.726																																					p.R328C	Esophageal Squamous(136;1368 1743 5685 7935 50360)	Atlas-SNP	.											.	HOXA3	62	.	0			c.C982T						PASS	.						6	8	7					7																	27147884		2050	4012	6062	SO:0001583	missense	3200	exon3			TGTAGCGCTTCTG		CCDS5404.1	7p15.2	2011-06-20	2005-12-22		ENSG00000105997	ENSG00000105997		"Homeoboxes / ANTP class : HOXL subclass"	5104	protein-coding gene	gene with protein product		142954	"homeo box A3"	HOX1E, HOX1		1973146, 1358459	Standard	XM_005249730		Approved		uc011jzl.2	O43365	OTTHUMG00000023209	ENST00000396352.4:c.982C>T	chr7.hg19:g.27147884G>A	ENSP00000379640:p.Arg328Cys	26.0	0.0	.		19.0	5.0	.	NM_030661	A4D181	Missense_Mutation	SNP	ENST00000396352.4	hg19	CCDS5404.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.104964	0.37145	.	.	ENSG00000105997	ENST00000396352;ENST00000317201;ENST00000396350	D;D	0.86769	-2.17;-2.17	5.68	4.8	0.61643	.	0.046305	0.85682	D	0.000000	D	0.89842	0.6832	M	0.79123	2.44	0.80722	D	1	D	0.62365	0.991	P	0.50231	0.635	D	0.90827	0.4713	10	0.87932	D	0	.	13.1397	0.59428	0.0:0.0:0.5656:0.4344	.	328	O43365	HXA3_HUMAN	C	328;328;170	ENSP00000379640:R328C;ENSP00000324884:R328C	ENSP00000324884:R328C	R	-	1	0	HOXA3	27114409	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	3.812000	0.55628	1.395000	0.46643	0.655000	0.94253	CGC	.	.	.	none		0.726	HOXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358708.2			A	27147884	G	A	27147884	3	1	209	1	0	0	0	0	1	0	0	0	7300	1087	38	1	353	1	HOXA3	7	27147884	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08		27147884	131990779	32	12695											
ABCA13	154664	hgsc.bcm.edu	37	chr7	48411809	48411809	+	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	ccagtgatccatttcctggcCtggttcctggagaacatggc	7	11	11	12	0	0	2	0	1	0	1	3	3	3	2	5	4	1	1	5	4	1	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr7:48411809C>A	ENST00000435803.1	+	33	10872	c.10848C>A	c.(10846-10848)gcC>gcA	p.A3616A		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	3616					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						ATTTCCTGGCCTGGTTCCTGG	0.463																																					p.A3616A		Atlas-SNP	.											.	ABCA13	1192	.	0			c.C10848A						PASS	.						178	170	173					7																	48411809		2026	4187	6213	SO:0001819	synonymous_variant	154664	exon33			CCTGGCCTGGTTC	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.10848C>A	chr7.hg19:g.48411809C>A		98.0	0.0	.		84.0	32.0	.	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	hg19	CCDS47584.1																																																																																			.	.	.	none		0.463	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48411809	C	A	48411809	2	1	209	1	0	0	0	0	0	0	0	1	31	668	24	4		4	ABCA13	7	48411809	Silent	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	21263925	48411809	110726854	33	12696											
TMEM139	135932	hgsc.bcm.edu	37	chr7	142983611	142983611	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agttggaccaaccaccccccTacagcactgttgtgataccc	10	8	7	16	0	0	1	0	1	0	0	0	2	0	2	6	1	4	3	6	1	3	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr7:142983611T>C	ENST00000359333.3	+	3	853	c.340T>C	c.(340-342)Tac>Cac	p.Y114H	TMEM139_ENST00000471161.1_3'UTR|TMEM139_ENST00000410004.1_Missense_Mutation_p.Y114H|TMEM139_ENST00000409102.1_Missense_Mutation_p.Y114H|TMEM139_ENST00000409541.1_Missense_Mutation_p.Y114H|CASP2_ENST00000310447.5_5'Flank|AC073342.12_ENST00000446192.1_RNA|CASP2_ENST00000392925.2_5'Flank|AC073342.12_ENST00000427392.1_RNA|TMEM139_ENST00000409244.1_Missense_Mutation_p.Y114H	NM_001242775.2|NM_001282876.1|NM_001282877.1	NP_001229704.1|NP_001269805.1|NP_001269806.1	Q8IV31	TM139_HUMAN	transmembrane protein 139	114						integral component of membrane (GO:0016021)				endometrium(1)|lung(4)|ovary(1)|prostate(1)	7	Melanoma(164;0.059)					ACCACCCCCCTACAGCACTGT	0.577																																					p.Y114H		Atlas-SNP	.											.	TMEM139	18	.	0			c.T340C						PASS	.						72	77	75					7																	142983611		2203	4300	6503	SO:0001583	missense	135932	exon4			CCCCCCTACAGCA	AK075067	CCDS5878.1	7q34	2006-03-17			ENSG00000178826	ENSG00000178826			22058	protein-coding gene	gene with protein product							Standard	NM_153345		Approved	FLJ90586	uc003wck.4	Q8IV31	OTTHUMG00000152652	ENST00000359333.3:c.340T>C	chr7.hg19:g.142983611T>C	ENSP00000352284:p.Tyr114His	207.0	0.0	.		148.0	46.0	.	NM_001242773	B2RCL5|D3DXD4|Q6ZME2|Q8NC22|Q96AU8	Missense_Mutation	SNP	ENST00000359333.3	hg19	CCDS5878.1	.	.	.	.	.	.	.	.	.	.	T	17.45	3.391665	0.62066	.	.	ENSG00000178826	ENST00000409102;ENST00000359333;ENST00000409244;ENST00000409541;ENST00000410004	.	.	.	5.1	5.1	0.69264	.	0.000000	0.56097	D	0.000028	T	0.72423	0.3458	M	0.65498	2.005	0.36979	D	0.894208	D	0.89917	1.0	D	0.91635	0.999	T	0.79264	-0.1875	9	0.87932	D	0	-14.1344	11.6253	0.51142	0.0:0.0:0.0:1.0	.	114	Q8IV31	TM139_HUMAN	H	114	.	ENSP00000352284:Y114H	Y	+	1	0	TMEM139	142693733	0.999000	0.42202	0.998000	0.56505	0.511000	0.34104	3.868000	0.56055	2.076000	0.62316	0.456000	0.33151	TAC	.	.	.	none		0.577	TMEM139-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327145.1	NM_153345		C	142983611	T	C	142983611	3	2	209	1	0	0	0	0	1	0	0	0	16066	1522	53	3	346	3	TMEM139	7	142983611	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08	94571802	142983611	16155052	34	12697											
CA8	767	hgsc.bcm.edu	37	chr8	61192348	61192348	+	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	gagaggcggacatccaacagCgaggggtcatacctagcctc	11	5	13	12	2	1	1	1	0	0	1	3	4	2	2	3	4	4	0	3	4	3	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr8:61192348C>T	ENST00000317995.4	-	2	456	c.192G>A	c.(190-192)tcG>tcA	p.S64S		NM_004056.4	NP_004047.3	P35219	CAH8_HUMAN	carbonic anhydrase VIII	64					one-carbon metabolic process (GO:0006730)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasm (GO:0005737)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(6)|prostate(2)|skin(1)	16		all_cancers(86;0.172)|all_epithelial(80;0.0383)|all_lung(136;0.0413)|Lung NSC(129;0.0474)			Zonisamide(DB00909)	CATCCAACAGCGAGGGGTCAT	0.473																																					p.S64S		Atlas-SNP	.											.	CA8	31	.	0			c.G192A						PASS	.						92	86	88					8																	61192348		2203	4300	6503	SO:0001819	synonymous_variant	767	exon2			CAACAGCGAGGGG	L04656	CCDS6174.1	8q12.1	2012-08-21			ENSG00000178538	ENSG00000178538		"Carbonic anhydrases"	1382	protein-coding gene	gene with protein product		114815		CALS		17219437	Standard	NM_004056		Approved	CARP	uc003xtz.1	P35219	OTTHUMG00000165325	ENST00000317995.4:c.192G>A	chr8.hg19:g.61192348C>T		104.0	0.0	.		103.0	66.0	.	NM_004056	A8K0A5|B3KQZ7|Q32MY2	Silent	SNP	ENST00000317995.4	hg19	CCDS6174.1																																																																																			.	.	.	none		0.473	CA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383445.1			T	61192348	C	T	61192348	2	4	209	1	0	0	0	0	0	0	0	1	2525	755	27	1		1	CA8	8	61192348	Silent	SNP	C	TCGA-IZ-8195-01A-31D-2396-08		61192348	85171674	35	12698											
ZC3H3	23144	hgsc.bcm.edu	37	chr8	144550696	144550696	+	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	gccggatgatggccaggctgCgctgcactgcccggctgcag	5	6	16	14	3	0	1	0	1	0	0	0	2	0	2	3	4	4	5	3	4	0	0			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr8:144550696C>T	ENST00000262577.5	-	7	1992	c.1961G>A	c.(1960-1962)cGc>cAc	p.R654H		NM_015117.2	NP_055932.2	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3	654					mRNA polyadenylation (GO:0006378)|poly(A)+ mRNA export from nucleus (GO:0016973)|regulation of mRNA export from nucleus (GO:0010793)	nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23	all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107)			GGCCAGGCTGCGCTGCACTGC	0.677																																					p.R654H		Atlas-SNP	.											ZC3H3,caecum,carcinoma,0,1	ZC3H3	75	.	0			c.G1961A						PASS	.						24	30	28					8																	144550696		2191	4297	6488	SO:0001583	missense	23144	exon7			AGGCTGCGCTGCA	D63484	CCDS6402.1	8q24.3	2012-07-05	2005-06-02	2005-06-02	ENSG00000014164	ENSG00000014164		"Zinc fingers, CCCH-type domain containing"	28972	protein-coding gene	gene with protein product			"zinc finger CCCH-type domain containing 3"	ZC3HDC3		8590280	Standard	NM_015117		Approved	KIAA0150	uc003yyd.2	Q8IXZ2	OTTHUMG00000165127	ENST00000262577.5:c.1961G>A	chr8.hg19:g.144550696C>T	ENSP00000262577:p.Arg654His	17.0	0.0	.		28.0	2.0	.	NM_015117	Q14163|Q8N4E2|Q9BUS4	Missense_Mutation	SNP	ENST00000262577.5	hg19	CCDS6402.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.864699	0.91511	.	.	ENSG00000014164	ENST00000262577	T	0.04049	3.72	5.01	5.01	0.66863	.	0.000000	0.64402	D	0.000001	T	0.21267	0.0512	M	0.68952	2.095	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.00382	-1.1775	10	0.72032	D	0.01	-20.1301	18.3055	0.90179	0.0:1.0:0.0:0.0	.	654	Q8IXZ2	ZC3H3_HUMAN	H	654	ENSP00000262577:R654H	ENSP00000262577:R654H	R	-	2	0	ZC3H3	144621839	1.000000	0.71417	1.000000	0.80357	0.787000	0.44495	7.212000	0.77941	2.348000	0.79779	0.561000	0.74099	CGC	.	.	.	none		0.677	ZC3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382011.2	NM_015117		T	144550696	C	T	144550696	3	4	209	1	0	0	0	0	1	0	0	0	17581	768	27	1	909	1	ZC3H3	8	144550696	Missense_Mutation	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	83358348	144550696	1813326	36	12699											
GPT	2875	hgsc.bcm.edu	37	chr8	145732311	145732312	+	Frame_Shift_Ins	INS	-	-	A																															ggatgaccattctgccccccINSttggagaaactgcggctgct																										TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr8:145732311_145732312insA	ENST00000528431.1	+	12	1576_1577	c.1419_1420insA	c.(1420-1422)ttgfs	p.L474fs	MFSD3_ENST00000301327.4_5'Flank|GPT_ENST00000394955.2_Frame_Shift_Ins_p.L474fs			P24298	ALAT1_HUMAN	glutamic-pyruvate transaminase (alanine aminotransferase)	474					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-alanine catabolic process (GO:0042853)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	L-alanine:2-oxoglutarate aminotransferase activity (GO:0004021)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(1)|lung(2)|ovary(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)		L-Alanine(DB00160)|Phenelzine(DB00780)	TTCTGCCCCCCTTGGAGAAACT	0.629																																					p.P473fs		Atlas-INDEL	.											.	GPT	31	.	0			c.1419_1420insA						PASS	.																																			SO:0001589	frameshift_variant	2875	exon11			.		CCDS6430.1	8q24.3	2013-09-19			ENSG00000167701	ENSG00000167701	2.6.1.2		4552	protein-coding gene	gene with protein product		138200					Standard	NM_005309		Approved	ALT1, GPT1	uc003zdh.4	P24298	OTTHUMG00000165176	Exception_encountered	chr8.hg19:g.145732311_145732312insA	ENSP00000433586:p.Leu474fs	109.0	0.0	0		109.0	36.0	0.330275	NM_005309	B0YJ18|D3DWM7|P78398|Q93076	Frame_Shift_Ins	INS	ENST00000528431.1	hg19	CCDS6430.1																																																																																			.	.	.	none		0.629	GPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382471.1			A	145732312	-	A	145732311	7	5	209	1	0	1	1	0	0	0	0	0	6744	668	24	0	1461	0	GPT	8	145732311	Frame_Shift_Ins	INS	-	TCGA-IZ-8195-01A-31D-2396-08	1181615	145732311	631711	37	12700											
C9orf5	23731	hgsc.bcm.edu	37	chr9	111853340	111853340	+	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	cgttcctatttcaggccttcGtctgcccagagtaggtgaag	7	12	11	11	2	2	2	1	1	1	1	4	2	3	2	3	2	1	2	3	2	3	5			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr9:111853340G>A	ENST00000374586.3	-	5	1043	c.1012C>T	c.(1012-1014)Cga>Tga	p.R338*		NM_032012.3	NP_114401.2	Q9H330	TM245_HUMAN	transmembrane protein 245	338						integral component of membrane (GO:0016021)											TCAGGCCTTCGTCTGCCCAGA	0.502																																					p.R338X		Atlas-SNP	.											.	.	.	.	0			c.C1012T						PASS	.						102	105	104					9																	111853340		1918	4124	6042	SO:0001587	stop_gained	23731	exon5			GCCTTCGTCTGCC	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.1012C>T	chr9.hg19:g.111853340G>A	ENSP00000363714:p.Arg338*	97.0	0.0	.		85.0	15.0	.	NM_032012	B4DSW7|Q5JTQ5|Q5SS43|Q6ZME3|Q8NDJ5|Q96CG6	Nonsense_Mutation	SNP	ENST00000374586.3	hg19	CCDS43858.1	.	.	.	.	.	.	.	.	.	.	G	36	5.709073	0.96821	.	.	ENSG00000106771	ENST00000374587;ENST00000374586;ENST00000223608	.	.	.	5.68	3.78	0.43462	.	0.612323	0.16965	N	0.192324	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.7849	16.3662	0.83325	0.0:0.2216:0.7784:0.0	.	.	.	.	X	338	.	ENSP00000223608:R338X	R	-	1	2	C9orf5	110893161	1.000000	0.71417	0.646000	0.29493	0.959000	0.62525	3.441000	0.52893	0.708000	0.31955	0.563000	0.77884	CGA	.	.	.	none		0.502	TMEM245-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053587.2	NM_032012		A	111853340	G	A	111853340	4	1	209	1	0	0	0	0	0	1	0	0	2488	1153	40	1	1683	1	C9orf5	9	111853340	Nonsense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08		111853340	29360091	38	12701											
C9orf171	389799	hgsc.bcm.edu	37	chr9	135447853	135447853	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaccgggaagagtgtgccGtgcgccaggggaccctgcgg	6	4	17	14	4	0	1	0	0	0	1	0	3	0	3	5	4	3	0	5	4	1	0			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr9:135447853G>A	ENST00000343036.2	+	7	967	c.919G>A	c.(919-921)Gtg>Atg	p.V307M	C9orf171_ENST00000393216.2_Missense_Mutation_p.V271M	NM_207417.1	NP_997300.1	Q6ZQR2	CI171_HUMAN	chromosome 9 open reading frame 171	307										large_intestine(7)|lung(9)|ovary(4)|prostate(3)	23						AGAGTGTGCCGTGCGCCAGGG	0.602																																					p.V307M		Atlas-SNP	.											.	C9orf171	53	.	0			c.G919A						PASS	.						54	52	53					9																	135447853		2203	4300	6503	SO:0001583	missense	389799	exon7			TGTGCCGTGCGCC	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.919G>A	chr9.hg19:g.135447853G>A	ENSP00000343290:p.Val307Met	84.0	0.0	.		62.0	32.0	.	NM_207417	Q147X1	Missense_Mutation	SNP	ENST00000343036.2	hg19	CCDS6949.1	.	.	.	.	.	.	.	.	.	.	G	18.55	3.648988	0.67358	.	.	ENSG00000188523	ENST00000343036;ENST00000393216	T;T	0.24350	1.87;1.86	5.53	4.62	0.57501	.	0.411149	0.21865	N	0.067979	T	0.34193	0.0889	L	0.36672	1.1	0.21897	N	0.999488	D;D	0.76494	0.995;0.999	P;P	0.60117	0.578;0.869	T	0.07195	-1.0785	10	0.56958	D	0.05	.	10.6586	0.45690	0.0906:0.0:0.9094:0.0	.	271;307	Q6ZQR2-2;Q6ZQR2	.;CI171_HUMAN	M	307;271	ENSP00000343290:V307M;ENSP00000376909:V271M	ENSP00000343290:V307M	V	+	1	0	C9orf171	134437674	0.997000	0.39634	0.952000	0.39060	0.875000	0.50365	3.331000	0.52075	2.617000	0.88574	0.542000	0.68232	GTG	.	.	.	none		0.602	C9orf171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254589.1	NM_207417		A	135447853	G	A	135447853	3	1	209	1	0	0	0	0	1	0	0	0	2472	1145	40	1	945	1	C9orf171	9	135447853	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	23594513	135447853	5765578	39	12702											
GTPBP4	23560	hgsc.bcm.edu	37	chr10	1061760	1061760	+	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	aagaaagcgggaagactctgCtcccccgtcctctgtggccc	8	7	11	15	2	2	2	0	0	2	2	4	3	4	3	4	2	2	1	4	2	3	0			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr10:1061760C>A	ENST00000360803.4	+	16	1758	c.1676C>A	c.(1675-1677)gCt>gAt	p.A559D	GTPBP4_ENST00000545048.1_Missense_Mutation_p.A512D|GTPBP4_ENST00000538293.1_Missense_Mutation_p.A443D	NM_012341.2	NP_036473.2	Q9BZE4	NOG1_HUMAN	GTP binding protein 4	559					GTP catabolic process (GO:0006184)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of collagen binding (GO:0033342)|negative regulation of DNA replication (GO:0008156)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein stabilization (GO:0050821)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|ribosome biogenesis (GO:0042254)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(1)	21		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)		GAAGACTCTGCTCCCCCGTCC	0.552																																					p.A559D		Atlas-SNP	.											.	GTPBP4	57	.	0			c.C1676A						PASS	.						137	124	128					10																	1061760		2203	4300	6503	SO:0001583	missense	23560	exon16			ACTCTGCTCCCCC	AK001548	CCDS31132.1	10p15-p14	2007-07-27			ENSG00000107937	ENSG00000107937			21535	protein-coding gene	gene with protein product	"G protein-binding protein CRFG", " GTP-binding protein"					11316846	Standard	NM_012341		Approved	CRFG, NGB, FLJ10690, FLJ10686, NOG1	uc001ift.3	Q9BZE4	OTTHUMG00000017538	ENST00000360803.4:c.1676C>A	chr10.hg19:g.1061760C>A	ENSP00000354040:p.Ala559Asp	198.0	0.0	.		166.0	55.0	.	NM_012341	B3KMC5|B4DY13|B7Z7A3|O95446|Q5T3R8|Q9NVJ8	Missense_Mutation	SNP	ENST00000360803.4	hg19	CCDS31132.1	.	.	.	.	.	.	.	.	.	.	C	4.232	0.041906	0.08196	.	.	ENSG00000107937	ENST00000360803;ENST00000538293;ENST00000545048	T;T;T	0.32753	1.44;1.45;1.44	5.67	2.86	0.33363	.	0.344788	0.32868	N	0.005550	T	0.13628	0.0330	N	0.14661	0.345	0.34292	D	0.683401	B	0.10296	0.003	B	0.17098	0.017	T	0.20638	-1.0269	10	0.12103	T	0.63	-11.4058	4.131	0.10149	0.2318:0.1869:0.0:0.5813	.	559	Q9BZE4	NOG1_HUMAN	D	559;443;512	ENSP00000354040:A559D;ENSP00000444277:A443D;ENSP00000445473:A512D	ENSP00000354040:A559D	A	+	2	0	GTPBP4	1051760	0.537000	0.26386	0.749000	0.31150	0.005000	0.04900	0.845000	0.27668	0.256000	0.21614	-0.218000	0.12543	GCT	.	.	.	none		0.552	GTPBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046412.1	NM_012341		A	1061760	C	A	1061760	3	1	209	1	0	0	0	0	1	0	0	0	6889	797	28	4	1738	4	GTPBP4	10	1061760	Missense_Mutation	SNP	C	TCGA-IZ-8195-01A-31D-2396-08		1061760	134472987	40	12703											
KLF6	1316	hgsc.bcm.edu	37	chr10	3822362	3822362	+	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	tcggaagtgcctggttaactCatcacttcttgcaaaacgcc	10	11	8	12	2	3	0	2	0	1	0	4	1	3	1	2	2	4	2	2	2	4	3			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr10:3822362C>T	ENST00000497571.1	-	3	996	c.736G>A	c.(736-738)Gag>Aag	p.E246K	KLF6_ENST00000542957.1_Intron|KLF6_ENST00000173785.4_5'UTR	NM_001160124.1|NM_001300.5	NP_001153596.1|NP_001291.3	Q99612	KLF6_HUMAN	Kruppel-like factor 6	246					B cell differentiation (GO:0030183)|cytokine-mediated signaling pathway (GO:0019221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(3)|endometrium(1)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16				Colorectal(1;0.238)		CTGGTTAACTCATCACTTCTT	0.542																																					p.E246K		Atlas-SNP	.											KLF6,colon,carcinoma,0,1	KLF6	38	.	0			c.G736A						PASS	.						222	168	186					10																	3822362		2203	4300	6503	SO:0001583	missense	1316	exon3			TTAACTCATCACT	U51869	CCDS7060.1, CCDS53490.1	10p15	2013-01-08	2004-11-29	2004-12-01	ENSG00000067082	ENSG00000067082		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	2235	protein-coding gene	gene with protein product	"GC-rich binding factor"	602053	"core promoter element binding protein"	BCD1, ST12, COPEB		9503030, 9685731	Standard	NM_001300		Approved	CPBP, GBF, Zf9, PAC1	uc001iha.3	Q99612	OTTHUMG00000017567	ENST00000497571.1:c.736G>A	chr10.hg19:g.3822362C>T	ENSP00000419923:p.Glu246Lys	135.0	0.0	.		77.0	23.0	.	NM_001300	B2RE86|B4DDN0|D3DRR1|F5H3M5|Q5VUT7|Q5VUT8|Q9BT79	Missense_Mutation	SNP	ENST00000497571.1	hg19	CCDS7060.1	.	.	.	.	.	.	.	.	.	.	C	36	5.975022	0.97162	.	.	ENSG00000067082	ENST00000497571	T	0.51071	0.72	5.67	5.67	0.87782	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.053414	0.85682	D	0.000000	T	0.56156	0.1966	N	0.17379	0.485	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.995;0.998	T	0.62234	-0.6897	10	0.87932	D	0	.	18.7705	0.91890	0.0:1.0:0.0:0.0	.	204;246	D3GC14;Q99612	.;KLF6_HUMAN	K	246	ENSP00000419923:E246K	ENSP00000419923:E246K	E	-	1	0	KLF6	3812362	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.702000	0.84576	2.677000	0.91161	0.561000	0.74099	GAG	.	.	.	none		0.542	KLF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046495.1			T	3822362	C	T	3822362	3	4	209	1	0	0	0	0	1	0	0	0	8357	835	29	2	123	2	KLF6	10	3822362	Missense_Mutation	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	2760602	3822362	131712385	41	12704											
KIN	509	hgsc.bcm.edu	37	chr10	7829859	7829859	+	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	1	0	0	0	0	0	0	0	0	ccttggacttgatcctgttgGcgatagccttgggagtaaga	8	12	13	8	1	0	2	0	1	0	1	1	5	1	4	3	3	1	2	3	3	2	6			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr10:7829859G>C	ENST00000356708.7	+	0	0				KIN_ENST00000379562.4_Missense_Mutation_p.A13G|KIN_ENST00000543003.1_5'UTR|ATP5C1_ENST00000541227.1_5'Flank|ATP5C1_ENST00000335698.4_5'Flank|KIN_ENST00000535925.1_Missense_Mutation_p.A13G	NM_001001973.1	NP_001001973.1	P36542	ATPG_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1						ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, catalytic core F(1) (GO:0000275)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)			breast(2)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	16						GATCCTGTTGGCGATAGCCTT	0.612																																					p.A13G	Melanoma(143;1012 1820 16249 30920 33158)	Atlas-SNP	.											.	KIN	39	.	0			c.C38G						PASS	.						108	107	108					10																	7829859		2203	4300	6503	SO:0001631	upstream_gene_variant	22944	exon1			CTGTTGGCGATAG	D16561	CCDS7081.1, CCDS31142.1	10p14	2012-10-12			ENSG00000165629	ENSG00000165629		"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	833	protein-coding gene	gene with protein product		108729		ATP5CL1, ATP5C		8168843, 8227057	Standard	NM_005174		Approved		uc001iju.3	P36542	OTTHUMG00000017639		chr10.hg19:g.7829859G>C	Exception_encountered	203.0	0.0	.		145.0	67.0	.	NM_012311	A8KA31|Q5VYP3|Q6I9V2|Q96AS8	Missense_Mutation	SNP	ENST00000356708.7	hg19	CCDS31142.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.942900	0.73672	.	.	ENSG00000151657	ENST00000535925;ENST00000379562	.	.	.	5.97	5.97	0.96955	.	0.224004	0.45606	D	0.000341	T	0.48714	0.1515	L	0.41236	1.265	0.80722	D	1	P;P	0.40970	0.734;0.734	B;B	0.28991	0.097;0.097	T	0.53387	-0.8446	9	0.52906	T	0.07	-11.2701	20.4301	0.99081	0.0:0.0:1.0:0.0	.	13;13	B4DX32;O60870	.;KIN17_HUMAN	G	13	.	ENSP00000368881:A13G	A	-	2	0	KIN	7869865	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.909000	0.48758	2.834000	0.97654	0.557000	0.71058	GCC	.	.	.	none		0.612	ATP5C1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046708.1	NM_005174		C	7829859	G	C	7829859	1	2	209	0	1	0	0	0	0	0	0	0	8322	1203	42	4		4	KIN	10	7829859	5'Flank	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	4007497	7829859	127704888	42	12705											
MGEA5	10724	hgsc.bcm.edu	37	chr10	103563517	103563517	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actacatcttttctcactccAttcatgtttgatttgtacca	9	18	3	11	0	3	1	2	1	2	0	5	1	4	1	2	0	2	2	2	0	2	7			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr10:103563517A>G	ENST00000361464.3	-	7	1406	c.1011T>C	c.(1009-1011)aaT>aaC	p.N337N	MGEA5_ENST00000439817.1_Silent_p.N337N|MGEA5_ENST00000370094.3_Silent_p.N337N|MGEA5_ENST00000357797.5_Silent_p.N337N	NM_012215.3	NP_036347.1	O60502	OGA_HUMAN	meningioma expressed antigen 5 (hyaluronidase)	337					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)		TTCTCACTCCATTCATGTTTG	0.438																																					p.N337N		Atlas-SNP	.											.	MGEA5	53	.	0			c.T1011C						PASS	.						113	107	109					10																	103563517		2203	4300	6503	SO:0001819	synonymous_variant	10724	exon7			CACTCCATTCATG	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.1011T>C	chr10.hg19:g.103563517A>G		148.0	0.0	.		116.0	9.0	.	NM_001142434	B7WPB9|D3DR79|E9PGF9|O75166|Q86WV0|Q8IV98|Q9BVA5|Q9HAR0	Silent	SNP	ENST00000361464.3	hg19	CCDS7520.1																																																																																			.	.	.	none		0.438	MGEA5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049987.1	NM_012215		G	103563517	A	G	103563517	2	3	209	1	0	0	0	0	0	0	0	1	9562	214	8	3		3	MGEA5	10	103563517	Silent	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	95733658	103563517	31971230	43	12706											
NPS	594857	hgsc.bcm.edu	37	chr10	129347639	129347639	+	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	ttgggaagtccaaaatgattAggtaaaaggctacgtttttc	13	13	10	5	1	0	1	0	1	0	0	2	2	1	2	1	3	1	3	1	3	7	6			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr10:129347639A>G	ENST00000398023.1	+	1	27	c.7A>G	c.(7-9)Agc>Ggc	p.S3G		NM_001030013.1	NP_001025184.1	P0C0P6	NPS_HUMAN	neuropeptide S	3					neuropeptide signaling pathway (GO:0007218)|positive regulation of action potential (GO:0045760)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|visual learning (GO:0008542)	extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|lung(4)	5						CAAAATGATTAGGTAAAAGGC	0.348																																					p.S3G		Atlas-SNP	.											.	NPS	14	.	0			c.A7G						PASS	.						120	114	116					10																	129347639		1824	4084	5908	SO:0001630	splice_region_variant	594857	exon1			ATGATTAGGTAAA	BC148465	CCDS41577.1	10q26.2	2013-02-26			ENSG00000214285	ENSG00000214285		"Endogenous ligands"	33940	protein-coding gene	gene with protein product	"prepro-neuropeptide S"	609513				18181564, 15312648	Standard	NM_001030013		Approved		uc001ljx.1	P0C0P6		ENST00000398023.1:c.8+1A>G	chr10.hg19:g.129347639A>G		48.0	0.0	.		37.0	4.0	.	NM_001030013		Missense_Mutation	SNP	ENST00000398023.1	hg19	CCDS41577.1	.	.	.	.	.	.	.	.	.	.	A	1.347	-0.592491	0.03799	.	.	ENSG00000214285	ENST00000398023	T	0.33216	1.42	5.72	0.828	0.18841	.	0.509696	0.13562	N	0.378760	T	0.14056	0.0340	.	.	.	0.21861	N	0.999501	B	0.14805	0.011	B	0.14578	0.011	T	0.34875	-0.9811	9	0.08599	T	0.76	2.0E-4	9.0261	0.36230	0.7136:0.0:0.2864:0.0	.	3	P0C0P6	NPS_HUMAN	G	3	ENSP00000381105:S3G	ENSP00000381105:S3G	S	+	1	0	NPS	129237629	0.925000	0.31364	0.777000	0.31699	0.054000	0.15201	1.856000	0.39389	-0.032000	0.13758	-0.899000	0.02877	AGC	.	.	.	none		0.348	NPS-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001030013	Missense_Mutation	G	129347639	A	G	129347639	5	3	209	1	0	0	0	0	0	0	1	0	10606	434	15	3	9	3	NPS	10	129347639	Splice_Site	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	25784122	129347639	6187108	44	12707											
DCHS1	8642	hgsc.bcm.edu	37	chr11	6662595	6662595	+	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	tgtgcccacgccgctgccctCttgggcagagatgaagtaca	8	8	12	13	2	1	2	0	1	1	1	1	3	1	2	3	1	3	3	3	1	2	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr11:6662595C>G	ENST00000299441.3	-	2	661	c.250G>C	c.(250-252)Gag>Cag	p.E84Q		NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	84	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCGCTGCCCTCTTGGGCAGAG	0.627																																					p.E84Q		Atlas-SNP	.											.	DCHS1	277	.	0			c.G250C						PASS	.						35	35	35					11																	6662595		2201	4296	6497	SO:0001583	missense	8642	exon2			TGCCCTCTTGGGC	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.250G>C	chr11.hg19:g.6662595C>G	ENSP00000299441:p.Glu84Gln	55.0	0.0	.		49.0	20.0	.	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	hg19	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	C	19.15	3.772553	0.69992	.	.	ENSG00000166341	ENST00000299441	T	0.38401	1.14	5.41	5.41	0.78517	Cadherin (3);Cadherin-like (1);	0.000000	0.47093	D	0.000243	T	0.50103	0.1596	L	0.33245	0.995	0.54753	D	0.999986	D	0.69078	0.997	D	0.75020	0.985	T	0.42344	-0.9457	10	0.40728	T	0.16	.	18.1884	0.89799	0.0:1.0:0.0:0.0	.	84	Q96JQ0	PCD16_HUMAN	Q	84	ENSP00000299441:E84Q	ENSP00000299441:E84Q	E	-	1	0	DCHS1	6619171	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.783000	0.85696	2.536000	0.85505	0.643000	0.83706	GAG	.	.	.	none		0.627	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		G	6662595	C	G	6662595	3	3	209	1	0	0	0	0	1	0	0	0	4289	922	32	4	9726	4	DCHS1	11	6662595	Missense_Mutation	SNP	C	TCGA-IZ-8195-01A-31D-2396-08		6662595	128343921	45	12708											
OR5F1	338674	hgsc.bcm.edu	37	chr11	55761615	55761615	+	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	acagaatgacaagctgctgaCatggcttgtgttgaccatga	12	10	11	8	0	0	5	0	4	0	1	0	5	0	5	1	1	2	4	1	1	2	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr11:55761615C>T	ENST00000278409.1	-	1	486	c.487G>A	c.(487-489)Gtc>Atc	p.V163I		NM_003697.1	NP_003688.1	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F, member 1	163					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(11)|liver(1)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	58	Esophageal squamous(21;0.00448)					AAGCTGCTGACATGGCTTGTG	0.483																																					p.V163I		Atlas-SNP	.											.	OR5F1	116	.	0			c.G487A						PASS	.						73	69	71					11																	55761615		2201	4296	6497	SO:0001583	missense	338674	exon1			TGCTGACATGGCT	AF065863	CCDS31515.1	11q11	2012-08-09			ENSG00000149133	ENSG00000149133		"GPCR / Class A : Olfactory receptors"	8343	protein-coding gene	gene with protein product		608492				9787077	Standard	NM_003697		Approved	OR11-10	uc010riv.2	O95221	OTTHUMG00000166825	ENST00000278409.1:c.487G>A	chr11.hg19:g.55761615C>T	ENSP00000278409:p.Val163Ile	96.0	0.0	.		108.0	48.0	.	NM_003697	Q495D1|Q6IFB9	Missense_Mutation	SNP	ENST00000278409.1	hg19	CCDS31515.1	.	.	.	.	.	.	.	.	.	.	C	1.364	-0.588052	0.03799	.	.	ENSG00000149133	ENST00000278409	T	0.00099	8.73	2.8	-5.6	0.02497	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00073	0.0002	N	0.02111	-0.68	0.09310	N	1	B	0.14012	0.009	B	0.15870	0.014	T	0.02975	-1.1087	9	0.33141	T	0.24	.	7.0422	0.25027	0.1404:0.1464:0.0:0.7132	.	163	O95221	OR5F1_HUMAN	I	163	ENSP00000278409:V163I	ENSP00000278409:V163I	V	-	1	0	OR5F1	55518191	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-2.797000	0.00763	-0.940000	0.03705	0.297000	0.19635	GTC	.	.	.	none		0.483	OR5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391532.1	NM_003697		T	55761615	C	T	55761615	3	4	209	1	0	0	0	0	1	0	0	0	11165	478	17	2	460	2	OR5F1	11	55761615	Missense_Mutation	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	49099020	55761615	79244901	46	12709			1	28		2	2	22	N	C_A	4.884116e-05
OR5F1	338674	hgsc.bcm.edu	37	chr11	55761636	55761636	+	Missense_Mutation	SNP	A	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	atggcttgtgttgaccatgaAgttcagcaaccctgcagcaa	11	10	10	10	0	1	2	1	2	0	0	1	2	1	2	2	1	4	6	2	1	3	3			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr11:55761636A>C	ENST00000278409.1	-	1	465	c.466T>G	c.(466-468)Ttc>Gtc	p.F156V		NM_003697.1	NP_003688.1	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F, member 1	156					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(11)|liver(1)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	58	Esophageal squamous(21;0.00448)					TTGACCATGAAGTTCAGCAAC	0.507																																					p.F156V		Atlas-SNP	.											.	OR5F1	116	.	0			c.T466G						PASS	.						56	55	55					11																	55761636		2201	4296	6497	SO:0001583	missense	338674	exon1			CCATGAAGTTCAG	AF065863	CCDS31515.1	11q11	2012-08-09			ENSG00000149133	ENSG00000149133		"GPCR / Class A : Olfactory receptors"	8343	protein-coding gene	gene with protein product		608492				9787077	Standard	NM_003697		Approved	OR11-10	uc010riv.2	O95221	OTTHUMG00000166825	ENST00000278409.1:c.466T>G	chr11.hg19:g.55761636A>C	ENSP00000278409:p.Phe156Val	88.0	0.0	.		95.0	31.0	.	NM_003697	Q495D1|Q6IFB9	Missense_Mutation	SNP	ENST00000278409.1	hg19	CCDS31515.1	.	.	.	.	.	.	.	.	.	.	A	4.403	0.074536	0.08485	.	.	ENSG00000149133	ENST00000278409	T	0.36157	1.27	2.96	1.42	0.22433	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.15089	0.0364	N	0.02286	-0.61	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19095	-1.0316	9	0.87932	D	0	.	7.3055	0.26445	0.7399:0.0:0.0:0.2601	.	156	O95221	OR5F1_HUMAN	V	156	ENSP00000278409:F156V	ENSP00000278409:F156V	F	-	1	0	OR5F1	55518212	0.000000	0.05858	0.976000	0.42696	0.068000	0.16541	-0.848000	0.04326	1.136000	0.42199	0.155000	0.16302	TTC	.	.	.	none		0.507	OR5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391532.1	NM_003697		C	55761636	A	C	55761636	3	2	209	1	0	0	0	0	1	0	0	0	11165	72	3	5	481	5	OR5F1	11	55761636	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	21	55761636	79244880	47	12710			1	28		2	2	22	N	C_A	4.884116e-05
MYO7A	4647	hgsc.bcm.edu	37	chr11	76903188	76903188	+	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	cagggcgcccaggagcgcaaCgccccctggaggctcttctt	6	6	13	16	3	2	0	0	0	2	0	2	2	2	2	3	4	2	2	3	4	1	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr11:76903188C>T	ENST00000409709.3	+	31	4289	c.4017C>T	c.(4015-4017)aaC>aaT	p.N1339N	MYO7A_ENST00000458637.2_Silent_p.N1339N|MYO7A_ENST00000409619.2_Silent_p.N1328N	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	1339	FERM 1. {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						AGGAGCGCAACGCCCCCTGGA	0.662											OREG0021258	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N1339N		Atlas-SNP	.											.	MYO7A	164	.	0			c.C4017T						PASS	.						59	69	66					11																	76903188		2114	4216	6330	SO:0001819	synonymous_variant	4647	exon31			GCGCAACGCCCCC	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.4017C>T	chr11.hg19:g.76903188C>T		106.0	0.0	.	1171	77.0	35.0	.	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Silent	SNP	ENST00000409709.3	hg19	CCDS53683.1																																																																																			.	.	.	none		0.662	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		T	76903188	C	T	76903188	2	4	209	1	0	0	0	0	0	0	0	1	10089	535	19	1		1	MYO7A	11	76903188	Silent	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	21141552	76903188	58103328	48	12711											
LRP1	4035	hgsc.bcm.edu	37	chr12	57573720	57573720	+	Missense_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	tggagcagccccatggccttGtcgtccaccctctgcgtggg	4	9	13	15	2	1	0	0	0	1	0	3	1	2	1	5	3	3	1	5	3	0	1			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr12:57573720G>A	ENST00000243077.3	+	30	5588	c.5122G>A	c.(5122-5124)Gtc>Atc	p.V1708I		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	1708					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)	CCATGGCCTTGTCGTCCACCC	0.622																																					p.V1708I		Atlas-SNP	.											.	LRP1	428	.	0			c.G5122A						PASS	.						80	84	82					12																	57573720		2203	4300	6503	SO:0001583	missense	4035	exon30			GGCCTTGTCGTCC	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.5122G>A	chr12.hg19:g.57573720G>A	ENSP00000243077:p.Val1708Ile	200.0	0.0	.		127.0	54.0	.	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	hg19	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.135943	0.77662	.	.	ENSG00000123384	ENST00000243077	D	0.91792	-2.91	5.01	5.01	0.66863	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000008	D	0.94814	0.8325	L	0.58669	1.825	0.80722	D	1	D	0.58970	0.984	D	0.68192	0.956	D	0.94336	0.7566	10	0.46703	T	0.11	.	17.2551	0.87053	0.0:0.0:1.0:0.0	.	1708	Q07954	LRP1_HUMAN	I	1708	ENSP00000243077:V1708I	ENSP00000243077:V1708I	V	+	1	0	LRP1	55859987	1.000000	0.71417	0.994000	0.49952	0.978000	0.69477	9.622000	0.98378	2.606000	0.88127	0.655000	0.94253	GTC	.	.	.	none		0.622	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		A	57573720	G	A	57573720	3	1	209	1	0	0	0	0	1	0	0	0	8958	1377	48	2	5240	2	LRP1	12	57573720	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08		57573720	76278175	49	12712											
C12orf51	283450	hgsc.bcm.edu	37	chr12	112668608	112668608	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccacatgcccactgatgaaGggacgcacaggatcagtcct	11	6	11	13	1	1	2	1	2	0	0	2	4	2	4	3	2	1	1	3	2	1	0			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr12:112668608G>A	ENST00000430131.2	-	39	6098	c.4953C>T	c.(4951-4953)ccC>ccT	p.P1651P	HECTD4_ENST00000377560.5_Silent_p.P1901P|HECTD4_ENST00000550722.1_Silent_p.P1927P			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	1651					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)										CACTGATGAAGGGACGCACAG	0.498																																					p.P1939P		Atlas-SNP	.											.	.	.	.	0			c.C5817T						PASS	.						84	76	79					12																	112668608		2068	4230	6298	SO:0001819	synonymous_variant	283450	exon40			GATGAAGGGACGC	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.4953C>T	chr12.hg19:g.112668608G>A		23.0	0.0	.		15.0	5.0	.	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	hg19																																																																																				.	.	.	none		0.498	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		A	112668608	G	A	112668608	2	1	209	1	0	0	0	0	0	0	0	1	1698	987	35	2		2	C12orf51	12	112668608	Silent	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	55094888	112668608	21183287	50	12713											
MTMR6	9107	hgsc.bcm.edu	37	chr13	25823587	25823587	+	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	ctgaatgtaacaattccttgGtgaggatgccatctgtttgc	9	14	10	8	0	1	2	0	2	1	0	2	3	2	3	2	2	3	2	2	2	3	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr13:25823587G>C	ENST00000381801.5	-	14	2410	c.1649C>G	c.(1648-1650)aCc>aGc	p.T550S	MTMR6_ENST00000540661.1_Intron|AL590787.1_ENST00000408397.1_RNA	NM_004685.3	NP_004676.3	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6	550					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)		CAATTCCTTGGTGAGGATGCC	0.353																																					p.T550S		Atlas-SNP	.											.	MTMR6	75	.	0			c.C1649G						PASS	.						145	137	139					13																	25823587		2203	4300	6503	SO:0001583	missense	9107	exon14			TCCTTGGTGAGGA	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.1649C>G	chr13.hg19:g.25823587G>C	ENSP00000371221:p.Thr550Ser	79.0	0.0	.		58.0	24.0	.	NM_004685	B2RBB5|B3KSB4|Q5JRG6|Q86TB7|Q86YH4|Q96P80	Missense_Mutation	SNP	ENST00000381801.5	hg19	CCDS9313.1	.	.	.	.	.	.	.	.	.	.	G	10.08	1.252375	0.22880	.	.	ENSG00000139505	ENST00000381801;ENST00000319298	D	0.94092	-3.35	5.65	4.76	0.60689	.	0.280543	0.39210	N	0.001422	D	0.82701	0.5094	N	0.12182	0.205	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.74551	-0.3628	10	0.15066	T	0.55	.	6.229	0.20724	0.0787:0.1336:0.6502:0.1375	.	550	Q9Y217	MTMR6_HUMAN	S	550;118	ENSP00000371221:T550S	ENSP00000317987:T118S	T	-	2	0	MTMR6	24721587	0.998000	0.40836	0.987000	0.45799	0.992000	0.81027	0.947000	0.29082	2.833000	0.97629	0.655000	0.94253	ACC	.	.	.	none		0.353	MTMR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044225.1	NM_004685		C	25823587	G	C	25823587	3	2	209	1	0	0	0	0	1	0	0	0	9954	1261	44	4	220	4	MTMR6	13	25823587	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08		25823587	89346291	51	12714											
IPO5	3843	hgsc.bcm.edu	37	chr13	98652854	98652854	+	Missense_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	gcggacttggtggaaagctcGttctgccgatgatcaaggaa	10	9	14	8	3	2	1	1	1	1	0	3	5	2	4	1	4	2	2	1	4	3	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr13:98652854G>A	ENST00000490680.1	+	10	1128	c.1063G>A	c.(1063-1065)Gtt>Att	p.V355I	IPO5_ENST00000261574.5_Missense_Mutation_p.V373I|IPO5_ENST00000539640.1_Missense_Mutation_p.V230I			O00410	IPO5_HUMAN	importin 5	355	Ran-GTP binding. {ECO:0000250}.				cellular response to amino acid stimulus (GO:0071230)|negative regulation of catalytic activity (GO:0043086)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein import into nucleus (GO:0042307)|ribosomal protein import into nucleus (GO:0006610)|viral process (GO:0016032)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|Ran GTPase binding (GO:0008536)			breast(2)|endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	27						TGGAAAGCTCGTTCTGCCGAT	0.418																																					p.V373I		Atlas-SNP	.											.	IPO5	90	.	0			c.G1117A						PASS	.						138	119	125					13																	98652854		2203	4300	6503	SO:0001583	missense	3843	exon13			AAGCTCGTTCTGC	U72761	CCDS31999.1	13q32.2	2012-05-02	2008-04-15	2008-04-15	ENSG00000065150	ENSG00000065150		"Importins"	6402	protein-coding gene	gene with protein product		602008	"karyopherin (importin) beta 3", "RAN binding protein 5"	KPNB3, RANBP5		9114010, 9271386, 17005651	Standard	NM_002271		Approved	IMB3, MGC2068, Pse1	uc001vne.3	O00410	OTTHUMG00000017244	ENST00000490680.1:c.1063G>A	chr13.hg19:g.98652854G>A	ENSP00000418393:p.Val355Ile	88.0	0.0	.		67.0	33.0	.	NM_002271	B4DZA0|O15257|Q5T578|Q86XC7	Missense_Mutation	SNP	ENST00000490680.1	hg19		.	.	.	.	.	.	.	.	.	.	G	14.28	2.486959	0.44249	.	.	ENSG00000065150	ENST00000261574;ENST00000357602;ENST00000490680;ENST00000539640	T;T;T;T	0.18338	2.22;2.22;2.22;2.22	5.99	5.99	0.97316	Armadillo-like helical (1);Armadillo-type fold (1);	0.052583	0.85682	D	0.000000	T	0.10465	0.0256	N	0.05280	-0.08	0.58432	D	0.999996	B;B;B	0.17852	0.024;0.013;0.023	B;B;B	0.23716	0.021;0.013;0.048	T	0.21177	-1.0253	10	0.07644	T	0.81	-0.6551	20.4756	0.99175	0.0:0.0:1.0:0.0	.	230;355;373	B4E0R6;O00410;O00410-3	.;IPO5_HUMAN;.	I	373;355;355;230	ENSP00000261574:V373I;ENSP00000350219:V355I;ENSP00000418393:V355I;ENSP00000445126:V230I	ENSP00000261574:V373I	V	+	1	0	IPO5	97450855	1.000000	0.71417	0.795000	0.32087	0.974000	0.67602	6.319000	0.72871	2.847000	0.97988	0.655000	0.94253	GTT	.	.	.	none		0.418	IPO5-006	NOVEL	alternative_5_UTR|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000354655.1	NM_002271		A	98652854	G	A	98652854	3	1	209	1	0	0	0	0	1	0	0	0	7803	1145	40	1	1159	1	IPO5	13	98652854	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	72829267	98652854	16517024	52	12715											
FARP1	10160	hgsc.bcm.edu	37	chr13	99037979	99037979	+	Missense_Mutation	SNP	A	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	agattgcccgtcggctagagAtgtatggaatccggttgcac	9	10	13	9	3	0	2	0	0	0	2	2	4	1	3	2	3	2	4	2	3	3	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr13:99037979A>C	ENST00000319562.6	+	8	935	c.670A>C	c.(670-672)Atg>Ctg	p.M224L	FARP1_ENST00000376586.2_Missense_Mutation_p.M224L|FARP1_ENST00000595437.1_Missense_Mutation_p.M224L	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)	224	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			TCGGCTAGAGATGTATGGAAT	0.488																																					p.M224L		Atlas-SNP	.											.	FARP1	207	.	0			c.A670C						PASS	.						102	98	99					13																	99037979		2203	4300	6503	SO:0001583	missense	10160	exon8			CTAGAGATGTATG	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.670A>C	chr13.hg19:g.99037979A>C	ENSP00000322926:p.Met224Leu	183.0	0.0	.		110.0	39.0	.	NM_005766	Q5JVI9|Q6IQ29	Missense_Mutation	SNP	ENST00000319562.6	hg19	CCDS9487.1	.	.	.	.	.	.	.	.	.	.	A	15.46	2.839552	0.51057	.	.	ENSG00000152767	ENST00000376586;ENST00000319562	D;D	0.82619	-1.63;-1.63	5.85	4.63	0.57726	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);	0.075237	0.85682	D	0.000000	D	0.88555	0.6468	M	0.63428	1.95	0.58432	D	0.999996	B;D	0.60575	0.019;0.988	B;D	0.77557	0.026;0.99	D	0.86464	0.1781	10	0.32370	T	0.25	.	12.9994	0.58666	0.8652:0.1348:0.0:0.0	.	224;224	Q9Y4F1;C9JME2	FARP1_HUMAN;.	L	224	ENSP00000365771:M224L;ENSP00000322926:M224L	ENSP00000322926:M224L	M	+	1	0	FARP1	97835980	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.144000	0.71762	0.994000	0.38892	0.533000	0.62120	ATG	.	.	.	none		0.488	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766		C	99037979	A	C	99037979	3	2	209	1	0	0	0	0	1	0	0	0	5683	333	12	5	919	5	FARP1	13	99037979	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	385125	99037979	16131899	53	12716											
LRP10	26020	hgsc.bcm.edu	37	chr14	23345117	23345117	+	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	ccctgtggcttaggctctggCctgggagctggcgaaggcct	4	9	16	12	1	1	0	0	0	1	0	1	2	1	1	3	6	1	3	3	6	2	1			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr14:23345117C>T	ENST00000359591.4	+	5	1651	c.960C>T	c.(958-960)ggC>ggT	p.G320G	LRP10_ENST00000546834.1_Silent_p.G320G	NM_014045.3	NP_054764.2	Q7Z4F1	LRP10_HUMAN	low density lipoprotein receptor-related protein 10	320	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.				endocytosis (GO:0006897)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(2)	32	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.00549)		TAGGCTCTGGCCTGGGAGCTG	0.607																																					p.G320G		Atlas-SNP	.											.	LRP10	72	.	0			c.C960T						PASS	.						70	65	67					14																	23345117		2203	4300	6503	SO:0001819	synonymous_variant	26020	exon5			CTCTGGCCTGGGA	AF131760	CCDS9578.1	14q11.2	2013-05-29			ENSG00000197324	ENSG00000197324		"Low density lipoprotein receptors"	14553	protein-coding gene	gene with protein product		609921				11123907	Standard	XM_005267510		Approved	DKFZP564C1940, MGC8675, LRP9, MST087, MSTP087	uc001whd.3	Q7Z4F1	OTTHUMG00000028705	ENST00000359591.4:c.960C>T	chr14.hg19:g.23345117C>T		145.0	0.0	.		100.0	4.0	.	NM_014045	A8K4R5|D3DS31|O95882|Q14CK7|Q86T02|Q8NCZ4|Q9HC42|Q9UG33	Silent	SNP	ENST00000359591.4	hg19	CCDS9578.1	.	.	.	.	.	.	.	.	.	.	C	4.733	0.136334	0.09032	.	.	ENSG00000197324	ENST00000551466	.	.	.	5.97	3.99	0.46301	.	.	.	.	.	T	0.55909	0.1950	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53401	-0.8444	4	.	.	.	-15.5777	6.558	0.22471	0.1566:0.6785:0.0:0.1649	.	.	.	.	S	222	.	.	P	+	1	0	LRP10	22414957	0.997000	0.39634	0.992000	0.48379	0.682000	0.39822	0.651000	0.24873	1.544000	0.49359	0.655000	0.94253	CCT	.	.	.	none		0.607	LRP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071663.3			T	23345117	C	T	23345117	2	4	209	1	0	0	0	0	0	0	0	1	8959	726	26	2		2	LRP10	14	23345117	Silent	SNP	C	TCGA-IZ-8195-01A-31D-2396-08		23345117	84004423	54	12717											
RYR3	6263	hgsc.bcm.edu	37	chr15	33961646	33961646	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatttccatgaggaccttcTccttcactgtggtaagctgc	7	14	9	11	0	2	2	1	2	1	0	4	3	3	3	3	2	2	2	3	2	1	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr15:33961646T>C	ENST00000389232.4	+	37	5781	c.5711T>C	c.(5710-5712)cTc>cCc	p.L1904P	RYR3_ENST00000415757.3_Missense_Mutation_p.L1904P	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	1904	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)		GAGGACCTTCTCCTTCACTGT	0.463																																					p.L1904P		Atlas-SNP	.											.	RYR3	760	.	0			c.T5711C						PASS	.						86	83	84					15																	33961646		1868	4102	5970	SO:0001583	missense	6263	exon37			ACCTTCTCCTTCA		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.5711T>C	chr15.hg19:g.33961646T>C	ENSP00000373884:p.Leu1904Pro	82.0	0.0	.		53.0	21.0	.	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	T	15.50	2.851326	0.51270	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	T;T	0.71341	-0.54;-0.56	5.65	4.53	0.55603	.	0.156082	0.44097	D	0.000496	T	0.69771	0.3148	M	0.61703	1.905	0.54753	D	0.999987	P;P	0.44195	0.787;0.828	B;B	0.43413	0.419;0.296	T	0.72821	-0.4177	10	0.87932	D	0	.	11.6133	0.51074	0.0:0.0688:0.0:0.9312	.	1904;1904	Q15413-2;Q15413	.;RYR3_HUMAN	P	1904	ENSP00000373884:L1904P;ENSP00000399610:L1904P	ENSP00000354735:L1904P	L	+	2	0	RYR3	31748938	1.000000	0.71417	0.639000	0.29394	0.964000	0.63967	3.815000	0.55651	1.158000	0.42547	0.533000	0.62120	CTC	.	.	.	none		0.463	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			C	33961646	T	C	33961646	3	2	209	1	0	0	0	0	1	0	0	0	13783	1551	54	3	5857	3	RYR3	15	33961646	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08		33961646	68569746	55	12718											
THBS1	7057	hgsc.bcm.edu	37	chr15	39885784	39885784	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggctcagggatactcgggccTttctgtgaaagttgtaaact	9	12	12	8	1	2	1	1	1	1	0	3	2	2	2	1	3	2	3	1	3	4	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr15:39885784T>C	ENST00000260356.5	+	19	3347	c.3182T>C	c.(3181-3183)cTt>cCt	p.L1061P	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	1061	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		TACTCGGGCCTTTCTGTGAAA	0.582																																					p.L1061P		Atlas-SNP	.											.	THBS1	106	.	0			c.T3182C						PASS	.						107	105	106					15																	39885784		2200	4297	6497	SO:0001583	missense	7057	exon19			CGGGCCTTTCTGT		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.3182T>C	chr15.hg19:g.39885784T>C	ENSP00000260356:p.Leu1061Pro	257.0	0.0	.		179.0	67.0	.	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	hg19	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.514534	0.85389	.	.	ENSG00000137801	ENST00000260356	D	0.95853	-3.83	5.77	5.77	0.91146	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.000000	0.32357	N	0.006219	D	0.97049	0.9036	L	0.57536	1.79	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.989;1.0	D	0.97737	1.0206	10	0.87932	D	0	-8.1512	16.0747	0.80960	0.0:0.0:0.0:1.0	.	976;1061	B4E3J7;P07996	.;TSP1_HUMAN	P	1061	ENSP00000260356:L1061P	ENSP00000260356:L1061P	L	+	2	0	THBS1	37673076	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	8.036000	0.88901	2.190000	0.69967	0.533000	0.62120	CTT	.	.	.	none		0.582	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		C	39885784	T	C	39885784	3	2	209	1	0	0	0	0	1	0	0	0	15865	1609	56	3	3252	3	THBS1	15	39885784	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08	5924138	39885784	62645608	56	12719											
HMG20A	10363	hgsc.bcm.edu	37	chr15	77759508	77759508	+	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	cttcgagacagcaatgcaccCaaatccccccttacaggata	13	7	6	15	1	0	1	0	0	0	1	2	3	1	2	4	1	3	2	4	1	4	3			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr15:77759508C>A	ENST00000381714.3	+	5	737	c.309C>A	c.(307-309)ccC>ccA	p.P103P	HMG20A_ENST00000336216.4_Silent_p.P103P	NM_018200.2	NP_060670.1	Q9NP66	HM20A_HUMAN	high mobility group 20A	103					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						GCAATGCACCCAAATCCCCCC	0.428																																					p.P103P		Atlas-SNP	.											.	HMG20A	48	.	0			c.C309A						PASS	.						92	88	90					15																	77759508		2196	4294	6490	SO:0001819	synonymous_variant	10363	exon5			TGCACCCAAATCC	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.309C>A	chr15.hg19:g.77759508C>A		116.0	0.0	.		75.0	28.0	.	NM_018200	A6NHY3|D3DW78|Q53G31|Q9NSF6	Silent	SNP	ENST00000381714.3	hg19	CCDS10295.1																																																																																			.	.	.	none		0.428	HMG20A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419512.2	NM_018200		A	77759508	C	A	77759508	2	1	209	1	0	0	0	0	0	0	0	1	7228	581	21	4		4	HMG20A	15	77759508	Silent	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	37873724	77759508	24771884	57	12720											
MLST8	64223	hgsc.bcm.edu	37	chr16	2258565	2258565	+	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	cccggggagtcctcccgcggCtggatgtggggctgcgcctt	2	8	17	14	4	0	0	0	0	0	0	2	2	2	2	4	6	1	2	4	6	0	1			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr16:2258565C>T	ENST00000569417.1	+	8	1167	c.813C>T	c.(811-813)ggC>ggT	p.G271G	MLST8_ENST00000301724.10_Silent_p.G271G|MLST8_ENST00000397124.1_Silent_p.G271G|MLST8_ENST00000564088.1_Silent_p.G271G|MLST8_ENST00000565250.1_Silent_p.G271G|MLST8_ENST00000301725.7_3'UTR|MLST8_ENST00000382450.4_Silent_p.G270G	NM_022372.4	NP_071767.3	Q9BVC4	LST8_HUMAN	MTOR associated protein, LST8 homolog (S. cerevisiae)	271					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 actin filament polymerization (GO:0030838)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of TOR signaling (GO:0032008)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of Rac GTPase activity (GO:0032314)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				large_intestine(3)|lung(2)|skin(1)	6						CCTCCCGCGGCTGGATGTGGG	0.677																																					p.G271G		Atlas-SNP	.											.	MLST8	60	.	0			c.C813T						PASS	.						61	74	70					16																	2258565		2030	4167	6197	SO:0001819	synonymous_variant	64223	exon8			CCGCGGCTGGATG		CCDS10462.2, CCDS58409.1	16p13.3	2013-01-09			ENSG00000167965	ENSG00000167965		"WD repeat domain containing"	24825	protein-coding gene	gene with protein product	"G protein beta subunit like"	612190				12477932	Standard	NM_022372		Approved	Lst8, Pop3, GBL, GbetaL	uc002cpc.3	Q9BVC4	OTTHUMG00000128827	ENST00000569417.1:c.813C>T	chr16.hg19:g.2258565C>T		276.0	0.0	.		198.0	45.0	.	NM_001199174	B3KMM4|B4DY00|D3DU88|Q5M800|Q86Y18|Q8WUI5|Q9HA66|Q9UJV6	Silent	SNP	ENST00000569417.1	hg19	CCDS10462.2																																																																																			.	.	.	none		0.677	MLST8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250763.2	NM_022372		T	2258565	C	T	2258565	2	4	209	1	0	0	0	0	0	0	0	1	9641	784	28	2		2	MLST8	16	2258565	Silent	SNP	C	TCGA-IZ-8195-01A-31D-2396-08		2258565	88096188	58	12721											
PPP4C	5531	hgsc.bcm.edu	37	chr16	30094761	30094761	+	Missense_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	gatccggggcaaccatgagaGtcgccagatcacgcaggtct	10	6	13	12	3	2	2	1	1	1	2	4	4	3	2	3	3	1	2	3	3	1	0			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr16:30094761G>A	ENST00000279387.7	+	6	518	c.350G>A	c.(349-351)aGt>aAt	p.S117N	PPP4C_ENST00000561610.1_Missense_Mutation_p.S117N	NM_002720.1	NP_002711.1	P60510	PP4C_HUMAN	protein phosphatase 4, catalytic subunit	117					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						AACCATGAGAGTCGCCAGATC	0.592																																					p.S117N		Atlas-SNP	.											.	PPP4C	25	.	0			c.G350A						PASS	.						101	92	95					16																	30094761		2197	4300	6497	SO:0001583	missense	5531	exon6			ATGAGAGTCGCCA		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.350G>A	chr16.hg19:g.30094761G>A	ENSP00000279387:p.Ser117Asn	156.0	0.0	.		165.0	102.0	.	NM_002720	P33172	Missense_Mutation	SNP	ENST00000279387.7	hg19	CCDS10669.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.690325	0.88735	.	.	ENSG00000149923	ENST00000279387	D	0.85861	-2.04	5.83	5.83	0.93111	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (2);Metallophosphoesterase domain (1);	0.136138	0.64402	D	0.000003	D	0.94751	0.8306	H	0.97315	3.98	0.80722	D	1	P	0.44380	0.834	P	0.55785	0.784	D	0.95816	0.8845	10	0.87932	D	0	1.9966	18.8865	0.92379	0.0:0.0:1.0:0.0	.	117	P60510	PP4C_HUMAN	N	117	ENSP00000279387:S117N	ENSP00000279387:S117N	S	+	2	0	PPP4C	30002262	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	2.862000	0.48388	2.761000	0.94854	0.650000	0.86243	AGT	.	.	.	none		0.592	PPP4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255155.2	NM_002720		A	30094761	G	A	30094761	3	1	209	1	0	0	0	0	1	0	0	0	12412	1029	36	2	368	2	PPP4C	16	30094761	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	27836196	30094761	60259992	59	12722											
ITFG1	81533	hgsc.bcm.edu	37	chr16	47189669	47189669	+	Frame_Shift_Del	DEL	T	T	-																															aaccggtgggcttcttgtcgTttttctctatcatctgcttt																										TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr16:47189669delT	ENST00000320640.6	-	18	2028	c.1800delA	c.(1798-1800)aaafs	p.K600fs	ITFG1_ENST00000544001.2_3'UTR|ITFG1_ENST00000568047.1_5'UTR|RP11-329J18.2_ENST00000564705.1_RNA|RP11-329J18.2_ENST00000565694.1_RNA	NM_030790.3	NP_110417.2	Q8TB96	TIP_HUMAN	integrin alpha FG-GAP repeat containing 1	600						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)				CTTCTTGTCGTTTTTCTCTAT	0.328																																					p.R601fs		Atlas-INDEL	.											.	ITFG1	49	.	0			c.1801delC						PASS	.						158	171	167					16																	47189669		2202	4300	6502	SO:0001589	frameshift_variant	81533	exon18			.	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.1800delA	chr16.hg19:g.47189669delT	ENSP00000319918:p.Lys600fs	175.0	0.0	0		239.0	77.0	0.322176	NM_030790	Q96SR4|Q9BRE2|Q9H2V9	Frame_Shift_Del	DEL	ENST00000320640.6	hg19	CCDS10728.1																																																																																			.	.	.	none		0.328	ITFG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256768.3	NM_030790		-	47189669	T	-	47189669	7	5	209	1	0	1	0	1	0	0	0	0	7876	1722	60	0	42	0	ITFG1	16	47189669	Frame_Shift_Del	DEL	T	TCGA-IZ-8195-01A-31D-2396-08	17094908	47189669	43165084	60	12723											
MARVELD3	91862	hgsc.bcm.edu	37	chr16	71663293	71663293	+	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	acccccttcggagagatatcTgccctcgacccccaggcctg	7	7	9	18	2	1	1	0	0	1	1	3	4	1	2	6	2	1	0	6	2	1	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr16:71663293T>A	ENST00000268485.3	+	2	535	c.491T>A	c.(490-492)cTg>cAg	p.L164Q	RP11-432I5.2_ENST00000562763.1_RNA|MARVELD3_ENST00000565261.1_Missense_Mutation_p.C110S|MARVELD3_ENST00000567501.1_5'UTR|MARVELD3_ENST00000299952.4_Missense_Mutation_p.L164Q|MARVELD3_ENST00000567566.1_Missense_Mutation_p.L164Q	NM_052858.4	NP_443090.4	Q96A59	MALD3_HUMAN	MARVEL domain containing 3	164	Pro-rich.				cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|tight junction (GO:0005923)				NS(1)|endometrium(3)|large_intestine(5)|lung(6)|skin(2)	17		Ovarian(137;0.125)				GAGAGATATCTGCCCTCGACC	0.502																																					p.L164Q		Atlas-SNP	.											.	MARVELD3	63	.	0			c.T491A						PASS	.						97	90	92					16																	71663293		2198	4300	6498	SO:0001583	missense	91862	exon2			GATATCTGCCCTC	BC013376	CCDS10904.1, CCDS32478.1, CCDS59270.1	16q22.2	2008-02-05	2004-07-12	2004-07-14	ENSG00000140832	ENSG00000140832			30525	protein-coding gene	gene with protein product		614094	"MARVEL (membrane-associating) domain containing 3"	MRVLDC3			Standard	NM_001017967		Approved		uc002fat.4	Q96A59	OTTHUMG00000137591	ENST00000268485.3:c.491T>A	chr16.hg19:g.71663293T>A	ENSP00000268485:p.Leu164Gln	118.0	0.0	.		121.0	5.0	.	NM_001017967	A8K820|H3BQM5|Q96MJ4	Missense_Mutation	SNP	ENST00000268485.3	hg19	CCDS10904.1	.	.	.	.	.	.	.	.	.	.	T	9.698	1.153699	0.21371	.	.	ENSG00000140832	ENST00000268485;ENST00000299952	T;T	0.49139	0.79;0.84	5.57	3.3	0.37823	.	0.821835	0.11320	N	0.576170	T	0.48857	0.1523	L	0.34521	1.04	0.09310	N	0.999993	D;D;D	0.71674	0.958;0.958;0.998	P;P;P	0.62560	0.66;0.66;0.904	T	0.28776	-1.0033	10	0.18276	T	0.48	-13.3398	6.9002	0.24279	0.0:0.1987:0.0:0.8013	.	164;164;187	Q96A59-2;Q96A59;Q9BSH2	.;MALD3_HUMAN;.	Q	164	ENSP00000268485:L164Q;ENSP00000299952:L164Q	ENSP00000268485:L164Q	L	+	2	0	MARVELD3	70220794	0.001000	0.12720	0.001000	0.08648	0.051000	0.14879	0.598000	0.24074	0.958000	0.37956	0.459000	0.35465	CTG	.	.	.	none		0.502	MARVELD3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268991.2	NM_052858		A	71663293	T	A	71663293	3	1	209	1	0	0	0	0	1	0	0	0	9326	1580	55	5	497	5	MARVELD3	16	71663293	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08	24473624	71663293	18691460	61	12724											
ABR	29	hgsc.bcm.edu	37	chr17	916353	916353	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccccggctcaccccgttcaTctcaatcacgtccgtgtgcc	5	10	7	19	4	4	0	4	0	1	0	7	0	6	0	6	1	1	2	6	1	1	1			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr17:916353T>C	ENST00000302538.5	-	17	1989	c.1843A>G	c.(1843-1845)Atg>Gtg	p.M615V	ABR_ENST00000291107.2_Missense_Mutation_p.M578V|ABR_ENST00000544583.2_Missense_Mutation_p.M569V|ABR_ENST00000574437.1_Missense_Mutation_p.M569V|ABR_ENST00000572441.1_Missense_Mutation_p.M66V|ABR_ENST00000543210.2_Missense_Mutation_p.M66V|ABR_ENST00000536794.2_Missense_Mutation_p.M397V	NM_001282149.1|NM_021962.3	NP_001269078.1|NP_068781.2	Q12979	ABR_HUMAN	active BCR-related	615					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)		ACCCCGTTCATCTCAATCACG	0.632																																					p.M615V	Esophageal Squamous(197;2016 2115 4129 29033 46447)	Atlas-SNP	.											.	ABR	119	.	0			c.A1843G						PASS	.						232	177	196					17																	916353		2203	4300	6503	SO:0001583	missense	29	exon17			CGTTCATCTCAAT	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.1843A>G	chr17.hg19:g.916353T>C	ENSP00000303909:p.Met615Val	129.0	0.0	.		129.0	39.0	.	NM_021962	B3KW89|B7Z6H7|D3DTH3|D3DTH4|F5H3S2|F5H8B3|Q13693|Q13694	Missense_Mutation	SNP	ENST00000302538.5	hg19	CCDS10999.1	.	.	.	.	.	.	.	.	.	.	T	16.54	3.152234	0.57259	.	.	ENSG00000159842	ENST00000302538;ENST00000544583;ENST00000291107;ENST00000536794;ENST00000543210	T;T;T;T;T	0.19532	2.17;2.18;2.14;3.39;3.13	5.77	5.77	0.91146	C2 calcium/lipid-binding domain, CaLB (1);	0.046264	0.85682	D	0.000000	T	0.39733	0.1089	M	0.65975	2.015	0.41941	D	0.990616	B;B;P;B	0.43578	0.128;0.452;0.811;0.129	B;P;P;B	0.60789	0.101;0.455;0.879;0.045	T	0.15037	-1.0451	10	0.16896	T	0.51	.	12.5258	0.56085	0.0:0.0:0.0:1.0	.	397;66;578;615	B7Z683;F5H3S2;Q12979-2;Q12979	.;.;.;ABR_HUMAN	V	615;569;578;397;66	ENSP00000303909:M615V;ENSP00000442048:M569V;ENSP00000291107:M578V;ENSP00000437429:M397V;ENSP00000445198:M66V	ENSP00000291107:M578V	M	-	1	0	ABR	863103	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	3.919000	0.56439	2.220000	0.72140	0.529000	0.55759	ATG	.	.	.	none		0.632	ABR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206675.4			C	916353	T	C	916353	3	2	209	1	0	0	0	0	1	0	0	0	99	1435	50	3	764	3	ABR	17	916353	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08		916353	80278857	62	12725											
CTNS	1497	hgsc.bcm.edu	37	chr17	3550808	3550808	+	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	agctcgaccaacgtcagcctCaccctgcggtaagttcctgg	8	8	10	15	3	2	0	2	0	0	0	4	1	3	0	4	2	4	3	4	2	2	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr17:3550808C>T	ENST00000046640.3	+	4	725	c.132C>T	c.(130-132)ctC>ctT	p.L44L	CTNS_ENST00000488623.1_3'UTR|CTNS_ENST00000414524.2_Intron|CTNS_ENST00000399306.2_Silent_p.L44L|CTNS_ENST00000381870.3_Silent_p.L44L|CTNS_ENST00000441220.2_Intron	NM_004937.2	NP_004928.2	O60931	CTNS_HUMAN	cystinosin, lysosomal cystine transporter	44					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)	ACGTCAGCCTCACCCTGCGGT	0.602																																					p.L44L		Atlas-SNP	.											.	CTNS	42	.	0			c.C132T						PASS	.						135	100	112					17																	3550808		2203	4300	6503	SO:0001819	synonymous_variant	1497	exon4			CAGCCTCACCCTG	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.132C>T	chr17.hg19:g.3550808C>T		68.0	0.0	.		94.0	13.0	.	NM_001031681	D3DTJ5|Q8IZ01|Q9UNK6	Silent	SNP	ENST00000046640.3	hg19	CCDS11031.1																																																																																			.	.	.	none		0.602	CTNS-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317696.1	NM_004937		T	3550808	C	T	3550808	2	4	209	1	0	0	0	0	0	0	0	1	4023	813	29	2		2	CTNS	17	3550808	Silent	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	2634455	3550808	77644402	63	12726											
GPR179	440435	hgsc.bcm.edu	37	chr17	36486249	36486249	+	Missense_Mutation	SNP	A	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	ggctgtgggatttagggaagAtcttgggcctgtcttcgtcc	5	13	15	8	1	2	1	0	0	2	1	4	3	3	3	2	4	0	1	2	4	2	4			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr17:36486249A>C	ENST00000342292.4	-	11	3223	c.3203T>G	c.(3202-3204)aTc>aGc	p.I1068S	GPR179_ENST00000584976.1_5'Flank	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	1068					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)				TTTAGGGAAGATCTTGGGCCT	0.562																																					p.I1068S		Atlas-SNP	.											.	GPR179	170	.	0			c.T3203G						PASS	.						70	76	74					17																	36486249		2078	4209	6287	SO:0001583	missense	440435	exon11			GGGAAGATCTTGG		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.3203T>G	chr17.hg19:g.36486249A>C	ENSP00000345060:p.Ile1068Ser	112.0	0.0	.		113.0	28.0	.	NM_001004334		Missense_Mutation	SNP	ENST00000342292.4	hg19	CCDS42308.1	.	.	.	.	.	.	.	.	.	.	A	0.624	-0.819832	0.02776	.	.	ENSG00000188888	ENST00000342292	T	0.52295	0.67	5.14	2.9	0.33743	.	0.633204	0.14796	N	0.297947	T	0.28200	0.0696	N	0.24115	0.695	0.18873	N	0.999981	B	0.15473	0.013	B	0.14023	0.01	T	0.17592	-1.0364	10	0.25106	T	0.35	-0.9541	3.9932	0.09546	0.6254:0.1793:0.1953:0.0	.	1068	Q6PRD1	GP179_HUMAN	S	1068	ENSP00000345060:I1068S	ENSP00000345060:I1068S	I	-	2	0	GPR179	33739775	0.000000	0.05858	0.494000	0.27515	0.138000	0.21146	-0.354000	0.07681	0.427000	0.26145	0.379000	0.24179	ATC	.	.	.	none		0.562	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			C	36486249	A	C	36486249	3	2	209	1	0	0	0	0	1	0	0	0	6681	333	12	5	3904	5	GPR179	17	36486249	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	32935441	36486249	44708961	64	12727											
FOXK2	3607	hgsc.bcm.edu	37	chr17	80543893	80543893	+	Frame_Shift_Del	DEL	C	C	-																															tgaccacctcgacctcccagCcacccgtcgtgcagacggtt																										TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr17:80543893delC	ENST00000335255.5	+	7	1567	c.1393delC	c.(1393-1395)ccafs	p.P466fs	RP13-638C3.3_ENST00000575085.1_RNA	NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	466					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)			GACCTCCCAGCCACCCGTCGT	0.632																																					p.Q464fs		Atlas-INDEL	.											.	FOXK2	46	.	0			c.1392delG						PASS	.						69	56	60					17																	80543893		2200	4294	6494	SO:0001589	frameshift_variant	3607	exon7			.	U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"Forkhead boxes"	6036	protein-coding gene	gene with protein product		147685	"interleukin enhancer binding factor 1"	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.1393delC	chr17.hg19:g.80543893delC	ENSP00000335677:p.Pro466fs	86.0	0.0	0		70.0	22.0	0.314286	NM_004514	A6NEP5|Q13622|Q13623|Q13624	Frame_Shift_Del	DEL	ENST00000335255.5	hg19	CCDS11813.1																																																																																			.	.	.	none		0.632	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430		-	80543893	C	-	80543893	7	5	209	1	0	1	0	1	0	0	0	0	6022	739	26	0	1419	0	FOXK2	17	80543893	Frame_Shift_Del	DEL	C	TCGA-IZ-8195-01A-31D-2396-08	44057644	80543893	651317	65	12728											
IL29	282618	hgsc.bcm.edu	37	chr19	39787490	39787490	+	Missense_Mutation	SNP	T	T	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	ggagttgcagctctcctgtcTtccccgggaattgggacctg	5	11	13	12	1	2	0	0	0	2	0	4	3	3	3	4	3	2	3	4	3	1	3			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr19:39787490T>G	ENST00000333625.2	+	2	314	c.217T>G	c.(217-219)Ttc>Gtc	p.F73V		NM_172140.1	NP_742152.1	Q8IU54	IFNL1_HUMAN	interferon, lambda 1	73					defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|negative regulation of cell proliferation (GO:0008285)|negative regulation of interleukin-13 production (GO:0032696)|negative regulation of interleukin-5 production (GO:0032714)|negative regulation of memory T cell differentiation (GO:0043381)|negative regulation of T cell differentiation (GO:0045581)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of immune response (GO:0050778)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-28 receptor complex (GO:0032002)	interleukin-28 receptor binding (GO:0032003)|receptor binding (GO:0005102)										CTCTCCTGTCTTCCCCGGGAA	0.572																																					p.F73V		Atlas-SNP	.											.	.	.	.	0			c.T217G						PASS	.						91	86	88					19																	39787490		2203	4300	6503	SO:0001583	missense	282618	exon2			CCTGTCTTCCCCG	AY129150	CCDS12531.1	19q13.13	2014-05-22	2012-11-26	2012-11-26	ENSG00000182393	ENSG00000182393		"Interferons"	18363	protein-coding gene	gene with protein product		607403	"interleukin 29", "interleukin 29 (interferon, lambda 1)"	IL29			Standard	NM_172140		Approved	IL-29	uc002okv.3	Q8IU54		ENST00000333625.2:c.217T>G	chr19.hg19:g.39787490T>G	ENSP00000329991:p.Phe73Val	106.0	0.0	.		55.0	23.0	.	NM_172140	A0AV25|Q17R34	Missense_Mutation	SNP	ENST00000333625.2	hg19	CCDS12531.1	.	.	.	.	.	.	.	.	.	.	T	17.77	3.470360	0.63625	.	.	ENSG00000182393	ENST00000333625	T	0.35421	1.31	3.69	3.69	0.42338	.	0.094954	0.46758	D	0.000269	T	0.59770	0.2218	M	0.84846	2.72	0.25011	N	0.991407	D	0.71674	0.998	D	0.71870	0.975	T	0.54098	-0.8344	10	0.66056	D	0.02	-28.5284	10.3642	0.44012	0.0:0.0:0.0:1.0	.	73	Q8IU54	IL29_HUMAN	V	73	ENSP00000329991:F73V	ENSP00000329991:F73V	F	+	1	0	IL29	44479330	0.956000	0.32656	0.939000	0.37840	0.068000	0.16541	1.113000	0.31184	1.553000	0.49476	0.374000	0.22700	TTC	.	.	.	none		0.572	IFNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463834.1	NM_172140		G	39787490	T	G	39787490	3	3	209	1	0	0	0	0	1	0	0	0	7692	1609	56	5	223	5	IL29	19	39787490	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08		39787490	19341493	66	12729											
PRR19	284338	hgsc.bcm.edu	37	chr19	42814766	42814766	+	Silent	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	ctgcctcagccttcatcaccCctgttgccccgaacctctgt	5	11	6	19	1	4	0	3	0	1	0	4	1	4	0	7	0	4	1	7	0	1	2			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr19:42814766C>T	ENST00000499536.2	+	2	1756	c.945C>T	c.(943-945)ccC>ccT	p.P315P	PRR19_ENST00000598490.1_3'UTR|TMEM145_ENST00000301204.3_5'Flank|TMEM145_ENST00000598766.1_5'Flank|PRR19_ENST00000341747.3_Silent_p.P315P			A6NJB7	PRR19_HUMAN	proline rich 19	315	Pro-rich.									NS(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	10		Prostate(69;0.00682)				CTTCATCACCCCTGTTGCCCC	0.652																																					p.P315P		Atlas-SNP	.											.	PRR19	30	.	0			c.C945T						PASS	.						71	82	78					19																	42814766		2203	4300	6503	SO:0001819	synonymous_variant	284338	exon3			ATCACCCCTGTTG	AK124116	CCDS33036.1	19q13.2	2007-12-17				ENSG00000188368			33728	protein-coding gene	gene with protein product							Standard	NM_199285		Approved	MGC70924	uc002oti.3	A6NJB7		ENST00000499536.2:c.945C>T	chr19.hg19:g.42814766C>T		300.0	0.0	.		218.0	83.0	.	NM_199285	A8K663|B3KW48|Q6P584	Silent	SNP	ENST00000499536.2	hg19	CCDS33036.1																																																																																			.	.	.	none		0.652	PRR19-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463735.1	NM_199285		T	42814766	C	T	42814766	2	4	209	1	0	0	0	0	0	0	0	1	12601	610	22	2		2	PRR19	19	42814766	Silent	SNP	C	TCGA-IZ-8195-01A-31D-2396-08	3027276	42814766	16314217	67	12730											
RSPH6A	81492	hgsc.bcm.edu	37	chr19	46317875	46317875	+	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	gctcgggctcaggcacctggGcactgtagtgtgggaagccc	6	7	16	12	1	1	0	1	0	0	0	2	1	1	1	2	4	1	5	2	4	2	1			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr19:46317875G>C	ENST00000221538.3	-	1	702	c.560C>G	c.(559-561)gCc>gGc	p.A187G	RSPH6A_ENST00000597055.1_Missense_Mutation_p.A187G|SYMPK_ENST00000598155.1_5'Flank	NM_030785.3	NP_110412.1	Q9H0K4	RSH6A_HUMAN	radial spoke head 6 homolog A (Chlamydomonas)	187						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						AGGCACCTGGGCACTGTAGTG	0.612																																					p.A187G		Atlas-SNP	.											.	RSPH6A	70	.	0			c.C560G						PASS	.						41	42	42					19																	46317875		2203	4300	6503	SO:0001583	missense	81492	exon1			ACCTGGGCACTGT	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.560C>G	chr19.hg19:g.46317875G>C	ENSP00000221538:p.Ala187Gly	108.0	0.0	.		67.0	24.0	.	NM_030785	Q53FE2|Q6PEZ9	Missense_Mutation	SNP	ENST00000221538.3	hg19	CCDS12675.1	.	.	.	.	.	.	.	.	.	.	G	7.970	0.748802	0.15710	.	.	ENSG00000104941	ENST00000221538	T	0.14022	2.54	4.76	-7.87	0.01183	.	1.573020	0.03646	N	0.240221	T	0.05273	0.0140	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.35822	-0.9773	10	0.12766	T	0.61	-6.7105	6.8603	0.24064	0.3005:0.342:0.3575:0.0	.	187	Q9H0K4	RSH6A_HUMAN	G	187	ENSP00000221538:A187G	ENSP00000221538:A187G	A	-	2	0	RSPH6A	51009715	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.503000	0.06383	-1.022000	0.03346	-0.274000	0.10170	GCC	.	.	.	none		0.612	RSPH6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461657.1			C	46317875	G	C	46317875	3	2	209	1	0	0	0	0	1	0	0	0	13720	1203	42	4	1617	4	RSPH6A	19	46317875	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	3503109	46317875	12811108	68	12731											
TMEM190	147744	hgsc.bcm.edu	37	chr19	55889354	55889354	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccctgcaggtgggccaagcGccgggacgtgctgcatatgc	6	7	15	13	3	0	0	0	0	0	0	1	1	1	1	3	3	5	3	3	3	2	1			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr19:55889354G>A	ENST00000291934.3	+	5	335	c.317G>A	c.(316-318)cGc>cAc	p.R106H	CTD-2105E13.15_ENST00000595064.1_RNA	NM_139172.1	NP_631911.1	Q8WZ59	TM190_HUMAN	transmembrane protein 190	106					hematopoietic progenitor cell differentiation (GO:0002244)	inner acrosomal membrane (GO:0002079)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	5	Breast(117;0.191)		BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		TGGGCCAAGCGCCGGGACGTG	0.716																																					p.R106H		Atlas-SNP	.											TMEM190,NS,carcinoma,0,1	TMEM190	17	.	0			c.G317A						PASS	.						26	25	26					19																	55889354		2197	4281	6478	SO:0001583	missense	147744	exon5			CCAAGCGCCGGGA	AF442729	CCDS33113.1	19q13.42	2011-09-28				ENSG00000160472			29632	protein-coding gene	gene with protein product						21273369	Standard	NM_139172		Approved	MDAC1	uc002qkt.1	Q8WZ59		ENST00000291934.3:c.317G>A	chr19.hg19:g.55889354G>A	ENSP00000291934:p.Arg106His	60.0	0.0	.		47.0	2.0	.	NM_139172	A6NJL5	Missense_Mutation	SNP	ENST00000291934.3	hg19	CCDS33113.1	.	.	.	.	.	.	.	.	.	.	G	14.61	2.587005	0.46110	.	.	ENSG00000160472	ENST00000291934	.	.	.	3.02	3.02	0.34903	.	0.000000	0.41938	D	0.000798	T	0.51329	0.1668	L	0.27053	0.805	0.33174	D	0.548688	D	0.76494	0.999	D	0.78314	0.991	T	0.62530	-0.6835	9	0.87932	D	0	-26.0952	9.7157	0.40274	0.0:0.0:1.0:0.0	.	106	Q8WZ59	TM190_HUMAN	H	106	.	ENSP00000291934:R106H	R	+	2	0	TMEM190	60581166	0.763000	0.28462	0.922000	0.36590	0.142000	0.21351	2.515000	0.45512	1.995000	0.58328	0.313000	0.20887	CGC	.	.	.	none		0.716	TMEM190-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453042.1	NM_139172		A	55889354	G	A	55889354	3	1	209	1	0	0	0	0	1	0	0	0	16126	1087	38	1	335	1	TMEM190	19	55889354	Missense_Mutation	SNP	G	TCGA-IZ-8195-01A-31D-2396-08	9571479	55889354	3239629	69	12732											
PEG3	5178	hgsc.bcm.edu	37	chr19	57325186	57325186	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgttcgatgtagcctgagcActccccaaaggcatttgcag	10	9	10	12	2	0	1	0	1	0	0	2	2	1	1	3	1	3	5	3	1	2	3	rs530969342		TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr19:57325186A>G	ENST00000326441.9	-	10	4987	c.4624T>C	c.(4624-4626)Tgc>Cgc	p.C1542R	ZIM2_ENST00000221722.5_Intron|ZIM2_ENST00000593711.1_Intron|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000601070.1_Intron|PEG3_ENST00000423103.2_Missense_Mutation_p.C1542R|PEG3_ENST00000593695.1_Missense_Mutation_p.C1416R|PEG3_ENST00000598410.1_Missense_Mutation_p.C1418R|ZIM2_ENST00000391708.3_Intron	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	1542					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)		TAGCCTGAGCACTCCCCAAAG	0.488													A|||	0	0	0	0	5008	,	,		21323	0		0	False		,,,				2504	0				p.C1542R		Atlas-SNP	.											.	PEG3	414	.	0			c.T4624C						PASS	.						158	137	144					19																	57325186		2203	4300	6503	SO:0001583	missense	5178	exon9			CTGAGCACTCCCC	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.4624T>C	chr19.hg19:g.57325186A>G	ENSP00000326581:p.Cys1542Arg	186.0	0.0	.		114.0	35.0	.	NM_001146184	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	hg19	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	A	10.68	1.417219	0.25552	.	.	ENSG00000198300	ENST00000326441;ENST00000423103	T;T	0.03330	3.97;3.97	3.95	-1.91	0.07641	.	0.139082	0.33712	N	0.004636	T	0.01800	0.0057	N	0.19112	0.55	.	.	.	B;B;B	0.29432	0.159;0.244;0.244	B;B;B	0.29176	0.031;0.047;0.099	T	0.41324	-0.9515	9	0.23302	T	0.38	-3.4232	0.998	0.01471	0.2243:0.3544:0.1312:0.2901	.	1418;1542;1477	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	R	1542	ENSP00000326581:C1542R;ENSP00000403051:C1542R	ENSP00000326581:C1542R	C	-	1	0	ZIM2	62016998	0.001000	0.12720	0.008000	0.14137	0.951000	0.60555	0.315000	0.19451	-0.525000	0.06391	0.482000	0.46254	TGC	.	.	.	none		0.488	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			G	57325186	A	G	57325186	3	3	209	1	0	0	0	0	1	0	0	0	11727	159	6	3	146	3	PEG3	19	57325186	Missense_Mutation	SNP	A	TCGA-IZ-8195-01A-31D-2396-08	1435832	57325186	1803797	70	12733											
SAMHD1	25939	hgsc.bcm.edu	37	chr20	35532631	35532631	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttagcactggcaacctcttTtggaagagattcatagtcct	10	14	8	9	0	2	1	1	0	1	1	3	3	3	2	2	2	2	2	2	2	4	6			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr20:35532631T>C	ENST00000262878.4	-	13	1631	c.1432A>G	c.(1432-1434)Aaa>Gaa	p.K478E		NM_015474.3	NP_056289.2	Q9Y3Z3	SAMH1_HUMAN	SAM domain and HD domain 1	478					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)				GCAACCTCTTTTGGAAGAGAT	0.388																																					p.K478E		Atlas-SNP	.											.	SAMHD1	62	.	0			c.A1432G						PASS	.						167	160	163					20																	35532631		2203	4300	6503	SO:0001583	missense	25939	exon13			CCTCTTTTGGAAG	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.1432A>G	chr20.hg19:g.35532631T>C	ENSP00000262878:p.Lys478Glu	209.0	0.0	.		210.0	124.0	.	NM_015474	B4E2A5|E1P5V2|Q5JXG8|Q8N491|Q9H004|Q9H005|Q9H3U9	Missense_Mutation	SNP	ENST00000262878.4	hg19	CCDS13288.1	.	.	.	.	.	.	.	.	.	.	T	3.335	-0.135924	0.06711	.	.	ENSG00000101347	ENST00000262878	D	0.95035	-3.59	5.58	-1.17	0.09648	.	0.908554	0.09627	N	0.776782	T	0.81880	0.4916	N	0.05012	-0.13	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.70040	-0.4981	10	0.12103	T	0.63	-4.9058	2.7471	0.05270	0.1081:0.3573:0.2665:0.2681	.	478	Q9Y3Z3	SAMH1_HUMAN	E	478	ENSP00000262878:K478E	ENSP00000262878:K478E	K	-	1	0	SAMHD1	34966045	0.001000	0.12720	0.005000	0.12908	0.362000	0.29581	-0.100000	0.10990	-0.173000	0.10761	0.460000	0.39030	AAA	.	.	.	none		0.388	SAMHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079062.2	NM_015474		C	35532631	T	C	35532631	3	2	209	1	0	0	0	0	1	0	0	0	13841	1850	64	3	464	3	SAMHD1	20	35532631	Missense_Mutation	SNP	T	TCGA-IZ-8195-01A-31D-2396-08		35532631	27492889	71	12734											
SFRS15	57466	hgsc.bcm.edu	37	chr21	33057763	33057763	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggaatggatactggtggAgttataggaggtgggggtcc	9	9	20	3	0	0	0	0	0	0	0	1	5	1	5	1	9	1	1	1	9	4	3			TCGA-IZ-8195-01A-31D-2396-08	TCGA-IZ-8195-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fcdb724c-08ad-42b7-9fef-e4d84edaf2fe	5d320b5a-a67a-4a11-908d-9c5e8c70e16a	g.chr21:33057763A>G	ENST00000286835.7	-	18	2626	c.2244T>C	c.(2242-2244)acT>acC	p.T748T	SCAF4_ENST00000434667.3_Silent_p.T733T|SCAF4_ENST00000399804.1_Silent_p.T748T	NM_020706.2	NP_065757.1	O95104	SFR15_HUMAN	SR-related CTD-associated factor 4	748						nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(11)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						ATACTGGTGGAGTTATAGGAG	0.433																																					p.T748T		Atlas-SNP	.											.	SCAF4	142	.	0			c.T2244C						PASS	.						92	94	93					21																	33057763		2203	4300	6503	SO:0001819	synonymous_variant	57466	exon18			TGGTGGAGTTATA	AB032998	CCDS33537.1, CCDS46644.1, CCDS54482.1	21q22.1	2013-02-12	2011-01-10	2011-01-10	ENSG00000156304	ENSG00000156304		"RNA binding motif (RRM) containing"	19304	protein-coding gene	gene with protein product			"splicing factor, arginine/serine-rich 15"	SFRS15		10574461	Standard	NM_020706		Approved	KIAA1172, DKFZp434E098, SRA4	uc002ypd.2	O95104	OTTHUMG00000084903	ENST00000286835.7:c.2244T>C	chr21.hg19:g.33057763A>G		139.0	0.0	.		96.0	5.0	.	NM_020706	C9JLZ0|Q0P5W8|Q6P1M5|Q8N3I8|Q9UFM1|Q9ULP8	Silent	SNP	ENST00000286835.7	hg19	CCDS33537.1																																																																																			.	.	.	none		0.433	SCAF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000192659.1	XM_047889		G	33057763	A	G	33057763	2	3	209	1	0	0	0	0	0	0	0	1	14184	291	11	3		3	SFRS15	21	33057763	Silent	SNP	A	TCGA-IZ-8195-01A-31D-2396-08		33057763	15072132	72	12735											
DDI2	84301	hgsc.bcm.edu	37	chr1	15956839	15956839	+	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	gacttaccccgaatagatttCagtagtatagctgtgcctgg	10	12	10	9	1	1	1	1	0	0	1	1	3	1	1	3	1	3	3	3	1	6	6			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr1:15956839C>T	ENST00000480945.1	+	3	459	c.288C>T	c.(286-288)ttC>ttT	p.F96F		NM_032341.4	NP_115717.3	Q5TDH0	DDI2_HUMAN	DNA-damage inducible 1 homolog 2 (S. cerevisiae)	96							aspartic-type endopeptidase activity (GO:0004190)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|stomach(1)	17		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00327)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.03e-07)|COAD - Colon adenocarcinoma(227;4.48e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)		GAATAGATTTCAGTAGTATAG	0.463																																					p.F96F		Atlas-SNP	.											.	DDI2	38	.	0			c.C288T						PASS	.						87	90	89					1																	15956839		2203	4300	6503	SO:0001819	synonymous_variant	84301	exon3			AGATTTCAGTAGT		CCDS30607.1	1p36.13	2010-05-04	2010-05-04		ENSG00000197312	ENSG00000197312			24578	protein-coding gene	gene with protein product			"DDI1, DNA-damage inducible 1, homolog 2 (S. cerevisiae)"				Standard	NM_032341		Approved	MGC14844	uc001awx.2	Q5TDH0	OTTHUMG00000002381	ENST00000480945.1:c.288C>T	chr1.hg19:g.15956839C>T		168.0	0.0	.		133.0	66.0	.	NM_032341	A8KAE1|Q7RTZ0|Q9BRT1	Silent	SNP	ENST00000480945.1	hg19	CCDS30607.1																																																																																			.	.	.	none		0.463	DDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006826.1	NM_032341		T	15956839	C	T	15956839	2	4	210	1	0	0	0	0	0	0	0	1	4331	825	29	2		2	DDI2	1	15956839	Silent	SNP	C	TCGA-IZ-8196-01A-11D-2396-08		15956839	233293782	1	12736											
MSH4	4438	hgsc.bcm.edu	37	chr1	76269502	76269502	+	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	caagctcatcttctgcacgaGatactaattatcctcaaaca	14	11	4	12	1	4	1	2	0	2	1	5	2	5	1	1	0	4	2	1	0	5	4			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr1:76269502G>A	ENST00000263187.3	+	2	435	c.331G>A	c.(331-333)Gat>Aat	p.D111N		NM_002440.3	NP_002431.2	O15457	MSH4_HUMAN	mutS homolog 4	111					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|female gamete generation (GO:0007292)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						TTCTGCACGAGATACTAATTA	0.363								Mismatch excision repair (MMR)																													p.D111N		Atlas-SNP	.											MSH4,NS,carcinoma,0,1	MSH4	147	.	0			c.G331A						PASS	.						97	101	100					1																	76269502		2203	4300	6503	SO:0001583	missense	4438	exon2			GCACGAGATACTA	U89293	CCDS670.1	1p31	2013-09-12	2013-09-12		ENSG00000057468	ENSG00000057468			7327	protein-coding gene	gene with protein product		602105	"mutS (E. coli) homolog 4", "mutS homolog 4 (E. coli)"			9299235	Standard	NM_002440		Approved		uc001dhd.2	O15457	OTTHUMG00000009788	ENST00000263187.3:c.331G>A	chr1.hg19:g.76269502G>A	ENSP00000263187:p.Asp111Asn	60.0	0.0	.		110.0	52.0	.	NM_002440	Q5T4U6|Q8NEB3|Q9UNP8	Missense_Mutation	SNP	ENST00000263187.3	hg19	CCDS670.1	.	.	.	.	.	.	.	.	.	.	G	10.35	1.326532	0.24080	.	.	ENSG00000057468	ENST00000263187	D	0.87256	-2.23	4.73	3.81	0.43845	.	0.591556	0.15780	N	0.245000	T	0.61776	0.2374	N	0.24115	0.695	0.09310	N	1	B	0.19817	0.039	B	0.11329	0.006	T	0.55392	-0.8148	10	0.49607	T	0.09	-16.9831	6.3049	0.21133	0.16:0.0:0.6929:0.147	.	111	O15457	MSH4_HUMAN	N	111	ENSP00000263187:D111N	ENSP00000263187:D111N	D	+	1	0	MSH4	76042090	0.920000	0.31207	0.889000	0.34880	0.806000	0.45545	3.225000	0.51246	0.984000	0.38629	-0.266000	0.10368	GAT	.	.	.	none		0.363	MSH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026983.1	NM_002440		A	76269502	G	A	76269502	3	1	210	1	0	0	0	0	1	0	0	0	9879	942	33	2	337	2	MSH4	1	76269502	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	60312663	76269502	172981119	2	12737											
LRRC8C	84230	hgsc.bcm.edu	37	chr1	90180228	90180228	+	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	tgacattcgatttatcccccCtgaaattggagttctacaaa	12	13	6	10	1	1	2	0	2	1	0	3	4	2	3	3	1	1	1	3	1	4	6			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr1:90180228C>A	ENST00000370454.4	+	3	2354	c.2099C>A	c.(2098-2100)cCt>cAt	p.P700H	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	700					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)		TTTATCCCCCCTGAAATTGGA	0.383																																					p.P700H		Atlas-SNP	.											.	LRRC8C	73	.	0			c.C2099A						PASS	.						68	63	65					1																	90180228		2203	4299	6502	SO:0001583	missense	84230	exon3			TCCCCCCTGAAAT		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.2099C>A	chr1.hg19:g.90180228C>A	ENSP00000359483:p.Pro700His	43.0	0.0	.		77.0	29.0	.	NM_032270	B3KXS9|Q29RV6|Q9H075	Missense_Mutation	SNP	ENST00000370454.4	hg19	CCDS725.1	.	.	.	.	.	.	.	.	.	.	C	12.14	1.849986	0.32699	.	.	ENSG00000171488	ENST00000370454	T	0.25414	1.8	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.24353	0.0590	M	0.78049	2.395	0.80722	D	1	B	0.25351	0.124	B	0.24269	0.052	T	0.02789	-1.1110	10	0.35671	T	0.21	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	700	Q8TDW0	LRC8C_HUMAN	H	700	ENSP00000359483:P700H	ENSP00000359483:P700H	P	+	2	0	LRRC8C	89952816	1.000000	0.71417	0.801000	0.32222	0.989000	0.77384	6.050000	0.71063	2.941000	0.99782	0.655000	0.94253	CCT	.	.	.	none		0.383	LRRC8C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028435.2	NM_032270		A	90180228	C	A	90180228	3	1	210	1	0	0	0	0	1	0	0	0	9030	681	24	4	2105	4	LRRC8C	1	90180228	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	13910726	90180228	159070393	3	12738											
RBM15	64783	hgsc.bcm.edu	37	chr1	110882978	110882978	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcttggccgcctgcccccTccacctccgccaccattgcc	3	8	7	23	2	1	0	0	0	1	0	3	0	3	0	10	1	2	1	10	1	0	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr1:110882978T>C	ENST00000369784.3	+	1	1851	c.951T>C	c.(949-951)ccT>ccC	p.P317P	RBM15_ENST00000602849.1_Silent_p.P317P|RP5-1074L1.1_ENST00000449169.1_RNA|RBM15_ENST00000487146.2_Silent_p.P317P	NM_022768.4	NP_073605.4	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	317					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)		GCCTGCCCCCTCCACCTCCGC	0.607			T	MKL1	acute megakaryocytic leukemia																																p.P317P		Atlas-SNP	.		Dom	yes		1	1p13	64783	RNA binding motif protein 15		L	.	RBM15	93	.	0			c.T951C						PASS	.						46	52	50					1																	110882978		2203	4300	6503	SO:0001819	synonymous_variant	64783	exon1			GCCCCCTCCACCT	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.951T>C	chr1.hg19:g.110882978T>C		214.0	1.0	.		112.0	53.0	.	NM_022768	A1A693|Q3ZB86|Q4V760|Q5D058|Q5T613|Q86VW9|Q96PE4|Q96SC5|Q96SC6|Q96SC9|Q96SD0|Q96T38|Q9BRA5|Q9H6R8|Q9H9Y0	Silent	SNP	ENST00000369784.3	hg19	CCDS822.1																																																																																			.	.	.	none		0.607	RBM15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000031114.2	NM_022768		C	110882978	T	C	110882978	2	2	210	1	0	0	0	0	0	0	0	1	13129	1538	54	3		3	RBM15	1	110882978	Silent	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	20702750	110882978	138367643	4	12739											
ANKRD35	148741	hgsc.bcm.edu	37	chr1	145561688	145561688	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggccctgatcatgctgaccAgctgcctgctggtcagaagg	7	9	13	12	0	2	3	2	2	0	1	2	3	2	3	3	3	4	3	3	3	1	0			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr1:145561688A>G	ENST00000355594.4	+	10	1463	c.1376A>G	c.(1375-1377)cAg>cGg	p.Q459R		NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	459										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)					CATGCTGACCAGCTGCCTGCT	0.592																																					p.Q459R	Melanoma(9;127 754 22988 51047)	Atlas-SNP	.											.	ANKRD35	96	.	0			c.A1376G						PASS	.						55	63	60					1																	145561688		2203	4300	6503	SO:0001583	missense	148741	exon10			CTGACCAGCTGCC	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.1376A>G	chr1.hg19:g.145561688A>G	ENSP00000347802:p.Gln459Arg	169.0	0.0	.		113.0	48.0	.	NM_144698	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	hg19	CCDS919.1	.	.	.	.	.	.	.	.	.	.	a	0.294	-0.978340	0.02197	.	.	ENSG00000198483	ENST00000453670;ENST00000355594	T	0.67698	-0.28	5.54	0.0734	0.14390	.	0.859396	0.09865	N	0.745663	T	0.33760	0.0874	M	0.63428	1.95	0.09310	N	1	B	0.26935	0.164	B	0.22601	0.04	T	0.16158	-1.0412	10	0.27785	T	0.31	-2.3373	2.517	0.04670	0.4852:0.2931:0.0804:0.1412	.	459	Q8N283	ANR35_HUMAN	R	368;459	ENSP00000347802:Q459R	ENSP00000347802:Q459R	Q	+	2	0	ANKRD35	144273045	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	1.054000	0.30455	0.044000	0.15775	-0.253000	0.11424	CAG	.	.	.	none		0.592	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698		G	145561688	A	G	145561688	3	3	210	1	0	0	0	0	1	0	0	0	664	188	7	3	1414	3	ANKRD35	1	145561688	Missense_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	34678710	145561688	103688933	5	12740											
ATP8B2	57198	hgsc.bcm.edu	37	chr1	154314963	154314968	+	In_Frame_Del	DEL	GTTTGA	GTTTGA	-																															tggctgtatgtaggtgatgtGtttgacgtcctgggacacaa																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	GTTTGA	GTTTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr1:154314963_154314968delGTTTGA	ENST00000368489.3	+	14	1350_1355	c.1350_1355delGTTTGA	c.(1348-1356)gtgtttgac>gtc	p.FD451del		NM_020452.3	NP_065185.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	437					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)		IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			TAGGTGATGTGTTTGACGTCCTGGGA	0.49																																					p.450_452del		Atlas-INDEL	.											.	ATP8B2	158	.	0			c.1349_1354del						PASS	.																																			SO:0001651	inframe_deletion	57198	exon14			.	AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515		"ATPases / P-type"	13534	protein-coding gene	gene with protein product		605867	"ATPase, class I, type 8B, member 2"			10574461, 11015572	Standard	NM_020452		Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368489.3:c.1350_1355delGTTTGA	chr1.hg19:g.154314963_154314968delGTTTGA	ENSP00000357475:p.Phe451_Asp452del	101.0	0.0	0		67.0	13.0	0.19403	NM_020452	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	In_Frame_Del	DEL	ENST00000368489.3	hg19	CCDS1066.1																																																																																			.	.	.	none		0.49	ATP8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087658.2	NM_020452		-	154314968	GTTTGA	-	154314963	7	5	210	1	0	1	0	1	0	0	0	0	1195	1364	48	0	1534	0	ATP8B2	1	154314963	In_Frame_Del	DEL	GTTTGA	TCGA-IZ-8196-01A-11D-2396-08	8753275	154314963	94935658	6	12741											
MAEL	84944	hgsc.bcm.edu	37	chr1	166974561	166974561	+	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	ggatctaccaacaaaaatttCtcaaggagccctctaagact	15	9	6	11	0	3	1	1	0	3	1	4	3	3	3	2	2	3	0	2	2	6	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr1:166974561C>A	ENST00000367872.4	+	8	1016	c.772C>A	c.(772-774)Ctc>Atc	p.L258I	MAEL_ENST00000367870.2_Missense_Mutation_p.L227I|RNA5SP65_ENST00000363166.1_RNA|MAEL_ENST00000491055.1_3'UTR	NM_032858.1	NP_116247.1	Q96JY0	MAEL_HUMAN	maelstrom spermatogenic transposon silencer	258					cell differentiation (GO:0030154)|cell morphogenesis (GO:0000902)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|piRNA metabolic process (GO:0034587)|regulation of organ growth (GO:0046620)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	autosome (GO:0030849)|chromatin (GO:0000785)|chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|perinuclear region of cytoplasm (GO:0048471)|piP-body (GO:0071547)|XY body (GO:0001741)	DNA binding (GO:0003677)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(12)|skin(4)	28						ACAAAAATTTCTCAAGGAGCC	0.398																																					p.L258I		Atlas-SNP	.											.	MAEL	95	.	0			c.C772A						PASS	.						73	78	76					1																	166974561		2203	4300	6503	SO:0001583	missense	84944	exon8			AAATTTCTCAAGG	AK027810, DQ076156	CCDS1257.1, CCDS65712.1, CCDS72975.1	1q24.1	2013-10-11	2012-12-18		ENSG00000143194	ENSG00000143194			25929	protein-coding gene	gene with protein product	"cancer/testis antigen 128", "spermatogenesis associated 35"	611368	"maelstrom homolog (Drosophila)"			19693694, 18694567	Standard	NM_001286378		Approved	FLJ14904, CT128, SPATA35	uc001gdy.1	Q96JY0	OTTHUMG00000034432	ENST00000367872.4:c.772C>A	chr1.hg19:g.166974561C>A	ENSP00000356846:p.Leu258Ile	33.0	0.0	.		62.0	28.0	.	NM_032858	B4DY43|E9JVC3|Q49AP9|Q5VZP8|Q9UIW6	Missense_Mutation	SNP	ENST00000367872.4	hg19	CCDS1257.1	.	.	.	.	.	.	.	.	.	.	C	12.06	1.825645	0.32237	.	.	ENSG00000143194	ENST00000367872;ENST00000367870;ENST00000447624	T;T;T	0.47869	0.85;0.83;0.85	5.66	4.75	0.60458	.	0.324591	0.26193	N	0.025795	T	0.13927	0.0337	N	0.08118	0	0.23765	N	0.996906	B;B	0.32071	0.301;0.355	B;B	0.38225	0.209;0.268	T	0.05920	-1.0856	10	0.42905	T	0.14	.	7.8331	0.29355	0.0:0.7505:0.1634:0.086	.	227;258	E9JVC3;Q96JY0	.;MAEL_HUMAN	I	258;227;227	ENSP00000356846:L258I;ENSP00000356844:L227I;ENSP00000402143:L227I	ENSP00000356844:L227I	L	+	1	0	MAEL	165241185	0.611000	0.26992	0.982000	0.44146	0.989000	0.77384	1.344000	0.33941	1.389000	0.46526	0.591000	0.81541	CTC	.	.	.	none		0.398	MAEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083239.1	NM_032858		A	166974561	C	A	166974561	3	1	210	1	0	0	0	0	1	0	0	0	9161	913	32	4	802	4	MAEL	1	166974561	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	12659598	166974561	82276060	7	12742											
CNTN2	6900	hgsc.bcm.edu	37	chr1	205028742	205028742	+	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	tttgcacccagcatcaaggcCcggttcccagcagagaccta	10	7	9	15	1	1	1	1	0	0	1	2	2	2	1	4	2	3	4	4	2	2	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr1:205028742C>A	ENST00000331830.4	+	7	1013	c.729C>A	c.(727-729)gcC>gcA	p.A243A	AL583832.1_ENST00000515887.1_RNA	NM_005076.3	NP_005067.1	Q02246	CNTN2_HUMAN	contactin 2 (axonal)	243	Ig-like C2-type 3.				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)			GCATCAAGGCCCGGTTCCCAG	0.582																																					p.A243A	Melanoma(183;2548 2817 37099 41192)	Atlas-SNP	.											.	CNTN2	116	.	0			c.C729A						PASS	.						90	91	91					1																	205028742		2203	4300	6503	SO:0001819	synonymous_variant	6900	exon7			CAAGGCCCGGTTC	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.729C>A	chr1.hg19:g.205028742C>A		287.0	0.0	.		155.0	53.0	.	NM_005076	P78432|Q5T054	Silent	SNP	ENST00000331830.4	hg19	CCDS1449.1																																																																																			.	.	.	none		0.582	CNTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090080.3	NM_005076		A	205028742	C	A	205028742	2	1	210	1	0	0	0	0	0	0	0	1	3643	610	22	4		4	CNTN2	1	205028742	Silent	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	38054181	205028742	44221879	8	12743											
AHCTF1	25909	hgsc.bcm.edu	37	chr1	247070995	247070995	+	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	ctggaaacacagatggcgccCttgtctcattacactttctc	9	12	7	13	1	2	1	1	0	2	1	4	2	2	2	1	2	2	0	1	2	2	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr1:247070995C>T	ENST00000391829.2	-	5	745	c.622G>A	c.(622-624)Ggg>Agg	p.G208R	AHCTF1_ENST00000366508.1_Missense_Mutation_p.G243R|AHCTF1_ENST00000326225.3_Missense_Mutation_p.G217R			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	208	Necessary for cytoplasmic localization. {ECO:0000250}.|Seven-bladed beta propeller repeats. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			AGATGGCGCCCTTGTCTCATT	0.383																																					p.G217R	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.G649A						PASS	.						135	127	130					1																	247070995		2203	4300	6503	SO:0001583	missense	25909	exon5			GGCGCCCTTGTCT		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.622G>A	chr1.hg19:g.247070995C>T	ENSP00000375705:p.Gly208Arg	62.0	0.0	.		124.0	58.0	.	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Missense_Mutation	SNP	ENST00000391829.2	hg19		.	.	.	.	.	.	.	.	.	.	C	22.0	4.223797	0.79576	.	.	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	T;T;T	0.20738	2.05;2.05;2.05	5.76	5.76	0.90799	.	0.051494	0.85682	D	0.000000	T	0.26195	0.0639	N	0.19112	0.55	0.58432	D	0.999999	D;D	0.59767	0.986;0.981	P;P	0.56474	0.799;0.706	T	0.00761	-1.1577	10	0.37606	T	0.19	-24.8597	15.7857	0.78300	0.0:0.8645:0.1355:0.0	.	243;208	Q8WYP5-2;Q8WYP5	.;ELYS_HUMAN	R	243;217;208	ENSP00000355464:G243R;ENSP00000355465:G217R;ENSP00000375705:G208R	ENSP00000355465:G217R	G	-	1	0	AHCTF1	245137618	1.000000	0.71417	0.982000	0.44146	0.994000	0.84299	5.686000	0.68211	2.880000	0.98712	0.650000	0.86243	GGG	.	.	.	none		0.383	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446		T	247070995	C	T	247070995	3	4	210	1	0	0	0	0	1	0	0	0	408	681	24	2	6306	2	AHCTF1	1	247070995	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	42042253	247070995	2179626	9	12744											
OR2L8	391190	hgsc.bcm.edu	37	chr1	248112473	248112473	+	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	tcagagtttcttcttcttggCattaggaggtgcagaagcac	9	13	11	8	0	4	2	1	0	3	2	4	3	4	3	0	3	2	4	0	3	2	5			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr1:248112473C>T	ENST00000357191.3	+	1	314	c.314C>T	c.(313-315)gCa>gTa	p.A105V	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	105						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)			TTCTTCTTGGCATTAGGAGGT	0.433																																					p.A105V		Atlas-SNP	.											.	OR2L8	92	.	0			c.C314T						PASS	.						335	270	292					1																	248112473		2203	4300	6503	SO:0001583	missense	391190	exon1			TCTTGGCATTAGG	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.314C>T	chr1.hg19:g.248112473C>T	ENSP00000349719:p.Ala105Val	233.0	0.0	.		393.0	140.0	.	NM_001001963	Q6IF03	Missense_Mutation	SNP	ENST00000357191.3	hg19	CCDS31101.1	.	.	.	.	.	.	.	.	.	.	.	8.579	0.881879	0.17467	.	.	ENSG00000196936	ENST00000357191	T	0.00349	7.99	1.64	1.64	0.23874	GPCR, rhodopsin-like superfamily (1);	0.542717	0.13750	U	0.365321	T	0.00178	0.0005	N	0.20483	0.58	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.41805	-0.9488	10	0.87932	D	0	.	3.6931	0.08354	0.0:0.5144:0.0:0.4856	.	105	Q8NGY9	OR2L8_HUMAN	V	105	ENSP00000349719:A105V	ENSP00000349719:A105V	A	+	2	0	OR2L8	246179096	0.000000	0.05858	0.699000	0.30290	0.027000	0.11550	-0.195000	0.09546	0.905000	0.36596	0.479000	0.44913	GCA	.	.	.	none		0.433	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2			T	248112473	C	T	248112473	3	4	210	1	0	0	0	0	1	0	0	0	11016	710	25	2	316	2	OR2L8	1	248112473	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	1041478	248112473	1138148	10	12745											
MBOAT2	129642	hgsc.bcm.edu	37	chr2	9002791	9002791	+	Frame_Shift_Del	DEL	A	A	-																															tcctgggtataccccgtgccAaatggcagagagaatgaacg																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:9002791delA	ENST00000305997.3	-	11	1312	c.1114delT	c.(1114-1116)tggfs	p.W372fs	MBOAT2_ENST00000486484.1_5'UTR	NM_138799.2	NP_620154.2	Q6ZWT7	MBOA2_HUMAN	membrane bound O-acyltransferase domain containing 2	372					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)					ACCCCGTGCCAAATGGCAGAG	0.408																																					p.W372fs	Ovarian(194;1699 3813 22401)	Atlas-INDEL	.											.	MBOAT2	36	.	0			c.1115delG						PASS	.						96	91	93					2																	9002791		2203	4300	6503	SO:0001589	frameshift_variant	129642	exon11			.	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.1114delT	chr2.hg19:g.9002791delA	ENSP00000302177:p.Trp372fs	61.0	0.0	0		86.0	39.0	0.453488	NM_138799	A9EDR2|Q8NCE7|Q96KY4	Frame_Shift_Del	DEL	ENST00000305997.3	hg19	CCDS1660.1																																																																																			.	.	.	none		0.408	MBOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206735.1	NM_138799		-	9002791	A	-	9002791	7	5	210	1	0	1	0	1	0	0	0	0	9364	130	5	0	460	0	MBOAT2	2	9002791	Frame_Shift_Del	DEL	A	TCGA-IZ-8196-01A-11D-2396-08		9002791	234196582	11	12746											
LPIN1	23175	hgsc.bcm.edu	37	chr2	11960558	11960558	+	Missense_Mutation	SNP	G	G	C																															atgtgtattcatacaagcaaGtaggagtgtctttgaataga																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:11960558G>C	ENST00000256720.2	+	19	2524	c.2431G>C	c.(2431-2433)Gta>Cta	p.V811L	LPIN1_ENST00000396099.1_Missense_Mutation_p.V853L|LPIN1_ENST00000449576.2_Missense_Mutation_p.V896L|LPIN1_ENST00000396097.1_Missense_Mutation_p.V541L|LPIN1_ENST00000404113.2_Missense_Mutation_p.V312L|LPIN1_ENST00000425416.2_Missense_Mutation_p.V817L	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	811	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)		ATACAAGCAAGTAGGAGTGTC	0.348																																					p.V896L		Atlas-SNP	.											.	LPIN1	99	.	0			c.G2686C						PASS	.						117	110	112					2																	11960558		2203	4300	6503	SO:0001583	missense	23175	exon21			AAGCAAGTAGGAG	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.2431G>C	chr2.hg19:g.11960558G>C	ENSP00000256720:p.Val811Leu	51.0	0.0	.		74.0	28.0	.	NM_001261428	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Missense_Mutation	SNP	ENST00000256720.2	hg19	CCDS1682.1	.	.	.	.	.	.	.	.	.	.	G	35	5.510636	0.96386	.	.	ENSG00000134324	ENST00000449576;ENST00000396099;ENST00000425416;ENST00000256720;ENST00000396097;ENST00000404113	T;T;T;T;T;T	0.79454	-1.27;-1.27;-1.27;-1.27;-1.27;-1.27	6.02	6.02	0.97574	HAD-like domain (2);LNS2, Lipin/Ned1/Smp2 (2);	0.055717	0.64402	D	0.000001	D	0.90007	0.6880	M	0.87682	2.9	0.80722	D	1	D;D;D	0.64830	0.994;0.988;0.975	D;P;P	0.68039	0.955;0.907;0.883	D	0.90458	0.4444	10	0.87932	D	0	-24.1549	20.5407	0.99260	0.0:0.0:1.0:0.0	.	312;896;811	B4DET9;F5GY24;Q14693	.;.;LPIN1_HUMAN	L	896;853;817;811;541;312	ENSP00000397908:V896L;ENSP00000379406:V853L;ENSP00000401522:V817L;ENSP00000256720:V811L;ENSP00000379404:V541L;ENSP00000386120:V312L	ENSP00000256720:V811L	V	+	1	0	LPIN1	11878009	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.357000	0.97099	2.865000	0.98341	0.655000	0.94253	GTA	.	.	.	none		0.348	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693		C	11960558	G	C	11960558	3	2	210	1	0	0	0	0	1	0	0	0	8925	1029	36	4	2501	4	LPIN1	2	11960558	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	2957767	11960558	231238815	12	12747	124	2									
LPIN1	23175	hgsc.bcm.edu	37	chr2	11960560	11960560	+	Silent	SNP	A	A	G																															gtgtattcatacaagcaagtAggagtgtctttgaatagaat																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:11960560A>G	ENST00000256720.2	+	19	2526	c.2433A>G	c.(2431-2433)gtA>gtG	p.V811V	LPIN1_ENST00000396099.1_Silent_p.V853V|LPIN1_ENST00000449576.2_Silent_p.V896V|LPIN1_ENST00000396097.1_Silent_p.V541V|LPIN1_ENST00000404113.2_Silent_p.V312V|LPIN1_ENST00000425416.2_Silent_p.V817V	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	811	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)		ACAAGCAAGTAGGAGTGTCTT	0.348																																					p.V896V		Atlas-SNP	.											.	LPIN1	99	.	0			c.A2688G						PASS	.						118	111	113					2																	11960560		2203	4300	6503	SO:0001819	synonymous_variant	23175	exon21			GCAAGTAGGAGTG	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.2433A>G	chr2.hg19:g.11960560A>G		50.0	0.0	.		75.0	29.0	.	NM_001261428	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Silent	SNP	ENST00000256720.2	hg19	CCDS1682.1																																																																																			.	.	.	none		0.348	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693		G	11960560	A	G	11960560	2	3	210	1	0	0	0	0	0	0	0	1	8925	407	15	3		3	LPIN1	2	11960560	Silent	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	2	11960560	231238813	13	12748	124	2									
KIF3C	3797	hgsc.bcm.edu	37	chr2	26178417	26178417	+	Missense_Mutation	SNP	A	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	tgcagcgtctcaccttcttgAgtttcttggttttgacctcc	4	17	8	12	1	3	2	1	2	3	0	5	2	4	2	3	1	2	3	3	1	0	6			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:26178417A>C	ENST00000264712.3	-	3	2342	c.1763T>G	c.(1762-1764)cTc>cGc	p.L588R	KIF3C_ENST00000405914.1_Missense_Mutation_p.L588R	NM_002254.6	NP_002245	O14782	KIF3C_HUMAN	kinesin family member 3C	588					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)					CACCTTCTTGAGTTTCTTGGT	0.587																																					p.L588R		Atlas-SNP	.											.	KIF3C	79	.	0			c.T1763G						PASS	.						229	186	200					2																	26178417		2203	4300	6503	SO:0001583	missense	3797	exon3			TTCTTGAGTTTCT		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.1763T>G	chr2.hg19:g.26178417A>C	ENSP00000264712:p.Leu588Arg	299.0	0.0	.		155.0	62.0	.	NM_002254	O43544|Q4ZG18|Q53SX5|Q562F7	Missense_Mutation	SNP	ENST00000264712.3	hg19	CCDS1719.1	.	.	.	.	.	.	.	.	.	.	A	18.30	3.593287	0.66219	.	.	ENSG00000084731	ENST00000264712;ENST00000542511;ENST00000405914	T;T	0.78481	-1.18;-1.18	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.81669	0.4871	M	0.92026	3.265	0.80722	D	1	B;B	0.30686	0.095;0.29	B;B	0.28638	0.037;0.092	D	0.83422	0.0033	10	0.72032	D	0.01	.	13.0867	0.59144	1.0:0.0:0.0:0.0	.	588;588	B7ZM25;O14782	.;KIF3C_HUMAN	R	588;394;588	ENSP00000264712:L588R;ENSP00000385030:L588R	ENSP00000264712:L588R	L	-	2	0	KIF3C	26031921	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.119000	0.94362	1.998000	0.58463	0.459000	0.35465	CTC	.	.	.	none		0.587	KIF3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211611.1			C	26178417	A	C	26178417	3	2	210	1	0	0	0	0	1	0	0	0	8309	304	11	5	642	5	KIF3C	2	26178417	Missense_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	14217857	26178417	217020956	14	12749											
RBKS	64080	hgsc.bcm.edu	37	chr2	28004505	28004506	+	Frame_Shift_Ins	INS	-	-	T																															aacagagtaagcggaaggtcINSttttttgtaagggtaagatg																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:28004505_28004506insT	ENST00000302188.3	-	8	1697_1698	c.945_946insA	c.(943-948)aaagacfs	p.D316fs	AC110084.1_ENST00000601759.1_Intron	NM_022128.1	NP_071411.1	Q9H477	RBSK_HUMAN	ribokinase	316					D-ribose catabolic process (GO:0019303)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ribokinase activity (GO:0004747)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	7	Acute lymphoblastic leukemia(172;0.155)					AGCGGAAGGTCTTTTTTGTAAG	0.421																																					p.D316fs		Atlas-INDEL	.											.	RBKS	23	.	0			c.946_947insA						PASS	.																																			SO:0001589	frameshift_variant	64080	exon8			.	BC017425	CCDS1762.1	2p23.3	2008-02-05			ENSG00000171174	ENSG00000171174	2.7.1.15		30325	protein-coding gene	gene with protein product		611132				8382990	Standard	NM_022128		Approved	DKFZp686G13268, RBSK	uc002rlo.1	Q9H477	OTTHUMG00000097833	ENST00000302188.3:c.946dupA	chr2.hg19:g.28004511_28004511dupT	ENSP00000306817:p.Asp316fs	108.0	0.0	0		134.0	42.0	0.313433	NM_022128	A9UK04|B4DV96	Frame_Shift_Ins	INS	ENST00000302188.3	hg19	CCDS1762.1																																																																																			.	.	.	none		0.421	RBKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215118.1	NM_022128		T	28004506	-	T	28004505	7	5	210	1	0	1	1	0	0	0	0	0	13121	913	32	0	26	0	RBKS	2	28004505	Frame_Shift_Ins	INS	-	TCGA-IZ-8196-01A-11D-2396-08	1826088	28004505	215194868	15	12750											
CLIP4	79745	hgsc.bcm.edu	37	chr2	29379236	29379236	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaggattaatgacatcaaaAaaagatagtgcttctgagtc	17	10	8	6	0	2	3	1	2	1	1	3	4	2	4	0	1	1	1	0	1	6	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:29379236A>G	ENST00000320081.5	+	10	1437	c.1182A>G	c.(1180-1182)aaA>aaG	p.K394K	CLIP4_ENST00000401617.2_Silent_p.K287K|CLIP4_ENST00000404424.1_Silent_p.K394K|CLIP4_ENST00000401605.1_Silent_p.K394K	NM_024692.4	NP_078968.3	Q8N3C7	CLIP4_HUMAN	CAP-GLY domain containing linker protein family, member 4	394										endometrium(4)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(1)	26	Acute lymphoblastic leukemia(172;0.155)					TGACATCAAAAAAAGATAGTG	0.313																																					p.K394K		Atlas-SNP	.											CLIP4,colon,carcinoma,0,1	CLIP4	69	.	0			c.A1182G						PASS	.						73	74	74					2																	29379236		2203	4298	6501	SO:0001819	synonymous_variant	79745	exon10			ATCAAAAAAAGAT	AK024722	CCDS1770.1, CCDS74502.1	2p23	2013-01-10	2007-01-04	2007-01-04	ENSG00000115295	ENSG00000115295		"Ankyrin repeat domain containing"	26108	protein-coding gene	gene with protein product			"restin-like 2"	RSNL2			Standard	XM_005264562		Approved	FLJ21069	uc002rmv.3	Q8N3C7	OTTHUMG00000097837	ENST00000320081.5:c.1182A>G	chr2.hg19:g.29379236A>G		22.0	0.0	.		47.0	2.0	.	NM_024692	A0AV10|B2RMQ3|B7Z7N8|Q7Z4U3|Q96BR7|Q96MA5|Q9H7C0	Silent	SNP	ENST00000320081.5	hg19	CCDS1770.1																																																																																			.	.	.	none		0.313	CLIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215123.2	NM_024692		G	29379236	A	G	29379236	2	3	210	1	0	0	0	0	0	0	0	1	3537	11	1	3		3	CLIP4	2	29379236	Silent	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	1374731	29379236	213820137	16	12751											
PLEKHH2	130271	hgsc.bcm.edu	37	chr2	43953471	43953471	+	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	aagaggttgacagatcttgtGattcagatgaagattatgaa	15	12	11	3	0	2	8	1	4	1	4	2	8	2	8	0	1	0	1	0	1	4	4			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:43953471G>T	ENST00000282406.4	+	17	2712	c.2602G>T	c.(2602-2604)Gat>Tat	p.D868Y		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	868	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				CAGATCTTGTGATTCAGATGA	0.388																																					p.D868Y		Atlas-SNP	.											.	PLEKHH2	156	.	0			c.G2602T						PASS	.						108	102	104					2																	43953471		2203	4300	6503	SO:0001583	missense	130271	exon17			TCTTGTGATTCAG	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.2602G>T	chr2.hg19:g.43953471G>T	ENSP00000282406:p.Asp868Tyr	42.0	0.0	.		74.0	27.0	.	NM_172069	Q5JPJ6|Q6P4Q1|Q8N3Q3	Missense_Mutation	SNP	ENST00000282406.4	hg19	CCDS1812.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.667945	0.88348	.	.	ENSG00000152527	ENST00000282406	T	0.77750	-1.12	5.57	5.57	0.84162	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.049073	0.85682	D	0.000000	D	0.88887	0.6559	M	0.77313	2.365	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.991	D	0.89680	0.3890	10	0.87932	D	0	-23.2912	19.5645	0.95388	0.0:0.0:1.0:0.0	.	868;305	Q8IVE3;Q8IVE3-2	PKHH2_HUMAN;.	Y	868	ENSP00000282406:D868Y	ENSP00000282406:D868Y	D	+	1	0	PLEKHH2	43806975	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.386000	0.97228	2.599000	0.87857	0.650000	0.86243	GAT	.	.	.	none		0.388	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069		T	43953471	G	T	43953471	3	4	210	1	0	0	0	0	1	0	0	0	12084	1290	45	4	2664	4	PLEKHH2	2	43953471	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	14574235	43953471	199245902	17	12752											
DNAH6	1768	hgsc.bcm.edu	37	chr2	84777109	84777109	+	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	aaccatctcactgacaagctAaaacgaacaccttcagcaga	17	6	5	13	1	2	2	2	1	1	1	3	3	2	2	2	0	5	2	2	0	5	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:84777109A>T	ENST00000237449.6	+	8	1421	c.1413A>T	c.(1411-1413)ctA>ctT	p.L471L	DNAH6_ENST00000389394.3_Silent_p.L471L|DNAH6_ENST00000398278.2_Silent_p.L471L			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	471	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						CTGACAAGCTAAAACGAACAC	0.358																																					p.L471L		Atlas-SNP	.											.	DNAH6	194	.	0			c.A1413T						PASS	.						94	83	87					2																	84777109		2203	4300	6503	SO:0001819	synonymous_variant	1768	exon9			CAAGCTAAAACGA	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.1413A>T	chr2.hg19:g.84777109A>T		34.0	0.0	.		66.0	25.0	.	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	hg19	CCDS46348.1																																																																																			.	.	.	none		0.358	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		T	84777109	A	T	84777109	2	4	210	1	0	0	0	0	0	0	0	1	4607	349	13	5		5	DNAH6	2	84777109	Silent	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	40823638	84777109	158422264	18	12753											
POTEF	728378	hgsc.bcm.edu	37	chr2	130872496	130872496	+	Frame_Shift_Del	DEL	T	T	-																															gcaccatataagagcagtgcTttggccattaatttatcttc																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:130872496delT	ENST00000409914.2	-	5	1167	c.768delA	c.(766-768)aaafs	p.K256fs	POTEF_ENST00000360967.5_Frame_Shift_Del_p.K256fs|POTEF_ENST00000357462.5_Frame_Shift_Del_p.K256fs|POTEF_ENST00000361163.4_Frame_Shift_Del_p.K266fs	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	256					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						AGAGCAGTGCTTTGGCCATTA	0.338																																					p.A257fs		Atlas-INDEL	.											POTEF,NS,carcinoma,0,2	POTEF	140	.	0			c.769delG						PASS	.						3	3	3					2																	130872496		1247	2882	4129	SO:0001589	frameshift_variant	728378	exon5			.	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.768delA	chr2.hg19:g.130872496delT	ENSP00000386786:p.Lys256fs	91.0	0.0	0		114.0	18.0	0.157895	NM_001099771	A6NC34	Frame_Shift_Del	DEL	ENST00000409914.2	hg19	CCDS46409.1																																																																																			.	.	.	none		0.338	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771		-	130872496	T	-	130872496	7	5	210	1	0	1	0	1	0	0	0	0	12272	1606	56	0	2511	0	POTEF	2	130872496	Frame_Shift_Del	DEL	T	TCGA-IZ-8196-01A-11D-2396-08	46095387	130872496	112326877	19	12754											
POTEE	445582	hgsc.bcm.edu	37	chr2	131981572	131981572	+	Frame_Shift_Del	DEL	A	A	-																															atgaagataaattaatggccAaagcactgctcttatatggt																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:131981572delA	ENST00000356920.5	+	3	860	c.766delA	c.(766-768)aaafs	p.K256fs	PLEKHB2_ENST00000303908.3_Intron|PLEKHB2_ENST00000404460.1_Intron|POTEE_ENST00000358087.5_Frame_Shift_Del_p.K266fs	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	256					retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											ATTAATGGCCAAAGCACTGCT	0.338																																					p.A255fs		Atlas-INDEL	.											.	.	.	.	0			c.765delC						PASS	.						1	1	1					2																	131981572		992	2313	3305	SO:0001589	frameshift_variant	445582	exon3			.	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.766delA	chr2.hg19:g.131981572delA	ENSP00000439189:p.Lys256fs	69.0	0.0	0		131.0	29.0	0.221374	NM_001083538	Q6S8J4|Q6S8J5|Q6S8J8	Frame_Shift_Del	DEL	ENST00000356920.5	hg19	CCDS46414.1																																																																																			.	.	.	none		0.338	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538		-	131981572	A	-	131981572	7	5	210	1	0	1	0	1	0	0	0	0	12271	131	5	0	776	0	POTEE	2	131981572	Frame_Shift_Del	DEL	A	TCGA-IZ-8196-01A-11D-2396-08	1109076	131981572	111217801	20	12755											
MCM6	4175	hgsc.bcm.edu	37	chr2	136620201	136620202	+	Missense_Mutation	DNP	CT	CT	AG																															gaaattggctcttagctgtaCttgggtcaccaacaatgcaa																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:136620201_136620202CT>AG	ENST00000264156.2	-	8	1255_1256	c.1195_1196AG>CT	c.(1195-1197)AGt>CTt	p.S399L	MCM6_ENST00000492091.1_5'UTR	NM_005915.5	NP_005906.2	Q14566	MCM6_HUMAN	minichromosome maintenance complex component 6	399	MCM.				DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|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)		CTTAGCTGTACTTGGGTCACCA	0.485																																					p.S399I|p.S399R	Ovarian(196;141 2104 8848 24991 25939)	Atlas-SNP	.											.	MCM6	64	.	0			c.G1196T|c.A1195C						PASS	.																																			SO:0001583	missense	4175	exon8			GCTGTACTTGGGT|CTGTACTTGGGTC		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.1195_1196delinsAG	chr2.hg19:g.136620201_136620202delinsAG	ENSP00000264156:p.Ser399Leu	142.0	0.0	.		180.0|179.0	78.0	.	NM_005915	B2R6H2|Q13504|Q99859	Missense_Mutation	SNP	ENST00000264156.2	hg19	CCDS2179.1																																																																																			.	.	.	none		0.485	MCM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254658.1	NM_005915		AG	136620202	CT	AG	136620201	3	1	210	1	0	0	0	0	1	0	0	0	9398	565	20	4	1309	4	MCM6	2	136620201	Missense_Mutation	DNP	CT	TCGA-IZ-8196-01A-11D-2396-08	4638629	136620201	106579172	21	12756											
ATG9A	79065	hgsc.bcm.edu	37	chr2	220090289	220090289	+	Missense_Mutation	SNP	A	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	tgaaggcaaccacaaagaggAactgcctggggagttgggaa	14	5	15	7	0	0	2	0	1	0	1	0	5	0	5	2	5	3	2	2	5	5	1			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:220090289A>C	ENST00000409618.1	-	6	657	c.218T>G	c.(217-219)tTc>tGc	p.F73C	AC068946.1_ENST00000408417.1_RNA|ATG9A_ENST00000488833.1_5'Flank|ATG9A_ENST00000361242.4_Missense_Mutation_p.F73C|ATG9A_ENST00000409422.1_Missense_Mutation_p.F12C|ATG9A_ENST00000396761.2_Missense_Mutation_p.F73C			Q7Z3C6	ATG9A_HUMAN	autophagy related 9A	73					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)		CACAAAGAGGAACTGCCTGGG	0.532																																					p.F73C		Atlas-SNP	.											.	ATG9A	50	.	0			c.T218G						PASS	.						71	74	73					2																	220090289		2019	4190	6209	SO:0001583	missense	79065	exon6			AAGAGGAACTGCC	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.218T>G	chr2.hg19:g.220090289A>C	ENSP00000386710:p.Phe73Cys	63.0	0.0	.		59.0	22.0	.	NM_001077198	Q3ZAQ6|Q6P0N7|Q7Z317|Q7Z320|Q8NDK6|Q8WU65|Q9BVL5|Q9H6L1|Q9HAG7	Missense_Mutation	SNP	ENST00000409618.1	hg19	CCDS42820.1	.	.	.	.	.	.	.	.	.	.	A	17.32	3.360020	0.61403	.	.	ENSG00000198925	ENST00000396761;ENST00000409618;ENST00000361242;ENST00000409422;ENST00000436856;ENST00000457841;ENST00000428226;ENST00000432520;ENST00000439812;ENST00000443140;ENST00000434939	T;T;T;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;-0.7;-0.7;-0.7	5.05	5.05	0.67936	.	0.057192	0.64402	D	0.000001	T	0.73513	0.3596	M	0.78916	2.43	0.58432	D	0.999995	D	0.58620	0.983	B	0.43783	0.431	T	0.79808	-0.1647	10	0.72032	D	0.01	.	15.2471	0.73513	1.0:0.0:0.0:0.0	.	73	Q7Z3C6	ATG9A_HUMAN	C	73;73;73;12;73;73;73;73;73;73;73	ENSP00000379983:F73C;ENSP00000386710:F73C;ENSP00000355173:F73C;ENSP00000386535:F12C;ENSP00000401530:F73C;ENSP00000404750:F73C;ENSP00000409164:F73C;ENSP00000406785:F73C;ENSP00000413569:F73C;ENSP00000416435:F73C;ENSP00000394345:F73C	ENSP00000355173:F73C	F	-	2	0	ATG9A	219798533	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.040000	0.93783	2.251000	0.74343	0.482000	0.46254	TTC	.	.	.	none		0.532	ATG9A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335930.1	NM_024085		C	220090289	A	C	220090289	3	2	210	1	0	0	0	0	1	0	0	0	1102	246	9	5	2345	5	ATG9A	2	220090289	Missense_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	83470088	220090289	23109084	22	12757											
SPHKAP	80309	hgsc.bcm.edu	37	chr2	228860230	228860230	+	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	gggaagagcaggtacctcatGgatcgctcactgagctggag	10	7	15	9	1	2	2	2	1	0	1	3	5	2	5	1	4	3	4	1	4	2	1			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr2:228860230G>C	ENST00000392056.3	-	8	4675	c.4629C>G	c.(4627-4629)tcC>tcG	p.S1543S	SPHKAP_ENST00000344657.5_Silent_p.S1543S	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1543						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)		GGTACCTCATGGATCGCTCAC	0.483																																					p.S1543S		Atlas-SNP	.											.	SPHKAP	750	.	0			c.C4629G						PASS	.						226	197	207					2																	228860230		2203	4300	6503	SO:0001819	synonymous_variant	80309	exon8			CCTCATGGATCGC		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.4629C>G	chr2.hg19:g.228860230G>C		298.0	1.0	.		283.0	107.0	.	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Silent	SNP	ENST00000392056.3	hg19	CCDS46537.1																																																																																			.	.	.	none		0.483	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		C	228860230	G	C	228860230	2	2	210	1	0	0	0	0	0	0	0	1	15060	1335	47	4		4	SPHKAP	2	228860230	Silent	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	8769941	228860230	14339143	23	12758											
CAMK1	8536	hgsc.bcm.edu	37	chr3	9802445	9802445	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcatagaagggagggtaacCgcagagcctgggcagggaga	12	4	18	7	1	1	3	1	0	0	3	1	5	1	4	2	4	2	3	2	4	3	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr3:9802445C>T	ENST00000256460.3	-	8	817	c.640G>A	c.(640-642)Ggt>Agt	p.G214S	OGG1_ENST00000349503.5_Intron|OGG1_ENST00000302008.8_Intron|OGG1_ENST00000449570.2_Intron|OGG1_ENST00000383826.5_Intron|OGG1_ENST00000302036.7_Intron	NM_003656.4	NP_003647.1	Q14012	KCC1A_HUMAN	calcium/calmodulin-dependent protein kinase I	214	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)	p.G214S(1)		endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	12	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.0475)		GGAGGGTAACCGCAGAGCCTG	0.552																																					p.G214S		Atlas-SNP	.											CAMK1,NS,carcinoma,0,1	CAMK1	32	.	1	Substitution - Missense(1)	endometrium(1)	c.G640A						PASS	.						82	77	78					3																	9802445		2203	4300	6503	SO:0001583	missense	8536	exon8			GGTAACCGCAGAG	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.640G>A	chr3.hg19:g.9802445C>T	ENSP00000256460:p.Gly214Ser	76.0	0.0	.		46.0	22.0	.	NM_003656	Q3KPF6	Missense_Mutation	SNP	ENST00000256460.3	hg19	CCDS2582.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.258485|5.258485	0.95368|0.95368	.|.	.|.	ENSG00000134072|ENSG00000134072	ENST00000256460|ENST00000421120	T|.	0.58210|.	0.35|.	5.13|5.13	5.13|5.13	0.70059|0.70059	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.82962|0.82962	0.5151|0.5151	M|M	0.87269|0.87269	2.87|2.87	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.80764|.	0.994|.	D|D	0.85554|0.85554	0.1223|0.1223	10|5	0.87932|.	D|.	0|.	-14.0937|-14.0937	17.3689|17.3689	0.87371|0.87371	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	214|.	Q14012|.	KCC1A_HUMAN|.	S|Q	214|60	ENSP00000256460:G214S|.	ENSP00000256460:G214S|.	G|R	-|-	1|2	0|0	CAMK1|CAMK1	9777445|9777445	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.793000|0.793000	0.44817|0.44817	7.648000|7.648000	0.83479|0.83479	2.384000|2.384000	0.81235|0.81235	0.655000|0.655000	0.94253|0.94253	GGT|CGG	.	.	.	none		0.552	CAMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250206.1	NM_003656		T	9802445	C	T	9802445	3	4	210	1	0	0	0	0	1	0	0	0	2598	652	23	1	492	1	CAMK1	3	9802445	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08		9802445	188219985	24	12759											
C3orf71	646450	hgsc.bcm.edu	37	chr3	48956091	48956091	+	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	aacatctcgacgggagacgcTggtaggcgaatagtggctcc	10	7	14	10	4	1	1	0	0	1	1	3	4	2	1	1	4	1	3	1	4	4	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr3:48956091T>A	ENST00000408959.2	-	1	727	c.492A>T	c.(490-492)ccA>ccT	p.P164P	ARIH2_ENST00000356401.4_5'Flank|ARIH2_ENST00000449376.1_5'Flank	NM_001123040.1	NP_001116512.1	Q8N7S6	ARI2O_HUMAN	ariadne homolog 2 opposite strand	164						integral component of membrane (GO:0016021)											CGGGAGACGCTGGTAGGCGAA	0.587																																					p.P164P		Atlas-SNP	.											.	.	.	.	0			c.A492T						PASS	.						47	49	49					3																	48956091		1568	3582	5150	SO:0001819	synonymous_variant	646450	exon1			AGACGCTGGTAGG	DA461567	CCDS43088.1	3p21.31	2012-10-08	2012-10-08	2012-10-08	ENSG00000221883	ENSG00000221883			34425	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 71"	C3orf71			Standard	NM_001123040		Approved		uc010hkk.1	Q8N7S6	OTTHUMG00000156672	ENST00000408959.2:c.492A>T	chr3.hg19:g.48956091T>A		100.0	0.0	.		58.0	34.0	.	NM_001123040		Silent	SNP	ENST00000408959.2	hg19	CCDS43088.1																																																																																			.	.	.	none		0.587	ARIH2OS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345247.1	NM_001123040		A	48956091	T	A	48956091	2	1	210	1	0	0	0	0	0	0	0	1	2245	1567	55	5		5	C3orf71	3	48956091	Silent	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	39153646	48956091	149066339	25	12760											
ARHGEF3	50650	hgsc.bcm.edu	37	chr3	56789065	56789065	+	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	attgacgcacacatcgaaggTctcactccacagcttgctat	11	10	7	13	2	1	1	1	1	1	0	4	2	2	1	1	1	2	3	1	1	2	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr3:56789065T>A	ENST00000296315.3	-	3	487	c.319A>T	c.(319-321)Acc>Tcc	p.T107S	ARHGEF3_ENST00000496106.1_Missense_Mutation_p.T113S|ARHGEF3_ENST00000498517.1_5'UTR|ARHGEF3_ENST00000495373.1_Missense_Mutation_p.T107S|ARHGEF3_ENST00000413728.2_Missense_Mutation_p.T113S|ARHGEF3_ENST00000497267.1_Missense_Mutation_p.T78S|ARHGEF3_ENST00000338458.4_Missense_Mutation_p.T139S	NM_019555.2	NP_062455.1	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor (GEF) 3	107					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)		ACATCGAAGGTCTCACTCCAC	0.587																																					p.T139S		Atlas-SNP	.											.	ARHGEF3	128	.	0			c.A415T						PASS	.						165	147	153					3																	56789065		2203	4300	6503	SO:0001583	missense	50650	exon6			CGAAGGTCTCACT	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.319A>T	chr3.hg19:g.56789065T>A	ENSP00000296315:p.Thr107Ser	267.0	1.0	.		184.0	87.0	.	NM_001128615	A8K5U7|Q4FZB6|Q4QQI5|Q4QQQ0|Q59F00|Q6NUN3|Q7Z4U2|Q7Z5T2|Q9H7T4	Missense_Mutation	SNP	ENST00000296315.3	hg19	CCDS2878.1	.	.	.	.	.	.	.	.	.	.	T	35	5.460720	0.96240	.	.	ENSG00000163947	ENST00000296315;ENST00000338458;ENST00000413728;ENST00000496106;ENST00000497267;ENST00000495373;ENST00000468727;ENST00000473779	T;T;T;T;T;T;T;T	0.67345	1.6;1.6;1.6;1.6;1.6;1.6;-0.26;-0.26	5.32	5.32	0.75619	Dbl homology (DH) domain (1);	0.000000	0.85682	D	0.000000	T	0.79476	0.4452	M	0.74881	2.28	0.54753	D	0.999988	D;P;P;D;D;D	0.58268	0.969;0.938;0.882;0.982;0.982;0.982	P;P;P;P;P;P	0.60682	0.798;0.628;0.55;0.878;0.855;0.878	T	0.81760	-0.0785	10	0.59425	D	0.04	-11.4376	15.6104	0.76713	0.0:0.0:0.0:1.0	.	113;78;107;139;107;113	E9PG37;E7EU49;C9J586;Q9NR81-2;Q9NR81;Q9NR81-3	.;.;.;.;ARHG3_HUMAN;.	S	107;139;113;113;78;107;108;125	ENSP00000296315:T107S;ENSP00000341071:T139S;ENSP00000410922:T113S;ENSP00000420420:T113S;ENSP00000418826:T78S;ENSP00000417986:T107S;ENSP00000417087:T108S;ENSP00000420402:T125S	ENSP00000296315:T107S	T	-	1	0	ARHGEF3	56764105	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.991000	0.88244	2.156000	0.67533	0.533000	0.62120	ACC	.	.	.	none		0.587	ARHGEF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352431.2	NM_019555		A	56789065	T	A	56789065	3	1	210	1	0	0	0	0	1	0	0	0	904	1667	58	5	1293	5	ARHGEF3	3	56789065	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	7832974	56789065	141233365	26	12761											
RNF13	11342	hgsc.bcm.edu	37	chr3	149678575	149678575	+	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	gctaactaaaaccaaaaaaaCctgtccagtgtgcaagcaaa	19	6	6	10	0	0	0	0	0	0	0	1	0	1	0	3	0	5	3	3	0	8	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr3:149678575C>G	ENST00000344229.3	+	11	1532	c.830C>G	c.(829-831)aCc>aGc	p.T277S	RNF13_ENST00000361785.6_Missense_Mutation_p.T158S|RNF13_ENST00000392894.3_Missense_Mutation_p.T277S	NM_007282.4	NP_009213.1	O43567	RNF13_HUMAN	ring finger protein 13	277					protein autoubiquitination (GO:0051865)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(2)	11		all_neural(597;0.0138)|Myeloproliferative disorder(1037;0.0255)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			ACCAAAAAAACCTGTCCAGTG	0.398																																					p.T277S		Atlas-SNP	.											.	RNF13	57	.	0			c.C830G						PASS	.						67	66	66					3																	149678575		2203	4300	6503	SO:0001583	missense	11342	exon11			AAAAAACCTGTCC	AF037204	CCDS3146.1	3q25.1	2013-01-09			ENSG00000082996	ENSG00000082996		"RING-type (C3HC4) zinc fingers"	10057	protein-coding gene	gene with protein product		609247					Standard	NM_183381		Approved	RZF	uc003exp.4	O43567	OTTHUMG00000150338	ENST00000344229.3:c.830C>G	chr3.hg19:g.149678575C>G	ENSP00000341361:p.Thr277Ser	61.0	0.0	.		69.0	24.0	.	NM_007282	A6NC87|B3KR12|Q05D66|Q6IBJ9	Missense_Mutation	SNP	ENST00000344229.3	hg19	CCDS3146.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.38|17.38	3.374025|3.374025	0.61735|0.61735	.|.	.|.	ENSG00000082996|ENSG00000082996	ENST00000468289|ENST00000392894;ENST00000344229;ENST00000491086;ENST00000543506;ENST00000361785;ENST00000482083	.|T;T;T;T;T	.|0.41065	.|1.01;1.01;1.01;1.01;1.01	6.06|6.06	6.06|6.06	0.98353|0.98353	.|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|T	0.46852|0.46852	0.1414|0.1414	L|L	0.32530|0.32530	0.975|0.975	0.80722|0.80722	D|D	1|1	.|B;P	.|0.38565	.|0.213;0.637	.|B;P	.|0.46452	.|0.193;0.517	T|T	0.19745|0.19745	-1.0296|-1.0296	5|10	.|0.41790	.|T	.|0.15	-20.7775|-20.7775	20.6397|20.6397	0.99537|0.99537	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|158;277	.|B3KR12;O43567	.|.;RNF13_HUMAN	K|S	78|277;277;158;277;158;158	.|ENSP00000376628:T277S;ENSP00000341361:T277S;ENSP00000420667:T158S;ENSP00000355268:T158S;ENSP00000418863:T158S	.|ENSP00000341361:T277S	N|T	+|+	3|2	2|0	RNF13|RNF13	151161265|151161265	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.487000|7.487000	0.81328|0.81328	2.880000|2.880000	0.98712|0.98712	0.650000|0.650000	0.86243|0.86243	AAC|ACC	.	.	.	none		0.398	RNF13-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356876.1	NM_183384		G	149678575	C	G	149678575	3	3	210	1	0	0	0	0	1	0	0	0	13450	507	18	4	864	4	RNF13	3	149678575	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	92889510	149678575	48343855	27	12762											
GABRA2	2555	hgsc.bcm.edu	37	chr4	46312218	46312218	+	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	aatttcagaggacatgaatgAgcatccattgggaaatcctc	14	10	9	8	0	1	3	1	2	0	1	4	5	3	5	2	2	1	1	2	2	3	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr4:46312218A>T	ENST00000510861.1	-	6	704	c.531T>A	c.(529-531)gcT>gcA	p.A177A	GABRA2_ENST00000540012.1_Silent_p.A122A|GABRA2_ENST00000514090.1_Silent_p.A177A|GABRA2_ENST00000356504.1_Silent_p.A177A|GABRA2_ENST00000507069.1_Silent_p.A177A|GABRA2_ENST00000381620.4_Silent_p.A177A|GABRA2_ENST00000515082.1_Silent_p.A177A			P47869	GBRA2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 2	177					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|neurotransmitter transport (GO:0006836)|regulation of neurotransmitter levels (GO:0001505)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of synaptic vesicle membrane (GO:0030285)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	56					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198)	GACATGAATGAGCATCCATTG	0.388																																					p.A177A		Atlas-SNP	.											.	GABRA2	134	.	0			c.T531A						PASS	.						135	130	132					4																	46312218		2203	4300	6503	SO:0001819	synonymous_variant	2555	exon6			TGAATGAGCATCC		CCDS3471.1	4p12	2012-06-22			ENSG00000151834	ENSG00000151834		"GABA receptors", "Ligand-gated ion channels / GABA(A) receptors"	4076	protein-coding gene	gene with protein product	"GABA(A) receptor, alpha 2"	137140					Standard	NM_000807		Approved		uc010igc.2	P47869	OTTHUMG00000044266	ENST00000510861.1:c.531T>A	chr4.hg19:g.46312218A>T		67.0	0.0	.		125.0	52.0	.	NM_000807	A8K0U7|B7Z1H8|Q59G14	Silent	SNP	ENST00000510861.1	hg19	CCDS3471.1																																																																																			.	.	.	none		0.388	GABRA2-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360848.2			T	46312218	A	T	46312218	2	4	210	1	0	0	0	0	0	0	0	1	6168	291	11	5		5	GABRA2	4	46312218	Silent	SNP	A	TCGA-IZ-8196-01A-11D-2396-08		46312218	144842058	28	12763											
GALNTL6	442117	hgsc.bcm.edu	37	chr4	173269759	173269759	+	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	aaggttggacttcactcctgCggaccatacacagtataatt	12	11	8	10	1	1	0	1	0	0	0	2	2	2	2	2	3	2	2	2	3	4	6			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr4:173269759C>T	ENST00000506823.1	+	5	1129	c.472C>T	c.(472-474)Cgg>Tgg	p.R158W	GALNTL6_ENST00000457021.1_3'UTR|GALNTL6_ENST00000508122.1_Missense_Mutation_p.R141W	NM_001034845.2	NP_001030017.2	Q49A17	GLTL6_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 6	158	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						TTCACTCCTGCGGACCATACA	0.428																																					p.R158W		Atlas-SNP	.											.	GALNTL6	102	.	0			c.C472T						PASS	.						141	132	135					4																	173269759		2203	4300	6503	SO:0001583	missense	442117	exon5			CTCCTGCGGACCA		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.472C>T	chr4.hg19:g.173269759C>T	ENSP00000423313:p.Arg158Trp	73.0	0.0	.		171.0	88.0	.	NM_001034845	Q2L4S6	Missense_Mutation	SNP	ENST00000506823.1	hg19	CCDS34104.1	.	.	.	.	.	.	.	.	.	.	C	17.39	3.376971	0.61735	.	.	ENSG00000174473	ENST00000506823;ENST00000404275;ENST00000508122	T;T	0.63913	-0.07;-0.07	5.38	1.32	0.21799	Glycosyl transferase, family 2 (1);	0.730958	0.11188	N	0.590274	D	0.88228	0.6380	H	0.99425	4.56	0.48341	D	0.999638	D	0.89917	1.0	D	0.97110	1.0	D	0.89622	0.3849	10	0.87932	D	0	.	14.8011	0.69916	0.6209:0.3791:0.0:0.0	.	158	Q49A17	GLTL6_HUMAN	W	158;158;141	ENSP00000423313:R158W;ENSP00000423827:R141W	ENSP00000385382:R158W	R	+	1	2	GALNTL6	173506334	0.987000	0.35691	1.000000	0.80357	0.979000	0.70002	0.342000	0.19926	0.212000	0.20703	-0.470000	0.05040	CGG	.	.	.	none		0.428	GALNTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362395.1	NM_001034845		T	173269759	C	T	173269759	3	4	210	1	0	0	0	0	1	0	0	0	6232	759	27	1	486	1	GALNTL6	4	173269759	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	126957541	173269759	17884517	29	12764											
SLC9A3	6550	hgsc.bcm.edu	37	chr5	476140	476140	+	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	gggcccccagcgcacctttcTccttgatggtgaaattctgc	6	11	10	14	1	2	2	0	2	2	0	3	2	2	2	4	2	2	1	4	2	1	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr5:476140T>A	ENST00000264938.3	-	14	2144	c.2135A>T	c.(2134-2136)gAg>gTg	p.E712V	CTD-2228K2.7_ENST00000607286.1_RNA|CTD-2228K2.7_ENST00000607005.1_RNA|CTD-2228K2.7_ENST00000606288.1_RNA|CTD-2228K2.7_ENST00000606319.1_RNA|CTD-2228K2.5_ENST00000342584.3_5'Flank|SLC9A3_ENST00000514375.1_Missense_Mutation_p.E703V	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	712					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)			CGCACCTTTCTCCTTGATGGT	0.642																																					p.E712V		Atlas-SNP	.											.	SLC9A3	89	.	0			c.A2135T						PASS	.						24	26	25					5																	476140		2203	4300	6503	SO:0001583	missense	6550	exon14			CCTTTCTCCTTGA		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.2135A>T	chr5.hg19:g.476140T>A	ENSP00000264938:p.Glu712Val	77.0	0.0	.		24.0	9.0	.	NM_004174	B7ZKR2|E9PF67|Q3MIW3	Missense_Mutation	SNP	ENST00000264938.3	hg19	CCDS3855.1	.	.	.	.	.	.	.	.	.	.	T	9.100	1.003901	0.19199	.	.	ENSG00000066230	ENST00000264938;ENST00000514375	T;T	0.72942	-0.7;-0.7	3.93	3.93	0.45458	.	11.221700	0.00508	N	0.000168	T	0.70360	0.3215	M	0.64997	1.995	0.30953	N	0.724513	B;P	0.35433	0.222;0.501	B;B	0.35470	0.059;0.203	T	0.57470	-0.7806	10	0.25106	T	0.35	.	9.4489	0.38714	0.0:0.0:0.0:1.0	.	703;712	E9PF67;P48764	.;SL9A3_HUMAN	V	712;703	ENSP00000264938:E712V;ENSP00000422983:E703V	ENSP00000264938:E712V	E	-	2	0	SLC9A3	529140	0.009000	0.17119	0.998000	0.56505	0.230000	0.25150	0.875000	0.28079	1.565000	0.49641	0.155000	0.16302	GAG	.	.	.	none		0.642	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174		A	476140	T	A	476140	3	1	210	1	0	0	0	0	1	0	0	0	14726	1551	54	5	385	5	SLC9A3	5	476140	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08		476140	180439120	30	12765											
ADAMTS16	170690	hgsc.bcm.edu	37	chr5	5235155	5235155	+	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	atggagggaagttctgtgagGgctccactcgcactctgaag	9	9	14	9	1	2	2	0	2	2	0	4	4	3	4	1	3	0	3	1	3	2	1			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr5:5235155G>C	ENST00000274181.7	+	13	2017	c.1879G>C	c.(1879-1881)Ggc>Cgc	p.G627R	ADAMTS16_ENST00000513709.1_3'UTR	NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	627	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						GTTCTGTGAGGGCTCCACTCG	0.443																																					p.G627R		Atlas-SNP	.											.	ADAMTS16	543	.	0			c.G1879C						PASS	.						66	69	68					5																	5235155		1926	4118	6044	SO:0001583	missense	170690	exon13			TGTGAGGGCTCCA	AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536		"ADAM metallopeptidases with thrombospondin type 1 motif"	17108	protein-coding gene	gene with protein product		607510	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16"			11867212	Standard	NM_139056		Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.1879G>C	chr5.hg19:g.5235155G>C	ENSP00000274181:p.Gly627Arg	126.0	0.0	.		81.0	34.0	.	NM_139056	C6G490|Q8IVE2	Missense_Mutation	SNP	ENST00000274181.7	hg19	CCDS43299.1	.	.	.	.	.	.	.	.	.	.	G	17.23	3.337693	0.60963	.	.	ENSG00000145536	ENST00000274181;ENST00000536857	T	0.09163	3.01	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.54886	0.1886	H	0.99565	4.63	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.76984	-0.2756	10	0.72032	D	0.01	.	17.2614	0.87071	0.0:0.0:1.0:0.0	.	627;627	Q8TE57;Q8TE57-2	ATS16_HUMAN;.	R	627	ENSP00000274181:G627R	ENSP00000274181:G627R	G	+	1	0	ADAMTS16	5288155	1.000000	0.71417	0.963000	0.40424	0.056000	0.15407	9.323000	0.96364	2.446000	0.82766	0.655000	0.94253	GGC	.	.	.	none		0.443	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056		C	5235155	G	C	5235155	3	2	210	1	0	0	0	0	1	0	0	0	261	1232	43	4	1929	4	ADAMTS16	5	5235155	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	4759015	5235155	175680105	31	12766											
IL7R	3575	hgsc.bcm.edu	37	chr5	35876145	35876145	+	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	gccagattcatagggtggatGacattcaagctagagatgaa	14	9	12	6	0	2	4	2	2	0	2	2	6	2	5	1	2	1	1	1	2	4	4			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr5:35876145G>T	ENST00000303115.3	+	8	1066	c.937G>T	c.(937-939)Gac>Tac	p.D313Y	IL7R_ENST00000343305.4_3'UTR	NM_002185.3	NP_002176.2	P16871	IL7RA_HUMAN	interleukin 7 receptor	313					B cell proliferation (GO:0042100)|cell growth (GO:0016049)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|immune response (GO:0006955)|immunoglobulin production (GO:0002377)|interleukin-7-mediated signaling pathway (GO:0038111)|lymph node development (GO:0048535)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|positive regulation of gene expression (GO:0010628)|positive regulation of T cell differentiation in thymus (GO:0033089)|regulation of cell size (GO:0008361)|regulation of DNA recombination (GO:0000018)|signal transduction (GO:0007165)|T cell differentiation (GO:0030217)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|interleukin-7 receptor activity (GO:0004917)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(78)|kidney(2)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|skin(5)|stomach(3)	126	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)			TAGGGTGGATGACATTCAAGC	0.438			"Mis, O"		"ALL, ETP ALL"		Severe combined immune deficiency																														p.D313Y		Atlas-SNP	.		Dom	yes		5	5p13	146661	interleukin 7 receptor	yes	L	.	IL7R	200	.	0			c.G937T						PASS	.						89	84	85					5																	35876145		2203	4300	6503	SO:0001583	missense	3575	exon8			GTGGATGACATTC	M29696	CCDS3911.1	5p13	2014-09-17			ENSG00000168685	ENSG00000168685		"Interleukins and interleukin receptors", "CD molecules", "Fibronectin type III domain containing"	6024	protein-coding gene	gene with protein product		146661				2317865	Standard	NM_002185		Approved	CD127	uc003jjs.4	P16871	OTTHUMG00000090791	ENST00000303115.3:c.937G>T	chr5.hg19:g.35876145G>T	ENSP00000306157:p.Asp313Tyr	62.0	0.0	.		87.0	37.0	.	NM_002185	B2RCS6|B4DVT1|Q05CU8|Q6NSP4|Q6NWM0|Q6NWM1|Q6NWM2|Q6NWM3|Q6SV45|Q9UPC1	Missense_Mutation	SNP	ENST00000303115.3	hg19	CCDS3911.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.199424	0.79015	.	.	ENSG00000168685	ENST00000303115;ENST00000505875	T;T	0.35421	1.9;1.31	6.06	6.06	0.98353	.	0.458345	0.25467	N	0.030468	T	0.30854	0.0778	N	0.14661	0.345	0.80722	D	1	D	0.56521	0.976	P	0.46975	0.533	T	0.09885	-1.0654	10	0.72032	D	0.01	-1.5157	16.1283	0.81408	0.0:0.0:1.0:0.0	.	313	P16871	IL7RA_HUMAN	Y	313;79	ENSP00000306157:D313Y;ENSP00000420923:D79Y	ENSP00000306157:D313Y	D	+	1	0	IL7R	35911902	1.000000	0.71417	0.998000	0.56505	0.961000	0.63080	3.729000	0.54999	2.871000	0.98454	0.655000	0.94253	GAC	.	.	.	none		0.438	IL7R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207577.2			T	35876145	G	T	35876145	3	4	210	1	0	0	0	0	1	0	0	0	7712	1290	45	4	967	4	IL7R	5	35876145	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	30640990	35876145	145039115	32	12767											
PPIC	5480	hgsc.bcm.edu	37	chr5	122359696	122359696	+	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	agctctatggagtgcaccacTgtctggtgagagaaaagtag	12	9	13	7	0	2	2	0	1	2	1	2	4	2	3	1	2	2	3	1	2	4	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr5:122359696T>A	ENST00000306442.4	-	5	628	c.513A>T	c.(511-513)acA>acT	p.T171T	RN7SL689P_ENST00000577215.1_RNA	NM_000943.4	NP_000934.1	P45877	PPIC_HUMAN	peptidylprolyl isomerase C (cyclophilin C)	171	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				protein folding (GO:0006457)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	6		all_cancers(142;0.0168)|Prostate(80;0.0322)|Lung NSC(810;0.102)|all_lung(232;0.163)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000331)|Epithelial(69;0.000553)|all cancers(49;0.00505)	L-Proline(DB00172)	AGTGCACCACTGTCTGGTGAG	0.478																																					p.T171T	Ovarian(99;690 1502 20765 45543 49568)	Atlas-SNP	.											.	PPIC	18	.	0			c.A513T						PASS	.						203	187	192					5																	122359696		2203	4300	6503	SO:0001819	synonymous_variant	5480	exon5			CACCACTGTCTGG	S71018	CCDS4133.1	5q23.2	2008-02-05			ENSG00000168938	ENSG00000168938	5.2.1.8		9256	protein-coding gene	gene with protein product		123842				1383094, 8031755	Standard	NM_000943		Approved	CYPC	uc003kth.3	P45877	OTTHUMG00000128921	ENST00000306442.4:c.513A>T	chr5.hg19:g.122359696T>A		177.0	0.0	.		188.0	76.0	.	NM_000943	A4LBB5	Silent	SNP	ENST00000306442.4	hg19	CCDS4133.1																																																																																			.	.	.	none		0.478	PPIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250898.2	NM_000943		A	122359696	T	A	122359696	2	1	210	1	0	0	0	0	0	0	0	1	12330	1567	55	5		5	PPIC	5	122359696	Silent	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	86483551	122359696	58555564	33	12768											
PCDHA8	56140	hgsc.bcm.edu	37	chr5	140223201	140223201	+	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	tgctctggtgaggggccaccGaagacggacctcatggcctt	7	8	14	12	2	2	2	1	1	1	1	2	4	2	3	4	5	1	1	4	5	1	1			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr5:140223201G>A	ENST00000531613.1	+	1	2295	c.2295G>A	c.(2293-2295)ccG>ccA	p.P765P	PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA8_ENST00000378123.3_Silent_p.P765P|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	765					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)			AGGGGCCACCGAAGACGGACC	0.592																																					p.P765P		Atlas-SNP	.											.	PCDHA8	366	.	0			c.G2295A						PASS	.						59	60	60					5																	140223201		2196	4262	6458	SO:0001819	synonymous_variant	56140	exon1			GCCACCGAAGACG	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.2295G>A	chr5.hg19:g.140223201G>A		64.0	0.0	.		40.0	32.0	.	NM_031856	B9EGT7|O75281	Silent	SNP	ENST00000531613.1	hg19	CCDS54919.1																																																																																			.	.	.	none		0.592	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911		A	140223201	G	A	140223201	2	1	210	1	0	0	0	0	0	0	0	1	11537	1045	37	1		1	PCDHA8	5	140223201	Silent	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	17863505	140223201	40692059	34	12769											
PCDHGA12	26025	hgsc.bcm.edu	37	chr5	140811805	140811805	+	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	atcacttattccctggctgaGaacaccatccaaggggcaag	12	8	9	12	0	1	1	1	1	0	1	3	2	3	1	3	3	1	2	3	3	4	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr5:140811805G>A	ENST00000252085.3	+	1	1621	c.1479G>A	c.(1477-1479)gaG>gaA	p.E493E	PCDHGB2_ENST00000522605.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	493	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCCTGGCTGAGAACACCATCC	0.557																																					p.E493E		Atlas-SNP	.											.	PCDHGA12	271	.	0			c.G1479A						PASS	.						75	81	79					5																	140811805		2203	4300	6503	SO:0001819	synonymous_variant	26025	exon1			GGCTGAGAACACC	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.1479G>A	chr5.hg19:g.140811805G>A		161.0	0.0	.		87.0	36.0	.	NM_032094	O15100|Q6UW70|Q9Y5D7	Silent	SNP	ENST00000252085.3	hg19	CCDS4260.1																																																																																			.	.	.	none		0.557	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735		A	140811805	G	A	140811805	2	1	210	1	0	0	0	0	0	0	0	1	11560	933	33	2		2	PCDHGA12	5	140811805	Silent	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	588604	140811805	40103455	35	12770											
LARP1	23367	hgsc.bcm.edu	37	chr5	154183178	154183178	+	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	ccgctctctaccaaccactgTcccagagtcaccaaactacc	11	7	4	19	1	2	1	1	0	1	1	4	1	3	1	6	0	4	1	6	0	4	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr5:154183178T>A	ENST00000336314.4	+	13	2105	c.2081T>A	c.(2080-2082)gTc>gAc	p.V694D		NM_015315.3	NP_056130.2	Q6PKG0	LARP1_HUMAN	La ribonucleoprotein domain family, member 1	771					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)			CCAACCACTGTCCCAGAGTCA	0.582																																					p.V694D		Atlas-SNP	.											.	LARP1	187	.	0			c.T2081A						PASS	.						153	132	139					5																	154183178		2203	4300	6503	SO:0001583	missense	23367	exon13			CCACTGTCCCAGA	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.2081T>A	chr5.hg19:g.154183178T>A	ENSP00000336721:p.Val694Asp	98.0	0.0	.		64.0	29.0	.	NM_015315	O94836|Q8N4M2|Q8NB73|Q9UFD7	Missense_Mutation	SNP	ENST00000336314.4	hg19	CCDS4328.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.11|18.11	3.551818|3.551818	0.65311|0.65311	.|.	.|.	ENSG00000155506|ENSG00000155506	ENST00000518677|ENST00000336314;ENST00000518297;ENST00000524248	.|T;T;T	.|0.38240	.|1.67;1.15;1.22	5.67|5.67	5.67|5.67	0.87782|0.87782	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.59459|0.59459	0.2195|0.2195	M|M	0.72118|0.72118	2.19|2.19	0.80722|0.80722	D|D	1|1	.|D;D	.|0.71674	.|0.997;0.998	.|D;D	.|0.74348	.|0.92;0.983	T|T	0.60551|0.60551	-0.7241|-0.7241	5|10	.|0.48119	.|T	.|0.1	-16.9963|-16.9963	15.9212|15.9212	0.79575|0.79575	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|771;694	.|Q6PKG0;Q6PKG0-3	.|LARP1_HUMAN;.	T|D	85|694;771;566	.|ENSP00000336721:V694D;ENSP00000428589:V771D;ENSP00000429904:V566D	.|ENSP00000336721:V694D	S|V	+|+	1|2	0|0	LARP1|LARP1	154163371|154163371	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.186000|0.186000	0.23388|0.23388	7.633000|7.633000	0.83260|0.83260	2.155000|2.155000	0.67459|0.67459	0.460000|0.460000	0.39030|0.39030	TCC|GTC	.	.	.	none		0.582	LARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252509.1	NM_033551		A	154183178	T	A	154183178	3	1	210	1	0	0	0	0	1	0	0	0	8635	1667	58	5	2131	5	LARP1	5	154183178	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	13371373	154183178	26732082	36	12771											
PANK3	79646	hgsc.bcm.edu	37	chr5	167995656	167995656	+	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	gtaaaagatacctactgtgcGaaaatctttttcaaacttgt	14	14	6	7	1	2	1	1	0	1	1	2	2	2	1	1	0	4	1	1	0	7	6			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr5:167995656G>A	ENST00000239231.6	-	2	692	c.376C>T	c.(376-378)Cgc>Tgc	p.R126C	PANK3_ENST00000520504.1_5'Flank	NM_024594.3	NP_078870.1	Q9H999	PANK3_HUMAN	pantothenate kinase 3	126					coenzyme A biosynthetic process (GO:0015937)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)	p.R126C(1)		NS(1)|cervix(2)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	16	Renal(175;0.000159)|Lung NSC(126;0.0441)|all_lung(126;0.0909)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0989)|OV - Ovarian serous cystadenocarcinoma(192;0.147)|Epithelial(171;0.188)		CCTACTGTGCGAAAATCTTTT	0.373																																					p.R126C		Atlas-SNP	.											PANK3,NS,carcinoma,0,2	PANK3	39	.	1	Substitution - Missense(1)	cervix(1)	c.C376T						PASS	.						80	77	78					5																	167995656		2203	4300	6503	SO:0001583	missense	79646	exon2			CTGTGCGAAAATC	AK022961	CCDS4368.1	5q35.1	2008-02-05			ENSG00000120137	ENSG00000120137			19365	protein-coding gene	gene with protein product		606161				11479594	Standard	NM_024594		Approved	FLJ12899	uc003lzz.2	Q9H999	OTTHUMG00000130410	ENST00000239231.6:c.376C>T	chr5.hg19:g.167995656G>A	ENSP00000239231:p.Arg126Cys	71.0	0.0	.		102.0	36.0	.	NM_024594	D3DQL1|Q53FJ9|Q7RTX4	Missense_Mutation	SNP	ENST00000239231.6	hg19	CCDS4368.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.021887	0.75275	.	.	ENSG00000120137	ENST00000239231;ENST00000522176	D;D	0.99582	-6.22;-6.22	5.81	5.81	0.92471	.	0.045054	0.85682	D	0.000000	D	0.99387	0.9784	M	0.72118	2.19	0.80722	D	1	D	0.61697	0.99	P	0.54856	0.762	D	0.99429	1.0935	10	0.54805	T	0.06	-7.4746	19.0666	0.93114	0.0:0.0:1.0:0.0	.	126	Q9H999	PANK3_HUMAN	C	126;111	ENSP00000239231:R126C;ENSP00000428631:R111C	ENSP00000239231:R126C	R	-	1	0	PANK3	167928234	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	5.446000	0.66600	2.736000	0.93811	0.655000	0.94253	CGC	.	.	.	none		0.373	PANK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252793.2	NM_024594		A	167995656	G	A	167995656	3	1	210	1	0	0	0	0	1	0	0	0	11425	1058	37	1	760	1	PANK3	5	167995656	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	13812478	167995656	12919604	37	12772											
DHX16	8449	hgsc.bcm.edu	37	chr6	30640454	30640454	+	Silent	SNP	G	G	T																															aagtcccgggccggcccactGagatccaaggtatcagtgtc																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr6:30640454G>T	ENST00000376442.3	-	1	360	c.165C>A	c.(163-165)ctC>ctA	p.L55L		NM_001164239.1|NM_003587.4	NP_001157711.1|NP_003578.2	O60231	DHX16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 16	55					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			kidney(2)|ovary(2)	4						CCGGCCCACTGAGATCCAAGG	0.652																																					p.L55L		Atlas-SNP	.											.	DHX16	119	.	0			c.C165A						PASS	.						51	54	53					6																	30640454		1508	2709	4217	SO:0001819	synonymous_variant	8449	exon1			CCCACTGAGATCC	AB001601	CCDS4685.1	6p21.3	2010-02-17	2003-06-13	2003-06-20	ENSG00000204560	ENSG00000204560		"DEAH-boxes"	2739	protein-coding gene	gene with protein product		603405	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 16"	DDX16		9547260	Standard	NM_003587		Approved	DBP2, Prp2, PRPF2	uc003nqz.3	O60231	OTTHUMG00000031060	ENST00000376442.3:c.165C>A	chr6.hg19:g.30640454G>T		174.0	0.0	.		66.0	24.0	.	NM_003587	O60322|Q5JP45|Q969X7|Q96QC1	Silent	SNP	ENST00000376442.3	hg19	CCDS4685.1																																																																																			.	.	.	none		0.652	DHX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076076.2	NM_003587		T	30640454	G	T	30640454	2	4	210	1	0	0	0	0	0	0	0	1	4504	1277	45	4		4	DHX16	6	30640454	Silent	SNP	G	TCGA-IZ-8196-01A-11D-2396-08		30640454	140474613	38	12773	125	2									
DHX16	8449	hgsc.bcm.edu	37	chr6	30640464	30640464	+	Missense_Mutation	SNP	G	G	T																															ccggcccactgagatccaagGtatcagtgtctcgtaggcgc																								rs375439029		TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr6:30640464G>T	ENST00000376442.3	-	1	350	c.155C>A	c.(154-156)aCc>aAc	p.T52N		NM_001164239.1|NM_003587.4	NP_001157711.1|NP_003578.2	O60231	DHX16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 16	52					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			kidney(2)|ovary(2)	4						GAGATCCAAGGTATCAGTGTC	0.647																																					p.T52N		Atlas-SNP	.											.	DHX16	119	.	0			c.C155A						PASS	.						52	55	54					6																	30640464		1509	2709	4218	SO:0001583	missense	8449	exon1			TCCAAGGTATCAG	AB001601	CCDS4685.1	6p21.3	2010-02-17	2003-06-13	2003-06-20	ENSG00000204560	ENSG00000204560		"DEAH-boxes"	2739	protein-coding gene	gene with protein product		603405	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 16"	DDX16		9547260	Standard	NM_003587		Approved	DBP2, Prp2, PRPF2	uc003nqz.3	O60231	OTTHUMG00000031060	ENST00000376442.3:c.155C>A	chr6.hg19:g.30640464G>T	ENSP00000365625:p.Thr52Asn	177.0	0.0	.		70.0	23.0	.	NM_003587	O60322|Q5JP45|Q969X7|Q96QC1	Missense_Mutation	SNP	ENST00000376442.3	hg19	CCDS4685.1	.	.	.	.	.	.	.	.	.	.	G	14.67	2.604490	0.46423	.	.	ENSG00000204560	ENST00000376442	T	0.02709	4.19	4.61	4.61	0.57282	.	0.054721	0.64402	D	0.000001	T	0.01661	0.0053	L	0.52364	1.645	0.80722	D	1	P	0.41673	0.759	B	0.37267	0.245	T	0.63844	-0.6545	10	0.17832	T	0.49	.	16.3585	0.83245	0.0:0.0:1.0:0.0	.	52	O60231	DHX16_HUMAN	N	52	ENSP00000365625:T52N	ENSP00000365625:T52N	T	-	2	0	DHX16	30748443	1.000000	0.71417	0.876000	0.34364	0.601000	0.36947	7.517000	0.81783	2.395000	0.81488	0.400000	0.26472	ACC	.	.	.	alt		0.647	DHX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076076.2	NM_003587		T	30640464	G	T	30640464	3	4	210	1	0	0	0	0	1	0	0	0	4504	1261	44	4	3050	4	DHX16	6	30640464	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	10	30640464	140474603	39	12774	125	2									
TNF	7124	hgsc.bcm.edu	37	chr6	31545047	31545049	+	In_Frame_Del	DEL	CCC	CCC	-																															ctcttcaagggccaaggctgCccctccacccatgtgctcct																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	CCC	CCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr6:31545047_31545049delCCC	ENST00000449264.2	+	4	610_612	c.435_437delCCC	c.(433-438)tgcccc>tgc	p.P146del		NM_000594.3	NP_000585.2	P01375	TNFA_HUMAN	tumor necrosis factor	146					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)	GCCAAGGCTGCCCCTCCACCCAT	0.611									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of																												p.145_146del		Atlas-INDEL	.											.	TNF	15	.	0			c.434_436del						PASS	.																																			SO:0001651	inframe_deletion	7124	exon4	Familial Cancer Database	incl.: Familial Head and Neck Cancer	.	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.435_437delCCC	chr6.hg19:g.31545047_31545049delCCC	ENSP00000398698:p.Pro146del	259.0	0.0	0		119.0	42.0	0.352941	NM_000594	O43647|Q9P1Q2|Q9UIV3	In_Frame_Del	DEL	ENST00000449264.2	hg19	CCDS4702.1																																																																																			.	.	.	none		0.611	TNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076390.2			-	31545049	CCC	-	31545047	7	5	210	1	0	1	0	1	0	0	0	0	16283	747	26	0	449	0	TNF	6	31545047	In_Frame_Del	DEL	CCC	TCGA-IZ-8196-01A-11D-2396-08	904583	31545047	139570020	40	12775											
DAXX	1616	hgsc.bcm.edu	37	chr6	33287821	33287822	+	Frame_Shift_Ins	INS	-	-	A																															tcctcttcgtcctcctcttcINSatcatcctcctgaccctcct																								rs145347312		TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr6:33287821_33287822insA	ENST00000374542.5	-	5	1635_1636	c.1431_1432insT	c.(1429-1434)gatgaafs	p.E478fs	ZBTB22_ENST00000431845.2_5'Flank|ZBTB22_ENST00000418724.1_5'Flank|DAXX_ENST00000414083.2_Frame_Shift_Ins_p.E403fs|DAXX_ENST00000477162.1_5'UTR|DAXX_ENST00000266000.6_Frame_Shift_Ins_p.E478fs	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	478	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						tcctcctcttcatcatcctcct	0.505			"Mis, F, N"		Pancreatic neuroendocrine tumors. Paediatric GBM																																p.E490_E491delinsX		Atlas-INDEL	.		Rec	yes		6	6p21.3	1616	death-domain associated protein		E	.	DAXX	111	.	0			c.1468_1469insT						PASS	.																																			SO:0001589	frameshift_variant	1616	exon5			.	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.1432dupT	chr6.hg19:g.33287822_33287822dupA	ENSP00000363668:p.Glu478fs	30.0	0.0	0		22.0	10.0	0.454545	NM_001141970	B4E1I3|F5H082|O14747|O15141|O15208|Q5STK9|Q9BWI3	Frame_Shift_Ins	INS	ENST00000374542.5	hg19	CCDS4776.1																																																																																			.	.	.	none		0.505	DAXX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076403.1			A	33287822	-	A	33287821	7	5	210	1	0	1	1	0	0	0	0	0	4245	835	29	0	806	0	DAXX	6	33287821	Frame_Shift_Ins	INS	-	TCGA-IZ-8196-01A-11D-2396-08	1742774	33287821	137827246	41	12776											
MDN1	23195	hgsc.bcm.edu	37	chr6	90426453	90426453	+	Missense_Mutation	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	tgtcaacccattcaaatgtgCcatggctatggccactggcc	9	10	9	13	0	2	0	2	0	0	0	2	0	2	0	4	3	2	1	4	3	3	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr6:90426453C>T	ENST00000369393.3	-	44	6774	c.6659G>A	c.(6658-6660)gGc>gAc	p.G2220D	MDN1_ENST00000428876.1_Missense_Mutation_p.G2220D			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	2220					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)		TTCAAATGTGCCATGGCTATG	0.473																																					p.G2220D		Atlas-SNP	.											.	MDN1	478	.	0			c.G6659A						PASS	.						114	95	101					6																	90426453		2203	4300	6503	SO:0001583	missense	23195	exon44			AATGTGCCATGGC	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.6659G>A	chr6.hg19:g.90426453C>T	ENSP00000358400:p.Gly2220Asp	73.0	0.0	.		94.0	38.0	.	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	hg19	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	C	19.83	3.900696	0.72754	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.58210	0.35;0.35	5.35	5.35	0.76521	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.000000	0.85682	D	0.000000	T	0.75428	0.3848	M	0.91768	3.24	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	T	0.77640	-0.2512	10	0.42905	T	0.14	.	19.4391	0.94811	0.0:1.0:0.0:0.0	.	2220	Q9NU22	MDN1_HUMAN	D	2220	ENSP00000358400:G2220D;ENSP00000413970:G2220D	ENSP00000358400:G2220D	G	-	2	0	MDN1	90483174	1.000000	0.71417	1.000000	0.80357	0.822000	0.46500	7.600000	0.82769	2.660000	0.90430	0.557000	0.71058	GGC	.	.	.	none		0.473	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			T	90426453	C	T	90426453	3	4	210	1	0	0	0	0	1	0	0	0	9422	739	26	2	10367	2	MDN1	6	90426453	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	57138632	90426453	80688614	42	12777											
SIM1	6492	hgsc.bcm.edu	37	chr6	100895187	100895187	+	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	gatacagtgtggcctggaggAgcgactgttgtgcacgatgg	8	9	17	7	2	0	0	0	0	0	0	0	5	0	2	1	4	3	2	1	4	1	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr6:100895187A>T	ENST00000369208.3	-	9	1737	c.955T>A	c.(955-957)Tcc>Acc	p.S319T	SIM1_ENST00000262901.4_Missense_Mutation_p.S319T			P81133	SIM1_HUMAN	single-minded family bHLH transcription factor 1	319	PAC.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(1)|large_intestine(15)|lung(34)|ovary(4)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	79		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		GGCCTGGAGGAGCGACTGTTG	0.597																																					p.S319T		Atlas-SNP	.											.	SIM1	173	.	0			c.T955A						PASS	.						165	123	137					6																	100895187		2203	4300	6503	SO:0001583	missense	6492	exon8			TGGAGGAGCGACT	U70212	CCDS5045.1	6q16.3	2013-10-17	2013-10-17		ENSG00000112246	ENSG00000112246		"Basic helix-loop-helix proteins"	10882	protein-coding gene	gene with protein product		603128	"single-minded (Drosophila) homolog 1", "single-minded homolog 1 (Drosophila)"			9199934, 11448938	Standard	NM_005068		Approved	bHLHe14	uc003pqj.4	P81133	OTTHUMG00000015275	ENST00000369208.3:c.955T>A	chr6.hg19:g.100895187A>T	ENSP00000358210:p.Ser319Thr	100.0	0.0	.		59.0	22.0	.	NM_005068	Q5TDP7	Missense_Mutation	SNP	ENST00000369208.3	hg19	CCDS5045.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.772481	0.90108	.	.	ENSG00000112246	ENST00000369208;ENST00000262901	T;T	0.16457	2.34;2.34	6.17	6.17	0.99709	PAS fold-3 (1);	0.000000	0.85682	D	0.000000	T	0.23766	0.0575	L	0.39085	1.19	0.58432	D	0.999999	D	0.76494	0.999	D	0.73380	0.98	T	0.01273	-1.1399	10	0.49607	T	0.09	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	319	P81133	SIM1_HUMAN	T	319	ENSP00000358210:S319T;ENSP00000262901:S319T	ENSP00000262901:S319T	S	-	1	0	SIM1	101001908	1.000000	0.71417	0.998000	0.56505	0.971000	0.66376	7.296000	0.78790	2.371000	0.80710	0.533000	0.62120	TCC	.	.	.	none		0.597	SIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041628.3	NM_005068		T	100895187	A	T	100895187	3	4	210	1	0	0	0	0	1	0	0	0	14336	304	11	5	1361	5	SIM1	6	100895187	Missense_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	10468734	100895187	70219880	43	12778											
REV3L	5980	hgsc.bcm.edu	37	chr6	111695488	111695488	+	Frame_Shift_Del	DEL	T	T	-																															gattggaaaggtcaaatataTttttttgaattaacgttgat																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr6:111695488delT	ENST00000358835.3	-	14	4524	c.4070delA	c.(4069-4071)aatfs	p.N1357fs	REV3L_ENST00000435970.1_Frame_Shift_Del_p.N1279fs|REV3L_ENST00000368802.3_Frame_Shift_Del_p.N1357fs|REV3L_ENST00000368805.1_Frame_Shift_Del_p.N1357fs			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	1357					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)		GTCAAATATATTTTTTTGAAT	0.308								DNA polymerases (catalytic subunits)																													p.N1357fs		Atlas-INDEL	.											.	REV3L	386	.	0			c.4071delT						PASS	.						63	69	67					6																	111695488		2201	4296	6497	SO:0001589	frameshift_variant	5980	exon13			.	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.4070delA	chr6.hg19:g.111695488delT	ENSP00000351697:p.Asn1357fs	55.0	0.0	0		134.0	52.0	0.38806	NM_002912	O43214|Q5TC33	Frame_Shift_Del	DEL	ENST00000358835.3	hg19	CCDS5091.2																																																																																			.	.	.	none		0.308	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		-	111695488	T	-	111695488	7	5	210	1	0	1	0	1	0	0	0	0	13253	1493	52	0	5402	0	REV3L	6	111695488	Frame_Shift_Del	DEL	T	TCGA-IZ-8196-01A-11D-2396-08	10800301	111695488	59419579	44	12779											
AHR	196	hgsc.bcm.edu	37	chr7	17362177	17362177	+	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	ggaggccaggataactgtagAgcagcaaatttcagagaagg	15	6	14	6	0	1	2	1	0	0	2	1	5	1	4	1	4	3	3	1	4	4	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr7:17362177A>T	ENST00000242057.4	+	3	949	c.306A>T	c.(304-306)agA>agT	p.R102S		NM_001621.4	NP_001612.1	P35869	AHR_HUMAN	aryl hydrocarbon receptor	102					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)	ATAACTGTAGAGCAGCAAATT	0.333																																					p.R102S		Atlas-SNP	.											.	AHR	89	.	0			c.A306T						PASS	.						67	68	68					7																	17362177		2203	4299	6502	SO:0001583	missense	196	exon3			CTGTAGAGCAGCA	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.306A>T	chr7.hg19:g.17362177A>T	ENSP00000242057:p.Arg102Ser	24.0	0.0	.		102.0	47.0	.	NM_001621	A4D130|Q13728|Q13803|Q13804	Missense_Mutation	SNP	ENST00000242057.4	hg19	CCDS5366.1	.	.	.	.	.	.	.	.	.	.	A	2.672	-0.277392	0.05679	.	.	ENSG00000106546	ENST00000242057	T	0.05199	3.48	0.235	-0.47	0.12131	.	0.875214	0.10272	N	0.694599	T	0.07503	0.0189	M	0.69823	2.125	0.09310	N	1	B	0.29162	0.235	B	0.30401	0.115	T	0.42015	-0.9476	9	0.22706	T	0.39	.	.	.	.	.	102	P35869	AHR_HUMAN	S	102	ENSP00000242057:R102S	ENSP00000242057:R102S	R	+	3	2	AHR	17328702	0.648000	0.27313	0.005000	0.12908	0.666000	0.39218	-0.535000	0.06142	-0.797000	0.04450	-0.818000	0.03119	AGA	.	.	.	none		0.333	AHR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314620.2	NM_001621		T	17362177	A	T	17362177	3	4	210	1	0	0	0	0	1	0	0	0	416	301	11	5	316	5	AHR	7	17362177	Missense_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08		17362177	141776486	45	12780											
PDE1C	5137	hgsc.bcm.edu	37	chr7	31877507	31877507	+	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	tctggctgctgcagagcagtCttcattgctttgatttgttg	5	17	11	8	0	3	2	1	1	2	1	3	2	3	2	0	1	4	6	0	1	0	5			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr7:31877507C>T	ENST00000396191.1	-	10	1514	c.1059G>A	c.(1057-1059)aaG>aaA	p.K353K	PDE1C_ENST00000396182.2_Silent_p.K353K|PDE1C_ENST00000396193.1_Silent_p.K413K|PDE1C_ENST00000396184.3_Silent_p.K353K|PDE1C_ENST00000321453.7_Silent_p.K353K	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	353	Catalytic. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	GCAGAGCAGTCTTCATTGCTT	0.433																																					p.K413K		Atlas-SNP	.											.	PDE1C	465	.	0			c.G1239A						PASS	.						194	187	189					7																	31877507		2203	4300	6503	SO:0001819	synonymous_variant	5137	exon11			AGCAGTCTTCATT	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.1059G>A	chr7.hg19:g.31877507C>T		130.0	0.0	.		416.0	169.0	.	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Silent	SNP	ENST00000396191.1	hg19	CCDS55099.1																																																																																			.	.	.	none		0.433	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1			T	31877507	C	T	31877507	2	4	210	1	0	0	0	0	0	0	0	1	11642	912	32	2		2	PDE1C	7	31877507	Silent	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	14515330	31877507	127261156	46	12781											
PCLO	27445	hgsc.bcm.edu	37	chr7	82579067	82579067	+	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	ggatttgggtggggaaggagCcagctgtactgtggaatctg	8	10	18	5	0	1	0	0	0	1	0	1	4	1	4	1	6	3	2	1	6	3	2	rs370030206		TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr7:82579067C>A	ENST00000333891.9	-	6	11174	c.10837G>T	c.(10837-10839)Gct>Tct	p.A3613S	PCLO_ENST00000423517.2_Missense_Mutation_p.A3613S|PCLO_ENST00000437081.1_Missense_Mutation_p.A333S	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						GGGGAAGGAGCCAGCTGTACT	0.483																																					p.A3613S		Atlas-SNP	.											.	PCLO	1506	.	0			c.G10837T						PASS	.	C	SER/ALA,SER/ALA	1,4111		0,1,2055	106	107	106		10837,10837	5.6	1	7		106	1,8435		0,1,4217	no	missense,missense	PCLO	NM_033026.5,NM_014510.2	99,99	0,2,6272	AA,AC,CC		0.0119,0.0243,0.0159	benign,benign	3613/5143,3613/4936	82579067	2,12546	2056	4218	6274	SO:0001583	missense	27445	exon6			AAGGAGCCAGCTG	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.10837G>T	chr7.hg19:g.82579067C>A	ENSP00000334319:p.Ala3613Ser	87.0	0.0	.		234.0	127.0	.	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	11.09	1.536177	0.27475	2.43E-4	1.19E-4	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517;ENST00000437081	T;T	0.15603	2.41;2.41	5.61	5.61	0.85477	.	.	.	.	.	T	0.19327	0.0464	L	0.33485	1.01	0.30557	N	0.764896	B;B;B	0.28419	0.008;0.211;0.211	B;B;B	0.29716	0.004;0.106;0.106	T	0.09443	-1.0674	9	0.87932	D	0	.	19.6465	0.95778	0.0:1.0:0.0:0.0	.	3544;3613;3613	Q9Y6V0;Q9Y6V0-5;Q9Y6V0-6	PCLO_HUMAN;.;.	S	3544;3613;3613;333	ENSP00000334319:A3613S;ENSP00000388393:A3613S	ENSP00000334319:A3613S	A	-	1	0	PCLO	82417003	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.155000	0.58131	2.642000	0.89623	0.650000	0.86243	GCT	.	.	.	weak		0.483	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82579067	C	A	82579067	3	1	210	1	0	0	0	0	1	0	0	0	11590	739	26	4	4688	4	PCLO	7	82579067	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	50701560	82579067	76559596	47	12782											
MET	4233	hgsc.bcm.edu	37	chr7	116422117	116422117	+	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	aatatcttgcaagcaaaaagTttgtccacagagacttggct	14	11	8	8	0	1	1	0	0	1	1	2	2	2	1	1	1	2	4	1	1	5	4			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr7:116422117T>A	ENST00000318493.6	+	18	3839	c.3652T>A	c.(3652-3654)Ttt>Att	p.F1218I	MET_ENST00000397752.3_Missense_Mutation_p.F1200I|MET_ENST00000539704.1_Missense_Mutation_p.F70I			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.F1218V(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)			AAGCAAAAAGTTTGTCCACAG	0.393			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.F1218I		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	Substitution - Missense(1)	kidney(1)	c.T3652A						PASS	.						57	55	56					7																	116422117		1836	4092	5928	SO:0001583	missense	4233	exon18	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	AAAAAGTTTGTCC	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.3652T>A	chr7.hg19:g.116422117T>A	ENSP00000317272:p.Phe1218Ile	22.0	0.0	.		75.0	31.0	.	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.735740	0.89482	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000539704	T;T;T	0.25414	1.8;1.8;1.8	5.87	5.87	0.94306	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	0.37128	0.0992	N	0.16862	0.45	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.35201	-0.9798	10	0.87932	D	0	.	16.5764	0.84681	0.0:0.0:0.0:1.0	.	1218;1200	P08581-2;P08581	.;MET_HUMAN	I	1200;1218;70	ENSP00000380860:F1200I;ENSP00000317272:F1218I;ENSP00000445020:F70I	ENSP00000317272:F1218I	F	+	1	0	MET	116209353	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.972000	0.88022	2.371000	0.80710	0.533000	0.62120	TTT	.	.	.	none		0.393	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			A	116422117	T	A	116422117	3	1	210	1	0	0	0	0	1	0	0	0	9492	1725	60	5	3718	5	MET	7	116422117	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	33843050	116422117	42716546	48	12783											
CTTNBP2	83992	hgsc.bcm.edu	37	chr7	117431390	117431391	+	Frame_Shift_Ins	INS	-	-	C																															cacagcctgcaggtgccacaINSgttaaatctatggatggttt																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr7:117431390_117431391insC	ENST00000160373.3	-	4	1950_1951	c.1859_1860insG	c.(1858-1860)actfs	p.T620fs	CTTNBP2_ENST00000487820.1_5'Flank	NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	620					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)		CAGGTGCCACAGTTAAATCTAT	0.559																																					p.T620fs		Atlas-INDEL	.											.	CTTNBP2	200	.	0			c.1860_1861insG						PASS	.																																			SO:0001589	frameshift_variant	83992	exon4			.		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.1859_1860insG	chr7.hg19:g.117431390_117431391insC	ENSP00000160373:p.Thr620fs	102.0	0.0	0		103.0	55.0	0.533981	NM_033427	O43389|Q7LG11|Q9C0A5	Frame_Shift_Ins	INS	ENST00000160373.3	hg19	CCDS5774.1																																																																																			.	.	.	none		0.559	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		C	117431391	-	C	117431390	7	5	210	1	0	1	1	0	0	0	0	0	4047	175	7	0	3211	0	CTTNBP2	7	117431390	Frame_Shift_Ins	INS	-	TCGA-IZ-8196-01A-11D-2396-08	1009273	117431390	41707273	49	12784											
CHRNB3	1142	hgsc.bcm.edu	37	chr8	42565553	42565553	+	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	gatgaaaagaatcagctgatGacaaccaatgtgtggctcaa	16	8	10	7	0	2	4	2	3	0	1	2	5	2	4	1	1	2	2	1	1	6	0			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr8:42565553G>A	ENST00000289957.2	+	3	353	c.225G>A	c.(223-225)atG>atA	p.M75I	RP11-412B14.1_ENST00000527318.1_RNA	NM_000749.3	NP_000740.1	Q05901	ACHB3_HUMAN	cholinergic receptor, nicotinic, beta 3 (neuronal)	75					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|drug binding (GO:0008144)			endometrium(4)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25	all_lung(13;5.7e-12)|Lung NSC(13;1.6e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00026)|Lung NSC(58;0.000992)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	Lung(22;0.0199)|LUSC - Lung squamous cell carcinoma(45;0.0869)		Galantamine(DB00674)|Nicotine(DB00184)	ATCAGCTGATGACAACCAATG	0.313																																					p.M75I		Atlas-SNP	.											.	CHRNB3	74	.	0			c.G225A						PASS	.						72	73	72					8																	42565553		2203	4300	6503	SO:0001583	missense	1142	exon3			GCTGATGACAACC	U62438	CCDS6134.1	8p11.21	2012-02-11	2012-02-07		ENSG00000147432	ENSG00000147432		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1963	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, beta 3 (neuronal)"	118508	"cholinergic receptor, nicotinic, beta polypeptide 3"			1505988	Standard	NM_000749		Approved		uc003xpi.1	Q05901	OTTHUMG00000165262	ENST00000289957.2:c.225G>A	chr8.hg19:g.42565553G>A	ENSP00000289957:p.Met75Ile	44.0	0.0	.		37.0	21.0	.	NM_000749	Q15827	Missense_Mutation	SNP	ENST00000289957.2	hg19	CCDS6134.1	.	.	.	.	.	.	.	.	.	.	g	19.35	3.810373	0.70797	.	.	ENSG00000147432	ENST00000534391;ENST00000289957	T	0.78816	-1.21	6.03	6.03	0.97812	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	T	0.76702	0.4024	L	0.33624	1.015	0.80722	D	1	P	0.36712	0.566	B	0.43990	0.438	T	0.77763	-0.2466	10	0.87932	D	0	.	18.1139	0.89545	0.0:0.0:1.0:0.0	.	75	Q05901	ACHB3_HUMAN	I	1;75	ENSP00000289957:M75I	ENSP00000289957:M75I	M	+	3	0	CHRNB3	42684710	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.752000	0.91632	2.876000	0.98609	0.644000	0.83932	ATG	.	.	.	none		0.313	CHRNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383055.1			A	42565553	G	A	42565553	3	1	210	1	0	0	0	0	1	0	0	0	3394	1290	45	2	235	2	CHRNB3	8	42565553	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08		42565553	103798469	50	12785											
RBM12B	389677	hgsc.bcm.edu	37	chr8	94747484	94747484	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagagtatttttgtgaaacAtgtccgggcctatctctctc	8	15	9	9	1	2	2	0	2	2	1	5	3	3	2	2	1	1	1	2	1	3	4			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr8:94747484A>G	ENST00000399300.2	-	3	1368	c.1155T>C	c.(1153-1155)caT>caC	p.H385H	RBM12B_ENST00000517700.1_Silent_p.H385H|RBM12B_ENST00000520961.1_Intron|RP11-10N23.4_ENST00000517998.1_RNA	NM_203390.2	NP_976324.2	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	385							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	30	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			TTTGTGAAACATGTCCGGGCC	0.368																																					p.H385H		Atlas-SNP	.											.	RBM12B	78	.	0			c.T1155C						PASS	.						124	121	122					8																	94747484		1836	4085	5921	SO:0001819	synonymous_variant	389677	exon3			TGAAACATGTCCG		CCDS43755.1	8q22	2014-05-20			ENSG00000183808	ENSG00000183808		"RNA binding motif (RRM) containing"	32310	protein-coding gene	gene with protein product							Standard	NM_203390		Approved		uc003yfz.3	Q8IXT5	OTTHUMG00000164317	ENST00000399300.2:c.1155T>C	chr8.hg19:g.94747484A>G		133.0	0.0	.		236.0	96.0	.	NM_203390	A8MYB5	Silent	SNP	ENST00000399300.2	hg19	CCDS43755.1																																																																																			.	.	.	none		0.368	RBM12B-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383603.1	NM_203390		G	94747484	A	G	94747484	2	3	210	1	0	0	0	0	0	0	0	1	13127	214	8	3		3	RBM12B	8	94747484	Silent	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	52181931	94747484	51616538	51	12786											
VPS13B	157680	hgsc.bcm.edu	37	chr8	100514063	100514063	+	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	tactataaagctctttgctcCagatcctgaaaataaaggca	15	11	6	9	0	1	2	0	1	1	1	3	2	3	2	2	1	3	3	2	1	8	5			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr8:100514063C>T	ENST00000358544.2	+	26	4130	c.4019C>T	c.(4018-4020)cCa>cTa	p.P1340L	VPS13B_ENST00000395996.1_Missense_Mutation_p.P1340L|VPS13B_ENST00000357162.2_Missense_Mutation_p.P1340L	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	1340					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)			CTCTTTGCTCCAGATCCTGAA	0.483																																					p.P1340L	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.C4019T						PASS	.						132	135	134					8																	100514063		2203	4300	6503	SO:0001583	missense	157680	exon26			TTGCTCCAGATCC	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.4019C>T	chr8.hg19:g.100514063C>T	ENSP00000351346:p.Pro1340Leu	111.0	0.0	.		140.0	54.0	.	NM_152564	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	hg19	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	C	14.34	2.507355	0.44558	.	.	ENSG00000132549	ENST00000357162;ENST00000358544;ENST00000395996	T;T;T	0.45276	0.9;0.9;0.9	5.22	5.22	0.72569	.	0.215869	0.38548	N	0.001641	T	0.32315	0.0825	L	0.34521	1.04	0.53688	D	0.999974	B;B;B;B	0.09022	0.001;0.002;0.001;0.001	B;B;B;B	0.10450	0.005;0.004;0.004;0.002	T	0.06807	-1.0806	10	0.31617	T	0.26	.	12.4938	0.55916	0.0:0.9229:0.0:0.0771	.	1339;1340;1340;1340	Q7Z7G8-6;Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3	.;.;VP13B_HUMAN;.	L	1340	ENSP00000349685:P1340L;ENSP00000351346:P1340L;ENSP00000379318:P1340L	ENSP00000349685:P1340L	P	+	2	0	VPS13B	100583239	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	5.508000	0.67006	2.589000	0.87451	0.557000	0.71058	CCA	.	.	.	none		0.483	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		T	100514063	C	T	100514063	3	4	210	1	0	0	0	0	1	0	0	0	17202	594	21	2	4240	2	VPS13B	8	100514063	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	5766579	100514063	45849959	52	12787											
C10orf18	54906	hgsc.bcm.edu	37	chr10	5788364	5788364	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccagtgatatgtcagagcTctgtgtacggcacccttgaa	10	10	11	10	1	2	3	1	2	1	1	2	3	2	3	2	1	3	3	2	1	3	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr10:5788364T>C	ENST00000328090.5	+	15	3605	c.2980T>C	c.(2980-2982)Tct>Cct	p.S994P	RP11-336A10.2_ENST00000411512.2_RNA	NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	994																	ATGTCAGAGCTCTGTGTACGG	0.483																																					p.S994P		Atlas-SNP	.											.	.	.	.	0			c.T2980C						PASS	.						102	100	100					10																	5788364		2007	4170	6177	SO:0001583	missense	54906	exon15			CAGAGCTCTGTGT	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.2980T>C	chr10.hg19:g.5788364T>C	ENSP00000328426:p.Ser994Pro	80.0	0.0	.		113.0	55.0	.	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Missense_Mutation	SNP	ENST00000328090.5	hg19	CCDS41485.1	.	.	.	.	.	.	.	.	.	.	T	5.833	0.337978	0.11013	.	.	ENSG00000108021	ENST00000328090	D	0.97811	-4.55	5.37	2.97	0.34412	.	0.115838	0.39407	N	0.001362	D	0.94601	0.8260	L	0.43701	1.375	0.09310	N	1	B	0.34161	0.439	B	0.37422	0.249	D	0.88914	0.3361	10	0.48119	T	0.1	.	4.643	0.12558	0.1675:0.0913:0.0:0.7412	.	994	Q5VWN6	F208B_HUMAN	P	994	ENSP00000328426:S994P	ENSP00000328426:S994P	S	+	1	0	C10orf18	5828370	0.079000	0.21365	0.210000	0.23637	0.008000	0.06430	0.877000	0.28106	0.304000	0.22809	0.460000	0.39030	TCT	.	.	.	none		0.483	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782		C	5788364	T	C	5788364	3	2	210	1	0	0	0	0	1	0	0	0	1598	1551	54	3	3026	3	C10orf18	10	5788364	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08		5788364	129746383	53	12788											
C1QL3	389941	hgsc.bcm.edu	37	chr10	16556595	16556595	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttcctccatgggctttccCgccatctaatttgatataga	8	15	7	11	1	1	2	0	1	1	1	4	2	4	2	4	1	0	2	4	1	3	6			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr10:16556595C>T	ENST00000298943.3	-	2	1639	c.700G>A	c.(700-702)Ggg>Agg	p.G234R		NM_001010908.1	NP_001010908.1	Q5VWW1	C1QL3_HUMAN	complement component 1, q subcomponent-like 3	234	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				regulation of synapse organization (GO:0050807)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)		p.G234W(1)		breast(1)|endometrium(3)|kidney(1)|lung(4)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	13						TGGGCTTTCCCGCCATCTAAT	0.393																																					p.G234R		Atlas-SNP	.											.	C1QL3	27	.	1	Substitution - Missense(1)	lung(1)	c.G700A						PASS	.						148	137	141					10																	16556595		2203	4300	6503	SO:0001583	missense	389941	exon2			CTTTCCCGCCATC		CCDS31156.1	10p13	2012-03-26			ENSG00000165985	ENSG00000165985			19359	protein-coding gene	gene with protein product		615227				21378161	Standard	NM_001010908		Approved	K100, C1ql, C1QTNF13, CTRP13	uc001ioj.1	Q5VWW1	OTTHUMG00000017738	ENST00000298943.3:c.700G>A	chr10.hg19:g.16556595C>T	ENSP00000298943:p.Gly234Arg	101.0	0.0	.		118.0	47.0	.	NM_001010908	A0PJY4|A0PJY5	Missense_Mutation	SNP	ENST00000298943.3	hg19	CCDS31156.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.486586	0.84854	.	.	ENSG00000165985	ENST00000298943;ENST00000448557	T	0.25749	1.78	5.71	5.71	0.89125	Tumour necrosis factor-like (2);Complement C1q protein (3);	0.000000	0.85682	D	0.000000	T	0.52322	0.1727	M	0.68317	2.08	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.44907	-0.9297	10	0.48119	T	0.1	.	19.8415	0.96690	0.0:1.0:0.0:0.0	.	234	Q5VWW1	C1QL3_HUMAN	R	234;211	ENSP00000298943:G234R	ENSP00000298943:G234R	G	-	1	0	C1QL3	16596601	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	7.818000	0.86416	2.700000	0.92200	0.655000	0.94253	GGG	.	.	.	none		0.393	C1QL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047003.1	XM_372305		T	16556595	C	T	16556595	3	4	210	1	0	0	0	0	1	0	0	0	1962	652	23	1	71	1	C1QL3	10	16556595	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	10768231	16556595	118978152	54	12789											
ITGB1	3688	hgsc.bcm.edu	37	chr10	33201013	33201013	+	Frame_Shift_Del	DEL	G	G	-																															tcactgttaacttcatctgtGctgcattcacaatgtctacc																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr10:33201013delG	ENST00000396033.2	-	12	1644	c.1509delC	c.(1507-1509)agcfs	p.S503fs	ITGB1_ENST00000302278.3_Frame_Shift_Del_p.S503fs|ITGB1_ENST00000374956.4_Frame_Shift_Del_p.S503fs|ITGB1_ENST00000423113.1_Frame_Shift_Del_p.S503fs	NM_133376.2	NP_596867.1	P05556	ITB1_HUMAN	integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)	503	Cysteine-rich tandem repeats.				axon extension (GO:0048675)|axon guidance (GO:0007411)|B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cardiac muscle cell differentiation (GO:0055007)|cell fate specification (GO:0001708)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular calcium ion homeostasis (GO:0006874)|cellular defense response (GO:0006968)|cellular response to ionizing radiation (GO:0071479)|cellular response to mechanical stimulus (GO:0071260)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|formation of radial glial scaffolds (GO:0021943)|G1/S transition of mitotic cell cycle (GO:0000082)|germ cell migration (GO:0008354)|heterotypic cell-cell adhesion (GO:0034113)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|maternal process involved in female pregnancy (GO:0060135)|mesodermal cell differentiation (GO:0048333)|negative regulation of anoikis (GO:2000811)|negative regulation of cell projection organization (GO:0031345)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of apoptotic process (GO:0043065)|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 endocytosis (GO:0045807)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein transport within lipid bilayer (GO:0032594)|regulation of cell cycle (GO:0051726)|regulation of collagen catabolic process (GO:0010710)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of immune response (GO:0050776)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|response to transforming growth factor beta (GO:0071559)|sarcomere organization (GO:0045214)|tight junction assembly (GO:0070830)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	acrosomal vesicle (GO:0001669)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha1-beta1 complex (GO:0034665)|integrin alpha10-beta1 complex (GO:0034680)|integrin alpha11-beta1 complex (GO:0034681)|integrin alpha2-beta1 complex (GO:0034666)|integrin alpha3-beta1 complex (GO:0034667)|integrin alpha7-beta1 complex (GO:0034677)|integrin alpha8-beta1 complex (GO:0034678)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|intercalated disc (GO:0014704)|invadopodium membrane (GO:0071438)|membrane (GO:0016020)|membrane raft (GO:0045121)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|cell adhesion molecule binding (GO:0050839)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|peptide binding (GO:0042277)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|virus receptor activity (GO:0001618)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Ovarian(717;1.34e-05)|Breast(68;0.0634)			Antithymocyte globulin(DB00098)	CTTCATCTGTGCTGCATTCAC	0.413																																					p.T504fs		Atlas-INDEL	.											.	ITGB1	156	.	0			c.1510delA						PASS	.						143	120	128					10																	33201013		2203	4300	6503	SO:0001589	frameshift_variant	3688	exon12			.	BC020057	CCDS7174.1	10p11.2	2010-10-13			ENSG00000150093	ENSG00000150093		"CD molecules", "Integrins"	6153	protein-coding gene	gene with protein product		135630		FNRB, MSK12, MDF2		2524991	Standard	NM_033668		Approved	CD29, GPIIA	uc001iwt.4	P05556	OTTHUMG00000017928	ENST00000396033.2:c.1509delC	chr10.hg19:g.33201013delG	ENSP00000379350:p.Ser503fs	69.0	0.0	0		95.0	41.0	0.431579	NM_133376	A8K6N2|D3DRX9|D3DRY3|D3DRY4|D3DRY5|P78466|P78467|Q13089|Q13090|Q13091|Q13212|Q14622|Q14647|Q29RW2|Q7Z3V1|Q8WUM6	Frame_Shift_Del	DEL	ENST00000396033.2	hg19	CCDS7174.1																																																																																			.	.	.	none		0.413	ITGB1-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047496.1	NM_002211		-	33201013	G	-	33201013	7	5	210	1	0	1	0	1	0	0	0	0	7897	1310	46	0	1145	0	ITGB1	10	33201013	Frame_Shift_Del	DEL	G	TCGA-IZ-8196-01A-11D-2396-08	16644418	33201013	102333734	55	12790											
TPP1	1200	hgsc.bcm.edu	37	chr11	6638089	6638089	+	Splice_Site	DEL	A	A	-																															catggaaatactgctccaggAactatggagggagtcagagc																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr11:6638089delA	ENST00000299427.6	-	7	749	c.689delT	c.(688-690)ttc>tc	p.F230fs	RP11-732A19.9_ENST00000545572.1_RNA|TPP1_ENST00000533371.1_5'UTR|TPP1_ENST00000534644.1_5'Flank	NM_000391.3	NP_000382.3	P49638	TTPA_HUMAN	tripeptidyl peptidase I	0	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				embryonic placenta development (GO:0001892)|intermembrane transport (GO:0046909)|intracellular pH reduction (GO:0051452)|lipid metabolic process (GO:0006629)|negative regulation of cell death (GO:0060548)|negative regulation of establishment of blood-brain barrier (GO:0090212)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|response to toxic substance (GO:0009636)|transport (GO:0006810)|vitamin E metabolic process (GO:0042360)|vitamin transport (GO:0051180)	cytosol (GO:0005829)|late endosome (GO:0005770)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|transporter activity (GO:0005215)|vitamin E binding (GO:0008431)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;3.45e-09)|BRCA - Breast invasive adenocarcinoma(625;0.131)	Vitamin E(DB00163)	CTGCTCCAGGAACTATGGAGG	0.567																																					p.F230fs		Atlas-INDEL	.											.	TPP1	71	.	0			c.690delC						PASS	.						84	82	83					11																	6638089		2201	4296	6497	SO:0001630	splice_region_variant	1200	exon7			.	AF017456	CCDS7770.1	11p15.4	2014-09-17	2004-12-09	2004-12-10	ENSG00000166340	ENSG00000166340			2073	protein-coding gene	gene with protein product	"TPP I"	607998	"ceroid-lipofuscinosis, neuronal 2, late infantile (Jansky-Bielschowsky disease)", "spinocerebellar ataxia, autosomal recessive 7"	CLN2, SCAR7		9653647, 23418007	Standard	NM_000391		Approved		uc001mel.1	O14773	OTTHUMG00000133404	ENST00000299427.6:c.688-1T>-	chr11.hg19:g.6638089delA		171.0	0.0	0		103.0	54.0	0.524272	NM_000391	Q71V64	Frame_Shift_Del	DEL	ENST00000299427.6	hg19	CCDS7770.1																																																																																			.	.	.	none		0.567	TPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257261.2		Frame_Shift_Del	-	6638089	A	-	6638089	8	5	210	1	0	1	0	1	0	0	1	0	16423	260	9	0	1030	0	TPP1	11	6638089	Splice_Site	DEL	A	TCGA-IZ-8196-01A-11D-2396-08		6638089	128368427	56	12791											
API5	8539	hgsc.bcm.edu	37	chr11	43342441	43342441	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttcctcgagtggcagataTactaacgcaacttttgcaga	11	12	8	10	2	1	2	0	0	1	2	3	3	2	2	1	1	4	3	1	1	4	6			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr11:43342441T>C	ENST00000531273.1	+	3	441	c.302T>C	c.(301-303)aTa>aCa	p.I101T	API5_ENST00000455725.2_Missense_Mutation_p.I90T|API5_ENST00000378852.3_Missense_Mutation_p.I101T|API5_ENST00000534600.1_Missense_Mutation_p.I101T|API5_ENST00000534695.1_Intron|API5_ENST00000420461.2_Missense_Mutation_p.I47T			Q9BZZ5	API5_HUMAN	apoptosis inhibitor 5	101	ARM-like and Heat-like helical repeats.				apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|negative regulation of fibroblast apoptotic process (GO:2000270)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	fibroblast growth factor binding (GO:0017134)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(2)|urinary_tract(1)	20						GTGGCAGATATACTAACGCAA	0.343																																					p.I101T	Pancreas(1;98 122 5625 20895 49453)	Atlas-SNP	.											.	API5	91	.	0			c.T302C						PASS	.						83	85	84					11																	43342441		2203	4300	6503	SO:0001583	missense	8539	exon3			CAGATATACTAAC	U83857	CCDS31465.1, CCDS44572.1, CCDS44573.1	11p12	2010-09-30			ENSG00000166181	ENSG00000166181			594	protein-coding gene	gene with protein product	"API5-like 1", "fibroblast growth factor 2-interacting factor 2", "migration-inducing protein MIG8"	609774				9307294	Standard	NR_024625		Approved	AAC-11, API5L1, AAC11	uc010rfh.1	Q9BZZ5	OTTHUMG00000166395	ENST00000531273.1:c.302T>C	chr11.hg19:g.43342441T>C	ENSP00000431391:p.Ile101Thr	65.0	0.0	.		93.0	42.0	.	NM_006595	B4DGR0|B4DRJ2|D3DR21|O15441|Q9Y4J7	Missense_Mutation	SNP	ENST00000531273.1	hg19	CCDS44572.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.975544	0.74360	.	.	ENSG00000166181	ENST00000455725;ENST00000531273;ENST00000420461;ENST00000378852;ENST00000534600	T;T;T;T;T	0.20738	2.05;2.05;2.05;2.05;2.05	6.13	6.13	0.99165	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.36220	0.0959	L	0.45422	1.42	0.58432	D	0.999999	P;P;D;P	0.61697	0.951;0.92;0.99;0.952	P;P;P;P	0.61722	0.675;0.551;0.893;0.6	T	0.01570	-1.1322	10	0.34782	T	0.22	-2.8866	16.4795	0.84153	0.0:0.0:0.0:1.0	.	47;101;90;101	B4DGR0;Q9BZZ5;B4E283;Q9BZZ5-2	.;API5_HUMAN;.;.	T	90;101;47;101;101	ENSP00000399341:I90T;ENSP00000431391:I101T;ENSP00000402540:I47T;ENSP00000368129:I101T;ENSP00000434462:I101T	ENSP00000368129:I101T	I	+	2	0	API5	43299017	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	7.981000	0.88123	2.367000	0.80283	0.529000	0.55759	ATA	.	.	.	none		0.343	API5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389545.1	NM_006595		C	43342441	T	C	43342441	3	2	210	1	0	0	0	0	1	0	0	0	773	1406	49	3	312	3	API5	11	43342441	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	36704352	43342441	91664075	57	12792											
OR8I2	120586	hgsc.bcm.edu	37	chr11	55861616	55861616	+	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	ggtggcatctgtattctataCgattgtcattcccatgctga	8	15	9	9	1	3	1	1	1	2	0	4	2	4	1	1	2	2	3	1	2	3	6	rs140206966	byFrequency	TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr11:55861616C>T	ENST00000302124.2	+	1	864	c.833C>T	c.(832-834)aCg>aTg	p.T278M		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	278						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T278M(1)		NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					GTATTCTATACGATTGTCATT	0.408																																					p.T278M		Atlas-SNP	.											OR8I2,NS,carcinoma,0,2	OR8I2	119	.	1	Substitution - Missense(1)	endometrium(1)	c.C833T						PASS	.						62	61	62					11																	55861616		2201	4296	6497	SO:0001583	missense	120586	exon1			TCTATACGATTGT	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.833C>T	chr11.hg19:g.55861616C>T	ENSP00000303864:p.Thr278Met	52.0	0.0	.		96.0	8.0	.	NM_001003750	B2RNN4|Q6IFC0|Q96RC5	Missense_Mutation	SNP	ENST00000302124.2	hg19	CCDS31517.1	.	.	.	.	.	.	.	.	.	.	C	12.23	1.876897	0.33162	.	.	ENSG00000172154	ENST00000302124	T	0.00262	8.4	4.33	4.33	0.51752	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41605	U	0.000856	T	0.00608	0.0020	M	0.83118	2.625	0.32279	N	0.567785	D	0.89917	1.0	D	0.70935	0.971	T	0.50988	-0.8762	10	0.87932	D	0	-16.3432	15.8041	0.78481	0.0:1.0:0.0:0.0	.	278	Q8N0Y5	OR8I2_HUMAN	M	278	ENSP00000303864:T278M	ENSP00000303864:T278M	T	+	2	0	OR8I2	55618192	0.000000	0.05858	0.985000	0.45067	0.054000	0.15201	0.638000	0.24674	2.120000	0.65058	0.447000	0.29281	ACG	.	C|0.999;A|0.001	.	alt		0.408	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750		T	55861616	C	T	55861616	3	4	210	1	0	0	0	0	1	0	0	0	11247	536	19	1	835	1	OR8I2	11	55861616	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	12519175	55861616	79144900	58	12793											
HNRNPUL2	221092	hgsc.bcm.edu	37	chr11	62488862	62488862	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aactaaaaggtctcggctttTggggtccatctctggctcct	7	13	10	11	1	2	0	0	0	2	0	6	0	4	0	2	5	1	2	2	5	3	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr11:62488862T>C	ENST00000301785.5	-	9	1708	c.1516A>G	c.(1516-1518)Aaa>Gaa	p.K506E	HNRNPUL2-BSCL2_ENST00000403734.2_Missense_Mutation_p.K506E	NM_001079559.2	NP_001073027.1	Q1KMD3	HNRL2_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 2	506						membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						TCTCGGCTTTTGGGGTCCATC	0.428																																					p.K506E		Atlas-SNP	.											.	HNRNPUL2	41	.	0			c.A1516G						PASS	.						153	158	157					11																	62488862		1846	4094	5940	SO:0001583	missense	221092	exon9			GGCTTTTGGGGTC		CCDS41659.1	11q12	2013-07-16		2008-04-18	ENSG00000214753	ENSG00000214753			25451	protein-coding gene	gene with protein product				HNRPUL2			Standard	NM_001079559		Approved	DKFZp762N1910	uc001nuw.3	Q1KMD3	OTTHUMG00000167773	ENST00000301785.5:c.1516A>G	chr11.hg19:g.62488862T>C	ENSP00000301785:p.Lys506Glu	180.0	0.0	.		214.0	87.0	.	NM_001079559	Q8N3B3	Missense_Mutation	SNP	ENST00000301785.5	hg19	CCDS41659.1	.	.	.	.	.	.	.	.	.	.	T	18.84	3.709456	0.68730	.	.	ENSG00000214753	ENST00000301785	T	0.40756	1.02	5.99	5.99	0.97316	Zeta toxin domain (1);	0.158288	0.64402	D	0.000020	T	0.40719	0.1128	N	0.25286	0.73	0.35130	D	0.767875	P	0.51791	0.948	P	0.51866	0.682	T	0.49934	-0.8886	10	0.30854	T	0.27	-16.7044	14.4463	0.67352	0.0:0.0:0.0:1.0	.	506	Q1KMD3	HNRL2_HUMAN	E	506	ENSP00000301785:K506E	ENSP00000301785:K506E	K	-	1	0	HNRNPUL2	62245438	0.897000	0.30589	1.000000	0.80357	0.995000	0.86356	1.144000	0.31565	2.291000	0.77112	0.533000	0.62120	AAA	.	.	.	none		0.428	HNRNPUL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396208.2	XM_495877		C	62488862	T	C	62488862	3	2	210	1	0	0	0	0	1	0	0	0	7282	1821	63	3	751	3	HNRNPUL2	11	62488862	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	6627246	62488862	72517654	59	12794											
PCF11	51585	hgsc.bcm.edu	37	chr11	82877727	82877727	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttccaagtctgccaaaagAtggaaatctggttgggaaga	14	9	12	6	0	2	2	0	0	2	2	3	4	3	4	2	3	1	2	2	3	5	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr11:82877727A>G	ENST00000298281.4	+	5	2240	c.1788A>G	c.(1786-1788)agA>agG	p.R596R		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	596					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						CTGCCAAAAGATGGAAATCTG	0.343																																					p.R596R		Atlas-SNP	.											.	PCF11	220	.	0			c.A1788G						PASS	.						74	75	75					11																	82877727		1755	3854	5609	SO:0001819	synonymous_variant	51585	exon5			CAAAAGATGGAAA	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.1788A>G	chr11.hg19:g.82877727A>G		67.0	0.0	.		135.0	65.0	.	NM_015885	A6H8W7|O43671|Q6P0X8	Silent	SNP	ENST00000298281.4	hg19	CCDS44689.1																																																																																			.	.	.	none		0.343	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		G	82877727	A	G	82877727	2	3	210	1	0	0	0	0	0	0	0	1	11580	330	12	3		3	PCF11	11	82877727	Silent	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	20388865	82877727	52128789	60	12795											
NCAM1	4684	hgsc.bcm.edu	37	chr11	113078684	113078684	+	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	atctgcattgctgagaacaaGgctggcgagcaggatgcgac	11	7	14	9	2	1	1	0	1	1	1	1	5	1	2	0	3	5	4	0	3	2	1			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr11:113078684G>C	ENST00000533760.1	+	7	1121	c.522G>C	c.(520-522)aaG>aaC	p.K174N	NCAM1_ENST00000316851.7_Missense_Mutation_p.K282N|NCAM1_ENST00000401611.2_Missense_Mutation_p.K291N|NCAM1_ENST00000397957.4_3'UTR	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1	292	Ig-like C2-type 2.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		CTGAGAACAAGGCTGGCGAGC	0.532																																					p.K292N		Atlas-SNP	.											.	NCAM1	372	.	0			c.G876C						PASS	.						61	61	61					11																	113078684		2078	4216	6294	SO:0001583	missense	4684	exon8			GAACAAGGCTGGC		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"CD molecules", "Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.522G>C	chr11.hg19:g.113078684G>C	ENSP00000473281:p.Lys174Asn	27.0	0.0	.		20.0	6.0	.	NM_001242608	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Missense_Mutation	SNP	ENST00000533760.1	hg19		.	.	.	.	.	.	.	.	.	.	G	18.41	3.617792	0.66787	.	.	ENSG00000149294	ENST00000531044;ENST00000401611;ENST00000316851	T;T	0.68181	-0.31;-0.31	5.57	3.47	0.39725	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.041493	0.85682	D	0.000000	T	0.78400	0.4277	.	.	.	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.997;0.995;0.994;0.983	D;D;D;D;D	0.71870	0.963;0.917;0.975;0.952;0.925	T	0.79697	-0.1695	9	0.87932	D	0	-16.9107	8.6894	0.34258	0.2821:0.0:0.7179:0.0	.	292;292;292;292;292	P13591-5;P13591-1;P13591;P13591-3;P13591-6	.;.;NCAM1_HUMAN;.;.	N	174;291;282	ENSP00000384055:K291N;ENSP00000318472:K282N	ENSP00000318472:K282N	K	+	3	2	NCAM1	112583894	1.000000	0.71417	1.000000	0.80357	0.714000	0.41099	3.113000	0.50376	1.347000	0.45714	0.655000	0.94253	AAG	.	.	.	none		0.532	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615		C	113078684	G	C	113078684	3	2	210	1	0	0	0	0	1	0	0	0	10209	991	35	4	903	4	NCAM1	11	113078684	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	30200957	113078684	21927832	61	12796											
C3AR1	719	hgsc.bcm.edu	37	chr12	8211578	8211578	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggagtttctgggtcagtaaGcaatgacaggactccaaaaa	14	8	12	7	0	2	1	1	1	1	0	3	3	3	3	1	3	1	3	1	3	4	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr12:8211578G>A	ENST00000307637.4	-	2	1407	c.1204C>T	c.(1204-1206)Ctt>Ttt	p.L402F		NM_004054.2	NP_004045.1	Q16581	C3AR_HUMAN	complement component 3a receptor 1	402					blood circulation (GO:0008015)|chemotaxis (GO:0006935)|complement receptor mediated signaling pathway (GO:0002430)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation vascular endothelial growth factor production (GO:0010575)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C3a anaphylatoxin receptor activity (GO:0004943)|complement component C3a receptor activity (GO:0004876)|G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)	20				Kidney(36;0.0893)		GGGTCAGTAAGCAATGACAGG	0.483																																					p.L402F		Atlas-SNP	.											.	C3AR1	61	.	0			c.C1204T						PASS	.						73	68	70					12																	8211578		2203	4300	6503	SO:0001583	missense	719	exon2			CAGTAAGCAATGA	U28488	CCDS8588.1	12p13.31	2012-08-10				ENSG00000171860		"Complement system", "GPCR / Class A : Complement component receptors"	1319	protein-coding gene	gene with protein product		605246				8605247	Standard	NM_004054		Approved	C3AR, AZ3B	uc001qtv.1	Q16581		ENST00000307637.4:c.1204C>T	chr12.hg19:g.8211578G>A	ENSP00000302079:p.Leu402Phe	69.0	0.0	.		67.0	8.0	.	NM_004054	O43771|Q92868	Missense_Mutation	SNP	ENST00000307637.4	hg19	CCDS8588.1	.	.	.	.	.	.	.	.	.	.	G	0.033	-1.321727	0.01320	.	.	ENSG00000171860	ENST00000307637	T	0.37235	1.21	5.26	0.103	0.14526	GPCR, rhodopsin-like superfamily (1);	1.231120	0.05729	N	0.599303	T	0.12518	0.0304	N	0.01800	-0.715	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.23332	-1.0191	10	0.15499	T	0.54	.	3.1161	0.06375	0.4472:0.0:0.2539:0.2989	.	402	Q16581	C3AR_HUMAN	F	402	ENSP00000302079:L402F	ENSP00000302079:L402F	L	-	1	0	C3AR1	8102845	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.859000	0.04277	0.118000	0.18165	-0.238000	0.12139	CTT	.	.	.	none		0.483	C3AR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400254.1			A	8211578	G	A	8211578	3	1	210	1	0	0	0	0	1	0	0	0	2207	971	34	2	248	2	C3AR1	12	8211578	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08		8211578	125640317	62	12797											
ESPL1	9700	hgsc.bcm.edu	37	chr12	53687232	53687232	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttggggctgcacctatagccTatggcttgcctgtctctctg	4	14	11	12	0	2	0	0	0	2	0	3	0	2	0	3	3	3	3	3	3	3	5			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr12:53687232T>C	ENST00000257934.4	+	31	6428	c.6337T>C	c.(6337-6339)Tat>Cat	p.Y2113H	PFDN5_ENST00000550846.1_5'Flank|ESPL1_ENST00000552462.1_Missense_Mutation_p.Y2113H|PFDN5_ENST00000551018.1_5'Flank|PFDN5_ENST00000351500.3_5'Flank|PFDN5_ENST00000334478.4_5'Flank	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	2113					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						ACCTATAGCCTATGGCTTGCC	0.527																																					p.Y2113H	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											.	ESPL1	158	.	0			c.T6337C						PASS	.						64	65	65					12																	53687232		2203	4300	6503	SO:0001583	missense	9700	exon31			ATAGCCTATGGCT	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.6337T>C	chr12.hg19:g.53687232T>C	ENSP00000257934:p.Tyr2113His	133.0	0.0	.		97.0	45.0	.	NM_012291		Missense_Mutation	SNP	ENST00000257934.4	hg19	CCDS8852.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.234561	0.79800	.	.	ENSG00000135476	ENST00000257934;ENST00000552671;ENST00000552462	T;T	0.56444	0.46;0.46	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.76702	0.4024	M	0.90198	3.095	0.53688	D	0.999976	D	0.89917	1.0	D	0.87578	0.998	T	0.82204	-0.0573	10	0.87932	D	0	.	13.8969	0.63778	0.0:0.0:0.0:1.0	.	2113	Q14674	ESPL1_HUMAN	H	2113;1788;2113	ENSP00000257934:Y2113H;ENSP00000449831:Y2113H	ENSP00000257934:Y2113H	Y	+	1	0	ESPL1	51973499	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.612000	0.82975	2.178000	0.69098	0.460000	0.39030	TAT	.	.	.	none		0.527	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291		C	53687232	T	C	53687232	3	2	210	1	0	0	0	0	1	0	0	0	5255	1522	53	3	6455	3	ESPL1	12	53687232	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	45475654	53687232	80164663	63	12798											
DUSP6	1848	hgsc.bcm.edu	37	chr12	89743102	89743107	+	In_Frame_Del	DEL	CTGGAA	CTGGAA	-																															ggtaaaatacagctgctgtgCtggaaccctgttgtcacatg																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	CTGGAA	CTGGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr12:89743102_89743107delCTGGAA	ENST00000279488.7	-	3	2301_2306	c.1070_1075delTTCCAG	c.(1069-1077)gttccagca>gca	p.VP357del	DUSP6_ENST00000308385.6_In_Frame_Del_p.VP211del|DUSP6_ENST00000547291.1_In_Frame_Del_p.VP232del|DUSP6_ENST00000547140.1_5'Flank	NM_001946.2	NP_001937.2	Q16828	DUS6_HUMAN	dual specificity phosphatase 6	357	Tyrosine-protein phosphatase.				cell differentiation (GO:0030154)|dorsal/ventral pattern formation (GO:0009953)|inactivation of MAPK activity (GO:0000188)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of apoptotic process (GO:0043065)|regulation of endodermal cell fate specification (GO:0042663)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of heart growth (GO:0060420)|response to drug (GO:0042493)|response to nitrosative stress (GO:0051409)|response to organic cyclic compound (GO:0014070)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)			large_intestine(5)|lung(8)|skin(2)|urinary_tract(1)	16						AGCTGCTGTGCTGGAACCCTGTTGTC	0.5																																					p.357_359del	Colon(132;3456 5224)	Atlas-INDEL	.											.	DUSP6	30	.	0			c.1071_1076del						PASS	.																																			SO:0001651	inframe_deletion	1848	exon3			.	BC037236	CCDS9033.1, CCDS9034.1	12q22-q23	2011-06-09				ENSG00000139318		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3072	protein-coding gene	gene with protein product		602748				8626780, 9205128	Standard	NM_001946		Approved	MKP-3, PYST1	uc001tay.3	Q16828		ENST00000279488.7:c.1070_1075delTTCCAG	chr12.hg19:g.89743102_89743107delCTGGAA	ENSP00000279488:p.Val357_Pro358del	146.0	0.0	0		129.0	41.0	0.317829	NM_001946	O75109|Q53Y75|Q9BSH6	In_Frame_Del	DEL	ENST00000279488.7	hg19	CCDS9033.1																																																																																			.	.	.	none		0.5	DUSP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406534.2	NM_001946, NM_022652		-	89743107	CTGGAA	-	89743102	7	5	210	1	0	1	0	1	0	0	0	0	4831	797	28	0	74	0	DUSP6	12	89743102	In_Frame_Del	DEL	CTGGAA	TCGA-IZ-8196-01A-11D-2396-08	36055870	89743102	44108793	64	12799											
ALDH2	217	hgsc.bcm.edu	37	chr12	112227694	112227694	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgacggagacttcttcagcTacacacgccatgaacctgtg	10	10	9	12	2	2	3	1	2	1	1	2	4	2	3	2	1	3	1	2	1	2	4			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr12:112227694T>C	ENST00000261733.2	+	5	569	c.508T>C	c.(508-510)Tac>Cac	p.Y170H	RP11-162P23.2_ENST00000546840.2_Silent_p.A166A|ALDH2_ENST00000416293.3_Missense_Mutation_p.Y123H	NM_000690.3	NP_000681.2	P05091	ALDH2_HUMAN	aldehyde dehydrogenase 2 family (mitochondrial)	170					alcohol metabolic process (GO:0006066)|carbohydrate metabolic process (GO:0005975)|ethanol catabolic process (GO:0006068)|ethanol oxidation (GO:0006069)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|electron carrier activity (GO:0009055)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|stomach(1)	22					Amyl Nitrite(DB01612)|Benzyl alcohol(DB06770)|Disulfiram(DB00822)|Guanidine(DB00536)|Nitric Oxide(DB00435)|Nitroglycerin(DB00727)	CTTCTTCAGCTACACACGCCA	0.527			T	HMGA2	leiomyoma																																p.Y170H		Atlas-SNP	.		Dom	yes		12	12q24.2	217	aldehyde dehydrogenase 2 family (mitochondrial)		M	.	ALDH2	91	.	0			c.T508C						PASS	.						100	87	91					12																	112227694		2203	4300	6503	SO:0001583	missense	217	exon5			TTCAGCTACACAC	M26760	CCDS9155.1, CCDS55885.1	12q24.12	2007-12-14				ENSG00000111275	1.2.1.3	"Aldehyde dehydrogenases"	404	protein-coding gene	gene with protein product		100650				4015823, 2987944	Standard	NM_000690		Approved		uc001tst.3	P05091	OTTHUMG00000169603	ENST00000261733.2:c.508T>C	chr12.hg19:g.112227694T>C	ENSP00000261733:p.Tyr170His	81.0	0.0	.		61.0	21.0	.	NM_000690	B4DW54|E7EUE5|Q03639|Q6IB13|Q6IV71	Missense_Mutation	SNP	ENST00000261733.2	hg19	CCDS9155.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.792458	0.90453	.	.	ENSG00000257767;ENSG00000111275;ENSG00000111275;ENSG00000111275;ENSG00000111275	ENST00000546840;ENST00000416293;ENST00000261733;ENST00000553044;ENST00000552234	T;T	0.77620	-1.11;-1.11	5.17	5.17	0.71159	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.172373	0.53938	D	0.000059	D	0.89612	0.6765	M	0.88105	2.93	0.53688	D	0.999979	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.87578	0.987;0.997;0.998	D	0.91609	0.5301	10	0.72032	D	0.01	.	15.3139	0.74059	0.0:0.0:0.0:1.0	.	123;170;170	E7EUE5;F8VXI5;P05091	.;.;ALDH2_HUMAN	H	151;123;170;170;30	ENSP00000403349:Y123H;ENSP00000261733:Y170H	ENSP00000261733:Y170H	Y	+	1	0	ALDH2;RP11-162P23.2	110712077	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.655000	0.83696	2.071000	0.62044	0.460000	0.39030	TAC	.	.	.	none		0.527	ALDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405008.1	NM_000690		C	112227694	T	C	112227694	3	2	210	1	0	0	0	0	1	0	0	0	496	1522	53	3	526	3	ALDH2	12	112227694	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	22484592	112227694	21624201	65	12800											
HNF1A	6927	hgsc.bcm.edu	37	chr12	121437158	121437158	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcaccgacaccaccaaccTgagcgccctggccagcctca	10	4	7	20	2	2	1	2	1	0	0	2	2	2	1	7	1	3	0	7	1	1	0			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr12:121437158T>C	ENST00000257555.6	+	8	1815	c.1589T>C	c.(1588-1590)cTg>cCg	p.L530P	HNF1A_ENST00000544413.1_Missense_Mutation_p.L530P|RP11-216P16.2_ENST00000606238.1_RNA|HNF1A_ENST00000541395.1_Missense_Mutation_p.L530P			P20823	HNF1A_HUMAN	HNF1 homeobox A	530					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)					ACCACCAACCTGAGCGCCCTG	0.687									Hepatic Adenoma, Familial Clustering of																												p.L530P		Atlas-SNP	.											.	HNF1A	302	.	0			c.T1589C						PASS	.						83	85	84					12																	121437158		2203	4300	6503	SO:0001583	missense	6927	exon8	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CCAACCTGAGCGC	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.1589T>C	chr12.hg19:g.121437158T>C	ENSP00000257555:p.Leu530Pro	399.0	0.0	.		116.0	54.0	.	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Missense_Mutation	SNP	ENST00000257555.6	hg19	CCDS9209.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.760491	0.89932	.	.	ENSG00000135100	ENST00000257555;ENST00000535125;ENST00000537424;ENST00000543027;ENST00000541395;ENST00000544413	D;D;D	0.98617	-5.03;-5.03;-5.03	5.52	5.52	0.82312	Hepatocyte nuclear factor 1, beta isoform, C-terminal (1);	0.000000	0.48286	D	0.000189	D	0.98658	0.9550	L	0.52573	1.65	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.83275	0.993;0.996	D	0.99890	1.1133	10	0.72032	D	0.01	-15.5351	14.8565	0.70341	0.0:0.0:0.0:1.0	.	530;530	F5H0K0;P20823	.;HNF1A_HUMAN	P	530;422;530;351;530;530	ENSP00000257555:L530P;ENSP00000443112:L530P;ENSP00000438804:L530P	ENSP00000257555:L530P	L	+	2	0	HNF1A	119921541	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.616000	0.83018	2.104000	0.64026	0.528000	0.53228	CTG	.	.	.	none		0.687	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		C	121437158	T	C	121437158	3	2	210	1	0	0	0	0	1	0	0	0	7258	1580	55	3	1619	3	HNF1A	12	121437158	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	9209464	121437158	12414737	66	12801											
BRCA2	675	hgsc.bcm.edu	37	chr13	32907353	32907353	+	Missense_Mutation	SNP	A	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	ctttgaagaatgcaggtttaAtatccactttgaaaaagaaa	17	12	7	5	0	0	4	0	2	0	2	1	4	1	4	1	1	1	2	1	1	7	5			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr13:32907353A>C	ENST00000380152.3	+	10	1971	c.1738A>C	c.(1738-1740)Ata>Cta	p.I580L	BRCA2_ENST00000544455.1_Missense_Mutation_p.I580L			P51587	BRCA2_HUMAN	breast cancer 2, early onset	580					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)		TGCAGGTTTAATATCCACTTT	0.338			"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.I580L	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.A1738C						PASS	.						44	49	47					13																	32907353		2203	4300	6503	SO:0001583	missense	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)	GGTTTAATATCCA	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.1738A>C	chr13.hg19:g.32907353A>C	ENSP00000369497:p.Ile580Leu	55.0	0.0	.		93.0	49.0	.	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	hg19	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	A	14.91	2.677622	0.47886	.	.	ENSG00000139618	ENST00000380152;ENST00000544455;ENST00000530893	T;T	0.00776	5.71;5.71	5.5	4.32	0.51571	.	0.150989	0.47093	D	0.000244	T	0.00906	0.0030	M	0.70275	2.135	0.25438	N	0.988123	P;B	0.39748	0.686;0.402	B;B	0.32211	0.088;0.142	T	0.45190	-0.9278	10	0.15952	T	0.53	.	5.4332	0.16464	0.7537:0.0:0.0834:0.1629	.	580;580	P51587;A1YBP1	BRCA2_HUMAN;.	L	580;580;578	ENSP00000369497:I580L;ENSP00000439902:I580L	ENSP00000369497:I580L	I	+	1	0	BRCA2	31805353	0.997000	0.39634	0.995000	0.50966	0.698000	0.40448	0.972000	0.29409	1.016000	0.39470	0.528000	0.53228	ATA	.	.	.	none		0.338	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		C	32907353	A	C	32907353	3	2	210	1	0	0	0	0	1	0	0	0	1501	101	4	5	1772	5	BRCA2	13	32907353	Missense_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08		32907353	82262525	67	12802											
ESD	2098	hgsc.bcm.edu	37	chr13	47354151	47354151	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtacagggttgcaaattggAgcaaatgctgacacagactt	14	9	11	7	0	0	2	0	1	0	1	0	3	0	3	0	2	4	5	0	2	3	4			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr13:47354151A>G	ENST00000378720.3	-	8	701	c.519T>C	c.(517-519)gcT>gcC	p.A173A	ESD_ENST00000495654.1_5'UTR|ESD_ENST00000378697.1_Silent_p.A144A	NM_001984.1	NP_001975.1	P10768	ESTD_HUMAN	esterase D	173					formaldehyde catabolic process (GO:0046294)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carboxylic ester hydrolase activity (GO:0052689)|hydrolase activity, acting on ester bonds (GO:0016788)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)|S-formylglutathione hydrolase activity (GO:0018738)			endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)	9		all_lung(13;3.54e-08)|Lung NSC(96;9.1e-06)|Breast(56;0.000148)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)		GBM - Glioblastoma multiforme(144;2.66e-05)	Glutathione(DB00143)	TGCAAATTGGAGCAAATGCTG	0.333																																					p.A173A		Atlas-SNP	.											.	ESD	23	.	0			c.T519C						PASS	.						91	91	91					13																	47354151		2203	4299	6502	SO:0001819	synonymous_variant	2098	exon8			AATTGGAGCAAAT	M13450	CCDS9404.1	13q14.1-q14.2	2014-05-13	2010-05-07		ENSG00000139684	ENSG00000139684	3.1.2.12		3465	protein-coding gene	gene with protein product	"S-formylglutathione hydrolase"	133280	"esterase D/formylglutathione hydrolase"				Standard	NM_001984		Approved		uc001vbn.3	P10768	OTTHUMG00000016878	ENST00000378720.3:c.519T>C	chr13.hg19:g.47354151A>G		76.0	0.0	.		101.0	42.0	.	NM_001984	Q5TBU8|Q5TBV0|Q5TBV2|Q9BVJ2	Silent	SNP	ENST00000378720.3	hg19	CCDS9404.1	.	.	.	.	.	.	.	.	.	.	A	9.962	1.223120	0.22457	.	.	ENSG00000139684	ENST00000412582	.	.	.	6.16	3.7	0.42460	.	.	.	.	.	T	0.57140	0.2033	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50717	-0.8795	4	.	.	.	-8.9614	7.2303	0.26038	0.6488:0.2815:0.0697:0.0	.	.	.	.	P	121	.	.	L	-	2	0	ESD	46252152	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.509000	0.35780	0.536000	0.28733	-0.299000	0.09455	CTC	.	.	.	none		0.333	ESD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044826.1			G	47354151	A	G	47354151	2	3	210	1	0	0	0	0	0	0	0	1	5252	291	11	3		3	ESD	13	47354151	Silent	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	14446798	47354151	67815727	68	12803											
OR11G2	390439	hgsc.bcm.edu	37	chr14	20666034	20666034	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgaccagacgtctctgtacCaatcttgtggtcaattgctg	9	13	9	10	1	3	2	1	1	2	1	4	2	3	2	2	1	2	2	2	1	3	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr14:20666034C>T	ENST00000357366.3	+	1	540	c.540C>T	c.(538-540)acC>acT	p.T180T		NM_001005503.1	NP_001005503.1	Q8NGC1	O11G2_HUMAN	olfactory receptor, family 11, subfamily G, member 2	180						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(95;0.00108)		Epithelial(56;9.76e-07)|all cancers(55;5.61e-06)	GBM - Glioblastoma multiforme(265;0.0144)		GTCTCTGTACCAATCTTGTGG	0.448																																					p.T180T		Atlas-SNP	.											.	OR11G2	73	.	0			c.C540T						PASS	.						111	94	100					14																	20666034		2203	4300	6503	SO:0001819	synonymous_variant	390439	exon1			CTGTACCAATCTT		CCDS32032.1	14q11.2	2013-09-24			ENSG00000196832	ENSG00000196832		"GPCR / Class A : Olfactory receptors"	15346	protein-coding gene	gene with protein product							Standard	NM_001005503		Approved		uc010tlb.2	Q8NGC1	OTTHUMG00000167700	ENST00000357366.3:c.540C>T	chr14.hg19:g.20666034C>T		63.0	0.0	.		112.0	39.0	.	NM_001005503	Q6IF09|Q96R33	Silent	SNP	ENST00000357366.3	hg19	CCDS32032.1																																																																																			.	.	.	none		0.448	OR11G2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395722.1			T	20666034	C	T	20666034	2	4	210	1	0	0	0	0	0	0	0	1	10932	581	21	2		2	OR11G2	14	20666034	Silent	SNP	C	TCGA-IZ-8196-01A-11D-2396-08		20666034	86683506	69	12804											
C14orf37	145407	hgsc.bcm.edu	37	chr14	58563683	58563683	+	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	tcttcttcatcctcttcatcCtcatcttcttgtccctctag	4	19	2	16	0	9	0	3	0	6	0	12	0	12	0	3	0	0	0	3	0	1	6			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr14:58563683C>G	ENST00000267485.7	-	5	2042	c.1848G>C	c.(1846-1848)gaG>gaC	p.E616D		NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	616	Glu-rich.					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						cctcttcatcctcatcttctt	0.398																																					p.E616D		Atlas-SNP	.											.	C14orf37	87	.	0			c.G1848C						PASS	.						195	145	162					14																	58563683		2203	4300	6503	SO:0001583	missense	145407	exon5			TTCATCCTCATCT		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.1848G>C	chr14.hg19:g.58563683C>G	ENSP00000267485:p.Glu616Asp	31.0	0.0	.		55.0	27.0	.	NM_001001872	A8K8Z8|Q6P5Q1|Q86TY1	Missense_Mutation	SNP	ENST00000267485.7	hg19	CCDS32089.1	.	.	.	.	.	.	.	.	.	.	C	12.96	2.093373	0.36952	.	.	ENSG00000139971	ENST00000267485;ENST00000438670	T	0.11063	2.81	4.97	-3.62	0.04543	Armadillo-like helical (1);	0.466239	0.19773	N	0.106394	T	0.07143	0.0181	L	0.38531	1.155	0.30330	N	0.786721	B;B;B	0.24576	0.106;0.106;0.106	B;B;B	0.26770	0.073;0.073;0.073	T	0.12016	-1.0564	10	0.87932	D	0	-0.7422	5.8628	0.18759	0.0:0.3161:0.242:0.4419	.	654;616;616	B4DMS4;A8K990;Q86TY3	.;.;CN037_HUMAN	D	616;654	ENSP00000267485:E616D	ENSP00000267485:E616D	E	-	3	2	C14orf37	57633436	0.186000	0.23225	0.976000	0.42696	0.636000	0.38137	-1.104000	0.03326	-0.558000	0.06118	0.561000	0.74099	GAG	.	.	.	none		0.398	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872		G	58563683	C	G	58563683	3	3	210	1	0	0	0	0	1	0	0	0	1773	680	24	4	492	4	C14orf37	14	58563683	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	37897649	58563683	48785857	70	12805											
SYNE2	23224	hgsc.bcm.edu	37	chr14	64596614	64596614	+	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	tactccaggaggtttacaaaTtagaggtatgcctgagcaga	13	10	11	7	0	0	3	0	1	0	2	1	4	1	4	2	3	4	3	2	3	5	5			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr14:64596614T>A	ENST00000344113.4	+	75	14346	c.14134T>A	c.(14134-14136)Tta>Ata	p.L4712I	SYNE2_ENST00000555002.1_Missense_Mutation_p.L1346I|SYNE2_ENST00000357395.3_Missense_Mutation_p.L1097I|SYNE2_ENST00000358025.3_Missense_Mutation_p.L4712I|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000394768.2_Missense_Mutation_p.L1097I|SYNE2_ENST00000554584.1_Missense_Mutation_p.L4629I	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	4712					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)		GGTTTACAAATTAGAGGTATG	0.458																																					p.L4712I		Atlas-SNP	.											.	SYNE2	577	.	0			c.T14134A						PASS	.						113	112	112					14																	64596614		2203	4300	6503	SO:0001583	missense	23224	exon75			TACAAATTAGAGG	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.14134T>A	chr14.hg19:g.64596614T>A	ENSP00000341781:p.Leu4712Ile	54.0	0.0	.		59.0	29.0	.	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	T	10.90	1.481904	0.26598	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	T;T;T;T;T;T	0.71934	1.34;1.34;1.34;-0.61;1.34;1.34	5.23	1.55	0.23275	.	0.000000	0.40144	N	0.001175	T	0.76300	0.3968	M	0.72894	2.215	0.80722	D	1	D;D;D	0.69078	0.997;0.987;0.995	D;P;D	0.67231	0.95;0.841;0.926	T	0.70197	-0.4938	10	0.27785	T	0.31	.	5.4414	0.16511	0.0:0.2145:0.1349:0.6506	.	1097;4712;4712	Q8WXH0-7;Q8WXH0;Q8WXH0-2	.;SYNE2_HUMAN;.	I	4712;1097;4712;4629;4629;1346;1097	ENSP00000350719:L4712I;ENSP00000349969:L1097I;ENSP00000341781:L4712I;ENSP00000452570:L4629I;ENSP00000450831:L1346I;ENSP00000378249:L1097I	ENSP00000261678:L4629I	L	+	1	2	SYNE2	63666367	1.000000	0.71417	0.996000	0.52242	0.717000	0.41224	0.934000	0.28910	0.084000	0.17077	-0.274000	0.10170	TTA	.	.	.	none		0.458	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		A	64596614	T	A	64596614	3	1	210	1	0	0	0	0	1	0	0	0	15458	1490	52	5	14428	5	SYNE2	14	64596614	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	6032931	64596614	42752926	71	12806											
TTC8	123016	hgsc.bcm.edu	37	chr14	89307438	89307438	+	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	ctcaggcccagcacgcagagTggaaggccaggcactatgga	11	4	14	12	1	1	1	1	0	0	1	1	3	1	3	2	5	1	3	2	5	2	1			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr14:89307438T>A	ENST00000345383.5	+	4	441	c.357T>A	c.(355-357)agT>agA	p.S119R	TTC8_ENST00000354441.6_Intron|Y_RNA_ENST00000384612.1_RNA|TTC8_ENST00000338104.6_Missense_Mutation_p.S119R|TTC8_ENST00000346301.4_Missense_Mutation_p.S119R|TTC8_ENST00000380656.2_Missense_Mutation_p.S129R|TTC8_ENST00000358622.5_5'Flank|TTC8_ENST00000536576.1_5'UTR	NM_198309.2	NP_938051.1	Q8TAM2	TTC8_HUMAN	tetratricopeptide repeat domain 8	129					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						GCACGCAGAGTGGAAGGCCAG	0.498																																					p.S129R		Atlas-SNP	.											.	TTC8	42	.	0			c.T387A						PASS	.						67	75	72					14																	89307438		2203	4300	6503	SO:0001583	missense	123016	exon5			GCAGAGTGGAAGG	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.357T>A	chr14.hg19:g.89307438T>A	ENSP00000339486:p.Ser119Arg	114.0	0.0	.		127.0	52.0	.	NM_144596	A6NFG2|B3KWA5|Q67B97|Q86SY0|Q86TV9|Q86U26|Q8NDH9|Q96DG8	Missense_Mutation	SNP	ENST00000345383.5	hg19	CCDS9885.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	17.54|17.54|17.54	3.414274|3.414274|3.414274	0.62511|0.62511|0.62511	.|.|.	.|.|.	ENSG00000165533|ENSG00000165533|ENSG00000165533	ENST00000345383;ENST00000346301;ENST00000338104;ENST00000380656;ENST00000556651|ENST00000554686|ENST00000343648	T;T;T;T|.|.	0.80738|.|.	-1.3;-1.39;-1.41;-1.3|.|.	5.46|5.46|5.46	1.8|1.8|1.8	0.24995|0.24995|0.24995	.|.|.	0.153416|.|.	0.56097|.|.	D|.|.	0.000029|.|.	T|T|T	0.68613|0.68613|0.68613	0.3020|0.3020|0.3020	M|M|M	0.76574|0.76574|0.76574	2.34|2.34|2.34	0.80722|0.80722|0.80722	D|D|D	1|1|1	P;D;B;D;B|.|.	0.54601|.|.	0.808;0.967;0.012;0.967;0.012|.|.	B;P;B;P;B|.|.	0.51918|.|.	0.368;0.595;0.054;0.684;0.054|.|.	T|T|T	0.64045|0.64045|0.64045	-0.6499|-0.6499|-0.6499	10|5|5	0.66056|.|.	D|.|.	0.02|.|.	-16.3432|-16.3432|-16.3432	9.1746|9.1746|9.1746	0.37105|0.37105|0.37105	0.0:0.2088:0.0:0.7912|0.0:0.2088:0.0:0.7912|0.0:0.2088:0.0:0.7912	.|.|.	129;119;129;119;129|.|.	Q8TAM2;G3V2Z9;Q8TAM2-3;G3V324;Q8TAM2-4|.|.	TTC8_HUMAN;.;.;.;.|.|.	R|E|R	119;119;119;129;119|109|171	ENSP00000339486:S119R;ENSP00000298324:S119R;ENSP00000337653:S119R;ENSP00000370031:S129R|.|.	ENSP00000337653:S119R|.|.	S|V|W	+|+|+	3|2|1	2|0|0	TTC8|TTC8|TTC8	88377191|88377191|88377191	0.719000|0.719000|0.719000	0.27986|0.27986|0.27986	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.989000|0.989000|0.989000	0.77384|0.77384|0.77384	-0.225000|-0.225000|-0.225000	0.09151|0.09151|0.09151	0.065000|0.065000|0.065000	0.16485|0.16485|0.16485	0.460000|0.460000|0.460000	0.39030|0.39030|0.39030	AGT|GTG|TGG	.	.	.	none		0.498	TTC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410861.1	NM_144596		A	89307438	T	A	89307438	3	1	210	1	0	0	0	0	1	0	0	0	16726	1693	59	5	405	5	TTC8	14	89307438	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	24710824	89307438	18042102	72	12807											
CDC42BPB	9578	hgsc.bcm.edu	37	chr14	103438368	103438368	+	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	gctgccgggacaccttctgcTtctgggcacggagctctgcc	4	9	13	15	2	3	0	0	0	3	0	3	2	3	2	3	3	4	4	3	3	0	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr14:103438368T>A	ENST00000361246.2	-	13	2060	c.1772A>T	c.(1771-1773)aAg>aTg	p.K591M		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)		CACCTTCTGCTTCTGGGCACG	0.617																																					p.K591M		Atlas-SNP	.											.	CDC42BPB	123	.	0			c.A1772T						PASS	.						112	95	100					14																	103438368		2203	4300	6503	SO:0001583	missense	9578	exon13			TTCTGCTTCTGGG	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.1772A>T	chr14.hg19:g.103438368T>A	ENSP00000355237:p.Lys591Met	293.0	0.0	.		132.0	60.0	.	NM_006035		Missense_Mutation	SNP	ENST00000361246.2	hg19	CCDS9978.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.560047	0.86335	.	.	ENSG00000198752	ENST00000361246	D	0.82619	-1.63	5.31	4.15	0.48705	.	0.045881	0.85682	D	0.000000	D	0.90456	0.7011	M	0.84948	2.725	0.80722	D	1	D	0.76494	0.999	D	0.70935	0.971	D	0.90167	0.4232	10	0.56958	D	0.05	.	10.9197	0.47156	0.0:0.0743:0.0:0.9257	.	591	Q9Y5S2	MRCKB_HUMAN	M	591	ENSP00000355237:K591M	ENSP00000355237:K591M	K	-	2	0	CDC42BPB	102508121	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.228000	0.72288	0.860000	0.35481	0.460000	0.39030	AAG	.	.	.	none		0.617	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415711.1	NM_006035		A	103438368	T	A	103438368	3	1	210	1	0	0	0	0	1	0	0	0	3075	1609	56	5	3463	5	CDC42BPB	14	103438368	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	14130930	103438368	3911172	73	12808											
KIAA0284	283638	hgsc.bcm.edu	37	chr14	105353612	105353612	+	Missense_Mutation	SNP	T	T	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	cagtcctcagagaggcagcaTcacccacttggcccgacgga	10	5	11	15	2	2	1	2	0	0	1	3	4	3	2	3	3	1	2	3	3	0	1			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr14:105353612T>G	ENST00000414716.3	+	12	3264	c.3036T>G	c.(3034-3036)caT>caG	p.H1012Q	CEP170B_ENST00000418279.1_Missense_Mutation_p.H942Q|CEP170B_ENST00000556508.1_Missense_Mutation_p.H942Q|CEP170B_ENST00000453495.1_Missense_Mutation_p.H1013Q	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	1012						cytoplasm (GO:0005737)|microtubule (GO:0005874)											AGAGGCAGCATCACCCACTTG	0.687																																					p.H1012Q		Atlas-SNP	.											.	.	.	.	0			c.T3036G						PASS	.						11	15	14					14																	105353612		2073	4183	6256	SO:0001583	missense	283638	exon12			GCAGCATCACCCA	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.3036T>G	chr14.hg19:g.105353612T>G	ENSP00000404151:p.His1012Gln	74.0	0.0	.		35.0	14.0	.	NM_001112726	Q2KHR7|Q86TI7	Missense_Mutation	SNP	ENST00000414716.3	hg19	CCDS45175.1	.	.	.	.	.	.	.	.	.	.	T	4.535	0.099232	0.08681	.	.	ENSG00000099814	ENST00000556508;ENST00000414716;ENST00000453495;ENST00000418279	T;T;T;T	0.40756	1.02;1.02;1.02;1.02	3.85	-6.94	0.01633	.	1.152450	0.06494	N	0.735156	T	0.24736	0.0600	N	0.22421	0.69	0.09310	N	1	B;B;B	0.23735	0.002;0.09;0.01	B;B;B	0.16722	0.008;0.016;0.014	T	0.31971	-0.9924	10	0.59425	D	0.04	-0.1639	8.1321	0.31033	0.0:0.3657:0.4378:0.1965	.	1012;1012;942	Q9Y4F5-2;Q9Y4F5;E9PFC1	.;K0284_HUMAN;.	Q	942;1012;1013;942	ENSP00000451249:H942Q;ENSP00000404151:H1012Q;ENSP00000407238:H1013Q;ENSP00000415006:H942Q	ENSP00000404151:H1012Q	H	+	3	2	KIAA0284	104424657	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-3.141000	0.00586	-1.631000	0.01543	-0.537000	0.04273	CAT	.	.	.	none		0.687	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726		G	105353612	T	G	105353612	3	3	210	1	0	0	0	0	1	0	0	0	8173	1432	50	5	3078	5	KIAA0284	14	105353612	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	1915244	105353612	1995928	74	12809											
CATSPER2	117155	hgsc.bcm.edu	37	chr15	43928412	43928412	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgttaccagggaattcgggAggtccctaaagaaaaagaca	15	7	11	8	1	0	2	0	0	0	2	2	4	1	4	2	3	1	1	2	3	6	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr15:43928412A>G	ENST00000321596.5	-	8	1047	c.848T>C	c.(847-849)cTc>cCc	p.L283P	RNU6-610P_ENST00000384264.1_RNA|CATSPER2_ENST00000396879.1_Missense_Mutation_p.L283P|CATSPER2_ENST00000354127.4_Missense_Mutation_p.L283P|STRC_ENST00000541030.1_Intron|CATSPER2_ENST00000355438.2_Missense_Mutation_p.L283P|CATSPER2_ENST00000381761.1_Missense_Mutation_p.L289P			Q96P56	CTSR2_HUMAN	cation channel, sperm associated 2	283					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)		GGAATTCGGGAGGTCCCTAAA	0.413																																					p.L283P		Atlas-SNP	.											.	CATSPER2	49	.	0			c.T848C						PASS	.						53	54	53					15																	43928412		2199	4296	6495	SO:0001583	missense	117155	exon8			TTCGGGAGGTCCC	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.848T>C	chr15.hg19:g.43928412A>G	ENSP00000321463:p.Leu283Pro	52.0	0.0	.		73.0	28.0	.	NM_054020	Q8NHT9|Q96P54|Q96P55	Missense_Mutation	SNP	ENST00000321596.5	hg19	CCDS10099.1	.	.	.	.	.	.	.	.	.	.	A	5.296	0.239992	0.10023	.	.	ENSG00000166762	ENST00000396879;ENST00000299989;ENST00000381761;ENST00000321596;ENST00000354127;ENST00000355438	D;D;D;D;D	0.98585	-5.01;-5.01;-5.01;-5.01;-5.01	4.81	4.81	0.61882	Ion transport (1);	0.856615	0.09979	N	0.731205	D	0.97885	0.9305	M	0.82823	2.61	0.33841	D	0.631417	B;B	0.29481	0.206;0.245	B;B	0.35727	0.133;0.209	D	0.99974	1.2121	10	0.87932	D	0	.	10.6643	0.45721	1.0:0.0:0.0:0.0	.	289;283	F8W9H2;Q96P56	.;CTSR2_HUMAN	P	283;283;289;283;283;283	ENSP00000380088:L283P;ENSP00000371180:L289P;ENSP00000321463:L283P;ENSP00000339137:L283P;ENSP00000347613:L283P	ENSP00000299989:L283P	L	-	2	0	CATSPER2	41715704	0.211000	0.23529	0.127000	0.21898	0.013000	0.08279	3.770000	0.55310	2.013000	0.59113	0.533000	0.62120	CTC	.	.	.	none		0.413	CATSPER2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133151.2	NM_054020		G	43928412	A	G	43928412	3	3	210	1	0	0	0	0	1	0	0	0	2690	304	11	3	768	3	CATSPER2	15	43928412	Missense_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08		43928412	58602980	75	12810											
NEO1	4756	hgsc.bcm.edu	37	chr15	73590713	73590713	+	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	cgttcgaaatacccccagcaCtgacaccatgccagcctctt	10	8	6	17	2	1	1	0	1	1	0	2	2	1	1	5	0	4	2	5	0	2	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr15:73590713C>T	ENST00000339362.5	+	28	4373	c.3926C>T	c.(3925-3927)aCt>aTt	p.T1309I	NEO1_ENST00000558964.1_Missense_Mutation_p.T1298I|NEO1_ENST00000560262.1_Missense_Mutation_p.T1256I|NEO1_ENST00000261908.6_Missense_Mutation_p.T1309I			Q92859	NEO1_HUMAN	neogenin 1	1309					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|iron ion homeostasis (GO:0055072)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						ACCCCCAGCACTGACACCATG	0.483																																					p.T1309I		Atlas-SNP	.											.	NEO1	102	.	0			c.C3926T						PASS	.						81	76	78					15																	73590713		2198	4297	6495	SO:0001583	missense	4756	exon27			CCAGCACTGACAC	U61262	CCDS10247.1, CCDS53957.1, CCDS58378.1	15q22.3-q23	2014-06-20	2010-06-24		ENSG00000067141	ENSG00000067141		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7754	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 2"	601907	"neogenin (chicken) homolog 1"			9121761	Standard	NM_002499		Approved	NGN, HsT17534, IGDCC2, NTN1R2	uc002avm.4	Q92859	OTTHUMG00000133509	ENST00000339362.5:c.3926C>T	chr15.hg19:g.73590713C>T	ENSP00000341198:p.Thr1309Ile	88.0	0.0	.		70.0	36.0	.	NM_002499	B7ZKM9|B7ZKN0|O00340|Q17RX1	Missense_Mutation	SNP	ENST00000339362.5	hg19	CCDS10247.1	.	.	.	.	.	.	.	.	.	.	C	19.96	3.924141	0.73213	.	.	ENSG00000067141	ENST00000339362;ENST00000379842;ENST00000261908	T	0.42900	0.96	5.28	5.28	0.74379	Neogenin, C-terminal (1);	0.294982	0.37857	N	0.001913	T	0.32704	0.0838	N	0.14661	0.345	0.41912	D	0.990476	B;B;B;P	0.37594	0.408;0.408;0.372;0.601	B;B;B;B	0.42959	0.304;0.324;0.295;0.403	T	0.16247	-1.0409	10	0.36615	T	0.2	-15.6613	14.1931	0.65652	0.0:0.8505:0.1495:0.0	.	1256;1298;1020;1309	B7ZKM9;B7ZKN0;E7EUX3;Q92859	.;.;.;NEO1_HUMAN	I	1256;1020;1309	ENSP00000261908:T1309I	ENSP00000261908:T1309I	T	+	2	0	NEO1	71377766	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.492000	0.66893	2.479000	0.83701	0.655000	0.94253	ACT	.	.	.	none		0.483	NEO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257472.2	NM_002499		T	73590713	C	T	73590713	3	4	210	1	0	0	0	0	1	0	0	0	10343	565	20	2	4032	2	NEO1	15	73590713	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	29662301	73590713	28940679	76	12811											
IREB2	3658	hgsc.bcm.edu	37	chr15	78755356	78755356	+	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	aggaagatgttatgaacattTtagactggaaaaccaaacaa	19	9	8	5	0	0	3	0	1	0	2	0	5	0	5	1	2	3	1	1	2	8	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr15:78755356T>A	ENST00000258886.8	+	3	348	c.199T>A	c.(199-201)Tta>Ata	p.L67I	IREB2_ENST00000560440.1_Missense_Mutation_p.L67I	NM_004136.2	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2	67					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)		TATGAACATTTTAGACTGGAA	0.378																																					p.L67I	NSCLC(200;764 2208 35157 49871 50830)	Atlas-SNP	.											.	IREB2	106	.	0			c.T199A						PASS	.						214	201	205					15																	78755356		2196	4293	6489	SO:0001583	missense	3658	exon3			AACATTTTAGACT	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.199T>A	chr15.hg19:g.78755356T>A	ENSP00000258886:p.Leu67Ile	107.0	0.0	.		183.0	75.0	.	NM_004136	A8KAC7|E1CJT9|H0YKU0|Q13095|Q1HE21|Q59FQ7|Q8WVK6|Q9UF17	Missense_Mutation	SNP	ENST00000258886.8	hg19	CCDS10302.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.018887	0.75275	.	.	ENSG00000136381	ENST00000258886	T	0.44881	0.91	5.87	3.57	0.40892	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3 (1);Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha (2);	0.000000	0.85682	D	0.000000	T	0.53254	0.1785	L	0.52573	1.65	0.51482	D	0.999929	D;P	0.69078	0.997;0.577	D;P	0.91635	0.999;0.774	T	0.42616	-0.9441	10	0.23891	T	0.37	.	10.2319	0.43260	0.0:0.1334:0.0:0.8666	.	67;67	P48200;Q8WVK6	IREB2_HUMAN;.	I	67	ENSP00000258886:L67I	ENSP00000258886:L67I	L	+	1	2	IREB2	76542411	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	0.725000	0.25970	0.574000	0.29417	0.533000	0.62120	TTA	.	.	.	none		0.378	IREB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290109.3	NM_004136		A	78755356	T	A	78755356	3	1	210	1	0	0	0	0	1	0	0	0	7833	1838	64	5	209	5	IREB2	15	78755356	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	5164643	78755356	23776036	77	12812											
KIAA1199	57214	hgsc.bcm.edu	37	chr15	81166242	81166242	+	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	tgggagctgctgggaggcagGacttcctcttcaaggccatg	7	9	15	10	0	2	0	1	0	1	0	3	3	3	3	2	5	2	3	2	5	1	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr15:81166242G>C	ENST00000394685.3	+	3	441	c.22G>C	c.(22-24)Gac>Cac	p.D8H	KIAA1199_ENST00000356249.5_Missense_Mutation_p.D8H|KIAA1199_ENST00000220244.3_Missense_Mutation_p.D8H			Q8WUJ3	CEMIP_HUMAN		8					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)	p.D8N(1)		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						TGGGAGGCAGGACTTCCTCTT	0.577																																					p.D8H		Atlas-SNP	.											KIAA1199,NS,carcinoma,0,1	KIAA1199	118	.	1	Substitution - Missense(1)	kidney(1)	c.G22C						PASS	.						70	54	60					15																	81166242		2202	4298	6500	SO:0001583	missense	57214	exon2			AGGCAGGACTTCC																												ENST00000394685.3:c.22G>C	chr15.hg19:g.81166242G>C	ENSP00000378177:p.Asp8His	15.0	0.0	.		8.0	2.0	.	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Missense_Mutation	SNP	ENST00000394685.3	hg19	CCDS10315.1	.	.	.	.	.	.	.	.	.	.	G	8.342	0.828847	0.16749	.	.	ENSG00000103888	ENST00000220244;ENST00000394685;ENST00000356249;ENST00000394683	T;T;T	0.66460	-0.21;-0.21;-0.21	4.92	-2.97	0.05530	.	6.948940	0.00166	N	0.000000	T	0.48537	0.1505	L	0.27053	0.805	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.17806	-1.0357	10	0.14656	T	0.56	-8.0685	5.165	0.15081	0.3585:0.2796:0.3619:0.0	.	8	Q8WUJ3	K1199_HUMAN	H	8	ENSP00000220244:D8H;ENSP00000378177:D8H;ENSP00000348583:D8H	ENSP00000220244:D8H	D	+	1	0	KIAA1199	78953297	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.356000	0.02609	-0.329000	0.08527	-0.165000	0.13383	GAC	.	.	.	none		0.577	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1			C	81166242	G	C	81166242	3	2	210	1	0	0	0	0	1	0	0	0	8220	1174	41	4	24	4	KIAA1199	15	81166242	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	2410886	81166242	21365150	78	12813											
SRCAP	10847	hgsc.bcm.edu	37	chr16	30733503	30733503	+	Frame_Shift_Del	DEL	C	C	-																															acaacgtccagtggctaatgCagggggaagcaaacctctca																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr16:30733503delC	ENST00000262518.4	+	22	3987	c.3602delC	c.(3601-3603)gcafs	p.A1201fs	SRCAP_ENST00000344771.4_Frame_Shift_Del_p.A1105fs|SRCAP_ENST00000395059.2_Frame_Shift_Del_p.A1201fs	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1201	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)			GTGGCTAATGCAGGGGGAAGC	0.577																																					p.A1201fs		Atlas-INDEL	.											.	SRCAP	298	.	0			c.3601delG						PASS	.						128	106	113					16																	30733503		2197	4300	6497	SO:0001589	frameshift_variant	10847	exon22			.	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.3602delC	chr16.hg19:g.30733503delC	ENSP00000262518:p.Ala1201fs	238.0	0.0	0		97.0	33.0	0.340206	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Frame_Shift_Del	DEL	ENST00000262518.4	hg19	CCDS10689.2																																																																																			.	.	.	none		0.577	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		-	30733503	C	-	30733503	7	5	210	1	0	1	0	1	0	0	0	0	15147	710	25	0	3680	0	SRCAP	16	30733503	Frame_Shift_Del	DEL	C	TCGA-IZ-8196-01A-11D-2396-08		30733503	59621250	79	12814	126	2									
SRCAP	10847	hgsc.bcm.edu	37	chr16	30733505	30733505	+	Missense_Mutation	SNP	G	G	A																															aacgtccagtggctaatgcaGggggaagcaaacctctcacc																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr16:30733505G>A	ENST00000262518.4	+	22	3989	c.3604G>A	c.(3604-3606)Ggg>Agg	p.G1202R	SRCAP_ENST00000344771.4_Missense_Mutation_p.G1106R|SRCAP_ENST00000395059.2_Missense_Mutation_p.G1202R	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1202	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)			GGCTAATGCAGGGGGAAGCAA	0.572																																					p.G1202R		Atlas-SNP	.											.	SRCAP	298	.	0			c.G3604A						PASS	.						129	107	114					16																	30733505		2197	4300	6497	SO:0001583	missense	10847	exon22			AATGCAGGGGGAA	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.3604G>A	chr16.hg19:g.30733505G>A	ENSP00000262518:p.Gly1202Arg	245.0	0.0	.		102.0	38.0	.	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	hg19	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	G	15.91	2.973443	0.53614	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.90900	-2.71;-2.68;-2.75	4.68	4.68	0.58851	.	0.000000	0.49305	D	0.000153	D	0.85961	0.5819	N	0.14661	0.345	0.20821	N	0.999846	P;D;P	0.53462	0.859;0.96;0.933	P;P;P	0.51229	0.572;0.663;0.462	T	0.78420	-0.2211	10	0.31617	T	0.26	-8.9406	12.9347	0.58307	0.0:0.1644:0.8356:0.0	.	1106;1202;1202	Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2	.;.;SRCAP_HUMAN	R	1202;1202;1106	ENSP00000262518:G1202R;ENSP00000378499:G1202R;ENSP00000343042:G1106R	ENSP00000262518:G1202R	G	+	1	0	SRCAP	30641006	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.941000	0.49011	2.414000	0.81942	0.462000	0.41574	GGG	.	.	.	none		0.572	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		A	30733505	G	A	30733505	3	1	210	1	0	0	0	0	1	0	0	0	15147	1000	35	2	3682	2	SRCAP	16	30733505	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	2	30733505	59621248	80	12815	126	2									
CDH8	1006	hgsc.bcm.edu	37	chr16	61851550	61851550	+	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	gtcgccgtgtctttaaagggCcccctgccactgaagcgtgg	6	9	13	13	3	1	1	0	1	1	0	2	1	1	1	4	2	2	0	4	2	3	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr16:61851550C>T	ENST00000577390.1	-	7	2064	c.1110G>A	c.(1108-1110)ggG>ggA	p.G370G	CDH8_ENST00000577730.1_Silent_p.G370G|CDH8_ENST00000584337.1_Silent_p.G370G|CDH8_ENST00000299345.6_Silent_p.G370G	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	370	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|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)		CTTTAAAGGGCCCCCTGCCAC	0.468																																					p.G370G		Atlas-SNP	.											.	CDH8	273	.	0			c.G1110A						PASS	.						86	68	74					16																	61851550		2203	4300	6503	SO:0001819	synonymous_variant	1006	exon7			AAAGGGCCCCCTG	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.1110G>A	chr16.hg19:g.61851550C>T		82.0	0.0	.		90.0	44.0	.	NM_001796	B3KWC1|Q14DC6|Q9ULB2	Silent	SNP	ENST00000577390.1	hg19	CCDS10802.1																																																																																			.	.	.	none		0.468	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		T	61851550	C	T	61851550	2	4	210	1	0	0	0	0	0	0	0	1	3118	726	26	2		2	CDH8	16	61851550	Silent	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	31118045	61851550	28503203	81	12816											
CDT1	81620	hgsc.bcm.edu	37	chr16	88872437	88872437	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcgtcccacagaggctgacGgagcagccccccagctcacg	8	4	11	18	3	1	2	1	1	0	1	3	3	2	3	4	2	3	3	4	2	0	0	rs368718178		TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr16:88872437G>A	ENST00000301019.4	+	6	1460	c.841G>A	c.(841-843)Gga>Aga	p.G281R		NM_030928.3	NP_112190.2			chromatin licensing and DNA replication factor 1											central_nervous_system(1)|endometrium(2)|kidney(1)|lung(3)	7				BRCA - Breast invasive adenocarcinoma(80;0.0476)		AGAGGCTGACGGAGCAGCCCC	0.672																																					p.G281R	Melanoma(159;511 3380 30971)	Atlas-SNP	.											.	CDT1	30	.	0			c.G841A						PASS	.	G	ARG/GLY	1,4361		0,1,2180	15	17	16		841	-3.5	0	16		16	0,8566		0,0,4283	no	missense	CDT1	NM_030928.3	125	0,1,6463	AA,AG,GG		0.0,0.0229,0.0077	possibly-damaging	281/547	88872437	1,12927	2181	4283	6464	SO:0001583	missense	81620	exon6			GCTGACGGAGCAG	AF070552	CCDS32510.1	16q24.3	2014-08-12			ENSG00000167513	ENSG00000167513			24576	protein-coding gene	gene with protein product		605525				11896191, 11555648	Standard	NM_030928		Approved	DUP, RIS2	uc002flu.3	Q9H211	OTTHUMG00000173467	ENST00000301019.4:c.841G>A	chr16.hg19:g.88872437G>A	ENSP00000301019:p.Gly281Arg	36.0	0.0	.		12.0	5.0	.	NM_030928		Missense_Mutation	SNP	ENST00000301019.4	hg19	CCDS32510.1	.	.	.	.	.	.	.	.	.	.	G	13.49	2.253471	0.39797	2.29E-4	0.0	ENSG00000167513	ENST00000301019	T	0.23552	1.9	4.83	-3.49	0.04724	.	1.014200	0.07884	N	0.970068	T	0.13030	0.0316	L	0.35487	1.065	0.30312	N	0.788448	P	0.51351	0.944	B	0.38458	0.274	T	0.37033	-0.9723	10	0.20046	T	0.44	.	4.4942	0.11828	0.0996:0.2944:0.5056:0.1004	.	281	Q9H211	CDT1_HUMAN	R	281	ENSP00000301019:G281R	ENSP00000301019:G281R	G	+	1	0	CDT1	87399938	0.003000	0.15002	0.000000	0.03702	0.004000	0.04260	0.790000	0.26900	-0.552000	0.06167	0.462000	0.41574	GGA	.	.	.	weak		0.672	CDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000423215.1	NM_030928		A	88872437	G	A	88872437	3	1	210	1	0	0	0	0	1	0	0	0	3182	1117	39	1	863	1	CDT1	16	88872437	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08	27020887	88872437	1482316	82	12817											
MAP2K4	6416	hgsc.bcm.edu	37	chr17	12016635	12016635	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtggacagcttgtggactcTattgccaagacaagagatgc	12	9	12	8	0	1	2	0	0	1	2	1	5	1	4	1	2	3	1	1	2	3	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr17:12016635T>C	ENST00000353533.5	+	7	834	c.771T>C	c.(769-771)tcT>tcC	p.S257S	MAP2K4_ENST00000581941.1_3'UTR|MAP2K4_ENST00000415385.3_Silent_p.S268S	NM_003010.2	NP_003001.1	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4	257	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron apoptotic process (GO:0043525)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|nucleus (GO:0005634)|perikaryon (GO:0043204)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.0?(10)|p.?(1)		NS(1)|biliary_tract(2)|breast(22)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(26)|lung(15)|ovary(8)|pancreas(11)|skin(3)|stomach(2)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	100		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)		TTGTGGACTCTATTGCCAAGA	0.453			"D, Mis, N"		"pancreatic, breast, colorectal"																																p.S257S		Atlas-SNP	.		Rec	yes		17	17p11.2	6416	mitogen-activated protein kinase kinase 4		E	.	MAP2K4	176	.	11	Whole gene deletion(10)|Unknown(1)	ovary(4)|breast(4)|biliary_tract(1)|large_intestine(1)|pancreas(1)	c.T771C						PASS	.						105	101	102					17																	12016635		2203	4300	6503	SO:0001819	synonymous_variant	6416	exon7			GGACTCTATTGCC	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.771T>C	chr17.hg19:g.12016635T>C		81.0	0.0	.		159.0	104.0	.	NM_003010	B2R7N7|B3KYB2|D3DTS5|Q5U0B8|Q6FHX4|Q6P9H2|Q6PIE6	Silent	SNP	ENST00000353533.5	hg19	CCDS11162.1																																																																																			.	.	.	none		0.453	MAP2K4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441226.1			C	12016635	T	C	12016635	2	2	210	1	0	0	0	0	0	0	0	1	9246	1509	53	3		3	MAP2K4	17	12016635	Silent	SNP	T	TCGA-IZ-8196-01A-11D-2396-08		12016635	69178575	83	12818											
NAGLU	4669	hgsc.bcm.edu	37	chr17	40695935	40695935	+	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	agtgaggccgaggccgatttCtacgagcagaacagccgcta	11	6	13	11	4	1	2	0	1	1	1	1	5	1	2	3	2	4	2	3	2	3	3			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr17:40695935C>T	ENST00000225927.2	+	6	2012	c.1911C>T	c.(1909-1911)ttC>ttT	p.F637F	RP11-400F19.8_ENST00000585572.1_RNA	NM_000263.3	NP_000254.2	P54802	ANAG_HUMAN	N-acetylglucosaminidase, alpha	637					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)	AGGCCGATTTCTACGAGCAGA	0.627																																					p.F637F		Atlas-SNP	.											.	NAGLU	36	.	0			c.C1911T						PASS	.						25	21	22					17																	40695935		2202	4295	6497	SO:0001819	synonymous_variant	4669	exon6			CGATTTCTACGAG		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.1911C>T	chr17.hg19:g.40695935C>T		43.0	0.0	.		21.0	10.0	.	NM_000263		Silent	SNP	ENST00000225927.2	hg19	CCDS11427.1																																																																																			.	.	.	none		0.627	NAGLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450385.1	NM_000263		T	40695935	C	T	40695935	2	4	210	1	0	0	0	0	0	0	0	1	10150	912	32	2		2	NAGLU	17	40695935	Silent	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	28679300	40695935	40499275	84	12819											
LSM12	124801	hgsc.bcm.edu	37	chr17	42117589	42117589	+	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	attgcataggcctggctcagCttctcctccttctctgtccg	4	14	8	15	1	3	0	1	0	2	0	7	0	5	0	4	2	2	3	4	2	1	4			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr17:42117589C>T	ENST00000591247.1	-	4	616	c.294G>A	c.(292-294)aaG>aaA	p.K98K	LSM12_ENST00000293406.3_Silent_p.K98K|LSM12_ENST00000585388.1_Silent_p.K98K	NM_152344.3	NP_689557.1	Q3MHD2	LSM12_HUMAN	LSM12 homolog (S. cerevisiae)	98										NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)	6		Breast(137;0.0313)|Prostate(33;0.0861)		BRCA - Breast invasive adenocarcinoma(366;0.115)		CCTGGCTCAGCTTCTCCTCCT	0.517																																					p.K98K		Atlas-SNP	.											.	LSM12	16	.	0			c.G294A						PASS	.						99	72	81					17																	42117589		2203	4300	6503	SO:0001819	synonymous_variant	124801	exon4			GCTCAGCTTCTCC	BC044587	CCDS11475.1	17q21.31	2007-08-21				ENSG00000161654			26407	protein-coding gene	gene with protein product		611793				15225602	Standard	NM_152344		Approved	FLJ30656	uc002iev.3	Q3MHD2		ENST00000591247.1:c.294G>A	chr17.hg19:g.42117589C>T		60.0	0.0	.		67.0	42.0	.	NM_152344	Q86YB1|Q96NL5	Silent	SNP	ENST00000591247.1	hg19	CCDS11475.1																																																																																			.	.	.	none		0.517	LSM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457672.1	NM_152344		T	42117589	C	T	42117589	2	4	210	1	0	0	0	0	0	0	0	1	9060	796	28	2		2	LSM12	17	42117589	Silent	SNP	C	TCGA-IZ-8196-01A-11D-2396-08	1421654	42117589	39077621	85	12820											
AMH	268	hgsc.bcm.edu	37	chr19	2249551	2249551	+	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	gctcccccctgcgggtggtgGgggctctaagcgcctatgag	4	8	16	13	2	1	1	0	1	1	0	2	1	2	1	4	4	2	2	4	4	2	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr19:2249551G>T	ENST00000221496.4	+	1	242	c.220G>T	c.(220-222)Ggg>Tgg	p.G74W	MIR4321_ENST00000592276.1_RNA	NM_000479.3	NP_000470	P03971	MIS_HUMAN	anti-Mullerian hormone	74					aging (GO:0007568)|cell-cell signaling (GO:0007267)|gonadal mesoderm development (GO:0007506)|Mullerian duct regression (GO:0001880)|positive regulation of gene expression (GO:0010628)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|preantral ovarian follicle growth (GO:0001546)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|sex determination (GO:0007530)|sex differentiation (GO:0007548)|urogenital system development (GO:0001655)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)|receptor binding (GO:0005102)			lung(2)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCGGGTGGTGGGGGCTCTAAG	0.692									Persistant Mullerian Duct Syndrome (type I and II)																												p.G74W		Atlas-SNP	.											.	AMH	12	.	0			c.G220T						PASS	.						8	11	10					19																	2249551		2163	4282	6445	SO:0001583	missense	268	exon1	Familial Cancer Database	PMDS, Persistent Oviduct Syndrome	GTGGTGGGGGCTC	K03474	CCDS12085.1	19p13.3	2014-01-30				ENSG00000104899		"Endogenous ligands"	464	protein-coding gene	gene with protein product		600957				3754790, 18784351	Standard	NM_000479		Approved	MIS	uc002lvh.2	P03971		ENST00000221496.4:c.220G>T	chr19.hg19:g.2249551G>T	ENSP00000221496:p.Gly74Trp	33.0	0.0	.		11.0	6.0	.	NM_000479	O75246|Q6GTN3	Missense_Mutation	SNP	ENST00000221496.4	hg19	CCDS12085.1	.	.	.	.	.	.	.	.	.	.	G	11.06	1.527815	0.27299	.	.	ENSG00000104899	ENST00000221496	D	0.94687	-3.49	3.75	3.75	0.43078	.	0.168909	0.38548	U	0.001642	D	0.95010	0.8385	L	0.34521	1.04	0.44555	D	0.997518	D	0.89917	1.0	D	0.91635	0.999	D	0.95614	0.8675	10	0.87932	D	0	-23.8931	14.1364	0.65291	0.0:0.0:1.0:0.0	.	74	P03971	MIS_HUMAN	W	74	ENSP00000221496:G74W	ENSP00000221496:G74W	G	+	1	0	AMH	2200551	1.000000	0.71417	0.103000	0.21229	0.001000	0.01503	5.367000	0.66127	1.657000	0.50732	0.462000	0.41574	GGG	.	.	.	none		0.692	AMH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451276.3	NM_000479		T	2249551	G	T	2249551	3	4	210	1	0	0	0	0	1	0	0	0	572	1232	43	4	222	4	AMH	19	2249551	Missense_Mutation	SNP	G	TCGA-IZ-8196-01A-11D-2396-08		2249551	56879432	86	12821											
CLEC4M	10332	hgsc.bcm.edu	37	chr19	7832420	7832420	+	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	agaacttcctacagctgcagActtccaggagtaaccgcttc	11	9	8	13	1	0	2	0	0	0	2	3	3	2	3	3	1	5	4	3	1	3	5			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr19:7832420A>T	ENST00000327325.5	+	6	1073	c.955A>T	c.(955-957)Act>Tct	p.T319S	CLEC4M_ENST00000359059.5_Missense_Mutation_p.T252S|CLEC4M_ENST00000248228.4_Missense_Mutation_p.T297S|CLEC4M_ENST00000595496.1_Missense_Mutation_p.T183S|CLEC4M_ENST00000596707.1_Missense_Mutation_p.T252S|CLEC4M_ENST00000596363.1_Intron|CLEC4M_ENST00000394122.2_Missense_Mutation_p.T307S|CLEC4M_ENST00000334806.5_Missense_Mutation_p.T268S|CLEC4M_ENST00000597522.1_Intron|CLEC4M_ENST00000357361.2_Intron	NM_001144909.1|NM_014257.4	NP_001138381.1|NP_055072.3	Q9H2X3	CLC4M_HUMAN	C-type lectin domain family 4, member M	319	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				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						ACAGCTGCAGACTTCCAGGAG	0.552																																					p.T319S		Atlas-SNP	.											CLEC4M,NS,carcinoma,0,1	CLEC4M	58	.	0			c.A955T						PASS	.						102	89	94					19																	7832420		2203	4300	6503	SO:0001583	missense	10332	exon6			CTGCAGACTTCCA	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.955A>T	chr19.hg19:g.7832420A>T	ENSP00000316228:p.Thr319Ser	100.0	0.0	.		90.0	6.0	.	NM_014257	A6NKI4|A8K8B3|Q69F40|Q969M4|Q96QP3|Q96QP4|Q96QP5|Q96QP6|Q9BXS3|Q9H2Q9|Q9H8F0|Q9Y2A8	Missense_Mutation	SNP	ENST00000327325.5	hg19	CCDS12187.1	.	.	.	.	.	.	.	.	.	.	A	0.007	-1.947181	0.00475	.	.	ENSG00000104938	ENST00000327325;ENST00000394122;ENST00000248228;ENST00000334806;ENST00000359059	T;T;T;T;T	0.16897	2.31;2.31;2.31;2.31;2.31	2.42	-4.84	0.03151	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	.	.	.	.	T	0.08044	0.0201	N	0.25426	0.745	0.09310	N	0.999998	B;B;B;B;B;B	0.09022	0.002;0.0;0.001;0.0;0.001;0.001	B;B;B;B;B;B	0.13407	0.007;0.0;0.004;0.007;0.002;0.009	T	0.38735	-0.9647	9	0.13108	T	0.6	.	3.4919	0.07641	0.3644:0.0:0.3242:0.3114	.	268;252;319;307;296;183	B4E2Z5;Q9H2X3-5;Q9H2X3;E7ENS9;Q9H2X3-8;Q9H2X3-7	.;.;CLC4M_HUMAN;.;.;.	S	319;307;297;268;252	ENSP00000316228:T319S;ENSP00000377680:T307S;ENSP00000248228:T297S;ENSP00000335228:T268S;ENSP00000351954:T252S	ENSP00000248228:T297S	T	+	1	0	CLEC4M	7738420	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.311000	0.08124	-2.225000	0.00724	-2.665000	0.00146	ACT	.	.	.	none		0.552	CLEC4M-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461161.1	NM_014257		T	7832420	A	T	7832420	3	4	210	1	0	0	0	0	1	0	0	0	3520	275	10	5	998	5	CLEC4M	19	7832420	Missense_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	5582869	7832420	51296563	87	12822											
CD97	976	hgsc.bcm.edu	37	chr19	14518917	14518918	+	Frame_Shift_Ins	INS	-	-	A																															ctccaggccctcagggcatcINSagagtccggcatatgaaggc																										TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr19:14518917_14518918insA	ENST00000242786.5	+	20	2572_2573	c.2492_2493insA	c.(2491-2496)tcagagfs	p.E832fs	CTC-548K16.5_ENST00000590626.1_RNA|CD97_ENST00000357355.3_Frame_Shift_Ins_p.E783fs|DDX39A_ENST00000592927.1_5'Flank|CD97_ENST00000358600.3_Frame_Shift_Ins_p.E739fs	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	832					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						CTCAGGGCATCAGAGTCCGGCA	0.663																																					p.S831fs		Atlas-INDEL	.											.	CD97	86	.	0			c.2492_2493insA						PASS	.																																			SO:0001589	frameshift_variant	976	exon20			.		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.2493dupA	chr19.hg19:g.14518918_14518918dupA	ENSP00000242786:p.Glu832fs	98.0	0.0	0		47.0	18.0	0.382979	NM_078481	A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	Frame_Shift_Ins	INS	ENST00000242786.5	hg19	CCDS32929.1																																																																																			.	.	.	none		0.663	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459821.2	NM_078481		A	14518918	-	A	14518917	7	5	210	1	0	1	1	0	0	0	0	0	3051	838	29	0	2570	0	CD97	19	14518917	Frame_Shift_Ins	INS	-	TCGA-IZ-8196-01A-11D-2396-08	6686497	14518917	44610066	88	12823											
SNPH	9751	hgsc.bcm.edu	37	chr20	1286555	1286555	+	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	cctggctttgccgctcccagCggcgccagggccagcccatc	4	6	12	19	3	0	0	0	0	0	0	2	0	1	0	6	3	3	2	6	3	0	1			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr20:1286555C>T	ENST00000381873.3	+	6	1578	c.1342C>T	c.(1342-1344)Cgg>Tgg	p.R448W	SNPH_ENST00000381867.1_Missense_Mutation_p.R492W	NM_014723.2	NP_055538.2	O15079	SNPH_HUMAN	syntaphilin	448					brain development (GO:0007420)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|synaptic vesicle docking involved in exocytosis (GO:0016081)	cell junction (GO:0030054)|cytoplasmic microtubule (GO:0005881)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)	syntaxin-1 binding (GO:0017075)			endometrium(2)|large_intestine(4)|lung(10)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						CCGCTCCCAGCGGCGCCAGGG	0.672																																					p.R448W		Atlas-SNP	.											.	SNPH	89	.	0			c.C1342T						PASS	.						16	10	12					20																	1286555		2131	4210	6341	SO:0001583	missense	9751	exon6			TCCCAGCGGCGCC		CCDS13012.1	20p13	2008-07-02			ENSG00000101298	ENSG00000101298			15931	protein-coding gene	gene with protein product		604942				10707983	Standard	NM_014723		Approved	bA314N13.5	uc002wes.3	O15079	OTTHUMG00000031662	ENST00000381873.3:c.1342C>T	chr20.hg19:g.1286555C>T	ENSP00000371297:p.Arg448Trp	33.0	0.0	.		13.0	7.0	.	NM_014723	Q8IYI3	Missense_Mutation	SNP	ENST00000381873.3	hg19	CCDS13012.1	.	.	.	.	.	.	.	.	.	.	C	15.03	2.712880	0.48517	.	.	ENSG00000101298	ENST00000381873;ENST00000381867	.	.	.	4.24	1.16	0.20824	.	0.431073	0.21513	N	0.073349	T	0.59729	0.2215	M	0.62723	1.935	0.31113	N	0.709748	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.992	T	0.61088	-0.7133	9	0.87932	D	0	-28.0671	7.7271	0.28765	0.5262:0.3946:0.0:0.0791	.	492;448	O15079-2;O15079	.;SNPH_HUMAN	W	448;492	.	ENSP00000371291:R492W	R	+	1	2	SNPH	1234555	0.992000	0.36948	0.981000	0.43875	0.898000	0.52572	0.375000	0.20518	0.083000	0.17047	-0.268000	0.10319	CGG	.	.	.	none		0.672	SNPH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145240.2	NM_014723		T	1286555	C	T	1286555	3	4	210	1	0	0	0	0	1	0	0	0	14863	759	27	1	1356	1	SNPH	20	1286555	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08		1286555	61738965	89	12824											
BRWD1	54014	hgsc.bcm.edu	37	chr21	40641908	40641908	+	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	atgtcctgcagataacataaTtctggaatcaaagggatgtg	14	11	10	6	0	2	1	1	0	1	1	3	3	3	3	1	2	2	1	1	2	4	3	rs540249994		TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr21:40641908T>A	ENST00000333229.2	-	15	1774	c.1447A>T	c.(1447-1449)Att>Ttt	p.I483F	BRWD1_ENST00000342449.3_Missense_Mutation_p.I483F|BRWD1_ENST00000380800.3_Missense_Mutation_p.I483F	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	483					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)				GATAACATAATTCTGGAATCA	0.333																																					p.I483F	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.A1447T						PASS	.						105	99	101					21																	40641908		2203	4300	6503	SO:0001583	missense	54014	exon15			ACATAATTCTGGA	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.1447A>T	chr21.hg19:g.40641908T>A	ENSP00000330753:p.Ile483Phe	20.0	0.0	.		48.0	26.0	.	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	hg19	CCDS13662.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.9|25.9	4.681151|4.681151	0.88542|0.88542	.|.	.|.	ENSG00000185658|ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800|ENST00000455867	T;T;T|.	0.59224|.	0.28;0.28;0.28|.	5.57|5.57	5.57|5.57	0.84162|0.84162	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.080378|.	0.53938|.	D|.	0.000059|.	T|T	0.45337|0.45337	0.1337|0.1337	L|L	0.27944|0.27944	0.81|0.81	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	0.999;0.999;1.0|.	D;D;D|.	0.91635|.	0.996;0.999;0.99|.	T|T	0.38200|0.38200	-0.9672|-0.9672	10|5	0.87932|.	D|.	0|.	-10.9067|-10.9067	10.1398|10.1398	0.42728|0.42728	0.0:0.0743:0.0:0.9257|0.0:0.0743:0.0:0.9257	.|.	194;483;483|.	Q5R2U6;Q9NSI6-2;Q9NSI6|.	.;.;BRWD1_HUMAN|.	F|I	483|194	ENSP00000330753:I483F;ENSP00000344333:I483F;ENSP00000370178:I483F|.	ENSP00000330753:I483F|.	I|N	-|-	1|2	0|0	BRWD1|BRWD1	39563778|39563778	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	3.879000|3.879000	0.56138|0.56138	2.130000|2.130000	0.65690|0.65690	0.455000|0.455000	0.32223|0.32223	ATT|AAT	.	.	.	none		0.333	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		A	40641908	T	A	40641908	3	1	210	1	0	0	0	0	1	0	0	0	1527	1493	52	5	5866	5	BRWD1	21	40641908	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08		40641908	7487987	90	12825											
PDE9A	5152	hgsc.bcm.edu	37	chr21	44152003	44152003	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttgaaagtggacaggtagAgcccaggcccagagagcccc	12	5	13	11	0	0	3	0	1	0	2	0	5	0	4	4	3	2	1	4	3	2	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr21:44152003A>G	ENST00000291539.6	+	5	446	c.386A>G	c.(385-387)gAg>gGg	p.E129G	PDE9A_ENST00000398236.3_Intron|PDE9A_ENST00000335440.6_Intron|PDE9A_ENST00000335512.4_Intron|PDE9A_ENST00000380328.2_Intron|PDE9A_ENST00000349112.3_Intron|PDE9A_ENST00000398225.3_Missense_Mutation_p.E88G|PDE9A_ENST00000470987.1_Intron|PDE9A_ENST00000398232.3_Missense_Mutation_p.E62G|AP001627.1_ENST00000437426.1_RNA|PDE9A_ENST00000539837.1_Intron|PDE9A_ENST00000398227.3_Intron|PDE9A_ENST00000328862.6_Missense_Mutation_p.E103G|PDE9A_ENST00000398224.3_Intron|PDE9A_ENST00000398234.3_Intron|PDE9A_ENST00000398229.3_Intron	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	129					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)	GGACAGGTAGAGCCCAGGCCC	0.652																																					p.E129G		Atlas-SNP	.											.	PDE9A	69	.	0			c.A386G						PASS	.						56	59	58					21																	44152003		2203	4300	6503	SO:0001583	missense	5152	exon5			AGGTAGAGCCCAG	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.386A>G	chr21.hg19:g.44152003A>G	ENSP00000291539:p.Glu129Gly	121.0	0.0	.		50.0	26.0	.	NM_002606	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	Missense_Mutation	SNP	ENST00000291539.6	hg19	CCDS13690.1	.	.	.	.	.	.	.	.	.	.	A	5.981	0.364909	0.11296	.	.	ENSG00000160191	ENST00000291539;ENST00000398232;ENST00000328862;ENST00000398225	T;T;T;T	0.69435	-0.37;-0.4;-0.39;-0.38	2.62	-5.23	0.02798	.	2.493450	0.01301	N	0.010305	T	0.41026	0.1141	N	0.08118	0	0.09310	N	1	B;B;B;B	0.19706	0.038;0.003;0.003;0.002	B;B;B;B	0.19391	0.025;0.001;0.001;0.0	T	0.17930	-1.0353	10	0.49607	T	0.09	.	0.789	0.01054	0.4523:0.1816:0.1307:0.2354	.	62;103;88;129	O76083-13;O76083-15;O76083-14;O76083	.;.;.;PDE9A_HUMAN	G	129;62;103;88	ENSP00000291539:E129G;ENSP00000381287:E62G;ENSP00000328699:E103G;ENSP00000381281:E88G	ENSP00000291539:E129G	E	+	2	0	PDE9A	43025072	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	0.271000	0.18626	-2.215000	0.00733	0.383000	0.25322	GAG	.	.	.	none		0.652	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1			G	44152003	A	G	44152003	3	3	210	1	0	0	0	0	1	0	0	0	11662	304	11	3	484	3	PDE9A	21	44152003	Missense_Mutation	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	3510095	44152003	3977892	91	12826											
CYTSA	23384	hgsc.bcm.edu	37	chr22	24734414	24734414	+	Missense_Mutation	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	gagcccaagtcctatgaaaaCccctcctgcagcagctgtgt	10	8	9	14	0	0	1	0	1	0	0	2	2	2	1	5	0	5	3	5	0	4	1			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr22:24734414C>T	ENST00000314328.9	+	10	2906	c.2621C>T	c.(2620-2622)aCc>aTc	p.T874I	SPECC1L_ENST00000437398.1_Missense_Mutation_p.T874I|SPECC1L-ADORA2A_ENST00000358654.2_Missense_Mutation_p.T874I|SPECC1L_ENST00000541492.1_Missense_Mutation_p.T874I	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	874					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						CCTATGAAAACCCCTCCTGCA	0.498																																					p.T874I		Atlas-SNP	.											.	SPECC1L	85	.	0			c.C2621T						PASS	.						162	158	160					22																	24734414		2203	4300	6503	SO:0001583	missense	23384	exon9			TGAAAACCCCTCC	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.2621C>T	chr22.hg19:g.24734414C>T	ENSP00000325785:p.Thr874Ile	242.0	0.0	.		216.0	89.0	.	NM_001145468	B7Z758|F5H1H6|O15081	Missense_Mutation	SNP	ENST00000314328.9	hg19	CCDS33619.1	.	.	.	.	.	.	.	.	.	.	c	29.1	4.976045	0.92982	.	.	ENSG00000100014	ENST00000398280;ENST00000437398;ENST00000314328;ENST00000541492	T;T;T	0.53640	0.61;0.61;0.61	5.69	5.69	0.88448	.	0.050156	0.85682	D	0.000000	T	0.69124	0.3076	M	0.68593	2.085	0.80722	D	1	D;P	0.89917	1.0;0.906	D;P	0.91635	0.999;0.521	T	0.69614	-0.5098	10	0.72032	D	0.01	-23.2113	19.1962	0.93690	0.0:1.0:0.0:0.0	.	874;874	F5H1H6;Q69YQ0	.;CYTSA_HUMAN	I	902;874;874;874	ENSP00000393363:T874I;ENSP00000325785:T874I;ENSP00000439633:T874I	ENSP00000325785:T874I	T	+	2	0	SPECC1L	23064414	1.000000	0.71417	0.982000	0.44146	0.996000	0.88848	5.103000	0.64578	2.865000	0.98341	0.655000	0.94253	ACC	.	.	.	none		0.498	SPECC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319986.2	NM_015330		T	24734414	C	T	24734414	3	4	210	1	0	0	0	0	1	0	0	0	4211	507	18	2	2651	2	CYTSA	22	24734414	Missense_Mutation	SNP	C	TCGA-IZ-8196-01A-11D-2396-08		24734414	26570152	92	12827											
GGT1	2678	hgsc.bcm.edu	37	chr22	25023938	25023938	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccctcacctgccaatttcaTccagccaggtatggggtgga	8	9	10	14	0	2	0	2	0	0	0	3	1	3	1	6	4	2	1	6	4	2	2			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr22:25023938T>C	ENST00000400382.1	+	13	2083	c.1328T>C	c.(1327-1329)aTc>aCc	p.I443T	GGT1_ENST00000403838.1_Missense_Mutation_p.I99T|GGT1_ENST00000401885.1_Missense_Mutation_p.I99T|GGT1_ENST00000406383.2_Missense_Mutation_p.I443T|GGT1_ENST00000404920.1_Missense_Mutation_p.I99T|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000400380.1_Missense_Mutation_p.I443T|GGT1_ENST00000400383.1_Missense_Mutation_p.I443T|GGT1_ENST00000248923.4_Missense_Mutation_p.I443T|GGT1_ENST00000404532.1_Missense_Mutation_p.I99T|GGT1_ENST00000404223.1_Missense_Mutation_p.I99T			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	443					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)	GCCAATTTCATCCAGCCAGGT	0.617																																					p.I443T		Atlas-SNP	.											.	GGT1	68	.	0			c.T1328C						PASS	.						42	50	47					22																	25023938		2202	4297	6499	SO:0001583	missense	2678	exon13			ATTTCATCCAGCC	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.1328T>C	chr22.hg19:g.25023938T>C	ENSP00000383232:p.Ile443Thr	225.0	0.0	.		99.0	48.0	.	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	ENST00000400382.1	hg19	CCDS42992.1	.	.	.	.	.	.	.	.	.	.	.	13.53	2.265969	0.40095	.	.	ENSG00000100031	ENST00000248923;ENST00000412658;ENST00000400382;ENST00000400383;ENST00000400380;ENST00000406383;ENST00000401885;ENST00000404532;ENST00000403838;ENST00000404223;ENST00000404920	T;T;T;T;T;T;T;T;T;T;T	0.09073	3.02;3.02;3.02;3.02;3.02;3.02;3.02;3.02;3.02;3.02;3.02	3.49	3.49	0.39957	.	0.000000	0.85682	D	0.000000	T	0.42086	0.1187	H	0.98256	4.185	0.46901	D	0.999246	D	0.89917	1.0	D	0.79784	0.993	T	0.61232	-0.7104	10	0.87932	D	0	-34.9439	11.6793	0.51448	0.0:0.0:0.0:1.0	.	443	P19440	GGT1_HUMAN	T	443;443;443;443;443;443;99;99;99;99;99	ENSP00000248923:I443T;ENSP00000393537:I443T;ENSP00000383232:I443T;ENSP00000383233:I443T;ENSP00000383231:I443T;ENSP00000385975:I443T;ENSP00000384381:I99T;ENSP00000385445:I99T;ENSP00000384820:I99T;ENSP00000385016:I99T;ENSP00000385001:I99T	ENSP00000248923:I443T	I	+	2	0	GGT1	23353938	1.000000	0.71417	0.952000	0.39060	0.028000	0.11728	7.217000	0.77982	1.593000	0.50029	0.373000	0.22412	ATC	.	.	.	none		0.617	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430		C	25023938	T	C	25023938	3	2	210	1	0	0	0	0	1	0	0	0	6368	1435	50	3	1362	3	GGT1	22	25023938	Missense_Mutation	SNP	T	TCGA-IZ-8196-01A-11D-2396-08	289524	25023938	26280628	93	12828											
CHKB	1120	hgsc.bcm.edu	37	chr22	51018475	51018475	+	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	tcctcgtgagtataatcataAacccactcacaaaaatggtt	15	11	5	10	1	2	1	2	1	0	0	4	1	3	1	2	1	1	2	2	1	6	4			TCGA-IZ-8196-01A-11D-2396-08	TCGA-IZ-8196-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dccd5469-1539-42f2-9023-47320e9e4275	d5a2fa8f-8c51-4867-b806-5f49d4b33c1a	g.chr22:51018475A>C	ENST00000406938.2	-	8	1072	c.855T>G	c.(853-855)gtT>gtG	p.V285V	CHKB-CPT1B_ENST00000452668.1_5'Flank|CPT1B_ENST00000405237.3_5'Flank|CHKB_ENST00000463053.1_5'Flank|CHKB-CPT1B_ENST00000453634.1_5'Flank|CPT1B_ENST00000440709.1_5'Flank|CHKB-AS1_ENST00000380711.3_RNA|CPT1B_ENST00000312108.7_5'Flank|CPT1B_ENST00000395650.2_5'Flank|CPT1B_ENST00000434492.2_5'Flank|CPT1B_ENST00000360719.2_5'Flank|CPT1B_ENST00000457250.1_5'Flank	NM_005198.4	NP_005189.2	Q9Y259	CHKB_HUMAN	choline kinase beta	285					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|choline kinase activity (GO:0004103)|ethanolamine kinase activity (GO:0004305)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(5)|ovary(3)|skin(1)|urinary_tract(1)	15		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;4.04e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.79e-74)|Epithelial(4;6.17e-70)|GBM - Glioblastoma multiforme(4;5.68e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.205)	Choline(DB00122)	TATAATCATAAACCCACTCAC	0.522																																					p.V285V		Atlas-SNP	.											.	CHKB	40	.	0			c.T855G						PASS	.						88	94	92					22																	51018475		2203	4300	6503	SO:0001819	synonymous_variant	1120	exon8			ATCATAAACCCAC	AB029886	CCDS14099.1	22q13.33	2011-02-16	2004-04-19	2004-04-19	ENSG00000100288	ENSG00000100288			1938	protein-coding gene	gene with protein product		612395	"choline kinase-like"	CHKL		9224698, 15003397	Standard	NM_005198		Approved	CHETK	uc003bmv.3	Q9Y259	OTTHUMG00000150275	ENST00000406938.2:c.855T>G	chr22.hg19:g.51018475A>C		125.0	0.0	.		134.0	54.0	.	NM_005198	A0PJM6|Q13388	Silent	SNP	ENST00000406938.2	hg19	CCDS14099.1																																																																																			.	.	.	none		0.522	CHKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317267.3	NM_005198		C	51018475	A	C	51018475	2	2	210	1	0	0	0	0	0	0	0	1	3350	1	1	5		5	CHKB	22	51018475	Silent	SNP	A	TCGA-IZ-8196-01A-11D-2396-08	25994537	51018475	286091	94	12829											
PLCH2	9651	hgsc.bcm.edu	37	chr1	2418423	2418423	+	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	ccagaaaacaagagtaagggGctgctgggcattgatggtga	13	7	15	6	0	0	4	0	2	0	2	0	4	0	4	1	4	2	4	1	4	4	2			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:2418423G>A	ENST00000419816.2	+	6	1168	c.894G>A	c.(892-894)ggG>ggA	p.G298G	PLCH2_ENST00000449969.1_Silent_p.G271G|PLCH2_ENST00000288766.5_Intron|PLCH2_ENST00000378486.3_Silent_p.G298G|PLCH2_ENST00000378488.3_Silent_p.G298G			O75038	PLCH2_HUMAN	phospholipase C, eta 2	298					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)		AGAGTAAGGGGCTGCTGGGCA	0.632																																					p.G298G		Atlas-SNP	.											.	PLCH2	131	.	0			c.G894A						PASS	.						55	59	57					1																	2418423		2096	4214	6310	SO:0001819	synonymous_variant	9651	exon6			TAAGGGGCTGCTG	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.894G>A	chr1.hg19:g.2418423G>A		52.0	0.0	.		45.0	10.0	.	NM_014638	A2VCM3|B9DI80|Q3LUA8|Q86XJ2|Q86XU1|Q86YU7|Q8TEH5|Q8WUS6	Silent	SNP	ENST00000419816.2	hg19																																																																																				.	.	.	none		0.632	PLCH2-009	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467514.1	NM_014638		A	2418423	G	A	2418423	2	1	211	1	0	0	0	0	0	0	0	1	12045	1190	42	2		2	PLCH2	1	2418423	Silent	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10		2418423	246832198	1	12830											
CASZ1	54897	hgsc.bcm.edu	37	chr1	10714628	10714628	+	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	atcacgtcagacgtgctcgtGtacaccttgttacagcccac	9	10	8	14	3	2	1	2	0	0	1	3	1	2	1	2	0	4	3	2	0	2	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:10714628G>A	ENST00000377022.3	-	10	2003	c.1686C>T	c.(1684-1686)taC>taT	p.Y562Y	CASZ1_ENST00000344008.5_Silent_p.Y562Y|RP4-734G22.3_ENST00000606802.1_RNA	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	562					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)		ACGTGCTCGTGTACACCTTGT	0.597																																					p.Y562Y		Atlas-SNP	.											.	CASZ1	150	.	0			c.C1686T						PASS	.						210	193	199					1																	10714628		2203	4300	6503	SO:0001819	synonymous_variant	54897	exon10			GCTCGTGTACACC	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.1686C>T	chr1.hg19:g.10714628G>A		158.0	0.0	.		165.0	52.0	.	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Silent	SNP	ENST00000377022.3	hg19	CCDS41246.1																																																																																			.	.	.	none		0.597	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766		A	10714628	G	A	10714628	2	1	211	1	0	0	0	0	0	0	0	1	2687	1372	48	2		2	CASZ1	1	10714628	Silent	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10	8296205	10714628	238535993	2	12831											
KDM1A	23028	hgsc.bcm.edu	37	chr1	23380289	23380289	+	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	gataatccaaagattcagctGacatttgaggctactctcca	13	11	7	10	0	2	3	1	2	1	1	4	4	3	3	2	1	2	2	2	1	3	4			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:23380289G>A	ENST00000356634.3	+	4	836	c.687G>A	c.(685-687)ctG>ctA	p.L229L	RP1-184J9.2_ENST00000427154.1_RNA|KDM1A_ENST00000400181.4_Silent_p.L249L|KDM1A_ENST00000542151.1_Silent_p.L249L	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A	229	SWIRM. {ECO:0000255|PROSITE- ProRule:PRU00247}.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|histone H3-K4 demethylation (GO:0034720)|histone H3-K9 demethylation (GO:0033169)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of DNA binding (GO:0043392)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of protein binding (GO:0032091)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pituitary gland development (GO:0021983)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein demethylation (GO:0006482)|regulation of primitive erythrocyte differentiation (GO:0010725)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|demethylase activity (GO:0032451)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-K4 specific) (GO:0032453)|histone demethylase activity (H3-K9 specific) (GO:0032454)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|MRF binding (GO:0043426)|oxidoreductase activity (GO:0016491)|p53 binding (GO:0002039)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(2)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						AGATTCAGCTGACATTTGAGG	0.323																																					p.L249L		Atlas-SNP	.											.	KDM1A	49	.	0			c.G747A						PASS	.						92	84	87					1																	23380289		2203	4300	6503	SO:0001819	synonymous_variant	23028	exon5			TCAGCTGACATTT	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.687G>A	chr1.hg19:g.23380289G>A		314.0	1.0	.		133.0	47.0	.	NM_001009999	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Silent	SNP	ENST00000356634.3	hg19	CCDS30627.1																																																																																			.	.	.	none		0.323	KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013		A	23380289	G	A	23380289	2	1	211	1	0	0	0	0	0	0	0	1	8129	1277	45	2		2	KDM1A	1	23380289	Silent	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10	12665661	23380289	225870332	3	12832											
WDR65	149465	hgsc.bcm.edu	37	chr1	43675436	43675439	+	Frame_Shift_Del	DEL	TTGA	TTGA	-																															ccttcgagagatatcggcgtTtgatgtcacctacaccgcca																										TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	TTGA	TTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:43675436_43675439delTTGA	ENST00000372492.4	+	11	2102_2105	c.1778_1781delTTGA	c.(1777-1782)tttgatfs	p.FD593fs	WDR65_ENST00000528956.1_Frame_Shift_Del_p.FD593fs	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		593										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)				ATATCGGCGTTTGATGTCACCTAC	0.574																																					p.593_594del		Atlas-Indel,Pindel	.											.	WDR65	76	.	0			c.1777_1780del						PASS	.																																			SO:0001589	frameshift_variant	149465	exon11			.																												ENST00000372492.4:c.1778_1781delTTGA	chr1.hg19:g.43675436_43675439delTTGA	ENSP00000361570:p.Phe593fs	59.0	0.0	0		67.0	19.0	0.283582	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Frame_Shift_Del	DEL	ENST00000372492.4	hg19																																																																																				.	.	.	none		0.574	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1			-	43675439	TTGA	-	43675436	7	5	211	1	0	1	0	1	0	0	0	0	17328	1841	64	0	1816	0	WDR65	1	43675436	Frame_Shift_Del	DEL	TTGA	TCGA-IZ-A6M8-01A-11D-A31X-10	20295147	43675436	205575185	4	12833											
TESK2	10420	hgsc.bcm.edu	37	chr1	45812448	45812448	+	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	agcatcatagtccagcccgaAattctgtggatgggtatgga	11	10	12	8	1	2	0	1	0	1	0	3	3	3	2	2	3	2	2	2	3	3	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:45812448A>T	ENST00000372086.3	-	9	1196	c.796T>A	c.(796-798)Ttc>Atc	p.F266I	TESK2_ENST00000538496.1_Missense_Mutation_p.F183I|TESK2_ENST00000341771.6_Intron|TESK2_ENST00000486676.1_5'UTR|TESK2_ENST00000372084.1_Intron	NM_007170.2	NP_009101.2	Q96S53	TESK2_HUMAN	testis-specific kinase 2	266	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|focal adhesion assembly (GO:0048041)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	32	Acute lymphoblastic leukemia(166;0.155)					TCCAGCCCGAAATTCTGTGGA	0.502																																					p.F266I		Atlas-SNP	.											.	TESK2	60	.	0			c.T796A						PASS	.						79	82	81					1																	45812448		1949	4153	6102	SO:0001583	missense	10420	exon9			GCCCGAAATTCTG	AJ132545	CCDS41323.1	1p32	2010-04-27			ENSG00000070759	ENSG00000070759	2.7.12.1		11732	protein-coding gene	gene with protein product		604746				10512679	Standard	NM_007170		Approved		uc001cns.1	Q96S53	OTTHUMG00000007680	ENST00000372086.3:c.796T>A	chr1.hg19:g.45812448A>T	ENSP00000361158:p.Phe266Ile	107.0	0.0	.		116.0	47.0	.	NM_007170	Q5T422|Q5T423|Q8N520|Q9Y3Q6	Missense_Mutation	SNP	ENST00000372086.3	hg19	CCDS41323.1	.	.	.	.	.	.	.	.	.	.	A	34	5.297190	0.95574	.	.	ENSG00000070759	ENST00000372086;ENST00000372083;ENST00000538496	D;D	0.81579	-1.51;-1.51	6.08	6.08	0.98989	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000002	D	0.86573	0.5965	L	0.42581	1.335	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.87288	0.2297	10	0.62326	D	0.03	-8.8357	16.6438	0.85155	1.0:0.0:0.0:0.0	.	266	Q96S53	TESK2_HUMAN	I	266;250;183	ENSP00000361158:F266I;ENSP00000441746:F183I	ENSP00000361155:F250I	F	-	1	0	TESK2	45585035	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	9.317000	0.96327	2.333000	0.79357	0.533000	0.62120	TTC	.	.	.	none		0.502	TESK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020523.1	NM_007170		T	45812448	A	T	45812448	3	4	211	1	0	0	0	0	1	0	0	0	15780	14	1	5	931	5	TESK2	1	45812448	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	2137012	45812448	203438173	5	12834											
ELTD1	64123	hgsc.bcm.edu	37	chr1	79470814	79470814	+	Frame_Shift_Del	DEL	C	C	-																															tgcaatagcaggcttcaattCcattgcgtatttcacatttt																										TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:79470814delC	ENST00000370742.3	-	2	176	c.113delG	c.(112-114)ggafs	p.G38fs		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	38	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.G38E(1)		NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		GGCTTCAATTCCATTGCGTAT	0.348																																					p.G38fs		Atlas-Indel,Pindel	.											.	ELTD1	143	.	1	Substitution - Missense(1)	endometrium(1)	c.114delA						PASS	.						140	127	131					1																	79470814		1864	4103	5967	SO:0001589	frameshift_variant	64123	exon2			.	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"-", "GPCR / Class B : Orphans"	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.113delG	chr1.hg19:g.79470814delC	ENSP00000359778:p.Gly38fs	175.0	0.0	0		82.0	20.0	0.243902	NM_022159	B1AR71|Q5KU34	Frame_Shift_Del	DEL	ENST00000370742.3	hg19	CCDS41352.1																																																																																			.	.	.	none		0.348	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159		-	79470814	C	-	79470814	7	5	211	1	0	1	0	1	0	0	0	0	5086	855	30	0	2015	0	ELTD1	1	79470814	Frame_Shift_Del	DEL	C	TCGA-IZ-A6M8-01A-11D-A31X-10	33658366	79470814	169779807	6	12835											
MCOLN3	55283	hgsc.bcm.edu	37	chr1	85506767	85506767	+	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	atatgtgtcatccattcggtCcatatatccttttaggaaaa	12	15	6	8	1	1	0	1	0	0	0	5	1	4	1	3	2	0	0	3	2	6	6			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:85506767C>G	ENST00000370589.2	-	3	374	c.322G>C	c.(322-324)Gac>Cac	p.D108H	MCOLN3_ENST00000341115.4_Intron|MCOLN3_ENST00000370587.1_Missense_Mutation_p.D108H|WDR63_ENST00000370596.1_Intron	NM_018298.10	NP_060768.8	Q8TDD5	MCLN3_HUMAN	mucolipin 3	108					auditory receptor cell differentiation (GO:0042491)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|locomotory behavior (GO:0007626)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(6)|kidney(3)|large_intestine(9)|lung(12)|prostate(3)|skin(1)	34				all cancers(265;0.00957)|Epithelial(280;0.0254)		TCCATTCGGTCCATATATCCT	0.378																																					p.D108H		Atlas-SNP	.											.	MCOLN3	74	.	0			c.G322C						PASS	.						235	209	217					1																	85506767		2203	4300	6503	SO:0001583	missense	55283	exon3			TTCGGTCCATATA	AF475085	CCDS701.1, CCDS58009.1	1p22.3	2011-12-16			ENSG00000055732	ENSG00000055732		"Voltage-gated ion channels / Transient receptor potential cation channels"	13358	protein-coding gene	gene with protein product		607400				16382100	Standard	NM_018298		Approved	TRPML3, FLJ11006, TRP-ML3	uc001dkp.3	Q8TDD5	OTTHUMG00000009955	ENST00000370589.2:c.322G>C	chr1.hg19:g.85506767C>G	ENSP00000359621:p.Asp108His	213.0	0.0	.		125.0	44.0	.	NM_018298	Q5T4H5|Q5T4H6|Q9NV09	Missense_Mutation	SNP	ENST00000370589.2	hg19	CCDS701.1	.	.	.	.	.	.	.	.	.	.	C	18.86	3.712652	0.68730	.	.	ENSG00000055732	ENST00000370589;ENST00000302814;ENST00000370587	T;T	0.62364	0.03;0.03	5.76	5.76	0.90799	.	0.048278	0.85682	D	0.000000	T	0.77239	0.4101	M	0.77820	2.39	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.69824	0.966;0.965	T	0.77608	-0.2524	10	0.56958	D	0.05	-2.0809	19.9857	0.97347	0.0:1.0:0.0:0.0	.	108;108	B1ANB7;Q8TDD5	.;MCLN3_HUMAN	H	108	ENSP00000359621:D108H;ENSP00000359619:D108H	ENSP00000304843:D108H	D	-	1	0	MCOLN3	85279355	1.000000	0.71417	0.506000	0.27664	0.660000	0.38997	5.767000	0.68850	2.706000	0.92434	0.655000	0.94253	GAC	.	.	.	none		0.378	MCOLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027569.2	NM_018298		G	85506767	C	G	85506767	3	3	211	1	0	0	0	0	1	0	0	0	9404	855	30	4	1383	4	MCOLN3	1	85506767	Missense_Mutation	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	6035953	85506767	163743854	7	12836											
TRIM45	80263	hgsc.bcm.edu	37	chr1	117660955	117660955	+	Missense_Mutation	SNP	T	T	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	ccttctgcagctgcagggaaTtttccttctgggcccgtatg	5	13	11	12	1	2	0	0	0	2	0	3	1	3	1	3	2	3	4	3	2	2	5			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:117660955T>G	ENST00000256649.4	-	2	1449	c.923A>C	c.(922-924)aAt>aCt	p.N308T	TRIM45_ENST00000369464.3_Missense_Mutation_p.N308T|TRIM45_ENST00000369461.3_Missense_Mutation_p.N251T	NM_025188.3	NP_079464.2	Q9H8W5	TRI45_HUMAN	tripartite motif containing 45	308					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)		CTGCAGGGAATTTTCCTTCTG	0.567																																					p.N308T		Atlas-SNP	.											.	TRIM45	55	.	0			c.A923C						PASS	.						76	74	74					1																	117660955		2203	4300	6503	SO:0001583	missense	80263	exon2			AGGGAATTTTCCT		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.923A>C	chr1.hg19:g.117660955T>G	ENSP00000256649:p.Asn308Thr	101.0	0.0	.		99.0	33.0	.	NM_001145635	Q53GN0|Q5T2K4|Q5T2K5|Q8IYV6	Missense_Mutation	SNP	ENST00000256649.4	hg19	CCDS893.1	.	.	.	.	.	.	.	.	.	.	T	10.44	1.352209	0.24512	.	.	ENSG00000134253	ENST00000256649;ENST00000369464;ENST00000369461	D;D;D	0.85629	-2.01;-2.01;-2.01	5.11	3.96	0.45880	.	0.242716	0.47852	N	0.000216	T	0.66557	0.2801	L	0.35723	1.085	0.44254	D	0.997108	B;B	0.16802	0.019;0.011	B;B	0.15870	0.014;0.006	T	0.63594	-0.6602	10	0.37606	T	0.19	-26.5032	11.6751	0.51425	0.0:0.0:0.1477:0.8522	.	308;308	Q9H8W5-2;Q9H8W5	.;TRI45_HUMAN	T	308;308;251	ENSP00000256649:N308T;ENSP00000358476:N308T;ENSP00000358473:N251T	ENSP00000256649:N308T	N	-	2	0	TRIM45	117462478	1.000000	0.71417	0.823000	0.32752	0.520000	0.34377	2.680000	0.46918	0.932000	0.37266	0.533000	0.62120	AAT	.	.	.	none		0.567	TRIM45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033503.1	NM_025188		G	117660955	T	G	117660955	3	3	211	1	0	0	0	0	1	0	0	0	16532	1493	52	5	839	5	TRIM45	1	117660955	Missense_Mutation	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10	32154188	117660955	131589666	8	12837											
SETDB1	9869	hgsc.bcm.edu	37	chr1	150900339	150900347	+	In_Frame_Del	DEL	AGATGGATT	AGATGGATT	-																															catcgatgaggaactggagaAgatggattgtgtacagcaac																								rs201917860|rs200122173		TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	AGATGGATT	AGATGGATT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:150900339_150900347delAGATGGATT	ENST00000271640.5	+	2	339_347	c.149_157delAGATGGATT	c.(148-159)aagatggattgt>agt	p.50_53KMDC>S	SETDB1_ENST00000459773.1_3'UTR|SETDB1_ENST00000368963.1_In_Frame_Del_p.50_53KMDC>S|SETDB1_ENST00000368969.4_In_Frame_Del_p.50_53KMDC>S|SETDB1_ENST00000368962.2_In_Frame_Del_p.50_53KMDC>S	NM_001145415.1|NM_012432.3	NP_001138887.1|NP_036564.3	Q15047	SETB1_HUMAN	SET domain, bifurcated 1	50					bone development (GO:0060348)|histone H3-K9 trimethylation (GO:0036124)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)			GAACTGGAGAAGATGGATTGTGTACAGCA	0.474																																					p.50_52del		Atlas-Indel,Pindel	.											.	SETDB1	204	.	0			c.148_156del						PASS	.																																			SO:0001651	inframe_deletion	9869	exon2			.	D31891	CCDS972.1, CCDS44217.1, CCDS58026.1	1q21	2013-01-23			ENSG00000143379	ENSG00000143379		"Chromatin-modifying enzymes / K-methyltransferases", "Tudor domain containing"	10761	protein-coding gene	gene with protein product	"tudor domain containing 21"	604396				10343109	Standard	NM_001145415		Approved	KG1T, KIAA0067, ESET, KMT1E, TDRD21	uc001evu.2	Q15047	OTTHUMG00000035003	ENST00000271640.5:c.149_157delAGATGGATT	chr1.hg19:g.150900339_150900347delAGATGGATT	ENSP00000271640:p.Lys50_Cys53delinsSer	261.0	0.0	0		219.0	59.0	0.269406	NM_012432	A6NEW2|Q5SZD8|Q5SZD9|Q5SZE0|Q5SZE7|Q96GM9	In_Frame_Del	DEL	ENST00000271640.5	hg19	CCDS44217.1																																																																																			.	.	.	none		0.474	SETDB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084717.2			-	150900347	AGATGGATT	-	150900339	7	5	211	1	0	1	0	1	0	0	0	0	14151	72	3	0	151	0	SETDB1	1	150900339	In_Frame_Del	DEL	AGATGGATT	TCGA-IZ-A6M8-01A-11D-A31X-10	33239384	150900339	98350282	9	12838											
ZNF281	23528	hgsc.bcm.edu	37	chr1	200378264	200378264	+	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	agtaatacgtcacggtggtgCtgggctggttgctgctggac	6	11	16	8	2	1	0	1	0	0	0	1	1	1	1	0	5	4	6	0	5	2	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:200378264C>T	ENST00000294740.3	-	2	694	c.570G>A	c.(568-570)caG>caA	p.Q190Q	ZNF281_ENST00000367353.1_Silent_p.Q190Q|ZNF281_ENST00000367352.3_Silent_p.Q154Q	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	190					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						CACGGTGGTGCTGGGCTGGTT	0.562																																					p.Q190Q		Atlas-SNP	.											.	ZNF281	74	.	0			c.G570A						PASS	.						101	97	98					1																	200378264		2203	4300	6503	SO:0001819	synonymous_variant	23528	exon2			GTGGTGCTGGGCT	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.570G>A	chr1.hg19:g.200378264C>T		78.0	0.0	.		87.0	35.0	.	NM_012482	A6NF48|B3KMX2|Q5RKW5|Q9NY92	Silent	SNP	ENST00000294740.3	hg19	CCDS1402.1																																																																																			.	.	.	none		0.562	ZNF281-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086879.2	NM_012482		T	200378264	C	T	200378264	2	4	211	1	0	0	0	0	0	0	0	1	17830	796	28	2		2	ZNF281	1	200378264	Silent	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	49477925	200378264	48872357	10	12839											
LBR	3930	hgsc.bcm.edu	37	chr1	225600280	225600280	+	Missense_Mutation	SNP	A	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	agaaaatgactgtacacgtaAtgaaactctacgccctggaa	16	8	8	9	2	1	3	0	2	1	1	1	4	1	4	1	1	3	2	1	1	7	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr1:225600280A>C	ENST00000338179.2	-	8	1085	c.960T>G	c.(958-960)caT>caG	p.H320Q	AC092811.1_ENST00000366845.2_5'Flank|LBR_ENST00000272163.4_Missense_Mutation_p.H320Q	NM_194442.2	NP_919424.1	Q14739	LBR_HUMAN	lamin B receptor	320					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)		TGTACACGTAATGAAACTCTA	0.413																																					p.H320Q		Atlas-SNP	.											.	LBR	54	.	0			c.T960G						PASS	.						79	80	80					1																	225600280		2203	4300	6503	SO:0001583	missense	3930	exon8			CACGTAATGAAAC	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.960T>G	chr1.hg19:g.225600280A>C	ENSP00000339883:p.His320Gln	540.0	1.0	.		407.0	97.0	.	NM_194442	B2R5P3|Q14740|Q53GU7|Q59FE6	Missense_Mutation	SNP	ENST00000338179.2	hg19	CCDS1545.1	.	.	.	.	.	.	.	.	.	.	A	10.74	1.434732	0.25813	.	.	ENSG00000143815	ENST00000272163;ENST00000338179	D;D	0.97811	-4.55;-4.55	6.07	-0.357	0.12579	.	1.680490	0.02408	N	0.081343	D	0.92440	0.7600	N	0.04203	-0.255	0.09310	N	1	B	0.23128	0.08	B	0.18263	0.021	D	0.86742	0.1955	10	0.29301	T	0.29	3.4658	9.9056	0.41375	0.6743:0.0:0.3257:0.0	.	320	Q14739	LBR_HUMAN	Q	320	ENSP00000272163:H320Q;ENSP00000339883:H320Q	ENSP00000272163:H320Q	H	-	3	2	LBR	223666903	0.080000	0.21391	0.000000	0.03702	0.029000	0.11900	0.526000	0.22971	-0.299000	0.08909	0.533000	0.62120	CAT	.	.	.	none		0.413	LBR-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091398.1	NM_002296		C	225600280	A	C	225600280	3	2	211	1	0	0	0	0	1	0	0	0	8659	98	4	5	915	5	LBR	1	225600280	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	25222016	225600280	23650341	11	12840											
SULT6B1	391365	hgsc.bcm.edu	37	chr2	37414574	37414575	+	Frame_Shift_Ins	INS	-	-	T																															ttttttagaaacagcatataINSttaattcactgacaatgtgg																										TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr2:37414574_37414575insT	ENST00000535679.1	-	2	234_235	c.235_236insA	c.(235-237)atafs	p.I79fs	SULT6B1_ENST00000260637.3_Frame_Shift_Ins_p.I41fs|SULT6B1_ENST00000407963.1_Frame_Shift_Ins_p.I41fs|SULT6B1_ENST00000379149.2_Frame_Shift_Ins_p.I79fs			Q6IMI4	ST6B1_HUMAN	sulfotransferase family, cytosolic, 6B, member 1	79						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)				AACAGCATATATTAATTCACTG	0.327																																					p.I41fs		Pindel	.											.	SULT6B1	46	.	0			c.122_123insA						PASS	.																																			SO:0001589	frameshift_variant	391365	exon2			.	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.236dupA	chr2.hg19:g.37414576_37414576dupT	ENSP00000444081:p.Ile79fs	166.0	0.0	.		104.0	30.0	0.288	NM_001032377	B2RTS7	Frame_Shift_Ins	INS	ENST00000535679.1	hg19																																																																																				.	.	.	none		0.327	SULT6B1-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001032377		T	37414575	-	T	37414574	7	5	211	1	0	1	1	0	0	0	0	0	15396	449	16	0	699	0	SULT6B1	2	37414574	Frame_Shift_Ins	INS	-	TCGA-IZ-A6M8-01A-11D-A31X-10		37414574	205784799	12	12841											
GMCL1	64395	hgsc.bcm.edu	37	chr2	70096993	70096993	+	Missense_Mutation	SNP	T	T	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	gcctcgaaggagcatagcatTtaggtaggatgagatttccc	11	10	12	8	1	0	1	0	1	0	1	2	5	1	3	2	3	2	3	2	3	4	5			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr2:70096993T>G	ENST00000282570.3	+	12	1612	c.1361T>G	c.(1360-1362)tTt>tGt	p.F454C		NM_178439.3	NP_848526.1	Q96IK5	GMCL1_HUMAN	germ cell-less, spermatogenesis associated 1	454					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)	nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)				endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	15						AGCATAGCATTTAGGTAGGAT	0.398																																					p.F454C		Atlas-SNP	.											.	GMCL1	50	.	0			c.T1361G						PASS	.						138	118	125					2																	70096993		2203	4300	6503	SO:0001583	missense	64395	exon12			TAGCATTTAGGTA	AK023119	CCDS1895.1	2p13.3	2013-01-09	2012-08-20		ENSG00000087338	ENSG00000087338		"BTB/POZ domain containing"	23843	protein-coding gene	gene with protein product	"spermatogenesis associated 29"		"germ cell-less homolog 1 (Drosophila)"				Standard	NM_178439		Approved	FLJ13057, BTBD13, GCL1, SPATA29	uc002sfu.3	Q96IK5	OTTHUMG00000129643	ENST00000282570.3:c.1361T>G	chr2.hg19:g.70096993T>G	ENSP00000282570:p.Phe454Cys	63.0	0.0	.		56.0	20.0	.	NM_178439	Q9H826|Q9H8V7|Q9H927	Missense_Mutation	SNP	ENST00000282570.3	hg19	CCDS1895.1	.	.	.	.	.	.	.	.	.	.	T	15.07	2.723230	0.48728	.	.	ENSG00000087338	ENST00000282570	T	0.56103	0.48	5.22	5.22	0.72569	.	0.108148	0.64402	D	0.000004	T	0.63534	0.2519	L	0.44542	1.39	0.46113	D	0.99887	D	0.76494	0.999	D	0.70227	0.968	T	0.64478	-0.6398	10	0.51188	T	0.08	-38.9046	13.3387	0.60533	0.0:0.0:0.0:1.0	.	454	Q96IK5	GMCL1_HUMAN	C	454	ENSP00000282570:F454C	ENSP00000282570:F454C	F	+	2	0	GMCL1	69950497	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.799000	0.55529	2.090000	0.63153	0.533000	0.62120	TTT	.	.	.	none		0.398	GMCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251841.2	NM_178439		G	70096993	T	G	70096993	3	3	211	1	0	0	0	0	1	0	0	0	6492	1841	64	5	1407	5	GMCL1	2	70096993	Missense_Mutation	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10	32682419	70096993	173102380	13	12842											
PCDP1	200373	hgsc.bcm.edu	37	chr2	120362785	120362785	+	Missense_Mutation	SNP	A	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	cagggcactgaaatttcaaaAacgagacagatgaaggaggc	17	5	12	7	1	1	4	1	2	0	2	1	6	1	5	0	3	1	1	0	3	4	1			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr2:120362785A>C	ENST00000413369.3	+	11	1140	c.1053A>C	c.(1051-1053)aaA>aaC	p.K351N	PCDP1_ENST00000602047.1_Missense_Mutation_p.K65N|PCDP1_ENST00000597189.1_3'UTR	NM_001271049.1	NP_001257978																Colorectal(110;0.196)					AAATTTCAAAAACGAGACAGA	0.383																																					p.K351N		Atlas-SNP	.											.	.	.	.	0			c.A1053C						PASS	.						67	70	69					2																	120362785		2203	4300	6503	SO:0001583	missense	0	exon11			TTCAAAAACGAGA																												ENST00000413369.3:c.1053A>C	chr2.hg19:g.120362785A>C	ENSP00000393222:p.Lys351Asn	419.0	0.0	.		280.0	80.0	.	NM_001271049		Missense_Mutation	SNP	ENST00000413369.3	hg19	CCDS33282.2	.	.	.	.	.	.	.	.	.	.	A	14.44	2.535164	0.45176	.	.	ENSG00000163075	ENST00000295220;ENST00000413369	T	0.19938	2.11	5.22	2.87	0.33458	.	0.239906	0.36338	N	0.002660	T	0.12433	0.0302	L	0.34521	1.04	0.80722	D	1	P;B	0.35011	0.48;0.291	B;B	0.27715	0.082;0.082	T	0.13872	-1.0493	10	0.27082	T	0.32	-25.951	8.4885	0.33086	0.8403:0.0:0.1597:0.0	.	195;351	Q4G0U5-3;Q4G0U5	.;PCDP1_HUMAN	N	65;351	ENSP00000393222:K351N	ENSP00000295220:K65N	K	+	3	2	AC069154.2	120079255	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	1.660000	0.37397	0.460000	0.27045	0.533000	0.62120	AAA	.	.	.	none		0.383	PCDP1-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464236.1			C	120362785	A	C	120362785	3	2	211	1	0	0	0	0	1	0	0	0	11579	11	1	5	205	5	PCDP1	2	120362785	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	50265792	120362785	122836588	14	12843											
PTPN23	25930	hgsc.bcm.edu	37	chr3	47452317	47452317	+	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	gcctggggtcctggggcagcCgccaccccccctacacaccc	5	4	11	21	1	0	0	0	0	0	0	1	0	1	0	8	4	2	1	8	4	1	1			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr3:47452317C>G	ENST00000265562.4	+	20	3106	c.3029C>G	c.(3028-3030)cCg>cGg	p.P1010R	PTPN23_ENST00000431726.1_Missense_Mutation_p.P884R	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	1010	His.|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)		CTGGGGCAGCCGCCACCCCCC	0.687																																					p.P1010R		Atlas-SNP	.											.	PTPN23	85	.	0			c.C3029G						PASS	.						15	20	18					3																	47452317		2139	4247	6386	SO:0001583	missense	25930	exon20			GGCAGCCGCCACC	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.3029C>G	chr3.hg19:g.47452317C>G	ENSP00000265562:p.Pro1010Arg	108.0	0.0	.		130.0	35.0	.	NM_015466	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Missense_Mutation	SNP	ENST00000265562.4	hg19	CCDS2754.1	.	.	.	.	.	.	.	.	.	.	C	12.39	1.923200	0.33908	.	.	ENSG00000076201	ENST00000265562	T	0.02763	4.17	4.29	3.18	0.36537	.	0.362779	0.25154	N	0.032736	T	0.02342	0.0072	N	0.19112	0.55	0.41800	D	0.989917	P;P	0.37824	0.609;0.609	B;B	0.39738	0.308;0.308	T	0.62310	-0.6881	10	0.37606	T	0.19	-4.7843	6.2976	0.21095	0.0:0.6978:0.0:0.3022	.	884;1010	B4DST5;Q9H3S7	.;PTN23_HUMAN	R	1010	ENSP00000265562:P1010R	ENSP00000265562:P1010R	P	+	2	0	PTPN23	47427321	0.000000	0.05858	0.892000	0.35008	0.632000	0.37999	0.244000	0.18124	0.976000	0.38417	0.557000	0.71058	CCG	.	.	.	none		0.687	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466		G	47452317	C	G	47452317	3	3	211	1	0	0	0	0	1	0	0	0	12801	652	23	4	3107	4	PTPN23	3	47452317	Missense_Mutation	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10		47452317	150570113	15	12844											
IL17RD	54756	hgsc.bcm.edu	37	chr3	57136553	57136553	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgaagagcgtcgcgaatgcCgatatgactaccagtggcac	11	7	13	10	4	0	3	0	2	0	1	1	5	0	3	2	1	3	1	2	1	4	2			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr3:57136553C>T	ENST00000296318.7	-	10	1021	c.933G>A	c.(931-933)tcG>tcA	p.S311S	IL17RD_ENST00000320057.5_Silent_p.S167S|IL17RD_ENST00000463523.1_Silent_p.S167S|IL17RD_ENST00000427856.2_Silent_p.S287S	NM_017563.3	NP_060033.3	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D	311					signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)	16				KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204)		TCGCGAATGCCGATATGACTA	0.547																																					p.S311S		Atlas-SNP	.											.	IL17RD	93	.	0			c.G933A						PASS	.						70	69	69					3																	57136553		2203	4300	6503	SO:0001819	synonymous_variant	54756	exon10			GAATGCCGATATG	AF494208	CCDS2880.2	3p21.1	2008-02-05			ENSG00000144730	ENSG00000144730		"Interleukins and interleukin receptors"	17616	protein-coding gene	gene with protein product		606807				11802164, 12604616	Standard	NM_017563		Approved	SEF, IL17RLM, FLJ35755, IL-17RD	uc003dil.3	Q8NFM7	OTTHUMG00000150171	ENST00000296318.7:c.933G>A	chr3.hg19:g.57136553C>T		145.0	0.0	.		138.0	37.0	.	NM_017563	Q2NKP7|Q58EZ7|Q6RVF4|Q6UWI5|Q8N113|Q8NFS0|Q9UFA0	Silent	SNP	ENST00000296318.7	hg19	CCDS2880.2																																																																																			.	.	.	none		0.547	IL17RD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316680.1	NM_017563		T	57136553	C	T	57136553	2	4	211	1	0	0	0	0	0	0	0	1	7649	639	23	1		1	IL17RD	3	57136553	Silent	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	9684236	57136553	140885877	16	12845											
DNAJC13	23317	hgsc.bcm.edu	37	chr3	132207851	132207851	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acacacataccaaacaggctTtcaagtcagaagaggtaagc	17	6	8	10	0	2	2	2	0	0	2	2	2	2	2	1	2	3	2	1	2	5	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr3:132207851T>C	ENST00000260818.6	+	31	3702	c.3454T>C	c.(3454-3456)Ttc>Ctc	p.F1152L		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	1152					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						CAAACAGGCTTTCAAGTCAGA	0.333																																					p.F1152L		Atlas-SNP	.											.	DNAJC13	253	.	0			c.T3454C						PASS	.						64	65	64					3																	132207851		2203	4300	6503	SO:0001583	missense	23317	exon31			CAGGCTTTCAAGT	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.3454T>C	chr3.hg19:g.132207851T>C	ENSP00000260818:p.Phe1152Leu	106.0	0.0	.		44.0	13.0	.	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	hg19	CCDS33857.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.653771	0.88056	.	.	ENSG00000138246	ENST00000260818	T	0.18174	2.23	5.57	5.57	0.84162	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.16171	0.0389	L	0.47716	1.5	0.80722	D	1	P	0.52463	0.953	B	0.39217	0.294	T	0.04708	-1.0932	10	0.25106	T	0.35	.	15.7007	0.77538	0.0:0.0:0.0:1.0	.	1152	O75165	DJC13_HUMAN	L	1152	ENSP00000260818:F1152L	ENSP00000260818:F1152L	F	+	1	0	DNAJC13	133690541	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.807000	0.75201	2.236000	0.73375	0.528000	0.53228	TTC	.	.	.	none		0.333	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		C	132207851	T	C	132207851	3	2	211	1	0	0	0	0	1	0	0	0	4634	1841	64	3	3572	3	DNAJC13	3	132207851	Missense_Mutation	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10	75071298	132207851	65814579	17	12846											
WHSC1	7468	hgsc.bcm.edu	37	chr4	1977074	1977074	+	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	gtctgggcaatgaaaaaacgGtctgccggtgtggagcctcc	9	8	14	10	2	2	1	0	1	2	0	3	2	3	2	3	4	3	1	3	4	4	0			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr4:1977074G>C	ENST00000382895.3	+	22	3999	c.3568G>C	c.(3568-3570)Gtc>Ctc	p.V1190L	WHSC1_ENST00000382888.3_Missense_Mutation_p.V538L|WHSC1_ENST00000382892.2_Missense_Mutation_p.V1190L|WHSC1_ENST00000482415.2_3'UTR|WHSC1_ENST00000382891.5_Missense_Mutation_p.V1190L|WHSC1_ENST00000508803.1_Missense_Mutation_p.V1190L|SCARNA22_ENST00000503991.1_RNA	NM_133330.2	NP_579877.1	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1	1190	Post-SET. {ECO:0000255|PROSITE- ProRule:PRU00155}.				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)		TGAAAAAACGGTCTGCCGGTG	0.532			T	IGH@	MM																																p.V1190L		Atlas-SNP	.		Dom	yes		4	4p16.3	7468	Wolf-Hirschhorn syndrome candidate 1(MMSET)		L	.	WHSC1	180	.	0			c.G3568C						PASS	.						101	93	96					4																	1977074		2203	4300	6503	SO:0001583	missense	7468	exon20			AAAACGGTCTGCC	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.3568G>C	chr4.hg19:g.1977074G>C	ENSP00000372351:p.Val1190Leu	99.0	0.0	.		111.0	24.0	.	NM_133335	A2A2T2|A2A2T3|A2A2T4|A7MCZ1|D3DVQ2|O96031|Q4VBY8|Q672J1|Q6IS00|Q86V01|Q9BZB4|Q9UI92|Q9UPR2	Missense_Mutation	SNP	ENST00000382895.3	hg19	CCDS33940.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.627438	0.46944	.	.	ENSG00000109685	ENST00000508803;ENST00000382891;ENST00000382892;ENST00000382895;ENST00000382888	D;D;D;D;D	0.97066	-3.61;-3.61;-3.61;-3.61;-4.23	4.91	4.91	0.64330	Post-SET domain (2);	0.000000	0.49916	D	0.000140	D	0.93523	0.7933	L	0.42008	1.315	0.80722	D	1	B;B	0.30361	0.009;0.277	B;B	0.21151	0.012;0.033	D	0.91080	0.4899	10	0.30854	T	0.27	.	12.0537	0.53522	0.0793:0.0:0.9207:0.0	.	538;1190	A2A2T2;O96028	.;NSD2_HUMAN	L	1190;1190;1190;1190;538	ENSP00000423972:V1190L;ENSP00000372347:V1190L;ENSP00000372348:V1190L;ENSP00000372351:V1190L;ENSP00000372344:V538L	ENSP00000372344:V538L	V	+	1	0	WHSC1	1946872	1.000000	0.71417	0.974000	0.42286	0.874000	0.50279	5.102000	0.64572	2.719000	0.93026	0.655000	0.94253	GTC	.	.	.	none		0.532	WHSC1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366269.2	NM_133330		C	1977074	G	C	1977074	3	2	211	1	0	0	0	0	1	0	0	0	17374	1261	44	4	3718	4	WHSC1	4	1977074	Missense_Mutation	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10		1977074	189177202	18	12847											
WDR19	57728	hgsc.bcm.edu	37	chr4	39205336	39205336	+	Missense_Mutation	SNP	A	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	gaccgaacctctgctgctgaAagcatggtaagaattctaat	13	10	9	9	1	2	2	0	1	2	1	2	4	2	2	2	1	4	4	2	1	5	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr4:39205336A>C	ENST00000399820.3	+	7	751	c.597A>C	c.(595-597)gaA>gaC	p.E199D	WDR19_ENST00000288634.7_Missense_Mutation_p.E39D|WDR19_ENST00000506503.1_Missense_Mutation_p.E199D	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	199					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						CTGCTGCTGAAAGCATGGTAA	0.353																																					p.E199D		Atlas-SNP	.											.	WDR19	96	.	0			c.A597C						PASS	.						92	83	86					4																	39205336		1872	4111	5983	SO:0001583	missense	57728	exon7			TGCTGAAAGCATG	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.597A>C	chr4.hg19:g.39205336A>C	ENSP00000382717:p.Glu199Asp	133.0	0.0	.		66.0	21.0	.	NM_025132	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Missense_Mutation	SNP	ENST00000399820.3	hg19	CCDS47042.1	.	.	.	.	.	.	.	.	.	.	A	14.28	2.488399	0.44249	.	.	ENSG00000157796	ENST00000399820;ENST00000509560;ENST00000512112;ENST00000288634;ENST00000506503;ENST00000399836	T;T;T;T	0.66099	3.42;2.2;-0.19;3.42	5.64	1.62	0.23740	WD40 repeat-like-containing domain (1);	0.134922	0.64402	D	0.000003	T	0.51941	0.1704	M	0.64080	1.96	0.38720	D	0.953425	B;B	0.19445	0.002;0.036	B;B	0.20767	0.007;0.031	T	0.38714	-0.9648	10	0.23891	T	0.37	-17.3314	6.2227	0.20691	0.6749:0.1242:0.2008:0.0	.	199;199	Q8NEZ3;D6R9P6	WDR19_HUMAN;.	D	199;140;39;39;199;198	ENSP00000382717:E199D;ENSP00000426918:E140D;ENSP00000288634:E39D;ENSP00000423491:E199D	ENSP00000288634:E39D	E	+	3	2	WDR19	38881731	1.000000	0.71417	0.974000	0.42286	0.955000	0.61496	0.886000	0.28241	0.111000	0.17947	0.455000	0.32223	GAA	.	.	.	none		0.353	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1			C	39205336	A	C	39205336	3	2	211	1	0	0	0	0	1	0	0	0	17291	11	1	5	623	5	WDR19	4	39205336	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	37228262	39205336	151948940	19	12848											
EXOC1	55763	hgsc.bcm.edu	37	chr4	56737307	56737307	+	Missense_Mutation	SNP	A	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	aggtcatataaaggcccttcAggaaggagatcttgcttctt	11	12	10	8	0	4	1	2	0	2	1	4	3	4	2	1	4	1	1	1	4	4	6			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr4:56737307A>C	ENST00000381295.2	+	7	1220	c.872A>C	c.(871-873)cAg>cCg	p.Q291P	EXOC1_ENST00000349598.6_Missense_Mutation_p.Q291P|EXOC1_ENST00000346134.7_Missense_Mutation_p.Q291P	NM_001024924.1	NP_001020095.1	Q9NV70	EXOC1_HUMAN	exocyst complex component 1	291					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)					AAGGCCCTTCAGGAAGGAGAT	0.453																																					p.Q291P		Atlas-SNP	.											.	EXOC1	103	.	0			c.A872C						PASS	.						95	83	87					4																	56737307		2203	4300	6503	SO:0001583	missense	55763	exon7			CCCTTCAGGAAGG	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.872A>C	chr4.hg19:g.56737307A>C	ENSP00000370695:p.Gln291Pro	98.0	0.0	.		53.0	18.0	.	NM_018261	Q504V4|Q8WUE7|Q96T15|Q9NZE4	Missense_Mutation	SNP	ENST00000381295.2	hg19	CCDS3502.1	.	.	.	.	.	.	.	.	.	.	A	14.67	2.604708	0.46423	.	.	ENSG00000090989	ENST00000381295;ENST00000346134;ENST00000349598	.	.	.	5.97	4.77	0.60923	.	0.224009	0.46758	D	0.000269	T	0.57489	0.2057	L	0.53249	1.67	0.54753	D	0.999985	P;P	0.47191	0.891;0.626	P;P	0.46885	0.466;0.53	T	0.54200	-0.8329	9	0.30854	T	0.27	.	12.5014	0.55957	0.8746:0.0:0.0:0.1254	.	291;291	Q9NV70-2;Q9NV70	.;EXOC1_HUMAN	P	291	.	ENSP00000326514:Q291P	Q	+	2	0	EXOC1	56432064	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	5.837000	0.69381	1.053000	0.40415	-0.480000	0.04831	CAG	.	.	.	none		0.453	EXOC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361799.1	NM_018261		C	56737307	A	C	56737307	3	2	211	1	0	0	0	0	1	0	0	0	5303	188	7	5	894	5	EXOC1	4	56737307	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	17531971	56737307	134416969	20	12849											
DDX60L	91351	hgsc.bcm.edu	37	chr4	169315621	169315621	+	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	aagaaatttacctaccctaaTaagcccttttacaaagagta	17	11	4	9	0	0	2	0	0	0	2	0	2	0	2	3	0	4	1	3	0	9	8			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr4:169315621T>A	ENST00000511577.1	-	28	4052	c.3805A>T	c.(3805-3807)Att>Ttt	p.I1269F	DDX60L_ENST00000260184.7_Missense_Mutation_p.I1269F|DDX60L_ENST00000505890.1_Missense_Mutation_p.I1270F			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1269	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		CCTACCCTAATAAGCCCTTTT	0.323																																					p.I1269F		Atlas-SNP	.											.	DDX60L	116	.	0			c.A3805T						PASS	.						67	62	63					4																	169315621		1803	4068	5871	SO:0001583	missense	91351	exon28			CCCTAATAAGCCC	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.3805A>T	chr4.hg19:g.169315621T>A	ENSP00000422423:p.Ile1269Phe	95.0	0.0	.		46.0	12.0	.	NM_001012967	Q96ND6	Missense_Mutation	SNP	ENST00000511577.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.62|13.62	2.293047|2.293047	0.40594|0.40594	.|.	.|.	ENSG00000181381|ENSG00000181381	ENST00000260184;ENST00000511577;ENST00000505890|ENST00000514580	T;T;T|.	0.59224|.	0.28;0.28;0.28|.	3.16|3.16	1.95|1.95	0.26073|0.26073	Helicase, C-terminal (3);|.	0.000000|.	0.36591|.	U|.	0.002501|.	T|T	0.60183|0.60183	0.2249|0.2249	M|M	0.87682|0.87682	2.9|2.9	0.09310|0.09310	N|N	0.999999|0.999999	D;D|.	0.71674|.	0.994;0.998|.	D;D|.	0.65773|.	0.922;0.938|.	T|T	0.52961|0.52961	-0.8505|-0.8505	10|5	0.66056|.	D|.	0.02|.	.|.	7.0872|7.0872	0.25264|0.25264	0.0:0.118:0.0:0.882|0.0:0.118:0.0:0.882	.|.	1270;1269|.	D6R906;Q5H9U9|.	.;DDX6L_HUMAN|.	F|F	1269;1269;1270|156	ENSP00000260184:I1269F;ENSP00000422423:I1269F;ENSP00000422202:I1270F|.	ENSP00000260184:I1269F|.	I|Y	-|-	1|2	0|0	DDX60L|DDX60L	169552196|169552196	0.721000|0.721000	0.28007|0.28007	0.002000|0.002000	0.10522|0.10522	0.093000|0.093000	0.18481|0.18481	1.244000|1.244000	0.32778|0.32778	0.248000|0.248000	0.21435|0.21435	0.383000|0.383000	0.25322|0.25322	ATT|TAT	.	.	.	none		0.323	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		A	169315621	T	A	169315621	3	1	211	1	0	0	0	0	1	0	0	0	4381	1406	49	5	1359	5	DDX60L	4	169315621	Missense_Mutation	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10	112578314	169315621	21838655	21	12850											
DMXL1	1657	hgsc.bcm.edu	37	chr5	118479556	118479556	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaatatgttggtgaagtcttTaacatcgtcagtcaacaatc	14	13	7	7	1	3	1	2	1	1	0	5	1	3	1	0	1	2	1	0	1	6	4			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr5:118479556T>C	ENST00000311085.8	+	14	2477	c.2397T>C	c.(2395-2397)ttT>ttC	p.F799F	DMXL1_ENST00000539542.1_Silent_p.F799F	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	799										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)		GTGAAGTCTTTAACATCGTCA	0.299																																					p.F799F		Atlas-SNP	.											.	DMXL1	268	.	0			c.T2397C						PASS	.						110	116	114					5																	118479556		2201	4299	6500	SO:0001819	synonymous_variant	1657	exon14			AGTCTTTAACATC	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.2397T>C	chr5.hg19:g.118479556T>C		601.0	1.0	.		303.0	97.0	.	NM_005509		Silent	SNP	ENST00000311085.8	hg19	CCDS4125.1																																																																																			.	.	.	none		0.299	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		C	118479556	T	C	118479556	2	2	211	1	0	0	0	0	0	0	0	1	4596	1751	61	3		3	DMXL1	5	118479556	Silent	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10		118479556	62435704	22	12851											
MEGF10	84466	hgsc.bcm.edu	37	chr5	126705695	126705695	+	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	agggaccaactgctccagtgGtaagtttccacctgctgttg	8	11	11	11	0	0	0	0	0	0	0	2	1	2	1	4	2	3	5	4	2	2	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr5:126705695G>T	ENST00000274473.6	+	6	679		c.e6+1		MEGF10_ENST00000508365.1_Splice_Site|MEGF10_ENST00000418761.2_Splice_Site|MEGF10_ENST00000503335.2_Splice_Site	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10						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)		TGCTCCAGTGGTAAGTTTCCA	0.537																																					.		Atlas-SNP	.											.	MEGF10	152	.	0			c.412+1G>T						PASS	.						176	140	152					5																	126705695		2203	4300	6503	SO:0001630	splice_region_variant	84466	exon5			CCAGTGGTAAGTT	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.412+1G>T	chr5.hg19:g.126705695G>T		33.0	0.0	.		42.0	13.0	.	NM_001256545	Q68DE5|Q8WUL3	Splice_Site	SNP	ENST00000274473.6	hg19	CCDS4142.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.749510	0.89753	.	.	ENSG00000145794	ENST00000503335;ENST00000508365;ENST00000418761;ENST00000274473	.	.	.	5.34	5.34	0.76211	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.1131	0.93326	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MEGF10	126733594	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.844000	0.99494	2.506000	0.84524	0.558000	0.71614	.	.	.	.	none		0.537	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446	Intron	T	126705695	G	T	126705695	5	4	211	1	0	0	0	0	0	0	1	0	9467	1275	44	4	427	4	MEGF10	5	126705695	Splice_Site	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10	8226139	126705695	54209565	23	12852											
PIK3CG	5294	hgsc.bcm.edu	37	chr7	106508582	106508582	+	Frame_Shift_Del	DEL	C	C	-																															gcggaggtggccagccgcgaCcccaagctctacgccatgca																								rs377396894		TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr7:106508582delC	ENST00000359195.3	+	2	886	c.576delC	c.(574-576)gacfs	p.D192fs	PIK3CG_ENST00000440650.2_Frame_Shift_Del_p.D192fs|PIK3CG_ENST00000496166.1_Frame_Shift_Del_p.D192fs	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	192					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						CCAGCCGCGACCCCAAGCTCT	0.617																																					p.D192fs		Atlas-Indel,Pindel	.											.	PIK3CG	279	.	0			c.575delA						PASS	.						70	74	73					7																	106508582		2203	4300	6503	SO:0001589	frameshift_variant	5294	exon2			.		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.576delC	chr7.hg19:g.106508582delC	ENSP00000352121:p.Asp192fs	49.0	0.0	0		82.0	22.0	0.268293	NM_002649	A4D0Q6|Q8IV23|Q9BZC8	Frame_Shift_Del	DEL	ENST00000359195.3	hg19	CCDS5739.1																																																																																			.	.	.	none		0.617	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1			-	106508582	C	-	106508582	7	5	211	1	0	1	0	1	0	0	0	0	11923	506	18	0	578	0	PIK3CG	7	106508582	Frame_Shift_Del	DEL	C	TCGA-IZ-A6M8-01A-11D-A31X-10		106508582	52630081	24	12853											
RAB11FIP1	80223	hgsc.bcm.edu	37	chr8	37729061	37729061	+	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	attgtccagggatgtgccagGaggcgggcttggactcccat	7	9	15	10	1	0	0	0	0	0	0	2	3	2	3	3	5	1	1	3	5	0	2			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr8:37729061G>C	ENST00000330843.4	-	4	3271	c.3259C>G	c.(3259-3261)Cct>Gct	p.P1087A	RAB11FIP1_ENST00000287263.4_Intron|RAB11FIP1_ENST00000524118.1_Intron|RAB11FIP1_ENST00000522727.1_Intron|RAB11FIP1_ENST00000523182.1_5'UTR	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	1087					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)			GATGTGCCAGGAGGCGGGCTT	0.552											OREG0018713	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P1087A		Atlas-SNP	.											.	RAB11FIP1	105	.	0			c.C3259G						PASS	.						190	202	198					8																	37729061		2203	4300	6503	SO:0001583	missense	80223	exon4			TGCCAGGAGGCGG	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.3259C>G	chr8.hg19:g.37729061G>C	ENSP00000331342:p.Pro1087Ala	45.0	0.0	.	872	69.0	30.0	.	NM_001002814	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Missense_Mutation	SNP	ENST00000330843.4	hg19	CCDS34882.1	.	.	.	.	.	.	.	.	.	.	G	10.50	1.368051	0.24771	.	.	ENSG00000156675	ENST00000330843	T	0.11712	2.75	5.24	0.717	0.18196	.	0.271342	0.26499	N	0.024035	T	0.05823	0.0152	L	0.36672	1.1	0.09310	N	0.999994	P;B	0.37101	0.582;0.057	B;B	0.33392	0.163;0.02	T	0.32481	-0.9905	10	0.19590	T	0.45	-8.4888	3.2151	0.06696	0.4377:0.2192:0.3431:0.0	.	416;1087	Q67C35;Q6WKZ4	.;RFIP1_HUMAN	A	1087	ENSP00000331342:P1087A	ENSP00000331342:P1087A	P	-	1	0	RAB11FIP1	37848219	0.746000	0.28272	0.013000	0.15412	0.003000	0.03518	1.420000	0.34804	0.206000	0.20587	-0.136000	0.14681	CCT	.	.	.	none		0.552	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151		C	37729061	G	C	37729061	3	2	211	1	0	0	0	0	1	0	0	0	12906	1174	41	4	604	4	RAB11FIP1	8	37729061	Missense_Mutation	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10		37729061	108634961	25	12854											
DOCK8	81704	hgsc.bcm.edu	37	chr9	441958	441958	+	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	ttggatgaacaggagtttgtCtacaaagagcctgcaattac	13	11	10	7	0	1	2	0	1	1	1	1	4	1	4	1	2	5	2	1	2	5	4			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr9:441958C>T	ENST00000453981.1	+	42	5551	c.5439C>T	c.(5437-5439)gtC>gtT	p.V1813V	DOCK8_ENST00000432829.2_Silent_p.V1745V|DOCK8_ENST00000382329.1_Silent_p.V1280V|DOCK8_ENST00000469391.1_Silent_p.V1713V			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1813	DHR-2.				blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		AGGAGTTTGTCTACAAAGAGC	0.403																																					p.V1813V		Atlas-SNP	.											.	DOCK8	401	.	0			c.C5439T						PASS	.						111	106	108					9																	441958		2203	4300	6503	SO:0001819	synonymous_variant	81704	exon42			GTTTGTCTACAAA	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.5439C>T	chr9.hg19:g.441958C>T		141.0	0.0	.		83.0	35.0	.	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Silent	SNP	ENST00000453981.1	hg19	CCDS6440.2																																																																																			.	.	.	none		0.403	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307		T	441958	C	T	441958	2	4	211	1	0	0	0	0	0	0	0	1	4695	900	32	2		2	DOCK8	9	441958	Silent	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10		441958	140771473	26	12855											
SHB	6461	hgsc.bcm.edu	37	chr9	37956019	37956019	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcccgcgaaggtgagggggAtgactgccgcttctcgttgc	5	9	16	11	4	1	2	0	2	1	0	3	4	2	3	2	3	2	2	2	3	1	2			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr9:37956019A>G	ENST00000377707.3	-	4	1652	c.1087T>C	c.(1087-1089)Tcc>Ccc	p.S363P	RP11-613M10.9_ENST00000540557.1_3'UTR	NM_003028.2	NP_003019.2	Q15464	SHB_HUMAN	Src homology 2 domain containing adaptor protein B	363	Mediates interaction with LAT, PTK2/FAK1, JAK1 and JAK3.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(2)|endometrium(4)|lung(1)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)	11		all_epithelial(88;0.122)		GBM - Glioblastoma multiforme(29;3.27e-05)|Lung(182;0.0658)		GGTGAGGGGGATGACTGCCGC	0.602																																					p.S363P		Atlas-SNP	.											SHB,colon,carcinoma,0,1	SHB	31	.	0			c.T1087C						PASS	.						39	33	35					9																	37956019		1990	4146	6136	SO:0001583	missense	6461	exon4			AGGGGGATGACTG		CCDS43806.1	9p13.2	2013-09-23	2005-05-24		ENSG00000107338	ENSG00000107338		"SH2 domain containing"	10838	protein-coding gene	gene with protein product		600314	"SHB adaptor protein (a Src homology 2 protein)", "SHB (Src homology 2 domain containing) adaptor protein B"			7713524	Standard	NM_003028		Approved		uc004aax.3	Q15464	OTTHUMG00000019936	ENST00000377707.3:c.1087T>C	chr9.hg19:g.37956019A>G	ENSP00000366936:p.Ser363Pro	105.0	0.0	.		86.0	4.0	.	NM_003028	B9EGM0|D3DRQ5|Q504U5|Q5VUM8	Missense_Mutation	SNP	ENST00000377707.3	hg19	CCDS43806.1	.	.	.	.	.	.	.	.	.	.	A	15.42	2.827960	0.50845	.	.	ENSG00000107338	ENST00000377707	T	0.36520	1.25	5.68	5.68	0.88126	.	0.117982	0.39341	N	0.001400	T	0.33760	0.0874	N	0.12182	0.205	0.80722	D	1	D	0.61697	0.99	P	0.53649	0.731	T	0.24297	-1.0164	10	0.52906	T	0.07	-16.6295	13.8702	0.63615	1.0:0.0:0.0:0.0	.	363	Q15464	SHB_HUMAN	P	363	ENSP00000366936:S363P	ENSP00000366936:S363P	S	-	1	0	SHB	37946019	1.000000	0.71417	0.999000	0.59377	0.957000	0.61999	6.114000	0.71560	2.161000	0.67846	0.460000	0.39030	TCC	.	.	.	none		0.602	SHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052490.1			G	37956019	A	G	37956019	3	3	211	1	0	0	0	0	1	0	0	0	14281	333	12	3	454	3	SHB	9	37956019	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	37514061	37956019	103257412	27	12856											
PRKACG	5568	hgsc.bcm.edu	37	chr9	71628289	71628289	+	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	atctggatgggctggtcggcGtagaagggtgggaagcccac	8	7	18	8	2	1	1	0	0	1	1	2	3	1	3	1	6	1	2	1	6	3	1	rs140133619		TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr9:71628289G>A	ENST00000377276.2	-	1	750	c.720C>T	c.(718-720)taC>taT	p.Y240Y		NM_002732.3	NP_002723.2	P22612	KAPCG_HUMAN	protein kinase, cAMP-dependent, catalytic, gamma	240	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)|carbohydrate metabolic process (GO:0005975)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|male gonad development (GO:0008584)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)	p.Y240Y(1)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						GCTGGTCGGCGTAGAAGGGTG	0.602																																					p.Y240Y	Esophageal Squamous(110;2236 2623 32146)	Atlas-SNP	.											PRKACG,mouth,carcinoma,0,1	PRKACG	65	.	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C720T						PASS	.						70	68	68					9																	71628289		2203	4300	6503	SO:0001819	synonymous_variant	5568	exon1			GTCGGCGTAGAAG	M34182	CCDS6625.1	9q13	2012-10-02			ENSG00000165059	ENSG00000165059	2.7.11.1		9382	protein-coding gene	gene with protein product		176893				2342480, 9598317	Standard	NM_002732		Approved	PKACg	uc004agy.3	P22612	OTTHUMG00000019974	ENST00000377276.2:c.720C>T	chr9.hg19:g.71628289G>A		90.0	0.0	.		91.0	28.0	.	NM_002732	O60850|Q5VZ02|Q86YI1	Silent	SNP	ENST00000377276.2	hg19	CCDS6625.1																																																																																			.	G|1.000;C|0.000	.	alt		0.602	PRKACG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052559.1			A	71628289	G	A	71628289	2	1	211	1	0	0	0	0	0	0	0	1	12509	1140	40	1		1	PRKACG	9	71628289	Silent	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10	33672270	71628289	69585142	28	12857											
MAMDC4	158056	hgsc.bcm.edu	37	chr9	139748712	139748712	+	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	caccactgccagaacaaggtCtgcgtggagccccagcagct	10	5	11	15	1	1	1	0	0	1	1	1	2	1	2	4	2	6	2	4	2	2	0			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr9:139748712C>T	ENST00000317446.2	+	7	770	c.720C>T	c.(718-720)gtC>gtT	p.V240V	MAMDC4_ENST00000445819.1_Silent_p.V240V|MAMDC4_ENST00000485732.1_3'UTR	NM_206920.2	NP_996803.2			MAM domain containing 4											breast(4)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	19	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)		AGAACAAGGTCTGCGTGGAGC	0.667																																					p.V240V		Atlas-SNP	.											.	MAMDC4	117	.	0			c.C720T						PASS	.						25	27	26					9																	139748712		2193	4296	6489	SO:0001819	synonymous_variant	158056	exon7			CAAGGTCTGCGTG	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.720C>T	chr9.hg19:g.139748712C>T		106.0	0.0	.		130.0	38.0	.	NM_206920		Silent	SNP	ENST00000317446.2	hg19	CCDS7010.1																																																																																			.	.	.	none		0.667	MAMDC4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254642.3	NM_206920		T	139748712	C	T	139748712	2	4	211	1	0	0	0	0	0	0	0	1	9211	900	32	2		2	MAMDC4	9	139748712	Silent	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	68120423	139748712	1464719	29	12858											
GPAM	57678	hgsc.bcm.edu	37	chr10	113913352	113913352	+	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	atattctagaagtttttgtcGgttgcattgaggtagaaaag	12	15	11	3	1	1	3	0	1	1	2	2	3	1	3	0	2	1	4	0	2	6	8			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr10:113913352G>A	ENST00000348367.4	-	22	2640	c.2443C>T	c.(2443-2445)Cga>Tga	p.R815*	GPAM_ENST00000423155.1_Nonsense_Mutation_p.R815*			Q9HCL2	GPAT1_HUMAN	glycerol-3-phosphate acyltransferase, mitochondrial	815					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)		AGTTTTTGTCGGTTGCATTGA	0.383																																					p.R815X	Ovarian(161;1017 2606 18293 52943)	Atlas-SNP	.											.	GPAM	68	.	0			c.C2443T						PASS	.						126	131	129					10																	113913352		2203	4300	6503	SO:0001587	stop_gained	57678	exon22			TTTGTCGGTTGCA	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.2443C>T	chr10.hg19:g.113913352G>A	ENSP00000265276:p.Arg815*	106.0	0.0	.		91.0	30.0	.	NM_001244949	Q5VW51|Q86TA3	Nonsense_Mutation	SNP	ENST00000348367.4	hg19	CCDS7570.1	.	.	.	.	.	.	.	.	.	.	G	40	8.137750	0.98672	.	.	ENSG00000119927	ENST00000348367;ENST00000423155	.	.	.	5.59	4.63	0.57726	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.7284	11.4195	0.49974	0.0:0.0:0.7192:0.2808	.	.	.	.	X	815	.	ENSP00000265276:R815X	R	-	1	2	GPAM	113903342	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.487000	0.45268	2.640000	0.89533	0.655000	0.94253	CGA	.	.	.	none		0.383	GPAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050377.1	NM_020918		A	113913352	G	A	113913352	4	1	211	1	0	0	0	0	0	1	0	0	6595	1124	39	1	47	1	GPAM	10	113913352	Nonsense_Mutation	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10		113913352	21621395	30	12859											
DCHS1	8642	hgsc.bcm.edu	37	chr11	6652589	6652589	+	Frame_Shift_Del	DEL	T	T	-																															tctccccctcatctggatccTtcgcctgcagagtcgtcacc																										TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr11:6652589delT	ENST00000299441.3	-	8	4136	c.3725delA	c.(3724-3726)aagfs	p.K1242fs	RP11-732A19.6_ENST00000526633.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	1242	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)		ATCTGGATCCTTCGCCTGCAG	0.552																																					p.K1242fs		Atlas-Indel,Pindel	.											.	DCHS1	277	.	0			c.3726delG						PASS	.						206	169	181					11																	6652589		2201	4296	6497	SO:0001589	frameshift_variant	8642	exon8			.	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.3725delA	chr11.hg19:g.6652589delT	ENSP00000299441:p.Lys1242fs	78.0	0.0	0		77.0	21.0	0.272727	NM_003737	O15098	Frame_Shift_Del	DEL	ENST00000299441.3	hg19	CCDS7771.1																																																																																			.	.	.	none		0.552	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		-	6652589	T	-	6652589	7	5	211	1	0	1	0	1	0	0	0	0	4289	1609	56	0	6227	0	DCHS1	11	6652589	Frame_Shift_Del	DEL	T	TCGA-IZ-A6M8-01A-11D-A31X-10		6652589	128353927	31	12860											
IGSF22	283284	hgsc.bcm.edu	37	chr11	18731076	18731076	+	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	caggtgcctgagatggggatCtttgtgcacttggaccactc	7	11	13	10	0	1	1	0	1	1	1	2	4	1	3	2	4	2	1	2	4	0	2			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr11:18731076C>A	ENST00000513874.1	-	18	2995	c.2856G>T	c.(2854-2856)aaG>aaT	p.K952N	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	851										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						AGATGGGGATCTTTGTGCACT	0.577																																					p.K952N		Atlas-SNP	.											.	IGSF22	211	.	0			c.G2856T						PASS	.						100	105	104					11																	18731076		1974	4152	6126	SO:0001583	missense	283284	exon18			GGGGATCTTTGTG	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.2856G>T	chr11.hg19:g.18731076C>A	ENSP00000421191:p.Lys952Asn	97.0	0.0	.		102.0	34.0	.	NM_173588	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	hg19	CCDS41625.2	.	.	.	.	.	.	.	.	.	.	C	13.80	2.345544	0.41498	.	.	ENSG00000179057	ENST00000513874	T	0.56776	0.44	4.39	2.46	0.29980	.	.	.	.	.	T	0.47948	0.1473	N	0.12182	0.205	0.09310	N	0.999997	D	0.69078	0.997	D	0.80764	0.994	T	0.34104	-0.9842	9	0.18276	T	0.48	.	7.069	0.25167	0.0:0.7288:0.1744:0.0969	.	952	D6RGV7	.	N	952	ENSP00000421191:K952N	ENSP00000322422:K851N	K	-	3	2	IGSF22	18687652	0.000000	0.05858	0.578000	0.28575	0.994000	0.84299	-0.453000	0.06778	0.464000	0.27142	0.655000	0.94253	AAG	.	.	.	none		0.577	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588		A	18731076	C	A	18731076	3	1	211	1	0	0	0	0	1	0	0	0	7607	912	32	4	1148	4	IGSF22	11	18731076	Missense_Mutation	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	12078487	18731076	116275440	32	12861											
GRIN2B	2904	hgsc.bcm.edu	37	chr12	13768093	13768093	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccattgctgcgtgacaccaTgacactgatgcctgtctcta	8	11	8	14	1	1	3	0	3	1	0	2	3	1	3	3	0	3	1	3	0	1	2			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr12:13768093T>C	ENST00000609686.1	-	7	1818	c.1609A>G	c.(1609-1611)Atg>Gtg	p.M537V		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	537					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)	CGTGACACCATGACACTGATG	0.517																																					p.M537V		Atlas-SNP	.											.	GRIN2B	303	.	0			c.A1609G						PASS	.						195	151	166					12																	13768093		2203	4300	6503	SO:0001583	missense	2904	exon7			ACACCATGACACT		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.1609A>G	chr12.hg19:g.13768093T>C	ENSP00000477455:p.Met537Val	93.0	0.0	.		82.0	21.0	.	NM_000834	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Missense_Mutation	SNP	ENST00000609686.1	hg19	CCDS8662.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.266041	0.80358	.	.	ENSG00000150086	ENST00000279593	T	0.22134	1.97	6.17	6.17	0.99709	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	T	0.42720	0.1215	L	0.53780	1.695	0.80722	D	1	D	0.76494	0.999	D	0.67382	0.951	T	0.21655	-1.0239	10	0.87932	D	0	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	537	Q13224	NMDE2_HUMAN	V	537	ENSP00000279593:M537V	ENSP00000279593:M537V	M	-	1	0	GRIN2B	13659360	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.035000	0.88872	2.371000	0.80710	0.533000	0.62120	ATG	.	.	.	none		0.517	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2			C	13768093	T	C	13768093	3	2	211	1	0	0	0	0	1	0	0	0	6787	1464	51	3	2873	3	GRIN2B	12	13768093	Missense_Mutation	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10		13768093	120083802	33	12862											
AMHR2	269	hgsc.bcm.edu	37	chr12	53825014	53825014	+	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	tgttgggatgcagacccagaAgcacggctgacagctgagtg	10	7	15	9	1	0	4	0	2	0	2	0	5	0	5	1	2	3	5	1	2	1	1			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr12:53825014A>T	ENST00000257863.4	+	11	1559	c.1479A>T	c.(1477-1479)gaA>gaT	p.E493D	AMHR2_ENST00000550311.1_3'UTR|AMHR2_ENST00000379791.3_Missense_Mutation_p.E398D	NM_001164690.1|NM_020547.2	NP_001158162.1|NP_065434.1	Q16671	AMHR2_HUMAN	anti-Mullerian hormone receptor, type II	493	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				Mullerian duct regression (GO:0001880)|negative regulation of anti-Mullerian hormone signaling pathway (GO:1902613)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	integral component of plasma membrane (GO:0005887)	anti-Mullerian hormone receptor activity (GO:1990272)|ATP binding (GO:0005524)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor activity, type II (GO:0005026)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|skin(2)	34					Adenosine triphosphate(DB00171)	CAGACCCAGAAGCACGGCTGA	0.607																																					p.E493D		Atlas-SNP	.											.	AMHR2	61	.	0			c.A1479T						PASS	.						88	84	86					12																	53825014		2203	4300	6503	SO:0001583	missense	269	exon11			CCCAGAAGCACGG	AF172932	CCDS8858.1, CCDS53798.1, CCDS55829.1	12q13	2013-03-14							465	protein-coding gene	gene with protein product	"Muellerian inhibiting substance type II receptor"	600956				7493017	Standard	NM_001164690		Approved	MISR2, MISRII	uc001scx.2	Q16671	OTTHUMG00000170048	ENST00000257863.4:c.1479A>T	chr12.hg19:g.53825014A>T	ENSP00000257863:p.Glu493Asp	59.0	0.0	.		68.0	22.0	.	NM_020547	A0AVE1|B9EGB7|E9PGD2|F8W1D2|Q13762|Q647K2	Missense_Mutation	SNP	ENST00000257863.4	hg19	CCDS8858.1	.	.	.	.	.	.	.	.	.	.	A	19.53	3.844229	0.71488	.	.	ENSG00000135409	ENST00000257863;ENST00000379791	T;D	0.93659	-0.22;-3.26	4.86	3.72	0.42706	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.38959	N	0.001503	D	0.92512	0.7622	N	0.25094	0.71	0.29470	N	0.857082	D	0.76494	0.999	D	0.80764	0.994	D	0.87493	0.2428	10	0.62326	D	0.03	.	8.3026	0.32023	0.9085:0.0:0.0915:0.0	.	493	Q16671	AMHR2_HUMAN	D	493;398	ENSP00000257863:E493D;ENSP00000369117:E398D	ENSP00000257863:E493D	E	+	3	2	AMHR2	52111281	0.998000	0.40836	0.998000	0.56505	0.971000	0.66376	0.443000	0.21644	0.998000	0.38996	0.460000	0.39030	GAA	.	.	.	none		0.607	AMHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407048.1	NM_020547		T	53825014	A	T	53825014	3	4	211	1	0	0	0	0	1	0	0	0	573	69	3	5	1521	5	AMHR2	12	53825014	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	40056921	53825014	80026881	34	12863											
TARBP2	8620	hgsc.bcm.edu	37	chr12	53899840	53899840	+	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	0	0	0	0	0	0	0	ccacccagccggccactgtgTgtcatggctctgcaaccacc	7	7	9	18	1	2	0	1	0	1	0	2	0	2	0	6	2	3	2	6	2	1	0			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr12:53899840T>C	ENST00000267017.3	-	0	592				TARBP2_ENST00000266987.2_Missense_Mutation_p.C337R|TARBP2_ENST00000456234.2_Missense_Mutation_p.C316R|TARBP2_ENST00000552857.1_3'UTR|TARBP2_ENST00000394357.2_Missense_Mutation_p.C316R	NM_003717.2	NP_003708.1	O15130	NPFF_HUMAN	neuropeptide FF-amide peptide precursor						acute inflammatory response to antigenic stimulus (GO:0002438)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of appetite (GO:0032099)|negative regulation of heart rate (GO:0010459)|negative regulation of insulin secretion (GO:0046676)|neuropeptide signaling pathway (GO:0007218)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane depolarization (GO:0003254)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|response to morphine (GO:0043278)|somatostatin secretion (GO:0070253)|spinal cord development (GO:0021510)|synaptic transmission (GO:0007268)|vasopressin secretion (GO:0030103)	axon terminus (GO:0043679)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|perikaryon (GO:0043204)|vesicle (GO:0031982)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(1)|prostate(1)|urinary_tract(1)	3						GGCCACTGTGTGTCATGGCTC	0.632																																					p.C337R		Atlas-SNP	.											.	TARBP2	35	.	0			c.T1009C						PASS	.						48	44	46					12																	53899840		2203	4300	6503	SO:0001628	intergenic_variant	6895	exon9			ACTGTGTGTCATG	AF005271	CCDS8862.1	12q13.13	2013-02-26			ENSG00000139574	ENSG00000139574		"Endogenous ligands"	7901	protein-coding gene	gene with protein product		604643				9224703	Standard	NM_003717		Approved	FMRFAL	uc001sdw.1	O15130	OTTHUMG00000169856		chr12.hg19:g.53899840T>C		78.0	0.0	.		71.0	20.0	.	NM_134323	Q3SXL4	Missense_Mutation	SNP	ENST00000267017.3	hg19	CCDS8862.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.437352	0.83885	.	.	ENSG00000139546	ENST00000266987;ENST00000456234;ENST00000394357	D;D;D	0.82255	-1.59;-1.59;-1.59	5.15	5.15	0.70609	Double-stranded RNA-binding (2);	0.000000	0.85682	D	0.000000	D	0.91047	0.7183	M	0.83223	2.63	0.80722	D	1	D	0.65815	0.995	D	0.72982	0.979	D	0.92199	0.5766	10	0.66056	D	0.02	-6.1074	14.2562	0.66053	0.0:0.0:0.0:1.0	.	337	Q15633	TRBP2_HUMAN	R	337;316;316	ENSP00000266987:C337R;ENSP00000416077:C316R;ENSP00000377885:C316R	ENSP00000266987:C337R	C	+	1	0	TARBP2	52186107	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	4.900000	0.63252	2.075000	0.62263	0.402000	0.26972	TGT	.	.	.	none		0.632	NPFF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406301.1	NM_003717		C	53899840	T	C	53899840	1	2	211	0	1	0	0	0	0	0	0	0	15568	1696	59	3		3	TARBP2	12	53899840	IGR	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10	74826	53899840	79952055	35	12864											
MON2	23041	hgsc.bcm.edu	37	chr12	62931886	62931886	+	Frame_Shift_Del	DEL	G	G	-																															aattttacagcatcttgtgtGgattctgggattaaagccta																										TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr12:62931886delG	ENST00000393632.2	+	17	2520	c.2129delG	c.(2128-2130)tggfs	p.W710fs	MON2_ENST00000552738.1_Frame_Shift_Del_p.W687fs|MON2_ENST00000552115.1_Frame_Shift_Del_p.W710fs|MON2_ENST00000393630.3_Frame_Shift_Del_p.W710fs|MON2_ENST00000546600.1_Frame_Shift_Del_p.W710fs|MON2_ENST00000280379.6_Frame_Shift_Del_p.W710fs|MON2_ENST00000393629.2_Frame_Shift_Del_p.W710fs	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	710					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)		CATCTTGTGTGGATTCTGGGA	0.353																																					p.W710fs		Pindel	.											.	MON2	160	.	0			c.2128delT						PASS	.						43	49	47					12																	62931886		2202	4300	6502	SO:0001589	frameshift_variant	23041	exon17			.		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.2129delG	chr12.hg19:g.62931886delG	ENSP00000377252:p.Trp710fs	163.0	0.0	.		90.0	10.0	0.111	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Frame_Shift_Del	DEL	ENST00000393632.2	hg19	CCDS31849.1																																																																																			.	.	.	none		0.353	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		-	62931886	G	-	62931886	7	5	211	1	0	1	0	1	0	0	0	0	9707	1357	47	0	2195	0	MON2	12	62931886	Frame_Shift_Del	DEL	G	TCGA-IZ-A6M8-01A-11D-A31X-10	9032046	62931886	70920009	36	12865											
SBNO1	55206	hgsc.bcm.edu	37	chr12	123815855	123815855	+	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	ctgctatcgtccttccttttCctacaccggcaccatcacct	6	13	4	18	2	1	0	1	0	0	0	5	0	4	0	6	1	2	2	6	1	2	5			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr12:123815855C>G	ENST00000602398.1	-	8	1104	c.977G>C	c.(976-978)gGa>gCa	p.G326A	SBNO1_ENST00000420886.2_Missense_Mutation_p.G326A|SBNO1_ENST00000602750.1_Missense_Mutation_p.G325A|SBNO1_ENST00000267176.4_Missense_Mutation_p.G325A			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	326					regulation of transcription, DNA-templated (GO:0006355)					NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		CCTTCCTTTTCCTACACCGGC	0.408																																					p.G326A		Atlas-SNP	.											.	SBNO1	138	.	0			c.G977C						PASS	.						152	138	143					12																	123815855		2203	4300	6503	SO:0001583	missense	55206	exon7			CCTTTTCCTACAC	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"sno, strawberry notch homolog 1 (Drosophila)"				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.977G>C	chr12.hg19:g.123815855C>G	ENSP00000473665:p.Gly326Ala	92.0	0.0	.		94.0	33.0	.	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Missense_Mutation	SNP	ENST00000602398.1	hg19	CCDS53844.1	.	.	.	.	.	.	.	.	.	.	C	32	5.164386	0.94727	.	.	ENSG00000139697	ENST00000420886;ENST00000267176;ENST00000442601	D;D	0.99940	-8.38;-8.38	5.83	5.83	0.93111	Helicase/UvrB domain (1);	0.000000	0.85682	D	0.000000	D	0.99955	0.9981	H	0.96015	3.755	0.80722	D	1	D;D;D	0.89917	1.0;0.998;0.999	D;D;D	0.91635	0.999;0.993;0.998	D	0.96352	0.9259	10	0.87932	D	0	-27.8907	20.1218	0.97964	0.0:1.0:0.0:0.0	.	326;325;324	A3KN83;A3KN83-2;A3KN83-3	SBNO1_HUMAN;.;.	A	326;325;325	ENSP00000387361:G326A;ENSP00000267176:G325A	ENSP00000267176:G325A	G	-	2	0	SBNO1	122381808	1.000000	0.71417	0.958000	0.39756	0.998000	0.95712	7.794000	0.85869	2.763000	0.94921	0.561000	0.74099	GGA	.	.	.	none		0.408	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183		G	123815855	C	G	123815855	3	3	211	1	0	0	0	0	1	0	0	0	13875	855	30	4	3304	4	SBNO1	12	123815855	Missense_Mutation	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	60883969	123815855	10036040	37	12866											
ABHD13	84945	hgsc.bcm.edu	37	chr13	108882148	108882149	+	Missense_Mutation	DNP	GG	GG	TT																															tttctttttggccgttccttGggtggagcagtggctattca																										TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr13:108882148_108882149GG>TT	ENST00000375898.3	+	2	883_884	c.582_583GG>TT	c.(580-585)ttGGgt>ttTTgt	p.194_195LG>FC		NM_032859.2	NP_116248.2	Q7L211	ABHDD_HUMAN	abhydrolase domain containing 13	194						integral component of membrane (GO:0016021)|membrane (GO:0016020)	hydrolase activity (GO:0016787)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	17	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					GCCGTTCCTTGGGTGGAGCAGT	0.406																																					p.L194F|p.G195C	Pancreas(22;506 789 38166 45896 51596)	Atlas-SNP	.											.	ABHD13	39	.	0			c.G582T|c.G583T						PASS	.																																			SO:0001583	missense	84945	exon2			TTCCTTGGGTGGA|TCCTTGGGTGGAG	AK027812	CCDS32007.1	13q33.2	2007-04-03	2006-03-10	2006-03-10	ENSG00000139826	ENSG00000139826		"Abhydrolase domain containing"	20293	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 6"	C13orf6			Standard	NM_032859		Approved	bA153I24.2, FLJ14906, BEM46L1	uc001vqq.3	Q7L211	OTTHUMG00000017330	Exception_encountered	chr13.hg19:g.108882148_108882149delinsTT	ENSP00000365063:p.L194_G195delinsFC	129.0	0.0	.		90.0|89.0	25.0	.	NM_032859	B3KWE7|Q8NBW1|Q96JX9	Missense_Mutation	SNP	ENST00000375898.3	hg19	CCDS32007.1																																																																																			.	.	.	none		0.406	ABHD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045743.1	NM_032859		TT	108882149	GG	TT	108882148	3	4	211	1	0	0	0	0	1	0	0	0	78	1339	47	4	584	4	ABHD13	13	108882148	Missense_Mutation	DNP	GG	TCGA-IZ-A6M8-01A-11D-A31X-10		108882148	6287730	38	12867											
SNX6	58533	hgsc.bcm.edu	37	chr14	35062293	35062293	+	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	atcagatttagcagatgcatCcttaactcggttatgatact	12	14	7	8	1	1	3	1	1	0	2	3	3	2	3	1	1	4	3	1	1	4	5			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr14:35062293C>A	ENST00000362031.4	-	8	742	c.712G>T	c.(712-714)Gat>Tat	p.D238Y	SNX6_ENST00000396526.3_Missense_Mutation_p.D110Y|SNX6_ENST00000355110.5_Missense_Mutation_p.D114Y|SNX6_ENST00000396534.3_Missense_Mutation_p.D110Y	NM_152233.2	NP_689419.2	Q9UNH7	SNX6_HUMAN	sorting nexin 6	226					intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|intracellular (GO:0005622)|nucleus (GO:0005634)	phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)			endometrium(4)|lung(1)|ovary(1)	6	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00199)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.0245)		GCAGATGCATCCTTAACTCGG	0.299																																					p.D238Y		Atlas-SNP	.											.	SNX6	21	.	0			c.G712T						PASS	.						75	74	74					14																	35062293		2202	4298	6500	SO:0001583	missense	58533	exon8			ATGCATCCTTAAC	AF121856	CCDS9648.1, CCDS41942.1	14q13	2010-08-05			ENSG00000129515	ENSG00000129515		"Sorting nexins"	14970	protein-coding gene	gene with protein product		606098				11279102	Standard	XM_006720224		Approved		uc001wsf.1	Q9UNH7	OTTHUMG00000140213	ENST00000362031.4:c.712G>T	chr14.hg19:g.35062293C>A	ENSP00000355217:p.Asp238Tyr	269.0	0.0	.		127.0	31.0	.	NM_152233	C0H5W9|Q9Y449	Missense_Mutation	SNP	ENST00000362031.4	hg19	CCDS41942.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.345615	0.82022	.	.	ENSG00000129515	ENST00000396526;ENST00000396534;ENST00000362031;ENST00000355110;ENST00000557265	T;T;T;T;T	0.54071	1.5;1.5;1.5;1.5;0.59	4.69	4.69	0.59074	Vps5 C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.75317	0.3833	M	0.82630	2.6	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.80360	-0.1415	10	0.87932	D	0	-17.283	17.6053	0.88036	0.0:1.0:0.0:0.0	.	114;226	B4DJS7;Q9UNH7	.;SNX6_HUMAN	Y	110;110;238;114;201	ENSP00000379779:D110Y;ENSP00000379785:D110Y;ENSP00000355217:D238Y;ENSP00000347230:D114Y;ENSP00000452577:D201Y	ENSP00000347230:D114Y	D	-	1	0	SNX6	34132044	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.993000	0.76245	2.340000	0.79590	0.561000	0.74099	GAT	.	.	.	none		0.299	SNX6-002	KNOWN	downstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276642.3			A	35062293	C	A	35062293	3	1	211	1	0	0	0	0	1	0	0	0	14919	855	30	4	572	4	SNX6	14	35062293	Missense_Mutation	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10		35062293	72287247	39	12868											
LTBP2	4053	hgsc.bcm.edu	37	chr14	75019017	75019017	+	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	ataggcaggtggcagaacttCccggtggagttggcggggca	8	7	18	8	2	0	1	0	0	0	1	1	2	1	2	1	8	1	4	1	8	2	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr14:75019017C>G	ENST00000261978.4	-	6	1658	c.1272G>C	c.(1270-1272)ggG>ggC	p.G424G	LTBP2_ENST00000557425.1_Intron|LTBP2_ENST00000556690.1_Silent_p.G424G|CTD-2207P18.1_ENST00000554552.1_lincRNA	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	424	EGF-like 2. {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)		GGCAGAACTTCCCGGTGGAGT	0.652																																					p.G424G		Atlas-SNP	.											.	LTBP2	158	.	0			c.G1272C						PASS	.						39	41	40					14																	75019017		2203	4300	6503	SO:0001819	synonymous_variant	4053	exon6			GAACTTCCCGGTG		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.1272G>C	chr14.hg19:g.75019017C>G		67.0	0.0	.		83.0	26.0	.	NM_000428	Q99907|Q9NS51	Silent	SNP	ENST00000261978.4	hg19	CCDS9831.1																																																																																			.	.	.	none		0.652	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428		G	75019017	C	G	75019017	2	3	211	1	0	0	0	0	0	0	0	1	9081	842	30	4		4	LTBP2	14	75019017	Silent	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	39956724	75019017	32330523	40	12869											
TJP1	7082	hgsc.bcm.edu	37	chr15	30019082	30019082	+	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	ggacataacctcattctcatTgtttttactccttgcttaga	9	17	5	10	0	2	1	2	0	1	1	4	2	3	2	2	1	3	2	2	1	3	8			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr15:30019082T>G	ENST00000346128.6	-	17	2688	c.2214A>C	c.(2212-2214)acA>acC	p.T738T	TJP1_ENST00000400011.2_Silent_p.T742T|RP11-680F8.4_ENST00000560740.1_RNA|TJP1_ENST00000545208.2_Silent_p.T738T|TJP1_ENST00000356107.6_Silent_p.T738T	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	738	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				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)		TCATTCTCATTGTTTTTACTC	0.363																																					p.T738T	Melanoma(77;681 1843 6309 6570)	Atlas-SNP	.											.	TJP1	140	.	0			c.A2214C						PASS	.						161	147	151					15																	30019082		1861	4096	5957	SO:0001819	synonymous_variant	7082	exon17			TCTCATTGTTTTT		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.2214A>C	chr15.hg19:g.30019082T>G		131.0	0.0	.		110.0	26.0	.	NM_175610	B4E3K1|Q2NKP3|Q4ZGJ6	Silent	SNP	ENST00000346128.6	hg19	CCDS42007.1																																																																																			.	.	.	none		0.363	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		G	30019082	T	G	30019082	2	3	211	1	0	0	0	0	0	0	0	1	15941	1799	63	5		5	TJP1	15	30019082	Silent	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10		30019082	72512310	41	12870											
HMG20A	10363	hgsc.bcm.edu	37	chr15	77750833	77750833	+	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	gagagtaatgatctggctacCactgggtaagcagctgcttt	10	11	12	8	0	1	2	0	1	1	1	1	3	1	2	1	2	4	6	1	2	3	4			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr15:77750833C>G	ENST00000381714.3	+	3	512	c.84C>G	c.(82-84)acC>acG	p.T28T	HMG20A_ENST00000336216.4_Silent_p.T28T	NM_018200.2	NP_060670.1	Q9NP66	HM20A_HUMAN	high mobility group 20A	28					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						ATCTGGCTACCACTGGGTAAG	0.453																																					p.T28T		Atlas-SNP	.											.	HMG20A	48	.	0			c.C84G						PASS	.						92	88	89					15																	77750833		2196	4294	6490	SO:0001819	synonymous_variant	10363	exon3			GGCTACCACTGGG	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.84C>G	chr15.hg19:g.77750833C>G		64.0	0.0	.		45.0	15.0	.	NM_018200	A6NHY3|D3DW78|Q53G31|Q9NSF6	Silent	SNP	ENST00000381714.3	hg19	CCDS10295.1																																																																																			.	.	.	none		0.453	HMG20A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419512.2	NM_018200		G	77750833	C	G	77750833	2	3	211	1	0	0	0	0	0	0	0	1	7228	581	21	4		4	HMG20A	15	77750833	Silent	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	47731751	77750833	24780559	42	12871											
MEFV	4210	hgsc.bcm.edu	37	chr16	3304171	3304171	+	Frame_Shift_Del	DEL	T	T	-																															aatttaccggtgaccgaatgTtctggatttccagggccttc																										TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr16:3304171delT	ENST00000219596.1	-	2	936	c.897delA	c.(895-897)gaafs	p.E299fs	MEFV_ENST00000536379.1_Intron|MEFV_ENST00000541159.1_Intron|MEFV_ENST00000339854.4_Intron	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	299					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						tgacCGAATGTTCTGGATTTC	0.562																																					p.H300fs		Atlas-Indel,Pindel	.											.	MEFV	170	.	0			c.898delC						PASS	.						53	56	55					16																	3304171		2197	4300	6497	SO:0001589	frameshift_variant	4210	exon2			.	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"Tripartite motif containing / Tripartite motif containing"	6998	protein-coding gene	gene with protein product	"pyrin"	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.897delA	chr16.hg19:g.3304171delT	ENSP00000219596:p.Glu299fs	53.0	0.0	0		62.0	14.0	0.225806	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Frame_Shift_Del	DEL	ENST00000219596.1	hg19	CCDS10498.1																																																																																			.	.	.	none		0.562	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243		-	3304171	T	-	3304171	7	5	211	1	0	1	0	1	0	0	0	0	9466	1722	60	0	1484	0	MEFV	16	3304171	Frame_Shift_Del	DEL	T	TCGA-IZ-A6M8-01A-11D-A31X-10		3304171	87050582	43	12872											
APOB48R	55911	hgsc.bcm.edu	37	chr16	28509637	28509637	+	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	tctgaggcatgatgggacccCggtgccagccaggagaaggc	9	5	16	11	1	1	3	0	2	1	1	1	5	1	4	4	5	2	1	4	5	1	0			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr16:28509637C>G	ENST00000431282.1	+	4	3174	c.3164C>G	c.(3163-3165)cCg>cGg	p.P1055R	CLN3_ENST00000567160.1_5'Flank|APOBR_ENST00000564831.1_Missense_Mutation_p.P1064R|APOBR_ENST00000328423.5_Intron|CLN3_ENST00000569430.1_5'Flank			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor	1055					cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						GATGGGACCCCGGTGCCAGCC	0.672																																					p.P1064R		Atlas-SNP	.											.	APOBR	89	.	0			c.C3191G						PASS	.						16	21	19					16																	28509637		1941	4148	6089	SO:0001583	missense	55911	exon3			GGACCCCGGTGCC	AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"apolipoprotein B48 receptor", "apolipoprotein B100 receptor"	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83		ENST00000431282.1:c.3164C>G	chr16.hg19:g.28509637C>G	ENSP00000416094:p.Pro1055Arg	55.0	0.0	.		93.0	10.0	.	NM_018690	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Missense_Mutation	SNP	ENST00000431282.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.49	2.251925	0.39797	.	.	ENSG00000184730	ENST00000431282	T	0.61742	0.08	4.84	4.84	0.62591	.	.	.	.	.	T	0.62962	0.2471	L	0.34521	1.04	0.34997	D	0.755616	D;D	0.71674	0.998;0.998	D;D	0.64687	0.928;0.928	T	0.69026	-0.5254	8	.	.	.	-4.4525	13.4548	0.61193	0.0:1.0:0.0:0.0	.	1055;1055	Q0VD83;Q9NS13	APOBR_HUMAN;.	R	1055	ENSP00000416094:P1055R	.	P	+	2	0	APOBR	28417138	0.950000	0.32346	0.996000	0.52242	0.736000	0.42039	2.535000	0.45685	2.236000	0.73375	0.457000	0.33378	CCG	.	.	.	none		0.672	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_182804		G	28509637	C	G	28509637	3	3	211	1	0	0	0	0	1	0	0	0	786	652	23	4	3178	4	APOB48R	16	28509637	Missense_Mutation	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	25205466	28509637	61845116	44	12873											
SF3B3	23450	hgsc.bcm.edu	37	chr16	70605581	70605581	+	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	ttctccatatcttagaatgtGattgatggagacctctgtga	10	15	9	7	0	3	5	0	3	3	2	4	6	3	5	2	1	0	0	2	1	3	4			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr16:70605581G>A	ENST00000302516.5	+	26	3730	c.3519G>A	c.(3517-3519)gtG>gtA	p.V1173V		NM_012426.4	NP_036558.3	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3, 130kDa	1173					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein complex assembly (GO:0006461)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleic acid binding (GO:0003676)			breast(2)|endometrium(8)|kidney(2)|large_intestine(8)|liver(3)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	53		Ovarian(137;0.0694)				CTTAGAATGTGATTGATGGAG	0.428																																					p.V1173V		Atlas-SNP	.											.	SF3B3	99	.	0			c.G3519A						PASS	.						51	48	49					16																	70605581		2198	4300	6498	SO:0001819	synonymous_variant	23450	exon26			GAATGTGATTGAT	AJ001443	CCDS10894.1	16q22	2008-08-01	2002-08-29		ENSG00000189091	ENSG00000189091			10770	protein-coding gene	gene with protein product		605592	"splicing factor 3b, subunit 3, 130kD"			10490618	Standard	NM_012426		Approved	SAP130, SF3b130, RSE1, KIAA0017	uc002ezf.3	Q15393	OTTHUMG00000137582	ENST00000302516.5:c.3519G>A	chr16.hg19:g.70605581G>A		73.0	0.0	.		93.0	24.0	.	NM_012426	Q6NTI8|Q96GC0|Q9BPY2|Q9UFX7|Q9UJ29	Silent	SNP	ENST00000302516.5	hg19	CCDS10894.1																																																																																			.	.	.	none		0.428	SF3B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268972.1	NM_012426		A	70605581	G	A	70605581	2	1	211	1	0	0	0	0	0	0	0	1	14165	1277	45	2		2	SF3B3	16	70605581	Silent	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10	42095944	70605581	19749172	45	12874											
C17orf39	79018	hgsc.bcm.edu	37	chr17	17962263	17962263	+	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	aagagctgaagaatggagacTacgtcttcatgaggtggaag	14	8	14	5	1	2	5	1	2	1	3	2	7	2	6	0	3	2	1	0	3	5	2			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr17:17962263T>A	ENST00000268719.4	+	4	861	c.688T>A	c.(688-690)Tac>Aac	p.Y230N		NM_024052.4	NP_076957.3	Q8IVV7	GID4_HUMAN	GID complex subunit 4	230																	GAATGGAGACTACGTCTTCAT	0.458																																					p.Y230N		Atlas-SNP	.											.	.	.	.	0			c.T688A						PASS	.						75	68	71					17																	17962263		2203	4300	6503	SO:0001583	missense	79018	exon4			GGAGACTACGTCT	AK127580	CCDS11190.1	17p11.2	2013-07-31	2013-07-31	2012-07-20	ENSG00000141034	ENSG00000141034			28453	protein-coding gene	gene with protein product	"vacuolar import and degradation 24"		"chromosome 17 open reading frame 39", "GID complex subunit 4, VID24 homolog (S. cerevisiae)"	C17orf39		11997338	Standard	NM_024052		Approved	VID24	uc002gsg.1	Q8IVV7	OTTHUMG00000059398	ENST00000268719.4:c.688T>A	chr17.hg19:g.17962263T>A	ENSP00000268719:p.Tyr230Asn	111.0	0.0	.		125.0	33.0	.	NM_024052	Q8TEB5|Q9BW50	Missense_Mutation	SNP	ENST00000268719.4	hg19	CCDS11190.1	.	.	.	.	.	.	.	.	.	.	T	15.99	2.995621	0.54147	.	.	ENSG00000141034	ENST00000268719	.	.	.	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.55862	0.1947	L	0.48642	1.525	0.80722	D	1	B	0.24317	0.101	B	0.20184	0.028	T	0.51387	-0.8712	9	0.23302	T	0.38	-15.1166	16.1549	0.81657	0.0:0.0:0.0:1.0	.	230	Q8IVV7	CQ039_HUMAN	N	230	.	ENSP00000268719:Y230N	Y	+	1	0	C17orf39	17902988	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	7.797000	0.85911	2.209000	0.71365	0.533000	0.62120	TAC	.	.	.	none		0.458	GID4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132071.2	NM_024052		A	17962263	T	A	17962263	3	1	211	1	0	0	0	0	1	0	0	0	1857	1522	53	5	702	5	C17orf39	17	17962263	Missense_Mutation	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10		17962263	63232947	46	12875											
TOP2A	7153	hgsc.bcm.edu	37	chr17	38562843	38562844	+	Frame_Shift_Ins	INS	-	-	T																															ttcattacaaacctttgtaaINStatttgactttccatttttt																										TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr17:38562843_38562844insT	ENST00000423485.1	-	15	1993_1994	c.1835_1836insA	c.(1834-1836)tatfs	p.Y612fs		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	612					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)	AACCTTTGTAATATTTGACTTT	0.317																																					p.Y612_Y613delinsX		Atlas-Indel,Pindel	.											.	TOP2A	124	.	0			c.1836_1837insA						PASS	.																																			SO:0001589	frameshift_variant	7153	exon15			.		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.1836dupA	chr17.hg19:g.38562844_38562844dupT	ENSP00000411532:p.Tyr612fs	103.0	0.0	0		70.0	31.0	0.442857	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Frame_Shift_Ins	INS	ENST00000423485.1	hg19	CCDS45672.1																																																																																			.	.	.	none		0.317	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1			T	38562844	-	T	38562843	7	5	211	1	0	1	1	0	0	0	0	0	16377	108	4	0	2843	0	TOP2A	17	38562843	Frame_Shift_Ins	INS	-	TCGA-IZ-A6M8-01A-11D-A31X-10	20600580	38562843	42632367	47	12876											
TEX14	56155	hgsc.bcm.edu	37	chr17	56676917	56676918	+	Frame_Shift_Del	DEL	GA	GA	-																															cataaatggagcagggcaagGagcatcttgattctgagtct																										TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr17:56676917_56676918delGA	ENST00000240361.8	-	14	1891_1892	c.1806_1807delTC	c.(1804-1809)gctcctfs	p.P603fs	TEX14_ENST00000349033.5_Frame_Shift_Del_p.P597fs|TEX14_ENST00000389934.3_Frame_Shift_Del_p.P597fs			Q8IWB6	TEX14_HUMAN	testis expressed 14	603					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GCAGGGCAAGGAGCATCTTGAT	0.53																																					p.603_603del		Atlas-Indel,Pindel	.											.	TEX14	343	.	0			c.1807_1808del						PASS	.																																			SO:0001589	frameshift_variant	56155	exon14			.	AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"cancer/testis antigen 113"	605792	"testis expressed sequence 14"			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.1806_1807delTC	chr17.hg19:g.56676917_56676918delGA	ENSP00000240361:p.Pro603fs	62.0	0.0	0		81.0	35.0	0.432099	NM_001201457	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Frame_Shift_Del	DEL	ENST00000240361.8	hg19	CCDS56042.1																																																																																			.	.	.	none		0.53	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1			-	56676918	GA	-	56676917	7	5	211	1	0	1	0	1	0	0	0	0	15790	1174	41	0	2766	0	TEX14	17	56676917	Frame_Shift_Del	DEL	GA	TCGA-IZ-A6M8-01A-11D-A31X-10	18114074	56676917	24518293	48	12877											
FASN	2194	hgsc.bcm.edu	37	chr17	80047603	80047603	+	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	acactcctcccaggacaagcCtatggcagagccagcctcag	11	5	9	16	0	1	1	1	0	0	1	3	2	3	2	5	2	3	1	5	2	2	1			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr17:80047603C>G	ENST00000306749.2	-	12	2089		c.e12-1			NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase						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)	CAGGACAAGCCTATGGCAGAG	0.652																																					.	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.1871-1G>C						PASS	.						16	15	16					17																	80047603		2171	4272	6443	SO:0001630	splice_region_variant	2194	exon13			ACAAGCCTATGGC	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.1871-1G>C	chr17.hg19:g.80047603C>G		84.0	0.0	.		92.0	15.0	.	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Splice_Site	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	C	15.55	2.865470	0.51588	.	.	ENSG00000169710	ENST00000306749	.	.	.	4.4	4.4	0.53042	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.9623	0.86275	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	FASN	77640892	1.000000	0.71417	0.168000	0.22838	0.067000	0.16453	5.505000	0.66981	1.997000	0.58415	0.561000	0.74099	.	.	.	.	none		0.652	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104	Intron	G	80047603	C	G	80047603	5	3	211	1	0	0	0	0	0	0	1	0	5690	695	24	4	5793	4	FASN	17	80047603	Splice_Site	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	23370686	80047603	1147607	49	12878											
ANKRD29	147463	hgsc.bcm.edu	37	chr18	21214112	21214112	+	Splice_Site	DEL	T	T	-																															ccaacagggcggtgcccccgTcctatggacatgcaaagtat																										TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr18:21214112delT	ENST00000592179.1	-	5	486	c.332delA	c.(331-333)gac>gc	p.D111fs	ANKRD29_ENST00000284207.7_Splice_Site_p.D111fs|ANKRD29_ENST00000322980.9_Splice_Site_p.D111fs	NM_173505.2	NP_775776.2	Q8N6D5	ANR29_HUMAN	ankyrin repeat domain 29	111										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)					GGTGCCCCCGTCCTATGGACA	0.498																																					p.D111fs		Atlas-INDEL	.											.	ANKRD29	24	.	0			c.333delC						PASS	.						74	59	64					18																	21214112		2203	4300	6503	SO:0001630	splice_region_variant	147463	exon5			.	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.331-1A>-	chr18.hg19:g.21214112delT		55.0	0.0	0		53.0	16.0	0.301887	NM_173505	B2R972|Q6ZWE8|Q96LU9	Frame_Shift_Del	DEL	ENST00000592179.1	hg19	CCDS11879.1																																																																																			.	.	.	none		0.498	ANKRD29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254825.1	NM_173505	Frame_Shift_Del	-	21214112	T	-	21214112	8	5	211	1	0	1	0	1	0	0	1	0	657	1681	58	0	597	0	ANKRD29	18	21214112	Splice_Site	DEL	T	TCGA-IZ-A6M8-01A-11D-A31X-10		21214112	56863136	50	12879											
MUC16	94025	hgsc.bcm.edu	37	chr19	9057871	9057871	+	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	cctagtctcagagaaggcagGatttgatgtgaaaacagtgg	13	9	13	6	0	1	3	1	2	1	1	2	5	1	4	1	3	1	1	1	3	4	2			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr19:9057871G>A	ENST00000397910.4	-	3	29778	c.29575C>T	c.(29575-29577)Cct>Tct	p.P9859S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9861	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						GAGAAGGCAGGATTTGATGTG	0.478																																					p.P9859S		Atlas-SNP	.											.	MUC16	4315	.	0			c.C29575T						PASS	.						147	138	141					19																	9057871		1987	4169	6156	SO:0001583	missense	94025	exon3			AGGCAGGATTTGA	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.29575C>T	chr19.hg19:g.9057871G>A	ENSP00000381008:p.Pro9859Ser	140.0	0.0	.		123.0	36.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	3.787	-0.044427	0.07452	.	.	ENSG00000181143	ENST00000397910	T	0.26223	1.75	2.62	0.396	0.16309	.	.	.	.	.	T	0.23330	0.0564	N	0.14661	0.345	.	.	.	D	0.54207	0.965	P	0.59703	0.862	T	0.26503	-1.0101	8	0.87932	D	0	.	3.8274	0.08859	0.1494:0.2545:0.5961:0.0	.	9859	B5ME49	.	S	9859	ENSP00000381008:P9859S	ENSP00000381008:P9859S	P	-	1	0	MUC16	8918871	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-1.124000	0.03260	0.181000	0.19994	-1.109000	0.02080	CCT	.	.	.	none		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9057871	G	A	9057871	3	1	211	1	0	0	0	0	1	0	0	0	9980	1174	41	2	14276	2	MUC16	19	9057871	Missense_Mutation	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10		9057871	50071112	51	12880											
ZNF45	7596	hgsc.bcm.edu	37	chr19	44419046	44419046	+	Missense_Mutation	SNP	A	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	ctgcatgagccctttggttaAtttgaagatgagagctccag	10	12	11	8	0	0	4	0	3	0	2	1	5	1	4	2	1	3	3	2	1	2	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr19:44419046A>C	ENST00000269973.5	-	10	1632	c.542T>G	c.(541-543)aTt>aGt	p.I181S	ZNF45_ENST00000589703.1_Missense_Mutation_p.I181S|RP11-15A1.2_ENST00000586247.1_RNA	NM_003425.3	NP_003416.1	Q02386	ZNF45_HUMAN	zinc finger protein 45	181					gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	17						CCTTTGGTTAATTTGAAGATG	0.443																																					p.I181S		Atlas-SNP	.											.	ZNF45	51	.	0			c.T542G						PASS	.						126	128	127					19																	44419046		2203	4300	6503	SO:0001583	missense	7596	exon10			TGGTTAATTTGAA	M67509	CCDS12632.1	19q13.2	2013-01-08	2005-01-11			ENSG00000124459		"Zinc fingers, C2H2-type", "-"	13111	protein-coding gene	gene with protein product		194554	"zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide)", "zinc finger protein 13"	ZNF13		9067431	Standard	NM_003425		Approved		uc002oxw.2	Q02386		ENST00000269973.5:c.542T>G	chr19.hg19:g.44419046A>C	ENSP00000269973:p.Ile181Ser	86.0	0.0	.		74.0	25.0	.	NM_003425	P17016|P78472|Q9P1U9	Missense_Mutation	SNP	ENST00000269973.5	hg19	CCDS12632.1	.	.	.	.	.	.	.	.	.	.	A	6.279	0.419509	0.11928	.	.	ENSG00000124459	ENST00000269973;ENST00000328762	T	0.15139	2.45	3.91	-3.04	0.05412	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	2.004110	0.02863	N	0.130523	T	0.07279	0.0184	N	0.13299	0.325	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.18178	-1.0345	10	0.08179	T	0.78	0.9799	0.481	0.00547	0.3318:0.133:0.2741:0.2611	.	181	Q02386	ZNF45_HUMAN	S	181	ENSP00000269973:I181S	ENSP00000269973:I181S	I	-	2	0	ZNF45	49110886	0.000000	0.05858	0.000000	0.03702	0.251000	0.25915	-5.448000	0.00121	-0.856000	0.04120	0.260000	0.18958	ATT	.	.	.	none		0.443	ZNF45-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459919.1	NM_003425		C	44419046	A	C	44419046	3	2	211	1	0	0	0	0	1	0	0	0	17933	101	4	5	1510	5	ZNF45	19	44419046	Missense_Mutation	SNP	A	TCGA-IZ-A6M8-01A-11D-A31X-10	35361175	44419046	14709937	52	12881											
ZNF534	147658	hgsc.bcm.edu	37	chr19	52941044	52941044	+	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	cacttaaaaatcaacatggaTtaactcttcagttacatctg	15	13	4	9	0	4	0	2	0	2	0	4	1	4	1	0	1	3	1	0	1	6	4			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr19:52941044T>A	ENST00000332323.6	+	4	431	c.370T>A	c.(370-372)Tta>Ata	p.L124I	ZNF534_ENST00000301085.4_Intron|ZNF534_ENST00000432303.2_Intron|ZNF534_ENST00000433050.1_Missense_Mutation_p.L111I	NM_001143939.1	NP_001137411.1	Q76KX8	ZN534_HUMAN	zinc finger protein 534	124					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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						TCAACATGGATTAACTCTTCA	0.353																																					p.L124I		Atlas-SNP	.											.	ZNF534	105	.	0			c.T370A						PASS	.						71	60	63					19																	52941044		1568	3582	5150	SO:0001583	missense	147658	exon4			CATGGATTAACTC	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.370T>A	chr19.hg19:g.52941044T>A	ENSP00000327538:p.Leu124Ile	455.0	0.0	.		257.0	82.0	.	NM_001143939	Q76KX9	Missense_Mutation	SNP	ENST00000332323.6	hg19	CCDS46165.1	.	.	.	.	.	.	.	.	.	.	T	9.193	1.026520	0.19512	.	.	ENSG00000198633	ENST00000332323;ENST00000433050;ENST00000391790	T;T	0.07444	3.19;3.23	1.69	1.69	0.24217	.	.	.	.	.	T	0.11750	0.0286	M	0.62723	1.935	0.09310	N	1	P;P	0.44344	0.833;0.524	P;B	0.45276	0.475;0.095	T	0.14309	-1.0477	9	0.45353	T	0.12	.	6.6481	0.22947	0.0:0.0:0.0:1.0	.	111;124	Q76KX8-2;Q76KX8	.;ZN534_HUMAN	I	124;111;123	ENSP00000327538:L124I;ENSP00000391358:L111I	ENSP00000327538:L124I	L	+	1	2	ZNF534	57632856	0.001000	0.12720	0.012000	0.15200	0.302000	0.27658	-0.032000	0.12266	0.751000	0.32900	0.172000	0.16884	TTA	.	.	.	none		0.353	ZNF534-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460877.1	NM_182512		A	52941044	T	A	52941044	3	1	211	1	0	0	0	0	1	0	0	0	17985	1490	52	5	384	5	ZNF534	19	52941044	Missense_Mutation	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10	8521998	52941044	6187939	53	12882											
CRNKL1	51340	hgsc.bcm.edu	37	chr20	20033152	20033152	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcgcttgagccgtgacggaGgcggcaccgtttccatggtg	5	9	15	12	5	0	2	0	2	0	0	2	3	1	3	3	4	1	3	3	4	0	2	rs140622884		TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr20:20033152G>A	ENST00000377340.2	-	2	349	c.318C>T	c.(316-318)gcC>gcT	p.A106A	C20orf26_ENST00000245957.5_5'Flank|CRNKL1_ENST00000377327.4_Silent_p.A94A|C20orf26_ENST00000377309.2_5'Flank|C20orf26_ENST00000389656.3_5'Flank|C20orf26_ENST00000377306.1_5'Flank|CRNKL1_ENST00000536226.1_5'Flank	NM_001278628.1|NM_016652.4	NP_001265557.1|NP_057736.4	Q9BZJ0	CRNL1_HUMAN	crooked neck pre-mRNA splicing factor 1	106					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						CCGTGACGGAGGCGGCACCGT	0.607																																					p.A106A		Atlas-SNP	.											.	CRNKL1	101	.	0			c.C318T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	74	70	71		318	-9	0	20	dbSNP_134	71	0,8600		0,0,4300	no	coding-synonymous	CRNKL1	NM_016652.4		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		106/849	20033152	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	51340	exon2			GACGGAGGCGGCA	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.318C>T	chr20.hg19:g.20033152G>A		86.0	0.0	.		131.0	38.0	.	NM_016652	A8K9T4|Q5JY64|Q8WYI5|Q9BZI9|Q9BZJ1|Q9BZJ2|Q9GZW7|Q9H8F8|Q9NQH5|Q9NYD8	Silent	SNP	ENST00000377340.2	hg19	CCDS33446.1																																																																																			.	G|1.000;A|0.000	0.000	weak		0.607	CRNKL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000127787.1			A	20033152	G	A	20033152	2	1	211	1	0	0	0	0	0	0	0	1	3893	987	35	2		2	CRNKL1	20	20033152	Silent	SNP	G	TCGA-IZ-A6M8-01A-11D-A31X-10		20033152	42992368	54	12883											
TM9SF4	9777	hgsc.bcm.edu	37	chr20	30730877	30730877	+	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	acgtaccgtgtcgtccgcttCgaggtgattccccagagcat	7	10	11	13	5	0	2	0	1	0	1	4	3	2	2	4	1	2	3	4	1	1	3			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chr20:30730877C>T	ENST00000398022.2	+	6	856	c.621C>T	c.(619-621)ttC>ttT	p.F207F	TM9SF4_ENST00000217315.5_Silent_p.F190F	NM_014742.3	NP_055557.2	Q92544	TM9S4_HUMAN	transmembrane 9 superfamily protein member 4	207						integral component of membrane (GO:0016021)				central_nervous_system(2)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			TCGTCCGCTTCGAGGTGATTC	0.597																																					p.F207F		Atlas-SNP	.											TM9SF4,NS,carcinoma,0,1	TM9SF4	65	.	0			c.C621T						PASS	.						151	107	122					20																	30730877		2203	4300	6503	SO:0001819	synonymous_variant	9777	exon6			CCGCTTCGAGGTG	BC021107	CCDS13196.2	20q11.21	2004-04-19			ENSG00000101337	ENSG00000101337			30797	protein-coding gene	gene with protein product						9039502	Standard	NM_014742		Approved	KIAA0255, dJ836N17.2	uc002wxj.2	Q92544	OTTHUMG00000032206	ENST00000398022.2:c.621C>T	chr20.hg19:g.30730877C>T		97.0	0.0	.		69.0	17.0	.	NM_014742	B0QYT7|Q9NUA3	Silent	SNP	ENST00000398022.2	hg19	CCDS13196.2																																																																																			.	.	.	none		0.597	TM9SF4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323568.1	NM_014742		T	30730877	C	T	30730877	2	4	211	1	0	0	0	0	0	0	0	1	15992	883	31	1		1	TM9SF4	20	30730877	Silent	SNP	C	TCGA-IZ-A6M8-01A-11D-A31X-10	10697725	30730877	32294643	55	12884											
ATP7A	538	hgsc.bcm.edu	37	chrX	77268391	77268391	+	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	tgcagtttttcggaggctggTacttctacattcaggcttat	7	16	10	8	1	2	0	1	0	1	0	3	1	2	1	0	4	3	5	0	4	3	7			TCGA-IZ-A6M8-01A-11D-A31X-10	TCGA-IZ-A6M8-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4dfdbda6-c66f-4c67-8b66-e44364185d82	63f41eeb-2753-4768-a87a-f24b16256074	g.chrX:77268391T>A	ENST00000341514.6	+	10	2343	c.2188T>A	c.(2188-2190)Tac>Aac	p.Y730N	ATP7A_ENST00000343533.5_Intron|ATP7A_ENST00000350425.4_Intron	NM_000052.5	NP_000043.4	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	730					blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cartilage development (GO:0051216)|catecholamine metabolic process (GO:0006584)|cellular copper ion homeostasis (GO:0006878)|central nervous system neuron development (GO:0021954)|cerebellar Purkinje cell differentiation (GO:0021702)|collagen fibril organization (GO:0030199)|copper ion export (GO:0060003)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detoxification of copper ion (GO:0010273)|dopamine metabolic process (GO:0042417)|elastic fiber assembly (GO:0048251)|elastin biosynthetic process (GO:0051542)|epinephrine metabolic process (GO:0042414)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|lung alveolus development (GO:0048286)|mitochondrion organization (GO:0007005)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of neuron apoptotic process (GO:0043524)|neuron projection morphogenesis (GO:0048812)|norepinephrine biosynthetic process (GO:0042421)|norepinephrine metabolic process (GO:0042415)|peptidyl-lysine modification (GO:0018205)|pigmentation (GO:0043473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|pyramidal neuron development (GO:0021860)|regulation of gene expression (GO:0010468)|regulation of oxidative phosphorylation (GO:0002082)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|response to iron(III) ion (GO:0010041)|response to zinc ion (GO:0010043)|serotonin metabolic process (GO:0042428)|skin development (GO:0043588)|T-helper cell differentiation (GO:0042093)|transmembrane transport (GO:0055085)|tryptophan metabolic process (GO:0006568)|tyrosine metabolic process (GO:0006570)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|copper-dependent protein binding (GO:0032767)|copper-exporting ATPase activity (GO:0004008)|superoxide dismutase copper chaperone activity (GO:0016532)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(26)|pancreas(1)|prostate(1)|urinary_tract(1)	53					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	CGGAGGCTGGTACTTCTACAT	0.343																																					p.Y730N		Atlas-SNP	.											.	ATP7A	248	.	0			c.T2188A						PASS	.						139	122	127					X																	77268391		2203	4296	6499	SO:0001583	missense	538	exon10			GGCTGGTACTTCT	L06133	CCDS35339.1, CCDS75997.1	Xq21.1	2012-10-22	2008-07-31		ENSG00000165240	ENSG00000165240	3.6.3.4	"ATPases / P-type"	869	protein-coding gene	gene with protein product	"copper pump 1", "copper-transporting ATPase 1"	300011	"Menkes syndrome"	MNK		10079817	Standard	NM_000052		Approved		uc004ecx.4	Q04656	OTTHUMG00000021885	ENST00000341514.6:c.2188T>A	chrX.hg19:g.77268391T>A	ENSP00000345728:p.Tyr730Asn	48.0	0.0	.		38.0	22.0	.	NM_000052	B1AT72|O00227|O00745|Q9BYY8	Missense_Mutation	SNP	ENST00000341514.6	hg19	CCDS35339.1	.	.	.	.	.	.	.	.	.	.	T	17.13	3.309564	0.60414	.	.	ENSG00000165240	ENST00000341514	T	0.75938	-0.98	5.64	-1.38	0.09027	.	0.505078	0.21943	N	0.066860	T	0.73345	0.3575	L	0.51422	1.61	0.80722	D	1	P	0.38729	0.644	P	0.48654	0.585	T	0.71629	-0.4535	10	0.59425	D	0.04	-15.6701	11.7399	0.51786	0.0:0.5586:0.0:0.4414	.	730	Q04656	ATP7A_HUMAN	N	730	ENSP00000345728:Y730N	ENSP00000345728:Y730N	Y	+	1	0	ATP7A	77155047	1.000000	0.71417	0.995000	0.50966	0.993000	0.82548	0.785000	0.26830	-0.249000	0.09569	0.381000	0.24937	TAC	.	.	.	none		0.343	ATP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057306.1	NM_000052		A	77268391	T	A	77268391	3	1	211	1	0	0	0	0	1	0	0	0	1190	1638	57	5	2222	5	ATP7A	23	77268391	Missense_Mutation	SNP	T	TCGA-IZ-A6M8-01A-11D-A31X-10		77268391	78002169	56	12885											
CLSTN1	22883	hgsc.bcm.edu	37	chr1	9809529	9809529	+	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	gtctccttaccacagagccgGtggagggacttctctgagta	8	10	12	11	1	2	2	0	1	2	1	4	4	2	4	3	3	2	1	3	3	2	3			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr1:9809529G>A	ENST00000377298.4	-	7	1767	c.975C>T	c.(973-975)caC>caT	p.H325H	CLSTN1_ENST00000361311.4_Silent_p.H315H|CLSTN1_ENST00000377288.3_Silent_p.H325H	NM_001009566.1	NP_001009566.1	O94985	CSTN1_HUMAN	calsyntenin 1	325					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)|calcium ion binding (GO:0005509)|kinesin binding (GO:0019894)|X11-like protein binding (GO:0042988)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(9)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	36	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)		CACAGAGCCGGTGGAGGGACT	0.557																																					p.H325H		Atlas-SNP	.											.	CLSTN1	88	.	0			c.C975T						PASS	.						100	102	101					1																	9809529		2203	4300	6503	SO:0001819	synonymous_variant	22883	exon7			GAGCCGGTGGAGG	AB020718	CCDS105.1, CCDS30580.1	1p36.22	2011-07-01			ENSG00000171603	ENSG00000171603		"Cadherins / Cadherin-related"	17447	protein-coding gene	gene with protein product	"cadherin-related family member 12"	611321				10048485	Standard	XM_005263432		Approved	CSTN1, KIAA0911, CDHR12	uc001aqh.3	O94985	OTTHUMG00000001451	ENST00000377298.4:c.975C>T	chr1.hg19:g.9809529G>A		89.0	0.0	.		74.0	32.0	.	NM_001009566	A8K183|Q5SR52|Q5UE58|Q71MN0|Q8N4K9	Silent	SNP	ENST00000377298.4	hg19	CCDS30580.1																																																																																			.	.	.	none		0.557	CLSTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004239.1			A	9809529	G	A	9809529	2	1	212	1	0	0	0	0	0	0	0	1	3563	1252	44	2		2	CLSTN1	1	9809529	Silent	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10		9809529	239441092	1	12886											
CSDE1	7812	hgsc.bcm.edu	37	chr1	115277116	115277116	+	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	ttgtttctttttcaacagcaTaatgttgcgagcacttacag	10	16	7	8	1	2	0	1	0	1	0	2	1	2	0	0	0	5	4	0	0	3	7	rs200868850		TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr1:115277116T>A	ENST00000358528.4	-	7	955	c.529A>T	c.(529-531)Atg>Ttg	p.M177L	CSDE1_ENST00000369530.1_Missense_Mutation_p.M192L|CSDE1_ENST00000438362.2_Missense_Mutation_p.M223L|CSDE1_ENST00000339438.6_Missense_Mutation_p.M146L|CSDE1_ENST00000261443.5_Missense_Mutation_p.M146L|CSDE1_ENST00000534699.1_Missense_Mutation_p.M177L|CSDE1_ENST00000530886.1_Missense_Mutation_p.M47L	NM_001007553.2	NP_001007554.1	O75534	CSDE1_HUMAN	cold shock domain containing E1, RNA-binding	177	CSD 2; truncated.				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)		TTCAACAGCATAATGTTGCGA	0.388																																					p.M223L		Atlas-SNP	.											.	CSDE1	145	.	0			c.A667T						PASS	.						80	80	80					1																	115277116		2203	4300	6503	SO:0001583	missense	7812	exon8			ACAGCATAATGTT		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.529A>T	chr1.hg19:g.115277116T>A	ENSP00000351329:p.Met177Leu	389.0	0.0	.		295.0	34.0	.	NM_001242891	A8K281|E9PGZ0|G5E9Q2|O94961|Q5TF04|Q5TF05|Q68DF1|Q68DI9|Q9Y2S4	Missense_Mutation	SNP	ENST00000358528.4	hg19	CCDS30812.1	.	.	.	.	.	.	.	.	.	.	T	15.16	2.752407	0.49362	.	.	ENSG00000009307	ENST00000339438;ENST00000438362;ENST00000358528;ENST00000261443;ENST00000530886;ENST00000369530;ENST00000534699;ENST00000529046	.	.	.	5.82	4.67	0.58626	Nucleic acid-binding, OB-fold-like (1);	0.141721	0.64402	D	0.000006	T	0.42337	0.1198	L	0.29908	0.895	0.36744	D	0.882387	B;B;B	0.29805	0.04;0.0;0.257	B;B;P	0.44623	0.008;0.0;0.455	T	0.48198	-0.9056	9	0.42905	T	0.14	-0.4958	13.0463	0.58928	0.0:0.0:0.1344:0.8656	.	192;177;223	E9PGZ0;O75534;G5E9Q2	.;CSDE1_HUMAN;.	L	146;223;177;146;47;192;177;47	.	ENSP00000261443:M146L	M	-	1	0	CSDE1	115078639	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.781000	0.55394	0.999000	0.39023	0.460000	0.39030	ATG	.	.	.	alt		0.388	CSDE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033397.1	NM_007158		A	115277116	T	A	115277116	3	1	212	1	0	0	0	0	1	0	0	0	3931	1406	49	5	1923	5	CSDE1	1	115277116	Missense_Mutation	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10	105467587	115277116	133973505	2	12887											
RPRD2	23248	hgsc.bcm.edu	37	chr1	150443766	150443766	+	Missense_Mutation	SNP	A	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	agatgaaagctacccccgagAgctctccaattctgtatcta	12	10	7	12	1	3	3	0	1	3	2	4	4	3	3	3	0	3	3	3	0	5	4			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr1:150443766A>C	ENST00000369068.4	+	11	2346	c.2342A>C	c.(2341-2343)gAg>gCg	p.E781A	RPRD2_ENST00000539519.1_Missense_Mutation_p.E755A|RPRD2_ENST00000492220.1_3'UTR|RPRD2_ENST00000401000.4_Missense_Mutation_p.E755A	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	781	Ser-rich.					DNA-directed RNA polymerase II, holoenzyme (GO:0016591)				central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						TACCCCCGAGAGCTCTCCAAT	0.498																																					p.E781A		Atlas-SNP	.											.	RPRD2	189	.	0			c.A2342C						PASS	.						84	79	81					1																	150443766		1895	4111	6006	SO:0001583	missense	23248	exon11			CCCGAGAGCTCTC	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.2342A>C	chr1.hg19:g.150443766A>C	ENSP00000358064:p.Glu781Ala	127.0	0.0	.		109.0	43.0	.	NM_015203	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Missense_Mutation	SNP	ENST00000369068.4	hg19	CCDS44216.1	.	.	.	.	.	.	.	.	.	.	A	18.04	3.534839	0.64972	.	.	ENSG00000163125	ENST00000401000;ENST00000539519;ENST00000369068	T;T;T	0.53206	0.63;0.63;0.63	5.21	5.21	0.72293	.	0.000000	0.64402	D	0.000001	T	0.22781	0.0550	N	0.24115	0.695	0.32162	N	0.582853	B;P;P	0.46784	0.319;0.816;0.884	B;B;B	0.40477	0.048;0.177;0.33	T	0.14035	-1.0487	10	0.59425	D	0.04	-7.9453	15.2872	0.73835	1.0:0.0:0.0:0.0	.	755;781;755	B4E2Q6;Q5VT52;Q5VT52-3	.;RPRD2_HUMAN;.	A	755;755;781	ENSP00000383785:E755A;ENSP00000445482:E755A;ENSP00000358064:E781A	ENSP00000358064:E781A	E	+	2	0	RPRD2	148710390	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.543000	0.73874	2.194000	0.70268	0.529000	0.55759	GAG	.	.	.	none		0.498	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203		C	150443766	A	C	150443766	3	2	212	1	0	0	0	0	1	0	0	0	13630	304	11	5	2384	5	RPRD2	1	150443766	Missense_Mutation	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10	35166650	150443766	98806855	3	12888											
KIAA1614	57710	hgsc.bcm.edu	37	chr1	180885446	180885457	+	In_Frame_Del	DEL	TCCCAGGGTATG	TCCCAGGGTATG	-																															agcctgatggccccccagccTcccagggtatggggagtaca																								rs377550267		TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	TCCCAGGGTATG	TCCCAGGGTATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr1:180885446_180885457delTCCCAGGGTATG	ENST00000367588.4	+	2	262_273	c.207_218delTCCCAGGGTATG	c.(205-219)cctcccagggtatgg>ccg	p.PRVW70del		NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	70										NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						CCCCCCAGCCTCCCAGGGTATGGGGAGTACAG	0.599																																					p.69_73del		Atlas-Indel,Pindel	.											KIAA1614,NS,chondrosarcoma,0,1	KIAA1614	75	.	0			c.206_217del						PASS	.																																			SO:0001651	inframe_deletion	57710	exon2			.	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.207_218delTCCCAGGGTATG	chr1.hg19:g.180885446_180885457delTCCCAGGGTATG	ENSP00000356560:p.Pro70_Trp73del	67.0	0.0	0		53.0	17.0	0.320755	NM_020950	Q5VZ45|Q9HCF8	In_Frame_Del	DEL	ENST00000367588.4	hg19	CCDS41442.1																																																																																			.	.	.	none		0.599	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531		-	180885457	TCCCAGGGTATG	-	180885446	7	5	212	1	0	1	0	1	0	0	0	0	8255	1538	54	0	213	0	KIAA1614	1	180885446	In_Frame_Del	DEL	TCCCAGGGTATG	TCGA-IZ-A6M9-01A-11D-A31X-10	30441680	180885446	68365175	4	12889											
KDM5B	10765	hgsc.bcm.edu	37	chr1	202701002	202701002	+	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	gttgagaagggggagtgcaaAtatgaggttctgttgtccca	10	11	15	5	0	1	2	0	2	1	1	2	4	2	3	1	3	1	4	1	3	3	4			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr1:202701002A>C	ENST00000367265.3	-	24	5139	c.3975T>G	c.(3973-3975)taT>taG	p.Y1325*	KDM5B_ENST00000367264.2_Nonsense_Mutation_p.Y1361*	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	1325					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						GGGAGTGCAAATATGAGGTTC	0.408																																					p.Y1325X		Atlas-SNP	.											.	KDM5B	166	.	0			c.T3975G						PASS	.						111	106	108					1																	202701002		2203	4300	6503	SO:0001587	stop_gained	10765	exon24			GTGCAAATATGAG	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.3975T>G	chr1.hg19:g.202701002A>C	ENSP00000356234:p.Tyr1325*	61.0	0.0	.		70.0	21.0	.	NM_006618	O95811|Q15752|Q9Y3Q5	Nonsense_Mutation	SNP	ENST00000367265.3	hg19	CCDS30974.1	.	.	.	.	.	.	.	.	.	.	A	47	13.303743	0.99733	.	.	ENSG00000117139	ENST00000367265;ENST00000538292;ENST00000367264;ENST00000235790	.	.	.	5.78	3.41	0.39046	.	0.229878	0.47093	D	0.000247	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.4004	7.269	0.26246	0.7476:0.1297:0.1226:0.0	.	.	.	.	X	1325;1167;1361;1167	.	ENSP00000235790:Y1167X	Y	-	3	2	KDM5B	200967625	0.999000	0.42202	0.375000	0.26029	0.998000	0.95712	1.112000	0.31172	1.096000	0.41439	0.533000	0.62120	TAT	.	.	.	none		0.408	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618		C	202701002	A	C	202701002	4	2	212	1	0	0	0	0	0	1	0	0	8141	108	4	5	675	5	KDM5B	1	202701002	Nonsense_Mutation	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10	21815556	202701002	46549619	5	12890											
PLXNA2	5362	hgsc.bcm.edu	37	chr1	208234136	208234136	+	Missense_Mutation	SNP	A	A	T																															gacccaggttcacgccatggAtggtcactcgcgtccctcct																										TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr1:208234136A>T	ENST00000367033.3	-	13	3390	c.2633T>A	c.(2632-2634)aTc>aAc	p.I878N		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	878	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)		CACGCCATGGATGGTCACTCG	0.582																																					p.I878N		Atlas-SNP	.											.	PLXNA2	178	.	0			c.T2633A						PASS	.						64	59	60					1																	208234136		2203	4300	6503	SO:0001583	missense	5362	exon13			CCATGGATGGTCA	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.2633T>A	chr1.hg19:g.208234136A>T	ENSP00000356000:p.Ile878Asn	128.0	0.0	.		89.0	39.0	.	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	hg19	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.751914	0.89753	.	.	ENSG00000076356	ENST00000367033	T	0.70869	-0.52	4.75	4.75	0.60458	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.87744	0.6254	H	0.94847	3.59	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	D	0.91215	0.5002	10	0.87932	D	0	.	14.2819	0.66219	1.0:0.0:0.0:0.0	.	878	O75051	PLXA2_HUMAN	N	878	ENSP00000356000:I878N	ENSP00000356000:I878N	I	-	2	0	PLXNA2	206300759	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.956000	0.93066	1.787000	0.52448	0.533000	0.62120	ATC	.	.	.	none		0.582	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		T	208234136	A	T	208234136	3	4	212	1	0	0	0	0	1	0	0	0	12127	333	12	5	3131	5	PLXNA2	1	208234136	Missense_Mutation	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10	5533134	208234136	41016485	6	12891	127	2									
PLXNA2	5362	hgsc.bcm.edu	37	chr1	208234142	208234142	+	Missense_Mutation	SNP	A	A	G																															ggttcacgccatggatggtcActcgcgtccctccttccggc																										TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr1:208234142A>G	ENST00000367033.3	-	13	3384	c.2627T>C	c.(2626-2628)gTg>gCg	p.V876A		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	876	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)		ATGGATGGTCACTCGCGTCCC	0.587																																					p.V876A		Atlas-SNP	.											.	PLXNA2	178	.	0			c.T2627C						PASS	.						62	57	59					1																	208234142		2203	4300	6503	SO:0001583	missense	5362	exon13			ATGGTCACTCGCG	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.2627T>C	chr1.hg19:g.208234142A>G	ENSP00000356000:p.Val876Ala	121.0	0.0	.		84.0	38.0	.	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	hg19	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	A	29.5	5.008254	0.93346	.	.	ENSG00000076356	ENST00000367033	T	0.66815	-0.23	4.75	4.75	0.60458	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.81917	0.4924	M	0.91920	3.255	0.80722	D	1	D	0.54397	0.966	P	0.55824	0.785	D	0.86680	0.1916	10	0.87932	D	0	.	14.2819	0.66219	1.0:0.0:0.0:0.0	.	876	O75051	PLXA2_HUMAN	A	876	ENSP00000356000:V876A	ENSP00000356000:V876A	V	-	2	0	PLXNA2	206300765	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.956000	0.93066	1.787000	0.52448	0.533000	0.62120	GTG	.	.	.	none		0.587	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		G	208234142	A	G	208234142	3	3	212	1	0	0	0	0	1	0	0	0	12127	159	6	3	3137	3	PLXNA2	1	208234142	Missense_Mutation	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10	6	208234142	41016479	7	12892	127	2									
PTPN14	5784	hgsc.bcm.edu	37	chr1	214557537	214557537	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcttaagcatgtgggccgtgCtgtagttatggctgccctgc	5	13	13	10	1	1	0	0	0	1	0	1	0	1	0	2	2	4	5	2	2	3	3			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr1:214557537C>T	ENST00000366956.5	-	13	1855	c.1661G>A	c.(1660-1662)aGc>aAc	p.S554N	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	554					lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)			NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		GTGGGCCGTGCTGTAGTTATG	0.632																																					p.S554N	Colon(92;557 1424 24372 34121 40073)	Atlas-SNP	.											.	PTPN14	168	.	0			c.G1661A						PASS	.						67	69	68					1																	214557537		2203	4300	6503	SO:0001583	missense	5784	exon13			GCCGTGCTGTAGT	X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.1661G>A	chr1.hg19:g.214557537C>T	ENSP00000355923:p.Ser554Asn	61.0	0.0	.		50.0	20.0	.	NM_005401	Q5VSI0	Missense_Mutation	SNP	ENST00000366956.5	hg19	CCDS1514.1	.	.	.	.	.	.	.	.	.	.	C	5.545	0.285458	0.10513	.	.	ENSG00000152104	ENST00000366956	T	0.67523	-0.27	5.51	-1.94	0.07571	.	0.544215	0.22141	N	0.064056	T	0.36635	0.0974	N	0.11560	0.145	0.28282	N	0.923954	B	0.02656	0.0	B	0.01281	0.0	T	0.21759	-1.0236	10	0.14252	T	0.57	.	6.8274	0.23891	0.113:0.4191:0.0:0.468	.	554	Q15678	PTN14_HUMAN	N	554	ENSP00000355923:S554N	ENSP00000355923:S554N	S	-	2	0	PTPN14	212624160	0.001000	0.12720	0.056000	0.19401	0.764000	0.43329	-0.747000	0.04823	-0.259000	0.09432	0.650000	0.86243	AGC	.	.	.	none		0.632	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401		T	214557537	C	T	214557537	3	4	212	1	0	0	0	0	1	0	0	0	12794	797	28	2	1930	2	PTPN14	1	214557537	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	6323395	214557537	34693084	8	12893											
DNAJC5G	285126	hgsc.bcm.edu	37	chr2	27500675	27500675	+	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	gtatcacctgggtaggaaacTggccttgcggtatcatcccg	8	10	12	11	2	2	0	2	0	0	0	3	1	3	1	3	4	2	3	3	4	4	4			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr2:27500675T>A	ENST00000296097.3	+	4	585	c.167T>A	c.(166-168)cTg>cAg	p.L56Q	DNAJC5G_ENST00000404433.1_Missense_Mutation_p.L40Q|SLC30A3_ENST00000447008.2_5'Flank|DNAJC5G_ENST00000406962.1_Intron|DNAJC5G_ENST00000402462.1_Missense_Mutation_p.L56Q	NM_173650.1	NP_775921.1	Q8N7S2	DNJ5G_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 5 gamma	56	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.					membrane (GO:0016020)				cervix(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGTAGGAAACTGGCCTTGCGG	0.488																																					p.L56Q		Atlas-SNP	.											.	DNAJC5G	19	.	0			c.T167A						PASS	.						107	102	104					2																	27500675		2203	4300	6503	SO:0001583	missense	285126	exon4			GGAAACTGGCCTT	AF368277	CCDS1744.1	2p23	2011-09-02			ENSG00000163793	ENSG00000163793		"Heat shock proteins / DNAJ (HSP40)"	24844	protein-coding gene	gene with protein product		613946					Standard	NM_173650		Approved	FLJ40417, CSP-gamma	uc002rjl.1	Q8N7S2	OTTHUMG00000097079	ENST00000296097.3:c.167T>A	chr2.hg19:g.27500675T>A	ENSP00000296097:p.Leu56Gln	108.0	0.0	.		79.0	21.0	.	NM_173650	B4DY29|Q53SY5|Q8IYQ4|Q96RJ8	Missense_Mutation	SNP	ENST00000296097.3	hg19	CCDS1744.1	.	.	.	.	.	.	.	.	.	.	T	17.86	3.492169	0.64074	.	.	ENSG00000163793	ENST00000296097;ENST00000402462;ENST00000404433	T;T;T	0.46819	0.86;0.86;0.86	5.09	5.09	0.68999	Heat shock protein DnaJ, N-terminal (5);	0.000000	0.40554	N	0.001066	T	0.65780	0.2724	M	0.69248	2.105	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.69247	-0.5195	10	0.72032	D	0.01	.	12.8356	0.57771	0.0:0.0:0.0:1.0	.	56	Q8N7S2	DNJ5G_HUMAN	Q	56;56;40	ENSP00000296097:L56Q;ENSP00000384305:L56Q;ENSP00000385829:L40Q	ENSP00000296097:L56Q	L	+	2	0	DNAJC5G	27354179	1.000000	0.71417	1.000000	0.80357	0.243000	0.25628	7.834000	0.86773	1.926000	0.55796	0.455000	0.32223	CTG	.	.	.	none		0.488	DNAJC5G-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214200.1	NM_173650		A	27500675	T	A	27500675	3	1	212	1	0	0	0	0	1	0	0	0	4654	1580	55	5	173	5	DNAJC5G	2	27500675	Missense_Mutation	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10		27500675	215698698	9	12894											
POTEE	445582	hgsc.bcm.edu	37	chr2	131976330	131976330	+	Missense_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	gcggcaagagcaaggtgggcGcttggggagactacgatgac	10	5	18	8	3	0	3	0	1	0	2	0	5	0	3	0	5	2	3	0	5	3	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr2:131976330G>A	ENST00000356920.5	+	1	449	c.355G>A	c.(355-357)Gct>Act	p.A119T	PLEKHB2_ENST00000303908.3_Intron|PLEKHB2_ENST00000404460.1_Intron|POTEE_ENST00000358087.5_Missense_Mutation_p.A119T	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	119					retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											CAAGGTGGGCGCTTGGGGAGA	0.597																																					p.A119T		Atlas-SNP	.											.	.	.	.	0			c.G355A						PASS	.						121	119	120					2																	131976330		2203	4300	6503	SO:0001583	missense	445582	exon1			GTGGGCGCTTGGG	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.355G>A	chr2.hg19:g.131976330G>A	ENSP00000439189:p.Ala119Thr	239.0	0.0	.		230.0	80.0	.	NM_001083538	Q6S8J4|Q6S8J5|Q6S8J8	Missense_Mutation	SNP	ENST00000356920.5	hg19	CCDS46414.1	.	.	.	.	.	.	.	.	.	.	.	9.510	1.105419	0.20632	.	.	ENSG00000188219	ENST00000356920;ENST00000358087	T;T	0.76839	-1.05;1.61	0.399	0.399	0.16325	.	.	.	.	.	T	0.49983	0.1589	N	0.12746	0.255	0.09310	N	1	P	0.52463	0.953	B	0.32149	0.141	T	0.44236	-0.9341	8	0.36615	T	0.2	.	.	.	.	.	119	Q6S8J3	POTEE_HUMAN	T	119	ENSP00000439189:A119T;ENSP00000443049:A119T	ENSP00000439189:A119T	A	+	1	0	AC131180.1	131692800	0.000000	0.05858	0.002000	0.10522	0.009000	0.06853	-0.980000	0.03770	0.440000	0.26502	0.162000	0.16502	GCT	.	.	.	none		0.597	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538		A	131976330	G	A	131976330	3	1	212	1	0	0	0	0	1	0	0	0	12271	1087	38	1	357	1	POTEE	2	131976330	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	104475655	131976330	111223043	10	12895											
GPR39	2863	hgsc.bcm.edu	37	chr2	133403162	133403162	+	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	ctgctgcagagaatggttttCaggagcatgaagtttgaatg	11	12	13	5	0	1	3	1	2	0	1	1	5	1	4	0	2	3	5	0	2	3	3			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr2:133403162C>A	ENST00000329321.3	+	2	1814	c.1345C>A	c.(1345-1347)Cag>Aag	p.Q449K	LYPD1_ENST00000397463.2_3'UTR|GPR39_ENST00000470071.1_3'UTR	NM_001508.2	NP_001499.1	O43194	GPR39_HUMAN	G protein-coupled receptor 39	449					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						GAATGGTTTTCAGGAGCATGA	0.532																																					p.Q449K		Atlas-SNP	.											.	GPR39	60	.	0			c.C1345A						PASS	.						54	58	57					2																	133403162		2203	4300	6503	SO:0001583	missense	2863	exon2			GGTTTTCAGGAGC	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.1345C>A	chr2.hg19:g.133403162C>A	ENSP00000327417:p.Gln449Lys	58.0	0.0	.		64.0	30.0	.	NM_001508	B2RC12|B6V9G4|Q08AS2|Q53R01	Missense_Mutation	SNP	ENST00000329321.3	hg19	CCDS2170.1	.	.	.	.	.	.	.	.	.	.	C	0.009	-1.834578	0.00579	.	.	ENSG00000183840	ENST00000329321	T	0.65178	-0.14	5.15	3.18	0.36537	.	3.248910	0.01165	N	0.006739	T	0.56992	0.2023	L	0.57536	1.79	0.37755	D	0.926099	B	0.02656	0.0	B	0.01281	0.0	T	0.51741	-0.8667	10	0.16896	T	0.51	.	4.3592	0.11194	0.4322:0.446:0.0:0.1219	.	449	O43194	GPR39_HUMAN	K	449	ENSP00000327417:Q449K	ENSP00000327417:Q449K	Q	+	1	0	GPR39	133119632	0.326000	0.24669	0.628000	0.29241	0.050000	0.14768	0.714000	0.25808	1.393000	0.46605	-0.188000	0.12872	CAG	.	.	.	none		0.532	GPR39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254582.1			A	133403162	C	A	133403162	3	1	212	1	0	0	0	0	1	0	0	0	6700	827	29	4	1351	4	GPR39	2	133403162	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	1426832	133403162	109796211	11	12896											
NEB	4703	hgsc.bcm.edu	37	chr2	152382499	152382499	+	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	acatgcttggtcacttccttGacgtgaacagtgtcccgggt	7	12	11	11	2	1	2	1	2	0	0	3	2	3	2	2	2	2	1	2	2	1	3			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr2:152382499G>A	ENST00000172853.10	-	122	17178	c.17031C>T	c.(17029-17031)gtC>gtT	p.V5677V	NEB_ENST00000427231.2_Silent_p.V7378V|NEB_ENST00000409198.1_Silent_p.V5677V|NEB_ENST00000397345.3_Silent_p.V7378V|NEB_ENST00000603639.1_Silent_p.V7378V|NEB_ENST00000604864.1_Silent_p.V7378V			P20929	NEBU_HUMAN	nebulin	5677					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.V5677V(1)|p.V7378V(1)		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)		TCACTTCCTTGACGTGAACAG	0.483																																					p.V7413V		Atlas-SNP	.											NEB_ENST00000427231,NS,carcinoma,0,3	NEB	1697	.	2	Substitution - coding silent(2)	lung(2)	c.C22239T						PASS	.						300	294	296					2																	152382499		2038	4201	6239	SO:0001819	synonymous_variant	4703	exon151			TTCCTTGACGTGA	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.17031C>T	chr2.hg19:g.152382499G>A		126.0	0.0	.		102.0	25.0	.	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	hg19		.	.	.	.	.	.	.	.	.	.	G	10.46	1.355381	0.24512	.	.	ENSG00000183091	ENST00000434685	.	.	.	6.07	5.2	0.72013	.	.	.	.	.	T	0.63885	0.2549	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62756	-0.6787	4	.	.	.	.	12.0778	0.53653	0.0656:0.1214:0.813:0.0	.	.	.	.	L	1	.	.	S	-	2	0	NEB	152090745	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.792000	0.62467	1.582000	0.49881	0.655000	0.94253	TCA	.	.	.	none		0.483	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152382499	G	A	152382499	2	1	212	1	0	0	0	0	0	0	0	1	10309	1277	45	2		2	NEB	2	152382499	Silent	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	18979337	152382499	90816874	12	12897											
COL3A1	1281	hgsc.bcm.edu	37	chr2	189867767	189867767	+	Silent	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	cctcctggagttgcaggaccCcctggaggttctggacctgc	5	9	13	14	0	1	0	0	0	1	0	2	4	2	4	5	5	2	3	5	5	0	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr2:189867767C>T	ENST00000304636.3	+	36	2702	c.2532C>T	c.(2530-2532)ccC>ccT	p.P844P	COL3A1_ENST00000317840.5_Intron	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	844	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)	TTGCAGGACCCCCTGGAGGTT	0.493																																					p.P844P		Atlas-SNP	.											.	COL3A1	292	.	0			c.C2532T						PASS	.						51	61	58					2																	189867767		2068	4020	6088	SO:0001819	synonymous_variant	1281	exon36			AGGACCCCCTGGA	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.2532C>T	chr2.hg19:g.189867767C>T		103.0	0.0	.		79.0	26.0	.	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Silent	SNP	ENST00000304636.3	hg19	CCDS2297.1																																																																																			.	.	.	none		0.493	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		T	189867767	C	T	189867767	2	4	212	1	0	0	0	0	0	0	0	1	3690	610	22	2		2	COL3A1	2	189867767	Silent	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	37485268	189867767	53331606	13	12898											
SCHIP1	100505385	hgsc.bcm.edu	37	chr3	159606614	159606614	+	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	cctttgtatcttcagctgccAcacatgcctcatataagtga	10	13	6	12	0	3	1	2	1	1	0	3	1	3	1	3	0	3	2	3	0	3	5			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr3:159606614A>T	ENST00000460298.1	+	6	1321	c.1080A>T	c.(1078-1080)ccA>ccT	p.P360P	SCHIP1_ENST00000482804.1_Silent_p.P173P|IQCJ-SCHIP1_ENST00000337808.6_Silent_p.P400P|IQCJ-SCHIP1_ENST00000476809.1_Silent_p.P449P|IQCJ-SCHIP1_ENST00000527095.1_Silent_p.P168P|IQCJ-SCHIP1_ENST00000485419.1_Silent_p.P476P|SCHIP1_ENST00000445224.2_Silent_p.P157P|IQCJ-SCHIP1_ENST00000412423.2_Silent_p.P387P					IQCJ-SCHIP1 readthrough											central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(7)	12						TTCAGCTGCCACACATGCCTC	0.433																																					p.P476P		Atlas-SNP	.											.	IQCJ-SCHIP1	40	.	0			c.A1428T						PASS	.						138	130	132					3																	159606614		2203	4300	6503	SO:0001819	synonymous_variant	100505385	exon9			GCTGCCACACATG		CCDS56289.1, CCDS56291.1	3q25.33	2011-03-24			ENSG00000250588	ENSG00000250588			38842	other	readthrough							Standard	NM_001197113		Approved		uc003fcq.2		OTTHUMG00000162426	ENST00000460298.1:c.1080A>T	chr3.hg19:g.159606614A>T		92.0	0.0	.		81.0	63.0	.	NM_001197113		Silent	SNP	ENST00000460298.1	hg19																																																																																				.	.	.	none		0.433	IQCJ-SCHIP1-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000352558.2	NM_001197113		T	159606614	A	T	159606614	2	4	212	1	0	0	0	0	0	0	0	1	13917	146	6	5		5	SCHIP1	3	159606614	Silent	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10		159606614	38415816	14	12899											
FAM193A	8603	hgsc.bcm.edu	37	chr4	2632748	2632748	+	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	ggagatgaaggtccgcctgcTccggcagctgtcggctgcgg	5	7	17	12	4	0	2	0	1	0	1	3	3	2	2	3	5	3	4	3	5	1	0			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr4:2632748T>A	ENST00000324666.5	+	3	368	c.17T>A	c.(16-18)cTc>cAc	p.L6H	FAM193A_ENST00000545951.1_Missense_Mutation_p.L6H|FAM193A_ENST00000505311.1_Missense_Mutation_p.L6H|FAM193A_ENST00000382839.3_Missense_Mutation_p.L6H|FAM193A_ENST00000502458.1_Missense_Mutation_p.L6H	NM_001256666.1	NP_001243595.1	P78312	F193A_HUMAN	family with sequence similarity 193, member A	6										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						GTCCGCCTGCTCCGGCAGCTG	0.632																																					p.L6H		Atlas-SNP	.											.	FAM193A	103	.	0			c.T17A						PASS	.						42	45	44					4																	2632748		2202	4300	6502	SO:0001583	missense	8603	exon3			GCCTGCTCCGGCA	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.17T>A	chr4.hg19:g.2632748T>A	ENSP00000324587:p.Leu6His	76.0	0.0	.		60.0	18.0	.	NM_003704	B7ZM85|B9EGR0|E9PFA1|O43607|P78311|P78313|Q9UEG8	Missense_Mutation	SNP	ENST00000324666.5	hg19	CCDS58875.1	.	.	.	.	.	.	.	.	.	.	T	28.0	4.881897	0.91740	.	.	ENSG00000125386	ENST00000509050;ENST00000382839;ENST00000324666;ENST00000545951;ENST00000502458	T;T;T;T	0.53640	0.63;1.02;0.61;0.67	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.65460	0.2693	L	0.59436	1.845	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;0.996;0.999	T	0.68534	-0.5383	10	0.87932	D	0	-27.2496	14.8927	0.70620	0.0:0.0:0.0:1.0	.	6;6;6;6;6	B9EGR0;E9PFA1;P78312;B7ZM85;P78312-2	.;.;F193A_HUMAN;.;.	H	6	ENSP00000372290:L6H;ENSP00000324587:L6H;ENSP00000443617:L6H;ENSP00000427505:L6H	ENSP00000324587:L6H	L	+	2	0	FAM193A	2602546	1.000000	0.71417	0.996000	0.52242	0.879000	0.50718	7.680000	0.84062	2.108000	0.64289	0.533000	0.62120	CTC	.	.	.	none		0.632	FAM193A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360903.1	NM_003704		A	2632748	T	A	2632748	3	1	212	1	0	0	0	0	1	0	0	0	5528	1551	54	5	19	5	FAM193A	4	2632748	Missense_Mutation	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10		2632748	188521528	15	12900											
LNX1	84708	hgsc.bcm.edu	37	chr4	54343069	54343069	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgagtactatcgaggatgaTgttcttttcaataatgccac	11	15	8	7	1	2	2	1	2	1	0	3	4	2	3	1	1	2	2	1	1	4	7	rs151307935		TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr4:54343069T>C	ENST00000263925.7	-	9	2057	c.1743A>G	c.(1741-1743)acA>acG	p.T581T	LNX1_ENST00000306888.2_Silent_p.T485T|FIP1L1_ENST00000507166.1_Intron	NM_001126328.2	NP_001119800.1	Q8TBB1	LNX1_HUMAN	ligand of numb-protein X 1, E3 ubiquitin protein ligase	581	PDZ 3. {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)			TCGAGGATGATGTTCTTTTCA	0.512																																					p.T581T		Atlas-SNP	.											.	LNX1	139	.	0			c.A1743G						PASS	.						180	180	180					4																	54343069		2203	4300	6503	SO:0001819	synonymous_variant	84708	exon9			GGATGATGTTCTT	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.1743A>G	chr4.hg19:g.54343069T>C		69.0	0.0	.		46.0	21.0	.	NM_001126328	Q4W5K7|Q8N4C2|Q96MJ7|Q9BY20	Silent	SNP	ENST00000263925.7	hg19	CCDS47057.1																																																																																			.	T|1.000;G|0.000	.	alt		0.512	LNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219934.2			C	54343069	T	C	54343069	2	2	212	1	0	0	0	0	0	0	0	1	8872	1451	51	3		3	LNX1	4	54343069	Silent	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10	51710321	54343069	136811207	16	12901											
CEP135	9662	hgsc.bcm.edu	37	chr4	56876035	56876035	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaggaaaacagaagactgcAagatgacctggctacaatgg	17	6	11	7	0	0	4	0	1	0	3	0	5	0	5	1	3	3	2	1	3	7	2	rs148279836		TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr4:56876035A>G	ENST00000257287.4	+	19	2595	c.2471A>G	c.(2470-2472)cAa>cGa	p.Q824R		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	824					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)					AGAAGACTGCAAGATGACCTG	0.388																																					p.Q824R		Atlas-SNP	.											.	CEP135	115	.	0			c.A2471G						PASS	.	A	ARG/GLN	1,4405	2.1+/-5.4	0,1,2202	83	82	82		2471	5.5	1	4	dbSNP_134	82	0,8600		0,0,4300	no	missense	CEP135	NM_025009.3	43	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	probably-damaging	824/1141	56876035	1,13005	2203	4300	6503	SO:0001583	missense	9662	exon19			GACTGCAAGATGA	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.2471A>G	chr4.hg19:g.56876035A>G	ENSP00000257287:p.Gln824Arg	251.0	0.0	.		144.0	45.0	.	NM_025009	B2RMY0|O75130|Q58F25|Q9H8H7	Missense_Mutation	SNP	ENST00000257287.4	hg19	CCDS33986.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.375961	0.82682	2.27E-4	0.0	ENSG00000174799	ENST00000257287	T	0.09911	2.93	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.30854	0.0778	M	0.66939	2.045	0.58432	D	0.999998	D	0.89917	1.0	D	0.85130	0.997	T	0.01508	-1.1337	10	0.28530	T	0.3	.	15.8895	0.79286	1.0:0.0:0.0:0.0	.	824	Q66GS9	CP135_HUMAN	R	824	ENSP00000257287:Q824R	ENSP00000257287:Q824R	Q	+	2	0	CEP135	56570792	1.000000	0.71417	0.999000	0.59377	0.951000	0.60555	8.565000	0.90730	2.207000	0.71202	0.533000	0.62120	CAA	.	A|1.000;G|0.000	0.000	weak		0.388	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009		G	56876035	A	G	56876035	3	3	212	1	0	0	0	0	1	0	0	0	3249	130	5	3	2541	3	CEP135	4	56876035	Missense_Mutation	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10	2532966	56876035	134278241	17	12902											
DNAH8	1769	hgsc.bcm.edu	37	chr6	38825504	38825504	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccatgtgcatcagagagatAtttttgatgacttggtaagg	11	14	11	5	0	1	4	1	2	0	2	2	5	2	4	1	2	1	2	1	2	2	5			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr6:38825504A>G	ENST00000359357.3	+	40	5547	c.5293A>G	c.(5293-5295)Att>Gtt	p.I1765V	DNAH8_ENST00000449981.2_Missense_Mutation_p.I1982V|DNAH8_ENST00000441566.1_Missense_Mutation_p.I1765V			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1765					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						TCAGAGAGATATTTTTGATGA	0.308																																					p.I1982V		Atlas-SNP	.											.	DNAH8	1239	.	0			c.A5944G						PASS	.						110	106	107					6																	38825504		2203	4300	6503	SO:0001583	missense	1769	exon42			AGAGATATTTTTG	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.5293A>G	chr6.hg19:g.38825504A>G	ENSP00000352312:p.Ile1765Val	130.0	0.0	.		111.0	53.0	.	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	A	21.7	4.181365	0.78677	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.20332	2.09;2.09;2.08	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.21590	0.0520	L	0.46670	1.46	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.06862	-1.0803	10	0.02654	T	1	.	16.0707	0.80928	1.0:0.0:0.0:0.0	.	1765	Q96JB1	DYH8_HUMAN	V	1970;1970;1765;1765	ENSP00000333363:I1970V;ENSP00000352312:I1765V;ENSP00000402294:I1765V	ENSP00000333363:I1970V	I	+	1	0	DNAH8	38933482	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.271000	0.95698	2.194000	0.70268	0.533000	0.62120	ATT	.	.	.	none		0.308	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		G	38825504	A	G	38825504	3	3	212	1	0	0	0	0	1	0	0	0	4609	449	16	3	5443	3	DNAH8	6	38825504	Missense_Mutation	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10		38825504	132289563	18	12903											
EZR	7430	hgsc.bcm.edu	37	chr6	159188095	159188095	+	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	ctcatctcgggcctgggacaGctcgctgctcagcgtctgta	5	10	12	14	3	4	0	2	0	2	0	6	1	4	1	1	2	3	4	1	2	1	1	rs367907031		TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr6:159188095G>C	ENST00000367075.3	-	14	1780	c.1612C>G	c.(1612-1614)Ctg>Gtg	p.L538V	EZR_ENST00000337147.7_Missense_Mutation_p.L538V|EZR_ENST00000392177.4_Missense_Mutation_p.L506V|MIR3918_ENST00000581555.1_RNA	NM_001111077.1	NP_001104547.1	P15311	EZRI_HUMAN	ezrin	538	Interaction with SCYL3.				actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of endothelial barrier (GO:0061028)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|filopodium assembly (GO:0046847)|leukocyte cell-cell adhesion (GO:0007159)|membrane to membrane docking (GO:0022614)|positive regulation of gene expression (GO:0010628)|receptor internalization (GO:0031623)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|astrocyte projection (GO:0097449)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell tip (GO:0051286)|ciliary basal body (GO:0036064)|cortical cytoskeleton (GO:0030863)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|microspike (GO:0044393)|microvillus (GO:0005902)|microvillus membrane (GO:0031528)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|Schwann cell microvillus (GO:0097454)|T-tubule (GO:0030315)|uropod (GO:0001931)|vesicle (GO:0031982)	actin filament binding (GO:0051015)|cell adhesion molecule binding (GO:0050839)|poly(A) RNA binding (GO:0044822)		EZR/ROS1(4)	breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)	15		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-17)|BRCA - Breast invasive adenocarcinoma(81;6.58e-06)		GCCTGGGACAGCTCGCTGCTC	0.562			T	ROS1	NSCLC																																p.L538V		Atlas-SNP	.		Dom	yes		6	6q25.3	7430	ezrin		E	.	EZR	44	.	0			c.C1612G						PASS	.						180	157	165					6																	159188095		2203	4300	6503	SO:0001583	missense	7430	exon13			GGGACAGCTCGCT	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.1612C>G	chr6.hg19:g.159188095G>C	ENSP00000356042:p.Leu538Val	89.0	0.0	.		95.0	32.0	.	NM_003379	E1P5A8|P23714|Q4VX75|Q96CU8|Q9NSJ4	Missense_Mutation	SNP	ENST00000367075.3	hg19	CCDS5258.1	.	.	.	.	.	.	.	.	.	.	G	19.03	3.747324	0.69533	.	.	ENSG00000092820	ENST00000337147;ENST00000367075;ENST00000392177	D;D;D	0.88586	-2.4;-2.4;-2.4	5.37	0.447	0.16608	Moesin (1);Ezrin/radixin/moesin, C-terminal (1);	0.067471	0.64402	D	0.000011	D	0.92074	0.7488	M	0.87617	2.895	0.58432	D	0.999996	D;D	0.71674	0.998;0.989	D;D	0.75484	0.986;0.976	D	0.91442	0.5174	10	0.87932	D	0	.	9.9553	0.41663	0.3142:0.0:0.6858:0.0	.	506;538	E7EQR4;P15311	.;EZRI_HUMAN	V	538;538;506	ENSP00000338934:L538V;ENSP00000356042:L538V;ENSP00000376016:L506V	ENSP00000338934:L538V	L	-	1	2	EZR	159108083	1.000000	0.71417	0.995000	0.50966	0.980000	0.70556	3.249000	0.51437	0.007000	0.14760	0.561000	0.74099	CTG	.	.	.	alt		0.562	EZR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042878.1	NM_003379		C	159188095	G	C	159188095	3	2	212	1	0	0	0	0	1	0	0	0	5337	962	34	4	152	4	EZR	6	159188095	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	120362591	159188095	11926972	19	12904											
TBP	6908	hgsc.bcm.edu	37	chr6	170871004	170871004	+	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	gagcaacaaaggcagcagcaGcaacaacaacagcagcagca	19	0	10	12	0	0	0	0	0	0	0	0	1	0	0	0	1	11	8	0	1	5	0			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr6:170871004G>A	ENST00000392092.2	+	3	459	c.180G>A	c.(178-180)caG>caA	p.Q60Q	TBP_ENST00000540980.1_Silent_p.Q40Q|TBP_ENST00000230354.6_Silent_p.Q60Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	60	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		Ggcagcagcagcaacaacaac	0.542																																					p.Q60Q		Atlas-SNP	.											.	TBP	58	.	0			c.G180A						PASS	.						43	45	44					6																	170871004		2203	4300	6503	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAACAA	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"General transcription factors"	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.180G>A	chr6.hg19:g.170871004G>A		47.0	0.0	.		41.0	5.0	.	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	hg19	CCDS5315.1																																																																																			.	.	.	none		0.542	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		A	170871004	G	A	170871004	2	1	212	1	0	0	0	0	0	0	0	1	15656	962	34	2		2	TBP	6	170871004	Silent	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	11682909	170871004	244063	20	12905											
AUTS2	26053	hgsc.bcm.edu	37	chr7	70255844	70255844	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaacaagacccctccgacAgcagcgctgagcgcacctcc	10	4	8	19	3	1	2	1	1	0	1	3	3	3	2	5	0	4	3	5	0	2	0			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr7:70255844A>G	ENST00000342771.4	+	19	3963	c.3642A>G	c.(3640-3642)acA>acG	p.T1214T	AUTS2_ENST00000406775.2_Silent_p.T1190T	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	1214										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)		CCCCTCCGACAGCAGCGCTGA	0.672																																					p.T1214T		Atlas-SNP	.											.	AUTS2	173	.	0			c.A3642G						PASS	.						41	45	43					7																	70255844		2203	4299	6502	SO:0001819	synonymous_variant	26053	exon19			TCCGACAGCAGCG	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.3642A>G	chr7.hg19:g.70255844A>G		80.0	0.0	.		106.0	30.0	.	NM_015570	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Silent	SNP	ENST00000342771.4	hg19	CCDS5539.1																																																																																			.	.	.	none		0.672	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			G	70255844	A	G	70255844	2	3	212	1	0	0	0	0	0	0	0	1	1225	175	7	3		3	AUTS2	7	70255844	Silent	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10		70255844	88882819	21	12906											
MTFR1	9650	hgsc.bcm.edu	37	chr8	66617127	66617127	+	Missense_Mutation	SNP	A	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	ctcagagctcagattgccaaAattgtgacccagcaggagca	13	7	10	11	0	2	3	2	1	0	2	2	4	2	4	2	1	4	3	2	1	2	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr8:66617127A>C	ENST00000262146.4	+	5	606	c.480A>C	c.(478-480)aaA>aaC	p.K160N	MTFR1_ENST00000458689.2_Missense_Mutation_p.K127N|MTFR1_ENST00000517944.1_3'UTR	NM_014637.3	NP_055452.3	Q15390	MTFR1_HUMAN	mitochondrial fission regulator 1	160					aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(1)|pancreas(1)|urinary_tract(1)	11			Epithelial(68;0.0526)|BRCA - Breast invasive adenocarcinoma(89;0.156)|all cancers(69;0.171)|OV - Ovarian serous cystadenocarcinoma(28;0.194)			AGATTGCCAAAATTGTGACCC	0.458																																					p.K160N		Atlas-SNP	.											.	MTFR1	26	.	0			c.A480C						PASS	.						27	28	27					8																	66617127		2203	4300	6503	SO:0001583	missense	9650	exon5			TGCCAAAATTGTG		CCDS6182.1, CCDS55240.1	8q13.1	2012-11-30							29510	protein-coding gene	gene with protein product	"likely ortholog of chicken chondrocyte protein with a poly proline region"					7584026, 7584028, 15389597	Standard	NM_014637		Approved	CHPPR, KIAA0009, FAM54A2	uc003xvn.2	Q15390		ENST00000262146.4:c.480A>C	chr8.hg19:g.66617127A>C	ENSP00000262146:p.Lys160Asn	122.0	0.0	.		127.0	51.0	.	NM_014637	E7EP84|Q6IB94|Q7Z669|Q86XH5|Q8IVD7	Missense_Mutation	SNP	ENST00000262146.4	hg19	CCDS6182.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.72|19.72	3.879273|3.879273	0.72294|0.72294	.|.	.|.	ENSG00000066855|ENSG00000066855	ENST00000518609;ENST00000262146;ENST00000458689|ENST00000518800	T;T|T	0.50813|0.49432	0.73;0.73|0.78	5.24|5.24	1.59|1.59	0.23543|0.23543	.|.	0.095465|0.095465	0.64402|0.64402	D|D	0.000001|0.000001	T|T	0.59932|0.59932	0.2230|0.2230	M|M	0.84683|0.84683	2.71|2.71	0.44789|0.44789	D|D	0.997793|0.997793	P;D;D;D|.	0.76494|.	0.947;0.992;0.998;0.999|.	P;D;D;D|.	0.74674|.	0.905;0.954;0.94;0.984|.	T|T	0.56044|0.56044	-0.8044|-0.8044	10|8	0.42905|0.41790	T|T	0.14|0.15	-28.337|-28.337	7.9704|7.9704	0.30124|0.30124	0.6814:0.0:0.3186:0.0|0.6814:0.0:0.3186:0.0	.|.	160;144;127;160|.	B4E3G8;E5RJS5;E7EP84;Q15390|.	.;.;.;MTFR1_HUMAN|.	N|T	144;160;127|118	ENSP00000262146:K160N;ENSP00000391502:K127N|ENSP00000430621:K118T	ENSP00000262146:K160N|ENSP00000430621:K118T	K|K	+|+	3|2	2|0	MTFR1|MTFR1	66779681|66779681	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.987000|0.987000	0.75469|0.75469	1.601000|1.601000	0.36773|0.36773	0.035000|0.035000	0.15519|0.15519	0.460000|0.460000	0.39030|0.39030	AAA|AAA	.	.	.	none		0.458	MTFR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378894.1	NM_014637		C	66617127	A	C	66617127	3	2	212	1	0	0	0	0	1	0	0	0	9932	11	1	5	494	5	MTFR1	8	66617127	Missense_Mutation	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10		66617127	79746895	22	12907											
SULF1	23213	hgsc.bcm.edu	37	chr8	70488224	70488224	+	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	gggtccctgcaagtcatgaaCaaaacgagaaagattatgga	16	7	11	7	1	1	3	1	1	0	2	2	5	2	4	1	2	3	1	1	2	6	1			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr8:70488224C>G	ENST00000260128.4	+	6	909	c.192C>G	c.(190-192)aaC>aaG	p.N64K	SULF1_ENST00000419716.3_Missense_Mutation_p.N64K|SULF1_ENST00000458141.2_Missense_Mutation_p.N64K|SULF1_ENST00000402687.4_Missense_Mutation_p.N64K	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	64					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)			AAGTCATGAACAAAACGAGAA	0.522																																					p.N64K		Atlas-SNP	.											.	SULF1	153	.	0			c.C192G						PASS	.						80	67	71					8																	70488224		2203	4300	6503	SO:0001583	missense	23213	exon6			CATGAACAAAACG	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.192C>G	chr8.hg19:g.70488224C>G	ENSP00000260128:p.Asn64Lys	91.0	0.0	.		89.0	33.0	.	NM_001128205	Q86YV8|Q8NCA2|Q9UPS5	Missense_Mutation	SNP	ENST00000260128.4	hg19	CCDS6204.1	.	.	.	.	.	.	.	.	.	.	C	11.47	1.648999	0.29336	.	.	ENSG00000137573	ENST00000458141;ENST00000260128;ENST00000529134;ENST00000402687;ENST00000419716;ENST00000528783;ENST00000525999	D;D;D;D;D;T;D	0.96265	-3.96;-3.96;-3.23;-3.96;-3.96;0.86;-3.96	5.23	2.96	0.34315	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.93861	0.8036	M	0.67397	2.05	0.53688	D	0.999974	B	0.06786	0.001	B	0.10450	0.005	D	0.89996	0.4111	10	0.22109	T	0.4	.	10.5049	0.44828	0.0:0.7019:0.0:0.2981	.	64	Q8IWU6	SULF1_HUMAN	K	64	ENSP00000403040:N64K;ENSP00000260128:N64K;ENSP00000432178:N64K;ENSP00000385704:N64K;ENSP00000390315:N64K;ENSP00000436949:N64K;ENSP00000431753:N64K	ENSP00000260128:N64K	N	+	3	2	SULF1	70650778	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.135000	0.31454	1.123000	0.41961	0.650000	0.86243	AAC	.	.	.	none		0.522	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378885.2	NM_015170		G	70488224	C	G	70488224	3	3	212	1	0	0	0	0	1	0	0	0	15382	477	17	4	198	4	SULF1	8	70488224	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	3871097	70488224	75875798	23	12908											
DPYS	1807	hgsc.bcm.edu	37	chr8	105393497	105393499	+	In_Frame_Del	DEL	CTT	CTT	-																															tctggatttcagtgtggcgaCttctcccttatagggtgcac																								rs148864394	byFrequency	TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr8:105393497_105393499delCTT	ENST00000351513.2	-	9	1619_1621	c.1487_1489delAAG	c.(1486-1491)gaagtc>gtc	p.E496del	DPYS_ENST00000521601.1_5'UTR	NM_001385.2	NP_001376.1	Q14117	DPYS_HUMAN	dihydropyrimidinase	496					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)			AGTGTGGCGACTTCTCCCTTATA	0.483																																					p.496_497del		Atlas-Indel,Pindel	.											.	DPYS	107	.	0			c.1488_1490del						PASS	.																																			SO:0001651	inframe_deletion	1807	exon9			.	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.1487_1489delAAG	chr8.hg19:g.105393497_105393499delCTT	ENSP00000276651:p.Glu496del	69.0	0.0	0		55.0	26.0	0.472727	NM_001385		In_Frame_Del	DEL	ENST00000351513.2	hg19	CCDS6302.1																																																																																			.	.	.	none		0.483	DPYS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380814.1	NM_001385		-	105393499	CTT	-	105393497	7	5	212	1	0	1	0	1	0	0	0	0	4748	565	20	0	74	0	DPYS	8	105393497	In_Frame_Del	DEL	CTT	TCGA-IZ-A6M9-01A-11D-A31X-10	34905273	105393497	40970525	24	12909											
CSMD3	114788	hgsc.bcm.edu	37	chr8	114326898	114326898	+	Missense_Mutation	SNP	A	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	tgaaaaacaatttgtattctAtttcgttcttctgctattat	11	20	4	6	1	3	1	0	1	3	0	4	1	3	1	0	0	2	3	0	0	7	9			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr8:114326898A>C	ENST00000297405.5	-	2	547	c.303T>G	c.(301-303)aaT>aaG	p.N101K	CSMD3_ENST00000352409.3_Missense_Mutation_p.N101K|CSMD3_ENST00000343508.3_Missense_Mutation_p.N61K|CSMD3_ENST00000455883.2_Missense_Mutation_p.N101K	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	101	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.N101N(1)|p.N61N(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						TTTGTATTCTATTTCGTTCTT	0.353										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.N101K		Atlas-SNP	.											CSMD3_ENST00000343508,NS,carcinoma,0,2	CSMD3	2325	.	2	Substitution - coding silent(2)	lung(2)	c.T303G						PASS	.						171	162	165					8																	114326898		2203	4300	6503	SO:0001583	missense	114788	exon2			TATTCTATTTCGT	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.303T>G	chr8.hg19:g.114326898A>C	ENSP00000297405:p.Asn101Lys	136.0	0.0	.		131.0	52.0	.	NM_052900	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	A	14.73	2.621352	0.46736	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000455883;ENST00000352409	T;T;T;T	0.27256	1.68;1.68;1.68;1.68	5.72	3.38	0.38709	CUB (5);	0.077066	0.47455	D	0.000223	T	0.24699	0.0599	L	0.28740	0.885	0.28547	N	0.911799	P;P;D;P;B	0.69078	0.827;0.93;0.997;0.77;0.395	B;P;P;B;B	0.61132	0.275;0.526;0.884;0.253;0.341	T	0.09796	-1.0658	10	0.09338	T	0.73	.	4.6113	0.12404	0.5913:0.0:0.4087:0.0	.	101;101;101;101;61	Q7Z407-3;Q7Z407-4;Q7Z407-5;Q7Z407;Q7Z407-2	.;.;.;CSMD3_HUMAN;.	K	61;101;101;101	ENSP00000345799:N61K;ENSP00000297405:N101K;ENSP00000412263:N101K;ENSP00000343124:N101K	ENSP00000297405:N101K	N	-	3	2	CSMD3	114396074	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.778000	0.55371	0.998000	0.38996	0.455000	0.32223	AAT	.	.	.	none		0.353	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		C	114326898	A	C	114326898	3	2	212	1	0	0	0	0	1	0	0	0	3948	446	16	5	11100	5	CSMD3	8	114326898	Missense_Mutation	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10	8933401	114326898	32037124	25	12910											
SIGMAR1	10280	hgsc.bcm.edu	37	chr9	34637563	34637563	+	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	ccagcgtactgccgcgccaaCtgcgctatctcttcgcgctg	5	9	10	17	6	1	0	0	0	1	0	3	0	1	0	3	0	5	3	3	0	3	3			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr9:34637563C>G	ENST00000277010.4	-	1	205	c.132G>C	c.(130-132)caG>caC	p.Q44H	SIGMAR1_ENST00000477726.1_Missense_Mutation_p.Q44H|SIGMAR1_ENST00000461426.1_5'UTR|SIGMAR1_ENST00000378892.1_5'UTR	NM_001282208.1|NM_005866.2	NP_001269137.1|NP_005857.1	Q99720	SGMR1_HUMAN	sigma non-opioid intracellular receptor 1	44					cell death (GO:0008219)|lipid transport (GO:0006869)|nervous system development (GO:0007399)|regulation of neuron apoptotic process (GO:0043523)	cell junction (GO:0030054)|cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lipid particle (GO:0005811)|nuclear envelope (GO:0005635)	drug binding (GO:0008144)|opioid receptor activity (GO:0004985)			large_intestine(1)|lung(1)	2					Amitriptyline(DB00321)|Dextromethorphan(DB00514)|Nortriptyline(DB00540)|Pentazocine(DB00652)|Remoxipride(DB00409)	GCCGCGCCAACTGCGCTATCT	0.701																																					p.Q44H		Atlas-SNP	.											.	SIGMAR1	6	.	0			c.G132C						PASS	.						15	18	17					9																	34637563		2195	4292	6487	SO:0001583	missense	10280	exon1			CGCCAACTGCGCT	BC004899	CCDS6562.1, CCDS6563.1	9p13.3	2008-12-18	2008-12-18	2008-12-18	ENSG00000147955	ENSG00000147955			8157	protein-coding gene	gene with protein product		601978	"opioid receptor, sigma 1"	OPRS1		8954936, 9453537	Standard	NM_005866		Approved	SR-BP1	uc003zvb.3	Q99720	OTTHUMG00000019829	ENST00000277010.4:c.132G>C	chr9.hg19:g.34637563C>G	ENSP00000277010:p.Gln44His	37.0	0.0	.		33.0	7.0	.	NM_005866	D3DRM7|O00673|O00725|Q0Z9W6|Q153Z1|Q2TSD1|Q53GN2|Q7Z653|Q8N7H3|Q9NYX0	Missense_Mutation	SNP	ENST00000277010.4	hg19	CCDS6562.1	.	.	.	.	.	.	.	.	.	.	C	14.79	2.641021	0.47153	.	.	ENSG00000147955	ENST00000277010;ENST00000477726	T;T	0.64618	-0.11;-0.11	4.7	3.8	0.43715	.	0.332724	0.31519	N	0.007517	T	0.63757	0.2538	L	0.52011	1.625	0.29794	N	0.832985	D;D;P	0.59357	0.958;0.985;0.879	P;P;P	0.52598	0.574;0.703;0.559	T	0.63897	-0.6533	10	0.56958	D	0.05	-7.6325	9.982	0.41819	0.3691:0.6309:0.0:0.0	.	44;44;44	B4DR71;A2A3U5;Q99720	.;.;SGMR1_HUMAN	H	44	ENSP00000277010:Q44H;ENSP00000420022:Q44H	ENSP00000277010:Q44H	Q	-	3	2	SIGMAR1	34627563	0.996000	0.38824	1.000000	0.80357	0.969000	0.65631	1.763000	0.38461	1.194000	0.43101	0.561000	0.74099	CAG	.	.	.	none		0.701	SIGMAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052204.1	NM_005866		G	34637563	C	G	34637563	3	3	212	1	0	0	0	0	1	0	0	0	14329	564	20	4	555	4	SIGMAR1	9	34637563	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10		34637563	106575868	26	12911											
TMOD1	7111	hgsc.bcm.edu	37	chr9	100286582	100286582	+	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	aaaatgagctggatgagctgGaccctgatgtgagtaggtgc	11	9	15	6	0	0	4	0	4	0	0	0	6	0	6	1	3	3	3	1	3	3	1			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr9:100286582G>A	ENST00000259365.4	+	2	325	c.112G>A	c.(112-114)Gac>Aac	p.D38N	TMOD1_ENST00000395211.2_Missense_Mutation_p.D38N	NM_003275.3	NP_003266.1	P28289	TMOD1_HUMAN	tropomodulin 1	38					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)		p.D38N(1)		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)		GGATGAGCTGGACCCTGATGT	0.512																																					p.D38N		Atlas-SNP	.											TMOD1,NS,carcinoma,0,1	TMOD1	29	.	1	Substitution - Missense(1)	kidney(1)	c.G112A						PASS	.						138	112	121					9																	100286582		2203	4300	6503	SO:0001583	missense	7111	exon2			GAGCTGGACCCTG		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.112G>A	chr9.hg19:g.100286582G>A	ENSP00000259365:p.Asp38Asn	101.0	0.0	.		77.0	30.0	.	NM_001166116	B2RB77|Q5T7W3|Q9BUF1	Missense_Mutation	SNP	ENST00000259365.4	hg19	CCDS6726.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.821210	0.90873	.	.	ENSG00000136842	ENST00000395211;ENST00000259365	T;T	0.54279	0.58;0.58	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.76814	0.4040	M	0.87097	2.86	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.81468	-0.0919	10	0.87932	D	0	-31.3023	17.3565	0.87337	0.0:0.0:1.0:0.0	.	38	P28289	TMOD1_HUMAN	N	38	ENSP00000378637:D38N;ENSP00000259365:D38N	ENSP00000259365:D38N	D	+	1	0	TMOD1	99326403	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.283000	0.78640	2.534000	0.85438	0.585000	0.79938	GAC	.	.	.	none		0.512	TMOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053320.2	NM_003275		A	100286582	G	A	100286582	3	1	212	1	0	0	0	0	1	0	0	0	16245	1174	41	2	114	2	TMOD1	9	100286582	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	65649019	100286582	40926849	27	12912											
PRDM12	59335	hgsc.bcm.edu	37	chr9	133556745	133556745	+	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	tgcgctcgcacatgcgcatcCacacgctggacaagcccttc	8	7	9	17	4	0	0	0	0	0	0	3	1	1	1	2	1	3	4	2	1	1	1			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr9:133556745C>T	ENST00000253008.2	+	5	853	c.793C>T	c.(793-795)Cac>Tac	p.H265Y		NM_021619.2	NP_067632.2	Q9H4Q4	PRD12_HUMAN	PR domain containing 12	265					neurogenesis (GO:0022008)|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)			kidney(2)|large_intestine(3)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	11		all_hematologic(13;0.0433)|Acute lymphoblastic leukemia(5;0.0534)		OV - Ovarian serous cystadenocarcinoma(145;0.000344)		CATGCGCATCCACACGCTGGA	0.711																																					p.H265Y		Atlas-SNP	.											.	PRDM12	24	.	0			c.C793T						PASS	.						11	13	12					9																	133556745		2188	4269	6457	SO:0001583	missense	59335	exon5			CGCATCCACACGC	AY004252	CCDS6934.1	9q33-q34	2013-01-08			ENSG00000130711	ENSG00000130711		"Zinc fingers, C2H2-type"	13997	protein-coding gene	gene with protein product	"PR-domain containing protein 12", "PR-domain zinc finger protein 12"					14523459	Standard	NM_021619		Approved		uc004bzt.1	Q9H4Q4	OTTHUMG00000020808	ENST00000253008.2:c.793C>T	chr9.hg19:g.133556745C>T	ENSP00000253008:p.His265Tyr	77.0	0.0	.		73.0	29.0	.	NM_021619	A3KFK9	Missense_Mutation	SNP	ENST00000253008.2	hg19	CCDS6934.1	.	.	.	.	.	.	.	.	.	.	C	35	5.424499	0.96111	.	.	ENSG00000130711	ENST00000253008	T	0.67523	-0.27	4.31	4.31	0.51392	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.84120	0.5402	M	0.89353	3.025	0.54753	D	0.999986	D	0.76494	0.999	D	0.87578	0.998	D	0.88039	0.2780	10	0.87932	D	0	-38.3997	15.763	0.78101	0.0:1.0:0.0:0.0	.	265	Q9H4Q4	PRD12_HUMAN	Y	265	ENSP00000253008:H265Y	ENSP00000253008:H265Y	H	+	1	0	PRDM12	132546566	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.432000	0.80349	1.954000	0.56735	0.561000	0.74099	CAC	.	.	.	none		0.711	PRDM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054664.1	NM_021619		T	133556745	C	T	133556745	3	4	212	1	0	0	0	0	1	0	0	0	12463	594	21	2	811	2	PRDM12	9	133556745	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	33270163	133556745	7656686	28	12913											
GDI2	2665	hgsc.bcm.edu	37	chr10	5855180	5855180	+	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	tcagccctggcgcccaccgtCaggccggtgcccagcacgat	6	5	12	18	4	2	0	2	0	0	0	2	1	2	0	5	3	3	1	5	3	0	0			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr10:5855180C>A	ENST00000380191.4	-	1	332	c.42G>T	c.(40-42)ctG>ctT	p.L14L	GDI2_ENST00000380181.3_Silent_p.L14L|GDI2_ENST00000380132.4_5'UTR|RP11-318E3.9_ENST00000608273.1_lincRNA	NM_001115156.1|NM_001494.3	NP_001108628.1|NP_001485.2	P50395	GDIB_HUMAN	GDP dissociation inhibitor 2	14					protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|Rab GDP-dissociation inhibitor activity (GO:0005093)|Rab GTPase activator activity (GO:0005097)			NS(1)|breast(1)|large_intestine(1)|lung(6)|urinary_tract(1)	10						CGCCCACCGTCAGGCCGGTGC	0.751																																					p.L14L		Atlas-SNP	.											.	GDI2	26	.	0			c.G42T						PASS	.						8	9	9					10																	5855180		2144	4238	6382	SO:0001819	synonymous_variant	2665	exon1			CACCGTCAGGCCG	D13988	CCDS7071.1, CCDS44352.1	10p15	2010-03-16			ENSG00000057608	ENSG00000057608			4227	protein-coding gene	gene with protein product	"rab GDP-dissociation"	600767				9434952	Standard	NM_001494		Approved	RABGDIB	uc001iil.4	P50395	OTTHUMG00000017607	ENST00000380191.4:c.42G>T	chr10.hg19:g.5855180C>A		66.0	0.0	.		50.0	24.0	.	NM_001115156	O43928|Q5SX88|Q9UQM6	Silent	SNP	ENST00000380191.4	hg19	CCDS7071.1																																																																																			.	.	.	none		0.751	GDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046580.1	NM_001494		A	5855180	C	A	5855180	2	1	212	1	0	0	0	0	0	0	0	1	6328	813	29	4		4	GDI2	10	5855180	Silent	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10		5855180	129679567	29	12914											
COL17A1	1308	hgsc.bcm.edu	37	chr10	105795252	105795252	+	Missense_Mutation	SNP	T	T	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	ctcgcagcaaggagaggagcTcctcataggaggttcccggc	9	6	14	12	2	1	1	1	0	0	1	4	4	3	3	2	5	2	4	2	5	2	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr10:105795252T>G	ENST00000353479.5	-	49	3778	c.3488A>C	c.(3487-3489)gAg>gCg	p.E1163A	COL17A1_ENST00000369733.3_Missense_Mutation_p.E1118A	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	1163	Triple-helical region.				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|hemidesmosome (GO:0030056)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				NS(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|liver(1)|lung(22)|ovary(5)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	62		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		GGAGAGGAGCTCCTCATAGGA	0.627																																					p.E1163A		Atlas-SNP	.											.	COL17A1	149	.	0			c.A3488C						PASS	.						29	33	32					10																	105795252		2203	4300	6503	SO:0001583	missense	1308	exon49			AGGAGCTCCTCAT	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.3488A>C	chr10.hg19:g.105795252T>G	ENSP00000340937:p.Glu1163Ala	116.0	0.0	.		105.0	16.0	.	NM_000494	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Missense_Mutation	SNP	ENST00000353479.5	hg19	CCDS7554.1	.	.	.	.	.	.	.	.	.	.	T	10.22	1.290516	0.23478	.	.	ENSG00000065618	ENST00000353479;ENST00000369733	D;D	0.91740	-2.9;-2.8	4.83	3.68	0.42216	.	0.150217	0.30329	N	0.009864	D	0.84633	0.5515	L	0.34521	1.04	0.80722	D	1	B	0.30406	0.278	B	0.30179	0.112	T	0.76542	-0.2921	10	0.10902	T	0.67	-20.9225	9.6783	0.40054	0.1549:0.0:0.0:0.8451	.	1163	Q9UMD9	COHA1_HUMAN	A	1163;1118	ENSP00000340937:E1163A;ENSP00000358748:E1118A	ENSP00000340937:E1163A	E	-	2	0	COL17A1	105785242	1.000000	0.71417	1.000000	0.80357	0.007000	0.05969	2.356000	0.44116	0.845000	0.35118	-0.695000	0.03696	GAG	.	.	.	none		0.627	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494		G	105795252	T	G	105795252	3	3	212	1	0	0	0	0	1	0	0	0	3676	1551	54	5	1037	5	COL17A1	10	105795252	Missense_Mutation	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10	99940072	105795252	29739495	30	12915											
SMPD1	6609	hgsc.bcm.edu	37	chr11	6412728	6412728	+	Missense_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	acctctttgaggatgacatgGtggaggtgtggagacgctca	9	10	15	7	1	2	3	1	2	1	1	2	6	2	5	1	5	0	1	1	5	0	1			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr11:6412728G>A	ENST00000342245.4	+	2	601	c.433G>A	c.(433-435)Gtg>Atg	p.V145M	SMPD1_ENST00000527275.1_Missense_Mutation_p.V144M|SMPD1_ENST00000533196.1_Intron|SMPD1_ENST00000356761.2_Missense_Mutation_p.V145M|SMPD1_ENST00000299397.3_Missense_Mutation_p.V145M	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	143	Saposin B-type. {ECO:0000255|PROSITE- ProRule:PRU00415}.				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)	GGATGACATGGTGGAGGTGTG	0.582																																					p.V145M		Atlas-SNP	.											.	SMPD1	108	.	0			c.G433A						PASS	.						76	63	68					11																	6412728		2201	4296	6497	SO:0001583	missense	6609	exon2			GACATGGTGGAGG	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.433G>A	chr11.hg19:g.6412728G>A	ENSP00000340409:p.Val145Met	55.0	0.0	.		52.0	19.0	.	NM_000543	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Missense_Mutation	SNP	ENST00000342245.4	hg19	CCDS44531.1	.	.	.	.	.	.	.	.	.	.	G	18.12	3.553731	0.65425	.	.	ENSG00000166311	ENST00000299397;ENST00000356761;ENST00000342245;ENST00000527275	D;D;D;D	0.97731	-4.51;-4.51;-4.51;-4.51	5.11	5.11	0.69529	Saposin-like (2);Saposin B (2);	0.178891	0.37857	N	0.001919	D	0.96892	0.8985	L	0.54323	1.7	0.42449	D	0.99274	P;P;P	0.46706	0.818;0.883;0.579	B;P;P	0.51516	0.366;0.672;0.472	D	0.96137	0.9097	10	0.49607	T	0.09	-7.0221	9.6331	0.39791	0.0956:0.0:0.9044:0.0	.	144;145;143	E9PKS3;G3XAB5;P17405	.;.;ASM_HUMAN	M	145;145;145;144	ENSP00000299397:V145M;ENSP00000349203:V145M;ENSP00000340409:V145M;ENSP00000435350:V144M	ENSP00000299397:V145M	V	+	1	0	SMPD1	6369304	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.869000	0.48444	2.382000	0.81193	0.650000	0.86243	GTG	.	.	.	none		0.582	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543		A	6412728	G	A	6412728	3	1	212	1	0	0	0	0	1	0	0	0	14817	1261	44	2	439	2	SMPD1	11	6412728	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10		6412728	128593788	31	12916											
PEX16	9409	hgsc.bcm.edu	37	chr11	45936221	45936221	+	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	ggactgctcatggttgccagGgctgtggtcaccatctagca	7	10	13	11	0	3	0	2	0	1	0	3	1	3	1	2	4	3	4	2	4	1	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr11:45936221G>A	ENST00000378750.5	-	6	718	c.475C>T	c.(475-477)Cct>Tct	p.P159S	PEX16_ENST00000532554.1_5'UTR|PEX16_ENST00000532681.1_Missense_Mutation_p.P64S|PEX16_ENST00000241041.3_Missense_Mutation_p.P159S			Q9Y5Y5	PEX16_HUMAN	peroxisomal biogenesis factor 16	159					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)	p.P159T(1)		large_intestine(2)|lung(2)|ovary(2)|skin(1)	7				GBM - Glioblastoma multiforme(35;0.223)		TGGTTGCCAGGGCTGTGGTCA	0.582																																					p.P159S		Atlas-SNP	.											PEX16,colon,carcinoma,0,1	PEX16	24	.	1	Substitution - Missense(1)	large_intestine(1)	c.C475T						PASS	.						154	129	137					11																	45936221		2203	4299	6502	SO:0001583	missense	9409	exon6			TGCCAGGGCTGTG	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.475C>T	chr11.hg19:g.45936221G>A	ENSP00000368024:p.Pro159Ser	51.0	0.0	.		59.0	21.0	.	NM_004813	Q9BWB9	Missense_Mutation	SNP	ENST00000378750.5	hg19	CCDS31472.1	.	.	.	.	.	.	.	.	.	.	G	0.052	-1.248308	0.01469	.	.	ENSG00000121680	ENST00000241041;ENST00000378750;ENST00000532681;ENST00000533151;ENST00000525192	T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16	6.04	-5.2	0.02823	.	1.274680	0.04746	N	0.423709	T	0.05868	0.0153	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.28744	-1.0034	10	0.06236	T	0.91	2.692	1.5964	0.02665	0.2746:0.3442:0.2067:0.1744	.	159;159	Q9Y5Y5;Q9Y5Y5-2	PEX16_HUMAN;.	S	159;159;64;55;64	ENSP00000241041:P159S;ENSP00000368024:P159S;ENSP00000434654:P64S;ENSP00000433045:P55S;ENSP00000431309:P64S	ENSP00000241041:P159S	P	-	1	0	PEX16	45892797	0.000000	0.05858	0.001000	0.08648	0.474000	0.32979	-1.251000	0.02882	-0.602000	0.05775	0.561000	0.74099	CCT	.	.	.	none		0.582	PEX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392398.1	NM_057174		A	45936221	G	A	45936221	3	1	212	1	0	0	0	0	1	0	0	0	11750	1232	43	2	652	2	PEX16	11	45936221	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	39523493	45936221	89070295	32	12917											
C11orf57	55216	hgsc.bcm.edu	37	chr11	111953315	111953315	+	Frame_Shift_Del	DEL	C	C	-																															aagcagaaaaaaaggtcacaCaaaaaacagaagaaaagcaa																										TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr11:111953315delC	ENST00000280352.9	+	6	1134	c.498delC	c.(496-498)cacfs	p.H166fs	C11orf57_ENST00000393047.3_Frame_Shift_Del_p.H167fs|TIMM8B_ENST00000507614.1_5'Flank|C11orf57_ENST00000420986.2_Frame_Shift_Del_p.H166fs|C11orf57_ENST00000532163.1_Frame_Shift_Del_p.H138fs	NM_001082970.1|NM_018195.3	NP_001076439.1|NP_060665.3	Q6ZUT1	CK057_HUMAN	chromosome 11 open reading frame 57	166	Lys-rich.									autonomic_ganglia(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)	12		all_cancers(61;9.8e-15)|all_epithelial(67;6.57e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;3.6e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;7.01e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0521)		AAAGGTCACACAAAAAACAGA	0.413																																					p.H167fs		Atlas-Indel,Pindel	.											.	C11orf57	41	.	0			c.500delA						PASS	.						99	105	103					11																	111953315		2201	4297	6498	SO:0001589	frameshift_variant	55216	exon6			.	BX538107	CCDS8356.2, CCDS41715.1, CCDS73383.1	11q23.1	2006-03-09			ENSG00000150776	ENSG00000150776			25569	protein-coding gene	gene with protein product						12477932	Standard	NM_001082970		Approved	FLJ10726	uc001pmw.4	Q6ZUT1	OTTHUMG00000150213	ENST00000280352.9:c.498delC	chr11.hg19:g.111953315delC	ENSP00000339076:p.His166fs	256.0	0.0	0		209.0	79.0	0.37799	NM_001082969	Q5RL41|Q6IN53|Q7Z357|Q8N2T3	Frame_Shift_Del	DEL	ENST00000280352.9	hg19	CCDS41715.1																																																																																			.	.	.	none		0.413	C11orf57-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316852.1	NM_018195		-	111953315	C	-	111953315	7	5	212	1	0	1	0	1	0	0	0	0	1652	477	17	0	519	0	C11orf57	11	111953315	Frame_Shift_Del	DEL	C	TCGA-IZ-A6M9-01A-11D-A31X-10	66017094	111953315	23053201	33	12918											
DNAJC22	79962	hgsc.bcm.edu	37	chr12	49745201	49745201	+	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	cacaacctggaccagacagaGgaggcacagaggcacttcct	13	4	11	13	0	0	3	0	0	0	3	1	5	1	5	3	4	1	2	3	4	1	1			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr12:49745201G>T	ENST00000549441.2	+	4	2146	c.942G>T	c.(940-942)gaG>gaT	p.E314D	DNAJC22_ENST00000395069.3_Missense_Mutation_p.E314D			Q8N4W6	DJC22_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 22	314	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.					integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(2)|lung(1)|ovary(1)|pancreas(1)	10						ACCAGACAGAGGAGGCACAGA	0.547																																					p.E314D		Atlas-SNP	.											.	DNAJC22	29	.	0			c.G942T						PASS	.						59	59	59					12																	49745201		2203	4300	6503	SO:0001583	missense	79962	exon3			GACAGAGGAGGCA	AK055747	CCDS8785.1	12q13.12	2011-09-02		2008-07-08	ENSG00000178401	ENSG00000178401		"Heat shock proteins / DNAJ (HSP40)"	25802	protein-coding gene	gene with protein product	"wurst homolog (Drosophila)"					17558392	Standard	NM_024902		Approved	wus, FLJ13236	uc001rua.3	Q8N4W6		ENST00000549441.2:c.942G>T	chr12.hg19:g.49745201G>T	ENSP00000446830:p.Glu314Asp	132.0	0.0	.		120.0	5.0	.	NM_024902	B3KP54	Missense_Mutation	SNP	ENST00000549441.2	hg19	CCDS8785.1	.	.	.	.	.	.	.	.	.	.	G	18.17	3.564963	0.65651	.	.	ENSG00000178401	ENST00000549441;ENST00000395069	T;T	0.33438	1.41;1.41	5.5	3.53	0.40419	Heat shock protein DnaJ, N-terminal (5);	0.154813	0.56097	D	0.000021	T	0.18882	0.0453	N	0.20357	0.565	0.47511	D	0.999446	P	0.36354	0.549	B	0.40038	0.317	T	0.05517	-1.0880	10	0.37606	T	0.19	-7.4243	4.2702	0.10783	0.1957:0.0:0.6268:0.1776	.	314	Q8N4W6	DJC22_HUMAN	D	314	ENSP00000446830:E314D;ENSP00000378508:E314D	ENSP00000378508:E314D	E	+	3	2	DNAJC22	48031468	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	0.731000	0.26058	0.748000	0.32831	0.555000	0.69702	GAG	.	.	.	none		0.547	DNAJC22-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404302.2	NM_024902		T	49745201	G	T	49745201	3	4	212	1	0	0	0	0	1	0	0	0	4643	991	35	4	948	4	DNAJC22	12	49745201	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10		49745201	84106694	34	12919											
ARL6IP4	23457	hgsc.bcm.edu	37	chr12	123465766	123465770	+	5'UTR	DEL	AGAGC	AGAGC	-																															gtcggaaaagagaaagaagaAgagcaggaaagacacctcga																										TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	AGAGC	AGAGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr12:123465766_123465770delAGAGC	ENST00000542678.1	-	0	426_430				ARL6IP4_ENST00000454885.2_Frame_Shift_Del_p.KS27fs|ARL6IP4_ENST00000412505.2_Frame_Shift_Del_p.KS27fs|ARL6IP4_ENST00000439686.2_Frame_Shift_Del_p.KS27fs|ARL6IP4_ENST00000543566.1_Frame_Shift_Del_p.KS150fs|ARL6IP4_ENST00000426960.2_Frame_Shift_Del_p.KS27fs|RP11-197N18.2_ENST00000540866.2_RNA|ARL6IP4_ENST00000315580.5_Frame_Shift_Del_p.KS150fs|ARL6IP4_ENST00000453766.2_Frame_Shift_Del_p.KS150fs|ARL6IP4_ENST00000392435.2_Frame_Shift_Del_p.KS150fs|ARL6IP4_ENST00000357866.4_Frame_Shift_Del_p.KS27fs			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)		AGAAAGAAGAAGAGCAGGAAAGACA	0.683																																					p.150_151del	Ovarian(49;786 1333 9175 38236)	Atlas-Indel,Pindel	.											.	ARL6IP4	14	.	0			c.448_452del						PASS	.																																			SO:0001623	5_prime_UTR_variant	51329	exon2			.	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.-2413GCTCT>-	chr12.hg19:g.123465766_123465770delAGAGC		155.0	0.0	0		144.0	31.0	0.215278	NM_018694	B4E2J0|Q5W9G7|Q769F3|Q769F4|Q96AB1|Q9P208	Frame_Shift_Del	DEL	ENST00000542678.1	hg19	CCDS9241.1																																																																																			.	.	.	none		0.683	ABCB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400956.1	NM_019624		-	123465770	AGAGC	-	123465766	6	5	212	0	1	1	0	1	0	0	0	0	943	72	3	0		0	ARL6IP4	12	123465766	5'UTR	DEL	AGAGC	TCGA-IZ-A6M9-01A-11D-A31X-10	73720565	123465766	10386129	35	12920											
NUFIP1	26747	hgsc.bcm.edu	37	chr13	45563329	45563329	+	Frame_Shift_Del	DEL	G	G	-																															ccgggaagaatctgggcgtcGaaggggggcggagccccggg																										TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr13:45563329delG	ENST00000379161.4	-	1	289	c.243delC	c.(241-243)ttcfs	p.F81fs	GPALPP1_ENST00000379151.4_5'Flank|RP11-321C24.1_ENST00000437748.2_lincRNA|GPALPP1_ENST00000361121.2_5'Flank	NM_012345.2	NP_036477.2	Q9UHK0	NUFP1_HUMAN	nuclear fragile X mental retardation protein interacting protein 1	81	Pro-rich.				box C/D snoRNP assembly (GO:0000492)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|RNA processing (GO:0006396)	cytosolic ribosome (GO:0022626)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|pre-snoRNP complex (GO:0070761)|presynaptic active zone (GO:0048786)|transcription elongation factor complex (GO:0008023)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)|RNA binding (GO:0003723)			breast(2)|cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(4)|skin(3)	18		Lung NSC(96;8.23e-05)|Breast(139;0.00378)|Prostate(109;0.0107)|all_hematologic(4;0.014)|Lung SC(185;0.0262)|Hepatocellular(98;0.0524)|Acute lymphoblastic leukemia(4;0.143)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000306)|BRCA - Breast invasive adenocarcinoma(63;0.125)		TCTGGGCGTCGAAGGGGGGCG	0.657																																					p.D82fs		Atlas-INDEL	.											.	NUFIP1	41	.	0			c.244delG						PASS	.						14	17	16					13																	45563329		2189	4285	6474	SO:0001589	frameshift_variant	26747	exon1			.	AF159548	CCDS9393.1	13q14	2008-02-05			ENSG00000083635	ENSG00000083635			8057	protein-coding gene	gene with protein product		604354				10556305, 10894927	Standard	NM_012345		Approved	NUFIP	uc001uzp.2	Q9UHK0	OTTHUMG00000016842	ENST00000379161.4:c.243delC	chr13.hg19:g.45563329delG	ENSP00000368459:p.Phe81fs	130.0	0.0	0		113.0	22.0	0.19469	NM_012345	Q8WVM5|Q96SG1	Frame_Shift_Del	DEL	ENST00000379161.4	hg19	CCDS9393.1																																																																																			.	.	.	none		0.657	NUFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044755.2	NM_012345		-	45563329	G	-	45563329	7	5	212	1	0	1	0	1	0	0	0	0	10755	1049	37	0	1284	0	NUFIP1	13	45563329	Frame_Shift_Del	DEL	G	TCGA-IZ-A6M9-01A-11D-A31X-10		45563329	69606549	36	12921											
LMO7	4008	hgsc.bcm.edu	37	chr13	76395479	76395497	+	Frame_Shift_Del	DEL	AAAGAAGATTCTACCACTT	AAAGAAGATTCTACCACTT	-																															cttatccttcagaaattcccAaagaagattctaccactttt																								rs200351536|rs532984694|rs149099643	byFrequency	TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	AAAGAAGATTCTACCACTT	AAAGAAGATTCTACCACTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr13:76395479_76395497delAAAGAAGATTCTACCACTT	ENST00000321797.8	+	12	2396_2414	c.1675_1693delAAAGAAGATTCTACCACTT	c.(1675-1695)aaagaagattctaccacttttfs	p.KEDSTTF559fs	LMO7_ENST00000465261.2_Frame_Shift_Del_p.KEDSTTF559fs|LMO7_ENST00000357063.3_Frame_Shift_Del_p.KEDSTTF844fs|LMO7_ENST00000377534.3_Frame_Shift_Del_p.KEDSTTF844fs|LMO7_ENST00000341547.4_Frame_Shift_Del_p.KEDSTTF510fs|LMO7_ENST00000526202.1_Frame_Shift_Del_p.KEDSTTF409fs			Q8WWI1	LMO7_HUMAN	LIM domain 7	844					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)		AGAAATTCCCAAAGAAGATTCTACCACTTTTGCAAAAAG	0.457																																					p.558_564del		Atlas-Indel,Pindel	.											.	LMO7	334	.	0			c.1674_1692del						PASS	.																																			SO:0001589	frameshift_variant	4008	exon11			.	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.1675_1693delAAAGAAGATTCTACCACTT	chr13.hg19:g.76395479_76395497delAAAGAAGATTCTACCACTT	ENSP00000317802:p.Lys559fs	161.0	0.0	0		104.0	28.0	0.269231	NM_015842	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Frame_Shift_Del	DEL	ENST00000321797.8	hg19																																																																																				.	.	.	none		0.457	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358		-	76395497	AAAGAAGATTCTACCACTT	-	76395479	7	5	212	1	0	1	0	1	0	0	0	0	8862	131	5	0	2588	0	LMO7	13	76395479	Frame_Shift_Del	DEL	AAAGAAGATTCTACCACTT	TCGA-IZ-A6M9-01A-11D-A31X-10	30832150	76395479	38774399	37	12922											
TMTC4	84899	hgsc.bcm.edu	37	chr13	101287091	101287091	+	Missense_Mutation	SNP	T	T	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	gggacacacagacagagcacTtctgaaaagctgttcctcac	13	7	9	12	0	2	3	1	1	1	2	3	4	3	4	1	1	2	3	1	1	2	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr13:101287091T>G	ENST00000376234.3	-	11	1606	c.1417A>C	c.(1417-1419)Agt>Cgt	p.S473R	TMTC4_ENST00000328767.5_Missense_Mutation_p.S362R|TMTC4_ENST00000462211.1_5'UTR|TMTC4_ENST00000342624.5_Missense_Mutation_p.S492R	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	473						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)					GACAGAGCACTTCTGAAAAGC	0.493																																					p.S492R		Atlas-SNP	.											.	TMTC4	103	.	0			c.A1474C						PASS	.						135	140	139					13																	101287091		2203	4300	6503	SO:0001583	missense	84899	exon12			GAGCACTTCTGAA		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.1417A>C	chr13.hg19:g.101287091T>G	ENSP00000365408:p.Ser473Arg	95.0	0.0	.		62.0	21.0	.	NM_032813	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Missense_Mutation	SNP	ENST00000376234.3	hg19	CCDS41904.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.428259	0.83667	.	.	ENSG00000125247	ENST00000376234;ENST00000342624;ENST00000328767	T;T;T	0.52526	0.66;0.66;0.66	5.55	5.55	0.83447	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.75406	0.3845	M	0.91663	3.23	0.80722	D	1	D;D;D;P	0.89917	1.0;0.999;1.0;0.737	D;D;D;P	0.97110	0.997;0.994;1.0;0.565	T	0.81901	-0.0720	10	0.87932	D	0	.	15.7439	0.77922	0.0:0.0:0.0:1.0	.	362;473;473;492	B7Z666;Q5T4D3-2;Q5T4D3;Q5T4D3-3	.;.;TMTC4_HUMAN;.	R	473;492;362	ENSP00000365408:S473R;ENSP00000343871:S492R;ENSP00000365409:S362R	ENSP00000365409:S362R	S	-	1	0	TMTC4	100085092	1.000000	0.71417	0.954000	0.39281	0.652000	0.38707	7.590000	0.82653	2.134000	0.65973	0.456000	0.33151	AGT	.	.	.	none		0.493	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813		G	101287091	T	G	101287091	3	3	212	1	0	0	0	0	1	0	0	0	16275	1609	56	5	840	5	TMTC4	13	101287091	Missense_Mutation	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10	24891612	101287091	13882787	38	12923											
MTA1	9112	hgsc.bcm.edu	37	chr14	105927271	105927271	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaatatgggaaggatttcaCggacattcagcaagattttg	15	11	10	5	1	2	1	2	0	0	1	2	4	2	4	0	3	1	1	0	3	5	5			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr14:105927271C>T	ENST00000331320.7	+	10	1137	c.923C>T	c.(922-924)aCg>aTg	p.T308M	MTA1_ENST00000435036.2_5'Flank|MTA1_ENST00000405646.1_Missense_Mutation_p.T291M|MTA1_ENST00000406191.1_Missense_Mutation_p.T308M	NM_001203258.1|NM_004689.3	NP_001190187.1|NP_004680.2	Q13330	MTA1_HUMAN	metastasis associated 1	308	SANT. {ECO:0000255|PROSITE- ProRule:PRU00624}.				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)		AAGGATTTCACGGACATTCAG	0.597																																					p.T308M		Atlas-SNP	.											.	MTA1	61	.	0			c.C923T						PASS	.						109	108	109					14																	105927271		2203	4300	6503	SO:0001583	missense	9112	exon10			ATTTCACGGACAT	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.923C>T	chr14.hg19:g.105927271C>T	ENSP00000333633:p.Thr308Met	155.0	0.0	.		98.0	4.0	.	NM_004689	A5PLK4|Q86SW2|Q8NFI8|Q96GI8	Missense_Mutation	SNP	ENST00000331320.7	hg19	CCDS32169.1	.	.	.	.	.	.	.	.	.	.	C	19.61	3.860017	0.71834	.	.	ENSG00000182979	ENST00000414153;ENST00000331320;ENST00000406191;ENST00000405646;ENST00000498644;ENST00000434050	T;T;T;T	0.45668	0.89;0.89;0.89;0.89	4.38	3.47	0.39725	SANT domain, DNA binding (1);Homeodomain-like (1);SANT, eukarya (1);	0.053947	0.85682	D	0.000000	T	0.41096	0.1144	N	0.08118	0	0.80722	D	1	D;D	0.89917	1.0;0.977	D;P	0.67382	0.951;0.571	T	0.47774	-0.9091	10	0.66056	D	0.02	-8.7686	12.2148	0.54400	0.172:0.828:0.0:0.0	.	100;308	Q59FW1;Q13330	.;MTA1_HUMAN	M	217;308;308;291;222;100	ENSP00000333633:T308M;ENSP00000385702:T308M;ENSP00000384180:T291M;ENSP00000394106:T100M	ENSP00000333633:T308M	T	+	2	0	MTA1	104998316	0.994000	0.37717	0.923000	0.36655	0.976000	0.68499	3.151000	0.50670	0.814000	0.34374	0.655000	0.94253	ACG	.	.	.	none		0.597	MTA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317849.15			T	105927271	C	T	105927271	3	4	212	1	0	0	0	0	1	0	0	0	9915	536	19	1	961	1	MTA1	14	105927271	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10		105927271	1422269	39	12924											
CNOT1	23019	hgsc.bcm.edu	37	chr16	58592566	58592570	+	Frame_Shift_Del	DEL	CAAGA	CAAGA	-																															actaagagatgtcattccagCaagagggtcaatctaaagaa																										TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	CAAGA	CAAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr16:58592566_58592570delCAAGA	ENST00000317147.5	-	18	2471_2475	c.2139_2143delTCTTG	c.(2137-2145)cctcttgctfs	p.LA714fs	CNOT1_ENST00000569240.1_Frame_Shift_Del_p.LA714fs|CNOT1_ENST00000441024.2_Frame_Shift_Del_p.LA714fs|CNOT1_ENST00000569732.1_5'Flank|SNORA50_ENST00000384225.2_RNA	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	714					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)		GTCATTCCAGCAAGAGGGTCAATCT	0.4																																					p.714_715del		Atlas-Indel,Pindel	.											CNOT1_ENST00000441024,NS,lymphoid_neoplasm,0,2	CNOT1	359	.	0			c.2140_2144del						PASS	.																																			SO:0001589	frameshift_variant	23019	exon18			.	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.2139_2143delTCTTG	chr16.hg19:g.58592566_58592570delCAAGA	ENSP00000320949:p.Leu714fs	102.0	0.0	0		97.0	46.0	0.474227	NM_001265612	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Frame_Shift_Del	DEL	ENST00000317147.5	hg19	CCDS10799.1																																																																																			.	.	.	none		0.4	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		-	58592570	CAAGA	-	58592566	7	5	212	1	0	1	0	1	0	0	0	0	3619	710	25	0	5337	0	CNOT1	16	58592566	Frame_Shift_Del	DEL	CAAGA	TCGA-IZ-A6M9-01A-11D-A31X-10		58592566	31762187	40	12925											
PDPR	55066	hgsc.bcm.edu	37	chr16	70163023	70163023	+	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	ggcaagtgctgcctcccaaaAtggtgagcaggtttttgcat	9	11	12	9	0	0	1	0	1	0	0	1	1	1	1	2	3	4	5	2	3	3	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr16:70163023A>T	ENST00000288050.4	+	6	1562	c.605A>T	c.(604-606)aAt>aTt	p.N202I	PDPR_ENST00000398122.3_Missense_Mutation_p.N102I|PDPR_ENST00000568530.1_Missense_Mutation_p.N202I	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	202					cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		GCCTCCCAAAATGGTGAGCAG	0.512																																					p.N202I		Atlas-SNP	.											.	PDPR	66	.	0			c.A605T						PASS	.						111	104	106					16																	70163023		1953	4159	6112	SO:0001583	missense	55066	exon6			CCCAAAATGGTGA		CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857			30264	protein-coding gene	gene with protein product						9395502	Standard	NM_017990		Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.605A>T	chr16.hg19:g.70163023A>T	ENSP00000288050:p.Asn202Ile	379.0	0.0	.		473.0	124.0	.	NM_017990	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Missense_Mutation	SNP	ENST00000288050.4	hg19	CCDS45520.1	.	.	.	.	.	.	.	.	.	.	A	13.30	2.196035	0.38806	.	.	ENSG00000090857	ENST00000288050;ENST00000398122	D;D	0.82167	-1.58;-1.58	4.5	3.4	0.38934	FAD dependent oxidoreductase (1);	0.236187	0.40385	N	0.001112	T	0.77765	0.4179	L	0.55213	1.73	0.80722	D	1	B	0.23806	0.091	B	0.28784	0.094	T	0.69224	-0.5201	10	0.31617	T	0.26	.	9.0915	0.36614	0.9111:0.0:0.0889:0.0	.	202	Q8NCN5	PDPR_HUMAN	I	202;102	ENSP00000288050:N202I;ENSP00000381190:N102I	ENSP00000288050:N202I	N	+	2	0	PDPR	68720524	1.000000	0.71417	0.967000	0.41034	0.965000	0.64279	5.368000	0.66133	0.581000	0.29539	0.455000	0.32223	AAT	.	.	.	none		0.512	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1	NM_017990		T	70163023	A	T	70163023	3	4	212	1	0	0	0	0	1	0	0	0	11696	101	4	5	619	5	PDPR	16	70163023	Missense_Mutation	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10	11570457	70163023	20191730	41	12926											
KARS	3735	hgsc.bcm.edu	37	chr16	75678300	75678300	+	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	ttgcgcagggaccccctaacAagccttacagcagcttgcgt	9	8	10	14	2	0	0	0	0	0	0	0	1	0	1	3	1	7	3	3	1	3	4			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr16:75678300A>T	ENST00000302445.3	-	2	102				KARS_ENST00000319410.5_Silent_p.L9L|KARS_ENST00000568378.1_Silent_p.L9L	NM_005548.2	NP_005539.1	Q15046	SYK_HUMAN	lysyl-tRNA synthetase						cell death (GO:0008219)|diadenosine tetraphosphate biosynthetic process (GO:0015966)|gene expression (GO:0010467)|lysyl-tRNA aminoacylation (GO:0006430)|tRNA aminoacylation for protein translation (GO:0006418)|tRNA processing (GO:0008033)|viral process (GO:0016032)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|microtubule cytoskeleton (GO:0015630)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	amino acid binding (GO:0016597)|ATP binding (GO:0005524)|lysine-tRNA ligase activity (GO:0004824)|metal ion binding (GO:0046872)|tRNA binding (GO:0000049)			kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	18					L-Lysine(DB00123)	ACCCCCTAACAAGCCTTACAG	0.552																																					p.L9L		Atlas-SNP	.											.	KARS	77	.	0			c.T27A						PASS	.						50	47	48					16																	75678300		1568	3582	5150	SO:0001627	intron_variant	3735	exon2			CCTAACAAGCCTT	AF285758	CCDS10923.1, CCDS45532.1	16q23.1	2014-09-17			ENSG00000065427	ENSG00000065427	6.1.1.6	"Aminoacyl tRNA synthetases / Class II"	6215	protein-coding gene	gene with protein product	"lysine tRNA ligase"	601421	"deafness, autosomal recessive 89"	DFNB89		8812440, 9278442, 23768514	Standard	NM_005548		Approved	KARS2, KARS1	uc002fer.3	Q15046	OTTHUMG00000137609	ENST00000302445.3:c.63-2679T>A	chr16.hg19:g.75678300A>T		87.0	0.0	.		96.0	54.0	.	NM_001130089	A8MSK1|D3DUK4|O14946|Q96J25|Q9HB23	Silent	SNP	ENST00000302445.3	hg19	CCDS10923.1																																																																																			.	.	.	none		0.552	KARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269023.1	NM_005548		T	75678300	A	T	75678300	1	4	212	0	1	0	0	0	0	0	0	0	7987	117	5	5		5	KARS	16	75678300	Intron	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10	5515277	75678300	14676453	42	12927											
MYH4	4622	hgsc.bcm.edu	37	chr17	10358389	10358389	+	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	cccagcaggccagctttgaaGaaaaccttatgaaagaacaa	17	6	8	10	0	0	4	0	2	0	2	0	4	0	4	3	1	4	2	3	1	7	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr17:10358389G>T	ENST00000255381.2	-	21	2414	c.2304C>A	c.(2302-2304)ttC>ttA	p.F768L	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	768	Actin-binding. {ECO:0000250}.|Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						CAGCTTTGAAGAAAACCTTAT	0.403																																					p.F768L		Atlas-SNP	.											.	MYH4	349	.	0			c.C2304A						PASS	.						169	108	129					17																	10358389		2203	4300	6503	SO:0001583	missense	4622	exon21			TTTGAAGAAAACC		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.2304C>A	chr17.hg19:g.10358389G>T	ENSP00000255381:p.Phe768Leu	104.0	0.0	.		115.0	31.0	.	NM_017533		Missense_Mutation	SNP	ENST00000255381.2	hg19	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.962237	0.74016	.	.	ENSG00000141048	ENST00000255381	D	0.94280	-3.39	5.04	5.04	0.67666	Myosin head, motor domain (2);	0.000000	0.39475	U	0.001344	D	0.97340	0.9130	H	0.96691	3.865	0.58432	D	0.999998	P	0.40794	0.729	P	0.51229	0.663	D	0.98383	1.0559	10	0.62326	D	0.03	.	18.7298	0.91731	0.0:0.0:1.0:0.0	.	768	Q9Y623	MYH4_HUMAN	L	768	ENSP00000255381:F768L	ENSP00000255381:F768L	F	-	3	2	MYH4	10299114	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	3.989000	0.56958	2.497000	0.84241	0.313000	0.20887	TTC	.	.	.	none		0.403	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		T	10358389	G	T	10358389	3	4	212	1	0	0	0	0	1	0	0	0	10044	933	33	4	3595	4	MYH4	17	10358389	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10		10358389	70836821	43	12928											
C17orf48	56985	hgsc.bcm.edu	37	chr17	10608594	10608594	+	Missense_Mutation	SNP	T	T	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	catgaattctataacttcagTagagagtatttaacacactc	15	13	5	8	0	2	2	1	1	1	1	3	3	2	2	0	0	2	2	0	0	6	8			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr17:10608594T>G	ENST00000379774.4	+	2	442	c.351T>G	c.(349-351)agT>agG	p.S117R	ADPRM_ENST00000609540.1_Missense_Mutation_p.S117R	NM_020233.4	NP_064618.3	Q3LIE5	ADPRM_HUMAN	ADP-ribose/CDP-alcohol diphosphatase, manganese-dependent	117							ADP-ribose diphosphatase activity (GO:0047631)|CDP-glycerol diphosphatase activity (GO:0047734)|metal ion binding (GO:0046872)										ATAACTTCAGTAGAGAGTATT	0.358																																					p.S117R		Atlas-SNP	.											.	.	.	.	0			c.T351G						PASS	.						83	78	80					17																	10608594		2203	4300	6503	SO:0001583	missense	56985	exon2			CTTCAGTAGAGAG	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.351T>G	chr17.hg19:g.10608594T>G	ENSP00000369099:p.Ser117Arg	113.0	0.0	.		149.0	81.0	.	NM_020233	A8K9B4|D3DTS4|Q9BVD4|Q9NRU8	Missense_Mutation	SNP	ENST00000379774.4	hg19	CCDS11159.2	.	.	.	.	.	.	.	.	.	.	T	13.35	2.211314	0.39102	.	.	ENSG00000170222	ENST00000379774	D	0.84800	-1.9	5.64	-3.05	0.05396	Metallophosphoesterase domain (1);	0.000000	0.85682	D	0.000000	T	0.80919	0.4716	M	0.65498	2.005	0.80722	D	1	B	0.22080	0.064	B	0.27380	0.079	T	0.67264	-0.5714	10	0.21014	T	0.42	-25.0558	14.2725	0.66159	0.0:0.7691:0.1179:0.113	.	117	Q3LIE5	ADPRM_HUMAN	R	117	ENSP00000369099:S117R	ENSP00000369099:S117R	S	+	3	2	C17orf48	10549319	0.999000	0.42202	0.983000	0.44433	0.902000	0.53008	0.629000	0.24538	-0.424000	0.07382	-0.299000	0.09455	AGT	.	.	.	none		0.358	ADPRM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252732.2	NM_020233		G	10608594	T	G	10608594	3	3	212	1	0	0	0	0	1	0	0	0	1861	1635	57	5	353	5	C17orf48	17	10608594	Missense_Mutation	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10	250205	10608594	70586616	44	12929											
SUPT6H	6830	hgsc.bcm.edu	37	chr17	27014486	27014486	+	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	cggaaagggacccacctcctGaaggtaggattggagtgaat	12	7	14	8	1	0	2	0	2	0	0	1	6	1	6	3	5	0	1	3	5	4	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr17:27014486G>T	ENST00000314616.6	+	23	3286	c.3003G>T	c.(3001-3003)ctG>ctT	p.L1001L	SUPT6H_ENST00000347486.4_Silent_p.L1001L	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	1001	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)					CCCACCTCCTGAAGGTAGGAT	0.458																																					p.L1001L		Atlas-SNP	.											.	SUPT6H	165	.	0			c.G3003T						PASS	.						46	41	43					17																	27014486		2203	4300	6503	SO:0001819	synonymous_variant	6830	exon23			CCTCCTGAAGGTA	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.3003G>T	chr17.hg19:g.27014486G>T		45.0	0.0	.		44.0	10.0	.	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Silent	SNP	ENST00000314616.6	hg19	CCDS32596.1																																																																																			.	.	.	none		0.458	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		T	27014486	G	T	27014486	2	4	212	1	0	0	0	0	0	0	0	1	15412	1277	45	4		4	SUPT6H	17	27014486	Silent	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	16405892	27014486	54180724	45	12930											
CACNB1	782	hgsc.bcm.edu	37	chr17	37341119	37341119	+	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	aggggggcacatgctctgtcTggggggggaagcagggaggg	7	5	23	6	0	2	0	0	0	2	0	2	2	2	2	0	9	2	3	0	9	1	0			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr17:37341119T>A	ENST00000394303.3	-	8	856		c.e8-2		CACNB1_ENST00000344140.5_Splice_Site|CACNB1_ENST00000582877.1_5'Flank|CACNB1_ENST00000394310.3_Splice_Site	NM_000723.4	NP_000714.3	Q02641	CACB1_HUMAN	calcium channel, voltage-dependent, beta 1 subunit						axon guidance (GO:0007411)|protein targeting to membrane (GO:0006612)|transport (GO:0006810)	sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	16					Dronedarone(DB04855)|Ibutilide(DB00308)|Magnesium Sulfate(DB00653)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	ATGCTCTGTCTGGGGGGGGAA	0.627																																					.	Esophageal Squamous(5;100 366 38393 41452 45827)	Atlas-SNP	.											.	CACNB1	89	.	0			c.649-2A>T						PASS	.						33	30	31					17																	37341119		2203	4300	6503	SO:0001630	splice_region_variant	782	exon9			TCTGTCTGGGGGG		CCDS11334.1, CCDS42311.1, CCDS45665.1	17q21-q22	2013-03-20			ENSG00000067191	ENSG00000067191		"Calcium channel subunits"	1401	protein-coding gene	gene with protein product		114207		CACNLB1		8381767, 8395940	Standard	NM_000723		Approved		uc002hrm.2	Q02641	OTTHUMG00000133217	ENST00000394303.3:c.649-2A>T	chr17.hg19:g.37341119T>A		102.0	0.0	.		83.0	50.0	.	NM_000723	A8K114|O15331|Q02639|Q02640|Q8N3X9|Q9C085|Q9UD79	Splice_Site	SNP	ENST00000394303.3	hg19	CCDS42311.1	.	.	.	.	.	.	.	.	.	.	T	18.41	3.618558	0.66787	.	.	ENSG00000067191	ENST00000539338;ENST00000394303;ENST00000344140;ENST00000394310;ENST00000536613	.	.	.	5.28	5.28	0.74379	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.1992	0.65690	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	CACNB1	34594645	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	7.867000	0.87062	1.992000	0.58205	0.454000	0.30748	.	.	.	.	weak		0.627	CACNB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256945.3		Intron	A	37341119	T	A	37341119	5	1	212	1	0	0	0	0	0	0	1	0	2554	1594	55	5	1282	5	CACNB1	17	37341119	Splice_Site	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10	10326633	37341119	43854091	46	12931											
ERBB2	2064	hgsc.bcm.edu	37	chr17	37883597	37883597	+	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	ggagccctctgaagaggaggCccccaggtctccactggcac	8	5	13	15	0	2	2	0	1	2	1	3	4	2	4	4	5	1	1	4	5	1	0			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr17:37883597C>T	ENST00000269571.5	+	26	3368	c.3209C>T	c.(3208-3210)gCc>gTc	p.A1070V	MIEN1_ENST00000474210.1_5'Flank|MIR4728_ENST00000580969.1_RNA|ERBB2_ENST00000541774.1_Missense_Mutation_p.A1055V|ERBB2_ENST00000584450.1_Intron|ERBB2_ENST00000445658.2_Missense_Mutation_p.A794V|ERBB2_ENST00000540147.1_Missense_Mutation_p.A1040V|ERBB2_ENST00000406381.2_Missense_Mutation_p.A1040V|ERBB2_ENST00000584601.1_Missense_Mutation_p.A1040V			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	1070					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)	GAAGAGGAGGCCCCCAGGTCT	0.617		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)																											p.A1070V		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.C3209T						PASS	.						35	39	38					17																	37883597		2203	4300	6503	SO:0001583	missense	2064	exon26			AGGAGGCCCCCAG	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.3209C>T	chr17.hg19:g.37883597C>T	ENSP00000269571:p.Ala1070Val	73.0	0.0	.		74.0	21.0	.	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	hg19	CCDS32642.1	.	.	.	.	.	.	.	.	.	.	C	12.57	1.978099	0.34942	.	.	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147	T;T;T;T;T	0.75704	-0.95;-0.95;-0.93;-0.96;-0.95	5.41	5.41	0.78517	.	.	.	.	.	T	0.63260	0.2496	L	0.29908	0.895	0.58432	D	0.99999	B;B;B	0.19817	0.017;0.019;0.039	B;B;B	0.18561	0.01;0.022;0.01	T	0.57854	-0.7739	9	0.17369	T	0.5	.	15.9084	0.79447	0.0:1.0:0.0:0.0	.	794;1055;1070	B4DTR1;P04626-4;P04626	.;.;ERBB2_HUMAN	V	1040;1055;794;1070;1040	ENSP00000385185:A1040V;ENSP00000446466:A1055V;ENSP00000404047:A794V;ENSP00000269571:A1070V;ENSP00000443562:A1040V	ENSP00000269571:A1070V	A	+	2	0	ERBB2	35137123	0.667000	0.27484	0.997000	0.53966	0.976000	0.68499	2.804000	0.47931	2.515000	0.84797	0.561000	0.74099	GCC	.	.	.	none		0.617	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			T	37883597	C	T	37883597	3	4	212	1	0	0	0	0	1	0	0	0	5208	739	26	2	3311	2	ERBB2	17	37883597	Missense_Mutation	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10	542478	37883597	43311613	47	12932											
C17orf77	146723	hgsc.bcm.edu	37	chr17	72588562	72588562	+	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	cagtgtatgttgcaaggtgtGcccaaacttttgtgcatgtg	8	14	12	7	0	0	0	0	0	0	0	0	0	0	0	1	1	4	4	1	1	3	4			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr17:72588562G>T	ENST00000392620.1	+	3	739	c.377G>T	c.(376-378)tGc>tTc	p.C126F	C17orf77_ENST00000328023.2_Missense_Mutation_p.C126F|CD300LD_ENST00000375352.1_5'Flank	NM_152460.2	NP_689673.2	Q96MU5	CQ077_HUMAN	chromosome 17 open reading frame 77	126	Cys-rich.					extracellular region (GO:0005576)				breast(2)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	11						TGCAAGGTGTGCCCAAACTTT	0.458																																					p.C126F		Atlas-SNP	.											.	C17orf77	31	.	0			c.G377T						PASS	.						151	143	145					17																	72588562		2203	4300	6503	SO:0001583	missense	146723	exon3			AGGTGTGCCCAAA		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.377G>T	chr17.hg19:g.72588562G>T	ENSP00000376396:p.Cys126Phe	70.0	0.0	.		65.0	18.0	.	NM_152460		Missense_Mutation	SNP	ENST00000392620.1	hg19	CCDS32721.1	.	.	.	.	.	.	.	.	.	.	G	2.196	-0.384056	0.04966	.	.	ENSG00000182352	ENST00000392620;ENST00000328023	T;T	0.55760	0.5;0.5	2.64	1.62	0.23740	.	.	.	.	.	T	0.39436	0.1078	N	0.08118	0	0.09310	N	1	D	0.59767	0.986	P	0.53861	0.736	T	0.18650	-1.0330	8	.	.	.	.	7.2654	0.26227	0.0:0.2771:0.7229:0.0	.	126	Q96MU5	CQ077_HUMAN	F	126	ENSP00000376396:C126F;ENSP00000329353:C126F	.	C	+	2	0	C17orf77	70100157	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.150000	0.16263	0.651000	0.30788	0.609000	0.83330	TGC	.	.	.	none		0.458	C17orf77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145090.2	NM_152460		T	72588562	G	T	72588562	3	4	212	1	0	0	0	0	1	0	0	0	1884	1319	46	4	379	4	C17orf77	17	72588562	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	34704965	72588562	8606648	48	12933											
MARCH2	51257	hgsc.bcm.edu	37	chr19	8503277	8503277	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agggctgccccacaggtctcCttccgctaccactgccagct	6	8	9	18	1	1	0	0	0	1	0	3	0	2	0	6	2	4	3	6	2	1	2			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr19:8503277C>T	ENST00000602117.1	+	5	1043	c.588C>T	c.(586-588)tcC>tcT	p.S196S	MARCH2_ENST00000215555.2_Silent_p.S196S|MARCH2_ENST00000381035.4_Silent_p.S126S|MARCH2_ENST00000601283.1_Intron|MARCH2_ENST00000393944.1_Silent_p.S196S			Q9P0N8	MARH2_HUMAN	membrane-associated ring finger (C3HC4) 2, E3 ubiquitin protein ligase	196					endocytosis (GO:0006897)|protein ubiquitination (GO:0016567)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(3)|ovary(3)|skin(1)|urinary_tract(1)	10						CACAGGTCTCCTTCCGCTACC	0.637																																					p.S196S		Atlas-SNP	.											.	MARCH2	17	.	0			c.C588T						PASS	.						54	54	54					19																	8503277		2203	4300	6503	SO:0001819	synonymous_variant	51257	exon5			GGTCTCCTTCCGC	AF151074	CCDS12202.1, CCDS32894.1	19p13.2	2013-01-09	2012-02-23			ENSG00000099785		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	28038	protein-coding gene	gene with protein product		613332	"membrane-associated ring finger (C3HC4) 2"			11042152, 14722266	Standard	NM_016496		Approved	HSPC240, MARCH-II, RNF172	uc002mjw.3	Q9P0N8		ENST00000602117.1:c.588C>T	chr19.hg19:g.8503277C>T		87.0	0.0	.		62.0	22.0	.	NM_001005415	A6NP10|Q5H785|Q8N5A3|Q96B78	Silent	SNP	ENST00000602117.1	hg19	CCDS12202.1																																																																																			.	.	.	none		0.637	MARCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460361.2	NM_016496		T	8503277	C	T	8503277	2	4	212	1	0	0	0	0	0	0	0	1	9308	668	24	2		2	MARCH2	19	8503277	Silent	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10		8503277	50625706	49	12934											
MAG	4099	hgsc.bcm.edu	37	chr19	35804347	35804347	+	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	agctgagtatgctgaaatccGggtcaagtgaaggagctggg	11	8	16	6	1	1	3	1	3	0	0	2	4	2	4	1	3	3	4	1	3	4	1			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr19:35804347G>T	ENST00000392213.3	+	11	2030	c.1871G>T	c.(1870-1872)cGg>cTg	p.R624L	MAG_ENST00000361922.4_3'UTR|MAG_ENST00000537831.2_Missense_Mutation_p.R599L	NM_002361.3	NP_002352.1	P20916	MAG_HUMAN	myelin associated glycoprotein	624					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)			GCTGAAATCCGGGTCAAGTGA	0.627																																					p.R624L		Atlas-SNP	.											MAG_ENST00000392213,colon,carcinoma,0,1	MAG	172	.	0			c.G1871T						PASS	.						53	44	47					19																	35804347		2203	4300	6503	SO:0001583	missense	4099	exon11			AAATCCGGGTCAA	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.1871G>T	chr19.hg19:g.35804347G>T	ENSP00000376048:p.Arg624Leu	35.0	0.0	.		37.0	2.0	.	NM_002361	B7Z2E5|F5GYC0|Q567S4	Missense_Mutation	SNP	ENST00000392213.3	hg19	CCDS12455.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.992488	0.74703	.	.	ENSG00000105695	ENST00000262624;ENST00000392213;ENST00000537831	T;T	0.70399	-0.48;-0.38	4.43	4.43	0.53597	.	0.205101	0.40554	N	0.001064	T	0.64193	0.2576	N	0.19112	0.55	0.36382	D	0.861966	D	0.63880	0.993	P	0.51229	0.663	T	0.74247	-0.3727	10	0.72032	D	0.01	.	12.4	0.55407	0.0:0.0:1.0:0.0	.	624	P20916	MAG_HUMAN	L	661;624;599	ENSP00000376048:R624L;ENSP00000440695:R599L	ENSP00000262624:R661L	R	+	2	0	MAG	40496187	1.000000	0.71417	0.939000	0.37840	0.958000	0.62258	5.034000	0.64152	2.274000	0.75844	0.462000	0.41574	CGG	.	.	.	none		0.627	MAG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466071.1	NM_080600		T	35804347	G	T	35804347	3	4	212	1	0	0	0	0	1	0	0	0	9169	1116	39	4	1942	4	MAG	19	35804347	Missense_Mutation	SNP	G	TCGA-IZ-A6M9-01A-11D-A31X-10	27301070	35804347	23324636	50	12935											
EPB41L1	2036	hgsc.bcm.edu	37	chr20	34765954	34765956	+	In_Frame_Del	DEL	CTT	CTT	-																															aaggactacttcggcctgacCttctgtgatgctgacagcca																										TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr20:34765954_34765956delCTT	ENST00000338074.2	+	4	584_586	c.423_425delCTT	c.(421-426)accttc>acc	p.F142del	EPB41L1_ENST00000373946.3_In_Frame_Del_p.F111del|EPB41L1_ENST00000373950.2_Intron|EPB41L1_ENST00000441639.1_In_Frame_Del_p.F80del|EPB41L1_ENST00000373941.1_In_Frame_Del_p.F142del|EPB41L1_ENST00000202028.5_In_Frame_Del_p.F80del	NM_001258329.1|NM_012156.2	NP_001245258.1|NP_036288.2	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	142	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)					TCGGCCTGACCTTCTGTGATGCT	0.576																																					p.141_142del		Atlas-Indel,Pindel	.											.	EPB41L1	111	.	0			c.422_424del						PASS	.																																			SO:0001651	inframe_deletion	2036	exon5			.	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.423_425delCTT	chr20.hg19:g.34765954_34765956delCTT	ENSP00000337168:p.Phe142del	64.0	0.0	0		50.0	20.0	0.4	NM_001258329	O15046|Q4VXM6|Q4VXM7|Q4VXM8|Q4VXN4|Q6ZT61|Q8IUU7|Q96CV5|Q96L65	In_Frame_Del	DEL	ENST00000338074.2	hg19	CCDS13271.1																																																																																			.	.	.	none		0.576	EPB41L1-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078978.3	NM_012156		-	34765956	CTT	-	34765954	7	5	212	1	0	1	0	1	0	0	0	0	5154	668	24	0	433	0	EPB41L1	20	34765954	In_Frame_Del	DEL	CTT	TCGA-IZ-A6M9-01A-11D-A31X-10		34765954	28259566	51	12936											
MORC2	22880	hgsc.bcm.edu	37	chr22	31345772	31345772	+	Missense_Mutation	SNP	T	T	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	cccgtactgcccaatctgagTagactcaggtgttcgcttgg	7	11	11	12	2	2	2	1	1	1	1	3	2	2	2	2	2	2	4	2	2	3	4			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chr22:31345772T>G	ENST00000397641.3	-	5	691	c.283A>C	c.(283-285)Act>Cct	p.T95P	MORC2_ENST00000215862.4_Missense_Mutation_p.T33P			Q9Y6X9	MORC2_HUMAN	MORC family CW-type zinc finger 2	95						cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	21						CCAATCTGAGTAGACTCAGGT	0.463																																					p.T33P		Atlas-SNP	.											.	MORC2	78	.	0			c.A97C						PASS	.						139	127	131					22																	31345772		2203	4300	6503	SO:0001583	missense	22880	exon6			TCTGAGTAGACTC	AB020659	CCDS33636.1	22q12.2	2005-06-15	2005-06-15	2005-06-15	ENSG00000133422	ENSG00000133422			23573	protein-coding gene	gene with protein product			"zinc finger, CW-type with coiled-coil domain 1", "zinc finger, CW type with coiled-coil domain 1"	ZCWCC1		14607086	Standard	XM_005261391		Approved	ZCW3, KIAA0852, AC004542.C22.1	uc003aje.1	Q9Y6X9	OTTHUMG00000151193	ENST00000397641.3:c.283A>C	chr22.hg19:g.31345772T>G	ENSP00000380763:p.Thr95Pro	82.0	0.0	.		59.0	23.0	.	NM_014941	B2RNB1|Q9UF28|Q9Y6V2	Missense_Mutation	SNP	ENST00000397641.3	hg19		.	.	.	.	.	.	.	.	.	.	T	26.9	4.777606	0.90195	.	.	ENSG00000133422	ENST00000397641;ENST00000215862	D;D	0.95205	-3.64;-3.64	5.62	5.62	0.85841	ATPase-like, ATP-binding domain (4);	0.050861	0.85682	D	0.000000	D	0.94968	0.8372	L	0.35341	1.055	0.80722	D	1	D	0.89917	1.0	D	0.70487	0.969	D	0.94117	0.7376	10	0.30854	T	0.27	.	15.8169	0.78608	0.0:0.0:0.0:1.0	.	95	Q9Y6X9	MORC2_HUMAN	P	95;33	ENSP00000380763:T95P;ENSP00000215862:T33P	ENSP00000215862:T33P	T	-	1	0	MORC2	29675772	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.698000	0.84413	2.151000	0.67156	0.482000	0.46254	ACT	.	.	.	none		0.463	MORC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321710.2	NM_014941		G	31345772	T	G	31345772	3	3	212	1	0	0	0	0	1	0	0	0	9709	1638	57	5	2903	5	MORC2	22	31345772	Missense_Mutation	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10		31345772	19958794	52	12937											
MAGED2	10916	hgsc.bcm.edu	37	chrX	54841947	54841947	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagtgccagcactggtgcCagtaccagtaccaataacag	12	6	11	12	0	0	0	0	0	0	0	0	0	0	0	4	2	6	4	4	2	4	3			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chrX:54841947C>T	ENST00000375068.1	+	12	1886	c.1653C>T	c.(1651-1653)gcC>gcT	p.A551A	MAGED2_ENST00000396224.1_Silent_p.A551A|MAGED2_ENST00000375062.4_Silent_p.A466A|MAGED2_ENST00000347546.4_Silent_p.A533A|MAGED2_ENST00000375053.2_Silent_p.A551A|SNORA11_ENST00000408789.1_RNA|MAGED2_ENST00000218439.4_Silent_p.A551A|MAGED2_ENST00000375060.1_Silent_p.A466A|MAGED2_ENST00000375058.1_Silent_p.A551A			Q9UNF1	MAGD2_HUMAN	melanoma antigen family D, 2	551						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						gcactggtgccagtaccagta	0.602																																					p.A551A		Atlas-SNP	.											.	MAGED2	74	.	0			c.C1653T						PASS	.						35	28	30					X																	54841947		2197	4291	6488	SO:0001819	synonymous_variant	10916	exon12			TGGTGCCAGTACC	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.1653C>T	chrX.hg19:g.54841947C>T		48.0	0.0	.		47.0	4.0	.	NM_201222	A6NMX0|O76058|Q5BJF3|Q8NAL6|Q9H218|Q9P0U9|Q9UM52	Silent	SNP	ENST00000375068.1	hg19	CCDS14362.1																																																																																			.	.	.	none		0.602	MAGED2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056821.2	NM_014599		T	54841947	C	T	54841947	2	4	212	1	0	0	0	0	0	0	0	1	9191	581	21	2		2	MAGED2	23	54841947	Silent	SNP	C	TCGA-IZ-A6M9-01A-11D-A31X-10		54841947	100428613	53	12938											
TCEAL4	79921	hgsc.bcm.edu	37	chrX	102841929	102841929	+	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	tgaaggagagccagggagtgAaacaagggctgcaggaaagc	15	3	17	6	0	0	3	0	2	0	1	0	6	0	5	1	4	4	2	1	4	4	0			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chrX:102841929A>T	ENST00000472745.1	+	3	878	c.326A>T	c.(325-327)gAa>gTa	p.E109V	TCEAL4_ENST00000494801.1_Missense_Mutation_p.E109V|TCEAL4_ENST00000415568.2_Missense_Mutation_p.E109V|TCEAL4_ENST00000468024.1_Missense_Mutation_p.E109V|TCEAL4_ENST00000472484.1_Missense_Mutation_p.E109V|TCEAL4_ENST00000372629.4_Missense_Mutation_p.E252V			Q96EI5	TCAL4_HUMAN	transcription elongation factor A (SII)-like 4	109	Glu-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(2)|skin(2)	6						CCAGGGAGTGAAACAAGGGCT	0.507																																					p.E109V		Atlas-SNP	.											.	TCEAL4	18	.	0			c.A326T						PASS	.						67	67	67					X																	102841929		2203	4300	6503	SO:0001583	missense	79921	exon3			GGAGTGAAACAAG	AF314542	CCDS14510.2, CCDS76004.1	Xq22.2	2014-03-21			ENSG00000133142	ENSG00000133142			26121	protein-coding gene	gene with protein product						14702039, 16221301	Standard	XM_005262192		Approved	FLJ21174, WEX7	uc004ekn.3	Q96EI5	OTTHUMG00000022103	ENST00000472745.1:c.326A>T	chrX.hg19:g.102841929A>T	ENSP00000424314:p.Glu109Val	153.0	1.0	.		126.0	104.0	.	NM_001006935	Q8WY12|Q9H2H1|Q9H775	Missense_Mutation	SNP	ENST00000472745.1	hg19	CCDS14510.2	.	.	.	.	.	.	.	.	.	.	A	10.28	1.307826	0.23821	.	.	ENSG00000133142	ENST00000372629;ENST00000468024;ENST00000472484;ENST00000415568;ENST00000414064;ENST00000472745;ENST00000494801;ENST00000469586	T;T;T;T;T;T;T	0.35973	1.32;1.28;1.28;1.28;1.28;1.28;1.44	3.99	1.55	0.23275	.	0.216564	0.23312	N	0.049559	T	0.38214	0.1032	M	0.63843	1.955	0.09310	N	1	P	0.38250	0.624	P	0.45577	0.486	T	0.25187	-1.0139	10	0.56958	D	0.05	.	5.2758	0.15649	0.7556:0.0:0.2444:0.0	.	109	Q96EI5	TCAL4_HUMAN	V	252;109;109;109;80;109;109;109	ENSP00000361712:E252V;ENSP00000421857:E109V;ENSP00000421156:E109V;ENSP00000415564:E109V;ENSP00000424314:E109V;ENSP00000427494:E109V;ENSP00000427053:E109V	ENSP00000361712:E252V	E	+	2	0	TCEAL4	102728585	0.003000	0.15002	0.001000	0.08648	0.387000	0.30353	1.156000	0.31712	0.221000	0.20879	-0.681000	0.03757	GAA	.	.	.	none		0.507	TCEAL4-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252339.2	NM_024863		T	102841929	A	T	102841929	3	4	212	1	0	0	0	0	1	0	0	0	15685	246	9	5	328	5	TCEAL4	23	102841929	Missense_Mutation	SNP	A	TCGA-IZ-A6M9-01A-11D-A31X-10	47999982	102841929	52428631	54	12939											
SLC25A5	292	hgsc.bcm.edu	37	chrX	118603720	118603720	+	Missense_Mutation	SNP	T	T	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	aggagcagggagttctgtccTtctggcgcggtaacctggcc	6	9	15	11	2	2	0	0	0	2	0	3	2	3	2	3	5	2	3	3	5	1	3			TCGA-IZ-A6M9-01A-11D-A31X-10	TCGA-IZ-A6M9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0541b2e4-13f8-4845-a6ba-6dfde158bc09	558c1803-c4c2-42cb-82cb-f3e277bf9beb	g.chrX:118603720T>G	ENST00000317881.8	+	2	324	c.208T>G	c.(208-210)Ttc>Gtc	p.F70V	SLC25A5_ENST00000460013.1_3'UTR|SLC25A5-AS1_ENST00000446986.1_RNA	NM_001152.4	NP_001143.2	P05141	ADT2_HUMAN	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 5	70					adenine transport (GO:0015853)|chromosome segregation (GO:0007059)|energy reserve metabolic process (GO:0006112)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)|positive regulation of cell proliferation (GO:0008284)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|MMXD complex (GO:0071817)|nucleus (GO:0005634)	adenine transmembrane transporter activity (GO:0015207)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|stomach(2)	12					Clodronate(DB00720)	AGTTCTGTCCTTCTGGCGCGG	0.498																																					p.F70V		Atlas-SNP	.											.	SLC25A5	33	.	0			c.T208G						PASS	.						166	157	160					X																	118603720		2203	4300	6503	SO:0001583	missense	292	exon2			CTGTCCTTCTGGC	BC068199	CCDS14578.1	Xq24	2013-08-09			ENSG00000005022	ENSG00000005022		"Solute carriers"	10991	protein-coding gene	gene with protein product		300150		ANT2		2168878, 2829183	Standard	NM_001152		Approved	T2, 2F1, T3	uc004erh.4	P05141	OTTHUMG00000022715	ENST00000317881.8:c.208T>G	chrX.hg19:g.118603720T>G	ENSP00000360671:p.Phe70Val	40.0	0.0	.		63.0	45.0	.	NM_001152	B2RCV1|O43350	Missense_Mutation	SNP	ENST00000317881.8	hg19	CCDS14578.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.010876	0.75046	.	.	ENSG00000005022	ENST00000317881	T	0.80214	-1.35	4.18	4.18	0.49190	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.90290	0.6963	M	0.90198	3.095	0.58432	D	0.999999	D	0.63880	0.993	D	0.69824	0.966	D	0.91908	0.5537	10	0.87932	D	0	.	12.1849	0.54231	0.0:0.0:0.0:1.0	.	70	P05141	ADT2_HUMAN	V	70	ENSP00000360671:F70V	ENSP00000360671:F70V	F	+	1	0	SLC25A5	118487748	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.575000	0.82447	1.622000	0.50330	0.430000	0.28490	TTC	.	.	.	none		0.498	SLC25A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058952.2	NM_001152		G	118603720	T	G	118603720	3	3	212	1	0	0	0	0	1	0	0	0	14525	1609	56	5	214	5	SLC25A5	23	118603720	Missense_Mutation	SNP	T	TCGA-IZ-A6M9-01A-11D-A31X-10	15761791	118603720	36666840	55	12940											
SFN	2810	hgsc.bcm.edu	37	chr1	27189915	27189915	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tattgagcagaaaagcaacgAggagggctcggaggagaagg	15	4	17	5	2	0	3	0	1	0	2	1	7	0	5	0	5	3	3	0	5	5	2			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr1:27189915A>G	ENST00000339276.4	+	1	283	c.212A>G	c.(211-213)gAg>gGg	p.E71G		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)		AAAAGCAACGAGGAGGGCTCG	0.627																																					p.E71G		Atlas-SNP	.											.	SFN	20	.	0			c.A212G						PASS	.						69	74	72					1																	27189915		2203	4300	6503	SO:0001583	missense	2810	exon1			GCAACGAGGAGGG	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.212A>G	chr1.hg19:g.27189915A>G	ENSP00000340989:p.Glu71Gly	106.0	0.0	.		116.0	46.0	.	NM_006142	B2R532|Q32Q18|Q53FT1|Q6FIC6|Q9UFY7	Missense_Mutation	SNP	ENST00000339276.4	hg19	CCDS288.1	.	.	.	.	.	.	.	.	.	.	A	11.09	1.535187	0.27475	.	.	ENSG00000175793	ENST00000339276;ENST00000538651	T	0.39787	1.06	5.96	5.96	0.96718	14-3-3 domain (4);	0.106868	0.41396	D	0.000892	T	0.16938	0.0407	N	0.00873	-1.125	0.27459	N	0.9532	B	0.02656	0.0	B	0.04013	0.001	T	0.13818	-1.0495	10	0.54805	T	0.06	-27.1227	12.0125	0.53295	0.8558:0.1442:0.0:0.0	.	71	P31947	1433S_HUMAN	G	71	ENSP00000340989:E71G	ENSP00000340989:E71G	E	+	2	0	SFN	27062502	1.000000	0.71417	0.994000	0.49952	0.719000	0.41307	4.148000	0.58085	2.270000	0.75569	0.533000	0.62120	GAG	.	.	.	none		0.627	SFN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011709.1	NM_006142		G	27189915	A	G	27189915	3	3	213	1	0	0	0	0	1	0	0	0	14172	304	11	3	214	3	SFN	1	27189915	Missense_Mutation	SNP	A	TCGA-J7-6720-01A-11D-2136-08		27189915	222060706	1	12941											
GPR3	2827	hgsc.bcm.edu	37	chr1	27720330	27720350	+	In_Frame_Del	DEL	GCCTGGCTCTCAGCTGGCTCA	GCCTGGCTCTCAGCTGGCTCA	-																															ggggtgcaggcagccctctgGcctggctctcagctggctca																										TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	GCCTGGCTCTCAGCTGGCTCA	GCCTGGCTCTCAGCTGGCTCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr1:27720330_27720350delGCCTGGCTCTCAGCTGGCTCA	ENST00000374024.3	+	2	127_147	c.28_48delGCCTGGCTCTCAGCTGGCTCA	c.(28-48)gcctggctctcagctggctcadel	p.AWLSAGS10del		NM_005281.3	NP_005272.1	P46089	GPR3_HUMAN	G protein-coupled receptor 3	10					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|regulation of meiosis (GO:0040020)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|lung(3)|ovary(1)|skin(1)	8		Breast(348;1.53e-05)|Ovarian(437;0.0606)|all_lung(284;0.157)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;2.81e-26)|Colorectal(126;1.24e-08)|KIRC - Kidney renal clear cell carcinoma(1967;3.23e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;4.45e-06)|Lung(427;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|LUSC - Lung squamous cell carcinoma(448;0.008)|READ - Rectum adenocarcinoma(331;0.0419)		CAGCCCTCTGGCCTGGCTCTCAGCTGGCTCAGGCAACGTGA	0.633																																					p.9_16del		Atlas-INDEL	.											.	GPR3	23	.	0			c.27_47del						PASS	.																																			SO:0001651	inframe_deletion	2827	exon2			.	BC032702	CCDS303.1	1p36.1-p35	2012-08-21			ENSG00000181773	ENSG00000181773		"GPCR / Class A : Orphans"	4484	protein-coding gene	gene with protein product		600241				7851889	Standard	NM_005281		Approved	ACCA	uc001bod.4	P46089	OTTHUMG00000003397	ENST00000374024.3:c.28_48delGCCTGGCTCTCAGCTGGCTCA	chr1.hg19:g.27720330_27720350delGCCTGGCTCTCAGCTGGCTCA	ENSP00000363136:p.Ala10_Ser16del	232.0	0.0	0		213.0	24.0	0.112676	NM_005281	A8K570	In_Frame_Del	DEL	ENST00000374024.3	hg19	CCDS303.1																																																																																			.	.	.	none		0.633	GPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009522.1	NM_005281		-	27720350	GCCTGGCTCTCAGCTGGCTCA	-	27720330	7	5	213	1	0	1	0	1	0	0	0	0	6693	1203	42	0	30	0	GPR3	1	27720330	In_Frame_Del	DEL	GCCTGGCTCTCAGCTGGCTCA	TCGA-J7-6720-01A-11D-2136-08	530415	27720330	221530291	2	12942											
PIAS3	10401	hgsc.bcm.edu	37	chr1	145578967	145578967	+	Missense_Mutation	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	cagagaggttctgccaggagCcaaatgtgattataccatac	13	9	10	9	0	1	2	0	1	1	1	1	4	1	3	3	2	4	1	3	2	4	4			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr1:145578967C>T	ENST00000393045.2	+	4	635	c.545C>T	c.(544-546)gCc>gTc	p.A182V	PIAS3_ENST00000369298.1_Missense_Mutation_p.A147V|PIAS3_ENST00000369299.3_Missense_Mutation_p.A173V	NM_006099.3	NP_006090.2	Q9Y6X2	PIAS3_HUMAN	protein inhibitor of activated STAT, 3	182	PINIT. {ECO:0000255|PROSITE- ProRule:PRU00799}.				positive regulation of gene expression (GO:0010628)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein sumoylation (GO:0033235)|protein sumoylation (GO:0016925)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|nucleus (GO:0005634)|synapse (GO:0045202)	enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|potassium channel regulator activity (GO:0015459)|protein C-terminus binding (GO:0008022)|SUMO ligase activity (GO:0019789)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)	28	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CTGCCAGGAGCCAAATGTGAT	0.527																																					p.A182V		Atlas-SNP	.											.	PIAS3	96	.	0			c.C545T						PASS	.						109	97	101					1																	145578967		2203	4300	6503	SO:0001583	missense	10401	exon4			CAGGAGCCAAATG	AB021868	CCDS72866.1	1q21	2011-10-11			ENSG00000131788	ENSG00000131788		"Zinc fingers, MIZ-type"	16861	protein-coding gene	gene with protein product	"zinc finger, MIZ-type containing 5"	605987				10319586	Standard	NM_006099		Approved	FLJ14651, ZMIZ5	uc001eoc.1	Q9Y6X2	OTTHUMG00000013750	ENST00000393045.2:c.545C>T	chr1.hg19:g.145578967C>T	ENSP00000376765:p.Ala182Val	126.0	0.0	.		131.0	48.0	.	NM_006099	Q9UFI3	Missense_Mutation	SNP	ENST00000393045.2	hg19	CCDS920.2	.	.	.	.	.	.	.	.	.	.	C	14.25	2.478871	0.44044	.	.	ENSG00000131788	ENST00000393046;ENST00000369299;ENST00000393045;ENST00000369298	T;T;T;T	0.44881	0.93;0.91;1.54;1.51	4.33	4.33	0.51752	PINIT domain (1);	0.000000	0.49916	D	0.000123	T	0.13841	0.0335	N	0.17474	0.49	0.38130	D	0.938123	B;P	0.47841	0.024;0.901	B;B	0.41088	0.061;0.347	T	0.03240	-1.1057	10	0.13108	T	0.6	-12.7129	14.3972	0.67020	0.0:1.0:0.0:0.0	.	173;182	F8WA94;Q9Y6X2	.;PIAS3_HUMAN	V	173;173;182;147	ENSP00000376766:A173V;ENSP00000358305:A173V;ENSP00000376765:A182V;ENSP00000358304:A147V	ENSP00000358304:A147V	A	+	2	0	PIAS3	144290324	0.999000	0.42202	1.000000	0.80357	0.582000	0.36321	1.616000	0.36933	2.230000	0.72887	0.655000	0.94253	GCC	.	.	.	none		0.527	PIAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038533.4	NM_006099		T	145578967	C	T	145578967	3	4	213	1	0	0	0	0	1	0	0	0	11884	739	26	2	559	2	PIAS3	1	145578967	Missense_Mutation	SNP	C	TCGA-J7-6720-01A-11D-2136-08	117858637	145578967	103671654	3	12943											
C1orf182	128229	hgsc.bcm.edu	37	chr1	156309583	156309583	+	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	tagtcatcctaacagaaaagGtgtgtgttggaggccctgct	10	11	12	8	0	1	1	1	0	0	1	2	2	2	2	2	3	2	2	2	3	4	3	rs113369857		TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr1:156309583G>C	ENST00000368255.3	+	2	394		c.e2+1		TSACC_ENST00000470342.1_Splice_Site|CCT3_ENST00000368261.3_5'Flank|CCT3_ENST00000472765.2_5'Flank|CCT3_ENST00000295688.3_5'Flank|TSACC_ENST00000368253.2_Splice_Site|CCT3_ENST00000368256.3_5'Flank|TSACC_ENST00000481479.1_Splice_Site|TSACC_ENST00000368252.1_Splice_Site|TSACC_ENST00000368254.1_Splice_Site|TSACC_ENST00000368251.1_Splice_Site|TSACC_ENST00000466306.1_Splice_Site|CCT3_ENST00000368259.2_5'Flank	NM_144627.3	NP_653228.1	Q96A04	TSACC_HUMAN	TSSK6 activating co-chaperone							cytoplasm (GO:0005737)	chaperone binding (GO:0051087)										AACAGAAAAGGTGTGTGTTGG	0.483																																					.		Atlas-SNP	.											.	.	.	.	0			c.34+1G>C						PASS	.						147	127	134					1																	156309583		2203	4300	6503	SO:0001630	splice_region_variant	128229	exon2			GAAAAGGTGTGTG	AY048672	CCDS1141.1	1q22	2012-08-16	2012-08-16	2012-08-16	ENSG00000163467	ENSG00000163467			30636	protein-coding gene	gene with protein product	"SSTK-interacting protein"		"chromosome 1 open reading frame 182"	C1orf182		20829357	Standard	NM_144627		Approved	SSTK-IP, SIP	uc001foo.3	Q96A04	OTTHUMG00000024060	ENST00000368255.3:c.34+1G>C	chr1.hg19:g.156309583G>C		68.0	0.0	.		59.0	17.0	.	NM_144627	D3DVB9	Splice_Site	SNP	ENST00000368255.3	hg19	CCDS1141.1	.	.	.	.	.	.	.	.	.	.	G	15.30	2.792835	0.50102	.	.	ENSG00000163467	ENST00000368255;ENST00000368254;ENST00000368253;ENST00000368252;ENST00000368251	.	.	.	2.76	2.76	0.32466	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.1866	0.37174	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C1orf182	154576207	1.000000	0.71417	0.995000	0.50966	0.965000	0.64279	2.090000	0.41682	1.852000	0.53769	0.467000	0.42956	.	.	.	.	alt		0.483	TSACC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060594.1	NM_144627	Intron	C	156309583	G	C	156309583	5	2	213	1	0	0	0	0	0	0	1	0	2020	1275	44	4	37	4	C1orf182	1	156309583	Splice_Site	SNP	G	TCGA-J7-6720-01A-11D-2136-08	10730616	156309583	92941038	4	12944											
CALCRL	10203	hgsc.bcm.edu	37	chr2	188245425	188245425	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgatggatcaaagtcctgaaAgtaatcagggcagagctgca	14	8	12	7	0	2	3	2	2	0	1	3	4	3	4	1	2	2	4	1	2	3	1			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr2:188245425A>G	ENST00000409998.1	-	7	1055	c.274T>C	c.(274-276)Ttt>Ctt	p.F92L	AC007319.1_ENST00000453517.1_RNA|CALCRL_ENST00000392370.3_Missense_Mutation_p.F92L|CALCRL_ENST00000410068.1_Missense_Mutation_p.F92L|AC007319.1_ENST00000412276.1_RNA			Q16602	CALRL_HUMAN	calcitonin receptor-like	92					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)			AAGTCCTGAAAGTAATCAGGG	0.418																																					p.F92L		Atlas-SNP	.											.	CALCRL	73	.	0			c.T274C						PASS	.						68	66	67					2																	188245425		2203	4300	6503	SO:0001583	missense	10203	exon5			CCTGAAAGTAATC	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.274T>C	chr2.hg19:g.188245425A>G	ENSP00000386972:p.Phe92Leu	41.0	0.0	.		67.0	34.0	.	NM_001271751	A8K6G5|A8KAD3|Q53S02|Q53TS5	Missense_Mutation	SNP	ENST00000409998.1	hg19	CCDS2293.1	.	.	.	.	.	.	.	.	.	.	A	31	5.083990	0.94100	.	.	ENSG00000064989	ENST00000392370;ENST00000409998;ENST00000410068	T;T;T	0.64803	-0.12;-0.12;-0.12	5.29	5.29	0.74685	GPCR, family 2, extracellular hormone receptor domain (3);	0.000000	0.64402	D	0.000002	T	0.54886	0.1886	L	0.42008	1.315	0.80722	D	1	P	0.46220	0.874	B	0.42495	0.389	T	0.53041	-0.8494	10	0.25751	T	0.34	.	13.2254	0.59912	1.0:0.0:0.0:0.0	.	92	Q16602	CALRL_HUMAN	L	92	ENSP00000376177:F92L;ENSP00000386972:F92L;ENSP00000387190:F92L	ENSP00000376177:F92L	F	-	1	0	CALCRL	187953670	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.861000	0.75478	2.221000	0.72209	0.455000	0.32223	TTT	.	.	.	none		0.418	CALCRL-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334648.1	NM_005795		G	188245425	A	G	188245425	3	3	213	1	0	0	0	0	1	0	0	0	2582	72	3	3	1151	3	CALCRL	2	188245425	Missense_Mutation	SNP	A	TCGA-J7-6720-01A-11D-2136-08		188245425	54953948	5	12945											
WDR12	55759	hgsc.bcm.edu	37	chr2	203762106	203762106	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccttccaaggaccagatcCgagaagtcttatcataagaa	14	10	7	10	1	2	3	1	0	1	3	5	5	5	4	4	1	0	0	4	1	5	4			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr2:203762106C>T	ENST00000261015.4	-	5	1120	c.371G>A	c.(370-372)cGg>cAg	p.R124Q	WDR12_ENST00000477723.1_5'Flank	NM_018256.3	NP_060726.3			WD repeat domain 12											endometrium(3)|large_intestine(1)|liver(1)|lung(6)|prostate(1)|skin(1)	13						GGACCAGATCCGAGAAGTCTT	0.383																																					p.R124Q		Atlas-SNP	.											.	WDR12	35	.	0			c.G371A						PASS	.						105	97	100					2																	203762106		2203	4300	6503	SO:0001583	missense	55759	exon5			CAGATCCGAGAAG	AF242546	CCDS2356.1	2q33.1	2013-01-09			ENSG00000138442	ENSG00000138442		"WD repeat domain containing"	14098	protein-coding gene	gene with protein product						16043514, 17353269	Standard	NM_018256		Approved	YTM1, FLJ10881	uc002uzl.3	Q9GZL7	OTTHUMG00000132855	ENST00000261015.4:c.371G>A	chr2.hg19:g.203762106C>T	ENSP00000261015:p.Arg124Gln	120.0	0.0	.		107.0	26.0	.	NM_018256		Missense_Mutation	SNP	ENST00000261015.4	hg19	CCDS2356.1	.	.	.	.	.	.	.	.	.	.	C	14.97	2.695498	0.48202	.	.	ENSG00000138442	ENST00000261015	T	0.67865	-0.29	5.33	4.45	0.53987	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.056455	0.64402	N	0.000001	T	0.70570	0.3239	M	0.87827	2.91	0.53688	D	0.999978	B;B	0.21753	0.06;0.06	B;B	0.13407	0.009;0.009	T	0.71034	-0.4709	10	0.56958	D	0.05	-7.5369	13.8674	0.63596	0.0:0.9263:0.0:0.0737	.	124;124	Q53T99;Q9GZL7	.;WDR12_HUMAN	Q	124	ENSP00000261015:R124Q	ENSP00000261015:R124Q	R	-	2	0	WDR12	203470351	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.869000	0.63028	1.229000	0.43630	-0.218000	0.12543	CGG	.	.	.	none		0.383	WDR12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256329.4	NM_018256		T	203762106	C	T	203762106	3	4	213	1	0	0	0	0	1	0	0	0	17286	652	23	1	936	1	WDR12	2	203762106	Missense_Mutation	SNP	C	TCGA-J7-6720-01A-11D-2136-08	15516681	203762106	39437267	6	12946											
COL4A3	1285	hgsc.bcm.edu	37	chr2	228145271	228145271	+	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	tggacttccaggtctccctgGaactccaggaaatgaagggc	10	8	12	11	0	1	1	0	1	1	0	4	4	3	4	3	5	1	0	3	5	3	1			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr2:228145271G>T	ENST00000396578.3	+	30	2501	c.2339G>T	c.(2338-2340)gGa>gTa	p.G780V	AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000433324.1_RNA|AC097662.2_ENST00000439598.2_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	780	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)		GGTCTCCCTGGAACTCCAGGA	0.498																																					p.G780V		Atlas-SNP	.											.	COL4A3	293	.	0			c.G2339T	GRCh37	CM034405	COL4A3	M		PASS	.						102	104	103					2																	228145271		1895	4117	6012	SO:0001583	missense	1285	exon30			TCCCTGGAACTCC		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.2339G>T	chr2.hg19:g.228145271G>T	ENSP00000379823:p.Gly780Val	175.0	0.0	.		198.0	66.0	.	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	ENST00000396578.3	hg19	CCDS42829.1	.	.	.	.	.	.	.	.	.	.	G	16.90	3.249670	0.59212	.	.	ENSG00000169031	ENST00000396578;ENST00000328380;ENST00000335583;ENST00000396574;ENST00000315699	D	0.99353	-5.77	5.49	5.49	0.81192	.	0.000000	0.56097	D	0.000033	D	0.99542	0.9836	M	0.93016	3.37	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	0.98235	1.0485	10	0.87932	D	0	.	16.2931	0.82759	0.0:0.0:1.0:0.0	.	780;780;780;780	Q01955-5;Q01955-4;Q01955-2;Q01955	.;.;.;CO4A3_HUMAN	V	780	ENSP00000379823:G780V	ENSP00000323334:G780V	G	+	2	0	COL4A3	227853515	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.405000	0.66351	2.596000	0.87737	0.557000	0.71058	GGA	.	.	.	none		0.498	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091		T	228145271	G	T	228145271	3	4	213	1	0	0	0	0	1	0	0	0	3693	1174	41	4	2457	4	COL4A3	2	228145271	Missense_Mutation	SNP	G	TCGA-J7-6720-01A-11D-2136-08	24383165	228145271	15054102	7	12947											
FBXO36	130888	hgsc.bcm.edu	37	chr2	230875429	230875429	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagctgtgcatgtctgataaActgtgggaacagatagtcca	12	10	11	8	0	1	2	0	1	1	1	2	3	2	3	1	1	4	2	1	1	4	2			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr2:230875429A>G	ENST00000283946.3	+	4	414	c.396A>G	c.(394-396)aaA>aaG	p.K132K	FBXO36_ENST00000409992.1_Silent_p.K112K|FBXO36_ENST00000373652.3_Silent_p.K101K	NM_174899.4	NP_777559.3	Q8NEA4	FBX36_HUMAN	F-box protein 36	132	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.									endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	7		Renal(207;0.0112)|all_lung(227;0.0179)|Lung NSC(271;0.0804)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;7.56e-14)|all cancers(144;7.74e-11)|Lung(119;0.00488)|LUSC - Lung squamous cell carcinoma(224;0.008)		TGTCTGATAAACTGTGGGAAC	0.532																																					p.K132K		Atlas-SNP	.											.	FBXO36	22	.	0			c.A396G						PASS	.						63	56	58					2																	230875429		2203	4300	6503	SO:0001819	synonymous_variant	130888	exon4			TGATAAACTGTGG	BC033935	CCDS2472.1	2q37.1	2008-02-05	2004-06-15		ENSG00000153832	ENSG00000153832		"F-boxes /  "other""	27020	protein-coding gene	gene with protein product		609105	"F-box only protein 36"			12477932	Standard	NM_174899		Approved	Fbx36, FLJ37592	uc002vqa.3	Q8NEA4	OTTHUMG00000133206	ENST00000283946.3:c.396A>G	chr2.hg19:g.230875429A>G		46.0	0.0	.		64.0	17.0	.	NM_174899	B3KVQ6|Q53TE6|Q8WWD4	Silent	SNP	ENST00000283946.3	hg19	CCDS2472.1																																																																																			.	.	.	none		0.532	FBXO36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256919.2	NM_174899		G	230875429	A	G	230875429	2	3	213	1	0	0	0	0	0	0	0	1	5752	40	2	3		3	FBXO36	2	230875429	Silent	SNP	A	TCGA-J7-6720-01A-11D-2136-08	2730158	230875429	12323944	8	12948											
ACY1	95	hgsc.bcm.edu	37	chr3	52020519	52020519	+	Splice_Site	DEL	G	G	-																															gcaggctttgccctggatgaGggtgagcaggttggcaagcc																										TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr3:52020519delG	ENST00000404366.2	+	7	671	c.525delG	c.(523-525)gag>ga	p.E175fs	ACY1_ENST00000476854.1_Splice_Site_p.E175fs|ABHD14A-ACY1_ENST00000463937.1_Splice_Site_p.E276fs|ACY1_ENST00000458031.2_Splice_Site_p.E265fs|ACY1_ENST00000476351.1_Splice_Site_p.E140fs|ACY1_ENST00000494103.1_Intron	NM_000666.2|NM_001198895.1	NP_000657.1|NP_001185824.1	Q03154	ACY1_HUMAN	aminoacylase 1	175					cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aminoacylase activity (GO:0004046)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Acetylcysteine(DB06151)|L-Aspartic Acid(DB00128)	CCCTGGATGAGGGTGAGCAGG	0.612																																					p.E175fs		Atlas-INDEL	.											.	ACY1	35	.	0			c.524delA						PASS	.						60	60	60					3																	52020519		2203	4300	6503	SO:0001630	splice_region_variant	95	exon7			.	L07548	CCDS2844.1, CCDS56261.1, CCDS56262.1, CCDS56263.1	3p21.2	2006-02-02			ENSG00000243989	ENSG00000243989	3.5.1.14		177	protein-coding gene	gene with protein product		104620				1707030, 6948533	Standard	NM_000666		Approved		uc003dcq.3	Q03154	OTTHUMG00000157815	ENST00000404366.2:c.526+1G>-	chr3.hg19:g.52020519delG		72.0	0.0	0		85.0	37.0	0.435294	NM_001198895	C9J6I6|C9J9D8|C9JWD4	Frame_Shift_Del	DEL	ENST00000404366.2	hg19	CCDS2844.1																																																																																			.	.	.	none		0.612	ACY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349657.1	NM_000666	Frame_Shift_Del	-	52020519	G	-	52020519	8	5	213	1	0	1	0	1	0	0	1	0	226	1014	35	0	547	0	ACY1	3	52020519	Splice_Site	DEL	G	TCGA-J7-6720-01A-11D-2136-08		52020519	146001911	9	12949											
TWF2	11344	hgsc.bcm.edu	37	chr3	52269098	52269098	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agccagcccgtgccttggcaAagaattccttcagctcttcc	8	10	8	15	1	2	1	1	0	1	1	4	1	4	1	5	1	4	2	5	1	2	4			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr3:52269098A>G	ENST00000305533.5	-	2	293	c.50T>C	c.(49-51)tTt>tCt	p.F17S	TLR9_ENST00000597542.1_5'UTR|TWF2_ENST00000499914.2_Missense_Mutation_p.F17S	NM_007284.3	NP_009215.1	Q6IBS0	TWF2_HUMAN	twinfilin actin-binding protein 2	17	ADF-H 1. {ECO:0000255|PROSITE- ProRule:PRU00599}.				barbed-end actin filament capping (GO:0051016)|cell projection organization (GO:0030030)|cellular response to growth factor stimulus (GO:0071363)|cellular response to retinoic acid (GO:0071300)|negative regulation of actin filament polymerization (GO:0030837)|positive regulation of axon extension (GO:0045773)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of microvillus length (GO:0032532)|sequestering of actin monomers (GO:0042989)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|myofibril (GO:0030016)|perinuclear region of cytoplasm (GO:0048471)|stereocilium (GO:0032420)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|poly(A) RNA binding (GO:0044822)|protein kinase C binding (GO:0005080)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|stomach(1)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;2.43e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		TGCCTTGGCAAAGAATTCCTT	0.572																																					p.F17S		Atlas-SNP	.											.	TWF2	33	.	0			c.T50C						PASS	.						112	98	103					3																	52269098		2203	4300	6503	SO:0001583	missense	11344	exon2			TTGGCAAAGAATT	Y17169	CCDS2849.1	3p21.1	2013-04-25	2013-04-25	2006-11-13	ENSG00000247596	ENSG00000247596			9621	protein-coding gene	gene with protein product		607433	"protein tyrosine kinase 9-like (A6-related protein)", "PTK9L protein tyrosine kinase 9-like (A6-related protein)", "twinfilin, actin-binding protein, homolog 2 (Drosophila)"	PTK9L		10406962, 12807912	Standard	NM_007284		Approved	A6RP, A6r		Q6IBS0	OTTHUMG00000158105	ENST00000305533.5:c.50T>C	chr3.hg19:g.52269098A>G	ENSP00000303908:p.Phe17Ser	80.0	0.0	.		103.0	33.0	.	NM_007284	Q9Y3F5	Missense_Mutation	SNP	ENST00000305533.5	hg19	CCDS2849.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.727062	0.89390	.	.	ENSG00000247596	ENST00000305533;ENST00000499914	T;T	0.46063	0.88;0.88	4.58	4.58	0.56647	Actin-binding, cofilin/tropomyosin type (2);	.	.	.	.	T	0.71863	0.3390	M	0.93375	3.41	0.48288	D	0.999623	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.80141	-0.1506	9	0.87932	D	0	.	13.2613	0.60106	1.0:0.0:0.0:0.0	.	17;17	D6RG15;Q6IBS0	.;TWF2_HUMAN	S	17	ENSP00000303908:F17S;ENSP00000426464:F17S	ENSP00000303908:F17S	F	-	2	0	TWF2	52244138	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.871000	0.92346	1.927000	0.55829	0.459000	0.35465	TTT	.	.	.	none		0.572	TWF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350199.2			G	52269098	A	G	52269098	3	3	213	1	0	0	0	0	1	0	0	0	16794	14	1	3	1031	3	TWF2	3	52269098	Missense_Mutation	SNP	A	TCGA-J7-6720-01A-11D-2136-08	248579	52269098	145753332	10	12950											
KALRN	8997	hgsc.bcm.edu	37	chr3	124438147	124438147	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggcggcccacagcagccAcatgcttgcagcatccatgg	9	5	13	14	1	0	0	0	0	0	0	1	1	1	1	3	4	5	4	3	4	0	1			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr3:124438147A>G	ENST00000291478.5	+	27	3863	c.3700A>G	c.(3700-3702)Aca>Gca	p.T1234A	KALRN_ENST00000360013.3_Missense_Mutation_p.T2931A|KALRN_ENST00000428018.2_Missense_Mutation_p.T1202A	NM_007064.3	NP_008995.2	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	2930					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						CACAGCAGCCACATGCTTGCA	0.532																																					p.T2931A		Atlas-SNP	.											.	KALRN	556	.	0			c.A8791G						PASS	.						49	52	51					3																	124438147		2203	4300	6503	SO:0001583	missense	8997	exon60			GCAGCCACATGCT	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.3700A>G	chr3.hg19:g.124438147A>G	ENSP00000291478:p.Thr1234Ala	91.0	0.0	.		105.0	5.0	.	NM_001024660	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Missense_Mutation	SNP	ENST00000291478.5	hg19	CCDS3028.1	.	.	.	.	.	.	.	.	.	.	A	8.186	0.794821	0.16327	.	.	ENSG00000160145	ENST00000360013;ENST00000291478;ENST00000428018	T;T;T	0.38560	1.13;1.13;1.13	5.3	5.3	0.74995	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.136740	0.50627	D	0.000115	T	0.16896	0.0406	N	0.01209	-0.955	0.29636	N	0.845117	B;B	0.13594	0.008;0.001	B;B	0.14023	0.01;0.003	T	0.05666	-1.0871	10	0.09843	T	0.71	.	15.4077	0.74893	1.0:0.0:0.0:0.0	.	1234;2930	C9JQ37;O60229	.;KALRN_HUMAN	A	2931;1234;1202	ENSP00000353109:T2931A;ENSP00000291478:T1234A;ENSP00000402419:T1202A	ENSP00000291478:T1234A	T	+	1	0	KALRN	125920837	0.999000	0.42202	1.000000	0.80357	0.478000	0.33099	1.735000	0.38176	2.225000	0.72522	0.460000	0.39030	ACA	.	.	.	none		0.532	KALRN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000246891.5	NM_003947		G	124438147	A	G	124438147	3	3	213	1	0	0	0	0	1	0	0	0	7982	159	6	3	9185	3	KALRN	3	124438147	Missense_Mutation	SNP	A	TCGA-J7-6720-01A-11D-2136-08	72169049	124438147	73584283	11	12951											
FNDC3B	64778	hgsc.bcm.edu	37	chr3	172025192	172025192	+	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	tccgtaaagggatcctgctcCgagcctgttagcttcaccac	8	10	9	14	2	1	0	1	0	0	0	4	2	4	1	5	1	3	4	5	1	3	3	rs145255541		TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr3:172025192C>G	ENST00000336824.4	+	10	1200	c.1101C>G	c.(1099-1101)tcC>tcG	p.S367S	FNDC3B_ENST00000416957.1_Silent_p.S367S|FNDC3B_ENST00000415807.2_Silent_p.S367S	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	367	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)		GATCCTGCTCCGAGCCTGTTA	0.502																																					p.S367S		Atlas-SNP	.											.	FNDC3B	118	.	0			c.C1101G						PASS	.						154	129	138					3																	172025192		2203	4300	6503	SO:0001819	synonymous_variant	64778	exon10			CTGCTCCGAGCCT	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.1101C>G	chr3.hg19:g.172025192C>G		106.0	0.0	.		131.0	39.0	.	NM_001135095	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Silent	SNP	ENST00000336824.4	hg19	CCDS3217.1																																																																																			.	C|1.000;T|0.000	.	alt		0.502	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763		G	172025192	C	G	172025192	2	3	213	1	0	0	0	0	0	0	0	1	5977	639	23	4		4	FNDC3B	3	172025192	Silent	SNP	C	TCGA-J7-6720-01A-11D-2136-08	47587045	172025192	25997238	12	12952											
TBC1D14	57533	hgsc.bcm.edu	37	chr4	7026865	7026865	+	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	gctgttcgaggacatcctgaCcaagatggacttcattcaca	11	10	9	11	1	2	2	2	1	0	1	4	5	3	4	2	2	0	2	2	2	1	3			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr4:7026865C>A	ENST00000409757.4	+	13	2016	c.1892C>A	c.(1891-1893)aCc>aAc	p.T631N	TBC1D14_ENST00000451522.2_Missense_Mutation_p.T351N|TBC1D14_ENST00000448507.1_Missense_Mutation_p.T631N|TBC1D14_ENST00000446947.2_Missense_Mutation_p.T278N|TBC1D14_ENST00000410031.1_Missense_Mutation_p.T403N	NM_020773.2	NP_065824.2	Q9P2M4	TBC14_HUMAN	TBC1 domain family, member 14	631					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						GACATCCTGACCAAGATGGAC	0.612																																					p.T631N		Atlas-SNP	.											.	TBC1D14	110	.	0			c.C1892A						PASS	.						145	117	127					4																	7026865		2203	4300	6503	SO:0001583	missense	57533	exon13			TCCTGACCAAGAT	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.1892C>A	chr4.hg19:g.7026865C>A	ENSP00000386921:p.Thr631Asn	134.0	0.0	.		168.0	45.0	.	NM_001113361	B9A6L5|D3DVT4|E9PAZ6|Q8IW15|Q8NDK3	Missense_Mutation	SNP	ENST00000409757.4	hg19	CCDS3394.2	.	.	.	.	.	.	.	.	.	.	C	14.93	2.681226	0.47886	.	.	ENSG00000132405	ENST00000448507;ENST00000409757;ENST00000410031;ENST00000451522;ENST00000446947	T;T;T;T;T	0.22134	1.97;1.97;1.97;1.97;1.97	5.15	5.15	0.70609	Rab-GAP/TBC domain (2);	0.162937	0.53938	D	0.000045	T	0.19287	0.0463	N	0.08118	0	0.58432	D	0.999994	B;B;B	0.34372	0.451;0.02;0.187	B;B;B	0.43838	0.242;0.104;0.433	T	0.25082	-1.0142	10	0.66056	D	0.02	-12.687	17.6366	0.88124	0.0:1.0:0.0:0.0	.	278;351;631	F5GXK4;Q9P2M4-2;Q9P2M4	.;.;TBC14_HUMAN	N	631;631;403;351;278	ENSP00000404041:T631N;ENSP00000386921:T631N;ENSP00000386343:T403N;ENSP00000388886:T351N;ENSP00000405875:T278N	ENSP00000386921:T631N	T	+	2	0	TBC1D14	7077766	0.256000	0.24012	1.000000	0.80357	0.994000	0.84299	1.090000	0.30902	2.409000	0.81822	0.561000	0.74099	ACC	.	.	.	none		0.612	TBC1D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206981.3	NM_020773		A	7026865	C	A	7026865	3	1	213	1	0	0	0	0	1	0	0	0	15615	507	18	4	1945	4	TBC1D14	4	7026865	Missense_Mutation	SNP	C	TCGA-J7-6720-01A-11D-2136-08		7026865	184127411	13	12953											
PDLIM5	10611	hgsc.bcm.edu	37	chr4	95496927	95496927	+	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	atcaccatcgtctgccttcaCcccagcccatgcgaccacct	8	8	5	20	2	3	0	2	0	1	0	4	1	3	0	7	0	3	0	7	0	0	1	rs200734812		TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr4:95496927C>G	ENST00000317968.4	+	5	588	c.452C>G	c.(451-453)aCc>aGc	p.T151S	PDLIM5_ENST00000514743.1_Intron|PDLIM5_ENST00000538141.1_Intron|PDLIM5_ENST00000437932.1_Intron|PDLIM5_ENST00000318007.5_Intron|PDLIM5_ENST00000450793.1_Intron|PDLIM5_ENST00000508216.1_Intron|PDLIM5_ENST00000542407.1_Missense_Mutation_p.T29S|PDLIM5_ENST00000380180.3_Intron	NM_001256428.1|NM_006457.4	NP_001243357.1|NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5	151					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)		TCTGCCTTCACCCCAGCCCAT	0.542																																					p.T151S		Atlas-SNP	.											.	PDLIM5	76	.	0			c.C452G						PASS	.						332	281	299					4																	95496927		2203	4300	6503	SO:0001583	missense	10611	exon5			CCTTCACCCCAGC	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.452C>G	chr4.hg19:g.95496927C>G	ENSP00000321746:p.Thr151Ser	346.0	0.0	.		408.0	111.0	.	NM_006457	A8K6F9|D6RB78|E9PBF5|O60705|Q56VN4|Q5UW38|Q8WVK0	Missense_Mutation	SNP	ENST00000317968.4	hg19	CCDS3641.1	.	.	.	.	.	.	.	.	.	.	C	15.94	2.981800	0.53827	.	.	ENSG00000163110	ENST00000317968;ENST00000542407	T;T	0.58940	0.72;0.3	5.25	5.25	0.73442	.	0.106561	0.64402	D	0.000004	T	0.72566	0.3476	M	0.65975	2.015	0.80722	D	1	D	0.69078	0.997	D	0.70716	0.97	T	0.66337	-0.5949	10	0.13470	T	0.59	.	19.2104	0.93751	0.0:1.0:0.0:0.0	.	151	Q96HC4	PDLI5_HUMAN	S	151;29	ENSP00000321746:T151S;ENSP00000442187:T29S	ENSP00000321746:T151S	T	+	2	0	PDLIM5	95715950	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.993000	0.63895	2.590000	0.87494	0.655000	0.94253	ACC	.	C|0.999;T|0.001	.	alt		0.542	PDLIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253586.1			G	95496927	C	G	95496927	3	3	213	1	0	0	0	0	1	0	0	0	11690	507	18	4	466	4	PDLIM5	4	95496927	Missense_Mutation	SNP	C	TCGA-J7-6720-01A-11D-2136-08	88470062	95496927	95657349	14	12954											
SH3RF1	57630	hgsc.bcm.edu	37	chr4	170028338	170028338	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcgccagaaagcaacttcaAcaaaccctttttttctttct	11	13	5	12	1	3	1	1	0	2	1	3	1	3	1	2	1	4	1	2	1	4	5			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr4:170028338A>G	ENST00000284637.9	-	11	2499	c.2158T>C	c.(2158-2160)Ttg>Ctg	p.L720L		NM_020870.3	NP_065921.2	Q7Z6J0	SH3R1_HUMAN	SH3 domain containing ring finger 1	720					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)		AGCAACTTCAACAAACCCTTT	0.468																																					p.L720L		Atlas-SNP	.											.	SH3RF1	60	.	0			c.T2158C						PASS	.						26	30	29					4																	170028338		2196	4289	6485	SO:0001819	synonymous_variant	57630	exon11			ACTTCAACAAACC	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.2158T>C	chr4.hg19:g.170028338A>G		63.0	0.0	.		77.0	23.0	.	NM_020870	Q05BT2|Q8IW46|Q9HAM2|Q9P234	Silent	SNP	ENST00000284637.9	hg19	CCDS34099.1																																																																																			.	.	.	none		0.468	SH3RF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363382.3	NM_020870		G	170028338	A	G	170028338	2	3	213	1	0	0	0	0	0	0	0	1	14271	40	2	3		3	SH3RF1	4	170028338	Silent	SNP	A	TCGA-J7-6720-01A-11D-2136-08	74531411	170028338	21125938	15	12955											
GIN1	54826	hgsc.bcm.edu	37	chr5	102444326	102444335	+	Frame_Shift_Del	DEL	AGTGTAGTTG	AGTGTAGTTG	-																															tgccacttctctcacttggcAgtgtagttgaatgatattca																								rs371302288		TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	AGTGTAGTTG	AGTGTAGTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr5:102444326_102444335delAGTGTAGTTG	ENST00000399004.2	-	2	171_180	c.77_86delCAACTACACT	c.(76-87)tcaactacactgfs	p.STTL26fs	GIN1_ENST00000508629.1_Frame_Shift_Del_p.STTL26fs	NM_017676.2	NP_060146.2	Q9NXP7	GIN1_HUMAN	gypsy retrotransposon integrase 1	26					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)		CTCACTTGGCAGTGTAGTTGAATGATATTC	0.343																																					p.26_29del		Atlas-INDEL	.											.	GIN1	53	.	0			c.78_87del						PASS	.																																			SO:0001589	frameshift_variant	54826	exon2			.	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.77_86delCAACTACACT	chr5.hg19:g.102444326_102444335delAGTGTAGTTG	ENSP00000381970:p.Ser26fs	67.0	0.0	0		71.0	16.0	0.225352	NM_017676	B2RXF7|B4DIV4|Q6AI03|Q96BR2	Frame_Shift_Del	DEL	ENST00000399004.2	hg19	CCDS43349.1																																																																																			.	.	.	none		0.343	GIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370478.3	NM_017676		-	102444335	AGTGTAGTTG	-	102444326	7	5	213	1	0	1	0	1	0	0	0	0	6393	188	7	0	1510	0	GIN1	5	102444326	Frame_Shift_Del	DEL	AGTGTAGTTG	TCGA-J7-6720-01A-11D-2136-08		102444326	78470934	16	12956											
HINT1	3094	hgsc.bcm.edu	37	chr5	130500845	130500845	+	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	ttgcggatgatcttcccaaaGatcgtgtcgccaccaggccg	8	9	11	13	4	1	2	0	1	1	1	4	3	2	3	4	2	1	0	4	2	1	2			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr5:130500845G>T	ENST00000304043.5	-	1	333	c.54C>A	c.(52-54)atC>atA	p.I18I	HINT1_ENST00000506908.1_Silent_p.I18I|HINT1_ENST00000508488.1_Silent_p.I18I|HINT1_ENST00000513012.1_Silent_p.I18I|HINT1_ENST00000506207.1_Intron	NM_005340.6	NP_005331.1	P49773	HINT1_HUMAN	histidine triad nucleotide binding protein 1	18	HIT. {ECO:0000255|PROSITE- ProRule:PRU00464}.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|purine ribonucleotide catabolic process (GO:0009154)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|nucleotide binding (GO:0000166)|protein kinase C binding (GO:0005080)			endometrium(1)|large_intestine(1)|lung(3)	5		all_cancers(142;0.0452)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Adenosine monophosphate(DB00131)	TCTTCCCAAAGATCGTGTCGC	0.587																																					p.I18I		Atlas-SNP	.											.	HINT1	7	.	0			c.C54A						PASS	.						83	74	77					5																	130500845		2203	4300	6503	SO:0001819	synonymous_variant	3094	exon1			CCCAAAGATCGTG	BC007090	CCDS4147.1	5q31.2	2010-03-30	2001-11-28	2002-03-08	ENSG00000169567	ENSG00000169567			4912	protein-coding gene	gene with protein product		601314	"histidine triad nucleotide-binding protein"	PRKCNH1, HINT		8812426	Standard	NM_005340		Approved	PKCI-1	uc003kve.4	P49773	OTTHUMG00000128995	ENST00000304043.5:c.54C>A	chr5.hg19:g.130500845G>T		70.0	0.0	.		107.0	40.0	.	NM_005340	Q9H5W8	Silent	SNP	ENST00000304043.5	hg19	CCDS4147.1																																																																																			.	.	.	none		0.587	HINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250984.1	NM_005340		T	130500845	G	T	130500845	2	4	213	1	0	0	0	0	0	0	0	1	7118	932	33	4		4	HINT1	5	130500845	Silent	SNP	G	TCGA-J7-6720-01A-11D-2136-08	28056519	130500845	50414415	17	12957											
TBC1D9B	23061	hgsc.bcm.edu	37	chr5	179326225	179326225	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acgaaggtggtgatatcttcCtcactgtcgaagatggacag	11	10	12	8	2	2	2	1	1	1	1	4	5	3	3	1	3	0	0	1	3	3	2			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr5:179326225C>T	ENST00000356834.3	-	3	349	c.312G>A	c.(310-312)gaG>gaA	p.E104E	TBC1D9B_ENST00000355235.3_Silent_p.E104E	NM_198868.2	NP_942568.2	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	104						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)			TGATATCTTCCTCACTGTCGA	0.478																																					p.E104E		Atlas-SNP	.											.	TBC1D9B	157	.	0			c.G312A						PASS	.						186	155	166					5																	179326225		2203	4300	6503	SO:0001819	synonymous_variant	23061	exon3			ATCTTCCTCACTG	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.312G>A	chr5.hg19:g.179326225C>T		45.0	0.0	.		59.0	19.0	.	NM_198868	D3DWQ5|D3DWQ6|O75163|Q53EY0|Q6MZI2|Q96H49	Silent	SNP	ENST00000356834.3	hg19	CCDS43408.1																																																																																			.	.	.	none		0.478	TBC1D9B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253501.3	NM_015043		T	179326225	C	T	179326225	2	4	213	1	0	0	0	0	0	0	0	1	15640	680	24	2		2	TBC1D9B	5	179326225	Silent	SNP	C	TCGA-J7-6720-01A-11D-2136-08	48825380	179326225	1589035	18	12958											
CDKAL1	54901	hgsc.bcm.edu	37	chr6	20846322	20846322	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acaggtgtctcaatgcttgtAcctactgcaaaactaaacac	14	10	6	11	0	1	0	1	0	1	0	2	0	1	0	1	1	6	3	1	1	7	4			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr6:20846322A>G	ENST00000378610.1	+	7	665	c.655A>G	c.(655-657)Acc>Gcc	p.T219A	CDKAL1_ENST00000378624.4_Missense_Mutation_p.T149A|CDKAL1_ENST00000274695.4_Missense_Mutation_p.T219A			Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein 1-like 1	219					maintenance of translational fidelity (GO:1990145)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|N6-threonylcarbomyladenosine methylthiotransferase activity (GO:0035598)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|stomach(1)	29	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			CAATGCTTGTACCTACTGCAA	0.343																																					p.T219A		Atlas-SNP	.											.	CDKAL1	55	.	0			c.A655G						PASS	.						75	75	75					6																	20846322		2203	4300	6503	SO:0001583	missense	54901	exon9			GCTTGTACCTACT	AK000349	CCDS4546.1	6p22.2	2008-02-05			ENSG00000145996	ENSG00000145996			21050	protein-coding gene	gene with protein product		611259					Standard	NM_017774		Approved	FLJ20342	uc003ndd.2	Q5VV42	OTTHUMG00000014340	ENST00000378610.1:c.655A>G	chr6.hg19:g.20846322A>G	ENSP00000367873:p.Thr219Ala	73.0	0.0	.		69.0	23.0	.	NM_017774	A8K6S0|Q6P385|Q6ZR27|Q9NXB3	Missense_Mutation	SNP	ENST00000378610.1	hg19	CCDS4546.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.612488	0.87258	.	.	ENSG00000145996	ENST00000274695;ENST00000378624;ENST00000378610	T;T;T	0.24151	1.87;1.87;1.87	5.81	5.81	0.92471	Elongator protein 3/MiaB/NifB (1);Radical SAM, alpha/beta horseshoe (1);Methylthiotransferase, conserved site (1);Radical SAM (1);	0.000000	0.85682	D	0.000000	T	0.42607	0.1210	M	0.66378	2.025	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;0.951	T	0.42378	-0.9455	10	0.87932	D	0	.	16.1616	0.81721	1.0:0.0:0.0:0.0	.	149;219	Q5VV42-2;Q5VV42	.;CDKAL_HUMAN	A	219;149;219	ENSP00000274695:T219A;ENSP00000367889:T149A;ENSP00000367873:T219A	ENSP00000274695:T219A	T	+	1	0	CDKAL1	20954301	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.971000	0.76105	2.218000	0.71995	0.377000	0.23210	ACC	.	.	.	none		0.343	CDKAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039986.1	NM_017774		G	20846322	A	G	20846322	3	3	213	1	0	0	0	0	1	0	0	0	3154	391	14	3	681	3	CDKAL1	6	20846322	Missense_Mutation	SNP	A	TCGA-J7-6720-01A-11D-2136-08		20846322	150268745	19	12959											
TJAP1	93643	hgsc.bcm.edu	37	chr6	43472653	43472653	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gccggagtctctactgctcaAttcagcccagtcaggcagcg	8	8	11	14	2	4	0	3	0	1	0	5	1	4	1	2	2	4	2	2	2	2	2			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr6:43472653A>G	ENST00000372445.5	+	11	1110	c.734A>G	c.(733-735)aAt>aGt	p.N245S	TJAP1_ENST00000438588.2_Missense_Mutation_p.N245S|TJAP1_ENST00000372444.2_Missense_Mutation_p.N235S|TJAP1_ENST00000483640.1_3'UTR|TJAP1_ENST00000436109.2_Missense_Mutation_p.N235S|TJAP1_ENST00000372452.1_Missense_Mutation_p.N235S|TJAP1_ENST00000372449.1_Missense_Mutation_p.N245S|TJAP1_ENST00000259751.1_Missense_Mutation_p.N235S	NM_001146016.1	NP_001139488.1	Q5JTD0	TJAP1_HUMAN	tight junction associated protein 1 (peripheral)	245					Golgi organization (GO:0007030)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)|trans-Golgi network (GO:0005802)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|urinary_tract(2)	21	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			CTACTGCTCAATTCAGCCCAG	0.637																																					p.N245S		Atlas-SNP	.											.	TJAP1	35	.	0			c.A734G						PASS	.						88	89	88					6																	43472653		2203	4300	6503	SO:0001583	missense	93643	exon11			TGCTCAATTCAGC	AK024269	CCDS4898.1, CCDS55004.1	6p21.1	2008-02-05	2005-07-05	2005-07-05	ENSG00000137221	ENSG00000137221			17949	protein-coding gene	gene with protein product		612658	"tight junction protein 4 (peripheral)"	TJP4		11602598	Standard	NM_001146016		Approved	PILT	uc011dvh.1	Q5JTD0	OTTHUMG00000014736	ENST00000372445.5:c.734A>G	chr6.hg19:g.43472653A>G	ENSP00000361522:p.Asn245Ser	161.0	0.0	.		182.0	20.0	.	NM_001146016	Q05BH9|Q5JTD1|Q5JWW1|Q68DB2|Q6P2P3|Q9H7V7	Missense_Mutation	SNP	ENST00000372445.5	hg19	CCDS55004.1	.	.	.	.	.	.	.	.	.	.	A	18.71	3.681816	0.68042	.	.	ENSG00000137221	ENST00000372444;ENST00000372445;ENST00000436109;ENST00000259751;ENST00000372454;ENST00000372452;ENST00000372449;ENST00000438588	T;T;T;T;T;T;T	0.20881	2.04;2.04;2.04;2.04;2.04;2.04;2.04	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.21022	0.0506	L	0.31664	0.95	0.58432	D	0.999999	D;D	0.89917	0.998;1.0	D;D	0.83275	0.987;0.996	T	0.05037	-1.0910	10	0.20046	T	0.44	-53.1615	14.9298	0.70906	1.0:0.0:0.0:0.0	.	245;235	Q5JTD0;Q5JTD0-2	TJAP1_HUMAN;.	S	235;245;235;235;235;235;245;245	ENSP00000361521:N235S;ENSP00000361522:N245S;ENSP00000407080:N235S;ENSP00000259751:N235S;ENSP00000361530:N235S;ENSP00000361527:N245S;ENSP00000408769:N245S	ENSP00000259751:N235S	N	+	2	0	TJAP1	43580631	1.000000	0.71417	0.995000	0.50966	0.806000	0.45545	8.900000	0.92551	1.912000	0.55364	0.459000	0.35465	AAT	.	.	.	none		0.637	TJAP1-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040629.1	NM_080604		G	43472653	A	G	43472653	3	3	213	1	0	0	0	0	1	0	0	0	15940	101	4	3	764	3	TJAP1	6	43472653	Missense_Mutation	SNP	A	TCGA-J7-6720-01A-11D-2136-08	22626331	43472653	127642414	20	12960											
ZDHHC14	79683	hgsc.bcm.edu	37	chr6	158093775	158093785	+	Frame_Shift_Del	DEL	TTCAGAGCACC	TTCAGAGCACC	-																															gtgcgaccaagaccagtgcaTtcagagcaccaaattcgttt																										TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	TTCAGAGCACC	TTCAGAGCACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr6:158093775_158093785delTTCAGAGCACC	ENST00000359775.5	+	9	1977_1987	c.1088_1098delTTCAGAGCACC	c.(1087-1098)attcagagcaccfs	p.IQST363fs	ZDHHC14_ENST00000341375.8_3'UTR|ZDHHC14_ENST00000414563.2_Intron			Q8IZN3	ZDH14_HUMAN	zinc finger, DHHC-type containing 14	363					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)		GACCAGTGCATTCAGAGCACCAAATTCGTTT	0.664																																					p.363_366del		Atlas-INDEL	.											.	ZDHHC14	39	.	0			c.1087_1097del						PASS	.																																			SO:0001589	frameshift_variant	79683	exon9			.	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.1088_1098delTTCAGAGCACC	chr6.hg19:g.158093775_158093785delTTCAGAGCACC	ENSP00000352821:p.Ile363fs	63.0	0.0	0		71.0	11.0	0.15493	NM_024630	A6NDB7|Q5JS07|Q5JS08|Q6PHS4|Q8IZN2|Q9H7F1	Frame_Shift_Del	DEL	ENST00000359775.5	hg19	CCDS5252.1																																																																																			.	.	.	none		0.664	ZDHHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042841.2	NM_153746		-	158093785	TTCAGAGCACC	-	158093775	7	5	213	1	0	1	0	1	0	0	0	0	17616	1493	52	0	1122	0	ZDHHC14	6	158093775	Frame_Shift_Del	DEL	TTCAGAGCACC	TCGA-J7-6720-01A-11D-2136-08	114621122	158093775	13021292	21	12961											
THBS2	7058	hgsc.bcm.edu	37	chr6	169642014	169642014	+	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	tggtgacatgcggacccaggCgcagcgtctctgtgttctca	6	10	13	12	3	2	1	1	1	2	0	4	2	2	2	1	3	2	2	1	3	0	1			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr6:169642014C>G	ENST00000366787.3	-	6	983	c.734G>C	c.(733-735)cGc>cCc	p.R245P	XXyac-YX65C7_A.2_ENST00000444188.1_RNA	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	245					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)		CGGACCCAGGCGCAGCGTCTC	0.647																																					p.R245P	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-SNP	.											.	THBS2	230	.	0			c.G734C						PASS	.						50	45	47					6																	169642014		2202	4300	6502	SO:0001583	missense	7058	exon6			CCCAGGCGCAGCG		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.734G>C	chr6.hg19:g.169642014C>G	ENSP00000355751:p.Arg245Pro	92.0	0.0	.		91.0	34.0	.	NM_003247	A6H8N1|A7E232|Q5RI52	Missense_Mutation	SNP	ENST00000366787.3	hg19	CCDS34574.1	.	.	.	.	.	.	.	.	.	.	C	6.539	0.467797	0.12402	.	.	ENSG00000186340	ENST00000366787	T	0.80994	-1.44	4.75	0.174	0.15040	.	0.371764	0.19184	U	0.120604	T	0.47525	0.1450	N	0.22421	0.69	0.22412	N	0.999129	B	0.26845	0.161	B	0.25506	0.061	T	0.44922	-0.9296	10	0.46703	T	0.11	-42.5921	9.6944	0.40147	0.0:0.2486:0.0:0.7513	.	245	P35442	TSP2_HUMAN	P	245	ENSP00000355751:R245P	ENSP00000355751:R245P	R	-	2	0	THBS2	169383939	0.998000	0.40836	0.177000	0.23020	0.004000	0.04260	0.342000	0.19926	0.182000	0.20032	-0.658000	0.03865	CGC	.	.	.	none		0.647	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247		G	169642014	C	G	169642014	3	3	213	1	0	0	0	0	1	0	0	0	15866	768	27	4	2856	4	THBS2	6	169642014	Missense_Mutation	SNP	C	TCGA-J7-6720-01A-11D-2136-08	11548239	169642014	1473053	22	12962											
ZNF679	168417	hgsc.bcm.edu	37	chr7	63726979	63726979	+	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	aattcatactggagagaaacCctacacatgtgaagaatgtg	16	9	9	7	0	1	3	1	1	0	2	1	5	1	4	1	1	3	0	1	1	6	3			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr7:63726979C>G	ENST00000421025.1	+	5	1237	c.968C>G	c.(967-969)cCc>cGc	p.P323R	ZNF679_ENST00000255746.4_Missense_Mutation_p.P323R	NM_001159524.1|NM_153363.2	NP_001152996.1|NP_699194.2	Q8IYX0	ZN679_HUMAN	zinc finger protein 679	323					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						GGAGAGAAACCCTACACATGT	0.398																																					p.P323R		Atlas-SNP	.											.	ZNF679	80	.	0			c.C968G						PASS	.						26	27	27					7																	63726979		692	1591	2283	SO:0001583	missense	168417	exon5			AGAAACCCTACAC	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.968C>G	chr7.hg19:g.63726979C>G	ENSP00000416809:p.Pro323Arg	36.0	0.0	.		99.0	34.0	.	NM_153363		Missense_Mutation	SNP	ENST00000421025.1	hg19	CCDS47592.1	.	.	.	.	.	.	.	.	.	.	C	11.23	1.576050	0.28092	.	.	ENSG00000197123	ENST00000421025;ENST00000255746	T;T	0.17213	2.29;2.29	0.81	0.81	0.18732	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.28962	0.0719	L	0.46819	1.47	0.37644	D	0.922144	D	0.89917	1.0	D	0.97110	1.0	T	0.11641	-1.0579	9	0.72032	D	0.01	.	6.9761	0.24677	0.0:1.0:0.0:0.0	.	323	Q8IYX0	ZN679_HUMAN	R	323	ENSP00000416809:P323R;ENSP00000255746:P323R	ENSP00000255746:P323R	P	+	2	0	ZNF679	63364414	0.775000	0.28604	0.437000	0.26809	0.440000	0.31957	3.755000	0.55197	0.181000	0.19994	0.184000	0.17185	CCC	.	.	.	none		0.398	ZNF679-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344317.2	NM_153363		G	63726979	C	G	63726979	3	3	213	1	0	0	0	0	1	0	0	0	18098	623	22	4	982	4	ZNF679	7	63726979	Missense_Mutation	SNP	C	TCGA-J7-6720-01A-11D-2136-08		63726979	95411684	23	12963											
RELN	5649	hgsc.bcm.edu	37	chr7	103292216	103292216	+	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	accaggagcgcccatggttgGtagaaaattccaagctgaca	13	7	11	10	1	0	2	0	1	0	1	1	3	1	3	3	3	2	3	3	3	4	3			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr7:103292216G>C	ENST00000428762.1	-	15	1943	c.1784C>G	c.(1783-1785)aCc>aGc	p.T595S	RELN_ENST00000343529.5_Missense_Mutation_p.T595S|RELN_ENST00000424685.2_Missense_Mutation_p.T595S	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	595					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)		CCCATGGTTGGTAGAAAATTC	0.463																																					p.T595S	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.C1784G						PASS	.						64	52	56					7																	103292216		2203	4300	6503	SO:0001583	missense	5649	exon15			TGGTTGGTAGAAA		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.1784C>G	chr7.hg19:g.103292216G>C	ENSP00000392423:p.Thr595Ser	29.0	0.0	.		90.0	43.0	.	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	hg19	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.770518	0.90108	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.25085	1.82;1.82;1.82	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.47801	0.1465	L	0.46157	1.445	0.58432	D	0.999998	D;D	0.76494	0.999;0.982	D;D	0.77557	0.99;0.952	T	0.34279	-0.9835	10	0.66056	D	0.02	.	20.0693	0.97712	0.0:0.0:1.0:0.0	.	595;595	P78509-2;P78509	.;RELN_HUMAN	S	595	ENSP00000392423:T595S;ENSP00000345694:T595S;ENSP00000388446:T595S	ENSP00000345694:T595S	T	-	2	0	RELN	103079452	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	9.476000	0.97823	2.758000	0.94735	0.563000	0.77884	ACC	.	.	.	none		0.463	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		C	103292216	G	C	103292216	3	2	213	1	0	0	0	0	1	0	0	0	13233	1261	44	4	8802	4	RELN	7	103292216	Missense_Mutation	SNP	G	TCGA-J7-6720-01A-11D-2136-08	39565237	103292216	55846447	24	12964											
JPH1	56704	hgsc.bcm.edu	37	chr8	75227665	75227665	+	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	aagttgagcacgaaaccgccGcgggtgccggccgggctgtc	7	5	16	13	6	0	1	0	1	0	0	1	2	0	1	4	3	3	3	4	3	2	1			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr8:75227665G>A	ENST00000342232.4	-	2	610	c.570C>T	c.(568-570)cgC>cgT	p.R190R		NM_020647.2	NP_065698.1	Q9HDC5	JPH1_HUMAN	junctophilin 1	190					calcium ion transport into cytosol (GO:0060402)|muscle organ development (GO:0007517)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	24	Breast(64;0.00576)		BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)			CGAAACCGCCGCGGGTGCCGG	0.682																																					p.R190R		Atlas-SNP	.											.	JPH1	77	.	0			c.C570T						PASS	.						14	18	16					8																	75227665		2161	4223	6384	SO:0001819	synonymous_variant	56704	exon2			ACCGCCGCGGGTG	AB042634	CCDS6217.1	8q21	2008-07-03			ENSG00000104369	ENSG00000104369			14201	protein-coding gene	gene with protein product		605266				10891348, 10949023	Standard	XM_005251273		Approved	JP-1	uc003yae.3	Q9HDC5	OTTHUMG00000164524	ENST00000342232.4:c.570C>T	chr8.hg19:g.75227665G>A		54.0	0.0	.		73.0	24.0	.	NM_020647	B2RTZ0	Silent	SNP	ENST00000342232.4	hg19	CCDS6217.1																																																																																			.	.	.	none		0.682	JPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379102.1			A	75227665	G	A	75227665	2	1	213	1	0	0	0	0	0	0	0	1	7967	1074	38	1		1	JPH1	8	75227665	Silent	SNP	G	TCGA-J7-6720-01A-11D-2136-08		75227665	71136357	25	12965											
FAM135B	51059	hgsc.bcm.edu	37	chr8	139180285	139180285	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagggacagctggctgtgcgTctgtatcctggggagcacat	7	9	15	10	1	1	0	0	0	1	0	2	2	2	2	1	4	3	4	1	4	1	1			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr8:139180285T>C	ENST00000395297.1	-	12	1281	c.1111A>G	c.(1111-1113)Acg>Gcg	p.T371A		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	371										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)			TGGCTGTGCGTCTGTATCCTG	0.587										HNSCC(54;0.14)																											p.T371A		Atlas-SNP	.											.	FAM135B	423	.	0			c.A1111G						PASS	.						84	91	89					8																	139180285		2108	4234	6342	SO:0001583	missense	51059	exon12			TGTGCGTCTGTAT	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.1111A>G	chr8.hg19:g.139180285T>C	ENSP00000378710:p.Thr371Ala	114.0	0.0	.		167.0	7.0	.	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	hg19	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	T	12.75	2.032813	0.35893	.	.	ENSG00000147724	ENST00000395297	D	0.88201	-2.35	5.66	3.16	0.36331	.	0.611892	0.17190	N	0.183555	D	0.85852	0.5793	M	0.63428	1.95	0.27501	N	0.951993	B	0.19817	0.039	B	0.16722	0.016	T	0.75422	-0.3323	10	0.38643	T	0.18	-6.9288	10.1146	0.42583	0.2674:0.0:0.0:0.7326	.	371	Q49AJ0	F135B_HUMAN	A	371	ENSP00000378710:T371A	ENSP00000276737:T371A	T	-	1	0	FAM135B	139249467	0.993000	0.37304	0.963000	0.40424	0.275000	0.26752	2.562000	0.45914	0.433000	0.26313	0.533000	0.62120	ACG	.	.	.	none		0.587	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		C	139180285	T	C	139180285	3	2	213	1	0	0	0	0	1	0	0	0	5453	1667	58	3	3145	3	FAM135B	8	139180285	Missense_Mutation	SNP	T	TCGA-J7-6720-01A-11D-2136-08	63952620	139180285	7183737	26	12966											
CYP11B1	1584	hgsc.bcm.edu	37	chr8	143956729	143956729	+	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	acagacccacagggtagagcCtggaggtgggggcatccata	11	5	15	10	0	0	2	0	0	0	2	1	3	1	3	3	5	1	2	3	5	2	2			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr8:143956729C>G	ENST00000292427.4	-	7	1154		c.e7-1		CYP11B1_ENST00000517471.1_Splice_Site|CYP11B1_ENST00000377675.3_Splice_Site	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1						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)	AGGGTAGAGCCTGGAGGTGGG	0.602									Familial Hyperaldosteronism type I																												.		Atlas-SNP	.											.	CYP11B1	128	.	0			c.1122-1G>C						PASS	.						39	43	41					8																	143956729		2203	4300	6503	SO:0001630	splice_region_variant	1584	exon8	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	TAGAGCCTGGAGG	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.1122-1G>C	chr8.hg19:g.143956729C>G		35.0	0.0	.		40.0	16.0	.	NM_001026213	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Splice_Site	SNP	ENST00000292427.4	hg19	CCDS6392.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	13.78|13.78	2.338412|2.338412	0.41398|0.41398	.|.	.|.	ENSG00000160882|ENSG00000160882	ENST00000292427;ENST00000517471;ENST00000377675|ENST00000519285	.|D	.|0.97480	.|-4.4	3.12|3.12	3.12|3.12	0.35913|0.35913	.|.	.|.	.|.	.|.	.|.	.|D	.|0.96836	.|0.8967	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|D	.|0.95728	.|0.8772	.|5	.|.	.|.	.|.	.|.	12.4777|12.4777	0.55823|0.55823	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	.|T	-1|52	.|ENSP00000430144:R52T	.|.	.|R	-|-	.|2	.|0	CYP11B1|CYP11B1	143953731|143953731	1.000000|1.000000	0.71417|0.71417	0.985000|0.985000	0.45067|0.45067	0.194000|0.194000	0.23727|0.23727	4.120000|4.120000	0.57897|0.57897	2.055000|2.055000	0.61198|0.61198	0.555000|0.555000	0.69702|0.69702	.|AGG	.	.	.	none		0.602	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379475.2		Intron	G	143956729	C	G	143956729	5	3	213	1	0	0	0	0	0	0	1	0	4147	695	24	4	402	4	CYP11B1	8	143956729	Splice_Site	SNP	C	TCGA-J7-6720-01A-11D-2136-08	4776444	143956729	2407293	27	12967											
SCRIB	23513	hgsc.bcm.edu	37	chr8	144895667	144895667	+	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	gggacttgagcaggttctccCggagctccagggtcaccagg	7	7	15	12	1	2	1	1	1	1	0	4	3	3	3	3	5	2	3	3	5	0	2			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr8:144895667C>A	ENST00000320476.3	-	5	482	c.476G>T	c.(475-477)cGg>cTg	p.R159L	SCRIB_ENST00000356994.2_Missense_Mutation_p.R159L|SCRIB_ENST00000377533.3_Missense_Mutation_p.R78L|MIR937_ENST00000401271.1_RNA	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	159	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)			CAGGTTCTCCCGGAGCTCCAG	0.647																																					p.R159L	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.G476T						PASS	.						41	39	40					8																	144895667		2203	4300	6503	SO:0001583	missense	23513	exon5			TTCTCCCGGAGCT	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.476G>T	chr8.hg19:g.144895667C>A	ENSP00000322938:p.Arg159Leu	45.0	0.0	.		76.0	4.0	.	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Missense_Mutation	SNP	ENST00000320476.3	hg19	CCDS6411.1	.	.	.	.	.	.	.	.	.	.	C	35	5.538622	0.96474	.	.	ENSG00000180900	ENST00000356994;ENST00000320476;ENST00000377533	T;T;T	0.11277	2.79;2.79;2.79	4.55	4.55	0.56014	.	.	.	.	.	T	0.30417	0.0764	L	0.60012	1.86	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.03503	-1.1030	9	0.87932	D	0	.	16.6416	0.85128	0.0:1.0:0.0:0.0	.	159;159	Q14160;Q14160-3	SCRIB_HUMAN;.	L	159;159;78	ENSP00000349486:R159L;ENSP00000322938:R159L;ENSP00000366756:R78L	ENSP00000322938:R159L	R	-	2	0	SCRIB	144967655	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.446000	0.60014	2.222000	0.72286	0.563000	0.77884	CGG	.	.	.	none		0.647	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356		A	144895667	C	A	144895667	3	1	213	1	0	0	0	0	1	0	0	0	13950	652	23	4	4623	4	SCRIB	8	144895667	Missense_Mutation	SNP	C	TCGA-J7-6720-01A-11D-2136-08	938938	144895667	1468355	28	12968											
ING4	51147	hgsc.bcm.edu	37	chr12	6761549	6761549	+	Frame_Shift_Del	DEL	C	C	-																															catcagaggggtggacactgCcaaaggtcactgagggcatc																										TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr12:6761549delC	ENST00000396807.4	-	6	574	c.536delG	c.(535-537)ggcfs	p.G179fs	ING4_ENST00000423703.2_Intron|ING4_ENST00000446105.2_Frame_Shift_Del_p.G175fs|ING4_ENST00000486287.1_Intron|ING4_ENST00000444704.2_Frame_Shift_Del_p.G155fs|ING4_ENST00000412586.2_Frame_Shift_Del_p.G176fs|ING4_ENST00000341550.4_Frame_Shift_Del_p.G178fs	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	179					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						GTGGACACTGCCAAAGGTCAC	0.512																																					p.G179fs		Atlas-INDEL	.											.	ING4	31	.	0			c.537delC						PASS	.						186	161	169					12																	6761549		2203	4300	6503	SO:0001589	frameshift_variant	51147	exon6			.	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.536delG	chr12.hg19:g.6761549delC	ENSP00000380024:p.Gly179fs	189.0	0.0	0		169.0	49.0	0.289941	NM_001127582	A4KYM4|A4KYM6|D3DUR8|Q0EF62|Q0EF63|Q4VBQ6|Q96E15|Q9H3J0	Frame_Shift_Del	DEL	ENST00000396807.4	hg19	CCDS44813.1																																																																																			.	.	.	none		0.512	ING4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280467.2	NM_198287		-	6761549	C	-	6761549	7	5	213	1	0	1	0	1	0	0	0	0	7745	739	26	0	225	0	ING4	12	6761549	Frame_Shift_Del	DEL	C	TCGA-J7-6720-01A-11D-2136-08		6761549	127090346	29	12969											
FGD4	121512	hgsc.bcm.edu	37	chr12	32777967	32777968	+	In_Frame_Ins	INS	-	-	TTTTTT																															tgaaaccttcagaaatgcaaINSttgcaaaggataatgacatt																										TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr12:32777967_32777968insTTTTTT	ENST00000427716.2	+	13	2024_2025	c.1600_1601insTTTTTT	c.(1600-1602)att>aTTTTTTtt	p.534_535insFF	FGD4_ENST00000534526.2_In_Frame_Ins_p.671_672insFF|FGD4_ENST00000546442.1_In_Frame_Ins_p.441_442insFF|FGD4_ENST00000266482.3_In_Frame_Ins_p.286_287insFF|FGD4_ENST00000525053.1_In_Frame_Ins_p.646_647insFF|FGD4_ENST00000531134.1_In_Frame_Ins_p.619_620insFF	NM_139241.2	NP_640334.2	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	534					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)					CAGAAATGCAATTGCAAAGGAT	0.347																																					p.I534delinsIFF		Atlas-INDEL	.											.	FGD4	86	.	0			c.1600_1601insTTTTTT						PASS	.																																			SO:0001652	inframe_insertion	121512	exon13			.	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	Exception_encountered	chr12.hg19:g.32777967_32777968insTTTTTT	ENSP00000394487:p.Ile534_Ala535insPhePhe	194.0	0.0	0		186.0	19.0	0.102151	NM_139241	Q6ULS2|Q8TCP6	In_Frame_Ins	INS	ENST00000427716.2	hg19	CCDS8727.1																																																																																			.	.	.	none		0.347	FGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268017.1	NM_139241		TTTTTT	32777968	-	TTTTTT	32777967	7	5	213	1	0	1	1	0	0	0	0	0	5842	101	4	0	1642	0	FGD4	12	32777967	In_Frame_Ins	INS	-	TCGA-J7-6720-01A-11D-2136-08	26016418	32777967	101073928	30	12970											
DGKH	160851	hgsc.bcm.edu	37	chr13	42742631	42742632	+	Missense_Mutation	DNP	GG	GG	AT																															ttcttgtttgtggaggcgatGgaagtgtaggttgggttttg																										TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr13:42742631_42742632GG>AT	ENST00000337343.4	+	10	1195_1196	c.1174_1175GG>AT	c.(1174-1176)GGa>ATa	p.G392I	DGKH_ENST00000379274.2_Missense_Mutation_p.G256I|DGKH_ENST00000538674.1_Missense_Mutation_p.G147I|DGKH_ENST00000261491.5_Missense_Mutation_p.G392I|DGKH_ENST00000536612.1_Missense_Mutation_p.G256I|DGKH_ENST00000540693.1_Missense_Mutation_p.G392I|DGKH_ENST00000498255.2_3'UTR	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	392	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)|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)		TGGAGGCGATGGAAGTGTAGGT	0.322																																					p.G392R|p.G392V		Atlas-SNP	.											.	DGKH	106	.	0			c.G1174A|c.G1175T						PASS	.																																			SO:0001583	missense	160851	exon11			GGCGATGGAAGTG|GCGATGGAAGTGT	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	Exception_encountered	chr13.hg19:g.42742631_42742632delinsAT	ENSP00000337572:p.Gly392Ile	82.0|80.0	0.0	.		69.0	19.0	.	NM_001204504	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Missense_Mutation	SNP	ENST00000337343.4	hg19	CCDS9381.1																																																																																			.	.	.	none		0.322	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009		AT	42742632	GG	AT	42742631	3	1	213	1	0	0	0	0	1	0	0	0	4472	1349	47	2	1212	2	DGKH	13	42742631	Missense_Mutation	DNP	GG	TCGA-J7-6720-01A-11D-2136-08		42742631	72427247	31	12971											
HAUS4	54930	hgsc.bcm.edu	37	chr14	23415759	23415759	+	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	ggtagaccttgctgaactccTggagggcccaccgcttgttc	6	10	12	13	1	0	2	0	1	0	1	2	3	1	3	4	3	2	4	4	3	2	4			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr14:23415759T>A	ENST00000206474.7	-	10	1319	c.1067A>T	c.(1066-1068)cAg>cTg	p.Q356L	HAUS4_ENST00000541587.1_Missense_Mutation_p.Q356L|HAUS4_ENST00000554446.1_5'UTR|HAUS4_ENST00000555367.1_Missense_Mutation_p.Q311L|HAUS4_ENST00000342454.8_Missense_Mutation_p.Q311L|RP11-298I3.1_ENST00000548322.1_RNA|RP11-298I3.1_ENST00000548819.1_RNA|HAUS4_ENST00000397409.4_Missense_Mutation_p.Q230L|RP11-298I3.5_ENST00000555074.1_Silent_p.P185P|HAUS4_ENST00000490506.1_Missense_Mutation_p.Q232L|HAUS4_ENST00000347758.2_Missense_Mutation_p.Q230L|HAUS4_ENST00000555986.1_Missense_Mutation_p.Q311L			Q9H6D7	HAUS4_HUMAN	HAUS augmin-like complex, subunit 4	356					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						GCTGAACTCCTGGAGGGCCCA	0.562																																					p.Q356L		Atlas-SNP	.											.	HAUS4	34	.	0			c.A1067T						PASS	.						71	64	66					14																	23415759		2203	4300	6503	SO:0001583	missense	54930	exon10			AACTCCTGGAGGG	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.1067A>T	chr14.hg19:g.23415759T>A	ENSP00000206474:p.Gln356Leu	90.0	0.0	.		89.0	5.0	.	NM_001166269	B7WP17|D3DS34|Q86T15|Q86T16|Q86U43|Q9NX59	Missense_Mutation	SNP	ENST00000206474.7	hg19	CCDS9580.1	.	.	.	.	.	.	.	.	.	.	T	13.26	2.185415	0.38609	.	.	ENSG00000092036;ENSG00000092036;ENSG00000092036;ENSG00000092036;ENSG00000092036;ENSG00000092036;ENSG00000092036;ENSG00000092036;ENSG00000259132	ENST00000206474;ENST00000490506;ENST00000541587;ENST00000342454;ENST00000347758;ENST00000397409;ENST00000555367;ENST00000555986;ENST00000555074	.	.	.	5.8	3.46	0.39613	.	0.358284	0.32328	N	0.006245	T	0.33904	0.0879	L	0.50333	1.59	0.30627	N	0.757909	B;P;B	0.42518	0.0;0.782;0.001	B;B;B	0.40256	0.003;0.324;0.004	T	0.40136	-0.9579	9	0.52906	T	0.07	-10.115	5.9375	0.19173	0.1466:0.0786:0.0:0.7748	.	311;230;356	Q9H6D7-4;Q9H6D7-2;Q9H6D7	.;.;HAUS4_HUMAN	L	356;232;356;311;230;230;311;311;133	.	ENSP00000206474:Q356L	Q	-	2	0	RP11-298I3.5;HAUS4	22485599	1.000000	0.71417	1.000000	0.80357	0.718000	0.41266	0.712000	0.25779	1.014000	0.39417	-0.409000	0.06214	CAG	.	.	.	none		0.562	HAUS4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071680.3			A	23415759	T	A	23415759	3	1	213	1	0	0	0	0	1	0	0	0	6975	1580	55	5	28	5	HAUS4	14	23415759	Missense_Mutation	SNP	T	TCGA-J7-6720-01A-11D-2136-08		23415759	83933781	32	12972											
ACIN1	22985	hgsc.bcm.edu	37	chr14	23549776	23549776	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tccatcatctcctctggtttTactctaggtatctcttcccc	5	17	4	15	0	5	0	1	0	4	0	9	0	7	0	4	2	1	2	4	2	3	5			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr14:23549776T>C	ENST00000262710.1	-	6	1269	c.942A>G	c.(940-942)gtA>gtG	p.V314V	ACIN1_ENST00000555352.1_5'Flank|ACIN1_ENST00000555053.1_Silent_p.V314V|ACIN1_ENST00000605057.1_Silent_p.V256V|ACIN1_ENST00000457657.1_Silent_p.V274V	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	314	Glu-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		CCTCTGGTTTTACTCTAGGTA	0.453																																					p.V314V		Atlas-SNP	.											.	ACIN1	147	.	0			c.A942G						PASS	.						246	213	224					14																	23549776		2203	4300	6503	SO:0001819	synonymous_variant	22985	exon6			TGGTTTTACTCTA	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.942A>G	chr14.hg19:g.23549776T>C		160.0	0.0	.		182.0	54.0	.	NM_001164814	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Silent	SNP	ENST00000262710.1	hg19	CCDS9587.1																																																																																			.	.	.	none		0.453	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977		C	23549776	T	C	23549776	2	2	213	1	0	0	0	0	0	0	0	1	142	1741	61	3		3	ACIN1	14	23549776	Silent	SNP	T	TCGA-J7-6720-01A-11D-2136-08	134017	23549776	83799764	33	12973											
ADCY4	196883	hgsc.bcm.edu	37	chr14	24793367	24793367	+	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	accaggccagacagtgcaggCagccagtgcagcatcttggg	10	5	14	12	0	1	1	0	0	1	1	1	1	1	1	3	3	4	4	3	3	0	1			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr14:24793367C>A	ENST00000310677.4	-	17	2060	c.1947G>T	c.(1945-1947)ctG>ctT	p.L649L	ADCY4_ENST00000418030.2_Silent_p.L649L|ADCY4_ENST00000396747.3_Silent_p.L342L|ADCY4_ENST00000554068.2_Silent_p.L649L	NM_001198568.1|NM_001198592.1|NM_139247.3	NP_001185497.1|NP_001185521.1|NP_640340.2	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4	649					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)		ACAGTGCAGGCAGCCAGTGCA	0.612																																					p.L649L		Atlas-SNP	.											.	ADCY4	86	.	0			c.G1947T						PASS	.						64	63	63					14																	24793367		2203	4300	6503	SO:0001819	synonymous_variant	196883	exon17			TGCAGGCAGCCAG	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.1947G>T	chr14.hg19:g.24793367C>A		66.0	0.0	.		80.0	6.0	.	NM_001198592	B3KV74|D3DS75|Q17R40|Q6ZTM6|Q96ML7	Silent	SNP	ENST00000310677.4	hg19	CCDS9627.1																																																																																			.	.	.	none		0.612	ADCY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073200.4			A	24793367	C	A	24793367	2	1	213	1	0	0	0	0	0	0	0	1	296	697	25	4		4	ADCY4	14	24793367	Silent	SNP	C	TCGA-J7-6720-01A-11D-2136-08	1243591	24793367	82556173	34	12974											
JKAMP	51528	hgsc.bcm.edu	37	chr14	59965574	59965574	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaaagtatttatgctgcactTtacttcttcccaattttaac	12	17	3	9	0	1	0	0	0	1	0	2	0	2	0	1	0	4	3	1	0	7	9			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr14:59965574T>C	ENST00000261247.9	+	5	735	c.588T>C	c.(586-588)ctT>ctC	p.L196L	JKAMP_ENST00000425728.2_Silent_p.L190L|JKAMP_ENST00000356057.5_Silent_p.L204L|RP11-701B16.2_ENST00000554253.1_RNA|JKAMP_ENST00000554271.1_Silent_p.L210L	NM_001098625.1|NM_001284203.1|NM_016475.3	NP_001092095.1|NP_001271132.1|NP_057559.2	Q9P055	JKAMP_HUMAN	JNK1/MAPK8-associated membrane protein	211					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(1)|kidney(1)|lung(3)	6						ATGCTGCACTTTACTTCTTCC	0.373																																					p.L196L		Atlas-SNP	.											.	JKAMP	49	.	0			c.T588C						PASS	.						125	113	117					14																	59965574		1831	4097	5928	SO:0001819	synonymous_variant	51528	exon5			TGCACTTTACTTC	AF212245	CCDS45116.1, CCDS45117.1, CCDS61462.1, CCDS61463.1	14q22.3	2014-02-14	2009-08-13	2009-08-13	ENSG00000050130	ENSG00000050130			20184	protein-coding gene	gene with protein product	"Jun N-terminal kinase 1-associated membrane protein"	611176	"chromosome 14 open reading frame 100"	C14orf100		16166642, 19269966	Standard	NM_001284202		Approved	HSPC213, JAMP, HSPC327, CDA06	uc001xef.4	Q9P055	OTTHUMG00000171054	ENST00000261247.9:c.588T>C	chr14.hg19:g.59965574T>C		19.0	0.0	.		31.0	12.0	.	NM_016475	B4DP67|Q6FIB6|Q6IAJ2|Q7Z5D4|Q86SY6|Q9H0Q6|Q9H2W0|Q9HAH5|Q9P0R3	Silent	SNP	ENST00000261247.9	hg19	CCDS45116.1																																																																																			.	.	.	none		0.373	JKAMP-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411430.1	NM_001098625		C	59965574	T	C	59965574	2	2	213	1	0	0	0	0	0	0	0	1	7956	1828	64	3		3	JKAMP	14	59965574	Silent	SNP	T	TCGA-J7-6720-01A-11D-2136-08	35172207	59965574	47383966	35	12975											
KIAA1199	57214	hgsc.bcm.edu	37	chr15	81221510	81221511	+	Frame_Shift_Del	DEL	AG	AG	-																															agcggaaggaccctccctatAggccagtaggtttgcaacca																								rs201251202		TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr15:81221510_81221511delAG	ENST00000394685.3	+	21	3026_3027	c.2607_2608delAG	c.(2605-2610)ataggcfs	p.IG869fs	RP11-351M8.2_ENST00000560873.1_RNA|KIAA1199_ENST00000220244.3_Frame_Shift_Del_p.IG869fs|KIAA1199_ENST00000356249.5_Frame_Shift_Del_p.IG869fs			Q8WUJ3	CEMIP_HUMAN		869					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						CCCTCCCTATAGGCCAGTAGGT	0.51																																					p.869_869del		Atlas-INDEL	.											.	KIAA1199	118	.	0			c.2606_2607del						PASS	.																																			SO:0001589	frameshift_variant	57214	exon20			.																												ENST00000394685.3:c.2607_2608delAG	chr15.hg19:g.81221510_81221511delAG	ENSP00000378177:p.Ile869fs	97.0	0.0	0		141.0	54.0	0.382979	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Frame_Shift_Del	DEL	ENST00000394685.3	hg19	CCDS10315.1																																																																																			.	.	.	none		0.51	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1			-	81221511	AG	-	81221510	7	5	213	1	0	1	0	1	0	0	0	0	8220	410	15	0	2681	0	KIAA1199	15	81221510	Frame_Shift_Del	DEL	AG	TCGA-J7-6720-01A-11D-2136-08		81221510	21309882	36	12976											
SBK1	388228	hgsc.bcm.edu	37	chr16	28330355	28330355	+	Missense_Mutation	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	gtttgtgaacaagagcaaaaCcaagctgaagaacttcctac	16	8	8	9	0	0	4	0	2	0	2	1	4	1	4	2	0	6	3	2	0	8	3			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr16:28330355C>T	ENST00000341901.4	+	3	1055	c.266C>T	c.(265-267)aCc>aTc	p.T89I		NM_001024401.2	NP_001019572.1	Q52WX2	SBK1_HUMAN	SH3 domain binding kinase 1	89	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|lung(3)|ovary(1)	5						AAGAGCAAAACCAAGCTGAAG	0.532																																					p.T89I		Atlas-SNP	.											.	SBK1	36	.	0			c.C266T						PASS	.						170	156	161					16																	28330355		2197	4300	6497	SO:0001583	missense	388228	exon3			GCAAAACCAAGCT		CCDS32416.1	16p11.2	2013-09-27	2013-09-27			ENSG00000188322			17699	protein-coding gene	gene with protein product			"SH3-binding domain kinase 1"				Standard	XM_005255315		Approved	Sbk	uc002dpd.3	Q52WX2		ENST00000341901.4:c.266C>T	chr16.hg19:g.28330355C>T	ENSP00000343248:p.Thr89Ile	211.0	0.0	.		250.0	85.0	.	NM_001024401		Missense_Mutation	SNP	ENST00000341901.4	hg19	CCDS32416.1	.	.	.	.	.	.	.	.	.	.	c	20.4	3.991381	0.74703	.	.	ENSG00000188322	ENST00000341901	T	0.65549	-0.16	4.98	4.03	0.46877	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	0.62732	0.2452	L	0.33339	1.005	0.54753	D	0.999985	D	0.52996	0.957	P	0.57324	0.818	T	0.59958	-0.7356	10	0.35671	T	0.21	-23.5445	11.1208	0.48289	0.0:0.9084:0.0:0.0916	.	89	Q52WX2	SBK1_HUMAN	I	89	ENSP00000343248:T89I	ENSP00000343248:T89I	T	+	2	0	SBK1	28237856	1.000000	0.71417	0.989000	0.46669	0.901000	0.52897	7.769000	0.85360	1.089000	0.41292	-0.141000	0.14075	ACC	.	.	.	none		0.532	SBK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387677.1	XM_370948		T	28330355	C	T	28330355	3	4	213	1	0	0	0	0	1	0	0	0	13873	507	18	2	272	2	SBK1	16	28330355	Missense_Mutation	SNP	C	TCGA-J7-6720-01A-11D-2136-08		28330355	62024398	37	12977											
PSG2	5670	hgsc.bcm.edu	37	chr19	43585217	43585217	+	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	attatttgaccgtctactacAtatgatgtaatgtaatggta	13	16	7	5	1	1	2	0	2	1	0	1	2	1	2	1	1	2	3	1	1	7	8			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr19:43585217A>T	ENST00000406487.1	-	2	344	c.246T>A	c.(244-246)taT>taA	p.Y82*	PSG2_ENST00000491995.1_5'Flank	NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	82	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)				CGTCTACTACATATGATGTAA	0.438																																					p.Y82X		Atlas-SNP	.											.	PSG2	84	.	0			c.T246A						PASS	.						170	174	173					19																	43585217		2203	4298	6501	SO:0001587	stop_gained	5670	exon2			TACTACATATGAT		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.246T>A	chr19.hg19:g.43585217A>T	ENSP00000385706:p.Tyr82*	456.0	0.0	.		513.0	141.0	.	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Nonsense_Mutation	SNP	ENST00000406487.1	hg19	CCDS12616.1	.	.	.	.	.	.	.	.	.	.	N	10.75	1.438722	0.25900	.	.	ENSG00000242221	ENST00000406487;ENST00000329509;ENST00000401942;ENST00000406917	.	.	.	0.569	-0.723	0.11181	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	.	.	.	.	.	.	.	X	82	.	ENSP00000332984:Y82X	Y	-	3	2	PSG2	48277057	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.017000	0.12590	-0.394000	0.07727	0.155000	0.16302	TAT	.	.	.	none		0.438	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246		T	43585217	A	T	43585217	4	4	213	1	0	0	0	0	0	1	0	0	12665	224	8	5	777	5	PSG2	19	43585217	Nonsense_Mutation	SNP	A	TCGA-J7-6720-01A-11D-2136-08		43585217	15543766	38	12978											
ZNF347	84671	hgsc.bcm.edu	37	chr19	53643573	53643575	+	In_Frame_Del	DEL	TGA	TGA	-																															tctctccactatgaattctgTgatggcttgcaaggtttgaa																										TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr19:53643573_53643575delTGA	ENST00000334197.7	-	5	2574_2576	c.2506_2508delTCA	c.(2506-2508)tcadel	p.S836del	ZNF347_ENST00000601469.2_In_Frame_Del_p.S837del|ZNF347_ENST00000601804.1_Intron|ZNF347_ENST00000452676.2_In_Frame_Del_p.S837del	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	836					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		ATGAATTCTGTGATGGCTTGCAA	0.394																																					p.837_838del	Melanoma(64;205 1597 17324 45721)	Atlas-INDEL	.											.	ZNF347	87	.	0			c.2510_2512del						PASS	.																																			SO:0001651	inframe_deletion	84671	exon5			.	AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937		"Zinc fingers, C2H2-type", "-"	16447	protein-coding gene	gene with protein product							Standard	NM_032584		Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000334197.7:c.2506_2508delTCA	chr19.hg19:g.53643573_53643575delTGA	ENSP00000334146:p.Ser836del	193.0	0.0	0		170.0	46.0	0.270588	NM_001172675	B3KU77|B9EG59|G5E9N4|Q8TCN1	In_Frame_Del	DEL	ENST00000334197.7	hg19	CCDS33097.1																																																																																			.	.	.	none		0.394	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584		-	53643575	TGA	-	53643573	7	5	213	1	0	1	0	1	0	0	0	0	17873	1683	59	0	15	0	ZNF347	19	53643573	In_Frame_Del	DEL	TGA	TCGA-J7-6720-01A-11D-2136-08	10058356	53643573	5485410	39	12979											
TGM6	343641	hgsc.bcm.edu	37	chr20	2384361	2384361	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtggcacgaggatgagagcCgggagcgtgtatactcaaac	11	7	15	8	3	1	1	1	1	0	1	1	5	1	3	1	3	4	2	1	3	3	2			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr20:2384361C>T	ENST00000202625.2	+	9	1289	c.1228C>T	c.(1228-1230)Cgg>Tgg	p.R410W	TGM6_ENST00000381423.1_Missense_Mutation_p.R410W	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	410					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)	GGATGAGAGCCGGGAGCGTGT	0.582																																					p.R410W		Atlas-SNP	.											.	TGM6	126	.	0			c.C1228T						PASS	.						117	102	107					20																	2384361		2203	4300	6503	SO:0001583	missense	343641	exon9			GAGAGCCGGGAGC	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.1228C>T	chr20.hg19:g.2384361C>T	ENSP00000202625:p.Arg410Trp	109.0	0.0	.		126.0	6.0	.	NM_198994	Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	Missense_Mutation	SNP	ENST00000202625.2	hg19	CCDS13025.1	.	.	.	.	.	.	.	.	.	.	C	15.01	2.707089	0.48412	.	.	ENSG00000166948	ENST00000202625;ENST00000381423	T;T	0.74526	-0.85;-0.85	4.84	2.82	0.32997	.	0.503753	0.20705	N	0.087198	T	0.76905	0.4053	L	0.49126	1.545	0.25334	N	0.989007	D;D	0.71674	0.998;0.997	P;P	0.56916	0.809;0.628	T	0.67933	-0.5542	10	0.66056	D	0.02	-13.0667	10.1216	0.42623	0.3642:0.6358:0.0:0.0	.	410;410	O95932-2;O95932	.;TGM3L_HUMAN	W	410	ENSP00000202625:R410W;ENSP00000370831:R410W	ENSP00000202625:R410W	R	+	1	2	TGM6	2332361	0.001000	0.12720	0.983000	0.44433	0.361000	0.29550	0.639000	0.24690	0.711000	0.32018	0.549000	0.68633	CGG	.	.	.	none		0.582	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994		T	2384361	C	T	2384361	3	4	213	1	0	0	0	0	1	0	0	0	15846	643	23	1	1262	1	TGM6	20	2384361	Missense_Mutation	SNP	C	TCGA-J7-6720-01A-11D-2136-08		2384361	60641159	40	12980											
COL6A2	1292	hgsc.bcm.edu	37	chr21	47542788	47542788	+	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	aacatgtgttccctgtcacaGggaggccgaggcgactttgg	8	9	14	10	2	1	0	1	0	0	0	2	3	2	1	2	4	1	1	2	4	1	2			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr21:47542788G>A	ENST00000300527.4	+	21	1712		c.e21-1		COL6A2_ENST00000357838.4_Splice_Site|COL6A2_ENST00000397763.1_Splice_Site|COL6A2_ENST00000409416.1_Splice_Site|COL6A2_ENST00000310645.5_Splice_Site	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		CCCTGTCACAGGGAGGCCGAG	0.547																																					.		Atlas-SNP	.											.	COL6A2	351	.	0			c.1609-1G>A						PASS	.						86	75	79					21																	47542788		2203	4298	6501	SO:0001630	splice_region_variant	1292	exon21			GTCACAGGGAGGC	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.1609-1G>A	chr21.hg19:g.47542788G>A		91.0	0.0	.		93.0	31.0	.	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Splice_Site	SNP	ENST00000300527.4	hg19	CCDS13728.1	.	.	.	.	.	.	.	.	.	.	G	12.89	2.073193	0.36566	.	.	ENSG00000142173	ENST00000300527;ENST00000357838;ENST00000310645;ENST00000409416;ENST00000397763;ENST00000413758	.	.	.	3.54	3.54	0.40534	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9711	0.80019	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	COL6A2	46367216	1.000000	0.71417	0.991000	0.47740	0.337000	0.28794	7.524000	0.81866	1.909000	0.55274	0.491000	0.48974	.	.	.	.	none		0.547	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		Intron	A	47542788	G	A	47542788	5	1	213	1	0	0	0	0	0	0	1	0	3702	1014	35	2	1686	2	COL6A2	21	47542788	Splice_Site	SNP	G	TCGA-J7-6720-01A-11D-2136-08		47542788	587107	41	12981											
PCNT	5116	hgsc.bcm.edu	37	chr21	47809247	47809247	+	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	agctttctcatgagcccagaAagtgtgcgggagtgtgagca	10	9	14	8	1	1	3	1	2	1	1	2	4	1	4	1	1	4	2	1	1	1	1			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr21:47809247A>T	ENST00000359568.5	+	19	3848	c.3741A>T	c.(3739-3741)gaA>gaT	p.E1247D	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1247					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)					TGAGCCCAGAAAGTGTGCGGG	0.587																																					p.E1247D		Atlas-SNP	.											.	PCNT	283	.	0			c.A3741T						PASS	.						95	94	94					21																	47809247		2203	4300	6503	SO:0001583	missense	5116	exon19			CCCAGAAAGTGTG	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.3741A>T	chr21.hg19:g.47809247A>T	ENSP00000352572:p.Glu1247Asp	208.0	0.0	.		197.0	71.0	.	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	hg19	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	A	15.19	2.761428	0.49468	.	.	ENSG00000160299	ENST00000359568	T	0.02032	4.49	5.44	-10.3	0.00346	.	.	.	.	.	T	0.07279	0.0184	M	0.70275	2.135	0.09310	N	1	B;D	0.76494	0.193;0.999	B;D	0.78314	0.08;0.991	T	0.02269	-1.1185	9	0.66056	D	0.02	.	8.9466	0.35762	0.6619:0.2264:0.1118:0.0	.	1129;1247	O95613-2;O95613	.;PCNT_HUMAN	D	1247	ENSP00000352572:E1247D	ENSP00000352572:E1247D	E	+	3	2	PCNT	46633675	0.000000	0.05858	0.000000	0.03702	0.169000	0.22640	-1.857000	0.01660	-1.903000	0.01093	-0.456000	0.05471	GAA	.	.	.	none		0.587	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		T	47809247	A	T	47809247	3	4	213	1	0	0	0	0	1	0	0	0	11597	11	1	5	3815	5	PCNT	21	47809247	Missense_Mutation	SNP	A	TCGA-J7-6720-01A-11D-2136-08	266459	47809247	320648	42	12982											
OSBP2	23762	hgsc.bcm.edu	37	chr22	31137192	31137192	+	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	gtgccgtggaaccatcaaccTgtccaccgcgcacattgaca	10	7	9	15	3	1	1	1	1	0	0	2	2	2	2	5	1	3	1	5	1	2	1			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr22:31137192T>A	ENST00000332585.6	+	2	793	c.689T>A	c.(688-690)cTg>cAg	p.L230Q	OSBP2_ENST00000446658.2_Missense_Mutation_p.L230Q|OSBP2_ENST00000382310.3_Missense_Mutation_p.L230Q|OSBP2_ENST00000403222.3_Missense_Mutation_p.L65Q|OSBP2_ENST00000407373.1_Missense_Mutation_p.L57Q	NM_001282739.1|NM_001282740.1|NM_001282741.1|NM_001282742.1|NM_030758.3	NP_001269668.1|NP_001269669.1|NP_001269670.1|NP_001269671.1|NP_110385.1	Q969R2	OSBP2_HUMAN	oxysterol binding protein 2	230	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				lipid transport (GO:0006869)	membrane (GO:0016020)	cholesterol binding (GO:0015485)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(6)|ovary(1)|skin(3)|urinary_tract(1)	19						ACCATCAACCTGTCCACCGCG	0.567																																					p.L230Q		Atlas-SNP	.											.	OSBP2	52	.	0			c.T689A						PASS	.						51	53	53					22																	31137192		2028	4163	6191	SO:0001583	missense	23762	exon2			TCAACCTGTCCAC		CCDS43002.1, CCDS63448.1, CCDS63449.1, CCDS63450.1, CCDS63451.1	22q12.2	2013-01-10			ENSG00000184792	ENSG00000184792		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	8504	protein-coding gene	gene with protein product		606729		OSBPL1		10591208, 11278871, 11802775	Standard	NM_001282738		Approved	KIAA1664, ORP-4, ORP4	uc003aiy.1	Q969R2	OTTHUMG00000151153	ENST00000332585.6:c.689T>A	chr22.hg19:g.31137192T>A	ENSP00000332576:p.Leu230Gln	71.0	0.0	.		79.0	4.0	.	NM_030758	B0QYG1|B4DK24|B4DKE4|B4DTR3|F5H2A3|O60396|Q0VF99|Q8NA37|Q9BY96|Q9BZF0	Missense_Mutation	SNP	ENST00000332585.6	hg19	CCDS43002.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.662468	0.88251	.	.	ENSG00000184792	ENST00000438716;ENST00000403222;ENST00000407373;ENST00000332585;ENST00000382310;ENST00000446658	T;T;D;D;D	0.84146	-0.42;-0.41;-1.81;-1.81;-1.81	5.38	5.38	0.77491	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.64402	D	0.000005	D	0.95943	0.8679	H	0.99516	4.605	0.80722	D	1	D;D;D;D;D	0.89917	0.998;1.0;1.0;0.999;1.0	D;D;D;D;D	0.81914	0.989;0.98;0.98;0.995;0.995	D	0.97875	1.0288	10	0.87932	D	0	-22.7415	15.0591	0.71939	0.0:0.0:0.0:1.0	.	230;65;57;230;230	B4DFA8;B4DKE4;Q6ZN50;Q0VF99;Q969R2	.;.;.;.;OSBP2_HUMAN	Q	65;65;57;230;230;230	ENSP00000384213:L65Q;ENSP00000385237:L57Q;ENSP00000332576:L230Q;ENSP00000371747:L230Q;ENSP00000392080:L230Q	ENSP00000332576:L230Q	L	+	2	0	OSBP2	29467192	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	8.040000	0.89188	2.040000	0.60383	0.379000	0.24179	CTG	.	.	.	none		0.567	OSBP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321547.2	NM_030758		A	31137192	T	A	31137192	3	1	213	1	0	0	0	0	1	0	0	0	11281	1580	55	5	695	5	OSBP2	22	31137192	Missense_Mutation	SNP	T	TCGA-J7-6720-01A-11D-2136-08		31137192	20167374	43	12983											
TTLL12	23170	hgsc.bcm.edu	37	chr22	43579135	43579149	+	In_Frame_Del	DEL	CACTTCCCCAGCGTC	CACTTCCCCAGCGTC	-																															tccacttgcatgatcccaaaCacttccccagcgtcgaaaac																								rs146360108|rs571455195		TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	CACTTCCCCAGCGTC	CACTTCCCCAGCGTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chr22:43579135_43579149delCACTTCCCCAGCGTC	ENST00000216129.6	-	2	247_261	c.184_198delGACGCTGGGGAAGTG	c.(184-198)gacgctggggaagtgdel	p.DAGEV62del		NM_015140.3	NP_055955.1	Q14166	TTL12_HUMAN	tubulin tyrosine ligase-like family, member 12	62					cellular protein modification process (GO:0006464)			p.D62D(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	13		Ovarian(80;0.221)|Glioma(61;0.222)				TGATCCCAAACACTTCCCCAGCGTCGAAAACCTGG	0.637																																					p.62_67del		Atlas-INDEL	.											.	TTLL12	50	.	1	Substitution - coding silent(1)	large_intestine(1)	c.185_199del						PASS	.																																			SO:0001651	inframe_deletion	23170	exon2			.	D63487	CCDS14047.1	22q13.31	2013-02-14	2006-02-02		ENSG00000100304	ENSG00000100304		"Tubulin tyrosine ligase-like family"	28974	protein-coding gene	gene with protein product						15890843	Standard	NM_015140		Approved	KIAA0153	uc003bdp.3	Q14166	OTTHUMG00000150682	ENST00000216129.6:c.184_198delGACGCTGGGGAAGTG	chr22.hg19:g.43579135_43579149delCACTTCCCCAGCGTC	ENSP00000216129:p.Asp62_Val66del	192.0	0.0	0		195.0	16.0	0.0820513	NM_015140	Q20WK5|Q9UGU3	In_Frame_Del	DEL	ENST00000216129.6	hg19	CCDS14047.1																																																																																			.	.	.	none		0.637	TTLL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319611.1	NM_015140		-	43579149	CACTTCCCCAGCGTC	-	43579135	7	5	213	1	0	1	0	1	0	0	0	0	16737	465	17	0	1788	0	TTLL12	22	43579135	In_Frame_Del	DEL	CACTTCCCCAGCGTC	TCGA-J7-6720-01A-11D-2136-08	12441943	43579135	7725431	44	12984											
SLITRK4	139065	hgsc.bcm.edu	37	chrX	142718336	142718336	+	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	gccaatgtgttccagaacccCgatataagggagcttctgga	11	9	11	10	1	1	1	0	0	1	1	2	4	2	3	4	2	2	2	4	2	4	4			TCGA-J7-6720-01A-11D-2136-08	TCGA-J7-6720-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f51e571-67b3-4e0a-a5b5-bdc9a788d1d1	ee153c70-16dc-47aa-b326-e5341dc09b2f	g.chrX:142718336C>A	ENST00000381779.4	-	2	814	c.589G>T	c.(589-591)Ggg>Tgg	p.G197W	SLITRK4_ENST00000356928.1_Missense_Mutation_p.G197W|SLITRK4_ENST00000338017.4_Missense_Mutation_p.G197W	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	197						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)					TCCAGAACCCCGATATAAGGG	0.433																																					p.G197W		Atlas-SNP	.											.	SLITRK4	162	.	0			c.G589T						PASS	.						78	76	77					X																	142718336		2203	4300	6503	SO:0001583	missense	139065	exon2			GAACCCCGATATA	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.589G>T	chrX.hg19:g.142718336C>A	ENSP00000371198:p.Gly197Trp	64.0	0.0	.		94.0	4.0	.	NM_001184750	Q5JXG3|Q8TCM8|Q96DL3	Missense_Mutation	SNP	ENST00000381779.4	hg19	CCDS14679.1	.	.	.	.	.	.	.	.	.	.	C	17.15	3.315367	0.60524	.	.	ENSG00000179542	ENST00000381779;ENST00000356928;ENST00000338017	T;T;T	0.55413	0.52;0.52;0.52	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.79034	0.4378	M	0.91038	3.17	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84122	0.0407	10	0.87932	D	0	-6.8478	17.0529	0.86524	0.0:1.0:0.0:0.0	.	197	Q8IW52	SLIK4_HUMAN	W	197	ENSP00000371198:G197W;ENSP00000349400:G197W;ENSP00000336627:G197W	ENSP00000336627:G197W	G	-	1	0	SLITRK4	142546002	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	7.818000	0.86416	2.347000	0.79759	0.600000	0.82982	GGG	.	.	.	none		0.433	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078		A	142718336	C	A	142718336	3	1	213	1	0	0	0	0	1	0	0	0	14758	652	23	4	1928	4	SLITRK4	23	142718336	Missense_Mutation	SNP	C	TCGA-J7-6720-01A-11D-2136-08		142718336	12552224	45	12985											
PRDM16	63976	hgsc.bcm.edu	37	chr1	3334451	3334451	+	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	tttgcagccatgaaggcggaCtcgggcagctccctgcagcc	7	7	13	14	2	0	1	0	1	0	0	2	2	1	2	3	3	5	4	3	3	1	1			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr1:3334451C>T	ENST00000270722.5	+	11	2800	c.2751C>T	c.(2749-2751)gaC>gaT	p.D917D	PRDM16_ENST00000378398.3_Silent_p.D917D|PRDM16_ENST00000514189.1_Silent_p.D917D|PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000378391.2_Silent_p.D917D|PRDM16_ENST00000442529.2_Silent_p.D916D|PRDM16_ENST00000511072.1_Silent_p.D918D|PRDM16_ENST00000441472.2_Silent_p.D916D			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	917	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)		TGAAGGCGGACTCGGGCAGCT	0.602			T	EVI1	"MDS, AML"																																p.D917D		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.C2751T						PASS	.						97	108	104					1																	3334451		2039	4191	6230	SO:0001819	synonymous_variant	63976	exon11			GGCGGACTCGGGC	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.2751C>T	chr1.hg19:g.3334451C>T		178.0	0.0	.		311.0	80.0	.	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Silent	SNP	ENST00000270722.5	hg19	CCDS41236.2																																																																																			.	.	.	none		0.602	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114		T	3334451	C	T	3334451	2	4	214	1	0	0	0	0	0	0	0	1	12467	564	20	2		2	PRDM16	1	3334451	Silent	SNP	C	TCGA-J7-8537-01A-11D-2396-08		3334451	245916170	1	12986											
TAS1R2	80834	hgsc.bcm.edu	37	chr1	19176018	19176018	+	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	tggtggtccaggagagtgaaGttgaccttccagatctcctc	8	11	12	10	0	1	4	0	2	1	2	5	5	3	4	4	3	0	1	4	3	1	2			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr1:19176018G>T	ENST00000375371.3	-	4	1305	c.1284C>A	c.(1282-1284)aaC>aaA	p.N428K	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	428					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)	GGAGAGTGAAGTTGACCTTCC	0.552																																					p.N428K		Atlas-SNP	.											.	TAS1R2	134	.	0			c.C1284A						PASS	.						64	59	61					1																	19176018		2203	4300	6503	SO:0001583	missense	80834	exon4			AGTGAAGTTGACC		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.1284C>A	chr1.hg19:g.19176018G>T	ENSP00000364520:p.Asn428Lys	79.0	0.0	.		121.0	30.0	.	NM_152232	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	hg19	CCDS187.1	.	.	.	.	.	.	.	.	.	.	G	16.45	3.127587	0.56721	.	.	ENSG00000179002	ENST00000375371	D	0.86497	-2.13	5.16	2.1	0.27182	Extracellular ligand-binding receptor (1);	0.344112	0.24479	N	0.038174	D	0.87908	0.6296	L	0.48935	1.535	0.28764	N	0.900721	D	0.71674	0.998	D	0.66979	0.948	T	0.79815	-0.1644	10	0.52906	T	0.07	.	5.3671	0.16119	0.194:0.1632:0.6428:0.0	.	428	Q8TE23	TS1R2_HUMAN	K	428	ENSP00000364520:N428K	ENSP00000364520:N428K	N	-	3	2	TAS1R2	19048605	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	0.985000	0.29578	0.518000	0.28383	0.561000	0.74099	AAC	.	.	.	none		0.552	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1			T	19176018	G	T	19176018	3	4	214	1	0	0	0	0	1	0	0	0	15575	1020	36	4	1247	4	TAS1R2	1	19176018	Missense_Mutation	SNP	G	TCGA-J7-8537-01A-11D-2396-08	15841567	19176018	230074603	2	12987											
ALDH4A1	8659	hgsc.bcm.edu	37	chr1	19201049	19201049	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccggcagcattcctcagcAcctttgtggcctcctgcacg	5	10	10	16	2	1	0	1	0	0	0	3	0	3	0	5	2	4	4	5	2	0	2			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr1:19201049A>G	ENST00000375341.3	-	14	1744	c.1487T>C	c.(1486-1488)gTg>gCg	p.V496A	RP13-279N23.2_ENST00000494072.3_3'UTR|ALDH4A1_ENST00000538309.1_Missense_Mutation_p.V436A|ALDH4A1_ENST00000290597.5_Missense_Mutation_p.V496A|ALDH4A1_ENST00000538839.1_Missense_Mutation_p.V445A	NM_003748.3	NP_003739.2	P30038	AL4A1_HUMAN	aldehyde dehydrogenase 4 family, member A1	496					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)		ATTCCTCAGCACCTTTGTGGC	0.617																																					p.V496A		Atlas-SNP	.											.	ALDH4A1	72	.	0			c.T1487C						PASS	.						183	149	160					1																	19201049		2203	4300	6503	SO:0001583	missense	8659	exon14			CTCAGCACCTTTG	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.1487T>C	chr1.hg19:g.19201049A>G	ENSP00000364490:p.Val496Ala	177.0	0.0	.		290.0	67.0	.	NM_003748	A8K1Q7|B4DGE4|D2D4A3|Q16882|Q53HU4|Q5JNV6|Q8IZ38|Q96IF0|Q9UDI6	Missense_Mutation	SNP	ENST00000375341.3	hg19	CCDS188.1	.	.	.	.	.	.	.	.	.	.	A	0.577	-0.838870	0.02692	.	.	ENSG00000159423	ENST00000290597;ENST00000375341;ENST00000538839;ENST00000538309	T;T;T;T	0.74632	-0.86;-0.86;1.68;-0.86	5.36	4.24	0.50183	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.644592	0.17853	N	0.159761	T	0.42471	0.1204	N	0.02697	-0.525	0.23113	N	0.998271	B	0.02656	0.0	B	0.06405	0.002	T	0.33574	-0.9863	10	0.07644	T	0.81	-25.7928	5.0242	0.14376	0.7201:0.1868:0.0931:0.0	.	496	P30038	AL4A1_HUMAN	A	496;496;445;436	ENSP00000290597:V496A;ENSP00000364490:V496A;ENSP00000446071:V445A;ENSP00000442988:V436A	ENSP00000290597:V496A	V	-	2	0	ALDH4A1	19073636	0.387000	0.25188	0.907000	0.35723	0.356000	0.29392	3.436000	0.52856	2.025000	0.59659	0.459000	0.35465	GTG	.	.	.	none		0.617	ALDH4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006954.1			G	19201049	A	G	19201049	3	3	214	1	0	0	0	0	1	0	0	0	501	159	6	3	212	3	ALDH4A1	1	19201049	Missense_Mutation	SNP	A	TCGA-J7-8537-01A-11D-2396-08	25031	19201049	230049572	3	12988											
ARID1A	8289	hgsc.bcm.edu	37	chr1	27106580	27106580	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaaaacaccttggttacacTcgccaacatctcggggcagt	11	8	10	12	2	1	0	0	0	1	0	3	1	1	1	2	4	3	2	2	4	4	2			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr1:27106580T>C	ENST00000324856.7	+	20	6562	c.6191T>C	c.(6190-6192)cTc>cCc	p.L2064P	ARID1A_ENST00000457599.2_Missense_Mutation_p.L1847P|ARID1A_ENST00000374152.2_Missense_Mutation_p.L1681P|ARID1A_ENST00000540690.1_Missense_Mutation_p.L392P	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	2064					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)		TTGGTTACACTCGCCAACATC	0.557			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.L2064P		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.T6191C						PASS	.						136	137	137					1																	27106580		2203	4300	6503	SO:0001583	missense	8289	exon20			TTACACTCGCCAA	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.6191T>C	chr1.hg19:g.27106580T>C	ENSP00000320485:p.Leu2064Pro	194.0	0.0	.		238.0	58.0	.	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	hg19	CCDS285.1	.	.	.	.	.	.	.	.	.	.	T	19.26	3.793741	0.70452	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152;ENST00000540690	T;T;T;T	0.71698	0.88;0.88;0.88;-0.59	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	D	0.84447	0.5474	M	0.81239	2.535	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.999	D	0.86848	0.2021	10	0.87932	D	0	-10.1896	15.3414	0.74300	0.0:0.0:0.0:1.0	.	1681;2064;1847	O14497-3;O14497;O14497-2	.;ARI1A_HUMAN;.	P	2064;1847;1681;392	ENSP00000320485:L2064P;ENSP00000387636:L1847P;ENSP00000363267:L1681P;ENSP00000442437:L392P	ENSP00000320485:L2064P	L	+	2	0	ARID1A	26979167	1.000000	0.71417	0.585000	0.28666	0.975000	0.68041	7.676000	0.84012	2.273000	0.75805	0.482000	0.46254	CTC	.	.	.	none		0.557	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		C	27106580	T	C	27106580	3	2	214	1	0	0	0	0	1	0	0	0	913	1551	54	3	6269	3	ARID1A	1	27106580	Missense_Mutation	SNP	T	TCGA-J7-8537-01A-11D-2396-08	7905531	27106580	222144041	4	12989											
HIVEP3	59269	hgsc.bcm.edu	37	chr1	42047804	42047804	+	Missense_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	ctgggcaagtgtctggctgcGctggggccattggaactcct	5	10	15	11	1	1	0	0	0	1	0	2	1	2	1	2	5	2	3	2	5	2	1			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr1:42047804G>A	ENST00000372583.1	-	4	3550	c.2665C>T	c.(2665-2667)Cgc>Tgc	p.R889C	HIVEP3_ENST00000247584.5_Missense_Mutation_p.R889C|HIVEP3_ENST00000372584.1_Missense_Mutation_p.R889C|HIVEP3_ENST00000429157.2_Missense_Mutation_p.R889C|HIVEP3_ENST00000460604.1_5'Flank	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	889	No DNA binding activity or transactivation activity, but complete prevention of TRAF-dependent NF-Kappa-B activation; associates with TRAF2 and JUN. {ECO:0000250}.				positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R889C(1)		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)				GTCTGGCTGCGCTGGGGCCAT	0.597																																					p.R889C		Atlas-SNP	.											HIVEP3,colon,carcinoma,0,1	HIVEP3	235	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2665T						PASS	.						54	63	60					1																	42047804		2203	4300	6503	SO:0001583	missense	59269	exon4			GGCTGCGCTGGGG	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.2665C>T	chr1.hg19:g.42047804G>A	ENSP00000361664:p.Arg889Cys	159.0	0.0	.		299.0	70.0	.	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Missense_Mutation	SNP	ENST00000372583.1	hg19	CCDS463.1	.	.	.	.	.	.	.	.	.	.	G	18.70	3.679130	0.68042	.	.	ENSG00000127124	ENST00000372584;ENST00000372583;ENST00000247584;ENST00000429157	T;T;T;T	0.61859	0.07;0.07;0.07;0.07	4.95	4.95	0.65309	.	0.000000	0.53938	D	0.000060	T	0.73466	0.3590	M	0.76727	2.345	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.76107	-0.3080	10	0.87932	D	0	2.8066	11.1037	0.48190	0.0:0.0:0.6936:0.3063	.	889;889	Q5T1R4-2;Q5T1R4	.;ZEP3_HUMAN	C	889	ENSP00000361665:R889C;ENSP00000361664:R889C;ENSP00000247584:R889C;ENSP00000410828:R889C	ENSP00000247584:R889C	R	-	1	0	HIVEP3	41820391	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	5.841000	0.69409	2.562000	0.86427	0.462000	0.41574	CGC	.	.	.	none		0.597	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		A	42047804	G	A	42047804	3	1	214	1	0	0	0	0	1	0	0	0	7195	1087	38	1	4579	1	HIVEP3	1	42047804	Missense_Mutation	SNP	G	TCGA-J7-8537-01A-11D-2396-08	14941224	42047804	207202817	5	12990											
FNBP1L	54874	hgsc.bcm.edu	37	chr1	94009756	94009756	+	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	gaacttaacagagaactacaGaaagaatcagaccaaaagta	22	5	7	7	0	1	4	1	0	0	4	1	6	1	4	1	0	4	1	1	0	9	3			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr1:94009756G>A	ENST00000271234.7	+	12	1408	c.1257G>A	c.(1255-1257)caG>caA	p.Q419Q	FNBP1L_ENST00000370253.2_Silent_p.Q361Q|FNBP1L_ENST00000604705.1_Silent_p.Q419Q|FNBP1L_ENST00000370256.4_Silent_p.Q414Q|FNBP1L_ENST00000260506.8_Silent_p.Q361Q	NM_001164473.2	NP_001157945.1	Q5T0N5	FBP1L_HUMAN	formin binding protein 1-like	419	Interaction with CDC42.				autophagy (GO:0006914)|clathrin-mediated endocytosis (GO:0072583)|membrane budding (GO:0006900)|membrane invagination (GO:0010324)|membrane tubulation (GO:0097320)|positive regulation of filopodium assembly (GO:0051491)|vesicle organization (GO:0016050)|vesicle transport along actin filament (GO:0030050)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			breast(2)|kidney(2)|large_intestine(4)|lung(2)|urinary_tract(1)	11		all_lung(203;0.00206)|Lung NSC(277;0.00902)|Melanoma(281;0.155)		all cancers(265;0.00666)|GBM - Glioblastoma multiforme(16;0.0378)|Epithelial(280;0.111)		GAGAACTACAGAAAGAATCAG	0.373																																					p.Q419Q		Atlas-SNP	.											.	FNBP1L	56	.	0			c.G1257A						PASS	.						71	67	68					1																	94009756		1827	4080	5907	SO:0001819	synonymous_variant	54874	exon12			ACTACAGAAAGAA		CCDS53343.1, CCDS53344.1, CCDS60192.1	1p22.1	2008-02-05	2004-11-16	2004-11-17	ENSG00000137942	ENSG00000137942			20851	protein-coding gene	gene with protein product		608848	"chromosome 1 open reading frame 39"	C1orf39		14654988	Standard	NM_017737		Approved	TOCA1, FLJ20275	uc010otk.2	Q5T0N5	OTTHUMG00000010863	ENST00000271234.7:c.1257G>A	chr1.hg19:g.94009756G>A		58.0	0.0	.		59.0	17.0	.	NM_001164473	J3QSS4|Q5T0N6|Q6B097|Q6P653|Q6R4Q4|Q9NXG1	Silent	SNP	ENST00000271234.7	hg19	CCDS53343.1																																																																																			.	.	.	none		0.373	FNBP1L-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_017737		A	94009756	G	A	94009756	2	1	214	1	0	0	0	0	0	0	0	1	5973	933	33	2		2	FNBP1L	1	94009756	Silent	SNP	G	TCGA-J7-8537-01A-11D-2396-08	51961952	94009756	155240865	6	12991											
FLG	2312	hgsc.bcm.edu	37	chr1	152277075	152277075	+	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	ccacgaatggtgtcctgaccCtcttgggacgctgagtgcct	6	10	12	13	2	1	2	0	2	1	0	2	4	2	3	4	2	1	1	4	2	1	1			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr1:152277075C>A	ENST00000368799.1	-	3	10322	c.10287G>T	c.(10285-10287)gaG>gaT	p.E3429D	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3429	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)			TGTCCTGACCCTCTTGGGACG	0.612									Ichthyosis																												p.E3429D		Atlas-SNP	.											.	FLG	900	.	0			c.G10287T						PASS	.						245	252	250					1																	152277075		2203	4299	6502	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTGACCCTCTTGG	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.10287G>T	chr1.hg19:g.152277075C>A	ENSP00000357789:p.Glu3429Asp	584.0	1.0	.		1349.0	247.0	.	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	13.64	2.296547	0.40594	.	.	ENSG00000143631	ENST00000368799	T	0.01705	4.68	4.17	-5.64	0.02466	.	.	.	.	.	T	0.00754	0.0025	L	0.41824	1.3	0.09310	N	1	P	0.44478	0.836	P	0.54499	0.754	T	0.31943	-0.9925	9	0.20046	T	0.44	.	0.6472	0.00820	0.3782:0.2562:0.1242:0.2414	.	3429	P20930	FILA_HUMAN	D	3429	ENSP00000357789:E3429D	ENSP00000357789:E3429D	E	-	3	2	FLG	150543699	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-6.083000	0.00082	-1.572000	0.01661	0.454000	0.30748	GAG	.	.	.	none		0.612	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152277075	C	A	152277075	3	1	214	1	0	0	0	0	1	0	0	0	5929	680	24	4	1902	4	FLG	1	152277075	Missense_Mutation	SNP	C	TCGA-J7-8537-01A-11D-2396-08	58267319	152277075	96973546	7	12992											
CEP350	9857	hgsc.bcm.edu	37	chr1	180047678	180047678	+	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	ccattccagaagaattaggcAgccctgctgttgaatatgta	12	11	9	9	0	0	3	0	1	0	2	1	3	1	3	3	1	2	4	3	1	6	5			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr1:180047678A>T	ENST00000367607.3	+	29	6266	c.5848A>T	c.(5848-5850)Agc>Tgc	p.S1950C		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	1950					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						AGAATTAGGCAGCCCTGCTGT	0.433																																					p.S1950C		Atlas-SNP	.											.	CEP350	418	.	0			c.A5848T						PASS	.						65	63	63					1																	180047678		2203	4300	6503	SO:0001583	missense	9857	exon29			TTAGGCAGCCCTG	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.5848A>T	chr1.hg19:g.180047678A>T	ENSP00000356579:p.Ser1950Cys	44.0	0.0	.		55.0	10.0	.	NM_014810	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	hg19	CCDS1336.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.0|21.0	4.087658|4.087658	0.76642|0.76642	.|.	.|.	ENSG00000135837|ENSG00000135837	ENST00000429851|ENST00000367607	.|T	.|0.57907	.|0.37	5.31|5.31	5.31|5.31	0.75309|0.75309	.|.	.|0.000000	.|0.53938	.|D	.|0.000045	T|T	0.70254|0.70254	0.3203|0.3203	M|M	0.71581|0.71581	2.175|2.175	0.49299|0.49299	D|D	0.999774|0.999774	.|D;D	.|0.76494	.|0.999;0.999	.|D;D	.|0.79784	.|0.993;0.988	T|T	0.71573|0.71573	-0.4552|-0.4552	5|9	.|.	.|.	.|.	.|.	14.1282|14.1282	0.65235|0.65235	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|1950;1950	.|E7EU22;Q5VT06	.|.;CE350_HUMAN	L|C	124|1950	.|ENSP00000356579:S1950C	.|.	Q|S	+|+	2|1	0|0	CEP350|CEP350	178314301|178314301	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.777000|0.777000	0.43975|0.43975	4.336000|4.336000	0.59304|0.59304	2.140000|2.140000	0.66376|0.66376	0.482000|0.482000	0.46254|0.46254	CAG|AGC	.	.	.	none		0.433	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		T	180047678	A	T	180047678	3	4	214	1	0	0	0	0	1	0	0	0	3256	188	7	5	5958	5	CEP350	1	180047678	Missense_Mutation	SNP	A	TCGA-J7-8537-01A-11D-2396-08	27770603	180047678	69202943	8	12993											
RYR2	6262	hgsc.bcm.edu	37	chr1	237617770	237617770	+	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	ccgtaagcctaagtctgcagGatctcattggctacttccac	9	11	8	13	1	2	0	1	0	2	0	4	1	3	1	3	2	3	3	3	2	3	5			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr1:237617770G>T	ENST00000366574.2	+	15	1689	c.1372G>T	c.(1372-1374)Gat>Tat	p.D458Y	RYR2_ENST00000360064.6_Missense_Mutation_p.D456Y|RYR2_ENST00000542537.1_Missense_Mutation_p.D442Y	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	458					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)			AAGTCTGCAGGATCTCATTGG	0.463																																					p.D458Y		Atlas-SNP	.											.	RYR2	1273	.	0			c.G1372T						PASS	.						84	82	82					1																	237617770		1919	4125	6044	SO:0001583	missense	6262	exon15			CTGCAGGATCTCA	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.1372G>T	chr1.hg19:g.237617770G>T	ENSP00000355533:p.Asp458Tyr	70.0	0.0	.		104.0	22.0	.	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	17.49	3.403612	0.62288	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.91180	-2.8;-2.8;-2.8	5.8	5.8	0.92144	Intracellular calcium-release channel (1);	0.000000	0.64402	U	0.000006	D	0.96131	0.8739	M	0.87180	2.865	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	D	0.96166	0.9119	10	0.87932	D	0	.	20.0679	0.97707	0.0:0.0:1.0:0.0	.	458	Q92736	RYR2_HUMAN	Y	458;456;442	ENSP00000355533:D458Y;ENSP00000353174:D456Y;ENSP00000443798:D442Y	ENSP00000353174:D456Y	D	+	1	0	RYR2	235684393	1.000000	0.71417	1.000000	0.80357	0.023000	0.10783	9.804000	0.99143	2.747000	0.94245	0.551000	0.68910	GAT	.	.	.	none		0.463	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237617770	G	T	237617770	3	4	214	1	0	0	0	0	1	0	0	0	13782	1174	41	4	1430	4	RYR2	1	237617770	Missense_Mutation	SNP	G	TCGA-J7-8537-01A-11D-2396-08	57570092	237617770	11632851	9	12994											
GEN1	348654	hgsc.bcm.edu	37	chr2	17962008	17962008	+	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	gaattccaagttaaattcggGgatttcccctgatcctacat	11	13	7	10	1	0	1	0	1	0	0	4	3	3	2	4	2	1	1	4	2	5	5			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr2:17962008G>A	ENST00000381254.2	+	14	1743	c.1529G>A	c.(1528-1530)gGg>gAg	p.G510E	GEN1_ENST00000317402.7_Missense_Mutation_p.G510E|SMC6_ENST00000402989.1_Intron	NM_001130009.1	NP_001123481.1	Q17RS7	GEN_HUMAN	GEN1 Holliday junction 5' flap endonuclease	510					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)					TTAAATTCGGGGATTTCCCCT	0.373								Homologous recombination																													p.G510E		Atlas-SNP	.											.	GEN1	79	.	0			c.G1529A						PASS	.						82	80	80					2																	17962008		2203	4300	6503	SO:0001583	missense	348654	exon14			ATTCGGGGATTTC	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.1529G>A	chr2.hg19:g.17962008G>A	ENSP00000370653:p.Gly510Glu	97.0	0.0	.		98.0	15.0	.	NM_182625	Q17RS9|Q6ZN37	Missense_Mutation	SNP	ENST00000381254.2	hg19	CCDS1691.1	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.178672	0.00308	.	.	ENSG00000178295	ENST00000317402;ENST00000381254;ENST00000528873;ENST00000536097	T;T;T	0.38560	1.96;1.96;1.13	5.46	1.86	0.25419	.	0.276329	0.30742	N	0.008968	T	0.11196	0.0273	N	0.01048	-1.04	0.09310	N	0.999996	B	0.02656	0.0	B	0.01281	0.0	T	0.36939	-0.9727	10	0.02654	T	1	-9.6119	7.6912	0.28569	0.7505:0.0:0.2495:0.0	.	510	Q17RS7	GEN_HUMAN	E	510;510;281;147	ENSP00000318977:G510E;ENSP00000370653:G510E;ENSP00000431542:G281E	ENSP00000318977:G510E	G	+	2	0	GEN1	17825489	0.204000	0.23447	0.429000	0.26710	0.003000	0.03518	1.257000	0.32932	0.473000	0.27368	-0.469000	0.05056	GGG	.	.	.	none		0.373	GEN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241661.2	NM_182625		A	17962008	G	A	17962008	3	1	214	1	0	0	0	0	1	0	0	0	6342	1232	43	2	1579	2	GEN1	2	17962008	Missense_Mutation	SNP	G	TCGA-J7-8537-01A-11D-2396-08		17962008	225237365	10	12995											
APOB	338	hgsc.bcm.edu	37	chr2	21238283	21238283	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggaaactgtggagccataaGctgtagcagatgagtccatt	12	10	12	7	0	0	2	0	1	0	1	1	4	1	4	2	2	4	3	2	2	3	3			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr2:21238283G>A	ENST00000233242.1	-	22	3594	c.3467C>T	c.(3466-3468)gCt>gTt	p.A1156V		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1156					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)					GGAGCCATAAGCTGTAGCAGA	0.507																																					p.A1156V		Atlas-SNP	.											.	APOB	761	.	0			c.C3467T						PASS	.						140	121	128					2																	21238283		2203	4300	6503	SO:0001583	missense	338	exon22			CCATAAGCTGTAG	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.3467C>T	chr2.hg19:g.21238283G>A	ENSP00000233242:p.Ala1156Val	96.0	0.0	.		201.0	35.0	.	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	15.43	2.830038	0.50845	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.00686	5.85	5.49	5.49	0.81192	.	0.100022	0.44483	D	0.000457	T	0.01870	0.0059	M	0.67953	2.075	0.80722	D	1	D	0.58620	0.983	P	0.53313	0.723	T	0.63216	-0.6687	10	0.06099	T	0.92	.	13.2457	0.60022	0.0756:0.0:0.9244:0.0	.	1156	P04114	APOB_HUMAN	V	1156	ENSP00000233242:A1156V	ENSP00000233242:A1156V	A	-	2	0	APOB	21091788	0.822000	0.29219	0.991000	0.47740	0.903000	0.53119	1.269000	0.33074	2.767000	0.95098	0.655000	0.94253	GCT	.	.	.	none		0.507	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21238283	G	A	21238283	3	1	214	1	0	0	0	0	1	0	0	0	785	971	34	2	10256	2	APOB	2	21238283	Missense_Mutation	SNP	G	TCGA-J7-8537-01A-11D-2396-08	3276275	21238283	221961090	11	12996											
LRP1B	53353	hgsc.bcm.edu	37	chr2	141607702	141607702	+	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	acagtttctaacccagttccGttaataaaagctcgtttaat	13	14	5	9	2	1	0	0	0	1	0	3	0	2	0	2	0	2	5	2	0	5	7	rs368565366		TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr2:141607702G>A	ENST00000389484.3	-	29	5879	c.4908C>T	c.(4906-4908)aaC>aaT	p.N1636N		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1636					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)		ACCCAGTTCCGTTAATAAAAG	0.318										TSP Lung(27;0.18)																											p.N1636N	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											LRP1B,rectum,carcinoma,0,1	LRP1B	1315	.	0			c.C4908T						PASS	.	A		1,4405	4.2+/-10.8	0,1,2202	162	169	167		4908	0.2	1	2		167	0,8600		0,0,4300	no	coding-synonymous	LRP1B	NM_018557.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		1636/4600	141607702	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	53353	exon29			AGTTCCGTTAATA	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.4908C>T	chr2.hg19:g.141607702G>A		123.0	0.0	.		123.0	25.0	.	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	hg19	CCDS2182.1																																																																																			.	.	.	weak		0.318	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141607702	G	A	141607702	2	1	214	1	0	0	0	0	0	0	0	1	8962	1136	40	1		1	LRP1B	2	141607702	Silent	SNP	G	TCGA-J7-8537-01A-11D-2396-08	120369419	141607702	101591671	12	12997											
IGSF10	285313	hgsc.bcm.edu	37	chr3	151161388	151161388	+	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	ttctgagacaactgtttggtTtgcaagaatccaggtaactg	11	13	10	7	0	1	2	0	1	1	2	2	3	2	2	1	2	3	4	1	2	4	4			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr3:151161388T>A	ENST00000282466.3	-	5	5346	c.5347A>T	c.(5347-5349)Aac>Tac	p.N1783Y	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	1783	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)			ACTGTTTGGTTTGCAAGAATC	0.498																																					p.N1783Y		Atlas-SNP	.											.	IGSF10	279	.	0			c.A5347T						PASS	.						125	112	116					3																	151161388		2203	4300	6503	SO:0001583	missense	285313	exon5			TTTGGTTTGCAAG	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.5347A>T	chr3.hg19:g.151161388T>A	ENSP00000282466:p.Asn1783Tyr	98.0	0.0	.		170.0	45.0	.	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	hg19	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	T	18.09	3.546893	0.65198	.	.	ENSG00000152580	ENST00000282466;ENST00000544042	T	0.80909	-1.43	5.25	5.25	0.73442	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.52532	D	0.000074	D	0.89522	0.6739	M	0.85099	2.735	0.58432	D	0.999991	D	0.89917	1.0	D	0.97110	1.0	D	0.90304	0.4332	9	.	.	.	.	11.1386	0.48390	0.0:0.0747:0.0:0.9253	.	1783	Q6WRI0	IGS10_HUMAN	Y	1783;410	ENSP00000282466:N1783Y	.	N	-	1	0	IGSF10	152644078	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.209000	0.58493	1.989000	0.58080	0.477000	0.44152	AAC	.	.	.	none		0.498	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		A	151161388	T	A	151161388	3	1	214	1	0	0	0	0	1	0	0	0	7604	1841	64	5	2580	5	IGSF10	3	151161388	Missense_Mutation	SNP	T	TCGA-J7-8537-01A-11D-2396-08		151161388	46861042	13	12998											
GOLIM4	27333	hgsc.bcm.edu	37	chr3	167742778	167742778	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actttgtttttgctcttcatTttcatctggcaaattttctt	6	23	4	8	0	5	0	2	0	3	0	5	0	5	0	0	1	1	3	0	1	1	9			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr3:167742778T>C	ENST00000470487.1	-	13	2418	c.1729A>G	c.(1729-1731)Aat>Gat	p.N577D	GOLIM4_ENST00000309027.4_Missense_Mutation_p.N549D	NM_014498.3	NP_055313.1	O00461	GOLI4_HUMAN	golgi integral membrane protein 4	577	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						TGCTCTTCATTTTCATCTGGC	0.408																																					p.N577D		Atlas-SNP	.											.	GOLIM4	71	.	0			c.A1729G						PASS	.						220	192	202					3																	167742778		2203	4300	6503	SO:0001583	missense	27333	exon13			CTTCATTTTCATC	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.1729A>G	chr3.hg19:g.167742778T>C	ENSP00000417354:p.Asn577Asp	156.0	0.0	.		194.0	36.0	.	NM_014498		Missense_Mutation	SNP	ENST00000470487.1	hg19	CCDS3204.1	.	.	.	.	.	.	.	.	.	.	T	18.56	3.649660	0.67358	.	.	ENSG00000173905	ENST00000470487;ENST00000309027	.	.	.	6.0	6.0	0.97389	.	0.224151	0.53938	D	0.000046	T	0.55577	0.1929	M	0.69823	2.125	0.35647	D	0.811481	P;P	0.40875	0.731;0.731	B;B	0.36845	0.234;0.234	T	0.63937	-0.6524	9	0.15499	T	0.54	-6.4985	16.56	0.84537	0.0:0.0:0.0:1.0	.	549;577	F8W785;O00461	.;GOLI4_HUMAN	D	577;549	.	ENSP00000309893:N549D	N	-	1	0	GOLIM4	169225472	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.450000	0.60041	2.313000	0.78055	0.454000	0.30748	AAT	.	.	.	none		0.408	GOLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351278.2			C	167742778	T	C	167742778	3	2	214	1	0	0	0	0	1	0	0	0	6573	1841	64	3	377	3	GOLIM4	3	167742778	Missense_Mutation	SNP	T	TCGA-J7-8537-01A-11D-2396-08	16581390	167742778	30279652	14	12999											
CENPE	1062	hgsc.bcm.edu	37	chr4	104117119	104117119	+	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	tcatgaattgccctgggtatAactcccaaatgatcttctga	11	13	7	10	0	3	3	1	3	2	0	4	3	4	3	2	1	2	1	2	1	4	4			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr4:104117119A>C	ENST00000265148.3	-	4	404	c.315T>G	c.(313-315)gtT>gtG	p.V105V	CENPE_ENST00000380026.3_Silent_p.V105V	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	105	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)|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)		CCCTGGGTATAACTCCCAAAT	0.358																																					p.V105V		Atlas-SNP	.											.	CENPE	253	.	0			c.T315G						PASS	.						106	101	103					4																	104117119		2202	4300	6502	SO:0001819	synonymous_variant	1062	exon4			GGGTATAACTCCC	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.315T>G	chr4.hg19:g.104117119A>C		54.0	0.0	.		49.0	10.0	.	NM_001813	A6NKY9|A8K2U7|Q4LE75	Silent	SNP	ENST00000265148.3	hg19	CCDS34042.1																																																																																			.	.	.	none		0.358	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	104117119	A	C	104117119	2	2	214	1	0	0	0	0	0	0	0	1	3232	349	13	5		5	CENPE	4	104117119	Silent	SNP	A	TCGA-J7-8537-01A-11D-2396-08		104117119	87037157	15	13000											
IL6ST	3572	hgsc.bcm.edu	37	chr5	55247844	55247844	+	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	aacaggaagttggtcccactCtaagacagcttcgtttttcc	10	12	8	11	1	1	1	0	0	1	1	4	2	3	2	2	2	2	3	2	2	3	5			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr5:55247844C>G	ENST00000381298.2	-	13	1924	c.1612G>C	c.(1612-1614)Gag>Cag	p.E538Q	IL6ST_ENST00000502326.3_Missense_Mutation_p.E538Q|IL6ST_ENST00000536319.1_3'UTR|IL6ST_ENST00000522633.2_3'UTR|IL6ST_ENST00000381293.2_Intron|IL6ST_ENST00000381286.3_Intron|IL6ST_ENST00000336909.5_Missense_Mutation_p.E538Q|IL6ST_ENST00000381294.3_Missense_Mutation_p.E477Q|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	538	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				TGGTCCCACTCTAAGACAGCT	0.348			O		hepatocellular ca																																p.E538Q		Atlas-SNP	.		Dom	yes		5	5q11	3572	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"		E	.	IL6ST	75	.	0			c.G1612C						PASS	.						75	64	68					5																	55247844		2203	4300	6503	SO:0001583	missense	3572	exon13			CCCACTCTAAGAC	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.1612G>C	chr5.hg19:g.55247844C>G	ENSP00000370698:p.Glu538Gln	70.0	0.0	.		64.0	6.0	.	NM_002184	A0N0L4|Q5FC04|Q9UQ41	Missense_Mutation	SNP	ENST00000381298.2	hg19	CCDS3971.1	.	.	.	.	.	.	.	.	.	.	C	12.30	1.897415	0.33535	.	.	ENSG00000134352	ENST00000381298;ENST00000336909;ENST00000381294	T;T;T	0.57273	0.41;0.41;0.41	5.83	5.83	0.93111	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.455228	0.26089	N	0.026407	T	0.22085	0.0532	N	0.01352	-0.895	0.80722	D	1	B;B;B	0.18610	0.008;0.029;0.008	B;B;B	0.21151	0.011;0.033;0.011	T	0.29181	-1.0020	10	0.13853	T	0.58	.	9.4221	0.38557	0.0:0.7741:0.1461:0.0799	.	538;477;538	Q17RA0;Q5FC04;P40189	.;.;IL6RB_HUMAN	Q	538;538;477	ENSP00000370698:E538Q;ENSP00000338799:E538Q;ENSP00000370694:E477Q	ENSP00000338799:E538Q	E	-	1	0	IL6ST	55283601	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	0.907000	0.28531	2.770000	0.95276	0.655000	0.94253	GAG	.	.	.	none		0.348	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		G	55247844	C	G	55247844	3	3	214	1	0	0	0	0	1	0	0	0	7710	922	32	4	1164	4	IL6ST	5	55247844	Missense_Mutation	SNP	C	TCGA-J7-8537-01A-11D-2396-08		55247844	125667416	16	13001											
PCDHGA1	56114	hgsc.bcm.edu	37	chr5	140712677	140712677	+	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	ggaaccattttctcaggtaaActtttgtgatgaatgtatca	12	15	8	6	0	2	2	2	2	1	0	3	3	2	3	1	2	2	2	1	2	5	6			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr5:140712677A>G	ENST00000517417.1	+	1	2421				PCDHGA1_ENST00000378105.3_Missense_Mutation_p.N809S	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1						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)			TCTCAGGTAAACTTTTGTGAT	0.388																																					p.N809S		Atlas-SNP	.											.	PCDHGA1	397	.	0			c.A2426G						PASS	.						50	53	52					5																	140712677		2203	4300	6503	SO:0001627	intron_variant	56114	exon1			AGGTAAACTTTTG	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.2421+5A>G	chr5.hg19:g.140712677A>G		104.0	0.0	.		173.0	34.0	.	NM_031993	Q2M273|Q9Y5D6	Missense_Mutation	SNP	ENST00000517417.1	hg19	CCDS54922.1	.	.	.	.	.	.	.	.	.	.	.	2.192	-0.385092	0.04966	.	.	ENSG00000204956	ENST00000378105	T	0.47869	0.83	4.15	0.129	0.14739	.	0.924660	0.08888	U	0.879068	T	0.21427	0.0516	N	0.08118	0	0.09310	N	0.999996	B	0.13145	0.007	B	0.09377	0.004	T	0.20174	-1.0283	9	.	.	.	.	2.5439	0.04732	0.462:0.0:0.194:0.344	.	809	Q9Y5H4-2	.	S	809	ENSP00000367345:N809S	.	N	+	2	0	PCDHGA1	140692861	0.001000	0.12720	0.351000	0.25721	0.671000	0.39405	-0.689000	0.05144	-0.058000	0.13177	-0.468000	0.05107	AAC	.	.	.	none		0.388	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		G	140712677	A	G	140712677	1	3	214	0	1	0	0	0	0	0	0	0	11557	43	2	3		3	PCDHGA1	5	140712677	Intron	SNP	A	TCGA-J7-8537-01A-11D-2396-08	85464833	140712677	40202583	17	13002											
CSF1R	1436	hgsc.bcm.edu	37	chr5	149433707	149433707	+	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	tcgcagcaggtcaggtgctcActagagctctcctcctccag	7	9	10	15	1	3	1	2	0	1	1	7	1	5	1	3	2	3	4	3	2	1	1			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr5:149433707A>T	ENST00000286301.3	-	22	3135	c.2844T>A	c.(2842-2844)agT>agA	p.S948R		NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	948					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)	TCAGGTGCTCACTAGAGCTCT	0.602																																					p.S948R		Atlas-SNP	.											.	CSF1R	250	.	0			c.T2844A						PASS	.						38	35	36					5																	149433707		2203	4300	6503	SO:0001583	missense	1436	exon22			GTGCTCACTAGAG	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.2844T>A	chr5.hg19:g.149433707A>T	ENSP00000286301:p.Ser948Arg	28.0	0.0	.		67.0	14.0	.	NM_005211	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Missense_Mutation	SNP	ENST00000286301.3	hg19	CCDS4302.1	.	.	.	.	.	.	.	.	.	.	A	9.983	1.228611	0.22542	.	.	ENSG00000182578	ENST00000286301	T	0.30182	1.54	5.25	-4.77	0.03219	.	0.092077	0.47852	D	0.000212	T	0.23133	0.0559	L	0.50333	1.59	0.54753	D	0.999989	D	0.54397	0.966	B	0.44315	0.446	T	0.11792	-1.0573	10	0.51188	T	0.08	.	7.9653	0.30095	0.2777:0.0:0.6023:0.12	.	948	P07333	CSF1R_HUMAN	R	948	ENSP00000286301:S948R	ENSP00000286301:S948R	S	-	3	2	CSF1R	149413900	0.078000	0.21339	0.618000	0.29105	0.009000	0.06853	-0.609000	0.05635	-0.866000	0.04068	-0.490000	0.04691	AGT	.	.	.	none		0.602	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211		T	149433707	A	T	149433707	3	4	214	1	0	0	0	0	1	0	0	0	3934	156	6	5	78	5	CSF1R	5	149433707	Missense_Mutation	SNP	A	TCGA-J7-8537-01A-11D-2396-08	8721030	149433707	31481553	18	13003											
ZNF184	7738	hgsc.bcm.edu	37	chr6	27420221	27420223	+	In_Frame_Del	DEL	TGG	TGG	-																															ttgagtaaggtgtgtgctccTggtgaaggttttatcacatt																										TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	TGG	TGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr6:27420221_27420223delTGG	ENST00000211936.6	-	6	1399_1401	c.1115_1117delCCA	c.(1114-1119)accagg>agg	p.T372del	ZNF184_ENST00000377419.1_In_Frame_Del_p.T372del	NM_007149.2	NP_009080.2	Q99676	ZN184_HUMAN	zinc finger protein 184	372					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|kidney(9)|large_intestine(13)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						TGTGTGCTCCTGGTGAAGGTTTT	0.379																																					p.372_373del		Atlas-INDEL	.											.	ZNF184	89	.	0			c.1116_1118del						PASS	.																																			SO:0001651	inframe_deletion	7738	exon6			.	U66561	CCDS4624.1	6p21.3	2013-01-08	2006-06-28		ENSG00000096654	ENSG00000096654		"Zinc fingers, C2H2-type", "-"	12975	protein-coding gene	gene with protein product		602277	"zinc finger protein 184 (Kruppel-like)"				Standard	NM_007149		Approved		uc003nji.3	Q99676	OTTHUMG00000014478	ENST00000211936.6:c.1115_1117delCCA	chr6.hg19:g.27420221_27420223delTGG	ENSP00000211936:p.Thr372del	89.0	0.0	0		103.0	20.0	0.194175	NM_007149	B2R715|O60792|Q8TBA9	In_Frame_Del	DEL	ENST00000211936.6	hg19	CCDS4624.1																																																																																			.	.	.	none		0.379	ZNF184-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040146.1	NM_007149		-	27420223	TGG	-	27420221	7	5	214	1	0	1	0	1	0	0	0	0	17763	1579	55	0	1142	0	ZNF184	6	27420221	In_Frame_Del	DEL	TGG	TCGA-J7-8537-01A-11D-2396-08		27420221	143694846	19	13004											
VARS	7407	hgsc.bcm.edu	37	chr6	31762754	31762754	+	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	tgggccccccaggcctgctgGccacagcagctgggccacag	6	4	14	17	0	0	0	0	0	0	0	0	0	0	0	6	4	3	3	6	4	0	0			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr6:31762754G>T	ENST00000375663.3	-	2	681	c.241C>A	c.(241-243)Cca>Aca	p.P81T	VARS_ENST00000444930.2_Intron|LSM2_ENST00000491421.1_5'Flank	NM_006295.2	NP_006286.1	P26640	SYVC_HUMAN	valyl-tRNA synthetase	81					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)	AGGCCTGCTGGCCACAGCAGC	0.711																																					p.P81T		Atlas-SNP	.											.	VARS	76	.	0			c.C241A						PASS	.						13	19	16					6																	31762754		1478	2637	4115	SO:0001583	missense	7407	exon2			CTGCTGGCCACAG	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.241C>A	chr6.hg19:g.31762754G>T	ENSP00000364815:p.Pro81Thr	59.0	0.0	.		86.0	15.0	.	NM_006295	B0V1N1|B4DZ61|Q5JQ90|Q96E77|Q9UQM2	Missense_Mutation	SNP	ENST00000375663.3	hg19	CCDS34412.1	.	.	.	.	.	.	.	.	.	.	G	14.34	2.505254	0.44558	.	.	ENSG00000204394	ENST00000375663;ENST00000440048	T;T	0.06849	3.25;3.25	5.24	5.24	0.73138	Glutathione S-transferase, N-terminal (1);	0.142308	0.47455	D	0.000231	T	0.04003	0.0112	N	0.24115	0.695	0.80722	D	1	P	0.44139	0.827	P	0.45276	0.475	T	0.29366	-1.0014	10	0.87932	D	0	-2.2071	9.8609	0.41114	0.0931:0.0:0.9069:0.0	.	81	P26640	SYVC_HUMAN	T	81	ENSP00000364815:P81T;ENSP00000413925:P81T	ENSP00000364815:P81T	P	-	1	0	VARS	31870733	1.000000	0.71417	0.999000	0.59377	0.392000	0.30506	2.707000	0.47143	2.461000	0.83175	0.462000	0.41574	CCA	.	.	.	none		0.711	VARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076619.2	NM_006295		T	31762754	G	T	31762754	3	4	214	1	0	0	0	0	1	0	0	0	17135	1203	42	4	3669	4	VARS	6	31762754	Missense_Mutation	SNP	G	TCGA-J7-8537-01A-11D-2396-08	4342533	31762754	139352313	20	13005											
AARS2	57505	hgsc.bcm.edu	37	chr6	44272835	44272835	+	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	agtagttgtacttggggctgTcgtcagttgggggcactcct	5	13	15	8	1	1	0	1	0	0	0	3	0	2	0	1	4	1	6	1	4	2	5			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr6:44272835T>A	ENST00000244571.4	-	11	1537	c.1535A>T	c.(1534-1536)gAc>gTc	p.D512V	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)			CTTGGGGCTGTCGTCAGTTGG	0.607											OREG0017473	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D512V		Atlas-SNP	.											.	AARS2	77	.	0			c.A1535T						PASS	.						128	121	123					6																	44272835		2203	4300	6503	SO:0001583	missense	57505	exon11			GGGCTGTCGTCAG	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.1535A>T	chr6.hg19:g.44272835T>A	ENSP00000244571:p.Asp512Val	179.0	0.0	.	922	370.0	34.0	.	NM_020745		Missense_Mutation	SNP	ENST00000244571.4	hg19	CCDS34464.1	.	.	.	.	.	.	.	.	.	.	T	13.94	2.385639	0.42308	.	.	ENSG00000124608	ENST00000244571	T	0.72725	-0.68	5.01	3.83	0.44106	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);	0.096640	0.64402	D	0.000001	T	0.77478	0.4136	M	0.73598	2.24	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79962	-0.1582	10	0.87932	D	0	-17.649	12.7414	0.57255	0.0:0.0715:0.0:0.9285	.	512	Q5JTZ9	SYAM_HUMAN	V	512	ENSP00000244571:D512V	ENSP00000244571:D512V	D	-	2	0	AARS2	44380813	1.000000	0.71417	0.925000	0.36789	0.052000	0.14988	5.622000	0.67750	0.272000	0.22027	-1.186000	0.01703	GAC	.	.	.	none		0.607	AARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040741.2	NM_020745		A	44272835	T	A	44272835	3	1	214	1	0	0	0	0	1	0	0	0	20	1667	58	5	1470	5	AARS2	6	44272835	Missense_Mutation	SNP	T	TCGA-J7-8537-01A-11D-2396-08	12510081	44272835	126842232	21	13006											
SAMD3	154075	hgsc.bcm.edu	37	chr6	130505262	130505262	+	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	acttacgaagccacagccatCctcatccaggaaagggtggg	12	6	11	12	1	1	0	1	0	0	0	3	2	3	1	4	3	3	0	4	3	3	1			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr6:130505262C>T	ENST00000368134.2	-	9	1248	c.640G>A	c.(640-642)Gat>Aat	p.D214N	SAMD3_ENST00000324172.6_Missense_Mutation_p.D214N|SAMD3_ENST00000437477.2_Missense_Mutation_p.D214N|SAMD3_ENST00000457563.2_Missense_Mutation_p.D238N|SAMD3_ENST00000439090.2_Missense_Mutation_p.D214N|SAMD3_ENST00000532763.1_Missense_Mutation_p.D212N|SAMD3_ENST00000533296.1_5'UTR	NM_001258275.1	NP_001245204.1	Q8N6K7	SAMD3_HUMAN	sterile alpha motif domain containing 3	214										breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(3)|lung(15)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	29				GBM - Glioblastoma multiforme(226;0.00594)|OV - Ovarian serous cystadenocarcinoma(155;0.128)		CCACAGCCATCCTCATCCAGG	0.473																																					p.D214N		Atlas-SNP	.											.	SAMD3	98	.	0			c.G640A						PASS	.						101	86	91					6																	130505262		2203	4300	6503	SO:0001583	missense	154075	exon7			AGCCATCCTCATC	AK091351	CCDS34539.1, CCDS64525.1	6q23.1	2013-01-10			ENSG00000164483	ENSG00000164483		"Sterile alpha motif (SAM) domain containing"	21574	protein-coding gene	gene with protein product							Standard	NM_001017373		Approved	bA73O6.2, FLJ34032	uc031spp.1	Q8N6K7	OTTHUMG00000015556	ENST00000368134.2:c.640G>A	chr6.hg19:g.130505262C>T	ENSP00000357116:p.Asp214Asn	50.0	0.0	.		103.0	5.0	.	NM_001017373	B4DY20|E1P576|J3KQK4|Q4VXD8|Q8NAY1|Q8NB96	Missense_Mutation	SNP	ENST00000368134.2	hg19	CCDS34539.1	.	.	.	.	.	.	.	.	.	.	C	17.32	3.359379	0.61403	.	.	ENSG00000164483	ENST00000368134;ENST00000457563;ENST00000439090;ENST00000437477;ENST00000532763;ENST00000324172	T;T;T;T;T;T	0.56444	0.88;0.87;0.88;0.88;0.8;0.46	5.53	4.66	0.58398	.	0.237830	0.36854	N	0.002379	T	0.34164	0.0888	M	0.73598	2.24	0.37596	D	0.920378	B;P;B;B	0.38788	0.256;0.647;0.068;0.098	B;B;B;B	0.31495	0.055;0.131;0.039;0.025	T	0.45086	-0.9285	10	0.66056	D	0.02	.	10.1892	0.43017	0.0:0.845:0.0:0.155	.	238;213;214;214	B4DY20;Q4VXD9;Q8N6K7-2;Q8N6K7	.;.;.;SAMD3_HUMAN	N	214;238;214;214;212;214	ENSP00000357116:D214N;ENSP00000402092:D238N;ENSP00000403565:D214N;ENSP00000391163:D214N;ENSP00000436088:D212N;ENSP00000324874:D214N	ENSP00000324874:D214N	D	-	1	0	SAMD3	130546955	0.996000	0.38824	0.997000	0.53966	0.991000	0.79684	2.562000	0.45914	1.300000	0.44818	0.655000	0.94253	GAT	.	.	.	none		0.473	SAMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042197.3	NM_152552		T	130505262	C	T	130505262	3	4	214	1	0	0	0	0	1	0	0	0	13833	855	30	2	962	2	SAMD3	6	130505262	Missense_Mutation	SNP	C	TCGA-J7-8537-01A-11D-2396-08	86232427	130505262	40609805	22	13007											
PUS7	54517	hgsc.bcm.edu	37	chr7	105099624	105099624	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtaaacttaccagaagcaaAaactggtggtgtcttccctt	13	11	8	9	0	1	1	0	0	1	1	2	1	2	1	2	2	4	2	2	2	6	4			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr7:105099624A>G	ENST00000356362.2	-	15	2054	c.1840T>C	c.(1840-1842)Ttt>Ctt	p.F614L	PUS7_ENST00000469408.1_Missense_Mutation_p.F614L	NM_019042.3	NP_061915.2	Q96PZ0	PUS7_HUMAN	pseudouridylate synthase 7 (putative)	614					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						CCAGAAGCAAAAACTGGTGGT	0.353																																					p.F614L	Colon(138;2387 3051 17860)	Atlas-SNP	.											.	PUS7	59	.	0			c.T1840C						PASS	.						136	115	122					7																	105099624		2203	4300	6503	SO:0001583	missense	54517	exon15			AAGCAAAAACTGG	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.1840T>C	chr7.hg19:g.105099624A>G	ENSP00000348722:p.Phe614Leu	100.0	0.0	.		85.0	16.0	.	NM_019042	Q75MG4|Q9NX19	Missense_Mutation	SNP	ENST00000356362.2	hg19	CCDS34725.1	.	.	.	.	.	.	.	.	.	.	A	10.52	1.372308	0.24857	.	.	ENSG00000091127	ENST00000356362;ENST00000544995;ENST00000469408	T;T	0.40756	1.02;1.02	5.28	5.28	0.74379	Pseudouridine synthase, catalytic domain (1);	0.171422	0.52532	N	0.000075	T	0.17831	0.0428	N	0.03608	-0.345	0.40339	D	0.979018	B;B	0.11235	0.004;0.004	B;B	0.14023	0.01;0.005	T	0.14699	-1.0463	10	0.10377	T	0.69	-1.6592	8.8965	0.35467	0.9072:0.0:0.0928:0.0	.	614;614	B3KY42;Q96PZ0	.;PUS7_HUMAN	L	614	ENSP00000348722:F614L;ENSP00000417402:F614L	ENSP00000348722:F614L	F	-	1	0	PUS7	104886860	1.000000	0.71417	0.993000	0.49108	0.860000	0.49131	5.995000	0.70631	1.995000	0.58328	0.460000	0.39030	TTT	.	.	.	none		0.353	PUS7-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348681.1	NM_019042		G	105099624	A	G	105099624	3	3	214	1	0	0	0	0	1	0	0	0	12846	14	1	3	153	3	PUS7	7	105099624	Missense_Mutation	SNP	A	TCGA-J7-8537-01A-11D-2396-08		105099624	54039039	23	13008											
C8orf79	57604	hgsc.bcm.edu	37	chr8	12879058	12879058	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtccagccttccagacactcTagtttagactttgatcacca	10	12	6	13	0	2	3	1	1	1	2	4	3	4	3	4	0	1	1	4	0	2	5			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr8:12879058T>C	ENST00000524591.2	+	5	1359	c.870T>C	c.(868-870)tcT>tcC	p.S290S	KIAA1456_ENST00000447063.2_Intron	NM_001099677.1|NM_020844.2	NP_001093147.1|NP_065895.2	Q9P272	K1456_HUMAN	KIAA1456	290							methyltransferase activity (GO:0008168)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7						CCAGACACTCTAGTTTAGACT	0.423																																					p.S290S		Atlas-SNP	.											.	KIAA1456	20	.	0			c.T870C						PASS	.						79	77	78					8																	12879058		1869	4097	5966	SO:0001819	synonymous_variant	57604	exon5			ACACTCTAGTTTA	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.870T>C	chr8.hg19:g.12879058T>C		64.0	0.0	.		110.0	26.0	.	NM_020844	Q96AW6	Silent	SNP	ENST00000524591.2	hg19	CCDS47808.1																																																																																			.	.	.	none		0.423	KIAA1456-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383262.2	NM_001099677		C	12879058	T	C	12879058	2	2	214	1	0	0	0	0	0	0	0	1	2440	1509	53	3		3	C8orf79	8	12879058	Silent	SNP	T	TCGA-J7-8537-01A-11D-2396-08		12879058	133484964	24	13009											
ST8SIA6	338596	hgsc.bcm.edu	37	chr10	17495608	17495608	+	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	gggctccggagcgtcctcagCgctgcgggggtgccgtgggt	2	7	20	12	5	1	0	1	0	0	0	3	1	3	1	3	5	4	2	3	5	0	0			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr10:17495608C>T	ENST00000377602.4	-	2	224	c.150G>A	c.(148-150)gcG>gcA	p.A50A		NM_001004470.1	NP_001004470.1	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	50					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						GCGTCCTCAGCGCTGCGGGGG	0.706																																					p.A50A		Atlas-SNP	.											.	ST8SIA6	85	.	0			c.G150A						PASS	.						8	10	9					10																	17495608		2170	4271	6441	SO:0001819	synonymous_variant	338596	exon2			CCTCAGCGCTGCG		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.150G>A	chr10.hg19:g.17495608C>T		17.0	0.0	.		25.0	9.0	.	NM_001004470	B0YJ97|B9EH72|Q5VZH4	Silent	SNP	ENST00000377602.4	hg19	CCDS31158.1																																																																																			.	.	.	none		0.706	ST8SIA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047036.1	NM_001004470		T	17495608	C	T	17495608	2	4	214	1	0	0	0	0	0	0	0	1	15248	755	27	1		1	ST8SIA6	10	17495608	Silent	SNP	C	TCGA-J7-8537-01A-11D-2396-08		17495608	118039139	25	13010											
MKI67	4288	hgsc.bcm.edu	37	chr10	129910454	129910454	+	Missense_Mutation	SNP	T	T	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	ggaacatatcatctgtaaaaTatcatgttgacttcggctga	13	13	8	7	1	3	2	2	2	1	0	4	3	3	3	0	2	1	3	0	2	5	5			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr10:129910454T>G	ENST00000368654.3	-	9	2287	c.1912A>C	c.(1912-1914)Att>Ctt	p.I638L	MKI67_ENST00000484853.1_5'UTR|MKI67_ENST00000368653.3_Missense_Mutation_p.I278L	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	638					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)				ATCTGTAAAATATCATGTTGA	0.398																																					p.I638L		Atlas-SNP	.											.	MKI67	363	.	0			c.A1912C						PASS	.						96	89	91					10																	129910454		2203	4300	6503	SO:0001583	missense	4288	exon9			GTAAAATATCATG	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.1912A>C	chr10.hg19:g.129910454T>G	ENSP00000357643:p.Ile638Leu	152.0	0.0	.		175.0	39.0	.	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	hg19	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	T	15.38	2.815996	0.50527	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609;ENST00000368652	T;T	0.01369	5.0;4.97	4.47	2.03	0.26663	.	0.382408	0.22081	N	0.064888	T	0.01765	0.0056	M	0.63428	1.95	0.09310	N	1	B;B;B	0.32573	0.376;0.376;0.259	B;B;B	0.36418	0.224;0.224;0.112	T	0.42137	-0.9469	10	0.35671	T	0.21	.	0.8729	0.01218	0.167:0.161:0.1731:0.4989	.	637;278;638	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	L	638;278;637;213	ENSP00000357643:I638L;ENSP00000357642:I278L	ENSP00000357641:I213L	I	-	1	0	MKI67	129800444	0.000000	0.05858	0.002000	0.10522	0.491000	0.33493	-0.129000	0.10515	0.725000	0.32318	0.533000	0.62120	ATT	.	.	.	none		0.398	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		G	129910454	T	G	129910454	3	3	214	1	0	0	0	0	1	0	0	0	9605	1406	49	5	7886	5	MKI67	10	129910454	Missense_Mutation	SNP	T	TCGA-J7-8537-01A-11D-2396-08	112414846	129910454	5624293	26	13011											
TSG101	7251	hgsc.bcm.edu	37	chr11	18541141	18541142	+	Frame_Shift_Del	DEL	TG	TG	-																															ttcacgtacagttaggtctcTgtatttgtactgaaaagcaa																										TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr11:18541141_18541142delTG	ENST00000251968.3	-	2	466_467	c.51_52delCA	c.(49-54)tacagafs	p.YR17fs	TSG101_ENST00000536719.1_Frame_Shift_Del_p.YR17fs|TSG101_ENST00000357193.3_Intron	NM_006292.3	NP_006283.1	Q99816	TS101_HUMAN	tumor susceptibility 101	17	UEV. {ECO:0000255|PROSITE- ProRule:PRU00652}.				cell cycle arrest (GO:0007050)|cell division (GO:0051301)|cellular protein modification process (GO:0006464)|endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|keratinocyte differentiation (GO:0030216)|membrane organization (GO:0061024)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell growth (GO:0001558)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|viral budding (GO:0046755)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|multivesicular body (GO:0005771)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transcription corepressor activity (GO:0003714)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	22						GTTAGGTCTCTGTATTTGTACT	0.307																																					p.18_18del	GBM(99;1348 1396 8611 26475 50572)	Atlas-INDEL	.											.	TSG101	43	.	0			c.52_53del						PASS	.																																			SO:0001589	frameshift_variant	7251	exon2			.	U82130	CCDS7842.1	11p15	2013-08-22	2013-08-22		ENSG00000074319	ENSG00000074319			15971	protein-coding gene	gene with protein product		601387	"tumor susceptibility gene 10", "tumor susceptibility gene 101"	TSG10		9019400, 9241264	Standard	NM_006292		Approved	VPS23	uc001mor.3	Q99816	OTTHUMG00000167725	ENST00000251968.3:c.51_52delCA	chr11.hg19:g.18541141_18541142delTG	ENSP00000251968:p.Tyr17fs	161.0	0.0	0		136.0	24.0	0.176471	NM_006292	Q9BUM5	Frame_Shift_Del	DEL	ENST00000251968.3	hg19	CCDS7842.1																																																																																			.	.	.	none		0.307	TSG101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395906.1	NM_006292		-	18541142	TG	-	18541141	7	5	214	1	0	1	0	1	0	0	0	0	16628	1588	55	0	1156	0	TSG101	11	18541141	Frame_Shift_Del	DEL	TG	TCGA-J7-8537-01A-11D-2396-08		18541141	116465375	27	13012											
ANAPC5	51433	hgsc.bcm.edu	37	chr12	121766167	121766168	+	Missense_Mutation	DNP	TC	TC	CA																															ttttctgtgcgatgctgataTcgatgagctctgacaggctg																										TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr12:121766167_121766168TC>CA	ENST00000261819.3	-	10	1376_1377	c.1255_1256GA>TG	c.(1255-1257)GAt>TGt	p.D419C	ANAPC5_ENST00000441917.2_Missense_Mutation_p.D307C|ANAPC5_ENST00000541887.1_Missense_Mutation_p.D406C|ANAPC5_ENST00000535482.1_Missense_Mutation_p.D85C|ANAPC5_ENST00000544314.1_5'UTR|ANAPC5_ENST00000344395.4_Missense_Mutation_p.D307C	NM_016237.4	NP_057321.2	Q9UJX4	APC5_HUMAN	anaphase promoting complex subunit 5	419					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)			breast(6)|endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(3)	31	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GATGCTGATATCGATGAGCTCT	0.545																																					p.D419G|p.D419Y		Atlas-SNP	.											.	ANAPC5	60	.	0			c.A1256G|c.G1255T						PASS	.																																			SO:0001583	missense	51433	exon10			CTGATATCGATGA|TGATATCGATGAG	AF191339	CCDS9220.1, CCDS45000.1	12q24.31	2014-08-12			ENSG00000089053	ENSG00000089053		"Anaphase promoting complex subunits"	15713	protein-coding gene	gene with protein product		606948				9469815	Standard	NM_016237		Approved	APC5	uc001uag.3	Q9UJX4	OTTHUMG00000169157	ENST00000261819.3:c.1255_1256delinsCA	chr12.hg19:g.121766167_121766168delinsCA	ENSP00000261819:p.Asp419Cys	76.0	0.0	.		120.0|121.0	17.0|18.0	.	NM_016237	E9PFB2|Q8N4H7|Q9BQD4	Missense_Mutation	SNP	ENST00000261819.3	hg19	CCDS9220.1																																																																																			.	.	.	none		0.545	ANAPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402582.1			CA	121766168	TC	CA	121766167	3	2	214	1	0	0	0	0	1	0	0	0	605	1435	50	3	1043	3	ANAPC5	12	121766167	Missense_Mutation	DNP	TC	TCGA-J7-8537-01A-11D-2396-08		121766167	12085728	28	13013											
MCF2L	23263	hgsc.bcm.edu	37	chr13	113741757	113741757	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agctccctcctacagctacaAgcagtccttaaacgtaagtg	12	9	7	13	1	0	0	0	0	0	0	3	0	3	0	3	0	6	4	3	0	6	4			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr13:113741757A>G	ENST00000375608.3	+	23	2730	c.2672A>G	c.(2671-2673)aAg>aGg	p.K891R	MCF2L_ENST00000375597.4_Missense_Mutation_p.K859R|MCF2L_ENST00000421756.1_Missense_Mutation_p.K865R|MCF2L_ENST00000397030.1_Missense_Mutation_p.K894R|MCF2L_ENST00000375604.2_Missense_Mutation_p.K918R|MCF2L_ENST00000442652.2_Missense_Mutation_p.K891R|MCF2L_ENST00000423482.2_Missense_Mutation_p.K859R|MCF2L_ENST00000535094.2_Missense_Mutation_p.K861R|MCF2L_ENST00000375601.3_Missense_Mutation_p.K865R|MCF2L_ENST00000434480.2_Missense_Mutation_p.K867R			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	891	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 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)				TACAGCTACAAGCAGTCCTTA	0.592																																					p.K861R		Atlas-SNP	.											.	MCF2L	182	.	0			c.A2582G						PASS	.						45	39	41					13																	113741757		2202	4299	6501	SO:0001583	missense	23263	exon22			GCTACAAGCAGTC	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.2672A>G	chr13.hg19:g.113741757A>G	ENSP00000364758:p.Lys891Arg	22.0	0.0	.		56.0	12.0	.	NM_001112732	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Missense_Mutation	SNP	ENST00000375608.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.93|19.93	3.918654|3.918654	0.73098|0.73098	.|.	.|.	ENSG00000126217|ENSG00000126217	ENST00000375608;ENST00000442652;ENST00000375604;ENST00000397030;ENST00000535094;ENST00000421756;ENST00000375601;ENST00000434480;ENST00000423482;ENST00000375597;ENST00000440749|ENST00000413354;ENST00000261963	T;T;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;2.0;2.0|.	5.08|5.08	5.08|5.08	0.68730|0.68730	Pleckstrin homology-type (1);Pleckstrin homology domain (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.84678|0.84678	0.5525|0.5525	M|M	0.92367|0.92367	3.3|3.3	0.58432|0.58432	D|D	0.999999|0.999999	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;0.998;0.996;0.999|.	D|D	0.88684|0.88684	0.3204|0.3204	10|5	0.87932|.	D|.	0|.	.|.	14.8626|14.8626	0.70392|0.70392	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	859;861;918;859;891|.	E9PDN8;O15068-9;G5E9A1;O15068-4;O15068|.	.;.;.;.;MCF2L_HUMAN|.	R|G	891;891;918;894;861;865;865;867;859;859;702|91;32	ENSP00000364758:K891R;ENSP00000401422:K891R;ENSP00000364754:K918R;ENSP00000380225:K894R;ENSP00000440374:K861R;ENSP00000397285:K865R;ENSP00000364751:K865R;ENSP00000407722:K867R;ENSP00000405639:K859R;ENSP00000364747:K859R|.	ENSP00000364747:K859R|.	K|S	+|+	2|1	0|0	MCF2L|MCF2L	112789758|112789758	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.524000|0.524000	0.34500|0.34500	9.084000|9.084000	0.94076|0.94076	1.902000|1.902000	0.55061|0.55061	0.533000|0.533000	0.62120|0.62120	AAG|AGC	.	.	.	none		0.592	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4			G	113741757	A	G	113741757	3	3	214	1	0	0	0	0	1	0	0	0	9386	72	3	3	2934	3	MCF2L	13	113741757	Missense_Mutation	SNP	A	TCGA-J7-8537-01A-11D-2396-08		113741757	1428121	29	13014											
HSPA2	3306	hgsc.bcm.edu	37	chr14	65009419	65009419	+	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	gcaaactttaccaaggtggtCctggcggcggcagcggcggc	7	6	16	12	4	0	0	0	0	0	0	1	0	1	0	2	7	3	2	2	7	3	2			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr14:65009419C>A	ENST00000394709.1	+	2	1928	c.1852C>A	c.(1852-1854)Cct>Act	p.P618T	HSPA2_ENST00000247207.6_Missense_Mutation_p.P618T|RP11-973N13.4_ENST00000554918.1_RNA			P54652	HSP72_HUMAN	heat shock 70kDa protein 2	618					male meiosis (GO:0007140)|male meiosis I (GO:0007141)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle (GO:0031662)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)|spermatid development (GO:0007286)|synaptonemal complex disassembly (GO:0070194)	blood microparticle (GO:0072562)|CatSper complex (GO:0036128)|cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycolipid binding (GO:0051861)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00515)|OV - Ovarian serous cystadenocarcinoma(108;0.00584)|BRCA - Breast invasive adenocarcinoma(234;0.045)		CCAAGGTGGTCCTggcggcgg	0.552																																					p.P618T	Pancreas(136;1211 1835 24894 31984 38227)	Atlas-SNP	.											.	HSPA2	83	.	0			c.C1852A						PASS	.						48	50	50					14																	65009419		2203	4300	6503	SO:0001583	missense	3306	exon1			GGTGGTCCTGGCG	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.1852C>A	chr14.hg19:g.65009419C>A	ENSP00000378199:p.Pro618Thr	59.0	0.0	.		106.0	30.0	.	NM_021979	Q15508|Q53XM3|Q9UE78	Missense_Mutation	SNP	ENST00000394709.1	hg19	CCDS9766.1	.	.	.	.	.	.	.	.	.	.	C	3.079	-0.189353	0.06299	.	.	ENSG00000126803	ENST00000394709;ENST00000247207;ENST00000545222	T;T	0.13538	2.58;2.58	5.43	2.55	0.30701	.	1.329050	0.05831	U	0.617584	T	0.08447	0.0210	N	0.11201	0.11	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.40365	-0.9567	10	0.29301	T	0.29	0.1445	7.9468	0.29991	0.0:0.6354:0.2799:0.0847	.	618	P54652	HSP72_HUMAN	T	618;618;392	ENSP00000378199:P618T;ENSP00000247207:P618T	ENSP00000247207:P618T	P	+	1	0	HSPA2	64079172	1.000000	0.71417	0.954000	0.39281	0.732000	0.41865	2.213000	0.42844	0.254000	0.21573	-0.230000	0.12252	CCT	.	.	.	none		0.552	HSPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280651.1			A	65009419	C	A	65009419	3	1	214	1	0	0	0	0	1	0	0	0	7418	855	30	4	1854	4	HSPA2	14	65009419	Missense_Mutation	SNP	C	TCGA-J7-8537-01A-11D-2396-08		65009419	42340121	30	13015											
EIF2AK4	440275	hgsc.bcm.edu	37	chr15	40324962	40324962	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtgtgtattcacaggtggAtctacccaaagaaacaatat	14	12	8	7	0	2	1	1	0	1	1	2	2	2	2	1	2	2	1	1	2	6	5			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr15:40324962A>G	ENST00000263791.5	+	37	4776	c.4733A>G	c.(4732-4734)gAt>gGt	p.D1578G	EIF2AK4_ENST00000382727.2_Missense_Mutation_p.D1550G	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	1578					cellular response to starvation (GO:0009267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of translation (GO:0017148)|protein phosphorylation (GO:0006468)|regulation of translational initiation (GO:0006446)|regulation of translational initiation in response to stress (GO:0043558)	cytosolic ribosome (GO:0022626)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		TCACAGGTGGATCTACCCAAA	0.388																																					p.D1578G		Atlas-SNP	.											.	EIF2AK4	107	.	0			c.A4733G						PASS	.						110	106	107					15																	40324962		1929	4132	6061	SO:0001583	missense	440275	exon37			AGGTGGATCTACC	AB037759	CCDS42016.1	15q13.3	2008-08-18				ENSG00000128829			19687	protein-coding gene	gene with protein product		609280				10504407	Standard	XM_005254392		Approved	GCN2, KIAA1338	uc001zkm.1	Q9P2K8		ENST00000263791.5:c.4733A>G	chr15.hg19:g.40324962A>G	ENSP00000263791:p.Asp1578Gly	87.0	0.0	.		78.0	16.0	.	NM_001013703	C9JEC4|Q69YL7|Q6DC97|Q96GN6|Q9H5K1|Q9NSQ3|Q9NSZ5|Q9UJ56	Missense_Mutation	SNP	ENST00000263791.5	hg19	CCDS42016.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.042322	0.75732	.	.	ENSG00000128829	ENST00000263791;ENST00000382727	T;T	0.61742	0.08;0.08	5.89	5.89	0.94794	Serine/threonine-protein kinase GCN2, anticodon binding domain (1);	0.000000	0.85682	D	0.000000	T	0.65238	0.2672	N	0.24115	0.695	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.69577	-0.5108	10	0.72032	D	0.01	-24.8288	15.9741	0.80044	1.0:0.0:0.0:0.0	.	1550;1578	Q9P2K8-2;Q9P2K8	.;E2AK4_HUMAN	G	1578;1550	ENSP00000263791:D1578G;ENSP00000372174:D1550G	ENSP00000263791:D1578G	D	+	2	0	EIF2AK4	38112254	1.000000	0.71417	1.000000	0.80357	0.848000	0.48234	5.973000	0.70456	2.246000	0.74042	0.533000	0.62120	GAT	.	.	.	none		0.388	EIF2AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418395.1			G	40324962	A	G	40324962	3	3	214	1	0	0	0	0	1	0	0	0	5001	333	12	3	4879	3	EIF2AK4	15	40324962	Missense_Mutation	SNP	A	TCGA-J7-8537-01A-11D-2396-08		40324962	62206430	31	13016											
TMC7	79905	hgsc.bcm.edu	37	chr16	19051691	19051691	+	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	atcacgctggccaattttatCaccccaatgatctttgccaa	11	12	5	13	1	3	1	2	1	1	0	3	1	3	1	4	1	1	1	4	1	4	3			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr16:19051691C>A	ENST00000304381.5	+	9	1390	c.1260C>A	c.(1258-1260)atC>atA	p.I420I	TMC7_ENST00000569532.1_Silent_p.I420I|TMC7_ENST00000421369.3_Silent_p.I310I	NM_024847.3	NP_079123.3	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7	420					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						CCAATTTTATCACCCCAATGA	0.418																																					p.I420I		Atlas-SNP	.											.	TMC7	75	.	0			c.C1260A						PASS	.						142	121	128					16																	19051691		2197	4300	6497	SO:0001819	synonymous_variant	79905	exon9			TTTTATCACCCCA	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.1260C>A	chr16.hg19:g.19051691C>A		157.0	0.0	.		184.0	37.0	.	NM_024847	E7ERB6|Q5H9Q8|Q7Z5M4|Q86WX0|Q9H766	Silent	SNP	ENST00000304381.5	hg19	CCDS10573.1																																																																																			.	.	.	none		0.418	TMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254276.3	NM_024847		A	19051691	C	A	19051691	2	1	214	1	0	0	0	0	0	0	0	1	16002	816	29	4		4	TMC7	16	19051691	Silent	SNP	C	TCGA-J7-8537-01A-11D-2396-08		19051691	71303062	32	13017											
NETO2	81831	hgsc.bcm.edu	37	chr16	47117430	47117430	+	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	agcgggaggcggtggaggagCgccgcatcttctggtagttg	6	8	19	8	4	2	0	0	0	2	0	2	3	2	3	1	6	2	3	1	6	1	3	rs372424394		TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr16:47117430C>T	ENST00000562435.1	-	9	1664	c.1280G>A	c.(1279-1281)cGc>cAc	p.R427H	NETO2_ENST00000303155.5_Missense_Mutation_p.R420H	NM_018092.4	NP_060562.3	Q8NC67	NETO2_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 2	427					regulation of kainate selective glutamate receptor activity (GO:2000312)	kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)				breast(1)|cervix(1)|endometrium(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	29		all_cancers(37;0.00114)|all_lung(18;0.00432)|Lung NSC(13;0.0384)|Breast(268;0.174)				GGTGGAGGAGCGCCGCATCTT	0.537										HNSCC(25;0.065)			C|||	1	0.000199681	0	0.0014	5008	,	,		16407	0		0	False		,,,				2504	0				p.R427H		Atlas-SNP	.											.	NETO2	67	.	0			c.G1280A						PASS	.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	92	85	87		1280,1259	3.8	1	16		87	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	NETO2	NM_018092.4,NM_001201477.1	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	427/526,420/519	47117430	1,13005	2203	4300	6503	SO:0001583	missense	81831	exon9			GAGGAGCGCCGCA	AK001292	CCDS10727.1, CCDS58460.1	16q11.2	2008-08-04			ENSG00000171208	ENSG00000171208			14644	protein-coding gene	gene with protein product		607974				11943477	Standard	NM_018092		Approved	FLJ10430, NEOT2	uc002eer.2	Q8NC67	OTTHUMG00000133101	ENST00000562435.1:c.1280G>A	chr16.hg19:g.47117430C>T	ENSP00000455169:p.Arg427His	154.0	0.0	.		372.0	78.0	.	NM_018092	J3KNF1|Q7Z381|Q8ND51|Q96SP4|Q9NVY8	Missense_Mutation	SNP	ENST00000562435.1	hg19	CCDS10727.1	.	.	.	.	.	.	.	.	.	.	C	18.06	3.539890	0.65085	0.0	1.16E-4	ENSG00000171208	ENST00000303155	.	.	.	5.78	3.83	0.44106	.	0.048904	0.85682	N	0.000000	T	0.48677	0.1513	L	0.52126	1.63	0.53005	D	0.999961	P;B;B	0.37914	0.611;0.244;0.357	B;B;B	0.32022	0.139;0.033;0.072	T	0.51268	-0.8727	9	0.66056	D	0.02	.	12.2767	0.54739	0.0:0.8634:0.0:0.1366	.	284;427;103	B7Z4I7;Q8NC67;Q8NC67-2	.;NETO2_HUMAN;.	H	427	.	ENSP00000306726:R427H	R	-	2	0	NETO2	45674931	1.000000	0.71417	1.000000	0.80357	0.800000	0.45204	4.088000	0.57678	0.801000	0.34066	0.655000	0.94253	CGC	.	.	.	weak		0.537	NETO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256766.2	NM_018092		T	47117430	C	T	47117430	3	4	214	1	0	0	0	0	1	0	0	0	10347	768	27	1	301	1	NETO2	16	47117430	Missense_Mutation	SNP	C	TCGA-J7-8537-01A-11D-2396-08	28065739	47117430	43237323	33	13018											
EIF4A1	1973	hgsc.bcm.edu	37	chr17	7478578	7478578	+	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	tcgagaattggctcagcaggTaagagtggcttctattccct	9	12	11	9	1	2	2	1	0	1	2	4	3	3	2	1	3	1	4	1	3	3	5			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr17:7478578T>G	ENST00000293831.8	+	4	361		c.e4+2		SNORA48_ENST00000386847.1_RNA|EIF4A1_ENST00000582746.1_Splice_Site|SNORD10_ENST00000459579.1_RNA|SNORA67_ENST00000384423.1_RNA|EIF4A1_ENST00000577269.1_Splice_Site|SENP3-EIF4A1_ENST00000579777.1_RNA|EIF4A1_ENST00000380512.5_Missense_Mutation_p.V100G	NM_001416.3	NP_001407.1	P60842	IF4A1_HUMAN	eukaryotic translation initiation factor 4A1						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)|organ regeneration (GO:0031100)|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)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|mRNA binding (GO:0003729)|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)			NS(1)|breast(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	22						GCTCAGCAGGTAAGAGTGGCT	0.488																																					.	Melanoma(120;278 1668 15796 27423 46368)	Atlas-SNP	.											.	EIF4A1	38	.	0			c.345+2T>G						PASS	.						73	70	71					17																	7478578		2203	4300	6503	SO:0001630	splice_region_variant	1973	exon4			AGCAGGTAAGAGT	D13748	CCDS11113.1, CCDS58511.1	17p13	2012-02-23	2010-02-10		ENSG00000161960	ENSG00000161960		"DEAD-boxes"	3282	protein-coding gene	gene with protein product		602641	"eukaryotic translation initiation factor 4A, isoform 1"	EIF4A		8493113, 9790779	Standard	NM_001416		Approved	DDX2A, EIF-4A		P60842	OTTHUMG00000108149	ENST00000293831.8:c.345+2T>G	chr17.hg19:g.7478578T>G		134.0	0.0	.		190.0	41.0	.	NM_001204510	B2R6L8|D3DTP9|J3QLC4|P04765|Q5U018|Q61516	Splice_Site	SNP	ENST00000293831.8	hg19	CCDS11113.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.7|20.7	4.031827|4.031827	0.75504|0.75504	.|.	.|.	ENSG00000161960|ENSG00000161960	ENST00000293831|ENST00000380512	.|T	.|0.17213	.|2.29	5.43|5.43	5.43|5.43	0.79202|0.79202	.|.	.|.	.|.	.|.	.|.	.|T	.|0.29749	.|0.0743	.|.	.|.	.|.	0.48511|0.48511	D|D	0.999669|0.999669	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.01195	.|-1.1422	.|5	.|.	.|.	.|.	.|.	13.4334|13.4334	0.61068|0.61068	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	.|G	-1|100	.|ENSP00000369881:V100G	.|.	.|V	+|+	.|2	.|0	EIF4A1|EIF4A1	7419302|7419302	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.957000|0.957000	0.61999|0.61999	7.698000|7.698000	0.84413|0.84413	2.077000|2.077000	0.62373|0.62373	0.459000|0.459000	0.35465|0.35465	.|GTA	.	.	.	none		0.488	EIF4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226952.6	NM_001416	Intron	G	7478578	T	G	7478578	5	3	214	1	0	0	0	0	0	0	1	0	5026	1652	57	5	361	5	EIF4A1	17	7478578	Splice_Site	SNP	T	TCGA-J7-8537-01A-11D-2396-08		7478578	73716632	34	13019											
MED24	9862	hgsc.bcm.edu	37	chr17	38187790	38187790	+	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	ggtgaccaggggagctcataCttgcagcgctggtcagcttt	7	10	14	10	1	2	1	2	1	0	0	2	2	2	2	1	4	5	4	1	4	1	3			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr17:38187790C>G	ENST00000394128.2	-	11	1149		c.e11+1		MED24_ENST00000479829.1_5'Flank|MED24_ENST00000501516.3_Splice_Site|MED24_ENST00000394127.2_Splice_Site|MED24_ENST00000394126.1_Splice_Site|MED24_ENST00000356271.3_Splice_Site	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24						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)					GGAGCTCATACTTGCAGCGCT	0.557																																					.		Atlas-SNP	.											.	MED24	89	.	0			c.1028+1G>C						PASS	.						84	82	82					17																	38187790		2203	4300	6503	SO:0001630	splice_region_variant	9862	exon11			CTCATACTTGCAG	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.1067+1G>C	chr17.hg19:g.38187790C>G		156.0	0.0	.		356.0	55.0	.	NM_001079518	A8K4S5|B3KMR9|Q14143|Q9NNY5	Splice_Site	SNP	ENST00000394128.2	hg19	CCDS11359.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.948640	0.73787	.	.	ENSG00000008838	ENST00000394126;ENST00000356271;ENST00000394128;ENST00000535071;ENST00000394127;ENST00000536318;ENST00000431269	.	.	.	4.56	4.56	0.56223	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.4676	0.87638	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MED24	35441316	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	3.743000	0.55104	2.533000	0.85409	0.561000	0.74099	.	.	.	.	none		0.557	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815	Intron	G	38187790	C	G	38187790	5	3	214	1	0	0	0	0	0	0	1	0	9449	579	20	4	1965	4	MED24	17	38187790	Splice_Site	SNP	C	TCGA-J7-8537-01A-11D-2396-08	30709212	38187790	43007420	35	13020											
NPEPPS	9520	hgsc.bcm.edu	37	chr17	45669357	45669357	+	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	ccatctgaggttgatgagatAtttgatgctatatcatatag	12	15	9	5	0	2	4	1	4	1	1	2	5	2	4	1	1	1	2	1	1	5	7			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr17:45669357A>T	ENST00000322157.4	+	11	1533	c.1296A>T	c.(1294-1296)atA>atT	p.I432I	NPEPPS_ENST00000530173.1_Silent_p.I428I|NPEPPS_ENST00000525037.1_3'UTR|NPEPPS_ENST00000544660.1_Silent_p.I352I	NM_006310.3	NP_006301.3	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	432					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						TTGATGAGATATTTGATGCTA	0.383																																					p.I432I		Atlas-SNP	.											.	NPEPPS	59	.	0			c.A1296T						PASS	.						123	78	93					17																	45669357		2021	4151	6172	SO:0001819	synonymous_variant	9520	exon11			TGAGATATTTGAT	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.1296A>T	chr17.hg19:g.45669357A>T		76.0	0.0	.		133.0	17.0	.	NM_006310	B7Z463|Q6P145|Q9NP16|Q9UEM2	Silent	SNP	ENST00000322157.4	hg19	CCDS45721.1																																																																																			.	.	.	none		0.383	NPEPPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384269.1	NM_006310		T	45669357	A	T	45669357	2	4	214	1	0	0	0	0	0	0	0	1	10582	439	16	5		5	NPEPPS	17	45669357	Silent	SNP	A	TCGA-J7-8537-01A-11D-2396-08	7481567	45669357	35525853	36	13021											
CCDC45	90799	hgsc.bcm.edu	37	chr17	62532827	62532827	+	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	gaacaaaggagacgccaccaGgatgaactggactccatgga	15	4	12	10	1	0	2	0	1	0	1	1	7	1	5	3	4	2	0	3	4	3	0			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr17:62532827G>C	ENST00000556440.2	+	18	2688	c.2178G>C	c.(2176-2178)caG>caC	p.Q726H	CEP95_ENST00000553412.1_Missense_Mutation_p.Q562H	NM_138363.1	NP_612372.1	Q96GE4	CEP95_HUMAN	centrosomal protein 95kDa	726						centrosome (GO:0005813)|cytoplasm (GO:0005737)|spindle pole (GO:0000922)				endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)	13						GACGCCACCAGGATGAACTGG	0.458																																					p.Q726H		Atlas-SNP	.											.	CEP95	103	.	0			c.G2178C						PASS	.						78	82	81					17																	62532827		2022	4184	6206	SO:0001583	missense	90799	exon18			CCACCAGGATGAA	AL832822	CCDS45763.1	17q24.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000258890	ENSG00000258890			25141	protein-coding gene	gene with protein product			"coiled-coil domain containing 45"	CCDC45		21399614	Standard	NM_138363		Approved	DKFZp667E1824	uc002jem.3	Q96GE4	OTTHUMG00000179174	ENST00000556440.2:c.2178G>C	chr17.hg19:g.62532827G>C	ENSP00000450461:p.Gln726His	62.0	0.0	.		155.0	47.0	.	NM_138363	B4DMD2|Q96M81	Missense_Mutation	SNP	ENST00000556440.2	hg19	CCDS45763.1	.	.	.	.	.	.	.	.	.	.	G	16.52	3.146995	0.57151	.	.	ENSG00000258890	ENST00000553956;ENST00000556440;ENST00000553412	T;T	0.37411	1.25;1.2	5.48	3.5	0.40072	.	0.125921	0.53938	D	0.000047	T	0.51839	0.1698	L	0.59436	1.845	0.35792	D	0.822454	D	0.89917	1.0	D	0.73380	0.98	T	0.61964	-0.6954	10	0.72032	D	0.01	-13.7497	9.6268	0.39754	0.275:0.0:0.725:0.0	.	726	Q96GE4	CEP95_HUMAN	H	661;726;562	ENSP00000450461:Q726H;ENSP00000450906:Q562H	ENSP00000438458:Q661H	Q	+	3	2	CEP95	59963289	1.000000	0.71417	1.000000	0.80357	0.728000	0.41692	0.926000	0.28804	0.805000	0.34159	0.650000	0.86243	CAG	.	.	.	none		0.458	CEP95-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445100.2	NM_138363		C	62532827	G	C	62532827	3	2	214	1	0	0	0	0	1	0	0	0	2818	991	35	4	2248	4	CCDC45	17	62532827	Missense_Mutation	SNP	G	TCGA-J7-8537-01A-11D-2396-08	16863470	62532827	18662383	37	13022											
ZNF419	79744	hgsc.bcm.edu	37	chr19	58005060	58005060	+	Missense_Mutation	SNP	T	T	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	agtgcagcgactgtgggaaaTtttttacccaatgctcaagc	11	11	10	9	1	1	0	1	0	0	0	1	2	1	1	1	1	5	2	1	1	4	3			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr19:58005060T>G	ENST00000221735.7	+	5	1321	c.1135T>G	c.(1135-1137)Ttt>Gtt	p.F379V	ZNF419_ENST00000424930.2_Missense_Mutation_p.F380V|ZNF419_ENST00000426954.2_Missense_Mutation_p.F367V|ZNF419_ENST00000347466.6_Missense_Mutation_p.F347V|ZNF419_ENST00000354197.4_Missense_Mutation_p.F367V|AC003005.4_ENST00000601674.1_Intron|ZNF419_ENST00000415379.2_Missense_Mutation_p.F333V|ZNF419_ENST00000442920.2_Missense_Mutation_p.F366V			Q96HQ0	ZN419_HUMAN	zinc finger protein 419	379					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0252)|Lung(386;0.171)		CTGTGGGAAATTTTTTACCCA	0.408																																					p.F380V		Atlas-SNP	.											.	ZNF419	134	.	0			c.T1138G						PASS	.						81	85	84					19																	58005060		2200	4297	6497	SO:0001583	missense	79744	exon5			GGGAAATTTTTTA	AK026886	CCDS42637.1, CCDS46211.1, CCDS54325.1, CCDS54326.1, CCDS54327.1, CCDS54328.1	19q13.43	2013-01-08	2006-12-15	2006-12-15	ENSG00000105136	ENSG00000105136		"Zinc fingers, C2H2-type", "-"	20648	protein-coding gene	gene with protein product			"zinc finger protein 419A"	ZNF419A			Standard	NM_001098492		Approved		uc010ety.1	Q96HQ0	OTTHUMG00000037073	ENST00000221735.7:c.1135T>G	chr19.hg19:g.58005060T>G	ENSP00000221735:p.Phe379Val	178.0	0.0	.		227.0	42.0	.	NM_001098491	B4DXU7|B4E348|B7ZA41|E9PCP4|E9PED0|E9PET3|E9PFX9|Q9H5P0	Missense_Mutation	SNP	ENST00000221735.7	hg19	CCDS54326.1	.	.	.	.	.	.	.	.	.	.	T	10.63	1.405079	0.25378	.	.	ENSG00000105136	ENST00000284020;ENST00000424930;ENST00000426954;ENST00000354197;ENST00000442920;ENST00000517598;ENST00000347466;ENST00000415379;ENST00000221735	T;T;T;T;T;T;T	0.16743	3.25;3.25;3.25;3.25;3.25;2.32;3.25	2.26	1.16	0.20824	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.14614	0.0353	N	0.02539	-0.55	0.23454	N	0.997643	D;D;D;D;B;D;B	0.69078	0.985;0.991;0.997;0.991;0.292;0.996;0.292	D;D;D;D;B;D;B	0.79108	0.966;0.982;0.992;0.988;0.071;0.986;0.071	T	0.25222	-1.0138	9	0.38643	T	0.18	.	7.3178	0.26511	0.0:0.0:0.2246:0.7754	.	333;333;366;367;380;347;379	E9PFX9;B4DXU7;E9PCP4;E9PET3;E9PED0;Q96HQ0-2;Q96HQ0	.;.;.;.;.;.;ZN419_HUMAN	V	354;380;367;367;366;380;347;333;379	ENSP00000388864:F380V;ENSP00000390916:F367V;ENSP00000346136:F367V;ENSP00000414709:F366V;ENSP00000299860:F347V;ENSP00000392129:F333V;ENSP00000221735:F379V	ENSP00000221735:F379V	F	+	1	0	ZNF419	62696872	0.000000	0.05858	0.044000	0.18714	0.111000	0.19643	-1.253000	0.02877	0.101000	0.17610	0.260000	0.18958	TTT	.	.	.	none		0.408	ZNF419-006	KNOWN	NAGNAG_splice_site|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378506.1	NM_024691		G	58005060	T	G	58005060	3	3	214	1	0	0	0	0	1	0	0	0	17908	1493	52	5	1156	5	ZNF419	19	58005060	Missense_Mutation	SNP	T	TCGA-J7-8537-01A-11D-2396-08		58005060	1123923	38	13023											
C20orf7	79133	hgsc.bcm.edu	37	chr20	13775537	13775537	+	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	agcgttttagctgatgaagaAttccttcccttcaaagaaaa	14	12	7	8	1	1	4	1	2	0	2	3	4	3	4	2	0	2	2	2	0	6	5			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr20:13775537A>T	ENST00000378106.5	+	5	548	c.429A>T	c.(427-429)gaA>gaT	p.E143D	NDUFAF5_ENST00000463598.1_Intron|NDUFAF5_ENST00000475968.1_Intron	NM_024120.4	NP_077025.2	Q5TEU4	NDUF5_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 5	143					mitochondrial respiratory chain complex I assembly (GO:0032981)	extrinsic component of mitochondrial inner membrane (GO:0031314)	methyltransferase activity (GO:0008168)										CTGATGAAGAATTCCTTCCCT	0.318																																					p.E143D		Atlas-SNP	.											.	.	.	.	0			c.A429T						PASS	.						105	105	105					20																	13775537		2203	4300	6503	SO:0001583	missense	79133	exon5			TGAAGAATTCCTT		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.429A>T	chr20.hg19:g.13775537A>T	ENSP00000367346:p.Glu143Asp	45.0	0.0	.		48.0	6.0	.	NM_024120	A8K166|Q6GPH3|Q9H6F4	Missense_Mutation	SNP	ENST00000378106.5	hg19	CCDS13118.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.282700	0.80692	.	.	ENSG00000101247	ENST00000378106;ENST00000536501	D	0.85484	-1.99	5.93	2.37	0.29283	Methyltransferase type 11 (1);	0.000000	0.85682	D	0.000000	D	0.88362	0.6416	L	0.49513	1.565	0.80722	D	1	D;D	0.89917	1.0;0.985	D;D	0.81914	0.995;0.951	D	0.86347	0.1708	10	0.72032	D	0.01	-15.2415	9.9234	0.41478	0.7238:0.0:0.2762:0.0	.	143;143	Q5TEU4;B3KR61	CT007_HUMAN;.	D	143	ENSP00000367346:E143D	ENSP00000437325:E143D	E	+	3	2	C20orf7	13723537	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	2.111000	0.41883	0.126000	0.18424	-0.408000	0.06270	GAA	.	.	.	none		0.318	NDUFAF5-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078057.2	NM_001039375		T	13775537	A	T	13775537	3	4	214	1	0	0	0	0	1	0	0	0	2117	98	4	5	467	5	C20orf7	20	13775537	Missense_Mutation	SNP	A	TCGA-J7-8537-01A-11D-2396-08		13775537	49249983	39	13024											
GART	2618	hgsc.bcm.edu	37	chr21	34904710	34904710	+	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	gctctttgcaacaatcacccCttttccagctgcaagaccac	10	10	5	16	0	2	1	1	0	1	1	3	1	3	1	4	0	4	4	4	0	3	3			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr21:34904710C>T	ENST00000381831.3	-	5	732	c.469G>A	c.(469-471)Ggg>Agg	p.G157R	GART_ENST00000381815.4_Missense_Mutation_p.G157R|GART_ENST00000381839.3_Missense_Mutation_p.G157R|GART_ENST00000361093.5_Missense_Mutation_p.G157R|GART_ENST00000497313.1_5'UTR	NM_001136005.1	NP_001129477.1	P22102	PUR2_HUMAN	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	157	ATP-grasp.				'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|glycine metabolic process (GO:0006544)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|phosphoribosylamine-glycine ligase activity (GO:0004637)|phosphoribosylformylglycinamidine cyclo-ligase activity (GO:0004641)|phosphoribosylglycinamide formyltransferase activity (GO:0004644)			NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(13)|ovary(3)|prostate(5)|urinary_tract(1)	31					Pemetrexed(DB00642)	ACAATCACCCCTTTTCCAGCT	0.428																																					p.G157R		Atlas-SNP	.											.	GART	81	.	0			c.G469A						PASS	.						213	227	222					21																	34904710		2203	4300	6503	SO:0001583	missense	2618	exon5			TCACCCCTTTTCC	M32082	CCDS13627.1, CCDS13628.1	21q22.11	2012-10-02			ENSG00000159131	ENSG00000159131	2.1.2.2, 6.3.3.1, 6.3.4.13		4163	protein-coding gene	gene with protein product		138440		PRGS, PGFT		2050105	Standard	NM_001136005		Approved		uc002yrx.3	P22102	OTTHUMG00000065628	ENST00000381831.3:c.469G>A	chr21.hg19:g.34904710C>T	ENSP00000371253:p.Gly157Arg	402.0	0.0	.		627.0	130.0	.	NM_001136005	A8K945|A8KA32|D3DSF3|D3DSF4|O14659|Q52M77	Missense_Mutation	SNP	ENST00000381831.3	hg19	CCDS13627.1	.	.	.	.	.	.	.	.	.	.	C	35	5.450836	0.96205	.	.	ENSG00000159131	ENST00000381815;ENST00000381831;ENST00000381839;ENST00000361093;ENST00000430874;ENST00000426819	T;T;T;T;T;T	0.67698	0.46;0.46;0.46;0.38;-0.15;-0.28	6.07	6.07	0.98685	ATP-grasp fold (1);ATP-grasp fold, subdomain 1 (1);Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain (1);	0.000000	0.85682	D	0.000000	D	0.87787	0.6265	H	0.94542	3.55	0.80722	D	1	D	0.89917	1.0	D	0.72625	0.978	D	0.89842	0.4003	10	0.87932	D	0	-20.8496	20.6593	0.99626	0.0:1.0:0.0:0.0	.	157	P22102	PUR2_HUMAN	R	157	ENSP00000371236:G157R;ENSP00000371253:G157R;ENSP00000371261:G157R;ENSP00000354388:G157R;ENSP00000413040:G157R;ENSP00000398631:G157R	ENSP00000354388:G157R	G	-	1	0	GART	33826580	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.487000	0.81328	2.885000	0.99019	0.655000	0.94253	GGG	.	.	.	none		0.428	GART-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140626.3	NM_000819		T	34904710	C	T	34904710	3	4	214	1	0	0	0	0	1	0	0	0	6250	681	24	2	2639	2	GART	21	34904710	Missense_Mutation	SNP	C	TCGA-J7-8537-01A-11D-2396-08		34904710	13225185	40	13025											
ADORA2A	135	hgsc.bcm.edu	37	chr22	24837246	24837246	+	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	ccgtctcaacggccacccgcCaggagtgtgggccaacggca	8	4	13	16	4	1	0	1	0	1	0	2	1	1	1	5	4	2	1	5	4	2	0			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chr22:24837246C>T	ENST00000337539.7	+	3	1487	c.1028C>T	c.(1027-1029)cCa>cTa	p.P343L	ADORA2A-AS1_ENST00000543438.1_RNA|SPECC1L-ADORA2A_ENST00000358654.2_3'UTR|ADORA2A-AS1_ENST00000427813.2_RNA|ADORA2A-AS1_ENST00000326341.4_RNA	NM_000675.4|NM_001278497.1|NM_001278498.1|NM_001278499.1|NM_001278500.1	NP_000666.2|NP_001265426.1|NP_001265427.1|NP_001265428.1|NP_001265429.1	P29274	AA2AR_HUMAN	adenosine A2a receptor	343					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|apoptotic process (GO:0006915)|blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cAMP biosynthetic process (GO:0006171)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|central nervous system development (GO:0007417)|inflammatory response (GO:0006954)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phagocytosis (GO:0006909)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|sensory perception (GO:0007600)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|G-protein coupled adenosine receptor activity (GO:0001609)|identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|skin(1)	21	Colorectal(2;0.196)				Adenosine(DB00640)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Mefloquine(DB00358)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Regadenoson(DB06213)|Theobromine(DB01412)|Theophylline(DB00277)	GGCCACCCGCCAGGAGTGTGG	0.662																																					p.P343L		Atlas-SNP	.											.	ADORA2A	44	.	0			c.C1028T						PASS	.						25	22	23					22																	24837246		2202	4299	6501	SO:0001583	missense	135	exon3			ACCCGCCAGGAGT	X68486	CCDS13826.1	22q11.23	2012-08-08			ENSG00000128271	ENSG00000128271		"GPCR / Class A : Adenosine receptors"	263	protein-coding gene	gene with protein product		102776		ADORA2		1662665, 2541503	Standard	NM_001278497		Approved	RDC8	uc002zzy.4	P29274	OTTHUMG00000150761	ENST00000337539.7:c.1028C>T	chr22.hg19:g.24837246C>T	ENSP00000336630:p.Pro343Leu	41.0	0.0	.		71.0	17.0	.	NM_000675	B2R7E0	Missense_Mutation	SNP	ENST00000337539.7	hg19	CCDS13826.1	.	.	.	.	.	.	.	.	.	.	C	1.893	-0.454933	0.04540	.	.	ENSG00000128271	ENST00000444262;ENST00000541988;ENST00000337539;ENST00000417596	T;T	0.62941	0.01;-0.01	4.95	0.288	0.15719	.	0.374401	0.24291	N	0.039802	T	0.37972	0.1023	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08722	-1.0708	10	0.26408	T	0.33	-1.5144	3.3452	0.07132	0.1839:0.3375:0.0:0.4785	.	343	P29274	AA2AR_HUMAN	L	343	ENSP00000414802:P343L;ENSP00000336630:P343L	ENSP00000336630:P343L	P	+	2	0	ADORA2A	23167246	0.000000	0.05858	0.000000	0.03702	0.511000	0.34104	0.577000	0.23758	0.177000	0.19895	0.462000	0.41574	CCA	.	.	.	none		0.662	ADORA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319971.2	NM_000675		T	24837246	C	T	24837246	3	4	214	1	0	0	0	0	1	0	0	0	327	594	21	2	1034	2	ADORA2A	22	24837246	Missense_Mutation	SNP	C	TCGA-J7-8537-01A-11D-2396-08		24837246	26467320	41	13026											
GRPR	2925	hgsc.bcm.edu	37	chrX	16168549	16168550	+	Frame_Shift_Ins	INS	-	-	C																															cattccagaggccgtgttttINSctgacctccatcccttccat																										TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chrX:16168549_16168550insC	ENST00000380289.2	+	2	933_934	c.535_536insC	c.(535-537)tctfs	p.S179fs	RP11-431J24.2_ENST00000422438.1_RNA|RP11-431J24.2_ENST00000435789.1_RNA|RP11-431J24.2_ENST00000454712.2_RNA	NM_005314.2	NP_005305.1	P30550	GRPR_HUMAN	gastrin-releasing peptide receptor	179					cell proliferation (GO:0008283)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of cell proliferation (GO:0042127)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bombesin receptor activity (GO:0004946)|G-protein coupled peptide receptor activity (GO:0008528)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(3)|stomach(1)|upper_aerodigestive_tract(3)	25	Hepatocellular(33;0.183)					GGCCGTGTTTTCTGACCTCCAT	0.505																																					p.S179fs		Atlas-INDEL	.											.	GRPR	51	.	0			c.535_536insC						PASS	.																																			SO:0001589	frameshift_variant	2925	exon2			.		CCDS14174.1	Xp22.2	2014-02-21			ENSG00000126010	ENSG00000126010		"GPCR / Class A : Bombesin receptors"	4609	protein-coding gene	gene with protein product	"bombesin receptor 2"	305670					Standard	NM_005314		Approved	BB2	uc004cxj.3	P30550	OTTHUMG00000021189	ENST00000380289.2:c.536dupC	chrX.hg19:g.16168550_16168550dupC	ENSP00000369643:p.Ser179fs	158.0	0.0	0		376.0	68.0	0.180851	NM_005314	B2R910	Frame_Shift_Ins	INS	ENST00000380289.2	hg19	CCDS14174.1																																																																																			.	.	.	none		0.505	GRPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055901.1	NM_005314		C	16168550	-	C	16168549	7	5	214	1	0	1	1	0	0	0	0	0	6815	1783	62	0	541	0	GRPR	23	16168549	Frame_Shift_Ins	INS	-	TCGA-J7-8537-01A-11D-2396-08		16168549	139102011	42	13027											
RP2	6102	hgsc.bcm.edu	37	chrX	46713306	46713306	+	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	aaagatgcagggctaagtatCttcaacaatacatggagtaa	17	9	9	6	0	2	1	1	0	1	1	2	2	2	2	0	2	3	4	0	2	7	5			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chrX:46713306C>G	ENST00000218340.3	+	2	659	c.498C>G	c.(496-498)atC>atG	p.I166M		NM_006915.2	NP_008846.2	O75695	XRP2_HUMAN	retinitis pigmentosa 2 (X-linked recessive)	166	C-CAP/cofactor C-like. {ECO:0000255|PROSITE-ProRule:PRU00659}.				cell morphogenesis (GO:0000902)|CTP biosynthetic process (GO:0006241)|cytoskeleton organization (GO:0007010)|GTP biosynthetic process (GO:0006183)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein transport (GO:0015031)|UTP biosynthetic process (GO:0006228)|visual perception (GO:0007601)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|periciliary membrane compartment (GO:1990075)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|nucleoside diphosphate kinase activity (GO:0004550)|unfolded protein binding (GO:0051082)			NS(1)|large_intestine(4)|lung(5)|stomach(1)	11						GGCTAAGTATCTTCAACAATA	0.403																																					p.I166M		Atlas-SNP	.											.	RP2	37	.	0			c.C498G						PASS	.						111	97	101					X																	46713306		2203	4300	6503	SO:0001583	missense	6102	exon2			AAGTATCTTCAAC	AJ007590	CCDS14270.1	Xp11.3	2013-01-08			ENSG00000102218	ENSG00000102218			10274	protein-coding gene	gene with protein product		300757				6325945, 9697692, 19852809	Standard	NM_006915		Approved	TBCCD2, NME10, NM23-H10	uc004dgw.4	O75695	OTTHUMG00000021430	ENST00000218340.3:c.498C>G	chrX.hg19:g.46713306C>G	ENSP00000218340:p.Ile166Met	193.0	0.0	.		229.0	34.0	.	NM_006915	Q86XJ7|Q9NU67	Missense_Mutation	SNP	ENST00000218340.3	hg19	CCDS14270.1	.	.	.	.	.	.	.	.	.	.	C	14.78	2.637203	0.47049	.	.	ENSG00000102218	ENST00000218340	D	0.86627	-2.15	5.64	3.89	0.44902	Tubulin binding cofactor C (1);C-CAP/cofactor C-like domain (1);	0.093345	0.64402	D	0.000001	D	0.89646	0.6775	M	0.65975	2.015	0.48632	D	0.999683	P	0.52316	0.952	P	0.57324	0.818	D	0.87427	0.2386	10	0.48119	T	0.1	-23.7323	9.0313	0.36260	0.0:0.7697:0.0:0.2303	.	166	O75695	XRP2_HUMAN	M	166	ENSP00000218340:I166M	ENSP00000218340:I166M	I	+	3	3	RP2	46598250	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.459000	0.35234	0.558000	0.29135	-0.191000	0.12829	ATC	.	.	.	none		0.403	RP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056375.1	NM_006915		G	46713306	C	G	46713306	3	3	214	1	0	0	0	0	1	0	0	0	13547	903	32	4	504	4	RP2	23	46713306	Missense_Mutation	SNP	C	TCGA-J7-8537-01A-11D-2396-08	30544757	46713306	108557254	43	13028											
SLITRK2	84631	hgsc.bcm.edu	37	chrX	144904238	144904238	+	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	acctaggtaacaacgggttaCaggagatccgaacgggggca	13	5	14	9	3	0	1	0	0	0	1	1	3	1	1	2	5	4	3	2	5	5	3			TCGA-J7-8537-01A-11D-2396-08	TCGA-J7-8537-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3cf4b130-0aa3-407e-9fea-bd8ddd8b7d5b	56af51d5-45a7-4a64-ba3e-f810d95407f8	g.chrX:144904238C>T	ENST00000370490.1	+	1	4550	c.295C>T	c.(295-297)Cag>Tag	p.Q99*	SLITRK2_ENST00000428560.2_Nonsense_Mutation_p.Q99*|SLITRK2_ENST00000434188.2_Nonsense_Mutation_p.Q99*|SLITRK2_ENST00000413937.2_Nonsense_Mutation_p.Q99*|SLITRK2_ENST00000447897.2_Nonsense_Mutation_p.Q99*			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	99					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)					CAACGGGTTACAGGAGATCCG	0.458																																					p.Q99X		Atlas-SNP	.											.	SLITRK2	221	.	0			c.C295T						PASS	.						77	69	72					X																	144904238		2203	4300	6503	SO:0001587	stop_gained	84631	exon5			GGGTTACAGGAGA	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.295C>T	chrX.hg19:g.144904238C>T	ENSP00000359521:p.Gln99*	155.0	0.0	.		243.0	48.0	.	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Nonsense_Mutation	SNP	ENST00000370490.1	hg19	CCDS14680.1	.	.	.	.	.	.	.	.	.	.	C	59	34.326611	0.99982	.	.	ENSG00000185985	ENST00000335565;ENST00000447897;ENST00000370490;ENST00000434188;ENST00000413937;ENST00000428560	.	.	.	4.88	4.01	0.46588	.	0.066024	0.64402	U	0.000007	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	-7.1777	12.0035	0.53246	0.0:0.8284:0.1716:0.0	.	.	.	.	X	99	.	ENSP00000334374:Q99X	Q	+	1	0	SLITRK2	144711930	1.000000	0.71417	0.996000	0.52242	0.494000	0.33585	7.818000	0.86416	0.832000	0.34804	-0.218000	0.12543	CAG	.	.	.	none		0.458	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		T	144904238	C	T	144904238	4	4	214	1	0	0	0	0	0	1	0	0	14756	479	17	2	297	2	SLITRK2	23	144904238	Nonsense_Mutation	SNP	C	TCGA-J7-8537-01A-11D-2396-08	98190932	144904238	10366322	44	13029											
DMRTA2	63950	hgsc.bcm.edu	37	chr1	50885395	50885395	+	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	aggaaacaggtcaaacttctGcaacttggcctctgggaggg	11	8	13	9	0	3	0	1	0	2	0	3	2	3	2	1	5	4	1	1	5	3	2			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr1:50885395G>C	ENST00000404795.3	-	3	963	c.571C>G	c.(571-573)Cag>Gag	p.Q191E	DMRTA2_ENST00000418121.1_Missense_Mutation_p.Q191E	NM_032110.2	NP_115486.1	Q96SC8	DMTA2_HUMAN	DMRT-like family A2	191	Gly-rich.				cerebral cortex regionalization (GO:0021796)|dopaminergic neuron differentiation (GO:0071542)|neuron fate specification (GO:0048665)|positive regulation of neuroblast proliferation (GO:0002052)|skeletal muscle cell differentiation (GO:0035914)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(4)|pancreas(1)	6						TCAAACTTCTGCAACTTGGCC	0.617																																					p.Q191E	Colon(196;1651 2045 3292 36497 38236)|Esophageal Squamous(2;257 258 11567 27043 43804)	Atlas-SNP	.											.	DMRTA2	17	.	0			c.C571G						PASS	.						14	15	15					1																	50885395		1951	4137	6088	SO:0001583	missense	63950	exon3			ACTTCTGCAACTT	AJ301580	CCDS44141.1	1p33	2008-08-04			ENSG00000142700	ENSG00000142700			13908	protein-coding gene	gene with protein product		614804				11863363	Standard	NM_032110		Approved		uc010onb.2	Q96SC8	OTTHUMG00000007884	ENST00000404795.3:c.571C>G	chr1.hg19:g.50885395G>C	ENSP00000383909:p.Gln191Glu	175.0	0.0	.		171.0	9.0	.	NM_032110	Q5TFQ3	Missense_Mutation	SNP	ENST00000404795.3	hg19	CCDS44141.1	.	.	.	.	.	.	.	.	.	.	G	10.52	1.372316	0.24857	.	.	ENSG00000142700	ENST00000404795;ENST00000418121	T;T	0.32023	1.47;1.47	3.98	3.98	0.46160	.	0.740013	0.12457	N	0.467217	T	0.27454	0.0674	L	0.52573	1.65	0.49915	D	0.999837	P	0.44090	0.826	B	0.40940	0.344	T	0.13926	-1.0491	10	0.02654	T	1	-9.7172	15.3449	0.74327	0.0:0.0:1.0:0.0	.	191	Q96SC8	DMTA2_HUMAN	E	191	ENSP00000383909:Q191E;ENSP00000399370:Q191E	ENSP00000383909:Q191E	Q	-	1	0	DMRTA2	50657982	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.385000	0.90163	2.194000	0.70268	0.462000	0.41574	CAG	.	.	.	none		0.617	DMRTA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351074.1	NM_032110		C	50885395	G	C	50885395	3	2	215	1	0	0	0	0	1	0	0	0	4591	1328	46	4	1061	4	DMRTA2	1	50885395	Missense_Mutation	SNP	G	TCGA-J7-A8I2-01A-12D-A35Z-10		50885395	198365226	1	13030											
PPAP2B	8613	hgsc.bcm.edu	37	chr1	56989998	56989998	+	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	tctgcatctgtagttctgaaTgtagccttcagagcagttga	9	14	10	8	0	4	3	1	2	3	1	4	3	4	3	1	0	3	6	1	0	3	5			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr1:56989998T>A	ENST00000371250.3	-	3	1077	c.526A>T	c.(526-528)Att>Ttt	p.I176F		NM_003713.4	NP_003704.3	O14495	LPP3_HUMAN	phosphatidic acid phosphatase type 2B	176					Bergmann glial cell differentiation (GO:0060020)|blood vessel development (GO:0001568)|canonical Wnt signaling pathway involved in positive regulation of cell-cell adhesion (GO:0044329)|canonical Wnt signaling pathway involved in positive regulation of endothelial cell migration (GO:0044328)|canonical Wnt signaling pathway involved in positive regulation of wound healing (GO:0044330)|dephosphorylation (GO:0016311)|gastrulation with mouth forming second (GO:0001702)|germ cell migration (GO:0008354)|homotypic cell-cell adhesion (GO:0034109)|lipid metabolic process (GO:0006629)|negative regulation of protein phosphorylation (GO:0001933)|phospholipid metabolic process (GO:0006644)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein stabilization (GO:0050821)|regulation of sphingolipid mediated signaling pathway (GO:1902068)|regulation of Wnt signaling pathway (GO:0030111)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	adherens junction (GO:0005912)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid phosphatase activity (GO:0042577)|phosphatidate phosphatase activity (GO:0008195)|phosphoprotein phosphatase activity (GO:0004721)|sphingosine-1-phosphate phosphatase activity (GO:0042392)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	17						TAGTTCTGAATGTAGCCTTCA	0.527																																					p.I176F		Atlas-SNP	.											.	PPAP2B	30	.	0			c.A526T						PASS	.						144	141	142					1																	56989998		2203	4300	6503	SO:0001583	missense	8613	exon3			TCTGAATGTAGCC	AB000889	CCDS604.1	1p32.2	2009-05-27			ENSG00000162407	ENSG00000162407	3.1.3.4		9229	protein-coding gene	gene with protein product		607125				9305923	Standard	NM_003713		Approved	PAP-2b, LPP3	uc001cyj.2	O14495	OTTHUMG00000008160	ENST00000371250.3:c.526A>T	chr1.hg19:g.56989998T>A	ENSP00000360296:p.Ile176Phe	145.0	0.0	.		150.0	74.0	.	NM_003713	B2R651|D3DQ52|Q5U0F7|Q96GW0|Q99782	Missense_Mutation	SNP	ENST00000371250.3	hg19	CCDS604.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.131509	0.77549	.	.	ENSG00000162407	ENST00000371250	T	0.36340	1.26	5.56	3.21	0.36854	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.156720	0.56097	D	0.000033	T	0.55625	0.1932	M	0.78637	2.42	0.80722	D	1	P	0.45212	0.853	P	0.62885	0.908	T	0.57004	-0.7885	10	0.87932	D	0	.	8.5688	0.33556	0.0:0.2073:0.0:0.7927	.	176	O14495	LPP3_HUMAN	F	176	ENSP00000360296:I176F	ENSP00000360296:I176F	I	-	1	0	PPAP2B	56762586	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.446000	0.52928	0.926000	0.37118	0.533000	0.62120	ATT	.	.	.	none		0.527	PPAP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022334.2	NM_003713		A	56989998	T	A	56989998	3	1	215	1	0	0	0	0	1	0	0	0	12298	1464	51	5	425	5	PPAP2B	1	56989998	Missense_Mutation	SNP	T	TCGA-J7-A8I2-01A-12D-A35Z-10	6104603	56989998	192260623	2	13031											
TPO	7173	hgsc.bcm.edu	37	chr2	1481209	1481209	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agacccgcgggccctgcttcCtggccggagacggccgcgcc	4	4	15	18	6	0	2	0	0	0	2	1	3	1	2	6	4	1	1	6	4	0	1			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr2:1481209C>T	ENST00000345913.4	+	8	1262	c.1171C>T	c.(1171-1173)Ctg>Ttg	p.L391L	TPO_ENST00000329066.4_Silent_p.L391L|TPO_ENST00000382201.3_Silent_p.L391L|TPO_ENST00000497517.2_Intron|TPO_ENST00000382198.1_Intron|TPO_ENST00000337415.3_Silent_p.L391L|TPO_ENST00000349624.3_Intron|TPO_ENST00000346956.3_Silent_p.L391L	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	391					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)	GCCCTGCTTCCTGGCCGGAGA	0.771																																					p.L391L		Atlas-SNP	.											.	TPO	224	.	0			c.C1171T						PASS	.						1	1	1					2																	1481209		1216	2495	3711	SO:0001819	synonymous_variant	7173	exon8			TGCTTCCTGGCCG		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.1171C>T	chr2.hg19:g.1481209C>T		672.0	1.0	.		626.0	273.0	.	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Silent	SNP	ENST00000345913.4	hg19	CCDS1643.1																																																																																			.	.	.	none		0.771	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		T	1481209	C	T	1481209	2	4	215	1	0	0	0	0	0	0	0	1	16422	680	24	2		2	TPO	2	1481209	Silent	SNP	C	TCGA-J7-A8I2-01A-12D-A35Z-10		1481209	241718164	3	13032											
KCNF1	3754	hgsc.bcm.edu	37	chr2	11053663	11053663	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatcatcaccatgaccaccGtcggctacggcgacatctac	10	7	7	17	4	3	1	2	1	1	0	4	2	3	1	4	2	2	1	4	2	2	2			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr2:11053663G>A	ENST00000295082.1	+	1	1601	c.1111G>A	c.(1111-1113)Gtc>Atc	p.V371I		NM_002236.4	NP_002227.2	Q9H3M0	KCNF1_HUMAN	potassium voltage-gated channel, subfamily F, member 1	371					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			NS(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(2)|skin(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.128)		CATGACCACCGTCGGCTACGG	0.607																																					p.V371I		Atlas-SNP	.											.	KCNF1	70	.	0			c.G1111A						PASS	.						126	97	106					2																	11053663		2203	4300	6503	SO:0001583	missense	3754	exon1			ACCACCGTCGGCT	AF033382	CCDS1676.1	2p25	2011-07-05			ENSG00000162975	ENSG00000162975		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6246	protein-coding gene	gene with protein product		603787		KCNF		9434767, 16382104	Standard	NM_002236		Approved	Kv5.1, kH1, IK8	uc002rax.3	Q9H3M0	OTTHUMG00000119054	ENST00000295082.1:c.1111G>A	chr2.hg19:g.11053663G>A	ENSP00000295082:p.Val371Ile	61.0	0.0	.		74.0	40.0	.	NM_002236	O43527|Q585L3	Missense_Mutation	SNP	ENST00000295082.1	hg19	CCDS1676.1	.	.	.	.	.	.	.	.	.	.	g	24.4	4.523021	0.85600	.	.	ENSG00000162975	ENST00000295082	D	0.97575	-4.44	5.32	5.32	0.75619	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98327	0.9445	M	0.76433	2.335	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.99316	1.0905	10	0.87932	D	0	.	19.3693	0.94479	0.0:0.0:1.0:0.0	.	371	Q9H3M0	KCNF1_HUMAN	I	371	ENSP00000295082:V371I	ENSP00000295082:V371I	V	+	1	0	KCNF1	10971114	1.000000	0.71417	0.399000	0.26333	0.996000	0.88848	9.813000	0.99286	2.640000	0.89533	0.651000	0.88453	GTC	.	.	.	none		0.607	KCNF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239265.1	NM_002236		A	11053663	G	A	11053663	3	1	215	1	0	0	0	0	1	0	0	0	8033	1145	40	1	1113	1	KCNF1	2	11053663	Missense_Mutation	SNP	G	TCGA-J7-A8I2-01A-12D-A35Z-10	9572454	11053663	232145710	4	13033											
C2orf28	8884	hgsc.bcm.edu	37	chr2	27435095	27435095	+	De_novo_Start_OutOfFrame	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaccagcgcagagctccaCgagcaggaaaagcccccaag	15	1	11	14	2	0	2	0	0	0	2	1	4	1	3	4	1	4	3	4	1	4	0			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr2:27435095C>T	ENST00000310574.3	-	0	59				SLC5A6_ENST00000408041.1_5'Flank|ATRAID_ENST00000405489.3_5'Flank|ATRAID_ENST00000380171.3_Silent_p.H8H|ATRAID_ENST00000606999.1_5'Flank	NM_021095.2	NP_066918.2	Q9Y289	SC5A6_HUMAN	solute carrier family 5 (sodium/multivitamin and iodide cotransporter), member 6						biotin metabolic process (GO:0006768)|biotin transport (GO:0015878)|pantothenate metabolic process (GO:0015939)|pantothenate transmembrane transport (GO:0015887)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)			endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|ovary(3)|prostate(1)|skin(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Biotin(DB00121)|gabapentin enacarbil(DB08872)|Lipoic Acid(DB00166)	CAGAGCTCCACGAGCAGGAAA	0.701																																					p.H8H		Atlas-SNP	.											.	.	.	.	0			c.C24T						PASS	.						6	8	7					2																	27435095		2097	4118	6215			51374	exon1			GCTCCACGAGCAG	AF069307	CCDS1740.1	2p23	2013-07-19	2013-07-19		ENSG00000138074	ENSG00000138074		"Solute carriers"	11041	protein-coding gene	gene with protein product		604024	"solute carrier family 5 (sodium-dependent vitamin transporter), member 6"			9516450, 10329687	Standard	NM_021095		Approved	SMVT	uc002rjd.3	Q9Y289	OTTHUMG00000097075	ENST00000310574.3:c.-415G>A	chr2.hg19:g.27435095C>T		374.0	0.0	.		349.0	166.0	.	NM_080592	B2RB85|D6W549|Q969Y5	Silent	SNP	ENST00000310574.3	hg19	CCDS1740.1																																																																																			.	.	.	none		0.701	SLC5A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214194.1	NM_021095		T	27435095	C	T	27435095	1	4	215	1	0	1	0	0	0	0	0	0	2162	535	19	1		1	C2orf28	2	27435095	De_novo_Start_OutOfFrame	SNP	C	TCGA-J7-A8I2-01A-12D-A35Z-10	16381432	27435095	215764278	5	13034											
ALK	238	hgsc.bcm.edu	37	chr2	29456516	29456516	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcacacggatttcttcttctAtcacattgttctctccaatg	8	17	4	12	1	6	0	2	0	4	0	8	1	7	1	1	1	0	1	1	1	2	6			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr2:29456516A>G	ENST00000389048.3	-	14	3308	c.2402T>C	c.(2401-2403)aTa>aCa	p.I801T	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	801					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)	TTCTTCTTCTATCACATTGTT	0.478			"T, Mis, A"	"NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"	"ALCL, NSCLC, Neuroblastoma"	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.I801T		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	.	ALK	533	.	0			c.T2402C						PASS	.						193	177	182					2																	29456516		2203	4300	6503	SO:0001583	missense	238	exon14	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	TCTTCTATCACAT	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.2402T>C	chr2.hg19:g.29456516A>G	ENSP00000373700:p.Ile801Thr	123.0	0.0	.		124.0	61.0	.	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	hg19	CCDS33172.1	.	.	.	.	.	.	.	.	.	.	A	17.50	3.405704	0.62288	.	.	ENSG00000171094	ENST00000389048	T	0.41065	1.01	5.29	5.29	0.74685	.	0.000000	0.51477	D	0.000085	T	0.44808	0.1311	L	0.49126	1.545	0.80722	D	1	P	0.38250	0.624	B	0.43445	0.42	T	0.31558	-0.9939	9	.	.	.	.	15.2522	0.73556	1.0:0.0:0.0:0.0	.	801	Q9UM73	ALK_HUMAN	T	801	ENSP00000373700:I801T	.	I	-	2	0	ALK	29310020	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.230000	0.65321	2.007000	0.58848	0.459000	0.35465	ATA	.	.	.	none		0.478	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		G	29456516	A	G	29456516	3	3	215	1	0	0	0	0	1	0	0	0	525	449	16	3	2524	3	ALK	2	29456516	Missense_Mutation	SNP	A	TCGA-J7-A8I2-01A-12D-A35Z-10	2021421	29456516	213742857	6	13035											
PNPT1	87178	hgsc.bcm.edu	37	chr2	55870498	55870498	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaagtctcttgcctcatgcaTagcactgggtgttggtgcaa	8	12	12	9	0	2	0	1	0	1	0	3	1	2	0	1	2	4	4	1	2	3	3			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr2:55870498T>C	ENST00000447944.2	-	24	2055	c.1969A>G	c.(1969-1971)Atg>Gtg	p.M657V		NM_033109.3	NP_149100.2	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	657	KH. {ECO:0000255|PROSITE- ProRule:PRU00117}.				cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA polyadenylation (GO:0097222)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA 5'-end processing (GO:0000964)|mitochondrial RNA catabolic process (GO:0000957)|mitochondrion morphogenesis (GO:0070584)|mitotic cell cycle arrest (GO:0071850)|mRNA catabolic process (GO:0006402)|negative regulation of growth (GO:0045926)|nuclear polyadenylation-dependent mRNA catabolic process (GO:0071042)|positive regulation of miRNA catabolic process (GO:2000627)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|positive regulation of mRNA catabolic process (GO:0061014)|protein homooligomerization (GO:0051260)|protein homotrimerization (GO:0070207)|regulation of cellular respiration (GO:0043457)|regulation of cellular senescence (GO:2000772)|RNA catabolic process (GO:0006401)|RNA import into mitochondrion (GO:0035927)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA polyadenylation (GO:0043631)|rRNA import into mitochondrion (GO:0035928)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrial degradosome (GO:0045025)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	3'-5'-exoribonuclease activity (GO:0000175)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|polyribonucleotide nucleotidyltransferase activity (GO:0004654)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			GCCTCATGCATAGCACTGGGT	0.313																																					p.M657V		Atlas-SNP	.											.	PNPT1	68	.	0			c.A1969G						PASS	.						142	134	137					2																	55870498		2203	4300	6503	SO:0001583	missense	87178	exon24			CATGCATAGCACT	BC053660	CCDS1856.1	2p15	2013-01-08			ENSG00000138035	ENSG00000138035			23166	protein-coding gene	gene with protein product	"polynucleotide phosphorylase", "3'-5' RNA exonuclease"	610316	"deafness, autosomal recessive 70"	DFNB70		12419256	Standard	NM_033109		Approved	PNPase, OLD35, old-35	uc002rzf.3	Q8TCS8	OTTHUMG00000129335	ENST00000447944.2:c.1969A>G	chr2.hg19:g.55870498T>C	ENSP00000400646:p.Met657Val	435.0	0.0	.		420.0	162.0	.	NM_033109	Q53SU0|Q68CN1|Q7Z7D1|Q8IWX1|Q96T05|Q9BRU3|Q9BVX0	Missense_Mutation	SNP	ENST00000447944.2	hg19	CCDS1856.1	.	.	.	.	.	.	.	.	.	.	T	19.06	3.753568	0.69648	.	.	ENSG00000138035	ENST00000447944	T	0.17370	2.28	5.17	4.01	0.46588	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.084629	0.85682	D	0.000000	T	0.30947	0.0781	M	0.62154	1.92	0.58432	D	0.999999	P	0.47604	0.898	P	0.57548	0.823	T	0.01688	-1.1295	10	0.26408	T	0.33	-22.0783	11.4955	0.50406	0.1346:0.0:0.0:0.8654	.	657	Q8TCS8	PNPT1_HUMAN	V	657	ENSP00000400646:M657V	ENSP00000393953:M657V	M	-	1	0	PNPT1	55724002	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	5.814000	0.69208	0.811000	0.34303	-0.544000	0.04233	ATG	.	.	.	none		0.313	PNPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251481.2	NM_033109		C	55870498	T	C	55870498	3	2	215	1	0	0	0	0	1	0	0	0	12180	1406	49	3	402	3	PNPT1	2	55870498	Missense_Mutation	SNP	T	TCGA-J7-A8I2-01A-12D-A35Z-10	26413982	55870498	187328875	7	13036											
ALMS1	7840	hgsc.bcm.edu	37	chr2	73680351	73680351	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggctgatgacagagttgtaAtaaataaaccagaatctgca	17	9	9	6	0	1	4	0	2	1	2	1	4	1	4	1	1	2	4	1	1	6	4			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr2:73680351A>G	ENST00000264448.6	+	8	6805	c.6694A>G	c.(6694-6696)Ata>Gta	p.I2232V	ALMS1_ENST00000409009.1_Missense_Mutation_p.I2190V|ALMS1_ENST00000377715.1_Missense_Mutation_p.I2232V	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2232					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						CAGAGTTGTAATAAATAAACC	0.353																																					p.I2232V		Atlas-SNP	.											.	ALMS1	384	.	0			c.A6694G						PASS	.						54	53	53					2																	73680351		1831	4094	5925	SO:0001583	missense	7840	exon8			GTTGTAATAAATA	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.6694A>G	chr2.hg19:g.73680351A>G	ENSP00000264448:p.Ile2232Val	147.0	0.0	.		159.0	74.0	.	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	A	10.19	1.282885	0.23392	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.15017	3.34;3.34;2.46	6.03	3.6	0.41247	.	0.109289	0.41712	D	0.000822	T	0.13543	0.0328	L	0.48642	1.525	0.09310	N	1	B;B;B	0.33940	0.23;0.433;0.433	B;B;B	0.32677	0.15;0.134;0.134	T	0.19160	-1.0314	10	0.46703	T	0.11	.	5.3339	0.15947	0.7629:0.0:0.0823:0.1548	.	2232;2190;2232	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	V	2190;2232;2232	ENSP00000386627:I2190V;ENSP00000264448:I2232V;ENSP00000366944:I2232V	ENSP00000264448:I2232V	I	+	1	0	ALMS1	73533859	0.183000	0.23186	0.175000	0.22980	0.402000	0.30811	1.065000	0.30592	0.485000	0.27652	0.533000	0.62120	ATA	.	.	.	none		0.353	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		G	73680351	A	G	73680351	3	3	215	1	0	0	0	0	1	0	0	0	535	101	4	3	6724	3	ALMS1	2	73680351	Missense_Mutation	SNP	A	TCGA-J7-A8I2-01A-12D-A35Z-10	17809853	73680351	169519022	8	13037											
CLASP1	23332	hgsc.bcm.edu	37	chr2	122216460	122216460	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aacaccagatgtggccataaTtttggcactgtttggaatta	12	13	9	7	0	0	1	0	0	0	1	0	2	0	2	2	3	1	2	2	3	4	5			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr2:122216460T>C	ENST00000263710.4	-	13	1659	c.1270A>G	c.(1270-1272)Att>Gtt	p.I424V	CLASP1_ENST00000455322.2_Missense_Mutation_p.I424V|CLASP1_ENST00000545861.1_Missense_Mutation_p.I192V|CLASP1_ENST00000397587.3_Missense_Mutation_p.I424V|CLASP1_ENST00000409078.3_Missense_Mutation_p.I424V|CLASP1_ENST00000430234.1_5'Flank|CLASP1_ENST00000541859.1_Missense_Mutation_p.I193V|CLASP1_ENST00000541377.1_Missense_Mutation_p.I424V	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	424					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)					GTGGCCATAATTTTGGCACTG	0.378																																					p.I424V		Atlas-SNP	.											.	CLASP1	135	.	0			c.A1270G						PASS	.						102	102	102					2																	122216460		1850	4097	5947	SO:0001583	missense	23332	exon13			CCATAATTTTGGC	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.1270A>G	chr2.hg19:g.122216460T>C	ENSP00000263710:p.Ile424Val	109.0	0.0	.		128.0	63.0	.	NM_001207051	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Missense_Mutation	SNP	ENST00000263710.4	hg19		.	.	.	.	.	.	.	.	.	.	T	3.808	-0.040404	0.07497	.	.	ENSG00000074054	ENST00000263710;ENST00000455322;ENST00000397587;ENST00000541377;ENST00000541859;ENST00000409078;ENST00000545861	T;T;T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67;0.67;0.67	5.35	4.19	0.49359	Armadillo-like helical (1);Armadillo-type fold (1);CLASP N-terminal domain (1);	0.150369	0.64402	D	0.000012	T	0.12305	0.0299	N	0.00422	-1.515	0.33312	D	0.566265	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.09377	0.002;0.001;0.002;0.004	T	0.28170	-1.0052	10	0.02654	T	1	-1.4012	7.7836	0.29078	0.0:0.2102:0.0:0.7898	.	424;424;424;424	E7EUA5;F5GWS0;B7ZLX3;Q7Z460	.;.;.;CLAP1_HUMAN	V	424;424;424;424;193;424;192	ENSP00000263710:I424V;ENSP00000389372:I424V;ENSP00000380717:I424V;ENSP00000441625:I424V;ENSP00000441770:I193V;ENSP00000386442:I424V;ENSP00000438620:I192V	ENSP00000263710:I424V	I	-	1	0	CLASP1	121932930	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.415000	0.44635	0.971000	0.38288	0.533000	0.62120	ATT	.	.	.	none		0.378	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282		C	122216460	T	C	122216460	3	2	215	1	0	0	0	0	1	0	0	0	3456	1493	52	3	3510	3	CLASP1	2	122216460	Missense_Mutation	SNP	T	TCGA-J7-A8I2-01A-12D-A35Z-10	48536109	122216460	120982913	9	13038											
TSN	7247	hgsc.bcm.edu	37	chr2	122513374	122513374	+	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	ccatgtctgtgagcgagatcTtcgtggagctgcagggcttt	6	12	14	9	2	2	2	0	1	2	1	3	4	2	3	1	2	3	3	1	2	0	2			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr2:122513374T>A	ENST00000389682.3	+	1	266	c.19T>A	c.(19-21)Ttc>Atc	p.F7I	TSN_ENST00000498545.1_3'UTR|TSN_ENST00000536142.1_Missense_Mutation_p.F7I|TSN_ENST00000409193.1_5'Flank	NM_001261401.1|NM_004622.2	NP_001248330.1|NP_004613.1	Q15631	TSN_HUMAN	translin	7					DNA recombination (GO:0006310)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|mRNA binding (GO:0003729)|sequence-specific DNA binding (GO:0043565)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|large_intestine(1)|liver(1)|lung(3)|skin(1)	12		Ovarian(717;0.0563)|Prostate(154;0.116)				GAGCGAGATCTTCGTGGAGCT	0.612																																					p.F7I		Atlas-SNP	.											.	TSN	31	.	0			c.T19A						PASS	.						78	80	79					2																	122513374		2203	4300	6503	SO:0001583	missense	7247	exon1			GAGATCTTCGTGG	X78627	CCDS33284.1, CCDS58723.1	2q21.1	2008-05-23			ENSG00000211460	ENSG00000211460			12379	protein-coding gene	gene with protein product	"recombination hotspot associated factor"	600575				7947454, 9244443	Standard	NM_004622		Approved	TRSLN, BCLF-1, REHF-1	uc002tnl.3	Q15631	OTTHUMG00000153334	ENST00000389682.3:c.19T>A	chr2.hg19:g.122513374T>A	ENSP00000374332:p.Phe7Ile	27.0	0.0	.		33.0	16.0	.	NM_004622	B7Z3X8|Q5U0K7	Missense_Mutation	SNP	ENST00000389682.3	hg19	CCDS33284.1	.	.	.	.	.	.	.	.	.	.	T	34	5.366476	0.95900	.	.	ENSG00000211460	ENST00000389682;ENST00000536142;ENST00000413418	.	.	.	4.18	4.18	0.49190	Translin, N-terminal (1);	0.225178	0.46758	D	0.000261	T	0.80303	0.4598	M	0.88906	2.99	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.995;0.999	T	0.83027	-0.0164	9	0.59425	D	0.04	-0.0926	11.0851	0.48082	0.0:0.0:0.0:1.0	.	7;7	B7Z3X8;Q15631	.;TSN_HUMAN	I	7	.	ENSP00000374332:F7I	F	+	1	0	TSN	122229844	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.462000	0.60121	1.761000	0.52028	0.460000	0.39030	TTC	.	.	.	none		0.612	TSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330767.1	NM_004622		A	122513374	T	A	122513374	3	1	215	1	0	0	0	0	1	0	0	0	16641	1609	56	5	21	5	TSN	2	122513374	Missense_Mutation	SNP	T	TCGA-J7-A8I2-01A-12D-A35Z-10	296914	122513374	120685999	10	13039											
NFE2L2	4780	hgsc.bcm.edu	37	chr2	178096314	178096314	+	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	atgccggagtcagaatcattGaattctgctgtgctttcagg	9	13	11	8	1	4	2	3	1	1	1	4	3	4	3	1	2	3	2	1	2	2	3			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr2:178096314G>C	ENST00000397062.3	-	5	1571	c.1017C>G	c.(1015-1017)ttC>ttG	p.F339L	NFE2L2_ENST00000446151.2_Missense_Mutation_p.F316L|NFE2L2_ENST00000464747.1_Missense_Mutation_p.F323L|NFE2L2_ENST00000397063.4_Missense_Mutation_p.F323L	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	339					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			CAGAATCATTGAATTCTGCTG	0.453			Mis		"NSCLC, HNSCC"					HNSCC(56;0.16)																											p.F339L		Atlas-SNP	.		Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	.	NFE2L2	225	.	0			c.C1017G						PASS	.						131	136	134					2																	178096314		2196	4299	6495	SO:0001583	missense	4780	exon5			ATCATTGAATTCT		CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"basic leucine zipper proteins"	7782	protein-coding gene	gene with protein product	"NF-E2-related factor 2"	600492	"nuclear factor (erythroid-derived 2)-like 2"			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.1017C>G	chr2.hg19:g.178096314G>C	ENSP00000380252:p.Phe339Leu	171.0	0.0	.		216.0	94.0	.	NM_006164	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	hg19	CCDS42782.1	.	.	.	.	.	.	.	.	.	.	G	6.841	0.524426	0.13066	.	.	ENSG00000116044	ENST00000397063;ENST00000397062;ENST00000446151;ENST00000449627	T;T;T;T	0.29142	2.3;2.3;2.3;1.58	5.83	2.66	0.31614	.	0.423208	0.29846	N	0.011059	T	0.23727	0.0574	L	0.53249	1.67	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.05750	-1.0866	10	0.09843	T	0.71	-2.2964	9.1144	0.36748	0.3416:0.0:0.6584:0.0	.	316;339	E9PGJ7;Q16236	.;NF2L2_HUMAN	L	323;339;316;67	ENSP00000380253:F323L;ENSP00000380252:F339L;ENSP00000411575:F316L;ENSP00000391590:F67L	ENSP00000380252:F339L	F	-	3	2	NFE2L2	177804560	0.997000	0.39634	0.999000	0.59377	0.988000	0.76386	0.667000	0.25112	0.823000	0.34589	0.563000	0.77884	TTC	.	.	.	none		0.453	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4	NM_006164		C	178096314	G	C	178096314	3	2	215	1	0	0	0	0	1	0	0	0	10375	1281	45	4	804	4	NFE2L2	2	178096314	Missense_Mutation	SNP	G	TCGA-J7-A8I2-01A-12D-A35Z-10	55582940	178096314	65103059	11	13040											
PLEKHA3	65977	hgsc.bcm.edu	37	chr2	179358605	179358605	+	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	agtgaaaccagtgaatcgctGaaaaccaaaatgtctgaact	17	8	8	8	1	1	4	0	4	1	0	2	4	1	4	2	0	3	1	2	0	7	0			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr2:179358605G>T	ENST00000234453.5	+	4	741	c.339G>T	c.(337-339)ctG>ctT	p.L113L	PLEKHA3_ENST00000461474.1_3'UTR	NM_019091.3	NP_061964.3	Q9HB20	PKHA3_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3	113						Golgi apparatus (GO:0005794)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)			GTGAATCGCTGAAAACCAAAA	0.323																																					p.L113L		Atlas-SNP	.											.	PLEKHA3	25	.	0			c.G339T						PASS	.						77	72	74					2																	179358605		2203	4300	6503	SO:0001819	synonymous_variant	65977	exon4			ATCGCTGAAAACC	AF286162	CCDS33336.1	2q31.2	2013-01-10	2002-01-14		ENSG00000116095	ENSG00000116095		"Pleckstrin homology (PH) domain containing"	14338	protein-coding gene	gene with protein product	"four-phosphate-adaptor protein 1"	607774	"pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3"			11001876, 15107860	Standard	NM_019091		Approved	FAPP1	uc002umn.3	Q9HB20	OTTHUMG00000154446	ENST00000234453.5:c.339G>T	chr2.hg19:g.179358605G>T		288.0	1.0	.		284.0	125.0	.	NM_019091	Q4ZG69|Q86TQ1|Q9NXT3	Silent	SNP	ENST00000234453.5	hg19	CCDS33336.1																																																																																			.	.	.	none		0.323	PLEKHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335241.2	NM_019091		T	179358605	G	T	179358605	2	4	215	1	0	0	0	0	0	0	0	1	12064	1277	45	4		4	PLEKHA3	2	179358605	Silent	SNP	G	TCGA-J7-A8I2-01A-12D-A35Z-10	1262291	179358605	63840768	12	13041											
SGOL1	151648	hgsc.bcm.edu	37	chr3	20215950	20215950	+	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	cagactcgttgttttcttctCtattagagtcattgctcact	7	18	6	10	1	4	2	2	0	2	2	6	2	4	2	0	0	1	3	0	0	2	7			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr3:20215950C>G	ENST00000263753.4	-	6	1212	c.1073G>C	c.(1072-1074)aGa>aCa	p.R358T	SGOL1-AS1_ENST00000448208.1_RNA|SGOL1_ENST00000425061.1_Intron|SGOL1_ENST00000421451.1_Missense_Mutation_p.R358T|SGOL1_ENST00000383774.1_Intron|SGOL1_ENST00000412997.1_Missense_Mutation_p.R358T|SGOL1_ENST00000419233.2_Intron|SGOL1_ENST00000443724.1_Intron|SGOL1_ENST00000442720.1_Intron|SGOL1_ENST00000437051.1_Intron|SGOL1_ENST00000429446.3_Intron|SGOL1_ENST00000417364.1_Intron|SGOL1-AS1_ENST00000441442.1_RNA|SGOL1_ENST00000412868.1_Missense_Mutation_p.R358T|SGOL1_ENST00000306698.2_Intron|SGOL1_ENST00000452020.1_Intron	NM_001012410.3|NM_001199252.1	NP_001012410.1|NP_001186181.1	Q5FBB7	SGOL1_HUMAN	shugoshin-like 1 (S. pombe)	358					attachment of spindle microtubules to kinetochore (GO:0008608)|centriole-centriole cohesion (GO:0010457)|chromosome segregation (GO:0007059)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|chromosome, centromeric region (GO:0000775)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)|spindle pole (GO:0000922)	kinase binding (GO:0019900)			kidney(1)|large_intestine(4)|lung(6)|skin(1)|urinary_tract(2)	14						GTTTTCTTCTCTATTAGAGTC	0.398																																					p.R358T		Atlas-SNP	.											.	SGOL1	55	.	0			c.G1073C						PASS	.						142	129	134					3																	20215950		2203	4300	6503	SO:0001583	missense	151648	exon6			TCTTCTCTATTAG	BC001339	CCDS2635.1, CCDS33716.1, CCDS46771.1, CCDS46772.1, CCDS46773.1, CCDS46774.1, CCDS56243.1	3p24.3	2005-07-27			ENSG00000129810	ENSG00000129810			25088	protein-coding gene	gene with protein product		609168				12747765	Standard	NM_001199251		Approved	NY-BR-85	uc003cbu.3	Q5FBB7	OTTHUMG00000130479	ENST00000263753.4:c.1073G>C	chr3.hg19:g.20215950C>G	ENSP00000263753:p.Arg358Thr	154.0	0.0	.		187.0	78.0	.	NM_001012409	Q588H5|Q5FBB4|Q5FBB5|Q5FBB6|Q5FBB8|Q8N579|Q8WVL0|Q9BVA8|Q9H275	Missense_Mutation	SNP	ENST00000263753.4	hg19	CCDS33716.1	.	.	.	.	.	.	.	.	.	.	C	3.154	-0.173522	0.06421	.	.	ENSG00000129810	ENST00000263753;ENST00000421451;ENST00000412997;ENST00000412868	T;T;T;T	0.31769	1.48;1.48;1.5;1.5	5.76	-0.651	0.11454	.	0.794180	0.11812	N	0.527060	T	0.16342	0.0393	L	0.38838	1.175	0.20196	N	0.999927	B;B	0.21381	0.055;0.055	B;B	0.15052	0.012;0.012	T	0.25398	-1.0133	10	0.19590	T	0.45	.	0.7717	0.01025	0.2512:0.323:0.1118:0.314	.	358;358	B5BUA4;Q5FBB7	.;SGOL1_HUMAN	T	358	ENSP00000263753:R358T;ENSP00000414129:R358T;ENSP00000410458:R358T;ENSP00000406880:R358T	ENSP00000263753:R358T	R	-	2	0	SGOL1	20190954	0.000000	0.05858	0.024000	0.17045	0.228000	0.25075	-0.798000	0.04565	0.030000	0.15379	0.561000	0.74099	AGA	.	.	.	none		0.398	SGOL1-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340498.1	NM_138484		G	20215950	C	G	20215950	3	3	215	1	0	0	0	0	1	0	0	0	14229	913	32	4	648	4	SGOL1	3	20215950	Missense_Mutation	SNP	C	TCGA-J7-A8I2-01A-12D-A35Z-10		20215950	177806480	13	13042											
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113383247	113383247	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaaggcttggtccaggatcaTattcttgctctgtccaagaa	11	12	9	9	0	3	1	1	0	2	1	5	2	5	2	2	3	1	2	2	3	4	4			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr3:113383247T>C	ENST00000478658.1	-	4	186	c.169A>G	c.(169-171)Atg>Gtg	p.M57V	KIAA2018_ENST00000316407.4_Missense_Mutation_p.M57V|KIAA2018_ENST00000491165.1_Missense_Mutation_p.M57V			Q68DE3	K2018_HUMAN	KIAA2018	57	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.					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						TCCAGGATCATATTCTTGCTC	0.318																																					p.M57V		Atlas-SNP	.											.	KIAA2018	180	.	0			c.A169G						PASS	.						84	77	79					3																	113383247		1794	4067	5861	SO:0001583	missense	205717	exon6			GGATCATATTCTT	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.169A>G	chr3.hg19:g.113383247T>C	ENSP00000420721:p.Met57Val	107.0	0.0	.		103.0	40.0	.	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Missense_Mutation	SNP	ENST00000478658.1	hg19	CCDS43133.1	.	.	.	.	.	.	.	.	.	.	T	16.86	3.238796	0.58995	.	.	ENSG00000176542	ENST00000491165;ENST00000316407;ENST00000478658	D;D;D	0.97906	-4.6;-4.6;-4.6	4.83	4.83	0.62350	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.97120	0.9059	N	0.20685	0.6	0.58432	D	0.999998	D	0.76494	0.999	D	0.79108	0.992	D	0.98417	1.0575	10	0.87932	D	0	-13.03	14.8689	0.70441	0.0:0.0:0.0:1.0	.	57	Q68DE3	K2018_HUMAN	V	57	ENSP00000420752:M57V;ENSP00000320794:M57V;ENSP00000420721:M57V	ENSP00000320794:M57V	M	-	1	0	KIAA2018	114865937	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.431000	0.80335	2.167000	0.68274	0.528000	0.53228	ATG	.	.	.	none		0.318	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		C	113383247	T	C	113383247	3	2	215	1	0	0	0	0	1	0	0	0	8275	1406	49	3	6576	3	KIAA2018	3	113383247	Missense_Mutation	SNP	T	TCGA-J7-A8I2-01A-12D-A35Z-10	93167297	113383247	84639183	14	13043											
CCDC37	348807	hgsc.bcm.edu	37	chr3	126137471	126137471	+	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	cagtatgccctggatgtcaaGcggagagagatccagcggct	10	7	14	10	2	1	2	1	0	0	2	2	5	2	3	2	3	3	2	2	3	2	1			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr3:126137471G>C	ENST00000352312.1	+	7	603	c.504G>C	c.(502-504)aaG>aaC	p.K168N	CCDC37_ENST00000505024.1_Missense_Mutation_p.K169N|CCDC37_ENST00000393425.1_Missense_Mutation_p.K169N	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37	168										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)		TGGATGTCAAGCGGAGAGAGA	0.672																																					p.K168N		Atlas-SNP	.											.	CCDC37	69	.	0			c.G504C						PASS	.						29	32	31					3																	126137471		2200	4298	6498	SO:0001583	missense	348807	exon7			TGTCAAGCGGAGA	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.504G>C	chr3.hg19:g.126137471G>C	ENSP00000344749:p.Lys168Asn	73.0	0.0	.		75.0	5.0	.	NM_182628	D3DNA8|Q494V1|Q494V4|Q8N838	Missense_Mutation	SNP	ENST00000352312.1	hg19	CCDS3037.1	.	.	.	.	.	.	.	.	.	.	G	9.840	1.190832	0.21954	.	.	ENSG00000163885	ENST00000352312;ENST00000393425;ENST00000505024	T;T;T	0.23754	1.89;1.89;1.89	4.74	1.94	0.25998	.	0.000000	0.85682	D	0.000000	T	0.52837	0.1759	M	0.89840	3.065	0.44762	D	0.997769	D;D	0.76494	0.999;0.999	D;D	0.80764	0.99;0.994	T	0.50955	-0.8766	10	0.52906	T	0.07	-39.2628	9.3746	0.38275	0.3372:0.0:0.6628:0.0	.	169;168	Q494V2-2;Q494V2	.;CCD37_HUMAN	N	168;169;169	ENSP00000344749:K168N;ENSP00000377076:K169N;ENSP00000423046:K169N	ENSP00000344749:K168N	K	+	3	2	CCDC37	127620161	0.996000	0.38824	0.111000	0.21465	0.005000	0.04900	1.465000	0.35299	-0.116000	0.11893	-1.579000	0.00862	AAG	.	.	.	none		0.672	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628		C	126137471	G	C	126137471	3	2	215	1	0	0	0	0	1	0	0	0	2811	962	34	4	526	4	CCDC37	3	126137471	Missense_Mutation	SNP	G	TCGA-J7-A8I2-01A-12D-A35Z-10	12754224	126137471	71884959	15	13044											
FGFR3	2261	hgsc.bcm.edu	37	chr4	1806099	1806099	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgacgaggcgggcagtgtgtAtgcaggcatcctcagctacg	8	8	15	10	3	1	1	1	1	0	0	2	2	2	1	1	3	3	5	1	3	2	2	rs121913485		TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr4:1806099A>G	ENST00000260795.2	+	8	1220	c.1118A>G	c.(1117-1119)tAt>tGt	p.Y373C	FGFR3_ENST00000412135.2_Intron|FGFR3_ENST00000340107.4_Missense_Mutation_p.Y375C|FGFR3_ENST00000481110.2_Missense_Mutation_p.Y373C|FGFR3_ENST00000352904.1_Intron|FGFR3_ENST00000440486.2_Missense_Mutation_p.Y373C			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	373			Y -> C (in KERSEB and TD1; disulfide- linked dimer with constitutive kinase activation). {ECO:0000269|PubMed:10360402, ECO:0000269|PubMed:15772091, ECO:0000269|PubMed:8845844, ECO:0000269|PubMed:9207791}.		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)	p.Y373C(395)		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)	GGCAGTGTGTATGCAGGCATC	0.682	Y373C(KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	1	"Mis, T"	"IGH@, ETV6"	"bladder, MM, T-cell lymphoma"		"Hypochondroplasia, Thanatophoric dysplasia"		Saethre-Chotzen syndrome;Muenke syndrome																												p.Y375C		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"L, E"	FGFR3_ENST00000340107,bladder,carcinoma,0,407	FGFR3	3320	.	395	Substitution - Missense(395)	urinary_tract(371)|skin(16)|haematopoietic_and_lymphoid_tissue(8)	c.A1124G	GRCh37	CM960657	FGFR3	M	rs121913485	PASS	.						141	134	137					4																	1806099		2203	4300	6503	SO:0001583	missense	2261	exon9	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	GTGTGTATGCAGG	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.1118A>G	chr4.hg19:g.1806099A>G	ENSP00000260795:p.Tyr373Cys	44.0	0.0	.		54.0	24.0	.	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Missense_Mutation	SNP	ENST00000260795.2	hg19	CCDS3353.1	.	.	.	.	.	.	.	.	.	.	a	12.61	1.990190	0.35131	.	.	ENSG00000068078	ENST00000481110;ENST00000340107;ENST00000440486;ENST00000260795	D;D;D;D	0.88201	-2.35;-2.35;-2.35;-2.35	4.68	1.93	0.25924	.	0.343855	0.31061	N	0.008340	D	0.93148	0.7818	M	0.82517	2.595	0.80722	A	1	D;D;D	0.76494	0.992;0.994;0.999	D;P;D	0.72625	0.94;0.896;0.978	D	0.94049	0.7316	9	0.72032	D	0.01	.	8.9873	0.36001	0.7079:0.0:0.0:0.2921	.	375;373;373	P22607-2;P22607;F8W9L4	.;FGFR3_HUMAN;.	C	373;375;373;373	ENSP00000420533:Y373C;ENSP00000339824:Y375C;ENSP00000414914:Y373C;ENSP00000260795:Y373C	ENSP00000260795:Y373C	Y	+	2	0	FGFR3	1775897	0.999000	0.42202	0.495000	0.27527	0.084000	0.17831	4.274000	0.58921	0.715000	0.32103	0.379000	0.24179	TAT	.	.	.	weak		0.682	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142		G	1806099	A	G	1806099	3	3	215	1	0	0	0	0	1	0	0	0	5874	449	16	3	1303	3	FGFR3	4	1806099	Missense_Mutation	SNP	A	TCGA-J7-A8I2-01A-12D-A35Z-10		1806099	189348177	16	13045											
ABLIM2	84448	hgsc.bcm.edu	37	chr4	8082456	8082456	+	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	cagctcttgcacttaaaacaGcccaagtgccagtgcttgtc	10	10	8	13	0	1	0	0	0	1	0	2	0	1	0	2	0	6	3	2	0	3	3			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr4:8082456G>A	ENST00000341937.5	-	5	592	c.528C>T	c.(526-528)ggC>ggT	p.G176G	ABLIM2_ENST00000546334.1_Silent_p.G176G|ABLIM2_ENST00000447017.2_Silent_p.G176G|ABLIM2_ENST00000545242.1_Silent_p.G176G|ABLIM2_ENST00000407564.3_Silent_p.G176G|ABLIM2_ENST00000361581.5_Silent_p.G176G|ABLIM2_ENST00000318888.4_5'UTR|ABLIM2_ENST00000296372.8_Silent_p.G176G|ABLIM2_ENST00000428004.2_Silent_p.G176G|ABLIM2_ENST00000361737.5_Silent_p.G176G|ABLIM2_ENST00000505872.1_Silent_p.G176G	NM_001130084.1	NP_001123556.1	Q6H8Q1	ABLM2_HUMAN	actin binding LIM protein family, member 2	176	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				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						ACTTAAAACAGCCCAAGTGCC	0.557																																					p.G176G		Atlas-SNP	.											.	ABLIM2	59	.	0			c.C528T						PASS	.						65	70	68					4																	8082456		1977	4158	6135	SO:0001819	synonymous_variant	84448	exon5			AAAACAGCCCAAG	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.528C>T	chr4.hg19:g.8082456G>A		141.0	0.0	.		145.0	67.0	.	NM_001130083	E9PF39|Q08E71|Q19VH0|Q6H8Q0|Q6NX73|Q8N3C5|Q8N9E9|Q8N9G2|Q96JL7	Silent	SNP	ENST00000341937.5	hg19	CCDS47013.1																																																																																			.	.	.	none		0.557	ABLIM2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358862.2	NM_001130083		A	8082456	G	A	8082456	2	1	215	1	0	0	0	0	0	0	0	1	95	958	34	2		2	ABLIM2	4	8082456	Silent	SNP	G	TCGA-J7-A8I2-01A-12D-A35Z-10	6276357	8082456	183071820	17	13046											
PCDH18	54510	hgsc.bcm.edu	37	chr4	138451594	138451594	+	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	ccagttgcttcgggcttcctCcatctcttgcttctaccaca	5	14	6	16	1	2	0	0	0	2	0	6	0	4	0	4	1	3	4	4	1	1	6			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr4:138451594C>G	ENST00000344876.4	-	1	2035	c.1649G>C	c.(1648-1650)gGa>gCa	p.G550A	PCDH18_ENST00000510305.1_Intron|PCDH18_ENST00000507846.1_Missense_Mutation_p.G330A|PCDH18_ENST00000412923.2_Missense_Mutation_p.G550A|PCDH18_ENST00000511115.1_Intron	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	550	Cadherin 5. {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)					CGGGCTTCCTCCATCTCTTGC	0.443																																					p.G550A		Atlas-SNP	.											.	PCDH18	229	.	0			c.G1649C						PASS	.						140	138	139					4																	138451594		2203	4300	6503	SO:0001583	missense	54510	exon1			CTTCCTCCATCTC	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.1649G>C	chr4.hg19:g.138451594C>G	ENSP00000355082:p.Gly550Ala	80.0	0.0	.		76.0	26.0	.	NM_019035	A8K7K3|B7ZKT1|Q52LS2	Missense_Mutation	SNP	ENST00000344876.4	hg19	CCDS34064.1	.	.	.	.	.	.	.	.	.	.	C	5.574	0.290786	0.10567	.	.	ENSG00000189184	ENST00000344876;ENST00000412923;ENST00000507846	T;T;T	0.50277	0.75;0.75;0.75	5.93	5.93	0.95920	Cadherin (4);Cadherin-like (1);	0.000000	0.42420	D	0.000720	T	0.42291	0.1196	L	0.39566	1.225	0.80722	D	1	B;B;P	0.35628	0.145;0.016;0.513	B;B;B	0.35470	0.141;0.049;0.203	T	0.17715	-1.0360	10	0.13853	T	0.58	.	20.3437	0.98782	0.0:1.0:0.0:0.0	.	330;550;550	D6RIG4;Q9HCL0-2;Q9HCL0	.;.;PCD18_HUMAN	A	550;550;330	ENSP00000355082:G550A;ENSP00000390688:G550A;ENSP00000425903:G330A	ENSP00000355082:G550A	G	-	2	0	PCDH18	138671044	0.994000	0.37717	0.999000	0.59377	0.339000	0.28857	2.566000	0.45948	2.802000	0.96397	0.563000	0.77884	GGA	.	.	.	none		0.443	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		G	138451594	C	G	138451594	3	3	215	1	0	0	0	0	1	0	0	0	11520	855	30	4	1774	4	PCDH18	4	138451594	Missense_Mutation	SNP	C	TCGA-J7-A8I2-01A-12D-A35Z-10	130369138	138451594	52702682	18	13047											
FBXW7	55294	hgsc.bcm.edu	37	chr4	153273874	153273874	+	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	agtatcaaaccgcttctcggGacacacatacatacatgcag	14	8	7	12	2	2	0	1	0	1	0	3	1	2	1	1	1	4	3	1	1	4	4			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr4:153273874G>A	ENST00000281708.4	-	3	1731				FBXW7_ENST00000603841.1_Intron|FBXW7_ENST00000263981.5_Silent_p.V3V|FBXW7_ENST00000603548.1_Intron|FBXW7_ENST00000296555.5_Intron	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase						cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)			NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				CGCTTCTCGGGACACACATAC	0.468			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																p.V3V		Atlas-SNP	.		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	.	FBXW7	2157	.	0			c.C9T						PASS	.						66	63	64					4																	153273874		2203	4300	6503	SO:0001627	intron_variant	55294	exon1			TCTCGGGACACAC	AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.502-2598C>T	chr4.hg19:g.153273874G>A		59.0	0.0	.		59.0	31.0	.	NM_018315	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Silent	SNP	ENST00000281708.4	hg19	CCDS3777.1																																																																																			.	.	.	none		0.468	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			A	153273874	G	A	153273874	1	1	215	0	1	0	0	0	0	0	0	0	5776	1161	41	2		2	FBXW7	4	153273874	Intron	SNP	G	TCGA-J7-A8I2-01A-12D-A35Z-10	14822280	153273874	37880402	19	13048											
MAP1B	4131	hgsc.bcm.edu	37	chr5	71403432	71403432	+	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	caacccggcggcgtccacctCgcctagcctgtcgcaccgct	5	6	10	20	6	0	0	0	0	0	0	3	0	1	0	6	2	2	2	6	2	2	1			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr5:71403432C>T	ENST00000296755.7	+	1	372	c.74C>T	c.(73-75)tCg>tTg	p.S25L	MAP1B_ENST00000504183.1_3'UTR	NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	25					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)		GCGTCCACCTCGCCTAGCCTG	0.682																																					p.S25L	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.C74T						PASS	.						28	25	26					5																	71403432		2201	4299	6500	SO:0001583	missense	4131	exon1			CCACCTCGCCTAG	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.74C>T	chr5.hg19:g.71403432C>T	ENSP00000296755:p.Ser25Leu	74.0	0.0	.		72.0	35.0	.	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	hg19	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.696927	0.88830	.	.	ENSG00000131711	ENST00000512974;ENST00000296755;ENST00000511641	T;T	0.06449	3.86;3.3	5.02	5.02	0.67125	.	0.000000	0.47455	D	0.000230	T	0.19005	0.0456	L	0.50333	1.59	0.58432	D	0.999996	D	0.76494	0.999	P	0.61275	0.886	T	0.00144	-1.1994	10	0.66056	D	0.02	-7.1031	18.5265	0.90974	0.0:1.0:0.0:0.0	.	25	P46821	MAP1B_HUMAN	L	25	ENSP00000296755:S25L;ENSP00000423444:S25L	ENSP00000296755:S25L	S	+	2	0	MAP1B	71439188	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	5.355000	0.66046	2.606000	0.88127	0.561000	0.74099	TCG	.	.	.	none		0.682	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		T	71403432	C	T	71403432	3	4	215	1	0	0	0	0	1	0	0	0	9235	893	31	1	76	1	MAP1B	5	71403432	Missense_Mutation	SNP	C	TCGA-J7-A8I2-01A-12D-A35Z-10		71403432	109511828	20	13049											
SCIN	85477	hgsc.bcm.edu	37	chr7	12689143	12689143	+	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	atgatttagctgaagatgatGtcatgttactagatgcttgg	11	15	11	4	0	1	5	1	3	0	2	1	5	1	5	0	1	3	3	0	1	4	5			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr7:12689143G>T	ENST00000297029.5	+	14	2034	c.1933G>T	c.(1933-1935)Gtc>Ttc	p.V645F	SCIN_ENST00000519209.1_Missense_Mutation_p.V398F|SCIN_ENST00000445618.2_Missense_Mutation_p.V398F	NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	645	Ca(2+)-dependent actin binding.				actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	17				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		TGAAGATGATGTCATGTTACT	0.353																																					p.V645F		Atlas-SNP	.											.	SCIN	105	.	0			c.G1933T						PASS	.						98	92	94					7																	12689143		1869	4107	5976	SO:0001583	missense	85477	exon14			GATGATGTCATGT	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.1933G>T	chr7.hg19:g.12689143G>T	ENSP00000297029:p.Val645Phe	110.0	0.0	.		158.0	69.0	.	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Missense_Mutation	SNP	ENST00000297029.5	hg19	CCDS47545.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.872781	0.91587	.	.	ENSG00000006747	ENST00000297029;ENST00000519209;ENST00000445618	T;T;T	0.30448	1.53;1.53;1.53	5.6	5.6	0.85130	Gelsolin domain (1);	0.058409	0.64402	D	0.000003	T	0.70842	0.3270	H	0.96080	3.765	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.80169	-0.1494	10	0.87932	D	0	-21.0868	20.0086	0.97443	0.0:0.0:1.0:0.0	.	645	Q9Y6U3	ADSV_HUMAN	F	645;398;398	ENSP00000297029:V645F;ENSP00000430997:V398F;ENSP00000390189:V398F	ENSP00000297029:V645F	V	+	1	0	SCIN	12655668	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.174000	0.94824	2.814000	0.96858	0.655000	0.94253	GTC	.	.	.	none		0.353	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128		T	12689143	G	T	12689143	3	4	215	1	0	0	0	0	1	0	0	0	13918	1377	48	4	1987	4	SCIN	7	12689143	Missense_Mutation	SNP	G	TCGA-J7-A8I2-01A-12D-A35Z-10		12689143	146449520	21	13050											
RALA	5898	hgsc.bcm.edu	37	chr7	39736427	39736427	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaatgttaactacgtggaaaCatctgctaaaacacgagcta	16	9	8	8	2	1	0	0	0	1	0	1	3	1	1	0	1	6	3	0	1	7	4			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr7:39736427C>T	ENST00000005257.2	+	4	847	c.467C>T	c.(466-468)aCa>aTa	p.T156I	RALA_ENST00000468201.1_3'UTR	NM_005402.3	NP_005393.2	P11233	RALA_HUMAN	v-ral simian leukemia viral oncogene homolog A (ras related)	156					actin cytoskeleton reorganization (GO:0031532)|chemotaxis (GO:0006935)|cytokinesis (GO:0000910)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|membrane raft localization (GO:0051665)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of filopodium assembly (GO:0051491)|Ras protein signal transduction (GO:0007265)|regulation of exocytosis (GO:0017157)|signal transduction (GO:0007165)|viral process (GO:0016032)	cell surface (GO:0009986)|cleavage furrow (GO:0032154)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	Edg-2 lysophosphatidic acid receptor binding (GO:0031755)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(9)|skin(3)	16						TACGTGGAAACATCTGCTAAA	0.378																																					p.T156I		Atlas-SNP	.											.	RALA	39	.	0			c.C467T						PASS	.						108	99	102					7																	39736427		2203	4300	6503	SO:0001583	missense	5898	exon4			TGGAAACATCTGC		CCDS5460.1	7p22-p15	2014-05-09			ENSG00000006451	ENSG00000006451			9839	protein-coding gene	gene with protein product	"RAS-like protein A", "Ras-related protein Ral-A", "Ras family small GTP binding protein RALA", "ras related GTP binding protein A"	179550		RAL		3292391	Standard	NM_005402		Approved		uc003thd.3	P11233	OTTHUMG00000128775	ENST00000005257.2:c.467C>T	chr7.hg19:g.39736427C>T	ENSP00000005257:p.Thr156Ile	308.0	0.0	.		318.0	137.0	.	NM_005402	A4D1W3	Missense_Mutation	SNP	ENST00000005257.2	hg19	CCDS5460.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.750870	0.89753	.	.	ENSG00000006451	ENST00000005257	T	0.80653	-1.4	4.84	4.84	0.62591	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.91136	0.7209	M	0.86953	2.85	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92791	0.6248	10	0.87932	D	0	.	18.3322	0.90274	0.0:1.0:0.0:0.0	.	156	P11233	RALA_HUMAN	I	156	ENSP00000005257:T156I	ENSP00000005257:T156I	T	+	2	0	RALA	39702952	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.814000	0.86154	2.396000	0.81511	0.563000	0.77884	ACA	.	.	.	none		0.378	RALA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250696.2	NM_005402		T	39736427	C	T	39736427	3	4	215	1	0	0	0	0	1	0	0	0	13023	478	17	2	477	2	RALA	7	39736427	Missense_Mutation	SNP	C	TCGA-J7-A8I2-01A-12D-A35Z-10	27047284	39736427	119402236	22	13051											
COL14A1	7373	hgsc.bcm.edu	37	chr8	121243856	121243856	+	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	tgaggaagaagtcataggaaCggtctgtataaattcaactg	15	10	11	5	1	3	2	2	1	1	1	3	4	3	4	0	3	2	1	0	3	8	4	rs145606030		TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr8:121243856C>T	ENST00000297848.3	+	19	2618	c.2348C>T	c.(2347-2349)aCg>aTg	p.T783M	COL14A1_ENST00000247781.3_Splice_Site_p.T688M|COL14A1_ENST00000309791.4_Splice_Site_p.T783M|COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000537875.1_3'UTR	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1											NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			GTCATAGGAACGGTCTGTATA	0.443																																					p.T783M		Atlas-SNP	.											.	COL14A1	292	.	0			c.C2348T						PASS	.	C	MET/THR	2,4404	4.2+/-10.8	0,2,2201	78	72	74		2348	3.7	1	8	dbSNP_134	74	0,8600		0,0,4300	yes	missense-near-splice	COL14A1	NM_021110.1	81	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging	783/1797	121243856	2,13004	2203	4300	6503	SO:0001630	splice_region_variant	7373	exon19			TAGGAACGGTCTG		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.2349+1C>T	chr8.hg19:g.121243856C>T		126.0	0.0	.		112.0	54.0	.	NM_021110		Missense_Mutation	SNP	ENST00000297848.3	hg19	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	C	16.23	3.063760	0.55432	4.54E-4	0.0	ENSG00000187955	ENST00000309791;ENST00000297848;ENST00000247781;ENST00000434620	T;T;T;T	0.58652	0.32;0.32;0.32;0.32	5.55	3.66	0.41972	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.236035	0.30109	N	0.010396	T	0.59142	0.2172	L	0.36672	1.1	0.80722	D	1	D;B	0.71674	0.998;0.359	P;B	0.58660	0.843;0.142	T	0.58612	-0.7606	10	0.62326	D	0.03	.	8.7818	0.34795	0.0:0.8126:0.0:0.1874	.	783;783	Q05707-2;Q05707	.;COEA1_HUMAN	M	783;783;688;596	ENSP00000311809:T783M;ENSP00000297848:T783M;ENSP00000247781:T688M;ENSP00000409461:T596M	ENSP00000247781:T688M	T	+	2	0	COL14A1	121313037	1.000000	0.71417	1.000000	0.80357	0.740000	0.42216	0.599000	0.24089	0.640000	0.30582	-0.367000	0.07326	ACG	.	C|1.000;T|0.000	0.000	weak		0.443	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110	Missense_Mutation	T	121243856	C	T	121243856	5	4	215	1	0	0	0	0	0	0	1	0	3673	550	19	1	2418	1	COL14A1	8	121243856	Splice_Site	SNP	C	TCGA-J7-A8I2-01A-12D-A35Z-10		121243856	25120166	23	13052											
EPPK1	83481	hgsc.bcm.edu	37	chr8	144946578	144946578	+	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	ggccacgctgccggtaccctCcaggtagcgccgcacctcgg	5	5	13	18	5	0	0	0	0	0	0	2	0	1	0	6	4	3	4	6	4	2	2			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr8:144946578C>A	ENST00000525985.1	-	2	915	c.844G>T	c.(844-846)Gag>Tag	p.E282*				P58107	EPIPL_HUMAN	epiplakin 1	282						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)			CCGGTACCCTCCAGGTAGCGC	0.687																																					p.E282X		Atlas-SNP	.											.	EPPK1	199	.	0			c.G844T						PASS	.						20	26	24					8																	144946578		2160	4242	6402	SO:0001587	stop_gained	83481	exon1			TACCCTCCAGGTA	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.844G>T	chr8.hg19:g.144946578C>A	ENSP00000436337:p.Glu282*	54.0	0.0	.		54.0	21.0	.	NM_031308	Q76E58|Q9NSU9	Nonsense_Mutation	SNP	ENST00000525985.1	hg19		.	.	.	.	.	.	.	.	.	.	C	18.67	3.673779	0.67928	.	.	ENSG00000227184	ENST00000525985	.	.	.	4.81	-0.522	0.11928	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.13108	T	0.6	.	11.5156	0.50520	0.0:0.2877:0.6244:0.0879	.	.	.	.	X	282	.	ENSP00000436337:E282X	E	-	1	0	EPPK1	145018566	0.000000	0.05858	0.799000	0.32177	0.177000	0.22998	-0.810000	0.04505	-0.304000	0.08843	0.511000	0.50034	GAG	.	.	.	none		0.687	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		A	144946578	C	A	144946578	4	1	215	1	0	0	0	0	0	1	0	0	5192	864	30	4	6422	4	EPPK1	8	144946578	Nonsense_Mutation	SNP	C	TCGA-J7-A8I2-01A-12D-A35Z-10	23702722	144946578	1417444	24	13053											
HKDC1	80201	hgsc.bcm.edu	37	chr10	71010157	71010157	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtacaacaagatcttcgccaTccccctggagatcatgcagg	11	8	9	13	1	2	2	1	0	1	2	4	3	3	2	3	2	3	2	3	2	3	2			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr10:71010157T>C	ENST00000354624.5	+	11	1815	c.1682T>C	c.(1681-1683)aTc>aCc	p.I561T	HKDC1_ENST00000395086.2_Missense_Mutation_p.I561T	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	561	Hexokinase type-1 2.				carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)	cytosol (GO:0005829)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|mannokinase activity (GO:0019158)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						ATCTTCGCCATCCCCCTGGAG	0.592																																					p.I561T		Atlas-SNP	.											.	HKDC1	98	.	0			c.T1682C						PASS	.						114	99	104					10																	71010157		2203	4300	6503	SO:0001583	missense	80201	exon11			TCGCCATCCCCCT		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.1682T>C	chr10.hg19:g.71010157T>C	ENSP00000346643:p.Ile561Thr	79.0	0.0	.		86.0	5.0	.	NM_025130	B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Missense_Mutation	SNP	ENST00000354624.5	hg19	CCDS7288.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.417035	0.83449	.	.	ENSG00000156510	ENST00000354624;ENST00000395087;ENST00000395086	D;D	0.98717	-5.09;-5.09	4.98	4.98	0.66077	Hexokinase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99217	0.9728	M	0.90542	3.125	0.54753	D	0.999989	P	0.48230	0.907	D	0.69479	0.964	D	0.99075	1.0835	10	0.72032	D	0.01	-20.7428	14.8099	0.69985	0.0:0.0:0.0:1.0	.	561	Q2TB90	HKDC1_HUMAN	T	561	ENSP00000346643:I561T;ENSP00000378521:I561T	ENSP00000346643:I561T	I	+	2	0	HKDC1	70680163	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.831000	0.86748	2.090000	0.63153	0.459000	0.35465	ATC	.	.	.	none		0.592	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048389.1	NM_025130		C	71010157	T	C	71010157	3	2	215	1	0	0	0	0	1	0	0	0	7200	1435	50	3	1724	3	HKDC1	10	71010157	Missense_Mutation	SNP	T	TCGA-J7-A8I2-01A-12D-A35Z-10		71010157	64524590	25	13054											
USP47	55031	hgsc.bcm.edu	37	chr11	11971443	11971443	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttatatttctagccatgcaAgtttctgctagatgctgtgt	8	18	8	7	0	2	1	0	0	2	1	2	1	2	1	1	0	4	4	1	0	5	7			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr11:11971443A>G	ENST00000399455.2	+	24	3536	c.3416A>G	c.(3415-3417)aAg>aGg	p.K1139R	USP47_ENST00000539466.1_5'UTR|USP47_ENST00000527733.1_Missense_Mutation_p.K1119R|USP47_ENST00000339865.5_Missense_Mutation_p.K1051R	NM_001282659.1	NP_001269588.1	Q96K76	UBP47_HUMAN	ubiquitin specific peptidase 47	1139					base-excision repair (GO:0006284)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell growth (GO:0030307)|response to drug (GO:0042493)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-specific protease activity (GO:0004843)|WD40-repeat domain binding (GO:0071987)			breast(4)|endometrium(7)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46				Epithelial(150;0.000339)		TAGCCATGCAAGTTTCTGCTA	0.323																																					p.K1051R		Atlas-SNP	.											.	USP47	91	.	0			c.A3152G						PASS	.						113	102	105					11																	11971443		1857	4090	5947	SO:0001583	missense	55031	exon22			CATGCAAGTTTCT	AK027362	CCDS41619.1, CCDS60725.1	11p15.2	2008-02-05	2005-08-08		ENSG00000170242	ENSG00000170242		"Ubiquitin-specific peptidases"	20076	protein-coding gene	gene with protein product		614460	"Trf (TATA binding protein-related factor)-proximal homolog (Drosophila)", "ubiquitin specific protease 47"			12838346	Standard	XM_005252997		Approved		uc001mjr.3	Q96K76	OTTHUMG00000165685	ENST00000399455.2:c.3416A>G	chr11.hg19:g.11971443A>G	ENSP00000382382:p.Lys1139Arg	115.0	0.0	.		130.0	43.0	.	NM_017944	B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1	Missense_Mutation	SNP	ENST00000399455.2	hg19		.	.	.	.	.	.	.	.	.	.	A	12.79	2.044265	0.36085	.	.	ENSG00000170242	ENST00000339865;ENST00000527733;ENST00000399455	D;D;D	0.94687	-3.49;-3.49;-3.49	5.37	4.22	0.49857	.	0.045749	0.85682	D	0.000000	D	0.94873	0.8343	L	0.40543	1.245	0.80722	D	1	D;D	0.63880	0.993;0.974	D;D	0.70935	0.971;0.969	D	0.94365	0.7591	10	0.51188	T	0.08	.	11.5397	0.50659	0.9251:0.0:0.0749:0.0	.	1119;1051	E9PM46;Q96K76-2	.;.	R	1051;1119;1139	ENSP00000339957:K1051R;ENSP00000433146:K1119R;ENSP00000382382:K1139R	ENSP00000339957:K1051R	K	+	2	0	USP47	11928019	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.423000	0.80229	2.138000	0.66242	0.533000	0.62120	AAG	.	.	.	none		0.323	USP47-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000385853.2	NM_017944		G	11971443	A	G	11971443	3	3	215	1	0	0	0	0	1	0	0	0	17090	72	3	3	3238	3	USP47	11	11971443	Missense_Mutation	SNP	A	TCGA-J7-A8I2-01A-12D-A35Z-10		11971443	123035073	26	13055											
SLC22A24	283238	hgsc.bcm.edu	37	chr11	62911071	62911071	+	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	gagggtcccggtatcattgtCagacacagtgtcattgtcca	9	11	11	10	1	3	1	3	0	0	1	5	2	5	1	2	2	0	1	2	2	1	3			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr11:62911071C>T	ENST00000417740.1	-	1	622	c.181G>A	c.(181-183)Gac>Aac	p.D61N	SLC22A10_ENST00000525620.1_Intron|SLC22A24_ENST00000326192.5_Missense_Mutation_p.D61N	NM_001136506.2	NP_001129978.2	Q8N4F4	S22AO_HUMAN	solute carrier family 22, member 24	61					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				kidney(1)|stomach(1)	2						GTATCATTGTCAGACACAGTG	0.517																																					p.D61N		Atlas-SNP	.											.	SLC22A24	31	.	0			c.G181A						PASS	.						109	108	108					11																	62911071		692	1591	2283	SO:0001583	missense	283238	exon1			CATTGTCAGACAC		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.181G>A	chr11.hg19:g.62911071C>T	ENSP00000396586:p.Asp61Asn	124.0	0.0	.		108.0	49.0	.	NM_001136506		Missense_Mutation	SNP	ENST00000417740.1	hg19		.	.	.	.	.	.	.	.	.	.	C	2.174	-0.389127	0.04932	.	.	ENSG00000197658	ENST00000417740;ENST00000531535;ENST00000326192	T;T	0.34859	1.34;1.34	2.29	-0.153	0.13403	.	2.737860	0.02513	N	0.091716	T	0.31638	0.0803	L	0.42686	1.345	0.09310	N	1	B	0.23442	0.085	B	0.23852	0.049	T	0.19549	-1.0302	10	0.17832	T	0.49	.	9.282	0.37733	0.0:0.5823:0.4177:0.0	.	61	C9JC66	.	N	61	ENSP00000396586:D61N;ENSP00000321549:D61N	ENSP00000321549:D61N	D	-	1	0	SLC22A24	62667647	0.000000	0.05858	0.024000	0.17045	0.632000	0.37999	-0.569000	0.05902	0.298000	0.22638	-0.890000	0.02929	GAC	.	.	.	none		0.517	SLC22A24-003	PUTATIVE	non_canonical_polymorphism|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000383747.1	NM_173586		T	62911071	C	T	62911071	3	4	215	1	0	0	0	0	1	0	0	0	14466	826	29	2	1512	2	SLC22A24	11	62911071	Missense_Mutation	SNP	C	TCGA-J7-A8I2-01A-12D-A35Z-10	50939628	62911071	72095445	27	13056											
KLC2	64837	hgsc.bcm.edu	37	chr11	66026154	66026155	+	Frame_Shift_Del	DEL	CT	CT	-																															tgtcatccagggactggagaCtctgcgtggggagcatcgtg																								rs546719017		TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr11:66026154_66026155delCT	ENST00000417856.1	+	2	332_333	c.89_90delCT	c.(88-90)actfs	p.T30fs	KLC2_ENST00000421552.1_Frame_Shift_Del_p.T30fs|KLC2_ENST00000394067.2_Frame_Shift_Del_p.T30fs|KLC2_ENST00000394065.2_5'Flank|KLC2_ENST00000316924.5_Frame_Shift_Del_p.T30fs|RP11-755F10.3_ENST00000533576.1_RNA|KLC2_ENST00000394066.2_Frame_Shift_Del_p.T30fs|KLC2_ENST00000394078.1_Frame_Shift_Del_p.T30fs	NM_001134775.1	NP_001128247.1	Q9H0B6	KLC2_HUMAN	kinesin light chain 2	30					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon cargo transport (GO:0008088)|blood coagulation (GO:0007596)|microtubule-based movement (GO:0007018)	ciliary rootlet (GO:0035253)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinesin I complex (GO:0016938)|membrane (GO:0016020)|microtubule (GO:0005874)|neuron projection (GO:0043005)|protein complex (GO:0043234)	kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)			breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	24						GGACTGGAGACTCTGCGTGGGG	0.653											OREG0021097	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.30_30del		Atlas-Indel,Pindel	.											.	KLC2	50	.	0			c.88_89del						PASS	.																																			SO:0001589	frameshift_variant	64837	exon2			.	AK022449	CCDS8130.1, CCDS44653.1	11q13.1	2013-01-10			ENSG00000174996	ENSG00000174996		"Tetratricopeptide (TTC) repeat domain containing"	20716	protein-coding gene	gene with protein product		611729				9624122	Standard	NM_022822		Approved	FLJ12387	uc001ohb.2	Q9H0B6	OTTHUMG00000133757	ENST00000417856.1:c.89_90delCT	chr11.hg19:g.66026156_66026157delCT	ENSP00000399403:p.Thr30fs	103.0	0.0	0	1088	103.0	50.0	0.485437	NM_001134774	A8MXL7|B2RDY4|Q9H9C8|Q9HA20	Frame_Shift_Del	DEL	ENST00000417856.1	hg19	CCDS8130.1																																																																																			.	.	.	none		0.653	KLC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258200.1	NM_022822		-	66026155	CT	-	66026154	7	5	215	1	0	1	0	1	0	0	0	0	8341	565	20	0	91	0	KLC2	11	66026154	Frame_Shift_Del	DEL	CT	TCGA-J7-A8I2-01A-12D-A35Z-10	3115083	66026154	68980362	28	13057											
NPAS4	266743	hgsc.bcm.edu	37	chr11	66190272	66190272	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctactgggcaggaaatccCgtgttcacagctttctgtgc	7	11	11	12	1	2	0	1	0	1	0	3	1	3	1	2	2	3	3	2	2	2	3	rs569596792		TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr11:66190272C>T	ENST00000311034.2	+	4	734	c.558C>T	c.(556-558)ccC>ccT	p.P186P		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	186					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						CAGGAAATCCCGTGTTCACAG	0.637																																					p.P186P		Atlas-SNP	.											.	NPAS4	133	.	0			c.C558T						PASS	.						104	102	103					11																	66190272		2200	4295	6495	SO:0001819	synonymous_variant	266743	exon4			AAATCCCGTGTTC	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.558C>T	chr11.hg19:g.66190272C>T		88.0	0.0	.		88.0	47.0	.	NM_178864	B7ZL81|Q8N8S5|Q8N9Q9	Silent	SNP	ENST00000311034.2	hg19	CCDS8138.1																																																																																			.	.	.	none		0.637	NPAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392634.1	NM_178864		T	66190272	C	T	66190272	2	4	215	1	0	0	0	0	0	0	0	1	10572	639	23	1		1	NPAS4	11	66190272	Silent	SNP	C	TCGA-J7-A8I2-01A-12D-A35Z-10	164118	66190272	68816244	29	13058											
YAP1	10413	hgsc.bcm.edu	37	chr11	102033201	102033201	+	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	tcttagtcacatcgatcagaCaacaacatggcaggacccca	14	7	7	13	1	3	1	2	0	1	1	4	3	3	2	2	2	2	1	2	2	3	1			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr11:102033201C>T	ENST00000282441.5	+	3	975	c.587C>T	c.(586-588)aCa>aTa	p.T196I	YAP1_ENST00000524575.1_Missense_Mutation_p.T18I|YAP1_ENST00000531439.1_Missense_Mutation_p.T196I|YAP1_ENST00000345877.2_Missense_Mutation_p.T196I|YAP1_ENST00000526343.1_Missense_Mutation_p.T196I|YAP1_ENST00000537274.1_Missense_Mutation_p.T196I	NM_001130145.2|NM_001282101.1	NP_001123617.1|NP_001269030.1	P46937	YAP1_HUMAN	Yes-associated protein 1	196	WW 1. {ECO:0000255|PROSITE- ProRule:PRU00224}.				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)		ATCGATCAGACAACAACATGG	0.473																																					p.T196I	Colon(50;247 1103 7861 28956)	Atlas-SNP	.											.	YAP1	45	.	0			c.C587T						PASS	.						184	181	182					11																	102033201		2203	4299	6502	SO:0001583	missense	10413	exon3			ATCAGACAACAAC		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.587C>T	chr11.hg19:g.102033201C>T	ENSP00000282441:p.Thr196Ile	67.0	0.0	.		88.0	37.0	.	NM_001130145	B4DTY1|B7ZA01|E3WEB5|E3WEB6|E9PRV2|F5H202|K0KQ18|K0KYZ8|K0L195|K0L1G3|Q7Z574|Q8IUY9	Missense_Mutation	SNP	ENST00000282441.5	hg19	CCDS44716.1	.	.	.	.	.	.	.	.	.	.	C	15.30	2.791911	0.50102	.	.	ENSG00000137693	ENST00000526343;ENST00000282441;ENST00000537274;ENST00000345877;ENST00000445250;ENST00000531439;ENST00000524575	D;D;D;D;D;T	0.83837	-1.77;-1.77;-1.77;-1.77;-1.77;0.86	5.59	5.59	0.84812	WW/Rsp5/WWP (6);	0.000000	0.85682	D	0.000000	D	0.84483	0.5482	L	0.37750	1.13	0.80722	D	1	P;B;B;P;D	0.61080	0.915;0.151;0.167;0.822;0.989	P;B;B;P;P	0.53450	0.653;0.129;0.053;0.494;0.726	D	0.84620	0.0683	10	0.48119	T	0.1	.	19.5866	0.95492	0.0:1.0:0.0:0.0	.	111;196;196;196;196	F5GWC5;E9PRV2;P46937-2;P46937;P46937-3	.;.;.;YAP1_HUMAN;.	I	196;196;196;196;111;196;18	ENSP00000434134:T196I;ENSP00000282441:T196I;ENSP00000445635:T196I;ENSP00000331023:T196I;ENSP00000431574:T196I;ENSP00000435602:T18I	ENSP00000282441:T196I	T	+	2	0	YAP1	101538411	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.463000	0.73530	2.620000	0.88729	0.555000	0.69702	ACA	.	.	.	none		0.473	YAP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394151.1	NM_006106		T	102033201	C	T	102033201	3	4	215	1	0	0	0	0	1	0	0	0	17478	478	17	2	597	2	YAP1	11	102033201	Missense_Mutation	SNP	C	TCGA-J7-A8I2-01A-12D-A35Z-10	35842929	102033201	32973315	30	13059											
SH2B3	10019	hgsc.bcm.edu	37	chr12	111885593	111885593	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggcgccgcctgtgatgtccGgctctccagctacgtggtag	4	9	14	14	5	1	1	0	1	1	0	3	1	2	1	4	3	2	3	4	3	2	2			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr12:111885593G>A	ENST00000341259.2	+	7	1727	c.1370G>A	c.(1369-1371)cGg>cAg	p.R457Q	SH2B3_ENST00000538307.1_Missense_Mutation_p.R255Q	NM_005475.2	NP_005466.1	Q9UQQ2	SH2B3_HUMAN	SH2B adaptor protein 3	457	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|embryonic hemopoiesis (GO:0035162)|intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)	phosphate ion binding (GO:0042301)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	10					Pazopanib(DB06589)	TGTGATGTCCGGCTCTCCAGC	0.632																																					p.R457Q		Atlas-SNP	.											.	SH2B3	62	.	0			c.G1370A						PASS	.						69	61	64					12																	111885593		2203	4300	6503	SO:0001583	missense	10019	exon7			ATGTCCGGCTCTC	AF055581	CCDS9153.1	12q24.12	2014-09-17				ENSG00000111252		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	29605	protein-coding gene	gene with protein product	"lymphocyte adaptor protein"	605093				10799879	Standard	NM_005475		Approved	LNK, IDDM20	uc001tse.3	Q9UQQ2		ENST00000341259.2:c.1370G>A	chr12.hg19:g.111885593G>A	ENSP00000345492:p.Arg457Gln	89.0	0.0	.		82.0	43.0	.	NM_005475	B9EGG5|O95184	Missense_Mutation	SNP	ENST00000341259.2	hg19	CCDS9153.1	.	.	.	.	.	.	.	.	.	.	G	14.58	2.577538	0.45902	.	.	ENSG00000111252	ENST00000341259;ENST00000551001;ENST00000538307	T;T	0.53857	0.6;0.6	4.96	3.81	0.43845	SH2 motif (1);	0.405045	0.26251	N	0.025457	T	0.26666	0.0652	N	0.08118	0	0.32839	D	0.505132	B;B;B	0.31351	0.123;0.222;0.32	B;B;B	0.28465	0.04;0.013;0.09	T	0.28618	-1.0038	10	0.26408	T	0.33	.	7.2579	0.26187	0.2705:0.0:0.7295:0.0	.	255;321;457	F5GYM4;Q59H48;Q9UQQ2	.;.;SH2B3_HUMAN	Q	457;267;255	ENSP00000345492:R457Q;ENSP00000440597:R255Q	ENSP00000345492:R457Q	R	+	2	0	SH2B3	110369976	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	3.131000	0.50515	2.474000	0.83562	0.462000	0.41574	CGG	.	.	.	none		0.632	SH2B3-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000404779.1	NM_005475		A	111885593	G	A	111885593	3	1	215	1	0	0	0	0	1	0	0	0	14242	1116	39	1	1392	1	SH2B3	12	111885593	Missense_Mutation	SNP	G	TCGA-J7-A8I2-01A-12D-A35Z-10		111885593	21966302	31	13060											
C12orf51	283450	hgsc.bcm.edu	37	chr12	112607423	112607423	+	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	ctgaggccagctgcctggcaGcctgacagaagtaggagttt	9	8	14	10	0	0	3	0	2	0	1	0	4	0	4	3	3	3	4	3	3	2	2			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr12:112607423G>C	ENST00000430131.2	-	69	11971	c.10826C>G	c.(10825-10827)gCt>gGt	p.A3609G	HECTD4_ENST00000550722.1_Missense_Mutation_p.A3885G|HECTD4_ENST00000377560.5_Missense_Mutation_p.A3859G			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3609					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)										CTGCCTGGCAGCCTGACAGAA	0.602																																					p.A3897G		Atlas-SNP	.											.	.	.	.	0			c.C11690G						PASS	.						46	53	50					12																	112607423		2042	4189	6231	SO:0001583	missense	283450	exon70			CTGGCAGCCTGAC	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.10826C>G	chr12.hg19:g.112607423G>C	ENSP00000404379:p.Ala3609Gly	46.0	0.0	.		48.0	24.0	.	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	G	33	5.232023	0.95207	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722;ENST00000547085	T;T;T	0.50813	0.73;0.74;0.73	5.88	5.88	0.94601	.	.	.	.	.	T	0.58192	0.2105	N	0.24115	0.695	0.58432	D	0.999999	D	0.58970	0.984	D	0.68192	0.956	T	0.61197	-0.7111	9	0.87932	D	0	.	20.2207	0.98324	0.0:0.0:1.0:0.0	.	3609	Q9Y4D8	K0614_HUMAN	G	3859;3609;3885;74	ENSP00000366783:A3859G;ENSP00000404379:A3609G;ENSP00000449784:A3885G	ENSP00000366783:A3859G	A	-	2	0	C12orf51	111091806	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.240000	0.95396	2.790000	0.95986	0.591000	0.81541	GCT	.	.	.	none		0.602	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		C	112607423	G	C	112607423	3	2	215	1	0	0	0	0	1	0	0	0	1698	971	34	4	1192	4	C12orf51	12	112607423	Missense_Mutation	SNP	G	TCGA-J7-A8I2-01A-12D-A35Z-10	721830	112607423	21244472	32	13061											
LPAR6	10161	hgsc.bcm.edu	37	chr13	48985593	48985593	+	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	gttatgctgaataaaattctCtgcaccatgaacttcagaga	14	12	7	8	0	2	3	1	2	1	1	3	4	2	3	1	0	3	3	1	0	5	4			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr13:48985593C>T	ENST00000378434.4	-	7	2591	c.967G>A	c.(967-969)Gag>Aag	p.E323K	LPAR6_ENST00000345941.2_Missense_Mutation_p.E323K|RB1_ENST00000267163.4_Intron	NM_005767.5	NP_005758.2	P43657	LPAR6_HUMAN	lysophosphatidic acid receptor 6	323						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.0?(15)|p.?(4)		NS(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	14						ATAAAATTCTCTGCACCATGA	0.358																																					p.E323K		Atlas-SNP	.											.	LPAR6	38	.	19	Whole gene deletion(15)|Unknown(4)	bone(10)|breast(4)|adrenal_gland(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	c.G967A						PASS	.						79	85	83					13																	48985593		2203	4300	6503	SO:0001583	missense	10161	exon5			AATTCTCTGCACC	AF000546	CCDS9410.1	13q14	2012-08-08	2009-06-23	2009-06-23	ENSG00000139679	ENSG00000139679		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	15520	protein-coding gene	gene with protein product		609239	"purinergic receptor P2Y, G-protein coupled, 5"	P2RY5		11004484, 9755289, 19386608	Standard	NM_005767		Approved	P2Y5	uc010acu.3	P43657	OTTHUMG00000016895	ENST00000378434.4:c.967G>A	chr13.hg19:g.48985593C>T	ENSP00000367691:p.Glu323Lys	145.0	0.0	.		151.0	53.0	.	NM_001162497	A4FTW9|B3KVF2|F2YGU4|O15133|Q3KPF5|Q53FA0|Q5VW44|Q7Z3S0|Q7Z3S6	Missense_Mutation	SNP	ENST00000378434.4	hg19	CCDS9410.1	.	.	.	.	.	.	.	.	.	.	C	14.07	2.426889	0.43020	.	.	ENSG00000139679	ENST00000378434;ENST00000345941	T;T	0.63913	-0.07;-0.07	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.38772	0.1053	N	0.08118	0	0.49687	D	0.999819	P	0.34562	0.457	B	0.27608	0.081	T	0.44544	-0.9321	10	0.06236	T	0.91	.	19.6656	0.95891	0.0:1.0:0.0:0.0	.	323	P43657	LPAR6_HUMAN	K	323	ENSP00000367691:E323K;ENSP00000344353:E323K	ENSP00000344353:E323K	E	-	1	0	LPAR6	47883594	1.000000	0.71417	0.971000	0.41717	0.477000	0.33069	7.445000	0.80570	2.713000	0.92767	0.455000	0.32223	GAG	.	.	.	none		0.358	LPAR6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276280.2	NM_005767		T	48985593	C	T	48985593	3	4	215	1	0	0	0	0	1	0	0	0	8916	922	32	2	71	2	LPAR6	13	48985593	Missense_Mutation	SNP	C	TCGA-J7-A8I2-01A-12D-A35Z-10		48985593	66184285	33	13062											
DZIP1	22873	hgsc.bcm.edu	37	chr13	96264392	96264392	+	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	attgcttgcatttagatcatCtatcattgaggttcgaagtt	10	17	8	6	1	3	2	2	1	1	1	4	3	3	2	0	1	2	4	0	1	3	8			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr13:96264392C>G	ENST00000376829.2	-	11	2064	c.1213G>C	c.(1213-1215)Gat>Cat	p.D405H	DZIP1_ENST00000361156.3_Missense_Mutation_p.D405H|DZIP1_ENST00000347108.3_Missense_Mutation_p.D405H|DZIP1_ENST00000361396.2_Missense_Mutation_p.D405H	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	405					cilium assembly (GO:0042384)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(20)|lung(11)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	38	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			tttagatcatctatcattgAG	0.393																																					p.D405H		Atlas-SNP	.											.	DZIP1	195	.	0			c.G1213C						PASS	.						132	127	129					13																	96264392		2203	4300	6503	SO:0001583	missense	22873	exon11			GATCATCTATCAT	AB023213	CCDS9477.1, CCDS9478.1	13q32.1	2013-05-22	2013-05-22		ENSG00000134874	ENSG00000134874		"Zinc fingers, C2H2-type"	20908	protein-coding gene	gene with protein product		608671	"DAZ interacting protein 1"				Standard	NM_014934		Approved	KIAA0996, DZIP	uc001vmk.4	Q86YF9	OTTHUMG00000017224	ENST00000376829.2:c.1213G>C	chr13.hg19:g.96264392C>G	ENSP00000366025:p.Asp405His	55.0	0.0	.		65.0	24.0	.	NM_014934	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Missense_Mutation	SNP	ENST00000376829.2	hg19	CCDS9478.1	.	.	.	.	.	.	.	.	.	.	C	17.12	3.309415	0.60414	.	.	ENSG00000134874	ENST00000347108;ENST00000361156;ENST00000361396;ENST00000376829	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.88	5.03	0.67393	.	0.467342	0.23349	N	0.049157	T	0.43743	0.1261	L	0.47716	1.5	0.28469	N	0.915509	D;P	0.53151	0.958;0.855	P;B	0.48627	0.584;0.38	T	0.43426	-0.9392	10	0.59425	D	0.04	-3.0786	11.3767	0.49733	0.0:0.914:0.0:0.086	.	405;405	Q86YF9-2;Q86YF9	.;DZIP1_HUMAN	H	405	ENSP00000257312:D405H;ENSP00000355018:D405H;ENSP00000355175:D405H;ENSP00000366025:D405H	ENSP00000257312:D405H	D	-	1	0	DZIP1	95062393	0.996000	0.38824	0.977000	0.42913	0.780000	0.44128	1.178000	0.31981	1.458000	0.47871	0.655000	0.94253	GAT	.	.	.	none		0.393	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934		G	96264392	C	G	96264392	3	3	215	1	0	0	0	0	1	0	0	0	4865	913	32	4	1442	4	DZIP1	13	96264392	Missense_Mutation	SNP	C	TCGA-J7-A8I2-01A-12D-A35Z-10	47278799	96264392	18905486	34	13063											
SIX1	6495	hgsc.bcm.edu	37	chr14	61115779	61115780	+	Frame_Shift_Ins	INS	-	-	A																															gtacgctctcgttcttgtgcINSaggtggtcgcaggcgggcag																										TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr14:61115779_61115780insA	ENST00000247182.6	-	1	400_401	c.128_129insT	c.(127-129)ctgfs	p.L43fs	SIX1_ENST00000554986.1_Intron	NM_005982.3	NP_005973.1	Q15475	SIX1_HUMAN	SIX homeobox 1	43					aorta morphogenesis (GO:0035909)|apoptotic process (GO:0006915)|branching involved in ureteric bud morphogenesis (GO:0001658)|cochlea morphogenesis (GO:0090103)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic skeletal system morphogenesis (GO:0048704)|epithelial cell differentiation (GO:0030855)|facial nerve morphogenesis (GO:0021610)|generation of neurons (GO:0048699)|inner ear development (GO:0048839)|inner ear morphogenesis (GO:0042472)|kidney development (GO:0001822)|mesonephric tubule formation (GO:0072172)|metanephric mesenchyme development (GO:0072075)|middle ear morphogenesis (GO:0042474)|myoblast migration (GO:0051451)|negative regulation of branching involved in ureteric bud morphogenesis (GO:0090191)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate specification (GO:0048665)|organ induction (GO:0001759)|otic vesicle development (GO:0071599)|outflow tract morphogenesis (GO:0003151)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of mesenchymal cell proliferation involved in ureter development (GO:2000729)|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)|positive regulation of ureteric bud formation (GO:0072107)|protein localization to nucleus (GO:0034504)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of neuron differentiation (GO:0045664)|regulation of protein localization (GO:0032880)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|skeletal muscle tissue development (GO:0007519)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	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)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	13				OV - Ovarian serous cystadenocarcinoma(108;0.0201)		CGTTCTTGTGCAGGTGGTCGCA	0.634																																					p.L43fs		Atlas-Indel,Pindel	.											.	SIX1	40	.	0			c.129_130insT						PASS	.																																			SO:0001589	frameshift_variant	6495	exon1			.	X91868	CCDS9748.1	14q23.1	2011-06-20	2007-07-13		ENSG00000126778	ENSG00000126778		"Homeoboxes / SINE class"	10887	protein-coding gene	gene with protein product		601205	"sine oculis homeobox (Drosophila) homolog 1", "sine oculis homeobox homolog 1 (Drosophila)", "deafness, autosomal dominant 23"	DFNA23		8617500, 15141091	Standard	NM_005982		Approved		uc001xfb.4	Q15475	OTTHUMG00000140334	ENST00000247182.6:c.129dupT	chr14.hg19:g.61115780_61115780dupA	ENSP00000247182:p.Leu43fs	100.0	0.0	0		79.0	33.0	0.417722	NM_005982	Q53Y16|Q96H64	Frame_Shift_Ins	INS	ENST00000247182.6	hg19	CCDS9748.1																																																																																			.	.	.	none		0.634	SIX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276951.3			A	61115780	-	A	61115779	7	5	215	1	0	1	1	0	0	0	0	0	14359	697	25	0	733	0	SIX1	14	61115779	Frame_Shift_Ins	INS	-	TCGA-J7-A8I2-01A-12D-A35Z-10		61115779	46233761	35	13064											
HIF1A	3091	hgsc.bcm.edu	37	chr14	62213681	62213681	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtagactgctggggcaatcaAtggatgaaagtggattacca	13	9	13	6	0	1	2	1	1	0	1	1	4	1	4	1	4	2	3	1	4	5	2			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr14:62213681A>G	ENST00000337138.4	+	15	2624	c.2359A>G	c.(2359-2361)Atg>Gtg	p.M787V	HIF1A-AS2_ENST00000554254.1_lincRNA|RP11-618G20.1_ENST00000555937.1_RNA|HIF1A_ENST00000394997.1_Missense_Mutation_p.M788V|HIF1A_ENST00000539097.1_Missense_Mutation_p.M811V|HIF1A_ENST00000323441.6_3'UTR|HIF1A_ENST00000557538.1_Missense_Mutation_p.M728V	NM_001530.3	NP_001521.1	Q16665	HIF1A_HUMAN	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	787	CTAD.				angiogenesis (GO:0001525)|axon transport of mitochondrion (GO:0019896)|B-1 B cell homeostasis (GO:0001922)|cardiac ventricle morphogenesis (GO:0003208)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cerebral cortex development (GO:0021987)|collagen metabolic process (GO:0032963)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|digestive tract morphogenesis (GO:0048546)|dopaminergic neuron differentiation (GO:0071542)|elastin metabolic process (GO:0051541)|embryonic hemopoiesis (GO:0035162)|embryonic placenta development (GO:0001892)|epithelial cell differentiation involved in mammary gland alveolus development (GO:0061030)|epithelial to mesenchymal transition (GO:0001837)|glucose homeostasis (GO:0042593)|heart looping (GO:0001947)|hemoglobin biosynthetic process (GO:0042541)|intestinal epithelial cell maturation (GO:0060574)|lactate metabolic process (GO:0006089)|lactation (GO:0007595)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of bone mineralization (GO:0030502)|negative regulation of growth (GO:0045926)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of thymocyte apoptotic process (GO:0070244)|negative regulation of TOR signaling (GO:0032007)|neural crest cell migration (GO:0001755)|neural fold elevation formation (GO:0021502)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|oxygen homeostasis (GO:0032364)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine production (GO:0032722)|positive regulation of chemokine-mediated signaling pathway (GO:0070101)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to muscle activity (GO:0014850)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|vascular endothelial growth factor production (GO:0010573)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|Hsp90 protein binding (GO:0051879)|nuclear hormone receptor binding (GO:0035257)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|endometrium(8)|kidney(6)|large_intestine(3)|lung(4)	23				OV - Ovarian serous cystadenocarcinoma(108;1.62e-09)|BRCA - Breast invasive adenocarcinoma(234;0.189)	Carvedilol(DB01136)	GGGGCAATCAATGGATGAAAG	0.378																																					p.M811V		Atlas-SNP	.											.	HIF1A	120	.	0			c.A2431G						PASS	.						176	166	169					14																	62213681		2203	4300	6503	SO:0001583	missense	3091	exon15			CAATCAATGGATG	U22431	CCDS9753.1, CCDS9754.1, CCDS58324.1	14q23.2	2013-05-21	2008-12-02		ENSG00000100644	ENSG00000100644		"Basic helix-loop-helix proteins"	4910	protein-coding gene	gene with protein product		603348				8786149, 9079689	Standard	NM_001530		Approved	MOP1, HIF-1alpha, PASD8, HIF1, bHLHe78	uc001xfq.2	Q16665	OTTHUMG00000140344	ENST00000337138.4:c.2359A>G	chr14.hg19:g.62213681A>G	ENSP00000338018:p.Met787Val	100.0	0.0	.		125.0	61.0	.	NM_001243084	C0LZJ3|Q53XP6|Q96PT9|Q9UPB1	Missense_Mutation	SNP	ENST00000337138.4	hg19	CCDS9753.1	.	.	.	.	.	.	.	.	.	.	A	7.232	0.599557	0.13939	.	.	ENSG00000100644	ENST00000539494;ENST00000394988;ENST00000337138;ENST00000394997;ENST00000557538;ENST00000539097	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.61	4.44	0.53790	HIF-1 alpha, transactivation domain, C-terminal (1);	0.904790	0.09913	N	0.739514	T	0.25827	0.0629	N	0.08118	0	0.33434	D	0.581479	B;B	0.16802	0.019;0.019	B;B	0.24701	0.055;0.055	T	0.28332	-1.0047	10	0.41790	T	0.15	.	8.144	0.31100	0.7257:0.1403:0.0:0.134	.	788;787	A8MYV6;Q16665	.;HIF1A_HUMAN	V	538;728;787;788;728;811	ENSP00000338018:M787V;ENSP00000378446:M788V;ENSP00000451696:M728V;ENSP00000437955:M811V	ENSP00000338018:M787V	M	+	1	0	HIF1A	61283434	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.513000	0.45494	1.028000	0.39785	0.533000	0.62120	ATG	.	.	.	none		0.378	HIF1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276977.2	NM_001530		G	62213681	A	G	62213681	3	3	215	1	0	0	0	0	1	0	0	0	7110	101	4	3	2417	3	HIF1A	14	62213681	Missense_Mutation	SNP	A	TCGA-J7-A8I2-01A-12D-A35Z-10	1097902	62213681	45135859	36	13065											
TRPM7	54822	hgsc.bcm.edu	37	chr15	50866612	50866612	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttctaaattctccagtcaTacattcttccacagcaaacc	12	14	2	13	0	4	0	1	0	3	0	6	0	5	0	3	0	3	1	3	0	4	7			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr15:50866612T>C	ENST00000313478.7	-	36	5448	c.5167A>G	c.(5167-5169)Atg>Gtg	p.M1723V	TRPM7_ENST00000561443.1_5'UTR|TRPM7_ENST00000560955.1_Missense_Mutation_p.M1722V	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	1723	Alpha-type protein kinase. {ECO:0000255|PROSITE-ProRule:PRU00501}.				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)		TCTCCAGTCATACATTCTTCC	0.348																																					p.M1723V		Atlas-SNP	.											TRPM7,colon,carcinoma,0,2	TRPM7	145	.	0			c.A5167G						PASS	.						60	57	58					15																	50866612		1807	4073	5880	SO:0001583	missense	54822	exon36			CAGTCATACATTC	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.5167A>G	chr15.hg19:g.50866612T>C	ENSP00000320239:p.Met1723Val	77.0	0.0	.		85.0	33.0	.	NM_017672	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	Missense_Mutation	SNP	ENST00000313478.7	hg19	CCDS42035.1	.	.	.	.	.	.	.	.	.	.	T	13.62	2.292013	0.40594	.	.	ENSG00000092439	ENST00000313478	T	0.13657	2.57	4.98	4.98	0.66077	MHCK/EF2 kinase (3);Protein kinase-like domain (1);	0.044676	0.85682	D	0.000000	T	0.14614	0.0353	L	0.37630	1.12	0.45295	D	0.998291	B	0.30193	0.272	B	0.33196	0.159	T	0.04320	-1.0960	10	0.87932	D	0	-18.4568	14.8475	0.70270	0.0:0.0:0.0:1.0	.	1723	Q96QT4	TRPM7_HUMAN	V	1723	ENSP00000320239:M1723V	ENSP00000320239:M1723V	M	-	1	0	TRPM7	48653904	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.942000	0.70203	2.074000	0.62210	0.528000	0.53228	ATG	.	.	.	none		0.348	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672		C	50866612	T	C	50866612	3	2	215	1	0	0	0	0	1	0	0	0	16603	1406	49	3	446	3	TRPM7	15	50866612	Missense_Mutation	SNP	T	TCGA-J7-A8I2-01A-12D-A35Z-10		50866612	51664780	37	13066											
TRPM7	54822	hgsc.bcm.edu	37	chr15	50904864	50904864	+	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	tttagccattgattcttcacCatgttgccataaaaaacggg	12	13	7	9	1	2	1	1	1	1	0	2	1	2	1	3	1	3	1	3	1	4	7			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr15:50904864C>A	ENST00000313478.7	-	16	2214	c.1933G>T	c.(1933-1935)Ggt>Tgt	p.G645C	TRPM7_ENST00000560955.1_Missense_Mutation_p.G645C	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	645					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)	p.G645C(1)		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)		GATTCTTCACCATGTTGCCAT	0.413																																					p.G645C		Atlas-SNP	.											TRPM7,NS,carcinoma,0,1	TRPM7	145	.	1	Substitution - Missense(1)	lung(1)	c.G1933T						PASS	.						163	152	156					15																	50904864		1884	4115	5999	SO:0001583	missense	54822	exon16			CTTCACCATGTTG	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.1933G>T	chr15.hg19:g.50904864C>A	ENSP00000320239:p.Gly645Cys	129.0	0.0	.		109.0	50.0	.	NM_017672	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	Missense_Mutation	SNP	ENST00000313478.7	hg19	CCDS42035.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.878977	0.91740	.	.	ENSG00000092439	ENST00000313478	T	0.73681	-0.77	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	D	0.87406	0.6169	M	0.87381	2.88	0.80722	D	1	D	0.67145	0.996	P	0.61940	0.896	D	0.89507	0.3768	10	0.87932	D	0	-7.094	19.1653	0.93555	0.0:1.0:0.0:0.0	.	645	Q96QT4	TRPM7_HUMAN	C	645	ENSP00000320239:G645C	ENSP00000320239:G645C	G	-	1	0	TRPM7	48692156	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.730000	0.84881	2.603000	0.88011	0.585000	0.79938	GGT	.	.	.	none		0.413	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672		A	50904864	C	A	50904864	3	1	215	1	0	0	0	0	1	0	0	0	16603	594	21	4	3760	4	TRPM7	15	50904864	Missense_Mutation	SNP	C	TCGA-J7-A8I2-01A-12D-A35Z-10	38252	50904864	51626528	38	13067											
SPPL2A	84888	hgsc.bcm.edu	37	chr15	51014331	51014331	+	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	aaaaatttaccaactgtagaCgaaacatagtatatgtaaga	20	10	6	5	1	0	2	0	0	0	2	0	3	0	2	1	0	3	3	1	0	10	7			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr15:51014331C>T	ENST00000261854.5	-	13	1591	c.1317G>A	c.(1315-1317)tcG>tcA	p.S439S	SPPL2A_ENST00000559293.1_5'Flank	NM_032802.3	NP_116191.2	Q8TCT8	SPP2A_HUMAN	signal peptide peptidase like 2A	439					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)		CAACTGTAGACGAAACATAGT	0.294																																					p.S439S	Melanoma(50;790 1209 4069 22965 33125)	Atlas-SNP	.											.	SPPL2A	26	.	0			c.G1317A						PASS	.						72	70	71					15																	51014331		2196	4294	6490	SO:0001819	synonymous_variant	84888	exon13			TGTAGACGAAACA		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.1317G>A	chr15.hg19:g.51014331C>T		78.0	0.0	.		68.0	27.0	.	NM_032802	B2RDS0|Q8TAW1|Q96SZ8	Silent	SNP	ENST00000261854.5	hg19	CCDS10138.1																																																																																			.	.	.	none		0.294	SPPL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254543.3	NM_032802		T	51014331	C	T	51014331	2	4	215	1	0	0	0	0	0	0	0	1	15100	523	19	1		1	SPPL2A	15	51014331	Silent	SNP	C	TCGA-J7-A8I2-01A-12D-A35Z-10	109467	51014331	51517061	39	13068											
NEDD4	4734	hgsc.bcm.edu	37	chr15	56207684	56207684	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcttcgtaaaataccatggTttttgttcatctgtgaatgt	9	19	7	6	1	3	1	1	1	2	0	4	1	3	1	1	1	1	3	1	1	4	7			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr15:56207684T>C	ENST00000508342.1	-	1	1645	c.1346A>G	c.(1345-1347)aAc>aGc	p.N449S	NEDD4_ENST00000506154.1_Missense_Mutation_p.N449S|NEDD4_ENST00000338963.2_Missense_Mutation_p.N449S|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	449					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)		AATACCATGGTTTTTGTTCAT	0.378																																					p.N449S		Atlas-SNP	.											.	NEDD4	167	.	0			c.A1346G						PASS	.						121	120	120					15																	56207684		2193	4292	6485	SO:0001583	missense	4734	exon1			CCATGGTTTTTGT	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.1346A>G	chr15.hg19:g.56207684T>C	ENSP00000424827:p.Asn449Ser	122.0	0.0	.		149.0	70.0	.	NM_198400	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Missense_Mutation	SNP	ENST00000508342.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.169|0.169	-1.073075|-1.073075	0.01918|0.01918	.|.	.|.	ENSG00000069869|ENSG00000069869	ENST00000508342;ENST00000338963;ENST00000506154|ENST00000508871	T;T;T|.	0.18174|.	2.24;2.23;2.24|.	5.46|5.46	-0.0555|-0.0555	0.13809|0.13809	.|.	.|.	.|.	.|.	.|.	T|T	0.36880|0.36880	0.0983|0.0983	L|L	0.47716|0.47716	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|.	0.06405|.	0.002;0.001;0.001|.	T|T	0.31641|0.31641	-0.9936|-0.9936	9|5	0.46703|.	T|.	0.11|.	.|.	6.7263|6.7263	0.23359|0.23359	0.0:0.28:0.1625:0.5575|0.0:0.28:0.1625:0.5575	.|.	449;449;449|.	P46934-2;P46934;P46934-3|.	.;NEDD4_HUMAN;.|.	S|A	449|57	ENSP00000424827:N449S;ENSP00000345530:N449S;ENSP00000422705:N449S|.	ENSP00000345530:N449S|.	N|T	-|-	2|1	0|0	NEDD4|NEDD4	53994976|53994976	0.533000|0.533000	0.26354|0.26354	0.362000|0.362000	0.25862|0.25862	0.881000|0.881000	0.50899|0.50899	-0.132000|-0.132000	0.10467|0.10467	0.072000|0.072000	0.16694|0.16694	0.377000|0.377000	0.23210|0.23210	AAC|ACC	.	.	.	none		0.378	NEDD4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000359817.1	NM_198400		C	56207684	T	C	56207684	3	2	215	1	0	0	0	0	1	0	0	0	10317	1725	60	3	2713	3	NEDD4	15	56207684	Missense_Mutation	SNP	T	TCGA-J7-A8I2-01A-12D-A35Z-10	5193353	56207684	46323708	40	13069											
HERC1	8925	hgsc.bcm.edu	37	chr15	63956789	63956789	+	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	ctctgtatgatccaaattatCagggctacaagtgcaagtga	13	11	9	8	0	2	2	1	2	1	0	3	2	3	2	1	1	2	3	1	1	6	3			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr15:63956789C>T	ENST00000443617.2	-	43	8647	c.8560G>A	c.(8560-8562)Gat>Aat	p.D2854N		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	2854					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						TCCAAATTATCAGGGCTACAA	0.413																																					p.D2854N		Atlas-SNP	.											HERC1_ENST00000443617,right_upper_lobe,carcinoma,0,2	HERC1	624	.	0			c.G8560A						PASS	.						78	76	77					15																	63956789		1915	4128	6043	SO:0001583	missense	8925	exon43			AATTATCAGGGCT	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.8560G>A	chr15.hg19:g.63956789C>T	ENSP00000390158:p.Asp2854Asn	90.0	0.0	.		81.0	32.0	.	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.578366	0.86645	.	.	ENSG00000103657	ENST00000443617	T	0.24151	1.87	5.79	5.79	0.91817	.	0.063428	0.64402	D	0.000010	T	0.21022	0.0506	N	0.22421	0.69	0.80722	D	1	P	0.34522	0.455	B	0.30105	0.111	T	0.02781	-1.1111	10	0.54805	T	0.06	.	20.024	0.97514	0.0:1.0:0.0:0.0	.	2854	Q15751	HERC1_HUMAN	N	2854	ENSP00000390158:D2854N	ENSP00000390158:D2854N	D	-	1	0	HERC1	61743842	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.638000	0.74309	2.718000	0.92993	0.655000	0.94253	GAT	.	.	.	none		0.413	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		T	63956789	C	T	63956789	3	4	215	1	0	0	0	0	1	0	0	0	7064	826	29	2	6169	2	HERC1	15	63956789	Missense_Mutation	SNP	C	TCGA-J7-A8I2-01A-12D-A35Z-10	7749105	63956789	38574603	41	13070											
HERC1	8925	hgsc.bcm.edu	37	chr15	63958332	63958332	+	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	gacagtgatattctgggcatCagcctctcccctagcaccta	9	10	8	14	0	3	1	1	1	2	0	4	2	3	1	4	1	2	2	4	1	3	4			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr15:63958332C>T	ENST00000443617.2	-	42	8428	c.8341G>A	c.(8341-8343)Gat>Aat	p.D2781N		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	2781					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						TTCTGGGCATCAGCCTCTCCC	0.502																																					p.D2781N		Atlas-SNP	.											.	HERC1	624	.	0			c.G8341A						PASS	.						32	33	33					15																	63958332		1999	4164	6163	SO:0001583	missense	8925	exon42			GGGCATCAGCCTC	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.8341G>A	chr15.hg19:g.63958332C>T	ENSP00000390158:p.Asp2781Asn	146.0	0.0	.		169.0	73.0	.	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.978618	0.92982	.	.	ENSG00000103657	ENST00000443617	T	0.36340	1.26	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.52661	0.1748	L	0.40543	1.245	0.80722	D	1	D	0.63880	0.993	D	0.74674	0.984	T	0.34551	-0.9824	10	0.30078	T	0.28	.	19.8218	0.96599	0.0:1.0:0.0:0.0	.	2781	Q15751	HERC1_HUMAN	N	2781	ENSP00000390158:D2781N	ENSP00000390158:D2781N	D	-	1	0	HERC1	61745385	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.800000	0.85949	2.678000	0.91216	0.655000	0.94253	GAT	.	.	.	none		0.502	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		T	63958332	C	T	63958332	3	4	215	1	0	0	0	0	1	0	0	0	7064	826	29	2	6392	2	HERC1	15	63958332	Missense_Mutation	SNP	C	TCGA-J7-A8I2-01A-12D-A35Z-10	1543	63958332	38573060	42	13071											
BCL2A1	597	hgsc.bcm.edu	37	chr15	80263200	80263200	+	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	tgcaaatatggttacaattcTtccccagttaatgatgccgt	11	14	7	9	1	1	1	0	1	1	0	2	1	2	1	3	1	3	3	3	1	5	5			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr15:80263200T>G	ENST00000267953.3	-	1	588	c.262A>C	c.(262-264)Aga>Cga	p.R88R	BCL2A1_ENST00000335661.6_Silent_p.R88R	NM_004049.3	NP_004040.1	Q16548	B2LA1_HUMAN	BCL2-related protein A1	88					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						GTTACAATTCTTCCCCAGTTA	0.393																																					p.R88R		Atlas-SNP	.											.	BCL2A1	28	.	0			c.A262C						PASS	.						206	195	199					15																	80263200		2203	4300	6503	SO:0001819	synonymous_variant	597	exon1			CAATTCTTCCCCA		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.262A>C	chr15.hg19:g.80263200T>G		187.0	0.0	.		166.0	11.0	.	NM_001114735	Q6FGZ4|Q6FH19|Q86W13|Q99524	Silent	SNP	ENST00000267953.3	hg19	CCDS10312.1																																																																																			.	.	.	none		0.393	BCL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291372.1	NM_004049		G	80263200	T	G	80263200	2	3	215	1	0	0	0	0	0	0	0	1	1366	1617	56	5		5	BCL2A1	15	80263200	Silent	SNP	T	TCGA-J7-A8I2-01A-12D-A35Z-10	16304868	80263200	22268192	43	13072											
ABCC12	94160	hgsc.bcm.edu	37	chr16	48180293	48180293	+	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	aaaggatctccgccggcctcGctggtccagatctgagataa	10	8	11	12	3	2	2	0	1	2	2	5	4	3	3	4	3	0	1	4	3	2	1	rs561243035	byFrequency	TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr16:48180293G>A	ENST00000311303.3	-	1	388	c.43C>T	c.(43-45)Cga>Tga	p.R15*	ABCC12_ENST00000448542.1_Nonsense_Mutation_p.R15*|ABCC12_ENST00000416054.1_Nonsense_Mutation_p.R15*	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	15						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)				CGCCGGCCTCGCTGGTCCAGA	0.562													G|||	2	0.000399361	0	0	5008	,	,		20388	0.002		0	False		,,,				2504	0				p.R15X		Atlas-SNP	.											.	ABCC12	190	.	0			c.C43T						PASS	.						120	106	110					16																	48180293		2201	4300	6501	SO:0001587	stop_gained	94160	exon1			GGCCTCGCTGGTC	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.43C>T	chr16.hg19:g.48180293G>A	ENSP00000311030:p.Arg15*	79.0	0.0	.		85.0	35.0	.	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Nonsense_Mutation	SNP	ENST00000311303.3	hg19	CCDS10730.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.994178	0.74703	.	.	ENSG00000140798	ENST00000311303;ENST00000448542;ENST00000449939;ENST00000416054;ENST00000527640	.	.	.	5.55	-6.59	0.01830	.	0.286455	0.31484	N	0.007571	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	.	12.0598	0.53557	0.0767:0.0:0.1475:0.7758	.	.	.	.	X	15	.	ENSP00000311030:R15X	R	-	1	2	ABCC12	46737794	0.056000	0.20664	0.885000	0.34714	0.786000	0.44442	0.094000	0.15107	-0.795000	0.04462	-0.243000	0.11985	CGA	.	.	.	none		0.562	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226		A	48180293	G	A	48180293	4	1	215	1	0	0	0	0	0	1	0	0	52	1095	38	1	4152	1	ABCC12	16	48180293	Nonsense_Mutation	SNP	G	TCGA-J7-A8I2-01A-12D-A35Z-10		48180293	42174460	44	13073											
LLGL1	3996	hgsc.bcm.edu	37	chr17	18137219	18137219	+	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	ccctgaccctgctcgaggggCagacgcttgccccaggcgag	6	5	14	16	3	0	2	0	1	0	1	1	4	0	2	4	3	2	3	4	3	0	1			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr17:18137219C>G	ENST00000316843.4	+	5	616	c.520C>G	c.(520-522)Cag>Gag	p.Q174E		NM_004140.3	NP_004131	Q15334	L2GL1_HUMAN	lethal giant larvae homolog 1 (Drosophila)	174					axonogenesis (GO:0007409)|cortical actin cytoskeleton organization (GO:0030866)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|maintenance of apical/basal cell polarity (GO:0035090)|positive regulation of Rab GTPase activity (GO:0032851)|protein complex assembly (GO:0006461)	cell projection (GO:0042995)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome membrane (GO:0031901)|Golgi cis cisterna (GO:0000137)|myelin sheath abaxonal region (GO:0035748)|trans-Golgi network membrane (GO:0032588)	protein kinase binding (GO:0019901)|Rab GTPase activator activity (GO:0005097)|structural molecule activity (GO:0005198)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21	all_neural(463;0.228)					GCTCGAGGGGCAGACGCTTGC	0.647																																					p.Q174E		Atlas-SNP	.											.	LLGL1	61	.	0			c.C520G						PASS	.						60	61	61					17																	18137219		2203	4300	6503	SO:0001583	missense	3996	exon5			GAGGGGCAGACGC		CCDS32586.1	17p11.2	2013-01-10	2001-11-28		ENSG00000131899	ENSG00000131899		"WD repeat domain containing"	6628	protein-coding gene	gene with protein product		600966	"lethal giant larvae (Drosophila) homolog 1"	DLG4, LLGL, HUGL, HUGL-1		7542763, 8565641	Standard	XM_005256643		Approved		uc002gsp.3	Q15334	OTTHUMG00000059396	ENST00000316843.4:c.520C>G	chr17.hg19:g.18137219C>G	ENSP00000321537:p.Gln174Glu	42.0	0.0	.		27.0	23.0	.	NM_004140	A7MBM7|O00188|Q58F11|Q86UK6	Missense_Mutation	SNP	ENST00000316843.4	hg19	CCDS32586.1	.	.	.	.	.	.	.	.	.	.	C	6.290	0.421674	0.11928	.	.	ENSG00000131899	ENST00000316843	T	0.04502	3.61	5.87	4.89	0.63831	WD40 repeat-like-containing domain (1);	0.513993	0.23041	N	0.052615	T	0.04770	0.0129	L	0.29908	0.895	0.29734	N	0.837684	B	0.18013	0.025	B	0.15870	0.014	T	0.17319	-1.0373	10	0.23891	T	0.37	-18.3441	13.5421	0.61681	0.3898:0.6102:0.0:0.0	.	174	Q15334	L2GL1_HUMAN	E	174	ENSP00000321537:Q174E	ENSP00000321537:Q174E	Q	+	1	0	LLGL1	18077944	0.397000	0.25270	0.996000	0.52242	0.797000	0.45037	0.360000	0.20250	1.470000	0.48102	0.650000	0.86243	CAG	.	.	.	none		0.647	LLGL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132067.3			G	18137219	C	G	18137219	3	3	215	1	0	0	0	0	1	0	0	0	8840	711	25	4	538	4	LLGL1	17	18137219	Missense_Mutation	SNP	C	TCGA-J7-A8I2-01A-12D-A35Z-10		18137219	63057991	45	13074											
HOXB2	3212	hgsc.bcm.edu	37	chr17	46622084	46622084	+	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	cttttggctcctgggtctctGaagggtggaggcgccgggct	3	11	17	10	2	1	1	0	1	1	0	3	2	2	2	2	6	0	2	2	6	1	2			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr17:46622084G>A	ENST00000330070.4	-	1	1357	c.190C>T	c.(190-192)Cag>Tag	p.Q64*	HOXB-AS1_ENST00000435312.1_RNA|HOXB2_ENST00000504772.3_5'Flank|HOXB-AS1_ENST00000508688.1_RNA|HOXB-AS1_ENST00000502764.2_RNA|HOXB-AS1_ENST00000504972.3_RNA	NM_002145.3	NP_002136.1	P14652	HXB2_HUMAN	homeobox B2	64					anterior/posterior pattern specification (GO:0009952)|blood circulation (GO:0008015)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|facial nerve structural organization (GO:0021612)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|neural nucleus development (GO:0048857)|rhombomere 3 development (GO:0021569)|rhombomere 4 development (GO:0021570)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	11						CTGGGTCTCTGAAGGGTGGAG	0.637																																					p.Q64X		Atlas-SNP	.											.	HOXB2	23	.	0			c.C190T						PASS	.						24	32	29					17																	46622084		2202	4300	6502	SO:0001587	stop_gained	3212	exon1			GTCTCTGAAGGGT		CCDS11527.1	17q21.32	2012-02-22	2005-12-22		ENSG00000173917	ENSG00000173917		"Homeoboxes / ANTP class : HOXL subclass"	5113	protein-coding gene	gene with protein product		142967	"homeo box B2"	HOX2, HOX2H		1973146, 1358459	Standard	XM_005257276		Approved		uc002inm.3	P14652	OTTHUMG00000159930	ENST00000330070.4:c.190C>T	chr17.hg19:g.46622084G>A	ENSP00000331741:p.Gln64*	121.0	0.0	.		161.0	105.0	.	NM_002145	P10913|P17485	Nonsense_Mutation	SNP	ENST00000330070.4	hg19	CCDS11527.1	.	.	.	.	.	.	.	.	.	.	G	47	13.489855	0.99745	.	.	ENSG00000173917	ENST00000330070	.	.	.	5.05	5.05	0.67936	.	0.154045	0.46442	D	0.000285	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	.	17.3735	0.87385	0.0:0.0:1.0:0.0	.	.	.	.	X	64	.	ENSP00000331741:Q64X	Q	-	1	0	HOXB2	43977083	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.950000	0.56676	2.629000	0.89072	0.650000	0.86243	CAG	.	.	.	none		0.637	HOXB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358384.2			A	46622084	G	A	46622084	4	1	215	1	0	0	0	0	0	1	0	0	7308	1299	45	2	888	2	HOXB2	17	46622084	Nonsense_Mutation	SNP	G	TCGA-J7-A8I2-01A-12D-A35Z-10	28484865	46622084	34573126	46	13075											
UBE2O	63893	hgsc.bcm.edu	37	chr17	74393911	74393911	+	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	tgatggtctttgagttgtcaGcccacaccacctccaccttg	7	12	8	14	0	2	2	1	2	1	0	3	2	3	2	5	1	1	1	5	1	0	3			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr17:74393911G>C	ENST00000319380.7	-	13	2148	c.2084C>G	c.(2083-2085)gCt>gGt	p.A695G	UBE2O_ENST00000587581.1_5'UTR	NM_022066.3	NP_071349.3	Q9C0C9	UBE2O_HUMAN	ubiquitin-conjugating enzyme E2O	695					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						TGAGTTGTCAGCCCACACCAC	0.642											OREG0024751	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A695G		Atlas-SNP	.											.	UBE2O	207	.	0			c.C2084G						PASS	.						137	126	130					17																	74393911		2203	4300	6503	SO:0001583	missense	63893	exon13			TTGTCAGCCCACA	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.2084C>G	chr17.hg19:g.74393911G>C	ENSP00000323687:p.Ala695Gly	79.0	0.0	.	1152	80.0	27.0	.	NM_022066	A6NDU5|Q69YP4|Q6PIZ2|Q86UA4|Q8N425|Q8TBN1|Q9BSW1|Q9H6E6|Q9H7E4|Q9H9B2	Missense_Mutation	SNP	ENST00000319380.7	hg19	CCDS32742.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.497940	0.85069	.	.	ENSG00000175931	ENST00000319380	T	0.75477	-0.94	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.83954	0.5366	M	0.70595	2.14	0.50813	D	0.999893	D	0.67145	0.996	P	0.58266	0.836	D	0.83575	0.0114	10	0.46703	T	0.11	-10.7482	19.7404	0.96228	0.0:0.0:1.0:0.0	.	695	Q9C0C9	UBE2O_HUMAN	G	695	ENSP00000323687:A695G	ENSP00000323687:A695G	A	-	2	0	UBE2O	71905506	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.906000	0.87423	2.661000	0.90470	0.650000	0.86243	GCT	.	.	.	none		0.642	UBE2O-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450123.1	NM_022066		C	74393911	G	C	74393911	3	2	215	1	0	0	0	0	1	0	0	0	16880	971	34	4	1818	4	UBE2O	17	74393911	Missense_Mutation	SNP	G	TCGA-J7-A8I2-01A-12D-A35Z-10	27771827	74393911	6801299	47	13076											
SETBP1	26040	hgsc.bcm.edu	37	chr18	42531807	42531807	+	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	aagctgtctccacccagactGatggccaactccccttcaca	10	8	6	17	0	2	2	1	1	1	1	4	2	3	2	5	1	2	1	5	1	2	1			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr18:42531807G>A	ENST00000282030.5	+	4	2798	c.2502G>A	c.(2500-2502)ctG>ctA	p.L834L		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	834						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)		CACCCAGACTGATGGCCAACT	0.537									Schinzel-Giedion syndrome																												p.L834L		Atlas-SNP	.											.	SETBP1	577	.	0			c.G2502A						PASS	.						95	73	80					18																	42531807		2203	4300	6503	SO:0001819	synonymous_variant	26040	exon4	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	CAGACTGATGGCC	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.2502G>A	chr18.hg19:g.42531807G>A		62.0	0.0	.		55.0	24.0	.	NM_015559	A6H8W5|Q6P6C3|Q9UEF3	Silent	SNP	ENST00000282030.5	hg19	CCDS11923.2																																																																																			.	.	.	none		0.537	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110		A	42531807	G	A	42531807	2	1	215	1	0	0	0	0	0	0	0	1	14142	1277	45	2		2	SETBP1	18	42531807	Silent	SNP	G	TCGA-J7-A8I2-01A-12D-A35Z-10		42531807	35545441	48	13077											
ANKRD27	84079	hgsc.bcm.edu	37	chr19	33119054	33119054	+	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	tggagaatggagtgacaactGagggatcattcaacctccta	13	9	11	8	0	2	3	2	2	0	1	3	6	3	5	2	3	2	0	2	3	4	2			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr19:33119054G>A	ENST00000306065.4	-	15	1513	c.1355C>T	c.(1354-1356)tCa>tTa	p.S452L		NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	452					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)					AGTGACAACTGAGGGATCATT	0.542																																					p.S452L		Atlas-SNP	.											.	ANKRD27	86	.	0			c.C1355T						PASS	.						117	112	114					19																	33119054		2203	4300	6503	SO:0001583	missense	84079	exon15			ACAACTGAGGGAT	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.1355C>T	chr19.hg19:g.33119054G>A	ENSP00000304292:p.Ser452Leu	84.0	0.0	.		89.0	41.0	.	NM_032139	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Missense_Mutation	SNP	ENST00000306065.4	hg19	CCDS32986.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.677180	0.88445	.	.	ENSG00000105186	ENST00000306065	T	0.65916	-0.18	5.37	5.37	0.77165	Ankyrin repeat-containing domain (1);	0.000000	0.50627	D	0.000113	T	0.69441	0.3111	L	0.31120	0.905	0.80722	D	1	D	0.76494	0.999	D	0.71656	0.974	T	0.65529	-0.6146	10	0.26408	T	0.33	-14.3157	19.1028	0.93281	0.0:0.0:1.0:0.0	.	452	Q96NW4	ANR27_HUMAN	L	452	ENSP00000304292:S452L	ENSP00000304292:S452L	S	-	2	0	ANKRD27	37810894	1.000000	0.71417	0.242000	0.24170	0.787000	0.44495	8.928000	0.92853	2.511000	0.84671	0.655000	0.94253	TCA	.	.	.	none		0.542	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1	NM_032139		A	33119054	G	A	33119054	3	1	215	1	0	0	0	0	1	0	0	0	655	1294	45	2	1857	2	ANKRD27	19	33119054	Missense_Mutation	SNP	G	TCGA-J7-A8I2-01A-12D-A35Z-10		33119054	26009929	49	13078											
FKBP1A	2280	hgsc.bcm.edu	37	chr20	1352846	1352846	+	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	gtggcaccataggcataatcTggagatatagtcagtttggc	11	11	12	7	0	2	1	1	0	1	1	2	2	2	1	1	4	0	3	1	4	4	5			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr20:1352846T>G	ENST00000400137.4	-	4	400	c.237A>C	c.(235-237)ccA>ccC	p.P79P	SDCBP2-AS1_ENST00000609285.1_RNA|SDCBP2-AS1_ENST00000609470.1_RNA|FKBP1A_ENST00000381724.3_Silent_p.P74P|FKBP1A_ENST00000460490.1_5'Flank|FKBP1A_ENST00000381719.3_Silent_p.P79P|FKBP1A_ENST00000381715.1_Silent_p.P74P|SDCBP2-AS1_ENST00000446423.1_RNA|FKBP1A_ENST00000439640.2_Silent_p.P63P	NM_000801.4	NP_000792.1	P62942	FKB1A_HUMAN	FK506 binding protein 1A, 12kDa	79	PPIase FKBP-type. {ECO:0000255|PROSITE- ProRule:PRU00277}.				'de novo' protein folding (GO:0006458)|amyloid fibril formation (GO:1990000)|calcium ion transmembrane transport (GO:0070588)|chaperone-mediated protein folding (GO:0061077)|extracellular fibril organization (GO:0043206)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein binding (GO:0032092)|positive regulation of protein ubiquitination (GO:0031398)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)|protein peptidyl-prolyl isomerization (GO:0000413)|protein refolding (GO:0042026)|regulation of activin receptor signaling pathway (GO:0032925)|regulation of amyloid precursor protein catabolic process (GO:1902991)|regulation of immune response (GO:0050776)|regulation of protein localization (GO:0032880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|SMAD protein complex assembly (GO:0007183)|T cell activation (GO:0042110)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|terminal cisterna (GO:0014802)|Z disc (GO:0030018)	activin binding (GO:0048185)|FK506 binding (GO:0005528)|ion channel binding (GO:0044325)|macrolide binding (GO:0005527)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|type I transforming growth factor beta receptor binding (GO:0034713)			central_nervous_system(1)|lung(1)|upper_aerodigestive_tract(1)	3					Pimecrolimus(DB00337)|Sirolimus(DB00877)|Tacrolimus(DB00864)	AGGCATAATCTGGAGATATAG	0.498																																					p.P79P		Atlas-SNP	.											.	FKBP1A	6	.	0			c.A237C						PASS	.						72	62	66					20																	1352846		2203	4298	6501	SO:0001819	synonymous_variant	2280	exon4			ATAATCTGGAGAT	M92423	CCDS13014.1, CCDS74688.1	20p13	2013-03-20	2002-08-29		ENSG00000088832	ENSG00000088832			3711	protein-coding gene	gene with protein product	"calstabin 1"	186945	"FK506-binding protein 1A (12kD)"	FKBP1		1930186	Standard	NM_000801		Approved	FKBP-12, FKBP12, PKC12, PPIASE, FKBP12C	uc002wey.3	P62942	OTTHUMG00000031666	ENST00000400137.4:c.237A>C	chr20.hg19:g.1352846T>G		177.0	0.0	.		286.0	170.0	.	NM_054014	D3DVW6|P20071|Q4VC47|Q6FGD9|Q6LEU3|Q9H103|Q9H566	Silent	SNP	ENST00000400137.4	hg19	CCDS13014.1																																																																																			.	.	.	none		0.498	FKBP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077534.2			G	1352846	T	G	1352846	2	3	215	1	0	0	0	0	0	0	0	1	5913	1567	55	5		5	FKBP1A	20	1352846	Silent	SNP	T	TCGA-J7-A8I2-01A-12D-A35Z-10		1352846	61672674	50	13079											
GGT7	2686	hgsc.bcm.edu	37	chr20	33447370	33447371	+	Frame_Shift_Ins	INS	-	-	G																															cgagccaggtagtggcgggcINSggcccgatggcaggaacgtc																										TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr20:33447370_33447371insG	ENST00000336431.5	-	7	933_934	c.889_890insC	c.(889-891)cgcfs	p.R297fs		NM_178026.2	NP_821158.2	Q9UJ14	GGT7_HUMAN	gamma-glutamyltransferase 7	297					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)	p.R297H(1)		NS(2)|breast(1)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)	20						TAGTGGCGGGCGGCCCGATGGC	0.688																																					p.R297fs		Atlas-INDEL	.											GGT7,NS,carcinoma,0,1	GGT7	41	.	1	Substitution - Missense(1)	lung(1)	c.890_891insC						PASS	.																																			SO:0001589	frameshift_variant	2686	exon7			.	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.890dupC	chr20.hg19:g.33447372_33447372dupG	ENSP00000338964:p.Arg297fs	96.0	0.0	0		123.0	10.0	0.0813008	NM_178026	Q8N899|Q8NF66|Q9BYP5|Q9BYP6	Frame_Shift_Ins	INS	ENST00000336431.5	hg19	CCDS13242.2																																																																																			.	.	.	none		0.688	GGT7-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078816.2	NM_178026		G	33447371	-	G	33447370	7	5	215	1	0	1	1	0	0	0	0	0	6371	768	27	0	1134	0	GGT7	20	33447370	Frame_Shift_Ins	INS	-	TCGA-J7-A8I2-01A-12D-A35Z-10	32094524	33447370	29578150	51	13080											
CEP250	11190	hgsc.bcm.edu	37	chr20	34099427	34099427	+	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	agtcctgctacaccccagccCcagcactacccaagccgcct	9	5	6	21	1	0	0	0	0	0	0	1	0	1	0	8	0	6	2	8	0	3	2			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr20:34099427C>T	ENST00000397527.1	+	35	8021	c.7301C>T	c.(7300-7302)cCc>cTc	p.P2434L	CEP250_ENST00000342580.4_Missense_Mutation_p.P2378L	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	2434					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)			CACCCCAGCCCCAGCACTACC	0.627																																					p.P2434L		Atlas-SNP	.											.	CEP250	141	.	0			c.C7301T						PASS	.						38	39	39					20																	34099427		2203	4300	6503	SO:0001583	missense	11190	exon35			CCAGCCCCAGCAC	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.7301C>T	chr20.hg19:g.34099427C>T	ENSP00000380661:p.Pro2434Leu	100.0	0.0	.		119.0	72.0	.	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	hg19	CCDS13255.1	.	.	.	.	.	.	.	.	.	.	C	14.30	2.494922	0.44352	.	.	ENSG00000126001	ENST00000397527;ENST00000342580;ENST00000422671	T;T;T	0.48836	2.76;2.74;0.8	4.65	2.7	0.31948	.	0.277119	0.25890	N	0.027635	T	0.29882	0.0747	L	0.38838	1.175	0.31610	N	0.651583	B	0.02656	0.0	B	0.06405	0.002	T	0.17531	-1.0366	10	0.20046	T	0.44	.	3.6764	0.08294	0.1943:0.5961:0.0:0.2096	.	2434	Q9BV73	CP250_HUMAN	L	2434;2378;869	ENSP00000380661:P2434L;ENSP00000341541:P2378L;ENSP00000395992:P869L	ENSP00000341541:P2378L	P	+	2	0	CEP250	33562841	0.729000	0.28090	0.775000	0.31657	0.850000	0.48378	1.914000	0.39966	0.561000	0.29186	0.561000	0.74099	CCC	.	.	.	none		0.627	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		T	34099427	C	T	34099427	3	4	215	1	0	0	0	0	1	0	0	0	3254	623	22	2	7427	2	CEP250	20	34099427	Missense_Mutation	SNP	C	TCGA-J7-A8I2-01A-12D-A35Z-10	652057	34099427	28926093	52	13081											
LAMA5	3911	hgsc.bcm.edu	37	chr20	60906117	60906117	+	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	ccaaaggcgccgtggctgctGatgcagctgacccggggctc	6	6	15	14	3	0	2	0	2	0	0	1	2	0	2	3	4	3	5	3	4	1	0			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr20:60906117G>A	ENST00000252999.3	-	29	3687	c.3621C>T	c.(3619-3621)atC>atT	p.I1207I	MIR4758_ENST00000577688.1_RNA	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1207	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)	p.I1207I(1)		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)			CGTGGCTGCTGATGCAGCTGA	0.692																																					p.I1207I		Atlas-SNP	.											LAMA5,NS,carcinoma,-2,1	LAMA5	268	.	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C3621T						PASS	.						22	25	24					20																	60906117		2197	4298	6495	SO:0001819	synonymous_variant	3911	exon29			GCTGCTGATGCAG	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.3621C>T	chr20.hg19:g.60906117G>A		184.0	0.0	.		241.0	166.0	.	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	hg19	CCDS33502.1																																																																																			.	.	.	none		0.692	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		A	60906117	G	A	60906117	2	1	215	1	0	0	0	0	0	0	0	1	8616	1280	45	2		2	LAMA5	20	60906117	Silent	SNP	G	TCGA-J7-A8I2-01A-12D-A35Z-10	26806690	60906117	2119403	53	13082											
SLC37A1	54020	hgsc.bcm.edu	37	chr21	43979172	43979172	+	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	gggagtggcacggccgccatCagcttcacaggggccttgaa	8	6	15	12	2	2	1	2	1	0	0	2	2	2	2	3	5	1	2	3	5	1	2			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr21:43979172C>G	ENST00000352133.2	+	11	1936	c.954C>G	c.(952-954)atC>atG	p.I318M	AP001625.6_ENST00000442605.1_RNA|SLC37A1_ENST00000398341.3_Missense_Mutation_p.I318M			P57057	GLPT_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 1	318					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						CGGCCGCCATCAGCTTCACAG	0.592																																					p.I318M		Atlas-SNP	.											.	SLC37A1	48	.	0			c.C954G						PASS	.						45	45	45					21																	43979172		2203	4300	6503	SO:0001583	missense	54020	exon12			CGCCATCAGCTTC	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.954C>G	chr21.hg19:g.43979172C>G	ENSP00000344648:p.Ile318Met	82.0	0.0	.		97.0	45.0	.	NM_018964	D3DSJ7|Q9HAQ1	Missense_Mutation	SNP	ENST00000352133.2	hg19	CCDS13689.1	.	.	.	.	.	.	.	.	.	.	C	14.47	2.543831	0.45280	.	.	ENSG00000160190	ENST00000398341;ENST00000352133	T;T	0.59364	0.27;0.27	5.7	5.7	0.88788	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.054132	0.64402	D	0.000001	T	0.79724	0.4495	M	0.91818	3.245	0.58432	D	0.999993	D	0.76494	0.999	D	0.75484	0.986	D	0.83363	0.0003	10	0.72032	D	0.01	-27.3918	12.3411	0.55095	0.1685:0.8315:0.0:0.0	.	318	P57057	GLPT_HUMAN	M	318	ENSP00000381383:I318M;ENSP00000344648:I318M	ENSP00000344648:I318M	I	+	3	3	SLC37A1	42852241	1.000000	0.71417	1.000000	0.80357	0.021000	0.10359	2.026000	0.41069	2.688000	0.91661	0.655000	0.94253	ATC	.	.	.	none		0.592	SLC37A1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195377.1			G	43979172	C	G	43979172	3	3	215	1	0	0	0	0	1	0	0	0	14610	816	29	4	992	4	SLC37A1	21	43979172	Missense_Mutation	SNP	C	TCGA-J7-A8I2-01A-12D-A35Z-10		43979172	4150723	54	13083											
LIF	3976	hgsc.bcm.edu	37	chr22	30639798	30639798	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcacaggcggcacagcaCgttgctaaggaggcctcgca	9	5	14	13	3	0	0	0	0	0	0	1	1	0	1	1	4	3	7	1	4	1	2			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr22:30639798C>T	ENST00000249075.3	-	3	606	c.451G>A	c.(451-453)Gtg>Atg	p.V151M	RP1-102K2.8_ENST00000608354.1_RNA|LIF_ENST00000403987.3_3'UTR|RP1-102K2.8_ENST00000593843.1_RNA	NM_002309.4	NP_002300.1	P15018	LIF_HUMAN	leukemia inhibitory factor	151					blood vessel remodeling (GO:0001974)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|immune response (GO:0006955)|leukemia inhibitory factor signaling pathway (GO:0048861)|lung alveolus development (GO:0048286)|lung lobe morphogenesis (GO:0060463)|lung vasculature development (GO:0060426)|multicellular organismal development (GO:0007275)|muscle organ morphogenesis (GO:0048644)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of hormone secretion (GO:0046888)|negative regulation of meiosis (GO:0045835)|neuron development (GO:0048666)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cell proliferation (GO:0008284)|positive regulation of histone H3-K27 acetylation (GO:1901676)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein localization to nucleus (GO:1900182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|spongiotrophoblast differentiation (GO:0060708)|stem cell maintenance (GO:0019827)|transcription from RNA polymerase II promoter (GO:0006366)|trophoblast giant cell differentiation (GO:0060707)|tyrosine phosphorylation of Stat3 protein (GO:0042503)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|leukemia inhibitory factor receptor binding (GO:0005146)|receptor binding (GO:0005102)|RNA polymerase II transcription factor recruiting transcription factor activity (GO:0001135)			breast(1)|lung(3)|skin(3)	7			Epithelial(10;0.171)			CGGCACAGCACGTTGCTAAGG	0.612																																					p.V151M		Atlas-SNP	.											LIF,NS,carcinoma,0,1	LIF	18	.	0			c.G451A						PASS	.						202	172	182					22																	30639798		2203	4300	6503	SO:0001583	missense	3976	exon3			ACAGCACGTTGCT		CCDS13872.1, CCDS58799.1	22q12.2	2012-02-09	2012-02-09		ENSG00000128342	ENSG00000128342			6596	protein-coding gene	gene with protein product	"differentiation inhibitory activity", "differentiation-inducing factor", "hepatocyte-stimulating factor III", "cholinergic differentiation factor", "human interleukin in DA cells"	159540				1714745, 8058719	Standard	NM_002309		Approved	CDF, DIA, HILDA	uc003agz.3	P15018	OTTHUMG00000150910	ENST00000249075.3:c.451G>A	chr22.hg19:g.30639798C>T	ENSP00000249075:p.Val151Met	107.0	0.0	.		91.0	27.0	.	NM_002309	B2RCW7|B5MC23|Q52LZ2	Missense_Mutation	SNP	ENST00000249075.3	hg19	CCDS13872.1	.	.	.	.	.	.	.	.	.	.	C	19.76	3.886813	0.72410	.	.	ENSG00000128342	ENST00000249075	T	0.80304	-1.36	4.99	3.93	0.45458	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.095837	0.44688	D	0.000429	D	0.85999	0.5828	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.86414	0.1750	10	0.66056	D	0.02	-23.106	10.622	0.45484	0.0:0.6769:0.3231:0.0	.	151	P15018	LIF_HUMAN	M	151	ENSP00000249075:V151M	ENSP00000249075:V151M	V	-	1	0	LIF	28969798	0.967000	0.33354	0.998000	0.56505	0.932000	0.56968	1.735000	0.38176	2.294000	0.77228	0.561000	0.74099	GTG	.	.	.	none		0.612	LIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320508.1	NM_002309		T	30639798	C	T	30639798	3	4	215	1	0	0	0	0	1	0	0	0	8786	536	19	1	161	1	LIF	22	30639798	Missense_Mutation	SNP	C	TCGA-J7-A8I2-01A-12D-A35Z-10		30639798	20664768	55	13084											
EP300	2033	hgsc.bcm.edu	37	chr22	41553171	41553201	+	Splice_Site	DEL	GAGTAATGTTTGATGTCACTTGTCTTTCTAG	GAGTAATGTTTGATGTCACTTGTCTTTCTAG	-																															ttgatgtcacttgtctttctAggattactttgatattgtga																										TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	GAGTAATGTTTGATGTCACTTGTCTTTCTAG	GAGTAATGTTTGATGTCACTTGTCTTTCTAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chr22:41553171_41553201delGAGTAATGTTTGATGTCACTTGTCTTTCTAG	ENST00000263253.7	+	18	4480_4509	c.3261_3290delGAGTAATGTTTGATGTCACTTGTCTTTCTAG	c.(3259-3291)ccgagtaatgtttgatgtcacttgtctttctag>ccg	p.SNV*CHLSF*1088fs		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1088	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				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.F1090L(1)|p.S1095I(1)|p.?(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						TTGTCTTTCTAGGATTACTTTGATATTGTGAAGAGCCCCATGGATCTTTCT	0.385			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												.		Atlas-Indel,Pindel	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300	367	.	3	Substitution - Missense(2)|Unknown(1)	urinary_tract(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)	.						PASS	.																																			SO:0001630	splice_region_variant	2033	.	Familial Cancer Database	Broad Thumb-Hallux syndrome	.	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.3262-1GAGTAATGTTTGATGTCACTTGTCTTTCTAG>-	chr22.hg19:g.41553171_41553201delGAGTAATGTTTGATGTCACTTGTCTTTCTAG		94.0	0.0	0		91.0	27.0	0.296703	.	B1AKC2	Splice_Site	DEL	ENST00000263253.7	hg19	CCDS14010.1																																																																																			.	.	.	none		0.385	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429	Frame_Shift_Del	-	41553201	GAGTAATGTTTGATGTCACTTGTCTTTCTAG	-	41553171	8	5	215	1	0	1	0	1	0	0	1	0	5150	434	15	0	3330	0	EP300	22	41553171	Splice_Site	DEL	GAGTAATGTTTGATGTCACTTGTCTTTCTAG	TCGA-J7-A8I2-01A-12D-A35Z-10	10913373	41553171	9751395	56	13085											
KDM6A	7403	hgsc.bcm.edu	37	chrX	44970638	44970638	+	Frame_Shift_Del	DEL	A	A	-																															tattttcaggctcctccattAccatccgcctcatcttgata																										TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chrX:44970638delA	ENST00000377967.4	+	29	4229	c.4188delA	c.(4186-4188)ttafs	p.L1396fs	KDM6A_ENST00000382899.4_Frame_Shift_Del_p.L1403fs|KDM6A_ENST00000536777.1_Frame_Shift_Del_p.L1351fs|KDM6A_ENST00000543216.1_Frame_Shift_Del_p.L1317fs	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	1396					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						CTCCTCCATTACCATCCGCCT	0.373			"D, N, F, S"		"renal, oesophageal SCC, MM"																																p.L1396fs	Colon(129;1273 1667 15230 27352 52914)	Atlas-Indel,Pindel	.		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.4187delT						PASS	.						178	147	158					X																	44970638		2203	4300	6503	SO:0001589	frameshift_variant	7403	exon29			.	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.4188delA	chrX.hg19:g.44970638delA	ENSP00000367203:p.Leu1396fs	38.0	0.0	0		47.0	43.0	0.914894	NM_021140	Q52LL9|Q5JVQ7	Frame_Shift_Del	DEL	ENST00000377967.4	hg19	CCDS14265.1																																																																																			.	.	.	none		0.373	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140		-	44970638	A	-	44970638	7	5	215	1	0	1	0	1	0	0	0	0	8144	388	14	0	4302	0	KDM6A	23	44970638	Frame_Shift_Del	DEL	A	TCGA-J7-A8I2-01A-12D-A35Z-10		44970638	110299922	57	13086											
APEX2	27301	hgsc.bcm.edu	37	chrX	55033281	55033281	+	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	ctgcaaaacagtgcccacctCtgtgcacccgcttcctccct	7	9	6	19	1	1	0	0	0	1	0	3	0	3	0	5	0	4	3	5	0	2	1			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chrX:55033281C>T	ENST00000374987.3	+	6	1036	c.970C>T	c.(970-972)Ctg>Ttg	p.L324L	ALAS2_ENST00000498636.1_5'Flank	NM_014481.2	NP_055296.2	Q9UBZ4	APEX2_HUMAN	APEX nuclease (apurinic/apyrimidinic endonuclease) 2	324					base-excision repair (GO:0006284)|cell cycle (GO:0007049)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)	mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008311)|zinc ion binding (GO:0008270)			breast(1)|endometrium(8)|large_intestine(4)|lung(6)|prostate(1)|urinary_tract(1)	21						GTGCCCACCTCTGTGCACCCG	0.577								Other BER factors																													p.L324L		Atlas-SNP	.											.	APEX2	50	.	0			c.C970T						PASS	.						55	47	49					X																	55033281		2203	4300	6503	SO:0001819	synonymous_variant	27301	exon6			CCACCTCTGTGCA	AB021260	CCDS14365.1	Xp11.23	2014-02-18			ENSG00000169188	ENSG00000169188	4.2.99.18		17889	protein-coding gene	gene with protein product	"zinc finger, GRF-type containing 2"	300773				11376153	Standard	NM_014481		Approved	APEXL2, APE2, XTH2, ZGRF2	uc004dtz.4	Q9UBZ4	OTTHUMG00000021642	ENST00000374987.3:c.970C>T	chrX.hg19:g.55033281C>T		76.0	0.0	.		62.0	57.0	.	NM_014481	Q9Y5X7	Silent	SNP	ENST00000374987.3	hg19	CCDS14365.1																																																																																			.	.	.	none		0.577	APEX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056845.1			T	55033281	C	T	55033281	2	4	215	1	0	0	0	0	0	0	0	1	770	912	32	2		2	APEX2	23	55033281	Silent	SNP	C	TCGA-J7-A8I2-01A-12D-A35Z-10	10062643	55033281	100237279	58	13087											
ZMYM3	9203	hgsc.bcm.edu	37	chrX	70472979	70472979	+	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	gccagggggggcccatcctcGagttggggcagtctgggatt	5	8	18	10	1	1	0	0	0	1	0	3	2	2	1	3	6	0	2	3	6	0	2			TCGA-J7-A8I2-01A-12D-A35Z-10	TCGA-J7-A8I2-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9aace64d-14b2-435a-ab63-3891e2ae6bca	643d9c03-6b50-48da-aab4-0d369ca2392c	g.chrX:70472979G>A	ENST00000353904.2	-	2	314	c.127C>T	c.(127-129)Cga>Tga	p.R43*	ZMYM3_ENST00000373988.1_Nonsense_Mutation_p.R43*|ZMYM3_ENST00000314425.5_Nonsense_Mutation_p.R43*|ZMYM3_ENST00000373978.1_Nonsense_Mutation_p.R43*|ZMYM3_ENST00000373981.1_Nonsense_Mutation_p.R43*|ZMYM3_ENST00000373998.1_Nonsense_Mutation_p.R43*|ZMYM3_ENST00000373982.1_Nonsense_Mutation_p.R43*|ZMYM3_ENST00000489332.1_5'UTR|ZMYM3_ENST00000373984.3_Nonsense_Mutation_p.R43*	NM_005096.3	NP_005087.1	Q14202	ZMYM3_HUMAN	zinc finger, MYM-type 3	43					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)					GCCCATCCTCGAGTTGGGGCA	0.592											OREG0019858	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R43X		Atlas-SNP	.											.	ZMYM3	137	.	0			c.C127T						PASS	.						13	15	15					X																	70472979		2155	4235	6390	SO:0001587	stop_gained	9203	exon2			ATCCTCGAGTTGG	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.127C>T	chrX.hg19:g.70472979G>A	ENSP00000343909:p.Arg43*	276.0	2.0	.	1122	224.0	207.0	.	NM_005096	D3DVV3|O15089|Q96E26	Nonsense_Mutation	SNP	ENST00000353904.2	hg19	CCDS14409.1	.	.	.	.	.	.	.	.	.	.	g	36	5.732897	0.96856	.	.	ENSG00000147130	ENST00000314425;ENST00000373998;ENST00000353904;ENST00000373984;ENST00000373988;ENST00000373982;ENST00000373981;ENST00000373978	.	.	.	4.64	4.64	0.57946	.	0.369189	0.19624	N	0.109848	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.5077	15.0413	0.71793	0.0:0.0:1.0:0.0	.	.	.	.	X	43	.	ENSP00000322845:R43X	R	-	1	2	ZMYM3	70389704	1.000000	0.71417	0.993000	0.49108	0.962000	0.63368	4.218000	0.58554	1.898000	0.54952	0.287000	0.19450	CGA	.	.	.	none		0.592	ZMYM3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057154.1	NM_201599		A	70472979	G	A	70472979	4	1	215	1	0	0	0	0	0	1	0	0	17713	1066	37	1	4099	1	ZMYM3	23	70472979	Nonsense_Mutation	SNP	G	TCGA-J7-A8I2-01A-12D-A35Z-10	15439698	70472979	84797581	59	13088											
CTTNBP2NL	55917	hgsc.bcm.edu	37	chr1	112999075	112999075	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagagagttttccagcagaaAgaacccatgggagcaacata	16	6	10	9	0	0	3	0	0	0	3	1	5	1	4	2	1	4	3	2	1	4	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr1:112999075A>G	ENST00000271277.6	+	6	1186	c.961A>G	c.(961-963)Aga>Gga	p.R321G		NM_018704.2	NP_061174.1	Q9P2B4	CT2NL_HUMAN	CTTNBP2 N-terminal like	321					negative regulation of transmembrane transport (GO:0034763)|negative regulation of transporter activity (GO:0032410)|protein dephosphorylation (GO:0006470)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	protein phosphatase 2A binding (GO:0051721)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	29		all_cancers(81;0.00064)|all_epithelial(167;0.000415)|all_lung(203;0.00045)|Lung NSC(69;0.000705)		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)		TCCAGCAGAAAGAACCCATGG	0.483																																					p.R321G		Atlas-SNP	.											.	CTTNBP2NL	65	.	0			c.A961G						PASS	.						136	140	138					1																	112999075		2203	4300	6503	SO:0001583	missense	55917	exon6			GCAGAAAGAACCC	AB037854	CCDS845.1	1p13.2	2008-02-05			ENSG00000143079	ENSG00000143079			25330	protein-coding gene	gene with protein product		615100				10718198	Standard	NM_018704		Approved	DKFZp547A023	uc001ebx.3	Q9P2B4	OTTHUMG00000011154	ENST00000271277.6:c.961A>G	chr1.hg19:g.112999075A>G	ENSP00000271277:p.Arg321Gly	145.0	0.0	.		118.0	20.0	.	NM_018704	B3KMS5|Q96B40	Missense_Mutation	SNP	ENST00000271277.6	hg19	CCDS845.1	.	.	.	.	.	.	.	.	.	.	A	2.835	-0.241767	0.05906	.	.	ENSG00000143079	ENST00000271277	T	0.22945	1.93	5.88	4.73	0.59995	.	0.247257	0.38778	N	0.001578	T	0.08714	0.0216	L	0.44542	1.39	0.09310	N	1	B	0.17038	0.02	B	0.14023	0.01	T	0.22208	-1.0223	10	0.22109	T	0.4	-12.5708	12.215	0.54402	0.8572:0.1428:0.0:0.0	.	321	Q9P2B4	CT2NL_HUMAN	G	321	ENSP00000271277:R321G	ENSP00000271277:R321G	R	+	1	2	CTTNBP2NL	112800598	0.600000	0.26899	0.921000	0.36526	0.055000	0.15305	1.467000	0.35321	1.017000	0.39495	0.533000	0.62120	AGA	.	.	.	none		0.483	CTTNBP2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030686.1	NM_018704		G	112999075	A	G	112999075	3	3	216	1	0	0	0	0	1	0	0	0	4048	64	3	3	975	3	CTTNBP2NL	1	112999075	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10		112999075	136251546	1	13089											
ANKRD35	148741	hgsc.bcm.edu	37	chr1	145561841	145561841	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgagaaaaggatgctgcccGgggggctttgtcaagaccgg	9	6	17	9	3	1	2	1	0	0	2	1	4	1	3	2	5	2	2	2	5	3	1	rs201815402		TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr1:145561841G>A	ENST00000355594.4	+	10	1616	c.1529G>A	c.(1528-1530)cGg>cAg	p.R510Q		NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	510										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)					GATGCTGCCCGGGGGGCTTTG	0.632																																					p.R510Q	Melanoma(9;127 754 22988 51047)	Atlas-SNP	.											.	ANKRD35	96	.	0			c.G1529A						PASS	.						87	104	98					1																	145561841		2201	4300	6501	SO:0001583	missense	148741	exon10			CTGCCCGGGGGGC	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.1529G>A	chr1.hg19:g.145561841G>A	ENSP00000347802:p.Arg510Gln	115.0	0.0	.		96.0	11.0	.	NM_144698	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	hg19	CCDS919.1	.	.	.	.	.	.	.	.	.	.	g	13.79	2.341545	0.41498	.	.	ENSG00000198483	ENST00000453670;ENST00000355594	T	0.67865	-0.29	5.23	4.31	0.51392	.	0.342769	0.20873	N	0.084127	T	0.46756	0.1409	M	0.70595	2.14	0.80722	D	1	B	0.32324	0.364	B	0.24006	0.05	T	0.51364	-0.8715	10	0.34782	T	0.22	-6.7716	11.0303	0.47769	0.0:0.0:0.8146:0.1853	.	510	Q8N283	ANR35_HUMAN	Q	419;510	ENSP00000347802:R510Q	ENSP00000347802:R510Q	R	+	2	0	ANKRD35	144273198	0.749000	0.28305	0.965000	0.40720	0.652000	0.38707	1.901000	0.39838	1.405000	0.46838	0.651000	0.88453	CGG	.	G|1.000;T|0.000	.	alt		0.632	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698		A	145561841	G	A	145561841	3	1	216	1	0	0	0	0	1	0	0	0	664	1116	39	1	1567	1	ANKRD35	1	145561841	Missense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	32562766	145561841	103688780	2	13090											
ILDR2	387597	hgsc.bcm.edu	37	chr1	166890003	166890003	+	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	gttgctgtggtagggcaggtCgcggccgcggtaggacgggc	4	7	21	9	5	0	0	0	0	0	0	1	1	0	1	1	7	1	5	1	7	2	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr1:166890003C>T	ENST00000271417.3	-	9	1880	c.1825G>A	c.(1825-1827)Gac>Aac	p.D609N	ILDR2_ENST00000529387.1_Intron|ILDR2_ENST00000528703.1_Missense_Mutation_p.D550N|ILDR2_ENST00000526687.1_Missense_Mutation_p.D501N|ILDR2_ENST00000469934.2_Intron|ILDR2_ENST00000525740.1_Missense_Mutation_p.D482N|ILDR2_ENST00000529071.1_Missense_Mutation_p.D590N	NM_199351.2	NP_955383.1	Q71H61	ILDR2_HUMAN	immunoglobulin-like domain containing receptor 2	609					cell differentiation (GO:0030154)|homeostasis of number of cells within a tissue (GO:0048873)|insulin secretion (GO:0030073)|pancreas development (GO:0031016)|response to glucose (GO:0009749)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(3)|breast(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	22						TAGGGCAGGTCGCGGCCGCGG	0.687																																					p.D609N		Atlas-SNP	.											.	ILDR2	79	.	0			c.G1825A						PASS	.						6	9	8					1																	166890003		2076	4108	6184	SO:0001583	missense	387597	exon9			GCAGGTCGCGGCC	AF503509	CCDS1256.1	1q24.1	2008-12-18	2008-12-18	2008-12-18	ENSG00000143195	ENSG00000143195			18131	protein-coding gene	gene with protein product	"LISCH-like"		"chromosome 1 open reading frame 32"	C1orf32			Standard	NM_199351		Approved		uc001gdx.2	Q71H61	OTTHUMG00000034320	ENST00000271417.3:c.1825G>A	chr1.hg19:g.166890003C>T	ENSP00000271417:p.Asp609Asn	36.0	0.0	.		31.0	7.0	.	NM_199351		Missense_Mutation	SNP	ENST00000271417.3	hg19	CCDS1256.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.069172	0.76301	.	.	ENSG00000143195	ENST00000271417;ENST00000525740;ENST00000529071;ENST00000526687;ENST00000528703	T;T;T;T;T	0.77750	0.5;-1.12;0.5;-1.12;-0.12	4.76	4.76	0.60689	.	3.853080	0.00892	N	0.002254	T	0.64638	0.2616	L	0.56769	1.78	0.35061	D	0.761595	P	0.49358	0.923	B	0.36030	0.216	T	0.57464	-0.7807	9	0.62326	D	0.03	.	12.8493	0.57848	0.1631:0.8369:0.0:0.0	.	609	Q71H61	ILDR2_HUMAN	N	609;482;590;501;550	ENSP00000271417:D609N;ENSP00000436120:D482N;ENSP00000436882:D590N;ENSP00000434273:D501N;ENSP00000432750:D550N	ENSP00000271417:D609N	D	-	1	0	ILDR2	165156627	1.000000	0.71417	0.997000	0.53966	0.735000	0.41995	4.789000	0.62446	2.171000	0.68590	0.561000	0.74099	GAC	.	.	.	none		0.687	ILDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082880.2	NM_199351		T	166890003	C	T	166890003	3	4	216	1	0	0	0	0	1	0	0	0	7717	884	31	1	102	1	ILDR2	1	166890003	Missense_Mutation	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	21328162	166890003	82360618	3	13091											
TPR	7175	hgsc.bcm.edu	37	chr1	186316562	186316562	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttagctgactcacaagatcAtccacatcttctttgttgct	9	15	5	12	0	4	2	2	1	2	1	5	2	5	2	1	0	2	3	1	0	2	4			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr1:186316562A>G	ENST00000367478.4	-	22	3101	c.2805T>C	c.(2803-2805)gaT>gaC	p.D935D		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	935					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)		TCACAAGATCATCCACATCTT	0.368			T	NTRK1	papillary thyroid																																p.D935D		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.T2805C						PASS	.						213	200	204					1																	186316562		1964	4159	6123	SO:0001819	synonymous_variant	7175	exon22			AAGATCATCCACA	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.2805T>C	chr1.hg19:g.186316562A>G		108.0	0.0	.		70.0	4.0	.	NM_003292	Q15655|Q5SWY0|Q99968	Silent	SNP	ENST00000367478.4	hg19	CCDS41446.1																																																																																			.	.	.	none		0.368	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		G	186316562	A	G	186316562	2	3	216	1	0	0	0	0	0	0	0	1	16428	214	8	3		3	TPR	1	186316562	Silent	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	19426559	186316562	62934059	4	13092											
ASPM	259266	hgsc.bcm.edu	37	chr1	197072290	197072290	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctcactttcataccacgatAagctgactgtaaagttacta	13	13	5	10	1	2	1	2	1	1	0	3	2	2	1	1	0	3	3	1	0	6	6			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr1:197072290A>G	ENST00000367409.4	-	18	6347	c.6091T>C	c.(6091-6093)Tat>Cat	p.Y2031H	ASPM_ENST00000294732.7_Intron|ASPM_ENST00000367408.1_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2031	IQ 14. {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						ATACCACGATAAGCTGACTGT	0.328																																					p.Y2031H		Atlas-SNP	.											.	ASPM	444	.	0			c.T6091C						PASS	.						94	99	97					1																	197072290		2203	4298	6501	SO:0001583	missense	259266	exon18			CACGATAAGCTGA	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.6091T>C	chr1.hg19:g.197072290A>G	ENSP00000356379:p.Tyr2031His	155.0	0.0	.		100.0	17.0	.	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	hg19	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	a	19.52	3.842459	0.71488	.	.	ENSG00000066279	ENST00000367409	T	0.27557	1.66	5.6	4.46	0.54185	.	0.174809	0.40302	N	0.001123	T	0.59959	0.2232	M	0.90650	3.135	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.63541	-0.6614	10	0.41790	T	0.15	.	11.3347	0.49496	0.8639:0.0:0.0:0.1361	.	2031	Q8IZT6	ASPM_HUMAN	H	2031	ENSP00000356379:Y2031H	ENSP00000356379:Y2031H	Y	-	1	0	ASPM	195338913	1.000000	0.71417	0.632000	0.29296	0.972000	0.66771	7.212000	0.77941	0.930000	0.37217	0.524000	0.50904	TAT	.	.	.	none		0.328	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		G	197072290	A	G	197072290	3	3	216	1	0	0	0	0	1	0	0	0	1056	362	13	3	4386	3	ASPM	1	197072290	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	10755728	197072290	52178331	5	13093											
IFT172	26160	hgsc.bcm.edu	37	chr2	27702392	27702392	+	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	ttacctggctaggtcccacaTacgtcaactcaaacttgttc	10	12	6	13	1	2	0	2	0	0	0	4	0	3	0	2	2	4	2	2	2	5	5			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr2:27702392T>A	ENST00000260570.3	-	10	1092	c.989A>T	c.(988-990)tAt>tTt	p.Y330F	IFT172_ENST00000359466.6_Missense_Mutation_p.Y330F|IFT172_ENST00000416524.2_Missense_Mutation_p.Y309F	NM_015662.1	NP_056477.1	Q9UG01	IF172_HUMAN	intraflagellar transport 172	330					bone development (GO:0060348)|brain development (GO:0007420)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|epidermis development (GO:0008544)|heart looping (GO:0001947)|hindgut development (GO:0061525)|left/right axis specification (GO:0070986)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)	axoneme (GO:0005930)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(17)|lung(17)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	43	Acute lymphoblastic leukemia(172;0.155)					AGGTCCCACATACGTCAACTC	0.507																																					p.Y330F		Atlas-SNP	.											.	IFT172	119	.	0			c.A989T						PASS	.						164	142	150					2																	27702392		2203	4300	6503	SO:0001583	missense	26160	exon10			CCCACATACGTCA	AB033005	CCDS1755.1	2p23.3	2014-07-03	2014-07-03		ENSG00000138002	ENSG00000138002		"Intraflagellar transport homologs", "WD repeat domain containing"	30391	protein-coding gene	gene with protein product	"wimple homolog"	607386	"intraflagellar transport 172 homolog (Chlamydomonas)"			10788441, 10574461, 24140113	Standard	XM_005264254		Approved	SLB, wim, osm-1, NPHP17	uc002rku.3	Q9UG01	OTTHUMG00000128425	ENST00000260570.3:c.989A>T	chr2.hg19:g.27702392T>A	ENSP00000260570:p.Tyr330Phe	71.0	0.0	.		97.0	12.0	.	NM_015662	A5PKZ0|B2RNU5|Q86X44|Q96HW4|Q9UFJ9|Q9ULP1	Missense_Mutation	SNP	ENST00000260570.3	hg19	CCDS1755.1	.	.	.	.	.	.	.	.	.	.	T	18.09	3.547345	0.65311	.	.	ENSG00000138002	ENST00000260570;ENST00000359466;ENST00000416524	T;T;T	0.23147	1.92;1.92;1.92	5.64	5.64	0.86602	WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.30230	0.0758	M	0.64404	1.975	0.80722	D	1	B;P;B;B	0.35821	0.394;0.523;0.394;0.322	B;B;B;B	0.38378	0.228;0.272;0.144;0.2	T	0.04320	-1.0960	10	0.25106	T	0.35	-9.0488	14.6686	0.68926	0.0:0.0:0.0:1.0	.	330;330;330;330	A5PKZ0;Q9UG01-2;E7EP25;Q9UG01	.;.;.;IF172_HUMAN	F	330;330;309	ENSP00000260570:Y330F;ENSP00000352443:Y330F;ENSP00000407408:Y309F	ENSP00000260570:Y330F	Y	-	2	0	IFT172	27555896	1.000000	0.71417	0.988000	0.46212	0.937000	0.57800	7.558000	0.82253	2.138000	0.66242	0.533000	0.62120	TAT	.	.	.	none		0.507	IFT172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250213.2	NM_015662		A	27702392	T	A	27702392	3	1	216	1	0	0	0	0	1	0	0	0	7564	1406	49	5	4416	5	IFT172	2	27702392	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10		27702392	215496981	6	13094											
TCF7L1	83439	hgsc.bcm.edu	37	chr2	85361150	85361150	+	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	cctccgcaggcggagaggcgCccgcagcccgtccgggacac	6	2	15	18	6	0	1	0	0	0	1	2	3	2	2	5	4	1	2	5	4	0	0			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr2:85361150C>G	ENST00000282111.3	+	2	536	c.261C>G	c.(259-261)cgC>cgG	p.R87R		NM_031283.2	NP_112573.1	Q9HCS4	TF7L1_HUMAN	transcription factor 7-like 1 (T-cell specific, HMG-box)	87					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						CGGAGAGGCGCCCGCAGCCCG	0.697																																					p.R87R		Atlas-SNP	.											.	TCF7L1	44	.	0			c.C261G						PASS	.						19	25	23					2																	85361150		2200	4299	6499	SO:0001819	synonymous_variant	83439	exon2			GAGGCGCCCGCAG	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.261C>G	chr2.hg19:g.85361150C>G		90.0	0.0	.		117.0	19.0	.	NM_031283	Q53R97|Q6PD70|Q9NP00	Silent	SNP	ENST00000282111.3	hg19	CCDS1971.1																																																																																			.	.	.	none		0.697	TCF7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252301.2	NM_031283		G	85361150	C	G	85361150	2	3	216	1	0	0	0	0	0	0	0	1	15709	726	26	4		4	TCF7L1	2	85361150	Silent	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	57658758	85361150	157838223	7	13095											
RNF103	7844	hgsc.bcm.edu	37	chr2	86832185	86832185	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atggcatattatatatgccaAtatctgtcatataactcttg	13	16	5	7	0	3	0	1	0	2	0	3	0	3	0	1	1	2	1	1	1	8	8			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr2:86832185A>G	ENST00000237455.4	-	4	1807	c.839T>C	c.(838-840)aTt>aCt	p.I280T	CHMP3_ENST00000439940.2_Intron|RNF103_ENST00000477307.1_5'UTR|AC015971.2_ENST00000597638.1_RNA|AC015971.2_ENST00000424788.1_RNA|AC015971.2_ENST00000426549.1_RNA|AC015971.2_ENST00000439077.1_RNA|RNF103-CHMP3_ENST00000604011.1_Intron	NM_001198951.1|NM_005667.3	NP_001185880.1|NP_005658.1	O00237	RN103_HUMAN	ring finger protein 103	280					central nervous system development (GO:0007417)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(7)|skin(2)	25						ATATATGCCAATATCTGTCAT	0.353																																					p.I280T		Atlas-SNP	.											.	RNF103	58	.	0			c.T839C						PASS	.						45	48	47					2																	86832185		2203	4300	6503	SO:0001583	missense	7844	exon4			ATGCCAATATCTG	D76444	CCDS33237.1	2p11.2	2013-01-09	2003-05-14	2003-05-16	ENSG00000239305	ENSG00000239305		"RING-type (C3HC4) zinc fingers"	12859	protein-coding gene	gene with protein product		602507	"zinc finger protein 103 homolog (mouse)"	ZFP103		9070305	Standard	NM_005667		Approved	hkf-1, KF1	uc021vkg.1	O00237	OTTHUMG00000153197	ENST00000237455.4:c.839T>C	chr2.hg19:g.86832185A>G	ENSP00000237455:p.Ile280Thr	133.0	0.0	.		133.0	8.0	.	NM_005667	A6NFV6|B2RAG4|Q53SU6|Q8IVB9	Missense_Mutation	SNP	ENST00000237455.4	hg19	CCDS33237.1	.	.	.	.	.	.	.	.	.	.	A	11.95	1.790231	0.31685	.	.	ENSG00000239305	ENST00000237455	T	0.48522	0.81	5.1	5.1	0.69264	.	0.052243	0.85682	D	0.000000	T	0.43033	0.1229	L	0.51422	1.61	0.53688	D	0.999973	B	0.20052	0.041	B	0.16289	0.015	T	0.28073	-1.0055	10	0.30078	T	0.28	-13.0155	14.881	0.70534	1.0:0.0:0.0:0.0	.	280	O00237	RN103_HUMAN	T	280	ENSP00000237455:I280T	ENSP00000237455:I280T	I	-	2	0	RNF103	86685696	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.953000	0.93041	1.937000	0.56155	0.377000	0.23210	ATT	.	.	.	none		0.353	RNF103-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330041.2	NM_005667		G	86832185	A	G	86832185	3	3	216	1	0	0	0	0	1	0	0	0	13436	101	4	3	1222	3	RNF103	2	86832185	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	1471035	86832185	156367188	8	13096											
MALL	7851	hgsc.bcm.edu	37	chr2	110873286	110873286	+	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	agctcgggcaggaagaaggcGaaagggatggtgaggaacag	14	3	19	5	2	0	2	0	1	0	1	1	6	0	5	0	6	2	2	0	6	4	0			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr2:110873286G>A	ENST00000272462.2	-	1	857	c.84C>T	c.(82-84)ttC>ttT	p.F28F	MALL_ENST00000427178.1_Silent_p.F28F	NM_005434.4	NP_005425.1	Q13021	MALL_HUMAN	mal, T-cell differentiation protein-like	28	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				cholesterol homeostasis (GO:0042632)	clathrin-coated vesicle (GO:0030136)|cytoplasmic membrane-bounded vesicle (GO:0016023)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	9				Epithelial(1;0.0546)|STAD - Stomach adenocarcinoma(1;0.18)		GGAAGAAGGCGAAAGGGATGG	0.726																																					p.F28F		Atlas-SNP	.											.	MALL	14	.	0			c.C84T						PASS	.						21	22	21					2																	110873286		2184	4286	6470	SO:0001819	synonymous_variant	7851	exon1			GAAGGCGAAAGGG	U17077	CCDS2085.1	2q13	2008-02-05			ENSG00000144063	ENSG00000144063			6818	protein-coding gene	gene with protein product		602022				9326933	Standard	NM_005434		Approved	BENE	uc002tfk.3	Q13021	OTTHUMG00000131196	ENST00000272462.2:c.84C>T	chr2.hg19:g.110873286G>A		133.0	0.0	.		178.0	22.0	.	NM_005434	B3KWR6|Q9BTU0	Silent	SNP	ENST00000272462.2	hg19	CCDS2085.1																																																																																			.	.	.	none		0.726	MALL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253921.1	NM_005434		A	110873286	G	A	110873286	2	1	216	1	0	0	0	0	0	0	0	1	9208	1049	37	1		1	MALL	2	110873286	Silent	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	24041101	110873286	132326087	9	13097											
SLC20A1	6574	hgsc.bcm.edu	37	chr2	113418053	113418053	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacaccaatatggcttctacTctatggtggtgttggtatct	9	15	9	8	0	3	0	0	0	3	0	3	0	3	0	1	4	2	3	1	4	6	6			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr2:113418053T>C	ENST00000272542.3	+	9	2236	c.1697T>C	c.(1696-1698)cTc>cCc	p.L566P		NM_005415.4	NP_005406.3	Q8WUM9	S20A1_HUMAN	solute carrier family 20 (phosphate transporter), member 1	566					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						TGGCTTCTACTCTATGGTGGT	0.458																																					p.L566P		Atlas-SNP	.											.	SLC20A1	59	.	0			c.T1697C						PASS	.						180	174	176					2																	113418053		2203	4300	6503	SO:0001583	missense	6574	exon9			TTCTACTCTATGG		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.1697T>C	chr2.hg19:g.113418053T>C	ENSP00000272542:p.Leu566Pro	211.0	0.0	.		176.0	29.0	.	NM_005415	Q08344|Q6DHX8|Q9UQ82	Missense_Mutation	SNP	ENST00000272542.3	hg19	CCDS2099.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.570460	0.86542	.	.	ENSG00000144136	ENST00000272542	D	0.91996	-2.95	5.81	5.81	0.92471	.	0.062816	0.64402	D	0.000004	D	0.95191	0.8441	M	0.68593	2.085	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.79108	0.992;0.992	D	0.95405	0.8493	10	0.66056	D	0.02	-33.1091	14.1127	0.65132	0.0:0.0:0.0:1.0	.	566;566	A7LNJ1;Q8WUM9	.;S20A1_HUMAN	P	566	ENSP00000272542:L566P	ENSP00000272542:L566P	L	+	2	0	SLC20A1	113134524	1.000000	0.71417	0.926000	0.36857	0.997000	0.91878	8.040000	0.89188	2.226000	0.72624	0.482000	0.46254	CTC	.	.	.	none		0.458	SLC20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254086.2	NM_005415		C	113418053	T	C	113418053	3	2	216	1	0	0	0	0	1	0	0	0	14451	1551	54	3	1727	3	SLC20A1	2	113418053	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10	2544767	113418053	129781320	10	13098											
INHBB	3625	hgsc.bcm.edu	37	chr2	121106693	121106693	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agatggcctcgcctcctcccGggtccgcctatacttcttca	5	11	8	17	3	2	1	1	0	1	1	6	1	5	1	6	2	1	0	6	2	2	4			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr2:121106693G>A	ENST00000295228.3	+	2	513	c.467G>A	c.(466-468)cGg>cAg	p.R156Q		NM_002193.2	NP_002184.2	P09529	INHBB_HUMAN	inhibin, beta B	156					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)	p.R156Q(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(4)|pancreas(2)|skin(2)	15		Prostate(154;0.122)				GCCTCCTCCCGGGTCCGCCTA	0.557																																					p.R156Q		Atlas-SNP	.											INHBB,NS,adenocarcinoma,0,2	INHBB	29	.	1	Substitution - Missense(1)	large_intestine(1)	c.G467A						PASS	.						53	58	56					2																	121106693		2203	4300	6503	SO:0001583	missense	3625	exon2			CCTCCCGGGTCCG		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.467G>A	chr2.hg19:g.121106693G>A	ENSP00000295228:p.Arg156Gln	133.0	0.0	.		96.0	5.0	.	NM_002193	Q53T31|Q8N1D3	Missense_Mutation	SNP	ENST00000295228.3	hg19	CCDS2132.1	.	.	.	.	.	.	.	.	.	.	G	10.96	1.497539	0.26861	.	.	ENSG00000163083	ENST00000295228	T	0.66995	-0.24	5.09	5.09	0.68999	Transforming growth factor-beta, N-terminal (1);	0.555848	0.17053	N	0.188863	T	0.53850	0.1822	L	0.31664	0.95	0.33909	D	0.639429	B	0.24823	0.112	B	0.26094	0.066	T	0.59316	-0.7477	10	0.30854	T	0.27	-3.725	11.2497	0.49017	0.0848:0.0:0.9151:0.0	.	156	P09529	INHBB_HUMAN	Q	156	ENSP00000295228:R156Q	ENSP00000295228:R156Q	R	+	2	0	INHBB	120823163	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	5.966000	0.70395	2.804000	0.96469	0.655000	0.94253	CGG	.	.	.	none		0.557	INHBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254234.1			A	121106693	G	A	121106693	3	1	216	1	0	0	0	0	1	0	0	0	7749	1116	39	1	473	1	INHBB	2	121106693	Missense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	7688640	121106693	122092680	11	13099											
ANKRD44	91526	hgsc.bcm.edu	37	chr2	197878244	197878244	+	Frame_Shift_Del	DEL	G	G	-																															acaagacctacctgaggcatGaagtggggttcttttggtta																										TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr2:197878244delG	ENST00000328737.2	-	18	1916	c.1840delC	c.(1840-1842)catfs	p.H614fs	ANKRD44_ENST00000282272.8_Frame_Shift_Del_p.H631fs|ANKRD44_ENST00000337207.5_Frame_Shift_Del_p.H614fs|ANKRD44_ENST00000450567.1_Frame_Shift_Del_p.H614fs			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	639										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)			CCTGAGGCATGAAGTGGGGTT	0.443																																					p.H639fs		Atlas-Indel,Pindel	.											.	ANKRD44	281	.	0			c.1916delA						PASS	.						168	160	163					2																	197878244		2203	4300	6503	SO:0001589	frameshift_variant	91526	exon18			.	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.1840delC	chr2.hg19:g.197878244delG	ENSP00000331516:p.His614fs	141.0	0.0	0		134.0	31.0	0.231343	NM_001195144	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Frame_Shift_Del	DEL	ENST00000328737.2	hg19																																																																																				.	.	.	none		0.443	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697		-	197878244	G	-	197878244	7	5	216	1	0	1	0	1	0	0	0	0	672	1290	45	0	955	0	ANKRD44	2	197878244	Frame_Shift_Del	DEL	G	TCGA-KV-A6GD-01A-11D-A31X-10	76771551	197878244	45321129	12	13100											
EEF1B2	1933	hgsc.bcm.edu	37	chr2	207027278	207027278	+	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	cttgggatgatgagacagatAtggcgaaattagaggagtgc	13	9	15	4	1	0	4	0	2	0	3	0	8	0	6	0	3	1	0	0	3	3	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr2:207027278A>T	ENST00000392222.2	+	5	838	c.463A>T	c.(463-465)Atg>Ttg	p.M155L	NDUFS1_ENST00000233190.6_5'Flank|EEF1B2_ENST00000236957.5_Missense_Mutation_p.M155L|SNORA41_ENST00000384675.1_RNA|EEF1B2_ENST00000392221.1_Missense_Mutation_p.M155L|SNORD51_ENST00000384320.2_RNA	NM_001959.3	NP_001950.1	P24534	EF1B_HUMAN	eukaryotic translation elongation factor 1 beta 2	155					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						TGAGACAGATATGGCGAAATT	0.388																																					p.M155L		Atlas-SNP	.											.	EEF1B2	58	.	0			c.A463T						PASS	.						125	132	129					2																	207027278		2203	4300	6503	SO:0001583	missense	1933	exon6			ACAGATATGGCGA	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.463A>T	chr2.hg19:g.207027278A>T	ENSP00000376056:p.Met155Leu	206.0	0.0	.		209.0	28.0	.	NM_021121	A8K795|Q6IBH9	Missense_Mutation	SNP	ENST00000392222.2	hg19	CCDS2367.1	.	.	.	.	.	.	.	.	.	.	A	15.97	2.990128	0.54041	.	.	ENSG00000114942	ENST00000236957;ENST00000392221;ENST00000392222	.	.	.	5.24	5.24	0.73138	Translation elongation factor EF1B/ribosomal protein S6 (1);Translation elongation factor EF1B, beta/delta subunit, guanine nucleotide exchange (3);	0.071117	0.85682	D	0.000000	T	0.54902	0.1887	L	0.39245	1.2	0.80722	D	1	B	0.02656	0.0	B	0.20384	0.029	T	0.50651	-0.8803	9	0.33940	T	0.23	-16.9302	15.1403	0.72607	1.0:0.0:0.0:0.0	.	155	P24534	EF1B_HUMAN	L	155	.	ENSP00000236957:M155L	M	+	1	0	EEF1B2	206735523	1.000000	0.71417	0.994000	0.49952	0.958000	0.62258	9.237000	0.95368	1.984000	0.57885	0.533000	0.62120	ATG	.	.	.	none		0.388	EEF1B2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336436.1	NM_001037663		T	207027278	A	T	207027278	3	4	216	1	0	0	0	0	1	0	0	0	4927	449	16	5	481	5	EEF1B2	2	207027278	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	9149034	207027278	36172095	13	13101											
RAB17	64284	hgsc.bcm.edu	37	chr2	238494741	238494741	+	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	cccaggagaaccagcttgaaCacacggggctggctgggggc	9	4	16	12	1	0	2	0	1	0	1	0	3	0	2	2	6	3	3	2	6	2	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr2:238494741C>A	ENST00000264601.3	-	2	686	c.57G>T	c.(55-57)gtG>gtT	p.V19V	RAB17_ENST00000538644.1_5'UTR|RAB17_ENST00000409576.1_Intron|RAB17_ENST00000409822.1_Intron|RAB17_ENST00000416106.1_5'UTR	NM_022449.3	NP_071894.1	Q9H0T7	RAB17_HUMAN	RAB17, member RAS oncogene family	19			V -> A (in dbSNP:rs3751112). {ECO:0000269|Ref.3}.		cilium assembly (GO:0042384)|endocytic recycling (GO:0032456)|establishment of melanosome localization (GO:0032401)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|melanosome transport (GO:0032402)|protein transport (GO:0015031)|regulation of dendrite development (GO:0050773)|regulation of filopodium assembly (GO:0051489)|regulation of synapse assembly (GO:0051963)|small GTPase mediated signal transduction (GO:0007264)|transcytosis (GO:0045056)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|dendrite (GO:0030425)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|melanosome (GO:0042470)|neuronal cell body (GO:0043025)|recycling endosome (GO:0055037)|recycling endosome membrane (GO:0055038)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(1)	4		Renal(207;0.00272)|Breast(86;0.00297)|all_hematologic(139;0.182)|Ovarian(221;0.221)		Epithelial(121;9.36e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.26e-10)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000354)|Lung(119;0.011)|LUSC - Lung squamous cell carcinoma(224;0.026)		CCAGCTTGAACACACGGGGCT	0.597																																					p.V19V	Colon(56;987 1029 6466 13943 27336)	Atlas-SNP	.											.	RAB17	17	.	0			c.G57T						PASS	.						57	57	57					2																	238494741		2203	4300	6503	SO:0001819	synonymous_variant	64284	exon2			CTTGAACACACGG	AK022600	CCDS2520.1	2q37.3	2008-05-23			ENSG00000124839	ENSG00000124839		"RAB, member RAS oncogene"	16523	protein-coding gene	gene with protein product		602206				9624171	Standard	NM_022449		Approved		uc002vwz.2	Q9H0T7	OTTHUMG00000133299	ENST00000264601.3:c.57G>T	chr2.hg19:g.238494741C>A		116.0	0.0	.		120.0	18.0	.	NM_022449	Q53QV6|Q6IA73|Q6PJZ0|Q9BVU1|Q9H9U9	Silent	SNP	ENST00000264601.3	hg19	CCDS2520.1	.	.	.	.	.	.	.	.	.	.	C	6.279	0.419620	0.11928	.	.	ENSG00000124839	ENST00000430445	.	.	.	4.69	-3.2	0.05156	.	.	.	.	.	T	0.49029	0.1533	.	.	.	0.58432	D	0.999991	.	.	.	.	.	.	T	0.40515	-0.9559	4	.	.	.	-6.0609	5.8207	0.18526	0.0869:0.4881:0.2678:0.1572	.	.	.	.	F	1	.	.	C	-	2	0	RAB17	238159480	0.001000	0.12720	0.004000	0.12327	0.070000	0.16714	-0.140000	0.10342	-0.948000	0.03668	-1.094000	0.02160	TGT	.	.	.	none		0.597	RAB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257084.2			A	238494741	C	A	238494741	2	1	216	1	0	0	0	0	0	0	0	1	12915	465	17	4		4	RAB17	2	238494741	Silent	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	31467463	238494741	4704632	14	13102											
SLC6A6	6533	hgsc.bcm.edu	37	chr3	14508107	14508107	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgctgccgggcgcgggcgcAggcatcaagttctatctgta	7	8	14	12	5	3	0	1	0	2	0	3	0	3	0	1	3	1	5	1	3	3	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr3:14508107A>G	ENST00000454876.2	+	7	1145	c.816A>G	c.(814-816)gcA>gcG	p.A272A	SLC6A6_ENST00000360861.3_Silent_p.A272A			P31641	SC6A6_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 6	272				A -> R (in Ref. 1; CAA79481). {ECO:0000305}.	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						GCGCGGGCGCAGGCATCAAGT	0.632																																					p.A272A		Atlas-SNP	.											.	SLC6A6	58	.	0			c.A816G						PASS	.						80	70	73					3																	14508107		2203	4300	6503	SO:0001819	synonymous_variant	6533	exon7			GGGCGCAGGCATC		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.816A>G	chr3.hg19:g.14508107A>G		60.0	0.0	.		64.0	9.0	.	NM_003043	B2RNU7|Q9BRI2|Q9BXB0	Silent	SNP	ENST00000454876.2	hg19	CCDS33705.1																																																																																			.	.	.	none		0.632	SLC6A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340507.1	NM_003043		G	14508107	A	G	14508107	2	3	216	1	0	0	0	0	0	0	0	1	14701	175	7	3		3	SLC6A6	3	14508107	Silent	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10		14508107	183514323	15	13103											
TMEM115	11070	hgsc.bcm.edu	37	chr3	50396218	50396218	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcagctccaaggccccccAgaggggctccagcaaacgcc	10	2	12	17	1	0	1	0	0	0	1	2	2	2	1	6	3	4	4	6	3	2	0			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr3:50396218A>G	ENST00000266025.3	-	1	823	c.277T>C	c.(277-279)Tgg>Cgg	p.W93R	XXcos-LUCA11.5_ENST00000606589.1_Intron	NM_007024.4	NP_008955.1	Q12893	TM115_HUMAN	transmembrane protein 115	93					negative regulation of cell proliferation (GO:0008285)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(2)|endometrium(1)|lung(1)|prostate(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		AAGGCCCCCCAGAGGGGCTCC	0.622																																					p.W93R		Atlas-SNP	.											.	TMEM115	20	.	0			c.T277C						PASS	.						55	68	64					3																	50396218		2203	4300	6503	SO:0001583	missense	11070	exon1			CCCCCCAGAGGGG	BC011948	CCDS2828.1	3p21.31	2008-11-04			ENSG00000126062	ENSG00000126062			30055	protein-coding gene	gene with protein product	"placental protein 6"	607069				11085536	Standard	NM_007024		Approved	PL6	uc003dan.1	Q12893	OTTHUMG00000044212	ENST00000266025.3:c.277T>C	chr3.hg19:g.50396218A>G	ENSP00000266025:p.Trp93Arg	89.0	0.0	.		86.0	12.0	.	NM_007024	A2IDB7|O14568|Q6IAY4|Q9UIX3	Missense_Mutation	SNP	ENST00000266025.3	hg19	CCDS2828.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.371161	0.82573	.	.	ENSG00000126062	ENST00000266025	T	0.11712	2.75	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.39682	0.1087	M	0.89414	3.03	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.46555	-0.9183	10	0.87932	D	0	.	14.4388	0.67301	1.0:0.0:0.0:0.0	.	93	Q12893	TM115_HUMAN	R	93	ENSP00000266025:W93R	ENSP00000266025:W93R	W	-	1	0	TMEM115	50371222	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	8.943000	0.92975	2.110000	0.64415	0.460000	0.39030	TGG	.	.	.	none		0.622	TMEM115-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102784.3	NM_007024		G	50396218	A	G	50396218	3	3	216	1	0	0	0	0	1	0	0	0	16041	188	7	3	786	3	TMEM115	3	50396218	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	35888111	50396218	147626212	16	13104											
P2RY1	5028	hgsc.bcm.edu	37	chr3	152554007	152554007	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttgtttctgacatgcatcAgtgcccaccggtacagcggt	7	12	10	12	2	3	1	1	1	2	0	3	1	3	1	2	2	4	3	2	2	1	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr3:152554007A>G	ENST00000305097.3	+	1	1272	c.436A>G	c.(436-438)Agt>Ggt	p.S146G		NM_002563.3	NP_002554.1	P47900	P2RY1_HUMAN	purinergic receptor P2Y, G-protein coupled, 1	146					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)			GACATGCATCAGTGCCCACCG	0.507																																					p.S146G		Atlas-SNP	.											.	P2RY1	49	.	0			c.A436G						PASS	.						91	79	83					3																	152554007		2203	4300	6503	SO:0001583	missense	5028	exon1			TGCATCAGTGCCC	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.436A>G	chr3.hg19:g.152554007A>G	ENSP00000304767:p.Ser146Gly	82.0	0.0	.		90.0	5.0	.	NM_002563		Missense_Mutation	SNP	ENST00000305097.3	hg19	CCDS3169.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.164790	0.78339	.	.	ENSG00000169860	ENST00000305097	T	0.80994	-1.44	5.76	5.76	0.90799	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.90844	0.7124	M	0.92122	3.275	0.58432	D	0.999999	D	0.63046	0.992	P	0.60012	0.867	D	0.92885	0.6326	10	0.72032	D	0.01	.	15.2728	0.73717	1.0:0.0:0.0:0.0	.	146	P47900	P2RY1_HUMAN	G	146	ENSP00000304767:S146G	ENSP00000304767:S146G	S	+	1	0	P2RY1	154036697	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	9.210000	0.95106	2.186000	0.69663	0.533000	0.62120	AGT	.	.	.	none		0.507	P2RY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356943.1	NM_002563		G	152554007	A	G	152554007	3	3	216	1	0	0	0	0	1	0	0	0	11353	188	7	3	438	3	P2RY1	3	152554007	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	102157789	152554007	45468423	17	13105											
FGFR3	2261	hgsc.bcm.edu	37	chr4	1807653	1807653	+	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	tggcccggggcatggagtacTtggcctcccagaaggtgggc	6	7	17	11	1	0	1	0	0	0	1	1	2	1	2	3	7	1	2	3	7	2	2			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr4:1807653T>A	ENST00000260795.2	+	12	1924	c.1822T>A	c.(1822-1824)Ttg>Atg	p.L608M	FGFR3_ENST00000481110.2_Missense_Mutation_p.L609M|FGFR3_ENST00000412135.2_Missense_Mutation_p.L496M|FGFR3_ENST00000352904.1_Missense_Mutation_p.L496M|FGFR3_ENST00000340107.4_Missense_Mutation_p.L610M|FGFR3_ENST00000440486.2_Missense_Mutation_p.L608M			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	608	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)			NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	CATGGAGTACTTGGCCTCCCA	0.662		1	"Mis, T"	"IGH@, ETV6"	"bladder, MM, T-cell lymphoma"		"Hypochondroplasia, Thanatophoric dysplasia"		Saethre-Chotzen syndrome;Muenke syndrome																												p.L610M		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"L, E"	.	FGFR3	3320	.	0			c.T1828A						PASS	.						39	47	44					4																	1807653		2203	4299	6502	SO:0001583	missense	2261	exon13	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	GAGTACTTGGCCT	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.1822T>A	chr4.hg19:g.1807653T>A	ENSP00000260795:p.Leu608Met	57.0	0.0	.		55.0	17.0	.	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Missense_Mutation	SNP	ENST00000260795.2	hg19	CCDS3353.1	.	.	.	.	.	.	.	.	.	.	c	11.98	1.799537	0.31869	.	.	ENSG00000068078	ENST00000481110;ENST00000340107;ENST00000440486;ENST00000412135;ENST00000260795;ENST00000352904	D;D;D;D;D;D	0.92446	-3.04;-3.04;-3.04;-3.04;-3.04;-3.04	4.18	1.33	0.21861	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000001	D	0.95586	0.8565	M	0.86805	2.84	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;0.999;0.998;0.991	D	0.94568	0.7768	10	0.87932	D	0	.	10.2771	0.43517	0.0:0.681:0.0:0.319	.	610;496;608;609	P22607-2;P22607-3;P22607;F8W9L4	.;.;FGFR3_HUMAN;.	M	609;610;608;496;608;496	ENSP00000420533:L609M;ENSP00000339824:L610M;ENSP00000414914:L608M;ENSP00000412903:L496M;ENSP00000260795:L608M;ENSP00000231803:L496M	ENSP00000260795:L608M	L	+	1	2	FGFR3	1777451	0.995000	0.38212	0.995000	0.50966	0.390000	0.30446	0.568000	0.23623	0.311000	0.23014	-1.193000	0.01689	TTG	.	.	.	none		0.662	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142		A	1807653	T	A	1807653	3	1	216	1	0	0	0	0	1	0	0	0	5874	1606	56	5	2023	5	FGFR3	4	1807653	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10		1807653	189346623	18	13106											
SLC4A4	8671	hgsc.bcm.edu	37	chr4	72413388	72413388	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acaaagagtcactggaacccTtgtgtttattctgactggtc	10	13	9	9	0	2	2	1	1	1	1	3	3	2	3	1	2	1	1	1	2	3	4			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr4:72413388T>C	ENST00000264485.5	+	20	2762	c.2645T>C	c.(2644-2646)cTt>cCt	p.L882P	SLC4A4_ENST00000351898.6_Intron|SLC4A4_ENST00000340595.3_Missense_Mutation_p.L838P|SLC4A4_ENST00000425175.1_Missense_Mutation_p.L882P	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	882					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)	ACTGGAACCCTTGTGTTTATT	0.373																																					p.L882P		Atlas-SNP	.											.	SLC4A4	269	.	0			c.T2645C						PASS	.						217	212	214					4																	72413388		2203	4300	6503	SO:0001583	missense	8671	exon20			GAACCCTTGTGTT	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.2645T>C	chr4.hg19:g.72413388T>C	ENSP00000264485:p.Leu882Pro	109.0	0.0	.		82.0	7.0	.	NM_001098484	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	hg19	CCDS43236.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.277920	0.80692	.	.	ENSG00000080493	ENST00000264485;ENST00000425175;ENST00000340595	D;D;D	0.82167	-1.58;-1.58;-1.58	5.81	5.81	0.92471	Bicarbonate transporter, C-terminal (1);	0.329506	0.33980	N	0.004364	D	0.87661	0.6233	M	0.80183	2.485	0.80722	D	1	P;P;B	0.40230	0.708;0.481;0.242	P;B;B	0.46208	0.507;0.419;0.427	D	0.89124	0.3505	10	0.87932	D	0	.	16.167	0.81768	0.0:0.0:0.0:1.0	.	882;838;882	A5JJ20;Q9Y6R1-2;Q9Y6R1	.;.;S4A4_HUMAN	P	882;882;838	ENSP00000264485:L882P;ENSP00000393557:L882P;ENSP00000344272:L838P	ENSP00000264485:L882P	L	+	2	0	SLC4A4	72632252	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.184000	0.72008	2.210000	0.71456	0.533000	0.62120	CTT	.	.	.	none		0.373	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		C	72413388	T	C	72413388	3	2	216	1	0	0	0	0	1	0	0	0	14669	1609	56	3	2840	3	SLC4A4	4	72413388	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10	70605735	72413388	118740888	19	13107											
ISL1	3670	hgsc.bcm.edu	37	chr5	50680410	50680410	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctatgtgttggttgcggcAatcagattcacgatcagtat	9	13	10	9	2	3	1	3	0	0	1	3	2	3	1	1	2	1	4	1	2	3	5			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr5:50680410A>G	ENST00000230658.7	+	2	649	c.64A>G	c.(64-66)Aat>Gat	p.N22D	ISL1_ENST00000511384.1_Missense_Mutation_p.N22D|CTD-2314G24.2_ENST00000559112.2_RNA	NM_002202.2	NP_002193.2	P61371	ISL1_HUMAN	ISL LIM homeobox 1	22	LIM zinc-binding 1. {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)				TGGTTGCGGCAATCAGATTCA	0.393																																					p.N22D		Atlas-SNP	.											.	ISL1	65	.	0			c.A64G						PASS	.						141	131	134					5																	50680410		1856	4100	5956	SO:0001583	missense	3670	exon2			TGCGGCAATCAGA	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.64A>G	chr5.hg19:g.50680410A>G	ENSP00000230658:p.Asn22Asp	189.0	0.0	.		173.0	47.0	.	NM_002202	P20663|P47894	Missense_Mutation	SNP	ENST00000230658.7	hg19	CCDS43314.1	.	.	.	.	.	.	.	.	.	.	A	14.93	2.682347	0.47991	.	.	ENSG00000016082	ENST00000230658;ENST00000503187;ENST00000511384	D;D	0.87029	-2.2;-2.2	6.16	6.16	0.99307	Zinc finger, LIM-type (5);	0.000000	0.85682	D	0.000000	T	0.79040	0.4379	N	0.13098	0.295	0.58432	D	0.999993	P	0.36183	0.542	B	0.36030	0.216	T	0.78427	-0.2208	10	0.31617	T	0.26	.	16.8061	0.85666	1.0:0.0:0.0:0.0	.	22	P61371	ISL1_HUMAN	D	22	ENSP00000230658:N22D;ENSP00000422676:N22D	ENSP00000230658:N22D	N	+	1	0	ISL1	50716167	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.543000	0.82106	2.367000	0.80283	0.528000	0.53228	AAT	.	.	.	none		0.393	ISL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368413.3	NM_002202		G	50680410	A	G	50680410	3	3	216	1	0	0	0	0	1	0	0	0	7863	130	5	3	70	3	ISL1	5	50680410	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10		50680410	130234850	20	13108											
SEC24A	10802	hgsc.bcm.edu	37	chr5	134060676	134060676	+	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	cttttattcctaagggatgaGagtccaatgaaagcaaactt	14	12	8	7	0	0	2	0	2	0	1	2	4	2	3	2	1	2	1	2	1	5	5			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr5:134060676G>C	ENST00000398844.2	+	23	3462	c.3174G>C	c.(3172-3174)gaG>gaC	p.E1058D		NM_021982.2	NP_068817.1	O95486	SC24A_HUMAN	SEC24 family member A	1058					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of protein secretion (GO:0050714)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045714)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	36			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TAAGGGATGAGAGTCCAATGA	0.323																																					p.E1058D		Atlas-SNP	.											.	SEC24A	77	.	0			c.G3174C						PASS	.						60	56	57					5																	134060676		1806	4068	5874	SO:0001583	missense	10802	exon23			GGATGAGAGTCCA	AJ131244	CCDS43363.1, CCDS58967.1	5q31.1	2013-10-21	2013-10-21		ENSG00000113615	ENSG00000113615			10703	protein-coding gene	gene with protein product		607183	"SEC24 (S. cerevisiae) related gene family, member A", "SEC24 family, member A (S. cerevisiae)"			10075675, 10329445	Standard	NM_021982		Approved		uc003kzs.3	O95486	OTTHUMG00000163064	ENST00000398844.2:c.3174G>C	chr5.hg19:g.134060676G>C	ENSP00000381823:p.Glu1058Asp	409.0	0.0	.		404.0	43.0	.	NM_021982	A8MVW3|Q8WUV2|Q96GP7	Missense_Mutation	SNP	ENST00000398844.2	hg19	CCDS43363.1	.	.	.	.	.	.	.	.	.	.	G	7.791	0.711484	0.15239	.	.	ENSG00000113615	ENST00000398844	T	0.28666	1.6	5.68	5.68	0.88126	.	0.045285	0.85682	D	0.000000	T	0.11623	0.0283	N	0.04260	-0.245	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29731	-1.0002	10	0.10902	T	0.67	-12.469	5.5239	0.16947	0.1812:0.1697:0.6491:0.0	.	822;1058	B4E205;O95486	.;SC24A_HUMAN	D	1058	ENSP00000381823:E1058D	ENSP00000381823:E1058D	E	+	3	2	SEC24A	134088575	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.734000	0.26101	2.691000	0.91804	0.650000	0.86243	GAG	.	.	.	none		0.323	SEC24A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371563.1			C	134060676	G	C	134060676	3	2	216	1	0	0	0	0	1	0	0	0	14007	933	33	4	3264	4	SEC24A	5	134060676	Missense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	83380266	134060676	46854584	21	13109											
HNRNPA0	10949	hgsc.bcm.edu	37	chr5	137088931	137088931	+	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	ccccagctactgcctccaccGccgccgccgccgccgctctt	3	6	8	24	6	1	0	0	0	1	0	2	0	2	0	10	0	3	2	10	0	1	2			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr5:137088931G>A	ENST00000314940.4	-	1	1108	c.825C>T	c.(823-825)ggC>ggT	p.G275G		NM_006805.3	NP_006796.1	Q13151	ROA0_HUMAN	heterogeneous nuclear ribonucleoprotein A0	275	Gly-rich.				3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|inflammatory response (GO:0006954)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|response to lipopolysaccharide (GO:0032496)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)	p.G275G(1)		large_intestine(1)|lung(2)|skin(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			Tgcctccaccgccgccgccgc	0.632																																					p.G275G		Atlas-SNP	.											HNRNPA0,colon,carcinoma,0,1	HNRNPA0	17	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C825T						PASS	.						9	13	11					5																	137088931		1925	3891	5816	SO:0001819	synonymous_variant	10949	exon1			TCCACCGCCGCCG	U23803	CCDS4193.1	5q31	2013-02-12		2007-08-16	ENSG00000177733	ENSG00000177733		"RNA binding motif (RRM) containing"	5030	protein-coding gene	gene with protein product		609409		HNRPA0		7585247	Standard	NM_006805		Approved	hnRNPA0	uc003lbt.3	Q13151	OTTHUMG00000129156	ENST00000314940.4:c.825C>T	chr5.hg19:g.137088931G>A		70.0	1.0	.		85.0	7.0	.	NM_006805	Q6IB18	Silent	SNP	ENST00000314940.4	hg19	CCDS4193.1																																																																																			.	.	.	none		0.632	HNRNPA0-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251221.1	NM_006805		A	137088931	G	A	137088931	2	1	216	1	0	0	0	0	0	0	0	1	7263	1074	38	1		1	HNRNPA0	5	137088931	Silent	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	3028255	137088931	43826329	22	13110											
C5orf41	153222	hgsc.bcm.edu	37	chr5	172518246	172518246	+	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	gccaactaaatgcagtcctgAagaagatgaggaggacgagg	15	5	14	7	1	0	4	0	2	0	2	1	7	1	6	2	3	2	1	2	3	5	1	rs374100928		TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr5:172518246A>T	ENST00000296953.2	+	4	1383	c.1064A>T	c.(1063-1065)gAa>gTa	p.E355V	CREBRF_ENST00000540014.1_Missense_Mutation_p.E355V|CREBRF_ENST00000520420.1_Missense_Mutation_p.E355V|CREBRF_ENST00000522692.1_Missense_Mutation_p.E355V	NM_153607.2	NP_705835.2	Q8IUR6	CRERF_HUMAN	CREB3 regulatory factor	355	Glu-rich.				negative regulation of endoplasmic reticulum unfolded protein response (GO:1900102)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of intracellular transport (GO:0032388)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein transport (GO:0051222)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TGCAGTCCtgaagaagatgag	0.443																																					p.E355V		Atlas-SNP	.											.	.	.	.	0			c.A1064T						PASS	.						63	50	54					5																	172518246		2203	4300	6503	SO:0001583	missense	153222	exon4			GTCCTGAAGAAGA	AY139008	CCDS34293.1, CCDS54948.1	5q35.2	2012-03-06	2012-03-06	2012-03-06	ENSG00000164463	ENSG00000164463			24050	protein-coding gene	gene with protein product	"luman/CREB3 recruitment factor"		"chromosome 5 open reading frame 41"	C5orf41		18391022	Standard	NM_153607		Approved	LRF	uc003mch.3	Q8IUR6	OTTHUMG00000163322	ENST00000296953.2:c.1064A>T	chr5.hg19:g.172518246A>T	ENSP00000296953:p.Glu355Val	190.0	0.0	.		169.0	32.0	.	NM_153607	B3DFH2|B3KW49|D3DQM2|F5GXN3|Q5HYG4|Q5HYK0|Q86YR3|Q8IZG1	Missense_Mutation	SNP	ENST00000296953.2	hg19	CCDS34293.1	.	.	.	.	.	.	.	.	.	.	A	17.18	3.323089	0.60634	.	.	ENSG00000164463	ENST00000522692;ENST00000296953;ENST00000540014;ENST00000520420;ENST00000538538;ENST00000393776	T;T;T;T	0.70749	-0.51;2.19;2.19;-0.51	5.52	5.52	0.82312	.	0.433677	0.23268	N	0.050045	T	0.75525	0.3861	N	0.24115	0.695	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.83275	0.991;0.996	T	0.78703	-0.2101	10	0.66056	D	0.02	.	15.3153	0.74069	1.0:0.0:0.0:0.0	.	355;355	Q8IUR6;Q8IUR6-2	CE041_HUMAN;.	V	355	ENSP00000431107:E355V;ENSP00000296953:E355V;ENSP00000440075:E355V;ENSP00000428290:E355V	ENSP00000296953:E355V	E	+	2	0	C5orf41	172450852	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.297000	0.72757	2.103000	0.63969	0.533000	0.62120	GAA	.	.	.	none		0.443	CREBRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372667.1	NM_153607		T	172518246	A	T	172518246	3	4	216	1	0	0	0	0	1	0	0	0	2302	246	9	5	1074	5	C5orf41	5	172518246	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	35429315	172518246	8397014	23	13111											
SESN1	27244	hgsc.bcm.edu	37	chr6	109309823	109309823	+	Frame_Shift_Del	DEL	T	T	-																															ttcaggagtgcaaacaacagTtttgatataaactttaaagc																										TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr6:109309823delT	ENST00000356644.7	-	9	1409	c.1315delA	c.(1315-1317)actfs	p.T439fs	SESN1_ENST00000302071.2_Frame_Shift_Del_p.T373fs|SESN1_ENST00000436639.2_Frame_Shift_Del_p.T498fs	NM_001199933.1	NP_001186862.1	Q9Y6P5	SESN1_HUMAN	sestrin 1	439					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of cell proliferation (GO:0008285)|regulation of protein kinase B signaling (GO:0051896)|regulation of response to reactive oxygen species (GO:1901031)	nucleus (GO:0005634)				cervix(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	10		all_cancers(87;6.45e-05)|Acute lymphoblastic leukemia(125;3.55e-10)|all_hematologic(75;1.68e-07)|all_epithelial(87;0.0106)|Colorectal(196;0.0637)		Epithelial(106;0.0014)|BRCA - Breast invasive adenocarcinoma(108;0.00146)|all cancers(137;0.0031)|OV - Ovarian serous cystadenocarcinoma(136;0.0117)		CAAACAACAGTTTTGATATAA	0.343																																					p.T498fs		Atlas-Indel,Pindel	.											.	SESN1	29	.	0			c.1493delC						PASS	.						83	75	77					6																	109309823		2203	4300	6503	SO:0001589	frameshift_variant	27244	exon9			.	AF033120	CCDS5070.1, CCDS56444.1, CCDS56445.1	6q21	2008-10-23			ENSG00000080546	ENSG00000080546			21595	protein-coding gene	gene with protein product		606103				9926927, 7938006	Standard	NM_014454		Approved	SEST1, PA26	uc003psu.3	Q9Y6P5	OTTHUMG00000015338	ENST00000356644.7:c.1315delA	chr6.hg19:g.109309823delT	ENSP00000349061:p.Thr439fs	51.0	0.0	0		56.0	13.0	0.232143	NM_014454	Q2M2B7|Q5T316|Q9NV00|Q9UPD5|Q9Y6P6	Frame_Shift_Del	DEL	ENST00000356644.7	hg19	CCDS56445.1																																																																																			.	.	.	none		0.343	SESN1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041738.4	NM_014454		-	109309823	T	-	109309823	7	5	216	1	0	1	0	1	0	0	0	0	14137	1725	60	0	171	0	SESN1	6	109309823	Frame_Shift_Del	DEL	T	TCGA-KV-A6GD-01A-11D-A31X-10		109309823	61805244	24	13112											
HIVEP2	3097	hgsc.bcm.edu	37	chr6	143090738	143090738	+	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	atgtaagcttgccggttccaGgcctatgcatagcagccaga	10	9	11	11	1	0	1	0	0	0	1	1	1	1	1	4	2	5	5	4	2	3	5			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr6:143090738G>T	ENST00000367604.1	-	4	5777	c.5138C>A	c.(5137-5139)cCt>cAt	p.P1713H	HIVEP2_ENST00000012134.2_Missense_Mutation_p.P1713H|HIVEP2_ENST00000367603.2_Missense_Mutation_p.P1713H			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	1713					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		GCCGGTTCCAGGCCTATGCAT	0.433																																					p.P1713H	Esophageal Squamous(107;843 1510 13293 16805 42198)	Atlas-SNP	.											.	HIVEP2	225	.	0			c.C5138A						PASS	.						118	109	112					6																	143090738		1861	4116	5977	SO:0001583	missense	3097	exon5			GTTCCAGGCCTAT	M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"Zinc fingers, C2H2-type"	4921	protein-coding gene	gene with protein product	"c-myc intron binding protein 1"	143054	"human immunodeficiency virus type I enhancer-binding protein 2"			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.5138C>A	chr6.hg19:g.143090738G>T	ENSP00000356576:p.Pro1713His	133.0	0.0	.		93.0	17.0	.	NM_006734	Q02646|Q5THT5|Q9NS05	Missense_Mutation	SNP	ENST00000367604.1	hg19	CCDS43510.1	.	.	.	.	.	.	.	.	.	.	G	16.83	3.231189	0.58777	.	.	ENSG00000010818	ENST00000367604;ENST00000367603;ENST00000012134	T;T;T	0.02863	4.13;4.13;4.13	5.95	4.11	0.48088	.	0.192613	0.56097	D	0.000024	T	0.04907	0.0132	M	0.72894	2.215	0.47407	D	0.999417	D	0.67145	0.996	P	0.58013	0.831	T	0.10019	-1.0648	10	0.87932	D	0	-17.5678	8.3283	0.32171	0.135:0.1282:0.7368:0.0	.	1713	P31629	ZEP2_HUMAN	H	1713	ENSP00000356576:P1713H;ENSP00000356575:P1713H;ENSP00000012134:P1713H	ENSP00000012134:P1713H	P	-	2	0	HIVEP2	143132431	1.000000	0.71417	0.975000	0.42487	0.991000	0.79684	6.728000	0.74769	1.514000	0.48869	0.655000	0.94253	CCT	.	.	.	none		0.433	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1			T	143090738	G	T	143090738	3	4	216	1	0	0	0	0	1	0	0	0	7194	1000	35	4	2226	4	HIVEP2	6	143090738	Missense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	33780915	143090738	28024329	25	13113											
EIF2AK1	27102	hgsc.bcm.edu	37	chr7	6084205	6084205	+	Missense_Mutation	SNP	T	T	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	cggcttacctcgtggctgaaTcacatgaacatgttctatcc	9	12	8	12	2	2	2	1	2	1	0	4	2	3	2	2	2	2	3	2	2	4	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr7:6084205T>G	ENST00000199389.6	-	7	864	c.718A>C	c.(718-720)Att>Ctt	p.I240L	EIF2AK1_ENST00000495565.1_5'UTR|EIF2AK1_ENST00000536084.1_Missense_Mutation_p.I116L	NM_001134335.1|NM_014413.3	NP_001127807.1|NP_055228.2	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 1	240	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of cell proliferation (GO:0008285)|negative regulation of hemoglobin biosynthetic process (GO:0046986)|negative regulation of translational initiation by iron (GO:0045993)|protein autophosphorylation (GO:0046777)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|response to external stimulus (GO:0009605)|response to stress (GO:0006950)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	27		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)		CGTGGCTGAATCACATGAACA	0.468																																					p.I240L		Atlas-SNP	.											.	EIF2AK1	76	.	0			c.A718C						PASS	.						99	79	86					7																	6084205		2203	4300	6503	SO:0001583	missense	27102	exon7			GCTGAATCACATG	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.718A>C	chr7.hg19:g.6084205T>G	ENSP00000199389:p.Ile240Leu	31.0	0.0	.		41.0	6.0	.	NM_001134335	A8K2R2|Q549K6|Q8NBW3|Q9HC02|Q9NYE0|Q9P0V6|Q9P1J5|Q9P2H8|Q9UHG4	Missense_Mutation	SNP	ENST00000199389.6	hg19	CCDS5345.1	.	.	.	.	.	.	.	.	.	.	.	1.012	-0.687440	0.03328	.	.	ENSG00000086232	ENST00000199389;ENST00000536084	T;T	0.14144	2.53;2.53	5.2	2.36	0.29203	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.526065	0.21443	N	0.074457	T	0.06826	0.0174	N	0.17723	0.515	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.11329	0.006;0.002;0.002	T	0.42932	-0.9422	10	0.11485	T	0.65	-0.4159	5.4401	0.16504	0.0:0.4964:0.2696:0.234	.	116;240;240	B4DIP4;Q9BQI3-2;Q9BQI3	.;.;E2AK1_HUMAN	L	240;116	ENSP00000199389:I240L;ENSP00000445784:I116L	ENSP00000199389:I240L	I	-	1	0	EIF2AK1	6050731	0.000000	0.05858	0.062000	0.19696	0.277000	0.26821	-0.787000	0.04618	0.180000	0.19960	-0.248000	0.11899	ATT	.	.	.	none		0.468	EIF2AK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207373.2	NM_014413		G	6084205	T	G	6084205	3	3	216	1	0	0	0	0	1	0	0	0	4998	1435	50	5	1210	5	EIF2AK1	7	6084205	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10		6084205	153054458	26	13114											
CLCN1	1180	hgsc.bcm.edu	37	chr7	143049049	143049049	+	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	gaggaggatgaggatgaactGatcctttgaccccctcccac	10	8	11	12	0	0	4	0	4	0	0	2	8	2	7	4	3	1	0	4	3	1	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr7:143049049G>A	ENST00000343257.2	+	23	3045	c.2958G>A	c.(2956-2958)ctG>ctA	p.L986L		NM_000083.2	NP_000074	P35523	CLCN1_HUMAN	chloride channel, voltage-sensitive 1	986					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)					AGGATGAACTGATCCTTTGAC	0.617																																					p.L986L		Atlas-SNP	.											.	CLCN1	141	.	0			c.G2958A						PASS	.						85	83	84					7																	143049049		2203	4300	6503	SO:0001819	synonymous_variant	1180	exon23			TGAACTGATCCTT	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.2958G>A	chr7.hg19:g.143049049G>A		110.0	0.0	.		105.0	23.0	.	NM_000083	A4D2H5|Q2M202	Silent	SNP	ENST00000343257.2	hg19	CCDS5881.1																																																																																			.	.	.	none		0.617	CLCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327420.1	NM_000083		A	143049049	G	A	143049049	2	1	216	1	0	0	0	0	0	0	0	1	3464	1277	45	2		2	CLCN1	7	143049049	Silent	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	136964844	143049049	16089614	27	13115											
TRPM3	80036	hgsc.bcm.edu	37	chr9	73151135	73151136	+	Frame_Shift_Ins	INS	-	-	T																															ttgttggacagggttctctcINStgagttatcaccctcctggg																										TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr9:73151135_73151136insT	ENST00000377110.3	-	25	5100_5101	c.4857_4858insA	c.(4855-4860)tcagagfs	p.E1620fs	TRPM3_ENST00000423814.3_Frame_Shift_Ins_p.E1647fs|TRPM3_ENST00000377105.1_Frame_Shift_Ins_p.E1479fs|TRPM3_ENST00000396292.4_Frame_Shift_Ins_p.E1492fs|TRPM3_ENST00000358082.3_Frame_Shift_Ins_p.E1482fs|TRPM3_ENST00000408909.2_Frame_Shift_Ins_p.E1479fs|TRPM3_ENST00000396280.5_Frame_Shift_Ins_p.E1469fs|TRPM3_ENST00000377111.2_Intron|TRPM3_ENST00000357533.2_Frame_Shift_Ins_p.E1624fs|TRPM3_ENST00000396285.1_Frame_Shift_Ins_p.E1479fs|TRPM3_ENST00000360823.2_Frame_Shift_Ins_p.E1482fs|TRPM3_ENST00000377106.1_Frame_Shift_Ins_p.E1492fs			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						AGGGTTCTCTCTGAGTTATCAC	0.55																																					p.E1620fs		Atlas-Indel,Pindel	.											.	TRPM3	700	.	0			c.4858_4859insA						PASS	.																																			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.4858dupA	chr9.hg19:g.73151136_73151136dupT	ENSP00000366314:p.Glu1620fs	148.0	0.0	0		129.0	15.0	0.116279	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Frame_Shift_Ins	INS	ENST00000377110.3	hg19	CCDS43835.1																																																																																			.	.	.	none		0.55	TRPM3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214158.3	NM_206945		T	73151136	-	T	73151135	7	5	216	1	0	1	1	0	0	0	0	0	16599	922	32	0	269	0	TRPM3	9	73151135	Frame_Shift_Ins	INS	-	TCGA-KV-A6GD-01A-11D-A31X-10		73151135	68062296	28	13116											
CTSL1	1514	hgsc.bcm.edu	37	chr9	90344596	90344596	+	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	aggcagttgcaactgtggggCccatttctgttgctattgat	7	14	12	8	0	1	1	0	1	1	0	1	1	1	1	1	3	3	5	1	3	2	5			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr9:90344596C>T	ENST00000343150.5	+	6	1620	c.730C>T	c.(730-732)Ccc>Tcc	p.P244S	CTSL_ENST00000340342.6_Missense_Mutation_p.P244S|CTSL_ENST00000495822.1_3'UTR			P07711	CATL1_HUMAN	cathepsin L	244					adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|macrophage apoptotic process (GO:0071888)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|nucleus (GO:0005634)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|fibronectin binding (GO:0001968)|histone binding (GO:0042393)|proteoglycan binding (GO:0043394)										AACTGTGGGGCCCATTTCTGT	0.428																																					p.P244S		Atlas-SNP	.											.	CTSL1	43	.	0			c.C730T						PASS	.						153	147	149					9																	90344596		2203	4300	6503	SO:0001583	missense	1514	exon6			GTGGGGCCCATTT	X12451	CCDS6675.1	9q21.33	2013-06-27	2013-06-27	2013-06-27	ENSG00000135047	ENSG00000135047	3.4.22.15	"Cathepsins"	2537	protein-coding gene	gene with protein product		116880	"cathepsin L1"	CTSL1		8419312, 2835398	Standard	NM_145918		Approved	FLJ31037	uc004apk.4	P07711	OTTHUMG00000020149	ENST00000343150.5:c.730C>T	chr9.hg19:g.90344596C>T	ENSP00000345344:p.Pro244Ser	108.0	0.0	.		81.0	16.0	.	NM_145918	Q6IAV1|Q96QJ0	Missense_Mutation	SNP	ENST00000343150.5	hg19	CCDS6675.1	.	.	.	.	.	.	.	.	.	.	C	18.16	3.562005	0.65538	.	.	ENSG00000135047	ENST00000343150;ENST00000340342	T;T	0.58652	0.32;0.32	4.19	4.19	0.49359	Peptidase C1A, papain C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.86167	0.5868	H	0.99156	4.45	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92638	0.6122	10	0.87932	D	0	.	16.7092	0.85380	0.0:1.0:0.0:0.0	.	244	P07711	CATL1_HUMAN	S	244	ENSP00000345344:P244S;ENSP00000365061:P244S	ENSP00000365061:P244S	P	+	1	0	CTSL1	89534416	1.000000	0.71417	0.118000	0.21660	0.300000	0.27592	6.804000	0.75186	2.134000	0.65973	0.655000	0.94253	CCC	.	.	.	none		0.428	CTSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052936.1	NM_001912		T	90344596	C	T	90344596	3	4	216	1	0	0	0	0	1	0	0	0	4040	739	26	2	748	2	CTSL1	9	90344596	Missense_Mutation	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	17193461	90344596	50868835	29	13117											
MASTL	84930	hgsc.bcm.edu	37	chr10	27456144	27456144	+	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	ccagtagtcaatcccacaccTtcatatccagtgtggaatca	12	10	6	13	0	3	0	3	0	0	0	5	1	5	1	4	1	0	1	4	1	4	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr10:27456144T>A	ENST00000375940.4	+	7	982	c.925T>A	c.(925-927)Ttc>Atc	p.F309I	MASTL_ENST00000375946.4_Missense_Mutation_p.F309I|MASTL_ENST00000342386.6_Missense_Mutation_p.F309I			Q96GX5	GWL_HUMAN	microtubule associated serine/threonine kinase-like	309	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						ATCCCACACCTTCATATCCAG	0.438																																					p.F309I		Atlas-SNP	.											.	MASTL	81	.	0			c.T925A						PASS	.						98	94	95					10																	27456144		2203	4300	6503	SO:0001583	missense	84930	exon7			CACACCTTCATAT	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.925T>A	chr10.hg19:g.27456144T>A	ENSP00000365107:p.Phe309Ile	96.0	0.0	.		86.0	4.0	.	NM_032844	Q5T8D5|Q5T8D7|Q8NCD6|Q96SJ5	Missense_Mutation	SNP	ENST00000375940.4	hg19	CCDS53502.1	.	.	.	.	.	.	.	.	.	.	T	19.40	3.821148	0.71028	.	.	ENSG00000120539	ENST00000375946;ENST00000342386;ENST00000375940	T;T;T	0.66280	-0.1;-0.2;-0.09	6.16	6.16	0.99307	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.182060	0.49305	D	0.000145	T	0.69415	0.3108	M	0.67953	2.075	0.09310	N	1	D;P;D	0.60575	0.96;0.932;0.988	P;B;P	0.55455	0.579;0.397;0.776	T	0.64698	-0.6346	10	0.29301	T	0.29	-21.7995	10.7305	0.46093	0.0:0.1106:0.0:0.8894	.	309;309;309	Q96GX5-2;Q96GX5;Q96GX5-3	.;GWL_HUMAN;.	I	309	ENSP00000365113:F309I;ENSP00000343446:F309I;ENSP00000365107:F309I	ENSP00000343446:F309I	F	+	1	0	MASTL	27496150	0.046000	0.20272	0.950000	0.38849	0.998000	0.95712	0.873000	0.28052	2.367000	0.80283	0.528000	0.53228	TTC	.	.	.	none		0.438	MASTL-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047320.1	NM_032844		A	27456144	T	A	27456144	3	1	216	1	0	0	0	0	1	0	0	0	9335	1609	56	5	951	5	MASTL	10	27456144	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10		27456144	108078603	30	13118											
IFIT5	24138	hgsc.bcm.edu	37	chr10	91177012	91177012	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgttggagttagaatgtcAttttacatggaatttactta	11	18	8	4	0	2	1	1	0	1	1	2	3	2	3	0	2	2	2	0	2	6	7			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr10:91177012A>G	ENST00000371795.4	+	2	269	c.56A>G	c.(55-57)cAt>cGt	p.H19R	IFIT5_ENST00000416601.1_Missense_Mutation_p.H19R|LIPA_ENST00000371837.1_5'Flank	NM_012420.2	NP_036552.1	Q13325	IFIT5_HUMAN	interferon-induced protein with tetratricopeptide repeats 5	19					defense response to virus (GO:0051607)|innate immune response (GO:0045087)	actin cytoskeleton (GO:0015629)|apical part of cell (GO:0045177)|ruffle membrane (GO:0032587)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)|tRNA binding (GO:0000049)			endometrium(1)|large_intestine(4)|lung(4)	9						TTAGAATGTCATTTTACATGG	0.318																																					p.H19R		Atlas-SNP	.											.	IFIT5	32	.	0			c.A56G						PASS	.						69	71	70					10																	91177012		2203	4300	6503	SO:0001583	missense	24138	exon2			AATGTCATTTTAC	U34605	CCDS7403.1	10q23.31	2013-01-10			ENSG00000152778	ENSG00000152778		"Tetratricopeptide (TTC) repeat domain containing"	13328	protein-coding gene	gene with protein product	"retinoic acid- and interferon-inducible protein (58kD)"					9398535	Standard	NM_012420		Approved	RI58	uc010qnh.2	Q13325	OTTHUMG00000018713	ENST00000371795.4:c.56A>G	chr10.hg19:g.91177012A>G	ENSP00000360860:p.His19Arg	148.0	0.0	.		125.0	16.0	.	NM_012420	B2R5X9|B4DDV1|Q5T7I9|Q6IAX3	Missense_Mutation	SNP	ENST00000371795.4	hg19	CCDS7403.1	.	.	.	.	.	.	.	.	.	.	A	19.78	3.890598	0.72524	.	.	ENSG00000152778	ENST00000371795;ENST00000416601	T;T	0.60797	0.16;0.16	6.16	6.16	0.99307	.	0.045911	0.85682	D	0.000000	T	0.77253	0.4103	M	0.80847	2.515	0.53688	D	0.999979	D;D	0.89917	1.0;1.0	D;D	0.71414	0.973;0.973	T	0.80284	-0.1447	10	0.87932	D	0	-13.583	15.9872	0.80168	1.0:0.0:0.0:0.0	.	19;19	Q13325;B4DDV1	IFIT5_HUMAN;.	R	19	ENSP00000360860:H19R;ENSP00000414042:H19R	ENSP00000360860:H19R	H	+	2	0	IFIT5	91166992	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.666000	0.68059	2.367000	0.80283	0.528000	0.53228	CAT	.	.	.	none		0.318	IFIT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049303.1	NM_012420		G	91177012	A	G	91177012	3	3	216	1	0	0	0	0	1	0	0	0	7532	217	8	3	62	3	IFIT5	10	91177012	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	63720868	91177012	44357735	31	13119											
USH1C	10083	hgsc.bcm.edu	37	chr11	17542471	17542471	+	Missense_Mutation	SNP	A	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	agcagtgatggttttaggcaAgagtagctgttcctttgagc	9	13	13	6	0	0	3	0	2	0	1	1	3	1	3	1	2	3	6	1	2	3	5			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:17542471A>C	ENST00000318024.4	-	14	1264	c.1156T>G	c.(1156-1158)Ttg>Gtg	p.L386V	USH1C_ENST00000005226.7_Missense_Mutation_p.L386V|USH1C_ENST00000527020.1_Missense_Mutation_p.L367V|USH1C_ENST00000527720.1_Missense_Mutation_p.L355V	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)	386					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						GTTTTAGGCAAGAGTAGCTGT	0.488																																					p.L386V		Atlas-SNP	.											.	USH1C	157	.	0			c.T1156G						PASS	.						457	438	444					11																	17542471		2200	4293	6493	SO:0001583	missense	10083	exon14			TAGGCAAGAGTAG	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.1156T>G	chr11.hg19:g.17542471A>C	ENSP00000317018:p.Leu386Val	134.0	0.0	.		87.0	9.0	.	NM_005709	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Missense_Mutation	SNP	ENST00000318024.4	hg19	CCDS31438.1	.	.	.	.	.	.	.	.	.	.	A	9.184	1.024225	0.19433	.	.	ENSG00000006611	ENST00000318024;ENST00000527720;ENST00000527020;ENST00000005226	T;T;T;T	0.63913	1.77;1.77;2.01;-0.07	5.7	-8.8	0.00817	.	0.781295	0.12318	N	0.479554	T	0.26159	0.0638	N	0.08118	0	0.09310	N	1	B;B;B	0.14438	0.01;0.006;0.0	B;B;B	0.15870	0.014;0.006;0.001	T	0.28554	-1.0040	10	0.11485	T	0.65	.	3.9214	0.09245	0.2554:0.0946:0.4467:0.2034	.	367;386;386	Q9Y6N9-4;Q9Y6N9;Q7RTU8	.;USH1C_HUMAN;.	V	386;355;367;386	ENSP00000317018:L386V;ENSP00000432944:L355V;ENSP00000436934:L367V;ENSP00000005226:L386V	ENSP00000005226:L386V	L	-	1	2	USH1C	17499047	0.000000	0.05858	0.002000	0.10522	0.642000	0.38348	-1.114000	0.03293	-1.238000	0.02535	-1.039000	0.02377	TTG	.	.	.	none		0.488	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709		C	17542471	A	C	17542471	3	2	216	1	0	0	0	0	1	0	0	0	17046	69	3	5	1677	5	USH1C	11	17542471	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10		17542471	117464045	32	13120											
OR5M3	219482	hgsc.bcm.edu	37	chr11	56237348	56237348	+	Missense_Mutation	SNP	A	A	T																															aagagatgataattacagtcAgggaatatgtgaagttaatg																										TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:56237348A>T	ENST00000312240.2	-	1	666	c.626T>A	c.(625-627)cTg>cAg	p.L209Q		NM_001004742.2	NP_001004742.2	Q8NGP4	OR5M3_HUMAN	olfactory receptor, family 5, subfamily M, member 3	209						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)					AATTACAGTCAGGGAATATGT	0.438																																					p.L209Q		Atlas-SNP	.											.	OR5M3	103	.	0			c.T626A						PASS	.						111	109	110					11																	56237348		2201	4296	6497	SO:0001583	missense	219482	exon1			ACAGTCAGGGAAT	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.626T>A	chr11.hg19:g.56237348A>T	ENSP00000312208:p.Leu209Gln	206.0	0.0	.		173.0	20.0	.	NM_001004742	B2RNM7|Q6IEW4|Q96RC0	Missense_Mutation	SNP	ENST00000312240.2	hg19	CCDS31532.1	.	.	.	.	.	.	.	.	.	.	A	7.810	0.715500	0.15306	.	.	ENSG00000174937	ENST00000312240	T	0.49432	0.78	5.08	5.08	0.68730	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33854	N	0.004500	T	0.71753	0.3377	H	0.97240	3.965	0.09310	N	1	B	0.19445	0.036	B	0.40038	0.317	T	0.68884	-0.5291	10	0.72032	D	0.01	-8.3442	12.8019	0.57591	1.0:0.0:0.0:0.0	.	209	Q8NGP4	OR5M3_HUMAN	Q	209	ENSP00000312208:L209Q	ENSP00000312208:L209Q	L	-	2	0	OR5M3	55993924	0.207000	0.23482	0.002000	0.10522	0.005000	0.04900	4.573000	0.60893	1.897000	0.54924	0.448000	0.29417	CTG	.	.	.	none		0.438	OR5M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391639.1	NM_001004742		T	56237348	A	T	56237348	3	4	216	1	0	0	0	0	1	0	0	0	11182	188	7	5	299	5	OR5M3	11	56237348	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	38694877	56237348	78769168	33	13121	128	2									
OR5M3	219482	hgsc.bcm.edu	37	chr11	56237358	56237358	+	Missense_Mutation	SNP	T	T	A																															aattacagtcagggaatatgTgaagttaatgccggcaagta																										TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:56237358T>A	ENST00000312240.2	-	1	656	c.616A>T	c.(616-618)Aca>Tca	p.T206S		NM_001004742.2	NP_001004742.2	Q8NGP4	OR5M3_HUMAN	olfactory receptor, family 5, subfamily M, member 3	206						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)					AGGGAATATGTGAAGTTAATG	0.428																																					p.T206S		Atlas-SNP	.											.	OR5M3	103	.	0			c.A616T						PASS	.						120	118	119					11																	56237358		2201	4296	6497	SO:0001583	missense	219482	exon1			AATATGTGAAGTT	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.616A>T	chr11.hg19:g.56237358T>A	ENSP00000312208:p.Thr206Ser	205.0	0.0	.		172.0	20.0	.	NM_001004742	B2RNM7|Q6IEW4|Q96RC0	Missense_Mutation	SNP	ENST00000312240.2	hg19	CCDS31532.1	.	.	.	.	.	.	.	.	.	.	T	3.617	-0.078287	0.07184	.	.	ENSG00000174937	ENST00000312240	T	0.37058	1.22	5.08	-0.403	0.12400	GPCR, rhodopsin-like superfamily (1);	0.993240	0.08161	N	0.988433	T	0.16981	0.0408	N	0.11255	0.115	0.09310	N	1	B	0.14012	0.009	B	0.23150	0.044	T	0.31194	-0.9952	10	0.22706	T	0.39	-3.9091	3.5764	0.07936	0.2773:0.1679:0.0:0.5548	.	206	Q8NGP4	OR5M3_HUMAN	S	206	ENSP00000312208:T206S	ENSP00000312208:T206S	T	-	1	0	OR5M3	55993934	0.000000	0.05858	0.552000	0.28243	0.327000	0.28475	-0.845000	0.04340	0.248000	0.21435	0.448000	0.29417	ACA	.	.	.	none		0.428	OR5M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391639.1	NM_001004742		A	56237358	T	A	56237358	3	1	216	1	0	0	0	0	1	0	0	0	11182	1696	59	5	309	5	OR5M3	11	56237358	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10	10	56237358	78769158	34	13122	128	2									
SSRP1	6749	hgsc.bcm.edu	37	chr11	57100282	57100282	+	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	aagatgcagatggcatctccCgtggcctggattacatccgc	9	9	11	12	2	1	2	0	0	1	2	3	3	2	3	3	3	2	2	3	3	2	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:57100282C>A	ENST00000278412.2	-	6	851	c.585G>T	c.(583-585)acG>acT	p.T195T		NM_003146.2	NP_003137.1	Q08945	SSRP1_HUMAN	structure specific recognition protein 1	195					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						TGGCATCTCCCGTGGCCTGGA	0.562																																					p.T195T	Colon(89;1000 1340 6884 23013 41819)	Atlas-SNP	.											.	SSRP1	75	.	0			c.G585T						PASS	.						65	63	64					11																	57100282		2201	4296	6497	SO:0001819	synonymous_variant	6749	exon6			ATCTCCCGTGGCC	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.585G>T	chr11.hg19:g.57100282C>A		98.0	0.0	.		72.0	15.0	.	NM_003146	Q5BJG8	Silent	SNP	ENST00000278412.2	hg19	CCDS7952.1																																																																																			.	.	.	none		0.562	SSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392460.1	NM_003146		A	57100282	C	A	57100282	2	1	216	1	0	0	0	0	0	0	0	1	15206	639	23	4		4	SSRP1	11	57100282	Silent	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	862924	57100282	77906234	35	13123											
SYVN1	84447	hgsc.bcm.edu	37	chr11	64900251	64900251	+	Splice_Site	DEL	T	T	-																															gatgttggggctgcgttccaTctgaggcagagcacagaaga																										TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:64900251delT	ENST00000377190.3	-	5	473	c.379delA	c.(379-381)atg>tg	p.M127fs	SYVN1_ENST00000526060.1_Splice_Site_p.M127fs|SYVN1_ENST00000526121.1_5'Flank|SYVN1_ENST00000307289.6_Intron|SYVN1_ENST00000294256.8_Splice_Site_p.M127fs	NM_172230.2	NP_757385.1	Q86TM6	SYVN1_HUMAN	synovial apoptosis inhibitor 1, synoviolin	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)|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						CTGCGTTCCATCTGAGGCAGA	0.612																																					p.M127fs		Atlas-INDEL	.											.	SYVN1	55	.	0			c.380delT						PASS	.						97	97	97					11																	64900251		2201	4297	6498	SO:0001630	splice_region_variant	84447	exon5			.	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.379-1A>-	chr11.hg19:g.64900251delT		76.0	0.0	0		49.0	11.0	0.22449	NM_032431	Q8N3K3|Q8N6E8|Q96JL5|Q96PK3	Frame_Shift_Del	DEL	ENST00000377190.3	hg19	CCDS31605.1																																																																																			.	.	.	none		0.612	SYVN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385274.1	NM_032431	Frame_Shift_Del	-	64900251	T	-	64900251	8	5	216	1	0	1	0	1	0	0	1	0	15499	1449	50	0	1522	0	SYVN1	11	64900251	Splice_Site	DEL	T	TCGA-KV-A6GD-01A-11D-A31X-10	7799969	64900251	70106265	36	13124											
FRMD8	83786	hgsc.bcm.edu	37	chr11	65168213	65168213	+	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	agcatgtcctgctgggcctgCgcttccaggagctgtcgtgg	4	10	15	12	2	0	0	0	0	0	0	3	1	2	1	3	3	4	4	3	3	0	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:65168213C>T	ENST00000317568.5	+	9	1109	c.946C>T	c.(946-948)Cgc>Tgc	p.R316C	FRMD8_ENST00000355991.5_Missense_Mutation_p.R260C|FRMD8_ENST00000416776.2_Missense_Mutation_p.R282C	NM_031904.3	NP_114110.1	Q9BZ67	FRMD8_HUMAN	FERM domain containing 8	316	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoskeleton (GO:0005856)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|urinary_tract(1)	17						GCTGGGCCTGCGCTTCCAGGA	0.657																																					p.R316C		Atlas-SNP	.											.	FRMD8	28	.	0			c.C946T						PASS	.						48	38	41					11																	65168213		2201	4296	6497	SO:0001583	missense	83786	exon9			GGCCTGCGCTTCC	AK074850	CCDS8102.1, CCDS73320.1	11q13.1	2007-08-14			ENSG00000126391	ENSG00000126391			25462	protein-coding gene	gene with protein product						12477932	Standard	NM_031904		Approved	FLJ90369, FKSG44	uc001odu.4	Q9BZ67	OTTHUMG00000166275	ENST00000317568.5:c.946C>T	chr11.hg19:g.65168213C>T	ENSP00000319726:p.Arg316Cys	76.0	0.0	.		82.0	13.0	.	NM_031904	B4E2P1|Q86V56|Q8NCB5	Missense_Mutation	SNP	ENST00000317568.5	hg19	CCDS8102.1	.	.	.	.	.	.	.	.	.	.	C	14.69	2.609302	0.46527	.	.	ENSG00000126391	ENST00000317568;ENST00000355991;ENST00000416776	D;T;D	0.84223	-1.81;-1.22;-1.82	4.49	3.56	0.40772	FERM domain (1);	0.572355	0.18795	N	0.130960	D	0.84813	0.5555	.	.	.	0.48452	D	0.999659	B;B;D	0.71674	0.041;0.175;0.998	B;B;P	0.48654	0.01;0.028;0.585	D	0.83999	0.0342	9	0.56958	D	0.05	-14.6802	9.9641	0.41715	0.3682:0.6317:0.0:0.0	.	282;260;316	B4E2P1;Q9BZ67-2;Q9BZ67	.;.;FRMD8_HUMAN	C	316;260;282	ENSP00000319726:R316C;ENSP00000348270:R260C;ENSP00000392111:R282C	ENSP00000319726:R316C	R	+	1	0	FRMD8	64924789	0.940000	0.31905	1.000000	0.80357	0.991000	0.79684	1.023000	0.30065	0.998000	0.38996	0.549000	0.68633	CGC	.	.	.	none		0.657	FRMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388833.1	NM_031904		T	65168213	C	T	65168213	3	4	216	1	0	0	0	0	1	0	0	0	6063	768	27	1	976	1	FRMD8	11	65168213	Missense_Mutation	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	267962	65168213	69838303	37	13125											
MUS81	80198	hgsc.bcm.edu	37	chr11	65631192	65631192	+	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	agaccaatcctagagacccaGgtgaagggccgtggacaggc	12	4	14	11	1	0	3	0	1	0	2	1	5	1	4	4	4	0	0	4	4	3	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:65631192G>A	ENST00000308110.4	+	9	1310	c.961G>A	c.(961-963)Gca>Aca	p.A321T	EFEMP2_ENST00000532648.1_5'Flank|MUS81_ENST00000533035.1_Splice_Site_p.A246T|CFL1_ENST00000534769.1_5'Flank	NM_025128.4	NP_079404.3	Q96NY9	MUS81_HUMAN	MUS81 structure-specific endonuclease subunit	321	ERCC4.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	intercellular bridge (GO:0045171)|nucleus (GO:0005634)	3'-flap endonuclease activity (GO:0048257)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	13				READ - Rectum adenocarcinoma(159;0.166)		TAGAGACCCAGGTGAAGGGCC	0.637								Homologous recombination																													p.A321T		Atlas-SNP	.											.	MUS81	68	.	0			c.G961A						PASS	.						59	64	63					11																	65631192		2201	4296	6497	SO:0001630	splice_region_variant	80198	exon9			GACCCAGGTGAAG		CCDS8115.1	11q13	2013-07-03	2013-07-03			ENSG00000172732			29814	protein-coding gene	gene with protein product	"SLX3 structure-specific endonuclease subunit homolog (S. cerevisiae)"	606591	"MUS81 endonuclease homolog (yeast)", "MUS81 endonuclease homolog (S. cerevisiae)"			11741546, 12374758	Standard	NM_025128		Approved	FLJ44872, SLX3	uc001ofv.4	Q96NY9		ENST00000308110.4:c.961+1G>A	chr11.hg19:g.65631192G>A		132.0	0.0	.		110.0	21.0	.	NM_025128	Q9H7D9	Missense_Mutation	SNP	ENST00000308110.4	hg19	CCDS8115.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.03|11.03	1.519664|1.519664	0.27211|0.27211	.|.	.|.	ENSG00000172732|ENSG00000172732	ENST00000533035;ENST00000308110;ENST00000437855|ENST00000529374	T;T|.	0.22945|.	1.93;1.93|.	5.14|5.14	3.2|3.2	0.36748|0.36748	DNA repair nuclease, XPF-type/Helicase (1);Restriction endonuclease, type II-like (1);ERCC4 domain (2);|.	0.343384|.	0.32430|.	N|.	0.006119|.	T|T	0.43656|0.43656	0.1257|0.1257	L|L	0.35288|0.35288	1.05|1.05	0.36284|0.36284	D|D	0.855981|0.855981	B|.	0.29805|.	0.257|.	B|.	0.31442|.	0.13|.	T|T	0.46317|0.46317	-0.9200|-0.9200	10|5	0.13470|.	T|.	0.59|.	-1.6633|-1.6633	6.6325|6.6325	0.22865|0.22865	0.0927:0.0:0.7303:0.177|0.0927:0.0:0.7303:0.177	.|.	321|.	Q96NY9|.	MUS81_HUMAN|.	T|N	246;321;321|245	ENSP00000432287:A246T;ENSP00000307853:A321T|.	ENSP00000307853:A321T|.	A|S	+|+	1|2	0|0	MUS81|MUS81	65387768|65387768	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.034000|0.034000	0.12701|0.12701	3.588000|3.588000	0.53964|0.53964	1.370000|1.370000	0.46153|0.46153	0.563000|0.563000	0.77884|0.77884	GCA|AGC	.	.	.	none		0.637	MUS81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390941.3	NM_025128	Missense_Mutation	A	65631192	G	A	65631192	5	1	216	1	0	0	0	0	0	0	1	0	9995	1014	35	2	995	2	MUS81	11	65631192	Splice_Site	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	462979	65631192	69375324	38	13126											
INPPL1	3636	hgsc.bcm.edu	37	chr11	71948603	71948603	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcccccaggcccctcaccAgccagcactttcctggggga	6	6	10	19	0	1	0	1	0	0	0	2	1	2	1	7	3	3	1	7	3	0	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:71948603A>G	ENST00000298229.2	+	26	3519	c.3315A>G	c.(3313-3315)ccA>ccG	p.P1105P	INPPL1_ENST00000538751.1_Silent_p.P863P|INPPL1_ENST00000541756.1_Silent_p.P863P|PHOX2A_ENST00000544057.1_5'Flank	NM_001567.3	NP_001558.3	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	1105	Pro-rich.				actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|endochondral ossification (GO:0001958)|endocytosis (GO:0006897)|glucose metabolic process (GO:0006006)|immune system process (GO:0002376)|inositol phosphate metabolic process (GO:0043647)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|post-embryonic development (GO:0009791)|response to insulin (GO:0032868)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|SH2 domain binding (GO:0042169)			breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						GCCCCTCACCAGCCAGCACTT	0.692																																					p.P1105P		Atlas-SNP	.											.	INPPL1	120	.	0			c.A3315G						PASS	.						19	21	20					11																	71948603		2108	4155	6263	SO:0001819	synonymous_variant	3636	exon26			CTCACCAGCCAGC	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.3315A>G	chr11.hg19:g.71948603A>G		93.0	0.0	.		72.0	17.0	.	NM_001567	B2RTX5|Q13577|Q13578	Silent	SNP	ENST00000298229.2	hg19	CCDS8213.1																																																																																			.	.	.	none		0.692	INPPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396789.1	NM_001567		G	71948603	A	G	71948603	2	3	216	1	0	0	0	0	0	0	0	1	7768	175	7	3		3	INPPL1	11	71948603	Silent	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	6317411	71948603	63057913	39	13127											
C2CD3	26005	hgsc.bcm.edu	37	chr11	73796809	73796809	+	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	agaactcagggcagaaagaaCaggccacagggtgggttcgg	13	4	16	8	1	1	3	1	0	0	3	2	3	1	3	1	5	2	2	1	5	3	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:73796809C>G	ENST00000334126.7	-	21	3990	c.3764G>C	c.(3763-3765)tGt>tCt	p.C1255S	C2CD3_ENST00000313663.7_Missense_Mutation_p.C1255S			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1255	C2 1.				brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					GCAGAAAGAACAGGCCACAGG	0.547																																					p.C1255S		Atlas-SNP	.											.	C2CD3	288	.	0			c.G3764C						PASS	.						86	75	79					11																	73796809		2200	4293	6493	SO:0001583	missense	26005	exon21			AAAGAACAGGCCA	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.3764G>C	chr11.hg19:g.73796809C>G	ENSP00000334379:p.Cys1255Ser	140.0	0.0	.		132.0	19.0	.	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	hg19		.	.	.	.	.	.	.	.	.	.	C	20.1	3.935426	0.73442	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681;ENST00000414160	T;T;T	0.37411	1.2;1.2;1.2	5.8	4.88	0.63580	.	0.169348	0.50627	D	0.000102	T	0.27241	0.0668	L	0.29908	0.895	0.42377	D	0.992478	P	0.47910	0.902	B	0.40066	0.318	T	0.03008	-1.1083	10	0.37606	T	0.19	-9.4621	13.9561	0.64150	0.0:0.9267:0.0:0.0733	.	1255	Q4AC94-1	.	S	1255;1255;1255;63	ENSP00000334379:C1255S;ENSP00000323339:C1255S;ENSP00000388750:C63S	ENSP00000323339:C1255S	C	-	2	0	C2CD3	73474457	0.998000	0.40836	1.000000	0.80357	0.951000	0.60555	3.590000	0.53979	2.742000	0.94016	0.655000	0.94253	TGT	.	.	.	none		0.547	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		G	73796809	C	G	73796809	3	3	216	1	0	0	0	0	1	0	0	0	2156	478	17	4	2171	4	C2CD3	11	73796809	Missense_Mutation	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	1848206	73796809	61209707	40	13128											
YAP1	10413	hgsc.bcm.edu	37	chr11	102100555	102100555	+	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	gagatggaatgaacatagaaGgagaggagctgatgccaagt	16	6	15	4	0	0	5	0	2	0	3	0	9	0	7	1	3	3	1	1	3	5	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:102100555G>T	ENST00000282441.5	+	9	1787	c.1399G>T	c.(1399-1401)Gga>Tga	p.G467*	YAP1_ENST00000528834.1_3'UTR|YAP1_ENST00000531439.1_Nonsense_Mutation_p.G451*|YAP1_ENST00000526343.1_Nonsense_Mutation_p.G413*|RP11-864G5.3_ENST00000526310.1_RNA|YAP1_ENST00000537274.1_Nonsense_Mutation_p.G455*|YAP1_ENST00000524575.1_Nonsense_Mutation_p.G289*|YAP1_ENST00000345877.2_Nonsense_Mutation_p.G417*	NM_001130145.2|NM_001282101.1	NP_001123617.1|NP_001269030.1	P46937	YAP1_HUMAN	Yes-associated protein 1	467	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)		GAACATAGAAGGAGAGGAGCT	0.483																																					p.G467X	Colon(50;247 1103 7861 28956)	Atlas-SNP	.											.	YAP1	45	.	0			c.G1399T						PASS	.						131	123	126					11																	102100555		2203	4299	6502	SO:0001587	stop_gained	10413	exon9			ATAGAAGGAGAGG		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.1399G>T	chr11.hg19:g.102100555G>T	ENSP00000282441:p.Gly467*	128.0	0.0	.		94.0	15.0	.	NM_001130145	B4DTY1|B7ZA01|E3WEB5|E3WEB6|E9PRV2|F5H202|K0KQ18|K0KYZ8|K0L195|K0L1G3|Q7Z574|Q8IUY9	Nonsense_Mutation	SNP	ENST00000282441.5	hg19	CCDS44716.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	40|40	8.303129|8.303129	0.98750|0.98750	.|.	.|.	ENSG00000137693|ENSG00000137693	ENST00000526343;ENST00000282441;ENST00000537274;ENST00000345877;ENST00000445250;ENST00000531439;ENST00000524575|ENST00000529029	.|.	.|.	.|.	6.17|6.17	6.17|6.17	0.99709|0.99709	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.77638	.|0.4160	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73658	.|-0.3913	.|4	0.87932|.	D|.	0|.	.|.	20.8794|20.8794	0.99867|0.99867	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|N	413;467;455;417;384;451;289|220	.|.	ENSP00000282441:G467X|.	G|K	+|+	1|3	0|2	YAP1|YAP1	101605765|101605765	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.981000|0.981000	0.71138|0.71138	9.441000|9.441000	0.97557|0.97557	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	GGA|AAG	.	.	.	none		0.483	YAP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394151.1	NM_006106		T	102100555	G	T	102100555	4	4	216	1	0	0	0	0	0	1	0	0	17478	1001	35	4	1445	4	YAP1	11	102100555	Nonsense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	28303746	102100555	32905961	41	13129											
ARHGAP32	9743	hgsc.bcm.edu	37	chr11	128933815	128933815	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctctaaggtcagttcgtcAggggcccgagcagtgtacct	8	9	12	12	2	3	0	2	0	1	0	4	1	3	0	3	3	2	3	3	3	2	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr11:128933815A>G	ENST00000310343.9	-	8	824	c.825T>C	c.(823-825)ccT>ccC	p.P275P	ARHGAP32_ENST00000524655.1_Silent_p.P201P	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	275	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						TCAGTTCGTCAGGGGCCCGAG	0.433																																					p.P275P		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.T825C						PASS	.						162	158	160					11																	128933815		1566	3579	5145	SO:0001819	synonymous_variant	9743	exon8			TTCGTCAGGGGCC	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.825T>C	chr11.hg19:g.128933815A>G		158.0	0.0	.		139.0	24.0	.	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Silent	SNP	ENST00000310343.9	hg19	CCDS44769.1																																																																																			.	.	.	none		0.433	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		G	128933815	A	G	128933815	2	3	216	1	0	0	0	0	0	0	0	1	881	175	7	3		3	ARHGAP32	11	128933815	Silent	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	26833260	128933815	6072701	42	13130											
CLSTN3	9746	hgsc.bcm.edu	37	chr12	7302198	7302198	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggtgggggatgacctggaTcccgagcgggaaagcctgct	7	7	17	10	2	0	1	0	1	0	0	1	5	1	4	3	5	3	1	3	5	1	0			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr12:7302198T>C	ENST00000266546.6	+	14	2604	c.2154T>C	c.(2152-2154)gaT>gaC	p.D718D	CLSTN3_ENST00000537408.1_Silent_p.D730D	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	718					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						ATGACCTGGATCCCGAGCGGG	0.572																																					p.D718D		Atlas-SNP	.											.	CLSTN3	84	.	0			c.T2154C						PASS	.						86	78	80					12																	7302198		2203	4300	6503	SO:0001819	synonymous_variant	9746	exon14			CCTGGATCCCGAG	AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182		"Cadherins / Cadherin-related"	18371	protein-coding gene	gene with protein product	"cadherin-related family member 14"	611324				12498782	Standard	NM_014718		Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167	ENST00000266546.6:c.2154T>C	chr12.hg19:g.7302198T>C		110.0	0.0	.		67.0	21.0	.	NM_014718	D3DUT6|O94831|Q2T9J5|Q5UE57	Silent	SNP	ENST00000266546.6	hg19	CCDS8575.1																																																																																			.	.	.	none		0.572	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398560.2	NM_014718		C	7302198	T	C	7302198	2	2	216	1	0	0	0	0	0	0	0	1	3565	1432	50	3		3	CLSTN3	12	7302198	Silent	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10		7302198	126549697	43	13131											
MON2	23041	hgsc.bcm.edu	37	chr12	62954577	62954577	+	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	tgagcttgaagatttgaatcTatggtgggctgcgtggaata	10	13	14	4	1	1	4	0	3	1	1	1	5	1	5	0	3	2	2	0	3	5	4			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr12:62954577T>A	ENST00000393632.2	+	26	4107	c.3716T>A	c.(3715-3717)cTa>cAa	p.L1239Q	MON2_ENST00000280379.6_Missense_Mutation_p.L1240Q|MON2_ENST00000552738.1_Missense_Mutation_p.L1216Q|MON2_ENST00000393629.2_Missense_Mutation_p.L1239Q|MON2_ENST00000393630.3_Missense_Mutation_p.L1240Q|MON2_ENST00000546600.1_Missense_Mutation_p.L1239Q	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	1239					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)		GATTTGAATCTATGGTGGGCT	0.393																																					p.L1239Q		Atlas-SNP	.											.	MON2	160	.	0			c.T3716A						PASS	.						92	90	91					12																	62954577		2203	4300	6503	SO:0001583	missense	23041	exon26			TGAATCTATGGTG		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.3716T>A	chr12.hg19:g.62954577T>A	ENSP00000377252:p.Leu1239Gln	116.0	0.0	.		99.0	22.0	.	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	ENST00000393632.2	hg19	CCDS31849.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.100011	0.76983	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000552738;ENST00000393629	T;T;T;T;T;T	0.70282	-0.47;-0.47;-0.47;-0.47;-0.47;-0.47	5.03	5.03	0.67393	.	0.000000	0.64402	D	0.000001	T	0.79857	0.4518	L	0.52759	1.655	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.997;0.979;1.0;1.0	D;P;P;D;D	0.83275	0.99;0.861;0.793;0.994;0.996	T	0.79308	-0.1857	9	.	.	.	-5.6366	15.0609	0.71951	0.0:0.0:0.0:1.0	.	1239;1216;1239;114;1239	B9EGP5;F8VWA6;F8W1Z6;Q7Z3U7-3;Q7Z3U7-4	.;.;.;.;.	Q	1239;1240;1240;1239;1216;1239	ENSP00000377252:L1239Q;ENSP00000377250:L1240Q;ENSP00000280379:L1240Q;ENSP00000447407:L1239Q;ENSP00000449215:L1216Q;ENSP00000377249:L1239Q	.	L	+	2	0	MON2	61240844	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.787000	0.85759	2.031000	0.59945	0.377000	0.23210	CTA	.	.	.	none		0.393	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		A	62954577	T	A	62954577	3	1	216	1	0	0	0	0	1	0	0	0	9707	1522	53	5	3818	5	MON2	12	62954577	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10	55652379	62954577	70897318	44	13132											
MRPS31	10240	hgsc.bcm.edu	37	chr13	41323388	41323388	+	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	tgtggctaactgcttagcaaAttccacatcccaaagtgaag	13	10	8	10	0	0	1	0	1	0	0	2	1	2	1	2	1	3	3	2	1	5	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr13:41323388A>T	ENST00000323563.6	-	6	880	c.844T>A	c.(844-846)Ttt>Att	p.F282I	MRPS31_ENST00000498078.1_5'UTR	NM_005830.3	NP_005821.2	Q92665	RT31_HUMAN	mitochondrial ribosomal protein S31	282						mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	13		Lung NSC(96;3.55e-06)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;1.52e-08)|Epithelial(112;7.63e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000192)|GBM - Glioblastoma multiforme(144;0.00233)|BRCA - Breast invasive adenocarcinoma(63;0.0706)		TGCTTAGCAAATTCCACATCC	0.368																																					p.F282I		Atlas-SNP	.											.	MRPS31	30	.	0			c.T844A						PASS	.						103	90	94					13																	41323388		2203	4300	6503	SO:0001583	missense	10240	exon6			TAGCAAATTCCAC	Z68747	CCDS9372.1	13q14.11	2012-09-13			ENSG00000102738	ENSG00000102738		"Mitochondrial ribosomal proteins / small subunits"	16632	protein-coding gene	gene with protein product		611992				11279123, 8567980	Standard	NM_005830		Approved	IMOGN38	uc001uxm.4	Q92665	OTTHUMG00000016777	ENST00000323563.6:c.844T>A	chr13.hg19:g.41323388A>T	ENSP00000315397:p.Phe282Ile	122.0	0.0	.		88.0	8.0	.	NM_005830	B2RCS3|Q5VYC8|Q8WTV8	Missense_Mutation	SNP	ENST00000323563.6	hg19	CCDS9372.1	.	.	.	.	.	.	.	.	.	.	A	16.70	3.196191	0.58126	.	.	ENSG00000102738	ENST00000323563	T	0.30182	1.54	5.17	5.17	0.71159	.	0.105571	0.64402	D	0.000003	T	0.50973	0.1647	M	0.80982	2.52	0.40731	D	0.982746	D	0.71674	0.998	D	0.65233	0.933	T	0.54255	-0.8321	10	0.37606	T	0.19	.	8.5691	0.33558	0.912:0.0:0.088:0.0	.	282	Q92665	RT31_HUMAN	I	282	ENSP00000315397:F282I	ENSP00000315397:F282I	F	-	1	0	MRPS31	40221388	1.000000	0.71417	0.995000	0.50966	0.613000	0.37349	2.868000	0.48436	1.947000	0.56498	0.524000	0.50904	TTT	.	.	.	none		0.368	MRPS31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044640.2			T	41323388	A	T	41323388	3	4	216	1	0	0	0	0	1	0	0	0	9848	101	4	5	351	5	MRPS31	13	41323388	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10		41323388	73846490	45	13133											
COL4A2	1284	hgsc.bcm.edu	37	chr13	111117912	111117912	+	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	cttacctggaccaccaggctTcctgggccctcctggccccg	4	8	10	19	1	0	0	0	0	0	0	2	1	2	1	8	4	1	1	8	4	1	2			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr13:111117912T>A	ENST00000360467.5	+	25	2243	c.1937T>A	c.(1936-1938)tTc>tAc	p.F646Y	COL4A2-AS2_ENST00000458403.2_RNA	NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	646	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)			CCACCAGGCTTCCTGGGCCCT	0.597																																					p.F646Y		Atlas-SNP	.											.	COL4A2	178	.	0			c.T1937A						PASS	.						29	34	32					13																	111117912		1873	4094	5967	SO:0001583	missense	1284	exon25			CAGGCTTCCTGGG	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.1937T>A	chr13.hg19:g.111117912T>A	ENSP00000353654:p.Phe646Tyr	158.0	0.0	.		124.0	14.0	.	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Missense_Mutation	SNP	ENST00000360467.5	hg19	CCDS41907.1	.	.	.	.	.	.	.	.	.	.	T	0.019	-1.456320	0.01071	.	.	ENSG00000134871	ENST00000360467;ENST00000257309	D	0.93247	-3.19	4.82	3.55	0.40652	.	0.654622	0.13725	N	0.367070	D	0.84942	0.5584	N	0.17674	0.51	0.09310	N	0.999999	B	0.23650	0.089	B	0.17098	0.017	T	0.72966	-0.4131	10	0.29301	T	0.29	.	5.8702	0.18799	0.1497:0.0841:0.0:0.7662	.	646	P08572	CO4A2_HUMAN	Y	646	ENSP00000353654:F646Y	ENSP00000257309:F646Y	F	+	2	0	COL4A2	109915913	0.000000	0.05858	0.103000	0.21229	0.102000	0.19082	0.319000	0.19522	1.802000	0.52723	0.379000	0.24179	TTC	.	.	.	none		0.597	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846		A	111117912	T	A	111117912	3	1	216	1	0	0	0	0	1	0	0	0	3692	1783	62	5	2031	5	COL4A2	13	111117912	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10	69794524	111117912	4051966	46	13134											
GTF2A1	2957	hgsc.bcm.edu	37	chr14	81659105	81659105	+	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	aggtataacttgagtcttatTtcctgtaaataagatttgct	12	17	7	5	0	1	2	0	1	1	1	2	2	2	2	1	1	2	3	1	1	6	8			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr14:81659105T>A	ENST00000553612.1	-	7	1094	c.691A>T	c.(691-693)Aat>Tat	p.N231Y	GTF2A1_ENST00000434192.2_Missense_Mutation_p.N192Y	NM_001278940.1|NM_015859.3	NP_001265869.1|NP_056943.1	P52655	TF2AA_HUMAN	general transcription factor IIA, 1, 19/37kDa	231					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)		TGAGTCTTATTTCCTGTAAAT	0.502																																					p.N231Y		Atlas-SNP	.											.	GTF2A1	34	.	0			c.A691T						PASS	.						174	172	173					14																	81659105		2203	4300	6503	SO:0001583	missense	2957	exon7			TCTTATTTCCTGT	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.691A>T	chr14.hg19:g.81659105T>A	ENSP00000452454:p.Asn231Tyr	84.0	0.0	.		77.0	9.0	.	NM_015859	Q3KNQ9	Missense_Mutation	SNP	ENST00000553612.1	hg19	CCDS9873.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.444489	0.83993	.	.	ENSG00000165417	ENST00000553612;ENST00000344860;ENST00000434192	T;T	0.44083	0.93;0.93	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.62588	0.2440	M	0.68952	2.095	0.80722	D	1	D	0.69078	0.997	D	0.81914	0.995	T	0.64723	-0.6340	10	0.52906	T	0.07	-21.9526	15.3673	0.74531	0.0:0.0:0.0:1.0	.	231	P52655	TF2AA_HUMAN	Y	231;192;192	ENSP00000452454:N231Y;ENSP00000409492:N192Y	ENSP00000298173:N231Y	N	-	1	0	GTF2A1	80728858	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.643000	0.83403	2.084000	0.62774	0.533000	0.62120	AAT	.	.	.	none		0.502	GTF2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413309.1	NM_015859		A	81659105	T	A	81659105	3	1	216	1	0	0	0	0	1	0	0	0	6859	1841	64	5	451	5	GTF2A1	14	81659105	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10		81659105	25690435	47	13135											
SETD3	84193	hgsc.bcm.edu	37	chr14	99929881	99929881	+	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	atctgcacatactcttcccaCtcttttcctgggccaggcgc	6	12	7	16	1	3	0	0	0	3	0	5	0	5	0	3	2	2	1	3	2	1	4			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr14:99929881C>T	ENST00000331768.5	-	3	297	c.138G>A	c.(136-138)gaG>gaA	p.E46E	SETD3_ENST00000329331.3_Silent_p.E46E|SETD3_ENST00000453938.1_5'UTR|SETD3_ENST00000436070.2_Silent_p.E46E	NM_032233.2	NP_115609.2	Q86TU7	SETD3_HUMAN	SET domain containing 3	46					histone H3-K36 methylation (GO:0010452)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|peptidyl-lysine trimethylation (GO:0018023)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25		all_cancers(154;0.224)|all_epithelial(191;0.0644)|Melanoma(154;0.0866)				ACTCTTCCCACTCTTTTCCTG	0.413																																					p.E46E		Atlas-SNP	.											.	SETD3	56	.	0			c.G138A						PASS	.						84	71	76					14																	99929881		2203	4300	6503	SO:0001819	synonymous_variant	84193	exon3			TTCCCACTCTTTT	AK026680	CCDS9951.1, CCDS9952.1	14q32.2	2006-02-15	2006-02-15	2006-02-15	ENSG00000183576	ENSG00000183576			20493	protein-coding gene	gene with protein product		615671	"chromosome 14 open reading frame 154"	C14orf154			Standard	NM_032233		Approved	FLJ23027	uc001ygc.3	Q86TU7	OTTHUMG00000028970	ENST00000331768.5:c.138G>A	chr14.hg19:g.99929881C>T		85.0	0.0	.		63.0	11.0	.	NM_032233	A0PJU3|A5PLP0|B4DZE8|Q0VAQ2|Q659C0|Q86TU8|Q96GY9|Q9H5U5	Silent	SNP	ENST00000331768.5	hg19	CCDS9951.1																																																																																			.	.	.	none		0.413	SETD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072339.3	NM_032233		T	99929881	C	T	99929881	2	4	216	1	0	0	0	0	0	0	0	1	14145	564	20	2		2	SETD3	14	99929881	Silent	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	18270776	99929881	7419659	48	13136											
MTMR15	22909	hgsc.bcm.edu	37	chr15	31197838	31197838	+	Missense_Mutation	SNP	T	T	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	gattcagaggcaaaatctcaTagttctgcagatgatgcttc	12	12	9	8	0	3	3	2	1	2	2	5	4	3	3	0	1	2	4	0	1	3	4			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr15:31197838T>G	ENST00000362065.4	+	2	1263	c.972T>G	c.(970-972)caT>caG	p.H324Q	FAN1_ENST00000561594.1_Missense_Mutation_p.H324Q|FAN1_ENST00000561607.1_Missense_Mutation_p.H324Q|FAN1_ENST00000565466.1_Missense_Mutation_p.H324Q	NM_014967.4	NP_055782.3	Q9Y2M0	FAN1_HUMAN	FANCD2/FANCI-associated nuclease 1	324					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						CAAAATCTCATAGTTCTGCAG	0.418								Direct reversal of damage																													p.H324Q		Atlas-SNP	.											.	FAN1	77	.	0			c.T972G						PASS	.						71	67	68					15																	31197838		2202	4300	6502	SO:0001583	missense	22909	exon2			ATCTCATAGTTCT		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.972T>G	chr15.hg19:g.31197838T>G	ENSP00000354497:p.His324Gln	97.0	0.0	.		86.0	16.0	.	NM_001146095	A8K4M2|Q86WU8	Missense_Mutation	SNP	ENST00000362065.4	hg19	CCDS32186.1	.	.	.	.	.	.	.	.	.	.	T	3.821	-0.037772	0.07497	.	.	ENSG00000198690	ENST00000362065	T	0.40756	1.02	5.46	-9.68	0.00528	.	2.519990	0.00901	N	0.002356	T	0.18299	0.0439	N	0.16478	0.41	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.17228	-1.0376	10	0.12766	T	0.61	0.1551	2.0377	0.03543	0.2596:0.2533:0.3519:0.1352	.	324;324	Q9Y2M0;Q9Y2M0-2	FAN1_HUMAN;.	Q	324	ENSP00000354497:H324Q	ENSP00000354497:H324Q	H	+	3	2	FAN1	28985130	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-3.615000	0.00414	-2.231000	0.00718	-0.291000	0.09656	CAT	.	.	.	none		0.418	FAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430740.1	NM_014967		G	31197838	T	G	31197838	3	3	216	1	0	0	0	0	1	0	0	0	9950	1403	49	5	974	5	MTMR15	15	31197838	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10		31197838	71333554	49	13137											
SIN3A	25942	hgsc.bcm.edu	37	chr15	75705130	75705130	+	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	gactttggcaggtgggggctGaggagctggctgggcaggag	6	7	22	6	0	0	1	0	1	0	0	0	4	0	3	0	8	1	5	0	8	0	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr15:75705130G>A	ENST00000394947.3	-	5	1044	c.730C>T	c.(730-732)Cag>Tag	p.Q244*	SIN3A_ENST00000360439.4_Nonsense_Mutation_p.Q244*|SIN3A_ENST00000394949.4_Nonsense_Mutation_p.Q244*	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						GGTGggggctgaggagctggc	0.552																																					p.Q244X		Atlas-SNP	.											.	SIN3A	152	.	0			c.C730T						PASS	.						81	75	77					15																	75705130		2197	4294	6491	SO:0001587	stop_gained	25942	exon5			GGGGCTGAGGAGC	AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"SIN3 homolog A, transcription regulator (yeast)", "SIN3 transcription regulator homolog A (yeast)"			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.730C>T	chr15.hg19:g.75705130G>A	ENSP00000378402:p.Gln244*	131.0	0.0	.		89.0	12.0	.	NM_001145358		Nonsense_Mutation	SNP	ENST00000394947.3	hg19	CCDS10279.1	.	.	.	.	.	.	.	.	.	.	G	37	6.213995	0.97380	.	.	ENSG00000169375	ENST00000394947;ENST00000394949;ENST00000360439	.	.	.	6.04	5.12	0.69794	.	0.098566	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	-11.3013	14.2887	0.66263	0.0708:0.0:0.9292:0.0	.	.	.	.	X	244	.	ENSP00000353622:Q244X	Q	-	1	0	SIN3A	73492183	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.867000	0.99620	1.557000	0.49525	0.561000	0.74099	CAG	.	.	.	none		0.552	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477		A	75705130	G	A	75705130	4	1	216	1	0	0	0	0	0	1	0	0	14338	1299	45	2	3159	2	SIN3A	15	75705130	Nonsense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	44507292	75705130	26826262	50	13138											
RASGRF1	5923	hgsc.bcm.edu	37	chr15	79350728	79350728	+	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	catcctcgatctgctgccgaAgctgcttggccacggtcttc	5	11	10	15	3	2	0	0	0	2	0	5	2	3	0	3	2	4	3	3	2	1	2			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr15:79350728A>T	ENST00000419573.3	-	3	753	c.479T>A	c.(478-480)cTt>cAt	p.L160H	RASGRF1_ENST00000560334.1_5'UTR|RASGRF1_ENST00000558480.2_Missense_Mutation_p.L160H	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	160					activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						CTGCTGCCGAAGCTGCTTGGC	0.602																																					p.L160H		Atlas-SNP	.											.	RASGRF1	168	.	0			c.T479A						PASS	.						124	101	109					15																	79350728		2196	4293	6489	SO:0001583	missense	5923	exon3			TGCCGAAGCTGCT	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.479T>A	chr15.hg19:g.79350728A>T	ENSP00000405963:p.Leu160His	46.0	0.0	.		44.0	4.0	.	NM_001145648	F8VPA5|H0YKF2|J3KQP9|Q16027	Missense_Mutation	SNP	ENST00000419573.3	hg19	CCDS10309.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.982389	0.74474	.	.	ENSG00000058335	ENST00000419573;ENST00000394741	T	0.46819	0.86	4.59	4.59	0.56863	.	0.000000	0.64402	D	0.000005	T	0.62258	0.2413	L	0.55481	1.735	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.85130	0.954;0.984;0.993;0.997	T	0.65492	-0.6155	10	0.87932	D	0	.	11.9588	0.52997	1.0:0.0:0.0:0.0	.	160;160;160;160	A8K270;Q8IUU5;Q13972;F8VPA5	.;.;RGRF1_HUMAN;.	H	160	ENSP00000405963:L160H	ENSP00000378224:L160H	L	-	2	0	RASGRF1	77137783	1.000000	0.71417	0.997000	0.53966	0.677000	0.39632	8.730000	0.91510	1.917000	0.55516	0.443000	0.29094	CTT	.	.	.	none		0.602	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891		T	79350728	A	T	79350728	3	4	216	1	0	0	0	0	1	0	0	0	13085	72	3	5	3446	5	RASGRF1	15	79350728	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10	3645598	79350728	23180664	51	13139											
GRIN2A	2903	hgsc.bcm.edu	37	chr16	9858489	9858489	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttattgaggttatccttcTgccggttggccacaaatgtt	8	15	10	8	1	1	1	0	1	1	0	2	1	2	1	3	3	1	4	3	3	3	6			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr16:9858489T>C	ENST00000396573.2	-	14	3221	c.2912A>G	c.(2911-2913)cAg>cGg	p.Q971R	GRIN2A_ENST00000562109.1_Missense_Mutation_p.Q971R|GRIN2A_ENST00000396575.2_Missense_Mutation_p.Q971R|GRIN2A_ENST00000330684.3_Missense_Mutation_p.Q971R|GRIN2A_ENST00000404927.2_Missense_Mutation_p.Q971R|GRIN2A_ENST00000535259.1_Missense_Mutation_p.Q814R	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	971					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)	GTTATCCTTCTGCCGGTTGGC	0.468																																					p.Q971R		Atlas-SNP	.											.	GRIN2A	366	.	0			c.A2912G						PASS	.						151	131	137					16																	9858489		2197	4300	6497	SO:0001583	missense	2903	exon14			TCCTTCTGCCGGT		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.2912A>G	chr16.hg19:g.9858489T>C	ENSP00000379818:p.Gln971Arg	96.0	0.0	.		84.0	27.0	.	NM_000833	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	hg19	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	T	5.637	0.302152	0.10678	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000535259;ENST00000330684;ENST00000396575	T;T;T;T;T	0.11712	2.75;2.75;2.76;2.75;2.75	5.33	5.33	0.75918	Glutamate [NMDA] receptor, epsilon subunit, C-terminal (1);	0.088776	0.85682	D	0.000000	T	0.08714	0.0216	L	0.27053	0.805	0.23293	N	0.997962	B;B;B	0.24317	0.034;0.101;0.005	B;B;B	0.29440	0.062;0.102;0.008	T	0.32428	-0.9907	9	.	.	.	.	10.6354	0.45563	0.0:0.0:0.1607:0.8393	.	814;971;971	F5GZ52;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	R	971;971;814;971;971	ENSP00000379818:Q971R;ENSP00000385872:Q971R;ENSP00000441572:Q814R;ENSP00000332549:Q971R;ENSP00000379820:Q971R	.	Q	-	2	0	GRIN2A	9765990	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	4.691000	0.61738	2.016000	0.59253	0.533000	0.62120	CAG	.	.	.	none		0.468	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			C	9858489	T	C	9858489	3	2	216	1	0	0	0	0	1	0	0	0	6786	1580	55	3	1486	3	GRIN2A	16	9858489	Missense_Mutation	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10		9858489	80496264	52	13140											
ITGAX	3687	hgsc.bcm.edu	37	chr16	31373395	31373395	+	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	cctggaatccttttctcccaGgatggccccgttctgggggc	4	11	12	14	1	2	0	0	0	2	0	4	2	3	2	5	5	0	1	5	5	1	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr16:31373395G>A	ENST00000268296.4	+	11	1207		c.e11-1		ITGAX_ENST00000562522.1_Splice_Site	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)						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						TTTTCTCCCAGGATGGCCCCG	0.592																																					.		Atlas-SNP	.											.	ITGAX	198	.	0			c.1087-1G>A						PASS	.						82	87	86					16																	31373395		2197	4300	6497	SO:0001630	splice_region_variant	3687	exon11			CTCCCAGGATGGC	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.1087-1G>A	chr16.hg19:g.31373395G>A		94.0	0.0	.		74.0	10.0	.	NM_000887	Q8IVA6	Splice_Site	SNP	ENST00000268296.4	hg19	CCDS10711.1	.	.	.	.	.	.	.	.	.	.	g	13.52	2.262216	0.39995	.	.	ENSG00000140678	ENST00000268296	.	.	.	4.5	4.5	0.54988	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4899	0.67645	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ITGAX	31280896	1.000000	0.71417	1.000000	0.80357	0.483000	0.33249	5.608000	0.67654	2.217000	0.71921	0.580000	0.79431	.	.	.	.	none		0.592	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887	Intron	A	31373395	G	A	31373395	5	1	216	1	0	0	0	0	0	0	1	0	7896	1014	35	2	1128	2	ITGAX	16	31373395	Splice_Site	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	21514906	31373395	58981358	53	13141											
ITGAX	3687	hgsc.bcm.edu	37	chr16	31383064	31383064	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgagccgagtccgagtcctcGggctgaaggcacactgtgaa	9	7	14	11	3	0	3	0	3	0	0	3	5	2	3	3	2	1	2	3	2	2	0	rs368436373		TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr16:31383064G>A	ENST00000268296.4	+	17	2240	c.2119G>A	c.(2119-2121)Ggg>Agg	p.G707R	ITGAX_ENST00000562522.1_Missense_Mutation_p.G707R	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	707					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						CCGAGTCCTCGGGCTGAAGGC	0.652																																					p.G707R		Atlas-SNP	.											.	ITGAX	198	.	0			c.G2119A						PASS	.	G	ARG/GLY	0,4394		0,0,2197	60	54	56		2119	4.4	0	16		56	2,8598	2.2+/-6.3	0,2,4298	no	missense	ITGAX	NM_000887.3	125	0,2,6495	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	707/1164	31383064	2,12992	2197	4300	6497	SO:0001583	missense	3687	exon17			GTCCTCGGGCTGA	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.2119G>A	chr16.hg19:g.31383064G>A	ENSP00000268296:p.Gly707Arg	59.0	0.0	.		54.0	5.0	.	NM_000887	Q8IVA6	Missense_Mutation	SNP	ENST00000268296.4	hg19	CCDS10711.1	.	.	.	.	.	.	.	.	.	.	G	15.13	2.741680	0.49151	0.0	2.33E-4	ENSG00000140678	ENST00000268296	T	0.44881	0.91	5.4	4.43	0.53597	Integrin alpha-2 (1);	.	.	.	.	T	0.51398	0.1672	L	0.55834	1.745	0.09310	N	1	D	0.59767	0.986	P	0.56514	0.8	T	0.38436	-0.9661	9	0.49607	T	0.09	.	10.5956	0.45336	0.0933:0.0:0.9067:0.0	.	707	P20702	ITAX_HUMAN	R	707	ENSP00000268296:G707R	ENSP00000268296:G707R	G	+	1	0	ITGAX	31290565	0.076000	0.21285	0.028000	0.17463	0.033000	0.12548	2.282000	0.43461	2.662000	0.90505	0.655000	0.94253	GGG	.	.	.	weak		0.652	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887		A	31383064	G	A	31383064	3	1	216	1	0	0	0	0	1	0	0	0	7896	1116	39	1	2185	1	ITGAX	16	31383064	Missense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	9669	31383064	58971689	54	13142											
COL1A1	1277	hgsc.bcm.edu	37	chr17	48277127	48277127	+	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	gccgcacctgagccgtcgggGcagacgggacagcactcgcc	7	3	15	16	5	0	2	0	1	0	1	2	3	0	3	4	3	2	3	4	3	0	0			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr17:48277127G>A	ENST00000225964.5	-	2	403	c.285C>T	c.(283-285)tgC>tgT	p.C95C		NM_000088.3	NP_000079	P02452	CO1A1_HUMAN	collagen, type I, alpha 1	95	VWFC. {ECO:0000255|PROSITE- ProRule:PRU00220}.				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)	AGCCGTCGGGGCAGACGGGAC	0.726			T	"PDGFB, USP6"	"dermatofibrosarcoma protuberans, aneurysmal bone cyst "		Osteogenesis imperfecta																														p.C95C		Atlas-SNP	.		Dom	yes		17	17q21.31-q22	1277	"collagen, type I, alpha 1"	yes	M	.	COL1A1	158	.	0			c.C285T						PASS	.						47	49	48					17																	48277127		2202	4300	6502	SO:0001819	synonymous_variant	1277	exon2			GTCGGGGCAGACG	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.285C>T	chr17.hg19:g.48277127G>A		34.0	0.0	.		59.0	6.0	.	NM_000088	O76045|P78441|Q13896|Q13902|Q13903|Q14037|Q14992|Q15176|Q15201|Q16050|Q59F64|Q7KZ30|Q7KZ34|Q8IVI5|Q8N473|Q9UML6|Q9UMM7	Silent	SNP	ENST00000225964.5	hg19	CCDS11561.1																																																																																			.	.	.	none		0.726	COL1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309036.2			A	48277127	G	A	48277127	2	1	216	1	0	0	0	0	0	0	0	1	3679	1195	42	2		2	COL1A1	17	48277127	Silent	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10		48277127	32918083	55	13143											
SFRS1	6426	hgsc.bcm.edu	37	chr17	56083837	56083837	+	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	ggaaactccacccgcagacgGtacccatcgtaatcatagcc	12	6	8	15	3	1	1	1	0	0	1	3	2	2	2	4	2	3	3	4	2	4	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr17:56083837G>T	ENST00000258962.4	-	2	454	c.246C>A	c.(244-246)taC>taA	p.Y82*	SRSF1_ENST00000585096.1_Intron|SRSF1_ENST00000582730.2_Nonsense_Mutation_p.Y82*|SRSF1_ENST00000581497.1_5'Flank|RP11-159D12.5_ENST00000578794.1_5'Flank|SRSF1_ENST00000584773.1_Nonsense_Mutation_p.Y82*	NM_006924.4	NP_008855.1	Q07955	SRSF1_HUMAN	serine/arginine-rich splicing factor 1	82	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)	p.Y82*(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						CCCGCAGACGGTACCCATCGT	0.637																																					p.Y82X		Atlas-SNP	.											SRSF1,NS,lymphoid_neoplasm,0,2	SRSF1	41	.	1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C246A						PASS	.						30	28	29					17																	56083837		2203	4298	6501	SO:0001587	stop_gained	6426	exon2			CAGACGGTACCCA		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.246C>A	chr17.hg19:g.56083837G>T	ENSP00000258962:p.Tyr82*	223.0	0.0	.		206.0	20.0	.	NM_006924	B2R6Z7|D3DTZ3|Q13809	Nonsense_Mutation	SNP	ENST00000258962.4	hg19	CCDS11600.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.149607	0.78001	.	.	ENSG00000136450	ENST00000258962	.	.	.	5.96	-2.82	0.05787	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	.	13.3631	0.60667	0.5712:0.0:0.4287:0.0	.	.	.	.	X	82	.	ENSP00000258962:Y82X	Y	-	3	2	SRSF1	53438836	1.000000	0.71417	0.931000	0.37212	0.911000	0.54048	0.912000	0.28597	-0.291000	0.09012	-0.794000	0.03295	TAC	.	.	.	none		0.637	SRSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443335.1	NM_006924		T	56083837	G	T	56083837	4	4	216	1	0	0	0	0	0	1	0	0	14178	1256	44	4	566	4	SFRS1	17	56083837	Nonsense_Mutation	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	7806710	56083837	25111373	56	13144											
NETO1	81832	hgsc.bcm.edu	37	chr18	70450990	70450990	+	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	cccacatgcggatcaccccaAgacccgtgcgtagcatgaca	11	5	9	16	3	1	2	1	1	0	1	1	3	1	3	4	1	3	2	4	1	2	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr18:70450990A>T	ENST00000327305.6	-	7	1448	c.791T>A	c.(790-792)cTt>cAt	p.L264H	NETO1_ENST00000299430.2_Missense_Mutation_p.L263H|NETO1_ENST00000583169.1_Missense_Mutation_p.L264H	NM_138966.3	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 1	264	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				memory (GO:0007613)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|receptor localization to synapse (GO:0097120)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|visual learning (GO:0008542)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				NS(3)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(36)|ovary(2)|prostate(3)|skin(3)|stomach(1)	63		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		GATCACCCCAAGACCCGTGCG	0.478																																					p.L264H		Atlas-SNP	.											.	NETO1	178	.	0			c.T791A						PASS	.						193	165	174					18																	70450990		2203	4300	6503	SO:0001583	missense	81832	exon7			ACCCCAAGACCCG	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.791T>A	chr18.hg19:g.70450990A>T	ENSP00000313088:p.Leu264His	74.0	0.0	.		88.0	7.0	.	NM_001201465	Q86W85|Q8ND78|Q8TDF4	Missense_Mutation	SNP	ENST00000327305.6	hg19	CCDS12000.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.261669	0.80358	.	.	ENSG00000166342	ENST00000327305;ENST00000299430	T;T	0.18174	2.23;2.23	5.27	5.27	0.74061	CUB (5);	0.000000	0.53938	D	0.000058	T	0.36082	0.0954	L	0.47716	1.5	0.80722	D	1	D;D	0.89917	1.0;0.994	D;D	0.87578	0.998;0.957	T	0.08146	-1.0736	10	0.72032	D	0.01	-10.3986	15.5016	0.75703	1.0:0.0:0.0:0.0	.	263;264	Q8TDF5-2;Q8TDF5	.;NETO1_HUMAN	H	264;263	ENSP00000313088:L264H;ENSP00000299430:L263H	ENSP00000299430:L263H	L	-	2	0	NETO1	68601970	1.000000	0.71417	0.058000	0.19502	0.790000	0.44656	9.287000	0.95975	2.102000	0.63906	0.528000	0.53228	CTT	.	.	.	none		0.478	NETO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256301.2	NM_138999		T	70450990	A	T	70450990	3	4	216	1	0	0	0	0	1	0	0	0	10346	72	3	5	826	5	NETO1	18	70450990	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10		70450990	7626258	57	13145											
DOT1L	84444	hgsc.bcm.edu	37	chr19	2226194	2226194	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgccaggtggtggcttggCgggaaggaagcccgcgcccg	5	7	18	11	4	0	0	0	0	0	0	0	2	0	2	3	6	2	1	3	6	2	2			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr19:2226194C>T	ENST00000398665.3	+	27	3710	c.3674C>T	c.(3673-3675)gCg>gTg	p.A1225V		NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	1225					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)		GGTGGCTTGGCGGGAAGGAAG	0.677																																					p.A1225V		Atlas-SNP	.											.	DOT1L	205	.	0			c.C3674T						PASS	.						12	16	15					19																	2226194		1920	4101	6021	SO:0001583	missense	84444	exon27			GCTTGGCGGGAAG	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.3674C>T	chr19.hg19:g.2226194C>T	ENSP00000381657:p.Ala1225Val	63.0	0.0	.		68.0	12.0	.	NM_032482	O60379|Q96JL1	Missense_Mutation	SNP	ENST00000398665.3	hg19	CCDS42460.1	.	.	.	.	.	.	.	.	.	.	C	10.54	1.379238	0.24944	.	.	ENSG00000104885	ENST00000398665;ENST00000221482;ENST00000457590	T;T	0.30182	1.95;1.54	4.54	-0.654	0.11443	.	1.117080	0.06764	N	0.782394	T	0.21103	0.0508	L	0.31294	0.92	0.09310	N	1	B;B	0.16396	0.002;0.017	B;B	0.09377	0.001;0.004	T	0.32719	-0.9896	10	0.87932	D	0	-8.2664	5.1085	0.14796	0.0:0.5858:0.1604:0.2538	.	1225;1225	Q8TEK3;Q8TEK3-2	DOT1L_HUMAN;.	V	1225;1225;105	ENSP00000381657:A1225V;ENSP00000407411:A105V	ENSP00000221482:A1225V	A	+	2	0	DOT1L	2177194	0.000000	0.05858	0.000000	0.03702	0.225000	0.24961	0.096000	0.15147	-0.246000	0.09611	0.491000	0.48974	GCG	.	.	.	none		0.677	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482		T	2226194	C	T	2226194	3	4	216	1	0	0	0	0	1	0	0	0	4711	768	27	1	3780	1	DOT1L	19	2226194	Missense_Mutation	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10		2226194	56902789	58	13146											
RYR1	6261	hgsc.bcm.edu	37	chr19	38948847	38948847	+	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	accgagggctacaccccctaCcctggggccggcgagggctg	6	4	15	16	3	0	0	0	0	0	0	0	2	0	0	5	5	2	2	5	5	2	2			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr19:38948847C>G	ENST00000359596.3	+	18	2082	c.2082C>G	c.(2080-2082)taC>taG	p.Y694*	RYR1_ENST00000360985.3_Nonsense_Mutation_p.Y694*|RYR1_ENST00000355481.4_Nonsense_Mutation_p.Y694*			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	694	B30.2/SPRY 1. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	ACACCCCCTACCCTGGGGCCG	0.637																																					p.Y694X		Atlas-SNP	.											.	RYR1	708	.	0			c.C2082G						PASS	.						52	51	51					19																	38948847		2203	4300	6503	SO:0001587	stop_gained	6261	exon18			CCCCTACCCTGGG	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.2082C>G	chr19.hg19:g.38948847C>G	ENSP00000352608:p.Tyr694*	55.0	0.0	.		46.0	8.0	.	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Nonsense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	C	41	8.988435	0.99027	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	.	.	.	5.02	5.02	0.67125	.	0.000000	0.64402	U	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.9369	0.58320	0.0:0.9196:0.0:0.0804	.	.	.	.	X	694	.	ENSP00000347667:Y694X	Y	+	3	2	RYR1	43640687	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.109000	0.41863	2.623000	0.88846	0.549000	0.68633	TAC	.	.	.	none		0.637	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			G	38948847	C	G	38948847	4	3	216	1	0	0	0	0	0	1	0	0	13781	518	18	4	2152	4	RYR1	19	38948847	Nonsense_Mutation	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	36722653	38948847	20180136	59	13147											
PSG5	5673	hgsc.bcm.edu	37	chr19	43679366	43679366	+	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	aggatgctgggatccacttaCcagagacttcgactgtcatg	10	10	11	10	1	1	1	1	0	0	1	3	5	2	3	2	2	2	1	2	2	1	2			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr19:43679366C>T	ENST00000366175.3	-	4	1095		c.e4+1		PSG5_ENST00000407568.1_Intron|PSG5_ENST00000404580.1_Missense_Mutation_p.G322D|PSG5_ENST00000407356.1_Splice_Site|PSG5_ENST00000599812.1_Splice_Site|PSG5_ENST00000342951.6_Splice_Site			Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5						female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(18)|prostate(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(69;0.00899)				GATCCACTTACCAGAGACTTC	0.463																																					.		Atlas-SNP	.											.	PSG5	58	.	0			c.964+1G>A						PASS	.						125	148	140					19																	43679366		2202	4292	6494	SO:0001630	splice_region_variant	5673	exon5			CACTTACCAGAGA		CCDS12617.1	19q13.2	2013-01-29			ENSG00000204941	ENSG00000204941		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9522	protein-coding gene	gene with protein product	"pregnancy-specific beta-1 glycoprotein", "pregnancy-specific beta 1 glycoprotein"	176394				2735907	Standard	NM_002781		Approved	FL-NCA-3, PSG	uc002ovx.3	Q15238	OTTHUMG00000151539	ENST00000366175.3:c.964+1G>A	chr19.hg19:g.43679366C>T		153.0	0.0	.		114.0	12.0	.	NM_002781	Q15239|Q96QJ1|Q9UQ75	Splice_Site	SNP	ENST00000366175.3	hg19	CCDS12617.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|c	5.814|5.814	0.334421|0.334421	0.11013|0.11013	.|.	.|.	ENSG00000204941|ENSG00000204941	ENST00000366175;ENST00000407356;ENST00000342951|ENST00000404580	.|T	.|0.01252	.|5.1	1.25|1.25	1.25|1.25	0.21368|0.21368	.|.	.|.	.|.	.|.	.|.	.|T	.|0.00967	.|0.0032	.|.	.|.	.|.	0.23661|0.23661	N|N	0.99718|0.99718	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.49634	.|-0.8919	.|6	.|0.15499	.|T	.|0.54	.|.	5.8107|5.8107	0.18465|0.18465	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	.|D	-1|322	.|ENSP00000385250:G322D	.|ENSP00000385250:G322D	.|G	-|-	.|2	.|0	PSG5|PSG5	48371206|48371206	0.321000|0.321000	0.24625|0.24625	0.181000|0.181000	0.23098|0.23098	0.040000|0.040000	0.13550|0.13550	0.696000|0.696000	0.25541|0.25541	0.644000|0.644000	0.30656|0.30656	0.184000|0.184000	0.17185|0.17185	.|GGT	.	.	.	none		0.463	PSG5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323055.1	NM_002781	Intron	T	43679366	C	T	43679366	5	4	216	1	0	0	0	0	0	0	1	0	12668	521	18	2	50	2	PSG5	19	43679366	Splice_Site	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	4730519	43679366	15449617	60	13148											
NLRP8	126205	hgsc.bcm.edu	37	chr19	56487643	56487643	+	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	ctgtgtgaggccctgaagaaCcctgactgtacattacagat	11	10	10	10	0	0	5	0	3	0	2	0	5	0	5	2	1	3	1	2	1	4	2			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr19:56487643C>T	ENST00000291971.3	+	8	2921	c.2850C>T	c.(2848-2850)aaC>aaT	p.N950N	NLRP8_ENST00000590542.1_Silent_p.N931N	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	950					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)		CCCTGAAGAACCCTGACTGTA	0.453																																					p.N950N		Atlas-SNP	.											.	NLRP8	225	.	0			c.C2850T						PASS	.						139	135	136					19																	56487643		2203	4300	6503	SO:0001819	synonymous_variant	126205	exon8			GAAGAACCCTGAC	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.2850C>T	chr19.hg19:g.56487643C>T		188.0	0.0	.		151.0	22.0	.	NM_176811	Q7RTR4	Silent	SNP	ENST00000291971.3	hg19	CCDS12937.1																																																																																			.	.	.	none		0.453	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811		T	56487643	C	T	56487643	2	4	216	1	0	0	0	0	0	0	0	1	10490	506	18	2		2	NLRP8	19	56487643	Silent	SNP	C	TCGA-KV-A6GD-01A-11D-A31X-10	12808277	56487643	2641340	61	13149											
ACTR5	79913	hgsc.bcm.edu	37	chr20	37383625	37383625	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cacaaatggcggtgtcctgaTtattatgagaataatgtcca	13	12	9	7	1	0	2	0	2	0	1	2	3	2	2	2	2	0	0	2	2	5	3			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr20:37383625T>C	ENST00000243903.4	+	4	838	c.801T>C	c.(799-801)gaT>gaC	p.D267D		NM_024855.3	NP_079131.3	Q9H9F9	ARP5_HUMAN	ARP5 actin-related protein 5 homolog (yeast)	267					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)				GGTGTCCTGATTATTATGAGA	0.418																																					p.D267D		Atlas-SNP	.											.	ACTR5	44	.	0			c.T801C						PASS	.						67	71	70					20																	37383625		2203	4300	6503	SO:0001819	synonymous_variant	79913	exon4			TCCTGATTATTAT	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.801T>C	chr20.hg19:g.37383625T>C		245.0	0.0	.		256.0	56.0	.	NM_024855	Q86WF7|Q8IUY5|Q8N724|Q9BRN0|Q9BVB7	Silent	SNP	ENST00000243903.4	hg19	CCDS13308.1																																																																																			.	.	.	none		0.418	ACTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079205.2	NM_024855		C	37383625	T	C	37383625	2	2	216	1	0	0	0	0	0	0	0	1	215	1490	52	3		3	ACTR5	20	37383625	Silent	SNP	T	TCGA-KV-A6GD-01A-11D-A31X-10		37383625	25641895	62	13150											
PREX1	57580	hgsc.bcm.edu	37	chr20	47361658	47361658	+	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	aaatccttatgaacttccagGatgtcttcgatgttcgagaa	12	13	8	8	2	1	2	0	1	1	1	5	5	3	3	2	1	1	1	2	1	4	4			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr20:47361658G>A	ENST00000371941.3	-	3	340	c.318C>T	c.(316-318)atC>atT	p.I106I	PREX1_ENST00000396220.1_Silent_p.I106I	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	106	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			GAACTTCCAGGATGTCTTCGA	0.473																																					p.I106I		Atlas-SNP	.											.	PREX1	441	.	0			c.C318T						PASS	.						159	163	162					20																	47361658		2203	4300	6503	SO:0001819	synonymous_variant	57580	exon3			TTCCAGGATGTCT	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.318C>T	chr20.hg19:g.47361658G>A		130.0	0.0	.		79.0	22.0	.	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	hg19	CCDS13410.1																																																																																			.	.	.	none		0.473	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		A	47361658	G	A	47361658	2	1	216	1	0	0	0	0	0	0	0	1	12486	1164	41	2		2	PREX1	20	47361658	Silent	SNP	G	TCGA-KV-A6GD-01A-11D-A31X-10	9978033	47361658	15663862	63	13151											
GSTT1	2952	hgsc.bcm.edu	37	chr22	24384206	24384206	+	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	cgcggcagggctgggacagcAggtccaggtacagctccagg	8	4	17	12	2	0	0	0	0	0	0	2	1	2	1	2	6	3	5	2	6	1	1			TCGA-KV-A6GD-01A-11D-A31X-10	TCGA-KV-A6GD-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	971ca777-b810-45b5-bcca-7100b2935d0f	92ae44d5-c386-489b-b4aa-c3e169713c55	g.chr22:24384206A>T	ENST00000248935.5	-	1	78	c.26T>A	c.(25-27)cTg>cAg	p.L9Q	GSTT1_ENST00000439996.2_5'UTR	NM_000853.2	NP_000844.2	P30711	GSTT1_HUMAN		9	GST N-terminal.				glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione peroxidase activity (GO:0004602)|glutathione transferase activity (GO:0004364)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|ovary(1)|prostate(1)|skin(1)	6					Carboplatin(DB00958)|Cisplatin(DB00515)|Etoposide(DB00773)|Glutathione(DB00143)|Oxaliplatin(DB00526)	CTGGGACAGCAGGTCCAGGTA	0.592									Myelodysplasia and Acute Myeloid Leukemia (AML), Familial																												p.L9Q		Atlas-SNP	.											.	GSTT1	14	.	0			c.T26A						PASS	.						77	72	74					22																	24384206		1700	3601	5301	SO:0001583	missense	2952	exon1	Familial Cancer Database	incl.: Familial Myelodysplastic syndrome (late-onset), Familial AML, Familial Monocytic Leukemia, Familial Monosomy 7 and AML	GACAGCAGGTCCA																												ENST00000248935.5:c.26T>A	chr22.hg19:g.24384206A>T	ENSP00000248935:p.Leu9Gln	86.0	0.0	.		84.0	22.0	.	NM_000853	O00226|Q5TZY2|Q6IC69|Q969K8|Q96IY3	Missense_Mutation	SNP	ENST00000248935.5	hg19	CCDS13822.1	.	.	.	.	.	.	.	.	.	.	.	28.3	4.911220	0.92178	.	.	ENSG00000184674	ENST00000248935;ENST00000382792;ENST00000452369;ENST00000417870;ENST00000447865	T;T;T	0.64085	-0.08;-0.08;-0.08	5.31	5.31	0.75309	Glutathione S-transferase, N-terminal (1);Thioredoxin-like fold (2);	0.000000	0.64402	U	0.000006	T	0.77922	0.4203	M	0.80508	2.5	0.80722	D	1	D	0.63046	0.992	D	0.63957	0.92	T	0.81464	-0.0921	10	0.87932	D	0	-11.7318	13.568	0.61830	1.0:0.0:0.0:0.0	.	9	P30711	GSTT1_HUMAN	Q	9	ENSP00000248935:L9Q;ENSP00000406003:L9Q;ENSP00000397362:L9Q	ENSP00000248935:L9Q	L	-	2	0	GSTT1	22714206	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	8.005000	0.88553	2.163000	0.67991	0.451000	0.29950	CTG	.	.	.	none		0.592	GSTT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320184.2			T	24384206	A	T	24384206	3	4	216	1	0	0	0	0	1	0	0	0	6852	188	7	5	716	5	GSTT1	22	24384206	Missense_Mutation	SNP	A	TCGA-KV-A6GD-01A-11D-A31X-10		24384206	26920360	64	13152											
PIK3C2B	5287	hgsc.bcm.edu	37	chr1	204413511	204413511	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagcatctgagagtgagccaAtccactgcacagccatacga	13	6	9	13	1	1	2	0	2	1	1	2	4	2	2	3	0	5	2	3	0	2	1			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr1:204413511A>G	ENST00000367187.3	-	18	3276	c.2720T>C	c.(2719-2721)aTt>aCt	p.I907T	PIK3C2B_ENST00000424712.2_Missense_Mutation_p.I879T	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	907	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				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)			GAGTGAGCCAATCCACTGCAC	0.582																																					p.I907T		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.T2720C						PASS	.						83	68	73					1																	204413511		2203	4300	6503	SO:0001583	missense	5287	exon18			GAGCCAATCCACT	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.2720T>C	chr1.hg19:g.204413511A>G	ENSP00000356155:p.Ile907Thr	54.0	0.0	.		43.0	23.0	.	NM_002646	O95666|Q5SW99	Missense_Mutation	SNP	ENST00000367187.3	hg19	CCDS1446.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.730234	0.89390	.	.	ENSG00000133056	ENST00000367187;ENST00000424712	T;T	0.67345	-0.26;-0.26	5.98	5.98	0.97165	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.045667	0.85682	D	0.000000	D	0.82559	0.5063	M	0.85197	2.74	0.51482	D	0.999921	D;D	0.61697	0.98;0.99	P;P	0.62885	0.908;0.903	D	0.85512	0.1198	10	0.87932	D	0	.	16.1192	0.81329	1.0:0.0:0.0:0.0	.	879;907	F5GWN5;O00750	.;P3C2B_HUMAN	T	907;879	ENSP00000356155:I907T;ENSP00000400561:I879T	ENSP00000356155:I907T	I	-	2	0	PIK3C2B	202680134	1.000000	0.71417	0.999000	0.59377	0.902000	0.53008	9.339000	0.96797	2.288000	0.76882	0.482000	0.46254	ATT	.	.	.	none		0.582	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646		G	204413511	A	G	204413511	3	3	217	1	0	0	0	0	1	0	0	0	11917	101	4	3	2252	3	PIK3C2B	1	204413511	Missense_Mutation	SNP	A	TCGA-KV-A6GE-01A-11D-A31X-10		204413511	44837110	1	13153											
TLR5	7100	hgsc.bcm.edu	37	chr1	223286235	223286235	+	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	cagcaggagcctctcagtggTgttgaggacctgggggacct	7	8	16	10	0	1	1	1	1	1	0	2	4	1	4	3	5	2	2	3	5	0	1			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr1:223286235T>A	ENST00000540964.1	-	4	600	c.139A>T	c.(139-141)Acc>Tcc	p.T47S	TLR5_ENST00000342210.6_Missense_Mutation_p.T47S			O60602	TLR5_HUMAN	toll-like receptor 5	47					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)		CTCTCAGTGGTGTTGAGGACC	0.547																																					p.T47S		Atlas-SNP	.											.	TLR5	86	.	0			c.A139T						PASS	.						62	63	62					1																	223286235		2203	4300	6503	SO:0001583	missense	7100	exon6			CAGTGGTGTTGAG		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.139A>T	chr1.hg19:g.223286235T>A	ENSP00000440643:p.Thr47Ser	140.0	0.0	.		168.0	70.0	.	NM_003268	B1AZ05|B3Y633|B9VJ63|D1CS80|D3DTB8|O15456|Q32MI2|Q32MI3	Missense_Mutation	SNP	ENST00000540964.1	hg19	CCDS31033.1	.	.	.	.	.	.	.	.	.	.	T	10.90	1.480409	0.26598	.	.	ENSG00000187554	ENST00000540964;ENST00000366881;ENST00000342210	D;D;D	0.82526	-1.62;-1.62;-1.62	4.75	3.6	0.41247	.	0.354369	0.30510	N	0.009461	T	0.70430	0.3223	L	0.48362	1.52	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.50516	-0.8819	10	0.09084	T	0.74	.	3.4825	0.07607	0.0:0.2019:0.2085:0.5896	.	47	O60602	TLR5_HUMAN	S	47	ENSP00000440643:T47S;ENSP00000355846:T47S;ENSP00000340089:T47S	ENSP00000340089:T47S	T	-	1	0	TLR5	221352858	0.318000	0.24598	0.004000	0.12327	0.995000	0.86356	0.650000	0.24858	0.751000	0.32900	0.533000	0.62120	ACC	.	.	.	none		0.547	TLR5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003268		A	223286235	T	A	223286235	3	1	217	1	0	0	0	0	1	0	0	0	15966	1696	59	5	2441	5	TLR5	1	223286235	Missense_Mutation	SNP	T	TCGA-KV-A6GE-01A-11D-A31X-10	18872724	223286235	25964386	2	13154											
TTN	7273	hgsc.bcm.edu	37	chr2	179424419	179424419	+	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	agagtcatttctgttggcatTttcaatggtcagtgatgtac	9	16	10	6	0	4	2	3	1	1	1	4	2	4	2	0	2	1	3	0	2	2	5			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr2:179424419T>A	ENST00000591111.1	-	276	81741	c.81517A>T	c.(81517-81519)Aat>Tat	p.N27173Y	TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.N26246Y|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.N19749Y|TTN_ENST00000359218.5_Missense_Mutation_p.N19874Y|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.N28814Y|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.N19941Y|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	27173	Ig-like 129.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTGTTGGCATTTTCAATGGTC	0.423																																					p.N28814Y		Atlas-SNP	.											.	TTN	18412	.	0			c.A86440T						PASS	.						167	157	160					2																	179424419		2006	4191	6197	SO:0001583	missense	7273	exon326			TGGCATTTTCAAT	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.81517A>T	chr2.hg19:g.179424419T>A	ENSP00000465570:p.Asn27173Tyr	104.0	0.0	.		163.0	44.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	11.56	1.673934	0.29693	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.50001	0.76;0.76;0.76;0.76	5.77	5.77	0.91146	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.51941	0.1704	M	0.70595	2.14	0.39978	D	0.974889	P;P;P;P	0.49253	0.921;0.921;0.921;0.921	B;B;B;B	0.42163	0.378;0.378;0.378;0.378	T	0.62742	-0.6790	9	0.87932	D	0	.	16.383	0.83481	0.0:0.0:0.0:1.0	.	19749;19874;19941;27173	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	Y	26246;19749;19941;19874;19746	ENSP00000343764:N26246Y;ENSP00000434586:N19749Y;ENSP00000340554:N19941Y;ENSP00000352154:N19874Y	ENSP00000340554:N19941Y	N	-	1	0	TTN	179132665	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.039000	0.57325	2.326000	0.78906	0.533000	0.62120	AAT	.	.	.	none		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179424419	T	A	179424419	3	1	217	1	0	0	0	0	1	0	0	0	16747	1841	64	5	21687	5	TTN	2	179424419	Missense_Mutation	SNP	T	TCGA-KV-A6GE-01A-11D-A31X-10		179424419	63774954	3	13155											
EDEM1	9695	hgsc.bcm.edu	37	chr3	5229984	5229984	+	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	ccactgccgcggccgtgggcCcgaccgcggggacccgtgag	4	3	17	17	7	0	1	0	1	0	0	0	3	0	2	6	4	1	0	6	4	0	0			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr3:5229984C>G	ENST00000256497.4	+	1	627	c.494C>G	c.(493-495)cCc>cGc	p.P165R	EDEM1_ENST00000445686.1_5'Flank|AC026202.1_ENST00000600805.1_5'Flank|AC026202.3_ENST00000439325.1_RNA	NM_014674.2	NP_055489.1	Q92611	EDEM1_HUMAN	ER degradation enhancer, mannosidase alpha-like 1	165					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)		GGCCGTGGGCCCGACCGCGGG	0.736																																					p.P165R		Atlas-SNP	.											.	EDEM1	45	.	0			c.C494G						PASS	.						8	10	10					3																	5229984		2079	4182	6261	SO:0001583	missense	9695	exon1			GTGGGCCCGACCG	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.494C>G	chr3.hg19:g.5229984C>G	ENSP00000256497:p.Pro165Arg	44.0	0.0	.		54.0	32.0	.	NM_014674	A8K9C8|B4DXP3	Missense_Mutation	SNP	ENST00000256497.4	hg19	CCDS33686.1	.	.	.	.	.	.	.	.	.	.	C	14.92	2.679794	0.47886	.	.	ENSG00000134109	ENST00000256497	T	0.81415	-1.49	4.81	4.81	0.61882	.	0.109188	0.64402	D	0.000005	T	0.69097	0.3073	N	0.25957	0.775	0.80722	D	1	B	0.32653	0.379	B	0.34180	0.177	T	0.66685	-0.5861	10	0.05959	T	0.93	-8.2011	17.4653	0.87631	0.0:1.0:0.0:0.0	.	165	Q92611	EDEM1_HUMAN	R	165	ENSP00000256497:P165R	ENSP00000256497:P165R	P	+	2	0	EDEM1	5204984	1.000000	0.71417	0.691000	0.30163	0.932000	0.56968	5.419000	0.66435	2.199000	0.70637	0.491000	0.48974	CCC	.	.	.	none		0.736	EDEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337566.2	NM_014674		G	5229984	C	G	5229984	3	3	217	1	0	0	0	0	1	0	0	0	4913	623	22	4	496	4	EDEM1	3	5229984	Missense_Mutation	SNP	C	TCGA-KV-A6GE-01A-11D-A31X-10		5229984	192792446	4	13156											
ACY1	95	hgsc.bcm.edu	37	chr3	52022828	52022828	+	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	tgcctgctgccactgacaacCgctatatccgcgcggtgagc	7	8	11	15	4	0	2	0	2	0	0	1	2	1	2	4	1	5	2	4	1	3	2			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr3:52022828C>A	ENST00000404366.2	+	14	1194	c.1048C>A	c.(1048-1050)Cgc>Agc	p.R350S	ACY1_ENST00000494103.1_Missense_Mutation_p.R278S|ACY1_ENST00000458031.2_Missense_Mutation_p.R440S|ABHD14A-ACY1_ENST00000463937.1_Missense_Mutation_p.R451S|ACY1_ENST00000476351.1_Missense_Mutation_p.R315S|ACY1_ENST00000476854.1_Missense_Mutation_p.R285S	NM_000666.2|NM_001198895.1	NP_000657.1|NP_001185824.1	Q03154	ACY1_HUMAN	aminoacylase 1	350					cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aminoacylase activity (GO:0004046)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Acetylcysteine(DB06151)|L-Aspartic Acid(DB00128)	CACTGACAACCGCTATATCCG	0.567																																					p.R350S		Atlas-SNP	.											.	ACY1	35	.	0			c.C1048A						PASS	.						160	172	168					3																	52022828		2203	4300	6503	SO:0001583	missense	95	exon14			GACAACCGCTATA	L07548	CCDS2844.1, CCDS56261.1, CCDS56262.1, CCDS56263.1	3p21.2	2006-02-02			ENSG00000243989	ENSG00000243989	3.5.1.14		177	protein-coding gene	gene with protein product		104620				1707030, 6948533	Standard	NM_000666		Approved		uc003dcq.3	Q03154	OTTHUMG00000157815	ENST00000404366.2:c.1048C>A	chr3.hg19:g.52022828C>A	ENSP00000384296:p.Arg350Ser	85.0	0.0	.		138.0	65.0	.	NM_001198895	C9J6I6|C9J9D8|C9JWD4	Missense_Mutation	SNP	ENST00000404366.2	hg19	CCDS2844.1	.	.	.	.	.	.	.	.	.	.	C	18.84	3.709106	0.68615	.	.	ENSG00000114786;ENSG00000114786;ENSG00000114786;ENSG00000243989;ENSG00000243989;ENSG00000243989;ENSG00000243989	ENST00000458031;ENST00000463937;ENST00000232907;ENST00000476854;ENST00000476351;ENST00000494103;ENST00000404366	T;T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73;0.73	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.75766	0.3894	M	0.91872	3.25	0.80722	D	1	D;D	0.76494	0.991;0.999	D;D	0.68039	0.955;0.951	T	0.80522	-0.1345	10	0.62326	D	0.03	-13.0341	19.4166	0.94703	0.0:1.0:0.0:0.0	.	440;350	B4DNW0;Q03154	.;ACY1_HUMAN	S	440;451;350;285;315;278;350	ENSP00000390557:R440S;ENSP00000420487:R451S;ENSP00000419262:R285S;ENSP00000417056:R315S;ENSP00000417618:R278S;ENSP00000384296:R350S	ENSP00000384296:R350S	R	+	1	0	ACY1;RP11-155D18.11	51997868	1.000000	0.71417	1.000000	0.80357	0.175000	0.22909	6.896000	0.75665	2.679000	0.91253	0.655000	0.94253	CGC	.	.	.	none		0.567	ACY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349657.1	NM_000666		A	52022828	C	A	52022828	3	1	217	1	0	0	0	0	1	0	0	0	226	652	23	4	1098	4	ACY1	3	52022828	Missense_Mutation	SNP	C	TCGA-KV-A6GE-01A-11D-A31X-10	46792844	52022828	145999602	5	13157											
PLXND1	23129	hgsc.bcm.edu	37	chr3	129281631	129281631	+	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	tgcccccattcccacccaccAaggtcgacgtcctctgcacg	7	7	7	20	3	1	0	0	0	1	0	4	1	3	0	6	1	2	1	6	1	1	1			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr3:129281631A>G	ENST00000324093.4	-	27	5002	c.4824T>C	c.(4822-4824)ctT>ctC	p.L1608L	PLXND1_ENST00000393239.1_Splice_Site_p.L1608L	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1608					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						CCCACCCACCAAGGTCGACGT	0.627																																					p.L1608L	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.T4824C						PASS	.						64	56	58					3																	129281631		2203	4300	6503	SO:0001630	splice_region_variant	23129	exon27			CCCACCAAGGTCG	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.4825+1T>C	chr3.hg19:g.129281631A>G		25.0	0.0	.		50.0	25.0	.	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Silent	SNP	ENST00000324093.4	hg19	CCDS33854.1																																																																																			.	.	.	none		0.627	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	Silent	G	129281631	A	G	129281631	5	3	217	1	0	0	0	0	0	0	1	0	12134	144	5	3	993	3	PLXND1	3	129281631	Splice_Site	SNP	A	TCGA-KV-A6GE-01A-11D-A31X-10	77258803	129281631	68740799	6	13158											
F13A1	2162	hgsc.bcm.edu	37	chr6	6222265	6222266	+	Splice_Site	INS	-	-	CACA																															ccattgtcaatcaaactcacINScacactgaatccttggtgag																										TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr6:6222265_6222266insCACA	ENST00000264870.3	-	8	1377_1378		c.e8+1			NM_000129.3	NP_000120.2	P00488	F13A_HUMAN	coagulation factor XIII, A1 polypeptide						blood coagulation (GO:0007596)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	62	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	ATCAAACTCACCACACTGAATC	0.376																																					.		Atlas-Indel,Pindel	.											.	F13A1	135	.	0			c.1112+1->TGTG						PASS	.																																			SO:0001630	splice_region_variant	2162	exon9			.	M14539	CCDS4496.1	6p24.2-p23	2014-01-24			ENSG00000124491	ENSG00000124491		"Transglutaminases"	3531	protein-coding gene	gene with protein product		134570		F13A			Standard	NM_000129		Approved		uc003mwv.3	P00488	OTTHUMG00000014186	ENST00000264870.3:c.1112+1->TGTG	chr6.hg19:g.6222266_6222269dupCACA		55.0	0.0	0		56.0	22.0	0.392857	NM_000129	Q59HA7|Q8N6X2|Q96P24|Q9BX29	Splice_Site	INS	ENST00000264870.3	hg19	CCDS4496.1																																																																																			.	.	.	none		0.376	F13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039756.3	NM_000129	Intron	CACA	6222266	-	CACA	6222265	8	5	217	1	0	1	1	0	0	0	1	0	5342	521	18	0	1117	0	F13A1	6	6222265	Splice_Site	INS	-	TCGA-KV-A6GE-01A-11D-A31X-10		6222265	164892802	7	13159											
MDGA1	266727	hgsc.bcm.edu	37	chr6	37622225	37622225	+	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	gaccactgcagctgggggagGggatcaccgcctgtcagcag	8	5	16	12	1	2	0	2	0	0	0	2	3	2	2	3	4	3	3	3	4	0	0			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr6:37622225G>T	ENST00000434837.3	-	6	1985	c.807C>A	c.(805-807)ccC>ccA	p.P269P	MDGA1_ENST00000297153.7_Silent_p.P269P|MDGA1_ENST00000505425.1_Silent_p.P269P	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	269	Ig-like 3.				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						GCTGGGGGAGGGGATCACCGC	0.642																																					p.P269P		Atlas-SNP	.											.	MDGA1	104	.	0			c.C807A						PASS	.						45	48	47					6																	37622225		2076	4205	6281	SO:0001819	synonymous_variant	266727	exon6			GGGGAGGGGATCA	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.807C>A	chr6.hg19:g.37622225G>T		115.0	0.0	.		79.0	34.0	.	NM_153487	A6NHG0|Q8NBE3	Silent	SNP	ENST00000434837.3	hg19	CCDS47417.1																																																																																			.	.	.	none		0.642	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3			T	37622225	G	T	37622225	2	4	217	1	0	0	0	0	0	0	0	1	9413	1219	43	4		4	MDGA1	6	37622225	Silent	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10	31399960	37622225	133492842	8	13160											
USP45	85015	hgsc.bcm.edu	37	chr6	99894085	99894085	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaccggatccactactggaTctgaacagcccagtctgctt	10	9	8	14	1	2	1	0	1	2	0	3	3	3	3	3	2	4	1	3	2	2	2			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr6:99894085T>C	ENST00000327681.6	-	14	2095	c.1563A>G	c.(1561-1563)agA>agG	p.R521R	USP45_ENST00000369233.2_Silent_p.R473R|USP45_ENST00000539675.1_Intron|USP45_ENST00000500704.2_Silent_p.R521R|USP45_ENST00000392738.2_Silent_p.R201R	NM_001080481.1	NP_001073950.1	Q70EL2	UBP45_HUMAN	ubiquitin specific peptidase 45	521	USP.		R -> T (in dbSNP:rs41288947). {ECO:0000269|PubMed:15489334}.		protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(2)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	22		all_cancers(76;0.000208)|Acute lymphoblastic leukemia(125;8.41e-11)|all_hematologic(75;2.56e-07)|all_epithelial(107;0.122)|Colorectal(196;0.133)		BRCA - Breast invasive adenocarcinoma(108;0.0718)		CACTACTGGATCTGAACAGCC	0.483																																					p.R521R		Atlas-SNP	.											.	USP45	56	.	0			c.A1563G						PASS	.						83	69	74					6																	99894085		2203	4300	6503	SO:0001819	synonymous_variant	85015	exon14			ACTGGATCTGAAC	AL832030	CCDS34501.1	6q16.2	2008-02-05	2005-08-08		ENSG00000123552	ENSG00000123552		"Ubiquitin-specific peptidases"	20080	protein-coding gene	gene with protein product			"ubiquitin specific protease 45"			12838346	Standard	NM_001080481		Approved	MGC14793	uc003ppx.2	Q70EL2	OTTHUMG00000015267	ENST00000327681.6:c.1563A>G	chr6.hg19:g.99894085T>C		69.0	0.0	.		60.0	23.0	.	NM_001080481	B2RXG0|Q5T062|Q86T44|Q86TC0|Q9BRU1	Silent	SNP	ENST00000327681.6	hg19	CCDS34501.1																																																																																			.	.	.	none		0.483	USP45-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041609.2	NM_032929		C	99894085	T	C	99894085	2	2	217	1	0	0	0	0	0	0	0	1	17088	1432	50	3		3	USP45	6	99894085	Silent	SNP	T	TCGA-KV-A6GE-01A-11D-A31X-10	62271860	99894085	71220982	9	13161											
ENPP1	5167	hgsc.bcm.edu	37	chr6	132211511	132211511	+	Frame_Shift_Del	DEL	G	G	-																															atgactcctcatgggttgaaGaattgttaatgttacacaga																										TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr6:132211511delG	ENST00000360971.2	+	25	2658	c.2638delG	c.(2638-2640)gaafs	p.E880fs		NM_006208.2	NP_006199.2	P22413	ENPP1_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 1	880	Nuclease.				3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|ATP catabolic process (GO:0006200)|biomineral tissue development (GO:0031214)|bone remodeling (GO:0046849)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to insulin stimulus (GO:0032869)|generation of precursor metabolites and energy (GO:0006091)|immune response (GO:0006955)|inorganic diphosphate transport (GO:0030505)|negative regulation of cell growth (GO:0030308)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of ossification (GO:0030279)|negative regulation of protein autophosphorylation (GO:0031953)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)|regulation of bone mineralization (GO:0030500)|riboflavin metabolic process (GO:0006771)|sequestering of triglyceride (GO:0030730)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|insulin receptor binding (GO:0005158)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|protein homodimerization activity (GO:0042803)|scavenger receptor activity (GO:0005044)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(22)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	46	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)	ATGGGTTGAAGAATTGTTAAT	0.388																																					p.E879fs	Colon(104;336 1535 5856 11019 33782)	Atlas-INDEL	.											.	ENPP1	108	.	0			c.2637delA						PASS	.						132	123	126					6																	132211511		2203	4300	6503	SO:0001589	frameshift_variant	5167	exon25			.	M57736	CCDS5150.2	6q22-q23	2008-02-07			ENSG00000197594	ENSG00000197594	3.1.4.1, 3.6.1.9		3356	protein-coding gene	gene with protein product		173335		NPPS, M6S1, PDNP1		1315502	Standard	NM_006208		Approved	PC-1, PCA1	uc011ecf.2	P22413	OTTHUMG00000015572	ENST00000360971.2:c.2638delG	chr6.hg19:g.132211511delG	ENSP00000354238:p.Glu880fs	165.0	0.0	0		167.0	46.0	0.275449	NM_006208	Q5T9R6|Q9NPZ3|Q9P1P6|Q9UP61|Q9Y6K3	Frame_Shift_Del	DEL	ENST00000360971.2	hg19	CCDS5150.2																																																																																			.	.	.	none		0.388	ENPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042238.2			-	132211511	G	-	132211511	7	5	217	1	0	1	0	1	0	0	0	0	5131	943	33	0	2736	0	ENPP1	6	132211511	Frame_Shift_Del	DEL	G	TCGA-KV-A6GE-01A-11D-A31X-10	32317426	132211511	38903556	10	13162											
ARHGEF5	7984	hgsc.bcm.edu	37	chr7	144063479	144063479	+	Frame_Shift_Del	DEL	G	G	-																															ccagccgtggagaaacatccGggaccctcagacactgttgt																										TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr7:144063479delG	ENST00000056217.5	+	3	3360	c.3186delG	c.(3184-3186)ccgfs	p.P1062fs	ARHGEF5_ENST00000471847.2_5'UTR	NM_005435.3	NP_005426.2	Q12774	ARHG5_HUMAN	Rho guanine nucleotide exchange factor (GEF) 5	1062					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)					AGAAACATCCGGGACCCTCAG	0.483																																					p.P1062fs		Atlas-INDEL	.											.	ARHGEF5	73	.	0			c.3185delC						PASS	.						41	40	40					7																	144063479		2196	4273	6469	SO:0001589	frameshift_variant	7984	exon3			.	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.3186delG	chr7.hg19:g.144063479delG	ENSP00000056217:p.Pro1062fs	514.0	0.0	0		900.0	80.0	0.0888889	NM_005435	A6NNJ2|Q6ZML7	Frame_Shift_Del	DEL	ENST00000056217.5	hg19	CCDS34771.1																																																																																			.	.	.	none		0.483	ARHGEF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349981.1	NM_005435		-	144063479	G	-	144063479	7	5	217	1	0	1	0	1	0	0	0	0	909	1103	39	0	3192	0	ARHGEF5	7	144063479	Frame_Shift_Del	DEL	G	TCGA-KV-A6GE-01A-11D-A31X-10		144063479	15075184	11	13163											
CREB3	57704	hgsc.bcm.edu	37	chr9	35736272	35736272	+	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	0	0	0	0	0	0	0	ttgtacctgctatgtactccTctgacacaagggggagcctg	8	11	11	11	0	1	1	0	1	1	0	2	2	2	2	3	2	4	3	3	2	4	4			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr9:35736272T>C	ENST00000378103.3	-	0	3611				CREB3_ENST00000486056.1_3'UTR|CREB3_ENST00000353704.2_Missense_Mutation_p.S249P|GBA2_ENST00000467252.1_5'Flank	NM_020944.2	NP_065995.1	Q9HCG7	GBA2_HUMAN	glucosidase, beta (bile acid) 2						bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|central nervous system neuron development (GO:0021954)|glucosylceramide catabolic process (GO:0006680)|glycoside catabolic process (GO:0016139)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)	beta-glucosidase activity (GO:0008422)|glucosylceramidase activity (GO:0004348)			NS(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(4)|skin(3)	21	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TATGTACTCCTCTGACACAAG	0.552											OREG0019176	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S249P		Atlas-SNP	.											.	CREB3	24	.	0			c.T745C						PASS	.						220	207	211					9																	35736272		2203	4300	6503	SO:0001628	intergenic_variant	10488	exon8			TACTCCTCTGACA	AJ309567	CCDS6589.1	9p13.2	2013-09-11			ENSG00000070610	ENSG00000070610			18986	protein-coding gene	gene with protein product	"bile acid beta-glucosidase", "non-lysosomal glucosylceramidase"	609471	"spastic paraplegia 46 (autosomal recessive)"	SPG46		11489889, 23332916, 23332917	Standard	NM_020944		Approved	KIAA1605, AD035, DKFZp762K054	uc003zxw.3	Q9HCG7	OTTHUMG00000021024		chr9.hg19:g.35736272T>C		75.0	0.0	.	857	55.0	23.0	.	NM_006368	D3DRP2|Q5TCV6|Q96A51|Q96LY1|Q96SJ2|Q9H2L8	Missense_Mutation	SNP	ENST00000378103.3	hg19	CCDS6589.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.018246	0.75275	.	.	ENSG00000107175	ENST00000353704	T	0.67865	-0.29	5.68	4.56	0.56223	.	0.238919	0.43260	D	0.000597	T	0.74068	0.3668	L	0.56769	1.78	0.42787	D	0.993883	D;D	0.76494	0.999;0.996	D;D	0.66196	0.942;0.919	T	0.71394	-0.4606	10	0.26408	T	0.33	.	10.8203	0.46601	0.0:0.0743:0.0:0.9257	.	273;249	O43889;O43889-2	CREB3_HUMAN;.	P	249	ENSP00000342136:S249P	ENSP00000342136:S249P	S	+	1	0	CREB3	35726272	0.999000	0.42202	0.698000	0.30274	0.980000	0.70556	3.862000	0.56009	2.182000	0.69389	0.533000	0.62120	TCT	.	.	.	none		0.552	GBA2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055456.1	NM_020944		C	35736272	T	C	35736272	1	2	217	0	1	0	0	0	0	0	0	0	3857	1551	54	3		3	CREB3	9	35736272	IGR	SNP	T	TCGA-KV-A6GE-01A-11D-A31X-10		35736272	105477159	12	13164											
MAP3K8	1326	hgsc.bcm.edu	37	chr10	30748425	30748425	+	Missense_Mutation	SNP	T	T	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	gctggaacttcctgagaacaTtgctggtagggacaccctgc	9	9	12	11	0	0	1	0	1	0	1	1	4	1	3	2	3	4	3	2	3	3	3			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr10:30748425T>G	ENST00000263056.1	+	8	1964	c.1268T>G	c.(1267-1269)aTt>aGt	p.I423S	MAP3K8_ENST00000542547.1_Missense_Mutation_p.I423S|MAP3K8_ENST00000375321.1_Missense_Mutation_p.I423S	NM_001244134.1|NM_005204.3	NP_001231063.1|NP_005195.2	P41279	M3K8_HUMAN	mitogen-activated protein kinase kinase kinase 8	423			Missing (in oncogenic form).		cell cycle (GO:0007049)|protein phosphorylation (GO:0006468)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		Prostate(175;0.151)				CCTGAGAACATTGCTGGTAGG	0.527																																					p.I423S		Atlas-SNP	.											.	MAP3K8	46	.	0			c.T1268G						PASS	.						70	62	65					10																	30748425		2203	4300	6503	SO:0001583	missense	1326	exon7			AGAACATTGCTGG	D14497	CCDS7166.1	10p11.2	2011-06-09			ENSG00000107968	ENSG00000107968		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6860	protein-coding gene	gene with protein product		191195		COT, ESTF		2072910, 8479752	Standard	NM_005204		Approved	Tpl-2, EST, c-COT, MEKK8	uc009xlf.2	P41279	OTTHUMG00000017889	ENST00000263056.1:c.1268T>G	chr10.hg19:g.30748425T>G	ENSP00000263056:p.Ile423Ser	48.0	0.0	.		42.0	17.0	.	NM_001244134	A8K2Q5|D3DRX1|Q14275|Q5T855|Q9HC81	Missense_Mutation	SNP	ENST00000263056.1	hg19	CCDS7166.1	.	.	.	.	.	.	.	.	.	.	T	15.81	2.944339	0.53079	.	.	ENSG00000107968	ENST00000375328;ENST00000263056;ENST00000542547;ENST00000375321	T;T;T	0.70749	-0.51;-0.51;-0.51	4.91	4.91	0.64330	Protein kinase-like domain (1);	0.048008	0.85682	D	0.000000	T	0.52517	0.1739	N	0.24115	0.695	0.80722	D	1	P	0.35575	0.51	B	0.32211	0.142	T	0.52638	-0.8549	10	0.08599	T	0.76	.	14.5659	0.68176	0.0:0.0:0.0:1.0	.	423	P41279	M3K8_HUMAN	S	423	ENSP00000263056:I423S;ENSP00000443610:I423S;ENSP00000364470:I423S	ENSP00000263056:I423S	I	+	2	0	MAP3K8	30788431	1.000000	0.71417	0.979000	0.43373	0.850000	0.48378	5.323000	0.65858	1.850000	0.53721	0.519000	0.50382	ATT	.	.	.	none		0.527	MAP3K8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047416.2	NM_005204		G	30748425	T	G	30748425	3	3	217	1	0	0	0	0	1	0	0	0	9263	1493	52	5	1290	5	MAP3K8	10	30748425	Missense_Mutation	SNP	T	TCGA-KV-A6GE-01A-11D-A31X-10		30748425	104786322	13	13165											
DNHD1	144132	hgsc.bcm.edu	37	chr11	6592937	6592937	+	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	gggctacaggtcctacatgcGgagtgggacccaatagctgg	9	7	15	10	1	0	0	0	0	0	0	1	2	1	2	2	5	4	2	2	5	4	3	rs544585664		TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr11:6592937G>T	ENST00000527990.2	+	41	13983	c.13983G>T	c.(13981-13983)gcG>gcT	p.A4661A	DNHD1_ENST00000254579.6_Silent_p.A4661A			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	4661					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)		TCCTACATGCGGAGTGGGACC	0.627																																					p.A4661A		Atlas-SNP	.											.	DNHD1	198	.	0			c.G13983T						PASS	.						36	46	43					11																	6592937		2097	4219	6316	SO:0001819	synonymous_variant	144132	exon43			ACATGCGGAGTGG	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.13983G>T	chr11.hg19:g.6592937G>T		92.0	0.0	.		74.0	4.0	.	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Silent	SNP	ENST00000527990.2	hg19	CCDS44532.1																																																																																			.	.	.	none		0.627	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		T	6592937	G	T	6592937	2	4	217	1	0	0	0	0	0	0	0	1	4670	1103	39	4		4	DNHD1	11	6592937	Silent	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10		6592937	128413579	14	13166											
VSIG10	54621	hgsc.bcm.edu	37	chr12	118506351	118506351	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcctcctcctcctcctcCtcttcctcttctgaatccac	3	15	1	22	0	3	1	0	1	3	0	12	1	12	1	9	0	0	0	9	0	1	2	rs373328738		TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr12:118506351C>T	ENST00000359236.5	-	8	1674	c.1398G>A	c.(1396-1398)gaG>gaA	p.E466E		NM_019086.5	NP_061959.2	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	466	Glu-rich.					integral component of membrane (GO:0016021)				endometrium(5)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|urinary_tract(1)	17						cctcctcctcctcttcctctt	0.458																																					p.E466E		Atlas-SNP	.											.	VSIG10	41	.	0			c.G1398A						PASS	.						96	91	92					12																	118506351		2045	4191	6236	SO:0001819	synonymous_variant	54621	exon8			CTCCTCCTCTTCC		CCDS44992.1	12q24.23	2013-01-29			ENSG00000176834	ENSG00000176834		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26078	protein-coding gene	gene with protein product						12477932	Standard	NM_019086		Approved		uc001tws.3	Q8N0Z9		ENST00000359236.5:c.1398G>A	chr12.hg19:g.118506351C>T		100.0	0.0	.		132.0	8.0	.	NM_019086	Q9NWQ7	Silent	SNP	ENST00000359236.5	hg19	CCDS44992.1																																																																																			.	.	.	weak		0.458	VSIG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401273.2	NM_019086		T	118506351	C	T	118506351	2	4	217	1	0	0	0	0	0	0	0	1	17235	680	24	2		2	VSIG10	12	118506351	Silent	SNP	C	TCGA-KV-A6GE-01A-11D-A31X-10		118506351	15345544	15	13167											
PRMT5	10419	hgsc.bcm.edu	37	chr14	23397402	23397402	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccatggagaaagctttcccAcaattagcgtattccagtct	11	12	7	11	1	1	1	0	0	1	1	4	2	4	1	3	1	2	2	3	1	4	4			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr14:23397402A>G	ENST00000324366.8	-	3	471	c.248T>C	c.(247-249)gTg>gCg	p.V83A	PRMT5_ENST00000553641.1_5'UTR|PRMT5_ENST00000553897.1_Intron|PRMT5-AS1_ENST00000595662.1_RNA|RP11-298I3.1_ENST00000548322.1_RNA|PRMT5_ENST00000216350.8_Intron|PRMT5_ENST00000397440.4_Missense_Mutation_p.V66A|PRMT5_ENST00000397441.2_Missense_Mutation_p.V66A|PRMT5-AS1_ENST00000587245.2_RNA|PRMT5_ENST00000538452.1_5'UTR|RP11-298I3.1_ENST00000548819.1_RNA|PRMT5-AS1_ENST00000590290.1_RNA|PRMT5-AS1_ENST00000599580.2_RNA	NM_006109.3	NP_006100.2	O14744	ANM5_HUMAN	protein arginine methyltransferase 5	83	TIM barrel. {ECO:0000269|PubMed:23071334}.				cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|endothelial cell activation (GO:0042118)|gene expression (GO:0010467)|histone H4-R3 methylation (GO:0043985)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|peptidyl-arginine N-methylation (GO:0035246)|regulation of mitosis (GO:0007088)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|methylosome (GO:0034709)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|histone-arginine N-methyltransferase activity (GO:0008469)|methyltransferase activity (GO:0008168)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|transcription corepressor activity (GO:0003714)			endometrium(4)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	25	all_cancers(95;2.76e-05)			GBM - Glioblastoma multiforme(265;0.0126)		AAGCTTTCCCACAATTAGCGT	0.433																																					p.V83A		Atlas-SNP	.											.	PRMT5	101	.	0			c.T248C						PASS	.						92	82	85					14																	23397402		2203	4300	6503	SO:0001583	missense	10419	exon3			TTTCCCACAATTA	AF015913	CCDS9579.1, CCDS41922.1, CCDS61394.1, CCDS61395.1, CCDS61396.1	14q11.2	2014-06-12	2006-02-16	2006-02-16	ENSG00000100462	ENSG00000100462	2.1.1.125	"Protein arginine methyltransferases"	10894	protein-coding gene	gene with protein product		604045	"skb1 (S. pombe) homolog", "SKB1 homolog (S. pombe)"	HRMT1L5, SKB1		9843966	Standard	NM_001282955		Approved	SKB1Hs	uc001whm.1	O14744	OTTHUMG00000028709	ENST00000324366.8:c.248T>C	chr14.hg19:g.23397402A>G	ENSP00000319169:p.Val83Ala	59.0	0.0	.		85.0	33.0	.	NM_006109	A8MTP3|A8MZ91|B4DX49|B4DY30|B5BU10|D3DS33|E2QRE7|Q6IBR1|Q9UKH1	Missense_Mutation	SNP	ENST00000324366.8	hg19	CCDS9579.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.564340	0.86335	.	.	ENSG00000100462	ENST00000324366;ENST00000397441;ENST00000397440;ENST00000553550;ENST00000554867;ENST00000556616;ENST00000554910;ENST00000421938	.	.	.	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	T	0.80534	0.4641	M	0.84683	2.71	0.80722	D	1	D;D;D	0.71674	0.963;0.991;0.998	D;P;D	0.68765	0.959;0.73;0.96	D	0.83988	0.0336	9	0.87932	D	0	-13.1665	14.9141	0.70781	1.0:0.0:0.0:0.0	.	66;83;66	A8MTP3;O14744;A8MZ91	.;ANM5_HUMAN;.	A	83;66;66;83;83;45;41;93	.	ENSP00000319169:V83A	V	-	2	0	PRMT5	22467242	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.199000	0.89731	2.176000	0.68965	0.455000	0.32223	GTG	.	.	.	none		0.433	PRMT5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071674.3			G	23397402	A	G	23397402	3	3	217	1	0	0	0	0	1	0	0	0	12549	159	6	3	1725	3	PRMT5	14	23397402	Missense_Mutation	SNP	A	TCGA-KV-A6GE-01A-11D-A31X-10		23397402	83952138	16	13168											
PRMT7	54496	hgsc.bcm.edu	37	chr16	68386313	68386313	+	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	ctgtggttgtggagttcaggGtaggccacccaggggatgtt	6	11	17	7	0	1	0	1	0	0	0	1	2	1	2	2	6	0	4	2	6	1	4			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr16:68386313G>A	ENST00000339507.5	+	15	2405		c.e15+1		PRMT7_ENST00000441236.1_Splice_Site|PRMT7_ENST00000348497.4_Splice_Site|PRMT7_ENST00000449359.3_Splice_Site			Q9NVM4	ANM7_HUMAN	protein arginine methyltransferase 7						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)		GGAGTTCAGGGTAGGCCACCC	0.622																																					.		Atlas-SNP	.											.	PRMT7	51	.	0			c.1425+1G>A						PASS	.						40	38	39					16																	68386313		2198	4300	6498	SO:0001630	splice_region_variant	54496	exon13			TTCAGGGTAGGCC	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.1575+1G>A	chr16.hg19:g.68386313G>A		12.0	0.0	.		22.0	9.0	.	NM_001184824	B3KPR0|B3KUG9|B4E379|Q96PV5|Q9H9L0	Splice_Site	SNP	ENST00000339507.5	hg19	CCDS10866.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.947713	0.73787	.	.	ENSG00000132600	ENST00000449359;ENST00000441236;ENST00000348497;ENST00000339507	.	.	.	5.1	5.1	0.69264	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9994	0.80280	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PRMT7	66943814	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	9.352000	0.97076	2.392000	0.81423	0.655000	0.94253	.	.	.	.	none		0.622	PRMT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268892.3	NM_019023	Intron	A	68386313	G	A	68386313	5	1	217	1	0	0	0	0	0	0	1	0	12551	1275	44	2	1626	2	PRMT7	16	68386313	Splice_Site	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10		68386313	21968440	17	13169											
BLMH	642	hgsc.bcm.edu	37	chr17	28614937	28614937	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctgggctgtgtccacaaaaGcactcaagaagaaataacag	16	7	9	9	0	2	2	1	0	1	2	3	2	3	2	1	1	2	2	1	1	6	1			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr17:28614937G>A	ENST00000261714.6	-	4	524	c.350C>T	c.(349-351)gCt>gTt	p.A117V	BLMH_ENST00000582669.1_5'Flank|BLMH_ENST00000394819.3_Missense_Mutation_p.A30V|RNU6-1267P_ENST00000410747.1_RNA	NM_000386.3	NP_000377.1	Q13867	BLMH_HUMAN	bleomycin hydrolase	117					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|carboxypeptidase activity (GO:0004180)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|stomach(1)	13					Bleomycin(DB00290)	GTCCACAAAAGCACTCAAGAA	0.388																																					p.A117V	Pancreas(127;628 1772 12912 33293 36203)	Atlas-SNP	.											.	BLMH	42	.	0			c.C350T						PASS	.						88	85	86					17																	28614937		2203	4300	6503	SO:0001583	missense	642	exon4			ACAAAAGCACTCA	X92106	CCDS32604.1	17q11.2	2004-02-16				ENSG00000108578			1059	protein-coding gene	gene with protein product		602403				9407121, 9331073	Standard	NM_000386		Approved	BH	uc002hez.2	Q13867		ENST00000261714.6:c.350C>T	chr17.hg19:g.28614937G>A	ENSP00000261714:p.Ala117Val	75.0	0.0	.		76.0	17.0	.	NM_000386	B2R796|Q53F86|Q9UER9	Missense_Mutation	SNP	ENST00000261714.6	hg19	CCDS32604.1	.	.	.	.	.	.	.	.	.	.	G	19.14	3.769945	0.69992	.	.	ENSG00000108578	ENST00000261714;ENST00000394819	T;T	0.44881	0.91;0.91	5.95	5.95	0.96441	.	0.197192	0.52532	D	0.000067	T	0.45637	0.1352	M	0.63208	1.945	0.51233	D	0.999918	B;B	0.23540	0.087;0.036	B;B	0.25759	0.063;0.039	T	0.31530	-0.9940	10	0.49607	T	0.09	-8.7167	17.5491	0.87871	0.0:0.0:1.0:0.0	.	30;117	E7EMN3;Q13867	.;BLMH_HUMAN	V	117;30	ENSP00000261714:A117V;ENSP00000378296:A30V	ENSP00000261714:A117V	A	-	2	0	BLMH	25639063	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.945000	0.63568	2.824000	0.97209	0.655000	0.94253	GCT	.	.	.	none		0.388	BLMH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447940.1	NM_000386		A	28614937	G	A	28614937	3	1	217	1	0	0	0	0	1	0	0	0	1446	971	34	2	1053	2	BLMH	17	28614937	Missense_Mutation	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10		28614937	52580273	18	13170											
ZNF677	342926	hgsc.bcm.edu	37	chr19	53740610	53740610	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atttattacatttgtaaggtTtttctccagtgtgaattctc	9	20	6	6	0	2	1	0	1	2	0	4	1	2	1	1	1	1	2	1	1	4	8			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr19:53740610T>C	ENST00000598513.1	-	5	1520	c.1370A>G	c.(1369-1371)aAa>aGa	p.K457R	ZNF677_ENST00000333952.4_Missense_Mutation_p.K457R	NM_182609.2	NP_872415.1	Q86XU0	ZN677_HUMAN	zinc finger protein 677	457					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			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)		TTTGTAAGGTTTTTCTCCAGT	0.378																																					p.K457R		Atlas-SNP	.											.	ZNF677	94	.	0			c.A1370G						PASS	.						54	52	53					19																	53740610		2203	4300	6503	SO:0001583	missense	342926	exon5			TAAGGTTTTTCTC	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.1370A>G	chr19.hg19:g.53740610T>C	ENSP00000469391:p.Lys457Arg	65.0	0.0	.		80.0	23.0	.	NM_182609		Missense_Mutation	SNP	ENST00000598513.1	hg19	CCDS12861.1	.	.	.	.	.	.	.	.	.	.	T	16.82	3.227295	0.58668	.	.	ENSG00000197928	ENST00000333952	T	0.24908	1.83	2.21	1.14	0.20703	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.37393	N	0.002104	T	0.26085	0.0636	N	0.13272	0.32	0.25071	N	0.990998	D	0.67145	0.996	D	0.69142	0.962	T	0.05194	-1.0900	10	0.72032	D	0.01	.	6.5871	0.22626	0.0:0.0:0.2456:0.7543	.	457	Q86XU0	ZN677_HUMAN	R	457	ENSP00000334394:K457R	ENSP00000334394:K457R	K	-	2	0	ZNF677	58432422	0.880000	0.30214	0.998000	0.56505	0.997000	0.91878	0.417000	0.21214	0.277000	0.22141	0.533000	0.62120	AAA	.	.	.	none		0.378	ZNF677-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464189.1	NM_182609		C	53740610	T	C	53740610	3	2	217	1	0	0	0	0	1	0	0	0	18096	1841	64	3	388	3	ZNF677	19	53740610	Missense_Mutation	SNP	T	TCGA-KV-A6GE-01A-11D-A31X-10		53740610	5388373	19	13171											
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385790	58385790	+	Missense_Mutation	SNP	G	G	T																															cacattctccacattcataaGgtcttttcccagtgtgaact																								rs111727691		TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr19:58385790G>T	ENST00000435989.2	-	3	1202	c.968C>A	c.(967-969)cCt>cAt	p.P323H	ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000600634.1_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	chr19.hg19:g.58385790G>T	ENSP00000410545:p.Pro323His	87.0	0.0	.		115.0	8.0	.	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	hg19	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	217	1	0	0	0	0	1	0	0	0	18188	1000	35	4	1603	4	ZNF814	19	58385790	Missense_Mutation	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10	4645180	58385790	743193	20	13172	129	2									
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385793	58385793	+	Missense_Mutation	SNP	C	C	T																															attctccacattcataaggtCttttcccagtgtgaactctc																								rs113623532		TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr19:58385793C>T	ENST00000435989.2	-	3	1199	c.965G>A	c.(964-966)aGa>aAa	p.R322K	ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000600634.1_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	chr19.hg19:g.58385793C>T	ENSP00000410545:p.Arg322Lys	81.0	0.0	.		107.0	8.0	.	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	hg19	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	217	1	0	0	0	0	1	0	0	0	18188	913	32	2	1606	2	ZNF814	19	58385793	Missense_Mutation	SNP	C	TCGA-KV-A6GE-01A-11D-A31X-10	3	58385793	743190	21	13173	129	2									
TRAPPC10	7109	hgsc.bcm.edu	37	chr21	45502876	45502876	+	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	ctaccggaagactgcggagtGgcttaccaagcacaagacgt	12	6	12	11	3	0	2	0	0	0	2	0	4	0	4	2	3	4	2	2	3	5	2			TCGA-KV-A6GE-01A-11D-A31X-10	TCGA-KV-A6GE-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aff18e57-af36-44a3-8a58-5c8633a7ae20	24f06120-19b5-449d-88bf-45b846e314f7	g.chr21:45502876G>A	ENST00000291574.4	+	14	2106	c.1931G>A	c.(1930-1932)tGg>tAg	p.W644*		NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	644					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						ACTGCGGAGTGGCTTACCAAG	0.512																																					p.W644X		Atlas-SNP	.											.	TRAPPC10	109	.	0			c.G1931A						PASS	.						162	150	154					21																	45502876		2203	4300	6503	SO:0001587	stop_gained	7109	exon14			CGGAGTGGCTTAC	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.1931G>A	chr21.hg19:g.45502876G>A	ENSP00000291574:p.Trp644*	121.0	0.0	.		67.0	32.0	.	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Nonsense_Mutation	SNP	ENST00000291574.4	hg19	CCDS13704.1	.	.	.	.	.	.	.	.	.	.	G	38	7.254018	0.98168	.	.	ENSG00000160218	ENST00000291574	.	.	.	5.58	5.58	0.84498	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	.	19.1791	0.93615	0.0:0.0:1.0:0.0	.	.	.	.	X	644	.	ENSP00000291574:W644X	W	+	2	0	TRAPPC10	44327304	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	5.397000	0.66302	2.622000	0.88805	0.655000	0.94253	TGG	.	.	.	none		0.512	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274		A	45502876	G	A	45502876	4	1	217	1	0	0	0	0	0	1	0	0	16469	1357	47	2	1985	2	TRAPPC10	21	45502876	Nonsense_Mutation	SNP	G	TCGA-KV-A6GE-01A-11D-A31X-10		45502876	2627019	22	13174											
LRP1B	53353	hgsc.bcm.edu	37	chr2	141122239	141122239	+	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	aaatgccataccacacatatCaggggcttcatcagagttgt	13	10	8	10	0	3	1	3	0	0	1	3	1	3	1	2	2	2	2	2	2	3	4	rs200747526	byFrequency	TCGA-KV-A74V-01A-11D-A33Q-10	TCGA-KV-A74V-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	df25a569-f993-4bbe-9766-cdc2a7c40750	9a716ea4-aa7c-4d1a-b9ec-9fb71edb7024	g.chr2:141122239C>A	ENST00000389484.3	-	72	12093	c.11122G>T	c.(11122-11124)Gat>Tat	p.D3708Y		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	3708	LDL-receptor class A 30. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CCACACATATCAGGGGCTTCA	0.443										TSP Lung(27;0.18)																											p.D3708Y	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.G11122T						PASS	.						97	94	95					2																	141122239		2203	4300	6503	SO:0001583	missense	53353	exon72			ACATATCAGGGGC	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.11122G>T	chr2.hg19:g.141122239C>A	ENSP00000374135:p.Asp3708Tyr	233.0	0.0	.		258.0	27.0	.	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	17.60	3.430671	0.62844	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.87571	-2.27	5.48	5.48	0.80851	.	0.124779	0.52532	D	0.000065	D	0.87569	0.6210	N	0.19112	0.55	0.53005	D	0.999963	P	0.45474	0.859	P	0.55455	0.776	D	0.88303	0.2951	10	0.54805	T	0.06	.	19.711	0.96096	0.0:1.0:0.0:0.0	.	3708	Q9NZR2	LRP1B_HUMAN	Y	3708;3646	ENSP00000374135:D3708Y	ENSP00000374135:D3708Y	D	-	1	0	LRP1B	140838709	1.000000	0.71417	0.994000	0.49952	0.984000	0.73092	4.566000	0.60843	2.726000	0.93360	0.655000	0.94253	GAT	.	C|1.000;G|0.000	.	alt		0.443	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141122239	C	A	141122239	3	1	218	1	0	0	0	0	1	0	0	0	8962	826	29	4	2757	4	LRP1B	2	141122239	Missense_Mutation	SNP	C	TCGA-KV-A74V-01A-11D-A33Q-10		141122239	102077134	1	13175											
DHRS9	10170	hgsc.bcm.edu	37	chr2	169952139	169952139	+	Missense_Mutation	SNP	T	T	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	atggaccacgctctaacaagTctcttccctaagactcatta	12	11	5	13	1	3	1	1	0	2	1	5	2	4	2	2	1	1	1	2	1	4	4			TCGA-KV-A74V-01A-11D-A33Q-10	TCGA-KV-A74V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	df25a569-f993-4bbe-9766-cdc2a7c40750	9a716ea4-aa7c-4d1a-b9ec-9fb71edb7024	g.chr2:169952139T>G	ENST00000327239.4	+	8	2326	c.822T>G	c.(820-822)agT>agG	p.S274R	DHRS9_ENST00000428522.1_Missense_Mutation_p.S274R|DHRS9_ENST00000602501.1_Missense_Mutation_p.S274R|DHRS9_ENST00000436483.2_Missense_Mutation_p.S274R|DHRS9_ENST00000357546.2_Missense_Mutation_p.S274R|DHRS9_ENST00000432060.2_Missense_Mutation_p.S334R|DHRS9_ENST00000412271.1_Missense_Mutation_p.S274R|DHRS9_ENST00000421653.1_Missense_Mutation_p.S127R	NM_005771.4	NP_005762.2	Q9BPW9	DHRS9_HUMAN	dehydrogenase/reductase (SDR family) member 9	274					9-cis-retinoic acid biosynthetic process (GO:0042904)|androgen metabolic process (GO:0008209)|epithelial cell differentiation (GO:0030855)|progesterone metabolic process (GO:0042448)|retinol metabolic process (GO:0042572)	integral component of endoplasmic reticulum membrane (GO:0030176)	alcohol dehydrogenase (NAD) activity (GO:0004022)|racemase and epimerase activity (GO:0016854)|retinol dehydrogenase activity (GO:0004745)|testosterone dehydrogenase (NAD+) activity (GO:0047035)			breast(1)|endometrium(3)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	13						CTCTAACAAGTCTCTTCCCTA	0.428																																					p.S274R		Atlas-SNP	.											.	DHRS9	29	.	0			c.T822G						PASS	.						143	137	139					2																	169952139		2203	4300	6503	SO:0001583	missense	10170	exon8			AACAAGTCTCTTC	AF067174	CCDS2231.1, CCDS74600.1	2q31.1	2011-09-14			ENSG00000073737	ENSG00000073737		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	16888	protein-coding gene	gene with protein product	"NADP-dependent retinol dehydrogenase/reductase", "3-alpha hydroxysteroid dehydrogenase", "retinol dehydrogenase homolog", "short chain dehydrogenase/reductase family 9C, member 4"	612131				11304534, 11294878, 19027726	Standard	NM_001142270		Approved	RDHL, 3alpha-HSD, RETSDR8, RDH15, SDR9C4	uc010zde.2	Q9BPW9	OTTHUMG00000132180	ENST00000327239.4:c.822T>G	chr2.hg19:g.169952139T>G	ENSP00000316670:p.Ser274Arg	220.0	0.0	.		275.0	181.0	.	NM_005771	B7Z416|D3DPC1|Q5RKX1|Q9NRA9|Q9NRB0	Missense_Mutation	SNP	ENST00000327239.4	hg19	CCDS2231.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.239485	0.79800	.	.	ENSG00000073737	ENST00000327239;ENST00000357546;ENST00000432060;ENST00000428522;ENST00000421653;ENST00000436483;ENST00000412271	D;D;D;D;D;D;D	0.85258	-1.96;-1.96;-1.96;-1.96;-1.96;-1.96;-1.96	5.93	3.6	0.41247	NAD(P)-binding domain (1);	0.083052	0.85682	D	0.000000	D	0.91436	0.7297	M	0.89353	3.025	0.43683	D	0.996124	D;D	0.76494	0.999;0.998	D;D	0.72338	0.969;0.977	D	0.90197	0.4254	10	0.56958	D	0.05	.	6.2354	0.20760	0.0:0.3359:0.0:0.6641	.	334;274	B7Z416;Q9BPW9	.;DHRS9_HUMAN	R	274;274;334;274;127;274;274	ENSP00000316670:S274R;ENSP00000350154:S274R;ENSP00000389241:S334R;ENSP00000388564:S274R;ENSP00000388066:S127R;ENSP00000407167:S274R;ENSP00000407747:S274R	ENSP00000316670:S274R	S	+	3	2	DHRS9	169660385	0.908000	0.30866	1.000000	0.80357	0.991000	0.79684	1.156000	0.31712	1.081000	0.41110	0.533000	0.62120	AGT	.	.	.	none		0.428	DHRS9-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333612.3	NM_005771		G	169952139	T	G	169952139	3	3	218	1	0	0	0	0	1	0	0	0	4500	1664	58	5	836	5	DHRS9	2	169952139	Missense_Mutation	SNP	T	TCGA-KV-A74V-01A-11D-A33Q-10	28829900	169952139	73247234	2	13176											
TTLL4	9654	hgsc.bcm.edu	37	chr2	219617904	219617904	+	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	agttgtctctgattctgctcCagtggtgagtgctgccagtg	5	14	13	9	0	2	2	0	2	2	0	4	2	3	2	2	1	3	3	2	1	0	2			TCGA-KV-A74V-01A-11D-A33Q-10	TCGA-KV-A74V-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	df25a569-f993-4bbe-9766-cdc2a7c40750	9a716ea4-aa7c-4d1a-b9ec-9fb71edb7024	g.chr2:219617904C>A	ENST00000392102.1	+	18	3594	c.3254C>A	c.(3253-3255)cCa>cAa	p.P1085Q	TTLL4_ENST00000457313.1_Missense_Mutation_p.P920Q|TTLL4_ENST00000442769.1_Missense_Mutation_p.P1021Q|TTLL4_ENST00000258398.4_Missense_Mutation_p.P1085Q	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	1085					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)		GATTCTGCTCCAGTGGTGAGT	0.537																																					p.P1085Q	GBM(172;1818 2053 15407 20943 49753)	Atlas-SNP	.											.	TTLL4	96	.	0			c.C3254A						PASS	.						201	188	193					2																	219617904		2203	4300	6503	SO:0001583	missense	9654	exon18			CTGCTCCAGTGGT		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.3254C>A	chr2.hg19:g.219617904C>A	ENSP00000375951:p.Pro1085Gln	68.0	0.0	.		65.0	40.0	.	NM_014640	A8K6V5|Q8WW29	Missense_Mutation	SNP	ENST00000392102.1	hg19	CCDS2422.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.48|12.48	1.950870|1.950870	0.34471|0.34471	.|.	.|.	ENSG00000135912|ENSG00000135912	ENST00000457313;ENST00000392102;ENST00000442769;ENST00000258398|ENST00000417855	T;T;T;T|.	0.03982|.	3.95;4.16;3.74;4.16|.	5.17|5.17	5.17|5.17	0.71159|0.71159	.|.	0.860350|.	0.10371|.	N|.	0.682880|.	T|T	0.57858|0.57858	0.2082|0.2082	L|L	0.43701|0.43701	1.375|1.375	0.39078|0.39078	D|D	0.960852|0.960852	B;B;P|.	0.40834|.	0.085;0.158;0.73|.	B;B;B|.	0.35550|.	0.017;0.031;0.205|.	T|T	0.56432|0.56432	-0.7980|-0.7980	10|5	0.12430|.	T|.	0.62|.	.|.	11.2543|11.2543	0.49045|0.49045	0.1951:0.8049:0.0:0.0|0.1951:0.8049:0.0:0.0	.|.	920;1021;1085|.	E9PH58;E7EX20;Q14679|.	.;.;TTLL4_HUMAN|.	Q|K	920;1085;1021;1085|109	ENSP00000393332:P920Q;ENSP00000375951:P1085Q;ENSP00000396555:P1021Q;ENSP00000258398:P1085Q|.	ENSP00000258398:P1085Q|.	P|Q	+|+	2|1	0|0	TTLL4|TTLL4	219326148|219326148	0.819000|0.819000	0.29175|0.29175	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	2.040000|2.040000	0.41203|0.41203	2.683000|2.683000	0.91414|0.91414	0.655000|0.655000	0.94253|0.94253	CCA|CAG	.	.	.	none		0.537	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640		A	219617904	C	A	219617904	3	1	218	1	0	0	0	0	1	0	0	0	16741	594	21	4	3316	4	TTLL4	2	219617904	Missense_Mutation	SNP	C	TCGA-KV-A74V-01A-11D-A33Q-10	49665765	219617904	23581469	3	13177											
LYAR	55646	hgsc.bcm.edu	37	chr4	4270271	4270271	+	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	ccatacctttttccttagctTtttgatggttatttcattgt	6	22	5	8	0	1	1	1	1	0	0	2	1	2	1	3	1	2	2	3	1	3	9			TCGA-KV-A74V-01A-11D-A33Q-10	TCGA-KV-A74V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	df25a569-f993-4bbe-9766-cdc2a7c40750	9a716ea4-aa7c-4d1a-b9ec-9fb71edb7024	g.chr4:4270271T>A	ENST00000343470.4	-	9	1231	c.991A>T	c.(991-993)Aag>Tag	p.K331*	LYAR_ENST00000452476.1_Nonsense_Mutation_p.K331*	NM_017816.2	NP_060286	Q9NX58	LYAR_HUMAN	Ly1 antibody reactive	331	Lys-rich.					nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(6)|liver(2)|lung(5)|ovary(1)|prostate(1)	17				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		TTCCTTAGCTTTTTGATGGTT	0.318																																					p.K331X		Atlas-SNP	.											.	LYAR	36	.	0			c.A991T						PASS	.						222	211	215					4																	4270271		2203	4300	6503	SO:0001587	stop_gained	55646	exon9			TTAGCTTTTTGAT	AL136750	CCDS3374.1	4p16.3	2013-01-10	2012-12-07		ENSG00000145220	ENSG00000145220		"Zinc fingers, C2HC-type containing"	26021	protein-coding gene	gene with protein product			"Ly1 antibody reactive homolog (mouse)"			11230166, 8491376	Standard	NM_001145725		Approved	ZC2HC2, ZLYAR	uc003ght.3	Q9NX58	OTTHUMG00000125477	ENST00000343470.4:c.991A>T	chr4.hg19:g.4270271T>A	ENSP00000345917:p.Lys331*	89.0	0.0	.		62.0	9.0	.	NM_017816	D3DVS4|Q6FI78|Q9NYS1	Nonsense_Mutation	SNP	ENST00000343470.4	hg19	CCDS3374.1	.	.	.	.	.	.	.	.	.	.	T	39	7.639047	0.98406	.	.	ENSG00000145220	ENST00000343470;ENST00000452476	.	.	.	5.93	5.93	0.95920	.	0.088101	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-35.5133	16.0564	0.80809	0.0:0.0:0.0:1.0	.	.	.	.	X	331	.	ENSP00000345917:K331X	K	-	1	0	LYAR	4321172	1.000000	0.71417	0.989000	0.46669	0.871000	0.50021	6.068000	0.71201	2.271000	0.75665	0.459000	0.35465	AAG	.	.	.	none		0.318	LYAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246800.2	NM_017816		A	4270271	T	A	4270271	4	1	218	1	0	0	0	0	0	1	0	0	9110	1850	64	5	156	5	LYAR	4	4270271	Nonsense_Mutation	SNP	T	TCGA-KV-A74V-01A-11D-A33Q-10		4270271	186884005	4	13178											
SULT1B1	27284	hgsc.bcm.edu	37	chr4	70620844	70620844	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtctgctatggaactgttcaAttttttcccagttgcttgca	7	17	8	9	0	2	0	1	0	1	0	3	1	3	1	1	1	4	5	1	1	3	7			TCGA-KV-A74V-01A-11D-A33Q-10	TCGA-KV-A74V-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	df25a569-f993-4bbe-9766-cdc2a7c40750	9a716ea4-aa7c-4d1a-b9ec-9fb71edb7024	g.chr4:70620844A>G	ENST00000310613.3	-	2	389	c.92T>C	c.(91-93)aTt>aCt	p.I31T		NM_014465.3	NP_055280.2	O43704	ST1B1_HUMAN	sulfotransferase family, cytosolic, 1B, member 1	31					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						GAACTGTTCAATTTTTTCCCA	0.408																																					p.I31T		Atlas-SNP	.											.	SULT1B1	46	.	0			c.T92C						PASS	.						153	149	151					4																	70620844		2203	4300	6503	SO:0001583	missense	27284	exon2			TGTTCAATTTTTT	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.92T>C	chr4.hg19:g.70620844A>G	ENSP00000308770:p.Ile31Thr	106.0	0.0	.		98.0	10.0	.	NM_014465	O15497|Q96FI1|Q9UK34	Missense_Mutation	SNP	ENST00000310613.3	hg19	CCDS3530.1	.	.	.	.	.	.	.	.	.	.	A	14.36	2.511687	0.44660	.	.	ENSG00000173597	ENST00000310613;ENST00000510821;ENST00000512870	T;T;T	0.01918	4.56;4.56;4.56	4.97	2.53	0.30540	.	0.374774	0.22569	N	0.058373	T	0.02380	0.0073	N	0.08118	0	0.09310	N	1	B	0.32939	0.391	P	0.46758	0.526	T	0.44544	-0.9321	10	0.62326	D	0.03	.	6.2024	0.20583	0.73:0.1821:0.0879:0.0	.	31	O43704	ST1B1_HUMAN	T	31;31;12	ENSP00000308770:I31T;ENSP00000425464:I31T;ENSP00000427536:I12T	ENSP00000308770:I31T	I	-	2	0	SULT1B1	70655433	0.070000	0.21116	0.000000	0.03702	0.011000	0.07611	3.739000	0.55075	0.329000	0.23460	0.482000	0.46254	ATT	.	.	.	none		0.408	SULT1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251563.2	NM_014465		G	70620844	A	G	70620844	3	3	218	1	0	0	0	0	1	0	0	0	15388	101	4	3	826	3	SULT1B1	4	70620844	Missense_Mutation	SNP	A	TCGA-KV-A74V-01A-11D-A33Q-10	66350573	70620844	120533432	5	13179											
AFF1	4299	hgsc.bcm.edu	37	chr4	88048262	88048262	+	Frame_Shift_Del	DEL	T	T	-																															cagggaagcctcaagtgaagTttgacaagtaagacttcaga																										TCGA-KV-A74V-01A-11D-A33Q-10	TCGA-KV-A74V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	df25a569-f993-4bbe-9766-cdc2a7c40750	9a716ea4-aa7c-4d1a-b9ec-9fb71edb7024	g.chr4:88048262delT	ENST00000307808.6	+	14	3295	c.2875delT	c.(2875-2877)tttfs	p.F959fs	AFF1_ENST00000395146.4_Frame_Shift_Del_p.F966fs|AFF1_ENST00000544085.1_Frame_Shift_Del_p.F597fs	NM_005935.2	NP_005926.1	P51825	AFF1_HUMAN	AF4/FMR2 family, member 1	959					positive regulation of transcription, DNA-templated (GO:0045893)	transcription elongation factor complex (GO:0008023)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(2)	3		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		TCAAGTGAAGTTTGACAAGTA	0.438																																					p.K965fs		Atlas-Indel,Pindel	.											.	AFF1	102	.	0			c.2895delG						PASS	.						111	114	113					4																	88048262		2203	4300	6503	SO:0001589	frameshift_variant	4299	exon15			.	L22179	CCDS3616.1, CCDS54775.1	4q21.3	2009-08-04	2005-06-27	2005-06-27	ENSG00000172493	ENSG00000172493			7135	protein-coding gene	gene with protein product		159557	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 2", "pre-B-cell monocytic leukemia partner 1"	PBM1, MLLT2		7689231, 1423625, 8353274	Standard	NM_005935		Approved	AF-4, AF4	uc011ccz.2	P51825	OTTHUMG00000130603	ENST00000307808.6:c.2875delT	chr4.hg19:g.88048262delT	ENSP00000305689:p.Phe959fs	69.0	0.0	0		61.0	25.0	0.409836	NM_001166693	B4DTU1|E9PBM3	Frame_Shift_Del	DEL	ENST00000307808.6	hg19	CCDS3616.1																																																																																			.	.	.	none		0.438	AFF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253053.3	NM_005935		-	88048262	T	-	88048262	7	5	218	1	0	1	0	1	0	0	0	0	356	1725	60	0	2971	0	AFF1	4	88048262	Frame_Shift_Del	DEL	T	TCGA-KV-A74V-01A-11D-A33Q-10	17427418	88048262	103106014	6	13180											
ATOH1	474	hgsc.bcm.edu	37	chr4	94750489	94750489	+	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	tgaaaggcggggtggtggtaGacgagctgggctgcagccgc	7	6	20	8	3	0	2	0	1	0	1	0	3	0	2	1	6	3	4	1	6	2	1			TCGA-KV-A74V-01A-11D-A33Q-10	TCGA-KV-A74V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	df25a569-f993-4bbe-9766-cdc2a7c40750	9a716ea4-aa7c-4d1a-b9ec-9fb71edb7024	g.chr4:94750489G>T	ENST00000306011.3	+	1	448	c.412G>T	c.(412-414)Gac>Tac	p.D138Y		NM_005172.1	NP_005163.1	Q92858	ATOH1_HUMAN	atonal homolog 1 (Drosophila)	138					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)		GGTGGTGGTAGACGAGCTGGG	0.667																																					p.D138Y		Atlas-SNP	.											.	ATOH1	40	.	0			c.G412T						PASS	.						30	40	37					4																	94750489		2203	4299	6502	SO:0001583	missense	474	exon1			GTGGTAGACGAGC	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.412G>T	chr4.hg19:g.94750489G>T	ENSP00000302216:p.Asp138Tyr	114.0	0.0	.		101.0	48.0	.	NM_005172	Q14CT9	Missense_Mutation	SNP	ENST00000306011.3	hg19	CCDS3638.1	.	.	.	.	.	.	.	.	.	.	G	10.03	1.238517	0.22711	.	.	ENSG00000172238	ENST00000306011	D	0.97752	-4.52	4.27	4.27	0.50696	.	0.421469	0.22988	N	0.053226	D	0.93789	0.8014	N	0.19112	0.55	0.27027	N	0.964335	P	0.39576	0.679	B	0.37833	0.259	D	0.90439	0.4430	10	0.62326	D	0.03	-14.0929	12.1655	0.54127	0.0:0.0:1.0:0.0	.	138	Q92858	ATOH1_HUMAN	Y	138	ENSP00000302216:D138Y	ENSP00000302216:D138Y	D	+	1	0	ATOH1	94969512	1.000000	0.71417	0.923000	0.36655	0.915000	0.54546	4.756000	0.62205	2.229000	0.72834	0.543000	0.68304	GAC	.	.	.	none		0.667	ATOH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253585.1	NM_005172		T	94750489	G	T	94750489	3	4	218	1	0	0	0	0	1	0	0	0	1112	942	33	4	414	4	ATOH1	4	94750489	Missense_Mutation	SNP	G	TCGA-KV-A74V-01A-11D-A33Q-10	6702227	94750489	96403787	7	13181											
ARHGEF38	54848	hgsc.bcm.edu	37	chr4	106473951	106473951	+	Frame_Shift_Del	DEL	A	A	-																															caaagaagccactgggaaagAaaacatggtcaccaagaaaa																										TCGA-KV-A74V-01A-11D-A33Q-10	TCGA-KV-A74V-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	df25a569-f993-4bbe-9766-cdc2a7c40750	9a716ea4-aa7c-4d1a-b9ec-9fb71edb7024	g.chr4:106473951delA	ENST00000420470.2	+	1	173	c.29delA	c.(28-30)gaafs	p.E10fs	ARHGEF38_ENST00000265154.2_Frame_Shift_Del_p.E10fs|AC004066.3_ENST00000514879.1_RNA	NM_001242729.1	NP_001229658.1	Q9NXL2	ARH38_HUMAN	Rho guanine nucleotide exchange factor (GEF) 38	10						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(3)	11						ACTGGGAAAGAAAACATGGTC	0.473																																					p.E10fs		Atlas-Indel,Pindel	.											.	ARHGEF38	52	.	0			c.28delG						PASS	.						87	85	86					4																	106473951		2203	4300	6503	SO:0001589	frameshift_variant	54848	exon1			.	AK000191	CCDS3670.1, CCDS56338.1	4q24	2012-07-24			ENSG00000236699	ENSG00000236699		"Rho guanine nucleotide exchange factors"	25968	protein-coding gene	gene with protein product							Standard	NM_001242729		Approved	FLJ20184	uc003hxv.2	Q9NXL2	OTTHUMG00000154752	ENST00000420470.2:c.29delA	chr4.hg19:g.106473951delA	ENSP00000416125:p.Glu10fs	89.0	0.0	0		83.0	13.0	0.156627	NM_017700	C9JIB4	Frame_Shift_Del	DEL	ENST00000420470.2	hg19	CCDS56338.1																																																																																			.	.	.	none		0.473	ARHGEF38-001	PUTATIVE	basic|appris_principal|readthrough_transcript|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000336934.3	NM_017700		-	106473951	A	-	106473951	7	5	218	1	0	1	0	1	0	0	0	0	907	246	9	0	31	0	ARHGEF38	4	106473951	Frame_Shift_Del	DEL	A	TCGA-KV-A74V-01A-11D-A33Q-10	11723462	106473951	84680325	8	13182											
LPL	4023	hgsc.bcm.edu	37	chr8	19813385	19813385	+	Missense_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	agtgaagtgctcccacgagcGctccattcatctcttcatcg	8	11	8	14	3	3	1	2	1	1	0	7	2	5	1	2	0	2	2	2	0	1	2	rs118204062		TCGA-KV-A74V-01A-11D-A33Q-10	TCGA-KV-A74V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	df25a569-f993-4bbe-9766-cdc2a7c40750	9a716ea4-aa7c-4d1a-b9ec-9fb71edb7024	g.chr8:19813385G>A	ENST00000311322.8	+	6	1279	c.809G>A	c.(808-810)cGc>cAc	p.R270H		NM_000237.2	NP_000228.1	P06858	LIPL_HUMAN	lipoprotein lipase	270			R -> C (in LPL deficiency). {ECO:0000269|PubMed:15256764, ECO:0000269|PubMed:7906986, ECO:0000269|PubMed:8778602, ECO:0000269|PubMed:9279761}.|R -> H (in LPL deficiency; loss of activity). {ECO:0000269|PubMed:15256764, ECO:0000269|PubMed:1619366, ECO:0000269|PubMed:1702428, ECO:0000269|PubMed:1752947, ECO:0000269|PubMed:7906986, ECO:0000269|PubMed:9714430}.		chylomicron remodeling (GO:0034371)|fatty acid biosynthetic process (GO:0006633)|lipoprotein metabolic process (GO:0042157)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of sequestering of triglyceride (GO:0010890)|response to cold (GO:0009409)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|triglyceride metabolic process (GO:0006641)|very-low-density lipoprotein particle remodeling (GO:0034372)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|lipoprotein lipase activity (GO:0004465)|phospholipase activity (GO:0004620)|receptor binding (GO:0005102)|triglyceride binding (GO:0017129)|triglyceride lipase activity (GO:0004806)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	36				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	AST-120(DB05269)|Tyloxapol(DB06439)	TCCCACGAGCGCTCCATTCAT	0.458																																					p.R270H		Atlas-SNP	.											.	LPL	78	.	0			c.G809A	GRCh37	CM910265|CM962613	LPL	M	rs118204062	PASS	.						93	95	94					8																	19813385		2203	4300	6503	SO:0001583	missense	4023	exon6			ACGAGCGCTCCAT		CCDS6012.1	8p22	2012-10-02			ENSG00000175445	ENSG00000175445	3.1.1.34		6677	protein-coding gene	gene with protein product		609708		LIPD			Standard	NM_000237		Approved		uc003wzk.4	P06858	OTTHUMG00000036645	ENST00000311322.8:c.809G>A	chr8.hg19:g.19813385G>A	ENSP00000309757:p.Arg270His	83.0	0.0	.		86.0	25.0	.	NM_000237	B2R5T9|Q16282|Q16283|Q96FC4	Missense_Mutation	SNP	ENST00000311322.8	hg19	CCDS6012.1	.	.	.	.	.	.	.	.	.	.	G	35	5.534310	0.96460	.	.	ENSG00000175445	ENST00000311322;ENST00000538071;ENST00000535763	D	0.97209	-4.29	6.07	6.07	0.98685	Lipase, N-terminal (1);	0.043982	0.85682	N	0.000000	D	0.98570	0.9522	M	0.85630	2.765	0.41185	D	0.986265	D	0.89917	1.0	D	0.97110	1.0	D	0.98779	1.0731	8	.	.	.	-20.7835	18.2083	0.89861	0.0:0.0:1.0:0.0	.	270	P06858	LIPL_HUMAN	H	270;194;256	ENSP00000309757:R270H	.	R	+	2	0	LPL	19857665	1.000000	0.71417	0.997000	0.53966	0.982000	0.71751	9.807000	0.99171	2.902000	0.99343	0.650000	0.86243	CGC	.	.	.	weak		0.458	LPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089113.3			A	19813385	G	A	19813385	3	1	218	1	0	0	0	0	1	0	0	0	8928	1087	38	1	831	1	LPL	8	19813385	Missense_Mutation	SNP	G	TCGA-KV-A74V-01A-11D-A33Q-10		19813385	126550637	9	13183											
ZFAND1	79752	hgsc.bcm.edu	37	chr8	82615255	82615255	+	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	agcctggctagagaagcggcAaagtctatggcctttccaat	11	9	11	10	1	1	1	0	0	1	1	2	2	2	1	3	3	2	2	3	3	5	3			TCGA-KV-A74V-01A-11D-A33Q-10	TCGA-KV-A74V-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	df25a569-f993-4bbe-9766-cdc2a7c40750	9a716ea4-aa7c-4d1a-b9ec-9fb71edb7024	g.chr8:82615255A>T	ENST00000220669.5	-	7	603	c.585T>A	c.(583-585)ttT>ttA	p.F195L	ZFAND1_ENST00000519523.1_Missense_Mutation_p.F195L|ZFAND1_ENST00000521895.1_Missense_Mutation_p.F88L|ZFAND1_ENST00000517588.1_Missense_Mutation_p.F88L|ZFAND1_ENST00000523096.1_Missense_Mutation_p.F188L|ZFAND1_ENST00000519338.1_5'UTR|ZFAND1_ENST00000521287.1_Missense_Mutation_p.F88L|ZFAND1_ENST00000522520.1_Missense_Mutation_p.F88L	NM_024699.2	NP_078975.2	Q8TCF1	ZFAN1_HUMAN	zinc finger, AN1-type domain 1	195							zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						GAGAAGCGGCAAAGTCTATGG	0.338																																					p.F195L		Atlas-SNP	.											.	ZFAND1	29	.	0			c.T585A						PASS	.						28	24	26					8																	82615255		2201	4300	6501	SO:0001583	missense	79752	exon7			AGCGGCAAAGTCT		CCDS6232.1, CCDS55250.1, CCDS55251.1	8q21.13	2006-07-07						"Zinc fingers, AN1-type domain containing"	25858	protein-coding gene	gene with protein product						12477932	Standard	NM_024699		Approved	FLJ14007	uc003ycj.2	Q8TCF1		ENST00000220669.5:c.585T>A	chr8.hg19:g.82615255A>T	ENSP00000220669:p.Phe195Leu	160.0	0.0	.		135.0	49.0	.	NM_001170797	E5RIG0|E5RJ99|Q658R7|Q6IA32|Q6PGQ6|Q9H810	Missense_Mutation	SNP	ENST00000220669.5	hg19	CCDS6232.1	.	.	.	.	.	.	.	.	.	.	A	7.672	0.687266	0.14973	.	.	ENSG00000104231	ENST00000523096;ENST00000220669;ENST00000522520;ENST00000521895;ENST00000521287;ENST00000520635;ENST00000517588;ENST00000519523;ENST00000520604	.	.	.	5.83	-0.666	0.11399	.	0.284392	0.41097	D	0.000944	T	0.39708	0.1088	L	0.33137	0.985	0.41542	D	0.988525	B;B	0.21905	0.062;0.062	B;B	0.21546	0.024;0.035	T	0.13388	-1.0511	9	0.15952	T	0.53	.	10.4054	0.44254	0.7039:0.0:0.2961:0.0	.	188;195	E5RIG0;Q8TCF1	.;ZFAN1_HUMAN	L	188;195;88;88;88;88;88;195;88	.	ENSP00000220669:F195L	F	-	3	2	ZFAND1	82777810	0.829000	0.29322	0.165000	0.22776	0.449000	0.32228	0.912000	0.28597	-0.326000	0.08564	0.477000	0.44152	TTT	.	.	.	none		0.338	ZFAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379739.1	NM_024699		T	82615255	A	T	82615255	3	4	218	1	0	0	0	0	1	0	0	0	17638	127	5	5	277	5	ZFAND1	8	82615255	Missense_Mutation	SNP	A	TCGA-KV-A74V-01A-11D-A33Q-10	62801870	82615255	63748767	10	13184											
PSD	5662	hgsc.bcm.edu	37	chr10	104173691	104173691	+	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	taccagaatccggttcaagaGgggcaagtggggcgggagct	10	6	17	8	2	1	2	1	0	0	2	2	3	2	3	2	6	2	3	2	6	4	2			TCGA-KV-A74V-01A-11D-A33Q-10	TCGA-KV-A74V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	df25a569-f993-4bbe-9766-cdc2a7c40750	9a716ea4-aa7c-4d1a-b9ec-9fb71edb7024	g.chr10:104173691G>T	ENST00000020673.5	-	5	1914	c.1388C>A	c.(1387-1389)cCt>cAt	p.P463H	PSD_ENST00000492902.2_5'Flank|PSD_ENST00000406432.1_Missense_Mutation_p.P463H	NM_001270966.1|NM_002779.4	NP_001257895.1|NP_002770.3	A5PKW4	PSD1_HUMAN	pleckstrin and Sec7 domain containing	463	Pro-rich.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)		CGGTTCAAGAGGGGCAAGTGG	0.667																																					p.P463H		Atlas-SNP	.											.	PSD	164	.	0			c.C1388A						PASS	.						38	45	43					10																	104173691		2203	4299	6502	SO:0001583	missense	5662	exon6			TCAAGAGGGGCAA	X99688	CCDS31272.1, CCDS73187.1	10q24	2013-01-10	2004-04-28		ENSG00000059915	ENSG00000059915		"Pleckstrin homology (PH) domain containing"	9507	protein-coding gene	gene with protein product		602327	"pleckstrin and Sec7 domain protein"			9417912	Standard	NM_002779		Approved	KIAA2011, TYL, PSD1	uc009xxd.2	A5PKW4	OTTHUMG00000018954	ENST00000020673.5:c.1388C>A	chr10.hg19:g.104173691G>T	ENSP00000020673:p.Pro463His	147.0	0.0	.		103.0	38.0	.	NM_001270965	B1AKX7|D3DR87|Q15673|Q8IVG0	Missense_Mutation	SNP	ENST00000020673.5	hg19	CCDS31272.1	.	.	.	.	.	.	.	.	.	.	G	10.87	1.472957	0.26423	.	.	ENSG00000059915	ENST00000020673;ENST00000541902;ENST00000406432	T;T	0.44482	0.92;0.92	4.65	2.76	0.32466	.	0.402362	0.25006	N	0.033862	T	0.19208	0.0461	N	0.08118	0	0.29532	N	0.85272	B	0.25609	0.13	B	0.17098	0.017	T	0.09530	-1.0670	10	0.41790	T	0.15	.	5.7397	0.18087	0.1616:0.0:0.587:0.2514	.	463	A5PKW4	PSD1_HUMAN	H	463;366;463	ENSP00000020673:P463H;ENSP00000384830:P463H	ENSP00000020673:P463H	P	-	2	0	PSD	104163681	0.999000	0.42202	0.798000	0.32154	0.751000	0.42716	1.776000	0.38594	0.390000	0.25115	0.456000	0.33151	CCT	.	.	.	none		0.667	PSD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050041.2			T	104173691	G	T	104173691	3	4	218	1	0	0	0	0	1	0	0	0	12656	1000	35	4	1738	4	PSD	10	104173691	Missense_Mutation	SNP	G	TCGA-KV-A74V-01A-11D-A33Q-10		104173691	31361056	11	13185			1	29		2	2	14	N	G_C	7.558901e-06
PSD	5662	hgsc.bcm.edu	37	chr10	104173704	104173704	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcaagaggggcaagtggggCgggagctggtgggtcgggcc	6	6	22	7	2	1	1	1	0	0	1	2	2	1	2	1	8	1	2	1	8	2	1			TCGA-KV-A74V-01A-11D-A33Q-10	TCGA-KV-A74V-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	df25a569-f993-4bbe-9766-cdc2a7c40750	9a716ea4-aa7c-4d1a-b9ec-9fb71edb7024	g.chr10:104173704C>T	ENST00000020673.5	-	5	1901	c.1375G>A	c.(1375-1377)Gcc>Acc	p.A459T	PSD_ENST00000492902.2_5'Flank|PSD_ENST00000406432.1_Missense_Mutation_p.A459T	NM_001270966.1|NM_002779.4	NP_001257895.1|NP_002770.3	A5PKW4	PSD1_HUMAN	pleckstrin and Sec7 domain containing	459	Pro-rich.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)		GCAAGTGGGGCGGGAGCTGGT	0.657																																					p.A459T		Atlas-SNP	.											.	PSD	164	.	0			c.G1375A						PASS	.						36	44	42					10																	104173704		2203	4298	6501	SO:0001583	missense	5662	exon6			GTGGGGCGGGAGC	X99688	CCDS31272.1, CCDS73187.1	10q24	2013-01-10	2004-04-28		ENSG00000059915	ENSG00000059915		"Pleckstrin homology (PH) domain containing"	9507	protein-coding gene	gene with protein product		602327	"pleckstrin and Sec7 domain protein"			9417912	Standard	NM_002779		Approved	KIAA2011, TYL, PSD1	uc009xxd.2	A5PKW4	OTTHUMG00000018954	ENST00000020673.5:c.1375G>A	chr10.hg19:g.104173704C>T	ENSP00000020673:p.Ala459Thr	134.0	0.0	.		99.0	40.0	.	NM_001270965	B1AKX7|D3DR87|Q15673|Q8IVG0	Missense_Mutation	SNP	ENST00000020673.5	hg19	CCDS31272.1	.	.	.	.	.	.	.	.	.	.	C	15.49	2.847795	0.51164	.	.	ENSG00000059915	ENST00000020673;ENST00000541902;ENST00000406432	T;T	0.49720	0.77;0.77	4.78	4.78	0.61160	.	0.277670	0.29396	N	0.012273	T	0.31544	0.0800	L	0.27053	0.805	0.35766	D	0.820535	P	0.35551	0.509	B	0.20184	0.028	T	0.37314	-0.9711	10	0.19147	T	0.46	.	17.8792	0.88835	0.0:1.0:0.0:0.0	.	459	A5PKW4	PSD1_HUMAN	T	459;362;459	ENSP00000020673:A459T;ENSP00000384830:A459T	ENSP00000020673:A459T	A	-	1	0	PSD	104163694	1.000000	0.71417	0.995000	0.50966	0.271000	0.26615	5.034000	0.64152	2.224000	0.72417	0.555000	0.69702	GCC	.	.	.	none		0.657	PSD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050041.2			T	104173704	C	T	104173704	3	4	218	1	0	0	0	0	1	0	0	0	12656	768	27	1	1751	1	PSD	10	104173704	Missense_Mutation	SNP	C	TCGA-KV-A74V-01A-11D-A33Q-10	13	104173704	31361043	12	13186			1	29		2	2	14	N	G_C	7.558901e-06
MAP1A	4130	hgsc.bcm.edu	37	chr15	43819753	43819753	+	Missense_Mutation	SNP	T	T	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	tctcacccaagagcctccagTctgacactccaaccttcagc	10	8	5	18	0	3	2	2	1	2	1	6	2	5	2	5	0	3	0	5	0	2	1			TCGA-KV-A74V-01A-11D-A33Q-10	TCGA-KV-A74V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	df25a569-f993-4bbe-9766-cdc2a7c40750	9a716ea4-aa7c-4d1a-b9ec-9fb71edb7024	g.chr15:43819753T>G	ENST00000300231.5	+	4	6532	c.6082T>G	c.(6082-6084)Tct>Gct	p.S2028A	MAP1A_ENST00000399453.1_Missense_Mutation_p.S2028A|MAP1A_ENST00000382031.1_Missense_Mutation_p.S2266A			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	2028					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)	GAGCCTCCAGTCTGACACTCC	0.607																																					p.S2028A		Atlas-SNP	.											.	MAP1A	189	.	0			c.T6082G						PASS	.						62	65	64					15																	43819753		2017	4190	6207	SO:0001583	missense	4130	exon4			CTCCAGTCTGACA	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.6082T>G	chr15.hg19:g.43819753T>G	ENSP00000300231:p.Ser2028Ala	55.0	0.0	.		47.0	26.0	.	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	hg19	CCDS42031.1	.	.	.	.	.	.	.	.	.	.	T	8.252	0.809130	0.16537	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.01388	4.95;4.95;4.95	4.9	-3.21	0.05140	.	0.508000	0.14891	N	0.292432	T	0.01029	0.0034	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45848	-0.9233	10	0.62326	D	0.03	0.7505	2.4176	0.04440	0.1129:0.2765:0.3846:0.2261	.	2028	P78559	MAP1A_HUMAN	A	2266;2028;2028	ENSP00000371462:S2266A;ENSP00000382380:S2028A;ENSP00000300231:S2028A	ENSP00000300231:S2028A	S	+	1	0	MAP1A	41607045	0.000000	0.05858	0.351000	0.25721	0.994000	0.84299	-1.453000	0.02383	-0.183000	0.10585	0.533000	0.62120	TCT	.	.	.	none		0.607	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373		G	43819753	T	G	43819753	3	3	218	1	0	0	0	0	1	0	0	0	9234	1667	58	5	6084	5	MAP1A	15	43819753	Missense_Mutation	SNP	T	TCGA-KV-A74V-01A-11D-A33Q-10		43819753	58711639	13	13187											
TSC2	7249	hgsc.bcm.edu	37	chr16	2135239	2135240	+	Frame_Shift_Ins	INS	-	-	T																															gtgtgccacagtcacagtccINStttgagcggtcggtgcagct																								rs45514391|rs137854329|rs137854407		TCGA-KV-A74V-01A-11D-A33Q-10	TCGA-KV-A74V-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	df25a569-f993-4bbe-9766-cdc2a7c40750	9a716ea4-aa7c-4d1a-b9ec-9fb71edb7024	g.chr16:2135239_2135240insT	ENST00000219476.3	+	36	5208_5209	c.4578_4579insT	c.(4579-4581)tttfs	p.F1527fs	TSC2_ENST00000382538.6_Frame_Shift_Ins_p.F1412fs|TSC2_ENST00000353929.4_Frame_Shift_Ins_p.F1484fs|TSC2_ENST00000401874.2_Frame_Shift_Ins_p.F1460fs|TSC2_ENST00000568454.1_Frame_Shift_Ins_p.F1471fs|TSC2_ENST00000350773.4_Frame_Shift_Ins_p.F1504fs|TSC2_ENST00000439673.2_Frame_Shift_Ins_p.F1424fs	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	1527					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)				AGTCACAGTCCTTTGAGCGGTC	0.668			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.S1526fs		Atlas-INDEL	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	.	TSC2	364	.	0			c.4578_4579insT						PASS	.																																			SO:0001589	frameshift_variant	7249	exon36	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	.	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 160"	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.4581dupT	chr16.hg19:g.2135242_2135242dupT	ENSP00000219476:p.Phe1527fs	76.0	0.0	0		93.0	10.0	0.107527	NM_000548	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Frame_Shift_Ins	INS	ENST00000219476.3	hg19	CCDS10458.1																																																																																			.	.	.	none		0.668	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		T	2135240	-	T	2135239	7	5	218	1	0	1	1	0	0	0	0	0	16618	668	24	0	4716	0	TSC2	16	2135239	Frame_Shift_Ins	INS	-	TCGA-KV-A74V-01A-11D-A33Q-10		2135239	88219514	14	13188											
RTTN	25914	hgsc.bcm.edu	37	chr18	67816232	67816232	+	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	gaacttgctttgcttagaagGagaatgcagttacccagagg	12	10	12	7	0	0	3	0	0	0	3	0	5	0	3	1	2	5	4	1	2	5	4			TCGA-KV-A74V-01A-11D-A33Q-10	TCGA-KV-A74V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	df25a569-f993-4bbe-9766-cdc2a7c40750	9a716ea4-aa7c-4d1a-b9ec-9fb71edb7024	g.chr18:67816232G>T	ENST00000255674.6	-	17	2500	c.2214C>A	c.(2212-2214)ctC>ctA	p.L738L	RTTN_ENST00000454359.1_Silent_p.L738L|RTTN_ENST00000437017.1_Silent_p.L738L	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	738					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)				TGCTTAGAAGGAGAATGCAGT	0.393																																					p.L738L		Atlas-SNP	.											.	RTTN	184	.	0			c.C2214A						PASS	.						158	149	151					18																	67816232		1857	4100	5957	SO:0001819	synonymous_variant	25914	exon17			TAGAAGGAGAATG	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.2214C>A	chr18.hg19:g.67816232G>T		117.0	0.0	.		71.0	12.0	.	NM_173630	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Silent	SNP	ENST00000255674.6	hg19	CCDS42443.1																																																																																			.	.	.	none		0.393	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630		T	67816232	G	T	67816232	2	4	218	1	0	0	0	0	0	0	0	1	13750	1161	41	4		4	RTTN	18	67816232	Silent	SNP	G	TCGA-KV-A74V-01A-11D-A33Q-10		67816232	10261016	15	13189											
HUNK	30811	hgsc.bcm.edu	37	chr21	33371184	33371184	+	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	atccggaagcatgtcgcctcTccatactcctttgcatccaa	9	11	6	15	2	1	0	0	0	1	0	6	1	4	1	5	1	3	2	5	1	3	2			TCGA-KV-A74V-01A-11D-A33Q-10	TCGA-KV-A74V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	df25a569-f993-4bbe-9766-cdc2a7c40750	9a716ea4-aa7c-4d1a-b9ec-9fb71edb7024	g.chr21:33371184T>A	ENST00000270112.2	+	11	2192	c.1832T>A	c.(1831-1833)cTc>cAc	p.L611H		NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	611					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						ATGTCGCCTCTCCATACTCCT	0.572																																					p.L611H		Atlas-SNP	.											.	HUNK	74	.	0			c.T1832A						PASS	.						53	50	51					21																	33371184		2203	4300	6503	SO:0001583	missense	30811	exon11			CGCCTCTCCATAC	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.1832T>A	chr21.hg19:g.33371184T>A	ENSP00000270112:p.Leu611His	101.0	0.0	.		41.0	34.0	.	NM_014586		Missense_Mutation	SNP	ENST00000270112.2	hg19	CCDS13610.1	.	.	.	.	.	.	.	.	.	.	T	11.43	1.635034	0.29068	.	.	ENSG00000142149	ENST00000270112	T	0.69561	-0.41	4.39	1.92	0.25849	.	0.706815	0.12389	N	0.473175	T	0.49321	0.1550	N	0.19112	0.55	0.09310	N	0.999995	D	0.57257	0.979	P	0.46975	0.533	T	0.31998	-0.9923	10	0.15499	T	0.54	-12.9944	5.8389	0.18623	0.0:0.1007:0.1799:0.7194	.	611	P57058	HUNK_HUMAN	H	611	ENSP00000270112:L611H	ENSP00000270112:L611H	L	+	2	0	HUNK	32293055	0.002000	0.14202	0.023000	0.16930	0.286000	0.27126	0.915000	0.28638	0.712000	0.32039	0.402000	0.26972	CTC	.	.	.	none		0.572	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192782.1	NM_014586		A	33371184	T	A	33371184	3	1	218	1	0	0	0	0	1	0	0	0	7465	1551	54	5	1874	5	HUNK	21	33371184	Missense_Mutation	SNP	T	TCGA-KV-A74V-01A-11D-A33Q-10		33371184	14758711	16	13190											
NEFH	4744	hgsc.bcm.edu	37	chr22	29885585	29885586	+	In_Frame_Ins	INS	-	-	AAGTCCCCTGAGAAGGCC																															caaagtcccctgagaaggccINSaagtccccagagaaggaaga																								rs200984527|rs267607533		TCGA-KV-A74V-01A-11D-A33Q-10	TCGA-KV-A74V-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	df25a569-f993-4bbe-9766-cdc2a7c40750	9a716ea4-aa7c-4d1a-b9ec-9fb71edb7024	g.chr22:29885585_29885586insAAGTCCCCTGAGAAGGCC	ENST00000310624.6	+	4	1989_1990	c.1956_1957insAAGTCCCCTGAGAAGGCC	c.(1957-1959)aag>AAGTCCCCTGAGAAGGCCaag	p.653_653K>KSPEKAK		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	659	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						CTGAGAAGGCCAAGTCCCCAGA	0.564																																					p.A652delinsAKSPEKA		Atlas-INDEL	.											.,1	NEFH	178	.	0			c.1956_1957insAAGTCCCCTGAGAAGGCC						PASS	.																																			SO:0001652	inframe_insertion	4744	exon4			.		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1939_1956dupAAGTCCCCTGAGAAGGCC	chr22.hg19:g.29885585_29885586insAAGTCCCCTGAGAAGGCC	ENSP00000311997:p.SerProGluLysAlaLys653dup	142.0	0.0	0		142.0	33.0	0.232394	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.	.	none		0.564	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		AAGTCCCCTGAGAAGGCC	29885586	-	AAGTCCCCTGAGAAGGCC	29885585	7	5	218	1	0	1	1	0	0	0	0	0	10321	581	21	0	1970	0	NEFH	22	29885585	In_Frame_Ins	INS	-	TCGA-KV-A74V-01A-11D-A33Q-10		29885585	21418981	17	13191											
BRD1	23774	hgsc.bcm.edu	37	chr22	50170697	50170697	+	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	ctcaccggctgcgatcctggCcgccttggcgtagttcccat	4	10	11	16	4	1	0	1	0	0	0	3	1	3	0	5	3	1	3	5	3	1	3			TCGA-KV-A74V-01A-11D-A33Q-10	TCGA-KV-A74V-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	df25a569-f993-4bbe-9766-cdc2a7c40750	9a716ea4-aa7c-4d1a-b9ec-9fb71edb7024	g.chr22:50170697C>T	ENST00000216267.8	-	9	3199	c.2713G>A	c.(2713-2715)Gcc>Acc	p.A905T	BRD1_ENST00000404034.1_Missense_Mutation_p.A905T|BRD1_ENST00000342989.5_Missense_Mutation_p.A631T|BRD1_ENST00000404760.1_Missense_Mutation_p.A1036T|BRD1_ENST00000457780.2_3'UTR|BRD1_ENST00000542442.1_Missense_Mutation_p.A593T	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	905					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)		GCGATCCTGGCCGCCTTGGCG	0.647																																					p.A905T		Atlas-SNP	.											.	BRD1	144	.	0			c.G2713A						PASS	.						70	68	69					22																	50170697		2203	4300	6503	SO:0001583	missense	23774	exon9			TCCTGGCCGCCTT	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.2713G>A	chr22.hg19:g.50170697C>T	ENSP00000216267:p.Ala905Thr	83.0	0.0	.		80.0	35.0	.	NM_014577	A6ZJA4	Missense_Mutation	SNP	ENST00000216267.8	hg19	CCDS14080.1	.	.	.	.	.	.	.	.	.	.	C	18.16	3.561093	0.65538	.	.	ENSG00000100425	ENST00000216267;ENST00000404034;ENST00000404760;ENST00000542442;ENST00000342989;ENST00000419212	T;T;T;T;T	0.31510	2.45;2.45;2.48;1.49;1.87	4.98	4.98	0.66077	.	0.105193	0.64402	D	0.000004	T	0.51618	0.1685	M	0.63428	1.95	0.80722	D	1	D;D;D;D	0.89917	0.967;0.988;1.0;0.989	P;P;D;D	0.80764	0.629;0.815;0.994;0.91	T	0.41998	-0.9477	10	0.16896	T	0.51	.	18.245	0.89982	0.0:1.0:0.0:0.0	.	1036;631;905;1036	Q86X06;B7Z926;O95696;O95696-2	.;.;BRD1_HUMAN;.	T	905;905;1036;593;631;496	ENSP00000216267:A905T;ENSP00000384076:A905T;ENSP00000385858:A1036T;ENSP00000437514:A593T;ENSP00000345886:A631T	ENSP00000216267:A905T	A	-	1	0	BRD1	48556701	1.000000	0.71417	0.874000	0.34290	0.485000	0.33311	5.458000	0.66679	2.300000	0.77407	0.655000	0.94253	GCC	.	.	.	none		0.647	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577		T	50170697	C	T	50170697	3	4	218	1	0	0	0	0	1	0	0	0	1503	739	26	2	479	2	BRD1	22	50170697	Missense_Mutation	SNP	C	TCGA-KV-A74V-01A-11D-A33Q-10	20285112	50170697	1133869	18	13192											
UBR4	23352	hgsc.bcm.edu	37	chr1	19482811	19482811	+	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	ctaactcggtctgtgaaccaGgtaaccacacggctttgatg	10	10	10	11	2	1	2	0	2	1	0	2	2	1	2	2	3	3	2	2	3	3	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr1:19482811G>A	ENST00000375254.3	-	42	6053	c.6026C>T	c.(6025-6027)cCt>cTt	p.P2009L	UBR4_ENST00000375267.2_Missense_Mutation_p.P2009L|UBR4_ENST00000375226.2_Missense_Mutation_p.P2009L|UBR4_ENST00000375217.2_Missense_Mutation_p.P2009L	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	2009					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)		CTGTGAACCAGGTAACCACAC	0.438																																					p.P2009L		Atlas-SNP	.											.	UBR4	415	.	0			c.C6026T						PASS	.						139	122	128					1																	19482811		2203	4300	6503	SO:0001583	missense	23352	exon42			GAACCAGGTAACC	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.6026C>T	chr1.hg19:g.19482811G>A	ENSP00000364403:p.Pro2009Leu	474.0	1.0	.		418.0	155.0	.	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	hg19	CCDS189.1	.	.	.	.	.	.	.	.	.	.	G	34	5.380190	0.95945	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000417040;ENST00000419533	T;T;T;T;T	0.27720	1.65;1.65;1.65;1.65;2.69	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.63402	0.2508	M	0.87827	2.91	0.80722	D	1	D	0.71674	0.998	D	0.76071	0.987	T	0.68800	-0.5313	10	0.87932	D	0	.	19.3843	0.94550	0.0:0.0:1.0:0.0	.	2009	Q5T4S7	UBR4_HUMAN	L	2009;2009;2009;2009;719;1225	ENSP00000364403:P2009L;ENSP00000364416:P2009L;ENSP00000364365:P2009L;ENSP00000364374:P2009L;ENSP00000404897:P719L	ENSP00000364365:P2009L	P	-	2	0	UBR4	19355398	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.969000	0.93411	2.814000	0.96858	0.591000	0.81541	CCT	.	.	.	none		0.438	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		A	19482811	G	A	19482811	3	1	219	1	0	0	0	0	1	0	0	0	16916	1000	35	2	9785	2	UBR4	1	19482811	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10		19482811	229767810	1	13193											
STK40	83931	hgsc.bcm.edu	37	chr1	36820910	36820910	+	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	cgtagtgctgcaggttgatgAggtcagcggtcttatcgctg	6	12	15	8	3	2	2	1	2	1	0	3	2	2	2	0	3	3	5	0	3	2	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr1:36820910A>T	ENST00000373129.3	-	6	873	c.467T>A	c.(466-468)cTc>cAc	p.L156H	STK40_ENST00000373130.3_Missense_Mutation_p.L161H|STK40_ENST00000359297.2_Missense_Mutation_p.L156H|STK40_ENST00000482458.1_5'UTR|STK40_ENST00000373132.3_Missense_Mutation_p.L156H	NM_032017.1	NP_114406.1	Q8N2I9	STK40_HUMAN	serine/threonine kinase 40	156	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				glycogen metabolic process (GO:0005977)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|regulation of MAPK cascade (GO:0043408)|respiratory system process (GO:0003016)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)|stomach(1)	13		Myeloproliferative disorder(586;0.0393)				CAGGTTGATGAGGTCAGCGGT	0.557																																					p.L156H		Atlas-SNP	.											.	STK40	53	.	0			c.T467A						PASS	.						278	239	252					1																	36820910		2203	4300	6503	SO:0001583	missense	83931	exon6			TTGATGAGGTCAG	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.467T>A	chr1.hg19:g.36820910A>T	ENSP00000362221:p.Leu156His	215.0	0.0	.		187.0	66.0	.	NM_032017	D3DPS8|Q5VTK8|Q5VTK9|Q6ZMN1|Q8N2J8|Q8N3I6|Q96HN6|Q96I44|Q9BSA3|Q9H7H6	Missense_Mutation	SNP	ENST00000373129.3	hg19	CCDS407.1	.	.	.	.	.	.	.	.	.	.	A	29.4	5.006207	0.93287	.	.	ENSG00000196182	ENST00000373129;ENST00000359297;ENST00000373130;ENST00000373132	T;T;T;T	0.69175	-0.38;1.96;1.96;-0.38	5.91	5.91	0.95273	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.064019	0.64402	D	0.000004	D	0.87200	0.6118	H	0.95043	3.615	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.999;0.958;0.975	D	0.90870	0.4745	10	0.87932	D	0	-15.2233	15.5237	0.75885	1.0:0.0:0.0:0.0	.	156;161;156	Q8N2I9-3;Q8N2I9-4;Q8N2I9	.;.;STK40_HUMAN	H	156;156;161;156	ENSP00000362221:L156H;ENSP00000352245:L156H;ENSP00000362222:L161H;ENSP00000362224:L156H	ENSP00000352245:L156H	L	-	2	0	STK40	36593497	1.000000	0.71417	0.999000	0.59377	0.926000	0.56050	8.857000	0.92250	2.263000	0.75096	0.379000	0.24179	CTC	.	.	.	none		0.557	STK40-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022592.1	NM_032017		T	36820910	A	T	36820910	3	4	219	1	0	0	0	0	1	0	0	0	15319	304	11	5	868	5	STK40	1	36820910	Missense_Mutation	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	17338099	36820910	212429711	2	13194											
CELSR2	1952	hgsc.bcm.edu	37	chr1	109807154	109807154	+	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	agagcatcaacgtggagcaaGgctgtagcctgcctgaccct	10	7	12	12	1	1	2	1	1	0	1	1	3	1	3	3	2	5	4	3	2	3	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr1:109807154G>A	ENST00000271332.3	+	11	5429	c.5368G>A	c.(5368-5370)Ggc>Agc	p.G1790S		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	1790	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		CGTGGAGCAAGGCTGTAGCCT	0.587																																					p.G1790S	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.G5368A						PASS	.						190	170	177					1																	109807154		2203	4300	6503	SO:0001583	missense	1952	exon11			GAGCAAGGCTGTA	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.5368G>A	chr1.hg19:g.109807154G>A	ENSP00000271332:p.Gly1790Ser	135.0	0.0	.		126.0	50.0	.	NM_001408	Q5T2Y7|Q92566	Missense_Mutation	SNP	ENST00000271332.3	hg19	CCDS796.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.643501	0.87859	.	.	ENSG00000143126	ENST00000271332	D	0.87179	-2.22	4.79	4.79	0.61399	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	.	.	.	.	D	0.93190	0.7831	M	0.82517	2.595	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93620	0.6947	9	0.62326	D	0.03	.	18.0161	0.89241	0.0:0.0:1.0:0.0	.	1790	Q9HCU4	CELR2_HUMAN	S	1790	ENSP00000271332:G1790S	ENSP00000271332:G1790S	G	+	1	0	CELSR2	109608677	1.000000	0.71417	0.996000	0.52242	0.712000	0.41017	9.202000	0.95026	2.504000	0.84457	0.561000	0.74099	GGC	.	.	.	none		0.587	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		A	109807154	G	A	109807154	3	1	219	1	0	0	0	0	1	0	0	0	3224	1000	35	2	5410	2	CELSR2	1	109807154	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	72986244	109807154	139443467	3	13195											
ADAMTSL4	54507	hgsc.bcm.edu	37	chr1	150531493	150531493	+	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	ctctgtggtctgccttgggaGtggggcagccctcgggccag	3	9	17	12	1	2	0	0	0	2	0	3	1	2	1	3	5	2	1	3	5	0	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr1:150531493G>T	ENST00000369038.2	+	14	2816	c.2615G>T	c.(2614-2616)aGt>aTt	p.S872I	RP11-54A4.2_ENST00000442435.2_RNA|ADAMTSL4_ENST00000271643.4_Missense_Mutation_p.S872I|ADAMTSL4_ENST00000369039.5_Missense_Mutation_p.S895I			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	872	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|positive regulation of apoptotic process (GO:0043065)	interstitial matrix (GO:0005614)	metalloendopeptidase activity (GO:0004222)|protease binding (GO:0002020)			breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			TGCCTTGGGAGTGGGGCAGCC	0.692																																					p.S872I		Atlas-SNP	.											.	ADAMTSL4	101	.	0			c.G2615T						PASS	.						15	19	18					1																	150531493		2201	4296	6497	SO:0001583	missense	54507	exon16			TTGGGAGTGGGGC	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.2615G>T	chr1.hg19:g.150531493G>T	ENSP00000358034:p.Ser872Ile	21.0	0.0	.		29.0	19.0	.	NM_019032	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Missense_Mutation	SNP	ENST00000369038.2	hg19	CCDS955.1	.	.	.	.	.	.	.	.	.	.	G	18.00	3.525215	0.64747	.	.	ENSG00000143382	ENST00000271643;ENST00000407995;ENST00000369039;ENST00000369038	T;T;T	0.60797	0.16;0.16;0.16	5.63	5.63	0.86233	.	.	.	.	.	T	0.66973	0.2844	L	0.53617	1.68	0.46564	D	0.999104	D;D;D	0.89917	1.0;0.998;0.999	D;D;D	0.74674	0.981;0.984;0.973	T	0.68315	-0.5441	9	0.62326	D	0.03	.	17.1708	0.86830	0.0:0.0:1.0:0.0	.	833;895;872	B7ZMJ3;F8WAD0;Q6UY14	.;.;ATL4_HUMAN	I	872;410;895;872	ENSP00000271643:S872I;ENSP00000358035:S895I;ENSP00000358034:S872I	ENSP00000271643:S872I	S	+	2	0	ADAMTSL4	148798117	0.765000	0.28485	0.987000	0.45799	0.293000	0.27360	2.637000	0.46553	2.655000	0.90218	0.462000	0.41574	AGT	.	.	.	none		0.692	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032		T	150531493	G	T	150531493	3	4	219	1	0	0	0	0	1	0	0	0	277	1029	36	4	2744	4	ADAMTSL4	1	150531493	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	40724339	150531493	98719128	4	13196											
ROBLD3	28956	hgsc.bcm.edu	37	chr1	156027791	156027791	+	Frame_Shift_Del	DEL	G	G	-																															gggccgtgtagccatcacccGagtggccaaccttctgctgt																										TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr1:156027791delG	ENST00000368305.4	+	3	392	c.254delG	c.(253-255)cgafs	p.R85fs	LAMTOR2_ENST00000368302.3_Frame_Shift_Del_p.R85fs|LAMTOR2_ENST00000368304.5_Intron	NM_014017.3	NP_054736.1	Q9Y2Q5	LTOR2_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 2	85					activation of MAPKK activity (GO:0000186)|cell growth (GO:0016049)|cellular protein localization (GO:0034613)|cellular response to amino acid stimulus (GO:0071230)|positive regulation of GTPase activity (GO:0043547)|positive regulation of TOR signaling (GO:0032008)	extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|Ragulator complex (GO:0071986)				breast(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	7						GCCATCACCCGAGTGGCCAAC	0.577																																					p.R85fs		Atlas-Indel,Pindel	.											LAMTOR2,colon,carcinoma,0,1	LAMTOR2	13	.	0			c.253delC						PASS	.						205	152	170					1																	156027791		2203	4300	6503	SO:0001589	frameshift_variant	28956	exon3			.	BC024190	CCDS1128.1, CCDS44243.1	1q22	2014-09-17	2011-02-15	2011-02-15	ENSG00000116586	ENSG00000116586			29796	protein-coding gene	gene with protein product	"mitogen activated protein binding protein interacting protein", "MAPKSP1 adaptor protein", "endosomal adaptor protein"	610389	"roadblock domain containing 3"	ROBLD3		11042152	Standard	NM_014017		Approved	MAPBPIP, MAPKSP1AP, p14, ENDAP, Ragulator2	uc001fnb.3	Q9Y2Q5	OTTHUMG00000017462	ENST00000368305.4:c.254delG	chr1.hg19:g.156027791delG	ENSP00000357288:p.Arg85fs	311.0	0.0	0		315.0	118.0	0.374603	NM_014017	Q5VY97|Q5VY98|Q5VY99	Frame_Shift_Del	DEL	ENST00000368305.4	hg19	CCDS1128.1																																																																																			.	.	.	none		0.577	LAMTOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046197.1	NM_014017		-	156027791	G	-	156027791	7	5	219	1	0	1	0	1	0	0	0	0	13525	1058	37	0	264	0	ROBLD3	1	156027791	Frame_Shift_Del	DEL	G	TCGA-MH-A55W-01A-11D-A26P-10	5496298	156027791	93222830	5	13197											
ELK4	2005	hgsc.bcm.edu	37	chr1	205588957	205588957	+	Intron	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	atgagaaatggggtaactttCacatgacagtcacacataac	16	9	8	8	0	2	2	2	2	0	1	2	3	2	2	0	2	2	1	0	2	3	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr1:205588957C>G	ENST00000357992.4	-	3	1420				ELK4_ENST00000468523.1_5'Flank|ELK4_ENST00000289703.4_Nonstop_Mutation_p.*406S	NM_001973.3	NP_001964.2	P28324	ELK4_HUMAN	ELK4, ETS-domain protein (SRF accessory protein 1)						cell differentiation (GO:0030154)|histone H3 deacetylation (GO:0070932)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|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 cofactor activity (GO:0003712)		SLC45A3/ELK4(18)	breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|skin(1)	12	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0908)			GGGTAACTTTCACATGACAGT	0.289			T	SLC45A3	prostate																																p.X406S		Atlas-SNP	.		Dom	yes		1	1q32	2005	"ELK4, ETS-domain protein (SRF accessory protein 1)"		E	.	ELK4	45	.	0			c.G1217C						PASS	.						48	48	48					1																	205588957		2203	4300	6503	SO:0001627	intron_variant	2005	exon3			AACTTTCACATGA	M85165	CCDS1456.1, CCDS1457.1	1q32	2008-02-05			ENSG00000158711	ENSG00000158711			3326	protein-coding gene	gene with protein product		600246				7851904, 8575773	Standard	NM_001973		Approved	SAP1		P28324	OTTHUMG00000037221	ENST00000357992.4:c.1080+136G>C	chr1.hg19:g.205588957C>G		58.0	0.0	.		75.0	27.0	.	NM_021795	P28323|Q6GSJ2	Missense_Mutation	SNP	ENST00000357992.4	hg19	CCDS1456.1	.	.	.	.	.	.	.	.	.	.	C	11.79	1.744796	0.30865	.	.	ENSG00000158711	ENST00000289703	.	.	.	4.73	4.73	0.59995	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5541	0.61749	0.0:1.0:0.0:0.0	.	.	.	.	S	406	.	.	X	-	2	2	ELK4	203855580	0.000000	0.05858	0.860000	0.33809	0.233000	0.25261	0.118000	0.15605	2.344000	0.79699	0.655000	0.94253	TGA	.	.	.	none		0.289	ELK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090615.1	NM_021795		G	205588957	C	G	205588957	1	3	219	0	1	0	0	0	0	0	0	0	5063	837	29	4		4	ELK4	1	205588957	Intron	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	49561166	205588957	43661664	6	13198											
OR13G1	441933	hgsc.bcm.edu	37	chr1	247836182	247836182	+	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	agaaggaaaacatacatgggCgtatgcaaggtgttgttata	15	10	12	4	1	0	1	0	0	0	1	0	2	0	2	0	3	3	4	0	3	8	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr1:247836182C>A	ENST00000359688.2	-	1	183	c.162G>T	c.(160-162)acG>acT	p.T54T	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005487.1	NP_001005487.1	Q8NGZ3	O13G1_HUMAN	olfactory receptor, family 13, subfamily G, member 1	54						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(1)|large_intestine(2)|lung(28)|skin(2)	35	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			CATACATGGGCGTATGCAAGG	0.418																																					p.T54T		Atlas-SNP	.											OR13G1,NS,carcinoma,-1,4	OR13G1	78	.	0			c.G162T						PASS	.						90	70	77					1																	247836182		2203	4300	6503	SO:0001819	synonymous_variant	441933	exon1			CATGGGCGTATGC	AB065623	CCDS31094.1	1q44	2012-08-09			ENSG00000197437	ENSG00000197437		"GPCR / Class A : Olfactory receptors"	14999	protein-coding gene	gene with protein product		611677					Standard	NM_001005487		Approved		uc001idi.1	Q8NGZ3	OTTHUMG00000040212	ENST00000359688.2:c.162G>T	chr1.hg19:g.247836182C>A		129.0	0.0	.		157.0	52.0	.	NM_001005487	B2RN80|Q5T2T2|Q6IF86	Silent	SNP	ENST00000359688.2	hg19	CCDS31094.1																																																																																			.	.	.	none		0.418	OR13G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096869.1	NM_001005487		A	247836182	C	A	247836182	2	1	219	1	0	0	0	0	0	0	0	1	10949	755	27	4		4	OR13G1	1	247836182	Silent	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	42247225	247836182	1414439	7	13199											
GEN1	348654	hgsc.bcm.edu	37	chr2	17962535	17962535	+	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	ttacaaaattatcatatcctCaggataatctacaaccagat	17	12	3	9	0	3	1	2	0	1	1	4	2	4	2	2	1	3	0	2	1	8	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr2:17962535C>G	ENST00000381254.2	+	14	2270	c.2056C>G	c.(2056-2058)Cag>Gag	p.Q686E	GEN1_ENST00000317402.7_Missense_Mutation_p.Q686E|SMC6_ENST00000402989.1_Intron	NM_001130009.1	NP_001123481.1	Q17RS7	GEN_HUMAN	GEN1 Holliday junction 5' flap endonuclease	686					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)					ATCATATCCTCAGGATAATCT	0.348								Homologous recombination																													p.Q686E		Atlas-SNP	.											.	GEN1	79	.	0			c.C2056G						PASS	.						75	82	79					2																	17962535		2203	4300	6503	SO:0001583	missense	348654	exon14			TATCCTCAGGATA	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.2056C>G	chr2.hg19:g.17962535C>G	ENSP00000370653:p.Gln686Glu	32.0	0.0	.		108.0	54.0	.	NM_182625	Q17RS9|Q6ZN37	Missense_Mutation	SNP	ENST00000381254.2	hg19	CCDS1691.1	.	.	.	.	.	.	.	.	.	.	C	2.631	-0.286254	0.05605	.	.	ENSG00000178295	ENST00000317402;ENST00000381254;ENST00000536097	T;T	0.24723	1.84;1.84	5.41	2.48	0.30137	.	0.967756	0.08453	N	0.943658	T	0.25494	0.0620	M	0.62723	1.935	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.31888	-0.9927	10	0.59425	D	0.04	0.3588	4.3539	0.11169	0.1364:0.6005:0.1325:0.1307	.	686	Q17RS7	GEN_HUMAN	E	686;686;323	ENSP00000318977:Q686E;ENSP00000370653:Q686E	ENSP00000318977:Q686E	Q	+	1	0	GEN1	17826016	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	0.195000	0.17155	0.717000	0.32145	0.655000	0.94253	CAG	.	.	.	none		0.348	GEN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241661.2	NM_182625		G	17962535	C	G	17962535	3	3	219	1	0	0	0	0	1	0	0	0	6342	827	29	4	2106	4	GEN1	2	17962535	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10		17962535	225236838	8	13200											
ITSN2	50618	hgsc.bcm.edu	37	chr2	24469667	24469667	+	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	aattaacccacttccataccAggatgaaaggcaggtgtggc	13	8	10	10	0	0	1	0	1	0	0	1	2	1	2	3	4	2	1	3	4	4	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr2:24469667A>G	ENST00000355123.4	-	28	3827	c.3384T>C	c.(3382-3384)ccT>ccC	p.P1128P	ITSN2_ENST00000361999.3_Splice_Site_p.P1101P|ITSN2_ENST00000406921.3_Splice_Site_p.P1128P	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	1128	SH3 5. {ECO:0000255|PROSITE- ProRule:PRU00192}.				endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTCCATACCAGGATGAAAGG	0.383																																					p.P1128P		Atlas-SNP	.											.	ITSN2	224	.	0			c.T3384C						PASS	.						87	87	87					2																	24469667		2203	4300	6503	SO:0001630	splice_region_variant	50618	exon28			CATACCAGGATGA	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.3385+1T>C	chr2.hg19:g.24469667A>G		28.0	0.0	.		71.0	35.0	.	NM_147152	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Silent	SNP	ENST00000355123.4	hg19	CCDS1710.2	.	.	.	.	.	.	.	.	.	.	A	11.59	1.683791	0.29872	.	.	ENSG00000198399	ENST00000416160	.	.	.	5.59	-2.45	0.06481	.	.	.	.	.	T	0.43122	0.1233	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35624	-0.9781	4	.	.	.	.	4.57	0.12205	0.3227:0.0:0.2426:0.4346	.	.	.	.	P	56	.	.	L	-	2	0	ITSN2	24323171	1.000000	0.71417	0.998000	0.56505	0.972000	0.66771	1.158000	0.31737	-0.097000	0.12307	0.383000	0.25322	CTG	.	.	.	none		0.383	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277	Silent	G	24469667	A	G	24469667	5	3	219	1	0	0	0	0	0	0	1	0	7934	202	7	3	1812	3	ITSN2	2	24469667	Splice_Site	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	6507132	24469667	218729706	9	13201											
NRBP1	29959	hgsc.bcm.edu	37	chr2	27660178	27660178	+	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	agagtcctcatatgtgccacAggaagccatcagcagtgcca	12	7	10	12	0	2	1	2	0	0	1	3	2	3	2	4	1	4	1	4	1	2	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr2:27660178A>T	ENST00000233557.3	+	11	1686	c.854A>T	c.(853-855)cAg>cTg	p.Q285L	NRBP1_ENST00000379852.3_Missense_Mutation_p.Q285L|NRBP1_ENST00000379863.3_Missense_Mutation_p.Q293L			Q9UHY1	NRBP_HUMAN	nuclear receptor binding protein 1	285	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				ER to Golgi vesicle-mediated transport (GO:0006888)|gene expression (GO:0010467)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell projection (GO:0042995)|endomembrane system (GO:0012505)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19	Acute lymphoblastic leukemia(172;0.155)					TATGTGCCACAGGAAGCCATC	0.463																																					p.Q285L		Atlas-SNP	.											.	NRBP1	40	.	0			c.A854T						PASS	.						78	72	74					2																	27660178		2203	4300	6503	SO:0001583	missense	29959	exon10			TGCCACAGGAAGC	AF113249	CCDS1753.1	2p23	2008-02-05	2005-12-22	2005-12-22	ENSG00000115216	ENSG00000115216			7993	protein-coding gene	gene with protein product		606010	"nuclear receptor binding protein"	NRBP		10843813, 11956649	Standard	NM_013392		Approved	BCON3, MUDPNP, MADM	uc002rkp.3	Q9UHY1	OTTHUMG00000097789	ENST00000233557.3:c.854A>T	chr2.hg19:g.27660178A>T	ENSP00000233557:p.Gln285Leu	381.0	2.0	.		415.0	233.0	.	NM_013392	B3KV40|D6W558|Q53FZ5|Q96SU3	Missense_Mutation	SNP	ENST00000233557.3	hg19	CCDS1753.1	.	.	.	.	.	.	.	.	.	.	A	16.36	3.100500	0.56183	.	.	ENSG00000115216	ENST00000233557;ENST00000421823;ENST00000379852;ENST00000379863	T;T;T	0.32272	1.46;1.46;1.46	5.63	5.63	0.86233	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	0.28928	0.0718	L	0.28014	0.82	0.80722	D	1	B;B;B	0.32862	0.387;0.049;0.06	B;B;B	0.40256	0.324;0.039;0.021	T	0.08513	-1.0718	10	0.40728	T	0.16	-13.0877	14.6481	0.68774	1.0:0.0:0.0:0.0	.	265;293;285	B4DW31;F8W6G1;Q9UHY1	.;.;NRBP_HUMAN	L	285;265;285;293	ENSP00000233557:Q285L;ENSP00000369181:Q285L;ENSP00000369192:Q293L	ENSP00000233557:Q285L	Q	+	2	0	NRBP1	27513682	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.394000	0.79862	2.138000	0.66242	0.533000	0.62120	CAG	.	.	.	none		0.463	NRBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215033.1	NM_013392		T	27660178	A	T	27660178	3	4	219	1	0	0	0	0	1	0	0	0	10649	188	7	5	888	5	NRBP1	2	27660178	Missense_Mutation	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	3190511	27660178	215539195	10	13202											
RANBP2	5903	hgsc.bcm.edu	37	chr2	109380179	109380179	+	Frame_Shift_Del	DEL	A	A	-																															cccctcctgcagcttacagtAacagtgaaagccttttaggt																								rs201854838		TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr2:109380179delA	ENST00000283195.6	+	20	3310	c.3184delA	c.(3184-3186)aacfs	p.N1062fs		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	1062					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						AGCTTACAGTAACAGTGAAAG	0.443																																					p.S1061fs		Atlas-Indel,Pindel	.											.	RANBP2	488	.	0			c.3183delT						PASS	.						74	77	76					2																	109380179		2203	4300	6503	SO:0001589	frameshift_variant	5903	exon20			.	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.3184delA	chr2.hg19:g.109380179delA	ENSP00000283195:p.Asn1062fs	88.0	0.0	0		110.0	53.0	0.481818	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Frame_Shift_Del	DEL	ENST00000283195.6	hg19	CCDS2079.1																																																																																			.	.	.	none		0.443	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		-	109380179	A	-	109380179	7	5	219	1	0	1	0	1	0	0	0	0	13041	362	13	0	3262	0	RANBP2	2	109380179	Frame_Shift_Del	DEL	A	TCGA-MH-A55W-01A-11D-A26P-10	81720001	109380179	133819194	11	13203											
NPHP1	4867	hgsc.bcm.edu	37	chr2	110922202	110922202	+	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	tcttccacagtctccatcctAtttcgcatcagaactattag	10	14	4	13	1	3	1	1	0	2	1	7	1	5	1	3	0	1	1	3	0	4	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr2:110922202A>T	ENST00000393272.3	-	8	931	c.834T>A	c.(832-834)aaT>aaA	p.N278K	NPHP1_ENST00000417665.1_Intron|NPHP1_ENST00000445609.2_Intron|NPHP1_ENST00000316534.4_Missense_Mutation_p.N278K|NPHP1_ENST00000355301.4_Intron	NM_000272.3|NM_207181.2	NP_000263.2|NP_997064.2	O15259	NPHP1_HUMAN	nephronophthisis 1 (juvenile)	278					actin cytoskeleton organization (GO:0030036)|cell projection organization (GO:0030030)|cellular protein localization (GO:0034613)|excretion (GO:0007588)|photoreceptor cell outer segment organization (GO:0035845)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|spermatid differentiation (GO:0048515)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|motile cilium (GO:0031514)|photoreceptor connecting cilium (GO:0032391)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(2)	24						TCTCCATCCTATTTCGCATCA	0.463																																					p.N278K		Atlas-SNP	.											.	NPHP1	68	.	0			c.T834A						PASS	.						185	182	183					2																	110922202		2203	4300	6503	SO:0001583	missense	4867	exon8			CATCCTATTTCGC	AF023674	CCDS2086.1, CCDS46384.1, CCDS46385.1, CCDS46386.1	2q13	2014-01-28			ENSG00000144061	ENSG00000144061			7905	protein-coding gene	gene with protein product	"nephrocystin-1"	607100		NPH1			Standard	NM_000272		Approved	JBTS4, SLSN1	uc002tfm.4	O15259	OTTHUMG00000131195	ENST00000393272.3:c.834T>A	chr2.hg19:g.110922202A>T	ENSP00000376953:p.Asn278Lys	88.0	0.0	.		130.0	38.0	.	NM_207181	O14837	Missense_Mutation	SNP	ENST00000393272.3	hg19	CCDS46385.1	.	.	.	.	.	.	.	.	.	.	A	11.00	1.510348	0.27036	.	.	ENSG00000144061	ENST00000316534;ENST00000393272	T;T	0.60171	0.21;0.21	4.36	-3.69	0.04450	.	1.449030	0.04895	U	0.450299	T	0.35038	0.0918	N	0.22421	0.69	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.001;0.003	T	0.09335	-1.0679	10	0.23302	T	0.38	-2.1995	1.7177	0.02905	0.4617:0.1409:0.2537:0.1437	.	278;278	O15259;O15259-4	NPHP1_HUMAN;.	K	278	ENSP00000313169:N278K;ENSP00000376953:N278K	ENSP00000313169:N278K	N	-	3	2	NPHP1	110279491	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.481000	0.06552	-0.376000	0.07943	-1.092000	0.02172	AAT	.	.	.	none		0.463	NPHP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253919.3	NM_000272		T	110922202	A	T	110922202	3	4	219	1	0	0	0	0	1	0	0	0	10586	446	16	5	1419	5	NPHP1	2	110922202	Missense_Mutation	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	1542023	110922202	132277171	12	13204											
CLASP1	23332	hgsc.bcm.edu	37	chr2	122161975	122161975	+	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	gagggtcagcaaacatccgaGtgaagatctcacacaacctt	14	7	9	11	1	2	2	2	1	1	1	4	4	3	2	2	1	3	1	2	1	3	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr2:122161975G>C	ENST00000263710.4	-	26	3094	c.2705C>G	c.(2704-2706)aCt>aGt	p.T902S	CLASP1_ENST00000409078.3_Missense_Mutation_p.T874S|CLASP1_ENST00000455322.2_Missense_Mutation_p.T874S|CLASP1_ENST00000541859.1_Missense_Mutation_p.T635S|CLASP1_ENST00000541377.1_Missense_Mutation_p.T880S|CLASP1_ENST00000545861.1_Missense_Mutation_p.T649S|CLASP1_ENST00000397587.3_Missense_Mutation_p.T882S	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	902					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)					AAACATCCGAGTGAAGATCTC	0.408																																					p.T902S		Atlas-SNP	.											.	CLASP1	135	.	0			c.C2705G						PASS	.						102	99	100					2																	122161975		1978	4156	6134	SO:0001583	missense	23332	exon26			ATCCGAGTGAAGA	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.2705C>G	chr2.hg19:g.122161975G>C	ENSP00000263710:p.Thr902Ser	154.0	0.0	.		160.0	44.0	.	NM_015282	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Missense_Mutation	SNP	ENST00000263710.4	hg19		.	.	.	.	.	.	.	.	.	.	G	29.9	5.041443	0.93685	.	.	ENSG00000074054	ENST00000263710;ENST00000455322;ENST00000397587;ENST00000541377;ENST00000541859;ENST00000409078;ENST00000545861	T;T;T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16;-0.16;-0.16	5.37	5.37	0.77165	Armadillo-like helical (1);Armadillo-type fold (1);	0.045519	0.85682	D	0.000000	T	0.76615	0.4012	L	0.55481	1.735	0.58432	D	0.999999	D;D;P;P	0.76494	0.999;0.999;0.865;0.74	D;D;P;P	0.79108	0.992;0.968;0.604;0.617	T	0.77496	-0.2566	10	0.59425	D	0.04	-15.1313	19.1123	0.93321	0.0:0.0:1.0:0.0	.	874;882;880;902	E7EUA5;F5GWS0;B7ZLX3;Q7Z460	.;.;.;CLAP1_HUMAN	S	902;874;882;880;635;874;649	ENSP00000263710:T902S;ENSP00000389372:T874S;ENSP00000380717:T882S;ENSP00000441625:T880S;ENSP00000441770:T635S;ENSP00000386442:T874S;ENSP00000438620:T649S	ENSP00000263710:T902S	T	-	2	0	CLASP1	121878445	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.496000	0.97967	2.518000	0.84900	0.563000	0.77884	ACT	.	.	.	none		0.408	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282		C	122161975	G	C	122161975	3	2	219	1	0	0	0	0	1	0	0	0	3456	1029	36	4	1967	4	CLASP1	2	122161975	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	11239773	122161975	121037398	13	13205											
KIF1A	547	hgsc.bcm.edu	37	chr2	241725900	241725900	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggttcaggaggtcacggaCgcgctcacagtaaatctcca	10	7	13	11	3	4	0	3	0	1	0	5	2	4	2	1	5	0	3	1	5	2	2			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr2:241725900C>T	ENST00000320389.7	-	6	618	c.460G>A	c.(460-462)Gtc>Atc	p.V154I	KIF1A_ENST00000498729.2_Missense_Mutation_p.V154I	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	154	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				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)		AGGTCACGGACGCGCTCACAG	0.652																																					p.V154I		Atlas-SNP	.											.	KIF1A	152	.	0			c.G460A						PASS	.						112	117	115					2																	241725900		2085	4227	6312	SO:0001583	missense	547	exon6			CACGGACGCGCTC	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.460G>A	chr2.hg19:g.241725900C>T	ENSP00000322791:p.Val154Ile	203.0	0.0	.		238.0	22.0	.	NM_001244008	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Missense_Mutation	SNP	ENST00000320389.7	hg19	CCDS46561.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.399825	0.83120	.	.	ENSG00000130294	ENST00000320389;ENST00000498729;ENST00000373308;ENST00000404283	T;T;T	0.74315	-0.83;-0.83;-0.83	4.55	4.55	0.56014	Kinesin, motor domain (4);	0.000000	0.64402	U	0.000001	T	0.80681	0.4669	L	0.35414	1.06	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.85130	0.997;0.983;0.996	D	0.83722	0.0193	10	0.87932	D	0	.	17.3339	0.87274	0.0:1.0:0.0:0.0	.	154;154;154	F5H045;Q12756-2;Q12756	.;.;KIF1A_HUMAN	I	154	ENSP00000322791:V154I;ENSP00000438388:V154I;ENSP00000384231:V154I	ENSP00000322791:V154I	V	-	1	0	KIF1A	241374573	1.000000	0.71417	0.911000	0.35937	0.436000	0.31835	5.859000	0.69539	2.087000	0.62958	0.643000	0.83706	GTC	.	.	.	none		0.652	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483		T	241725900	C	T	241725900	3	4	219	1	0	0	0	0	1	0	0	0	8290	536	19	1	4780	1	KIF1A	2	241725900	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	119563925	241725900	1473473	14	13206											
FYCO1	79443	hgsc.bcm.edu	37	chr3	46009857	46009857	+	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	tccttctctgctgctcctagCtccaggccctgcaggcatgt	4	12	9	16	0	1	0	0	0	1	0	5	0	4	0	4	2	4	5	4	2	1	2	rs372875711		TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr3:46009857C>A	ENST00000296137.2	-	8	1174	c.969G>T	c.(967-969)gaG>gaT	p.E323D	FYCO1_ENST00000535325.1_Missense_Mutation_p.E323D	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	323					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)		CTGCTCCTAGCTCCAGGCCCT	0.627																																					p.E323D		Atlas-SNP	.											.	FYCO1	115	.	0			c.G969T						PASS	.						71	64	66					3																	46009857		2203	4300	6503	SO:0001583	missense	79443	exon8			TCCTAGCTCCAGG	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.969G>T	chr3.hg19:g.46009857C>A	ENSP00000296137:p.Glu323Asp	79.0	0.0	.		47.0	11.0	.	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	hg19	CCDS2734.1	.	.	.	.	.	.	.	.	.	.	C	19.41	3.822936	0.71028	.	.	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.28454	1.61;1.69	5.66	5.66	0.87406	.	0.237259	0.43260	D	0.000588	T	0.42539	0.1207	M	0.67953	2.075	0.34032	D	0.653899	D;P	0.63880	0.993;0.932	P;B	0.56127	0.792;0.362	T	0.54390	-0.8301	10	0.28530	T	0.3	-23.5428	8.7704	0.34728	0.0:0.8728:0.0:0.1272	.	323;323	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	D	323	ENSP00000296137:E323D;ENSP00000441178:E323D	ENSP00000296137:E323D	E	-	3	2	FYCO1	45984861	0.931000	0.31567	0.984000	0.44739	0.507000	0.33981	1.633000	0.37113	2.671000	0.90904	0.655000	0.94253	GAG	.	.	.	alt		0.627	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513		A	46009857	C	A	46009857	3	1	219	1	0	0	0	0	1	0	0	0	6132	796	28	4	3511	4	FYCO1	3	46009857	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10		46009857	152012573	15	13207											
RBM5	10181	hgsc.bcm.edu	37	chr3	50155814	50155814	+	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	ggagccaaaggcagcgcataTggtttgtcgggcgccgattc	8	8	15	10	4	0	0	0	0	0	0	2	2	0	1	2	4	2	3	2	4	2	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr3:50155814T>A	ENST00000347869.3	+	25	2548	c.2373T>A	c.(2371-2373)taT>taA	p.Y791*	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	791	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)		GCAGCGCATATGGTTTGTCGG	0.557																																					p.Y791X		Atlas-SNP	.											.	RBM5	76	.	0			c.T2373A						PASS	.						93	81	85					3																	50155814		2203	4300	6503	SO:0001587	stop_gained	10181	exon25			CGCATATGGTTTG	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.2373T>A	chr3.hg19:g.50155814T>A	ENSP00000343054:p.Tyr791*	172.0	0.0	.		150.0	63.0	.	NM_005778	B2RA45|B4DM16|B4DMF9|B4DZ63|Q93021|Q9BU14|Q9HDA6|Q9UKY8|Q9UL24	Nonsense_Mutation	SNP	ENST00000347869.3	hg19	CCDS2810.1	.	.	.	.	.	.	.	.	.	.	T	35	5.436728	0.96168	.	.	ENSG00000003756	ENST00000347869;ENST00000543047;ENST00000544851	.	.	.	5.56	0.508	0.16972	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.522	10.6385	0.45579	0.0:0.4157:0.0:0.5843	.	.	.	.	X	791;790;481	.	ENSP00000343054:Y791X	Y	+	3	2	RBM5	50130818	0.435000	0.25577	0.988000	0.46212	0.413000	0.31143	-0.355000	0.07671	0.075000	0.16796	0.528000	0.53228	TAT	.	.	.	none		0.557	RBM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345797.3	NM_005778		A	50155814	T	A	50155814	4	1	219	1	0	0	0	0	0	1	0	0	13156	1471	51	5	2467	5	RBM5	3	50155814	Nonsense_Mutation	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	4145957	50155814	147866616	16	13208											
WDR52	55779	hgsc.bcm.edu	37	chr3	113120585	113120585	+	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	ctattgtctcaaaatcccatAtcttgtaaaatgaaaagaaa	18	12	4	7	0	2	2	1	1	2	1	4	2	3	2	1	0	0	1	1	0	9	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr3:113120585A>C	ENST00000295868.2	-	10	1334	c.1172T>G	c.(1171-1173)aTa>aGa	p.I391R	WDR52_ENST00000393845.2_Splice_Site_p.I391R|WDR52-AS1_ENST00000498480.1_RNA|WDR52-AS1_ENST00000473329.1_RNA	NM_018338.3	NP_060808.2														breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						AAAATCCCATATCTTGTAAAA	0.308																																					p.I391R		Atlas-SNP	.											.	WDR52	151	.	0			c.T1172G						PASS	.						60	60	60					3																	113120585		2203	4298	6501	SO:0001630	splice_region_variant	55779	exon10			TCCCATATCTTGT																												ENST00000295868.2:c.1171-1T>G	chr3.hg19:g.113120585A>C		38.0	0.0	.		81.0	36.0	.	NM_001164496		Missense_Mutation	SNP	ENST00000295868.2	hg19	CCDS2972.1	.	.	.	.	.	.	.	.	.	.	A	19.49	3.838251	0.71373	.	.	ENSG00000206530	ENST00000393845;ENST00000295868	T;T	0.70631	-0.5;3.01	5.63	5.63	0.86233	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	.	.	.	.	T	0.79446	0.4447	L	0.59436	1.845	0.80722	D	1	D	0.69078	0.997	P	0.59012	0.85	T	0.81839	-0.0748	9	0.87932	D	0	.	15.8341	0.78787	1.0:0.0:0.0:0.0	.	391	Q96MT7	WDR52_HUMAN	R	391	ENSP00000377428:I391R;ENSP00000295868:I391R	ENSP00000295868:I391R	I	-	2	0	WDR52	114603275	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	4.300000	0.59079	2.144000	0.66660	0.533000	0.62120	ATA	.	.	.	none		0.308	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3		Missense_Mutation	C	113120585	A	C	113120585	5	2	219	1	0	0	0	0	0	0	1	0	17316	463	16	5	4511	5	WDR52	3	113120585	Splice_Site	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	62964771	113120585	84901845	17	13209											
IFT122	55764	hgsc.bcm.edu	37	chr3	129214436	129214436	+	Frame_Shift_Del	DEL	T	T	-																															tgtacaccgacctctgcatgTttgagtatgccaaggtaacc																										TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr3:129214436delT	ENST00000348417.2	+	18	2271	c.2194delT	c.(2194-2196)tttfs	p.F732fs	IFT122_ENST00000349441.2_Frame_Shift_Del_p.F621fs|IFT122_ENST00000507564.1_Frame_Shift_Del_p.F724fs|IFT122_ENST00000440957.2_Frame_Shift_Del_p.F523fs|IFT122_ENST00000504021.1_Frame_Shift_Del_p.F608fs|IFT122_ENST00000347300.2_Frame_Shift_Del_p.F673fs|IFT122_ENST00000513932.1_3'UTR|IFT122_ENST00000296266.3_Frame_Shift_Del_p.F783fs|IFT122_ENST00000431818.2_Frame_Shift_Del_p.F582fs	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	732					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						CCTCTGCATGTTTGAGTATGC	0.537																																					p.M782fs		Atlas-Indel,Pindel	.											.	IFT122	117	.	0			c.2346delG						PASS	.						118	106	110					3																	129214436		2203	4300	6503	SO:0001589	frameshift_variant	55764	exon19			.	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.2194delT	chr3.hg19:g.129214436delT	ENSP00000324005:p.Phe732fs	294.0	0.0	0		251.0	114.0	0.454183	NM_052985	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Frame_Shift_Del	DEL	ENST00000348417.2	hg19	CCDS3061.1																																																																																			.	.	.	none		0.537	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262		-	129214436	T	-	129214436	7	5	219	1	0	1	0	1	0	0	0	0	7562	1725	60	0	2421	0	IFT122	3	129214436	Frame_Shift_Del	DEL	T	TCGA-MH-A55W-01A-11D-A26P-10	16093851	129214436	68807994	18	13210											
MYNN	55892	hgsc.bcm.edu	37	chr3	169496621	169496621	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggaagaggtggtcactaaatGcaaaataaagatggaagatt	18	8	12	3	0	1	3	1	0	0	3	1	5	1	5	0	4	1	1	0	4	8	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr3:169496621G>A	ENST00000349841.5	+	3	995	c.332G>A	c.(331-333)tGc>tAc	p.C111Y	MYNN_ENST00000544106.1_Missense_Mutation_p.C111Y|RP11-362K14.5_ENST00000602342.1_RNA|MYNN_ENST00000356716.4_Missense_Mutation_p.C111Y|MYNN_ENST00000392733.1_Missense_Mutation_p.C111Y	NM_018657.4	NP_061127.1	Q9NPC7	MYNN_HUMAN	myoneurin	111					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_cancers(22;9.55e-22)|all_epithelial(15;2.04e-26)|all_lung(20;5.05e-16)|Lung NSC(18;2.19e-15)|Ovarian(172;0.000223)|Breast(254;0.197)		Epithelial(2;4.03e-64)|all cancers(2;2.19e-58)|Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00676)			GTCACTAAATGCAAAATAAAG	0.348																																					p.C111Y		Atlas-SNP	.											.	MYNN	36	.	0			c.G332A						PASS	.						92	98	96					3																	169496621		2203	4300	6503	SO:0001583	missense	55892	exon4			CTAAATGCAAAAT	AF148848	CCDS3207.1, CCDS54671.1	3q26.31	2013-01-09			ENSG00000085274	ENSG00000085274		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	14955	protein-coding gene	gene with protein product		606042				10873615	Standard	NM_001185118		Approved	SBBIZ1, ZBTB31, ZNF902	uc010hwo.3	Q9NPC7		ENST00000349841.5:c.332G>A	chr3.hg19:g.169496621G>A	ENSP00000326240:p.Cys111Tyr	75.0	0.0	.		81.0	32.0	.	NM_001185118	B2R6C9|Q6QHA6|Q6QHA7|Q6R3G1|Q6R3G2|Q6R4A0|Q7Z716|Q7Z717|Q86Z11|Q86Z12|Q9NS01|Q9UIW8	Missense_Mutation	SNP	ENST00000349841.5	hg19	CCDS3207.1	.	.	.	.	.	.	.	.	.	.	G	17.29	3.352343	0.61293	.	.	ENSG00000085274	ENST00000356716;ENST00000349841;ENST00000392733;ENST00000544106	T;T;T;T	0.78364	-1.17;-1.17;-1.17;-1.17	5.54	5.54	0.83059	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.93530	0.7935	H	0.98802	4.335	0.49915	D	0.999837	D;D	0.76494	0.999;0.998	D;D	0.81914	0.995;0.992	D	0.95900	0.8914	10	0.87932	D	0	.	19.4966	0.95075	0.0:0.0:1.0:0.0	.	111;111	Q9NPC7-2;Q9NPC7	.;MYNN_HUMAN	Y	111	ENSP00000349150:C111Y;ENSP00000326240:C111Y;ENSP00000376492:C111Y;ENSP00000440637:C111Y	ENSP00000326240:C111Y	C	+	2	0	MYNN	170979315	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.825000	0.69286	2.616000	0.88540	0.650000	0.86243	TGC	.	.	.	none		0.348	MYNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467801.1	NM_018657		A	169496621	G	A	169496621	3	1	219	1	0	0	0	0	1	0	0	0	10068	1319	46	2	338	2	MYNN	3	169496621	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	40282185	169496621	28525809	19	13211											
KNG1	3827	hgsc.bcm.edu	37	chr3	186435425	186435425	+	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	aaattgactgcaatgacaagGatttatttaaagctgtggat	15	13	9	4	0	0	2	0	2	0	0	0	4	0	4	0	2	2	2	0	2	6	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr3:186435425G>T	ENST00000265023.4	+	1	306	c.94G>T	c.(94-96)Gat>Tat	p.D32Y	RP11-573D15.8_ENST00000599314.1_RNA|KNG1_ENST00000287611.2_Missense_Mutation_p.D32Y|KNG1_ENST00000447445.1_Missense_Mutation_p.D32Y	NM_001102416.2	NP_001095886.1	P01042	KNG1_HUMAN	kininogen 1	32	Cystatin kininogen-type 1. {ECO:0000255|PROSITE-ProRule:PRU00979}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|inflammatory response (GO:0006954)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|smooth muscle contraction (GO:0006939)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			endometrium(1)|lung(15)|prostate(1)|skin(2)|stomach(2)	21	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)		CAATGACAAGGATTTATTTAA	0.393																																					p.D32Y		Atlas-SNP	.											.	KNG1	129	.	0			c.G94T						PASS	.						119	121	121					3																	186435425		2203	4299	6502	SO:0001583	missense	3827	exon1			GACAAGGATTTAT		CCDS3281.1, CCDS43183.1, CCDS54695.1	3q27.3	2014-05-15	2004-05-21	2004-05-26	ENSG00000113889	ENSG00000113889		"Endogenous ligands"	6383	protein-coding gene	gene with protein product	"alpha-2-thiol proteinase inhibitor", "bradykinin"	612358	"kininogen"	KNG, BDK		1733668	Standard	NM_000893		Approved	BK	uc011bsa.2	P01042	OTTHUMG00000150348	ENST00000265023.4:c.94G>T	chr3.hg19:g.186435425G>T	ENSP00000265023:p.Asp32Tyr	129.0	0.0	.		157.0	37.0	.	NM_000893	A8K474|B2RCR2|C9JEX1|P01043|Q53EQ0|Q6PAU9|Q7M4P1	Missense_Mutation	SNP	ENST00000265023.4	hg19	CCDS43183.1	.	.	.	.	.	.	.	.	.	.	G	13.29	2.192786	0.38707	.	.	ENSG00000113889	ENST00000287611;ENST00000265023;ENST00000447445;ENST00000432028	T;T;T	0.29655	1.56;1.56;1.56	5.2	4.31	0.51392	Proteinase inhibitor I25, cystatin (2);	0.603229	0.15391	N	0.264803	T	0.51805	0.1696	M	0.71581	2.175	0.22017	N	0.999412	D;D	0.89917	0.994;1.0	D;D	0.72075	0.976;0.975	T	0.39014	-0.9634	10	0.51188	T	0.08	-6.5792	10.4191	0.44340	0.0929:0.0:0.9071:0.0	.	32;32	P01042;P01042-2	KNG1_HUMAN;.	Y	32;32;32;20	ENSP00000287611:D32Y;ENSP00000265023:D32Y;ENSP00000396025:D32Y	ENSP00000265023:D32Y	D	+	1	0	KNG1	187918119	0.221000	0.23642	0.035000	0.18076	0.403000	0.30841	2.124000	0.42006	1.302000	0.44855	0.455000	0.32223	GAT	.	.	.	none		0.393	KNG1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317738.1	NM_001102416		T	186435425	G	T	186435425	3	4	219	1	0	0	0	0	1	0	0	0	8434	1174	41	4	96	4	KNG1	3	186435425	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	16938804	186435425	11587005	20	13212											
TBC1D19	55296	hgsc.bcm.edu	37	chr4	26585819	26585819	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggctagggcaggggaaatgTtgcaggaggagtcggacctc	9	6	19	7	1	0	0	0	0	0	0	2	4	0	4	1	7	1	4	1	7	2	2			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr4:26585819T>C	ENST00000264866.4	+	1	282	c.4T>C	c.(4-6)Ttg>Ctg	p.L2L	TBC1D19_ENST00000511789.1_Silent_p.L2L	NM_018317.2	NP_060787.2	Q8N5T2	TBC19_HUMAN	TBC1 domain family, member 19	2							Rab GTPase activator activity (GO:0005097)			breast(4)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	17		Breast(46;0.0503)				AGGGGAAATGTTGCAGGAGGA	0.627																																					p.L2L		Atlas-SNP	.											.	TBC1D19	53	.	0			c.T4C						PASS	.						44	45	45					4																	26585819		2203	4298	6501	SO:0001819	synonymous_variant	55296	exon1			GAAATGTTGCAGG	AK001944	CCDS3439.1, CCDS75115.1	4p15.2	2008-02-05			ENSG00000109680	ENSG00000109680			25624	protein-coding gene	gene with protein product							Standard	XM_006713967		Approved	FLJ11082	uc003gsf.4	Q8N5T2	OTTHUMG00000097797	ENST00000264866.4:c.4T>C	chr4.hg19:g.26585819T>C		54.0	0.0	.		70.0	29.0	.	NM_018317	B9A6M0|Q9NUX1	Silent	SNP	ENST00000264866.4	hg19	CCDS3439.1																																																																																			.	.	.	none		0.627	TBC1D19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215052.2	NM_018317		C	26585819	T	C	26585819	2	2	219	1	0	0	0	0	0	0	0	1	15619	1722	60	3		3	TBC1D19	4	26585819	Silent	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10		26585819	164568457	21	13213											
GRSF1	2926	hgsc.bcm.edu	37	chr4	71702003	71702003	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catactcagggggtggtggaAggtcttccaggtaagtagtt	9	11	15	6	0	2	0	1	0	1	0	3	1	3	1	1	6	1	3	1	6	4	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr4:71702003A>G	ENST00000254799.6	-	2	503	c.386T>C	c.(385-387)cTt>cCt	p.L129P	GRSF1_ENST00000502323.1_5'UTR|GRSF1_ENST00000545193.1_Missense_Mutation_p.L11P|GRSF1_ENST00000508091.1_5'UTR|GRSF1_ENST00000439371.1_5'UTR	NM_002092.3	NP_002083	Q12849	GRSF1_HUMAN	G-rich RNA sequence binding factor 1	129	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				anterior/posterior pattern specification (GO:0009952)|morphogenesis of embryonic epithelium (GO:0016331)|mRNA polyadenylation (GO:0006378)|tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|upper_aerodigestive_tract(2)	17		all_hematologic(202;0.21)	Lung(101;0.235)			GGGTGGTGGAAGGTCTTCCAG	0.413																																					p.L129P		Atlas-SNP	.											.	GRSF1	35	.	0			c.T386C						PASS	.						82	84	83					4																	71702003		1848	4089	5937	SO:0001583	missense	2926	exon2			GGTGGAAGGTCTT	BC040485	CCDS47069.1, CCDS47070.1	4q13	2013-07-16				ENSG00000132463		"RNA binding motif (RRM) containing"	4610	protein-coding gene	gene with protein product		604851				8036161	Standard	NM_001098477		Approved		uc010iia.1	Q12849		ENST00000254799.6:c.386T>C	chr4.hg19:g.71702003A>G	ENSP00000254799:p.Leu129Pro	141.0	0.0	.		154.0	46.0	.	NM_002092	B3KPW0|Q4W5S5|Q6ZST3|Q8IWD6|Q8NBD2	Missense_Mutation	SNP	ENST00000254799.6	hg19	CCDS47069.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.72|14.72	2.619082|2.619082	0.46736|0.46736	.|.	.|.	ENSG00000132463|ENSG00000132463	ENST00000514161|ENST00000254799;ENST00000540657;ENST00000499044;ENST00000545193	.|T;T;T	.|0.21734	.|2.05;2.03;1.99	4.51|4.51	4.51|4.51	0.55191|0.55191	.|RNA recognition motif domain (1);	.|0.718315	.|0.12425	.|N	.|0.470117	T|T	0.15998|0.15998	0.0385|0.0385	N|N	0.22421|0.22421	0.69|0.69	0.80722|0.80722	D|D	1|1	.|P;P	.|0.47350	.|0.79;0.894	.|B;P	.|0.45037	.|0.202;0.467	T|T	0.02917|0.02917	-1.1094|-1.1094	5|10	.|0.45353	.|T	.|0.12	-2.599|-2.599	5.3313|5.3313	0.15934|0.15934	0.6438:0.1816:0.0:0.1746|0.6438:0.1816:0.0:0.1746	.|.	.|42;129	.|B7Z5F9;Q12849	.|.;GRSF1_HUMAN	L|P	66|129;61;102;11	.|ENSP00000254799:L129P;ENSP00000427354:L102P;ENSP00000443380:L11P	.|ENSP00000254799:L129P	F|L	-|-	1|2	0|0	GRSF1|GRSF1	71920867|71920867	0.827000|0.827000	0.29292|0.29292	0.959000|0.959000	0.39883|0.39883	0.674000|0.674000	0.39518|0.39518	3.964000|3.964000	0.56780|0.56780	1.881000|1.881000	0.54492|0.54492	0.533000|0.533000	0.62120|0.62120	TTC|CTT	.	.	.	none		0.413	GRSF1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362642.1	NM_002092		G	71702003	A	G	71702003	3	3	219	1	0	0	0	0	1	0	0	0	6816	72	3	3	1088	3	GRSF1	4	71702003	Missense_Mutation	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	45116184	71702003	119452273	22	13214											
TBC1D9	23158	hgsc.bcm.edu	37	chr4	141600812	141600812	+	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	taaaagcaaaggtggttaatGctgaggtacatccaaccctg	14	9	10	8	0	0	1	0	1	0	0	1	1	1	1	2	3	4	4	2	3	6	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr4:141600812G>A	ENST00000442267.2	-	4	620	c.546C>T	c.(544-546)agC>agT	p.S182S		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	182	GRAM 1.						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)				GGTGGTTAATGCTGAGGTACA	0.448																																					p.S182S		Atlas-SNP	.											.	TBC1D9	198	.	0			c.C546T						PASS	.						69	67	67					4																	141600812		1837	4092	5929	SO:0001819	synonymous_variant	23158	exon4			GTTAATGCTGAGG	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.546C>T	chr4.hg19:g.141600812G>A		61.0	0.0	.		82.0	30.0	.	NM_015130	A6H8U8|D3DNZ1|O94958	Silent	SNP	ENST00000442267.2	hg19	CCDS47136.1																																																																																			.	.	.	none		0.448	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	NM_015130		A	141600812	G	A	141600812	2	1	219	1	0	0	0	0	0	0	0	1	15639	1310	46	2		2	TBC1D9	4	141600812	Silent	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	69898809	141600812	49553464	23	13215											
AHRR	57491	hgsc.bcm.edu	37	chr5	434928	434928	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctggtcccgccccaagcttcGgggtgcacattcctgccata	6	9	10	16	2	0	0	0	0	0	0	3	0	2	0	5	3	3	2	5	3	2	3	rs368088592		TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr5:434928G>A	ENST00000505113.1	+	11	2129	c.2085G>A	c.(2083-2085)tcG>tcA	p.S695S	AHRR_ENST00000316418.5_Silent_p.S713S|AHRR_ENST00000506456.1_Silent_p.S551S|AHRR_ENST00000512529.1_Silent_p.S541S	NM_001242412.1	NP_001229341.1	A9YTQ3	AHRR_HUMAN	aryl-hydrocarbon receptor repressor	695	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)			CCCAAGCTTCGGGGTGCACAT	0.627																																					p.S713S		Atlas-SNP	.											.	AHRR	67	.	0			c.G2139A						PASS	.	G	,	0,4188		0,0,2094	10	15	14		2085,2139	-8.4	0	5		14	1,8379		0,1,4189	no	coding-synonymous,coding-synonymous	AHRR	NM_001242412.1,NM_020731.4	,	0,1,6283	AA,AG,GG		0.0119,0.0,0.0080	,	695/702,713/720	434928	1,12567	2094	4190	6284	SO:0001819	synonymous_variant	57491	exon12			AGCTTCGGGGTGC	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.2085G>A	chr5.hg19:g.434928G>A		121.0	0.0	.		126.0	6.0	.	NM_020731	A7MBN5|D6RAZ1|Q9HAZ3|Q9ULI6	Silent	SNP	ENST00000505113.1	hg19	CCDS56355.1																																																																																			.	.	.	weak		0.627	AHRR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367720.1	NM_020731		A	434928	G	A	434928	2	1	219	1	0	0	0	0	0	0	0	1	417	1103	39	1		1	AHRR	5	434928	Silent	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10		434928	180480332	24	13216											
EGFLAM	133584	hgsc.bcm.edu	37	chr5	38418272	38418272	+	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	acaaaccgaggctttcaaggCtgtgtgcagtcgctcgctgt	8	10	12	11	3	1	0	1	0	0	0	3	1	1	0	1	2	2	5	1	2	2	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr5:38418272C>A	ENST00000354891.3	+	12	1945	c.1599C>A	c.(1597-1599)ggC>ggA	p.G533G	EGFLAM_ENST00000322350.5_Silent_p.G533G|EGFLAM_ENST00000397202.2_Intron|EGFLAM_ENST00000336740.6_Silent_p.G299G	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	533	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)					GCTTTCAAGGCTGTGTGCAGT	0.542																																					p.G533G	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.C1599A						PASS	.						96	100	98					5																	38418272		2203	4300	6503	SO:0001819	synonymous_variant	133584	exon12			TCAAGGCTGTGTG	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.1599C>A	chr5.hg19:g.38418272C>A		153.0	0.0	.		120.0	35.0	.	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Silent	SNP	ENST00000354891.3	hg19	CCDS56363.1																																																																																			.	.	.	none		0.542	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403		A	38418272	C	A	38418272	2	1	219	1	0	0	0	0	0	0	0	1	4968	784	28	4		4	EGFLAM	5	38418272	Silent	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	37983344	38418272	142496988	25	13217											
GPR98	84059	hgsc.bcm.edu	37	chr5	89979468	89979468	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacatagactctgatcctgaTggtgatctcgccttcacctc	9	12	7	13	1	3	4	1	3	2	1	6	4	4	4	3	1	1	0	3	1	2	2			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr5:89979468T>C	ENST00000405460.2	+	28	5826	c.5730T>C	c.(5728-5730)gaT>gaC	p.D1910D		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1910	Calx-beta 13. {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)		CTGATCCTGATGGTGATCTCG	0.418																																					p.D1910D		Atlas-SNP	.											.	GPR98	605	.	0			c.T5730C						PASS	.						69	70	70					5																	89979468		1951	4141	6092	SO:0001819	synonymous_variant	84059	exon28			TCCTGATGGTGAT	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.5730T>C	chr5.hg19:g.89979468T>C		97.0	0.0	.		108.0	38.0	.	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	hg19	CCDS47246.1																																																																																			.	.	.	none		0.418	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		C	89979468	T	C	89979468	2	2	219	1	0	0	0	0	0	0	0	1	6728	1461	51	3		3	GPR98	5	89979468	Silent	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	51561196	89979468	90935792	26	13218											
STK10	6793	hgsc.bcm.edu	37	chr5	171471934	171471934	+	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	aagaacttggcggccttgctTggggtggaggggtttgggca	6	10	19	6	1	0	1	0	0	0	1	0	2	0	2	1	8	2	3	1	8	2	4			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr5:171471934T>G	ENST00000176763.5	-	19	3202	c.2859A>C	c.(2857-2859)ccA>ccC	p.P953P		NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	953					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)			CGGCCTTGCTTGGGGTGGAGG	0.607																																					p.P953P		Atlas-SNP	.											.	STK10	100	.	0			c.A2859C						PASS	.						83	77	79					5																	171471934		2203	4300	6503	SO:0001819	synonymous_variant	6793	exon19			CTTGCTTGGGGTG	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.2859A>C	chr5.hg19:g.171471934T>G		95.0	0.0	.		98.0	5.0	.	NM_005990	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Silent	SNP	ENST00000176763.5	hg19	CCDS34290.1																																																																																			.	.	.	none		0.607	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990		G	171471934	T	G	171471934	2	3	219	1	0	0	0	0	0	0	0	1	15298	1799	63	5		5	STK10	5	171471934	Silent	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	81492466	171471934	9443326	27	13219											
NSD1	64324	hgsc.bcm.edu	37	chr5	176709581	176709584	+	Splice_Site	DEL	AAGT	AAGT	-																															ctatatgctcaccctagacaAagtaagtaatgggaaatgct																										TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	AAGT	AAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr5:176709581_176709584delAAGT	ENST00000439151.2	+	19	6053_6054	c.6008_6009delAAGT	c.(6007-6009)aaa>a	p.K2003fs	NSD1_ENST00000361032.4_Splice_Site_p.K1900fs|NSD1_ENST00000354179.4_Splice_Site_p.K1734fs|NSD1_ENST00000347982.4_Splice_Site_p.K1734fs	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2003	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				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)		ACCCTAGACAAAGTAAGTAATGGG	0.397			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.2003_2003del		Atlas-Indel,Pindel	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.6007_6009del						PASS	.																																			SO:0001630	splice_region_variant	64324	exon19	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	.	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	14234	protein-coding gene	gene with protein product		606681	"Sotos syndrome"	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.6009+1AAGT>-	chr5.hg19:g.176709585_176709588delAAGT		101.0	0.0	0		83.0	24.0	0.289157	NM_022455	Q96PD8|Q96RN7	In_Frame_Del	DEL	ENST00000439151.2	hg19	CCDS4412.1																																																																																			.	.	.	none		0.397	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349	Frame_Shift_Del	-	176709584	AAGT	-	176709581	8	5	219	1	0	1	0	1	0	0	1	0	10676	28	1	0	6078	0	NSD1	5	176709581	Splice_Site	DEL	AAGT	TCGA-MH-A55W-01A-11D-A26P-10	5237647	176709581	4205679	28	13220											
TNXB	7148	hgsc.bcm.edu	37	chr6	32038155	32038155	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacccacagctccccaaggCggggtggggcccctgggctg	5	5	15	16	1	1	0	1	0	0	0	2	0	2	0	5	6	1	2	5	6	1	0			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr6:32038155C>T	ENST00000375244.3	-	14	5228	c.5027G>A	c.(5026-5028)cGc>cAc	p.R1676H	TNXB_ENST00000375247.2_Missense_Mutation_p.R1676H			P22105	TENX_HUMAN	tenascin XB	1758	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CTCCCCAAGGCGGGGTGGGGC	0.597																																					p.R1676H		Atlas-SNP	.											.	TNXB	553	.	0			c.G5027A						PASS	.						14	16	15					6																	32038155		1903	4094	5997	SO:0001583	missense	7148	exon14			CCAAGGCGGGGTG	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.5027G>A	chr6.hg19:g.32038155C>T	ENSP00000364393:p.Arg1676His	49.0	0.0	.		82.0	27.0	.	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	hg19		.	.	.	.	.	.	.	.	.	.	C	11.28	1.593489	0.28357	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.04603	3.59;3.59	4.34	0.318	0.15867	.	0.470849	0.16112	N	0.229047	T	0.03263	0.0095	M	0.88241	2.94	0.23773	N	0.996888	B	0.26775	0.159	B	0.23716	0.048	T	0.22173	-1.0224	10	0.49607	T	0.09	.	8.1222	0.30978	0.0:0.6178:0.0:0.3822	.	1676	P22105-3	.	H	1676	ENSP00000364393:R1676H;ENSP00000364396:R1676H	ENSP00000364393:R1676H	R	-	2	0	TNXB	32146133	0.991000	0.36638	0.989000	0.46669	0.365000	0.29674	0.675000	0.25232	0.160000	0.19432	-0.302000	0.09304	CGC	.	.	.	none		0.597	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		T	32038155	C	T	32038155	3	4	219	1	0	0	0	0	1	0	0	0	16358	768	27	1	9810	1	TNXB	6	32038155	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10		32038155	139076912	29	13221											
KCNK5	8645	hgsc.bcm.edu	37	chr6	39159405	39159412	+	Frame_Shift_Del	DEL	TTGTGGAC	TTGTGGAC	-																															gccgccgcttcttaatggctTtgtggacttccacaaacatg																								rs13208158	byFrequency	TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	TTGTGGAC	TTGTGGAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr6:39159405_39159412delTTGTGGAC	ENST00000359534.3	-	5	1092_1099	c.754_761delGTCCACAA	c.(754-762)gtccacaaafs	p.VHK252fs		NM_003740.3	NP_003731.1	O95279	KCNK5_HUMAN	potassium channel, subfamily K, member 5	252					excretion (GO:0007588)|potassium ion transport (GO:0006813)	integral component of plasma membrane (GO:0005887)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(4)|skin(3)	19						CTTAATGGCTTTGTGGACTTCCACAAAC	0.591																																					p.252_254del		Atlas-Indel,Pindel	.											.	KCNK5	57	.	0			c.755_762del						PASS	.																																			SO:0001589	frameshift_variant	8645	exon5			.	AF084830	CCDS4841.1	6p21	2012-03-07			ENSG00000164626	ENSG00000164626		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6280	protein-coding gene	gene with protein product		603493				9812978, 16382106	Standard	XM_005249456		Approved	K2p5.1, TASK-2	uc003oon.3	O95279	OTTHUMG00000014642	ENST00000359534.3:c.754_761delGTCCACAA	chr6.hg19:g.39159405_39159412delTTGTGGAC	ENSP00000352527:p.Val252fs	169.0	0.0	0		95.0	20.0	0.210526	NM_003740	B2RAQ6|B5TJL2|Q5VV76	Frame_Shift_Del	DEL	ENST00000359534.3	hg19	CCDS4841.1																																																																																			.	.	.	none		0.591	KCNK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040449.1	NM_003740		-	39159412	TTGTGGAC	-	39159405	7	5	219	1	0	1	0	1	0	0	0	0	8076	1841	64	0	742	0	KCNK5	6	39159405	Frame_Shift_Del	DEL	TTGTGGAC	TCGA-MH-A55W-01A-11D-A26P-10	7121250	39159405	131955662	30	13222											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51768400	51768400	+	Missense_Mutation	SNP	T	T	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	agctgaacatcttacctctaTaacattggtgggactgcaga	12	11	9	9	0	2	2	0	1	2	1	2	3	2	3	1	2	5	2	1	2	4	4			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr6:51768400T>G	ENST00000371117.3	-	43	7266	c.6991A>C	c.(6991-6993)Ata>Cta	p.I2331L	PKHD1_ENST00000340994.4_Missense_Mutation_p.I2331L	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2331			I -> K (in ARPKD). {ECO:0000269|PubMed:11919560, ECO:0000269|PubMed:12506140}.		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)					CTTACCTCTATAACATTGGTG	0.478																																					p.I2331L		Atlas-SNP	.											.	PKHD1	927	.	0			c.A6991C						PASS	.						173	163	167					6																	51768400		2203	4300	6503	SO:0001583	missense	5314	exon43			CCTCTATAACATT	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.6991A>C	chr6.hg19:g.51768400T>G	ENSP00000360158:p.Ile2331Leu	97.0	0.0	.		118.0	41.0	.	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	T	7.897	0.733493	0.15574	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.82803	-1.65;-1.65	5.87	-2.49	0.06403	Pectin lyase fold/virulence factor (1);Pectin lyase fold (1);	0.766468	0.11605	N	0.547353	T	0.44074	0.1276	N	0.12182	0.205	0.09310	N	1	B;B;B	0.15141	0.012;0.006;0.012	B;B;B	0.17722	0.008;0.007;0.019	T	0.39440	-0.9614	10	0.44086	T	0.13	.	6.1429	0.20269	0.0:0.2716:0.2385:0.4899	.	2331;2331;2331	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	L	2331	ENSP00000360158:I2331L;ENSP00000341097:I2331L	ENSP00000341097:I2331L	I	-	1	0	PKHD1	51876359	0.002000	0.14202	0.004000	0.12327	0.326000	0.28443	-0.160000	0.10041	-0.465000	0.06953	0.528000	0.53228	ATA	.	.	.	none		0.478	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		G	51768400	T	G	51768400	3	3	219	1	0	0	0	0	1	0	0	0	11978	1406	49	5	5372	5	PKHD1	6	51768400	Missense_Mutation	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	12608995	51768400	119346667	31	13223											
GCM1	8521	hgsc.bcm.edu	37	chr6	52993368	52993369	+	In_Frame_Ins	INS	-	-	AAA																															gctggtcagaggaaaaggatINSaattggaataacagttgtca																										TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr6:52993368_52993369insAAA	ENST00000259803.7	-	6	1157_1158	c.946_947insTTT	c.(946-948)tat>tTTTat	p.315_316insF	RP11-506E9.3_ENST00000566420.1_RNA	NM_003643.3	NP_003634.2	Q9NP62	GCM1_HUMAN	glial cells missing homolog 1 (Drosophila)	315					anatomical structure morphogenesis (GO:0009653)|astrocyte fate commitment (GO:0060018)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|cell differentiation involved in embryonic placenta development (GO:0060706)|positive regulation of syncytium formation by plasma membrane fusion (GO:0060143)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|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)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|skin(1)	24	Lung NSC(77;0.0755)					AGGAAAAGGATAATTGGAATAA	0.48																																					p.Y316delinsFY		Pindel	.											.	GCM1	47	.	0			c.947_948insTTT						PASS	.																																			SO:0001652	inframe_insertion	8521	exon6			.	D88613	CCDS4950.1	6p21-p12	2008-08-29	2001-11-28	2002-09-27	ENSG00000137270	ENSG00000137270			4197	protein-coding gene	gene with protein product		603715	"glial cells missing (Drosophila) homolog a"	GCMA		8962155	Standard	NM_003643		Approved	hGCMa	uc003pbp.3	Q9NP62	OTTHUMG00000014871	ENST00000259803.7:c.946_947insTTT	chr6.hg19:g.52993368_52993369insAAA	ENSP00000259803:p.Asn315_Tyr316insPhe	140.0	0.0	.		112.0	22.0	0.196	NM_003643	Q4VAQ7|Q5T0X0|Q99468|Q9P1X3	In_Frame_Ins	INS	ENST00000259803.7	hg19	CCDS4950.1																																																																																			.	.	.	none		0.48	GCM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040953.1			AAA	52993369	-	AAA	52993368	7	5	219	1	0	1	1	0	0	0	0	0	6304	1406	49	0	367	0	GCM1	6	52993368	In_Frame_Ins	INS	-	TCGA-MH-A55W-01A-11D-A26P-10	1224968	52993368	118121699	32	13224											
AKAP12	9590	hgsc.bcm.edu	37	chr6	151671659	151671659	+	Frame_Shift_Del	DEL	C	C	-																															aaagcaatgggaggagaccaCcagaaagctgatgaggccgg																										TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr6:151671659delC	ENST00000253332.1	+	3	2322	c.2133delC	c.(2131-2133)cacfs	p.H711fs	AKAP12_ENST00000402676.2_Frame_Shift_Del_p.H711fs|AKAP12_ENST00000359755.5_Frame_Shift_Del_p.H606fs|AKAP12_ENST00000354675.6_Frame_Shift_Del_p.H613fs			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	711					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		GAGGAGACCACCAGAAAGCTG	0.532																																					p.H711fs	Melanoma(141;1616 1805 10049 24534 51979)	Atlas-Indel,Pindel	.											.	AKAP12	170	.	0			c.2132delA						PASS	.						96	106	103					6																	151671659		2203	4300	6503	SO:0001589	frameshift_variant	9590	exon4			.	U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"A-kinase anchor proteins"	370	protein-coding gene	gene with protein product	"gravin", "Src-Suppressed C Kinase Substrate"	604698	"A kinase (PRKA) anchor protein (gravin) 12"			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.2133delC	chr6.hg19:g.151671659delC	ENSP00000253332:p.His711fs	155.0	0.0	0		142.0	50.0	0.352113	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Frame_Shift_Del	DEL	ENST00000253332.1	hg19	CCDS5229.1																																																																																			.	.	.	none		0.532	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1			-	151671659	C	-	151671659	7	5	219	1	0	1	0	1	0	0	0	0	448	506	18	0	2172	0	AKAP12	6	151671659	Frame_Shift_Del	DEL	C	TCGA-MH-A55W-01A-11D-A26P-10	98678291	151671659	19443408	33	13225											
ZBTB2	57621	hgsc.bcm.edu	37	chr6	151686673	151686676	+	Frame_Shift_Del	DEL	TTTC	TTTC	-																															cattcagtctagtaagacggTttcttgttcctttttgatgg																								rs143773461		TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	TTTC	TTTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr6:151686673_151686676delTTTC	ENST00000325144.4	-	3	1665_1668	c.1525_1528delGAAA	c.(1525-1530)gaaaccfs	p.ET509fs		NM_020861.1	NP_065912.1	Q8N680	ZBTB2_HUMAN	zinc finger and BTB domain containing 2	509					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E509K(2)		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)		AGTAAGACGGTTTCTTGTTCCTTT	0.446																																					p.509_510del		Atlas-Indel,Pindel	.											.	ZBTB2	30	.	2	Substitution - Missense(2)	lung(1)|skin(1)	c.1526_1529del						PASS	.																																			SO:0001589	frameshift_variant	57621	exon3			.	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.1525_1528delGAAA	chr6.hg19:g.151686673_151686676delTTTC	ENSP00000323183:p.Glu509fs	137.0	0.0	0		127.0	39.0	0.307087	NM_020861	A8K7C7|Q5SZ81|Q9P245	Frame_Shift_Del	DEL	ENST00000325144.4	hg19	CCDS5231.1																																																																																			.	.	.	none		0.446	ZBTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042715.1	NM_020861		-	151686676	TTTC	-	151686673	7	5	219	1	0	1	0	1	0	0	0	0	17540	1725	60	0	20	0	ZBTB2	6	151686673	Frame_Shift_Del	DEL	TTTC	TCGA-MH-A55W-01A-11D-A26P-10	15014	151686673	19428394	34	13226											
BBS9	27241	hgsc.bcm.edu	37	chr7	33380559	33380559	+	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	acttgaacgtttctgtcgtgGtttctcctaactttgattca	7	18	7	9	2	3	2	1	2	2	0	5	2	3	2	1	1	2	2	1	1	2	6			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr7:33380559G>C	ENST00000242067.6	+	11	1770	c.1249G>C	c.(1249-1251)Gtt>Ctt	p.V417L	BBS9_ENST00000354265.4_Missense_Mutation_p.V417L|BBS9_ENST00000396127.2_Missense_Mutation_p.V417L|BBS9_ENST00000355070.2_Missense_Mutation_p.V417L|BBS9_ENST00000350941.3_Missense_Mutation_p.V417L	NM_198428.2	NP_940820.1	Q3SYG4	PTHB1_HUMAN	Bardet-Biedl syndrome 9	417					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)			TTCTGTCGTGGTTTCTCCTAA	0.338									Bardet-Biedl syndrome																												p.V417L		Atlas-SNP	.											.	BBS9	194	.	0			c.G1249C						PASS	.						187	175	179					7																	33380559		2203	4300	6503	SO:0001583	missense	27241	exon11	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GTCGTGGTTTCTC		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.1249G>C	chr7.hg19:g.33380559G>C	ENSP00000242067:p.Val417Leu	19.0	0.0	.		94.0	34.0	.	NM_014451	E9PDC9|P78514|Q7KYS6|Q7KYS7|Q8N570|Q99844|Q99854|Q9Y699|Q9Y6A0	Missense_Mutation	SNP	ENST00000242067.6	hg19	CCDS43566.1	.	.	.	.	.	.	.	.	.	.	G	14.37	2.515586	0.44763	.	.	ENSG00000122507	ENST00000242067;ENST00000350941;ENST00000396127;ENST00000355070;ENST00000354265;ENST00000396132;ENST00000396125;ENST00000537775	D;D;D;D;D	0.84516	-1.86;-1.86;-1.86;-1.86;-1.86	4.48	4.48	0.54585	.	0.000000	0.85682	D	0.000000	D	0.84727	0.5536	M	0.62723	1.935	0.80722	D	1	P;P;B;P	0.34864	0.473;0.473;0.245;0.473	B;B;B;B	0.42112	0.133;0.376;0.169;0.376	T	0.82524	-0.0414	10	0.31617	T	0.26	-21.4487	12.2466	0.54574	0.0859:0.0:0.9141:0.0	.	417;417;417;417	Q3SYG4-2;E9PDC9;Q3SYG4-4;Q3SYG4	.;.;.;PTHB1_HUMAN	L	417;417;417;417;417;417;417;295	ENSP00000242067:V417L;ENSP00000313122:V417L;ENSP00000379433:V417L;ENSP00000347182:V417L;ENSP00000346214:V417L	ENSP00000242067:V417L	V	+	1	0	BBS9	33347084	0.998000	0.40836	0.341000	0.25589	0.957000	0.61999	3.026000	0.49689	2.433000	0.82419	0.650000	0.86243	GTT	.	.	.	none		0.338	BBS9-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329064.1			C	33380559	G	C	33380559	3	2	219	1	0	0	0	0	1	0	0	0	1342	1261	44	4	1287	4	BBS9	7	33380559	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10		33380559	125758104	35	13227											
GBAS	2631	hgsc.bcm.edu	37	chr7	56046042	56046042	+	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	ttgaattttcttttgtttcaGttcacaatgttaaaccggaa	11	18	6	6	1	3	1	2	1	1	0	3	2	3	2	1	1	1	3	1	1	5	8			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr7:56046042G>C	ENST00000322090.3	+	3	261		c.e3-1		GBAS_ENST00000446778.1_Intron|GBAS_ENST00000487370.1_Splice_Site	NM_001483.2	NP_001474.1	O75323	NIPS2_HUMAN	glioblastoma amplified sequence						ATP biosynthetic process (GO:0006754)|negative regulation of ATP citrate synthase activity (GO:2000984)|oxidative phosphorylation (GO:0006119)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrion (GO:0005739)				breast(1)|central_nervous_system(1)|large_intestine(1)|lung(2)	5	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			TTTTGTTTCAGTTCACAATGT	0.323																																					.		Atlas-SNP	.											.	GBAS	16	.	0			c.233-1G>C						PASS	.						178	160	166					7																	56046042		2203	4300	6503	SO:0001630	splice_region_variant	2631	exon3			GTTTCAGTTCACA	AF029786	CCDS5521.1, CCDS56488.1	7p12	2014-03-11			ENSG00000146729	ENSG00000146729			4179	protein-coding gene	gene with protein product		603004				9615231, 9661659, 20888800	Standard	NM_001483		Approved	NIPSNAP2	uc003tre.2	O75323	OTTHUMG00000022932	ENST00000322090.3:c.233-1G>C	chr7.hg19:g.56046042G>C		102.0	0.0	.		213.0	89.0	.	NM_001483	C9IYJ3|O43801|Q53X96	Splice_Site	SNP	ENST00000322090.3	hg19	CCDS5521.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.279038	0.80692	.	.	ENSG00000146729	ENST00000322090	.	.	.	5.8	5.8	0.92144	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.0588	0.93078	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GBAS	56013536	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.510000	0.98004	2.744000	0.94065	0.655000	0.94253	.	.	.	.	none		0.323	GBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251524.1	NM_001483	Intron	C	56046042	G	C	56046042	5	2	219	1	0	0	0	0	0	0	1	0	6276	1043	36	4	242	4	GBAS	7	56046042	Splice_Site	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	22665483	56046042	103092621	36	13228											
TAF6	6878	hgsc.bcm.edu	37	chr7	99711723	99711723	+	Frame_Shift_Del	DEL	T	T	-																															tgacctcatccgttagcagcTggcaggtctcctcctgaatc																										TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr7:99711723delT	ENST00000344095.4	-	2	635	c.110delA	c.(109-111)cagfs	p.Q37fs	TAF6_ENST00000497233.1_5'Flank|TAF6_ENST00000452041.1_Frame_Shift_Del_p.Q37fs|RP11-506M12.1_ENST00000494221.1_RNA|TAF6_ENST00000418432.2_5'UTR|TAF6_ENST00000472509.1_Frame_Shift_Del_p.Q94fs|TAF6_ENST00000453269.2_Frame_Shift_Del_p.Q37fs|TAF6_ENST00000437822.2_Frame_Shift_Del_p.Q74fs	NM_005641.3	NP_005632.1	P49848	TAF6_HUMAN	TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80kDa	37					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)					CGTTAGCAGCTGGCAGGTCTC	0.582																																					p.Q74fs		Atlas-Indel,Pindel	.											TAF6,NS,carcinoma,0,1	TAF6	55	.	0			c.222delG						PASS	.						140	126	130					7																	99711723		2203	4300	6503	SO:0001589	frameshift_variant	6878	exon2			.		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.110delA	chr7.hg19:g.99711723delT	ENSP00000344537:p.Gln37fs	276.0	0.0	0		421.0	177.0	0.420428	NM_001190415	A4D2B2|A4D2B3|B4DT11|D6W5U2|Q6AI29	Frame_Shift_Del	DEL	ENST00000344095.4	hg19	CCDS5686.1																																																																																			.	.	.	none		0.582	TAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337024.2	NM_005641		-	99711723	T	-	99711723	7	5	219	1	0	1	0	1	0	0	0	0	15542	1580	55	0	1979	0	TAF6	7	99711723	Frame_Shift_Del	DEL	T	TCGA-MH-A55W-01A-11D-A26P-10	43665681	99711723	59426940	37	13229											
GOLGA2	2801	hgsc.bcm.edu	37	chr9	131021446	131021446	+	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	gccctcaccaactccctcacCtgggtttcctgcaactcttg	6	11	6	18	0	3	0	2	0	1	0	5	0	5	0	5	1	3	2	5	1	2	2			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr9:131021446C>T	ENST00000421699.2	-	19	2028	c.2016G>A	c.(2014-2016)caG>caA	p.Q672Q	GOLGA2_ENST00000609374.1_Splice_Site_p.Q660Q|AL590708.1_ENST00000408370.1_RNA	NM_004486.4	NP_004477.3	Q08379	GOGA2_HUMAN	golgin A2	672					mitotic cell cycle (GO:0000278)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34						ACTCCCTCACCTGGGTTTCCT	0.632																																					p.Q672Q		Atlas-SNP	.											.	GOLGA2	69	.	0			c.G2016A						PASS	.						42	46	45					9																	131021446		2203	4300	6503	SO:0001630	splice_region_variant	2801	exon19			CCTCACCTGGGTT	L06147	CCDS6896.2	9q34.13	2010-06-28	2010-02-12		ENSG00000167110	ENSG00000167110			4425	protein-coding gene	gene with protein product	"Golgi matrix protein GM130", "SY11 protein"	602580	"golgi autoantigen, golgin subfamily a, 2"			8315394	Standard	NM_004486		Approved	GM130, golgin-95	uc011maw.2	Q08379	OTTHUMG00000020732	ENST00000421699.2:c.2016+1G>A	chr9.hg19:g.131021446C>T		73.0	0.0	.		61.0	22.0	.	NM_004486	Q6GRM9|Q9BRB0|Q9NYF9	Silent	SNP	ENST00000421699.2	hg19	CCDS6896.2																																																																																			.	.	.	none		0.632	GOLGA2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054358.2	NM_004486	Silent	T	131021446	C	T	131021446	5	4	219	1	0	0	0	0	0	0	1	0	6559	695	24	2	1024	2	GOLGA2	9	131021446	Splice_Site	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10		131021446	10191985	38	13230											
NRG3	10718	hgsc.bcm.edu	37	chr10	83635808	83635808	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcctcctaccttcacgatTctactccctcctggaccctg	5	12	4	20	1	2	0	1	0	1	0	6	2	6	1	7	1	2	0	7	1	2	4			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr10:83635808T>C	ENST00000404547.1	+	1	712	c.712T>C	c.(712-714)Tct>Cct	p.S238P	NRG3_ENST00000372141.2_Missense_Mutation_p.S238P|NRG3_ENST00000404576.2_5'Flank|NRG3_ENST00000372142.2_5'Flank|NRG3_ENST00000556918.1_5'Flank			P56975	NRG3_HUMAN	neuregulin 3	238	Ser/Thr-rich.				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)		CCTTCACGATTCTACTCCCTC	0.602																																					p.S238P		Atlas-SNP	.											.	NRG3	301	.	0			c.T712C						PASS	.						100	74	83					10																	83635808		2203	4300	6503	SO:0001583	missense	10718	exon1			CACGATTCTACTC	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.712T>C	chr10.hg19:g.83635808T>C	ENSP00000384796:p.Ser238Pro	125.0	0.0	.		150.0	62.0	.	NM_001165972	A4D7U1|Q0PEH2|Q5VYH3	Missense_Mutation	SNP	ENST00000404547.1	hg19	CCDS31233.1	.	.	.	.	.	.	.	.	.	.	T	17.05	3.288753	0.59976	.	.	ENSG00000185737	ENST00000372141;ENST00000404547;ENST00000537287	T;T	0.32515	1.45;1.46	4.14	4.14	0.48551	.	0.174325	0.27831	N	0.017667	T	0.35913	0.0948	L	0.36672	1.1	0.80722	D	1	D;D	0.64830	0.994;0.994	P;P	0.54759	0.76;0.76	T	0.13282	-1.0515	10	0.59425	D	0.04	-18.5043	11.474	0.50286	0.0:0.0:0.0:1.0	.	238;238	B9EGV5;P56975-4	.;.	P	238	ENSP00000361214:S238P;ENSP00000384796:S238P	ENSP00000361214:S238P	S	+	1	0	NRG3	83625788	0.998000	0.40836	0.059000	0.19551	0.993000	0.82548	5.633000	0.67825	1.879000	0.54435	0.529000	0.55759	TCT	.	.	.	none		0.602	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086		C	83635808	T	C	83635808	3	2	219	1	0	0	0	0	1	0	0	0	10656	1783	62	3	714	3	NRG3	10	83635808	Missense_Mutation	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10		83635808	51898939	39	13231											
CYP2C8	1558	hgsc.bcm.edu	37	chr10	96818110	96818110	+	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	acctgctccattttgatcagGaagcaatcgataaagtcccg	12	10	8	11	2	1	1	1	1	0	0	4	3	3	2	3	1	2	2	3	1	4	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr10:96818110G>C	ENST00000371270.3	-	5	895	c.801C>G	c.(799-801)ttC>ttG	p.F267L	CYP2C8_ENST00000539050.1_Missense_Mutation_p.F181L|CYP2C8_ENST00000535898.1_Missense_Mutation_p.F165L	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	267					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)	TTTTGATCAGGAAGCAATCGA	0.353																																					p.F267L		Atlas-SNP	.											CYP2C8,NS,carcinoma,0,1	CYP2C8	73	.	0			c.C801G						PASS	.						163	145	151					10																	96818110		2203	4300	6503	SO:0001583	missense	1558	exon5			GATCAGGAAGCAA	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.801C>G	chr10.hg19:g.96818110G>C	ENSP00000360317:p.Phe267Leu	68.0	0.0	.		121.0	48.0	.	NM_000770	A8K9N8|B0AZN2|B7Z1F6|Q5VX93|Q8WWB1|Q9UCZ9	Missense_Mutation	SNP	ENST00000371270.3	hg19	CCDS7438.1	.	.	.	.	.	.	.	.	.	.	G	11.16	1.557052	0.27827	.	.	ENSG00000138115	ENST00000371270;ENST00000535868;ENST00000535898;ENST00000539050	T;T;T	0.06687	3.27;3.27;3.27	4.17	-0.451	0.12214	.	0.000000	0.85682	U	0.000000	T	0.07638	0.0192	L	0.29908	0.895	0.29573	N	0.849721	P;P;P;P	0.50617	0.922;0.937;0.779;0.937	P;P;P;P	0.50109	0.459;0.594;0.631;0.49	T	0.16424	-1.0403	10	0.49607	T	0.09	.	4.5328	0.12013	0.2874:0.0:0.5591:0.1535	.	181;165;235;267	F5H7Q9;B7Z1F6;B7Z8S1;P10632	.;.;.;CP2C8_HUMAN	L	267;234;165;181	ENSP00000360317:F267L;ENSP00000445062:F165L;ENSP00000442343:F181L	ENSP00000360317:F267L	F	-	3	2	CYP2C8	96808100	0.998000	0.40836	0.741000	0.31004	0.173000	0.22820	0.270000	0.18607	0.011000	0.14865	0.305000	0.20034	TTC	.	.	.	none		0.353	CYP2C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049499.2	NM_000770		C	96818110	G	C	96818110	3	2	219	1	0	0	0	0	1	0	0	0	4169	1165	41	4	691	4	CYP2C8	10	96818110	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	13182302	96818110	38716637	40	13232											
SORBS1	10580	hgsc.bcm.edu	37	chr10	97096528	97096528	+	Missense_Mutation	SNP	T	T	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	cgcctgcccccctctctgctTtcctctcatattgtccactc	3	14	4	20	1	2	0	1	0	2	0	7	0	4	0	6	0	2	1	6	0	1	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr10:97096528T>G	ENST00000361941.3	-	28	3415	c.3389A>C	c.(3388-3390)aAa>aCa	p.K1130T	SORBS1_ENST00000393949.1_Intron|SORBS1_ENST00000277982.5_Missense_Mutation_p.K989T|SORBS1_ENST00000607232.1_Intron|SORBS1_ENST00000354106.3_Intron|SORBS1_ENST00000371241.1_Intron|SORBS1_ENST00000371249.2_Intron|SORBS1_ENST00000306402.6_Intron|SORBS1_ENST00000371247.2_Missense_Mutation_p.K1130T|SORBS1_ENST00000371239.1_Intron|SORBS1_ENST00000371245.3_Intron|SORBS1_ENST00000353505.5_Intron|SORBS1_ENST00000371246.2_Missense_Mutation_p.K989T|SORBS1_ENST00000347291.4_Intron|SORBS1_ENST00000371227.4_Missense_Mutation_p.K1084T	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)		CCTCTCTGCTTTCCTCTCATA	0.552																																					p.K1130T		Atlas-SNP	.											.	SORBS1	185	.	0			c.A3389C						PASS	.						74	71	72					10																	97096528		2203	4300	6503	SO:0001583	missense	10580	exon28			TCTGCTTTCCTCT	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.3389A>C	chr10.hg19:g.97096528T>G	ENSP00000355136:p.Lys1130Thr	93.0	0.0	.		116.0	50.0	.	NM_001034954		Missense_Mutation	SNP	ENST00000361941.3	hg19	CCDS31255.1	.	.	.	.	.	.	.	.	.	.	T	12.02	1.813778	0.32053	.	.	ENSG00000095637	ENST00000371247;ENST00000371227;ENST00000371246;ENST00000361941;ENST00000277982	T;T;T;T;T	0.08984	3.09;3.03;3.38;3.09;3.38	5.58	3.22	0.36961	.	0.488362	0.17388	N	0.176042	T	0.04815	0.0130	N	0.19112	0.55	0.80722	D	1	B;B;B	0.30281	0.275;0.079;0.275	B;B;B	0.27076	0.076;0.035;0.076	T	0.46331	-0.9199	10	0.15499	T	0.54	-0.5924	7.5752	0.27931	0.0:0.1794:0.0:0.8206	.	1084;1130;989	Q9BX66-11;Q9BX66;Q9BX66-2	.;SRBS1_HUMAN;.	T	1130;1084;989;1130;989	ENSP00000360293:K1130T;ENSP00000360271:K1084T;ENSP00000360292:K989T;ENSP00000355136:K1130T;ENSP00000277982:K989T	ENSP00000277982:K989T	K	-	2	0	SORBS1	97086518	0.873000	0.30073	0.996000	0.52242	0.854000	0.48673	0.144000	0.16135	0.406000	0.25560	0.459000	0.35465	AAA	.	.	.	none		0.552	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049517.1			G	97096528	T	G	97096528	3	3	219	1	0	0	0	0	1	0	0	0	14940	1841	64	5	569	5	SORBS1	10	97096528	Missense_Mutation	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	278418	97096528	38438219	41	13233											
GPR123	84435	hgsc.bcm.edu	37	chr10	134912186	134912187	+	Frame_Shift_Del	DEL	TT	TT	-																															ggccggcacacgctcctgaaTttctgcttccacgcggccct																										TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr10:134912186_134912187delTT	ENST00000392607.3	+	4	610_611	c.174_175delTT	c.(172-177)aatttcfs	p.F59fs	GPR123_ENST00000607359.1_Frame_Shift_Del_p.F779fs	NM_001083909.1	NP_001077378.1	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	59					G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(3)	14		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		CGCTCCTGAATTTCTGCTTCCA	0.658																																					p.58_58del		Atlas-Indel,Pindel	.											.	GPR123	118	.	0			c.173_174del						PASS	.																																			SO:0001589	frameshift_variant	84435	exon4			.	AB058731	CCDS41580.1	10q26	2014-08-08			ENSG00000197177	ENSG00000197177		"-", "GPCR / Class B : Orphans"	13838	protein-coding gene	gene with protein product		612302				12565841	Standard	XM_005252695		Approved	KIAA1828	uc001llw.3	Q86SQ6	OTTHUMG00000019304	ENST00000392607.3:c.174_175delTT	chr10.hg19:g.134912186_134912187delTT	ENSP00000376384:p.Phe59fs	45.0	0.0	0		55.0	18.0	0.327273	NM_001083909	A5HL16|A6NG50|Q5T234|Q86SN7|Q96JJ9	Frame_Shift_Del	DEL	ENST00000392607.3	hg19	CCDS41580.1																																																																																			.	.	.	none		0.658	GPR123-003	NOVEL	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051113.2			-	134912187	TT	-	134912186	7	5	219	1	0	1	0	1	0	0	0	0	6644	1490	52	0	184	0	GPR123	10	134912186	Frame_Shift_Del	DEL	TT	TCGA-MH-A55W-01A-11D-A26P-10	37815658	134912186	622561	42	13234											
MARK2	2011	hgsc.bcm.edu	37	chr11	63671476	63671476	+	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	agcctaaccatgccagggtcCcgggcctccacggcttctgc	6	7	11	17	2	1	0	0	0	1	0	3	0	3	0	6	3	4	1	6	3	1	2			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr11:63671476C>G	ENST00000509502.2	+	15	1894	c.1431C>G	c.(1429-1431)tcC>tcG	p.S477S	MARK2_ENST00000377809.4_Silent_p.S511S|MARK2_ENST00000508192.1_Intron|MARK2_ENST00000425897.2_Intron|MARK2_ENST00000513765.2_Silent_p.S478S|MARK2_ENST00000402010.2_Silent_p.S511S|MARK2_ENST00000502399.3_Silent_p.S510S|MARK2_ENST00000377810.3_Intron|MARK2_ENST00000315032.8_Silent_p.S511S|MARK2_ENST00000350490.7_Intron|MARK2_ENST00000413835.2_Intron|MARK2_ENST00000408948.3_Intron|MARK2_ENST00000361128.5_Intron	NM_017490.3	NP_059672.2			MAP/microtubule affinity-regulating kinase 2											autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33						TGCCAGGGTCCCGGGCCTCCA	0.652																																					p.S511S		Atlas-SNP	.											.	MARK2	91	.	0			c.C1533G						PASS	.						39	41	40					11																	63671476		1818	4074	5892	SO:0001819	synonymous_variant	2011	exon15			AGGGTCCCGGGCC	BC008771	CCDS8051.1, CCDS41665.1, CCDS8051.2, CCDS53649.1, CCDS53650.1, CCDS53651.1	11q13.1	2013-06-27	2002-07-26	2002-08-01	ENSG00000072518	ENSG00000072518			3332	protein-coding gene	gene with protein product	"ELKL motif kinase 1", "serine/threonine kinase", "protein-serine/threonine kinase", "Ser/Thr protein kinase PAR-1B"	600526	"ELKL motif kinase"	EMK1		9730619, 10516437	Standard	NM_017490		Approved	PAR-1, Par1b, PAR-1B	uc001nxw.3	Q7KZI7	OTTHUMG00000160504	ENST00000509502.2:c.1431C>G	chr11.hg19:g.63671476C>G		24.0	0.0	.		38.0	13.0	.	NM_001039469		Silent	SNP	ENST00000509502.2	hg19	CCDS41665.1																																																																																			.	.	.	none		0.652	MARK2-003	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000360862.2	NM_017490		G	63671476	C	G	63671476	2	3	219	1	0	0	0	0	0	0	0	1	9320	610	22	4		4	MARK2	11	63671476	Silent	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10		63671476	71335040	43	13235											
DPF2	5977	hgsc.bcm.edu	37	chr11	65107956	65107956	+	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	gcctgcctttcttggactcaCagaccggagtagcccagagc	8	8	11	14	1	2	2	1	0	1	2	2	4	2	4	4	2	3	1	4	2	1	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr11:65107956C>G	ENST00000528416.1	+	2	266	c.133C>G	c.(133-135)Cag>Gag	p.Q45E	DPF2_ENST00000252268.4_Missense_Mutation_p.Q45E|DPF2_ENST00000532264.1_Intron|DPF2_ENST00000415073.2_Missense_Mutation_p.Q45E	NM_006268.4	NP_006259.1	Q92785	REQU_HUMAN	D4, zinc and double PHD fingers family 2	45					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						CTTGGACTCACAGACCGGAGT	0.562																																					p.Q45E		Atlas-SNP	.											.	DPF2	54	.	0			c.C133G						PASS	.						102	103	103					11																	65107956		2201	4297	6498	SO:0001583	missense	5977	exon2			GACTCACAGACCG	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.133C>G	chr11.hg19:g.65107956C>G	ENSP00000436901:p.Gln45Glu	165.0	0.0	.		137.0	53.0	.	NM_006268	A8K7C9|B4DT58	Missense_Mutation	SNP	ENST00000528416.1	hg19	CCDS8100.1	.	.	.	.	.	.	.	.	.	.	C	32	5.118519	0.94385	.	.	ENSG00000133884	ENST00000528416;ENST00000415073;ENST00000252268	D;D;D	0.92647	-3.06;-3.06;-3.08	5.52	5.52	0.82312	.	0.000000	0.35870	N	0.002937	D	0.96269	0.8783	M	0.83953	2.67	0.80722	D	1	D;D;D	0.76494	0.963;0.999;0.963	D;D;D	0.91635	0.973;0.999;0.973	D	0.96656	0.9485	10	0.87932	D	0	-25.3906	16.9414	0.86219	0.0:1.0:0.0:0.0	.	45;45;45	B4DT58;E9PN04;Q92785	.;.;REQU_HUMAN	E	45	ENSP00000436901:Q45E;ENSP00000399714:Q45E;ENSP00000252268:Q45E	ENSP00000252268:Q45E	Q	+	1	0	DPF2	64864532	1.000000	0.71417	0.968000	0.41197	0.994000	0.84299	7.818000	0.86416	2.588000	0.87417	0.655000	0.94253	CAG	.	.	.	none		0.562	DPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387293.3	NM_006268		G	65107956	C	G	65107956	3	3	219	1	0	0	0	0	1	0	0	0	4719	479	17	4	139	4	DPF2	11	65107956	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	1436480	65107956	69898560	44	13236											
FAT3	120114	hgsc.bcm.edu	37	chr11	92599961	92599961	+	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	gcggcagcggccctggaatcTtgggcatctcgggccgtgct	4	8	16	13	4	2	0	0	0	2	0	3	1	2	1	2	5	2	3	2	5	1	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr11:92599961T>A	ENST00000298047.6	+	21	11730	c.11713T>A	c.(11713-11715)Ttg>Atg	p.L3905M	FAT3_ENST00000409404.2_Missense_Mutation_p.L3905M|FAT3_ENST00000525166.1_Missense_Mutation_p.L3755M|FAT3_ENST00000533797.1_Missense_Mutation_p.L240M			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3905	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				CCCTGGAATCTTGGGCATCTC	0.592										TCGA Ovarian(4;0.039)																											p.L3905M		Atlas-SNP	.											.	FAT3	1822	.	0			c.T11713A						PASS	.						29	34	32					11																	92599961		2046	4196	6242	SO:0001583	missense	120114	exon21			GGAATCTTGGGCA	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.11713T>A	chr11.hg19:g.92599961T>A	ENSP00000298047:p.Leu3905Met	88.0	0.0	.		102.0	43.0	.	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	hg19		.	.	.	.	.	.	.	.	.	.	T	14.78	2.638068	0.47153	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166;ENST00000533797	T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.66	5.77	-6.79	0.01715	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	T	0.65688	0.2715	L	0.35414	1.06	0.80722	D	1	P;P	0.39601	0.68;0.645	B;B	0.43194	0.249;0.411	T	0.61367	-0.7077	9	0.49607	T	0.09	.	24.6348	0.99991	0.0:0.8789:0.0:0.1211	.	3905;3905	Q8TDW7-3;Q8TDW7	.;FAT3_HUMAN	M	3905;3905;3755;240	ENSP00000298047:L3905M;ENSP00000387040:L3905M;ENSP00000432586:L3755M;ENSP00000436399:L240M	ENSP00000298047:L3905M	L	+	1	2	FAT3	92239609	0.086000	0.21541	0.260000	0.24451	0.815000	0.46073	-0.484000	0.06528	-1.317000	0.02292	-0.379000	0.06801	TTG	.	.	.	none		0.592	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		A	92599961	T	A	92599961	3	1	219	1	0	0	0	0	1	0	0	0	5698	1606	56	5	11795	5	FAT3	11	92599961	Missense_Mutation	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	27492005	92599961	42406555	45	13237											
C2CD2L	9854	hgsc.bcm.edu	37	chr11	118984691	118984704	+	Splice_Site	DEL	TTTCCAAGGTAACA	TTTCCAAGGTAACA	-																															cactctcatcatctctggtgTttccaaggtaacagggctct																										TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	TTTCCAAGGTAACA	TTTCCAAGGTAACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr11:118984691_118984704delTTTCCAAGGTAACA	ENST00000528586.1	+	8	930_937	c.860_867delTTTCCAAGGTAACA	c.(859-867)gtttccaag>g	p.VSK287fs	C2CD2L_ENST00000336702.3_Splice_Site_p.VSK540fs			O14523	C2C2L_HUMAN	C2CD2-like	539						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|large_intestine(2)|lung(8)|prostate(1)	13						ATCTCTGGTGTTTCCAAGGTAACAGGGCTCTGGG	0.598																																					p.540_542del		Atlas-Indel,Pindel	.											.	C2CD2L	39	.	0			c.1618_1626del						PASS	.																																			SO:0001630	splice_region_variant	9854	exon12			.	AK025223	CCDS8413.1	11q23.3	2008-04-22	2008-04-22	2008-04-22		ENSG00000172375			29000	protein-coding gene	gene with protein product			"transmembrane protein 24"	TMEM24		15289880	Standard	XM_005271738		Approved	KIAA0285	uc001pvn.3	O14523		ENST00000528586.1:c.867+1TTTCCAAGGTAACA>-	chr11.hg19:g.118984691_118984704delTTTCCAAGGTAACA		141.0	0.0	0		126.0	30.0	0.238095	NM_014807	Q86UT7|Q86V04|Q8N522|Q8TBN4|Q96G10	In_Frame_Del	DEL	ENST00000528586.1	hg19																																																																																				.	.	.	none		0.598	C2CD2L-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000388199.2	NM_014807	Frame_Shift_Del	-	118984704	TTTCCAAGGTAACA	-	118984691	8	5	219	1	0	1	0	1	0	0	1	0	2155	1725	60	0	1665	0	C2CD2L	11	118984691	Splice_Site	DEL	TTTCCAAGGTAACA	TCGA-MH-A55W-01A-11D-A26P-10	26384730	118984691	16021825	46	13238											
CCDC15	80071	hgsc.bcm.edu	37	chr11	124847425	124847425	+	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	ggataaatacaggaataagaGgagagttgcccattaaggtc	16	8	12	5	0	0	2	0	0	0	2	1	5	0	4	1	4	2	1	1	4	6	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr11:124847425G>C	ENST00000344762.5	+	6	941	c.682G>C	c.(682-684)Gga>Cga	p.G228R	CCDC15_ENST00000529051.1_Missense_Mutation_p.G228R	NM_025004.2	NP_079280.2	Q0P6D6	CCD15_HUMAN	coiled-coil domain containing 15	228						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)		AGGAATAAGAGGAGAGTTGCC	0.378																																					p.G228R		Atlas-SNP	.											.	CCDC15	134	.	0			c.G682C						PASS	.						67	65	66					11																	124847425		1828	4076	5904	SO:0001583	missense	80071	exon6			ATAAGAGGAGAGT	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.682G>C	chr11.hg19:g.124847425G>C	ENSP00000341684:p.Gly228Arg	24.0	0.0	.		57.0	19.0	.	NM_025004	Q9H8U7	Missense_Mutation	SNP	ENST00000344762.5	hg19	CCDS44756.1	.	.	.	.	.	.	.	.	.	.	G	2.444	-0.327892	0.05314	.	.	ENSG00000149548	ENST00000529051;ENST00000344762	T;T	0.31510	1.49;1.57	3.57	0.63	0.17693	.	.	.	.	.	T	0.20455	0.0492	L	0.31926	0.97	0.09310	N	1	B	0.12013	0.005	B	0.10450	0.005	T	0.22591	-1.0212	9	0.46703	T	0.11	-1.5802	5.3366	0.15961	0.3864:0.0:0.6136:0.0	.	228	Q0P6D6	CCD15_HUMAN	R	228	ENSP00000435403:G228R;ENSP00000341684:G228R	ENSP00000341684:G228R	G	+	1	0	CCDC15	124352635	0.000000	0.05858	0.006000	0.13384	0.005000	0.04900	0.169000	0.16641	0.314000	0.23086	-0.363000	0.07495	GGA	.	.	.	none		0.378	CCDC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387131.1	NM_025004		C	124847425	G	C	124847425	3	2	219	1	0	0	0	0	1	0	0	0	2786	1001	35	4	700	4	CCDC15	11	124847425	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	5862734	124847425	10159091	47	13239											
STT3A	3703	hgsc.bcm.edu	37	chr11	125478106	125478106	+	Missense_Mutation	SNP	T	T	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	gcaagttgaatccacaacaaTttgaagttcttttccggagc	12	12	8	9	1	1	2	0	2	1	0	3	3	3	3	2	1	2	3	2	1	5	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr11:125478106T>G	ENST00000529196.1	+	10	1089	c.883T>G	c.(883-885)Ttt>Gtt	p.F295V	STT3A_ENST00000392708.4_Missense_Mutation_p.F295V|STT3A_ENST00000531491.1_Missense_Mutation_p.F203V			P46977	STT3A_HUMAN	STT3A, subunit of the oligosaccharyltransferase complex (catalytic)	295					cellular protein metabolic process (GO:0044267)|co-translational protein modification (GO:0043686)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			NS(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	33	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)		TCCACAACAATTTGAAGTTCT	0.507																																					p.F295V		Atlas-SNP	.											.	STT3A	52	.	0			c.T883G						PASS	.						145	136	139					11																	125478106		2201	4299	6500	SO:0001583	missense	3703	exon9			CAACAATTTGAAG	BC020965	CCDS8458.1, CCDS60998.1	11q23.3	2013-03-06	2013-03-06	2006-02-07	ENSG00000134910	ENSG00000134910	2.4.99.18		6172	protein-coding gene	gene with protein product	"dolichyl-diphosphooligosaccharide protein glycotransferase"	601134	"integral membrane protein 1", "STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)", "STT3A, cataylic subunit of the oligosaccharyltransferase complex"	ITM1		8941377, 8634329, 10234787	Standard	NM_152713		Approved	TMC, MGC9042, STT3-A	uc001qcd.2	P46977	OTTHUMG00000165852	ENST00000529196.1:c.883T>G	chr11.hg19:g.125478106T>G	ENSP00000436962:p.Phe295Val	105.0	0.0	.		96.0	43.0	.	NM_152713	B4DJ24|E9PNQ1|Q86XU9|Q8TE35|Q8WUB4	Missense_Mutation	SNP	ENST00000529196.1	hg19	CCDS8458.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	34|34	5.361297|5.361297	0.95877|0.95877	.|.	.|.	ENSG00000134910|ENSG00000134910	ENST00000392708;ENST00000529196;ENST00000531491|ENST00000526726	.|.	.|.	.|.	5.64|5.64	5.64|5.64	0.86602|0.86602	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.84561|0.84561	0.5499|0.5499	M|M	0.91818|0.91818	3.245|3.245	0.80722|0.80722	D|D	1|1	P;P;D|.	0.53151|.	0.923;0.925;0.958|.	P;P;P|.	0.59012|.	0.622;0.85;0.85|.	D|D	0.88159|0.88159	0.2856|0.2856	9|5	0.66056|.	D|.	0.02|.	-19.0074|-19.0074	15.5287|15.5287	0.75932|0.75932	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	203;203;295|.	B4DJ24;E9PNQ1;P46977|.	.;.;STT3A_HUMAN|.	V|K	295;295;203|52	.|.	ENSP00000376472:F295V|.	F|N	+|+	1|3	0|2	STT3A|STT3A	124983316|124983316	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.990000|0.990000	0.78478|0.78478	8.040000|8.040000	0.89188|0.89188	2.148000|2.148000	0.66965|0.66965	0.533000|0.533000	0.62120|0.62120	TTT|AAT	.	.	.	none		0.507	STT3A-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386691.1	NM_152713		G	125478106	T	G	125478106	3	3	219	1	0	0	0	0	1	0	0	0	15345	1493	52	5	913	5	STT3A	11	125478106	Missense_Mutation	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	630681	125478106	9528410	48	13240											
IQSEC3	440073	hgsc.bcm.edu	37	chr12	275007	275007	+	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	cagaagttcgtggaggacctGaaggagtccattgctgaggt	10	9	15	7	1	0	3	0	2	0	1	2	6	1	6	2	4	1	2	2	4	2	2			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr12:275007G>A	ENST00000538872.1	+	11	3040	c.2922G>A	c.(2920-2922)ctG>ctA	p.L974L	RP11-598F7.6_ENST00000537295.1_lincRNA|RP11-598F7.5_ENST00000540136.1_RNA|IQSEC3_ENST00000382841.2_Silent_p.L671L|IQSEC3_ENST00000326261.4_Silent_p.L974L			Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	974	PH.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		TGGAGGACCTGAAGGAGTCCA	0.602																																					p.L974L		Atlas-SNP	.											.	IQSEC3	154	.	0			c.G2922A						PASS	.						80	76	77					12																	275007		2203	4300	6503	SO:0001819	synonymous_variant	440073	exon11			GGACCTGAAGGAG	AB029033	CCDS31725.1, CCDS53728.1	12p13.33	2014-03-18			ENSG00000120645	ENSG00000120645			29193	protein-coding gene	gene with protein product		612118				10470851	Standard	NM_001170738		Approved	KIAA1110, MGC30156	uc001qhw.2	Q9UPP2	OTTHUMG00000167975	ENST00000538872.1:c.2922G>A	chr12.hg19:g.275007G>A		143.0	0.0	.		195.0	100.0	.	NM_001170738	A6NIF2|A6NKV9|Q8TB43	Silent	SNP	ENST00000538872.1	hg19	CCDS53728.1																																																																																			.	.	.	none		0.602	IQSEC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397382.3	XM_495902		A	275007	G	A	275007	2	1	219	1	0	0	0	0	0	0	0	1	7826	1277	45	2		2	IQSEC3	12	275007	Silent	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10		275007	133576888	49	13241											
SFRS2IP	9169	hgsc.bcm.edu	37	chr12	46342224	46342224	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaagttaatcactaaccttaTacagcttttagaattttcat	15	16	3	7	0	2	1	2	0	0	1	2	1	2	1	1	0	3	2	1	0	7	8			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr12:46342224T>C	ENST00000369367.3	-	5	627	c.394A>G	c.(394-396)Ata>Gta	p.I132V	SCAF11_ENST00000419565.2_Missense_Mutation_p.I132V	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	132					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						ACTAACCTTATACAGCTTTTA	0.308																																					p.I132V		Atlas-SNP	.											.	SCAF11	145	.	0			c.A394G						PASS	.						116	104	108					12																	46342224		1804	4076	5880	SO:0001583	missense	9169	exon5			ACCTTATACAGCT	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.394A>G	chr12.hg19:g.46342224T>C	ENSP00000358374:p.Ile132Val	25.0	0.0	.		25.0	13.0	.	NM_004719	A6NEU9|A6NLW5|Q8IW59	Missense_Mutation	SNP	ENST00000369367.3	hg19	CCDS8748.2	.	.	.	.	.	.	.	.	.	.	T	0.096	-1.159474	0.01686	.	.	ENSG00000139218	ENST00000369367;ENST00000419565;ENST00000547018	T;T;T	0.40756	1.02;1.02;1.02	5.76	2.03	0.26663	.	2.058940	0.02882	U	0.132917	T	0.21103	0.0508	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21895	-1.0232	10	0.10377	T	0.69	.	7.6398	0.28288	0.0:0.2476:0.0:0.7524	.	132	Q99590	SCAFB_HUMAN	V	132;132;72	ENSP00000358374:I132V;ENSP00000413036:I132V;ENSP00000446746:I72V	ENSP00000358374:I132V	I	-	1	0	SCAF11	44628491	0.005000	0.15991	0.024000	0.17045	0.748000	0.42578	-0.080000	0.11339	0.095000	0.17434	0.460000	0.39030	ATA	.	.	.	none		0.308	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719		C	46342224	T	C	46342224	3	2	219	1	0	0	0	0	1	0	0	0	14190	1406	49	3	4041	3	SFRS2IP	12	46342224	Missense_Mutation	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	46067217	46342224	87509671	50	13242											
MTERFD3	80298	hgsc.bcm.edu	37	chr12	107371368	107371368	+	Missense_Mutation	SNP	A	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	tttaatggtgccacagggttAaataatggccttactttttt	10	17	8	6	0	0	0	0	0	0	0	0	0	0	0	2	3	2	1	2	3	5	8			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr12:107371368A>C	ENST00000552029.1	-	2	3193	c.1125T>G	c.(1123-1125)ttT>ttG	p.F375L	C12orf23_ENST00000551237.1_Intron|MTERFD3_ENST00000240050.4_Missense_Mutation_p.F375L|MTERFD3_ENST00000392830.2_Missense_Mutation_p.F375L			Q49AM1	MTEF2_HUMAN		375					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)	transcription regulatory region DNA binding (GO:0044212)			breast(1)|kidney(1)|large_intestine(2)|lung(3)	7						CCACAGGGTTAAATAATGGCC	0.353																																					p.F375L		Atlas-SNP	.											.	MTERFD3	32	.	0			c.T1125G						PASS	.						114	112	113					12																	107371368		2202	4300	6502	SO:0001583	missense	80298	exon3			AGGGTTAAATAAT																												ENST00000552029.1:c.1125T>G	chr12.hg19:g.107371368A>C	ENSP00000447651:p.Phe375Leu	54.0	0.0	.		124.0	68.0	.	NM_001033050	Q53HM2|Q9H4L6|Q9H7Y9	Missense_Mutation	SNP	ENST00000552029.1	hg19	CCDS9111.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.167376	0.78339	.	.	ENSG00000120832	ENST00000392830;ENST00000240050;ENST00000552029	T;T;T	0.26373	1.74;1.74;1.74	5.95	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.33614	0.0869	M	0.63843	1.955	0.58432	D	0.999997	P	0.48503	0.911	P	0.49387	0.609	T	0.11867	-1.0570	10	0.87932	D	0	7.5321	8.7341	0.34516	0.859:0.0:0.141:0.0	.	375	Q49AM1	MTER3_HUMAN	L	375	ENSP00000376575:F375L;ENSP00000240050:F375L;ENSP00000447651:F375L	ENSP00000240050:F375L	F	-	3	2	MTERFD3	105895498	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	5.017000	0.64047	2.272000	0.75746	0.460000	0.39030	TTT	.	.	.	none		0.353	MTERFD3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406835.1			C	107371368	A	C	107371368	3	2	219	1	0	0	0	0	1	0	0	0	9928	359	13	5	36	5	MTERFD3	12	107371368	Missense_Mutation	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	61029144	107371368	26480527	51	13243											
MMP17	4326	hgsc.bcm.edu	37	chr12	132334421	132334421	+	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	ccgtctccgacttcagcctcCcgcctggcggcatcgacgct	4	8	10	19	6	2	0	1	0	1	0	5	2	3	0	5	2	1	2	5	2	0	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr12:132334421C>T	ENST00000360564.1	+	9	1381	c.1279C>T	c.(1279-1281)Ccg>Tcg	p.P427S	MMP17_ENST00000535004.1_Intron|MMP17_ENST00000535291.1_Missense_Mutation_p.P343S	NM_016155.4	NP_057239.4	Q9ULZ9	MMP17_HUMAN	matrix metallopeptidase 17 (membrane-inserted)	427					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)	CTTCAGCCTCCCGCCTGGCGG	0.587																																					p.P427S		Atlas-SNP	.											.	MMP17	77	.	0			c.C1279T						PASS	.						105	109	108					12																	132334421		2203	4300	6503	SO:0001583	missense	4326	exon9			AGCCTCCCGCCTG	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.1279C>T	chr12.hg19:g.132334421C>T	ENSP00000353767:p.Pro427Ser	217.0	0.0	.		270.0	85.0	.	NM_016155	Q14850	Missense_Mutation	SNP	ENST00000360564.1	hg19	CCDS31927.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.629492	0.87660	.	.	ENSG00000198598	ENST00000360564;ENST00000535291;ENST00000534865;ENST00000542648	T;T;T;T	0.04603	3.59;3.59;3.59;3.59	4.48	4.48	0.54585	Hemopexin/matrixin (2);	0.064020	0.64402	D	0.000006	T	0.23492	0.0568	M	0.83483	2.645	0.80722	D	1	D	0.65815	0.995	D	0.68039	0.955	T	0.04509	-1.0946	10	0.72032	D	0.01	.	17.1756	0.86841	0.0:1.0:0.0:0.0	.	427	Q9ULZ9	MMP17_HUMAN	S	427;343;268;57	ENSP00000353767:P427S;ENSP00000441106:P343S;ENSP00000442104:P268S;ENSP00000439542:P57S	ENSP00000353767:P427S	P	+	1	0	MMP17	130900374	1.000000	0.71417	0.995000	0.50966	0.701000	0.40568	7.727000	0.84838	2.054000	0.61138	0.471000	0.43371	CCG	.	.	.	none		0.587	MMP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397757.1	NM_016155		T	132334421	C	T	132334421	3	4	219	1	0	0	0	0	1	0	0	0	9663	623	22	2	1313	2	MMP17	12	132334421	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	24963053	132334421	1517474	52	13244											
STK24	8428	hgsc.bcm.edu	37	chr13	99127511	99127511	+	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	gatgtcctcttacctttaatGtctctgtggattttcttctc	5	20	6	10	0	4	0	0	0	4	0	7	2	5	1	2	1	1	0	2	1	2	6			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr13:99127511G>T	ENST00000376547.3	-	4	613	c.468C>A	c.(466-468)gaC>gaA	p.D156E	STK24_ENST00000397517.2_Missense_Mutation_p.D144E|STK24_ENST00000539966.1_Missense_Mutation_p.D125E	NM_003576.3	NP_003567.2	Q9Y6E0	STK24_HUMAN	serine/threonine kinase 24	156	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of cell migration (GO:0030336)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of axon regeneration (GO:0048679)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	17	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			TACCTTTAATGTCTCTGTGGA	0.443																																					p.D156E		Atlas-SNP	.											.	STK24	40	.	0			c.C468A						PASS	.						108	99	102					13																	99127511		2203	4300	6503	SO:0001583	missense	8428	exon4			TTTAATGTCTCTG	AF024636	CCDS9488.1, CCDS32001.1, CCDS66573.1	13q31.2-q32.3	2010-06-25	2010-06-25		ENSG00000102572	ENSG00000102572			11403	protein-coding gene	gene with protein product	"STE20-like kinase 3", "sterile 20-like kinase 3"	604984	"serine/threonine kinase 24 (Ste20, yeast homolog)"			9353338, 10644707	Standard	NM_003576		Approved	MST-3, MST3, MST3B, STK3, STE20	uc001vnn.1	Q9Y6E0	OTTHUMG00000017250	ENST00000376547.3:c.468C>A	chr13.hg19:g.99127511G>T	ENSP00000365730:p.Asp156Glu	119.0	0.0	.		123.0	25.0	.	NM_003576	O14840|Q5JV92	Missense_Mutation	SNP	ENST00000376547.3	hg19	CCDS9488.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.3|20.3	3.964958|3.964958	0.74131|0.74131	.|.	.|.	ENSG00000102572|ENSG00000102572	ENST00000397517;ENST00000376547;ENST00000539966;ENST00000376533;ENST00000543110|ENST00000444574	D;D;D|.	0.92911|.	-3.13;-3.13;-3.13|.	4.93|4.93	-3.84|-3.84	0.04256|0.04256	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|.	U|.	0.000020|.	D|D	0.84361|0.84361	0.5455|0.5455	H|H	0.97340|0.97340	3.985|3.985	0.58432|0.58432	D|D	0.999999|0.999999	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.91635|.	0.999;0.999;0.999|.	D|D	0.85372|0.85372	0.1114|0.1114	10|5	0.87932|.	D|.	0|.	.|.	11.1814|11.1814	0.48631|0.48631	0.5388:0.0:0.4612:0.0|0.5388:0.0:0.4612:0.0	.|.	125;144;156|.	B4DR80;Q5U0E6;Q9Y6E0|.	.;.;STK24_HUMAN|.	E|N	144;156;125;132;144|62	ENSP00000380651:D144E;ENSP00000365730:D156E;ENSP00000442539:D125E|.	ENSP00000365716:D132E|.	D|H	-|-	3|1	2|0	STK24|STK24	97925512|97925512	0.972000|0.972000	0.33761|0.33761	0.957000|0.957000	0.39632|0.39632	0.955000|0.955000	0.61496|0.61496	0.333000|0.333000	0.19768|0.19768	-0.885000|-0.885000	0.03971|0.03971	-0.390000|-0.390000	0.06520|0.06520	GAC|CAT	.	.	.	none		0.443	STK24-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045549.2	NM_003576		T	99127511	G	T	99127511	3	4	219	1	0	0	0	0	1	0	0	0	15305	1368	48	4	895	4	STK24	13	99127511	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10		99127511	16042367	53	13245											
CIDEB	27141	hgsc.bcm.edu	37	chr14	24775587	24775587	+	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	ataggcctcttacccttgtaGggctccagctctgaccagac	8	10	9	14	0	2	2	0	1	2	1	3	2	3	2	4	2	2	3	4	2	3	4			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr14:24775587G>C	ENST00000336557.5	-	6	1631	c.329C>G	c.(328-330)cCt>cGt	p.P110R	CIDEB_ENST00000554411.1_Missense_Mutation_p.P110R|CIDEB_ENST00000258807.5_Missense_Mutation_p.P110R|NOP9_ENST00000267425.3_3'UTR|LTB4R2_ENST00000528054.1_5'Flank			Q9UHD4	CIDEB_HUMAN	cell death-inducing DFFA-like effector b	110	CIDE-N. {ECO:0000255|PROSITE- ProRule:PRU00447}.				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)		TACCCTTGTAGGGCTCCAGCT	0.562																																					p.P110R		Atlas-SNP	.											.	CIDEB	17	.	0			c.C329G						PASS	.						140	111	121					14																	24775587		2203	4300	6503	SO:0001583	missense	27141	exon5			CTTGTAGGGCTCC	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.329C>G	chr14.hg19:g.24775587G>C	ENSP00000337731:p.Pro110Arg	139.0	0.0	.		150.0	51.0	.	NM_014430	D3DS73|Q546V8|Q9NNW9	Missense_Mutation	SNP	ENST00000336557.5	hg19	CCDS32056.1	.	.	.	.	.	.	.	.	.	.	G	14.46	2.541298	0.45280	.	.	ENSG00000136305	ENST00000554411;ENST00000336557;ENST00000258807;ENST00000541830	T;T;T	0.48522	0.81;0.81;0.81	4.43	4.43	0.53597	Caspase-activated nuclease CIDE-N (2);	0.163888	0.56097	D	0.000036	T	0.67468	0.2896	M	0.87827	2.91	0.80722	D	1	P	0.37038	0.579	P	0.53224	0.721	T	0.72371	-0.4314	10	0.72032	D	0.01	-12.5195	11.7635	0.51918	0.0:0.0:0.8233:0.1767	.	110	Q9UHD4	CIDEB_HUMAN	R	110	ENSP00000451089:P110R;ENSP00000337731:P110R;ENSP00000258807:P110R	ENSP00000258807:P110R	P	-	2	0	CIDEB	23845427	0.995000	0.38212	0.513000	0.27749	0.217000	0.24651	2.732000	0.47352	2.307000	0.77673	0.561000	0.74099	CCT	.	.	.	none		0.562	CIDEB-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414120.1			C	24775587	G	C	24775587	3	2	219	1	0	0	0	0	1	0	0	0	3428	1000	35	4	342	4	CIDEB	14	24775587	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10		24775587	82573953	54	13246											
ACTR10	55860	hgsc.bcm.edu	37	chr14	58680398	58680398	+	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	ttggggagcactacccctagGaggaaaagctcttcacaagt	12	8	11	10	0	2	0	1	0	1	0	2	3	2	3	2	4	3	2	2	4	5	4			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr14:58680398G>C	ENST00000254286.4	+	6	580	c.500G>C	c.(499-501)gGa>gCa	p.G167A		NM_018477.2	NP_060947.1	Q9NZ32	ARP10_HUMAN	actin-related protein 10 homolog (S. cerevisiae)	167					microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|dynactin complex (GO:0005869)				central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	13						CTACCCCTAGGAGGAAAAGCT	0.363																																					p.G167A		Atlas-SNP	.											.	ACTR10	33	.	0			c.G500C						PASS	.						68	66	67					14																	58680398		2203	4300	6503	SO:0001583	missense	55860	exon6			CCCTAGGAGGAAA	AF220190	CCDS32090.1	14q23.1	2014-08-08			ENSG00000131966	ENSG00000131966			17372	protein-coding gene	gene with protein product						12857853	Standard	NM_018477		Approved	HARP11, ACTR11, Arp11	uc001xdf.3	Q9NZ32	OTTHUMG00000171049	ENST00000254286.4:c.500G>C	chr14.hg19:g.58680398G>C	ENSP00000254286:p.Gly167Ala	34.0	0.0	.		27.0	16.0	.	NM_018477	Q9H9Y5|Q9NWY2	Missense_Mutation	SNP	ENST00000254286.4	hg19	CCDS32090.1	.	.	.	.	.	.	.	.	.	.	G	16.72	3.201439	0.58234	.	.	ENSG00000131966	ENST00000543474;ENST00000254286	D	0.94497	-3.44	5.8	5.8	0.92144	.	0.101891	0.64402	D	0.000002	D	0.88066	0.6337	N	0.13003	0.285	0.80722	D	1	B	0.27166	0.17	B	0.30716	0.119	D	0.83755	0.0211	10	0.02654	T	1	-16.7897	17.2104	0.86929	0.0:0.0:1.0:0.0	.	167	Q9NZ32	ARP10_HUMAN	A	167	ENSP00000254286:G167A	ENSP00000254286:G167A	G	+	2	0	ACTR10	57750151	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.523000	0.81856	2.748000	0.94277	0.655000	0.94253	GGA	.	.	.	none		0.363	ACTR10-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411405.1			C	58680398	G	C	58680398	3	2	219	1	0	0	0	0	1	0	0	0	208	1174	41	4	522	4	ACTR10	14	58680398	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	33904811	58680398	48669142	55	13247											
SPTLC2	9517	hgsc.bcm.edu	37	chr14	78036838	78036838	+	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	agctcctctagttcttcatgCttgtccaggtttcctgtgtg	4	17	9	11	0	3	0	1	0	2	0	6	0	6	0	3	1	2	4	3	1	1	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr14:78036838C>A	ENST00000216484.2	-	5	838	c.645G>T	c.(643-645)aaG>aaT	p.K215N		NM_004863.3	NP_004854.1	O15270	SPTC2_HUMAN	serine palmitoyltransferase, long chain base subunit 2	215					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphinganine biosynthetic process (GO:0046511)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|serine C-palmitoyltransferase complex (GO:0017059)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(5)	19			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0346)	L-Serine(DB00133)	GTTCTTCATGCTTGTCCAGGT	0.368																																					p.K215N		Atlas-SNP	.											.	SPTLC2	55	.	0			c.G645T						PASS	.						128	115	119					14																	78036838		2203	4300	6503	SO:0001583	missense	9517	exon5			TTCATGCTTGTCC	AB011098	CCDS9865.1	14q24.3	2014-09-17			ENSG00000100596	ENSG00000100596	2.3.1.50		11278	protein-coding gene	gene with protein product		605713				8921873, 9363775	Standard	NM_004863		Approved	KIAA0526, LCB2, LCB2A, hLCB2a	uc001xub.3	O15270		ENST00000216484.2:c.645G>T	chr14.hg19:g.78036838C>A	ENSP00000216484:p.Lys215Asn	64.0	0.0	.		75.0	34.0	.	NM_004863	Q16685	Missense_Mutation	SNP	ENST00000216484.2	hg19	CCDS9865.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.04|12.04	1.817411|1.817411	0.32145|0.32145	.|.	.|.	ENSG00000100596|ENSG00000100596	ENST00000554901|ENST00000216484	.|D	.|0.90444	.|-2.67	5.49|5.49	1.55|1.55	0.23275|0.23275	.|Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	.|0.169622	.|0.56097	.|D	.|0.000039	D|D	0.82559|0.82559	0.5063|0.5063	L|L	0.27053|0.27053	0.805|0.805	0.54753|0.54753	D|D	0.999983|0.999983	.|B	.|0.17038	.|0.02	.|B	.|0.20577	.|0.03	T|T	0.71119|0.71119	-0.4685|-0.4685	5|10	.|0.34782	.|T	.|0.22	-25.2504|-25.2504	10.0683|10.0683	0.42317|0.42317	0.0:0.4966:0.0:0.5034|0.0:0.4966:0.0:0.5034	.|.	.|215	.|O15270	.|SPTC2_HUMAN	S|N	152|215	.|ENSP00000216484:K215N	.|ENSP00000216484:K215N	A|K	-|-	1|3	0|2	SPTLC2|SPTLC2	77106591|77106591	0.942000|0.942000	0.31987|0.31987	0.999000|0.999000	0.59377|0.59377	0.996000|0.996000	0.88848|0.88848	0.022000|0.022000	0.13511|0.13511	0.071000|0.071000	0.16664|0.16664	-0.137000|-0.137000	0.14449|0.14449	GCA|AAG	.	.	.	none		0.368	SPTLC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414030.1	NM_004863		A	78036838	C	A	78036838	3	1	219	1	0	0	0	0	1	0	0	0	15136	796	28	4	1075	4	SPTLC2	14	78036838	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	19356440	78036838	29312702	56	13248											
C14orf159	80017	hgsc.bcm.edu	37	chr14	91681816	91681816	+	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	ctgtactcatgtgctgtccaCagtcagtacctgaggaaagc	10	10	10	11	0	2	1	2	1	0	0	3	2	3	2	2	1	4	3	2	1	3	2			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr14:91681816C>T	ENST00000523771.1	+	13	2220	c.1617C>T	c.(1615-1617)caC>caT	p.H539H	C14orf159_ENST00000523816.1_Silent_p.H539H|C14orf159_ENST00000412671.2_Silent_p.H544H|C14orf159_ENST00000525393.2_Silent_p.H415H|C14orf159_ENST00000520328.1_Silent_p.H487H|C14orf159_ENST00000256324.10_Silent_p.H544H|C14orf159_ENST00000518868.1_Silent_p.H544H|C14orf159_ENST00000521077.2_Silent_p.H504H|C14orf159_ENST00000428926.2_Silent_p.H539H|C14orf159_ENST00000522322.1_Silent_p.H539H			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	539						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)		GTGCTGTCCACAGTCAGTACC	0.552																																					p.H544H		Atlas-SNP	.											.	C14orf159	57	.	0			c.C1632T						PASS	.						117	103	108					14																	91681816		2203	4300	6503	SO:0001819	synonymous_variant	80017	exon13			TGTCCACAGTCAG	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.1617C>T	chr14.hg19:g.91681816C>T		117.0	0.0	.		95.0	39.0	.	NM_001102368	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Silent	SNP	ENST00000523771.1	hg19	CCDS32141.1	.	.	.	.	.	.	.	.	.	.	C	3.836	-0.034789	0.07543	.	.	ENSG00000133943	ENST00000522816	.	.	.	5.34	-3.48	0.04739	.	.	.	.	.	T	0.28466	0.0704	.	.	.	0.09310	N	0.999996	.	.	.	.	.	.	T	0.34900	-0.9810	4	.	.	.	.	7.4016	0.26967	0.0:0.1871:0.1388:0.6741	.	.	.	.	I	140	.	.	T	+	2	0	C14orf159	90751569	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.541000	0.06099	-0.508000	0.06540	-0.175000	0.13238	ACA	.	.	.	none		0.552	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952		T	91681816	C	T	91681816	2	4	219	1	0	0	0	0	0	0	0	1	1757	477	17	2		2	C14orf159	14	91681816	Silent	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	13644978	91681816	15667724	57	13249											
MARK3	4140	hgsc.bcm.edu	37	chr14	103969341	103969341	+	Frame_Shift_Del	DEL	G	G	-																															ggacatgatgcgggaaatccGcaaagtgttggacgccaata																										TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr14:103969341delG	ENST00000429436.2	+	18	2549	c.2039delG	c.(2038-2040)cgcfs	p.R680fs	MARK3_ENST00000416682.2_Frame_Shift_Del_p.R679fs|MARK3_ENST00000216288.7_Frame_Shift_Del_p.R640fs|MARK3_ENST00000440884.3_Frame_Shift_Del_p.R586fs|MARK3_ENST00000553942.1_Frame_Shift_Del_p.R671fs|MARK3_ENST00000303622.9_Frame_Shift_Del_p.R656fs|MARK3_ENST00000335102.5_Frame_Shift_Del_p.R703fs|MARK3_ENST00000561071.1_3'UTR	NM_001128918.1|NM_001128919.1	NP_001122390.1|NP_001122391.1	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	680						plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.I639_K641del(2)		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)			CGGGAAATCCGCAAAGTGTTG	0.532																																					p.R680fs		Atlas-Indel,Pindel	.											MARK3,NS,carcinoma,0,1	MARK3	86	.	2	Deletion - In frame(2)	central_nervous_system(2)	c.2038delC						PASS	.						69	71	71					14																	103969341		2055	4220	6275	SO:0001589	frameshift_variant	4140	exon18			.	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.2039delG	chr14.hg19:g.103969341delG	ENSP00000411397:p.Arg680fs	303.0	0.0	0		203.0	69.0	0.339901	NM_001128918	O60219|Q86TT8|Q8TB41|Q8WX83|Q96RG1|Q9UMY9|Q9UN34	Frame_Shift_Del	DEL	ENST00000429436.2	hg19	CCDS45165.1																																																																																			.	.	.	none		0.532	MARK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415144.1	NM_001128918		-	103969341	G	-	103969341	7	5	219	1	0	1	0	1	0	0	0	0	9321	1087	38	0	2109	0	MARK3	14	103969341	Frame_Shift_Del	DEL	G	TCGA-MH-A55W-01A-11D-A26P-10	12287525	103969341	3380199	58	13250											
FAM63B	54629	hgsc.bcm.edu	37	chr15	59139573	59139573	+	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	tgggaaagcctacacaacgtAgatggtgatggaaatttctg	13	10	12	6	1	1	2	0	1	1	1	1	4	1	4	1	3	3	1	1	3	5	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr15:59139573A>T	ENST00000559228.1	+	7	1528	c.1446A>T	c.(1444-1446)gtA>gtT	p.V482V	FAM63B_ENST00000450403.2_Silent_p.V482V			Q8NBR6	FA63B_HUMAN	family with sequence similarity 63, member B	482										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						TACACAACGTAGATGGTGATG	0.388																																					p.V482V		Atlas-SNP	.											.	FAM63B	33	.	0			c.A1446T						PASS	.						143	132	135					15																	59139573		1828	4082	5910	SO:0001819	synonymous_variant	54629	exon7			CAACGTAGATGGT	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.1446A>T	chr15.hg19:g.59139573A>T		37.0	0.0	.		48.0	17.0	.	NM_001040450	B2RTT8|Q9ULQ6	Silent	SNP	ENST00000559228.1	hg19	CCDS42046.1																																																																																			.	.	.	none		0.388	FAM63B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416230.1	NM_019092		T	59139573	A	T	59139573	2	4	219	1	0	0	0	0	0	0	0	1	5604	407	15	5		5	FAM63B	15	59139573	Silent	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10		59139573	43391819	59	13251											
ACAN	176	hgsc.bcm.edu	37	chr15	89400337	89400337	+	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	tctggaatagaggatgtcagTgaacttccttcaggagaagg	12	10	13	6	0	3	3	2	1	1	2	4	6	4	5	1	4	1	0	1	4	4	3			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr15:89400337T>A	ENST00000561243.1	+	11	4521	c.4521T>A	c.(4519-4521)agT>agA	p.S1507R	ACAN_ENST00000352105.7_Missense_Mutation_p.S1507R|ACAN_ENST00000439576.2_Missense_Mutation_p.S1507R|ACAN_ENST00000559004.1_Missense_Mutation_p.S1507R			P16112	PGCA_HUMAN	aggrecan	1508	CS-2.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			AGGATGTCAGTGAACTTCCTT	0.493																																					p.S1507R		Atlas-SNP	.											.	ACAN	220	.	0			c.T4521A						PASS	.						69	70	70					15																	89400337		1870	4099	5969	SO:0001583	missense	176	exon12			TGTCAGTGAACTT	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.4521T>A	chr15.hg19:g.89400337T>A	ENSP00000453342:p.Ser1507Arg	39.0	0.0	.		50.0	13.0	.	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	hg19	CCDS53970.1	.	.	.	.	.	.	.	.	.	.	T	14.33	2.503317	0.44558	.	.	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	D;D	0.97016	-4.21;-4.21	3.27	0.774	0.18521	.	.	.	.	.	D	0.97309	0.9120	M	0.79926	2.475	0.09310	N	1	D;D	0.76494	0.999;0.998	D;D	0.72982	0.979;0.953	D	0.91248	0.5027	9	0.56958	D	0.05	.	6.8295	0.23902	0.0:0.3522:0.0:0.6478	.	1507;1507	E7ENV9;E7EX88	.;.	R	1507;1507;1393	ENSP00000387356:S1507R;ENSP00000341615:S1507R	ENSP00000268134:S1393R	S	+	3	2	ACAN	87201341	0.000000	0.05858	0.002000	0.10522	0.944000	0.59088	-0.304000	0.08199	0.050000	0.15949	0.260000	0.18958	AGT	.	.	.	none		0.493	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		A	89400337	T	A	89400337	3	1	219	1	0	0	0	0	1	0	0	0	117	1693	59	5	4563	5	ACAN	15	89400337	Missense_Mutation	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	30260764	89400337	13131055	60	13252											
RBBP6	5930	hgsc.bcm.edu	37	chr16	24581079	24581079	+	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	tgataaaaccaaacggaagaAtgatggatctgctgtgtcca	15	9	10	7	1	1	3	0	2	1	1	2	5	2	5	2	2	3	1	2	2	5	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr16:24581079A>T	ENST00000319715.4	+	17	3500	c.3068A>T	c.(3067-3069)aAt>aTt	p.N1023I	RBBP6_ENST00000348022.2_Missense_Mutation_p.N989I|RBBP6_ENST00000381039.3_Intron	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1023	Interaction with RB1. {ECO:0000250}.				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)		AAACGGAAGAATGATGGATCT	0.383																																					p.N1023I		Atlas-SNP	.											.	RBBP6	158	.	0			c.A3068T						PASS	.						89	93	92					16																	24581079		2197	4300	6497	SO:0001583	missense	5930	exon17			GGAAGAATGATGG		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.3068A>T	chr16.hg19:g.24581079A>T	ENSP00000317872:p.Asn1023Ile	37.0	0.0	.		80.0	28.0	.	NM_006910	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Missense_Mutation	SNP	ENST00000319715.4	hg19	CCDS10621.1	.	.	.	.	.	.	.	.	.	.	A	14.65	2.597918	0.46318	.	.	ENSG00000122257	ENST00000319715;ENST00000348022	T;T	0.14516	2.5;2.5	5.66	1.57	0.23409	.	0.405156	0.23413	N	0.048451	T	0.06280	0.0162	N	0.19112	0.55	0.23724	N	0.997013	B;B	0.22983	0.078;0.047	B;B	0.21151	0.033;0.014	T	0.31971	-0.9924	10	0.28530	T	0.3	-9.0723	1.0512	0.01580	0.2899:0.3403:0.1901:0.1797	.	989;1023	Q7Z6E9-2;Q7Z6E9	.;RBBP6_HUMAN	I	1023;989	ENSP00000317872:N1023I;ENSP00000316291:N989I	ENSP00000317872:N1023I	N	+	2	0	RBBP6	24488580	0.343000	0.24818	0.990000	0.47175	0.994000	0.84299	0.309000	0.19332	-0.006000	0.14370	0.533000	0.62120	AAT	.	.	.	none		0.383	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910		T	24581079	A	T	24581079	3	4	219	1	0	0	0	0	1	0	0	0	13116	101	4	5	3188	5	RBBP6	16	24581079	Missense_Mutation	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10		24581079	65773674	61	13253											
ARHGEF15	22899	hgsc.bcm.edu	37	chr17	8215790	8215790	+	Missense_Mutation	SNP	T	T	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	tggctcagaatggctctgccTcagctcctggcactgtgcgg	5	10	13	13	1	3	1	2	0	1	1	4	1	4	1	2	4	3	4	2	4	1	0			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr17:8215790T>G	ENST00000361926.3	+	2	543	c.433T>G	c.(433-435)Tca>Gca	p.S145A	ARHGEF15_ENST00000421050.1_Missense_Mutation_p.S145A	NM_173728.3	NP_776089.2	O94989	ARHGF_HUMAN	Rho guanine nucleotide exchange factor (GEF) 15	145					negative regulation of synapse maturation (GO:2000297)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|regulation of catalytic activity (GO:0050790)|retina vasculature morphogenesis in camera-type eye (GO:0061299)	cytoplasm (GO:0005737)|dendrite (GO:0030425)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(9)|large_intestine(5)|lung(11)|ovary(5)|prostate(3)|skin(2)|urinary_tract(1)	37						TGGCTCTGCCTCAGCTCCTGG	0.672																																					p.S145A		Atlas-SNP	.											.	ARHGEF15	97	.	0			c.T433G						PASS	.						54	54	54					17																	8215790		2203	4300	6503	SO:0001583	missense	22899	exon2			TCTGCCTCAGCTC	AB020722	CCDS11139.1	17p13.1	2011-11-16			ENSG00000198844	ENSG00000198844		"Rho guanine nucleotide exchange factors"	15590	protein-coding gene	gene with protein product	"Rho guanine exchange factor (GEF) 15"	608504				10048485	Standard	NM_173728		Approved	KIAA0915, Vsm-RhoGEF, ARGEF15, FLJ13791, MGC44868	uc002glc.3	O94989	OTTHUMG00000108187	ENST00000361926.3:c.433T>G	chr17.hg19:g.8215790T>G	ENSP00000355026:p.Ser145Ala	54.0	0.0	.		74.0	35.0	.	NM_025014	A8K6G1|Q8N449|Q9H8B4	Missense_Mutation	SNP	ENST00000361926.3	hg19	CCDS11139.1	.	.	.	.	.	.	.	.	.	.	T	11.22	1.574696	0.28092	.	.	ENSG00000198844	ENST00000361926;ENST00000455564;ENST00000421050	T;T	0.74632	-0.86;-0.86	5.12	4.03	0.46877	.	1.787260	0.03046	N	0.153884	T	0.79569	0.4468	L	0.29908	0.895	0.24301	N	0.99513	D;D;P	0.58268	0.982;0.982;0.884	D;D;B	0.67548	0.952;0.952;0.262	T	0.62053	-0.6935	10	0.45353	T	0.12	-10.5299	7.7269	0.28765	0.0:0.0947:0.0:0.9053	.	145;145;46	D3DTR7;O94989;B4DTR5	.;ARHGF_HUMAN;.	A	145;46;145	ENSP00000355026:S145A;ENSP00000412505:S145A	ENSP00000355026:S145A	S	+	1	0	ARHGEF15	8156515	0.954000	0.32549	0.913000	0.36048	0.921000	0.55340	1.645000	0.37238	0.969000	0.38237	0.454000	0.30748	TCA	.	.	.	none		0.672	ARHGEF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226993.2	NM_173728		G	8215790	T	G	8215790	3	3	219	1	0	0	0	0	1	0	0	0	898	1551	54	5	435	5	ARHGEF15	17	8215790	Missense_Mutation	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10		8215790	72979420	62	13254											
FBXO47	494188	hgsc.bcm.edu	37	chr17	37099134	37099134	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtttccacttagcattaggAgacgtgcattattctctaga	10	15	8	8	1	1	2	0	0	1	2	3	3	2	2	1	1	2	3	1	1	4	6			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr17:37099134A>G	ENST00000378079.2	-	9	1179	c.980T>C	c.(979-981)cTc>cCc	p.L327P		NM_001008777.2	NP_001008777.2	Q5MNV8	FBX47_HUMAN	F-box protein 47	327										NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)	20						TAGCATTAGGAGACGTGCATT	0.403																																					p.L327P		Atlas-SNP	.											.	FBXO47	34	.	0			c.T980C						PASS	.						98	91	93					17																	37099134		2203	4300	6503	SO:0001583	missense	494188	exon9			ATTAGGAGACGTG		CCDS32639.1	17q12	2014-08-12			ENSG00000204952	ENSG00000204952		"F-boxes /  "other""	31969	protein-coding gene	gene with protein product		609498				15723337	Standard	NM_001008777		Approved		uc002hrc.2	Q5MNV8	OTTHUMG00000178945	ENST00000378079.2:c.980T>C	chr17.hg19:g.37099134A>G	ENSP00000367319:p.Leu327Pro	86.0	0.0	.		101.0	34.0	.	NM_001008777	B2RTZ4	Missense_Mutation	SNP	ENST00000378079.2	hg19	CCDS32639.1	.	.	.	.	.	.	.	.	.	.	A	17.39	3.378341	0.61735	.	.	ENSG00000204952	ENST00000378079	T	0.61158	0.13	5.9	4.8	0.61643	.	0.254055	0.40385	N	0.001113	T	0.71626	0.3362	M	0.66939	2.045	0.58432	D	0.999995	D	0.76494	0.999	D	0.67231	0.95	T	0.73902	-0.3836	10	0.87932	D	0	-13.2646	12.1337	0.53957	0.8566:0.1434:0.0:0.0	.	327	Q5MNV8	FBX47_HUMAN	P	327	ENSP00000367319:L327P	ENSP00000367319:L327P	L	-	2	0	FBXO47	34352660	1.000000	0.71417	0.996000	0.52242	0.995000	0.86356	7.161000	0.77505	1.013000	0.39391	0.482000	0.46254	CTC	.	.	.	none		0.403	FBXO47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444073.1	NM_001008777		G	37099134	A	G	37099134	3	3	219	1	0	0	0	0	1	0	0	0	5763	304	11	3	390	3	FBXO47	17	37099134	Missense_Mutation	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	28883344	37099134	44096076	63	13255											
AMZ2	51321	hgsc.bcm.edu	37	chr17	66246341	66246341	+	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	tttgttagatgcaaataataCggcactccgaacagacacta	15	10	7	9	2	0	2	0	0	0	2	1	3	1	2	1	1	3	3	1	1	6	5	rs532820909		TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr17:66246341C>T	ENST00000359904.3	+	2	1145	c.13C>T	c.(13-15)Cgg>Tgg	p.R5W	AMZ2_ENST00000577273.1_Missense_Mutation_p.R5W|RP11-147L13.2_ENST00000577698.1_RNA|AMZ2_ENST00000392720.2_Missense_Mutation_p.R5W|AMZ2_ENST00000359783.4_Missense_Mutation_p.R5W|AMZ2_ENST00000577866.1_Missense_Mutation_p.R5W|AMZ2_ENST00000577985.1_Missense_Mutation_p.R5W|AMZ2_ENST00000580753.1_Missense_Mutation_p.R5W|AMZ2_ENST00000585050.1_Intron	NM_016627.4	NP_057711.3	Q86W34	AMZ2_HUMAN	archaelysin family metallopeptidase 2	5							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	all_cancers(12;1.12e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)			GCAAATAATACGGCACTCCGA	0.343													C|||	1	0.000199681	0	0	5008	,	,		20400	0		0	False		,,,				2504	0.001				p.R5W		Atlas-SNP	.											.	AMZ2	15	.	0			c.C13T						PASS	.						75	79	78					17																	66246341		2203	4300	6503	SO:0001583	missense	51321	exon2			ATAATACGGCACT	CR609550	CCDS11674.1, CCDS32714.1	17q24.2	2010-04-08			ENSG00000196704	ENSG00000196704			28041	protein-coding gene	gene with protein product	"archaemetzincin-2"	615169				15972818	Standard	XM_005257436		Approved		uc002jgr.1	Q86W34		ENST00000359904.3:c.13C>T	chr17.hg19:g.66246341C>T	ENSP00000352976:p.Arg5Trp	30.0	0.0	.		59.0	5.0	.	NM_001033574	A6NLD9|B3KR44|Q5XKF1|Q9NZE2	Missense_Mutation	SNP	ENST00000359904.3	hg19	CCDS11674.1	.	.	.	.	.	.	.	.	.	.	C	0.090	-1.168251	0.01660	.	.	ENSG00000196704	ENST00000359904;ENST00000359783;ENST00000392720	T;T;T	0.19938	2.11;2.11;2.11	3.71	1.58	0.23477	.	0.721746	0.11673	N	0.540610	T	0.21718	0.0523	L	0.57536	1.79	0.09310	N	1	D;D	0.61697	0.978;0.99	B;B	0.43623	0.425;0.425	T	0.14090	-1.0485	10	0.87932	D	0	-32.5953	7.065	0.25147	0.1861:0.451:0.3629:0.0	.	5;5	A6NLD9;Q86W34	.;AMZ2_HUMAN	W	5	ENSP00000352976:R5W;ENSP00000352831:R5W;ENSP00000376481:R5W	ENSP00000352831:R5W	R	+	1	2	AMZ2	63757936	0.001000	0.12720	0.000000	0.03702	0.006000	0.05464	0.302000	0.19192	0.320000	0.23234	0.456000	0.33151	CGG	.	.	.	none		0.343	AMZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448261.1	NM_016627		T	66246341	C	T	66246341	3	4	219	1	0	0	0	0	1	0	0	0	597	527	19	1	15	1	AMZ2	17	66246341	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	29147207	66246341	14948869	64	13256											
C17orf70	80233	hgsc.bcm.edu	37	chr17	79518169	79518169	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcaggcatcggggtccacAgggatcacgggggaaggctg	9	5	18	9	2	1	0	1	0	0	0	3	2	2	2	1	7	1	3	1	7	1	0			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr17:79518169A>G	ENST00000327787.8	-	3	397	c.351T>C	c.(349-351)ccT>ccC	p.P117P	C17orf70_ENST00000537152.1_5'UTR|C17orf70_ENST00000425898.2_5'Flank			Q0VG06	FP100_HUMAN	chromosome 17 open reading frame 70	117					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)			CGGGGTCCACAGGGATCACGG	0.647																																					p.P117P		Atlas-SNP	.											.	C17orf70	79	.	0			c.T351C						PASS	.						6	8	7					17																	79518169		1251	2219	3470	SO:0001819	synonymous_variant	80233	exon3			GTCCACAGGGATC	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.351T>C	chr17.hg19:g.79518169A>G		446.0	1.0	.		559.0	133.0	.	NM_025161	A6NNM1|Q8N3F7|Q9BV13|Q9H6K7|Q9H7E8	Silent	SNP	ENST00000327787.8	hg19	CCDS32765.2																																																																																			.	.	.	none		0.647	C17orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396170.1	NM_025161		G	79518169	A	G	79518169	2	3	219	1	0	0	0	0	0	0	0	1	1879	175	7	3		3	C17orf70	17	79518169	Silent	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	13271828	79518169	1677041	65	13257											
DLGAP1	9229	hgsc.bcm.edu	37	chr18	3508641	3508641	+	Missense_Mutation	SNP	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	gttgggcactgcccactgcgGttcggatttttcctagaact	6	13	11	11	2	0	1	0	0	0	1	2	2	1	2	2	3	3	3	2	3	2	5	rs538990113		TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr18:3508641G>A	ENST00000315677.3	-	11	3093	c.2498C>T	c.(2497-2499)aCc>aTc	p.T833I	DLGAP1_ENST00000581527.1_Missense_Mutation_p.T833I|DLGAP1_ENST00000515196.2_Missense_Mutation_p.T833I|DLGAP1_ENST00000584874.1_Missense_Mutation_p.T833I|DLGAP1_ENST00000534970.1_Missense_Mutation_p.T517I|DLGAP1_ENST00000539435.1_Missense_Mutation_p.T541I|DLGAP1_ENST00000400150.3_Missense_Mutation_p.T549I|DLGAP1_ENST00000400147.2_Missense_Mutation_p.T531I|DLGAP1_ENST00000400155.1_Missense_Mutation_p.T539I|DLGAP1_ENST00000400149.3_Missense_Mutation_p.T523I|DLGAP1_ENST00000581699.1_Missense_Mutation_p.T539I|DLGAP1_ENST00000400145.2_Missense_Mutation_p.T531I	NM_004746.3	NP_004737.2	O14490	DLGP1_HUMAN	discs, large (Drosophila) homolog-associated protein 1	833					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)				GCCCACTGCGGTTCGGATTTT	0.413																																					p.T833I		Atlas-SNP	.											.	DLGAP1	201	.	0			c.C2498T						PASS	.						64	58	60					18																	3508641		2203	4300	6503	SO:0001583	missense	9229	exon11			ACTGCGGTTCGGA	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.2498C>T	chr18.hg19:g.3508641G>A	ENSP00000316377:p.Thr833Ile	66.0	0.0	.		70.0	24.0	.	NM_001242761	A8MWN8|B2RMU8|B7WPA1|B7Z2H2|B7Z2I2|B7Z9Y4|O14489|P78335	Missense_Mutation	SNP	ENST00000315677.3	hg19	CCDS11836.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.008210	0.75046	.	.	ENSG00000170579	ENST00000315677;ENST00000400147;ENST00000400150;ENST00000400149;ENST00000400155;ENST00000534970;ENST00000539435;ENST00000400145;ENST00000515196	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	5.66	4.74	0.60224	.	0.160479	0.56097	D	0.000030	T	0.24812	0.0602	L	0.48362	1.52	0.44908	D	0.997921	D;P;P;P;P;D;P;P	0.54397	0.966;0.939;0.758;0.662;0.758;0.958;0.758;0.714	P;P;P;B;P;B;P;B	0.47705	0.522;0.522;0.555;0.398;0.555;0.387;0.555;0.419	T	0.00885	-1.1527	10	0.87932	D	0	-22.5862	11.1457	0.48430	0.0:0.1378:0.7192:0.1429	.	833;517;529;539;541;531;833;531	B7Z9Y4;B7Z2H2;B7Z2J5;A8MWN8;B7Z2I2;O14490-3;O14490;O14490-2	.;.;.;.;.;.;DLGP1_HUMAN;.	I	833;531;549;523;539;517;541;531;833	ENSP00000316377:T833I;ENSP00000383011:T531I;ENSP00000383014:T549I;ENSP00000383013:T523I;ENSP00000383019:T539I;ENSP00000437817:T517I;ENSP00000446312:T541I;ENSP00000383010:T531I;ENSP00000445973:T833I	ENSP00000316377:T833I	T	-	2	0	DLGAP1	3498641	1.000000	0.71417	0.969000	0.41365	0.997000	0.91878	4.878000	0.63093	2.656000	0.90262	0.655000	0.94253	ACC	.	.	.	none		0.413	DLGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254394.4			A	3508641	G	A	3508641	3	1	219	1	0	0	0	0	1	0	0	0	4561	1261	44	2	447	2	DLGAP1	18	3508641	Missense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10		3508641	74568607	66	13258											
DSG2	1829	hgsc.bcm.edu	37	chr18	29116286	29116286	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatgcagagtatgtgaatgtTactgcagaggacctggatgg	11	10	15	5	0	0	3	0	1	0	2	0	6	0	5	1	3	3	4	1	3	3	2			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr18:29116286T>C	ENST00000261590.8	+	11	1754	c.1545T>C	c.(1543-1545)gtT>gtC	p.V515V		NM_001943.3	NP_001934.2	Q14126	DSG2_HUMAN	desmoglein 2	515			V -> I (in dbSNP:rs2230235).		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)			ATGTGAATGTTACTGCAGAGG	0.483																																					p.V515V		Atlas-SNP	.											.	DSG2	115	.	0			c.T1545C						PASS	.						94	89	90					18																	29116286		1963	4174	6137	SO:0001819	synonymous_variant	1829	exon11			GAATGTTACTGCA	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.1545T>C	chr18.hg19:g.29116286T>C		118.0	0.0	.		109.0	35.0	.	NM_001943	Q4KKU6	Silent	SNP	ENST00000261590.8	hg19	CCDS42423.1																																																																																			.	.	.	none		0.483	DSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447506.1	NM_001943		C	29116286	T	C	29116286	2	2	219	1	0	0	0	0	0	0	0	1	4779	1741	61	3		3	DSG2	18	29116286	Silent	SNP	T	TCGA-MH-A55W-01A-11D-A26P-10	25607645	29116286	48960962	67	13259											
RDH13	112724	hgsc.bcm.edu	37	chr19	55570627	55570627	+	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	ggccttgctggggcaagcccCaccggtgacatagtccctga	7	7	13	14	1	0	2	0	2	0	0	1	2	1	2	5	4	2	2	5	4	2	2			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr19:55570627C>A	ENST00000415061.3	-	2	225	c.82G>T	c.(82-84)Ggg>Tgg	p.G28W	RDH13_ENST00000396247.3_5'UTR	NM_001145971.1	NP_001139443.1	Q8NBN7	RDH13_HUMAN	retinol dehydrogenase 13 (all-trans/9-cis)	28					eye photoreceptor cell development (GO:0042462)|response to high light intensity (GO:0009644)|retina layer formation (GO:0010842)	mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.199)	GBM - Glioblastoma multiforme(193;0.0504)	Vitamin A(DB00162)	GGGCAAGCCCCACCGGTGACA	0.632																																					p.G28W		Atlas-SNP	.											.	RDH13	43	.	0			c.G82T						PASS	.						28	27	27					19																	55570627		1567	3580	5147	SO:0001583	missense	112724	exon2			AAGCCCCACCGGT		CCDS42627.1, CCDS54320.1	19q13.42	2011-09-14	2006-05-09			ENSG00000160439	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	19978	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 7C, member 3"		"retinol dehydrogenase 13 (all-trans and 9-cis)"			12226107, 19027726	Standard	NM_138412		Approved	SDR7C3	uc002qio.3	Q8NBN7		ENST00000415061.3:c.82G>T	chr19.hg19:g.55570627C>A	ENSP00000391121:p.Gly28Trp	69.0	0.0	.		87.0	37.0	.	NM_001145971	Q6UX79|Q96G88	Missense_Mutation	SNP	ENST00000415061.3	hg19	CCDS54320.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.395156	0.83011	.	.	ENSG00000160439	ENST00000415061;ENST00000291892	D;D	0.83673	-1.75;-1.63	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	D	0.88930	0.6571	L	0.56769	1.78	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.89139	0.3515	10	0.59425	D	0.04	.	14.7528	0.69540	0.0:1.0:0.0:0.0	.	28	Q8NBN7	RDH13_HUMAN	W	28	ENSP00000391121:G28W;ENSP00000291892:G28W	ENSP00000291892:G28W	G	-	1	0	RDH13	60262439	0.988000	0.35896	0.311000	0.25182	0.164000	0.22412	3.974000	0.56852	2.635000	0.89317	0.650000	0.86243	GGG	.	.	.	none		0.632	RDH13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451470.1	NM_138412		A	55570627	C	A	55570627	3	1	219	1	0	0	0	0	1	0	0	0	13205	594	21	4	937	4	RDH13	19	55570627	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10		55570627	3558356	68	13260											
SLC32A1	140679	hgsc.bcm.edu	37	chr20	37353586	37353607	+	Frame_Shift_Del	DEL	GGGCGCTGAAGCGCCCGTCGAG	GGGCGCTGAAGCGCCCGTCGAG	-																															ggagagccctgcggggacgaGggcgctgaagcgcccgtcga																								rs148951877		TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	GGGCGCTGAAGCGCCCGTCGAG	GGGCGCTGAAGCGCCCGTCGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr20:37353586_37353607delGGGCGCTGAAGCGCCCGTCGAG	ENST00000217420.1	+	1	482_503	c.219_240delGGGCGCTGAAGCGCCCGTCGAG	c.(217-240)gagggcgctgaagcgcccgtcgagfs	p.EGAEAPVE73fs		NM_080552.2	NP_542119.1	Q9H598	VIAAT_HUMAN	solute carrier family 32 (GABA vesicular transporter), member 1	73					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)	GCGGGGACGAGGGCGCTGAAGCGCCCGTCGAGGGAGACATCC	0.671																																					p.73_80del		Atlas-Indel,Pindel	.											.	SLC32A1	81	.	0			c.218_239del						PASS	.																																			SO:0001589	frameshift_variant	140679	exon1			.	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.219_240delGGGCGCTGAAGCGCCCGTCGAG	chr20.hg19:g.37353586_37353607delGGGCGCTGAAGCGCCCGTCGAG	ENSP00000217420:p.Glu73fs	27.0	0.0	0		107.0	33.0	0.308411	NM_080552	Q8N489	Frame_Shift_Del	DEL	ENST00000217420.1	hg19	CCDS13307.1																																																																																			.	.	.	none		0.671	SLC32A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079206.1	NM_080552		-	37353607	GGGCGCTGAAGCGCCCGTCGAG	-	37353586	7	5	219	1	0	1	0	1	0	0	0	0	14578	991	35	0	221	0	SLC32A1	20	37353586	Frame_Shift_Del	DEL	GGGCGCTGAAGCGCCCGTCGAG	TCGA-MH-A55W-01A-11D-A26P-10		37353586	25671934	69	13261											
NCOA3	8202	hgsc.bcm.edu	37	chr20	46254225	46254225	+	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	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-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr20:46254225G>A	ENST00000371998.3	+	5	548	c.357G>A	c.(355-357)caG>caA	p.Q119Q	NCOA3_ENST00000341724.6_Splice_Site_p.Q119Q|NCOA3_ENST00000372004.3_Splice_Site_p.Q119Q|NCOA3_ENST00000371997.3_Splice_Site_p.Q119Q			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.Q119Q		Atlas-SNP	.											.	NCOA3	156	.	0			c.G357A						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>A	chr20.hg19:g.46254225G>A		18.0	0.0	.		42.0	15.0	.	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Silent	SNP	ENST00000371998.3	hg19	CCDS13407.1																																																																																			.	.	.	none		0.343	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	Silent	A	46254225	G	A	46254225	5	1	219	1	0	0	0	0	0	0	1	0	10237	1014	35	2	367	2	NCOA3	20	46254225	Splice_Site	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	8900639	46254225	16771295	70	13262											
ADNP	23394	hgsc.bcm.edu	37	chr20	49509272	49509272	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatggatacatttgtaggtgAgctttttctcaactggatga	11	15	10	5	0	1	2	1	2	1	0	2	4	1	4	0	3	3	2	0	3	4	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr20:49509272A>G	ENST00000396029.3	-	5	2546	c.1979T>C	c.(1978-1980)cTc>cCc	p.L660P	ADNP_ENST00000396032.3_Missense_Mutation_p.L660P|ADNP_ENST00000349014.3_Missense_Mutation_p.L660P|ADNP_ENST00000371602.4_Missense_Mutation_p.L660P	NM_001282531.1|NM_015339.2	NP_001269460.1|NP_056154.1	Q9H2P0	ADNP_HUMAN	activity-dependent neuroprotector homeobox	660					negative regulation of neuron apoptotic process (GO:0043524)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|endometrium(7)|kidney(1)|large_intestine(13)|lung(7)|ovary(2)|prostate(2)|skin(2)	39						TTTGTAGGTGAGCTTTTTCTC	0.458																																					p.L660P		Atlas-SNP	.											.	ADNP	106	.	0			c.T1979C						PASS	.						168	159	162					20																	49509272		2203	4300	6503	SO:0001583	missense	23394	exon5			TAGGTGAGCTTTT	AF250860	CCDS13433.1	20q13.13	2011-06-20	2007-07-17		ENSG00000101126	ENSG00000101126		"Homeoboxes / ZF class"	15766	protein-coding gene	gene with protein product	"ADNP homeobox 1"	611386	"activity-dependent neuroprotector"			9872452, 11013255	Standard	NM_015339		Approved	KIAA0784, ADNP1	uc002xvu.1	Q9H2P0	OTTHUMG00000032737	ENST00000396029.3:c.1979T>C	chr20.hg19:g.49509272A>G	ENSP00000379346:p.Leu660Pro	220.0	0.0	.		233.0	102.0	.	NM_015339	E1P5Y2|O94881|Q5BKU2|Q9UG34	Missense_Mutation	SNP	ENST00000396029.3	hg19	CCDS13433.1	.	.	.	.	.	.	.	.	.	.	A	12.33	1.907002	0.33628	.	.	ENSG00000101126	ENST00000371602;ENST00000349014;ENST00000396029;ENST00000396032	.	.	.	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.45276	0.1334	N	0.17082	0.46	0.80722	D	1	B	0.25486	0.127	B	0.25140	0.058	T	0.40720	-0.9548	9	0.54805	T	0.06	-14.7154	16.4177	0.83748	1.0:0.0:0.0:0.0	.	660	Q9H2P0	ADNP_HUMAN	P	660	.	ENSP00000342905:L660P	L	-	2	0	ADNP	48942679	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.941000	0.92964	2.267000	0.75376	0.528000	0.53228	CTC	.	.	.	none		0.458	ADNP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079705.2	NM_181442		G	49509272	A	G	49509272	3	3	219	1	0	0	0	0	1	0	0	0	323	304	11	3	1333	3	ADNP	20	49509272	Missense_Mutation	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10	3255047	49509272	13516248	71	13263											
LIPI	149998	hgsc.bcm.edu	37	chr21	15561570	15561570	+	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	aagccagactgttttcttttGtgtgttgaaattaacattaa	12	17	7	5	0	1	2	0	1	1	1	1	2	1	2	1	0	2	2	1	0	4	7	rs569460311		TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr21:15561570G>A	ENST00000536861.1	-	2	216	c.217C>T	c.(217-219)Caa>Taa	p.Q73*	LIPI_ENST00000344577.2_Nonsense_Mutation_p.Q94*			Q6XZB0	LIPI_HUMAN	lipase, member I	73					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		GTTTTCTTTTGTGTGTTGAAA	0.378																																					p.Q94X		Atlas-SNP	.											.	LIPI	95	.	0			c.C280T						PASS	.						140	125	130					21																	15561570		2203	4300	6503	SO:0001587	stop_gained	149998	exon2			TCTTTTGTGTGTT	BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"membrane-associated phospholipase A1 beta", "cancer/testis antigen 17"	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.217C>T	chr21.hg19:g.15561570G>A	ENSP00000440381:p.Gln73*	94.0	0.0	.		155.0	46.0	.	NM_198996	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Nonsense_Mutation	SNP	ENST00000536861.1	hg19		.	.	.	.	.	.	.	.	.	.	G	25.4	4.631384	0.87660	.	.	ENSG00000188992	ENST00000344577;ENST00000536861	.	.	.	5.3	-2.36	0.06663	.	1.079770	0.06983	N	0.820308	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	.	1.3793	0.02227	0.1755:0.2196:0.1309:0.474	.	.	.	.	X	94;73	.	ENSP00000343331:Q94X	Q	-	1	0	LIPI	14483441	0.000000	0.05858	0.001000	0.08648	0.986000	0.74619	0.242000	0.18087	-0.342000	0.08363	-0.152000	0.13540	CAA	.	.	.	none		0.378	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996		A	15561570	G	A	15561570	4	1	219	1	0	0	0	0	0	1	0	0	8832	1386	48	2	1201	2	LIPI	21	15561570	Nonsense_Mutation	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10		15561570	32568325	72	13264											
HLCS	3141	hgsc.bcm.edu	37	chr21	38309141	38309141	+	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	gtctctgagagcactgtcctCcagcaggtggtagagaatat	10	10	12	9	0	1	2	0	1	1	2	4	4	3	2	2	2	2	3	2	2	3	2	rs148324626		TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr21:38309141C>G	ENST00000399120.1	-	5	1834	c.604G>C	c.(604-606)Gag>Cag	p.E202Q	HLCS_ENST00000336648.4_Missense_Mutation_p.E202Q	NM_001242784.1	NP_001229713.1	P50747	BPL1_HUMAN	holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase)	202					biotin metabolic process (GO:0006768)|cell proliferation (GO:0008283)|histone biotinylation (GO:0071110)|histone modification (GO:0016570)|protein biotinylation (GO:0009305)|response to biotin (GO:0070781)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin-[acetyl-CoA-carboxylase] ligase activity (GO:0004077)|biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity (GO:0004078)|biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity (GO:0004079)|biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity (GO:0004080)|biotin-protein ligase activity (GO:0018271)|enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(46;0.0422)			Biotin(DB00121)	GCACTGTCCTCCAGCAGGTGG	0.582																																					p.E202Q		Atlas-SNP	.											.	HLCS	64	.	0			c.G604C						PASS	.	C	GLN/GLU,GLN/GLU,GLN/GLU	1,4405	2.1+/-5.4	0,1,2202	70	73	72		604,604,604	3	0	21	dbSNP_134	72	0,8600		0,0,4300	no	missense,missense,missense	HLCS	NM_000411.6,NM_001242784.1,NM_001242785.1	29,29,29	0,1,6502	GG,GC,CC		0.0,0.0227,0.0077	benign,benign,benign	202/727,202/727,202/727	38309141	1,13005	2203	4300	6503	SO:0001583	missense	3141	exon5			TGTCCTCCAGCAG		CCDS13647.1	21q22.1	2012-07-13	2010-04-30		ENSG00000159267	ENSG00000159267	6.3.4.9, 6.3.4.10, 6.3.4.11, 6.3.4.15		4976	protein-coding gene	gene with protein product		609018	"holocarboxylase synthetase (biotin-[proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)", "holocarboxylase synthetase (biotin-(proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)) ligase)"			7842009	Standard	NM_000411		Approved	HCS	uc021wjb.1	P50747	OTTHUMG00000086636	ENST00000399120.1:c.604G>C	chr21.hg19:g.38309141C>G	ENSP00000382071:p.Glu202Gln	184.0	0.0	.		154.0	54.0	.	NM_000411	B2RAH1|D3DSG6|Q99451	Missense_Mutation	SNP	ENST00000399120.1	hg19	CCDS13647.1	.	.	.	.	.	.	.	.	.	.	C	9.293	1.051089	0.19827	2.27E-4	0.0	ENSG00000159267	ENST00000399120;ENST00000336648	D;D	0.98164	-4.76;-4.76	5.91	2.99	0.34606	.	0.383875	0.32258	N	0.006346	D	0.94745	0.8304	L	0.35723	1.085	0.09310	N	1	B;B	0.13145	0.007;0.003	B;B	0.09377	0.004;0.004	D	0.84732	0.0746	10	0.15952	T	0.53	.	10.2355	0.43280	0.0:0.6608:0.2659:0.0733	.	202;202	B2RAH1;P50747	.;BPL1_HUMAN	Q	202	ENSP00000382071:E202Q;ENSP00000338387:E202Q	ENSP00000338387:E202Q	E	-	1	0	HLCS	37231011	0.279000	0.24239	0.001000	0.08648	0.283000	0.27025	1.771000	0.38542	0.335000	0.23614	0.655000	0.94253	GAG	.	C|1.000;G|0.000	0.000	weak		0.582	HLCS-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194687.2			G	38309141	C	G	38309141	3	3	219	1	0	0	0	0	1	0	0	0	7220	864	30	4	1608	4	HLCS	21	38309141	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	22747571	38309141	9820754	73	13265											
C21orf29	54084	hgsc.bcm.edu	37	chr21	45949793	45949793	+	Silent	SNP	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	ctgctgggacacagccttggGgtggcgtctgagcccggcag	5	7	17	12	2	1	1	0	1	1	0	1	2	1	2	2	5	3	2	2	5	0	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr21:45949793G>A	ENST00000323084.4	-	5	743	c.678C>T	c.(676-678)acC>acT	p.T226T	TSPEAR_ENST00000397916.1_Silent_p.T158T	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	226	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						ACAGCCTTGGGGTGGCGTCTG	0.662																																					p.T226T		Atlas-SNP	.											.	TSPEAR	110	.	0			c.C678T						PASS	.						35	39	37					21																	45949793		2203	4300	6503	SO:0001819	synonymous_variant	54084	exon5			CCTTGGGGTGGCG	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.678C>T	chr21.hg19:g.45949793G>A		23.0	0.0	.		28.0	12.0	.	NM_144991		Silent	SNP	ENST00000323084.4	hg19	CCDS13712.1																																																																																			.	.	.	none		0.662	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098761.1	NM_144991		A	45949793	G	A	45949793	2	1	219	1	0	0	0	0	0	0	0	1	2126	1219	43	2		2	C21orf29	21	45949793	Silent	SNP	G	TCGA-MH-A55W-01A-11D-A26P-10	7640652	45949793	2180102	74	13266											
IL17RA	23765	hgsc.bcm.edu	37	chr22	17566096	17566096	+	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	ccctgcgactcctggaccacCgggcgctggtctgctcccag	4	7	12	18	3	1	0	0	0	1	0	3	2	3	1	5	3	2	2	5	3	0	0			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr22:17566096C>A	ENST00000319363.6	+	1	248	c.115C>A	c.(115-117)Cgg>Agg	p.R39R	IL17RA_ENST00000477874.1_3'UTR	NM_014339.5	NP_055154.3	Q96F46	I17RA_HUMAN	interleukin 17 receptor A	39					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)		CCTGGACCACCGGGCGCTGGT	0.766																																					p.R39R		Atlas-SNP	.											.	IL17RA	62	.	0			c.C115A						PASS	.						2	2	2					22																	17566096		1628	3503	5131	SO:0001819	synonymous_variant	23765	exon1			GACCACCGGGCGC	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.115C>A	chr22.hg19:g.17566096C>A		1.0	0.0	.		8.0	8.0	.	NM_014339	O43844|Q20WK1	Silent	SNP	ENST00000319363.6	hg19	CCDS13739.1																																																																																			.	.	.	none		0.766	IL17RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315820.1	NM_014339		A	17566096	C	A	17566096	2	1	219	1	0	0	0	0	0	0	0	1	7646	643	23	4		4	IL17RA	22	17566096	Silent	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10		17566096	33738470	75	13267											
CSNK1E	1454	hgsc.bcm.edu	37	chr22	38690131	38690131	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacctgtgaggctgggatcCgggagacctcttgccgccca	6	8	13	14	2	2	2	1	1	1	1	3	4	3	3	5	3	1	1	5	3	0	1			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr22:38690131C>T	ENST00000396832.1	-	9	1462	c.1202G>A	c.(1201-1203)cGg>cAg	p.R401Q	CSNK1E_ENST00000359867.3_Missense_Mutation_p.R401Q|CSNK1E_ENST00000498529.1_5'Flank|CSNK1E_ENST00000403904.1_Missense_Mutation_p.R401Q|CSNK1E_ENST00000400206.2_Missense_Mutation_p.R401Q	NM_152221.2	NP_689407.1	P49674	KC1E_HUMAN	casein kinase 1, epsilon	401					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)					GGCTGGGATCCGGGAGACCTC	0.662																																					p.R401Q	Esophageal Squamous(119;108 755 9651 12170 13692 17603 24932 28315 37982 41601)	Atlas-SNP	.											.	CSNK1E	143	.	0			c.G1202A						PASS	.						26	27	27					22																	38690131		2201	4300	6501	SO:0001583	missense	1454	exon9			GGGATCCGGGAGA		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.1202G>A	chr22.hg19:g.38690131C>T	ENSP00000380044:p.Arg401Gln	51.0	0.0	.		53.0	14.0	.	NM_001894		Missense_Mutation	SNP	ENST00000396832.1	hg19	CCDS13970.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.1|25.1	4.600758|4.600758	0.87055|0.87055	.|.	.|.	ENSG00000213923|ENSG00000213923	ENST00000366216|ENST00000359867;ENST00000396832;ENST00000402865;ENST00000400206;ENST00000403904	.|T;T;T;T	.|0.57436	.|0.4;0.4;0.4;0.4	5.8|5.8	5.8|5.8	0.92144|0.92144	.|.	.|0.055638	.|0.64402	.|D	.|0.000001	T|T	0.59211|0.59211	0.2177|0.2177	N|N	0.12182|0.12182	0.205|0.205	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.83275	.|0.996	T|T	0.65175|0.65175	-0.6232|-0.6232	5|10	.|0.56958	.|D	.|0.05	.|.	20.063|20.063	0.97692|0.97692	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|401	.|P49674	.|KC1E_HUMAN	R|Q	104|401	.|ENSP00000352929:R401Q;ENSP00000380044:R401Q;ENSP00000383067:R401Q;ENSP00000384074:R401Q	.|ENSP00000352929:R401Q	G|R	-|-	1|2	0|0	CSNK1E|CSNK1E	37020077|37020077	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.254000|0.254000	0.26022|0.26022	7.482000|7.482000	0.81143|0.81143	2.735000|2.735000	0.93741|0.93741	0.655000|0.655000	0.94253|0.94253	GGA|CGG	.	.	.	none		0.662	CSNK1E-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321462.1	NM_001894		T	38690131	C	T	38690131	3	4	219	1	0	0	0	0	1	0	0	0	3955	652	23	1	56	1	CSNK1E	22	38690131	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	21124035	38690131	12614435	76	13268											
SHANK3	85358	hgsc.bcm.edu	37	chr22	51160300	51160300	+	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	agcccagcagtgagccacccCctgcccctgagtctgcagcc	7	5	10	19	0	1	2	0	2	1	0	1	2	1	2	7	0	6	2	7	0	0	0			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chr22:51160300C>G	ENST00000414786.2	+	21	4224	c.3997C>G	c.(3997-3999)Cct>Gct	p.P1333A	SHANK3_ENST00000445220.2_Missense_Mutation_p.P1349A|SHANK3_ENST00000262795.3_Missense_Mutation_p.P1363A			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	1347	Pro-rich.		V -> G. {ECO:0000269|PubMed:20385823}.		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)		TGAGCCACCCCCTGCCCCTGA	0.711																																					p.P1333A		Atlas-SNP	.											.	SHANK3	96	.	0			c.C3997G						PASS	.						8	10	9					22																	51160300		1900	4008	5908	SO:0001583	missense	85358	exon21			CCACCCCCTGCCC	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.3997C>G	chr22.hg19:g.51160300C>G	ENSP00000464552:p.Pro1333Ala	34.0	0.0	.		36.0	10.0	.	NM_033517	D7UT47|Q8TET3	Missense_Mutation	SNP	ENST00000414786.2	hg19		.	.	.	.	.	.	.	.	.	.	C	15.71	2.913103	0.52439	.	.	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.18960	2.18;2.18	5.11	5.11	0.69529	.	0.073236	0.56097	D	0.000028	T	0.28167	0.0695	M	0.78456	2.415	0.28658	N	0.906287	B;B;B	0.28512	0.176;0.096;0.214	B;B;B	0.25884	0.064;0.036;0.052	T	0.13683	-1.0500	10	0.34782	T	0.22	.	16.0382	0.80645	0.0:1.0:0.0:0.0	.	1347;1348;1363	D7UT47;Q9BYB0;F2Z3L0	.;SHAN3_HUMAN;.	A	1363;1349	ENSP00000442518:P1363A;ENSP00000446078:P1349A	ENSP00000442518:P1363A	P	+	1	0	SHANK3	49507166	0.230000	0.23740	0.974000	0.42286	0.986000	0.74619	1.882000	0.39648	2.381000	0.81170	0.462000	0.41574	CCT	.	.	.	none		0.711	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420		G	51160300	C	G	51160300	3	3	219	1	0	0	0	0	1	0	0	0	14279	623	22	4	4173	4	SHANK3	22	51160300	Missense_Mutation	SNP	C	TCGA-MH-A55W-01A-11D-A26P-10	12470169	51160300	144266	77	13269											
WWC3	55841	hgsc.bcm.edu	37	chrX	10066562	10066562	+	Missense_Mutation	SNP	A	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	aaagtttgtctttgatgataAaacaagacttgtagaccgag	15	12	9	5	1	1	4	0	2	1	2	1	5	1	4	1	0	1	2	1	0	5	5			TCGA-MH-A55W-01A-11D-A26P-10	TCGA-MH-A55W-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2425a532-f562-423a-88f5-228642f53875	38fa8b8f-1a31-4331-9acc-15e845c9a9b8	g.chrX:10066562A>C	ENST00000380861.4	+	8	1065	c.674A>C	c.(673-675)aAa>aCa	p.K225T	WWC3_ENST00000454666.1_Missense_Mutation_p.K225T	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	225					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						TTTGATGATAAAACAAGACTT	0.353																																					p.K225T		Atlas-SNP	.											.	WWC3	142	.	0			c.A674C						PASS	.						78	73	75					X																	10066562		2203	4300	6503	SO:0001583	missense	55841	exon8			ATGATAAAACAAG	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.674A>C	chrX.hg19:g.10066562A>C	ENSP00000370242:p.Lys225Thr	25.0	0.0	.		38.0	27.0	.	NM_015691	A8KA96|Q659C1|Q9BTQ1	Missense_Mutation	SNP	ENST00000380861.4	hg19	CCDS14136.1	.	.	.	.	.	.	.	.	.	.	A	16.55	3.155337	0.57259	.	.	ENSG00000047644	ENST00000380861;ENST00000454666;ENST00000398613	T;T	0.05199	3.48;3.48	5.49	5.49	0.81192	.	0.217302	0.48286	D	0.000185	T	0.07954	0.0199	L	0.51422	1.61	0.39975	D	0.974846	P	0.39424	0.673	B	0.37144	0.242	T	0.38845	-0.9642	10	0.19590	T	0.45	-27.9526	14.6222	0.68594	1.0:0.0:0.0:0.0	.	225	Q9ULE0	WWC3_HUMAN	T	225	ENSP00000370242:K225T;ENSP00000399584:K225T	ENSP00000370242:K225T	K	+	2	0	WWC3	10026562	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	3.309000	0.51903	1.834000	0.53371	0.339000	0.21740	AAA	.	.	.	none		0.353	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691		C	10066562	A	C	10066562	3	2	219	1	0	0	0	0	1	0	0	0	17425	14	1	5	700	5	WWC3	23	10066562	Missense_Mutation	SNP	A	TCGA-MH-A55W-01A-11D-A26P-10		10066562	145203998	78	13270											
UBR4	23352	hgsc.bcm.edu	37	chr1	19504023	19504023	+	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	atcaaagatgagaaggaggcGagccaagataagcggcacga	17	3	14	7	3	1	3	1	1	0	3	1	7	1	4	1	3	2	1	1	3	4	1			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr1:19504023G>C	ENST00000375254.3	-	19	2596	c.2569C>G	c.(2569-2571)Cgc>Ggc	p.R857G	UBR4_ENST00000375226.2_Missense_Mutation_p.R857G|UBR4_ENST00000375267.2_Missense_Mutation_p.R857G|UBR4_ENST00000375217.2_Missense_Mutation_p.R857G	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	857					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)		AGAAGGAGGCGAGCCAAGATA	0.498																																					p.R857G		Atlas-SNP	.											.	UBR4	415	.	0			c.C2569G						PASS	.						133	126	128					1																	19504023		2203	4300	6503	SO:0001583	missense	23352	exon19			GGAGGCGAGCCAA	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.2569C>G	chr1.hg19:g.19504023G>C	ENSP00000364403:p.Arg857Gly	248.0	0.0	.		256.0	130.0	.	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	hg19	CCDS189.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.909893	0.92107	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000419533	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.60728	0.2291	L	0.50333	1.59	0.80722	D	1	D	0.60160	0.987	D	0.67725	0.953	T	0.61043	-0.7142	10	0.87932	D	0	.	19.4792	0.95002	0.0:0.0:1.0:0.0	.	857	Q5T4S7	UBR4_HUMAN	G	857;857;857;857;73	ENSP00000364403:R857G;ENSP00000364416:R857G;ENSP00000364365:R857G;ENSP00000364374:R857G	ENSP00000364365:R857G	R	-	1	0	UBR4	19376610	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.238000	0.95380	2.713000	0.92767	0.655000	0.94253	CGC	.	.	.	none		0.498	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		C	19504023	G	C	19504023	3	2	220	1	0	0	0	0	1	0	0	0	16916	1058	37	4	13334	4	UBR4	1	19504023	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10		19504023	229746598	1	13271											
GJB5	2709	hgsc.bcm.edu	37	chr1	35223633	35223633	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcatcacccccacggtacCacctcttcctgcaaacaaga	11	7	6	17	1	3	1	2	0	1	1	4	1	4	1	5	2	3	2	5	2	3	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr1:35223633C>T	ENST00000338513.1	+	2	875	c.702C>T	c.(700-702)acC>acT	p.T234T	GJB4_ENST00000339480.1_5'Flank	NM_005268.3	NP_005259.1	O95377	CXB5_HUMAN	gap junction protein, beta 5, 31.1kDa	234					cell communication (GO:0007154)|epidermis development (GO:0008544)|labyrinthine layer morphogenesis (GO:0060713)|spongiotrophoblast differentiation (GO:0060708)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|stomach(1)	10		Myeloproliferative disorder(586;0.0393)				CCCACGGTACCACCTCTTCCT	0.572																																					p.T234T		Atlas-SNP	.											.	GJB5	35	.	0			c.C702T						PASS	.						156	129	138					1																	35223633		2203	4300	6503	SO:0001819	synonymous_variant	2709	exon2			CGGTACCACCTCT	BC004379	CCDS382.1	1p34.3	2008-05-14	2007-11-06		ENSG00000189280	ENSG00000189280		"Ion channels / Gap junction proteins (connexins)"	4287	protein-coding gene	gene with protein product	"connexin 31.1"	604493	"gap junction protein, beta 5 (connexin 31.1)", "gap junction protein, beta 5"			9843209	Standard	NM_005268		Approved	CX31.1	uc001bxu.4	O95377	OTTHUMG00000004053	ENST00000338513.1:c.702C>T	chr1.hg19:g.35223633C>T		415.0	0.0	.		332.0	145.0	.	NM_005268	Q9UPA3	Silent	SNP	ENST00000338513.1	hg19	CCDS382.1																																																																																			.	.	.	none		0.572	GJB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011561.1	NM_005268		T	35223633	C	T	35223633	2	4	220	1	0	0	0	0	0	0	0	1	6418	581	21	2		2	GJB5	1	35223633	Silent	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	15719610	35223633	214026988	2	13272											
GNL2	29889	hgsc.bcm.edu	37	chr1	38040324	38040324	+	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	gaaagtcctcagcattctccCaagaatcaatcttgtatgtt	12	13	6	10	0	4	1	2	0	2	1	6	2	5	1	2	0	1	3	2	0	5	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr1:38040324C>G	ENST00000373062.3	-	11	1342	c.1244G>C	c.(1243-1245)tGg>tCg	p.W415S		NM_013285.2	NP_037417.1	Q13823	NOG2_HUMAN	guanine nucleotide binding protein-like 2 (nucleolar)	415					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)				AGCATTCTCCCAAGAATCAAT	0.418																																					p.W415S		Atlas-SNP	.											.	GNL2	58	.	0			c.G1244C						PASS	.						92	85	88					1																	38040324		2203	4300	6503	SO:0001583	missense	29889	exon11			TTCTCCCAAGAAT	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.1244G>C	chr1.hg19:g.38040324C>G	ENSP00000362153:p.Trp415Ser	93.0	0.0	.		92.0	46.0	.	NM_013285	Q9BWN7	Missense_Mutation	SNP	ENST00000373062.3	hg19	CCDS421.1	.	.	.	.	.	.	.	.	.	.	C	33	5.223863	0.95139	.	.	ENSG00000134697	ENST00000373062	T	0.12774	2.65	5.87	5.87	0.94306	GTP-binding protein, orthogonal bundle domain (1);	0.000000	0.85682	D	0.000000	T	0.45438	0.1342	M	0.86420	2.815	0.80722	D	1	D	0.63046	0.992	D	0.66497	0.944	T	0.44143	-0.9347	10	0.72032	D	0.01	-11.3487	20.5827	0.99408	0.0:1.0:0.0:0.0	.	415	Q13823	NOG2_HUMAN	S	415	ENSP00000362153:W415S	ENSP00000362153:W415S	W	-	2	0	GNL2	37812911	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.786000	0.85741	2.941000	0.99782	0.655000	0.94253	TGG	.	.	.	none		0.418	GNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012478.1	NM_013285		G	38040324	C	G	38040324	3	3	220	1	0	0	0	0	1	0	0	0	6543	595	21	4	975	4	GNL2	1	38040324	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	2816691	38040324	211210297	3	13273											
ATP1A1	476	hgsc.bcm.edu	37	chr1	116941337	116941337	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatggggattgctggctcagAtgtgtccaagcaagctgctg	8	11	14	8	0	1	1	1	0	0	1	2	2	2	2	1	3	4	5	1	3	3	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr1:116941337A>G	ENST00000295598.5	+	16	2471	c.2219A>G	c.(2218-2220)gAt>gGt	p.D740G	ATP1A1_ENST00000369496.4_Missense_Mutation_p.D709G|ATP1A1_ENST00000537345.1_Missense_Mutation_p.D740G	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	740					ATP biosynthetic process (GO:0006754)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|membrane hyperpolarization (GO:0060081)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of glucocorticoid biosynthetic process (GO:0031947)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart contraction (GO:0045823)|positive regulation of striated muscle contraction (GO:0045989)|potassium ion import (GO:0010107)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of sodium ion transport (GO:0002028)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|chaperone binding (GO:0051087)|phosphatase activity (GO:0016791)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(2)|breast(2)|cervix(3)|endometrium(2)|kidney(5)|large_intestine(9)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Ciclopirox(DB01188)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Ethacrynic acid(DB00903)|Hydroflumethiazide(DB00774)|Ouabain(DB01092)|Trichlormethiazide(DB01021)	GCTGGCTCAGATGTGTCCAAG	0.493																																					p.D740G		Atlas-SNP	.											.	ATP1A1	87	.	0			c.A2219G						PASS	.						201	191	194					1																	116941337		2203	4300	6503	SO:0001583	missense	476	exon16			GCTCAGATGTGTC	D00099	CCDS887.1, CCDS53351.1, CCDS53352.1	1p13	2012-10-22			ENSG00000163399	ENSG00000163399	3.6.3.9	"ATPases / P-type"	799	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit alpha-1", "sodium pump subunit alpha-1", "sodium-potassium ATPase catalytic subunit alpha-1"	182310					Standard	NM_000701		Approved		uc001ege.3	P05023	OTTHUMG00000012109	ENST00000295598.5:c.2219A>G	chr1.hg19:g.116941337A>G	ENSP00000295598:p.Asp740Gly	165.0	0.0	.		152.0	60.0	.	NM_001160233	B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Missense_Mutation	SNP	ENST00000295598.5	hg19	CCDS887.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.803837	0.90623	.	.	ENSG00000163399	ENST00000295598;ENST00000537345;ENST00000369496	D;D;D	0.83419	-1.72;-1.72;-1.72	5.23	5.23	0.72850	HAD-like domain (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.92622	0.7656	H	0.94847	3.59	0.80722	D	1	D;D	0.89917	1.0;0.995	D;D	0.97110	1.0;0.999	D	0.94580	0.7778	10	0.87932	D	0	.	15.2911	0.73868	1.0:0.0:0.0:0.0	.	740;740	F5H3A1;P05023	.;AT1A1_HUMAN	G	740;740;709	ENSP00000295598:D740G;ENSP00000445306:D740G;ENSP00000358508:D709G	ENSP00000295598:D740G	D	+	2	0	ATP1A1	116742860	1.000000	0.71417	0.550000	0.28217	0.991000	0.79684	9.139000	0.94554	2.195000	0.70347	0.533000	0.62120	GAT	.	.	.	none		0.493	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5	NM_001160233		G	116941337	A	G	116941337	3	3	220	1	0	0	0	0	1	0	0	0	1128	333	12	3	2297	3	ATP1A1	1	116941337	Missense_Mutation	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	78901013	116941337	132309284	4	13274											
LCE2A	353139	hgsc.bcm.edu	37	chr1	152671534	152671534	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccagctctgggggctgctgcGgctccagctctgggggctgc	2	8	17	14	1	2	0	0	0	2	0	3	0	3	0	2	5	5	6	2	5	0	0			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr1:152671534G>A	ENST00000368779.1	+	2	208	c.157G>A	c.(157-159)Ggc>Agc	p.G53S		NM_178428.3	NP_848515.1	Q5TA79	LCE2A_HUMAN	late cornified envelope 2A	53	Cys-rich.				keratinization (GO:0031424)			p.C51_G64delCCGSSSGGCCSSGG(2)		breast(1)|large_intestine(1)|liver(2)|lung(4)	8	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGGCTGCTGCGGCTCCAGCTC	0.692																																					p.G53S		Atlas-SNP	.											LCE2A,NS,carcinoma,0,1	LCE2A	22	.	2	Deletion - In frame(2)	liver(2)	c.G157A						PASS	.						48	61	56					1																	152671534		2203	4299	6502	SO:0001583	missense	353139	exon2			TGCTGCGGCTCCA		CCDS1021.1	1q21.3	2008-02-05			ENSG00000187173	ENSG00000187173		"Late cornified envelopes"	29469	protein-coding gene	gene with protein product		612609				11698679	Standard	NM_178428		Approved	LEP9	uc001faj.3	Q5TA79	OTTHUMG00000012392	ENST00000368779.1:c.157G>A	chr1.hg19:g.152671534G>A	ENSP00000357768:p.Gly53Ser	16.0	0.0	.		40.0	6.0	.	NM_178428	A4QMZ9	Missense_Mutation	SNP	ENST00000368779.1	hg19	CCDS1021.1	.	.	.	.	.	.	.	.	.	.	-	6.374	0.437046	0.12104	.	.	ENSG00000187173	ENST00000368779	T	0.03717	3.83	3.72	2.79	0.32731	.	.	.	.	.	T	0.01222	0.0040	L	0.51853	1.615	0.09310	N	1	P	0.39964	0.697	B	0.29353	0.101	T	0.47394	-0.9121	9	0.87932	D	0	.	6.8388	0.23951	0.1374:0.0:0.8626:0.0	.	53	Q5TA79	LCE2A_HUMAN	S	53	ENSP00000357768:G53S	ENSP00000357768:G53S	G	+	1	0	LCE2A	150938158	0.982000	0.34865	0.111000	0.21465	0.270000	0.26580	0.561000	0.23515	0.525000	0.28522	0.580000	0.79431	GGC	.	.	.	none		0.692	LCE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034512.1	NM_178428		A	152671534	G	A	152671534	3	1	220	1	0	0	0	0	1	0	0	0	8672	1116	39	1	159	1	LCE2A	1	152671534	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	35730197	152671534	96579087	5	13275											
OR6Y1	391112	hgsc.bcm.edu	37	chr1	158517180	158517180	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtggagaatgccttttggCggccctgagcagaagggatc	9	8	16	8	1	0	3	0	1	0	2	1	5	0	4	2	5	2	1	2	5	2	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr1:158517180C>T	ENST00000302617.3	-	1	715	c.716G>A	c.(715-717)cGc>cAc	p.R239H		NM_001005189.1	NP_001005189.1	Q8NGX8	OR6Y1_HUMAN	olfactory receptor, family 6, subfamily Y, member 1	239						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)					TGCCTTTTGGCGGCCCTGAGC	0.522																																					p.R239H		Atlas-SNP	.											.	OR6Y1	73	.	0			c.G716A						PASS	.						137	136	137					1																	158517180		2202	4300	6502	SO:0001583	missense	391112	exon1			TTTTGGCGGCCCT	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.716G>A	chr1.hg19:g.158517180C>T	ENSP00000304807:p.Arg239His	179.0	0.0	.		173.0	81.0	.	NM_001005189	Q6IFS0	Missense_Mutation	SNP	ENST00000302617.3	hg19	CCDS30899.1	.	.	.	.	.	.	.	.	.	.	C	17.84	3.487953	0.64074	.	.	ENSG00000197532	ENST00000302617	T	0.00333	8.07	5.34	4.41	0.53225	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42964	D	0.000631	T	0.00524	0.0017	M	0.90759	3.145	0.09310	N	1	D	0.89917	1.0	D	0.81914	0.995	T	0.30297	-0.9983	10	0.87932	D	0	.	13.4384	0.61096	0.0:0.9214:0.0:0.0786	.	239	Q8NGX8	OR6Y1_HUMAN	H	239	ENSP00000304807:R239H	ENSP00000304807:R239H	R	-	2	0	OR6Y1	156783804	0.003000	0.15002	0.951000	0.38953	0.889000	0.51656	1.500000	0.35682	2.763000	0.94921	0.655000	0.94253	CGC	.	.	.	none		0.522	OR6Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051844.1	NM_001005189		T	158517180	C	T	158517180	3	4	220	1	0	0	0	0	1	0	0	0	11220	768	27	1	263	1	OR6Y1	1	158517180	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	5845646	158517180	90733441	6	13276											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228469852	228469852	+	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	ctgcaccaagtgatgccgggGaggtggtcttctctgtgcgg	5	10	16	10	2	2	1	0	1	2	0	3	2	2	2	2	5	3	1	2	5	1	1			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr1:228469852G>T	ENST00000422127.1	+	31	8460	c.8416G>T	c.(8416-8418)Gag>Tag	p.E2806*	OBSCN_ENST00000284548.11_Nonsense_Mutation_p.E2806*|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000570156.2_Nonsense_Mutation_p.E3235*|OBSCN_ENST00000359599.6_Nonsense_Mutation_p.E1653*	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2806	Ig-like 27.				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)				TGATGCCGGGGAGGTGGTCTT	0.647																																					p.E3235X		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G9703T						PASS	.						32	38	36					1																	228469852		1989	4156	6145	SO:0001587	stop_gained	84033	exon36			GCCGGGGAGGTGG	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.8416G>T	chr1.hg19:g.228469852G>T	ENSP00000409493:p.Glu2806*	154.0	0.0	.		232.0	108.0	.	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Nonsense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	17.68	3.448476	0.63178	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000359599;ENST00000366706;ENST00000366704	.	.	.	4.21	4.21	0.49690	.	0.000000	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09843	T	0.71	.	16.9495	0.86240	0.0:0.0:1.0:0.0	.	.	.	.	X	2806;2806;1653;505;212	.	ENSP00000284548:E2806X	E	+	1	0	OBSCN	226536475	1.000000	0.71417	0.992000	0.48379	0.321000	0.28281	9.350000	0.97070	2.063000	0.61619	0.462000	0.41574	GAG	.	.	.	none		0.647	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228469852	G	T	228469852	4	4	220	1	0	0	0	0	0	1	0	0	10819	1175	41	4	8534	4	OBSCN	1	228469852	Nonsense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	69952672	228469852	20780769	7	13277											
LYST	1130	hgsc.bcm.edu	37	chr1	235884164	235884164	+	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	ccatattccagaagattaggGaggttatttgtgagtatatt	12	15	10	4	0	0	3	0	1	0	2	1	4	1	4	2	2	0	2	2	2	6	8			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr1:235884164G>A	ENST00000389794.3	-	40	9531	c.9357C>T	c.(9355-9357)ctC>ctT	p.L3119L	LYST_ENST00000473037.1_5'UTR|LYST_ENST00000389793.2_Silent_p.L3119L			Q99698	LYST_HUMAN	lysosomal trafficking regulator	3119					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)			GAAGATTAGGGAGGTTATTTG	0.328																																					p.L3119L		Atlas-SNP	.											.	LYST	370	.	0			c.C9357T						PASS	.						121	119	120					1																	235884164		2203	4300	6503	SO:0001819	synonymous_variant	1130	exon40			ATTAGGGAGGTTA	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.9357C>T	chr1.hg19:g.235884164G>A		76.0	0.0	.		71.0	28.0	.	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	hg19	CCDS31062.1																																																																																			.	.	.	none		0.328	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			A	235884164	G	A	235884164	2	1	220	1	0	0	0	0	0	0	0	1	9135	1161	41	2		2	LYST	1	235884164	Silent	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	7414312	235884164	13366457	8	13278											
FAM110C	642273	hgsc.bcm.edu	37	chr2	45688	45688	+	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	ccgcggtgaagttctccctcCccagggcctccaccacctcg	5	7	9	20	3	1	1	0	1	1	0	5	1	3	1	8	2	0	1	8	2	1	1			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:45688C>T	ENST00000327669.4	-	1	697	c.698G>A	c.(697-699)gGg>gAg	p.G233E	FAM110C_ENST00000460464.1_5'Flank	NM_001077710.2	NP_001071178.2	Q1W6H9	F110C_HUMAN	family with sequence similarity 110, member C	233					positive regulation of cell migration (GO:0030335)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell projection assembly (GO:0060491)	cell cortex (GO:0005938)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)			central_nervous_system(1)|kidney(1)|lung(2)	4	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.00221)		all cancers(51;0.000815)|Epithelial(75;0.00379)|OV - Ovarian serous cystadenocarcinoma(76;0.0127)|GBM - Glioblastoma multiforme(21;0.232)		GTTCTCCCTCCCCAGGGCCTC	0.682																																					p.G233E		Atlas-SNP	.											.	FAM110C	11	.	0			c.G698A						PASS	.						12	15	14					2																	45688		2074	4200	6274	SO:0001583	missense	642273	exon1			TCCCTCCCCAGGG	DQ431183	CCDS42645.1	2p25.3	2011-12-01			ENSG00000184731	ENSG00000184731			33340	protein-coding gene	gene with protein product		611395				17499476, 19698782	Standard	NM_001077710		Approved		uc010yim.2	Q1W6H9	OTTHUMG00000151321	ENST00000327669.4:c.698G>A	chr2.hg19:g.45688C>T	ENSP00000328347:p.Gly233Glu	15.0	0.0	.		18.0	10.0	.	NM_001077710		Missense_Mutation	SNP	ENST00000327669.4	hg19	CCDS42645.1	.	.	.	.	.	.	.	.	.	.	C	18.41	3.618544	0.66787	.	.	ENSG00000184731	ENST00000327669	T	0.50548	0.74	4.64	4.64	0.57946	.	0.000000	0.85682	D	0.000000	T	0.67011	0.2848	M	0.70595	2.14	0.42278	D	0.992084	D	0.71674	0.998	D	0.74674	0.984	T	0.71879	-0.4459	10	0.72032	D	0.01	-10.2308	15.3421	0.74306	0.0:1.0:0.0:0.0	.	233	Q1W6H9	F110C_HUMAN	E	233	ENSP00000328347:G233E	ENSP00000328347:G233E	G	-	2	0	FAM110C	35688	0.991000	0.36638	0.057000	0.19452	0.348000	0.29142	3.654000	0.54453	2.277000	0.76020	0.561000	0.74099	GGG	.	.	.	none		0.682	FAM110C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322220.1	NM_001077710		T	45688	C	T	45688	3	4	220	1	0	0	0	0	1	0	0	0	5402	623	22	2	275	2	FAM110C	2	45688	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10		45688	243153685	9	13279											
DNMT3A	1788	hgsc.bcm.edu	37	chr2	25469542	25469542	+	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	gctggaagccccccagggccCattcaatcatgggcttgttc	7	9	11	14	0	2	0	2	0	0	0	3	1	2	1	4	3	1	3	4	3	2	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:25469542C>T	ENST00000264709.3	-	10	1563	c.1226G>A	c.(1225-1227)tGg>tAg	p.W409*	DNMT3A_ENST00000402667.1_Nonsense_Mutation_p.W186*|DNMT3A_ENST00000380746.4_Nonsense_Mutation_p.W220*|DNMT3A_ENST00000321117.5_Nonsense_Mutation_p.W409*|DNMT3A_ENST00000474887.1_5'Flank	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	409					C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCCCAGGGCCCATTCAATCAT	0.647			"Mis, F, N, S"		AML																																p.W409X		Atlas-SNP	.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	.	DNMT3A	1807	.	0			c.G1226A						PASS	.						61	61	61					2																	25469542		2203	4298	6501	SO:0001587	stop_gained	1788	exon10			AGGGCCCATTCAA		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.1226G>A	chr2.hg19:g.25469542C>T	ENSP00000264709:p.Trp409*	124.0	0.0	.		112.0	48.0	.	NM_175629	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Nonsense_Mutation	SNP	ENST00000264709.3	hg19	CCDS33157.1	.	.	.	.	.	.	.	.	.	.	C	37	6.406269	0.97542	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	.	.	.	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.0978	15.5438	0.76077	0.0:1.0:0.0:0.0	.	.	.	.	X	220;409;409;186	.	ENSP00000264709:W409X	W	-	2	0	DNMT3A	25323046	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	7.528000	0.81941	2.535000	0.85469	0.655000	0.94253	TGG	.	.	.	none		0.647	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552		T	25469542	C	T	25469542	4	4	220	1	0	0	0	0	0	1	0	0	4678	595	21	2	1568	2	DNMT3A	2	25469542	Nonsense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	25423854	25469542	217729831	10	13280											
C2orf16	84226	hgsc.bcm.edu	37	chr2	27801772	27801772	+	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	gacagatattttgcagcctgAagagacctatatagacccta	14	10	8	9	0	0	4	0	1	0	3	0	6	0	4	3	0	2	1	3	0	6	7			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:27801772A>T	ENST00000408964.2	+	1	2384	c.2333A>T	c.(2332-2334)gAa>gTa	p.E778V	AC074091.1_ENST00000408604.1_RNA	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	778						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)					TTGCAGCCTGAAGAGACCTAT	0.403																																					p.E778V		Atlas-SNP	.											.	C2orf16	357	.	0			c.A2333T						PASS	.						170	168	168					2																	27801772		1824	4081	5905	SO:0001583	missense	84226	exon1			AGCCTGAAGAGAC	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.2333A>T	chr2.hg19:g.27801772A>T	ENSP00000386190:p.Glu778Val	44.0	0.0	.		39.0	16.0	.	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	hg19	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	A	12.72	2.022880	0.35701	.	.	ENSG00000221843	ENST00000408964	T	0.06768	3.26	5.39	-2.51	0.06365	.	.	.	.	.	T	0.05868	0.0153	N	0.24115	0.695	0.09310	N	1	P	0.46512	0.879	P	0.45449	0.481	T	0.28681	-1.0036	9	0.66056	D	0.02	.	2.4234	0.04454	0.285:0.1502:0.4258:0.139	.	778	Q68DN1	CB016_HUMAN	V	778	ENSP00000386190:E778V	ENSP00000386190:E778V	E	+	2	0	C2orf16	27655276	0.056000	0.20664	0.033000	0.17914	0.105000	0.19272	0.158000	0.16422	-0.136000	0.11475	0.459000	0.35465	GAA	.	.	.	none		0.403	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		T	27801772	A	T	27801772	3	4	220	1	0	0	0	0	1	0	0	0	2159	246	9	5	2335	5	C2orf16	2	27801772	Missense_Mutation	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	2332230	27801772	215397601	11	13281											
GEMIN6	79833	hgsc.bcm.edu	37	chr2	39008788	39008788	+	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	gagaagctgatgcatttgttCacgtctggagactgcaaagc	11	10	12	8	1	2	3	1	1	1	2	2	5	2	3	0	1	4	4	0	1	2	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:39008788C>T	ENST00000281950.3	+	3	374	c.258C>T	c.(256-258)ttC>ttT	p.F86F	GEMIN6_ENST00000409011.1_3'UTR|GEMIN6_ENST00000409566.1_3'UTR	NM_024775.9	NP_079051.9	Q8WXD5	GEMI6_HUMAN	gem (nuclear organelle) associated protein 6	86					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|spliceosomal complex assembly (GO:0000245)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				kidney(1)|large_intestine(3)|pancreas(1)	5		all_hematologic(82;0.21)				TGCATTTGTTCACGTCTGGAG	0.478																																					p.F86F		Atlas-SNP	.											.	GEMIN6	13	.	0			c.C258T						PASS	.						102	88	92					2																	39008788		2203	4300	6503	SO:0001819	synonymous_variant	79833	exon3			TTTGTTCACGTCT	AF453443	CCDS1799.1	2p22.1	2014-05-14			ENSG00000152147	ENSG00000152147			20044	protein-coding gene	gene with protein product		607006				11748230	Standard	NM_024775		Approved	FLJ23459	uc002rrc.3	Q8WXD5	OTTHUMG00000128588	ENST00000281950.3:c.258C>T	chr2.hg19:g.39008788C>T		127.0	0.0	.		127.0	43.0	.	NM_024775	B2RDP8|Q53SI5|Q8WVB4|Q9H5G6	Silent	SNP	ENST00000281950.3	hg19	CCDS1799.1																																																																																			.	.	.	none		0.478	GEMIN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250441.3			T	39008788	C	T	39008788	2	4	220	1	0	0	0	0	0	0	0	1	6339	825	29	2		2	GEMIN6	2	39008788	Silent	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	11207016	39008788	204190585	12	13282											
ZNF638	27332	hgsc.bcm.edu	37	chr2	71607375	71607375	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaagaggtgaagaaaaagacTttagagtcaaagaaagtatc	21	7	10	3	0	1	6	1	1	0	5	2	6	1	6	0	1	0	1	0	1	8	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:71607375T>C	ENST00000409544.1	+	9	2919	c.2289T>C	c.(2287-2289)acT>acC	p.T763T	ZNF638_ENST00000355812.3_Silent_p.T763T|ZNF638_ENST00000264447.4_Silent_p.T763T|ZNF638_ENST00000410075.1_3'UTR|ZNF638_ENST00000377802.2_Silent_p.T763T|RNU6-105P_ENST00000363909.1_RNA	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	763					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						AGAAAAAGACTTTAGAGTCAA	0.249																																					p.T763T		Atlas-SNP	.											.	ZNF638	179	.	0			c.T2289C						PASS	.						33	33	33					2																	71607375		2189	4242	6431	SO:0001819	synonymous_variant	27332	exon9			AAAGACTTTAGAG	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.2289T>C	chr2.hg19:g.71607375T>C		85.0	0.0	.		118.0	49.0	.	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Silent	SNP	ENST00000409544.1	hg19	CCDS1917.1																																																																																			.	.	.	none		0.249	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		C	71607375	T	C	71607375	2	2	220	1	0	0	0	0	0	0	0	1	18067	1596	56	3		3	ZNF638	2	71607375	Silent	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	32598587	71607375	171591998	13	13283											
FER1L5	90342	hgsc.bcm.edu	37	chr2	97359251	97359251	+	RNA	SNP	A	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	ctacccctccagggcccttcAttcgggtggtcttcctgaac	5	11	9	16	1	2	1	1	1	1	0	5	1	4	1	5	3	2	0	5	3	2	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:97359251A>T	ENST00000457909.1	+	0	1760							A0AVI2	FR1L5_HUMAN	fer-1-like family member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(9)|large_intestine(9)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	38						AGGGCCCTTCATTCGGGTGGT	0.612																																					p.I1128F		Atlas-SNP	.											.	FER1L5	113	.	0			c.A3382T						PASS	.						58	69	66					2																	97359251		692	1591	2283			90342	exon31			CCCTTCATTCGGG	BC126368		2q11.2	2014-06-27	2014-06-27		ENSG00000249715	ENSG00000249715			19044	protein-coding gene	gene with protein product			"fer-1-like 5 (C. elegans)"				Standard	XM_006712826		Approved	DKFZp434I0121	uc010fia.3	A0AVI2	OTTHUMG00000154929		chr2.hg19:g.97359251A>T		78.0	0.0	.		85.0	34.0	.	NM_001113382	Q17RH2|Q6ZU24	Missense_Mutation	SNP	ENST00000457909.1	hg19		.	.	.	.	.	.	.	.	.	.	A	9.661	1.144037	0.21205	.	.	ENSG00000214272	ENST00000414152;ENST00000436930	.	.	.	5.31	-0.268	0.12934	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	T	0.57651	0.2068	M	0.62723	1.935	.	.	.	P	0.50369	0.934	P	0.52856	0.711	T	0.66508	-0.5906	7	0.66056	D	0.02	-3.7442	9.6818	0.40074	0.4125:0.0:0.5875:0.0	.	1128	A0AVI2	FR1L5_HUMAN	F	1128;1086	.	ENSP00000444148:I1128F	I	+	1	0	FER1L5	96722978	0.149000	0.22717	0.255000	0.24374	0.514000	0.34195	1.218000	0.32467	-0.049000	0.13379	0.459000	0.35465	ATT	.	.	.	none		0.612	FER1L5-001	KNOWN	basic|exp_conf	retained_intron	pseudogene	OTTHUMT00000339030.1	NM_001077400		T	97359251	A	T	97359251	1	4	220	0	1	0	0	0	0	0	0	0	5821	217	8	5		5	FER1L5	2	97359251	RNA	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	25751876	97359251	145840122	14	13284											
ST6GAL2	84620	hgsc.bcm.edu	37	chr2	107459932	107459932	+	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	cttcacccgcctcctctggaCctgtgcagccggaaaagccc	7	7	9	18	2	2	0	1	0	1	0	3	2	3	2	6	2	3	1	6	2	2	1			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:107459932C>G	ENST00000409382.3	-	2	1112	c.502G>C	c.(502-504)Gtc>Ctc	p.V168L	ST6GAL2_ENST00000409087.3_Missense_Mutation_p.V168L|AC016994.2_ENST00000425419.1_RNA|ST6GAL2_ENST00000361686.4_Missense_Mutation_p.V168L	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	168					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						CTCCTCTGGACCTGTGCAGCC	0.662																																					p.V168L		Atlas-SNP	.											.	ST6GAL2	159	.	0			c.G502C						PASS	.						78	90	86					2																	107459932		2203	4300	6503	SO:0001583	missense	84620	exon2			TCTGGACCTGTGC	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.502G>C	chr2.hg19:g.107459932C>G	ENSP00000386942:p.Val168Leu	123.0	0.0	.		165.0	63.0	.	NM_032528	D3DVK3|Q53QP4|Q86Y44|Q8IUG7|Q96HE4	Missense_Mutation	SNP	ENST00000409382.3	hg19	CCDS2073.1	.	.	.	.	.	.	.	.	.	.	C	1.093	-0.663505	0.03428	.	.	ENSG00000144057	ENST00000361686;ENST00000409382;ENST00000409087	T;T;T	0.30714	2.53;2.53;1.52	2.52	1.61	0.23674	.	2.704170	0.01639	N	0.023935	T	0.17109	0.0411	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.17501	-1.0367	10	0.19147	T	0.46	.	6.3831	0.21546	0.0:0.6285:0.0:0.3715	.	168;168	Q96JF0-2;Q96JF0	.;SIAT2_HUMAN	L	168	ENSP00000355273:V168L;ENSP00000386942:V168L;ENSP00000387332:V168L	ENSP00000355273:V168L	V	-	1	0	ST6GAL2	106826364	0.000000	0.05858	0.000000	0.03702	0.186000	0.23388	0.013000	0.13310	0.339000	0.23719	0.561000	0.74099	GTC	.	.	.	none		0.662	ST6GAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330065.1	NM_032528		G	107459932	C	G	107459932	3	3	220	1	0	0	0	0	1	0	0	0	15234	507	18	4	1194	4	ST6GAL2	2	107459932	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	10100681	107459932	135739441	15	13285											
TNFAIP6	7130	hgsc.bcm.edu	37	chr2	152235994	152235994	+	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	gtcaaggaaaaaatacaagtActacttctactggaaataaa	20	9	6	6	0	2	0	1	0	1	0	2	2	2	2	0	2	4	1	0	2	12	6			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:152235994A>T	ENST00000243347.3	+	6	856	c.781A>T	c.(781-783)Act>Tct	p.T261S		NM_007115.3	NP_009046.2	P98066	TSG6_HUMAN	tumor necrosis factor, alpha-induced protein 6	261					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|inflammatory response (GO:0006954)|signal transduction (GO:0007165)		hyaluronic acid binding (GO:0005540)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.131)	Hyaluronan(DB08818)	AAATACAAGTACTACTTCTAC	0.333																																					p.T261S		Atlas-SNP	.											.	TNFAIP6	98	.	0			c.A781T						PASS	.						84	90	88					2																	152235994		2203	4300	6503	SO:0001583	missense	7130	exon6			ACAAGTACTACTT		CCDS2193.1	2q23.3	2008-11-18			ENSG00000123610	ENSG00000123610			11898	protein-coding gene	gene with protein product		600410				1730767, 8568267, 15060082	Standard	NM_007115		Approved	TSG6, TSG-6	uc002txk.3	P98066	OTTHUMG00000131884	ENST00000243347.3:c.781A>T	chr2.hg19:g.152235994A>T	ENSP00000243347:p.Thr261Ser	56.0	0.0	.		83.0	39.0	.	NM_007115	Q53TI7|Q8WWI9	Missense_Mutation	SNP	ENST00000243347.3	hg19	CCDS2193.1	.	.	.	.	.	.	.	.	.	.	A	8.550	0.875364	0.17395	.	.	ENSG00000123610	ENST00000243347	T	0.18174	2.23	5.56	1.83	0.25207	.	0.332619	0.29185	N	0.012896	T	0.07773	0.0195	N	0.17082	0.46	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.33497	-0.9866	10	0.21540	T	0.41	.	3.4438	0.07473	0.6522:0.0:0.1812:0.1666	.	261	P98066	TSG6_HUMAN	S	261	ENSP00000243347:T261S	ENSP00000243347:T261S	T	+	1	0	TNFAIP6	151944240	0.044000	0.20184	0.250000	0.24296	0.441000	0.31987	1.210000	0.32370	0.063000	0.16370	0.533000	0.62120	ACT	.	.	.	none		0.333	TNFAIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254834.2	NM_007115		T	152235994	A	T	152235994	3	4	220	1	0	0	0	0	1	0	0	0	16287	391	14	5	803	5	TNFAIP6	2	152235994	Missense_Mutation	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	44776062	152235994	90963379	16	13286											
SMARCAL1	50485	hgsc.bcm.edu	37	chr2	217285132	217285132	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gacaggccggccttccatcaGctccatccctttcatttgtc	6	12	7	16	1	2	0	2	0	0	0	6	1	5	0	5	2	1	1	5	2	0	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:217285132G>A	ENST00000357276.4	+	5	1303	c.973G>A	c.(973-975)Gct>Act	p.A325T	SMARCAL1_ENST00000358207.5_Missense_Mutation_p.A325T	NM_014140.3	NP_054859.2	Q9NZC9	SMAL1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	325					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)		CCTTCCATCAGCTCCATCCCT	0.562									Schimke Immuno-Osseous Dysplasia																												p.A325T		Atlas-SNP	.											.	SMARCAL1	93	.	0			c.G973A						PASS	.						121	100	108					2																	217285132		2203	4300	6503	SO:0001583	missense	50485	exon5	Familial Cancer Database	SIOD	CCATCAGCTCCAT	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.973G>A	chr2.hg19:g.217285132G>A	ENSP00000349823:p.Ala325Thr	237.0	0.0	.		249.0	93.0	.	NM_014140	A6NEH0|Q53R00|Q96AY1|Q9NXQ5|Q9UFH3|Q9UI93	Missense_Mutation	SNP	ENST00000357276.4	hg19	CCDS2403.1	.	.	.	.	.	.	.	.	.	.	G	14.62	2.590173	0.46214	.	.	ENSG00000138375	ENST00000357276;ENST00000358207;ENST00000427645;ENST00000392128;ENST00000412913	D;D;T;D;T	0.86097	-2.04;-2.04;1.45;-2.07;0.63	4.85	4.85	0.62838	.	0.704849	0.14015	N	0.347188	T	0.80711	0.4675	L	0.59436	1.845	0.09310	N	1	P	0.37612	0.602	B	0.31290	0.127	T	0.71968	-0.4432	10	0.28530	T	0.3	-12.6293	13.2969	0.60303	0.0:0.1601:0.8399:0.0	.	325	Q9NZC9	SMAL1_HUMAN	T	325;325;224;189;45	ENSP00000349823:A325T;ENSP00000350940:A325T;ENSP00000392997:A224T;ENSP00000375974:A189T;ENSP00000390248:A45T	ENSP00000349823:A325T	A	+	1	0	SMARCAL1	216993377	0.682000	0.27624	0.373000	0.26003	0.202000	0.24057	4.009000	0.57110	2.531000	0.85337	0.561000	0.74099	GCT	.	.	.	none		0.562	SMARCAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256671.2			A	217285132	G	A	217285132	3	1	220	1	0	0	0	0	1	0	0	0	14786	971	34	2	983	2	SMARCAL1	2	217285132	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	65049138	217285132	25914241	17	13287											
KCNJ13	3769	hgsc.bcm.edu	37	chr2	233633228	233633228	+	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	tgctggagcagagtagccagAggacttgatggtgtaatgga	11	9	16	5	0	0	3	0	1	0	2	0	6	0	6	1	4	3	4	1	4	2	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:233633228A>T	ENST00000233826.3	-	3	895	c.756T>A	c.(754-756)ccT>ccA	p.P252P	GIGYF2_ENST00000373566.3_Intron|KCNJ13_ENST00000409779.1_3'UTR|GIGYF2_ENST00000409480.1_Intron|GIGYF2_ENST00000409451.3_Intron|GIGYF2_ENST00000409547.1_Intron|KCNJ13_ENST00000410029.1_Silent_p.P252P|GIGYF2_ENST00000409196.3_Intron|GIGYF2_ENST00000452341.2_Intron|GIGYF2_ENST00000373563.4_Intron|AC064852.4_ENST00000427571.1_RNA	NM_002242.4	NP_002233.2	O60928	KCJ13_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 13	252					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	inward rectifier potassium channel activity (GO:0005242)			endometrium(3)|large_intestine(2)|lung(2)|stomach(1)|urinary_tract(1)	9		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0306)|Lung NSC(271;0.0908)		Epithelial(121;5.9e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0617)		GAGTAGCCAGAGGACTTGATG	0.443																																					p.P252P		Atlas-SNP	.											.	KCNJ13	18	.	0			c.T756A						PASS	.						129	118	122					2																	233633228		2203	4300	6503	SO:0001819	synonymous_variant	3769	exon3			AGCCAGAGGACTT	AJ006128	CCDS2498.1, CCDS54437.1	2q37	2014-01-28			ENSG00000115474	ENSG00000115474		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6259	protein-coding gene	gene with protein product		603208				9878260, 9620703, 16382105	Standard	NM_002242		Approved	Kir7.1, Kir1.4, LCA16	uc002vtp.3	O60928	OTTHUMG00000153292	ENST00000233826.3:c.756T>A	chr2.hg19:g.233633228A>T		164.0	0.0	.		200.0	87.0	.	NM_002242	A0PGH1|O76023|Q53SA1|Q8N3Y4	Silent	SNP	ENST00000233826.3	hg19	CCDS2498.1																																																																																			.	.	.	none		0.443	KCNJ13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257036.1	NM_002242		T	233633228	A	T	233633228	2	4	220	1	0	0	0	0	0	0	0	1	8054	291	11	5		5	KCNJ13	2	233633228	Silent	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	16348096	233633228	9566145	18	13288											
GIGYF2	26058	hgsc.bcm.edu	37	chr2	233659498	233659498	+	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	cagcccctgtcgcagattccTtcagatacagcctctcctct	7	11	6	17	1	3	2	1	0	2	2	6	2	4	2	5	0	3	1	5	0	1	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr2:233659498T>A	ENST00000409547.1	+	15	1634	c.1323T>A	c.(1321-1323)ccT>ccA	p.P441P	GIGYF2_ENST00000373566.3_Silent_p.P463P|GIGYF2_ENST00000409480.1_Silent_p.P463P|GIGYF2_ENST00000409451.3_Silent_p.P462P|GIGYF2_ENST00000409196.3_Silent_p.P435P|GIGYF2_ENST00000452341.2_Silent_p.P272P|GIGYF2_ENST00000373563.4_Silent_p.P441P	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	441	Pro-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)		CGCAGATTCCTTCAGATACAG	0.478																																					p.P462P		Atlas-SNP	.											.	GIGYF2	288	.	0			c.T1386A						PASS	.						292	293	293					2																	233659498		2203	4300	6503	SO:0001819	synonymous_variant	26058	exon15			GATTCCTTCAGAT	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.1323T>A	chr2.hg19:g.233659498T>A		94.0	0.0	.		92.0	44.0	.	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Silent	SNP	ENST00000409547.1	hg19	CCDS33401.1																																																																																			.	.	.	none		0.478	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		A	233659498	T	A	233659498	2	1	220	1	0	0	0	0	0	0	0	1	6385	1596	56	5		5	GIGYF2	2	233659498	Silent	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	26270	233659498	9539875	19	13289											
KIAA1407	57577	hgsc.bcm.edu	37	chr3	113697143	113697143	+	Missense_Mutation	SNP	A	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	ttttgaagaaaatgtacacaAaattttcttacttcttcctg	13	17	4	7	0	2	2	0	1	2	1	3	2	3	2	1	0	2	1	1	0	7	8			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr3:113697143A>C	ENST00000295878.3	-	16	2642	c.2496T>G	c.(2494-2496)ttT>ttG	p.F832L		NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	832										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						AATGTACACAAAATTTTCTTA	0.393																																					p.F832L		Atlas-SNP	.											.	KIAA1407	80	.	0			c.T2496G						PASS	.						73	74	74					3																	113697143		2203	4300	6503	SO:0001583	missense	57577	exon16			TACACAAAATTTT	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.2496T>G	chr3.hg19:g.113697143A>C	ENSP00000295878:p.Phe832Leu	45.0	0.0	.		63.0	27.0	.	NM_020817	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	hg19	CCDS2977.1	.	.	.	.	.	.	.	.	.	.	A	7.654	0.683498	0.14907	.	.	ENSG00000163617	ENST00000295878	T	0.28666	1.6	4.46	-2.16	0.07080	.	0.462954	0.22456	N	0.059825	T	0.05135	0.0137	N	0.00413	-1.525	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38415	-0.9662	10	0.05620	T	0.96	.	5.5621	0.17150	0.256:0.3712:0.3728:0.0	.	832	Q8NCU4	K1407_HUMAN	L	832	ENSP00000295878:F832L	ENSP00000295878:F832L	F	-	3	2	KIAA1407	115179833	0.000000	0.05858	0.000000	0.03702	0.745000	0.42441	-1.005000	0.03674	-0.297000	0.08934	0.528000	0.53228	TTT	.	.	.	none		0.393	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817		C	113697143	A	C	113697143	3	2	220	1	0	0	0	0	1	0	0	0	8236	11	1	5	322	5	KIAA1407	3	113697143	Missense_Mutation	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10		113697143	84325287	20	13290											
ABCC5	10057	hgsc.bcm.edu	37	chr3	183669307	183669307	+	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	aaacttcatagggcttcgaaGgatccttcggaaaagctcgt	12	10	10	9	3	1	0	1	0	0	0	5	3	2	2	1	3	2	2	1	3	5	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr3:183669307G>C	ENST00000334444.6	-	20	3106	c.2866C>G	c.(2866-2868)Ctt>Gtt	p.L956V	ABCC5_ENST00000265586.6_Missense_Mutation_p.L956V	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	956	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	GGGCTTCGAAGGATCCTTCGG	0.542																																					p.L956V		Atlas-SNP	.											.	ABCC5	142	.	0			c.C2866G						PASS	.						74	79	77					3																	183669307		2004	4191	6195	SO:0001583	missense	10057	exon20			TTCGAAGGATCCT	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.2866C>G	chr3.hg19:g.183669307G>C	ENSP00000333926:p.Leu956Val	86.0	0.0	.		71.0	41.0	.	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Missense_Mutation	SNP	ENST00000334444.6	hg19	CCDS43176.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.299975	0.81136	.	.	ENSG00000114770	ENST00000334444;ENST00000265586	D;D	0.91843	-2.92;-2.92	6.11	5.23	0.72850	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	0.92616	0.7654	M	0.74647	2.275	0.58432	D	0.999996	P;P	0.43024	0.771;0.798	P;B	0.44422	0.449;0.387	D	0.92434	0.5956	10	0.49607	T	0.09	-14.3754	15.2019	0.73147	0.067:0.0:0.933:0.0	.	956;956	Q86UX3;O15440	.;MRP5_HUMAN	V	956	ENSP00000333926:L956V;ENSP00000265586:L956V	ENSP00000265586:L956V	L	-	1	0	ABCC5	185152001	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	6.461000	0.73522	1.590000	0.49995	0.655000	0.94253	CTT	.	.	.	none		0.542	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688		C	183669307	G	C	183669307	3	2	220	1	0	0	0	0	1	0	0	0	56	1000	35	4	1491	4	ABCC5	3	183669307	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	69972164	183669307	14353123	21	13291											
KIAA0226	9711	hgsc.bcm.edu	37	chr3	197408102	197408102	+	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	ttaatgagcaggtccttggaGaagttgctgacgtagtactt	10	13	12	6	1	0	3	0	2	0	1	1	4	1	3	1	2	3	5	1	2	4	6			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr3:197408102G>A	ENST00000296343.5	-	16	2327	c.2328C>T	c.(2326-2328)ttC>ttT	p.F776F	KIAA0226_ENST00000389665.5_Silent_p.F801F|KIAA0226_ENST00000273582.5_Silent_p.F731F	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	776					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)		GGTCCTTGGAGAAGTTGCTGA	0.522																																					p.F776F	Esophageal Squamous(3;167 355 3763 15924)	Atlas-SNP	.											.	KIAA0226	136	.	0			c.C2328T						PASS	.						154	149	151					3																	197408102		2046	4228	6274	SO:0001819	synonymous_variant	9711	exon16			CTTGGAGAAGTTG	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.2328C>T	chr3.hg19:g.197408102G>A		177.0	0.0	.		154.0	72.0	.	NM_014687	Q96CK5	Silent	SNP	ENST00000296343.5	hg19	CCDS43195.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.648|8.648	0.897483|0.897483	0.17686|0.17686	.|.	.|.	ENSG00000145016|ENSG00000145016	ENST00000413360|ENST00000415452	.|.	.|.	.|.	4.55|4.55	3.66|3.66	0.41972|0.41972	.|.	.|.	.|.	.|.	.|.	T|T	0.63046|0.63046	0.2478|0.2478	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.61667|0.61667	-0.7016|-0.7016	4|4	.|.	.|.	.|.	.|.	12.4295|12.4295	0.55565|0.55565	0.0825:0.0:0.9175:0.0|0.0825:0.0:0.9175:0.0	.|.	.|.	.|.	.|.	F|F	738|560	.|.	.|.	L|S	-|-	1|2	0|0	KIAA0226|KIAA0226	198892499|198892499	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.909000|0.909000	0.53808|0.53808	2.466000|2.466000	0.45084|0.45084	1.244000|1.244000	0.43870|0.43870	0.555000|0.555000	0.69702|0.69702	CTC|TCT	.	.	.	none		0.522	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901		A	197408102	G	A	197408102	2	1	220	1	0	0	0	0	0	0	0	1	8169	933	33	2		2	KIAA0226	3	197408102	Silent	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	13738795	197408102	614328	22	13292											
GAK	2580	hgsc.bcm.edu	37	chr4	882734	882734	+	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	ccaggaagccgccatacggcTggtcgtactccgccagcgcc	7	5	12	17	5	0	0	0	0	0	0	2	1	1	1	6	3	4	2	6	3	3	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:882734T>A	ENST00000314167.4	-	11	1216	c.1106A>T	c.(1105-1107)cAg>cTg	p.Q369L	GAK_ENST00000511163.1_Missense_Mutation_p.Q290L	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	369					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)		GCCATACGGCTGGTCGTACTC	0.662																																					p.Q369L		Atlas-SNP	.											.	GAK	104	.	0			c.A1106T						PASS	.						45	40	42					4																	882734		2200	4293	6493	SO:0001583	missense	2580	exon11			TACGGCTGGTCGT	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.1106A>T	chr4.hg19:g.882734T>A	ENSP00000314499:p.Gln369Leu	46.0	0.0	.		63.0	29.0	.	NM_005255	Q5U4P5|Q9BVY6	Missense_Mutation	SNP	ENST00000314167.4	hg19	CCDS3340.1	.	.	.	.	.	.	.	.	.	.	T	16.66	3.185496	0.57909	.	.	ENSG00000178950	ENST00000314167;ENST00000511163	T;T	0.79352	-0.8;-1.26	4.55	4.55	0.56014	.	0.739757	0.13112	N	0.412872	T	0.80544	0.4643	M	0.76002	2.32	0.58432	D	0.999999	D;P;P;P	0.54772	0.968;0.883;0.944;0.937	P;P;B;B	0.48654	0.585;0.48;0.4;0.256	T	0.79271	-0.1872	10	0.45353	T	0.12	-33.1852	10.2933	0.43610	0.0:0.0:0.0:1.0	.	290;290;369;265	Q5U4P5;E9PGR2;O14976;Q59HA5	.;.;GAK_HUMAN;.	L	369;290	ENSP00000314499:Q369L;ENSP00000421361:Q290L	ENSP00000314499:Q369L	Q	-	2	0	GAK	872734	1.000000	0.71417	0.993000	0.49108	0.052000	0.14988	6.860000	0.75473	1.679000	0.50963	0.459000	0.35465	CAG	.	.	.	none		0.662	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255		A	882734	T	A	882734	3	1	220	1	0	0	0	0	1	0	0	0	6202	1580	55	5	2901	5	GAK	4	882734	Missense_Mutation	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10		882734	190271542	23	13293											
ADD1	118	hgsc.bcm.edu	37	chr4	2916729	2916729	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaccgtgagctggaggagtAccgcagggaggtggagagga	11	4	20	6	2	0	3	0	1	0	2	0	8	0	7	2	6	2	3	2	6	1	1			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:2916729A>G	ENST00000398129.1	+	12	1744	c.1724A>G	c.(1723-1725)tAc>tGc	p.Y575C	ADD1_ENST00000513328.2_Missense_Mutation_p.Y575C|ADD1_ENST00000398125.1_Missense_Mutation_p.Y606C|ADD1_ENST00000355842.3_Missense_Mutation_p.Y606C|ADD1_ENST00000446856.1_Missense_Mutation_p.Y575C|ADD1_ENST00000264758.7_Missense_Mutation_p.Y606C|ADD1_ENST00000398123.2_Missense_Mutation_p.Y606C|ADD1_ENST00000503455.2_Missense_Mutation_p.Y606C			P35611	ADDA_HUMAN	adducin 1 (alpha)	575					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)		CTGGAGGAGTACCGCAGGGAG	0.587																																					p.Y606C	Esophageal Squamous(71;505 1201 20414 34538 37449)	Atlas-SNP	.											.	ADD1	56	.	0			c.A1817G						PASS	.						100	95	96					4																	2916729		2203	4300	6503	SO:0001583	missense	118	exon13			AGGAGTACCGCAG	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.1724A>G	chr4.hg19:g.2916729A>G	ENSP00000381197:p.Tyr575Cys	197.0	0.0	.		196.0	89.0	.	NM_176801	A2A3N8|A2A3P0|B4DI79|D3DVR3|D3DVR4|D3DVR5|Q13734|Q14729|Q16156|Q86XM2|Q9UJB6	Missense_Mutation	SNP	ENST00000398129.1	hg19	CCDS43205.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	26.3|26.3	4.720674|4.720674	0.89205|0.89205	.|.	.|.	ENSG00000087274|ENSG00000087274	ENST00000514940;ENST00000541843|ENST00000264758;ENST00000446856;ENST00000398125;ENST00000513328;ENST00000503455;ENST00000355842;ENST00000398123;ENST00000398129	.|T;T;T;T;T;T;T;T	.|0.31247	.|1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5	5.44|5.44	5.44|5.44	0.79542|0.79542	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.56775|0.56775	0.2008|0.2008	M|M	0.73430|0.73430	2.235|2.235	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.89917	.|0.993;1.0;1.0;0.997;1.0	.|D;D;D;P;D	.|0.87578	.|0.928;0.977;0.998;0.863;0.992	T|T	0.61816|0.61816	-0.6985|-0.6985	5|10	.|0.87932	.|D	.|0	-15.9835|-15.9835	15.4885|15.4885	0.75587|0.75587	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|606;575;606;575;606	.|Q86XM2;P35611;P35611-3;P35611-2;A2A3N8	.|.;ADDA_HUMAN;.;.;.	A|C	312;21|606;575;606;575;606;606;606;575	.|ENSP00000264758:Y606C;ENSP00000399828:Y575C;ENSP00000381193:Y606C;ENSP00000421907:Y575C;ENSP00000423024:Y606C;ENSP00000348100:Y606C;ENSP00000381191:Y606C;ENSP00000381197:Y575C	.|ENSP00000264758:Y606C	T|Y	+|+	1|2	0|0	ADD1|ADD1	2886527|2886527	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	8.766000|8.766000	0.91728|0.91728	2.060000|2.060000	0.61445|0.61445	0.460000|0.460000	0.39030|0.39030	ACC|TAC	.	.	.	none		0.587	ADD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242840.1	NM_014189		G	2916729	A	G	2916729	3	3	220	1	0	0	0	0	1	0	0	0	304	391	14	3	1863	3	ADD1	4	2916729	Missense_Mutation	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	2033995	2916729	188237547	24	13294											
SLC10A4	201780	hgsc.bcm.edu	37	chr4	48487158	48487158	+	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	ggtggctgactacattgtgaAggtaaggccccctcttccct	7	11	11	12	0	1	2	0	2	1	0	2	2	2	2	3	4	1	2	3	4	3	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:48487158A>C	ENST00000273861.4	+	2	1019	c.800A>C	c.(799-801)aAg>aCg	p.K267T		NM_152679.3	NP_689892.1	Q96EP9	NTCP4_HUMAN	solute carrier family 10, member 4	267						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						TACATTGTGAAGGTAAGGCCC	0.522																																					p.K267T		Atlas-SNP	.											.	SLC10A4	23	.	0			c.A800C						PASS	.						73	72	72					4																	48487158		2203	4300	6503	SO:0001630	splice_region_variant	201780	exon2			TTGTGAAGGTAAG	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.801+1A>C	chr4.hg19:g.48487158A>C		157.0	0.0	.		198.0	71.0	.	NM_152679	Q8WUZ2	Missense_Mutation	SNP	ENST00000273861.4	hg19	CCDS3482.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.242171	0.79912	.	.	ENSG00000145248	ENST00000273861	T	0.10763	2.84	5.03	5.03	0.67393	.	0.044192	0.85682	D	0.000000	T	0.19967	0.0480	L	0.56340	1.77	0.80722	D	1	P	0.51537	0.946	P	0.51550	0.673	T	0.00480	-1.1714	10	0.44086	T	0.13	-29.9309	15.2283	0.73367	1.0:0.0:0.0:0.0	.	267	Q96EP9	NTCP4_HUMAN	T	267	ENSP00000273861:K267T	ENSP00000273861:K267T	K	+	2	0	SLC10A4	48181915	1.000000	0.71417	1.000000	0.80357	0.468000	0.32798	8.506000	0.90518	2.237000	0.73441	0.460000	0.39030	AAG	.	.	.	none		0.522	SLC10A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219926.3	NM_152679	Missense_Mutation	C	48487158	A	C	48487158	5	2	220	1	0	0	0	0	0	0	1	0	14389	86	3	5	806	5	SLC10A4	4	48487158	Splice_Site	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	45570429	48487158	142667118	25	13295											
KIAA1211	57482	hgsc.bcm.edu	37	chr4	57182735	57182735	+	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	cctcgcccccaggccccgagGaaaggaagggacagaagagg	12	1	15	13	2	0	2	0	0	0	2	1	6	0	5	5	5	0	0	5	5	3	0			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:57182735G>A	ENST00000504228.1	+	6	3172	c.3067G>A	c.(3067-3069)Gaa>Aaa	p.E1023K	KIAA1211_ENST00000264229.6_Missense_Mutation_p.E1023K|KIAA1211_ENST00000541073.1_Missense_Mutation_p.E1016K			Q6ZU35	K1211_HUMAN	KIAA1211	1023										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)					AGGCCCCGAGGAAAGGAAGGG	0.647																																					p.E1023K		Atlas-SNP	.											.	KIAA1211	178	.	0			c.G3067A						PASS	.						16	19	18					4																	57182735		1988	4152	6140	SO:0001583	missense	57482	exon8			CCCGAGGAAAGGA	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.3067G>A	chr4.hg19:g.57182735G>A	ENSP00000423366:p.Glu1023Lys	68.0	0.0	.		66.0	18.0	.	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	hg19	CCDS43230.1	.	.	.	.	.	.	.	.	.	.	G	14.11	2.437122	0.43224	.	.	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073	T;T;T	0.78003	-1.14;-1.14;-1.14	5.24	3.44	0.39384	.	.	.	.	.	T	0.67970	0.2950	L	0.44542	1.39	0.09310	N	1	B;B;B	0.28350	0.208;0.084;0.084	B;B;B	0.21917	0.022;0.037;0.037	T	0.58301	-0.7660	9	0.44086	T	0.13	-11.2684	8.9225	0.35621	0.2382:0.0:0.7618:0.0	.	1016;1016;1023	B7ZVZ4;F5H1N7;Q6ZU35	.;.;K1211_HUMAN	K	1023;1023;1016	ENSP00000264229:E1023K;ENSP00000423366:E1023K;ENSP00000444006:E1016K	ENSP00000264229:E1023K	E	+	1	0	KIAA1211	56877492	0.169000	0.23002	0.190000	0.23270	0.164000	0.22412	2.380000	0.44327	1.140000	0.42260	0.561000	0.74099	GAA	.	.	.	none		0.647	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722		A	57182735	G	A	57182735	3	1	220	1	0	0	0	0	1	0	0	0	8222	1175	41	2	3085	2	KIAA1211	4	57182735	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	8695577	57182735	133971541	26	13296											
C4orf17	84103	hgsc.bcm.edu	37	chr4	100434294	100434294	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgagggcaaaggcagccataTtatggctagaaatgtaagct	14	8	12	7	1	0	1	0	0	0	1	0	2	0	1	1	3	2	5	1	3	6	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:100434294T>C	ENST00000326581.4	+	2	418	c.56T>C	c.(55-57)aTt>aCt	p.I19T	C4orf17_ENST00000514652.1_Missense_Mutation_p.I19T	NM_032149.2	NP_115525.2	Q53FE4	CD017_HUMAN	chromosome 4 open reading frame 17	19										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)		GGCAGCCATATTATGGCTAGA	0.468																																					p.I19T		Atlas-SNP	.											.	C4orf17	42	.	0			c.T56C						PASS	.						102	86	92					4																	100434294		2203	4300	6503	SO:0001583	missense	84103	exon2			GCCATATTATGGC	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.56T>C	chr4.hg19:g.100434294T>C	ENSP00000322582:p.Ile19Thr	132.0	0.0	.		151.0	65.0	.	NM_032149	Q6FI84|Q6IS77|Q8NA78|Q9H0D9	Missense_Mutation	SNP	ENST00000326581.4	hg19	CCDS3649.1	.	.	.	.	.	.	.	.	.	.	T	10.04	1.242808	0.22796	.	.	ENSG00000138813	ENST00000326581;ENST00000514652	T;T	0.18338	2.22;2.22	4.76	-9.53	0.00575	.	1.807420	0.02601	N	0.101018	T	0.15089	0.0364	L	0.57536	1.79	0.09310	N	1	B	0.24426	0.103	B	0.25140	0.058	T	0.39354	-0.9618	10	0.66056	D	0.02	1.4304	5.5029	0.16838	0.1118:0.1614:0.5637:0.1631	.	19	Q53FE4	CD017_HUMAN	T	19	ENSP00000322582:I19T;ENSP00000427663:I19T	ENSP00000322582:I19T	I	+	2	0	C4orf17	100653317	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.503000	0.06383	-1.204000	0.02648	-0.256000	0.11100	ATT	.	.	.	none		0.468	C4orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253670.2	NM_032149		C	100434294	T	C	100434294	3	2	220	1	0	0	0	0	1	0	0	0	2254	1493	52	3	58	3	C4orf17	4	100434294	Missense_Mutation	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	43251559	100434294	90719982	27	13297											
TBCK	93627	hgsc.bcm.edu	37	chr4	107163709	107163709	+	Frame_Shift_Del	DEL	C	C	-																															gaccttgtccaaagctttcaCcatcctcaaagagaaaactg																								rs371959745		TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:107163709delC	ENST00000273980.5	-	13	1535	c.1088delG	c.(1087-1089)ggtfs	p.G363fs	TBCK_ENST00000432496.2_Frame_Shift_Del_p.G363fs|TBCK_ENST00000394708.2_Frame_Shift_Del_p.G363fs|TBCK_ENST00000361687.4_Frame_Shift_Del_p.G300fs|TBCK_ENST00000394706.3_Frame_Shift_Del_p.G324fs					TBC1 domain containing kinase											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						AAAGCTTTCACCATCCTCAAA	0.313																																					p.G363fs		Atlas-Indel,Pindel	.											.	TBCK	89	.	0			c.1089delT						PASS	.						67	65	66					4																	107163709		2203	4300	6503	SO:0001589	frameshift_variant	93627	exon12			.		CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.1088delG	chr4.hg19:g.107163709delC	ENSP00000273980:p.Gly363fs	27.0	0.0	0		28.0	17.0	0.607143	NM_001163435		Frame_Shift_Del	DEL	ENST00000273980.5	hg19	CCDS54788.1																																																																																			.	.	.	none		0.313	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115		-	107163709	C	-	107163709	7	5	220	1	0	1	0	1	0	0	0	0	15648	507	18	0	1653	0	TBCK	4	107163709	Frame_Shift_Del	DEL	C	TCGA-MH-A55Z-01A-11D-A26P-10	6729415	107163709	83990567	28	13298											
SH3D19	152503	hgsc.bcm.edu	37	chr4	152096316	152096316	+	Missense_Mutation	SNP	T	T	A																															tctcagtcccagagtcccacTctccagaagctctgttagca																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:152096316T>A	ENST00000409252.2	-	6	907	c.200A>T	c.(199-201)gAg>gTg	p.E67V	SH3D19_ENST00000455740.1_Missense_Mutation_p.E67V|SH3D19_ENST00000427414.2_Missense_Mutation_p.E67V|SH3D19_ENST00000514152.1_Missense_Mutation_p.E67V|SH3D19_ENST00000409598.4_Missense_Mutation_p.E67V|SH3D19_ENST00000304527.4_Missense_Mutation_p.E67V|SH3D19_ENST00000424281.1_Missense_Mutation_p.E67V|SH3D19_ENST00000604030.1_5'Flank			Q5HYK7	SH319_HUMAN	SH3 domain containing 19	67					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)				AGAGTCCCACTCTCCAGAAGC	0.517																																					p.E67V		Atlas-SNP	.											.	SH3D19	54	.	0			c.A200T						PASS	.						85	85	85					4																	152096316		2203	4300	6503	SO:0001583	missense	152503	exon1			TCCCACTCTCCAG	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.200A>T	chr4.hg19:g.152096316T>A	ENSP00000386848:p.Glu67Val	80.0	0.0	.		76.0	34.0	.	NM_001128924	B7Z296|Q08EK1|Q32N10|Q5U3B8|Q86XB3|Q8N5E7|Q9UFC8	Missense_Mutation	SNP	ENST00000409252.2	hg19	CCDS34077.2	.	.	.	.	.	.	.	.	.	.	T	21.3	4.134175	0.77662	.	.	ENSG00000109686	ENST00000409598;ENST00000304527;ENST00000455740;ENST00000424281;ENST00000427414;ENST00000409252;ENST00000514152	T;T;T;T;T;T;T	0.06449	3.3;3.3;3.3;3.3;3.3;3.3;3.3	6.07	3.59	0.41128	.	2.410060	0.02778	U	0.120587	T	0.23451	0.0567	M	0.62723	1.935	0.38335	D	0.943906	D;D;D	0.63046	0.969;0.982;0.992	P;P;P	0.61397	0.625;0.849;0.888	T	0.00024	-1.2325	10	0.87932	D	0	-8.5478	10.825	0.46627	0.0:0.1277:0.0:0.8723	.	67;67;67	Q5HYK7;Q5HYK7-2;Q5HYK7-3	SH319_HUMAN;.;.	V	67	ENSP00000387030:E67V;ENSP00000302913:E67V;ENSP00000416708:E67V;ENSP00000404542:E67V;ENSP00000415694:E67V;ENSP00000386848:E67V;ENSP00000423449:E67V	ENSP00000302913:E67V	E	-	2	0	SH3D19	152315766	0.997000	0.39634	0.976000	0.42696	0.954000	0.61252	2.976000	0.49289	0.514000	0.28300	0.533000	0.62120	GAG	.	.	.	none		0.517	SH3D19-002	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335132.3	NM_001009555		A	152096316	T	A	152096316	3	1	220	1	0	0	0	0	1	0	0	0	14262	1551	54	5	2232	5	SH3D19	4	152096316	Missense_Mutation	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	44932607	152096316	39057960	29	13299	130	3									
SH3D19	152503	hgsc.bcm.edu	37	chr4	152096322	152096322	+	Missense_Mutation	SNP	G	G	A																															tcccagagtcccactctccaGaagctctgttagcagctggt																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:152096322G>A	ENST00000409252.2	-	6	901	c.194C>T	c.(193-195)tCt>tTt	p.S65F	SH3D19_ENST00000455740.1_Missense_Mutation_p.S65F|SH3D19_ENST00000427414.2_Missense_Mutation_p.S65F|SH3D19_ENST00000514152.1_Missense_Mutation_p.S65F|SH3D19_ENST00000409598.4_Missense_Mutation_p.S65F|SH3D19_ENST00000304527.4_Missense_Mutation_p.S65F|SH3D19_ENST00000424281.1_Missense_Mutation_p.S65F|SH3D19_ENST00000604030.1_5'Flank			Q5HYK7	SH319_HUMAN	SH3 domain containing 19	65					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)				CCACTCTCCAGAAGCTCTGTT	0.527																																					p.S65F		Atlas-SNP	.											.	SH3D19	54	.	0			c.C194T						PASS	.						85	85	85					4																	152096322		2203	4300	6503	SO:0001583	missense	152503	exon1			TCTCCAGAAGCTC	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.194C>T	chr4.hg19:g.152096322G>A	ENSP00000386848:p.Ser65Phe	85.0	0.0	.		83.0	40.0	.	NM_001128924	B7Z296|Q08EK1|Q32N10|Q5U3B8|Q86XB3|Q8N5E7|Q9UFC8	Missense_Mutation	SNP	ENST00000409252.2	hg19	CCDS34077.2	.	.	.	.	.	.	.	.	.	.	G	19.49	3.838322	0.71373	.	.	ENSG00000109686	ENST00000409598;ENST00000304527;ENST00000455740;ENST00000424281;ENST00000427414;ENST00000409252;ENST00000514152	T;T;T;T;T;T;T	0.06068	3.35;3.35;3.35;3.35;3.35;3.35;3.35	6.07	4.34	0.51931	.	0.591075	0.16731	N	0.201834	T	0.21674	0.0522	M	0.64997	1.995	0.35608	D	0.808417	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	T	0.08534	-1.0717	10	0.87932	D	0	-5.1533	12.0719	0.53622	0.0648:0.1217:0.8135:0.0	.	65;65;65	Q5HYK7;Q5HYK7-2;Q5HYK7-3	SH319_HUMAN;.;.	F	65	ENSP00000387030:S65F;ENSP00000302913:S65F;ENSP00000416708:S65F;ENSP00000404542:S65F;ENSP00000415694:S65F;ENSP00000386848:S65F;ENSP00000423449:S65F	ENSP00000302913:S65F	S	-	2	0	SH3D19	152315772	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	5.083000	0.64456	0.883000	0.36040	0.655000	0.94253	TCT	.	.	.	none		0.527	SH3D19-002	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335132.3	NM_001009555		A	152096322	G	A	152096322	3	1	220	1	0	0	0	0	1	0	0	0	14262	942	33	2	2238	2	SH3D19	4	152096322	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	6	152096322	39057954	30	13300	130	3									
SH3D19	152503	hgsc.bcm.edu	37	chr4	152096326	152096326	+	Frame_Shift_Del	DEL	C	C	-																															agagtcccactctccagaagCtctgttagcagctggtttgg																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:152096326delC	ENST00000409252.2	-	6	897	c.190delG	c.(190-192)gctfs	p.A64fs	SH3D19_ENST00000455740.1_Frame_Shift_Del_p.A64fs|SH3D19_ENST00000427414.2_Frame_Shift_Del_p.A64fs|SH3D19_ENST00000514152.1_Frame_Shift_Del_p.A64fs|SH3D19_ENST00000409598.4_Frame_Shift_Del_p.A64fs|SH3D19_ENST00000304527.4_Frame_Shift_Del_p.A64fs|SH3D19_ENST00000424281.1_Frame_Shift_Del_p.A64fs|SH3D19_ENST00000604030.1_5'Flank			Q5HYK7	SH319_HUMAN	SH3 domain containing 19	64					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)				TCTCCAGAAGCTCTGTTAGCA	0.532																																					p.A64fs		Atlas-Indel,Pindel	.											.	SH3D19	54	.	0			c.191delC						PASS	.						86	86	86					4																	152096326		2203	4300	6503	SO:0001589	frameshift_variant	152503	exon1			.	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.190delG	chr4.hg19:g.152096326delC	ENSP00000386848:p.Ala64fs	84.0	0.0	0		81.0	39.0	0.481481	NM_001128924	B7Z296|Q08EK1|Q32N10|Q5U3B8|Q86XB3|Q8N5E7|Q9UFC8	Frame_Shift_Del	DEL	ENST00000409252.2	hg19	CCDS34077.2																																																																																			.	.	.	none		0.532	SH3D19-002	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335132.3	NM_001009555		-	152096326	C	-	152096326	7	5	220	1	0	1	0	1	0	0	0	0	14262	797	28	0	2242	0	SH3D19	4	152096326	Frame_Shift_Del	DEL	C	TCGA-MH-A55Z-01A-11D-A26P-10	4	152096326	39057950	31	13301	130	3									
FSTL5	56884	hgsc.bcm.edu	37	chr4	162307106	162307106	+	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	agtggttccttgagactcttTatcatcttgaccttcccaga	8	15	7	11	0	3	3	1	2	2	2	5	4	5	3	3	1	0	1	3	1	1	6			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:162307106T>A	ENST00000306100.5	-	16	2773	c.2337A>T	c.(2335-2337)atA>atT	p.I779I	FSTL5_ENST00000379164.4_Silent_p.I778I|FSTL5_ENST00000536695.1_Silent_p.I778I|RP11-234O6.2_ENST00000508189.1_RNA|FSTL5_ENST00000427802.2_Silent_p.I769I	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	779						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)		TGAGACTCTTTATCATCTTGA	0.458																																					p.I779I		Atlas-SNP	.											.	FSTL5	207	.	0			c.A2337T						PASS	.						179	163	168					4																	162307106		2203	4300	6503	SO:0001819	synonymous_variant	56884	exon16			ACTCTTTATCATC	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.2337A>T	chr4.hg19:g.162307106T>A		132.0	0.0	.		153.0	74.0	.	NM_020116	E9PCP6|Q9NSW7|Q9ULF7	Silent	SNP	ENST00000306100.5	hg19	CCDS3802.1																																																																																			.	.	.	none		0.458	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116		A	162307106	T	A	162307106	2	1	220	1	0	0	0	0	0	0	0	1	6087	1744	61	5		5	FSTL5	4	162307106	Silent	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	10210780	162307106	28847170	32	13302											
WDR17	116966	hgsc.bcm.edu	37	chr4	177089815	177089815	+	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	gaagtgtccccttttgttacGttaacaggaatttggcagct	9	14	10	8	1	0	0	0	0	0	0	1	2	1	1	2	2	3	4	2	2	4	5	rs371828424		TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr4:177089815G>C	ENST00000280190.4	+	25	3256	c.3100G>C	c.(3100-3102)Gtt>Ctt	p.V1034L	WDR17_ENST00000393643.2_Missense_Mutation_p.V1010L|WDR17_ENST00000508596.1_Intron|WDR17_ENST00000507824.2_Intron			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	1034										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)		CTTTTGTTACGTTAACAGGAA	0.338																																					p.V1034L		Atlas-SNP	.											.	WDR17	198	.	0			c.G3100C						PASS	.						134	127	129					4																	177089815		2203	4300	6503	SO:0001583	missense	116966	exon25			TGTTACGTTAACA	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.3100G>C	chr4.hg19:g.177089815G>C	ENSP00000280190:p.Val1034Leu	63.0	0.0	.		77.0	30.0	.	NM_170710	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	hg19	CCDS3825.1	.	.	.	.	.	.	.	.	.	.	g	1.369	-0.586595	0.03827	.	.	ENSG00000150627	ENST00000393643;ENST00000280190;ENST00000507824	T;T	0.54866	0.61;0.55	5.1	-2.02	0.07388	.	0.528184	0.15689	N	0.249514	T	0.20292	0.0488	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27773	-1.0064	10	0.02654	T	1	0.4761	4.7601	0.13104	0.4883:0.0:0.3534:0.1582	.	1034	Q8IZU2	WDR17_HUMAN	L	1010;1034;1010	ENSP00000377258:V1010L;ENSP00000280190:V1034L	ENSP00000280190:V1034L	V	+	1	0	WDR17	177326809	0.081000	0.21417	0.000000	0.03702	0.003000	0.03518	-0.019000	0.12546	-0.243000	0.09653	-1.290000	0.01357	GTT	.	.	.	alt		0.338	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2			C	177089815	G	C	177089815	3	2	220	1	0	0	0	0	1	0	0	0	17289	1145	40	4	3194	4	WDR17	4	177089815	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	14782709	177089815	14064461	33	13303											
TNPO1	3842	hgsc.bcm.edu	37	chr5	72183032	72183032	+	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	agaatcaggcattttggtttTaggagcaattgctgaaggta	12	13	12	4	0	1	2	1	1	0	1	1	3	1	3	0	4	2	5	0	4	5	6			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr5:72183032T>G	ENST00000337273.5	+	12	1712	c.1286T>G	c.(1285-1287)tTa>tGa	p.L429*	TNPO1_ENST00000523768.1_Nonsense_Mutation_p.L379*|TNPO1_ENST00000506351.2_Nonsense_Mutation_p.L421*|TNPO1_ENST00000454282.1_Nonsense_Mutation_p.L379*	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1	429					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)		ATTTTGGTTTTAGGAGCAATT	0.358																																					p.L429X		Atlas-SNP	.											.	TNPO1	90	.	0			c.T1286G						PASS	.						99	97	98					5																	72183032		2203	4300	6503	SO:0001587	stop_gained	3842	exon12			TGGTTTTAGGAGC	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.1286T>G	chr5.hg19:g.72183032T>G	ENSP00000336712:p.Leu429*	72.0	0.0	.		72.0	10.0	.	NM_002270	B4DVC6|Q92957|Q92975	Nonsense_Mutation	SNP	ENST00000337273.5	hg19	CCDS43329.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.770905	0.90108	.	.	ENSG00000083312	ENST00000337273;ENST00000454282;ENST00000523768;ENST00000506351	.	.	.	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.9103	15.3454	0.74334	0.0:0.0:0.0:1.0	.	.	.	.	X	429;379;379;421	.	ENSP00000336712:L429X	L	+	2	0	TNPO1	72218788	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	7.651000	0.83577	2.099000	0.63709	0.528000	0.53228	TTA	.	.	.	none		0.358	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	NM_002270		G	72183032	T	G	72183032	4	3	220	1	0	0	0	0	0	1	0	0	16347	1764	61	5	1332	5	TNPO1	5	72183032	Nonsense_Mutation	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10		72183032	108732228	34	13304											
SLC23A1	9963	hgsc.bcm.edu	37	chr5	138718252	138718252	+	Missense_Mutation	SNP	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	gtacaacatgtcaaacttagGctctgtgggtagcggggtcg	9	10	14	8	2	2	0	1	0	1	0	3	0	2	0	0	4	4	3	0	4	5	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr5:138718252G>A	ENST00000348729.3	-	2	125	c.79C>T	c.(79-81)Cct>Tct	p.P27S	SLC23A1_ENST00000503919.1_5'UTR|SLC23A1_ENST00000353963.3_Missense_Mutation_p.P27S	NM_005847.4	NP_005838	Q9UHI7	S23A1_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 1	27					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)	TCAAACTTAGGCTCTGTGGGT	0.582																																					p.P27S		Atlas-SNP	.											.	SLC23A1	51	.	0			c.C79T						PASS	.						134	111	118					5																	138718252		2203	4300	6503	SO:0001583	missense	9963	exon2			ACTTAGGCTCTGT	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.79C>T	chr5.hg19:g.138718252G>A	ENSP00000302701:p.Pro27Ser	199.0	0.0	.		170.0	76.0	.	NM_005847	O95191|Q8WWB6|Q9UGH4|Q9UI39	Missense_Mutation	SNP	ENST00000348729.3	hg19	CCDS4212.1	.	.	.	.	.	.	.	.	.	.	G	10.65	1.410755	0.25465	.	.	ENSG00000170482	ENST00000353963;ENST00000348729;ENST00000339881;ENST00000453898;ENST00000508270	T;T	0.17370	2.28;2.29	4.68	2.9	0.33743	.	0.428794	0.24659	N	0.036652	T	0.08670	0.0215	N	0.08118	0	0.31262	N	0.692759	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.06552	-1.0820	10	0.87932	D	0	-27.6722	8.6703	0.34145	0.1818:0.0:0.8182:0.0	.	27;27	Q9UHI7;Q9UHI7-2	S23A1_HUMAN;.	S	27;27;27;27;101	ENSP00000302851:P27S;ENSP00000302701:P27S	ENSP00000343584:P27S	P	-	1	0	SLC23A1	138746151	0.993000	0.37304	0.987000	0.45799	0.446000	0.32137	1.322000	0.33689	0.600000	0.29862	0.456000	0.33151	CCT	.	.	.	none		0.582	SLC23A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374185.1	NM_152685		A	138718252	G	A	138718252	3	1	220	1	0	0	0	0	1	0	0	0	14475	1203	42	2	1781	2	SLC23A1	5	138718252	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	66535220	138718252	42197008	35	13305											
FAT2	2196	hgsc.bcm.edu	37	chr5	150911353	150911353	+	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	accaccgagactgtgacggtGcccagcgtggacagcggtat	9	6	14	12	4	0	2	0	1	0	1	0	4	0	3	3	3	3	1	3	3	1	1			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr5:150911353G>A	ENST00000261800.5	-	13	9618	c.9606C>T	c.(9604-9606)ggC>ggT	p.G3202G		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3202	Cadherin 28. {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)			CTGTGACGGTGCCCAGCGTGG	0.672																																					p.G3202G		Atlas-SNP	.											.	FAT2	465	.	0			c.C9606T						PASS	.						101	89	93					5																	150911353		2203	4300	6503	SO:0001819	synonymous_variant	2196	exon13			GACGGTGCCCAGC	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.9606C>T	chr5.hg19:g.150911353G>A		9.0	0.0	.		16.0	7.0	.	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	hg19	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	5.409	0.260626	0.10239	.	.	ENSG00000086570	ENST00000520200	.	.	.	5.34	3.55	0.40652	.	.	.	.	.	T	0.55673	0.1935	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49133	-0.8971	4	.	.	.	.	6.8949	0.24251	0.1533:0.1441:0.7025:0.0	.	.	.	.	Y	61	.	.	H	-	1	0	FAT2	150891546	1.000000	0.71417	1.000000	0.80357	0.436000	0.31835	2.210000	0.42816	0.630000	0.30394	0.557000	0.71058	CAC	.	.	.	none		0.672	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		A	150911353	G	A	150911353	2	1	220	1	0	0	0	0	0	0	0	1	5697	1306	46	2		2	FAT2	5	150911353	Silent	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	12193101	150911353	30003907	36	13306											
LCP2	3937	hgsc.bcm.edu	37	chr5	169680134	169680134	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctcttacctcttcctccgCgggggatgggggccgaggtt	3	11	14	13	3	2	0	0	0	2	0	5	2	4	1	4	5	1	1	4	5	1	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr5:169680134C>T	ENST00000046794.5	-	18	1849	c.1234G>A	c.(1234-1236)Gcg>Acg	p.A412T	LCP2_ENST00000521416.1_Missense_Mutation_p.A207T	NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	412					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)		TCTTCCTCCGCGGGGGATGGG	0.458																																					p.A412T		Atlas-SNP	.											.	LCP2	133	.	0			c.G1234A						PASS	.						36	34	35					5																	169680134		1815	4077	5892	SO:0001583	missense	3937	exon18			CCTCCGCGGGGGA		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.1234G>A	chr5.hg19:g.169680134C>T	ENSP00000046794:p.Ala412Thr	38.0	0.0	.		43.0	12.0	.	NM_005565	A8KA25|Q53XV4	Missense_Mutation	SNP	ENST00000046794.5	hg19	CCDS47339.1	.	.	.	.	.	.	.	.	.	.	C	10.23	1.293873	0.23564	.	.	ENSG00000043462	ENST00000046794;ENST00000521416	D;D	0.92805	-3.11;-3.11	5.74	3.01	0.34805	.	0.541975	0.19974	N	0.101934	T	0.75481	0.3855	N	0.02539	-0.55	0.09310	N	1	B;B	0.18610	0.029;0.001	B;B	0.08055	0.003;0.001	T	0.62835	-0.6770	9	.	.	.	-3.3438	5.838	0.18617	0.154:0.685:0.0:0.1611	.	207;412	E7ESF6;Q13094	.;LCP2_HUMAN	T	412;207	ENSP00000046794:A412T;ENSP00000428871:A207T	.	A	-	1	0	LCP2	169612712	0.001000	0.12720	0.002000	0.10522	0.112000	0.19704	0.873000	0.28052	0.445000	0.26639	0.563000	0.77884	GCG	.	.	.	none		0.458	LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1	NM_005565		T	169680134	C	T	169680134	3	4	220	1	0	0	0	0	1	0	0	0	8699	768	27	1	383	1	LCP2	5	169680134	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	18768781	169680134	11235126	37	13307											
CANX	821	hgsc.bcm.edu	37	chr5	179136997	179136997	+	Frame_Shift_Del	DEL	C	C	-																															cgggtatctatgaagaaaaaCatgctaagaggccagatgca																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr5:179136997delC	ENST00000247461.4	+	7	852	c.652delC	c.(652-654)catfs	p.H218fs	CANX_ENST00000512607.2_Frame_Shift_Del_p.H110fs|CANX_ENST00000415618.2_Frame_Shift_Del_p.H253fs|CANX_ENST00000452673.2_Frame_Shift_Del_p.H218fs|CANX_ENST00000504734.1_Frame_Shift_Del_p.H218fs|CANX_ENST00000503126.1_3'UTR	NM_001746.3	NP_001737.1	P27824	CALX_HUMAN	calnexin	218					aging (GO:0007568)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein folding (GO:0061077)|clathrin-mediated endocytosis (GO:0072583)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|protein secretion (GO:0009306)|synaptic vesicle endocytosis (GO:0048488)	axon (GO:0030424)|dendrite cytoplasm (GO:0032839)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|ER-mitochondrion membrane contact site (GO:0044233)|extracellular vesicular exosome (GO:0070062)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ribosome (GO:0005840)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|kidney(4)|large_intestine(2)|lung(7)|prostate(2)|urinary_tract(3)	22	all_cancers(89;0.000129)|all_epithelial(37;5.59e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0413)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Antihemophilic Factor(DB00025)|Tenecteplase(DB00031)	TGAAGAAAAACATGCTAAGAG	0.373																																					p.K217fs		Pindel	.											.	CANX	47	.	0			c.651delA						PASS	.						132	135	134					5																	179136997		2203	4300	6503	SO:0001589	frameshift_variant	821	exon7			.	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.652delC	chr5.hg19:g.179136997delC	ENSP00000247461:p.His218fs	61.0	0.0	.		59.0	19.0	0.322	NM_001746	B2R5V8|B4DGP8|B4E2T8|D3DWQ3|D6R9K3	Frame_Shift_Del	DEL	ENST00000247461.4	hg19	CCDS4447.1																																																																																			.	.	.	none		0.373	CANX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253500.2	NM_001024649		-	179136997	C	-	179136997	7	5	220	1	0	1	0	1	0	0	0	0	2620	478	17	0	674	0	CANX	5	179136997	Frame_Shift_Del	DEL	C	TCGA-MH-A55Z-01A-11D-A26P-10	9456863	179136997	1778263	38	13308											
ZSCAN12	9753	hgsc.bcm.edu	37	chr6	28359289	28359289	+	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	tctctgatgttcagtatggtCagagttctcagtcaggctta	8	15	10	8	0	5	2	4	1	2	1	7	2	5	2	0	2	0	4	0	2	2	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr6:28359289C>G	ENST00000361028.1	-	4	923	c.778G>C	c.(778-780)Gac>Cac	p.D260H	ZSCAN12_ENST00000396827.3_Missense_Mutation_p.D260H			O43309	ZSC12_HUMAN	zinc finger and SCAN domain containing 12	260					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|urinary_tract(1)	6						TCAGTATGGTCAGAGTTCTCA	0.433																																					p.D260H		Atlas-SNP	.											.	ZSCAN12	35	.	0			c.G778C						PASS	.						219	181	192					6																	28359289		692	1591	2283	SO:0001583	missense	9753	exon4			TATGGTCAGAGTT	AB007886		6p21	2013-01-08	2007-02-20	2007-02-20	ENSG00000158691	ENSG00000158691		"-", "Zinc fingers, C2H2-type"	13172	protein-coding gene	gene with protein product		603978	"zinc finger protein 305", "zinc finger protein 96"	ZNF305, ZNF96		9244436	Standard	NM_001163391		Approved	KIAA0426, ZNF29K1, ZFP96, dJ29K1.2	uc011dlh.2	O43309	OTTHUMG00000014522	ENST00000361028.1:c.778G>C	chr6.hg19:g.28359289C>G	ENSP00000354305:p.Asp260His	161.0	0.0	.		141.0	51.0	.	NM_001163391	O43724	Missense_Mutation	SNP	ENST00000361028.1	hg19		.	.	.	.	.	.	.	.	.	.	C	3.906	-0.021133	0.07634	.	.	ENSG00000158691	ENST00000361028;ENST00000396827	T;T	0.27557	1.66;1.66	3.93	-0.342	0.12635	.	0.768215	0.10643	N	0.650758	T	0.02342	0.0072	N	0.02539	-0.55	0.09310	N	1	P;B	0.47302	0.893;0.38	B;B	0.34301	0.179;0.054	T	0.24548	-1.0157	10	0.22706	T	0.39	.	4.3597	0.11196	0.1506:0.4779:0.0:0.3715	.	260;260	A8K187;O43309	.;ZSC12_HUMAN	H	260	ENSP00000354305:D260H;ENSP00000380039:D260H	ENSP00000354305:D260H	D	-	1	0	ZSCAN12	28467268	0.000000	0.05858	0.000000	0.03702	0.383000	0.30230	-1.601000	0.02081	0.004000	0.14682	0.650000	0.86243	GAC	.	.	.	none		0.433	ZSCAN12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040190.1	NM_014724		G	28359289	C	G	28359289	3	3	220	1	0	0	0	0	1	0	0	0	18240	826	29	4	1061	4	ZSCAN12	6	28359289	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10		28359289	142755778	39	13309											
C6orf211	79624	hgsc.bcm.edu	37	chr6	151790234	151790234	+	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	atggaatatttcagtacgatGgtcccctttgacttgattta	10	16	8	7	1	1	2	1	2	0	0	2	4	2	3	2	2	1	1	2	2	4	7			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr6:151790234G>A	ENST00000367294.3	+	5	1574	c.1315G>A	c.(1315-1317)Ggt>Agt	p.G439S	C6orf211_ENST00000545879.1_Missense_Mutation_p.G320S	NM_024573.1	NP_078849.1	Q9H993	CF211_HUMAN	chromosome 6 open reading frame 211	439										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)		TCAGTACGATGGTCCCCTTTG	0.507																																					p.G439S		Atlas-SNP	.											.	C6orf211	30	.	0			c.G1315A						PASS	.						21	22	22					6																	151790234		1959	4161	6120	SO:0001583	missense	79624	exon5			TACGATGGTCCCC	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.1315G>A	chr6.hg19:g.151790234G>A	ENSP00000356263:p.Gly439Ser	65.0	0.0	.		64.0	24.0	.	NM_024573	Q96FC6|Q9UFY5	Missense_Mutation	SNP	ENST00000367294.3	hg19	CCDS5233.1	.	.	.	.	.	.	.	.	.	.	G	11.75	1.730830	0.30684	.	.	ENSG00000146476	ENST00000367294;ENST00000545879	T;T	0.13089	3.04;2.62	6.16	5.3	0.74995	.	0.212744	0.47852	D	0.000212	T	0.05181	0.0138	L	0.45352	1.415	0.41042	D	0.985231	B	0.22983	0.078	B	0.20184	0.028	T	0.18777	-1.0326	10	0.15499	T	0.54	.	13.6292	0.62186	0.0707:0.0:0.9293:0.0	.	439	Q9H993	CF211_HUMAN	S	439;320	ENSP00000356263:G439S;ENSP00000444121:G320S	ENSP00000356263:G439S	G	+	1	0	C6orf211	151831927	0.998000	0.40836	0.986000	0.45419	0.154000	0.21943	2.502000	0.45398	1.626000	0.50381	0.650000	0.86243	GGT	.	.	.	none		0.507	C6orf211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042724.1	NM_024573		A	151790234	G	A	151790234	3	1	220	1	0	0	0	0	1	0	0	0	2356	1348	47	2	1333	2	C6orf211	6	151790234	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	123430945	151790234	19324833	40	13310											
EIF2AK1	27102	hgsc.bcm.edu	37	chr7	6078295	6078296	+	Frame_Shift_Ins	INS	-	-	A																															gatgtgcagcatcaggtggtINSactgtgcctaggagaggaca																								rs150001751		TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr7:6078295_6078296insA	ENST00000199389.6	-	10	1272_1273	c.1126_1127insT	c.(1126-1128)tacfs	p.Y376fs	EIF2AK1_ENST00000536084.1_Frame_Shift_Ins_p.Y252fs|EIF2AK1_ENST00000495565.1_5'Flank	NM_001134335.1|NM_014413.3	NP_001127807.1|NP_055228.2	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 1	376	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of cell proliferation (GO:0008285)|negative regulation of hemoglobin biosynthetic process (GO:0046986)|negative regulation of translational initiation by iron (GO:0045993)|protein autophosphorylation (GO:0046777)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|response to external stimulus (GO:0009605)|response to stress (GO:0006950)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	27		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)		CATCAGGTGGTACTGTGCCTAG	0.505																																					p.Y376fs		Atlas-INDEL	.											.	EIF2AK1	76	.	0			c.1127_1128insT						PASS	.																																			SO:0001589	frameshift_variant	27102	exon10			.	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.1127dupT	chr7.hg19:g.6078296_6078296dupA	ENSP00000199389:p.Tyr376fs	92.0	0.0	0		137.0	20.0	0.145985	NM_014413	A8K2R2|Q549K6|Q8NBW3|Q9HC02|Q9NYE0|Q9P0V6|Q9P1J5|Q9P2H8|Q9UHG4	Frame_Shift_Ins	INS	ENST00000199389.6	hg19	CCDS5345.1																																																																																			.	.	.	none		0.505	EIF2AK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207373.2	NM_014413		A	6078296	-	A	6078295	7	5	220	1	0	1	1	0	0	0	0	0	4998	1638	57	0	789	0	EIF2AK1	7	6078295	Frame_Shift_Ins	INS	-	TCGA-MH-A55Z-01A-11D-A26P-10		6078295	153060368	41	13311	131	3									
EIF2AK1	27102	hgsc.bcm.edu	37	chr7	6078297	6078297	+	Missense_Mutation	SNP	C	C	G																															atgtgcagcatcaggtggtaCtgtgcctaggagaggacaca																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr7:6078297C>G	ENST00000199389.6	-	10	1271	c.1125G>C	c.(1123-1125)caG>caC	p.Q375H	EIF2AK1_ENST00000536084.1_Missense_Mutation_p.Q251H|EIF2AK1_ENST00000495565.1_5'Flank	NM_001134335.1|NM_014413.3	NP_001127807.1|NP_055228.2	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 1	375	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of cell proliferation (GO:0008285)|negative regulation of hemoglobin biosynthetic process (GO:0046986)|negative regulation of translational initiation by iron (GO:0045993)|protein autophosphorylation (GO:0046777)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|response to external stimulus (GO:0009605)|response to stress (GO:0006950)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	27		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)		TCAGGTGGTACTGTGCCTAGG	0.507																																					p.Q375H		Atlas-SNP	.											.	EIF2AK1	76	.	0			c.G1125C						PASS	.						108	94	99					7																	6078297		2203	4300	6503	SO:0001583	missense	27102	exon10			GTGGTACTGTGCC	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.1125G>C	chr7.hg19:g.6078297C>G	ENSP00000199389:p.Gln375His	93.0	0.0	.		134.0	21.0	.	NM_014413	A8K2R2|Q549K6|Q8NBW3|Q9HC02|Q9NYE0|Q9P0V6|Q9P1J5|Q9P2H8|Q9UHG4	Missense_Mutation	SNP	ENST00000199389.6	hg19	CCDS5345.1	.	.	.	.	.	.	.	.	.	.	.	9.811	1.183288	0.21870	.	.	ENSG00000086232	ENST00000199389;ENST00000536084;ENST00000426957	T;T	0.65549	-0.16;-0.16	5.57	2.56	0.30785	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.521490	0.21777	N	0.069272	T	0.53334	0.1790	M	0.64630	1.985	0.31933	N	0.61189	B;B;B	0.20368	0.044;0.007;0.005	B;B;B	0.22386	0.039;0.009;0.01	T	0.56062	-0.8041	10	0.37606	T	0.19	-7.4865	5.5568	0.17121	0.1395:0.6391:0.0:0.2214	.	251;374;375	B4DIP4;Q9BQI3-2;Q9BQI3	.;.;E2AK1_HUMAN	H	375;251;2	ENSP00000199389:Q375H;ENSP00000445784:Q251H	ENSP00000199389:Q375H	Q	-	3	2	EIF2AK1	6044823	1.000000	0.71417	0.996000	0.52242	0.286000	0.27126	0.647000	0.24812	1.341000	0.45600	0.650000	0.86243	CAG	.	.	.	none		0.507	EIF2AK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207373.2	NM_014413		G	6078297	C	G	6078297	3	3	220	1	0	0	0	0	1	0	0	0	4998	564	20	4	791	4	EIF2AK1	7	6078297	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	2	6078297	153060366	42	13312	131	3									
EIF2AK1	27102	hgsc.bcm.edu	37	chr7	6078298	6078299	+	Frame_Shift_Ins	INS	-	-	A																															gtgcagcatcaggtggtactINSgtgcctaggagaggacacag																								rs372398524		TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr7:6078298_6078299insA	ENST00000199389.6	-	10	1269_1270	c.1123_1124insT	c.(1123-1125)cagfs	p.Q375fs	EIF2AK1_ENST00000536084.1_Frame_Shift_Ins_p.Q251fs|EIF2AK1_ENST00000495565.1_5'Flank	NM_001134335.1|NM_014413.3	NP_001127807.1|NP_055228.2	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 1	375	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of cell proliferation (GO:0008285)|negative regulation of hemoglobin biosynthetic process (GO:0046986)|negative regulation of translational initiation by iron (GO:0045993)|protein autophosphorylation (GO:0046777)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|response to external stimulus (GO:0009605)|response to stress (GO:0006950)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	27		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)		CAGGTGGTACTGTGCCTAGGAG	0.51																																					p.Q375fs		Atlas-INDEL	.											.	EIF2AK1	76	.	0			c.1124_1125insT						PASS	.																																			SO:0001589	frameshift_variant	27102	exon10			.	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.1123_1124insT	chr7.hg19:g.6078298_6078299insA	ENSP00000199389:p.Gln375fs	92.0	0.0	0		134.0	20.0	0.149254	NM_014413	A8K2R2|Q549K6|Q8NBW3|Q9HC02|Q9NYE0|Q9P0V6|Q9P1J5|Q9P2H8|Q9UHG4	Frame_Shift_Ins	INS	ENST00000199389.6	hg19	CCDS5345.1																																																																																			.	.	.	none		0.51	EIF2AK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207373.2	NM_014413		A	6078299	-	A	6078298	7	5	220	1	0	1	1	0	0	0	0	0	4998	1580	55	0	792	0	EIF2AK1	7	6078298	Frame_Shift_Ins	INS	-	TCGA-MH-A55Z-01A-11D-A26P-10	1	6078298	153060365	43	13313	131	3									
NFE2L3	9603	hgsc.bcm.edu	37	chr7	26224635	26224636	+	Frame_Shift_Del	DEL	CT	CT	-																															atcaagtctaattcctctcaCtctgtgtgtgatgaaggtgc																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr7:26224635_26224636delCT	ENST00000056233.3	+	4	1576_1577	c.1317_1318delCT	c.(1315-1320)cactctfs	p.S440fs		NM_004289.6	NP_004280.5	Q9Y4A8	NF2L3_HUMAN	nuclear factor, erythroid 2-like 3	440					transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(5)|urinary_tract(7)	29						ATTCCTCTCACTCTGTGTGTGA	0.421																																					p.439_439del		Atlas-Indel,Pindel	.											.	NFE2L3	77	.	0			c.1316_1317del						PASS	.																																			SO:0001589	frameshift_variant	9603	exon4			.	AB010812	CCDS5396.1	7p15.2	2013-08-23	2013-08-23		ENSG00000050344	ENSG00000050344		"basic leucine zipper proteins"	7783	protein-coding gene	gene with protein product		604135	"nuclear factor (erythroid-derived 2)-like 3"			10037736	Standard	NM_004289		Approved	Nrf3	uc003sxq.3	Q9Y4A8	OTTHUMG00000023882	ENST00000056233.3:c.1317_1318delCT	chr7.hg19:g.26224637_26224638delCT	ENSP00000056233:p.Ser440fs	97.0	0.0	0		172.0	42.0	0.244186	NM_004289	Q6NUS0|Q7Z498|Q86UJ4|Q86VR5|Q9UQA4	Frame_Shift_Del	DEL	ENST00000056233.3	hg19	CCDS5396.1																																																																																			.	.	.	none		0.421	NFE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214088.1			-	26224636	CT	-	26224635	7	5	220	1	0	1	0	1	0	0	0	0	10376	564	20	0	1331	0	NFE2L3	7	26224635	Frame_Shift_Del	DEL	CT	TCGA-MH-A55Z-01A-11D-A26P-10	20146337	26224635	132914028	44	13314											
PLEKHA8	84725	hgsc.bcm.edu	37	chr7	30094389	30094389	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatcatgacaataacttgacTcagtctggatcagactcaag	15	10	7	9	0	5	3	4	2	1	1	5	4	5	4	0	1	1	0	0	1	4	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr7:30094389T>C	ENST00000449726.1	+	8	1211	c.861T>C	c.(859-861)acT>acC	p.T287T	PLEKHA8_ENST00000396259.1_Silent_p.T287T|PLEKHA8_ENST00000396257.2_Silent_p.T287T|PLEKHA8_ENST00000258679.7_Silent_p.T287T	NM_001197027.1	NP_001183956.1	Q96JA3	PKHA8_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8	287				T -> S (in Ref. 1; AAK55424). {ECO:0000305}.	ER to Golgi ceramide transport (GO:0035621)|lipid transport (GO:0006869)|protein transport (GO:0015031)	membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ceramide binding (GO:0097001)|glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)|phosphatidylinositol-4-phosphate binding (GO:0070273)			breast(4)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)	17						ATAACTTGACTCAGTCTGGAT	0.383																																					p.T287T		Atlas-SNP	.											.	PLEKHA8	68	.	0			c.T861C						PASS	.						149	143	145					7																	30094389		2203	4300	6503	SO:0001819	synonymous_variant	84725	exon8			CTTGACTCAGTCT	BC053990	CCDS5424.1, CCDS56473.1, CCDS75574.1	7p21-p11.2	2013-01-10			ENSG00000106086	ENSG00000106086		"Pleckstrin homology (PH) domain containing"	30037	protein-coding gene	gene with protein product		608639				11001876	Standard	NM_001197027		Approved	FAPP2, MGC3358	uc003taq.3	Q96JA3	OTTHUMG00000097751	ENST00000449726.1:c.861T>C	chr7.hg19:g.30094389T>C		143.0	0.0	.		353.0	139.0	.	NM_001197027	B4DH00|Q7Z5V8|Q9BU78|Q9H274|Q9H8Z7	Silent	SNP	ENST00000449726.1	hg19	CCDS56473.1																																																																																			.	.	.	none		0.383	PLEKHA8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032639		C	30094389	T	C	30094389	2	2	220	1	0	0	0	0	0	0	0	1	12069	1538	54	3		3	PLEKHA8	7	30094389	Silent	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	3869754	30094389	129044274	45	13315											
POLM	27434	hgsc.bcm.edu	37	chr7	44114102	44114102	+	Missense_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	catcggaccgcaggactgggGtgctcaggtcctggtggtgc	5	8	17	11	2	1	0	1	0	0	0	3	2	2	2	2	7	2	2	2	7	0	0			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr7:44114102G>A	ENST00000242248.5	-	7	964	c.863C>T	c.(862-864)aCc>aTc	p.T288I	POLM_ENST00000492971.1_5'UTR|POLM_ENST00000395831.3_Silent_p.H242H|POLM_ENST00000335195.6_Silent_p.H285H	NM_013284.2	NP_037416.1	Q9NP87	DPOLM_HUMAN	polymerase (DNA directed), mu	288					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						CAGGACTGGGGTGCTCAGGTC	0.697								DNA polymerases (catalytic subunits)																													p.T288I		Atlas-SNP	.											.	POLM	50	.	0			c.C863T						PASS	.						21	19	20					7																	44114102		2201	4299	6500	SO:0001583	missense	27434	exon7			ACTGGGGTGCTCA	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.863C>T	chr7.hg19:g.44114102G>A	ENSP00000242248:p.Thr288Ile	31.0	0.0	.		130.0	40.0	.	NM_013284	D3DVK4|Q6P5X8|Q86WQ9	Missense_Mutation	SNP	ENST00000242248.5	hg19	CCDS34625.1	.	.	.	.	.	.	.	.	.	.	G	13.05	2.122221	0.37436	.	.	ENSG00000122678	ENST00000242248	T	0.44083	0.93	5.38	1.23	0.21249	DNA-directed DNA polymerase X (1);DNA polymerase lambda, fingers domain (1);	.	.	.	.	T	0.42471	0.1204	M	0.68317	2.08	0.80722	D	1	P	0.40211	0.707	B	0.42959	0.403	T	0.33803	-0.9854	9	0.56958	D	0.05	-0.2386	8.6696	0.34143	0.0841:0.4398:0.4761:0.0	.	288	Q9NP87	DPOLM_HUMAN	I	288	ENSP00000242248:T288I	ENSP00000242248:T288I	T	-	2	0	POLM	44080627	0.013000	0.17824	0.506000	0.27664	0.637000	0.38172	0.038000	0.13862	0.231000	0.21079	0.555000	0.69702	ACC	.	.	.	none		0.697	POLM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339594.1	NM_013284		A	44114102	G	A	44114102	3	1	220	1	0	0	0	0	1	0	0	0	12213	1261	44	2	641	2	POLM	7	44114102	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	14019713	44114102	115024561	46	13316											
OGDH	4967	hgsc.bcm.edu	37	chr7	44735721	44735721	+	Missense_Mutation	SNP	G	G	T																															gcactggctggactctccctGgcctggtgagtgaagaaaca																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr7:44735721G>T	ENST00000222673.5	+	13	1808	c.1766G>T	c.(1765-1767)tGg>tTg	p.W589L	OGDH_ENST00000444676.1_Missense_Mutation_p.W604L|OGDH_ENST00000449767.1_Missense_Mutation_p.W585L|OGDH_ENST00000439616.2_Missense_Mutation_p.W439L|OGDH_ENST00000447398.1_Missense_Mutation_p.W600L|OGDH_ENST00000543843.1_Missense_Mutation_p.W540L	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	589					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)	GACTCTCCCTGGCCTGGTGAG	0.438																																					p.W589L		Atlas-SNP	.											.	OGDH	145	.	0			c.G1766T						PASS	.						71	67	68					7																	44735721		2203	4300	6503	SO:0001583	missense	4967	exon13			CTCCCTGGCCTGG	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.1766G>T	chr7.hg19:g.44735721G>T	ENSP00000222673:p.Trp589Leu	84.0	0.0	.		155.0	35.0	.	NM_002541	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Missense_Mutation	SNP	ENST00000222673.5	hg19	CCDS34627.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.713754	0.89112	.	.	ENSG00000105953	ENST00000439616;ENST00000449767;ENST00000447398;ENST00000444676;ENST00000222673;ENST00000543843	T;T;T;T;T;T	0.06608	3.33;3.28;3.29;3.29;3.29;3.3	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.36303	0.0962	M	0.94021	3.485	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	0.51132	-0.8744	10	0.87932	D	0	-15.9477	17.8672	0.88799	0.0:0.0:1.0:0.0	.	384;439;585;600;491;589	B4E3E9;E9PFG7;E9PBM1;E9PDF2;A2VCT2;Q02218	.;.;.;.;.;ODO1_HUMAN	L	439;585;600;604;589;540	ENSP00000398576:W439L;ENSP00000392878:W585L;ENSP00000388183:W600L;ENSP00000414662:W604L;ENSP00000222673:W589L;ENSP00000443821:W540L	ENSP00000222673:W589L	W	+	2	0	OGDH	44702246	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	9.657000	0.98554	2.556000	0.86216	0.655000	0.94253	TGG	.	.	.	none		0.438	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1			T	44735721	G	T	44735721	3	4	220	1	0	0	0	0	1	0	0	0	10846	1357	47	4	1985	4	OGDH	7	44735721	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	621619	44735721	114402942	47	13317	132	2									
OGDH	4967	hgsc.bcm.edu	37	chr7	44735723	44735723	+	Missense_Mutation	SNP	C	C	A																															actggctggactctccctggCctggtgagtgaagaaacagt																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr7:44735723C>A	ENST00000222673.5	+	13	1810	c.1768C>A	c.(1768-1770)Cct>Act	p.P590T	OGDH_ENST00000444676.1_Missense_Mutation_p.P605T|OGDH_ENST00000449767.1_Missense_Mutation_p.P586T|OGDH_ENST00000439616.2_Missense_Mutation_p.P440T|OGDH_ENST00000447398.1_Missense_Mutation_p.P601T|OGDH_ENST00000543843.1_Missense_Mutation_p.P541T	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	590					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)	CTCTCCCTGGCCTGGTGAGTG	0.438																																					p.P590T		Atlas-SNP	.											.	OGDH	145	.	0			c.C1768A						PASS	.						69	65	67					7																	44735723		2203	4300	6503	SO:0001583	missense	4967	exon13			CCCTGGCCTGGTG	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.1768C>A	chr7.hg19:g.44735723C>A	ENSP00000222673:p.Pro590Thr	81.0	0.0	.		153.0	34.0	.	NM_002541	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Missense_Mutation	SNP	ENST00000222673.5	hg19	CCDS34627.1	.	.	.	.	.	.	.	.	.	.	C	12.81	2.050408	0.36181	.	.	ENSG00000105953	ENST00000439616;ENST00000449767;ENST00000447398;ENST00000444676;ENST00000222673;ENST00000543843	T;T;T;T;T;T	0.05199	3.49;3.48;3.48;3.48;3.48;3.49	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.06554	0.0168	L	0.31294	0.92	0.80722	D	1	B;B;B;B;B;B	0.17268	0.007;0.007;0.01;0.01;0.001;0.021	B;B;B;B;B;B	0.16289	0.004;0.004;0.015;0.015;0.002;0.009	T	0.40194	-0.9576	10	0.19590	T	0.45	-15.3111	17.8673	0.88799	0.0:1.0:0.0:0.0	.	385;440;586;601;492;590	B4E3E9;E9PFG7;E9PBM1;E9PDF2;A2VCT2;Q02218	.;.;.;.;.;ODO1_HUMAN	T	440;586;601;605;590;541	ENSP00000398576:P440T;ENSP00000392878:P586T;ENSP00000388183:P601T;ENSP00000414662:P605T;ENSP00000222673:P590T;ENSP00000443821:P541T	ENSP00000222673:P590T	P	+	1	0	OGDH	44702248	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	7.651000	0.83577	2.556000	0.86216	0.655000	0.94253	CCT	.	.	.	none		0.438	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1			A	44735723	C	A	44735723	3	1	220	1	0	0	0	0	1	0	0	0	10846	739	26	4	1987	4	OGDH	7	44735723	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	2	44735723	114402940	48	13318	132	2									
CSPP1	10565	hgsc.bcm.edu	37	chr8	68107797	68107797	+	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	0	0	0	0	0	0	0	0	0	0	tggaaaaccaggcactttcaCttggcagggcctgtcgactg	9	9	12	11	1	1	0	1	0	0	0	2	2	1	1	2	4	1	2	2	4	2	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr8:68107797C>T	ENST00000262215.3	-	0	7225				CSPP1_ENST00000262210.5_Missense_Mutation_p.T1212I|ARFGEF1_ENST00000520381.1_Intron|ARFGEF1_ENST00000517955.1_5'Flank|CSPP1_ENST00000412460.1_Missense_Mutation_p.T867I	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)						endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)			breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			GGCACTTTCACTTGGCAGGGC	0.493																																					p.T1212I		Atlas-SNP	.											.	CSPP1	129	.	0			c.C3635T						PASS	.						50	51	51					8																	68107797		1953	4158	6111	SO:0001628	intergenic_variant	79848	exon29			CTTTCACTTGGCA	AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777			15772	protein-coding gene	gene with protein product		604141				10212200, 8917509	Standard	NM_006421		Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626		chr8.hg19:g.68107797C>T		222.0	0.0	.		263.0	84.0	.	NM_024790	Q9NV46|Q9UFV2|Q9UNL0	Missense_Mutation	SNP	ENST00000262215.3	hg19	CCDS6199.1	.	.	.	.	.	.	.	.	.	.	C	6.942	0.543635	0.13250	.	.	ENSG00000104218	ENST00000262210;ENST00000389042;ENST00000412460;ENST00000519668	T;T;T	0.32272	1.46;1.48;1.48	5.51	-0.424	0.12321	.	0.554792	0.18305	N	0.145291	T	0.21550	0.0519	L	0.44542	1.39	0.09310	N	1	B;P;P	0.41569	0.256;0.755;0.755	B;B;B	0.35470	0.176;0.203;0.203	T	0.10177	-1.0641	10	0.66056	D	0.02	-1.672	10.1481	0.42776	0.2208:0.5604:0.2188:0.0	.	867;1212;1247	Q1MSJ5-2;Q1MSJ5-1;Q1MSJ5	.;.;CSPP1_HUMAN	I	1212;1247;867;867	ENSP00000262210:T1212I;ENSP00000415782:T867I;ENSP00000430092:T867I	ENSP00000262210:T1212I	T	+	2	0	CSPP1	68270351	0.000000	0.05858	0.008000	0.14137	0.141000	0.21300	0.200000	0.17257	-0.223000	0.09943	-0.181000	0.13052	ACT	.	.	.	none		0.493	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421		T	68107797	C	T	68107797	1	4	220	0	1	0	0	0	0	0	0	0	3964	565	20	2		2	CSPP1	8	68107797	IGR	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10		68107797	78256225	49	13319											
PUF60	22827	hgsc.bcm.edu	37	chr8	144902839	144902839	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgagcatttctattgaccgaTtgcaaaggtgagagaggatc	12	11	12	6	1	1	4	0	3	1	1	2	7	1	5	1	2	2	2	1	2	2	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr8:144902839T>C	ENST00000526683.1	-	5	900	c.345A>G	c.(343-345)caA>caG	p.Q115Q	PUF60_ENST00000524570.1_5'UTR|PUF60_ENST00000313352.7_Intron|PUF60_ENST00000453551.2_Silent_p.Q72Q|PUF60_ENST00000527197.1_Intron|PUF60_ENST00000349157.6_Intron|PUF60_ENST00000456095.2_Silent_p.Q86Q	NM_001271098.1|NM_078480.2	NP_001258027.1|NP_510965.1	Q9UHX1	PUF60_HUMAN	poly-U binding splicing factor 60KDa	115	Inhibits homodimerization.|Inhibits transcriptional repression, interaction with ERCC3 and apoptosis induction.				apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(1)|kidney(3)|lung(7)|prostate(2)	14	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			TATTGACCGATTGCAAAGGTG	0.562																																					p.Q115Q		Atlas-SNP	.											.	PUF60	26	.	0			c.A345G						PASS	.						199	208	205					8																	144902839		2085	4208	6293	SO:0001819	synonymous_variant	22827	exon5			GACCGATTGCAAA	AF114818	CCDS47933.1, CCDS47934.1, CCDS47935.1, CCDS59514.1, CCDS59515.1, CCDS59516.1	8q24.3	2013-02-12	2007-07-27		ENSG00000179950	ENSG00000179950		"RNA binding motif (RRM) containing"	17042	protein-coding gene	gene with protein product	"siah binding protein 1", "FBP interacting repressor", "pyrimidine tract binding splicing factor", "Ro ribonucleoprotein binding protein 1"	604819				10668799, 10882074, 17579712	Standard	NM_078480		Approved	FIR, SIAHBP1, RoBPI	uc003yzs.4	Q9UHX1	OTTHUMG00000165155	ENST00000526683.1:c.345A>G	chr8.hg19:g.144902839T>C		82.0	0.0	.		62.0	26.0	.	NM_078480	A8K8K8|Q969E7|Q96D94|Q96H63|Q99628|Q9NZA0|Q9UJY7	Silent	SNP	ENST00000526683.1	hg19	CCDS47934.1	.	.	.	.	.	.	.	.	.	.	T	9.393	1.076050	0.20227	.	.	ENSG00000179950	ENST00000527744	.	.	.	5.28	4.14	0.48551	.	.	.	.	.	T	0.59972	0.2233	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55927	-0.8063	4	.	.	.	.	9.9314	0.41525	0.0:0.0798:0.0:0.9202	.	.	.	.	S	113	.	.	N	-	2	0	PUF60	144974827	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.482000	0.60257	0.868000	0.35678	0.533000	0.62120	AAT	.	.	.	none		0.562	PUF60-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382222.1	NM_014281		C	144902839	T	C	144902839	2	2	220	1	0	0	0	0	0	0	0	1	12837	1490	52	3		3	PUF60	8	144902839	Silent	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	76795042	144902839	1461183	50	13320											
VLDLR	7436	hgsc.bcm.edu	37	chr9	2643309	2643310	+	In_Frame_Ins	INS	-	-	GCA																															tggcgcccatgagttccagtINSgcagcacctcctcctgcatc																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr9:2643309_2643310insGCA	ENST00000382100.3	+	5	954_955	c.598_599insGCA	c.(598-600)tgc>tGCAgc	p.201_202insS	RP11-125B21.2_ENST00000599229.1_RNA|VLDLR_ENST00000382099.2_In_Frame_Ins_p.201_202insS	NM_003383.3	NP_003374.3	P98155	VLDLR_HUMAN	very low density lipoprotein receptor	201	LDL-receptor class A 5. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cholesterol metabolic process (GO:0008203)|glycoprotein transport (GO:0034436)|lipid transport (GO:0006869)|memory (GO:0007613)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|positive regulation of dendrite development (GO:1900006)|positive regulation of protein kinase activity (GO:0045860)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|signal transduction (GO:0007165)|ventral spinal cord development (GO:0021517)|very-low-density lipoprotein particle clearance (GO:0034447)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|glycoprotein binding (GO:0001948)|glycoprotein transporter activity (GO:0034437)|low-density lipoprotein receptor activity (GO:0005041)|reelin receptor activity (GO:0038025)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(50;0.0668)|Lung(218;0.123)		TGAGTTCCAGTGCAGCACCTCC	0.589																																					p.C200delinsCS		Atlas-Indel,Pindel	.											.	VLDLR	68	.	0			c.598_599insGCA						PASS	.																																			SO:0001652	inframe_insertion	7436	exon5			.		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.602_604dupGCA	chr9.hg19:g.2643313_2643315dupGCA	ENSP00000371532:p.Ser203_Ser204dup	131.0	0.0	0		141.0	52.0	0.368794	NM_003383	B2RMZ7|D3DRH6|Q5VVF6	In_Frame_Ins	INS	ENST00000382100.3	hg19	CCDS6446.1																																																																																			.	.	.	none		0.589	VLDLR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051519.2	NM_003383		GCA	2643310	-	GCA	2643309	7	5	220	1	0	1	1	0	0	0	0	0	17186	1696	59	0	616	0	VLDLR	9	2643309	In_Frame_Ins	INS	-	TCGA-MH-A55Z-01A-11D-A26P-10		2643309	138570122	51	13321											
ZNF438	220929	hgsc.bcm.edu	37	chr10	31134006	31134006	+	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	gtgcttccagtggtggaggaGgtcctctttccgtcccagca	5	11	13	12	1	1	0	0	0	1	0	5	2	5	2	4	4	2	2	4	4	0	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr10:31134006G>A	ENST00000361310.3	-	7	2700	c.2371C>T	c.(2371-2373)Ctc>Ttc	p.L791F	ZNF438_ENST00000331737.6_Missense_Mutation_p.L781F|ZNF438_ENST00000444692.2_Missense_Mutation_p.L781F|ZNF438_ENST00000538351.2_Missense_Mutation_p.L742F|ZNF438_ENST00000375311.1_Missense_Mutation_p.L355F|ZNF438_ENST00000436087.2_Missense_Mutation_p.L791F|ZNF438_ENST00000452305.1_Missense_Mutation_p.L781F|ZNF438_ENST00000413025.1_Missense_Mutation_p.L791F|ZNF438_ENST00000442986.1_Missense_Mutation_p.L791F			Q7Z4V0	ZN438_HUMAN	zinc finger protein 438	791					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)				TGGTGGAGGAGGTCCTCTTTC	0.537																																					p.L791F		Atlas-SNP	.											.	ZNF438	90	.	0			c.C2371T						PASS	.						188	181	184					10																	31134006		2203	4300	6503	SO:0001583	missense	220929	exon8			GGAGGAGGTCCTC	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.2371C>T	chr10.hg19:g.31134006G>A	ENSP00000354663:p.Leu791Phe	152.0	0.0	.		143.0	53.0	.	NM_182755	A2A3J4|A8K9L5|Q5T426|Q658Q4|Q6ZN65	Missense_Mutation	SNP	ENST00000361310.3	hg19	CCDS7168.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.766477	0.90020	.	.	ENSG00000183621	ENST00000331737;ENST00000361310;ENST00000436087;ENST00000442986;ENST00000413025;ENST00000452305;ENST00000444692;ENST00000538351;ENST00000430896;ENST00000375311	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;2.29	5.5	3.62	0.41486	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.115961	0.64402	D	0.000014	T	0.37293	0.0998	M	0.68593	2.085	0.36439	D	0.865386	D;D	0.89917	1.0;1.0	D;D	0.77557	0.976;0.99	T	0.44498	-0.9324	10	0.87932	D	0	-20.022	11.0268	0.47748	0.0708:0.1293:0.7998:0.0	.	791;781	Q7Z4V0;Q7Z4V0-2	ZN438_HUMAN;.	F	781;791;791;791;791;781;781;742;510;355	ENSP00000333571:L781F;ENSP00000354663:L791F;ENSP00000406934:L791F;ENSP00000412363:L791F;ENSP00000387546:L791F;ENSP00000413060:L781F;ENSP00000410898:L781F;ENSP00000445461:L742F;ENSP00000364460:L355F	ENSP00000333571:L781F	L	-	1	0	ZNF438	31174012	1.000000	0.71417	0.008000	0.14137	0.846000	0.48090	3.398000	0.52579	0.770000	0.33336	0.655000	0.94253	CTC	.	.	.	none		0.537	ZNF438-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277006.1	NM_182755		A	31134006	G	A	31134006	3	1	220	1	0	0	0	0	1	0	0	0	17922	1000	35	2	119	2	ZNF438	10	31134006	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10		31134006	104400741	52	13322											
ZNF33B	7582	hgsc.bcm.edu	37	chr10	43088357	43088357	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgctttctctcatgtaaaaTaagtcctgacttcacacaga	12	13	6	10	0	3	2	2	1	1	1	5	2	4	2	1	0	1	2	1	0	3	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr10:43088357T>C	ENST00000359467.3	-	5	2155	c.2041A>G	c.(2041-2043)Att>Gtt	p.I681V	ZNF33B_ENST00000486187.1_RNA	NM_006955.1	NP_008886.1	Q06732	ZN33B_HUMAN	zinc finger protein 33B	681					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|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						TCATGTAAAATAAGTCCTGAC	0.403																																					p.I681V	Melanoma(137;1247 1767 16772 25727 43810)	Atlas-SNP	.											.	ZNF33B	78	.	0			c.A2041G						PASS	.						123	121	122					10																	43088357		2203	4300	6503	SO:0001583	missense	7582	exon5			GTAAAATAAGTCC	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.2041A>G	chr10.hg19:g.43088357T>C	ENSP00000352444:p.Ile681Val	60.0	0.0	.		76.0	32.0	.	NM_006955	Q06731|Q32MA2|Q86XY8|Q8NDW3	Missense_Mutation	SNP	ENST00000359467.3	hg19	CCDS7198.1	.	.	.	.	.	.	.	.	.	.	T	4.006	-0.001564	0.07819	.	.	ENSG00000196693	ENST00000359467;ENST00000395836	T	0.35605	1.3	2.54	0.118	0.14667	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.852537	0.09554	N	0.786508	T	0.12902	0.0313	N	0.02842	-0.48	0.19300	N	0.999972	B	0.09022	0.002	B	0.09377	0.004	T	0.23404	-1.0189	10	0.30854	T	0.27	.	2.2255	0.03983	0.2309:0.2698:0.0:0.4993	.	681	Q06732	ZN33B_HUMAN	V	681;647	ENSP00000352444:I681V	ENSP00000352444:I681V	I	-	1	0	ZNF33B	42408363	0.000000	0.05858	0.917000	0.36280	0.797000	0.45037	-1.573000	0.02134	0.016000	0.14998	0.336000	0.21669	ATT	.	.	.	none		0.403	ZNF33B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_006955		C	43088357	T	C	43088357	3	2	220	1	0	0	0	0	1	0	0	0	17867	1406	49	3	299	3	ZNF33B	10	43088357	Missense_Mutation	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	11954351	43088357	92446390	53	13323											
AFAP1L2	84632	hgsc.bcm.edu	37	chr10	116100456	116100456	+	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	tcctggtcaagaatcttgagGaagtcatccaactctgtcag	11	11	9	10	0	5	2	3	1	2	1	7	3	7	3	2	2	1	0	2	2	4	1			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr10:116100456G>A	ENST00000304129.4	-	2	80	c.51C>T	c.(49-51)ttC>ttT	p.F17F	AFAP1L2_ENST00000369271.3_Silent_p.F17F|AFAP1L2_ENST00000545353.1_Silent_p.F17F			Q8N4X5	AF1L2_HUMAN	actin filament associated protein 1-like 2	17					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)		GAATCTTGAGGAAGTCATCCA	0.537																																					p.F17F		Atlas-SNP	.											.	AFAP1L2	90	.	0			c.C51T						PASS	.						87	85	86					10																	116100456		2203	4300	6503	SO:0001819	synonymous_variant	84632	exon2			CTTGAGGAAGTCA	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.51C>T	chr10.hg19:g.116100456G>A		106.0	0.0	.		95.0	33.0	.	NM_032550	A8K6P7|B3KVQ8|Q2UZW3|Q8TB54|Q96PX4|Q96SY5	Silent	SNP	ENST00000304129.4	hg19	CCDS31286.1																																																																																			.	.	.	none		0.537	AFAP1L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050462.1	NM_032550		A	116100456	G	A	116100456	2	1	220	1	0	0	0	0	0	0	0	1	355	1165	41	2		2	AFAP1L2	10	116100456	Silent	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	73012099	116100456	19434291	54	13324											
MKI67	4288	hgsc.bcm.edu	37	chr10	129902143	129902143	+	Frame_Shift_Del	DEL	G	G	-																															gttcctcttctactgggtttGgtttcttctttgcacgttgc																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr10:129902143delG	ENST00000368654.3	-	13	8336	c.7961delC	c.(7960-7962)ccafs	p.P2654fs	MKI67_ENST00000368653.3_Frame_Shift_Del_p.P2294fs	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2654	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)				TACTGGGTTTGGTTTCTTCTT	0.522																																					p.P2654fs		Atlas-Indel,Pindel	.											.	MKI67	363	.	0			c.7962delA						PASS	.						171	175	174					10																	129902143		2203	4300	6503	SO:0001589	frameshift_variant	4288	exon13			.	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.7961delC	chr10.hg19:g.129902143delG	ENSP00000357643:p.Pro2654fs	131.0	0.0	0		118.0	50.0	0.423729	NM_002417	Q5VWH2	Frame_Shift_Del	DEL	ENST00000368654.3	hg19	CCDS7659.1																																																																																			.	.	.	none		0.522	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		-	129902143	G	-	129902143	7	5	220	1	0	1	0	1	0	0	0	0	9605	1348	47	0	1821	0	MKI67	10	129902143	Frame_Shift_Del	DEL	G	TCGA-MH-A55Z-01A-11D-A26P-10	13801687	129902143	5632604	55	13325											
OR51G2	81282	hgsc.bcm.edu	37	chr11	4936503	4936503	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atagtgcaaggggtggcagaTagccacaaagcggtcaaagg	14	5	15	7	1	1	1	1	0	0	1	1	1	1	1	1	5	3	2	1	5	5	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr11:4936503T>C	ENST00000322013.3	-	1	419	c.391A>G	c.(391-393)Atc>Gtc	p.I131V	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001005238.1	NP_001005238.1	Q8NGK0	O51G2_HUMAN	olfactory receptor, family 51, subfamily G, member 2	131						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)		GGGTGGCAGATAGCCACAAAG	0.493																																					p.I131V		Atlas-SNP	.											.	OR51G2	70	.	0			c.A391G						PASS	.						81	80	80					11																	4936503		2201	4298	6499	SO:0001583	missense	81282	exon1			GGCAGATAGCCAC	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.391A>G	chr11.hg19:g.4936503T>C	ENSP00000322593:p.Ile131Val	52.0	0.0	.		56.0	23.0	.	NM_001005238	Q6IFH7	Missense_Mutation	SNP	ENST00000322013.3	hg19	CCDS31365.1	.	.	.	.	.	.	.	.	.	.	T	16.52	3.145321	0.57044	.	.	ENSG00000176893	ENST00000322013	T	0.50813	0.73	5.58	5.58	0.84498	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000099	T	0.55097	0.1899	M	0.86573	2.825	0.44719	D	0.997717	B	0.29301	0.241	B	0.25987	0.065	T	0.60835	-0.7184	10	0.66056	D	0.02	.	14.7227	0.69320	0.0:0.0:0.0:1.0	.	131	Q8NGK0	O51G2_HUMAN	V	131	ENSP00000322593:I131V	ENSP00000322593:I131V	I	-	1	0	OR51G2	4893079	1.000000	0.71417	0.999000	0.59377	0.952000	0.60782	7.646000	0.83445	2.343000	0.79666	0.533000	0.62120	ATC	.	.	.	none		0.493	OR51G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142174.1	NM_001005238		C	4936503	T	C	4936503	3	2	220	1	0	0	0	0	1	0	0	0	11106	1406	49	3	557	3	OR51G2	11	4936503	Missense_Mutation	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10		4936503	130070013	56	13326											
BDNF	627	hgsc.bcm.edu	37	chr11	27680049	27680056	+	Frame_Shift_Del	DEL	CATGGGGG	CATGGGGG	-																															cctcggatgtttgcttctttCatgggggcagccttcatgca																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	CATGGGGG	CATGGGGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr11:27680049_27680056delCATGGGGG	ENST00000525528.1	-	1	1149_1156	c.56_63delCCCCCATG	c.(55-63)gcccccatgfs	p.APM19fs	BDNF-AS_ENST00000499568.2_RNA|BDNF_ENST00000314915.6_Frame_Shift_Del_p.APM27fs|BDNF_ENST00000395983.3_Frame_Shift_Del_p.APM19fs|BDNF_ENST00000525950.1_Frame_Shift_Del_p.APM19fs|BDNF_ENST00000533131.1_Frame_Shift_Del_p.APM19fs|BDNF-AS_ENST00000502161.2_RNA|BDNF_ENST00000438929.1_Frame_Shift_Del_p.APM101fs|BDNF_ENST00000395980.2_Frame_Shift_Del_p.APM19fs|BDNF_ENST00000533246.1_Frame_Shift_Del_p.APM19fs|BDNF_ENST00000418212.1_Frame_Shift_Del_p.APM19fs|BDNF_ENST00000395986.2_Frame_Shift_Del_p.APM34fs|BDNF-AS_ENST00000530686.1_RNA|BDNF_ENST00000530861.1_Frame_Shift_Del_p.APM19fs|BDNF-AS_ENST00000499008.3_RNA|BDNF_ENST00000356660.4_Frame_Shift_Del_p.APM19fs|BDNF-AS_ENST00000500662.2_RNA|BDNF_ENST00000439476.2_Frame_Shift_Del_p.APM19fs|BDNF-AS_ENST00000501176.2_RNA|BDNF_ENST00000532997.1_Frame_Shift_Del_p.APM19fs|BDNF_ENST00000584049.1_5'UTR|BDNF_ENST00000395981.3_Frame_Shift_Del_p.APM19fs|BDNF-AS_ENST00000532965.1_RNA|BDNF-AS_ENST00000530313.1_RNA|BDNF_ENST00000420794.1_Frame_Shift_Del_p.APM19fs|BDNF_ENST00000395978.3_Frame_Shift_Del_p.APM19fs	NM_170735.5	NP_733931.1	P23560	BDNF_HUMAN	brain-derived neurotrophic factor	19					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						TTGCTTCTTTCATGGGGGCAGCCTTCAT	0.514																																					p.101_104del		Atlas-Indel,Pindel	.											.	BDNF	63	.	0			c.303_310del						PASS	.																																			SO:0001589	frameshift_variant	627	exon3			.	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.56_63delCCCCCATG	chr11.hg19:g.27680049_27680056delCATGGGGG	ENSP00000437138:p.Ala19fs	121.0	0.0	0		91.0	27.0	0.296703	NM_001143810	A7LA85|A7LA92|D3DQZ2|Q598Q1|Q6DN19|Q6YNR2|Q6YNR3|Q9BYY7|Q9UC24	Frame_Shift_Del	DEL	ENST00000525528.1	hg19	CCDS7866.1																																																																																			.	.	.	none		0.514	BDNF-016	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388135.1	NM_170735		-	27680056	CATGGGGG	-	27680049	7	5	220	1	0	1	0	1	0	0	0	0	1394	826	29	0	684	0	BDNF	11	27680049	Frame_Shift_Del	DEL	CATGGGGG	TCGA-MH-A55Z-01A-11D-A26P-10	22743546	27680049	107326467	57	13327											
SYT13	57586	hgsc.bcm.edu	37	chr11	45277229	45277229	+	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	acccctaccattctgagggaGgatgaacagctcctctgtga	10	9	10	12	0	2	3	0	3	2	0	3	5	3	5	4	2	3	1	4	2	2	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr11:45277229G>C	ENST00000020926.3	-	2	508	c.397C>G	c.(397-399)Ctc>Gtc	p.L133V	CTD-2560E9.5_ENST00000534342.1_RNA|CTD-2560E9.5_ENST00000531663.1_RNA	NM_001247987.1|NM_020826.2	NP_001234916.1|NP_065877.1	Q7L8C5	SYT13_HUMAN	synaptotagmin XIII	133					vesicle-mediated transport (GO:0016192)	integral component of plasma membrane (GO:0005887)|transport vesicle (GO:0030133)				breast(1)|large_intestine(3)|lung(16)|ovary(1)|skin(2)	23						TTCTGAGGGAGGATGAACAGC	0.592																																					p.L133V		Atlas-SNP	.											.	SYT13	45	.	0			c.C397G						PASS	.						53	47	49					11																	45277229		2203	4299	6502	SO:0001583	missense	57586	exon2			GAGGGAGGATGAA	AB037848	CCDS31470.1	11p12-p11	2013-01-21			ENSG00000019505	ENSG00000019505		"Synaptotagmins"	14962	protein-coding gene	gene with protein product		607716				11171101	Standard	NM_020826		Approved	KIAA1427	uc001myq.2	Q7L8C5	OTTHUMG00000166504	ENST00000020926.3:c.397C>G	chr11.hg19:g.45277229G>C	ENSP00000020926:p.Leu133Val	52.0	0.0	.		39.0	17.0	.	NM_020826	A8K4P4|D3DQP1|Q9BQS3|Q9H041|Q9P2C0	Missense_Mutation	SNP	ENST00000020926.3	hg19	CCDS31470.1	.	.	.	.	.	.	.	.	.	.	G	15.36	2.810428	0.50421	.	.	ENSG00000019505	ENST00000020926	T	0.08370	3.1	5.39	5.39	0.77823	.	0.077197	0.52532	D	0.000067	T	0.06917	0.0176	N	0.24115	0.695	0.33493	D	0.588914	B	0.23650	0.089	B	0.21917	0.037	T	0.17501	-1.0367	10	0.30078	T	0.28	.	13.5218	0.61572	0.0:0.0:0.8444:0.1556	.	133	Q7L8C5	SYT13_HUMAN	V	133	ENSP00000020926:L133V	ENSP00000020926:L133V	L	-	1	0	SYT13	45233805	1.000000	0.71417	0.997000	0.53966	0.983000	0.72400	3.496000	0.53288	2.679000	0.91253	0.561000	0.74099	CTC	.	.	.	none		0.592	SYT13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390110.1	NM_020826		C	45277229	G	C	45277229	3	2	220	1	0	0	0	0	1	0	0	0	15481	1000	35	4	903	4	SYT13	11	45277229	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	17597180	45277229	89729287	58	13328											
LTBP3	4054	hgsc.bcm.edu	37	chr11	65319017	65319017	+	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	ccatctgggttctcatactcActgagtccgtggtcacccct	6	12	8	15	1	4	1	3	1	2	0	6	1	5	1	4	2	1	1	4	2	1	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr11:65319017A>T	ENST00000301873.5	-	9	1817		c.e9+1		LTBP3_ENST00000532932.1_5'Flank|LTBP3_ENST00000536982.1_Splice_Site|LTBP3_ENST00000322147.4_Splice_Site	NM_001130144.2	NP_001123616.1	Q9NS15	LTBP3_HUMAN	latent transforming growth factor beta binding protein 3						bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|extracellular matrix organization (GO:0030198)|lung saccule development (GO:0060430)|negative regulation of bone mineralization (GO:0030502)|negative regulation of chondrocyte differentiation (GO:0032331)|positive regulation of bone resorption (GO:0045780)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of mesenchymal stem cell proliferation (GO:1902462)|transforming growth factor beta activation (GO:0036363)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(3)	23						TCTCATACTCACTGAGTCCGT	0.592																																					.		Atlas-SNP	.											.	LTBP3	55	.	0			c.1197+2T>A						PASS	.						68	58	62					11																	65319017		2201	4297	6498	SO:0001630	splice_region_variant	4054	exon10			ATACTCACTGAGT	AF135960	CCDS8103.1, CCDS44647.1	11q12	2011-10-20			ENSG00000168056	ENSG00000168056		"Latent transforming growth factor, beta binding proteins"	6716	protein-coding gene	gene with protein product		602090		LTBP2		7719025	Standard	NM_001164266		Approved		uc001oej.3	Q9NS15	OTTHUMG00000166575	ENST00000301873.5:c.1548+1T>A	chr11.hg19:g.65319017A>T		128.0	0.0	.		107.0	35.0	.	NM_001164266	O15107|Q96HB9|Q9H7K2|Q9UFN4	Splice_Site	SNP	ENST00000301873.5	hg19	CCDS44647.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.029156	0.75504	.	.	ENSG00000168056	ENST00000322147;ENST00000301873;ENST00000526927;ENST00000536982;ENST00000530866	.	.	.	4.96	4.96	0.65561	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.0038	0.47622	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	LTBP3	65075593	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	4.837000	0.62796	1.861000	0.53984	0.329000	0.21502	.	.	.	.	none		0.592	LTBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390538.1	NM_021070	Intron	T	65319017	A	T	65319017	5	4	220	1	0	0	0	0	0	0	1	0	9082	173	6	5	2441	5	LTBP3	11	65319017	Splice_Site	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	20041788	65319017	69687499	59	13329											
SIPA1	6494	hgsc.bcm.edu	37	chr11	65412463	65412463	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtgggcatcctgtactgccGggcgggccagggctcggagg	4	6	20	11	3	0	0	0	0	0	0	2	1	1	1	3	7	2	3	3	7	1	1	rs146916012		TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr11:65412463G>A	ENST00000394224.3	+	5	1318	c.1022G>A	c.(1021-1023)cGg>cAg	p.R341Q	SIPA1_ENST00000527525.1_Missense_Mutation_p.R341Q|SIPA1_ENST00000394227.3_Missense_Mutation_p.R341Q|SIPA1_ENST00000534313.1_Missense_Mutation_p.R341Q	NM_153253.29	NP_694985.29	Q96FS4	SIPA1_HUMAN	signal-induced proliferation-associated 1	341	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				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						CTGTACTGCCGGGCGGGCCAG	0.622																																					p.R341Q		Atlas-SNP	.											.	SIPA1	45	.	0			c.G1022A						PASS	.	G	GLN/ARG,GLN/ARG	0,4402		0,0,2201	86	88	87		1022,1022	4.8	1	11	dbSNP_134	87	2,8592	2.2+/-6.3	0,2,4295	yes	missense,missense	SIPA1	NM_006747.3,NM_153253.29	43,43	0,2,6496	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging	341/1043,341/1043	65412463	2,12994	2201	4297	6498	SO:0001583	missense	6494	exon5			ACTGCCGGGCGGG	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.1022G>A	chr11.hg19:g.65412463G>A	ENSP00000377771:p.Arg341Gln	142.0	0.0	.		187.0	88.0	.	NM_006747	O14518|O60484|O60618|Q2YD83	Missense_Mutation	SNP	ENST00000394224.3	hg19	CCDS8108.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.872939	0.91664	0.0	2.33E-4	ENSG00000213445	ENST00000534313;ENST00000527525;ENST00000394224;ENST00000394227	D;D;D;D	0.93859	-3.3;-3.3;-3.3;-3.3	4.78	4.78	0.61160	Rap/ran-GAP (1);	0.123367	0.30667	U	0.009135	D	0.94499	0.8229	L	0.41027	1.25	0.47994	D	0.999563	D;D	0.89917	1.0;1.0	D;D	0.69824	0.966;0.926	D	0.94259	0.7500	10	0.45353	T	0.12	-21.0415	15.6687	0.77255	0.0:0.0:1.0:0.0	.	341;341	F6RY50;Q96FS4	.;SIPA1_HUMAN	Q	341	ENSP00000436269:R341Q;ENSP00000433686:R341Q;ENSP00000377771:R341Q;ENSP00000377774:R341Q	ENSP00000377771:R341Q	R	+	2	0	SIPA1	65169039	0.996000	0.38824	0.989000	0.46669	0.990000	0.78478	1.561000	0.36342	2.368000	0.80403	0.561000	0.74099	CGG	.	G|1.000;A|0.000	0.000	weak		0.622	SIPA1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390356.1	NM_006747		A	65412463	G	A	65412463	3	1	220	1	0	0	0	0	1	0	0	0	14341	1116	39	1	1036	1	SIPA1	11	65412463	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	93446	65412463	69594053	60	13330											
CHEK1	1111	hgsc.bcm.edu	37	chr11	125497532	125497532	+	Missense_Mutation	SNP	A	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	gctgtgaatagagtaactgaAgaagcagtcgcagtgaagat	15	8	13	5	1	0	6	0	3	0	3	1	6	0	6	0	0	2	4	0	0	6	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr11:125497532A>C	ENST00000534070.1	+	3	351	c.96A>C	c.(94-96)gaA>gaC	p.E32D	CHEK1_ENST00000278916.3_Missense_Mutation_p.E32D|CHEK1_ENST00000438015.1_Missense_Mutation_p.E32D|CHEK1_ENST00000428830.2_Missense_Mutation_p.E32D|CHEK1_ENST00000427383.2_Intron|CHEK1_ENST00000524737.1_Missense_Mutation_p.E32D|CHEK1_ENST00000532449.1_Intron|CHEK1_ENST00000544373.1_Missense_Mutation_p.E32D	NM_001274.5	NP_001265.2	O14757	CHK1_HUMAN	checkpoint kinase 1	32	Interaction with CLSPN. {ECO:0000250}.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to caffeine (GO:0071313)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to mechanical stimulus (GO:0071260)|chromatin-mediated maintenance of transcription (GO:0048096)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of mitosis (GO:0045839)|peptidyl-threonine phosphorylation (GO:0018107)|regulation of cell proliferation (GO:0042127)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of histone H3-K9 acetylation (GO:2000615)|regulation of mitotic centrosome separation (GO:0046602)|regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010767)|replicative senescence (GO:0090399)	centrosome (GO:0005813)|chromatin (GO:0000785)|condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	ATP binding (GO:0005524)|histone kinase activity (H3-T11 specific) (GO:0035402)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(3)|endometrium(3)|large_intestine(2)|lung(16)|skin(1)|upper_aerodigestive_tract(1)	26	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0748)		GAGTAACTGAAGAAGCAGTCG	0.328								Other conserved DNA damage response genes																													p.E32D		Atlas-SNP	.											.	CHEK1	44	.	0			c.A96C						PASS	.						50	54	52					11																	125497532		2201	4299	6500	SO:0001583	missense	1111	exon3			AACTGAAGAAGCA	AF016582, BC017575	CCDS8459.1, CCDS58191.1	11q24.2	2011-11-11	2011-11-11		ENSG00000149554	ENSG00000149554			1925	protein-coding gene	gene with protein product		603078	"CHK1 (checkpoint, S.pombe) homolog", "CHK1 checkpoint homolog (S. pombe)"			9278511, 9382850	Standard	NM_001114121		Approved	CHK1	uc001qcg.4	O14757	OTTHUMG00000165853	ENST00000534070.1:c.96A>C	chr11.hg19:g.125497532A>C	ENSP00000435371:p.Glu32Asp	61.0	0.0	.		71.0	34.0	.	NM_001244846	A8K934|B4DDD0|B4DSK3|B5BTY6|F5H7S4|H2BI51	Missense_Mutation	SNP	ENST00000534070.1	hg19	CCDS8459.1	.	.	.	.	.	.	.	.	.	.	A	10.22	1.289544	0.23478	.	.	ENSG00000149554	ENST00000438015;ENST00000525396;ENST00000428830;ENST00000544373;ENST00000527013;ENST00000526937;ENST00000534685;ENST00000533778;ENST00000534070;ENST00000524737;ENST00000278916	T;T;T;T;T;T;T;T;T;T;T	0.41400	1.9;1.9;1.9;1.9;1.9;1.9;1.9;1.0;1.9;1.9;1.9	5.21	4.09	0.47781	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	0.23171	0.0560	N	0.05383	-0.06	0.53688	D	0.999972	B;B;B	0.19200	0.027;0.034;0.034	B;B;B	0.25405	0.036;0.06;0.06	T	0.04537	-1.0944	10	0.37606	T	0.19	.	8.9327	0.35680	0.8441:0.0:0.1559:0.0	.	32;32;32	F5H7S4;B5BTY6;O14757	.;.;CHK1_HUMAN	D	32	ENSP00000388648:E32D;ENSP00000434141:E32D;ENSP00000412504:E32D;ENSP00000442317:E32D;ENSP00000431525:E32D;ENSP00000431815:E32D;ENSP00000432470:E32D;ENSP00000433103:E32D;ENSP00000435371:E32D;ENSP00000432890:E32D;ENSP00000278916:E32D	ENSP00000278916:E32D	E	+	3	2	CHEK1	125002742	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	0.843000	0.27640	0.957000	0.37930	0.477000	0.44152	GAA	.	.	.	none		0.328	CHEK1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386714.1	NM_001274		C	125497532	A	C	125497532	3	2	220	1	0	0	0	0	1	0	0	0	3336	69	3	5	102	5	CHEK1	11	125497532	Missense_Mutation	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	60085069	125497532	9508984	61	13331											
NFRKB	4798	hgsc.bcm.edu	37	chr11	129747271	129747271	+	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	gtgctgggacgcaccacataGtcagttcttctggaatataa	11	11	10	9	1	3	0	1	0	2	0	3	2	3	2	1	2	1	3	1	2	4	5			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr11:129747271G>A	ENST00000446488.3	-	15	1624	c.1521C>T	c.(1519-1521)gaC>gaT	p.D507D	NFRKB_ENST00000304521.5_Silent_p.D507D|NFRKB_ENST00000524746.1_Silent_p.D507D|NFRKB_ENST00000524794.1_Silent_p.D532D	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	507					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)		GCACCACATAGTCAGTTCTTC	0.507																																					p.D532D		Atlas-SNP	.											.	NFRKB	101	.	0			c.C1596T						PASS	.						161	149	153					11																	129747271		2201	4297	6498	SO:0001819	synonymous_variant	4798	exon14			CACATAGTCAGTT		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.1521C>T	chr11.hg19:g.129747271G>A		111.0	0.0	.		74.0	27.0	.	NM_006165	Q12869|Q15312|Q9H048	Silent	SNP	ENST00000446488.3	hg19	CCDS44770.1																																																																																			.	.	.	none		0.507	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2	NM_006165		A	129747271	G	A	129747271	2	1	220	1	0	0	0	0	0	0	0	1	10391	1020	36	2		2	NFRKB	11	129747271	Silent	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	4249739	129747271	5259245	62	13332											
C12orf57	113246	hgsc.bcm.edu	37	chr12	7053729	7053729	+	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	taacgcctgcaacgacatggGtaagatgctgcaattcgtgc	11	9	11	10	3	0	1	0	0	0	1	1	2	0	1	1	1	6	4	1	1	4	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr12:7053729G>T	ENST00000229281.5	+	2	242	c.143G>T	c.(142-144)gGt>gTt	p.G48V	C12orf57_ENST00000540506.2_Missense_Mutation_p.G13V|U47924.31_ENST00000607421.1_RNA|C12orf57_ENST00000537087.1_Splice_Site|C12orf57_ENST00000544681.1_Missense_Mutation_p.G48V|PTPN6_ENST00000447931.2_5'Flank|C12orf57_ENST00000542222.1_3'UTR|RNU7-1_ENST00000458811.1_RNA|PTPN6_ENST00000399448.1_5'Flank	NM_138425.2	NP_612434.1	Q99622	C10_HUMAN	chromosome 12 open reading frame 57	48						cytoplasm (GO:0005737)				kidney(1)|large_intestine(1)	2						AACGACATGGGTAAGATGCTG	0.627											OREG0021642	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G48V		Atlas-SNP	.											.	C12orf57	10	.	0			c.G143T						PASS	.						90	66	74					12																	7053729		2203	4300	6503	SO:0001583	missense	113246	exon2			ACATGGGTAAGAT	U47924	CCDS8571.1	12p13.31	2012-05-30			ENSG00000111678	ENSG00000111678			29521	protein-coding gene	gene with protein product		615140				9445485	Standard	NM_138425		Approved	GRCC10, C10	uc009zfj.2	Q99622	OTTHUMG00000169017	ENST00000229281.5:c.143G>T	chr12.hg19:g.7053729G>T	ENSP00000229281:p.Gly48Val	95.0	0.0	.	638	203.0	118.0	.	NM_138425	B2R4Q6	Missense_Mutation	SNP	ENST00000229281.5	hg19	CCDS8571.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.6|24.6	4.552280|4.552280	0.86127|0.86127	.|.	.|.	ENSG00000111678|ENSG00000111678	ENST00000537087|ENST00000545581;ENST00000229281	.|T;T	.|0.75938	.|-0.98;-0.98	3.74|3.74	3.74|3.74	0.42951|0.42951	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.74412	.|0.3713	L|L	0.31664|0.31664	0.95|0.95	0.80722|0.80722	D|D	1|1	.|D;B	.|0.76494	.|0.999;0.106	.|D;B	.|0.74023	.|0.982;0.013	.|T	.|0.67673	.|-0.5610	.|10	.|0.06625	.|T	.|0.88	.|-25.1478	14.5671|14.5671	0.68185|0.68185	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|48;48	.|F5GXW5;Q99622	.|.;C10_HUMAN	.|V	-1|48	.|ENSP00000440602:G48V;ENSP00000229281:G48V	.|ENSP00000229281:G48V	.|G	+|+	.|2	.|0	C12orf57|C12orf57	6923990|6923990	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	9.007000|9.007000	0.93597|0.93597	2.373000|2.373000	0.80994|0.80994	0.561000|0.561000	0.74099|0.74099	.|GGT	.	.	.	none		0.627	C12orf57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401959.1	NM_138425		T	7053729	G	T	7053729	3	4	220	1	0	0	0	0	1	0	0	0	1703	1261	44	4	149	4	C12orf57	12	7053729	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10		7053729	126798166	63	13333											
TAS2R43	259289	hgsc.bcm.edu	37	chr12	11244149	11244149	+	Frame_Shift_Del	DEL	G	G	-																															aggagatcacagtttgcaaaGcttttatgtggaccttggtg																								rs73064964	byFrequency	TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr12:11244149delG	ENST00000531678.1	-	1	763	c.680delC	c.(679-681)gctfs	p.A227fs	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176884.2	NP_795365.2	P59537	T2R43_HUMAN	taste receptor, type 2, member 43	227					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)		AGTTTGCAAAGCTTTTATGTG	0.393																																					p.A227fs		Atlas-INDEL	.											.	TAS2R43	19	.	0			c.681delT						PASS	.						137	119	125					12																	11244149		2179	4249	6428	SO:0001589	frameshift_variant	259289	exon1			.	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.680delC	chr12.hg19:g.11244149delG	ENSP00000431719:p.Ala227fs	10.0	0.0	0		32.0	17.0	0.53125	NM_176884	P59546|Q645X4	Frame_Shift_Del	DEL	ENST00000531678.1	hg19	CCDS53749.1																																																																																			.	.	.	none		0.393	TAS2R43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383561.1	NM_176884		-	11244149	G	-	11244149	7	5	220	1	0	1	0	1	0	0	0	0	15593	971	34	0	253	0	TAS2R43	12	11244149	Frame_Shift_Del	DEL	G	TCGA-MH-A55Z-01A-11D-A26P-10	4190420	11244149	122607746	64	13334											
PLEKHA5	54477	hgsc.bcm.edu	37	chr12	19500042	19500042	+	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	gctccttgctctgttatagcAggggcccagttcatctgcct	5	13	10	13	0	3	0	1	0	2	0	4	0	4	0	3	2	3	5	3	2	2	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr12:19500042A>G	ENST00000299275.6	+	18	2406				PLEKHA5_ENST00000429027.2_Missense_Mutation_p.R942G|PLEKHA5_ENST00000539256.1_Intron|PLEKHA5_ENST00000359180.3_Intron|PLEKHA5_ENST00000538714.1_Intron|PLEKHA5_ENST00000355397.3_Intron|PLEKHA5_ENST00000317589.4_Missense_Mutation_p.R839G|PLEKHA5_ENST00000543806.1_Missense_Mutation_p.R758G|PLEKHA5_ENST00000424268.1_Missense_Mutation_p.R765G	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5						reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					CTGTTATAGCAGGGGCCCAGT	0.498																																					p.R942G	Pancreas(196;329 2193 11246 14234 19524)	Atlas-SNP	.											.	PLEKHA5	198	.	0			c.A2824G						PASS	.						91	80	83					12																	19500042		692	1591	2283	SO:0001627	intron_variant	54477	exon24			TATAGCAGGGGCC	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"Pleckstrin homology (PH) domain containing"	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.2400+1220A>G	chr12.hg19:g.19500042A>G		118.0	0.0	.		172.0	47.0	.	NM_001256470	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Missense_Mutation	SNP	ENST00000299275.6	hg19	CCDS8682.1	.	.	.	.	.	.	.	.	.	.	A	17.44	3.391185	0.62066	.	.	ENSG00000052126	ENST00000317589;ENST00000542828;ENST00000429027;ENST00000424268;ENST00000543806;ENST00000536974	T;T;T;T;T	0.10005	2.92;2.92;2.92;2.92;2.92	5.66	4.53	0.55603	.	0.154367	0.42420	D	0.000712	T	0.11196	0.0273	.	.	.	0.80722	D	1	B;B;B;B;B	0.27625	0.08;0.183;0.115;0.115;0.115	B;B;B;B;B	0.33690	0.12;0.168;0.081;0.081;0.031	T	0.06534	-1.0821	9	0.72032	D	0.01	-15.471	7.1521	0.25616	0.7782:0.1481:0.0737:0.0	.	839;758;765;937;942	Q9HAU0-4;F5H0I0;E7EME8;B4DHK5;E9PHQ3	.;.;.;.;.	G	839;938;942;765;758;731	ENSP00000325155:R839G;ENSP00000404296:R942G;ENSP00000400411:R765G;ENSP00000439837:R758G;ENSP00000440371:R731G	ENSP00000325155:R839G	R	+	1	2	PLEKHA5	19391309	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.764000	0.62264	2.137000	0.66172	0.528000	0.53228	AGG	.	.	.	none		0.498	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012		G	19500042	A	G	19500042	1	3	220	0	1	0	0	0	0	0	0	0	12066	179	7	3		3	PLEKHA5	12	19500042	Intron	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	8255893	19500042	114351853	65	13335											
SPRYD4	283377	hgsc.bcm.edu	37	chr12	56862411	56862411	+	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	gcacgttctttgcgcttgtgCcgctggggagccaaacgatt	6	11	13	11	4	1	0	0	0	1	0	1	2	1	1	2	2	4	4	2	2	1	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr12:56862411C>T	ENST00000338146.5	+	1	111	c.36C>T	c.(34-36)tgC>tgT	p.C12C	MIP_ENST00000555551.1_Intron	NM_207344.3	NP_997227	Q8WW59	SPRY4_HUMAN	SPRY domain containing 4	12	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					mitochondrion (GO:0005739)|nucleus (GO:0005634)				kidney(1)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)	7						TGCGCTTGTGCCGCTGGGGAG	0.567																																					p.C12C		Atlas-SNP	.											.	SPRYD4	13	.	0			c.C36T						PASS	.						136	125	129					12																	56862411		2203	4300	6503	SO:0001819	synonymous_variant	283377	exon1			CTTGTGCCGCTGG	AL832247	CCDS8920.1	12q13.3	2006-03-09				ENSG00000176422			27468	protein-coding gene	gene with protein product							Standard	NM_207344		Approved	DKFZp686N0877	uc001sli.4	Q8WW59		ENST00000338146.5:c.36C>T	chr12.hg19:g.56862411C>T		85.0	0.0	.		110.0	5.0	.	NM_207344	A8K7A5	Silent	SNP	ENST00000338146.5	hg19	CCDS8920.1																																																																																			.	.	.	none		0.567	SPRYD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_207344		T	56862411	C	T	56862411	2	4	220	1	0	0	0	0	0	0	0	1	15122	747	26	2		2	SPRYD4	12	56862411	Silent	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	37362369	56862411	76989484	66	13336											
SLC5A8	160728	hgsc.bcm.edu	37	chr12	101588897	101588897	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcagtagaatgtgcagacCacccccgttgccactaccgc	9	7	10	15	2	0	2	0	0	0	2	0	2	0	2	5	0	4	4	5	0	3	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr12:101588897C>T	ENST00000536262.2	-	4	1071	c.513G>A	c.(511-513)gtG>gtA	p.V171V		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						ATGTGCAGACCACCCCCGTTG	0.403																																					p.V171V	GBM(60;420 1056 13605 22380 47675)	Atlas-SNP	.											.	SLC5A8	102	.	0			c.G513A						PASS	.						99	86	90					12																	101588897		2203	4300	6503	SO:0001819	synonymous_variant	160728	exon4			GCAGACCACCCCC	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.513G>A	chr12.hg19:g.101588897C>T		101.0	0.0	.		108.0	61.0	.	NM_145913		Silent	SNP	ENST00000536262.2	hg19	CCDS9080.1																																																																																			.	.	.	none		0.403	SLC5A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409401.1	NM_145913		T	101588897	C	T	101588897	2	4	220	1	0	0	0	0	0	0	0	1	14684	581	21	2		2	SLC5A8	12	101588897	Silent	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	44726486	101588897	32262998	67	13337											
BTBD11	121551	hgsc.bcm.edu	37	chr12	107713245	107713245	+	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	ctgtcctggggcctggccgcGcactgtacggcggctgcgct	2	8	16	15	5	0	0	0	0	0	0	1	0	1	0	3	5	2	4	3	5	1	1			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr12:107713245G>A	ENST00000280758.5	+	1	1056	c.528G>A	c.(526-528)gcG>gcA	p.A176A	BTBD11_ENST00000420571.2_Silent_p.A176A|BTBD11_ENST00000490090.2_Silent_p.A176A	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	176						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						GCCTGGCCGCGCACTGTACGG	0.697																																					p.A176A		Atlas-SNP	.											.	BTBD11	122	.	0			c.G528A						PASS	.						11	10	10					12																	107713245		2095	4067	6162	SO:0001819	synonymous_variant	121551	exon1			GGCCGCGCACTGT	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.528G>A	chr12.hg19:g.107713245G>A		2.0	0.0	.		10.0	7.0	.	NM_001018072	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Silent	SNP	ENST00000280758.5	hg19	CCDS31893.1																																																																																			.	.	.	none		0.697	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322		A	107713245	G	A	107713245	2	1	220	1	0	0	0	0	0	0	0	1	1541	1074	38	1		1	BTBD11	12	107713245	Silent	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	6124348	107713245	26138650	68	13338											
GPC6	10082	hgsc.bcm.edu	37	chr13	94197565	94197565	+	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	tatacatgctgcaccacagaAatggaagacaagttaagcca	17	7	8	9	0	0	2	0	0	0	2	0	3	0	3	2	1	4	3	2	1	6	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr13:94197565A>T	ENST00000377047.4	+	2	825	c.210A>T	c.(208-210)gaA>gaT	p.E70D		NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6	70					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)				GCACCACAGAAATGGAAGACA	0.408																																					p.E70D		Atlas-SNP	.											.	GPC6	102	.	0			c.A210T						PASS	.						154	142	146					13																	94197565		2203	4300	6503	SO:0001583	missense	10082	exon2			CACAGAAATGGAA	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.210A>T	chr13.hg19:g.94197565A>T	ENSP00000366246:p.Glu70Asp	82.0	0.0	.		95.0	42.0	.	NM_005708	A8K279|Q96SG5|Q96SG8|Q9H1P4	Missense_Mutation	SNP	ENST00000377047.4	hg19	CCDS9469.1	.	.	.	.	.	.	.	.	.	.	A	14.65	2.598483	0.46318	.	.	ENSG00000183098	ENST00000377047	T	0.52983	0.64	5.0	3.82	0.43975	.	0.074354	0.51477	D	0.000081	T	0.43919	0.1269	L	0.51853	1.615	0.31140	N	0.706753	B;B	0.21452	0.031;0.056	B;B	0.30646	0.118;0.101	T	0.50110	-0.8866	10	0.46703	T	0.11	.	10.667	0.45736	0.9242:0.0:0.0758:0.0	.	70;70	B4E2M1;Q9Y625	.;GPC6_HUMAN	D	70	ENSP00000366246:E70D	ENSP00000366246:E70D	E	+	3	2	GPC6	92995566	0.997000	0.39634	1.000000	0.80357	0.999000	0.98932	0.672000	0.25187	0.867000	0.35654	0.524000	0.50904	GAA	.	.	.	none		0.408	GPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045460.4	NM_005708		T	94197565	A	T	94197565	3	4	220	1	0	0	0	0	1	0	0	0	6609	11	1	5	216	5	GPC6	13	94197565	Missense_Mutation	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10		94197565	20972313	69	13339											
LRFN5	145581	hgsc.bcm.edu	37	chr14	42360768	42360768	+	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	cacaaggtcaccaaggttagCaatgtttattcccaaactaa	15	10	6	10	0	1	0	1	0	0	0	2	0	2	0	2	2	2	3	2	2	7	5			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr14:42360768C>T	ENST00000298119.4	+	4	2890	c.1701C>T	c.(1699-1701)agC>agT	p.S567S	LRFN5_ENST00000554171.1_Intron|LRFN5_ENST00000554120.1_Intron	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	567						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)		CCAAGGTTAGCAATGTTTATT	0.458										HNSCC(30;0.082)																											p.S567S		Atlas-SNP	.											.	LRFN5	269	.	0			c.C1701T						PASS	.						103	99	100					14																	42360768		2203	4300	6503	SO:0001819	synonymous_variant	145581	exon4			GGTTAGCAATGTT	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.1701C>T	chr14.hg19:g.42360768C>T		102.0	0.0	.		113.0	43.0	.	NM_152447	B3KU78|Q86XL2	Silent	SNP	ENST00000298119.4	hg19	CCDS9678.1																																																																																			.	.	.	none		0.458	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	NM_152447		T	42360768	C	T	42360768	2	4	220	1	0	0	0	0	0	0	0	1	8948	709	25	2		2	LRFN5	14	42360768	Silent	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10		42360768	64988772	70	13340											
NEK9	91754	hgsc.bcm.edu	37	chr14	75558059	75558059	+	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	gattaaaccttccattcctcGgtctgcttccattgttcctc	6	16	5	14	1	1	0	0	0	1	0	7	1	5	0	5	1	2	2	5	1	2	6			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr14:75558059G>A	ENST00000238616.5	-	19	2514	c.2356C>T	c.(2356-2358)Cga>Tga	p.R786*		NM_033116.4	NP_149107.4	Q8TD19	NEK9_HUMAN	NIMA-related kinase 9	786	Interaction with NEK6.|Pro/Ser/Thr-rich.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00718)		TCCATTCCTCGGTCTGCTTCC	0.567																																					p.R786X		Atlas-SNP	.											.	NEK9	64	.	0			c.C2356T						PASS	.						116	104	108					14																	75558059		2203	4300	6503	SO:0001587	stop_gained	91754	exon19			TTCCTCGGTCTGC	AY048580	CCDS9839.1	14q24.2	2012-11-15	2012-11-15		ENSG00000119638	ENSG00000119638			18591	protein-coding gene	gene with protein product		609798	"NIMA (never in mitosis gene a)- related kinase 9"			11864968	Standard	NM_033116		Approved	Nek8, NERCC, DKFZp434D0935, MGC16714	uc001xrl.3	Q8TD19	OTTHUMG00000171768	ENST00000238616.5:c.2356C>T	chr14.hg19:g.75558059G>A	ENSP00000238616:p.Arg786*	74.0	0.0	.		70.0	32.0	.	NM_033116	Q52LK6|Q8NCN0|Q8TCY4|Q9UPI4|Q9Y6S4|Q9Y6S5|Q9Y6S6	Nonsense_Mutation	SNP	ENST00000238616.5	hg19	CCDS9839.1	.	.	.	.	.	.	.	.	.	.	G	41	9.014481	0.99037	.	.	ENSG00000119638	ENST00000238616	.	.	.	5.66	5.66	0.87406	.	0.295996	0.31673	N	0.007256	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.752	0.96271	0.0:0.0:1.0:0.0	.	.	.	.	X	786	.	ENSP00000238616:R786X	R	-	1	2	NEK9	74627812	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.628000	0.61282	2.668000	0.90789	0.462000	0.41574	CGA	.	.	.	none		0.567	NEK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415021.1	NM_033116		A	75558059	G	A	75558059	4	1	220	1	0	0	0	0	0	1	0	0	10338	1124	39	1	599	1	NEK9	14	75558059	Nonsense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	33197291	75558059	31791481	71	13341											
MTMR10	54893	hgsc.bcm.edu	37	chr15	31251264	31251264	+	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	cttctcccaacaaaagaatgGgaaaagatctttagatcttg	15	11	7	8	0	3	3	0	0	3	3	4	4	3	4	1	1	1	0	1	1	7	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr15:31251264G>C	ENST00000435680.1	-	8	916	c.819C>G	c.(817-819)tcC>tcG	p.S273S	MTMR10_ENST00000563714.1_Silent_p.S191S|RNU6-466P_ENST00000391224.1_RNA|MTMR10_ENST00000425768.1_3'UTR|MTMR10_ENST00000314404.8_Silent_p.S25S	NM_017762.2	NP_060232.2	Q9NXD2	MTMRA_HUMAN	myotubularin related protein 10	273	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)		CAAAAGAATGGGAAAAGATCT	0.383																																					p.S273S		Atlas-SNP	.											.	MTMR10	74	.	0			c.C819G						PASS	.						67	63	64					15																	31251264		1866	4106	5972	SO:0001819	synonymous_variant	54893	exon8			AGAATGGGAAAAG	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.819C>G	chr15.hg19:g.31251264G>C		82.0	0.0	.		85.0	38.0	.	NM_017762	Q6P4Q6	Silent	SNP	ENST00000435680.1	hg19	CCDS45204.1																																																																																			.	.	.	none		0.383	MTMR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430747.1	NM_017762		C	31251264	G	C	31251264	2	2	220	1	0	0	0	0	0	0	0	1	9946	1219	43	4		4	MTMR10	15	31251264	Silent	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10		31251264	71280128	72	13342											
COPS2	9318	hgsc.bcm.edu	37	chr15	49421727	49421727	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggcttaattaattttataaGcacttgtgttctgatgtttc	10	19	7	5	0	1	1	0	1	1	0	2	1	1	1	0	1	1	4	0	1	4	8			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr15:49421727G>A	ENST00000388901.5	-	11	1148	c.1075C>T	c.(1075-1077)Ctt>Ttt	p.L359F	COPS2_ENST00000299259.6_Missense_Mutation_p.L366F|COPS2_ENST00000542928.1_Missense_Mutation_p.L295F	NM_001143887.1|NM_004236.3	NP_001137359.1|NP_004227.1	P61201	CSN2_HUMAN	COP9 signalosome subunit 2	359	PCI.				cell proliferation (GO:0008283)|cullin deneddylation (GO:0010388)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(2)	18		all_lung(180;0.0428)		all cancers(107;1.34e-07)|GBM - Glioblastoma multiforme(94;3.02e-05)		AATTTTATAAGCACTTGTGTT	0.229																																					p.L366F	NSCLC(36;322 1063 10349 30082 48062)|Esophageal Squamous(122;685 1633 15569 21293 52803)	Atlas-SNP	.											.	COPS2	41	.	0			c.C1096T						PASS	.						24	25	24					15																	49421727		2132	4209	6341	SO:0001583	missense	9318	exon11			TTATAAGCACTTG	AF212227	CCDS32235.1, CCDS45257.1	15q21.2	2013-03-14	2013-03-14						30747	protein-coding gene	gene with protein product		604508	"COP9 constitutive photomorphogenic homolog subunit 2 (Arabidopsis)"			7776974, 9535219	Standard	NM_004236		Approved	TRIP15, ALIEN, CSN2	uc001zxh.3	P61201		ENST00000388901.5:c.1075C>T	chr15.hg19:g.49421727G>A	ENSP00000373553:p.Leu359Phe	104.0	0.0	.		85.0	35.0	.	NM_001143887	O88950|Q15647|Q6FGP4|Q9BY54|Q9R249|Q9UNI2|Q9UNQ5	Missense_Mutation	SNP	ENST00000388901.5	hg19	CCDS32235.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.868385	0.91587	.	.	ENSG00000166200	ENST00000299259;ENST00000388901;ENST00000542928	T;T;T	0.44083	0.93;0.93;0.93	5.05	5.05	0.67936	Winged helix-turn-helix transcription repressor DNA-binding (1);Proteasome component (PCI) domain (2);	0.000000	0.85682	D	0.000000	T	0.76737	0.4029	H	0.96208	3.785	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.995;0.995;0.998	D	0.84887	0.0834	10	0.72032	D	0.01	-18.1449	18.7719	0.91896	0.0:0.0:1.0:0.0	.	295;367;359	B4DIH5;Q59EL2;P61201	.;.;CSN2_HUMAN	F	366;359;295	ENSP00000299259:L366F;ENSP00000373553:L359F;ENSP00000443664:L295F	ENSP00000299259:L366F	L	-	1	0	COPS2	47209019	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.747000	0.98863	2.498000	0.84270	0.655000	0.94253	CTT	.	.	.	none		0.229	COPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417840.1	NM_004236		A	49421727	G	A	49421727	3	1	220	1	0	0	0	0	1	0	0	0	3735	971	34	2	268	2	COPS2	15	49421727	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	18170463	49421727	53109665	73	13343											
AP4E1	23431	hgsc.bcm.edu	37	chr15	51294808	51294808	+	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	ttcagatcctcctgttctacTcttcctgactatttactgta	7	18	4	12	0	3	2	1	1	2	1	6	2	6	2	3	0	2	2	3	0	4	8			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr15:51294808T>G	ENST00000261842.5	+	21	3469	c.3363T>G	c.(3361-3363)acT>acG	p.T1121T	AP4E1_ENST00000560508.1_Silent_p.T1046T|AP4E1_ENST00000561397.1_3'UTR	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	1121					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)		CCTGTTCTACTCTTCCTGACT	0.463																																					p.T1121T		Atlas-SNP	.											.	AP4E1	78	.	0			c.T3363G						PASS	.						275	213	234					15																	51294808		2196	4294	6490	SO:0001819	synonymous_variant	23431	exon21			TTCTACTCTTCCT	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.3363T>G	chr15.hg19:g.51294808T>G		169.0	0.0	.		128.0	69.0	.	NM_007347	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Silent	SNP	ENST00000261842.5	hg19	CCDS32240.1																																																																																			.	.	.	none		0.463	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1			G	51294808	T	G	51294808	2	3	220	1	0	0	0	0	0	0	0	1	752	1538	54	5		5	AP4E1	15	51294808	Silent	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	1873081	51294808	51236584	74	13344											
ADCY9	115	hgsc.bcm.edu	37	chr16	4164714	4164714	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacccccagacacaaactcaGgtacaaaggtaagtgcatga	16	5	8	12	0	1	2	1	1	0	1	1	2	1	2	2	2	3	3	2	2	4	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr16:4164714G>A	ENST00000294016.3	-	2	1268	c.730C>T	c.(730-732)Ctg>Ttg	p.L244L		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	244					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						CACAAACTCAGGTACAAAGGT	0.552																																					p.L244L		Atlas-SNP	.											.	ADCY9	151	.	0			c.C730T						PASS	.						58	46	50					16																	4164714		2196	4299	6495	SO:0001819	synonymous_variant	115	exon2			AACTCAGGTACAA	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.730C>T	chr16.hg19:g.4164714G>A		170.0	0.0	.		154.0	55.0	.	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Silent	SNP	ENST00000294016.3	hg19	CCDS32382.1																																																																																			.	.	.	none		0.552	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1			A	4164714	G	A	4164714	2	1	220	1	0	0	0	0	0	0	0	1	301	991	35	2		2	ADCY9	16	4164714	Silent	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10		4164714	86190039	75	13345											
MPRIP	23164	hgsc.bcm.edu	37	chr17	17075111	17075111	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctccagaggcagcaccagcGggagctagagaaacttcgag	12	5	13	11	2	1	2	0	0	1	2	3	5	1	3	2	2	4	3	2	2	2	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr17:17075111G>A	ENST00000341712.4	+	16	2243	c.2243G>A	c.(2242-2244)cGg>cAg	p.R748Q	MPRIP_ENST00000395804.3_Missense_Mutation_p.R748Q|RP11-45M22.3_ENST00000584203.1_RNA|MPRIP_ENST00000395811.5_Missense_Mutation_p.R748Q|RNU6-767P_ENST00000384132.1_RNA|MPRIP_ENST00000444976.1_Missense_Mutation_p.R710Q			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	748	Interaction with RHOA.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						CAGCACCAGCGGGAGCTAGAG	0.572																																					p.R748Q		Atlas-SNP	.											.	MPRIP	87	.	0			c.G2243A						PASS	.						71	85	80					17																	17075111		2203	4300	6503	SO:0001583	missense	23164	exon16			ACCAGCGGGAGCT	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.2243G>A	chr17.hg19:g.17075111G>A	ENSP00000342379:p.Arg748Gln	195.0	0.0	.		288.0	176.0	.	NM_015134	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Missense_Mutation	SNP	ENST00000341712.4	hg19	CCDS32578.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	29.7|29.7	5.027583|5.027583	0.93518|0.93518	.|.	.|.	ENSG00000133030|ENSG00000133030	ENST00000414263|ENST00000444976;ENST00000395811;ENST00000395804;ENST00000341712	.|T;T;T;T	.|0.25579	.|1.79;2.12;2.13;2.13	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	.|0.126948	.|0.50627	.|D	.|0.000103	T|T	0.44307|0.44307	0.1287|0.1287	L|L	0.37850|0.37850	1.14|1.14	0.44373|0.44373	D|D	0.99727|0.99727	.|D;P;D	.|0.89917	.|1.0;0.777;1.0	.|D;B;D	.|0.79108	.|0.992;0.346;0.992	T|T	0.12941|0.12941	-1.0528|-1.0528	5|10	.|0.46703	.|T	.|0.11	-16.1602|-16.1602	20.032|20.032	0.97543|0.97543	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1112;748;748	.|Q9Y6X7;Q6WCQ1-2;Q6WCQ1	.|.;.;MPRIP_HUMAN	R|Q	814|710;748;748;748	.|ENSP00000400189:R710Q;ENSP00000379156:R748Q;ENSP00000379149:R748Q;ENSP00000342379:R748Q	.|ENSP00000342379:R748Q	G|R	+|+	1|2	0|0	MPRIP|MPRIP	17015836|17015836	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	9.387000|9.387000	0.97232|0.97232	2.743000|2.743000	0.94032|0.94032	0.655000|0.655000	0.94253|0.94253	GGG|CGG	.	.	.	none		0.572	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134		A	17075111	G	A	17075111	3	1	220	1	0	0	0	0	1	0	0	0	9750	1116	39	1	2305	1	MPRIP	17	17075111	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10		17075111	64120099	76	13346											
PSMC3IP	29893	hgsc.bcm.edu	37	chr17	40729246	40729246	+	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	ctcacctgatccgcaaaataGatcttctgcttgccgtacat	10	12	6	13	2	3	2	1	1	2	1	4	2	4	2	3	0	3	3	3	0	4	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr17:40729246G>C	ENST00000393795.3	-	3	318	c.210C>G	c.(208-210)atC>atG	p.I70M	PSMC3IP_ENST00000590760.1_De_novo_Start_OutOfFrame|PSMC3IP_ENST00000253789.5_Missense_Mutation_p.I70M|PSMC3IP_ENST00000587209.1_Missense_Mutation_p.I7M	NM_001256015.1|NM_001256016.1|NM_016556.3	NP_001242944.1|NP_001242945.1|NP_057640.1	Q9P2W1	HOP2_HUMAN	PSMC3 interacting protein	70					DNA recombination (GO:0006310)|meiotic nuclear division (GO:0007126)|regulation of RNA biosynthetic process (GO:2001141)	nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			endometrium(2)|large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(2)	7		all_cancers(22;0.00426)|Breast(137;0.00116)|all_epithelial(22;0.0395)		BRCA - Breast invasive adenocarcinoma(366;0.13)		CCGCAAAATAGATCTTCTGCT	0.532																																					p.I70M		Atlas-SNP	.											PSMC3IP,NS,carcinoma,0,1	PSMC3IP	23	.	0			c.C210G						PASS	.						163	113	130					17																	40729246		2203	4300	6503	SO:0001583	missense	29893	exon3			AAAATAGATCTTC	AB030304, NM_013290, BC008792	CCDS11431.1, CCDS45688.1, CCDS59289.1	17q21.2	2012-04-10				ENSG00000131470		"Proteasome (prosome, macropain) subunits"	17928	protein-coding gene	gene with protein product	"TBP-1 interacting protein"	608665				7490091, 10806355, 11739747	Standard	NM_016556		Approved	TBPIP, GT198, HUMGT198A	uc002iai.3	Q9P2W1		ENST00000393795.3:c.210C>G	chr17.hg19:g.40729246G>C	ENSP00000377384:p.Ile70Met	118.0	0.0	.		173.0	66.0	.	NM_016556	C5ILB7|Q14458|Q8WXG2|Q96HA2	Missense_Mutation	SNP	ENST00000393795.3	hg19	CCDS45688.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.105854	0.77096	.	.	ENSG00000131470	ENST00000393795;ENST00000253789	T;T	0.60797	0.16;0.16	5.8	-1.78	0.07957	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.051811	0.85682	D	0.000000	T	0.71753	0.3377	M	0.81802	2.56	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.992	T	0.71738	-0.4502	10	0.72032	D	0.01	-11.3368	11.3412	0.49533	0.0598:0.0:0.3656:0.5746	.	70;70	Q9P2W1-2;Q9P2W1	.;HOP2_HUMAN	M	70	ENSP00000377384:I70M;ENSP00000253789:I70M	ENSP00000253789:I70M	I	-	3	3	PSMC3IP	37982772	0.947000	0.32204	0.954000	0.39281	0.978000	0.69477	-0.022000	0.12480	-0.533000	0.06323	0.655000	0.94253	ATC	.	.	.	none		0.532	PSMC3IP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450427.1	NM_013290		C	40729246	G	C	40729246	3	2	220	1	0	0	0	0	1	0	0	0	12698	932	33	4	467	4	PSMC3IP	17	40729246	Missense_Mutation	SNP	G	TCGA-MH-A55Z-01A-11D-A26P-10	23654135	40729246	40465964	77	13347											
TRIM25	7706	hgsc.bcm.edu	37	chr17	54969126	54969126	+	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	ccagaaagccgggtacaaagCctcagtaaagtccaccctga	14	5	9	13	1	1	2	1	1	0	1	2	2	2	2	5	1	3	2	5	1	5	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr17:54969126C>G	ENST00000316881.4	-	9	1877	c.1828G>C	c.(1828-1830)Gct>Cct	p.A610P	TRIM25_ENST00000537230.1_Missense_Mutation_p.A610P|MIR3614_ENST00000581261.1_RNA|TRIM25_ENST00000573108.1_5'Flank|RP11-670E13.5_ENST00000574826.1_RNA	NM_005082.4	NP_005073.2	Q14258	TRI25_HUMAN	tripartite motif containing 25	610	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)					GGGTACAAAGCCTCAGTAAAG	0.547																																					p.A610P		Atlas-SNP	.											.	TRIM25	52	.	0			c.G1828C						PASS	.						58	50	53					17																	54969126		2203	4300	6503	SO:0001583	missense	7706	exon9			ACAAAGCCTCAGT	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.1828G>C	chr17.hg19:g.54969126C>G	ENSP00000323889:p.Ala610Pro	138.0	0.0	.		194.0	116.0	.	NM_005082		Missense_Mutation	SNP	ENST00000316881.4	hg19	CCDS11591.1	.	.	.	.	.	.	.	.	.	.	C	15.89	2.967214	0.53507	.	.	ENSG00000121060	ENST00000316881;ENST00000537230	T;T	0.56103	0.48;0.48	4.87	4.87	0.63330	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.122762	0.36374	N	0.002631	T	0.44787	0.1310	N	0.02345	-0.59	0.58432	D	0.999993	D	0.89917	1.0	D	0.83275	0.996	T	0.43798	-0.9369	10	0.02654	T	1	.	18.0042	0.89205	0.0:1.0:0.0:0.0	.	610	Q14258	TRI25_HUMAN	P	610	ENSP00000323889:A610P;ENSP00000445961:A610P	ENSP00000323889:A610P	A	-	1	0	TRIM25	52324125	0.999000	0.42202	0.446000	0.26920	0.105000	0.19272	3.797000	0.55514	2.251000	0.74343	0.561000	0.74099	GCT	.	.	.	none		0.547	TRIM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440609.1	NM_005082		G	54969126	C	G	54969126	3	3	220	1	0	0	0	0	1	0	0	0	16511	739	26	4	68	4	TRIM25	17	54969126	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	14239880	54969126	26226084	78	13348											
SLC38A10	124565	hgsc.bcm.edu	37	chr17	79225020	79225080	+	Intron	DEL	GGGGAGCAAGGGAGATAAAACGGTAATCACAAGCCATGTGACGATGCCGCAGGTGTTTAAA	GGGGAGCAAGGGAGATAAAACGGTAATCACAAGCCATGTGACGATGCCGCAGGTGTTTAAA	-																															aatgccgcaggtgttttaaaGgggagcaagggagataaaac																								rs142504417|rs113882474|rs67972063|rs113562695|rs557587675|rs116990218|rs374319971|rs386799869|rs147245242|rs565704741|rs140396168	byFrequency	TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	GGGGAGCAAGGGAGATAAAACGGTAATCACAAGCCATGTGACGATGCCGCAGGTGTTTAAA	GGGGAGCAAGGGAGATAAAACGGTAATCACAAGCCATGTGACGATGCCGCAGGTGTTTAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr17:79225020_79225080delGGGGAGCAAGGGAGATAAAACGGTAATCACAAGCCATGTGACGATGCCGCAGGTGTTTAAA	ENST00000374759.3	-	14	2449				SLC38A10_ENST00000288439.5_Frame_Shift_Del_p.FKHLRHRHMACDYRFISLAPL760fs	NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10						amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.K761fs*>20(1)		NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			GTGTTTTAAAGGGGAGCAAGGGAGATAAAACGGTAATCACAAGCCATGTGACGATGCCGCAGGTGTTTAAAGGGGAGTAAG	0.483																																					p.760_780del		Pindel	.											.	SLC38A10	133	.	1	Deletion - Frameshift(1)	skin(1)	c.2279_2339del						PASS	.																																			SO:0001627	intron_variant	124565	exon14			.	BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637		"Solute carriers"	28237	protein-coding gene	gene with protein product							Standard	XM_005257019		Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.2065+212TTTAAACACCTGCGGCATCGTCACATGGCTTGTGATTACCGTTTTATCTCCCTTGCTCCCC>-	chr17.hg19:g.79225020_79225080delGGGGAGCAAGGGAGATAAAACGGTAATCACAAGCCATGTGACGATGCCGCAGGTGTTTAAA		138.0	0.0	.		138.0	16.0	0.116	NM_138570	Q6ZRC5|Q8NA99|Q96C66	Frame_Shift_Del	DEL	ENST00000374759.3	hg19	CCDS42397.1																																																																																			.	.	.	none		0.483	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	NM_138570		-	79225080	GGGGAGCAAGGGAGATAAAACGGTAATCACAAGCCATGTGACGATGCCGCAGGTGTTTAAA	-	79225020	6	5	220	0	1	1	0	1	0	0	0	0	14615	1000	35	0		0	SLC38A10	17	79225020	Intron	DEL	GGGGAGCAAGGGAGATAAAACGGTAATCACAAGCCATGTGACGATGCCGCAGGTGTTTAAA	TCGA-MH-A55Z-01A-11D-A26P-10	24255894	79225020	1970190	79	13349											
LAMA3	3909	hgsc.bcm.edu	37	chr18	21508090	21508090	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctgtgttcgtaatcagattTaacatttctacgcctgcttt	8	18	6	9	2	3	1	1	0	2	1	4	1	3	1	1	0	3	3	1	0	3	7			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr18:21508090T>C	ENST00000313654.9	+	63	8422	c.8181T>C	c.(8179-8181)ttT>ttC	p.F2727F	LAMA3_ENST00000587184.1_Silent_p.F1062F|LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000269217.6_Silent_p.F1118F|LAMA3_ENST00000399516.3_Silent_p.F2671F	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2727	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)					TAATCAGATTTAACATTTCTA	0.408																																					p.F2727F		Atlas-SNP	.											.	LAMA3	397	.	0			c.T8181C						PASS	.						114	97	103					18																	21508090		2203	4300	6503	SO:0001819	synonymous_variant	3909	exon63			CAGATTTAACATT	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.8181T>C	chr18.hg19:g.21508090T>C		117.0	0.0	.		137.0	50.0	.	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	hg19	CCDS42419.1																																																																																			.	.	.	none		0.408	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		C	21508090	T	C	21508090	2	2	220	1	0	0	0	0	0	0	0	1	8614	1751	61	3		3	LAMA3	18	21508090	Silent	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10		21508090	56569158	80	13350											
ZNF407	55628	hgsc.bcm.edu	37	chr18	72345617	72345618	+	Missense_Mutation	DNP	GC	GC	AT																															tcaccagtatagttatttatGcaaagtgtgtaagtattaca																										TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr18:72345617_72345618GC>AT	ENST00000299687.5	+	1	2642_2643	c.2642_2643GC>AT	c.(2641-2643)tGC>tAT	p.C881Y	ZNF407_ENST00000582337.1_Missense_Mutation_p.C881Y|ZNF407_ENST00000577538.1_Missense_Mutation_p.C881Y|ZNF407_ENST00000309902.6_Missense_Mutation_p.C881Y	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	881					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)		AGTTATTTATGCAAAGTGTGTA	0.401																																					p.C881Y|p.C881C		Atlas-SNP	.											.	ZNF407	231	.	0			c.G2642A|c.C2643T						PASS	.																																			SO:0001583	missense	55628	exon1			ATTTATGCAAAGT|TTTATGCAAAGTG	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		Exception_encountered	chr18.hg19:g.72345617_72345618delinsAT	ENSP00000299687:p.Cys881Tyr	126.0	0.0	.		136.0|132.0	39.0|38.0	.	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation|Silent	SNP	ENST00000299687.5	hg19	CCDS45885.1																																																																																			.	.	.	none		0.401	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		AT	72345618	GC	AT	72345617	3	1	220	1	0	0	0	0	1	0	0	0	17899	1319	46	2	2644	2	ZNF407	18	72345617	Missense_Mutation	DNP	GC	TCGA-MH-A55Z-01A-11D-A26P-10	50837527	72345617	5731631	81	13351											
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11134305	11134305	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcgaggcccagttgcccgaaAaggtgatggagttttgaggg	9	9	16	7	2	0	2	0	2	0	0	1	5	0	3	2	4	1	2	2	4	2	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr19:11134305A>G	ENST00000429416.3	+	21	3252	c.2971A>G	c.(2971-2973)Aag>Gag	p.K991E	SMARCA4_ENST00000344626.4_Missense_Mutation_p.K991E|SMARCA4_ENST00000589677.1_Missense_Mutation_p.K991E|SMARCA4_ENST00000444061.3_Missense_Mutation_p.K991E|SMARCA4_ENST00000358026.2_Missense_Mutation_p.K991E|SMARCA4_ENST00000413806.3_Missense_Mutation_p.K991E|SMARCA4_ENST00000590574.1_Missense_Mutation_p.K991E|SMARCA4_ENST00000450717.3_Missense_Mutation_p.K991E|SMARCA4_ENST00000541122.2_Missense_Mutation_p.K991E	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	991					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)				GTTGCCCGAAAAGGTGATGGA	0.607			"F, N, Mis"		NSCLC																																p.K991E		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.A2971G						PASS	.						37	34	35					19																	11134305		2202	4299	6501	SO:0001583	missense	6597	exon20			CCCGAAAAGGTGA	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.2971A>G	chr19.hg19:g.11134305A>G	ENSP00000395654:p.Lys991Glu	106.0	0.0	.		86.0	32.0	.	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.303884	0.81136	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.94576	-3.46;-3.46;-3.46;-3.46;-3.46;-3.46;-3.46	4.9	4.9	0.64082	SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.98601	0.9532	H	0.99705	4.715	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;0.999;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.91635	0.996;0.996;0.996;0.992;0.981;0.999;0.996;0.996	D	0.99004	1.0812	10	0.87932	D	0	-39.7655	13.6333	0.62208	1.0:0.0:0.0:0.0	.	991;991;991;991;991;211;991;991	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;A7E2E1;P51532	.;.;.;.;.;.;.;SMCA4_HUMAN	E	991;991;1055;991;991;991;991;991	ENSP00000395654:K991E;ENSP00000350720:K991E;ENSP00000343896:K991E;ENSP00000445036:K991E;ENSP00000392837:K991E;ENSP00000397783:K991E;ENSP00000414727:K991E	ENSP00000343896:K991E	K	+	1	0	SMARCA4	10995305	1.000000	0.71417	0.964000	0.40570	0.535000	0.34838	8.855000	0.92236	2.055000	0.61198	0.533000	0.62120	AAG	.	.	.	none		0.607	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		G	11134305	A	G	11134305	3	3	220	1	0	0	0	0	1	0	0	0	14783	15	1	3	3045	3	SMARCA4	19	11134305	Missense_Mutation	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10		11134305	47994678	82	13352											
CYP2A13	1553	hgsc.bcm.edu	37	chr19	41599643	41599643	+	Missense_Mutation	SNP	T	T	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	gcaccaccctgcgctacggtTtcctgctgctcatgaagcac	7	9	9	16	2	1	1	1	1	0	0	2	1	2	1	3	1	5	6	3	1	2	2			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr19:41599643T>G	ENST00000330436.3	+	6	940	c.940T>G	c.(940-942)Ttc>Gtc	p.F314V		NM_000766.4	NP_000757.2	Q16696	CP2AD_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 13	314					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)	GCGCTACGGTTTCCTGCTGCT	0.567																																					p.F314V		Atlas-SNP	.											.	CYP2A13	90	.	0			c.T940G						PASS	.						89	77	81					19																	41599643		2203	4300	6503	SO:0001583	missense	1553	exon6			TACGGTTTCCTGC	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.940T>G	chr19.hg19:g.41599643T>G	ENSP00000332679:p.Phe314Val	116.0	0.0	.		113.0	43.0	.	NM_000766	Q53YR8|Q6R569|Q6R570|Q9H2X2	Missense_Mutation	SNP	ENST00000330436.3	hg19	CCDS12571.1	.	.	.	.	.	.	.	.	.	.	.	12.81	2.049285	0.36181	.	.	ENSG00000197838	ENST00000330436	T	0.70045	-0.45	4.58	4.58	0.56647	.	0.157726	0.43919	D	0.000512	T	0.63698	0.2533	N	0.17082	0.46	0.29694	N	0.840704	P	0.51537	0.946	P	0.61003	0.882	T	0.62310	-0.6881	10	0.66056	D	0.02	.	8.6585	0.34077	0.1706:0.0:0.0:0.8293	.	314	Q16696	CP2AD_HUMAN	V	314	ENSP00000332679:F314V	ENSP00000332679:F314V	F	+	1	0	CYP2A13	46291483	0.124000	0.22315	0.995000	0.50966	0.015000	0.08874	0.497000	0.22514	1.945000	0.56424	0.397000	0.26171	TTC	.	.	.	none		0.567	CYP2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463505.1	NM_000766		G	41599643	T	G	41599643	3	3	220	1	0	0	0	0	1	0	0	0	4163	1841	64	5	962	5	CYP2A13	19	41599643	Missense_Mutation	SNP	T	TCGA-MH-A55Z-01A-11D-A26P-10	30465338	41599643	17529340	83	13353											
C20orf117	140710	hgsc.bcm.edu	37	chr20	35438421	35438421	+	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	ttgaaattgtcggcctcctcCtttcgtagctgccgctcctg	4	14	9	14	3	0	1	0	1	0	0	5	1	3	1	5	1	2	3	5	1	2	4			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr20:35438421C>G	ENST00000357779.3	-	7	2159	c.1833G>C	c.(1831-1833)aaG>aaC	p.K611N	SOGA1_ENST00000456801.2_Missense_Mutation_p.K452N|SOGA1_ENST00000279034.6_Missense_Mutation_p.K611N|SOGA1_ENST00000237536.4_Missense_Mutation_p.K849N			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	611					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						CGGCCTCCTCCTTTCGTAGCT	0.602																																					p.K849N		Atlas-SNP	.											.	SOGA1	136	.	0			c.G2547C						PASS	.						30	32	31					20																	35438421		1994	4177	6171	SO:0001583	missense	140710	exon7			CTCCTCCTTTCGT	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.1833G>C	chr20.hg19:g.35438421C>G	ENSP00000350424:p.Lys611Asn	61.0	0.0	.		69.0	26.0	.	NM_080627	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Missense_Mutation	SNP	ENST00000357779.3	hg19		.	.	.	.	.	.	.	.	.	.	C	19.13	3.768785	0.69878	.	.	ENSG00000149639	ENST00000237536;ENST00000279034;ENST00000456801;ENST00000357779	T;T;T;T	0.40756	1.02;1.02;1.02;1.02	5.15	0.757	0.18427	.	0.174867	0.47852	D	0.000216	T	0.30417	0.0764	L	0.36672	1.1	0.34718	D	0.728409	P	0.51351	0.944	B	0.44163	0.443	T	0.38564	-0.9655	10	0.31617	T	0.26	-53.0208	8.3632	0.32372	0.0:0.5833:0.0:0.4167	.	611	O94964-4	.	N	849;611;452;611	ENSP00000237536:K849N;ENSP00000279034:K611N;ENSP00000413886:K452N;ENSP00000350424:K611N	ENSP00000237536:K849N	K	-	3	2	KIAA0889	34871835	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	0.612000	0.24283	0.319000	0.23209	0.561000	0.74099	AAG	.	.	.	none		0.602	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181		G	35438421	C	G	35438421	3	3	220	1	0	0	0	0	1	0	0	0	2085	680	24	4	2536	4	C20orf117	20	35438421	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10		35438421	27587099	84	13354											
NPEPL1	79716	hgsc.bcm.edu	37	chr20	57282247	57282247	+	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	ctgggggccttcagagccgcAatcaagcaggtgagtgggcc	8	6	16	11	1	2	2	2	1	0	1	2	2	2	2	3	4	2	2	3	4	2	1			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr20:57282247A>C	ENST00000356091.6	+	7	1179	c.891A>C	c.(889-891)gcA>gcC	p.A297A	NPEPL1_ENST00000525967.1_Silent_p.A269A|NPEPL1_ENST00000525817.1_Silent_p.A249A|STX16-NPEPL1_ENST00000530122.1_3'UTR	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	297						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)			TCAGAGCCGCAATCAAGCAGG	0.687																																					p.A297A		Atlas-SNP	.											.	NPEPL1	36	.	0			c.A891C						PASS	.						11	17	15					20																	57282247		1969	4059	6028	SO:0001819	synonymous_variant	79716	exon7			AGCCGCAATCAAG	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.891A>C	chr20.hg19:g.57282247A>C		30.0	0.0	.		20.0	9.0	.	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Silent	SNP	ENST00000356091.6	hg19	CCDS46621.1																																																																																			.	.	.	none		0.687	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663		C	57282247	A	C	57282247	2	2	220	1	0	0	0	0	0	0	0	1	10581	117	5	5		5	NPEPL1	20	57282247	Silent	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10	21843826	57282247	5743273	85	13355											
BID	637	hgsc.bcm.edu	37	chr22	18226632	18226632	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atcagtctgcagctcatcgtAgccctcccactggggagcca	8	8	10	15	1	3	0	2	0	1	0	5	1	4	1	3	2	4	3	3	2	1	1			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chr22:18226632A>G	ENST00000399774.3	-	3	329	c.160T>C	c.(160-162)Tac>Cac	p.Y54H	BID_ENST00000551952.1_Missense_Mutation_p.Y54H|BID_ENST00000317361.7_Missense_Mutation_p.Y100H|BID_ENST00000399767.1_5'UTR|BID_ENST00000399765.1_Intron|BID_ENST00000342111.5_Missense_Mutation_p.Y54H|BID_ENST00000473439.1_5'UTR	NM_001196.3|NM_001244569.1	NP_001187.1|NP_001231498.1	P55957	BID_HUMAN	BH3 interacting domain death agonist	54					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|brain development (GO:0007420)|establishment of protein localization to membrane (GO:0090150)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|glial cell apoptotic process (GO:0034349)|intrinsic apoptotic signaling pathway (GO:0097193)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of protein homooligomerization (GO:0032464)|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 release of cytochrome c from mitochondria (GO:0090200)|protein homooligomerization (GO:0051260)|protein targeting to mitochondrion (GO:0006626)|regulation of cell proliferation (GO:0042127)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|release of cytochrome c from mitochondria (GO:0001836)|response to estradiol (GO:0032355)|signal transduction in response to DNA damage (GO:0042770)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of mitochondrial membrane (GO:0032592)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	death receptor binding (GO:0005123)			large_intestine(2)|ovary(1)	3		all_epithelial(15;0.198)		Lung(27;0.0419)		AGCTCATCGTAGCCCTCCCAC	0.632																																					p.Y100H		Atlas-SNP	.											.	BID	18	.	0			c.T298C						PASS	.						49	50	50					22																	18226632		2203	4300	6503	SO:0001583	missense	637	exon3			CATCGTAGCCCTC	AF042083	CCDS13747.1, CCDS13748.1, CCDS13749.1	22q11.2	2014-03-07			ENSG00000015475	ENSG00000015475		"Endogenous ligands"	1050	protein-coding gene	gene with protein product		601997				8918887, 9721221	Standard	NM_001244567		Approved		uc002znc.2	P55957	OTTHUMG00000150087	ENST00000399774.3:c.160T>C	chr22.hg19:g.18226632A>G	ENSP00000382674:p.Tyr54His	61.0	0.0	.		58.0	16.0	.	NM_197966	Q549M7|Q71T04|Q7Z4M9|Q8IY86	Missense_Mutation	SNP	ENST00000399774.3	hg19	CCDS13748.1	.	.	.	.	.	.	.	.	.	.	A	14.79	2.641884	0.47153	.	.	ENSG00000015475	ENST00000317361;ENST00000399774;ENST00000342111;ENST00000551952	T;T;T;T	0.21734	1.99;1.99;1.99;1.99	5.08	-10.2	0.00374	.	2.388480	0.01610	N	0.022462	T	0.11623	0.0283	L	0.29908	0.895	0.09310	N	0.999994	B;B	0.02656	0.0;0.0	B;B	0.10450	0.002;0.005	T	0.13818	-1.0495	10	0.14656	T	0.56	.	7.3234	0.26540	0.4392:0.3405:0.2203:0.0	.	54;100	P55957;P55957-2	BID_HUMAN;.	H	100;54;54;54	ENSP00000318822:Y100H;ENSP00000382674:Y54H;ENSP00000344594:Y54H;ENSP00000449236:Y54H	ENSP00000318822:Y100H	Y	-	1	0	BID	16606632	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-2.197000	0.01240	-1.410000	0.02035	-0.429000	0.05907	TAC	.	.	.	none		0.632	BID-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316178.1	NM_197966		G	18226632	A	G	18226632	3	3	220	1	0	0	0	0	1	0	0	0	1430	420	15	3	443	3	BID	22	18226632	Missense_Mutation	SNP	A	TCGA-MH-A55Z-01A-11D-A26P-10		18226632	33077934	86	13356											
SFRS17A	8227	hgsc.bcm.edu	37	chrX	1719998	1719998	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agctcctgtcgtgtggtcccCgaggatggctctccagagaa	7	9	13	12	2	1	1	0	0	1	1	5	4	3	2	4	3	1	2	4	3	1	0			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chrX:1719998C>T	ENST00000313871.3	+	5	1795	c.1599C>T	c.(1597-1599)ccC>ccT	p.P533P		NM_005088.2	NP_005079.2	Q02040	AK17A_HUMAN	A kinase (PRKA) anchor protein 17A	533					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						GTGTGGTCCCCGAGGATGGCT	0.657													c|||	1	0.000199681	0	0	5008	,	,		14923	0.001		0	False		,,,				2504	0				p.P533P		Atlas-SNP	.											.	AKAP17A	46	.	0			c.C1599T						PASS	.						57	56	56					X																	1719998		2203	4296	6499	SO:0001819	synonymous_variant	8227	exon5			GGTCCCCGAGGAT	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.1599C>T	chrX.hg19:g.1719998C>T		113.0	0.0	.		96.0	7.0	.	NM_005088	Q02832|Q2TB98|Q5JQ74|Q5JQ76|Q8N6U9	Silent	SNP	ENST00000313871.3	hg19	CCDS14116.1																																																																																			.	.	.	none		0.657	AKAP17A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055609.2	NM_005088		T	1719998	C	T	1719998	2	4	220	1	0	0	0	0	0	0	0	1	14186	639	23	1		1	SFRS17A	23	1719998	Silent	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10		1719998	153550562	87	13357											
LPAR4	2846	hgsc.bcm.edu	37	chrX	78010716	78010716	+	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	ctgcaagatctctggaactgCattccttaccaacatctatg	11	12	6	12	0	2	1	0	0	2	1	4	2	3	2	2	1	5	2	2	1	5	3			TCGA-MH-A55Z-01A-11D-A26P-10	TCGA-MH-A55Z-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b19ec4cd-2876-4a2b-bcb9-b3c8db54fc15	3d292f02-ebb2-457b-b5a3-1590b60833a6	g.chrX:78010716C>A	ENST00000435339.3	+	2	736	c.350C>A	c.(349-351)gCa>gAa	p.A117E		NM_005296.2	NP_005287.1	Q99677	LPAR4_HUMAN	lysophosphatidic acid receptor 4	117					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)|lipid binding (GO:0008289)			breast(3)|endometrium(3)|kidney(4)|large_intestine(4)|lung(16)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	38						TCTGGAACTGCATTCCTTACC	0.423																																					p.A117E		Atlas-SNP	.											.	LPAR4	83	.	0			c.C350A						PASS	.						190	152	165					X																	78010716		2203	4299	6502	SO:0001583	missense	2846	exon2			GAACTGCATTCCT	U90322	CCDS14441.1	Xq21.1	2012-08-08	2008-04-11	2008-04-11	ENSG00000147145	ENSG00000147145		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	4478	protein-coding gene	gene with protein product		300086	"G protein-coupled receptor 23"	GPR23			Standard	NM_005296		Approved	P2Y9, P2Y5-LIKE, P2RY9, LPA4	uc010nme.3	Q99677	OTTHUMG00000021895	ENST00000435339.3:c.350C>A	chrX.hg19:g.78010716C>A	ENSP00000408205:p.Ala117Glu	128.0	0.0	.		110.0	92.0	.	NM_005296	B2RAC7|O15132|Q502U9|Q6NSP5	Missense_Mutation	SNP	ENST00000435339.3	hg19	CCDS14441.1	.	.	.	.	.	.	.	.	.	.	C	16.01	3.002367	0.54254	.	.	ENSG00000147145	ENST00000435339;ENST00000373301	T;T	0.38077	1.16;1.16	4.21	4.21	0.49690	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.59293	0.2183	M	0.80183	2.485	0.50171	D	0.999859	D	0.63880	0.993	D	0.63877	0.919	T	0.66771	-0.5839	10	0.72032	D	0.01	.	14.3969	0.67018	0.0:1.0:0.0:0.0	.	117	Q99677	LPAR4_HUMAN	E	117	ENSP00000408205:A117E;ENSP00000362398:A117E	ENSP00000362398:A117E	A	+	2	0	LPAR4	77897372	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	4.452000	0.60054	1.943000	0.56356	0.422000	0.28245	GCA	.	.	.	none		0.423	LPAR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057322.2	NM_005296		A	78010716	C	A	78010716	3	1	220	1	0	0	0	0	1	0	0	0	8914	710	25	4	352	4	LPAR4	23	78010716	Missense_Mutation	SNP	C	TCGA-MH-A55Z-01A-11D-A26P-10	76290718	78010716	77259844	88	13358											
MECR	51102	hgsc.bcm.edu	37	chr1	29557328	29557328	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatgcggagtaggaggaggCggcaggtccgtgacagccag	9	4	20	8	3	0	1	0	1	0	0	1	5	1	5	2	7	2	2	2	7	1	1			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr1:29557328C>T	ENST00000263702.6	-	1	116	c.91G>A	c.(91-93)Gcc>Acc	p.A31T	MECR_ENST00000489248.1_5'UTR|MECR_ENST00000373791.3_5'UTR			Q9BV79	MECR_HUMAN	mitochondrial trans-2-enoyl-CoA reductase	31					fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)	11		Colorectal(325;0.000389)|Breast(348;0.00765)|Lung NSC(340;0.0081)|all_lung(284;0.00914)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.39e-07)|COAD - Colon adenocarcinoma(152;2.04e-05)|STAD - Stomach adenocarcinoma(196;0.0195)|BRCA - Breast invasive adenocarcinoma(304;0.053)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.137)		TAGGAGGAGGCGGCAGGTCCG	0.701																																					p.A31T		Atlas-SNP	.											.	MECR	31	.	0			c.G91A						PASS	.						9	12	11					1																	29557328		2186	4279	6465	SO:0001583	missense	51102	exon1			AGGAGGCGGCAGG		CCDS30659.1, CCDS30660.1	1p35.3	2012-09-20			ENSG00000116353	ENSG00000116353	1.3.1.38		19691	protein-coding gene	gene with protein product	"nuclear receptor binding factor 1", "mitochondrial 2-enoyl thioester reductase"	608205				9795230, 12654921	Standard	XM_005245885		Approved	CGI-63, NRBF1, FASN2B	uc001brq.1	Q9BV79	OTTHUMG00000059082	ENST00000263702.6:c.91G>A	chr1.hg19:g.29557328C>T	ENSP00000263702:p.Ala31Thr	44.0	0.0	.		30.0	20.0	.	NM_016011	B3KT72|Q5SYU0|Q5SYU1|Q5SYU2|Q6IBU9|Q9Y373	Missense_Mutation	SNP	ENST00000263702.6	hg19	CCDS30659.1	.	.	.	.	.	.	.	.	.	.	C	13.00	2.106638	0.37145	.	.	ENSG00000116353	ENST00000263702	T	0.03496	3.91	4.92	-0.97	0.10306	.	1.626230	0.03313	N	0.190804	T	0.02807	0.0084	N	0.19112	0.55	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.44817	-0.9303	9	.	.	.	.	4.5591	0.12151	0.5172:0.3021:0.0:0.1807	.	31	Q9BV79	MECR_HUMAN	T	31	ENSP00000263702:A31T	.	A	-	1	0	MECR	29429915	0.000000	0.05858	0.002000	0.10522	0.434000	0.31775	-1.074000	0.03427	-0.262000	0.09392	-0.140000	0.14226	GCC	.	.	.	none		0.701	MECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130740.1	NM_016011		T	29557328	C	T	29557328	3	4	221	1	0	0	0	0	1	0	0	0	9431	768	27	1	1070	1	MECR	1	29557328	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10		29557328	219693293	1	13359											
EIF2C3	192669	hgsc.bcm.edu	37	chr1	36475164	36475164	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caaggcaacagcaagatctgCaccagatagacaagaggaaa	19	3	10	9	0	1	4	0	0	1	4	1	5	1	5	1	2	3	3	1	2	6	1			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr1:36475164C>T	ENST00000373191.4	+	9	1467	c.1118C>T	c.(1117-1119)gCa>gTa	p.A373V	RP4-665N4.8_ENST00000479395.2_RNA|AGO3_ENST00000246314.6_Missense_Mutation_p.A139V|RP4-665N4.8_ENST00000466576.2_RNA	NM_024852.3	NP_079128.2	Q9H9G7	AGO3_HUMAN	argonaute RISC catalytic component 3	373					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)										GCAAGATCTGCACCAGATAGA	0.378																																					p.A373V		Atlas-SNP	.											.	.	.	.	0			c.C1118T						PASS	.						105	98	100					1																	36475164		2203	4300	6503	SO:0001583	missense	192669	exon9			GATCTGCACCAGA	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.1118C>T	chr1.hg19:g.36475164C>T	ENSP00000362287:p.Ala373Val	309.0	0.0	.		254.0	99.0	.	NM_024852	B1ALI0|Q5TA55|Q9H1U6	Missense_Mutation	SNP	ENST00000373191.4	hg19	CCDS399.1	.	.	.	.	.	.	.	.	.	.	C	36	5.888335	0.97068	.	.	ENSG00000126070	ENST00000373191;ENST00000246314	T;T	0.10960	2.82;2.82	6.17	6.17	0.99709	Argonaute/Dicer protein, PAZ (1);	0.000000	0.85682	D	0.000000	T	0.45135	0.1327	M	0.93283	3.4	0.80722	D	1	D	0.71674	0.998	P	0.62491	0.903	T	0.55023	-0.8205	10	0.87932	D	0	-12.0124	20.8794	0.99867	0.0:1.0:0.0:0.0	.	373	Q9H9G7	AGO3_HUMAN	V	373;139	ENSP00000362287:A373V;ENSP00000246314:A139V	ENSP00000246314:A139V	A	+	2	0	EIF2C3	36247751	1.000000	0.71417	0.995000	0.50966	0.982000	0.71751	7.818000	0.86416	2.941000	0.99782	0.655000	0.94253	GCA	.	.	.	none		0.378	AGO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019831.4	NM_024852		T	36475164	C	T	36475164	3	4	221	1	0	0	0	0	1	0	0	0	5009	710	25	2	1152	2	EIF2C3	1	36475164	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	6917836	36475164	212775457	2	13360											
INTS3	65123	hgsc.bcm.edu	37	chr1	153740253	153740253	+	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	tggacatgaaggcctgccagGaggacgatgtgcggctcctg	8	7	16	10	2	0	1	0	1	0	0	1	5	1	4	3	5	2	1	3	5	1	0			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr1:153740253G>T	ENST00000318967.2	+	21	2762	c.2194G>T	c.(2194-2196)Gag>Tag	p.E732*	INTS3_ENST00000476843.1_3'UTR|INTS3_ENST00000512605.1_Nonsense_Mutation_p.E526*|INTS3_ENST00000435409.2_Nonsense_Mutation_p.E732*|INTS3_ENST00000456435.1_Nonsense_Mutation_p.E526*	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	733					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)			GGCCTGCCAGGAGGACGATGT	0.612																																					p.E732X		Atlas-SNP	.											.	INTS3	83	.	0			c.G2194T						PASS	.						113	94	100					1																	153740253		2203	4300	6503	SO:0001587	stop_gained	65123	exon21			TGCCAGGAGGACG	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.2194G>T	chr1.hg19:g.153740253G>T	ENSP00000318641:p.Glu732*	78.0	0.0	.		95.0	33.0	.	NM_023015	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Nonsense_Mutation	SNP	ENST00000318967.2	hg19	CCDS1052.1	.	.	.	.	.	.	.	.	.	.	G	42	9.404468	0.99161	.	.	ENSG00000143624	ENST00000318967;ENST00000456435;ENST00000435409;ENST00000512605	.	.	.	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	.	15.6279	0.76878	0.0:0.0:1.0:0.0	.	.	.	.	X	732;526;732;526	.	ENSP00000318641:E732X	E	+	1	0	INTS3	152006877	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	9.055000	0.93873	2.768000	0.95171	0.561000	0.74099	GAG	.	.	.	none		0.612	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015		T	153740253	G	T	153740253	4	4	221	1	0	0	0	0	0	1	0	0	7786	1175	41	4	2276	4	INTS3	1	153740253	Nonsense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	117265089	153740253	95510368	3	13361											
CFH	3075	hgsc.bcm.edu	37	chr1	196654324	196654324	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaacccggggaaatacagcAaaatgcacaagtactggctg	15	5	11	10	1	0	0	0	0	0	0	0	1	0	1	1	3	5	5	1	3	7	2	rs1061147	byFrequency	TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr1:196654324A>G	ENST00000359637.2	+	6	791	c.729A>G	c.(727-729)gcA>gcG	p.A243A	CFH_ENST00000439155.2_Silent_p.A307A|CFH_ENST00000367429.4_Silent_p.A307A			P08603	CFAH_HUMAN	complement factor H	307	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)			NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						GAAATACAGCAAAATGCACAA	0.393																																					p.A307A		Atlas-SNP	.											.	CFH	251	.	0			c.A921G	GRCh37	CM057396	CFH	M	rs1061147	PASS	.						119	108	112					1																	196654324		2203	4300	6503	SO:0001819	synonymous_variant	3075	exon7			TACAGCAAAATGC	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.729A>G	chr1.hg19:g.196654324A>G		292.0	0.0	.		239.0	84.0	.	NM_001014975	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Silent	SNP	ENST00000359637.2	hg19																																																																																				.	A|0.352;C|0.648	.	alt		0.393	CFH-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000087502.1	NM_000186		G	196654324	A	G	196654324	2	3	221	1	0	0	0	0	0	0	0	1	3285	117	5	3		3	CFH	1	196654324	Silent	SNP	A	TCGA-MH-A560-01A-11D-A26P-10	42914071	196654324	52596297	4	13362											
PTPRC	5788	hgsc.bcm.edu	37	chr1	198678922	198678922	+	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	aataaccacaagtttactaaCgcaagtaaaattattaaaac	21	10	3	7	1	0	0	0	0	0	0	0	0	0	0	1	0	4	3	1	0	11	7	rs200643724		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr1:198678922C>T	ENST00000367376.2	+	11	1305	c.1134C>T	c.(1132-1134)aaC>aaT	p.N378N	PTPRC_ENST00000352140.3_Silent_p.N330N|PTPRC_ENST00000594404.1_Silent_p.N217N|PTPRC_ENST00000348564.6_Silent_p.N219N|PTPRC_ENST00000442510.2_Silent_p.N380N	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	378					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						AGTTTACTAACGCAAGTAAAA	0.269																																					p.N380N		Atlas-SNP	.											.	PTPRC	229	.	0			c.C1140T						PASS	.	C	,	0,4398		0,0,2199	74	89	84		1134,651	-9	0	1		84	2,8534	2.2+/-6.3	0,2,4266	no	coding-synonymous,coding-synonymous	PTPRC	NM_002838.3,NM_080921.2	,	0,2,6465	TT,TC,CC		0.0234,0.0,0.0155	,	378/1305,217/1144	198678922	2,12932	2199	4268	6467	SO:0001819	synonymous_variant	5788	exon11			TACTAACGCAAGT	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.1134C>T	chr1.hg19:g.198678922C>T		222.0	0.0	.		149.0	40.0	.	NM_002838	A8K7W6|Q16614|Q9H0Y6	Silent	SNP	ENST00000367376.2	hg19																																																																																				.	C|0.999;T|0.001	0.001	weak		0.269	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding				T	198678922	C	T	198678922	2	4	221	1	0	0	0	0	0	0	0	1	12810	535	19	1		1	PTPRC	1	198678922	Silent	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	2024598	198678922	50571699	5	13363											
GPR37L1	9283	hgsc.bcm.edu	37	chr1	202097357	202097357	+	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	gtctacgccttctgcaccctCccagagaacgtctgcaacat	9	9	7	16	2	3	1	0	0	3	1	4	2	4	1	3	0	5	2	3	0	3	2			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr1:202097357C>T	ENST00000367282.5	+	2	1225	c.1119C>T	c.(1117-1119)ctC>ctT	p.L373L		NM_004767.3	NP_004758.3	O60883	ETBR2_HUMAN	G protein-coupled receptor 37 like 1	373					negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	18						TCTGCACCCTCCCAGAGAACG	0.622																																					p.L373L		Atlas-SNP	.											.	GPR37L1	33	.	0			c.C1119T						PASS	.						157	139	145					1																	202097357		2203	4300	6503	SO:0001819	synonymous_variant	9283	exon2			CACCCTCCCAGAG	AJ310210	CCDS1420.1	1q32	2012-08-21	2006-02-15		ENSG00000170075	ENSG00000170075		"GPCR / Class A : Orphans"	14923	protein-coding gene	gene with protein product						9539149	Standard	NM_004767		Approved	ETBR-LP-2	uc001gxj.3	O60883	OTTHUMG00000035924	ENST00000367282.5:c.1119C>T	chr1.hg19:g.202097357C>T		124.0	0.0	.		108.0	8.0	.	NM_004767	B2R7M9|Q5SXP7|Q86VP7	Silent	SNP	ENST00000367282.5	hg19	CCDS1420.1																																																																																			.	.	.	none		0.622	GPR37L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087496.2	NM_004767		T	202097357	C	T	202097357	2	4	221	1	0	0	0	0	0	0	0	1	6699	842	30	2		2	GPR37L1	1	202097357	Silent	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	3418435	202097357	47153264	6	13364											
RCOR3	55758	hgsc.bcm.edu	37	chr1	211449723	211449723	+	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	cctatttgaacaagcctttaGttttcatggaaagagctttc	11	15	7	8	0	1	2	1	1	0	1	2	3	1	3	2	1	3	2	2	1	5	7			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr1:211449723G>C	ENST00000367005.4	+	4	446	c.305G>C	c.(304-306)aGt>aCt	p.S102T	RCOR3_ENST00000419091.2_Missense_Mutation_p.S160T|RCOR3_ENST00000452621.2_Missense_Mutation_p.S160T|RCOR3_ENST00000367006.4_Missense_Mutation_p.S160T	NM_018254.3	NP_060724.1	Q9P2K3	RCOR3_HUMAN	REST corepressor 3	102	SANT 1. {ECO:0000255|PROSITE- ProRule:PRU00624}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.00961)|all cancers(67;0.0999)|Epithelial(68;0.171)		CAAGCCTTTAGTTTTCATGGA	0.363																																					p.S160T		Atlas-SNP	.											.	RCOR3	51	.	0			c.G479C						PASS	.						164	162	163					1																	211449723		2203	4300	6503	SO:0001583	missense	55758	exon5			CCTTTAGTTTTCA	AK001738	CCDS31016.1, CCDS44312.1, CCDS44313.1, CCDS44314.1	1q32.3	2008-02-05			ENSG00000117625	ENSG00000117625			25594	protein-coding gene	gene with protein product						10718198	Standard	NM_018254		Approved	FLJ10876	uc010psw.2	Q9P2K3	OTTHUMG00000036996	ENST00000367005.4:c.305G>C	chr1.hg19:g.211449723G>C	ENSP00000355972:p.Ser102Thr	105.0	0.0	.		104.0	9.0	.	NM_001136223	B3KYA2|B4DYY7|Q5VT47|Q7L9I5|Q8N5U3|Q9NV83	Missense_Mutation	SNP	ENST00000367005.4	hg19	CCDS31016.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.435982	0.83885	.	.	ENSG00000117625	ENST00000533469;ENST00000367006;ENST00000452621;ENST00000419091;ENST00000367005	T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6	5.02	5.02	0.67125	SANT domain, DNA binding (1);Homeodomain-like (1);SANT, eukarya (1);	0.000000	0.85682	D	0.000000	T	0.45377	0.1339	L	0.35542	1.07	0.80722	D	1	D;B;B;B	0.56035	0.974;0.065;0.364;0.389	D;B;B;B	0.70487	0.969;0.066;0.341;0.198	T	0.21177	-1.0253	9	.	.	.	-4.1499	18.6937	0.91593	0.0:0.0:1.0:0.0	.	160;102;160;160	Q9P2K3-3;Q9P2K3;Q9P2K3-2;Q9P2K3-4	.;RCOR3_HUMAN;.;.	T	102;160;160;160;102	ENSP00000436838:S102T;ENSP00000355973:S160T;ENSP00000398558:S160T;ENSP00000413929:S160T;ENSP00000355972:S102T	.	S	+	2	0	RCOR3	209516346	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.639000	0.98448	2.495000	0.84180	0.484000	0.47621	AGT	.	.	.	none		0.363	RCOR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089821.1	NM_018254		C	211449723	G	C	211449723	3	2	221	1	0	0	0	0	1	0	0	0	13197	1029	36	4	497	4	RCOR3	1	211449723	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	9352366	211449723	37800898	7	13365											
CENPF	1063	hgsc.bcm.edu	37	chr1	214815375	214815375	+	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	aggaaagtgagaaggagaagGagtgcctgcagcatgaatta	16	6	15	4	0	0	3	0	2	0	2	0	7	0	5	1	3	3	2	1	3	5	1			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr1:214815375G>T	ENST00000366955.3	+	12	3862	c.3694G>T	c.(3694-3696)Gag>Tag	p.E1232*		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)	p.E1232*(1)		NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		GAAGGAGAAGGAGTGCCTGCA	0.373																																					p.E1232X	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											CENPF,NS,carcinoma,0,1	CENPF	321	.	1	Substitution - Nonsense(1)	lung(1)	c.G3694T						PASS	.						42	46	45					1																	214815375		2203	4298	6501	SO:0001587	stop_gained	1063	exon12			GAGAAGGAGTGCC	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.3694G>T	chr1.hg19:g.214815375G>T	ENSP00000355922:p.Glu1232*	187.0	1.0	.		118.0	33.0	.	NM_016343	Q13171|Q13246|Q5VVM7	Nonsense_Mutation	SNP	ENST00000366955.3	hg19	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	G	42	9.517275	0.99193	.	.	ENSG00000117724	ENST00000366955	.	.	.	5.17	2.19	0.27852	.	1.270870	0.05898	N	0.629477	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	.	6.3943	0.21603	0.1645:0.1498:0.6857:0.0	.	.	.	.	X	1232	.	ENSP00000355922:E1232X	E	+	1	0	CENPF	212881998	0.848000	0.29623	0.000000	0.03702	0.898000	0.52572	0.913000	0.28611	0.168000	0.19655	0.511000	0.50034	GAG	.	.	.	none		0.373	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		T	214815375	G	T	214815375	4	4	221	1	0	0	0	0	0	1	0	0	3233	1175	41	4	3736	4	CENPF	1	214815375	Nonsense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	3365652	214815375	34435246	8	13366											
SNAP47	116841	hgsc.bcm.edu	37	chr1	227946738	227946738	+	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	cctgcttggtggccctttagCtccaagctttggaagacacc	7	11	10	13	0	0	1	0	0	0	1	1	2	1	2	4	3	3	3	4	3	3	4			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr1:227946738C>A	ENST00000366759.4	+	3	1089	c.675C>A	c.(673-675)agC>agA	p.S225R	SNAP47_ENST00000366760.1_5'UTR|SNAP47_ENST00000315781.5_Missense_Mutation_p.S225R	NM_053052.3	NP_444280.2	Q5SQN1	SNP47_HUMAN	synaptosomal-associated protein, 47kDa	225					long-term synaptic potentiation (GO:0060291)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				endometrium(1)|large_intestine(5)|liver(2)|lung(6)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	17						GGCCCTTTAGCTCCAAGCTTT	0.433																																					p.S225R		Atlas-SNP	.											.	SNAP47	42	.	0			c.C675A						PASS	.						86	94	91					1																	227946738		2203	4300	6503	SO:0001583	missense	116841	exon3			CTTTAGCTCCAAG	AY090635	CCDS1562.1	1q42.13	2013-10-11	2008-10-27	2008-10-27	ENSG00000143740	ENSG00000143740			30669	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 142"	C1orf142		16621800	Standard	NM_053052		Approved	SVAP1, SNAP-47	uc001hrf.2	Q5SQN1	OTTHUMG00000037697	ENST00000366759.4:c.675C>A	chr1.hg19:g.227946738C>A	ENSP00000355721:p.Ser225Arg	91.0	0.0	.		73.0	4.0	.	NM_053052	B6EDE0|Q5HYB5|Q5TBZ3|Q8N558|Q8TB31|Q8TCW8|Q8WV46|Q96CQ3|Q96FE1|Q96I66|Q96NU3|Q9BT10|Q9BVB2	Missense_Mutation	SNP	ENST00000366759.4	hg19	CCDS1562.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.74|10.74	1.434984|1.434984	0.25813|0.25813	.|.	.|.	ENSG00000143740|ENSG00000143740	ENST00000418653;ENST00000426344|ENST00000366759;ENST00000315781	.|T;T	.|0.17054	.|2.3;2.3	4.95|4.95	0.434|0.434	0.16539|0.16539	.|.	.|0.129162	.|0.64402	.|D	.|0.000001	T|T	0.31231|0.31231	0.0790|0.0790	M|M	0.78637|0.78637	2.42|2.42	0.30113|0.30113	N|N	0.8064|0.8064	.|D;D	.|0.67145	.|0.989;0.996	.|P;P	.|0.61201	.|0.885;0.885	T|T	0.20638|0.20638	-1.0269|-1.0269	5|10	.|0.26408	.|T	.|0.33	-7.4349|-7.4349	8.0504|8.0504	0.30575|0.30575	0.0:0.4696:0.0:0.5304|0.0:0.4696:0.0:0.5304	.|.	.|225;225	.|Q5SQN1;Q5SQN1-2	.|SNP47_HUMAN;.	I|R	38;217|225	.|ENSP00000355721:S225R;ENSP00000314157:S225R	.|ENSP00000314157:S225R	L|S	+|+	1|3	0|2	SNAP47|SNAP47	226013361|226013361	0.994000|0.994000	0.37717|0.37717	0.678000|0.678000	0.29963|0.29963	0.565000|0.565000	0.35776|0.35776	0.206000|0.206000	0.17375|0.17375	-0.047000|-0.047000	0.13423|0.13423	0.561000|0.561000	0.74099|0.74099	CTC|AGC	.	.	.	none		0.433	SNAP47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091961.1	NM_053052		A	227946738	C	A	227946738	3	1	221	1	0	0	0	0	1	0	0	0	14845	796	28	4	685	4	SNAP47	1	227946738	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	13131363	227946738	21303883	9	13367											
SDCCAG8	10806	hgsc.bcm.edu	37	chr1	243419490	243419490	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgtgcatggcgaagtccccGgagaactctaccctggagga	9	6	14	12	3	1	1	0	0	1	1	2	5	2	3	3	4	3	1	3	4	3	1			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr1:243419490G>A	ENST00000366541.3	+	1	133	c.15G>A	c.(13-15)ccG>ccA	p.P5P	SDCCAG8_ENST00000391846.1_Silent_p.P5P|SDCCAG8_ENST00000355875.4_Silent_p.P5P|CEP170_ENST00000366544.1_5'Flank|CEP170_ENST00000366543.1_5'Flank|SDCCAG8_ENST00000343783.6_5'UTR|CEP170_ENST00000366542.1_5'Flank	NM_006642.3	NP_006633.1	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8	5					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)		CGAAGTCCCCGGAGAACTCTA	0.617																																					p.P5P		Atlas-SNP	.											.	SDCCAG8	73	.	0			c.G15A						PASS	.						78	79	78					1																	243419490		2203	4300	6503	SO:0001819	synonymous_variant	10806	exon1			GTCCCCGGAGAAC	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.15G>A	chr1.hg19:g.243419490G>A		146.0	0.0	.		123.0	7.0	.	NM_006642	O60527|Q3ZCR6|Q8N5F2|Q9P0F1	Silent	SNP	ENST00000366541.3	hg19	CCDS31075.1																																																																																			.	.	.	none		0.617	SDCCAG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096485.1	NM_006642		A	243419490	G	A	243419490	2	1	221	1	0	0	0	0	0	0	0	1	13972	1103	39	1		1	SDCCAG8	1	243419490	Silent	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	15472752	243419490	5831131	10	13368											
MOGS	7841	hgsc.bcm.edu	37	chr2	74688599	74688599	+	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	ccgagcctggtgaggaccctCcagatgcccatagtggtgga	8	7	14	12	1	0	2	0	1	0	1	1	5	1	4	5	4	2	0	5	4	1	1			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr2:74688599C>T	ENST00000233616.4	-	4	2479	c.2317G>A	c.(2317-2319)Gag>Aag	p.E773K	MOGS_ENST00000462443.1_5'Flank|MOGS_ENST00000409065.1_3'UTR|MOGS_ENST00000452063.2_Missense_Mutation_p.E667K	NM_006302.2	NP_006293.2	Q13724	MOGS_HUMAN	mannosyl-oligosaccharide glucosidase	773					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						TGAGGACCCTCCAGATGCCCA	0.592																																					p.E773K		Atlas-SNP	.											.	MOGS	58	.	0			c.G2317A						PASS	.						80	88	85					2																	74688599		2075	4200	6275	SO:0001583	missense	7841	exon4			GACCCTCCAGATG	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.2317G>A	chr2.hg19:g.74688599C>T	ENSP00000233616:p.Glu773Lys	248.0	0.0	.		197.0	56.0	.	NM_006302	A8K938|F5H6D0|Q17RN9|Q8TCT5	Missense_Mutation	SNP	ENST00000233616.4	hg19	CCDS42700.1	.	.	.	.	.	.	.	.	.	.	C	7.668	0.686371	0.14973	.	.	ENSG00000115275	ENST00000233616;ENST00000452063	T;T	0.48522	0.81;0.81	4.48	0.633	0.17712	Six-hairpin glycosidase-like (1);	0.109437	0.64402	N	0.000010	T	0.35508	0.0934	L	0.55103	1.725	0.80722	D	1	B	0.06786	0.001	B	0.14023	0.01	T	0.14008	-1.0488	10	0.11794	T	0.64	-2.6164	8.6268	0.33895	0.0:0.6721:0.0:0.3279	.	773	Q13724	MOGS_HUMAN	K	773;667	ENSP00000233616:E773K;ENSP00000388201:E667K	ENSP00000233616:E773K	E	-	1	0	MOGS	74542107	0.580000	0.26733	0.793000	0.32043	0.621000	0.37620	1.175000	0.31944	0.004000	0.14682	-0.244000	0.11960	GAG	.	.	.	none		0.592	MOGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328382.1	NM_006302		T	74688599	C	T	74688599	3	4	221	1	0	0	0	0	1	0	0	0	9704	864	30	2	200	2	MOGS	2	74688599	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10		74688599	168510774	11	13369											
ACMSD	130013	hgsc.bcm.edu	37	chr2	135621133	135621133	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgaaagagctgggctttcccGgggtccaaattggcacccac	9	8	12	12	1	0	2	0	1	0	1	2	2	2	2	3	4	1	3	3	4	2	2			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr2:135621133G>A	ENST00000356140.5	+	5	554	c.418G>A	c.(418-420)Ggg>Agg	p.G140R	ACMSD_ENST00000392928.1_Missense_Mutation_p.G82R|ACMSD_ENST00000283054.4_Missense_Mutation_p.G82R|AC016725.4_ENST00000392929.2_RNA	NM_138326.2	NP_612199.2	Q8TDX5	ACMSD_HUMAN	aminocarboxymuconate semialdehyde decarboxylase	140					cellular nitrogen compound metabolic process (GO:0034641)|quinolinate metabolic process (GO:0046874)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aminocarboxymuconate-semialdehyde decarboxylase activity (GO:0001760)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(4)|lung(6)|skin(1)	14				BRCA - Breast invasive adenocarcinoma(221;0.115)		GGGCTTTCCCGGGGTCCAAAT	0.632																																					p.G140R		Atlas-SNP	.											.	ACMSD	43	.	0			c.G418A						PASS	.						71	58	62					2																	135621133		2203	4300	6503	SO:0001583	missense	130013	exon5			TTTCCCGGGGTCC	AB071418	CCDS2173.2	2q21.3	2008-03-11			ENSG00000153086	ENSG00000153086	4.1.1.45		19288	protein-coding gene	gene with protein product		608889				12140278	Standard	NM_138326		Approved		uc002ttz.3	Q8TDX5	OTTHUMG00000131711	ENST00000356140.5:c.418G>A	chr2.hg19:g.135621133G>A	ENSP00000348459:p.Gly140Arg	116.0	0.0	.		98.0	6.0	.	NM_138326	Q3B7X3|Q53SR5|Q96KY2	Missense_Mutation	SNP	ENST00000356140.5	hg19	CCDS2173.2	.	.	.	.	.	.	.	.	.	.	G	28.8	4.950082	0.92660	.	.	ENSG00000153086	ENST00000356140;ENST00000283054;ENST00000392928	.	.	.	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.90518	0.7029	H	0.97315	3.98	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93490	0.6835	9	0.87932	D	0	-10.2027	19.6085	0.95589	0.0:0.0:1.0:0.0	.	82;140	Q53SR5;Q8TDX5	.;ACMSD_HUMAN	R	140;82;82	.	ENSP00000283054:G82R	G	+	1	0	ACMSD	135337603	1.000000	0.71417	0.959000	0.39883	0.755000	0.42902	9.463000	0.97652	2.618000	0.88619	0.561000	0.74099	GGG	.	.	.	none		0.632	ACMSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254627.1			A	135621133	G	A	135621133	3	1	221	1	0	0	0	0	1	0	0	0	144	1116	39	1	436	1	ACMSD	2	135621133	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	60932534	135621133	107578240	12	13370											
SSFA2	6744	hgsc.bcm.edu	37	chr2	182774650	182774650	+	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	aaagtacggagggagaagctCctcatgttccagccacttac	12	8	10	11	1	1	1	1	0	0	1	3	3	3	2	3	2	4	3	3	2	4	3			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr2:182774650C>G	ENST00000431877.2	+	9	1617	c.1438C>G	c.(1438-1440)Cct>Gct	p.P480A	SSFA2_ENST00000428267.2_Missense_Mutation_p.P327A|SSFA2_ENST00000320370.7_Missense_Mutation_p.P480A|SSFA2_ENST00000409136.1_5'Flank|SSFA2_ENST00000409001.1_Missense_Mutation_p.P480A	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	480						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)			GGGAGAAGCTCCTCATGTTCC	0.368																																					p.P480A		Atlas-SNP	.											.	SSFA2	130	.	0			c.C1438G						PASS	.						71	62	65					2																	182774650		2203	4300	6503	SO:0001583	missense	6744	exon9			GAAGCTCCTCATG	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.1438C>G	chr2.hg19:g.182774650C>G	ENSP00000388731:p.Pro480Ala	120.0	0.0	.		92.0	39.0	.	NM_001130445	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Missense_Mutation	SNP	ENST00000431877.2	hg19	CCDS46467.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.304280	0.81136	.	.	ENSG00000138434	ENST00000431877;ENST00000320370;ENST00000409001;ENST00000428267	T;T;T;T	0.15372	2.66;2.43;2.66;2.66	5.98	5.98	0.97165	.	0.175872	0.50627	D	0.000116	T	0.44138	0.1279	M	0.73598	2.24	0.58432	D	0.999993	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.997;0.997;0.997	T	0.04946	-1.0916	10	0.33141	T	0.24	-18.1989	18.6367	0.91380	0.0:1.0:0.0:0.0	.	327;480;480;480	E7END2;E9PHV5;P28290;P28290-3	.;.;SSFA2_HUMAN;.	A	480;480;480;327	ENSP00000388731:P480A;ENSP00000314669:P480A;ENSP00000387319:P480A;ENSP00000409867:P327A	ENSP00000314669:P480A	P	+	1	0	SSFA2	182482895	0.994000	0.37717	1.000000	0.80357	0.889000	0.51656	3.435000	0.52849	2.847000	0.97988	0.591000	0.81541	CCT	.	.	.	none		0.368	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2	NM_006751		G	182774650	C	G	182774650	3	3	221	1	0	0	0	0	1	0	0	0	15195	855	30	4	1472	4	SSFA2	2	182774650	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	47153517	182774650	60424723	13	13371											
KCNH8	131096	hgsc.bcm.edu	37	chr3	19554559	19554559	+	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	ggaggaagaggaggcagtctCcctctctcccatctgcacaa	10	7	11	13	0	3	1	0	0	3	1	6	4	4	4	2	4	1	2	2	4	2	0			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr3:19554559C>T	ENST00000328405.2	+	13	2443	c.2177C>T	c.(2176-2178)tCc>tTc	p.S726F		NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	726					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	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						gaggCAGTCTCCCTCTCTCCC	0.532																																					p.S726F	NSCLC(124;1625 1765 8018 24930 42026)	Atlas-SNP	.											KCNH8,NS,malignant_melanoma,0,1	KCNH8	189	.	0			c.C2177T						PASS	.						67	55	59					3																	19554559		2203	4300	6503	SO:0001583	missense	131096	exon13			CAGTCTCCCTCTC	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.2177C>T	chr3.hg19:g.19554559C>T	ENSP00000328813:p.Ser726Phe	248.0	0.0	.		265.0	13.0	.	NM_144633	B7Z2I7|Q59GQ6	Missense_Mutation	SNP	ENST00000328405.2	hg19	CCDS2632.1	.	.	.	.	.	.	.	.	.	.	C	14.12	2.441905	0.43326	.	.	ENSG00000183960	ENST00000328405	D	0.98792	-5.14	5.44	5.44	0.79542	.	0.000000	0.31709	U	0.007193	D	0.97495	0.9180	L	0.47716	1.5	0.80722	D	1	P	0.37158	0.585	B	0.42188	0.379	D	0.97417	1.0006	9	.	.	.	.	17.4503	0.87590	0.0:1.0:0.0:0.0	.	726	Q96L42	KCNH8_HUMAN	F	726	ENSP00000328813:S726F	.	S	+	2	0	KCNH8	19529563	0.164000	0.22935	0.087000	0.20705	0.252000	0.25951	1.912000	0.39946	2.559000	0.86315	0.585000	0.79938	TCC	.	.	.	none		0.532	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633		T	19554559	C	T	19554559	3	4	221	1	0	0	0	0	1	0	0	0	8045	855	30	2	2227	2	KCNH8	3	19554559	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10		19554559	178467871	14	13372											
TRANK1	9881	hgsc.bcm.edu	37	chr3	36874430	36874430	+	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	ctaaacacttggcttcacaaCgccgcagaggcctgtgaaaa	13	7	9	12	2	1	2	1	1	0	1	1	2	1	2	2	2	2	2	2	2	5	3	rs370553712		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr3:36874430C>T	ENST00000429976.2	-	21	6759	c.6512G>A	c.(6511-6513)cGt>cAt	p.R2171H	TRANK1_ENST00000301807.6_Missense_Mutation_p.R1621H|TRANK1_ENST00000428977.2_Missense_Mutation_p.R1621H	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	2171							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						GGCTTCACAACGCCGCAGAGG	0.438																																					p.R2171H		Atlas-SNP	.											.	TRANK1	398	.	0			c.G6512A						PASS	.	C	HIS/ARG	0,3780		0,0,1890	32	32	32		6512	5.2	0.9	3		32	1,8203		0,1,4101	no	missense	TRANK1	NM_014831.2	29	0,1,5991	TT,TC,CC		0.0122,0.0,0.0083	probably-damaging	2171/2926	36874430	1,11983	1890	4102	5992	SO:0001583	missense	9881	exon21			TCACAACGCCGCA	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.6512G>A	chr3.hg19:g.36874430C>T	ENSP00000416168:p.Arg2171His	42.0	0.0	.		22.0	10.0	.	NM_014831	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	hg19	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	C	15.37	2.812080	0.50527	0.0	1.22E-4	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.34667	1.35;1.76;1.35	5.16	5.16	0.70880	.	0.000000	0.48767	D	0.000162	T	0.40743	0.1129	L	0.34521	1.04	0.22156	N	0.999323	D	0.76494	0.999	P	0.57324	0.818	T	0.28459	-1.0043	10	0.72032	D	0.01	.	9.7288	0.40348	0.0:0.8452:0.0:0.1548	.	2171	O15050	TRNK1_HUMAN	H	1621;2171;1621	ENSP00000416826:R1621H;ENSP00000416168:R2171H;ENSP00000301807:R1621H	ENSP00000301807:R1621H	R	-	2	0	TRANK1	36849434	0.977000	0.34250	0.855000	0.33649	0.731000	0.41821	3.068000	0.50018	2.562000	0.86427	0.555000	0.69702	CGT	.	.	.	weak		0.438	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		T	36874430	C	T	36874430	3	4	221	1	0	0	0	0	1	0	0	0	16466	536	19	1	2277	1	TRANK1	3	36874430	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	17319871	36874430	161148000	15	13373											
BAP1	8314	hgsc.bcm.edu	37	chr3	52439271	52439271	+	Frame_Shift_Del	DEL	G	G	-																															tgttgggagggctgtgggatGgggcttgtgcgcatgaacca																										TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr3:52439271delG	ENST00000460680.1	-	11	1442	c.971delC	c.(970-972)ccafs	p.P324fs	BAP1_ENST00000296288.5_Frame_Shift_Del_p.P306fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P324fs*11(1)|p.A323fs*71(1)|p.P324fs*7(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		GCTGTGGGATGGGGCTTGTGC	0.592			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.P324fs	GBM(101;493 1458 7992 21037 25532)	Atlas-Indel,Pindel	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	3	Deletion - Frameshift(3)	eye(1)|kidney(1)|pleura(1)	c.972delA						PASS	.						115	120	118					3																	52439271		2203	4300	6503	SO:0001589	frameshift_variant	8314	exon11			.	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.971delC	chr3.hg19:g.52439271delG	ENSP00000417132:p.Pro324fs	100.0	0.0	0		81.0	60.0	0.740741	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Frame_Shift_Del	DEL	ENST00000460680.1	hg19	CCDS2853.1																																																																																			.	.	.	none		0.592	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			-	52439271	G	-	52439271	7	5	221	1	0	1	0	1	0	0	0	0	1311	1348	47	0	1246	0	BAP1	3	52439271	Frame_Shift_Del	DEL	G	TCGA-MH-A560-01A-11D-A26P-10	15564841	52439271	145583159	16	13374	133	2									
BAP1	8314	hgsc.bcm.edu	37	chr3	52439275	52439275	+	Missense_Mutation	SNP	C	C	A																															gggagggctgtgggatggggCttgtgcgcatgaaccagccg																										TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr3:52439275C>A	ENST00000460680.1	-	11	1438	c.967G>T	c.(967-969)Gcc>Tcc	p.A323S	BAP1_ENST00000296288.5_Missense_Mutation_p.A305S	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P324fs*7(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		TGGGATGGGGCTTGTGCGCAT	0.592			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.A323S	GBM(101;493 1458 7992 21037 25532)	Atlas-SNP	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	1	Deletion - Frameshift(1)	pleura(1)	c.G967T						PASS	.						113	118	116					3																	52439275		2203	4300	6503	SO:0001583	missense	8314	exon11			ATGGGGCTTGTGC	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.967G>T	chr3.hg19:g.52439275C>A	ENSP00000417132:p.Ala323Ser	99.0	0.0	.		84.0	65.0	.	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Missense_Mutation	SNP	ENST00000460680.1	hg19	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	C	10.53	1.375375	0.24857	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	T;T	0.55588	0.51;0.51	5.7	4.82	0.62117	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (1);	0.290995	0.39341	N	0.001388	T	0.41789	0.1174	L	0.44542	1.39	0.21782	N	0.999546	B	0.09022	0.002	B	0.14023	0.01	T	0.24512	-1.0158	10	0.24483	T	0.36	-12.9423	9.1237	0.36801	0.0:0.8178:0.0:0.1822	.	323	Q92560	BAP1_HUMAN	S	323;305	ENSP00000417132:A323S;ENSP00000296288:A305S	ENSP00000296288:A305S	A	-	1	0	BAP1	52414315	0.962000	0.33011	0.955000	0.39395	0.115000	0.19883	0.927000	0.28818	1.398000	0.46701	0.655000	0.94253	GCC	.	.	.	none		0.592	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			A	52439275	C	A	52439275	3	1	221	1	0	0	0	0	1	0	0	0	1311	797	28	4	1250	4	BAP1	3	52439275	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	4	52439275	145583155	17	13375	133	2									
OSBPL11	114885	hgsc.bcm.edu	37	chr3	125250787	125250787	+	Missense_Mutation	SNP	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	tcctctgacgttcttccaggGtatgcttatgctctgtggcc	4	15	10	12	1	3	1	0	1	3	0	5	1	5	1	3	2	2	4	3	2	2	4			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr3:125250787G>A	ENST00000296220.5	-	12	2385	c.2096C>T	c.(2095-2097)aCc>aTc	p.T699I		NM_022776.4	NP_073613.2	Q9BXB4	OSB11_HUMAN	oxysterol binding protein-like 11	699					fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|positive regulation of sequestering of triglyceride (GO:0010890)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)			NS(1)|breast(1)|cervix(1)|kidney(2)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	27						TTCTTCCAGGGTATGCTTATG	0.403																																					p.T699I		Atlas-SNP	.											.	OSBPL11	64	.	0			c.C2096T						PASS	.						177	165	169					3																	125250787		2203	4300	6503	SO:0001583	missense	114885	exon12			TCCAGGGTATGCT	AF392454	CCDS3033.1	3q21	2013-01-10			ENSG00000144909	ENSG00000144909		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16397	protein-coding gene	gene with protein product		606739					Standard	NM_022776		Approved	ORP-11, ORP11, FLJ13012, FLJ13164	uc003eic.3	Q9BXB4	OTTHUMG00000159571	ENST00000296220.5:c.2096C>T	chr3.hg19:g.125250787G>A	ENSP00000296220:p.Thr699Ile	118.0	0.0	.		102.0	5.0	.	NM_022776	A8K9I7	Missense_Mutation	SNP	ENST00000296220.5	hg19	CCDS3033.1	.	.	.	.	.	.	.	.	.	.	G	12.16	1.853695	0.32791	.	.	ENSG00000144909	ENST00000296220	T	0.30182	1.54	4.59	4.59	0.56863	.	0.550827	0.19443	N	0.114129	T	0.16981	0.0408	N	0.04508	-0.205	0.21355	N	0.999719	B	0.20164	0.042	B	0.15870	0.014	T	0.09207	-1.0685	10	0.23891	T	0.37	-2.1904	17.9326	0.89002	0.0:0.0:1.0:0.0	.	699	Q9BXB4	OSB11_HUMAN	I	699	ENSP00000296220:T699I	ENSP00000296220:T699I	T	-	2	0	OSBPL11	126733477	1.000000	0.71417	0.715000	0.30552	0.961000	0.63080	4.367000	0.59498	2.542000	0.85734	0.462000	0.41574	ACC	.	.	.	none		0.403	OSBPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356295.1	NM_022776		A	125250787	G	A	125250787	3	1	221	1	0	0	0	0	1	0	0	0	11283	1261	44	2	155	2	OSBPL11	3	125250787	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	72811512	125250787	72771643	18	13376											
CLDN11	5010	hgsc.bcm.edu	37	chr3	170141043	170141043	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgactgttcttccctgcatcCggatgggccaggagcccggt	5	10	13	13	2	1	1	0	1	1	0	3	3	3	3	4	4	2	2	4	4	0	2			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr3:170141043C>T	ENST00000064724.3	+	2	521	c.319C>T	c.(319-321)Cgg>Tgg	p.R107W	CLDN11_ENST00000486975.1_Missense_Mutation_p.R107W|CLDN11_ENST00000489485.1_3'UTR|CLDN11_ENST00000451576.1_Missense_Mutation_p.R107W	NM_005602.5	NP_005593.2	O75508	CLD11_HUMAN	claudin 11	107					axon ensheathment (GO:0008366)|calcium-independent cell-cell adhesion (GO:0016338)|spermatogenesis (GO:0007283)	basal part of cell (GO:0045178)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			central_nervous_system(2)|endometrium(2)|large_intestine(1)|liver(2)|lung(3)|ovary(2)	12	all_cancers(22;5.62e-23)|all_epithelial(15;7.54e-28)|all_lung(20;2.51e-17)|Lung NSC(18;1.02e-16)|Ovarian(172;0.000567)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			TCCCTGCATCCGGATGGGCCA	0.607																																					p.R107W		Atlas-SNP	.											.	CLDN11	28	.	0			c.C319T						PASS	.						111	105	107					3																	170141043		2203	4300	6503	SO:0001583	missense	5010	exon2			TGCATCCGGATGG	AF068863	CCDS3213.1	3q26.2-q26.3	2008-08-01	2008-08-01		ENSG00000013297	ENSG00000013297		"Claudins"	8514	protein-coding gene	gene with protein product		601326	"oligodendrocyte transmembrane protein"	OTM		8661061, 8797478	Standard	NM_005602		Approved	OSP	uc003fgx.3	O75508	OTTHUMG00000158940	ENST00000064724.3:c.319C>T	chr3.hg19:g.170141043C>T	ENSP00000064724:p.Arg107Trp	210.0	0.0	.		174.0	15.0	.	NM_005602	B2R7C1|D3DNQ5|Q5U0P3	Missense_Mutation	SNP	ENST00000064724.3	hg19	CCDS3213.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.128510	0.77549	.	.	ENSG00000013297	ENST00000064724;ENST00000486975;ENST00000451576	D;D;D	0.89681	-2.55;-2.55;-2.55	5.81	4.91	0.64330	.	0.175301	0.50627	D	0.000106	D	0.94265	0.8158	M	0.79123	2.44	0.47621	D	0.999477	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.949	D	0.94887	0.8044	10	0.87932	D	0	.	15.8994	0.79362	0.1364:0.8636:0.0:0.0	.	107;107	B4DFI2;O75508	.;CLD11_HUMAN	W	107	ENSP00000064724:R107W;ENSP00000417434:R107W;ENSP00000410185:R107W	ENSP00000064724:R107W	R	+	1	2	CLDN11	171623737	1.000000	0.71417	1.000000	0.80357	0.799000	0.45148	2.422000	0.44696	1.391000	0.46566	0.557000	0.71058	CGG	.	.	.	none		0.607	CLDN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352403.1	NM_005602		T	170141043	C	T	170141043	3	4	221	1	0	0	0	0	1	0	0	0	3475	643	23	1	325	1	CLDN11	3	170141043	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	44890256	170141043	27881387	19	13377											
MFN1	55669	hgsc.bcm.edu	37	chr3	179082985	179082985	+	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	caataatcgttgggatgcctCtgcatcagagccagaatata	13	10	9	9	1	2	2	1	0	1	2	3	3	2	3	2	1	3	2	2	1	5	4			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr3:179082985C>G	ENST00000471841.1	+	7	851	c.725C>G	c.(724-726)tCt>tGt	p.S242C	MFN1_ENST00000280653.7_Missense_Mutation_p.S242C|MFN1_ENST00000263969.5_Missense_Mutation_p.S242C	NM_033540.2	NP_284941	Q8IWA4	MFN1_HUMAN	mitofusin 1	242	Dynamin-type G.				mitochondrial fusion (GO:0008053)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(3)|prostate(1)|urinary_tract(1)	31	all_cancers(143;1.67e-16)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.00225)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			TGGGATGCCTCTGCATCAGAG	0.328																																					p.S242C		Atlas-SNP	.											.	MFN1	72	.	0			c.C725G						PASS	.						50	54	53					3																	179082985		2203	4300	6503	SO:0001583	missense	55669	exon7			ATGCCTCTGCATC	AF054986	CCDS3228.1	3q26.32	2006-12-13			ENSG00000171109	ENSG00000171109			18262	protein-coding gene	gene with protein product		608506				8358434, 11181170	Standard	NM_033540		Approved	FLJ20693	uc003fjs.3	Q8IWA4	OTTHUMG00000157385	ENST00000471841.1:c.725C>G	chr3.hg19:g.179082985C>G	ENSP00000420617:p.Ser242Cys	120.0	0.0	.		86.0	66.0	.	NM_033540	B2RAR1|D3DNR6|O15323|O60639|Q9BZB5|Q9NWQ2	Missense_Mutation	SNP	ENST00000471841.1	hg19	CCDS3228.1	.	.	.	.	.	.	.	.	.	.	C	19.98	3.927490	0.73327	.	.	ENSG00000171109	ENST00000471841;ENST00000280653;ENST00000539169;ENST00000263969;ENST00000489329;ENST00000474903	D;D;D;D;D	0.95447	-3.71;-3.71;-3.71;-3.66;-3.66	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	D	0.98128	0.9382	M	0.88241	2.94	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.998	D;P;P	0.87578	0.998;0.907;0.907	D	0.98003	1.0361	10	0.48119	T	0.1	-19.0836	19.7394	0.96219	0.0:1.0:0.0:0.0	.	242;270;242	Q8IWA4-3;Q4AEJ4;Q8IWA4	.;.;MFN1_HUMAN	C	242;242;242;242;95;105	ENSP00000420617:S242C;ENSP00000280653:S242C;ENSP00000263969:S242C;ENSP00000420148:S95C;ENSP00000419926:S105C	ENSP00000263969:S242C	S	+	2	0	MFN1	180565679	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.739000	0.68622	2.649000	0.89929	0.563000	0.77884	TCT	.	.	.	none		0.328	MFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348654.2	NM_017927		G	179082985	C	G	179082985	3	3	221	1	0	0	0	0	1	0	0	0	9530	913	32	4	747	4	MFN1	3	179082985	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	8941942	179082985	18939445	20	13378											
FGG	2266	hgsc.bcm.edu	37	chr4	155526043	155526043	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttccgcagggtgctctggTctgacctgtttggctccccc	2	13	12	14	1	2	1	0	1	2	0	4	1	4	1	4	3	1	5	4	3	0	2			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr4:155526043T>C	ENST00000336098.3	-	9	1343	c.1305A>G	c.(1303-1305)agA>agG	p.R435R	FGG_ENST00000407946.1_Silent_p.R443R|FGG_ENST00000404648.3_Intron|FGG_ENST00000405164.1_Intron	NM_021870.2	NP_068656.2	P02679	FIBG_HUMAN	fibrinogen gamma chain	435	Platelet aggregation and Staphylococcus clumping.			R -> Y (in Ref. 15; AA sequence). {ECO:0000305}.	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)	GGTGCTCTGGTCTGACCTGTT	0.433																																					p.R435R		Atlas-SNP	.											.	FGG	71	.	0			c.A1305G						PASS	.						198	188	192					4																	155526043		2203	4300	6503	SO:0001819	synonymous_variant	2266	exon9			CTCTGGTCTGACC		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.1305A>G	chr4.hg19:g.155526043T>C		66.0	0.0	.		93.0	37.0	.	NM_021870	A8K057|P04469|P04470|Q53Y18|Q96A14|Q96KJ3|Q9UC62|Q9UC63|Q9UCF3	Silent	SNP	ENST00000336098.3	hg19	CCDS3788.1																																																																																			.	.	.	none		0.433	FGG-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317581.1	NM_021870		C	155526043	T	C	155526043	2	2	221	1	0	0	0	0	0	0	0	1	5877	1664	58	3		3	FGG	4	155526043	Silent	SNP	T	TCGA-MH-A560-01A-11D-A26P-10		155526043	35628233	21	13379											
PAPD4	167153	hgsc.bcm.edu	37	chr5	78941013	78941013	+	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	gtgaagttcagggataaagtCaggtaaataattaatgagct	16	11	11	3	0	2	2	2	2	0	0	2	3	2	3	0	2	1	3	0	2	7	5			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr5:78941013C>T	ENST00000296783.3	+	9	1118	c.819C>T	c.(817-819)gtC>gtT	p.V273V	PAPD4_ENST00000504233.1_Silent_p.V273V|PAPD4_ENST00000423041.2_Silent_p.V269V|PAPD4_ENST00000453514.1_Silent_p.V273V|PAPD4_ENST00000428308.2_Silent_p.V273V			Q6PIY7	GLD2_HUMAN	PAP associated domain containing 4	273					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)		GGGATAAAGTCAGGTAAATAA	0.338																																					p.V273V		Atlas-SNP	.											.	PAPD4	51	.	0			c.C819T						PASS	.						91	94	93					5																	78941013		2203	4300	6503	SO:0001819	synonymous_variant	167153	exon9			TAAAGTCAGGTAA	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.819C>T	chr5.hg19:g.78941013C>T		121.0	0.0	.		100.0	4.0	.	NM_173797	Q86WZ2|Q8N927	Silent	SNP	ENST00000296783.3	hg19	CCDS4048.1																																																																																			.	.	.	none		0.338	PAPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226967.1	NM_173797		T	78941013	C	T	78941013	2	4	221	1	0	0	0	0	0	0	0	1	11431	813	29	2		2	PAPD4	5	78941013	Silent	SNP	C	TCGA-MH-A560-01A-11D-A26P-10		78941013	101974247	22	13380											
THSD7A	221981	hgsc.bcm.edu	37	chr7	11675888	11675888	+	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	ctctttttcttaataagctcGcgggcttctggatcctttac	6	17	7	11	2	3	0	0	0	3	0	5	1	4	1	1	2	2	2	1	2	3	7	rs375820480		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr7:11675888G>A	ENST00000423059.4	-	2	1142	c.891C>T	c.(889-891)cgC>cgT	p.R297R	THSD7A_ENST00000480061.1_5'Flank	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	297					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)		TAATAAGCTCGCGGGCTTCTG	0.463										HNSCC(18;0.044)																											p.R297R		Atlas-SNP	.											.	THSD7A	219	.	0			c.C891T						PASS	.	G		0,3716		0,0,1858	137	131	133		891	-11.2	0.6	7		133	1,8219		0,1,4109	no	coding-synonymous	THSD7A	NM_015204.2		0,1,5967	AA,AG,GG		0.0122,0.0,0.0084		297/1658	11675888	1,11935	1858	4110	5968	SO:0001819	synonymous_variant	221981	exon2			AAGCTCGCGGGCT		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.891C>T	chr7.hg19:g.11675888G>A		80.0	0.0	.		46.0	21.0	.	NM_015204		Silent	SNP	ENST00000423059.4	hg19	CCDS47543.1																																																																																			.	.	.	weak		0.463	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		A	11675888	G	A	11675888	2	1	221	1	0	0	0	0	0	0	0	1	15891	1074	38	1		1	THSD7A	7	11675888	Silent	SNP	G	TCGA-MH-A560-01A-11D-A26P-10		11675888	147462775	23	13381											
IMMP2L	83943	hgsc.bcm.edu	37	chr7	111161447	111161447	+	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	gccacaggcaccgccacaaaGaagcctttacaaaaggcctt	14	5	8	14	1	0	1	0	0	0	1	0	1	0	1	5	2	2	1	5	2	5	3			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr7:111161447G>A	ENST00000405709.2	-	2	499	c.57C>T	c.(55-57)ttC>ttT	p.F19F	IMMP2L_ENST00000452895.1_Silent_p.F19F|IMMP2L_ENST00000437687.1_Silent_p.F19F|IMMP2L_ENST00000447215.1_Silent_p.F19F|IMMP2L_ENST00000415362.1_Silent_p.F19F|IMMP2L_ENST00000331762.3_Silent_p.F19F	NM_032549.3	NP_115938.1	Q96T52	IMP2L_HUMAN	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	19					ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|protein processing involved in protein targeting to mitochondrion (GO:0006627)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|mitochondrial inner membrane peptidase complex (GO:0042720)	peptidase activity (GO:0008233)|serine-type peptidase activity (GO:0008236)			endometrium(3)|large_intestine(6)|lung(5)	14				UCEC - Uterine corpus endometrioid carcinoma (4;0.053)|Epithelial(3;2.27e-07)|all cancers(3;1.36e-05)|STAD - Stomach adenocarcinoma(3;0.00148)|KIRC - Kidney renal clear cell carcinoma(11;0.0339)|Lung(3;0.0375)|Kidney(11;0.0415)|LUSC - Lung squamous cell carcinoma(290;0.173)		CCGCCACAAAGAAGCCTTTAC	0.433																																					p.F19F		Atlas-SNP	.											.	IMMP2L	32	.	0			c.C57T						PASS	.						107	106	106					7																	111161447		2203	4300	6503	SO:0001819	synonymous_variant	83943	exon2			CACAAAGAAGCCT	AF359563	CCDS5753.1	7q31	2014-01-06	2005-08-17		ENSG00000184903	ENSG00000184903			14598	protein-coding gene	gene with protein product		605977	"IMP2 inner mitochondrial membrane protease-like (S. cerevisiae)", "IMMP2L intronic transcript 1 (non-protein coding)"	IMMP2L-IT1		11254443	Standard	NM_032549		Approved	IMP2	uc010ljr.2	Q96T52	OTTHUMG00000155023	ENST00000405709.2:c.57C>T	chr7.hg19:g.111161447G>A		86.0	0.0	.		58.0	17.0	.	NM_032549	Q75MF1|Q75MN9|Q75MP0|Q75MS5|Q75MS8|Q96HJ2	Silent	SNP	ENST00000405709.2	hg19	CCDS5753.1																																																																																			.	.	.	none		0.433	IMMP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338109.4	NM_032549		A	111161447	G	A	111161447	2	1	221	1	0	0	0	0	0	0	0	1	7724	933	33	2		2	IMMP2L	7	111161447	Silent	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	99485559	111161447	47977216	24	13382											
KIAA1147	57189	hgsc.bcm.edu	37	chr7	141365048	141365048	+	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	gccacgttcacgtagaagaaAggtttggactcaggaatggt	12	9	13	7	2	2	2	2	0	0	2	2	4	2	4	1	4	0	3	1	4	4	3			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr7:141365048A>T	ENST00000536163.1	-	6	890	c.891T>A	c.(889-891)ccT>ccA	p.P297P	KIAA1147_ENST00000482493.1_Silent_p.P193P|RP5-894A10.6_ENST00000602609.1_RNA	NM_001080392.1	NP_001073861.1	A4D1U4	LCHN_HUMAN	KIAA1147	297										breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|ovary(1)|skin(1)	12	Melanoma(164;0.0171)					CGTAGAAGAAAGGTTTGGACT	0.597																																					p.P297P		Atlas-SNP	.											.	KIAA1147	32	.	0			c.T891A						PASS	.						82	89	87					7																	141365048		2145	4228	6373	SO:0001819	synonymous_variant	57189	exon6			GAAGAAAGGTTTG	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.891T>A	chr7.hg19:g.141365048A>T		250.0	0.0	.		190.0	65.0	.	NM_001080392	Q9ULS3	Silent	SNP	ENST00000536163.1	hg19	CCDS47726.1																																																																																			.	.	.	none		0.597	KIAA1147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349104.1			T	141365048	A	T	141365048	2	4	221	1	0	0	0	0	0	0	0	1	8217	59	3	5		5	KIAA1147	7	141365048	Silent	SNP	A	TCGA-MH-A560-01A-11D-A26P-10	30203601	141365048	17773615	25	13383											
CUL1	8454	hgsc.bcm.edu	37	chr7	148496376	148496376	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgttgcataggcggccatcGtgagaatcatgaagatgagg	11	10	14	6	2	1	4	1	3	0	2	2	5	1	4	1	3	1	2	1	3	3	3			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr7:148496376G>A	ENST00000325222.4	+	21	2425	c.2146G>A	c.(2146-2148)Gtg>Atg	p.V716M	CUL1_ENST00000602748.1_Missense_Mutation_p.V716M|CUL1_ENST00000409469.1_Missense_Mutation_p.V716M	NM_003592.2	NP_003583.2	Q13616	CUL1_HUMAN	cullin 1	716					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)			GGCGGCCATCGTGAGAATCAT	0.478																																					p.V716M		Atlas-SNP	.											.	CUL1	80	.	0			c.G2146A						PASS	.						139	106	117					7																	148496376		2203	4300	6503	SO:0001583	missense	8454	exon21			GCCATCGTGAGAA	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.2146G>A	chr7.hg19:g.148496376G>A	ENSP00000326804:p.Val716Met	181.0	0.0	.		114.0	42.0	.	NM_003592	D3DWG3|O60719|Q08AL6|Q8IYW1	Missense_Mutation	SNP	ENST00000325222.4	hg19	CCDS34772.1	.	.	.	.	.	.	.	.	.	.	.	28.3	4.905971	0.92107	.	.	ENSG00000055130	ENST00000409469;ENST00000325222;ENST00000433865	D;D	0.89270	-2.49;-2.49	5.3	5.3	0.74995	Cullin protein, neddylation domain (2);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.96417	0.8831	H	0.96633	3.855	0.80722	D	1	D;D	0.76494	0.999;0.999	D;P	0.65233	0.933;0.64	D	0.97776	1.0229	10	0.87932	D	0	-16.3531	18.9531	0.92647	0.0:0.0:1.0:0.0	.	643;716	E7EWR0;Q13616	.;CUL1_HUMAN	M	716;716;643	ENSP00000387160:V716M;ENSP00000326804:V716M	ENSP00000326804:V716M	V	+	1	0	CUL1	148127309	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	9.472000	0.97709	2.467000	0.83353	0.557000	0.71058	GTG	.	.	.	none		0.478	CUL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467785.1	NM_003592		A	148496376	G	A	148496376	3	1	221	1	0	0	0	0	1	0	0	0	4056	1145	40	1	2224	1	CUL1	7	148496376	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	7131328	148496376	10642287	26	13384											
DEFA6	1671	hgsc.bcm.edu	37	chr8	6783427	6783427	+	Missense_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	cggcaaagtcctggtcatttGccccacgctgctcctgggca	6	9	11	15	2	1	0	1	0	0	0	3	0	3	0	4	3	2	4	4	3	1	1	rs371286175		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr8:6783427G>A	ENST00000297436.2	-	1	171	c.131C>T	c.(130-132)gCa>gTa	p.A44V	GS1-24F4.3_ENST00000526235.1_RNA	NM_001926.3	NP_001917.1	Q01524	DEF6_HUMAN	defensin, alpha 6, Paneth cell-specific	44					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)				lung(4)	4			STAD - Stomach adenocarcinoma(24;0.0322)	COAD - Colon adenocarcinoma(149;0.0572)|READ - Rectum adenocarcinoma(644;0.121)		CTGGTCATTTGCCCCACGCTG	0.557																																					p.A44V		Atlas-SNP	.											.	DEFA6	9	.	0			c.C131T						PASS	.	G	VAL/ALA	0,4406		0,0,2203	70	58	62		131	-3.3	0	8		62	1,8599		0,1,4299	no	missense	DEFA6	NM_001926.3	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	44/101	6783427	1,13005	2203	4300	6503	SO:0001583	missense	1671	exon1			TCATTTGCCCCAC	M98331	CCDS5960.1	8p23.1	2007-02-20			ENSG00000164822	ENSG00000164822		"Defensins, alpha"	2765	protein-coding gene	gene with protein product		600471				8417977	Standard	NM_001926		Approved	HD-6, DEF6	uc003wqt.3	Q01524	OTTHUMG00000149984	ENST00000297436.2:c.131C>T	chr8.hg19:g.6783427G>A	ENSP00000297436:p.Ala44Val	101.0	0.0	.		65.0	25.0	.	NM_001926	Q6EZF9	Missense_Mutation	SNP	ENST00000297436.2	hg19	CCDS5960.1	.	.	.	.	.	.	.	.	.	.	.	2.180	-0.387804	0.04932	0.0	1.16E-4	ENSG00000164822	ENST00000297436	T	0.32023	1.47	1.85	-3.35	0.04928	Defensin propeptide (1);	2.198720	0.02497	N	0.090070	T	0.24624	0.0597	L	0.39245	1.2	0.09310	N	1	B	0.30763	0.294	B	0.29942	0.109	T	0.12293	-1.0553	10	0.44086	T	0.13	.	5.9699	0.19346	0.0:0.1529:0.3749:0.4722	.	44	Q01524	DEF6_HUMAN	V	44	ENSP00000297436:A44V	ENSP00000297436:A44V	A	-	2	0	DEFA6	6770837	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.753000	0.04792	-1.668000	0.01471	-1.471000	0.01009	GCA	.	.	.	weak		0.557	DEFA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206739.1	NM_001926		A	6783427	G	A	6783427	3	1	221	1	0	0	0	0	1	0	0	0	4395	1319	46	2	179	2	DEFA6	8	6783427	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10		6783427	139580595	27	13385											
MFHAS1	9258	hgsc.bcm.edu	37	chr8	8655002	8655002	+	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	gggctgactcagcaactcccCtgtaggaggagagagaaaaa	14	5	13	9	0	1	3	1	1	0	2	2	6	2	4	2	3	2	3	2	3	4	1			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr8:8655002C>A	ENST00000276282.6	-	2	3585		c.e2-1		MFHAS1_ENST00000520091.1_Splice_Site	NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1											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)		AGCAACTCCCCTGTAGGAGGA	0.547																																					.	Melanoma(103;1201 2045 17515 28966)	Atlas-SNP	.											.	MFHAS1	58	.	0			c.2999-1G>T						PASS	.						78	66	70					8																	8655002		2203	4300	6503	SO:0001630	splice_region_variant	9258	exon3			ACTCCCCTGTAGG	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.2999-1G>T	chr8.hg19:g.8655002C>A		120.0	0.0	.		116.0	47.0	.	NM_004225	Q96CI0	Splice_Site	SNP	ENST00000276282.6	hg19	CCDS34844.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.752676	0.89753	.	.	ENSG00000147324	ENST00000276282	.	.	.	5.73	5.73	0.89815	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.882	0.92358	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MFHAS1	8692412	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.251000	0.78297	2.703000	0.92315	0.551000	0.68910	.	.	.	.	none		0.547	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225	Intron	A	8655002	C	A	8655002	5	1	221	1	0	0	0	0	0	0	1	0	9528	695	24	4	168	4	MFHAS1	8	8655002	Splice_Site	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	1871575	8655002	137709020	28	13386											
SETX	23064	hgsc.bcm.edu	37	chr9	135163729	135163729	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcgcctgaacatgagaaggtAactctttttctaataaaaat	15	13	6	7	1	2	2	0	2	2	1	3	3	2	2	1	1	2	1	1	1	7	5			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr9:135163729A>G	ENST00000224140.5	-	17	6400	c.6218T>C	c.(6217-6219)tTa>tCa	p.L2073S	SETX_ENST00000372169.2_Missense_Mutation_p.L2073S|SETX_ENST00000393220.1_Missense_Mutation_p.L2073S	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	2073					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)		ATGAGAAGGTAACTCTTTTTC	0.358																																					p.L2073S		Atlas-SNP	.											.	SETX	234	.	0			c.T6218C						PASS	.						33	32	32					9																	135163729		2203	4300	6503	SO:0001583	missense	23064	exon17			GAAGGTAACTCTT	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.6218T>C	chr9.hg19:g.135163729A>G	ENSP00000224140:p.Leu2073Ser	78.0	0.0	.		63.0	25.0	.	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	hg19	CCDS6947.1	.	.	.	.	.	.	.	.	.	.	A	13.01	2.108442	0.37242	.	.	ENSG00000107290	ENST00000224140;ENST00000436441;ENST00000372169;ENST00000393220	D;D;D;D	0.90900	-2.18;-2.75;-2.26;-1.87	5.5	5.5	0.81552	.	0.381500	0.24779	N	0.035673	D	0.89406	0.6706	L	0.31476	0.935	0.39629	D	0.970154	B;D;D	0.76494	0.203;0.999;0.998	B;D;P	0.68483	0.075;0.958;0.876	D	0.85262	0.1051	10	0.09338	T	0.73	.	8.5286	0.33319	0.9131:0.0:0.0869:0.0	.	2073;2073;2073	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	S	2073;315;2073;2073	ENSP00000224140:L2073S;ENSP00000409143:L315S;ENSP00000361242:L2073S;ENSP00000376913:L2073S	ENSP00000224140:L2073S	L	-	2	0	SETX	134153550	0.972000	0.33761	0.996000	0.52242	0.786000	0.44442	2.256000	0.43231	2.221000	0.72209	0.528000	0.53228	TTA	.	.	.	none		0.358	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		G	135163729	A	G	135163729	3	3	221	1	0	0	0	0	1	0	0	0	14154	372	13	3	1855	3	SETX	9	135163729	Missense_Mutation	SNP	A	TCGA-MH-A560-01A-11D-A26P-10		135163729	6049702	29	13387											
TAF3	83860	hgsc.bcm.edu	37	chr10	8007636	8007636	+	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	gagaaggagaagaaggagaaGgaaagagagaaagagaagag	23	0	18	0	0	0	8	0	0	0	8	0	14	0	9	0	3	0	0	0	3	7	0			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr10:8007636G>C	ENST00000344293.5	+	3	2369	c.2163G>C	c.(2161-2163)aaG>aaC	p.K721N		NM_031923.3	NP_114129.1	Q5VWG9	TAF3_HUMAN	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140kDa	721	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						agaaggagaaggaaagagaga	0.383																																					p.K721N		Atlas-SNP	.											.	TAF3	93	.	0			c.G2163C						PASS	.						18	18	18					10																	8007636		1856	4075	5931	SO:0001583	missense	83860	exon3			GGAGAAGGAAAGA	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.2163G>C	chr10.hg19:g.8007636G>C	ENSP00000340271:p.Lys721Asn	66.0	0.0	.		82.0	21.0	.	NM_031923	Q05DA0|Q6GMS5|Q6P6B5|Q86VY6|Q9BQS9|Q9UFI8	Missense_Mutation	SNP	ENST00000344293.5	hg19	CCDS41487.1	.	.	.	.	.	.	.	.	.	.	G	11.76	1.735163	0.30774	.	.	ENSG00000165632	ENST00000344293	T	0.08634	3.07	5.68	4.59	0.56863	.	0.459877	0.21158	N	0.079203	T	0.13798	0.0334	M	0.81802	2.56	0.49299	D	0.999772	P	0.46706	0.883	B	0.40375	0.327	T	0.02301	-1.1180	10	0.36615	T	0.2	-14.6137	13.0132	0.58743	0.1321:0.0:0.8679:0.0	.	721	Q5VWG9	TAF3_HUMAN	N	721	ENSP00000340271:K721N	ENSP00000340271:K721N	K	+	3	2	TAF3	8047642	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	2.385000	0.44371	2.689000	0.91719	0.655000	0.94253	AAG	.	.	.	none		0.383	TAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046725.1	NM_031923		C	8007636	G	C	8007636	3	2	221	1	0	0	0	0	1	0	0	0	15537	991	35	4	2173	4	TAF3	10	8007636	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10		8007636	127527111	30	13388											
DHTKD1	55526	hgsc.bcm.edu	37	chr10	12139749	12139749	+	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	ggcggactcatgacgcaggaGgaggtgtctgaaataaaatc	13	7	14	7	2	2	2	1	2	1	0	3	5	2	5	0	5	0	1	0	5	3	1			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr10:12139749G>C	ENST00000263035.4	+	8	1487	c.1425G>C	c.(1423-1425)gaG>gaC	p.E475D	DHTKD1_ENST00000465617.1_3'UTR	NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	475					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)			TGACGCAGGAGGAGGTGTCTG	0.488																																					p.E475D		Atlas-SNP	.											.	DHTKD1	104	.	0			c.G1425C						PASS	.						67	62	64					10																	12139749		2203	4300	6503	SO:0001583	missense	55526	exon8			GCAGGAGGAGGTG	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.1425G>C	chr10.hg19:g.12139749G>C	ENSP00000263035:p.Glu475Asp	116.0	0.0	.		125.0	53.0	.	NM_018706	Q68CU5|Q9BUM8|Q9HCE2	Missense_Mutation	SNP	ENST00000263035.4	hg19	CCDS7087.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.11|12.11	1.839538|1.839538	0.32513|0.32513	.|.	.|.	ENSG00000181192|ENSG00000181192	ENST00000263035|ENST00000448829	T|.	0.16196|.	2.36|.	5.35|5.35	1.27|1.27	0.21489|0.21489	Dehydrogenase, E1 component (1);|.	0.112246|.	0.64402|.	D|.	0.000014|.	T|T	0.35770|0.35770	0.0943|0.0943	N|N	0.25144|0.25144	0.715|0.715	0.41129|0.41129	D|D	0.985874|0.985874	B|.	0.14012|.	0.009|.	B|.	0.17979|.	0.02|.	T|T	0.07046|0.07046	-1.0793|-1.0793	10|5	0.24483|.	T|.	0.36|.	-13.3397|-13.3397	4.01|4.01	0.09618|0.09618	0.3596:0.0:0.3864:0.254|0.3596:0.0:0.3864:0.254	.|.	475|.	Q96HY7|.	DHTK1_HUMAN|.	D|R	475|27	ENSP00000263035:E475D|.	ENSP00000263035:E475D|.	E|G	+|+	3|1	2|0	DHTKD1|DHTKD1	12179755|12179755	0.982000|0.982000	0.34865|0.34865	1.000000|1.000000	0.80357|0.80357	0.863000|0.863000	0.49368|0.49368	0.093000|0.093000	0.15086|0.15086	0.264000|0.264000	0.21851|0.21851	0.462000|0.462000	0.41574|0.41574	GAG|GGA	.	.	.	none		0.488	DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046777.1	NM_018706		C	12139749	G	C	12139749	3	2	221	1	0	0	0	0	1	0	0	0	4502	991	35	4	1455	4	DHTKD1	10	12139749	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	4132113	12139749	123394998	31	13389											
DNA2	1763	hgsc.bcm.edu	37	chr10	70182074	70182074	+	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	gtcagcataaaattccagttCcagcttcacatctttaaagt	13	13	5	10	0	3	0	2	0	1	0	5	0	5	0	2	0	2	3	2	0	4	6	rs369018277		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr10:70182074C>T	ENST00000358410.3	-	17	2655	c.2605G>A	c.(2605-2607)Gaa>Aaa	p.E869K	DNA2_ENST00000399180.2_Missense_Mutation_p.E955K|DNA2_ENST00000399179.2_Intron	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2	869	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						AATTCCAGTTCCAGCTTCACA	0.393																																					p.E869K		Atlas-SNP	.											.	DNA2	76	.	0			c.G2605A						PASS	.	C	LYS/GLU	0,3782		0,0,1891	90	87	88		2605	3	1	10		88	1,8241		0,1,4120	no	missense	DNA2	NM_001080449.2	56	0,1,6011	TT,TC,CC		0.0121,0.0,0.0083	possibly-damaging	869/1061	70182074	1,12023	1891	4121	6012	SO:0001583	missense	1763	exon17			CCAGTTCCAGCTT	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.2605G>A	chr10.hg19:g.70182074C>T	ENSP00000351185:p.Glu869Lys	156.0	0.0	.		167.0	58.0	.	NM_001080449	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Missense_Mutation	SNP	ENST00000358410.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.14|16.14	3.040039|3.040039	0.55003|0.55003	0.0|0.0	1.21E-4|1.21E-4	ENSG00000138346|ENSG00000138346	ENST00000399180;ENST00000358410|ENST00000440722	D;D|.	0.91464|.	-2.85;-2.83|.	4.93|4.93	3.02|3.02	0.34903|0.34903	.|.	1.268580|.	0.05029|.	N|.	0.474288|.	T|T	0.58779|0.58779	0.2146|0.2146	L|L	0.49350|0.49350	1.555|1.555	0.80722|0.80722	D|D	1|1	P|.	0.49358|.	0.923|.	P|.	0.46796|.	0.527|.	T|T	0.54931|0.54931	-0.8219|-0.8219	10|5	0.11182|.	T|.	0.66|.	.|.	10.956|10.956	0.47358|0.47358	0.0:0.845:0.0:0.155|0.0:0.845:0.0:0.155	.|.	869|.	P51530|.	DNA2L_HUMAN|.	K|E	955;869|190	ENSP00000382133:E955K;ENSP00000351185:E869K|.	ENSP00000351185:E869K|.	E|G	-|-	1|2	0|0	DNA2|DNA2	69852080|69852080	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.905000|0.905000	0.53344|0.53344	2.929000|2.929000	0.48916|0.48916	1.035000|1.035000	0.39972|0.39972	0.655000|0.655000	0.94253|0.94253	GAA|GGA	.	.	.	none		0.393	DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2			T	70182074	C	T	70182074	3	4	221	1	0	0	0	0	1	0	0	0	4598	864	30	2	597	2	DNA2	10	70182074	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	58042325	70182074	65352673	32	13390											
HPSE2	60495	hgsc.bcm.edu	37	chr10	100481443	100481443	+	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	agggcgatgacattcttcctCggccgcccaatattagggcc	8	9	11	13	3	1	1	0	1	1	0	3	2	2	1	4	3	0	0	4	3	3	4	rs200916817		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr10:100481443C>T	ENST00000370552.3	-	5	986	c.927G>A	c.(925-927)ccG>ccA	p.P309P	HPSE2_ENST00000370549.1_Silent_p.P251P|HPSE2_ENST00000404542.1_Silent_p.P197P|HPSE2_ENST00000370546.1_Silent_p.P309P	NM_021828.4	NP_068600.4	Q8WWQ2	HPSE2_HUMAN	heparanase 2 (inactive)	309					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)		CATTCTTCCTCGGCCGCCCAA	0.438																																					p.P309P		Atlas-SNP	.											.	HPSE2	203	.	0			c.G927A						PASS	.						55	54	54					10																	100481443		2203	4300	6503	SO:0001819	synonymous_variant	60495	exon5			CTTCCTCGGCCGC	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.927G>A	chr10.hg19:g.100481443C>T		59.0	0.0	.		64.0	7.0	.	NM_001166246	Q5VUH4|Q5VUH5|Q5VUH6|Q8WWQ1|Q9HB37|Q9HB38|Q9HB39	Silent	SNP	ENST00000370552.3	hg19	CCDS7477.1																																																																																			.	C|0.999;T|0.001	0.001	weak		0.438	HPSE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049789.1	NM_021828		T	100481443	C	T	100481443	2	4	221	1	0	0	0	0	0	0	0	1	7352	871	31	1		1	HPSE2	10	100481443	Silent	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	30299369	100481443	35053304	33	13391											
GBF1	8729	hgsc.bcm.edu	37	chr10	104123472	104123472	+	Frame_Shift_Del	DEL	A	A	-																															tcttcctactcctagctgacAaaaagtttgcccggaagcca																										TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr10:104123472delA	ENST00000369983.3	+	17	2280	c.2020delA	c.(2020-2022)aaafs	p.K675fs		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	675					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		CCTAGCTGACAAAAAGTTTGC	0.423																																					p.D674fs		Atlas-Indel,Pindel	.											.	GBF1	142	.	0			c.2022delC						PASS	.						113	119	117					10																	104123472		2203	4300	6503	SO:0001589	frameshift_variant	8729	exon17			.	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.2020delA	chr10.hg19:g.104123472delA	ENSP00000359000:p.Lys675fs	76.0	0.0	0		69.0	19.0	0.275362	NM_001199378	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Frame_Shift_Del	DEL	ENST00000369983.3	hg19	CCDS7533.1																																																																																			.	.	.	none		0.423	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			-	104123472	A	-	104123472	7	5	221	1	0	1	0	1	0	0	0	0	6278	131	5	0	2082	0	GBF1	10	104123472	Frame_Shift_Del	DEL	A	TCGA-MH-A560-01A-11D-A26P-10	3642029	104123472	31411275	34	13392											
CARNS1	57571	hgsc.bcm.edu	37	chr11	67186592	67186592	+	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	agccgccggggctgctgcggGgaggggatgccagcctaggg	5	4	21	11	3	0	0	0	0	0	0	0	2	0	2	4	7	5	2	4	7	1	1			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr11:67186592G>C	ENST00000307823.3	+	4	813	c.361G>C	c.(361-363)Gga>Cga	p.G121R	CARNS1_ENST00000445895.2_Missense_Mutation_p.G244R|CARNS1_ENST00000423745.2_Missense_Mutation_p.G121R|CARNS1_ENST00000531040.1_Missense_Mutation_p.G244R	NM_020811.1	NP_065862.1	A5YM72	CRNS1_HUMAN	carnosine synthase 1	121					ATP catabolic process (GO:0006200)|carnosine biosynthetic process (GO:0035499)		ATP binding (GO:0005524)|ATPase activity (GO:0016887)|carnosine synthase activity (GO:0047730)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)	11						GCTGCTGCGGGGAGGGGATGC	0.652																																					p.G244R		Atlas-SNP	.											.	CARNS1	60	.	0			c.G730C						PASS	.						5	7	6					11																	67186592		1871	3990	5861	SO:0001583	missense	57571	exon5			CTGCGGGGAGGGG		CCDS44658.1, CCDS53667.1	11q13.1	2010-03-25	2010-03-25	2010-03-25	ENSG00000172508	ENSG00000172508			29268	protein-coding gene	gene with protein product		613368	"ATP-grasp domain containing 1"	ATPGD1		20097752	Standard	NM_020811		Approved	KIAA1394	uc010rpr.2	A5YM72		ENST00000307823.3:c.361G>C	chr11.hg19:g.67186592G>C	ENSP00000308268:p.Gly121Arg	46.0	0.0	.		37.0	20.0	.	NM_001166222	A8K1M3|B4DFC6|E9PK38|F5H427|Q8N467|Q9P2F3	Missense_Mutation	SNP	ENST00000307823.3	hg19	CCDS44658.1	.	.	.	.	.	.	.	.	.	.	G	9.966	1.224062	0.22457	.	.	ENSG00000172508	ENST00000531040;ENST00000307823;ENST00000542831;ENST00000539452;ENST00000423745;ENST00000445895	T;T;T;T	0.32753	1.44;1.47;1.47;1.47	4.38	2.5	0.30297	.	.	.	.	.	T	0.31765	0.0807	N	0.19112	0.55	0.09310	N	1	D;P;D	0.62365	0.982;0.94;0.991	P;P;P	0.60068	0.868;0.605;0.868	T	0.09552	-1.0669	9	0.41790	T	0.15	.	7.4523	0.27246	0.2888:0.0:0.7112:0.0	.	244;121;260	F5H427;A5YM72;A5YM72-3	.;CRNS1_HUMAN;.	R	244;121;244;260;121;244	ENSP00000431670:G244R;ENSP00000308268:G121R;ENSP00000401519:G121R;ENSP00000389009:G244R	ENSP00000308268:G121R	G	+	1	0	CARNS1	66943168	0.111000	0.22076	0.569000	0.28460	0.012000	0.07955	2.541000	0.45735	0.487000	0.27698	0.561000	0.74099	GGA	.	.	.	none		0.652	CARNS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395501.1	NM_020811		C	67186592	G	C	67186592	3	2	221	1	0	0	0	0	1	0	0	0	2658	1233	43	4	744	4	CARNS1	11	67186592	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10		67186592	67819924	35	13393											
C11orf53	341032	hgsc.bcm.edu	37	chr11	111156468	111156468	+	Missense_Mutation	SNP	A	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	tgaccttgccacccagcacgAgttgcctctcccagcttgag	7	9	9	16	1	1	2	0	2	1	0	2	3	1	2	5	0	4	3	5	0	0	3			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr11:111156468A>C	ENST00000280325.4	+	4	547	c.400A>C	c.(400-402)Agt>Cgt	p.S134R		NM_198498.1	NP_940900.1	Q8IXP5	CK053_HUMAN	chromosome 11 open reading frame 53	134										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)		ACCCAGCACGAGTTGCCTCTC	0.632																																					p.S134R		Atlas-SNP	.											.	C11orf53	17	.	0			c.A400C						PASS	.						76	69	71					11																	111156468		2201	4297	6498	SO:0001583	missense	341032	exon4			AGCACGAGTTGCC	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.400A>C	chr11.hg19:g.111156468A>C	ENSP00000280325:p.Ser134Arg	101.0	0.0	.		50.0	16.0	.	NM_198498		Missense_Mutation	SNP	ENST00000280325.4	hg19	CCDS31674.1	.	.	.	.	.	.	.	.	.	.	A	15.69	2.908387	0.52333	.	.	ENSG00000150750	ENST00000280325	.	.	.	4.8	0.97	0.19692	.	0.382752	0.29198	N	0.012842	T	0.39009	0.1062	L	0.55481	1.735	0.09310	N	0.999997	P	0.43701	0.815	P	0.45681	0.49	T	0.21415	-1.0246	9	0.42905	T	0.14	-1.3318	7.5852	0.27989	0.7125:0.0:0.2875:0.0	.	134	Q8IXP5	CK053_HUMAN	R	134	.	ENSP00000280325:S134R	S	+	1	0	C11orf53	110661678	0.055000	0.20627	0.041000	0.18516	0.940000	0.58332	1.282000	0.33226	-0.088000	0.12506	0.459000	0.35465	AGT	.	.	.	none		0.632	C11orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390989.1	NM_198498		C	111156468	A	C	111156468	3	2	221	1	0	0	0	0	1	0	0	0	1650	304	11	5	410	5	C11orf53	11	111156468	Missense_Mutation	SNP	A	TCGA-MH-A560-01A-11D-A26P-10	43969876	111156468	23850048	36	13394											
C14orf39	317761	hgsc.bcm.edu	37	chr14	60921717	60921717	+	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	aacttttggcttctcatattAcctgatctgatgagatttct	9	18	6	8	0	3	3	1	3	3	1	4	4	3	3	1	1	2	1	1	1	3	6			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr14:60921717A>T	ENST00000321731.3	-	16	1663		c.e16+1			NM_174978.2	NP_777638	Q8N1H7	S6OS1_HUMAN	chromosome 14 open reading frame 39						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)		TTCTCATATTACCTGATCTGA	0.313																																					.		Atlas-SNP	.											.	C14orf39	79	.	0			c.1503+2T>A						PASS	.						36	39	38					14																	60921717		2198	4285	6483	SO:0001630	splice_region_variant	317761	exon17			CATATTACCTGAT	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.1503+1T>A	chr14.hg19:g.60921717A>T		24.0	0.0	.		15.0	8.0	.	NM_174978	Q08AQ4	Splice_Site	SNP	ENST00000321731.3	hg19	CCDS9746.1	.	.	.	.	.	.	.	.	.	.	A	18.17	3.563953	0.65651	.	.	ENSG00000179008	ENST00000321731	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5881	0.61944	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C14orf39	59991470	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	5.199000	0.65152	2.234000	0.73211	0.459000	0.35465	.	.	.	.	none		0.313	C14orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276948.1	NM_174978	Intron	T	60921717	A	T	60921717	5	4	221	1	0	0	0	0	0	0	1	0	1774	405	14	5	270	5	C14orf39	14	60921717	Splice_Site	SNP	A	TCGA-MH-A560-01A-11D-A26P-10		60921717	46427823	37	13395											
FAM98B	283742	hgsc.bcm.edu	37	chr15	38776827	38776827	+	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	ggtggtggtggtggtggtggTggtggtggaggaggtggata	4	11	26	0	0	0	0	0	0	0	0	0	3	0	3	0	13	0	0	0	13	1	1			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr15:38776827T>A	ENST00000491535.1	+	0	3111				FAM98B_ENST00000397609.2_Silent_p.G423G	NM_001042429.1	NP_001035894.1	Q52LJ0	FA98B_HUMAN	family with sequence similarity 98, member B							cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-splicing ligase complex (GO:0072669)	poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|skin(1)	8		all_cancers(109;3.11e-17)|all_epithelial(112;2.64e-15)|Lung NSC(122;2.11e-11)|all_lung(180;5.61e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;9e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0209)		gtggtggtggtggtggtggag	0.443																																					p.G423G		Atlas-SNP	.											FAM98B_ENST00000397609,NS,carcinoma,0,1	FAM98B	53	.	0			c.T1269A						PASS	.						19	18	18					15																	38776827		1515	3413	4928	SO:0001628	intergenic_variant	283742	exon8			TGGTGGTGGTGGT		CCDS10047.2	15q14	2006-11-29		2005-11-20	ENSG00000171262	ENSG00000171262			26773	protein-coding gene	gene with protein product						12477932	Standard	NM_173611		Approved	FLJ38426	uc001zkc.3	Q52LJ0	OTTHUMG00000129831		chr15.hg19:g.38776827T>A		17.0	0.0	.		18.0	4.0	.	NM_173611	A8MUW5|Q8N935	Silent	SNP	ENST00000491535.1	hg19	CCDS42015.1																																																																																			.	.	.	none		0.443	FAM98B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252071.2	NM_173611		A	38776827	T	A	38776827	1	1	221	0	1	0	0	0	0	0	0	0	5664	1683	59	5		5	FAM98B	15	38776827	IGR	SNP	T	TCGA-MH-A560-01A-11D-A26P-10		38776827	63754565	38	13396											
ATAD5	79915	hgsc.bcm.edu	37	chr17	29162089	29162089	+	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	gttcttgcacaggttcacccTattccgcccaaaaagacagg	11	9	8	13	1	2	1	1	0	1	1	3	1	3	1	3	2	1	3	3	2	3	5			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr17:29162089T>A	ENST00000321990.4	+	2	1368	c.990T>A	c.(988-990)ccT>ccA	p.P330P	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	330					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)				AGGTTCACCCTATTCCGCCCA	0.378																																					p.P330P		Atlas-SNP	.											.	ATAD5	150	.	0			c.T990A						PASS	.						49	51	50					17																	29162089		2139	4265	6404	SO:0001819	synonymous_variant	79915	exon2			TCACCCTATTCCG		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.990T>A	chr17.hg19:g.29162089T>A		189.0	0.0	.		167.0	75.0	.	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Silent	SNP	ENST00000321990.4	hg19	CCDS11260.1																																																																																			.	.	.	none		0.378	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		A	29162089	T	A	29162089	2	1	221	1	0	0	0	0	0	0	0	1	1076	1509	53	5		5	ATAD5	17	29162089	Silent	SNP	T	TCGA-MH-A560-01A-11D-A26P-10		29162089	52033121	39	13397											
ORMDL3	94103	hgsc.bcm.edu	37	chr17	38078866	38078866	+	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	ggcagcttggggataagcacGctcatcagggacacggtgtt	9	8	15	9	2	2	0	2	0	0	0	2	2	2	2	0	5	2	5	0	5	1	3			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr17:38078866G>C	ENST00000394169.1	-	6	1893	c.399C>G	c.(397-399)agC>agG	p.S133R	ORMDL3_ENST00000304046.2_Missense_Mutation_p.S133R|ORMDL3_ENST00000584220.1_Missense_Mutation_p.S117R|ORMDL3_ENST00000579695.1_Missense_Mutation_p.S133R			Q8N138	ORML3_HUMAN	ORMDL sphingolipid biosynthesis regulator 3	133					ceramide metabolic process (GO:0006672)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|SPOTS complex (GO:0035339)				endometrium(3)|kidney(1)|lung(1)	5	Colorectal(19;0.000442)		Lung(15;0.0234)			GGATAAGCACGCTCATCAGGG	0.557																																					p.S133R		Atlas-SNP	.											.	ORMDL3	15	.	0			c.C399G						PASS	.						149	142	144					17																	38078866		2203	4300	6503	SO:0001583	missense	94103	exon4			AAGCACGCTCATC		CCDS11355.1	17q12	2014-06-16	2014-06-16		ENSG00000172057	ENSG00000172057			16038	protein-coding gene	gene with protein product		610075	"ORM1 (S. cerevisiae)-like 3", "ORM1-like 3 (S. cerevisiae)"			23066021	Standard	NM_139280		Approved		uc002htj.2	Q8N138	OTTHUMG00000133249	ENST00000394169.1:c.399C>G	chr17.hg19:g.38078866G>C	ENSP00000377724:p.Ser133Arg	159.0	0.0	.		141.0	29.0	.	NM_139280	B3KS83|Q6UY83	Missense_Mutation	SNP	ENST00000394169.1	hg19	CCDS11355.1	.	.	.	.	.	.	.	.	.	.	G	18.25	3.582713	0.65992	.	.	ENSG00000172057	ENST00000304046;ENST00000394169	.	.	.	5.39	-5.34	0.02705	.	0.110120	0.64402	D	0.000008	T	0.59432	0.2193	M	0.65975	2.015	0.34860	D	0.74254	P	0.37573	0.6	P	0.47744	0.556	T	0.65915	-0.6052	9	0.51188	T	0.08	-14.1116	13.4255	0.61022	0.658:0.0:0.342:0.0	.	133	Q8N138	ORML3_HUMAN	R	133	.	ENSP00000304858:S133R	S	-	3	2	ORMDL3	35332392	0.062000	0.20869	0.906000	0.35671	0.939000	0.58152	-0.588000	0.05774	-1.031000	0.03308	-0.345000	0.07892	AGC	.	.	.	none		0.557	ORMDL3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257003.1	NM_139280		C	38078866	G	C	38078866	3	2	221	1	0	0	0	0	1	0	0	0	11278	1078	38	4	66	4	ORMDL3	17	38078866	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	8916777	38078866	43116344	40	13398											
HELZ	9931	hgsc.bcm.edu	37	chr17	65110487	65110487	+	Missense_Mutation	SNP	T	T	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	tggtgttcgaatcttattaaTttcaggtccggaattatttg	9	18	9	5	2	2	0	1	0	1	0	4	2	3	1	1	3	0	1	1	3	5	6			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr17:65110487T>G	ENST00000358691.5	-	28	4037	c.3871A>C	c.(3871-3873)Att>Ctt	p.I1291L	HELZ_ENST00000580168.1_Missense_Mutation_p.I1292L	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	1291						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)					ATCTTATTAATTTCAGGTCCG	0.348																																					p.I1291L		Atlas-SNP	.											.	HELZ	160	.	0			c.A3871C						PASS	.						152	136	141					17																	65110487		1802	4071	5873	SO:0001583	missense	9931	exon28			TATTAATTTCAGG	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.3871A>C	chr17.hg19:g.65110487T>G	ENSP00000351524:p.Ile1291Leu	21.0	0.0	.		47.0	31.0	.	NM_014877	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	hg19	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	T	12.72	2.022328	0.35701	.	.	ENSG00000198265	ENST00000358691	D	0.82344	-1.6	5.65	4.56	0.56223	.	0.541833	0.21875	N	0.067829	T	0.64283	0.2584	N	0.14661	0.345	0.28505	N	0.913814	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.50625	-0.8806	10	0.10111	T	0.7	-10.9431	7.073	0.25189	0.0:0.078:0.1469:0.7752	.	1292;1291	B7ZLW2;P42694	.;HELZ_HUMAN	L	1291	ENSP00000351524:I1291L	ENSP00000351524:I1291L	I	-	1	0	HELZ	62540949	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	2.522000	0.45572	2.154000	0.67381	0.445000	0.29226	ATT	.	.	.	none		0.348	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		G	65110487	T	G	65110487	3	3	221	1	0	0	0	0	1	0	0	0	7056	1493	52	5	1981	5	HELZ	17	65110487	Missense_Mutation	SNP	T	TCGA-MH-A560-01A-11D-A26P-10	27031621	65110487	16084723	41	13399											
UNC13D	201294	hgsc.bcm.edu	37	chr17	73831821	73831821	+	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	tctctggggacactacatcaCccacaaccgtcgtgtggtcc	8	9	9	15	2	2	0	1	0	1	0	5	1	3	1	3	3	2	0	3	3	2	1			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr17:73831821C>T	ENST00000207549.4	-	19	2013	c.1634G>A	c.(1633-1635)gGt>gAt	p.G545D	UNC13D_ENST00000412096.2_Missense_Mutation_p.G545D	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	545					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)			CACTACATCACCCACAACCGT	0.617									Familial Hemophagocytic Lymphohistiocytosis																												p.G545D		Atlas-SNP	.											.	UNC13D	68	.	0			c.G1634A						PASS	.						66	65	65					17																	73831821		2203	4300	6503	SO:0001583	missense	201294	exon19	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	ACATCACCCACAA	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.1634G>A	chr17.hg19:g.73831821C>T	ENSP00000207549:p.Gly545Asp	129.0	0.0	.		123.0	5.0	.	NM_199242	B4DWG9|Q9H7K5	Missense_Mutation	SNP	ENST00000207549.4	hg19	CCDS11730.1	.	.	.	.	.	.	.	.	.	.	C	2.310	-0.358240	0.05138	.	.	ENSG00000092929	ENST00000207549;ENST00000412096;ENST00000448606	T;T	0.70164	-0.44;-0.46	4.81	4.81	0.61882	.	0.476497	0.22373	N	0.060904	T	0.56441	0.1985	L	0.43152	1.355	0.09310	N	0.999998	B;B	0.06786	0.001;0.001	B;B	0.10450	0.005;0.002	T	0.37957	-0.9683	10	0.14656	T	0.56	-0.4305	13.3603	0.60652	0.0:1.0:0.0:0.0	.	545;545	Q70J99-3;Q70J99	.;UN13D_HUMAN	D	545	ENSP00000207549:G545D;ENSP00000388093:G545D	ENSP00000207549:G545D	G	-	2	0	UNC13D	71343416	0.024000	0.19004	0.057000	0.19452	0.016000	0.09150	2.518000	0.45537	2.202000	0.70862	0.561000	0.74099	GGT	.	.	.	none		0.617	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950		T	73831821	C	T	73831821	3	4	221	1	0	0	0	0	1	0	0	0	16999	507	18	2	1694	2	UNC13D	17	73831821	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10	8721334	73831821	7363389	42	13400											
LAMA3	3909	hgsc.bcm.edu	37	chr18	21511115	21511115	+	Frame_Shift_Del	DEL	G	G	-																															atttttaaatctccacagacGtatatggatggtttactgca																								rs546328935		TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr18:21511115delG	ENST00000313654.9	+	65	8767	c.8526delG	c.(8524-8526)acgfs	p.T2842fs	LAMA3_ENST00000399516.3_Frame_Shift_Del_p.T2786fs|LAMA3_ENST00000269217.6_Frame_Shift_Del_p.T1233fs|LAMA3_ENST00000587184.1_Frame_Shift_Del_p.T1177fs|LAMA3_ENST00000588770.1_3'UTR	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2842	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)					CTCCACAGACGTATATGGATG	0.428																																					p.T2842fs		Atlas-INDEL	.											.	LAMA3	397	.	0			c.8525delC						PASS	.						110	110	110					18																	21511115		2203	4300	6503	SO:0001589	frameshift_variant	3909	exon65			.	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.8526delG	chr18.hg19:g.21511115delG	ENSP00000324532:p.Thr2842fs	52.0	0.0	0		49.0	13.0	0.265306	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Frame_Shift_Del	DEL	ENST00000313654.9	hg19	CCDS42419.1																																																																																			.	.	.	none		0.428	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		-	21511115	G	-	21511115	7	5	221	1	0	1	0	1	0	0	0	0	8614	1132	40	0	8959	0	LAMA3	18	21511115	Frame_Shift_Del	DEL	G	TCGA-MH-A560-01A-11D-A26P-10		21511115	56566133	43	13401	134	2									
LAMA3	3909	hgsc.bcm.edu	37	chr18	21511118	21511118	+	Frame_Shift_Del	DEL	T	T	-																															tttaaatctccacagacgtaTatggatggtttactgcatta																										TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr18:21511118delT	ENST00000313654.9	+	65	8770	c.8529delT	c.(8527-8529)tatfs	p.Y2843fs	LAMA3_ENST00000399516.3_Frame_Shift_Del_p.Y2787fs|LAMA3_ENST00000269217.6_Frame_Shift_Del_p.Y1234fs|LAMA3_ENST00000587184.1_Frame_Shift_Del_p.Y1178fs|LAMA3_ENST00000588770.1_3'UTR	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2843	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)					CACAGACGTATATGGATGGTT	0.428																																					p.Y2843fs		Atlas-INDEL	.											.	LAMA3	397	.	0			c.8528delA						PASS	.						112	111	111					18																	21511118		2203	4300	6503	SO:0001589	frameshift_variant	3909	exon65			.	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.8529delT	chr18.hg19:g.21511118delT	ENSP00000324532:p.Tyr2843fs	54.0	0.0	0		57.0	13.0	0.22807	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Frame_Shift_Del	DEL	ENST00000313654.9	hg19	CCDS42419.1																																																																																			.	.	.	none		0.428	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		-	21511118	T	-	21511118	7	5	221	1	0	1	0	1	0	0	0	0	8614	1413	49	0	8962	0	LAMA3	18	21511118	Frame_Shift_Del	DEL	T	TCGA-MH-A560-01A-11D-A26P-10	3	21511118	56566130	44	13402	134	2									
CREB3L3	84699	hgsc.bcm.edu	37	chr19	4171149	4171149	+	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	tgcagtccaccagcaagtcaGcccagacaggcacctgtgtc	10	6	10	15	0	1	1	1	0	0	1	3	1	2	1	4	1	3	3	4	1	1	0			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr19:4171149G>T	ENST00000078445.2	+	8	1099	c.952G>T	c.(952-954)Gcc>Tcc	p.A318S	CREB3L3_ENST00000595923.1_Missense_Mutation_p.A317S|CREB3L3_ENST00000252587.3_Intron|CREB3L3_ENST00000602147.1_Missense_Mutation_p.S282I|CREB3L3_ENST00000602257.1_Missense_Mutation_p.A316S	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	318					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)		CAGCAAGTCAGCCCAGACAGG	0.607																																					p.A318S		Atlas-SNP	.											.	CREB3L3	53	.	0			c.G952T						PASS	.						75	70	72					19																	4171149		2203	4300	6503	SO:0001583	missense	84699	exon8			AAGTCAGCCCAGA		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.952G>T	chr19.hg19:g.4171149G>T	ENSP00000078445:p.Ala318Ser	147.0	0.0	.		115.0	42.0	.	NM_032607	B2R7S6|B7ZL69|M0QYW7|Q6ZMC5|Q96TB9	Missense_Mutation	SNP	ENST00000078445.2	hg19	CCDS12121.1	.	.	.	.	.	.	.	.	.	.	G	10.83	1.462217	0.26248	.	.	ENSG00000060566	ENST00000078445;ENST00000381943	D	0.84800	-1.9	4.58	4.58	0.56647	.	0.130552	0.51477	D	0.000098	D	0.87172	0.6111	M	0.67569	2.06	0.52099	D	0.999947	D;P;P	0.62365	0.991;0.712;0.589	P;B;B	0.57204	0.815;0.396;0.223	D	0.84697	0.0726	10	0.26408	T	0.33	-0.2402	8.6838	0.34225	0.1062:0.0:0.8938:0.0	.	316;317;318	B7ZL69;Q68CJ9-2;Q68CJ9	.;.;CR3L3_HUMAN	S	318;276	ENSP00000078445:A318S	ENSP00000078445:A318S	A	+	1	0	CREB3L3	4122149	0.995000	0.38212	0.954000	0.39281	0.235000	0.25334	4.071000	0.57556	2.093000	0.63338	0.561000	0.74099	GCC	.	.	.	none		0.607	CREB3L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457922.1	NM_032607		T	4171149	G	T	4171149	3	4	221	1	0	0	0	0	1	0	0	0	3860	971	34	4	982	4	CREB3L3	19	4171149	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10		4171149	54957834	45	13403											
ZNF227	7770	hgsc.bcm.edu	37	chr19	44739325	44739325	+	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	agaaattacccttaggagagAaaccccatccatgtggtgag	14	8	10	9	0	0	3	0	1	0	2	1	5	1	4	4	2	2	0	4	2	4	2			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr19:44739325A>T	ENST00000313040.7	+	6	947	c.742A>T	c.(742-744)Aaa>Taa	p.K248*	ZNF227_ENST00000589005.1_Nonsense_Mutation_p.K197*|ZNF227_ENST00000391961.2_Nonsense_Mutation_p.K197*	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	248					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				CTTAGGAGAGAAACCCCATCC	0.428																																					p.K248X		Atlas-SNP	.											.	ZNF227	62	.	0			c.A742T						PASS	.						50	52	51					19																	44739325		2203	4300	6503	SO:0001587	stop_gained	7770	exon6			GGAGAGAAACCCC	AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"Zinc fingers, C2H2-type", "-"	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.742A>T	chr19.hg19:g.44739325A>T	ENSP00000321049:p.Lys248*	99.0	0.0	.		73.0	29.0	.	NM_182490	B3KRU7|B7Z5P9	Nonsense_Mutation	SNP	ENST00000313040.7	hg19	CCDS12636.1	.	.	.	.	.	.	.	.	.	.	A	37	6.426321	0.97559	.	.	ENSG00000131115	ENST00000313040;ENST00000328297;ENST00000391961;ENST00000418980	.	.	.	4.04	1.86	0.25419	.	.	.	.	.	.	.	.	.	.	.	0.23150	N	0.99822	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.6647	0.23035	0.7832:0.0:0.2168:0.0	.	.	.	.	X	248;205;197;227	.	ENSP00000321049:K248X	K	+	1	0	ZNF227	49431165	0.006000	0.16342	0.000000	0.03702	0.751000	0.42716	2.219000	0.42899	0.218000	0.20820	0.460000	0.39030	AAA	.	.	.	none		0.428	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490		T	44739325	A	T	44739325	4	4	221	1	0	0	0	0	0	1	0	0	17793	247	9	5	756	5	ZNF227	19	44739325	Nonsense_Mutation	SNP	A	TCGA-MH-A560-01A-11D-A26P-10	40568176	44739325	14389658	46	13404											
SIGLEC5	8778	hgsc.bcm.edu	37	chr19	52131213	52131213	+	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	cccggtattggagatgggggTggcgttcagggcaggggagc	6	7	21	7	2	1	1	1	0	0	1	1	3	1	2	1	8	1	3	1	8	1	3			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr19:52131213T>A	ENST00000534261.2	-	6	1270	c.871A>T	c.(871-873)Acc>Tcc	p.T291S	SIGLEC5_ENST00000599649.1_Missense_Mutation_p.T291S|SIGLEC5_ENST00000429354.3_Missense_Mutation_p.T291S|SIGLEC5_ENST00000222107.4_Missense_Mutation_p.T291S|SIGLEC5_ENST00000570106.2_Missense_Mutation_p.T291S			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5	291	Ig-like C2-type 2.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(9)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		GAGATGGGGGTGGCGTTCAGG	0.647																																					p.T291S		Atlas-SNP	.											.	SIGLEC5	67	.	0			c.A871T						PASS	.						64	71	69					19																	52131213		2203	4300	6503	SO:0001583	missense	8778	exon5			TGGGGGTGGCGTT	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.871A>T	chr19.hg19:g.52131213T>A	ENSP00000473238:p.Thr291Ser	82.0	0.0	.		93.0	37.0	.	NM_003830		Missense_Mutation	SNP	ENST00000534261.2	hg19	CCDS33088.1	.	.	.	.	.	.	.	.	.	.	T	3.867	-0.028769	0.07589	.	.	ENSG00000105501	ENST00000222107;ENST00000429354	T;T	0.13420	2.59;2.59	3.76	-6.36	0.01969	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.943120	0.02702	N	0.111846	T	0.04952	0.0133	N	0.11560	0.145	0.09310	N	1	B	0.32829	0.386	B	0.35931	0.214	T	0.26883	-1.0090	10	0.02654	T	1	.	1.2256	0.01932	0.4652:0.1053:0.2382:0.1914	.	291	O15389	SIGL5_HUMAN	S	291	ENSP00000222107:T291S;ENSP00000415200:T291S	ENSP00000222107:T291S	T	-	1	0	SIGLEC5	56823025	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-1.639000	0.02011	-1.347000	0.02208	0.383000	0.25322	ACC	.	.	.	none		0.647	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830		A	52131213	T	A	52131213	3	1	221	1	0	0	0	0	1	0	0	0	14324	1696	59	5	804	5	SIGLEC5	19	52131213	Missense_Mutation	SNP	T	TCGA-MH-A560-01A-11D-A26P-10	7391888	52131213	6997770	47	13405											
TGIF2	60436	hgsc.bcm.edu	37	chr20	35219589	35219589	+	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	agctggagtctcccaagcccCtggtgacccctggtagcaca	8	7	11	15	0	1	1	0	1	1	0	2	2	1	2	5	3	3	3	5	3	2	1			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr20:35219589C>A	ENST00000373874.2	+	3	668	c.469C>A	c.(469-471)Ctg>Atg	p.L157M	RP5-977B1.11_ENST00000561134.1_RNA|TGIF2_ENST00000373872.4_Missense_Mutation_p.L157M|TGIF2-C20orf24_ENST00000558530.1_Intron	NM_001199514.1|NM_001199515.1	NP_001186443.1|NP_001186444.1	Q9GZN2	TGIF2_HUMAN	TGFB-induced factor homeobox 2	157	Repressive function.				gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nodal signaling pathway (GO:0038092)|positive regulation of neuron differentiation (GO:0045666)|regulation of gastrulation (GO:0010470)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(3)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	14	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)				TCCCAAGCCCCTGGTGACCCC	0.632																																					p.L157M		Atlas-SNP	.											.	TGIF2	26	.	0			c.C469A						PASS	.						36	42	40					20																	35219589		2203	4300	6503	SO:0001583	missense	60436	exon3			AAGCCCCTGGTGA	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.469C>A	chr20.hg19:g.35219589C>A	ENSP00000362981:p.Leu157Met	89.0	0.0	.		53.0	30.0	.	NM_021809	B2R9U3|E1P5T9|H0YNI0	Missense_Mutation	SNP	ENST00000373874.2	hg19	CCDS13278.1	.	.	.	.	.	.	.	.	.	.	C	13.95	2.390012	0.42410	.	.	ENSG00000118707	ENST00000373874;ENST00000373872	T;T	0.65732	-0.17;-0.17	5.57	2.49	0.30216	.	3.072470	0.00622	N	0.000451	T	0.50718	0.1632	N	0.14661	0.345	0.80722	D	1	P	0.47106	0.89	P	0.44990	0.466	T	0.35822	-0.9773	10	0.46703	T	0.11	-14.2668	5.1002	0.14754	0.1452:0.6315:0.0:0.2233	.	157	Q9GZN2	TGIF2_HUMAN	M	157	ENSP00000362981:L157M;ENSP00000362979:L157M	ENSP00000362979:L157M	L	+	1	2	TGIF2	34653003	0.043000	0.20138	0.816000	0.32577	0.586000	0.36452	0.322000	0.19576	0.262000	0.21774	0.561000	0.74099	CTG	.	.	.	none		0.632	TGIF2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079004.2	NM_021809		A	35219589	C	A	35219589	3	1	221	1	0	0	0	0	1	0	0	0	15838	680	24	4	475	4	TGIF2	20	35219589	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10		35219589	27805931	48	13406											
HNF4A	3172	hgsc.bcm.edu	37	chr20	43052875	43052876	+	Frame_Shift_Ins	INS	-	-	C																															ccaagattgacaacctgttgINScaggagatgctgctgggagg																										TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr20:43052875_43052876insC	ENST00000316099.4	+	8	1199_1200	c.1110_1111insC	c.(1111-1113)cagfs	p.Q371fs	HNF4A_ENST00000457232.1_Frame_Shift_Ins_p.Q349fs|HNF4A_ENST00000609795.1_Frame_Shift_Ins_p.Q349fs|AL132772.1_ENST00000581483.1_RNA|HNF4A_ENST00000415691.2_Frame_Shift_Ins_p.Q371fs|HNF4A_ENST00000443598.2_Frame_Shift_Ins_p.Q371fs|HNF4A_ENST00000316673.4_Frame_Shift_Ins_p.Q349fs	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	371					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)			ACAACCTGTTGCAGGAGATGCT	0.609																																					p.L370fs	Colon(79;2 1269 8820 14841 52347)	Atlas-Indel,Pindel	.											.	HNF4A	150	.	0			c.1110_1111insC						PASS	.																																			SO:0001589	frameshift_variant	3172	exon8			.	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.1111dupC	chr20.hg19:g.43052876_43052876dupC	ENSP00000312987:p.Gln371fs	185.0	0.0	0		148.0	50.0	0.337838	NM_178849	A5JW41|B2RPP8|O00659|O00723|Q14540|Q5QPB8|Q6B4V5|Q6B4V6|Q6B4V7|Q92653|Q92654|Q92655|Q99864|Q9NQH0	Frame_Shift_Ins	INS	ENST00000316099.4	hg19	CCDS13330.1																																																																																			.	.	.	none		0.609	HNF4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079363.3			C	43052876	-	C	43052875	7	5	221	1	0	1	1	0	0	0	0	0	7260	1310	46	0	1193	0	HNF4A	20	43052875	Frame_Shift_Ins	INS	-	TCGA-MH-A560-01A-11D-A26P-10	7833286	43052875	19972645	49	13407											
SUSD2	56241	hgsc.bcm.edu	37	chr22	24583996	24583996	+	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	caacaggtacctggcgggttCcaccatctacttccactgtg	8	10	9	14	1	1	0	0	0	1	0	3	0	3	0	4	3	3	2	4	3	3	4			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr22:24583996C>A	ENST00000358321.3	+	13	2495	c.2234C>A	c.(2233-2235)tCc>tAc	p.S745Y		NM_019601.3	NP_062547.1	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2	745	Sushi. {ECO:0000255|PROSITE- ProRule:PRU00302}.				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						CTGGCGGGTTCCACCATCTAC	0.642																																					p.S745Y		Atlas-SNP	.											.	SUSD2	68	.	0			c.C2234A						PASS	.						80	82	81					22																	24583996		2203	4300	6503	SO:0001583	missense	56241	exon13			CGGGTTCCACCAT	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.2234C>A	chr22.hg19:g.24583996C>A	ENSP00000351075:p.Ser745Tyr	472.0	0.0	.		357.0	138.0	.	NM_019601	Q9H5Y6	Missense_Mutation	SNP	ENST00000358321.3	hg19	CCDS13824.1	.	.	.	.	.	.	.	.	.	.	C	17.35	3.366350	0.61513	.	.	ENSG00000099994	ENST00000358321	T	0.68181	-0.31	4.75	4.75	0.60458	Complement control module (2);Sushi/SCR/CCP (3);	0.119454	0.64402	D	0.000016	D	0.83403	0.5247	M	0.89414	3.03	0.41536	D	0.988484	D	0.76494	0.999	D	0.77004	0.989	D	0.86729	0.1947	10	0.72032	D	0.01	-53.0137	13.6888	0.62533	0.0:1.0:0.0:0.0	.	745	Q9UGT4	SUSD2_HUMAN	Y	745	ENSP00000351075:S745Y	ENSP00000351075:S745Y	S	+	2	0	SUSD2	22913996	0.999000	0.42202	0.998000	0.56505	0.451000	0.32288	4.155000	0.58131	2.383000	0.81215	0.505000	0.49811	TCC	.	.	.	none		0.642	SUSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320088.1	NM_019601		A	24583996	C	A	24583996	3	1	221	1	0	0	0	0	1	0	0	0	15420	855	30	4	2284	4	SUSD2	22	24583996	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10		24583996	26720570	50	13408											
CACNG2	10369	hgsc.bcm.edu	37	chr22	37098581	37098581	+	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	aggcagcgaaagcaccaacgGtggttaaaagcatttgaaca	16	6	11	8	2	0	1	0	1	0	0	0	2	0	1	1	3	5	4	1	3	5	2			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chr22:37098581G>T	ENST00000300105.6	-	1	1022	c.41C>A	c.(40-42)aCc>aAc	p.T14N	RP1-293L6.1_ENST00000430281.1_RNA	NM_006078.3	NP_006069.1	Q9Y698	CCG2_HUMAN	calcium channel, voltage-dependent, gamma subunit 2	14					membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|neuromuscular junction development (GO:0007528)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	18						AGCACCAACGGTGGTTAAAAG	0.488																																					p.T14N		Atlas-SNP	.											.	CACNG2	43	.	0			c.C41A						PASS	.						154	142	146					22																	37098581		2203	4300	6503	SO:0001583	missense	10369	exon1			CCAACGGTGGTTA	AF096322	CCDS13931.1	22q13.1	2006-08-01			ENSG00000166862	ENSG00000166862		"Calcium channel subunits"	1406	protein-coding gene	gene with protein product		602911					Standard	NM_006078		Approved	stargazin, MGC138502, MGC138504	uc003aps.2	Q9Y698	OTTHUMG00000030612	ENST00000300105.6:c.41C>A	chr22.hg19:g.37098581G>T	ENSP00000300105:p.Thr14Asn	104.0	0.0	.		149.0	56.0	.	NM_006078	Q2M1M1|Q5TGT3|Q9UGZ7	Missense_Mutation	SNP	ENST00000300105.6	hg19	CCDS13931.1	.	.	.	.	.	.	.	.	.	.	g	19.64	3.865847	0.71949	.	.	ENSG00000166862	ENST00000300105	D	0.89681	-2.55	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	D	0.94971	0.8373	M	0.84948	2.725	0.80722	D	1	D	0.62365	0.991	D	0.76071	0.987	D	0.95765	0.8804	10	0.72032	D	0.01	-20.8031	17.8661	0.88795	0.0:0.0:1.0:0.0	.	14	Q9Y698	CCG2_HUMAN	N	14	ENSP00000300105:T14N	ENSP00000300105:T14N	T	-	2	0	CACNG2	35428527	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.265000	0.95647	2.192000	0.70111	0.546000	0.68486	ACC	.	.	.	none		0.488	CACNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075500.2			T	37098581	G	T	37098581	3	4	221	1	0	0	0	0	1	0	0	0	2559	1261	44	4	946	4	CACNG2	22	37098581	Missense_Mutation	SNP	G	TCGA-MH-A560-01A-11D-A26P-10	12514585	37098581	14205985	51	13409											
FAM47A	158724	hgsc.bcm.edu	37	chrX	34148936	34148936	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgagtggagactggacctcCgacgtgtcttgggatgttcc	6	10	15	10	3	1	1	0	0	1	1	3	6	3	3	3	3	0	1	3	3	0	2			TCGA-MH-A560-01A-11D-A26P-10	TCGA-MH-A560-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cf5deb22-f7eb-409d-a0e4-882716199c39	8fa7c1a8-e64c-4ee8-9012-187aa9da1210	g.chrX:34148936C>T	ENST00000346193.3	-	1	1511	c.1460G>A	c.(1459-1461)cGg>cAg	p.R487Q		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	487								p.R487Q(1)		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						ACTGGACCTCCGACGTGTCTT	0.642																																					p.R487Q		Atlas-SNP	.											.	FAM47A	249	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1460A						PASS	.						47	54	51					X																	34148936		2192	4286	6478	SO:0001583	missense	158724	exon1			GACCTCCGACGTG	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.1460G>A	chrX.hg19:g.34148936C>T	ENSP00000345029:p.Arg487Gln	91.0	0.0	.		70.0	4.0	.	NM_203408	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	hg19	CCDS43926.1	.	.	.	.	.	.	.	.	.	.	c	9.489	1.100058	0.20552	.	.	ENSG00000185448	ENST00000346193	T	0.16196	2.36	0.446	0.446	0.16602	.	.	.	.	.	T	0.10380	0.0254	N	0.24115	0.695	0.09310	N	1	D	0.62365	0.991	P	0.44811	0.461	T	0.23762	-1.0179	8	0.13470	T	0.59	.	.	.	.	.	487	Q5JRC9	FA47A_HUMAN	Q	487	ENSP00000345029:R487Q	ENSP00000345029:R487Q	R	-	2	0	FAM47A	34058857	0.022000	0.18835	0.006000	0.13384	0.016000	0.09150	0.010000	0.13242	0.435000	0.26365	0.183000	0.17082	CGG	.	.	.	none		0.642	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		T	34148936	C	T	34148936	3	4	221	1	0	0	0	0	1	0	0	0	5576	652	23	1	919	1	FAM47A	23	34148936	Missense_Mutation	SNP	C	TCGA-MH-A560-01A-11D-A26P-10		34148936	121121624	52	13410											
RBP7	116362	hgsc.bcm.edu	37	chr1	10068242	10068242	+	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	ttcatgcagagtttggttatCtgggacaatgacaggctcac	10	12	11	8	0	3	2	2	1	1	1	3	3	3	3	0	3	1	4	0	3	2	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:10068242C>G	ENST00000294435.7	+	3	307	c.264C>G	c.(262-264)atC>atG	p.I88M		NM_052960.2	NP_443192.1	Q96R05	RET7_HUMAN	retinol binding protein 7, cellular	88						cytoplasm (GO:0005737)	retinal binding (GO:0016918)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			endometrium(1)|large_intestine(1)	2		all_lung(284;0.000407)|Renal(390;0.000469)|Lung NSC(185;0.000577)|Colorectal(325;0.0062)|Breast(348;0.00686)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.5e-08)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;0.000249)|BRCA - Breast invasive adenocarcinoma(304;0.000302)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00856)|READ - Rectum adenocarcinoma(331;0.0419)	Vitamin A(DB00162)	GTTTGGTTATCTGGGACAATG	0.468																																					p.I88M		Atlas-SNP	.											.	RBP7	11	.	0			c.C264G						PASS	.						112	104	107					1																	10068242		2203	4300	6503	SO:0001583	missense	116362	exon3			GGTTATCTGGGAC	AF399927	CCDS109.1	1p36.22	2013-03-01			ENSG00000162444	ENSG00000162444		"Fatty acid binding protein family"	30316	protein-coding gene	gene with protein product		608604				12177003	Standard	NM_052960		Approved	CRBPIV	uc001aqq.3	Q96R05	OTTHUMG00000001798	ENST00000294435.7:c.264C>G	chr1.hg19:g.10068242C>G	ENSP00000294435:p.Ile88Met	194.0	0.0	.		148.0	15.0	.	NM_052960	B2R517|Q5SWJ4	Missense_Mutation	SNP	ENST00000294435.7	hg19	CCDS109.1	.	.	.	.	.	.	.	.	.	.	C	6.871	0.529995	0.13127	.	.	ENSG00000162444	ENST00000315901;ENST00000294435	T	0.07688	3.17	4.07	0.988	0.19796	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.599344	0.15592	N	0.254321	T	0.07143	0.0181	N	0.19112	0.55	0.09310	N	0.99999	B	0.23650	0.089	B	0.37601	0.254	T	0.37526	-0.9702	10	0.87932	D	0	.	6.2468	0.20823	0.1332:0.6539:0.1302:0.0827	.	88	Q96R05	RET7_HUMAN	M	135;88	ENSP00000294435:I88M	ENSP00000294435:I88M	I	+	3	3	RBP7	9990829	0.000000	0.05858	0.746000	0.31095	0.291000	0.27294	-1.010000	0.03656	0.945000	0.37605	0.644000	0.83932	ATC	.	.	.	none		0.468	RBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005027.2	NM_052960		G	10068242	C	G	10068242	3	3	222	1	0	0	0	0	1	0	0	0	13173	903	32	4	274	4	RBP7	1	10068242	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10		10068242	239182379	1	13411											
PRDM2	7799	hgsc.bcm.edu	37	chr1	14108836	14108836	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaacagcaaccaccgcagaCggacagcggatgcggagatt	13	4	13	11	4	0	2	0	0	0	2	0	5	0	4	2	3	5	3	2	3	2	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:14108836C>T	ENST00000235372.7	+	8	5402	c.4546C>T	c.(4546-4548)Cgg>Tgg	p.R1516W	PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000343137.4_Missense_Mutation_p.R1315W|PRDM2_ENST00000413440.1_Missense_Mutation_p.R1315W|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000311066.5_Missense_Mutation_p.R1516W	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	1516					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)		CCACCGCAGACGGACAGCGGA	0.512																																					p.R1516W		Atlas-SNP	.											.	PRDM2	147	.	0			c.C4546T						PASS	.						72	82	79					1																	14108836		2203	4300	6503	SO:0001583	missense	7799	exon8			CGCAGACGGACAG	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.4546C>T	chr1.hg19:g.14108836C>T	ENSP00000235372:p.Arg1516Trp	121.0	0.0	.		107.0	39.0	.	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Missense_Mutation	SNP	ENST00000235372.7	hg19	CCDS150.1	.	.	.	.	.	.	.	.	.	.	C	16.45	3.127315	0.56721	.	.	ENSG00000116731	ENST00000235372;ENST00000311066;ENST00000400800;ENST00000413440;ENST00000343137	T;T;T;T	0.02032	4.6;4.49;4.49;4.49	5.98	4.06	0.47325	.	0.060868	0.64402	D	0.000003	T	0.09598	0.0236	M	0.69823	2.125	0.49051	D	0.999741	D;B;B	0.89917	1.0;0.14;0.445	D;B;B	0.73708	0.981;0.015;0.034	T	0.00638	-1.1632	10	0.87932	D	0	.	8.67	0.34145	0.1498:0.7733:0.0:0.0769	.	1374;1516;1516	Q5THJ0;Q13029;Q13029-2	.;PRDM2_HUMAN;.	W	1516;1516;1516;1315;1315	ENSP00000235372:R1516W;ENSP00000312352:R1516W;ENSP00000411103:R1315W;ENSP00000341621:R1315W	ENSP00000235372:R1516W	R	+	1	2	PRDM2	13981423	0.364000	0.24997	0.793000	0.32043	0.983000	0.72400	0.980000	0.29513	0.815000	0.34398	0.591000	0.81541	CGG	.	.	.	none		0.512	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231		T	14108836	C	T	14108836	3	4	222	1	0	0	0	0	1	0	0	0	12468	527	19	1	4572	1	PRDM2	1	14108836	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	4040594	14108836	235141785	2	13412											
E2F2	1870	hgsc.bcm.edu	37	chr1	23848337	23848337	+	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	ccaggcactcacacccactgGatgttgttcttggccttctt	6	13	8	14	0	3	0	1	0	2	0	3	1	3	1	3	3	0	3	3	3	0	5			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:23848337G>C	ENST00000361729.2	-	3	996	c.570C>G	c.(568-570)atC>atG	p.I190M	E2F2_ENST00000487237.1_5'Flank	NM_004091.3	NP_004082.1	Q14209	E2F2_HUMAN	E2F transcription factor 2	190					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)		ACACCCACTGGATGTTGTTCT	0.612																																					p.I190M		Atlas-SNP	.											.	E2F2	31	.	0			c.C570G						PASS	.						123	104	110					1																	23848337		2203	4300	6503	SO:0001583	missense	1870	exon3			CCACTGGATGTTG	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.570C>G	chr1.hg19:g.23848337G>C	ENSP00000355249:p.Ile190Met	156.0	0.0	.		118.0	45.0	.	NM_004091	B2R9W1|Q7Z6H1	Missense_Mutation	SNP	ENST00000361729.2	hg19	CCDS236.1	.	.	.	.	.	.	.	.	.	.	G	17.41	3.382364	0.61845	.	.	ENSG00000007968	ENST00000361729	T	0.15256	2.44	5.35	4.42	0.53409	Transcription factor E2F/dimerisation partner (TDP) (1);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.058637	0.64402	D	0.000003	T	0.48840	0.1522	M	0.93241	3.395	0.58432	D	0.999998	D	0.56968	0.978	D	0.65323	0.934	T	0.60865	-0.7178	10	0.87932	D	0	-24.1713	11.9214	0.52793	0.0:0.0:0.6839:0.3161	.	190	Q14209	E2F2_HUMAN	M	190	ENSP00000355249:I190M	ENSP00000355249:I190M	I	-	3	3	E2F2	23720924	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.406000	0.44557	1.212000	0.43366	0.591000	0.81541	ATC	.	.	.	none		0.612	E2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008885.1	NM_004091		C	23848337	G	C	23848337	3	2	222	1	0	0	0	0	1	0	0	0	4869	1164	41	4	763	4	E2F2	1	23848337	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	9739501	23848337	225402284	3	13413											
CD52	1043	hgsc.bcm.edu	37	chr1	26646661	26646661	+	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	atcccacttctcctcctacaGatacaaactggactctcagg	11	10	5	15	0	2	1	1	0	2	1	6	2	4	2	3	2	3	0	3	2	3	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:26646661G>T	ENST00000374213.2	+	2	115		c.e2-1		UBXN11_ENST00000374217.2_5'Flank|UBXN11_ENST00000374222.1_5'Flank	NM_001803.2	NP_001794.2	P31358	CD52_HUMAN	CD52 molecule						positive regulation of cytosolic calcium ion concentration (GO:0007204)|respiratory burst (GO:0045730)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				large_intestine(1)	1		all_cancers(24;5.02e-24)|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;7.56e-28)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0137)|READ - Rectum adenocarcinoma(331;0.0649)	Alemtuzumab(DB00087)	TCCTCCTACAGATACAAACTG	0.488																																					.		Atlas-SNP	.											.	CD52	7	.	0			c.55-1G>T						PASS	.						108	108	108					1																	26646661		2203	4300	6503	SO:0001630	splice_region_variant	1043	exon2			CCTACAGATACAA		CCDS30647.1	1p36	2008-02-05	2006-03-28	2005-02-07	ENSG00000169442	ENSG00000169442		"CD molecules"	1804	protein-coding gene	gene with protein product		114280	"CD52 antigen (CAMPATH-1 antigen)"	CDW52		1711975	Standard	NM_001803		Approved		uc001bmc.3	P31358	OTTHUMG00000003491	ENST00000374213.2:c.55-1G>T	chr1.hg19:g.26646661G>T		52.0	0.0	.		42.0	6.0	.	NM_001803	Q5T138|Q9BW46	Splice_Site	SNP	ENST00000374213.2	hg19	CCDS30647.1	.	.	.	.	.	.	.	.	.	.	G	13.65	2.299548	0.40694	.	.	ENSG00000169442	ENST00000374213	.	.	.	3.6	3.6	0.41247	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.042	0.47835	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CD52	26519248	0.969000	0.33509	0.935000	0.37517	0.213000	0.24496	3.220000	0.51207	2.312000	0.78011	0.655000	0.94253	.	.	.	.	none		0.488	CD52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009704.1	NM_001803	Intron	T	26646661	G	T	26646661	5	4	222	1	0	0	0	0	0	0	1	0	3024	956	33	4	60	4	CD52	1	26646661	Splice_Site	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	2798324	26646661	222603960	4	13414											
COL8A2	1296	hgsc.bcm.edu	37	chr1	36564106	36564106	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctaggcccctggtcacctcgAatgccaggcactcctggggg	6	7	13	15	1	1	0	1	0	0	0	3	1	2	0	5	5	1	1	5	5	2	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:36564106A>G	ENST00000397799.1	-	4	1400	c.1176T>C	c.(1174-1176)atT>atC	p.I392I	COL8A2_ENST00000303143.4_Silent_p.I392I|COL8A2_ENST00000481785.1_Silent_p.I327I			P25067	CO8A2_HUMAN	collagen, type VIII, alpha 2	392	Triple-helical region.				angiogenesis (GO:0001525)|camera-type eye morphogenesis (GO:0048593)|collagen catabolic process (GO:0030574)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			NS(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GGTCACCTCGAATGCCAGGCA	0.692																																					p.I392I		Atlas-SNP	.											.	COL8A2	41	.	0			c.T1176C						PASS	.						9	10	10					1																	36564106		2188	4274	6462	SO:0001819	synonymous_variant	1296	exon2			ACCTCGAATGCCA	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.1176T>C	chr1.hg19:g.36564106A>G		187.0	0.0	.		108.0	32.0	.	NM_005202	Q5JV31|Q8TEJ5	Silent	SNP	ENST00000397799.1	hg19	CCDS403.1																																																																																			.	.	.	none		0.692	COL8A2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313674.1	NM_005202		G	36564106	A	G	36564106	2	3	222	1	0	0	0	0	0	0	0	1	3708	242	9	3		3	COL8A2	1	36564106	Silent	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	9917445	36564106	212686515	5	13415											
CDC20	991	hgsc.bcm.edu	37	chr1	43826814	43826814	+	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	gtagcatggtgtccctggcaGtccaatgtcctggcaacagg	8	9	13	11	0	0	0	0	0	0	0	3	0	3	0	3	4	2	4	3	4	3	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:43826814G>C	ENST00000372462.1	+	8	1304	c.1101G>C	c.(1099-1101)caG>caC	p.Q367H	ELOVL1_ENST00000470769.1_5'Flank|CDC20_ENST00000310955.6_Missense_Mutation_p.Q367H|RP1-92O14.3_ENST00000424948.1_RNA			Q12834	CDC20_HUMAN	cell division cycle 20	367					activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell cycle (GO:0007049)|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 cell proliferation (GO:0008284)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein ubiquitination (GO:0016567)|regulation of dendrite development (GO:0050773)|regulation of meiosis (GO:0040020)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|spindle (GO:0005819)	enzyme binding (GO:0019899)|protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	15	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GTCCCTGGCAGTCCAATGTCC	0.572																																					p.Q367H	Esophageal Squamous(137;1154 1759 10362 10401 46925)	Atlas-SNP	.											.	CDC20	34	.	0			c.G1101C						PASS	.						85	76	79					1																	43826814		2203	4300	6503	SO:0001583	missense	991	exon9			CTGGCAGTCCAAT	U05340	CCDS484.1	1p34.1	2013-01-17	2013-01-17		ENSG00000117399	ENSG00000117399		"WD repeat domain containing"	1723	protein-coding gene	gene with protein product		603618	"CDC20 (cell division cycle 20, S. cerevisiae, homolog)", "CDC20 cell division cycle 20 homolog (S. cerevisiae)", "cell division cycle 20 homolog (S. cerevisiae)"			7513050, 9353311	Standard	NM_001255		Approved	p55CDC, CDC20A	uc001cix.3	Q12834	OTTHUMG00000007420	ENST00000372462.1:c.1101G>C	chr1.hg19:g.43826814G>C	ENSP00000361540:p.Gln367His	118.0	0.0	.		82.0	32.0	.	NM_001255	B2R6Z6|D3DPJ1|Q5JUY4|Q9BW56|Q9UQI9	Missense_Mutation	SNP	ENST00000372462.1	hg19	CCDS484.1	.	.	.	.	.	.	.	.	.	.	G	15.62	2.886198	0.51908	.	.	ENSG00000117399	ENST00000437896;ENST00000310955;ENST00000372462	T;T	0.29397	1.57;1.57	5.73	0.649	0.17806	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	0.27098	0.0664	L	0.33668	1.02	0.58432	D	0.999997	P	0.38992	0.653	P	0.45099	0.469	T	0.04481	-1.0948	10	0.62326	D	0.03	-17.7133	9.4478	0.38708	0.4049:0.0:0.5951:0.0	.	367	Q12834	CDC20_HUMAN	H	343;367;367	ENSP00000308450:Q367H;ENSP00000361540:Q367H	ENSP00000308450:Q367H	Q	+	3	2	CDC20	43599401	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	3.104000	0.50306	0.090000	0.17273	-0.291000	0.09656	CAG	.	.	.	none		0.572	CDC20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019488.1	NM_001255		C	43826814	G	C	43826814	3	2	222	1	0	0	0	0	1	0	0	0	3061	1020	36	4	1131	4	CDC20	1	43826814	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	7262708	43826814	205423807	6	13416											
KLF17	128209	hgsc.bcm.edu	37	chr1	44595144	44595144	+	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	tttcctcacagcgcagagatGctggggtcccctttggtgtc	5	12	12	12	1	1	1	1	0	0	1	4	2	3	1	3	3	2	2	3	3	0	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:44595144G>T	ENST00000372299.3	+	2	259	c.201G>T	c.(199-201)atG>atT	p.M67I	KLF17_ENST00000476802.1_3'UTR	NM_173484.3	NP_775755.3	Q5JT82	KLF17_HUMAN	Kruppel-like factor 17	67					gamete generation (GO:0007276)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|central_nervous_system(1)|large_intestine(1)|lung(6)|ovary(3)|prostate(1)|skin(2)|stomach(1)	18	Acute lymphoblastic leukemia(166;0.155)					GCGCAGAGATGCTGGGGTCCC	0.547																																					p.M67I		Atlas-SNP	.											.	KLF17	92	.	0			c.G201T						PASS	.						77	68	71					1																	44595144		2203	4300	6503	SO:0001583	missense	128209	exon2			AGAGATGCTGGGG	BC049844	CCDS508.1	1p34.1	2011-11-15	2006-02-17	2006-02-17	ENSG00000171872	ENSG00000171872		"Zinc fingers, C2H2-type", "Kruppel-like transcription factors"	18830	protein-coding gene	gene with protein product		609602	"zinc finger protein 393"	ZNF393		16460907	Standard	NM_173484		Approved	Zfp393, FLJ40160	uc001clp.3	Q5JT82	OTTHUMG00000009664	ENST00000372299.3:c.201G>T	chr1.hg19:g.44595144G>T	ENSP00000361373:p.Met67Ile	136.0	0.0	.		112.0	5.0	.	NM_173484	Q86VQ7|Q8N805	Missense_Mutation	SNP	ENST00000372299.3	hg19	CCDS508.1	.	.	.	.	.	.	.	.	.	.	G	12.28	1.890870	0.33348	.	.	ENSG00000171872	ENST00000372299	T	0.07327	3.2	4.58	3.66	0.41972	.	0.565978	0.16022	N	0.233274	T	0.05960	0.0155	N	0.19112	0.55	0.09310	N	1	B	0.26809	0.16	B	0.19946	0.027	T	0.30179	-0.9987	10	0.49607	T	0.09	.	10.2955	0.43620	0.0:0.0:0.804:0.196	.	67	Q5JT82	KLF17_HUMAN	I	67	ENSP00000361373:M67I	ENSP00000361373:M67I	M	+	3	0	KLF17	44367731	0.376000	0.25098	0.006000	0.13384	0.003000	0.03518	1.800000	0.38833	1.520000	0.48965	0.650000	0.86243	ATG	.	.	.	none		0.547	KLF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026646.1	NM_173484		T	44595144	G	T	44595144	3	4	222	1	0	0	0	0	1	0	0	0	8352	1319	46	4	207	4	KLF17	1	44595144	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	768330	44595144	204655477	7	13417											
GPBP1L1	60313	hgsc.bcm.edu	37	chr1	46124748	46124748	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccaagcaggaacaaaatcAtgctgcgccatttaggtcca	14	7	9	11	1	1	0	1	0	0	0	2	1	2	1	3	2	5	2	3	2	5	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:46124748A>G	ENST00000290795.3	-	3	1233	c.12T>C	c.(10-12)caT>caC	p.H4H	GPBP1L1_ENST00000355105.3_Silent_p.H4H			Q9HC44	GPBL1_HUMAN	GC-rich promoter binding protein 1-like 1	4					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)					GAACAAAATCATGCTGCGCCA	0.428																																					p.H4H		Atlas-SNP	.											.	GPBP1L1	43	.	0			c.T12C						PASS	.						146	137	140					1																	46124748		2203	4300	6503	SO:0001819	synonymous_variant	60313	exon4			AAAATCATGCTGC		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.12T>C	chr1.hg19:g.46124748A>G		97.0	0.0	.		89.0	13.0	.	NM_021639	D3DQ10|Q9H751	Silent	SNP	ENST00000290795.3	hg19	CCDS528.1																																																																																			.	.	.	none		0.428	GPBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098375.1	NM_021639		G	46124748	A	G	46124748	2	3	222	1	0	0	0	0	0	0	0	1	6603	214	8	3		3	GPBP1L1	1	46124748	Silent	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	1529604	46124748	203125873	8	13418											
AGBL4	84871	hgsc.bcm.edu	37	chr1	48999847	48999847	+	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	tcccaggactccgtgtctttAaaaaggggttgaagggtctt	9	12	12	8	1	2	1	0	1	2	0	4	2	4	2	2	4	0	1	2	4	4	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:48999847A>G	ENST00000371839.1	-	14	1626	c.1510T>C	c.(1510-1512)Taa>Caa	p.*504Q	AGBL4_ENST00000334103.7_Nonstop_Mutation_p.*228Q	NM_032785.3	NP_116174.3	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4	0					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)		CCGTGTCTTTAAAAAGGGGTT	0.507																																					p.X504Q		Atlas-SNP	.											.	AGBL4	54	.	0			c.T1510C						PASS	.						168	152	157					1																	48999847		692	1591	2283	SO:0001578	stop_lost	84871	exon14			GTCTTTAAAAAGG	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.1510T>C	chr1.hg19:g.48999847A>G	ENSP00000360905:p.*504Gluext*27	179.0	0.0	.		156.0	20.0	.	NM_032785	B3KT26|B4DG37	Missense_Mutation	SNP	ENST00000371839.1	hg19	CCDS44137.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.7|21.7	4.181371|4.181371	0.78677|0.78677	.|.	.|.	ENSG00000186094|ENSG00000186094	ENST00000411952|ENST00000371839;ENST00000334103	.|.	.|.	.|.	5.35|5.35	5.35|5.35	0.76521|0.76521	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.18873|0.18873	N|N	0.999988|0.999988	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	11.9|11.9	0.52678|0.52678	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|.	.|.	.|.	.|Q	-1|504;228	.|.	.|.	.|X	-|-	.|1	.|0	AGBL4|AGBL4	48772434|48772434	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.851000|0.851000	0.48451|0.48451	3.026000|3.026000	0.49689|0.49689	2.371000|2.371000	0.80710|0.80710	0.533000|0.533000	0.62120|0.62120	.|TAA	.	.	.	none		0.507	AGBL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021346.4	NM_032785		G	48999847	A	G	48999847	4	3	222	1	0	0	0	0	0	0	0	0	377	375	13	3	5	3	AGBL4	1	48999847	Nonstop_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	2875099	48999847	200250774	9	13419											
FNBP1L	54874	hgsc.bcm.edu	37	chr1	93965136	93965136	+	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	aacagaactatgcgaaacaaTtgaggtaagttaattttttt	16	14	7	4	1	0	2	0	1	0	1	0	3	0	2	0	1	4	2	0	1	7	7			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:93965136T>A	ENST00000271234.7	+	2	287	c.136T>A	c.(136-138)Ttg>Atg	p.L46M	FNBP1L_ENST00000604705.1_Missense_Mutation_p.L46M|FNBP1L_ENST00000260506.8_Missense_Mutation_p.L46M|FNBP1L_ENST00000370253.2_Missense_Mutation_p.L46M|FNBP1L_ENST00000370256.4_Missense_Mutation_p.L46M	NM_001164473.2	NP_001157945.1	Q5T0N5	FBP1L_HUMAN	formin binding protein 1-like	46	F-BAR domain. {ECO:0000250}.|FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				autophagy (GO:0006914)|clathrin-mediated endocytosis (GO:0072583)|membrane budding (GO:0006900)|membrane invagination (GO:0010324)|membrane tubulation (GO:0097320)|positive regulation of filopodium assembly (GO:0051491)|vesicle organization (GO:0016050)|vesicle transport along actin filament (GO:0030050)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			breast(2)|kidney(2)|large_intestine(4)|lung(2)|urinary_tract(1)	11		all_lung(203;0.00206)|Lung NSC(277;0.00902)|Melanoma(281;0.155)		all cancers(265;0.00666)|GBM - Glioblastoma multiforme(16;0.0378)|Epithelial(280;0.111)		TGCGAAACAATTGAGGTAAGT	0.308																																					p.L46M		Atlas-SNP	.											.	FNBP1L	56	.	0			c.T136A						PASS	.						46	44	45					1																	93965136		1815	4062	5877	SO:0001583	missense	54874	exon2			AAACAATTGAGGT		CCDS53343.1, CCDS53344.1, CCDS60192.1	1p22.1	2008-02-05	2004-11-16	2004-11-17	ENSG00000137942	ENSG00000137942			20851	protein-coding gene	gene with protein product		608848	"chromosome 1 open reading frame 39"	C1orf39		14654988	Standard	NM_017737		Approved	TOCA1, FLJ20275	uc010otk.2	Q5T0N5	OTTHUMG00000010863	ENST00000271234.7:c.136T>A	chr1.hg19:g.93965136T>A	ENSP00000271234:p.Leu46Met	91.0	0.0	.		97.0	44.0	.	NM_001164473	J3QSS4|Q5T0N6|Q6B097|Q6P653|Q6R4Q4|Q9NXG1	Missense_Mutation	SNP	ENST00000271234.7	hg19	CCDS53343.1	.	.	.	.	.	.	.	.	.	.	T	18.19	3.568848	0.65765	.	.	ENSG00000137942	ENST00000370256;ENST00000271234;ENST00000260506;ENST00000370253	T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21	5.55	2.05	0.26809	.	0.000000	0.85682	D	0.000000	T	0.69223	0.3087	M	0.84326	2.69	0.80722	D	1	D;P	0.54207	0.965;0.938	P;P	0.61328	0.887;0.855	T	0.69847	-0.5034	10	0.54805	T	0.06	-7.6767	6.8376	0.23945	0.0:0.465:0.0:0.535	.	46;46	Q5T0N5-4;Q5T0N5-3	.;.	M	46	ENSP00000359278:L46M;ENSP00000271234:L46M;ENSP00000260506:L46M;ENSP00000359275:L46M	ENSP00000260506:L46M	L	+	1	2	FNBP1L	93737724	0.711000	0.27906	0.997000	0.53966	0.913000	0.54294	0.165000	0.16564	0.401000	0.25424	-0.605000	0.04089	TTG	.	.	.	none		0.308	FNBP1L-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_017737		A	93965136	T	A	93965136	3	1	222	1	0	0	0	0	1	0	0	0	5973	1490	52	5	142	5	FNBP1L	1	93965136	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	44965289	93965136	155285485	10	13420											
ABCA4	24	hgsc.bcm.edu	37	chr1	94522320	94522320	+	Frame_Shift_Del	DEL	A	A	-																															gcatgatggtggcagtggagAaagccaacaagaacaggaag																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:94522320delA	ENST00000370225.3	-	15	2305	c.2219delT	c.(2218-2220)ttcfs	p.F740fs	ABCA4_ENST00000535735.1_Intron	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	740					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)		GGCAGTGGAGAAAGCCAACAA	0.517																																					p.F740fs		Pindel	.											.	ABCA4	275	.	0			c.2220delC						PASS	.						111	98	102					1																	94522320		2203	4300	6503	SO:0001589	frameshift_variant	24	exon15			.	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.2219delT	chr1.hg19:g.94522320delA	ENSP00000359245:p.Phe740fs	322.0	0.0	.		231.0	60.0	0.260	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Frame_Shift_Del	DEL	ENST00000370225.3	hg19	CCDS747.1																																																																																			.	.	.	none		0.517	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		-	94522320	A	-	94522320	7	5	222	1	0	1	0	1	0	0	0	0	34	246	9	0	4746	0	ABCA4	1	94522320	Frame_Shift_Del	DEL	A	TCGA-MH-A561-01A-11D-A26P-10	557184	94522320	154728301	11	13421											
AQP10	89872	hgsc.bcm.edu	37	chr1	154296801	154296801	+	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	tgcctgtggtggcccctctgGtgggggccaccgttggcaca	3	9	16	13	1	1	0	0	0	1	0	1	0	1	0	5	6	1	2	5	6	0	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:154296801G>T	ENST00000324978.3	+	6	791	c.751G>T	c.(751-753)Gtg>Ttg	p.V251L	ATP8B2_ENST00000368487.3_5'Flank|AQP10_ENST00000484864.1_3'UTR	NM_080429.2	NP_536354.2	Q96PS8	AQP10_HUMAN	aquaporin 10	251					response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(14)|stomach(2)|upper_aerodigestive_tract(1)	23	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			GGCCCCTCTGGTGGGGGCCAC	0.602											OREG0013832	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V251L		Atlas-SNP	.											.	AQP10	44	.	0			c.G751T						PASS	.						32	35	34					1																	154296801		2201	4290	6491	SO:0001583	missense	89872	exon6			CCTCTGGTGGGGG	AF159174	CCDS1065.1	1q21.3	2008-02-05			ENSG00000143595	ENSG00000143595		"Ion channels / Aquaporins"	16029	protein-coding gene	gene with protein product		606578				11573934	Standard	NM_080429		Approved		uc001feu.3	Q96PS8	OTTHUMG00000035980	ENST00000324978.3:c.751G>T	chr1.hg19:g.154296801G>T	ENSP00000318355:p.Val251Leu	41.0	0.0	.	1762	33.0	16.0	.	NM_080429	Q5VYD3|Q5VYD4|Q8NG70	Missense_Mutation	SNP	ENST00000324978.3	hg19	CCDS1065.1	.	.	.	.	.	.	.	.	.	.	G	5.726	0.318459	0.10845	.	.	ENSG00000143595	ENST00000324978	D	0.88124	-2.34	4.46	4.46	0.54185	Aquaporin-like (2);	0.142496	0.45126	D	0.000385	T	0.65688	0.2715	L	0.28608	0.87	0.80722	D	1	B	0.32939	0.391	B	0.34722	0.188	T	0.67345	-0.5694	10	0.02654	T	1	.	12.9205	0.58230	0.0:0.1648:0.8352:0.0	.	251	Q96PS8	AQP10_HUMAN	L	251	ENSP00000318355:V251L	ENSP00000318355:V251L	V	+	1	0	AQP10	152563425	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	1.571000	0.36450	2.510000	0.84645	0.555000	0.69702	GTG	.	.	.	none		0.602	AQP10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087661.1	NM_080429		T	154296801	G	T	154296801	3	4	222	1	0	0	0	0	1	0	0	0	822	1261	44	4	773	4	AQP10	1	154296801	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	59774481	154296801	94953820	12	13422											
CENPL	91687	hgsc.bcm.edu	37	chr1	173772297	173772298	+	Frame_Shift_Ins	INS	-	-	T																															ttttgcatcctctggatgtaINSttgcgaaagaaatgtccaga																								rs139873333	byFrequency	TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:173772297_173772298insT	ENST00000345664.6	-	4	979_980	c.766_767insA	c.(766-768)atafs	p.I256fs	CENPL_ENST00000356198.2_Frame_Shift_Ins_p.I302fs|CENPL_ENST00000367710.3_Frame_Shift_Ins_p.I256fs	NM_001171182.1	NP_001164653.1	Q8N0S6	CENPL_HUMAN	centromere protein L	256					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						CTCTGGATGTATTGCGAAAGAA	0.45																																					p.I302fs		Atlas-INDEL	.											.	CENPL	26	.	0			c.905_906insA						PASS	.																																			SO:0001589	frameshift_variant	91687	exon6			.	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.767dupA	chr1.hg19:g.173772299_173772299dupT	ENSP00000323543:p.Ile256fs	123.0	0.0	0		74.0	18.0	0.243243	NM_001127181	Q5TEL5|Q96ND4	Frame_Shift_Ins	INS	ENST00000345664.6	hg19	CCDS30938.1																																																																																			.	.	.	none		0.45	CENPL-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084213.1	NM_033319		T	173772298	-	T	173772297	7	5	222	1	0	1	1	0	0	0	0	0	3238	449	16	0	275	0	CENPL	1	173772297	Frame_Shift_Ins	INS	-	TCGA-MH-A561-01A-11D-A26P-10	19475496	173772297	75478324	13	13423	135	2									
CENPL	91687	hgsc.bcm.edu	37	chr1	173772300	173772300	+	Missense_Mutation	SNP	G	G	T																															ttgcatcctctggatgtattGcgaaagaaatgtccagactt																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:173772300G>T	ENST00000345664.6	-	4	977	c.764C>A	c.(763-765)gCa>gAa	p.A255E	CENPL_ENST00000356198.2_Missense_Mutation_p.A301E|CENPL_ENST00000367710.3_Missense_Mutation_p.A255E	NM_001171182.1	NP_001164653.1	Q8N0S6	CENPL_HUMAN	centromere protein L	255					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						TGGATGTATTGCGAAAGAAAT	0.458																																					p.A301E		Atlas-SNP	.											.	CENPL	26	.	0			c.C902A						PASS	.						95	97	96					1																	173772300		2203	4300	6503	SO:0001583	missense	91687	exon6			TGTATTGCGAAAG	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.764C>A	chr1.hg19:g.173772300G>T	ENSP00000323543:p.Ala255Glu	122.0	0.0	.		75.0	19.0	.	NM_001127181	Q5TEL5|Q96ND4	Missense_Mutation	SNP	ENST00000345664.6	hg19	CCDS30938.1	.	.	.	.	.	.	.	.	.	.	G	18.51	3.640619	0.67244	.	.	ENSG00000120334	ENST00000356198;ENST00000345664;ENST00000367710	T;T;T	0.41758	1.58;0.99;0.99	5.24	5.24	0.73138	.	0.172946	0.50627	D	0.000109	T	0.47691	0.1459	L	0.43152	1.355	0.39487	D	0.967975	D;P	0.69078	0.997;0.896	D;P	0.63283	0.913;0.602	T	0.50882	-0.8775	10	0.72032	D	0.01	-5.8243	17.633	0.88114	0.0:0.0:1.0:0.0	.	301;255	Q8N0S6-2;Q8N0S6	.;CENPL_HUMAN	E	301;255;255	ENSP00000348527:A301E;ENSP00000323543:A255E;ENSP00000356683:A255E	ENSP00000323543:A255E	A	-	2	0	CENPL	172038923	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	5.635000	0.67841	2.456000	0.83038	0.655000	0.94253	GCA	.	.	.	none		0.458	CENPL-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084213.1	NM_033319		T	173772300	G	T	173772300	3	4	222	1	0	0	0	0	1	0	0	0	3238	1319	46	4	278	4	CENPL	1	173772300	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	3	173772300	75478321	14	13424	135	2									
RFWD2	64326	hgsc.bcm.edu	37	chr1	175996826	175996826	+	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	ttggtagaccacagcttcacTaagggcaaaggacaataaaa	17	7	9	8	0	1	1	1	0	0	1	1	2	1	2	1	3	1	3	1	3	6	5			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:175996826T>C	ENST00000367669.3	-	15	2127		c.e15-2		RFWD2_ENST00000308769.8_Splice_Site	NM_022457.5	NP_071902.2	Q8NHY2	RFWD2_HUMAN	ring finger and WD repeat domain 2, E3 ubiquitin protein ligase						DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin protein ligase activity (GO:0061630)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						ACAGCTTCACTAAGGGCAAAG	0.388																																					.	Ovarian(134;1413 1765 5706 35534 51541)	Atlas-SNP	.											.	RFWD2	67	.	0			c.1613-2A>G						PASS	.						63	54	57					1																	175996826		2203	4300	6503	SO:0001630	splice_region_variant	64326	exon16			CTTCACTAAGGGC	AK001278	CCDS30944.1, CCDS44279.1	1q25.1-q25.2	2013-01-09	2012-02-23		ENSG00000143207	ENSG00000143207		"WD repeat domain containing", "RING-type (C3HC4) zinc fingers"	17440	protein-coding gene	gene with protein product		608067	"ring finger and WD repeat domain 2"			10395541	Standard	XM_005245447		Approved	FLJ10416, COP1, RNF200	uc001gku.1	Q8NHY2	OTTHUMG00000034986	ENST00000367669.3:c.1613-2A>G	chr1.hg19:g.175996826T>C		72.0	0.0	.		78.0	31.0	.	NM_022457	E9PKI0|Q504W6|Q6H103|Q9H6L7|X5D9B4	Splice_Site	SNP	ENST00000367669.3	hg19	CCDS30944.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.586435	0.86851	.	.	ENSG00000143207	ENST00000367665;ENST00000367669;ENST00000367666;ENST00000308769	.	.	.	5.73	5.73	0.89815	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6701	0.77267	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	RFWD2	174263449	1.000000	0.71417	0.986000	0.45419	0.994000	0.84299	7.563000	0.82314	2.174000	0.68829	0.528000	0.53228	.	.	.	.	none		0.388	RFWD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084672.2	NM_022457	Intron	C	175996826	T	C	175996826	5	2	222	1	0	0	0	0	0	0	1	0	13273	1536	53	3	608	3	RFWD2	1	175996826	Splice_Site	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	2224526	175996826	73253795	15	13425											
CEP350	9857	hgsc.bcm.edu	37	chr1	179959644	179959645	+	Frame_Shift_Del	DEL	GA	GA	-																															atggtgtttaaactttagctGagacacattgaaaataaatt																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:179959644_179959645delGA	ENST00000367607.3	+	4	541_542	c.123_124delGA	c.(121-126)ctgagafs	p.R42fs		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	42					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						AACTTTAGCTGAGACACATTGA	0.337																																					p.41_41del		Atlas-Indel,Pindel	.											.	CEP350	418	.	0			c.122_123del						PASS	.																																			SO:0001589	frameshift_variant	9857	exon4			.	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.123_124delGA	chr1.hg19:g.179959646_179959647delGA	ENSP00000356579:p.Arg42fs	67.0	0.0	0		66.0	14.0	0.212121	NM_014810	O75068|Q8TDK3|Q8WY20	Frame_Shift_Del	DEL	ENST00000367607.3	hg19	CCDS1336.1																																																																																			.	.	.	none		0.337	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		-	179959645	GA	-	179959644	7	5	222	1	0	1	0	1	0	0	0	0	3256	1277	45	0	133	0	CEP350	1	179959644	Frame_Shift_Del	DEL	GA	TCGA-MH-A561-01A-11D-A26P-10	3962818	179959644	69290977	16	13426											
ETNK2	55224	hgsc.bcm.edu	37	chr1	204101322	204101322	+	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	gggtggctggtcactttggcAtctccaaggctgacgcttga	6	11	14	10	1	2	2	1	2	1	0	3	2	2	2	1	5	0	4	1	5	1	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:204101322A>T	ENST00000367202.4	-	8	1301	c.1151T>A	c.(1150-1152)aTg>aAg	p.M384K	RP11-74C13.4_ENST00000565388.1_RNA|ETNK2_ENST00000367199.2_Missense_Mutation_p.M315K|ETNK2_ENST00000367198.2_Missense_Mutation_p.M206K|ETNK2_ENST00000367201.3_3'UTR|ETNK2_ENST00000367197.1_Missense_Mutation_p.M66K	NM_018208.2	NP_060678.2	Q9NVF9	EKI2_HUMAN	ethanolamine kinase 2	384					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)			TCACTTTGGCATCTCCAAGGC	0.557																																					p.M384K		Atlas-SNP	.											.	ETNK2	48	.	0			c.T1151A						PASS	.						80	77	78					1																	204101322		1564	3580	5144	SO:0001583	missense	55224	exon8			TTTGGCATCTCCA	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.1151T>A	chr1.hg19:g.204101322A>T	ENSP00000356170:p.Met384Lys	165.0	0.0	.		101.0	34.0	.	NM_018208	B7Z7K1|Q5SXX5|Q68CK3|Q96G05	Missense_Mutation	SNP	ENST00000367202.4	hg19	CCDS1442.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.99|18.99	3.740600|3.740600	0.69304|0.69304	.|.	.|.	ENSG00000143845|ENSG00000143845	ENST00000422072|ENST00000367202;ENST00000367199;ENST00000455266;ENST00000367198;ENST00000367197	.|T;T;T;T	.|0.64260	.|0.34;-0.02;-0.02;-0.09	5.0|5.0	3.82|3.82	0.43975|0.43975	.|.	.|.	.|.	.|.	.|.	T|T	0.62780|0.62780	0.2456|0.2456	L|L	0.58669|0.58669	1.825|1.825	0.38499|0.38499	D|D	0.948185|0.948185	.|P;P	.|0.46859	.|0.877;0.885	.|P;B	.|0.50754	.|0.649;0.446	T|T	0.62305|0.62305	-0.6882|-0.6882	5|9	.|0.28530	.|T	.|0.3	.|.	8.0791|8.0791	0.30733|0.30733	0.7042:0.0:0.0:0.2958|0.7042:0.0:0.0:0.2958	.|.	.|343;384	.|Q9NVF9-3;Q9NVF9	.|.;EKI2_HUMAN	S|K	147|384;315;250;206;66	.|ENSP00000356170:M384K;ENSP00000356167:M315K;ENSP00000356166:M206K;ENSP00000356165:M66K	.|ENSP00000356165:M66K	C|M	-|-	1|2	0|0	ETNK2|ETNK2	202367945|202367945	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.878000|0.878000	0.50629|0.50629	6.504000|6.504000	0.73704|0.73704	1.880000|1.880000	0.54463|0.54463	0.533000|0.533000	0.62120|0.62120	TGC|ATG	.	.	.	none		0.557	ETNK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087893.1	NM_018208		T	204101322	A	T	204101322	3	4	222	1	0	0	0	0	1	0	0	0	5276	217	8	5	13	5	ETNK2	1	204101322	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	24141678	204101322	45149299	17	13427											
C1orf107	27042	hgsc.bcm.edu	37	chr1	210006562	210006562	+	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	ctgctgaccctgagggaaaaGaagatggggaagagccaccg	13	4	15	9	1	0	5	0	2	0	3	0	7	0	7	3	3	2	1	3	3	4	0			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:210006562G>T	ENST00000491415.2	+	4	478	c.421G>T	c.(421-423)Gaa>Taa	p.E141*		NM_014388.6	NP_055203.4	Q68CQ4	DIEXF_HUMAN	digestive organ expansion factor homolog (zebrafish)	141	Glu-rich.				multicellular organismal development (GO:0007275)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(15)|large_intestine(7)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(2)	53						TGAGGGAAAAGAAGATGGGGA	0.398																																					p.E141X		Atlas-SNP	.											.	DIEXF	97	.	0			c.G421T						PASS	.						59	56	57					1																	210006562		2203	4300	6503	SO:0001587	stop_gained	27042	exon4			GGAAAAGAAGATG	BC022964	CCDS1493.1	1q32.2	2011-08-12	2011-02-16	2011-02-16	ENSG00000117597	ENSG00000117597			28440	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 107"	C1orf107		16322560	Standard	NM_014388		Approved	MGC29875, DEF, UTP25	uc001hhr.2	Q68CQ4	OTTHUMG00000036654	ENST00000491415.2:c.421G>T	chr1.hg19:g.210006562G>T	ENSP00000419005:p.Glu141*	59.0	0.0	.		51.0	17.0	.	NM_014388	O75992|Q4VY00|Q63HL9	Nonsense_Mutation	SNP	ENST00000491415.2	hg19	CCDS1493.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.380543	0.82792	.	.	ENSG00000117597	ENST00000491415	.	.	.	0.225	0.225	0.15325	.	1.807870	0.04544	U	0.388703	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	.	.	.	.	.	.	.	.	X	141	.	ENSP00000419005:E141X	E	+	1	0	DIEXF	208073185	0.949000	0.32298	0.212000	0.23672	0.934000	0.57294	0.364000	0.20325	0.300000	0.22699	0.305000	0.20034	GAA	.	.	.	none		0.398	DIEXF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089127.2	NM_014388		T	210006562	G	T	210006562	4	4	222	1	0	0	0	0	0	1	0	0	1983	943	33	4	435	4	C1orf107	1	210006562	Nonsense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	5905240	210006562	39244059	18	13428											
CENPF	1063	hgsc.bcm.edu	37	chr1	214820696	214820696	+	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	gttcttacaagaatctagagAatgagcttgaattgacaaaa	17	11	8	5	0	2	5	0	3	2	2	2	6	2	5	0	0	2	2	0	0	8	5			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr1:214820696A>T	ENST00000366955.3	+	13	7951	c.7783A>T	c.(7783-7785)Aat>Tat	p.N2595Y		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2691	Sufficient for centromere localization.|Sufficient for self-association.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		GAATCTAGAGAATGAGCTTGA	0.378																																					p.N2595Y	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.A7783T						PASS	.						37	37	37					1																	214820696		2203	4300	6503	SO:0001583	missense	1063	exon13			CTAGAGAATGAGC	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.7783A>T	chr1.hg19:g.214820696A>T	ENSP00000355922:p.Asn2595Tyr	66.0	0.0	.		55.0	24.0	.	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	hg19	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	A	12.11	1.839067	0.32513	.	.	ENSG00000117724	ENST00000366955	T	0.03301	3.98	5.61	3.16	0.36331	.	0.728326	0.11309	N	0.577293	T	0.03608	0.0103	N	0.19112	0.55	0.25270	N	0.989526	P	0.51653	0.947	P	0.44732	0.459	T	0.45963	-0.9225	10	0.59425	D	0.04	.	7.1052	0.25360	0.777:0.1469:0.0761:0.0	.	2691	P49454	CENPF_HUMAN	Y	2595	ENSP00000355922:N2595Y	ENSP00000355922:N2595Y	N	+	1	0	CENPF	212887319	1.000000	0.71417	0.126000	0.21872	0.167000	0.22549	1.705000	0.37867	0.427000	0.26145	0.496000	0.49642	AAT	.	.	.	none		0.378	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		T	214820696	A	T	214820696	3	4	222	1	0	0	0	0	1	0	0	0	3233	246	9	5	7829	5	CENPF	1	214820696	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	4814134	214820696	34429925	19	13429											
FBXO11	80204	hgsc.bcm.edu	37	chr2	48040950	48040950	+	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	cagaattataaactagaattCcaccattctgtcctccccag	13	11	4	13	0	1	2	0	0	1	2	4	2	4	2	5	0	1	0	5	0	6	5			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:48040950C>T	ENST00000403359.3	-	17	2135	c.2063G>A	c.(2062-2064)gGa>gAa	p.G688E	FBXO11_ENST00000316377.4_Missense_Mutation_p.G604E|FBXO11_ENST00000434523.2_Missense_Mutation_p.G112E|FBXO11_ENST00000402508.1_Missense_Mutation_p.G604E	NM_001190274.1	NP_001177203.1	Q86XK2	FBX11_HUMAN	F-box protein 11	688					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)			AACTAGAATTCCACCATTCTG	0.388			"Mis, F, D"		DLBCL																																p.G688E		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.G2063A						PASS	.						118	116	117					2																	48040950		2202	4300	6502	SO:0001583	missense	80204	exon17			AGAATTCCACCAT	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.2063G>A	chr2.hg19:g.48040950C>T	ENSP00000384823:p.Gly688Glu	61.0	0.0	.		44.0	5.0	.	NM_001190274	A1L491|Q52ZP1|Q53EP7|Q53RT5|Q8IXG3|Q96E90|Q9H6V8|Q9H9L1|Q9NR14|Q9UFK1|Q9UHI1|Q9UKC2	Missense_Mutation	SNP	ENST00000403359.3	hg19	CCDS54357.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	32|32	5.136371|5.136371	0.94517|0.94517	.|.	.|.	ENSG00000138081|ENSG00000138081	ENST00000402508;ENST00000403359;ENST00000316377;ENST00000434523|ENST00000493962	D;D;D;D|.	0.90133|.	-2.62;-2.62;-2.62;-2.62|.	5.43|5.43	5.43|5.43	0.79202|0.79202	Pectin lyase fold/virulence factor (2);Carbohydrate-binding/sugar hydrolysis domain (1);F-box domain, Skp2-like (1);Pectin lyase fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.86789|.	0.6017|.	M|M	0.92880|0.92880	3.355|3.355	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	0.998;1.0|.	D|.	0.89459|.	0.3735|.	10|.	0.66056|.	D|.	0.02|.	-12.1201|-12.1201	19.5994|19.5994	0.95554|0.95554	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	112;688|.	B3KUR1;Q86XK2|.	.;FBX11_HUMAN|.	E|X	604;688;604;112|479	ENSP00000385398:G604E;ENSP00000384823:G688E;ENSP00000323822:G604E;ENSP00000397359:G112E|.	ENSP00000323822:G604E|.	G|W	-|-	2|3	0|0	FBXO11|FBXO11	47894454|47894454	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.776000|7.776000	0.85560|0.85560	2.699000|2.699000	0.92147|0.92147	0.655000|0.655000	0.94253|0.94253	GGA|TGG	.	.	.	none		0.388	FBXO11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251181.3	NM_012167, NM_018693, NM_025133		T	48040950	C	T	48040950	3	4	222	1	0	0	0	0	1	0	0	0	5734	855	30	2	834	2	FBXO11	2	48040950	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10		48040950	195158423	20	13430											
AAK1	22848	hgsc.bcm.edu	37	chr2	69757189	69757189	+	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	cgagaattatcaggaattgtGaagtttccatcacaaattgc	14	12	8	7	1	2	2	2	1	0	1	3	4	3	3	1	1	1	1	1	1	5	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:69757189G>A	ENST00000409085.4	-	8	1198	c.822C>T	c.(820-822)ttC>ttT	p.F274F	AAK1_ENST00000406297.3_Silent_p.F274F|AAK1_ENST00000470281.1_5'Flank|AAK1_ENST00000409068.1_Silent_p.F274F	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	274	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				endocytosis (GO:0006897)|positive regulation of Notch signaling pathway (GO:0045747)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of clathrin-mediated endocytosis (GO:2000369)|regulation of protein localization (GO:0032880)	cell leading edge (GO:0031252)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extrinsic component of plasma membrane (GO:0019897)|terminal bouton (GO:0043195)	AP-2 adaptor complex binding (GO:0035612)|ATP binding (GO:0005524)|Notch binding (GO:0005112)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)	17						CAGGAATTGTGAAGTTTCCAT	0.313																																					p.F274F		Atlas-SNP	.											.	AAK1	121	.	0			c.C822T						PASS	.						58	54	55					2																	69757189		1830	4085	5915	SO:0001819	synonymous_variant	22848	exon8			AATTGTGAAGTTT	AB028971	CCDS1893.2	2p13.3	2012-07-10			ENSG00000115977	ENSG00000115977			19679	protein-coding gene	gene with protein product						11877461, 12471243	Standard	NM_014911		Approved	KIAA1048, DKFZp686K16132	uc002sfp.2	Q2M2I8	OTTHUMG00000129648	ENST00000409085.4:c.822C>T	chr2.hg19:g.69757189G>A		170.0	0.0	.		125.0	44.0	.	NM_014911	Q4ZFZ3|Q53RX6|Q9UPV4	Silent	SNP	ENST00000409085.4	hg19	CCDS1893.2																																																																																			.	.	.	none		0.313	AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251847.4	NM_014911		A	69757189	G	A	69757189	2	1	222	1	0	0	0	0	0	0	0	1	16	1281	45	2		2	AAK1	2	69757189	Silent	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	21716239	69757189	173442184	21	13431											
RTKN	6242	hgsc.bcm.edu	37	chr2	74668862	74668862	+	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	gtcgctgaagaggctgagtcGgaagcggccgcgtttgaact	8	8	16	9	5	0	4	0	3	0	1	2	5	0	5	1	3	2	3	1	3	3	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:74668862G>T	ENST00000272430.5	-	1	164	c.82C>A	c.(82-84)Cga>Aga	p.R28R	RTKN_ENST00000484453.1_5'UTR|RTKN_ENST00000305557.5_5'Flank|RTKN_ENST00000233330.6_5'Flank	NM_001015055.1	NP_001015055.1			rhotekin											endometrium(3)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	16						AGGCTGAGTCGGAAGCGGCCG	0.697																																					p.R28R		Atlas-SNP	.											.	RTKN	80	.	0			c.C82A						PASS	.						28	33	31					2																	74668862		2202	4300	6502	SO:0001819	synonymous_variant	6242	exon1			TGAGTCGGAAGCG	AF049227	CCDS1941.1, CCDS33226.1, CCDS42699.1	2p13.1	2013-01-10			ENSG00000114993	ENSG00000114993		"Pleckstrin homology (PH) domain containing"	10466	protein-coding gene	gene with protein product		602288				9073523, 10940294	Standard	XM_005264478		Approved	B5	uc002sle.3	Q9BST9	OTTHUMG00000129955	ENST00000272430.5:c.82C>A	chr2.hg19:g.74668862G>T		65.0	0.0	.		38.0	12.0	.	NM_001015055		Silent	SNP	ENST00000272430.5	hg19	CCDS33226.1																																																																																			.	.	.	none		0.697	RTKN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328234.1	NM_001015055		T	74668862	G	T	74668862	2	4	222	1	0	0	0	0	0	0	0	1	13735	1124	39	4		4	RTKN	2	74668862	Silent	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	4911673	74668862	168530511	22	13432											
AUP1	165545	hgsc.bcm.edu	37	chr2	74755401	74755401	+	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	tgatacaccgtgaaagggacGaaaagtgaccacagcagttc	15	6	11	9	2	0	3	0	3	0	0	1	5	0	4	2	1	2	2	2	1	4	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:74755401G>T	ENST00000404568.3	-	0	0				DQX1_ENST00000393951.2_5'Flank|AUP1_ENST00000377526.3_Missense_Mutation_p.F215L|HTRA2_ENST00000258080.3_5'Flank|HTRA2_ENST00000352222.3_5'Flank	NM_133637.2	NP_598376.2	Q8TE96	DQX1_HUMAN	DEAQ box RNA-dependent ATPase 1							nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	18						TGAAAGGGACGAAAAGTGACC	0.537																																					p.F215L		Atlas-SNP	.											.	AUP1	29	.	0			c.C645A						PASS	.						74	80	78					2																	74755401		2044	4193	6237	SO:0001631	upstream_gene_variant	550	exon6			AGGGACGAAAAGT	AK074337	CCDS1949.2	2p12	2010-04-20	2009-01-15		ENSG00000144045	ENSG00000144045			20410	protein-coding gene	gene with protein product			"DEAQ box polypeptide 1 (RNA-dependent ATPase)"				Standard	NM_133637		Approved	FLJ23757	uc010yrw.2	Q8TE96	OTTHUMG00000129965		chr2.hg19:g.74755401G>T	Exception_encountered	70.0	0.0	.		60.0	24.0	.	NM_181575	Q6B017|Q8NAM8	Missense_Mutation	SNP	ENST00000404568.3	hg19	CCDS1949.2	.	.	.	.	.	.	.	.	.	.	G	18.80	3.701042	0.68501	.	.	ENSG00000115307	ENST00000377526;ENST00000258081;ENST00000412627	D	0.92495	-3.05	5.1	3.01	0.34805	.	0.000000	0.85682	D	0.000000	D	0.94000	0.8078	M	0.66506	2.035	0.54753	D	0.999982	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.85130	0.984;0.992;0.997	D	0.91236	0.5018	10	0.33940	T	0.23	-15.5435	8.4169	0.32676	0.226:0.0:0.774:0.0	.	272;281;215	E7EU18;Q9Y679;Q9Y679-2	.;AUP1_HUMAN;.	L	215;279;217	ENSP00000366748:F215L	ENSP00000258081:F279L	F	-	3	2	AUP1	74608909	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.450000	0.35134	0.528000	0.28580	0.462000	0.41574	TTC	.	.	.	none		0.537	DQX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252230.3	NM_133637		T	74755401	G	T	74755401	1	4	222	0	1	0	0	0	0	0	0	0	1220	1049	37	4		4	AUP1	2	74755401	5'Flank	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	86539	74755401	168443972	23	13433											
LRP2	4036	hgsc.bcm.edu	37	chr2	170136009	170136009	+	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	ggtttccactagatagatttTattattaacccagtccacag	12	14	6	9	0	0	2	0	0	0	2	2	2	2	2	3	1	1	1	3	1	5	7			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:170136009T>A	ENST00000263816.3	-	12	1723	c.1438A>T	c.(1438-1440)Aaa>Taa	p.K480*	LRP2_ENST00000443831.1_Nonsense_Mutation_p.K480*	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	480					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)"	AGATAGATTTTATTATTAACC	0.393																																					p.K480X		Atlas-SNP	.											.	LRP2	751	.	0			c.A1438T						PASS	.						98	105	103					2																	170136009		2203	4300	6503	SO:0001587	stop_gained	4036	exon12			AGATTTTATTATT		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.1438A>T	chr2.hg19:g.170136009T>A	ENSP00000263816:p.Lys480*	72.0	0.0	.		81.0	26.0	.	NM_004525	O00711|Q16215	Nonsense_Mutation	SNP	ENST00000263816.3	hg19	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	T	39	7.557577	0.98358	.	.	ENSG00000081479	ENST00000263816;ENST00000443831	.	.	.	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7574	0.78046	0.0:0.0:0.0:1.0	.	.	.	.	X	480	.	.	K	-	1	0	LRP2	169844255	1.000000	0.71417	0.998000	0.56505	0.410000	0.31052	7.971000	0.88012	2.136000	0.66102	0.528000	0.53228	AAA	.	.	.	none		0.393	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		A	170136009	T	A	170136009	4	1	222	1	0	0	0	0	0	1	0	0	8963	1763	61	5	12801	5	LRP2	2	170136009	Nonsense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	95380608	170136009	73063364	24	13434											
GAD1	2571	hgsc.bcm.edu	37	chr2	171700591	171700591	+	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	gcaccagtgtttgtcctcatGgaacaaataacacttaagaa	15	10	7	9	0	1	1	1	0	0	1	2	2	2	2	2	1	2	2	2	1	5	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:171700591G>T	ENST00000358196.3	+	7	1225	c.675G>T	c.(673-675)atG>atT	p.M225I	GAD1_ENST00000429023.1_3'UTR	NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	225					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						TTGTCCTCATGGAACAAATAA	0.368																																					p.M225I		Atlas-SNP	.											.	GAD1	79	.	0			c.G675T						PASS	.						210	215	213					2																	171700591		2203	4300	6503	SO:0001583	missense	2571	exon7			CCTCATGGAACAA		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.675G>T	chr2.hg19:g.171700591G>T	ENSP00000350928:p.Met225Ile	122.0	0.0	.		119.0	40.0	.	NM_000817	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Missense_Mutation	SNP	ENST00000358196.3	hg19	CCDS2239.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.500461	0.85176	.	.	ENSG00000128683	ENST00000358196	T	0.36520	1.25	6.17	6.17	0.99709	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	T	0.37865	0.1019	L	0.33624	1.015	0.80722	D	1	B	0.30021	0.265	B	0.35312	0.2	T	0.15350	-1.0440	10	0.72032	D	0.01	-26.7667	20.8794	0.99867	0.0:0.0:1.0:0.0	.	225	Q99259	DCE1_HUMAN	I	225	ENSP00000350928:M225I	ENSP00000350928:M225I	M	+	3	0	GAD1	171408837	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.394000	0.97261	2.941000	0.99782	0.655000	0.94253	ATG	.	.	.	none		0.368	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2			T	171700591	G	T	171700591	3	4	222	1	0	0	0	0	1	0	0	0	6186	1348	47	4	738	4	GAD1	2	171700591	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	1564582	171700591	71498782	25	13435											
MSTN	2660	hgsc.bcm.edu	37	chr2	190927181	190927181	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctattcttgaagatttagTgttttgtctccaagtacatg	9	19	7	6	0	3	2	0	1	3	1	4	2	3	2	1	0	1	2	1	0	5	9			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:190927181T>C	ENST00000260950.4	-	1	274	c.142A>G	c.(142-144)Act>Gct	p.T48A	C2orf88_ENST00000478197.1_Intron	NM_005259.2	NP_005250.1	O14793	GDF8_HUMAN	myostatin	48					cellular response to dexamethasone stimulus (GO:0071549)|muscle organ development (GO:0007517)|negative regulation of muscle hypertrophy (GO:0014741)|negative regulation of skeletal muscle tissue growth (GO:0048632)|ovulation cycle process (GO:0022602)|positive regulation of transcription, DNA-templated (GO:0045893)|response to electrical stimulus (GO:0051602)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gravity (GO:0009629)|response to heat (GO:0009408)|response to muscle activity (GO:0014850)|response to testosterone (GO:0033574)|skeletal muscle atrophy (GO:0014732)|skeletal muscle tissue regeneration (GO:0043403)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|skin(1)	12			OV - Ovarian serous cystadenocarcinoma(117;0.000742)|Epithelial(96;0.0121)|all cancers(119;0.0395)			GAAGATTTAGTGTTTTGTCTC	0.378																																					p.T48A		Atlas-SNP	.											.	MSTN	46	.	0			c.A142G						PASS	.						198	194	195					2																	190927181		2203	4300	6503	SO:0001583	missense	2660	exon1			ATTTAGTGTTTTG	AF019627	CCDS2303.1	2q32.1	2014-09-17	2007-06-21	2007-06-21	ENSG00000138379	ENSG00000138379			4223	protein-coding gene	gene with protein product		601788	"growth differentiation factor 8"	GDF8		9288100, 10610713, 17003236	Standard	NM_005259		Approved		uc002urp.3	O14793	OTTHUMG00000132663	ENST00000260950.4:c.142A>G	chr2.hg19:g.190927181T>C	ENSP00000260950:p.Thr48Ala	52.0	0.0	.		49.0	22.0	.	NM_005259	A1C2J7|A1C2K0|Q6B0H2	Missense_Mutation	SNP	ENST00000260950.4	hg19	CCDS2303.1	.	.	.	.	.	.	.	.	.	.	T	13.67	2.307916	0.40895	.	.	ENSG00000138379	ENST00000260950	T	0.64085	-0.08	5.64	5.64	0.86602	Transforming growth factor-beta, N-terminal (1);	0.217803	0.48286	D	0.000186	T	0.51753	0.1693	L	0.29908	0.895	0.43195	D	0.995031	B	0.09022	0.002	B	0.15870	0.014	T	0.43877	-0.9364	10	0.30854	T	0.27	-11.9215	16.0238	0.80522	0.0:0.0:0.0:1.0	.	48	O14793	GDF8_HUMAN	A	48	ENSP00000260950:T48A	ENSP00000260950:T48A	T	-	1	0	MSTN	190635426	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	5.928000	0.70088	2.367000	0.80283	0.528000	0.53228	ACT	.	.	.	none		0.378	MSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255917.2	NM_005259		C	190927181	T	C	190927181	3	2	222	1	0	0	0	0	1	0	0	0	9900	1696	59	3	997	3	MSTN	2	190927181	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	19226590	190927181	52272192	26	13436											
C2orf69	205327	hgsc.bcm.edu	37	chr2	200789854	200789854	+	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	actggagtctagaaaatgttGctaccattttagcccaccgg	11	11	9	10	1	1	1	0	0	1	1	1	2	1	2	3	2	3	2	3	2	5	5			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:200789854G>T	ENST00000319974.5	+	2	586	c.403G>T	c.(403-405)Gct>Tct	p.A135S	C2orf69_ENST00000491721.1_Intron	NM_153689.5	NP_710156.3	Q8N8R5	CB069_HUMAN	chromosome 2 open reading frame 69	135						extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(2)|stomach(1)|urinary_tract(1)	11						AGAAAATGTTGCTACCATTTT	0.353																																					p.A135S		Atlas-SNP	.											.	C2orf69	17	.	0			c.G403T						PASS	.						51	48	48					2																	200789854		1819	4077	5896	SO:0001583	missense	205327	exon2			AATGTTGCTACCA		CCDS46482.1	2q33.1	2008-08-08			ENSG00000178074	ENSG00000178074			26799	protein-coding gene	gene with protein product	"hypothetical protein FLJ38973"					12477932	Standard	NM_153689		Approved	FLJ38973	uc010zhb.2	Q8N8R5	OTTHUMG00000154480	ENST00000319974.5:c.403G>T	chr2.hg19:g.200789854G>T	ENSP00000312770:p.Ala135Ser	56.0	0.0	.		92.0	31.0	.	NM_153689	Q8NE30	Missense_Mutation	SNP	ENST00000319974.5	hg19	CCDS46482.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.667963	0.88348	.	.	ENSG00000178074	ENST00000319974	.	.	.	6.03	6.03	0.97812	.	0.049006	0.85682	D	0.000000	D	0.82600	0.5072	M	0.76328	2.33	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.82600	-0.0377	9	0.62326	D	0.03	-10.3396	19.5548	0.95338	0.0:0.0:1.0:0.0	.	135	Q8N8R5	CB069_HUMAN	S	135	.	ENSP00000312770:A135S	A	+	1	0	C2orf69	200498099	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.827000	0.99397	2.854000	0.98071	0.655000	0.94253	GCT	.	.	.	none		0.353	C2orf69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335446.1	NM_153689		T	200789854	G	T	200789854	3	4	222	1	0	0	0	0	1	0	0	0	2190	1319	46	4	409	4	C2orf69	2	200789854	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	9862673	200789854	42409519	27	13437											
DGKD	8527	hgsc.bcm.edu	37	chr2	234368926	234368926	+	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	tgttccctgcacccggagatGctgtccgaggaggaggccac	7	7	14	13	2	0	1	0	0	0	1	2	5	2	3	4	4	2	3	4	4	0	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr2:234368926G>T	ENST00000264057.2	+	24	2928	c.2916G>T	c.(2914-2916)atG>atT	p.M972I	DGKD_ENST00000409813.3_Missense_Mutation_p.M928I	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	972					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)	ACCCGGAGATGCTGTCCGAGG	0.617																																					p.M972I		Atlas-SNP	.											.	DGKD	106	.	0			c.G2916T						PASS	.						87	79	81					2																	234368926		2203	4300	6503	SO:0001583	missense	8527	exon24			GGAGATGCTGTCC	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.2916G>T	chr2.hg19:g.234368926G>T	ENSP00000264057:p.Met972Ile	544.0	1.0	.		376.0	143.0	.	NM_152879	Q14158|Q6PK55|Q8NG53	Missense_Mutation	SNP	ENST00000264057.2	hg19	CCDS2504.1	.	.	.	.	.	.	.	.	.	.	G	7.872	0.728341	0.15507	.	.	ENSG00000077044	ENST00000264057;ENST00000409813	T;T	0.78364	-0.99;-1.17	4.93	3.12	0.35913	.	0.425083	0.24007	N	0.042416	T	0.41419	0.1158	N	0.00652	-1.29	0.20403	N	0.999909	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33214	-0.9877	10	0.21014	T	0.42	.	4.9917	0.14218	0.132:0.4809:0.3087:0.0784	.	928;972	Q16760-2;Q16760	.;DGKD_HUMAN	I	972;928	ENSP00000264057:M972I;ENSP00000386455:M928I	ENSP00000264057:M972I	M	+	3	0	DGKD	234033665	1.000000	0.71417	0.994000	0.49952	0.551000	0.35334	1.017000	0.29989	0.790000	0.33803	0.563000	0.77884	ATG	.	.	.	none		0.617	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648		T	234368926	G	T	234368926	3	4	222	1	0	0	0	0	1	0	0	0	4469	1319	46	4	3034	4	DGKD	2	234368926	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	33579072	234368926	8830447	28	13438											
SATB1	6304	hgsc.bcm.edu	37	chr3	18390936	18390936	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagacagagtctggatggccTcttcgtcagggtacaggccc	8	8	13	12	1	3	2	1	0	2	2	4	3	3	3	2	4	1	1	2	4	1	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr3:18390936T>C	ENST00000338745.6	-	11	3752	c.2018A>G	c.(2017-2019)gAg>gGg	p.E673G	SATB1_ENST00000417717.2_Missense_Mutation_p.E705G|TBC1D5_ENST00000414318.2_Intron|SATB1_ENST00000454909.2_Missense_Mutation_p.E673G	NM_002971.4	NP_002962.1	Q01826	SATB1_HUMAN	SATB homeobox 1	673					activated T cell proliferation (GO:0050798)|apoptotic process (GO:0006915)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|epidermis development (GO:0008544)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|reflex (GO:0060004)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|endometrium(6)|large_intestine(4)|lung(10)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	32						CTGGATGGCCTCTTCGTCAGG	0.517																																					p.E705G		Atlas-SNP	.											.	SATB1	96	.	0			c.A2114G						PASS	.						141	140	140					3																	18390936		2203	4300	6503	SO:0001583	missense	6304	exon12			ATGGCCTCTTCGT		CCDS2631.1, CCDS56242.1	3p24.3	2011-07-19	2007-02-15		ENSG00000182568	ENSG00000182568		"Homeoboxes / CUT class"	10541	protein-coding gene	gene with protein product		602075	"special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA)"			1505028	Standard	NM_002971		Approved		uc003cbj.3	Q01826	OTTHUMG00000129890	ENST00000338745.6:c.2018A>G	chr3.hg19:g.18390936T>C	ENSP00000341024:p.Glu673Gly	202.0	0.0	.		175.0	73.0	.	NM_001195470	B3KXF1|C9JTR6|Q59EQ0	Missense_Mutation	SNP	ENST00000338745.6	hg19	CCDS2631.1	.	.	.	.	.	.	.	.	.	.	T	17.36	3.370587	0.61624	.	.	ENSG00000182568	ENST00000338745;ENST00000454909;ENST00000417717	D;D;D	0.96745	-4.11;-4.11;-4.11	5.27	5.27	0.74061	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.049242	0.85682	N	0.000000	D	0.96642	0.8904	L	0.32530	0.975	0.80722	D	1	B;D	0.89917	0.013;1.0	B;D	0.97110	0.004;1.0	D	0.97662	1.0161	10	0.87932	D	0	-15.8047	15.186	0.73002	0.0:0.0:0.0:1.0	.	705;673	Q01826-2;Q01826	.;SATB1_HUMAN	G	673;673;705	ENSP00000341024:E673G;ENSP00000399708:E673G;ENSP00000399518:E705G	ENSP00000341024:E673G	E	-	2	0	SATB1	18365940	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.911000	0.87458	1.993000	0.58246	0.460000	0.39030	GAG	.	.	.	none		0.517	SATB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252138.4	NM_001131010		C	18390936	T	C	18390936	3	2	222	1	0	0	0	0	1	0	0	0	13866	1551	54	3	277	3	SATB1	3	18390936	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10		18390936	179631494	29	13439											
EPM2AIP1	9852	hgsc.bcm.edu	37	chr3	37033483	37033483	+	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	gttgttgcccctactgaaacCaagaacgcttccatttcttt	9	14	6	12	1	1	2	0	1	1	1	2	2	2	2	4	0	4	3	4	0	4	6			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr3:37033483C>A	ENST00000322716.5	-	1	1312	c.1086G>T	c.(1084-1086)ttG>ttT	p.L362F	MLH1_ENST00000536378.1_5'Flank|MLH1_ENST00000458205.2_5'Flank|MLH1_ENST00000435176.1_5'Flank|MLH1_ENST00000539477.1_5'Flank|MLH1_ENST00000455445.2_5'Flank|MLH1_ENST00000231790.2_5'Flank	NM_014805.3	NP_055620.1	Q7L775	EPMIP_HUMAN	EPM2A (laforin) interacting protein 1	362					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						CTACTGAAACCAAGAACGCTT	0.413																																					p.L362F		Atlas-SNP	.											.	EPM2AIP1	47	.	0			c.G1086T						PASS	.						190	192	191					3																	37033483		1871	4110	5981	SO:0001583	missense	9852	exon1			TGAAACCAAGAAC	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.1086G>T	chr3.hg19:g.37033483C>A	ENSP00000406027:p.Leu362Phe	62.0	0.0	.		62.0	10.0	.	NM_014805	O94866|Q9H3L3	Missense_Mutation	SNP	ENST00000322716.5	hg19	CCDS46790.1	.	.	.	.	.	.	.	.	.	.	C	17.00	3.275856	0.59649	.	.	ENSG00000178567	ENST00000322716	T	0.31247	1.5	4.71	4.71	0.59529	.	.	.	.	.	T	0.41834	0.1176	L	0.27053	0.805	0.47698	D	0.999499	D	0.76494	0.999	D	0.74674	0.984	T	0.29549	-1.0008	9	0.49607	T	0.09	-10.3057	15.1824	0.72968	0.0:1.0:0.0:0.0	.	362	Q7L775	EPMIP_HUMAN	F	362	ENSP00000406027:L362F	ENSP00000406027:L362F	L	-	3	2	EPM2AIP1	37008487	1.000000	0.71417	1.000000	0.80357	0.797000	0.45037	2.648000	0.46647	2.424000	0.82194	0.591000	0.81541	TTG	.	.	.	none		0.413	EPM2AIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470593.1	NM_014805		A	37033483	C	A	37033483	3	1	222	1	0	0	0	0	1	0	0	0	5186	593	21	4	741	4	EPM2AIP1	3	37033483	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	18642547	37033483	160988947	30	13440											
SCN10A	6336	hgsc.bcm.edu	37	chr3	38740016	38740018	+	In_Frame_Del	DEL	ACT	ACT	-																															aagagcgttggggagaagtaActttgaagtgacttaagaat																								rs200063383	byFrequency	TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	ACT	ACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr3:38740016_38740018delACT	ENST00000449082.2	-	27	4692_4694	c.4693_4695delAGT	c.(4693-4695)agtdel	p.S1565del		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1565					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)	GGGAGAAGTAACTTTGAAGTGAC	0.478																																					p.1565_1566del		Atlas-INDEL	.											.	SCN10A	359	.	0			c.4694_4696del						PASS	.																																			SO:0001651	inframe_deletion	6336	exon27			.	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.4693_4695delAGT	chr3.hg19:g.38740016_38740018delACT	ENSP00000390600:p.Ser1565del	164.0	0.0	0		118.0	18.0	0.152542	NM_006514	A6NDQ1	In_Frame_Del	DEL	ENST00000449082.2	hg19	CCDS33736.1																																																																																			.	.	.	none		0.478	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		-	38740018	ACT	-	38740016	7	5	222	1	0	1	0	1	0	0	0	0	13925	40	2	0	1179	0	SCN10A	3	38740016	In_Frame_Del	DEL	ACT	TCGA-MH-A561-01A-11D-A26P-10	1706533	38740016	159282414	31	13441	136	2									
SCN10A	6336	hgsc.bcm.edu	37	chr3	38740022	38740022	+	Frame_Shift_Del	DEL	A	A	-																															gttggggagaagtaactttgAagtgacttaagaattgcaga																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr3:38740022delA	ENST00000449082.2	-	27	4688	c.4689delT	c.(4687-4689)cttfs	p.L1563fs		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1563					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)	AGTAACTTTGAAGTGACTTAA	0.478																																					p.Q1564fs		Atlas-INDEL	.											.	SCN10A	359	.	0			c.4690delC						PASS	.						58	59	59					3																	38740022		2203	4300	6503	SO:0001589	frameshift_variant	6336	exon27			.	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"Sodium channels", "Voltage-gated ion channels / Sodium channels"	10582	protein-coding gene	gene with protein product		604427	"sodium channel, voltage-gated, type X, alpha polypeptide"			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.4689delT	chr3.hg19:g.38740022delA	ENSP00000390600:p.Leu1563fs	158.0	0.0	0		107.0	18.0	0.168224	NM_006514	A6NDQ1	Frame_Shift_Del	DEL	ENST00000449082.2	hg19	CCDS33736.1																																																																																			.	.	.	none		0.478	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		-	38740022	A	-	38740022	7	5	222	1	0	1	0	1	0	0	0	0	13925	233	9	0	1185	0	SCN10A	3	38740022	Frame_Shift_Del	DEL	A	TCGA-MH-A561-01A-11D-A26P-10	6	38740022	159282408	32	13442	136	2									
LIMD1	8994	hgsc.bcm.edu	37	chr3	45637412	45637412	+	Missense_Mutation	SNP	T	T	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	cccaaatcttacctttccagTtctgccccgtcatcctcgcc	6	12	4	19	2	3	0	1	0	2	0	6	0	5	0	7	0	2	1	7	0	2	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr3:45637412T>G	ENST00000273317.4	+	1	1062	c.1041T>G	c.(1039-1041)agT>agG	p.S347R	LIMD1_ENST00000465039.1_Intron|LIMD1_ENST00000440097.1_Missense_Mutation_p.S347R	NM_014240.2	NP_055055.1	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1	347					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)		ACCTTTCCAGTTCTGCCCCGT	0.622																																					p.S347R		Atlas-SNP	.											.	LIMD1	34	.	0			c.T1041G						PASS	.						78	78	78					3																	45637412		2203	4300	6503	SO:0001583	missense	8994	exon1			TTCCAGTTCTGCC	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.1041T>G	chr3.hg19:g.45637412T>G	ENSP00000273317:p.Ser347Arg	251.0	0.0	.		231.0	79.0	.	NM_014240	Q17RQ1|Q9BQQ9|Q9NQ47	Missense_Mutation	SNP	ENST00000273317.4	hg19	CCDS2729.1	.	.	.	.	.	.	.	.	.	.	T	9.543	1.113931	0.20795	.	.	ENSG00000144791	ENST00000440097;ENST00000273317	T;T	0.58506	0.33;0.53	4.73	1.1	0.20463	.	1.824180	0.02460	N	0.086523	T	0.44953	0.1318	L	0.29908	0.895	0.09310	N	1	B	0.15141	0.012	B	0.09377	0.004	T	0.14420	-1.0473	10	0.22706	T	0.39	.	6.3277	0.21253	0.0:0.4757:0.0:0.5243	.	347	Q9UGP4	LIMD1_HUMAN	R	347	ENSP00000394537:S347R;ENSP00000273317:S347R	ENSP00000273317:S347R	S	+	3	2	LIMD1	45612416	0.001000	0.12720	0.006000	0.13384	0.180000	0.23129	-0.032000	0.12266	0.203000	0.20529	0.533000	0.62120	AGT	.	.	.	none		0.622	LIMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257327.1	NM_014240		G	45637412	T	G	45637412	3	3	222	1	0	0	0	0	1	0	0	0	8805	1722	60	5	1043	5	LIMD1	3	45637412	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	6897390	45637412	152385018	33	13443											
DNAH1	25981	hgsc.bcm.edu	37	chr3	52416419	52416419	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatgtgaagaaggtcctgcTcaaggcgggcctacagaacc	11	7	13	10	1	1	4	1	2	0	2	2	4	2	4	3	3	3	1	3	3	5	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr3:52416419T>C	ENST00000420323.2	+	50	8150	c.7889T>C	c.(7888-7890)cTc>cCc	p.L2630P		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	2630	AAA 4. {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)		AAGGTCCTGCTCAAGGCGGGC	0.582																																					p.L2630P		Atlas-SNP	.											.	DNAH1	534	.	0			c.T7889C						PASS	.						169	177	175					3																	52416419		2125	4239	6364	SO:0001583	missense	25981	exon50			TCCTGCTCAAGGC	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.7889T>C	chr3.hg19:g.52416419T>C	ENSP00000401514:p.Leu2630Pro	197.0	0.0	.		143.0	57.0	.	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	hg19	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	T	18.02	3.529987	0.64860	.	.	ENSG00000114841	ENST00000420323	T	0.54279	0.58	4.49	4.49	0.54785	.	0.155058	0.30126	N	0.010343	T	0.76898	0.4052	M	0.93507	3.425	0.80722	D	1	D	0.61697	0.99	D	0.67725	0.953	T	0.80817	-0.1213	10	0.35671	T	0.21	.	13.9669	0.64213	0.0:0.0:0.0:1.0	.	2630	C9JXH6	.	P	2630	ENSP00000401514:L2630P	ENSP00000401514:L2630P	L	+	2	0	DNAH1	52391459	1.000000	0.71417	1.000000	0.80357	0.723000	0.41478	5.444000	0.66587	1.883000	0.54544	0.379000	0.24179	CTC	.	.	.	none		0.582	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		C	52416419	T	C	52416419	3	2	222	1	0	0	0	0	1	0	0	0	4599	1551	54	3	8083	3	DNAH1	3	52416419	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	6779007	52416419	145606011	34	13444											
IGSF10	285313	hgsc.bcm.edu	37	chr3	151166796	151166796	+	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	gaccatgttagcttcatttcCagactgatctgtcatattca	10	15	6	10	0	4	2	3	1	1	1	5	3	5	2	2	0	1	2	2	0	2	5			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr3:151166796C>T	ENST00000282466.3	-	4	972	c.973G>A	c.(973-975)Gga>Aga	p.G325R		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	325					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)			GCTTCATTTCCAGACTGATCT	0.433																																					p.G325R		Atlas-SNP	.											IGSF10,NS,malignant_melanoma,0,1	IGSF10	279	.	0			c.G973A						PASS	.						108	109	109					3																	151166796		2203	4300	6503	SO:0001583	missense	285313	exon4			CATTTCCAGACTG	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.973G>A	chr3.hg19:g.151166796C>T	ENSP00000282466:p.Gly325Arg	126.0	0.0	.		117.0	46.0	.	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	hg19	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	C	13.46	2.243180	0.39697	.	.	ENSG00000152580	ENST00000282466	T	0.75260	-0.92	5.37	4.5	0.54988	.	0.000000	0.47093	D	0.000256	T	0.67915	0.2944	M	0.64997	1.995	0.38362	D	0.944634	B	0.34200	0.441	B	0.26094	0.066	T	0.72513	-0.4270	10	0.87932	D	0	.	10.7221	0.46046	0.0:0.7971:0.1309:0.072	.	325	Q6WRI0	IGS10_HUMAN	R	325	ENSP00000282466:G325R	ENSP00000282466:G325R	G	-	1	0	IGSF10	152649486	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.805000	0.38883	1.270000	0.44297	0.650000	0.86243	GGA	.	.	.	none		0.433	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		T	151166796	C	T	151166796	3	4	222	1	0	0	0	0	1	0	0	0	7604	603	21	2	6958	2	IGSF10	3	151166796	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	98750377	151166796	46855634	35	13445											
BOD1L	259282	hgsc.bcm.edu	37	chr4	13601745	13601745	+	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	ggccctcacagtcttccaccGagctcgtagagatgatgcca	9	8	10	14	2	2	2	1	1	1	1	4	4	3	2	4	1	2	2	4	1	1	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr4:13601745G>A	ENST00000040738.5	-	10	6914	c.6779C>T	c.(6778-6780)tCg>tTg	p.S2260L		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	2260						nucleus (GO:0005634)	DNA binding (GO:0003677)										GTCTTCCACCGAGCTCGTAGA	0.542																																					p.S2260L		Atlas-SNP	.											BOD1L,colon,carcinoma,0,1	.	.	.	0			c.C6779T						PASS	.						79	69	72					4																	13601745		2203	4300	6503	SO:0001583	missense	259282	exon10			TCCACCGAGCTCG	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.6779C>T	chr4.hg19:g.13601745G>A	ENSP00000040738:p.Ser2260Leu	171.0	0.0	.		149.0	16.0	.	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	hg19	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	G	21.7	4.194306	0.78902	.	.	ENSG00000038219	ENST00000040738	T	0.12255	2.7	5.46	5.46	0.80206	.	0.000000	0.45126	D	0.000387	T	0.23727	0.0574	M	0.64997	1.995	0.30881	N	0.731467	D	0.63046	0.992	P	0.51055	0.657	T	0.15350	-1.0440	10	0.72032	D	0.01	-3.6924	11.8817	0.52579	0.0832:0.0:0.9168:0.0	.	2260	Q8NFC6	BOD1L_HUMAN	L	2260	ENSP00000040738:S2260L	ENSP00000040738:S2260L	S	-	2	0	BOD1L	13210843	0.993000	0.37304	0.944000	0.38274	0.889000	0.51656	2.414000	0.44627	2.573000	0.86826	0.650000	0.86243	TCG	.	.	.	none		0.542	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		A	13601745	G	A	13601745	3	1	222	1	0	0	0	0	1	0	0	0	1483	1059	37	1	2444	1	BOD1L	4	13601745	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10		13601745	177552531	36	13446											
RUFY3	22902	hgsc.bcm.edu	37	chr4	71588406	71588406	+	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	agtgtccatggatggagaatGgctctgcctgcgagagctgg	8	9	16	8	1	1	2	0	0	1	2	2	5	2	3	2	4	3	2	2	4	1	0			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr4:71588406G>T	ENST00000226328.4	+	1	679	c.116G>T	c.(115-117)tGg>tTg	p.W39L	RUFY3_ENST00000417478.2_Intron|RUFY3_ENST00000381006.3_Missense_Mutation_p.W39L|RUFY3_ENST00000536664.1_Missense_Mutation_p.W5L	NM_014961.3	NP_055776.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3	39					negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)				endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			GATGGAGAATGGCTCTGCCTG	0.532																																					p.W39L		Atlas-SNP	.											.	RUFY3	61	.	0			c.G116T						PASS	.						204	166	179					4																	71588406		2203	4300	6503	SO:0001583	missense	22902	exon1			GAGAATGGCTCTG	AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189		"Zinc fingers, FYVE domain containing"	30285	protein-coding gene	gene with protein product	"single axon-related 1"	611194				17439943	Standard	NM_001130709		Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910	ENST00000226328.4:c.116G>T	chr4.hg19:g.71588406G>T	ENSP00000226328:p.Trp39Leu	284.0	1.0	.		247.0	93.0	.	NM_001037442	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	Missense_Mutation	SNP	ENST00000226328.4	hg19	CCDS3547.1	.	.	.	.	.	.	.	.	.	.	G	19.28	3.797286	0.70567	.	.	ENSG00000018189	ENST00000381006;ENST00000226328;ENST00000536664	T;T;T	0.35973	1.81;1.28;2.13	5.51	5.51	0.81932	.	0.200815	0.47852	D	0.000210	T	0.57227	0.2039	L	0.52011	1.625	0.58432	D	0.999999	B;D;D	0.67145	0.001;0.996;0.967	B;D;P	0.78314	0.002;0.991;0.901	T	0.58301	-0.7660	10	0.87932	D	0	0.0099	19.4131	0.94683	0.0:0.0:1.0:0.0	.	5;39;39	B4DKC2;Q7L099-3;Q7L099	.;.;RUFY3_HUMAN	L	39;39;5	ENSP00000370394:W39L;ENSP00000226328:W39L;ENSP00000443652:W5L	ENSP00000226328:W39L	W	+	2	0	RUFY3	71807270	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.476000	0.97823	2.590000	0.87494	0.555000	0.69702	TGG	.	.	.	none		0.532	RUFY3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252161.2	NM_014961		T	71588406	G	T	71588406	3	4	222	1	0	0	0	0	1	0	0	0	13753	1357	47	4	480	4	RUFY3	4	71588406	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	57986661	71588406	119565870	37	13447											
FBXW7	55294	hgsc.bcm.edu	37	chr4	153250883	153250883	+	Frame_Shift_Del	DEL	G	G	-																															atcagaaccactaactattcGgttaccacaaaactgtaagc																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr4:153250883delG	ENST00000281708.4	-	8	2406	c.1177delC	c.(1177-1179)cgafs	p.R393fs	FBXW7_ENST00000393956.3_Frame_Shift_Del_p.R217fs|FBXW7_ENST00000603548.1_Frame_Shift_Del_p.R393fs|FBXW7_ENST00000263981.5_Frame_Shift_Del_p.R313fs|FBXW7_ENST00000296555.5_Frame_Shift_Del_p.R275fs|FBXW7_ENST00000603841.1_Frame_Shift_Del_p.R393fs	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	393					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R393*(7)|p.R313*(1)|p.R154*(1)|p.?(1)|p.R275*(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				CTAACTATTCGGTTACCACAA	0.343			"Mis, N, D, F"		"colorectal, endometrial, T-ALL"																																p.R393fs		Atlas-Indel,Pindel	.		Rec	yes		4	4q31.3	55294	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"		"E, L"	FBXW7_NM_018315_2,NS,carcinoma,-1,5	FBXW7	2157	.	11	Substitution - Nonsense(10)|Unknown(1)	endometrium(5)|large_intestine(4)|haematopoietic_and_lymphoid_tissue(1)|stomach(1)	c.1178delG						PASS	.						118	107	111					4																	153250883		2203	4300	6503	SO:0001589	frameshift_variant	55294	exon8			.	AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"F-boxes / WD-40 domains", "WD repeat domain containing"	16712	protein-coding gene	gene with protein product	"archipelago homolog (Drosophila)"	606278	"F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)", "F-box and WD repeat domain containing 7"			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1177delC	chr4.hg19:g.153250883delG	ENSP00000281708:p.Arg393fs	89.0	0.0	0		98.0	35.0	0.357143	NM_033632	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Frame_Shift_Del	DEL	ENST00000281708.4	hg19	CCDS3777.1																																																																																			.	.	.	none		0.343	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			-	153250883	G	-	153250883	7	5	222	1	0	1	0	1	0	0	0	0	5776	1124	39	0	966	0	FBXW7	4	153250883	Frame_Shift_Del	DEL	G	TCGA-MH-A561-01A-11D-A26P-10	81662477	153250883	37903393	38	13448											
TAF7	6879	hgsc.bcm.edu	37	chr5	140699374	140699374	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaaaaagtttttttatcaaTggttttcaagctttccataa	13	18	5	5	0	2	0	2	0	0	0	3	0	3	0	1	1	1	4	1	1	7	9			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr5:140699374T>C	ENST00000313368.5	-	1	956	c.238A>G	c.(238-240)Att>Gtt	p.I80V		NM_005642.2	NP_005633.2	Q15545	TAF7_HUMAN	TAF7 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 55kDa	80					DNA-templated transcription, initiation (GO:0006352)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of histone acetylation (GO:0035067)|negative regulation of protein kinase activity (GO:0006469)|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)|spermine transport (GO:0000296)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	histone acetyltransferase binding (GO:0035035)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|vitamin D receptor binding (GO:0042809)			central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTTTATCAATGGTTTTCAAG	0.443																																					p.I80V		Atlas-SNP	.											.	TAF7	28	.	0			c.A238G						PASS	.						120	113	116					5																	140699374		2203	4300	6503	SO:0001583	missense	6879	exon1			TATCAATGGTTTT	AF349038	CCDS4259.1	5q31	2008-02-05	2002-08-29	2001-12-07	ENSG00000178913	ENSG00000178913			11541	protein-coding gene	gene with protein product		600573	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, F, 55kD"	TAF2F		7824954	Standard	NM_005642		Approved	TAFII55	uc003ljg.3	Q15545	OTTHUMG00000129628	ENST00000313368.5:c.238A>G	chr5.hg19:g.140699374T>C	ENSP00000312709:p.Ile80Val	111.0	0.0	.		90.0	29.0	.	NM_005642	B2RBV9|Q13036	Missense_Mutation	SNP	ENST00000313368.5	hg19	CCDS4259.1	.	.	.	.	.	.	.	.	.	.	T	10.28	1.307342	0.23821	.	.	ENSG00000178913	ENST00000313368	T	0.23348	1.91	5.08	3.93	0.45458	TAFII55 protein, conserved region (1);	0.259807	0.37809	N	0.001931	T	0.13586	0.0329	N	0.17312	0.475	0.41194	D	0.986322	B	0.09022	0.002	B	0.12837	0.008	T	0.10567	-1.0624	10	0.19590	T	0.45	-6.4089	7.5444	0.27757	0.0:0.0947:0.0:0.9053	.	80	Q15545	TAF7_HUMAN	V	80	ENSP00000312709:I80V	ENSP00000312709:I80V	I	-	1	0	TAF7	140679558	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.373000	0.59537	1.092000	0.41356	0.533000	0.62120	ATT	.	.	.	none		0.443	TAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251823.2	NM_005642		C	140699374	T	C	140699374	3	2	222	1	0	0	0	0	1	0	0	0	15544	1464	51	3	815	3	TAF7	5	140699374	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10		140699374	40215886	39	13449											
TFAP2A	7020	hgsc.bcm.edu	37	chr6	10398689	10398689	+	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	tctttgtcactgcttttggcGttgttgtccgtgtggctgtt	1	20	12	8	2	2	0	1	0	1	0	3	0	3	0	1	2	1	5	1	2	0	6			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:10398689G>C	ENST00000482890.1	-	8	1627	c.1275C>G	c.(1273-1275)aaC>aaG	p.N425K	TFAP2A_ENST00000497266.1_5'Flank|TFAP2A_ENST00000379608.3_Missense_Mutation_p.N419K|TFAP2A_ENST00000319516.4_Missense_Mutation_p.N421K|TFAP2A_ENST00000379613.3_Missense_Mutation_p.N427K|TFAP2A_ENST00000379604.2_Missense_Mutation_p.N425K			P05549	AP2A_HUMAN	transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha)	425					anterior neuropore closure (GO:0021506)|basement membrane organization (GO:0071711)|bone morphogenesis (GO:0060349)|cellular response to iron ion (GO:0071281)|cornea development in camera-type eye (GO:0061303)|embryonic body morphogenesis (GO:0010172)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|embryonic pattern specification (GO:0009880)|epidermis morphogenesis (GO:0048730)|eyelid development in camera-type eye (GO:0061029)|face morphogenesis (GO:0060325)|forebrain neuron development (GO:0021884)|inner ear morphogenesis (GO:0042472)|keratinocyte development (GO:0003334)|kidney development (GO:0001822)|lens induction in camera-type eye (GO:0060235)|metanephric nephron development (GO:0072210)|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 neuron apoptotic process (GO:0043524)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|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)|neural crest cell development (GO:0014032)|oculomotor nerve formation (GO:0021623)|optic cup structural organization (GO:0003409)|optic vesicle morphogenesis (GO:0003404)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of tooth mineralization (GO:0070172)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell differentiation (GO:0045595)|regulation of neuron differentiation (GO:0045664)|retina layer formation (GO:0010842)|sensory perception of sound (GO:0007605)|sympathetic nervous system development (GO:0048485)|transcription from RNA polymerase II promoter (GO:0006366)|trigeminal nerve development (GO:0021559)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|protein dimerization activity (GO:0046983)|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 (GO:0000982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II 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)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)	13	Breast(50;0.0427)|Ovarian(93;0.0991)	all_hematologic(90;0.107)				TGCTTTTGGCGTTGTTGTCCG	0.637																																					p.N425K		Atlas-SNP	.											.	TFAP2A	129	.	0			c.C1275G						PASS	.						303	314	310					6																	10398689		2203	4300	6503	SO:0001583	missense	7020	exon7			TTTGGCGTTGTTG	X52611	CCDS4510.1, CCDS34337.1, CCDS43422.1	6p24.3	2013-09-19	2001-11-28		ENSG00000137203	ENSG00000137203			11742	protein-coding gene	gene with protein product		107580	"transcription factor AP-2 alpha (activating enhancer-binding protein 2 alpha)"	TFAP2, AP2TF		1916817, 3063603	Standard	NM_001032280		Approved	AP-2	uc003myr.3	P05549	OTTHUMG00000014235	ENST00000482890.1:c.1275C>G	chr6.hg19:g.10398689G>C	ENSP00000418541:p.Asn425Lys	193.0	0.0	.		146.0	46.0	.	NM_003220	Q13777|Q5TAV5|Q8N1C6	Missense_Mutation	SNP	ENST00000482890.1	hg19	CCDS4510.1	.	.	.	.	.	.	.	.	.	.	G	5.052	0.195211	0.09599	.	.	ENSG00000137203	ENST00000379613;ENST00000379604;ENST00000319516;ENST00000379608;ENST00000482890	D;D;D;D;D	0.96913	-4.17;-4.17;-4.17;-4.17;-4.17	5.41	5.41	0.78517	.	0.166295	0.64402	D	0.000003	T	0.82139	0.4972	N	0.02539	-0.55	0.34515	D	0.707504	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.74665	-0.3589	10	0.08381	T	0.77	-4.3896	19.197	0.93693	0.0:0.0:1.0:0.0	.	421;425;419	Q5TAV5;P05549;Q8N1C6	.;AP2A_HUMAN;.	K	427;425;421;419;425	ENSP00000368933:N427K;ENSP00000368924:N425K;ENSP00000316516:N421K;ENSP00000368928:N419K;ENSP00000418541:N425K	ENSP00000316516:N421K	N	-	3	2	TFAP2A	10506675	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.556000	0.53734	2.532000	0.85374	0.655000	0.94253	AAC	.	.	.	none		0.637	TFAP2A-007	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353619.2	NM_003220		C	10398689	G	C	10398689	3	2	222	1	0	0	0	0	1	0	0	0	15799	1136	40	4	42	4	TFAP2A	6	10398689	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10		10398689	160716378	40	13450											
KIF13A	63971	hgsc.bcm.edu	37	chr6	17817447	17817447	+	Missense_Mutation	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	ttgtttctccaggacctgaaCcacattttgaactgggtcta	9	14	8	10	0	2	2	0	2	2	0	3	3	2	3	3	2	2	1	3	2	3	5			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:17817447C>T	ENST00000259711.6	-	17	1909	c.1804G>A	c.(1804-1806)Gtt>Att	p.V602I	KIF13A_ENST00000378826.2_Missense_Mutation_p.V602I|KIF13A_ENST00000378816.5_Missense_Mutation_p.V602I|KIF13A_ENST00000378843.2_Missense_Mutation_p.V602I|KIF13A_ENST00000378814.5_Missense_Mutation_p.V602I|KIF13A_ENST00000503342.1_5'Flank	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	602					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)			AGGACCTGAACCACATTTTGA	0.532																																					p.V602I		Atlas-SNP	.											.	KIF13A	276	.	0			c.G1804A						PASS	.						74	79	78					6																	17817447		2040	4210	6250	SO:0001583	missense	63971	exon17			CCTGAACCACATT	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.1804G>A	chr6.hg19:g.17817447C>T	ENSP00000259711:p.Val602Ile	153.0	0.0	.		131.0	41.0	.	NM_001105567	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Missense_Mutation	SNP	ENST00000259711.6	hg19	CCDS47381.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.074673	0.76415	.	.	ENSG00000137177	ENST00000378814;ENST00000259711;ENST00000378826;ENST00000378843;ENST00000378816	T;T;T;T;T	0.71579	-0.58;-0.58;-0.58;-0.58;-0.58	5.92	5.92	0.95590	.	0.060329	0.64402	D	0.000003	T	0.43787	0.1263	L	0.27053	0.805	0.58432	D	0.99999	B;B;P;B;P	0.37731	0.112;0.094;0.48;0.112;0.607	B;B;B;B;B	0.34722	0.034;0.108;0.188;0.034;0.187	T	0.52064	-0.8625	10	0.08599	T	0.76	.	20.3248	0.98698	0.0:1.0:0.0:0.0	.	573;602;602;602;602	E7ER65;Q9H1H9-4;Q9H1H9-2;Q9H1H9;Q9H1H9-3	.;.;.;KI13A_HUMAN;.	I	602	ENSP00000368091:V602I;ENSP00000259711:V602I;ENSP00000368103:V602I;ENSP00000368120:V602I;ENSP00000368093:V602I	ENSP00000259711:V602I	V	-	1	0	KIF13A	17925426	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.432000	0.80349	2.818000	0.97014	0.655000	0.94253	GTT	.	.	.	none		0.532	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4			T	17817447	C	T	17817447	3	4	222	1	0	0	0	0	1	0	0	0	8281	507	18	2	3730	2	KIF13A	6	17817447	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	7418758	17817447	153297620	41	13451											
UHRF1BP1	54887	hgsc.bcm.edu	37	chr6	34825520	34825520	+	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	gttccttgtcctaatctctaCattcagttaaatggtctgac	9	16	6	10	0	3	1	1	1	2	0	6	1	5	1	2	1	1	2	2	1	4	6			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:34825520C>T	ENST00000192788.5	+	13	1764	c.1593C>T	c.(1591-1593)taC>taT	p.Y531Y	UHRF1BP1_ENST00000452449.2_Silent_p.Y531Y	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	531							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						CTAATCTCTACATTCAGTTAA	0.398																																					p.Y531Y		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.C1593T						PASS	.						158	148	151					6																	34825520		1859	4088	5947	SO:0001819	synonymous_variant	54887	exon13			TCTCTACATTCAG	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.1593C>T	chr6.hg19:g.34825520C>T		174.0	0.0	.		144.0	9.0	.	NM_017754	Q9NXE0	Silent	SNP	ENST00000192788.5	hg19	CCDS43455.1																																																																																			.	.	.	none		0.398	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754		T	34825520	C	T	34825520	2	4	222	1	0	0	0	0	0	0	0	1	16980	489	17	2		2	UHRF1BP1	6	34825520	Silent	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	17008073	34825520	136289547	42	13452											
COL12A1	1303	hgsc.bcm.edu	37	chr6	75861881	75861881	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcctttgtacggcaagttTgccacagcttgcaacaagct	9	11	8	13	1	0	0	0	0	0	0	1	0	1	0	3	1	6	6	3	1	4	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:75861881T>C	ENST00000322507.8	-	19	4110	c.3801A>G	c.(3799-3801)gcA>gcG	p.A1267A	COL12A1_ENST00000483888.2_Silent_p.A1267A|COL12A1_ENST00000416123.2_Silent_p.A1267A|COL12A1_ENST00000345356.6_Silent_p.A103A	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1267	VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						ACGGCAAGTTTGCCACAGCTT	0.473																																					p.A1267A		Atlas-SNP	.											.	COL12A1	385	.	0			c.A3801G						PASS	.						102	99	100					6																	75861881		1976	4162	6138	SO:0001819	synonymous_variant	1303	exon19			CAAGTTTGCCACA	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.3801A>G	chr6.hg19:g.75861881T>C		211.0	0.0	.		199.0	74.0	.	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	hg19	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	T	4.645	0.119852	0.08881	.	.	ENSG00000111799	ENST00000419671	.	.	.	5.94	-10.2	0.00374	.	.	.	.	.	T	0.24851	0.0603	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48570	-0.9024	4	.	.	.	.	5.2576	0.15555	0.078:0.3395:0.3536:0.2289	.	.	.	.	E	9	.	.	K	-	1	0	COL12A1	75918601	0.080000	0.21391	0.440000	0.26846	0.478000	0.33099	-0.719000	0.04974	-1.241000	0.02526	-1.293000	0.01348	AAA	.	.	.	none		0.473	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		C	75861881	T	C	75861881	2	2	222	1	0	0	0	0	0	0	0	1	3671	1799	63	3		3	COL12A1	6	75861881	Silent	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	41036361	75861881	95253186	43	13453											
TMEM30A	55754	hgsc.bcm.edu	37	chr6	75977367	75977367	+	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	aaacacagacctcaaatgacTtttccagtgtgaagttaatg	15	11	7	8	0	1	3	1	2	0	1	2	3	2	3	2	0	1	1	2	0	4	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:75977367T>A	ENST00000230461.6	-	2	664	c.335A>T	c.(334-336)aAg>aTg	p.K112M	TMEM30A_ENST00000475111.2_Intron|TMEM30A_ENST00000370050.5_De_novo_Start_InFrame	NM_018247.3	NP_060717.1	Q9NV96	CC50A_HUMAN	transmembrane protein 30A	112					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						CTCAAATGACTTTTCCAGTGT	0.363																																					p.K112M		Atlas-SNP	.											.	TMEM30A	40	.	0			c.A335T						PASS	.						130	135	133					6																	75977367		2203	4300	6503	SO:0001583	missense	55754	exon2			AATGACTTTTCCA	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.335A>T	chr6.hg19:g.75977367T>A	ENSP00000230461:p.Lys112Met	41.0	0.0	.		44.0	18.0	.	NM_018247	A8K9V8|E1P539|Q658Z3|Q96H09|Q9NSL9	Missense_Mutation	SNP	ENST00000230461.6	hg19	CCDS4983.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.082970	0.76642	.	.	ENSG00000112697	ENST00000230461;ENST00000545449	.	.	.	5.28	5.28	0.74379	.	0.326351	0.37761	N	0.001944	T	0.77890	0.4198	M	0.84326	2.69	0.80722	D	1	B	0.27264	0.173	P	0.47251	0.542	T	0.80511	-0.1350	9	0.66056	D	0.02	.	14.8721	0.70465	0.0:0.0:0.0:1.0	.	112	Q9NV96	CC50A_HUMAN	M	112;96	.	ENSP00000230461:K112M	K	-	2	0	TMEM30A	76034087	1.000000	0.71417	0.998000	0.56505	0.886000	0.51366	7.596000	0.82721	1.997000	0.58415	0.454000	0.30748	AAG	.	.	.	none		0.363	TMEM30A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041248.2	NM_018247		A	75977367	T	A	75977367	3	1	222	1	0	0	0	0	1	0	0	0	16165	1609	56	5	774	5	TMEM30A	6	75977367	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	115486	75977367	95137700	44	13454											
MAP3K7	6885	hgsc.bcm.edu	37	chr6	91226399	91226400	+	Splice_Site	DEL	GC	GC	-																															cagttctgcaactagttcttGcctacaaacaaataccacat																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:91226399_91226400delGC	ENST00000369329.3	-	17	1802_1803	c.1641_1642delGC	c.(1639-1644)aagcaa>aaaa	p.Q548fs	MAP3K7_ENST00000479630.1_5'UTR|MAP3K7_ENST00000369332.3_Splice_Site_p.Q521fs|MAP3K7_ENST00000369320.1_Splice_Site_p.Q202fs|MAP3K7_ENST00000369327.3_Splice_Site_p.A482fs|MAP3K7_ENST00000369325.3_Splice_Site_p.A509fs	NM_145331.2	NP_663304.1	O43318	M3K7_HUMAN	mitogen-activated protein kinase kinase kinase 7	548					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|Fc-epsilon receptor signaling pathway (GO:0038095)|histone H3 acetylation (GO:0043966)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of ripoptosome assembly involved in necroptotic process (GO:1902443)|neural tube formation (GO:0001841)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|regulation of reactive oxygen species metabolic process (GO:2000377)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase activity (GO:0004708)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)			endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	28		all_cancers(76;6.4e-08)|Acute lymphoblastic leukemia(125;1.43e-09)|Prostate(29;9.32e-09)|all_hematologic(105;3.69e-06)|all_epithelial(107;0.000187)|Ovarian(999;0.0164)		OV - Ovarian serous cystadenocarcinoma(136;2.05e-11)|all cancers(137;3.25e-11)|GBM - Glioblastoma multiforme(226;0.0416)|BRCA - Breast invasive adenocarcinoma(108;0.0429)		ACTAGTTCTTGCCTACAAACAA	0.351																																					p.548_548del		Atlas-INDEL	.											.	MAP3K7	100	.	0			c.1642_1643del						PASS	.																																			SO:0001630	splice_region_variant	6885	exon17			.	AB009356	CCDS5027.1, CCDS5028.1, CCDS5029.1, CCDS5030.1	6q15	2011-06-09			ENSG00000135341	ENSG00000135341		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6859	protein-coding gene	gene with protein product		602614		TAK1		9466656	Standard	NM_003188		Approved	MEKK7	uc003pnz.2	O43318	OTTHUMG00000015217	ENST00000369329.3:c.1641-1GC>-	chr6.hg19:g.91226399_91226400delGC		76.0	0.0	0		66.0	20.0	0.30303	NM_145331	B2RE27|E1P523|O43317|O43319|Q5TDN2|Q5TDN3|Q5TDT7|Q9NTR3|Q9NZ70	Frame_Shift_Del	DEL	ENST00000369329.3	hg19	CCDS5028.1																																																																																			.	.	.	none		0.351	MAP3K7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041530.1	NM_145331	Frame_Shift_Del	-	91226400	GC	-	91226399	8	5	222	1	0	1	0	1	0	0	1	0	9262	1333	46	0	182	0	MAP3K7	6	91226399	Splice_Site	DEL	GC	TCGA-MH-A561-01A-11D-A26P-10	15249032	91226399	79888668	45	13455											
GRIK2	2898	hgsc.bcm.edu	37	chr6	102513771	102513771	+	Intron	DEL	T	T	-																															catcaccatcttcatcatcaTtatcatcatgttcttaataa																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:102513771delT	ENST00000421544.1	+	16	3052				GRIK2_ENST00000369134.4_Intron|GRIK2_ENST00000369138.1_Frame_Shift_Del_p.L888fs|GRIK2_ENST00000369137.3_Intron|GRIK2_ENST00000413795.1_Intron	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2						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)	ttcatcatcattatcatcatG	0.363																																					p.S887fs		Atlas-Indel,Pindel	.											.	GRIK2	487	.	0			c.2661delA						PASS	.						287	228	246					6																	102513771		692	1590	2282	SO:0001627	intron_variant	2898	exon16			.		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.2563-2451T>-	chr6.hg19:g.102513771delT		96.0	0.0	0		80.0	37.0	0.4625	NM_001166247	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Frame_Shift_Del	DEL	ENST00000421544.1	hg19	CCDS5048.1																																																																																			.	.	.	none		0.363	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1			-	102513771	T	-	102513771	6	5	222	0	1	1	0	1	0	0	0	0	6781	1490	52	0		0	GRIK2	6	102513771	Intron	DEL	T	TCGA-MH-A561-01A-11D-A26P-10	11287372	102513771	68601296	46	13456											
HDAC2	3066	hgsc.bcm.edu	37	chr6	114264645	114264645	+	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	tctgagaattcttcatcacaAgctatccgcttgtctgatgc	9	14	7	11	1	5	2	2	2	3	1	6	3	6	2	1	0	2	2	1	0	3	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr6:114264645A>C	ENST00000519065.1	-	12	1624	c.1248T>G	c.(1246-1248)gcT>gcG	p.A416A	HDAC2_ENST00000519108.1_Silent_p.A386A|HDAC2_ENST00000398283.2_Silent_p.A510A|HDAC2_ENST00000368632.2_Silent_p.A386A			Q92769	HDAC2_HUMAN	histone deacetylase 2	416					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)	CTTCATCACAAGCTATCCGCT	0.363																																					p.A416A		Atlas-SNP	.											.	HDAC2	102	.	0			c.T1248G						PASS	.						126	110	115					6																	114264645		1841	4082	5923	SO:0001819	synonymous_variant	3066	exon12			ATCACAAGCTATC	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.1248T>G	chr6.hg19:g.114264645A>C		16.0	0.0	.		15.0	8.0	.	NM_001527	B3KRS5|B4DL58|E1P561|Q5SRI8|Q5SZ86|Q8NEH4	Silent	SNP	ENST00000519065.1	hg19	CCDS43493.2																																																																																			.	.	.	none		0.363	HDAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041909.2			C	114264645	A	C	114264645	2	2	222	1	0	0	0	0	0	0	0	1	7014	59	3	5		5	HDAC2	6	114264645	Silent	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	11750874	114264645	56850422	47	13457											
ELMO1	9844	hgsc.bcm.edu	37	chr7	37053037	37053037	+	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	ggaagtcgttgcaggtctcaCtagctggaggaaagagatgg	11	8	16	6	1	1	1	1	0	1	1	3	5	1	4	0	5	2	3	0	5	3	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr7:37053037C>T	ENST00000310758.4	-	16	1951	c.1304G>A	c.(1303-1305)aGt>aAt	p.S435N	ELMO1_ENST00000341056.3_Missense_Mutation_p.S137N|ELMO1-AS1_ENST00000419535.1_RNA|ELMO1_ENST00000448602.1_Missense_Mutation_p.S435N|ELMO1_ENST00000442504.1_Missense_Mutation_p.S435N	NM_001206480.1|NM_014800.10	NP_001193409.1|NP_055615.8	Q92556	ELMO1_HUMAN	engulfment and cell motility 1	435	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|phagocytosis, engulfment (GO:0006911)|Rac protein signal transduction (GO:0016601)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(28)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	58						GCAGGTCTCACTAGCTGGAGG	0.458																																					p.S435N		Atlas-SNP	.											.	ELMO1	141	.	0			c.G1304A						PASS	.						79	75	76					7																	37053037		2203	4300	6503	SO:0001583	missense	9844	exon16			GTCTCACTAGCTG	AF398885	CCDS5449.1, CCDS5450.1	7p14.1	2012-07-10	2006-01-20		ENSG00000155849	ENSG00000155849		"Engulfment and cell motility proteins"	16286	protein-coding gene	gene with protein product		606420	"engulfment and cell motility 1 (ced-12 homolog, C. elegans)"			11595183	Standard	NM_001039459		Approved	KIAA0281, CED12, ELMO-1, CED-12	uc003tfk.2	Q92556	OTTHUMG00000023701	ENST00000310758.4:c.1304G>A	chr7.hg19:g.37053037C>T	ENSP00000312185:p.Ser435Asn	122.0	0.0	.		88.0	31.0	.	NM_014800	A4D1X6|Q29R79|Q6ZTJ0|Q96PB0|Q9H0I1	Missense_Mutation	SNP	ENST00000310758.4	hg19	CCDS5449.1	.	.	.	.	.	.	.	.	.	.	C	15.24	2.774299	0.49786	.	.	ENSG00000155849	ENST00000341056;ENST00000310758;ENST00000361912;ENST00000442504;ENST00000448602	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	6.06	6.06	0.98353	Engulfment/cell motility, ELMO (2);	0.147484	0.64402	D	0.000020	T	0.21841	0.0526	N	0.12527	0.23	0.48571	D	0.999678	B	0.06786	0.001	B	0.12156	0.007	T	0.07366	-1.0776	10	0.22109	T	0.4	.	20.2348	0.98355	0.0:1.0:0.0:0.0	.	435	Q92556	ELMO1_HUMAN	N	137;435;339;435;435	ENSP00000342142:S137N;ENSP00000312185:S435N;ENSP00000406952:S435N;ENSP00000394458:S435N	ENSP00000312185:S435N	S	-	2	0	ELMO1	37019562	1.000000	0.71417	0.988000	0.46212	0.765000	0.43378	4.885000	0.63142	2.879000	0.98667	0.650000	0.86243	AGT	.	.	.	none		0.458	ELMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219830.4	NM_130442		T	37053037	C	T	37053037	3	4	222	1	0	0	0	0	1	0	0	0	5067	565	20	2	907	2	ELMO1	7	37053037	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10		37053037	122085626	48	13458											
MLL5	55904	hgsc.bcm.edu	37	chr7	104717538	104717538	+	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	agtgagggtgttcagagggaGgcacaaagaatagctctgag	13	7	16	5	0	2	4	1	2	1	2	2	5	2	5	0	3	1	3	0	3	3	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr7:104717538G>C	ENST00000311117.3	+	10	1442	c.897G>C	c.(895-897)gaG>gaC	p.E299D	KMT2E_ENST00000257745.4_Missense_Mutation_p.E299D|KMT2E_ENST00000334877.4_Missense_Mutation_p.E299D|KMT2E_ENST00000476671.1_Missense_Mutation_p.E299D|KMT2E_ENST00000334914.7_5'UTR	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	299					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										TTCAGAGGGAGGCACAAAGAA	0.393																																					p.E299D		Atlas-SNP	.											.	MLL5	173	.	0			c.G897C						PASS	.						125	115	118					7																	104717538		2203	4300	6503	SO:0001583	missense	55904	exon9			GAGGGAGGCACAA	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.897G>C	chr7.hg19:g.104717538G>C	ENSP00000312379:p.Glu299Asp	180.0	0.0	.		166.0	19.0	.	NM_018682	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	hg19	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	G	18.22	3.576129	0.65878	.	.	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745;ENST00000478990;ENST00000476671;ENST00000537308	D;D;D;D;D	0.95756	-2.92;-2.54;-2.92;-3.8;-3.28	6.07	4.28	0.50868	.	0.000000	0.64402	D	0.000001	D	0.94185	0.8134	L	0.44542	1.39	0.80722	D	1	D;P	0.67145	0.996;0.943	P;P	0.54499	0.754;0.576	D	0.91766	0.5424	10	0.14656	T	0.56	.	12.3705	0.55252	0.1346:0.0:0.8654:0.0	.	299;299	Q8IZD2;Q8IZD2-3	MLL5_HUMAN;.	D	299;299;299;299;299;157;299;233	ENSP00000312379:E299D;ENSP00000335599:E299D;ENSP00000257745:E299D;ENSP00000419883:E157D;ENSP00000417888:E299D	ENSP00000257745:E299D	E	+	3	2	MLL5	104504774	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.197000	0.72100	1.587000	0.49959	-0.136000	0.14681	GAG	.	.	.	none		0.393	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			C	104717538	G	C	104717538	3	2	222	1	0	0	0	0	1	0	0	0	9631	991	35	4	927	4	MLL5	7	104717538	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	67664501	104717538	54421125	49	13459											
LAMB4	22798	hgsc.bcm.edu	37	chr7	107732109	107732120	+	In_Frame_Del	DEL	CCTCGTAGAGAT	CCTCGTAGAGAT	-																															gagtgttgtggcttcctctgCctcgtagagatagaaattca																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	CCTCGTAGAGAT	CCTCGTAGAGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr7:107732109_107732120delCCTCGTAGAGAT	ENST00000388781.3	-	14	1735_1746	c.1652_1663delATCTCTACGAGG	c.(1651-1665)tatctctacgaggca>tca	p.551_555YLYEA>S	LAMB4_ENST00000418464.1_In_Frame_Del_p.551_555YLYEA>S|LAMB4_ENST00000205386.4_In_Frame_Del_p.551_555YLYEA>S|LAMB4_ENST00000388780.3_In_Frame_Del_p.551_555YLYEA>S|LAMB4_ENST00000414450.2_In_Frame_Del_p.551_555YLYEA>S	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	551	Laminin EGF-like 5; truncated. {ECO:0000255|PROSITE-ProRule:PRU00460}.|Laminin IV type B. {ECO:0000255|PROSITE- ProRule:PRU00462}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)		p.Y553D(1)		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						GCTTCCTCTGCCTCGTAGAGATAGAAATTCAA	0.491																																					p.551_555del		Atlas-Indel,Pindel	.											.	LAMB4	253	.	1	Substitution - Missense(1)	prostate(1)	c.1653_1664del						PASS	.																																			SO:0001651	inframe_deletion	22798	exon14			.	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.1652_1663delATCTCTACGAGG	chr7.hg19:g.107732109_107732120delCCTCGTAGAGAT	ENSP00000373433:p.Tyr551_Ala555delinsSer	174.0	0.0	0		119.0	23.0	0.193277	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	In_Frame_Del	DEL	ENST00000388781.3	hg19	CCDS34732.1																																																																																			.	.	.	none		0.491	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		-	107732120	CCTCGTAGAGAT	-	107732109	7	5	222	1	0	1	0	1	0	0	0	0	8620	739	26	0	3706	0	LAMB4	7	107732109	In_Frame_Del	DEL	CCTCGTAGAGAT	TCGA-MH-A561-01A-11D-A26P-10	3014571	107732109	51406554	50	13460											
MET	4233	hgsc.bcm.edu	37	chr7	116423474	116423474	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagctgccagtgaagtggaTggctttggaaagtctgcaaa	13	9	13	6	0	1	1	0	1	1	0	1	3	1	3	1	3	3	3	1	3	4	1	rs121913245		TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr7:116423474T>C	ENST00000318493.6	+	19	3990	c.3803T>C	c.(3802-3804)aTg>aCg	p.M1268T	MET_ENST00000539704.1_Missense_Mutation_p.M120T|MET_ENST00000397752.3_Missense_Mutation_p.M1250T			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.M1268T(4)		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)			GTGAAGTGGATGGCTTTGGAA	0.393			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.M1268T		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,rectum,carcinoma,+1,5	MET	412	.	4	Substitution - Missense(4)	kidney(4)	c.T3803C	GRCh37	CM992181	MET	M	rs121913245	PASS	.						93	92	92					7																	116423474		1872	4102	5974	SO:0001583	missense	4233	exon19	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	AGTGGATGGCTTT	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.3803T>C	chr7.hg19:g.116423474T>C	ENSP00000317272:p.Met1268Thr	98.0	0.0	.		83.0	27.0	.	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	T	18.99	3.740165	0.69304	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000539704	T;T;T	0.37752	1.18;1.18;1.18	5.68	5.68	0.88126	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	0.61714	0.2369	M	0.75264	2.295	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.97110	1.0;1.0	T	0.65734	-0.6096	10	0.87932	D	0	.	16.2225	0.82267	0.0:0.0:0.0:1.0	.	1268;1250	P08581-2;P08581	.;MET_HUMAN	T	1250;1268;120	ENSP00000380860:M1250T;ENSP00000317272:M1268T;ENSP00000445020:M120T	ENSP00000317272:M1268T	M	+	2	0	MET	116210710	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.997000	0.88414	2.289000	0.77006	0.460000	0.39030	ATG	.	.	.	weak		0.393	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			C	116423474	T	C	116423474	3	2	222	1	0	0	0	0	1	0	0	0	9492	1464	51	3	3873	3	MET	7	116423474	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	8691365	116423474	42715189	51	13461											
GPR37	2861	hgsc.bcm.edu	37	chr7	124405027	124405027	+	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	gagaagcgcgcccggggctcGcatggcttggtgagggcaca	7	5	18	11	4	0	2	0	1	0	1	1	3	0	2	1	5	1	4	1	5	1	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr7:124405027G>A	ENST00000303921.2	-	1	654	c.4C>T	c.(4-6)Cga>Tga	p.R2*		NM_005302.3	NP_005293.1	O15354	GPR37_HUMAN	G protein-coupled receptor 37 (endothelin receptor type B-like)	2					dopamine biosynthetic process (GO:0042416)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotion involved in locomotory behavior (GO:0031987)|positive regulation of dopamine metabolic process (GO:0045964)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ubiquitin ligase complex (GO:0000151)	G-protein coupled receptor activity (GO:0004930)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						CCCGGGGCTCGCATGGCTTGG	0.637																																					p.R2X		Atlas-SNP	.											.	GPR37	89	.	0			c.C4T						PASS	.						7	6	7					7																	124405027		2164	4249	6413	SO:0001587	stop_gained	2861	exon1			GGGCTCGCATGGC		CCDS5792.1	7q31	2012-08-21			ENSG00000170775	ENSG00000170775		"GPCR / Class A : Orphans"	4494	protein-coding gene	gene with protein product		602583				9339362	Standard	NM_005302		Approved	EDNRBL, hET(B)R-LP, PAELR	uc003vli.4	O15354	OTTHUMG00000157197	ENST00000303921.2:c.4C>T	chr7.hg19:g.124405027G>A	ENSP00000306449:p.Arg2*	4.0	0.0	.		6.0	4.0	.	NM_005302	A4D0Y6|O00348|O14768|Q8TD39	Nonsense_Mutation	SNP	ENST00000303921.2	hg19	CCDS5792.1	.	.	.	.	.	.	.	.	.	.	G	40	8.449312	0.98815	.	.	ENSG00000170775	ENST00000303921	.	.	.	5.31	3.45	0.39498	.	0.960325	0.08673	N	0.910555	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	-4.8252	6.6615	0.23016	0.0898:0.0:0.7349:0.1753	.	.	.	.	X	2	.	ENSP00000306449:R2X	R	-	1	2	GPR37	124192263	0.983000	0.35010	0.703000	0.30354	0.397000	0.30659	1.951000	0.40333	0.767000	0.33267	0.655000	0.94253	CGA	.	.	.	none		0.637	GPR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347873.1	NM_005302		A	124405027	G	A	124405027	4	1	222	1	0	0	0	0	0	1	0	0	6698	1095	38	1	1845	1	GPR37	7	124405027	Nonsense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	7981553	124405027	34733636	52	13462											
NRG1	3084	hgsc.bcm.edu	37	chr8	32616873	32616873	+	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	tgagcatattgttgagagagAagcagagacatccttttcca	13	11	10	7	0	0	4	0	2	0	3	2	7	2	4	2	0	2	3	2	0	2	5			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr8:32616873A>T	ENST00000405005.3	+	10	980	c.980A>T	c.(979-981)gAa>gTa	p.E327V	NRG1_ENST00000287842.3_Missense_Mutation_p.E324V|NRG1_ENST00000287845.5_Missense_Mutation_p.E298V|NRG1_ENST00000523079.1_Missense_Mutation_p.E324V|NRG1_ENST00000338921.4_Missense_Mutation_p.E335V|NRG1_ENST00000539990.1_Missense_Mutation_p.E170V|NRG1_ENST00000519301.1_Missense_Mutation_p.E277V|NRG1_ENST00000341377.5_3'UTR|NRG1_ENST00000356819.4_Missense_Mutation_p.E332V|NRG1_ENST00000521670.1_Missense_Mutation_p.E327V			Q02297	NRG1_HUMAN	neuregulin 1	327					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)		GTTGAGAGAGAAGCAGAGACA	0.408																																					p.E332V		Atlas-SNP	.											.	NRG1	260	.	0			c.A995T						PASS	.						201	169	180					8																	32616873		2203	4300	6503	SO:0001583	missense	3084	exon11			AGAGAGAAGCAGA	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.980A>T	chr8.hg19:g.32616873A>T	ENSP00000384620:p.Glu327Val	157.0	0.0	.		145.0	41.0	.	NM_013956	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Missense_Mutation	SNP	ENST00000405005.3	hg19	CCDS6085.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.300044	0.81136	.	.	ENSG00000157168	ENST00000518104;ENST00000519301;ENST00000523534;ENST00000523079;ENST00000338921;ENST00000356819;ENST00000287840;ENST00000287845;ENST00000287842;ENST00000405005;ENST00000521670;ENST00000539990	T;T;T;T;T;T;T;T;T;T;T;T	0.62364	0.03;0.03;0.03;0.03;0.03;0.03;0.03;0.03;0.03;0.03;0.03;0.03	6.16	6.16	0.99307	Neuregulin 1-related, C-terminal (1);	0.100274	0.64402	D	0.000002	T	0.70824	0.3268	L	0.41573	1.285	0.53688	D	0.999971	D;D;D;D;D;D;D;D;D;D;D	0.89917	0.996;1.0;1.0;1.0;1.0;1.0;0.983;0.999;0.999;1.0;1.0	D;D;D;D;D;D;P;D;D;D;D	0.97110	0.997;0.999;1.0;0.984;0.991;1.0;0.592;0.984;0.985;0.984;0.999	T	0.64694	-0.6347	10	0.14252	T	0.57	-8.3311	16.8061	0.85666	1.0:0.0:0.0:0.0	.	170;173;324;298;332;323;335;324;327;332;327	B7Z1E3;B7Z1D7;E9PHH4;F8W9E3;Q7RTW4;B0FYA9;Q02297-2;Q02297-7;Q02297;Q02297-6;Q02297-3	.;.;.;.;.;.;.;.;NRG1_HUMAN;.;.	V	294;277;400;324;335;332;327;298;324;327;327;170	ENSP00000430053:E294V;ENSP00000429582:E277V;ENSP00000429067:E400V;ENSP00000430120:E324V;ENSP00000343395:E335V;ENSP00000349275:E332V;ENSP00000287840:E327V;ENSP00000287845:E298V;ENSP00000287842:E324V;ENSP00000384620:E327V;ENSP00000428828:E327V;ENSP00000439276:E170V	ENSP00000287840:E327V	E	+	2	0	NRG1	32736415	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.312000	0.65792	2.367000	0.80283	0.528000	0.53228	GAA	.	.	.	none		0.408	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1			T	32616873	A	T	32616873	3	4	222	1	0	0	0	0	1	0	0	0	10654	246	9	5	2614	5	NRG1	8	32616873	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10		32616873	113747149	53	13463											
NKX6-3	157848	hgsc.bcm.edu	37	chr8	41504065	41504065	+	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	cgtccgagtcggggtccagcGgcttgttgtactcgtcgtcc	3	11	14	13	6	0	0	0	0	0	0	6	1	3	0	3	3	2	3	3	3	1	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr8:41504065G>T	ENST00000524115.2	-	2	314	c.311C>A	c.(310-312)cCg>cAg	p.P104Q		NM_152568.2	NP_689781.1	A6NJ46	NKX63_HUMAN	NK6 homeobox 3	234					cell fate determination (GO:0001709)|glandular epithelial cell differentiation (GO:0002067)|negative regulation of epithelial cell differentiation (GO:0030857)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			lung(1)	1	Ovarian(28;0.00541)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Esophageal squamous(32;0.0844)|Hepatocellular(245;0.154)	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)			GGGGTCCAGCGGCTTGTTGTA	0.731																																					p.P104Q		Atlas-SNP	.											.	NKX6-3	10	.	0			c.C311A						PASS	.						43	38	39					8																	41504065		2201	4300	6501	SO:0001583	missense	157848	exon2			TCCAGCGGCTTGT	AK057898	CCDS6118.1	8p11.21	2014-08-12	2007-07-09		ENSG00000165066	ENSG00000165066		"Homeoboxes / ANTP class : NKL subclass"	26328	protein-coding gene	gene with protein product		610772	"NK6 transcription factor related, locus 3 (Drosophila)"			16326147	Standard	XM_005273422		Approved	FLJ25169	uc003xoa.2	A6NJ46	OTTHUMG00000164083	ENST00000524115.2:c.311C>A	chr8.hg19:g.41504065G>T	ENSP00000429553:p.Pro104Gln	32.0	0.0	.		24.0	15.0	.	NM_152568	Q96LR0	Missense_Mutation	SNP	ENST00000524115.2	hg19	CCDS6118.1	.	.	.	.	.	.	.	.	.	.	G	32	5.124514	0.94429	.	.	ENSG00000165066	ENST00000524115;ENST00000425142;ENST00000518699	T;T	0.57907	0.37;0.37	4.9	4.02	0.46733	.	0.000000	0.85682	D	0.000000	T	0.70718	0.3256	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.73170	-0.4067	9	0.56958	D	0.05	.	12.1998	0.54319	0.0832:0.0:0.9168:0.0	.	104	A6NJ46-2	.	Q	104;234;234	ENSP00000429553:P104Q;ENSP00000428361:P234Q	ENSP00000414183:P234Q	P	-	2	0	NKX6-3	41623222	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	7.856000	0.86956	1.066000	0.40716	0.491000	0.48974	CCG	.	.	.	none		0.731	NKX6-3-002	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000377166.2	NM_152568		T	41504065	G	T	41504065	3	4	222	1	0	0	0	0	1	0	0	0	10466	1116	39	4	100	4	NKX6-3	8	41504065	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	8887192	41504065	104859957	54	13464											
NCOA2	10499	hgsc.bcm.edu	37	chr8	71053580	71053580	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctctcacagccgaactctgcGgtgcccattctccagatggc	7	9	9	16	2	3	1	1	0	3	1	5	2	3	1	3	2	4	0	3	2	1	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr8:71053580G>A	ENST00000452400.2	-	14	3048	c.2867C>T	c.(2866-2868)cCg>cTg	p.P956L	NCOA2_ENST00000267974.4_Missense_Mutation_p.P44L	NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	956					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)			CGAACTCTGCGGTGCCCATTC	0.532			T	"RUNXBP2, HEY1"	"AML, Chondrosarcoma"																																p.P956L		Atlas-SNP	.		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	NCOA2,NS,carcinoma,0,1	NCOA2	147	.	0			c.C2867T						PASS	.						57	60	59					8																	71053580		2052	4211	6263	SO:0001583	missense	10499	exon14			CTCTGCGGTGCCC	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.2867C>T	chr8.hg19:g.71053580G>A	ENSP00000399968:p.Pro956Leu	155.0	0.0	.		152.0	28.0	.	NM_006540	Q14CD2	Missense_Mutation	SNP	ENST00000452400.2	hg19	CCDS47872.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	1.585|1.585	-0.530666|-0.530666	0.04112|0.04112	.|.	.|.	ENSG00000140396|ENSG00000140396	ENST00000452400;ENST00000267974|ENST00000518363	T;T|.	0.06849|.	4.9;3.25|.	5.64|5.64	5.64|5.64	0.86602|0.86602	.|.	0.483437|.	0.22937|.	N|.	0.053835|.	T|T	0.28532|0.28532	0.0706|0.0706	N|N	0.04880|0.04880	-0.145|-0.145	0.09310|0.09310	N|N	0.999999|0.999999	P;B|.	0.35192|.	0.489;0.059|.	B;B|.	0.24974|.	0.057;0.01|.	T|T	0.19289|0.19289	-1.0310|-1.0310	10|5	0.02654|.	T|.	1|.	.|.	16.5528|16.5528	0.84476|0.84476	0.0:0.1389:0.8611:0.0|0.0:0.1389:0.8611:0.0	.|.	44;956|.	F8WAJ2;Q15596|.	.;NCOA2_HUMAN|.	L|C	956;44|57	ENSP00000399968:P956L;ENSP00000267974:P44L|.	ENSP00000267974:P44L|.	P|R	-|-	2|1	0|0	NCOA2|NCOA2	71216134|71216134	0.778000|0.778000	0.28640|0.28640	0.149000|0.149000	0.22428|0.22428	0.831000|0.831000	0.47069|0.47069	4.231000|4.231000	0.58639|0.58639	2.820000|2.820000	0.97059|0.97059	0.650000|0.650000	0.86243|0.86243	CCG|CGC	.	.	.	none		0.532	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1			A	71053580	G	A	71053580	3	1	222	1	0	0	0	0	1	0	0	0	10236	1116	39	1	1567	1	NCOA2	8	71053580	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	29549515	71053580	75310442	55	13465											
CSMD3	114788	hgsc.bcm.edu	37	chr8	113316994	113316994	+	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	tccaactccaagtaccattaGgaagacattcgatggaggca	14	8	9	10	1	0	1	0	0	0	1	3	4	2	3	3	3	2	2	3	3	5	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr8:113316994G>A	ENST00000297405.5	-	52	8466	c.8222C>T	c.(8221-8223)cCt>cTt	p.P2741L	CSMD3_ENST00000343508.3_Missense_Mutation_p.P2701L|CSMD3_ENST00000352409.3_Missense_Mutation_p.P2671L|CSMD3_ENST00000455883.2_Intron	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2741	Sushi 16. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						AGTACCATTAGGAAGACATTC	0.388										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.P2741L		Atlas-SNP	.											.	CSMD3	2325	.	0			c.C8222T						PASS	.						133	118	123					8																	113316994		2203	4300	6503	SO:0001583	missense	114788	exon52			CCATTAGGAAGAC	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.8222C>T	chr8.hg19:g.113316994G>A	ENSP00000297405:p.Pro2741Leu	151.0	0.0	.		136.0	53.0	.	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	15.64	2.891954	0.52014	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000352409	T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08	4.9	4.9	0.64082	Complement control module (2);Sushi/SCR/CCP (3);	0.178361	0.34200	N	0.004165	T	0.48259	0.1490	N	0.13272	0.32	0.54753	D	0.99998	B;B	0.30211	0.273;0.006	B;B	0.30105	0.111;0.026	T	0.47849	-0.9085	10	0.38643	T	0.18	.	18.4479	0.90691	0.0:0.0:1.0:0.0	.	2741;2701	Q7Z407;Q7Z407-2	CSMD3_HUMAN;.	L	2701;2741;2011;2671	ENSP00000345799:P2701L;ENSP00000297405:P2741L;ENSP00000341558:P2011L;ENSP00000343124:P2671L	ENSP00000297405:P2741L	P	-	2	0	CSMD3	113386170	1.000000	0.71417	1.000000	0.80357	0.427000	0.31564	9.775000	0.98995	2.385000	0.81259	0.561000	0.74099	CCT	.	.	.	none		0.388	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113316994	G	A	113316994	3	1	222	1	0	0	0	0	1	0	0	0	3948	1000	35	2	2981	2	CSMD3	8	113316994	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	42263414	113316994	33047028	56	13466											
PHF20L1	51105	hgsc.bcm.edu	37	chr8	133806739	133806739	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggagtcatcgttatgatgAgtggatttactgggatagca	10	13	13	5	1	1	2	1	2	0	0	2	5	1	5	0	3	2	2	0	3	3	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr8:133806739A>G	ENST00000395386.2	+	3	466	c.167A>G	c.(166-168)gAg>gGg	p.E56G	PHF20L1_ENST00000395390.2_Missense_Mutation_p.E56G|PHF20L1_ENST00000395376.1_Missense_Mutation_p.E56G|PHF20L1_ENST00000220847.7_5'UTR|PHF20L1_ENST00000395379.1_Missense_Mutation_p.E56G|PHF20L1_ENST00000337920.4_Missense_Mutation_p.E56G	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	56	Tudor 1.						zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			CGTTATGATGAGTGGATTTAC	0.408																																					p.E56G		Atlas-SNP	.											.	PHF20L1	129	.	0			c.A167G						PASS	.						134	122	126					8																	133806739		2203	4300	6503	SO:0001583	missense	51105	exon3			ATGATGAGTGGAT	AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"Tudor domain containing", "Zinc fingers, PHD-type"	24280	protein-coding gene	gene with protein product	"tudor domain containing 20B"					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.167A>G	chr8.hg19:g.133806739A>G	ENSP00000378784:p.Glu56Gly	130.0	0.0	.		140.0	48.0	.	NM_016018	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Missense_Mutation	SNP	ENST00000395386.2	hg19	CCDS6367.2	.	.	.	.	.	.	.	.	.	.	A	31	5.078557	0.94050	.	.	ENSG00000129292	ENST00000395383;ENST00000395379;ENST00000361997;ENST00000395386;ENST00000315808;ENST00000337920;ENST00000395376;ENST00000522580;ENST00000395390	T;T;T;T;T;T;T;T	0.56275	0.53;0.48;0.51;1.1;0.47;0.49;0.55;1.13	5.91	5.91	0.95273	Tudor-like, plant (1);Tudor domain (1);	0.000000	0.85682	D	0.000000	T	0.77942	0.4206	M	0.90759	3.145	0.80722	D	1	D;P;D;D;P	0.89917	1.0;0.735;1.0;1.0;0.714	D;P;D;D;P	0.91635	0.997;0.734;0.999;0.994;0.669	T	0.82833	-0.0262	10	0.87932	D	0	7.5356	15.5298	0.75948	1.0:0.0:0.0:0.0	.	56;56;56;56;56	F8W9L8;A8MW92;A8MW92-4;A8MW92-2;A8MUE8	.;P20L1_HUMAN;.;.;.	G	56;56;56;56;56;56;56;14;56	ENSP00000378781:E56G;ENSP00000378777:E56G;ENSP00000355301:E56G;ENSP00000378784:E56G;ENSP00000324519:E56G;ENSP00000338269:E56G;ENSP00000378775:E56G;ENSP00000378788:E56G	ENSP00000324519:E56G	E	+	2	0	PHF20L1	133875921	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.317000	0.96327	2.259000	0.74868	0.528000	0.53228	GAG	.	.	.	none		0.408	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018		G	133806739	A	G	133806739	3	3	222	1	0	0	0	0	1	0	0	0	11839	304	11	3	173	3	PHF20L1	8	133806739	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	20489745	133806739	12557283	57	13467											
PTPN3	5774	hgsc.bcm.edu	37	chr9	112219466	112219466	+	Frame_Shift_Del	DEL	C	C	-																															caccaaccttttaactgcttCctgatggctttgcttgcttc																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr9:112219466delC	ENST00000374541.2	-	4	380	c.276delG	c.(274-276)aggfs	p.R92fs	PTPN3_ENST00000262539.3_Frame_Shift_Del_p.E10fs	NM_001145368.1|NM_002829.3	NP_001138840.1|NP_002820.3	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type 3	92	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of mitotic cell cycle (GO:0045930)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of membrane depolarization during action potential (GO:0098902)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	ATPase binding (GO:0051117)|phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						TTAACTGCTTCCTGATGGCTT	0.413																																					p.K93fs		Atlas-Indel,Pindel	.											.	PTPN3	106	.	0			c.277delA						PASS	.						197	168	177					9																	112219466		2203	4300	6503	SO:0001589	frameshift_variant	5774	exon4			.		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.276delG	chr9.hg19:g.112219466delC	ENSP00000363667:p.Arg92fs	167.0	0.0	0		113.0	32.0	0.283186	NM_001145368	A0AUW9|E7EN99|E9PGU7	Frame_Shift_Del	DEL	ENST00000374541.2	hg19	CCDS6776.1																																																																																			.	.	.	none		0.413	PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4			-	112219466	C	-	112219466	7	5	222	1	0	1	0	1	0	0	0	0	12802	854	30	0	2557	0	PTPN3	9	112219466	Frame_Shift_Del	DEL	C	TCGA-MH-A561-01A-11D-A26P-10		112219466	28993965	58	13468											
PALM2	114299	hgsc.bcm.edu	37	chr9	112705604	112705604	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggccggtctcagacaccAcagagccctcatccccagaa	11	4	10	16	1	2	3	2	0	1	3	4	4	3	4	5	3	1	0	5	3	1	0			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr9:112705604A>G	ENST00000374531.2	+	7	1113	c.1039A>G	c.(1039-1041)Aca>Gca	p.T347A	PALM2_ENST00000314527.4_Missense_Mutation_p.T379A|PALM2_ENST00000448454.2_Missense_Mutation_p.T381A|PALM2-AKAP2_ENST00000302798.7_Intron|PALM2-AKAP2_ENST00000374530.3_Intron|AKAP2_ENST00000510514.5_Intron|PALM2_ENST00000483909.1_Missense_Mutation_p.T345A|AKAP2_ENST00000555236.1_Intron	NM_001037293.2	NP_001032370.1	Q8IXS6	PALM2_HUMAN	paralemmin 2	347					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						CTCAGACACCACAGAGCCCTC	0.552																																					p.T379A		Atlas-SNP	.											.	PALM2	51	.	0			c.A1135G						PASS	.						113	110	111					9																	112705604		2203	4300	6503	SO:0001583	missense	114299	exon7			GACACCACAGAGC	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.1039A>G	chr9.hg19:g.112705604A>G	ENSP00000363656:p.Thr347Ala	118.0	0.0	.		128.0	19.0	.	NM_053016	A9Z1X9|Q8N9D5|Q96DU1	Missense_Mutation	SNP	ENST00000374531.2	hg19	CCDS35099.1	.	.	.	.	.	.	.	.	.	.	A	15.03	2.711967	0.48517	.	.	ENSG00000243444;ENSG00000243444;ENSG00000243444;ENSG00000243444;ENSG00000157654	ENST00000374531;ENST00000448454;ENST00000483909;ENST00000314527;ENST00000413420	T;T;T;T;T	0.22945	2.36;2.36;2.36;2.36;1.93	5.86	5.86	0.93980	.	.	.	.	.	T	0.33498	0.0865	L	0.59436	1.845	0.80722	D	1	P;P	0.48503	0.788;0.911	P;P	0.51516	0.548;0.672	T	0.13710	-1.0499	9	0.05351	T	0.99	.	15.4456	0.75228	1.0:0.0:0.0:0.0	.	347;381	Q8IXS6;D3YTA4	PALM2_HUMAN;.	A	347;381;345;379;379	ENSP00000363656:T347A;ENSP00000400206:T381A;ENSP00000417525:T345A;ENSP00000323805:T379A;ENSP00000397839:T379A	ENSP00000397839:T379A	T	+	1	0	PALM2-AKAP2;PALM2	111745425	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	9.339000	0.96797	2.244000	0.73946	0.528000	0.53228	ACA	.	.	.	none		0.552	PALM2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053604.1	NM_001037293		G	112705604	A	G	112705604	3	3	222	1	0	0	0	0	1	0	0	0	11416	159	6	3	1171	3	PALM2	9	112705604	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	486138	112705604	28507827	59	13469											
FAM102A	399665	hgsc.bcm.edu	37	chr9	130707096	130707096	+	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	gtgaaatcctggctctgcacGatcttctccacgatggcatc	8	11	9	13	2	3	1	0	1	3	0	6	3	4	1	2	2	1	3	2	2	1	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr9:130707096G>A	ENST00000373095.1	-	9	1374	c.999C>T	c.(997-999)atC>atT	p.I333I	FAM102A_ENST00000300434.3_5'UTR|FAM102A_ENST00000373084.4_Silent_p.I191I	NM_001035254.2	NP_001030331.1	Q5T9C2	F102A_HUMAN	family with sequence similarity 102, member A	333										breast(1)|cervix(1)|large_intestine(3)|lung(1)|ovary(4)	10						GGCTCTGCACGATCTTCTCCA	0.672																																					p.I333I		Atlas-SNP	.											.	FAM102A	32	.	0			c.C999T						PASS	.						89	64	72					9																	130707096		2203	4300	6503	SO:0001819	synonymous_variant	399665	exon9			CTGCACGATCTTC		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.999C>T	chr9.hg19:g.130707096G>A		60.0	0.0	.		39.0	23.0	.	NM_001035254	A2A329|Q8TEL4	Silent	SNP	ENST00000373095.1	hg19	CCDS35150.1																																																																																			.	.	.	none		0.672	FAM102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054298.2			A	130707096	G	A	130707096	2	1	222	1	0	0	0	0	0	0	0	1	5386	1048	37	1		1	FAM102A	9	130707096	Silent	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	18001492	130707096	10506335	60	13470											
AKR1C2	1646	hgsc.bcm.edu	37	chr10	5038014	5038014	+	Frame_Shift_Del	DEL	A	A	-																															caatgtcttttgacttgcagAaatccagcagttttctctgg																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr10:5038014delA	ENST00000380753.4	-	6	801	c.614delT	c.(613-615)ttcfs	p.F205fs	RP11-499O7.7_ENST00000451575.2_RNA|AKR1C2_ENST00000407674.1_Frame_Shift_Del_p.F205fs|AKR1C2_ENST00000421196.3_Frame_Shift_Del_p.F179fs|RP11-499O7.7_ENST00000440414.1_RNA	NM_205845.2	NP_995317.1	P52895	AK1C2_HUMAN	aldo-keto reductase family 1, member C2	205					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)	TGACTTGCAGAAATCCAGCAG	0.393																																					p.F205fs		Atlas-Indel,Pindel	.											.	AKR1C2	68	.	0			c.615delC						PASS	.						62	57	59					10																	5038014		2203	4296	6499	SO:0001589	frameshift_variant	1646	exon8			.	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.614delT	chr10.hg19:g.5038014delA	ENSP00000370129:p.Phe205fs	706.0	0.0	0		638.0	51.0	0.0799373	NM_001354	A8K2N9|B4DKR9|Q14133|Q5SR16|Q7M4N1|Q96A71	Frame_Shift_Del	DEL	ENST00000380753.4	hg19	CCDS7062.1																																																																																			.	.	.	none		0.393	AKR1C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046531.1	NM_001354		-	5038014	A	-	5038014	7	5	222	1	0	1	0	1	0	0	0	0	470	246	9	0	373	0	AKR1C2	10	5038014	Frame_Shift_Del	DEL	A	TCGA-MH-A561-01A-11D-A26P-10		5038014	130496733	61	13471											
MTG1	92170	hgsc.bcm.edu	37	chr10	135209749	135209750	+	Frame_Shift_Ins	INS	-	-	GC																															gtcctcaacaagatggacttINSggcggatcttacagagcagc																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr10:135209749_135209750insGC	ENST00000317502.6	+	3	310_311	c.260_261insGC	c.(259-264)ttggcgfs	p.A88fs	RP11-108K14.8_ENST00000468317.2_Frame_Shift_Ins_p.A93fs|MTG1_ENST00000477902.2_Frame_Shift_Ins_p.A47fs	NM_138384.2	NP_612393.2	Q9BT17	MTG1_HUMAN	mitochondrial ribosome-associated GTPase 1	88	CP-type G. {ECO:0000255|PROSITE- ProRule:PRU01058}.				GTP catabolic process (GO:0006184)|regulation of mitochondrial translation (GO:0070129)|regulation of respiratory system process (GO:0044065)|ribosome biogenesis (GO:0042254)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial ribosome (GO:0005761)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|urinary_tract(1)	15		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.21e-06)|all cancers(32;1.69e-06)|Epithelial(32;1.94e-06)		AAGATGGACTTGGCGGATCTTA	0.515																																					p.L87fs		Atlas-Indel,Pindel	.											.	MTG1	38	.	0			c.260_261insGC						PASS	.																																			SO:0001589	frameshift_variant	92170	exon3			.		CCDS31320.1	10q26.3	2013-05-24	2013-05-24	2006-01-09	ENSG00000148824	ENSG00000148824			32159	protein-coding gene	gene with protein product			"GTP-binding protein 7", "GTP-binding protein 7 (putative)", "mitochondrial GTPase 1 homolog (S. cerevisiae)"	GTPBP7		12808030, 23396448	Standard	NM_138384		Approved		uc001lnd.3	Q9BT17	OTTHUMG00000166564	Exception_encountered	chr10.hg19:g.135209749_135209750insGC	ENSP00000323047:p.Ala88fs	139.0	0.0	0		108.0	42.0	0.388889	NM_138384	Q5VWX8|Q6PIY9|Q8IYJ4|Q8NC48|Q9BVU8	Frame_Shift_Ins	INS	ENST00000317502.6	hg19	CCDS31320.1																																																																																			.	.	.	none		0.515	MTG1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051166.1	NM_138384		GC	135209750	-	GC	135209749	7	5	222	1	0	1	1	0	0	0	0	0	9933	1821	63	0	270	0	MTG1	10	135209749	Frame_Shift_Ins	INS	-	TCGA-MH-A561-01A-11D-A26P-10	130171735	135209749	324998	62	13472											
INS	3630	hgsc.bcm.edu	37	chr11	2181135	2181135	+	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	gcagatgctggtacagcattGttccacaatgccacgcttct	9	11	9	12	1	1	1	0	0	1	1	2	1	2	1	2	1	4	6	2	1	2	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr11:2181135G>T	ENST00000397262.1	-	2	512	c.280C>A	c.(280-282)Caa>Aaa	p.Q94K	INS_ENST00000381330.4_Missense_Mutation_p.Q94K|INS_ENST00000512523.1_Missense_Mutation_p.Q82K|INS_ENST00000250971.3_Missense_Mutation_p.Q94K|INS-IGF2_ENST00000397270.1_Intron|INS-IGF2_ENST00000481781.1_5'Flank	NM_001185098.1	NP_001172027.1	P01308	INS_HUMAN	insulin	94					activation of protein kinase B activity (GO:0032148)|acute-phase response (GO:0006953)|alpha-beta T cell activation (GO:0046631)|cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|fatty acid homeostasis (GO:0055089)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|MAPK cascade (GO:0000165)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of fatty acid metabolic process (GO:0045922)|negative regulation of feeding behavior (GO:2000252)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of glycogen catabolic process (GO:0045818)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of protein secretion (GO:0050709)|negative regulation of proteolysis (GO:0045861)|negative regulation of respiratory burst involved in inflammatory response (GO:0060266)|negative regulation of vasodilation (GO:0045908)|positive regulation of brown fat cell differentiation (GO:0090336)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of respiratory burst (GO:0060267)|positive regulation of vasodilation (GO:0045909)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of insulin secretion (GO:0050796)|regulation of protein localization (GO:0032880)|regulation of protein secretion (GO:0050708)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transmembrane transporter activity (GO:0022898)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	endoplasmic reticulum lumen (GO:0005788)|endosome lumen (GO:0031904)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|secretory granule lumen (GO:0034774)	hormone activity (GO:0005179)|identical protein binding (GO:0042802)|insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|protease binding (GO:0002020)			haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)	5		Lung NSC(207;8.94e-06)|all_epithelial(84;3.17e-05)|all_lung(207;3.67e-05)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;0.0025)|LUSC - Lung squamous cell carcinoma(625;0.082)|Lung(200;0.14)		GTACAGCATTGTTCCACAATG	0.672																																					p.Q94K		Atlas-SNP	.											.	INS	10	.	0			c.C280A						PASS	.						63	53	57					11																	2181135		2187	4293	6480	SO:0001583	missense	3630	exon3			AGCATTGTTCCAC	X70508	CCDS7729.1	11p15.5	2014-02-03			ENSG00000254647	ENSG00000254647			6081	protein-coding gene	gene with protein product		176730	"insulin-dependent diabetes mellitus 2"	IDDM2, IDDM1		6243748, 7773291	Standard	NM_000207		Approved			P01308	OTTHUMG00000009558	ENST00000397262.1:c.280C>A	chr11.hg19:g.2181135G>T	ENSP00000380432:p.Gln94Lys	73.0	0.0	.		51.0	18.0	.	NM_001185097	Q5EEX2	Missense_Mutation	SNP	ENST00000397262.1	hg19	CCDS7729.1	.	.	.	.	.	.	.	.	.	.	G	14.14	2.445461	0.43429	.	.	ENSG00000254647	ENST00000397262;ENST00000250971;ENST00000381330;ENST00000512523	D;D;D;D	0.88431	-2.38;-2.38;-2.38;-2.38	3.68	2.73	0.32206	Insulin-like (4);	.	.	.	.	D	0.94466	0.8219	M	0.89534	3.04	0.52501	D	0.999953	D;B	0.60160	0.987;0.437	D;P	0.69307	0.963;0.511	D	0.94552	0.7754	9	0.72032	D	0.01	.	11.9365	0.52876	0.0:0.1778:0.8222:0.0	.	82;94	A6XGL2;P01308	.;INS_HUMAN	K	94;94;94;82	ENSP00000380432:Q94K;ENSP00000250971:Q94K;ENSP00000370731:Q94K;ENSP00000424008:Q82K	ENSP00000250971:Q94K	Q	-	1	0	INS	2137711	1.000000	0.71417	0.918000	0.36340	0.079000	0.17450	4.878000	0.63093	0.860000	0.35481	0.462000	0.41574	CAA	.	.	.	none		0.672	INS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026395.3	NM_000207		T	2181135	G	T	2181135	3	4	222	1	0	0	0	0	1	0	0	0	7769	1386	48	4	56	4	INS	11	2181135	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10		2181135	132825381	63	13473											
PDE3B	5140	hgsc.bcm.edu	37	chr11	14808189	14808189	+	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	ggattttacccctgttctgaAatagaggacccagctgagaa	12	10	10	9	0	1	3	0	2	1	2	1	6	1	5	3	2	2	2	3	2	4	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr11:14808189A>T	ENST00000282096.4	+	3	1589	c.1236A>T	c.(1234-1236)gaA>gaT	p.E412D	PDE3B_ENST00000455098.2_Intron	NM_000922.3	NP_000913.2	Q13370	PDE3B_HUMAN	phosphodiesterase 3B, cGMP-inhibited	412					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of lipid catabolic process (GO:0050995)|regulation of insulin secretion (GO:0050796)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)|protein kinase B binding (GO:0043422)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39					Caffeine(DB00201)	CCTGTTCTGAAATAGAGGACC	0.373																																					p.E412D		Atlas-SNP	.											.	PDE3B	98	.	0			c.A1236T						PASS	.						120	130	126					11																	14808189		2200	4294	6494	SO:0001583	missense	5140	exon3			TTCTGAAATAGAG	U38178	CCDS7817.1	11p15.2	2008-03-18			ENSG00000152270	ENSG00000152270	3.1.4.17	"Phosphodiesterases"	8779	protein-coding gene	gene with protein product		602047				8884271, 16395595	Standard	NM_000922		Approved	HcGIP1	uc001mln.3	Q13370	OTTHUMG00000165898	ENST00000282096.4:c.1236A>T	chr11.hg19:g.14808189A>T	ENSP00000282096:p.Glu412Asp	169.0	0.0	.		150.0	59.0	.	NM_000922	B7ZM37|O00639|Q14408|Q6SEI4	Missense_Mutation	SNP	ENST00000282096.4	hg19	CCDS7817.1	.	.	.	.	.	.	.	.	.	.	a	14.21	2.468783	0.43839	.	.	ENSG00000152270	ENST00000282096	T	0.34275	1.37	5.72	3.42	0.39159	.	0.151781	0.27749	U	0.018012	T	0.36552	0.0971	N	0.20986	0.625	0.80722	D	1	D	0.69078	0.997	D	0.72625	0.978	T	0.22312	-1.0220	10	0.05959	T	0.93	.	9.8395	0.40991	0.8619:0.0:0.1381:0.0	.	412	Q13370	PDE3B_HUMAN	D	412	ENSP00000282096:E412D	ENSP00000282096:E412D	E	+	3	2	PDE3B	14764765	1.000000	0.71417	0.992000	0.48379	0.978000	0.69477	3.979000	0.56888	0.452000	0.26830	0.456000	0.33151	GAA	.	.	.	none		0.373	PDE3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386974.1	NM_000922		T	14808189	A	T	14808189	3	4	222	1	0	0	0	0	1	0	0	0	11645	11	1	5	1246	5	PDE3B	11	14808189	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	12627054	14808189	120198327	64	13474											
CHRM1	1128	hgsc.bcm.edu	37	chr11	62677207	62677207	+	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	ctatcagcattggcgggaggGagtgcggtgcacggagccag	8	6	18	9	3	1	0	1	0	0	0	1	3	1	3	1	5	4	2	1	5	1	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr11:62677207G>A	ENST00000306960.3	-	2	1907	c.1366C>T	c.(1366-1368)Ccc>Tcc	p.P456S	AP000438.2_ENST00000543624.1_RNA	NM_000738.2	NP_000729.2	P11229	ACM1_HUMAN	cholinergic receptor, muscarinic 1	456					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cognition (GO:0050890)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|neuromuscular synaptic transmission (GO:0007274)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of ion transport (GO:0043270)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of locomotion (GO:0040012)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)			large_intestine(5)|lung(3)|stomach(1)	9					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Benzatropine(DB00245)|Biperiden(DB00810)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbachol(DB00411)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clidinium(DB00771)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyclopentolate(DB00979)|Cycrimine(DB00942)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Doxylamine(DB00366)|Escitalopram(DB01175)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Flupentixol(DB00875)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methantheline(DB00940)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Oxyphenonium(DB00219)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pirenzepine(DB00670)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propantheline(DB00782)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Trospium(DB00209)|Ziprasidone(DB00246)	TGGCGGGAGGGAGTGCGGTGC	0.667																																					p.P456S		Atlas-SNP	.											.	CHRM1	29	.	0			c.C1366T						PASS	.						72	79	77					11																	62677207		2201	4298	6499	SO:0001583	missense	1128	exon2			GGGAGGGAGTGCG	Y00508	CCDS8040.1	11q12-q13	2012-08-08				ENSG00000168539		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1950	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 1"	118510					Standard	NM_000738		Approved		uc001nwi.3	P11229		ENST00000306960.3:c.1366C>T	chr11.hg19:g.62677207G>A	ENSP00000306490:p.Pro456Ser	86.0	0.0	.		70.0	15.0	.	NM_000738	Q96RH1	Missense_Mutation	SNP	ENST00000306960.3	hg19	CCDS8040.1	.	.	.	.	.	.	.	.	.	.	G	15.52	2.857391	0.51376	.	.	ENSG00000168539	ENST00000306960	T	0.57595	0.39	4.53	3.58	0.41010	.	0.211607	0.23760	N	0.044839	T	0.37892	0.1020	N	0.24115	0.695	0.35793	D	0.822568	B	0.12630	0.006	B	0.14578	0.011	T	0.40289	-0.9571	10	0.42905	T	0.14	-15.4337	11.7385	0.51780	0.0:0.2317:0.7683:0.0	.	456	P11229	ACM1_HUMAN	S	456	ENSP00000306490:P456S	ENSP00000306490:P456S	P	-	1	0	CHRM1	62433783	1.000000	0.71417	0.993000	0.49108	0.930000	0.56654	5.691000	0.68249	0.995000	0.38917	0.561000	0.74099	CCC	.	.	.	none		0.667	CHRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396178.1	NM_000738		A	62677207	G	A	62677207	3	1	222	1	0	0	0	0	1	0	0	0	3378	1174	41	2	20	2	CHRM1	11	62677207	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	47869018	62677207	72329309	65	13475											
CHRM1	1128	hgsc.bcm.edu	37	chr11	62677510	62677510	+	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	cttctccttgaccagcgagaAggtcttccgcttggccagct	6	11	10	14	2	2	2	0	1	2	1	4	3	3	2	4	2	2	2	4	2	1	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr11:62677510A>T	ENST00000306960.3	-	2	1604	c.1063T>A	c.(1063-1065)Ttc>Atc	p.F355I	AP000438.2_ENST00000543624.1_RNA	NM_000738.2	NP_000729.2	P11229	ACM1_HUMAN	cholinergic receptor, muscarinic 1	355					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cognition (GO:0050890)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|neuromuscular synaptic transmission (GO:0007274)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of ion transport (GO:0043270)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of locomotion (GO:0040012)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)			large_intestine(5)|lung(3)|stomach(1)	9					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Benzatropine(DB00245)|Biperiden(DB00810)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbachol(DB00411)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clidinium(DB00771)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyclopentolate(DB00979)|Cycrimine(DB00942)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Doxylamine(DB00366)|Escitalopram(DB01175)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Flupentixol(DB00875)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methantheline(DB00940)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Oxyphenonium(DB00219)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pirenzepine(DB00670)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propantheline(DB00782)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Trospium(DB00209)|Ziprasidone(DB00246)	ACCAGCGAGAAGGTCTTCCGC	0.592																																					p.F355I		Atlas-SNP	.											.	CHRM1	29	.	0			c.T1063A						PASS	.						55	53	54					11																	62677510		2201	4298	6499	SO:0001583	missense	1128	exon2			GCGAGAAGGTCTT	Y00508	CCDS8040.1	11q12-q13	2012-08-08				ENSG00000168539		"Cholinergic receptors", "GPCR / Class A : Cholinergic receptors, muscarinic"	1950	protein-coding gene	gene with protein product	"acetylcholine receptor, muscarinic 1"	118510					Standard	NM_000738		Approved		uc001nwi.3	P11229		ENST00000306960.3:c.1063T>A	chr11.hg19:g.62677510A>T	ENSP00000306490:p.Phe355Ile	78.0	0.0	.		59.0	25.0	.	NM_000738	Q96RH1	Missense_Mutation	SNP	ENST00000306960.3	hg19	CCDS8040.1	.	.	.	.	.	.	.	.	.	.	A	11.63	1.696730	0.30142	.	.	ENSG00000168539	ENST00000306960;ENST00000543973	T;T	0.72051	-0.62;-0.62	4.49	4.49	0.54785	GPCR, rhodopsin-like superfamily (1);	0.232532	0.26293	N	0.025212	T	0.43634	0.1256	N	0.04275	-0.24	0.36087	D	0.843175	B	0.14805	0.011	B	0.17098	0.017	T	0.45920	-0.9228	10	0.17369	T	0.5	-24.428	7.3553	0.26714	0.8052:0.0:0.0:0.1948	.	355	P11229	ACM1_HUMAN	I	355	ENSP00000306490:F355I;ENSP00000441188:F355I	ENSP00000306490:F355I	F	-	1	0	CHRM1	62434086	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.101000	0.31037	1.870000	0.54199	0.459000	0.35465	TTC	.	.	.	none		0.592	CHRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396178.1	NM_000738		T	62677510	A	T	62677510	3	4	222	1	0	0	0	0	1	0	0	0	3378	72	3	5	323	5	CHRM1	11	62677510	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	303	62677510	72329006	66	13476											
SYTL2	54843	hgsc.bcm.edu	37	chr11	85409045	85409045	+	Missense_Mutation	SNP	A	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	ttaacaaaagaatttagatgActtccccttagcagtggtag	14	12	8	7	0	0	3	0	1	0	2	1	3	1	3	2	1	2	2	2	1	7	6	rs554484063		TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr11:85409045A>C	ENST00000528231.1	-	16	2707	c.2430T>G	c.(2428-2430)agT>agG	p.S810R	SYTL2_ENST00000354566.3_Missense_Mutation_p.S1148R|SYTL2_ENST00000529581.1_Missense_Mutation_p.S252R|SYTL2_ENST00000389960.4_Missense_Mutation_p.S786R|SYTL2_ENST00000524452.1_Missense_Mutation_p.S786R|SYTL2_ENST00000525702.1_Missense_Mutation_p.S252R|SYTL2_ENST00000527523.1_Missense_Mutation_p.S778R|SYTL2_ENST00000389958.3_Missense_Mutation_p.S241R|SYTL2_ENST00000359152.5_Missense_Mutation_p.S1656R|SYTL2_ENST00000533892.1_Missense_Mutation_p.S212R|SYTL2_ENST00000525423.1_Missense_Mutation_p.S1132R|SYTL2_ENST00000316356.4_Missense_Mutation_p.S811R	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	810	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		AATTTAGATGACTTCCCCTTA	0.393																																					p.S1148R		Atlas-SNP	.											.	SYTL2	231	.	0			c.T3444G						PASS	.						96	87	90					11																	85409045		2203	4299	6502	SO:0001583	missense	54843	exon11			TAGATGACTTCCC	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.2430T>G	chr11.hg19:g.85409045A>C	ENSP00000431701:p.Ser810Arg	52.0	0.0	.		50.0	7.0	.	NM_206927	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	hg19	CCDS53688.1	.	.	.	.	.	.	.	.	.	.	A	14.92	2.679575	0.47886	.	.	ENSG00000137501	ENST00000389960;ENST00000359152;ENST00000354566;ENST00000316356;ENST00000525702;ENST00000525423;ENST00000529581;ENST00000389958;ENST00000530351;ENST00000528231;ENST00000533892;ENST00000527523;ENST00000524452	T;T;T;T;T;T;T;T;T;T;T;T;T	0.08193	3.12;3.12;3.12;3.12;3.12;3.12;3.12;3.12;3.12;3.12;3.12;3.12;3.12	5.93	4.98	0.66077	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.357017	0.24240	N	0.040262	T	0.09335	0.0230	N	0.12637	0.245	0.30841	N	0.735693	B;B;B;B;B;D;P;D;B;B	0.54047	0.284;0.409;0.154;0.135;0.288;0.964;0.939;0.964;0.137;0.041	B;B;B;B;B;P;P;P;B;B	0.54346	0.091;0.091;0.148;0.091;0.091;0.749;0.681;0.749;0.091;0.023	T	0.10268	-1.0637	9	.	.	.	-1.3853	11.3673	0.49679	0.191:0.0:0.809:0.0	.	778;786;810;811;628;1108;1132;1148;241;212	Q9HCH5-14;Q9HCH5-6;Q9HCH5;Q9HCH5-13;Q9HCH5-15;Q9HCH5-11;Q9HCH5-7;Q9HCH5-8;Q9HCH5-9;Q9HCH5-4	.;.;SYTL2_HUMAN;.;.;.;.;.;.;.	R	786;1656;1148;811;252;1132;252;241;527;810;212;778;786	ENSP00000374610:S786R;ENSP00000352065:S1656R;ENSP00000346576:S1148R;ENSP00000318803:S811R;ENSP00000432996:S252R;ENSP00000432694:S1132R;ENSP00000435855:S252R;ENSP00000374608:S241R;ENSP00000435009:S527R;ENSP00000431701:S810R;ENSP00000432144:S212R;ENSP00000434010:S778R;ENSP00000435238:S786R	.	S	-	3	2	SYTL2	85086693	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.506000	0.45433	1.497000	0.48584	-0.177000	0.13119	AGT	.	.	.	none		0.393	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927		C	85409045	A	C	85409045	3	2	222	1	0	0	0	0	1	0	0	0	15495	272	10	5	386	5	SYTL2	11	85409045	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	22731535	85409045	49597471	67	13477											
NCAPD3	23310	hgsc.bcm.edu	37	chr11	134063948	134063948	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagactggagggcctgcttcCggacagacactgcagggtcc	8	6	15	12	1	0	2	0	0	0	2	2	5	2	4	3	4	2	2	3	4	0	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr11:134063948C>T	ENST00000534548.2	-	15	1851	c.1787G>A	c.(1786-1788)cGg>cAg	p.R596Q		NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	596					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)		GGCCTGCTTCCGGACAGACAC	0.443																																					p.R596Q		Atlas-SNP	.											.	NCAPD3	141	.	0			c.G1787A						PASS	.						70	67	68					11																	134063948		2201	4297	6498	SO:0001583	missense	23310	exon15			TGCTTCCGGACAG	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.1787G>A	chr11.hg19:g.134063948C>T	ENSP00000433681:p.Arg596Gln	101.0	0.0	.		100.0	14.0	.	NM_015261	A6NFS2|Q4KMQ9	Missense_Mutation	SNP	ENST00000534548.2	hg19	CCDS31723.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.777630	0.90195	.	.	ENSG00000151503	ENST00000534548	T	0.75938	-0.98	5.55	5.55	0.83447	Armadillo-like helical (1);Armadillo-type fold (1);	0.110622	0.64402	D	0.000010	D	0.87795	0.6267	M	0.83118	2.625	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	D	0.88588	0.3141	10	0.72032	D	0.01	-26.9521	19.8686	0.96842	0.0:1.0:0.0:0.0	.	596	P42695	CNDD3_HUMAN	Q	596	ENSP00000433681:R596Q	ENSP00000431612:R596Q	R	-	2	0	NCAPD3	133569158	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.278000	0.51662	2.768000	0.95171	0.655000	0.94253	CGG	.	.	.	none		0.443	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261		T	134063948	C	T	134063948	3	4	222	1	0	0	0	0	1	0	0	0	10213	652	23	1	2793	1	NCAPD3	11	134063948	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	48654903	134063948	942568	68	13478											
YARS2	51067	hgsc.bcm.edu	37	chr12	32908454	32908454	+	Frame_Shift_Del	DEL	G	G	-																															acggccgctcgggtctcccaGgcgcgccgtggcgcctccca																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr12:32908454delG	ENST00000324868.8	-	1	382	c.355delC	c.(355-357)ctgfs	p.L119fs		NM_001040436.2	NP_001035526.1	Q9Y2Z4	SYYM_HUMAN	tyrosyl-tRNA synthetase 2, mitochondrial	119					gene expression (GO:0010467)|mitochondrial tyrosyl-tRNA aminoacylation (GO:0070184)|translation (GO:0006412)|tRNA aminoacylation (GO:0043039)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)|tyrosine binding (GO:0072545)|tyrosine-tRNA ligase activity (GO:0004831)			endometrium(1)|large_intestine(4)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	16	Lung NSC(5;2.43e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)				L-Tyrosine(DB00135)	GGGTCTCCCAGGCGCGCCGTG	0.682											OREG0021729	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L119fs		Atlas-INDEL	.											YARS2,larynx,carcinoma,0,1	YARS2	33	.	0			c.356delT						PASS	.						14	16	16					12																	32908454		2196	4290	6486	SO:0001589	frameshift_variant	51067	exon1			.	AF132939	CCDS31770.1	12p11.21	2014-03-19	2007-02-23		ENSG00000139131	ENSG00000139131	6.1.1.1	"Aminoacyl tRNA synthetases / Class I"	24249	protein-coding gene	gene with protein product	"tyrosine tRNA ligase 2, mitochondrial"	610957				15779907, 15840810	Standard	NM_001040436		Approved	FLJ13995, CGI-04, mt-TyrRS	uc001rli.3	Q9Y2Z4	OTTHUMG00000169454	ENST00000324868.8:c.355delC	chr12.hg19:g.32908454delG	ENSP00000320658:p.Leu119fs	29.0	0.0	0	836	47.0	18.0	0.382979	NM_001040436	D3DUW8|Q9H817	Frame_Shift_Del	DEL	ENST00000324868.8	hg19	CCDS31770.1																																																																																			.	.	.	none		0.682	YARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404153.1	NM_015936		-	32908454	G	-	32908454	7	5	222	1	0	1	0	1	0	0	0	0	17480	991	35	0	1098	0	YARS2	12	32908454	Frame_Shift_Del	DEL	G	TCGA-MH-A561-01A-11D-A26P-10		32908454	100943441	69	13479											
GALNT6	11226	hgsc.bcm.edu	37	chr12	51758021	51758021	+	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	tggactctgcccctctggacGggcttggcgaactcaaaagt	8	9	12	12	2	3	0	1	0	2	0	3	3	3	2	2	4	2	1	2	4	3	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr12:51758021G>C	ENST00000543196.2	-	5	1138	c.933C>G	c.(931-933)ccC>ccG	p.P311P	GALNT6_ENST00000356317.3_Silent_p.P311P			Q8NCL4	GALT6_HUMAN	polypeptide N-acetylgalactosaminyltransferase 6	311					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(2)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						CCCTCTGGACGGGCTTGGCGA	0.577																																					p.P311P		Atlas-SNP	.											GALNT6,NS,carcinoma,0,1	GALNT6	63	.	0			c.C933G						PASS	.						97	90	92					12																	51758021		2203	4300	6503	SO:0001819	synonymous_variant	11226	exon6			CTGGACGGGCTTG	Y08565	CCDS8813.1	12q13	2014-03-13	2014-03-13		ENSG00000139629	ENSG00000139629		"Glycosyltransferase family 2 domain containing"	4128	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 6"	605148	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6)"			10464263	Standard	NM_007210		Approved	GalNAc-T6	uc001ryl.1	Q8NCL4		ENST00000543196.2:c.933C>G	chr12.hg19:g.51758021G>C		291.0	0.0	.		270.0	97.0	.	NM_007210	Q8IYH4|Q9H6G2|Q9UIV5	Silent	SNP	ENST00000543196.2	hg19	CCDS8813.1																																																																																			.	.	.	none		0.577	GALNT6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469735.1	NM_007210		C	51758021	G	C	51758021	2	2	222	1	0	0	0	0	0	0	0	1	6224	1103	39	4		4	GALNT6	12	51758021	Silent	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	18849567	51758021	82093874	70	13480											
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120569801	120569801	+	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	cacacagttcccctaggcacCcggctgaggagatgcgagtg	9	6	13	13	2	0	2	0	1	0	1	1	4	1	2	3	3	1	3	3	3	1	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr12:120569801C>T	ENST00000300648.6	-	54	7355	c.7343G>A	c.(7342-7344)gGg>gAg	p.G2448E		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	2448					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)					CCCTAGGCACCCGGCTGAGGA	0.567																																					p.G2448E		Atlas-SNP	.											.	GCN1L1	207	.	0			c.G7343A						PASS	.						58	60	60					12																	120569801		2016	4171	6187	SO:0001583	missense	10985	exon54			AGGCACCCGGCTG	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.7343G>A	chr12.hg19:g.120569801C>T	ENSP00000300648:p.Gly2448Glu	221.0	0.0	.		173.0	25.0	.	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	hg19	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.379586	0.82682	.	.	ENSG00000089154	ENST00000300648	T	0.61040	0.14	4.19	4.19	0.49359	Armadillo-like helical (1);Armadillo-type fold (1);	0.124142	0.53938	D	0.000052	T	0.75184	0.3815	M	0.77103	2.36	0.80722	D	1	D	0.71674	0.998	D	0.70935	0.971	T	0.76462	-0.2950	10	0.39692	T	0.17	-19.3318	17.0673	0.86562	0.0:1.0:0.0:0.0	.	2448	Q92616	GCN1L_HUMAN	E	2448	ENSP00000300648:G2448E	ENSP00000300648:G2448E	G	-	2	0	GCN1L1	119054184	1.000000	0.71417	0.969000	0.41365	0.975000	0.68041	6.918000	0.75788	2.330000	0.79161	0.655000	0.94253	GGG	.	.	.	none		0.567	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			T	120569801	C	T	120569801	3	4	222	1	0	0	0	0	1	0	0	0	6306	623	22	2	692	2	GCN1L1	12	120569801	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	68811780	120569801	13282094	71	13481											
ATP11A	23250	hgsc.bcm.edu	37	chr13	113526110	113526110	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatggtgttcacagttacacTaaaggtaagtggtctcgcgc	10	11	12	8	2	2	0	1	0	1	0	3	1	2	0	0	3	1	3	0	3	4	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr13:113526110T>C	ENST00000487903.1	+	26	3141	c.3053T>C	c.(3052-3054)cTa>cCa	p.L1018P	ATP11A_ENST00000283558.8_Missense_Mutation_p.L1018P|ATP11A_ENST00000375630.2_Missense_Mutation_p.L1018P|ATP11A_ENST00000375645.3_Missense_Mutation_p.L1018P			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	1018					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)				ACAGTTACACTAAAGGTAAGT	0.483																																					p.L1018P		Atlas-SNP	.											.	ATP11A	225	.	0			c.T3053C						PASS	.						159	151	154					13																	113526110		2203	4300	6503	SO:0001583	missense	23250	exon26			TTACACTAAAGGT	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.3053T>C	chr13.hg19:g.113526110T>C	ENSP00000420387:p.Leu1018Pro	99.0	0.0	.		77.0	33.0	.	NM_032189	Q5VXT2	Missense_Mutation	SNP	ENST00000487903.1	hg19	CCDS32011.1	.	.	.	.	.	.	.	.	.	.	T	16.06	3.016751	0.54468	.	.	ENSG00000068650	ENST00000487903;ENST00000375630;ENST00000375645;ENST00000283558;ENST00000419631	T;T;T;T;T	0.51325	0.71;0.71;0.71;0.71;0.71	4.15	4.15	0.48705	.	0.410679	0.24585	N	0.037266	T	0.75191	0.3816	H	0.96175	3.78	0.80722	D	1	D;D	0.67145	0.996;0.978	P;P	0.62014	0.897;0.841	D	0.83543	0.0097	10	0.66056	D	0.02	.	13.4786	0.61322	0.0:0.0:0.0:1.0	.	1018;1018	E9PEJ6;P98196	.;AT11A_HUMAN	P	1018;1018;1018;1018;10	ENSP00000420387:L1018P;ENSP00000364781:L1018P;ENSP00000364796:L1018P;ENSP00000283558:L1018P;ENSP00000410824:L10P	ENSP00000283558:L1018P	L	+	2	0	ATP11A	112574111	0.962000	0.33011	0.392000	0.26245	0.244000	0.25665	7.271000	0.78506	1.628000	0.50416	0.379000	0.24179	CTA	.	.	.	none		0.483	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205		C	113526110	T	C	113526110	3	2	222	1	0	0	0	0	1	0	0	0	1119	1522	53	3	3155	3	ATP11A	13	113526110	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10		113526110	1643768	72	13482											
GPHN	10243	hgsc.bcm.edu	37	chr14	67291218	67291218	+	Missense_Mutation	SNP	A	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	ctgatagattggtgtgatgaAaaggaacttaatttgatatt	14	15	10	2	0	0	5	0	4	0	1	0	6	0	6	0	2	1	0	0	2	6	6			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr14:67291218A>C	ENST00000315266.5	+	4	1349	c.228A>C	c.(226-228)gaA>gaC	p.E76D	GPHN_ENST00000543237.1_Missense_Mutation_p.E76D|GPHN_ENST00000478722.1_Missense_Mutation_p.E76D|GPHN_ENST00000305960.9_Intron|GPHN_ENST00000544752.2_3'UTR|GPHN_ENST00000459628.1_Intron	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	76	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)		GGTGTGATGAAAAGGAACTTA	0.393			T	MLL	AL																																p.E76D		Atlas-SNP	.		Dom	yes		14	14q24	10243	gephyrin (GPH)		L	.	GPHN	79	.	0			c.A228C						PASS	.						97	92	94					14																	67291218		2203	4300	6503	SO:0001583	missense	10243	exon4			TGATGAAAAGGAA	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.228A>C	chr14.hg19:g.67291218A>C	ENSP00000312771:p.Glu76Asp	94.0	0.0	.		70.0	19.0	.	NM_001024218	Q9H4E9|Q9P2G2	Missense_Mutation	SNP	ENST00000315266.5	hg19	CCDS32103.1	.	.	.	.	.	.	.	.	.	.	A	11.85	1.761655	0.31228	.	.	ENSG00000171723	ENST00000315266;ENST00000478722;ENST00000543237;ENST00000555456	T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13	5.48	4.33	0.51752	Molybdenum cofactor synthesis (1);Molybdopterin binding (4);	0.046743	0.85682	D	0.000000	T	0.56572	0.1994	N	0.10664	0.02	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.46721	-0.9171	10	0.16896	T	0.51	-9.6865	11.3654	0.49668	0.9283:0.0:0.0717:0.0	.	76;76;76	F5H039;Q9NQX3;Q9NQX3-2	.;GEPH_HUMAN;.	D	76;76;76;9	ENSP00000312771:E76D;ENSP00000417901:E76D;ENSP00000438404:E76D;ENSP00000450706:E9D	ENSP00000312771:E76D	E	+	3	2	GPHN	66360971	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	1.444000	0.35068	0.910000	0.36722	0.254000	0.18369	GAA	.	.	.	none		0.393	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806		C	67291218	A	C	67291218	3	2	222	1	0	0	0	0	1	0	0	0	6617	11	1	5	242	5	GPHN	14	67291218	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10		67291218	40058322	73	13483											
PPIP5K1	9677	hgsc.bcm.edu	37	chr15	43863609	43863609	+	Splice_Site	DEL	C	C	-																															ttcccaaggccctctcattaCctccatggaaccagcttttc																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr15:43863609delC	ENST00000396923.3	-	24	3089		c.e24+1		PPIP5K1_ENST00000432870.3_Splice_Site|PPIP5K1_ENST00000348806.6_Splice_Site|PPIP5K1_ENST00000360135.4_Splice_Site|PPIP5K1_ENST00000360301.4_Splice_Site|PPIP5K1_ENST00000381885.1_Splice_Site|PPIP5K1_ENST00000381879.4_Splice_Site|PPIP5K1_ENST00000420765.1_Splice_Site|PPIP5K1_ENST00000334933.4_Splice_Site			Q6PFW1	VIP1_HUMAN	diphosphoinositol pentakisphosphate kinase 1						inositol metabolic process (GO:0006020)|inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	acid phosphatase activity (GO:0003993)|ATP binding (GO:0005524)|diphosphoinositol-pentakisphosphate kinase activity (GO:0033857)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,3,4,5,6-pentakisphosphate kinase activity (GO:0000827)			large_intestine(1)	1						CCTCTCATTACCTCCATGGAA	0.557																																					.		Atlas-INDEL	.											.	PPIP5K1	34	.	0			c.2955+2G>-						PASS	.																																			SO:0001630	splice_region_variant	9677	exon25			.	AF502586	CCDS32215.1, CCDS45252.1, CCDS53937.1	15q15.3	2010-01-27	2010-01-26	2010-01-26	ENSG00000168781	ENSG00000168781	2.7.4.24		29023	protein-coding gene	gene with protein product		610979	"histidine acid phosphatase domain containing 2A"	HISPPD2A		17412958, 17690096, 18981179	Standard	NM_001190214		Approved	KIAA0377, IPS1, VIP1	uc001zrw.3	Q6PFW1	OTTHUMG00000059758	ENST00000396923.3:c.2967+1G>-	chr15.hg19:g.43863609delC		106.0	0.0	0		91.0	18.0	0.197802	NM_014659	O15082|Q5HYF8|Q7Z3A7|Q86TE7|Q86UV3|Q86UV4|Q86XW8|Q8IZN0	Splice_Site	DEL	ENST00000396923.3	hg19	CCDS45252.1																																																																																			.	.	.	none		0.557	PPIP5K1-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132907.1	NM_014659	Intron	-	43863609	C	-	43863609	8	5	222	1	0	1	0	1	0	0	1	0	12342	521	18	0	1485	0	PPIP5K1	15	43863609	Splice_Site	DEL	C	TCGA-MH-A561-01A-11D-A26P-10		43863609	58667783	74	13484											
VPS13C	54832	hgsc.bcm.edu	37	chr15	62211634	62211634	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agggatatttgcaacttctgTatatccatgaggtactaagg	12	13	10	6	0	1	1	0	1	1	0	2	2	2	2	1	3	3	3	1	3	6	7			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr15:62211634T>C	ENST00000261517.5	-	58	7565	c.7492A>G	c.(7492-7494)Aca>Gca	p.T2498A	VPS13C_ENST00000395898.3_Missense_Mutation_p.T2455A|VPS13C_ENST00000395896.4_Missense_Mutation_p.T2498A|VPS13C_ENST00000249837.3_Missense_Mutation_p.T2455A	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						GCAACTTCTGTATATCCATGA	0.378																																					p.T2498A		Atlas-SNP	.											.	VPS13C	506	.	0			c.A7492G						PASS	.						127	126	126					15																	62211634		2203	4299	6502	SO:0001583	missense	54832	exon58			CTTCTGTATATCC	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.7492A>G	chr15.hg19:g.62211634T>C	ENSP00000261517:p.Thr2498Ala	83.0	0.0	.		103.0	42.0	.	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	hg19	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	T	16.21	3.059562	0.55325	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.44881	0.92;0.91;1.09	5.08	5.08	0.68730	.	0.343050	0.31071	N	0.008307	T	0.38585	0.1046	M	0.69823	2.125	0.36345	D	0.85969	B;B;B;P	0.35745	0.257;0.171;0.257;0.518	B;B;B;B	0.30316	0.089;0.089;0.089;0.114	T	0.49753	-0.8906	10	0.30078	T	0.28	.	11.1995	0.48733	0.0:0.0745:0.0:0.9255	.	2455;2498;2455;2498	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	A	2455;2498;2498;2498	ENSP00000249837:T2455A;ENSP00000261517:T2498A;ENSP00000379233:T2498A	ENSP00000249837:T2455A	T	-	1	0	VPS13C	59998926	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	2.093000	0.41710	2.023000	0.59567	0.533000	0.62120	ACA	.	.	.	none		0.378	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		C	62211634	T	C	62211634	3	2	222	1	0	0	0	0	1	0	0	0	17203	1638	57	3	3909	3	VPS13C	15	62211634	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	18348025	62211634	40319758	75	13485											
RPL3L	6123	hgsc.bcm.edu	37	chr16	1995508	1995508	+	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	cggtgagctcaccatgaaggCcctcttctcttgggctgtct	5	12	11	13	1	4	2	1	2	3	0	5	2	4	2	2	3	1	2	2	3	1	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr16:1995508C>A	ENST00000268661.7	-	9	1253	c.1159G>T	c.(1159-1161)Gcc>Tcc	p.A387S	MSRB1_ENST00000564908.1_5'Flank|MSRB1_ENST00000361871.3_5'Flank|MSRB1_ENST00000399753.2_5'Flank	NM_005061.2	NP_005052.1	Q92901	RL3L_HUMAN	ribosomal protein L3-like	387					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						ACCATGAAGGCCCTCTTCTCT	0.597																																					p.A387S		Atlas-SNP	.											.	RPL3L	42	.	0			c.G1159T						PASS	.						55	46	50					16																	1995508		2199	4300	6499	SO:0001583	missense	6123	exon9			TGAAGGCCCTCTT	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.1159G>T	chr16.hg19:g.1995508C>A	ENSP00000268661:p.Ala387Ser	89.0	0.0	.		66.0	27.0	.	NM_005061		Missense_Mutation	SNP	ENST00000268661.7	hg19	CCDS10450.1	.	.	.	.	.	.	.	.	.	.	C	10.72	1.430672	0.25726	.	.	ENSG00000140986	ENST00000268661	T	0.32753	1.44	3.92	3.92	0.45320	.	0.259903	0.37178	N	0.002207	T	0.39384	0.1076	M	0.69248	2.105	0.50632	D	0.999888	P	0.44139	0.827	P	0.45856	0.495	T	0.40553	-0.9557	10	0.46703	T	0.11	-1.9802	15.4739	0.75461	0.0:1.0:0.0:0.0	.	387	Q92901	RL3L_HUMAN	S	387	ENSP00000268661:A387S	ENSP00000268661:A387S	A	-	1	0	RPL3L	1935509	1.000000	0.71417	0.999000	0.59377	0.185000	0.23345	4.700000	0.61803	2.185000	0.69588	0.563000	0.77884	GCC	.	.	.	none		0.597	RPL3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250582.2	NM_005061		A	1995508	C	A	1995508	3	1	222	1	0	0	0	0	1	0	0	0	13607	739	26	4	72	4	RPL3L	16	1995508	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10		1995508	88359245	76	13486											
SCNN1B	6338	hgsc.bcm.edu	37	chr16	23360139	23360139	+	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	tggggcatcttcatcaggacCtacttgagctgggaggtcag	8	10	14	9	0	4	1	3	1	1	0	4	3	4	3	1	5	2	2	1	5	1	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr16:23360139C>G	ENST00000343070.2	+	2	395	c.219C>G	c.(217-219)acC>acG	p.T73T	SCNN1B_ENST00000568085.1_Silent_p.T73T|SCNN1B_ENST00000307331.5_Silent_p.T118T|SCNN1B_ENST00000569789.1_3'UTR|SCNN1B_ENST00000568923.1_Silent_p.T73T	NM_000336.2	NP_000327.2	P51168	SCNNB_HUMAN	sodium channel, non-voltage-gated 1, beta subunit	73					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)	TCATCAGGACCTACTTGAGCT	0.587																																					p.T73T		Atlas-SNP	.											.	SCNN1B	81	.	0			c.C219G						PASS	.						84	69	74					16																	23360139		2197	4300	6497	SO:0001819	synonymous_variant	6338	exon2			CAGGACCTACTTG	X87159	CCDS10609.1	16p12.2-p12.1	2012-02-28	2012-02-28		ENSG00000168447	ENSG00000168447		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10600	protein-coding gene	gene with protein product	"Liddle syndrome"	600760	"sodium channel, nonvoltage-gated 1, beta", "sodium channel, non-voltage-gated 1, beta"				Standard	NM_000336		Approved	ENaCbeta	uc002dln.3	P51168	OTTHUMG00000131608	ENST00000343070.2:c.219C>G	chr16.hg19:g.23360139C>G		289.0	0.0	.		227.0	102.0	.	NM_000336	C5HTZ2|O60891|Q96KG2|Q9UJ32|Q9UMU5	Silent	SNP	ENST00000343070.2	hg19	CCDS10609.1																																																																																			.	.	.	none		0.587	SCNN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254495.2			G	23360139	C	G	23360139	2	3	222	1	0	0	0	0	0	0	0	1	13941	668	24	4		4	SCNN1B	16	23360139	Silent	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	21364631	23360139	66994614	77	13487											
MYLK3	91807	hgsc.bcm.edu	37	chr16	46781755	46781755	+	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	gccctgtccaccgcagccacCatcctgaagagggcctccag	8	5	10	18	1	0	2	0	1	0	1	3	2	3	2	8	1	1	1	8	1	1	0			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr16:46781755C>A	ENST00000394809.4	-	1	466	c.351G>T	c.(349-351)atG>atT	p.M117I	MYLK3_ENST00000536476.1_Intron	NM_182493.2	NP_872299.2	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3	117					cardiac myofibril assembly (GO:0055003)|cellular response to interleukin-1 (GO:0071347)|positive regulation of sarcomere organization (GO:0060298)|protein phosphorylation (GO:0006468)|regulation of vascular permeability involved in acute inflammatory response (GO:0002528)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(5)|stomach(3)	37		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				CCGCAGCCACCATCCTGAAGA	0.657																																					p.M117I		Atlas-SNP	.											.	MYLK3	82	.	0			c.G351T						PASS	.						45	40	42					16																	46781755		2203	4300	6503	SO:0001583	missense	91807	exon1			AGCCACCATCCTG	AJ247087	CCDS10723.2	16q11.2	2008-10-23			ENSG00000140795	ENSG00000140795			29826	protein-coding gene	gene with protein product	"MLC kinase"	612147				17885681	Standard	NM_182493		Approved	caMLCK, MLCK	uc002eei.4	Q32MK0	OTTHUMG00000132543	ENST00000394809.4:c.351G>T	chr16.hg19:g.46781755C>A	ENSP00000378288:p.Met117Ile	146.0	0.0	.		93.0	48.0	.	NM_182493	B5BUL9|B7Z5U8|Q32MK1|Q96DV1	Missense_Mutation	SNP	ENST00000394809.4	hg19	CCDS10723.2	.	.	.	.	.	.	.	.	.	.	C	14.42	2.530435	0.45073	.	.	ENSG00000140795	ENST00000394809	T	0.69435	-0.4	4.87	4.87	0.63330	.	0.000000	0.43260	D	0.000583	T	0.65101	0.2659	M	0.67953	2.075	0.80722	D	1	P	0.38922	0.651	B	0.33521	0.165	T	0.69942	-0.5008	10	0.46703	T	0.11	.	18.3666	0.90392	0.0:1.0:0.0:0.0	.	117	Q32MK0	MYLK3_HUMAN	I	117	ENSP00000378288:M117I	ENSP00000378288:M117I	M	-	3	0	MYLK3	45339256	1.000000	0.71417	1.000000	0.80357	0.273000	0.26683	2.195000	0.42677	2.394000	0.81467	0.491000	0.48974	ATG	.	.	.	none		0.657	MYLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255743.2	NM_182493		A	46781755	C	A	46781755	3	1	222	1	0	0	0	0	1	0	0	0	10065	594	21	4	2160	4	MYLK3	16	46781755	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	23421616	46781755	43572998	78	13488											
EDC4	23644	hgsc.bcm.edu	37	chr16	67910858	67910858	+	Missense_Mutation	SNP	T	T	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	tgctgtgtctaactccttctTggcctatgccattcggggtg	4	15	11	11	1	2	0	0	0	2	0	4	0	3	0	3	3	3	1	3	3	2	5			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr16:67910858T>G	ENST00000358933.5	+	4	673	c.434T>G	c.(433-435)tTg>tGg	p.L145W	EDC4_ENST00000574770.1_3'UTR|AC040162.1_ENST00000408599.1_RNA	NM_014329.4	NP_055144.3	Q6P2E9	EDC4_HUMAN	enhancer of mRNA decapping 4	145					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		AACTCCTTCTTGGCCTATGCC	0.507																																					p.L145W		Atlas-SNP	.											.	EDC4	101	.	0			c.T434G						PASS	.						136	130	132					16																	67910858		2198	4300	6498	SO:0001583	missense	23644	exon4			CCTTCTTGGCCTA	U17474	CCDS10849.1	16q22.1	2008-02-05			ENSG00000038358	ENSG00000038358			17157	protein-coding gene	gene with protein product		606030				9067524	Standard	NM_014329		Approved	RCD-8, Ge-1, HEDLS	uc002eur.3	Q6P2E9	OTTHUMG00000137543	ENST00000358933.5:c.434T>G	chr16.hg19:g.67910858T>G	ENSP00000351811:p.Leu145Trp	173.0	0.0	.		123.0	50.0	.	NM_014329	A6NGM1|A8K4T4|Q13025|Q13826|Q6ZR12|Q7Z6H7	Missense_Mutation	SNP	ENST00000358933.5	hg19	CCDS10849.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.935710	0.92458	.	.	ENSG00000038358	ENST00000358933;ENST00000536072	T	0.42131	0.98	5.83	5.83	0.93111	WD40 repeat-like-containing domain (1);	0.081121	0.51477	D	0.000086	T	0.62901	0.2466	M	0.69823	2.125	0.58432	D	0.999996	D;D	0.71674	0.998;0.997	D;P	0.65140	0.932;0.903	T	0.66740	-0.5847	10	0.87932	D	0	-7.7554	15.8624	0.79035	0.0:0.0:0.0:1.0	.	77;145	B7Z7V8;Q6P2E9	.;EDC4_HUMAN	W	145;77	ENSP00000351811:L145W	ENSP00000351811:L145W	L	+	2	0	EDC4	66468359	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.997000	0.88414	2.235000	0.73313	0.533000	0.62120	TTG	.	.	.	none		0.507	EDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268874.2	NM_014329		G	67910858	T	G	67910858	3	3	222	1	0	0	0	0	1	0	0	0	4910	1821	63	5	448	5	EDC4	16	67910858	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	21129103	67910858	22443895	79	13489											
MYO15A	51168	hgsc.bcm.edu	37	chr17	18057182	18057182	+	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	cttctacggctatcaggacgCcccctggaagatcttcctgc	7	10	9	15	2	3	1	1	0	2	1	4	3	4	3	3	3	2	1	3	3	3	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr17:18057182C>G	ENST00000205890.5	+	43	8398	c.8060C>G	c.(8059-8061)gCc>gGc	p.A2687G	MYO15A_ENST00000585180.1_5'Flank|MYO15A_ENST00000418233.3_5'UTR	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2687	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)					TATCAGGACGCCCCCTGGAAG	0.657																																					p.A2687G		Atlas-SNP	.											.	MYO15A	268	.	0			c.C8060G						PASS	.						45	46	46					17																	18057182		1888	4114	6002	SO:0001583	missense	51168	exon42			AGGACGCCCCCTG	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.8060C>G	chr17.hg19:g.18057182C>G	ENSP00000205890:p.Ala2687Gly	272.0	0.0	.		294.0	70.0	.	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	hg19	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	C	18.05	3.536404	0.65085	.	.	ENSG00000091536	ENST00000205890	D	0.88586	-2.4	5.07	2.79	0.32731	.	.	.	.	.	T	0.82263	0.4999	M	0.64997	1.995	0.80722	D	1	P	0.35433	0.501	B	0.27608	0.081	T	0.80400	-0.1398	9	0.87932	D	0	.	2.5033	0.04638	0.222:0.4596:0.0:0.3183	.	2687	Q9UKN7	MYO15_HUMAN	G	2687	ENSP00000205890:A2687G	ENSP00000205890:A2687G	A	+	2	0	MYO15A	17997907	1.000000	0.71417	0.800000	0.32199	0.904000	0.53231	2.694000	0.47035	1.107000	0.41642	0.563000	0.77884	GCC	.	.	.	none		0.657	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		G	18057182	C	G	18057182	3	3	222	1	0	0	0	0	1	0	0	0	10070	739	26	4	8222	4	MYO15A	17	18057182	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10		18057182	63138028	80	13490											
ITGA2B	3674	hgsc.bcm.edu	37	chr17	42449792	42449792	+	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	ttccgcttgaagaagccgacCtgggggtacacgggggccaa	9	6	15	11	3	0	2	0	1	0	1	1	3	1	2	4	4	2	2	4	4	4	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr17:42449792C>T	ENST00000262407.5	-	30	3092		c.e30-1		ITGA2B_ENST00000353281.4_Splice_Site	NM_000419.3	NP_000410.2	P08514	ITA2B_HUMAN	integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)						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)	AGAAGCCGACCTGGGGGTACA	0.577																																					.		Atlas-SNP	.											.	ITGA2B	88	.	0			c.3061-1G>A						PASS	.						58	44	49					17																	42449792		2203	4300	6503	SO:0001630	splice_region_variant	3674	exon31			GCCGACCTGGGGG		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.3061-1G>A	chr17.hg19:g.42449792C>T		84.0	0.0	.		97.0	22.0	.	NM_000419	B2RCY8|O95366|Q14443|Q17R67	Splice_Site	SNP	ENST00000262407.5	hg19	CCDS32665.1	.	.	.	.	.	.	.	.	.	.	C	17.11	3.306424	0.60305	.	.	ENSG00000005961	ENST00000262407;ENST00000353281	.	.	.	4.54	4.54	0.55810	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8074	0.69968	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ITGA2B	39805318	0.993000	0.37304	0.275000	0.24674	0.303000	0.27691	4.088000	0.57678	2.357000	0.79964	0.561000	0.74099	.	.	.	.	none		0.577	ITGA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439823.1		Intron	T	42449792	C	T	42449792	5	4	222	1	0	0	0	0	0	0	1	0	7883	695	24	2	63	2	ITGA2B	17	42449792	Splice_Site	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	24392610	42449792	38745418	81	13491											
C17orf104	284071	hgsc.bcm.edu	37	chr17	42744196	42744196	+	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	tcttgaagcaccactacagcAaaaaagggcagagatgtttc	15	8	9	9	0	1	2	0	1	1	1	2	3	1	2	1	1	3	4	1	1	5	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr17:42744196A>T	ENST00000409122.2	+	5	1059	c.917A>T	c.(916-918)cAa>cTa	p.Q306L	C17orf104_ENST00000359945.3_Missense_Mutation_p.Q306L|C17orf104_ENST00000409464.1_Missense_Mutation_p.Q140L	NM_001145080.2	NP_001138552.2	A2RUB1	CQ104_HUMAN	chromosome 17 open reading frame 104	306										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						CCACTACAGCAAAAAAGGGCA	0.348																																					p.Q306L		Atlas-SNP	.											.	C17orf104	75	.	0			c.A917T						PASS	.						27	28	28					17																	42744196		2202	4298	6500	SO:0001583	missense	284071	exon5			TACAGCAAAAAAG		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.917A>T	chr17.hg19:g.42744196A>T	ENSP00000386452:p.Gln306Leu	43.0	0.0	.		40.0	14.0	.	NM_001145080	B4DXJ2|B5MD93|B9EGQ6|C4AM97|Q4G0Y1|Q8IVZ7|Q8NA45	Missense_Mutation	SNP	ENST00000409122.2	hg19	CCDS45703.2	.	.	.	.	.	.	.	.	.	.	A	1.742	-0.491410	0.04322	.	.	ENSG00000180336	ENST00000359945;ENST00000409122;ENST00000432494;ENST00000409464	T;T;T;T	0.35421	1.31;1.31;1.37;1.31	5.45	4.38	0.52667	.	0.063895	0.64402	D	0.000008	T	0.25975	0.0633	N	0.24115	0.695	0.24874	N	0.992265	B;B;B	0.31548	0.328;0.161;0.161	B;B;B	0.35413	0.202;0.202;0.202	T	0.19257	-1.0311	10	0.59425	D	0.04	-14.3041	8.5529	0.33462	0.8008:0.1303:0.0689:0.0	.	306;306;140	A2RUB1-5;A2RUB1;A2RUB1-1	.;CQ104_HUMAN;.	L	306;306;140;140	ENSP00000353028:Q306L;ENSP00000386452:Q306L;ENSP00000399809:Q140L;ENSP00000386586:Q140L	ENSP00000353028:Q306L	Q	+	2	0	C17orf104	40099722	1.000000	0.71417	0.998000	0.56505	0.014000	0.08584	4.646000	0.61411	1.017000	0.39495	-0.388000	0.06559	CAA	.	.	.	none		0.348	C17orf104-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329171.2	NM_001145080		T	42744196	A	T	42744196	3	4	222	1	0	0	0	0	1	0	0	0	1853	130	5	5	935	5	C17orf104	17	42744196	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	294404	42744196	38451014	82	13492											
SPAG9	9043	hgsc.bcm.edu	37	chr17	49067112	49067112	+	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	gtaaagacatgctctgtgtaGacgccagtttgggagatgtc	10	11	13	7	1	1	3	0	0	1	3	2	4	1	3	1	1	1	4	1	1	3	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr17:49067112G>T	ENST00000262013.7	-	21	2947	c.2739C>A	c.(2737-2739)gtC>gtA	p.V913V	SPAG9_ENST00000505279.1_Silent_p.V903V|SPAG9_ENST00000357122.4_Silent_p.V899V|SPAG9_ENST00000510283.1_Silent_p.V756V	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	913					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)			GCTCTGTGTAGACGCCAGTTT	0.473																																					p.V913V		Atlas-SNP	.											.	SPAG9	151	.	0			c.C2739A						PASS	.						165	133	144					17																	49067112		2203	4300	6503	SO:0001819	synonymous_variant	9043	exon21			TGTGTAGACGCCA	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.2739C>A	chr17.hg19:g.49067112G>T		221.0	0.0	.		259.0	56.0	.	NM_001130528	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Silent	SNP	ENST00000262013.7	hg19	CCDS45740.1	.	.	.	.	.	.	.	.	.	.	G	9.197	1.027489	0.19512	.	.	ENSG00000008294	ENST00000513906	.	.	.	5.77	0.0229	0.14135	.	.	.	.	.	T	0.41627	0.1167	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.24548	-1.0157	4	.	.	.	-12.8707	1.4604	0.02394	0.2848:0.2293:0.3304:0.1555	.	.	.	.	Y	157	.	.	S	-	2	0	SPAG9	46422111	0.969000	0.33509	0.999000	0.59377	0.960000	0.62799	0.071000	0.14594	0.094000	0.17404	-1.467000	0.01014	TCT	.	.	.	none		0.473	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971		T	49067112	G	T	49067112	2	4	222	1	0	0	0	0	0	0	0	1	14998	929	33	4		4	SPAG9	17	49067112	Silent	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	6322916	49067112	32128098	83	13493											
C17orf95	124512	hgsc.bcm.edu	37	chr17	74729098	74729098	+	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	cttccaggaattttggctgcCaaatgtggtgcagaagtaat	11	12	11	7	0	0	1	0	0	0	1	1	2	1	2	2	3	2	3	2	3	4	4			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr17:74729098C>A	ENST00000341249.6	+	3	455	c.123C>A	c.(121-123)gcC>gcA	p.A41A	METTL23_ENST00000588822.1_5'UTR|MFSD11_ENST00000586622.1_5'Flank|METTL23_ENST00000590964.1_5'UTR|METTL23_ENST00000588302.1_5'UTR|RP11-318A15.7_ENST00000587459.1_Silent_p.A13A|METTL23_ENST00000586752.1_5'UTR|METTL23_ENST00000586200.1_Intron|METTL23_ENST00000588783.1_Silent_p.A41A|METTL23_ENST00000591571.1_5'UTR|METTL23_ENST00000586738.1_Silent_p.A41A|METTL23_ENST00000589977.1_Silent_p.A41A	NM_001206984.1	NP_001193913.1	Q86XA0	MET23_HUMAN	methyltransferase like 23	41						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	methyltransferase activity (GO:0008168)			large_intestine(2)|lung(1)	3						TTTTGGCTGCCAAATGTGGTG	0.438																																					p.A41A		Atlas-SNP	.											.	METTL23	19	.	0			c.C123A						PASS	.						26	24	25					17																	74729098		1915	4132	6047	SO:0001819	synonymous_variant	124512	exon3			GGCTGCCAAATGT		CCDS45787.1, CCDS59298.1	17q25.2	2011-03-03	2011-03-03	2011-03-03	ENSG00000181038	ENSG00000181038			26988	protein-coding gene	gene with protein product		615262	"chromosome 17 open reading frame 95"	C17orf95		12477932	Standard	NM_001080510		Approved	LOC124512	uc021udl.1	Q86XA0		ENST00000341249.6:c.123C>A	chr17.hg19:g.74729098C>A		74.0	0.0	.		80.0	13.0	.	NM_001206984	H9ZYJ0|K7EK32	Silent	SNP	ENST00000341249.6	hg19	CCDS45787.1																																																																																			.	.	.	none		0.438	METTL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451002.1	NM_001080510		A	74729098	C	A	74729098	2	1	222	1	0	0	0	0	0	0	0	1	1894	581	21	4		4	C17orf95	17	74729098	Silent	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	25661986	74729098	6466112	84	13494											
AATK	9625	hgsc.bcm.edu	37	chr17	79095314	79095314	+	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	ggcctcctccgagggaagtgGggctccctcctgggatgggg	4	7	18	12	1	0	0	0	0	0	0	4	3	4	2	5	7	0	1	5	7	1	0			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr17:79095314G>T	ENST00000326724.4	-	11	2446	c.2422C>A	c.(2422-2424)Cca>Aca	p.P808T	AATK_ENST00000417379.1_Missense_Mutation_p.P705T	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	808	Pro-rich.				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)			GAGGGAAGTGGGGCTCCCTCC	0.701																																					p.P808T		Atlas-SNP	.											.	AATK	102	.	0			c.C2422A						PASS	.						16	21	19					17																	79095314		2062	4182	6244	SO:0001583	missense	9625	exon11			GAAGTGGGGCTCC	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.2422C>A	chr17.hg19:g.79095314G>T	ENSP00000324196:p.Pro808Thr	69.0	0.0	.		60.0	15.0	.	NM_001080395	O75136|Q6ZN31|Q86X28	Missense_Mutation	SNP	ENST00000326724.4	hg19	CCDS45807.1	.	.	.	.	.	.	.	.	.	.	G	7.050	0.564179	0.13498	.	.	ENSG00000181409	ENST00000326724;ENST00000374792	T;T	0.78246	-1.06;-1.16	4.36	2.21	0.28008	.	0.938651	0.08819	U	0.889000	T	0.66366	0.2782	L	0.43152	1.355	0.19575	N	0.999966	B	0.15141	0.012	B	0.09377	0.004	T	0.50276	-0.8847	10	0.22706	T	0.39	.	5.0003	0.14261	0.1085:0.0:0.552:0.3395	.	808	Q6ZMQ8	LMTK1_HUMAN	T	808;772	ENSP00000324196:P808T;ENSP00000363924:P772T	ENSP00000324196:P808T	P	-	1	0	AATK	76709909	0.000000	0.05858	0.647000	0.29507	0.154000	0.21943	0.726000	0.25984	0.801000	0.34066	0.561000	0.74099	CCA	.	.	.	none		0.701	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920		T	79095314	G	T	79095314	3	4	222	1	0	0	0	0	1	0	0	0	26	1232	43	4	1718	4	AATK	17	79095314	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10	4366216	79095314	2099896	85	13495											
MALT1	10892	hgsc.bcm.edu	37	chr18	56400802	56400802	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttattggatatgtgtaggAaaaggtaagttttctaatct	12	17	9	3	0	3	0	0	0	3	0	3	2	3	2	0	3	0	3	0	3	7	8			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr18:56400802A>G	ENST00000348428.3	+	11	1654	c.1396A>G	c.(1396-1398)Aaa>Gaa	p.K466E	MALT1_ENST00000345724.3_Missense_Mutation_p.K455E|RP11-126O1.4_ENST00000588835.1_RNA	NM_006785.2|NM_173844.1	NP_006776.1|NP_776216.1	Q9UDY8	MALT1_HUMAN	mucosa associated lymphoid tissue lymphoma translocation gene 1	466	Caspase-like.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|B-1 B cell differentiation (GO:0001923)|defense response (GO:0006952)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|nuclear export (GO:0051168)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|protein oligomerization (GO:0051259)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of T cell receptor signaling pathway (GO:0050856)|response to fungus (GO:0009620)|response to molecule of bacterial origin (GO:0002237)|T cell proliferation (GO:0042098)|T cell receptor signaling pathway (GO:0050852)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)|protein self-association (GO:0043621)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|large_intestine(7)|lung(1)|ovary(2)|skin(1)	12						TATGTGTAGGAAAAGGTAAGT	0.313			T	BIRC3	MALT																																p.K466E		Atlas-SNP	.		Dom	yes		18	18q21	10892	mucosa associated lymphoid tissue lymphoma translocation gene 1		L	.	MALT1	55	.	0			c.A1396G						PASS	.						59	66	64					18																	56400802		2203	4299	6502	SO:0001583	missense	10892	exon11			TGTAGGAAAAGGT		CCDS11967.1, CCDS11968.1	18q21	2013-01-11			ENSG00000172175	ENSG00000172175		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6819	protein-coding gene	gene with protein product	"paracaspase"	604860		MLT		10339464, 10406266, 10523859	Standard	NM_006785		Approved		uc002lhm.1	Q9UDY8	OTTHUMG00000132761	ENST00000348428.3:c.1396A>G	chr18.hg19:g.56400802A>G	ENSP00000319279:p.Lys466Glu	59.0	0.0	.		66.0	5.0	.	NM_006785	Q9NTB7|Q9ULX4	Missense_Mutation	SNP	ENST00000348428.3	hg19	CCDS11967.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.599615	0.87055	.	.	ENSG00000172175	ENST00000348428;ENST00000345724	T;T	0.41400	1.0;1.0	5.52	5.52	0.82312	Peptidase C14, caspase catalytic (1);	0.000000	0.85682	D	0.000000	T	0.63390	0.2507	M	0.65975	2.015	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	T	0.66767	-0.5840	10	0.72032	D	0.01	.	15.304	0.73979	1.0:0.0:0.0:0.0	.	455;466	Q9UDY8-2;Q9UDY8	.;MALT1_HUMAN	E	466;455	ENSP00000319279:K466E;ENSP00000304161:K455E	ENSP00000304161:K455E	K	+	1	0	MALT1	54551782	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.153000	0.77428	2.106000	0.64143	0.528000	0.53228	AAA	.	.	.	none		0.313	MALT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256132.2			G	56400802	A	G	56400802	3	3	222	1	0	0	0	0	1	0	0	0	9209	247	9	3	1438	3	MALT1	18	56400802	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10		56400802	21676446	86	13496											
ZNF799	90576	hgsc.bcm.edu	37	chr19	12502161	12502161	+	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	tctttcatgacttttcagtgAactaggacaatcaaagcctt	12	14	6	9	0	4	2	3	2	1	0	4	3	4	3	1	1	2	0	1	1	4	5	rs541416821		TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr19:12502161A>T	ENST00000430385.3	-	4	1251	c.1051T>A	c.(1051-1053)Tca>Aca	p.S351T	CTD-3105H18.14_ENST00000435033.1_Intron|ZNF799_ENST00000419318.1_Missense_Mutation_p.S319T	NM_001080821.2	NP_001074290.1	Q96GE5	ZN799_HUMAN	zinc finger protein 799	351					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S351T(1)|p.S138T(1)		breast(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(2)	19						CTTTTCAGTGAACTAGGACAA	0.413																																					p.S351T		Atlas-SNP	.											ZNF799_ENST00000430385,NS,carcinoma,0,2	ZNF799	111	.	2	Substitution - Missense(2)	kidney(2)	c.T1051A						PASS	.						161	157	158					19																	12502161		2203	4300	6503	SO:0001583	missense	90576	exon4			TCAGTGAACTAGG	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.1051T>A	chr19.hg19:g.12502161A>T	ENSP00000411084:p.Ser351Thr	100.0	1.0	.		81.0	5.0	.	NM_001080821		Missense_Mutation	SNP	ENST00000430385.3	hg19	CCDS45989.1	.	.	.	.	.	.	.	.	.	.	A	11.22	1.574140	0.28092	.	.	ENSG00000196466	ENST00000419318;ENST00000430385	T;T	0.07567	3.18;3.18	1.31	1.31	0.21738	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09949	0.0244	N	0.16478	0.41	0.09310	N	1	D	0.60575	0.988	P	0.60173	0.87	T	0.34378	-0.9831	9	0.30078	T	0.28	.	6.6913	0.23174	1.0:0.0:0.0:0.0	.	351	Q96GE5	ZN799_HUMAN	T	319;351	ENSP00000415278:S319T;ENSP00000411084:S351T	ENSP00000415278:S319T	S	-	1	0	ZNF799	12363161	0.000000	0.05858	0.005000	0.12908	0.140000	0.21249	0.679000	0.25291	0.846000	0.35142	0.352000	0.21897	TCA	.	.	.	none		0.413	ZNF799-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344099.2	NM_001080821		T	12502161	A	T	12502161	3	4	222	1	0	0	0	0	1	0	0	0	18178	246	9	5	884	5	ZNF799	19	12502161	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10		12502161	46626822	87	13497											
SYDE1	85360	hgsc.bcm.edu	37	chr19	15220001	15220001	+	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	cacggggagcctacctgcaaAgcctggagcccagtagccgc	9	4	13	15	2	0	0	0	0	0	0	0	2	0	2	5	3	6	2	5	3	3	2			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr19:15220001A>T	ENST00000342784.2	+	2	254	c.223A>T	c.(223-225)Agc>Tgc	p.S75C	SYDE1_ENST00000600252.1_5'UTR|SYDE1_ENST00000600440.1_Intron	NM_033025.4	NP_149014.3	Q6ZW31	SYDE1_HUMAN	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	75	Pro-rich.				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						CTACCTGCAAAGCCTGGAGCC	0.706																																					p.S75C		Atlas-SNP	.											.	SYDE1	44	.	0			c.A223T						PASS	.						13	13	13					19																	15220001		2148	4200	6348	SO:0001583	missense	85360	exon2			CTGCAAAGCCTGG	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.223A>T	chr19.hg19:g.15220001A>T	ENSP00000341489:p.Ser75Cys	51.0	0.0	.		37.0	13.0	.	NM_033025	Q7L2I8|Q8N6J2|Q9H8K4	Missense_Mutation	SNP	ENST00000342784.2	hg19	CCDS12324.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.951011	0.73787	.	.	ENSG00000105137	ENST00000342784	T	0.13778	2.56	4.32	4.32	0.51571	.	0.000000	0.85682	D	0.000000	T	0.26484	0.0647	L	0.47716	1.5	0.27009	N	0.964736	D	0.76494	0.999	D	0.80764	0.994	T	0.02781	-1.1111	10	0.87932	D	0	.	8.0008	0.30295	0.7926:0.2074:0.0:0.0	.	75	Q6ZW31	SYDE1_HUMAN	C	75	ENSP00000341489:S75C	ENSP00000341489:S75C	S	+	1	0	SYDE1	15081001	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.770000	0.62309	1.598000	0.50083	0.533000	0.62120	AGC	.	.	.	none		0.706	SYDE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465666.1	NM_033025		T	15220001	A	T	15220001	3	4	222	1	0	0	0	0	1	0	0	0	15447	72	3	5	229	5	SYDE1	19	15220001	Missense_Mutation	SNP	A	TCGA-MH-A561-01A-11D-A26P-10	2717840	15220001	43908982	88	13498											
PDCD5	9141	hgsc.bcm.edu	37	chr19	33077794	33077794	+	Frame_Shift_Del	DEL	A	A	-																															aaggtttaatagaaatccttAaaaaagtaagccaacaaaca																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr19:33077794delA	ENST00000590247.2	+	5	483	c.289delA	c.(289-291)aaafs	p.K98fs	PDCD5_ENST00000379316.3_Intron|PDCD5_ENST00000592786.1_Stop_Codon_Del|PDCD5_ENST00000419343.3_3'UTR|PDCD5_ENST00000586035.1_Frame_Shift_Del_p.K60fs	NM_004708.3	NP_004699.1	O14737	PDCD5_HUMAN	programmed cell death 5	98					apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|large_intestine(2)|lung(1)|ovary(1)	5	Esophageal squamous(110;0.137)					AGAAATCCTTAAAAAAGTAAG	0.323																																					p.L96fs		Atlas-Indel,Pindel	.											.	PDCD5	18	.	0			c.288delT						PASS	.						81	87	85					19																	33077794		2203	4300	6503	SO:0001589	frameshift_variant	9141	exon5			.	AF014955	CCDS12423.1	19q13.11	2012-10-15			ENSG00000105185	ENSG00000105185			8764	protein-coding gene	gene with protein product	"TFAR19 novel apoptosis-related", "TF1 cell apoptosis-related gene 19"	604583				9920759	Standard	NM_004708		Approved	TFAR19, MGC9294	uc002ntm.3	O14737	OTTHUMG00000180224	ENST00000590247.2:c.289delA	chr19.hg19:g.33077794delA	ENSP00000466214:p.Lys98fs	144.0	0.0	0		124.0	43.0	0.346774	NM_004708	B4DE64|Q53YC9|Q6IB70	Frame_Shift_Del	DEL	ENST00000590247.2	hg19	CCDS12423.1																																																																																			.	.	.	none		0.323	PDCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450320.2	NM_004708		-	33077794	A	-	33077794	7	5	222	1	0	1	0	1	0	0	0	0	11629	363	13	0	307	0	PDCD5	19	33077794	Frame_Shift_Del	DEL	A	TCGA-MH-A561-01A-11D-A26P-10	17857793	33077794	26051189	89	13499											
ZNF792	126375	hgsc.bcm.edu	37	chr19	35450211	35450211	+	Frame_Shift_Del	DEL	T	T	-																															ttctgatagggttgtgtacgTtctgctgcacctgtttccgg																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr19:35450211delT	ENST00000404801.1	-	4	934	c.548delA	c.(547-549)aacfs	p.N183fs	ZNF792_ENST00000605484.1_Frame_Shift_Del_p.N116fs	NM_175872.4	NP_787068.3	Q3KQV3	ZN792_HUMAN	zinc finger protein 792	183					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(4)|kidney(1)|large_intestine(1)|lung(5)	12	all_lung(56;4.18e-08)|Lung NSC(56;6.62e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			GTTGTGTACGTTCTGCTGCAC	0.542																																					p.N183fs	GBM(1;7 183 21053 22581 22847)	Atlas-Indel,Pindel	.											.	ZNF792	46	.	0			c.549delC						PASS	.						256	248	251					19																	35450211		2203	4300	6503	SO:0001589	frameshift_variant	126375	exon4			.	AK095770	CCDS12440.2	19q13.11	2013-01-08			ENSG00000180884	ENSG00000180884		"Zinc fingers, C2H2-type", "-"	24751	protein-coding gene	gene with protein product						8889548	Standard	NM_175872		Approved	FLJ38451	uc002nxh.1	Q3KQV3	OTTHUMG00000150339	ENST00000404801.1:c.548delA	chr19.hg19:g.35450211delT	ENSP00000385099:p.Asn183fs	348.0	0.0	0		273.0	101.0	0.369963	NM_175872	B4E333|Q495L1|Q495L3|Q8N932	Frame_Shift_Del	DEL	ENST00000404801.1	hg19	CCDS12440.2																																																																																			.	.	.	none		0.542	ZNF792-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317673.1	NM_175872		-	35450211	T	-	35450211	7	5	222	1	0	1	0	1	0	0	0	0	18176	1725	60	0	1354	0	ZNF792	19	35450211	Frame_Shift_Del	DEL	T	TCGA-MH-A561-01A-11D-A26P-10	2372417	35450211	23678772	90	13500											
ZNF256	10172	hgsc.bcm.edu	37	chr19	58452565	58452565	+	Frame_Shift_Del	DEL	A	A	-																															tctccggtgtgacttctcctAtgtctaatgaggctggagct																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr19:58452565delA	ENST00000282308.3	-	3	1807	c.1611delT	c.(1609-1611)catfs	p.H537fs	ZNF256_ENST00000598928.1_3'UTR	NM_005773.2	NP_005764.2	Q9Y2P7	ZN256_HUMAN	zinc finger protein 256	537					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0155)		GACTTCTCCTATGTCTAATGA	0.468																																					p.R538fs	NSCLC(55;1313 1552 8040 11996)	Pindel	.											.	ZNF256	117	.	0			c.1612delA						PASS	.						66	58	61					19																	58452565		2203	4300	6503	SO:0001589	frameshift_variant	10172	exon3			.	AF067165	CCDS12966.1	19q13	2013-01-08				ENSG00000152454		"Zinc fingers, C2H2-type", "-"	13049	protein-coding gene	gene with protein product		606956					Standard	NM_005773		Approved	BMZF-3	uc002qqu.3	Q9Y2P7		ENST00000282308.3:c.1611delT	chr19.hg19:g.58452565delA	ENSP00000282308:p.His537fs	129.0	0.0	.		98.0	19.0	0.194	NM_005773	B2RA92|Q53Y85|Q9BV71	Frame_Shift_Del	DEL	ENST00000282308.3	hg19	CCDS12966.1																																																																																			.	.	.	none		0.468	ZNF256-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466702.1			-	58452565	A	-	58452565	7	5	222	1	0	1	0	1	0	0	0	0	17811	446	16	0	276	0	ZNF256	19	58452565	Frame_Shift_Del	DEL	A	TCGA-MH-A561-01A-11D-A26P-10	23002354	58452565	676418	91	13501											
PLTP	5360	hgsc.bcm.edu	37	chr20	44539886	44539886	+	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	agaaagcgcagcccctcctgCttcactgaagcagcagagaa	13	5	10	13	1	1	3	1	1	0	2	2	4	2	3	3	0	5	4	3	0	3	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr20:44539886C>T	ENST00000477313.1	-	2	699	c.105G>A	c.(103-105)aaG>aaA	p.K35K	PLTP_ENST00000372420.1_5'Flank|PLTP_ENST00000354050.4_Silent_p.K35K|PLTP_ENST00000542937.1_Silent_p.K55K|PLTP_ENST00000372431.3_Silent_p.K35K|PLTP_ENST00000420868.2_Silent_p.K35K			P55058	PLTP_HUMAN	phospholipid transfer protein	35					lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|sperm motility (GO:0030317)|vitamin E biosynthetic process (GO:0010189)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)			endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)	21		Myeloproliferative disorder(115;0.0122)				GCCCCTCCTGCTTCACTGAAG	0.602																																					p.K35K		Atlas-SNP	.											.	PLTP	49	.	0			c.G105A						PASS	.						70	71	71					20																	44539886		2203	4300	6503	SO:0001819	synonymous_variant	5360	exon3			CTCCTGCTTCACT	L26232	CCDS13386.1, CCDS13387.1, CCDS56196.1, CCDS56197.1	20q13.12	2011-08-16			ENSG00000100979	ENSG00000100979		"BPI fold containing"	9093	protein-coding gene	gene with protein product	"BPI fold containing family E"	172425					Standard	NM_006227		Approved	BPIFE	uc002xqn.2	P55058	OTTHUMG00000033047	ENST00000477313.1:c.105G>A	chr20.hg19:g.44539886C>T		124.0	0.0	.		91.0	32.0	.	NM_182676	A8K006|B4DDD5|B4DRB4|E1P5N8|E7EV16|Q8WTT1|Q9BR07|Q9BSH8	Silent	SNP	ENST00000477313.1	hg19	CCDS13386.1																																																																																			.	.	.	none		0.602	PLTP-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354633.1	NM_006227		T	44539886	C	T	44539886	2	4	222	1	0	0	0	0	0	0	0	1	12121	796	28	2		2	PLTP	20	44539886	Silent	SNP	C	TCGA-MH-A561-01A-11D-A26P-10		44539886	18485634	92	13502											
ZNF831	128611	hgsc.bcm.edu	37	chr20	57782069	57782069	+	Frame_Shift_Del	DEL	A	A	-																															ctcccgcacttgagggactgAagccatgcaggacccctggg																										TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr20:57782069delA	ENST00000371030.2	+	3	3985	c.3985delA	c.(3985-3987)aagfs	p.K1329fs		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1329							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)					TGAGGGACTGAAGCCATGCAG	0.577																																					p.L1328fs		Atlas-Indel,Pindel	.											.	ZNF831	287	.	0			c.3984delG						PASS	.						68	73	71					20																	57782069		1968	4144	6112	SO:0001589	frameshift_variant	128611	exon3			.	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.3985delA	chr20.hg19:g.57782069delA	ENSP00000360069:p.Lys1329fs	108.0	0.0	0		104.0	43.0	0.413462	NM_178457	Q5TDR4|Q8TCP0	Frame_Shift_Del	DEL	ENST00000371030.2	hg19	CCDS42894.1																																																																																			.	.	.	none		0.577	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		-	57782069	A	-	57782069	7	5	222	1	0	1	0	1	0	0	0	0	18197	247	9	0	3995	0	ZNF831	20	57782069	Frame_Shift_Del	DEL	A	TCGA-MH-A561-01A-11D-A26P-10	13242183	57782069	5243451	93	13503											
SAMSN1	64092	hgsc.bcm.edu	37	chr21	15889252	15889252	+	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	ttgatgtactttttacccacTtttttcttcattgtccatga	7	21	4	9	0	2	2	1	2	1	0	3	2	3	2	2	0	2	1	2	0	2	10			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr21:15889252T>A	ENST00000400566.1	-	3	321	c.240A>T	c.(238-240)aaA>aaT	p.K80N	SAMSN1_ENST00000285670.2_Missense_Mutation_p.K148N|SAMSN1_ENST00000400564.1_Intron	NM_022136.4	NP_071419.3	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization signals 1	80					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)		TTTTACCCACTTTTTTCTTCA	0.328																																					p.K148N		Atlas-SNP	.											.	SAMSN1	112	.	0			c.A444T						PASS	.						124	109	114					21																	15889252		1797	4068	5865	SO:0001583	missense	64092	exon4			ACCCACTTTTTTC	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.240A>T	chr21.hg19:g.15889252T>A	ENSP00000383411:p.Lys80Asn	47.0	0.0	.		51.0	21.0	.	NM_001256370	B3KWJ3|F8WAA1|Q8NFF7|Q9C041	Missense_Mutation	SNP	ENST00000400566.1	hg19	CCDS42906.1	.	.	.	.	.	.	.	.	.	.	T	14.39	2.520541	0.44866	.	.	ENSG00000155307	ENST00000285670;ENST00000400566	T;T	0.57752	0.38;0.38	5.35	5.35	0.76521	.	0.100854	0.64402	D	0.000003	T	0.66076	0.2753	M	0.83953	2.67	0.43750	D	0.996253	D;D	0.56746	0.977;0.962	P;P	0.55923	0.787;0.688	T	0.71500	-0.4574	10	0.87932	D	0	-16.1663	7.6865	0.28544	0.0:0.1638:0.0:0.8362	.	148;80	F8WAA1;Q9NSI8	.;SAMN1_HUMAN	N	148;80	ENSP00000285670:K148N;ENSP00000383411:K80N	ENSP00000285670:K148N	K	-	3	2	SAMSN1	14811123	1.000000	0.71417	0.880000	0.34516	0.214000	0.24535	2.251000	0.43187	2.033000	0.60031	0.533000	0.62120	AAA	.	.	.	none		0.328	SAMSN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157914.1			A	15889252	T	A	15889252	3	1	222	1	0	0	0	0	1	0	0	0	13843	1606	56	5	905	5	SAMSN1	21	15889252	Missense_Mutation	SNP	T	TCGA-MH-A561-01A-11D-A26P-10		15889252	32240643	94	13504											
TRPM2	7226	hgsc.bcm.edu	37	chr21	45825794	45825794	+	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	tgcccggcggccaggctcatCccggcgacgctgtaccccgg	4	5	14	18	6	1	0	1	0	0	0	2	1	2	0	5	5	2	3	5	5	1	1			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr21:45825794C>T	ENST00000397928.1	+	18	3109	c.2664C>T	c.(2662-2664)atC>atT	p.I888I	TRPM2_ENST00000300482.5_Silent_p.I888I|TRPM2_ENST00000300481.9_Silent_p.I868I|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000397932.2_Silent_p.I888I	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	888					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						CCAGGCTCATCCCGGCGACGC	0.642																																					p.I888I		Atlas-SNP	.											.	TRPM2	196	.	0			c.C2664T						PASS	.						67	71	70					21																	45825794		2203	4297	6500	SO:0001819	synonymous_variant	7226	exon18			GCTCATCCCGGCG	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.2664C>T	chr21.hg19:g.45825794C>T		18.0	0.0	.		19.0	10.0	.	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Silent	SNP	ENST00000397928.1	hg19	CCDS13710.1																																																																																			.	.	.	none		0.642	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307		T	45825794	C	T	45825794	2	4	222	1	0	0	0	0	0	0	0	1	16598	845	30	2		2	TRPM2	21	45825794	Silent	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	29936542	45825794	2304101	95	13505											
ADORA2A	135	hgsc.bcm.edu	37	chr22	24836558	24836558	+	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	ctcttctccccaggtacaatGgcttggtgaccggcacgagg	7	9	12	13	2	2	1	0	1	2	0	3	2	2	1	3	5	1	3	3	5	2	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chr22:24836558G>T	ENST00000337539.7	+	3	799	c.340G>T	c.(340-342)Ggc>Tgc	p.G114C	ADORA2A-AS1_ENST00000427813.2_RNA|SPECC1L-ADORA2A_ENST00000358654.2_3'UTR|ADORA2A-AS1_ENST00000543438.1_RNA|ADORA2A-AS1_ENST00000326341.4_RNA|ADORA2A_ENST00000496497.1_3'UTR	NM_000675.4|NM_001278497.1|NM_001278498.1|NM_001278499.1|NM_001278500.1	NP_000666.2|NP_001265426.1|NP_001265427.1|NP_001265428.1|NP_001265429.1	P29274	AA2AR_HUMAN	adenosine A2a receptor	114					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|apoptotic process (GO:0006915)|blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cAMP biosynthetic process (GO:0006171)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|central nervous system development (GO:0007417)|inflammatory response (GO:0006954)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phagocytosis (GO:0006909)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|sensory perception (GO:0007600)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|G-protein coupled adenosine receptor activity (GO:0001609)|identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|skin(1)	21	Colorectal(2;0.196)				Adenosine(DB00640)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Mefloquine(DB00358)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Regadenoson(DB06213)|Theobromine(DB01412)|Theophylline(DB00277)	CAGGTACAATGGCTTGGTGAC	0.567																																					p.G114C		Atlas-SNP	.											.	ADORA2A	44	.	0			c.G340T						PASS	.						107	101	103					22																	24836558		2203	4300	6503	SO:0001583	missense	135	exon3			TACAATGGCTTGG	X68486	CCDS13826.1	22q11.23	2012-08-08			ENSG00000128271	ENSG00000128271		"GPCR / Class A : Adenosine receptors"	263	protein-coding gene	gene with protein product		102776		ADORA2		1662665, 2541503	Standard	NM_001278497		Approved	RDC8	uc002zzy.4	P29274	OTTHUMG00000150761	ENST00000337539.7:c.340G>T	chr22.hg19:g.24836558G>T	ENSP00000336630:p.Gly114Cys	155.0	0.0	.		129.0	50.0	.	NM_000675	B2R7E0	Missense_Mutation	SNP	ENST00000337539.7	hg19	CCDS13826.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.71|15.71	2.914051|2.914051	0.52546|0.52546	.|.	.|.	ENSG00000128271|ENSG00000258555	ENST00000444262;ENST00000541988;ENST00000337539;ENST00000417596|ENST00000493440	T;T|.	0.20332|.	2.08;2.08|.	4.97|4.97	3.95|3.95	0.45737|0.45737	GPCR, rhodopsin-like superfamily (1);|.	0.205313|.	0.49305|.	D|.	0.000152|.	T|T	0.56217|0.56217	0.1970|0.1970	L|L	0.45470|0.45470	1.425|1.425	0.43814|0.43814	D|D	0.996375|0.996375	D|.	0.65815|.	0.995|.	P|.	0.62014|.	0.897|.	T|T	0.51872|0.51872	-0.8650|-0.8650	10|5	0.59425|.	D|.	0.04|.	-27.3119|-27.3119	9.0177|9.0177	0.36179|0.36179	0.1684:0.0:0.8316:0.0|0.1684:0.0:0.8316:0.0	.|.	114|.	P29274|.	AA2AR_HUMAN|.	C|I	114|46	ENSP00000414802:G114C;ENSP00000336630:G114C|.	ENSP00000336630:G114C|.	G|M	+|+	1|3	0|0	ADORA2A|KB-1896H10.1	23166558|23166558	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.973000|0.973000	0.67179|0.67179	3.477000|3.477000	0.53151|0.53151	1.213000|1.213000	0.43380|0.43380	0.563000|0.563000	0.77884|0.77884	GGC|ATG	.	.	.	none		0.567	ADORA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319971.2	NM_000675		T	24836558	G	T	24836558	3	4	222	1	0	0	0	0	1	0	0	0	327	1348	47	4	346	4	ADORA2A	22	24836558	Missense_Mutation	SNP	G	TCGA-MH-A561-01A-11D-A26P-10		24836558	26468008	96	13506											
SMC1A	8243	hgsc.bcm.edu	37	chrX	53440302	53440302	+	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	tttcgcttgtcatactcctgCgccagctccccagaacgact	7	11	7	16	3	1	1	1	0	0	1	4	2	3	1	4	0	4	2	4	0	2	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chrX:53440302C>G	ENST00000322213.4	-	4	622	c.495G>C	c.(493-495)gcG>gcC	p.A165A	SMC1A_ENST00000375340.6_Intron	NM_006306.2	NP_006297.2	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	165					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)	p.A165A(1)		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						CATACTCCTGCGCCAGCTCCC	0.463																																					p.A165A		Atlas-SNP	.											.	SMC1A	112	.	1	Substitution - coding silent(1)	lung(1)	c.G495C						PASS	.						138	124	129					X																	53440302		2203	4300	6503	SO:0001819	synonymous_variant	8243	exon4			CTCCTGCGCCAGC	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.495G>C	chrX.hg19:g.53440302C>G		102.0	0.0	.		50.0	40.0	.	NM_006306	O14995|Q16351|Q2M228	Silent	SNP	ENST00000322213.4	hg19	CCDS14352.1	.	.	.	.	.	.	.	.	.	.	C	5.699	0.313435	0.10789	.	.	ENSG00000072501	ENST00000428014	.	.	.	4.63	0.543	0.17179	.	.	.	.	.	T	0.41971	0.1182	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.20773	-1.0265	4	.	.	.	.	1.4228	0.02316	0.1701:0.1318:0.2791:0.419	.	.	.	.	P	170	.	.	R	-	2	0	SMC1A	53457027	0.002000	0.14202	0.996000	0.52242	0.942000	0.58702	-1.093000	0.03362	-0.226000	0.09899	-1.768000	0.00664	CGC	.	.	.	none		0.463	SMC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056756.2	NM_006306		G	53440302	C	G	53440302	2	3	222	1	0	0	0	0	0	0	0	1	14794	755	27	4		4	SMC1A	23	53440302	Silent	SNP	C	TCGA-MH-A561-01A-11D-A26P-10		53440302	101830258	97	13507											
GLRA4	441509	hgsc.bcm.edu	37	chrX	102973934	102973934	+	Intron	SNP	T	T	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	ggagggcacattgggatgaaTgggaaatggggtactctatg	11	9	17	4	0	1	1	0	1	1	0	1	4	1	4	0	6	1	2	0	6	4	3			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chrX:102973934T>A	ENST00000372617.4	-	7	1354				GLRA4_ENST00000469567.1_5'Flank	NM_001024452.2	NP_001019623.2	Q5JXX5	GLRA4_HUMAN	glycine receptor, alpha 4							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						TTGGGATGAATGGGAAATGGG	0.522																																					p.P328P		Atlas-SNP	.											.	GLRA4	86	.	0			c.A984T						PASS	.						30	32	31					X																	102973934		2194	4293	6487	SO:0001627	intron_variant	441509	exon7			GATGAATGGGAAA	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.933+50A>T	chrX.hg19:g.102973934T>A		100.0	0.0	.		86.0	22.0	.	NM_001172285		Silent	SNP	ENST00000372617.4	hg19	CCDS43980.2																																																																																			.	.	.	none		0.522	GLRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057742.2	NM_001024452		A	102973934	T	A	102973934	1	1	222	0	1	0	0	0	0	0	0	0	6464	1451	51	5		5	GLRA4	23	102973934	Intron	SNP	T	TCGA-MH-A561-01A-11D-A26P-10	49533632	102973934	52296626	98	13508											
UPF3B	65109	hgsc.bcm.edu	37	chrX	118985467	118985467	+	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	ccaggactcacctttattgtCaaggaatacataaccatcaa	15	10	5	11	0	3	0	3	0	0	0	3	2	3	2	3	2	2	0	3	2	6	5			TCGA-MH-A561-01A-11D-A26P-10	TCGA-MH-A561-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2e8ad1cd-d5d5-4bb4-8bbd-e9bef45088da	ebf9ee83-790d-43a8-ae04-e32e2f61bfa6	g.chrX:118985467C>G	ENST00000276201.2	-	3	430	c.361G>C	c.(361-363)Gac>Cac	p.D121H	UPF3B_ENST00000345865.2_Missense_Mutation_p.D121H	NM_080632.2	NP_542199.1	Q9BZI7	REN3B_HUMAN	UPF3 regulator of nonsense transcripts homolog B (yeast)	121	Necessary for interaction with UPF2.|Sufficient for association with EJC core.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|prostate(1)	30						CCTTTATTGTCAAGGAATACA	0.363																																					p.D121H		Atlas-SNP	.											.	UPF3B	74	.	0			c.G361C						PASS	.						104	86	92					X																	118985467		2203	4300	6503	SO:0001583	missense	65109	exon3			TATTGTCAAGGAA	AF318576	CCDS14587.1, CCDS14588.1	Xq25-q26	2014-01-31			ENSG00000125351	ENSG00000125351			20439	protein-coding gene	gene with protein product		300298	"mental retardation, X-linked 62"	MRX62		11113196, 11163187, 19238151	Standard	NM_023010		Approved	RENT3B, UPF3X, HUPF3B	uc004erz.2	Q9BZI7	OTTHUMG00000022282	ENST00000276201.2:c.361G>C	chrX.hg19:g.118985467C>G	ENSP00000276201:p.Asp121His	214.0	1.0	.		159.0	121.0	.	NM_023010	D3DWI3|D3DWI4|Q0VAK8|Q9H1J0	Missense_Mutation	SNP	ENST00000276201.2	hg19	CCDS14588.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.031576	0.75504	.	.	ENSG00000125351	ENST00000276201;ENST00000345865;ENST00000439808	T;T	0.74526	-0.85;-0.85	5.1	5.1	0.69264	Regulator of nonsense-mediated decay, UPF3 (1);Nucleotide-binding, alpha-beta plait (1);	0.000000	0.85682	D	0.000000	D	0.90246	0.6950	H	0.95079	3.62	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.93290	0.6667	10	0.87932	D	0	.	16.142	0.81534	0.0:1.0:0.0:0.0	.	121;121	Q9BZI7-2;Q9BZI7	.;REN3B_HUMAN	H	121	ENSP00000276201:D121H;ENSP00000245418:D121H	ENSP00000276201:D121H	D	-	1	0	UPF3B	118869495	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.226000	0.78060	2.111000	0.64477	0.600000	0.82982	GAC	.	.	.	none		0.363	UPF3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058068.1			G	118985467	C	G	118985467	3	3	222	1	0	0	0	0	1	0	0	0	17018	826	29	4	1126	4	UPF3B	23	118985467	Missense_Mutation	SNP	C	TCGA-MH-A561-01A-11D-A26P-10	16011533	118985467	36285093	99	13509											
ZMPSTE24	10269	hgsc.bcm.edu	37	chr1	40724033	40724033	+	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	0	0	0	0	0	0	0	0	0	ctgctcttttcctggacagtGtatctttgggagaccttcct	5	16	9	11	0	2	1	0	0	2	1	4	3	4	2	3	2	1	2	3	2	1	5			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr1:40724033G>C	ENST00000372759.3	+	1	255	c.90G>C	c.(88-90)gtG>gtC	p.V30V	ZMPSTE24_ENST00000479131.1_3'UTR|RP1-39G22.7_ENST00000567508.1_RNA	NM_005857.4	NP_005848.2	O75844	FACE1_HUMAN	zinc metallopeptidase STE24	30					CAAX-box protein processing (GO:0071586)|nuclear envelope organization (GO:0006998)|prenylated protein catabolic process (GO:0030327)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metalloexopeptidase activity (GO:0008235)			endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	16	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;6.3e-18)			CCTGGACAGTGTATCTTTGGG	0.622																																					p.V30V		Atlas-SNP	.											.	ZMPSTE24	50	.	0			c.G90C						PASS	.						121	104	109					1																	40724033		2203	4300	6503	SO:0001819	synonymous_variant	10269	exon1			GACAGTGTATCTT	Y13834	CCDS449.1	1p34	2014-09-17	2012-12-10		ENSG00000084073	ENSG00000084073	3.4.24.84		12877	protein-coding gene	gene with protein product	"Hutchinson-Gilford progeria syndrome", "CAAX prenyl protease 1 homolog"	606480	"zinc metalloproteinase (STE24 homolog, yeast)", "zinc metallopeptidase (STE24 homolog, yeast)", "zinc metallopeptidase STE24 homolog (S. cerevisiae)"			10373325, 9700155, 16671095	Standard	NM_005857		Approved	FACE-1, Ste24p, STE24, HGPS, PRO1	uc001cfg.4	O75844	OTTHUMG00000005762	ENST00000372759.3:c.90G>C	chr1.hg19:g.40724033G>C		83.0	0.0	.		99.0	32.0	.	NM_005857	B3KQI7|D3DPU7|Q8NDZ8|Q9UBQ2	Silent	SNP	ENST00000372759.3	hg19	CCDS449.1																																																																																			.	.	.	none		0.622	ZMPSTE24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015766.1			C	40724033	G	C	40724033	2	2	223	1	0	0	0	0	0	0	0	1	17710	1364	48	4		4	ZMPSTE24	1	40724033	Silent	SNP	G	TCGA-MH-A562-01A-11D-A26P-10		40724033	208526588	1	13510											
GSTM4	2948	hgsc.bcm.edu	37	chr1	110201466	110201466	+	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	agccagaatacttggaggaaCttcctacaatgatgcagcac	14	8	9	10	0	0	2	0	1	0	1	1	4	1	4	2	2	6	2	2	2	5	4			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr1:110201466C>A	ENST00000369836.4	+	6	700	c.391C>A	c.(391-393)Ctt>Att	p.L131I	GSTM4_ENST00000369833.1_Missense_Mutation_p.L90I|GSTM4_ENST00000326729.5_Missense_Mutation_p.L131I|GSTM4_ENST00000495742.1_3'UTR|GSTM4_ENST00000336075.5_Missense_Mutation_p.L70I	NM_000850.4	NP_000841.1	Q03013	GSTM4_HUMAN	glutathione S-transferase mu 4	131	GST C-terminal.				glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic catabolic process (GO:0042178)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	enzyme binding (GO:0019899)|glutathione binding (GO:0043295)|glutathione transferase activity (GO:0004364)|protein homodimerization activity (GO:0042803)			endometrium(3)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	12		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		all cancers(265;0.0123)|Colorectal(144;0.0129)|Epithelial(280;0.0147)|Lung(183;0.0422)|COAD - Colon adenocarcinoma(174;0.0471)|LUSC - Lung squamous cell carcinoma(189;0.227)	Glutathione(DB00143)	CTTGGAGGAACTTCCTACAAT	0.517																																					p.L131I		Atlas-SNP	.											.	GSTM4	38	.	0			c.C391A						PASS	.						164	158	160					1																	110201466		2203	4300	6503	SO:0001583	missense	2948	exon6			GAGGAACTTCCTA	M96234	CCDS806.1, CCDS807.1	1p13.3	2012-06-22	2008-11-26		ENSG00000168765	ENSG00000168765	2.5.1.18	"Glutathione S-transferases / Soluble"	4636	protein-coding gene	gene with protein product		138333	"glutathione S-transferase M4"			8276420	Standard	NM_000850		Approved		uc001dyf.3	Q03013	OTTHUMG00000011642	ENST00000369836.4:c.391C>A	chr1.hg19:g.110201466C>A	ENSP00000358851:p.Leu131Ile	327.0	0.0	.		303.0	97.0	.	NM_000850	A8K765|Q05465|Q32NC1|Q4JNT8|Q6FH87	Missense_Mutation	SNP	ENST00000369836.4	hg19	CCDS807.1	.	.	.	.	.	.	.	.	.	.	C	15.16	2.750271	0.49257	.	.	ENSG00000168765	ENST00000369836;ENST00000336075;ENST00000326729;ENST00000369833	T;T;T;T	0.04603	3.59;4.46;3.59;3.59	4.0	-0.554	0.11811	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.201178	0.32473	N	0.006046	T	0.01940	0.0061	L	0.41961	1.31	0.38907	D	0.957449	B;B;B	0.17852	0.024;0.007;0.0	B;B;B	0.23716	0.035;0.048;0.009	T	0.40346	-0.9568	10	0.44086	T	0.13	-16.1138	11.7266	0.51712	0.6127:0.3873:0.0:0.0	.	70;131;131	Q4JNT8;Q03013-2;Q03013	.;.;GSTM4_HUMAN	I	131;70;131;90	ENSP00000358851:L131I;ENSP00000336744:L70I;ENSP00000316471:L131I;ENSP00000358848:L90I	ENSP00000316471:L131I	L	+	1	0	GSTM4	110002989	0.010000	0.17322	0.005000	0.12908	0.847000	0.48162	0.193000	0.17116	-0.165000	0.10908	-0.901000	0.02856	CTT	.	.	.	none		0.517	GSTM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032187.1	NM_000850		A	110201466	C	A	110201466	3	1	223	1	0	0	0	0	1	0	0	0	6847	565	20	4	413	4	GSTM4	1	110201466	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	69477433	110201466	139049155	2	13511											
IGSF3	3321	hgsc.bcm.edu	37	chr1	117120184	117120184	+	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	tgatggactggagggtgggaCctgaaaagaatcatgagaga	14	7	16	4	0	1	5	1	3	0	2	1	9	1	8	1	4	0	0	1	4	3	0			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr1:117120184C>G	ENST00000369486.3	-	11	4100	c.3335G>C	c.(3334-3336)aGt>aCt	p.S1112T	IGSF3_ENST00000318837.6_Splice_Site_p.S1132T|IGSF3_ENST00000369483.1_Splice_Site_p.S1132T	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	1112					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)		GAGGGTGGGACCTGAAAAGAA	0.493																																					p.S1132T		Atlas-SNP	.											.	IGSF3	294	.	0			c.G3395C						PASS	.						98	102	101					1																	117120184		2203	4300	6503	SO:0001630	splice_region_variant	3321	exon12			GTGGGACCTGAAA	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.3335-1G>C	chr1.hg19:g.117120184C>G		57.0	0.0	.		88.0	30.0	.	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	hg19	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	C	7.587	0.670001	0.14776	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.02890	4.12;4.13;4.13	4.88	4.88	0.63580	.	0.310318	0.31199	N	0.008076	T	0.00695	0.0023	N	0.08118	0	0.32760	N	0.505191	B;B	0.24368	0.084;0.102	B;B	0.22386	0.028;0.039	T	0.52845	-0.8521	10	0.31617	T	0.26	.	9.0162	0.36170	0.0:0.9027:0.0:0.0973	.	1112;1132	O75054;A6NJZ6	IGSF3_HUMAN;.	T	1112;1132;1132	ENSP00000358498:S1112T;ENSP00000358495:S1132T;ENSP00000321184:S1132T	ENSP00000321184:S1132T	S	-	2	0	IGSF3	116921707	0.997000	0.39634	1.000000	0.80357	0.699000	0.40488	3.210000	0.51129	2.536000	0.85505	0.655000	0.94253	AGT	.	.	.	none		0.493	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542	Missense_Mutation	G	117120184	C	G	117120184	5	3	223	1	0	0	0	0	0	0	1	0	7608	521	18	4	253	4	IGSF3	1	117120184	Splice_Site	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	6918718	117120184	132130437	3	13512											
DENND4B	9909	hgsc.bcm.edu	37	chr1	153907305	153907305	+	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	ctgctgctgctgctgctgctGttgctgctgctgctgctgtt	0	16	13	12	0	0	0	0	0	0	0	0	0	0	0	0	0	11	13	0	0	0	2	rs35902206|rs557071025	byFrequency	TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr1:153907305G>C	ENST00000361217.4	-	18	3122	c.2704C>G	c.(2704-2706)Cag>Gag	p.Q902E	DENND4B_ENST00000474386.1_5'Flank	NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	902	Gln-rich.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			tgctgctgctgttgctgctgc	0.647																																					p.Q902E		Atlas-SNP	.											DENND4B_ENST00000361217,bladder,carcinoma,+2,2	DENND4B	210	.	0			c.C2704G						PASS	.						31	40	37					1																	153907305		2185	4281	6466	SO:0001583	missense	9909	exon18			GCTGCTGTTGCTG	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"DENN/MADD domain containing"	29044	protein-coding gene	gene with protein product			"KIAA0476"	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.2704C>G	chr1.hg19:g.153907305G>C	ENSP00000354597:p.Gln902Glu	49.0	1.0	.		102.0	24.0	.	NM_014856	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	hg19	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	G	0.055	-1.239891	0.01493	.	.	ENSG00000198837	ENST00000361217;ENST00000368646	T;T	0.06142	3.34;3.34	2.98	2.04	0.26737	.	0.726574	0.13139	N	0.410851	T	0.00845	0.0028	N	0.08118	0	0.22656	N	0.998883	B	0.12630	0.006	B	0.10450	0.005	T	0.47598	-0.9105	10	0.11794	T	0.64	-1.3144	7.3114	0.26477	0.0:0.0:0.7377:0.2623	.	902	O75064	DEN4B_HUMAN	E	902;913	ENSP00000354597:Q902E;ENSP00000357635:Q913E	ENSP00000354597:Q902E	Q	-	1	0	DENND4B	152173929	0.997000	0.39634	1.000000	0.80357	0.860000	0.49131	0.803000	0.27083	0.811000	0.34303	0.442000	0.29010	CAG	.	.	.	none		0.647	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806		C	153907305	G	C	153907305	3	2	223	1	0	0	0	0	1	0	0	0	4436	1386	48	4	1830	4	DENND4B	1	153907305	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	36787121	153907305	95343316	4	13513											
INSRR	3645	hgsc.bcm.edu	37	chr1	156824054	156824054	+	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	gctgcagttctccagctgacGaagctctgccacctctgagc	7	9	10	15	1	3	2	0	2	3	0	4	3	3	2	3	0	5	5	3	0	1	1	rs140386495		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr1:156824054G>A	ENST00000368195.3	-	2	523	c.127C>T	c.(127-129)Cgt>Tgt	p.R43C	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	43					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)					TCCAGCTGACGAAGCTCTGCC	0.622																																					p.R43C		Atlas-SNP	.											.	INSRR	309	.	0			c.C127T						PASS	.	G	,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	37	39	39		,127	3.1	1	1	dbSNP_134	39	2,8598	2.2+/-6.3	0,2,4298	yes	intron,missense	INSRR,NTRK1	NM_001007792.1,NM_014215.2	,180	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	,probably-damaging	,43/1298	156824054	3,13003	2203	4300	6503	SO:0001583	missense	3645	exon2			GCTGACGAAGCTC	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.127C>T	chr1.hg19:g.156824054G>A	ENSP00000357178:p.Arg43Cys	57.0	0.0	.		59.0	14.0	.	NM_014215	O60724|Q5VZS3	Missense_Mutation	SNP	ENST00000368195.3	hg19	CCDS1160.1	.	.	.	.	.	.	.	.	.	.	G	15.00	2.703881	0.48412	2.27E-4	2.33E-4	ENSG00000027644	ENST00000368195	T	0.32272	1.46	5.06	3.13	0.36017	.	0.000000	0.43416	D	0.000563	T	0.19604	0.0471	.	.	.	0.48288	D	0.999626	D	0.67145	0.996	P	0.46885	0.53	T	0.03403	-1.1040	9	0.72032	D	0.01	.	7.1713	0.25721	0.0913:0.0:0.7361:0.1726	.	43	P14616	INSRR_HUMAN	C	43	ENSP00000357178:R43C	ENSP00000357178:R43C	R	-	1	0	INSRR	155090678	0.003000	0.15002	1.000000	0.80357	0.342000	0.28953	1.267000	0.33050	1.098000	0.41479	0.557000	0.71058	CGT	.	G|1.000;A|0.000	0.000	weak		0.622	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		A	156824054	G	A	156824054	3	1	223	1	0	0	0	0	1	0	0	0	7781	1058	37	1	3849	1	INSRR	1	156824054	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	2916749	156824054	92426567	5	13514											
KLHDC9	126823	hgsc.bcm.edu	37	chr1	161069269	161069269	+	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	tagctgaaccagaagtagctGggcattggagtcatgggaaa	13	8	14	6	0	1	2	1	1	0	1	1	4	1	4	1	3	3	4	1	3	5	3			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr1:161069269G>A	ENST00000368011.4	+	2	803	c.661G>A	c.(661-663)Ggg>Agg	p.G221R	PFDN2_ENST00000468311.1_5'Flank|KLHDC9_ENST00000392192.2_Missense_Mutation_p.G221R|KLHDC9_ENST00000490724.2_3'UTR	NM_152366.4	NP_689579.3	Q8NEP7	KLDC9_HUMAN	kelch domain containing 9	221										lung(5)|upper_aerodigestive_tract(1)	6	all_cancers(52;1.28e-19)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			AGAAGTAGCTGGGCATTGGAG	0.498																																					p.G221R		Atlas-SNP	.											.	KLHDC9	16	.	0			c.G661A						PASS	.						120	122	121					1																	161069269		2203	4300	6503	SO:0001583	missense	126823	exon2			GTAGCTGGGCATT	BC022077	CCDS30919.1, CCDS41425.1	1q23.3	2008-02-05			ENSG00000162755	ENSG00000162755			28489	protein-coding gene	gene with protein product	"kelch/ankyrin repeat containing cyclin A1 interacting protein"					15159402	Standard	NM_152366		Approved	KARCA1	uc001fxr.3	Q8NEP7	OTTHUMG00000031479	ENST00000368011.4:c.661G>A	chr1.hg19:g.161069269G>A	ENSP00000356990:p.Gly221Arg	193.0	0.0	.		230.0	70.0	.	NM_001007255	Q5SY56|Q6NXT9|Q6PKN4|Q8N5E1|Q8NA16	Missense_Mutation	SNP	ENST00000368011.4	hg19	CCDS30919.1	.	.	.	.	.	.	.	.	.	.	G	14.59	2.580835	0.46006	.	.	ENSG00000162755	ENST00000368011;ENST00000392192	T;T	0.59364	1.77;0.27	4.47	3.55	0.40652	Galactose oxidase/kelch, beta-propeller (1);	0.000000	0.64402	D	0.000018	T	0.64583	0.2611	M	0.72118	2.19	0.35694	D	0.815117	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.68500	-0.5392	10	0.46703	T	0.11	-6.0987	13.2992	0.60315	0.0878:0.0:0.9122:0.0	.	221;221	Q8NEP7-2;Q8NEP7	.;KLDC9_HUMAN	R	221	ENSP00000356990:G221R;ENSP00000376030:G221R	ENSP00000356990:G221R	G	+	1	0	KLHDC9	159335893	1.000000	0.71417	0.955000	0.39395	0.891000	0.51852	3.599000	0.54045	0.526000	0.28541	-0.797000	0.03246	GGG	.	.	.	none		0.498	KLHDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077092.1	NM_152366		A	161069269	G	A	161069269	3	1	223	1	0	0	0	0	1	0	0	0	8371	1348	47	2	667	2	KLHDC9	1	161069269	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	4245215	161069269	88181352	6	13515											
IARS2	55699	hgsc.bcm.edu	37	chr1	220311360	220311360	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aattggcccatccgtgctcaAtgctgccagagatgatatta	11	11	9	10	1	1	2	1	1	0	1	2	3	2	2	3	1	3	2	3	1	4	3			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr1:220311360A>G	ENST00000302637.5	+	17	2254	c.2150A>G	c.(2149-2151)aAt>aGt	p.N717S	snoU13_ENST00000459443.1_RNA|IARS2_ENST00000366922.1_Missense_Mutation_p.N645S	NM_018060.3	NP_060530.3	Q9NSE4	SYIM_HUMAN	isoleucyl-tRNA synthetase 2, mitochondrial	717					gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)			NS(1)|breast(1)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(7)|lung(17)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)	TCCGTGCTCAATGCTGCCAGA	0.408																																					p.N717S		Atlas-SNP	.											.	IARS2	106	.	0			c.A2150G						PASS	.						141	126	131					1																	220311360		2203	4300	6503	SO:0001583	missense	55699	exon17			TGCTCAATGCTGC	AK022665	CCDS1523.1	1q41	2011-07-01	2007-02-26		ENSG00000067704	ENSG00000067704	6.1.1.5	"Aminoacyl tRNA synthetases / Class I"	29685	protein-coding gene	gene with protein product	"isoleucine tRNA ligase 2, mitochondrial"	612801					Standard	NM_018060		Approved	FLJ10326	uc001hmc.3	Q9NSE4	OTTHUMG00000037287	ENST00000302637.5:c.2150A>G	chr1.hg19:g.220311360A>G	ENSP00000303279:p.Asn717Ser	141.0	0.0	.		142.0	11.0	.	NM_018060	B2RPG8|Q1M2P9|Q6PI85|Q7L439|Q86WU9|Q96D91|Q9H9Q8|Q9NW42	Missense_Mutation	SNP	ENST00000302637.5	hg19	CCDS1523.1	.	.	.	.	.	.	.	.	.	.	A	15.56	2.868965	0.51588	.	.	ENSG00000067704	ENST00000366922;ENST00000302637	T;T	0.41758	0.99;0.99	5.94	-2.49	0.06403	.	0.500458	0.25060	N	0.033452	T	0.22820	0.0551	N	0.26162	0.8	0.29693	N	0.840771	B	0.06786	0.001	B	0.08055	0.003	T	0.05289	-1.0894	10	0.54805	T	0.06	-2.622	5.3859	0.16218	0.4679:0.2548:0.2773:0.0	.	717	Q9NSE4	SYIM_HUMAN	S	645;717	ENSP00000355889:N645S;ENSP00000303279:N717S	ENSP00000303279:N717S	N	+	2	0	IARS2	218377983	0.015000	0.18098	0.161000	0.22692	0.442000	0.32017	0.217000	0.17603	-0.335000	0.08451	-0.385000	0.06624	AAT	.	.	.	none		0.408	IARS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018060		G	220311360	A	G	220311360	3	3	223	1	0	0	0	0	1	0	0	0	7481	101	4	3	2216	3	IARS2	1	220311360	Missense_Mutation	SNP	A	TCGA-MH-A562-01A-11D-A26P-10	59242091	220311360	28939261	7	13516											
URB2	9816	hgsc.bcm.edu	37	chr1	229771821	229771821	+	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	gctgctgaggcactgaggcaGcctgtgctggcctcgggccc	4	7	16	14	1	0	2	0	2	0	0	1	2	0	2	3	4	3	5	3	4	0	0			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr1:229771821G>A	ENST00000258243.2	+	4	1597	c.1461G>A	c.(1459-1461)caG>caA	p.Q487Q		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	487						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						CACTGAGGCAGCCTGTGCTGG	0.582																																					p.Q487Q		Atlas-SNP	.											.	URB2	152	.	0			c.G1461A						PASS	.						111	119	116					1																	229771821		2203	4300	6503	SO:0001819	synonymous_variant	9816	exon4			GAGGCAGCCTGTG	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.1461G>A	chr1.hg19:g.229771821G>A		114.0	0.0	.		117.0	55.0	.	NM_014777	Q5VYC9	Silent	SNP	ENST00000258243.2	hg19	CCDS31052.1																																																																																			.	.	.	none		0.582	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777		A	229771821	G	A	229771821	2	1	223	1	0	0	0	0	0	0	0	1	17037	962	34	2		2	URB2	1	229771821	Silent	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	9460461	229771821	19478800	8	13517											
HNRNPU	3192	hgsc.bcm.edu	37	chr1	245018785	245018785	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtagttccctctgtttgagtAactaccacggccaggaaaaa	12	10	9	10	1	1	1	0	1	1	0	2	2	2	2	3	2	2	4	3	2	5	5			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr1:245018785A>G	ENST00000283179.9	-	12	2456	c.2293T>C	c.(2293-2295)Tac>Cac	p.Y765H	HNRNPU-AS1_ENST00000475997.1_RNA|HNRNPU_ENST00000444376.2_Missense_Mutation_p.Y746H|HNRNPU-AS1_ENST00000489705.1_RNA			Q00839	HNRPU_HUMAN	heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A)	765	Gly-rich.				CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasmic ribonucleoprotein granule (GO:0036464)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20	all_cancers(71;6.97e-06)|all_epithelial(71;0.000104)|all_neural(11;0.0269)|Breast(184;0.0545)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0989)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.00868)			CTGTTTGAGTAACTACCACGG	0.512																																					p.Y765H	NSCLC(33;911 1010 3329 23631 49995)	Atlas-SNP	.											.	HNRNPU	64	.	0			c.T2293C						PASS	.						169	168	168					1																	245018785		2203	4300	6503	SO:0001583	missense	3192	exon12			TTGAGTAACTACC	X65488	CCDS31081.1, CCDS41479.1	1q44	2011-10-24		2007-08-16	ENSG00000153187	ENSG00000153187			5048	protein-coding gene	gene with protein product		602869		HNRPU		7509195, 8068679	Standard	NM_031844		Approved	SAF-A, hnRNPU	uc001iaz.1	Q00839	OTTHUMG00000040396	ENST00000283179.9:c.2293T>C	chr1.hg19:g.245018785A>G	ENSP00000283179:p.Tyr765His	138.0	0.0	.		119.0	45.0	.	NM_031844	O75507|Q8N174|Q96HY9|Q9BQ09	Missense_Mutation	SNP	ENST00000283179.9	hg19	CCDS41479.1	.	.	.	.	.	.	.	.	.	.	A	16.34	3.094744	0.56075	.	.	ENSG00000153187	ENST00000444376;ENST00000283179;ENST00000427948	T;T	0.47177	0.85;0.86	5.51	5.51	0.81932	.	0.337558	0.31936	N	0.006827	T	0.42177	0.1191	N	0.04508	-0.205	0.44289	D	0.997152	D;D;P	0.69078	0.997;0.995;0.919	P;P;P	0.62184	0.899;0.795;0.543	T	0.42732	-0.9434	10	0.15952	T	0.53	-5.3765	15.623	0.76824	1.0:0.0:0.0:0.0	.	746;765;489	Q00839-2;Q00839;Q5RI19	.;HNRPU_HUMAN;.	H	746;765;690	ENSP00000393151:Y746H;ENSP00000283179:Y765H	ENSP00000283179:Y765H	Y	-	1	0	HNRNPU	243085408	1.000000	0.71417	0.798000	0.32154	0.954000	0.61252	6.268000	0.72552	2.088000	0.63022	0.482000	0.46254	TAC	.	.	.	none		0.512	HNRNPU-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000097163.3	NM_031844		G	245018785	A	G	245018785	3	3	223	1	0	0	0	0	1	0	0	0	7280	362	13	3	196	3	HNRNPU	1	245018785	Missense_Mutation	SNP	A	TCGA-MH-A562-01A-11D-A26P-10	15246964	245018785	4231836	9	13518											
RAD51AP2	729475	hgsc.bcm.edu	37	chr2	17692220	17692220	+	Frame_Shift_Del	DEL	T	T	-																															aatgccatgtggaaagtgacTacctaaaaatataagacaat																										TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr2:17692220delT	ENST00000399080.2	-	3	3354	c.3331delA	c.(3331-3333)agtfs	p.S1111fs		NM_001099218.2	NP_001092688.1	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	1111	Interaction with RAD51.									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)					GGAAAGTGACTACCTAAAAAT	0.313																																					p.S1111fs		Atlas-Indel,Pindel	.											.	RAD51AP2	134	.	0			c.3332delG						PASS	.						82	72	75					2																	17692220		1815	4072	5887	SO:0001589	frameshift_variant	729475	exon3			.	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.3331delA	chr2.hg19:g.17692220delT	ENSP00000382030:p.Ser1111fs	87.0	0.0	0		105.0	17.0	0.161905	NM_001099218		Frame_Shift_Del	DEL	ENST00000399080.2	hg19	CCDS42656.1																																																																																			.	.	.	none		0.313	RAD51AP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323801.3	NM_001099218		-	17692220	T	-	17692220	7	5	223	1	0	1	0	1	0	0	0	0	13000	1522	53	0	152	0	RAD51AP2	2	17692220	Frame_Shift_Del	DEL	T	TCGA-MH-A562-01A-11D-A26P-10		17692220	225507153	10	13519											
OSR1	130497	hgsc.bcm.edu	37	chr2	19552164	19552164	+	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	gaagggcttctctttggagtGaatatatctgagggcagaaa	12	11	13	5	0	2	3	0	2	2	1	3	5	2	4	0	3	0	2	0	3	5	4			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr2:19552164G>A	ENST00000272223.2	-	3	1017	c.673C>T	c.(673-675)Cac>Tac	p.H225Y	OSR1_ENST00000536433.1_Missense_Mutation_p.H225Y	NM_145260.2	NP_660303.1	Q8TAX0	OSR1_HUMAN	odd-skipped related transciption factor 1	225					cell differentiation (GO:0030154)|cell proliferation involved in kidney development (GO:0072111)|cellular response to retinoic acid (GO:0071300)|chondrocyte differentiation (GO:0002062)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal joint development (GO:0072498)|embryonic skeletal joint morphogenesis (GO:0060272)|embryonic skeletal limb joint morphogenesis (GO:0036023)|gonad development (GO:0008406)|heart development (GO:0007507)|intermediate mesoderm development (GO:0048389)|mesangial cell development (GO:0072143)|mesonephric duct morphogenesis (GO:0072180)|mesonephros development (GO:0001823)|metanephric cap mesenchymal cell proliferation involved in metanephros development (GO:0090094)|metanephric epithelium development (GO:0072207)|metanephric glomerulus vasculature development (GO:0072239)|metanephric interstitial fibroblast development (GO:0072259)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchyme development (GO:0072075)|metanephric mesenchyme morphogenesis (GO:0072133)|metanephric nephron tubule development (GO:0072234)|metanephric smooth muscle tissue development (GO:0072208)|middle ear morphogenesis (GO:0042474)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of nephron tubule epithelial cell differentiation (GO:0072183)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis (GO:0042476)|palate development (GO:0060021)|pattern specification involved in metanephros development (GO:0072268)|positive regulation of bone mineralization (GO:0030501)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gastrulation (GO:2000543)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posterior mesonephric tubule development (GO:0072166)|pronephros development (GO:0048793)|renal vesicle progenitor cell differentiation (GO:0072184)|specification of anterior mesonephric tubule identity (GO:0072168)|specification of posterior mesonephric tubule identity (GO:0072169)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)|ureter urothelium development (GO:0072190)|ureteric bud development (GO:0001657)|urogenital system development (GO:0001655)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(1)|large_intestine(2)|lung(4)|ovary(1)	8	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	Acute lymphoblastic leukemia(84;0.221)				TCTTTGGAGTGAATATATCTG	0.493																																					p.H225Y		Atlas-SNP	.											.	OSR1	29	.	0			c.C673T						PASS	.						119	109	112					2																	19552164		2203	4300	6503	SO:0001583	missense	130497	exon3			TGGAGTGAATATA	BC025712	CCDS1694.1	2p24.1	2013-10-17	2013-10-17	2004-11-26	ENSG00000143867	ENSG00000143867		"Zinc fingers, C2H2-type"	8111	protein-coding gene	gene with protein product		608891	"odd-skipped (Drosophila) homolog", "odd-skipped related 1 (Drosophila)"	ODD		2120051, 12119563	Standard	XM_006711942		Approved		uc002rdc.3	Q8TAX0	OTTHUMG00000088793	ENST00000272223.2:c.673C>T	chr2.hg19:g.19552164G>A	ENSP00000272223:p.His225Tyr	107.0	0.0	.		101.0	9.0	.	NM_145260	B3KV97|D6W521	Missense_Mutation	SNP	ENST00000272223.2	hg19	CCDS1694.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.550306	0.86127	.	.	ENSG00000143867	ENST00000272223;ENST00000536433	D;D	0.88896	-2.44;-2.44	5.01	5.01	0.66863	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.049292	0.85682	D	0.000000	D	0.95245	0.8458	M	0.93283	3.4	0.58432	D	0.999996	P	0.38148	0.62	P	0.52758	0.708	D	0.95373	0.8466	9	.	.	.	-8.151	18.0945	0.89485	0.0:0.0:1.0:0.0	.	225	Q8TAX0	OSR1_HUMAN	Y	225	ENSP00000272223:H225Y;ENSP00000441801:H225Y	.	H	-	1	0	OSR1	19415645	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.595000	0.98260	2.606000	0.88127	0.561000	0.74099	CAC	.	.	.	none		0.493	OSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000201432.2	NM_145260		A	19552164	G	A	19552164	3	1	223	1	0	0	0	0	1	0	0	0	11300	1290	45	2	131	2	OSR1	2	19552164	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	1859944	19552164	223647209	11	13520											
MPHOSPH10	10199	hgsc.bcm.edu	37	chr2	71368372	71368378	+	Frame_Shift_Del	DEL	ATGTAGT	ATGTAGT	-																															tatgtttcaggcttgggatgAtgtagtacgtaaagaaaaac																										TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	ATGTAGT	ATGTAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr2:71368372_71368378delATGTAGT	ENST00000244230.2	+	7	1671_1677	c.1319_1325delATGTAGT	c.(1318-1326)gatgtagtafs	p.DVV440fs		NM_005791.2	NP_005782.1	O00566	MPP10_HUMAN	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	440					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						GCTTGGGATGATGTAGTACGTAAAGAA	0.324																																					p.440_442del		Atlas-Indel,Pindel	.											.	MPHOSPH10	81	.	0			c.1318_1324del						PASS	.																																			SO:0001589	frameshift_variant	10199	exon7			.	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.1319_1325delATGTAGT	chr2.hg19:g.71368372_71368378delATGTAGT	ENSP00000244230:p.Asp440fs	186.0	0.0	0		151.0	16.0	0.10596	NM_005791	A0AVJ8	Frame_Shift_Del	DEL	ENST00000244230.2	hg19	CCDS1916.1																																																																																			.	.	.	none		0.324	MPHOSPH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251924.2	NM_005791		-	71368378	ATGTAGT	-	71368372	7	5	223	1	0	1	0	1	0	0	0	0	9732	333	12	0	1345	0	MPHOSPH10	2	71368372	Frame_Shift_Del	DEL	ATGTAGT	TCGA-MH-A562-01A-11D-A26P-10	51816208	71368372	171831001	12	13521											
IP6K2	51447	hgsc.bcm.edu	37	chr3	48728866	48728866	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttcttctctacagtgtagtAcaagacttcagatttcttta	10	17	5	9	0	4	2	1	0	3	2	5	2	4	2	0	0	2	2	0	0	5	9			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr3:48728866A>G	ENST00000328631.5	-	4	701	c.478T>C	c.(478-480)Tac>Cac	p.Y160H		NM_001005909.2|NM_016291.3	NP_001005909.1|NP_057375.2	Q9UHH9	IP6K2_HUMAN	inositol hexakisphosphate kinase 2	160					cytokine-mediated signaling pathway (GO:0019221)|inositol phosphate metabolic process (GO:0043647)|negative regulation of cell growth (GO:0030308)|phosphate ion transport (GO:0006817)|phosphatidylinositol phosphorylation (GO:0046854)|positive regulation of apoptotic process (GO:0043065)|small molecule metabolic process (GO:0044281)|type I interferon signaling pathway (GO:0060337)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			biliary_tract(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)	15						ACAGTGTAGTACAAGACTTCA	0.363																																					p.Y160H		Atlas-SNP	.											.	IP6K2	63	.	0			c.T478C						PASS	.						154	146	149					3																	48728866		2203	4300	6503	SO:0001583	missense	51447	exon4			TGTAGTACAAGAC	AF177145	CCDS2777.1, CCDS33752.1, CCDS54579.1, CCDS54580.1, CCDS54581.1	3p21.31	2009-01-05	2009-01-05	2008-12-22	ENSG00000068745	ENSG00000068745			17313	protein-coding gene	gene with protein product		606992	"inositol hexaphosphate kinase 2"	IHPK2		10574768	Standard	NM_016291		Approved		uc003cup.3	Q9UHH9	OTTHUMG00000133543	ENST00000328631.5:c.478T>C	chr3.hg19:g.48728866A>G	ENSP00000331103:p.Tyr160His	171.0	0.0	.		146.0	51.0	.	NM_016291	A8K3B1|B4E3G6|G8JLL6|Q6P0N8|Q9BSZ6|Q9BUW3|Q9H4P7|Q9NT63|Q9UFU6	Missense_Mutation	SNP	ENST00000328631.5	hg19	CCDS2777.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.109209	0.77096	.	.	ENSG00000068745	ENST00000328631	T	0.18657	2.2	5.6	5.6	0.85130	.	0.169966	0.53938	D	0.000049	T	0.23330	0.0564	L	0.58101	1.795	0.80722	D	1	P	0.49447	0.924	B	0.40782	0.34	T	0.03852	-1.0998	10	0.22706	T	0.39	-18.3925	15.8359	0.78796	1.0:0.0:0.0:0.0	.	160	Q9UHH9	IP6K2_HUMAN	H	160	ENSP00000331103:Y160H	ENSP00000331103:Y160H	Y	-	1	0	IP6K2	48703870	1.000000	0.71417	0.993000	0.49108	0.991000	0.79684	7.511000	0.81718	2.141000	0.66446	0.524000	0.50904	TAC	.	.	.	none		0.363	IP6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257521.2	NM_016291		G	48728866	A	G	48728866	3	3	223	1	0	0	0	0	1	0	0	0	7796	391	14	3	814	3	IP6K2	3	48728866	Missense_Mutation	SNP	A	TCGA-MH-A562-01A-11D-A26P-10		48728866	149293564	13	13522											
OR5H2	79310	hgsc.bcm.edu	37	chr3	98001882	98001882	+	Missense_Mutation	SNP	A	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	ttgtgtggaaccttggtctgAttgctcttatctggaatgac	7	16	11	7	0	3	2	0	2	3	0	3	4	3	4	1	3	2	1	1	3	3	4			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr3:98001882A>C	ENST00000355273.2	+	1	151	c.151A>C	c.(151-153)Att>Ctt	p.I51L	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005482.1	NP_001005482.1	Q8NGV7	OR5H2_HUMAN	olfactory receptor, family 5, subfamily H, member 2	51						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						CCTTGGTCTGATTGCTCTTAT	0.433																																					p.I51L		Atlas-SNP	.											.	OR5H2	63	.	0			c.A151C						PASS	.						359	331	340					3																	98001882		2203	4300	6503	SO:0001583	missense	79310	exon1			GGTCTGATTGCTC		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.151A>C	chr3.hg19:g.98001882A>C	ENSP00000347418:p.Ile51Leu	252.0	0.0	.		275.0	97.0	.	NM_001005482	Q6IF87	Missense_Mutation	SNP	ENST00000355273.2	hg19	CCDS33801.1	.	.	.	.	.	.	.	.	.	.	A	9.652	1.141906	0.21205	.	.	ENSG00000197938	ENST00000355273	T	0.00614	6.21	3.2	3.2	0.36748	GPCR, rhodopsin-like superfamily (1);	0.180712	0.26582	U	0.023580	T	0.01061	0.0035	L	0.52905	1.665	0.09310	N	1	P	0.45768	0.866	P	0.46585	0.521	T	0.48864	-0.8997	10	0.72032	D	0.01	.	5.7492	0.18138	0.7608:0.0:0.0:0.2391	.	51	Q8NGV7	OR5H2_HUMAN	L	51	ENSP00000347418:I51L	ENSP00000347418:I51L	I	+	1	0	OR5H2	99484572	0.003000	0.15002	0.516000	0.27786	0.041000	0.13682	0.917000	0.28665	1.458000	0.47871	0.443000	0.29094	ATT	.	.	.	none		0.433	OR5H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359113.2			C	98001882	A	C	98001882	3	2	223	1	0	0	0	0	1	0	0	0	11169	333	12	5	153	5	OR5H2	3	98001882	Missense_Mutation	SNP	A	TCGA-MH-A562-01A-11D-A26P-10	49273016	98001882	100020548	14	13523											
RG9MTD1	54931	hgsc.bcm.edu	37	chr3	101284160	101284160	+	Frame_Shift_Del	DEL	T	T	-																															ataaacagaaaaactttctaTttttacgactttgggatagg																										TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr3:101284160delT	ENST00000309922.6	+	2	689	c.535delT	c.(535-537)tttfs	p.F179fs		NM_017819.2	NP_060289.2	Q7L0Y3	MRRP1_HUMAN	tRNA methyltransferase 10 homolog C (S. cerevisiae)	179					mitochondrial RNA 5'-end processing (GO:0000964)|tRNA processing (GO:0008033)	mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)										AAACTTTCTATTTTTACGACT	0.408																																					p.L178fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.534delA						PASS	.						84	80	81					3																	101284160		1827	4080	5907	SO:0001589	frameshift_variant	54931	exon2			.	AK000439	CCDS43122.1	3q12.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000174173	ENSG00000174173			26022	protein-coding gene	gene with protein product	"mitochondrial RNase P subunit 1"	615423	"RNA (guanine-9-) methyltransferase domain containing 1"	RG9MTD1		18984158	Standard	NM_017819		Approved	FLJ20432, MRPP1	uc003duz.4	Q7L0Y3	OTTHUMG00000159114	ENST00000309922.6:c.535delT	chr3.hg19:g.101284160delT	ENSP00000312356:p.Phe179fs	30.0	0.0	0		46.0	18.0	0.391304	NM_017819	Q9NRG5|Q9NX54|Q9Y596	Frame_Shift_Del	DEL	ENST00000309922.6	hg19	CCDS43122.1																																																																																			.	.	.	none		0.408	TRMT10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353400.2	NM_017819		-	101284160	T	-	101284160	7	5	223	1	0	1	0	1	0	0	0	0	13284	1493	52	0	537	0	RG9MTD1	3	101284160	Frame_Shift_Del	DEL	T	TCGA-MH-A562-01A-11D-A26P-10	3282278	101284160	96738270	15	13524											
TPRA1	131601	hgsc.bcm.edu	37	chr3	127292425	127292425	+	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	tgatgctgccagtgtggcagGgcatggaagcgatgtcatcc	8	9	15	9	1	1	1	1	1	0	0	2	3	2	2	2	3	3	3	2	3	1	0	rs201165800	byFrequency	TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr3:127292425G>C	ENST00000355552.3	-	11	1437	c.1061C>G	c.(1060-1062)cCc>cGc	p.P354R	TPRA1_ENST00000450633.2_Missense_Mutation_p.P354R|TPRA1_ENST00000465915.1_5'Flank|TPRA1_ENST00000489960.1_Missense_Mutation_p.P354R|TPRA1_ENST00000296210.7_3'UTR	NM_001136053.1	NP_001129525.1	Q86W33	TPRA1_HUMAN	transmembrane protein, adipocyte asscociated 1	354					aging (GO:0007568)|G-protein coupled receptor signaling pathway (GO:0007186)|lipid metabolic process (GO:0006629)	integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	9						AGTGTGGCAGGGCATGGAAGC	0.657																																					p.P354R		Atlas-SNP	.											.	TPRA1	21	.	0			c.C1061G						PASS	.						47	48	47					3																	127292425		2202	4300	6502	SO:0001583	missense	131601	exon11			TGGCAGGGCATGG	AK056759	CCDS3042.1, CCDS46899.1	3q21.2	2012-08-22	2009-07-08	2009-07-08	ENSG00000163870	ENSG00000163870		"GPCR / Unclassified : 7TM orphan receptors"	30413	protein-coding gene	gene with protein product	"transmembrane protein 227"	608336	"G protein-coupled receptor 175"	GPR175		10342878	Standard	NM_001136053		Approved	TPRA40, FLJ32197, TMEM227	uc003ejn.3	Q86W33	OTTHUMG00000159639	ENST00000355552.3:c.1061C>G	chr3.hg19:g.127292425G>C	ENSP00000347748:p.Pro354Arg	66.0	0.0	.		74.0	24.0	.	NM_001136053	A8MVB8|D3DNA9|Q8WZ24|Q96AJ6|Q9P2R4	Missense_Mutation	SNP	ENST00000355552.3	hg19	CCDS3042.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.553183	0.86127	.	.	ENSG00000163870	ENST00000450633;ENST00000355552;ENST00000489960	.	.	.	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.66489	0.2794	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.70135	-0.4955	9	0.56958	D	0.05	-26.1417	18.2482	0.89993	0.0:0.0:1.0:0.0	.	354	Q86W33	TPRA1_HUMAN	R	354	.	ENSP00000347748:P354R	P	-	2	0	TPRA1	128775115	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	9.058000	0.93896	2.305000	0.77605	0.491000	0.48974	CCC	.	G|0.999;A|0.001	.	alt		0.657	TPRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356624.1	NM_016372		C	127292425	G	C	127292425	3	2	223	1	0	0	0	0	1	0	0	0	16429	1232	43	4	64	4	TPRA1	3	127292425	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	26008265	127292425	70730005	16	13525											
ADD1	118	hgsc.bcm.edu	37	chr4	2883755	2883755	+	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	accaaatgtctacccagcagCtccgcaaggagggatggctg	11	6	12	12	1	1	0	0	0	1	0	2	2	2	2	3	3	3	4	3	3	3	1			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr4:2883755C>A	ENST00000398129.1	+	2	346	c.326C>A	c.(325-327)gCt>gAt	p.A109D	ADD1_ENST00000513328.2_Missense_Mutation_p.A109D|ADD1_ENST00000398125.1_Missense_Mutation_p.A109D|ADD1_ENST00000355842.3_Missense_Mutation_p.A109D|ADD1_ENST00000398123.2_Missense_Mutation_p.A109D|ADD1_ENST00000446856.1_Missense_Mutation_p.A109D|ADD1_ENST00000503455.2_Missense_Mutation_p.A109D|ADD1_ENST00000264758.7_Missense_Mutation_p.A109D			P35611	ADDA_HUMAN	adducin 1 (alpha)	109					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)		TACCCAGCAGCTCCGCAAGGA	0.423																																					p.A109D	Esophageal Squamous(71;505 1201 20414 34538 37449)	Atlas-SNP	.											.	ADD1	56	.	0			c.C326A						PASS	.						152	144	147					4																	2883755		2203	4300	6503	SO:0001583	missense	118	exon3			CAGCAGCTCCGCA	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.326C>A	chr4.hg19:g.2883755C>A	ENSP00000381197:p.Ala109Asp	161.0	0.0	.		220.0	91.0	.	NM_014190	A2A3N8|A2A3P0|B4DI79|D3DVR3|D3DVR4|D3DVR5|Q13734|Q14729|Q16156|Q86XM2|Q9UJB6	Missense_Mutation	SNP	ENST00000398129.1	hg19	CCDS43205.1	.	.	.	.	.	.	.	.	.	.	C	15.64	2.894195	0.52121	.	.	ENSG00000087274	ENST00000264758;ENST00000446856;ENST00000398125;ENST00000398124;ENST00000511797;ENST00000513328;ENST00000503455;ENST00000355842;ENST00000398123;ENST00000398129	T;T;T;T;T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.25717	0.0626	N	0.22421	0.69	0.80722	D	1	B;B;P;B;B;P;B	0.42556	0.003;0.0;0.783;0.005;0.014;0.741;0.19	B;B;B;B;B;B;B	0.40477	0.006;0.002;0.33;0.01;0.022;0.238;0.042	T	0.04386	-1.0955	10	0.45353	T	0.12	-22.0196	18.2285	0.89926	0.0:1.0:0.0:0.0	.	109;109;109;109;109;109;109	E7ENY0;B4DI79;Q86XM2;P35611;P35611-3;P35611-2;A2A3N8	.;.;.;ADDA_HUMAN;.;.;.	D	109	ENSP00000264758:A109D;ENSP00000399828:A109D;ENSP00000381193:A109D;ENSP00000421918:A109D;ENSP00000421907:A109D;ENSP00000423024:A109D;ENSP00000348100:A109D;ENSP00000381191:A109D;ENSP00000381197:A109D	ENSP00000264758:A109D	A	+	2	0	ADD1	2853553	1.000000	0.71417	0.863000	0.33907	0.601000	0.36947	5.634000	0.67833	2.540000	0.85666	0.491000	0.48974	GCT	.	.	.	none		0.423	ADD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242840.1	NM_014189		A	2883755	C	A	2883755	3	1	223	1	0	0	0	0	1	0	0	0	304	797	28	4	332	4	ADD1	4	2883755	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10		2883755	188270521	17	13526											
SLC34A2	10568	hgsc.bcm.edu	37	chr4	25676246	25676246	+	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	gcaatgcattgaggagttcaCtccaggtcaggacttggggc	9	9	14	9	0	2	1	2	1	0	0	3	3	3	3	1	5	1	3	1	5	1	3	rs375377923		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr4:25676246C>G	ENST00000382051.3	+	12	1503	c.1453C>G	c.(1453-1455)Ctc>Gtc	p.L485V	SLC34A2_ENST00000504570.1_Missense_Mutation_p.L484V|SLC34A2_ENST00000503434.1_Missense_Mutation_p.L484V	NM_001177998.1|NM_006424.2	NP_001171469.1|NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 2	485					aging (GO:0007568)|cellular phosphate ion homeostasis (GO:0030643)|in utero embryonic development (GO:0001701)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|response to fructose (GO:0009750)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	phosphate ion binding (GO:0042301)|sodium ion binding (GO:0031402)|sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)		SLC34A2/ROS1(14)	breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(4)	41		Breast(46;0.0503)				GAGGAGTTCACTCCAGGTCAG	0.602			T	ROS1	NSCLC																																p.L485V		Atlas-SNP	.		Dom	yes		4	4p15.2	10568	"solute carrier family 34 (sodium phosphate), member 2"		E	.	SLC34A2	93	.	0			c.C1453G						PASS	.						69	74	72					4																	25676246		2203	4300	6503	SO:0001583	missense	10568	exon12			AGTTCACTCCAGG	AF111856	CCDS3435.1, CCDS54750.1	4p15.2	2013-07-17	2013-07-17		ENSG00000157765	ENSG00000157765		"Solute carriers"	11020	protein-coding gene	gene with protein product		604217	"solute carrier family 34 (sodium phosphate), member 2"			10329428, 10610722	Standard	NM_006424		Approved	NAPI-3B	uc003grr.3	O95436	OTTHUMG00000097757	ENST00000382051.3:c.1453C>G	chr4.hg19:g.25676246C>G	ENSP00000371483:p.Leu485Val	174.0	0.0	.		206.0	80.0	.	NM_006424	A5PL17|Q8N2K2|Q8WYA9|Q9P0V7	Missense_Mutation	SNP	ENST00000382051.3	hg19	CCDS3435.1	.	.	.	.	.	.	.	.	.	.	C	3.915	-0.019199	0.07634	.	.	ENSG00000157765	ENST00000504570;ENST00000382051;ENST00000503434	D;D;D	0.86497	-2.13;-2.13;-2.13	5.31	3.54	0.40534	.	0.068142	0.64402	D	0.000012	D	0.84079	0.5393	L	0.55103	1.725	0.42232	D	0.991895	P;P	0.35944	0.473;0.529	B;P	0.44696	0.336;0.458	T	0.78534	-0.2167	10	0.37606	T	0.19	-25.8301	2.7152	0.05185	0.3196:0.4244:0.1554:0.1006	.	484;485	O95436-2;O95436	.;NPT2B_HUMAN	V	484;485;484	ENSP00000425501:L484V;ENSP00000371483:L485V;ENSP00000423021:L484V	ENSP00000371483:L485V	L	+	1	0	SLC34A2	25285344	0.105000	0.21958	0.623000	0.29173	0.023000	0.10783	0.614000	0.24314	0.698000	0.31739	0.561000	0.74099	CTC	.	.	.	alt		0.602	SLC34A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214990.1	NM_006424		G	25676246	C	G	25676246	3	3	223	1	0	0	0	0	1	0	0	0	14581	565	20	4	1495	4	SLC34A2	4	25676246	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	22792491	25676246	165478030	18	13527											
CWH43	80157	hgsc.bcm.edu	37	chr4	49032879	49032879	+	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	attttggagagtgatgcttcTaagccctatatggggaacaa	12	12	11	6	0	1	2	0	1	1	1	1	4	1	3	1	3	3	1	1	3	5	6			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr4:49032879T>G	ENST00000226432.4	+	11	1593	c.1410T>G	c.(1408-1410)tcT>tcG	p.S470S	CWH43_ENST00000513409.1_Silent_p.S443S	NM_025087.2	NP_079363.2	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog (S. cerevisiae)	470					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						GTGATGCTTCTAAGCCCTATA	0.403																																					p.S470S		Atlas-SNP	.											.	CWH43	101	.	0			c.T1410G						PASS	.						130	131	130					4																	49032879		2203	4300	6503	SO:0001819	synonymous_variant	80157	exon11			TGCTTCTAAGCCC		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.1410T>G	chr4.hg19:g.49032879T>G		142.0	0.0	.		115.0	41.0	.	NM_025087	B2RPD7	Silent	SNP	ENST00000226432.4	hg19	CCDS3486.1																																																																																			.	.	.	none		0.403	CWH43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250496.2	NM_025087		G	49032879	T	G	49032879	2	3	223	1	0	0	0	0	0	0	0	1	4075	1509	53	5		5	CWH43	4	49032879	Silent	SNP	T	TCGA-MH-A562-01A-11D-A26P-10	23356633	49032879	142121397	19	13528											
PRKG2	5593	hgsc.bcm.edu	37	chr4	82061797	82061797	+	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	cttatacacttcatagcaaaAgcaacattctcattttttac	14	15	2	10	0	2	0	2	0	1	0	3	0	2	0	0	0	5	2	0	0	7	8			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr4:82061797A>T	ENST00000395578.1	-	12	1550	c.1434T>A	c.(1432-1434)gcT>gcA	p.A478A	PRKG2_ENST00000509169.1_5'UTR|PRKG2_ENST00000418486.2_Silent_p.A449A|PRKG2_ENST00000264399.1_Silent_p.A478A|PRKG2_ENST00000545647.1_Silent_p.A58A			Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	478	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						TCATAGCAAAAGCAACATTCT	0.353																																					p.A478A		Atlas-SNP	.											.	PRKG2	195	.	0			c.T1434A						PASS	.						130	116	121					4																	82061797		2203	4300	6503	SO:0001819	synonymous_variant	5593	exon11			AGCAAAAGCAACA	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.1434T>A	chr4.hg19:g.82061797A>T		139.0	0.0	.		156.0	37.0	.	NM_006259	B4DMX3|E7EPE6|O00125|O60916	Silent	SNP	ENST00000395578.1	hg19	CCDS3589.1																																																																																			.	.	.	none		0.353	PRKG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252639.1	NM_006259		T	82061797	A	T	82061797	2	4	223	1	0	0	0	0	0	0	0	1	12533	59	3	5		5	PRKG2	4	82061797	Silent	SNP	A	TCGA-MH-A562-01A-11D-A26P-10	33028918	82061797	109092479	20	13529											
FAT1	2195	hgsc.bcm.edu	37	chr4	187627969	187627969	+	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	agaaactggctttcccttgtCtttggccctcacagtgagat	8	13	9	11	0	2	2	1	1	1	2	3	3	3	2	2	2	1	1	2	2	1	3			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr4:187627969C>T	ENST00000441802.2	-	2	3222	c.3013G>A	c.(3013-3015)Gac>Aac	p.D1005N		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1005	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TTTCCCTTGTCTTTGGCCCTC	0.458										HNSCC(5;0.00058)																											p.D1005N	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.G3013A						PASS	.						108	110	109					4																	187627969		1971	4147	6118	SO:0001583	missense	2195	exon2			CCTTGTCTTTGGC	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.3013G>A	chr4.hg19:g.187627969C>T	ENSP00000406229:p.Asp1005Asn	219.0	0.0	.		262.0	91.0	.	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	hg19	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.374390	0.82573	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.65364	-0.15	4.55	4.55	0.56014	Cadherin (5);Cadherin-like (1);	0.106734	0.64402	D	0.000008	T	0.79191	0.4404	M	0.82132	2.575	0.80722	D	1	D	0.59767	0.986	D	0.63703	0.917	T	0.82963	-0.0196	10	0.87932	D	0	.	17.8551	0.88760	0.0:1.0:0.0:0.0	.	1005	Q14517	FAT1_HUMAN	N	1005	ENSP00000406229:D1005N	ENSP00000260147:D1005N	D	-	1	0	FAT1	187864963	1.000000	0.71417	1.000000	0.80357	0.733000	0.41908	7.606000	0.82863	2.508000	0.84585	0.491000	0.48974	GAC	.	.	.	none		0.458	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		T	187627969	C	T	187627969	3	4	223	1	0	0	0	0	1	0	0	0	5696	913	32	2	10857	2	FAT1	4	187627969	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	105566172	187627969	3526307	21	13530											
SKIV2L2	23517	hgsc.bcm.edu	37	chr5	54635905	54635905	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagcccaattaaggctctgAgtaaccaaaaataccgtgaa	16	7	7	11	1	1	2	0	2	1	0	1	2	1	2	4	1	3	2	4	1	7	3			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr5:54635905A>G	ENST00000230640.5	+	6	837	c.583A>G	c.(583-585)Agt>Ggt	p.S195G	SKIV2L2_ENST00000545714.1_Missense_Mutation_p.S94G	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	195	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)				TAAGGCTCTGAGTAACCAAAA	0.363																																					p.S195G	Melanoma(2;92 134 23744 29976 33782)	Atlas-SNP	.											.	SKIV2L2	104	.	0			c.A583G						PASS	.						141	137	139					5																	54635905		2203	4300	6503	SO:0001583	missense	23517	exon6			GCTCTGAGTAACC	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.583A>G	chr5.hg19:g.54635905A>G	ENSP00000230640:p.Ser195Gly	102.0	0.0	.		80.0	24.0	.	NM_015360	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Missense_Mutation	SNP	ENST00000230640.5	hg19	CCDS3967.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.543682	0.86022	.	.	ENSG00000039123	ENST00000230640;ENST00000545714	T;T	0.15139	2.45;2.45	5.98	5.98	0.97165	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.088703	0.85682	D	0.000000	T	0.55289	0.1911	H	0.94345	3.525	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.993;0.999	T	0.68704	-0.5338	10	0.87932	D	0	-18.2935	16.4566	0.84019	1.0:0.0:0.0:0.0	.	94;195	F5H7E2;P42285	.;SK2L2_HUMAN	G	195;94	ENSP00000230640:S195G;ENSP00000442583:S94G	ENSP00000230640:S195G	S	+	1	0	SKIV2L2	54671662	1.000000	0.71417	0.999000	0.59377	0.970000	0.65996	7.102000	0.77005	2.293000	0.77203	0.477000	0.44152	AGT	.	.	.	none		0.363	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1			G	54635905	A	G	54635905	3	3	223	1	0	0	0	0	1	0	0	0	14373	304	11	3	605	3	SKIV2L2	5	54635905	Missense_Mutation	SNP	A	TCGA-MH-A562-01A-11D-A26P-10		54635905	126279355	22	13531											
VCAN	1462	hgsc.bcm.edu	37	chr5	82815685	82815685	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctgtaactgaaacaccattGgtaactgcaagaatgatcct	14	10	7	10	0	0	3	0	2	0	1	1	3	1	3	3	1	4	3	3	1	5	3			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr5:82815685G>A	ENST00000265077.3	+	7	2125	c.1560G>A	c.(1558-1560)ttG>ttA	p.L520L	VCAN_ENST00000512590.2_Silent_p.L472L|VCAN_ENST00000343200.5_Intron|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Silent_p.L520L	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	520	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)	AAACACCATTGGTAACTGCAA	0.393																																					p.L520L		Atlas-SNP	.											.	VCAN	498	.	0			c.G1560A						PASS	.						127	127	127					5																	82815685		2203	4300	6503	SO:0001819	synonymous_variant	1462	exon7			ACCATTGGTAACT	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.1560G>A	chr5.hg19:g.82815685G>A		148.0	0.0	.		134.0	43.0	.	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	hg19	CCDS4060.1																																																																																			.	.	.	none		0.393	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		A	82815685	G	A	82815685	2	1	223	1	0	0	0	0	0	0	0	1	17150	1339	47	2		2	VCAN	5	82815685	Silent	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	28179780	82815685	98099575	23	13532											
PHACTR1	221692	hgsc.bcm.edu	37	chr6	13283687	13283687	+	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	ccacggtggaagagcttcggGaaagaaagatcctcatccgc	12	6	12	11	3	1	3	1	0	0	3	4	5	3	5	3	3	1	1	3	3	3	1			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr6:13283687G>C	ENST00000379335.3	+	3	340	c.235G>C	c.(235-237)Gaa>Caa	p.E79Q	RP1-257A7.4_ENST00000606150.1_RNA|PHACTR1_ENST00000332995.7_Missense_Mutation_p.E515Q|PHACTR1_ENST00000379329.1_Missense_Mutation_p.E79Q|PHACTR1_ENST00000457702.2_Missense_Mutation_p.E370Q|RP1-257A7.4_ENST00000399446.2_RNA			Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1	515					actin cytoskeleton reorganization (GO:0031532)|actomyosin structure organization (GO:0031032)|cell motility (GO:0048870)|stress fiber assembly (GO:0043149)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)|synapse (GO:0045202)	actin binding (GO:0003779)|protein phosphatase inhibitor activity (GO:0004864)			breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	26	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)			AGAGCTTCGGGAAAGAAAGAT	0.597																																					p.E515Q		Atlas-SNP	.											.	PHACTR1	94	.	0			c.G1543C						PASS	.						125	138	134					6																	13283687		2033	4200	6233	SO:0001583	missense	221692	exon13			CTTCGGGAAAGAA	AB051520	CCDS75401.1	6p23	2013-01-24	2004-05-20	2004-05-21	ENSG00000112137	ENSG00000112137		"Phosphatase and actin regulators"	20990	protein-coding gene	gene with protein product		608723	"RPEL repeat containing 1"	RPEL1		11214970, 15107502	Standard	NM_030948		Approved	KIAA1733, dJ257A7.2	uc010jpc.3	Q9C0D0	OTTHUMG00000014270	ENST00000379335.3:c.235G>C	chr6.hg19:g.13283687G>C	ENSP00000368639:p.Glu79Gln	78.0	0.0	.		124.0	43.0	.	NM_030948	A8K1V2|Q3MJ93|Q5JSJ2	Missense_Mutation	SNP	ENST00000379335.3	hg19		.	.	.	.	.	.	.	.	.	.	G	21.1	4.095811	0.76870	.	.	ENSG00000112137	ENST00000332995;ENST00000457702;ENST00000379335;ENST00000379329	T;T	0.32988	1.43;1.43	5.78	5.78	0.91487	.	0.094270	0.64402	D	0.000001	T	0.32224	0.0822	N	0.21448	0.665	0.80722	D	1	D	0.63046	0.992	D	0.67548	0.952	T	0.03193	-1.1062	10	0.33940	T	0.23	-15.365	19.0064	0.92852	0.0:0.0:1.0:0.0	.	515	Q9C0D0	PHAR1_HUMAN	Q	515;370;79;79	ENSP00000329880:E515Q;ENSP00000397669:E370Q	ENSP00000329880:E515Q	E	+	1	0	PHACTR1	13391666	1.000000	0.71417	0.985000	0.45067	0.919000	0.55068	9.623000	0.98386	2.738000	0.93877	0.655000	0.94253	GAA	.	.	.	none		0.597	PHACTR1-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000039878.1	XM_166420		C	13283687	G	C	13283687	3	2	223	1	0	0	0	0	1	0	0	0	11816	1175	41	4	1585	4	PHACTR1	6	13283687	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10		13283687	157831380	24	13533											
ZFP57	346171	hgsc.bcm.edu	37	chr6	29643249	29643249	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtgattagctctggcttaTgcagaaagattctggctgat	9	14	12	6	0	2	4	0	2	2	2	2	4	2	4	0	3	2	4	0	3	3	3			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr6:29643249T>C	ENST00000488757.1	-	3	416	c.266A>G	c.(265-267)cAt>cGt	p.H89R	ZFP57_ENST00000376881.3_Missense_Mutation_p.H69R|ZFP57_ENST00000376883.1_Missense_Mutation_p.H69R	NM_001109809.2	NP_001103279.2	Q9NU63	ZFP57_HUMAN	ZFP57 zinc finger protein	61					DNA methylation involved in embryo development (GO:0043045)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peripheral nervous system development (GO:0007422)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription, DNA-templated (GO:0006351)	nuclear heterochromatin (GO:0005720)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(16)|ovary(4)|skin(4)|urinary_tract(5)	44						CTCTGGCTTATGCAGAAAGAT	0.483																																					p.H89R		Atlas-SNP	.											.	ZFP57	80	.	0			c.A266G						PASS	.						221	207	212					6																	29643249		1947	4153	6100	SO:0001583	missense	346171	exon3			GGCTTATGCAGAA	AL050328	CCDS43436.1, CCDS43436.2	6p22.1	2013-01-08	2012-11-27	2005-07-20	ENSG00000204644	ENSG00000204644		"Zinc fingers, C2H2-type", "-"	18791	protein-coding gene	gene with protein product		612192	"chromosome 6 open reading frame 40", "zinc finger protein 57 homolog (mouse)"	C6orf40			Standard	NM_001109809		Approved	ZNF698, bA145L22, bA145L22.2	uc011dlw.2	Q9NU63	OTTHUMG00000031158	ENST00000488757.1:c.266A>G	chr6.hg19:g.29643249T>C	ENSP00000418259:p.His89Arg	223.0	0.0	.		218.0	91.0	.	NM_001109809	B0S894|B0V254|B2RXJ7|Q5SSB1	Missense_Mutation	SNP	ENST00000488757.1	hg19	CCDS43436.2	.	.	.	.	.	.	.	.	.	.	T	4.922	0.171264	0.09391	.	.	ENSG00000204644	ENST00000488757;ENST00000376881;ENST00000376883	T;T;T	0.00768	5.72;5.72;5.72	4.36	0.288	0.15719	.	0.866899	0.09598	N	0.780620	T	0.00210	0.0006	N	0.14661	0.345	0.09310	N	1	B;B	0.25169	0.119;0.119	B;B	0.23574	0.047;0.047	T	0.25152	-1.0140	10	0.34782	T	0.22	0.7587	4.8209	0.13390	0.173:0.0:0.599:0.2281	.	89;69	Q9NU63-3;Q9NU63-2	.;.	R	89;69;69	ENSP00000418259:H89R;ENSP00000366078:H69R;ENSP00000366080:H69R	ENSP00000366078:H69R	H	-	2	0	ZFP57	29751228	0.003000	0.15002	0.001000	0.08648	0.153000	0.21895	0.428000	0.21395	-0.071000	0.12886	-0.313000	0.08912	CAT	.	.	.	none		0.483	ZFP57-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355773.1	XM_294093		C	29643249	T	C	29643249	3	2	223	1	0	0	0	0	1	0	0	0	17663	1464	51	3	1352	3	ZFP57	6	29643249	Missense_Mutation	SNP	T	TCGA-MH-A562-01A-11D-A26P-10	16359562	29643249	141471818	25	13534											
BAT5	7920	hgsc.bcm.edu	37	chr6	31657863	31657863	+	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	agatggtctcaccgtgcttcCagcaaagcctggatgattcc	9	10	10	12	1	1	2	1	1	1	1	4	3	3	3	4	2	3	2	4	2	1	2			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr6:31657863C>T	ENST00000395952.3	-	11	1111	c.949G>A	c.(949-951)Gga>Aga	p.G317R	ABHD16A_ENST00000375842.4_Missense_Mutation_p.G98R|XXbac-BPG32J3.20_ENST00000461287.1_3'UTR|ABHD16A_ENST00000471644.1_5'UTR|ABHD16A_ENST00000440843.2_Missense_Mutation_p.G284R	NM_021160.2	NP_066983.1	O95870	ABHGA_HUMAN	abhydrolase domain containing 16A	317						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	10						ACCGTGCTTCCAGCAAAGCCT	0.547																																					p.G317R		Atlas-SNP	.											.	ABHD16A	34	.	0			c.G949A						PASS	.						68	56	60					6																	31657863		1511	2709	4220	SO:0001583	missense	7920	exon11			TGCTTCCAGCAAA	AF129756	CCDS4713.1, CCDS54988.1	6p21.3	2013-01-17	2010-12-09	2010-12-09	ENSG00000204427	ENSG00000204427		"Abhydrolase domain containing"	13921	protein-coding gene	gene with protein product		142620	"HLA-B associated transcript 5"	BAT5		2911734, 2813433	Standard	NM_021160		Approved	NG26, D6S82E	uc003nvy.2	O95870	OTTHUMG00000031177	ENST00000395952.3:c.949G>A	chr6.hg19:g.31657863C>T	ENSP00000379282:p.Gly317Arg	91.0	0.0	.		76.0	25.0	.	NM_021160	A2BEY3|B7Z4R6|Q5SRR1|Q5SRR2|Q8WYH0|Q9NW33	Missense_Mutation	SNP	ENST00000395952.3	hg19	CCDS4713.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.733977	0.89482	.	.	ENSG00000204427	ENST00000395952;ENST00000375842;ENST00000440843	T;T;T	0.21191	2.02;2.02;2.02	5.4	5.4	0.78164	.	0.108527	0.64402	D	0.000008	T	0.30792	0.0776	L	0.55834	1.745	0.80722	D	1	D;D	0.76494	0.96;0.999	P;D	0.71656	0.772;0.974	T	0.00909	-1.1518	10	0.30078	T	0.28	-9.9061	16.6668	0.85255	0.0:1.0:0.0:0.0	.	284;317	B7Z4R6;O95870	.;ABHGA_HUMAN	R	317;98;284	ENSP00000379282:G317R;ENSP00000365002:G98R;ENSP00000410347:G284R	ENSP00000365002:G98R	G	-	1	0	ABHD16A	31765842	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.008000	0.63991	2.536000	0.85505	0.655000	0.94253	GGA	.	.	.	none		0.547	ABHD16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076342.4			T	31657863	C	T	31657863	3	4	223	1	0	0	0	0	1	0	0	0	1324	603	21	2	767	2	BAT5	6	31657863	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	2014614	31657863	139457204	26	13535											
GRB10	2887	hgsc.bcm.edu	37	chr7	50742288	50742288	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgtctgactgcatgctgcaGgccgagtacaggctctccag	7	9	13	12	1	2	1	0	1	2	0	3	2	2	1	2	2	4	5	2	2	1	1			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr7:50742288G>A	ENST00000401949.1	-	6	676	c.207C>T	c.(205-207)gcC>gcT	p.A69A	GRB10_ENST00000357271.5_Silent_p.A69A|GRB10_ENST00000407526.1_Silent_p.A11A|GRB10_ENST00000406641.1_Silent_p.A11A|GRB10_ENST00000439599.1_Silent_p.A63A|GRB10_ENST00000402497.1_Silent_p.A11A|GRB10_ENST00000402578.1_Silent_p.A11A|GRB10_ENST00000398812.2_Silent_p.A69A|GRB10_ENST00000335866.3_Silent_p.A11A|GRB10_ENST00000403097.1_Silent_p.A63A|GRB10_ENST00000398810.2_Silent_p.A11A			Q13322	GRB10_HUMAN	growth factor receptor-bound protein 10	69					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)					GCATGCTGCAGGCCGAGTACA	0.587									Russell-Silver syndrome																												p.A69A		Atlas-SNP	.											.	GRB10	155	.	0			c.C207T						PASS	.						57	63	61					7																	50742288		2066	4214	6280	SO:0001819	synonymous_variant	2887	exon3	Familial Cancer Database	Silver-Russell Dwarfism, Silver-Russell syndrome, SRS, Russel-Silver Dwarfism	GCTGCAGGCCGAG		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.207C>T	chr7.hg19:g.50742288G>A		51.0	0.0	.		91.0	8.0	.	NM_005311	A4D258|A7VJ95|A8K0E6|D3DVM9|O00427|O00701|O75222|Q92606|Q92907|Q92948	Silent	SNP	ENST00000401949.1	hg19	CCDS43582.1																																																																																			.	.	.	none		0.587	GRB10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319157.1			A	50742288	G	A	50742288	2	1	223	1	0	0	0	0	0	0	0	1	6763	987	35	2		2	GRB10	7	50742288	Silent	SNP	G	TCGA-MH-A562-01A-11D-A26P-10		50742288	108396375	27	13536											
WDR91	29062	hgsc.bcm.edu	37	chr7	134893687	134893687	+	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	aaaccaatccttccactcagCctggttctggagttccgtgg	8	11	9	13	1	2	0	1	0	1	0	5	1	5	1	5	3	2	2	5	3	2	3			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr7:134893687C>A	ENST00000354475.4	-	3	398	c.367G>T	c.(367-369)Gct>Tct	p.A123S	WDR91_ENST00000485942.1_5'Flank|WDR91_ENST00000344400.5_Missense_Mutation_p.A123S|WDR91_ENST00000423565.1_Missense_Mutation_p.A88S	NM_014149.3	NP_054868.3	A4D1P6	WDR91_HUMAN	WD repeat domain 91	123										breast(3)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	40						TTCCACTCAGCCTGGTTCTGG	0.537																																					p.A123S		Atlas-SNP	.											.	WDR91	82	.	0			c.G367T						PASS	.						184	155	165					7																	134893687		2203	4300	6503	SO:0001583	missense	29062	exon3			ACTCAGCCTGGTT	AF161534	CCDS34758.1	7q33	2013-01-09			ENSG00000105875	ENSG00000105875		"WD repeat domain containing"	24997	protein-coding gene	gene with protein product						11042152, 11230166	Standard	NM_014149		Approved	HSPC049	uc003vsp.2	A4D1P6	OTTHUMG00000155414	ENST00000354475.4:c.367G>T	chr7.hg19:g.134893687C>A	ENSP00000346466:p.Ala123Ser	290.0	0.0	.		521.0	195.0	.	NM_014149	A6NK54|C9JMI4|Q6FI65|Q6MZQ1|Q6P4I1|Q96AE5|Q96G63|Q9H062|Q9H9B6|Q9NVG7|Q9NZY6	Missense_Mutation	SNP	ENST00000354475.4	hg19	CCDS34758.1	.	.	.	.	.	.	.	.	.	.	C	10.92	1.488114	0.26686	.	.	ENSG00000105875	ENST00000344400;ENST00000354475;ENST00000423565	D;D;D	0.91521	-2.86;-2.86;-2.86	5.77	4.89	0.63831	.	0.145674	0.64402	D	0.000009	D	0.82733	0.5101	N	0.25890	0.77	0.58432	D	0.999999	P	0.41524	0.753	B	0.35278	0.199	T	0.81028	-0.1118	10	0.18276	T	0.48	-19.4769	15.1712	0.72875	0.0:0.9322:0.0:0.0678	.	123	A4D1P6	WDR91_HUMAN	S	123;123;88	ENSP00000340877:A123S;ENSP00000346466:A123S;ENSP00000392555:A88S	ENSP00000340877:A123S	A	-	1	0	WDR91	134544227	1.000000	0.71417	0.998000	0.56505	0.041000	0.13682	4.739000	0.62080	1.587000	0.49959	-0.145000	0.13849	GCT	.	.	.	none		0.537	WDR91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340019.1	NM_014149		A	134893687	C	A	134893687	3	1	223	1	0	0	0	0	1	0	0	0	17350	739	26	4	1928	4	WDR91	7	134893687	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	84151399	134893687	24244976	28	13537											
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77616434	77616434	+	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	gtgccagagaaagttgcaggGatggagcctgacagggaaaa	14	5	16	6	0	0	2	0	1	0	1	0	6	0	5	2	3	3	2	2	3	3	1			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr8:77616434G>A	ENST00000521891.2	+	2	559	c.111G>A	c.(109-111)ggG>ggA	p.G37G	ZFHX4_ENST00000518282.1_Silent_p.G37G|ZFHX4_ENST00000455469.2_Silent_p.G37G|ZFHX4_ENST00000050961.6_Silent_p.G37G|ZFHX4_ENST00000517683.1_Intron	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	37					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)			AAGTTGCAGGGATGGAGCCTG	0.502										HNSCC(33;0.089)																											p.G37G		Atlas-SNP	.											.	ZFHX4	878	.	0			c.G111A						PASS	.						64	67	66					8																	77616434		2025	4211	6236	SO:0001819	synonymous_variant	79776	exon2			TGCAGGGATGGAG		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.111G>A	chr8.hg19:g.77616434G>A		238.0	0.0	.		274.0	84.0	.	NM_024721	G3V138|Q18PS0|Q6ZN20	Silent	SNP	ENST00000521891.2	hg19	CCDS47878.2																																																																																			.	.	.	none		0.502	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		A	77616434	G	A	77616434	2	1	223	1	0	0	0	0	0	0	0	1	17647	1161	41	2		2	ZFHX4	8	77616434	Silent	SNP	G	TCGA-MH-A562-01A-11D-A26P-10		77616434	68747588	29	13538											
NFKBIL2	4796	hgsc.bcm.edu	37	chr8	145654714	145654714	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccaggggaccctggacggCgcagcctgcggaggggaaga	8	2	19	12	3	0	1	0	0	0	1	0	5	0	5	3	7	2	1	3	7	1	0			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr8:145654714C>T	ENST00000409379.3	-	26	3978	c.3949G>A	c.(3949-3951)Gcc>Acc	p.A1317T	VPS28_ENST00000526054.1_5'Flank|VPS28_ENST00000526734.1_5'Flank|VPS28_ENST00000292510.4_5'Flank|VPS28_ENST00000377348.2_5'Flank|VPS28_ENST00000529182.1_5'Flank	NM_013432.4	NP_038460.4	Q96HA7	TONSL_HUMAN	tonsoku-like, DNA repair protein	1317					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						CCCTGGACGGCGCAGCCTGCG	0.706																																					p.A1317T		Atlas-SNP	.											.	TONSL	128	.	0			c.G3949A						PASS	.						5	5	5					8																	145654714		2056	4038	6094	SO:0001583	missense	4796	exon26			GGACGGCGCAGCC		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.3949G>A	chr8.hg19:g.145654714C>T	ENSP00000386239:p.Ala1317Thr	0.0	0.0	.		7.0	5.0	.	NM_013432	B5MDP0|C9JKB1|C9JNV8|Q13006|Q9UGJ2	Missense_Mutation	SNP	ENST00000409379.3	hg19	CCDS34968.2	.	.	.	.	.	.	.	.	.	.	c	8.974	0.973627	0.18736	.	.	ENSG00000160949	ENST00000409379;ENST00000422691	T	0.52983	0.64	5.39	0.26	0.15588	.	0.776034	0.12482	N	0.465083	T	0.35624	0.0938	L	0.47016	1.485	0.09310	N	1	B	0.20052	0.041	B	0.06405	0.002	T	0.28522	-1.0041	10	0.54805	T	0.06	-3.5453	5.4749	0.16690	0.5793:0.2411:0.0:0.1796	.	1317	Q96HA7	TONSL_HUMAN	T	1317;1316	ENSP00000386239:A1317T	ENSP00000386239:A1317T	A	-	1	0	TONSL	145625522	0.000000	0.05858	0.421000	0.26609	0.136000	0.21042	-0.691000	0.05133	0.097000	0.17492	0.511000	0.50034	GCC	.	.	.	none		0.706	TONSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329668.2	NM_013432		T	145654714	C	T	145654714	3	4	223	1	0	0	0	0	1	0	0	0	10389	768	27	1	191	1	NFKBIL2	8	145654714	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	68038280	145654714	709308	30	13539											
OPN4	94233	hgsc.bcm.edu	37	chr10	88419072	88419072	+	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	aggcgcctacgtgcccgaggGgttgctgacatcctgctcct	5	9	13	14	3	0	1	0	1	0	0	2	2	2	1	4	3	4	3	4	3	1	2			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr10:88419072G>A	ENST00000241891.5	+	5	814	c.647G>A	c.(646-648)gGg>gAg	p.G216E	OPN4_ENST00000372071.2_Missense_Mutation_p.G227E	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4	216					phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|rhodopsin mediated signaling pathway (GO:0016056)|rhythmic process (GO:0048511)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	11-cis retinal binding (GO:0005502)|G-protein coupled photoreceptor activity (GO:0008020)	p.G227V(2)		breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(5)|ovary(3)	18						GTGCCCGAGGGGTTGCTGACA	0.612																																					p.G227E		Atlas-SNP	.											OPN4,NS,carcinoma,0,2	OPN4	61	.	2	Substitution - Missense(2)	liver(2)	c.G680A						PASS	.						167	135	146					10																	88419072		2203	4300	6503	SO:0001583	missense	94233	exon6			CCGAGGGGTTGCT	AF147788	CCDS7376.1, CCDS31237.1	10q22	2012-08-08	2008-04-16		ENSG00000122375	ENSG00000122375		"GPCR / Class A : Opsin receptors"	14449	protein-coding gene	gene with protein product	"melanopsin"	606665	"opsin 4 (melanopsin)"			10632589	Standard	NM_001030015		Approved	MOP, melanopsin	uc001kdp.3	Q9UHM6	OTTHUMG00000018654	ENST00000241891.5:c.647G>A	chr10.hg19:g.88419072G>A	ENSP00000241891:p.Gly216Glu	56.0	0.0	.		77.0	29.0	.	NM_001030015	B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Missense_Mutation	SNP	ENST00000241891.5	hg19	CCDS7376.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.985781	0.93044	.	.	ENSG00000122375	ENST00000372071;ENST00000241891;ENST00000443292	T;T;T	0.70282	-0.47;-0.47;-0.47	5.15	5.15	0.70609	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.86694	0.5994	M	0.87269	2.87	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	0.89121	0.3503	10	0.87932	D	0	.	18.6376	0.91384	0.0:0.0:1.0:0.0	.	227;216;227	C9JWU6;Q9UHM6;Q9UHM6-2	.;OPN4_HUMAN;.	E	227;216;227	ENSP00000361141:G227E;ENSP00000241891:G216E;ENSP00000393132:G227E	ENSP00000241891:G216E	G	+	2	0	OPN4	88409052	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	9.705000	0.98719	2.397000	0.81536	0.655000	0.94253	GGG	.	.	.	none		0.612	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2	NM_033282		A	88419072	G	A	88419072	3	1	223	1	0	0	0	0	1	0	0	0	10889	1232	43	2	702	2	OPN4	10	88419072	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10		88419072	47115675	31	13540											
MUC2	4583	hgsc.bcm.edu	37	chr11	1093204	1093204	+	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	ccggcacacagtccccaaccCcaacagccatcaccaccacc	12	2	4	23	1	1	0	1	0	0	0	2	0	2	0	9	1	3	1	9	1	2	0	rs56299570		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr11:1093204C>A	ENST00000441003.2	+	30	5050	c.5023C>A	c.(5023-5025)Cca>Aca	p.P1675T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.P1642T|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)		p.P1675T(1)|p.P1642T(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)	gtccccaaccccaacagccat	0.627																																					p.P1675T		Atlas-SNP	.											MUC2_ENST00000441003,caecum,carcinoma,0,4	MUC2	614	.	2	Substitution - Missense(2)	kidney(2)	c.C5023A						PASS	.																																			SO:0001583	missense	4583	exon30			CCAACCCCAACAG	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.5023C>A	chr11.hg19:g.1093204C>A	ENSP00000415183:p.Pro1675Thr	130.0	2.0	.		144.0	8.0	.	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	C	0.954	-0.705464	0.03255	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.09073	3.02;3.53	1.75	-3.49	0.04724	.	0.575351	0.10542	U	0.662513	T	0.04092	0.0114	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45381	-0.9265	9	0.16896	T	0.51	.	6.9769	0.24681	0.6778:0.3222:0.0:0.0	rs56299570	1675	E7EUV1	.	T	1675;1642	ENSP00000415183:P1675T;ENSP00000351956:P1642T	ENSP00000351956:P1642T	P	+	1	0	MUC2	1083204	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-3.268000	0.00533	-1.450000	0.01936	0.184000	0.17185	CCA	.	.	.	weak		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1093204	C	A	1093204	3	1	223	1	0	0	0	0	1	0	0	0	9982	623	22	4	5141	4	MUC2	11	1093204	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10		1093204	133913312	32	13541											
KCNA4	3739	hgsc.bcm.edu	37	chr11	30034138	30034138	+	Missense_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	ggagtgagcaagcctctcccGctcccgggcccgggcctggg	4	5	16	16	3	1	1	0	1	1	0	3	2	2	2	5	4	2	2	5	4	1	0			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr11:30034138G>A	ENST00000328224.6	-	2	1321	c.88C>T	c.(88-90)Cgg>Tgg	p.R30W	KCNA4_ENST00000526518.1_5'Flank	NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	30					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	AGCCTCTCCCGCTCCCGGGCC	0.637																																					p.R30W		Atlas-SNP	.											.	KCNA4	158	.	0			c.C88T						PASS	.						58	60	59					11																	30034138		1910	4113	6023	SO:0001583	missense	3739	exon2			TCTCCCGCTCCCG	M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6222	protein-coding gene	gene with protein product		176266	"potassium voltage-gated channel, shaker-related subfamily, member 4-like"	KCNA4L		2263489, 16382104	Standard	NM_002233		Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.88C>T	chr11.hg19:g.30034138G>A	ENSP00000328511:p.Arg30Trp	14.0	0.0	.		12.0	5.0	.	NM_002233		Missense_Mutation	SNP	ENST00000328224.6	hg19	CCDS41629.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.988463	0.53934	.	.	ENSG00000182255	ENST00000328224	D	0.98012	-4.66	4.97	2.88	0.33553	Potassium channel, voltage dependent, Kv1.4, tandem inactivation (2);	269.221000	0.00166	N	0.000002	D	0.95290	0.8472	N	0.24115	0.695	0.47276	D	0.999375	B	0.29671	0.254	B	0.21360	0.034	T	0.80362	-0.1414	10	0.87932	D	0	.	14.4391	0.67303	0.0:0.0:0.6478:0.3522	.	30	P22459	KCNA4_HUMAN	W	30	ENSP00000328511:R30W	ENSP00000328511:R30W	R	-	1	2	KCNA4	29990714	1.000000	0.71417	0.992000	0.48379	0.963000	0.63663	0.619000	0.24388	1.065000	0.40693	0.655000	0.94253	CGG	.	.	.	none		0.637	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388074.2	NM_002233		A	30034138	G	A	30034138	3	1	223	1	0	0	0	0	1	0	0	0	8012	1086	38	1	1877	1	KCNA4	11	30034138	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	28940934	30034138	104972378	33	13542											
API5	8539	hgsc.bcm.edu	37	chr11	43350300	43350300	+	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	ccagaagaggcagaaaatggAgagaatgctggtaatgaaga	18	5	14	4	0	0	6	0	1	0	5	0	8	0	7	1	3	1	3	1	3	6	1			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr11:43350300A>T	ENST00000531273.1	+	9	1123	c.984A>T	c.(982-984)ggA>ggT	p.G328G	API5_ENST00000378852.3_Silent_p.G328G|API5_ENST00000534695.1_Intron|Y_RNA_ENST00000516843.1_RNA|API5_ENST00000455725.2_Silent_p.G317G|API5_ENST00000420461.2_Silent_p.G274G|API5_ENST00000534600.1_Silent_p.G328G|RP11-484D2.2_ENST00000526220.1_RNA			Q9BZZ5	API5_HUMAN	apoptosis inhibitor 5	328	ARM-like and Heat-like helical repeats.				apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|negative regulation of fibroblast apoptotic process (GO:2000270)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	fibroblast growth factor binding (GO:0017134)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(2)|urinary_tract(1)	20						CAGAAAATGGAGAGAATGCTG	0.373																																					p.G328G	Pancreas(1;98 122 5625 20895 49453)	Atlas-SNP	.											.	API5	91	.	0			c.A984T						PASS	.						82	72	75					11																	43350300		2203	4300	6503	SO:0001819	synonymous_variant	8539	exon9			AAATGGAGAGAAT	U83857	CCDS31465.1, CCDS44572.1, CCDS44573.1	11p12	2010-09-30			ENSG00000166181	ENSG00000166181			594	protein-coding gene	gene with protein product	"API5-like 1", "fibroblast growth factor 2-interacting factor 2", "migration-inducing protein MIG8"	609774				9307294	Standard	NR_024625		Approved	AAC-11, API5L1, AAC11	uc010rfh.1	Q9BZZ5	OTTHUMG00000166395	ENST00000531273.1:c.984A>T	chr11.hg19:g.43350300A>T		244.0	0.0	.		234.0	73.0	.	NM_006595	B4DGR0|B4DRJ2|D3DR21|O15441|Q9Y4J7	Silent	SNP	ENST00000531273.1	hg19	CCDS44572.1																																																																																			.	.	.	none		0.373	API5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389545.1	NM_006595		T	43350300	A	T	43350300	2	4	223	1	0	0	0	0	0	0	0	1	773	291	11	5		5	API5	11	43350300	Silent	SNP	A	TCGA-MH-A562-01A-11D-A26P-10	13316162	43350300	91656216	34	13543											
MCAM	4162	hgsc.bcm.edu	37	chr11	119185945	119185945	+	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	tccacctccaccagctcaggCgcaggctgctcagcctctcc	6	7	8	20	1	3	0	2	0	1	0	6	0	5	0	6	2	3	4	6	2	0	0	rs558009680		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr11:119185945C>T	ENST00000264036.4	-	2	110	c.96G>A	c.(94-96)gcG>gcA	p.A32A	MCAM_ENST00000530144.2_5'UTR|MCAM_ENST00000392814.1_5'Flank	NM_006500.2	NP_006491.2	P43121	MUC18_HUMAN	melanoma cell adhesion molecule	32	Ig-like V-type 1.				anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|glomerular filtration (GO:0003094)|vascular wound healing (GO:0061042)	external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|skin(1)	22		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.78e-05)		CCAGCTCAGGCGCAGGCTGCT	0.682													C|||	1	0.000199681	8e-04	0	5008	,	,		15849	0		0	False		,,,				2504	0				p.A32A		Atlas-SNP	.											.	MCAM	57	.	0			c.G96A						PASS	.						41	37	38					11																	119185945		2199	4294	6493	SO:0001819	synonymous_variant	4162	exon2			CTCAGGCGCAGGC	X68264	CCDS31690.1	11q23.3	2013-01-29				ENSG00000076706		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6934	protein-coding gene	gene with protein product	"Gicerin"	155735				2602381, 10702685	Standard	XM_005271552		Approved	MUC18, CD146	uc001pwf.3	P43121		ENST00000264036.4:c.96G>A	chr11.hg19:g.119185945C>T		42.0	0.0	.		48.0	5.0	.	NM_006500	O95812|Q59E86|Q6PHR3|Q6ZTR2	Silent	SNP	ENST00000264036.4	hg19	CCDS31690.1																																																																																			.	.	.	none		0.682	MCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388332.2			T	119185945	C	T	119185945	2	4	223	1	0	0	0	0	0	0	0	1	9375	755	27	1		1	MCAM	11	119185945	Silent	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	75835645	119185945	15820571	35	13544											
GLI1	2735	hgsc.bcm.edu	37	chr12	57861257	57861257	+	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	ccagtgaccgagccaagcacCagaatcggacccattccaat	13	5	8	15	2	0	2	0	1	0	1	2	4	1	3	6	1	2	1	6	1	3	1			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr12:57861257C>A	ENST00000228682.2	+	9	1145	c.1054C>A	c.(1054-1056)Cag>Aag	p.Q352K	GLI1_ENST00000543426.1_Missense_Mutation_p.Q224K|GLI1_ENST00000546141.1_Missense_Mutation_p.Q311K	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	352					cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			AGCCAAGCACCAGAATCGGAC	0.547																																					p.Q352K	Pancreas(157;841 1936 10503 41495 50368)	Atlas-SNP	.											.	GLI1	141	.	0			c.C1054A						PASS	.						120	80	94					12																	57861257		2203	4300	6503	SO:0001583	missense	2735	exon9			AAGCACCAGAATC		CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"Zinc fingers, C2H2-type"	4317	protein-coding gene	gene with protein product		165220	"glioma-associated oncogene homolog 1 (zinc finger protein)", "glioma-associated oncogene family zinc finger 1"	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.1054C>A	chr12.hg19:g.57861257C>A	ENSP00000228682:p.Gln352Lys	214.0	0.0	.		368.0	92.0	.	NM_005269	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Missense_Mutation	SNP	ENST00000228682.2	hg19	CCDS8940.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.001063	0.93227	.	.	ENSG00000111087	ENST00000543426;ENST00000228682;ENST00000546141;ENST00000528467;ENST00000443131	T;T;T;T	0.24151	1.87;1.87;1.87;1.87	4.77	4.77	0.60923	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49916	D	0.000133	T	0.34454	0.0898	N	0.14661	0.345	0.80722	D	1	D	0.59357	0.985	D	0.68765	0.96	T	0.34601	-0.9822	10	0.87932	D	0	.	17.1156	0.86688	0.0:1.0:0.0:0.0	.	352	P08151	GLI1_HUMAN	K	224;352;311;311;224	ENSP00000437607:Q224K;ENSP00000228682:Q352K;ENSP00000441006:Q311K;ENSP00000434408:Q311K	ENSP00000228682:Q352K	Q	+	1	0	GLI1	56147524	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.578000	0.82498	2.644000	0.89710	0.655000	0.94253	CAG	.	.	.	none		0.547	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269		A	57861257	C	A	57861257	3	1	223	1	0	0	0	0	1	0	0	0	6444	595	21	4	1084	4	GLI1	12	57861257	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10		57861257	75990638	36	13545											
PAWR	5074	hgsc.bcm.edu	37	chr12	80083606	80083606	+	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	ctttcctggcactggggcccGagctcttgcccttctctggg	2	12	12	15	1	2	0	0	0	2	0	4	1	3	0	3	4	2	2	3	4	0	3	rs369162125		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr12:80083606G>A	ENST00000328827.4	-	2	791	c.419C>T	c.(418-420)tCg>tTg	p.S140L	RP11-530C5.1_ENST00000551995.1_lincRNA|PAWR_ENST00000547571.1_5'UTR	NM_002583.2	NP_002574.2	Q96IZ0	PAWR_HUMAN	PRKC, apoptosis, WT1, regulator	140					actin filament bundle assembly (GO:0051017)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|interleukin-2 biosynthetic process (GO:0042094)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of amyloid precursor protein biosynthetic process (GO:0042986)|positive regulation of apoptotic process (GO:0043065)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|enzyme binding (GO:0019899)|leucine zipper domain binding (GO:0043522)|transcription corepressor activity (GO:0003714)			NS(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						ACTGGGGCCCGAGCTCTTGCC	0.706																																					p.S140L		Atlas-SNP	.											.	PAWR	14	.	0			c.C419T						PASS	.	G	LEU/SER	0,4392		0,0,2196	11	11	11		419	2.6	1	12		11	1,8579		0,1,4289	no	missense	PAWR	NM_002583.2	145	0,1,6485	AA,AG,GG		0.0117,0.0,0.0077	possibly-damaging	140/341	80083606	1,12971	2196	4290	6486	SO:0001583	missense	5074	exon2			GGGCCCGAGCTCT	U63809	CCDS31863.1	12q21.2	2013-03-07			ENSG00000177425	ENSG00000177425			8614	protein-coding gene	gene with protein product	"prostate apoptosis response-4"	601936				8943350, 9790775	Standard	NM_002583		Approved	par-4, PAR4	uc001syx.3	Q96IZ0	OTTHUMG00000170080	ENST00000328827.4:c.419C>T	chr12.hg19:g.80083606G>A	ENSP00000328088:p.Ser140Leu	40.0	0.0	.		100.0	5.0	.	NM_002583	O75796|Q6FHY9|Q8N700	Missense_Mutation	SNP	ENST00000328827.4	hg19	CCDS31863.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.494262	0.85069	0.0	1.17E-4	ENSG00000177425	ENST00000328827	T	0.10192	2.9	3.48	2.59	0.31030	.	0.352131	0.26887	N	0.021991	T	0.08133	0.0203	L	0.50333	1.59	0.42430	D	0.992671	P	0.35944	0.529	B	0.28305	0.088	T	0.29274	-1.0017	9	.	.	.	-1.0638	6.7459	0.23460	0.0988:0.1793:0.7219:0.0	.	140	Q96IZ0	PAWR_HUMAN	L	140	ENSP00000328088:S140L	.	S	-	2	0	PAWR	78607737	1.000000	0.71417	1.000000	0.80357	0.788000	0.44548	6.058000	0.71126	0.650000	0.30769	0.563000	0.77884	TCG	.	.	.	weak		0.706	PAWR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407175.1	NM_002583		A	80083606	G	A	80083606	3	1	223	1	0	0	0	0	1	0	0	0	11484	1059	37	1	627	1	PAWR	12	80083606	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	22222349	80083606	53768289	37	13546											
P2RX2	22953	hgsc.bcm.edu	37	chr12	133197702	133197702	+	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	caagcacgtgcctgcctcgtCaggctacaacttcaggtgct	8	9	10	14	2	2	0	2	0	0	0	3	0	2	0	2	2	6	3	2	2	3	2			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr12:133197702C>T	ENST00000389110.3	+	8	927	c.890C>T	c.(889-891)tCa>tTa	p.S297L	P2RX2_ENST00000343948.4_Missense_Mutation_p.S297L|P2RX2_ENST00000352418.4_Missense_Mutation_p.S225L|P2RX2_ENST00000348800.5_Missense_Mutation_p.S297L|P2RX2_ENST00000351222.4_Missense_Mutation_p.S205L|P2RX2_ENST00000449132.2_Missense_Mutation_p.S263L|P2RX2_ENST00000350048.5_Missense_Mutation_p.S273L	NM_170682.2|NM_170683.2|NM_174873.1	NP_733782.1|NP_733783.1|NP_777362.1	Q9UBL9	P2RX2_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 2	297					behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of hypoxic conditions in blood by carotid body chemoreceptor signaling (GO:0003029)|ion transmembrane transport (GO:0034220)|neuromuscular junction development (GO:0007528)|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 heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to hypoxia (GO:0001666)|sensory perception of sound (GO:0007605)|sensory perception of taste (GO:0050909)|skeletal muscle fiber development (GO:0048741)|urinary bladder smooth muscle contraction (GO:0014832)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|dendritic spine (GO:0043197)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|cadmium ion binding (GO:0046870)|cobalt ion binding (GO:0050897)|copper ion binding (GO:0005507)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|identical protein binding (GO:0042802)|ligand-gated ion channel activity (GO:0015276)|mercury ion binding (GO:0045340)|nickel cation binding (GO:0016151)|phosphatidylinositol binding (GO:0035091)|purinergic nucleotide receptor activity (GO:0001614)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|kidney(2)|large_intestine(2)|liver(2)|lung(8)|ovary(1)|prostate(3)	20	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0767)		OV - Ovarian serous cystadenocarcinoma(86;2.32e-08)|Epithelial(86;8.62e-08)|all cancers(50;4.5e-06)		CCTGCCTCGTCAGGCTACAAC	0.607																																					p.S297L		Atlas-SNP	.											.	P2RX2	49	.	0			c.C890T						PASS	.						103	84	90					12																	133197702		2203	4300	6503	SO:0001583	missense	22953	exon8			CCTCGTCAGGCTA	AF109387	CCDS31930.1, CCDS31931.1, CCDS31932.1, CCDS31933.1, CCDS31934.1, CCDS31935.1, CCDS61286.1, CCDS73548.1	12q24.33	2013-03-22			ENSG00000187848	ENSG00000187848		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	15459	protein-coding gene	gene with protein product		600844	"deafness, autosomal dominant 41"	DFNA41		10570044, 7523952, 23345450	Standard	XM_005266154		Approved	P2X2	uc001ukk.1	Q9UBL9	OTTHUMG00000168018	ENST00000389110.3:c.890C>T	chr12.hg19:g.133197702C>T	ENSP00000373762:p.Ser297Leu	124.0	0.0	.		182.0	11.0	.	NM_170683	A6NGB4|A6NH93|A6NHC2|A6NHU3|A6NIG9|Q6V9R6|Q9NR37|Q9NR38|Q9UHD5|Q9UHD6|Q9UHD7|Q9Y637|Q9Y638	Missense_Mutation	SNP	ENST00000389110.3	hg19	CCDS31931.1	.	.	.	.	.	.	.	.	.	.	C	16.49	3.138279	0.56936	.	.	ENSG00000187848	ENST00000389110;ENST00000449132;ENST00000343948;ENST00000352418;ENST00000350048;ENST00000351222;ENST00000348800	T;T;T;T;T;T;T	0.04406	3.63;3.63;3.63;3.63;3.63;3.63;3.63	4.96	4.96	0.65561	.	0.120057	0.64402	D	0.000017	T	0.13628	0.0330	M	0.76002	2.32	0.28672	N	0.905593	P;P;P;D;P;P;P;P	0.53745	0.751;0.58;0.928;0.962;0.716;0.716;0.849;0.575	P;P;P;B;B;P;P;B	0.49887	0.527;0.476;0.625;0.341;0.407;0.487;0.622;0.392	T	0.01375	-1.1371	10	0.54805	T	0.06	-13.2945	16.1502	0.81611	0.0:1.0:0.0:0.0	.	297;263;205;225;273;297;297;297	Q32MC3;Q9UBL9-7;Q9UBL9-5;Q9UBL9-6;Q9UBL9-3;Q9UBL9-4;Q9UBL9;Q9UBL9-2	.;.;.;.;.;.;P2RX2_HUMAN;.	L	297;263;297;225;273;205;297	ENSP00000373762:S297L;ENSP00000405531:S263L;ENSP00000343339:S297L;ENSP00000341419:S225L;ENSP00000343904:S273L;ENSP00000344502:S205L;ENSP00000345095:S297L	ENSP00000343339:S297L	S	+	2	0	P2RX2	131707775	0.343000	0.24818	0.655000	0.29622	0.406000	0.30931	3.786000	0.55431	2.584000	0.87258	0.561000	0.74099	TCA	.	.	.	none		0.607	P2RX2-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397542.1			T	133197702	C	T	133197702	3	4	223	1	0	0	0	0	1	0	0	0	11347	838	29	2	920	2	P2RX2	12	133197702	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	53114096	133197702	654193	38	13547											
POU4F1	5457	hgsc.bcm.edu	37	chr13	79175599	79175599	+	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	tctgcttctgtctctggttgCaaaaccacacccgcaccacg	8	10	7	16	2	3	0	0	0	3	0	4	0	3	0	3	1	3	4	3	1	2	2			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr13:79175599C>A	ENST00000377208.5	-	2	1422	c.1211G>T	c.(1210-1212)tGc>tTc	p.C404F	RNF219-AS1_ENST00000607860.1_RNA|RNF219-AS1_ENST00000606376.1_RNA|RNF219-AS1_ENST00000607220.1_RNA|RNF219-AS1_ENST00000444769.3_RNA|RNF219-AS1_ENST00000606429.1_RNA|RNF219-AS1_ENST00000560584.2_RNA|RNF219-AS1_ENST00000606124.1_RNA|RP11-52L5.6_ENST00000607269.1_RNA|RNF219-AS1_ENST00000560209.2_RNA|RNF219-AS1_ENST00000430549.2_RNA|RNF219-AS1_ENST00000607205.1_RNA	NM_006237.3	NP_006228.3	Q01851	PO4F1_HUMAN	POU class 4 homeobox 1	404					axonogenesis (GO:0007409)|cell migration in hindbrain (GO:0021535)|central nervous system neuron differentiation (GO:0021953)|habenula development (GO:0021986)|innervation (GO:0060384)|mesoderm development (GO:0007498)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate specification (GO:0048665)|peripheral nervous system neuron development (GO:0048935)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proprioception involved in equilibrioception (GO:0051355)|regulation of neurogenesis (GO:0050767)|sensory system development (GO:0048880)|suckling behavior (GO:0001967)|synapse assembly (GO:0007416)|transcription from RNA polymerase II promoter (GO:0006366)|trigeminal nerve development (GO:0021559)|ventricular compact myocardium morphogenesis (GO:0003223)	neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)	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)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(5)|ovary(1)	16		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.129)		TCTCTGGTTGCAAAACCACAC	0.597																																					p.C404F	Melanoma(109;347 2166 14574 42843)|Ovarian(81;1394 1854 22417 48351)	Atlas-SNP	.											.	POU4F1	43	.	0			c.G1211T						PASS	.						91	88	89					13																	79175599		2203	4300	6503	SO:0001583	missense	5457	exon2			TGGTTGCAAAACC	X64624	CCDS31996.1	13q31.1	2011-06-20	2007-07-13		ENSG00000152192	ENSG00000152192		"Homeoboxes / POU class"	9218	protein-coding gene	gene with protein product		601632	"POU domain class 4, transcription factor 1"	BRN3A		1357630	Standard	NM_006237		Approved	RDC-1	uc001vkv.3	Q01851	OTTHUMG00000017119	ENST00000377208.5:c.1211G>T	chr13.hg19:g.79175599C>A	ENSP00000366413:p.Cys404Phe	48.0	0.0	.		43.0	12.0	.	NM_006237	Q14986|Q15318|Q5T227	Missense_Mutation	SNP	ENST00000377208.5	hg19	CCDS31996.1	.	.	.	.	.	.	.	.	.	.	C	16.94	3.260312	0.59431	.	.	ENSG00000152192	ENST00000377208	D	0.96232	-3.95	4.35	4.35	0.52113	Homeodomain-related (1);Homeobox (3);POU (1);Homeodomain-like (1);Homeobox, conserved site (1);	0.053289	0.85682	U	0.000000	D	0.98239	0.9417	M	0.87758	2.905	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.99560	1.0968	10	0.87932	D	0	.	16.8947	0.86097	0.0:1.0:0.0:0.0	.	404	Q01851	PO4F1_HUMAN	F	404	ENSP00000366413:C404F	ENSP00000366413:C404F	C	-	2	0	POU4F1	78073600	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.629000	0.83207	2.159000	0.67721	0.499000	0.49734	TGC	.	.	.	none		0.597	POU4F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045360.3			A	79175599	C	A	79175599	3	1	223	1	0	0	0	0	1	0	0	0	12285	710	25	4	52	4	POU4F1	13	79175599	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10		79175599	35994279	39	13548											
CTAGE5	4253	hgsc.bcm.edu	37	chr14	39815176	39815179	+	Frame_Shift_Del	DEL	CTGT	CTGT	-																															tttgttctaattctggtagaCtgtctggaccagcagaactc																										TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	CTGT	CTGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr14:39815176_39815179delCTGT	ENST00000280083.3	+	21	2214_2217	c.1900_1903delCTGT	c.(1900-1905)ctgtctfs	p.LS634fs	CTAGE5_ENST00000557038.1_Frame_Shift_Del_p.LS554fs|CTAGE5_ENST00000396165.4_Frame_Shift_Del_p.LS605fs|CTAGE5_ENST00000553352.1_Frame_Shift_Del_p.LS605fs|CTAGE5_ENST00000348007.3_Frame_Shift_Del_p.LS591fs|CTAGE5_ENST00000341502.5_Frame_Shift_Del_p.LS634fs|RP11-407N17.3_ENST00000603904.1_Frame_Shift_Del_p.LS605fs|CTAGE5_ENST00000341749.3_Frame_Shift_Del_p.LS622fs|RP11-407N17.3_ENST00000553728.1_Frame_Shift_Del_p.LS1169fs|CTAGE5_ENST00000396158.2_Frame_Shift_Del_p.LS639fs|CTAGE5_ENST00000556148.1_Frame_Shift_Del_p.LS559fs			O15320	CTGE5_HUMAN	CTAGE family, member 5	634	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)		TTCTGGTAGACTGTCTGGACCAGC	0.353																																					p.638_639del		Pindel	.											.	CTAGE5	75	.	0			c.1914_1917del						PASS	.																																			SO:0001589	frameshift_variant	4253	exon21			.	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.1900_1903delCTGT	chr14.hg19:g.39815176_39815179delCTGT	ENSP00000280083:p.Leu634fs	219.0	0.0	.		200.0	11.0	0.055	NM_001247989	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Frame_Shift_Del	DEL	ENST00000280083.3	hg19	CCDS9674.1																																																																																			.	.	.	none		0.353	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930		-	39815179	CTGT	-	39815176	7	5	223	1	0	1	0	1	0	0	0	0	3996	564	20	0	2013	0	CTAGE5	14	39815176	Frame_Shift_Del	DEL	CTGT	TCGA-MH-A562-01A-11D-A26P-10		39815176	67534364	40	13549											
DCAF5	8816	hgsc.bcm.edu	37	chr14	69521317	69521317	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgggttgtctttgtggctggTtcctgctctcccttcatctg	1	18	11	11	0	4	0	1	0	3	0	6	0	5	0	2	3	1	4	2	3	0	4			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr14:69521317T>C	ENST00000341516.5	-	9	2233	c.2086A>G	c.(2086-2088)Acc>Gcc	p.T696A	DCAF5_ENST00000556847.1_Missense_Mutation_p.T614A|DCAF5_ENST00000553293.1_5'Flank|DCAF5_ENST00000557386.1_Missense_Mutation_p.T695A|DCAF5_ENST00000554215.1_Missense_Mutation_p.T614A	NM_001284206.1|NM_001284207.1|NM_003861.2	NP_001271135.1|NP_001271136.1|NP_003852.1	Q96JK2	DCAF5_HUMAN	DDB1 and CUL4 associated factor 5	696					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|mitochondrion (GO:0005739)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|upper_aerodigestive_tract(2)	29						TTGTGGCTGGTTCCTGCTCTC	0.527																																					p.T696A		Atlas-SNP	.											.	DCAF5	67	.	0			c.A2086G						PASS	.						110	118	115					14																	69521317		2203	4300	6503	SO:0001583	missense	8816	exon9			GGCTGGTTCCTGC	AB058727	CCDS32106.1, CCDS61480.1, CCDS61481.1, CCDS73646.1	14q23-q24.1	2013-01-09	2009-07-17	2009-07-17				"WD repeat domain containing", "DDB1 and CUL4 associated factors"	20224	protein-coding gene	gene with protein product		603812	"WD repeat domain 22"	WDR22		9740667, 9521877	Standard	NM_003861		Approved	BCRP2, D14S1461E, BCRG2, KIAA1824	uc001xkp.3	Q96JK2		ENST00000341516.5:c.2086A>G	chr14.hg19:g.69521317T>C	ENSP00000341351:p.Thr696Ala	60.0	0.0	.		68.0	21.0	.	NM_003861	B2RN31|G3V4J7|O60559|Q8N3V3|Q8N3V5	Missense_Mutation	SNP	ENST00000341516.5	hg19	CCDS32106.1	.	.	.	.	.	.	.	.	.	.	T	15.58	2.875191	0.51695	.	.	ENSG00000139990	ENST00000341516;ENST00000554215;ENST00000556847;ENST00000557386	T;T;T;T	0.71461	-0.57;-0.41;-0.41;0.08	4.99	3.83	0.44106	.	0.081881	0.51477	D	0.000095	T	0.56292	0.1975	L	0.29908	0.895	0.80722	D	1	P;P	0.37864	0.61;0.476	B;B	0.35114	0.196;0.096	T	0.53056	-0.8492	10	0.33141	T	0.24	-17.9216	11.9573	0.52988	0.0:0.0:0.1454:0.8546	.	695;696	G3V4J7;Q96JK2	.;DCAF5_HUMAN	A	696;614;614;695	ENSP00000341351:T696A;ENSP00000451551:T614A;ENSP00000452052:T614A;ENSP00000451845:T695A	ENSP00000341351:T696A	T	-	1	0	DCAF5	68591070	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.462000	0.53042	0.902000	0.36520	0.459000	0.35465	ACC	.	.	.	none		0.527	DCAF5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414806.2	NM_003861		C	69521317	T	C	69521317	3	2	223	1	0	0	0	0	1	0	0	0	4275	1725	60	3	746	3	DCAF5	14	69521317	Missense_Mutation	SNP	T	TCGA-MH-A562-01A-11D-A26P-10	29706141	69521317	37828223	41	13550											
IGDCC4	57722	hgsc.bcm.edu	37	chr15	65684246	65684246	+	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	ggcgccttctccgtcttgccCttccacactgctgcatagcc	4	11	8	18	2	2	0	0	0	2	0	4	0	3	0	5	1	4	2	5	1	1	4			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr15:65684246C>G	ENST00000352385.2	-	12	2405	c.2196G>C	c.(2194-2196)aaG>aaC	p.K732N		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	732	Fibronectin type-III 3. {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						CCGTCTTGCCCTTCCACACTG	0.612																																					p.K732N		Atlas-SNP	.											.	IGDCC4	95	.	0			c.G2196C						PASS	.						122	120	121					15																	65684246		2201	4299	6500	SO:0001583	missense	57722	exon12			CTTGCCCTTCCAC		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.2196G>C	chr15.hg19:g.65684246C>G	ENSP00000319623:p.Lys732Asn	92.0	0.0	.		112.0	40.0	.	NM_020962	Q9HCE4	Missense_Mutation	SNP	ENST00000352385.2	hg19	CCDS10206.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.416366	0.83449	.	.	ENSG00000103742	ENST00000352385;ENST00000356152	T	0.59638	0.25	5.15	4.22	0.49857	Fibronectin, type III (2);	0.055747	0.64402	D	0.000002	T	0.62708	0.2450	L	0.59436	1.845	0.48135	D	0.999599	D	0.65815	0.995	P	0.52856	0.711	T	0.64799	-0.6322	10	0.49607	T	0.09	-22.1714	12.3562	0.55176	0.0:0.9194:0.0:0.0806	.	732	Q8TDY8	IGDC4_HUMAN	N	732;461	ENSP00000319623:K732N	ENSP00000319623:K732N	K	-	3	2	IGDCC4	63471299	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	1.066000	0.30604	2.406000	0.81754	0.561000	0.74099	AAG	.	.	.	none		0.612	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962		G	65684246	C	G	65684246	3	3	223	1	0	0	0	0	1	0	0	0	7576	680	24	4	1592	4	IGDCC4	15	65684246	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10		65684246	36847146	42	13551											
SGK269	79834	hgsc.bcm.edu	37	chr15	77472613	77472613	+	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	acatttggtccagttccactAgtaattagttctactttagg	10	16	7	8	0	1	0	0	0	1	0	3	0	3	0	2	2	1	3	2	2	5	9			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr15:77472613A>T	ENST00000560626.2	-	4	2131	c.1656T>A	c.(1654-1656)acT>acA	p.T552T	PEAK1_ENST00000558305.1_Silent_p.T552T|PEAK1_ENST00000312493.4_Silent_p.T552T			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	552					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										CAGTTCCACTAGTAATTAGTT	0.413																																					p.T552T		Atlas-SNP	.											.	.	.	.	0			c.T1656A						PASS	.						217	198	204					15																	77472613		1881	4115	5996	SO:0001819	synonymous_variant	0	exon5			TCCACTAGTAATT		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.1656T>A	chr15.hg19:g.77472613A>T		140.0	0.0	.		110.0	35.0	.	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Silent	SNP	ENST00000560626.2	hg19	CCDS42062.1																																																																																			.	.	.	none		0.413	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3			T	77472613	A	T	77472613	2	4	223	1	0	0	0	0	0	0	0	1	14224	407	15	5		5	SGK269	15	77472613	Silent	SNP	A	TCGA-MH-A562-01A-11D-A26P-10	11788367	77472613	25058779	43	13552											
CARHSP1	23589	hgsc.bcm.edu	37	chr16	8953055	8953055	+	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	aggtcctcgtccggcgagtgGgcagtgggcttgggaccacg	5	7	18	11	4	0	0	0	0	0	0	3	2	2	1	3	5	0	2	3	5	0	1			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr16:8953055G>A	ENST00000396593.2	-	2	490	c.131C>T	c.(130-132)cCc>cTc	p.P44L	CARHSP1_ENST00000562843.1_Missense_Mutation_p.P44L|RP11-77H9.2_ENST00000565934.1_RNA|CARHSP1_ENST00000567554.1_Missense_Mutation_p.P44L|CARHSP1_ENST00000311052.5_Missense_Mutation_p.P44L|CARHSP1_ENST00000567626.1_5'Flank|CARHSP1_ENST00000561530.1_Missense_Mutation_p.P44L	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	44					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						CCGGCGAGTGGGCAGTGGGCT	0.652																																					p.P44L		Atlas-SNP	.											CARHSP1,NS,carcinoma,0,2	CARHSP1	12	.	0			c.C131T						PASS	.						27	23	25					16																	8953055		2195	4300	6495	SO:0001583	missense	23589	exon2			CGAGTGGGCAGTG	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.131C>T	chr16.hg19:g.8953055G>A	ENSP00000379838:p.Pro44Leu	110.0	0.0	.		112.0	42.0	.	NM_001042476	B2R4C3|D3DUF5|Q2YDX5|Q9BQ53	Missense_Mutation	SNP	ENST00000396593.2	hg19	CCDS10537.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.292618	0.80914	.	.	ENSG00000153048	ENST00000396593;ENST00000311052	.	.	.	5.35	4.38	0.52667	.	0.000000	0.85682	D	0.000000	T	0.77811	0.4186	M	0.85299	2.745	0.80722	D	1	D	0.89917	1.0	D	0.64877	0.93	T	0.77389	-0.2606	9	0.19590	T	0.45	-3.558	14.7061	0.69191	0.0:0.1461:0.8539:0.0	.	44	Q9Y2V2	CHSP1_HUMAN	L	44	.	ENSP00000311847:P44L	P	-	2	0	CARHSP1	8860556	1.000000	0.71417	0.996000	0.52242	0.993000	0.82548	9.057000	0.93889	1.221000	0.43506	0.563000	0.77884	CCC	.	.	.	none		0.652	CARHSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251902.1	NM_014316		A	8953055	G	A	8953055	3	1	223	1	0	0	0	0	1	0	0	0	2655	1232	43	2	324	2	CARHSP1	16	8953055	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10		8953055	81401698	44	13553											
IL4R	3566	hgsc.bcm.edu	37	chr16	27374134	27374134	+	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	aacctgacttgcacagagacGcccctcgtcatcgcaggcaa	11	6	9	15	3	1	2	1	1	0	1	3	3	1	2	3	1	2	3	3	1	2	1			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr16:27374134G>A	ENST00000395762.2	+	11	1720	c.1461G>A	c.(1459-1461)acG>acA	p.T487T	IL4R_ENST00000543915.2_Silent_p.T487T|IL4R_ENST00000170630.2_Silent_p.T487T|IL4R_ENST00000380922.3_Silent_p.T472T	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	487	Required for IRS1 activation and IL4- induced cell growth.				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						GCACAGAGACGCCCCTCGTCA	0.642																																					p.T487T		Atlas-SNP	.											.	IL4R	70	.	0			c.G1461A						PASS	.						91	94	93					16																	27374134		2197	4300	6497	SO:0001819	synonymous_variant	3566	exon11			AGAGACGCCCCTC	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.1461G>A	chr16.hg19:g.27374134G>A		86.0	0.0	.		117.0	40.0	.	NM_000418	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Silent	SNP	ENST00000395762.2	hg19	CCDS10629.1																																																																																			.	.	.	none		0.642	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4			A	27374134	G	A	27374134	2	1	223	1	0	0	0	0	0	0	0	1	7705	1074	38	1		1	IL4R	16	27374134	Silent	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	18421079	27374134	62980619	45	13554											
SETD1A	9739	hgsc.bcm.edu	37	chr16	30970101	30970101	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaggccccgagcttccagTggcggaactacaagctcatc	11	6	11	13	2	1	1	1	0	0	1	3	3	2	2	3	3	4	2	3	3	4	2			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr16:30970101T>C	ENST00000262519.8	+	2	735	c.49T>C	c.(49-51)Tgg>Cgg	p.W17R		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	17					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						GAGCTTCCAGTGGCGGAACTA	0.557																																					p.W17R		Atlas-SNP	.											.	SETD1A	143	.	0			c.T49C						PASS	.						109	105	107					16																	30970101		2197	4300	6497	SO:0001583	missense	9739	exon2			TTCCAGTGGCGGA	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.49T>C	chr16.hg19:g.30970101T>C	ENSP00000262519:p.Trp17Arg	136.0	0.0	.		152.0	46.0	.	NM_014712	A6NP62|Q6PIF3|Q8TAJ6	Missense_Mutation	SNP	ENST00000262519.8	hg19	CCDS32435.1	.	.	.	.	.	.	.	.	.	.	T	17.44	3.389372	0.61956	.	.	ENSG00000099381	ENST00000262519;ENST00000452917;ENST00000449974	D	0.94828	-3.53	5.1	5.1	0.69264	.	0.000000	0.64402	U	0.000001	D	0.96494	0.8856	M	0.68593	2.085	0.58432	D	0.999997	D	0.89917	1.0	D	0.87578	0.998	D	0.96642	0.9475	10	0.56958	D	0.05	.	13.8869	0.63714	0.0:0.0:0.0:1.0	.	17	O15047	SET1A_HUMAN	R	17	ENSP00000262519:W17R	ENSP00000262519:W17R	W	+	1	0	SETD1A	30877602	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.599000	0.82757	1.920000	0.55613	0.533000	0.62120	TGG	.	.	.	none		0.557	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712		C	30970101	T	C	30970101	3	2	223	1	0	0	0	0	1	0	0	0	14143	1696	59	3	51	3	SETD1A	16	30970101	Missense_Mutation	SNP	T	TCGA-MH-A562-01A-11D-A26P-10	3595967	30970101	59384652	46	13555											
SALL1	6299	hgsc.bcm.edu	37	chr16	51171349	51171349	+	Missense_Mutation	SNP	A	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	tgccgccaaatccttctggaAcatttctgggaacttgacgg	9	11	10	11	2	2	1	0	1	2	0	3	3	3	3	3	3	3	0	3	3	3	3			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr16:51171349A>C	ENST00000251020.4	-	3	3682	c.3649T>G	c.(3649-3651)Ttc>Gtc	p.F1217V	SALL1_ENST00000566102.1_3'UTR|SALL1_ENST00000541611.1_Missense_Mutation_p.F40V|SALL1_ENST00000440970.1_Missense_Mutation_p.F1120V	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	1217					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)			TCCTTCTGGAACATTTCTGGG	0.562																																					p.F1217V	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.T3649G						PASS	.						54	51	52					16																	51171349		2198	4300	6498	SO:0001583	missense	6299	exon3			TCTGGAACATTTC	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.3649T>G	chr16.hg19:g.51171349A>C	ENSP00000251020:p.Phe1217Val	133.0	0.0	.		116.0	29.0	.	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	hg19	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	A	15.45	2.837676	0.50951	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559;ENST00000541611	T;T;T	0.47869	3.22;3.21;0.83	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.66752	0.2821	M	0.76170	2.325	0.80722	D	1	D;B	0.76494	0.999;0.372	D;B	0.78314	0.991;0.083	T	0.64188	-0.6466	10	0.20046	T	0.44	.	15.6652	0.77225	1.0:0.0:0.0:0.0	.	1217;40	Q9NSC2;F5H733	SALL1_HUMAN;.	V	1217;1120;1181;40	ENSP00000251020:F1217V;ENSP00000407914:F1120V;ENSP00000442827:F40V	ENSP00000251020:F1217V	F	-	1	0	SALL1	49728850	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.311000	0.96282	2.104000	0.64026	0.523000	0.50628	TTC	.	.	.	none		0.562	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		C	51171349	A	C	51171349	3	2	223	1	0	0	0	0	1	0	0	0	13823	43	2	5	329	5	SALL1	16	51171349	Missense_Mutation	SNP	A	TCGA-MH-A562-01A-11D-A26P-10	20201248	51171349	39183404	47	13556											
RANBP10	57610	hgsc.bcm.edu	37	chr16	67761787	67761787	+	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	ccccgcagagctgccgccgaGgatgcctgtcatctgcatcc	6	7	11	17	3	2	1	1	0	1	1	3	3	3	2	6	1	4	3	6	1	0	0			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr16:67761787G>T	ENST00000317506.3	-	12	1602	c.1487C>A	c.(1486-1488)cCt>cAt	p.P496H	RANBP10_ENST00000536251.1_Missense_Mutation_p.P267H|RANBP10_ENST00000411657.2_Missense_Mutation_p.P409H|RANBP10_ENST00000448631.2_Missense_Mutation_p.P470H|RANBP10_ENST00000602677.1_Missense_Mutation_p.P526H	NM_020850.1	NP_065901.1	Q6VN20	RBP10_HUMAN	RAN binding protein 10	496					microtubule cytoskeleton organization (GO:0000226)	cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)	Ran guanyl-nucleotide exchange factor activity (GO:0005087)			endometrium(5)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|skin(1)	23		Acute lymphoblastic leukemia(13;4.34e-06)|all_hematologic(13;0.000643)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00522)|Epithelial(162;0.025)|all cancers(182;0.157)		CTGCCGCCGAGGATGCCTGTC	0.622																																					p.P496H		Atlas-SNP	.											.	RANBP10	56	.	0			c.C1487A						PASS	.						34	31	32					16																	67761787		2198	4300	6498	SO:0001583	missense	57610	exon12			CGCCGAGGATGCC	AB040897	CCDS32469.1	16q22	2008-02-05				ENSG00000141084			29285	protein-coding gene	gene with protein product		614031				14684163	Standard	NM_020850		Approved	KIAA1464	uc002eud.3	Q6VN20		ENST00000317506.3:c.1487C>A	chr16.hg19:g.67761787G>T	ENSP00000316589:p.Pro496His	118.0	0.0	.		108.0	32.0	.	NM_020850	A4FTY2|B4DID0|B4DQH9|E7EW27|Q9P264	Missense_Mutation	SNP	ENST00000317506.3	hg19	CCDS32469.1	.	.	.	.	.	.	.	.	.	.	G	12.84	2.057947	0.36277	.	.	ENSG00000141084	ENST00000317506;ENST00000448631;ENST00000536251;ENST00000411657	.	.	.	5.93	5.93	0.95920	.	0.631540	0.17547	N	0.170307	T	0.69006	0.3063	M	0.62723	1.935	0.80722	D	1	P;B;B	0.37573	0.6;0.006;0.012	P;B;B	0.46110	0.504;0.007;0.02	T	0.67413	-0.5677	9	0.48119	T	0.1	-12.1716	15.4231	0.75028	0.0:0.1386:0.8614:0.0	.	409;470;496	B4DID0;B4DQH9;Q6VN20	.;.;RBP10_HUMAN	H	496;470;267;409	.	ENSP00000316589:P496H	P	-	2	0	RANBP10	66319288	0.996000	0.38824	0.997000	0.53966	0.794000	0.44872	4.807000	0.62576	2.814000	0.96858	0.563000	0.77884	CCT	.	.	.	none		0.622	RANBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467896.1	NM_020850		T	67761787	G	T	67761787	3	4	223	1	0	0	0	0	1	0	0	0	13039	1000	35	4	387	4	RANBP10	16	67761787	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	16590438	67761787	22592966	48	13557											
CDK10	8558	hgsc.bcm.edu	37	chr16	89760632	89760632	+	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	accacgcagaccaccagcatCgacatgtggtgaggagatac	13	5	11	12	2	0	3	0	1	0	2	1	5	0	3	3	2	2	2	3	2	1	1			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr16:89760632C>T	ENST00000353379.7	+	9	703	c.660C>T	c.(658-660)atC>atT	p.I220I	CDK10_ENST00000331006.8_Silent_p.I173I|CDK10_ENST00000505473.1_Silent_p.I149I	NM_001098533.2|NM_001160367.1|NM_052988.4	NP_001092003.2|NP_001153839.1|NP_443714.3	Q15131	CDK10_HUMAN	cyclin-dependent kinase 10	220	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of cell proliferation (GO:0008285)|traversing start control point of mitotic cell cycle (GO:0007089)		ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			ovary(1)	1		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0276)		CCACCAGCATCGACATGTGGT	0.632																																					p.I220I		Atlas-SNP	.											.	CDK10	26	.	0			c.C660T						PASS	.						102	78	86					16																	89760632		2198	4300	6498	SO:0001819	synonymous_variant	8558	exon9			CAGCATCGACATG	L33264	CCDS10984.2, CCDS32514.1, CCDS32514.2	16q24.3	2011-11-08	2007-11-21		ENSG00000185324	ENSG00000185324		"Cyclin-dependent kinases"	1770	protein-coding gene	gene with protein product		603464	"cyclin-dependent kinase (CDC2-like) 10"			8208557, 8084611	Standard	NM_052988		Approved	PISSLRE	uc010cio.3	Q15131	OTTHUMG00000138049	ENST00000353379.7:c.660C>T	chr16.hg19:g.89760632C>T		169.0	0.0	.		158.0	65.0	.	NM_052988	A8K370|A8K8I6|A8MXU6|B3KQJ3|B7Z420|D3DX82|D3DX83|Q0VGZ7|Q15130|Q6PJC0	Silent	SNP	ENST00000353379.7	hg19	CCDS10984.2																																																																																			.	.	.	none		0.632	CDK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269925.2			T	89760632	C	T	89760632	2	4	223	1	0	0	0	0	0	0	0	1	3127	874	31	1		1	CDK10	16	89760632	Silent	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	21998845	89760632	594121	49	13558											
CAMTA2	23125	hgsc.bcm.edu	37	chr17	4877742	4877742	+	Missense_Mutation	SNP	T	T	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	agctgctgcgatctctgccaTccgcttctccatctgctcca	5	12	7	17	2	3	0	0	0	3	0	7	1	5	0	4	0	5	4	4	0	0	1			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr17:4877742T>G	ENST00000348066.3	-	12	2077	c.1954A>C	c.(1954-1956)Atg>Ctg	p.M652L	CAMTA2_ENST00000572543.1_Missense_Mutation_p.M657L|CAMTA2_ENST00000361571.5_Missense_Mutation_p.M651L|CAMTA2_ENST00000381311.5_Missense_Mutation_p.M654L|CAMTA2_ENST00000414043.3_Missense_Mutation_p.M675L|RP5-1050D4.2_ENST00000430920.1_RNA|CAMTA2_ENST00000358183.4_Missense_Mutation_p.M652L	NM_015099.3	NP_055914.2	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	652					cardiac muscle hypertrophy in response to stress (GO:0014898)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						ATCTCTGCCATCCGCTTCTCC	0.597																																					p.M675L		Atlas-SNP	.											.	CAMTA2	93	.	0			c.A2023C						PASS	.						155	119	132					17																	4877742		2203	4300	6503	SO:0001583	missense	23125	exon12			CTGCCATCCGCTT	AB020716	CCDS11063.1, CCDS54071.1, CCDS54072.1, CCDS54073.1	17p13.3	2004-09-01			ENSG00000108509	ENSG00000108509			18807	protein-coding gene	gene with protein product		611508				11925432	Standard	NM_015099		Approved	KIAA0909	uc010cku.2	O94983	OTTHUMG00000099417	ENST00000348066.3:c.1954A>C	chr17.hg19:g.4877742T>G	ENSP00000321813:p.Met652Leu	153.0	0.0	.		193.0	89.0	.	NM_001171167	B9EGL0|D3DTL5|E7EWU5|Q7Z6M8|Q8N3V0|Q8NDG4|Q96G17	Missense_Mutation	SNP	ENST00000348066.3	hg19	CCDS11063.1	.	.	.	.	.	.	.	.	.	.	T	16.40	3.111402	0.56398	.	.	ENSG00000108509	ENST00000414043;ENST00000381311;ENST00000361571;ENST00000358183;ENST00000348066	T;T;T;T;T	0.27557	2.87;1.91;1.66;1.91;1.69	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.30885	0.0779	N	0.11560	0.145	0.44454	D	0.997389	B;B;P;B;P	0.43024	0.077;0.077;0.471;0.34;0.798	B;B;P;P;P	0.60236	0.045;0.152;0.65;0.448;0.871	T	0.11891	-1.0569	10	0.13108	T	0.6	-18.4138	13.2241	0.59905	0.0:0.0:0.0:1.0	.	628;675;654;652;651	B7ZM30;E7EWU5;O94983-3;O94983;O94983-4	.;.;.;CMTA2_HUMAN;.	L	675;654;651;652;652	ENSP00000412886:M675L;ENSP00000370712:M654L;ENSP00000354828:M651L;ENSP00000350910:M652L;ENSP00000321813:M652L	ENSP00000321813:M652L	M	-	1	0	CAMTA2	4818466	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.777000	0.85628	2.232000	0.73038	0.482000	0.46254	ATG	.	.	.	none		0.597	CAMTA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216876.1	NM_015099		G	4877742	T	G	4877742	3	3	223	1	0	0	0	0	1	0	0	0	2616	1435	50	5	1752	5	CAMTA2	17	4877742	Missense_Mutation	SNP	T	TCGA-MH-A562-01A-11D-A26P-10		4877742	76317468	50	13559											
EZH1	2145	hgsc.bcm.edu	37	chr17	40880917	40880920	+	Frame_Shift_Del	DEL	AGTA	AGTA	-																															agatttcacttttcttttccAgtaagtgatacatttggagg																										TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	AGTA	AGTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr17:40880917_40880920delAGTA	ENST00000428826.2	-	3	161_164	c.40_43delTACT	c.(40-45)tactggfs	p.YW14fs	EZH1_ENST00000590078.1_Intron|EZH1_ENST00000592743.1_Frame_Shift_Del_p.YW14fs|EZH1_ENST00000435174.1_5'UTR|EZH1_ENST00000585893.1_Frame_Shift_Del_p.YW14fs|EZH1_ENST00000415827.2_Frame_Shift_Del_p.YW14fs			Q92800	EZH1_HUMAN	enhancer of zeste 1 polycomb repressive complex 2 subunit	14					anatomical structure morphogenesis (GO:0009653)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)			breast(1)|endometrium(4)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	27		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0784)		TTTCTTTTCCAGTAAGTGATACAT	0.373																																					p.14_15del		Atlas-Indel,Pindel	.											.	EZH1	62	.	0			c.41_44del						PASS	.																																			SO:0001589	frameshift_variant	2145	exon3			.		CCDS32659.1	17q21.1-q21.3	2014-05-28	2014-05-28			ENSG00000108799		"Chromatin-modifying enzymes / K-methyltransferases"	3526	protein-coding gene	gene with protein product		601674	"enhancer of zeste (Drosophila) homolog 1", "enhancer of zeste homolog 1 (Drosophila)"			8921387	Standard	NM_001991		Approved	KIAA0388, KMT6B	uc002iaz.3	Q92800		ENST00000428826.2:c.40_43delTACT	chr17.hg19:g.40880917_40880920delAGTA	ENSP00000404658:p.Tyr14fs	78.0	0.0	0		93.0	26.0	0.27957	NM_001991	A6NCH6|B4DIJ1|B4DIZ7|B4DSS2|B4E3R7|O43287|Q14459|Q53XP3	Frame_Shift_Del	DEL	ENST00000428826.2	hg19	CCDS32659.1																																																																																			.	.	.	none		0.373	EZH1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452347.1	NM_001991		-	40880920	AGTA	-	40880917	7	5	223	1	0	1	0	1	0	0	0	0	5335	188	7	0	2276	0	EZH1	17	40880917	Frame_Shift_Del	DEL	AGTA	TCGA-MH-A562-01A-11D-A26P-10	36003175	40880917	40314293	51	13560											
SCRN2	90507	hgsc.bcm.edu	37	chr17	45916860	45916860	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctgtctccagcacccacGcctcagtgcggtcagccagc	7	6	10	18	2	3	0	2	0	1	0	4	0	3	0	4	1	5	2	4	1	0	0			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr17:45916860G>A	ENST00000290216.9	-	4	631	c.506C>T	c.(505-507)gCg>gTg	p.A169V	SCRN2_ENST00000584123.1_Missense_Mutation_p.A177V|SCRN2_ENST00000407215.3_Missense_Mutation_p.A169V	NM_001145023.1|NM_138355.3	NP_001138495.1|NP_612364.2	Q96FV2	SCRN2_HUMAN	secernin 2	169						extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)			cervix(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	14						CAGCACCCACGCCTCAGTGCG	0.612																																					p.A169V		Atlas-SNP	.											.	SCRN2	35	.	0			c.C506T						PASS	.						78	72	74					17																	45916860		2203	4300	6503	SO:0001583	missense	90507	exon4			ACCCACGCCTCAG	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.506C>T	chr17.hg19:g.45916860G>A	ENSP00000290216:p.Ala169Val	170.0	0.0	.		220.0	108.0	.	NM_138355	A8K3N1|B7Z8S7|E9PBV5|Q96AC3|Q9BU04	Missense_Mutation	SNP	ENST00000290216.9	hg19	CCDS11519.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.593412	0.86953	.	.	ENSG00000141295	ENST00000290216;ENST00000407215	T;T	0.17370	2.28;2.28	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.44705	0.1306	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	0.999;0.999;0.999	T	0.42207	-0.9465	10	0.87932	D	0	-27.8264	17.8079	0.88607	0.0:0.0:1.0:0.0	.	169;169;169	E9PBV5;Q96FV2;B7Z8S7	.;SCRN2_HUMAN;.	V	169	ENSP00000290216:A169V;ENSP00000383935:A169V	ENSP00000290216:A169V	A	-	2	0	SCRN2	43271859	1.000000	0.71417	0.935000	0.37517	0.396000	0.30629	9.756000	0.98918	2.504000	0.84457	0.561000	0.74099	GCG	.	.	.	none		0.612	SCRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441383.1	NM_138355		A	45916860	G	A	45916860	3	1	223	1	0	0	0	0	1	0	0	0	13952	1087	38	1	809	1	SCRN2	17	45916860	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	5035943	45916860	35278350	52	13561											
NXPH3	11248	hgsc.bcm.edu	37	chr17	47656051	47656051	+	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	ggccccgggtgcctcggaagCggggccacatctcacctaag	7	5	14	15	3	1	0	1	0	1	0	3	1	1	1	5	5	2	0	5	5	2	1			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr17:47656051C>T	ENST00000328741.5	+	2	510	c.148C>T	c.(148-150)Cgg>Tgg	p.R50W	RP5-1029K10.4_ENST00000503624.1_RNA|NXPH3_ENST00000513748.1_Missense_Mutation_p.R50W	NM_007225.2	NP_009156.2	O95157	NXPH3_HUMAN	neurexophilin 3	50	II.				neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				endometrium(2)|large_intestine(3)|lung(4)|pancreas(1)|skin(2)	12	all_cancers(4;7.45e-14)|Breast(4;1.08e-27)|all_epithelial(4;2.27e-17)					GCCTCGGAAGCGGGGCCACAT	0.677																																					p.R50W		Atlas-SNP	.											.	NXPH3	31	.	0			c.C148T						PASS	.						35	39	37					17																	47656051		2203	4299	6502	SO:0001583	missense	11248	exon2			CGGAAGCGGGGCC	AF043468	CCDS11550.1	17q	2008-07-03				ENSG00000182575			8077	protein-coding gene	gene with protein product		604636				9570794	Standard	NM_007225		Approved	NPH3	uc002ipa.3	O95157		ENST00000328741.5:c.148C>T	chr17.hg19:g.47656051C>T	ENSP00000329295:p.Arg50Trp	72.0	0.0	.		169.0	101.0	.	NM_007225	Q8NDC3|Q8TBF6|Q9ULR1	Missense_Mutation	SNP	ENST00000328741.5	hg19	CCDS11550.1	.	.	.	.	.	.	.	.	.	.	c	16.57	3.159520	0.57368	.	.	ENSG00000182575	ENST00000328741;ENST00000513748	.	.	.	4.55	3.56	0.40772	.	0.310331	0.31381	N	0.007749	T	0.34250	0.0891	N	0.08118	0	0.09310	N	1	D;D	0.89917	1.0;0.998	D;P	0.70935	0.971;0.834	T	0.07578	-1.0765	9	0.72032	D	0.01	-23.4594	7.973	0.30138	0.428:0.4299:0.1421:0.0	.	50;50	D6RGW2;O95157	.;NXPH3_HUMAN	W	50	.	ENSP00000329295:R50W	R	+	1	2	NXPH3	45011050	0.037000	0.19845	1.000000	0.80357	0.994000	0.84299	0.755000	0.26405	1.110000	0.41699	0.556000	0.70494	CGG	.	.	.	none		0.677	NXPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365143.1			T	47656051	C	T	47656051	3	4	223	1	0	0	0	0	1	0	0	0	10799	759	27	1	154	1	NXPH3	17	47656051	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	1739191	47656051	33539159	53	13562											
SCN4A	6329	hgsc.bcm.edu	37	chr17	62045582	62045582	+	Silent	SNP	C	C	T																															ggcgggggccagcgcacacaCttctgcctcaggtttcccat																										TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr17:62045582C>T	ENST00000435607.1	-	6	913	c.837G>A	c.(835-837)aaG>aaA	p.K279K	SCN4A_ENST00000578147.1_Silent_p.K279K	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	279					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)	AGCGCACACACTTCTGCCTCA	0.547																																					p.K279K		Atlas-SNP	.											.	SCN4A	205	.	0			c.G837A						PASS	.																																			SO:0001819	synonymous_variant	6329	exon6			CACACACTTCTGC	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.837G>A	chr17.hg19:g.62045582C>T		365.0	0.0	.		518.0	129.0	.	NM_000334	Q15478|Q16447|Q7Z6B1	Silent	SNP	ENST00000435607.1	hg19	CCDS45761.1																																																																																			.	.	.	none		0.547	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		T	62045582	C	T	62045582	2	4	223	1	0	0	0	0	0	0	0	1	13933	564	20	2		2	SCN4A	17	62045582	Silent	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	14389531	62045582	19149628	54	13563	137	2									
SCN4A	6329	hgsc.bcm.edu	37	chr17	62045585	62045585	+	Silent	SNP	C	C	T																															gggggccagcgcacacacttCtgcctcaggtttcccatgaa																										TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr17:62045585C>T	ENST00000435607.1	-	6	910	c.834G>A	c.(832-834)caG>caA	p.Q278Q	SCN4A_ENST00000578147.1_Silent_p.Q278Q	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	278					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)	GCACACACTTCTGCCTCAGGT	0.542																																					p.Q278Q		Atlas-SNP	.											.	SCN4A	205	.	0			c.G834A						PASS	.						136	140	139					17																	62045585		2180	4283	6463	SO:0001819	synonymous_variant	6329	exon6			ACACTTCTGCCTC	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.834G>A	chr17.hg19:g.62045585C>T		359.0	0.0	.		504.0	125.0	.	NM_000334	Q15478|Q16447|Q7Z6B1	Silent	SNP	ENST00000435607.1	hg19	CCDS45761.1																																																																																			.	.	.	none		0.542	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		T	62045585	C	T	62045585	2	4	223	1	0	0	0	0	0	0	0	1	13933	912	32	2		2	SCN4A	17	62045585	Silent	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	3	62045585	19149625	55	13564	137	2									
DENND1C	79958	hgsc.bcm.edu	37	chr19	6475944	6475944	+	Missense_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	aggacgcgtggacgcacgagGtcagctggggagcgatggcg	8	4	20	9	6	1	0	1	0	0	0	1	5	1	3	0	6	2	2	0	6	0	0			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr19:6475944G>A	ENST00000381480.2	-	11	795	c.683C>T	c.(682-684)aCc>aTc	p.T228I	DENND1C_ENST00000543576.1_Missense_Mutation_p.T184I|DENND1C_ENST00000591030.1_5'Flank	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	228	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(3)|kidney(3)|large_intestine(1)|lung(3)	10						GACGCACGAGGTCAGCTGGGG	0.672																																					p.T228I		Atlas-SNP	.											.	DENND1C	93	.	0			c.C683T						PASS	.						8	10	9					19																	6475944		2158	4249	6407	SO:0001583	missense	79958	exon11			CACGAGGTCAGCT	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.683C>T	chr19.hg19:g.6475944G>A	ENSP00000370889:p.Thr228Ile	4.0	0.0	.		8.0	6.0	.	NM_024898	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Missense_Mutation	SNP	ENST00000381480.2	hg19	CCDS45938.1	.	.	.	.	.	.	.	.	.	.	G	32	5.166750	0.94768	.	.	ENSG00000205744	ENST00000381480;ENST00000543576	T;T	0.13089	2.62;2.62	5.31	5.31	0.75309	DENN (3);	0.054596	0.64402	D	0.000001	T	0.47040	0.1424	M	0.90870	3.155	0.50171	D	0.999858	D	0.67145	0.996	D	0.79784	0.993	T	0.58211	-0.7676	10	0.87932	D	0	-9.2935	16.4592	0.84031	0.0:0.0:1.0:0.0	.	228	Q8IV53	DEN1C_HUMAN	I	228;184	ENSP00000370889:T228I;ENSP00000437805:T184I	ENSP00000370889:T228I	T	-	2	0	DENND1C	6426944	1.000000	0.71417	0.950000	0.38849	0.890000	0.51754	8.957000	0.93082	2.498000	0.84270	0.561000	0.74099	ACC	.	.	.	none		0.672	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898		A	6475944	G	A	6475944	3	1	223	1	0	0	0	0	1	0	0	0	4430	1261	44	2	1774	2	DENND1C	19	6475944	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10		6475944	52653039	56	13565											
CYP4F22	126410	hgsc.bcm.edu	37	chr19	15651480	15651480	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgaggcctggcttaaggcCaagcaggggaagaccttgga	10	5	16	10	1	0	1	0	0	0	1	0	4	0	3	4	6	1	2	4	6	3	2			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr19:15651480C>T	ENST00000269703.3	+	8	1090	c.891C>T	c.(889-891)gcC>gcT	p.A297A	CYP4F22_ENST00000601005.2_Silent_p.A297A	NM_173483.3	NP_775754.2	Q6NT55	CP4FN_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 22	297						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			endometrium(6)|large_intestine(9)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	37						GGCTTAAGGCCAAGCAGGGGA	0.652																																					p.A297A		Atlas-SNP	.											.	CYP4F22	74	.	0			c.C891T						PASS	.						52	47	49					19																	15651480		2203	4300	6503	SO:0001819	synonymous_variant	126410	exon8			TAAGGCCAAGCAG		CCDS12331.1	19p13.12	2013-11-11			ENSG00000171954	ENSG00000171954		"Cytochrome P450s"	26820	protein-coding gene	gene with protein product		611495				16436457	Standard	NM_173483		Approved	FLJ39501	uc002nbh.4	Q6NT55	OTTHUMG00000182451	ENST00000269703.3:c.891C>T	chr19.hg19:g.15651480C>T		98.0	0.0	.		102.0	23.0	.	NM_173483	Q8N8H4	Silent	SNP	ENST00000269703.3	hg19	CCDS12331.1																																																																																			.	.	.	none		0.652	CYP4F22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461338.2	NM_173483		T	15651480	C	T	15651480	2	4	223	1	0	0	0	0	0	0	0	1	4191	581	21	2		2	CYP4F22	19	15651480	Silent	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	9175536	15651480	43477503	57	13566											
CAPN12	147968	hgsc.bcm.edu	37	chr19	39226166	39226166	+	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	agagactgcaggtctgcgctGatcacgtcgtcgatctccct	7	10	11	13	4	3	2	1	1	2	1	6	4	3	2	1	1	2	2	1	1	0	0	rs267605468		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr19:39226166G>T	ENST00000328867.4	-	13	1910	c.1602C>A	c.(1600-1602)atC>atA	p.I534I	CTD-2540F13.2_ENST00000602255.1_RNA|CAPN12_ENST00000601953.1_Silent_p.I385I	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	534	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)			GGTCTGCGCTGATCACGTCGT	0.642																																					p.I534I		Atlas-SNP	.											.	CAPN12	43	.	0			c.C1602A						PASS	.						38	36	37					19																	39226166		2192	4295	6487	SO:0001819	synonymous_variant	147968	exon13			TGCGCTGATCACG	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.1602C>A	chr19.hg19:g.39226166G>T		89.0	0.0	.		75.0	26.0	.	NM_144691		Silent	SNP	ENST00000328867.4	hg19	CCDS12519.1																																																																																			.	.	.	none		0.642	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1			T	39226166	G	T	39226166	2	4	223	1	0	0	0	0	0	0	0	1	2627	1280	45	4		4	CAPN12	19	39226166	Silent	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	23574686	39226166	19902817	58	13567											
PSG5	5673	hgsc.bcm.edu	37	chr19	43689069	43689069	+	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	tgcattggaatatactgtttCtcgtccagtgtatgcaggcc	8	14	10	9	1	1	0	0	0	1	0	3	1	2	1	2	2	3	4	2	2	4	5			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr19:43689069C>A	ENST00000366175.3	-	2	425	c.295G>T	c.(295-297)Gaa>Taa	p.E99*	PSG5_ENST00000342951.6_Nonsense_Mutation_p.E99*|PSG5_ENST00000407356.1_Nonsense_Mutation_p.E99*|PSG5_ENST00000404580.1_Nonsense_Mutation_p.E99*|PSG5_ENST00000599812.1_Nonsense_Mutation_p.E99*|PSG5_ENST00000401992.1_5'UTR|PSG5_ENST00000407568.1_Nonsense_Mutation_p.E99*			Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	99	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(18)|prostate(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(69;0.00899)				TATACTGTTTCTCGTCCAGTG	0.438																																					p.E99X		Atlas-SNP	.											.	PSG5	58	.	0			c.G295T						PASS	.						331	309	317					19																	43689069		2203	4295	6498	SO:0001587	stop_gained	5673	exon2			CTGTTTCTCGTCC		CCDS12617.1	19q13.2	2013-01-29			ENSG00000204941	ENSG00000204941		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9522	protein-coding gene	gene with protein product	"pregnancy-specific beta-1 glycoprotein", "pregnancy-specific beta 1 glycoprotein"	176394				2735907	Standard	NM_002781		Approved	FL-NCA-3, PSG	uc002ovx.3	Q15238	OTTHUMG00000151539	ENST00000366175.3:c.295G>T	chr19.hg19:g.43689069C>A	ENSP00000382334:p.Glu99*	254.0	0.0	.		252.0	79.0	.	NM_002781	Q15239|Q96QJ1|Q9UQ75	Nonsense_Mutation	SNP	ENST00000366175.3	hg19	CCDS12617.1	.	.	.	.	.	.	.	.	.	.	N	17.25	3.342999	0.61073	.	.	ENSG00000204941	ENST00000366175;ENST00000407356;ENST00000407568;ENST00000342951;ENST00000404580;ENST00000401992	.	.	.	1.58	1.58	0.23477	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	6.6423	0.22917	0.0:1.0:0.0:0.0	.	.	.	.	X	99	.	ENSP00000344413:E99X	E	-	1	0	PSG5	48380909	0.000000	0.05858	0.161000	0.22692	0.021000	0.10359	-0.245000	0.08890	1.195000	0.43115	0.423000	0.28283	GAA	.	.	.	none		0.438	PSG5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323055.1	NM_002781		A	43689069	C	A	43689069	4	1	223	1	0	0	0	0	0	1	0	0	12668	922	32	4	728	4	PSG5	19	43689069	Nonsense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10	4462903	43689069	15439914	59	13568											
LILRB3	11025	hgsc.bcm.edu	37	chr19	54721052	54721052	+	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	tcagttgccttccgtctaagGgtcaagctgtgcagctgggc	6	11	13	11	1	3	0	2	0	1	0	4	0	4	0	2	2	4	4	2	2	2	3			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr19:54721052G>T	ENST00000391750.1	-	14	1942	c.1806C>A	c.(1804-1806)acC>acA	p.T602T	LILRB3_ENST00000469273.1_5'UTR|LILRA6_ENST00000419410.2_Silent_p.T603T|LILRB3_ENST00000424807.1_Silent_p.T602T|LILRA6_ENST00000391735.3_3'UTR|LILRB3_ENST00000346401.6_Silent_p.T614T|LILRA6_ENST00000440558.2_Silent_p.T602T|LILRB3_ENST00000245620.9_Silent_p.T603T|LILRB3_ENST00000407860.2_Silent_p.T619T|LILRA6_ENST00000270464.5_Silent_p.T603T			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	602					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)		TCCGTCTAAGGGTCAAGCTGT	0.632																																					p.T603T		Atlas-SNP	.											.	LILRB3	67	.	0			c.C1809A						PASS	.						104	105	105					19																	54721052		2202	4300	6502	SO:0001819	synonymous_variant	11025	exon13			TCTAAGGGTCAAG	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.1806C>A	chr19.hg19:g.54721052G>T		180.0	0.0	.		189.0	101.0	.	NM_001081450	C9J1P3|C9JIP1|O15471|Q86U49	Silent	SNP	ENST00000391750.1	hg19	CCDS33105.1																																																																																			.	.	.	none		0.632	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864		T	54721052	G	T	54721052	2	4	223	1	0	0	0	0	0	0	0	1	8799	1219	43	4		4	LILRB3	19	54721052	Silent	SNP	G	TCGA-MH-A562-01A-11D-A26P-10	11031983	54721052	4407931	60	13569											
BCL2L1	598	hgsc.bcm.edu	37	chr20	30253881	30253881	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgttcccatagagttccacAaaagtatcctgcagggagag	12	10	10	9	0	0	2	0	0	0	2	3	3	3	2	3	1	1	4	3	1	4	5			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr20:30253881A>G	ENST00000307677.4	-	3	983	c.573T>C	c.(571-573)ttT>ttC	p.F191F	BCL2L1_ENST00000376055.4_Silent_p.F128F|BCL2L1_ENST00000420653.1_Silent_p.F191F|BCL2L1_ENST00000376062.2_Silent_p.F191F	NM_138578.1	NP_612815.1	Q07817	B2CL1_HUMAN	BCL2-like 1	191					apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|apoptotic process in bone marrow (GO:0071839)|cell proliferation (GO:0008283)|cellular process regulating host cell cycle in response to virus (GO:0060154)|cellular response to alkaloid (GO:0071312)|cellular response to amino acid stimulus (GO:0071230)|cellular response to gamma radiation (GO:0071480)|cytokinesis (GO:0000910)|endocytosis (GO:0006897)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fertilization (GO:0009566)|germ cell development (GO:0007281)|growth (GO:0040007)|hepatocyte apoptotic process (GO:0097284)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|male gonad development (GO:0008584)|mitochondrion morphogenesis (GO:0070584)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of autophagy (GO:0010507)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of execution phase of apoptosis (GO:1900118)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|ovarian follicle development (GO:0001541)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|release of cytochrome c from mitochondria (GO:0001836)|response to cycloheximide (GO:0046898)|response to cytokine (GO:0034097)|spermatogenesis (GO:0007283)|suppression by virus of host apoptotic process (GO:0019050)	Bcl-2 family protein complex (GO:0097136)|cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synapse (GO:0045202)	BH3 domain binding (GO:0051434)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(4)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	all_cancers(5;3.47e-06)|all_epithelial(3;1.83e-06)|Lung NSC(7;2.08e-06)|all_lung(7;3.63e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;2.97e-06)|all cancers(5;3.21e-05)|OV - Ovarian serous cystadenocarcinoma(3;0.00052)|Colorectal(19;0.0055)|COAD - Colon adenocarcinoma(19;0.0264)			AGAGTTCCACAAAAGTATCCT	0.567																																					p.F191F	Colon(51;693 1004 1401 20431 21026)	Atlas-SNP	.											.	BCL2L1	23	.	0			c.T573C						PASS	.						84	78	80					20																	30253881		2203	4300	6503	SO:0001819	synonymous_variant	598	exon3			TTCCACAAAAGTA	Z23115	CCDS13188.1, CCDS13189.1	20q11.21	2014-03-07			ENSG00000171552	ENSG00000171552		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	992	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 52"	600039				8358789	Standard	NM_001191		Approved	BCLX, BCL2L, Bcl-X, bcl-xL, bcl-xS, PPP1R52	uc002wwl.3	Q07817	OTTHUMG00000032192	ENST00000307677.4:c.573T>C	chr20.hg19:g.30253881A>G		84.0	0.0	.		137.0	71.0	.	NM_138578	E1P5L6|Q5CZ89|Q5TE65|Q92976	Silent	SNP	ENST00000307677.4	hg19	CCDS13189.1																																																																																			.	.	.	none		0.567	BCL2L1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078575.1	NM_138578		G	30253881	A	G	30253881	2	3	223	1	0	0	0	0	0	0	0	1	1367	127	5	3		3	BCL2L1	20	30253881	Silent	SNP	A	TCGA-MH-A562-01A-11D-A26P-10		30253881	32771639	61	13570											
ADAMTS5	11096	hgsc.bcm.edu	37	chr21	28305272	28305272	+	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	ttctgggagcagggttattaCagtgacgataggcaaactgc	11	10	13	7	1	1	1	0	1	1	0	1	3	1	2	0	3	4	3	0	3	4	4			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr21:28305272C>G	ENST00000284987.5	-	5	1902	c.1781G>C	c.(1780-1782)tGt>tCt	p.C594S	AP001601.2_ENST00000426771.1_RNA	NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	594	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				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						AGGGTTATTACAGTGACGATA	0.567																																					p.C594S	Esophageal Squamous(53;683 1080 10100 14424 45938)	Atlas-SNP	.											.	ADAMTS5	184	.	0			c.G1781C						PASS	.						152	105	121					21																	28305272		2203	4300	6503	SO:0001583	missense	11096	exon5			TTATTACAGTGAC	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.1781G>C	chr21.hg19:g.28305272C>G	ENSP00000284987:p.Cys594Ser	163.0	0.0	.		198.0	57.0	.	NM_007038	Q52LV4|Q9UKP2	Missense_Mutation	SNP	ENST00000284987.5	hg19	CCDS13579.1	.	.	.	.	.	.	.	.	.	.	C	33	5.248311	0.95305	.	.	ENSG00000154736	ENST00000284987	T	0.69040	-0.37	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	D	0.91778	0.7399	H	0.99922	4.955	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.95071	0.8204	10	0.87932	D	0	.	20.5666	0.99351	0.0:1.0:0.0:0.0	.	594	Q9UNA0	ATS5_HUMAN	S	594	ENSP00000284987:C594S	ENSP00000284987:C594S	C	-	2	0	ADAMTS5	27227143	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.487000	0.81328	2.854000	0.98071	0.655000	0.94253	TGT	.	.	.	none		0.567	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1			G	28305272	C	G	28305272	3	3	223	1	0	0	0	0	1	0	0	0	269	478	17	4	1027	4	ADAMTS5	21	28305272	Missense_Mutation	SNP	C	TCGA-MH-A562-01A-11D-A26P-10		28305272	19824623	62	13571											
SEZ6L	23544	hgsc.bcm.edu	37	chr22	26761491	26761491	+	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	gaccatccgctgcatcctggGacagccatcccactggaacg	9	6	10	16	2	0	0	0	0	0	0	3	3	3	2	5	2	3	2	5	2	1	0			TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chr22:26761491G>A	ENST00000248933.6	+	13	2848	c.2753G>A	c.(2752-2754)gGa>gAa	p.G918E	SEZ6L_ENST00000343706.4_Intron|SEZ6L_ENST00000411842.2_Missense_Mutation_p.G115E|SEZ6L_ENST00000529632.2_Missense_Mutation_p.G918E|SEZ6L_ENST00000404234.3_Missense_Mutation_p.G918E|SEZ6L_ENST00000494013.1_3'UTR|SEZ6L_ENST00000360929.3_Missense_Mutation_p.G854E|SEZ6L_ENST00000402979.1_Missense_Mutation_p.G691E|SEZ6L_ENST00000403121.1_Intron			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	918	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)				breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						TGCATCCTGGGACAGCCATCC	0.582																																					p.G918E		Atlas-SNP	.											.	SEZ6L	174	.	0			c.G2753A						PASS	.						82	73	76					22																	26761491		2203	4300	6503	SO:0001583	missense	23544	exon13			TCCTGGGACAGCC	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.2753G>A	chr22.hg19:g.26761491G>A	ENSP00000248933:p.Gly918Glu	174.0	0.0	.		149.0	49.0	.	NM_021115	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	hg19	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.605986	0.87157	.	.	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000402979;ENST00000411842	T;T;T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01;-0.01;-0.01	5.27	5.27	0.74061	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.53938	D	0.000046	T	0.80884	0.4709	M	0.80332	2.49	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.83060	-0.0148	10	0.87932	D	0	.	18.0747	0.89423	0.0:0.0:1.0:0.0	.	918;918;854;918;918	B7ZLJ8;B7ZLJ6;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;SE6L1_HUMAN	E	918;918;854;918;691;115	ENSP00000384772:G918E;ENSP00000437037:G918E;ENSP00000354185:G854E;ENSP00000248933:G918E;ENSP00000384733:G691E;ENSP00000397274:G115E	ENSP00000248933:G918E	G	+	2	0	SEZ6L	25091491	1.000000	0.71417	0.997000	0.53966	0.731000	0.41821	8.973000	0.93428	2.735000	0.93741	0.655000	0.94253	GGA	.	.	.	none		0.582	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3			A	26761491	G	A	26761491	3	1	223	1	0	0	0	0	1	0	0	0	14156	1174	41	2	2803	2	SEZ6L	22	26761491	Missense_Mutation	SNP	G	TCGA-MH-A562-01A-11D-A26P-10		26761491	24543075	63	13572											
PLS3	5358	hgsc.bcm.edu	37	chrX	114880464	114880465	+	Frame_Shift_Ins	INS	-	-	A																															ctgttgactggagtaaggttINSaataaacctccatacccgaa																										TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	g.chrX:114880464_114880465insA	ENST00000420625.2	+	12	1469_1470	c.1335_1336insA	c.(1336-1338)aatfs	p.N446fs	PLS3_ENST00000543070.1_Frame_Shift_Ins_p.N40fs|PLS3_ENST00000289290.3_Frame_Shift_Ins_p.N410fs|PLS3_ENST00000537301.1_Frame_Shift_Ins_p.N433fs|PLS3_ENST00000355899.3_Frame_Shift_Ins_p.N446fs|PLS3_ENST00000539310.1_Frame_Shift_Ins_p.N401fs	NM_001136025.3|NM_001172335.1|NM_001282338.1	NP_001129497.1|NP_001165806.1|NP_001269267.1	P13797	PLST_HUMAN	plastin 3	446	Actin-binding 2.|CH 3. {ECO:0000255|PROSITE- ProRule:PRU00044}.				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						GGAGTAAGGTTAATAAACCTCC	0.322																																					p.V445fs	Colon(160;1047 1864 8490 12969 29601)	Atlas-Indel,Pindel	.											.	PLS3	60	.	0			c.1335_1336insA						PASS	.																																			SO:0001589	frameshift_variant	5358	exon12			.	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.1337dupA	chrX.hg19:g.114880466_114880466dupA	ENSP00000398945:p.Asn446fs	140.0	0.0	0		141.0	92.0	0.652482	NM_005032	A8K579|B1AQ09|B4DGB4|B7Z6M1|Q86YI6	Frame_Shift_Ins	INS	ENST00000420625.2	hg19	CCDS14568.1																																																																																			.	.	.	none		0.322	PLS3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057976.2			A	114880465	-	A	114880464	7	5	223	1	0	1	1	0	0	0	0	0	12115	1741	61	0	1377	0	PLS3	23	114880464	Frame_Shift_Ins	INS	-	TCGA-MH-A562-01A-11D-A26P-10		114880464	40390096	64	13573											
AGTRAP	57085	hgsc.bcm.edu	37	chr1	11808542	11808542	+	Missense_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	catcttctacccgcgggtcaGcctcacggacacgggccgct	6	7	11	17	5	4	0	2	0	2	0	4	1	4	1	3	3	2	1	3	3	1	2			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr1:11808542G>A	ENST00000314340.5	+	4	293	c.239G>A	c.(238-240)aGc>aAc	p.S80N	AGTRAP_ENST00000376629.4_Missense_Mutation_p.S80N|AGTRAP_ENST00000452018.2_Silent_p.Q112Q|AGTRAP_ENST00000491346.1_3'UTR|AGTRAP_ENST00000510878.1_Missense_Mutation_p.A45T|AGTRAP_ENST00000376627.2_Silent_p.Q124Q|AGTRAP_ENST00000376637.3_Silent_p.Q68Q|AGTRAP_ENST00000400895.2_Silent_p.Q112Q	NM_020350.4	NP_065083.3	Q6RW13	ATRAP_HUMAN	angiotensin II receptor-associated protein	80					regulation of blood pressure (GO:0008217)|response to hypoxia (GO:0001666)	cell cortex (GO:0005938)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	angiotensin type II receptor activity (GO:0004945)		AGTRAP/BRAF(2)	endometrium(1)|lung(3)|prostate(1)	5	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;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.46e-06)|COAD - Colon adenocarcinoma(227;0.000256)|BRCA - Breast invasive adenocarcinoma(304;0.0003)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		CCGCGGGTCAGCCTCACGGAC	0.602																																					p.S80N		Atlas-SNP	.											.	AGTRAP	9	.	0			c.G239A						PASS	.						125	94	105					1																	11808542		2203	4300	6503	SO:0001583	missense	57085	exon4			GGGTCAGCCTCAC	AF165187	CCDS136.1, CCDS30585.1, CCDS30586.1, CCDS41248.1, CCDS44056.1	1p36.22	2008-02-05			ENSG00000177674	ENSG00000177674			13539	protein-coding gene	gene with protein product		608729				11733189	Standard	NM_001040194		Approved	ATRAP	uc001asv.3	Q6RW13	OTTHUMG00000002230	ENST00000314340.5:c.239G>A	chr1.hg19:g.11808542G>A	ENSP00000319713:p.Ser80Asn	60.0	0.0	.		50.0	21.0	.	NM_001040194	A8MVQ5|Q5SNV4|Q5SNV5|Q96AC0|Q96PL4|Q9NRW9	Missense_Mutation	SNP	ENST00000314340.5	hg19	CCDS136.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	3.143|3.143	-0.175891|-0.175891	0.06421|0.06421	.|.	.|.	ENSG00000177674|ENSG00000177674	ENST00000510878|ENST00000376629;ENST00000314340	.|T;T	.|0.40225	.|1.04;1.04	4.06|4.06	-8.12|-8.12	0.01078|0.01078	.|.	.|1.568190	.|0.04398	.|N	.|0.363603	T|T	0.17323|0.17323	0.0416|0.0416	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.04013	.|0.0;0.001	T|T	0.12477|0.12477	-1.0546|-1.0546	5|9	0.87932|0.14656	D|T	0|0.56	4.0859|4.0859	3.1848|3.1848	0.06597|0.06597	0.3059:0.3606:0.2425:0.0911|0.3059:0.3606:0.2425:0.0911	.|.	.|80;80	.|Q6RW13-2;Q6RW13	.|.;ATRAP_HUMAN	T|N	45|80	.|ENSP00000365816:S80N;ENSP00000319713:S80N	ENSP00000422647:A45T|ENSP00000319713:S80N	A|S	+|+	1|2	0|0	AGTRAP|AGTRAP	11731129|11731129	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.004000|0.004000	0.04260|0.04260	-1.508000|-1.508000	0.02266|0.02266	-1.874000|-1.874000	0.01133|0.01133	-1.263000|-1.263000	0.01449|0.01449	GCC|AGC	.	.	.	none		0.602	AGTRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006335.1	NM_020350		A	11808542	G	A	11808542	3	1	224	1	0	0	0	0	1	0	0	0	403	971	34	2	354	2	AGTRAP	1	11808542	Missense_Mutation	SNP	G	TCGA-MH-A854-01A-11D-A34Z-10		11808542	237442079	1	13574											
ALPL	249	hgsc.bcm.edu	37	chr1	21890580	21890580	+	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	acgagagtgaaccatgccacCcccagcgccgcctacgccca	10	3	9	19	4	0	2	0	1	0	1	0	3	0	2	7	0	4	0	7	0	2	1			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr1:21890580C>A	ENST00000374840.3	+	6	769	c.519C>A	c.(517-519)acC>acA	p.T173T	ALPL_ENST00000468526.1_3'UTR|ALPL_ENST00000374832.1_Silent_p.T173T|ALPL_ENST00000539907.1_Silent_p.T96T|ALPL_ENST00000540617.1_Silent_p.T118T|ALPL_ENST00000425315.2_Silent_p.T173T	NM_000478.4	NP_000469.3	P05186	PPBT_HUMAN	alkaline phosphatase, liver/bone/kidney	173					cellular response to organic cyclic compound (GO:0071407)|cementum mineralization (GO:0071529)|developmental process involved in reproduction (GO:0003006)|endochondral ossification (GO:0001958)|osteoblast differentiation (GO:0001649)|response to antibiotic (GO:0046677)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to vitamin D (GO:0033280)|skeletal system development (GO:0001501)	anchored component of membrane (GO:0031225)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	26		all_lung(284;2.19e-05)|Lung NSC(340;2.22e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;8.7e-28)|COAD - Colon adenocarcinoma(152;1.57e-05)|GBM - Glioblastoma multiforme(114;2.66e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000177)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00856)|READ - Rectum adenocarcinoma(331;0.0623)|Lung(427;0.146)	Amifostine(DB01143)|Fospropofol(DB06716)	ACCATGCCACCCCCAGCGCCG	0.627																																					p.T173T		Atlas-SNP	.											.	ALPL	50	.	0			c.C519A						PASS	.						75	70	72					1																	21890580		2203	4300	6503	SO:0001819	synonymous_variant	249	exon6			TGCCACCCCCAGC	BC021289	CCDS217.1, CCDS53274.1, CCDS53275.1	1p36.12	2008-02-05			ENSG00000162551	ENSG00000162551	3.1.3.1		438	protein-coding gene	gene with protein product		171760		HOPS		3532105, 3446011	Standard	NM_001127501		Approved	TNSALP	uc001bet.3	P05186	OTTHUMG00000002949	ENST00000374840.3:c.519C>A	chr1.hg19:g.21890580C>A		22.0	0.0	.		28.0	12.0	.	NM_000478	A1A4E7|B2RMP8|B7Z387|B7Z4Y6|O75090|Q2TAI7|Q59EJ7|Q5BKZ5|Q5VTG5|Q6NZI8|Q8WU32|Q9UBK0	Silent	SNP	ENST00000374840.3	hg19	CCDS217.1																																																																																			.	.	.	none		0.627	ALPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000008202.1	NM_000478		A	21890580	C	A	21890580	2	1	224	1	0	0	0	0	0	0	0	1	547	610	22	4		4	ALPL	1	21890580	Silent	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	10082038	21890580	227360041	2	13575											
KIAA0467	23334	hgsc.bcm.edu	37	chr1	43893320	43893320	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cccggacccggtgtcctgtcTacatctacagctgttcactg	6	11	9	15	2	3	0	1	0	2	0	4	1	4	1	3	2	3	2	3	2	2	3			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr1:43893320T>C	ENST00000562955.1	+	25	3547	c.3547T>C	c.(3547-3549)Tac>Cac	p.Y1183H	SZT2_ENST00000372442.1_Missense_Mutation_p.Y341H	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	1240					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						GTGTCCTGTCTACATCTACAG	0.597																																					p.Y1183H		Atlas-SNP	.											.	SZT2	383	.	0			c.T3547C						PASS	.						60	66	64					1																	43893320		2203	4300	6503	SO:0001583	missense	23334	exon25			CCTGTCTACATCT	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.3547T>C	chr1.hg19:g.43893320T>C	ENSP00000457168:p.Tyr1183His	41.0	0.0	.		41.0	14.0	.	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Missense_Mutation	SNP	ENST00000562955.1	hg19	CCDS30694.2	.	.	.	.	.	.	.	.	.	.	T	20.6	4.016875	0.75161	.	.	ENSG00000198198	ENST00000372442	.	.	.	5.26	5.26	0.73747	.	0.222108	0.39615	N	0.001304	T	0.61615	0.2361	M	0.63843	1.955	0.25906	N	0.983298	D	0.54964	0.969	P	0.57620	0.824	T	0.59568	-0.7430	9	0.87932	D	0	.	15.3531	0.74405	0.0:0.0:0.0:1.0	.	1183	Q5T011-5	.	H	341	.	ENSP00000361519:Y341H	Y	+	1	0	SZT2	43665907	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.185000	0.77714	2.207000	0.71202	0.533000	0.62120	TAC	.	.	.	none		0.597	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		C	43893320	T	C	43893320	3	2	224	1	0	0	0	0	1	0	0	0	8185	1522	53	3	1055	3	KIAA0467	1	43893320	Missense_Mutation	SNP	T	TCGA-MH-A854-01A-11D-A34Z-10	22002740	43893320	205357301	3	13576											
C8B	732	hgsc.bcm.edu	37	chr1	57409426	57409426	+	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	agacacacccagactgacgtAgacctcttcaatggcaccac	13	6	7	15	1	2	4	1	1	1	3	2	4	2	4	3	1	0	2	3	1	2	2			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr1:57409426A>T	ENST00000371237.4	-	8	1243	c.1177T>A	c.(1177-1179)Tac>Aac	p.Y393N	C8B_ENST00000535057.1_Missense_Mutation_p.Y331N|C8B_ENST00000543257.1_Missense_Mutation_p.Y341N	NM_000066.2	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide	393	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						AGACTGACGTAGACCTCTTCA	0.398																																					p.Y393N		Atlas-SNP	.											.	C8B	107	.	0			c.T1177A						PASS	.						234	201	212					1																	57409426		2203	4300	6503	SO:0001583	missense	732	exon8			TGACGTAGACCTC	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.1177T>A	chr1.hg19:g.57409426A>T	ENSP00000360281:p.Tyr393Asn	122.0	0.0	.		126.0	54.0	.	NM_000066	A1L4K7	Missense_Mutation	SNP	ENST00000371237.4	hg19	CCDS30730.1	.	.	.	.	.	.	.	.	.	.	A	12.59	1.984073	0.35036	.	.	ENSG00000021852	ENST00000371237;ENST00000543257;ENST00000535057	T;T;T	0.26223	1.91;1.92;1.75	4.59	2.17	0.27698	Membrane attack complex component/perforin (MACPF) domain (3);	0.397983	0.29246	N	0.012719	T	0.31295	0.0792	M	0.80183	2.485	0.38163	D	0.939107	P;P;P	0.42871	0.753;0.753;0.792	B;B;P	0.44860	0.332;0.332;0.462	T	0.15093	-1.0449	10	0.25106	T	0.35	-7.8974	7.3585	0.26733	0.708:0.1492:0.0:0.1428	.	341;331;393	F5H7G1;F5GY80;P07358	.;.;CO8B_HUMAN	N	393;341;331	ENSP00000360281:Y393N;ENSP00000442548:Y341N;ENSP00000440113:Y331N	ENSP00000360281:Y393N	Y	-	1	0	C8B	57182014	0.422000	0.25473	0.042000	0.18584	0.025000	0.11179	0.822000	0.27352	0.461000	0.27071	0.533000	0.62120	TAC	.	.	.	none		0.398	C8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022886.2			T	57409426	A	T	57409426	3	4	224	1	0	0	0	0	1	0	0	0	2419	420	15	5	618	5	C8B	1	57409426	Missense_Mutation	SNP	A	TCGA-MH-A854-01A-11D-A34Z-10	13516106	57409426	191841195	4	13577											
CCBL2	56267	hgsc.bcm.edu	37	chr1	89409051	89409051	+	Frame_Shift_Del	DEL	T	T	-																															accttatgtttagtcatccaTttcacaaacttatagtcata																										TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr1:89409051delT	ENST00000260508.4	-	12	1534	c.1197delA	c.(1195-1197)aaafs	p.K399fs	CCBL2_ENST00000370491.3_Frame_Shift_Del_p.K365fs|CCBL2_ENST00000370485.2_3'UTR|CCBL2_ENST00000446900.2_5'UTR	NM_001008661.2	NP_001008661.1	Q6YP21	KAT3_HUMAN	cysteine conjugate-beta lyase 2	399					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)		TAGTCATCCATTTCACAAACT	0.308																																					p.W400fs		Atlas-INDEL	.											.	CCBL2	138	.	0			c.1198delT						PASS	.						99	99	99					1																	89409051		2203	4300	6503	SO:0001589	frameshift_variant	56267	exon12			.	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.1197delA	chr1.hg19:g.89409051delT	ENSP00000260508:p.Lys399fs	195.0	0.0	0		196.0	69.0	0.352041	NM_001008661	B3KQ13|O95335|Q5JS27|Q5T9T7|Q5T9T8|Q6AI27|Q6ICW1|Q9BVY5	Frame_Shift_Del	DEL	ENST00000260508.4	hg19	CCDS30766.1																																																																																			.	.	.	none		0.308	CCBL2-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000029300.3	NM_001008661		-	89409051	T	-	89409051	7	5	224	1	0	1	0	1	0	0	0	0	2735	1490	52	0	179	0	CCBL2	1	89409051	Frame_Shift_Del	DEL	T	TCGA-MH-A854-01A-11D-A34Z-10	31999625	89409051	159841570	5	13578	138	3									
CCBL2	56267	hgsc.bcm.edu	37	chr1	89409052	89409053	+	Frame_Shift_Del	DEL	TT	TT	-																															ccttatgtttagtcatccatTtcacaaacttatagtcataa																										TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr1:89409052_89409053delTT	ENST00000260508.4	-	12	1532_1533	c.1195_1196delAA	c.(1195-1197)aaafs	p.K399fs	CCBL2_ENST00000370491.3_Frame_Shift_Del_p.K365fs|CCBL2_ENST00000370485.2_3'UTR|CCBL2_ENST00000446900.2_5'UTR	NM_001008661.2	NP_001008661.1	Q6YP21	KAT3_HUMAN	cysteine conjugate-beta lyase 2	399					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)		AGTCATCCATTTCACAAACTTA	0.312																																					p.399_399del		Pindel	.											.	CCBL2	138	.	0			c.1196_1197del						PASS	.																																			SO:0001589	frameshift_variant	56267	exon12			.	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.1195_1196delAA	chr1.hg19:g.89409052_89409053delTT	ENSP00000260508:p.Lys399fs	200.0	0.0	.		196.0	51.0	0.260	NM_001008661	B3KQ13|O95335|Q5JS27|Q5T9T7|Q5T9T8|Q6AI27|Q6ICW1|Q9BVY5	Frame_Shift_Del	DEL	ENST00000260508.4	hg19	CCDS30766.1																																																																																			.	.	.	none		0.312	CCBL2-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000029300.3	NM_001008661		-	89409053	TT	-	89409052	7	5	224	1	0	1	0	1	0	0	0	0	2735	1841	64	0	180	0	CCBL2	1	89409052	Frame_Shift_Del	DEL	TT	TCGA-MH-A854-01A-11D-A34Z-10	1	89409052	159841569	6	13579	138	3									
CCBL2	56267	hgsc.bcm.edu	37	chr1	89409053	89409053	+	Nonsense_Mutation	SNP	T	T	A																															cttatgtttagtcatccattTcacaaacttatagtcataag																										TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr1:89409053T>A	ENST00000260508.4	-	12	1532	c.1195A>T	c.(1195-1197)Aaa>Taa	p.K399*	CCBL2_ENST00000370491.3_Nonsense_Mutation_p.K365*|CCBL2_ENST00000370485.2_3'UTR|CCBL2_ENST00000446900.2_5'UTR	NM_001008661.2	NP_001008661.1	Q6YP21	KAT3_HUMAN	cysteine conjugate-beta lyase 2	399					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)		GTCATCCATTTCACAAACTTA	0.313																																					p.K399X		Atlas-SNP	.											.	CCBL2	138	.	0			c.A1195T						PASS	.						99	99	99					1																	89409053		2203	4300	6503	SO:0001587	stop_gained	56267	exon12			TCCATTTCACAAA	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.1195A>T	chr1.hg19:g.89409053T>A	ENSP00000260508:p.Lys399*	197.0	0.0	.		193.0	69.0	.	NM_001008661	B3KQ13|O95335|Q5JS27|Q5T9T7|Q5T9T8|Q6AI27|Q6ICW1|Q9BVY5	Nonsense_Mutation	SNP	ENST00000260508.4	hg19	CCDS30766.1	.	.	.	.	.	.	.	.	.	.	T	38	6.926121	0.97940	.	.	ENSG00000137944	ENST00000370491;ENST00000260508	.	.	.	5.65	5.65	0.86999	.	0.046579	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-19.8953	12.9534	0.58413	0.0:0.0:0.1346:0.8654	.	.	.	.	X	365;399	.	ENSP00000260508:K399X	K	-	1	0	CCBL2	89181641	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.403000	0.66338	2.149000	0.67028	0.460000	0.39030	AAA	.	.	.	none		0.313	CCBL2-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000029300.3	NM_001008661		A	89409053	T	A	89409053	4	1	224	1	0	0	0	0	0	1	0	0	2735	1792	62	5	181	5	CCBL2	1	89409053	Nonsense_Mutation	SNP	T	TCGA-MH-A854-01A-11D-A34Z-10	1	89409053	159841568	7	13580	138	3									
ZNF644	84146	hgsc.bcm.edu	37	chr1	91405923	91405923	+	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	gtctactgcttgtagctcttCattttgttctagaaagtcta	8	18	7	8	0	5	1	1	0	4	1	5	1	5	1	0	0	3	4	0	0	5	9			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr1:91405923C>T	ENST00000370440.1	-	3	1205	c.988G>A	c.(988-990)Gaa>Aaa	p.E330K	ZNF644_ENST00000347275.5_Intron|ZNF644_ENST00000467231.1_Intron|ZNF644_ENST00000337393.5_Missense_Mutation_p.E330K|ZNF644_ENST00000361321.5_Intron			Q9H582	ZN644_HUMAN	zinc finger protein 644	330					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(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)		TGTAGCTCTTCATTTTGTTCT	0.358																																					p.E330K		Atlas-SNP	.											.	ZNF644	120	.	0			c.G988A						PASS	.						100	99	99					1																	91405923		2203	4299	6502	SO:0001583	missense	84146	exon3			GCTCTTCATTTTG	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.988G>A	chr1.hg19:g.91405923C>T	ENSP00000359469:p.Glu330Lys	84.0	0.0	.		87.0	26.0	.	NM_201269	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Missense_Mutation	SNP	ENST00000370440.1	hg19	CCDS731.1	.	.	.	.	.	.	.	.	.	.	C	11.75	1.732778	0.30684	.	.	ENSG00000122482	ENST00000370440;ENST00000337393	T;T	0.00596	6.32;6.32	5.58	5.58	0.84498	.	0.230912	0.44688	D	0.000434	T	0.00524	0.0017	L	0.29908	0.895	0.46564	D	0.999104	D	0.56521	0.976	P	0.47603	0.551	D	0.85156	0.0989	10	0.72032	D	0.01	-17.5126	19.5736	0.95432	0.0:1.0:0.0:0.0	.	330	Q9H582	ZN644_HUMAN	K	330	ENSP00000359469:E330K;ENSP00000337008:E330K	ENSP00000337008:E330K	E	-	1	0	ZNF644	91178511	1.000000	0.71417	0.999000	0.59377	0.521000	0.34408	2.652000	0.46682	2.636000	0.89361	0.655000	0.94253	GAA	.	.	.	none		0.358	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186		T	91405923	C	T	91405923	3	4	224	1	0	0	0	0	1	0	0	0	18072	835	29	2	3011	2	ZNF644	1	91405923	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	1996870	91405923	157844698	8	13581											
OVGP1	5016	hgsc.bcm.edu	37	chr1	111957099	111957099	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggggcttaggcttcttcaTccacagcagagttttctggg	7	12	13	9	0	3	1	1	0	2	1	4	2	4	1	1	4	1	4	1	4	1	5			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr1:111957099T>C	ENST00000369732.3	-	11	2079	c.2024A>G	c.(2023-2025)gAt>gGt	p.D675G		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	675					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)		GGCTTCTTCATCCACAGCAGA	0.453																																					p.D675G		Atlas-SNP	.											.	OVGP1	177	.	0			c.A2024G						PASS	.						66	72	70					1																	111957099		2202	4300	6502	SO:0001583	missense	5016	exon11			TCTTCATCCACAG	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.2024A>G	chr1.hg19:g.111957099T>C	ENSP00000358747:p.Asp675Gly	48.0	0.0	.		47.0	14.0	.	NM_002557	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	hg19	CCDS834.1	.	.	.	.	.	.	.	.	.	.	T	10.09	1.254760	0.22965	.	.	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000434331	T	0.05717	3.4	4.92	2.54	0.30619	.	22.625600	0.00748	N	0.001042	T	0.01835	0.0058	N	0.22421	0.69	0.09310	N	1	B;B	0.15719	0.014;0.005	B;B	0.12156	0.007;0.004	T	0.41378	-0.9512	10	0.72032	D	0.01	.	6.616	0.22776	0.0:0.2102:0.0:0.7898	.	675;739	Q12889;Q59HH5	OVGP1_HUMAN;.	G	675;739;483	ENSP00000358747:D675G	ENSP00000358743:D739G	D	-	2	0	OVGP1	111758622	0.000000	0.05858	0.004000	0.12327	0.364000	0.29643	0.283000	0.18846	0.418000	0.25898	0.477000	0.44152	GAT	.	.	.	none		0.453	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557		C	111957099	T	C	111957099	3	2	224	1	0	0	0	0	1	0	0	0	11332	1435	50	3	16	3	OVGP1	1	111957099	Missense_Mutation	SNP	T	TCGA-MH-A854-01A-11D-A34Z-10	20551176	111957099	137293522	9	13582											
DDX20	11218	hgsc.bcm.edu	37	chr1	112299304	112299304	+	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	taaatctggcaccgggaaaaCctgtgtgttctccaccatag	11	10	9	11	1	2	0	0	0	2	0	3	1	2	1	4	2	1	2	4	2	5	3			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr1:112299304C>G	ENST00000369702.4	+	2	958	c.338C>G	c.(337-339)aCc>aGc	p.T113S	DDX20_ENST00000536167.1_Missense_Mutation_p.T113S|FAM212B_ENST00000412270.1_5'Flank|FAM212B_ENST00000444059.2_5'Flank	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	113	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				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)		ACCGGGAAAACCTGTGTGTTC	0.433																																					p.T113S		Atlas-SNP	.											.	DDX20	50	.	0			c.C338G						PASS	.						113	106	108					1																	112299304		2203	4300	6503	SO:0001583	missense	11218	exon2			GGAAAACCTGTGT	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.338C>G	chr1.hg19:g.112299304C>G	ENSP00000358716:p.Thr113Ser	95.0	0.0	.		85.0	21.0	.	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Missense_Mutation	SNP	ENST00000369702.4	hg19	CCDS842.1	.	.	.	.	.	.	.	.	.	.	C	32	5.118880	0.94385	.	.	ENSG00000064703	ENST00000369702;ENST00000536167	T;T	0.72505	0.88;-0.66	5.61	5.61	0.85477	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.86062	0.5843	M	0.90922	3.16	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	D	0.88501	0.3082	10	0.72032	D	0.01	-14.8317	17.412	0.87488	0.0:1.0:0.0:0.0	.	113	Q9UHI6	DDX20_HUMAN	S	113	ENSP00000358716:T113S;ENSP00000439026:T113S	ENSP00000358716:T113S	T	+	2	0	DDX20	112100827	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.770000	0.74990	2.644000	0.89710	0.561000	0.74099	ACC	.	.	.	none		0.433	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204		G	112299304	C	G	112299304	3	3	224	1	0	0	0	0	1	0	0	0	4350	507	18	4	344	4	DDX20	1	112299304	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	342205	112299304	136951317	10	13583											
S100A16	140576	hgsc.bcm.edu	37	chr1	153580138	153580138	+	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	ggcatccaggttctggatgaGcttatccgcagccttccggt	6	11	12	12	2	1	1	0	1	1	0	4	2	4	2	4	4	2	4	4	4	1	3			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr1:153580138G>C	ENST00000368704.1	-	3	369	c.184C>G	c.(184-186)Ctc>Gtc	p.L62V	S100A16_ENST00000368703.2_Missense_Mutation_p.L62V|S100A16_ENST00000368705.2_Missense_Mutation_p.L62V|S100A16_ENST00000368706.4_Missense_Mutation_p.L62V|S100A16_ENST00000474991.1_5'UTR			Q96FQ6	S10AG_HUMAN	S100 calcium binding protein A16	62	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				response to calcium ion (GO:0051592)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			breast(1)|large_intestine(1)|prostate(1)	3	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)			TTCTGGATGAGCTTATCCGCA	0.587																																					p.L62V	Melanoma(71;1388 1729 37039 46098)	Atlas-SNP	.											.	S100A16	7	.	0			c.C184G						PASS	.						89	81	84					1																	153580138		2203	4300	6503	SO:0001583	missense	140576	exon3			GGATGAGCTTATC	BC010541	CCDS1045.1	1q21	2014-01-28			ENSG00000188643	ENSG00000188643		"S100 calcium binding proteins", "EF-hand domain containing"	20441	protein-coding gene	gene with protein product						9417904	Standard	NM_080388		Approved	S100F, DT1P1A7, MGC17528	uc001fcd.1	Q96FQ6	OTTHUMG00000013545	ENST00000368704.1:c.184C>G	chr1.hg19:g.153580138G>C	ENSP00000357693:p.Leu62Val	63.0	0.0	.		60.0	22.0	.	NM_080388	A8K439|D3DV52|Q5RHS6	Missense_Mutation	SNP	ENST00000368704.1	hg19	CCDS1045.1	.	.	.	.	.	.	.	.	.	.	G	16.29	3.082152	0.55861	.	.	ENSG00000188643	ENST00000368704;ENST00000368705;ENST00000368706;ENST00000368703	T;T;T;T	0.73258	-0.73;-0.73;-0.73;-0.73	4.38	4.38	0.52667	S100/Calbindin-D9k, conserved site (1);EF-hand-like domain (1);	0.140645	0.33110	N	0.005273	T	0.73737	0.3625	L	0.55481	1.735	0.42070	D	0.991207	D	0.64830	0.994	D	0.70716	0.97	T	0.70597	-0.4828	10	0.30078	T	0.28	-4.9853	14.8714	0.70459	0.0:0.0:1.0:0.0	.	62	Q96FQ6	S10AG_HUMAN	V	62	ENSP00000357693:L62V;ENSP00000357694:L62V;ENSP00000357695:L62V;ENSP00000357692:L62V	ENSP00000357692:L62V	L	-	1	0	S100A16	151846762	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	3.803000	0.55560	2.462000	0.83206	0.456000	0.33151	CTC	.	.	.	none		0.587	S100A16-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037713.1	NM_080388		C	153580138	G	C	153580138	3	2	224	1	0	0	0	0	1	0	0	0	13790	971	34	4	131	4	S100A16	1	153580138	Missense_Mutation	SNP	G	TCGA-MH-A854-01A-11D-A34Z-10	41280834	153580138	95670483	11	13584											
SLC19A2	10560	hgsc.bcm.edu	37	chr1	169454887	169454887	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaggctggcgaagaagccgtAggcgcagagcagcgcggtcg	9	3	19	10	6	0	2	0	0	0	2	1	4	0	2	1	4	3	4	1	4	3	1			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr1:169454887A>G	ENST00000236137.5	-	1	354	c.118T>C	c.(118-120)Tac>Cac	p.Y40H	SLC19A2_ENST00000367804.4_Missense_Mutation_p.Y40H	NM_006996.2	NP_008927.1	O60779	S19A2_HUMAN	solute carrier family 19 (thiamine transporter), member 2	40					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)	AAGAAGCCGTAGGCGCAGAGC	0.721																																					p.Y40H		Atlas-SNP	.											.	SLC19A2	35	.	0			c.T118C						PASS	.						7	9	8					1																	169454887		2081	4110	6191	SO:0001583	missense	10560	exon1			AGCCGTAGGCGCA	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.118T>C	chr1.hg19:g.169454887A>G	ENSP00000236137:p.Tyr40His	51.0	0.0	.		58.0	29.0	.	NM_006996	B2R9H0|B4E1X4|Q8WV87|Q9UBL7|Q9UKJ2|Q9UN31|Q9UN43	Missense_Mutation	SNP	ENST00000236137.5	hg19	CCDS1280.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.958638	0.74016	.	.	ENSG00000117479	ENST00000236137;ENST00000367804;ENST00000367802	D;D;D	0.89552	-2.53;-2.46;-2.53	4.38	4.38	0.52667	Major facilitator superfamily domain, general substrate transporter (1);	0.068558	0.64402	D	0.000011	D	0.91821	0.7412	M	0.80422	2.495	0.43977	D	0.996660	P;D	0.59357	0.834;0.985	B;P	0.60345	0.363;0.873	D	0.93069	0.6481	9	0.62326	D	0.03	-10.2171	13.7581	0.62948	1.0:0.0:0.0:0.0	.	40;40	O60779-2;O60779	.;S19A2_HUMAN	H	40	ENSP00000236137:Y40H;ENSP00000356778:Y40H;ENSP00000356776:Y40H	ENSP00000236137:Y40H	Y	-	1	0	SLC19A2	167721511	1.000000	0.71417	1.000000	0.80357	0.331000	0.28603	6.838000	0.75359	1.821000	0.53095	0.482000	0.46254	TAC	.	.	.	none		0.721	SLC19A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086106.1	NM_006996		G	169454887	A	G	169454887	3	3	224	1	0	0	0	0	1	0	0	0	14442	420	15	3	1399	3	SLC19A2	1	169454887	Missense_Mutation	SNP	A	TCGA-MH-A854-01A-11D-A34Z-10	15874749	169454887	79795734	12	13585											
ETNK2	55224	hgsc.bcm.edu	37	chr1	204118891	204118892	+	Missense_Mutation	DNP	TA	TA	CG																															ccacaccctgcatgtactcaTagcacagcccattctggaag																								rs377403947		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T|A	T|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr1:204118891_204118892TA>CG	ENST00000367202.4	-	2	607_608	c.457_458TA>CG	c.(457-459)TAt>CGt	p.Y153R	ETNK2_ENST00000367201.3_Missense_Mutation_p.Y153R|ETNK2_ENST00000367199.2_Missense_Mutation_p.Y125R|ETNK2_ENST00000367198.2_5'Flank	NM_018208.2	NP_060678.2	Q9NVF9	EKI2_HUMAN	ethanolamine kinase 2	153					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)			CATGTACTCATAGCACAGCCCA	0.584																																					p.Y153C|p.Y153H		Atlas-SNP	.											.	ETNK2	48	.	0			c.A458G|c.T457C						PASS	.																																			SO:0001583	missense	55224	exon2			TACTCATAGCACA|ACTCATAGCACAG	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.457_458delinsCG	chr1.hg19:g.204118891_204118892delinsCG	ENSP00000356170:p.Tyr153Arg	29.0	0.0	.		38.0|37.0	12.0	.	NM_018208	B7Z7K1|Q5SXX5|Q68CK3|Q96G05	Missense_Mutation	SNP	ENST00000367202.4	hg19	CCDS1442.2																																																																																			.	.	.	none		0.584	ETNK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087893.1	NM_018208		CG	204118892	TA	CG	204118891	3	2	224	1	0	0	0	0	1	0	0	0	5276	1406	49	3	730	3	ETNK2	1	204118891	Missense_Mutation	DNP	TA	TCGA-MH-A854-01A-11D-A34Z-10	34664004	204118891	45131730	13	13586											
USH2A	7399	hgsc.bcm.edu	37	chr1	215807830	215807830	+	Missense_Mutation	SNP	T	T	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	ttcccccggtgggtaaacatTcaatggagacatcctcttct	9	12	8	12	1	3	1	1	0	2	1	5	2	5	1	3	3	1	1	3	3	3	4			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr1:215807830T>G	ENST00000307340.3	-	70	15654	c.15268A>C	c.(15268-15270)Aat>Cat	p.N5090H	USH2A_ENST00000366943.2_Missense_Mutation_p.N5090H	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	5090					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)		GGGTAAACATTCAATGGAGAC	0.418										HNSCC(13;0.011)																											p.N5090H		Atlas-SNP	.											.	USH2A	1168	.	0			c.A15268C						PASS	.						101	103	102					1																	215807830		2203	4300	6503	SO:0001583	missense	7399	exon70			AAACATTCAATGG	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.15268A>C	chr1.hg19:g.215807830T>G	ENSP00000305941:p.Asn5090His	110.0	0.0	.		118.0	46.0	.	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	T	14.21	2.468710	0.43839	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.13196	2.62;2.61	5.74	4.61	0.57282	.	0.644992	0.13425	N	0.388859	T	0.13372	0.0324	L	0.36672	1.1	0.24098	N	0.995885	P	0.38642	0.641	B	0.37833	0.259	T	0.11036	-1.0604	10	0.59425	D	0.04	.	11.4143	0.49943	0.0:0.0705:0.0:0.9295	.	5090	O75445	USH2A_HUMAN	H	5090	ENSP00000305941:N5090H;ENSP00000355910:N5090H	ENSP00000305941:N5090H	N	-	1	0	USH2A	213874453	0.985000	0.35326	0.093000	0.20910	0.197000	0.23852	2.127000	0.42035	1.005000	0.39183	0.533000	0.62120	AAT	.	.	.	none		0.418	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		G	215807830	T	G	215807830	3	3	224	1	0	0	0	0	1	0	0	0	17048	1783	62	5	352	5	USH2A	1	215807830	Missense_Mutation	SNP	T	TCGA-MH-A854-01A-11D-A34Z-10	11688939	215807830	33442791	14	13587											
PARP1	142	hgsc.bcm.edu	37	chr1	226570809	226570809	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcgtggccgccacggaggCgctggtttctggggggaata	6	7	19	9	4	1	0	0	0	1	0	1	2	1	2	2	8	0	2	2	8	2	2			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr1:226570809C>T	ENST00000366794.5	-	8	1230	c.1087G>A	c.(1087-1089)Gcc>Acc	p.A363T		NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	363					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)		GCCACGGAGGCGCTGGTTTCT	0.498								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																													p.A363T		Atlas-SNP	.											.	PARP1	100	.	0			c.G1087A						PASS	.						102	128	119					1																	226570809		2203	4300	6503	SO:0001583	missense	142	exon8			CGGAGGCGCTGGT	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.1087G>A	chr1.hg19:g.226570809C>T	ENSP00000355759:p.Ala363Thr	72.0	0.0	.		68.0	30.0	.	NM_001618	B1ANJ4|Q8IUZ9	Missense_Mutation	SNP	ENST00000366794.5	hg19	CCDS1554.1	.	.	.	.	.	.	.	.	.	.	C	0.062	-1.220740	0.01530	.	.	ENSG00000143799	ENST00000366794	T	0.08896	3.04	5.26	-3.57	0.04612	.	0.543121	0.22223	N	0.062926	T	0.03011	0.0089	N	0.08118	0	0.35886	D	0.829289	B	0.02656	0.0	B	0.01281	0.0	T	0.49466	-0.8937	10	0.05833	T	0.94	.	12.1841	0.54227	0.0:0.4939:0.0:0.5061	.	363	P09874	PARP1_HUMAN	T	363	ENSP00000355759:A363T	ENSP00000355759:A363T	A	-	1	0	PARP1	224637432	0.014000	0.17966	0.001000	0.08648	0.056000	0.15407	0.261000	0.18442	-0.521000	0.06426	-0.266000	0.10368	GCC	.	.	.	none		0.498	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618		T	226570809	C	T	226570809	3	4	224	1	0	0	0	0	1	0	0	0	11461	768	27	1	2021	1	PARP1	1	226570809	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	10762979	226570809	22679812	15	13588											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228461691	228461691	+	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	ggcgcccaggttctggacagCgccatctacagctgccgtgt	6	8	13	14	3	2	0	0	0	2	0	2	1	2	1	3	3	4	2	3	3	1	2	rs374335072		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr1:228461691C>T	ENST00000422127.1	+	18	5402	c.5358C>T	c.(5356-5358)agC>agT	p.S1786S	OBSCN_ENST00000359599.6_Silent_p.S633S|OBSCN_ENST00000366709.4_5'UTR|RP5-1139B12.3_ENST00000602529.1_RNA|RP5-1139B12.2_ENST00000602517.1_RNA|RP5-1139B12.3_ENST00000602947.1_RNA|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.S1786S|OBSCN_ENST00000570156.2_Silent_p.S2161S	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1786	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)				TTCTGGACAGCGCCATCTACA	0.667																																					p.S2161S		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C6483T						PASS	.	T	,	1,4235		0,1,2117	18	23	21		5358,5358	-7.9	0.1	1		21	0,8424		0,0,4212	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	0,1,6329	TT,TC,CC		0.0,0.0236,0.0079	,	1786/7969,1786/6621	228461691	1,12659	2118	4212	6330	SO:0001819	synonymous_variant	84033	exon22			GGACAGCGCCATC	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.5358C>T	chr1.hg19:g.228461691C>T		76.0	0.0	.		56.0	20.0	.	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	hg19	CCDS58065.1																																																																																			.	.	.	none		0.667	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228461691	C	T	228461691	2	4	224	1	0	0	0	0	0	0	0	1	10819	767	27	1		1	OBSCN	1	228461691	Silent	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	1890882	228461691	20788930	16	13589											
GREB1	9687	hgsc.bcm.edu	37	chr2	11751041	11751041	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggcggtggtggcctatgAgcggctggcccacgtgcggg	3	7	19	12	4	0	1	0	1	0	0	0	1	0	1	3	7	2	1	3	7	1	1			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr2:11751041A>G	ENST00000381486.2	+	18	3194	c.2894A>G	c.(2893-2895)gAg>gGg	p.E965G	GREB1_ENST00000234142.5_Missense_Mutation_p.E965G|GREB1_ENST00000396123.1_5'Flank	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	965						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)		GTGGCCTATGAGCGGCTGGCC	0.682																																					p.E965G	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.A2894G						PASS	.						14	18	17					2																	11751041		2015	4146	6161	SO:0001583	missense	9687	exon18			CCTATGAGCGGCT		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.2894A>G	chr2.hg19:g.11751041A>G	ENSP00000370896:p.Glu965Gly	87.0	0.0	.		72.0	19.0	.	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	hg19	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.960016	0.74016	.	.	ENSG00000196208	ENST00000381486;ENST00000234142	T;T	0.50813	0.73;0.73	5.17	5.17	0.71159	.	0.219003	0.38897	N	0.001534	T	0.67832	0.2935	M	0.73217	2.22	0.42070	D	0.991201	D	0.89917	1.0	D	0.85130	0.997	T	0.72734	-0.4204	10	0.87932	D	0	-44.6127	15.0084	0.71530	1.0:0.0:0.0:0.0	.	965	Q4ZG55	GREB1_HUMAN	G	965	ENSP00000370896:E965G;ENSP00000234142:E965G	ENSP00000234142:E965G	E	+	2	0	GREB1	11668492	1.000000	0.71417	1.000000	0.80357	0.810000	0.45777	3.663000	0.54518	1.951000	0.56629	0.460000	0.39030	GAG	.	.	.	none		0.682	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		G	11751041	A	G	11751041	3	3	224	1	0	0	0	0	1	0	0	0	6767	304	11	3	3068	3	GREB1	2	11751041	Missense_Mutation	SNP	A	TCGA-MH-A854-01A-11D-A34Z-10		11751041	231448332	17	13590											
GKN1	56287	hgsc.bcm.edu	37	chr2	69207188	69207188	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acatacatggctgaggagatGcaaggtgagtagcatcccta	13	8	12	8	0	0	3	0	2	0	1	1	4	1	3	1	3	3	4	1	3	4	3			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr2:69207188G>A	ENST00000377938.2	+	5	564	c.501G>A	c.(499-501)atG>atA	p.M167I		NM_019617.3	NP_062563.3	Q9NS71	GKN1_HUMAN	gastrokine 1	167					digestion (GO:0007586)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)	extracellular region (GO:0005576)|secretory granule (GO:0030141)				breast(2)|large_intestine(4)|lung(5)	11						CTGAGGAGATGCAAGGTGAGT	0.502																																					p.M167I		Atlas-SNP	.											.	GKN1	24	.	0			c.G501A						PASS	.						141	101	115					2																	69207188		2203	4300	6503	SO:0001583	missense	56287	exon5			GGAGATGCAAGGT	AY139182	CCDS1891.2	2p13.3	2012-10-10			ENSG00000169605	ENSG00000169605		"BRICHOS domain containing"	23217	protein-coding gene	gene with protein product	"BRICHOS domain containing 1"	606402				12851218, 11562744	Standard	NM_019617		Approved	AMP18, CA11, BRICD1	uc002sfc.3	Q9NS71	OTTHUMG00000129574	ENST00000377938.2:c.501G>A	chr2.hg19:g.69207188G>A	ENSP00000367172:p.Met167Ile	58.0	0.0	.		43.0	24.0	.	NM_019617	Q8IUA9	Missense_Mutation	SNP	ENST00000377938.2	hg19	CCDS1891.2	.	.	.	.	.	.	.	.	.	.	G	0.082	-1.182600	0.01620	.	.	ENSG00000169605	ENST00000377938	T	0.39787	1.06	5.35	0.0642	0.14352	.	0.896583	0.09689	N	0.768723	T	0.16727	0.0402	N	0.04203	-0.255	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29912	-0.9996	10	0.08381	T	0.77	-3.1782	6.6465	0.22939	0.2552:0.0:0.4241:0.3207	.	167	Q9NS71	GKN1_HUMAN	I	167	ENSP00000367172:M167I	ENSP00000367172:M167I	M	+	3	0	GKN1	69060692	0.000000	0.05858	0.127000	0.21898	0.582000	0.36321	-0.098000	0.11024	-0.111000	0.12001	-1.506000	0.00953	ATG	.	.	.	none		0.502	GKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251769.2	NM_019617		A	69207188	G	A	69207188	3	1	224	1	0	0	0	0	1	0	0	0	6431	1319	46	2	519	2	GKN1	2	69207188	Missense_Mutation	SNP	G	TCGA-MH-A854-01A-11D-A34Z-10	57456147	69207188	173992185	18	13591											
KDM3A	55818	hgsc.bcm.edu	37	chr2	86709089	86709089	+	Missense_Mutation	SNP	T	T	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	gccaattttaaagaatgaaaTcaaatgccttccacccctcc	14	10	4	13	0	1	2	1	1	0	1	3	2	3	2	6	0	1	0	6	0	6	3			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr2:86709089T>G	ENST00000409556.1	+	18	2914	c.2549T>G	c.(2548-2550)aTc>aGc	p.I850S	KDM3A_ENST00000542128.1_Missense_Mutation_p.I798S|KDM3A_ENST00000409064.1_Missense_Mutation_p.I850S|KDM3A_ENST00000312912.5_Missense_Mutation_p.I850S			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	850					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						AAGAATGAAATCAAATGCCTT	0.363																																					p.I850S	NSCLC(96;1150 1523 6936 46253 49736)	Atlas-SNP	.											.	KDM3A	179	.	0			c.T2549G						PASS	.						127	120	122					2																	86709089		2203	4300	6503	SO:0001583	missense	55818	exon17			ATGAAATCAAATG	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.2549T>G	chr2.hg19:g.86709089T>G	ENSP00000386660:p.Ile850Ser	126.0	0.0	.		108.0	44.0	.	NM_001146688	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Missense_Mutation	SNP	ENST00000409556.1	hg19	CCDS1990.1	.	.	.	.	.	.	.	.	.	.	T	7.548	0.662024	0.14645	.	.	ENSG00000115548	ENST00000409556;ENST00000540058;ENST00000312912;ENST00000409064;ENST00000542128	T;T;T;T	0.55930	0.49;0.49;0.49;0.5	5.8	3.36	0.38483	.	0.221574	0.38778	N	0.001577	T	0.20251	0.0487	N	0.01874	-0.695	0.29435	N	0.859551	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.09975	-1.0650	10	0.20046	T	0.44	.	5.2614	0.15576	0.3072:0.0:0.128:0.5648	.	798;850	F5H070;Q9Y4C1	.;KDM3A_HUMAN	S	850;850;850;850;798	ENSP00000386660:I850S;ENSP00000323659:I850S;ENSP00000386516:I850S;ENSP00000438324:I798S	ENSP00000323659:I850S	I	+	2	0	KDM3A	86562600	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.125000	0.42016	2.216000	0.71823	0.533000	0.62120	ATC	.	.	.	none		0.363	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433		G	86709089	T	G	86709089	3	3	224	1	0	0	0	0	1	0	0	0	8133	1435	50	5	2611	5	KDM3A	2	86709089	Missense_Mutation	SNP	T	TCGA-MH-A854-01A-11D-A34Z-10	17501901	86709089	156490284	19	13592											
UBR3	130507	hgsc.bcm.edu	37	chr2	170936421	170936421	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtactaccacagaaaaacctGtagtgtctgcaccaaggttc	13	9	8	11	0	1	1	0	0	1	1	2	1	1	1	3	1	4	4	3	1	6	4			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr2:170936421G>A	ENST00000272793.5	+	37	5347	c.5297G>A	c.(5296-5298)tGt>tAt	p.C1766Y	UBR3_ENST00000392631.1_Missense_Mutation_p.C587Y|UBR3_ENST00000418381.1_Missense_Mutation_p.C1766Y			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	1766	Cys-rich.				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						AGAAAAACCTGTAGTGTCTGC	0.413																																					p.C1766Y		Atlas-SNP	.											.	UBR3	182	.	0			c.G5297A						PASS	.						136	125	129					2																	170936421		2203	4300	6503	SO:0001583	missense	130507	exon37			AAACCTGTAGTGT	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.5297G>A	chr2.hg19:g.170936421G>A	ENSP00000272793:p.Cys1766Tyr	227.0	0.0	.		207.0	78.0	.	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Missense_Mutation	SNP	ENST00000272793.5	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.8|25.8	4.675813|4.675813	0.88445|0.88445	.|.	.|.	ENSG00000144357|ENSG00000144357	ENST00000272793;ENST00000442603;ENST00000418381;ENST00000392631;ENST00000439681|ENST00000392632	T;T;T;T|.	0.71698|.	-0.59;-0.59;-0.59;-0.59|.	5.66|5.66	5.66|5.66	0.87406|0.87406	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.83225|0.83225	0.5208|0.5208	M|M	0.84511|0.84511	2.7|2.7	0.80722|0.80722	D|D	1|1	D;D;D|.	0.76494|.	0.995;0.999;0.98|.	D;D;D|.	0.83275|.	0.986;0.996;0.974|.	D|D	0.84171|0.84171	0.0434|0.0434	10|5	0.52906|.	T|.	0.07|.	.|.	19.7411|19.7411	0.96231|0.96231	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1766;587;1795|.	Q6ZT12;Q6ZT12-2;E7EVK3|.	UBR3_HUMAN;.;.|.	Y|I	1766;1795;1766;587;466|828	ENSP00000272793:C1766Y;ENSP00000396068:C1766Y;ENSP00000376408:C587Y;ENSP00000389097:C466Y|.	ENSP00000272793:C1766Y|.	C|V	+|+	2|1	0|0	UBR3|UBR3	170644667|170644667	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	9.476000|9.476000	0.97823|0.97823	2.653000|2.653000	0.90120|0.90120	0.650000|0.650000	0.86243|0.86243	TGT|GTA	.	.	.	none		0.413	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070		A	170936421	G	A	170936421	3	1	224	1	0	0	0	0	1	0	0	0	16915	1377	48	2	5443	2	UBR3	2	170936421	Missense_Mutation	SNP	G	TCGA-MH-A854-01A-11D-A34Z-10	84227332	170936421	72262952	20	13593											
ALS2	57679	hgsc.bcm.edu	37	chr2	202625787	202625787	+	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	gcatcgctgcttgtgatctgAgcacttactgcattcagttc	7	14	9	11	1	2	2	1	2	1	0	4	2	2	2	0	0	4	6	0	0	1	4			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr2:202625787A>T	ENST00000264276.6	-	4	1302	c.930T>A	c.(928-930)gcT>gcA	p.A310A	ALS2_ENST00000467448.1_Silent_p.A310A|ALS2_ENST00000496244.1_5'Flank	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	310					behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						TTGTGATCTGAGCACTTACTG	0.458																																					p.A310A		Atlas-SNP	.											.	ALS2	172	.	0			c.T930A						PASS	.						208	196	200					2																	202625787		2071	4220	6291	SO:0001819	synonymous_variant	57679	exon4			GATCTGAGCACTT	AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"Rho guanine nucleotide exchange factors"	443	protein-coding gene	gene with protein product	"alsin"	606352	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.930T>A	chr2.hg19:g.202625787A>T		233.0	0.0	.		239.0	106.0	.	NM_001135745	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Silent	SNP	ENST00000264276.6	hg19	CCDS42800.1																																																																																			.	.	.	none		0.458	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919		T	202625787	A	T	202625787	2	4	224	1	0	0	0	0	0	0	0	1	550	291	11	5		5	ALS2	2	202625787	Silent	SNP	A	TCGA-MH-A854-01A-11D-A34Z-10	31689366	202625787	40573586	21	13594											
XIRP1	165904	hgsc.bcm.edu	37	chr3	39226976	39226976	+	Missense_Mutation	SNP	T	T	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	gggcagctgcggcttcttctTtgggggcatggtggggtcca	3	11	18	9	1	2	0	0	0	2	0	3	0	3	0	1	7	2	4	1	7	0	3			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr3:39226976T>G	ENST00000340369.3	-	2	4189	c.3961A>C	c.(3961-3963)Aag>Cag	p.K1321Q	XIRP1_ENST00000396251.1_3'UTR|XIRP1_ENST00000421646.1_Missense_Mutation_p.K4Q	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	1321	Pro-rich.				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)		GGCTTCTTCTTTGGGGGCATG	0.607																																					p.K1321Q		Atlas-SNP	.											.	XIRP1	173	.	0			c.A3961C						PASS	.						39	46	44					3																	39226976		2195	4299	6494	SO:0001583	missense	165904	exon2			TCTTCTTTGGGGG	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.3961A>C	chr3.hg19:g.39226976T>G	ENSP00000343140:p.Lys1321Gln	62.0	0.0	.		36.0	16.0	.	NM_194293	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	hg19	CCDS2683.1	.	.	.	.	.	.	.	.	.	.	T	7.981	0.751161	0.15778	.	.	ENSG00000168334	ENST00000340369;ENST00000421646	T;T	0.19938	3.83;2.11	4.38	0.707	0.18139	.	2.505940	0.01310	N	0.010586	T	0.12178	0.0296	N	0.22421	0.69	0.09310	N	1	B	0.22276	0.067	B	0.17433	0.018	T	0.13953	-1.0490	10	0.11182	T	0.66	.	1.3649	0.02199	0.1779:0.0999:0.1852:0.537	.	1321	Q702N8	XIRP1_HUMAN	Q	1321;4	ENSP00000343140:K1321Q;ENSP00000391645:K4Q	ENSP00000343140:K1321Q	K	-	1	0	XIRP1	39201980	0.713000	0.27926	0.148000	0.22405	0.462000	0.32619	0.540000	0.23191	0.119000	0.18210	0.533000	0.62120	AAG	.	.	.	none		0.607	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522		G	39226976	T	G	39226976	3	3	224	1	0	0	0	0	1	0	0	0	17441	1850	64	5	1574	5	XIRP1	3	39226976	Missense_Mutation	SNP	T	TCGA-MH-A854-01A-11D-A34Z-10		39226976	158795454	22	13595											
CXCR6	10663	hgsc.bcm.edu	37	chr3	45988859	45988859	+	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	cctttgtcagcctgaagtttCgaaagaacttctggaaactt	11	13	8	9	1	2	2	1	1	1	1	3	4	2	3	2	1	3	1	2	1	4	4			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr3:45988859C>G	ENST00000458629.1	+	1	2349	c.886C>G	c.(886-888)Cga>Gga	p.R296G	FYCO1_ENST00000296137.2_Intron|FYCO1_ENST00000438446.1_Intron|CXCR6_ENST00000304552.4_Missense_Mutation_p.R296G|FYCO1_ENST00000535325.1_Intron|CXCR6_ENST00000457814.1_Missense_Mutation_p.R296G|CXCR6_ENST00000438735.1_Missense_Mutation_p.R296G			O00574	CXCR6_HUMAN	chemokine (C-X-C motif) receptor 6	296					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)		CCTGAAGTTTCGAAAGAACTT	0.478																																					p.R296G	Esophageal Squamous(63;1005 1117 15521 45762 47089)	Atlas-SNP	.											.	CXCR6	17	.	0			c.C886G						PASS	.						113	101	105					3																	45988859		2203	4300	6503	SO:0001583	missense	10663	exon2			AAGTTTCGAAAGA	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.886C>G	chr3.hg19:g.45988859C>G	ENSP00000395704:p.Arg296Gly	81.0	0.0	.		74.0	38.0	.	NM_006564	O00575|Q9HCA5	Missense_Mutation	SNP	ENST00000458629.1	hg19	CCDS2735.1	.	.	.	.	.	.	.	.	.	.	C	16.88	3.243587	0.58995	.	.	ENSG00000172215	ENST00000438735;ENST00000304552;ENST00000458629;ENST00000457814	T;T;T;T	0.58358	0.34;0.34;0.34;0.34	5.83	3.86	0.44501	.	0.049616	0.85682	D	0.000000	T	0.64853	0.2636	M	0.68952	2.095	0.40450	D	0.980135	D	0.64830	0.994	P	0.57911	0.829	T	0.71241	-0.4651	10	0.87932	D	0	.	13.1958	0.59738	0.3957:0.6043:0.0:0.0	.	296	O00574	CXCR6_HUMAN	G	296	ENSP00000396218:R296G;ENSP00000304414:R296G;ENSP00000395704:R296G;ENSP00000396886:R296G	ENSP00000304414:R296G	R	+	1	2	CXCR6	45963863	0.092000	0.21681	0.939000	0.37840	0.975000	0.68041	0.375000	0.20518	1.454000	0.47793	-0.314000	0.08810	CGA	.	.	.	none		0.478	CXCR6-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344395.1			G	45988859	C	G	45988859	3	3	224	1	0	0	0	0	1	0	0	0	4097	876	31	4	888	4	CXCR6	3	45988859	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	6761883	45988859	152033571	23	13596											
SLC38A3	10991	hgsc.bcm.edu	37	chr3	50254733	50254733	+	RNA	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	gtcaccatcattctgcccctGgcactgatgcggcagcttgg	6	10	11	14	1	3	1	2	1	1	0	3	1	3	1	3	3	3	3	3	3	0	2			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr3:50254733G>C	ENST00000420502.1	+	0	765									solute carrier family 38, member 3											breast(1)|cervix(1)|endometrium(1)|lung(3)	6				BRCA - Breast invasive adenocarcinoma(193;0.000275)|KIRC - Kidney renal clear cell carcinoma(197;0.00548)|Kidney(197;0.00615)		TTCTGCCCCTGGCACTGATGC	0.587																																					p.L204L		Atlas-SNP	.											.	SLC38A3	22	.	0			c.G612C						PASS	.						61	65	64					3																	50254733		2040	4208	6248			10991	exon8			GCCCCTGGCACTG	U49082	CCDS74940.1	3p21.3	2013-05-22			ENSG00000188338	ENSG00000188338		"Solute carriers"	18044	protein-coding gene	gene with protein product		604437				10619430, 10823827	Standard	XM_006712954		Approved	G17, SN1	uc003cyn.4	Q99624	OTTHUMG00000156764		chr3.hg19:g.50254733G>C		42.0	0.0	.		62.0	27.0	.	NM_006841		Silent	SNP	ENST00000420502.1	hg19																																																																																				.	.	.	none		0.587	SLC38A3-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000345635.2	NM_006841		C	50254733	G	C	50254733	1	2	224	0	1	0	0	0	0	0	0	0	14618	1335	47	4		4	SLC38A3	3	50254733	RNA	SNP	G	TCGA-MH-A854-01A-11D-A34Z-10	4265874	50254733	147767697	24	13597											
CACNA2D2	9254	hgsc.bcm.edu	37	chr3	50416403	50416403	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcatagttatgctgccccaCggagaaagtaaacacgcgca	13	7	10	11	3	1	1	1	0	0	1	1	2	1	1	2	1	3	4	2	1	5	3			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr3:50416403C>T	ENST00000479441.1	-	13	1281	c.1282G>A	c.(1282-1284)Gtg>Atg	p.V428M	CACNA2D2_ENST00000423994.2_Missense_Mutation_p.V428M|CACNA2D2_ENST00000424201.2_Missense_Mutation_p.V428M|CACNA2D2_ENST00000435965.1_Missense_Mutation_p.V428M|CACNA2D2_ENST00000266039.3_Missense_Mutation_p.V428M|CACNA2D2_ENST00000360963.3_Missense_Mutation_p.V359M|CACNA2D2_ENST00000395083.1_Missense_Mutation_p.V428M|CACNA2D2_ENST00000429770.1_Missense_Mutation_p.V428M			Q9NY47	CA2D2_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 2	428	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				energy reserve metabolic process (GO:0006112)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|positive regulation of organ growth (GO:0046622)|regulation of insulin secretion (GO:0050796)|regulation of multicellular organism growth (GO:0040014)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|cervix(1)|endometrium(4)|large_intestine(4)|lung(8)|ovary(2)|prostate(4)|skin(4)|urinary_tract(1)	31				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Amiodarone(DB01118)|Bepridil(DB01244)|Felodipine(DB01023)|Gabapentin(DB00996)|Isradipine(DB00270)|Nitrendipine(DB01054)|Spironolactone(DB00421)	TGCTGCCCCACGGAGAAAGTA	0.607																																					p.V428M		Atlas-SNP	.											.	CACNA2D2	82	.	0			c.G1282A						PASS	.						83	74	77					3																	50416403		2203	4300	6503	SO:0001583	missense	9254	exon13			GCCCCACGGAGAA	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.1282G>A	chr3.hg19:g.50416403C>T	ENSP00000418081:p.Val428Met	37.0	0.0	.		32.0	12.0	.	NM_001174051	A7MD15|Q9NY48|Q9UEW0|Q9Y268	Missense_Mutation	SNP	ENST00000479441.1	hg19	CCDS54588.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.412276	0.83340	.	.	ENSG00000007402	ENST00000423994;ENST00000429770;ENST00000266039;ENST00000360963;ENST00000435965;ENST00000395083;ENST00000424201;ENST00000479441	D;D;D;D;D;D;D;D	0.87029	-2.2;-2.2;-2.2;-2.2;-2.2;-2.2;-2.2;-2.2	4.3	4.3	0.51218	von Willebrand factor, type A (3);	0.063724	0.64402	D	0.000008	D	0.91178	0.7221	L	0.58810	1.83	0.58432	D	0.999995	D;D	0.65815	0.995;0.982	P;P	0.61328	0.887;0.493	D	0.92409	0.5936	10	0.87932	D	0	-16.6573	17.3344	0.87276	0.0:1.0:0.0:0.0	.	428;428	Q9NY47;Q9NY47-2	CA2D2_HUMAN;.	M	428;428;428;359;428;428;428;428	ENSP00000407393:V428M;ENSP00000404631:V428M;ENSP00000266039:V428M;ENSP00000354228:V359M;ENSP00000390526:V428M;ENSP00000378519:V428M;ENSP00000390329:V428M;ENSP00000418081:V428M	ENSP00000266039:V428M	V	-	1	0	CACNA2D2	50391407	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.689000	0.68234	2.396000	0.81511	0.557000	0.71058	GTG	.	.	.	none		0.607	CACNA2D2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346457.1	NM_006030		T	50416403	C	T	50416403	3	4	224	1	0	0	0	0	1	0	0	0	2551	536	19	1	2284	1	CACNA2D2	3	50416403	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	161670	50416403	147606027	25	13598											
STAB1	23166	hgsc.bcm.edu	37	chr3	52548199	52548199	+	Silent	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	tttgtgcccaccaaccgctcCctggaggcccagggcaacag	8	6	11	16	1	0	0	0	0	0	0	1	1	1	1	5	3	3	2	5	3	2	1			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr3:52548199C>T	ENST00000321725.6	+	33	3592	c.3516C>T	c.(3514-3516)tcC>tcT	p.S1172S		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	1172	FAS1 4. {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)		CCAACCGCTCCCTGGAGGCCC	0.637																																					p.S1172S		Atlas-SNP	.											.	STAB1	178	.	0			c.C3516T						PASS	.						68	68	68					3																	52548199		2203	4300	6503	SO:0001819	synonymous_variant	23166	exon33			CCGCTCCCTGGAG	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.3516C>T	chr3.hg19:g.52548199C>T		51.0	0.0	.		38.0	15.0	.	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Silent	SNP	ENST00000321725.6	hg19	CCDS33768.1																																																																																			.	.	.	none		0.637	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		T	52548199	C	T	52548199	2	4	224	1	0	0	0	0	0	0	0	1	15249	610	22	2		2	STAB1	3	52548199	Silent	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	2131796	52548199	145474231	26	13599											
NIT2	56954	hgsc.bcm.edu	37	chr3	100074091	100074091	+	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	aagcgatcagacctctatgcTgtggagatgaaaaagcccta	14	8	10	9	1	2	3	1	1	1	2	2	5	2	3	2	1	3	1	2	1	5	2	rs144496756		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr3:100074091T>A	ENST00000394140.4	+	10	901	c.810T>A	c.(808-810)gcT>gcA	p.A270A		NM_020202.4	NP_064587.1	Q9NQR4	NIT2_HUMAN	nitrilase family, member 2	270	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				asparagine metabolic process (GO:0006528)|glutamine metabolic process (GO:0006541)|oxaloacetate metabolic process (GO:0006107)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	omega-amidase activity (GO:0050152)			breast(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(1)	17						ACCTCTATGCTGTGGAGATGA	0.378																																					p.A270A		Atlas-SNP	.											.	NIT2	35	.	0			c.T810A						PASS	.						78	77	77					3																	100074091		2203	4300	6503	SO:0001819	synonymous_variant	56954	exon10			CTATGCTGTGGAG	AF284574	CCDS33806.1	3q12.3	2004-07-12			ENSG00000114021	ENSG00000114021			29878	protein-coding gene	gene with protein product						10959838	Standard	NM_020202		Approved		uc003dtv.3	Q9NQR4	OTTHUMG00000159066	ENST00000394140.4:c.810T>A	chr3.hg19:g.100074091T>A		62.0	0.0	.		82.0	24.0	.	NM_020202	B2R9A3|D3DN47|Q8WUF0	Silent	SNP	ENST00000394140.4	hg19	CCDS33806.1																																																																																			.	T|0.999;C|0.001	.	alt		0.378	NIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353142.2	NM_020202		A	100074091	T	A	100074091	2	1	224	1	0	0	0	0	0	0	0	1	10441	1567	55	5		5	NIT2	3	100074091	Silent	SNP	T	TCGA-MH-A854-01A-11D-A34Z-10	47525892	100074091	97948339	27	13600											
ADCY5	111	hgsc.bcm.edu	37	chr3	123038548	123038548	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctaagtcaggctccctgaaGgtcaggaggaacttgcggac	10	8	13	10	1	3	1	2	1	1	0	4	4	4	4	1	5	2	1	1	5	3	2			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr3:123038548G>A	ENST00000462833.1	-	10	3441	c.2229C>T	c.(2227-2229)acC>acT	p.T743T	ADCY5_ENST00000491190.1_Silent_p.T376T|ADCY5_ENST00000309879.5_Silent_p.T393T	NM_183357.2	NP_899200.1	O95622	ADCY5_HUMAN	adenylate cyclase 5	743					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(22)|ovary(5)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(114;0.0342)		GCTCCCTGAAGGTCAGGAGGA	0.577																																					p.T743T		Atlas-SNP	.											.	ADCY5	169	.	0			c.C2229T						PASS	.						87	76	79					3																	123038548		2203	4300	6503	SO:0001819	synonymous_variant	111	exon10			CCTGAAGGTCAGG	U65473	CCDS3022.1, CCDS56274.1	3q21.1	2013-02-04			ENSG00000173175	ENSG00000173175	4.6.1.1	"Adenylate cyclases"	236	protein-coding gene	gene with protein product		600293				10481931	Standard	NM_183357		Approved	AC5	uc003egh.2	O95622	OTTHUMG00000159517	ENST00000462833.1:c.2229C>T	chr3.hg19:g.123038548G>A		27.0	0.0	.		28.0	10.0	.	NM_183357	B7Z8A6|Q7RTV7|Q8NFM3	Silent	SNP	ENST00000462833.1	hg19	CCDS3022.1																																																																																			.	.	.	none		0.577	ADCY5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355889.4	XM_171048		A	123038548	G	A	123038548	2	1	224	1	0	0	0	0	0	0	0	1	297	987	35	2		2	ADCY5	3	123038548	Silent	SNP	G	TCGA-MH-A854-01A-11D-A34Z-10	22964457	123038548	74983882	28	13601											
ZNF639	51193	hgsc.bcm.edu	37	chr3	179050906	179050906	+	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	tctagaccacactgccttttCtacaggttgggggaactaat	10	12	9	10	0	2	1	0	0	2	1	2	2	2	2	2	3	3	1	2	3	4	6	rs75079502		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr3:179050906C>G	ENST00000326361.3	+	6	744	c.299C>G	c.(298-300)tCt>tGt	p.S100C	ZNF639_ENST00000484866.1_Missense_Mutation_p.S100C|ZNF639_ENST00000466663.1_3'UTR|ZNF639_ENST00000496856.1_Missense_Mutation_p.S100C	NM_016331.1	NP_057415.1	Q9UID6	ZN639_HUMAN	zinc finger protein 639	100					negative regulation by host of viral transcription (GO:0043922)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of cell growth (GO:0030307)|transcription, DNA-templated (GO:0006351)|viral entry into host cell (GO:0046718)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein self-association (GO:0043621)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(10)|urinary_tract(1)	16	all_cancers(143;7.9e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			actgcctTTTCTACAGGTTGG	0.353																																					p.S100C		Atlas-SNP	.											.	ZNF639	45	.	0			c.C299G						PASS	.						63	58	59					3																	179050906		2203	4298	6501	SO:0001583	missense	51193	exon6			CCTTTTCTACAGG	BC020500	CCDS3227.1	3q27.1	2010-03-26			ENSG00000121864	ENSG00000121864		"Zinc fingers, C2H2-type"	30950	protein-coding gene	gene with protein product	"zinc finger amplified in esophageal squamous cell carcinomas 1"					14522885	Standard	NM_016331		Approved	ANC-2H01, ZASC1	uc003fjr.1	Q9UID6	OTTHUMG00000157439	ENST00000326361.3:c.299C>G	chr3.hg19:g.179050906C>G	ENSP00000325634:p.Ser100Cys	75.0	0.0	.		56.0	13.0	.	NM_016331	A9X3Z9|D3DNR3	Missense_Mutation	SNP	ENST00000326361.3	hg19	CCDS3227.1	.	.	.	.	.	.	.	.	.	.	C	8.257	0.810266	0.16537	.	.	ENSG00000121864	ENST00000496856;ENST00000491818;ENST00000481587;ENST00000326361;ENST00000466264;ENST00000484866;ENST00000494234	T;T;T;T	0.03831	3.79;3.79;4.42;3.79	5.86	5.86	0.93980	.	0.861759	0.10491	N	0.668436	T	0.05410	0.0143	N	0.24115	0.695	0.23238	N	0.998063	P	0.34462	0.454	B	0.29942	0.109	T	0.40776	-0.9545	10	0.72032	D	0.01	.	16.0536	0.80779	0.0:1.0:0.0:0.0	.	100	Q9UID6	ZN639_HUMAN	C	100	ENSP00000417740:S100C;ENSP00000325634:S100C;ENSP00000419650:S100C;ENSP00000418766:S100C	ENSP00000325634:S100C	S	+	2	0	ZNF639	180533600	0.777000	0.28628	0.523000	0.27875	0.355000	0.29361	3.174000	0.50847	2.937000	0.99478	0.650000	0.86243	TCT	.	C|0.750;T|0.250	.	alt		0.353	ZNF639-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348855.1	NM_016331		G	179050906	C	G	179050906	3	3	224	1	0	0	0	0	1	0	0	0	18068	913	32	4	309	4	ZNF639	3	179050906	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	56012358	179050906	18971524	29	13602											
PPP1R2	5504	hgsc.bcm.edu	37	chr3	195251642	195251642	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctaagatgtctggcgccaTggcttcagtggcctcggtgt	5	11	15	10	2	2	1	1	0	1	1	3	1	2	1	2	5	0	2	2	5	1	2			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr3:195251642T>C	ENST00000328432.3	-	3	643	c.283A>G	c.(283-285)Atg>Gtg	p.M95V	RNU6ATAC24P_ENST00000516811.1_RNA	NM_006241.4	NP_006232.1	P41236	IPP2_HUMAN	protein phosphatase 1, regulatory (inhibitor) subunit 2	95					generation of precursor metabolites and energy (GO:0006091)|glycogen metabolic process (GO:0005977)|negative regulation of catalytic activity (GO:0043086)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of signal transduction (GO:0009966)		protein serine/threonine phosphatase inhibitor activity (GO:0004865)			endometrium(2)|kidney(1)|large_intestine(1)|urinary_tract(2)	6	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)		Epithelial(36;2.64e-22)|all cancers(36;2.69e-20)|OV - Ovarian serous cystadenocarcinoma(49;3.52e-19)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;9.55e-05)		TCTGGCGCCATGGCTTCAGTG	0.448																																					p.M95V		Atlas-SNP	.											.	PPP1R2	11	.	0			c.A283G						PASS	.						108	91	97					3																	195251642		2203	4300	6503	SO:0001583	missense	5504	exon3			GCGCCATGGCTTC	U68111	CCDS3309.1	3q29	2012-04-17			ENSG00000184203	ENSG00000184203	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9288	protein-coding gene	gene with protein product		601792				9126490, 8119416	Standard	XM_006713682		Approved	IPP2	uc003fup.3	P41236	OTTHUMG00000155887	ENST00000328432.3:c.283A>G	chr3.hg19:g.195251642T>C	ENSP00000328178:p.Met95Val	161.0	0.0	.		152.0	50.0	.	NM_006241		Missense_Mutation	SNP	ENST00000328432.3	hg19	CCDS3309.1	.	.	.	.	.	.	.	.	.	.	T	4.282	0.051444	0.08291	.	.	ENSG00000184203	ENST00000328432	.	.	.	5.46	-3.69	0.04450	.	0.286677	0.35096	N	0.003456	T	0.15305	0.0369	N	0.05230	-0.09	0.30048	N	0.812	B	0.02656	0.0	B	0.01281	0.0	T	0.33137	-0.9880	9	0.11182	T	0.66	.	9.8244	0.40903	0.0:0.1674:0.5827:0.2498	.	95	P41236	IPP2_HUMAN	V	95	.	ENSP00000328178:M95V	M	-	1	0	PPP1R2	196732931	0.317000	0.24589	0.499000	0.27577	0.039000	0.13416	-0.917000	0.04025	-0.316000	0.08690	-0.334000	0.08254	ATG	.	.	.	none		0.448	PPP1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342133.1	NM_006241		C	195251642	T	C	195251642	3	2	224	1	0	0	0	0	1	0	0	0	12380	1464	51	3	350	3	PPP1R2	3	195251642	Missense_Mutation	SNP	T	TCGA-MH-A854-01A-11D-A34Z-10	16200736	195251642	2770788	30	13603											
ADD1	118	hgsc.bcm.edu	37	chr4	2910285	2910285	+	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	cattaagacggctggccctcAgtcccaggttttgtgtggtg	6	12	13	10	1	1	1	1	0	0	1	2	1	2	1	2	4	0	2	2	4	1	3			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr4:2910285A>T	ENST00000398129.1	+	11	1579	c.1559A>T	c.(1558-1560)cAg>cTg	p.Q520L	ADD1_ENST00000503455.2_Missense_Mutation_p.Q551L|ADD1_ENST00000513328.2_Missense_Mutation_p.Q520L|ADD1_ENST00000398125.1_Missense_Mutation_p.Q551L|ADD1_ENST00000355842.3_Missense_Mutation_p.Q520L|ADD1_ENST00000264758.7_Missense_Mutation_p.Q551L|ADD1_ENST00000446856.1_Missense_Mutation_p.Q520L|ADD1_ENST00000398123.2_Missense_Mutation_p.Q551L			P35611	ADDA_HUMAN	adducin 1 (alpha)	520					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)		GCTGGCCCTCAGTCCCAGGTT	0.572																																					p.Q551L	Esophageal Squamous(71;505 1201 20414 34538 37449)	Atlas-SNP	.											.	ADD1	56	.	0			c.A1652T						PASS	.						175	139	151					4																	2910285		2203	4300	6503	SO:0001583	missense	118	exon12			GCCCTCAGTCCCA	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.1559A>T	chr4.hg19:g.2910285A>T	ENSP00000381197:p.Gln520Leu	73.0	0.0	.		81.0	33.0	.	NM_176801	A2A3N8|A2A3P0|B4DI79|D3DVR3|D3DVR4|D3DVR5|Q13734|Q14729|Q16156|Q86XM2|Q9UJB6	Missense_Mutation	SNP	ENST00000398129.1	hg19	CCDS43205.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	34|34	5.322861|5.322861	0.95708|0.95708	.|.	.|.	ENSG00000087274|ENSG00000087274	ENST00000264758;ENST00000446856;ENST00000398125;ENST00000513328;ENST00000503455;ENST00000355842;ENST00000398123;ENST00000398129;ENST00000536424|ENST00000514940	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|.	5.91|5.91	5.91|5.91	0.95273|0.95273	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.78704|0.78704	0.4325|0.4325	M|M	0.82823|0.82823	2.61|2.61	0.80722|0.80722	D|D	1|1	D;D;D;D;P|.	0.67145|.	0.985;0.996;0.958;0.992;0.93|.	D;D;P;D;P|.	0.74348|.	0.983;0.954;0.749;0.979;0.566|.	T|T	0.80329|0.80329	-0.1428|-0.1428	10|5	0.62326|.	D|.	0.03|.	-26.831|-26.831	16.3512|16.3512	0.83208|0.83208	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	520;520;551;520;551|.	Q86XM2;P35611;P35611-3;P35611-2;A2A3N8|.	.;ADDA_HUMAN;.;.;.|.	L|C	551;520;551;520;551;520;551;520;20|257	ENSP00000264758:Q551L;ENSP00000399828:Q520L;ENSP00000381193:Q551L;ENSP00000421907:Q520L;ENSP00000423024:Q551L;ENSP00000348100:Q520L;ENSP00000381191:Q551L;ENSP00000381197:Q520L;ENSP00000438069:Q20L|.	ENSP00000264758:Q551L|.	Q|S	+|+	2|1	0|0	ADD1|ADD1	2880083|2880083	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.845000|8.845000	0.92153|0.92153	2.266000|2.266000	0.75297|0.75297	0.533000|0.533000	0.62120|0.62120	CAG|AGT	.	.	.	none		0.572	ADD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242840.1	NM_014189		T	2910285	A	T	2910285	3	4	224	1	0	0	0	0	1	0	0	0	304	188	7	5	1694	5	ADD1	4	2910285	Missense_Mutation	SNP	A	TCGA-MH-A854-01A-11D-A34Z-10		2910285	188243991	31	13604											
C4orf23	152992	hgsc.bcm.edu	37	chr4	8456486	8456486	+	Missense_Mutation	SNP	T	T	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	cagcatccaggcagagggatTgatgtccgaagaagaaaaat	16	6	12	7	1	0	4	0	1	0	3	2	6	2	5	2	2	1	2	2	2	4	1			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr4:8456486T>G	ENST00000389737.4	+	6	1149	c.1149T>G	c.(1147-1149)atT>atG	p.I383M	TRMT44_ENST00000513449.2_Missense_Mutation_p.I142M|RP11-689P11.3_ENST00000515186.1_RNA	NM_152544.2	NP_689757.2	Q8IYL2	TRM44_HUMAN	tRNA methyltransferase 44 homolog (S. cerevisiae)	383					tRNA processing (GO:0008033)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)										GCAGAGGGATTGATGTCCGAA	0.393																																					p.I383M		Atlas-SNP	.											.	TRMT44	7	.	0			c.T1149G						PASS	.						126	122	123					4																	8456486		2203	4300	6503	SO:0001583	missense	152992	exon6			AGGGATTGATGTC	AK093044	CCDS3402.1, CCDS3402.2	4p16.1	2012-06-12	2012-06-12	2012-06-12	ENSG00000155275	ENSG00000155275			26653	protein-coding gene	gene with protein product	"tRNA methyltransferase 44 homolog (S. cerevisiae)"	614309	"chromosome 4 open reading frame 23", "methyltransferase like 19"	C4orf23, METTL19		21658913	Standard	NM_152544		Approved	FLJ35725, TRM44	uc003glg.2	Q8IYL2	OTTHUMG00000160935	ENST00000389737.4:c.1149T>G	chr4.hg19:g.8456486T>G	ENSP00000374387:p.Ile383Met	96.0	0.0	.		68.0	29.0	.	NM_152544	Q8NA95	Missense_Mutation	SNP	ENST00000389737.4	hg19	CCDS3402.2	.	.	.	.	.	.	.	.	.	.	t	17.24	3.340592	0.60963	.	.	ENSG00000155275	ENST00000513449;ENST00000389737	T;T	0.35789	1.29;1.29	4.33	-3.76	0.04359	.	0.063137	0.64402	U	0.000008	T	0.52661	0.1748	M	0.91300	3.195	0.58432	D	0.99999	P;D	0.56746	0.856;0.977	P;P	0.61477	0.858;0.889	T	0.53954	-0.8365	10	0.87932	D	0	-10.8156	3.5823	0.07958	0.2523:0.2232:0.0:0.5245	.	383;142	Q8IYL2;Q8IYL2-2	TRM44_HUMAN;.	M	142;383	ENSP00000424643:I142M;ENSP00000374387:I383M	ENSP00000374387:I383M	I	+	3	3	METTL19	8507386	0.954000	0.32549	0.962000	0.40283	0.990000	0.78478	-0.081000	0.11321	-0.892000	0.03935	0.524000	0.50904	ATT	.	.	.	none		0.393	TRMT44-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359197.2	NM_152544		G	8456486	T	G	8456486	3	3	224	1	0	0	0	0	1	0	0	0	2258	1800	63	5	1171	5	C4orf23	4	8456486	Missense_Mutation	SNP	T	TCGA-MH-A854-01A-11D-A34Z-10	5546201	8456486	182697790	32	13605											
NIPAL1	152519	hgsc.bcm.edu	37	chr4	48037631	48037631	+	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	atctccttggtgctgattttGattgtggctcccaagaaagg	8	14	11	8	0	1	3	0	2	1	1	3	3	2	3	2	3	1	2	2	3	2	4			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr4:48037631G>A	ENST00000295461.5	+	6	741	c.675G>A	c.(673-675)ttG>ttA	p.L225L		NM_207330.1	NP_997213.1	Q6NVV3	NIPA3_HUMAN	NIPA-like domain containing 1	225						integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			endometrium(2)|large_intestine(1)|lung(3)|skin(2)	8						TGCTGATTTTGATTGTGGCTC	0.383																																					p.L225L		Atlas-SNP	.											.	NIPAL1	29	.	0			c.G675A						PASS	.						117	117	117					4																	48037631		2203	4300	6503	SO:0001819	synonymous_variant	152519	exon6			GATTTTGATTGTG	BC067881	CCDS3479.1	4p12	2009-03-24		2009-03-24	ENSG00000163293	ENSG00000163293			27194	protein-coding gene	gene with protein product				NPAL1			Standard	NM_207330		Approved	DKFZp686A06115	uc003gxw.3	Q6NVV3	OTTHUMG00000128622	ENST00000295461.5:c.675G>A	chr4.hg19:g.48037631G>A		148.0	0.0	.		139.0	45.0	.	NM_207330	B3KTB0|Q68DA9	Silent	SNP	ENST00000295461.5	hg19	CCDS3479.1																																																																																			.	.	.	none		0.383	NIPAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250491.4	NM_207330		A	48037631	G	A	48037631	2	1	224	1	0	0	0	0	0	0	0	1	10431	1281	45	2		2	NIPAL1	4	48037631	Silent	SNP	G	TCGA-MH-A854-01A-11D-A34Z-10	39581145	48037631	143116645	33	13606											
EPHA5	2044	hgsc.bcm.edu	37	chr4	66201790	66201790	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attaactgatagagagcagcAggacaatccatggggcttgg	13	8	13	7	0	0	2	0	1	0	1	1	4	1	3	1	4	3	3	1	4	3	3			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr4:66201790A>G	ENST00000273854.3	-	16	3312	c.2712T>C	c.(2710-2712)ccT>ccC	p.P904P	EPHA5_ENST00000511294.1_Silent_p.P905P|EPHA5_ENST00000354839.4_Silent_p.P882P|EPHA5_ENST00000432638.2_Silent_p.P741P	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	904	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						AGAGAGCAGCAGGACAATCCA	0.453										TSP Lung(17;0.13)																											p.P904P		Atlas-SNP	.											.	EPHA5	315	.	0			c.T2712C						PASS	.						112	96	101					4																	66201790		2203	4299	6502	SO:0001819	synonymous_variant	2044	exon16			AGCAGCAGGACAA	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.2712T>C	chr4.hg19:g.66201790A>G		84.0	0.0	.		70.0	31.0	.	NM_004439	Q7Z3F2	Silent	SNP	ENST00000273854.3	hg19	CCDS3513.1																																																																																			.	.	.	none		0.453	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		G	66201790	A	G	66201790	2	3	224	1	0	0	0	0	0	0	0	1	5172	175	7	3		3	EPHA5	4	66201790	Silent	SNP	A	TCGA-MH-A854-01A-11D-A34Z-10	18164159	66201790	124952486	34	13607											
SH3TC2	79628	hgsc.bcm.edu	37	chr5	148407090	148407090	+	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	tgtctgagcattgggcaggcCaaggcagaaacttcacccca	11	7	11	12	0	2	2	1	1	1	1	2	2	2	2	3	3	2	3	3	3	2	2			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr5:148407090C>A	ENST00000515425.1	-	11	2306	c.2205G>T	c.(2203-2205)ttG>ttT	p.L735F	SH3TC2_ENST00000394358.2_Missense_Mutation_p.L620F|SH3TC2_ENST00000538184.1_Missense_Mutation_p.L282F|SH3TC2_ENST00000513340.1_5'Flank|SH3TC2_ENST00000512049.1_Missense_Mutation_p.L728F	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	735					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)			TTGGGCAGGCCAAGGCAGAAA	0.572																																					p.L735F		Atlas-SNP	.											.	SH3TC2	178	.	0			c.G2205T						PASS	.						61	64	63					5																	148407090		2203	4300	6503	SO:0001583	missense	79628	exon11			GCAGGCCAAGGCA	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.2205G>T	chr5.hg19:g.148407090C>A	ENSP00000423660:p.Leu735Phe	51.0	0.0	.		50.0	22.0	.	NM_024577	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Missense_Mutation	SNP	ENST00000515425.1	hg19	CCDS4293.1	.	.	.	.	.	.	.	.	.	.	C	12.13	1.846276	0.32606	.	.	ENSG00000169247	ENST00000538184;ENST00000515425;ENST00000512049;ENST00000394358	T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.38	6.16	6.16	0.99307	.	0.082696	0.51477	D	0.000086	T	0.78483	0.4290	L	0.59436	1.845	0.43814	D	0.996379	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.78314	0.991;0.972;0.972;0.972	T	0.78168	-0.2309	10	0.59425	D	0.04	-4.7214	13.9788	0.64291	0.0:0.9314:0.0:0.0686	.	620;728;735;735	C9JLC3;Q14CC0;E9PDF1;Q8TF17	.;.;.;S3TC2_HUMAN	F	282;735;728;620	ENSP00000441427:L282F;ENSP00000423660:L735F;ENSP00000421860:L728F;ENSP00000377886:L620F	ENSP00000377886:L620F	L	-	3	2	SH3TC2	148387283	0.991000	0.36638	0.997000	0.53966	0.200000	0.23975	0.534000	0.23098	2.937000	0.99478	0.650000	0.86243	TTG	.	.	.	none		0.572	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577		A	148407090	C	A	148407090	3	1	224	1	0	0	0	0	1	0	0	0	14275	593	21	4	1689	4	SH3TC2	5	148407090	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10		148407090	32508170	35	13608											
MGAT4B	11282	hgsc.bcm.edu	37	chr5	179225417	179225417	+	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	cggccctcctgcagggcctcCttgtctgactgagggttctg	3	11	13	14	1	2	2	0	2	2	0	4	2	4	2	4	3	1	2	4	3	0	2			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr5:179225417C>A	ENST00000292591.7	-	13	1790	c.1440G>T	c.(1438-1440)aaG>aaT	p.K480N	MGAT4B_ENST00000337755.5_Missense_Mutation_p.K495N|MIR1229_ENST00000408467.1_RNA|MGAT4B_ENST00000521305.1_5'Flank	NM_014275.4	NP_055090.1	Q9UQ53	MGT4B_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme B	480					cellular protein metabolic process (GO:0044267)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	13	all_cancers(89;0.000201)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0525)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCAGGGCCTCCTTGTCTGACT	0.662																																					p.K495N	GBM(13;414 434 4098 22176 23230)	Atlas-SNP	.											.	MGAT4B	41	.	0			c.G1485T						PASS	.						33	34	33					5																	179225417		2203	4299	6502	SO:0001583	missense	11282	exon12			GGCCTCCTTGTCT	AB000624	CCDS4448.1, CCDS4449.1	5q35	2013-02-25	2005-11-16		ENSG00000161013	ENSG00000161013	2.4.1.145	"Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"	7048	protein-coding gene	gene with protein product		604561	"mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme B"			10372966	Standard	NM_014275		Approved	GnT-Ivb	uc003mks.3	Q9UQ53	OTTHUMG00000130912	ENST00000292591.7:c.1440G>T	chr5.hg19:g.179225417C>A	ENSP00000292591:p.Lys480Asn	45.0	0.0	.		32.0	14.0	.	NM_054013	A8MPR0|Q86TF1|Q96GH4|Q9NSK6	Missense_Mutation	SNP	ENST00000292591.7	hg19	CCDS4448.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	23.8|23.8|23.8	4.456538|4.456538|4.456538	0.84317|0.84317|0.84317	.|.|.	.|.|.	ENSG00000161013|ENSG00000161013|ENSG00000161013	ENST00000518778;ENST00000520875|ENST00000337755;ENST00000292591;ENST00000519836|ENST00000520969;ENST00000518980;ENST00000518867	.|T;T|.	.|0.33654|.	.|1.4;1.42|.	5.09|5.09|5.09	2.14|2.14|2.14	0.27477|0.27477|0.27477	.|.|.	.|0.000000|.	.|0.85682|.	.|D|.	.|0.000000|.	.|T|T	.|0.54447|0.54447	.|0.1859|0.1859	L|L|L	0.50333|0.50333|0.50333	1.59|1.59|1.59	0.58432|0.58432|0.58432	D|D|D	0.999998|0.999998|0.999998	.|P;P;D|.	.|0.76494|.	.|0.906;0.906;0.999|.	.|B;B;D|.	.|0.78314|.	.|0.264;0.444;0.991|.	.|T|T	.|0.45891|0.45891	.|-0.9230|-0.9230	.|10|5	.|0.17832|.	.|T|.	.|0.49|.	-31.9236|-31.9236|-31.9236	6.435|6.435|6.435	0.21819|0.21819|0.21819	0.0:0.6875:0.1492:0.1633|0.0:0.6875:0.1492:0.1633|0.0:0.6875:0.1492:0.1633	.|.|.	.|480;495;479|.	.|Q9UQ53;A8MPR0;Q9UQ53-2|.	.|MGT4B_HUMAN;.;.|.	X|N|M	305;261|495;480;348|172;226;241	.|ENSP00000338487:K495N;ENSP00000292591:K480N|.	.|ENSP00000292591:K480N|.	G|K|R	-|-|-	1|3|2	0|2|0	MGAT4B|MGAT4B|MGAT4B	179158023|179158023|179158023	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.968000|0.968000|0.968000	0.65278|0.65278|0.65278	0.894000|0.894000|0.894000	0.28350|0.28350|0.28350	0.547000|0.547000|0.547000	0.28938|0.28938|0.28938	0.561000|0.561000|0.561000	0.74099|0.74099|0.74099	GGA|AAG|AGG	.	.	.	none		0.662	MGAT4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253503.3	NM_014275		A	179225417	C	A	179225417	3	1	224	1	0	0	0	0	1	0	0	0	9553	680	24	4	218	4	MGAT4B	5	179225417	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	30818327	179225417	1689843	36	13609											
VARS2	57176	hgsc.bcm.edu	37	chr6	30886640	30886640	+	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	aggaaccacaaggccagagaCgctgcctggagatgtggctg	11	5	15	10	1	0	2	0	0	0	2	0	5	0	3	3	4	2	2	3	4	2	0			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr6:30886640C>G	ENST00000321897.5	+	10	1654	c.1022C>G	c.(1021-1023)aCg>aGg	p.T341R	VARS2_ENST00000542001.1_Missense_Mutation_p.T201R|VARS2_ENST00000541562.1_Missense_Mutation_p.T371R|VARS2_ENST00000416670.2_Missense_Mutation_p.T341R			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	341					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						AGGCCAGAGACGCTGCCTGGA	0.547																																					p.T371R		Atlas-SNP	.											.	VARS2	60	.	0			c.C1112G						PASS	.						102	85	91					6																	30886640		1510	2707	4217	SO:0001583	missense	57176	exon11			CAGAGACGCTGCC	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.1022C>G	chr6.hg19:g.30886640C>G	ENSP00000316092:p.Thr341Arg	31.0	0.0	.		40.0	19.0	.	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Missense_Mutation	SNP	ENST00000321897.5	hg19	CCDS34387.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.432661	0.83776	.	.	ENSG00000137411	ENST00000321897;ENST00000416670;ENST00000542001;ENST00000541562	T;T;T;T	0.61158	0.13;0.13;0.13;0.13	4.54	4.54	0.55810	Valyl/Leucyl/Isoleucyl-tRNA synthetase, class Ia, editing domain (2);Aminoacyl-tRNA synthetase, class Ia (1);	0.000000	0.85682	D	0.000000	D	0.82715	0.5097	H	0.98446	4.235	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	0.89538	0.3790	10	0.87932	D	0	-12.4516	14.7942	0.69865	0.0:1.0:0.0:0.0	.	341;371;341	B7ZL25;F5GXJ0;Q5ST30	.;.;SYVM_HUMAN	R	341;341;201;371	ENSP00000316092:T341R;ENSP00000394802:T341R;ENSP00000438200:T201R;ENSP00000441000:T371R	ENSP00000316092:T341R	T	+	2	0	VARS2	30994619	1.000000	0.71417	0.934000	0.37439	0.976000	0.68499	6.793000	0.75130	2.093000	0.63338	0.563000	0.77884	ACG	.	.	.	none		0.547	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442		G	30886640	C	G	30886640	3	3	224	1	0	0	0	0	1	0	0	0	17136	536	19	4	1154	4	VARS2	6	30886640	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10		30886640	140228427	37	13610											
BRPF3	27154	hgsc.bcm.edu	37	chr6	36181792	36181792	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acctccaagcaggttcctaaAgcccagaaaggtggaagaag	15	5	11	10	0	0	2	0	0	0	2	2	3	2	3	4	3	2	2	4	3	6	2			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr6:36181792A>G	ENST00000357641.6	+	8	2871	c.2618A>G	c.(2617-2619)aAg>aGg	p.K873R	BRPF3_ENST00000443324.2_Intron|BRPF3_ENST00000339717.7_Intron|BRPF3_ENST00000534694.1_Intron|BRPF3_ENST00000534400.1_Missense_Mutation_p.K873R|BRPF3_ENST00000543502.1_Intron	NM_015695.2	NP_056510.2	Q9ULD4	BRPF3_HUMAN	bromodomain and PHD finger containing, 3	873					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						AGGTTCCTAAAGCCCAGAAAG	0.517																																					p.K873R		Atlas-SNP	.											.	BRPF3	93	.	0			c.A2618G						PASS	.						55	57	56					6																	36181792		2203	4300	6503	SO:0001583	missense	27154	exon8			TCCTAAAGCCCAG	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.2618A>G	chr6.hg19:g.36181792A>G	ENSP00000350267:p.Lys873Arg	44.0	0.0	.		41.0	18.0	.	NM_015695	A6ND56|A6NJE2|B7ZLN5|E7EX85|Q17RB6|Q5R3K8	Missense_Mutation	SNP	ENST00000357641.6	hg19	CCDS34437.1	.	.	.	.	.	.	.	.	.	.	A	15.26	2.780396	0.49891	.	.	ENSG00000096070	ENST00000357641;ENST00000534400;ENST00000394572	T;T	0.18338	2.41;2.22	5.86	5.86	0.93980	.	0.345140	0.33938	N	0.004413	T	0.05593	0.0147	L	0.43923	1.385	0.80722	D	1	B	0.25390	0.125	B	0.20184	0.028	T	0.13845	-1.0494	10	0.10377	T	0.69	.	10.7757	0.46348	0.9265:0.0:0.0735:0.0	.	873	Q9ULD4	BRPF3_HUMAN	R	873;873;287	ENSP00000350267:K873R;ENSP00000436504:K873R	ENSP00000350267:K873R	K	+	2	0	BRPF3	36289770	1.000000	0.71417	0.976000	0.42696	0.742000	0.42306	6.518000	0.73764	2.241000	0.73720	0.413000	0.27773	AAG	.	.	.	none		0.517	BRPF3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040335.3	NM_015695		G	36181792	A	G	36181792	3	3	224	1	0	0	0	0	1	0	0	0	1523	72	3	3	2644	3	BRPF3	6	36181792	Missense_Mutation	SNP	A	TCGA-MH-A854-01A-11D-A34Z-10	5295152	36181792	134933275	38	13611											
PNPLA1	285848	hgsc.bcm.edu	37	chr6	36259229	36259229	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtcctgcccgaggactcctAcaaggtcaccacggggaagc	9	5	13	14	2	1	0	1	0	0	0	3	3	3	2	4	5	3	0	4	5	3	1			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr6:36259229A>G	ENST00000394571.2	+	2	338	c.338A>G	c.(337-339)tAc>tGc	p.Y113C	PNPLA1_ENST00000388715.3_Missense_Mutation_p.Y18C|PNPLA1_ENST00000312917.5_Missense_Mutation_p.Y18C	NM_001145717.1	NP_001139189.2	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	113	Patatin.				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						GAGGACTCCTACAAGGTCACC	0.577																																					p.Y113C		Atlas-SNP	.											.	PNPLA1	92	.	0			c.A338G						PASS	.						90	79	83					6																	36259229		2203	4300	6503	SO:0001583	missense	285848	exon2			ACTCCTACAAGGT		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.338A>G	chr6.hg19:g.36259229A>G	ENSP00000378072:p.Tyr113Cys	53.0	0.0	.		45.0	21.0	.	NM_001145717	A3RMU3|J3JS20|Q2A6N1|Q3SY95|Q3SY96|Q5R3L2	Missense_Mutation	SNP	ENST00000394571.2	hg19	CCDS54997.1	.	.	.	.	.	.	.	.	.	.	A	16.47	3.131417	0.56828	.	.	ENSG00000180316	ENST00000388715;ENST00000312917;ENST00000457797;ENST00000394571	T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09	5.48	5.48	0.80851	Acyl transferase/acyl hydrolase/lysophospholipase (1);	0.087844	0.45606	D	0.000353	T	0.81791	0.4897	L	0.54323	1.7	0.46222	D	0.998936	P;D	0.89917	0.515;1.0	B;D	0.87578	0.141;0.998	D	0.84518	0.0626	10	0.72032	D	0.01	-22.4818	13.5137	0.61528	1.0:0.0:0.0:0.0	.	113;18	Q8N8W4;Q8N8W4-3	PLPL1_HUMAN;.	C	18;18;113;113	ENSP00000373367:Y18C;ENSP00000321116:Y18C;ENSP00000391868:Y113C;ENSP00000378072:Y113C	ENSP00000321116:Y18C	Y	+	2	0	PNPLA1	36367207	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	7.908000	0.87438	2.070000	0.61991	0.383000	0.25322	TAC	.	.	.	none		0.577	PNPLA1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_173676		G	36259229	A	G	36259229	3	3	224	1	0	0	0	0	1	0	0	0	12171	391	14	3	344	3	PNPLA1	6	36259229	Missense_Mutation	SNP	A	TCGA-MH-A854-01A-11D-A34Z-10	77437	36259229	134855838	39	13612											
ABCC10	89845	hgsc.bcm.edu	37	chr6	43403598	43403598	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtccttggaccggatccagcTtttcctcgaccttccaaacc	7	11	7	16	2	0	0	0	0	0	0	5	3	4	2	7	2	2	1	7	2	1	4			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr6:43403598T>C	ENST00000372530.4	+	5	1933	c.1718T>C	c.(1717-1719)cTt>cCt	p.L573P	ABCC10_ENST00000244533.3_Missense_Mutation_p.L530P	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	573					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)	CGGATCCAGCTTTTCCTCGAC	0.567																																					p.L573P		Atlas-SNP	.											.	ABCC10	118	.	0			c.T1718C						PASS	.						111	101	104					6																	43403598		2203	4300	6503	SO:0001583	missense	89845	exon5			TCCAGCTTTTCCT	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.1718T>C	chr6.hg19:g.43403598T>C	ENSP00000361608:p.Leu573Pro	94.0	0.0	.		77.0	37.0	.	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Missense_Mutation	SNP	ENST00000372530.4	hg19	CCDS56430.1	.	.	.	.	.	.	.	.	.	.	T	10.98	1.505257	0.26949	.	.	ENSG00000124574	ENST00000372515;ENST00000372530;ENST00000244533	D;D;D	0.94280	-3.39;-2.7;-2.71	5.12	3.32	0.38043	ABC transporter, transmembrane domain, type 1 (1);	0.651192	0.16159	N	0.226849	T	0.80199	0.4579	N	0.22421	0.69	0.37531	D	0.917901	B;B	0.21688	0.059;0.046	B;B	0.32677	0.15;0.026	T	0.71981	-0.4428	10	0.42905	T	0.14	-26.4903	4.7311	0.12964	0.2033:0.0:0.5197:0.277	.	530;573	Q5T3U5-2;Q5T3U5	.;MRP7_HUMAN	P	129;573;530	ENSP00000361593:L129P;ENSP00000361608:L573P;ENSP00000244533:L530P	ENSP00000244533:L530P	L	+	2	0	ABCC10	43511576	0.999000	0.42202	0.998000	0.56505	0.973000	0.67179	1.147000	0.31602	0.558000	0.29135	-0.656000	0.03901	CTT	.	.	.	none		0.567	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450		C	43403598	T	C	43403598	3	2	224	1	0	0	0	0	1	0	0	0	50	1609	56	3	1599	3	ABCC10	6	43403598	Missense_Mutation	SNP	T	TCGA-MH-A854-01A-11D-A34Z-10	7144369	43403598	127711469	40	13613											
KIAA1009	22832	hgsc.bcm.edu	37	chr6	84936099	84936099	+	Frame_Shift_Del	DEL	A	A	-																															ttcatctagctcttcttgggAacagttagccatagtcaaca																										TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr6:84936099delA	ENST00000403245.3	-	2	127	c.13delT	c.(13-15)tccfs	p.S5fs	KIAA1009_ENST00000257766.4_Intron	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)		TCTTCTTGGGAACAGTTAGCC	0.318																																					p.S5fs		Atlas-Indel,Pindel	.											.	KIAA1009	119	.	0			c.14delC						PASS	.						65	60	61					6																	84936099		1839	4066	5905	SO:0001589	frameshift_variant	22832	exon2			.																												ENST00000403245.3:c.13delT	chr6.hg19:g.84936099delA	ENSP00000385215:p.Ser5fs	71.0	0.0	0		71.0	34.0	0.478873	NM_014895		Frame_Shift_Del	DEL	ENST00000403245.3	hg19	CCDS34494.2																																																																																			.	.	.	none		0.318	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1			-	84936099	A	-	84936099	7	5	224	1	0	1	0	1	0	0	0	0	8210	246	9	0	4302	0	KIAA1009	6	84936099	Frame_Shift_Del	DEL	A	TCGA-MH-A854-01A-11D-A34Z-10	41532501	84936099	86178968	41	13614											
REV3L	5980	hgsc.bcm.edu	37	chr6	111680124	111680124	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtcagatgagatgcagtagaAcagagcacagattgggtcaa	15	7	13	6	0	2	5	2	1	0	5	2	6	2	5	0	1	3	3	0	1	3	2			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr6:111680124A>G	ENST00000358835.3	-	18	7427	c.6973T>C	c.(6973-6975)Ttc>Ctc	p.F2325L	REV3L_ENST00000435970.1_Missense_Mutation_p.F2247L|REV3L-IT1_ENST00000411895.1_RNA|REV3L_ENST00000368805.1_Missense_Mutation_p.F2325L|REV3L_ENST00000368802.3_Missense_Mutation_p.F2325L			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2325					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)		ATGCAGTAGAACAGAGCACAG	0.408								DNA polymerases (catalytic subunits)																													p.F2325L		Atlas-SNP	.											.	REV3L	386	.	0			c.T6973C						PASS	.						163	151	155					6																	111680124		2203	4300	6503	SO:0001583	missense	5980	exon17			AGTAGAACAGAGC	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.6973T>C	chr6.hg19:g.111680124A>G	ENSP00000351697:p.Phe2325Leu	125.0	0.0	.		121.0	48.0	.	NM_002912	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	hg19	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	A	33	5.272863	0.95429	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970;ENST00000543871	T;T;T;T	0.09163	3.01;3.01;3.01;3.01	5.65	5.65	0.86999	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.31104	0.0786	M	0.88310	2.945	0.53005	D	0.999969	P	0.51240	0.943	D	0.66716	0.946	T	0.22417	-1.0217	10	0.87932	D	0	.	15.883	0.79216	1.0:0.0:0.0:0.0	.	2325	O60673	DPOLZ_HUMAN	L	2325;2325;2325;2247;398	ENSP00000357792:F2325L;ENSP00000357795:F2325L;ENSP00000351697:F2325L;ENSP00000402003:F2247L	ENSP00000351697:F2325L	F	-	1	0	REV3L	111786817	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.721000	0.91446	2.150000	0.67090	0.455000	0.32223	TTC	.	.	.	none		0.408	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		G	111680124	A	G	111680124	3	3	224	1	0	0	0	0	1	0	0	0	13253	43	2	3	2483	3	REV3L	6	111680124	Missense_Mutation	SNP	A	TCGA-MH-A854-01A-11D-A34Z-10	26744025	111680124	59434943	42	13615											
KPNA5	3841	hgsc.bcm.edu	37	chr6	117023282	117023282	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tccgatttttatcaaacttcTtaattctgaacatgaagatg	13	16	5	7	1	3	3	1	2	2	1	4	4	4	3	1	0	2	0	1	0	5	6			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr6:117023282T>C	ENST00000368564.1	+	6	684	c.536T>C	c.(535-537)cTt>cCt	p.L179P	KPNA5_ENST00000356348.1_Missense_Mutation_p.L179P			O15131	IMA6_HUMAN	karyopherin alpha 5 (importin alpha 6)	176	NLS binding site (major). {ECO:0000250}.				cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)	protein transporter activity (GO:0008565)			breast(6)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0298)|all cancers(137;0.0461)|OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.212)		ATCAAACTTCTTAATTCTGAA	0.348																																					p.L179P		Atlas-SNP	.											.	KPNA5	57	.	0			c.T536C						PASS	.						103	102	102					6																	117023282		2203	4300	6503	SO:0001583	missense	3841	exon6			AACTTCTTAATTC	AF005361	CCDS5111.1	6q22.2	2013-02-14			ENSG00000196911	ENSG00000196911		"Importins", "Armadillo repeat containing"	6398	protein-coding gene	gene with protein product		604545				9395085	Standard	NM_002269		Approved	SRP6, IPOA6	uc003pxh.3	O15131	OTTHUMG00000015448	ENST00000368564.1:c.536T>C	chr6.hg19:g.117023282T>C	ENSP00000357552:p.Leu179Pro	113.0	0.0	.		100.0	39.0	.	NM_002269	B2RAI5|Q86X23	Missense_Mutation	SNP	ENST00000368564.1	hg19	CCDS5111.1	.	.	.	.	.	.	.	.	.	.	T	18.68	3.675139	0.67928	.	.	ENSG00000196911	ENST00000368564;ENST00000356348	D;D	0.84516	-1.86;-1.86	5.51	3.09	0.35607	Armadillo-like helical (1);Armadillo-type fold (1);	0.079936	0.50627	N	0.000102	D	0.92583	0.7644	H	0.97265	3.97	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91539	0.5248	10	0.87932	D	0	.	7.462	0.27300	0.1275:0.0696:0.0:0.8029	.	176	O15131	IMA5_HUMAN	P	179	ENSP00000357552:L179P;ENSP00000348704:L179P	ENSP00000348704:L179P	L	+	2	0	KPNA5	117129975	1.000000	0.71417	0.649000	0.29536	0.997000	0.91878	7.376000	0.79658	0.378000	0.24764	0.482000	0.46254	CTT	.	.	.	none		0.348	KPNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041967.1	NM_002269		C	117023282	T	C	117023282	3	2	224	1	0	0	0	0	1	0	0	0	8440	1609	56	3	558	3	KPNA5	6	117023282	Missense_Mutation	SNP	T	TCGA-MH-A854-01A-11D-A34Z-10	5343158	117023282	54091785	43	13616											
RFX6	222546	hgsc.bcm.edu	37	chr6	117246661	117246661	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctccgagttcatgctttcTggccaaccgtaataaaggga	10	12	9	10	2	3	0	1	0	2	0	4	2	3	1	3	2	2	3	3	2	4	5			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr6:117246661T>C	ENST00000332958.2	+	16	1740	c.1724T>C	c.(1723-1725)cTg>cCg	p.L575P		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	575					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						TCATGCTTTCTGGCCAACCGT	0.458																																					p.L575P		Atlas-SNP	.											.	RFX6	141	.	0			c.T1724C						PASS	.						136	137	137					6																	117246661		2203	4300	6503	SO:0001583	missense	222546	exon16			GCTTTCTGGCCAA	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.1724T>C	chr6.hg19:g.117246661T>C	ENSP00000332208:p.Leu575Pro	71.0	0.0	.		73.0	21.0	.	NM_173560	Q5T6B3	Missense_Mutation	SNP	ENST00000332958.2	hg19	CCDS5113.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.651636	0.88056	.	.	ENSG00000185002	ENST00000332958	T	0.70516	-0.49	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.78142	0.4237	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.78635	-0.2127	10	0.48119	T	0.1	-11.6703	16.5763	0.84648	0.0:0.0:0.0:1.0	.	575	Q8HWS3	RFX6_HUMAN	P	575	ENSP00000332208:L575P	ENSP00000332208:L575P	L	+	2	0	RFX6	117353354	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.649000	0.83500	2.317000	0.78254	0.459000	0.35465	CTG	.	.	.	none		0.458	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560		C	117246661	T	C	117246661	3	2	224	1	0	0	0	0	1	0	0	0	13280	1580	55	3	1786	3	RFX6	6	117246661	Missense_Mutation	SNP	T	TCGA-MH-A854-01A-11D-A34Z-10	223379	117246661	53868406	44	13617											
EPB41L2	2037	hgsc.bcm.edu	37	chr6	131216219	131216219	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctttgtaaatgagaagtccaTtagcacacacgcccagcttg	12	10	8	11	1	0	1	0	1	0	1	1	2	1	1	2	0	2	3	2	0	4	4			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr6:131216219T>C	ENST00000337057.3	-	9	1458	c.1277A>G	c.(1276-1278)aAt>aGt	p.N426S	EPB41L2_ENST00000528282.1_Missense_Mutation_p.N426S|EPB41L2_ENST00000530481.1_Missense_Mutation_p.N426S|EPB41L2_ENST00000527411.1_Missense_Mutation_p.N426S|EPB41L2_ENST00000525271.1_Missense_Mutation_p.N426S|EPB41L2_ENST00000529208.1_Missense_Mutation_p.N426S|EPB41L2_ENST00000392427.3_Missense_Mutation_p.N426S|EPB41L2_ENST00000445890.2_Missense_Mutation_p.N426S|EPB41L2_ENST00000525193.1_Missense_Mutation_p.N426S|EPB41L2_ENST00000368128.2_Missense_Mutation_p.N426S|EPB41L2_ENST00000527659.1_Missense_Mutation_p.N426S	NM_001431.3	NP_001422.1	O43491	E41L2_HUMAN	erythrocyte membrane protein band 4.1-like 2	426	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cortical actin cytoskeleton organization (GO:0030866)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|spectrin (GO:0008091)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(23)|prostate(1)|skin(2)	44	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)		GAGAAGTCCATTAGCACACAC	0.398																																					p.N426S		Atlas-SNP	.											.	EPB41L2	96	.	0			c.A1277G						PASS	.						166	146	153					6																	131216219		2203	4300	6503	SO:0001583	missense	2037	exon9			AGTCCATTAGCAC	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.1277A>G	chr6.hg19:g.131216219T>C	ENSP00000338481:p.Asn426Ser	69.0	0.0	.		57.0	27.0	.	NM_001135554	B4DHI8|E9PPD9|Q5T4F0|Q68DV2	Missense_Mutation	SNP	ENST00000337057.3	hg19	CCDS5141.1	.	.	.	.	.	.	.	.	.	.	T	9.975	1.226513	0.22542	.	.	ENSG00000079819	ENST00000528282;ENST00000530481;ENST00000445890;ENST00000337057;ENST00000392427;ENST00000425439;ENST00000368128;ENST00000527411;ENST00000525271;ENST00000525193;ENST00000527659;ENST00000529208	D;D;D;D;D;D;D;D;D;D;D	0.86366	-2.11;-2.11;-2.11;-2.11;-2.11;-2.11;-2.11;-2.11;-2.11;-2.11;-2.11	5.68	5.68	0.88126	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	T	0.72011	0.3408	N	0.01535	-0.81	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;1.0;0.999;0.999	D;D;D;D;D	0.87578	0.998;0.996;0.998;0.998;0.996	T	0.76258	-0.3025	10	0.02654	T	1	.	15.9369	0.79717	0.0:0.0:0.0:1.0	.	426;426;426;426;426	E9PHY5;B4DHI8;E9PPD9;O43491;Q68DV2	.;.;.;E41L2_HUMAN;.	S	426	ENSP00000434308:N426S;ENSP00000434576:N426S;ENSP00000402041:N426S;ENSP00000338481:N426S;ENSP00000376222:N426S;ENSP00000357110:N426S;ENSP00000436348:N426S;ENSP00000432803:N426S;ENSP00000431988:N426S;ENSP00000431647:N426S;ENSP00000436641:N426S	ENSP00000338481:N426S	N	-	2	0	EPB41L2	131257912	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	5.155000	0.64900	2.172000	0.68678	0.533000	0.62120	AAT	.	.	.	none		0.398	EPB41L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042204.3			C	131216219	T	C	131216219	3	2	224	1	0	0	0	0	1	0	0	0	5155	1493	52	3	1784	3	EPB41L2	6	131216219	Missense_Mutation	SNP	T	TCGA-MH-A854-01A-11D-A34Z-10	13969558	131216219	39898848	45	13618											
EYA4	2070	hgsc.bcm.edu	37	chr6	133849906	133849906	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atccagtcactcagacctccTggctctccaccaagcactgg	9	8	7	17	0	3	1	2	0	1	1	6	1	5	1	5	2	1	2	5	2	1	0			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr6:133849906T>C	ENST00000367895.5	+	20	2347	c.1883T>C	c.(1882-1884)cTg>cCg	p.L628P	EYA4_ENST00000431403.2_Missense_Mutation_p.L628P|EYA4_ENST00000355286.6_Missense_Mutation_p.L605P|EYA4_ENST00000525849.1_Missense_Mutation_p.L605P|EYA4_ENST00000531901.1_Missense_Mutation_p.L634P|EYA4_ENST00000452339.2_Missense_Mutation_p.L574P|EYA4_ENST00000355167.3_Missense_Mutation_p.L628P|EYA4_ENST00000430974.2_Intron|RP3-323P13.2_ENST00000607033.1_RNA	NM_004100.4	NP_004091.3	O95677	EYA4_HUMAN	EYA transcriptional coactivator and phosphatase 4	628					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)		TCAGACCTCCTGGCTCTCCAC	0.448																																					p.L628P	Melanoma(57;398 1237 3528 4702 7415)	Atlas-SNP	.											.	EYA4	196	.	0			c.T1883C						PASS	.						274	253	260					6																	133849906		2203	4300	6503	SO:0001583	missense	2070	exon20			ACCTCCTGGCTCT	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.1883T>C	chr6.hg19:g.133849906T>C	ENSP00000356870:p.Leu628Pro	164.0	0.0	.		137.0	47.0	.	NM_172105	B7Z7F7|O95464|O95679|Q8IW39|Q9NTR7	Missense_Mutation	SNP	ENST00000367895.5	hg19	CCDS5165.1	.	.	.	.	.	.	.	.	.	.	T	18.29	3.590941	0.66219	.	.	ENSG00000112319	ENST00000452339;ENST00000367895;ENST00000355167;ENST00000355286;ENST00000531901;ENST00000525849;ENST00000431403	D;D;D;D;D;D;D	0.89617	-2.54;-2.54;-2.54;-2.54;-2.54;-2.54;-2.54	6.07	6.07	0.98685	EYA (1);	0.000000	0.85682	D	0.000000	D	0.90817	0.7116	L	0.53249	1.67	0.80722	D	1	D;D;D;P;D	0.76494	0.96;0.998;0.999;0.871;0.96	P;P;D;P;P	0.68943	0.689;0.899;0.961;0.574;0.782	D	0.89304	0.3628	10	0.30854	T	0.27	-8.0266	16.6407	0.85098	0.0:0.0:0.0:1.0	.	634;574;605;628;628	F2Z2Y1;E7EN58;O95677-2;O95677-4;O95677	.;.;.;.;EYA4_HUMAN	P	574;628;628;605;634;605;628	ENSP00000395916:L574P;ENSP00000356870:L628P;ENSP00000347294:L628P;ENSP00000347434:L605P;ENSP00000432770:L634P;ENSP00000433219:L605P;ENSP00000404558:L628P	ENSP00000347294:L628P	L	+	2	0	EYA4	133891599	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.015000	0.88690	2.326000	0.78906	0.533000	0.62120	CTG	.	.	.	none		0.448	EYA4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042282.2	NM_004100		C	133849906	T	C	133849906	3	2	224	1	0	0	0	0	1	0	0	0	5333	1580	55	3	2062	3	EYA4	6	133849906	Missense_Mutation	SNP	T	TCGA-MH-A854-01A-11D-A34Z-10	2633687	133849906	37265161	46	13619											
NOX3	50508	hgsc.bcm.edu	37	chr6	155776915	155776915	+	Frame_Shift_Del	DEL	A	A	-																															tggtggagagaccctcattcAaaatccagcaccccatcatg																										TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr6:155776915delA	ENST00000159060.2	-	1	122	c.20delT	c.(19-21)ttgfs	p.L7fs		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	7					detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)			cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		ACCCTCATTCAAAATCCAGCA	0.378																																					p.L7fs		Atlas-Indel,Pindel	.											.	NOX3	93	.	0			c.21delG						PASS	.						96	91	93					6																	155776915		2203	4300	6503	SO:0001589	frameshift_variant	50508	exon1			.	AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.20delT	chr6.hg19:g.155776915delA	ENSP00000159060:p.Leu7fs	175.0	0.0	0		134.0	74.0	0.552239	NM_015718	Q9HBJ9	Frame_Shift_Del	DEL	ENST00000159060.2	hg19	CCDS5250.1																																																																																			.	.	.	none		0.378	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1			-	155776915	A	-	155776915	7	5	224	1	0	1	0	1	0	0	0	0	10564	131	5	0	1738	0	NOX3	6	155776915	Frame_Shift_Del	DEL	A	TCGA-MH-A854-01A-11D-A34Z-10	21927009	155776915	15338152	47	13620											
THSD7A	221981	hgsc.bcm.edu	37	chr7	11581118	11581118	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttccgttatctggctcgcAgtttcccagtctcactgctt	4	16	7	14	2	2	0	1	0	2	0	6	0	4	0	2	1	1	5	2	1	1	4			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr7:11581118A>G	ENST00000423059.4	-	6	2001	c.1750T>C	c.(1750-1752)Tgc>Cgc	p.C584R		NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	584					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)		TCTGGCTCGCAGTTTCCCAGT	0.498										HNSCC(18;0.044)																											p.C584R		Atlas-SNP	.											.	THSD7A	219	.	0			c.T1750C						PASS	.						101	101	101					7																	11581118		1996	4162	6158	SO:0001583	missense	221981	exon6			GCTCGCAGTTTCC		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.1750T>C	chr7.hg19:g.11581118A>G	ENSP00000406482:p.Cys584Arg	123.0	0.0	.		129.0	57.0	.	NM_015204		Missense_Mutation	SNP	ENST00000423059.4	hg19	CCDS47543.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.360480	0.82353	.	.	ENSG00000005108	ENST00000262042;ENST00000423059	T	0.76060	-0.99	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.91479	0.7310	H	0.98199	4.17	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94288	0.7526	10	0.62326	D	0.03	.	16.1381	0.81502	1.0:0.0:0.0:0.0	.	584	Q9UPZ6	THS7A_HUMAN	R	584	ENSP00000406482:C584R	ENSP00000262042:C584R	C	-	1	0	THSD7A	11547643	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	8.880000	0.92407	2.258000	0.74832	0.533000	0.62120	TGC	.	.	.	none		0.498	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		G	11581118	A	G	11581118	3	3	224	1	0	0	0	0	1	0	0	0	15891	188	7	3	3311	3	THSD7A	7	11581118	Missense_Mutation	SNP	A	TCGA-MH-A854-01A-11D-A34Z-10		11581118	147557545	48	13621											
LSM5	23658	hgsc.bcm.edu	37	chr7	32527353	32527353	+	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	taatttagtaatccttcttcCttctggtgtgatttcactaa	9	19	5	8	0	3	1	1	1	2	0	5	1	5	1	2	1	0	1	2	1	4	9			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr7:32527353C>T	ENST00000450169.2	-	4	239	c.187G>A	c.(187-189)Gga>Aga	p.G63R	LSM5_ENST00000409987.1_Silent_p.K58K|LSM5_ENST00000409292.1_Missense_Mutation_p.G34R|LSM5_ENST00000409952.3_Missense_Mutation_p.G34R|LSM5_ENST00000409909.3_Missense_Mutation_p.G34R|LSM5_ENST00000409782.1_Missense_Mutation_p.G34R|LSM5_ENST00000410044.1_Missense_Mutation_p.G34R	NM_001130710.1|NM_012322.2	NP_001124182.1|NP_036454.1	Q9Y4Y9	LSM5_HUMAN	LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae)	63					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)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	RNA binding (GO:0003723)			breast(1)|cervix(1)|large_intestine(1)|lung(1)|stomach(1)	5			GBM - Glioblastoma multiforme(11;0.152)			ATCCTTCTTCCTTCTGGTGTG	0.318																																					p.G63R		Atlas-SNP	.											.	LSM5	9	.	0			c.G187A						PASS	.						84	84	84					7																	32527353		2200	4297	6497	SO:0001583	missense	23658	exon4			TTCTTCCTTCTGG	AF182291	CCDS5438.1, CCDS47571.1	7p14.3	2003-02-17			ENSG00000106355	ENSG00000106355			17162	protein-coding gene	gene with protein product		607285				10369684, 12515382	Standard	NM_001130710		Approved	YER146W	uc003tct.2	Q9Y4Y9	OTTHUMG00000022913	ENST00000450169.2:c.187G>A	chr7.hg19:g.32527353C>T	ENSP00000410758:p.Gly63Arg	77.0	0.0	.		56.0	24.0	.	NM_012322		Missense_Mutation	SNP	ENST00000450169.2	hg19	CCDS5438.1	.	.	.	.	.	.	.	.	.	.	C	33	5.281048	0.95489	.	.	ENSG00000106355	ENST00000450169;ENST00000409909;ENST00000409292;ENST00000410044;ENST00000409782;ENST00000409952	.	.	.	6.17	6.17	0.99709	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	0.84028	0.5382	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83775	0.0222	8	0.62326	D	0.03	.	20.4745	0.99168	0.0:1.0:0.0:0.0	.	63	Q9Y4Y9	LSM5_HUMAN	R	63;34;34;34;34;34	.	ENSP00000386814:G34R	G	-	1	0	LSM5	32493878	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.191000	0.77763	2.941000	0.99782	0.655000	0.94253	GGA	.	.	.	none		0.318	LSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215102.2			T	32527353	C	T	32527353	3	4	224	1	0	0	0	0	1	0	0	0	9066	690	24	2	96	2	LSM5	7	32527353	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	20946235	32527353	126611310	49	13622											
PCLO	27445	hgsc.bcm.edu	37	chr7	82784425	82784425	+	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	ttgctgggccaggctgttgaGgtgggggttttgttgagcca	4	13	18	6	0	0	2	0	2	0	0	0	2	0	2	2	5	2	5	2	5	0	5			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr7:82784425G>A	ENST00000333891.9	-	2	1869	c.1532C>T	c.(1531-1533)cCt>cTt	p.P511L	PCLO_ENST00000423517.2_Missense_Mutation_p.P511L	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						AGGCTGTTGAGGTGGGGGTTT	0.597																																					p.P511L		Atlas-SNP	.											.	PCLO	1506	.	0			c.C1532T						PASS	.						134	143	140					7																	82784425		1971	4164	6135	SO:0001583	missense	27445	exon2			TGTTGAGGTGGGG	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.1532C>T	chr7.hg19:g.82784425G>A	ENSP00000334319:p.Pro511Leu	66.0	0.0	.		61.0	20.0	.	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	3.408	-0.120889	0.06838	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.16196	2.36;2.36	4.65	4.65	0.58169	.	.	.	.	.	T	0.14787	0.0357	L	0.35854	1.095	0.18873	N	0.999983	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.09164	-1.0687	9	0.87932	D	0	.	8.9393	0.35720	0.1036:0.0:0.8964:0.0	.	511;511	Q9Y6V0-5;Q9Y6V0-6	.;.	L	457;511;511	ENSP00000334319:P511L;ENSP00000388393:P511L	ENSP00000334319:P511L	P	-	2	0	PCLO	82622361	0.015000	0.18098	0.325000	0.25375	0.071000	0.16799	1.788000	0.38714	2.176000	0.68965	0.089000	0.15464	CCT	.	.	.	none		0.597	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82784425	G	A	82784425	3	1	224	1	0	0	0	0	1	0	0	0	11590	1000	35	2	14009	2	PCLO	7	82784425	Missense_Mutation	SNP	G	TCGA-MH-A854-01A-11D-A34Z-10	50257072	82784425	76354238	50	13623											
DMTF1	9988	hgsc.bcm.edu	37	chr7	86808921	86808921	+	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	tgtcaaaagacgaaagaaaaGatttctacaggactatagca	19	8	8	6	1	2	3	1	0	1	3	2	5	2	4	0	1	2	1	0	1	8	4			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr7:86808921G>C	ENST00000394703.5	+	10	1143	c.580G>C	c.(580-582)Gat>Cat	p.D194H	DMTF1_ENST00000432937.2_Missense_Mutation_p.D106H|DMTF1_ENST00000414194.2_5'UTR|DMTF1_ENST00000411766.2_Missense_Mutation_p.D153H|DMTF1_ENST00000331242.7_Missense_Mutation_p.D194H|DMTF1_ENST00000394702.3_Missense_Mutation_p.D194H|DMTF1_ENST00000413276.2_Missense_Mutation_p.D194H	NM_021145.3	NP_066968.3	Q9Y222	DMTF1_HUMAN	cyclin D binding myb-like transcription factor 1	194	Interaction with CCND1, CCND2 and CCND3. {ECO:0000250}.|Interaction with CCND2. {ECO:0000250}.|Required for DNA-binding. {ECO:0000250}.				cell cycle (GO:0007049)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)	16	Esophageal squamous(14;0.0058)					CGAAAGAAAAGATTTCTACAG	0.388																																					p.D194H		Atlas-SNP	.											.	DMTF1	48	.	0			c.G580C						PASS	.						78	75	76					7																	86808921		2203	4300	6503	SO:0001583	missense	9988	exon8			AGAAAAGATTTCT	AF084530	CCDS5601.1, CCDS47633.1	7q21	2014-06-25			ENSG00000135164	ENSG00000135164			14603	protein-coding gene	gene with protein product	"cyclin D-binding Myb-like protein"	608491				10095122, 24958102	Standard	NR_024549		Approved	DMP1, DMTF, hDMP1, MRUL	uc003uih.3	Q9Y222	OTTHUMG00000154135	ENST00000394703.5:c.580G>C	chr7.hg19:g.86808921G>C	ENSP00000378193:p.Asp194His	45.0	0.0	.		49.0	18.0	.	NM_001142327	B2RBE1|B4DJS5|Q05C48|Q59G79|Q6IS13|Q969T2|Q9H2Z2|Q9H2Z3	Missense_Mutation	SNP	ENST00000394703.5	hg19	CCDS5601.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.686016	0.88639	.	.	ENSG00000135164	ENST00000331242;ENST00000394702;ENST00000413276;ENST00000447863;ENST00000425406;ENST00000411766;ENST00000432937;ENST00000394703;ENST00000412139	T;T;T;T	0.50277	0.75;0.83;0.77;0.75	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.63710	0.2534	L	0.52573	1.65	0.80722	D	1	D	0.89917	1.0	D	0.72625	0.978	T	0.64093	-0.6488	10	0.51188	T	0.08	-18.0197	17.6427	0.88141	0.0:0.0:1.0:0.0	.	194	Q9Y222	DMTF1_HUMAN	H	194;194;194;194;153;153;106;194;194	ENSP00000332171:D194H;ENSP00000402627:D194H;ENSP00000412532:D106H;ENSP00000378193:D194H	ENSP00000332171:D194H	D	+	1	0	DMTF1	86646857	1.000000	0.71417	1.000000	0.80357	0.848000	0.48234	9.813000	0.99286	2.475000	0.83589	0.313000	0.20887	GAT	.	.	.	none		0.388	DMTF1-002	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334025.5	NM_021145		C	86808921	G	C	86808921	3	2	224	1	0	0	0	0	1	0	0	0	4594	942	33	4	602	4	DMTF1	7	86808921	Missense_Mutation	SNP	G	TCGA-MH-A854-01A-11D-A34Z-10	4024496	86808921	72329742	51	13624											
STEAP4	79689	hgsc.bcm.edu	37	chr7	87910335	87910335	+	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	ccaagtattcccaaagccacAtatgaatcactgagccaggc	14	7	7	13	0	1	2	1	2	0	0	2	2	2	2	4	1	2	1	4	1	5	3			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr7:87910335A>C	ENST00000380079.4	-	4	1145	c.1044T>G	c.(1042-1044)taT>taG	p.Y348*	STEAP4_ENST00000301959.5_Nonsense_Mutation_p.Y172*|AC003991.3_ENST00000595121.1_RNA|AC003991.3_ENST00000600908.1_RNA|AC003991.3_ENST00000434733.1_RNA|AC003991.3_ENST00000447758.1_RNA	NM_001205315.1|NM_024636.3	NP_001192244.1|NP_078912.2	Q687X5	STEA4_HUMAN	STEAP family member 4	348	Ferric oxidoreductase.				copper ion import (GO:0015677)|fat cell differentiation (GO:0045444)|ferric iron import into cell (GO:0097461)|iron ion homeostasis (GO:0055072)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cupric reductase activity (GO:0008823)|ferric-chelate reductase (NADPH) activity (GO:0052851)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(3)	15	Esophageal squamous(14;0.00802)					CCAAAGCCACATATGAATCAC	0.388																																					p.Y348X		Atlas-SNP	.											.	STEAP4	54	.	0			c.T1044G						PASS	.						91	89	89					7																	87910335		1881	4112	5993	SO:0001587	stop_gained	79689	exon5			AGCCACATATGAA	AK026806	CCDS43611.1, CCDS56494.1	7q21.13	2014-01-28	2005-06-15	2005-06-15	ENSG00000127954	ENSG00000127954			21923	protein-coding gene	gene with protein product		611098	"tumor necrosis factor, alpha-induced protein 9"	TNFAIP9		11443137, 15897894	Standard	NM_024636		Approved	FLJ23153, TIARP, STAMP2	uc003ujs.3	Q687X5	OTTHUMG00000153853	ENST00000380079.4:c.1044T>G	chr7.hg19:g.87910335A>C	ENSP00000369419:p.Tyr348*	78.0	0.0	.		76.0	34.0	.	NM_001205315	Q658Q9|Q687X4|Q8WWB0|Q9H5R1	Nonsense_Mutation	SNP	ENST00000380079.4	hg19	CCDS43611.1	.	.	.	.	.	.	.	.	.	.	A	19.81	3.896109	0.72639	.	.	ENSG00000127954	ENST00000380079;ENST00000301959	.	.	.	6.08	-0.826	0.10805	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.35668	D	0.81311	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.7158	12.1658	0.54129	0.5099:0.0:0.4901:0.0	.	.	.	.	X	348;172	.	ENSP00000305545:Y172X	Y	-	3	2	STEAP4	87748271	0.002000	0.14202	0.072000	0.20136	0.834000	0.47266	0.053000	0.14184	-0.081000	0.12662	0.482000	0.46254	TAT	.	.	.	none		0.388	STEAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332712.4	NM_024636		C	87910335	A	C	87910335	4	2	224	1	0	0	0	0	0	1	0	0	15292	224	8	5	343	5	STEAP4	7	87910335	Nonsense_Mutation	SNP	A	TCGA-MH-A854-01A-11D-A34Z-10	1101414	87910335	71228328	52	13625											
TFR2	7036	hgsc.bcm.edu	37	chr7	100238810	100238819	+	Frame_Shift_Del	DEL	ACGCTGGTAG	ACGCTGGTAG	-																															cctttccgggggccttccacAcgctggtagacggtctgaga																										TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	ACGCTGGTAG	ACGCTGGTAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr7:100238810_100238819delACGCTGGTAG	ENST00000462107.1	-	3	353_362	c.66_75delCTACCAGCGT	c.(64-75)gtctaccagcgtfs	p.VYQR22fs	TFR2_ENST00000223051.3_Frame_Shift_Del_p.VYQR22fs|TFR2_ENST00000431692.1_Frame_Shift_Del_p.VYQR22fs			Q9UP52	TFR2_HUMAN	transferrin receptor 2	22			V -> I (in HFE3). {ECO:0000269|PubMed:14633868}.		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)	p.R25H(1)		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)	GGCCTTCCACACGCTGGTAGACGGTCTGAG	0.638																																					p.23_26del		Atlas-Indel,Pindel	.											.	TFR2	53	.	1	Substitution - Missense(1)	large_intestine(1)	c.67_76del						PASS	.																																			SO:0001589	frameshift_variant	7036	exon2			.	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.66_75delCTACCAGCGT	chr7.hg19:g.100238810_100238819delACGCTGGTAG	ENSP00000420525:p.Val22fs	28.0	0.0	0		28.0	10.0	0.357143	NM_003227	A6NGM7|O75422|Q1HE13|Q9HA99|Q9NX67	Frame_Shift_Del	DEL	ENST00000462107.1	hg19	CCDS34707.1																																																																																			.	.	.	none		0.638	TFR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356392.3	NM_003227		-	100238819	ACGCTGGTAG	-	100238810	7	5	224	1	0	1	0	1	0	0	0	0	15823	146	6	0	2398	0	TFR2	7	100238810	Frame_Shift_Del	DEL	ACGCTGGTAG	TCGA-MH-A854-01A-11D-A34Z-10	12328475	100238810	58899853	53	13626											
SLC12A9	56996	hgsc.bcm.edu	37	chr7	100463464	100463464	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagggagggcagttccccagCtctgagcaccctgttccctc	6	8	11	16	0	1	1	0	1	1	0	4	2	3	2	4	2	2	5	4	2	0	2			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr7:100463464C>T	ENST00000354161.3	+	14	2107	c.1982C>T	c.(1981-1983)gCt>gTt	p.A661V	TRIP6_ENST00000200457.4_5'Flank	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	661					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)					AGTTCCCCAGCTCTGAGCACC	0.647																																					p.A661V		Atlas-SNP	.											.	SLC12A9	81	.	0			c.C1982T						PASS	.						48	50	49					7																	100463464		2203	4300	6503	SO:0001583	missense	56996	exon14			CCCCAGCTCTGAG	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.1982C>T	chr7.hg19:g.100463464C>T	ENSP00000275730:p.Ala661Val	77.0	0.0	.		58.0	18.0	.	NM_020246	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Missense_Mutation	SNP	ENST00000354161.3	hg19	CCDS5707.1	.	.	.	.	.	.	.	.	.	.	C	7.488	0.650158	0.14516	.	.	ENSG00000146828	ENST00000354161;ENST00000539308	D	0.91295	-2.82	4.92	4.92	0.64577	.	0.481191	0.19531	N	0.112040	T	0.79822	0.4512	N	0.08118	0	0.80722	D	1	B	0.22146	0.065	B	0.13407	0.009	T	0.74881	-0.3513	10	0.11182	T	0.66	.	15.6446	0.77039	0.0:1.0:0.0:0.0	.	661	Q9BXP2	S12A9_HUMAN	V	661;287	ENSP00000275730:A661V	ENSP00000275730:A661V	A	+	2	0	SLC12A9	100301400	0.967000	0.33354	0.857000	0.33713	0.106000	0.19336	2.366000	0.44204	2.564000	0.86499	0.555000	0.69702	GCT	.	.	.	none		0.647	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246		T	100463464	C	T	100463464	3	4	224	1	0	0	0	0	1	0	0	0	14403	797	28	2	2032	2	SLC12A9	7	100463464	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	224654	100463464	58675199	54	13627											
PSMC2	5701	hgsc.bcm.edu	37	chr7	103008247	103008247	+	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	tgttagcacgactgtgtccaAatagcactggtaagtagaaa	14	10	10	7	1	0	1	0	0	0	1	1	2	1	1	1	1	2	5	1	1	6	4			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr7:103008247A>T	ENST00000435765.1	+	12	1546	c.1135A>T	c.(1135-1137)Aat>Tat	p.N379Y	PSMC2_ENST00000292644.3_Missense_Mutation_p.N379Y|SLC26A5_ENST00000393735.2_Intron|SLC26A5_ENST00000356767.4_Intron|PSMC2_ENST00000544811.1_Missense_Mutation_p.N242Y|SLC26A5_ENST00000339444.6_Intron	NM_002803.3	NP_002794.1	P35998	PRS7_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 2	379					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|osteoblast differentiation (GO:0001649)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	21						ACTGTGTCCAAATAGCACTGG	0.388																																					p.N379Y		Atlas-SNP	.											.	PSMC2	38	.	0			c.A1135T						PASS	.						107	110	109					7																	103008247		2203	4300	6503	SO:0001583	missense	5701	exon11			TGTCCAAATAGCA	D11094	CCDS5731.1	7q22.1-q22.3	2010-04-21			ENSG00000161057	ENSG00000161057		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9548	protein-coding gene	gene with protein product	"proteasome 26S subunit, ATPase, 2", "mammalian suppressor of sgv-1 of yeast", "protease 26S subunit 7", "putative protein product of Nbla10058"	154365				9473509, 1377363	Standard	NM_002803		Approved	MSS1, S7, Nbla10058	uc003vbs.3	P35998	OTTHUMG00000157206	ENST00000435765.1:c.1135A>T	chr7.hg19:g.103008247A>T	ENSP00000391211:p.Asn379Tyr	94.0	0.0	.		92.0	41.0	.	NM_002803	A4D0Q1|B7Z5E2|Q3LIA5|Q9UDI3	Missense_Mutation	SNP	ENST00000435765.1	hg19	CCDS5731.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.217729	0.79352	.	.	ENSG00000161057	ENST00000435765;ENST00000292644;ENST00000544811	D;D;D	0.95137	-3.62;-3.62;-3.62	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	D	0.95893	0.8663	L	0.48877	1.53	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.96294	0.9216	10	0.62326	D	0.03	-31.875	14.9258	0.70878	1.0:0.0:0.0:0.0	.	379	P35998	PRS7_HUMAN	Y	379;379;242	ENSP00000391211:N379Y;ENSP00000292644:N379Y;ENSP00000445546:N242Y	ENSP00000292644:N379Y	N	+	1	0	PSMC2	102795483	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.978000	0.93450	1.917000	0.55516	0.524000	0.50904	AAT	.	.	.	none		0.388	PSMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347922.1	NM_002803		T	103008247	A	T	103008247	3	4	224	1	0	0	0	0	1	0	0	0	12696	14	1	5	1177	5	PSMC2	7	103008247	Missense_Mutation	SNP	A	TCGA-MH-A854-01A-11D-A34Z-10	2544783	103008247	56130416	55	13628											
DNAJB6	10049	hgsc.bcm.edu	37	chr7	157178258	157178258	+	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	tgtcgagaacggtcaagaaaGagtagaagttgaagaagatg	17	7	14	3	2	1	7	1	1	0	6	2	8	1	7	0	1	1	2	0	1	7	2			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr7:157178258G>T	ENST00000262177.4	+	8	849	c.644G>T	c.(643-645)aGa>aTa	p.R215I	DNAJB6_ENST00000429029.2_Missense_Mutation_p.R215I|DNAJB6_ENST00000452797.2_Missense_Mutation_p.R166I|DNAJB6_ENST00000443280.1_Intron	NM_058246.3	NP_490647.1	O75190	DNJB6_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 6	215	Interaction with KRT18.				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)		GGTCAAGAAAGAGTAGAAGTT	0.373																																					p.R215I	Esophageal Squamous(46;195 967 1350 20350 43814)	Atlas-SNP	.											.	DNAJB6	39	.	0			c.G644T						PASS	.						118	130	126					7																	157178258		2203	4300	6503	SO:0001583	missense	10049	exon8			AAGAAAGAGTAGA	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.644G>T	chr7.hg19:g.157178258G>T	ENSP00000262177:p.Arg215Ile	99.0	0.0	.		96.0	40.0	.	NM_058246	A4D232|A8K7D8|A8KAG0|B4DN73|E9PCZ2|O95806|Q53EN8|Q59EF2|Q6FIC8|Q75MA2|Q9UIK6	Missense_Mutation	SNP	ENST00000262177.4	hg19	CCDS5946.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.13|16.13	3.034822|3.034822	0.54896|0.54896	.|.	.|.	ENSG00000105993|ENSG00000105993	ENST00000421417|ENST00000429029;ENST00000262177;ENST00000417758;ENST00000452797	.|T;T;T;T	.|0.46819	.|0.86;0.86;0.86;0.86	5.58|5.58	3.62|3.62	0.41486|0.41486	.|.	.|0.106321	.|0.34088	.|N	.|0.004272	.|T	.|0.60881	.|0.2303	M|M	0.79693|0.79693	2.465|2.465	0.80722|0.80722	D|D	1|1	.|D;D;P;P	.|0.59357	.|0.985;0.974;0.883;0.498	.|P;P;P;B	.|0.51135	.|0.66;0.459;0.459;0.444	.|T	.|0.71159	.|-0.4674	.|10	0.18276|0.87932	T|D	0.48|0	.|.	15.4173|15.4173	0.74980|0.74980	0.0:0.2635:0.7365:0.0|0.0:0.2635:0.7365:0.0	.|.	.|166;215;215;215	.|B4DN73;A8KAG0;O75190;O75190-2	.|.;.;DNJB6_HUMAN;.	X|I	215|215;215;215;166	.|ENSP00000397556:R215I;ENSP00000262177:R215I;ENSP00000400665:R215I;ENSP00000402270:R166I	ENSP00000416129:E215X|ENSP00000262177:R215I	E|R	+|+	1|2	0|0	DNAJB6|DNAJB6	156871019|156871019	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	4.591000|4.591000	0.61019|0.61019	1.318000|1.318000	0.45170|0.45170	0.655000|0.655000	0.94253|0.94253	GAG|AGA	.	.	.	none		0.373	DNAJB6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000348119.2			T	157178258	G	T	157178258	3	4	224	1	0	0	0	0	1	0	0	0	4626	942	33	4	670	4	DNAJB6	7	157178258	Missense_Mutation	SNP	G	TCGA-MH-A854-01A-11D-A34Z-10	54170011	157178258	1960405	56	13629											
AGPAT5	55326	hgsc.bcm.edu	37	chr8	6590118	6590118	+	Frame_Shift_Del	DEL	A	A	-																															taaagcgcagtgccaaatttAacgagaaagagatgcgaaac																										TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr8:6590118delA	ENST00000285518.6	+	4	754	c.442delA	c.(442-444)aacfs	p.N148fs		NM_018361.3	NP_060831.2	Q9NUQ2	PLCE_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 5	148					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|hematopoietic progenitor cell differentiation (GO:0002244)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)		AGPAT5/MCPH1(2)	endometrium(2)|kidney(2)|large_intestine(4)|lung(3)	11			STAD - Stomach adenocarcinoma(24;0.0578)	READ - Rectum adenocarcinoma(644;0.156)|COAD - Colon adenocarcinoma(149;0.191)		TGCCAAATTTAACGAGAAAGA	0.418																																					p.F147fs		Atlas-Indel,Pindel	.											.	AGPAT5	31	.	0			c.441delT						PASS	.						67	66	66					8																	6590118		2203	4300	6503	SO:0001589	frameshift_variant	55326	exon4			.	AF375789	CCDS34796.1	8p23.1	2013-02-05	2013-02-05		ENSG00000155189	ENSG00000155189	2.3.1.51	"1-acylglycerol-3-phosphate O-acyltransferases"	20886	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, epsilon"	614796	"1-acylglycerol-3-phosphate O-acyltransferase 5 (lysophosphatidic acid acyltransferase, epsilon)"				Standard	NM_018361		Approved	FLJ11210, LPAAT-e, LPAAT-epsilon	uc003wqo.3	Q9NUQ2	OTTHUMG00000163656	ENST00000285518.6:c.442delA	chr8.hg19:g.6590118delA	ENSP00000285518:p.Asn148fs	271.0	0.0	0		280.0	128.0	0.457143	NM_018361	Q8IZ47|Q9BQG4	Frame_Shift_Del	DEL	ENST00000285518.6	hg19	CCDS34796.1																																																																																			.	.	.	none		0.418	AGPAT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374684.1	NM_018361		-	6590118	A	-	6590118	7	5	224	1	0	1	0	1	0	0	0	0	390	362	13	0	456	0	AGPAT5	8	6590118	Frame_Shift_Del	DEL	A	TCGA-MH-A854-01A-11D-A34Z-10		6590118	139773904	57	13630											
ZBTB10	65986	hgsc.bcm.edu	37	chr8	81399773	81399773	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcgcggcccaagtctctaaTgcagaagctccaatgctcct	9	8	9	15	3	1	1	0	0	1	1	4	1	3	1	3	1	3	3	3	1	4	1			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr8:81399773T>C	ENST00000430430.1	+	2	1507	c.728T>C	c.(727-729)aTg>aCg	p.M243T	Y_RNA_ENST00000605948.1_RNA|ZBTB10_ENST00000379091.4_Intron|ZBTB10_ENST00000455036.3_Missense_Mutation_p.M243T|ZBTB10_ENST00000426744.2_Missense_Mutation_p.M243T	NM_001277145.1	NP_001264074.1	Q96DT7	ZBT10_HUMAN	zinc finger and BTB domain containing 10	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(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(4)	20	all_cancers(3;1.68e-09)|all_epithelial(4;5.13e-11)|Lung NSC(7;1.75e-07)|all_lung(9;7.38e-07)|Breast(3;2.96e-06)		BRCA - Breast invasive adenocarcinoma(6;0.000434)|Epithelial(68;0.00486)|all cancers(69;0.0296)			AAGTCTCTAATGCAGAAGCTC	0.612																																					p.M243T		Atlas-SNP	.											.	ZBTB10	51	.	0			c.T728C						PASS	.						31	34	33					8																	81399773		2002	4174	6176	SO:0001583	missense	65986	exon1			CTCTAATGCAGAA	AK022814	CCDS47880.1, CCDS64920.1	8q13-q21.1	2013-01-09			ENSG00000205189	ENSG00000205189		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	30953	protein-coding gene	gene with protein product						12477932	Standard	NM_001105539		Approved	RINZF, FLJ12752	uc003ybx.5	Q96DT7	OTTHUMG00000155016	ENST00000430430.1:c.728T>C	chr8.hg19:g.81399773T>C	ENSP00000387462:p.Met243Thr	33.0	0.0	.		60.0	24.0	.	NM_023929	A4FVD0|Q86W96|Q8IXI9|Q96MH9	Missense_Mutation	SNP	ENST00000430430.1	hg19	CCDS47880.1	.	.	.	.	.	.	.	.	.	.	T	12.52	1.962697	0.34659	.	.	ENSG00000205189	ENST00000430430;ENST00000455036;ENST00000426744;ENST00000519370	T;T;T	0.09630	2.96;2.96;2.96	4.52	4.52	0.55395	.	0.171155	0.37095	N	0.002246	T	0.06600	0.0169	N	0.08118	0	0.33778	D	0.623847	B;B;B	0.26547	0.039;0.039;0.152	B;B;B	0.20955	0.01;0.01;0.032	T	0.12477	-1.0546	10	0.87932	D	0	.	13.9929	0.64378	0.0:0.0:0.0:1.0	.	99;243;243	A8E4L4;Q96DT7;Q96DT7-2	.;ZBT10_HUMAN;.	T	243;243;243;71	ENSP00000387462:M243T;ENSP00000412036:M243T;ENSP00000416134:M243T	ENSP00000416134:M243T	M	+	2	0	ZBTB10	81562328	1.000000	0.71417	0.977000	0.42913	0.191000	0.23601	6.246000	0.72405	1.878000	0.54408	0.533000	0.62120	ATG	.	.	.	none		0.612	ZBTB10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338055.2	NM_023929		C	81399773	T	C	81399773	3	2	224	1	0	0	0	0	1	0	0	0	17535	1464	51	3	730	3	ZBTB10	8	81399773	Missense_Mutation	SNP	T	TCGA-MH-A854-01A-11D-A34Z-10	74809655	81399773	64964249	58	13631											
SLC25A32	81034	hgsc.bcm.edu	37	chr8	104419932	104419932	+	Missense_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	tactccttgataaagtccccGtagtccatcaagtttccaaa	12	12	5	12	1	1	1	1	1	0	0	5	1	5	1	5	0	1	2	5	0	6	5			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr8:104419932G>A	ENST00000297578.4	-	2	401	c.235C>T	c.(235-237)Cgg>Tgg	p.R79W	SLC25A32_ENST00000543107.1_De_novo_Start_OutOfFrame	NM_030780.3	NP_110407.2	Q9H2D1	MFTC_HUMAN	solute carrier family 25 (mitochondrial folate carrier), member 32	79					folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	folic acid transporter activity (GO:0008517)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	9			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)		Folic Acid(DB00158)	TAAAGTCCCCGTAGTCCATCA	0.398																																					p.R79W		Atlas-SNP	.											.	SLC25A32	36	.	0			c.C235T						PASS	.						163	164	164					8																	104419932		2203	4300	6503	SO:0001583	missense	81034	exon2			GTCCCCGTAGTCC	AF283645	CCDS6300.1	8q22.3	2013-05-22	2013-03-15		ENSG00000164933	ENSG00000164933		"Solute carriers"	29683	protein-coding gene	gene with protein product		610815	"solute carrier family 25, member 32"			10978331	Standard	NM_030780		Approved	MFTC	uc003yll.4	Q9H2D1	OTTHUMG00000164790	ENST00000297578.4:c.235C>T	chr8.hg19:g.104419932G>A	ENSP00000297578:p.Arg79Trp	62.0	0.0	.		75.0	24.0	.	NM_030780	Q96JZ6|Q96SU7	Missense_Mutation	SNP	ENST00000297578.4	hg19	CCDS6300.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.514039	0.85389	.	.	ENSG00000164933	ENST00000297578;ENST00000424899	T	0.80909	-1.43	6.05	6.05	0.98169	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.92273	0.7549	M	0.90252	3.1	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.92648	0.6130	10	0.87932	D	0	-11.9646	20.6013	0.99457	0.0:0.0:1.0:0.0	.	79	Q9H2D1	MFTC_HUMAN	W	79;63	ENSP00000297578:R79W	ENSP00000297578:R79W	R	-	1	2	SLC25A32	104489108	1.000000	0.71417	0.959000	0.39883	0.987000	0.75469	5.692000	0.68256	2.878000	0.98634	0.650000	0.86243	CGG	.	.	.	none		0.398	SLC25A32-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380290.2	NM_030780		A	104419932	G	A	104419932	3	1	224	1	0	0	0	0	1	0	0	0	14509	1144	40	1	736	1	SLC25A32	8	104419932	Missense_Mutation	SNP	G	TCGA-MH-A854-01A-11D-A34Z-10	23020159	104419932	41944090	59	13632											
AQP3	360	hgsc.bcm.edu	37	chr9	33447468	33447468	+	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	ggccagcgcctgtcggagcaGccggtagcggatgtggagca	7	5	18	11	4	0	0	0	0	0	0	1	3	0	3	3	5	5	3	3	5	1	1			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr9:33447468G>A	ENST00000297991.4	-	1	141	c.61C>T	c.(61-63)Ctg>Ttg	p.L21L	AQP3_ENST00000493581.1_5'UTR	NM_004925.4	NP_004916.1	Q92482	AQP3_HUMAN	aquaporin 3 (Gill blood group)	21					excretion (GO:0007588)|odontogenesis (GO:0042476)|positive regulation of immune system process (GO:0002684)|regulation of keratinocyte differentiation (GO:0045616)|renal water absorption (GO:0070295)|response to calcium ion (GO:0051592)|response to retinoic acid (GO:0032526)|response to vitamin D (GO:0033280)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urea transport (GO:0015840)|water transport (GO:0006833)	basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycerol channel activity (GO:0015254)|transporter activity (GO:0005215)|water channel activity (GO:0015250)			endometrium(2)|large_intestine(3)|lung(2)|ovary(1)	8			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.0899)		TGTCGGAGCAGCCGGTAGCGG	0.711																																					p.L21L		Atlas-SNP	.											.	AQP3	18	.	0			c.C61T						PASS	.						18	21	20					9																	33447468		2188	4289	6477	SO:0001819	synonymous_variant	360	exon1			GGAGCAGCCGGTA		CCDS6542.1	9p13	2014-07-18	2006-02-23		ENSG00000165272	ENSG00000165272		"Ion channels / Aquaporins", "Blood group antigens"	636	protein-coding gene	gene with protein product	"Gill blood group"	600170	"aquaporin 3", "aquaporin 3 (GIL blood group)"			7558005	Standard	NM_004925		Approved	GIL	uc003zsx.3	Q92482	OTTHUMG00000019769	ENST00000297991.4:c.61C>T	chr9.hg19:g.33447468G>A		84.0	0.0	.		91.0	37.0	.	NM_004925	A8K843|B2RE16|D3DRL3|O00108|Q6FGT2|Q6FGW6	Silent	SNP	ENST00000297991.4	hg19	CCDS6542.1																																																																																			.	.	.	weak		0.711	AQP3-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052055.1	NM_004925		A	33447468	G	A	33447468	2	1	224	1	0	0	0	0	0	0	0	1	827	962	34	2		2	AQP3	9	33447468	Silent	SNP	G	TCGA-MH-A854-01A-11D-A34Z-10		33447468	107765963	60	13633											
SPTLC1	10558	hgsc.bcm.edu	37	chr9	94809499	94809499	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggcctcaattgctgcagcagCtaacaggggaggtaacgaag	12	6	14	9	1	1	0	1	0	0	0	1	2	1	1	1	4	6	5	1	4	4	3			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr9:94809499C>T	ENST00000262554.2	-	11	1041	c.1036G>A	c.(1036-1038)Gct>Act	p.A346T		NM_006415.2	NP_006406.1	O15269	SPTC1_HUMAN	serine palmitoyltransferase, long chain base subunit 1	346					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphinganine biosynthetic process (GO:0046511)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|serine C-palmitoyltransferase complex (GO:0017059)|SPOTS complex (GO:0035339)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			breast(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	14					L-Serine(DB00133)	GCTGCAGCAGCTAACAGGGGA	0.438																																					p.A346T		Atlas-SNP	.											.	SPTLC1	42	.	0			c.G1036A						PASS	.						147	141	143					9																	94809499		2203	4300	6503	SO:0001583	missense	10558	exon11			CAGCAGCTAACAG	Y08685	CCDS6692.1, CCDS6693.1	9q22.31	2014-09-17	2003-12-02		ENSG00000090054	ENSG00000090054	2.3.1.50		11277	protein-coding gene	gene with protein product		605712	"hereditary sensory neuropathy, type 1"	HSN1		9363775	Standard	NM_006415		Approved	LCB1, SPTI, HSAN1, hLCB1	uc004arl.1	O15269	OTTHUMG00000021047	ENST00000262554.2:c.1036G>A	chr9.hg19:g.94809499C>T	ENSP00000262554:p.Ala346Thr	43.0	0.0	.		43.0	10.0	.	NM_006415	A8K681|Q5VWB4|Q96IX6	Missense_Mutation	SNP	ENST00000262554.2	hg19	CCDS6692.1	.	.	.	.	.	.	.	.	.	.	C	33	5.247472	0.95305	.	.	ENSG00000090054	ENST00000262554	D	0.96200	-3.94	5.25	5.25	0.73442	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.048440	0.85682	D	0.000000	D	0.94785	0.8316	L	0.51422	1.61	0.80722	D	1	B;P	0.37914	0.314;0.611	B;B	0.43274	0.393;0.414	D	0.93830	0.7127	10	0.38643	T	0.18	-11.2377	19.0877	0.93212	0.0:1.0:0.0:0.0	.	346;346	Q6NUL7;O15269	.;SPTC1_HUMAN	T	346	ENSP00000262554:A346T	ENSP00000262554:A346T	A	-	1	0	SPTLC1	93849320	1.000000	0.71417	0.964000	0.40570	0.985000	0.73830	7.543000	0.82106	2.733000	0.93635	0.650000	0.86243	GCT	.	.	.	none		0.438	SPTLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055553.1	NM_006415		T	94809499	C	T	94809499	3	4	224	1	0	0	0	0	1	0	0	0	15135	797	28	2	405	2	SPTLC1	9	94809499	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	61362031	94809499	46403932	61	13634											
KLF4	9314	hgsc.bcm.edu	37	chr9	110249965	110249965	+	Missense_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	tgccgtactcgctgccagggGcgctcagcgacgccttcagc	5	7	13	16	5	2	0	2	0	0	0	3	1	2	0	3	2	5	3	3	2	1	2			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr9:110249965G>A	ENST00000374672.4	-	3	1183	c.710C>T	c.(709-711)gCc>gTc	p.A237V		NM_004235.4	NP_004226.3	O43474	KLF4_HUMAN	Kruppel-like factor 4 (gut)	237	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						GCTGCCAGGGGCGCTCAGCGA	0.701																																					p.A237V		Atlas-SNP	.											.	KLF4	106	.	0			c.C710T						PASS	.						10	11	11					9																	110249965		2160	4246	6406	SO:0001583	missense	9314	exon3			CCAGGGGCGCTCA	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.710C>T	chr9.hg19:g.110249965G>A	ENSP00000363804:p.Ala237Val	27.0	0.0	.		27.0	11.0	.	NM_004235	B2R8S4|B3KT79|L0R3I6|L0R4N5|P78338|Q5T3J8|Q5T3J9|Q8N717|Q9UNP3	Missense_Mutation	SNP	ENST00000374672.4	hg19	CCDS6770.2	.	.	.	.	.	.	.	.	.	.	G	13.71	2.317561	0.40996	.	.	ENSG00000136826	ENST00000374672;ENST00000411706	T	0.04809	3.55	3.38	3.38	0.38709	.	0.605659	0.13877	N	0.356593	T	0.02119	0.0066	N	0.03608	-0.345	0.21416	N	0.999697	B;B	0.11235	0.004;0.003	B;B	0.12156	0.007;0.004	T	0.40403	-0.9565	10	0.06099	T	0.92	.	10.5918	0.45314	0.0:0.0:1.0:0.0	.	237;237	O43474;O43474-1	KLF4_HUMAN;.	V	237;228	ENSP00000363804:A237V	ENSP00000363804:A237V	A	-	2	0	KLF4	109289786	1.000000	0.71417	0.914000	0.36105	0.647000	0.38526	2.120000	0.41968	2.191000	0.70037	0.655000	0.94253	GCC	.	.	.	none		0.701	KLF4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053556.2	NM_004235		A	110249965	G	A	110249965	3	1	224	1	0	0	0	0	1	0	0	0	8355	1203	42	2	741	2	KLF4	9	110249965	Missense_Mutation	SNP	G	TCGA-MH-A854-01A-11D-A34Z-10	15440466	110249965	30963466	62	13635											
RPL7A	6130	hgsc.bcm.edu	37	chr9	136216882	136216882	+	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	ggcaaaggggacgtcccaacGaagagaccacctgtccttcg	11	5	12	13	3	0	1	0	0	0	1	3	4	2	2	4	3	1	1	4	3	3	1	rs7700	byFrequency	TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr9:136216882G>T	ENST00000323345.6	+	4	420	c.390G>T	c.(388-390)acG>acT	p.T130T	SNORD36A_ENST00000362874.1_RNA|SNORD24_ENST00000383884.1_RNA|MED22_ENST00000471524.1_5'Flank|SURF1_ENST00000495952.1_5'Flank|RPL7A_ENST00000463740.1_3'UTR|SNORD36B_ENST00000363961.1_RNA|SNORD36C_ENST00000516733.1_RNA|MED22_ENST00000476080.1_5'Flank|MED22_ENST00000491289.1_5'Flank|MED22_ENST00000344469.5_5'Flank|MED22_ENST00000371999.1_5'Flank|RPL7A_ENST00000315731.4_Silent_p.T15T|MED22_ENST00000343730.5_5'Flank	NM_000972.2	NP_000963.1	P62424	RL7A_HUMAN	ribosomal protein L7a	130					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosome biogenesis (GO:0042254)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(1)|kidney(1)|lung(3)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(145;4.93e-07)|Epithelial(140;4.09e-06)|all cancers(34;3.78e-05)		ACGTCCCAACGAAGAGACCAC	0.557																																					p.T130T		Atlas-SNP	.											.	RPL7A	9	.	0			c.G390T						PASS	.						58	63	61					9																	136216882		2203	4300	6503	SO:0001819	synonymous_variant	6130	exon4			CCCAACGAAGAGA	BC005128	CCDS6965.1	9q34	2011-04-06			ENSG00000148303	ENSG00000148303		"L ribosomal proteins"	10364	protein-coding gene	gene with protein product	"surfeit 3", "PLA-X polypeptide", "surfeit locus protein 3", "60S ribosomal protein L7a", ";", "thyroid hormone receptor uncoupling protein"	185640				2403926, 2966065	Standard	NM_000972		Approved	SURF3, TRUP, L7A	uc004cde.1	P62424	OTTHUMG00000020864	ENST00000323345.6:c.390G>T	chr9.hg19:g.136216882G>T		32.0	0.0	.		27.0	11.0	.	NM_000972	P11518|Q5T8U4	Silent	SNP	ENST00000323345.6	hg19	CCDS6965.1																																																																																			.	G|0.942;A|0.058	.	alt		0.557	RPL7A-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054869.1	NM_000972		T	136216882	G	T	136216882	2	4	224	1	0	0	0	0	0	0	0	1	13613	1045	37	4		4	RPL7A	9	136216882	Silent	SNP	G	TCGA-MH-A854-01A-11D-A34Z-10	25966917	136216882	4996549	63	13636											
COL5A1	1289	hgsc.bcm.edu	37	chr9	137710604	137710604	+	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	gccttcgagggatccctggcCctgtggtgagtaggctgtga	5	10	16	10	1	0	2	0	2	0	0	2	4	1	3	3	4	0	2	3	4	1	2			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr9:137710604C>T	ENST00000371817.3	+	55	4747	c.4333C>T	c.(4333-4335)Cct>Tct	p.P1445S		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1445	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		GATCCCTGGCCCTGTGGTGAG	0.667																																					p.P1445S		Atlas-SNP	.											.	COL5A1	323	.	0			c.C4333T						PASS	.						22	23	23					9																	137710604		2203	4297	6500	SO:0001583	missense	1289	exon55			CCTGGCCCTGTGG	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.4333C>T	chr9.hg19:g.137710604C>T	ENSP00000360882:p.Pro1445Ser	41.0	0.0	.		28.0	10.0	.	NM_000093	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	hg19	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	C	11.73	1.726665	0.30593	.	.	ENSG00000130635	ENST00000371817	D	0.96802	-4.13	4.69	3.79	0.43588	.	0.068028	0.64402	U	0.000012	D	0.94889	0.8348	M	0.78049	2.395	0.53005	D	0.999969	B	0.30914	0.3	B	0.29077	0.098	D	0.92543	0.6043	10	0.29301	T	0.29	.	12.715	0.57109	0.0:0.9191:0.0:0.0809	.	1445	P20908	CO5A1_HUMAN	S	1445	ENSP00000360882:P1445S	ENSP00000360882:P1445S	P	+	1	0	COL5A1	136850425	0.994000	0.37717	0.977000	0.42913	0.632000	0.37999	3.040000	0.49799	0.968000	0.38212	0.448000	0.29417	CCT	.	.	.	none		0.667	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		T	137710604	C	T	137710604	3	4	224	1	0	0	0	0	1	0	0	0	3698	623	22	2	4551	2	COL5A1	9	137710604	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	1493722	137710604	3502827	64	13637											
TAF3	83860	hgsc.bcm.edu	37	chr10	8006138	8006138	+	Frame_Shift_Del	DEL	A	A	-																															actcagctcaataaatactcAaaagatcccaccaatgcttt																										TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr10:8006138delA	ENST00000344293.5	+	3	871	c.665delA	c.(664-666)caafs	p.Q222fs		NM_031923.3	NP_114129.1	Q5VWG9	TAF3_HUMAN	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140kDa	222					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						ATAAATACTCAAAAGATCCCA	0.507																																					p.Q222fs		Atlas-Indel,Pindel	.											.	TAF3	93	.	0			c.664delC						PASS	.						86	88	87					10																	8006138		1952	4142	6094	SO:0001589	frameshift_variant	83860	exon3			.	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.665delA	chr10.hg19:g.8006138delA	ENSP00000340271:p.Gln222fs	74.0	0.0	0		95.0	43.0	0.452632	NM_031923	Q05DA0|Q6GMS5|Q6P6B5|Q86VY6|Q9BQS9|Q9UFI8	Frame_Shift_Del	DEL	ENST00000344293.5	hg19	CCDS41487.1																																																																																			.	.	.	none		0.507	TAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046725.1	NM_031923		-	8006138	A	-	8006138	7	5	224	1	0	1	0	1	0	0	0	0	15537	130	5	0	675	0	TAF3	10	8006138	Frame_Shift_Del	DEL	A	TCGA-MH-A854-01A-11D-A34Z-10		8006138	127528609	65	13638											
ANK3	288	hgsc.bcm.edu	37	chr10	61842390	61842390	+	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	tacctttttatgtgctggcaGagtgatatttaagttgcaaa	11	16	9	5	0	0	2	0	1	0	1	0	2	0	2	1	1	3	4	1	1	5	8			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr10:61842390G>C	ENST00000280772.2	-	34	4497	c.4306C>G	c.(4306-4308)Ctg>Gtg	p.L1436V	ANK3_ENST00000373827.2_Missense_Mutation_p.L1430V|ANK3_ENST00000503366.1_Missense_Mutation_p.L1437V|ANK3_ENST00000355288.2_Missense_Mutation_p.L570V|Y_RNA_ENST00000365320.1_RNA	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	1436					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						TGTGCTGGCAGAGTGATATTT	0.413																																					p.L1437V		Atlas-SNP	.											.	ANK3	703	.	0			c.C4309G						PASS	.						183	178	180					10																	61842390		2203	4300	6503	SO:0001583	missense	288	exon35			CTGGCAGAGTGAT	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.4306C>G	chr10.hg19:g.61842390G>C	ENSP00000280772:p.Leu1436Val	72.0	0.0	.		76.0	32.0	.	NM_001204404	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	hg19	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	G	13.95	2.390947	0.42410	.	.	ENSG00000151150	ENST00000280772;ENST00000373827;ENST00000373820;ENST00000355288;ENST00000423532;ENST00000503366;ENST00000395299;ENST00000373817;ENST00000395293;ENST00000395304	T;T;D;T;T	0.82344	1.47;1.47;-1.6;1.47;1.47	5.89	4.05	0.47172	.	0.239554	0.21461	N	0.074162	D	0.88851	0.6549	M	0.64080	1.96	0.80722	D	1	B;D;D;B;D;P	0.89917	0.427;0.998;1.0;0.148;0.993;0.956	B;D;D;B;D;D	0.87578	0.342;0.99;0.998;0.089;0.946;0.931	D	0.88474	0.3064	10	0.87932	D	0	.	11.7562	0.51875	0.1961:0.0:0.8039:0.0	.	1437;570;1430;1436;671;570	E9PE32;A8KA62;Q5CZH9;Q12955;F5GXK0;B1AQT2	.;.;.;ANK3_HUMAN;.;.	V	1436;1430;19;570;570;1437;1416;671;1071;1071	ENSP00000280772:L1436V;ENSP00000362933:L1430V;ENSP00000362926:L19V;ENSP00000347436:L570V;ENSP00000425236:L1437V	ENSP00000280772:L1436V	L	-	1	2	ANK3	61512396	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.338000	0.52128	0.835000	0.34877	0.557000	0.71058	CTG	.	.	.	none		0.413	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		C	61842390	G	C	61842390	3	2	224	1	0	0	0	0	1	0	0	0	622	933	33	4	9180	4	ANK3	10	61842390	Missense_Mutation	SNP	G	TCGA-MH-A854-01A-11D-A34Z-10	53836252	61842390	73692357	66	13639											
PAPSS2	9060	hgsc.bcm.edu	37	chr10	89474565	89474566	+	Frame_Shift_Ins	INS	-	-	T																															gagcgtgtgcttaaaaccaaINStttgtccacagtgagtgact																										TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr10:89474565_89474566insT	ENST00000361175.4	+	5	953_954	c.584_585insT	c.(583-588)aatttgfs	p.L196fs	PAPSS2_ENST00000456849.1_Frame_Shift_Ins_p.L196fs|PAPSS2_ENST00000427144.2_Frame_Shift_Ins_p.L200fs	NM_004670.3	NP_004661.2	O95340	PAPS2_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 2	196					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|blood coagulation (GO:0007596)|bone development (GO:0060348)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	adenylylsulfate kinase activity (GO:0004020)|ATP binding (GO:0005524)|nucleotidyltransferase activity (GO:0016779)|sulfate adenylyltransferase (ATP) activity (GO:0004781)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|stomach(1)	20		Melanoma(5;0.019)|Colorectal(252;0.123)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00164)|Colorectal(12;0.000323)|COAD - Colon adenocarcinoma(12;0.00124)		CTTAAAACCAATTTGTCCACAG	0.401																																					p.N195fs		Atlas-Indel,Pindel	.											.	PAPSS2	46	.	0			c.584_585insT						PASS	.																																			SO:0001589	frameshift_variant	9060	exon5			.	AF091242	CCDS7385.1, CCDS44453.1	10q24	2008-02-07			ENSG00000198682	ENSG00000198682	2.7.7.4, 2.7.1.25		8604	protein-coding gene	gene with protein product		603005				9771708	Standard	NM_004670		Approved	ATPSK2	uc001kex.3	O95340	OTTHUMG00000018683	ENST00000361175.4:c.587dupT	chr10.hg19:g.89474568_89474568dupT	ENSP00000354436:p.Leu196fs	100.0	0.0	0		96.0	31.0	0.322917	NM_001015880	Q9BZL2|Q9P0G6|Q9UHM1|Q9UKD3|Q9UP30	Frame_Shift_Ins	INS	ENST00000361175.4	hg19	CCDS7385.1																																																																																			.	.	.	none		0.401	PAPSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049229.1			T	89474566	-	T	89474565	7	5	224	1	0	1	1	0	0	0	0	0	11442	101	4	0	602	0	PAPSS2	10	89474565	Frame_Shift_Ins	INS	-	TCGA-MH-A854-01A-11D-A34Z-10	27632175	89474565	46060182	67	13640											
GBF1	8729	hgsc.bcm.edu	37	chr10	104126202	104126202	+	Missense_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	cctctacctggaagccttccGtttgcctggggaagcaccag	7	9	11	14	1	1	0	0	0	1	0	2	2	2	2	6	3	4	2	6	3	3	3			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr10:104126202G>A	ENST00000369983.3	+	19	2629	c.2369G>A	c.(2368-2370)cGt>cAt	p.R790H		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	790	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		GAAGCCTTCCGTTTGCCTGGG	0.547																																					p.R791H		Atlas-SNP	.											.	GBF1	142	.	0			c.G2372A						PASS	.						124	105	112					10																	104126202		2203	4300	6503	SO:0001583	missense	8729	exon19			CCTTCCGTTTGCC	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.2369G>A	chr10.hg19:g.104126202G>A	ENSP00000359000:p.Arg790His	131.0	0.0	.		95.0	18.0	.	NM_001199378	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	hg19	CCDS7533.1	.	.	.	.	.	.	.	.	.	.	G	36	5.911085	0.97093	.	.	ENSG00000107862	ENST00000369983	T	0.58210	0.35	6.03	6.03	0.97812	SEC7-like, alpha orthogonal bundle (1);SEC7-like (4);	0.000000	0.85682	D	0.000000	T	0.79240	0.4412	M	0.89163	3.01	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.998	T	0.81497	-0.0906	10	0.87932	D	0	-13.0608	20.5568	0.99304	0.0:0.0:1.0:0.0	.	790;790;790	Q149P1;Q149P0;Q92538	.;.;GBF1_HUMAN	H	790	ENSP00000359000:R790H	ENSP00000359000:R790H	R	+	2	0	GBF1	104116192	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.824000	0.99380	2.861000	0.98227	0.655000	0.94253	CGT	.	.	.	none		0.547	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			A	104126202	G	A	104126202	3	1	224	1	0	0	0	0	1	0	0	0	6278	1145	40	1	2439	1	GBF1	10	104126202	Missense_Mutation	SNP	G	TCGA-MH-A854-01A-11D-A34Z-10	14651637	104126202	31408545	68	13641											
C10orf118	55088	hgsc.bcm.edu	37	chr10	115922488	115922488	+	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	cccttattcattccatttggTactcgatgttctgcaaactc	8	16	5	12	1	2	0	1	0	1	0	5	1	3	0	2	1	3	3	2	1	3	6			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr10:115922488T>G	ENST00000369287.3	-	2	806	c.540A>C	c.(538-540)gtA>gtC	p.V180V	C10orf118_ENST00000369285.3_Silent_p.V180V|C10orf118_ENST00000369286.1_Silent_p.V180V	NM_018017.2	NP_060487.2	Q7Z3E2	CC186_HUMAN		180										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)		TTCCATTTGGTACTCGATGTT	0.333																																					p.V180V		Atlas-SNP	.											.	C10orf118	70	.	0			c.A540C						PASS	.						76	72	73					10																	115922488		2202	4298	6500	SO:0001819	synonymous_variant	55088	exon2			ATTTGGTACTCGA																												ENST00000369287.3:c.540A>C	chr10.hg19:g.115922488T>G		255.0	0.0	.		176.0	66.0	.	NM_018017	Q2M2V6|Q3ZB81|Q6NS91|Q7RTP1|Q8N117|Q8N3G3|Q8N6C2|Q9NWA3	Silent	SNP	ENST00000369287.3	hg19	CCDS7587.1																																																																																			.	.	.	none		0.333	C10orf118-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050455.1			G	115922488	T	G	115922488	2	3	224	1	0	0	0	0	0	0	0	1	1589	1625	57	5		5	C10orf118	10	115922488	Silent	SNP	T	TCGA-MH-A854-01A-11D-A34Z-10	11796286	115922488	19612259	69	13642											
PSMC3	5702	hgsc.bcm.edu	37	chr11	47446781	47446781	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcatgggtgactctcaacActtcactcttcatgatctga	9	13	7	12	0	6	3	4	3	3	0	7	3	6	3	0	1	1	1	0	1	1	2			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr11:47446781A>G	ENST00000298852.3	-	3	333	c.176T>C	c.(175-177)gTg>gCg	p.V59A	PSMC3_ENST00000530912.1_Intron|PSMC3_ENST00000602866.1_Missense_Mutation_p.V43A	NM_002804.4	NP_002795.2	P17980	PRS6A_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 3	59					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of RNA biosynthetic process (GO:2001141)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(4)|urinary_tract(1)	17				Lung(87;0.0932)|BRCA - Breast invasive adenocarcinoma(625;0.13)		GACTCTCAACACTTCACTCTT	0.478																																					p.V59A		Atlas-SNP	.											.	PSMC3	35	.	0			c.T176C						PASS	.						195	170	178					11																	47446781		2201	4298	6499	SO:0001583	missense	5702	exon3			CTCAACACTTCAC	M34079	CCDS7935.1	11p11.2	2010-04-21			ENSG00000165916	ENSG00000165916		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9549	protein-coding gene	gene with protein product		186852				9048938, 9473509	Standard	NM_002804		Approved	TBP1, TBP-1	uc001nfh.2	P17980	OTTHUMG00000167692	ENST00000298852.3:c.176T>C	chr11.hg19:g.47446781A>G	ENSP00000298852:p.Val59Ala	100.0	0.0	.		84.0	37.0	.	NM_002804	B2R8V1|Q3B757|Q3B865|Q53HU5|Q6GPG8|Q6IBS1|Q96HD3	Missense_Mutation	SNP	ENST00000298852.3	hg19	CCDS7935.1	.	.	.	.	.	.	.	.	.	.	A	14.56	2.572615	0.45798	.	.	ENSG00000165916	ENST00000298852;ENST00000524447;ENST00000531051;ENST00000530887;ENST00000530651;ENST00000527906;ENST00000526993;ENST00000531653;ENST00000528362	D	0.94417	-3.42	5.5	5.5	0.81552	.	0.176985	0.48767	D	0.000178	D	0.92014	0.7470	L	0.53249	1.67	0.58432	D	0.999999	B	0.25441	0.126	B	0.24701	0.055	D	0.89317	0.3637	10	0.17369	T	0.5	-33.9881	15.6076	0.76685	1.0:0.0:0.0:0.0	.	59	P17980	PRS6A_HUMAN	A	59;24;24;24;24;24;67;43;43	ENSP00000298852:V59A	ENSP00000298852:V59A	V	-	2	0	PSMC3	47403357	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.576000	0.82467	2.094000	0.63399	0.454000	0.30748	GTG	.	.	.	none		0.478	PSMC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395660.2	NM_002804		G	47446781	A	G	47446781	3	3	224	1	0	0	0	0	1	0	0	0	12697	159	6	3	1183	3	PSMC3	11	47446781	Missense_Mutation	SNP	A	TCGA-MH-A854-01A-11D-A34Z-10		47446781	87559735	70	13643											
B3GAT3	26229	hgsc.bcm.edu	37	chr11	62388048	62388048	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaggggcagggggtggccGtcggagttccgcttgcagct	4	7	20	10	3	0	0	0	0	0	0	2	1	1	1	2	7	2	6	2	7	0	2	rs374687580		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr11:62388048G>A	ENST00000265471.5	-	2	405	c.178C>T	c.(178-180)Cgg>Tgg	p.R60W	B3GAT3_ENST00000534026.1_Missense_Mutation_p.R60W|B3GAT3_ENST00000531383.1_Missense_Mutation_p.R60W	NM_012200.3	NP_036332.2	O94766	B3GA3_HUMAN	beta-1,3-glucuronyltransferase 3	60					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity (GO:0015018)|glucuronosyltransferase activity (GO:0015020)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(2)|urinary_tract(1)	12						GGGGGTGGCCGTCGGAGTTCC	0.637																																					p.R60W		Atlas-SNP	.											.	B3GAT3	24	.	0			c.C178T						PASS	.						20	27	24					11																	62388048		2202	4293	6495	SO:0001583	missense	26229	exon2			GTGGCCGTCGGAG	AB009598	CCDS8025.1	11q12	2014-07-08	2014-07-08		ENSG00000149541	ENSG00000149541	2.4.1.135	"Beta-1,3-glucuronyltransferases"	923	protein-coding gene	gene with protein product	"glucuronosyltransferase I", "galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3"	606374	"beta-1,3-glucuronyltransferase 3 (glucuronosyltransferase I)"			9506957	Standard	NM_012200		Approved	GlcAT-I	uc001ntw.3	O94766	OTTHUMG00000167685	ENST00000265471.5:c.178C>T	chr11.hg19:g.62388048G>A	ENSP00000265471:p.Arg60Trp	39.0	0.0	.		49.0	18.0	.	NM_012200	B7ZAB3|Q96I06|Q9UEP0	Missense_Mutation	SNP	ENST00000265471.5	hg19	CCDS8025.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.668430	0.88348	.	.	ENSG00000149541	ENST00000265471;ENST00000531383;ENST00000534026;ENST00000534715	T;T;T;T	0.66460	-0.18;-0.19;-0.21;0.75	5.53	5.53	0.82687	.	0.436137	0.23323	N	0.049434	T	0.75184	0.3815	L	0.44542	1.39	0.49687	D	0.999812	D;D;D	0.89917	1.0;1.0;0.999	D;D;P	0.66979	0.948;0.948;0.824	T	0.76509	-0.2933	10	0.66056	D	0.02	.	14.9659	0.71193	0.0:0.0:1.0:0.0	.	60;66;60	B7ZAB3;Q5U676;O94766	.;.;B3GA3_HUMAN	W	60;60;60;83	ENSP00000265471:R60W;ENSP00000431359:R60W;ENSP00000432474:R60W;ENSP00000432854:R83W	ENSP00000265471:R60W	R	-	1	2	B3GAT3	62144624	0.941000	0.31946	0.966000	0.40874	0.882000	0.50991	2.038000	0.41184	2.599000	0.87857	0.655000	0.94253	CGG	.	.	.	alt		0.637	B3GAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395588.1	NM_012200		A	62388048	G	A	62388048	3	1	224	1	0	0	0	0	1	0	0	0	1255	1144	40	1	845	1	B3GAT3	11	62388048	Missense_Mutation	SNP	G	TCGA-MH-A854-01A-11D-A34Z-10	14941267	62388048	72618468	71	13644											
LRRC32	2615	hgsc.bcm.edu	37	chr11	76371152	76371152	+	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	ccgttgccctgcagtgccagGacctccaaggaggcctccag	7	6	12	16	1	0	0	0	0	0	0	2	2	2	2	7	3	3	2	7	3	1	1			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr11:76371152G>A	ENST00000407242.2	-	3	1727	c.1485C>T	c.(1483-1485)gtC>gtT	p.V495V	LRRC32_ENST00000404995.1_Silent_p.V495V|LRRC32_ENST00000464145.1_Intron|AP001189.4_ENST00000447519.1_RNA|LRRC32_ENST00000260061.5_Silent_p.V495V	NM_005512.2	NP_005503.1	Q14392	LRC32_HUMAN	leucine rich repeat containing 32	495					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						GCAGTGCCAGGACCTCCAAGG	0.647																																					p.V495V		Atlas-SNP	.											.	LRRC32	74	.	0			c.C1485T						PASS	.						27	28	27					11																	76371152		2200	4292	6492	SO:0001819	synonymous_variant	2615	exon3			TGCCAGGACCTCC	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.1485C>T	chr11.hg19:g.76371152G>A		34.0	0.0	.		23.0	14.0	.	NM_005512	Q86V06	Silent	SNP	ENST00000407242.2	hg19	CCDS8245.1																																																																																			.	.	.	none		0.647	LRRC32-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257926.2	NM_005512		A	76371152	G	A	76371152	2	1	224	1	0	0	0	0	0	0	0	1	8994	1161	41	2		2	LRRC32	11	76371152	Silent	SNP	G	TCGA-MH-A854-01A-11D-A34Z-10	13983104	76371152	58635364	72	13645											
CACNA2D4	93589	hgsc.bcm.edu	37	chr12	1993454	1993454	+	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	catgcggtcagcaaaagacaCttctctcccaatgaggtaag	13	8	9	11	1	2	2	1	1	1	1	4	2	3	2	1	2	2	2	1	2	4	2			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr12:1993454C>T	ENST00000382722.5	-	12	1668	c.1306G>A	c.(1306-1308)Gtg>Atg	p.V436M	CACNA2D4_ENST00000585732.1_Intron|CACNA2D4_ENST00000588077.1_Missense_Mutation_p.V372M|CACNA2D4_ENST00000586184.1_Missense_Mutation_p.V436M|CACNA2D4_ENST00000587995.1_Missense_Mutation_p.V436M|CACNA2D4_ENST00000585708.1_Missense_Mutation_p.V372M	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	436	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)		GCAAAAGACACTTCTCTCCCA	0.502																																					p.V436M	Colon(2;101 179 21030 23310 28141)	Atlas-SNP	.											.	CACNA2D4	220	.	0			c.G1306A						PASS	.						72	80	77					12																	1993454		2051	4204	6255	SO:0001583	missense	93589	exon12			AAGACACTTCTCT	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.1306G>A	chr12.hg19:g.1993454C>T	ENSP00000372169:p.Val436Met	29.0	0.0	.		57.0	33.0	.	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Missense_Mutation	SNP	ENST00000382722.5	hg19	CCDS44785.1	.	.	.	.	.	.	.	.	.	.	C	13.59	2.283451	0.40394	.	.	ENSG00000151062	ENST00000456077;ENST00000280663;ENST00000382722	T	0.08282	3.11	5.27	5.27	0.74061	von Willebrand factor, type A (3);	0.107037	0.64402	D	0.000003	T	0.09598	0.0236	L	0.28556	0.865	0.80722	D	1	B	0.12013	0.005	B	0.20384	0.029	T	0.15292	-1.0442	10	0.49607	T	0.09	.	18.8984	0.92433	0.0:1.0:0.0:0.0	.	436	Q7Z3S7	CA2D4_HUMAN	M	372;436;436	ENSP00000372169:V436M	ENSP00000280663:V436M	V	-	1	0	CACNA2D4	1863715	1.000000	0.71417	0.976000	0.42696	0.827000	0.46813	3.017000	0.49615	2.463000	0.83235	0.603000	0.83216	GTG	.	.	.	none		0.502	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2			T	1993454	C	T	1993454	3	4	224	1	0	0	0	0	1	0	0	0	2553	565	20	2	2215	2	CACNA2D4	12	1993454	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10		1993454	131858441	73	13646											
NCAPD2	9918	hgsc.bcm.edu	37	chr12	6639960	6639960	+	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	agcaggtagccagagagcgcCatcagccaagaaaccatcca	15	3	10	13	1	1	2	1	0	0	2	2	3	2	2	5	1	5	2	5	1	3	1			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr12:6639960C>A	ENST00000315579.5	+	30	4740	c.3941C>A	c.(3940-3942)cCa>cAa	p.P1314Q	RP5-940J5.3_ENST00000537921.1_RNA|NCAPD2_ENST00000545962.1_Missense_Mutation_p.P1269Q	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	1314					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						CAGAGAGCGCCATCAGCCAAG	0.512																																					p.P1314Q		Atlas-SNP	.											.	NCAPD2	99	.	0			c.C3941A						PASS	.						62	64	63					12																	6639960		2203	4300	6503	SO:0001583	missense	9918	exon30			GAGCGCCATCAGC	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.3941C>A	chr12.hg19:g.6639960C>A	ENSP00000325017:p.Pro1314Gln	38.0	0.0	.		47.0	16.0	.	NM_014865	D3DUR4|Q8N6U3	Missense_Mutation	SNP	ENST00000315579.5	hg19	CCDS8548.1	.	.	.	.	.	.	.	.	.	.	C	12.87	2.068903	0.36470	.	.	ENSG00000010292	ENST00000315579;ENST00000545962	T;T	0.17854	2.52;2.25	5.63	2.8	0.32819	.	0.513361	0.21089	N	0.080360	T	0.11024	0.0269	L	0.38838	1.175	0.09310	N	1	B;B	0.21071	0.025;0.051	B;B	0.18871	0.023;0.008	T	0.32455	-0.9906	10	0.22109	T	0.4	-3.6593	4.7752	0.13175	0.2099:0.5563:0.0:0.2337	.	1269;1314	F5GZJ1;Q15021	.;CND1_HUMAN	Q	1314;1269	ENSP00000325017:P1314Q;ENSP00000444417:P1269Q	ENSP00000325017:P1314Q	P	+	2	0	NCAPD2	6510221	0.000000	0.05858	0.403000	0.26384	0.250000	0.25880	0.275000	0.18698	0.305000	0.22832	0.561000	0.74099	CCA	.	.	.	none		0.512	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865		A	6639960	C	A	6639960	3	1	224	1	0	0	0	0	1	0	0	0	10212	594	21	4	4055	4	NCAPD2	12	6639960	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	4646506	6639960	127211935	74	13647											
GPR162	27239	hgsc.bcm.edu	37	chr12	6933104	6933104	+	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	gggcagaggaggcctccctgCgctccaacgcattgtcctgg	6	7	14	14	2	0	1	0	0	0	1	3	2	3	2	4	4	2	3	4	4	1	1			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr12:6933104C>T	ENST00000311268.3	+	2	827	c.40C>T	c.(40-42)Cgc>Tgc	p.R14C	GPR162_ENST00000382315.3_Intron|GPR162_ENST00000428545.2_Intron|GPR162_ENST00000541431.1_Intron	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162	14						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						GGCCTCCCTGCGCTCCAACGC	0.682																																					p.R14C		Atlas-SNP	.											.	GPR162	55	.	0			c.C40T						PASS	.						11	11	11					12																	6933104		2197	4291	6488	SO:0001583	missense	27239	exon2			TCCCTGCGCTCCA	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.40C>T	chr12.hg19:g.6933104C>T	ENSP00000311528:p.Arg14Cys	19.0	0.0	.		24.0	17.0	.	NM_019858	Q16664|Q59EH5|Q66K56	Missense_Mutation	SNP	ENST00000311268.3	hg19	CCDS8563.1	.	.	.	.	.	.	.	.	.	.	C	18.14	3.557714	0.65425	.	.	ENSG00000250510	ENST00000311268	T	0.09073	3.02	4.74	4.74	0.60224	.	.	.	.	.	T	0.07773	0.0195	N	0.08118	0	0.80722	D	1	D;D	0.76494	0.999;0.993	P;B	0.50490	0.642;0.348	T	0.36040	-0.9764	9	0.54805	T	0.06	.	12.9402	0.58337	0.162:0.838:0.0:0.0	.	14;14	B7Z3U3;Q16538	.;GP162_HUMAN	C	14	ENSP00000311528:R14C	ENSP00000311528:R14C	R	+	1	0	GPR162	6803365	1.000000	0.71417	1.000000	0.80357	0.724000	0.41520	3.946000	0.56644	2.464000	0.83262	0.561000	0.74099	CGC	.	.	.	none		0.682	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	NM_019858		T	6933104	C	T	6933104	3	4	224	1	0	0	0	0	1	0	0	0	6673	768	27	1	61	1	GPR162	12	6933104	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	293144	6933104	126918791	75	13648											
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-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_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,0,66	KRAS	30930	.	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	c.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	chr12.hg19:g.25398284C>A	ENSP00000256078:p.Gly12Val	155.0	0.0	.		201.0	132.0	.	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	hg19	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	224	1	0	0	0	0	1	0	0	0	8445	507	18	4	671	4	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	18465180	25398284	108453611	76	13649											
KRT83	3889	hgsc.bcm.edu	37	chr12	52710705	52710705	+	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	ggcaatgtcatcatactgtgCcttgatctcggcaacgatgc	9	11	10	11	2	3	1	2	1	1	0	4	2	3	1	1	2	4	2	1	2	3	2			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr12:52710705C>A	ENST00000293670.3	-	5	915	c.853G>T	c.(853-855)Gca>Tca	p.A285S		NM_002282.3	NP_002273.3	P78385	KRT83_HUMAN	keratin 83	285	Coil 2.|Rod.				aging (GO:0007568)|epidermis development (GO:0008544)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(4)|stomach(7)|upper_aerodigestive_tract(1)	32	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		TCATACTGTGCCTTGATCTCG	0.582																																					p.A285S	GBM(41;747 834 12702 24089 39393)|Esophageal Squamous(97;805 1414 12559 28198 31861)	Atlas-SNP	.											.	KRT83	64	.	0			c.G853T						PASS	.						174	143	154					12																	52710705		2203	4300	6503	SO:0001583	missense	3889	exon5			ACTGTGCCTTGAT	X99141	CCDS8823.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000170523	ENSG00000170523		"-", "Intermediate filaments type II, keratins (basic)"	6460	protein-coding gene	gene with protein product	"hard keratin type II"	602765	"keratin, hair, basic, 3"	KRTHB3		9084137, 16831889	Standard	NM_002282		Approved	Hb-3	uc001saf.2	P78385	OTTHUMG00000169632	ENST00000293670.3:c.853G>T	chr12.hg19:g.52710705C>A	ENSP00000293670:p.Ala285Ser	68.0	0.0	.		93.0	50.0	.	NM_002282	A1A4S9|B2RC21|Q6NT21|Q9NSB3	Missense_Mutation	SNP	ENST00000293670.3	hg19	CCDS8823.1	.	.	.	.	.	.	.	.	.	.	C	16.60	3.168355	0.57584	.	.	ENSG00000170523	ENST00000293670	T	0.76578	-1.03	3.9	3.9	0.45041	Filament (1);	0.184777	0.25490	U	0.030304	T	0.82107	0.4965	M	0.71581	2.175	0.38260	D	0.941851	P	0.36465	0.554	P	0.45506	0.483	D	0.86574	0.1849	10	0.66056	D	0.02	.	16.2457	0.82445	0.0:1.0:0.0:0.0	.	285	P78385	KRT83_HUMAN	S	285	ENSP00000293670:A285S	ENSP00000293670:A285S	A	-	1	0	KRT83	50996972	1.000000	0.71417	0.999000	0.59377	0.344000	0.29017	5.625000	0.67770	1.894000	0.54839	0.561000	0.74099	GCA	.	.	.	none		0.582	KRT83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405182.1	NM_002282		A	52710705	C	A	52710705	3	1	224	1	0	0	0	0	1	0	0	0	8504	739	26	4	648	4	KRT83	12	52710705	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	27312421	52710705	81141190	77	13650											
MYF6	4618	hgsc.bcm.edu	37	chr12	81102003	81102003	+	Frame_Shift_Del	DEL	C	C	-																															tggaccccttcagctacagaCccaaacaagaaaatgtaagc																										TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr12:81102003delC	ENST00000228641.3	+	1	727	c.505delC	c.(505-507)cccfs	p.P169fs		NM_002469.2	NP_002460.1	P23409	MYF6_HUMAN	myogenic factor 6 (herculin)	169				P -> S (in Ref. 3; CAG46563). {ECO:0000305}.	muscle cell differentiation (GO:0042692)|muscle cell fate commitment (GO:0042693)|muscle tissue morphogenesis (GO:0060415)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle tissue development (GO:0007519)|skeletal muscle tissue regeneration (GO:0043403)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|skin(1)	26						CAGCTACAGACCCAAACAAGA	0.577																																					p.R168fs		Atlas-Indel,Pindel	.											.	MYF6	74	.	0			c.504delA						PASS	.						32	36	35					12																	81102003		2201	4297	6498	SO:0001589	frameshift_variant	4618	exon1			.		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.505delC	chr12.hg19:g.81102003delC	ENSP00000228641:p.Pro169fs	19.0	0.0	0		19.0	12.0	0.631579	NM_002469	B2R898|Q53X80|Q6FHI9	Frame_Shift_Del	DEL	ENST00000228641.3	hg19	CCDS9019.1																																																																																			.	.	.	none		0.577	MYF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407756.1	NM_002469		-	81102003	C	-	81102003	7	5	224	1	0	1	0	1	0	0	0	0	10035	507	18	0	507	0	MYF6	12	81102003	Frame_Shift_Del	DEL	C	TCGA-MH-A854-01A-11D-A34Z-10	28391298	81102003	52749892	78	13651											
KDM2B	84678	hgsc.bcm.edu	37	chr12	121881963	121881963	+	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	ggggcgcctcctcacactcaCtcctccgcttggcaggttcc	4	9	10	18	2	2	0	2	0	0	0	6	0	6	0	5	4	0	3	5	4	0	2			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr12:121881963C>T	ENST00000377071.4	-	16	2375	c.2303G>A	c.(2302-2304)aGt>aAt	p.S768N	KDM2B_ENST00000536437.1_Intron|KDM2B_ENST00000542973.1_Missense_Mutation_p.S136N|KDM2B_ENST00000377069.4_Missense_Mutation_p.S737N	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	768					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						CTCACACTCACTCCTCCGCTT	0.632											OREG0022201	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S768N		Atlas-SNP	.											.	KDM2B	218	.	0			c.G2303A						PASS	.						82	86	85					12																	121881963		2058	4202	6260	SO:0001583	missense	84678	exon16			CACTCACTCCTCC	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.2303G>A	chr12.hg19:g.121881963C>T	ENSP00000366271:p.Ser768Asn	29.0	0.0	.	1514	29.0	15.0	.	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Missense_Mutation	SNP	ENST00000377071.4	hg19	CCDS41850.1	.	.	.	.	.	.	.	.	.	.	C	12.90	2.077467	0.36662	.	.	ENSG00000089094	ENST00000397480;ENST00000542973;ENST00000377069;ENST00000377071;ENST00000540043;ENST00000261824	T;T;T	0.24151	2.2;2.47;1.87	5.95	5.04	0.67666	.	0.487539	0.19689	N	0.108332	T	0.12944	0.0314	N	0.08118	0	0.80722	D	1	B;B;B;B	0.28128	0.054;0.055;0.201;0.128	B;B;B;B	0.18871	0.016;0.008;0.023;0.023	T	0.12041	-1.0563	10	0.17832	T	0.49	-2.6873	13.955	0.64142	0.2761:0.7239:0.0:0.0	.	208;768;737;211	B7ZB05;Q8NHM5;A8MRS1;B4DSN4	.;KDM2B_HUMAN;.;.	N	768;136;737;768;211;771	ENSP00000437821:S136N;ENSP00000366269:S737N;ENSP00000366271:S768N	ENSP00000261824:S771N	S	-	2	0	KDM2B	120366346	0.986000	0.35501	0.968000	0.41197	0.715000	0.41141	2.987000	0.49378	1.461000	0.47929	0.655000	0.94253	AGT	.	.	.	none		0.632	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590		T	121881963	C	T	121881963	3	4	224	1	0	0	0	0	1	0	0	0	8132	565	20	2	1791	2	KDM2B	12	121881963	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	40779960	121881963	11969932	79	13652											
GPR109A	338442	hgsc.bcm.edu	37	chr12	123187139	123187139	+	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	tggccaccaccatgatgaagGtgatggctctcttgatcttg	8	12	11	10	0	2	4	0	4	2	0	3	4	2	4	3	3	0	1	3	3	1	2			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr12:123187139G>T	ENST00000328880.5	-	1	751	c.692C>A	c.(691-693)aCc>aAc	p.T231N	RP11-324E6.6_ENST00000543611.1_lincRNA|HCAR1_ENST00000356987.2_Intron	NM_177551.3	NP_808219.1	Q8TDS4	HCAR2_HUMAN	hydroxycarboxylic acid receptor 2	231					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)	CATGATGAAGGTGATGGCTCT	0.567																																					p.T231N		Atlas-SNP	.											.	HCAR2	36	.	0			c.C692A						PASS	.						72	61	65					12																	123187139		2203	4297	6500	SO:0001583	missense	338442	exon1			ATGAAGGTGATGG	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.692C>A	chr12.hg19:g.123187139G>T	ENSP00000375066:p.Thr231Asn	146.0	0.0	.		174.0	37.0	.	NM_177551	A0PJL5|A7LGG3	Missense_Mutation	SNP	ENST00000328880.5	hg19	CCDS9235.1	.	.	.	.	.	.	.	.	.	.	G	4.367	0.067602	0.08436	.	.	ENSG00000182782	ENST00000328880;ENST00000536970	T	0.37584	1.19	4.97	0.684	0.18003	GPCR, rhodopsin-like superfamily (1);	0.595355	0.15261	N	0.271792	T	0.10294	0.0252	N	0.00879	-1.12	0.18873	N	0.999981	B	0.02656	0.0	B	0.06405	0.002	T	0.23976	-1.0173	10	0.39692	T	0.17	-13.1354	4.7774	0.13185	0.0:0.2263:0.1698:0.6039	.	231	Q8TDS4	HCAR2_HUMAN	N	231	ENSP00000375066:T231N	ENSP00000375066:T231N	T	-	2	0	HCAR2	121753092	0.000000	0.05858	0.962000	0.40283	0.413000	0.31143	-0.028000	0.12350	0.136000	0.18733	-0.457000	0.05445	ACC	.	.	.	none		0.567	HCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370202.1	NM_177551		T	123187139	G	T	123187139	3	4	224	1	0	0	0	0	1	0	0	0	6632	1261	44	4	403	4	GPR109A	12	123187139	Missense_Mutation	SNP	G	TCGA-MH-A854-01A-11D-A34Z-10	1305176	123187139	10664756	80	13653											
XPO4	64328	hgsc.bcm.edu	37	chr13	21370348	21370348	+	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	cctaaattattcttagaataCacttgcaacaaagtaaggca	17	11	5	8	0	1	1	0	0	1	1	1	1	1	1	1	1	3	3	1	1	9	7			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr13:21370348C>G	ENST00000255305.6	-	18	2735	c.2664G>C	c.(2662-2664)gtG>gtC	p.V888V	XPO4_ENST00000400602.2_Silent_p.V888V			Q9C0E2	XPO4_HUMAN	exportin 4	888					positive regulation of protein export from nucleus (GO:0046827)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(10)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	41		all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548)		TCTTAGAATACACTTGCAACA	0.353																																					p.V888V		Atlas-SNP	.											.	XPO4	153	.	0			c.G2664C						PASS	.						103	90	94					13																	21370348		1817	4081	5898	SO:0001819	synonymous_variant	64328	exon18			AGAATACACTTGC	AB051508	CCDS41872.1	13q11	2011-04-13			ENSG00000132953	ENSG00000132953		"Exportins"	17796	protein-coding gene	gene with protein product		611449				11214970, 10944119	Standard	NM_022459		Approved	FLJ13046, KIAA1721	uc001unq.4	Q9C0E2	OTTHUMG00000016528	ENST00000255305.6:c.2664G>C	chr13.hg19:g.21370348C>G		46.0	0.0	.		62.0	29.0	.	NM_022459	Q5VUZ5|Q8N3V6|Q9H934	Silent	SNP	ENST00000255305.6	hg19	CCDS41872.1																																																																																			.	.	.	none		0.353	XPO4-001	KNOWN	non_canonical_conserved|non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044096.1	NM_022459		G	21370348	C	G	21370348	2	3	224	1	0	0	0	0	0	0	0	1	17458	465	17	4		4	XPO4	13	21370348	Silent	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10		21370348	93799530	81	13654											
SMAD9	4093	hgsc.bcm.edu	37	chr13	37427774	37427774	+	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	gctgctgtcactcacgcactCggcatacacctctcccccga	7	8	7	19	3	3	0	2	0	1	0	5	1	3	0	3	1	2	4	3	1	1	1	rs375386551		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr13:37427774C>T	ENST00000399275.2	-	5	1181	c.1042G>A	c.(1042-1044)Gag>Aag	p.E348K	SMAD9_ENST00000350148.5_Missense_Mutation_p.E311K|SMAD9_ENST00000379826.4_Missense_Mutation_p.E348K			O15198	SMAD9_HUMAN	SMAD family member 9	348	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				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)		CTCACGCACTCGGCATACACC	0.562																																					p.E348K		Atlas-SNP	.											.	SMAD9	91	.	0			c.G1042A						PASS	.	C	LYS/GLU,LYS/GLU	0,4406		0,0,2203	148	92	111		1042,931	5.5	1	13		111	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	SMAD9	NM_001127217.2,NM_005905.5	56,56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	348/468,311/431	37427774	1,13005	2203	4300	6503	SO:0001583	missense	4093	exon6			CGCACTCGGCATA		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.1042G>A	chr13.hg19:g.37427774C>T	ENSP00000382216:p.Glu348Lys	52.0	0.0	.		54.0	23.0	.	NM_001127217	A2A2Y6|O14989|Q5TBA1	Missense_Mutation	SNP	ENST00000399275.2	hg19	CCDS45032.1	.	.	.	.	.	.	.	.	.	.	C	35	5.571853	0.96553	0.0	1.16E-4	ENSG00000120693	ENST00000399275;ENST00000350148;ENST00000379826	D;D;D	0.97455	-4.39;-4.28;-4.39	5.54	5.54	0.83059	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.97517	0.9187	M	0.81614	2.55	0.80722	D	1	P;D	0.56035	0.888;0.974	B;P	0.49301	0.325;0.606	D	0.97979	1.0348	10	0.62326	D	0.03	.	18.4694	0.90767	0.0:1.0:0.0:0.0	.	311;348	O15198-2;O15198	.;SMAD9_HUMAN	K	348;311;348	ENSP00000382216:E348K;ENSP00000239885:E311K;ENSP00000369154:E348K	ENSP00000239885:E311K	E	-	1	0	SMAD9	36325774	1.000000	0.71417	0.986000	0.45419	0.933000	0.57130	7.630000	0.83225	2.600000	0.87896	0.655000	0.94253	GAG	.	.	.	weak		0.562	SMAD9-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044525.2	NM_005905		T	37427774	C	T	37427774	3	4	224	1	0	0	0	0	1	0	0	0	14777	893	31	1	369	1	SMAD9	13	37427774	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	16057426	37427774	77742104	82	13655											
FAM124A	220108	hgsc.bcm.edu	37	chr13	51825756	51825756	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttccgggtgtccgagaggCgggcgtcccggcggcggcgg	2	6	21	12	8	0	1	0	0	0	1	3	2	3	1	3	7	0	1	3	7	0	1			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr13:51825756C>T	ENST00000322475.8	+	3	388	c.253C>T	c.(253-255)Cgg>Tgg	p.R85W	FAM124A_ENST00000280057.6_Missense_Mutation_p.R121W	NM_001242312.1	NP_001229241.1	Q86V42	F124A_HUMAN	family with sequence similarity 124A	85										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)		GTCCGAGAGGCGGGCGTCCCG	0.697																																					p.R121W		Atlas-SNP	.											.	FAM124A	61	.	0			c.C361T						PASS	.						11	11	11					13																	51825756		2185	4266	6451	SO:0001583	missense	220108	exon4			GAGAGGCGGGCGT	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.253C>T	chr13.hg19:g.51825756C>T	ENSP00000324625:p.Arg85Trp	35.0	0.0	.		53.0	16.0	.	NM_145019	A2A324|Q8N8P9|Q8NE66|Q96NJ9	Missense_Mutation	SNP	ENST00000322475.8	hg19	CCDS55900.1	.	.	.	.	.	.	.	.	.	.	C	12.44	1.938493	0.34189	.	.	ENSG00000150510	ENST00000322475;ENST00000280057	T;T	0.46063	0.88;0.88	5.79	-0.131	0.13494	.	0.245963	0.38720	N	0.001584	T	0.56217	0.1970	M	0.63843	1.955	0.33264	D	0.560112	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.984;0.997	T	0.64807	-0.6320	10	0.72032	D	0.01	-3.7704	10.7279	0.46079	0.2612:0.5921:0.1467:0.0	.	85;121;85	Q86V42;Q86V42-2;Q86V42-3	F124A_HUMAN;.;.	W	85;121	ENSP00000324625:R85W;ENSP00000280057:R121W	ENSP00000280057:R121W	R	+	1	2	FAM124A	50723757	0.880000	0.30214	0.002000	0.10522	0.008000	0.06430	0.233000	0.17911	-0.243000	0.09653	-0.176000	0.13171	CGG	.	.	.	none		0.697	FAM124A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045019.3	NM_145019		T	51825756	C	T	51825756	3	4	224	1	0	0	0	0	1	0	0	0	5429	759	27	1	375	1	FAM124A	13	51825756	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	14397982	51825756	63344122	83	13656											
CARKD	55739	hgsc.bcm.edu	37	chr13	111279816	111279816	+	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	aatgctgttcatgaggtggaGaagtggctgccccggctgca	8	9	15	9	1	1	2	1	1	0	1	1	3	1	2	2	4	3	5	2	4	2	1	rs553217045	byFrequency	TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr13:111279816G>T	ENST00000309957.2	+	5	431	c.417G>T	c.(415-417)gaG>gaT	p.E139D	CARKD_ENST00000458711.2_Intron|CARKD_ENST00000424185.2_Missense_Mutation_p.E29D|CARKD_ENST00000397191.4_Missense_Mutation_p.E76D|CARKD_ENST00000470164.2_3'UTR	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						ATGAGGTGGAGAAGTGGCTGC	0.478																																					p.E139D		Atlas-SNP	.											.	CARKD	36	.	0			c.G417T						PASS	.						117	98	104					13																	111279816		2203	4300	6503	SO:0001583	missense	55739	exon5			GGTGGAGAAGTGG	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.417G>T	chr13.hg19:g.111279816G>T	ENSP00000311984:p.Glu139Asp	89.0	0.0	.		90.0	36.0	.	NM_018210		Missense_Mutation	SNP	ENST00000309957.2	hg19	CCDS9513.1	.	.	.	.	.	.	.	.	.	.	G	7.687	0.690257	0.15039	.	.	ENSG00000213995	ENST00000424185;ENST00000439607;ENST00000397191;ENST00000309957	T;T;T	0.21932	1.98;1.98;1.98	5.13	-7.72	0.01250	Uncharacterised domain, carbohydrate kinase-related (3);	0.167564	0.51477	D	0.000087	T	0.06872	0.0175	N	0.17594	0.5	0.23492	N	0.997562	B;B;B;B;B	0.19200	0.004;0.002;0.034;0.005;0.002	B;B;B;B;B	0.21360	0.007;0.012;0.034;0.012;0.012	T	0.24333	-1.0163	10	0.15952	T	0.53	-16.6414	3.5533	0.07855	0.4722:0.2722:0.1641:0.0915	.	29;121;76;139;139	Q8IW45-4;B4DKX7;B7Z3Q0;Q8IW45-2;Q8IW45	.;.;.;.;CARKD_HUMAN	D	29;121;76;139	ENSP00000413191:E29D;ENSP00000380375:E76D;ENSP00000311984:E139D	ENSP00000311984:E139D	E	+	3	2	CARKD	110077817	0.116000	0.22171	0.001000	0.08648	0.319000	0.28217	-0.813000	0.04491	-1.320000	0.02283	-0.367000	0.07326	GAG	.	.	.	none		0.478	CARKD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045764.1	NM_018210		T	111279816	G	T	111279816	3	4	224	1	0	0	0	0	1	0	0	0	2656	933	33	4	435	4	CARKD	13	111279816	Missense_Mutation	SNP	G	TCGA-MH-A854-01A-11D-A34Z-10	59454060	111279816	3890062	84	13657											
ZNF828	283489	hgsc.bcm.edu	37	chr13	115089604	115089604	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaatggaatgataaaccaaAaaatcagttgaacaaagaaa	24	6	6	5	0	1	3	1	2	0	1	1	4	1	4	1	1	2	1	1	1	10	2			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr13:115089604A>G	ENST00000361283.1	+	3	596	c.287A>G	c.(286-288)aAa>aGa	p.K96R		NM_001164144.1|NM_001164145.1|NM_032436.2	NP_001157616.1|NP_001157617.1|NP_115812.1	Q96JM3	CHAP1_HUMAN	chromosome alignment maintaining phosphoprotein 1	96					attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|protein localization to kinetochore (GO:0034501)|protein localization to microtubule (GO:0035372)|sister chromatid biorientation (GO:0031134)	condensed chromosome (GO:0000793)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)										GATAAACCAAAAAATCAGTTG	0.408																																					p.K96R		Atlas-SNP	.											.	.	.	.	0			c.A287G						PASS	.						71	72	72					13																	115089604		2203	4300	6503	SO:0001583	missense	283489	exon3			AACCAAAAAATCA	AK074894	CCDS9545.1	13q34	2013-01-07	2011-10-07	2011-10-07	ENSG00000198824	ENSG00000198824		"Zinc fingers, C2H2-type"	20311	protein-coding gene	gene with protein product	"chromosome alignment-maintaining phosphoprotein"		"chromosome 13 open reading frame 8", "zinc finger protein 828"	C13orf8, ZNF828		21063390	Standard	NM_032436		Approved	CAMP, CHAMP	uc010ahb.3	Q96JM3	OTTHUMG00000017404	ENST00000361283.1:c.287A>G	chr13.hg19:g.115089604A>G	ENSP00000354730:p.Lys96Arg	97.0	0.0	.		72.0	28.0	.	NM_001164144	B3KU06|Q6P181|Q8NC88|Q9BST0	Missense_Mutation	SNP	ENST00000361283.1	hg19	CCDS9545.1	.	.	.	.	.	.	.	.	.	.	A	19.56	3.851053	0.71719	.	.	ENSG00000198824	ENST00000361283	T	0.01516	4.81	5.96	4.76	0.60689	.	0.095542	0.45361	D	0.000361	T	0.02047	0.0064	L	0.32530	0.975	0.34976	D	0.753647	P	0.51537	0.946	B	0.41860	0.368	T	0.62483	-0.6845	9	.	.	.	-12.7091	12.2897	0.54810	0.9335:0.0:0.0665:0.0	.	96	Q96JM3	ZN828_HUMAN	R	96	ENSP00000354730:K96R	.	K	+	2	0	ZNF828	114107706	1.000000	0.71417	0.793000	0.32043	0.806000	0.45545	3.930000	0.56522	1.046000	0.40249	0.533000	0.62120	AAA	.	.	.	none		0.408	CHAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045977.2	NM_032436		G	115089604	A	G	115089604	3	3	224	1	0	0	0	0	1	0	0	0	18193	14	1	3	289	3	ZNF828	13	115089604	Missense_Mutation	SNP	A	TCGA-MH-A854-01A-11D-A34Z-10	3809788	115089604	80274	85	13658											
SPTLC2	9517	hgsc.bcm.edu	37	chr14	78021667	78021667	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgcctccaatatatcctccAgaagcaccaaaactctttgt	12	12	4	13	0	1	1	0	0	1	1	4	1	4	1	5	0	3	1	5	0	6	4			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr14:78021667A>G	ENST00000216484.2	-	8	1345	c.1152T>C	c.(1150-1152)tcT>tcC	p.S384S	SPTLC2_ENST00000556264.1_5'Flank	NM_004863.3	NP_004854.1	O15270	SPTC2_HUMAN	serine palmitoyltransferase, long chain base subunit 2	384					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphinganine biosynthetic process (GO:0046511)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|serine C-palmitoyltransferase complex (GO:0017059)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(5)	19			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0346)	L-Serine(DB00133)	TATATCCTCCAGAAGCACCAA	0.502																																					p.S384S		Atlas-SNP	.											.	SPTLC2	55	.	0			c.T1152C						PASS	.						127	129	129					14																	78021667		2203	4300	6503	SO:0001819	synonymous_variant	9517	exon8			TCCTCCAGAAGCA	AB011098	CCDS9865.1	14q24.3	2014-09-17			ENSG00000100596	ENSG00000100596	2.3.1.50		11278	protein-coding gene	gene with protein product		605713				8921873, 9363775	Standard	NM_004863		Approved	KIAA0526, LCB2, LCB2A, hLCB2a	uc001xub.3	O15270		ENST00000216484.2:c.1152T>C	chr14.hg19:g.78021667A>G		52.0	0.0	.		23.0	17.0	.	NM_004863	Q16685	Silent	SNP	ENST00000216484.2	hg19	CCDS9865.1	.	.	.	.	.	.	.	.	.	.	A	9.959	1.222330	0.22457	.	.	ENSG00000100596	ENST00000554901	.	.	.	4.8	3.62	0.41486	.	.	.	.	.	T	0.59649	0.2209	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55829	-0.8079	4	.	.	.	-1.2399	9.9746	0.41774	0.7231:0.0:0.0:0.2769	.	.	.	.	R	321	.	.	W	-	1	0	SPTLC2	77091420	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	1.726000	0.38085	0.930000	0.37217	0.477000	0.44152	TGG	.	.	.	none		0.502	SPTLC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414030.1	NM_004863		G	78021667	A	G	78021667	2	3	224	1	0	0	0	0	0	0	0	1	15136	175	7	3		3	SPTLC2	14	78021667	Silent	SNP	A	TCGA-MH-A854-01A-11D-A34Z-10		78021667	29327873	86	13659											
TCF12	6938	hgsc.bcm.edu	37	chr15	57484401	57484401	+	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	ggcttgggagcccagcacagCtatcttcttcaggaaaacct	10	9	10	12	0	3	0	1	0	2	0	3	2	3	2	2	3	4	3	2	3	3	4			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr15:57484401C>A	ENST00000267811.5	+	7	740	c.436C>A	c.(436-438)Cta>Ata	p.L146I	TCF12_ENST00000557843.1_Missense_Mutation_p.L146I|TCF12_ENST00000333725.5_Missense_Mutation_p.L146I|TCF12_ENST00000452095.2_Missense_Mutation_p.L142I|TCF12_ENST00000438423.2_Missense_Mutation_p.L146I	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN	transcription factor 12	146					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)		CCCAGCACAGCTATCTTCTTC	0.473			T	TEC	extraskeletal myxoid chondrosarcoma																																p.L146I		Atlas-SNP	.		Dom	yes		15	15q21	6938	"transcription factor 12 (HTF4, helix-loop-helix transcription factors 4)"		M	.	TCF12	242	.	0			c.C436A						PASS	.						93	94	94					15																	57484401		2192	4292	6484	SO:0001583	missense	6938	exon7			GCACAGCTATCTT	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.436C>A	chr15.hg19:g.57484401C>A	ENSP00000267811:p.Leu146Ile	47.0	0.0	.		35.0	13.0	.	NM_207036	Q7Z3D9|Q86TC1|Q86VM2	Missense_Mutation	SNP	ENST00000267811.5	hg19	CCDS10159.1	.	.	.	.	.	.	.	.	.	.	C	13.68	2.309405	0.40895	.	.	ENSG00000140262	ENST00000543236;ENST00000267811;ENST00000438423;ENST00000452095;ENST00000333725	T;T;T;T	0.55234	0.53;0.53;0.53;0.53	5.57	2.22	0.28083	.	0.065136	0.64402	D	0.000010	T	0.55321	0.1913	L	0.41356	1.27	0.36082	D	0.842877	D;P;P;P	0.58268	0.982;0.587;0.478;0.612	D;B;B;B	0.67548	0.952;0.177;0.069;0.144	T	0.57556	-0.7791	10	0.27082	T	0.32	-7.5425	7.2908	0.26364	0.1392:0.6718:0.0:0.189	.	142;198;146;146	E9PGY0;F5H6Z6;Q99081;Q99081-3	.;.;HTF4_HUMAN;.	I	198;146;146;142;146	ENSP00000267811:L146I;ENSP00000388940:L146I;ENSP00000396881:L142I;ENSP00000331057:L146I	ENSP00000267811:L146I	L	+	1	2	TCF12	55271693	0.994000	0.37717	0.998000	0.56505	0.986000	0.74619	0.554000	0.23407	0.689000	0.31550	0.561000	0.74099	CTA	.	.	.	none		0.473	TCF12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255069.3	NM_003205		A	57484401	C	A	57484401	3	1	224	1	0	0	0	0	1	0	0	0	15699	796	28	4	458	4	TCF12	15	57484401	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10		57484401	45046991	87	13660											
CLCN7	1186	hgsc.bcm.edu	37	chr16	1507707	1507707	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgttacctttcccacggcCaggcccccgaccacggacag	7	8	9	17	3	0	0	0	0	0	0	1	2	1	1	6	3	1	1	6	3	1	3			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr16:1507707C>T	ENST00000382745.4	-	8	1331	c.726G>A	c.(724-726)ctG>ctA	p.L242L	CLCN7_ENST00000448525.1_Silent_p.L218L|CLCN7_ENST00000262318.8_Silent_p.L218L	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	242					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)				TTCCCACGGCCAGGCCCCCGA	0.632																																					p.L242L		Atlas-SNP	.											.	CLCN7	53	.	0			c.G726A						PASS	.						79	71	74					16																	1507707		2199	4300	6499	SO:0001819	synonymous_variant	1186	exon8			CACGGCCAGGCCC	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.726G>A	chr16.hg19:g.1507707C>T		21.0	0.0	.		26.0	19.0	.	NM_001287	A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	Silent	SNP	ENST00000382745.4	hg19	CCDS32361.1																																																																																			.	.	.	none		0.632	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287		T	1507707	C	T	1507707	2	4	224	1	0	0	0	0	0	0	0	1	3470	581	21	2		2	CLCN7	16	1507707	Silent	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10		1507707	88847046	88	13661											
TSC2	7249	hgsc.bcm.edu	37	chr16	2098730	2098730	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagggtaaacagacggagttTatcatcaccgcggaaatact	14	8	11	8	3	2	1	2	0	0	1	2	4	2	3	1	3	2	2	1	3	5	4	rs397515078		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr16:2098730T>C	ENST00000219476.3	+	2	744	c.114T>C	c.(112-114)ttT>ttC	p.F38F	TSC2_ENST00000353929.4_Silent_p.F38F|TSC2_ENST00000350773.4_Silent_p.F38F|TSC2_ENST00000401874.2_Silent_p.F38F|TSC2_ENST00000382538.6_Intron|TSC2_ENST00000568454.1_Silent_p.F49F|TSC2_ENST00000439673.2_Silent_p.F38F|NTHL1_ENST00000219066.1_5'Flank	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	38	Required for interaction with TSC1.				acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				AGACGGAGTTTATCATCACCG	0.498			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.F38F		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	.	TSC2	364	.	0			c.T114C	GRCh37	CD090959	TSC2	D	rs137854355	PASS	.						174	145	155					16																	2098730		2198	4299	6497	SO:0001819	synonymous_variant	7249	exon2	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	GGAGTTTATCATC	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.114T>C	chr16.hg19:g.2098730T>C		76.0	0.0	.		77.0	18.0	.	NM_001114382	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Silent	SNP	ENST00000219476.3	hg19	CCDS10458.1																																																																																			.	.	.	none		0.498	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		C	2098730	T	C	2098730	2	2	224	1	0	0	0	0	0	0	0	1	16618	1751	61	3		3	TSC2	16	2098730	Silent	SNP	T	TCGA-MH-A854-01A-11D-A34Z-10	591023	2098730	88256023	89	13662											
SRRM2	23524	hgsc.bcm.edu	37	chr16	2814755	2814755	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctcttcacctgtgcttgatgCtgtacccagaacaccctcga	8	11	7	15	1	2	2	1	1	1	1	3	3	2	2	3	0	4	3	3	0	2	3	rs141353583		TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr16:2814755C>T	ENST00000301740.8	+	11	4775	c.4226C>T	c.(4225-4227)gCt>gTt	p.A1409V		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	1409	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						GTGCTTGATGCTGTACCCAGA	0.478																																					p.A1409V		Atlas-SNP	.											.	SRRM2	263	.	0			c.C4226T						PASS	.						202	198	199					16																	2814755		2198	4300	6498	SO:0001583	missense	23524	exon11			TTGATGCTGTACC	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.4226C>T	chr16.hg19:g.2814755C>T	ENSP00000301740:p.Ala1409Val	30.0	0.0	.		42.0	10.0	.	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	hg19	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	C	6.871	0.530146	0.13127	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	T	0.25749	1.78	6.17	2.93	0.34026	.	0.538685	0.18243	N	0.147187	T	0.12347	0.0300	N	0.14661	0.345	0.22050	N	0.999392	B	0.09022	0.002	B	0.04013	0.001	T	0.24154	-1.0168	10	0.22109	T	0.4	-3.2971	5.9401	0.19187	0.118:0.5991:0.2041:0.0788	.	1409	Q9UQ35	SRRM2_HUMAN	V	1409;1409;661	ENSP00000301740:A1409V	ENSP00000301740:A1409V	A	+	2	0	SRRM2	2754756	0.061000	0.20836	0.898000	0.35279	0.656000	0.38851	0.077000	0.14738	0.920000	0.36970	-0.136000	0.14681	GCT	.	C|1.000;A|0.000	.	alt		0.478	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			T	2814755	C	T	2814755	3	4	224	1	0	0	0	0	1	0	0	0	15181	797	28	2	4264	2	SRRM2	16	2814755	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	716025	2814755	87539998	90	13663											
GTF3C1	2975	hgsc.bcm.edu	37	chr16	27480845	27480845	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcctcttcatcctcgtcaTcctccaggctgccgtccttc	4	13	5	19	2	3	0	2	0	1	0	10	0	8	0	6	1	1	1	6	1	0	2			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr16:27480845T>C	ENST00000356183.4	-	32	4856	c.4841A>G	c.(4840-4842)gAt>gGt	p.D1614G	GTF3C1_ENST00000561623.1_Missense_Mutation_p.D1614G	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	1614	Asp/Glu-rich (acidic).				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						ATCCTCGTCATCCTCCAGGCT	0.587																																					p.D1614G		Atlas-SNP	.											.	GTF3C1	210	.	0			c.A4841G						PASS	.						168	145	153					16																	27480845		2197	4300	6497	SO:0001583	missense	2975	exon32			TCGTCATCCTCCA	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.4841A>G	chr16.hg19:g.27480845T>C	ENSP00000348510:p.Asp1614Gly	92.0	0.0	.		111.0	33.0	.	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	hg19	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	T	12.98	2.100315	0.37048	.	.	ENSG00000077235	ENST00000356183;ENST00000388971	T	0.30981	1.51	4.7	4.7	0.59300	.	0.225071	0.37906	N	0.001883	T	0.29749	0.0743	L	0.34521	1.04	0.42457	D	0.992774	P;P	0.42692	0.605;0.787	B;P	0.46585	0.26;0.521	T	0.03384	-1.1042	10	0.21540	T	0.41	-9.7129	13.8623	0.63569	0.0:0.0:0.0:1.0	.	1614;1614	Q12789;Q12789-3	TF3C1_HUMAN;.	G	1614;1610	ENSP00000348510:D1614G	ENSP00000348510:D1614G	D	-	2	0	GTF3C1	27388346	1.000000	0.71417	0.324000	0.25361	0.042000	0.13812	7.485000	0.81204	1.757000	0.51966	0.402000	0.26972	GAT	.	.	.	none		0.587	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520		C	27480845	T	C	27480845	3	2	224	1	0	0	0	0	1	0	0	0	6879	1435	50	3	1512	3	GTF3C1	16	27480845	Missense_Mutation	SNP	T	TCGA-MH-A854-01A-11D-A34Z-10	24666090	27480845	62873908	91	13664											
MT1H	4496	hgsc.bcm.edu	37	chr16	56704825	56704826	+	Frame_Shift_Ins	INS	-	-	C																															ccaggctgctgctcctgttgINSccccctgggctgtgccaagt																										TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr16:56704825_56704826insC	ENST00000332374.4	+	3	181_182	c.110_111insC	c.(109-114)tgccccfs	p.CP37fs	MT1G_ENST00000444837.2_5'Flank|MT1H_ENST00000569155.1_3'UTR|MT1G_ENST00000379811.3_5'Flank|MT1G_ENST00000569500.1_5'Flank|MT1G_ENST00000568675.1_5'Flank	NM_005951.2	NP_005942.1	P80294	MT1H_HUMAN	metallothionein 1H	37	Alpha.				cellular response to cadmium ion (GO:0071276)|cellular response to zinc ion (GO:0071294)|negative regulation of growth (GO:0045926)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			lung(5)	5						TGCTCCTGTTGCCCCCTGGGCT	0.609																																					p.C37fs		Atlas-Indel,Pindel	.											.	MT1H	19	.	0			c.110_111insC						PASS	.																																			SO:0001589	frameshift_variant	4496	exon3			.	BC008408	CCDS10767.1	16q13	2008-02-05			ENSG00000205358	ENSG00000205358		"Metallothioneins"	7400	protein-coding gene	gene with protein product		156354		MT1		2286373, 8049263	Standard	NM_005951		Approved		uc002ejw.3	P80294	OTTHUMG00000133283	ENST00000332374.4:c.115dupC	chr16.hg19:g.56704830_56704830dupC	ENSP00000330587:p.Cys37fs	101.0	0.0	0		119.0	53.0	0.445378	NM_005951	B2RUY6	Frame_Shift_Ins	INS	ENST00000332374.4	hg19	CCDS10767.1																																																																																			.	.	.	none		0.609	MT1H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257063.1	NM_005951		C	56704826	-	C	56704825	7	5	224	1	0	1	1	0	0	0	0	0	9909	1319	46	0	120	0	MT1H	16	56704825	Frame_Shift_Ins	INS	-	TCGA-MH-A854-01A-11D-A34Z-10	29223980	56704825	33649928	92	13665											
NLGN2	57555	hgsc.bcm.edu	37	chr17	7317791	7317791	+	Missense_Mutation	SNP	A	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	acgtcattgtagccacgctcAactaccgtcttggggtgctc	7	11	10	13	3	3	0	2	0	1	0	4	0	3	0	2	2	4	3	2	2	3	4			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr17:7317791A>C	ENST00000302926.2	+	3	710	c.637A>C	c.(637-639)Aac>Cac	p.N213H	NLGN2_ENST00000575301.1_Missense_Mutation_p.N213H	NM_020795.2	NP_065846.1	Q8NFZ4	NLGN2_HUMAN	neuroligin 2	213					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)				AGCCACGCTCAACTACCGTCT	0.622																																					p.N213H		Atlas-SNP	.											.	NLGN2	61	.	0			c.A637C						PASS	.						105	91	95					17																	7317791		2203	4300	6503	SO:0001583	missense	57555	exon3			ACGCTCAACTACC	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.637A>C	chr17.hg19:g.7317791A>C	ENSP00000305288:p.Asn213His	44.0	0.0	.		39.0	17.0	.	NM_020795	Q9P2I1	Missense_Mutation	SNP	ENST00000302926.2	hg19	CCDS11103.1	.	.	.	.	.	.	.	.	.	.	A	17.81	3.481491	0.63849	.	.	ENSG00000169992	ENST00000302926	T	0.65178	-0.14	4.69	4.69	0.59074	Carboxylesterase, type B (1);	0.000000	0.85682	D	0.000000	D	0.83133	0.5188	H	0.94698	3.57	0.80722	D	1	D	0.89917	1.0	D	0.72075	0.976	D	0.87417	0.2379	10	0.87932	D	0	.	12.1593	0.54096	1.0:0.0:0.0:0.0	.	213	Q8NFZ4	NLGN2_HUMAN	H	213	ENSP00000305288:N213H	ENSP00000305288:N213H	N	+	1	0	NLGN2	7258515	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.079000	0.94032	1.989000	0.58080	0.379000	0.24179	AAC	.	.	.	none		0.622	NLGN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226941.2	NM_020795		C	7317791	A	C	7317791	3	2	224	1	0	0	0	0	1	0	0	0	10469	130	5	5	647	5	NLGN2	17	7317791	Missense_Mutation	SNP	A	TCGA-MH-A854-01A-11D-A34Z-10		7317791	73877419	93	13666											
NEUROD2	4761	hgsc.bcm.edu	37	chr17	37762540	37762540	+	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	catcttgcgcttcttgggccCgcgcttcttgggccgctcgc	1	12	12	16	5	3	0	0	0	3	0	4	0	3	0	2	2	1	3	2	2	0	5			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr17:37762540C>A	ENST00000302584.4	-	2	533	c.313G>T	c.(313-315)Ggg>Tgg	p.G105W		NM_006160.3	NP_006151.3	Q15784	NDF2_HUMAN	neuronal differentiation 2	105					associative learning (GO:0008306)|behavioral fear response (GO:0001662)|cellular response to calcium ion (GO:0071277)|cellular response to electrical stimulus (GO:0071257)|cerebellar cortex development (GO:0021695)|negative regulation of synapse maturation (GO:2000297)|nervous system development (GO:0007399)|neuron development (GO:0048666)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic plasticity (GO:0031915)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	E-box binding (GO:0070888)|protein heterodimerization activity (GO:0046982)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(1)|kidney(1)|large_intestine(2)|lung(4)	8	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)|Lung(15;0.00549)|LUAD - Lung adenocarcinoma(14;0.0664)			TTCTTGGGCCCGCGCTTCTTG	0.667																																					p.G105W		Atlas-SNP	.											.	NEUROD2	21	.	0			c.G313T						PASS	.						33	27	29					17																	37762540		2203	4300	6503	SO:0001583	missense	4761	exon2			TGGGCCCGCGCTT	U58681	CCDS11338.1	17q12	2013-05-21	2012-02-22		ENSG00000171532	ENSG00000171532		"Basic helix-loop-helix proteins"	7763	protein-coding gene	gene with protein product		601725	"neurogenic differentiation 2"			9119405	Standard	XM_005257409		Approved	NDRF, bHLHa1	uc002hry.3	Q15784	OTTHUMG00000133211	ENST00000302584.4:c.313G>T	chr17.hg19:g.37762540C>A	ENSP00000306754:p.Gly105Trp	38.0	0.0	.		43.0	17.0	.	NM_006160	Q8TBI7|Q9UQC6	Missense_Mutation	SNP	ENST00000302584.4	hg19	CCDS11338.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.995471	0.74703	.	.	ENSG00000171532	ENST00000302584	D	0.97378	-4.36	5.25	5.25	0.73442	.	0.000000	0.85682	U	0.000000	D	0.98124	0.9381	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99331	1.0909	10	0.87932	D	0	-5.6865	17.6108	0.88053	0.0:1.0:0.0:0.0	.	105	Q15784	NDF2_HUMAN	W	105	ENSP00000306754:G105W	ENSP00000306754:G105W	G	-	1	0	NEUROD2	35016066	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.661000	0.83786	2.451000	0.82905	0.511000	0.50034	GGG	.	.	.	none		0.667	NEUROD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256931.2	NM_006160		A	37762540	C	A	37762540	3	1	224	1	0	0	0	0	1	0	0	0	10356	652	23	4	839	4	NEUROD2	17	37762540	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	30444749	37762540	43432670	94	13667											
UBTF	7343	hgsc.bcm.edu	37	chr17	42288679	42288679	+	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	tcgaggaaacggagcagctcCacctcgtaatctttcttttt	9	13	8	11	3	2	0	0	0	2	0	5	3	3	2	2	2	3	3	2	2	2	4			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr17:42288679C>A	ENST00000302904.4	-	11	1560	c.1068G>T	c.(1066-1068)gtG>gtT	p.V356V	UBTF_ENST00000526094.1_Silent_p.V319V|UBTF_ENST00000436088.1_Silent_p.V356V|CTB-175E5.7_ENST00000586560.1_RNA|UBTF_ENST00000533177.1_Silent_p.V319V|UBTF_ENST00000529383.1_Silent_p.V356V|UBTF_ENST00000343638.5_Silent_p.V319V|UBTF_ENST00000393606.3_Silent_p.V319V|UBTF_ENST00000527034.1_Silent_p.V319V			P17480	UBF1_HUMAN	upstream binding transcription factor, RNA polymerase I	356					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)		GGAGCAGCTCCACCTCGTAAT	0.567																																					p.V356V		Atlas-SNP	.											.	UBTF	65	.	0			c.G1068T						PASS	.						79	68	72					17																	42288679		2203	4300	6503	SO:0001819	synonymous_variant	7343	exon11			CAGCTCCACCTCG	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.1068G>T	chr17.hg19:g.42288679C>A		40.0	0.0	.		32.0	12.0	.	NM_014233	A8K6R8	Silent	SNP	ENST00000302904.4	hg19	CCDS11480.1																																																																																			.	.	.	none		0.567	UBTF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395205.1	NM_014233		A	42288679	C	A	42288679	2	1	224	1	0	0	0	0	0	0	0	1	16921	581	21	4		4	UBTF	17	42288679	Silent	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	4526139	42288679	38906531	95	13668											
C17orf104	284071	hgsc.bcm.edu	37	chr17	42750780	42750780	+	Missense_Mutation	SNP	T	T	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	acgtcttcggagttctcttcTtcatgccagtatctctactg	6	16	7	12	2	5	0	1	0	4	0	8	1	5	1	1	1	2	2	1	1	2	6			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr17:42750780T>G	ENST00000409122.2	+	7	2646	c.2504T>G	c.(2503-2505)cTt>cGt	p.L835R	RP11-1072C15.4_ENST00000591628.1_RNA	NM_001145080.2	NP_001138552.2	A2RUB1	CQ104_HUMAN	chromosome 17 open reading frame 104	835										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						AGTTCTCTTCTTCATGCCAGT	0.388																																					p.L835R		Atlas-SNP	.											.	C17orf104	75	.	0			c.T2504G						PASS	.						226	189	201					17																	42750780		692	1591	2283	SO:0001583	missense	284071	exon7			CTCTTCTTCATGC		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.2504T>G	chr17.hg19:g.42750780T>G	ENSP00000386452:p.Leu835Arg	109.0	0.0	.		93.0	37.0	.	NM_001145080	B4DXJ2|B5MD93|B9EGQ6|C4AM97|Q4G0Y1|Q8IVZ7|Q8NA45	Missense_Mutation	SNP	ENST00000409122.2	hg19	CCDS45703.2	.	.	.	.	.	.	.	.	.	.	T	23.4	4.416623	0.83449	.	.	ENSG00000180336	ENST00000409122	T	0.39229	1.09	5.67	5.67	0.87782	.	.	.	.	.	T	0.51856	0.1699	L	0.38175	1.15	0.80722	D	1	D	0.54397	0.966	P	0.58970	0.849	T	0.54649	-0.8262	9	0.87932	D	0	-18.7971	15.9161	0.79521	0.0:0.0:0.0:1.0	.	835	A2RUB1	CQ104_HUMAN	R	835	ENSP00000386452:L835R	ENSP00000386452:L835R	L	+	2	0	C17orf104	40106306	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.948000	0.75965	2.171000	0.68590	0.528000	0.53228	CTT	.	.	.	none		0.388	C17orf104-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329171.2	NM_001145080		G	42750780	T	G	42750780	3	3	224	1	0	0	0	0	1	0	0	0	1853	1609	56	5	2530	5	C17orf104	17	42750780	Missense_Mutation	SNP	T	TCGA-MH-A854-01A-11D-A34Z-10	462101	42750780	38444430	96	13669											
MUC16	94025	hgsc.bcm.edu	37	chr19	9074934	9074934	+	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	atgtcaacaaaatattggaaGgcgaggttgtagcatggata	15	10	12	4	1	1	0	1	0	0	0	1	3	1	2	0	4	2	3	0	4	7	5			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr19:9074934G>C	ENST00000397910.4	-	3	12715	c.12512C>G	c.(12511-12513)cCt>cGt	p.P4171R		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4173	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						AATATTGGAAGGCGAGGTTGT	0.512																																					p.P4171R		Atlas-SNP	.											.	MUC16	4315	.	0			c.C12512G						PASS	.						157	145	149					19																	9074934		1973	4162	6135	SO:0001583	missense	94025	exon3			TTGGAAGGCGAGG	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.12512C>G	chr19.hg19:g.9074934G>C	ENSP00000381008:p.Pro4171Arg	97.0	0.0	.		96.0	35.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	5.519	0.280650	0.10458	.	.	ENSG00000181143	ENST00000397910	T	0.25250	1.81	1.49	1.49	0.22878	.	.	.	.	.	T	0.30417	0.0764	L	0.43152	1.355	.	.	.	D	0.65815	0.995	P	0.55011	0.766	T	0.40683	-0.9550	8	0.87932	D	0	.	6.41	0.21686	0.0:0.0:1.0:0.0	.	4171	B5ME49	.	R	4171	ENSP00000381008:P4171R	ENSP00000381008:P4171R	P	-	2	0	MUC16	8935934	0.002000	0.14202	0.001000	0.08648	0.416000	0.31233	1.136000	0.31467	1.138000	0.42230	0.313000	0.20887	CCT	.	.	.	none		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9074934	G	C	9074934	3	2	224	1	0	0	0	0	1	0	0	0	9980	1000	35	4	31339	4	MUC16	19	9074934	Missense_Mutation	SNP	G	TCGA-MH-A854-01A-11D-A34Z-10		9074934	50054049	97	13670											
ANO8	57719	hgsc.bcm.edu	37	chr19	17438617	17438617	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagggcgcacagcgccgccaGggggaaggcggacgagaaga	11	0	19	11	5	0	2	0	0	0	2	0	5	0	4	2	5	1	1	2	5	2	0			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr19:17438617G>A	ENST00000159087.4	-	14	2457	c.2299C>T	c.(2299-2301)Ctg>Ttg	p.L767L		NM_020959.2	NP_066010.1	Q9HCE9	ANO8_HUMAN	anoctamin 8	767					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						AGCGCCGCCAGGGGGAAGGCG	0.652																																					p.L767L		Atlas-SNP	.											.	ANO8	67	.	0			c.C2299T						PASS	.						112	102	105					19																	17438617		2203	4300	6503	SO:0001819	synonymous_variant	57719	exon14			CCGCCAGGGGGAA	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.2299C>T	chr19.hg19:g.17438617G>A		98.0	0.0	.		86.0	34.0	.	NM_020959	A6NIJ0	Silent	SNP	ENST00000159087.4	hg19	CCDS32949.1																																																																																			.	.	.	none		0.652	ANO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462943.1	XM_050644		A	17438617	G	A	17438617	2	1	224	1	0	0	0	0	0	0	0	1	703	991	35	2		2	ANO8	19	17438617	Silent	SNP	G	TCGA-MH-A854-01A-11D-A34Z-10	8363683	17438617	41690366	98	13671											
HNRNPUL1	11100	hgsc.bcm.edu	37	chr19	41774184	41774184	+	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	acgatacccaagtcatcaaaCaagaaaacgagtcaggctac	18	5	7	11	2	3	1	3	0	0	1	3	3	3	1	1	1	4	1	1	1	7	2			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr19:41774184C>T	ENST00000392006.3	+	2	525	c.352C>T	c.(352-354)Caa>Taa	p.Q118*	HNRNPUL1_ENST00000352456.3_Nonsense_Mutation_p.Q18*|HNRNPUL1_ENST00000263367.3_Nonsense_Mutation_p.Q29*|HNRNPUL1_ENST00000594207.1_3'UTR|HNRNPUL1_ENST00000593587.1_Nonsense_Mutation_p.Q18*|HNRNPUL1_ENST00000602130.1_Nonsense_Mutation_p.Q118*|HNRNPUL1_ENST00000378215.4_Nonsense_Mutation_p.Q75*|HNRNPUL1_ENST00000595018.1_Nonsense_Mutation_p.Q18*	NM_007040.3	NP_008971.2	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1	118					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						AGTCATCAAACAAGAAAACGA	0.443																																					p.Q118X		Atlas-SNP	.											.	HNRNPUL1	73	.	0			c.C352T						PASS	.						127	99	108					19																	41774184		2203	4300	6503	SO:0001587	stop_gained	11100	exon2			ATCAAACAAGAAA	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.352C>T	chr19.hg19:g.41774184C>T	ENSP00000375863:p.Gln118*	64.0	0.0	.		52.0	24.0	.	NM_007040	B3KMW7|O76022|Q6ZSZ0|Q7L8P4|Q8N6Z4|Q96G37|Q9HAL3|Q9UG75	Nonsense_Mutation	SNP	ENST00000392006.3	hg19	CCDS12576.1	.	.	.	.	.	.	.	.	.	.	C	37	6.423845	0.97555	.	.	ENSG00000105323	ENST00000352456;ENST00000392006;ENST00000378215;ENST00000263367	.	.	.	5.11	4.07	0.47477	.	0.259681	0.37437	N	0.002091	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-6.0125	11.2434	0.48982	0.1822:0.8178:0.0:0.0	.	.	.	.	X	18;118;75;29	.	ENSP00000263367:Q29X	Q	+	1	0	HNRNPUL1	46466024	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	2.263000	0.43293	1.524000	0.49035	0.655000	0.94253	CAA	.	.	.	none		0.443	HNRNPUL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463406.1	NM_144732, NM_007040		T	41774184	C	T	41774184	4	4	224	1	0	0	0	0	0	1	0	0	7281	479	17	2	358	2	HNRNPUL1	19	41774184	Nonsense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	24335567	41774184	17354799	99	13672											
FKRP	79147	hgsc.bcm.edu	37	chr19	47260096	47260096	+	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	ttcgtggcgcaggcgcctaaCaactaccgccgcttcctgga	7	8	11	15	5	0	0	0	0	0	0	2	1	1	1	4	3	3	2	4	3	3	4			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr19:47260096C>T	ENST00000318584.5	+	4	1686	c.1389C>T	c.(1387-1389)aaC>aaT	p.N463N	FKRP_ENST00000600646.1_Intron|FKRP_ENST00000391909.3_Silent_p.N463N	NM_001039885.2|NM_024301.4	NP_001034974.1|NP_077277.1	Q9H9S5	FKRP_HUMAN	fukutin related protein	463			N -> D (in MDDGB5). {ECO:0000269|PubMed:17336067}.		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)		AGGCGCCTAACAACTACCGCC	0.657																																					p.N463N		Atlas-SNP	.											.	FKRP	16	.	0			c.C1389T						PASS	.						12	12	12					19																	47260096		2197	4282	6479	SO:0001819	synonymous_variant	79147	exon4			GCCTAACAACTAC	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.1389C>T	chr19.hg19:g.47260096C>T		33.0	0.0	.		26.0	15.0	.	NM_024301	A8K5G7	Silent	SNP	ENST00000318584.5	hg19	CCDS12691.1																																																																																			.	.	.	none		0.657	FKRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465473.1	NM_024301		T	47260096	C	T	47260096	2	4	224	1	0	0	0	0	0	0	0	1	5924	477	17	2		2	FKRP	19	47260096	Silent	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10	5485912	47260096	11868887	100	13673											
DBP	1628	hgsc.bcm.edu	37	chr19	49136867	49136867	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaaggtcatcaacacctccAcggtgtctgggtccacaggg	10	7	11	13	1	3	0	2	0	1	0	5	0	5	0	3	4	1	0	3	4	2	0			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr19:49136867A>G	ENST00000222122.5	-	3	1039	c.596T>C	c.(595-597)gTg>gCg	p.V199A	DBP_ENST00000599385.1_5'UTR|DBP_ENST00000593500.1_5'UTR|DBP_ENST00000601104.1_Missense_Mutation_p.V199A	NM_001352.3	NP_001343.2	Q10586	DBP_HUMAN	D site of albumin promoter (albumin D-box) binding protein	199	Pro-rich (proline/acidic region (PAR)).				liver development (GO:0001889)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|rhythmic process (GO:0048511)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;9.98e-05)|all cancers(93;0.000112)|GBM - Glioblastoma multiforme(486;0.00615)|Epithelial(262;0.0155)		CAACACCTCCACGGTGTCTGG	0.557																																					p.V199A		Atlas-SNP	.											.	DBP	16	.	0			c.T596C						PASS	.						146	129	135					19																	49136867		2203	4300	6503	SO:0001583	missense	1628	exon3			ACCTCCACGGTGT	U06936	CCDS12728.1	19q13.33	2013-09-20			ENSG00000105516	ENSG00000105516			2697	protein-coding gene	gene with protein product		124097				1535333, 7835883	Standard	XR_243907		Approved	DABP	uc002pjx.4	Q10586	OTTHUMG00000183319	ENST00000222122.5:c.596T>C	chr19.hg19:g.49136867A>G	ENSP00000222122:p.Val199Ala	73.0	0.0	.		51.0	19.0	.	NM_001352	A2I2P4	Missense_Mutation	SNP	ENST00000222122.5	hg19	CCDS12728.1	.	.	.	.	.	.	.	.	.	.	A	17.21	3.331769	0.60853	.	.	ENSG00000105516	ENST00000222122	.	.	.	5.11	5.11	0.69529	.	0.834711	0.10336	U	0.686922	T	0.49915	0.1585	L	0.49126	1.545	0.30737	N	0.746626	B	0.19935	0.04	B	0.19148	0.024	T	0.49908	-0.8889	9	0.41790	T	0.15	-24.4839	13.1676	0.59579	1.0:0.0:0.0:0.0	.	199	Q10586	DBP_HUMAN	A	199	.	ENSP00000222122:V199A	V	-	2	0	DBP	53828679	0.997000	0.39634	0.998000	0.56505	0.998000	0.95712	5.022000	0.64078	2.064000	0.61679	0.533000	0.62120	GTG	.	.	.	none		0.557	DBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466167.1	NM_001352		G	49136867	A	G	49136867	3	3	224	1	0	0	0	0	1	0	0	0	4258	159	6	3	389	3	DBP	19	49136867	Missense_Mutation	SNP	A	TCGA-MH-A854-01A-11D-A34Z-10	1876771	49136867	9992116	101	13674											
ZNF749	388567	hgsc.bcm.edu	37	chr19	57956719	57956719	+	Frame_Shift_Del	DEL	A	A	-																															aatgtgggaaagacttcaacAaatgtaatactggtcagcgc																										TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr19:57956719delA	ENST00000334181.4	+	3	2453	c.2203delA	c.(2203-2205)aaafs	p.K735fs	AC004076.9_ENST00000596831.1_Intron	NM_001023561.2	NP_001018855.2	O43361	ZN749_HUMAN	zinc finger protein 749	735					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)|lung(3)|prostate(1)	13		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;0.0264)|Lung(386;0.177)		AGACTTCAACAAATGTAATAC	0.393																																					p.N734fs		Atlas-Indel,Pindel	.											.	ZNF749	75	.	0			c.2202delC						PASS	.						106	109	108					19																	57956719		2203	4300	6503	SO:0001589	frameshift_variant	388567	exon3			.	AK122740	CCDS33132.2	19q13.43	2013-01-08			ENSG00000186230	ENSG00000186230		"Zinc fingers, C2H2-type", "-"	32783	protein-coding gene	gene with protein product							Standard	NM_001023561		Approved	FLJ16360	uc002qoq.2	O43361	OTTHUMG00000150372	ENST00000334181.4:c.2203delA	chr19.hg19:g.57956719delA	ENSP00000333980:p.Lys735fs	67.0	0.0	0		59.0	27.0	0.457627	NM_001023561		Frame_Shift_Del	DEL	ENST00000334181.4	hg19	CCDS33132.2																																																																																			.	.	.	none		0.393	ZNF749-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317879.1	NM_001023561		-	57956719	A	-	57956719	7	5	224	1	0	1	0	1	0	0	0	0	18143	131	5	0	2213	0	ZNF749	19	57956719	Frame_Shift_Del	DEL	A	TCGA-MH-A854-01A-11D-A34Z-10	8819852	57956719	1172264	102	13675											
FITM2	128486	hgsc.bcm.edu	37	chr20	42935653	42935653	+	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	ggcactgctgcttgctctggTgttcctttctgaccccctcc	2	14	9	16	0	2	1	0	1	2	0	4	1	4	1	4	2	3	5	4	2	0	3			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr20:42935653T>A	ENST00000396825.3	-	2	421	c.401A>T	c.(400-402)cAc>cTc	p.H134L		NM_001080472.1	NP_001073941.1	Q8N6M3	FITM2_HUMAN	fat storage-inducing transmembrane protein 2	134					cellular triglyceride homeostasis (GO:0035356)|cytoskeleton organization (GO:0007010)|lipid particle organization (GO:0034389)|positive regulation of sequestering of triglyceride (GO:0010890)|regulation of cell morphogenesis (GO:0022604)|regulation of triglyceride biosynthetic process (GO:0010866)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|mitochondrion (GO:0005739)				endometrium(2)|lung(2)|skin(2)	6						CTTGCTCTGGTGTTCCTTTCT	0.567																																					p.H134L		Atlas-SNP	.											.	FITM2	15	.	0			c.A401T						PASS	.						119	87	98					20																	42935653		2203	4300	6503	SO:0001583	missense	128486	exon2			CTCTGGTGTTCCT	BC029662	CCDS33473.1	20q13.12	2009-04-29	2009-04-29	2009-04-29	ENSG00000197296	ENSG00000197296			16135	protein-coding gene	gene with protein product	"fat inducing transcript 2"	612029	"chromosome 20 open reading frame 142"	C20orf142		18160536	Standard	NM_001080472		Approved	dJ881L22.2, FIT2	uc002xlr.1	Q8N6M3	OTTHUMG00000032522	ENST00000396825.3:c.401A>T	chr20.hg19:g.42935653T>A	ENSP00000380037:p.His134Leu	46.0	0.0	.		44.0	13.0	.	NM_001080472	A1L492|B9EGQ4|Q5TE59|Q9H3Y1	Missense_Mutation	SNP	ENST00000396825.3	hg19	CCDS33473.1	.	.	.	.	.	.	.	.	.	.	T	9.891	1.204219	0.22205	.	.	ENSG00000197296	ENST00000396825	.	.	.	5.84	-4.83	0.03161	.	0.696249	0.15653	N	0.251278	T	0.13884	0.0336	N	0.17082	0.46	0.09310	N	1	B	0.18013	0.025	B	0.18871	0.023	T	0.29305	-1.0016	9	0.11794	T	0.64	.	4.3673	0.11230	0.2017:0.0597:0.4168:0.3218	.	134	Q8N6M3	FITM2_HUMAN	L	134	.	ENSP00000380037:H134L	H	-	2	0	FITM2	42369067	0.000000	0.05858	0.002000	0.10522	0.762000	0.43233	-1.102000	0.03332	-0.380000	0.07894	0.533000	0.62120	CAC	.	.	.	none		0.567	FITM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079342.2	XM_371399		A	42935653	T	A	42935653	3	1	224	1	0	0	0	0	1	0	0	0	5906	1696	59	5	391	5	FITM2	20	42935653	Missense_Mutation	SNP	T	TCGA-MH-A854-01A-11D-A34Z-10		42935653	20089867	103	13676											
ARFGEF2	10564	hgsc.bcm.edu	37	chr20	47568002	47568002	+	Missense_Mutation	SNP	T	T	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	aggggttcagttacaaataaTtaaggtatgcctatttgttt	12	16	9	4	0	1	0	1	0	0	0	1	0	1	0	1	3	2	4	1	3	6	8			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr20:47568002T>G	ENST00000371917.4	+	4	419	c.419T>G	c.(418-420)aTt>aGt	p.I140S		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	140	DCB; DCB:DCB domain and DCB:HUS domain interaction.				endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)			breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			TTACAAATAATTAAGGTATGC	0.423																																					p.I140S	Esophageal Squamous(176;1738 1974 26285 33069 35354)	Atlas-SNP	.											.	ARFGEF2	160	.	0			c.T419G						PASS	.						90	93	92					20																	47568002		2203	4300	6503	SO:0001583	missense	10564	exon4			AAATAATTAAGGT	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.419T>G	chr20.hg19:g.47568002T>G	ENSP00000360985:p.Ile140Ser	58.0	0.0	.		86.0	22.0	.	NM_006420	Q5TFT9|Q9NTS1	Missense_Mutation	SNP	ENST00000371917.4	hg19	CCDS13411.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.289541	0.80914	.	.	ENSG00000124198	ENST00000538445;ENST00000371917	T	0.31247	1.5	6.05	4.95	0.65309	Armadillo-type fold (1);	0.071289	0.85682	D	0.000000	T	0.57858	0.2082	M	0.88906	2.99	0.80722	D	1	D	0.67145	0.996	D	0.63703	0.917	T	0.64296	-0.6441	10	0.56958	D	0.05	.	11.9957	0.53201	0.0:0.0671:0.0:0.9329	.	140	Q9Y6D5	BIG2_HUMAN	S	140	ENSP00000360985:I140S	ENSP00000360985:I140S	I	+	2	0	ARFGEF2	47001409	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.040000	0.89188	1.118000	0.41863	0.528000	0.53228	ATT	.	.	.	none		0.423	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420		G	47568002	T	G	47568002	3	3	224	1	0	0	0	0	1	0	0	0	853	1493	52	5	433	5	ARFGEF2	20	47568002	Missense_Mutation	SNP	T	TCGA-MH-A854-01A-11D-A34Z-10	4632349	47568002	15457518	104	13677											
HSPA13	6782	hgsc.bcm.edu	37	chr21	15746414	15746414	+	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	ttccttcctgtcctgctcctCcaccgttagtaatactgaca	7	14	5	15	1	0	1	0	1	0	0	5	1	5	1	6	0	2	3	6	0	3	5			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr21:15746414C>T	ENST00000285667.3	-	5	1007	c.940G>A	c.(940-942)Gag>Aag	p.E314K	HSPA13_ENST00000544452.1_Missense_Mutation_p.E106K	NM_006948.4	NP_008879.3	P48723	HSP13_HUMAN	heat shock protein 70kDa family, member 13	314						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	13						TCCTGCTCCTCCACCGTTAGT	0.453																																					p.E314K		Atlas-SNP	.											.	HSPA13	44	.	0			c.G940A						PASS	.						116	89	98					21																	15746414		2203	4300	6503	SO:0001583	missense	6782	exon5			GCTCCTCCACCGT		CCDS13567.1	21q11.1	2011-09-02	2008-06-17	2008-06-17	ENSG00000155304	ENSG00000155304		"Heat shock proteins / HSP70"	11375	protein-coding gene	gene with protein product		601100	"stress 70 protein chaperone, microsome-associated, 60kD", "stress 70 protein chaperone, microsome-associated, 60kDa"	STCH		8825657	Standard	NM_006948		Approved		uc002yjt.3	P48723	OTTHUMG00000074261	ENST00000285667.3:c.940G>A	chr21.hg19:g.15746414C>T	ENSP00000285667:p.Glu314Lys	88.0	0.0	.		71.0	27.0	.	NM_006948	B2R616|Q8NE40	Missense_Mutation	SNP	ENST00000285667.3	hg19	CCDS13567.1	.	.	.	.	.	.	.	.	.	.	C	11.06	1.527733	0.27299	.	.	ENSG00000155304	ENST00000285667;ENST00000544452	T;T	0.00966	5.49;5.49	5.86	4.97	0.65823	.	0.638912	0.16716	N	0.202467	T	0.01320	0.0043	L	0.41415	1.275	0.09310	N	1	P	0.35226	0.491	B	0.34536	0.185	T	0.48854	-0.8998	10	0.87932	D	0	-14.9378	12.2841	0.54783	0.1155:0.7214:0.1631:0.0	.	314	P48723	HSP13_HUMAN	K	314;106	ENSP00000285667:E314K;ENSP00000441986:E106K	ENSP00000285667:E314K	E	-	1	0	HSPA13	14668285	1.000000	0.71417	0.890000	0.34922	0.117000	0.20001	2.613000	0.46351	1.598000	0.50083	0.650000	0.86243	GAG	.	.	.	none		0.453	HSPA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157815.1			T	15746414	C	T	15746414	3	4	224	1	0	0	0	0	1	0	0	0	7413	864	30	2	479	2	HSPA13	21	15746414	Missense_Mutation	SNP	C	TCGA-MH-A854-01A-11D-A34Z-10		15746414	32383481	105	13678											
CLIC6	54102	hgsc.bcm.edu	37	chr21	36080328	36080329	+	Frame_Shift_Del	DEL	AG	AG	-																															agtcaagacggatgtgaataAgatcgaggagttcttagagg																										TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr21:36080328_36080329delAG	ENST00000360731.3	+	4	1625_1626	c.1625_1626delAG	c.(1624-1626)aagfs	p.K542fs	CLIC6_ENST00000349499.2_Frame_Shift_Del_p.K524fs			Q96NY7	CLIC6_HUMAN	chloride intracellular channel 6	542						chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	voltage-gated chloride channel activity (GO:0005247)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19						GATGTGAATAAGATCGAGGAGT	0.485																																					p.524_524del		Atlas-Indel,Pindel	.											.	CLIC6	49	.	0			c.1570_1571del						PASS	.																																			SO:0001589	frameshift_variant	54102	exon3			.	AF426169	CCDS13638.1	21q22.12	2012-09-26			ENSG00000159212	ENSG00000159212		"Ion channels / Chloride channels : Intracellular"	2065	protein-coding gene	gene with protein product		615321		CLIC1L		10830953	Standard	NM_053277		Approved	CLIC5	uc002yuf.1	Q96NY7	OTTHUMG00000086237	ENST00000360731.3:c.1625_1626delAG	chr21.hg19:g.36080328_36080329delAG	ENSP00000353959:p.Lys542fs	52.0	0.0	0		61.0	23.0	0.377049	NM_053277	A8K0U8|Q8IX31	Frame_Shift_Del	DEL	ENST00000360731.3	hg19																																																																																				.	.	.	none		0.485	CLIC6-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000194156.1			-	36080329	AG	-	36080328	7	5	224	1	0	1	0	1	0	0	0	0	3532	72	3	0	1581	0	CLIC6	21	36080328	Frame_Shift_Del	DEL	AG	TCGA-MH-A854-01A-11D-A34Z-10	20333914	36080328	12049567	106	13679											
CABIN1	23523	hgsc.bcm.edu	37	chr22	24480737	24480737	+	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	cattgagggaacttcaactgAggtgggcccacaaccttgag	11	8	12	10	0	1	3	1	3	0	0	1	4	1	4	2	3	3	0	2	3	3	3			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr22:24480737A>T	ENST00000398319.2	+	21	3501	c.3116A>T	c.(3115-3117)gAg>gTg	p.E1039V	CABIN1_ENST00000405822.2_Splice_Site_p.E989V|CABIN1_ENST00000263119.5_Splice_Site_p.E1039V	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	1039					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						ACTTCAACTGAGGTGGGCCCA	0.547																																					p.E1039V		Atlas-SNP	.											.	CABIN1	153	.	0			c.A3116T						PASS	.						59	47	51					22																	24480737		2203	4300	6503	SO:0001630	splice_region_variant	23523	exon21			CAACTGAGGTGGG	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.3117+1A>T	chr22.hg19:g.24480737A>T		72.0	0.0	.		64.0	29.0	.	NM_001199281	G5E9F3|Q6PHY0|Q9Y460	Missense_Mutation	SNP	ENST00000398319.2	hg19	CCDS13823.1	.	.	.	.	.	.	.	.	.	.	A	16.41	3.115392	0.56505	.	.	ENSG00000099991	ENST00000263119;ENST00000405822;ENST00000398319	T;T;T	0.65364	0.06;-0.15;0.06	5.56	5.56	0.83823	.	0.051340	0.85682	D	0.000000	T	0.57301	0.2044	L	0.34521	1.04	0.80722	D	1	P;P	0.45827	0.867;0.791	P;B	0.44897	0.463;0.273	T	0.61987	-0.6949	10	0.59425	D	0.04	.	15.2547	0.73576	1.0:0.0:0.0:0.0	.	989;1039	G5E9F3;Q9Y6J0	.;CABIN_HUMAN	V	1039;989;1039	ENSP00000263119:E1039V;ENSP00000384694:E989V;ENSP00000381364:E1039V	ENSP00000263119:E1039V	E	+	2	0	CABIN1	22810737	1.000000	0.71417	0.993000	0.49108	0.260000	0.26232	8.121000	0.89582	2.259000	0.74868	0.529000	0.55759	GAG	.	.	.	none		0.547	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295	Missense_Mutation	T	24480737	A	T	24480737	5	4	224	1	0	0	0	0	0	0	1	0	2530	318	11	5	3194	5	CABIN1	22	24480737	Splice_Site	SNP	A	TCGA-MH-A854-01A-11D-A34Z-10		24480737	26823829	107	13680											
SMTN	6525	hgsc.bcm.edu	37	chr22	31487406	31487406	+	Missense_Mutation	SNP	A	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	cacattcaccatcgagatcaAggacggccgtggccaggcct	10	6	11	14	3	2	1	2	0	0	1	3	3	2	2	4	4	0	0	4	4	1	1			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chr22:31487406A>C	ENST00000347557.2	+	10	1615	c.1397A>C	c.(1396-1398)aAg>aCg	p.K466T	SMTN_ENST00000358743.1_Missense_Mutation_p.K466T|SMTN_ENST00000333137.7_Missense_Mutation_p.K466T|SMTN_ENST00000404574.1_5'Flank	NM_001207017.1|NM_006932.4	NP_001193946.1|NP_008863.3	P53814	SMTN_HUMAN	smoothelin	466					muscle organ development (GO:0007517)|smooth muscle contraction (GO:0006939)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)			breast(2)|endometrium(2)|large_intestine(5)|lung(9)|ovary(3)|pancreas(1)|prostate(3)	25						ATCGAGATCAAGGACGGCCGT	0.682																																					p.K522T		Atlas-SNP	.											.	SMTN	219	.	0			c.A1565C						PASS	.						22	26	25					22																	31487406		2050	4150	6200	SO:0001583	missense	6525	exon9			AGATCAAGGACGG	AY061972	CCDS13886.1, CCDS13887.1, CCDS13888.1, CCDS74845.1, CCDS74846.1	22q12	2006-01-27			ENSG00000183963	ENSG00000183963			11126	protein-coding gene	gene with protein product		602127				9244445, 8707825	Standard	NM_006932		Approved		uc011ale.2	P53814	OTTHUMG00000151203	ENST00000347557.2:c.1397A>C	chr22.hg19:g.31487406A>C	ENSP00000328635:p.Lys466Thr	20.0	0.0	.		21.0	9.0	.	NM_001207018	O00569|O95769|O95937|Q8N4H8|Q8WWW1|Q8WWW2|Q9P1S8|Q9UIT1|Q9UIT2	Missense_Mutation	SNP	ENST00000347557.2	hg19	CCDS13886.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.494882	0.85069	.	.	ENSG00000183963	ENST00000358743;ENST00000347557;ENST00000333137;ENST00000329852;ENST00000404496	T;T;T	0.76060	-0.55;-0.99;-0.99	5.07	5.07	0.68467	.	0.000000	0.36034	N	0.002826	D	0.84211	0.5422	M	0.65498	2.005	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;0.999;1.0	D;D;D;D;D;D	0.91635	0.997;0.996;0.991;0.997;0.991;0.999	D	0.86070	0.1537	10	0.87932	D	0	-35.7001	13.7041	0.62627	1.0:0.0:0.0:0.0	.	522;520;458;466;466;466	E7ETT8;B4E229;B5MC56;E7EWD0;P53814;P53814-5	.;.;.;.;SMTN_HUMAN;.	T	466;466;466;464;458	ENSP00000351593:K466T;ENSP00000328635:K466T;ENSP00000329532:K466T	ENSP00000329393:K464T	K	+	2	0	SMTN	29817406	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	6.535000	0.73838	2.049000	0.60858	0.402000	0.26972	AAG	.	.	.	none		0.682	SMTN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321766.1	NM_134270		C	31487406	A	C	31487406	3	2	224	1	0	0	0	0	1	0	0	0	14827	72	3	5	1431	5	SMTN	22	31487406	Missense_Mutation	SNP	A	TCGA-MH-A854-01A-11D-A34Z-10	7006669	31487406	19817160	108	13681											
MED12	9968	hgsc.bcm.edu	37	chrX	70355044	70355044	+	Missense_Mutation	SNP	T	T	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	tcacgtgtgagccacagggcTcccttatcgataccaagggc	9	8	11	13	2	1	1	1	1	0	0	3	2	2	1	3	2	2	1	3	2	3	2			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chrX:70355044T>G	ENST00000374080.3	+	36	4998	c.4966T>G	c.(4966-4968)Tcc>Gcc	p.S1656A	MED12_ENST00000333646.6_Missense_Mutation_p.S1656A|MED12_ENST00000374102.1_Missense_Mutation_p.S1656A			Q93074	MED12_HUMAN	mediator complex subunit 12	1656	Interaction with CTNNB1 and GLI3.				androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					GCCACAGGGCTCCCTTATCGA	0.557			"M, S"		uterine leiomyoma		Opitz-Kaveggia Syndrome																														p.S1656A		Atlas-SNP	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	0			c.T4966G						PASS	.						84	80	81					X																	70355044		2105	4205	6310	SO:0001583	missense	9968	exon36			CAGGGCTCCCTTA	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.4966T>G	chrX.hg19:g.70355044T>G	ENSP00000363193:p.Ser1656Ala	143.0	0.0	.		119.0	47.0	.	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Missense_Mutation	SNP	ENST00000374080.3	hg19	CCDS43970.1	.	.	.	.	.	.	.	.	.	.	-	16.44	3.124037	0.56613	.	.	ENSG00000184634	ENST00000333646;ENST00000536756;ENST00000374102;ENST00000374080;ENST00000430072;ENST00000439750	T;T;T;T;T	0.58652	0.33;0.32;0.32;0.33;1.37	3.97	3.97	0.46021	.	0.000000	0.85682	D	0.000000	T	0.60560	0.2278	L	0.34521	1.04	0.58432	D	0.999999	B;B;D;B	0.60160	0.383;0.342;0.987;0.264	B;B;P;B	0.61003	0.155;0.092;0.882;0.168	T	0.59257	-0.7488	10	0.36615	T	0.2	-13.3161	12.5429	0.56182	0.0:0.0:0.0:1.0	.	1656;1503;1656;1656	F5H3Y1;Q7Z3Z5;Q93074-3;Q93074	.;.;.;MED12_HUMAN	A	1656;1656;1656;1656;1624;401	ENSP00000333125:S1656A;ENSP00000363215:S1656A;ENSP00000363193:S1656A;ENSP00000414203:S1624A;ENSP00000408388:S401A	ENSP00000333125:S1656A	S	+	1	0	MED12	70271769	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.864000	0.87037	1.595000	0.50050	0.430000	0.28490	TCC	.	.	.	none		0.557	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120		G	70355044	T	G	70355044	3	3	224	1	0	0	0	0	1	0	0	0	9435	1551	54	5	5108	5	MED12	23	70355044	Missense_Mutation	SNP	T	TCGA-MH-A854-01A-11D-A34Z-10		70355044	84915516	109	13682											
WDR44	54521	hgsc.bcm.edu	37	chrX	117526785	117526785	+	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	agaatcccaaaaggcagagaGtcagaatacatttgaagaga	19	6	10	6	0	1	5	1	1	0	4	2	7	2	5	1	1	1	1	1	1	6	2			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chrX:117526785G>C	ENST00000254029.3	+	4	772	c.377G>C	c.(376-378)aGt>aCt	p.S126T	WDR44_ENST00000371825.3_Missense_Mutation_p.S126T|WDR44_ENST00000371822.5_Missense_Mutation_p.S101T|WDR44_ENST00000493448.1_3'UTR	NM_019045.4	NP_061918.3	Q5JSH3	WDR44_HUMAN	WD repeat domain 44	126	Binding activity.					endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	33						AAGGCAGAGAGTCAGAATACA	0.403																																					p.S126T		Atlas-SNP	.											.	WDR44	188	.	0			c.G377C						PASS	.						87	84	85					X																	117526785		2203	4300	6503	SO:0001583	missense	54521	exon4			CAGAGAGTCAGAA	AK001978	CCDS14572.1, CCDS55482.1, CCDS55483.1	Xq24	2013-01-09			ENSG00000131725	ENSG00000131725		"WD repeat domain containing"	30512	protein-coding gene	gene with protein product						12477932	Standard	NM_019045		Approved	DKFZp686L20145, RPH11, RAB11BP	uc004eqn.3	Q5JSH3	OTTHUMG00000022254	ENST00000254029.3:c.377G>C	chrX.hg19:g.117526785G>C	ENSP00000254029:p.Ser126Thr	124.0	0.0	.		154.0	73.0	.	NM_001184965	B4DSE9|F8W913|Q0JS52|Q0JTF3|Q5JSH2|Q6ZSC1|Q7Z365|Q7Z3P6|Q8NAU8|Q8NHU5|Q9NUV4	Missense_Mutation	SNP	ENST00000254029.3	hg19	CCDS14572.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.225|7.225	0.598130|0.598130	0.13939|0.13939	.|.	.|.	ENSG00000131725|ENSG00000131725	ENST00000371848|ENST00000371822;ENST00000254029;ENST00000371825	T|T;T;T	0.64803|0.73258	-0.12|-0.73;-0.15;-0.02	5.58|5.58	4.53|4.53	0.55603|0.55603	.|.	.|0.401797	.|0.29924	.|N	.|0.010857	T|T	0.48169|0.48169	0.1485|0.1485	N|N	0.14661|0.14661	0.345|0.345	0.19775|0.19775	N|N	0.999955|0.999955	.|B;B;B	.|0.09022	.|0.002;0.001;0.002	.|B;B;B	.|0.11329	.|0.006;0.002;0.002	T|T	0.21793|0.21793	-1.0235|-1.0235	7|10	0.18710|0.12430	T|T	0.47|0.62	-15.6424|-15.6424	8.5425|8.5425	0.33402|0.33402	0.2406:0.0:0.7594:0.0|0.2406:0.0:0.7594:0.0	.|.	.|101;126;126	.|F8W913;Q5JSH3-2;Q5JSH3	.|.;.;WDR44_HUMAN	D|T	25|101;126;126	ENSP00000360914:E25D|ENSP00000360887:S101T;ENSP00000254029:S126T;ENSP00000360890:S126T	ENSP00000360914:E25D|ENSP00000254029:S126T	E|S	+|+	3|2	2|0	WDR44|WDR44	117410813|117410813	0.461000|0.461000	0.25783|0.25783	0.998000|0.998000	0.56505|0.56505	0.467000|0.467000	0.32768|0.32768	0.667000|0.667000	0.25112|0.25112	2.333000|2.333000	0.79357|0.79357	0.600000|0.600000	0.82982|0.82982	GAG|AGT	.	.	.	none		0.403	WDR44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058001.1	NM_019045		C	117526785	G	C	117526785	3	2	224	1	0	0	0	0	1	0	0	0	17308	1029	36	4	391	4	WDR44	23	117526785	Missense_Mutation	SNP	G	TCGA-MH-A854-01A-11D-A34Z-10	47171741	117526785	37743775	110	13683			1	30		2	2	25	N	G_A	8.527672e-05
WDR44	54521	hgsc.bcm.edu	37	chrX	117526809	117526809	+	Frame_Shift_Del	DEL	A	A	-																															gaatacatttgaagagactgAattagaattaaaaaaatgct																										TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chrX:117526809delA	ENST00000254029.3	+	4	796	c.401delA	c.(400-402)gaafs	p.E134fs	WDR44_ENST00000371825.3_Frame_Shift_Del_p.E134fs|WDR44_ENST00000371822.5_Frame_Shift_Del_p.E109fs|WDR44_ENST00000493448.1_3'UTR	NM_019045.4	NP_061918.3	Q5JSH3	WDR44_HUMAN	WD repeat domain 44	134	Binding activity.					endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	33						GAAGAGACTGAATTAGAATTA	0.383																																					p.E134fs		Atlas-Indel,Pindel	.											.	WDR44	188	.	0			c.400delG						PASS	.						85	83	84					X																	117526809		2203	4300	6503	SO:0001589	frameshift_variant	54521	exon4			.	AK001978	CCDS14572.1, CCDS55482.1, CCDS55483.1	Xq24	2013-01-09			ENSG00000131725	ENSG00000131725		"WD repeat domain containing"	30512	protein-coding gene	gene with protein product						12477932	Standard	NM_019045		Approved	DKFZp686L20145, RPH11, RAB11BP	uc004eqn.3	Q5JSH3	OTTHUMG00000022254	ENST00000254029.3:c.401delA	chrX.hg19:g.117526809delA	ENSP00000254029:p.Glu134fs	118.0	0.0	0		131.0	64.0	0.48855	NM_001184965	B4DSE9|F8W913|Q0JS52|Q0JTF3|Q5JSH2|Q6ZSC1|Q7Z365|Q7Z3P6|Q8NAU8|Q8NHU5|Q9NUV4	Frame_Shift_Del	DEL	ENST00000254029.3	hg19	CCDS14572.1																																																																																			.	.	.	none		0.383	WDR44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058001.1	NM_019045		-	117526809	A	-	117526809	7	5	224	1	0	1	0	1	0	0	0	0	17308	246	9	0	415	0	WDR44	23	117526809	Frame_Shift_Del	DEL	A	TCGA-MH-A854-01A-11D-A34Z-10	24	117526809	37743751	111	13684			1	30		2	2	25	N	G_A	8.527672e-05
IKBKG	2539	hgsc.bcm.edu	37	chrX	153770658	153770658	+	Intron	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	tacaaggccagagctttctgGaagggggcagtaagtacctc	11	8	13	9	0	1	1	0	0	1	1	2	2	1	2	2	4	3	4	2	4	5	4			TCGA-MH-A854-01A-11D-A34Z-10	TCGA-MH-A854-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	cfe2ae5e-1b05-49e9-896c-0dfe0c7bb0e0	c013eb32-4377-46f2-8ed8-eb0f3d494642	g.chrX:153770658G>T	ENST00000393564.2	-	2	233				IKBKG_ENST00000369607.1_Intron|IKBKG_ENST00000369609.5_Missense_Mutation_p.W60C|G6PD_ENST00000369620.2_Intron|G6PD_ENST00000497281.1_Intron|G6PD_ENST00000393562.2_Intron	NM_001042351.1	NP_001035810.1	P11413	G6PD_HUMAN	glucose-6-phosphate dehydrogenase						carbohydrate metabolic process (GO:0005975)|cellular response to oxidative stress (GO:0034599)|cholesterol biosynthetic process (GO:0006695)|cytokine production (GO:0001816)|erythrocyte maturation (GO:0043249)|glucose 6-phosphate metabolic process (GO:0051156)|glutathione metabolic process (GO:0006749)|lipid metabolic process (GO:0006629)|NADP metabolic process (GO:0006739)|NADPH regeneration (GO:0006740)|negative regulation of protein glutathionylation (GO:0010734)|oxidation-reduction process (GO:0055114)|pentose biosynthetic process (GO:0019322)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, oxidative branch (GO:0009051)|regulation of neuron apoptotic process (GO:0043523)|response to ethanol (GO:0045471)|response to food (GO:0032094)|response to organic cyclic compound (GO:0014070)|ribose phosphate biosynthetic process (GO:0046390)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	glucose binding (GO:0005536)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(3)|ovary(4)	18	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)					GAGCTTTCTGGAAGGGGGCAG	0.582																																					p.W60C		Atlas-SNP	.											.	IKBKG	17	.	0			c.G180T						PASS	.						56	48	50					X																	153770658		1568	3582	5150	SO:0001627	intron_variant	8517	exon1			TTTCTGGAAGGGG	X03674	CCDS14756.2, CCDS44023.1	Xq28	2014-09-17			ENSG00000160211	ENSG00000160211	1.1.1.49		4057	protein-coding gene	gene with protein product		305900				3012556, 2428611	Standard	NM_000402		Approved	G6PD1	uc004flx.1	P11413	OTTHUMG00000024237	ENST00000393564.2:c.120+3592C>A	chrX.hg19:g.153770658G>T		53.0	0.0	.		44.0	21.0	.	NM_001099856	D3DWX9|Q16000|Q16765|Q8IU70|Q8IU88|Q8IUA6|Q96PQ2	Missense_Mutation	SNP	ENST00000393564.2	hg19	CCDS44023.1	.	.	.	.	.	.	.	.	.	.	G	11.29	1.593948	0.28445	.	.	ENSG00000073009	ENST00000369609	D	0.91843	-2.92	2.6	1.67	0.24075	.	.	.	.	.	D	0.87414	0.6171	.	.	.	0.09310	N	0.999993	P	0.44006	0.824	B	0.40285	0.325	T	0.79147	-0.1923	8	0.87932	D	0	.	5.8132	0.18477	0.0:0.0:0.6857:0.3143	.	60	Q9Y6K9-2	.	C	60	ENSP00000358622:W60C	ENSP00000358622:W60C	W	+	3	0	IKBKG	153423852	0.002000	0.14202	0.002000	0.10522	0.556000	0.35491	0.859000	0.27858	0.481000	0.27557	0.483000	0.47432	TGG	.	.	.	none		0.582	G6PD-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061170.3	NM_000402		T	153770658	G	T	153770658	1	4	224	0	1	0	0	0	0	0	0	0	7620	1183	41	4		4	IKBKG	23	153770658	Intron	SNP	G	TCGA-MH-A854-01A-11D-A34Z-10	36243849	153770658	1499902	112	13685											
CDK11B	984	hgsc.bcm.edu	37	chr1	1577073	1577078	+	In_Frame_Del	DEL	TCCTCT	TCCTCT	-																															tgctgccggtctcctcctccTcctcttcctcttcctcctcc																										TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	TCCTCT	TCCTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr1:1577073_1577078delTCCTCT	ENST00000407249.3	-	10	962_967	c.963_968delAGAGGA	c.(961-969)gaagaggag>gag	p.321_323EEE>E	CDK11B_ENST00000341832.6_In_Frame_Del_p.274_276EEE>E|CDK11B_ENST00000340677.5_In_Frame_Del_p.308_310EEE>E|CDK11B_ENST00000317673.7_In_Frame_Del_p.319_321EEE>E			P21127	CD11B_HUMAN	cyclin-dependent kinase 11B	331	Glu-rich.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|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)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(3)|lung(4)|skin(1)|stomach(2)	12						ctcctcctcctcctcttcctcttcct	0.563																																					p.317_318del		Pindel	.											.	CDK11B	37	.	0			c.949_954del						PASS	.																																			SO:0001651	inframe_deletion	984	exon9			.	AK000081	CCDS72682.1, CCDS72683.1, CCDS72684.1	1p36.33	2013-09-24	2009-12-16	2009-12-16	ENSG00000248333	ENSG00000248333		"Cyclin-dependent kinases"	1729	protein-coding gene	gene with protein product		176873	"cell division cycle 2-like 1 (PITSLRE proteins)"	CDC2L1		1774066, 14511641, 19884882	Standard	XM_006711061		Approved	CDK11-p110, CDK11-p58, CDK11-p46	uc001agv.1	P21127	OTTHUMG00000078638	ENST00000407249.3:c.963_968delAGAGGA	chr1.hg19:g.1577079_1577084delTCCTCT	ENSP00000464036:p.Glu325_Glu326del	87.0	0.0	.		108.0	10.0	0.093	NM_033486	O95265|Q12817|Q12818|Q12819|Q12820|Q12822|Q8N530|Q9NZS5|Q9UBJ0|Q9UBQ1|Q9UBR0|Q9UNY2|Q9UP57|Q9UP58|Q9UP59	In_Frame_Del	DEL	ENST00000407249.3	hg19																																																																																				.	.	.	none		0.563	CDK11B-204	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001787		-	1577078	TCCTCT	-	1577073	7	5	225	1	0	1	0	1	0	0	0	0	3129	1551	54	0	1437	0	CDK11B	1	1577073	In_Frame_Del	DEL	TCCTCT	TCGA-MH-A855-01A-11D-A34Z-10		1577073	247673548	1	13686											
CDK11A	728642	hgsc.bcm.edu	37	chr1	1640283	1640288	+	In_Frame_Del	DEL	TCCTCT	TCCTCT	-																															tgctgccggtctcctcctccTcctcttcctcttcctcctcc																										TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	TCCTCT	TCCTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr1:1640283_1640288delTCCTCT	ENST00000378633.1	-	9	1036_1041	c.957_962delAGAGGA	c.(955-963)gaagaggag>gag	p.319_321EEE>E	CDK11A_ENST00000356200.3_In_Frame_Del_p.282_284EEE>E|CDK11A_ENST00000358779.5_In_Frame_Del_p.306_308EEE>E|CDK11A_ENST00000378638.2_In_Frame_Del_p.282_284EEE>E|CDK11A_ENST00000404249.3_In_Frame_Del_p.316_318EEE>E|CDK11A_ENST00000378635.3_3'UTR|RP1-283E3.8_ENST00000598846.1_RNA|CDK11A_ENST00000357760.2_In_Frame_Del_p.315_317EEE>E			Q9UQ88	CD11A_HUMAN	cyclin-dependent kinase 11A	319	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						ctcctcctcctcctcttcctcttcct	0.563																																					p.317_318del	Pancreas(186;965 2119 30274 40311 50569)	Pindel	.											.	CDK11A	38	.	0			c.949_954del						PASS	.																																			SO:0001651	inframe_deletion	728642	exon9			.	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.957_962delAGAGGA	chr1.hg19:g.1640289_1640294delTCCTCT	ENSP00000367900:p.Glu323_Glu324del	114.0	0.0	.		85.0	12.0	0.141	NM_024011	O95227|O95228|O96012|Q12821|Q12853|Q12854|Q2TAJ0|Q5QPR0|Q5QPR1|Q5QPR2|Q9UBC4|Q9UBI3|Q9UEI1|Q9UEI2|Q9UP53|Q9UP54|Q9UP55|Q9UP56|Q9UQ86|Q9UQ87|Q9UQ89	In_Frame_Del	DEL	ENST00000378633.1	hg19																																																																																				.	.	.	none		0.563	CDK11A-005	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000001735.1	NM_024011		-	1640288	TCCTCT	-	1640283	7	5	225	1	0	1	0	1	0	0	0	0	3128	1551	54	0	1437	0	CDK11A	1	1640283	In_Frame_Del	DEL	TCCTCT	TCGA-MH-A855-01A-11D-A34Z-10	63210	1640283	247610338	2	13687											
KIF1B	23095	hgsc.bcm.edu	37	chr1	10435400	10435400	+	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	acatgaacgactggttgtatGccttcaacccacttctagct	10	12	7	12	1	2	1	1	1	1	0	2	2	2	1	2	1	4	3	2	1	4	5			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr1:10435400G>C	ENST00000377086.1	+	48	5579	c.5377G>C	c.(5377-5379)Gcc>Ccc	p.A1793P	KIF1B_ENST00000263934.6_Missense_Mutation_p.A1747P|KIF1B_ENST00000377081.1_Missense_Mutation_p.A1793P			O60333	KIF1B_HUMAN	kinesin family member 1B	1793	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)		CTGGTTGTATGCCTTCAACCC	0.448																																					p.A1747P		Atlas-SNP	.											.	KIF1B	242	.	0			c.G5239C						PASS	.						120	110	113					1																	10435400		2203	4300	6503	SO:0001583	missense	23095	exon46			TTGTATGCCTTCA	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.5377G>C	chr1.hg19:g.10435400G>C	ENSP00000366290:p.Ala1793Pro	178.0	0.0	.		150.0	34.0	.	NM_015074	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	hg19		.	.	.	.	.	.	.	.	.	.	G	35	5.472787	0.96274	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377086;ENST00000377081	T;T;T	0.79845	-1.31;-1.31;-1.31	5.38	5.38	0.77491	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	D	0.91925	0.7443	M	0.89534	3.04	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.999	D;D;D;D;D;D	0.97110	1.0;0.999;1.0;1.0;0.999;0.991	D	0.93192	0.6584	10	0.72032	D	0.01	.	19.1601	0.93527	0.0:0.0:1.0:0.0	.	1779;1753;1793;1767;1793;1747	Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2	.;.;.;.;KIF1B_HUMAN;.	P	1793;1747;1793;1793	ENSP00000263934:A1747P;ENSP00000366290:A1793P;ENSP00000366284:A1793P	ENSP00000263934:A1747P	A	+	1	0	KIF1B	10357987	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	9.864000	0.99589	2.520000	0.84964	0.585000	0.79938	GCC	.	.	.	none		0.448	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1			C	10435400	G	C	10435400	3	2	225	1	0	0	0	0	1	0	0	0	8291	1319	46	4	6906	4	KIF1B	1	10435400	Missense_Mutation	SNP	G	TCGA-MH-A855-01A-11D-A34Z-10	8795117	10435400	238815221	3	13688											
DHDDS	79947	hgsc.bcm.edu	37	chr1	26759444	26759444	+	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	ctggaaaagaactatgtcatGgatcaaggaaggagagctgt	15	8	13	5	0	2	2	2	0	0	2	2	6	2	5	0	4	2	1	0	4	6	1			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr1:26759444G>T	ENST00000236342.7	+	2	101	c.8G>T	c.(7-9)tGg>tTg	p.W3L	DHDDS_ENST00000427245.2_Missense_Mutation_p.W3L|DHDDS_ENST00000374185.3_Missense_Mutation_p.W3L|DHDDS_ENST00000525682.2_Missense_Mutation_p.W3L|DHDDS_ENST00000531955.1_3'UTR|DHDDS_ENST00000526219.1_Missense_Mutation_p.W3L|DHDDS_ENST00000360009.2_Missense_Mutation_p.W3L			Q86SQ9	DHDDS_HUMAN	dehydrodolichyl diphosphate synthase	3					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)	transferase activity, transferring alkyl or aryl (other than methyl) groups (GO:0016765)			breast(5)|endometrium(2)|large_intestine(2)|lung(4)|stomach(1)|urinary_tract(1)	15		all_cancers(24;2.04e-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;1.11e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.0161)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.166)|LUSC - Lung squamous cell carcinoma(448;0.239)		ACTATGTCATGGATCAAGGAA	0.468																																					p.W3L		Atlas-SNP	.											.	DHDDS	33	.	0			c.G8T						PASS	.						148	137	141					1																	26759444		2203	4300	6503	SO:0001583	missense	79947	exon2			TGTCATGGATCAA	AK023164	CCDS281.1, CCDS282.1, CCDS57984.1, CCDS57983.1	1p35.3	2014-01-28			ENSG00000117682	ENSG00000117682			20603	protein-coding gene	gene with protein product		608172				12591616	Standard	NM_024887		Approved	HDS, FLJ13102, DS, RP59	uc001bmk.3	Q86SQ9	OTTHUMG00000003554	ENST00000236342.7:c.8G>T	chr1.hg19:g.26759444G>T	ENSP00000236342:p.Trp3Leu	140.0	0.0	.		134.0	42.0	.	NM_001243564	B7Z4B9|B7ZB20|D3DPK7|D3DPK8|D3DPK9|E9KL43|Q5T0A4|Q8NE90|Q9BTG5|Q9BTK3|Q9H905	Missense_Mutation	SNP	ENST00000236342.7	hg19	CCDS282.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.435781	0.83885	.	.	ENSG00000117682	ENST00000427245;ENST00000525682;ENST00000236342;ENST00000526219;ENST00000374185;ENST00000360009;ENST00000533087;ENST00000531312;ENST00000525165;ENST00000525326;ENST00000525546;ENST00000436153;ENST00000530781;ENST00000430232	T;T;T;T;T	0.56103	0.55;0.5;0.55;0.48;0.71	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.73345	0.3575	M	0.87900	2.915	0.80722	D	1	D;P;P;D	0.59357	0.985;0.944;0.928;0.957	P;P;P;P	0.55667	0.728;0.448;0.609;0.781	T	0.77800	-0.2452	10	0.87932	D	0	-13.9392	19.2865	0.94077	0.0:0.0:1.0:0.0	.	3;3;3;3	B7Z4B9;Q86SQ9-3;Q86SQ9;Q86SQ9-2	.;.;DHDDS_HUMAN;.	L	3	ENSP00000434984:W3L;ENSP00000236342:W3L;ENSP00000434219:W3L;ENSP00000353104:W3L;ENSP00000397584:W3L	ENSP00000236342:W3L	W	+	2	0	DHDDS	26632031	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.358000	0.90090	2.802000	0.96397	0.655000	0.94253	TGG	.	.	.	none		0.468	DHDDS-011	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392504.1	NM_024887		T	26759444	G	T	26759444	3	4	225	1	0	0	0	0	1	0	0	0	4480	1357	47	4	10	4	DHDDS	1	26759444	Missense_Mutation	SNP	G	TCGA-MH-A855-01A-11D-A34Z-10	16324044	26759444	222491177	4	13689											
GON4L	54856	hgsc.bcm.edu	37	chr1	155785662	155785662	+	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	tcatctgaggaatcatcttcTtcaaggtggatatccacaaa	13	12	7	9	0	6	1	3	1	3	0	7	3	7	3	1	3	0	0	1	3	4	3			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr1:155785662T>A	ENST00000368331.1	-	8	1143	c.1095A>T	c.(1093-1095)gaA>gaT	p.E365D	GON4L_ENST00000471341.1_5'UTR|GON4L_ENST00000271883.5_Missense_Mutation_p.E365D|GON4L_ENST00000361040.5_Missense_Mutation_p.E365D|GON4L_ENST00000437809.1_Missense_Mutation_p.E365D	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	365					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					AATCATCTTCTTCAAGGTGGA	0.368																																					p.E365D		Atlas-SNP	.											.	GON4L	392	.	0			c.A1095T						PASS	.						92	84	87					1																	155785662		2203	4300	6503	SO:0001583	missense	54856	exon8			ATCTTCTTCAAGG	AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"gon-4 homolog (C.elegans)"	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.1095A>T	chr1.hg19:g.155785662T>A	ENSP00000357315:p.Glu365Asp	171.0	0.0	.		205.0	51.0	.	NM_001037533	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Missense_Mutation	SNP	ENST00000368331.1	hg19		.	.	.	.	.	.	.	.	.	.	T	19.44	3.828178	0.71143	.	.	ENSG00000116580	ENST00000437809;ENST00000368331;ENST00000271883;ENST00000539959;ENST00000361040	T;T;T;T	0.12774	2.87;2.85;2.87;2.65	5.28	2.78	0.32641	.	0.131508	0.51477	D	0.000095	T	0.11707	0.0285	L	0.49350	1.555	0.32400	N	0.552129	D;D;D;D;D	0.71674	0.986;0.998;0.998;0.997;0.998	P;D;D;D;D	0.77557	0.84;0.99;0.941;0.978;0.99	T	0.06250	-1.0837	10	0.28530	T	0.3	.	3.7085	0.08410	0.0:0.2293:0.1888:0.5819	.	59;365;365;365;365	Q9H5U2;A4PB68;Q3T8J9-2;Q3T8J9;Q3T8J9-3	.;.;.;GON4L_HUMAN;.	D	365	ENSP00000396117:E365D;ENSP00000357315:E365D;ENSP00000271883:E365D;ENSP00000354322:E365D	ENSP00000271883:E365D	E	-	3	2	GON4L	154052286	0.972000	0.33761	1.000000	0.80357	0.998000	0.95712	0.009000	0.13219	0.938000	0.37419	0.533000	0.62120	GAA	.	.	.	none		0.368	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292		A	155785662	T	A	155785662	3	1	225	1	0	0	0	0	1	0	0	0	6579	1606	56	5	5844	5	GON4L	1	155785662	Missense_Mutation	SNP	T	TCGA-MH-A855-01A-11D-A34Z-10	129026218	155785662	93464959	5	13690											
KDM3A	55818	hgsc.bcm.edu	37	chr2	86693629	86693629	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gattggaactggagacttgaAaattctgactgagccaaaag	15	9	11	6	0	1	4	0	3	1	1	1	7	1	5	1	2	2	0	1	2	5	3			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr2:86693629A>G	ENST00000409556.1	+	11	1507	c.1142A>G	c.(1141-1143)aAa>aGa	p.K381R	KDM3A_ENST00000312912.5_Missense_Mutation_p.K381R|KDM3A_ENST00000409064.1_Missense_Mutation_p.K381R|KDM3A_ENST00000542128.1_Missense_Mutation_p.K329R			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	381					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						GGAGACTTGAAAATTCTGACT	0.448																																					p.K381R	NSCLC(96;1150 1523 6936 46253 49736)	Atlas-SNP	.											.	KDM3A	179	.	0			c.A1142G						PASS	.						116	118	117					2																	86693629		2203	4300	6503	SO:0001583	missense	55818	exon10			ACTTGAAAATTCT	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.1142A>G	chr2.hg19:g.86693629A>G	ENSP00000386660:p.Lys381Arg	81.0	0.0	.		129.0	40.0	.	NM_001146688	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Missense_Mutation	SNP	ENST00000409556.1	hg19	CCDS1990.1	.	.	.	.	.	.	.	.	.	.	A	14.91	2.675086	0.47781	.	.	ENSG00000115548	ENST00000409556;ENST00000540058;ENST00000312912;ENST00000409064;ENST00000542128	T;T;T;T	0.59502	0.26;0.26;0.26;0.26	5.71	4.54	0.55810	.	0.336240	0.28914	N	0.013724	T	0.38558	0.1045	N	0.14661	0.345	0.24510	N	0.994213	B;B	0.28933	0.228;0.146	B;B	0.25140	0.058;0.038	T	0.26155	-1.0111	10	0.44086	T	0.13	.	10.9773	0.47473	0.8434:0.1566:0.0:0.0	.	329;381	F5H070;Q9Y4C1	.;KDM3A_HUMAN	R	381;381;381;381;329	ENSP00000386660:K381R;ENSP00000323659:K381R;ENSP00000386516:K381R;ENSP00000438324:K329R	ENSP00000323659:K381R	K	+	2	0	KDM3A	86547140	0.046000	0.20272	0.980000	0.43619	0.993000	0.82548	2.137000	0.42130	0.963000	0.38082	0.533000	0.62120	AAA	.	.	.	none		0.448	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433		G	86693629	A	G	86693629	3	3	225	1	0	0	0	0	1	0	0	0	8133	14	1	3	1176	3	KDM3A	2	86693629	Missense_Mutation	SNP	A	TCGA-MH-A855-01A-11D-A34Z-10		86693629	156505744	6	13691											
ADAM23	8745	hgsc.bcm.edu	37	chr2	207457453	207457453	+	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	accatcaaggccgggtgattGactgcaggtaacatattaaa	14	9	10	8	1	1	2	1	2	0	0	1	2	1	2	2	3	2	2	2	3	5	4			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr2:207457453G>C	ENST00000264377.3	+	22	2399	c.2071G>C	c.(2071-2073)Gac>Cac	p.D691H	ADAM23_ENST00000374415.3_Missense_Mutation_p.D691H|ADAM23_ENST00000374416.1_Missense_Mutation_p.D691H	NM_003812.2	NP_003803.1	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23	691					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)		CCGGGTGATTGACTGCAGGTA	0.353																																					p.D691H	Melanoma(194;1127 2130 19620 24042 27855)	Atlas-SNP	.											.	ADAM23	239	.	0			c.G2071C						PASS	.						117	102	107					2																	207457453		2203	4300	6503	SO:0001583	missense	8745	exon22			GTGATTGACTGCA	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.2071G>C	chr2.hg19:g.207457453G>C	ENSP00000264377:p.Asp691His	232.0	0.0	.		155.0	9.0	.	NM_003812	A2RU59	Missense_Mutation	SNP	ENST00000264377.3	hg19	CCDS2369.1	.	.	.	.	.	.	.	.	.	.	G	14.26	2.482645	0.44147	.	.	ENSG00000114948	ENST00000264377;ENST00000374416;ENST00000431817;ENST00000374415	T;T;T	0.21932	1.98;1.98;1.98	5.52	5.52	0.82312	ADAM, cysteine-rich (2);	0.000000	0.64402	D	0.000006	T	0.24275	0.0588	L	0.46157	1.445	0.80722	D	1	P	0.48016	0.904	P	0.44673	0.457	T	0.00742	-1.1585	10	0.48119	T	0.1	.	13.7002	0.62604	0.0741:0.0:0.9259:0.0	.	691	O75077	ADA23_HUMAN	H	691;691;585;691	ENSP00000264377:D691H;ENSP00000363537:D691H;ENSP00000363536:D691H	ENSP00000264377:D691H	D	+	1	0	ADAM23	207165698	1.000000	0.71417	1.000000	0.80357	0.174000	0.22865	5.445000	0.66594	2.593000	0.87608	0.591000	0.81541	GAC	.	.	.	none		0.353	ADAM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256431.2	NM_003812		C	207457453	G	C	207457453	3	2	225	1	0	0	0	0	1	0	0	0	245	1290	45	4	2157	4	ADAM23	2	207457453	Missense_Mutation	SNP	G	TCGA-MH-A855-01A-11D-A34Z-10	120763824	207457453	35741920	7	13692											
ZPLD1	131368	hgsc.bcm.edu	37	chr3	102171980	102171980	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagggctgtggaaacaacctGgtggtaagattagtgtgaca	12	9	15	5	0	0	2	0	1	0	1	0	4	0	3	1	4	2	2	1	4	4	2			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr3:102171980G>A	ENST00000491959.1	+	10	1206	c.324G>A	c.(322-324)ctG>ctA	p.L108L	ZPLD1_ENST00000466937.1_Silent_p.L108L|ZPLD1_ENST00000306176.1_Silent_p.L124L			Q8TCW7	ZPLD1_HUMAN	zona pellucida-like domain containing 1	108	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						GAAACAACCTGGTGGTAAGAT	0.433																																					p.L124L		Atlas-SNP	.											.	ZPLD1	82	.	0			c.G372A						PASS	.						63	55	58					3																	102171980		2203	4300	6503	SO:0001819	synonymous_variant	131368	exon3			CAACCTGGTGGTA	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.324G>A	chr3.hg19:g.102171980G>A		88.0	0.0	.		77.0	13.0	.	NM_175056	Q49AS1|Q8WU36	Silent	SNP	ENST00000491959.1	hg19																																																																																				.	.	.	none		0.433	ZPLD1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353984.1	NM_175056		A	102171980	G	A	102171980	2	1	225	1	0	0	0	0	0	0	0	1	18233	1335	47	2		2	ZPLD1	3	102171980	Silent	SNP	G	TCGA-MH-A855-01A-11D-A34Z-10		102171980	95850450	8	13693											
TNFSF10	8743	hgsc.bcm.edu	37	chr3	172232753	172232753	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgtcatcttcttttaagaaAcaagcaatgccacttttgga	12	14	6	9	0	3	1	1	0	2	1	3	2	3	2	1	1	3	1	1	1	4	5			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr3:172232753A>G	ENST00000241261.2	-	2	290	c.168T>C	c.(166-168)tgT>tgC	p.C56C	TNFSF10_ENST00000420541.2_Silent_p.C56C	NM_003810.3	NP_003801.1	P50591	TNF10_HUMAN	tumor necrosis factor (ligand) superfamily, member 10	56					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|immune response (GO:0006955)|male gonad development (GO:0008584)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to insulin (GO:0032868)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)			breast(2)|cervix(1)|large_intestine(1)|lung(6)|ovary(1)|skin(4)	15	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.67e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)			CTTTTAAGAAACAAGCAATGC	0.408																																					p.C56C		Atlas-SNP	.											.	TNFSF10	30	.	0			c.T168C						PASS	.						143	140	141					3																	172232753		2203	4300	6503	SO:0001819	synonymous_variant	8743	exon2			TAAGAAACAAGCA	U37518	CCDS3219.1, CCDS54680.1	3q26	2006-09-20			ENSG00000121858	ENSG00000121858		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11925	protein-coding gene	gene with protein product		603598				8777713, 8663110	Standard	NM_003810		Approved	TRAIL, Apo-2L, TL2, CD253	uc003fid.3	P50591	OTTHUMG00000156917	ENST00000241261.2:c.168T>C	chr3.hg19:g.172232753A>G		110.0	0.0	.		109.0	27.0	.	NM_003810	A1Y9B3	Silent	SNP	ENST00000241261.2	hg19	CCDS3219.1																																																																																			.	.	.	none		0.408	TNFSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346601.1			G	172232753	A	G	172232753	2	3	225	1	0	0	0	0	0	0	0	1	16313	41	2	3		3	TNFSF10	3	172232753	Silent	SNP	A	TCGA-MH-A855-01A-11D-A34Z-10	70060773	172232753	25789677	9	13694											
CCDC39	339829	hgsc.bcm.edu	37	chr3	180379790	180379790	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcacgctcccttgctttgcaAagagactacagaataacaca	14	9	6	12	1	1	2	1	0	0	2	2	3	2	2	1	0	4	3	1	0	4	4			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr3:180379790A>G	ENST00000442201.2	-	3	335	c.216T>C	c.(214-216)ctT>ctC	p.L72L	CCDC39_ENST00000273654.4_Silent_p.L156L	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	72					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)			TTGCTTTGCAAAGAGACTACA	0.323																																					p.L72L		Atlas-SNP	.											.	CCDC39	242	.	0			c.T216C						PASS	.						56	45	49					3																	180379790		1776	4011	5787	SO:0001819	synonymous_variant	339829	exon3			TTTGCAAAGAGAC	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.216T>C	chr3.hg19:g.180379790A>G		207.0	0.0	.		269.0	59.0	.	NM_181426	B4E2H1	Silent	SNP	ENST00000442201.2	hg19	CCDS46964.1																																																																																			.	.	.	none		0.323	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028		G	180379790	A	G	180379790	2	3	225	1	0	0	0	0	0	0	0	1	2813	1	1	3		3	CCDC39	3	180379790	Silent	SNP	A	TCGA-MH-A855-01A-11D-A34Z-10	8147037	180379790	17642640	10	13695											
CHRD	8646	hgsc.bcm.edu	37	chr3	184099117	184099117	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcctgtgggcagccgcgccAgctgccgggacactgctgcc	4	5	16	16	3	0	0	0	0	0	0	0	1	0	1	5	3	5	3	5	3	0	0			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr3:184099117A>G	ENST00000204604.1	+	3	593	c.347A>G	c.(346-348)cAg>cGg	p.Q116R	CHRD_ENST00000545352.1_5'Flank|EIF2B5_ENST00000444495.1_Intron|CHRD_ENST00000482805.1_3'UTR|CHRD_ENST00000348986.3_Missense_Mutation_p.Q116R|CHRD_ENST00000450923.1_Missense_Mutation_p.Q116R	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	116	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.			RQLP -> QVAA (in Ref. 4; AAC69835). {ECO:0000305}.	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)			CAGCCGCGCCAGCTGCCGGGA	0.692																																					p.Q116R		Atlas-SNP	.											.	CHRD	149	.	0			c.A347G						PASS	.						8	11	10					3																	184099117		2170	4243	6413	SO:0001583	missense	8646	exon3			CGCGCCAGCTGCC	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.347A>G	chr3.hg19:g.184099117A>G	ENSP00000204604:p.Gln116Arg	176.0	0.0	.		154.0	40.0	.	NM_003741	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Missense_Mutation	SNP	ENST00000204604.1	hg19	CCDS3266.1	.	.	.	.	.	.	.	.	.	.	A	17.95	3.514869	0.64634	.	.	ENSG00000090539	ENST00000204604;ENST00000450923;ENST00000348986	T;T;T	0.72282	-0.64;-0.64;-0.64	5.18	3.94	0.45596	von Willebrand factor, type C (3);	0.069374	0.64402	D	0.000016	T	0.37865	0.1019	N	0.02368	-0.58	0.80722	D	1	B;B	0.33318	0.101;0.408	B;B	0.31495	0.102;0.131	T	0.34925	-0.9809	10	0.11485	T	0.65	-21.1397	7.5131	0.27585	0.6909:0.0:0.0:0.3091	.	116;116	E7ESX1;Q9H2X0	.;CHRD_HUMAN	R	116	ENSP00000204604:Q116R;ENSP00000408972:Q116R;ENSP00000334036:Q116R	ENSP00000204604:Q116R	Q	+	2	0	CHRD	185581811	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	3.705000	0.54823	1.954000	0.56735	0.459000	0.35465	CAG	.	.	.	none		0.692	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741		G	184099117	A	G	184099117	3	3	225	1	0	0	0	0	1	0	0	0	3374	188	7	3	357	3	CHRD	3	184099117	Missense_Mutation	SNP	A	TCGA-MH-A855-01A-11D-A34Z-10	3719327	184099117	13923313	11	13696											
ZNF721	170960	hgsc.bcm.edu	37	chr4	436272	436272	+	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	actttgctctccagtaagaaTtttcgtgtgttgattcaggt	8	17	9	7	1	2	2	1	1	1	1	4	2	2	2	1	1	1	3	1	1	2	6			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr4:436272T>A	ENST00000338977.5	-	2	1996	c.1948A>T	c.(1948-1950)Att>Ttt	p.I650F	ZNF721_ENST00000511833.2_Missense_Mutation_p.I662F|ZNF721_ENST00000506646.1_Intron|ZNF721_ENST00000507078.1_Intron|ABCA11P_ENST00000451020.2_RNA			Q8TF20	ZN721_HUMAN	zinc finger protein 721	650					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						CCAGTAAGAATTTTCGTGTGT	0.408																																					p.L662L		Atlas-SNP	.											.	ZNF721	205	.	0			c.T1984T						PASS	.						151	158	156					4																	436272		2008	4191	6199	SO:0001583	missense	170960	exon3			TAAGAATTTTCGT	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.1948A>T	chr4.hg19:g.436272T>A	ENSP00000340524:p.Ile650Phe	271.0	0.0	.		339.0	94.0	.	NM_133474	Q69YG7	Silent	SNP	ENST00000338977.5	hg19		.	.	.	.	.	.	.	.	.	.	T	15.96	2.987248	0.53934	.	.	ENSG00000182903	ENST00000338977;ENST00000511833	T;T	0.17370	2.28;2.28	1.02	1.02	0.19986	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.22126	0.0533	M	0.75085	2.285	0.24841	N	0.992466	D;D;D	0.54601	0.967;0.967;0.96	P;P;B	0.45577	0.486;0.486;0.354	T	0.14448	-1.0472	9	0.66056	D	0.02	.	6.213	0.20640	0.0:0.0:0.0:1.0	.	650;662;662	Q8TF20;D9N162;Q8TF20-2	ZN721_HUMAN;.;.	F	650;662	ENSP00000340524:I650F;ENSP00000428878:I662F	ENSP00000340524:I650F	I	-	1	0	ZNF721	426272	0.100000	0.21855	0.009000	0.14445	0.110000	0.19582	1.945000	0.40273	0.733000	0.32492	0.155000	0.16302	ATT	.	.	.	none		0.408	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474		A	436272	T	A	436272	3	1	225	1	0	0	0	0	1	0	0	0	18134	1493	52	5	791	5	ZNF721	4	436272	Missense_Mutation	SNP	T	TCGA-MH-A855-01A-11D-A34Z-10		436272	190718004	12	13697											
TRIP13	9319	hgsc.bcm.edu	37	chr5	914652	914652	+	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	tgattggcttcattgaaaacAacgtgtcaaaattgagcctt	13	13	8	7	1	2	3	2	3	0	0	2	3	2	3	1	1	3	1	1	1	5	5			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr5:914652A>T	ENST00000166345.3	+	11	1449	c.1093A>T	c.(1093-1095)Aac>Tac	p.N365Y		NM_004237.3	NP_004228.1	Q15645	PCH2_HUMAN	thyroid hormone receptor interactor 13	365					double-strand break repair (GO:0006302)|female meiosis I (GO:0007144)|male meiosis I (GO:0007141)|oocyte maturation (GO:0001556)|oogenesis (GO:0048477)|reciprocal meiotic recombination (GO:0007131)|regulation of RNA biosynthetic process (GO:2001141)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|transcription from RNA polymerase II promoter (GO:0006366)	male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)	ATP binding (GO:0005524)|transcription cofactor activity (GO:0003712)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	18			Epithelial(17;0.00147)|OV - Ovarian serous cystadenocarcinoma(19;0.00271)|all cancers(22;0.00622)|Lung(60;0.165)			CATTGAAAACAACGTGTCAAA	0.428																																					p.N365Y		Atlas-SNP	.											.	TRIP13	41	.	0			c.A1093T						PASS	.						196	201	199					5																	914652		2203	4300	6503	SO:0001583	missense	9319	exon11			GAAAACAACGTGT	L40384	CCDS3858.1	5p15	2010-04-21			ENSG00000071539	ENSG00000071539		"ATPases / AAA-type"	12307	protein-coding gene	gene with protein product	"thyroid receptor interacting protein 13"	604507				7776974	Standard	NM_004237		Approved	16E1BP	uc003jbr.3	Q15645	OTTHUMG00000090349	ENST00000166345.3:c.1093A>T	chr5.hg19:g.914652A>T	ENSP00000166345:p.Asn365Tyr	63.0	0.0	.		42.0	10.0	.	NM_004237	C9K0T3|D3DTC0|O15324	Missense_Mutation	SNP	ENST00000166345.3	hg19	CCDS3858.1	.	.	.	.	.	.	.	.	.	.	.	15.36	2.811141	0.50527	.	.	ENSG00000071539	ENST00000166345	D	0.95307	-3.67	5.8	5.8	0.92144	.	0.218259	0.51477	D	0.000093	D	0.89856	0.6836	L	0.34521	1.04	0.51233	D	0.999919	B	0.33694	0.421	B	0.31337	0.128	D	0.88757	0.3254	10	0.51188	T	0.08	-5.4017	10.9531	0.47341	0.9266:0.0:0.0734:0.0	.	365	Q15645	PCH2_HUMAN	Y	365	ENSP00000166345:N365Y	ENSP00000166345:N365Y	N	+	1	0	TRIP13	967652	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	3.960000	0.56752	2.224000	0.72417	0.533000	0.62120	AAC	.	.	.	none		0.428	TRIP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206721.2	NM_004237		T	914652	A	T	914652	3	4	225	1	0	0	0	0	1	0	0	0	16569	130	5	5	1139	5	TRIP13	5	914652	Missense_Mutation	SNP	A	TCGA-MH-A855-01A-11D-A34Z-10		914652	180000608	13	13698											
PGBD1	84547	hgsc.bcm.edu	37	chr6	28268788	28268788	+	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	gttaaaggtatcatgtttccCagaaaagagttggaccaaaa	16	10	9	6	0	1	2	1	0	0	2	2	3	2	3	2	2	0	4	2	2	7	4			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr6:28268788C>T	ENST00000405948.2	+	7	1577	c.1157C>T	c.(1156-1158)cCa>cTa	p.P386L	PGBD1_ENST00000259883.3_Missense_Mutation_p.P386L	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	386						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						TCATGTTTCCCAGAAAAGAGT	0.433																																					p.P386L		Atlas-SNP	.											.	PGBD1	106	.	0			c.C1157T						PASS	.						64	68	67					6																	28268788		2203	4300	6503	SO:0001583	missense	84547	exon7			GTTTCCCAGAAAA	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.1157C>T	chr6.hg19:g.28268788C>T	ENSP00000385213:p.Pro386Leu	79.0	0.0	.		67.0	17.0	.	NM_001184743	Q53F43|Q6NTF5|Q8WWS4	Missense_Mutation	SNP	ENST00000405948.2	hg19	CCDS4648.1	.	.	.	.	.	.	.	.	.	.	C	10.60	1.396990	0.25205	.	.	ENSG00000137338	ENST00000405948;ENST00000259883	T;T	0.01347	4.99;4.99	4.54	3.65	0.41850	.	0.184961	0.26715	N	0.022869	T	0.00580	0.0019	L	0.34521	1.04	0.40026	D	0.97547	B	0.28378	0.209	B	0.21360	0.034	T	0.59026	-0.7531	10	0.42905	T	0.14	-10.7499	9.9021	0.41353	0.2033:0.7967:0.0:0.0	.	386	Q96JS3	PGBD1_HUMAN	L	386	ENSP00000385213:P386L;ENSP00000259883:P386L	ENSP00000259883:P386L	P	+	2	0	PGBD1	28376767	0.417000	0.25432	0.214000	0.23707	0.588000	0.36517	2.102000	0.41796	1.218000	0.43458	0.655000	0.94253	CCA	.	.	.	none		0.433	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2			T	28268788	C	T	28268788	3	4	225	1	0	0	0	0	1	0	0	0	11787	594	21	2	1179	2	PGBD1	6	28268788	Missense_Mutation	SNP	C	TCGA-MH-A855-01A-11D-A34Z-10		28268788	142846279	14	13699											
HOXA2	3199	hgsc.bcm.edu	37	chr7	27140420	27140420	+	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	aagctgtcagctgaaatatcTacgggactgtcgagggaacc	12	8	12	9	2	2	1	1	1	1	0	3	4	2	3	1	2	4	2	1	2	5	2			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr7:27140420T>A	ENST00000222718.5	-	2	1366	c.1056A>T	c.(1054-1056)gtA>gtT	p.V352V	HOTAIRM1_ENST00000593300.1_RNA|HOTAIRM1_ENST00000425358.2_RNA|HOTAIRM1_ENST00000434063.3_RNA|HOTAIRM1_ENST00000428939.3_RNA|HOTAIRM1_ENST00000429611.3_RNA	NM_006735.3	NP_006726.1	O43364	HXA2_HUMAN	homeobox A2	352					anterior/posterior pattern specification (GO:0009952)|brain segmentation (GO:0035284)|cell fate determination (GO:0001709)|dorsal/ventral pattern formation (GO:0009953)|embryonic viscerocranium morphogenesis (GO:0048703)|middle ear morphogenesis (GO:0042474)|motor neuron axon guidance (GO:0008045)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast development (GO:0002076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|rhombomere 2 development (GO:0021568)|rhombomere 3 morphogenesis (GO:0021658)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|cervix(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(1)	22						CTGAAATATCTACGGGACTGT	0.443																																					p.V352V		Atlas-SNP	.											.	HOXA2	56	.	0			c.A1056T						PASS	.						87	87	87					7																	27140420		2203	4300	6503	SO:0001819	synonymous_variant	3199	exon2			AATATCTACGGGA		CCDS5403.1	7p15.2	2011-06-20	2005-12-22		ENSG00000105996	ENSG00000105996		"Homeoboxes / ANTP class : HOXL subclass"	5103	protein-coding gene	gene with protein product		604685	"homeo box A2"	HOX1K		1358459	Standard	NM_006735		Approved		uc003syh.3	O43364	OTTHUMG00000023208	ENST00000222718.5:c.1056A>T	chr7.hg19:g.27140420T>A		174.0	0.0	.		201.0	52.0	.	NM_006735	A1L4K3|B2RMW3	Silent	SNP	ENST00000222718.5	hg19	CCDS5403.1																																																																																			.	.	.	none		0.443	HOXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358508.2			A	27140420	T	A	27140420	2	1	225	1	0	0	0	0	0	0	0	1	7299	1509	53	5		5	HOXA2	7	27140420	Silent	SNP	T	TCGA-MH-A855-01A-11D-A34Z-10		27140420	131998243	15	13700											
DPY19L1	23333	hgsc.bcm.edu	37	chr7	35006553	35006553	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tttacatatatcaatgtaccCgacaacatatactgcaaata	17	12	3	9	1	1	0	1	0	0	0	1	1	1	0	1	0	5	2	1	0	10	8			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr7:35006553C>T	ENST00000310974.4	-	10	970	c.826G>A	c.(826-828)Ggg>Agg	p.G276R	DPY19L1_ENST00000462134.2_5'UTR	NM_015283.1	NP_056098.1	Q2PZI1	D19L1_HUMAN	dpy-19-like 1 (C. elegans)	276						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						TCAATGTACCCGACAACATAT	0.249																																					p.G276R		Atlas-SNP	.											.	DPY19L1	56	.	0			c.G826A						PASS	.						43	40	41					7																	35006553		1783	4020	5803	SO:0001583	missense	23333	exon10			TGTACCCGACAAC	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.826G>A	chr7.hg19:g.35006553C>T	ENSP00000308695:p.Gly276Arg	216.0	0.0	.		209.0	11.0	.	NM_015283	O94954|Q4G151	Missense_Mutation	SNP	ENST00000310974.4	hg19	CCDS43567.1	.	.	.	.	.	.	.	.	.	.	C	18.56	3.649777	0.67358	.	.	ENSG00000173852	ENST00000310974;ENST00000446375	T;T	0.58358	0.34;0.34	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.68329	0.2989	L	0.60845	1.875	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	T	0.68221	-0.5466	10	0.44086	T	0.13	-13.2136	15.6504	0.77088	0.0:1.0:0.0:0.0	.	276	Q2PZI1	D19L1_HUMAN	R	276;75	ENSP00000308695:G276R;ENSP00000400510:G75R	ENSP00000308695:G276R	G	-	1	0	DPY19L1	34973078	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	5.342000	0.65970	2.365000	0.80145	0.555000	0.69702	GGG	.	.	.	none		0.249	DPY19L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337506.1			T	35006553	C	T	35006553	3	4	225	1	0	0	0	0	1	0	0	0	4742	652	23	1	1253	1	DPY19L1	7	35006553	Missense_Mutation	SNP	C	TCGA-MH-A855-01A-11D-A34Z-10	7866133	35006553	124132110	16	13701											
TRAPPC9	83696	hgsc.bcm.edu	37	chr8	141468506	141468506	+	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	1	0	0	0	0	0	0	0	0	0	cacggtaccccccgtgactcCcacggtcgtgccccccacgt	5	6	9	21	5	0	1	0	1	0	0	2	1	1	1	7	2	2	1	7	2	1	1	rs572038747	byFrequency	TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr8:141468506C>T	ENST00000438773.2	-	0	0				TRAPPC9_ENST00000389328.4_Missense_Mutation_p.G53E|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						CCCGTGACTCCCACGGTCGTG	0.721													C|||	66	0.0131789	0.0484	0.0029	5008	,	,		12228	0		0	False		,,,				2504	0				p.G53E		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.G158A						PASS	.						13	13	13					8																	141468506		2190	4273	6463	SO:0001631	upstream_gene_variant	83696	exon1			TGACTCCCACGGT	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		chr8.hg19:g.141468506C>T	Exception_encountered	66.0	0.0	.		83.0	17.0	.	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Missense_Mutation	SNP	ENST00000438773.2	hg19	CCDS55278.1	.	.	.	.	.	.	.	.	.	.	C	9.074	0.997622	0.19043	.	.	ENSG00000167632	ENST00000389328	.	.	.	0.857	-0.237	0.13061	.	.	.	.	.	T	0.16128	0.0388	N	0.08118	0	0.09310	N	0.999996	B	0.02656	0.0	B	0.01281	0.0	T	0.20505	-1.0273	8	0.87932	D	0	.	2.8882	0.05668	0.0:0.5548:0.0:0.4452	.	53	Q96Q05-2	.	E	53	.	ENSP00000373979:G53E	G	-	2	0	TRAPPC9	141537688	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.171000	0.16685	-0.127000	0.11661	0.498000	0.49722	GGG	.	.	.	none		0.721	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466		T	141468506	C	T	141468506	1	4	225	0	1	0	0	0	0	0	0	0	16477	623	22	2		2	TRAPPC9	8	141468506	5'Flank	SNP	C	TCGA-MH-A855-01A-11D-A34Z-10		141468506	4895516	17	13702											
CNTLN	54875	hgsc.bcm.edu	37	chr9	17298345	17298346	+	Frame_Shift_Ins	INS	-	-	A																															agctgaaagtatatcatatcINSaaaaagtatgcttttattct																								rs190561659		TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr9:17298345_17298346insA	ENST00000380647.3	+	7	1225_1226	c.1141_1142insA	c.(1141-1143)caafs	p.Q381fs	CNTLN_ENST00000262360.5_Frame_Shift_Ins_p.Q381fs|CNTLN_ENST00000425824.1_Frame_Shift_Ins_p.Q381fs|CNTLN_ENST00000380641.4_Frame_Shift_Ins_p.Q381fs			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	381					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)		TATATCATATCAAAAAGTATGC	0.307																																					p.Q381fs		Pindel	.											.	CNTLN	128	.	0			c.1141_1142insA						PASS	.																																			SO:0001589	frameshift_variant	54875	exon7			.	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.1146dupA	chr9.hg19:g.17298350_17298350dupA	ENSP00000370021:p.Gln381fs	252.0	0.0	.		225.0	49.0	0.218	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Frame_Shift_Ins	INS	ENST00000380647.3	hg19	CCDS43789.1																																																																																			.	.	.	none		0.307	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		A	17298346	-	A	17298345	7	5	225	1	0	1	1	0	0	0	0	0	3641	827	29	0	1167	0	CNTLN	9	17298345	Frame_Shift_Ins	INS	-	TCGA-MH-A855-01A-11D-A34Z-10		17298345	123915086	18	13703											
OR52J3	119679	hgsc.bcm.edu	37	chr11	5067977	5067977	+	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	ctttccactattgatttggcCctttctacaacctctgtgcc	6	16	5	14	0	2	1	0	1	2	0	3	1	3	1	4	1	3	0	4	1	3	6			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr11:5067977C>G	ENST00000380370.1	+	1	222	c.222C>G	c.(220-222)gcC>gcG	p.A74A		NM_001001916.2	NP_001001916.2	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J, member 3	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)|endometrium(1)|kidney(6)|large_intestine(6)|lung(19)|ovary(1)|skin(2)	36		Medulloblastoma(188;0.00131)|all_neural(188;0.0189)|Breast(177;0.0204)		Epithelial(150;9.29e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.19)		TTGATTTGGCCCTTTCTACAA	0.493																																					p.A74A		Atlas-SNP	.											.	OR52J3	77	.	0			c.C222G						PASS	.						131	111	118					11																	5067977		2201	4298	6499	SO:0001819	synonymous_variant	119679	exon1			TTTGGCCCTTTCT	AB065530	CCDS31370.1	11p15.4	2012-08-09			ENSG00000205495	ENSG00000205495		"GPCR / Class A : Olfactory receptors"	14799	protein-coding gene	gene with protein product							Standard	NM_001001916		Approved		uc010qyv.2	Q8NH60	OTTHUMG00000066600	ENST00000380370.1:c.222C>G	chr11.hg19:g.5067977C>G		186.0	0.0	.		191.0	29.0	.	NM_001001916	Q6IFE4	Silent	SNP	ENST00000380370.1	hg19	CCDS31370.1																																																																																			.	.	.	none		0.493	OR52J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142807.1	NM_001001916		G	5067977	C	G	5067977	2	3	225	1	0	0	0	0	0	0	0	1	11129	610	22	4		4	OR52J3	11	5067977	Silent	SNP	C	TCGA-MH-A855-01A-11D-A34Z-10		5067977	129938539	19	13704											
PLCB3	5331	hgsc.bcm.edu	37	chr11	64033788	64033788	+	Splice_Site	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	cccctgccggcttctccaggGagaagaaggagctgcagaag	10	5	14	12	1	1	3	0	0	1	3	2	5	1	4	4	3	3	3	4	3	3	1			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr11:64033788G>A	ENST00000540288.1	+	28	3371	c.3268G>A	c.(3268-3270)Gag>Aag	p.E1090K	PLCB3_ENST00000325234.5_Splice_Site_p.E1023K|PLCB3_ENST00000279230.6_Splice_Site_p.E1090K	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	1090				REKKELQKILDRKRHNSISEAKMRDKHKKEA -> SWPSWP RSVRSSGRGSPRRSAGACWARCRRG (in Ref. 2; CAA85776). {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						CTTCTCCAGGGAGAAGAAGGA	0.572																																					p.E1090K		Atlas-SNP	.											.	PLCB3	103	.	0			c.G3268A						PASS	.						54	60	58					11																	64033788		2201	4297	6498	SO:0001630	splice_region_variant	5331	exon28			TCCAGGGAGAAGA	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.3267-1G>A	chr11.hg19:g.64033788G>A		28.0	0.0	.		28.0	7.0	.	NM_000932	A5PKZ6|G5E960|Q8N1A4	Missense_Mutation	SNP	ENST00000540288.1	hg19	CCDS8064.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.957261	0.92726	.	.	ENSG00000149782	ENST00000279230;ENST00000540288;ENST00000325234	T;T;T	0.58652	0.32;0.32;0.32	5.17	5.17	0.71159	PLC-beta, C-terminal (1);	0.686476	0.15459	N	0.261221	T	0.75568	0.3867	M	0.65498	2.005	0.80722	D	1	D;P	0.76494	0.999;0.927	D;P	0.81914	0.995;0.842	T	0.76814	-0.2820	10	0.72032	D	0.01	.	17.4353	0.87550	0.0:0.0:1.0:0.0	.	1023;1090	G5E960;Q01970	.;PLCB3_HUMAN	K	1090;1090;1023	ENSP00000279230:E1090K;ENSP00000443631:E1090K;ENSP00000324660:E1023K	ENSP00000279230:E1090K	E	+	1	0	PLCB3	63790364	1.000000	0.71417	1.000000	0.80357	0.562000	0.35680	9.167000	0.94773	2.421000	0.82119	0.555000	0.69702	GAG	.	.	.	none		0.572	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1		Missense_Mutation	A	64033788	G	A	64033788	5	1	225	1	0	0	0	0	0	0	1	0	12036	1188	41	2	3378	2	PLCB3	11	64033788	Splice_Site	SNP	G	TCGA-MH-A855-01A-11D-A34Z-10	58965811	64033788	70972728	20	13705											
MMP28	79148	hgsc.bcm.edu	37	chr17	34122300	34122300	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgcgcagctcctggcctcCgcgctccgcgggctgggcgt	1	8	15	17	6	0	0	0	0	0	0	3	0	3	0	4	3	2	4	4	3	0	1	rs201598708	byFrequency	TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr17:34122300C>T	ENST00000250144.8	-	1	411	c.82G>A	c.(82-84)Gga>Aga	p.G28R		NM_001032278.1	NP_001027449.1	Q9H239	MMP28_HUMAN	matrix metallopeptidase 28	28					negative regulation of macrophage chemotaxis (GO:0010760)	cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|lung(7)|ovary(1)|skin(5)	16		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)	Marimastat(DB00786)	TCCTGGCCTCCGCGCTCCGCG	0.716																																					p.G28R		Atlas-SNP	.											.	MMP28	41	.	0			c.G82A						PASS	.						7	9	9					17																	34122300		1771	3550	5321	SO:0001583	missense	79148	exon1			GGCCTCCGCGCTC	AF315683	CCDS45651.1, CCDS74036.1	17q12	2014-08-12	2005-08-08		ENSG00000271447	ENSG00000271447			14366	protein-coding gene	gene with protein product		608417	"matrix metalloproteinase 28"			11121398, 11255011	Standard	NM_024302		Approved	MMP-25, MM28, EPILYSIN, MMP-28	uc002hjy.1	Q9H239	OTTHUMG00000188387	ENST00000250144.8:c.82G>A	chr17.hg19:g.34122300C>T	ENSP00000250144:p.Gly28Arg	48.0	0.0	.		41.0	13.0	.	NM_001032278	Q96F04|Q96TE2	Missense_Mutation	SNP	ENST00000250144.8	hg19	CCDS45651.1	.	.	.	.	.	.	.	.	.	.	C	12.85	2.062543	0.36373	.	.	ENSG00000129270	ENST00000338839;ENST00000538544;ENST00000250144	T	0.67171	-0.25	4.41	3.42	0.39159	.	1.443060	0.04714	N	0.418131	T	0.58090	0.2098	.	.	.	0.09310	N	1	D;P	0.54047	0.964;0.898	P;B	0.46299	0.511;0.108	T	0.46119	-0.9214	9	0.12430	T	0.62	.	9.8502	0.41053	0.2041:0.7959:0.0:0.0	.	28;28	Q9H239-2;Q9H239	.;MMP28_HUMAN	R	28	ENSP00000250144:G28R	ENSP00000250144:G28R	G	-	1	0	MMP28	31146413	0.000000	0.05858	0.001000	0.08648	0.130000	0.20726	0.615000	0.24329	1.428000	0.47296	-0.188000	0.12872	GGA	.	.	.	alt		0.716	MMP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449269.1	NM_024302		T	34122300	C	T	34122300	3	4	225	1	0	0	0	0	1	0	0	0	9672	661	23	1	1525	1	MMP28	17	34122300	Missense_Mutation	SNP	C	TCGA-MH-A855-01A-11D-A34Z-10		34122300	47072910	21	13706											
CBX4	8535	hgsc.bcm.edu	37	chr17	77807917	77807917	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgtcgtggtgggtgccgcTgccgccgccaccgccaccgc	2	5	15	19	7	0	0	0	0	0	0	1	0	0	0	8	2	2	1	8	2	0	0			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr17:77807917T>C	ENST00000269397.4	-	5	1701	c.1524A>G	c.(1522-1524)gcA>gcG	p.A508A		NM_003655.2	NP_003646.2	O00257	CBX4_HUMAN	chromobox homolog 4	508	Interaction with BMI1.|Poly-Ala.				chromatin modification (GO:0016568)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein sumoylation (GO:0016925)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|single-stranded RNA binding (GO:0003727)|SUMO binding (GO:0032183)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			TGGGTgccgctgccgccgcca	0.687																																					p.A508A		Atlas-SNP	.											.,1	CBX4	40	.	0			c.A1524G						PASS	.						16	24	21					17																	77807917		2078	4093	6171	SO:0001819	synonymous_variant	8535	exon5			TGCCGCTGCCGCC	AF013956	CCDS32758.1	17q25.3	2010-07-06	2010-06-24		ENSG00000141582	ENSG00000141582			1554	protein-coding gene	gene with protein product	"NS5ATP1-binding protein 16", "Pc class 2 homolog (Drosophila)"	603079	"chromobox homolog 4 (Drosophila Pc class)"			9315667	Standard	NM_003655		Approved	hPC2, PC2, NBP16	uc002jxe.3	O00257	OTTHUMG00000150415	ENST00000269397.4:c.1524A>G	chr17.hg19:g.77807917T>C		96.0	1.0	.		49.0	4.0	.	NM_003655	B1PJR7|Q6TPI8|Q96C04	Silent	SNP	ENST00000269397.4	hg19	CCDS32758.1																																																																																			.	.	.	none		0.687	CBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318007.1	NM_003655		C	77807917	T	C	77807917	2	2	225	1	0	0	0	0	0	0	0	1	2722	1567	55	3		3	CBX4	17	77807917	Silent	SNP	T	TCGA-MH-A855-01A-11D-A34Z-10	43685617	77807917	3387293	22	13707											
ATF5	22809	hgsc.bcm.edu	37	chr19	50436034	50436034	+	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	caggaggaagtggggatgccGcctctgcccccgccacagca	8	4	14	15	2	1	0	0	0	1	0	1	3	1	3	5	4	3	1	5	4	1	0	rs367836750	byFrequency	TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr19:50436034G>T	ENST00000423777.2	+	3	911	c.534G>T	c.(532-534)ccG>ccT	p.P178P	ATF5_ENST00000595125.1_Silent_p.P178P|MIR4751_ENST00000578027.1_RNA|CTC-326K19.6_ENST00000451973.1_Intron	NM_001193646.1	NP_001180575.1	Q9Y2D1	ATF5_HUMAN	activating transcription factor 5	178	Interaction with PTP4A1. {ECO:0000250}.				multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of astrocyte differentiation (GO:0048712)|olfactory bulb interneuron development (GO:0021891)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|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)|transcription corepressor activity (GO:0003714)			NS(1)|endometrium(2)|large_intestine(1)|skin(3)	7		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00221)|OV - Ovarian serous cystadenocarcinoma(262;0.017)	Pseudoephedrine(DB00852)	TGGGGATGCCGCCTCTGCCCC	0.672																																					p.P178P	GBM(48;768 989 9196 9511 26329)	Atlas-SNP	.											.	ATF5	27	.	0			c.G534T						PASS	.						29	23	25					19																	50436034		2201	4293	6494	SO:0001819	synonymous_variant	22809	exon4			GATGCCGCCTCTG	AF101388	CCDS12789.1	19q13.33	2013-09-20			ENSG00000169136	ENSG00000169136		"basic leucine zipper proteins"	790	protein-coding gene	gene with protein product		606398				10373550	Standard	NM_012068		Approved		uc002prd.3	Q9Y2D1	OTTHUMG00000183065	ENST00000423777.2:c.534G>T	chr19.hg19:g.50436034G>T		52.0	0.0	.		58.0	14.0	.	NM_012068	B3KND3|Q9BSA1|Q9UNQ3	Silent	SNP	ENST00000423777.2	hg19	CCDS12789.1																																																																																			.	.	.	alt		0.672	ATF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464915.2			T	50436034	G	T	50436034	2	4	225	1	0	0	0	0	0	0	0	1	1083	1074	38	4		4	ATF5	19	50436034	Silent	SNP	G	TCGA-MH-A855-01A-11D-A34Z-10		50436034	8692949	23	13708											
ZNF584	201514	hgsc.bcm.edu	37	chr19	58928550	58928550	+	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	gtgtaatgaatgtgggaaggCcttcagttacccgtctaagc	10	11	12	8	1	2	1	1	1	1	0	2	2	2	2	2	2	2	2	2	2	5	4			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr19:58928550C>A	ENST00000306910.4	+	4	1188	c.665C>A	c.(664-666)gCc>gAc	p.A222D	ZNF584_ENST00000599238.1_3'UTR|CTD-2619J13.16_ENST00000596296.1_lincRNA|ZNF584_ENST00000593920.1_Missense_Mutation_p.A177D	NM_173548.1	NP_775819.1	Q8IVC4	ZN584_HUMAN	zinc finger protein 584	222					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(3)|large_intestine(3)|lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14		all_cancers(17;5.3e-17)|all_epithelial(17;3.71e-12)|Lung NSC(17;8.3e-05)|Colorectal(82;0.000147)|all_lung(17;0.000386)|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;0.0271)		TGTGGGAAGGCCTTCAGTTAC	0.453																																					p.A222D		Atlas-SNP	.											.	ZNF584	31	.	0			c.C665A						PASS	.						65	64	65					19																	58928550		2203	4300	6503	SO:0001583	missense	201514	exon4			GGAAGGCCTTCAG	AK097218	CCDS12979.1	19q13.43	2013-01-08			ENSG00000171574	ENSG00000171574		"Zinc fingers, C2H2-type", "-"	27318	protein-coding gene	gene with protein product							Standard	NM_173548		Approved	FLJ39899	uc002qsp.3	Q8IVC4		ENST00000306910.4:c.665C>A	chr19.hg19:g.58928550C>A	ENSP00000306756:p.Ala222Asp	114.0	0.0	.		113.0	19.0	.	NM_173548	A8K203	Missense_Mutation	SNP	ENST00000306910.4	hg19	CCDS12979.1	.	.	.	.	.	.	.	.	.	.	C	14.39	2.520116	0.44866	.	.	ENSG00000171574	ENST00000306910;ENST00000354635	T	0.20069	2.1	3.78	1.63	0.23807	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.20861	0.0502	L	0.52011	1.625	0.09310	N	1	B	0.33413	0.411	B	0.39771	0.309	T	0.30387	-0.9980	9	0.87932	D	0	.	3.7	0.08379	0.0:0.5578:0.2082:0.2339	.	222	Q8IVC4	ZN584_HUMAN	D	222;81	ENSP00000306756:A222D	ENSP00000306756:A222D	A	+	2	0	ZNF584	63620362	0.000000	0.05858	0.653000	0.29593	0.797000	0.45037	0.033000	0.13754	0.935000	0.37341	0.555000	0.69702	GCC	.	.	.	none		0.453	ZNF584-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467022.1	NM_173548		A	58928550	C	A	58928550	3	1	225	1	0	0	0	0	1	0	0	0	18028	739	26	4	679	4	ZNF584	19	58928550	Missense_Mutation	SNP	C	TCGA-MH-A855-01A-11D-A34Z-10	8492516	58928550	200433	24	13709											
SEC23B	10483	hgsc.bcm.edu	37	chr20	18529410	18529410	+	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	ttactcctttcatgggccacCagaggtgaggctctacccaa	9	10	9	13	0	2	2	1	1	1	1	3	2	3	2	4	3	2	1	4	3	3	3	rs372083109		TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr20:18529410C>T	ENST00000336714.3	+	16	2333	c.1901C>T	c.(1900-1902)cCa>cTa	p.P634L	SEC23B_ENST00000377465.1_Missense_Mutation_p.P634L|SEC23B_ENST00000377475.3_Missense_Mutation_p.P634L|AL121893.1_ENST00000578930.1_RNA|SEC23B_ENST00000262544.2_Missense_Mutation_p.P634L	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)	634					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						CATGGGCCACCAGAGGTGAGG	0.433													C|||	1	0.000199681	0	0.0014	5008	,	,		16828	0		0	False		,,,				2504	0				p.P634L		Atlas-SNP	.											.	SEC23B	70	.	0			c.C1901T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	0,4406		0,0,2203	105	89	95		1901,1901,1901,1847,1901	4.4	1	20		95	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	SEC23B	NM_032986.3,NM_032985.4,NM_006363.4,NM_001172746.1,NM_001172745.1	98,98,98,98,98	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign,benign,benign	634/768,634/768,634/768,616/750,634/768	18529410	1,13005	2203	4300	6503	SO:0001583	missense	10483	exon16			GGCCACCAGAGGT	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.1901C>T	chr20.hg19:g.18529410C>T	ENSP00000338844:p.Pro634Leu	125.0	0.0	.		126.0	33.0	.	NM_032985	D3DW33|Q503A9|Q5W183|Q9BS15|Q9BSI2|Q9H1D7	Missense_Mutation	SNP	ENST00000336714.3	hg19	CCDS13137.1	.	.	.	.	.	.	.	.	.	.	C	16.61	3.171570	0.57584	0.0	1.16E-4	ENSG00000101310	ENST00000336714;ENST00000262544;ENST00000377475;ENST00000377465;ENST00000422877	T;T;T;T;D	0.93366	0.25;0.25;0.25;0.25;-3.21	4.44	4.44	0.53790	Gelsolin domain (1);	0.000000	0.85682	D	0.000000	D	0.97142	0.9066	M	0.93720	3.45	0.80722	D	1	P;B	0.49862	0.929;0.291	P;B	0.59825	0.864;0.363	D	0.98225	1.0480	10	0.87932	D	0	-11.4968	16.5981	0.84802	0.0:1.0:0.0:0.0	.	616;634	B4DJW8;Q15437	.;SC23B_HUMAN	L	634;634;634;634;142	ENSP00000338844:P634L;ENSP00000262544:P634L;ENSP00000366695:P634L;ENSP00000366685:P634L;ENSP00000409882:P142L	ENSP00000262544:P634L	P	+	2	0	SEC23B	18477410	1.000000	0.71417	0.968000	0.41197	0.039000	0.13416	7.525000	0.81892	2.467000	0.83353	0.563000	0.77884	CCA	.	.	.	weak		0.433	SEC23B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078184.5			T	18529410	C	T	18529410	3	4	225	1	0	0	0	0	1	0	0	0	14005	594	21	2	1959	2	SEC23B	20	18529410	Missense_Mutation	SNP	C	TCGA-MH-A855-01A-11D-A34Z-10		18529410	44496110	25	13710											
ZMYND8	23613	hgsc.bcm.edu	37	chr20	45878117	45878117	+	Missense_Mutation	SNP	A	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	gcttgggagagatgagaggaAcaggggtggactgttgctgg	9	8	20	4	0	0	2	0	1	0	2	0	7	0	5	0	6	2	3	0	6	1	2			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr20:45878117A>C	ENST00000311275.7	-	13	1881	c.1628T>G	c.(1627-1629)gTt>gGt	p.V543G	ZMYND8_ENST00000352431.2_Missense_Mutation_p.V563G|ZMYND8_ENST00000446994.2_Missense_Mutation_p.V480G|ZMYND8_ENST00000536340.1_Missense_Mutation_p.V570G|ZMYND8_ENST00000372023.3_Missense_Mutation_p.V538G|ZMYND8_ENST00000468376.2_5'UTR|ZMYND8_ENST00000360911.3_Missense_Mutation_p.V538G|ZMYND8_ENST00000262975.4_Missense_Mutation_p.V543G|ZMYND8_ENST00000355972.4_Missense_Mutation_p.V543G|ZMYND8_ENST00000471951.2_Missense_Mutation_p.V563G|ZMYND8_ENST00000396281.4_Missense_Mutation_p.V543G|ZMYND8_ENST00000540497.1_Missense_Mutation_p.V491G|ZMYND8_ENST00000458360.2_Missense_Mutation_p.V538G|ZMYND8_ENST00000461685.1_Missense_Mutation_p.V563G	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)			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)			GATGAGAGGAACAGGGGTGGA	0.488																																					p.V563G		Atlas-SNP	.											.	ZMYND8	166	.	0			c.T1688G						PASS	.						149	129	136					20																	45878117		2203	4300	6503	SO:0001583	missense	23613	exon13			AGAGGAACAGGGG	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.1628T>G	chr20.hg19:g.45878117A>C	ENSP00000312237:p.Val543Gly	101.0	0.0	.		100.0	30.0	.	NM_183047	B3KVL2|B7Z2A8|B7Z3E0|B7Z680|B7ZM62|E1P5U5|F5H0X3|H7C0U2|J3KPU3|Q13517|Q2HXV1|Q2HXV2|Q2HXV3|Q2HXV4|Q2HXV7|Q2HXV8|Q2HXV9|Q2HXW0|Q2HXW1|Q2HXW2|Q4JJ94|Q4JJ95|Q5TH09|Q5TH11|Q6MZM1|Q8WXC5|Q9H1F3|Q9H1F4|Q9H1F5|Q9H1L8|Q9H1L9|Q9H2G5|Q9NYN3|Q9UIX6	Missense_Mutation	SNP	ENST00000311275.7	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.737|0.737	-0.777934|-0.777934	0.02929|0.02929	.|.	.|.	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	.|0.90955	.|-1.91;-1.81;-1.94;-1.81;-1.92;-1.82;-1.82;-2.76;-1.81;-1.91;-1.88	5.7|5.7	3.47|3.47	0.39725|0.39725	.|.	.|0.203494	.|0.42294	.|D	.|0.000725	D|D	0.85270|0.85270	0.5658|0.5658	L|L	0.43152|0.43152	1.355|1.355	0.29997|0.29997	N|N	0.81633|0.81633	.|P;B;B;B;B;P;B;B;B;B;B;B;B;B;B;B;B;B	.|0.47762	.|0.9;0.438;0.17;0.17;0.143;0.481;0.234;0.029;0.118;0.029;0.029;0.17;0.083;0.083;0.17;0.161;0.064;0.17	.|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;0.243;0.314;0.138;0.096;0.156;0.096;0.096;0.217;0.297;0.297;0.217;0.053;0.122;0.217	T|T	0.81543|0.81543	-0.0885|-0.0885	5|10	.|0.72032	.|D	.|0.01	-17.669|-17.669	8.2758|8.2758	0.31871|0.31871	0.789:0.0:0.211:0.0|0.789:0.0:0.211:0.0	.|.	.|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;.;.;.;.;.;.	W|G	470|538;543;538;544;564;563;543;570;543;480;563;538;491	.|ENSP00000354166:V538G;ENSP00000312237:V543G;ENSP00000392964:V538G;ENSP00000335537:V563G;ENSP00000379577:V543G;ENSP00000439800:V570G;ENSP00000348246:V543G;ENSP00000396725:V480G;ENSP00000418210:V563G;ENSP00000361093:V538G;ENSP00000443086:V491G	.|ENSP00000262975:V544G	C|V	-|-	3|2	2|0	ZMYND8|ZMYND8	45311524|45311524	0.955000|0.955000	0.32602|0.32602	0.029000|0.029000	0.17559|0.17559	0.067000|0.067000	0.16453|0.16453	3.510000|3.510000	0.53393|0.53393	0.451000|0.451000	0.26802|0.26802	0.528000|0.528000	0.53228|0.53228	TGT|GTT	.	.	.	none		0.488	ZMYND8-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000079596.2	NM_183047		C	45878117	A	C	45878117	3	2	225	1	0	0	0	0	1	0	0	0	17723	43	2	5	1922	5	ZMYND8	20	45878117	Missense_Mutation	SNP	A	TCGA-MH-A855-01A-11D-A34Z-10	27348707	45878117	17147403	26	13711											
PRIC285	85441	hgsc.bcm.edu	37	chr20	62196757	62196757	+	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	cgggatggctgacgcccgctCgaaggtctctggcacgaaag	8	6	15	12	5	1	1	0	1	1	0	3	4	1	2	1	4	0	3	1	4	2	0			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr20:62196757C>T	ENST00000467148.1	-	8	3487	c.3418G>A	c.(3418-3420)Gag>Aag	p.E1140K	HELZ2_ENST00000427522.2_Missense_Mutation_p.E571K	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	1140					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)										GACGCCCGCTCGAAGGTCTCT	0.701																																					p.E1140K		Atlas-SNP	.											.	.	.	.	0			c.G3418A						PASS	.						12	13	13					20																	62196757		2172	4262	6434	SO:0001583	missense	85441	exon9			CCCGCTCGAAGGT	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.3418G>A	chr20.hg19:g.62196757C>T	ENSP00000417401:p.Glu1140Lys	59.0	0.0	.		41.0	16.0	.	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	hg19	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	C	10.97	1.502154	0.26949	.	.	ENSG00000130589	ENST00000427522;ENST00000467148	T;T	0.21361	2.01;2.01	4.81	3.85	0.44370	.	0.563900	0.18326	N	0.144647	T	0.18800	0.0451	L	0.50333	1.59	0.09310	N	0.999995	B;P	0.39352	0.336;0.669	B;B	0.30316	0.022;0.114	T	0.05209	-1.0899	10	0.44086	T	0.13	-17.4384	14.9232	0.70856	0.0:0.8558:0.1442:0.0	.	1140;571	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	K	571;1140	ENSP00000393257:E571K;ENSP00000417401:E1140K	ENSP00000393257:E571K	E	-	1	0	RP4-697K14.7	61667201	0.009000	0.17119	0.030000	0.17652	0.014000	0.08584	1.911000	0.39937	1.001000	0.39076	0.491000	0.48974	GAG	.	.	.	none		0.701	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		T	62196757	C	T	62196757	3	4	225	1	0	0	0	0	1	0	0	0	12495	893	31	1	4579	1	PRIC285	20	62196757	Missense_Mutation	SNP	C	TCGA-MH-A855-01A-11D-A34Z-10	16318640	62196757	828763	27	13712											
EFCAB6	64800	hgsc.bcm.edu	37	chr22	44064754	44064754	+	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	cattttgcttaattttacctCtcagaaagatctggctgctg	9	16	7	9	0	2	2	1	0	2	2	3	2	2	2	1	1	3	3	1	1	3	5			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chr22:44064754C>G	ENST00000262726.7	-	16	2065	c.1812G>C	c.(1810-1812)gaG>gaC	p.E604D	EFCAB6_ENST00000396231.2_Missense_Mutation_p.E452D	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	604					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				AATTTTACCTCTCAGAAAGAT	0.368																																					p.E604D		Atlas-SNP	.											.	EFCAB6	177	.	0			c.G1812C						PASS	.						93	86	89					22																	44064754		2203	4300	6503	SO:0001583	missense	64800	exon16			TTACCTCTCAGAA	Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"EF-hand domain containing"	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.1812G>C	chr22.hg19:g.44064754C>G	ENSP00000262726:p.Glu604Asp	303.0	0.0	.		299.0	70.0	.	NM_022785	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Missense_Mutation	SNP	ENST00000262726.7	hg19	CCDS14049.1	.	.	.	.	.	.	.	.	.	.	C	8.514	0.867300	0.17250	.	.	ENSG00000186976	ENST00000396231;ENST00000262726	T;T	0.16324	2.35;2.39	4.97	3.95	0.45737	.	0.983709	0.08286	N	0.969105	T	0.19327	0.0464	M	0.62723	1.935	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.05099	-1.0906	10	0.19590	T	0.45	-6.1905	9.2837	0.37744	0.0:0.9026:0.0:0.0974	.	604	Q5THR3	EFCB6_HUMAN	D	452;604	ENSP00000379533:E452D;ENSP00000262726:E604D	ENSP00000262726:E604D	E	-	3	2	EFCAB6	42396087	0.936000	0.31750	0.917000	0.36280	0.560000	0.35617	0.544000	0.23253	1.327000	0.45338	0.555000	0.69702	GAG	.	.	.	none		0.368	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785		G	44064754	C	G	44064754	3	3	225	1	0	0	0	0	1	0	0	0	4941	912	32	4	2761	4	EFCAB6	22	44064754	Missense_Mutation	SNP	C	TCGA-MH-A855-01A-11D-A34Z-10		44064754	7239812	28	13713											
SEPT6	23157	hgsc.bcm.edu	37	chrX	118809562	118809562	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccctggctgacggacttatTcaccagctggtcaggcaagc	8	8	12	13	1	2	1	2	1	0	0	2	2	2	2	2	4	2	3	2	4	2	2			TCGA-MH-A855-01A-11D-A34Z-10	TCGA-MH-A855-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45f692dd-7c11-4489-9e41-a3288880bb92	d3dee4f3-5666-47be-8e2e-f75389de1c43	g.chrX:118809562T>C	ENST00000343984.5	-	2	364	c.100A>G	c.(100-102)Aat>Gat	p.N34D	SEPT6_ENST00000394616.4_5'UTR|SEPT6_ENST00000489216.1_Missense_Mutation_p.N34D|SEPT6_ENST00000360156.7_Missense_Mutation_p.N34D|SEPT6_ENST00000354416.3_Missense_Mutation_p.N34D|SEPT6_ENST00000394610.1_Missense_Mutation_p.N34D|SEPT6_ENST00000354228.4_Missense_Mutation_p.N34D|SEPT6_ENST00000394617.2_Missense_Mutation_p.N64D	NM_015129.5	NP_055944.2	Q14141	SEPT6_HUMAN	septin 6	34					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						ACGGACTTATTCACCAGCTGG	0.493			T	MLL	AML																																p.N34D		Atlas-SNP	.		Dom	yes		X	Xq24	23157	septin 6		L	.	SEPT6	53	.	0			c.A100G						PASS	.						70	46	54					X																	118809562		2203	4300	6503	SO:0001583	missense	23157	exon2			ACTTATTCACCAG	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.100A>G	chrX.hg19:g.118809562T>C	ENSP00000341524:p.Asn34Asp	158.0	0.0	.		187.0	53.0	.	NM_145802	Q5JTK0|Q969W5|Q96A13|Q96GR1|Q96P86|Q96P87	Missense_Mutation	SNP	ENST00000343984.5	hg19	CCDS14584.1	.	.	.	.	.	.	.	.	.	.	T	18.73	3.685597	0.68157	.	.	ENSG00000125354	ENST00000360156;ENST00000354228;ENST00000489216;ENST00000354416;ENST00000394610;ENST00000343984;ENST00000394617;ENST00000520510	T;T;T;T;T;T;T	0.32988	1.43;1.43;1.43;1.43;1.43;1.43;1.43	5.82	5.82	0.92795	.	0.042909	0.85682	D	0.000000	T	0.45458	0.1343	L	0.56396	1.775	0.80722	D	1	P;B;B	0.48640	0.913;0.143;0.003	P;B;B	0.54544	0.755;0.173;0.005	T	0.33979	-0.9847	10	0.45353	T	0.12	.	14.1936	0.65654	0.0:0.0:0.0:1.0	.	64;34;34	F5H1J5;Q14141;Q548C9	.;SEPT6_HUMAN;.	D	34;34;34;34;34;34;64;34	ENSP00000353278:N34D;ENSP00000346169:N34D;ENSP00000418715:N34D;ENSP00000346397:N34D;ENSP00000378108:N34D;ENSP00000341524:N34D;ENSP00000378115:N64D	ENSP00000341524:N34D	N	-	1	0	SEPT6	118693590	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.698000	0.84413	1.950000	0.56595	0.417000	0.27973	AAT	.	.	.	none		0.493	SEPT6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058059.1	NM_145802		C	118809562	T	C	118809562	3	2	225	1	0	0	0	0	1	0	0	0	14081	1783	62	3	1262	3	SEPT6	23	118809562	Missense_Mutation	SNP	T	TCGA-MH-A855-01A-11D-A34Z-10		118809562	36460998	29	13714											
HCRTR1	3061	hgsc.bcm.edu	37	chr1	32092534	32092534	+	Missense_Mutation	SNP	A	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	gccgatgctccatctccaaaAtctctgagcatgtggtgctc	8	11	9	13	1	2	1	0	1	2	0	6	2	3	1	3	1	3	3	3	1	2	0			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr1:32092534A>C	ENST00000373706.5	+	7	1384	c.1231A>C	c.(1231-1233)Atc>Ctc	p.I411L	HCRTR1_ENST00000373705.1_Intron|HCRTR1_ENST00000403528.2_Missense_Mutation_p.I411L|HCRTR1_ENST00000468521.1_Intron			O43613	OX1R_HUMAN	hypocretin (orexin) receptor 1	411					feeding behavior (GO:0007631)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|orexin receptor activity (GO:0016499)|peptide hormone binding (GO:0017046)			breast(2)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	7		Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.053)		CATCTCCAAAATCTCTGAGCA	0.652																																					p.I411L		Atlas-SNP	.											.	HCRTR1	20	.	0			c.A1231C						PASS	.						103	101	102					1																	32092534		2203	4300	6503	SO:0001583	missense	3061	exon9			TCCAAAATCTCTG	AF041243	CCDS344.1	1p33	2012-08-08			ENSG00000121764	ENSG00000121764		"GPCR / Class A : Hypocretin (orexin) receptors"	4848	protein-coding gene	gene with protein product		602392				9491897	Standard	NM_001525		Approved	OX1R	uc009vtx.2	O43613	OTTHUMG00000003876	ENST00000373706.5:c.1231A>C	chr1.hg19:g.32092534A>C	ENSP00000362810:p.Ile411Leu	43.0	0.0	.		36.0	14.0	.	NM_001525	A8K3A6|Q9HBV6	Missense_Mutation	SNP	ENST00000373706.5	hg19	CCDS344.1	.	.	.	.	.	.	.	.	.	.	A	0.048	-1.258738	0.01445	.	.	ENSG00000121764	ENST00000403528;ENST00000373706	T;T	0.59364	0.27;0.27	4.58	0.0883	0.14454	.	0.624474	0.15468	N	0.260782	T	0.22898	0.0553	N	0.02916	-0.46	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.23226	-1.0194	10	0.06625	T	0.88	.	5.0151	0.14331	0.4204:0.1475:0.4321:0.0	.	411	O43613	OX1R_HUMAN	L	411	ENSP00000384387:I411L;ENSP00000362810:I411L	ENSP00000362810:I411L	I	+	1	0	HCRTR1	31865121	0.988000	0.35896	0.023000	0.16930	0.847000	0.48162	0.244000	0.18124	-0.388000	0.07797	-2.581000	0.00168	ATC	.	.	.	none		0.652	HCRTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011042.1	NM_001525		C	32092534	A	C	32092534	3	2	226	1	0	0	0	0	1	0	0	0	7008	101	4	5	1257	5	HCRTR1	1	32092534	Missense_Mutation	SNP	A	TCGA-MH-A856-01A-11D-A34Z-10		32092534	217158087	1	13715											
HIVEP3	59269	hgsc.bcm.edu	37	chr1	42047342	42047343	+	Frame_Shift_Ins	INS	-	-	T																															gcctgtctcaccaagaagcaINSttttcttctctctggcgggg																										TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr1:42047342_42047343insT	ENST00000372583.1	-	4	4011_4012	c.3126_3127insA	c.(3124-3129)aaatgcfs	p.C1043fs	HIVEP3_ENST00000247584.5_Frame_Shift_Ins_p.C1043fs|HIVEP3_ENST00000429157.2_Frame_Shift_Ins_p.C1043fs|HIVEP3_ENST00000460604.1_5'Flank|HIVEP3_ENST00000372584.1_Frame_Shift_Ins_p.C1043fs	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	1043	No DNA binding activity or transactivation activity, but complete prevention of TRAF-dependent NF-Kappa-B activation; associates with TRAF2 and JUN. {ECO:0000250}.				positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				ACCAAGAAGCATTTTCTTCTCT	0.589																																					p.C1043fs		Atlas-Indel,Pindel	.											.	HIVEP3	235	.	0			c.3127_3128insA						PASS	.																																			SO:0001589	frameshift_variant	59269	exon4			.	AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"Zinc fingers, C2H2-type"	13561	protein-coding gene	gene with protein product	"kappabinding protein-1"	606649	"human immunodeficiency virus type I enhancer-binding protein 3"			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.3127dupA	chr1.hg19:g.42047346_42047346dupT	ENSP00000361664:p.Cys1043fs	50.0	0.0	0		60.0	19.0	0.316667	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Frame_Shift_Ins	INS	ENST00000372583.1	hg19	CCDS463.1																																																																																			.	.	.	none		0.589	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		T	42047343	-	T	42047342	7	5	226	1	0	1	1	0	0	0	0	0	7195	217	8	0	4117	0	HIVEP3	1	42047342	Frame_Shift_Ins	INS	-	TCGA-MH-A856-01A-11D-A34Z-10	9954808	42047342	207203279	2	13716											
MUTYH	4595	hgsc.bcm.edu	37	chr1	45797966	45797966	+	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	tggccgggctgggtccaccaGctgctgggctagacccctaa	6	7	14	14	1	0	1	0	0	0	1	1	1	1	1	5	4	2	4	5	4	2	2			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr1:45797966G>C	ENST00000372098.3	-	10	929	c.796C>G	c.(796-798)Ctg>Gtg	p.L266V	MUTYH_ENST00000529984.1_Intron|MUTYH_ENST00000528332.2_Intron|MUTYH_ENST00000456914.2_Missense_Mutation_p.L241V|MUTYH_ENST00000372100.5_Missense_Mutation_p.L252V|MUTYH_ENST00000488731.2_Intron|MUTYH_ENST00000528013.2_Missense_Mutation_p.L255V|MUTYH_ENST00000355498.2_Missense_Mutation_p.L241V|MUTYH_ENST00000450313.1_Missense_Mutation_p.L269V|MUTYH_ENST00000372115.3_Missense_Mutation_p.L255V|MUTYH_ENST00000372110.3_Missense_Mutation_p.L256V|MUTYH_ENST00000354383.6_Missense_Mutation_p.L242V|MUTYH_ENST00000372104.1_Missense_Mutation_p.L241V|MUTYH_ENST00000448481.1_Missense_Mutation_p.L252V|MUTYH_ENST00000531105.1_Intron			Q9UIF7	MUTYH_HUMAN	mutY homolog	266					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA repair (GO:0006281)|mismatch repair (GO:0006298)	mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|metal ion binding (GO:0046872)|MutSalpha complex binding (GO:0032407)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					GGGTCCACCAGCTGCTGGGCT	0.592			Mis			colorectal		Base excision repair (BER), DNA glycosylases	MUTYH-associated polyposis																												p.L269V		Atlas-SNP	.	yes	Rec		Adenomatous polyposis coli	1	1p34.3-1p32.1	4595	mutY homolog (E. coli)		E	.	MUTYH	38	.	0			c.C805G						PASS	.						29	30	30					1																	45797966		2203	4300	6503	SO:0001583	missense	4595	exon10	Familial Cancer Database	MAP, MYH-associated polyposis	CCACCAGCTGCTG	U63329	CCDS520.1, CCDS41320.1, CCDS41321.1, CCDS41322.1, CCDS72776.1, CCDS72777.1	1p34.1	2014-09-17	2013-09-12		ENSG00000132781	ENSG00000132781			7527	protein-coding gene	gene with protein product		604933	"mutY (E. coli) homolog", "mutY homolog (E. coli)"			7823963, 10684930	Standard	NM_012222		Approved	MYH	uc009vxp.3	Q9UIF7	OTTHUMG00000007682	ENST00000372098.3:c.796C>G	chr1.hg19:g.45797966G>C	ENSP00000361170:p.Leu266Val	54.0	0.0	.		46.0	10.0	.	NM_001128425	D3DPZ4|Q15830|Q9UBP2|Q9UBS7|Q9UIF4|Q9UIF5|Q9UIF6	Missense_Mutation	SNP	ENST00000372098.3	hg19	CCDS520.1	.	.	.	.	.	.	.	.	.	.	G	11.99	1.803564	0.31869	.	.	ENSG00000132781	ENST00000372104;ENST00000448481;ENST00000456914;ENST00000354383;ENST00000355498;ENST00000372098;ENST00000372110;ENST00000372115;ENST00000450313;ENST00000372100;ENST00000525481;ENST00000412971;ENST00000435155	D;D;D;D;D;D;D;D;D;D;D;D	0.94138	-3.36;-3.36;-3.36;-3.36;-3.36;-3.36;-3.36;-3.36;-3.36;-3.36;-3.36;-3.36	5.64	3.71	0.42584	HhH-GPD domain (1);DNA glycosylase (1);Helix-turn-helix, base-excision DNA repair, C-terminal (1);	0.075116	0.53938	D	0.000042	D	0.94518	0.8235	M	0.68952	2.095	0.46317	D	0.998987	D;P;D;P;D;P;D	0.57571	0.965;0.695;0.98;0.695;0.965;0.92;0.965	P;B;P;B;P;P;P	0.57009	0.578;0.217;0.811;0.217;0.578;0.578;0.652	D	0.93723	0.7034	10	0.72032	D	0.01	-15.3824	11.2119	0.48804	0.1549:0.0:0.8451:0.0	.	269;266;256;266;255;149;242	E5KP25;E5KP26;Q9UIF7-2;Q9UIF7;E5KP27;D3DPZ6;E5KP28	.;.;.;MUTYH_HUMAN;.;.;.	V	241;252;241;242;241;266;256;255;269;252;113;113;252	ENSP00000361176:L241V;ENSP00000409718:L252V;ENSP00000407590:L241V;ENSP00000346354:L242V;ENSP00000347685:L241V;ENSP00000361170:L266V;ENSP00000361182:L256V;ENSP00000361187:L255V;ENSP00000408176:L269V;ENSP00000361172:L252V;ENSP00000410263:L113V;ENSP00000403655:L252V	ENSP00000346354:L242V	L	-	1	2	MUTYH	45570553	0.782000	0.28689	0.997000	0.53966	0.320000	0.28249	1.025000	0.30090	0.676000	0.31285	-0.150000	0.13652	CTG	.	.	.	none		0.592	MUTYH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020529.1	NM_012222		C	45797966	G	C	45797966	3	2	226	1	0	0	0	0	1	0	0	0	10000	962	34	4	872	4	MUTYH	1	45797966	Missense_Mutation	SNP	G	TCGA-MH-A856-01A-11D-A34Z-10	3750624	45797966	203452655	3	13717											
LRP8	7804	hgsc.bcm.edu	37	chr1	53722944	53722944	+	Missense_Mutation	SNP	A	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	ggttgctggttgcagggcttAgggtagacgggctgatgctg	5	11	19	6	1	0	2	0	1	0	1	0	2	0	2	0	5	3	8	0	5	2	4			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr1:53722944A>C	ENST00000306052.6	-	15	2503	c.2402T>G	c.(2401-2403)cTa>cGa	p.L801R	LRP8_ENST00000371454.2_Missense_Mutation_p.L801R|LRP8_ENST00000460214.1_5'UTR|LRP8_ENST00000465675.1_Missense_Mutation_p.L354R|LRP8_ENST00000347547.2_Missense_Mutation_p.L631R|LRP8_ENST00000354412.3_Intron	NM_004631.4	NP_004622.2	Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	801					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						TGCAGGGCTTAGGGTAGACGG	0.562																																					p.L801R		Atlas-SNP	.											.	LRP8	58	.	0			c.T2402G						PASS	.						175	154	161					1																	53722944		2203	4300	6503	SO:0001583	missense	7804	exon15			GGGCTTAGGGTAG	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.2402T>G	chr1.hg19:g.53722944A>C	ENSP00000303634:p.Leu801Arg	142.0	0.0	.		197.0	82.0	.	NM_004631	B1AMT6|B1AMT7|B1AMT8|O14968|Q86V27|Q99876|Q9BR78	Missense_Mutation	SNP	ENST00000306052.6	hg19	CCDS578.1	.	.	.	.	.	.	.	.	.	.	A	4.412	0.076180	0.08485	.	.	ENSG00000157193	ENST00000306052;ENST00000371454;ENST00000465675;ENST00000347547	T;T;T;T	0.22336	1.96;1.96;1.96;1.96	5.94	2.98	0.34508	.	.	.	.	.	T	0.08133	0.0203	N	0.08118	0	0.09310	N	1	B;B;P;B;B	0.34757	0.0;0.38;0.467;0.043;0.001	B;B;B;B;B	0.29176	0.001;0.076;0.099;0.021;0.002	T	0.31223	-0.9951	9	0.16420	T	0.52	.	5.4585	0.16604	0.2396:0.0:0.6203:0.1401	.	354;631;801;801;354	B3KU40;Q14114-4;Q14114-3;Q14114;E9PP15	.;.;.;LRP8_HUMAN;.	R	801;801;354;631	ENSP00000303634:L801R;ENSP00000360509:L801R;ENSP00000437009:L354R;ENSP00000334522:L631R	ENSP00000303634:L801R	L	-	2	0	LRP8	53495532	0.486000	0.25980	0.454000	0.27019	0.839000	0.47603	0.158000	0.16422	0.364000	0.24374	-0.248000	0.11899	CTA	.	.	.	none		0.562	LRP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024699.1	NM_004631		C	53722944	A	C	53722944	3	2	226	1	0	0	0	0	1	0	0	0	8970	420	15	5	509	5	LRP8	1	53722944	Missense_Mutation	SNP	A	TCGA-MH-A856-01A-11D-A34Z-10	7924978	53722944	195527677	4	13718											
PIGK	10026	hgsc.bcm.edu	37	chr1	77620232	77620232	+	Missense_Mutation	SNP	T	T	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	aaatcagttatcagtacattTttaggatccctctgaaaaag	15	13	6	7	0	3	1	2	1	1	0	4	2	4	2	1	1	1	2	1	1	6	5			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr1:77620232T>G	ENST00000370812.3	-	9	911	c.888A>C	c.(886-888)aaA>aaC	p.K296N	PIGK_ENST00000359130.1_Missense_Mutation_p.K296N|PIGK_ENST00000445065.1_Missense_Mutation_p.K202N|PIGK_ENST00000478391.1_5'UTR|PIGK_ENST00000370813.5_Missense_Mutation_p.K220N	NM_005482.2	NP_005473.1	Q92643	GPI8_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class K	296					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 folding (GO:0006457)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	cysteine-type endopeptidase activity (GO:0004197)|GPI-anchor transamidase activity (GO:0003923)|protein disulfide isomerase activity (GO:0003756)			endometrium(5)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	19						TCAGTACATTTTTAGGATCCC	0.358																																					p.K296N		Atlas-SNP	.											.	PIGK	46	.	0			c.A888C						PASS	.						107	103	104					1																	77620232		2203	4300	6503	SO:0001583	missense	10026	exon9			TACATTTTTAGGA	AF022913	CCDS674.1	1p31.1	2013-02-26	2006-06-28		ENSG00000142892	ENSG00000142892		"Phosphatidylinositol glycan anchor biosynthesis"	8965	protein-coding gene	gene with protein product	"GPI transamidase subunit"	605087	"phosphatidylinositol glycan, class K"			9356492	Standard	NM_005482		Approved	hGPI8, GPI8	uc001dhk.3	Q92643	OTTHUMG00000009686	ENST00000370812.3:c.888A>C	chr1.hg19:g.77620232T>G	ENSP00000359848:p.Lys296Asn	162.0	0.0	.		219.0	88.0	.	NM_005482	B2R7K3|B4E2M3|O14822|Q5TG77	Missense_Mutation	SNP	ENST00000370812.3	hg19	CCDS674.1	.	.	.	.	.	.	.	.	.	.	T	11.78	1.741690	0.30865	.	.	ENSG00000142892	ENST00000370812;ENST00000445065;ENST00000370813;ENST00000359130	T;T;T;T	0.46063	0.89;0.88;0.88;0.89	5.11	3.98	0.46160	.	0.370552	0.31897	N	0.006890	T	0.10035	0.0246	N	0.19112	0.55	0.33023	D	0.529102	B;B;B;B	0.06786	0.001;0.001;0.0;0.0	B;B;B;B	0.15052	0.012;0.008;0.008;0.008	T	0.12915	-1.0529	10	0.22109	T	0.4	-14.8515	4.9815	0.14168	0.1415:0.1428:0.0:0.7157	.	220;202;296;296	B4E2M3;B1AK81;A6NEM5;Q92643	.;.;.;GPI8_HUMAN	N	296;202;220;296	ENSP00000359848:K296N;ENSP00000388854:K202N;ENSP00000359849:K220N;ENSP00000352041:K296N	ENSP00000352041:K296N	K	-	3	2	PIGK	77392820	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.781000	0.26774	2.050000	0.60909	0.482000	0.46254	AAA	.	.	.	none		0.358	PIGK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026687.1	NM_005482		G	77620232	T	G	77620232	3	3	226	1	0	0	0	0	1	0	0	0	11897	1838	64	5	311	5	PIGK	1	77620232	Missense_Mutation	SNP	T	TCGA-MH-A856-01A-11D-A34Z-10	23897288	77620232	171630389	5	13719											
GON4L	54856	hgsc.bcm.edu	37	chr1	155823224	155823224	+	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	agttttcctttaccaatgtgTatattaagggggtgaaaaga	13	14	10	4	0	0	2	0	1	0	1	1	2	1	2	2	2	1	2	2	2	7	7			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr1:155823224T>G	ENST00000368331.1	-	2	396	c.348A>C	c.(346-348)atA>atC	p.I116I	GON4L_ENST00000437809.1_Silent_p.I116I|GON4L_ENST00000271883.5_Silent_p.I116I|GON4L_ENST00000361040.5_Silent_p.I116I|GON4L_ENST00000471341.1_5'UTR	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	116					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					TACCAATGTGTATATTAAGGG	0.458																																					p.I116I		Atlas-SNP	.											.	GON4L	392	.	0			c.A348C						PASS	.						123	121	122					1																	155823224		2203	4300	6503	SO:0001819	synonymous_variant	54856	exon2			AATGTGTATATTA	AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"gon-4 homolog (C.elegans)"	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.348A>C	chr1.hg19:g.155823224T>G		133.0	0.0	.		106.0	35.0	.	NM_001037533	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Silent	SNP	ENST00000368331.1	hg19																																																																																				.	.	.	none		0.458	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292		G	155823224	T	G	155823224	2	3	226	1	0	0	0	0	0	0	0	1	6579	1628	57	5		5	GON4L	1	155823224	Silent	SNP	T	TCGA-MH-A856-01A-11D-A34Z-10	78202992	155823224	93427397	6	13720											
FAM5B	57795	hgsc.bcm.edu	37	chr1	177245534	177245534	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctgctgcagatccaggacTcctgggccactcacaaccgg	8	6	11	16	1	1	1	1	0	0	1	3	2	3	2	5	3	3	2	5	3	1	0	rs368629885		TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr1:177245534T>C	ENST00000361539.4	+	6	1288	c.976T>C	c.(976-978)Tcc>Ccc	p.S326P	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	326					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)											GATCCAGGACTCCTGGGCCAC	0.567																																					p.S326P		Atlas-SNP	.											.	FAM5B	191	.	0			c.T976C						PASS	.						63	55	58					1																	177245534		2203	4300	6503	SO:0001583	missense	57795	exon6			CAGGACTCCTGGG		CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"family with sequence similarity 5, member B"	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.976T>C	chr1.hg19:g.177245534T>C	ENSP00000354481:p.Ser326Pro	117.0	0.0	.		150.0	59.0	.	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	hg19	CCDS1320.1	.	.	.	.	.	.	.	.	.	.	T	15.57	2.871574	0.51695	.	.	ENSG00000198797	ENST00000536589;ENST00000361539	T	0.15256	2.44	6.07	0.802	0.18686	.	0.390200	0.28209	N	0.016191	T	0.13114	0.0318	L	0.39898	1.24	0.36544	D	0.871453	B;P;B	0.37038	0.256;0.579;0.037	B;B;B	0.38755	0.189;0.281;0.029	T	0.12708	-1.0537	10	0.72032	D	0.01	-17.6413	6.0285	0.19667	0.3365:0.0:0.3715:0.2919	.	76;221;326	F5H8E0;Q9C0B6-2;Q9C0B6	.;.;FAM5B_HUMAN	P	76;326	ENSP00000354481:S326P	ENSP00000354481:S326P	S	+	1	0	FAM5B	175512157	0.029000	0.19370	1.000000	0.80357	0.994000	0.84299	0.314000	0.19432	0.475000	0.27415	0.533000	0.62120	TCC	.	.	.	none		0.567	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165		C	177245534	T	C	177245534	3	2	226	1	0	0	0	0	1	0	0	0	5600	1551	54	3	994	3	FAM5B	1	177245534	Missense_Mutation	SNP	T	TCGA-MH-A856-01A-11D-A34Z-10	21422310	177245534	72005087	7	13721											
JMJD4	65094	hgsc.bcm.edu	37	chr1	227921688	227921688	+	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	aactcattcagccagtcggaCgagaagtacacaggcagggt	13	6	12	10	2	2	1	2	0	0	1	3	3	2	2	1	3	3	2	1	3	3	2			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr1:227921688C>G	ENST00000366758.3	-	3	611	c.612G>C	c.(610-612)tcG>tcC	p.S204S	SNAP47_ENST00000366760.1_Intron|JMJD4_ENST00000438896.2_Silent_p.S204S|SNAP47_ENST00000366759.4_5'Flank|JMJD4_ENST00000485807.1_5'UTR|SNAP47_ENST00000315781.5_5'Flank|SNAP47_ENST00000480897.1_3'UTR	NM_023007.2	NP_075383.2	Q9H9V9	JMJD4_HUMAN	jumonji domain containing 4	204	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.									endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	9		Prostate(94;0.0885)				GCCAGTCGGACGAGAAGTACA	0.612																																					p.S204S		Atlas-SNP	.											.	JMJD4	28	.	0			c.G612C						PASS	.						145	115	125					1																	227921688		2203	4300	6503	SO:0001819	synonymous_variant	65094	exon3			GTCGGACGAGAAG	AK022579	CCDS1561.1, CCDS59203.1	1q42.13	2008-02-05			ENSG00000081692	ENSG00000081692			25724	protein-coding gene	gene with protein product						12477932	Standard	NM_023007		Approved	FLJ12517	uc001hrb.3	Q9H9V9	OTTHUMG00000037698	ENST00000366758.3:c.612G>C	chr1.hg19:g.227921688C>G		24.0	0.0	.		22.0	6.0	.	NM_023007	Q5TBZ1|Q5TBZ6|Q9H970	Silent	SNP	ENST00000366758.3	hg19	CCDS1561.1	.	.	.	.	.	.	.	.	.	.	.	0.076	-1.192619	0.01607	.	.	ENSG00000081692	ENST00000438896	.	.	.	4.16	-8.31	0.01001	.	.	.	.	.	T	0.42086	0.1187	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52616	-0.8552	4	.	.	.	-14.4929	3.4793	0.07597	0.176:0.329:0.3564:0.1386	.	.	.	.	P	197	.	.	R	-	2	0	JMJD4	225988311	0.000000	0.05858	0.022000	0.16811	0.139000	0.21198	-2.996000	0.00655	-3.988000	0.00084	-4.550000	0.00004	CGT	.	.	.	none		0.612	JMJD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091970.1	NM_023007		G	227921688	C	G	227921688	2	3	226	1	0	0	0	0	0	0	0	1	7958	523	19	4		4	JMJD4	1	227921688	Silent	SNP	C	TCGA-MH-A856-01A-11D-A34Z-10	50676154	227921688	21328933	8	13722											
ABCB10	23456	hgsc.bcm.edu	37	chr1	229666004	229666004	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgttgatttgccagaaccActtgggccaaccagtgccgt	9	10	10	12	1	0	2	0	1	0	1	0	2	0	2	5	1	4	1	5	1	2	3			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr1:229666004A>G	ENST00000344517.4	-	8	1629	c.1587T>C	c.(1585-1587)agT>agC	p.S529S		NM_012089.2	NP_036221.2	Q9NRK6	ABCBA_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 10	529	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)	31	Breast(184;0.143)|Ovarian(103;0.249)	Prostate(94;0.167)				TGCCAGAACCACTTGGGCCAA	0.537																																					p.S529S		Atlas-SNP	.											.	ABCB10	71	.	0			c.T1587C						PASS	.						111	102	105					1																	229666004		2203	4300	6503	SO:0001819	synonymous_variant	23456	exon8			AGAACCACTTGGG	U18237	CCDS1580.1	1q32	2012-03-14			ENSG00000135776	ENSG00000135776		"ATP binding cassette transporters / subfamily B"	41	protein-coding gene	gene with protein product	"ATP-binding cassette sub-family B member 10, mitochondrial", "ATP-binding cassette transporter 10", "ABC transporter 10 protein", "mitochondrial ATP-binding cassette 2"	605454				7766993	Standard	NM_012089		Approved	EST20237, M-ABC2, MTABC2	uc001htp.4	Q9NRK6	OTTHUMG00000039471	ENST00000344517.4:c.1587T>C	chr1.hg19:g.229666004A>G		27.0	0.0	.		34.0	14.0	.	NM_012089	Q13040|Q6P1Q8|Q9H3V0	Silent	SNP	ENST00000344517.4	hg19	CCDS1580.1																																																																																			.	.	.	none		0.537	ABCB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095240.1	NM_012089		G	229666004	A	G	229666004	2	3	226	1	0	0	0	0	0	0	0	1	41	156	6	3		3	ABCB10	1	229666004	Silent	SNP	A	TCGA-MH-A856-01A-11D-A34Z-10	1744316	229666004	19584617	9	13723											
TGOLN2	10618	hgsc.bcm.edu	37	chr2	85554384	85554384	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtctttttgggtctttgcCtccgcacccgacctgttggg	2	15	11	13	2	2	0	0	0	2	0	3	1	3	0	4	2	1	2	4	2	0	4			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr2:85554384C>T	ENST00000409232.3	-	2	532	c.471G>A	c.(469-471)gaG>gaA	p.E157E	TGOLN2_ENST00000409015.1_Silent_p.E157E|TGOLN2_ENST00000444342.2_Silent_p.E157E|TGOLN2_ENST00000398263.2_Silent_p.E157E|TGOLN2_ENST00000282120.2_Intron|TGOLN2_ENST00000377386.3_Silent_p.E157E			O43493	TGON2_HUMAN	trans-golgi network protein 2	157	14 X 14 AA tandem repeats.					Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)											GGGTCTTTGCCTCCGCACCCG	0.587																																					p.E157E		Atlas-SNP	.											.	TGOLN2	32	.	0			c.G471A						PASS	.						298	303	301					2																	85554384		1962	4150	6112	SO:0001819	synonymous_variant	10618	exon2			CTTTGCCTCCGCA	AF027515	CCDS46351.1, CCDS56126.1, CCDS56127.1	2p11.2	2012-06-25			ENSG00000152291	ENSG00000152291			15450	protein-coding gene	gene with protein product	"trans-Golgi network protein (46, 48, 51kD isoforms)"	603062				9422759, 21994457	Standard	NM_001206840		Approved	TGN51, TGN46, TGN48, TGN38, TTGN2	uc021vjw.1	O43493	OTTHUMG00000153017	ENST00000409232.3:c.471G>A	chr2.hg19:g.85554384C>T		237.0	0.0	.		159.0	63.0	.	NM_001206841	B2R686|B8ZZ88|D6W5K3|F8WBK2|O15282|O43492|O43499|O43500|O43501|Q53G68|Q53GV2|Q6MZV1|Q6ZTM7|Q8N6T8|Q92760|Q96QL2	Silent	SNP	ENST00000409232.3	hg19	CCDS56126.1																																																																																			.	.	.	none		0.587	TGOLN2-006	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000329045.2	NM_006464		T	85554384	C	T	85554384	2	4	226	1	0	0	0	0	0	0	0	1	15848	680	24	2		2	TGOLN2	2	85554384	Silent	SNP	C	TCGA-MH-A856-01A-11D-A34Z-10		85554384	157644989	10	13724											
GPR39	2863	hgsc.bcm.edu	37	chr2	133174849	133174849	+	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	atggtgagtttggcttgctcGgacatcttggtgttcctcat	5	16	12	8	1	2	1	1	1	1	0	4	2	3	2	1	4	1	4	1	4	0	4			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr2:133174849G>T	ENST00000329321.3	+	1	703	c.234G>T	c.(232-234)tcG>tcT	p.S78S		NM_001508.2	NP_001499.1	O43194	GPR39_HUMAN	G protein-coupled receptor 39	78					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						TGGCTTGCTCGGACATCTTGG	0.552																																					p.S78S		Atlas-SNP	.											.	GPR39	60	.	0			c.G234T						PASS	.						247	222	231					2																	133174849		2203	4300	6503	SO:0001819	synonymous_variant	2863	exon1			TTGCTCGGACATC	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.234G>T	chr2.hg19:g.133174849G>T		45.0	0.0	.		74.0	21.0	.	NM_001508	B2RC12|B6V9G4|Q08AS2|Q53R01	Silent	SNP	ENST00000329321.3	hg19	CCDS2170.1																																																																																			.	.	.	none		0.552	GPR39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254582.1			T	133174849	G	T	133174849	2	4	226	1	0	0	0	0	0	0	0	1	6700	1103	39	4		4	GPR39	2	133174849	Silent	SNP	G	TCGA-MH-A856-01A-11D-A34Z-10	47620465	133174849	110024524	11	13725											
R3HDM1	23518	hgsc.bcm.edu	37	chr2	136467748	136467748	+	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	aaaacaaatattactgtgatCaccagagaggacagaagtgt	18	8	9	6	0	1	3	1	1	0	2	1	5	1	4	1	1	2	0	1	1	6	2	rs143703596		TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr2:136467748C>G	ENST00000264160.4	+	22	2948	c.2578C>G	c.(2578-2580)Cac>Gac	p.H860D	R3HDM1_ENST00000409606.1_Missense_Mutation_p.H861D|R3HDM1_ENST00000409478.1_Missense_Mutation_p.H732D|R3HDM1_ENST00000329971.3_Missense_Mutation_p.H731D|R3HDM1_ENST00000410054.1_Missense_Mutation_p.H805D	NM_001282798.1|NM_015361.2	NP_001269727.1|NP_056176.2	Q15032	R3HD1_HUMAN	R3H domain containing 1	860							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)		TTACTGTGATCACCAGAGAGG	0.413											OREG0014997	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H860D		Atlas-SNP	.											.	R3HDM1	84	.	0			c.C2578G						PASS	.						138	124	129					2																	136467748		2203	4300	6503	SO:0001583	missense	23518	exon22			TGTGATCACCAGA	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.2578C>G	chr2.hg19:g.136467748C>G	ENSP00000264160:p.His860Asp	108.0	0.0	.	1626	88.0	31.0	.	NM_015361	A8K1V0|B3KXQ9|E9PBB4|E9PG42|G5E9G8|Q8IW32	Missense_Mutation	SNP	ENST00000264160.4	hg19	CCDS2177.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	4.899|4.899|4.899	0.167091|0.167091|0.167091	0.09339|0.09339|0.09339	.|.|.	.|.|.	ENSG00000048991|ENSG00000048991|ENSG00000048991	ENST00000409478;ENST00000264160;ENST00000329971;ENST00000410054;ENST00000409606|ENST00000445855|ENST00000429703	T;T;T;T;T|.|.	0.29655|.|.	1.57;1.56;1.57;1.56;1.56|.|.	5.49|5.49|5.49	3.66|3.66|3.66	0.41972|0.41972|0.41972	.|.|.	0.381500|.|.	0.28241|.|.	N|.|.	0.016076|.|.	T|T|.	0.35799|0.35799|.	0.0944|0.0944|.	L|L|L	0.33485|0.33485|0.33485	1.01|1.01|1.01	0.28870|0.28870|0.28870	N|N|N	0.89501|0.89501|0.89501	P;P;P;P|.|.	0.52316|.|.	0.952;0.704;0.651;0.651|.|.	P;B;B;B|.|.	0.49922|.|.	0.626;0.079;0.115;0.058|.|.	T|T|.	0.21759|0.21759|.	-1.0236|-1.0236|.	10|5|.	0.10902|.|.	T|.|.	0.67|.|.	-3.3318|-3.3318|-3.3318	10.1209|10.1209|10.1209	0.42621|0.42621|0.42621	0.1369:0.7911:0.0:0.072|0.1369:0.7911:0.0:0.072|0.1369:0.7911:0.0:0.072	.|.|.	732;861;805;860|.|.	G5E9G8;E9PBB4;E9PG42;Q15032|.|.	.;.;.;R3HD1_HUMAN|.|.	D|M|X	732;860;731;805;861|155|583	ENSP00000386457:H732D;ENSP00000264160:H860D;ENSP00000331396:H731D;ENSP00000386877:H805D;ENSP00000387010:H861D|.|.	ENSP00000264160:H860D|.|.	H|I|S	+|+|+	1|3|2	0|3|0	R3HDM1|R3HDM1|R3HDM1	136184218|136184218|136184218	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	5.896000|5.896000|5.896000	0.69822|0.69822|0.69822	0.652000|0.652000|0.652000	0.30806|0.30806|0.30806	0.650000|0.650000|0.650000	0.86243|0.86243|0.86243	CAC|ATC|TCA	.	C|1.000;T|0.000	.	alt		0.413	R3HDM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254659.1	NM_015361		G	136467748	C	G	136467748	3	3	226	1	0	0	0	0	1	0	0	0	12900	826	29	4	2656	4	R3HDM1	2	136467748	Missense_Mutation	SNP	C	TCGA-MH-A856-01A-11D-A34Z-10	3292899	136467748	106731625	12	13726											
GPR155	151556	hgsc.bcm.edu	37	chr2	175330526	175330526	+	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	aactcacctgtccacaggtaGgtgctatagagggagctgta	11	9	12	9	0	1	1	1	0	0	1	2	2	2	2	2	3	3	4	2	3	5	4			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr2:175330526G>T	ENST00000392552.2	-	7	1609	c.1371C>A	c.(1369-1371)acC>acA	p.T457T	GPR155_ENST00000392551.2_Silent_p.T457T|GPR155_ENST00000295500.4_Silent_p.T457T	NM_001267051.1|NM_152529.6	NP_001253980.1|NP_689742.4	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155	457					cognition (GO:0050890)|intracellular signal transduction (GO:0035556)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.T457T(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	26						TCCACAGGTAGGTGCTATAGA	0.393																																					p.T457T		Atlas-SNP	.											GPR155,NS,carcinoma,0,1	GPR155	76	.	1	Substitution - coding silent(1)	endometrium(1)	c.C1371A						PASS	.						48	51	50					2																	175330526		2203	4300	6503	SO:0001819	synonymous_variant	151556	exon8			CAGGTAGGTGCTA	AY255528	CCDS2259.1, CCDS74605.1	2q31.1	2012-04-10			ENSG00000163328	ENSG00000163328			22951	protein-coding gene	gene with protein product						12679517	Standard	NM_001033045		Approved	DEPDC3, DEP.7, FLJ31819, PGR22	uc002uiu.4	Q7Z3F1	OTTHUMG00000132336	ENST00000392552.2:c.1371C>A	chr2.hg19:g.175330526G>T		203.0	0.0	.		194.0	68.0	.	NM_001033045	B2RCI2|D3DPE2|Q4G0Y6|Q53SJ3|Q53TA8|Q69YG8|Q86SP9|Q8N261|Q8N639|Q8N8K3|Q96MV6	Silent	SNP	ENST00000392552.2	hg19	CCDS2259.1																																																																																			.	.	.	none		0.393	GPR155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255455.1	NM_152529		T	175330526	G	T	175330526	2	4	226	1	0	0	0	0	0	0	0	1	6667	987	35	4		4	GPR155	2	175330526	Silent	SNP	G	TCGA-MH-A856-01A-11D-A34Z-10	38862778	175330526	67868847	13	13727											
PER2	8864	hgsc.bcm.edu	37	chr2	239155118	239155118	+	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	gaaggaatatcttcctcataTggtatgcaaatattaccttt	13	15	6	7	0	2	0	1	0	1	0	3	2	3	1	2	2	2	2	2	2	8	7			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr2:239155118T>A	ENST00000254657.3	-	23	3945	c.3666A>T	c.(3664-3666)ccA>ccT	p.P1222P	PER2_ENST00000254658.3_3'UTR|AC096574.4_ENST00000456601.1_RNA	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	1222	CRY binding domain. {ECO:0000250|UniProtKB:Q9Z301}.				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)		CTTCCTCATATGGTATGCAAA	0.383																																					p.P1222P		Atlas-SNP	.											.	PER2	85	.	0			c.A3666T						PASS	.						94	81	86					2																	239155118		2203	4300	6503	SO:0001819	synonymous_variant	8864	exon23			CTCATATGGTATG	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.3666A>T	chr2.hg19:g.239155118T>A		53.0	0.0	.		68.0	26.0	.	NM_022817	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Silent	SNP	ENST00000254657.3	hg19	CCDS2528.1																																																																																			.	.	.	none		0.383	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817		A	239155118	T	A	239155118	2	1	226	1	0	0	0	0	0	0	0	1	11737	1451	51	5		5	PER2	2	239155118	Silent	SNP	T	TCGA-MH-A856-01A-11D-A34Z-10	63824592	239155118	4044255	14	13728											
KIF1A	547	hgsc.bcm.edu	37	chr2	241686666	241686666	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggtaccttttcaaaatgcTggtcatcaaaggagatttta	12	15	8	6	0	3	1	3	0	0	1	3	2	3	1	1	3	2	2	1	3	5	6			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr2:241686666T>C	ENST00000320389.7	-	27	2905	c.2747A>G	c.(2746-2748)cAg>cGg	p.Q916R	KIF1A_ENST00000498729.2_Missense_Mutation_p.Q1017R	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	916					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)		TTCAAAATGCTGGTCATCAAA	0.557																																					p.Q1017R		Atlas-SNP	.											.	KIF1A	152	.	0			c.A3050G						PASS	.						64	70	68					2																	241686666		1951	4152	6103	SO:0001583	missense	547	exon29			AAATGCTGGTCAT	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.2747A>G	chr2.hg19:g.241686666T>C	ENSP00000322791:p.Gln916Arg	38.0	0.0	.		49.0	18.0	.	NM_001244008	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Missense_Mutation	SNP	ENST00000320389.7	hg19	CCDS46561.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.81|15.81	2.943532|2.943532	0.53079|0.53079	.|.	.|.	ENSG00000130294|ENSG00000130294	ENST00000320389;ENST00000498729;ENST00000373308;ENST00000404283|ENST00000415042	T;T;T|.	0.72282|.	-0.64;-0.64;-0.64|.	4.61|4.61	4.61|4.61	0.57282|0.57282	.|.	0.062457|.	0.64402|.	U|.	0.000004|.	T|T	0.54224|0.54224	0.1845|0.1845	L|L	0.34521|0.34521	1.04|1.04	0.43399|0.43399	D|D	0.99552|0.99552	B;B;P|.	0.37122|.	0.01;0.29;0.583|.	B;B;B|.	0.29077|.	0.014;0.098;0.08|.	T|T	0.51419|0.51419	-0.8708|-0.8708	10|5	0.20519|.	T|.	0.43|.	.|.	12.9905|12.9905	0.58616|0.58616	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1017;1017;916|.	F5H045;Q12756-2;Q12756|.	.;.;KIF1A_HUMAN|.	R|G	916;1017;1017;1017|43	ENSP00000322791:Q916R;ENSP00000438388:Q1017R;ENSP00000384231:Q1017R|.	ENSP00000322791:Q916R|.	Q|S	-|-	2|1	0|0	KIF1A|KIF1A	241335339|241335339	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.876000|0.876000	0.50452|0.50452	4.868000|4.868000	0.63021|0.63021	1.728000|1.728000	0.51552|0.51552	0.383000|0.383000	0.25322|0.25322	CAG|AGC	.	.	.	none		0.557	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483		C	241686666	T	C	241686666	3	2	226	1	0	0	0	0	1	0	0	0	8290	1580	55	3	2409	3	KIF1A	2	241686666	Missense_Mutation	SNP	T	TCGA-MH-A856-01A-11D-A34Z-10	2531548	241686666	1512707	15	13729											
SEMA3F	6405	hgsc.bcm.edu	37	chr3	50222188	50222188	+	Frame_Shift_Del	DEL	T	T	-																															tccctaccgccttaccactaTtgccgtggaccaggtggatg																										TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr3:50222188delT	ENST00000002829.3	+	13	1881	c.1397delT	c.(1396-1398)attfs	p.I466fs	SEMA3F_ENST00000434342.1_Frame_Shift_Del_p.I435fs|SEMA3F_ENST00000413852.1_Frame_Shift_Del_p.I367fs	NM_004186.3	NP_004177.3	Q13275	SEM3F_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F	466	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|negative regulation of axon extension involved in axon guidance (GO:0048843)|nerve development (GO:0021675)|neural crest cell migration (GO:0001755)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	extracellular space (GO:0005615)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|receptor activity (GO:0004872)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	17				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)		CTTACCACTATTGCCGTGGAC	0.652																																					p.I466fs		Atlas-Indel,Pindel	.											.	SEMA3F	62	.	0			c.1396delA						PASS	.						69	58	61					3																	50222188		2203	4299	6502	SO:0001589	frameshift_variant	6405	exon13			.	U33920	CCDS2811.1	3p21.3	2013-01-11			ENSG00000001617	ENSG00000001617		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10728	protein-coding gene	gene with protein product	"sema IV"	601124				8786119, 8649831	Standard	NM_004186		Approved	SEMAK, Sema4	uc003cyj.3	Q13275	OTTHUMG00000156806	ENST00000002829.3:c.1397delT	chr3.hg19:g.50222188delT	ENSP00000002829:p.Ile466fs	66.0	0.0	0		73.0	23.0	0.315068	NM_004186	C9JQ85|Q13274|Q13372|Q15704|Q6GTR4	Frame_Shift_Del	DEL	ENST00000002829.3	hg19	CCDS2811.1																																																																																			.	.	.	none		0.652	SEMA3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345929.1	NM_004186		-	50222188	T	-	50222188	7	5	226	1	0	1	0	1	0	0	0	0	14042	1493	52	0	1443	0	SEMA3F	3	50222188	Frame_Shift_Del	DEL	T	TCGA-MH-A856-01A-11D-A34Z-10		50222188	147800242	16	13730											
CADPS	8618	hgsc.bcm.edu	37	chr3	62535723	62535723	+	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	aggatgcggtcttgttcatcGtcactggcaaatatcacggt	9	12	11	9	3	4	0	3	0	1	0	5	1	4	1	0	4	1	2	0	4	2	3	rs528317538		TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr3:62535723G>A	ENST00000383710.4	-	11	2170	c.1821C>T	c.(1819-1821)gaC>gaT	p.D607D	CADPS_ENST00000357948.3_Silent_p.D607D|CADPS_ENST00000283269.9_Silent_p.D607D	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	607	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)		CTTGTTCATCGTCACTGGCAA	0.552																																					p.D607D		Atlas-SNP	.											.	CADPS	387	.	0			c.C1821T						PASS	.						166	148	154					3																	62535723		2203	4300	6503	SO:0001819	synonymous_variant	8618	exon11			TTCATCGTCACTG	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.1821C>T	chr3.hg19:g.62535723G>A		111.0	0.0	.		136.0	6.0	.	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Silent	SNP	ENST00000383710.4	hg19	CCDS46858.1	.	.	.	.	.	.	.	.	.	.	G	9.080	0.999051	0.19121	.	.	ENSG00000163618	ENST00000478434	.	.	.	4.49	-2.99	0.05497	.	.	.	.	.	T	0.57592	0.2064	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57608	-0.7782	4	.	.	.	.	12.1907	0.54270	0.415:0.0:0.585:0.0	.	.	.	.	M	38	.	.	T	-	2	0	CADPS	62510763	0.985000	0.35326	0.989000	0.46669	0.989000	0.77384	0.352000	0.20113	-0.363000	0.08101	-0.224000	0.12420	ACG	.	.	.	none		0.552	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394		A	62535723	G	A	62535723	2	1	226	1	0	0	0	0	0	0	0	1	2572	1136	40	1		1	CADPS	3	62535723	Silent	SNP	G	TCGA-MH-A856-01A-11D-A34Z-10	12313535	62535723	135486707	17	13731											
EIF4A2	1974	hgsc.bcm.edu	37	chr3	186504962	186504962	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttgtacgagacactgaccaTtacacaggctgttatttttc	10	14	7	10	1	0	2	0	1	0	1	1	3	0	2	1	1	2	3	1	1	3	6	rs34583258		TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr3:186504962T>C	ENST00000323963.5	+	8	882	c.818T>C	c.(817-819)aTt>aCt	p.I273T	RP11-573D15.9_ENST00000577781.1_RNA|SNORA4_ENST00000584302.1_RNA|SNORA63_ENST00000363548.1_RNA|SNORD2_ENST00000459163.1_RNA|EIF4A2_ENST00000440191.2_Missense_Mutation_p.I274T|EIF4A2_ENST00000356531.5_Missense_Mutation_p.I178T|SNORA63_ENST00000363450.1_RNA|SNORA81_ENST00000408493.2_RNA			Q14240	IF4A2_HUMAN	eukaryotic translation initiation factor 4A2	273	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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)		ACACTGACCATTACACAGGCT	0.418			T	BCL6	NHL																																p.I273T		Atlas-SNP	.		Dom	yes		3	3q27.3	1974	"eukaryotic translation initiation factor 4A, isoform 2"		L	.	EIF4A2	55	.	0			c.T818C						PASS	.						117	117	117					3																	186504962		2203	4300	6503	SO:0001583	missense	1974	exon8			TGACCATTACACA	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.818T>C	chr3.hg19:g.186504962T>C	ENSP00000326381:p.Ile273Thr	212.0	0.0	.		165.0	56.0	.	NM_001967	D3DNU9|Q53XJ6|Q96B90|Q96EA8	Missense_Mutation	SNP	ENST00000323963.5	hg19	CCDS3282.1	.	.	.	.	.	.	.	.	.	.	T	15.09	2.729313	0.48833	.	.	ENSG00000156976	ENST00000323963;ENST00000440191;ENST00000356531	T;T;T	0.04654	3.58;3.58;3.58	5.12	5.12	0.69794	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.13586	0.0329	L	0.47078	1.49	0.80722	D	1	D;D;P;B	0.61080	0.989;0.978;0.499;0.366	P;P;B;B	0.62560	0.904;0.828;0.159;0.076	T	0.00293	-1.1841	10	0.87932	D	0	-13.5813	13.1874	0.59688	0.0:0.0:0.0:1.0	.	129;178;274;273	B4DJX6;Q9NZE6;Q14240-2;Q14240	.;.;.;IF4A2_HUMAN	T	273;274;178	ENSP00000326381:I273T;ENSP00000398370:I274T;ENSP00000348925:I178T	ENSP00000326381:I273T	I	+	2	0	EIF4A2	187987656	1.000000	0.71417	0.996000	0.52242	0.736000	0.42039	5.699000	0.68310	2.272000	0.75746	0.460000	0.39030	ATT	.	.	.	none		0.418	EIF4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344609.1	NM_001967		C	186504962	T	C	186504962	3	2	226	1	0	0	0	0	1	0	0	0	5027	1493	52	3	848	3	EIF4A2	3	186504962	Missense_Mutation	SNP	T	TCGA-MH-A856-01A-11D-A34Z-10	123969239	186504962	11517468	18	13732											
LSG1	55341	hgsc.bcm.edu	37	chr3	194366904	194366904	+	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	ttcacttacactgacatagtCcttcaggatgtagcgcgcag	10	11	9	11	2	2	1	2	1	0	0	3	2	3	2	1	1	2	2	1	1	3	5			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr3:194366904C>G	ENST00000265245.5	-	12	1926	c.1612G>C	c.(1612-1614)Gac>Cac	p.D538H	AC046143.3_ENST00000447139.1_RNA	NM_018385.2	NP_060855.2	Q9H089	LSG1_HUMAN	large 60S subunit nuclear export GTPase 1	538					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)		CTGACATAGTCCTTCAGGATG	0.448																																					p.D538H		Atlas-SNP	.											.	LSG1	38	.	0			c.G1612C						PASS	.						217	191	200					3																	194366904		2203	4300	6503	SO:0001583	missense	55341	exon12			CATAGTCCTTCAG		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.1612G>C	chr3.hg19:g.194366904C>G	ENSP00000265245:p.Asp538His	97.0	0.0	.		112.0	48.0	.	NM_018385	A0JLT4|A0PJK3|A6NI18|Q7L9H8|Q9NUK8	Missense_Mutation	SNP	ENST00000265245.5	hg19	CCDS33922.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.0|21.0	4.082680|4.082680	0.76528|0.76528	.|.	.|.	ENSG00000041802|ENSG00000041802	ENST00000265245|ENST00000437613	T|.	0.26810|.	1.71|.	5.58|5.58	5.58|5.58	0.84498|0.84498	GTP-binding protein, orthogonal bundle domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.84224|0.84224	0.5425|0.5425	M|M	0.87827|0.87827	2.91|2.91	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	D|D	0.85647|0.85647	0.1280|0.1280	10|5	0.62326|.	D|.	0.03|.	.|.	19.5831|19.5831	0.95478|0.95478	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	538|.	Q9H089|.	LSG1_HUMAN|.	H|S	538|254	ENSP00000265245:D538H|.	ENSP00000265245:D538H|.	D|R	-|-	1|3	0|2	LSG1|LSG1	195848193|195848193	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.451000|0.451000	0.32288|0.32288	7.783000|7.783000	0.85696|0.85696	2.641000|2.641000	0.89580|0.89580	0.563000|0.563000	0.77884|0.77884	GAC|AGG	.	.	.	none		0.448	LSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342740.1	NM_018385		G	194366904	C	G	194366904	3	3	226	1	0	0	0	0	1	0	0	0	9056	855	30	4	376	4	LSG1	3	194366904	Missense_Mutation	SNP	C	TCGA-MH-A856-01A-11D-A34Z-10	7861942	194366904	3655526	19	13733											
RGS12	6002	hgsc.bcm.edu	37	chr4	3418678	3418678	+	Missense_Mutation	SNP	T	T	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	tttgatagctacactcgcttTctgaagtccccgctgtacca	8	13	7	13	2	1	2	0	2	1	0	3	2	2	2	3	0	3	4	3	0	4	5			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr4:3418678T>G	ENST00000344733.5	+	8	3370	c.2466T>G	c.(2464-2466)ttT>ttG	p.F822L	RGS12_ENST00000543385.1_3'UTR|RGS12_ENST00000382788.3_Missense_Mutation_p.F822L|RGS12_ENST00000338806.4_Missense_Mutation_p.F174L|RGS12_ENST00000538395.1_Missense_Mutation_p.F164L|RGS12_ENST00000508158.1_3'UTR|RGS12_ENST00000336727.3_Missense_Mutation_p.F822L|RGS12_ENST00000306648.7_Missense_Mutation_p.F220L	NM_198229.2	NP_937872.1	O14924	RGS12_HUMAN	regulator of G-protein signaling 12	822	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				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)		ACACTCGCTTTCTGAAGTCCC	0.587																																					p.F822L		Atlas-SNP	.											.	RGS12	128	.	0			c.T2466G						PASS	.						79	81	80					4																	3418678		2203	4300	6503	SO:0001583	missense	6002	exon8			TCGCTTTCTGAAG	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.2466T>G	chr4.hg19:g.3418678T>G	ENSP00000339381:p.Phe822Leu	109.0	0.0	.		88.0	30.0	.	NM_002926	B1AQ30|B1AQ31|B1AQ32|B7Z764|E7EMN9|O14922|O14923|O43510|O75338|Q147X0|Q8WX95	Missense_Mutation	SNP	ENST00000344733.5	hg19	CCDS3366.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.249521	0.80024	.	.	ENSG00000159788	ENST00000344733;ENST00000336727;ENST00000382788;ENST00000306648;ENST00000338806;ENST00000538395	T;T;T;T;T;T	0.11495	2.77;2.77;2.77;2.77;2.77;2.77	4.5	-5.97	0.02227	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);	0.000000	0.85682	D	0.000000	T	0.36717	0.0977	H	0.94503	3.545	0.53688	D	0.99997	P;D;D;D;P;D;P;P;P	0.89917	0.947;0.966;1.0;0.966;0.889;0.985;0.947;0.798;0.759	P;P;D;P;P;D;P;P;P	0.97110	0.869;0.785;1.0;0.785;0.841;0.954;0.908;0.847;0.762	T	0.55811	-0.8082	10	0.87932	D	0	-21.6848	13.8554	0.63524	0.0:0.5296:0.0:0.4704	.	164;21;164;21;164;174;220;822;822	B7Z764;B3KVS7;B7Z8B8;A8K440;O14924-2;O14924-3;Q8WX95;O14924;O14924-4	.;.;.;.;.;.;.;RGS12_HUMAN;.	L	822;822;822;220;174;164	ENSP00000339381:F822L;ENSP00000338509:F822L;ENSP00000372238:F822L;ENSP00000304459:F220L;ENSP00000342133:F174L;ENSP00000438888:F164L	ENSP00000304459:F220L	F	+	3	2	RGS12	3388476	0.983000	0.35010	0.632000	0.29296	0.673000	0.39480	0.177000	0.16801	-1.100000	0.03030	-0.315000	0.08773	TTT	.	.	.	none		0.587	RGS12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206602.1	NM_002926		G	3418678	T	G	3418678	3	3	226	1	0	0	0	0	1	0	0	0	13308	1780	62	5	2550	5	RGS12	4	3418678	Missense_Mutation	SNP	T	TCGA-MH-A856-01A-11D-A34Z-10		3418678	187735598	20	13734											
SLC34A2	10568	hgsc.bcm.edu	37	chr4	25664375	25664375	+	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	gattgaacttctgccgtcctActccacggctacactgatag	9	11	8	13	2	1	2	0	2	1	0	3	3	3	2	3	1	4	1	3	1	4	5			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr4:25664375A>T	ENST00000382051.3	+	3	211	c.161A>T	c.(160-162)tAc>tTc	p.Y54F	SLC34A2_ENST00000503434.1_Missense_Mutation_p.Y53F|SLC34A2_ENST00000504570.1_Missense_Mutation_p.Y53F	NM_001177998.1|NM_006424.2	NP_001171469.1|NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 2	54					aging (GO:0007568)|cellular phosphate ion homeostasis (GO:0030643)|in utero embryonic development (GO:0001701)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|response to fructose (GO:0009750)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	phosphate ion binding (GO:0042301)|sodium ion binding (GO:0031402)|sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)		SLC34A2/ROS1(14)	breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(4)	41		Breast(46;0.0503)				CTGCCGTCCTACTCCACGGCT	0.517			T	ROS1	NSCLC																																p.Y54F		Atlas-SNP	.		Dom	yes		4	4p15.2	10568	"solute carrier family 34 (sodium phosphate), member 2"		E	.	SLC34A2	93	.	0			c.A161T						PASS	.						138	137	137					4																	25664375		2203	4300	6503	SO:0001583	missense	10568	exon3			CGTCCTACTCCAC	AF111856	CCDS3435.1, CCDS54750.1	4p15.2	2013-07-17	2013-07-17		ENSG00000157765	ENSG00000157765		"Solute carriers"	11020	protein-coding gene	gene with protein product		604217	"solute carrier family 34 (sodium phosphate), member 2"			10329428, 10610722	Standard	NM_006424		Approved	NAPI-3B	uc003grr.3	O95436	OTTHUMG00000097757	ENST00000382051.3:c.161A>T	chr4.hg19:g.25664375A>T	ENSP00000371483:p.Tyr54Phe	109.0	0.0	.		96.0	28.0	.	NM_006424	A5PL17|Q8N2K2|Q8WYA9|Q9P0V7	Missense_Mutation	SNP	ENST00000382051.3	hg19	CCDS3435.1	.	.	.	.	.	.	.	.	.	.	A	11.85	1.760566	0.31137	.	.	ENSG00000157765	ENST00000513204;ENST00000504570;ENST00000382051;ENST00000503434;ENST00000507530	T;T;T;T;T	0.55930	0.49;1.93;1.93;1.93;0.49	5.45	1.6	0.23607	.	0.529195	0.21573	N	0.072361	T	0.40956	0.1138	L	0.56769	1.78	0.09310	N	0.999994	B;B	0.14012	0.007;0.009	B;B	0.13407	0.009;0.004	T	0.25710	-1.0124	10	0.22706	T	0.39	-9.0718	4.4856	0.11788	0.6159:0.0:0.14:0.2441	.	53;54	O95436-2;O95436	.;NPT2B_HUMAN	F	53;53;54;53;54	ENSP00000423038:Y53F;ENSP00000425501:Y53F;ENSP00000371483:Y54F;ENSP00000423021:Y53F;ENSP00000424266:Y54F	ENSP00000371483:Y54F	Y	+	2	0	SLC34A2	25273473	0.137000	0.22531	0.004000	0.12327	0.176000	0.22953	1.990000	0.40717	0.052000	0.16007	0.528000	0.53228	TAC	.	.	.	none		0.517	SLC34A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214990.1	NM_006424		T	25664375	A	T	25664375	3	4	226	1	0	0	0	0	1	0	0	0	14581	391	14	5	167	5	SLC34A2	4	25664375	Missense_Mutation	SNP	A	TCGA-MH-A856-01A-11D-A34Z-10	22245697	25664375	165489901	21	13735											
KDR	3791	hgsc.bcm.edu	37	chr4	55979601	55979601	+	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	aaaaatttcttcatctcactCccagactgggtttttaggtc	10	15	6	10	0	3	1	2	0	2	1	6	1	4	1	1	2	0	1	1	2	3	5			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr4:55979601C>T	ENST00000263923.4	-	7	1141	c.846G>A	c.(844-846)ggG>ggA	p.G282G		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	282	Ig-like C2-type 3.				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)	TCATCTCACTCCCAGACTGGG	0.428			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)																											p.G282G		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	.	KDR	307	.	0			c.G846A						PASS	.						143	136	138					4																	55979601		2203	4300	6503	SO:0001819	synonymous_variant	3791	exon7			CTCACTCCCAGAC	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.846G>A	chr4.hg19:g.55979601C>T		133.0	0.0	.		134.0	53.0	.	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Silent	SNP	ENST00000263923.4	hg19	CCDS3497.1																																																																																			.	.	.	none		0.428	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			T	55979601	C	T	55979601	2	4	226	1	0	0	0	0	0	0	0	1	8146	842	30	2		2	KDR	4	55979601	Silent	SNP	C	TCGA-MH-A856-01A-11D-A34Z-10	30315226	55979601	135174675	22	13736											
C4orf32	132720	hgsc.bcm.edu	37	chr4	113066846	113066846	+	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	gaccgggtgggatcccggggCgagcccgcggcggcgcggac	4	2	21	14	8	0	0	0	0	0	0	1	4	1	2	3	7	1	0	3	7	0	0			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr4:113066846C>A	ENST00000309733.5	+	1	294	c.110C>A	c.(109-111)gCg>gAg	p.A37E		NM_152400.2	NP_689613.1	Q8N8J7	CD032_HUMAN	chromosome 4 open reading frame 32	37						integral component of membrane (GO:0016021)							Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.00198)		gatcccggggcgagcccgcgg	0.831																																					p.A37E		Atlas-SNP	.											.	C4orf32	6	.	0			c.C110A						PASS	.						2	4	4					4																	113066846		1213	2632	3845	SO:0001583	missense	132720	exon1			CCGGGGCGAGCCC	AK096689	CCDS3695.1	4q25	2008-02-05			ENSG00000174749	ENSG00000174749			26813	protein-coding gene	gene with protein product						12477932	Standard	NM_152400		Approved	FLJ39370	uc003iah.2	Q8N8J7	OTTHUMG00000132851	ENST00000309733.5:c.110C>A	chr4.hg19:g.113066846C>A	ENSP00000310182:p.Ala37Glu	3.0	0.0	.		12.0	9.0	.	NM_152400	Q49A91|Q4W5C7|Q8TBF9	Missense_Mutation	SNP	ENST00000309733.5	hg19	CCDS3695.1	.	.	.	.	.	.	.	.	.	.	C	15.27	2.783857	0.49891	.	.	ENSG00000174749	ENST00000309733	T	0.52526	0.66	3.18	1.33	0.21861	.	0.896444	0.09366	U	0.812075	T	0.36110	0.0955	L	0.44542	1.39	0.27426	N	0.954157	B	0.11235	0.004	B	0.16289	0.015	T	0.33137	-0.9880	10	0.45353	T	0.12	-0.8497	3.6435	0.08176	0.2659:0.5956:0.0:0.1385	.	37	Q8N8J7	CD032_HUMAN	E	37	ENSP00000310182:A37E	ENSP00000310182:A37E	A	+	2	0	C4orf32	113286295	0.732000	0.28121	0.982000	0.44146	0.008000	0.06430	0.121000	0.15667	0.147000	0.19030	0.305000	0.20034	GCG	.	.	.	none		0.831	C4orf32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256325.2	NM_152400		A	113066846	C	A	113066846	3	1	226	1	0	0	0	0	1	0	0	0	2264	768	27	4	112	4	C4orf32	4	113066846	Missense_Mutation	SNP	C	TCGA-MH-A856-01A-11D-A34Z-10	57087245	113066846	78087430	23	13737											
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123236769	123236769	+	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	aagacatagatgacattgctGacttaaattcagtgaacata	17	11	7	6	0	1	5	1	3	0	2	1	5	1	5	0	0	2	1	0	0	6	5			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr4:123236769G>A	ENST00000264501.4	+	61	10838	c.10465G>A	c.(10465-10467)Gac>Aac	p.D3489N	KIAA1109_ENST00000455637.1_Missense_Mutation_p.D3489N|KIAA1109_ENST00000388738.3_Missense_Mutation_p.D3489N			Q2LD37	K1109_HUMAN	KIAA1109	3489					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.D3489N(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						TGACATTGCTGACTTAAATTC	0.393																																					p.D3489N		Atlas-SNP	.											KIAA1109,NS,carcinoma,0,1	KIAA1109	424	.	1	Substitution - Missense(1)	lung(1)	c.G10465A						PASS	.						172	157	162					4																	123236769		1989	4174	6163	SO:0001583	missense	84162	exon59			ATTGCTGACTTAA	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.10465G>A	chr4.hg19:g.123236769G>A	ENSP00000264501:p.Asp3489Asn	103.0	0.0	.		114.0	44.0	.	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.	.	.	.	.	.	.	.	.	.	G	35	5.483944	0.96307	.	.	ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637;ENST00000438707;ENST00000421930	T;T;T;T	0.43294	2.43;2.43;1.84;0.95	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.60637	0.2284	L	0.51422	1.61	0.80722	D	1	D;D	0.67145	0.996;0.993	D;D	0.79784	0.993;0.984	T	0.57124	-0.7865	10	0.42905	T	0.14	.	19.379	0.94523	0.0:0.0:1.0:0.0	.	3489;3489	Q2LD37-6;Q2LD37	.;K1109_HUMAN	N	3489;3489;3489;105;63	ENSP00000264501:D3489N;ENSP00000373390:D3489N;ENSP00000389925:D3489N;ENSP00000410874:D105N	ENSP00000264501:D3489N	D	+	1	0	KIAA1109	123456219	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.787000	0.99055	2.653000	0.90120	0.650000	0.86243	GAC	.	.	.	none		0.393	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		A	123236769	G	A	123236769	3	1	226	1	0	0	0	0	1	0	0	0	8215	1290	45	2	10699	2	KIAA1109	4	123236769	Missense_Mutation	SNP	G	TCGA-MH-A856-01A-11D-A34Z-10	10169923	123236769	67917507	24	13738											
PHF17	79960	hgsc.bcm.edu	37	chr4	129793111	129793111	+	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	gtcaaagtgcctacaacaccTgccagcccagtgaaaaactg	14	6	8	13	0	1	1	1	1	0	0	1	1	1	1	4	0	6	0	4	0	5	1			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr4:129793111T>A	ENST00000226319.6	+	11	2503	c.2223T>A	c.(2221-2223)ccT>ccA	p.P741P	PHF17_ENST00000512960.1_Silent_p.P741P|PHF17_ENST00000452328.2_Silent_p.P729P	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						CTACAACACCTGCCAGCCCAG	0.547																																					p.P741P		Atlas-SNP	.											.	PHF17	63	.	0			c.T2223A						PASS	.						34	38	36					4																	129793111		2203	4299	6502	SO:0001819	synonymous_variant	79960	exon11			AACACCTGCCAGC																												ENST00000226319.6:c.2223T>A	chr4.hg19:g.129793111T>A		48.0	0.0	.		83.0	32.0	.	NM_199320		Silent	SNP	ENST00000226319.6	hg19	CCDS34062.1																																																																																			.	.	.	none		0.547	PHF17-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364280.1			A	129793111	T	A	129793111	2	1	226	1	0	0	0	0	0	0	0	1	11835	1567	55	5		5	PHF17	4	129793111	Silent	SNP	T	TCGA-MH-A856-01A-11D-A34Z-10	6556342	129793111	61361165	25	13739											
TARS	6897	hgsc.bcm.edu	37	chr5	33441209	33441209	+	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	gccaatgtttgaggagaaggCcagcagtccttcagggaaga	12	7	14	8	0	1	3	1	1	0	2	2	5	2	4	3	3	1	2	3	3	3	2			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr5:33441209C>A	ENST00000265112.3	+	1	328	c.17C>A	c.(16-18)gCc>gAc	p.A6D	TARS_ENST00000455217.2_Missense_Mutation_p.A6D|CTD-2203K17.1_ENST00000507251.1_RNA|TARS_ENST00000414361.2_5'UTR|TARS_ENST00000541634.1_5'UTR|TARS_ENST00000502553.1_Missense_Mutation_p.A6D	NM_152295.4	NP_689508.3	P26639	SYTC_HUMAN	threonyl-tRNA synthetase	6					gene expression (GO:0010467)|threonyl-tRNA aminoacylation (GO:0006435)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|threonine-tRNA ligase activity (GO:0004829)			NS(1)|biliary_tract(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)	29					L-Threonine(DB00156)	GAGGAGAAGGCCAGCAGTCCT	0.612																																					p.A6D		Atlas-SNP	.											.	TARS	66	.	0			c.C17A						PASS	.						86	74	78					5																	33441209		2203	4300	6503	SO:0001583	missense	6897	exon1			AGAAGGCCAGCAG	AK095852	CCDS3899.1, CCDS58943.1	5p13.2	2012-10-02			ENSG00000113407	ENSG00000113407	6.1.1.3	"Aminoacyl tRNA synthetases / Class II"	11572	protein-coding gene	gene with protein product	"threonine tRNA ligase 1, cytoplasmic"	187790					Standard	NM_152295		Approved		uc011coc.3	P26639	OTTHUMG00000090683	ENST00000265112.3:c.17C>A	chr5.hg19:g.33441209C>A	ENSP00000265112:p.Ala6Asp	82.0	0.0	.		61.0	28.0	.	NM_152295	A8K8I1|B4DEG8|Q96FP5|Q9BWA6	Missense_Mutation	SNP	ENST00000265112.3	hg19	CCDS3899.1	.	.	.	.	.	.	.	.	.	.	C	13.52	2.262597	0.39995	.	.	ENSG00000113407	ENST00000502553;ENST00000514259;ENST00000265112;ENST00000455217	T;T;T;T	0.48836	0.9;0.8;0.9;0.81	4.74	0.646	0.17789	.	0.527644	0.20999	N	0.081888	T	0.23370	0.0565	N	0.16478	0.41	0.21020	N	0.999804	B	0.24721	0.11	B	0.22386	0.039	T	0.08932	-1.0698	10	0.27082	T	0.32	-7.084	2.7791	0.05356	0.3274:0.4217:0.1591:0.0918	.	6	P26639	SYTC_HUMAN	D	6	ENSP00000424387:A6D;ENSP00000422130:A6D;ENSP00000265112:A6D;ENSP00000387710:A6D	ENSP00000265112:A6D	A	+	2	0	TARS	33476966	0.001000	0.12720	0.003000	0.11579	0.663000	0.39108	-0.265000	0.08644	-0.003000	0.14444	0.591000	0.81541	GCC	.	.	.	none		0.612	TARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207367.1	NM_152295		A	33441209	C	A	33441209	3	1	226	1	0	0	0	0	1	0	0	0	15571	739	26	4	19	4	TARS	5	33441209	Missense_Mutation	SNP	C	TCGA-MH-A856-01A-11D-A34Z-10		33441209	147474051	26	13740											
MOCS2	4338	hgsc.bcm.edu	37	chr5	52396318	52396318	+	Frame_Shift_Del	DEL	C	C	-																															aagagatgcagctctgtgggCtgaggacacagcaatgatta																										TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr5:52396318delC	ENST00000396954.3	-	6	1101	c.424delG	c.(424-426)gccfs	p.A142fs	MOCS2_ENST00000361377.4_3'UTR|MOCS2_ENST00000510818.2_Splice_Site|MOCS2_ENST00000582677.1_3'UTR|MOCS2_ENST00000527216.1_3'UTR|MOCS2_ENST00000508922.1_Intron|MOCS2_ENST00000584946.1_3'UTR|MOCS2_ENST00000450852.3_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)				GCTCTGTGGGCTGAGGACACA	0.393																																					p.A142fs		Atlas-Indel,Pindel	.											.	MOCS2	28	.	0			c.425delC						PASS	.						80	80	80					5																	52396318		2203	4300	6503	SO:0001589	frameshift_variant	4338	exon6			.	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.424delG	chr5.hg19:g.52396318delC	ENSP00000380157:p.Ala142fs	121.0	0.0	0		165.0	57.0	0.345455	NM_004531		Frame_Shift_Del	DEL	ENST00000396954.3	hg19	CCDS3958.1																																																																																			.	.	.	none		0.393	MOCS2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214053.3	NM_183418		-	52396318	C	-	52396318	7	5	226	1	0	1	0	1	0	0	0	0	9698	797	28	0	150	0	MOCS2	5	52396318	Frame_Shift_Del	DEL	C	TCGA-MH-A856-01A-11D-A34Z-10	18955109	52396318	128518942	27	13741											
EPB41L4A	64097	hgsc.bcm.edu	37	chr5	111594984	111594984	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagtgaacctttgtaatcCgaggcctaaaaaacaaagca	17	8	8	8	1	0	2	0	2	0	0	1	3	1	2	3	1	3	2	3	1	7	3	rs539290653		TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr5:111594984C>T	ENST00000261486.5	-	9	1013	c.737G>A	c.(736-738)cGg>cAg	p.R246Q	RP11-526F3.1_ENST00000504004.1_RNA	NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	246	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)		p.R246L(2)|p.R246Q(1)		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)		CTTTGTAATCCGAGGCCTAAA	0.393													C|||	1	0.000199681	0	0	5008	,	,		20668	0		0	False		,,,				2504	0.001				p.R246Q		Atlas-SNP	.											EPB41L4A,caecum,carcinoma,0,5	EPB41L4A	130	.	3	Substitution - Missense(3)	lung(2)|haematopoietic_and_lymphoid_tissue(1)	c.G737A						PASS	.						148	130	136					5																	111594984		1807	4092	5899	SO:0001583	missense	64097	exon9			GTAATCCGAGGCC	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.737G>A	chr5.hg19:g.111594984C>T	ENSP00000261486:p.Arg246Gln	56.0	0.0	.		73.0	33.0	.	NM_022140	A4FUI6	Missense_Mutation	SNP	ENST00000261486.5	hg19	CCDS43350.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.046182	0.93740	.	.	ENSG00000129595	ENST00000261486	D	0.82081	-1.57	5.28	5.28	0.74379	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	D	0.87830	0.6276	M	0.64997	1.995	0.40889	D	0.984053	D	0.69078	0.997	P	0.55545	0.778	D	0.89465	0.3739	10	0.87932	D	0	.	18.0454	0.89330	0.0:1.0:0.0:0.0	.	246	Q9HCS5	E41LA_HUMAN	Q	246	ENSP00000261486:R246Q	ENSP00000261486:R246Q	R	-	2	0	EPB41L4A	111622883	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.751000	0.68720	2.644000	0.89710	0.655000	0.94253	CGG	.	.	.	none		0.393	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1			T	111594984	C	T	111594984	3	4	226	1	0	0	0	0	1	0	0	0	5157	652	23	1	1383	1	EPB41L4A	5	111594984	Missense_Mutation	SNP	C	TCGA-MH-A856-01A-11D-A34Z-10	59198666	111594984	69320276	28	13742											
TRIM31	11074	hgsc.bcm.edu	37	chr6	30072974	30072974	+	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	tgtcatttttattcatgcttTtgaagaatctgttttcatct	8	22	5	6	0	5	2	3	1	2	1	5	2	5	2	0	0	1	2	0	0	3	8			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr6:30072974T>A	ENST00000376734.3	-	7	1054	c.929A>T	c.(928-930)aAa>aTa	p.K310I	TRIM31_ENST00000485864.1_5'UTR|TRIM31-AS1_ENST00000440874.1_RNA|TRIM31_ENST00000540829.1_Missense_Mutation_p.K310I	NM_007028.3	NP_008959.3	Q9BZY9	TRI31_HUMAN	tripartite motif containing 31	310					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral release from host cell (GO:1902186)	mitochondrion (GO:0005739)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(2)	15						ATTCATGCTTTTGAAGAATCT	0.413																																					p.K310I		Atlas-SNP	.											.	TRIM31	40	.	0			c.A929T						PASS	.						181	181	181					6																	30072974		1511	2709	4220	SO:0001583	missense	11074	exon7			ATGCTTTTGAAGA	AF230386	CCDS34374.1	6p21.3	2013-01-09	2011-01-25		ENSG00000204616	ENSG00000204616		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16289	protein-coding gene	gene with protein product		609316	"tripartite motif-containing 31"			11331580	Standard	XM_006714977		Approved	RNF, HCGI, C6orf13, HCG1	uc003npg.1	Q9BZY9	OTTHUMG00000031064	ENST00000376734.3:c.929A>T	chr6.hg19:g.30072974T>A	ENSP00000365924:p.Lys310Ile	190.0	0.0	.		171.0	59.0	.	NM_007028	A6NLX6|A9R9Q4|Q53H52|Q5RI37|Q5SRJ7|Q5SRJ8|Q5SS28|Q96AK4|Q96AP8|Q99579|Q9BZY8	Missense_Mutation	SNP	ENST00000376734.3	hg19	CCDS34374.1	.	.	.	.	.	.	.	.	.	.	T	12.66	2.004393	0.35320	.	.	ENSG00000204616	ENST00000376734;ENST00000376728;ENST00000540829	T;T	0.68331	-0.32;-0.32	4.05	-2.76	0.05896	.	.	.	.	.	T	0.19685	0.0473	N	0.14661	0.345	0.09310	N	1	P	0.46020	0.871	B	0.39935	0.314	T	0.14839	-1.0458	9	0.18710	T	0.47	.	5.621	0.17457	0.0:0.492:0.1825:0.3254	.	310	Q9BZY9	TRI31_HUMAN	I	310	ENSP00000365924:K310I;ENSP00000444311:K310I	ENSP00000365918:K310I	K	-	2	0	TRIM31	30180953	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.376000	0.07465	-0.375000	0.07955	-0.517000	0.04412	AAA	.	.	.	none		0.413	TRIM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076081.2			A	30072974	T	A	30072974	3	1	226	1	0	0	0	0	1	0	0	0	16517	1841	64	5	360	5	TRIM31	6	30072974	Missense_Mutation	SNP	T	TCGA-MH-A856-01A-11D-A34Z-10		30072974	141042093	29	13743											
COL11A2	1302	hgsc.bcm.edu	37	chr6	33137181	33137181	+	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	gggttccctttggggccatcAtcgcctgtggggcctttagg	3	12	15	11	1	1	0	1	0	0	0	3	0	2	0	4	6	0	1	4	6	1	4			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr6:33137181A>T	ENST00000374708.4	-	49	3777	c.3519T>A	c.(3517-3519)gaT>gaA	p.D1173E	COL11A2_ENST00000374712.1_Missense_Mutation_p.D1178E|COL11A2_ENST00000361917.1_Missense_Mutation_p.D1152E|COL11A2_ENST00000374713.1_Missense_Mutation_p.D1212E|COL11A2_ENST00000357486.1_Missense_Mutation_p.D1238E|COL11A2_ENST00000477772.1_Intron|COL11A2_ENST00000395197.1_Missense_Mutation_p.D1199E|COL11A2_ENST00000341947.2_Missense_Mutation_p.D1259E|COL11A2_ENST00000374714.1_Missense_Mutation_p.D1233E	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	1259	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						TGGGGCCATCATCGCCTGTGG	0.627																																					p.D1259E	Melanoma(1;90 116 3946 5341 17093)	Atlas-SNP	.											.	COL11A2	124	.	0			c.T3777A						PASS	.						47	42	44					6																	33137181		1510	2707	4217	SO:0001583	missense	1302	exon51			GCCATCATCGCCT	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.3519T>A	chr6.hg19:g.33137181A>T	ENSP00000363840:p.Asp1173Glu	31.0	0.0	.		17.0	8.0	.	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Missense_Mutation	SNP	ENST00000374708.4	hg19	CCDS43452.1	.	.	.	.	.	.	.	.	.	.	A	10.24	1.295457	0.23564	.	.	ENSG00000204248	ENST00000374708;ENST00000341947;ENST00000357486;ENST00000374714;ENST00000374713;ENST00000395197;ENST00000374712;ENST00000361917	D;D;D;D;D;D;D;D	0.94138	-3.36;-3.23;-3.23;-3.23;-3.36;-3.36;-3.36;-3.36	4.88	-5.47	0.02600	.	0.000000	0.85682	D	0.000000	D	0.84665	0.5522	N	0.05230	-0.09	0.48762	D	0.999704	D;D;D	0.61697	0.99;0.99;0.984	D;D;D	0.75484	0.986;0.986;0.967	D	0.84632	0.0690	10	0.23891	T	0.37	.	13.4632	0.61239	0.4166:0.0:0.5834:0.0	.	1152;1173;1259	P13942-8;P13942-6;P13942	.;.;COBA2_HUMAN	E	1173;1259;1238;1233;1212;1199;1178;1152	ENSP00000363840:D1173E;ENSP00000339915:D1259E;ENSP00000350079:D1238E;ENSP00000363846:D1233E;ENSP00000363845:D1212E;ENSP00000378623:D1199E;ENSP00000363844:D1178E;ENSP00000355123:D1152E	ENSP00000339915:D1259E	D	-	3	2	COL11A2	33245159	0.628000	0.27138	0.139000	0.22197	0.512000	0.34134	-0.096000	0.11059	-1.298000	0.02348	-0.398000	0.06409	GAT	.	.	.	none		0.627	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2			T	33137181	A	T	33137181	3	4	226	1	0	0	0	0	1	0	0	0	3670	214	8	5	1497	5	COL11A2	6	33137181	Missense_Mutation	SNP	A	TCGA-MH-A856-01A-11D-A34Z-10	3064207	33137181	137977886	30	13744											
FOXP4	116113	hgsc.bcm.edu	37	chr6	41553179	41553179	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acccccccagctacaggagtActacaagaagcagcaggagc	14	3	10	14	0	0	1	0	0	0	1	0	3	0	3	3	2	7	4	3	2	5	3			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr6:41553179A>G	ENST00000307972.4	+	4	446	c.434A>G	c.(433-435)tAc>tGc	p.Y145C	FOXP4_ENST00000373057.3_Missense_Mutation_p.Y143C|FOXP4_ENST00000373063.3_Missense_Mutation_p.Y145C|FOXP4_ENST00000373060.1_Missense_Mutation_p.Y145C|FOXP4_ENST00000409208.1_Missense_Mutation_p.Y145C			Q8IVH2	FOXP4_HUMAN	forkhead box P4	145	Gln-rich.				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)					CTACAGGAGTACTACAAGAAG	0.637																																					p.Y145C		Atlas-SNP	.											.	FOXP4	83	.	0			c.A434G						PASS	.						58	50	53					6																	41553179		2203	4300	6503	SO:0001583	missense	116113	exon5			AGGAGTACTACAA	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.434A>G	chr6.hg19:g.41553179A>G	ENSP00000309823:p.Tyr145Cys	110.0	0.0	.		100.0	30.0	.	NM_138457	Q5W098|Q7Z7F8|Q8IW55|Q96E19	Missense_Mutation	SNP	ENST00000307972.4	hg19	CCDS34447.1	.	.	.	.	.	.	.	.	.	.	A	17.48	3.401051	0.62288	.	.	ENSG00000137166	ENST00000373060;ENST00000373063;ENST00000409208;ENST00000373057;ENST00000307972	T;D;T;T;T	0.90620	1.32;-2.7;1.32;1.32;1.32	4.94	4.94	0.65067	.	0.000000	0.64402	D	0.000001	D	0.89462	0.6722	L	0.57536	1.79	0.47308	D	0.999388	D;D;D	0.67145	0.996;0.996;0.996	P;P;P	0.54372	0.75;0.75;0.75	D	0.90770	0.4671	10	0.72032	D	0.01	.	11.009	0.47652	0.8606:0.0:0.0:0.1394	.	145;143;145	Q8IW55;Q7Z7F8;Q8IVH2	.;.;FOXP4_HUMAN	C	145;145;145;143;145	ENSP00000362151:Y145C;ENSP00000362154:Y145C;ENSP00000386958:Y145C;ENSP00000362148:Y143C;ENSP00000309823:Y145C	ENSP00000309823:Y145C	Y	+	2	0	FOXP4	41661157	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	2.189000	0.42621	1.856000	0.53863	0.454000	0.30748	TAC	.	.	.	none		0.637	FOXP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106767.1	NM_138457		G	41553179	A	G	41553179	3	3	226	1	0	0	0	0	1	0	0	0	6036	391	14	3	448	3	FOXP4	6	41553179	Missense_Mutation	SNP	A	TCGA-MH-A856-01A-11D-A34Z-10	8415998	41553179	129561888	31	13745											
XPO5	57510	hgsc.bcm.edu	37	chr6	43499248	43499248	+	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	gagggtagagaagaaacgctGcattctttccaagacggttt	12	10	12	7	2	1	3	0	0	1	3	2	5	2	3	1	2	2	4	1	2	4	4			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr6:43499248G>T	ENST00000265351.7	-	22	2719	c.2509C>A	c.(2509-2511)Cag>Aag	p.Q837K		NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	837					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)			AAGAAACGCTGCATTCTTTCC	0.433																																					p.Q837K		Atlas-SNP	.											.	XPO5	79	.	0			c.C2509A						PASS	.						137	127	130					6																	43499248		1895	4125	6020	SO:0001583	missense	57510	exon22			AACGCTGCATTCT	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.2509C>A	chr6.hg19:g.43499248G>T	ENSP00000265351:p.Gln837Lys	115.0	0.0	.		105.0	40.0	.	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Missense_Mutation	SNP	ENST00000265351.7	hg19	CCDS47430.1	.	.	.	.	.	.	.	.	.	.	G	32	5.191726	0.94923	.	.	ENSG00000124571	ENST00000265351;ENST00000436943;ENST00000372258;ENST00000439465	T	0.66099	-0.19	5.61	5.61	0.85477	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.72137	0.3423	M	0.64567	1.98	0.80722	D	1	D	0.69078	0.997	D	0.73380	0.98	T	0.68652	-0.5352	10	0.39692	T	0.17	-16.0687	18.182	0.89781	0.0:0.0:1.0:0.0	.	837	Q9HAV4	XPO5_HUMAN	K	837;542;377;465	ENSP00000265351:Q837K	ENSP00000265351:Q837K	Q	-	1	0	XPO5	43607226	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.420000	0.97426	2.793000	0.96121	0.655000	0.94253	CAG	.	.	.	none		0.433	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750		T	43499248	G	T	43499248	3	4	226	1	0	0	0	0	1	0	0	0	17459	1328	46	4	1149	4	XPO5	6	43499248	Missense_Mutation	SNP	G	TCGA-MH-A856-01A-11D-A34Z-10	1946069	43499248	127615819	32	13746											
ARG1	383	hgsc.bcm.edu	37	chr6	131903762	131903762	+	Splice_Site	DEL	T	T	-																															gaaaacattgtaattttagaTtcccgatgtgccaggattct																								rs200319835		TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr6:131903762delT	ENST00000368087.3	+	5	606	c.467delT	c.(466-468)att>at	p.I156fs	MED23_ENST00000354577.4_Intron|ARG1_ENST00000356962.2_Splice_Site_p.I164fs			P05089	ARGI1_HUMAN	arginase 1	156					arginine catabolic process (GO:0006527)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to glucagon stimulus (GO:0071377)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-4 (GO:0071353)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|liver development (GO:0001889)|lung development (GO:0030324)|mammary gland involution (GO:0060056)|maternal process involved in female pregnancy (GO:0060135)|positive regulation of endothelial cell proliferation (GO:0001938)|protein homotrimerization (GO:0070207)|regulation of L-arginine import (GO:0010963)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to axon injury (GO:0048678)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to herbicide (GO:0009635)|response to manganese ion (GO:0010042)|response to methylmercury (GO:0051597)|response to selenium ion (GO:0010269)|response to vitamin A (GO:0033189)|response to vitamin E (GO:0033197)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	arginase activity (GO:0004053)|manganese ion binding (GO:0030145)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1)|skin(3)	14	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0106)|OV - Ovarian serous cystadenocarcinoma(155;0.0713)	L-Ornithine(DB00129)	TAATTTTAGATTCCCGATGTG	0.393																																					p.I164fs		Atlas-Indel,Pindel	.											.	ARG1	33	.	0			c.490delA						PASS	.						127	121	123					6																	131903762		2203	4300	6503	SO:0001630	splice_region_variant	383	exon5			.		CCDS5145.1, CCDS59038.1	6q23	2013-05-01	2013-05-01		ENSG00000118520	ENSG00000118520	3.5.3.1		663	protein-coding gene	gene with protein product		608313	"arginase, liver"			22959135	Standard	NM_000045		Approved		uc003qcp.2	P05089	OTTHUMG00000015566	ENST00000368087.3:c.466-1T>-	chr6.hg19:g.131903762delT		95.0	0.0	0		138.0	40.0	0.289855	NM_001244438	A6NEA0|Q5JWT5|Q5JWT6|Q8TE72|Q9BS50	Frame_Shift_Del	DEL	ENST00000368087.3	hg19	CCDS5145.1																																																																																			.	.	.	none		0.393	ARG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042223.1		Frame_Shift_Del	-	131903762	T	-	131903762	8	5	226	1	0	1	0	1	0	0	1	0	857	1507	52	0	485	0	ARG1	6	131903762	Splice_Site	DEL	T	TCGA-MH-A856-01A-11D-A34Z-10	88404514	131903762	39211305	33	13747											
HNRNPA2B1	3181	hgsc.bcm.edu	37	chr7	26235474	26235474	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggaaaactgacctccaggTcctcctccatacccattata	12	9	6	14	0	0	1	0	1	0	0	4	3	4	2	6	2	2	0	6	2	5	3			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr7:26235474T>C	ENST00000354667.4	-	8	918	c.750A>G	c.(748-750)ggA>ggG	p.G250G	HNRNPA2B1_ENST00000356674.7_Silent_p.G238G	NM_031243.2	NP_112533.1	P22626	ROA2_HUMAN	heterogeneous nuclear ribonucleoprotein A2/B1	250	Gly-rich.				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						GACCTCCAGGTCCTCCTCCAT	0.358			T	ETV1	prostate																																p.G250G		Atlas-SNP	.		Dom	yes		7	7p15	3181	heterogeneous nuclear ribonucleoprotein A2/B1		E	.	HNRNPA2B1	70	.	0			c.A750G						PASS	.						113	99	104					7																	26235474		2203	4300	6503	SO:0001819	synonymous_variant	3181	exon8			TCCAGGTCCTCCT	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.750A>G	chr7.hg19:g.26235474T>C		87.0	0.0	.		82.0	37.0	.	NM_031243	A8K064|P22627|Q9UC98|Q9UDJ2	Silent	SNP	ENST00000354667.4	hg19	CCDS43557.1	.	.	.	.	.	.	.	.	.	.	T	9.789	1.177349	0.21787	.	.	ENSG00000122566	ENST00000409814	.	.	.	5.93	0.584	0.17422	.	.	.	.	.	T	0.42404	0.1201	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.20907	-1.0261	4	.	.	.	.	1.8406	0.03149	0.1924:0.1811:0.0996:0.5269	.	.	.	.	G	184	.	.	D	-	2	0	HNRNPA2B1	26201999	0.999000	0.42202	0.998000	0.56505	0.941000	0.58515	0.264000	0.18497	-0.088000	0.12506	-2.424000	0.00217	GAC	.	.	.	none		0.358	HNRNPA2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214109.1	NM_002137		C	26235474	T	C	26235474	2	2	226	1	0	0	0	0	0	0	0	1	7266	1654	58	3		3	HNRNPA2B1	7	26235474	Silent	SNP	T	TCGA-MH-A856-01A-11D-A34Z-10		26235474	132903189	34	13748											
CACNA2D1	781	hgsc.bcm.edu	37	chr7	82072743	82072744	+	Frame_Shift_Ins	INS	-	-	A																															gcaaagattggaaaagtgtcINSagagtcaaggccagcaggca																										TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr7:82072743_82072744insA	ENST00000356253.5	-	1	287_288	c.32_33insT	c.(31-33)ctgfs	p.L11fs	CACNA2D1_ENST00000356860.3_Frame_Shift_Ins_p.L11fs|CACNA2D1_ENST00000423588.1_Frame_Shift_Ins_p.L11fs			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	11					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)	GGAAAAGTGTCAGAGTCAAGGC	0.673																																					p.L11fs		Atlas-Indel,Pindel	.											.	CACNA2D1	191	.	0			c.33_34insT						PASS	.																																			SO:0001589	frameshift_variant	781	exon1			.	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.33dupT	chr7.hg19:g.82072744_82072744dupA	ENSP00000348589:p.Leu11fs	74.0	0.0	0		68.0	22.0	0.323529	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Frame_Shift_Ins	INS	ENST00000356253.5	hg19																																																																																				.	.	.	none		0.673	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				A	82072744	-	A	82072743	7	5	226	1	0	1	1	0	0	0	0	0	2550	813	29	0	3398	0	CACNA2D1	7	82072743	Frame_Shift_Ins	INS	-	TCGA-MH-A856-01A-11D-A34Z-10	55837269	82072743	77065920	35	13749											
DMTF1	9988	hgsc.bcm.edu	37	chr7	86820330	86820330	+	Missense_Mutation	SNP	T	T	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	cagtggaacactacagacatTtgagattcttcccgtgagta	12	11	9	9	1	1	3	0	2	1	2	2	5	2	4	1	1	2	1	1	1	3	5			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr7:86820330T>G	ENST00000394703.5	+	16	2044	c.1481T>G	c.(1480-1482)tTt>tGt	p.F494C	DMTF1_ENST00000331242.7_Missense_Mutation_p.F494C|DMTF1_ENST00000432937.2_Missense_Mutation_p.F406C|DMTF1_ENST00000413276.2_Missense_Mutation_p.F424C|DMTF1_ENST00000414194.2_Missense_Mutation_p.F228C	NM_021145.3	NP_066968.3	Q9Y222	DMTF1_HUMAN	cyclin D binding myb-like transcription factor 1	494	Interaction with CCND1, CCND2 and CCND3. {ECO:0000250}.|Required for transcriptional activation. {ECO:0000250}.				cell cycle (GO:0007049)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)	16	Esophageal squamous(14;0.0058)					CTACAGACATTTGAGATTCTT	0.388																																					p.F494C		Atlas-SNP	.											DMTF1,colon,carcinoma,0,1	DMTF1	48	.	0			c.T1481G						PASS	.						173	135	148					7																	86820330		2203	4300	6503	SO:0001583	missense	9988	exon14			AGACATTTGAGAT	AF084530	CCDS5601.1, CCDS47633.1	7q21	2014-06-25			ENSG00000135164	ENSG00000135164			14603	protein-coding gene	gene with protein product	"cyclin D-binding Myb-like protein"	608491				10095122, 24958102	Standard	NR_024549		Approved	DMP1, DMTF, hDMP1, MRUL	uc003uih.3	Q9Y222	OTTHUMG00000154135	ENST00000394703.5:c.1481T>G	chr7.hg19:g.86820330T>G	ENSP00000378193:p.Phe494Cys	40.0	0.0	.		54.0	20.0	.	NM_001142327	B2RBE1|B4DJS5|Q05C48|Q59G79|Q6IS13|Q969T2|Q9H2Z2|Q9H2Z3	Missense_Mutation	SNP	ENST00000394703.5	hg19	CCDS5601.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.630090	0.87660	.	.	ENSG00000135164	ENST00000331242;ENST00000413276;ENST00000432937;ENST00000394703;ENST00000414194	T;T;T;T;T	0.65364	-0.15;0.15;-0.09;-0.15;-0.15	5.74	5.74	0.90152	.	0.125440	0.64402	D	0.000001	T	0.66915	0.2838	N	0.24115	0.695	0.58432	D	0.999997	D	0.76494	0.999	D	0.70716	0.97	T	0.67337	-0.5696	10	0.38643	T	0.18	-13.4366	15.2105	0.73219	0.0:0.0:0.0:1.0	.	494	Q9Y222	DMTF1_HUMAN	C	494;424;406;494;228	ENSP00000332171:F494C;ENSP00000402627:F424C;ENSP00000412532:F406C;ENSP00000378193:F494C;ENSP00000415910:F228C	ENSP00000332171:F494C	F	+	2	0	DMTF1	86658266	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.407000	0.80029	2.185000	0.69588	0.455000	0.32223	TTT	.	.	.	none		0.388	DMTF1-002	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334025.5	NM_021145		G	86820330	T	G	86820330	3	3	226	1	0	0	0	0	1	0	0	0	4594	1841	64	5	1527	5	DMTF1	7	86820330	Missense_Mutation	SNP	T	TCGA-MH-A856-01A-11D-A34Z-10	4747587	86820330	72318333	36	13750											
TMEM213	155006	hgsc.bcm.edu	37	chr7	138486107	138486107	+	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	acagctcaagcttgaccgctCaccacccagaccctgggacc	10	5	8	18	1	2	2	2	1	0	1	2	3	2	3	5	1	2	3	5	1	1	1			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr7:138486107C>A	ENST00000442682.2	+	2	271	c.118C>A	c.(118-120)Cac>Aac	p.H40N	TMEM213_ENST00000458494.1_Intron|TMEM213_ENST00000413208.1_Missense_Mutation_p.H40N|TMEM213_ENST00000422794.2_Missense_Mutation_p.H90N|TMEM213_ENST00000397602.3_Missense_Mutation_p.H39N	NM_001085429.1	NP_001078898.1	A2RRL7	TM213_HUMAN	transmembrane protein 213	40						integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|kidney(1)|lung(1)	6						CTTGACCGCTCACCACCCAGA	0.537																																					p.H40N		Atlas-SNP	.											.	TMEM213	20	.	0			c.C118A						PASS	.						38	44	42					7																	138486107		1966	4157	6123	SO:0001583	missense	155006	exon2			ACCGCTCACCACC		CCDS47722.1	7q34	2008-08-08			ENSG00000214128	ENSG00000214128			27220	protein-coding gene	gene with protein product							Standard	NM_001085429		Approved		uc010lna.3	A2RRL7	OTTHUMG00000157182	ENST00000442682.2:c.118C>A	chr7.hg19:g.138486107C>A	ENSP00000390407:p.His40Asn	62.0	0.0	.		46.0	17.0	.	NM_001085429	A4D1R3|C9JH49|C9JX41|C9K0P0	Missense_Mutation	SNP	ENST00000442682.2	hg19	CCDS47722.1	.	.	.	.	.	.	.	.	.	.	C	6.873	0.530421	0.13127	.	.	ENSG00000214128	ENST00000422794;ENST00000397602;ENST00000442682;ENST00000413208	.	.	.	5.33	5.33	0.75918	.	0.227351	0.21672	U	0.070852	T	0.38532	0.1044	L	0.34521	1.04	0.09310	N	0.999999	P;P	0.36535	0.557;0.557	B;B	0.41988	0.372;0.372	T	0.28004	-1.0057	9	0.30854	T	0.27	-30.7942	14.8724	0.70468	0.0:1.0:0.0:0.0	.	39;40	A2RRL7-3;A2RRL7	.;TM213_HUMAN	N	90;39;40;40	.	ENSP00000380727:H39N	H	+	1	0	TMEM213	138136647	0.005000	0.15991	0.294000	0.24946	0.007000	0.05969	1.234000	0.32660	2.636000	0.89361	0.655000	0.94253	CAC	.	.	.	none		0.537	TMEM213-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347800.2	NM_001085429		A	138486107	C	A	138486107	3	1	226	1	0	0	0	0	1	0	0	0	16148	826	29	4	124	4	TMEM213	7	138486107	Missense_Mutation	SNP	C	TCGA-MH-A856-01A-11D-A34Z-10	51665777	138486107	20652556	37	13751											
ADCK2	90956	hgsc.bcm.edu	37	chr7	140374550	140374550	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaatttgagaagctgatggTccaacaggtgagttctcctc	10	11	12	8	0	1	3	0	3	1	1	4	5	2	4	2	3	2	2	2	3	3	2			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr7:140374550T>C	ENST00000072869.4	+	2	1251	c.1073T>C	c.(1072-1074)gTc>gCc	p.V358A	ADCK2_ENST00000476491.1_Missense_Mutation_p.V358A	NM_052853.3	NP_443085.2	Q7Z695	ADCK2_HUMAN	aarF domain containing kinase 2	358	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)					AAGCTGATGGTCCAACAGGTG	0.458																																					p.V358A		Atlas-SNP	.											.	ADCK2	37	.	0			c.T1073C						PASS	.						122	105	110					7																	140374550		2203	4300	6503	SO:0001583	missense	90956	exon2			TGATGGTCCAACA	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.1073T>C	chr7.hg19:g.140374550T>C	ENSP00000072869:p.Val358Ala	99.0	0.0	.		99.0	49.0	.	NM_052853	Q96CN6|Q9Y6T5	Missense_Mutation	SNP	ENST00000072869.4	hg19	CCDS5861.1	.	.	.	.	.	.	.	.	.	.	T	11.45	1.641354	0.29157	.	.	ENSG00000133597	ENST00000072869;ENST00000476491	T;T	0.53640	0.61;0.61	5.35	4.21	0.49690	ABC-1 (1);	0.566619	0.18600	N	0.136484	T	0.31389	0.0795	L	0.31157	0.91	0.30831	N	0.736681	B;B	0.31153	0.129;0.31	B;B	0.30251	0.113;0.113	T	0.26395	-1.0104	10	0.15499	T	0.54	-42.3317	8.4754	0.33009	0.0:0.1506:0.0:0.8494	.	358;358	C9JE15;Q7Z695	.;ADCK2_HUMAN	A	358	ENSP00000072869:V358A;ENSP00000420512:V358A	ENSP00000072869:V358A	V	+	2	0	ADCK2	140021019	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	2.242000	0.43106	0.983000	0.38602	0.533000	0.62120	GTC	.	.	.	none		0.458	ADCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348734.1	NM_052853		C	140374550	T	C	140374550	3	2	226	1	0	0	0	0	1	0	0	0	289	1667	58	3	1079	3	ADCK2	7	140374550	Missense_Mutation	SNP	T	TCGA-MH-A856-01A-11D-A34Z-10	1888443	140374550	18764113	38	13752											
DDHD2	23259	hgsc.bcm.edu	37	chr8	38092031	38092031	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catcggaagtgagacgatgtAcgtggttttacaagggggac	11	9	15	6	3	0	1	0	1	0	1	1	5	0	3	0	4	2	2	0	4	4	3			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr8:38092031A>G	ENST00000397166.2	+	3	865	c.340A>G	c.(340-342)Acg>Gcg	p.T114A	DDHD2_ENST00000520272.2_Missense_Mutation_p.T114A	NM_015214.2	NP_056029.2	O94830	DDHD2_HUMAN	DDHD domain containing 2	114					cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|microtubule organizing center (GO:0005815)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)|urinary_tract(2)	28	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)			GAGACGATGTACGTGGTTTTA	0.433																																					p.T114A		Atlas-SNP	.											.	DDHD2	60	.	0			c.A340G						PASS	.						229	230	229					8																	38092031		2203	4300	6503	SO:0001583	missense	23259	exon3			CGATGTACGTGGT	AK056525	CCDS34883.1	8p11.23	2014-03-03	2004-04-05	2004-04-07				"Sterile alpha motif (SAM) domain containing"	29106	protein-coding gene	gene with protein product		615003	"SAM, WWE and DDHD domain containing 1"	SAMWD1		9872452, 11788596, 19632984, 20932832	Standard	NM_015214		Approved	KIAA0725, SPG54	uc003xlc.3	O94830		ENST00000397166.2:c.340A>G	chr8.hg19:g.38092031A>G	ENSP00000380352:p.Thr114Ala	153.0	0.0	.		126.0	44.0	.	NM_001164232	B3KWV2|B3KXB5|Q9H8X7	Missense_Mutation	SNP	ENST00000397166.2	hg19	CCDS34883.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.394179	0.83011	.	.	ENSG00000085788	ENST00000527834;ENST00000397166;ENST00000533100;ENST00000528358;ENST00000529642;ENST00000532222;ENST00000520272	T;T;T;T;T;T;T	0.34859	1.34;1.34;1.34;1.34;1.34;1.34;1.34	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.59528	0.2200	M	0.73217	2.22	0.80722	D	1	B;D	0.76494	0.157;0.999	B;D	0.78314	0.129;0.991	T	0.61802	-0.6988	10	0.56958	D	0.05	-16.5827	14.9594	0.71144	1.0:0.0:0.0:0.0	.	114;114	O94830;E9PKE6	DDHD2_HUMAN;.	A	114;114;114;112;18;114;114	ENSP00000432433:T114A;ENSP00000380352:T114A;ENSP00000432678:T114A;ENSP00000433118:T112A;ENSP00000436444:T18A;ENSP00000433578:T114A;ENSP00000429932:T114A	ENSP00000380352:T114A	T	+	1	0	DDHD2	38211188	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	8.398000	0.90195	2.207000	0.71202	0.533000	0.62120	ACG	.	.	.	none		0.433	DDHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377251.2	XM_291291		G	38092031	A	G	38092031	3	3	226	1	0	0	0	0	1	0	0	0	4329	391	14	3	346	3	DDHD2	8	38092031	Missense_Mutation	SNP	A	TCGA-MH-A856-01A-11D-A34Z-10		38092031	108271991	39	13753											
PLEC	5339	hgsc.bcm.edu	37	chr8	144997605	144997605	+	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	ttatgcttctccatctccgcGtcagctgcctgcttctgccg	3	14	8	16	3	4	0	1	0	3	0	6	0	4	0	4	0	5	3	4	0	1	3	rs575031901	byFrequency	TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr8:144997605G>A	ENST00000322810.4	-	31	7072	c.6903C>T	c.(6901-6903)gaC>gaT	p.D2301D	PLEC_ENST00000356346.3_Silent_p.D2150D|PLEC_ENST00000345136.3_Silent_p.D2164D|PLEC_ENST00000354589.3_Silent_p.D2164D|PLEC_ENST00000357649.2_Silent_p.D2168D|PLEC_ENST00000436759.2_Silent_p.D2191D|PLEC_ENST00000527096.1_Silent_p.D2187D|PLEC_ENST00000398774.2_Silent_p.D2132D|PLEC_ENST00000354958.2_Silent_p.D2142D	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2301	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						CCATCTCCGCGTCAGCTGCCT	0.672													G|||	3	0.000599042	0	0	5008	,	,		11719	0		0	False		,,,				2504	0.0031				p.D2301D		Atlas-SNP	.											.	PLEC	1144	.	0			c.C6903T						PASS	.						11	14	13					8																	144997605		2085	4221	6306	SO:0001819	synonymous_variant	5339	exon31			CTCCGCGTCAGCT	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.6903C>T	chr8.hg19:g.144997605G>A		86.0	0.0	.		66.0	6.0	.	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	hg19	CCDS43772.1																																																																																			.	.	.	none		0.672	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		A	144997605	G	A	144997605	2	1	226	1	0	0	0	0	0	0	0	1	12059	1136	40	1		1	PLEC	8	144997605	Silent	SNP	G	TCGA-MH-A856-01A-11D-A34Z-10	106905574	144997605	1366417	40	13754											
LOXL4	84171	hgsc.bcm.edu	37	chr10	100020789	100020789	+	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	cacacctgccgccagtggccCtcatacttcacctccacggc	7	7	7	20	2	2	0	2	0	0	0	3	0	3	0	6	2	2	0	6	2	1	2			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr10:100020789C>A	ENST00000260702.3	-	4	702	c.552G>T	c.(550-552)gaG>gaT	p.E184D		NM_032211.6	NP_115587.6	Q96JB6	LOXL4_HUMAN	lysyl oxidase-like 4	184	SRCR 2. {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)		GCCAGTGGCCCTCATACTTCA	0.667																																					p.E184D		Atlas-SNP	.											.	LOXL4	60	.	0			c.G552T						PASS	.						106	79	88					10																	100020789		2203	4300	6503	SO:0001583	missense	84171	exon4			GTGGCCCTCATAC	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.552G>T	chr10.hg19:g.100020789C>A	ENSP00000260702:p.Glu184Asp	56.0	0.0	.		60.0	24.0	.	NM_032211	Q5W0B3|Q96DY1|Q96PC0|Q9H6T5	Missense_Mutation	SNP	ENST00000260702.3	hg19	CCDS7473.1	.	.	.	.	.	.	.	.	.	.	C	8.607	0.888261	0.17540	.	.	ENSG00000138131	ENST00000260702	T	0.27557	1.66	5.53	-6.5	0.01884	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.474502	0.24985	N	0.034025	T	0.07863	0.0197	N	0.04508	-0.205	0.19300	N	0.999974	B	0.10296	0.003	B	0.13407	0.009	T	0.25572	-1.0128	10	0.12430	T	0.62	.	3.1247	0.06403	0.1631:0.1373:0.4253:0.2743	.	184	Q96JB6	LOXL4_HUMAN	D	184	ENSP00000260702:E184D	ENSP00000260702:E184D	E	-	3	2	LOXL4	100010779	0.004000	0.15560	0.578000	0.28575	0.859000	0.49053	-1.149000	0.03182	-1.027000	0.03325	-1.045000	0.02358	GAG	.	.	.	none		0.667	LOXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049766.1	NM_032211		A	100020789	C	A	100020789	3	1	226	1	0	0	0	0	1	0	0	0	8909	680	24	4	1766	4	LOXL4	10	100020789	Missense_Mutation	SNP	C	TCGA-MH-A856-01A-11D-A34Z-10		100020789	35513958	41	13755											
BIRC2	329	hgsc.bcm.edu	37	chr11	102220675	102220675	+	Missense_Mutation	SNP	T	T	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	gatagcacgatcttgtcagaTtggacaaacagcaacaaaca	17	7	8	9	1	2	1	1	0	1	1	2	4	2	2	0	1	5	2	0	1	4	3			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr11:102220675T>G	ENST00000227758.2	+	2	1489	c.90T>G	c.(88-90)gaT>gaG	p.D30E	BIRC2_ENST00000532672.1_Missense_Mutation_p.D9E|BIRC2_ENST00000530675.1_Intron|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	30					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)		TCTTGTCAGATTGGACAAACA	0.428																																					p.D30E		Atlas-SNP	.											.	BIRC2	51	.	0			c.T90G						PASS	.						121	118	119					11																	102220675		2203	4299	6502	SO:0001583	missense	329	exon2			GTCAGATTGGACA	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.90T>G	chr11.hg19:g.102220675T>G	ENSP00000227758:p.Asp30Glu	187.0	0.0	.		152.0	64.0	.	NM_001256163	B4E026|Q16516|Q4TTG0	Missense_Mutation	SNP	ENST00000227758.2	hg19	CCDS8316.1	.	.	.	.	.	.	.	.	.	.	T	11.47	1.647966	0.29336	.	.	ENSG00000110330	ENST00000227758;ENST00000541741;ENST00000532672;ENST00000527465	T;T;T	0.62232	2.13;2.12;0.04	5.5	3.2	0.36748	Baculoviral inhibition of apoptosis protein repeat (1);	0.583137	0.21661	N	0.071015	T	0.35885	0.0947	N	0.08118	0	0.09310	N	0.999993	B	0.13594	0.008	B	0.15484	0.013	T	0.15780	-1.0425	10	0.25106	T	0.35	-3.5714	5.9772	0.19387	0.0:0.1492:0.1389:0.7119	.	30	Q13490	BIRC2_HUMAN	E	30;30;9;9	ENSP00000227758:D30E;ENSP00000434979:D9E;ENSP00000434708:D9E	ENSP00000227758:D30E	D	+	3	2	BIRC2	101725885	0.069000	0.21087	0.937000	0.37676	0.729000	0.41735	0.134000	0.15932	0.519000	0.28406	-0.254000	0.11334	GAT	.	.	.	none		0.428	BIRC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394170.1	NM_001166		G	102220675	T	G	102220675	3	3	226	1	0	0	0	0	1	0	0	0	1435	1490	52	5	92	5	BIRC2	11	102220675	Missense_Mutation	SNP	T	TCGA-MH-A856-01A-11D-A34Z-10		102220675	32785841	42	13756											
DLAT	1737	hgsc.bcm.edu	37	chr11	111899514	111899514	+	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	atgcattctttctcttccttAggcctgaggatattgaggcc	7	15	9	10	0	2	2	0	2	2	0	4	3	3	3	3	3	1	1	3	3	2	6			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr11:111899514A>T	ENST00000280346.6	+	4	1165		c.e4-1		DLAT_ENST00000393051.1_Splice_Site|DLAT_ENST00000537636.1_Intron	NM_001931.4	NP_001922.2	P10515	ODP2_HUMAN	dihydrolipoamide S-acetyltransferase						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)		TCTCTTCCTTAGGCCTGAGGA	0.428																																					.		Atlas-SNP	.											.	DLAT	39	.	0			c.507-2A>T						PASS	.						70	78	76					11																	111899514		2201	4297	6498	SO:0001630	splice_region_variant	1737	exon4			TTCCTTAGGCCTG	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.507-1A>T	chr11.hg19:g.111899514A>T		99.0	0.0	.		68.0	25.0	.	NM_001931	Q16783|Q53EP3	Splice_Site	SNP	ENST00000280346.6	hg19	CCDS8354.1	.	.	.	.	.	.	.	.	.	.	A	19.61	3.860721	0.71834	.	.	ENSG00000150768	ENST00000280346;ENST00000534998;ENST00000393051	.	.	.	4.88	4.88	0.63580	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4904	0.67647	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DLAT	111404724	1.000000	0.71417	1.000000	0.80357	0.867000	0.49689	7.704000	0.84595	1.836000	0.53414	0.377000	0.23210	.	.	.	.	none		0.428	DLAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258167.1	NM_001931	Intron	T	111899514	A	T	111899514	5	4	226	1	0	0	0	0	0	0	1	0	4551	434	15	5	519	5	DLAT	11	111899514	Splice_Site	SNP	A	TCGA-MH-A856-01A-11D-A34Z-10	9678839	111899514	23107002	43	13757											
ARHGAP32	9743	hgsc.bcm.edu	37	chr11	128846491	128846491	+	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	gagagatgtaagagactcctCacttttagctgaacggaggg	12	9	13	7	1	1	3	1	1	0	2	2	7	2	4	1	2	2	2	1	2	3	3			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr11:128846491C>G	ENST00000310343.9	-	19	2118	c.2119G>C	c.(2119-2121)Gag>Cag	p.E707Q	ARHGAP32_ENST00000524655.1_Missense_Mutation_p.E633Q|ARHGAP32_ENST00000527272.1_Missense_Mutation_p.E358Q|ARHGAP32_ENST00000392657.3_Missense_Mutation_p.E358Q	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	707					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						AGAGACTCCTCACTTTTAGCT	0.363																																					p.E707Q		Atlas-SNP	.											ARHGAP32_ENST00000310343,right_lower_lobe,carcinoma,0,2	ARHGAP32	307	.	0			c.G2119C						PASS	.						107	108	108					11																	128846491		2201	4297	6498	SO:0001583	missense	9743	exon19			ACTCCTCACTTTT	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.2119G>C	chr11.hg19:g.128846491C>G	ENSP00000310561:p.Glu707Gln	151.0	0.0	.		182.0	67.0	.	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Missense_Mutation	SNP	ENST00000310343.9	hg19	CCDS44769.1	.	.	.	.	.	.	.	.	.	.	C	33	5.210996	0.95069	.	.	ENSG00000134909	ENST00000310343;ENST00000392657;ENST00000524655;ENST00000457677;ENST00000527272	T;T;T;T	0.23147	1.92;1.92;1.92;1.92	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.42314	0.1197	M	0.66939	2.045	0.58432	D	0.999999	P;P	0.52577	0.778;0.954	P;B	0.49451	0.611;0.393	T	0.17319	-1.0373	10	0.59425	D	0.04	.	20.6593	0.99626	0.0:1.0:0.0:0.0	.	641;707	Q86T64;A7KAX9	.;RHG32_HUMAN	Q	707;358;633;641;358	ENSP00000310561:E707Q;ENSP00000376425:E358Q;ENSP00000432468:E633Q;ENSP00000432862:E358Q	ENSP00000310561:E707Q	E	-	1	0	ARHGAP32	128351701	1.000000	0.71417	0.999000	0.59377	0.973000	0.67179	7.277000	0.78572	2.885000	0.99019	0.655000	0.94253	GAG	.	.	.	none		0.363	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		G	128846491	C	G	128846491	3	3	226	1	0	0	0	0	1	0	0	0	881	835	29	4	4160	4	ARHGAP32	11	128846491	Missense_Mutation	SNP	C	TCGA-MH-A856-01A-11D-A34Z-10	16946977	128846491	6160025	44	13758											
KRT5	3852	hgsc.bcm.edu	37	chr12	52910546	52910546	+	Silent	SNP	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	tcctgcttggccttctgcagGgcctcctccagctcggccag	3	10	11	17	1	1	0	0	0	1	0	5	0	4	0	6	3	3	3	6	3	0	2			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr12:52910546G>A	ENST00000252242.4	-	7	1704	c.1314C>T	c.(1312-1314)gcC>gcT	p.A438A		NM_000424.3	NP_000415.2	P13647	K2C5_HUMAN	keratin 5	438	Coil 2.|Rod.		A -> D (in WC-EBS). {ECO:0000269|PubMed:12655565}.		cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|hemidesmosome assembly (GO:0031581)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)			endometrium(5)|kidney(1)|large_intestine(8)|lung(15)|prostate(4)|skin(2)	35				BRCA - Breast invasive adenocarcinoma(357;0.189)		CCTTCTGCAGGGCCTCCTCCA	0.632																																					p.A438A		Atlas-SNP	.											KRT5,NS,haematopoietic_neoplasm,0,1	KRT5	88	.	0			c.C1314T						PASS	.						97	87	90					12																	52910546		2203	4300	6503	SO:0001819	synonymous_variant	3852	exon7			CTGCAGGGCCTCC		CCDS8830.1	12q13.13	2013-01-16	2008-08-01		ENSG00000186081	ENSG00000186081		"-", "Intermediate filaments type II, keratins (basic)"	6442	protein-coding gene	gene with protein product		148040	"epidermolysis bullosa simplex 2 Dowling-Meara/Kobner/Weber-Cockayne types", "keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types)"	EBS2		1713141, 16831889	Standard	NM_000424		Approved	KRT5A	uc001san.3	P13647	OTTHUMG00000169657	ENST00000252242.4:c.1314C>T	chr12.hg19:g.52910546G>A		76.0	0.0	.		73.0	24.0	.	NM_000424	Q6PI71|Q6UBJ0|Q8TA91	Silent	SNP	ENST00000252242.4	hg19	CCDS8830.1	.	.	.	.	.	.	.	.	.	.	G	11.13	1.547660	0.27652	.	.	ENSG00000186081	ENST00000548409	.	.	.	5.93	3.09	0.35607	.	.	.	.	.	T	0.55705	0.1937	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46707	-0.9172	4	.	.	.	.	7.3447	0.26656	0.2475:0.1167:0.6358:0.0	.	.	.	.	S	146	.	.	P	-	1	0	KRT5	51196813	0.156000	0.22821	0.991000	0.47740	0.976000	0.68499	-0.471000	0.06631	0.389000	0.25086	0.655000	0.94253	CCT	.	.	.	none		0.632	KRT5-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405312.1			A	52910546	G	A	52910546	2	1	226	1	0	0	0	0	0	0	0	1	8486	1219	43	2		2	KRT5	12	52910546	Silent	SNP	G	TCGA-MH-A856-01A-11D-A34Z-10		52910546	80941349	45	13759											
ESYT1	23344	hgsc.bcm.edu	37	chr12	56536880	56536880	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagacaagaaccgaggcaccAagaggaggacctcacagaag	17	1	12	11	1	1	4	1	0	0	4	1	7	1	6	3	3	1	1	3	3	4	0			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr12:56536880A>G	ENST00000394048.5	+	28	3331	c.3067A>G	c.(3067-3069)Aag>Gag	p.K1023E	ESYT1_ENST00000541590.1_Missense_Mutation_p.K1033E|ESYT1_ENST00000267113.4_Missense_Mutation_p.K1033E	NM_001184796.1|NM_015292.2	NP_001171725.1|NP_056107.1	Q9BSJ8	ESYT1_HUMAN	extended synaptotagmin-like protein 1	1023	C2 5. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Required for phosphatidylinositol 4,5- bisphosphate-dependent location at the cell membrane. {ECO:0000250}.				lipid transport (GO:0006869)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(4)|lung(10)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	28						CCGAGGCACCAAGAGGAGGAC	0.522																																					p.K1033E		Atlas-SNP	.											.	ESYT1	84	.	0			c.A3097G						PASS	.						133	127	129					12																	56536880		2203	4300	6503	SO:0001583	missense	23344	exon28			GGCACCAAGAGGA	AK074368	CCDS8904.1, CCDS53801.1	12q13.2	2014-07-02	2009-06-23	2009-06-23		ENSG00000139641		"Synaptotagmins"	29534	protein-coding gene	gene with protein product			"family with sequence similarity 62 (C2 domain containing), member A"	FAM62A		9872452, 10350628, 17672888	Standard	NM_015292		Approved	MBC2, KIAA0747	uc001sjr.3	Q9BSJ8		ENST00000394048.5:c.3067A>G	chr12.hg19:g.56536880A>G	ENSP00000377612:p.Lys1023Glu	66.0	0.0	.		53.0	26.0	.	NM_001184796	A0FGR7|A8K2S2|O94848|Q6PJN4|Q9H6J1|Q9H6W2|Q9Y416	Missense_Mutation	SNP	ENST00000394048.5	hg19	CCDS8904.1	.	.	.	.	.	.	.	.	.	.	A	26.5	4.744295	0.89663	.	.	ENSG00000139641	ENST00000394048;ENST00000402331;ENST00000267113;ENST00000541590	T;T;T	0.70869	-0.52;-0.52;-0.52	5.22	5.22	0.72569	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.107964	0.64402	D	0.000011	D	0.84570	0.5501	M	0.88512	2.96	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.91635	0.999;0.994	D	0.83962	0.0322	10	0.22109	T	0.4	-23.4658	12.9417	0.58348	1.0:0.0:0.0:0.0	.	1033;1023	Q9BSJ8-2;Q9BSJ8	.;ESYT1_HUMAN	E	1023;977;1033;1033	ENSP00000377612:K1023E;ENSP00000267113:K1033E;ENSP00000445952:K1033E	ENSP00000267113:K1033E	K	+	1	0	ESYT1	54823147	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.577000	0.67444	2.107000	0.64212	0.459000	0.35465	AAG	.	.	.	none		0.522	ESYT1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000407906.1	NM_015292		G	56536880	A	G	56536880	3	3	226	1	0	0	0	0	1	0	0	0	5266	131	5	3	3207	3	ESYT1	12	56536880	Missense_Mutation	SNP	A	TCGA-MH-A856-01A-11D-A34Z-10	3626334	56536880	77315015	46	13760											
SLC17A8	246213	hgsc.bcm.edu	37	chr12	100774514	100774514	+	Frame_Shift_Del	DEL	T	T	-																															aactgaggaagaagataacaTtgagctgaatgaagaaggaa																										TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr12:100774514delT	ENST00000323346.5	+	2	450	c.137delT	c.(136-138)attfs	p.I46fs	SLC17A8_ENST00000392989.3_Frame_Shift_Del_p.I46fs	NM_001145288.1|NM_139319.2	NP_001138760.1|NP_647480.1	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 8	46					ion transport (GO:0006811)|neurotransmitter transport (GO:0006836)|sensory perception of sound (GO:0007605)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|synaptic vesicle membrane (GO:0030672)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	44						GAAGATAACATTGAGCTGAAT	0.473																																					p.I46fs		Atlas-Indel,Pindel	.											.	SLC17A8	89	.	0			c.136delA						PASS	.						116	121	119					12																	100774514		2203	4300	6503	SO:0001589	frameshift_variant	246213	exon2			.	AJ459241	CCDS9077.1, CCDS44957.1	12q23.1	2013-07-18	2013-07-18		ENSG00000179520	ENSG00000179520		"Solute carriers"	20151	protein-coding gene	gene with protein product	"vesicular glutamate transporter 3"	607557	"deafness, autosomal dominant 25", "solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 8"	DFNA25		12151341	Standard	NM_139319		Approved	VGLUT3	uc010svi.2	Q8NDX2	OTTHUMG00000170358	ENST00000323346.5:c.137delT	chr12.hg19:g.100774514delT	ENSP00000316909:p.Ile46fs	112.0	0.0	0		99.0	33.0	0.333333	NM_001145288	B3KXZ6|B7ZKV4|Q17RQ8	Frame_Shift_Del	DEL	ENST00000323346.5	hg19	CCDS9077.1																																																																																			.	.	.	none		0.473	SLC17A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408673.2	NM_139319		-	100774514	T	-	100774514	7	5	226	1	0	1	0	1	0	0	0	0	14436	1493	52	0	143	0	SLC17A8	12	100774514	Frame_Shift_Del	DEL	T	TCGA-MH-A856-01A-11D-A34Z-10	44237634	100774514	33077381	47	13761											
IFT81	28981	hgsc.bcm.edu	37	chr12	110618356	110618356	+	Missense_Mutation	SNP	G	G	A																															aacttcttaagcaacgtcatGaaaatattcaacaacaactg																										TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr12:110618356G>A	ENST00000242591.5	+	12	1824	c.1318G>A	c.(1318-1320)Gaa>Aaa	p.E440K	IFT81_ENST00000552912.1_Missense_Mutation_p.E440K	NM_014055.3	NP_054774.2	Q8WYA0	IFT81_HUMAN	intraflagellar transport 81	440					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						GCAACGTCATGAAAATATTCA	0.353																																					p.E440K		Atlas-SNP	.											.	IFT81	86	.	0			c.G1318A						PASS	.						74	66	69					12																	110618356		1826	4083	5909	SO:0001583	missense	28981	exon12			CGTCATGAAAATA	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.1318G>A	chr12.hg19:g.110618356G>A	ENSP00000242591:p.Glu440Lys	77.0	0.0	.		61.0	21.0	.	NM_014055	Q2YDY1|Q8NB51|Q9BSV2|Q9UNY8	Missense_Mutation	SNP	ENST00000242591.5	hg19	CCDS41831.1	.	.	.	.	.	.	.	.	.	.	G	18.86	3.712746	0.68730	.	.	ENSG00000122970	ENST00000552912;ENST00000242591	T;T	0.16743	2.32;2.32	6.07	5.19	0.71726	.	0.346210	0.36815	N	0.002382	T	0.22475	0.0542	M	0.65975	2.015	0.80722	D	1	P	0.39862	0.692	B	0.39840	0.311	T	0.02852	-1.1102	10	0.22706	T	0.39	-12.7522	15.5714	0.76341	0.0659:0.0:0.9341:0.0	.	440	Q8WYA0	IFT81_HUMAN	K	440	ENSP00000449718:E440K;ENSP00000242591:E440K	ENSP00000242591:E440K	E	+	1	0	IFT81	109102739	1.000000	0.71417	0.996000	0.52242	0.908000	0.53690	5.664000	0.68045	1.580000	0.49851	-0.150000	0.13652	GAA	.	.	.	none		0.353	IFT81-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403529.1	NM_014055		A	110618356	G	A	110618356	3	1	226	1	0	0	0	0	1	0	0	0	7572	1291	45	2	1472	2	IFT81	12	110618356	Missense_Mutation	SNP	G	TCGA-MH-A856-01A-11D-A34Z-10	9843842	110618356	23233539	48	13762	139	2									
IFT81	28981	hgsc.bcm.edu	37	chr12	110618362	110618362	+	Missense_Mutation	SNP	A	A	T																															ttaagcaacgtcatgaaaatAttcaacaacaactggtaata																										TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr12:110618362A>T	ENST00000242591.5	+	12	1830	c.1324A>T	c.(1324-1326)Att>Ttt	p.I442F	IFT81_ENST00000552912.1_Missense_Mutation_p.I442F	NM_014055.3	NP_054774.2	Q8WYA0	IFT81_HUMAN	intraflagellar transport 81	442					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						TCATGAAAATATTCAACAACA	0.338																																					p.I442F		Atlas-SNP	.											.	IFT81	86	.	0			c.A1324T						PASS	.						70	63	66					12																	110618362		1829	4082	5911	SO:0001583	missense	28981	exon12			GAAAATATTCAAC	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.1324A>T	chr12.hg19:g.110618362A>T	ENSP00000242591:p.Ile442Phe	74.0	0.0	.		59.0	20.0	.	NM_014055	Q2YDY1|Q8NB51|Q9BSV2|Q9UNY8	Missense_Mutation	SNP	ENST00000242591.5	hg19	CCDS41831.1	.	.	.	.	.	.	.	.	.	.	A	13.74	2.326704	0.41197	.	.	ENSG00000122970	ENST00000552912;ENST00000242591	T;T	0.17691	2.26;2.26	6.07	4.92	0.64577	.	0.309061	0.39210	N	0.001424	T	0.14270	0.0345	L	0.38838	1.175	0.80722	D	1	B	0.12013	0.005	B	0.13407	0.009	T	0.05649	-1.0872	10	0.27785	T	0.31	-12.4757	12.5221	0.56065	0.9341:0.0:0.0659:0.0	.	442	Q8WYA0	IFT81_HUMAN	F	442	ENSP00000449718:I442F;ENSP00000242591:I442F	ENSP00000242591:I442F	I	+	1	0	IFT81	109102745	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	4.247000	0.58750	2.326000	0.78906	0.533000	0.62120	ATT	.	.	.	none		0.338	IFT81-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403529.1	NM_014055		T	110618362	A	T	110618362	3	4	226	1	0	0	0	0	1	0	0	0	7572	449	16	5	1478	5	IFT81	12	110618362	Missense_Mutation	SNP	A	TCGA-MH-A856-01A-11D-A34Z-10	6	110618362	23233533	49	13763	139	2									
KIAA1737	85457	hgsc.bcm.edu	37	chr14	77580331	77580331	+	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	ccactgtccgctaattatagCtcacctttatgggctgcaga	9	12	8	12	1	1	1	1	0	0	1	2	1	2	1	3	1	2	4	3	1	4	5			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr14:77580331C>T	ENST00000361786.2	+	4	1187	c.870C>T	c.(868-870)agC>agT	p.S290S	RP11-463C8.4_ENST00000557752.1_Intron	NM_033426.2	NP_219494.2	Q9C0C6	CIPC_HUMAN		290					negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(2)|lung(4)|prostate(3)	9			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0284)		CTAATTATAGCTCACCTTTAT	0.542																																					p.S290S		Atlas-SNP	.											.	KIAA1737	26	.	0			c.C870T						PASS	.						99	93	95					14																	77580331		2203	4300	6503	SO:0001819	synonymous_variant	85457	exon4			TTATAGCTCACCT																												ENST00000361786.2:c.870C>T	chr14.hg19:g.77580331C>T		80.0	0.0	.		62.0	26.0	.	NM_033426	B2RCI1|Q8N389|Q8NDZ1	Silent	SNP	ENST00000361786.2	hg19	CCDS9855.1																																																																																			.	.	.	none		0.542	KIAA1737-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414278.1			T	77580331	C	T	77580331	2	4	226	1	0	0	0	0	0	0	0	1	8262	796	28	2		2	KIAA1737	14	77580331	Silent	SNP	C	TCGA-MH-A856-01A-11D-A34Z-10		77580331	29769209	50	13764											
HMG20A	10363	hgsc.bcm.edu	37	chr15	77756629	77756629	+	Frame_Shift_Del	DEL	C	C	-																															tagtggcgccacatcatccaCcaacaatccagaatttgtgg																										TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr15:77756629delC	ENST00000381714.3	+	4	565	c.137delC	c.(136-138)accfs	p.T46fs	HMG20A_ENST00000336216.4_Frame_Shift_Del_p.T46fs	NM_018200.2	NP_060670.1	Q9NP66	HM20A_HUMAN	high mobility group 20A	46					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						ACATCATCCACCAACAATCCA	0.433																																					p.T46fs		Pindel	.											.	HMG20A	48	.	0			c.136delA						PASS	.						143	120	128					15																	77756629		2196	4294	6490	SO:0001589	frameshift_variant	10363	exon4			.	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.137delC	chr15.hg19:g.77756629delC	ENSP00000371133:p.Thr46fs	241.0	0.0	.		211.0	56.0	0.265	NM_018200	A6NHY3|D3DW78|Q53G31|Q9NSF6	Frame_Shift_Del	DEL	ENST00000381714.3	hg19	CCDS10295.1																																																																																			.	.	.	none		0.433	HMG20A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419512.2	NM_018200		-	77756629	C	-	77756629	7	5	226	1	0	1	0	1	0	0	0	0	7228	507	18	0	143	0	HMG20A	15	77756629	Frame_Shift_Del	DEL	C	TCGA-MH-A856-01A-11D-A34Z-10		77756629	24774763	51	13765											
CHTF18	63922	hgsc.bcm.edu	37	chr16	841194	841194	+	Missense_Mutation	SNP	T	T	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	gcctgctcaagtggctgaagTtgtgggacctggtggtgttt	5	13	16	7	0	1	1	1	1	0	0	1	2	1	2	2	4	1	4	2	4	2	2	rs374149034		TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr16:841194T>G	ENST00000262315.9	+	8	991	c.928T>G	c.(928-930)Ttg>Gtg	p.L310V	CHTF18_ENST00000317063.6_Missense_Mutation_p.L505V|CHTF18_ENST00000455171.2_Missense_Mutation_p.L338V|CHTF18_ENST00000491530.1_3'UTR|RPUSD1_ENST00000007264.2_5'Flank|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)	310					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)				GTGGCTGAAGTTGTGGGACCT	0.662																																					p.L310V		Atlas-SNP	.											.	CHTF18	52	.	0			c.T928G						PASS	.	T	VAL/LEU	0,4244		0,0,2122	20	25	23		928	2.8	1	16		23	1,8443		0,1,4221	no	missense	CHTF18	NM_022092.2	32	0,1,6343	GG,GT,TT		0.0118,0.0,0.0079	probably-damaging	310/976	841194	1,12687	2122	4222	6344	SO:0001583	missense	63922	exon8			CTGAAGTTGTGGG	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.928T>G	chr16.hg19:g.841194T>G	ENSP00000262315:p.Leu310Val	36.0	0.0	.		51.0	19.0	.	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Missense_Mutation	SNP	ENST00000262315.9	hg19	CCDS45371.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.44|15.44	2.832785|2.832785	0.50951|0.50951	0.0|0.0	1.18E-4|1.18E-4	ENSG00000127586|ENSG00000127586	ENST00000317063;ENST00000455171;ENST00000262315|ENST00000426047	T;T;T|.	0.17691|.	2.26;2.26;2.26|.	4.85|4.85	2.78|2.78	0.32641|0.32641	.|.	0.070845|.	0.56097|.	N|.	0.000026|.	T|T	0.73590|0.73590	0.3606|0.3606	M|M	0.85197|0.85197	2.74|2.74	0.58432|0.58432	D|D	0.999999|0.999999	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;0.999|.	T|T	0.72776|0.72776	-0.4191|-0.4191	10|5	0.30078|.	T|.	0.28|.	-21.219|-21.219	9.1807|9.1807	0.37141|0.37141	0.0:0.8168:0.0:0.1832|0.0:0.8168:0.0:0.1832	.|.	338;310|.	Q8WVB6-2;Q8WVB6|.	.;CTF18_HUMAN|.	V|G	505;338;310|205	ENSP00000313029:L505V;ENSP00000406252:L338V;ENSP00000262315:L310V|.	ENSP00000262315:L310V|.	L|V	+|+	1|2	2|0	CHTF18|CHTF18	781195|781195	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.967000|0.967000	0.64934|0.64934	3.942000|3.942000	0.56614|0.56614	0.564000|0.564000	0.29238|0.29238	-0.301000|-0.301000	0.09380|0.09380	TTG|GTT	.	.	.	weak		0.662	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092		G	841194	T	G	841194	3	3	226	1	0	0	0	0	1	0	0	0	3416	1722	60	5	958	5	CHTF18	16	841194	Missense_Mutation	SNP	T	TCGA-MH-A856-01A-11D-A34Z-10		841194	89513559	52	13766											
CREBBP	1387	hgsc.bcm.edu	37	chr16	3860645	3860645	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgaagtattcttgatatctgTagggaaggtgggcaaactgt	11	13	13	4	0	2	2	0	2	2	0	2	3	2	3	0	3	1	3	0	3	6	5			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr16:3860645T>C	ENST00000262367.5	-	3	1743	c.934A>G	c.(934-936)Aca>Gca	p.T312A	CREBBP_ENST00000382070.3_Missense_Mutation_p.T312A	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	312	Interaction with SRCAP.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		TTGATATCTGTAGGGAAGGTG	0.527			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.T312A		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.A934G						PASS	.						215	196	203					16																	3860645		2197	4300	6497	SO:0001583	missense	1387	exon3			TATCTGTAGGGAA	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.934A>G	chr16.hg19:g.3860645T>C	ENSP00000262367:p.Thr312Ala	121.0	0.0	.		95.0	29.0	.	NM_001079846	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	hg19	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	T	10.24	1.294678	0.23564	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	D;D	0.82433	-1.61;-1.52	5.28	-6.97	0.01616	.	0.454713	0.21929	N	0.067045	T	0.55847	0.1946	N	0.19112	0.55	0.22737	N	0.998795	B;B	0.24721	0.069;0.11	B;B	0.21546	0.035;0.011	T	0.60078	-0.7333	10	0.05525	T	0.97	-0.0051	5.1164	0.14836	0.2035:0.4842:0.0877:0.2246	.	380;312	Q4LE28;Q92793	.;CBP_HUMAN	A	312;380;312	ENSP00000262367:T312A;ENSP00000371502:T312A	ENSP00000262367:T312A	T	-	1	0	CREBBP	3800646	0.001000	0.12720	0.643000	0.29450	0.974000	0.67602	-0.279000	0.08479	-0.852000	0.04141	0.460000	0.39030	ACA	.	.	.	none		0.527	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		C	3860645	T	C	3860645	3	2	226	1	0	0	0	0	1	0	0	0	3863	1638	57	3	6510	3	CREBBP	16	3860645	Missense_Mutation	SNP	T	TCGA-MH-A856-01A-11D-A34Z-10	3019451	3860645	86494108	53	13767											
TMEM186	25880	hgsc.bcm.edu	37	chr16	8890188	8890188	+	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	gggagtacaagtaatagcctGgtggcaaagctaccactgtc	12	8	12	9	0	0	0	0	0	0	0	1	1	0	1	2	3	4	4	2	3	6	4			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr16:8890188G>A	ENST00000333050.6	-	2	296	c.263C>T	c.(262-264)cCa>cTa	p.P88L	PMM2_ENST00000537352.1_5'Flank|PMM2_ENST00000268261.4_5'Flank|TMEM186_ENST00000564869.1_Intron|PMM2_ENST00000566983.1_Intron|PMM2_ENST00000539622.1_5'Flank|PMM2_ENST00000569958.1_5'Flank	NM_015421.3	NP_056236.2	Q96B77	TM186_HUMAN	transmembrane protein 186	88						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	9						GTAATAGCCTGGTGGCAAAGC	0.527																																					p.P88L		Atlas-SNP	.											.	TMEM186	21	.	0			c.C263T						PASS	.						113	99	104					16																	8890188		2197	4300	6497	SO:0001583	missense	25880	exon2			TAGCCTGGTGGCA	BC015912	CCDS10535.1	16p13.2	2008-02-05	2007-02-08	2007-02-08	ENSG00000184857	ENSG00000184857			24530	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 51"	C16orf51		11230166	Standard	NM_015421		Approved	DKFZP564K2062	uc002cze.3	Q96B77	OTTHUMG00000129696	ENST00000333050.6:c.263C>T	chr16.hg19:g.8890188G>A	ENSP00000331640:p.Pro88Leu	70.0	0.0	.		57.0	23.0	.	NM_015421	B2RAY0|Q9Y4T4	Missense_Mutation	SNP	ENST00000333050.6	hg19	CCDS10535.1	.	.	.	.	.	.	.	.	.	.	G	12.72	2.022735	0.35701	.	.	ENSG00000184857	ENST00000333050	.	.	.	5.36	3.38	0.38709	.	0.000000	0.45606	D	0.000348	T	0.51126	0.1656	M	0.63428	1.95	0.54753	D	0.999989	P	0.37207	0.587	B	0.34242	0.178	T	0.54715	-0.8252	9	0.46703	T	0.11	-11.2014	10.9642	0.47403	0.1567:0.0:0.8433:0.0	.	88	Q96B77	TM186_HUMAN	L	88	.	ENSP00000331640:P88L	P	-	2	0	TMEM186	8797689	1.000000	0.71417	0.011000	0.14972	0.025000	0.11179	6.023000	0.70848	1.275000	0.44379	0.561000	0.74099	CCA	.	.	.	none		0.527	TMEM186-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251903.1	NM_015421		A	8890188	G	A	8890188	3	1	226	1	0	0	0	0	1	0	0	0	16120	1348	47	2	382	2	TMEM186	16	8890188	Missense_Mutation	SNP	G	TCGA-MH-A856-01A-11D-A34Z-10	5029543	8890188	81464565	54	13768											
SRCAP	10847	hgsc.bcm.edu	37	chr16	30731535	30731535	+	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	cctggaaggtcgtgtctctcGatatgaggcagacacatttc	9	11	11	10	2	1	2	0	1	1	1	5	4	1	3	1	3	0	1	1	3	2	2			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr16:30731535G>A	ENST00000262518.4	+	19	3255	c.2870G>A	c.(2869-2871)cGa>cAa	p.R957Q	SRCAP_ENST00000344771.4_Missense_Mutation_p.R957Q|SRCAP_ENST00000395059.2_Missense_Mutation_p.R957Q	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	957					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)			CGTGTCTCTCGATATGAGGCA	0.542																																					p.R957Q		Atlas-SNP	.											.	SRCAP	298	.	0			c.G2870A						PASS	.						183	184	183					16																	30731535		2197	4300	6497	SO:0001583	missense	10847	exon19			TCTCTCGATATGA	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.2870G>A	chr16.hg19:g.30731535G>A	ENSP00000262518:p.Arg957Gln	159.0	0.0	.		143.0	60.0	.	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	hg19	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	G	29.0	4.971261	0.92919	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.92249	-3.0;-2.87;-2.94	5.45	5.45	0.79879	.	0.000000	0.48286	D	0.000186	D	0.94574	0.8252	L	0.47716	1.5	0.43347	D	0.995408	D;D;D	0.89917	0.994;1.0;1.0	P;D;D	0.85130	0.884;0.997;0.994	D	0.94120	0.7378	10	0.45353	T	0.12	-7.4366	18.0556	0.89363	0.0:0.0:1.0:0.0	.	957;957;957	Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2	.;.;SRCAP_HUMAN	Q	957	ENSP00000262518:R957Q;ENSP00000378499:R957Q;ENSP00000343042:R957Q	ENSP00000262518:R957Q	R	+	2	0	SRCAP	30639036	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.067000	0.93955	2.569000	0.86673	0.484000	0.47621	CGA	.	.	.	none		0.542	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		A	30731535	G	A	30731535	3	1	226	1	0	0	0	0	1	0	0	0	15147	1058	37	1	2936	1	SRCAP	16	30731535	Missense_Mutation	SNP	G	TCGA-MH-A856-01A-11D-A34Z-10	21841347	30731535	59623218	55	13769											
CIRH1A	84916	hgsc.bcm.edu	37	chr16	69170698	69170698	+	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	atggcgagattatggagtatGatttacaggcgttaaacatc	13	12	11	5	2	0	2	0	1	0	1	1	4	0	3	0	3	2	2	0	3	5	5			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr16:69170698G>A	ENST00000314423.7	+	3	436	c.259G>A	c.(259-261)Gat>Aat	p.D87N	CIRH1A_ENST00000352319.4_Missense_Mutation_p.D87N|CIRH1A_ENST00000563094.1_Missense_Mutation_p.D87N			Q969X6	CIR1A_HUMAN	cirrhosis, autosomal recessive 1A (cirhin)	87					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)		TATGGAGTATGATTTACAGGC	0.488																																					p.D87N	Melanoma(69;1156 1278 4951 8715 52012)	Atlas-SNP	.											.	CIRH1A	48	.	0			c.G259A						PASS	.						239	237	238					16																	69170698		2198	4300	6498	SO:0001583	missense	84916	exon3			GAGTATGATTTAC	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.259G>A	chr16.hg19:g.69170698G>A	ENSP00000327179:p.Asp87Asn	304.0	0.0	.		226.0	85.0	.	NM_032830	Q8NCD9|Q8TF14|Q96SP0|Q96SR9|Q96SZ9|Q96T13|Q9BWK6	Missense_Mutation	SNP	ENST00000314423.7	hg19	CCDS10872.1	.	.	.	.	.	.	.	.	.	.	G	15.75	2.926883	0.52759	.	.	ENSG00000141076	ENST00000314423;ENST00000352319	T;T	0.44482	0.92;0.92	5.62	5.62	0.85841	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.50292	0.1607	L	0.52905	1.665	0.80722	D	1	P;D	0.61080	0.929;0.989	B;P	0.49683	0.296;0.619	T	0.37244	-0.9714	10	0.33940	T	0.23	.	19.6231	0.95667	0.0:0.0:1.0:0.0	.	87;87	Q969X6;Q969X6-3	CIR1A_HUMAN;.	N	87	ENSP00000327179:D87N;ENSP00000339164:D87N	ENSP00000327179:D87N	D	+	1	0	CIRH1A	67728199	1.000000	0.71417	1.000000	0.80357	0.486000	0.33341	8.755000	0.91646	2.818000	0.97014	0.655000	0.94253	GAT	.	.	.	none		0.488	CIRH1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268950.2	NM_032830		A	69170698	G	A	69170698	3	1	226	1	0	0	0	0	1	0	0	0	3436	1290	45	2	265	2	CIRH1A	16	69170698	Missense_Mutation	SNP	G	TCGA-MH-A856-01A-11D-A34Z-10	38439163	69170698	21184055	56	13770											
ATP2C2	9914	hgsc.bcm.edu	37	chr16	84482189	84482189	+	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	gccttggaagaggtgatccgCtactgcaccatgtacaacaa	12	8	10	11	1	0	2	0	1	0	1	1	3	1	3	3	2	4	3	3	2	5	3			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr16:84482189C>T	ENST00000262429.4	+	17	1643	c.1554C>T	c.(1552-1554)cgC>cgT	p.R518R	ATP2C2_ENST00000416219.2_Silent_p.R518R|ATP2C2_ENST00000420010.2_3'UTR	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	518					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						AGGTGATCCGCTACTGCACCA	0.532																																					p.R518R		Atlas-SNP	.											.	ATP2C2	75	.	0			c.C1554T						PASS	.						84	91	89					16																	84482189		1988	4150	6138	SO:0001819	synonymous_variant	9914	exon17			GATCCGCTACTGC	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.1554C>T	chr16.hg19:g.84482189C>T		91.0	0.0	.		80.0	24.0	.	NM_014861	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	Silent	SNP	ENST00000262429.4	hg19	CCDS42207.1																																																																																			.	.	.	none		0.532	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861		T	84482189	C	T	84482189	2	4	226	1	0	0	0	0	0	0	0	1	1144	784	28	2		2	ATP2C2	16	84482189	Silent	SNP	C	TCGA-MH-A856-01A-11D-A34Z-10	15311491	84482189	5872564	57	13771											
SLC25A11	8402	hgsc.bcm.edu	37	chr17	4841106	4841107	+	Frame_Shift_Ins	INS	-	-	G																															gatgaaggtgaggacggtgtINSgggggcccaggcgggcatag																										TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr17:4841106_4841107insG	ENST00000225665.7	-	8	1214_1215	c.874_875insC	c.(874-876)cacfs	p.H292fs	RNF167_ENST00000576229.1_5'Flank|RNF167_ENST00000571816.1_5'Flank|RNF167_ENST00000575111.1_5'Flank|RNF167_ENST00000572430.1_5'Flank|RNF167_ENST00000262482.6_5'Flank|SLC25A11_ENST00000544061.2_Frame_Shift_Ins_p.H241fs	NM_001165417.1|NM_003562.4	NP_001158889.1|NP_003553.2	Q02978	M2OM_HUMAN	solute carrier family 25 (mitochondrial carrier; oxoglutarate carrier), member 11	292					alpha-ketoglutarate transport (GO:0015742)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxoglutarate:malate antiporter activity (GO:0015367)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)	10						GAGGACGGTGTGGGGGCCCAGG	0.609																																					p.H292fs	Esophageal Squamous(144;1178 2388 18010 48797)	Atlas-Indel,Pindel	.											.	SLC25A11	22	.	0			c.875_876insC						PASS	.																																			SO:0001589	frameshift_variant	8402	exon8			.	X66114	CCDS11059.1, CCDS54069.1	17p13.3	2013-05-22			ENSG00000108528	ENSG00000108528		"Solute carriers"	10981	protein-coding gene	gene with protein product		604165		SLC20A4		10072597, 1457818	Standard	NM_003562		Approved	OGC	uc002fzo.2	Q02978	OTTHUMG00000099395	ENST00000225665.7:c.875dupC	chr17.hg19:g.4841111_4841111dupG	ENSP00000225665:p.His292fs	42.0	0.0	0		45.0	20.0	0.444444	NM_003562	F5GY65|O75537|Q969P7	Frame_Shift_Ins	INS	ENST00000225665.7	hg19	CCDS11059.1																																																																																			.	.	.	none		0.609	SLC25A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216852.4	NM_003562		G	4841107	-	G	4841106	7	5	226	1	0	1	1	0	0	0	0	0	14486	1696	59	0	73	0	SLC25A11	17	4841106	Frame_Shift_Ins	INS	-	TCGA-MH-A856-01A-11D-A34Z-10		4841106	76354104	58	13772											
MLLT6	4302	hgsc.bcm.edu	37	chr17	36865775	36865775	+	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	tgtgtgaggaagaagtgctgGaggtggacaacgtcaagtac	12	8	16	5	1	1	2	1	1	0	1	1	5	1	5	0	4	3	2	0	4	5	1			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr17:36865775G>C	ENST00000325718.7	+	6	590	c.499G>C	c.(499-501)Gag>Cag	p.E167Q	MLLT6_ENST00000378137.5_Missense_Mutation_p.E167Q	NM_005937.3	NP_005928	P55198	AF17_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6	167					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)					AGAAGTGCTGGAGGTGGACAA	0.562			T	MLL	AL																																p.E167Q		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.G499C						PASS	.						154	110	124					17																	36865775		2203	4300	6503	SO:0001583	missense	4302	exon6			GTGCTGGAGGTGG		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.499G>C	chr17.hg19:g.36865775G>C	ENSP00000316426:p.Glu167Gln	51.0	0.0	.		46.0	10.0	.	NM_005937	Q59F28|Q96IU3|Q9H5F6|Q9UF49	Missense_Mutation	SNP	ENST00000325718.7	hg19	CCDS11327.1	.	.	.	.	.	.	.	.	.	.	G	16.80	3.223152	0.58668	.	.	ENSG00000108292	ENST00000325718;ENST00000378137	T;T	0.14640	2.49;2.49	4.35	3.37	0.38596	Zinc finger, PHD-finger (1);Zinc finger, PHD-type (1);	0.066588	0.64402	D	0.000018	T	0.23926	0.0579	L	0.41356	1.27	0.45747	D	0.998647	D;D;D	0.63046	0.971;0.971;0.992	P;P;D	0.65233	0.786;0.786;0.933	T	0.01375	-1.1371	10	0.26408	T	0.33	.	13.395	0.60846	0.0:0.1591:0.8408:0.0	.	167;167;167	E9PEP1;Q6P2C6;P55198	.;.;AF17_HUMAN	Q	167	ENSP00000316426:E167Q;ENSP00000367377:E167Q	ENSP00000316426:E167Q	E	+	1	0	MLLT6	34119301	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.257000	0.95545	1.161000	0.42604	0.591000	0.81541	GAG	.	.	.	none		0.562	MLLT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256799.1	NM_005937		C	36865775	G	C	36865775	3	2	226	1	0	0	0	0	1	0	0	0	9637	1175	41	4	521	4	MLLT6	17	36865775	Missense_Mutation	SNP	G	TCGA-MH-A856-01A-11D-A34Z-10	32024669	36865775	44329435	59	13773											
ACLY	47	hgsc.bcm.edu	37	chr17	40054090	40054090	+	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	gctgtcctgctgggggctggCgtctggggtgagataaggag	5	9	20	7	1	1	1	0	1	1	1	2	3	2	2	1	6	1	3	1	6	1	1			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr17:40054090C>T	ENST00000352035.2	-	13	1471	c.1341G>A	c.(1339-1341)acG>acA	p.T447T	ACLY_ENST00000590151.1_Silent_p.T447T|ACLY_ENST00000393896.2_Silent_p.T447T|ACLY_ENST00000353196.1_Silent_p.T447T|ACLY_ENST00000537919.1_Silent_p.T186T	NM_001096.2	NP_001087.2	P53396	ACLY_HUMAN	ATP citrate lyase	447					ATP catabolic process (GO:0006200)|cellular carbohydrate metabolic process (GO:0044262)|cellular lipid metabolic process (GO:0044255)|citrate metabolic process (GO:0006101)|coenzyme A metabolic process (GO:0015936)|energy reserve metabolic process (GO:0006112)|lipid biosynthetic process (GO:0008610)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	citrate lyase complex (GO:0009346)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)		NTN1/ACLY(2)	breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	28		Breast(137;0.000143)				TGGGGGCTGGCGTCTGGGGTG	0.522																																					p.T447T	Colon(64;807 1396 15971 30971)	Atlas-SNP	.											.	ACLY	85	.	0			c.G1341A						PASS	.						37	38	38					17																	40054090		2203	4300	6503	SO:0001819	synonymous_variant	47	exon13			GGCTGGCGTCTGG	X64330	CCDS11412.1, CCDS11413.1	17q21.2	2010-04-27			ENSG00000131473	ENSG00000131473	2.3.3.8		115	protein-coding gene	gene with protein product	"ATP citrate synthase"	108728				1371749, 8088842	Standard	NM_001096		Approved	ATPCL, CLATP, ACL	uc002hyg.3	P53396	OTTHUMG00000133507	ENST00000352035.2:c.1341G>A	chr17.hg19:g.40054090C>T		31.0	0.0	.		35.0	15.0	.	NM_001096	B4DIM0|B4E3P0|Q13037|Q9BRL0	Silent	SNP	ENST00000352035.2	hg19	CCDS11412.1																																																																																			.	.	.	none		0.522	ACLY-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257465.1	NM_001096		T	40054090	C	T	40054090	2	4	226	1	0	0	0	0	0	0	0	1	143	755	27	1		1	ACLY	17	40054090	Silent	SNP	C	TCGA-MH-A856-01A-11D-A34Z-10	3188315	40054090	41141120	60	13774											
CABLES1	91768	hgsc.bcm.edu	37	chr18	20793942	20793942	+	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	tcttctttttattttttagaAtagtccttatcagtggcaga	9	20	6	6	0	3	2	1	0	2	2	4	2	4	2	1	1	0	1	1	1	5	9			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr18:20793942A>G	ENST00000256925.7	+	4	1012	c.1012A>G	c.(1012-1014)Ata>Gta	p.I338V	CABLES1_ENST00000420687.2_Splice_Site_p.I73V|CABLES1_ENST00000585061.1_Intron|TMEM241_ENST00000450466.2_Intron|CABLES1_ENST00000400473.2_Splice_Site_p.I11V	NM_001100619.2	NP_001094089.1	Q8TDN4	CABL1_HUMAN	Cdk5 and Abl enzyme substrate 1	338	Interacts with CDK3. {ECO:0000250}.				blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|nervous system development (GO:0007399)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)	cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			breast(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|stomach(1)	11	all_cancers(21;0.000102)|all_epithelial(16;2.48e-06)|Lung NSC(20;0.00696)|all_lung(20;0.0197)|Colorectal(14;0.0202)|Ovarian(20;0.127)					ATTTTTTAGAATAGTCCTTAT	0.348																																					p.I338V		Atlas-SNP	.											.	CABLES1	32	.	0			c.A1012G						PASS	.						82	75	77					18																	20793942		1857	4091	5948	SO:0001630	splice_region_variant	91768	exon4			TTTAGAATAGTCC	BC037218	CCDS42417.1, CCDS42418.1, CCDS58615.1	18q11.2	2005-08-16				ENSG00000134508			25097	protein-coding gene	gene with protein product		609194				12477932	Standard	NM_138375		Approved	HsT2563, FLJ35924	uc002kuc.2	Q8TDN4		ENST00000256925.7:c.1011-1A>G	chr18.hg19:g.20793942A>G		60.0	0.0	.		65.0	26.0	.	NM_001100619	B4DK60|Q8N3Y8|Q8NA22|Q9BTG1	Missense_Mutation	SNP	ENST00000256925.7	hg19	CCDS42417.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.339421	0.81911	.	.	ENSG00000134508	ENST00000400473;ENST00000256925;ENST00000420687	T;T;T	0.49432	0.78;0.78;0.82	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.62282	0.2415	L	0.56280	1.765	0.80722	D	1	P;D	0.59357	0.65;0.985	P;D	0.67548	0.743;0.952	T	0.57631	-0.7778	10	0.27082	T	0.32	-17.3786	15.8255	0.78703	1.0:0.0:0.0:0.0	.	73;338	Q8TDN4-2;Q8TDN4	.;CABL1_HUMAN	V	11;338;73	ENSP00000383321:I11V;ENSP00000256925:I338V;ENSP00000413851:I73V	ENSP00000256925:I338V	I	+	1	0	CABLES1	19047940	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.722000	0.91452	2.224000	0.72417	0.477000	0.44152	ATA	.	.	.	none		0.348	CABLES1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445198.2	NM_138375	Missense_Mutation	G	20793942	A	G	20793942	5	3	226	1	0	0	0	0	0	0	1	0	2531	115	4	3	1080	3	CABLES1	18	20793942	Splice_Site	SNP	A	TCGA-MH-A856-01A-11D-A34Z-10		20793942	57283306	61	13775											
EFNA2	1943	hgsc.bcm.edu	37	chr19	1295670	1295670	+	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	gccgagcgcatggagcactaCgtgctgtacatggtcaacgg	9	7	14	11	4	1	0	1	0	0	0	1	2	1	1	1	3	6	4	1	3	3	2	rs561395362		TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr19:1295670C>T	ENST00000215368.2	+	2	282	c.267C>T	c.(265-267)taC>taT	p.Y89Y	MUM1_ENST00000344663.3_Intron	NM_001405.3	NP_001396.2	O43921	EFNA2_HUMAN	ephrin-A2	89	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.				axon guidance (GO:0007411)|bone remodeling (GO:0046849)|cell-cell signaling (GO:0007267)|ephrin receptor signaling pathway (GO:0048013)|olfactory bulb development (GO:0021772)|osteoclast differentiation (GO:0030316)	anchored component of membrane (GO:0031225)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	ephrin receptor binding (GO:0046875)			lung(2)	2		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)		TGGAGCACTACGTGCTGTACA	0.706													C|||	1	0.000199681	0	0	5008	,	,		8346	0		0	False		,,,				2504	0.001				p.Y89Y		Atlas-SNP	.											.	EFNA2	8	.	0			c.C267T						PASS	.						25	21	22					19																	1295670		2198	4290	6488	SO:0001819	synonymous_variant	1943	exon2			GCACTACGTGCTG		CCDS12061.1	19p13	2011-03-09			ENSG00000099617	ENSG00000099617		"Ephrins"	3222	protein-coding gene	gene with protein product		602756		EPLG6			Standard	NM_001405		Approved	ELF-1, LERK6	uc002lry.2	O43921		ENST00000215368.2:c.267C>T	chr19.hg19:g.1295670C>T		54.0	0.0	.		52.0	22.0	.	NM_001405	O76020	Silent	SNP	ENST00000215368.2	hg19	CCDS12061.1																																																																																			.	.	.	none		0.706	EFNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450016.1	NM_001405		T	1295670	C	T	1295670	2	4	226	1	0	0	0	0	0	0	0	1	4953	547	19	1		1	EFNA2	19	1295670	Silent	SNP	C	TCGA-MH-A856-01A-11D-A34Z-10		1295670	57833313	62	13776											
DAZAP1	26528	hgsc.bcm.edu	37	chr19	1428952	1428953	+	Frame_Shift_Del	DEL	GG	GG	-																															acgctgccaatggctgggcaGgccagcccccgcccacgtgg																										TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr19:1428952_1428953delGG	ENST00000233078.4	+	8	819_820	c.658_659delGG	c.(658-660)ggcfs	p.G220fs	DAZAP1_ENST00000336761.6_Frame_Shift_Del_p.G220fs	NM_018959.2	NP_061832.2	Q96EP5	DAZP1_HUMAN	DAZ associated protein 1	220					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)		TGGCTGGGCAGGCCAGCCCCCG	0.688																																					p.219_220del		Atlas-Indel,Pindel	.											.	DAZAP1	52	.	0			c.657_658del						PASS	.																																			SO:0001589	frameshift_variant	26528	exon8			.		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.658_659delGG	chr19.hg19:g.1428952_1428953delGG	ENSP00000233078:p.Gly220fs	71.0	0.0	0		59.0	20.0	0.338983	NM_018959	Q96MJ3|Q9NRR9	Frame_Shift_Del	DEL	ENST00000233078.4	hg19	CCDS12065.1																																																																																			.	.	.	none		0.688	DAZAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449522.3	NM_170711		-	1428953	GG	-	1428952	7	5	226	1	0	1	0	1	0	0	0	0	4246	1000	35	0	688	0	DAZAP1	19	1428952	Frame_Shift_Del	DEL	GG	TCGA-MH-A856-01A-11D-A34Z-10	133282	1428952	57700031	63	13777											
KDM4B	23030	hgsc.bcm.edu	37	chr19	5039997	5039997	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggccatgacagtgggcgagTaccgccgcctggccaacagc	9	4	14	14	3	0	1	0	1	0	0	0	2	0	1	5	3	3	1	5	3	2	1			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr19:5039997T>C	ENST00000159111.4	+	4	510	c.292T>C	c.(292-294)Tac>Cac	p.Y98H	KDM4B_ENST00000536461.1_Missense_Mutation_p.Y98H|KDM4B_ENST00000381759.4_Missense_Mutation_p.Y98H	NM_015015.2	NP_055830	O94953	KDM4B_HUMAN	lysine (K)-specific demethylase 4B	98					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(1)|liver(1)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						AGTGGGCGAGTACCGCCGCCT	0.697																																					p.Y98H		Atlas-SNP	.											.	KDM4B	120	.	0			c.T292C						PASS	.						45	40	42					19																	5039997		2203	4300	6503	SO:0001583	missense	23030	exon4			GGCGAGTACCGCC	AB020683	CCDS12138.1	19p13.3	2013-01-23	2009-04-06	2009-04-06		ENSG00000127663		"Chromatin-modifying enzymes / K-demethylases", "Tudor domain containing"	29136	protein-coding gene	gene with protein product	"tudor domain containing 14B"	609765	"jumonji domain containing 2B"	JMJD2B		10048485, 15138608	Standard	NM_015015		Approved	KIAA0876, TDRD14B	uc002mbq.4	O94953		ENST00000159111.4:c.292T>C	chr19.hg19:g.5039997T>C	ENSP00000159111:p.Tyr98His	57.0	0.0	.		46.0	23.0	.	NM_015015	B9EGN8|D6W631|O75274|Q6P3R5|Q9P1V1|Q9UF40	Missense_Mutation	SNP	ENST00000159111.4	hg19	CCDS12138.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.505972	0.85282	.	.	ENSG00000127663	ENST00000159111;ENST00000381759;ENST00000536461	T;T;T	0.50277	0.75;0.75;0.75	4.04	4.04	0.47022	.	0.075962	0.56097	D	0.000036	T	0.67496	0.2899	M	0.76838	2.35	0.58432	D	0.999999	D;D;D	0.67145	0.996;0.993;0.994	D;D;D	0.74348	0.983;0.951;0.92	T	0.73170	-0.4067	10	0.87932	D	0	-36.4153	13.4363	0.61086	0.0:0.0:0.0:1.0	.	98;98;98	F5GX28;O94953-2;O94953	.;.;KDM4B_HUMAN	H	98	ENSP00000159111:Y98H;ENSP00000371178:Y98H;ENSP00000440495:Y98H	ENSP00000159111:Y98H	Y	+	1	0	KDM4B	4990997	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.730000	0.84881	1.817000	0.53016	0.379000	0.24179	TAC	.	.	.	none		0.697	KDM4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450558.1	NM_015015		C	5039997	T	C	5039997	3	2	226	1	0	0	0	0	1	0	0	0	8136	1638	57	3	298	3	KDM4B	19	5039997	Missense_Mutation	SNP	T	TCGA-MH-A856-01A-11D-A34Z-10	3611045	5039997	54088986	64	13778											
ANGPTL4	51129	hgsc.bcm.edu	37	chr19	8438718	8438718	+	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	gcggggccgctactacccgcTgcaggccaccaccatgttga	7	6	12	16	3	0	1	0	1	0	0	0	1	0	1	5	3	3	4	5	3	2	3			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr19:8438718T>A	ENST00000301455.2	+	7	1340	c.1169T>A	c.(1168-1170)cTg>cAg	p.L390Q	ANGPTL4_ENST00000541807.1_Missense_Mutation_p.L223Q|RAB11B-AS1_ENST00000597407.1_RNA|ANGPTL4_ENST00000393962.2_Missense_Mutation_p.L352Q|RAB11B-AS1_ENST00000597785.1_RNA|RAB11B-AS1_ENST00000593581.1_RNA	NM_139314.1	NP_647475.1	Q9BY76	ANGL4_HUMAN	angiopoietin-like 4	390	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				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						TACTACCCGCTGCAGGCCACC	0.622																																					p.L390Q		Atlas-SNP	.											.	ANGPTL4	21	.	0			c.T1169A						PASS	.						67	75	72					19																	8438718		2203	4300	6503	SO:0001583	missense	51129	exon7			ACCCGCTGCAGGC	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.1169T>A	chr19.hg19:g.8438718T>A	ENSP00000301455:p.Leu390Gln	59.0	0.0	.		47.0	19.0	.	NM_139314	A8MY84|B4E089|D6W670|F5H0I2|Q53HQ6|Q53HU1|Q6UXN0|Q9HBV4|Q9NZU4|Q9Y5B3	Missense_Mutation	SNP	ENST00000301455.2	hg19	CCDS12200.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.237776	0.79800	.	.	ENSG00000167772	ENST00000301455;ENST00000393962;ENST00000541807	T;T;T	0.80393	-1.37;-1.37;-1.37	5.62	5.62	0.85841	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1);	0.000000	0.64402	D	0.000004	D	0.92080	0.7490	M	0.93550	3.43	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.93951	0.7232	10	0.87932	D	0	.	14.6557	0.68831	0.0:0.0:0.0:1.0	.	352;390	A8MY84;Q9BY76	.;ANGL4_HUMAN	Q	390;352;223	ENSP00000301455:L390Q;ENSP00000377534:L352Q;ENSP00000439833:L223Q	ENSP00000301455:L390Q	L	+	2	0	ANGPTL4	8344718	1.000000	0.71417	0.934000	0.37439	0.634000	0.38068	7.489000	0.81451	2.136000	0.66102	0.533000	0.62120	CTG	.	.	.	none		0.622	ANGPTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460322.1	NM_139314		A	8438718	T	A	8438718	3	1	226	1	0	0	0	0	1	0	0	0	616	1580	55	5	1195	5	ANGPTL4	19	8438718	Missense_Mutation	SNP	T	TCGA-MH-A856-01A-11D-A34Z-10	3398721	8438718	50690265	65	13779											
RAD23A	5886	hgsc.bcm.edu	37	chr19	13060221	13060221	+	Splice_Site	DEL	A	A	-																															ggagaaccctcagcttttacAggtgtggtcccaagggcaga																										TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr19:13060221delA	ENST00000586534.1	+	7	873	c.812delA	c.(811-813)cag>cg	p.Q272fs	RAD23A_ENST00000588826.2_3'UTR|RAD23A_ENST00000541222.1_Splice_Site_p.Q107fs|RAD23A_ENST00000592268.1_Splice_Site_p.Q271fs|RAD23A_ENST00000316856.3_Splice_Site_p.Q271fs			P54725	RD23A_HUMAN	RAD23 homolog A (S. cerevisiae)	272					nucleotide-excision repair (GO:0006289)|positive regulation of viral genome replication (GO:0045070)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	damaged DNA binding (GO:0003684)|polyubiquitin binding (GO:0031593)|single-stranded DNA binding (GO:0003697)|ubiquitin-specific protease binding (GO:1990381)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)	12						CAGCTTTTACAGGTGTGGTCC	0.602								Nucleotide excision repair (NER)																													p.Q271fs		Atlas-Indel,Pindel	.											.	RAD23A	29	.	0			c.811delC						PASS	.						53	57	56					19																	13060221		2203	4300	6503	SO:0001630	splice_region_variant	5886	exon7			.		CCDS12289.1, CCDS59357.1, CCDS59358.1	19p13.2	2008-07-17	2001-11-28			ENSG00000179262			9812	protein-coding gene	gene with protein product	"RAD23, yeast homolog, A"	600061	"RAD23 (S. cerevisiae) homolog A"			7851894	Standard	NM_005053		Approved	HHR23A, MGC111083	uc002mvw.2	P54725		ENST00000586534.1:c.813+1A>-	chr19.hg19:g.13060221delA		65.0	0.0	0		52.0	25.0	0.480769	NM_005053	K7ESE3|Q59EU8|Q5M7Z1	Frame_Shift_Del	DEL	ENST00000586534.1	hg19	CCDS12289.1																																																																																			.	.	.	none		0.602	RAD23A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452752.1	NM_005053	Frame_Shift_Del	-	13060221	A	-	13060221	8	5	226	1	0	1	0	1	0	0	1	0	12995	202	7	0	838	0	RAD23A	19	13060221	Splice_Site	DEL	A	TCGA-MH-A856-01A-11D-A34Z-10	4621503	13060221	46068762	66	13780											
RASGRP4	115727	hgsc.bcm.edu	37	chr19	38903684	38903684	+	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	tcagggtcataattcttgaaCacagacttcagaggagtgtg	12	11	11	7	0	4	3	3	1	1	2	4	4	4	4	0	2	1	0	0	2	2	4			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr19:38903684C>T	ENST00000587738.1	-	12	1492	c.1422G>A	c.(1420-1422)gtG>gtA	p.V474V	RASGRP4_ENST00000586305.1_Silent_p.V460V|RASGRP4_ENST00000426920.2_Silent_p.V285V|RASGRP4_ENST00000433821.2_Silent_p.V382V|RASGRP4_ENST00000587753.1_Silent_p.V405V|RASGRP4_ENST00000293062.9_Silent_p.V377V|RASGRP4_ENST00000454404.2_Silent_p.V440V			Q8TDF6	GRP4_HUMAN	RAS guanyl releasing protein 4	474	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of phospholipase C activity (GO:0007202)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|myeloid cell differentiation (GO:0030099)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|response to extracellular stimulus (GO:0009991)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|GTP-dependent protein binding (GO:0030742)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			cervix(1)|kidney(1)|large_intestine(4)|lung(12)|pancreas(1)|prostate(3)|skin(1)	23	all_cancers(60;4.21e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			AATTCTTGAACACAGACTTCA	0.532																																					p.V474V		Atlas-SNP	.											.	RASGRP4	54	.	0			c.G1422A						PASS	.						50	53	52					19																	38903684		1927	4137	6064	SO:0001819	synonymous_variant	115727	exon12			CTTGAACACAGAC	AY048119	CCDS46068.1, CCDS54262.1, CCDS54263.1, CCDS54264.1	19q13.1	2013-01-10						"EF-hand domain containing"	18958	protein-coding gene	gene with protein product		607320				11956218	Standard	NM_170604		Approved		uc021uub.1	Q8TDF6		ENST00000587738.1:c.1422G>A	chr19.hg19:g.38903684C>T		53.0	0.0	.		40.0	19.0	.	NM_170604	A6H8M4|C0LTP2|C0LTP3|C0LTP4|C0LTP5|C0LTP7|C9J416|C9JHZ1|Q8N858|Q96QN5|Q96QN6|Q96QN7	Silent	SNP	ENST00000587738.1	hg19	CCDS46068.1																																																																																			.	.	.	none		0.532	RASGRP4-013	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460540.1	NM_170604		T	38903684	C	T	38903684	2	4	226	1	0	0	0	0	0	0	0	1	13090	465	17	2		2	RASGRP4	19	38903684	Silent	SNP	C	TCGA-MH-A856-01A-11D-A34Z-10	25843463	38903684	20225299	67	13781											
DLGAP4	22839	hgsc.bcm.edu	37	chr20	35060886	35060886	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcagtgggcacatgctcaaaAccaccaagaacaacactact	16	6	6	13	0	2	1	2	0	0	1	2	1	2	1	2	1	5	2	2	1	6	1			TCGA-MH-A856-01A-11D-A34Z-10	TCGA-MH-A856-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	08268f2c-7eb1-4f12-8ef8-7878585d4e39	e6f69dd8-8606-463e-a198-de6007153945	g.chr20:35060886A>G	ENST00000373907.2	+	2	965	c.766A>G	c.(766-768)Acc>Gcc	p.T256A	DLGAP4_ENST00000373913.3_Missense_Mutation_p.T256A|DLGAP4_ENST00000339266.5_Missense_Mutation_p.T256A|DLGAP4_ENST00000401952.2_Missense_Mutation_p.T256A			Q9Y2H0	DLGP4_HUMAN	discs, large (Drosophila) homolog-associated protein 4	256					cell-cell signaling (GO:0007267)	membrane (GO:0016020)|synapse (GO:0045202)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(20)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	37	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				CATGCTCAAAACCACCAAGAA	0.627																																					p.T256A		Atlas-SNP	.											.	DLGAP4	111	.	0			c.A766G						PASS	.						69	66	67					20																	35060886		2203	4300	6503	SO:0001583	missense	22839	exon2			CTCAAAACCACCA	AF088030	CCDS13274.1, CCDS13275.1	20q11.23	2010-02-05			ENSG00000080845	ENSG00000080845			24476	protein-coding gene	gene with protein product						9115257	Standard	XM_005260329		Approved	DAP4, KIAA0964, SAPAP4	uc010zvp.2	Q9Y2H0	OTTHUMG00000032390	ENST00000373907.2:c.766A>G	chr20.hg19:g.35060886A>G	ENSP00000363014:p.Thr256Ala	78.0	0.0	.		67.0	26.0	.	NM_014902	E1P5T5|Q5QPG4|Q5T2Y4|Q5T2Y5|Q9H137|Q9H138|Q9H1L7	Missense_Mutation	SNP	ENST00000373907.2	hg19		.	.	.	.	.	.	.	.	.	.	A	2.470	-0.322180	0.05350	.	.	ENSG00000080845	ENST00000373913;ENST00000401952;ENST00000373907;ENST00000339266	T;T;T;T	0.15834	2.39;2.39;2.39;2.39	5.37	-1.76	0.08006	.	0.677891	0.15516	N	0.258311	T	0.04952	0.0133	N	0.04018	-0.295	0.25098	N	0.990804	B	0.02656	0.0	B	0.01281	0.0	T	0.40496	-0.9560	10	0.09590	T	0.72	.	4.2281	0.10590	0.3059:0.0:0.3662:0.3279	.	256	Q9Y2H0-1	.	A	256	ENSP00000363023:T256A;ENSP00000384954:T256A;ENSP00000363014:T256A;ENSP00000341633:T256A	ENSP00000341633:T256A	T	+	1	0	DLGAP4	34494300	0.992000	0.36948	0.904000	0.35570	0.983000	0.72400	0.322000	0.19576	-0.216000	0.10048	-0.252000	0.11476	ACC	.	.	.	none		0.627	DLGAP4-007	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000079025.2	NM_014902		G	35060886	A	G	35060886	3	3	226	1	0	0	0	0	1	0	0	0	4564	43	2	3	768	3	DLGAP4	20	35060886	Missense_Mutation	SNP	A	TCGA-MH-A856-01A-11D-A34Z-10		35060886	27964634	68	13782											
MTOR	2475	hgsc.bcm.edu	37	chr1	11174395	11174395	+	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	tgtccatcagcctccagttcAgcaaggggtcatagacaaag	12	8	10	11	0	3	1	3	0	0	1	5	1	5	1	3	2	2	2	3	2	3	2			TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr1:11174395A>T	ENST00000361445.4	-	53	7356	c.7280T>A	c.(7279-7281)cTg>cAg	p.L2427Q	MTOR_ENST00000376838.1_Missense_Mutation_p.L632Q	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	2427	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	CCTCCAGTTCAGCAAGGGGTC	0.537																																					p.L2427Q		Atlas-SNP	.											MTOR,NS,carcinoma,+1,2	MTOR	327	.	0			c.T7280A						PASS	.						135	115	122					1																	11174395		2203	4300	6503	SO:0001583	missense	2475	exon53			CAGTTCAGCAAGG	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.7280T>A	chr1.hg19:g.11174395A>T	ENSP00000354558:p.Leu2427Gln	70.0	0.0	.		44.0	14.0	.	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	hg19	CCDS127.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.842624	0.91197	.	.	ENSG00000198793	ENST00000361445;ENST00000376838;ENST00000455339	T;T;T	0.80033	-1.33;-1.33;-1.33	5.89	5.89	0.94794	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.000000	0.85682	D	0.000000	D	0.89966	0.6868	M	0.82056	2.57	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.91209	0.4997	10	0.87932	D	0	-16.8498	15.497	0.75662	1.0:0.0:0.0:0.0	.	2427	P42345	MTOR_HUMAN	Q	2427;632;83	ENSP00000354558:L2427Q;ENSP00000366034:L632Q;ENSP00000398745:L83Q	ENSP00000354558:L2427Q	L	-	2	0	MTOR	11096982	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.923000	0.92808	2.254000	0.74563	0.533000	0.62120	CTG	.	.	.	none		0.537	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		T	11174395	A	T	11174395	3	4	227	1	0	0	0	0	1	0	0	0	9961	188	7	5	393	5	MTOR	1	11174395	Missense_Mutation	SNP	A	TCGA-MH-A857-01A-11D-A34Z-10		11174395	238076226	1	13783											
DENND2C	163259	hgsc.bcm.edu	37	chr1	115130431	115130431	+	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	aggaagtggcgtacacttcgGgaggtgtgggacttacggaa	10	8	17	6	3	0	0	0	0	0	0	1	4	0	4	0	6	2	1	0	6	4	3			TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr1:115130431G>T	ENST00000393274.1	-	19	3199	c.2574C>A	c.(2572-2574)tcC>tcA	p.S858S	DENND2C_ENST00000481894.1_5'UTR|DENND2C_ENST00000393277.1_Silent_p.S746S|DENND2C_ENST00000393276.3_Silent_p.S801S	NM_001256404.1	NP_001243333.1	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	858	dDENN. {ECO:0000255|PROSITE- ProRule:PRU00306}.				positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|breast(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|skin(3)	37	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTACACTTCGGGAGGTGTGGG	0.478																																					p.S858S		Atlas-SNP	.											.	DENND2C	105	.	0			c.C2574A						PASS	.						104	87	93					1																	115130431		2203	4300	6503	SO:0001819	synonymous_variant	163259	exon19			ACTTCGGGAGGTG		CCDS875.1, CCDS58018.1	1p13.2-p13.1	2012-10-03			ENSG00000175984	ENSG00000175984		"DENN/MADD domain containing"	24748	protein-coding gene	gene with protein product							Standard	NM_198459		Approved	FLJ37099, DKFZp686G0351, DKFZp779P1149, dJ1156J9.1, RP5-1156J9.1	uc001efd.1	Q68D51	OTTHUMG00000011893	ENST00000393274.1:c.2574C>A	chr1.hg19:g.115130431G>T		149.0	0.0	.		95.0	5.0	.	NM_001256404	B1AL26|Q5TCX6|Q6P3R3	Silent	SNP	ENST00000393274.1	hg19	CCDS58018.1																																																																																			.	.	.	none		0.478	DENND2C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000314822.1	NM_198459		T	115130431	G	T	115130431	2	4	227	1	0	0	0	0	0	0	0	1	4432	1219	43	4		4	DENND2C	1	115130431	Silent	SNP	G	TCGA-MH-A857-01A-11D-A34Z-10	103956036	115130431	134120190	2	13784											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228547456	228547466	+	Intron	DEL	GCAGGCCGGAG	GCAGGCCGGAG	-																															gccaggtgctggccagccccGcaggccggaggcagaaccag																								rs377484630|rs370692094		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	GCAGGCCGGAG	GCAGGCCGGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr1:228547456_228547466delGCAGGCCGGAG	ENST00000422127.1	+	80	18705				OBSCN_ENST00000570156.2_Intron|OBSCN_ENST00000366709.4_Frame_Shift_Del_p.RRPE3407fs|OBSCN_ENST00000284548.11_Frame_Shift_Del_p.RRPE6288fs|OBSCN_ENST00000366707.4_Intron	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF						apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GGCCAGCCCCGCAGGCCGGAGGCAGAACCAG	0.706																																					p.6288_6291del		Atlas-Indel,Pindel	.											.	OBSCN	2142	.	0			c.18862_18872del						PASS	.																																			SO:0001627	intron_variant	84033	exon81			.	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.18662-2811GCAGGCCGGAG>-	chr1.hg19:g.228547456_228547466delGCAGGCCGGAG		104.0	0.0	0		54.0	13.0	0.240741	NM_052843	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Frame_Shift_Del	DEL	ENST00000422127.1	hg19	CCDS58065.1																																																																																			.	.	.	none		0.706	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		-	228547466	GCAGGCCGGAG	-	228547456	6	5	227	0	1	1	0	1	0	0	0	0	10819	1087	38	0		0	OBSCN	1	228547456	Intron	DEL	GCAGGCCGGAG	TCGA-MH-A857-01A-11D-A34Z-10	113417025	228547456	20703165	3	13785											
LYST	1130	hgsc.bcm.edu	37	chr1	235827769	235827769	+	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	tccaaattcctcttaccttaCaattccattttctaatcccc	10	16	0	15	0	2	0	0	0	2	0	6	0	6	0	6	0	2	0	6	0	5	7			TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr1:235827769C>A	ENST00000389794.3	-	51	11365	c.11191G>T	c.(11191-11193)Gta>Tta	p.V3731L	LYST_ENST00000473037.1_5'UTR|LYST_ENST00000389793.2_Missense_Mutation_p.V3731L			Q99698	LYST_HUMAN	lysosomal trafficking regulator	3731					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)			TCTTACCTTACAATTCCATTT	0.373																																					p.V3731L		Atlas-SNP	.											.	LYST	370	.	0			c.G11191T						PASS	.						66	65	66					1																	235827769		2203	4300	6503	SO:0001583	missense	1130	exon51			ACCTTACAATTCC	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.11191G>T	chr1.hg19:g.235827769C>A	ENSP00000374444:p.Val3731Leu	81.0	0.0	.		60.0	20.0	.	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	hg19	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	C	34	5.390459	0.95988	.	.	ENSG00000143669	ENST00000389794;ENST00000389793	T;T	0.32988	1.43;1.43	5.98	5.98	0.97165	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	0.51176	0.1659	L	0.46614	1.455	0.80722	D	1	D	0.69078	0.997	D	0.66979	0.948	T	0.41233	-0.9520	10	0.59425	D	0.04	.	20.4581	0.99154	0.0:1.0:0.0:0.0	.	3731	Q99698	LYST_HUMAN	L	3731	ENSP00000374444:V3731L;ENSP00000374443:V3731L	ENSP00000374443:V3731L	V	-	1	0	LYST	233894392	1.000000	0.71417	0.994000	0.49952	0.950000	0.60333	7.818000	0.86416	2.835000	0.97688	0.650000	0.86243	GTA	.	.	.	none		0.373	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			A	235827769	C	A	235827769	3	1	227	1	0	0	0	0	1	0	0	0	9135	478	17	4	226	4	LYST	1	235827769	Missense_Mutation	SNP	C	TCGA-MH-A857-01A-11D-A34Z-10	7280313	235827769	13422852	4	13786											
B3GNT2	10678	hgsc.bcm.edu	37	chr2	62449390	62449390	+	Missense_Mutation	SNP	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	tcgaagaataaagttgttggGtatcctgatgatggcaaatg	13	12	12	4	1	0	3	0	2	0	1	2	4	1	3	1	2	0	4	1	2	6	4			TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr2:62449390G>A	ENST00000301998.4	+	2	287	c.35G>A	c.(34-36)gGt>gAt	p.G12D	B3GNT2_ENST00000405767.1_Missense_Mutation_p.G12D	NM_006577.5	NP_006568.2	Q9NY97	B3GN2_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	12					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)			AAGTTGTTGGGTATCCTGATG	0.343																																					p.G12D		Atlas-SNP	.											.	B3GNT2	34	.	0			c.G35A						PASS	.						80	81	81					2																	62449390		2203	4300	6503	SO:0001583	missense	10678	exon2			TGTTGGGTATCCT	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.35G>A	chr2.hg19:g.62449390G>A	ENSP00000305595:p.Gly12Asp	179.0	0.0	.		99.0	31.0	.	NM_006577	Q54AC1|Q9NQQ9|Q9NQR0|Q9NUT9	Missense_Mutation	SNP	ENST00000301998.4	hg19	CCDS1870.1	.	.	.	.	.	.	.	.	.	.	G	18.74	3.688762	0.68271	.	.	ENSG00000170340	ENST00000301998;ENST00000405767	T;T	0.28895	1.59;1.59	6.02	6.02	0.97574	.	0.540943	0.20145	N	0.098292	T	0.53302	0.1788	M	0.72118	2.19	0.54753	D	0.999986	D	0.60575	0.988	P	0.56398	0.797	T	0.51498	-0.8698	10	0.66056	D	0.02	.	20.5407	0.99260	0.0:0.0:1.0:0.0	.	12	Q9NY97	B3GN2_HUMAN	D	12	ENSP00000305595:G12D;ENSP00000384692:G12D	ENSP00000305595:G12D	G	+	2	0	B3GNT2	62302894	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.305000	0.51873	2.865000	0.98341	0.655000	0.94253	GGT	.	.	.	none		0.343	B3GNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251606.2	NM_006577		A	62449390	G	A	62449390	3	1	227	1	0	0	0	0	1	0	0	0	1257	1261	44	2	37	2	B3GNT2	2	62449390	Missense_Mutation	SNP	G	TCGA-MH-A857-01A-11D-A34Z-10		62449390	180749983	5	13787											
EFHB	151651	hgsc.bcm.edu	37	chr3	19947241	19947250	+	Splice_Site	DEL	CCTGTGGAAA	CCTGTGGAAA	-																															actttcggttctttgcctctCctgtggaaaaagaaaggaag																										TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	CCTGTGGAAA	CCTGTGGAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr3:19947241_19947250delCCTGTGGAAA	ENST00000295824.9	-	6	1450	c.1289delTTTCCACAGG	c.(1288-1290)gtt>gt	p.V430fs	EFHB_ENST00000344838.4_Splice_Site_p.V300fs|EFHB_ENST00000498089.1_5'UTR	NM_144715.3	NP_653316.3	Q8N7U6	EFHB_HUMAN	EF-hand domain family, member B	430							calcium ion binding (GO:0005509)			breast(2)|endometrium(4)|kidney(1)|lung(17)|prostate(1)|urinary_tract(1)	26						CTTTGCCTCTCCTGTGGAAAAAGAAAGGAA	0.381																																					p.430_430del		Atlas-Indel,Pindel	.											.	EFHB	186	.	0			c.1289_1290del						PASS	.																																			SO:0001630	splice_region_variant	151651	exon6			.	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.1289-1TTTCCACAGG>-	chr3.hg19:g.19947241_19947250delCCTGTGGAAA		124.0	0.0	0		65.0	15.0	0.230769	NM_144715	A6ND25|A8MPR3|Q6ZWK9|Q8IV58|Q96LQ6	Frame_Shift_Del	DEL	ENST00000295824.9	hg19	CCDS33715.2																																																																																			.	.	.	none		0.381	EFHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318673.2	NM_144715	Frame_Shift_Del	-	19947250	CCTGTGGAAA	-	19947241	8	5	227	1	0	1	0	1	0	0	1	0	4947	869	30	0	1244	0	EFHB	3	19947241	Splice_Site	DEL	CCTGTGGAAA	TCGA-MH-A857-01A-11D-A34Z-10		19947241	178075189	6	13788											
ST3GAL6	10402	hgsc.bcm.edu	37	chr3	98512536	98512536	+	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	tagaacgcgtatcacaatgtGactgcagagcagctcttttt	11	12	9	9	2	2	3	1	1	1	2	2	3	2	3	0	0	4	4	0	0	4	4			TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr3:98512536G>T	ENST00000483910.1	+	10	1216	c.927G>T	c.(925-927)gtG>gtT	p.V309V	ST3GAL6_ENST00000265261.6_Silent_p.V191V|ST3GAL6_ENST00000394162.1_Silent_p.V309V|ST3GAL6_ENST00000462152.1_3'UTR	NM_001271146.1	NP_001258075.1	Q9Y274	SIA10_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	309					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|cellular response to interleukin-6 (GO:0071354)|glycolipid metabolic process (GO:0006664)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,3-sialyltransferase activity (GO:0052798)			breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(1)	19						ATCACAATGTGACTGCAGAGC	0.353																																					p.V362V		Atlas-SNP	.											.	ST3GAL6	41	.	0			c.G1086T						PASS	.						115	120	118					3																	98512536		2203	4300	6503	SO:0001819	synonymous_variant	10402	exon10			CAATGTGACTGCA	AF119391	CCDS2933.1, CCDS59452.1, CCDS74968.1	3q12.2	2013-03-01	2005-02-07	2005-02-07	ENSG00000064225	ENSG00000064225		"Sialyltransferases"	18080	protein-coding gene	gene with protein product		607156	"sialyltransferase 10 (alpha-2,3-sialyltransferase VI)"	SIAT10		10206952	Standard	NM_006100		Approved	ST3GALVI	uc010hpd.4	Q9Y274	OTTHUMG00000159047	ENST00000483910.1:c.927G>T	chr3.hg19:g.98512536G>T		140.0	0.0	.		87.0	25.0	.	NM_001271145	B2RCH2|B3KMI1|D3DN39|F8W6U0	Silent	SNP	ENST00000483910.1	hg19	CCDS2933.1																																																																																			.	.	.	none		0.353	ST3GAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353013.2	NM_006100		T	98512536	G	T	98512536	2	4	227	1	0	0	0	0	0	0	0	1	15231	1277	45	4		4	ST3GAL6	3	98512536	Silent	SNP	G	TCGA-MH-A857-01A-11D-A34Z-10	78565295	98512536	99509894	7	13789											
DSPP	1834	hgsc.bcm.edu	37	chr4	88537513	88537513	+	Missense_Mutation	SNP	A	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	gacagcagtgacagcaatgaAagcagcgacagcagtgacag	16	3	13	9	1	0	3	0	3	0	0	0	5	0	3	0	0	5	4	0	0	2	0	rs112275895		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr4:88537513A>C	ENST00000282478.7	+	4	3732	c.3699A>C	c.(3697-3699)gaA>gaC	p.E1233D	DSPP_ENST00000399271.1_Missense_Mutation_p.E1233D|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1233	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcaatgaaagcagcgaca	0.547																																					p.E1233D		Atlas-SNP	.											.	DSPP	174	.	0			c.A3699C						PASS	.																																			SO:0001583	missense	1834	exon5			CAATGAAAGCAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3699A>C	chr4.hg19:g.88537513A>C	ENSP00000282478:p.Glu1233Asp	116.0	0.0	.		88.0	13.0	.	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	hg19	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.785366	0.00628	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88741	-2.42;-2.42	2.61	-5.21	0.02815	.	.	.	.	.	T	0.57213	0.2038	N	0.01048	-1.04	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.57347	-0.7827	9	0.02654	T	1	.	0.7125	0.00926	0.2623:0.1881:0.1298:0.4197	.	1233	Q9NZW4	DSPP_HUMAN	D	1233	ENSP00000382213:E1233D;ENSP00000282478:E1233D	ENSP00000282478:E1233D	E	+	3	2	DSPP	88756537	0.003000	0.15002	0.000000	0.03702	0.000000	0.00434	-2.769000	0.00780	-2.252000	0.00699	-3.496000	0.00033	GAA	.	A|0.500;C|0.500	0.500	weak		0.547	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		C	88537513	A	C	88537513	3	2	227	1	0	0	0	0	1	0	0	0	4784	11	1	5	3713	5	DSPP	4	88537513	Missense_Mutation	SNP	A	TCGA-MH-A857-01A-11D-A34Z-10		88537513	102616763	8	13790											
PCDHA10	56139	hgsc.bcm.edu	37	chr5	140236456	140236456	+	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	cggatgaaggaataaacaagGaaatgatgtattcatttagc	17	10	10	4	1	1	2	1	2	0	0	1	5	1	5	0	3	2	1	0	3	8	5			TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr5:140236456G>T	ENST00000307360.5	+	1	823	c.823G>T	c.(823-825)Gaa>Taa	p.E275*	PCDHA9_ENST00000532602.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000506939.2_Nonsense_Mutation_p.E275*|PCDHA4_ENST00000512229.2_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	275	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(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)			AATAAACAAGGAAATGATGTA	0.363																																					p.E275X		Atlas-SNP	.											.	PCDHA10	358	.	0			c.G823T						PASS	.						76	75	75					5																	140236456		2196	4270	6466	SO:0001587	stop_gained	56139	exon1			AACAAGGAAATGA	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.823G>T	chr5.hg19:g.140236456G>T	ENSP00000304234:p.Glu275*	158.0	0.0	.		127.0	52.0	.	NM_031859	A1L493|O75280|Q9NRU2	Nonsense_Mutation	SNP	ENST00000307360.5	hg19	CCDS54921.1	.	.	.	.	.	.	.	.	.	.	G	36	5.642740	0.96704	.	.	ENSG00000250120	ENST00000506939;ENST00000307360	.	.	.	4.29	4.29	0.51040	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	.	17.2947	0.87167	0.0:0.0:1.0:0.0	.	.	.	.	X	275	.	ENSP00000304234:E275X	E	+	1	0	PCDHA10	140216640	0.849000	0.29639	0.913000	0.36048	0.983000	0.72400	1.747000	0.38298	2.383000	0.81215	0.561000	0.74099	GAA	.	.	.	none		0.363	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		T	140236456	G	T	140236456	4	4	227	1	0	0	0	0	0	1	0	0	11527	1175	41	4	825	4	PCDHA10	5	140236456	Nonsense_Mutation	SNP	G	TCGA-MH-A857-01A-11D-A34Z-10		140236456	40678804	9	13791											
ERGIC1	57222	hgsc.bcm.edu	37	chr5	172362237	172362237	+	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	ccgcatcatccctgcaatctGgttccgctacgacctcagcc	7	9	7	18	3	3	0	2	0	1	0	5	1	5	0	5	1	3	4	5	1	2	2			TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr5:172362237G>T	ENST00000393784.3	+	9	828	c.689G>T	c.(688-690)tGg>tTg	p.W230L		NM_001031711.2	NP_001026881.1	Q969X5	ERGI1_HUMAN	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	230					ER to Golgi vesicle-mediated transport (GO:0006888)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)	9	Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CCTGCAATCTGGTTCCGCTAC	0.582																																					p.W230L		Atlas-SNP	.											.	ERGIC1	35	.	0			c.G689T						PASS	.						91	84	86					5																	172362237		2203	4300	6503	SO:0001583	missense	57222	exon9			CAATCTGGTTCCG	AF267855	CCDS34292.1	5q35.1	2009-11-06			ENSG00000113719	ENSG00000113719			29205	protein-coding gene	gene with protein product						10574461, 15308636	Standard	NM_001031711		Approved	ERGIC32, ERGIC-32, KIAA1181, NET24	uc003mbw.4	Q969X5	OTTHUMG00000130520	ENST00000393784.3:c.689G>T	chr5.hg19:g.172362237G>T	ENSP00000377374:p.Trp230Leu	113.0	0.0	.		83.0	4.0	.	NM_001031711	Q9H0L0|Q9H2J2|Q9ULN9	Missense_Mutation	SNP	ENST00000393784.3	hg19	CCDS34292.1	.	.	.	.	.	.	.	.	.	.	G	35	5.463136	0.96257	.	.	ENSG00000113719	ENST00000393784	.	.	.	5.88	5.88	0.94601	Domain of unknown function DUF1692 (1);	0.000000	0.85682	D	0.000000	D	0.83326	0.5230	M	0.77103	2.36	0.80722	D	1	D;D	0.89917	0.985;1.0	P;D	0.91635	0.783;0.999	D	0.84050	0.0369	9	0.72032	D	0.01	-17.8113	19.8311	0.96636	0.0:0.0:1.0:0.0	.	175;230	B4E0N6;Q969X5	.;ERGI1_HUMAN	L	230	.	ENSP00000377374:W230L	W	+	2	0	ERGIC1	172294843	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.141000	0.94612	2.790000	0.95986	0.591000	0.81541	TGG	.	.	.	none		0.582	ERGIC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252938.3	NM_020462		T	172362237	G	T	172362237	3	4	227	1	0	0	0	0	1	0	0	0	5225	1357	47	4	723	4	ERGIC1	5	172362237	Missense_Mutation	SNP	G	TCGA-MH-A857-01A-11D-A34Z-10	32125781	172362237	8553023	10	13792											
CDSN	170679	hgsc.bcm.edu	37	chr6	31085252	31085252	+	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	ggtcgttaggggaggtgataCgcgtggggtccttacaaggg	7	9	19	6	3	0	1	0	1	0	0	2	2	1	2	1	7	2	1	1	7	4	3	rs370680006	byFrequency	TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr6:31085252C>T	ENST00000259881.9	+	1	61				CDSN_ENST00000376288.2_Missense_Mutation_p.R47H|PSORS1C1_ENST00000467107.1_3'UTR	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						GGAGGTGATACGCGTGGGGTC	0.567													C|||	2	0.000399361	0.0015	0	5008	,	,		18117	0		0	False		,,,				2504	0				p.R47H		Atlas-SNP	.											.	CDSN	48	.	0			c.G140A						PASS	.	C	HIS/ARG,	0,3564		0,0,1782	16	10	12		140,	4.9	0	6		12	1,7003		0,1,3501	no	missense,intron	CDSN,PSORS1C1	NM_001264.4,NM_014068.2	29,	0,1,5283	TT,TC,CC		0.0143,0.0,0.0095	probably-damaging,	47/530,	31085252	1,10567	1782	3502	5284	SO:0001627	intron_variant	1041	exon2			GTGATACGCGTGG	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+2584C>T	chr6.hg19:g.31085252C>T		102.0	0.0	.		57.0	12.0	.	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	hg19	CCDS34390.1	.	.	.	.	.	.	.	.	.	.	C	11.70	1.717543	0.30413	0.0	1.43E-4	ENSG00000204539	ENST00000376288	T	0.12672	2.66	4.93	4.93	0.64822	.	0.000000	0.42682	D	0.000671	T	0.18923	0.0454	L	0.55990	1.75	0.09310	N	1	D	0.71674	0.998	D	0.63703	0.917	T	0.01371	-1.1372	10	0.72032	D	0.01	-8.1812	13.9681	0.64221	0.0:1.0:0.0:0.0	.	47	Q15517	CDSN_HUMAN	H	47	ENSP00000365465:R47H	ENSP00000365465:R47H	R	-	2	0	CDSN	31193231	0.055000	0.20627	0.016000	0.15963	0.057000	0.15508	3.491000	0.53252	2.461000	0.83175	0.549000	0.68633	CGT	.	.	.	weak		0.567	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068		T	31085252	C	T	31085252	1	4	227	0	1	0	0	0	0	0	0	0	3181	536	19	1		1	CDSN	6	31085252	Intron	SNP	C	TCGA-MH-A857-01A-11D-A34Z-10		31085252	140029815	11	13793											
NPC1L1	29881	hgsc.bcm.edu	37	chr7	44561797	44561797	+	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	tacaccggggcccccacctcGaagtagcggttcagaaagag	11	5	12	13	3	1	2	1	0	0	2	2	3	1	2	4	3	2	2	4	3	4	3	rs267601517		TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr7:44561797G>A	ENST00000289547.4	-	11	2737	c.2682C>T	c.(2680-2682)ttC>ttT	p.F894F	NPC1L1_ENST00000546276.1_Intron|NPC1L1_ENST00000381160.3_Silent_p.F894F	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	894					cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	CCCCCACCTCGAAGTAGCGGT	0.552																																					p.F894F		Atlas-SNP	.											.	NPC1L1	141	.	0			c.C2682T						PASS	.						58	56	57					7																	44561797		2203	4300	6503	SO:0001819	synonymous_variant	29881	exon11			CACCTCGAAGTAG		CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"NPC1 (Niemann-Pick disease, type C1, gene)-like 1"			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.2682C>T	chr7.hg19:g.44561797G>A		40.0	0.0	.		21.0	7.0	.	NM_001101648	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Silent	SNP	ENST00000289547.4	hg19	CCDS5491.1																																																																																			.	.	.	none		0.552	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389		A	44561797	G	A	44561797	2	1	227	1	0	0	0	0	0	0	0	1	10578	1049	37	1		1	NPC1L1	7	44561797	Silent	SNP	G	TCGA-MH-A857-01A-11D-A34Z-10		44561797	114576866	12	13794											
SEMA3E	9723	hgsc.bcm.edu	37	chr7	83037688	83037688	+	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	ttttcctcatccttacctttCaacagacgctcatcgtcatg	8	15	4	14	2	4	1	4	0	0	1	7	1	6	1	3	0	2	1	3	0	2	4			TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr7:83037688C>T	ENST00000307792.3	-	6	1133	c.666G>A	c.(664-666)ttG>ttA	p.L222L	SEMA3E_ENST00000427262.1_Silent_p.L162L	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	222	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)				CCTTACCTTTCAACAGACGCT	0.428																																					p.L222L		Atlas-SNP	.											.	SEMA3E	125	.	0			c.G666A						PASS	.						69	66	67					7																	83037688		2203	4300	6503	SO:0001819	synonymous_variant	9723	exon6			ACCTTTCAACAGA	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.666G>A	chr7.hg19:g.83037688C>T		171.0	0.0	.		108.0	27.0	.	NM_012431	B4E1P1|Q75M94|Q75M97	Silent	SNP	ENST00000307792.3	hg19	CCDS34674.1																																																																																			.	.	.	none		0.428	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431		T	83037688	C	T	83037688	2	4	227	1	0	0	0	0	0	0	0	1	14041	825	29	2		2	SEMA3E	7	83037688	Silent	SNP	C	TCGA-MH-A857-01A-11D-A34Z-10	38475891	83037688	76100975	13	13795											
SVIL	6840	hgsc.bcm.edu	37	chr10	29818641	29818641	+	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	tgtgggcacttacgtggctgCgatgaccacctcttcagtgg	6	11	13	11	2	2	1	1	1	1	0	2	2	2	1	2	3	2	2	2	3	1	2			TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr10:29818641C>T	ENST00000355867.4	-	12	2991	c.2239G>A	c.(2239-2241)Gca>Aca	p.A747T	SVIL_ENST00000375398.2_Missense_Mutation_p.A747T|SVIL_ENST00000375400.3_Missense_Mutation_p.A353T	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	747					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)				TACGTGGCTGCGATGACCACC	0.493																																					p.A747T		Atlas-SNP	.											.	SVIL	226	.	0			c.G2239A						PASS	.						113	97	102					10																	29818641		2203	4300	6503	SO:0001583	missense	6840	exon12			TGGCTGCGATGAC	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.2239G>A	chr10.hg19:g.29818641C>T	ENSP00000348128:p.Ala747Thr	98.0	0.0	.		60.0	4.0	.	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	hg19	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.836524	0.91117	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867	T;T;T	0.63255	-0.03;-0.03;-0.03	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.79981	0.4540	M	0.76328	2.33	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.79232	-0.1888	9	.	.	.	-17.2812	19.571	0.95419	0.0:1.0:0.0:0.0	.	353;747	O95425-2;O95425	.;SVIL_HUMAN	T	353;747;747	ENSP00000364549:A353T;ENSP00000364547:A747T;ENSP00000348128:A747T	.	A	-	1	0	SVIL	29858647	1.000000	0.71417	0.467000	0.27180	0.599000	0.36880	7.354000	0.79424	2.709000	0.92574	0.655000	0.94253	GCA	.	.	.	none		0.493	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			T	29818641	C	T	29818641	3	4	227	1	0	0	0	0	1	0	0	0	15433	768	27	1	4513	1	SVIL	10	29818641	Missense_Mutation	SNP	C	TCGA-MH-A857-01A-11D-A34Z-10		29818641	105716106	14	13796											
PIWIL4	143689	hgsc.bcm.edu	37	chr11	94300728	94300728	+	Missense_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	ggccagaggcatcgcccgcaGccccagtgccacagaagtgg	9	3	14	15	2	0	2	0	0	0	2	1	2	0	2	5	3	2	2	5	3	1	0			TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr11:94300728G>A	ENST00000299001.6	+	1	255	c.44G>A	c.(43-45)aGc>aAc	p.S15N	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	15					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)				ATCGCCCGCAGCCCCAGTGCC	0.557																																					p.S15N		Atlas-SNP	.											.	PIWIL4	70	.	0			c.G44A						PASS	.						59	44	49					11																	94300728		2199	4296	6495	SO:0001583	missense	143689	exon1			CCCGCAGCCCCAG	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.44G>A	chr11.hg19:g.94300728G>A	ENSP00000299001:p.Ser15Asn	105.0	0.0	.		71.0	25.0	.	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Missense_Mutation	SNP	ENST00000299001.6	hg19	CCDS31656.1	.	.	.	.	.	.	.	.	.	.	g	12.40	1.925406	0.34002	.	.	ENSG00000134627	ENST00000299001	T	0.03982	3.74	4.01	3.09	0.35607	.	0.865945	0.09952	N	0.734526	T	0.05456	0.0144	L	0.43152	1.355	0.21527	N	0.999656	B	0.23937	0.094	B	0.21917	0.037	T	0.39078	-0.9631	10	0.30854	T	0.27	-0.0873	7.5657	0.27876	0.1179:0.0:0.8821:0.0	.	15	Q7Z3Z4	PIWL4_HUMAN	N	15	ENSP00000299001:S15N	ENSP00000299001:S15N	S	+	2	0	PIWIL4	93940376	0.001000	0.12720	0.002000	0.10522	0.129000	0.20672	0.946000	0.29069	1.034000	0.39945	0.555000	0.69702	AGC	.	.	.	none		0.557	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431		A	94300728	G	A	94300728	3	1	227	1	0	0	0	0	1	0	0	0	11967	971	34	2	46	2	PIWIL4	11	94300728	Missense_Mutation	SNP	G	TCGA-MH-A857-01A-11D-A34Z-10		94300728	40705788	15	13797											
MLL	4297	hgsc.bcm.edu	37	chr11	118377019	118377019	+	Frame_Shift_Del	DEL	C	C	-																															caaaactgggattcattcttCccagcgtgatcttgattctg																										TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr11:118377019delC	ENST00000389506.5	+	27	10403	c.10403delC	c.(10402-10404)tccfs	p.S3468fs	KMT2A_ENST00000354520.4_Frame_Shift_Del_p.S3430fs|KMT2A_ENST00000534358.1_Frame_Shift_Del_p.S3471fs			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	3468					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)										ATTCATTCTTCCCAGCGTGAT	0.517																																					p.S3471fs		Atlas-Indel,Pindel	.											.	MLL	548	.	0			c.10411delT						PASS	.						129	119	123					11																	118377019		2200	4295	6495	SO:0001589	frameshift_variant	4297	exon27			.	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	7132	protein-coding gene	gene with protein product		159555	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.10403delC	chr11.hg19:g.118377019delC	ENSP00000374157:p.Ser3468fs	112.0	0.0	0		90.0	34.0	0.377778	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Frame_Shift_Del	DEL	ENST00000389506.5	hg19	CCDS31686.1																																																																																			.	.	.	none		0.517	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		-	118377019	C	-	118377019	7	5	227	1	0	1	0	1	0	0	0	0	9627	855	30	0	10509	0	MLL	11	118377019	Frame_Shift_Del	DEL	C	TCGA-MH-A857-01A-11D-A34Z-10	24076291	118377019	16629497	16	13798											
KIAA0528	9847	hgsc.bcm.edu	37	chr12	22676361	22676361	+	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	ttcattgattcatacttactCcttcatttctttggatgggg	7	19	7	8	0	4	1	3	1	1	0	5	2	5	2	1	3	2	0	1	3	2	8			TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr12:22676361C>T	ENST00000333957.4	-	7	1054	c.799G>A	c.(799-801)Gag>Aag	p.E267K	C2CD5_ENST00000396028.2_Splice_Site_p.E267K|C2CD5_ENST00000545552.1_Splice_Site_p.E267K|C2CD5_ENST00000446597.1_Splice_Site_p.E267K|C2CD5_ENST00000540703.1_5'UTR|C2CD5_ENST00000544930.1_Splice_Site_p.E69K|C2CD5_ENST00000542676.1_Splice_Site_p.E267K|C2CD5_ENST00000536386.1_Splice_Site_p.E267K	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	267					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)										CATACTTACTCCTTCATTTCT	0.363																																					p.E267K		Atlas-SNP	.											.	.	.	.	0			c.G799A						PASS	.						75	70	72					12																	22676361		2203	4300	6503	SO:0001630	splice_region_variant	9847	exon7			CTTACTCCTTCAT	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.800+1G>A	chr12.hg19:g.22676361C>T		133.0	0.0	.		104.0	29.0	.	NM_014802	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Missense_Mutation	SNP	ENST00000333957.4	hg19	CCDS31758.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.026154	0.93518	.	.	ENSG00000111731	ENST00000333957;ENST00000446597;ENST00000536386;ENST00000396028;ENST00000542676;ENST00000545552;ENST00000544930;ENST00000544281	T;T;T;T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69;0.69;0.69;0.69	5.24	5.24	0.73138	.	0.054847	0.64402	D	0.000001	T	0.61035	0.2315	L	0.47716	1.5	0.54753	D	0.999981	B;B;D;B;D;B	0.76494	0.216;0.397;0.997;0.138;0.999;0.192	B;B;D;B;D;B	0.75484	0.108;0.085;0.972;0.032;0.986;0.038	T	0.52888	-0.8515	10	0.13470	T	0.59	-15.5681	18.8083	0.92047	0.0:1.0:0.0:0.0	.	267;267;69;267;267;267	F5H2A1;B4DRN7;F5H3N1;B7ZLL0;Q86YS7-2;Q86YS7	.;.;.;.;.;K0528_HUMAN	K	267;267;267;267;267;267;69;66	ENSP00000334229:E267K;ENSP00000388756:E267K;ENSP00000439392:E267K;ENSP00000379345:E267K;ENSP00000441951:E267K;ENSP00000443204:E267K;ENSP00000445288:E69K;ENSP00000443479:E66K	ENSP00000334229:E267K	E	-	1	0	KIAA0528	22567628	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.474000	0.81024	2.426000	0.82243	0.591000	0.81541	GAG;GAG;GAG;GAG;GAG;GAG;GAG;GAA	.	.	.	none		0.363	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802	Missense_Mutation	T	22676361	C	T	22676361	5	4	227	1	0	0	0	0	0	0	1	0	8189	869	30	2	2279	2	KIAA0528	12	22676361	Splice_Site	SNP	C	TCGA-MH-A857-01A-11D-A34Z-10		22676361	111175534	17	13799											
PTPRR	5801	hgsc.bcm.edu	37	chr12	71286725	71286725	+	Missense_Mutation	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	actcttcttctgattaattgCcaaaaaatgatcattgtttc	12	17	4	8	0	4	2	1	2	3	0	5	2	4	2	1	0	1	1	1	0	4	6			TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr12:71286725C>T	ENST00000283228.2	-	2	543	c.91G>A	c.(91-93)Gca>Aca	p.A31T		NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	31					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)		TGATTAATTGCCAAAAAATGA	0.378																																					p.A31T		Atlas-SNP	.											.	PTPRR	109	.	0			c.G91A						PASS	.						93	99	97					12																	71286725		2203	4299	6502	SO:0001583	missense	5801	exon2			TAATTGCCAAAAA	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.91G>A	chr12.hg19:g.71286725C>T	ENSP00000283228:p.Ala31Thr	276.0	0.0	.		243.0	79.0	.	NM_002849	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Missense_Mutation	SNP	ENST00000283228.2	hg19	CCDS8998.1	.	.	.	.	.	.	.	.	.	.	C	16.59	3.166559	0.57476	.	.	ENSG00000153233	ENST00000283228	T	0.04156	3.69	5.86	4.92	0.64577	.	0.423542	0.16942	U	0.193232	T	0.04543	0.0124	L	0.27053	0.805	0.80722	D	1	B	0.13594	0.008	B	0.06405	0.002	T	0.40515	-0.9559	10	0.45353	T	0.12	-1.9248	10.8509	0.46769	0.0:0.7948:0.1326:0.0725	.	31	Q15256	PTPRR_HUMAN	T	31	ENSP00000283228:A31T	ENSP00000283228:A31T	A	-	1	0	PTPRR	69572992	1.000000	0.71417	0.991000	0.47740	0.990000	0.78478	2.095000	0.41729	2.776000	0.95493	0.650000	0.86243	GCA	.	.	.	none		0.378	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849		T	71286725	C	T	71286725	3	4	227	1	0	0	0	0	1	0	0	0	12823	739	26	2	1934	2	PTPRR	12	71286725	Missense_Mutation	SNP	C	TCGA-MH-A857-01A-11D-A34Z-10	48610364	71286725	62565170	18	13800											
RNF17	56163	hgsc.bcm.edu	37	chr13	25428149	25428149	+	Missense_Mutation	SNP	T	T	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	gaacagaaagtgtctgaattTcaggagaaaattctagaacc	17	9	9	6	0	3	4	1	1	2	3	3	6	3	4	1	1	2	0	1	1	7	3			TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr13:25428149T>G	ENST00000255324.5	+	25	3529	c.3477T>G	c.(3475-3477)ttT>ttG	p.F1159L	RNF17_ENST00000339524.3_Missense_Mutation_p.F211L|RNF17_ENST00000381921.1_Missense_Mutation_p.F1159L	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	1159					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)		TGTCTGAATTTCAGGAGAAAA	0.393																																					p.F1159L		Atlas-SNP	.											.	RNF17	259	.	0			c.T3477G						PASS	.						88	89	89					13																	25428149		2203	4300	6503	SO:0001583	missense	56163	exon25			TGAATTTCAGGAG	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.3477T>G	chr13.hg19:g.25428149T>G	ENSP00000255324:p.Phe1159Leu	121.0	0.0	.		98.0	27.0	.	NM_031277	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Missense_Mutation	SNP	ENST00000255324.5	hg19	CCDS9308.2	.	.	.	.	.	.	.	.	.	.	T	0.044	-1.274512	0.01410	.	.	ENSG00000132972	ENST00000255324;ENST00000381921;ENST00000429047;ENST00000418120;ENST00000339524	T;T;T;T	0.21361	3.62;3.62;2.85;2.01	4.95	0.786	0.18590	.	1.172140	0.06091	N	0.663694	T	0.13884	0.0336	L	0.44542	1.39	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	0.33803	-0.9854	10	0.08179	T	0.78	-0.6392	1.6021	0.02676	0.1715:0.0948:0.1782:0.5556	.	1155;211;1159;1159	B7Z7S1;Q5T6R1;Q9BXT8-5;Q9BXT8	.;.;.;RNF17_HUMAN	L	1159;1159;1018;483;211	ENSP00000255324:F1159L;ENSP00000371346:F1159L;ENSP00000388892:F483L;ENSP00000344776:F211L	ENSP00000255324:F1159L	F	+	3	2	RNF17	24326149	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-0.083000	0.11286	0.421000	0.25980	0.477000	0.44152	TTT	.	.	.	none		0.393	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994		G	25428149	T	G	25428149	3	3	227	1	0	0	0	0	1	0	0	0	13474	1780	62	5	3575	5	RNF17	13	25428149	Missense_Mutation	SNP	T	TCGA-MH-A857-01A-11D-A34Z-10		25428149	89741729	19	13801											
EML5	161436	hgsc.bcm.edu	37	chr14	89109293	89109293	+	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	tgtgataaattatatcatcaCcatcatttaaatagtgaaca	17	14	4	6	0	3	2	3	2	0	0	3	2	3	2	1	0	1	0	1	0	8	6			TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr14:89109293C>T	ENST00000380664.5	-	29	4156	c.4157G>A	c.(4156-4158)gGt>gAt	p.G1386D	EML5_ENST00000352093.5_Missense_Mutation_p.G1348D|EML5_ENST00000554922.1_Missense_Mutation_p.G1394D			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	1386						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						TATATCATCACCATCATTTAA	0.343																																					p.G1394D		Atlas-SNP	.											.	EML5	141	.	0			c.G4181A						PASS	.						102	98	99					14																	89109293		1855	4103	5958	SO:0001583	missense	161436	exon30			TCATCACCATCAT	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.4157G>A	chr14.hg19:g.89109293C>T	ENSP00000370039:p.Gly1386Asp	229.0	0.0	.		143.0	11.0	.	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	hg19	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.045975	0.93685	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.68181	-0.31;-0.31;-0.31	5.7	5.7	0.88788	HELP (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.83308	0.5226	M	0.77712	2.385	0.80722	D	1	D;D	0.89917	0.981;1.0	P;D	0.91635	0.9;0.999	D	0.84618	0.0682	10	0.87932	D	0	-24.0977	19.8242	0.96610	0.0:1.0:0.0:0.0	.	1394;1386	Q05BV3-5;Q05BV3	.;EMAL5_HUMAN	D	1394;1348;1386	ENSP00000451998:G1394D;ENSP00000298315:G1348D;ENSP00000370039:G1386D	ENSP00000298315:G1348D	G	-	2	0	EML5	88179046	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.442000	0.80503	2.669000	0.90835	0.591000	0.81541	GGT	.	.	.	none		0.343	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			T	89109293	C	T	89109293	3	4	227	1	0	0	0	0	1	0	0	0	5102	507	18	2	1808	2	EML5	14	89109293	Missense_Mutation	SNP	C	TCGA-MH-A857-01A-11D-A34Z-10		89109293	18240247	20	13802											
CGNL1	84952	hgsc.bcm.edu	37	chr15	57815687	57815687	+	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	cctttccctgccatttgcagGgaaatctgagtcagactacc	9	11	8	13	0	2	2	1	1	1	1	3	3	3	3	4	1	3	1	4	1	2	3			TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr15:57815687G>A	ENST00000281282.5	+	11	2794	c.2716G>A	c.(2716-2718)Gga>Aga	p.G906R		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	906						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)		CCATTTGCAGGGAAATCTGAG	0.502																																					p.G906R		Atlas-SNP	.											.	CGNL1	125	.	0			c.G2716A						PASS	.						68	66	67					15																	57815687		2192	4292	6484	SO:0001630	splice_region_variant	84952	exon12			TTGCAGGGAAATC	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.2716-1G>A	chr15.hg19:g.57815687G>A		87.0	0.0	.		53.0	17.0	.	NM_001252335	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Missense_Mutation	SNP	ENST00000281282.5	hg19	CCDS10161.1	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.607950	0.00842	.	.	ENSG00000128849	ENST00000281282	T	0.74209	-0.82	5.46	1.79	0.24919	.	0.721945	0.12888	N	0.430847	T	0.30727	0.0774	N	0.00135	-2.02	0.37102	D	0.899944	B	0.02656	0.0	B	0.04013	0.001	T	0.17228	-1.0376	9	.	.	.	-6.013	5.9639	0.19315	0.6491:0.1289:0.2219:0.0	.	906	Q0VF96	CGNL1_HUMAN	R	906	ENSP00000281282:G906R	.	G	+	1	0	CGNL1	55602979	1.000000	0.71417	0.610000	0.28997	0.079000	0.17450	2.572000	0.45999	0.112000	0.17975	-0.238000	0.12139	GGA	.	.	.	none		0.502	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866	Missense_Mutation	A	57815687	G	A	57815687	5	1	227	1	0	0	0	0	0	0	1	0	3306	1246	43	2	2754	2	CGNL1	15	57815687	Splice_Site	SNP	G	TCGA-MH-A857-01A-11D-A34Z-10		57815687	44715705	21	13803											
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43534423	43534423	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttagcattttggcaatcagaTgtcagagtaagcagctcagc	12	11	10	8	0	3	2	3	0	0	2	3	2	3	2	0	1	4	5	0	1	3	4			TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr18:43534423T>C	ENST00000282041.5	-	2	979	c.945A>G	c.(943-945)acA>acG	p.T315T		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	315					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						GGCAATCAGATGTCAGAGTAA	0.453																																					p.T315T		Atlas-SNP	.											.	EPG5	199	.	0			c.A945G						PASS	.						105	102	103					18																	43534423		1934	4155	6089	SO:0001819	synonymous_variant	57724	exon2			ATCAGATGTCAGA	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.945A>G	chr18.hg19:g.43534423T>C		174.0	0.0	.		113.0	38.0	.	NM_020964	A2BDF3|Q9H8C8	Silent	SNP	ENST00000282041.5	hg19	CCDS11926.2																																																																																			.	.	.	none		0.453	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		C	43534423	T	C	43534423	2	2	227	1	0	0	0	0	0	0	0	1	8256	1451	51	3		3	KIAA1632	18	43534423	Silent	SNP	T	TCGA-MH-A857-01A-11D-A34Z-10		43534423	34542825	22	13804											
MAG	4099	hgsc.bcm.edu	37	chr19	35802844	35802844	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaacgtgacagagagccccaGcttctcggcaggggacaacc	11	4	13	13	2	1	2	0	1	1	1	2	5	1	3	3	3	4	2	3	3	2	1			TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr19:35802844G>A	ENST00000392213.3	+	10	1799	c.1640G>A	c.(1639-1641)aGc>aAc	p.S547N	MAG_ENST00000361922.4_Missense_Mutation_p.S547N|MAG_ENST00000593348.1_3'UTR|MAG_ENST00000537831.2_Missense_Mutation_p.S522N	NM_002361.3	NP_002352.1	P20916	MAG_HUMAN	myelin associated glycoprotein	547					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)			GAGAGCCCCAGCTTCTCGGCA	0.607																																					p.S547N		Atlas-SNP	.											.	MAG	172	.	0			c.G1640A						PASS	.						50	37	41					19																	35802844		2203	4300	6503	SO:0001583	missense	4099	exon10			GCCCCAGCTTCTC	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.1640G>A	chr19.hg19:g.35802844G>A	ENSP00000376048:p.Ser547Asn	140.0	0.0	.		83.0	37.0	.	NM_080600	B7Z2E5|F5GYC0|Q567S4	Missense_Mutation	SNP	ENST00000392213.3	hg19	CCDS12455.1	.	.	.	.	.	.	.	.	.	.	g	22.6	4.314557	0.81358	.	.	ENSG00000105695	ENST00000262624;ENST00000361922;ENST00000392213;ENST00000537831	T;T;T	0.65549	0.01;-0.16;-0.09	5.26	5.26	0.73747	.	0.169147	0.52532	D	0.000066	T	0.63628	0.2527	N	0.19112	0.55	0.35505	D	0.800098	D;P;P	0.57899	0.981;0.948;0.941	D;P;P	0.65140	0.932;0.508;0.607	T	0.64381	-0.6421	10	0.16896	T	0.51	.	16.3569	0.83237	0.0:0.0:1.0:0.0	.	584;547;547	Q59GD9;P20916;Q567S4	.;MAG_HUMAN;.	N	584;547;547;522	ENSP00000355234:S547N;ENSP00000376048:S547N;ENSP00000440695:S522N	ENSP00000262624:S584N	S	+	2	0	MAG	40494684	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.547000	0.67249	2.466000	0.83321	0.556000	0.70494	AGC	.	.	.	none		0.607	MAG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466071.1	NM_080600		A	35802844	G	A	35802844	3	1	227	1	0	0	0	0	1	0	0	0	9169	971	34	2	1670	2	MAG	19	35802844	Missense_Mutation	SNP	G	TCGA-MH-A857-01A-11D-A34Z-10		35802844	23326139	23	13805											
SCAF1	58506	hgsc.bcm.edu	37	chr19	50156129	50156129	+	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	ctcgtcgtcctcctgttcttCccggaaggtgaagctgcagt	5	12	11	13	3	1	1	0	1	1	0	6	2	4	2	3	2	2	3	3	2	2	2			TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr19:50156129C>A	ENST00000360565.3	+	7	2607	c.2483C>A	c.(2482-2484)tCc>tAc	p.S828Y		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	828	Ser-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		TCCTGTTCTTCCCGGAAGGTG	0.692																																					p.S828Y		Atlas-SNP	.											.	SCAF1	78	.	0			c.C2483A						PASS	.						64	72	69					19																	50156129		2201	4300	6501	SO:0001583	missense	58506	exon7			GTTCTTCCCGGAA	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.2483C>A	chr19.hg19:g.50156129C>A	ENSP00000353769:p.Ser828Tyr	57.0	0.0	.		26.0	9.0	.	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Missense_Mutation	SNP	ENST00000360565.3	hg19	CCDS33074.1	.	.	.	.	.	.	.	.	.	.	C	3.923	-0.017817	0.07681	.	.	ENSG00000126461	ENST00000360565	T	0.36520	1.25	3.11	3.11	0.35812	.	0.761454	0.10799	N	0.632937	T	0.35307	0.0927	N	0.14661	0.345	0.09310	N	1	D	0.64830	0.994	P	0.59889	0.865	T	0.14282	-1.0478	9	.	.	.	-19.5321	9.2581	0.37595	0.0:0.6322:0.3678:0.0	.	828	Q9H7N4	SFR19_HUMAN	Y	828	ENSP00000353769:S828Y	.	S	+	2	0	SCAF1	54847941	.	.	0.243000	0.24186	0.174000	0.22865	.	.	2.046000	0.60703	0.561000	0.74099	TCC	.	.	.	none		0.692	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228		A	50156129	C	A	50156129	3	1	227	1	0	0	0	0	1	0	0	0	13881	855	30	4	2505	4	SCAF1	19	50156129	Missense_Mutation	SNP	C	TCGA-MH-A857-01A-11D-A34Z-10	14353285	50156129	8972854	24	13806											
NCOA6	23054	hgsc.bcm.edu	37	chr20	33329080	33329081	+	Frame_Shift_Del	DEL	AA	AA	-																															attattgaggatgaattgatAaagacaggtgtaatgaactg																										TCGA-MH-A857-01A-11D-A34Z-10	TCGA-MH-A857-10A-01D-A34Z-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0299221a-3d27-41da-acfa-e3d9a0bf59cf	66cc7636-90d2-4545-99c6-ea90745ba8b1	g.chr20:33329080_33329081delAA	ENST00000374796.2	-	12	7549_7550	c.4979_4980delTT	c.(4978-4980)tttfs	p.F1660fs	NCOA6_ENST00000359003.2_Frame_Shift_Del_p.F1660fs			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1660	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						ATGAATTGATAAAGACAGGTGT	0.49																																					p.1660_1661del		Atlas-Indel,Pindel	.											.	NCOA6	219	.	0			c.4980_4981del						PASS	.																																			SO:0001589	frameshift_variant	23054	exon11			.	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"nuclear receptor coactivator RAP250", "activating signal cointegrator-2", "peroxisome proliferator-activated receptor interacting protein"	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.4979_4980delTT	chr20.hg19:g.33329080_33329081delAA	ENSP00000363929:p.Phe1660fs	109.0	0.0	0		68.0	23.0	0.338235	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Frame_Shift_Del	DEL	ENST00000374796.2	hg19	CCDS13241.1																																																																																			.	.	.	none		0.49	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		-	33329081	AA	-	33329080	7	5	227	1	0	1	0	1	0	0	0	0	10240	359	13	0	1231	0	NCOA6	20	33329080	Frame_Shift_Del	DEL	AA	TCGA-MH-A857-01A-11D-A34Z-10		33329080	29696440	25	13807											
DNAJC11	55735	hgsc.bcm.edu	37	chr1	6705133	6705133	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcacacgagtctgatcgtcAtcttggaatttgtgctgata	9	15	9	8	2	4	2	2	2	2	0	5	4	4	3	0	1	1	1	0	1	2	4			TCGA-O9-A75Z-01A-11D-A33Q-10	TCGA-O9-A75Z-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11f95391-f644-4b23-b2b3-c3020648260b	b07e7c8d-9fc0-4376-89e2-8ceb9afcaa38	g.chr1:6705133A>G	ENST00000377577.5	-	9	1071	c.948T>C	c.(946-948)gaT>gaC	p.D316D	DNAJC11_ENST00000349363.6_Intron|DNAJC11_ENST00000465508.1_5'Flank|DNAJC11_ENST00000294401.7_Silent_p.D316D|DNAJC11_ENST00000542246.1_Silent_p.D278D|DNAJC11_ENST00000377573.5_Silent_p.D226D	NM_018198.3	NP_060668.2	Q9NVH1	DJC11_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 11	316						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)		TCTGATCGTCATCTTGGAATT	0.532																																					p.D316D		Atlas-SNP	.											.	DNAJC11	93	.	0			c.T948C						PASS	.						299	274	282					1																	6705133		2203	4300	6503	SO:0001819	synonymous_variant	55735	exon9			ATCGTCATCTTGG	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.948T>C	chr1.hg19:g.6705133A>G		77.0	0.0	.		73.0	26.0	.	NM_018198	Q4VWF5|Q5VZN0|Q6PK20|Q6PK70|Q8NDM2|Q96CL7	Silent	SNP	ENST00000377577.5	hg19	CCDS87.1																																																																																			.	.	.	none		0.532	DNAJC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004216.3	NM_018198		G	6705133	A	G	6705133	2	3	228	1	0	0	0	0	0	0	0	1	4632	214	8	3		3	DNAJC11	1	6705133	Silent	SNP	A	TCGA-O9-A75Z-01A-11D-A33Q-10		6705133	242545488	1	13808											
KDM4A	9682	hgsc.bcm.edu	37	chr1	44133641	44133641	+	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	acgaggaggagtgcccagagGaggacatggaaggggtggag	12	3	21	5	1	0	1	0	0	0	1	0	8	0	7	1	8	1	0	1	8	1	0			TCGA-O9-A75Z-01A-11D-A33Q-10	TCGA-O9-A75Z-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11f95391-f644-4b23-b2b3-c3020648260b	b07e7c8d-9fc0-4376-89e2-8ceb9afcaa38	g.chr1:44133641G>C	ENST00000372396.3	+	9	1248	c.1114G>C	c.(1114-1116)Gag>Cag	p.E372Q		NM_014663.2	NP_055478.2	O75164	KDM4A_HUMAN	lysine (K)-specific demethylase 4A	372					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						GTGCCCAGAGGAGGACATGGA	0.562																																					p.E372Q		Atlas-SNP	.											.	KDM4A	74	.	0			c.G1114C						PASS	.						145	139	141					1																	44133641		2203	4300	6503	SO:0001583	missense	9682	exon9			CCAGAGGAGGACA	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.1114G>C	chr1.hg19:g.44133641G>C	ENSP00000361473:p.Glu372Gln	151.0	0.0	.		105.0	34.0	.	NM_014663	Q5VVB1	Missense_Mutation	SNP	ENST00000372396.3	hg19	CCDS491.1	.	.	.	.	.	.	.	.	.	.	G	13.74	2.328538	0.41197	.	.	ENSG00000066135	ENST00000372396	T	0.16196	2.36	5.58	5.58	0.84498	.	0.765572	0.13019	N	0.420245	T	0.17152	0.0412	L	0.48362	1.52	0.33669	D	0.610687	B;B	0.30482	0.281;0.068	B;B	0.22152	0.038;0.031	T	0.18272	-1.0342	10	0.13470	T	0.59	-2.168	17.7576	0.88453	0.0:0.0:1.0:0.0	.	372;372	B4DT38;O75164	.;KDM4A_HUMAN	Q	372	ENSP00000361473:E372Q	ENSP00000361473:E372Q	E	+	1	0	KDM4A	43906228	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	8.613000	0.90913	2.617000	0.88574	0.555000	0.69702	GAG	.	.	.	none		0.562	KDM4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019960.1	NM_014663		C	44133641	G	C	44133641	3	2	228	1	0	0	0	0	1	0	0	0	8135	1175	41	4	1144	4	KDM4A	1	44133641	Missense_Mutation	SNP	G	TCGA-O9-A75Z-01A-11D-A33Q-10	37428508	44133641	205116980	2	13809											
AGT	183	hgsc.bcm.edu	37	chr1	230839940	230839940	+	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	gacacaggctcacacataccTcccccaccctgatgcggtca	10	6	7	18	1	2	1	2	1	0	0	3	2	3	1	4	2	2	1	4	2	1	1			TCGA-O9-A75Z-01A-11D-A33Q-10	TCGA-O9-A75Z-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11f95391-f644-4b23-b2b3-c3020648260b	b07e7c8d-9fc0-4376-89e2-8ceb9afcaa38	g.chr1:230839940T>C	ENST00000366667.4	-	4	1482	c.1268A>G	c.(1267-1269)gAg>gGg	p.E423G		NM_000029.3	NP_000020.1	P01019	ANGT_HUMAN	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	423					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)		CACACATACCTCCCCCACCCT	0.597																																					p.E423G		Atlas-SNP	.											AGT,colon,carcinoma,0,1	AGT	62	.	0			c.A1268G						PASS	.						159	123	135					1																	230839940		2203	4300	6503	SO:0001630	splice_region_variant	183	exon4			CATACCTCCCCCA	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.1269+1A>G	chr1.hg19:g.230839940T>C		122.0	0.0	.		96.0	4.0	.	NM_000029	Q16358|Q16359|Q96F91	Missense_Mutation	SNP	ENST00000366667.4	hg19	CCDS1585.1	.	.	.	.	.	.	.	.	.	.	T	16.31	3.086987	0.55861	.	.	ENSG00000135744	ENST00000366667;ENST00000430091	D	0.88046	-2.33	5.33	5.33	0.75918	Serpin domain (3);	0.348276	0.35555	N	0.003140	D	0.84951	0.5586	L	0.36672	1.1	0.34358	D	0.690613	P;P	0.49862	0.929;0.929	P;P	0.47251	0.542;0.542	D	0.90471	0.4453	10	0.72032	D	0.01	.	14.1269	0.65228	0.0:0.0:0.0:1.0	.	423;423	B0ZBE2;P01019	.;ANGT_HUMAN	G	423;341	ENSP00000355627:E423G	ENSP00000355627:E423G	E	-	2	0	AGT	228906563	1.000000	0.71417	0.884000	0.34674	0.012000	0.07955	4.445000	0.60007	2.020000	0.59435	0.533000	0.62120	GAG	.	.	.	none		0.597	AGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092102.1	NM_000029	Missense_Mutation	C	230839940	T	C	230839940	5	2	228	1	0	0	0	0	0	0	1	0	399	1565	54	3	197	3	AGT	1	230839940	Splice_Site	SNP	T	TCGA-O9-A75Z-01A-11D-A33Q-10	186706299	230839940	18410681	3	13810											
OR2W3	343171	hgsc.bcm.edu	37	chr1	248059782	248059782	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcagaaacagagaggtgaaGggggcactgggaaggttgct	12	6	17	6	0	1	3	1	1	0	2	1	5	1	4	0	5	2	3	0	5	3	1			TCGA-O9-A75Z-01A-11D-A33Q-10	TCGA-O9-A75Z-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11f95391-f644-4b23-b2b3-c3020648260b	b07e7c8d-9fc0-4376-89e2-8ceb9afcaa38	g.chr1:248059782G>A	ENST00000360358.3	+	1	894	c.894G>A	c.(892-894)aaG>aaA	p.K298K	OR2W3_ENST00000537741.1_Silent_p.K298K	NM_001001957.2	NP_001001957.2	Q7Z3T1	OR2W3_HUMAN	olfactory receptor, family 2, subfamily W, member 3	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)|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)			GAGAGGTGAAGGGGGCACTGG	0.537																																					p.K298K		Atlas-SNP	.											.	OR2W3	113	.	0			c.G894A						PASS	.						39	40	40					1																	248059782		2203	4300	6503	SO:0001819	synonymous_variant	343171	exon1			GGTGAAGGGGGCA	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.894G>A	chr1.hg19:g.248059782G>A		78.0	0.0	.		88.0	8.0	.	NM_001001957	Q6IF06|Q8NG86	Silent	SNP	ENST00000360358.3	hg19	CCDS31099.1																																																																																			.	.	.	none		0.537	OR2W3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096861.1	NM_001001957		A	248059782	G	A	248059782	2	1	228	1	0	0	0	0	0	0	0	1	11040	991	35	2		2	OR2W3	1	248059782	Silent	SNP	G	TCGA-O9-A75Z-01A-11D-A33Q-10	17219842	248059782	1190839	4	13811											
NLRC4	58484	hgsc.bcm.edu	37	chr2	32474767	32474767	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatcttctatggtgaggggActggcttccaccatgagaga	9	11	12	9	0	3	3	1	2	2	1	4	5	4	4	2	4	0	1	2	4	1	3			TCGA-O9-A75Z-01A-11D-A33Q-10	TCGA-O9-A75Z-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11f95391-f644-4b23-b2b3-c3020648260b	b07e7c8d-9fc0-4376-89e2-8ceb9afcaa38	g.chr2:32474767A>G	ENST00000404025.2	-	5	2654	c.2166T>C	c.(2164-2166)agT>agC	p.S722S	NLRC4_ENST00000402280.1_Silent_p.S722S|NLRC4_ENST00000360906.5_Silent_p.S722S|NLRC4_ENST00000342905.6_Intron			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	722					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)					TGGTGAGGGGACTGGCTTCCA	0.473																																					p.S722S		Atlas-SNP	.											.	NLRC4	165	.	0			c.T2166C						PASS	.						160	153	155					2																	32474767		2203	4300	6503	SO:0001819	synonymous_variant	58484	exon4			GAGGGGACTGGCT	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.2166T>C	chr2.hg19:g.32474767A>G		100.0	0.0	.		94.0	40.0	.	NM_001199138	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Silent	SNP	ENST00000404025.2	hg19	CCDS33174.1																																																																																			.	.	.	none		0.473	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209		G	32474767	A	G	32474767	2	3	228	1	0	0	0	0	0	0	0	1	10476	272	10	3		3	NLRC4	2	32474767	Silent	SNP	A	TCGA-O9-A75Z-01A-11D-A33Q-10		32474767	210724606	5	13812											
IQCJ	654502	hgsc.bcm.edu	37	chr3	158983179	158983179	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatagaaagacttggttttcTcaccctccagtgaatggacc	11	11	9	10	0	1	3	1	1	1	2	3	5	2	4	3	2	0	1	3	2	3	4			TCGA-O9-A75Z-01A-11D-A33Q-10	TCGA-O9-A75Z-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11f95391-f644-4b23-b2b3-c3020648260b	b07e7c8d-9fc0-4376-89e2-8ceb9afcaa38	g.chr3:158983179T>C	ENST00000451172.1	+	5	572	c.467T>C	c.(466-468)cTc>cCc	p.L156P	IQCJ-SCHIP1_ENST00000467442.1_Intron|IQCJ_ENST00000482126.1_Missense_Mutation_p.L129P|IQCJ-SCHIP1_ENST00000476809.1_Intron|IQCJ-SCHIP1_ENST00000485419.1_Intron	NM_001042705.2	NP_001036170.1	Q1A5X6	IQCJ_HUMAN	IQ motif containing J	156										cervix(1)|endometrium(2)|large_intestine(2)|lung(10)	15			LUSC - Lung squamous cell carcinoma(72;0.00523)|Lung(72;0.00534)			CTTGGTTTTCTCACCCTCCAG	0.478																																					p.L156P		Atlas-SNP	.											.	IQCJ	28	.	0			c.T467C						PASS	.						92	88	89					3																	158983179		1892	4130	6022	SO:0001583	missense	654502	exon5			GTTTTCTCACCCT	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.467T>C	chr3.hg19:g.158983179T>C	ENSP00000402153:p.Leu156Pro	129.0	0.0	.		87.0	4.0	.	NM_001042705	B7ZMM2|B9EH97|Q1A5X5	Missense_Mutation	SNP	ENST00000451172.1	hg19	CCDS46946.1	.	.	.	.	.	.	.	.	.	.	T	10.29	1.310205	0.23821	.	.	ENSG00000214216	ENST00000451172;ENST00000482126	.	.	.	3.53	-3.64	0.04515	.	.	.	.	.	T	0.22126	0.0533	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.20107	-1.0285	8	0.62326	D	0.03	.	6.7772	0.23626	0.1904:0.6487:0.0:0.1609	.	129;156	B7ZMM2;Q1A5X6	.;IQCJ_HUMAN	P	156;129	.	ENSP00000402153:L156P	L	+	2	0	IQCJ	160465873	0.000000	0.05858	0.000000	0.03702	0.062000	0.15995	-0.646000	0.05403	-0.782000	0.04541	-0.250000	0.11733	CTC	.	.	.	none		0.478	IQCJ-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352395.1	NM_001042705.1		C	158983179	T	C	158983179	3	2	228	1	0	0	0	0	1	0	0	0	7819	1551	54	3	533	3	IQCJ	3	158983179	Missense_Mutation	SNP	T	TCGA-O9-A75Z-01A-11D-A33Q-10		158983179	39039251	6	13813											
FBXL17	64839	hgsc.bcm.edu	37	chr5	107700635	107700635	+	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	acatactgcgacaatcagaaAtgttgatttcaattatattc	15	14	5	7	1	2	2	2	1	0	1	3	3	2	2	0	0	2	1	0	0	6	6			TCGA-O9-A75Z-01A-11D-A33Q-10	TCGA-O9-A75Z-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11f95391-f644-4b23-b2b3-c3020648260b	b07e7c8d-9fc0-4376-89e2-8ceb9afcaa38	g.chr5:107700635A>T	ENST00000542267.1	-	3	1584	c.1178T>A	c.(1177-1179)aTt>aAt	p.I393N	FBXL17_ENST00000496714.1_5'UTR|FBXL17_ENST00000359660.5_5'UTR	NM_001163315.2	NP_001156787.2	Q9UF56	FXL17_HUMAN	F-box and leucine-rich repeat protein 17	393										endometrium(1)|large_intestine(4)|lung(1)	6		all_cancers(142;0.00273)|all_epithelial(76;0.000362)|Prostate(80;0.0115)|Myeloproliferative disorder(839;0.0393)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;9.63e-11)|Epithelial(69;4.02e-10)		ACAATCAGAAATGTTGATTTC	0.328																																					p.I393N		Atlas-SNP	.											.	FBXL17	60	.	0			c.T1178A						PASS	.						85	86	85					5																	107700635		2202	4299	6501	SO:0001583	missense	64839	exon3			TCAGAAATGTTGA	AL133602	CCDS54886.1	5q21.3	2011-06-09	2004-06-15	2004-06-16	ENSG00000145743	ENSG00000145743		"F-boxes / Leucine-rich repeats"	13615	protein-coding gene	gene with protein product		609083	"F-box only protein 13"	FBXO13			Standard	NM_001163315		Approved	DKFZP434C1715, Fbx13, Fbl17	uc011cvc.2	Q9UF56	OTTHUMG00000159785	ENST00000542267.1:c.1178T>A	chr5.hg19:g.107700635A>T	ENSP00000437464:p.Ile393Asn	144.0	0.0	.		155.0	66.0	.	NM_001163315	A1A4E3	Missense_Mutation	SNP	ENST00000542267.1	hg19	CCDS54886.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.539746	0.85917	.	.	ENSG00000145743	ENST00000542267	T	0.03181	4.02	5.59	5.59	0.84812	.	.	.	.	.	T	0.10551	0.0258	L	0.39898	1.24	0.80722	D	1	D	0.67145	0.996	P	0.59171	0.853	T	0.01409	-1.1362	9	0.87932	D	0	.	16.0612	0.80839	1.0:0.0:0.0:0.0	.	393	Q9UF56	FXL17_HUMAN	N	393	ENSP00000437464:I393N	ENSP00000437464:I393N	I	-	2	0	FBXL17	107728534	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.870000	0.92336	2.250000	0.74265	0.477000	0.44152	ATT	.	.	.	none		0.328	FBXL17-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	107700635	A	T	107700635	3	4	228	1	0	0	0	0	1	0	0	0	5720	101	4	5	955	5	FBXL17	5	107700635	Missense_Mutation	SNP	A	TCGA-O9-A75Z-01A-11D-A33Q-10		107700635	73214625	7	13814											
LMNB1	4001	hgsc.bcm.edu	37	chr5	126154725	126154725	+	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	gagagatggcggaaataaggGatcaaatgcagcaacagctg	16	5	14	6	1	1	1	1	0	0	1	1	5	1	3	0	3	4	3	0	3	4	1			TCGA-O9-A75Z-01A-11D-A33Q-10	TCGA-O9-A75Z-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11f95391-f644-4b23-b2b3-c3020648260b	b07e7c8d-9fc0-4376-89e2-8ceb9afcaa38	g.chr5:126154725G>T	ENST00000261366.5	+	6	1412	c.1051G>T	c.(1051-1053)Gat>Tat	p.D351Y	LMNB1_ENST00000395354.1_Missense_Mutation_p.D351Y|LMNB1_ENST00000460265.1_3'UTR	NM_001198557.1|NM_005573.3	NP_001185486.1|NP_005564.1	P20700	LMNB1_HUMAN	lamin B1	351	Coil 2.|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)		GGAAATAAGGGATCAAATGCA	0.423																																					p.D351Y		Atlas-SNP	.											.	LMNB1	49	.	0			c.G1051T						PASS	.						123	120	121					5																	126154725		2203	4300	6503	SO:0001583	missense	4001	exon6			ATAAGGGATCAAA	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.1051G>T	chr5.hg19:g.126154725G>T	ENSP00000261366:p.Asp351Tyr	172.0	0.0	.		166.0	62.0	.	NM_005573	B2R6J6|Q3SYN7|Q96EI6	Missense_Mutation	SNP	ENST00000261366.5	hg19	CCDS4140.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.158723	0.78226	.	.	ENSG00000113368	ENST00000261366;ENST00000395354	D;D	0.89270	-2.49;-2.49	5.74	5.74	0.90152	Filament (1);	0.160581	0.53938	D	0.000058	D	0.92179	0.7520	M	0.72118	2.19	0.51767	D	0.999936	P	0.51791	0.948	P	0.56163	0.793	D	0.92360	0.5896	10	0.72032	D	0.01	.	13.954	0.64135	0.0783:0.0:0.9217:0.0	.	351	P20700	LMNB1_HUMAN	Y	351	ENSP00000261366:D351Y;ENSP00000378761:D351Y	ENSP00000261366:D351Y	D	+	1	0	LMNB1	126182624	1.000000	0.71417	0.994000	0.49952	0.975000	0.68041	3.942000	0.56614	2.873000	0.98535	0.563000	0.77884	GAT	.	.	.	none		0.423	LMNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250956.2	NM_005573		T	126154725	G	T	126154725	3	4	228	1	0	0	0	0	1	0	0	0	8856	1174	41	4	1073	4	LMNB1	5	126154725	Missense_Mutation	SNP	G	TCGA-O9-A75Z-01A-11D-A33Q-10	18454090	126154725	54760535	8	13815											
PCDHGA12	26025	hgsc.bcm.edu	37	chr5	140811391	140811391	+	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	ctcacctctctcgccagctcGgttcccgaaaactctcccag	7	9	6	19	3	3	0	1	0	2	0	8	1	4	0	4	1	2	2	4	1	2	1			TCGA-O9-A75Z-01A-11D-A33Q-10	TCGA-O9-A75Z-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11f95391-f644-4b23-b2b3-c3020648260b	b07e7c8d-9fc0-4376-89e2-8ceb9afcaa38	g.chr5:140811391G>T	ENST00000252085.3	+	1	1207	c.1065G>T	c.(1063-1065)tcG>tcT	p.S355S	PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	355	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCGCCAGCTCGGTTCCCGAAA	0.483																																					p.S355S		Atlas-SNP	.											.	PCDHGA12	271	.	0			c.G1065T						PASS	.						75	75	75					5																	140811391		2203	4300	6503	SO:0001819	synonymous_variant	26025	exon1			CAGCTCGGTTCCC	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.1065G>T	chr5.hg19:g.140811391G>T		125.0	0.0	.		112.0	5.0	.	NM_032094	O15100|Q6UW70|Q9Y5D7	Silent	SNP	ENST00000252085.3	hg19	CCDS4260.1																																																																																			.	.	.	none		0.483	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735		T	140811391	G	T	140811391	2	4	228	1	0	0	0	0	0	0	0	1	11560	1103	39	4		4	PCDHGA12	5	140811391	Silent	SNP	G	TCGA-O9-A75Z-01A-11D-A33Q-10	14656666	140811391	40103869	9	13816											
FOXP4	116113	hgsc.bcm.edu	37	chr6	41557563	41557563	+	Frame_Shift_Del	DEL	C	C	-																															tggcccacctgcacatgcggCcctcggagcccaagcccttc																										TCGA-O9-A75Z-01A-11D-A33Q-10	TCGA-O9-A75Z-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11f95391-f644-4b23-b2b3-c3020648260b	b07e7c8d-9fc0-4376-89e2-8ceb9afcaa38	g.chr6:41557563delC	ENST00000307972.4	+	9	1132	c.1120delC	c.(1120-1122)cccfs	p.P374fs	FOXP4_ENST00000409208.1_Frame_Shift_Del_p.P374fs|FOXP4_ENST00000373063.3_Frame_Shift_Del_p.P373fs|FOXP4_ENST00000373060.1_Frame_Shift_Del_p.P374fs|FOXP4_ENST00000373057.3_Frame_Shift_Del_p.P372fs			Q8IVH2	FOXP4_HUMAN	forkhead box P4	374					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)					GCACATGCGGCCCTCGGAGCC	0.692											OREG0004066	type=REGULATORY REGION|Gene=FOXP4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.R373fs		Atlas-INDEL	.											.	FOXP4	83	.	0			c.1119delG						PASS	.						34	37	36					6																	41557563		2203	4299	6502	SO:0001589	frameshift_variant	116113	exon10			.	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.1120delC	chr6.hg19:g.41557563delC	ENSP00000309823:p.Pro374fs	33.0	0.0	0	902	30.0	11.0	0.366667	NM_001012426	Q5W098|Q7Z7F8|Q8IW55|Q96E19	Frame_Shift_Del	DEL	ENST00000307972.4	hg19	CCDS34447.1																																																																																			.	.	.	none		0.692	FOXP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106767.1	NM_138457		-	41557563	C	-	41557563	7	5	228	1	0	1	0	1	0	0	0	0	6036	739	26	0	1154	0	FOXP4	6	41557563	Frame_Shift_Del	DEL	C	TCGA-O9-A75Z-01A-11D-A33Q-10		41557563	129557504	10	13817											
ERCC6	2074	hgsc.bcm.edu	37	chr10	50668440	50668440	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcacttctctgttggagaTgttgatgaaggatgctgcac	8	13	13	7	0	1	3	0	2	1	1	2	5	1	4	0	3	2	5	0	3	1	3			TCGA-O9-A75Z-01A-11D-A33Q-10	TCGA-O9-A75Z-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11f95391-f644-4b23-b2b3-c3020648260b	b07e7c8d-9fc0-4376-89e2-8ceb9afcaa38	g.chr10:50668440T>C	ENST00000355832.5	-	20	4119	c.4041A>G	c.(4039-4041)acA>acG	p.T1347T	ERCC6_ENST00000542458.1_Silent_p.T717T|ERCC6_ENST00000465653.1_5'UTR|RP11-123B3.2_ENST00000423283.1_RNA	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	1347					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						CTGTTGGAGATGTTGATGAAG	0.368								Direct reversal of damage;Nucleotide excision repair (NER)																													p.R1347R		Atlas-SNP	.											.	ERCC6	162	.	0			c.G4041G						PASS	.						117	115	115					10																	50668440		2203	4300	6503	SO:0001819	synonymous_variant	2074	exon20			TGGAGATGTTGAT	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.4041A>G	chr10.hg19:g.50668440T>C		75.0	0.0	.		49.0	20.0	.	NM_000124	D3DX94|Q5W0L9	Silent	SNP	ENST00000355832.5	hg19	CCDS7229.1																																																																																			.	.	.	none		0.368	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124		C	50668440	T	C	50668440	2	2	228	1	0	0	0	0	0	0	0	1	5219	1451	51	3		3	ERCC6	10	50668440	Silent	SNP	T	TCGA-O9-A75Z-01A-11D-A33Q-10		50668440	84866307	11	13818											
MKI67	4288	hgsc.bcm.edu	37	chr10	129904962	129904962	+	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	cttggtgtctggaagagctcGatgaagccggccaggtcttc	7	10	14	10	2	2	2	0	1	2	1	4	4	2	3	2	4	2	1	2	4	2	2	rs372451114		TCGA-O9-A75Z-01A-11D-A33Q-10	TCGA-O9-A75Z-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11f95391-f644-4b23-b2b3-c3020648260b	b07e7c8d-9fc0-4376-89e2-8ceb9afcaa38	g.chr10:129904962G>T	ENST00000368654.3	-	13	5517	c.5142C>A	c.(5140-5142)atC>atA	p.I1714I	MKI67_ENST00000368653.3_Silent_p.I1354I	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1714	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)				GGAAGAGCTCGATGAAGCCGG	0.493																																					p.I1714I		Atlas-SNP	.											.	MKI67	363	.	0			c.C5142A						PASS	.						109	98	102					10																	129904962		2203	4300	6503	SO:0001819	synonymous_variant	4288	exon13			GAGCTCGATGAAG	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.5142C>A	chr10.hg19:g.129904962G>T		57.0	0.0	.		62.0	4.0	.	NM_002417	Q5VWH2	Silent	SNP	ENST00000368654.3	hg19	CCDS7659.1																																																																																			.	.	.	none		0.493	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		T	129904962	G	T	129904962	2	4	228	1	0	0	0	0	0	0	0	1	9605	1048	37	4		4	MKI67	10	129904962	Silent	SNP	G	TCGA-O9-A75Z-01A-11D-A33Q-10	79236522	129904962	5629785	12	13819											
HSPA8	3312	hgsc.bcm.edu	37	chr11	122931977	122931977	+	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	cttttccgtgctggaaaacaCccacacaagagtaggtggtg	11	9	11	10	1	0	1	0	0	0	1	1	2	1	2	2	3	2	2	2	3	4	3			TCGA-O9-A75Z-01A-11D-A33Q-10	TCGA-O9-A75Z-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11f95391-f644-4b23-b2b3-c3020648260b	b07e7c8d-9fc0-4376-89e2-8ceb9afcaa38	g.chr11:122931977C>G	ENST00000532636.1	-	2	175	c.56G>C	c.(55-57)gGt>gCt	p.G19A	HSPA8_ENST00000526110.1_Missense_Mutation_p.G19A|HSPA8_ENST00000534319.1_5'Flank|SNORD14D_ENST00000384390.1_RNA|HSPA8_ENST00000453788.2_Missense_Mutation_p.G19A|HSPA8_ENST00000526862.1_5'Flank|HSPA8_ENST00000227378.3_Missense_Mutation_p.G19A|HSPA8_ENST00000533540.1_Missense_Mutation_p.G19A|HSPA8_ENST00000534624.1_Missense_Mutation_p.G19A|SNORD14C_ENST00000365382.1_RNA			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	19					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)		CTGGAAAACACCCACACAAGA	0.438																																					p.G19A	Colon(21;486 594 5900 6733 14272)	Atlas-SNP	.											.	HSPA8	168	.	0			c.G56C						PASS	.						65	58	61					11																	122931977		2202	4299	6501	SO:0001583	missense	3312	exon2			AAAACACCCACAC	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.56G>C	chr11.hg19:g.122931977C>G	ENSP00000437125:p.Gly19Ala	107.0	0.0	.		77.0	43.0	.	NM_006597	Q9H3R6	Missense_Mutation	SNP	ENST00000532636.1	hg19	CCDS8440.1	.	.	.	.	.	.	.	.	.	.	C	33	5.209267	0.95069	.	.	ENSG00000109971	ENST00000532636;ENST00000533540;ENST00000534624;ENST00000453788;ENST00000227378;ENST00000526110;ENST00000525463;ENST00000525624;ENST00000534567;ENST00000527387;ENST00000532182;ENST00000524590;ENST00000530391	T;T;T;T;T;T;T;T;T;T;T;T;T	0.02709	5.87;5.87;5.87;5.87;5.87;5.87;4.19;5.87;5.87;5.87;5.87;5.87;5.87	4.42	4.42	0.53409	.	0.000000	0.85682	D	0.000000	T	0.08358	0.0208	N	0.25094	0.71	0.80722	D	1	D;B;D;D;B	0.89917	0.993;0.337;1.0;1.0;0.337	P;P;D;D;P	0.80764	0.876;0.499;0.994;0.989;0.499	T	0.39522	-0.9610	10	0.87932	D	0	-19.7385	17.4081	0.87479	0.0:1.0:0.0:0.0	.	19;19;19;19;19	B4DTX2;Q53GZ6;E7ET08;P11142-2;P11142	.;.;.;.;HSP7C_HUMAN	A	19	ENSP00000437125:G19A;ENSP00000437189:G19A;ENSP00000432083:G19A;ENSP00000404372:G19A;ENSP00000227378:G19A;ENSP00000433584:G19A;ENSP00000436762:G19A;ENSP00000435154:G19A;ENSP00000431641:G19A;ENSP00000436183:G19A;ENSP00000434415:G19A;ENSP00000434565:G19A;ENSP00000434851:G19A	ENSP00000227378:G19A	G	-	2	0	HSPA8	122437187	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.818000	0.86416	2.151000	0.67156	0.484000	0.47621	GGT	.	.	.	none		0.438	HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1			G	122931977	C	G	122931977	3	3	228	1	0	0	0	0	1	0	0	0	7423	507	18	4	1916	4	HSPA8	11	122931977	Missense_Mutation	SNP	C	TCGA-O9-A75Z-01A-11D-A33Q-10		122931977	12074539	13	13820											
ATF7IP	55729	hgsc.bcm.edu	37	chr12	14576874	14576874	+	Frame_Shift_Del	DEL	A	A	-																															acagtttagaagaacctcagAaaaaagtctttaaggctcga																										TCGA-O9-A75Z-01A-11D-A33Q-10	TCGA-O9-A75Z-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11f95391-f644-4b23-b2b3-c3020648260b	b07e7c8d-9fc0-4376-89e2-8ceb9afcaa38	g.chr12:14576874delA	ENST00000540793.1	+	1	180	c.25delA	c.(25-27)aaafs	p.K10fs	ATF7IP_ENST00000543189.1_Frame_Shift_Del_p.K10fs|ATF7IP_ENST00000544627.1_Frame_Shift_Del_p.K18fs|ATF7IP_ENST00000541654.1_3'UTR|ATF7IP_ENST00000536444.1_Frame_Shift_Del_p.K10fs|ATF7IP_ENST00000261168.4_Frame_Shift_Del_p.K10fs			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	10					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						AGAACCTCAGAAAAAAGTCTT	0.353																																					p.Q8fs		Atlas-Indel,Pindel	.											.	ATF7IP	136	.	0			c.24delG						PASS	.						48	47	47					12																	14576874		2203	4300	6503	SO:0001589	frameshift_variant	55729	exon2			.	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.25delA	chr12.hg19:g.14576874delA	ENSP00000444589:p.Lys10fs	91.0	0.0	0		86.0	34.0	0.395349	NM_018179	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Frame_Shift_Del	DEL	ENST00000540793.1	hg19	CCDS8663.1																																																																																			.	.	.	none		0.353	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179		-	14576874	A	-	14576874	7	5	228	1	0	1	0	1	0	0	0	0	1087	247	9	0	27	0	ATF7IP	12	14576874	Frame_Shift_Del	DEL	A	TCGA-O9-A75Z-01A-11D-A33Q-10		14576874	119275021	14	13821											
FRMD6	122786	hgsc.bcm.edu	37	chr14	52156560	52156561	+	Frame_Shift_Ins	INS	-	-	A																															gtgcccaaaacacaatgaacINSaaattgaattttcataacaa																										TCGA-O9-A75Z-01A-11D-A33Q-10	TCGA-O9-A75Z-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11f95391-f644-4b23-b2b3-c3020648260b	b07e7c8d-9fc0-4376-89e2-8ceb9afcaa38	g.chr14:52156560_52156561insA	ENST00000344768.5	+	2	202_203	c.6_7insA	c.(7-9)aaafs	p.K3fs	RNA5SP385_ENST00000515947.1_RNA|FRMD6_ENST00000395718.2_Frame_Shift_Ins_p.K3fs|FRMD6_ENST00000356218.4_Frame_Shift_Ins_p.K3fs			Q96NE9	FRMD6_HUMAN	FERM domain containing 6	3					apical constriction (GO:0003383)|cellular protein localization (GO:0034613)|regulation of actin filament-based process (GO:0032970)	apical junction complex (GO:0043296)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_epithelial(31;0.0163)|Breast(41;0.089)					ACACAATGAACAAATTGAATTT	0.485																																					p.N2fs		Atlas-Indel,Pindel	.											.	FRMD6	100	.	0			c.6_7insA						PASS	.																																			SO:0001589	frameshift_variant	122786	exon3			.	BI465118	CCDS9704.1, CCDS58318.1, CCDS58319.1	14q22.1	2011-06-22	2005-07-20	2005-07-20	ENSG00000139926	ENSG00000139926			19839	protein-coding gene	gene with protein product	"expanded homolog"	614555	"chromosome 14 open reading frame 31"	C14orf31			Standard	NM_152330		Approved	MGC17921, willin, EX1	uc001wzd.3	Q96NE9	OTTHUMG00000140294	ENST00000344768.5:c.9dupA	chr14.hg19:g.52156563_52156563dupA	ENSP00000343899:p.Lys3fs	186.0	0.0	0		172.0	80.0	0.465116	NM_001042481	D3DSB9|Q5HYF2|Q8N2X1|Q8WUH7	Frame_Shift_Ins	INS	ENST00000344768.5	hg19	CCDS58318.1																																																																																			.	.	.	none		0.485	FRMD6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276881.1	NM_152330		A	52156561	-	A	52156560	7	5	228	1	0	1	1	0	0	0	0	0	6061	477	17	0	8	0	FRMD6	14	52156560	Frame_Shift_Ins	INS	-	TCGA-O9-A75Z-01A-11D-A33Q-10		52156560	55192980	15	13822											
MT1E	4493	hgsc.bcm.edu	37	chr16	56660835	56660835	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggctgtgccaagtgtgcccaGggctgcgtctgcaaaggggc	6	7	17	11	1	1	0	0	0	1	0	1	0	1	0	2	4	4	3	2	4	2	0			TCGA-O9-A75Z-01A-11D-A33Q-10	TCGA-O9-A75Z-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11f95391-f644-4b23-b2b3-c3020648260b	b07e7c8d-9fc0-4376-89e2-8ceb9afcaa38	g.chr16:56660835G>A	ENST00000306061.6	+	3	515	c.138G>A	c.(136-138)caG>caA	p.Q46Q	MT1E_ENST00000330439.6_3'UTR|MT1E_ENST00000568293.1_Silent_p.Q24Q	NM_175617.3	NP_783316.2	P04732	MT1E_HUMAN	metallothionein 1E	46	Alpha.				cellular response to cadmium ion (GO:0071276)|cellular response to zinc ion (GO:0071294)|negative regulation of growth (GO:0045926)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)										AGTGTGCCCAGGGCTGCGTCT	0.602																																					p.Q46Q		Atlas-SNP	.											.	MT1E	7	.	0			c.G138A						PASS	.						139	132	134					16																	56660835		2198	4300	6498	SO:0001819	synonymous_variant	4493	exon3			TGCCCAGGGCTGC	BC009699	CCDS10764.2	16q13	2008-08-11	2007-03-02		ENSG00000169715	ENSG00000169715		"Metallothioneins"	7397	protein-coding gene	gene with protein product		156351		MT1		6089206, 2581970	Standard	XM_005255956		Approved	MTD	uc002ejl.3	P04732	OTTHUMG00000133014	ENST00000306061.6:c.138G>A	chr16.hg19:g.56660835G>A		80.0	0.0	.		69.0	27.0	.	NM_175617	A2RRF7|Q86YX4|Q8TD51	Silent	SNP	ENST00000306061.6	hg19	CCDS10764.2																																																																																			.	.	.	none		0.602	MT1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256600.1	NM_175617		A	56660835	G	A	56660835	2	1	228	1	0	0	0	0	0	0	0	1	9906	991	35	2		2	MT1E	16	56660835	Silent	SNP	G	TCGA-O9-A75Z-01A-11D-A33Q-10		56660835	33693918	16	13823											
SIRT7	51547	hgsc.bcm.edu	37	chr17	79870320	79870320	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctttcttcctttttgtgcgtTttgtgcagcccctgccaaac	4	17	7	13	1	1	0	0	0	1	0	2	0	2	0	4	0	5	2	4	0	1	6			TCGA-O9-A75Z-01A-11D-A33Q-10	TCGA-O9-A75Z-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11f95391-f644-4b23-b2b3-c3020648260b	b07e7c8d-9fc0-4376-89e2-8ceb9afcaa38	g.chr17:79870320T>C	ENST00000328666.6	-	10	1237	c.1175A>G	c.(1174-1176)aAa>aGa	p.K392R	PCYT2_ENST00000331285.3_5'Flank|PCYT2_ENST00000538721.2_5'Flank|PCYT2_ENST00000570388.1_5'Flank|PCYT2_ENST00000570391.1_5'Flank|PCYT2_ENST00000538936.2_5'Flank|PCYT2_ENST00000571105.1_5'Flank	NM_016538.2	NP_057622.1	Q9NRC8	SIR7_HUMAN	sirtuin 7	392					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)			TTTTGTGCGTTTTGTGCAGCC	0.602																																					p.K392R		Atlas-SNP	.											.	SIRT7	37	.	0			c.A1175G						PASS	.						155	138	144					17																	79870320		2203	4299	6502	SO:0001583	missense	51547	exon10			GTGCGTTTTGTGC	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.1175A>G	chr17.hg19:g.79870320T>C	ENSP00000329466:p.Lys392Arg	81.0	0.0	.		97.0	4.0	.	NM_016538	A8K2K0|B3KSU8|Q3MIK4|Q9NSZ6|Q9NUS6	Missense_Mutation	SNP	ENST00000328666.6	hg19	CCDS11792.1	.	.	.	.	.	.	.	.	.	.	T	28.4	4.918735	0.92249	.	.	ENSG00000187531	ENST00000328666	T	0.38240	1.15	4.74	4.74	0.60224	.	0.000000	0.85682	D	0.000000	T	0.56906	0.2017	M	0.67953	2.075	0.54753	D	0.999987	D;D	0.63880	0.993;0.993	D;D	0.72625	0.978;0.978	T	0.61362	-0.7078	10	0.87932	D	0	-14.0698	13.3565	0.60631	0.0:0.0:0.0:1.0	.	392;392	A8K2K0;Q9NRC8	.;SIRT7_HUMAN	R	392	ENSP00000329466:K392R	ENSP00000329466:K392R	K	-	2	0	SIRT7	77463612	1.000000	0.71417	0.911000	0.35937	0.977000	0.68977	6.029000	0.70895	1.996000	0.58369	0.402000	0.26972	AAA	.	.	.	none		0.602	SIRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439961.1	NM_016538		C	79870320	T	C	79870320	3	2	228	1	0	0	0	0	1	0	0	0	14356	1841	64	3	31	3	SIRT7	17	79870320	Missense_Mutation	SNP	T	TCGA-O9-A75Z-01A-11D-A33Q-10		79870320	1324890	17	13824											
TSHZ3	57616	hgsc.bcm.edu	37	chr19	31768683	31768683	+	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	ttgcacccatcccgcgggggGctggggctgttctcctggct	2	10	15	14	2	1	0	0	0	1	0	3	0	2	0	3	6	1	5	3	6	0	2	rs373477520		TCGA-O9-A75Z-01A-11D-A33Q-10	TCGA-O9-A75Z-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11f95391-f644-4b23-b2b3-c3020648260b	b07e7c8d-9fc0-4376-89e2-8ceb9afcaa38	g.chr19:31768683G>A	ENST00000240587.4	-	2	2343	c.2016C>T	c.(2014-2016)agC>agT	p.S672S		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	672					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)					CCCGCGGGGGGCTGGGGCTGT	0.657																																					p.S672S		Atlas-SNP	.											.	TSHZ3	549	.	0			c.C2016T						PASS	.	G		1,4391		0,1,2195	22	25	24		2016	0.8	1	19		24	0,8584		0,0,4292	no	coding-synonymous	TSHZ3	NM_020856.2		0,1,6487	AA,AG,GG		0.0,0.0228,0.0077		672/1082	31768683	1,12975	2196	4292	6488	SO:0001819	synonymous_variant	57616	exon2			CGGGGGGCTGGGG	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.2016C>T	chr19.hg19:g.31768683G>A		66.0	0.0	.		52.0	23.0	.	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	hg19	CCDS12421.2																																																																																			.	.	.	weak		0.657	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		A	31768683	G	A	31768683	2	1	228	1	0	0	0	0	0	0	0	1	16637	1194	42	2		2	TSHZ3	19	31768683	Silent	SNP	G	TCGA-O9-A75Z-01A-11D-A33Q-10		31768683	27360300	18	13825											
C20orf195	79025	hgsc.bcm.edu	37	chr20	62187129	62187129	+	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	gctgctggaaccagaggcgtGgaagacctacaccgagcgcc	10	4	14	13	3	0	2	0	0	0	2	0	5	0	4	4	3	4	2	4	3	3	1			TCGA-O9-A75Z-01A-11D-A33Q-10	TCGA-O9-A75Z-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11f95391-f644-4b23-b2b3-c3020648260b	b07e7c8d-9fc0-4376-89e2-8ceb9afcaa38	g.chr20:62187129G>T	ENST00000370098.3	+	2	205	c.113G>T	c.(112-114)tGg>tTg	p.W38L	C20orf195_ENST00000370097.1_Missense_Mutation_p.W38L	NM_024059.2	NP_076964.1	Q9BVV2	CT195_HUMAN	chromosome 20 open reading frame 195	38						extracellular vesicular exosome (GO:0070062)				large_intestine(3)|lung(4)	7	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)			CCAGAGGCGTGGAAGACCTAC	0.647																																					p.W38L		Atlas-SNP	.											.	C20orf195	21	.	0			c.G113T						PASS	.						51	47	48					20																	62187129		2203	4300	6503	SO:0001583	missense	79025	exon2			AGGCGTGGAAGAC		CCDS13526.1	20q13.33	2014-02-12			ENSG00000125531	ENSG00000125531			28764	protein-coding gene	gene with protein product						12477932	Standard	NM_024059		Approved	MGC5356	uc002yfj.3	Q9BVV2	OTTHUMG00000032980	ENST00000370098.3:c.113G>T	chr20.hg19:g.62187129G>T	ENSP00000359116:p.Trp38Leu	78.0	0.0	.		64.0	25.0	.	NM_024059		Missense_Mutation	SNP	ENST00000370098.3	hg19	CCDS13526.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.877757	0.51801	.	.	ENSG00000125531	ENST00000370098;ENST00000370097	.	.	.	5.26	5.26	0.73747	.	0.000000	0.47093	D	0.000260	T	0.66703	0.2816	L	0.29908	0.895	0.41621	D	0.988965	D	0.89917	1.0	D	0.87578	0.998	T	0.70070	-0.4973	9	0.62326	D	0.03	-15.2825	16.61	0.84880	0.0:0.0:1.0:0.0	.	38	Q9BVV2	CT195_HUMAN	L	38	.	ENSP00000359115:W38L	W	+	2	0	C20orf195	61657573	1.000000	0.71417	0.991000	0.47740	0.053000	0.15095	4.172000	0.58243	2.444000	0.82710	0.655000	0.94253	TGG	.	.	.	none		0.647	C20orf195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080155.1	NM_024059		T	62187129	G	T	62187129	3	4	228	1	0	0	0	0	1	0	0	0	2102	1357	47	4	115	4	C20orf195	20	62187129	Missense_Mutation	SNP	G	TCGA-O9-A75Z-01A-11D-A33Q-10		62187129	838391	19	13826											
TRAPPC10	7109	hgsc.bcm.edu	37	chr21	45518268	45518268	+	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	acgtgaaggctgagatctttCccccttcgggaatggagtat	9	11	12	9	2	1	2	0	2	1	1	3	5	2	4	2	3	0	2	2	3	3	3			TCGA-O9-A75Z-01A-11D-A33Q-10	TCGA-O9-A75Z-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11f95391-f644-4b23-b2b3-c3020648260b	b07e7c8d-9fc0-4376-89e2-8ceb9afcaa38	g.chr21:45518268C>A	ENST00000291574.4	+	21	3374	c.3199C>A	c.(3199-3201)Ccc>Acc	p.P1067T		NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	1067					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						TGAGATCTTTCCCCCTTCGGG	0.483																																					p.P1067T		Atlas-SNP	.											.	TRAPPC10	109	.	0			c.C3199A						PASS	.						160	154	156					21																	45518268		2203	4300	6503	SO:0001583	missense	7109	exon21			ATCTTTCCCCCTT	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.3199C>A	chr21.hg19:g.45518268C>A	ENSP00000291574:p.Pro1067Thr	117.0	0.0	.		83.0	38.0	.	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Missense_Mutation	SNP	ENST00000291574.4	hg19	CCDS13704.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.867157	0.91511	.	.	ENSG00000160218	ENST00000291574;ENST00000542855	T	0.27104	1.69	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.45418	0.1341	L	0.47190	1.495	0.80722	D	1	D;D;D	0.59357	0.981;0.985;0.966	D;D;P	0.65233	0.91;0.933;0.773	T	0.12604	-1.0541	10	0.46703	T	0.11	.	19.8608	0.96783	0.0:1.0:0.0:0.0	.	172;326;1067	B4DV34;B4DI17;P48553	.;.;TPC10_HUMAN	T	1067;198	ENSP00000291574:P1067T	ENSP00000291574:P1067T	P	+	1	0	TRAPPC10	44342696	1.000000	0.71417	0.174000	0.22961	0.192000	0.23643	6.845000	0.75394	2.763000	0.94921	0.655000	0.94253	CCC	.	.	.	none		0.483	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274		A	45518268	C	A	45518268	3	1	228	1	0	0	0	0	1	0	0	0	16469	855	30	4	3281	4	TRAPPC10	21	45518268	Missense_Mutation	SNP	C	TCGA-O9-A75Z-01A-11D-A33Q-10		45518268	2611627	20	13827											
MYO18B	84700	hgsc.bcm.edu	37	chr22	26348362	26348362	+	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	ctagagaacaagacagagttCcagaaggtgcagattaagag	17	6	12	6	0	0	6	0	0	0	6	1	7	1	6	1	1	2	2	1	1	5	3			TCGA-O9-A75Z-01A-11D-A33Q-10	TCGA-O9-A75Z-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	11f95391-f644-4b23-b2b3-c3020648260b	b07e7c8d-9fc0-4376-89e2-8ceb9afcaa38	g.chr22:26348362C>G	ENST00000407587.2	+	38	6115	c.5946C>G	c.(5944-5946)ttC>ttG	p.F1982L	MYO18B_ENST00000335473.7_Missense_Mutation_p.F1981L|MYO18B_ENST00000536101.1_Missense_Mutation_p.F1981L			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1981	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						AGACAGAGTTCCAGAAGGTGC	0.507																																					p.F1981L		Atlas-SNP	.											.	MYO18B	322	.	0			c.C5943G						PASS	.						68	72	70					22																	26348362		2022	4201	6223	SO:0001583	missense	84700	exon38			AGAGTTCCAGAAG	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.5946C>G	chr22.hg19:g.26348362C>G	ENSP00000386096:p.Phe1982Leu	110.0	0.0	.		87.0	40.0	.	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	hg19		.	.	.	.	.	.	.	.	.	.	C	17.33	3.363118	0.61513	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.86497	-2.1;-2.1;-2.13	5.49	4.48	0.54585	.	0.000000	0.85682	D	0.000000	D	0.90407	0.6997	M	0.62016	1.91	0.39328	D	0.965364	P;P;D;P	0.89917	0.929;0.576;1.0;0.701	P;B;D;B	0.85130	0.597;0.073;0.997;0.153	D	0.87861	0.2664	10	0.12766	T	0.61	.	11.4231	0.49993	0.0:0.85:0.0:0.15	.	1494;1981;1982;1981	Q8IUG5-2;Q8IUG5;F5GXR6;F5GYU7	.;MY18B_HUMAN;.;.	L	1981;1981;1982	ENSP00000441229:F1981L;ENSP00000334563:F1981L;ENSP00000386096:F1982L	ENSP00000334563:F1981L	F	+	3	2	MYO18B	24678362	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.324000	0.33712	1.337000	0.45525	0.655000	0.94253	TTC	.	.	.	none		0.507	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		G	26348362	C	G	26348362	3	3	228	1	0	0	0	0	1	0	0	0	10073	854	30	4	6089	4	MYO18B	22	26348362	Missense_Mutation	SNP	C	TCGA-O9-A75Z-01A-11D-A33Q-10		26348362	24956204	21	13828											
GNB1	2782	hgsc.bcm.edu	37	chr1	1720557	1720557	+	Missense_Mutation	SNP	A	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	cgtcgtacccagcaaggaggAggcgcccgctcttggagaag	9	5	15	12	4	1	1	0	0	1	1	2	4	1	3	2	4	2	3	2	4	3	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:1720557A>C	ENST00000378609.4	-	10	1182	c.851T>G	c.(850-852)cTc>cGc	p.L284R		NM_001282539.1|NM_002074.3	NP_001269468.1|NP_002065.1	P62873	GBB1_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 1	284					adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|blood coagulation (GO:0007596)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|GTP catabolic process (GO:0006184)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|Ras protein signal transduction (GO:0007265)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	GTPase activity (GO:0003924)|GTPase binding (GO:0051020)|protein complex binding (GO:0032403)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	12	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.62e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.14e-35)|OV - Ovarian serous cystadenocarcinoma(86;7.31e-23)|GBM - Glioblastoma multiforme(42;3.1e-07)|COAD - Colon adenocarcinoma(227;0.000323)|Colorectal(212;0.000374)|Kidney(185;0.00392)|BRCA - Breast invasive adenocarcinoma(365;0.00573)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.0482)|Lung(427;0.236)		AGCAAGGAGGAGGCGCCCGCT	0.572											OREG0012998	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L284R		Atlas-SNP	.											.	GNB1	39	.	0			c.T851G						PASS	.						100	94	96					1																	1720557		2203	4300	6503	SO:0001583	missense	2782	exon10			AGGAGGAGGCGCC	BC004186	CCDS34.1, CCDS72685.1	1p36.33	2013-01-10			ENSG00000078369	ENSG00000078369		"WD repeat domain containing"	4396	protein-coding gene	gene with protein product		139380					Standard	NM_002074		Approved		uc001aif.3	P62873	OTTHUMG00000000940	ENST00000378609.4:c.851T>G	chr1.hg19:g.1720557A>C	ENSP00000367872:p.Leu284Arg	143.0	0.0	.	598	145.0	67.0	.	NM_002074	B1AJZ7|P04697|P04901|Q1RMY8	Missense_Mutation	SNP	ENST00000378609.4	hg19	CCDS34.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.4|22.4	4.290122|4.290122	0.80914|0.80914	.|.	.|.	ENSG00000078369|ENSG00000078369	ENST00000378609;ENST00000455156;ENST00000378606|ENST00000424622	T|.	0.62105|.	0.05|.	5.52|5.52	5.52|5.52	0.82312|0.82312	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.76528|0.76528	0.4000|0.4000	M|M	0.80847|0.80847	2.515|2.515	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.81914|.	0.995|.	T|T	0.78219|0.78219	-0.2289|-0.2289	10|5	0.51188|.	T|.	0.08|.	-9.8798|-9.8798	14.8181|14.8181	0.70050|0.70050	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	284|.	P62873|.	GBB1_HUMAN|.	R|A	284;184;284|142	ENSP00000367872:L284R|.	ENSP00000367869:L284R|.	L|S	-|-	2|1	0|0	GNB1|GNB1	1710417|1710417	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.885000|0.885000	0.51271|0.51271	9.126000|9.126000	0.94411|0.94411	2.096000|2.096000	0.63516|0.63516	0.533000|0.533000	0.62120|0.62120	CTC|TCC	.	.	.	none		0.572	GNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002762.3	NM_002074		C	1720557	A	C	1720557	3	2	229	1	0	0	0	0	1	0	0	0	6522	304	11	5	179	5	GNB1	1	1720557	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10		1720557	247530064	1	13829											
DNAJC16	23341	hgsc.bcm.edu	37	chr1	15855696	15855696	+	Missense_Mutation	SNP	A	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	ttggattttgacccatacagAgtcctaggggtcagccgaac	10	10	11	10	1	1	2	1	1	0	1	2	4	2	3	3	3	3	0	3	3	3	5			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:15855696A>C	ENST00000375847.3	+	2	260	c.96A>C	c.(94-96)agA>agC	p.R32S	CASP9_ENST00000469637.1_5'Flank|DNAJC16_ENST00000375838.1_Missense_Mutation_p.R32S|DNAJC16_ENST00000375849.1_Missense_Mutation_p.R32S	NM_015291.2	NP_056106.1	Q9Y2G8	DJC16_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 16	32	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(7)|urinary_tract(1)	18		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		ACCCATACAGAGTCCTAGGGG	0.443																																					p.R32S		Atlas-SNP	.											.	DNAJC16	59	.	0			c.A96C						PASS	.						109	107	108					1																	15855696		2203	4300	6503	SO:0001583	missense	23341	exon2			ATACAGAGTCCTA	AB023179	CCDS30606.1, CCDS72710.1	1p36.1	2011-09-02			ENSG00000116138	ENSG00000116138		"Heat shock proteins / DNAJ (HSP40)"	29157	protein-coding gene	gene with protein product							Standard	NM_015291		Approved	KIAA0962	uc001aws.3	Q9Y2G8	OTTHUMG00000002358	ENST00000375847.3:c.96A>C	chr1.hg19:g.15855696A>C	ENSP00000365007:p.Arg32Ser	106.0	0.0	.		120.0	47.0	.	NM_015291	Q68D57|Q86X32|Q8N5P4	Missense_Mutation	SNP	ENST00000375847.3	hg19	CCDS30606.1	.	.	.	.	.	.	.	.	.	.	A	14.92	2.678494	0.47886	.	.	ENSG00000116138	ENST00000375847;ENST00000375838;ENST00000375849;ENST00000546230	T;T;T	0.72282	-0.64;-0.64;-0.64	5.41	5.41	0.78517	Heat shock protein DnaJ, N-terminal (5);	0.092613	0.64402	D	0.000001	T	0.41465	0.1160	N	0.02111	-0.68	0.24628	N	0.99364	B;B	0.28208	0.166;0.203	B;B	0.24848	0.056;0.052	T	0.29518	-1.0009	10	0.38643	T	0.18	-23.0336	8.0421	0.30527	0.9101:0.0:0.0899:0.0	.	32;32	Q9Y2G8;Q5TDG9	DJC16_HUMAN;.	S	32	ENSP00000365007:R32S;ENSP00000364998:R32S;ENSP00000365009:R32S	ENSP00000364998:R32S	R	+	3	2	DNAJC16	15728283	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	3.233000	0.51311	2.060000	0.61445	0.460000	0.39030	AGA	.	.	.	none		0.443	DNAJC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006764.1	NM_015291		C	15855696	A	C	15855696	3	2	229	1	0	0	0	0	1	0	0	0	4637	301	11	5	98	5	DNAJC16	1	15855696	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	14135139	15855696	233394925	2	13830											
UBR4	23352	hgsc.bcm.edu	37	chr1	19500887	19500887	+	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	agctgcaagcagggctgtcaGtgcagcataaagctcatcat	12	8	11	10	0	3	0	3	0	0	0	3	0	3	0	0	1	6	7	0	1	3	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:19500887G>T	ENST00000375254.3	-	22	2935	c.2908C>A	c.(2908-2910)Ctg>Atg	p.L970M	UBR4_ENST00000375226.2_Missense_Mutation_p.L970M|UBR4_ENST00000375217.2_Missense_Mutation_p.L970M|UBR4_ENST00000375267.2_Missense_Mutation_p.L970M	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	970					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)		AGGGCTGTCAGTGCAGCATAA	0.438																																					p.L970M		Atlas-SNP	.											.	UBR4	415	.	0			c.C2908A						PASS	.						120	102	108					1																	19500887		2203	4300	6503	SO:0001583	missense	23352	exon22			CTGTCAGTGCAGC	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.2908C>A	chr1.hg19:g.19500887G>T	ENSP00000364403:p.Leu970Met	52.0	0.0	.		37.0	11.0	.	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	hg19	CCDS189.1	.	.	.	.	.	.	.	.	.	.	G	15.95	2.982527	0.53827	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000419533	T;T;T;T	0.36699	1.26;1.26;1.24;1.24	5.76	-1.65	0.08291	.	0.000000	0.64402	D	0.000001	T	0.44371	0.1290	L	0.39898	1.24	0.80722	D	1	D	0.65815	0.995	D	0.70487	0.969	T	0.26467	-1.0102	10	0.87932	D	0	.	11.0624	0.47955	0.5235:0.0:0.4765:0.0	.	970	Q5T4S7	UBR4_HUMAN	M	970;970;970;970;186	ENSP00000364403:L970M;ENSP00000364416:L970M;ENSP00000364365:L970M;ENSP00000364374:L970M	ENSP00000364365:L970M	L	-	1	2	UBR4	19373474	0.850000	0.29656	0.011000	0.14972	0.823000	0.46562	1.167000	0.31847	-0.623000	0.05618	-0.768000	0.03414	CTG	.	.	.	none		0.438	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		T	19500887	G	T	19500887	3	4	229	1	0	0	0	0	1	0	0	0	16916	1020	36	4	12983	4	UBR4	1	19500887	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	3645191	19500887	229749734	3	13831											
USP48	84196	hgsc.bcm.edu	37	chr1	22073615	22073615	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctgagaagccaatgtaggtAttcagctttttcttatgtcc	9	16	8	8	0	3	1	1	1	2	1	4	2	4	1	2	1	2	3	2	1	5	6			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:22073615A>G	ENST00000308271.9	-	8	1584	c.936T>C	c.(934-936)aaT>aaC	p.N312N	USP48_ENST00000400301.1_Silent_p.N312N|USP48_ENST00000421625.2_Silent_p.N312N|USP48_ENST00000529637.1_Silent_p.N312N	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	312	USP.				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)		CAATGTAGGTATTCAGCTTTT	0.313																																					p.N312N		Atlas-SNP	.											.	USP48	91	.	0			c.T936C						PASS	.						94	91	92					1																	22073615		2203	4300	6503	SO:0001819	synonymous_variant	84196	exon8			GTAGGTATTCAGC	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.936T>C	chr1.hg19:g.22073615A>G		18.0	0.0	.		18.0	5.0	.	NM_001032730	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Silent	SNP	ENST00000308271.9	hg19	CCDS30623.1																																																																																			.	.	.	none		0.313	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236		G	22073615	A	G	22073615	2	3	229	1	0	0	0	0	0	0	0	1	17091	446	16	3		3	USP48	1	22073615	Silent	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	2572728	22073615	227177006	4	13832											
MECR	51102	hgsc.bcm.edu	37	chr1	29520638	29520638	+	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	ggagcaggcaggggctgtgaGctggcctcggcggatgagat	7	6	20	8	2	0	2	0	2	0	1	1	5	0	4	1	7	2	4	1	7	0	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:29520638G>C	ENST00000263702.6	-	10	1043	c.1018C>G	c.(1018-1020)Ctc>Gtc	p.L340V	MECR_ENST00000373791.3_Missense_Mutation_p.L264V			Q9BV79	MECR_HUMAN	mitochondrial trans-2-enoyl-CoA reductase	340					fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)	11		Colorectal(325;0.000389)|Breast(348;0.00765)|Lung NSC(340;0.0081)|all_lung(284;0.00914)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.39e-07)|COAD - Colon adenocarcinoma(152;2.04e-05)|STAD - Stomach adenocarcinoma(196;0.0195)|BRCA - Breast invasive adenocarcinoma(304;0.053)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.137)		GGGGCTGTGAGCTGGCCTCGG	0.572																																					p.L340V		Atlas-SNP	.											.	MECR	31	.	0			c.C1018G						PASS	.						102	109	107					1																	29520638		2203	4300	6503	SO:0001583	missense	51102	exon10			CTGTGAGCTGGCC		CCDS30659.1, CCDS30660.1	1p35.3	2012-09-20			ENSG00000116353	ENSG00000116353	1.3.1.38		19691	protein-coding gene	gene with protein product	"nuclear receptor binding factor 1", "mitochondrial 2-enoyl thioester reductase"	608205				9795230, 12654921	Standard	XM_005245885		Approved	CGI-63, NRBF1, FASN2B	uc001brq.1	Q9BV79	OTTHUMG00000059082	ENST00000263702.6:c.1018C>G	chr1.hg19:g.29520638G>C	ENSP00000263702:p.Leu340Val	67.0	0.0	.		96.0	30.0	.	NM_016011	B3KT72|Q5SYU0|Q5SYU1|Q5SYU2|Q6IBU9|Q9Y373	Missense_Mutation	SNP	ENST00000263702.6	hg19	CCDS30659.1	.	.	.	.	.	.	.	.	.	.	G	18.13	3.554761	0.65425	.	.	ENSG00000116353	ENST00000373791;ENST00000263702	T;T	0.05199	3.48;3.49	5.48	5.48	0.80851	NAD(P)-binding domain (1);	0.133396	0.53938	D	0.000051	T	0.27169	0.0666	M	0.88181	2.935	0.58432	D	0.999999	P	0.45348	0.856	P	0.55749	0.783	T	0.01583	-1.1319	10	0.59425	D	0.04	.	16.849	0.85988	0.0:0.0:1.0:0.0	.	340	Q9BV79	MECR_HUMAN	V	264;340	ENSP00000362896:L264V;ENSP00000263702:L340V	ENSP00000263702:L340V	L	-	1	0	MECR	29393225	1.000000	0.71417	1.000000	0.80357	0.411000	0.31082	6.509000	0.73725	2.584000	0.87258	0.563000	0.77884	CTC	.	.	.	none		0.572	MECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130740.1	NM_016011		C	29520638	G	C	29520638	3	2	229	1	0	0	0	0	1	0	0	0	9431	971	34	4	107	4	MECR	1	29520638	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	7447023	29520638	219729983	5	13833											
INADL	10207	hgsc.bcm.edu	37	chr1	62271194	62271194	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgggtcctgattatgaagtaAtggtatgttaaaatgctcta	12	15	10	4	0	1	2	0	2	1	0	2	2	2	2	1	2	1	4	1	2	7	5			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:62271194A>G	ENST00000371158.2	+	13	1738	c.1624A>G	c.(1624-1626)Atg>Gtg	p.M542V	INADL_ENST00000316485.6_Missense_Mutation_p.M542V	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	542					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						TTATGAAGTAATGGTATGTTA	0.358																																					p.M542V		Atlas-SNP	.											.	INADL	179	.	0			c.A1624G						PASS	.						93	99	97					1																	62271194		2203	4300	6503	SO:0001583	missense	10207	exon13			GAAGTAATGGTAT	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.1624A>G	chr1.hg19:g.62271194A>G	ENSP00000360200:p.Met542Val	54.0	0.0	.		73.0	25.0	.	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	hg19	CCDS617.2	.	.	.	.	.	.	.	.	.	.	A	17.77	3.472247	0.63737	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000255202	T;T	0.08546	3.27;3.08	5.69	5.69	0.88448	PDZ/DHR/GLGF (1);	0.057835	0.64402	D	0.000002	T	0.21186	0.0510	M	0.62723	1.935	0.80722	D	1	D;D;P	0.67145	0.996;0.986;0.488	D;D;P	0.77557	0.99;0.965;0.508	T	0.08868	-1.0701	10	0.02654	T	1	.	14.5128	0.67800	1.0:0.0:0.0:0.0	.	542;542;542	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	V	542	ENSP00000360200:M542V;ENSP00000326199:M542V	ENSP00000255202:M542V	M	+	1	0	INADL	62043782	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.401000	0.52601	2.174000	0.68829	0.528000	0.53228	ATG	.	.	.	none		0.358	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		G	62271194	A	G	62271194	3	3	229	1	0	0	0	0	1	0	0	0	7738	101	4	3	1670	3	INADL	1	62271194	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	32750556	62271194	186979427	6	13834											
CCDC18	343099	hgsc.bcm.edu	37	chr1	93705010	93705043	+	Splice_Site	DEL	TAGAAAAGAAAACAAATGCTGGTAAGCAAGTGGT	TAGAAAAGAAAACAAATGCTGGTAAGCAAGTGGT	-																															agatcagacaaagacagagcTagaaaagaaaacaaatgctg																								rs550574161		TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	TAGAAAAGAAAACAAATGCTGGTAAGCAAGTGGT	TAGAAAAGAAAACAAATGCTGGTAAGCAAGTGGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:93705010_93705043delTAGAAAAGAAAACAAATGCTGGTAAGCAAGTGGT	ENST00000343253.7	+	20	3246_3266	c.2744_2764delTAGAAAAGAAAACAAATGCTGGTAAGCAAGTGGT	c.(2743-2766)ctagaaaagaaaacaaatgctggt>cgt	p.LEKKTNAG915fs	CCDC18_ENST00000421014.2_3'UTR|CCDC18_ENST00000557479.1_Splice_Site_p.LEKKTNAG1034fs|CCDC18_ENST00000334652.5_Splice_Site_p.LEKKTNAG211fs|CCDC18_ENST00000401026.3_Splice_Site_p.LEKKTNAG916fs|CCDC18_ENST00000338949.4_Splice_Site_p.LEKKTNAG671fs			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	915										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)		AAGACAGAGCTAGAAAAGAAAACAAATGCTGGTAAGCAAGTGGTTAGATGAGTA	0.363																																					p.916_923del		Pindel	.											.	CCDC18	93	.	0			c.2746_2767del						PASS	.																																			SO:0001630	splice_region_variant	343099	exon20			.			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.2764+1TAGAAAAGAAAACAAATGCTGGTAAGCAAGTGGT>-	chr1.hg19:g.93705010_93705043delTAGAAAAGAAAACAAATGCTGGTAAGCAAGTGGT		168.0	0.0	.		130.0	14.0	0.108	NM_206886	Q6ZU17	Frame_Shift_Del	DEL	ENST00000343253.7	hg19																																																																																				.	.	.	none		0.363	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886	Frame_Shift_Del	-	93705043	TAGAAAAGAAAACAAATGCTGGTAAGCAAGTGGT	-	93705010	8	5	229	1	0	1	0	1	0	0	1	0	2796	1522	53	0	3179	0	CCDC18	1	93705010	Splice_Site	DEL	TAGAAAAGAAAACAAATGCTGGTAAGCAAGTGGT	TCGA-P4-A5E6-01A-11D-A28G-10	31433816	93705010	155545611	7	13835											
PRMT6	55170	hgsc.bcm.edu	37	chr1	107599742	107599742	+	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	ctggaggaccgggtgcacgtCctgccgggaccagtggagac	7	5	17	12	3	0	1	0	0	0	1	1	5	1	4	4	5	2	1	4	5	0	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:107599742C>T	ENST00000370078.1	+	1	442	c.405C>T	c.(403-405)gtC>gtT	p.V135V	PRMT6_ENST00000361318.5_Silent_p.V76V			Q96LA8	ANM6_HUMAN	protein arginine methyltransferase 6	135	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				base-excision repair (GO:0006284)|histone H3-R2 methylation (GO:0034970)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	histone binding (GO:0042393)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H2A-R3 specific) (GO:0070612)|histone methyltransferase activity (H3-R2 specific) (GO:0070611)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)			biliary_tract(1)|breast(2)|kidney(1)|large_intestine(4)|lung(5)|urinary_tract(1)	14		all_epithelial(167;0.000429)|all_lung(203;0.00122)|Lung NSC(277;0.00185)		Lung(183;0.0305)|Epithelial(280;0.0765)|Colorectal(144;0.0998)|all cancers(265;0.14)|LUSC - Lung squamous cell carcinoma(189;0.173)|BRCA - Breast invasive adenocarcinoma(282;0.242)		GGGTGCACGTCCTGCCGGGAC	0.672																																					p.V135V		Atlas-SNP	.											.	PRMT6	55	.	0			c.C405T						PASS	.						72	85	81					1																	107599742		2178	4281	6459	SO:0001819	synonymous_variant	55170	exon1			GCACGTCCTGCCG	AK001421	CCDS41360.1, CCDS41360.2	1p13.2	2008-02-05	2006-02-16	2006-02-16	ENSG00000198890	ENSG00000198890		"Protein arginine methyltransferases"	18241	protein-coding gene	gene with protein product		608274	"HMT1 hnRNP methyltransferase-like 6 (S. cerevisiae)"	HRMT1L6		11724789	Standard	NM_018137		Approved	FLJ10559	uc010ous.2	Q96LA8	OTTHUMG00000010964	ENST00000370078.1:c.405C>T	chr1.hg19:g.107599742C>T		20.0	0.0	.		24.0	8.0	.	NM_018137	A3KME1|B4DID8|Q5T5Y5|Q6DKI4|Q9NVR8	Silent	SNP	ENST00000370078.1	hg19	CCDS41360.2	.	.	.	.	.	.	.	.	.	.	C	5.305	0.241690	0.10077	.	.	ENSG00000198890	ENST00000540389	.	.	.	5.75	1.4	0.22301	.	.	.	.	.	T	0.48537	0.1505	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53753	-0.8394	5	0.87932	D	0	-18.1897	6.1728	0.20427	0.0:0.3898:0.4219:0.1884	.	.	.	.	S	29	.	ENSP00000440829:P29S	P	+	1	0	PRMT6	107401265	0.574000	0.26684	0.997000	0.53966	0.007000	0.05969	-0.426000	0.07008	0.714000	0.32081	0.544000	0.68410	CCT	.	.	.	none		0.672	PRMT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030185.1	NM_018137		T	107599742	C	T	107599742	2	4	229	1	0	0	0	0	0	0	0	1	12550	842	30	2		2	PRMT6	1	107599742	Silent	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	13894732	107599742	141650879	8	13836											
CRNN	49860	hgsc.bcm.edu	37	chr1	152384603	152384603	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcaaactcttgctccaagAgtcttttcagctcccctcgg	7	11	8	15	2	3	1	1	0	2	1	6	1	5	1	3	2	3	3	3	2	2	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:152384603A>G	ENST00000271835.3	-	2	169	c.107T>C	c.(106-108)cTc>cCc	p.L36P	RP1-91G5.3_ENST00000411804.1_RNA	NM_016190.2	NP_057274.1	Q9UBG3	CRNN_HUMAN	cornulin	36					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)			TTGCTCCAAGAGTCTTTTCAG	0.557																																					p.L36P		Atlas-SNP	.											.	CRNN	78	.	0			c.T107C						PASS	.						152	132	139					1																	152384603		2203	4300	6503	SO:0001583	missense	49860	exon2			TCCAAGAGTCTTT	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.107T>C	chr1.hg19:g.152384603A>G	ENSP00000271835:p.Leu36Pro	136.0	0.0	.		170.0	74.0	.	NM_016190	B2RE60|Q8N613	Missense_Mutation	SNP	ENST00000271835.3	hg19	CCDS1010.1	.	.	.	.	.	.	.	.	.	.	A	17.97	3.518486	0.64634	.	.	ENSG00000143536	ENST00000271835;ENST00000451038	T	0.36340	1.26	4.78	3.65	0.41850	S100/CaBP-9k-type, calcium binding, subdomain (1);EF-hand-like domain (1);	0.164580	0.29021	N	0.013391	T	0.54175	0.1842	M	0.92507	3.315	0.51233	D	0.999918	D	0.89917	1.0	D	0.80764	0.994	T	0.61652	-0.7019	10	0.87932	D	0	.	7.0943	0.25301	0.8983:0.0:0.1017:0.0	.	36	Q9UBG3	CRNN_HUMAN	P	36	ENSP00000271835:L36P	ENSP00000271835:L36P	L	-	2	0	CRNN	150651227	0.903000	0.30736	0.739000	0.30968	0.985000	0.73830	3.133000	0.50531	0.861000	0.35504	0.482000	0.46254	CTC	.	.	.	none		0.557	CRNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034503.1	NM_016190		G	152384603	A	G	152384603	3	3	229	1	0	0	0	0	1	0	0	0	3894	304	11	3	1388	3	CRNN	1	152384603	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	44784861	152384603	96866018	9	13837											
DENND4B	9909	hgsc.bcm.edu	37	chr1	153907287	153907287	+	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	tgacacctgctcctgctgctGctgctgctgctgctgctgtt	2	14	11	14	0	0	1	0	1	0	0	1	1	1	1	2	0	9	10	2	0	0	1	rs3835302|rs199597671		TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:153907287G>C	ENST00000361217.4	-	18	3140	c.2722C>G	c.(2722-2724)Cag>Gag	p.Q908E	DENND4B_ENST00000474386.1_5'Flank	NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	908	Gln-rich.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			tcctgctgctgctgctgctgc	0.632																																					p.Q908E		Atlas-SNP	.											.	DENND4B	210	.	0			c.C2722G						PASS	.						23	27	26					1																	153907287		2184	4281	6465	SO:0001583	missense	9909	exon18			GCTGCTGCTGCTG	AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837		"DENN/MADD domain containing"	29044	protein-coding gene	gene with protein product			"KIAA0476"	KIAA0476		9455484, 12906859	Standard	NM_014856		Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.2722C>G	chr1.hg19:g.153907287G>C	ENSP00000354597:p.Gln908Glu	45.0	0.0	.		90.0	9.0	.	NM_014856	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	hg19	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	G	1.785	-0.481073	0.04383	.	.	ENSG00000198837	ENST00000361217;ENST00000368646	T;T	0.06294	3.33;3.32	2.67	0.673	0.17941	.	5.053470	0.00166	N	0.000001	T	0.00815	0.0027	N	0.14661	0.345	0.19300	N	0.999977	B	0.02656	0.0	B	0.04013	0.001	T	0.26573	-1.0099	10	0.02654	T	1	-2.4288	3.3651	0.07201	0.1454:0.0:0.5849:0.2697	.	908	O75064	DEN4B_HUMAN	E	908;919	ENSP00000354597:Q908E;ENSP00000357635:Q919E	ENSP00000354597:Q908E	Q	-	1	0	DENND4B	152173911	0.943000	0.32029	0.986000	0.45419	0.760000	0.43138	0.537000	0.23144	0.194000	0.20326	0.271000	0.19318	CAG	.	.	.	weak		0.632	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806		C	153907287	G	C	153907287	3	2	229	1	0	0	0	0	1	0	0	0	4436	1328	46	4	1812	4	DENND4B	1	153907287	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	1522684	153907287	95343334	10	13838											
HDGF	3068	hgsc.bcm.edu	37	chr1	156713547	156713547	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggaggcccccggccagagcCgggctcagagggggtgctat	6	4	19	12	2	1	2	1	0	0	2	1	3	1	3	4	6	2	2	4	6	1	1	rs375226201		TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:156713547C>T	ENST00000357325.5	-	5	927	c.613G>A	c.(613-615)Ggc>Agc	p.G205S	HDGF_ENST00000368206.5_Missense_Mutation_p.G221S|MRPL24_ENST00000361531.2_5'Flank|MRPL24_ENST00000368211.4_5'Flank|HDGF_ENST00000368209.5_Missense_Mutation_p.G198S|HDGF_ENST00000465180.1_5'UTR|HDGF_ENST00000416666.2_Missense_Mutation_p.G173S|HDGF_ENST00000537739.1_Missense_Mutation_p.G205S	NM_004494.2	NP_004485.1	P51858	HDGF_HUMAN	hepatoma-derived growth factor	205	Glu-rich.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription corepressor binding (GO:0001222)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9	all_hematologic(923;0.088)|Hepatocellular(266;0.158)	Breast(1374;0.198)		Colorectal(1306;0.018)		CGGCCAGAGCCGGGCTCAGAG	0.587																																					p.G221S		Atlas-SNP	.											.	HDGF	60	.	0			c.G661A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY	0,4406		0,0,2203	30	33	32		661,592,613	0.6	0.1	1		32	1,8599		0,1,4299	no	missense,missense,missense	HDGF	NM_001126050.1,NM_001126051.1,NM_004494.2	56,56,56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	221/257,198/234,205/241	156713547	1,13005	2203	4300	6503	SO:0001583	missense	3068	exon5			CAGAGCCGGGCTC	D16431	CCDS1156.1, CCDS44247.1, CCDS44248.1	1q23.1	2013-10-14	2010-03-19		ENSG00000143321	ENSG00000143321			4856	protein-coding gene	gene with protein product	"high-mobility group protein 1-like"	600339	"hepatoma-derived growth factor (high-mobility group protein 1-like)"			8833162	Standard	NM_004494		Approved	HMG1L2	uc001fpy.4	P51858	OTTHUMG00000041295	ENST00000357325.5:c.613G>A	chr1.hg19:g.156713547C>T	ENSP00000349878:p.Gly205Ser	28.0	0.0	.		63.0	33.0	.	NM_001126050	B3KU21|D3DVC9|Q5SZ07|Q5SZ08|Q5SZ09	Missense_Mutation	SNP	ENST00000357325.5	hg19	CCDS1156.1	.	.	.	.	.	.	.	.	.	.	C	10.45	1.352591	0.24512	0.0	1.16E-4	ENSG00000143321	ENST00000357325;ENST00000368209;ENST00000537739;ENST00000416666;ENST00000368206;ENST00000406805	T;T;T;T;T	0.30448	2.05;1.56;2.05;1.6;1.53	4.55	0.546	0.17196	.	1.032050	0.07707	N	0.941443	T	0.06280	0.0162	L	0.34521	1.04	0.09310	N	1	B;B;B;B	0.28291	0.206;0.206;0.034;0.014	B;B;B;B	0.14023	0.01;0.01;0.004;0.002	T	0.38628	-0.9652	10	0.15952	T	0.53	-2.1192	6.8306	0.23907	0.0:0.6085:0.0:0.3915	.	180;221;198;205	B7Z958;Q5SZ07;Q5SZ08;P51858	.;.;.;HDGF_HUMAN	S	205;198;205;173;221;228	ENSP00000349878:G205S;ENSP00000357192:G198S;ENSP00000443120:G205S;ENSP00000416752:G173S;ENSP00000357189:G221S	ENSP00000349878:G205S	G	-	1	0	HDGF	154980171	0.000000	0.05858	0.089000	0.20774	0.788000	0.44548	-0.589000	0.05767	-0.053000	0.13289	0.456000	0.33151	GGC	.	.	.	none		0.587	HDGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098946.1	NM_004494		T	156713547	C	T	156713547	3	4	229	1	0	0	0	0	1	0	0	0	7025	652	23	1	117	1	HDGF	1	156713547	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	2806260	156713547	92537074	11	13839											
IPO9	55705	hgsc.bcm.edu	37	chr1	201842054	201842054	+	Missense_Mutation	SNP	A	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	agaggagatctacagcatggAtgagggcatccgcacccgct	11	6	13	11	2	1	3	0	1	1	2	2	5	2	4	2	3	2	4	2	3	1	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:201842054A>C	ENST00000361565.4	+	20	2744	c.2675A>C	c.(2674-2676)gAt>gCt	p.D892A		NM_018085.4	NP_060555.2	Q96P70	IPO9_HUMAN	importin 9	892					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						TACAGCATGGATGAGGGCATC	0.532																																					p.D892A		Atlas-SNP	.											.	IPO9	98	.	0			c.A2675C						PASS	.						97	88	91					1																	201842054		2203	4300	6503	SO:0001583	missense	55705	exon20			GCATGGATGAGGG	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.2675A>C	chr1.hg19:g.201842054A>C	ENSP00000354742:p.Asp892Ala	180.0	0.0	.		181.0	78.0	.	NM_018085	B1ASV5|Q8N1Y1|Q8N3I2|Q8NCG9|Q96SU6|Q9NW01|Q9P0A8|Q9ULM8	Missense_Mutation	SNP	ENST00000361565.4	hg19	CCDS1415.1	.	.	.	.	.	.	.	.	.	.	A	15.53	2.859721	0.51376	.	.	ENSG00000198700	ENST00000361565	.	.	.	5.23	5.23	0.72850	Armadillo-like helical (1);Armadillo-type fold (1);	0.136301	0.64402	D	0.000004	T	0.40498	0.1119	N	0.17723	0.515	0.80722	D	1	B	0.17038	0.02	B	0.16722	0.016	T	0.26677	-1.0096	9	0.12103	T	0.63	-31.3306	13.3919	0.60829	1.0:0.0:0.0:0.0	.	892	Q96P70	IPO9_HUMAN	A	892	.	ENSP00000354742:D892A	D	+	2	0	IPO9	200108677	1.000000	0.71417	0.990000	0.47175	0.998000	0.95712	8.726000	0.91474	2.107000	0.64212	0.533000	0.62120	GAT	.	.	.	none		0.532	IPO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087088.1	NM_018085		C	201842054	A	C	201842054	3	2	229	1	0	0	0	0	1	0	0	0	7806	333	12	5	2753	5	IPO9	1	201842054	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	45128507	201842054	47408567	12	13840											
YOD1	55432	hgsc.bcm.edu	37	chr1	207222409	207222409	+	Frame_Shift_Del	DEL	C	C	-																															gcctgtctccttggcatgttCccttgcttctgcttgtccag																										TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:207222409delC	ENST00000315927.4	-	2	1049	c.1003delG	c.(1003-1005)gaafs	p.E335fs	YOD1_ENST00000391927.1_Frame_Shift_Del_p.E291fs|PFKFB2_ENST00000411990.2_5'Flank|YOD1_ENST00000367084.1_Frame_Shift_Del_p.E291fs	NM_018566.3	NP_061036.3	Q5VVQ6	OTU1_HUMAN	YOD1 deubiquitinase	335					cellular amino acid metabolic process (GO:0006520)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein K11-linked deubiquitination (GO:0035871)|protein K27-linked deubiquitination (GO:1990167)|protein K29-linked deubiquitination (GO:0035523)|protein K33-linked deubiquitination (GO:1990168)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)		Lys48-specific deubiquitinase activity (GO:1990380)|metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)			cervix(1)|endometrium(3)|large_intestine(1)|lung(3)|ovary(3)	11	Prostate(682;0.19)					TTGGCATGTTCCCTTGCTTCT	0.478																																					p.E335fs		Atlas-Indel,Pindel	.											.	YOD1	24	.	0			c.1004delA						PASS	.						271	251	257					1																	207222409		2203	4300	6503	SO:0001589	frameshift_variant	55432	exon2			.		CCDS31002.1, CCDS60402.1	1q32.2	2013-06-04	2013-06-04		ENSG00000180667	ENSG00000180667		"OTU domain containing"	25035	protein-coding gene	gene with protein product		612023	"YOD1 OTU deubiquinating enzyme 1 homolog ( yeast)", "YOD1 OTU deubiquinating enzyme 1 homolog (S. cerevisiae)"				Standard	NM_001276320		Approved	DKFZp451J1719, OTUD2, DUBA8	uc001hfe.1	Q5VVQ6	OTTHUMG00000036032	ENST00000315927.4:c.1003delG	chr1.hg19:g.207222409delC	ENSP00000326813:p.Glu335fs	141.0	0.0	0		131.0	40.0	0.305344	NM_018566	B2RNX3|Q5VVQ5|Q6ZRS6|Q86T63|Q9P1L8	Frame_Shift_Del	DEL	ENST00000315927.4	hg19	CCDS31002.1																																																																																			.	.	.	none		0.478	YOD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087837.1	NM_018566		-	207222409	C	-	207222409	7	5	229	1	0	1	0	1	0	0	0	0	17500	864	30	0	47	0	YOD1	1	207222409	Frame_Shift_Del	DEL	C	TCGA-P4-A5E6-01A-11D-A28G-10	5380355	207222409	42028212	13	13841											
CENPF	1063	hgsc.bcm.edu	37	chr1	214813548	214813548	+	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	aaactctgttttcttgttggAaaagtgaaaacgaaaaactt	16	13	7	5	1	2	1	0	1	2	0	2	3	2	2	0	1	3	2	0	1	7	5			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:214813548A>T	ENST00000366955.3	+	12	2035	c.1867A>T	c.(1867-1869)Aaa>Taa	p.K623*		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		TTCTTGTTGGAAAAGTGAAAA	0.333																																					p.K623X	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.A1867T						PASS	.						32	37	36					1																	214813548		2198	4298	6496	SO:0001587	stop_gained	1063	exon12			TGTTGGAAAAGTG	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.1867A>T	chr1.hg19:g.214813548A>T	ENSP00000355922:p.Lys623*	64.0	0.0	.		51.0	21.0	.	NM_016343	Q13171|Q13246|Q5VVM7	Nonsense_Mutation	SNP	ENST00000366955.3	hg19	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	A	40	8.443638	0.98813	.	.	ENSG00000117724	ENST00000366955	.	.	.	5.6	5.6	0.85130	.	0.000000	0.39407	N	0.001364	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.7907	0.78357	1.0:0.0:0.0:0.0	.	.	.	.	X	623	.	ENSP00000355922:K623X	K	+	1	0	CENPF	212880171	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.770000	0.85390	2.126000	0.65437	0.443000	0.29094	AAA	.	.	.	none		0.333	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		T	214813548	A	T	214813548	4	4	229	1	0	0	0	0	0	1	0	0	3233	247	9	5	1909	5	CENPF	1	214813548	Nonsense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	7591139	214813548	34437073	14	13842											
EPRS	2058	hgsc.bcm.edu	37	chr1	220154162	220154162	+	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	cctgccaaagaaattcacgaGtacgtaggaaaggctgagga	15	6	12	8	2	1	2	1	1	0	1	1	5	1	4	2	3	2	3	2	3	5	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:220154162G>C	ENST00000366923.3	-	25	3760	c.3491C>G	c.(3490-3492)aCt>aGt	p.T1164S		NM_004446.2	NP_004437.2	P07814	SYEP_HUMAN	glutamyl-prolyl-tRNA synthetase	1164	Proline--tRNA ligase.				cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|negative regulation of translation (GO:0017148)|prolyl-tRNA aminoacylation (GO:0006433)|protein complex assembly (GO:0006461)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|GAIT complex (GO:0097452)|membrane (GO:0016020)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|proline-tRNA ligase activity (GO:0004827)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(11)|kidney(2)|large_intestine(13)|lung(24)|ovary(1)|prostate(3)|skin(2)|stomach(2)|urinary_tract(3)	63				GBM - Glioblastoma multiforme(131;0.0735)	L-Proline(DB00172)	AAATTCACGAGTACGTAGGAA	0.388																																					p.T1164S		Atlas-SNP	.											.	EPRS	140	.	0			c.C3491G						PASS	.						64	60	61					1																	220154162		2203	4300	6503	SO:0001583	missense	2058	exon25			TCACGAGTACGTA	X54326	CCDS31027.1	1q41	2011-07-01			ENSG00000136628	ENSG00000136628	6.1.1.15, 6.1.1.17	"Aminoacyl tRNA synthetases / Class I", "Aminoacyl tRNA synthetases / Class II"	3418	protein-coding gene	gene with protein product	"glutamate tRNA ligase", "proline tRNA ligase"	138295		QPRS, QARS		1988429	Standard	NM_004446		Approved	EARS, PARS, GLUPRORS	uc001hly.1	P07814	OTTHUMG00000037433	ENST00000366923.3:c.3491C>G	chr1.hg19:g.220154162G>C	ENSP00000355890:p.Thr1164Ser	202.0	0.0	.		207.0	80.0	.	NM_004446	A0AVA9|B9EGH3|Q05BP6|Q05DF8|Q5DSM1|Q5H9S5|Q6PD57|Q86X73	Missense_Mutation	SNP	ENST00000366923.3	hg19	CCDS31027.1	.	.	.	.	.	.	.	.	.	.	G	32	5.174061	0.94807	.	.	ENSG00000136628	ENST00000366923	T	0.68025	-0.3	6.06	6.06	0.98353	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (G/ H/ P/ S), conserved domain (1);	0.000000	0.85682	D	0.000000	T	0.78046	0.4222	L	0.39326	1.205	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.76865	-0.2801	10	0.56958	D	0.05	-28.6459	20.6397	0.99537	0.0:0.0:1.0:0.0	.	1164	P07814	SYEP_HUMAN	S	1164	ENSP00000355890:T1164S	ENSP00000355890:T1164S	T	-	2	0	EPRS	218220785	1.000000	0.71417	0.980000	0.43619	0.980000	0.70556	9.577000	0.98196	2.880000	0.98712	0.650000	0.86243	ACT	.	.	.	none		0.388	EPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091133.2	NM_004446		C	220154162	G	C	220154162	3	2	229	1	0	0	0	0	1	0	0	0	5193	1029	36	4	1079	4	EPRS	1	220154162	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	5340614	220154162	29096459	15	13843											
TLR5	7100	hgsc.bcm.edu	37	chr1	223285316	223285316	+	Frame_Shift_Del	DEL	C	C	-																															gtagtccatagaaattcgaaCtgtaaagttcccccagaagg																										TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:223285316delC	ENST00000540964.1	-	4	1519	c.1058delG	c.(1057-1059)agtfs	p.S354fs	TLR5_ENST00000342210.6_Frame_Shift_Del_p.S354fs			O60602	TLR5_HUMAN	toll-like receptor 5	354					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)		GAAATTCGAACTGTAAAGTTC	0.353																																					p.S353fs		Atlas-Indel,Pindel	.											.	TLR5	86	.	0			c.1059delT						PASS	.						93	93	93					1																	223285316		2203	4300	6503	SO:0001589	frameshift_variant	7100	exon6			.		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.1058delG	chr1.hg19:g.223285316delC	ENSP00000440643:p.Ser354fs	46.0	0.0	0		57.0	25.0	0.438596	NM_003268	B1AZ05|B3Y633|B9VJ63|D1CS80|D3DTB8|O15456|Q32MI2|Q32MI3	Frame_Shift_Del	DEL	ENST00000540964.1	hg19	CCDS31033.1																																																																																			.	.	.	none		0.353	TLR5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003268		-	223285316	C	-	223285316	7	5	229	1	0	1	0	1	0	0	0	0	15966	565	20	0	1522	0	TLR5	1	223285316	Frame_Shift_Del	DEL	C	TCGA-P4-A5E6-01A-11D-A28G-10	3131154	223285316	25965305	16	13844											
C1orf65	164127	hgsc.bcm.edu	37	chr1	223567036	223567036	+	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	accccgcggcctcgcaggcgCgggtgctcagattcactgcg	5	6	14	16	6	2	1	2	0	0	1	3	1	2	1	3	3	2	2	3	3	0	1	rs369292167	byFrequency	TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:223567036C>T	ENST00000366875.3	+	1	322	c.219C>T	c.(217-219)cgC>cgT	p.R73R		NM_152610.2	NP_689823.2	Q8N715	CC185_HUMAN		73	Arg-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)		CTCGCAGGCGCGGGTGCTCAG	0.736													C|||	6	0.00119808	0.0045	0	5008	,	,		13138	0		0	False		,,,				2504	0				p.R73R		Atlas-SNP	.											.	C1orf65	71	.	0			c.C219T						PASS	.	C		15,3615		0,15,1800	4	6	5		219	0.3	0	1		5	0,7554		0,0,3777	no	coding-synonymous	C1orf65	NM_152610.2		0,15,5577	TT,TC,CC		0.0,0.4132,0.1341		73/624	223567036	15,11169	1815	3777	5592	SO:0001819	synonymous_variant	164127	exon1			CAGGCGCGGGTGC																												ENST00000366875.3:c.219C>T	chr1.hg19:g.223567036C>T		1.0	0.0	.		50.0	17.0	.	NM_152610	Q8N746|Q8NA93	Silent	SNP	ENST00000366875.3	hg19	CCDS1537.1																																																																																			.	.	.	none		0.736	C1orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092718.1			T	223567036	C	T	223567036	2	4	229	1	0	0	0	0	0	0	0	1	2057	755	27	1		1	C1orf65	1	223567036	Silent	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	281720	223567036	25683585	17	13845											
ITPKB	3707	hgsc.bcm.edu	37	chr1	226924770	226924784	+	In_Frame_Del	DEL	CTTCCTCTTGGCCTC	CTTCCTCTTGGCCTC	-																															tcgcgctgcaagatccgcagCttcctcttggcctcctccgg																								rs140396711|rs144653273|rs531138740|rs563769960	byFrequency	TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	CTTCCTCTTGGCCTC	CTTCCTCTTGGCCTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:226924770_226924784delCTTCCTCTTGGCCTC	ENST00000272117.3	-	1	375_389	c.376_390delGAGGCCAAGAGGAAG	c.(376-390)gaggccaagaggaagdel	p.EAKRK126del	ITPKB_ENST00000429204.1_In_Frame_Del_p.EAKRK126del|ITPKB_ENST00000366784.1_In_Frame_Del_p.EAKRK126del			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	126					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)	p.A127A(1)		central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				AGATCCGCAGCTTCCTCTTGGCCTCCTCCGGCCCT	0.656																																					p.126_131del	Colon(84;110 1851 5306 33547)	Atlas-Indel,Pindel	.											.	ITPKB	158	.	1	Substitution - coding silent(1)	large_intestine(1)	c.377_391del						PASS	.																																			SO:0001651	inframe_deletion	3707	exon2			.	AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"inositol 1,4,5-trisphosphate 3-kinase B"			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.376_390delGAGGCCAAGAGGAAG	chr1.hg19:g.226924770_226924784delCTTCCTCTTGGCCTC	ENSP00000272117:p.Glu126_Lys130del	58.0	0.0	0		78.0	17.0	0.217949	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	In_Frame_Del	DEL	ENST00000272117.3	hg19	CCDS1555.1																																																																																			.	.	.	none		0.656	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221		-	226924784	CTTCCTCTTGGCCTC	-	226924770	7	5	229	1	0	1	0	1	0	0	0	0	7925	796	28	0	2478	0	ITPKB	1	226924770	In_Frame_Del	DEL	CTTCCTCTTGGCCTC	TCGA-P4-A5E6-01A-11D-A28G-10	3357734	226924770	22325851	18	13846											
OR2M5	127059	hgsc.bcm.edu	37	chr1	248309355	248309355	+	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	gaggtgaccagagcactcagGaaagtgttaggaaagggcaa	15	5	15	6	0	1	2	1	1	0	1	1	5	1	4	1	4	1	3	1	4	4	1	rs201158893	byFrequency	TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr1:248309355G>A	ENST00000366476.1	+	1	906	c.906G>A	c.(904-906)agG>agA	p.R302R		NM_001004690.1	NP_001004690.1	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M, member 5	302						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	49	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)			GAGCACTCAGGAAAGTGTTAG	0.453													g|||	3	0.000599042	0	0	5008	,	,		17536	0		0	False		,,,				2504	0.0031				p.R302R		Atlas-SNP	.											.	OR2M5	117	.	0			c.G906A						PASS	.						62	58	59					1																	248309355		2203	4300	6503	SO:0001819	synonymous_variant	127059	exon1			ACTCAGGAAAGTG		CCDS31105.1	1q44	2012-08-09		2004-03-10	ENSG00000162727	ENSG00000162727		"GPCR / Class A : Olfactory receptors"	19576	protein-coding gene	gene with protein product				OR2M5P			Standard	NM_001004690		Approved		uc010pze.2	A3KFT3	OTTHUMG00000040447	ENST00000366476.1:c.906G>A	chr1.hg19:g.248309355G>A		137.0	0.0	.		175.0	8.0	.	NM_001004690		Silent	SNP	ENST00000366476.1	hg19	CCDS31105.1																																																																																			.	G|0.999;A|0.001	0.001	weak		0.453	OR2M5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097343.1	NM_001004690		A	248309355	G	A	248309355	2	1	229	1	0	0	0	0	0	0	0	1	11020	1165	41	2		2	OR2M5	1	248309355	Silent	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	21384585	248309355	941266	19	13847											
MXD1	4084	hgsc.bcm.edu	37	chr2	70165384	70165384	+	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	gcatcaagagaataaagctgCaggacagtcacaaggcgtgt	15	6	12	8	1	2	1	2	0	0	1	2	3	2	2	0	2	2	3	0	2	5	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr2:70165384C>G	ENST00000264444.2	+	6	894	c.634C>G	c.(634-636)Cag>Gag	p.Q212E	MXD1_ENST00000465446.1_3'UTR|MXD1_ENST00000540449.1_Missense_Mutation_p.Q202E	NM_001202513.1|NM_001202514.1|NM_002357.3	NP_001189442.1|NP_001189443.1|NP_002348.1	Q05195	MAD1_HUMAN	MAX dimerization protein 1	212					cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(1)	7						AATAAAGCTGCAGGACAGTCA	0.547																																					p.Q212E		Atlas-SNP	.											.	MXD1	23	.	0			c.C634G						PASS	.						103	101	101					2																	70165384		2203	4300	6503	SO:0001583	missense	4084	exon6			AAGCTGCAGGACA		CCDS1896.1, CCDS56123.1	2p13-p12	2010-07-07		2005-02-11	ENSG00000059728	ENSG00000059728		"MAX dimerization proteins", "Basic helix-loop-helix proteins"	6761	protein-coding gene	gene with protein product		600021		MAD		7829091	Standard	NM_002357		Approved	MAD1, bHLHc58	uc002sfy.3	Q05195	OTTHUMG00000129646	ENST00000264444.2:c.634C>G	chr2.hg19:g.70165384C>G	ENSP00000264444:p.Gln212Glu	328.0	0.0	.		335.0	22.0	.	NM_002357	B2R6V8|B7ZLI6|D6W5G2|Q6FI41	Missense_Mutation	SNP	ENST00000264444.2	hg19	CCDS1896.1	.	.	.	.	.	.	.	.	.	.	C	18.69	3.677983	0.68042	.	.	ENSG00000059728	ENST00000435990;ENST00000264444;ENST00000540449	T;T;T	0.45276	0.9;0.91;0.91	5.75	5.75	0.90469	.	0.527941	0.22156	N	0.063844	T	0.35537	0.0935	N	0.22421	0.69	0.47214	D	0.999358	B;B;B	0.23316	0.083;0.083;0.083	B;B;B	0.24006	0.05;0.05;0.05	T	0.13072	-1.0523	10	0.66056	D	0.02	.	18.875	0.92331	0.0:1.0:0.0:0.0	.	202;211;212	B7ZLI6;B7ZLI7;Q05195	.;.;MAD1_HUMAN	E	180;212;202	ENSP00000410672:Q180E;ENSP00000264444:Q212E;ENSP00000443935:Q202E	ENSP00000264444:Q212E	Q	+	1	0	MXD1	70018888	1.000000	0.71417	0.999000	0.59377	0.853000	0.48598	5.131000	0.64751	2.866000	0.98385	0.650000	0.86243	CAG	.	.	.	none		0.547	MXD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251845.3	NM_002357		G	70165384	C	G	70165384	3	3	229	1	0	0	0	0	1	0	0	0	10006	711	25	4	656	4	MXD1	2	70165384	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10		70165384	173033989	20	13848											
RGPD4	285190	hgsc.bcm.edu	37	chr2	108488583	108488583	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataaagatgttggtcaatggAaagaaaggggcattggtgat	15	10	14	2	0	1	3	1	1	0	2	1	4	1	4	0	5	0	2	0	5	5	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr2:108488583A>G	ENST00000408999.3	+	20	4200	c.4123A>G	c.(4123-4125)Aaa>Gaa	p.K1375E	RGPD4_ENST00000354986.4_Missense_Mutation_p.K1375E	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	1375	RanBD1 2. {ECO:0000255|PROSITE- ProRule:PRU00164}.				protein targeting to Golgi (GO:0000042)					breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						TGGTCAATGGAAAGAAAGGGG	0.353																																					p.K1375E		Atlas-SNP	.											.	RGPD4	112	.	0			c.A4123G						PASS	.						3	3	3					2																	108488583		568	1292	1860	SO:0001583	missense	285190	exon20			CAATGGAAAGAAA	BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"Tetratricopeptide (TTC) repeat domain containing"	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.4123A>G	chr2.hg19:g.108488583A>G	ENSP00000386810:p.Lys1375Glu	237.0	1.0	.		290.0	198.0	.	NM_182588	B9A029	Missense_Mutation	SNP	ENST00000408999.3	hg19	CCDS46381.1	.	.	.	.	.	.	.	.	.	.	-	12.87	2.068566	0.36470	.	.	ENSG00000196862	ENST00000354986;ENST00000408999	T;T	0.53423	0.62;0.62	2.33	2.33	0.28932	Pleckstrin homology-type (1);Ran binding protein 1 (3);	.	.	.	.	T	0.70745	0.3259	M	0.91406	3.205	0.37032	D	0.896721	D	0.76494	0.999	D	0.80764	0.994	T	0.77611	-0.2523	9	0.87932	D	0	-35.6834	9.2036	0.37275	1.0:0.0:0.0:0.0	.	1375	Q7Z3J3	RGPD4_HUMAN	E	1375	ENSP00000347081:K1375E;ENSP00000386810:K1375E	ENSP00000347081:K1375E	K	+	1	0	RGPD4	107855015	1.000000	0.71417	1.000000	0.80357	0.405000	0.30901	9.032000	0.93736	1.072000	0.40860	0.136000	0.15936	AAA	.	.	.	none		0.353	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581		G	108488583	A	G	108488583	3	3	229	1	0	0	0	0	1	0	0	0	13301	247	9	3	4201	3	RGPD4	2	108488583	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	38323199	108488583	134710790	21	13849											
SP5	389058	hgsc.bcm.edu	37	chr2	171572792	171572792	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgcacccccagcgcctccccGgacctgggcaagcactcgcc	6	3	10	22	4	0	0	0	0	0	0	2	1	1	1	7	2	2	3	7	2	1	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr2:171572792G>A	ENST00000375281.3	+	2	237	c.75G>A	c.(73-75)ccG>ccA	p.P25P	SP5_ENST00000487037.1_3'UTR|AC007405.2_ENST00000409786.1_5'Flank	NM_001003845.2	NP_001003845.1	Q6BEB4	SP5_HUMAN	Sp5 transcription factor	25					bone morphogenesis (GO:0060349)|post-anal tail morphogenesis (GO:0036342)|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)			NS(1)|endometrium(2)|lung(1)|prostate(1)	5						GCGCCTCCCCGGACCTGGGCA	0.736																																					p.P25P		Atlas-SNP	.											.	SP5	14	.	0			c.G75A						PASS	.						16	22	20					2																	171572792		2004	3993	5997	SO:0001819	synonymous_variant	389058	exon2			CTCCCCGGACCTG		CCDS33322.1	2q31	2013-01-08			ENSG00000204335	ENSG00000204335		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	14529	protein-coding gene	gene with protein product		609391					Standard	NM_001003845		Approved		uc002uge.3	Q6BEB4	OTTHUMG00000154053	ENST00000375281.3:c.75G>A	chr2.hg19:g.171572792G>A		1.0	0.0	.		5.0	5.0	.	NM_001003845		Silent	SNP	ENST00000375281.3	hg19	CCDS33322.1																																																																																			.	.	.	none		0.736	SP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333670.1	XM_371581		A	171572792	G	A	171572792	2	1	229	1	0	0	0	0	0	0	0	1	14980	1103	39	1		1	SP5	2	171572792	Silent	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	63084209	171572792	71626581	22	13850											
FZD7	8324	hgsc.bcm.edu	37	chr2	202900342	202900342	+	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	cgcttctcggacgatggctaCcgcacggtggcgcagggcac	6	6	15	14	6	1	0	0	0	1	0	2	2	1	1	1	5	1	5	1	5	1	2	rs571062625		TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr2:202900342C>G	ENST00000286201.1	+	1	1033	c.972C>G	c.(970-972)taC>taG	p.Y324*	RP11-107N15.1_ENST00000608741.1_lincRNA	NM_003507.1	NP_003498.1	O75084	FZD7_HUMAN	frizzled class receptor 7	324					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						ACGATGGCTACCGCACGGTGG	0.632											OREG0015146	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y324X		Atlas-SNP	.											.	FZD7	70	.	0			c.C972G						PASS	.						65	64	65					2																	202900342		2203	4300	6503	SO:0001587	stop_gained	8324	exon1			TGGCTACCGCACG	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.972C>G	chr2.hg19:g.202900342C>G	ENSP00000286201:p.Tyr324*	179.0	0.0	.	2133	217.0	67.0	.	NM_003507	O94816|Q53S59|Q96B74	Nonsense_Mutation	SNP	ENST00000286201.1	hg19	CCDS2351.1	.	.	.	.	.	.	.	.	.	.	C	36	5.730939	0.96856	.	.	ENSG00000155760	ENST00000286201	.	.	.	5.54	5.54	0.83059	.	0.140083	0.49916	D	0.000138	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.4882	0.95039	0.0:1.0:0.0:0.0	.	.	.	.	X	324	.	ENSP00000286201:Y324X	Y	+	3	2	FZD7	202608587	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.927000	0.63440	2.618000	0.88619	0.563000	0.77884	TAC	.	.	.	none		0.632	FZD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256314.1	NM_003507		G	202900342	C	G	202900342	4	3	229	1	0	0	0	0	0	1	0	0	6142	518	18	4	974	4	FZD7	2	202900342	Nonsense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	31327550	202900342	40299031	23	13851											
FAM117B	150864	hgsc.bcm.edu	37	chr2	203500481	203500481	+	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	gccgaagctcgccggagaagAggagccccagcgccccggtt	8	3	15	15	5	0	2	0	0	0	2	1	5	0	3	6	3	3	2	6	3	2	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr2:203500481A>C	ENST00000392238.2	+	1	571	c.571A>C	c.(571-573)Agg>Cgg	p.R191R	FAM117B_ENST00000303116.6_5'UTR			Q6P1L5	F117B_HUMAN	family with sequence similarity 117, member B	191										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)	17						GCCGGAGAAGAGGAGCCCCAG	0.731																																					p.R191R		Atlas-SNP	.											.	FAM117B	73	.	0			c.A571C						PASS	.						2	2	2					2																	203500481		404	1189	1593	SO:0001819	synonymous_variant	150864	exon1			GAGAAGAGGAGCC	AB053315	CCDS33362.1, CCDS33362.2	2q33	2008-08-18	2008-08-18	2008-08-18	ENSG00000138439	ENSG00000138439			14440	protein-coding gene	gene with protein product			"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13"	ALS2CR13		11586298	Standard	NM_173511		Approved	FLJ38771	uc010zhx.2	Q6P1L5	OTTHUMG00000154550	ENST00000392238.2:c.571A>C	chr2.hg19:g.203500481A>C		0.0	0.0	.		5.0	5.0	.	NM_173511	Q53QZ5|Q585T9|Q8N8W1|Q96Q34	Silent	SNP	ENST00000392238.2	hg19	CCDS33362.2																																																																																			.	.	.	none		0.731	FAM117B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335888.3	NM_173511		C	203500481	A	C	203500481	2	2	229	1	0	0	0	0	0	0	0	1	5414	295	11	5		5	FAM117B	2	203500481	Silent	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	600139	203500481	39698892	24	13852											
RPE	6120	hgsc.bcm.edu	37	chr2	210881324	210881324	+	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	tggttatgacagtggaaccgGggtttggagggcagaaattc	10	10	16	5	1	0	2	0	1	0	1	1	4	0	4	1	6	1	3	1	6	3	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr2:210881324G>A	ENST00000359429.6	+	4	533	c.436G>A	c.(436-438)Ggg>Agg	p.G146R	RPE_ENST00000354506.6_Missense_Mutation_p.G138R|RPE_ENST00000429921.1_Missense_Mutation_p.G96R|RPE_ENST00000452025.1_Missense_Mutation_p.G146R|RPE_ENST00000411934.2_Missense_Mutation_p.G78R|RPE_ENST00000454822.1_Missense_Mutation_p.G96R|RPE_ENST00000445268.1_Missense_Mutation_p.G78R|RPE_ENST00000429907.1_Missense_Mutation_p.G78R|RPE_ENST00000540255.1_Missense_Mutation_p.G146R|RPE_ENST00000438204.2_Missense_Mutation_p.G78R|RPE_ENST00000436630.2_Missense_Mutation_p.G96R|RPE_ENST00000435437.2_Missense_Mutation_p.G146R	NM_199229.1	NP_954699.1	Q96AT9	RPE_HUMAN	ribulose-5-phosphate-3-epimerase	146	Substrate binding.				carbohydrate metabolic process (GO:0005975)|pentose-phosphate shunt (GO:0006098)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|ribulose-phosphate 3-epimerase activity (GO:0004750)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(2)	9				Epithelial(149;0.00241)|Lung(261;0.041)|all cancers(144;0.0429)|LUSC - Lung squamous cell carcinoma(261;0.0431)		AGTGGAACCGGGGTTTGGAGG	0.438																																					p.G146R		Atlas-SNP	.											.	RPE	29	.	0			c.G436A						PASS	.						132	129	130					2																	210881324		2203	4300	6503	SO:0001583	missense	6120	exon4			GAACCGGGGTTTG		CCDS2388.1, CCDS42810.1, CCDS63107.1, CCDS63108.1	2q32-q33.3	2012-10-02			ENSG00000197713	ENSG00000197713	5.1.3.1		10293	protein-coding gene	gene with protein product		180480					Standard	NM_199229		Approved		uc002vdn.4	Q96AT9	OTTHUMG00000154690	ENST00000359429.6:c.436G>A	chr2.hg19:g.210881324G>A	ENSP00000352401:p.Gly146Arg	177.0	0.0	.		159.0	118.0	.	NM_199229	A8K4S0|B4E016|C9JPQ7|O43767|Q53TV9|Q8N215|Q96N34|Q9BSB5	Missense_Mutation	SNP	ENST00000359429.6	hg19	CCDS2388.1	.	.	.	.	.	.	.	.	.	.	G	34	5.304604	0.95601	.	.	ENSG00000197713	ENST00000359429;ENST00000436630;ENST00000408981;ENST00000454822;ENST00000429921;ENST00000540255;ENST00000438265;ENST00000429907;ENST00000441588;ENST00000445268;ENST00000452025;ENST00000438204;ENST00000411934;ENST00000435437;ENST00000354506	.	.	.	5.45	5.45	0.79879	Aldolase-type TIM barrel (1);Ribulose-phosphate binding barrel (1);	0.000000	0.85682	D	0.000000	D	0.85852	0.5793	M	0.90369	3.11	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	0.88209	0.2889	9	0.87932	D	0	-3.1604	19.2659	0.93985	0.0:0.0:1.0:0.0	.	146;138;146;146	B4E016;E7EW52;Q96AT9;C9J9T0	.;.;RPE_HUMAN;.	R	146;96;78;96;96;146;96;78;78;78;146;78;78;146;138	.	ENSP00000346501:G138R	G	+	1	0	RPE	210589569	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.777000	0.99008	2.725000	0.93324	0.655000	0.94253	GGG	.	.	.	none		0.438	RPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336574.2	NM_006916		A	210881324	G	A	210881324	3	1	229	1	0	0	0	0	1	0	0	0	13557	1232	43	2	508	2	RPE	2	210881324	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	7380843	210881324	32318049	25	13853											
CUL3	8452	hgsc.bcm.edu	37	chr2	225449678	225449678	+	Frame_Shift_Del	DEL	G	G	-																															caccggaaaggcccggatccGcatcttggtgtccttccggc																										TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr2:225449678delG	ENST00000264414.4	-	1	387	c.49delC	c.(49-51)cggfs	p.R17fs	CUL3_ENST00000344951.4_Frame_Shift_Del_p.R17fs	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	17					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)		GCCCGGATCCGCATCTTGGTG	0.736																																					p.R17fs		Atlas-INDEL	.											.	CUL3	96	.	0			c.50delG						PASS	.						37	35	35					2																	225449678		2200	4300	6500	SO:0001589	frameshift_variant	8452	exon1			.	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.49delC	chr2.hg19:g.225449678delG	ENSP00000264414:p.Arg17fs	76.0	0.0	0		126.0	89.0	0.706349	NM_001257197	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Frame_Shift_Del	DEL	ENST00000264414.4	hg19	CCDS2462.1																																																																																			.	.	.	none		0.736	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2			-	225449678	G	-	225449678	7	5	229	1	0	1	0	1	0	0	0	0	4058	1086	38	0	2321	0	CUL3	2	225449678	Frame_Shift_Del	DEL	G	TCGA-P4-A5E6-01A-11D-A28G-10	14568354	225449678	17749695	26	13854											
BHLHE40	8553	hgsc.bcm.edu	37	chr3	5024970	5024970	+	Missense_Mutation	SNP	A	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	tgggagaaaggatcggcgcaAttaagcaagagtccgaagaa	16	5	14	6	3	0	3	0	0	0	3	2	6	1	4	1	3	1	2	1	3	6	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr3:5024970A>C	ENST00000256495.3	+	5	1435	c.832A>C	c.(832-834)Att>Ctt	p.I278L		NM_003670.2	NP_003661.1	O14503	BHE40_HUMAN	basic helix-loop-helix family, member e40	278					circadian regulation of gene expression (GO:0032922)|entrainment of circadian clock by photoperiod (GO:0043153)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|MRF binding (GO:0043426)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(2)	12						GATCGGCGCAATTAAGCAAGA	0.537																																					p.I278L		Atlas-SNP	.											.	BHLHE40	35	.	0			c.A832C						PASS	.						76	77	77					3																	5024970		2203	4300	6503	SO:0001583	missense	8553	exon5			GGCGCAATTAAGC	AB004066	CCDS2565.1	3p26	2009-01-12	2009-01-12	2009-01-12	ENSG00000134107	ENSG00000134107		"Basic helix-loop-helix proteins"	1046	protein-coding gene	gene with protein product	"differentially expressed in chondrocytes 1", " differentiated embryo chondrocyte expressed gene 1"	604256	"basic helix-loop-helix domain containing, class B, 2"	STRA13, BHLHB2		9240428, 10449910, 18557763	Standard	NM_003670		Approved	DEC1, bHLHe40	uc003bqf.3	O14503	OTTHUMG00000119035	ENST00000256495.3:c.832A>C	chr3.hg19:g.5024970A>C	ENSP00000256495:p.Ile278Leu	82.0	0.0	.		96.0	38.0	.	NM_003670	Q96TD3	Missense_Mutation	SNP	ENST00000256495.3	hg19	CCDS2565.1	.	.	.	.	.	.	.	.	.	.	A	17.95	3.513068	0.64522	.	.	ENSG00000134107	ENST00000256495	T	0.79845	-1.31	5.62	4.47	0.54385	.	0.309371	0.35970	N	0.002872	D	0.85944	0.5815	M	0.75615	2.305	0.80722	D	1	D	0.56035	0.974	P	0.57911	0.829	D	0.85230	0.1032	10	0.46703	T	0.11	.	11.0922	0.48123	0.9283:0.0:0.0717:0.0	.	278	O14503	BHE40_HUMAN	L	278	ENSP00000256495:I278L	ENSP00000256495:I278L	I	+	1	0	BHLHE40	4999970	1.000000	0.71417	0.912000	0.35992	0.165000	0.22458	7.345000	0.79337	0.983000	0.38602	0.533000	0.62120	ATT	.	.	.	none		0.537	BHLHE40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239244.2	NM_003670		C	5024970	A	C	5024970	3	2	229	1	0	0	0	0	1	0	0	0	1423	101	4	5	850	5	BHLHE40	3	5024970	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10		5024970	192997460	27	13855											
XPC	7508	hgsc.bcm.edu	37	chr3	14188804	14188804	+	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	actgaccttgggcccgtagcGacgcttcagcctctccctga	6	9	10	16	3	2	2	1	2	1	0	3	3	2	2	4	1	2	2	4	1	1	3	rs373301509		TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr3:14188804G>C	ENST00000285021.7	-	15	2804	c.2590C>G	c.(2590-2592)Cgc>Ggc	p.R864G	RP11-434D12.1_ENST00000601399.1_Intron|RP11-434D12.1_ENST00000608606.1_Intron|XPC_ENST00000449060.2_Missense_Mutation_p.R827G|AC093495.4_ENST00000428681.3_RNA|AC093495.4_ENST00000420253.1_RNA	NM_001145769.1|NM_004628.4	NP_001139241.1|NP_004619.3	Q01831	XPC_HUMAN	xeroderma pigmentosum, complementation group C	864	Interaction with CETN2.|Interaction with ERCC2 and GTF2H1.				DNA repair (GO:0006281)|intra-S DNA damage checkpoint (GO:0031573)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to drug (GO:0042493)|response to UV-B (GO:0010224)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|XPC complex (GO:0071942)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|heteroduplex DNA loop binding (GO:0000404)|single-stranded DNA binding (GO:0003697)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GGCCCGTAGCGACGCTTCAGC	0.547			"Mis, N, F, S"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.R864G		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (C)	3	3p25	7508	"xeroderma pigmentosum, complementation group C"		E	.	XPC	60	.	0			c.C2590G						PASS	.						53	57	56					3																	14188804		1998	4157	6155	SO:0001583	missense	7508	exon15	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	CGTAGCGACGCTT		CCDS46763.1	3p25.1	2014-09-17			ENSG00000154767	ENSG00000154767			12816	protein-coding gene	gene with protein product	"xeroderma pigmentosum group C protein"	613208				1522891	Standard	NM_004628		Approved	XPCC, RAD4	uc011ave.2	Q01831	OTTHUMG00000155526	ENST00000285021.7:c.2590C>G	chr3.hg19:g.14188804G>C	ENSP00000285021:p.Arg864Gly	60.0	0.0	.		110.0	8.0	.	NM_004628	B4DIP3|E9PB96|E9PH69|Q53GT7|Q96AX0	Missense_Mutation	SNP	ENST00000285021.7	hg19	CCDS46763.1	.	.	.	.	.	.	.	.	.	.	G	19.14	3.770436	0.69992	.	.	ENSG00000154767	ENST00000285021;ENST00000449060	T;T	0.36157	1.27;1.29	5.18	4.3	0.51218	.	0.000000	0.85682	D	0.000000	T	0.59959	0.2232	M	0.78801	2.425	0.80722	D	1	D;D	0.76494	0.996;0.999	P;D	0.70716	0.903;0.97	T	0.64437	-0.6408	10	0.49607	T	0.09	-14.9319	15.159	0.72767	0.0:0.0:0.8577:0.1423	.	827;864	E9PH69;Q01831	.;XPC_HUMAN	G	864;827	ENSP00000285021:R864G;ENSP00000404002:R827G	ENSP00000285021:R864G	R	-	1	0	XPC	14163805	1.000000	0.71417	0.891000	0.34965	0.837000	0.47467	6.671000	0.74472	1.385000	0.46445	0.591000	0.81541	CGC	.	.	.	alt		0.547	XPC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340517.3	NM_004628		C	14188804	G	C	14188804	3	2	229	1	0	0	0	0	1	0	0	0	17453	1058	37	4	240	4	XPC	3	14188804	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	9163834	14188804	183833626	28	13856											
DAG1	1605	hgsc.bcm.edu	37	chr3	49568609	49568609	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagcttctcagaagtagagcTtcacaacatgaaattagtgc	14	10	9	8	0	2	3	2	1	1	2	3	4	2	3	0	0	4	3	0	0	5	4			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr3:49568609T>C	ENST00000539901.1	+	3	1223	c.665T>C	c.(664-666)cTt>cCt	p.L222P	DAG1_ENST00000545947.1_Missense_Mutation_p.L222P|DAG1_ENST00000308775.2_Missense_Mutation_p.L222P|DAG1_ENST00000515359.2_Missense_Mutation_p.L222P|DAG1_ENST00000538711.1_Missense_Mutation_p.L222P|DAG1_ENST00000541308.1_Missense_Mutation_p.L222P	NM_001177644.2	NP_001171115	Q14118	DAG1_HUMAN	dystroglycan 1 (dystrophin-associated glycoprotein 1)	222	Required for laminin recognition.				basement membrane organization (GO:0071711)|branching involved in salivary gland morphogenesis (GO:0060445)|calcium-dependent cell-matrix adhesion (GO:0016340)|commissural neuron axon guidance (GO:0071679)|cytoskeletal anchoring at plasma membrane (GO:0007016)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|microtubule anchoring (GO:0034453)|modulation by virus of host morphology or physiology (GO:0019048)|morphogenesis of an epithelial sheet (GO:0002011)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell migration (GO:0030336)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase B signaling (GO:0051898)|nerve maturation (GO:0021682)|NLS-bearing protein import into nucleus (GO:0006607)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell outer membrane (GO:0009279)|cell-cell adherens junction (GO:0005913)|contractile ring (GO:0070938)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystroglycan complex (GO:0016011)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|node of Ranvier (GO:0033268)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|alpha-actinin binding (GO:0051393)|calcium ion binding (GO:0005509)|laminin-1 binding (GO:0043237)|SH2 domain binding (GO:0042169)|structural constituent of muscle (GO:0008307)|tubulin binding (GO:0015631)|vinculin binding (GO:0017166)|virus receptor activity (GO:0001618)			NS(1)|autonomic_ganglia(2)|breast(2)|endometrium(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	23				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.00241)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		GAAGTAGAGCTTCACAACATG	0.493																																					p.L222P		Atlas-SNP	.											.	DAG1	60	.	0			c.T665C						PASS	.						76	81	80					3																	49568609		2203	4300	6503	SO:0001583	missense	1605	exon4			TAGAGCTTCACAA	L19711	CCDS2799.1	3p21	2014-09-17			ENSG00000173402	ENSG00000173402			2666	protein-coding gene	gene with protein product	"alpha-dystroglycan", "dystrophin-associated glycoprotein-1", "beta-dystroglycan"	128239				7774920, 1741056	Standard	NM_001177643		Approved	A3a, 156DAG, AGRNR, DAG	uc021wyd.1	Q14118	OTTHUMG00000156869	ENST00000539901.1:c.665T>C	chr3.hg19:g.49568609T>C	ENSP00000439334:p.Leu222Pro	124.0	0.0	.		116.0	47.0	.	NM_001177642	A8K6M7|Q969J9	Missense_Mutation	SNP	ENST00000539901.1	hg19	CCDS2799.1	.	.	.	.	.	.	.	.	.	.	T	11.97	1.798715	0.31777	.	.	ENSG00000173402	ENST00000515359;ENST00000308775;ENST00000545947;ENST00000541308;ENST00000539901;ENST00000538711;ENST00000415315	T;T;T;T;T;T	0.81163	-1.46;-1.46;-1.46;-1.46;-1.46;-1.46	5.92	3.55	0.40652	.	0.170769	0.52532	N	0.000062	T	0.76652	0.4017	M	0.65975	2.015	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.70368	-0.4891	10	0.51188	T	0.08	-12.03	9.6231	0.39734	0.0:0.1436:0.0:0.8564	.	222	Q14118	DAG1_HUMAN	P	222;222;222;222;222;222;21	ENSP00000440705:L222P;ENSP00000312435:L222P;ENSP00000442600:L222P;ENSP00000440590:L222P;ENSP00000439334:L222P;ENSP00000438421:L222P	ENSP00000312435:L222P	L	+	2	0	DAG1	49543613	1.000000	0.71417	0.997000	0.53966	0.982000	0.71751	4.211000	0.58507	0.496000	0.27904	0.533000	0.62120	CTT	.	.	.	none		0.493	DAG1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346326.1			C	49568609	T	C	49568609	3	2	229	1	0	0	0	0	1	0	0	0	4227	1609	56	3	671	3	DAG1	3	49568609	Missense_Mutation	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10	35379805	49568609	148453821	29	13857											
MAPKAPK3	7867	hgsc.bcm.edu	37	chr3	50685441	50685441	+	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	aggagaaaaaagcaggcaggCagctcctctgcctcacaggg	13	4	13	11	0	2	1	1	0	1	1	3	2	3	1	2	4	3	4	2	4	3	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr3:50685441C>G	ENST00000446044.1	+	13	1709	c.1113C>G	c.(1111-1113)ggC>ggG	p.G371G	MAPKAPK3_ENST00000357955.2_Silent_p.G371G	NM_001243926.1	NP_001230855.1	Q16644	MAPK3_HUMAN	mitogen-activated protein kinase-activated protein kinase 3	371					activation of MAPK activity (GO:0000187)|innate immune response (GO:0045087)|macropinocytosis (GO:0044351)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|Ras protein signal transduction (GO:0007265)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|response to stress (GO:0006950)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|ovary(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.0188)|Kidney(197;0.0223)		AGCAGGCAGGCAGCTCCTCTG	0.562																																					p.G371G		Atlas-SNP	.											.	MAPKAPK3	32	.	0			c.C1113G						PASS	.						69	69	69					3																	50685441		2203	4300	6503	SO:0001819	synonymous_variant	7867	exon11			GGCAGGCAGCTCC	U43784	CCDS2832.1	3p21.3	2004-03-10			ENSG00000114738	ENSG00000114738			6888	protein-coding gene	gene with protein product		602130				8626550, 8622688	Standard	NM_004635		Approved	3pK, MAPKAP3, 3PK	uc003dba.2	Q16644	OTTHUMG00000156850	ENST00000446044.1:c.1113C>G	chr3.hg19:g.50685441C>G		246.0	1.0	.		260.0	110.0	.	NM_004635	B5BU67	Silent	SNP	ENST00000446044.1	hg19	CCDS2832.1	.	.	.	.	.	.	.	.	.	.	C	9.156	1.017372	0.19355	.	.	ENSG00000114738	ENST00000451680	.	.	.	5.73	2.59	0.31030	.	.	.	.	.	T	0.53626	0.1808	.	.	.	0.45733	D	0.998639	.	.	.	.	.	.	T	0.49194	-0.8965	4	.	.	.	-29.6661	6.4693	0.21999	0.2822:0.5832:0.0:0.1346	.	.	.	.	E	86	.	.	Q	+	1	0	MAPKAPK3	50660445	0.089000	0.21612	0.973000	0.42090	0.978000	0.69477	0.290000	0.18975	1.409000	0.46915	0.655000	0.94253	CAG	.	.	.	none		0.562	MAPKAPK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346237.1	NM_004635		G	50685441	C	G	50685441	2	3	229	1	0	0	0	0	0	0	0	1	9297	697	25	4		4	MAPKAPK3	3	50685441	Silent	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	1116832	50685441	147336989	30	13858											
MAGI1	9223	hgsc.bcm.edu	37	chr3	65425597	65425597	+	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	tgctgctgctgctgttgctgCtgctgttgctgctgctgctg	0	16	14	11	0	0	0	0	0	0	0	0	0	0	0	0	0	11	13	0	0	0	2	rs571281009	byFrequency	TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr3:65425597C>T	ENST00000497477.2	-	9	1226	c.1227G>A	c.(1225-1227)caG>caA	p.Q409Q	MAGI1_ENST00000402939.2_Silent_p.Q409Q|MAGI1_ENST00000470990.1_5'UTR|MAGI1_ENST00000330909.8_Silent_p.Q409Q|MAGI1_ENST00000483466.1_Silent_p.Q409Q			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	409	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)		gctgttgctgctgctgttgct	0.532											OREG0015658	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	49	0.00978435	0.0325	0.0043	5008	,	,		14951	0.003		0	False		,,,				2504	0				p.Q409Q		Atlas-SNP	.											.	MAGI1	481	.	0			c.G1227A						PASS	.						68	64	65					3																	65425597		2202	4296	6498	SO:0001819	synonymous_variant	9223	exon9			TTGCTGCTGCTGT	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.1227G>A	chr3.hg19:g.65425597C>T		38.0	0.0	.	1084	41.0	7.0	.	NM_001033057	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Silent	SNP	ENST00000497477.2	hg19		.	.	.	.	.	.	.	.	.	.	C	1.115	-0.657141	0.03480	.	.	ENSG00000151276	ENST00000460329	.	.	.	3.23	1.37	0.22104	.	.	.	.	.	T	0.23014	0.0556	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.22277	-1.0221	4	.	.	.	0.0018	2.6711	0.05067	0.2253:0.507:0.0:0.2677	.	.	.	.	N	290	.	.	S	-	2	0	MAGI1	65400637	0.651000	0.27340	0.048000	0.18961	0.002000	0.02628	-0.987000	0.03743	0.095000	0.17434	-0.850000	0.03035	AGC	.	.	.	none		0.532	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742		T	65425597	C	T	65425597	2	4	229	1	0	0	0	0	0	0	0	1	9197	796	28	2		2	MAGI1	3	65425597	Silent	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	14740156	65425597	132596833	31	13859											
MYH15	22989	hgsc.bcm.edu	37	chr3	108174686	108174687	+	Frame_Shift_Ins	INS	-	-	T																															cttgctctttggaaaggtccINSttggattcagaatgcagtac																										TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr3:108174686_108174687insT	ENST00000273353.3	-	21	2274_2275	c.2218_2219insA	c.(2218-2220)aggfs	p.R740fs	MYH15_ENST00000495753.2_5'UTR	NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	740	Myosin motor.					cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						TGGAAAGGTCCTTGGATTCAGA	0.361																																					p.R740fs		Atlas-Indel,Pindel	.											.	MYH15	223	.	0			c.2219_2220insA						PASS	.																																			SO:0001589	frameshift_variant	22989	exon21			.	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.2219dupA	chr3.hg19:g.108174688_108174688dupT	ENSP00000273353:p.Arg740fs	38.0	0.0	0		55.0	15.0	0.272727	NM_014981		Frame_Shift_Ins	INS	ENST00000273353.3	hg19	CCDS43127.1																																																																																			.	.	.	none		0.361	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		T	108174687	-	T	108174686	7	5	229	1	0	1	1	0	0	0	0	0	10041	681	24	0	3709	0	MYH15	3	108174686	Frame_Shift_Ins	INS	-	TCGA-P4-A5E6-01A-11D-A28G-10	42749089	108174686	89847744	32	13860											
ABHD10	55347	hgsc.bcm.edu	37	chr3	111710242	111710242	+	Missense_Mutation	SNP	A	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	agctaaaaaaggaagtagagAtgaaaggtgtgtggagcatg	17	7	15	2	0	0	2	0	1	0	1	0	5	0	4	0	3	2	3	0	3	6	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr3:111710242A>C	ENST00000273359.3	+	5	622	c.595A>C	c.(595-597)Atg>Ctg	p.M199L	ABHD10_ENST00000494817.1_3'UTR|ABHD10_ENST00000534857.1_Missense_Mutation_p.M42L	NM_018394.2	NP_060864.1	Q9NUJ1	ABHDA_HUMAN	abhydrolase domain containing 10	199					glucuronoside catabolic process (GO:0019391)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			large_intestine(2)|lung(7)|skin(1)	10						GGAAGTAGAGATGAAAGGTGT	0.323																																					p.M199L		Atlas-SNP	.											.	ABHD10	20	.	0			c.A595C						PASS	.						79	75	76					3																	111710242		2203	4300	6503	SO:0001583	missense	55347	exon5			GTAGAGATGAAAG	AL713726	CCDS2963.1, CCDS63718.1	3q13.2	2012-03-26			ENSG00000144827	ENSG00000144827		"Abhydrolase domain containing"	25656	protein-coding gene	gene with protein product						22294686	Standard	NM_018394		Approved	FLJ11342	uc003dyk.5	Q9NUJ1	OTTHUMG00000159280	ENST00000273359.3:c.595A>C	chr3.hg19:g.111710242A>C	ENSP00000273359:p.Met199Leu	154.0	0.0	.		151.0	34.0	.	NM_018394	B7Z6A8|C9IZX5|D3DN63|Q8TCF9	Missense_Mutation	SNP	ENST00000273359.3	hg19	CCDS2963.1	.	.	.	.	.	.	.	.	.	.	A	12.86	2.064132	0.36373	.	.	ENSG00000144827	ENST00000534857;ENST00000273359	T;T	0.66099	1.02;-0.19	5.47	-3.29	0.05017	.	0.598228	0.18438	N	0.141217	T	0.33585	0.0868	N	0.19112	0.55	0.23445	N	0.997665	B	0.02656	0.0	B	0.06405	0.002	T	0.06661	-1.0814	10	0.30078	T	0.28	-12.4265	1.0289	0.01533	0.3041:0.125:0.3257:0.2452	.	199	Q9NUJ1	ABHDA_HUMAN	L	42;199	ENSP00000442932:M42L;ENSP00000273359:M199L	ENSP00000273359:M199L	M	+	1	0	ABHD10	113192932	1.000000	0.71417	0.986000	0.45419	0.987000	0.75469	1.234000	0.32660	-0.436000	0.07254	0.443000	0.29094	ATG	.	.	.	none		0.323	ABHD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354326.1	NM_018394		C	111710242	A	C	111710242	3	2	229	1	0	0	0	0	1	0	0	0	74	333	12	5	613	5	ABHD10	3	111710242	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	3535556	111710242	86312188	33	13861											
ARRDC3	57561	hgsc.bcm.edu	37	chr5	90669948	90669948	+	Missense_Mutation	SNP	A	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	taccttcaggtctttcaggaAgtgataaactgagccagttc	11	12	9	9	0	3	2	2	2	1	0	4	3	3	3	2	2	3	1	2	2	4	5			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr5:90669948A>C	ENST00000265138.3	-	6	1282	c.1016T>G	c.(1015-1017)cTt>cGt	p.L339R	ARRDC3_ENST00000503192.1_5'Flank	NM_020801.2	NP_065852.1	Q96B67	ARRD3_HUMAN	arrestin domain containing 3	339					fat pad development (GO:0060613)|negative regulation of heat generation (GO:0031651)|negative regulation of locomotion involved in locomotory behavior (GO:0090327)|negative regulation of multicellular organismal metabolic process (GO:0044252)|positive regulation of adrenergic receptor signaling pathway (GO:0071879)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|skin development (GO:0043588)|temperature homeostasis (GO:0001659)	endosome (GO:0005768)|plasma membrane (GO:0005886)	beta-3 adrenergic receptor binding (GO:0031699)			breast(2)|endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	18		all_cancers(142;2.22e-05)|all_epithelial(76;1.58e-07)|all_lung(232;0.000521)|Lung NSC(167;0.000548)|Ovarian(174;0.0798)|Colorectal(57;0.207)		OV - Ovarian serous cystadenocarcinoma(54;4.56e-30)|Epithelial(54;7.55e-26)|all cancers(79;3.63e-22)		TCTTTCAGGAAGTGATAAACT	0.373																																					p.L339R		Atlas-SNP	.											.	ARRDC3	56	.	0			c.T1016G						PASS	.						187	185	186					5																	90669948		2203	4300	6503	SO:0001583	missense	57561	exon6			TCAGGAAGTGATA	AB037797	CCDS34202.1	5q14.3	2013-10-11			ENSG00000113369	ENSG00000113369			29263	protein-coding gene	gene with protein product	"alpha-arrestin 3"	612464				10718198, 19605364	Standard	NM_020801		Approved	KIAA1376	uc003kjz.2	Q96B67	OTTHUMG00000162616	ENST00000265138.3:c.1016T>G	chr5.hg19:g.90669948A>C	ENSP00000265138:p.Leu339Arg	105.0	0.0	.		113.0	33.0	.	NM_020801	A8K6T8|Q9P2H1	Missense_Mutation	SNP	ENST00000265138.3	hg19	CCDS34202.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.263139	0.80358	.	.	ENSG00000113369	ENST00000265138	T	0.08984	3.03	5.77	5.77	0.91146	Immunoglobulin E-set (1);	0.000000	0.85682	D	0.000000	T	0.26085	0.0636	M	0.62723	1.935	0.80722	D	1	D	0.65815	0.995	D	0.72982	0.979	T	0.00473	-1.1718	10	0.34782	T	0.22	-10.2226	16.086	0.81049	1.0:0.0:0.0:0.0	.	339	Q96B67	ARRD3_HUMAN	R	339	ENSP00000265138:L339R	ENSP00000265138:L339R	L	-	2	0	ARRDC3	90705704	1.000000	0.71417	0.981000	0.43875	0.932000	0.56968	9.339000	0.96797	2.207000	0.71202	0.528000	0.53228	CTT	.	.	.	none		0.373	ARRDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369763.2	NM_020801		C	90669948	A	C	90669948	3	2	229	1	0	0	0	0	1	0	0	0	984	72	3	5	240	5	ARRDC3	5	90669948	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10		90669948	90245312	34	13862											
PAM	5066	hgsc.bcm.edu	37	chr5	102285295	102285295	+	Missense_Mutation	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	ttatccaatgcatgtctttgCctatagagttcacactcacc	10	14	5	12	0	3	1	2	0	1	1	4	1	4	1	3	0	2	2	3	0	4	5			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr5:102285295C>T	ENST00000438793.3	+	9	1168	c.698C>T	c.(697-699)gCc>gTc	p.A233V	PAM_ENST00000346918.2_Missense_Mutation_p.A233V|PAM_ENST00000379787.4_5'UTR|PAM_ENST00000455264.2_Missense_Mutation_p.A233V|PAM_ENST00000304400.7_Missense_Mutation_p.A233V|PAM_ENST00000274392.9_Missense_Mutation_p.A136V|PAM_ENST00000348126.2_Missense_Mutation_p.A233V	NM_000919.3|NM_001177306.1|NM_138766.2	NP_000910.2|NP_001170777.1|NP_620121.1	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	233	Peptidylglycine alpha-hydroxylating monooxygenase. {ECO:0000250}.				central nervous system development (GO:0007417)|heart development (GO:0007507)|lactation (GO:0007595)|limb development (GO:0060173)|long-chain fatty acid metabolic process (GO:0001676)|maternal process involved in female pregnancy (GO:0060135)|odontogenesis (GO:0042476)|ovulation cycle process (GO:0022602)|peptide amidation (GO:0001519)|protein amidation (GO:0018032)|protein homooligomerization (GO:0051260)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of protein secretion (GO:0050708)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to pH (GO:0009268)|toxin metabolic process (GO:0009404)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|L-ascorbic acid binding (GO:0031418)|peptidylamidoglycolate lyase activity (GO:0004598)|peptidylglycine monooxygenase activity (GO:0004504)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	25		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	CATGTCTTTGCCTATAGAGTT	0.323																																					p.A233V		Atlas-SNP	.											.	PAM	180	.	0			c.C698T						PASS	.						106	108	107					5																	102285295		2203	4297	6500	SO:0001583	missense	5066	exon9			TCTTTGCCTATAG	AB095007	CCDS4092.1, CCDS4093.1, CCDS4094.1, CCDS43348.1, CCDS54885.1	5q	2008-02-05			ENSG00000145730	ENSG00000145730	1.14.17.3		8596	protein-coding gene	gene with protein product	"peptidyl-alpha-hydroxyglycine alpha-amidating lyase", "peptidylglycine alpha-hydroxylating monooxygenase"	170270				2357221	Standard	NM_000919		Approved	PAL, PHM	uc003knt.3	P19021	OTTHUMG00000128729	ENST00000438793.3:c.698C>T	chr5.hg19:g.102285295C>T	ENSP00000396493:p.Ala233Val	264.0	0.0	.		259.0	24.0	.	NM_138822	A6NMR0|A8K293|O43211|O95080|Q16252|Q16253|Q54A45|Q86U53|Q8WVC7|Q9UCG0	Missense_Mutation	SNP	ENST00000438793.3	hg19	CCDS54885.1	.	.	.	.	.	.	.	.	.	.	C	32	5.156388	0.94686	.	.	ENSG00000145730	ENST00000438793;ENST00000346918;ENST00000348126;ENST00000304400;ENST00000274392;ENST00000455264	T;T;T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14;-1.14;-1.14	6.02	6.02	0.97574	Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-2 conserved site (1);PHM/PNGase F domain (1);Copper type II, ascorbate-dependent monooxygenase-like, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.91036	0.7180	M	0.90650	3.135	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.91659	0.5341	10	0.87932	D	0	.	20.5373	0.99239	0.0:1.0:0.0:0.0	.	136;233;233;233;233;233	F8WE90;P19021;P19021-4;P19021-3;P19021-5;P19021-2	.;AMD_HUMAN;.;.;.;.	V	233;233;233;233;136;233	ENSP00000396493:A233V;ENSP00000282992:A233V;ENSP00000314638:A233V;ENSP00000306100:A233V;ENSP00000274392:A136V;ENSP00000403461:A233V	ENSP00000274392:A136V	A	+	2	0	PAM	102313194	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.290000	0.72712	2.857000	0.98124	0.650000	0.86243	GCC	.	.	.	none		0.323	PAM-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250640.2	NM_000919		T	102285295	C	T	102285295	3	4	229	1	0	0	0	0	1	0	0	0	11419	739	26	2	732	2	PAM	5	102285295	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	11615347	102285295	78629965	35	13863											
PCDHGB6	56100	hgsc.bcm.edu	37	chr5	140788348	140788348	+	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	gatggtggcaaatacccagaGttatctctggagaaactcct	12	10	10	9	0	1	2	0	0	1	2	3	4	2	2	2	3	2	2	2	3	4	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr5:140788348G>T	ENST00000520790.1	+	1	579	c.579G>T	c.(577-579)gaG>gaT	p.E193D	PCDHGB4_ENST00000519479.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_018926.2|NM_032100.1	NP_061749.1|NP_115271.1	Q9Y5F9	PCDGI_HUMAN	protocadherin gamma subfamily B, 6	193	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|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)			AATACCCAGAGTTATCTCTGG	0.403																																					p.E193D		Atlas-SNP	.											.	PCDHGB6	120	.	0			c.G579T						PASS	.						26	26	26					5																	140788348		1835	4088	5923	SO:0001583	missense	56100	exon1			CCCAGAGTTATCT	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.579G>T	chr5.hg19:g.140788348G>T	ENSP00000428603:p.Glu193Asp	38.0	0.0	.		53.0	22.0	.	NM_032100	Q9Y5C5	Missense_Mutation	SNP	ENST00000520790.1	hg19	CCDS54929.1	.	.	.	.	.	.	.	.	.	.	g	13.81	2.348524	0.41599	.	.	ENSG00000253305	ENST00000520790	T	0.21734	1.99	5.34	1.01	0.19927	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.40909	0.1136	M	0.77616	2.38	0.09310	N	0.999999	D;D	0.71674	0.994;0.998	D;D	0.70016	0.948;0.967	T	0.12760	-1.0535	9	0.66056	D	0.02	.	6.0351	0.19702	0.382:0.0:0.4936:0.1244	.	193;193	Q9Y5F9;Q9Y5F9-2	PCDGI_HUMAN;.	D	193	ENSP00000428603:E193D	ENSP00000428603:E193D	E	+	3	2	PCDHGB6	140768532	0.000000	0.05858	0.987000	0.45799	0.966000	0.64601	-1.583000	0.02115	0.257000	0.21650	-0.373000	0.07131	GAG	.	.	.	none		0.403	PCDHGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374746.1	NM_018926		T	140788348	G	T	140788348	3	4	229	1	0	0	0	0	1	0	0	0	11574	1020	36	4	581	4	PCDHGB6	5	140788348	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	38503053	140788348	40126912	36	13864											
SPINK1	6690	hgsc.bcm.edu	37	chr5	147207646	147207646	+	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	tccatcagtcccacagacagGgtcatatatcttggtgcatc	10	11	8	12	0	3	1	2	0	1	1	6	1	5	1	2	2	1	1	2	2	2	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr5:147207646G>A	ENST00000296695.5	-	3	341	c.133C>T	c.(133-135)Cct>Tct	p.P45S	SPINK1_ENST00000510027.2_Missense_Mutation_p.P45S	NM_003122.3	NP_003113.2	P00995	ISK1_HUMAN	serine peptidase inhibitor, Kazal type 1	45	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)			CCACAGACAGGGTCATATATC	0.328									Hereditary Pancreatitis																												p.P45S		Atlas-SNP	.											.	SPINK1	9	.	0			c.C133T						PASS	.						126	119	121					5																	147207646		2203	4300	6503	SO:0001583	missense	6690	exon3	Familial Cancer Database		AGACAGGGTCATA		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.133C>T	chr5.hg19:g.147207646G>A	ENSP00000296695:p.Pro45Ser	106.0	0.0	.		114.0	24.0	.	NM_003122		Missense_Mutation	SNP	ENST00000296695.5	hg19	CCDS4286.1	.	.	.	.	.	.	.	.	.	.	G	16.15	3.042553	0.55003	.	.	ENSG00000164266	ENST00000296695;ENST00000510027	D;D	0.85339	-1.97;-1.97	4.9	4.9	0.64082	Proteinase inhibitor I1, Kazal (3);	0.000000	0.64402	D	0.000001	D	0.91991	0.7463	.	.	.	0.43708	D	0.996175	D	0.89917	1.0	D	0.97110	1.0	D	0.92165	0.5739	9	0.56958	D	0.05	-21.6312	15.9791	0.80094	0.0:0.0:1.0:0.0	.	45	P00995	ISK1_HUMAN	S	45	ENSP00000296695:P45S;ENSP00000427376:P45S	ENSP00000296695:P45S	P	-	1	0	SPINK1	147187839	1.000000	0.71417	0.938000	0.37757	0.224000	0.24922	4.936000	0.63506	2.725000	0.93324	0.655000	0.94253	CCT	.	.	.	none		0.328	SPINK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251940.2	NM_003122		A	147207646	G	A	147207646	3	1	229	1	0	0	0	0	1	0	0	0	15069	1232	43	2	114	2	SPINK1	5	147207646	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	6419298	147207646	33707614	37	13865											
C5orf40	408263	hgsc.bcm.edu	37	chr5	156770121	156770121	+	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	cctgtaagaccatcgcggctCatggcaacggacacaccaga	12	5	10	14	3	1	2	1	0	0	2	2	3	1	3	3	3	1	3	3	3	2	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr5:156770121C>A	ENST00000312349.4	-	2	611	c.424G>T	c.(424-426)Gag>Tag	p.E142*	CYFIP2_ENST00000521420.1_Intron|CYFIP2_ENST00000442283.2_Intron|CYFIP2_ENST00000377576.3_Intron|CYFIP2_ENST00000347377.6_Intron|CYFIP2_ENST00000435847.2_Intron|CYFIP2_ENST00000522463.1_Intron|CYFIP2_ENST00000318218.6_Intron|CYFIP2_ENST00000541131.1_Intron	NM_001001343.3	NP_001001343.2	Q8TBE3	FNDC9_HUMAN	fibronectin type III domain containing 9	142						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	9						CATCGCGGCTCATGGCAACGG	0.607											OREG0016977	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E142X		Atlas-SNP	.											.	FNDC9	22	.	0			c.G424T						PASS	.						64	62	63					5																	156770121		2203	4300	6503	SO:0001587	stop_gained	408263	exon2			GCGGCTCATGGCA	BC022570	CCDS4337.1	5q33.3	2013-02-11	2011-01-25	2011-01-25	ENSG00000172568	ENSG00000172568		"Fibronectin type III domain containing"	33547	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 40"	C5orf40			Standard	NM_001001343		Approved	MGC27121	uc003lwu.2	Q8TBE3	OTTHUMG00000130248	ENST00000312349.4:c.424G>T	chr5.hg19:g.156770121C>A	ENSP00000310594:p.Glu142*	116.0	0.0	.	1781	136.0	43.0	.	NM_001001343	A8K0Y6	Nonsense_Mutation	SNP	ENST00000312349.4	hg19	CCDS4337.1	.	.	.	.	.	.	.	.	.	.	C	19.32	3.805183	0.70682	.	.	ENSG00000172568	ENST00000312349;ENST00000520782	.	.	.	5.08	4.15	0.48705	.	0.241065	0.28784	N	0.014157	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	-4.2189	9.3255	0.37990	0.16:0.6848:0.1551:0.0	.	.	.	.	X	142	.	ENSP00000310594:E142X	E	-	1	0	FNDC9	156702699	0.304000	0.24472	0.997000	0.53966	0.674000	0.39518	0.688000	0.25422	2.369000	0.80426	0.491000	0.48974	GAG	.	.	.	none		0.607	FNDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252573.2	NM_001001343		A	156770121	C	A	156770121	4	1	229	1	0	0	0	0	0	1	0	0	2301	835	29	4	254	4	C5orf40	5	156770121	Nonsense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	9562475	156770121	24145139	38	13866											
FAM65B	9750	hgsc.bcm.edu	37	chr6	24843494	24843494	+	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	ggcaggttttctgggctcctCtgggtcttcctccttcaggt	2	15	12	12	0	4	0	1	0	3	0	7	0	7	0	3	5	0	3	3	5	0	4			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr6:24843494C>G	ENST00000259698.4	-	14	1691	c.1516G>C	c.(1516-1518)Gag>Cag	p.E506Q	FAM65B_ENST00000378023.4_Missense_Mutation_p.E456Q|FAM65B_ENST00000510784.2_Missense_Mutation_p.E490Q|FAM65B_ENST00000540914.1_Missense_Mutation_p.E456Q|FAM65B_ENST00000538035.1_Missense_Mutation_p.E485Q|FAM65B_ENST00000473070.1_5'Flank	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	506					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						CTGGGCTCCTCTGGGTCTTCC	0.577																																					p.E506Q		Atlas-SNP	.											.	FAM65B	134	.	0			c.G1516C						PASS	.						86	82	83					6																	24843494		1916	4115	6031	SO:0001583	missense	9750	exon14			GCTCCTCTGGGTC	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.1516G>C	chr6.hg19:g.24843494C>G	ENSP00000259698:p.Glu506Gln	83.0	0.0	.		99.0	33.0	.	NM_014722	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Missense_Mutation	SNP	ENST00000259698.4	hg19	CCDS47383.1	.	.	.	.	.	.	.	.	.	.	C	9.393	1.076084	0.20227	.	.	ENSG00000111913	ENST00000259698;ENST00000538035;ENST00000378023;ENST00000540914;ENST00000510784	T;T;T;T;T	0.32515	1.45;1.45;1.45;1.45;1.45	4.3	2.46	0.29980	.	1.536000	0.03262	N	0.183420	T	0.06917	0.0176	N	0.24115	0.695	0.09310	N	1	B;B;B;B	0.16396	0.017;0.004;0.009;0.004	B;B;B;B	0.11329	0.006;0.003;0.004;0.004	T	0.23404	-1.0189	10	0.13853	T	0.58	-0.5328	7.1945	0.25845	0.0:0.6914:0.1422:0.1664	.	490;485;456;506	B7Z6U4;F5GX51;Q9Y4F9-2;Q9Y4F9	.;.;.;FA65B_HUMAN	Q	506;485;456;456;490	ENSP00000259698:E506Q;ENSP00000441138:E485Q;ENSP00000367262:E456Q;ENSP00000438425:E456Q;ENSP00000441305:E490Q	ENSP00000259698:E506Q	E	-	1	0	FAM65B	24951473	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	0.333000	0.19768	0.417000	0.25871	0.655000	0.94253	GAG	.	.	.	none		0.577	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2			G	24843494	C	G	24843494	3	3	229	1	0	0	0	0	1	0	0	0	5607	922	32	4	1740	4	FAM65B	6	24843494	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10		24843494	146271573	39	13867											
HLA-E	3133	hgsc.bcm.edu	37	chr6	30459405	30459405	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctggagctgtggttgctgcTgtgatatggaggaagaagag	9	11	17	4	0	1	3	0	1	1	2	1	6	1	6	0	4	3	4	0	4	3	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr6:30459405T>C	ENST00000376630.4	+	5	1043	c.978T>C	c.(976-978)gcT>gcC	p.A326A		NM_005516.5	NP_005507.3	P13747	HLAE_HUMAN	major histocompatibility complex, class I, E	326					antigen processing and presentation of endogenous peptide antigen via MHC class Ib (GO:0002476)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of natural killer cell mediated immunity (GO:0002717)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protection from natural killer cell mediated cytotoxicity (GO:0042270)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	MHC class I protein binding (GO:0042288)|peptide antigen binding (GO:0042605)			breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(2)|lung(1)|ovary(3)|skin(1)|urinary_tract(1)	18						TGGTTGCTGCTGTGATATGGA	0.557																																					p.A326A		Atlas-SNP	.											.	HLA-E	35	.	0			c.T978C						PASS	.						153	162	159					6																	30459405		1509	2709	4218	SO:0001819	synonymous_variant	3133	exon5			TGCTGCTGTGATA	M20022	CCDS34379.1	6p21.3	2013-01-11			ENSG00000204592	ENSG00000204592		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4962	protein-coding gene	gene with protein product		143010				3131426	Standard	NM_005516		Approved		uc003nqg.3	P13747	OTTHUMG00000031155	ENST00000376630.4:c.978T>C	chr6.hg19:g.30459405T>C		100.0	0.0	.		100.0	27.0	.	NM_005516	Q30169|Q9BT83|Q9GIY7|Q9GIY8	Silent	SNP	ENST00000376630.4	hg19	CCDS34379.1																																																																																			.	.	.	none		0.557	HLA-E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076282.2	NM_005516		C	30459405	T	C	30459405	2	2	229	1	0	0	0	0	0	0	0	1	7217	1567	55	3		3	HLA-E	6	30459405	Silent	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10	5615911	30459405	140655662	40	13868											
PRICKLE4	29964	hgsc.bcm.edu	37	chr6	41751890	41751890	+	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	gtcctgcagttctgagcttgGgttccctttgcctggacacc	4	13	11	13	0	1	1	0	1	1	0	3	2	3	2	4	2	3	4	4	2	0	4			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr6:41751890G>A	ENST00000394260.1	+	1	34	c.34G>A	c.(34-36)Ggt>Agt	p.G12S	PRICKLE4_ENST00000458694.1_Missense_Mutation_p.G52S|PRICKLE4_ENST00000394259.1_Missense_Mutation_p.G12S|PRICKLE4_ENST00000394263.1_Missense_Mutation_p.G52S|PRICKLE4_ENST00000359201.5_Missense_Mutation_p.G52S			Q2TBC4	PRIC4_HUMAN	prickle homolog 4 (Drosophila)	12	PET. {ECO:0000255|PROSITE- ProRule:PRU00636}.					nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	13	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TCTGAGCTTGGGTTCCCTTTG	0.542																																					p.G52S		Atlas-SNP	.											.	PRICKLE4	29	.	0			c.G154A						PASS	.						140	115	123					6																	41751890		2203	4300	6503	SO:0001583	missense	29964	exon4			AGCTTGGGTTCCC	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.34G>A	chr6.hg19:g.41751890G>A	ENSP00000377803:p.Gly12Ser	154.0	0.0	.		169.0	58.0	.	NM_013397	A2A3M0|A6PVU1|B3KQ15|Q5T3D4|Q9NSV1	Missense_Mutation	SNP	ENST00000394260.1	hg19		.	.	.	.	.	.	.	.	.	.	G	15.41	2.826744	0.50739	.	.	ENSG00000124593	ENST00000458694;ENST00000359201;ENST00000394263;ENST00000394259;ENST00000394260	T;T;T;T;T	0.68624	-0.14;-0.33;-0.14;-0.34;-0.12	4.61	2.79	0.32731	.	0.160117	0.29892	N	0.010940	T	0.41442	0.1159	L	0.57536	1.79	0.09310	N	1	P	0.47910	0.902	P	0.46543	0.52	T	0.28650	-1.0037	10	0.15952	T	0.53	-8.6317	5.2819	0.15680	0.1041:0.0:0.6944:0.2015	.	52	Q2TBC4-3	.	S	52;52;52;12;12	ENSP00000404911:G52S;ENSP00000352128:G52S;ENSP00000377806:G52S;ENSP00000377802:G12S;ENSP00000377803:G12S	ENSP00000335185:G52S	G	+	1	0	PRICKLE4	41859868	0.041000	0.20044	0.003000	0.11579	0.193000	0.23685	1.999000	0.40806	0.540000	0.28808	0.491000	0.48974	GGT	.	.	.	none		0.542	PRICKLE4-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000303948.1	NM_013397		A	41751890	G	A	41751890	3	1	229	1	0	0	0	0	1	0	0	0	12499	1232	43	2	160	2	PRICKLE4	6	41751890	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	11292485	41751890	129363177	41	13869											
CASP8AP2	9994	hgsc.bcm.edu	37	chr6	90578032	90578032	+	RNA	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	tggaagaaatctcacactctGttggggaacatcttccaaac	13	10	8	10	0	3	1	1	0	3	1	5	3	4	3	1	3	2	1	1	3	4	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr6:90578032G>C	ENST00000551025.1	+	0	6460									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)		CTCACACTCTGTTGGGGAACA	0.378																																					p.V1675L	Colon(187;1656 2025 17045 31481 39901)	Atlas-SNP	.											.	CASP8AP2	108	.	0			c.G5023C						PASS	.						49	50	49					6																	90578032		1888	4122	6010			9994	exon8			CACTCTGTTGGGG	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"FLICE-associated huge protein"	606880	"CASP8 associated protein 2"			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		chr6.hg19:g.90578032G>C		75.0	0.0	.		62.0	29.0	.	NM_001137667		Missense_Mutation	SNP	ENST00000551025.1	hg19																																																																																				.	.	.	none		0.378	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667		C	90578032	G	C	90578032	1	2	229	0	1	0	0	0	0	0	0	0	2680	1377	48	4		4	CASP8AP2	6	90578032	RNA	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	48826142	90578032	80537035	42	13870											
RFX6	222546	hgsc.bcm.edu	37	chr6	117203548	117203548	+	Frame_Shift_Del	DEL	C	C	-																															agacaattcgccagaagtttCccctcctaacaacaaggcgg																										TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr6:117203548delC	ENST00000332958.2	+	4	539	c.523delC	c.(523-525)cccfs	p.P175fs		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	175					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						CCAGAAGTTTCCCCTCCTAAC	0.413																																					p.F174fs		Atlas-Indel,Pindel	.											.	RFX6	141	.	0			c.522delT						PASS	.						105	92	96					6																	117203548		2203	4300	6503	SO:0001589	frameshift_variant	222546	exon4			.	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.523delC	chr6.hg19:g.117203548delC	ENSP00000332208:p.Pro175fs	54.0	0.0	0		77.0	35.0	0.454545	NM_173560	Q5T6B3	Frame_Shift_Del	DEL	ENST00000332958.2	hg19	CCDS5113.1																																																																																			.	.	.	none		0.413	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560		-	117203548	C	-	117203548	7	5	229	1	0	1	0	1	0	0	0	0	13280	855	30	0	537	0	RFX6	6	117203548	Frame_Shift_Del	DEL	C	TCGA-P4-A5E6-01A-11D-A28G-10	26625516	117203548	53911519	43	13871											
NFE2L3	9603	hgsc.bcm.edu	37	chr7	26224503	26224503	+	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	tttgatgagataaacttaatGtcattggccacagaagacaa	16	11	8	6	0	1	4	1	2	0	3	1	5	1	4	1	1	1	0	1	1	5	4			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr7:26224503G>T	ENST00000056233.3	+	4	1444	c.1185G>T	c.(1183-1185)atG>atT	p.M395I		NM_004289.6	NP_004280.5	Q9Y4A8	NF2L3_HUMAN	nuclear factor, erythroid 2-like 3	395					transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(5)|urinary_tract(7)	29						TAAACTTAATGTCATTGGCCA	0.363																																					p.M395I		Atlas-SNP	.											NFE2L3,colon,carcinoma,0,1	NFE2L3	77	.	0			c.G1185T						PASS	.						89	93	92					7																	26224503		2203	4300	6503	SO:0001583	missense	9603	exon4			CTTAATGTCATTG	AB010812	CCDS5396.1	7p15.2	2013-08-23	2013-08-23		ENSG00000050344	ENSG00000050344		"basic leucine zipper proteins"	7783	protein-coding gene	gene with protein product		604135	"nuclear factor (erythroid-derived 2)-like 3"			10037736	Standard	NM_004289		Approved	Nrf3	uc003sxq.3	Q9Y4A8	OTTHUMG00000023882	ENST00000056233.3:c.1185G>T	chr7.hg19:g.26224503G>T	ENSP00000056233:p.Met395Ile	93.0	0.0	.		80.0	29.0	.	NM_004289	Q6NUS0|Q7Z498|Q86UJ4|Q86VR5|Q9UQA4	Missense_Mutation	SNP	ENST00000056233.3	hg19	CCDS5396.1	.	.	.	.	.	.	.	.	.	.	G	11.69	1.714423	0.30413	.	.	ENSG00000050344	ENST00000056233;ENST00000398175	T	0.32988	1.43	5.12	1.16	0.20824	.	0.373144	0.32328	N	0.006247	T	0.33030	0.0849	M	0.78049	2.395	0.28293	N	0.923461	B	0.14805	0.011	B	0.13407	0.009	T	0.34950	-0.9808	10	0.54805	T	0.06	-0.9264	10.7382	0.46137	0.3412:0.0:0.6588:0.0	.	395	Q9Y4A8	NF2L3_HUMAN	I	395;101	ENSP00000056233:M395I	ENSP00000056233:M395I	M	+	3	0	NFE2L3	26191028	0.998000	0.40836	0.717000	0.30585	0.799000	0.45148	2.503000	0.45407	0.259000	0.21709	-0.229000	0.12294	ATG	.	.	.	none		0.363	NFE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214088.1			T	26224503	G	T	26224503	3	4	229	1	0	0	0	0	1	0	0	0	10376	1377	48	4	1199	4	NFE2L3	7	26224503	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10		26224503	132914160	44	13872											
POU6F2	11281	hgsc.bcm.edu	37	chr7	39500162	39500162	+	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	acagatcctcaaacggcagcGggtgaggtggatggggttaa	11	7	16	7	2	1	2	1	1	0	1	2	3	2	3	1	6	2	2	1	6	2	1	rs548578851		TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr7:39500162G>T	ENST00000403058.1	+	10	1573	c.1419G>T	c.(1417-1419)gcG>gcT	p.A473A	POU6F2_ENST00000518318.2_Silent_p.A473A|POU6F2_ENST00000559001.1_Silent_p.A418A	NM_001166018.1|NM_007252.3	NP_001159490.1|NP_009183.3	P78424	PO6F2_HUMAN	POU class 6 homeobox 2	473					central nervous system development (GO:0007417)|ganglion mother cell fate determination (GO:0007402)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42						AAACGGCAGCGGGTGAGGTGG	0.473																																					p.A473A		Atlas-SNP	.											.	POU6F2	117	.	0			c.G1419T						PASS	.						55	49	51					7																	39500162		2203	4300	6503	SO:0001819	synonymous_variant	11281	exon10			GGCAGCGGGTGAG	U91934	CCDS34620.2, CCDS55103.1	7p14.1	2011-06-20	2007-07-13		ENSG00000106536	ENSG00000106536		"Homeoboxes / POU class"	21694	protein-coding gene	gene with protein product	"Retina-derived POU-domain factor-1"	609062	"POU domain, class 6, transcription factor 2"			8601806	Standard	NM_007252		Approved	RPF-1	uc003thb.2	P78424	OTTHUMG00000150803	ENST00000403058.1:c.1419G>T	chr7.hg19:g.39500162G>T		122.0	0.0	.		100.0	4.0	.	NM_007252	A4D1W2|C4AMB9|P78425|Q75ME8|Q86UM6|Q9UDS7	Silent	SNP	ENST00000403058.1	hg19	CCDS34620.2																																																																																			.	.	.	none		0.473	POU6F2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320146.3	NM_007252		T	39500162	G	T	39500162	2	4	229	1	0	0	0	0	0	0	0	1	12292	1103	39	4		4	POU6F2	7	39500162	Silent	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	13275659	39500162	119638501	45	13873											
COL14A1	7373	hgsc.bcm.edu	37	chr8	121357692	121357692	+	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	ccggactgtccaagggcctcCtggggagcctgggaggccag	6	5	17	13	1	0	0	0	0	0	0	2	3	2	3	6	6	1	0	6	6	1	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr8:121357692C>T	ENST00000297848.3	+	45	5237	c.4967C>T	c.(4966-4968)cCt>cTt	p.P1656L	COL14A1_ENST00000309791.4_Missense_Mutation_p.P1656L|COL14A1_ENST00000247781.3_Missense_Mutation_p.P1561L	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)			CAAGGGCCTCCTGGGGAGCCT	0.622																																					p.P1656L		Atlas-SNP	.											.	COL14A1	292	.	0			c.C4967T						PASS	.						59	58	58					8																	121357692		2203	4300	6503	SO:0001583	missense	7373	exon45			GGCCTCCTGGGGA		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.4967C>T	chr8.hg19:g.121357692C>T	ENSP00000297848:p.Pro1656Leu	103.0	0.0	.		97.0	40.0	.	NM_021110		Missense_Mutation	SNP	ENST00000297848.3	hg19	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.621078	0.87460	.	.	ENSG00000187955	ENST00000309791;ENST00000297848;ENST00000247781;ENST00000440844	D;D;D;D	0.98684	-3.87;-3.87;-3.87;-5.07	5.54	4.67	0.58626	.	0.048120	0.85682	D	0.000000	D	0.99032	0.9669	M	0.86502	2.82	0.80722	D	1	D	0.56746	0.977	D	0.69307	0.963	D	0.99226	1.0880	10	0.49607	T	0.09	.	12.3879	0.55343	0.0:0.9213:0.0:0.0787	.	1656	Q05707	COEA1_HUMAN	L	1656;1656;1561;3	ENSP00000311809:P1656L;ENSP00000297848:P1656L;ENSP00000247781:P1561L;ENSP00000403640:P3L	ENSP00000247781:P1561L	P	+	2	0	COL14A1	121426873	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	6.600000	0.74132	1.364000	0.46038	0.555000	0.69702	CCT	.	.	.	none		0.622	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		T	121357692	C	T	121357692	3	4	229	1	0	0	0	0	1	0	0	0	3673	681	24	2	5141	2	COL14A1	8	121357692	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10		121357692	25006330	46	13874											
EIF2C2	27161	hgsc.bcm.edu	37	chr8	141557696	141557696	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcactgcgtggccatccccAgcaccgtgtctcccacgcgc	5	6	10	20	5	1	0	0	0	1	0	3	0	2	0	5	1	2	2	5	1	0	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr8:141557696A>G	ENST00000220592.5	-	13	1731	c.1619T>C	c.(1618-1620)cTg>cCg	p.L540P	AGO2_ENST00000519980.1_Missense_Mutation_p.L540P	NM_012154.3	NP_036286.2	Q9UKV8	AGO2_HUMAN	argonaute RISC catalytic component 2	540	Interaction with guide RNA.|Piwi. {ECO:0000255|HAMAP-Rule:MF_03031}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|regulation of transcription, DNA-templated (GO:0006355)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|mRNA cap binding complex (GO:0005845)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|RISC complex (GO:0016442)	endoribonuclease activity (GO:0004521)|endoribonuclease activity, cleaving siRNA-paired mRNA (GO:0070551)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA 7-methylguanosine cap binding (GO:0000340)|siRNA binding (GO:0035197)|translation initiation factor activity (GO:0003743)										GGCCATCCCCAGCACCGTGTC	0.637																																					p.L540P		Atlas-SNP	.											.	.	.	.	0			c.T1619C						PASS	.						182	140	154					8																	141557696		2203	4300	6503	SO:0001583	missense	27161	exon13			ATCCCCAGCACCG	AF121255	CCDS6380.1, CCDS55279.1	8q24.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000123908	ENSG00000123908		"Argonaute/PIWI family"	3263	protein-coding gene	gene with protein product	"argonaute 2"	606229	"eukaryotic translation initiation factor 2C, 2"	EIF2C2		10534406, 12906857	Standard	NM_012154		Approved	hAGO2, Q10	uc003yvn.3	Q9UKV8	OTTHUMG00000164232	ENST00000220592.5:c.1619T>C	chr8.hg19:g.141557696A>G	ENSP00000220592:p.Leu540Pro	111.0	0.0	.		110.0	38.0	.	NM_012154	Q8TCZ5|Q8WV58|Q96ID1	Missense_Mutation	SNP	ENST00000220592.5	hg19	CCDS6380.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.212273	0.79240	.	.	ENSG00000123908	ENST00000220592;ENST00000519980	T;T	0.35236	1.32;1.32	5.49	5.49	0.81192	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.69958	0.3169	M	0.94021	3.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.995;0.997	T	0.79259	-0.1877	10	0.87932	D	0	-13.6154	15.5836	0.76465	1.0:0.0:0.0:0.0	.	540;540	Q9UKV8-2;Q9UKV8	.;AGO2_HUMAN	P	540	ENSP00000220592:L540P;ENSP00000430176:L540P	ENSP00000220592:L540P	L	-	2	0	EIF2C2	141626878	1.000000	0.71417	0.973000	0.42090	0.690000	0.40134	9.193000	0.94954	2.076000	0.62316	0.533000	0.62120	CTG	.	.	.	none		0.637	AGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377866.4			G	141557696	A	G	141557696	3	3	229	1	0	0	0	0	1	0	0	0	5008	188	7	3	988	3	EIF2C2	8	141557696	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	20200004	141557696	4806326	47	13875											
TRPM6	140803	hgsc.bcm.edu	37	chr9	77435298	77435298	+	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	agactaaagttgaaagtgttCtgaatcatgcagatgatctc	14	12	9	6	0	3	5	1	3	2	2	4	5	3	5	0	0	1	3	0	0	4	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr9:77435298C>G	ENST00000360774.1	-	9	1293	c.1056G>C	c.(1054-1056)caG>caC	p.Q352H	TRPM6_ENST00000361255.3_Missense_Mutation_p.Q347H|TRPM6_ENST00000449912.2_Missense_Mutation_p.Q347H|TRPM6_ENST00000451710.3_Missense_Mutation_p.Q352H|TRPM6_ENST00000376871.3_Missense_Mutation_p.Q352H|TRPM6_ENST00000376864.4_Missense_Mutation_p.Q352H|TRPM6_ENST00000376872.3_Missense_Mutation_p.Q352H|TRPM6_ENST00000483186.1_5'UTR	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	352					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						TGAAAGTGTTCTGAATCATGC	0.438																																					p.Q352H		Atlas-SNP	.											.	TRPM6	377	.	0			c.G1056C						PASS	.						148	135	140					9																	77435298		2203	4300	6503	SO:0001583	missense	140803	exon9			AGTGTTCTGAATC	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.1056G>C	chr9.hg19:g.77435298C>G	ENSP00000354006:p.Gln352His	83.0	0.0	.		87.0	8.0	.	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	hg19	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	C	18.08	3.544685	0.65198	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000376872;ENST00000376871;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449;ENST00000448641	T;T;T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21	5.37	4.36	0.52297	.	0.122952	0.64402	D	0.000020	T	0.79476	0.4452	M	0.78456	2.415	0.43617	D	0.995992	D;D;P;P	0.71674	0.998;0.998;0.951;0.896	D;D;P;P	0.67382	0.951;0.951;0.765;0.694	T	0.81861	-0.0738	10	0.87932	D	0	.	11.9834	0.53133	0.0:0.8466:0.0:0.1534	.	352;352;352;347	Q9BX84-6;Q9BX84-5;Q9BX84;Q9BX84-3	.;.;TRPM6_HUMAN;.	H	352;352;352;352;347;347;352;15;15	ENSP00000354006:Q352H;ENSP00000407341:Q352H;ENSP00000366068:Q352H;ENSP00000366067:Q352H;ENSP00000396672:Q347H;ENSP00000354962:Q347H;ENSP00000366060:Q352H	ENSP00000309693:Q15H	Q	-	3	2	TRPM6	76625118	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	0.737000	0.26144	2.500000	0.84329	0.655000	0.94253	CAG	.	.	.	none		0.438	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		G	77435298	C	G	77435298	3	3	229	1	0	0	0	0	1	0	0	0	16602	912	32	4	5136	4	TRPM6	9	77435298	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10		77435298	63778133	48	13876											
TEX10	54881	hgsc.bcm.edu	37	chr9	103109141	103109141	+	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	cttcactttctctcaacctaCtggatccatctgccaaggcc	8	12	5	16	0	4	0	2	0	2	0	6	1	5	1	4	2	3	0	4	2	3	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr9:103109141C>G	ENST00000374902.4	-	3	904	c.728G>C	c.(727-729)aGt>aCt	p.S243T	TEX10_ENST00000537512.1_Missense_Mutation_p.S178T|TEX10_ENST00000535814.1_Missense_Mutation_p.S246T	NM_017746.3	NP_060216.2	Q9NXF1	TEX10_HUMAN	testis expressed 10	243						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)		TCTCAACCTACTGGATCCATC	0.448																																					p.S246T		Atlas-SNP	.											.	TEX10	99	.	0			c.G737C						PASS	.						122	118	119					9																	103109141		2203	4300	6503	SO:0001583	missense	54881	exon3			AACCTACTGGATC	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.728G>C	chr9.hg19:g.103109141C>G	ENSP00000364037:p.Ser243Thr	83.0	0.0	.		84.0	28.0	.	NM_001161584	B4DYV2|Q5T722|Q5T723|Q8NCN8|Q8TDY0	Missense_Mutation	SNP	ENST00000374902.4	hg19	CCDS6748.1	.	.	.	.	.	.	.	.	.	.	C	9.748	1.166577	0.21621	.	.	ENSG00000136891	ENST00000535814;ENST00000374902;ENST00000444730;ENST00000537512	.	.	.	5.26	4.31	0.51392	Armadillo-type fold (1);	0.430875	0.29932	N	0.010833	T	0.29288	0.0729	N	0.12182	0.205	0.38372	D	0.944907	B;B;B;B;B	0.29766	0.002;0.007;0.11;0.256;0.002	B;B;B;B;B	0.21360	0.003;0.004;0.011;0.034;0.003	T	0.20638	-1.0269	9	0.29301	T	0.29	-9.3945	9.3406	0.38079	0.0:0.7187:0.1367:0.1446	.	178;246;111;111;243	B7Z9D5;B4DYV2;E7ERG2;B4DQR0;Q9NXF1	.;.;.;.;TEX10_HUMAN	T	246;243;111;178	.	ENSP00000364037:S243T	S	-	2	0	TEX10	102148962	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.669000	0.37492	2.450000	0.82876	0.655000	0.94253	AGT	.	.	.	none		0.448	TEX10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053416.1	NM_017746		G	103109141	C	G	103109141	3	3	229	1	0	0	0	0	1	0	0	0	15784	565	20	4	2113	4	TEX10	9	103109141	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	25673843	103109141	38104290	49	13877											
EGFL7	51162	hgsc.bcm.edu	37	chr9	139564703	139564703	+	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	agttactggtgccagtgttgGgaggggcacagcctgtctgc	6	10	16	9	0	1	0	0	0	1	0	1	1	1	1	2	4	4	3	2	4	1	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr9:139564703G>C	ENST00000371699.1	+	7	1403	c.492G>C	c.(490-492)tgG>tgC	p.W164C	EGFL7_ENST00000406555.3_Missense_Mutation_p.W164C|MIR126_ENST00000362291.1_RNA|EGFL7_ENST00000492002.1_3'UTR|EGFL7_ENST00000371698.3_Missense_Mutation_p.W164C|EGFL7_ENST00000308874.7_Missense_Mutation_p.W164C			Q9UHF1	EGFL7_HUMAN	EGF-like-domain, multiple 7	164	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				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)		GCCAGTGTTGGGAGGGGCACA	0.652																																					p.W164C		Atlas-SNP	.											.	EGFL7	11	.	0			c.G492C						PASS	.						28	30	29					9																	139564703		2198	4297	6495	SO:0001583	missense	51162	exon8			GTGTTGGGAGGGG	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.492G>C	chr9.hg19:g.139564703G>C	ENSP00000360764:p.Trp164Cys	129.0	0.0	.		157.0	47.0	.	NM_016215	B3KRP0|M9VTX9|Q5M7Y5|Q5VUD5|Q96EG0	Missense_Mutation	SNP	ENST00000371699.1	hg19	CCDS7002.1	.	.	.	.	.	.	.	.	.	.	G	15.33	2.802260	0.50315	.	.	ENSG00000172889	ENST00000371699;ENST00000308874;ENST00000406555;ENST00000371698	T;T;T;T	0.36157	1.27;1.27;1.27;1.27	5.26	2.31	0.28768	EGF-like calcium-binding (2);	1.149640	0.06146	N	0.673294	T	0.37785	0.1016	L	0.32530	0.975	0.45822	D	0.998694	D	0.56968	0.978	P	0.50754	0.649	T	0.04454	-1.0950	10	0.46703	T	0.11	-0.7885	7.8608	0.29509	0.1492:0.1325:0.7182:0.0	.	164	Q9UHF1	EGFL7_HUMAN	C	164	ENSP00000360764:W164C;ENSP00000307843:W164C;ENSP00000385639:W164C;ENSP00000360763:W164C	ENSP00000307843:W164C	W	+	3	0	EGFL7	138684524	0.247000	0.23920	0.257000	0.24404	0.612000	0.37316	0.439000	0.21575	0.188000	0.20168	0.561000	0.74099	TGG	.	.	.	none		0.652	EGFL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055094.1	NM_016215		C	139564703	G	C	139564703	3	2	229	1	0	0	0	0	1	0	0	0	4966	1241	43	4	510	4	EGFL7	9	139564703	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	36455562	139564703	1648728	50	13878											
TRAF2	7186	hgsc.bcm.edu	37	chr9	139794876	139794876	+	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	ggatattcctctccccaggcCttcccagataatgctgcccg	7	10	8	16	1	1	1	0	0	1	1	4	2	3	2	6	2	2	1	6	2	2	4			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr9:139794876C>G	ENST00000247668.2	+	4	322	c.270C>G	c.(268-270)gcC>gcG	p.A90A	TRAF2_ENST00000359662.3_Silent_p.A90A|TRAF2_ENST00000536468.1_Silent_p.A90A	NM_021138.3	NP_066961.2	Q12933	TRAF2_HUMAN	TNF receptor-associated factor 2	90					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)		CTCCCCAGGCCTTCCCAGATA	0.577																																					p.A90A		Atlas-SNP	.											.	TRAF2	46	.	0			c.C270G						PASS	.						43	38	39					9																	139794876		2203	4300	6503	SO:0001819	synonymous_variant	7186	exon4			CCAGGCCTTCCCA	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.270C>G	chr9.hg19:g.139794876C>G		51.0	0.0	.		50.0	14.0	.	NM_021138	A8K107|B4DPJ7|Q7Z337|Q96NT2	Silent	SNP	ENST00000247668.2	hg19	CCDS7013.1																																																																																			.	.	.	none		0.577	TRAF2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055166.1	NM_021138		G	139794876	C	G	139794876	2	3	229	1	0	0	0	0	0	0	0	1	16450	668	24	4		4	TRAF2	9	139794876	Silent	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	230173	139794876	1418555	51	13879											
VIM	7431	hgsc.bcm.edu	37	chr10	17278345	17278345	+	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	acccactcaaaaaggacactTctgattaagacggttgaaac	16	8	7	10	1	2	3	1	2	1	1	2	4	2	4	1	2	1	1	1	2	4	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr10:17278345T>G	ENST00000224237.5	+	8	1471	c.1326T>G	c.(1324-1326)ctT>ctG	p.L442L	RP11-124N14.3_ENST00000456355.1_RNA|VIM_ENST00000544301.1_Silent_p.L442L			P08670	VIME_HUMAN	vimentin	442	Tail.			L -> F (in Ref. 1; AAA61279). {ECO:0000305}.	apoptotic process (GO:0006915)|astrocyte development (GO:0014002)|Bergmann glial cell differentiation (GO:0060020)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular component movement (GO:0006928)|intermediate filament organization (GO:0045109)|lens fiber cell development (GO:0070307)|muscle filament sliding (GO:0030049)|negative regulation of neuron projection development (GO:0010977)|positive regulation of gene expression (GO:0010628)|viral process (GO:0016032)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|neuron projection (GO:0043005)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	double-stranded RNA binding (GO:0003725)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(18)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						AAAGGACACTTCTGATTAAGA	0.348																																					p.L442L		Atlas-SNP	.											.	VIM	71	.	0			c.T1326G						PASS	.						150	165	160					10																	17278345		2203	4300	6503	SO:0001819	synonymous_variant	7431	exon9			GACACTTCTGATT	M14144	CCDS7120.1	10p13	2013-01-16			ENSG00000026025	ENSG00000026025		"Intermediate filaments type III"	12692	protein-coding gene	gene with protein product		193060					Standard	NM_003380		Approved		uc001iou.2	P08670	OTTHUMG00000017744	ENST00000224237.5:c.1326T>G	chr10.hg19:g.17278345T>G		75.0	0.0	.		91.0	39.0	.	NM_003380	B0YJC2|D3DRU4|Q15867|Q15868|Q15869|Q548L2|Q6LER9|Q8N850|Q96ML2|Q9NTM3	Silent	SNP	ENST00000224237.5	hg19	CCDS7120.1																																																																																			.	.	.	none		0.348	VIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047015.1	NM_003380		G	17278345	T	G	17278345	2	3	229	1	0	0	0	0	0	0	0	1	17178	1770	62	5		5	VIM	10	17278345	Silent	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10		17278345	118256402	52	13880											
ARHGAP21	57584	hgsc.bcm.edu	37	chr10	24873742	24873742	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagttcagattctctctcccCgctctgctcatgcactttcc	6	14	5	16	1	5	1	2	0	3	1	8	1	6	1	3	0	2	4	3	0	1	3	rs370251256		TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr10:24873742C>T	ENST00000396432.2	-	26	5962	c.5476G>A	c.(5476-5478)Ggg>Agg	p.G1826R		NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	1825	Interaction with CTNNA1.				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						TCTCTCTCCCCGCTCTGCTCA	0.498																																					p.G1826R		Atlas-SNP	.											ARHGAP21,right_upper_lobe,carcinoma,0,1	ARHGAP21	185	.	0			c.G5476A						PASS	.	C	ARG/GLY	0,4406		0,0,2203	62	63	63		5476	3.3	0	10		63	1,8599	1.2+/-3.3	0,1,4299	no	missense	ARHGAP21	NM_020824.3	125	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	1826/1959	24873742	1,13005	2203	4300	6503	SO:0001583	missense	57584	exon26			TCTCCCCGCTCTG	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.5476G>A	chr10.hg19:g.24873742C>T	ENSP00000379709:p.Gly1826Arg	93.0	0.0	.		101.0	53.0	.	NM_020824	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000396432.2	hg19	CCDS7144.2	.	.	.	.	.	.	.	.	.	.	C	1.589	-0.529652	0.04112	0.0	1.16E-4	ENSG00000107863	ENST00000396432;ENST00000447364	T	0.11712	2.75	5.13	3.27	0.37495	.	1.152260	0.06177	N	0.678642	T	0.06416	0.0165	N	0.16307	0.4	0.18873	N	0.999984	B	0.09022	0.002	B	0.04013	0.001	T	0.42207	-0.9465	10	0.18710	T	0.47	.	2.6596	0.05023	0.2147:0.4829:0.0:0.3023	.	1825	Q5T5U3	RHG21_HUMAN	R	1826;1275	ENSP00000379709:G1826R	ENSP00000379709:G1826R	G	-	1	0	ARHGAP21	24913748	0.000000	0.05858	0.002000	0.10522	0.007000	0.05969	0.682000	0.25335	1.139000	0.42245	0.655000	0.94253	GGG	.	.	.	none		0.498	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824		T	24873742	C	T	24873742	3	4	229	1	0	0	0	0	1	0	0	0	871	652	23	1	404	1	ARHGAP21	10	24873742	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	7595397	24873742	110661005	53	13881											
RBP3	5949	hgsc.bcm.edu	37	chr10	48388918	48388918	+	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	ggtctgccccacgacctctgGccgagcatagtgggcctcca	6	7	12	16	2	2	0	0	0	2	0	3	2	3	0	6	3	2	1	6	3	1	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr10:48388918G>C	ENST00000224600.4	-	1	2073	c.1960C>G	c.(1960-1962)Cca>Gca	p.P654A	AL731561.2_ENST00000581861.1_RNA	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	654	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)	ACGACCTCTGGCCGAGCATAG	0.672																																					p.P654A		Atlas-SNP	.											.	RBP3	152	.	0			c.C1960G						PASS	.						16	18	17					10																	48388918		2197	4286	6483	SO:0001583	missense	5949	exon1			CCTCTGGCCGAGC	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.1960C>G	chr10.hg19:g.48388918G>C	ENSP00000224600:p.Pro654Ala	58.0	0.0	.		102.0	43.0	.	NM_002900	Q0QD34|Q5VSR0|Q8IXN0	Missense_Mutation	SNP	ENST00000224600.4	hg19	CCDS7218.1	.	.	.	.	.	.	.	.	.	.	G	7.421	0.636769	0.14386	.	.	ENSG00000107618	ENST00000224600	T	0.39997	1.05	5.53	5.53	0.82687	.	0.128692	0.53938	D	0.000058	T	0.47322	0.1439	M	0.76170	2.325	0.38359	D	0.944551	P	0.34562	0.457	B	0.31390	0.129	T	0.57894	-0.7732	10	0.87932	D	0	-14.2089	18.4586	0.90729	0.0:0.0:1.0:0.0	.	654	P10745	RET3_HUMAN	A	654	ENSP00000224600:P654A	ENSP00000224600:P654A	P	-	1	0	RBP3	48008924	1.000000	0.71417	0.047000	0.18901	0.002000	0.02628	5.637000	0.67854	2.628000	0.89032	0.561000	0.74099	CCA	.	.	.	none		0.672	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900		C	48388918	G	C	48388918	3	2	229	1	0	0	0	0	1	0	0	0	13170	1203	42	4	1799	4	RBP3	10	48388918	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	23515176	48388918	87145829	54	13882											
ERCC6	2074	hgsc.bcm.edu	37	chr10	50681040	50681040	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgacacctaagccgcccaccCgcgtggtcagaagaaacaca	13	4	9	15	3	1	3	1	1	0	2	1	3	1	3	4	1	2	0	4	1	3	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr10:50681040C>T	ENST00000355832.5	-	15	2822	c.2744G>A	c.(2743-2745)cGg>cAg	p.R915Q	ERCC6_ENST00000465653.1_5'Flank|RP11-123B3.2_ENST00000423283.1_RNA|ERCC6_ENST00000542458.1_Missense_Mutation_p.R285Q	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	915	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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						GCCGCCCACCCGCGTGGTCAG	0.498								Direct reversal of damage;Nucleotide excision repair (NER)																													p.T915N		Atlas-SNP	.											.	ERCC6	162	.	0			c.C2744A						PASS	.						66	61	63					10																	50681040		2203	4300	6503	SO:0001583	missense	2074	exon15			CCCACCCGCGTGG	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.2744G>A	chr10.hg19:g.50681040C>T	ENSP00000348089:p.Arg915Gln	224.0	0.0	.		231.0	92.0	.	NM_000124	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	hg19	CCDS7229.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.199652	0.79015	.	.	ENSG00000225830	ENST00000355832;ENST00000374129;ENST00000542458	T;T	0.74842	-0.88;-0.88	5.88	5.88	0.94601	Helicase, C-terminal (3);	.	.	.	.	D	0.88093	0.6344	M	0.83603	2.65	0.48341	D	0.999631	D;D	0.89917	1.0;0.999	D;D	0.76575	0.987;0.988	D	0.88520	0.3095	9	0.72032	D	0.01	-20.7418	20.2422	0.98381	0.0:1.0:0.0:0.0	.	915;292	Q03468;Q59FF6	ERCC6_HUMAN;.	Q	915;292;285	ENSP00000348089:R915Q;ENSP00000445134:R285Q	ENSP00000348089:R915Q	R	-	2	0	ERCC6	50351046	0.998000	0.40836	0.702000	0.30337	0.338000	0.28826	3.873000	0.56093	2.782000	0.95742	0.655000	0.94253	CGG	.	.	.	none		0.498	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124		T	50681040	C	T	50681040	3	4	229	1	0	0	0	0	1	0	0	0	5219	652	23	1	1765	1	ERCC6	10	50681040	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	2292122	50681040	84853707	55	13883											
CSTF2T	23283	hgsc.bcm.edu	37	chr10	53458361	53458361	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accaccaggagtcacgggtcCgcgaggtataggagctctag	10	6	14	11	3	2	0	1	0	1	0	3	3	3	2	3	4	1	2	3	4	3	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr10:53458361C>T	ENST00000331173.4	-	1	994	c.949G>A	c.(949-951)Gga>Aga	p.G317R	PRKG1_ENST00000401604.2_Intron|PRKG1_ENST00000373985.1_Intron|PRKG1_ENST00000373980.4_Intron	NM_015235.2	NP_056050.1	Q9H0L4	CSTFT_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant	317	Gly-rich.				mRNA processing (GO:0006397)	intracellular (GO:0005622)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.G317R(1)		NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30				COAD - Colon adenocarcinoma(2;0.00736)|Colorectal(2;0.00898)|all cancers(4;0.0188)|GBM - Glioblastoma multiforme(4;0.0778)|Epithelial(53;0.122)		GTCACGGGTCCGCGAGGTATA	0.567																																					p.G317R		Atlas-SNP	.											CSTF2T,rectum,carcinoma,0,1	CSTF2T	64	.	1	Substitution - Missense(1)	large_intestine(1)	c.G949A						PASS	.						72	68	70					10																	53458361		2203	4300	6503	SO:0001583	missense	23283	exon1			CGGGTCCGCGAGG	AB014589	CCDS7245.1	10q11	2013-02-12			ENSG00000177613	ENSG00000177613		"RNA binding motif (RRM) containing"	17086	protein-coding gene	gene with protein product		611968				12408968, 11113135	Standard	NM_015235		Approved	DKFZp434C1013, KIAA0689, CstF-64T	uc001jjp.3	Q9H0L4	OTTHUMG00000018246	ENST00000331173.4:c.949G>A	chr10.hg19:g.53458361C>T	ENSP00000332444:p.Gly317Arg	59.0	0.0	.		64.0	14.0	.	NM_015235	B2RAR9|O75174|Q53HK6|Q7LGE8|Q8N6T1	Missense_Mutation	SNP	ENST00000331173.4	hg19	CCDS7245.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.169805	0.78452	.	.	ENSG00000177613	ENST00000331173	T	0.22539	1.95	4.7	4.7	0.59300	.	0.449653	0.22819	N	0.055255	T	0.41994	0.1183	L	0.55481	1.735	0.53688	D	0.999972	D	0.89917	1.0	D	0.97110	1.0	T	0.13737	-1.0498	10	0.52906	T	0.07	-7.9329	15.5353	0.75998	0.0:1.0:0.0:0.0	.	317	Q9H0L4	CSTFT_HUMAN	R	317	ENSP00000332444:G317R	ENSP00000332444:G317R	G	-	1	0	CSTF2T	53128367	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.116000	0.71571	2.613000	0.88420	0.655000	0.94253	GGA	.	.	.	none		0.567	CSTF2T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048097.1	NM_015235		T	53458361	C	T	53458361	3	4	229	1	0	0	0	0	1	0	0	0	3987	661	23	1	905	1	CSTF2T	10	53458361	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	2777321	53458361	82076386	56	13884											
COL13A1	1305	hgsc.bcm.edu	37	chr10	71562297	71562297	+	Missense_Mutation	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	cggagcgcggcgcacggctgCcgagtccagggtcgtgcggg	4	4	20	13	8	0	0	0	0	0	0	2	2	1	1	2	5	3	2	2	5	0	0	rs561022104	byFrequency	TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr10:71562297C>T	ENST00000398978.3	+	1	610	c.118C>T	c.(118-120)Ccg>Tcg	p.P40S	COL13A1_ENST00000398971.3_Missense_Mutation_p.P40S|COL13A1_ENST00000354547.3_Missense_Mutation_p.P40S|COL13A1_ENST00000398969.3_Missense_Mutation_p.P40S|COL13A1_ENST00000520133.1_Missense_Mutation_p.P40S|COL13A1_ENST00000398972.3_Missense_Mutation_p.P40S|COL13A1_ENST00000398974.3_Missense_Mutation_p.P40S|COL13A1_ENST00000398973.3_Missense_Mutation_p.P40S|COL13A1_ENST00000356340.3_Missense_Mutation_p.P40S|COL13A1_ENST00000522165.1_Missense_Mutation_p.P40S|COL13A1_ENST00000357811.3_Missense_Mutation_p.P40S|COL13A1_ENST00000398964.3_Missense_Mutation_p.P40S|COL13A1_ENST00000520267.1_Missense_Mutation_p.P40S|COL13A1_ENST00000398966.3_Missense_Mutation_p.P40S|COL13A1_ENST00000398968.3_Missense_Mutation_p.P40S|COL13A1_ENST00000517713.1_Missense_Mutation_p.P40S	NM_001130103.1	NP_001123575.1			collagen, type XIII, alpha 1											endometrium(5)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	28						CGCACGGCTGCCGAGTCCAGG	0.766													C|||	2	0.000399361	0.0015	0	5008	,	,		8844	0		0	False		,,,				2504	0				p.P40S		Atlas-SNP	.											.	COL13A1	133	.	0			c.C118T						PASS	.						12	14	13					10																	71562297		1839	3975	5814	SO:0001583	missense	1305	exon1			CGGCTGCCGAGTC	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.118C>T	chr10.hg19:g.71562297C>T	ENSP00000381949:p.Pro40Ser	0.0	0.0	.		17.0	4.0	.	NM_080802		Missense_Mutation	SNP	ENST00000398978.3	hg19	CCDS44419.1	.	.	.	.	.	.	.	.	.	.	C	16.09	3.024834	0.54683	.	.	ENSG00000197467	ENST00000398974;ENST00000398971;ENST00000398968;ENST00000398966;ENST00000398964;ENST00000398969;ENST00000356340;ENST00000398972;ENST00000398973;ENST00000398978;ENST00000354547;ENST00000357811;ENST00000520267;ENST00000517713;ENST00000522165;ENST00000520133	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.91686	-2.74;-2.66;-2.7;-2.79;-2.89;-2.7;-2.73;-2.6;-2.72;-2.72;-2.7;-2.71;-2.66;-2.61;-2.66;-2.61	5.24	5.24	0.73138	.	0.000000	0.42294	D	0.000732	D	0.92172	0.7518	N	0.22421	0.69	0.29823	N	0.830659	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.69078	0.993;0.996;0.997;0.993;0.994;0.994;0.994;0.997;0.994;0.994;0.997;0.997;0.997;0.996;0.997;0.997;0.994;0.996	D;D;P;D;P;P;P;D;P;P;P;P;D;D;P;P;P;D	0.78314	0.979;0.991;0.9;0.979;0.796;0.796;0.796;0.986;0.796;0.723;0.9;0.9;0.986;0.991;0.9;0.9;0.796;0.991	D	0.88496	0.3079	10	0.44086	T	0.13	-5.5417	13.2925	0.60278	0.0:0.9204:0.0:0.0796	.	40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40	Q5TAT6;Q5TAT6-5;Q5TAT6-6;E9PEG9;E7ES55;E7ES51;E7ES47;E7ES46;E7ES49;E7EWL8;Q5TAT6-3;Q5TAT6-4;E7EX21;Q5TAT6-7;Q5TAT6-8;Q5TAT6-2;E7ES56;G5E987	CODA1_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	S	40	ENSP00000381946:P40S;ENSP00000381943:P40S;ENSP00000381940:P40S;ENSP00000381938:P40S;ENSP00000381936:P40S;ENSP00000381941:P40S;ENSP00000348695:P40S;ENSP00000381944:P40S;ENSP00000381945:P40S;ENSP00000381949:P40S;ENSP00000346553:P40S;ENSP00000350463:P40S;ENSP00000428057:P40S;ENSP00000430061:P40S;ENSP00000428342:P40S;ENSP00000430173:P40S	ENSP00000346553:P40S	P	+	1	0	COL13A1	71232303	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	3.084000	0.50143	2.462000	0.83206	0.456000	0.33151	CCG	.	.	.	none		0.766	COL13A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048468.1	NM_005203		T	71562297	C	T	71562297	3	4	229	1	0	0	0	0	1	0	0	0	3672	739	26	2	120	2	COL13A1	10	71562297	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	18103936	71562297	63972450	57	13885											
RNLS	55328	hgsc.bcm.edu	37	chr10	90342858	90342858	+	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	tcagccttgtcccacacagcAaggtacaagggaccggacgt	11	6	11	13	2	1	0	1	0	0	0	2	2	2	2	3	3	3	2	3	3	3	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr10:90342858A>C	ENST00000331772.4	-	1	112	c.90T>G	c.(88-90)ctT>ctG	p.L30L	Y_RNA_ENST00000364678.1_RNA|RNLS_ENST00000466945.1_5'UTR|RNLS_ENST00000437752.1_Silent_p.L30L|RNLS_ENST00000371947.3_Silent_p.L30L	NM_001031709.2	NP_001026879.2	Q5VYX0	RNLS_HUMAN	renalase, FAD-dependent amine oxidase	30					cardiac left ventricle morphogenesis (GO:0003214)|dopamine metabolic process (GO:0042417)|epinephrine metabolic process (GO:0042414)|heart contraction (GO:0060047)|norepinephrine metabolic process (GO:0042415)|phosphate ion homeostasis (GO:0055062)|regulation of systemic arterial blood pressure (GO:0003073)|response to epinephrine (GO:0071871)|response to ischemia (GO:0002931)|response to norepinephrine (GO:0071873)|response to salt (GO:1902074)	extracellular space (GO:0005615)	oxidoreductase activity (GO:0016491)			breast(1)|kidney(1)|lung(3)|ovary(1)|prostate(1)	7						CCCACACAGCAAGGTACAAGG	0.632											OREG0020353	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L30L		Atlas-SNP	.											.	RNLS	45	.	0			c.T90G						PASS	.						65	63	64					10																	90342858		2203	4300	6503	SO:0001819	synonymous_variant	55328	exon1			CACAGCAAGGTAC	BC005364	CCDS7388.1, CCDS31239.1	10q23.31	2009-04-22	2009-04-22	2009-04-22	ENSG00000184719	ENSG00000184719			25641	protein-coding gene	gene with protein product		609360	"chromosome 10 open reading frame 59"	C10orf59		15841207, 17565281	Standard	NM_001031709		Approved	FLJ11218, renalase	uc001kfe.3	Q5VYX0	OTTHUMG00000018692	ENST00000331772.4:c.90T>G	chr10.hg19:g.90342858A>C		121.0	0.0	.	1274	164.0	57.0	.	NM_001031709	Q9BS33|Q9NUP8	Silent	SNP	ENST00000331772.4	hg19	CCDS31239.1																																																																																			.	.	.	none		0.632	RNLS-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049250.1	NM_018363		C	90342858	A	C	90342858	2	2	229	1	0	0	0	0	0	0	0	1	13518	117	5	5		5	RNLS	10	90342858	Silent	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	18780561	90342858	45191889	58	13886											
NOC3L	64318	hgsc.bcm.edu	37	chr10	96121495	96121495	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctttcacagcttgccttagTttcctctgttcttttcggta	4	20	6	11	1	4	0	1	0	3	0	6	0	5	0	2	1	2	4	2	1	2	8			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr10:96121495T>C	ENST00000371361.3	-	2	244	c.144A>G	c.(142-144)aaA>aaG	p.K48K	NOC3L_ENST00000463649.1_5'UTR|NOC3L_ENST00000371350.1_Silent_p.K48K	NM_022451.9	NP_071896.8	Q8WTT2	NOC3L_HUMAN	nucleolar complex associated 3 homolog (S. cerevisiae)	48					fat cell differentiation (GO:0045444)	nuclear speck (GO:0016607)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(3)|large_intestine(17)|lung(5)|ovary(1)|skin(2)|stomach(1)	29		Colorectal(252;0.0897)				CTTGCCTTAGTTTCCTCTGTT	0.368																																					p.K48K		Atlas-SNP	.											.	NOC3L	67	.	0			c.A144G						PASS	.						308	272	284					10																	96121495		2203	4300	6503	SO:0001819	synonymous_variant	64318	exon2			CCTTAGTTTCCTC	AL355341	CCDS7433.1	10q23.33	2004-04-20	2005-08-01	2005-08-01	ENSG00000173145	ENSG00000173145			24034	protein-coding gene	gene with protein product		610769	"chromosome 10 open reading frame 117"	C10orf117		15564382	Standard	NM_022451		Approved	AD24, FLJ12820, FAD24	uc001kjq.1	Q8WTT2	OTTHUMG00000018788	ENST00000371361.3:c.144A>G	chr10.hg19:g.96121495T>C		93.0	0.0	.		79.0	27.0	.	NM_022451	Q9H5M6|Q9H9D8	Silent	SNP	ENST00000371361.3	hg19	CCDS7433.1																																																																																			.	.	.	none		0.368	NOC3L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049466.1	NM_022451		C	96121495	T	C	96121495	2	2	229	1	0	0	0	0	0	0	0	1	10521	1722	60	3		3	NOC3L	10	96121495	Silent	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10	5778637	96121495	39413252	59	13887											
PDZD8	118987	hgsc.bcm.edu	37	chr10	119134718	119134718	+	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	cccagcacggccgacgccagGatcatgagcagcagccccat	10	3	11	17	3	1	1	1	1	0	0	1	3	1	2	5	2	4	3	5	2	0	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr10:119134718G>T	ENST00000334464.5	-	1	260	c.21C>A	c.(19-21)atC>atA	p.I7I		NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	7					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)		CCGACGCCAGGATCATGAGCA	0.741																																					p.I7I		Atlas-SNP	.											.	PDZD8	85	.	0			c.C21A						PASS	.																																			SO:0001819	synonymous_variant	118987	exon1			CGCCAGGATCATG	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.21C>A	chr10.hg19:g.119134718G>T		10.0	0.0	.		59.0	38.0	.	NM_173791	Q86WE0|Q86WE5|Q9UFF1	Silent	SNP	ENST00000334464.5	hg19	CCDS7600.1																																																																																			.	.	.	none		0.741	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791		T	119134718	G	T	119134718	2	4	229	1	0	0	0	0	0	0	0	1	11712	1164	41	4		4	PDZD8	10	119134718	Silent	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	23013223	119134718	16400029	60	13888											
ZFP91	80829	hgsc.bcm.edu	37	chr11	58346868	58346868	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggccccctgaggcggtcgcGgcggcgcctgcagggaccac	4	3	17	17	6	0	1	0	1	0	0	1	2	0	2	4	6	1	1	4	6	0	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr11:58346868G>A	ENST00000316059.6	+	1	285	c.114G>A	c.(112-114)gcG>gcA	p.A38A	ZFP91-CNTF_ENST00000389919.4_Silent_p.A38A|LPXN_ENST00000528489.1_5'Flank|LPXN_ENST00000528954.1_5'Flank	NM_001197051.1|NM_053023.4	NP_001183980.1|NP_444251.1	Q96JP5	ZFP91_HUMAN	ZFP91 zinc finger protein	38	Ala-rich.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein K63-linked ubiquitination (GO:0070534)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(4)|kidney(4)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	26		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				AGGCGGTCGCGGCGGCGCCTG	0.771																																					p.A38A		Atlas-SNP	.											.	ZFP91	66	.	0			c.G114A						PASS	.						2	2	2					11																	58346868		1047	2260	3307	SO:0001819	synonymous_variant	80829	exon1			GGTCGCGGCGGCG	AB056107	CCDS31553.1	11q12	2012-11-27	2012-11-27		ENSG00000186660	ENSG00000186660		"Zinc fingers, C2H2-type"	14983	protein-coding gene	gene with protein product			"zinc finger protein homologous to Zfp91 in mouse", "zinc finger protein 91 homolog (mouse)"			12738986, 20682767	Standard	NM_053023		Approved	PZF, ZNF757	uc001nmx.4	Q96JP5	OTTHUMG00000137391	ENST00000316059.6:c.114G>A	chr11.hg19:g.58346868G>A		0.0	0.0	.		15.0	8.0	.	NM_001197051	A6NHC4|A8MSG7|Q86V47|Q96JP4|Q96QA3	Silent	SNP	ENST00000316059.6	hg19	CCDS31553.1																																																																																			.	.	.	none		0.771	ZFP91-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268674.1	NM_053023		A	58346868	G	A	58346868	2	1	229	1	0	0	0	0	0	0	0	1	17667	1103	39	1		1	ZFP91	11	58346868	Silent	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10		58346868	76659648	61	13889											
ATG2A	23130	hgsc.bcm.edu	37	chr11	64681557	64681557	+	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	ggaggggcctgctcaccagtCtcaatggtctgggcaaacat	9	8	13	11	0	3	0	2	0	2	0	4	1	3	1	2	5	2	2	2	5	2	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr11:64681557C>A	ENST00000377264.3	-	3	595	c.483G>T	c.(481-483)gaG>gaT	p.E161D	ATG2A_ENST00000421419.2_Missense_Mutation_p.E161D	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	161					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						GCTCACCAGTCTCAATGGTCT	0.667																																					p.E161D		Atlas-SNP	.											.	ATG2A	133	.	0			c.G483T						PASS	.						27	31	29					11																	64681557		2165	4236	6401	SO:0001583	missense	23130	exon3			ACCAGTCTCAATG		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.483G>T	chr11.hg19:g.64681557C>A	ENSP00000366475:p.Glu161Asp	129.0	0.0	.		154.0	54.0	.	NM_015104	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Missense_Mutation	SNP	ENST00000377264.3	hg19	CCDS31602.1	.	.	.	.	.	.	.	.	.	.	c	16.16	3.045338	0.55110	.	.	ENSG00000110046	ENST00000421419;ENST00000377264;ENST00000227459	T;T	0.56444	0.46;0.46	3.89	1.99	0.26369	.	0.000000	0.64402	D	0.000001	T	0.55449	0.1921	L	0.41236	1.265	0.44366	D	0.997264	D	0.63880	0.993	D	0.70016	0.967	T	0.49542	-0.8929	10	0.33940	T	0.23	.	5.9448	0.19213	0.0:0.666:0.0:0.334	.	161	Q2TAZ0	ATG2A_HUMAN	D	161	ENSP00000410522:E161D;ENSP00000366475:E161D	ENSP00000227459:E161D	E	-	3	2	ATG2A	64438133	1.000000	0.71417	0.998000	0.56505	0.950000	0.60333	0.697000	0.25556	0.439000	0.26476	0.457000	0.33378	GAG	.	.	.	none		0.667	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104		A	64681557	C	A	64681557	3	1	229	1	0	0	0	0	1	0	0	0	1093	912	32	4	5489	4	ATG2A	11	64681557	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	6334689	64681557	70324959	62	13890											
C11orf80	79703	hgsc.bcm.edu	37	chr11	66610492	66610492	+	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	agggagcaccgcgaggctcaCggcagggccctggcgccggg	6	2	19	14	5	1	0	1	0	0	0	1	2	1	1	3	6	1	3	3	6	0	0	rs369989753	byFrequency	TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr11:66610492C>T	ENST00000360962.4	+	16	1927	c.1920C>T	c.(1918-1920)caC>caT	p.H640H	C11orf80_ENST00000532565.2_Silent_p.H422H|RCE1_ENST00000525356.1_5'Flank|RCE1_ENST00000524506.1_5'Flank|RCE1_ENST00000309657.3_5'Flank|C11orf80_ENST00000346672.4_Silent_p.H449H|C11orf80_ENST00000525449.2_Silent_p.H448H|C11orf80_ENST00000540737.1_Silent_p.H474H|C11orf80_ENST00000527634.1_Silent_p.H423H	NM_024650.3	NP_078926.3	Q8N6T0	CK080_HUMAN	chromosome 11 open reading frame 80	640										autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	14						GCGAGGCTCACGGCAGGGCCC	0.766													C|||	13	0.00259585	0.0098	0	5008	,	,		10475	0		0	False		,,,				2504	0				p.H640H		Atlas-SNP	.											C11orf80,right_upper_lobe,carcinoma,0,1	C11orf80	31	.	0			c.C1920T						PASS	.	C		13,2905		0,13,1446	3	4	3		1920	1.1	0	11		3	0,6770		0,0,3385	no	coding-synonymous	C11orf80	NM_024650.3		0,13,4831	TT,TC,CC		0.0,0.4455,0.1342		640/678	66610492	13,9675	1459	3385	4844	SO:0001819	synonymous_variant	79703	exon16			GGCTCACGGCAGG			11q13.2	2012-05-30			ENSG00000173715	ENSG00000173715			26197	protein-coding gene	gene with protein product						18160775	Standard	NM_024650		Approved	FLJ22531	uc021qmd.1	Q8N6T0	OTTHUMG00000167164	ENST00000360962.4:c.1920C>T	chr11.hg19:g.66610492C>T		1.0	1.0	.		9.0	6.0	.	NM_024650	Q9H677	Silent	SNP	ENST00000360962.4	hg19	CCDS53664.1																																																																																			.	.	.	weak		0.766	C11orf80-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_024650		T	66610492	C	T	66610492	2	4	229	1	0	0	0	0	0	0	0	1	1666	535	19	1		1	C11orf80	11	66610492	Silent	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	1928935	66610492	68396024	63	13891											
FOLR2	2350	hgsc.bcm.edu	37	chr11	71931920	71931920	+	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	tcttccccacccagtgcagtCcctggaagaagaatgcctgc	9	8	9	15	0	1	2	0	0	1	2	3	3	3	3	5	1	3	1	5	1	3	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr11:71931920C>A	ENST00000298223.6	+	3	344	c.157C>A	c.(157-159)Ccc>Acc	p.P53T	FOLR2_ENST00000454954.2_Missense_Mutation_p.P12T|FOLR2_ENST00000449475.2_Missense_Mutation_p.P70T	NM_000803.4|NM_001113534.1|NM_001113535.1|NM_001113536.1	NP_000794.3|NP_001107006.1|NP_001107007.1|NP_001107008.1	P14207	FOLR2_HUMAN	folate receptor 2 (fetal)	53					folic acid transport (GO:0015884)	anchored component of external side of plasma membrane (GO:0031362)|extracellular region (GO:0005576)|membrane (GO:0016020)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)			breast(3)|large_intestine(3)|ovary(1)|skin(1)	8					Folic Acid(DB00158)	CCAGTGCAGTCCCTGGAAGAA	0.587																																					p.P53T		Atlas-SNP	.											FOLR2,NS,carcinoma,0,1	FOLR2	29	.	0			c.C157A						PASS	.						46	44	44					11																	71931920		2200	4293	6493	SO:0001583	missense	2350	exon3			TGCAGTCCCTGGA	AK222539	CCDS8212.1	11q13.3-q14.1	2010-04-08			ENSG00000165457	ENSG00000165457			3793	protein-coding gene	gene with protein product		136425				1133088, 7698003	Standard	NM_000803		Approved		uc009ytf.3	P14207	OTTHUMG00000150394	ENST00000298223.6:c.157C>A	chr11.hg19:g.71931920C>A	ENSP00000298223:p.Pro53Thr	103.0	2.0	.		105.0	37.0	.	NM_001113535	Q05CA5|Q6GTE8	Missense_Mutation	SNP	ENST00000298223.6	hg19	CCDS8212.1	.	.	.	.	.	.	.	.	.	.	c	17.57	3.422312	0.62622	.	.	ENSG00000165457	ENST00000449475;ENST00000298223;ENST00000413873;ENST00000454954;ENST00000541003;ENST00000539412;ENST00000536778;ENST00000535625;ENST00000321324;ENST00000538353	T;T;T;T;T;T;T;T;T	0.76448	-1.02;-1.02;-1.02;-1.02;-1.02;-1.02;-1.02;-1.02;-1.02	4.25	2.38	0.29361	Folate receptor-like (1);	0.000000	0.85682	D	0.000000	D	0.88976	0.6584	M	0.93678	3.445	0.39744	D	0.971793	D	0.89917	1.0	D	0.97110	1.0	D	0.88102	0.2820	10	0.56958	D	0.05	.	8.6185	0.33847	0.0:0.8112:0.0:0.1888	.	53	P14207	FOLR2_HUMAN	T	70;53;70;12;99;64;68;53;66;53	ENSP00000405638:P70T;ENSP00000298223:P53T;ENSP00000414094:P12T;ENSP00000443307:P99T;ENSP00000441547:P64T;ENSP00000438568:P68T;ENSP00000444794:P53T;ENSP00000321957:P66T;ENSP00000440337:P53T	ENSP00000298223:P53T	P	+	1	0	FOLR2	71609568	0.920000	0.31207	0.934000	0.37439	0.977000	0.68977	3.796000	0.55507	0.435000	0.26365	0.455000	0.32223	CCC	.	.	.	none		0.587	FOLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317923.2	NM_000803		A	71931920	C	A	71931920	3	1	229	1	0	0	0	0	1	0	0	0	5989	855	30	4	163	4	FOLR2	11	71931920	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	5321428	71931920	63074596	64	13892											
BARX2	8538	hgsc.bcm.edu	37	chr11	129321185	129321185	+	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	ctctcaggggcaggaggagcTctgtgaagcacaggaaccga	11	5	15	10	1	2	1	1	1	2	0	3	5	2	4	1	5	3	3	1	5	2	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr11:129321185T>A	ENST00000281437.4	+	4	824	c.728T>A	c.(727-729)cTc>cAc	p.L243H	BARX2_ENST00000531946.1_Missense_Mutation_p.L121H|BARX2_ENST00000526127.1_Missense_Mutation_p.L98H	NM_003658.4	NP_003649.2	Q9UMQ3	BARX2_HUMAN	BARX homeobox 2	243					cartilage condensation (GO:0001502)|catagen (GO:0042637)|myotube differentiation (GO:0014902)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(1)|central_nervous_system(1)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	20	all_hematologic(175;0.0749)	Lung NSC(97;0.000383)|all_lung(97;0.000824)|Breast(109;0.000962)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.00929)|Lung(977;0.0245)|LUSC - Lung squamous cell carcinoma(976;0.0253)		CAGGAGGAGCTCTGTGAAGCA	0.582																																					p.L243H		Atlas-SNP	.											.	BARX2	40	.	0			c.T728A						PASS	.						72	66	68					11																	129321185		2201	4297	6498	SO:0001583	missense	8538	exon4			AGGAGCTCTGTGA	AF031924	CCDS8481.1	11q24.3	2011-06-20	2007-07-09		ENSG00000043039	ENSG00000043039		"Homeoboxes / ANTP class : NKL subclass"	956	protein-coding gene	gene with protein product		604823	"BarH-like homeobox 2"			10644443	Standard	NM_003658		Approved		uc001qfc.4	Q9UMQ3	OTTHUMG00000165776	ENST00000281437.4:c.728T>A	chr11.hg19:g.129321185T>A	ENSP00000281437:p.Leu243His	143.0	0.0	.		134.0	53.0	.	NM_003658	O43518|Q6NT51	Missense_Mutation	SNP	ENST00000281437.4	hg19	CCDS8481.1	.	.	.	.	.	.	.	.	.	.	T	18.48	3.632445	0.67015	.	.	ENSG00000043039	ENST00000281437;ENST00000526127;ENST00000531946	D;D;D	0.90385	-2.66;-2.27;-2.27	5.51	-1.59	0.08453	.	0.906017	0.09601	N	0.780189	D	0.83769	0.5326	L	0.29908	0.895	0.09310	N	0.999999	P	0.45348	0.856	B	0.40101	0.319	T	0.72701	-0.4214	10	0.41790	T	0.15	.	12.1971	0.54303	0.0:0.6898:0.0:0.3102	.	243	Q9UMQ3	BARX2_HUMAN	H	243;98;121	ENSP00000281437:L243H;ENSP00000451113:L98H;ENSP00000450418:L121H	ENSP00000281437:L243H	L	+	2	0	BARX2	128826395	0.188000	0.23250	0.043000	0.18650	0.326000	0.28443	0.364000	0.20325	-0.288000	0.09051	0.533000	0.62120	CTC	.	.	.	none		0.582	BARX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386153.1	NM_003658		A	129321185	T	A	129321185	3	1	229	1	0	0	0	0	1	0	0	0	1316	1551	54	5	742	5	BARX2	11	129321185	Missense_Mutation	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10	57389265	129321185	5685331	65	13893											
SHMT2	6472	hgsc.bcm.edu	37	chr12	57624649	57624649	+	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	ctcagcacagcaacgcagccCagactcagactggggaagca	13	3	11	14	1	2	2	2	0	0	2	2	3	2	3	1	2	5	4	1	2	2	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr12:57624649C>G	ENST00000328923.3	+	2	549	c.97C>G	c.(97-99)Cag>Gag	p.Q33E	Y_RNA_ENST00000365197.1_RNA|SHMT2_ENST00000393827.4_5'UTR|SHMT2_ENST00000557487.1_Missense_Mutation_p.Q33E|SHMT2_ENST00000414700.3_Missense_Mutation_p.Q12E|SHMT2_ENST00000449049.3_Missense_Mutation_p.Q12E|SHMT2_ENST00000554600.1_3'UTR|SHMT2_ENST00000553474.1_Missense_Mutation_p.Q12E	NM_001166356.1|NM_005412.5	NP_001159828.1|NP_005403.2	P34897	GLYM_HUMAN	serine hydroxymethyltransferase 2 (mitochondrial)	33					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)	CAACGCAGCCCAGACTCAGAC	0.582																																					p.Q33E	Esophageal Squamous(150;1369 2416 49071 49364)	Atlas-SNP	.											.	SHMT2	40	.	0			c.C97G						PASS	.						92	77	82					12																	57624649		2203	4300	6503	SO:0001583	missense	6472	exon2			GCAGCCCAGACTC	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.97C>G	chr12.hg19:g.57624649C>G	ENSP00000333667:p.Gln33Glu	346.0	0.0	.		402.0	161.0	.	NM_005412	B7Z9F1|E7EQ19|E7EU43|O00740|Q8N1A5	Missense_Mutation	SNP	ENST00000328923.3	hg19	CCDS8934.1	.	.	.	.	.	.	.	.	.	.	C	8.946	0.966931	0.18659	.	.	ENSG00000182199	ENST00000328923;ENST00000557487;ENST00000556689;ENST00000414700;ENST00000557703;ENST00000553529;ENST00000554310;ENST00000557427;ENST00000553474;ENST00000555773;ENST00000554975;ENST00000449049;ENST00000556737	T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59	4.81	3.85	0.44370	.	0.335256	0.29537	N	0.011879	T	0.10551	0.0258	N	0.08118	0	0.80722	D	1	B;B	0.11235	0.004;0.002	B;B	0.12837	0.008;0.005	T	0.31586	-0.9938	10	0.02654	T	1	-12.6294	3.4496	0.07493	0.1727:0.5679:0.1666:0.0929	.	33;33	Q8N1A5;P34897	.;GLYM_HUMAN	E	33;33;33;12;12;12;12;12;12;12;12;12;12	ENSP00000333667:Q33E;ENSP00000452315:Q33E;ENSP00000406881:Q12E;ENSP00000452419:Q12E;ENSP00000413770:Q12E	ENSP00000333667:Q33E	Q	+	1	0	SHMT2	55910916	0.139000	0.22563	1.000000	0.80357	0.972000	0.66771	0.472000	0.22116	2.668000	0.90789	0.655000	0.94253	CAG	.	.	.	none		0.582	SHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412525.2	NM_005412		G	57624649	C	G	57624649	3	3	229	1	0	0	0	0	1	0	0	0	14299	595	21	4	103	4	SHMT2	12	57624649	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10		57624649	76227246	66	13894											
CCDC41	51134	hgsc.bcm.edu	37	chr12	94763803	94763804	+	Frame_Shift_Ins	INS	-	-	T																															agtttgtttgaatgtttaagINSttcttttacctgttgataat																										TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr12:94763803_94763804insT	ENST00000397809.5	-	9	1491_1492	c.942_943insA	c.(940-945)gaacttfs	p.L315fs	CCDC41_ENST00000547575.1_Frame_Shift_Ins_p.L315fs|CCDC41_ENST00000397807.2_Frame_Shift_Ins_p.L282fs|CCDC41_ENST00000339839.5_Frame_Shift_Ins_p.L315fs|CCDC41_ENST00000549352.1_5'UTR	NM_016122.2	NP_057206.2	Q9Y592	CEP83_HUMAN		307					cilium assembly (GO:0042384)|protein localization to centrosome (GO:0071539)|vesicle docking (GO:0048278)	centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|Golgi apparatus (GO:0005794)				breast(1)|central_nervous_system(3)|kidney(3)|large_intestine(8)|lung(8)|prostate(2)|skin(2)	27						GAATGTTTAAGTTCTTTTACCT	0.332																																					p.L315fs		Atlas-Indel,Pindel	.											.	CCDC41	59	.	0			c.943_944insA						PASS	.																																			SO:0001589	frameshift_variant	51134	exon8			.																												ENST00000397809.5:c.943dupA	chr12.hg19:g.94763805_94763805dupT	ENSP00000380911:p.Leu315fs	62.0	0.0	0		58.0	21.0	0.362069	NM_001042399	A4FVB1|Q08AP1	Frame_Shift_Ins	INS	ENST00000397809.5	hg19	CCDS41820.1																																																																																			.	.	.	none		0.332	CCDC41-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408147.3			T	94763804	-	T	94763803	7	5	229	1	0	1	1	0	0	0	0	0	2815	1029	36	0	1198	0	CCDC41	12	94763803	Frame_Shift_Ins	INS	-	TCGA-P4-A5E6-01A-11D-A28G-10	37139154	94763803	39088092	67	13895											
C12orf24	29902	hgsc.bcm.edu	37	chr12	110906786	110906786	+	Missense_Mutation	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	agcgtagctcttctgcagagCcgcccgctgtggccgggacc	5	7	14	15	4	2	1	0	0	2	1	2	2	2	2	4	2	4	4	4	2	1	2	rs202079205	byFrequency	TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr12:110906786C>T	ENST00000377673.5	+	1	618	c.106C>T	c.(106-108)Ccg>Tcg	p.P36S	GPN3_ENST00000228827.3_5'Flank|GPN3_ENST00000552180.1_5'UTR|GPN3_ENST00000537466.2_5'Flank|GPN3_ENST00000543199.1_5'Flank	NM_013300.2	NP_037432.2	Q8WUB2	F216A_HUMAN	family with sequence similarity 216, member A	36																	TTCTGCAGAGCCGCCCGCTGT	0.771													C|||	12	0.00239617	0.0091	0	5008	,	,		13111	0		0	False		,,,				2504	0				p.P36S		Atlas-SNP	.											.	.	.	.	0			c.C106T						PASS	.	C	SER/PRO	24,3054		0,24,1515	2	2	2		106	3.3	0.1	12		2	0,6186		0,0,3093	yes	missense	C12orf24	NM_013300.2	74	0,24,4608	TT,TC,CC		0.0,0.7797,0.2591	probably-damaging	36/274	110906786	24,9240	1539	3093	4632	SO:0001583	missense	29902	exon1			GCAGAGCCGCCCG	U79274	CCDS31899.1	12q24.11	2012-02-07	2012-02-07	2012-02-07	ENSG00000204856	ENSG00000204856			30180	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 24"	C12orf24			Standard	NM_013300		Approved	HSU79274	uc001tqu.4	Q8WUB2	OTTHUMG00000169526	ENST00000377673.5:c.106C>T	chr12.hg19:g.110906786C>T	ENSP00000366901:p.Pro36Ser	0.0	0.0	.		22.0	15.0	.	NM_013300	A6NH30|Q99776	Missense_Mutation	SNP	ENST00000377673.5	hg19	CCDS31899.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.171608	0.78452	0.007797	0.0	ENSG00000204856	ENST00000377673;ENST00000538285	T	0.51071	0.72	4.16	3.27	0.37495	.	0.000000	0.39544	N	0.001336	T	0.32645	0.0836	L	0.56769	1.78	0.27811	N	0.942126	B;B	0.30709	0.291;0.129	B;B	0.26693	0.072;0.031	T	0.41645	-0.9497	10	0.87932	D	0	-0.6948	9.2806	0.37727	0.0:0.8974:0.0:0.1026	.	36;36	F5GZE4;Q8WUB2	.;CL024_HUMAN	S	36	ENSP00000366901:P36S	ENSP00000366901:P36S	P	+	1	0	C12orf24	109391169	0.943000	0.32029	0.132000	0.22025	0.895000	0.52256	2.944000	0.49034	1.096000	0.41439	0.462000	0.41574	CCG	.	.	.	weak		0.771	FAM216A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404616.1	NM_013300		T	110906786	C	T	110906786	3	4	229	1	0	0	0	0	1	0	0	0	1680	739	26	2	108	2	C12orf24	12	110906786	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	16142983	110906786	22945109	68	13896											
CLYBL	171425	hgsc.bcm.edu	37	chr13	100258999	100258999	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgcggagctgcggcggcggCgctgctgaggctgtgagtgc	3	6	21	11	6	0	2	0	2	0	0	0	3	0	3	0	5	4	4	0	5	0	0	rs200020595		TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr13:100258999C>T	ENST00000376360.1	+	1	77	c.50C>T	c.(49-51)gCg>gTg	p.A17V	CLYBL_ENST00000339105.4_Missense_Mutation_p.A17V|CLYBL_ENST00000376354.1_Missense_Mutation_p.A17V|CLYBL_ENST00000376355.3_Missense_Mutation_p.A17V|CLYBL_ENST00000444838.2_Missense_Mutation_p.A17V			Q8N0X4	CLYBL_HUMAN	citrate lyase beta like	17						mitochondrion (GO:0005739)	lyase activity (GO:0016829)|metal ion binding (GO:0046872)			NS(1)|kidney(6)|large_intestine(6)|lung(10)|skin(2)	25	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					GCGGCGGCGGCGCTGCTGAGG	0.776																																					p.A17V		Atlas-SNP	.											.	CLYBL	48	.	0			c.C50T						PASS	.						6	8	7					13																	100258999		1843	3595	5438	SO:0001583	missense	171425	exon1			CGGCGGCGCTGCT	AF428253	CCDS32002.1	13q32.3	2011-04-08			ENSG00000125246	ENSG00000125246			18355	protein-coding gene	gene with protein product		609686					Standard	XM_005254030		Approved	CLB	uc001vok.3	Q8N0X4	OTTHUMG00000017278	ENST00000376360.1:c.50C>T	chr13.hg19:g.100258999C>T	ENSP00000365538:p.Ala17Val	0.0	0.0	.		16.0	12.0	.	NM_206808	Q5W0F7|Q8TDH8	Missense_Mutation	SNP	ENST00000376360.1	hg19	CCDS32002.1	.	.	.	.	.	.	.	.	.	.	C	11.61	1.689931	0.29962	.	.	ENSG00000125246	ENST00000376355;ENST00000376360;ENST00000444838;ENST00000376354;ENST00000339105	T;T;T;T;T	0.24350	1.86;1.88;1.86;1.86;1.88	3.41	1.64	0.23874	.	0.599921	0.15592	N	0.254333	T	0.10766	0.0263	N	0.08118	0	0.22552	N	0.998997	B;B;B	0.15719	0.014;0.01;0.003	B;B;B	0.10450	0.002;0.005;0.001	T	0.30357	-0.9981	10	0.23302	T	0.38	.	5.6733	0.17735	0.0:0.7452:0.0:0.2548	.	17;17;17	B4DU60;Q8N0X4-2;Q8N0X4	.;.;CLYBL_HUMAN	V	17	ENSP00000365533:A17V;ENSP00000365538:A17V;ENSP00000404768:A17V;ENSP00000365532:A17V;ENSP00000342991:A17V	ENSP00000342991:A17V	A	+	2	0	CLYBL	99057000	0.995000	0.38212	1.000000	0.80357	0.521000	0.34408	0.074000	0.14662	0.436000	0.26393	0.313000	0.20887	GCG	.	.	.	weak		0.776	CLYBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045611.1			T	100258999	C	T	100258999	3	4	229	1	0	0	0	0	1	0	0	0	3575	768	27	1	52	1	CLYBL	13	100258999	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10		100258999	14910879	69	13897											
LGALS3	3958	hgsc.bcm.edu	37	chr14	55604955	55604955	+	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	ctggagcacctggagcttatCccggagcacctgcacctgga	8	7	12	14	1	0	0	0	0	0	0	1	4	1	4	4	4	4	4	4	4	1	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr14:55604955C>T	ENST00000254301.9	+	3	472	c.211C>T	c.(211-213)Ccc>Tcc	p.P71S	LGALS3_ENST00000553755.1_3'UTR|LGALS3_ENST00000554715.1_Missense_Mutation_p.P71S	NM_002306.3	NP_002297.2	P17931	LEG3_HUMAN	lectin, galactoside-binding, soluble, 3	71	8 X 9 AA tandem repeats of Y-P-G-X(3)-P- G-A.				eosinophil chemotaxis (GO:0048245)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|mononuclear cell migration (GO:0071674)|mRNA processing (GO:0006397)|negative regulation of endocytosis (GO:0045806)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of immunological synapse formation (GO:2000521)|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 receptor signaling pathway (GO:0050860)|neutrophil chemotaxis (GO:0030593)|positive chemotaxis (GO:0050918)|positive regulation of calcium ion import (GO:0090280)|positive regulation of mononuclear cell migration (GO:0071677)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of T cell apoptotic process (GO:0070232)|regulation of T cell proliferation (GO:0042129)|RNA splicing (GO:0008380)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|spliceosomal complex (GO:0005681)	carbohydrate binding (GO:0030246)|chemoattractant activity (GO:0042056)|IgE binding (GO:0019863)|laminin binding (GO:0043236)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|prostate(1)	3						TGGAGCTTATCCCGGAGCACC	0.682																																					p.P71S		Atlas-SNP	.											.	LGALS3	10	.	0			c.C211T						PASS	.						21	24	23					14																	55604955		1813	4069	5882	SO:0001583	missense	3958	exon3			GCTTATCCCGGAG	M64303	CCDS41956.1	14q22.3	2014-03-19	2007-02-01		ENSG00000131981	ENSG00000131981		"Lectins, galactoside-binding", "Endogenous ligands"	6563	protein-coding gene	gene with protein product	"galectin 3"	153619		LGALS2		2009535, 8063692	Standard	NR_003225		Approved	MAC-2, GALIG	uc001xbr.3	P17931	OTTHUMG00000171030	ENST00000254301.9:c.211C>T	chr14.hg19:g.55604955C>T	ENSP00000254301:p.Pro71Ser	61.0	0.0	.		78.0	29.0	.	NM_002306	B2RC38|Q16005|Q6IBA7|Q96J47	Missense_Mutation	SNP	ENST00000254301.9	hg19	CCDS41956.1	.	.	.	.	.	.	.	.	.	.	C	7.633	0.679349	0.14907	.	.	ENSG00000131981	ENST00000553493;ENST00000254301;ENST00000554715	T;T;T	0.74315	-0.83;3.24;2.45	5.35	4.45	0.53987	.	0.209237	0.50627	N	0.000111	T	0.77751	0.4177	M	0.86178	2.8	0.45662	D	0.998582	B	0.11235	0.004	B	0.16722	0.016	T	0.73830	-0.3859	10	0.62326	D	0.03	.	14.3618	0.66776	0.0:0.921:0.0:0.079	.	71	P17931	LEG3_HUMAN	S	71	ENSP00000451526:P71S;ENSP00000254301:P71S;ENSP00000451381:P71S	ENSP00000254301:P71S	P	+	1	0	LGALS3	54674708	0.991000	0.36638	0.823000	0.32752	0.087000	0.18053	2.632000	0.46511	0.647000	0.30713	-0.797000	0.03246	CCC	.	.	.	none		0.682	LGALS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411309.1	NM_002306		T	55604955	C	T	55604955	3	4	229	1	0	0	0	0	1	0	0	0	8750	855	30	2	217	2	LGALS3	14	55604955	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10		55604955	51744585	70	13898											
ZFYVE26	23503	hgsc.bcm.edu	37	chr14	68268851	68268851	+	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	gctgaggccaggtcctcagaGaggctgtctttgcagtcctg	6	10	14	11	0	2	2	1	1	1	1	4	3	4	2	3	3	1	3	3	3	0	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr14:68268851G>T	ENST00000347230.4	-	10	1722	c.1584C>A	c.(1582-1584)ctC>ctA	p.L528L	ZFYVE26_ENST00000555452.1_Silent_p.L528L	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	528					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)		GGTCCTCAGAGAGGCTGTCTT	0.537																																					p.L528L		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.C1584A						PASS	.						139	126	130					14																	68268851		2203	4300	6503	SO:0001819	synonymous_variant	23503	exon10			CTCAGAGAGGCTG	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.1584C>A	chr14.hg19:g.68268851G>T		128.0	0.0	.		188.0	71.0	.	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Silent	SNP	ENST00000347230.4	hg19	CCDS9788.1																																																																																			.	.	.	none		0.537	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		T	68268851	G	T	68268851	2	4	229	1	0	0	0	0	0	0	0	1	17680	929	33	4		4	ZFYVE26	14	68268851	Silent	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	12663896	68268851	39080689	71	13899											
GPR65	8477	hgsc.bcm.edu	37	chr14	88478074	88478074	+	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	ttctgtactgttttgtaaccGaaacaggaagatatgatatg	13	14	9	5	1	1	2	0	1	1	1	1	4	1	3	1	1	3	3	1	1	6	7			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr14:88478074G>A	ENST00000267549.3	+	2	1441	c.883G>A	c.(883-885)Gaa>Aaa	p.E295K	RP11-300J18.2_ENST00000554433.1_RNA	NM_003608.3	NP_003599.2	Q8IYL9	PSYR_HUMAN	G protein-coupled receptor 65	295					actin cytoskeleton reorganization (GO:0031532)|activation of Rho GTPase activity (GO:0032862)|apoptotic process (GO:0006915)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|multicellular organismal development (GO:0007275)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of stress fiber assembly (GO:0051496)|response to acidic pH (GO:0010447)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)	16						TTTTGTAACCGAAACAGGAAG	0.353																																					p.E295K		Atlas-SNP	.											.	GPR65	48	.	0			c.G883A						PASS	.						95	90	91					14																	88478074		2203	4300	6503	SO:0001583	missense	8477	exon2			GTAACCGAAACAG	U95218	CCDS9879.1	14q31-q32.1	2012-08-21			ENSG00000140030	ENSG00000140030		"GPCR / Class A : Orphans"	4517	protein-coding gene	gene with protein product		604620				9655242	Standard	NM_003608		Approved	hTDAG8, TDAG8	uc001xvv.3	Q8IYL9	OTTHUMG00000028648	ENST00000267549.3:c.883G>A	chr14.hg19:g.88478074G>A	ENSP00000267549:p.Glu295Lys	204.0	0.0	.		185.0	10.0	.	NM_003608	O75819	Missense_Mutation	SNP	ENST00000267549.3	hg19	CCDS9879.1	.	.	.	.	.	.	.	.	.	.	G	31	5.063367	0.93898	.	.	ENSG00000140030	ENST00000267549	T	0.30714	1.52	5.98	5.98	0.97165	.	0.000000	0.56097	D	0.000037	T	0.33556	0.0867	N	0.08118	0	0.44417	D	0.99733	D	0.71674	0.998	P	0.58820	0.846	T	0.20009	-1.0288	10	0.29301	T	0.29	.	20.4581	0.99154	0.0:0.0:1.0:0.0	.	295	Q8IYL9	PSYR_HUMAN	K	295	ENSP00000267549:E295K	ENSP00000267549:E295K	E	+	1	0	GPR65	87547827	1.000000	0.71417	0.654000	0.29608	0.919000	0.55068	6.201000	0.72124	2.835000	0.97688	0.650000	0.86243	GAA	.	.	.	none		0.353	GPR65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071564.4			A	88478074	G	A	88478074	3	1	229	1	0	0	0	0	1	0	0	0	6713	1059	37	1	885	1	GPR65	14	88478074	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	20209223	88478074	18871466	72	13900											
KIAA0284	283638	hgsc.bcm.edu	37	chr14	105350539	105350539	+	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	agcgggagaagacagaggaaCggctgggcagcccctcgccc	10	2	16	13	3	0	3	0	0	0	3	1	5	0	4	3	4	3	2	3	4	2	0	rs373443985		TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr14:105350539C>T	ENST00000414716.3	+	9	1651	c.1423C>T	c.(1423-1425)Cgg>Tgg	p.R475W	CEP170B_ENST00000453495.1_Missense_Mutation_p.R476W|CEP170B_ENST00000418279.1_Missense_Mutation_p.R405W|CEP170B_ENST00000556508.1_Missense_Mutation_p.R405W	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	475						cytoplasm (GO:0005737)|microtubule (GO:0005874)											GACAGAGGAACGGCTGGGCAG	0.736																																					p.R475W		Atlas-SNP	.											.	.	.	.	0			c.C1423T						PASS	.	C	TRP/ARG,TRP/ARG	2,3338		0,2,1668	4	7	6		1423,1213	4.1	1	14		6	1,7387		0,1,3693	no	missense,missense	KIAA0284	NM_001112726.2,NM_015005.2	101,101	0,3,5361	TT,TC,CC		0.0135,0.0599,0.028	probably-damaging,probably-damaging	475/1555,405/1520	105350539	3,10725	1670	3694	5364	SO:0001583	missense	283638	exon9			GAGGAACGGCTGG	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.1423C>T	chr14.hg19:g.105350539C>T	ENSP00000404151:p.Arg475Trp	0.0	0.0	.		8.0	4.0	.	NM_001112726	Q2KHR7|Q86TI7	Missense_Mutation	SNP	ENST00000414716.3	hg19	CCDS45175.1	.	.	.	.	.	.	.	.	.	.	C	18.77	3.695399	0.68386	5.99E-4	1.35E-4	ENSG00000099814	ENST00000556508;ENST00000414716;ENST00000453495;ENST00000418279	T;T;T;T	0.51574	0.71;0.7;0.71;0.71	4.09	4.09	0.47781	.	0.577739	0.16725	N	0.202119	T	0.61751	0.2372	L	0.49350	1.555	0.52501	D	0.999953	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.995;0.989	T	0.62845	-0.6768	10	0.62326	D	0.03	-12.0906	12.3112	0.54929	0.1701:0.8299:0.0:0.0	.	475;475;405	Q9Y4F5-2;Q9Y4F5;E9PFC1	.;K0284_HUMAN;.	W	405;475;476;405	ENSP00000451249:R405W;ENSP00000404151:R475W;ENSP00000407238:R476W;ENSP00000415006:R405W	ENSP00000404151:R475W	R	+	1	2	KIAA0284	104421584	0.739000	0.28196	0.982000	0.44146	0.376000	0.30014	1.841000	0.39240	1.813000	0.52934	0.313000	0.20887	CGG	.	.	.	weak		0.736	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726		T	105350539	C	T	105350539	3	4	229	1	0	0	0	0	1	0	0	0	8173	527	19	1	1453	1	KIAA0284	14	105350539	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	16872465	105350539	1999001	73	13901											
C15orf2	23742	hgsc.bcm.edu	37	chr15	24923447	24923447	+	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	actttagtgagcagtgcctcTgcagcatcgttatccaagcc	9	11	9	12	1	1	1	0	1	1	0	3	1	2	1	3	0	5	4	3	0	3	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr15:24923447T>A	ENST00000329468.2	+	1	2907	c.2433T>A	c.(2431-2433)tcT>tcA	p.S811S		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	811					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											GCAGTGCCTCTGCAGCATCGT	0.522																																					p.S811S		Atlas-SNP	.											.	.	.	.	0			c.T2433A						PASS	.						138	133	135					15																	24923447		2203	4300	6503	SO:0001819	synonymous_variant	23742	exon1			TGCCTCTGCAGCA	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.2433T>A	chr15.hg19:g.24923447T>A		50.0	0.0	.		69.0	4.0	.	NM_018958		Silent	SNP	ENST00000329468.2	hg19	CCDS10015.1																																																																																			.	.	.	none		0.522	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		A	24923447	T	A	24923447	2	1	229	1	0	0	0	0	0	0	0	1	1786	1567	55	5		5	C15orf2	15	24923447	Silent	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10		24923447	77607945	74	13902											
OTUD7A	161725	hgsc.bcm.edu	37	chr15	31818596	31818596	+	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	ctgaagtgtgtgcgcggctcGctggaggccagcttcagcag	6	8	16	11	3	1	1	1	1	0	0	2	2	1	2	1	3	3	4	1	3	1	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr15:31818596G>A	ENST00000307050.4	-	6	920	c.828C>T	c.(826-828)agC>agT	p.S276S	OTUD7A_ENST00000382902.1_Silent_p.S283S	NM_130901.1	NP_570971.1	Q8TE49	OTU7A_HUMAN	OTU deubiquitinase 7A	276	Catalytic. {ECO:0000250}.|OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.|TRAF-binding. {ECO:0000250}.				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)		TGCGCGGCTCGCTGGAGGCCA	0.677																																					p.S276S		Atlas-SNP	.											.	OTUD7A	89	.	0			c.C828T						PASS	.						37	34	35					15																	31818596		2202	4300	6502	SO:0001819	synonymous_variant	161725	exon6			CGGCTCGCTGGAG	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.828C>T	chr15.hg19:g.31818596G>A		25.0	0.0	.		22.0	5.0	.	NM_130901	Q8IWK5	Silent	SNP	ENST00000307050.4	hg19	CCDS10026.1																																																																																			.	.	.	none		0.677	OTUD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251393.2	NM_130901		A	31818596	G	A	31818596	2	1	229	1	0	0	0	0	0	0	0	1	11325	1078	38	1		1	OTUD7A	15	31818596	Silent	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	6895149	31818596	70712796	75	13903											
C15orf53	400359	hgsc.bcm.edu	37	chr15	38988831	38988831	+	Missense_Mutation	SNP	A	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	ggagctacaaggggcccaagAggacctgggcatttccctct	9	7	13	12	0	1	1	0	0	1	1	2	3	2	3	3	5	2	2	3	5	3	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr15:38988831A>C	ENST00000318792.1	+	1	33	c.23A>C	c.(22-24)gAg>gCg	p.E8A		NM_207444.2	NP_997327.1	Q8NAA6	CO053_HUMAN	chromosome 15 open reading frame 53	8										endometrium(1)|large_intestine(1)|lung(2)|skin(1)|stomach(1)	6		all_cancers(109;1.75e-13)|all_epithelial(112;1.02e-11)|Lung NSC(122;1.9e-09)|all_lung(180;4.04e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)		GBM - Glioblastoma multiforme(113;8.39e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0321)		GGGGCCCAAGAGGACCTGGGC	0.562																																					p.E8A		Atlas-SNP	.											.	C15orf53	12	.	0			c.A23C						PASS	.						96	91	93					15																	38988831		2200	4297	6497	SO:0001583	missense	400359	exon1			CCCAAGAGGACCT		CCDS10048.1	15q14	2007-11-21			ENSG00000175779	ENSG00000175779			33796	protein-coding gene	gene with protein product							Standard	NM_207444		Approved	FLJ35695	uc001zkf.1	Q8NAA6	OTTHUMG00000129841	ENST00000318792.1:c.23A>C	chr15.hg19:g.38988831A>C	ENSP00000325144:p.Glu8Ala	134.0	0.0	.		159.0	46.0	.	NM_207444		Missense_Mutation	SNP	ENST00000318792.1	hg19	CCDS10048.1	.	.	.	.	.	.	.	.	.	.	A	9.365	1.069014	0.20147	.	.	ENSG00000175779	ENST00000318792	T	0.34667	1.35	3.31	-1.66	0.08265	.	.	.	.	.	T	0.23330	0.0564	N	0.08118	0	0.09310	N	1	D	0.54207	0.965	P	0.52554	0.702	T	0.12477	-1.0546	9	0.87932	D	0	.	3.0108	0.06044	0.4664:0.0:0.3378:0.1958	.	8	Q8NAA6	CO053_HUMAN	A	8	ENSP00000325144:E8A	ENSP00000325144:E8A	E	+	2	0	C15orf53	36776123	0.001000	0.12720	0.000000	0.03702	0.074000	0.17049	0.566000	0.23593	-0.349000	0.08274	-0.415000	0.06103	GAG	.	.	.	none		0.562	C15orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252081.1	NM_207444		C	38988831	A	C	38988831	3	2	229	1	0	0	0	0	1	0	0	0	1803	304	11	5	25	5	C15orf53	15	38988831	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	7170235	38988831	63542561	76	13904											
MYO5A	4644	hgsc.bcm.edu	37	chr15	52680095	52680096	+	Missense_Mutation	DNP	AC	AC	CA																															ttcttttcgagaaatccttcAcactggtattccacctgaaa																										TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr15:52680095_52680096AC>CA	ENST00000399231.3	-	14	1925_1926	c.1682_1683GT>TG	c.(1681-1683)tGT>tTG	p.C561L	MYO5A_ENST00000356338.6_Missense_Mutation_p.C561L|MYO5A_ENST00000399233.2_Missense_Mutation_p.C561L|MYO5A_ENST00000358212.6_Missense_Mutation_p.C561L|MYO5A_ENST00000553916.1_Missense_Mutation_p.C561L	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	561	Myosin motor.				actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		GAAATCCTTCACACTGGTATTC	0.307																																					p.C561W|p.C561F		Atlas-SNP	.											.	MYO5A	145	.	0			c.T1683G|c.G1682T						PASS	.																																			SO:0001583	missense	4644	exon14			TCCTTCACACTGG|CCTTCACACTGGT		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.1682_1683delinsCA	chr15.hg19:g.52680095_52680096delinsCA	ENSP00000382177:p.Cys561Leu	13.0	0.0	.		15.0|13.0	5.0	.	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	hg19	CCDS42037.1																																																																																			.	.	.	none		0.307	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259		CA	52680096	AC	CA	52680095	3	2	229	1	0	0	0	0	1	0	0	0	10085	157	6	5	3996	5	MYO5A	15	52680095	Missense_Mutation	DNP	AC	TCGA-P4-A5E6-01A-11D-A28G-10	13691264	52680095	49851297	77	13905											
WDR90	197335	hgsc.bcm.edu	37	chr16	707787	707787	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atggtatgcccggatgccccCgcgagccccagcgccctggc	5	5	13	18	4	0	0	0	0	0	0	0	2	0	1	6	3	4	1	6	3	1	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr16:707787C>T	ENST00000293879.4	+	21	2499	c.2499C>T	c.(2497-2499)ccC>ccT	p.P833P	WDR90_ENST00000549091.1_Silent_p.P833P|LA16c-349E10.1_ENST00000573609.1_RNA			Q96KV7	WDR90_HUMAN	WD repeat domain 90	833										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CGGATGCCCCCGCGAGCCCCA	0.726																																					p.P833P		Atlas-SNP	.											.	WDR90	107	.	0			c.C2499T						PASS	.						8	11	10					16																	707787		1929	4048	5977	SO:0001819	synonymous_variant	197335	exon21			TGCCCCCGCGAGC	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.2499C>T	chr16.hg19:g.707787C>T		35.0	0.0	.		281.0	89.0	.	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Silent	SNP	ENST00000293879.4	hg19	CCDS42092.1																																																																																			.	.	.	none		0.726	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294		T	707787	C	T	707787	2	4	229	1	0	0	0	0	0	0	0	1	17349	639	23	1		1	WDR90	16	707787	Silent	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10		707787	89646966	78	13906											
VASN	114990	hgsc.bcm.edu	37	chr16	4432672	4432672	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggtgggggcagcctactgTgtgcggcgggggcgggccat	3	6	22	10	4	0	0	0	0	0	0	0	0	0	0	2	7	3	1	2	7	1	1	rs370088997	byFrequency	TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr16:4432672T>C	ENST00000304735.3	+	2	1949	c.1794T>C	c.(1792-1794)tgT>tgC	p.C598C	CORO7_ENST00000537233.2_Intron|CORO7_ENST00000423908.2_Intron|CORO7_ENST00000251166.4_Intron|CORO7_ENST00000539968.1_Intron|CORO7-PAM16_ENST00000572467.1_Intron|CORO7_ENST00000574025.1_Intron	NM_138440.2	NP_612449.2	Q6EMK4	VASN_HUMAN	vasorin	598					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						CAGCCTACTGTGTGCGGCGGG	0.741													T|||	5	0.000998403	0.0038	0	5008	,	,		13454	0		0	False		,,,				2504	0				p.C598C		Atlas-SNP	.											.	VASN	21	.	0			c.T1794C						PASS	.	T	,,,,	8,3802		0,8,1897	4	7	6		,,,,1794	-1.7	1	16		6	0,7642		0,0,3821	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	,,,,	0,8,5718	CC,CT,TT		0.0,0.21,0.0699	,,,,	,,,,598/674	4432672	8,11444	1905	3821	5726	SO:0001819	synonymous_variant	114990	exon2			CTACTGTGTGCGG	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.1794T>C	chr16.hg19:g.4432672T>C		2.0	0.0	.		19.0	4.0	.	NM_138440	Q6UXL4|Q6UXL5|Q96CX1	Silent	SNP	ENST00000304735.3	hg19	CCDS10514.1																																																																																			.	.	.	weak		0.741	VASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251632.1	NM_138440		C	4432672	T	C	4432672	2	2	229	1	0	0	0	0	0	0	0	1	17139	1702	59	3		3	VASN	16	4432672	Silent	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10	3724885	4432672	85922081	79	13907											
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24788401	24788401	+	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	gcagcagcaacagcagcagcCgcagcagcagcagccacagc	13	0	12	16	1	0	0	0	0	0	0	0	0	0	0	2	0	11	9	2	0	1	0	rs112426081|rs575176088	byFrequency	TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr16:24788401C>A	ENST00000395799.3	+	5	440	c.311C>A	c.(310-312)cCg>cAg	p.P104Q	TNRC6A_ENST00000315183.7_Missense_Mutation_p.P104Q	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	104	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)		cagcagcagccgcagcagcag	0.587													C|||	5	0.000998403	0.0038	0	5008	,	,		10840	0		0	False		,,,				2504	0				p.P104Q		Atlas-SNP	.											TNRC6A,NS,carcinoma,0,1	TNRC6A	171	.	0			c.C311A						PASS	.						17	25	22					16																	24788401		2009	4030	6039	SO:0001583	missense	27327	exon5			AGCAGCCGCAGCA	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.311C>A	chr16.hg19:g.24788401C>A	ENSP00000379144:p.Pro104Gln	49.0	1.0	.		128.0	8.0	.	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	hg19	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.471905	0.00167	.	.	ENSG00000090905	ENST00000315183;ENST00000395799	T;T	0.10668	2.85;2.89	4.41	-2.9	0.05648	.	0.157308	0.30193	N	0.010181	T	0.03827	0.0108	N	0.08118	0	0.58432	D	0.999991	B	0.02656	0.0	B	0.01281	0.0	T	0.47711	-0.9096	10	0.12430	T	0.62	0.0105	8.8291	0.35074	0.3902:0.531:0.0787:0.0	.	104	Q8NDV7	TNR6A_HUMAN	Q	104	ENSP00000326900:P104Q;ENSP00000379144:P104Q	ENSP00000326900:P104Q	P	+	2	0	TNRC6A	24695902	0.031000	0.19500	0.019000	0.16419	0.020000	0.10135	-0.621000	0.05559	-0.679000	0.05217	-1.413000	0.01118	CCG	.	.	.	none		0.587	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		A	24788401	C	A	24788401	3	1	229	1	0	0	0	0	1	0	0	0	16352	652	23	4	329	4	TNRC6A	16	24788401	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	20355729	24788401	65566352	80	13908											
ITGAD	3681	hgsc.bcm.edu	37	chr16	31414951	31414951	+	Missense_Mutation	SNP	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	cctgacgttcacggccacggGcatcctgacagtggtgtaag	8	8	13	12	3	1	2	1	2	0	0	2	2	2	2	3	3	0	3	3	3	1	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr16:31414951G>A	ENST00000389202.2	+	7	738	c.689G>A	c.(688-690)gGc>gAc	p.G230D	RP11-120K18.2_ENST00000567545.1_RNA	NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	230	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						ACGGCCACGGGCATCCTGACA	0.607																																					p.G230D		Atlas-SNP	.											.	ITGAD	154	.	0			c.G689A						PASS	.						96	78	84					16																	31414951		2197	4300	6497	SO:0001583	missense	3681	exon7			CCACGGGCATCCT	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.689G>A	chr16.hg19:g.31414951G>A	ENSP00000373854:p.Gly230Asp	143.0	0.0	.		157.0	59.0	.	NM_005353	Q15575|Q15576	Missense_Mutation	SNP	ENST00000389202.2	hg19	CCDS32438.1	.	.	.	.	.	.	.	.	.	.	G	19.35	3.810704	0.70797	.	.	ENSG00000156886	ENST00000316569;ENST00000444228;ENST00000389202	D	0.86030	-2.06	4.7	3.7	0.42460	von Willebrand factor, type A (3);	.	.	.	.	D	0.92492	0.7616	M	0.86864	2.845	0.34300	D	0.684244	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.996;0.996	D	0.94979	0.8124	9	0.87932	D	0	.	12.6978	0.57014	0.0:0.1801:0.8199:0.0	.	230;246;230	B7Z6V7;Q59H14;Q13349	.;.;ITAD_HUMAN	D	94;246;230	ENSP00000373854:G230D	ENSP00000323325:G94D	G	+	2	0	ITGAD	31322452	1.000000	0.71417	0.706000	0.30403	0.134000	0.20937	1.683000	0.37638	2.434000	0.82447	0.508000	0.49915	GGC	.	.	.	none		0.607	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353		A	31414951	G	A	31414951	3	1	229	1	0	0	0	0	1	0	0	0	7891	1203	42	2	715	2	ITGAD	16	31414951	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	6626550	31414951	58939802	81	13909											
PHKB	5257	hgsc.bcm.edu	37	chr16	47622955	47622955	+	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	taaacgtttcttgagagatgGgtatagaacatcattggaag	14	12	11	4	1	2	3	1	1	1	2	2	5	2	4	0	2	2	2	0	2	6	6			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr16:47622955G>A	ENST00000323584.5	+	10	1034	c.1010G>A	c.(1009-1011)gGg>gAg	p.G337E	PHKB_ENST00000455779.1_Missense_Mutation_p.G330E|PHKB_ENST00000566044.1_Missense_Mutation_p.G330E|PHKB_ENST00000299167.8_Missense_Mutation_p.G337E|PHKB_ENST00000567402.1_3'UTR	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	337					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				TTGAGAGATGGGTATAGAACA	0.353																																					p.G337E		Atlas-SNP	.											.	PHKB	298	.	0			c.G1010A						PASS	.						70	74	73					16																	47622955		2201	4300	6501	SO:0001583	missense	5257	exon10			GAGATGGGTATAG		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.1010G>A	chr16.hg19:g.47622955G>A	ENSP00000313504:p.Gly337Glu	69.0	0.0	.		107.0	27.0	.	NM_000293	Q8N4T5	Missense_Mutation	SNP	ENST00000323584.5	hg19	CCDS10729.1	.	.	.	.	.	.	.	.	.	.	G	31	5.099043	0.94197	.	.	ENSG00000102893	ENST00000299167;ENST00000455779;ENST00000323584	D;D	0.91792	-2.91;-2.91	5.83	5.83	0.93111	Six-hairpin glycosidase-like (1);Glycoside hydrolase 15-related (1);	0.000000	0.85682	D	0.000000	D	0.97232	0.9095	M	0.92923	3.36	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.79108	0.992;0.918	D	0.97532	1.0080	10	0.87932	D	0	-10.5585	20.127	0.97984	0.0:0.0:1.0:0.0	.	337;330	Q93100;Q93100-4	KPBB_HUMAN;.	E	330;330;337	ENSP00000414345:G330E;ENSP00000313504:G337E	ENSP00000299167:G330E	G	+	2	0	PHKB	46180456	1.000000	0.71417	0.964000	0.40570	0.946000	0.59487	9.717000	0.98755	2.775000	0.95449	0.585000	0.79938	GGG	.	.	.	none		0.353	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1			A	47622955	G	A	47622955	3	1	229	1	0	0	0	0	1	0	0	0	11852	1232	43	2	1107	2	PHKB	16	47622955	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	16208004	47622955	42731798	82	13910											
DBNDD1	79007	hgsc.bcm.edu	37	chr16	90075270	90075270	+	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	ctcctggtccgacatgtcggTgagctcagtgaggtccagga	7	9	14	11	2	1	2	1	2	0	0	5	4	4	3	3	4	1	1	3	4	0	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr16:90075270T>A	ENST00000002501.6	-	3	372	c.241A>T	c.(241-243)Acc>Tcc	p.T81S	DBNDD1_ENST00000568838.1_Missense_Mutation_p.T201S|DBNDD1_ENST00000392973.3_Missense_Mutation_p.T87S|DBNDD1_ENST00000304733.3_Missense_Mutation_p.T101S	NM_001042610.1	NP_001036075.1	Q9H9R9	DBND1_HUMAN	dysbindin (dystrobrevin binding protein 1) domain containing 1	81						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)		GACATGTCGGTGAGCTCAGTG	0.642																																					p.T101S		Atlas-SNP	.											.	DBNDD1	9	.	0			c.A301T						PASS	.						32	37	35					16																	90075270		2016	4160	6176	SO:0001583	missense	79007	exon3			TGTCGGTGAGCTC	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.241A>T	chr16.hg19:g.90075270T>A	ENSP00000002501:p.Thr81Ser	61.0	0.0	.		119.0	28.0	.	NM_024043	B4DQS3|Q69YT2|Q9BW25	Missense_Mutation	SNP	ENST00000002501.6	hg19	CCDS42223.1	.	.	.	.	.	.	.	.	.	.	T	17.81	3.480743	0.63849	.	.	ENSG00000003249	ENST00000304733;ENST00000002501;ENST00000392973	T;T	0.34072	1.38;1.38	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.61274	0.2334	M	0.78637	2.42	0.49299	D	0.999773	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.994	T	0.64415	-0.6413	9	.	.	.	-34.7701	15.1222	0.72453	0.0:0.0:0.0:1.0	.	81;101	Q9H9R9;Q9H9R9-2	DBND1_HUMAN;.	S	101;81;201	ENSP00000306407:T101S;ENSP00000002501:T81S	.	T	-	1	0	DBNDD1	88602771	1.000000	0.71417	0.992000	0.48379	0.282000	0.26991	5.761000	0.68801	1.992000	0.58205	0.260000	0.18958	ACC	.	.	.	none		0.642	DBNDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272872.1	NM_024043		A	90075270	T	A	90075270	3	1	229	1	0	0	0	0	1	0	0	0	4255	1696	59	5	243	5	DBNDD1	16	90075270	Missense_Mutation	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10	42452315	90075270	279483	83	13911											
ZNF594	84622	hgsc.bcm.edu	37	chr17	5086862	5086862	+	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	ttccccctactgtggattctCtggtgcaggacaaggtttga	7	13	11	10	0	1	1	0	1	1	0	3	3	2	3	2	4	2	2	2	4	2	4			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr17:5086862C>G	ENST00000399604.4	-	1	830	c.690G>C	c.(688-690)caG>caC	p.Q230H	ZNF594_ENST00000575779.1_Missense_Mutation_p.Q230H			Q96JF6	ZN594_HUMAN	zinc finger protein 594	230					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.Q230H(1)		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						TGTGGATTCTCTGGTGCAGGA	0.438																																					p.Q230H		Atlas-SNP	.											ZNF594,NS,carcinoma,0,1	ZNF594	89	.	1	Substitution - Missense(1)	cervix(1)	c.G690C						PASS	.						104	107	106					17																	5086862		2051	4221	6272	SO:0001583	missense	84622	exon2			GATTCTCTGGTGC	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.690G>C	chr17.hg19:g.5086862C>G	ENSP00000382513:p.Gln230His	73.0	0.0	.		68.0	32.0	.	NM_032530	Q6RFS0	Missense_Mutation	SNP	ENST00000399604.4	hg19	CCDS42241.1	.	.	.	.	.	.	.	.	.	.	C	3.775	-0.046880	0.07407	.	.	ENSG00000180626	ENST00000399604	T	0.18502	2.21	2.36	1.36	0.22044	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.22859	0.0552	L	0.48986	1.54	0.20638	N	0.99988	D	0.57899	0.981	P	0.53035	0.716	T	0.08186	-1.0734	9	0.52906	T	0.07	.	6.6334	0.22869	0.0:0.8341:0.0:0.1659	.	230	Q96JF6	ZN594_HUMAN	H	230	ENSP00000382513:Q230H	ENSP00000382513:Q230H	Q	-	3	2	ZNF594	5027586	0.000000	0.05858	0.612000	0.29024	0.229000	0.25112	-0.361000	0.07612	1.314000	0.45095	0.462000	0.41574	CAG	.	.	.	none		0.438	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737		G	5086862	C	G	5086862	3	3	229	1	0	0	0	0	1	0	0	0	18036	912	32	4	1737	4	ZNF594	17	5086862	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10		5086862	76108348	84	13912											
KIAA0100	9703	hgsc.bcm.edu	37	chr17	26971163	26971163	+	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	atctttagctccgcctgcagCttccgctgacaccacttggt	6	12	8	15	2	1	1	0	1	1	0	3	1	3	1	4	1	3	4	4	1	1	4			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr17:26971163C>A	ENST00000528896.2	-	2	185	c.111G>T	c.(109-111)aaG>aaT	p.K37N	KIAA0100_ENST00000389003.3_5'UTR|KIAA0100_ENST00000544884.1_5'UTR	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	37						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)					CCGCCTGCAGCTTCCGCTGAC	0.488											OREG0024280	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K37N		Atlas-SNP	.											.	KIAA0100	175	.	0			c.G111T						PASS	.						59	69	65					17																	26971163		2203	4300	6503	SO:0001583	missense	9703	exon2			CTGCAGCTTCCGC	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.111G>T	chr17.hg19:g.26971163C>A	ENSP00000436773:p.Lys37Asn	90.0	0.0	.	790	77.0	25.0	.	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	hg19	CCDS32595.1	.	.	.	.	.	.	.	.	.	.	C	11.55	1.673269	0.29693	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896	T	0.26373	1.74	5.18	4.2	0.49525	FMP27, N-terminal (1);	0.354102	0.32719	N	0.005740	T	0.19127	0.0459	L	0.27053	0.805	0.80722	D	1	B;B	0.15141	0.012;0.0	B;B	0.12156	0.007;0.002	T	0.03619	-1.1019	10	0.62326	D	0.03	.	11.8337	0.52309	0.1379:0.7294:0.1327:0.0	.	37;37	F6XS94;Q14667	.;K0100_HUMAN	N	37	ENSP00000436773:K37N	ENSP00000005905:K37N	K	-	3	2	KIAA0100	23995290	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.047000	0.30367	1.295000	0.44724	-0.310000	0.09108	AAG	.	.	.	none		0.488	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		A	26971163	C	A	26971163	3	1	229	1	0	0	0	0	1	0	0	0	8161	796	28	4	6748	4	KIAA0100	17	26971163	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	21884301	26971163	54224047	85	13913											
NUFIP2	57532	hgsc.bcm.edu	37	chr17	27614566	27614566	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaatgaaattcttggttttaAttcctgctttcccaaaggtg	10	16	8	7	0	1	1	0	1	1	0	3	2	3	1	2	2	1	2	2	2	4	6			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr17:27614566A>G	ENST00000225388.4	-	2	504	c.446T>C	c.(445-447)aTt>aCt	p.I149T	NUFIP2_ENST00000579665.1_Intron	NM_020772.2	NP_065823.1	Q7Z417	NUFP2_HUMAN	nuclear fragile X mental retardation protein interacting protein 2	149						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)			CTTGGTTTTAATTCCTGCTTT	0.408																																					p.I149T		Atlas-SNP	.											.	NUFIP2	60	.	0			c.T446C						PASS	.						121	120	121					17																	27614566		2203	4300	6503	SO:0001583	missense	57532	exon2			GTTTTAATTCCTG	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.446T>C	chr17.hg19:g.27614566A>G	ENSP00000225388:p.Ile149Thr	60.0	0.0	.		67.0	4.0	.	NM_020772	A1L3A6|Q9P2M5	Missense_Mutation	SNP	ENST00000225388.4	hg19	CCDS32600.1	.	.	.	.	.	.	.	.	.	.	A	12.71	2.020017	0.35606	.	.	ENSG00000108256	ENST00000225388	.	.	.	6.17	6.17	0.99709	.	0.134082	0.52532	D	0.000080	T	0.41328	0.1154	N	0.12182	0.205	0.80722	D	1	B	0.24721	0.11	B	0.25291	0.059	T	0.37384	-0.9708	9	0.56958	D	0.05	-12.34	12.6398	0.56702	0.8623:0.1377:0.0:0.0	.	149	Q7Z417	NUFP2_HUMAN	T	149	.	ENSP00000225388:I149T	I	-	2	0	NUFIP2	24638692	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.852000	0.55934	2.371000	0.80710	0.533000	0.62120	ATT	.	.	.	none		0.408	NUFIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447015.2	NM_020772		G	27614566	A	G	27614566	3	3	229	1	0	0	0	0	1	0	0	0	10756	101	4	3	1653	3	NUFIP2	17	27614566	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10	643403	27614566	53580644	86	13914											
KLHL11	55175	hgsc.bcm.edu	37	chr17	40011371	40011371	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caaatctgaaagccagtctcTaatgagatggaaaggtaacg	16	8	10	7	1	2	2	0	2	2	1	3	4	2	3	1	2	2	1	1	2	5	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr17:40011371T>C	ENST00000319121.3	-	2	808	c.748A>G	c.(748-750)Aga>Gga	p.R250G		NM_018143.1	NP_060613.1	Q9NVR0	KLH11_HUMAN	kelch-like family member 11	250	BACK.									NS(2)|breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	17		Breast(137;0.00156)				AGCCAGTCTCTAATGAGATGG	0.398																																					p.R250G		Atlas-SNP	.											.	KLHL11	44	.	0			c.A748G						PASS	.						57	58	58					17																	40011371		2203	4300	6503	SO:0001583	missense	55175	exon2			AGTCTCTAATGAG		CCDS11411.1	17q21	2013-01-30	2013-01-30		ENSG00000178502	ENSG00000178502		"Kelch-like", "BTB/POZ domain containing"	19008	protein-coding gene	gene with protein product			"kelch-like 11 (Drosophila)"				Standard	NM_018143		Approved	FLJ10572	uc002hyf.1	Q9NVR0	OTTHUMG00000133506	ENST00000319121.3:c.748A>G	chr17.hg19:g.40011371T>C	ENSP00000314608:p.Arg250Gly	64.0	0.0	.		61.0	33.0	.	NM_018143		Missense_Mutation	SNP	ENST00000319121.3	hg19	CCDS11411.1	.	.	.	.	.	.	.	.	.	.	T	6.149	0.395748	0.11638	.	.	ENSG00000178502	ENST00000319121;ENST00000540254	T	0.69040	-0.37	4.99	4.01	0.46588	BTB/Kelch-associated (2);	0.068566	0.56097	D	0.000034	T	0.48892	0.1525	N	0.20986	0.625	0.50313	D	0.999866	P	0.46142	0.873	B	0.38264	0.269	T	0.41215	-0.9521	10	0.21540	T	0.41	-2.2119	13.3418	0.60549	0.0:0.0:0.5227:0.4773	.	250	Q9NVR0	KLH11_HUMAN	G	250;113	ENSP00000314608:R250G	ENSP00000314608:R250G	R	-	1	2	KLHL11	37264897	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.686000	0.37669	1.055000	0.40461	-0.452000	0.05504	AGA	.	.	.	none		0.398	KLHL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257464.2	NM_018143		C	40011371	T	C	40011371	3	2	229	1	0	0	0	0	1	0	0	0	8374	1530	53	3	1382	3	KLHL11	17	40011371	Missense_Mutation	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10	12396805	40011371	41183839	87	13915											
KAT2A	2648	hgsc.bcm.edu	37	chr17	40269761	40269761	+	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	ctcattgaccagctccatggGgatgtcacccatcacacgga	10	8	9	14	1	3	1	3	1	0	0	4	3	4	3	3	3	1	1	3	3	0	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr17:40269761G>C	ENST00000225916.5	-	9	1416	c.1363C>G	c.(1363-1365)Ccc>Gcc	p.P455A		NM_021078.2	NP_066564.2	Q92830	KAT2A_HUMAN	K(lysine) acetyltransferase 2A	455					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						AGCTCCATGGGGATGTCACCC	0.627																																					p.P455A		Atlas-SNP	.											.	KAT2A	54	.	0			c.C1363G						PASS	.						43	36	39					17																	40269761		2203	4300	6503	SO:0001583	missense	2648	exon9			CCATGGGGATGTC	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.1363C>G	chr17.hg19:g.40269761G>C	ENSP00000225916:p.Pro455Ala	107.0	0.0	.		132.0	53.0	.	NM_021078	Q8N1A2|Q9UCW1	Missense_Mutation	SNP	ENST00000225916.5	hg19	CCDS11417.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.470462	0.84533	.	.	ENSG00000108773	ENST00000225916	T	0.08634	3.07	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	T	0.31979	0.0814	M	0.84683	2.71	0.80722	D	1	D	0.61080	0.989	D	0.63192	0.912	T	0.28744	-1.0034	10	0.72032	D	0.01	-17.8967	17.6406	0.88135	0.0:0.0:1.0:0.0	.	455	Q92830	KAT2A_HUMAN	A	455	ENSP00000225916:P455A	ENSP00000225916:P455A	P	-	1	0	KAT2A	37523287	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.811000	0.99226	2.164000	0.68074	0.561000	0.74099	CCC	.	.	.	none		0.627	KAT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257458.1	NM_021078		C	40269761	G	C	40269761	3	2	229	1	0	0	0	0	1	0	0	0	7988	1232	43	4	1190	4	KAT2A	17	40269761	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	258390	40269761	40925449	88	13916											
MYST2	11143	hgsc.bcm.edu	37	chr17	47869395	47869395	+	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	ggctaagccagagttctcaaGgtaaaaaaaccttcattttt	14	12	7	8	0	2	1	2	0	1	1	3	1	2	1	2	2	2	3	2	2	6	6			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr17:47869395G>A	ENST00000259021.4	+	2	443	c.163G>A	c.(163-165)Gat>Aat	p.D55N	KAT7_ENST00000503935.2_5'UTR|KAT7_ENST00000454930.2_Splice_Site_p.G55R|KAT7_ENST00000510819.1_Splice_Site_p.G55R|KAT7_ENST00000424009.2_Splice_Site_p.D55N|KAT7_ENST00000435742.2_5'UTR|KAT7_ENST00000509773.1_Splice_Site_p.D55N	NM_007067.4	NP_008998.1	O95251	KAT7_HUMAN	K(lysine) acetyltransferase 7	55	Ser-rich.				chromatin organization (GO:0006325)|DNA replication (GO:0006260)|histone H3 acetylation (GO:0043966)|histone H4-K12 acetylation (GO:0043983)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										GAGTTCTCAAGGTAAAAAAAC	0.493																																					p.G55R		Atlas-SNP	.											.	.	.	.	0			c.G163A						PASS	.						72	69	70					17																	47869395		2203	4300	6503	SO:0001630	splice_region_variant	11143	exon2			TCTCAAGGTAAAA	AF074606	CCDS11554.1, CCDS56035.1, CCDS56036.1, CCDS56037.1, CCDS56038.1	17q21.32	2013-01-10	2011-07-21	2011-07-21	ENSG00000136504	ENSG00000136504	2.3.1.48	"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing"	17016	protein-coding gene	gene with protein product	"histone acetyltransferase binding to ORC1"	609880	"MYST histone acetyltransferase 2"	MYST2		10438470, 10930412	Standard	NM_001199155		Approved	HBOA, HBO1, ZC2HC7	uc002ipm.3	O95251	OTTHUMG00000161770	ENST00000259021.4:c.163+1G>A	chr17.hg19:g.47869395G>A		25.0	0.0	.		36.0	11.0	.	NM_001199158	B3KN74|B4DF85|B4DFB4|B4DFE0|B4DGY4|E7ER15|G5E9K7	Missense_Mutation	SNP	ENST00000259021.4	hg19	CCDS11554.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.224482|5.224482	0.95139|0.95139	.|.	.|.	ENSG00000136504|ENSG00000136504	ENST00000259021;ENST00000509773;ENST00000424009|ENST00000454930;ENST00000510819	.|.	.|.	.|.	5.56|5.56	5.56|5.56	0.83823|0.83823	.|.	0.153798|.	0.56097|.	D|.	0.000026|.	T|T	0.76385|0.76385	0.3980|0.3980	L|L	0.50333|0.50333	1.59|1.59	0.80722|0.80722	D|D	1|1	D;B;D|D;D	0.60575|0.89917	0.98;0.281;0.988|1.0;1.0	D;B;D|D;D	0.73708|0.97110	0.956;0.083;0.981|1.0;1.0	T|T	0.77747|0.77747	-0.2472|-0.2472	9|8	0.09843|0.87932	T|D	0.71|0	-15.7574|-15.7574	19.1747|19.1747	0.93599|0.93599	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	55;55;55|55;55	B4DFB4;O95251;G5E9K7|B4DFE0;E7ER15	.;KAT7_HUMAN;.|.;.	N|R	55|55	.|.	ENSP00000259021:D55N|ENSP00000413415:G55R	D|G	+|+	1|1	0|0	KAT7|KAT7	45224394|45224394	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	9.448000|9.448000	0.97600|0.97600	2.623000|2.623000	0.88846|0.88846	0.650000|0.650000	0.86243|0.86243	GAT|GGA	.	.	.	none		0.493	KAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366032.1	NM_007067	Missense_Mutation	A	47869395	G	A	47869395	5	1	229	1	0	0	0	0	0	0	1	0	10110	1014	35	2	169	2	MYST2	17	47869395	Splice_Site	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	7599634	47869395	33325815	89	13917											
FAM59A	64762	hgsc.bcm.edu	37	chr18	29867165	29867165	+	Frame_Shift_Del	DEL	A	A	-																															agagagcgagtgagaggctgAtggctgggcttgccttcctc																										TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr18:29867165delA	ENST00000269209.6	-	4	1398	c.1395delT	c.(1393-1395)catfs	p.H465fs	GAREM_ENST00000399218.4_Frame_Shift_Del_p.H465fs|GAREM_ENST00000578619.1_5'Flank|RP11-344B2.2_ENST00000579580.1_RNA			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	465					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)										TGAGAGGCTGATGGCTGGGCT	0.527																																					p.Q466fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.1396delC						PASS	.						104	102	103					18																	29867165		2203	4300	6503	SO:0001589	frameshift_variant	64762	exon4			.	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.1395delT	chr18.hg19:g.29867165delA	ENSP00000269209:p.His465fs	93.0	0.0	0		66.0	27.0	0.409091	NM_022751	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	Frame_Shift_Del	DEL	ENST00000269209.6	hg19	CCDS56057.1																																																																																			.	.	.	none		0.527	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255365.1	NM_022751		-	29867165	A	-	29867165	7	5	229	1	0	1	0	1	0	0	0	0	5599	330	12	0	1244	0	FAM59A	18	29867165	Frame_Shift_Del	DEL	A	TCGA-P4-A5E6-01A-11D-A28G-10		29867165	48210083	90	13918											
CELF5	60680	hgsc.bcm.edu	37	chr19	3285978	3285978	+	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	ccatcacgcccatcgcgcacAgcgtcccccagccgccgccc	6	3	8	24	6	1	0	1	0	0	0	3	0	2	0	7	0	2	1	7	0	0	0			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr19:3285978A>T	ENST00000292672.2	+	10	1178	c.1141A>T	c.(1141-1143)Agc>Tgc	p.S381C	CELF5_ENST00000588101.1_3'UTR|CELF5_ENST00000541430.2_Missense_Mutation_p.S356C	NM_021938.3	NP_068757.2	Q8N6W0	CELF5_HUMAN	CUGBP, Elav-like family member 5	381					mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)	13						CATCGCGCACAGCGTCCCCCA	0.756																																					p.S381C		Atlas-SNP	.											.	CELF5	32	.	0			c.A1141T						PASS	.						12	12	12					19																	3285978		2081	4145	6226	SO:0001583	missense	60680	exon10			GCGCACAGCGTCC	AF248649	CCDS12106.1, CCDS54197.1	19p13	2013-02-12	2010-02-19	2010-02-19		ENSG00000161082		"RNA binding motif (RRM) containing"	14058	protein-coding gene	gene with protein product		612680	"Bruno (Drosophila) -like 5, RNA binding protein", "bruno-like 5, RNA binding protein (Drosophila)"	BRUNOL5		10893231	Standard	NM_001172673		Approved		uc002lxm.3	Q8N6W0		ENST00000292672.2:c.1141A>T	chr19.hg19:g.3285978A>T	ENSP00000292672:p.Ser381Cys	4.0	0.0	.		67.0	37.0	.	NM_021938	D6W614|O75253|Q59GP2|Q86VW6|Q9BZC0|Q9NR86	Missense_Mutation	SNP	ENST00000292672.2	hg19	CCDS12106.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.488587	0.84854	.	.	ENSG00000161082	ENST00000292672;ENST00000541430;ENST00000334293	T;T;T	0.51071	0.72;1.66;1.56	4.15	4.15	0.48705	.	0.325407	0.28841	N	0.013971	T	0.53867	0.1823	L	0.36672	1.1	0.37559	D	0.919007	D;D;P	0.76494	0.985;0.999;0.944	P;D;P	0.63192	0.731;0.912;0.662	T	0.61451	-0.7060	10	0.62326	D	0.03	-4.5717	11.4083	0.49911	1.0:0.0:0.0:0.0	.	267;356;381	B4DFI3;Q8N6W0-2;Q8N6W0	.;.;CELF5_HUMAN	C	381;356;267	ENSP00000292672:S381C;ENSP00000443498:S356C;ENSP00000335182:S267C	ENSP00000292672:S381C	S	+	1	0	CELF5	3236978	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.948000	0.49066	1.666000	0.50821	0.402000	0.26972	AGC	.	.	.	none		0.756	CELF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452574.1	NM_021938		T	3285978	A	T	3285978	3	4	229	1	0	0	0	0	1	0	0	0	3221	188	7	5	1179	5	CELF5	19	3285978	Missense_Mutation	SNP	A	TCGA-P4-A5E6-01A-11D-A28G-10		3285978	55843005	91	13919											
ATP13A1	57130	hgsc.bcm.edu	37	chr19	19758062	19758062	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtaggccaggatgagggcaTtgagcgccaggatcttgaac	10	8	15	8	1	1	3	0	3	1	0	1	5	1	5	2	4	2	2	2	4	2	3			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr19:19758062T>C	ENST00000357324.6	-	22	3007	c.2981A>G	c.(2980-2982)aAt>aGt	p.N994S	ATP13A1_ENST00000291503.5_Missense_Mutation_p.N876S	NM_020410.2	NP_065143.2	Q9HD20	AT131_HUMAN	ATPase type 13A1	994						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						GATGAGGGCATTGAGCGCCAG	0.632																																					p.N994S	Esophageal Squamous(142;920 1789 9047 14684 24777)	Atlas-SNP	.											.	ATP13A1	82	.	0			c.A2981G						PASS	.						108	109	109					19																	19758062		2203	4300	6503	SO:0001583	missense	57130	exon22			AGGGCATTGAGCG	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.2981A>G	chr19.hg19:g.19758062T>C	ENSP00000349877:p.Asn994Ser	63.0	0.0	.		99.0	19.0	.	NM_020410	B3KPJ2|B3KTA7|Q6NT90|Q6ZMG7|Q9H6C6	Missense_Mutation	SNP	ENST00000357324.6	hg19	CCDS32970.2	.	.	.	.	.	.	.	.	.	.	T	22.3	4.274546	0.80580	.	.	ENSG00000105726	ENST00000291503;ENST00000357324	D;D	0.88354	-2.37;-2.37	4.75	4.75	0.60458	.	0.000000	0.85682	D	0.000000	D	0.91784	0.7401	M	0.75264	2.295	0.80722	D	1	D;D	0.59357	0.974;0.985	P;P	0.61592	0.78;0.891	D	0.89608	0.3839	10	0.11794	T	0.64	-19.537	12.2865	0.54795	0.0:0.0:0.0:1.0	.	994;876	Q9HD20;Q9HD20-2	AT131_HUMAN;.	S	876;994	ENSP00000291503:N876S;ENSP00000349877:N994S	ENSP00000291503:N876S	N	-	2	0	ATP13A1	19619062	1.000000	0.71417	0.855000	0.33649	0.995000	0.86356	7.576000	0.82467	1.789000	0.52484	0.529000	0.55759	AAT	.	.	.	none		0.632	ATP13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329005.1	NM_020410		C	19758062	T	C	19758062	3	2	229	1	0	0	0	0	1	0	0	0	1123	1493	52	3	653	3	ATP13A1	19	19758062	Missense_Mutation	SNP	T	TCGA-P4-A5E6-01A-11D-A28G-10	16472084	19758062	39370921	92	13920											
GRAMD1A	57655	hgsc.bcm.edu	37	chr19	35506763	35506763	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcttcccgacctctccggcCgcctcctcatcaactctgtc	4	11	6	20	3	4	0	2	0	2	0	8	1	6	0	6	1	2	1	6	1	1	1			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr19:35506763C>T	ENST00000317991.5	+	11	1297	c.1105C>T	c.(1105-1107)Cgc>Tgc	p.R369C	GRAMD1A_ENST00000411896.2_Missense_Mutation_p.R362C|GRAMD1A_ENST00000599564.1_Missense_Mutation_p.R456C|GRAMD1A_ENST00000504615.2_Missense_Mutation_p.R135C|CTD-2527I21.14_ENST00000605640.1_RNA	NM_020895.3	NP_065946.2	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A	369						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)			CCTCTCCGGCCGCCTCCTCAT	0.642																																					p.R369C		Atlas-SNP	.											.	GRAMD1A	39	.	0			c.C1105T						PASS	.						39	44	42					19																	35506763		2115	4223	6338	SO:0001583	missense	57655	exon11			TCCGGCCGCCTCC	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.1105C>T	chr19.hg19:g.35506763C>T	ENSP00000441032:p.Arg369Cys	93.0	0.0	.		106.0	43.0	.	NM_020895	A6NKY7|Q8NC77|Q9P1Z5	Missense_Mutation	SNP	ENST00000317991.5	hg19	CCDS42546.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.127959	0.77549	.	.	ENSG00000089351	ENST00000453966;ENST00000504615;ENST00000317991;ENST00000411896	T;T;T	0.60548	0.18;1.34;1.3	5.01	5.01	0.66863	.	0.067735	0.64402	D	0.000013	T	0.75398	0.3844	M	0.82323	2.585	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.80764	0.96;0.994;0.917;0.975	T	0.78443	-0.2202	10	0.87932	D	0	.	10.8825	0.46946	0.1875:0.8125:0.0:0.0	.	369;369;135;362	Q96CP6-3;Q96CP6;B3KQF7;Q96CP6-2	.;GRM1A_HUMAN;.;.	C	455;135;369;362	ENSP00000423728:R135C;ENSP00000441032:R369C;ENSP00000439267:R362C	ENSP00000441032:R369C	R	+	1	0	GRAMD1A	40198603	1.000000	0.71417	0.997000	0.53966	0.988000	0.76386	3.193000	0.50997	2.615000	0.88500	0.555000	0.69702	CGC	.	.	.	none		0.642	GRAMD1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461557.1	NM_020895		T	35506763	C	T	35506763	3	4	229	1	0	0	0	0	1	0	0	0	6754	652	23	1	1147	1	GRAMD1A	19	35506763	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	15748701	35506763	23622220	93	13921											
RSPH6A	81492	hgsc.bcm.edu	37	chr19	46305454	46305454	+	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	tctggcccctcatctgccttCtcttcctcctcccccaggtc	2	13	5	21	0	4	0	1	0	3	0	9	0	7	0	7	2	1	0	7	2	0	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr19:46305454C>G	ENST00000221538.3	-	4	1864	c.1722G>C	c.(1720-1722)gaG>gaC	p.E574D	RSPH6A_ENST00000597055.1_Missense_Mutation_p.E574D|RSPH6A_ENST00000600188.1_Missense_Mutation_p.E310D	NM_030785.3	NP_110412.1	Q9H0K4	RSH6A_HUMAN	radial spoke head 6 homolog A (Chlamydomonas)	574	Glu-rich.					intracellular (GO:0005622)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	32						catctgccttctcttcctcct	0.622																																					p.E574D		Atlas-SNP	.											.	RSPH6A	70	.	0			c.G1722C						PASS	.						111	73	86					19																	46305454		2203	4300	6503	SO:0001583	missense	81492	exon4			TGCCTTCTCTTCC	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.1722G>C	chr19.hg19:g.46305454C>G	ENSP00000221538:p.Glu574Asp	107.0	0.0	.		139.0	50.0	.	NM_030785	Q53FE2|Q6PEZ9	Missense_Mutation	SNP	ENST00000221538.3	hg19	CCDS12675.1	.	.	.	.	.	.	.	.	.	.	C	11.81	1.748680	0.30955	.	.	ENSG00000104941	ENST00000221538	T	0.19806	2.12	4.27	2.08	0.27032	.	0.108659	0.64402	D	0.000011	T	0.15912	0.0383	L	0.48986	1.54	0.27895	N	0.939171	P	0.41978	0.767	B	0.38985	0.287	T	0.08827	-1.0703	10	0.26408	T	0.33	-9.2878	6.3085	0.21151	0.0:0.764:0.0:0.236	.	574	Q9H0K4	RSH6A_HUMAN	D	574	ENSP00000221538:E574D	ENSP00000221538:E574D	E	-	3	2	RSPH6A	50997294	0.980000	0.34600	1.000000	0.80357	0.407000	0.30961	0.054000	0.14205	0.710000	0.31997	-0.390000	0.06520	GAG	.	.	.	none		0.622	RSPH6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461657.1			G	46305454	C	G	46305454	3	3	229	1	0	0	0	0	1	0	0	0	13720	912	32	4	443	4	RSPH6A	19	46305454	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	10798691	46305454	12823529	94	13922											
GLTSCR1	29998	hgsc.bcm.edu	37	chr19	48183987	48183987	+	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	atcctcacaaaccagaacctGgcgggcccactgagcctggg	10	5	11	15	1	1	2	1	1	0	1	2	2	2	2	5	3	3	0	5	3	2	0	rs377326337		TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr19:48183987G>T	ENST00000396720.3	+	6	1754	c.1560G>T	c.(1558-1560)ctG>ctT	p.L520L	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	520										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)		ACCAGAACCTGGCGGGCCCAC	0.726																																					p.L520L		Atlas-SNP	.											.	GLTSCR1	79	.	0			c.G1560T						PASS	.						26	32	30					19																	48183987		1884	4062	5946	SO:0001819	synonymous_variant	29998	exon6			GAACCTGGCGGGC	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.1560G>T	chr19.hg19:g.48183987G>T		25.0	0.0	.		108.0	42.0	.	NM_015711	A8MW01	Silent	SNP	ENST00000396720.3	hg19	CCDS46134.1																																																																																			.	.	.	alt		0.726	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711		T	48183987	G	T	48183987	2	4	229	1	0	0	0	0	0	0	0	1	6481	1335	47	4		4	GLTSCR1	19	48183987	Silent	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10	1878533	48183987	10944996	95	13923											
ZBTB46	140685	hgsc.bcm.edu	37	chr20	62378613	62378613	+	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	gcggcggacatgaagacgcgGctgcacaccttgcacacata	11	5	12	13	4	0	2	0	1	0	1	0	3	0	3	1	3	2	3	1	3	2	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr20:62378613G>T	ENST00000245663.4	-	5	1590	c.1440C>A	c.(1438-1440)agC>agA	p.S480R	ZBTB46_ENST00000302995.2_Missense_Mutation_p.S480R|ZBTB46_ENST00000395104.1_Missense_Mutation_p.S480R|RP4-583P15.10_ENST00000447343.2_RNA|RP4-583P15.10_ENST00000433905.2_RNA	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	480					negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					TGAAGACGCGGCTGCACACCT	0.701																																					p.S480R		Atlas-SNP	.											.	ZBTB46	72	.	0			c.C1440A						PASS	.						9	7	8					20																	62378613		2124	4163	6287	SO:0001583	missense	140685	exon5			GACGCGGCTGCAC	AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16094	protein-coding gene	gene with protein product	"BTB-ZF protein expressed in effector lymphocytes"	614639	"BTB (POZ) domain containing 4"	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.1440C>A	chr20.hg19:g.62378613G>T	ENSP00000245663:p.Ser480Arg	64.0	0.0	.		138.0	52.0	.	NM_025224	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Missense_Mutation	SNP	ENST00000245663.4	hg19	CCDS13538.1	.	.	.	.	.	.	.	.	.	.	G	14.61	2.585999	0.46110	.	.	ENSG00000130584	ENST00000245663;ENST00000302995;ENST00000395104	T;T;T	0.15487	2.42;2.42;2.42	4.29	3.16	0.36331	Zinc finger, C2H2-like (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.174840	0.48767	D	0.000179	T	0.11793	0.0287	L	0.28504	0.86	0.46336	D	0.998998	P	0.38048	0.616	B	0.35278	0.199	T	0.09509	-1.0671	10	0.39692	T	0.17	.	10.1961	0.43056	0.1118:0.0:0.8882:0.0	.	480	Q86UZ6	ZBT46_HUMAN	R	480	ENSP00000245663:S480R;ENSP00000303102:S480R;ENSP00000378536:S480R	ENSP00000245663:S480R	S	-	3	2	ZBTB46	61849057	1.000000	0.71417	0.991000	0.47740	0.822000	0.46500	2.148000	0.42235	0.504000	0.28082	0.462000	0.41574	AGC	.	.	.	none		0.701	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224		T	62378613	G	T	62378613	3	4	229	1	0	0	0	0	1	0	0	0	17559	1194	42	4	333	4	ZBTB46	20	62378613	Missense_Mutation	SNP	G	TCGA-P4-A5E6-01A-11D-A28G-10		62378613	646907	96	13924											
MICAL3	57553	hgsc.bcm.edu	37	chr22	18300505	18300505	+	Frame_Shift_Del	DEL	T	T	-																															caggccggcgctccttgcccTgggagggtgctgaggacgcc																										TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr22:18300505delT	ENST00000441493.2	-	26	5274	c.4922delA	c.(4921-4923)cagfs	p.Q1641fs	MICAL3_ENST00000580469.1_5'Flank	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	1641					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)		CTCCTTGCCCTGGGAGGGTGC	0.711																																					p.Q1641fs		Atlas-INDEL	.											.	MICAL3	53	.	0			c.4923delG						PASS	.						13	18	16					22																	18300505		1932	4104	6036	SO:0001589	frameshift_variant	57553	exon26			.	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.4922delA	chr22.hg19:g.18300505delT	ENSP00000416015:p.Gln1641fs	4.0	0.0	0		29.0	12.0	0.413793	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Frame_Shift_Del	DEL	ENST00000441493.2	hg19	CCDS46659.1																																																																																			.	.	.	none		0.711	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			-	18300505	T	-	18300505	7	5	229	1	0	1	0	1	0	0	0	0	9578	1580	55	0	1114	0	MICAL3	22	18300505	Frame_Shift_Del	DEL	T	TCGA-P4-A5E6-01A-11D-A28G-10		18300505	33004061	97	13925											
RRP7A	27341	hgsc.bcm.edu	37	chr22	42912080	42912080	+	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	gggctctcagccaggtccggCttctcctgcaactctacaga	7	9	10	15	1	3	1	1	0	3	1	6	1	4	1	3	3	4	3	3	3	2	2			TCGA-P4-A5E6-01A-11D-A28G-10	TCGA-P4-A5E6-11A-22D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c543688-1b5c-4af6-806b-9c9e444a740f	5b0f01b3-0aee-4950-87e0-0a6c395d73a4	g.chr22:42912080C>A	ENST00000323013.6	-	3	294	c.279G>T	c.(277-279)aaG>aaT	p.K93N		NM_015703.4	NP_056518.2	Q9Y3A4	RRP7A_HUMAN	ribosomal RNA processing 7 homolog A (S. cerevisiae)	93							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						CCAGGTCCGGCTTCTCCTGCA	0.617																																					p.K93N		Atlas-SNP	.											.	RRP7A	25	.	0			c.G279T						PASS	.						57	51	53					22																	42912080		2203	4300	6503	SO:0001583	missense	27341	exon3			GTCCGGCTTCTCC	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.279G>T	chr22.hg19:g.42912080C>A	ENSP00000321449:p.Lys93Asn	119.0	0.0	.		121.0	50.0	.	NM_015703	A4FTX2|B2RBG4|Q0VAD0|Q5JZ94|Q6P4B5|Q8IVR9|Q8IVY0|Q8N5Q3|Q8NEY6|Q9Y3H5	Missense_Mutation	SNP	ENST00000323013.6	hg19	CCDS14036.1	.	.	.	.	.	.	.	.	.	.	C	12.33	1.907011	0.33628	.	.	ENSG00000189306	ENST00000323013	T	0.15952	2.38	3.93	2.9	0.33743	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.106611	0.64402	D	0.000007	T	0.30103	0.0754	M	0.72576	2.205	0.51012	D	0.999906	D	0.56035	0.974	P	0.55577	0.779	T	0.03818	-1.1001	10	0.72032	D	0.01	-34.7209	8.4778	0.33023	0.0:0.7373:0.0:0.2627	.	93	Q9Y3A4	RRP7A_HUMAN	N	93	ENSP00000321449:K93N	ENSP00000321449:K93N	K	-	3	2	RRP7A	41242024	1.000000	0.71417	0.993000	0.49108	0.007000	0.05969	0.731000	0.26058	0.946000	0.37632	-0.346000	0.07831	AAG	.	.	.	none		0.617	RRP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320451.1	NM_015703		A	42912080	C	A	42912080	3	1	229	1	0	0	0	0	1	0	0	0	13702	796	28	4	583	4	RRP7A	22	42912080	Missense_Mutation	SNP	C	TCGA-P4-A5E6-01A-11D-A28G-10	24611575	42912080	8392486	98	13926											
HMGCL	3155	hgsc.bcm.edu	37	chr1	24151846	24151846	+	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	cggcggctcggggcacttacAgcccggagggacgccaagcc	7	3	16	15	5	0	0	0	0	0	0	1	2	0	2	3	6	3	2	3	6	2	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr1:24151846A>G	ENST00000374490.3	-	1	103	c.60T>C	c.(58-60)gcT>gcC	p.A20A	HMGCL_ENST00000374483.4_Intron|HMGCL_ENST00000509389.1_5'UTR|HMGCL_ENST00000436439.2_Splice_Site_p.A20A	NM_000191.2	NP_000182.2	P35914	HMGCL_HUMAN	3-hydroxymethyl-3-methylglutaryl-CoA lyase	20					acyl-CoA metabolic process (GO:0006637)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|ketone body biosynthetic process (GO:0046951)|leucine catabolic process (GO:0006552)|liver development (GO:0001889)|mitochondrion organization (GO:0007005)|protein tetramerization (GO:0051262)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	carboxylic acid binding (GO:0031406)|fatty-acyl-CoA binding (GO:0000062)|hydroxymethylglutaryl-CoA lyase activity (GO:0004419)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	12		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;0.0044)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.38e-24)|Colorectal(126;5.58e-08)|COAD - Colon adenocarcinoma(152;3.12e-06)|GBM - Glioblastoma multiforme(114;4.9e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000982)|KIRC - Kidney renal clear cell carcinoma(1967;0.0034)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0856)|LUSC - Lung squamous cell carcinoma(448;0.188)		GGGCACTTACAGCCCGGAGGG	0.706																																					p.A20A		Atlas-SNP	.											.	HMGCL	22	.	0			c.T60C						PASS	.						10	11	10					1																	24151846		2085	4077	6162	SO:0001630	splice_region_variant	3155	exon1			ACTTACAGCCCGG	BC010570	CCDS243.1, CCDS53279.1	1p36.1-p35	2010-04-30	2010-04-30		ENSG00000117305	ENSG00000117305	4.1.3.4		5005	protein-coding gene	gene with protein product	"hydroxymethylglutaricaciduria"	613898	"3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase"			8102917, 8978493	Standard	NM_001166059		Approved	HL	uc001bib.3	P35914	OTTHUMG00000002963	ENST00000374490.3:c.60+1T>C	chr1.hg19:g.24151846A>G		8.0	0.0	.		87.0	27.0	.	NM_000191	B4DUP4|B7UCC6|D3Y5K7|Q6IBC0|Q96FP8	Silent	SNP	ENST00000374490.3	hg19	CCDS243.1	.	.	.	.	.	.	.	.	.	.	A	16.83	3.232145	0.58777	.	.	ENSG00000117305	ENST00000235958	.	.	.	5.66	2.13	0.27403	.	.	.	.	.	T	0.54549	0.1865	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45483	-0.9258	4	.	.	.	-1.3076	6.689	0.23161	0.7318:0.0:0.2682:0.0	.	.	.	.	P	16	.	.	L	-	2	0	HMGCL	24024433	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	0.764000	0.26532	0.516000	0.28340	0.533000	0.62120	CTG	.	.	.	none		0.706	HMGCL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008253.2	NM_000191	Silent	G	24151846	A	G	24151846	5	3	230	1	0	0	0	0	0	0	1	0	7236	202	7	3	953	3	HMGCL	1	24151846	Splice_Site	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10		24151846	225098775	1	13927											
SYNC	81493	hgsc.bcm.edu	37	chr1	33161106	33161106	+	Missense_Mutation	SNP	T	T	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	cccggagcaatacaagctcaTggatgagctgatccctctcc	10	8	9	14	1	2	2	1	2	1	0	4	4	3	4	3	2	4	3	3	2	3	1	rs554437078		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr1:33161106T>G	ENST00000409190.3	-	2	1051	c.593A>C	c.(592-594)cAt>cCt	p.H198P	SYNC_ENST00000373484.3_Missense_Mutation_p.H198P	NM_030786.2	NP_110413	Q9H7C4	SYNCI_HUMAN	syncoilin, intermediate filament protein	198	Coil 1A.				intermediate filament-based process (GO:0045103)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	structural molecule activity (GO:0005198)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12						TACAAGCTCATGGATGAGCTG	0.567																																					p.H198P		Atlas-SNP	.											.	SYNC	36	.	0			c.A593C						PASS	.						89	78	82					1																	33161106		692	1591	2283	SO:0001583	missense	81493	exon2			AGCTCATGGATGA	AK024707	CCDS367.2, CCDS53294.1	1p35.1	2013-01-16	2008-09-19	2008-09-19	ENSG00000162520	ENSG00000162520		"Intermediate filaments type III"	28897	protein-coding gene	gene with protein product		611750	"syncoilin, intermediate filament 1"	SYNC1		11053421	Standard	NM_030786		Approved	SYNCOILIN	uc001bvt.2	Q9H7C4	OTTHUMG00000008087	ENST00000409190.3:c.593A>C	chr1.hg19:g.33161106T>G	ENSP00000386439:p.His198Pro	131.0	0.0	.		88.0	24.0	.	NM_001161708	B4DNK8|B4DY58|C9IY41	Missense_Mutation	SNP	ENST00000409190.3	hg19	CCDS367.2	.	.	.	.	.	.	.	.	.	.	T	16.44	3.123508	0.56613	.	.	ENSG00000162520	ENST00000373484;ENST00000409190	T;T	0.24350	1.86;1.86	4.57	4.57	0.56435	Filament (1);	.	.	.	.	T	0.27559	0.0677	N	0.14661	0.345	0.31839	N	0.623691	D;D	0.76494	0.998;0.999	P;D	0.75020	0.905;0.985	T	0.17471	-1.0368	9	0.31617	T	0.26	-9.3582	5.8491	0.18683	0.0:0.0877:0.1689:0.7435	.	198;198	Q9H7C4-2;Q9H7C4	.;SYNCI_HUMAN	P	198	ENSP00000362583:H198P;ENSP00000386439:H198P	ENSP00000362583:H198P	H	-	2	0	SYNC	32933693	0.988000	0.35896	0.997000	0.53966	0.958000	0.62258	1.916000	0.39986	1.853000	0.53794	0.459000	0.35465	CAT	.	.	.	none		0.567	SYNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022129.3	NM_030786		G	33161106	T	G	33161106	3	3	230	1	0	0	0	0	1	0	0	0	15455	1464	51	5	933	5	SYNC	1	33161106	Missense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10	9009260	33161106	216089515	2	13928											
ZC3H12A	80149	hgsc.bcm.edu	37	chr1	37949045	37949045	+	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	ctggcaggagcccgtggggcAgggcaggcagcctggccaag	7	3	19	12	1	0	0	0	0	0	0	0	1	0	1	3	7	2	4	3	7	1	0			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr1:37949045A>T	ENST00000373087.6	+	6	1749	c.1633A>T	c.(1633-1635)Agg>Tgg	p.R545W		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)				CCCGTGGGGCAGGGCAGGCAG	0.647																																					p.R545W		Atlas-SNP	.											.	ZC3H12A	58	.	0			c.A1633T						PASS	.						48	58	55					1																	37949045		2203	4300	6503	SO:0001583	missense	80149	exon6			TGGGGCAGGGCAG		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.1633A>T	chr1.hg19:g.37949045A>T	ENSP00000362179:p.Arg545Trp	135.0	0.0	.		196.0	53.0	.	NM_025079		Missense_Mutation	SNP	ENST00000373087.6	hg19	CCDS417.1	.	.	.	.	.	.	.	.	.	.	A	12.75	2.033050	0.35893	.	.	ENSG00000163874	ENST00000373087;ENST00000373082	T	0.45668	0.89	5.15	2.9	0.33743	.	0.653715	0.14763	N	0.299862	T	0.37544	0.1007	N	0.22421	0.69	0.09310	N	0.999998	D;P	0.59767	0.986;0.923	P;B	0.52554	0.702;0.221	T	0.14868	-1.0457	10	0.66056	D	0.02	-9.4135	7.823	0.29298	0.2651:0.0:0.7349:0.0	.	340;545	B3KSD3;Q5D1E8	.;ZC12A_HUMAN	W	545	ENSP00000362179:R545W	ENSP00000362174:R545W	R	+	1	2	ZC3H12A	37721632	0.000000	0.05858	0.097000	0.21041	0.675000	0.39556	0.003000	0.13083	0.284000	0.22305	0.459000	0.35465	AGG	.	.	.	none		0.647	ZC3H12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012154.2	NM_025079		T	37949045	A	T	37949045	3	4	230	1	0	0	0	0	1	0	0	0	17573	179	7	5	1651	5	ZC3H12A	1	37949045	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	4787939	37949045	211301576	3	13929											
KTI12	112970	hgsc.bcm.edu	37	chr1	52499078	52499078	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttctcgttcgcgcccgccAcctgaggtcccgcgatcggg	3	8	14	16	7	1	1	0	1	1	0	5	2	2	1	4	3	0	2	4	3	0	2	rs563103084|rs377187997	byFrequency	TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr1:52499078A>G	ENST00000371614.1	-	1	410	c.356T>C	c.(355-357)gTg>gCg	p.V119A	RP11-91A18.4_ENST00000425802.1_RNA|TXNDC12_ENST00000371626.4_Intron	NM_138417.2	NP_612426.1	Q96EK9	KTI12_HUMAN	KTI12 homolog, chromatin associated (S. cerevisiae)	119							ATP binding (GO:0005524)			central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)|ovary(1)|stomach(2)|urinary_tract(1)	12						CGCGCCCGCCACCTGAGGTCC	0.721																																					p.V119A		Atlas-SNP	.											.	KTI12	30	.	0			c.T356C						PASS	.						28	34	32					1																	52499078		2194	4277	6471	SO:0001583	missense	112970	exon1			CCCGCCACCTGAG		CCDS562.1	1p32.3	2008-02-05			ENSG00000198841	ENSG00000198841			25160	protein-coding gene	gene with protein product						11929532	Standard	NM_138417		Approved	TOT4, MGC20419, SBBI81	uc001ctj.1	Q96EK9	OTTHUMG00000008630	ENST00000371614.1:c.356T>C	chr1.hg19:g.52499078A>G	ENSP00000360676:p.Val119Ala	1.0	0.0	.		43.0	13.0	.	NM_138417		Missense_Mutation	SNP	ENST00000371614.1	hg19	CCDS562.1	.	.	.	.	.	.	.	.	.	.	A	9.740	1.164503	0.21538	.	.	ENSG00000198841	ENST00000371614	T	0.39997	1.05	4.93	-9.87	0.00470	.	.	.	.	.	T	0.11750	0.0286	N	0.04880	-0.145	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.15150	-1.0447	9	0.05959	T	0.93	.	2.3401	0.04257	0.1327:0.1704:0.3566:0.3403	.	119	Q96EK9	KTI12_HUMAN	A	119	ENSP00000360676:V119A	ENSP00000360676:V119A	V	-	2	0	KTI12	52271666	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-2.926000	0.00691	-2.213000	0.00735	-0.256000	0.11100	GTG	.	.	.	none		0.721	KTI12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023821.1	NM_138417		G	52499078	A	G	52499078	3	3	230	1	0	0	0	0	1	0	0	0	8591	159	6	3	712	3	KTI12	1	52499078	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	14550033	52499078	196751543	4	13930											
DHCR24	1718	hgsc.bcm.edu	37	chr1	55317995	55317995	+	Missense_Mutation	SNP	A	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	tcgcagcttgtggtacaaggAgccatcaaacatctcccaga	12	8	9	12	1	2	1	1	0	1	1	4	2	2	2	2	2	4	3	2	2	3	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr1:55317995A>C	ENST00000371269.3	-	9	1560	c.1462T>G	c.(1462-1464)Tcc>Gcc	p.S488A	DHCR24_ENST00000537443.1_Missense_Mutation_p.S272A|DHCR24_ENST00000535035.1_Missense_Mutation_p.S447A	NM_014762.3	NP_055577.1	Q15392	DHC24_HUMAN	24-dehydrocholesterol reductase	488					amyloid precursor protein catabolic process (GO:0042987)|apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cholesterol biosynthetic process (GO:0006695)|male genitalia development (GO:0030539)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|oxidation-reduction process (GO:0055114)|plasminogen activation (GO:0031639)|protein localization (GO:0008104)|Ras protein signal transduction (GO:0007265)|regulation of neuron death (GO:1901214)|response to hormone (GO:0009725)|response to oxidative stress (GO:0006979)|skin development (GO:0043588)|small molecule metabolic process (GO:0044281)|tissue development (GO:0009888)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	delta24(24-1) sterol reductase activity (GO:0000246)|delta24-sterol reductase activity (GO:0050614)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)|peptide antigen binding (GO:0042605)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			large_intestine(2)|liver(1)|lung(1)|pancreas(1)|prostate(1)|skin(1)	7						TGGTACAAGGAGCCATCAAAC	0.597																																					p.S488A	Pancreas(39;516 1021 24601 30715 32780)	Atlas-SNP	.											.	DHCR24	31	.	0			c.T1462G						PASS	.						141	123	130					1																	55317995		2203	4300	6503	SO:0001583	missense	1718	exon9			ACAAGGAGCCATC	AF261758	CCDS600.1	1p32.3	2008-02-05			ENSG00000116133	ENSG00000116133			2859	protein-coding gene	gene with protein product		606418				11519011	Standard	NM_014762		Approved	KIAA0018, seladin-1	uc001cyc.1	Q15392	OTTHUMG00000009989	ENST00000371269.3:c.1462T>G	chr1.hg19:g.55317995A>C	ENSP00000360316:p.Ser488Ala	94.0	0.0	.		90.0	4.0	.	NM_014762	B7Z817|D3DQ51|Q9HBA8	Missense_Mutation	SNP	ENST00000371269.3	hg19	CCDS600.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.52|13.52	2.262766|2.262766	0.39995|0.39995	.|.	.|.	ENSG00000116133|ENSG00000116133	ENST00000436604|ENST00000539536;ENST00000371269;ENST00000537443;ENST00000535035	.|T;T;T	.|0.69306	.|-0.39;-0.39;-0.39	5.45|5.45	5.45|5.45	0.79879|0.79879	.|.	.|0.277164	.|0.40064	.|N	.|0.001199	T|T	0.47451|0.47451	0.1446|0.1446	N|N	0.16478|0.16478	0.41|0.41	0.36209|0.36209	D|D	0.851231|0.851231	.|B;B;B	.|0.16166	.|0.016;0.007;0.016	.|B;B;B	.|0.14023	.|0.01;0.004;0.007	T|T	0.51236|0.51236	-0.8731|-0.8731	5|10	.|0.14252	.|T	.|0.57	-42.9406|-42.9406	11.5029|11.5029	0.50448|0.50448	0.8501:0.1499:0.0:0.0|0.8501:0.1499:0.0:0.0	.|.	.|447;447;488	.|B7Z817;B7ZAV4;Q15392	.|.;.;DHC24_HUMAN	R|A	125|214;488;272;447	.|ENSP00000360316:S488A;ENSP00000439852:S272A;ENSP00000440191:S447A	.|ENSP00000360316:S488A	L|S	-|-	2|1	0|0	DHCR24|DHCR24	55090583|55090583	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.827000|0.827000	0.46813|0.46813	3.617000|3.617000	0.54181|0.54181	2.079000|2.079000	0.62486|0.62486	0.379000|0.379000	0.24179|0.24179	CTC|TCC	.	.	.	none		0.597	DHCR24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027680.1	NM_014762		C	55317995	A	C	55317995	3	2	230	1	0	0	0	0	1	0	0	0	4478	304	11	5	92	5	DHCR24	1	55317995	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	2818917	55317995	193932626	5	13931											
NRAS	4893	hgsc.bcm.edu	37	chr1	115256491	115256491	+	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	acagaggaagccttcgcctgTcctcatgtattggtctctca	8	12	9	12	1	3	1	2	0	1	1	6	2	4	2	3	2	1	1	3	2	2	3			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr1:115256491T>A	ENST00000369535.4	-	3	473	c.220A>T	c.(220-222)Aca>Tca	p.T74S		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	74					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)			NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		CCTTCGCCTGTCCTCATGTAT	0.418		50	Mis		"melanoma, MM, AML, thyroid"				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																											p.T74S		Atlas-SNP	.		Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"L, E"	.	NRAS	3766	.	0			c.A220T						PASS	.						186	159	168					1																	115256491		2203	4300	6503	SO:0001583	missense	4893	exon3	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	CGCCTGTCCTCAT	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.220A>T	chr1.hg19:g.115256491T>A	ENSP00000358548:p.Thr74Ser	102.0	0.0	.		74.0	28.0	.	NM_002524	Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	hg19	CCDS877.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.602254	0.87055	.	.	ENSG00000213281	ENST00000369535	T	0.76186	-1.0	5.08	5.08	0.68730	Small GTP-binding protein domain (1);	0.000000	0.56097	U	0.000022	T	0.46054	0.1373	N	0.04373	-0.215	0.80722	D	1	B	0.31640	0.333	B	0.37833	0.259	T	0.59209	-0.7497	10	0.51188	T	0.08	.	15.0132	0.71565	0.0:0.0:0.0:1.0	.	74	P01111	RASN_HUMAN	S	74	ENSP00000358548:T74S	ENSP00000358548:T74S	T	-	1	0	NRAS	115058014	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.787000	0.85759	2.120000	0.65058	0.533000	0.62120	ACA	.	.	.	none		0.418	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524		A	115256491	T	A	115256491	3	1	230	1	0	0	0	0	1	0	0	0	10647	1667	58	5	361	5	NRAS	1	115256491	Missense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10	59938496	115256491	133994130	6	13932											
DDR2	4921	hgsc.bcm.edu	37	chr1	162729664	162729664	+	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	cagacccatgaataccacgtGtggcccggctatgactatgt	10	9	10	12	2	0	3	0	2	0	1	0	3	0	3	3	2	1	1	3	2	4	3			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr1:162729664G>A	ENST00000367922.3	+	9	1188	c.750G>A	c.(748-750)gtG>gtA	p.V250V	DDR2_ENST00000367921.3_Silent_p.V250V	NM_001014796.1	NP_001014796.1	Q16832	DDR2_HUMAN	discoidin domain receptor tyrosine kinase 2	250					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)	AATACCACGTGTGGCCCGGCT	0.532																																					p.V250V	NSCLC(161;314 2006 8283 19651 23192)	Atlas-SNP	.											.	DDR2	228	.	0			c.G750A						PASS	.						119	105	110					1																	162729664		2203	4300	6503	SO:0001819	synonymous_variant	4921	exon9			CCACGTGTGGCCC	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.750G>A	chr1.hg19:g.162729664G>A		198.0	0.0	.		172.0	52.0	.	NM_001014796	Q7Z730	Silent	SNP	ENST00000367922.3	hg19	CCDS1241.1																																																																																			.	.	.	none		0.532	DDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083213.2	NM_006182		A	162729664	G	A	162729664	2	1	230	1	0	0	0	0	0	0	0	1	4339	1364	48	2		2	DDR2	1	162729664	Silent	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	47473173	162729664	86520957	7	13933											
C1orf114	57821	hgsc.bcm.edu	37	chr1	169390718	169390718	+	Frame_Shift_Del	DEL	A	A	-																															gcagactgtgtcctgtgattAgatttcccattccctttact																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr1:169390718delA	ENST00000367806.3	-	3	1103	c.951delT	c.(949-951)tctfs	p.S317fs	CCDC181_ENST00000367805.3_Frame_Shift_Del_p.S317fs|CCDC181_ENST00000491570.1_5'UTR|CCDC181_ENST00000545005.1_Frame_Shift_Del_p.S317fs	NM_021179.1	NP_067002.1	Q5TID7	CC181_HUMAN	coiled-coil domain containing 181	317						nucleus (GO:0005634)											TCCTGTGATTAGATTTCCCAT	0.463																																					p.N318fs		Atlas-Indel,Pindel	.											.	C1orf114	67	.	0			c.952delA						PASS	.						159	145	150					1																	169390718		2203	4300	6503	SO:0001589	frameshift_variant	57821	exon3			.	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.951delT	chr1.hg19:g.169390718delA	ENSP00000356780:p.Ser317fs	73.0	0.0	0		77.0	35.0	0.454545	NM_021179	O60780|Q53FD5|Q5TID9|Q8TC48	Frame_Shift_Del	DEL	ENST00000367806.3	hg19																																																																																				.	.	.	none		0.463	CCDC181-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086099.1	NM_021179		-	169390718	A	-	169390718	7	5	230	1	0	1	0	1	0	0	0	0	1989	407	15	0	591	0	C1orf114	1	169390718	Frame_Shift_Del	DEL	A	TCGA-P4-A5E7-01A-31D-A28G-10	6661054	169390718	79859903	8	13934											
FAM98A	25940	hgsc.bcm.edu	37	chr2	33813426	33813426	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttcaatcccgctgaagaaTtggaacatagttatattggc	12	14	8	7	1	1	2	1	1	0	1	2	3	2	3	1	2	1	2	1	2	7	7	rs561820764		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr2:33813426T>C	ENST00000238823.8	-	4	638	c.498A>G	c.(496-498)caA>caG	p.Q166Q	FAM98A_ENST00000441530.2_Intron|FAM98A_ENST00000498340.1_Intron|FAM98A_ENST00000403368.1_Silent_p.Q166Q			Q8NCA5	FA98A_HUMAN	family with sequence similarity 98, member A	166							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)					CGCTGAAGAATTGGAACATAG	0.363																																					p.Q166Q		Atlas-SNP	.											.	FAM98A	42	.	0			c.A498G						PASS	.						173	175	174					2																	33813426		2203	4300	6503	SO:0001819	synonymous_variant	25940	exon4			GAAGAATTGGAAC		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.498A>G	chr2.hg19:g.33813426T>C		79.0	0.0	.		75.0	32.0	.	NM_015475	B2RNA2|Q9Y3Y6	Silent	SNP	ENST00000238823.8	hg19	CCDS33179.1																																																																																			.	.	.	none		0.363	FAM98A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325457.2	NM_015475		C	33813426	T	C	33813426	2	2	230	1	0	0	0	0	0	0	0	1	5663	1490	52	3		3	FAM98A	2	33813426	Silent	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10		33813426	209385947	9	13935											
TTC31	64427	hgsc.bcm.edu	37	chr2	74718487	74718487	+	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	ggaaacccagttcagggacaGtgtggtgaagaagaggtgag	13	6	17	5	0	1	4	1	2	0	2	1	6	1	6	1	4	1	1	1	4	3	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr2:74718487G>A	ENST00000233623.5	+	7	676	c.669G>A	c.(667-669)caG>caA	p.Q223Q	TTC31_ENST00000442235.2_Silent_p.Q79Q|TTC31_ENST00000463189.1_3'UTR|TTC31_ENST00000410003.1_Silent_p.Q223Q	NM_022492.4	NP_071937.4	Q49AM3	TTC31_HUMAN	tetratricopeptide repeat domain 31	223										breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9						TTCAGGGACAGTGTGGTGAAG	0.537																																					p.Q223Q		Atlas-SNP	.											.	TTC31	23	.	0			c.G669A						PASS	.						127	138	134					2																	74718487		1930	4124	6054	SO:0001819	synonymous_variant	64427	exon7			GGGACAGTGTGGT	AK026819	CCDS42701.1	2p13.1	2013-01-11			ENSG00000115282	ENSG00000115282		"Tetratricopeptide (TTC) repeat domain containing"	25759	protein-coding gene	gene with protein product						12477932	Standard	NM_022492		Approved	FLJ12788	uc002slt.2	Q49AM3	OTTHUMG00000152887	ENST00000233623.5:c.669G>A	chr2.hg19:g.74718487G>A		99.0	0.0	.		84.0	22.0	.	NM_022492	Q4KN40|Q53FD4|Q9H9F7	Silent	SNP	ENST00000233623.5	hg19	CCDS42701.1																																																																																			.	.	.	none		0.537	TTC31-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328422.1	NM_022492		A	74718487	G	A	74718487	2	1	230	1	0	0	0	0	0	0	0	1	16712	1020	36	2		2	TTC31	2	74718487	Silent	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	40905061	74718487	168480886	10	13936											
SUCLG1	8802	hgsc.bcm.edu	37	chr2	84652539	84652539	+	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	gggccactgttggagctcacCttgtagatcgtggttcccag	6	11	13	11	1	1	1	1	0	0	1	3	2	2	2	3	3	1	4	3	3	1	4			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr2:84652539C>T	ENST00000393868.2	-	8	1224	c.1014G>A	c.(1012-1014)aaG>aaA	p.K338K	SUCLG1_ENST00000491123.1_5'UTR	NM_003849.3	NP_003840.2	P53597	SUCA_HUMAN	succinate-CoA ligase, alpha subunit	338					cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|succinyl-CoA metabolic process (GO:0006104)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|succinate-CoA ligase complex (GDP-forming) (GO:0045244)	ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)|succinate-CoA ligase (GDP-forming) activity (GO:0004776)			kidney(4)|large_intestine(4)|lung(2)	10					Succinic acid(DB00139)	TGGAGCTCACCTTGTAGATCG	0.532																																					p.K338K	Ovarian(48;203 1101 37206 40305 50790)	Atlas-SNP	.											.	SUCLG1	30	.	0			c.G1014A						PASS	.						77	69	71					2																	84652539		2203	4300	6503	SO:0001630	splice_region_variant	8802	exon8			GCTCACCTTGTAG	Z68204	CCDS1967.2	2p11.3	2008-02-05	2008-01-08		ENSG00000163541	ENSG00000163541	6.2.1.4		11449	protein-coding gene	gene with protein product		611224	"succinate-CoA ligase, GDP-forming, alpha subunit"			9128182	Standard	NM_003849		Approved		uc002son.3	P53597	OTTHUMG00000130023	ENST00000393868.2:c.1014+1G>A	chr2.hg19:g.84652539C>T		98.0	0.0	.		119.0	36.0	.	NM_003849	Q9BWB0|Q9UNP6	Silent	SNP	ENST00000393868.2	hg19	CCDS1967.2																																																																																			.	.	.	none		0.532	SUCLG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252298.2	NM_003849	Silent	T	84652539	C	T	84652539	5	4	230	1	0	0	0	0	0	0	1	0	15376	695	24	2	34	2	SUCLG1	2	84652539	Splice_Site	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	9934052	84652539	158546834	11	13937											
KCNIP3	30818	hgsc.bcm.edu	37	chr2	95976175	95976175	+	Missense_Mutation	SNP	A	A	G																															cacttagcaagaaggagggtAtcaagtggcagaggccgagg																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr2:95976175A>G	ENST00000295225.5	+	2	223	c.88A>G	c.(88-90)Atc>Gtc	p.I30V	KCNIP3_ENST00000360990.3_Missense_Mutation_p.I30V|KCNIP3_ENST00000377181.2_Intron	NM_013434.4	NP_038462.1	Q9Y2W7	CSEN_HUMAN	Kv channel interacting protein 3, calsenilin	30					apoptotic process (GO:0006915)|behavioral response to pain (GO:0048266)|intracellular protein transport (GO:0006886)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of neuron apoptotic process (GO:0043523)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	axon terminus (GO:0043679)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sequence-specific DNA binding (GO:0043565)|transcription corepressor activity (GO:0003714)|voltage-gated ion channel activity (GO:0005244)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	16				READ - Rectum adenocarcinoma(193;0.13)		GAAGGAGGGTATCAAGTGGCA	0.622																																					p.I30V		Atlas-SNP	.											.	KCNIP3	52	.	0			c.A88G						PASS	.						79	86	84					2																	95976175		2203	4300	6503	SO:0001583	missense	30818	exon2			GAGGGTATCAAGT	AF199599	CCDS2013.1, CCDS33245.1	2q21.1	2013-01-10	2006-02-11	2006-02-11	ENSG00000115041	ENSG00000115041		"EF-hand domain containing"	15523	protein-coding gene	gene with protein product		604662	"calsenilin, presenilin-binding protein, EF hand transcription factor"	CSEN		9771752, 10078534	Standard	NM_013434		Approved	DREAM, KCHIP3, calsenilin	uc002sup.3	Q9Y2W7	OTTHUMG00000130392	ENST00000295225.5:c.88A>G	chr2.hg19:g.95976175A>G	ENSP00000295225:p.Ile30Val	356.0	1.0	.		364.0	110.0	.	NM_013434	H7BY46|Q3YAC3|Q3YAC4|Q53TJ5|Q96T40|Q9UJ84|Q9UJ85	Missense_Mutation	SNP	ENST00000295225.5	hg19	CCDS2013.1	.	.	.	.	.	.	.	.	.	.	A	0.862	-0.734899	0.03111	.	.	ENSG00000115041	ENST00000295225;ENST00000360990	T;T	0.69926	-0.27;-0.44	5.02	-2.69	0.06022	.	1.487590	0.04089	N	0.310881	T	0.38983	0.1061	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	0.23547	-1.0185	10	0.20519	T	0.43	.	11.1112	0.48235	0.6262:0.0:0.3738:0.0	.	30;30	Q9Y2W7;Q3YAC4	CSEN_HUMAN;.	V	30	ENSP00000295225:I30V;ENSP00000354261:I30V	ENSP00000295225:I30V	I	+	1	0	KCNIP3	95339902	0.154000	0.22792	0.361000	0.25849	0.847000	0.48162	0.311000	0.19380	-0.418000	0.07450	-0.810000	0.03169	ATC	.	.	.	none		0.622	KCNIP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252770.1	NM_013434		G	95976175	A	G	95976175	3	3	230	1	0	0	0	0	1	0	0	0	8048	449	16	3	94	3	KCNIP3	2	95976175	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	11323636	95976175	147223198	12	13938	140	2									
KCNIP3	30818	hgsc.bcm.edu	37	chr2	95976177	95976177	+	Silent	SNP	C	C	T																															cttagcaagaaggagggtatCaagtggcagaggccgaggct																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr2:95976177C>T	ENST00000295225.5	+	2	225	c.90C>T	c.(88-90)atC>atT	p.I30I	KCNIP3_ENST00000360990.3_Silent_p.I30I|KCNIP3_ENST00000377181.2_Intron	NM_013434.4	NP_038462.1	Q9Y2W7	CSEN_HUMAN	Kv channel interacting protein 3, calsenilin	30					apoptotic process (GO:0006915)|behavioral response to pain (GO:0048266)|intracellular protein transport (GO:0006886)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of neuron apoptotic process (GO:0043523)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	axon terminus (GO:0043679)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sequence-specific DNA binding (GO:0043565)|transcription corepressor activity (GO:0003714)|voltage-gated ion channel activity (GO:0005244)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	16				READ - Rectum adenocarcinoma(193;0.13)		AGGAGGGTATCAAGTGGCAGA	0.627																																					p.I30I		Atlas-SNP	.											.	KCNIP3	52	.	0			c.C90T						PASS	.						79	86	83					2																	95976177		2203	4300	6503	SO:0001819	synonymous_variant	30818	exon2			GGGTATCAAGTGG	AF199599	CCDS2013.1, CCDS33245.1	2q21.1	2013-01-10	2006-02-11	2006-02-11	ENSG00000115041	ENSG00000115041		"EF-hand domain containing"	15523	protein-coding gene	gene with protein product		604662	"calsenilin, presenilin-binding protein, EF hand transcription factor"	CSEN		9771752, 10078534	Standard	NM_013434		Approved	DREAM, KCHIP3, calsenilin	uc002sup.3	Q9Y2W7	OTTHUMG00000130392	ENST00000295225.5:c.90C>T	chr2.hg19:g.95976177C>T		352.0	1.0	.		361.0	109.0	.	NM_013434	H7BY46|Q3YAC3|Q3YAC4|Q53TJ5|Q96T40|Q9UJ84|Q9UJ85	Silent	SNP	ENST00000295225.5	hg19	CCDS2013.1																																																																																			.	.	.	none		0.627	KCNIP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252770.1	NM_013434		T	95976177	C	T	95976177	2	4	230	1	0	0	0	0	0	0	0	1	8048	816	29	2		2	KCNIP3	2	95976177	Silent	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	2	95976177	147223196	13	13939	140	2									
SLC5A7	60482	hgsc.bcm.edu	37	chr2	108604763	108604763	+	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	tggtggccgagatattggttTattggttggtggatttacca	7	16	14	4	1	0	1	0	0	0	1	0	3	0	2	2	6	1	2	2	6	3	8			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr2:108604763T>A	ENST00000264047.2	+	2	428	c.152T>A	c.(151-153)tTa>tAa	p.L51*	SLC5A7_ENST00000540517.1_Intron|SLC5A7_ENST00000409059.1_Nonsense_Mutation_p.L51*	NM_021815.2	NP_068587.1	Q9GZV3	SC5A7_HUMAN	solute carrier family 5 (sodium/choline cotransporter), member 7	51					acetylcholine biosynthetic process (GO:0008292)|cell death (GO:0008219)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	choline binding (GO:0033265)|choline transmembrane transporter activity (GO:0015220)|choline:sodium symporter activity (GO:0005307)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	49					Choline(DB00122)	GATATTGGTTTATTGGTTGGT	0.532																																					p.L51X		Atlas-SNP	.											.	SLC5A7	109	.	0			c.T152A						PASS	.						148	131	137					2																	108604763		2203	4300	6503	SO:0001587	stop_gained	60482	exon2			TTGGTTTATTGGT	AF276871	CCDS2074.1	2q12	2013-07-19	2013-07-19		ENSG00000115665	ENSG00000115665		"Solute carriers"	14025	protein-coding gene	gene with protein product		608761	"solute carrier family 5 (choline transporter), member 7"			11027560	Standard	NM_021815		Approved	hCHT, CHT1	uc002tdv.3	Q9GZV3	OTTHUMG00000130959	ENST00000264047.2:c.152T>A	chr2.hg19:g.108604763T>A	ENSP00000264047:p.Leu51*	133.0	0.0	.		142.0	41.0	.	NM_021815	Q53TF2	Nonsense_Mutation	SNP	ENST00000264047.2	hg19	CCDS2074.1	.	.	.	.	.	.	.	.	.	.	T	38	6.986976	0.97983	.	.	ENSG00000115665	ENST00000409059;ENST00000264047	.	.	.	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	-15.1779	16.3634	0.83296	0.0:0.0:0.0:1.0	.	.	.	.	X	51	.	ENSP00000264047:L51X	L	+	2	0	SLC5A7	107971195	1.000000	0.71417	0.256000	0.24389	0.386000	0.30323	7.655000	0.83696	2.324000	0.78689	0.533000	0.62120	TTA	.	.	.	none		0.532	SLC5A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253562.1			A	108604763	T	A	108604763	4	1	230	1	0	0	0	0	0	1	0	0	14683	1764	61	5	154	5	SLC5A7	2	108604763	Nonsense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10	12628586	108604763	134594610	14	13940											
ZRANB3	84083	hgsc.bcm.edu	37	chr2	135988115	135988115	+	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	gaggagtctcacacatttcaCaataaggtaactctgaatta	15	11	7	8	0	3	1	2	1	2	0	4	3	3	2	0	2	1	1	0	2	5	4			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr2:135988115C>T	ENST00000264159.6	-	13	2038	c.1922G>A	c.(1921-1923)tGt>tAt	p.C641Y	ZRANB3_ENST00000412849.1_5'UTR|ZRANB3_ENST00000401392.1_Missense_Mutation_p.C641Y|ZRANB3_ENST00000536680.1_Missense_Mutation_p.C641Y	NM_032143.2	NP_115519.2	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	641					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)		ACACATTTCACAATAAGGTAA	0.473																																					p.C641Y		Atlas-SNP	.											.	ZRANB3	109	.	0			c.G1922A						PASS	.						111	103	105					2																	135988115		1967	4164	6131	SO:0001583	missense	84083	exon13			ATTTCACAATAAG	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.1922G>A	chr2.hg19:g.135988115C>T	ENSP00000264159:p.Cys641Tyr	94.0	0.0	.		96.0	5.0	.	NM_032143	B3KYA1|B4E375|B5MDI3|D3DP76|E9PBP0|Q53SM1|Q6P2C4|Q8N1P4|Q9H0E8	Missense_Mutation	SNP	ENST00000264159.6	hg19	CCDS46419.1	.	.	.	.	.	.	.	.	.	.	C	17.32	3.360568	0.61403	.	.	ENSG00000121988	ENST00000538542;ENST00000283060;ENST00000401392;ENST00000264159;ENST00000536680	D;D;D	0.99797	-6.79;-6.79;-6.79	5.61	5.61	0.85477	Zinc finger, RanBP2-type (4);	0.047816	0.85682	D	0.000000	D	0.99864	0.9936	H	0.96175	3.78	0.49213	D	0.999763	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96707	0.9522	10	0.87932	D	0	-12.7436	17.4074	0.87477	0.0:1.0:0.0:0.0	.	641;641	Q5FWF4;Q5FWF4-3	ZRAB3_HUMAN;.	Y	106;106;641;641;641	ENSP00000383979:C641Y;ENSP00000264159:C641Y;ENSP00000441320:C641Y	ENSP00000264159:C641Y	C	-	2	0	ZRANB3	135704585	1.000000	0.71417	0.995000	0.50966	0.454000	0.32378	5.258000	0.65479	2.638000	0.89438	0.563000	0.77884	TGT	.	.	.	none		0.473	ZRANB3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318254.1	NM_032143		T	135988115	C	T	135988115	3	4	230	1	0	0	0	0	1	0	0	0	18236	478	17	2	1353	2	ZRANB3	2	135988115	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	27383352	135988115	107211258	15	13941											
SSB	6741	hgsc.bcm.edu	37	chr2	170667495	170667495	+	Missense_Mutation	SNP	A	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	agaaggagaggtggaaaaagAagcactgaagaaaataatag	22	4	13	2	0	0	5	0	1	0	4	0	7	0	6	0	3	1	1	0	3	9	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr2:170667495A>C	ENST00000409333.1	+	10	1185	c.938A>C	c.(937-939)gAa>gCa	p.E313A	METTL5_ENST00000409837.1_Intron|SSB_ENST00000260956.4_Missense_Mutation_p.E313A			P05455	LA_HUMAN	Sjogren syndrome antigen B (autoantigen La)	313					histone mRNA metabolic process (GO:0008334)|tRNA modification (GO:0006400)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			endometrium(3)|large_intestine(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						GTGGAAAAAGAAGCACTGAAG	0.348																																					p.E313A		Atlas-SNP	.											.	SSB	28	.	0			c.A938C						PASS	.						66	68	67					2																	170667495		2203	4299	6502	SO:0001583	missense	6741	exon10			AAAAAGAAGCACT		CCDS2237.1	2q31.1	2014-02-14		2005-06-16	ENSG00000138385	ENSG00000138385		"La ribonucleoprotein domain containing", "RNA binding motif (RRM) containing"	11316	protein-coding gene	gene with protein product	"La ribonucleoprotein domain family, member 3"	109090					Standard	NM_003142		Approved	LARP3, La, La/SSB	uc002ufk.3	P05455	OTTHUMG00000132212	ENST00000409333.1:c.938A>C	chr2.hg19:g.170667495A>C	ENSP00000386636:p.Glu313Ala	139.0	0.0	.		133.0	42.0	.	NM_003142	Q15367|Q53XJ4	Missense_Mutation	SNP	ENST00000409333.1	hg19	CCDS2237.1	.	.	.	.	.	.	.	.	.	.	A	13.37	2.217202	0.39201	.	.	ENSG00000138385	ENST00000260956;ENST00000409005;ENST00000409333	T;T	0.47528	0.84;0.84	4.86	-0.881	0.10607	Nucleotide-binding, alpha-beta plait (1);RNA-binding motif (1);	0.493908	0.22411	N	0.060419	T	0.49508	0.1561	M	0.85710	2.77	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.12156	0.003;0.007	T	0.50285	-0.8846	10	0.31617	T	0.26	-0.5081	14.1431	0.65331	0.4664:0.5336:0.0:0.0	.	313;313	E9PFH8;P05455	.;LA_HUMAN	A	313	ENSP00000260956:E313A;ENSP00000386636:E313A	ENSP00000260956:E313A	E	+	2	0	SSB	170375741	1.000000	0.71417	0.890000	0.34922	0.989000	0.77384	1.295000	0.33377	-0.310000	0.08766	0.383000	0.25322	GAA	.	.	.	none		0.348	SSB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333316.1	NM_003142		C	170667495	A	C	170667495	3	2	230	1	0	0	0	0	1	0	0	0	15190	246	9	5	972	5	SSB	2	170667495	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	34679380	170667495	72531878	16	13942											
TNS1	7145	hgsc.bcm.edu	37	chr2	218678511	218678511	+	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	tcgcggatgatgaaggccccCggctcctggtccttgaggag	6	8	15	12	3	0	3	0	3	0	0	3	5	2	5	4	5	0	1	4	5	1	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr2:218678511C>G	ENST00000171887.4	-	26	4898	c.4446G>C	c.(4444-4446)ccG>ccC	p.P1482P	TNS1_ENST00000430930.1_Silent_p.P1461P|TNS1_ENST00000419504.1_Silent_p.P1469P	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1482	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				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)	p.P1482P(1)		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)		TGAAGGCCCCCGGCTCCTGGT	0.572																																					p.P1482P		Atlas-SNP	.											TNS1,colon,carcinoma,0,1	TNS1	251	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G4446C						PASS	.						58	58	58					2																	218678511		2203	4300	6503	SO:0001819	synonymous_variant	7145	exon26			GGCCCCCGGCTCC	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.4446G>C	chr2.hg19:g.218678511C>G		124.0	0.0	.		110.0	34.0	.	NM_022648	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	hg19	CCDS2407.1																																																																																			.	.	.	none		0.572	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		G	218678511	C	G	218678511	2	3	230	1	0	0	0	0	0	0	0	1	16355	639	23	4		4	TNS1	2	218678511	Silent	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	48011016	218678511	24520862	17	13943											
ANKMY1	51281	hgsc.bcm.edu	37	chr2	241465102	241465102	+	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	gtggccaccggggggcttacCtggggctcaggtatggtccg	4	8	18	11	2	1	0	1	0	0	0	2	0	2	0	4	8	1	3	4	8	2	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr2:241465102C>T	ENST00000272972.3	-	6	1282	c.1068G>A	c.(1066-1068)caG>caA	p.Q356Q	ANKMY1_ENST00000361678.4_Splice_Site_p.Q215Q|ANKMY1_ENST00000401804.1_Splice_Site_p.Q445Q|ANKMY1_ENST00000403283.1_Splice_Site_p.Q294Q|ANKMY1_ENST00000406958.1_Splice_Site_p.Q215Q|ANKMY1_ENST00000462004.1_5'Flank|ANKMY1_ENST00000536462.1_Splice_Site_p.Q168Q|ANKMY1_ENST00000405002.1_Splice_Site_p.Q126Q|ANKMY1_ENST00000373318.2_Splice_Site_p.Q215Q|ANKMY1_ENST00000373320.4_Splice_Site_p.Q126Q|ANKMY1_ENST00000405523.3_Splice_Site_p.Q215Q|ANKMY1_ENST00000391987.1_Splice_Site_p.Q356Q	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	356							metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	30		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		GGGGGCTTACCTGGGGCTCAG	0.587																																					p.Q356Q		Atlas-SNP	.											.	ANKMY1	112	.	0			c.G1068A						PASS	.						78	68	72					2																	241465102		2202	4300	6502	SO:0001630	splice_region_variant	51281	exon6			GCTTACCTGGGGC	AB034636	CCDS2535.1, CCDS2536.1, CCDS63184.1, CCDS63185.1, CCDS74681.1	2q37.3	2013-01-10			ENSG00000144504	ENSG00000144504		"Zinc fingers, MYND-type", "Ankyrin repeat domain containing"	20987	protein-coding gene	gene with protein product							Standard	XM_005247020		Approved	FLJ20499, ZMYND13	uc002vyz.1	Q9P2S6	OTTHUMG00000133355	ENST00000272972.3:c.1068+1G>A	chr2.hg19:g.241465102C>T		118.0	0.0	.		121.0	45.0	.	NM_016552	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Silent	SNP	ENST00000272972.3	hg19	CCDS2536.1																																																																																			.	.	.	none		0.587	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2	NM_017844	Silent	T	241465102	C	T	241465102	5	4	230	1	0	0	0	0	0	0	1	0	634	695	24	2	1805	2	ANKMY1	2	241465102	Splice_Site	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	22786591	241465102	1734271	18	13944											
C3orf54	7318	hgsc.bcm.edu	37	chr3	49842183	49842183	+	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	1	0	0	0	0	0	0	0	ctgcctgagacagggagtgaAgggggtgacggaggtgggca	9	5	21	6	1	0	3	0	3	0	1	0	6	0	5	1	6	1	1	1	6	1	0			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr3:49842183A>C	ENST00000333486.3	-	0	3299				MIR5193_ENST00000584510.1_RNA|FAM212A_ENST00000333323.4_Missense_Mutation_p.E209D	NM_003335.2	NP_003326.2	P41226	UBA7_HUMAN	ubiquitin-like modifier activating enzyme 7						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)		CAGGGAGTGAAGGGGGTGACG	0.652																																					p.E209D		Atlas-SNP	.											.	.	.	.	0			c.A627C						PASS	.						78	78	78					3																	49842183		2203	4300	6503	SO:0001628	intergenic_variant	389119	exon2			GAGTGAAGGGGGT	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		chr3.hg19:g.49842183A>C		93.0	0.0	.		305.0	151.0	.	NM_203370	Q9BRB2	Missense_Mutation	SNP	ENST00000333486.3	hg19	CCDS2805.1	.	.	.	.	.	.	.	.	.	.	A	14.90	2.673205	0.47781	.	.	ENSG00000185614	ENST00000333323	.	.	.	5.64	-0.363	0.12556	.	0.000000	0.52532	D	0.000077	T	0.61627	0.2362	L	0.44542	1.39	0.39146	D	0.962132	D	0.71674	0.998	D	0.63488	0.915	T	0.62358	-0.6871	9	0.56958	D	0.05	.	10.7234	0.46052	0.5054:0.0:0.4946:0.0	.	207	Q96EL1	CC054_HUMAN	D	209	.	ENSP00000329735:E209D	E	+	3	2	C3orf54	49817187	1.000000	0.71417	0.885000	0.34714	0.348000	0.29142	0.471000	0.22100	-0.003000	0.14444	0.459000	0.35465	GAA	.	.	.	none		0.652	UBA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350503.1	NM_003335		C	49842183	A	C	49842183	1	2	230	0	1	0	0	0	0	0	0	0	2235	69	3	5		5	C3orf54	3	49842183	IGR	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10		49842183	148180247	19	13945											
ROBO1	6091	hgsc.bcm.edu	37	chr3	79639003	79639003	+	Frame_Shift_Del	DEL	T	T	-																															gctgggccagaaacaggtgaTttggggataagctgaggagt																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr3:79639003delT	ENST00000464233.1	-	2	172	c.59delA	c.(58-60)aatfs	p.N20fs		NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	20					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)		AAACAGGTGATTTGGGGATAA	0.393																																					p.N20fs		Atlas-INDEL	.											.	ROBO1	833	.	0			c.60delT						PASS	.						165	164	164					3																	79639003		1916	4117	6033	SO:0001589	frameshift_variant	6091	exon2			.	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	10249	protein-coding gene	gene with protein product		602430	"roundabout (axon guidance receptor, Drosophila) homolog 1"			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.59delA	chr3.hg19:g.79639003delT	ENSP00000420321:p.Asn20fs	153.0	0.0	0		165.0	11.0	0.0666667	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Frame_Shift_Del	DEL	ENST00000464233.1	hg19	CCDS54611.1																																																																																			.	.	.	none		0.393	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		-	79639003	T	-	79639003	7	5	230	1	0	1	0	1	0	0	0	0	13526	1493	52	0	5088	0	ROBO1	3	79639003	Frame_Shift_Del	DEL	T	TCGA-P4-A5E7-01A-31D-A28G-10	29796820	79639003	118383427	20	13946											
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121415217	121415217	+	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	atgttctaggccagcaatttGtagttggctgctttccaatt	8	16	9	8	0	1	0	0	0	1	0	2	0	2	0	2	2	2	6	2	2	4	7			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr3:121415217G>A	ENST00000340645.5	-	13	4263	c.4138C>T	c.(4138-4140)Caa>Taa	p.Q1380*	GOLGB1_ENST00000393667.3_Nonsense_Mutation_p.Q1385*	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	1380					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)		CCAGCAATTTGTAGTTGGCTG	0.413																																					p.Q1385X		Atlas-SNP	.											.	GOLGB1	319	.	0			c.C4153T						PASS	.						157	162	160					3																	121415217		2203	4299	6502	SO:0001587	stop_gained	2804	exon13			CAATTTGTAGTTG	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.4138C>T	chr3.hg19:g.121415217G>A	ENSP00000341848:p.Gln1380*	40.0	0.0	.		59.0	12.0	.	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Nonsense_Mutation	SNP	ENST00000340645.5	hg19	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	G	39	7.740962	0.98465	.	.	ENSG00000173230	ENST00000340645;ENST00000393667;ENST00000494517	.	.	.	6.17	3.41	0.39046	.	0.324362	0.26746	N	0.022716	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.993	0.19478	0.0:0.6622:0.1652:0.1726	.	.	.	.	X	1380;1385;1344	.	ENSP00000341848:Q1380X	Q	-	1	0	GOLGB1	122897907	0.273000	0.24181	0.748000	0.31131	0.666000	0.39218	0.959000	0.29240	0.464000	0.27142	-0.165000	0.13383	CAA	.	.	.	none		0.413	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		A	121415217	G	A	121415217	4	1	230	1	0	0	0	0	0	1	0	0	6572	1386	48	2	5681	2	GOLGB1	3	121415217	Nonsense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	41776214	121415217	76607213	21	13947											
ARMC8	25852	hgsc.bcm.edu	37	chr3	137982982	137982982	+	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	attctttgtagatgtttgcaCagtttatccagatctgtgca	9	17	8	7	0	2	2	0	0	2	2	3	2	3	2	1	0	2	5	1	0	2	6			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr3:137982982C>T	ENST00000469044.1	+	14	1498	c.1227C>T	c.(1225-1227)caC>caT	p.H409H	ARMC8_ENST00000491704.1_Silent_p.H367H|ARMC8_ENST00000538260.1_Silent_p.H378H|ARMC8_ENST00000485396.1_Silent_p.H336H|NME9_ENST00000484930.1_Intron|ARMC8_ENST00000481646.1_Silent_p.H395H|ARMC8_ENST00000393058.3_Silent_p.H399H|NME9_ENST00000383180.2_Intron|NME9_ENST00000536478.1_Intron|ARMC8_ENST00000461822.1_Silent_p.H342H|NME9_ENST00000317876.4_Intron|NME9_ENST00000341790.5_Intron	NM_001267041.1|NM_001267042.1	NP_001253970.1|NP_001253971.1	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8	409										endometrium(2)|kidney(1)|large_intestine(7)|lung(5)|upper_aerodigestive_tract(1)	16						GATGTTTGCACAGTTTATCCA	0.368																																					p.H395H		Atlas-SNP	.											.	ARMC8	79	.	0			c.C1185T						PASS	.						100	89	92					3																	137982982		1850	4099	5949	SO:0001819	synonymous_variant	25852	exon15			TTTGCACAGTTTA		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.1227C>T	chr3.hg19:g.137982982C>T		55.0	0.0	.		83.0	24.0	.	NM_015396	A8K0L2|B7Z441|B7Z453|D3DNE6|F5GWK4|Q6PIL2|Q96D19|Q96HZ5|Q9NV02|Q9NV94|Q9Y4R9	Silent	SNP	ENST00000469044.1	hg19																																																																																				.	.	.	none		0.368	ARMC8-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000357560.1	NM_015396		T	137982982	C	T	137982982	2	4	230	1	0	0	0	0	0	0	0	1	957	477	17	2		2	ARMC8	3	137982982	Silent	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	16567765	137982982	60039448	22	13948											
RBP1	5947	hgsc.bcm.edu	37	chr3	139237296	139237296	+	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	tcaccctcgatccactgggtCcagccacgcccctccttctc	5	9	6	21	2	2	0	1	0	1	0	7	1	5	0	7	1	1	0	7	1	0	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr3:139237296C>A	ENST00000232219.2	-	3	617	c.507G>T	c.(505-507)tgG>tgT	p.W169C	RP11-319G6.1_ENST00000515247.1_RNA	NM_002899.3	NP_002890.2	P09455	RET1_HUMAN	retinol binding protein 1, cellular	107					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)	TCCACTGGGTCCAGCCACGCC	0.592																																					p.W169C		Atlas-SNP	.											.	RBP1	39	.	0			c.G507T						PASS	.						120	95	104					3																	139237296		2203	4300	6503	SO:0001583	missense	5947	exon3			CTGGGTCCAGCCA		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	ENST00000232219.2:c.507G>T	chr3.hg19:g.139237296C>A	ENSP00000232219:p.Trp169Cys	69.0	0.0	.		86.0	25.0	.	NM_002899	A8K2Q0|B7Z7A0|E7EWV0|F2Z2F2|Q6FGX8	Missense_Mutation	SNP	ENST00000232219.2	hg19	CCDS3110.2	.	.	.	.	.	.	.	.	.	.	C	24.1	4.491184	0.84962	.	.	ENSG00000114115	ENST00000232219	T	0.23147	1.92	5.93	5.93	0.95920	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.000000	0.85682	D	0.000000	T	0.54759	0.1878	M	0.77616	2.38	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.55477	-0.8135	10	0.72032	D	0.01	.	17.8376	0.88704	0.0:1.0:0.0:0.0	.	107	P09455	RET1_HUMAN	C	169	ENSP00000232219:W169C	ENSP00000232219:W169C	W	-	3	0	RBP1	140719986	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.088000	0.76901	2.815000	0.96918	0.561000	0.74099	TGG	.	.	.	none		0.592	RBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341495.1	NM_002899		A	139237296	C	A	139237296	3	1	230	1	0	0	0	0	1	0	0	0	13168	856	30	4	94	4	RBP1	3	139237296	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	1254314	139237296	58785134	23	13949											
EXOC1	55763	hgsc.bcm.edu	37	chr4	56738102	56738102	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggagactggccagtcaccTcaacaatgtttttgttcaac	10	11	8	12	1	3	1	3	0	0	1	3	2	3	1	3	2	2	2	3	2	3	3			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr4:56738102T>C	ENST00000381295.2	+	8	1400	c.1052T>C	c.(1051-1053)cTc>cCc	p.L351P	EXOC1_ENST00000346134.7_Missense_Mutation_p.L351P|EXOC1_ENST00000349598.6_Missense_Mutation_p.L351P	NM_001024924.1	NP_001020095.1	Q9NV70	EXOC1_HUMAN	exocyst complex component 1	351					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)					GCCAGTCACCTCAACAATGTT	0.393																																					p.L351P		Atlas-SNP	.											.	EXOC1	103	.	0			c.T1052C						PASS	.						76	76	76					4																	56738102		2203	4300	6503	SO:0001583	missense	55763	exon8			GTCACCTCAACAA	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.1052T>C	chr4.hg19:g.56738102T>C	ENSP00000370695:p.Leu351Pro	129.0	0.0	.		73.0	4.0	.	NM_018261	Q504V4|Q8WUE7|Q96T15|Q9NZE4	Missense_Mutation	SNP	ENST00000381295.2	hg19	CCDS3502.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.548026	0.86022	.	.	ENSG00000090989	ENST00000381295;ENST00000346134;ENST00000349598	.	.	.	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.80813	0.4695	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	0.83261	-0.0048	9	0.87932	D	0	.	16.6245	0.84952	0.0:0.0:0.0:1.0	.	351;351	Q9NV70-2;Q9NV70	.;EXOC1_HUMAN	P	351	.	ENSP00000326514:L351P	L	+	2	0	EXOC1	56432859	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	7.546000	0.82137	2.323000	0.78572	0.528000	0.53228	CTC	.	.	.	none		0.393	EXOC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361799.1	NM_018261		C	56738102	T	C	56738102	3	2	230	1	0	0	0	0	1	0	0	0	5303	1551	54	3	1078	3	EXOC1	4	56738102	Missense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10		56738102	134416174	24	13950											
REST	5978	hgsc.bcm.edu	37	chr4	57797826	57797826	+	Missense_Mutation	SNP	A	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	acgccagagggtgaaactttAaatggtaaacatcagactga	16	8	10	7	1	1	4	1	2	0	2	1	4	1	4	1	2	2	1	1	2	5	3			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr4:57797826A>C	ENST00000309042.7	+	4	3116	c.2802A>C	c.(2800-2802)ttA>ttC	p.L934F		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	934					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)					GTGAAACTTTAAATGGTAAAC	0.393																																					p.L934F		Atlas-SNP	.											.	REST	104	.	0			c.A2802C						PASS	.						63	61	62					4																	57797826		2203	4300	6503	SO:0001583	missense	5978	exon4			AACTTTAAATGGT	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.2802A>C	chr4.hg19:g.57797826A>C	ENSP00000311816:p.Leu934Phe	153.0	0.0	.		110.0	43.0	.	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Missense_Mutation	SNP	ENST00000309042.7	hg19	CCDS3509.1	.	.	.	.	.	.	.	.	.	.	A	11.64	1.698194	0.30142	.	.	ENSG00000084093	ENST00000309042;ENST00000358605	T	0.09445	2.98	5.44	-0.433	0.12287	.	1.916850	0.03006	N	0.148774	T	0.10337	0.0253	L	0.44542	1.39	0.09310	N	1	B;B	0.22146	0.065;0.002	B;B	0.19946	0.027;0.003	T	0.36890	-0.9729	10	0.62326	D	0.03	3.7839	2.7257	0.05213	0.5094:0.2758:0.0816:0.1332	.	911;934	F8WAN5;Q13127	.;REST_HUMAN	F	934;911	ENSP00000311816:L934F	ENSP00000311816:L934F	L	+	3	2	REST	57492583	0.001000	0.12720	0.000000	0.03702	0.092000	0.18411	0.791000	0.26915	0.082000	0.17018	0.459000	0.35465	TTA	.	.	.	none		0.393	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612		C	57797826	A	C	57797826	3	2	230	1	0	0	0	0	1	0	0	0	13247	359	13	5	2812	5	REST	4	57797826	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	1059724	57797826	133356450	25	13951											
PIK3R1	5295	hgsc.bcm.edu	37	chr5	67588157	67588158	+	Frame_Shift_Ins	INS	-	-	G																															ataacaatatgtccttacaaINSgatgctgaatggtactgggg																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr5:67588157_67588158insG	ENST00000521381.1	+	8	1603_1604	c.987_988insG	c.(988-990)gatfs	p.D330fs	PIK3R1_ENST00000523872.1_5'Flank|PIK3R1_ENST00000336483.5_Frame_Shift_Ins_p.D60fs|PIK3R1_ENST00000396611.1_Frame_Shift_Ins_p.D330fs|PIK3R1_ENST00000521657.1_Frame_Shift_Ins_p.D330fs|PIK3R1_ENST00000320694.8_Frame_Shift_Ins_p.D30fs|PIK3R1_ENST00000274335.5_Frame_Shift_Ins_p.D330fs	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	330				D -> N (in Ref. 1; M61906). {ECO:0000305}.	B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.0?(1)|p.?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	TGTCCTTACAAGATGCTGAATG	0.396			"Mis, F, O"		"gliobastoma, ovarian, colorectal"					TCGA GBM(4;<1E-08)																											p.Q329fs		Atlas-Indel,Pindel	.		Rec	yes		5	5q13.1	5295	"phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"		"E, O"	.	PIK3R1	869	.	2	Whole gene deletion(1)|Unknown(1)	large_intestine(1)|lung(1)	c.987_988insG						PASS	.																																			SO:0001589	frameshift_variant	5295	exon8			.	M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"SH2 domain containing"	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.988dupG	chr5.hg19:g.67588158_67588158dupG	ENSP00000428056:p.Asp330fs	51.0	0.0	0		55.0	24.0	0.436364	NM_181523	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Frame_Shift_Ins	INS	ENST00000521381.1	hg19	CCDS3993.1																																																																																			.	.	.	none		0.396	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		G	67588158	-	G	67588157	7	5	230	1	0	1	1	0	0	0	0	0	11925	69	3	0	1143	0	PIK3R1	5	67588157	Frame_Shift_Ins	INS	-	TCGA-P4-A5E7-01A-31D-A28G-10		67588157	113327103	26	13952											
NAIP	4671	hgsc.bcm.edu	37	chr5	70279772	70279772	+	Frame_Shift_Del	DEL	T	T	-																															ctataaagcctctgctgtggTttaaatggagttcgatgcgc																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr5:70279772delT	ENST00000517649.1	-	12	3394	c.3104delA	c.(3103-3105)aacfs	p.N1035fs	NAIP_ENST00000508426.2_Frame_Shift_Del_p.N1035fs|NAIP_ENST00000194097.4_Frame_Shift_Del_p.N1035fs|NAIP_ENST00000503719.2_Frame_Shift_Del_p.N873fs|NAIP_ENST00000523981.1_Frame_Shift_Del_p.N873fs	NM_004536.2	NP_004527.2	Q13075	BIRC1_HUMAN	NLR family, apoptosis inhibitory protein	1035					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)		TCTGCTGTGGTTTAAATGGAG	0.468																																					p.N1035fs		Atlas-INDEL	.											.	NAIP	38	.	0			c.3105delC						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.3104delA	chr5.hg19:g.70279772delT	ENSP00000428657:p.Asn1035fs	221.0	0.0	0		221.0	17.0	0.0769231	NM_004536	B9EG72|E9PHD1|O75857|Q13730|Q59GI6|Q8TDZ4|Q99796	Frame_Shift_Del	DEL	ENST00000517649.1	hg19	CCDS4009.1																																																																																			.	.	.	none		0.468	NAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372649.6	NM_004536		-	70279772	T	-	70279772	7	5	230	1	0	1	0	1	0	0	0	0	10154	1725	60	0	1131	0	NAIP	5	70279772	Frame_Shift_Del	DEL	T	TCGA-P4-A5E7-01A-31D-A28G-10	2691615	70279772	110635488	27	13953											
NQO2	4835	hgsc.bcm.edu	37	chr6	3010268	3010268	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcctgatttaggtaagaaagTactcattgtctatgcacacc	12	13	7	9	0	2	2	1	1	1	1	3	2	3	2	2	1	2	3	2	1	5	6			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr6:3010268T>C	ENST00000338130.2	+	6	729	c.17T>C	c.(16-18)gTa>gCa	p.V6A	NQO2_ENST00000380430.1_Missense_Mutation_p.V6A|NQO2_ENST00000380441.1_Missense_Mutation_p.V6A|NQO2_ENST00000380454.4_Missense_Mutation_p.V6A|NQO2_ENST00000606474.1_3'UTR|NQO2_ENST00000380455.4_Missense_Mutation_p.V6A			P16083	NQO2_HUMAN	NAD(P)H dehydrogenase, quinone 2	6					memory (GO:0007613)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	dihydronicotinamide riboside quinone reductase activity (GO:0001512)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADPH dehydrogenase (quinone) activity (GO:0008753)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	7	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Dabigatran etexilate(DB06695)|Flavin adenine dinucleotide(DB03147)|Melatonin(DB01065)|Menadione(DB00170)|Primaquine(DB01087)	GGTAAGAAAGTACTCATTGTC	0.423																																					p.V6A		Atlas-SNP	.											.	NQO2	21	.	0			c.T17C						PASS	.						97	87	90					6																	3010268		2203	4300	6503	SO:0001583	missense	4835	exon3			AGAAAGTACTCAT	U07736	CCDS4481.1, CCDS75388.1	6p25.2	2012-09-20	2001-11-30	2001-12-07	ENSG00000124588	ENSG00000124588	1.6.5.2		7856	protein-coding gene	gene with protein product		160998	"NAD(P)H menadione oxidoreductase 2, dioxin-inducible"	NMOR2		1691923	Standard	XM_005249152		Approved	QR2, DHQV, DIA6	uc003mus.2	P16083	OTTHUMG00000014130	ENST00000338130.2:c.17T>C	chr6.hg19:g.3010268T>C	ENSP00000337773:p.Val6Ala	123.0	0.0	.		104.0	30.0	.	NM_000904	B2R492|Q5TD04	Missense_Mutation	SNP	ENST00000338130.2	hg19	CCDS4481.1	.	.	.	.	.	.	.	.	.	.	T	12.76	2.034069	0.35893	.	.	ENSG00000124588	ENST00000426637;ENST00000380472;ENST00000538898;ENST00000397717;ENST00000338130;ENST00000380441;ENST00000380455;ENST00000380454;ENST00000380430	T;T;T;T;T;T;T;T	0.11930	2.81;2.73;2.73;2.81;2.81;2.81;2.81;2.81	5.63	5.63	0.86233	Flavodoxin-like fold (1);	0.123571	0.56097	D	0.000034	T	0.18800	0.0451	L	0.52823	1.66	0.44771	D	0.997777	P;D	0.89917	0.613;1.0	P;D	0.91635	0.851;0.999	T	0.06516	-1.0822	10	0.16896	T	0.51	-27.3633	13.5807	0.61901	0.0:0.0:0.0:1.0	.	6;53	P16083;Q59EN2	NQO2_HUMAN;.	A	6;6;53;6;6;6;6;6;6	ENSP00000406951:V6A;ENSP00000369839:V6A;ENSP00000380829:V6A;ENSP00000337773:V6A;ENSP00000369806:V6A;ENSP00000369822:V6A;ENSP00000369821:V6A;ENSP00000369795:V6A	ENSP00000337773:V6A	V	+	2	0	NQO2	2955267	0.985000	0.35326	1.000000	0.80357	0.371000	0.29859	1.927000	0.40094	2.140000	0.66376	0.460000	0.39030	GTA	.	.	.	none		0.423	NQO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039651.1			C	3010268	T	C	3010268	3	2	230	1	0	0	0	0	1	0	0	0	10619	1638	57	3	23	3	NQO2	6	3010268	Missense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10		3010268	168104799	28	13954											
GABBR1	2550	hgsc.bcm.edu	37	chr6	29595420	29595420	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccgatgtacactgcgcgcCgttctgaggaggggtgcggg	5	7	17	12	5	1	1	0	1	1	0	1	3	1	2	3	4	3	2	3	4	1	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr6:29595420C>T	ENST00000377034.4	-	6	835	c.500G>A	c.(499-501)cGg>cAg	p.R167Q	GABBR1_ENST00000377012.4_Missense_Mutation_p.R50Q|GABBR1_ENST00000376977.3_Missense_Mutation_p.R167Q|GABBR1_ENST00000355973.3_Missense_Mutation_p.R50Q|GABBR1_ENST00000377016.4_Missense_Mutation_p.R105Q	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	167					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)	CACTGCGCGCCGTTCTGAGGA	0.716																																					p.R167Q		Atlas-SNP	.											.	GABBR1	95	.	0			c.G500A						PASS	.						5	5	5					6																	29595420		1961	3937	5898	SO:0001583	missense	2550	exon6			GCGCGCCGTTCTG	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.500G>A	chr6.hg19:g.29595420C>T	ENSP00000366233:p.Arg167Gln	5.0	0.0	.		34.0	14.0	.	NM_001470	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Missense_Mutation	SNP	ENST00000377034.4	hg19	CCDS4663.1	.	.	.	.	.	.	.	.	.	.	C	17.14	3.313674	0.60414	.	.	ENSG00000204681	ENST00000355973;ENST00000376977;ENST00000377016;ENST00000377012;ENST00000377034	D;T;D;D;T	0.82984	-1.67;-0.98;-1.57;-1.67;-0.45	3.25	3.25	0.37280	.	0.279410	0.27912	U	0.017356	T	0.57257	0.2041	L	0.46157	1.445	0.33376	D	0.574201	B;B;B;B	0.28208	0.071;0.065;0.063;0.203	B;B;B;B	0.21151	0.033;0.01;0.011;0.028	T	0.49263	-0.8958	10	0.22109	T	0.4	-24.9114	6.2007	0.20575	0.0:0.8596:0.0:0.1404	.	167;105;167;50	Q9UBS5-5;Q9UBS5-3;Q9UBS5;Q5SUJ9	.;.;GABR1_HUMAN;.	Q	50;167;105;50;167	ENSP00000348248:R50Q;ENSP00000366176:R167Q;ENSP00000366215:R105Q;ENSP00000366211:R50Q;ENSP00000366233:R167Q	ENSP00000348248:R50Q	R	-	2	0	GABBR1	29703399	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.661000	0.46758	1.645000	0.50612	0.455000	0.32223	CGG	.	.	.	none		0.716	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3			T	29595420	C	T	29595420	3	4	230	1	0	0	0	0	1	0	0	0	6162	652	23	1	2457	1	GABBR1	6	29595420	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	26585152	29595420	141519647	29	13955											
NFKBIL1	4795	hgsc.bcm.edu	37	chr6	31526116	31526116	+	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	accccagaggagcggggaggGgcagcctctggcgatttggt	7	6	18	10	2	1	1	0	0	1	1	1	4	1	3	3	7	2	1	3	7	0	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr6:31526116G>A	ENST00000376148.4	+	4	988	c.874G>A	c.(874-876)Ggc>Agc	p.G292S	NFKBIL1_ENST00000376145.4_Missense_Mutation_p.G277S	NM_005007.3	NP_004998.3	Q9UBC1	IKBL1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 1	292					cellular response to lipopolysaccharide (GO:0071222)|cytoplasmic sequestering of transcription factor (GO:0042994)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of tumor necrosis factor production (GO:0032720)	cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(1)|lung(2)|skin(1)	7						AGCGGGGAGGGGCAGCCTCTG	0.711																																					p.G292S		Atlas-SNP	.											.	NFKBIL1	17	.	0			c.G874A						PASS	.						7	7	7					6																	31526116		1474	2672	4146	SO:0001583	missense	4795	exon4			GGGAGGGGCAGCC	X77909	CCDS4700.1, CCDS47399.1, CCDS47400.1	6p21.3	2010-02-17			ENSG00000204498	ENSG00000204498			7800	protein-coding gene	gene with protein product		601022		NFKBIL		8081366	Standard	NM_005007		Approved	IKBL	uc003nub.3	Q9UBC1	OTTHUMG00000031038	ENST00000376148.4:c.874G>A	chr6.hg19:g.31526116G>A	ENSP00000365318:p.Gly292Ser	24.0	0.0	.		69.0	23.0	.	NM_005007	A6NL91|B4DUW1|Q14625|Q5HYU4|Q5RJ72|Q5ST96|Q5STV4|Q5STV5|Q9UBX4	Missense_Mutation	SNP	ENST00000376148.4	hg19	CCDS4700.1	.	.	.	.	.	.	.	.	.	.	G	13.38	2.218538	0.39201	.	.	ENSG00000204498	ENST00000376146;ENST00000376148;ENST00000376145	T;T;T	0.30448	1.53;1.53;1.53	5.95	3.09	0.35607	.	0.261597	0.36555	N	0.002538	T	0.04318	0.0119	N	0.11560	0.145	0.31038	N	0.71666	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.39820	-0.9595	10	0.17369	T	0.5	-13.1009	5.6448	0.17584	0.1708:0.1613:0.6679:0.0	.	269;277;292	Q5STV6;Q5STV4;Q9UBC1	.;.;IKBL1_HUMAN	S	269;292;277	ENSP00000365316:G269S;ENSP00000365318:G292S;ENSP00000365315:G277S	ENSP00000365315:G277S	G	+	1	0	NFKBIL1	31634095	0.998000	0.40836	0.997000	0.53966	0.980000	0.70556	0.920000	0.28705	0.863000	0.35553	0.563000	0.77884	GGC	.	.	.	none		0.711	NFKBIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076036.3	NM_005007		A	31526116	G	A	31526116	3	1	230	1	0	0	0	0	1	0	0	0	10388	1232	43	2	888	2	NFKBIL1	6	31526116	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	1930696	31526116	139588951	30	13956											
HCRTR2	3062	hgsc.bcm.edu	37	chr6	55039411	55039411	+	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	cggcaccaaattggaggactCccccccttgtcgcaactggt	8	8	10	15	2	0	0	0	0	0	0	2	2	1	2	4	4	1	2	4	4	2	2	rs76774128		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr6:55039411C>G	ENST00000370862.3	+	1	362	c.26C>G	c.(25-27)tCc>tGc	p.S9C		NM_001526.3	NP_001517.2	O43614	OX2R_HUMAN	hypocretin (orexin) receptor 2	9					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)	p.P11fs*11(1)		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)			TTGGAGGACTCCCCCCCTTGT	0.567																																					p.S9C		Atlas-SNP	.											.,3	HCRTR2	112	.	1	Deletion - Frameshift(1)	upper_aerodigestive_tract(1)	c.C26G						PASS	.						101	96	98					6																	55039411		2203	4300	6503	SO:0001583	missense	3062	exon1			AGGACTCCCCCCC	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.26C>G	chr6.hg19:g.55039411C>G	ENSP00000359899:p.Ser9Cys	91.0	0.0	.		130.0	47.0	.	NM_001526	Q5VTM0	Missense_Mutation	SNP	ENST00000370862.3	hg19	CCDS4956.1	.	.	.	.	.	.	.	.	.	.	C	12.39	1.922205	0.33908	.	.	ENSG00000137252	ENST00000370862	T	0.62232	0.04	4.81	3.94	0.45596	.	0.414369	0.27084	N	0.021005	T	0.30572	0.0769	L	0.36672	1.1	0.32083	N	0.592878	B	0.02656	0.0	B	0.04013	0.001	T	0.14227	-1.0480	10	0.42905	T	0.14	.	8.2548	0.31748	0.0:0.7582:0.1587:0.0831	.	9	O43614	OX2R_HUMAN	C	9	ENSP00000359899:S9C	ENSP00000359899:S9C	S	+	2	0	HCRTR2	55147370	0.019000	0.18553	1.000000	0.80357	0.907000	0.53573	0.521000	0.22893	1.246000	0.43901	-0.257000	0.10917	TCC	.	.	.	alt		0.567	HCRTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043392.1			G	55039411	C	G	55039411	3	3	230	1	0	0	0	0	1	0	0	0	7009	855	30	4	28	4	HCRTR2	6	55039411	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	23513295	55039411	116075656	31	13957											
COL12A1	1303	hgsc.bcm.edu	37	chr6	75848659	75848659	+	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	cttcagtaatctttaagtttGttggggctggcacgggtcct	6	15	12	8	1	2	0	1	0	1	0	3	0	3	0	1	4	0	5	1	4	2	6			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr6:75848659G>T	ENST00000322507.8	-	28	5285	c.4976C>A	c.(4975-4977)aCa>aAa	p.T1659K	COL12A1_ENST00000483888.2_Missense_Mutation_p.T1659K|COL12A1_ENST00000416123.2_Missense_Mutation_p.T1659K|COL12A1_ENST00000345356.6_Missense_Mutation_p.T495K	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1659	Fibronectin type-III 12. {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						CTTTAAGTTTGTTGGGGCTGG	0.403																																					p.T1659K		Atlas-SNP	.											.	COL12A1	385	.	0			c.C4976A						PASS	.						102	102	102					6																	75848659		1847	4078	5925	SO:0001583	missense	1303	exon28			AAGTTTGTTGGGG	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.4976C>A	chr6.hg19:g.75848659G>T	ENSP00000325146:p.Thr1659Lys	64.0	0.0	.		63.0	16.0	.	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	hg19	CCDS43482.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.188|0.188	-1.055736|-1.055736	0.01965|0.01965	.|.	.|.	ENSG00000111799|ENSG00000111799	ENST00000419671|ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	.|T;T;T;T	.|0.57752	.|0.38;0.38;0.38;0.38	5.95|5.95	4.98|4.98	0.66077|0.66077	.|Fibronectin, type III (4);Immunoglobulin-like fold (1);	.|0.429258	.|0.26428	.|N	.|0.024432	T|T	0.11410|0.11410	0.0278|0.0278	N|N	0.20685|0.20685	0.6|0.6	0.09310|0.09310	N|N	0.999999|0.999999	.|B;B	.|0.06786	.|0.0;0.001	.|B;B	.|0.08055	.|0.002;0.003	T|T	0.34850|0.34850	-0.9812|-0.9812	5|10	.|0.02654	.|T	.|1	.|.	5.5016|5.5016	0.16831|0.16831	0.1314:0.0:0.661:0.2076|0.1314:0.0:0.661:0.2076	.|.	.|495;1659	.|Q99715-2;Q99715	.|.;COCA1_HUMAN	K|K	400|1659;1659;495;1659;1659	.|ENSP00000325146:T1659K;ENSP00000305147:T495K;ENSP00000412864:T1659K;ENSP00000421216:T1659K	.|ENSP00000325146:T1659K	N|T	-|-	3|2	2|0	COL12A1|COL12A1	75905379|75905379	1.000000|1.000000	0.71417|0.71417	0.986000|0.986000	0.45419|0.45419	0.021000|0.021000	0.10359|0.10359	2.434000|2.434000	0.44802|0.44802	2.827000|2.827000	0.97445|0.97445	0.650000|0.650000	0.86243|0.86243	AAC|ACA	.	.	.	none		0.403	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		T	75848659	G	T	75848659	3	4	230	1	0	0	0	0	1	0	0	0	3671	1377	48	4	4371	4	COL12A1	6	75848659	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	20809248	75848659	95266408	32	13958											
RSPH3	83861	hgsc.bcm.edu	37	chr6	159398820	159398821	+	Frame_Shift_Del	DEL	TG	TG	-																															cctcgggttctggagactgaTgtgtgtcttccccatgctca																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr6:159398820_159398821delTG	ENST00000252655.1	-	8	1621_1622	c.1432_1433delCA	c.(1432-1434)catfs	p.H478fs	RSPH3_ENST00000607398.1_5'Flank|RSPH3_ENST00000297262.3_Frame_Shift_Del_p.H382fs|RSPH3_ENST00000449822.1_Frame_Shift_Del_p.H240fs|RSPH3_ENST00000367069.2_Frame_Shift_Del_p.H336fs	NM_031924.4	NP_114130.3	Q86UC2	RSPH3_HUMAN	radial spoke 3 homolog (Chlamydomonas)	478										endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|skin(1)|stomach(7)	23		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.36e-16)|BRCA - Breast invasive adenocarcinoma(81;5.92e-06)		TGGAGACTGATGTGTGTCTTCC	0.48																																					p.478_478del		Atlas-Indel,Pindel	.											.	RSPH3	48	.	0			c.1433_1434del						PASS	.																																			SO:0001589	frameshift_variant	83861	exon8			.	AF353618	CCDS5260.1	6q25.3	2014-05-16	2008-07-04	2007-06-26	ENSG00000130363	ENSG00000130363			21054	protein-coding gene	gene with protein product		615876	"radial spokehead-like 2"	RSHL2		12477932	Standard	NM_031924		Approved	dJ111C20.1, RSP3	uc003qrx.3	Q86UC2	OTTHUMG00000015924	ENST00000252655.1:c.1432_1433delCA	chr6.hg19:g.159398824_159398825delTG	ENSP00000252655:p.His478fs	72.0	0.0	0		77.0	23.0	0.298701	NM_031924	Q96LQ5|Q96LX2|Q9BX75	Frame_Shift_Del	DEL	ENST00000252655.1	hg19	CCDS5260.1																																																																																			.	.	.	none		0.48	RSPH3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031924		-	159398821	TG	-	159398820	7	5	230	1	0	1	0	1	0	0	0	0	13718	1464	51	0	253	0	RSPH3	6	159398820	Frame_Shift_Del	DEL	TG	TCGA-P4-A5E7-01A-31D-A28G-10	83550161	159398820	11716247	33	13959											
THSD7A	221981	hgsc.bcm.edu	37	chr7	11486930	11486931	+	Frame_Shift_Ins	INS	-	-	T																															aaaacttggaccagctggtcINSaattgacagtcatcctggca																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr7:11486930_11486931insT	ENST00000423059.4	-	12	2977_2978	c.2726_2727insA	c.(2725-2727)ttgfs	p.L909fs	AC004538.3_ENST00000445839.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	909	TSP type-1 9. {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)		ACCAGCTGGTCAATTGACAGTC	0.53										HNSCC(18;0.044)																											p.L909fs		Atlas-Indel,Pindel	.											.	THSD7A	219	.	0			c.2727_2728insA						PASS	.																																			SO:0001589	frameshift_variant	221981	exon12			.		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.2726_2727insA	chr7.hg19:g.11486930_11486931insT	ENSP00000406482:p.Leu909fs	85.0	0.0	0		167.0	84.0	0.502994	NM_015204		Frame_Shift_Ins	INS	ENST00000423059.4	hg19	CCDS47543.1																																																																																			.	.	.	none		0.53	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		T	11486931	-	T	11486930	7	5	230	1	0	1	1	0	0	0	0	0	15891	825	29	0	2310	0	THSD7A	7	11486930	Frame_Shift_Ins	INS	-	TCGA-P4-A5E7-01A-31D-A28G-10		11486930	147651733	34	13960											
AHR	196	hgsc.bcm.edu	37	chr7	17375399	17375399	+	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	gattatatcattgtaactcaGagaccactaacgtaagcaca	16	10	6	9	1	2	1	2	0	0	1	2	3	2	1	1	0	3	3	1	0	5	6			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr7:17375399G>C	ENST00000242057.4	+	9	1792	c.1149G>C	c.(1147-1149)caG>caC	p.Q383H	AHR_ENST00000492120.1_3'UTR	NM_001621.4	NP_001612.1	P35869	AHR_HUMAN	aryl hydrocarbon receptor	383	PAC.				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)	p.Q383H(2)		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)	TTGTAACTCAGAGACCACTAA	0.348																																					p.Q383H		Atlas-SNP	.											AHR,NS,carcinoma,0,1	AHR	89	.	2	Substitution - Missense(2)	lung(2)	c.G1149C						PASS	.						71	63	66					7																	17375399		2202	4300	6502	SO:0001583	missense	196	exon9			AACTCAGAGACCA	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.1149G>C	chr7.hg19:g.17375399G>C	ENSP00000242057:p.Gln383His	57.0	0.0	.		71.0	40.0	.	NM_001621	A4D130|Q13728|Q13803|Q13804	Missense_Mutation	SNP	ENST00000242057.4	hg19	CCDS5366.1	.	.	.	.	.	.	.	.	.	.	G	15.77	2.930150	0.52759	.	.	ENSG00000106546	ENST00000242057	T	0.05447	3.44	5.98	-1.41	0.08941	.	0.000000	0.85682	D	0.000000	T	0.06917	0.0176	L	0.43152	1.355	0.44798	D	0.997802	B	0.28128	0.201	B	0.31390	0.129	T	0.22277	-1.0221	10	0.62326	D	0.03	.	12.8346	0.57765	0.6126:0.0:0.3874:0.0	.	383	P35869	AHR_HUMAN	H	383	ENSP00000242057:Q383H	ENSP00000242057:Q383H	Q	+	3	2	AHR	17341924	0.995000	0.38212	0.977000	0.42913	0.859000	0.49053	0.361000	0.20267	-0.292000	0.08999	0.591000	0.81541	CAG	.	.	.	none		0.348	AHR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314620.2	NM_001621		C	17375399	G	C	17375399	3	2	230	1	0	0	0	0	1	0	0	0	416	933	33	4	1183	4	AHR	7	17375399	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	5888469	17375399	141763264	35	13961											
AUTS2	26053	hgsc.bcm.edu	37	chr7	69364300	69364300	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcacttaagcctcaggaacGtgtggagaaacgccagacgc	13	5	12	11	3	1	2	1	0	0	2	1	4	1	3	2	2	4	1	2	2	3	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr7:69364300G>A	ENST00000342771.4	+	2	659	c.338G>A	c.(337-339)cGt>cAt	p.R113H	AUTS2_ENST00000403018.2_Missense_Mutation_p.R113H|AUTS2_ENST00000406775.2_Missense_Mutation_p.R113H	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	113								p.R113L(1)		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)		CCTCAGGAACGTGTGGAGAAA	0.473																																					p.R113H		Atlas-SNP	.											AUTS2,caecum,carcinoma,+1,1	AUTS2	173	.	1	Substitution - Missense(1)	lung(1)	c.G338A						PASS	.						86	79	81					7																	69364300		2203	4300	6503	SO:0001583	missense	26053	exon2			AGGAACGTGTGGA	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.338G>A	chr7.hg19:g.69364300G>A	ENSP00000344087:p.Arg113His	73.0	0.0	.		130.0	22.0	.	NM_001127231	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Missense_Mutation	SNP	ENST00000342771.4	hg19	CCDS5539.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.345953	0.82022	.	.	ENSG00000158321	ENST00000406775;ENST00000342771;ENST00000403018	T;T	0.39787	1.06;1.08	5.65	5.65	0.86999	.	0.000000	0.64402	D	0.000019	T	0.56187	0.1968	L	0.46157	1.445	0.23872	N	0.9966	D;D;D	0.89917	0.997;0.994;1.0	P;P;D	0.69824	0.862;0.754;0.966	T	0.48980	-0.8986	9	.	.	.	-11.4592	14.7871	0.69810	0.0:0.2577:0.7423:0.0	.	113;113;113	Q8WXX7-2;Q8WXX7;Q6PJU5	.;AUTS2_HUMAN;.	H	113	ENSP00000385263:R113H;ENSP00000344087:R113H	.	R	+	2	0	AUTS2	69002236	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.796000	0.62496	2.941000	0.99782	0.655000	0.94253	CGT	.	.	.	none		0.473	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			A	69364300	G	A	69364300	3	1	230	1	0	0	0	0	1	0	0	0	1225	1145	40	1	344	1	AUTS2	7	69364300	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	51988901	69364300	89774363	36	13962											
BAZ1B	9031	hgsc.bcm.edu	37	chr7	72873963	72873963	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttttgcttgggagccatgAagccttggagaaatttcttt	8	16	10	7	0	2	2	0	1	2	1	2	4	2	3	2	2	3	1	2	2	2	6			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr7:72873963A>G	ENST00000339594.4	-	13	3673	c.3335T>C	c.(3334-3336)tTc>tCc	p.F1112S	BAZ1B_ENST00000404251.1_Missense_Mutation_p.F1112S	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	1112					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)				GGGAGCCATGAAGCCTTGGAG	0.398																																					p.F1112S	Esophageal Squamous(112;1167 1561 21085 43672 48228)	Atlas-SNP	.											.	BAZ1B	147	.	0			c.T3335C						PASS	.						146	140	142					7																	72873963		2203	4300	6503	SO:0001583	missense	9031	exon13			GCCATGAAGCCTT	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.3335T>C	chr7.hg19:g.72873963A>G	ENSP00000342434:p.Phe1112Ser	60.0	0.0	.		70.0	43.0	.	NM_032408	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Missense_Mutation	SNP	ENST00000339594.4	hg19	CCDS5549.1	.	.	.	.	.	.	.	.	.	.	A	28.2	4.902860	0.92035	.	.	ENSG00000009954	ENST00000339594;ENST00000404251	T;T	0.59364	0.27;0.27	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.64305	0.2586	L	0.32530	0.975	0.58432	D	0.999999	D	0.71674	0.998	D	0.71656	0.974	T	0.59963	-0.7355	10	0.22109	T	0.4	-20.6332	14.9627	0.71169	1.0:0.0:0.0:0.0	.	1112	Q9UIG0	BAZ1B_HUMAN	S	1112	ENSP00000342434:F1112S;ENSP00000385442:F1112S	ENSP00000342434:F1112S	F	-	2	0	BAZ1B	72511899	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.697000	0.91307	2.125000	0.65367	0.533000	0.62120	TTC	.	.	.	none		0.398	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408		G	72873963	A	G	72873963	3	3	230	1	0	0	0	0	1	0	0	0	1330	246	9	3	1144	3	BAZ1B	7	72873963	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	3509663	72873963	86264700	37	13963											
CUX1	1523	hgsc.bcm.edu	37	chr7	101882763	101882763	+	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	aaggaggcgctgaaacgagcGtatcagcaaaagccataccc	15	4	11	11	3	1	1	1	1	0	0	1	3	1	2	2	2	5	3	2	2	6	2	rs140169027		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr7:101882763G>A	ENST00000292535.7	+	23	3824	c.3786G>A	c.(3784-3786)gcG>gcA	p.A1262A	CUX1_ENST00000560541.1_Intron|CUX1_ENST00000546411.2_Silent_p.A1160A|AC005088.1_ENST00000580604.1_RNA|CUX1_ENST00000360264.3_Silent_p.A1273A|CUX1_ENST00000549414.2_Silent_p.A1240A|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000556210.1_Silent_p.A1104A|CUX1_ENST00000292538.4_Intron|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000550008.2_Silent_p.A1206A	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	1262					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						TGAAACGAGCGTATCAGCAAA	0.597																																					p.A1273A		Atlas-SNP	.											CUX1,colon,carcinoma,0,1	CUX1	253	.	0			c.G3819A						PASS	.	G	,,,,,,	0,4406		0,0,2203	113	109	110		3819,,,,,,3786	-9.8	0	7	dbSNP_134	110	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous	CUX1	NM_001202543.1,NM_001202544.1,NM_001202545.1,NM_001202546.1,NM_001913.3,NM_181500.2,NM_181552.3	,,,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,,,	1273/1517,,,,,,1262/1506	101882763	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1523	exon23			ACGAGCGTATCAG	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.3786G>A	chr7.hg19:g.101882763G>A		57.0	0.0	.		158.0	98.0	.	NM_001202543	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Silent	SNP	ENST00000292535.7	hg19	CCDS5721.1																																																																																			.	G|1.000;A|0.000	0.000	weak		0.597	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913		A	101882763	G	A	101882763	2	1	230	1	0	0	0	0	0	0	0	1	4066	1132	40	1		1	CUX1	7	101882763	Silent	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	29008800	101882763	57255900	38	13964											
MLL3	58508	hgsc.bcm.edu	37	chr7	151845991	151845991	+	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	cggcctgcaatcttcaaaccCaccatggacagctcttagcc	10	8	7	16	1	3	0	1	0	2	0	3	1	3	1	4	2	4	2	4	2	3	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr7:151845991C>A	ENST00000262189.6	-	52	13239	c.13021G>T	c.(13021-13023)Ggg>Tgg	p.G4341W	KMT2C_ENST00000355193.2_Missense_Mutation_p.G4398W	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	4341					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)										TCTTCAAACCCACCATGGACA	0.493																																					p.G4341W		Atlas-SNP	.											.	MLL3	1564	.	0			c.G13021T						PASS	.						63	59	60					7																	151845991		2203	4300	6503	SO:0001583	missense	58508	exon52			CAAACCCACCATG	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.13021G>T	chr7.hg19:g.151845991C>A	ENSP00000262189:p.Gly4341Trp	62.0	0.0	.		97.0	23.0	.	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.63|13.63	2.295838|2.295838	0.40594|0.40594	.|.	.|.	ENSG00000055609|ENSG00000055609	ENST00000262189;ENST00000355193;ENST00000424877|ENST00000360104	D;D;D|.	0.88975|.	-1.77;-1.77;-2.45|.	5.4|5.4	4.52|4.52	0.55395|0.55395	.|.	0.152286|.	0.29892|.	U|.	0.010923|.	T|T	0.64670|0.64670	0.2619|0.2619	M|M	0.65498|0.65498	2.005|2.005	0.80722|0.80722	D|D	1|1	D;D;D|.	0.69078|.	0.997;0.997;0.997|.	P;D;D|.	0.68483|.	0.907;0.958;0.958|.	T|T	0.63637|0.63637	-0.6592|-0.6592	10|5	0.49607|.	T|.	0.09|.	.|.	10.7105|10.7105	0.45980|0.45980	0.0:0.8351:0.0:0.1649|0.0:0.8351:0.0:0.1649	.|.	4341;3459;4398|.	Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3|.	MLL3_HUMAN;.;.|.	W|L	4341;4398;958|1901	ENSP00000262189:G4341W;ENSP00000347325:G4398W;ENSP00000410411:G958W|.	ENSP00000262189:G4341W|.	G|W	-|-	1|2	0|0	MLL3|MLL3	151476924|151476924	0.007000|0.007000	0.16637|0.16637	0.015000|0.015000	0.15790|0.15790	0.970000|0.970000	0.65996|0.65996	1.934000|1.934000	0.40163|0.40163	1.273000|1.273000	0.44346|0.44346	0.650000|0.650000	0.86243|0.86243	GGG|TGG	.	.	.	none		0.493	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			A	151845991	C	A	151845991	3	1	230	1	0	0	0	0	1	0	0	0	9629	594	21	4	1746	4	MLL3	7	151845991	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	49963228	151845991	7292672	39	13965											
MLL3	58508	hgsc.bcm.edu	37	chr7	151873882	151873883	+	Frame_Shift_Del	DEL	TT	TT	-																															atttgcactggggccagcagTttctcgattggttcttttct																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr7:151873882_151873883delTT	ENST00000262189.6	-	38	8873_8874	c.8655_8656delAA	c.(8653-8658)gaaactfs	p.ET2885fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.ET2885fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2885					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)										GGGCCAGCAGTTTCTCGATTGG	0.441																																					p.2886_2886del		Atlas-Indel,Pindel	.											.	MLL3	1564	.	0			c.8656_8657del						PASS	.																																			SO:0001589	frameshift_variant	58508	exon38			.	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.8655_8656delAA	chr7.hg19:g.151873882_151873883delTT	ENSP00000262189:p.Glu2885fs	98.0	0.0	0		164.0	98.0	0.597561	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	hg19	CCDS5931.1																																																																																			.	.	.	none		0.441	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			-	151873883	TT	-	151873882	7	5	230	1	0	1	0	1	0	0	0	0	9629	1725	60	0	6167	0	MLL3	7	151873882	Frame_Shift_Del	DEL	TT	TCGA-P4-A5E7-01A-31D-A28G-10	27891	151873882	7264781	40	13966											
VDAC3	7419	hgsc.bcm.edu	37	chr8	42259309	42259309	+	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	ttgtttgtttattgcagaaaGaagagtgggaaattgaaggc	13	13	13	2	0	0	4	0	1	0	3	0	5	0	5	0	2	1	3	0	2	5	6			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr8:42259309G>C	ENST00000022615.4	+	7	395	c.327G>C	c.(325-327)aaG>aaC	p.K109N	VDAC3_ENST00000392935.3_Missense_Mutation_p.K110N|VDAC3_ENST00000521158.1_Missense_Mutation_p.K110N|VDAC3_ENST00000522572.1_Missense_Mutation_p.K110N			Q9Y277	VDAC3_HUMAN	voltage-dependent anion channel 3	109					adenine transport (GO:0015853)	extracellular vesicular exosome (GO:0070062)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|pore complex (GO:0046930)	nucleotide binding (GO:0000166)|porin activity (GO:0015288)|voltage-gated anion channel activity (GO:0008308)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	7	all_cancers(6;3.86e-23)|all_lung(13;6.47e-12)|Lung NSC(13;1.08e-10)|Ovarian(28;0.00769)|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;3.48e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00266)|Lung(22;0.00849)|LUSC - Lung squamous cell carcinoma(45;0.024)		Dihydroxyaluminium(DB01375)	ATTGCAGAAAGAAGAGTGGGA	0.378																																					p.K110N		Atlas-SNP	.											.	VDAC3	17	.	0			c.G330C						PASS	.						100	100	100					8																	42259309		2203	4300	6503	SO:0001583	missense	7419	exon7			CAGAAAGAAGAGT	AF038962	CCDS6131.1, CCDS47850.1	8p11.21	2011-11-15			ENSG00000078668	ENSG00000078668		"Voltage-dependent anion channels"	12674	protein-coding gene	gene with protein product		610029				9653160, 9781040	Standard	NM_001135694		Approved	HD-VDAC3	uc003xpc.3	Q9Y277	OTTHUMG00000164168	ENST00000022615.4:c.327G>C	chr8.hg19:g.42259309G>C	ENSP00000022615:p.Lys109Asn	64.0	0.0	.		72.0	22.0	.	NM_001135694	Q9UIS0	Missense_Mutation	SNP	ENST00000022615.4	hg19	CCDS6131.1	.	.	.	.	.	.	.	.	.	.	G	19.10	3.761925	0.69763	.	.	ENSG00000078668	ENST00000518563;ENST00000392935;ENST00000520115;ENST00000522069;ENST00000522572;ENST00000521158;ENST00000022615	T;T;T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87;0.87;0.87	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.64713	0.2623	M	0.73962	2.25	0.80722	D	1	D	0.67145	0.996	D	0.70935	0.971	T	0.61936	-0.6960	10	0.40728	T	0.16	-12.3041	17.6115	0.88055	0.0:0.0:1.0:0.0	.	109	Q9Y277	VDAC3_HUMAN	N	77;110;109;109;110;110;109	ENSP00000428977:K77N;ENSP00000442811:K110N;ENSP00000428519:K109N;ENSP00000429006:K109N;ENSP00000428029:K110N;ENSP00000428845:K110N;ENSP00000022615:K109N	ENSP00000022615:K109N	K	+	3	2	VDAC3	42378466	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.582000	0.74049	2.832000	0.97577	0.650000	0.86243	AAG	.	.	.	none		0.378	VDAC3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000377574.1			C	42259309	G	C	42259309	3	2	230	1	0	0	0	0	1	0	0	0	17160	933	33	4	348	4	VDAC3	8	42259309	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10		42259309	104104713	41	13967											
SLC7A13	157724	hgsc.bcm.edu	37	chr8	87235298	87235298	+	Frame_Shift_Del	DEL	T	T	-																															ggtaacgcagtaaatatgcaTttgggaattgttgttctggg																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr8:87235298delT	ENST00000297524.3	-	2	823	c.720delA	c.(718-720)aaafs	p.K240fs	SLC7A13_ENST00000520624.1_5'UTR|SLC7A13_ENST00000419776.2_Frame_Shift_Del_p.K231fs	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	240						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						TAAATATGCATTTGGGAATTG	0.363																																					p.C241fs		Atlas-Indel,Pindel	.											.	SLC7A13	97	.	0			c.721delT						PASS	.						147	152	150					8																	87235298		2203	4300	6503	SO:0001589	frameshift_variant	157724	exon2			.	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.720delA	chr8.hg19:g.87235298delT	ENSP00000297524:p.Lys240fs	47.0	0.0	0		55.0	16.0	0.290909	NM_138817	Q05C37|Q08AH9|Q96N84	Frame_Shift_Del	DEL	ENST00000297524.3	hg19	CCDS34917.1																																																																																			.	.	.	none		0.363	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817		-	87235298	T	-	87235298	7	5	230	1	0	1	0	1	0	0	0	0	14708	1490	52	0	704	0	SLC7A13	8	87235298	Frame_Shift_Del	DEL	T	TCGA-P4-A5E7-01A-31D-A28G-10	44975989	87235298	59128724	42	13968											
SFMBT2	57713	hgsc.bcm.edu	37	chr10	7214001	7214001	+	Silent	SNP	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	cgcagggtgacggccctccgGggccgggccgagggcacctc	4	3	18	16	5	0	1	0	1	0	0	2	2	1	1	5	6	0	2	5	6	0	0	rs370293109		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr10:7214001G>A	ENST00000361972.4	-	19	2361	c.2271C>T	c.(2269-2271)ccC>ccT	p.P757P	SFMBT2_ENST00000397167.1_Silent_p.P757P	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	757					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						CGGCCCTCCGGGGCCGGGCCG	0.746																																					p.P757P		Atlas-SNP	.											.	SFMBT2	209	.	0			c.C2271T						PASS	.	G	,	0,4346		0,0,2173	12	15	14		2271,2271	0.9	1	10		14	1,8505		0,1,4252	no	coding-synonymous,coding-synonymous	SFMBT2	NM_001018039.1,NM_001029880.2	,	0,1,6425	AA,AG,GG		0.0118,0.0,0.0078	,	757/895,757/895	7214001	1,12851	2173	4253	6426	SO:0001819	synonymous_variant	57713	exon19			CCTCCGGGGCCGG	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.2271C>T	chr10.hg19:g.7214001G>A		1.0	0.0	.		8.0	6.0	.	NM_001029880	A7MD09|Q9HCF5	Silent	SNP	ENST00000361972.4	hg19	CCDS31138.1																																																																																			.	.	.	none		0.746	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880		A	7214001	G	A	7214001	2	1	230	1	0	0	0	0	0	0	0	1	14171	1219	43	2		2	SFMBT2	10	7214001	Silent	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10		7214001	128320746	43	13969											
PLXDC2	84898	hgsc.bcm.edu	37	chr10	20335920	20335920	+	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	gtgaagattcatggaatattGtccaatactcatcggcaagc	13	11	9	8	1	2	2	2	1	0	1	4	3	3	3	1	2	2	1	1	2	6	4			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr10:20335920G>T	ENST00000377252.4	+	3	1288	c.447G>T	c.(445-447)ttG>ttT	p.L149F	PLXDC2_ENST00000377238.2_3'UTR|PLXDC2_ENST00000377242.3_Intron	NM_001282736.1|NM_032812.7	NP_001269665.1|NP_116201.7	Q6UX71	PXDC2_HUMAN	plexin domain containing 2	149					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						ATGGAATATTGTCCAATACTC	0.373																																					p.L149F		Atlas-SNP	.											.	PLXDC2	108	.	0			c.G447T						PASS	.						95	93	93					10																	20335920		2203	4300	6503	SO:0001583	missense	84898	exon3			AATATTGTCCAAT	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.447G>T	chr10.hg19:g.20335920G>T	ENSP00000366460:p.Leu149Phe	56.0	0.0	.		58.0	5.0	.	NM_032812	Q96E59|Q96PD9|Q96SU9	Missense_Mutation	SNP	ENST00000377252.4	hg19	CCDS7132.1	.	.	.	.	.	.	.	.	.	.	G	17.07	3.294191	0.60086	.	.	ENSG00000120594	ENST00000377252;ENST00000377238;ENST00000536022	T	0.78364	-1.17	5.61	0.195	0.15151	.	0.000000	0.85682	D	0.000000	D	0.82499	0.5050	M	0.79343	2.45	0.58432	D	0.999999	D	0.89917	1.0	D	0.71414	0.973	T	0.77335	-0.2626	10	0.87932	D	0	.	2.1328	0.03754	0.1312:0.2504:0.2267:0.3917	.	149	Q6UX71	PXDC2_HUMAN	F	149;12;135	ENSP00000366460:L149F	ENSP00000366446:L12F	L	+	3	2	PLXDC2	20375926	0.996000	0.38824	0.683000	0.30040	0.886000	0.51366	0.297000	0.19101	-0.233000	0.09797	-0.133000	0.14855	TTG	.	.	.	none		0.373	PLXDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047101.2	NM_032812		T	20335920	G	T	20335920	3	4	230	1	0	0	0	0	1	0	0	0	12125	1368	48	4	457	4	PLXDC2	10	20335920	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	13121919	20335920	115198827	44	13970											
TET1	80312	hgsc.bcm.edu	37	chr10	70332130	70332130	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccatgcaaggccttccagatTagtcaggaaggaagatgtaa	14	8	11	8	0	1	2	1	0	0	2	2	4	2	4	3	3	1	2	3	3	5	3			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr10:70332130T>C	ENST00000373644.4	+	2	244	c.35T>C	c.(34-36)tTa>tCa	p.L12S		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	12					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						CCTTCCAGATTAGTCAGGAAG	0.433																																					p.L12S		Atlas-SNP	.											.	TET1	255	.	0			c.T35C						PASS	.						38	38	38					10																	70332130		2199	4299	6498	SO:0001583	missense	80312	exon2			CCAGATTAGTCAG	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.35T>C	chr10.hg19:g.70332130T>C	ENSP00000362748:p.Leu12Ser	93.0	0.0	.		85.0	28.0	.	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	hg19	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	T	13.35	2.210522	0.39102	.	.	ENSG00000138336	ENST00000373644	T	0.08458	3.09	5.24	0.299	0.15771	.	4.959980	0.00166	N	0.000012	T	0.06735	0.0172	N	0.19112	0.55	0.23501	N	0.997547	B	0.28512	0.214	B	0.21151	0.033	T	0.37502	-0.9703	10	0.28530	T	0.3	.	9.3061	0.37876	0.0:0.403:0.0:0.597	.	12	Q8NFU7	TET1_HUMAN	S	12	ENSP00000362748:L12S	ENSP00000362748:L12S	L	+	2	0	TET1	70002136	0.998000	0.40836	0.679000	0.29978	0.998000	0.95712	0.421000	0.21280	-0.188000	0.10499	0.460000	0.39030	TTA	.	.	.	none		0.433	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		C	70332130	T	C	70332130	3	2	230	1	0	0	0	0	1	0	0	0	15781	1764	61	3	37	3	TET1	10	70332130	Missense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10	49996210	70332130	65202617	45	13971											
PTEN	5728	hgsc.bcm.edu	37	chr10	89717690	89717690	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacgacgggaagacaagttcAtgtactttgagttccctcag	11	10	10	10	2	2	2	2	1	0	1	3	4	3	3	1	1	1	3	1	1	3	4			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr10:89717690A>G	ENST00000371953.3	+	7	2072	c.715A>G	c.(715-717)Atg>Gtg	p.M239V	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	239	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.?(1)|p.R234fs*9(1)|p.K237_Y240>N(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)		AGACAAGTTCATGTACTTTGA	0.418		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.M239V		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	3652	.	50	Whole gene deletion(37)|Deletion - Frameshift(10)|Complex - deletion inframe(1)|Deletion - In frame(1)|Unknown(1)	prostate(16)|central_nervous_system(10)|skin(6)|haematopoietic_and_lymphoid_tissue(4)|lung(4)|breast(4)|ovary(3)|urinary_tract(2)|soft_tissue(1)	c.A715G						PASS	.						153	130	138					10																	89717690		2203	4300	6503	SO:0001583	missense	5728	exon7	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	AAGTTCATGTACT	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.715A>G	chr10.hg19:g.89717690A>G	ENSP00000361021:p.Met239Val	163.0	0.0	.		171.0	49.0	.	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	hg19	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	12.58	1.980414	0.34942	.	.	ENSG00000171862	ENST00000371953	D	0.84660	-1.88	5.15	5.15	0.70609	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.038168	0.85682	D	0.000000	T	0.73567	0.3603	N	0.13352	0.335	0.80722	D	1	B	0.06786	0.001	B	0.10450	0.005	T	0.67983	-0.5529	9	.	.	.	-3.0578	14.9657	0.71193	1.0:0.0:0.0:0.0	.	239	P60484	PTEN_HUMAN	V	239	ENSP00000361021:M239V	.	M	+	1	0	PTEN	89707670	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.918000	0.92759	1.928000	0.55862	0.477000	0.44152	ATG	.	.	.	none		0.418	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89717690	A	G	89717690	3	3	230	1	0	0	0	0	1	0	0	0	12748	217	8	3	741	3	PTEN	10	89717690	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	19385560	89717690	45817057	46	13972											
PDZD8	118987	hgsc.bcm.edu	37	chr10	119043959	119043959	+	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	ttctagtgactatagccttaGgtgagggggcttccagtctc	7	13	12	9	0	2	2	0	2	2	0	4	2	3	2	2	3	1	1	2	3	4	6			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr10:119043959G>T	ENST00000334464.5	-	5	2524	c.2285C>A	c.(2284-2286)cCt>cAt	p.P762H	PDZD8_ENST00000482496.1_5'UTR	NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	762					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)		TATAGCCTTAGGTGAGGGGGC	0.403																																					p.P762H		Atlas-SNP	.											.	PDZD8	85	.	0			c.C2285A						PASS	.						125	111	116					10																	119043959		2203	4300	6503	SO:0001583	missense	118987	exon5			GCCTTAGGTGAGG	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.2285C>A	chr10.hg19:g.119043959G>T	ENSP00000334642:p.Pro762His	70.0	0.0	.		68.0	23.0	.	NM_173791	Q86WE0|Q86WE5|Q9UFF1	Missense_Mutation	SNP	ENST00000334464.5	hg19	CCDS7600.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.075899	0.76415	.	.	ENSG00000165650	ENST00000334464	D	0.87256	-2.23	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	D	0.90889	0.7137	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90836	0.4720	10	0.59425	D	0.04	-12.5235	20.4116	0.99017	0.0:0.0:1.0:0.0	.	762	Q8NEN9	PDZD8_HUMAN	H	762	ENSP00000334642:P762H	ENSP00000334642:P762H	P	-	2	0	PDZD8	119033949	1.000000	0.71417	0.991000	0.47740	0.986000	0.74619	9.869000	0.99810	2.827000	0.97445	0.655000	0.94253	CCT	.	.	.	none		0.403	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791		T	119043959	G	T	119043959	3	4	230	1	0	0	0	0	1	0	0	0	11712	1000	35	4	1183	4	PDZD8	10	119043959	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	29326269	119043959	16490788	47	13973											
PWWP2B	170394	hgsc.bcm.edu	37	chr10	134218416	134218416	+	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	ggctccgggacacgtacaagCtgtgggtgccccagccgccg	6	5	15	15	4	0	0	0	0	0	0	1	1	1	1	5	3	4	3	5	3	2	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr10:134218416C>T	ENST00000305233.5	+	2	471	c.412C>T	c.(412-414)Ctg>Ttg	p.L138L	PWWP2B_ENST00000368609.4_Silent_p.L138L	NM_138499.3	NP_612508.3	Q6NUJ5	PWP2B_HUMAN	PWWP domain containing 2B	138	Pro-rich.									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)		CACGTACAAGCTGTGGGTGCC	0.731																																					p.L138L		Atlas-SNP	.											.	PWWP2B	33	.	0			c.C412T						PASS	.						11	10	10					10																	134218416		1839	3661	5500	SO:0001819	synonymous_variant	170394	exon2			TACAAGCTGTGGG	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.412C>T	chr10.hg19:g.134218416C>T		0.0	0.0	.		5.0	4.0	.	NM_001098637	A6NM90|B5MDQ1|H9KV61|Q5SZI0|Q6ZQX5|Q96F43	Silent	SNP	ENST00000305233.5	hg19	CCDS7667.2																																																																																			.	.	.	none		0.731	PWWP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051075.3	NM_138499		T	134218416	C	T	134218416	2	4	230	1	0	0	0	0	0	0	0	1	12859	796	28	2		2	PWWP2B	10	134218416	Silent	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	15174457	134218416	1316331	48	13974											
MUC6	4588	hgsc.bcm.edu	37	chr11	1018068	1018068	+	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	agggactgctccctgtaggtGgggagtgtgtggtgaagggt	6	10	20	5	0	0	1	0	1	0	0	1	3	1	3	1	6	1	2	1	6	2	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr11:1018068G>A	ENST00000421673.2	-	31	4783	c.4733C>T	c.(4732-4734)cCa>cTa	p.P1578L		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1578	Pro-rich.|Thr-rich.		P -> S (in dbSNP:rs10736904).		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)		CCCTGTAGGTGGGGAGTGTGT	0.582																																					p.P1578L		Atlas-SNP	.											.	MUC6	408	.	0			c.C4733T						PASS	.						259	265	263					11																	1018068		2174	4263	6437	SO:0001583	missense	4588	exon31			GTAGGTGGGGAGT	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.4733C>T	chr11.hg19:g.1018068G>A	ENSP00000406861:p.Pro1578Leu	394.0	0.0	.		411.0	70.0	.	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	hg19	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	9.977	1.227087	0.22542	.	.	ENSG00000184956	ENST00000421673	T	0.15603	2.41	2.31	1.29	0.21616	.	.	.	.	.	T	0.12689	0.0308	L	0.46157	1.445	0.09310	N	1	B	0.24963	0.115	B	0.19946	0.027	T	0.38520	-0.9657	9	0.10902	T	0.67	.	8.0503	0.30575	0.0:0.0:0.7368:0.2632	.	1578	Q6W4X9	MUC6_HUMAN	L	1578	ENSP00000406861:P1578L	ENSP00000406861:P1578L	P	-	2	0	MUC6	1008068	0.000000	0.05858	0.001000	0.08648	0.150000	0.21749	-0.194000	0.09559	0.226000	0.20979	0.297000	0.19635	CCA	.	.	.	none		0.582	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		A	1018068	G	A	1018068	3	1	230	1	0	0	0	0	1	0	0	0	9987	1348	47	2	2598	2	MUC6	11	1018068	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10		1018068	133988448	49	13975											
KRTAP5-4	387267	hgsc.bcm.edu	37	chr11	1643254	1643254	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccccacagccagagccacAgcccccacagccggagccac	10	0	9	22	1	0	1	0	0	0	1	0	2	0	2	8	1	5	0	8	1	0	0			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr11:1643254A>G	ENST00000399682.1	-	1	114	c.70T>C	c.(70-72)Tgt>Cgt	p.C24R		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0						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)		ccagagccacagcccccacag	0.687																																					p.C24R		Atlas-SNP	.											.	KRTAP5-4	78	.	0			c.T70C						PASS	.						4	8	7					11																	1643254		641	1519	2160	SO:0001583	missense	387267	exon1			AGCCACAGCCCCC	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.70T>C	chr11.hg19:g.1643254A>G	ENSP00000382590:p.Cys24Arg	57.0	0.0	.		133.0	6.0	.	NM_001012709		Missense_Mutation	SNP	ENST00000399682.1	hg19		.	.	.	.	.	.	.	.	.	.	A	7.309	0.614523	0.14129	.	.	ENSG00000241598	ENST00000399682;ENST00000328953	T	0.01099	5.34	2.15	2.15	0.27550	.	.	.	.	.	T	0.06234	0.0161	M	0.87971	2.92	0.49389	D	0.999781	D	0.59357	0.985	D	0.70487	0.969	T	0.05273	-1.0895	9	0.56958	D	0.05	.	8.2253	0.31564	1.0:0.0:0.0:0.0	.	24	Q6L8H1	KRA54_HUMAN	R	24	ENSP00000382590:C24R	ENSP00000331603:C24R	C	-	1	0	KRTAP5-4	1599830	0.001000	0.12720	0.930000	0.37139	0.032000	0.12392	-0.060000	0.11712	1.242000	0.43836	0.367000	0.22151	TGT	.	.	.	none		0.687	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709		G	1643254	A	G	1643254	3	3	230	1	0	0	0	0	1	0	0	0	8570	188	7	3	620	3	KRTAP5-4	11	1643254	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	625186	1643254	133363262	50	13976											
EEF1G	1937	hgsc.bcm.edu	37	chr11	62334912	62334912	+	Missense_Mutation	SNP	A	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	cacacagtttcacttcgcccAagacagcccggaactggggc	10	6	10	15	2	1	1	1	0	0	1	2	2	1	2	2	3	2	1	2	3	2	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr11:62334912A>C	ENST00000329251.4	-	6	741	c.611T>G	c.(610-612)tTg>tGg	p.L204W	MIR3654_ENST00000496634.2_3'UTR|EEF1G_ENST00000378019.3_Missense_Mutation_p.L254W	NM_001404.4	NP_001395.1	P26641	EF1G_HUMAN	eukaryotic translation elongation factor 1 gamma	204	GST C-terminal.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to virus (GO:0009615)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	translation elongation factor activity (GO:0003746)			breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						CACTTCGCCCAAGACAGCCCG	0.552																																					p.L204W		Atlas-SNP	.											.	EEF1G	33	.	0			c.T611G						PASS	.						44	41	42					11																	62334912		1926	4135	6061	SO:0001583	missense	1937	exon6			TCGCCCAAGACAG	X63526	CCDS44626.1	11q12.3	2008-02-05			ENSG00000254772	ENSG00000254772			3213	protein-coding gene	gene with protein product		130593				1598220, 1461723	Standard	NM_001404		Approved	EF1G	uc001ntm.1	P26641	OTTHUMG00000167567	ENST00000329251.4:c.611T>G	chr11.hg19:g.62334912A>C	ENSP00000331901:p.Leu204Trp	70.0	0.0	.		99.0	32.0	.	NM_001404	B4DTG2|Q6PJ62|Q6PK31|Q96CU2|Q9P196	Missense_Mutation	SNP	ENST00000329251.4	hg19	CCDS44626.1	.	.	.	.	.	.	.	.	.	.	A	25.7	4.662133	0.88251	.	.	ENSG00000254772	ENST00000329251;ENST00000378019	T;T	0.21932	1.98;1.98	4.8	4.8	0.61643	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);	0.000000	0.64402	D	0.000002	T	0.54159	0.1841	M	0.92459	3.31	0.53005	D	0.999968	D;P	0.89917	1.0;0.905	D;P	0.80764	0.994;0.703	T	0.65487	-0.6156	10	0.72032	D	0.01	.	12.5918	0.56447	1.0:0.0:0.0:0.0	.	254;204	B4DTG2;P26641	.;EF1G_HUMAN	W	204;254	ENSP00000331901:L204W;ENSP00000367258:L254W	ENSP00000331901:L204W	L	-	2	0	EEF1G	62091488	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	8.903000	0.92573	1.928000	0.55862	0.459000	0.35465	TTG	.	.	.	weak		0.552	EEF1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395047.1	NM_001404		C	62334912	A	C	62334912	3	2	230	1	0	0	0	0	1	0	0	0	4930	131	5	5	722	5	EEF1G	11	62334912	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	60691658	62334912	72671604	51	13977											
DGAT2	84649	hgsc.bcm.edu	37	chr11	75509414	75509414	+	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	catgcatcttccatggtcgaGgcctcttctcctccgacacc	6	11	7	17	2	3	0	0	0	3	0	7	2	5	0	5	2	1	1	5	2	0	2	rs145750206		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr11:75509414G>C	ENST00000228027.7	+	7	1212	c.952G>C	c.(952-954)Ggc>Cgc	p.G318R	DGAT2_ENST00000376262.3_Missense_Mutation_p.G275R|RP11-535A19.1_ENST00000534354.1_RNA	NM_032564.4	NP_115953.2	Q96PD7	DGAT2_HUMAN	diacylglycerol O-acyltransferase 2	318					acylglycerol acyl-chain remodeling (GO:0036155)|cellular lipid metabolic process (GO:0044255)|cellular response to oleic acid (GO:0071400)|cellular triglyceride homeostasis (GO:0035356)|cholesterol homeostasis (GO:0042632)|diacylglycerol metabolic process (GO:0046339)|fat pad development (GO:0060613)|fatty acid homeostasis (GO:0055089)|glycerol metabolic process (GO:0006071)|glycerophospholipid biosynthetic process (GO:0046474)|lipid storage (GO:0019915)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid metabolic process (GO:0006644)|regulation of plasma lipoprotein particle levels (GO:0097006)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)	2-acylglycerol O-acyltransferase activity (GO:0003846)|diacylglycerol O-acyltransferase activity (GO:0004144)|protein homodimerization activity (GO:0042803)|retinol O-fatty-acyltransferase activity (GO:0050252)			endometrium(3)|large_intestine(5)|lung(5)|prostate(2)|skin(2)	17	Ovarian(111;0.103)					CCATGGTCGAGGCCTCTTCTC	0.582																																					p.G318R	Melanoma(35;811 1096 8354 24009 39363)	Atlas-SNP	.											.	DGAT2	37	.	0			c.G952C						PASS	.						84	72	76					11																	75509414		2200	4293	6493	SO:0001583	missense	84649	exon7			GGTCGAGGCCTCT		CCDS31642.1, CCDS58162.1	11q13.3	2010-06-24	2010-06-24		ENSG00000062282	ENSG00000062282			16940	protein-coding gene	gene with protein product		606983	"diacylglycerol O-acyltransferase homolog 2 (mouse)"			11481335, 14970677	Standard	NM_032564		Approved		uc001oxa.3	Q96PD7	OTTHUMG00000165338	ENST00000228027.7:c.952G>C	chr11.hg19:g.75509414G>C	ENSP00000228027:p.Gly318Arg	77.0	0.0	.		97.0	33.0	.	NM_032564	A6ND76|Q5U810|Q68CL3|Q68DJ0|Q8NDB7|Q96BS0|Q9BYE5	Missense_Mutation	SNP	ENST00000228027.7	hg19	CCDS31642.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.248066	0.80024	.	.	ENSG00000062282	ENST00000228027;ENST00000376262;ENST00000525612	T;T	0.18960	2.18;2.18	5.59	4.68	0.58851	.	0.090338	0.85682	D	0.000000	T	0.44498	0.1296	M	0.78456	2.415	0.80722	D	1	D;D	0.89917	1.0;0.993	D;D	0.74674	0.984;0.955	T	0.44862	-0.9300	10	0.87932	D	0	-19.5496	9.867	0.41150	0.1582:0.0:0.8418:0.0	.	275;318	Q96PD7-2;Q96PD7	.;DGAT2_HUMAN	R	318;275;272	ENSP00000228027:G318R;ENSP00000365438:G275R	ENSP00000228027:G318R	G	+	1	0	DGAT2	75187062	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.726000	0.68515	1.501000	0.48654	0.655000	0.94253	GGC	.	G|0.999;A|0.001	.	alt		0.582	DGAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383506.1	NM_032564		C	75509414	G	C	75509414	3	2	230	1	0	0	0	0	1	0	0	0	4460	1000	35	4	978	4	DGAT2	11	75509414	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	13174502	75509414	59497102	52	13978											
KLRC3	3823	hgsc.bcm.edu	37	chr12	10573086	10573086	+	Frame_Shift_Del	DEL	T	T	-																															tttattgcctttaggtttccTttgctgccactttgggtcct																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr12:10573086delT	ENST00000396439.2	-	1	108	c.64delA	c.(64-66)aggfs	p.R22fs	NKG2-E_ENST00000539033.1_Intron|KLRC3_ENST00000381904.2_Frame_Shift_Del_p.R22fs|KLRC3_ENST00000381903.2_Frame_Shift_Del_p.R22fs	NM_002261.2	NP_002252.2	Q07444	NKG2E_HUMAN	killer cell lectin-like receptor subfamily C, member 3	22					cellular defense response (GO:0006968)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			large_intestine(2)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11						TTAGGTTTCCTTTGCTGCCAC	0.438																																					p.R22fs		Atlas-INDEL	.											.	KLRC3	25	.	0			c.65delG						PASS	.						98	96	97					12																	10573086		2203	4297	6500	SO:0001589	frameshift_variant	3823	exon1			.	L14542	CCDS31744.1, CCDS41755.1	12p13	2008-08-05			ENSG00000205810	ENSG00000205810		"Killer cell lectin-like receptors"	6376	protein-coding gene	gene with protein product		602892				9598306	Standard	NM_002261		Approved	NKG2-E	uc001qyi.1	Q07444	OTTHUMG00000167149	ENST00000396439.2:c.64delA	chr12.hg19:g.10573086delT	ENSP00000379716:p.Arg22fs	68.0	0.0	0		48.0	13.0	0.270833	NM_007333	Q8WXA4|Q96RL0|Q9UP04	Frame_Shift_Del	DEL	ENST00000396439.2	hg19	CCDS41755.1																																																																																			.	.	.	none		0.438	KLRC3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393471.1	NM_002261		-	10573086	T	-	10573086	7	5	230	1	0	1	0	1	0	0	0	0	8424	1608	56	0	782	0	KLRC3	12	10573086	Frame_Shift_Del	DEL	T	TCGA-P4-A5E7-01A-31D-A28G-10		10573086	123278809	53	13979											
KLRC2	3823	hgsc.bcm.edu	37	chr12	10588522	10588522	+	Frame_Shift_Del	DEL	T	T	-																															tttattgcctttaggtttccTttgctgccgctttgggtcct																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr12:10588522delT	ENST00000539033.1	-	1	78	c.64delA	c.(64-66)aggfs	p.R22fs	KLRC2_ENST00000536833.2_Intron|KLRC2_ENST00000381902.2_Frame_Shift_Del_p.R22fs|KLRC2_ENST00000381901.1_Frame_Shift_Del_p.R22fs																							TTAGGTTTCCTTTGCTGCCGC	0.438																																					p.R22fs		Atlas-INDEL	.											.	KLRC2	29	.	0			c.65delG						PASS	.						250	250	250					12																	10588522		2203	4300	6503	SO:0001589	frameshift_variant	3822	exon1			.																												ENST00000539033.1:c.64delA	chr12.hg19:g.10588522delT	ENSP00000437563:p.Arg22fs	146.0	0.0	0		154.0	34.0	0.220779	NM_002260		Frame_Shift_Del	DEL	ENST00000539033.1	hg19																																																																																				.	.	.	none		0.438	NKG2-E-001	KNOWN	basic|appris_principal|readthrough_transcript	protein_coding	protein_coding	OTTHUMT00000400274.1			-	10588522	T	-	10588522	7	5	230	1	0	1	0	1	0	0	0	0	8423	1608	56	0	655	0	KLRC2	12	10588522	Frame_Shift_Del	DEL	T	TCGA-P4-A5E7-01A-31D-A28G-10	15436	10588522	123263373	54	13980											
DENND5B	160518	hgsc.bcm.edu	37	chr12	31551284	31551284	+	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	atgcctttccccagccaccgCccacatgggaatctggtagg	8	8	10	15	1	1	0	0	0	1	0	2	1	2	1	6	3	2	1	6	3	2	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr12:31551284C>T	ENST00000389082.5	-	17	3345	c.3081G>A	c.(3079-3081)ggG>ggA	p.G1027G	DENND5B_ENST00000536562.1_Silent_p.G1062G|RNU6-618P_ENST00000363518.1_RNA|DENND5B_ENST00000306833.6_Silent_p.G1062G	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	1027	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						CCAGCCACCGCCCACATGGGA	0.453																																					p.G1027G		Atlas-SNP	.											.	DENND5B	114	.	0			c.G3081A						PASS	.						45	41	42					12																	31551284		1778	3993	5771	SO:0001819	synonymous_variant	160518	exon17			CCACCGCCCACAT	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.3081G>A	chr12.hg19:g.31551284C>T		44.0	0.0	.		24.0	9.0	.	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Silent	SNP	ENST00000389082.5	hg19	CCDS44857.1																																																																																			.	.	.	none		0.453	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973		T	31551284	C	T	31551284	2	4	230	1	0	0	0	0	0	0	0	1	4439	726	26	2		2	DENND5B	12	31551284	Silent	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	20962762	31551284	102300611	55	13981											
PRPH	5630	hgsc.bcm.edu	37	chr12	49689459	49689459	+	Missense_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	gcgagagctggagctgttggGccgcgagcgtgaccgggtgc	5	6	20	10	5	0	2	0	1	0	1	0	5	0	3	2	3	4	3	2	3	0	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr12:49689459G>A	ENST00000257860.4	+	1	1975	c.476G>A	c.(475-477)gGc>gAc	p.G159D	RP11-161H23.9_ENST00000553259.1_RNA	NM_006262.3	NP_006253.2	P23942	PRPH2_HUMAN	peripherin	0					cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(8)|skin(1)	12						GAGCTGTTGGGCCGCGAGCGT	0.766																																					p.G159D		Atlas-SNP	.											.	PRPH	26	.	0			c.G476A						PASS	.						2	3	3					12																	49689459		1611	3196	4807	SO:0001583	missense	5630	exon1			TGTTGGGCCGCGA		CCDS8783.1	12q12-q13	2013-01-16						"Intermediate filaments type III"	9461	protein-coding gene	gene with protein product		170710		NEF4		1378416	Standard	XM_005269025		Approved	PRPH1	uc001rtu.3	P41219		ENST00000257860.4:c.476G>A	chr12.hg19:g.49689459G>A	ENSP00000257860:p.Gly159Asp	0.0	0.0	.		7.0	4.0	.	NM_006262	Q5TFH5|Q6DK65	Missense_Mutation	SNP	ENST00000257860.4	hg19	CCDS8783.1	.	.	.	.	.	.	.	.	.	.	G	17.57	3.422107	0.62622	.	.	ENSG00000135406	ENST00000257860;ENST00000451891	D	0.88741	-2.42	4.51	2.61	0.31194	Filament (1);	0.000000	0.40554	N	0.001080	D	0.89022	0.6597	L	0.58669	1.825	0.46096	D	0.998869	P	0.46987	0.888	P	0.52109	0.69	D	0.84585	0.0663	10	0.18710	T	0.47	.	12.3528	0.55157	0.0:0.3262:0.6738:0.0	.	159	P41219	PERI_HUMAN	D	159;46	ENSP00000257860:G159D	ENSP00000257860:G159D	G	+	2	0	PRPH	47975726	0.835000	0.29415	0.999000	0.59377	0.608000	0.37181	1.757000	0.38400	0.501000	0.28013	0.462000	0.41574	GGC	.	.	.	none		0.766	PRPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393381.1	NM_006262		A	49689459	G	A	49689459	3	1	230	1	0	0	0	0	1	0	0	0	12586	1203	42	2	478	2	PRPH	12	49689459	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	18138175	49689459	84162436	56	13982											
KRT2	3849	hgsc.bcm.edu	37	chr12	53045499	53045499	+	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	tgccaccagggtatcctccaGgcccaaagccaccaggaccc	10	4	9	18	0	0	0	0	0	0	0	2	1	2	1	8	3	2	1	8	3	2	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr12:53045499G>C	ENST00000309680.3	-	1	449	c.428C>G	c.(427-429)cCt>cGt	p.P143R		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	143	Head.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		GTATCCTCCAGGCCCAAAGCC	0.597																																					p.P143R		Atlas-SNP	.											.	KRT2	94	.	0			c.C428G						PASS	.						82	83	83					12																	53045499		2203	4300	6503	SO:0001583	missense	3849	exon1			CCTCCAGGCCCAA		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"-", "Intermediate filaments type II, keratins (basic)"	6439	protein-coding gene	gene with protein product	"epidermal ichthyosis bullosa of Siemens"	600194	"keratin 2A (epidermal ichthyosis bullosa of Siemens)"	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.428C>G	chr12.hg19:g.53045499G>C	ENSP00000310861:p.Pro143Arg	120.0	0.0	.		117.0	39.0	.	NM_000423	Q4VAQ2	Missense_Mutation	SNP	ENST00000309680.3	hg19	CCDS8835.1	.	.	.	.	.	.	.	.	.	.	G	15.79	2.938619	0.52972	.	.	ENSG00000172867	ENST00000309680	D	0.85556	-2.0	5.54	5.54	0.83059	.	.	.	.	.	D	0.92296	0.7556	M	0.83603	2.65	0.38710	D	0.953191	D	0.76494	0.999	D	0.69307	0.963	D	0.93716	0.7028	9	0.87932	D	0	.	15.3671	0.74531	0.0:0.0:1.0:0.0	.	143	P35908	K22E_HUMAN	R	143	ENSP00000310861:P143R	ENSP00000310861:P143R	P	-	2	0	KRT2	51331766	0.164000	0.22935	0.998000	0.56505	0.983000	0.72400	-0.229000	0.09098	2.791000	0.96007	0.655000	0.94253	CCT	.	.	.	none		0.597	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423		C	53045499	G	C	53045499	3	2	230	1	0	0	0	0	1	0	0	0	8464	1000	35	4	1527	4	KRT2	12	53045499	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	3356040	53045499	80806396	57	13983											
MDM1	56890	hgsc.bcm.edu	37	chr12	68696605	68696605	+	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	ggcagaggatcaactgttttTataccagcagctggagaagt	12	10	12	7	0	1	2	1	0	0	2	1	4	1	3	1	3	4	4	1	3	4	4			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr12:68696605T>A	ENST00000303145.7	-	12	1853	c.1767A>T	c.(1765-1767)atA>atT	p.I589I	MDM1_ENST00000411698.2_Silent_p.I554I|MDM1_ENST00000540418.1_Silent_p.I309I	NM_017440.4	NP_059136.2	Q8TC05	MDM1_HUMAN	Mdm1 nuclear protein homolog (mouse)	589					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)		CAACTGTTTTTATACCAGCAG	0.358																																					p.I589I		Atlas-SNP	.											.	MDM1	74	.	0			c.A1767T						PASS	.						90	92	91					12																	68696605		2203	4300	6503	SO:0001819	synonymous_variant	56890	exon12			TGTTTTTATACCA	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.1767A>T	chr12.hg19:g.68696605T>A		37.0	0.0	.		27.0	6.0	.	NM_017440	B4DM65|E7EPQ3|O43406|Q8WTV9|Q9NR04	Silent	SNP	ENST00000303145.7	hg19	CCDS8983.1																																																																																			.	.	.	none		0.358	MDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402402.1	NM_020128		A	68696605	T	A	68696605	2	1	230	1	0	0	0	0	0	0	0	1	9419	1744	61	5		5	MDM1	12	68696605	Silent	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10	15651106	68696605	65155290	58	13984											
SRRM4	84530	hgsc.bcm.edu	37	chr12	119583229	119583229	+	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	tgacctctttaccaaaacagCcagcccgctcaccacctcgc	10	7	5	19	2	2	1	1	1	1	0	3	1	2	1	6	0	4	1	6	0	3	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr12:119583229C>A	ENST00000267260.4	+	9	1203	c.815C>A	c.(814-816)gCc>gAc	p.A272D		NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	272	Ser-rich.				cell differentiation (GO:0030154)|mRNA processing (GO:0006397)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	mRNA binding (GO:0003729)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	24						ACCAAAACAGCCAGCCCGCTC	0.597																																					p.A272D		Atlas-SNP	.											.	SRRM4	131	.	0			c.C815A						PASS	.						27	29	29					12																	119583229		1987	4156	6143	SO:0001583	missense	84530	exon9			AAACAGCCAGCCC	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.815C>A	chr12.hg19:g.119583229C>A	ENSP00000267260:p.Ala272Asp	81.0	0.0	.		106.0	28.0	.	NM_194286	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Missense_Mutation	SNP	ENST00000267260.4	hg19	CCDS44994.1	.	.	.	.	.	.	.	.	.	.	C	14.09	2.431158	0.43122	.	.	ENSG00000139767	ENST00000267260	T	0.23147	1.92	5.48	3.26	0.37387	.	0.608931	0.17277	N	0.180174	T	0.16854	0.0405	L	0.40543	1.245	0.33704	D	0.614946	B	0.12013	0.005	B	0.09377	0.004	T	0.13469	-1.0508	9	.	.	.	-16.4361	4.1827	0.10383	0.2661:0.5295:0.1154:0.089	.	272	A7MD48	SRRM4_HUMAN	D	272	ENSP00000267260:A272D	.	A	+	2	0	SRRM4	118067612	0.997000	0.39634	1.000000	0.80357	0.996000	0.88848	1.389000	0.34453	1.274000	0.44362	0.655000	0.94253	GCC	.	.	.	none		0.597	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286		A	119583229	C	A	119583229	3	1	230	1	0	0	0	0	1	0	0	0	15183	739	26	4	849	4	SRRM4	12	119583229	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	50886624	119583229	14268666	59	13985											
RABGGTA	5875	hgsc.bcm.edu	37	chr14	24734893	24734893	+	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	atgcccaccgcttggcacagCgggttaccctgcaggttgag	7	8	13	13	2	0	1	0	1	0	0	0	1	0	1	3	3	4	5	3	3	1	3	rs369935041		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr14:24734893C>T	ENST00000399409.3	-	16	2115	c.1632G>A	c.(1630-1632)ccG>ccA	p.P544P	RABGGTA_ENST00000560777.1_Silent_p.P153P|TGM1_ENST00000544573.1_5'Flank|TGM1_ENST00000206765.6_5'Flank|RABGGTA_ENST00000216840.6_Silent_p.P544P	NM_004581.5	NP_004572.3	Q92696	PGTA_HUMAN	Rab geranylgeranyltransferase, alpha subunit	544					cellular protein modification process (GO:0006464)|protein geranylgeranylation (GO:0018344)|visual perception (GO:0007601)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)	12				GBM - Glioblastoma multiforme(265;0.0184)		CTTGGCACAGCGGGTTACCCT	0.612																																					p.P544P		Atlas-SNP	.											RABGGTA,NS,lymphoid_neoplasm,0,1	RABGGTA	43	.	0			c.G1632A						PASS	.	C	,	0,4034		0,0,2017	38	42	41		1632,1632	-4.9	0.9	14		41	1,8365		0,1,4182	no	coding-synonymous,coding-synonymous	RABGGTA	NM_004581.3,NM_182836.1	,	0,1,6199	TT,TC,CC		0.012,0.0,0.0081	,	544/568,544/568	24734893	1,12399	2017	4183	6200	SO:0001819	synonymous_variant	5875	exon16			GCACAGCGGGTTA		CCDS45088.1	14q11.2	2011-06-27				ENSG00000100949		"Prenyltransferase alpha subunit repeat containing"	9795	protein-coding gene	gene with protein product	"protein prenyltransferase alpha subunit repeat containing 3"	601905				8954794	Standard	NM_182836		Approved	PTAR3	uc001wog.4	Q92696		ENST00000399409.3:c.1632G>A	chr14.hg19:g.24734893C>T		119.0	0.0	.		116.0	40.0	.	NM_004581	A8K5N2|D3DS69	Silent	SNP	ENST00000399409.3	hg19	CCDS45088.1																																																																																			.	.	.	weak		0.612	RABGGTA-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415308.5	NM_182836		T	24734893	C	T	24734893	2	4	230	1	0	0	0	0	0	0	0	1	12980	755	27	1		1	RABGGTA	14	24734893	Silent	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10		24734893	82614647	60	13986											
RALGAPA1	253959	hgsc.bcm.edu	37	chr14	36143779	36143779	+	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	aaaacttgagcatgtatttcAggatccatgattgaatttac	14	14	7	6	0	1	3	1	3	0	0	2	4	2	4	1	1	3	2	1	1	5	6			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr14:36143779A>C	ENST00000389698.3	-	22	3633	c.3243T>G	c.(3241-3243)ccT>ccG	p.P1081P	RALGAPA1_ENST00000382366.3_Silent_p.P1094P|RALGAPA1_ENST00000258840.6_Silent_p.P1128P|RALGAPA1_ENST00000307138.6_Silent_p.P1081P	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	1081					activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						CATGTATTTCAGGATCCATGA	0.388																																					p.P1081P		Atlas-SNP	.											.	RALGAPA1	289	.	0			c.T3243G						PASS	.						26	27	27					14																	36143779		2201	4288	6489	SO:0001819	synonymous_variant	253959	exon22			TATTTCAGGATCC	AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"tuberin-like protein 1", "GAP-related interacting protein to E12"	608884	"GTPase activating RANGAP domain-like 1", "GTPase activating Rap/RanGAP domain-like 1"	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.3243T>G	chr14.hg19:g.36143779A>C		246.0	0.0	.		243.0	72.0	.	NM_194301	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Silent	SNP	ENST00000389698.3	hg19	CCDS32065.1																																																																																			.	.	.	none		0.388	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022		C	36143779	A	C	36143779	2	2	230	1	0	0	0	0	0	0	0	1	13026	175	7	5		5	RALGAPA1	14	36143779	Silent	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	11408886	36143779	71205761	61	13987											
TTLL5	23093	hgsc.bcm.edu	37	chr14	76243163	76243163	+	Frame_Shift_Del	DEL	A	A	-																															ggaagatggggtgaatatggAaaactttcaggagttcatca																								rs372279209		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr14:76243163delA	ENST00000298832.9	+	23	2562	c.2357delA	c.(2356-2358)gaafs	p.E786fs	TTLL5_ENST00000555422.1_3'UTR|TTLL5_ENST00000556893.1_Frame_Shift_Del_p.E337fs|TTLL5_ENST00000554510.1_Frame_Shift_Del_p.E295fs|TTLL5_ENST00000557636.1_Frame_Shift_Del_p.E800fs	NM_015072.4	NP_055887.3	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	786					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)		GTGAATATGGAAAACTTTCAG	0.403																																					p.E786fs		Atlas-Indel,Pindel	.											.	TTLL5	102	.	0			c.2356delG						PASS	.						130	127	128					14																	76243163		2203	4300	6503	SO:0001589	frameshift_variant	23093	exon23			.	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.2357delA	chr14.hg19:g.76243163delA	ENSP00000298832:p.Glu786fs	92.0	0.0	0		97.0	21.0	0.216495	NM_015072	B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4	Frame_Shift_Del	DEL	ENST00000298832.9	hg19	CCDS32124.1																																																																																			.	.	.	none		0.403	TTLL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414453.1	NM_015072		-	76243163	A	-	76243163	7	5	230	1	0	1	0	1	0	0	0	0	16742	246	9	0	2443	0	TTLL5	14	76243163	Frame_Shift_Del	DEL	A	TCGA-P4-A5E7-01A-31D-A28G-10	40099384	76243163	31106377	62	13988											
C15orf2	23742	hgsc.bcm.edu	37	chr15	24923342	24923342	+	Silent	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	cctcaacccaaatttggggcCcctgatgggccgcagcagaa	10	6	11	14	1	1	2	1	1	0	1	1	2	1	2	5	3	2	2	5	3	3	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr15:24923342C>T	ENST00000329468.2	+	1	2802	c.2328C>T	c.(2326-2328)gcC>gcT	p.A776A		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	776					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)		p.A776A(1)									AATTTGGGGCCCCTGATGGGC	0.552																																					p.A776A		Atlas-SNP	.											C15orf2,NS,carcinoma,0,1	.	.	.	1	Substitution - coding silent(1)	lung(1)	c.C2328T						PASS	.						109	128	121					15																	24923342		2203	4300	6503	SO:0001819	synonymous_variant	23742	exon1			TGGGGCCCCTGAT	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.2328C>T	chr15.hg19:g.24923342C>T		20.0	0.0	.		34.0	14.0	.	NM_018958		Silent	SNP	ENST00000329468.2	hg19	CCDS10015.1																																																																																			.	.	.	none		0.552	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		T	24923342	C	T	24923342	2	4	230	1	0	0	0	0	0	0	0	1	1786	610	22	2		2	C15orf2	15	24923342	Silent	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10		24923342	77608050	63	13989											
ZNF75A	7627	hgsc.bcm.edu	37	chr16	3363138	3363138	+	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	cagaaggccctctacaatgaTgtaatgcaggaaaactatga	16	8	9	8	0	1	3	0	2	1	1	1	4	1	4	1	2	3	2	1	2	7	3			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr16:3363138T>A	ENST00000574298.1	+	4	536	c.63T>A	c.(61-63)gaT>gaA	p.D21E	ZNF75A_ENST00000498240.2_Intron	NM_153028.2	NP_694573.1	Q96N20	ZN75A_HUMAN	zinc finger protein 75a	21	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|large_intestine(3)|lung(7)|prostate(1)	12						TCTACAATGATGTAATGCAGG	0.408																																					p.D21E		Atlas-SNP	.											.	ZNF75A	34	.	0			c.T63A						PASS	.						131	118	122					16																	3363138		2197	4300	6497	SO:0001583	missense	7627	exon4			CAATGATGTAATG	X91826	CCDS10501.1	16p13.11	2013-01-08			ENSG00000162086	ENSG00000162086		"Zinc fingers, C2H2-type", "-"	13146	protein-coding gene	gene with protein product		601473				8661144	Standard	NM_153028		Approved	FLJ31529	uc002cut.4	Q96N20	OTTHUMG00000129356	ENST00000574298.1:c.63T>A	chr16.hg19:g.3363138T>A	ENSP00000459566:p.Asp21Glu	112.0	0.0	.		170.0	84.0	.	NM_153028	Q0VDI8|Q92669	Missense_Mutation	SNP	ENST00000574298.1	hg19	CCDS10501.1	.	.	.	.	.	.	.	.	.	.	T	14.16	2.452955	0.43531	.	.	ENSG00000162086	ENST00000293995	.	.	.	3.48	1.13	0.20643	Krueppel-associated box (4);	.	.	.	.	T	0.40694	0.1127	L	0.42487	1.325	0.80722	D	1	B	0.16603	0.018	B	0.16722	0.016	T	0.12760	-1.0535	8	0.22706	T	0.39	.	2.7142	0.05183	0.1927:0.2235:0.0:0.5838	.	21	Q96N20	ZN75A_HUMAN	E	21	.	ENSP00000293995:D21E	D	+	3	2	ZNF75A	3303139	0.292000	0.24362	0.996000	0.52242	0.996000	0.88848	-0.885000	0.04161	0.207000	0.20607	0.379000	0.24179	GAT	.	.	.	none		0.408	ZNF75A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251506.2	NM_153028		A	3363138	T	A	3363138	3	1	230	1	0	0	0	0	1	0	0	0	18145	1461	51	5	65	5	ZNF75A	16	3363138	Missense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10		3363138	86991615	64	13990											
LOC81691	81691	hgsc.bcm.edu	37	chr16	20851720	20851720	+	Frame_Shift_Del	DEL	G	G	-																															tagcaaaaattgcaatctcaGggctctgaagaggctgttta																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr16:20851720delG	ENST00000261377.6	+	15	1765	c.1556delG	c.(1555-1557)aggfs	p.R519fs	ERI2_ENST00000564349.1_Intron|AC004381.6_ENST00000564274.1_Frame_Shift_Del_p.R519fs|AC004381.6_ENST00000348433.6_Frame_Shift_Del_p.R519fs	NM_001199053.1|NM_030941.2	NP_001185982.1|NP_112203.2																					TGCAATCTCAGGGCTCTGAAG	0.408																																					p.R519fs		Atlas-Indel,Pindel	.											.	LOC81691	41	.	0			c.1555delA						PASS	.						113	115	115					16																	20851720		2201	4300	6501	SO:0001589	frameshift_variant	0	exon15			.																												ENST00000261377.6:c.1556delG	chr16.hg19:g.20851720delG	ENSP00000261377:p.Arg519fs	71.0	0.0	0		70.0	34.0	0.485714	NM_001144924		Frame_Shift_Del	DEL	ENST00000261377.6	hg19	CCDS10591.1																																																																																			.	.	.	none		0.408	AC004381.6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254418.2			-	20851720	G	-	20851720	7	5	230	1	0	1	0	1	0	0	0	0	8897	1000	35	0	1610	0	LOC81691	16	20851720	Frame_Shift_Del	DEL	G	TCGA-P4-A5E7-01A-31D-A28G-10	17488582	20851720	69503033	65	13991											
ACADVL	37	hgsc.bcm.edu	37	chr17	7127679	7127679	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcctgagtctcagcggactTgtccacccggagttgagtcg	6	9	14	12	3	1	2	1	2	1	0	4	4	2	4	3	3	1	1	3	3	0	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr17:7127679T>C	ENST00000356839.5	+	16	1751	c.1572T>C	c.(1570-1572)ctT>ctC	p.L524L	ACADVL_ENST00000543245.2_Silent_p.L547L|MIR324_ENST00000362183.1_RNA|ACADVL_ENST00000350303.5_Silent_p.L502L	NM_000018.3|NM_001270448.1	NP_000009.1|NP_001257377.1	P49748	ACADV_HUMAN	acyl-CoA dehydrogenase, very long chain	524					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						TCAGCGGACTTGTCCACCCGG	0.657																																					p.L547L		Atlas-SNP	.											.	ACADVL	43	.	0			c.T1641C						PASS	.						54	54	54					17																	7127679		2203	4300	6503	SO:0001819	synonymous_variant	37	exon17			CGGACTTGTCCAC	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.1572T>C	chr17.hg19:g.7127679T>C		73.0	0.0	.		106.0	49.0	.	NM_001270447	B4DEB6|F5H2A9|O76056|Q8WUL0	Silent	SNP	ENST00000356839.5	hg19	CCDS11090.1																																																																																			.	.	.	none		0.657	ACADVL-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220001.5	NM_000018		C	7127679	T	C	7127679	2	2	230	1	0	0	0	0	0	0	0	1	116	1799	63	3		3	ACADVL	17	7127679	Silent	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10		7127679	74067531	66	13992											
POLR2A	5430	hgsc.bcm.edu	37	chr17	7405000	7405000	+	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	tctgaatacaataacttcaaGtctatggtcgtgtccggagc	11	12	9	9	2	3	1	1	1	2	0	5	2	4	2	1	2	3	0	1	2	6	4			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr17:7405000G>A	ENST00000322644.6	+	14	2700	c.2301G>A	c.(2299-2301)aaG>aaA	p.K767K		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	767					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)				ATAACTTCAAGTCTATGGTCG	0.488																																					p.K767K		Atlas-SNP	.											.	POLR2A	157	.	0			c.G2301A						PASS	.						71	67	68					17																	7405000		2203	4300	6503	SO:0001819	synonymous_variant	5430	exon14			CTTCAAGTCTATG			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.2301G>A	chr17.hg19:g.7405000G>A		88.0	0.0	.		140.0	34.0	.	NM_000937	A6NN93|B9EH88|Q6NX41	Silent	SNP	ENST00000322644.6	hg19	CCDS32548.1																																																																																			.	.	.	none		0.488	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937		A	7405000	G	A	7405000	2	1	230	1	0	0	0	0	0	0	0	1	12221	1020	36	2		2	POLR2A	17	7405000	Silent	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	277321	7405000	73790210	67	13993											
GPR179	440435	hgsc.bcm.edu	37	chr17	36492994	36492994	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acggtgtggcatccatgcagCtggtgcagccctcaggacat	8	8	13	12	1	1	0	1	0	0	0	2	1	2	1	2	4	4	4	2	4	0	0			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr17:36492994C>T	ENST00000342292.4	-	4	1114	c.1094G>A	c.(1093-1095)aGc>aAc	p.S365N		NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	365					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)				ATCCATGCAGCTGGTGCAGCC	0.632																																					p.S365N		Atlas-SNP	.											.	GPR179	170	.	0			c.G1094A						PASS	.						27	31	29					17																	36492994		2097	4237	6334	SO:0001583	missense	440435	exon4			ATGCAGCTGGTGC		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.1094G>A	chr17.hg19:g.36492994C>T	ENSP00000345060:p.Ser365Asn	25.0	0.0	.		78.0	14.0	.	NM_001004334		Missense_Mutation	SNP	ENST00000342292.4	hg19	CCDS42308.1	.	.	.	.	.	.	.	.	.	.	C	18.13	3.554853	0.65425	.	.	ENSG00000188888	ENST00000342292	T	0.52295	0.67	5.19	4.2	0.49525	.	0.000000	0.85682	D	0.000000	T	0.36248	0.0960	L	0.46157	1.445	0.32221	N	0.57526	B	0.34290	0.447	B	0.32149	0.141	T	0.46331	-0.9199	10	0.37606	T	0.19	-10.9887	7.967	0.30104	0.0:0.6539:0.2598:0.0863	.	365	Q6PRD1	GP179_HUMAN	N	365	ENSP00000345060:S365N	ENSP00000345060:S365N	S	-	2	0	GPR179	33746520	0.669000	0.27502	0.999000	0.59377	0.940000	0.58332	0.856000	0.27818	2.709000	0.92574	0.561000	0.74099	AGC	.	.	.	none		0.632	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			T	36492994	C	T	36492994	3	4	230	1	0	0	0	0	1	0	0	0	6681	797	28	2	6041	2	GPR179	17	36492994	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	29087994	36492994	44702216	68	13994											
GPATCH8	23131	hgsc.bcm.edu	37	chr17	42475173	42475176	+	Frame_Shift_Del	DEL	TGAG	TGAG	-																															gcagggtggccagggatgatTgagtgagtgaggtgggacaa																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	TGAG	TGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr17:42475173_42475176delTGAG	ENST00000591680.1	-	8	4299_4302	c.4269_4272delCTCA	c.(4267-4272)cactcafs	p.HS1423fs	GPATCH8_ENST00000434000.1_Frame_Shift_Del_p.HS1345fs	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	1423							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)		CAGGGATGATTGAGTGAGTGAGGT	0.588																																					p.1424_1425del		Atlas-Indel,Pindel	.											.	GPATCH8	114	.	0			c.4270_4273del						PASS	.																																			SO:0001589	frameshift_variant	23131	exon8			.	AB011125	CCDS32666.1	17q21.31	2013-01-28	2006-08-22	2006-12-13	ENSG00000186566	ENSG00000186566		"G patch domain containing"	29066	protein-coding gene	gene with protein product		614396	"KIAA0553"	KIAA0553, GPATC8		9628581	Standard	NM_001002909		Approved		uc002igw.2	Q9UKJ3	OTTHUMG00000181818	ENST00000591680.1:c.4269_4272delCTCA	chr17.hg19:g.42475181_42475184delTGAG	ENSP00000467556:p.His1423fs	206.0	0.0	0		263.0	112.0	0.425856	NM_001002909	B9EGP9|O60300|Q8TB99	Frame_Shift_Del	DEL	ENST00000591680.1	hg19	CCDS32666.1																																																																																			.	.	.	none		0.588	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909		-	42475176	TGAG	-	42475173	7	5	230	1	0	1	0	1	0	0	0	0	6601	1799	63	0	240	0	GPATCH8	17	42475173	Frame_Shift_Del	DEL	TGAG	TCGA-P4-A5E7-01A-31D-A28G-10	5982179	42475173	38720037	69	13995											
OTOP3	347741	hgsc.bcm.edu	37	chr17	72942796	72942796	+	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	ctgtgcctcaatgccaccgcGtgtgaagctttccggagagg	7	9	13	12	3	1	2	1	1	0	1	2	3	2	2	4	2	3	1	4	2	2	1	rs200903740		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr17:72942796G>A	ENST00000328801.4	+	6	846	c.846G>A	c.(844-846)gcG>gcA	p.A282A		NM_178233.1	NP_839947.1	Q7RTS5	OTOP3_HUMAN	otopetrin 3	282						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)					ATGCCACCGCGTGTGAAGCTT	0.567																																					p.A282A		Atlas-SNP	.											.	OTOP3	64	.	0			c.G846A						PASS	.	G		0,4406		0,0,2203	132	125	127		846	2.1	0.1	17		127	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	OTOP3	NM_178233.1		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		282/597	72942796	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	347741	exon6			CACCGCGTGTGAA	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.846G>A	chr17.hg19:g.72942796G>A		60.0	0.0	.		90.0	4.0	.	NM_178233		Silent	SNP	ENST00000328801.4	hg19	CCDS11709.1																																																																																			.	G|0.999;A|0.001	0.001	weak		0.567	OTOP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445308.1	NM_178233		A	72942796	G	A	72942796	2	1	230	1	0	0	0	0	0	0	0	1	11314	1132	40	1		1	OTOP3	17	72942796	Silent	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	30467623	72942796	8252414	70	13996											
HMHA1	23526	hgsc.bcm.edu	37	chr19	1081736	1081736	+	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	gcggcgggcgctgcgcaccaAggtgaggcgggggaggaagc	7	2	22	10	5	0	1	0	1	0	0	0	3	0	3	1	7	2	2	1	7	2	0			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr19:1081736A>C	ENST00000313093.2	+	18	2609	c.2378A>C	c.(2377-2379)aAg>aCg	p.K793T	HMHA1_ENST00000536472.1_Splice_Site_p.K661T|HMHA1_ENST00000539243.2_Splice_Site_p.K809T|HMHA1_ENST00000590214.1_Splice_Site_p.K820T|HMHA1_ENST00000543365.1_Splice_Site_p.K676T|HMHA1_ENST00000590577.1_Splice_Site_p.K428T|HMHA1_ENST00000586866.1_Splice_Site_p.K797T	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	793	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)		CTGCGCACCAAGGTGAGGCGG	0.731																																					p.K809T		Atlas-SNP	.											.	HMHA1	78	.	0			c.A2426C						PASS	.						6	7	7					19																	1081736		2129	4218	6347	SO:0001630	splice_region_variant	23526	exon18			GCACCAAGGTGAG	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.2379+1A>C	chr19.hg19:g.1081736A>C		2.0	0.0	.		31.0	10.0	.	NM_001258328	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Missense_Mutation	SNP	ENST00000313093.2	hg19	CCDS32863.1	.	.	.	.	.	.	.	.	.	.	a	22.3	4.273106	0.80580	.	.	ENSG00000180448	ENST00000539243;ENST00000313093;ENST00000544746;ENST00000536472;ENST00000412039;ENST00000543365	T;T;T;T	0.23147	1.92;1.92;1.92;1.92	4.55	4.55	0.56014	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.43787	0.1263	L	0.49455	1.56	0.58432	D	0.999996	D;D;D;D;D	0.69078	0.997;0.993;0.996;0.993;0.995	D;D;D;P;D	0.74674	0.928;0.945;0.984;0.892;0.967	T	0.40421	-0.9564	10	0.87932	D	0	-45.2741	13.1017	0.59224	1.0:0.0:0.0:0.0	.	661;809;428;676;793	F5H4A3;F6QP70;B3KVA9;F5H1R4;Q92619	.;.;.;.;HMHA1_HUMAN	T	809;793;793;661;787;676	ENSP00000439601:K809T;ENSP00000316772:K793T;ENSP00000445109:K661T;ENSP00000438979:K676T	ENSP00000316772:K793T	K	+	2	0	HMHA1	1032736	1.000000	0.71417	1.000000	0.80357	0.579000	0.36224	8.654000	0.91092	1.684000	0.51022	0.449000	0.29647	AAG	.	.	.	none		0.731	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1		Missense_Mutation	C	1081736	A	C	1081736	5	2	230	1	0	0	0	0	0	0	1	0	7247	86	3	5	2448	5	HMHA1	19	1081736	Splice_Site	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10		1081736	58047247	71	13997											
EVI5L	115704	hgsc.bcm.edu	37	chr19	7917990	7917990	+	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	agtacttccagagagtgatcCcccaccagttcgacagctgc	10	8	9	14	1	0	2	0	1	0	1	3	4	2	2	4	0	3	3	4	0	1	3			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr19:7917990C>G	ENST00000270530.4	+	9	1202	c.1006C>G	c.(1006-1008)Ccc>Gcc	p.P336A	EVI5L_ENST00000538904.2_Missense_Mutation_p.P336A	NM_145245.3	NP_660288.1	Q96CN4	EVI5L_HUMAN	ecotropic viral integration site 5-like	336					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						GAGAGTGATCCCCCACCAGTT	0.627											OREG0025211	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P336A		Atlas-SNP	.											.	EVI5L	43	.	0			c.C1006G						PASS	.						123	122	123					19																	7917990		2203	4300	6503	SO:0001583	missense	115704	exon8			GTGATCCCCCACC	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.1006C>G	chr19.hg19:g.7917990C>G	ENSP00000270530:p.Pro336Ala	79.0	0.0	.	645	112.0	43.0	.	NM_001159944	B9A6I9	Missense_Mutation	SNP	ENST00000270530.4	hg19	CCDS12188.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.277895	0.80692	.	.	ENSG00000142459	ENST00000270530;ENST00000538904	T;T	0.23147	1.92;1.92	3.8	3.8	0.43715	Rab-GAP/TBC domain (1);	0.000000	0.85682	D	0.000000	T	0.46639	0.1403	M	0.64567	1.98	0.58432	D	0.999999	D;P	0.89917	1.0;0.951	D;P	0.91635	0.999;0.727	T	0.47497	-0.9113	10	0.59425	D	0.04	-42.9871	13.5149	0.61535	0.0:1.0:0.0:0.0	.	336;336	B9A6I9;Q96CN4	.;EVI5L_HUMAN	A	336	ENSP00000270530:P336A;ENSP00000445905:P336A	ENSP00000270530:P336A	P	+	1	0	EVI5L	7823990	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.584000	0.82572	2.124000	0.65301	0.462000	0.41574	CCC	.	.	.	none		0.627	EVI5L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461347.1	NM_145245		G	7917990	C	G	7917990	3	3	230	1	0	0	0	0	1	0	0	0	5292	623	22	4	1036	4	EVI5L	19	7917990	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	6836254	7917990	51210993	72	13998											
HOOK2	29911	hgsc.bcm.edu	37	chr19	12874398	12874398	+	Frame_Shift_Del	DEL	T	T	-																															ctgctcccgctgacttcggcTtttctcaaagtccatctgtc																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr19:12874398delT	ENST00000397668.3	-	22	2027	c.1954delA	c.(1954-1956)agcfs	p.S652fs	HOOK2_ENST00000589965.1_5'Flank|HOOK2_ENST00000264827.5_Frame_Shift_Del_p.S650fs	NM_013312.2	NP_037444.2	Q96ED9	HOOK2_HUMAN	hook microtubule-tethering protein 2	652	Required for localization to the centrosome and induction of aggresome formation.|Sufficient for interaction with CNTRL.				early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	centrosome (GO:0005813)|FHF complex (GO:0070695)|microtubule (GO:0005874)	identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(5)|skin(1)	20						TGACTTCGGCTTTTCTCAAAG	0.522																																					p.S652fs		Atlas-Indel,Pindel	.											.	HOOK2	73	.	0			c.1955delG						PASS	.						185	194	191					19																	12874398		2203	4300	6503	SO:0001589	frameshift_variant	29911	exon22			.	AF044924	CCDS42507.1, CCDS42508.1	19p13.2	2013-08-21	2013-08-21						19885	protein-coding gene	gene with protein product		607824	"hook homolog 2 (Drosophila)"			9927460	Standard	NM_013312		Approved	HK2	uc002muy.2	Q96ED9		ENST00000397668.3:c.1954delA	chr19.hg19:g.12874398delT	ENSP00000380785:p.Ser652fs	121.0	0.0	0		118.0	40.0	0.338983	NM_013312	O60562	Frame_Shift_Del	DEL	ENST00000397668.3	hg19	CCDS42508.1																																																																																			.	.	.	none		0.522	HOOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451008.1	NM_013312		-	12874398	T	-	12874398	7	5	230	1	0	1	0	1	0	0	0	0	7290	1609	56	0	213	0	HOOK2	19	12874398	Frame_Shift_Del	DEL	T	TCGA-P4-A5E7-01A-31D-A28G-10	4956408	12874398	46254585	73	13999											
PGLYRP2	114770	hgsc.bcm.edu	37	chr19	15582776	15582776	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatgttggctgcgcagcgcGtgaagtccgtgcagggtggt	5	9	18	9	4	0	1	0	1	0	0	1	1	1	1	1	3	3	5	1	3	1	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr19:15582776G>A	ENST00000340880.4	-	3	1748	c.1268C>T	c.(1267-1269)aCg>aTg	p.T423M	PGLYRP2_ENST00000292609.4_Missense_Mutation_p.T423M	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	423					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						TGCGCAGCGCGTGAAGTCCGT	0.672																																					p.T423M		Atlas-SNP	.											.	PGLYRP2	116	.	0			c.C1268T						PASS	.						63	53	56					19																	15582776		2203	4300	6503	SO:0001583	missense	114770	exon3			CAGCGCGTGAAGT	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.1268C>T	chr19.hg19:g.15582776G>A	ENSP00000345968:p.Thr423Met	59.0	0.0	.		88.0	5.0	.	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Missense_Mutation	SNP	ENST00000340880.4	hg19	CCDS12330.2	.	.	.	.	.	.	.	.	.	.	G	6.484	0.457468	0.12342	.	.	ENSG00000161031	ENST00000340880;ENST00000292609	T;T	0.14391	2.51;2.51	4.62	-7.33	0.01431	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (4);	2.474620	0.01368	N	0.012465	T	0.17704	0.0425	L	0.60455	1.87	0.09310	N	1	P;P	0.52316	0.952;0.889	P;P	0.49597	0.616;0.505	T	0.48068	-0.9067	10	0.52906	T	0.07	-14.711	4.6458	0.12572	0.0767:0.2083:0.1616:0.5534	.	423;423	Q96PD5-2;Q96PD5	.;PGRP2_HUMAN	M	423	ENSP00000345968:T423M;ENSP00000292609:T423M	ENSP00000292609:T423M	T	-	2	0	PGLYRP2	15443776	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.143000	0.10296	-1.075000	0.03129	-1.001000	0.02504	ACG	.	.	.	none		0.672	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890		A	15582776	G	A	15582776	3	1	230	1	0	0	0	0	1	0	0	0	11801	1145	40	1	474	1	PGLYRP2	19	15582776	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	2708378	15582776	43546207	74	14000											
TMEM38A	79041	hgsc.bcm.edu	37	chr19	16793291	16793291	+	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	tccgaggggtctggaagccaGagaccaacgagatcctgcac	11	5	13	12	2	1	2	0	0	1	2	3	6	3	3	4	3	3	1	4	3	2	0			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr19:16793291G>C	ENST00000187762.2	+	4	617	c.526G>C	c.(526-528)Gag>Cag	p.E176Q		NM_024074.1	NP_076979.1	Q9H6F2	TM38A_HUMAN	transmembrane protein 38A	176						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|sarcoplasmic reticulum membrane (GO:0033017)	potassium channel activity (GO:0005267)			central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)	15						CTGGAAGCCAGAGACCAACGA	0.582																																					p.E176Q		Atlas-SNP	.											.	TMEM38A	32	.	0			c.G526C						PASS	.						149	123	132					19																	16793291		2203	4300	6503	SO:0001583	missense	79041	exon4			AAGCCAGAGACCA	AK025981	CCDS12349.1	19p13.11	2013-05-23				ENSG00000072954			28462	protein-coding gene	gene with protein product		611235				17611541	Standard	NM_024074		Approved	MGC3169, TRIC-A	uc002nes.3	Q9H6F2		ENST00000187762.2:c.526G>C	chr19.hg19:g.16793291G>C	ENSP00000187762:p.Glu176Gln	92.0	0.0	.		133.0	42.0	.	NM_024074	A8K9P9	Missense_Mutation	SNP	ENST00000187762.2	hg19	CCDS12349.1	.	.	.	.	.	.	.	.	.	.	g	24.0	4.482621	0.84747	.	.	ENSG00000072954	ENST00000187762	.	.	.	5.38	4.35	0.52113	.	0.053986	0.64402	D	0.000001	T	0.72835	0.3510	M	0.71206	2.165	0.58432	D	0.999998	D	0.57571	0.98	P	0.58130	0.833	T	0.74325	-0.3702	9	0.46703	T	0.11	-30.6059	13.1225	0.59336	0.077:0.0:0.923:0.0	.	176	Q9H6F2	TM38A_HUMAN	Q	176	.	ENSP00000187762:E176Q	E	+	1	0	TMEM38A	16654291	1.000000	0.71417	0.674000	0.29902	0.978000	0.69477	7.723000	0.84788	1.258000	0.44101	0.655000	0.94253	GAG	.	.	.	none		0.582	TMEM38A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462841.1	NM_024074		C	16793291	G	C	16793291	3	2	230	1	0	0	0	0	1	0	0	0	16171	943	33	4	540	4	TMEM38A	19	16793291	Missense_Mutation	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	1210515	16793291	42335692	75	14001											
C19orf62	29086	hgsc.bcm.edu	37	chr19	17384931	17384931	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagctgtctggcctgaccTccgacccccgcgagctctgt	4	9	11	17	3	2	1	0	1	2	0	3	3	3	1	5	1	3	3	5	1	0	0			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr19:17384931T>C	ENST00000359435.4	+	5	674	c.481T>C	c.(481-483)Tcc>Ccc	p.S161P	BABAM1_ENST00000601043.1_Missense_Mutation_p.S161P|BABAM1_ENST00000447614.2_Missense_Mutation_p.S161P|BABAM1_ENST00000448635.2_Intron|BABAM1_ENST00000595632.1_Intron|CTD-2278I10.6_ENST00000596542.1_Missense_Mutation_p.S83P|BABAM1_ENST00000598188.1_Missense_Mutation_p.S161P	NM_001033549.1	NP_001028721.1	Q9NWV8	BABA1_HUMAN	BRISC and BRCA1 A complex member 1	161	VWFA-like.				chromatin modification (GO:0016568)|double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of DNA repair (GO:0045739)|protein K63-linked deubiquitination (GO:0070536)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRISC complex (GO:0070552)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5						TGGCCTGACCTCCGACCCCCG	0.667																																					p.S161P		Atlas-SNP	.											.	BABAM1	14	.	0			c.T481C						PASS	.						57	66	63					19																	17384931		2060	4203	6263	SO:0001583	missense	29086	exon5			CTGACCTCCGACC	AK000578	CCDS46012.1, CCDS74310.1	19p13.11	2011-02-21	2011-02-21	2011-01-31	ENSG00000105393	ENSG00000105393			25008	protein-coding gene	gene with protein product	"Mediator of Rap80 Interactions and Targeting 40 kD", "new component of the BRCA1 A complex"	612766	"chromosome 19 open reading frame 62"	C19orf62		11042152	Standard	NM_001288756		Approved	FLJ20571, HSPC142, NBA1, MERIT40	uc002nfv.3	Q9NWV8		ENST00000359435.4:c.481T>C	chr19.hg19:g.17384931T>C	ENSP00000352408:p.Ser161Pro	40.0	0.0	.		51.0	23.0	.	NM_014173	A8MQT0|B4DRY9|B4DVR1|Q6FIA0|Q9P018	Missense_Mutation	SNP	ENST00000359435.4	hg19	CCDS46012.1	.	.	.	.	.	.	.	.	.	.	T	19.36	3.812432	0.70912	.	.	ENSG00000105393	ENST00000359435;ENST00000447614;ENST00000300965	.	.	.	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.76666	0.4019	M	0.66939	2.045	0.80722	D	1	D	0.71674	0.998	D	0.76575	0.988	T	0.77885	-0.2421	9	0.52906	T	0.07	-27.2018	14.0114	0.64498	0.0:0.0:0.0:1.0	.	161	Q9NWV8	BABA1_HUMAN	P	161;161;83	.	ENSP00000300965:S83P	S	+	1	0	BABAM1	17245931	1.000000	0.71417	0.979000	0.43373	0.276000	0.26787	5.510000	0.67018	2.192000	0.70111	0.533000	0.62120	TCC	.	.	.	none		0.667	BABAM1-005	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463471.1	NM_014173		C	17384931	T	C	17384931	3	2	230	1	0	0	0	0	1	0	0	0	1946	1551	54	3	495	3	C19orf62	19	17384931	Missense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10	591640	17384931	41744052	76	14002											
SFRS14	10147	hgsc.bcm.edu	37	chr19	19106027	19106027	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttccagcccatcttctgcagCatctggaagcccaggttctt	7	12	8	14	0	4	0	0	0	4	0	5	1	5	1	3	2	4	3	3	2	1	4			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr19:19106027C>T	ENST00000601879.1	-	9	3351	c.3054G>A	c.(3052-3054)atG>atA	p.M1018I	SUGP2_ENST00000456085.2_Missense_Mutation_p.M787I|SUGP2_ENST00000600377.1_Missense_Mutation_p.M1032I|AC004447.2_ENST00000594142.1_RNA|SUGP2_ENST00000452918.2_Missense_Mutation_p.M1018I|SUGP2_ENST00000337018.6_Missense_Mutation_p.M1018I			Q8IX01	SUGP2_HUMAN	SURP and G patch domain containing 2	1018	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						TCTTCTGCAGCATCTGGAAGC	0.627																																					p.M1018I		Atlas-SNP	.											.	SUGP2	107	.	0			c.G3054A						PASS	.						64	53	57					19																	19106027		2203	4300	6503	SO:0001583	missense	10147	exon9			CTGCAGCATCTGG	AB002363	CCDS12392.1	19p13	2013-01-28	2010-08-10	2010-08-10	ENSG00000064607	ENSG00000064607		"G patch domain containing"	18641	protein-coding gene	gene with protein product		607993	"splicing factor, arginine/serine-rich 14"	SFRS14		12594045	Standard	NM_014884		Approved	KIAA0365	uc002nkx.2	Q8IX01		ENST00000601879.1:c.3054G>A	chr19.hg19:g.19106027C>T	ENSP00000472286:p.Met1018Ile	61.0	0.0	.		57.0	19.0	.	NM_014884	C9JI71|O15071|O60369|Q5JPH7|Q8WUF7	Missense_Mutation	SNP	ENST00000601879.1	hg19	CCDS12392.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.017731	0.93404	.	.	ENSG00000064607	ENST00000337018;ENST00000330854;ENST00000452918;ENST00000456085	T;T;T;T	0.37235	1.21;1.21;1.21;1.21	5.05	5.05	0.67936	D111/G-patch (3);	0.000000	0.85682	D	0.000000	T	0.61236	0.2331	M	0.73962	2.25	0.58432	D	0.999999	D;D;D	0.59357	0.969;0.985;0.969	D;D;D	0.72338	0.968;0.977;0.951	T	0.65627	-0.6122	10	0.72032	D	0.01	-26.6822	16.9459	0.86230	0.0:1.0:0.0:0.0	.	787;1018;1018	E7ETX7;A8K5G0;Q8IX01	.;.;SUGP2_HUMAN	I	1018;966;1018;787	ENSP00000337926:M1018I;ENSP00000332373:M966I;ENSP00000389380:M1018I;ENSP00000409603:M787I	ENSP00000332373:M966I	M	-	3	0	SUGP2	18967027	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.709000	0.74665	2.349000	0.79799	0.462000	0.41574	ATG	.	.	.	none		0.627	SUGP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464627.1	NM_001017392		T	19106027	C	T	19106027	3	4	230	1	0	0	0	0	1	0	0	0	14183	710	25	2	202	2	SFRS14	19	19106027	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	1721096	19106027	40022956	77	14003											
ETHE1	23474	hgsc.bcm.edu	37	chr19	44030497	44030497	+	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	tggtccgcgtggcagtgggtAttcactgggagagagaggag	8	8	19	6	2	1	2	1	0	0	2	2	5	2	3	1	5	0	2	1	5	1	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr19:44030497A>T	ENST00000292147.2	-	3	297	c.231T>A	c.(229-231)aaT>aaA	p.N77K	ZNF575_ENST00000458714.2_Intron|ETHE1_ENST00000600651.1_Missense_Mutation_p.N77K	NM_014297.3	NP_055112.2	O95571	ETHE1_HUMAN	ethylmalonic encephalopathy 1	77					cellular nitrogen compound metabolic process (GO:0034641)|glutathione metabolic process (GO:0006749)|hydrogen sulfide metabolic process (GO:0070813)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	iron ion binding (GO:0005506)|sulfur dioxygenase activity (GO:0050313)			central_nervous_system(1)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	5		Prostate(69;0.0153)				GGCAGTGGGTATTCACTGGGA	0.637																																					p.N77K		Atlas-SNP	.											.	ETHE1	7	.	0			c.T231A						PASS	.						50	50	50					19																	44030497		2203	4300	6503	SO:0001583	missense	23474	exon3			GTGGGTATTCACT		CCDS12622.1	19q13.32	2014-06-20				ENSG00000105755	1.13.11.18		23287	protein-coding gene	gene with protein product		608451				19136963	Standard	NM_014297		Approved	YF13H12, HSCO	uc002owp.3	O95571		ENST00000292147.2:c.231T>A	chr19.hg19:g.44030497A>T	ENSP00000292147:p.Asn77Lys	143.0	0.0	.		131.0	43.0	.	NM_014297	Q96HR0|Q9H001	Missense_Mutation	SNP	ENST00000292147.2	hg19	CCDS12622.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.574665	0.86542	.	.	ENSG00000105755	ENST00000292147	T	0.80393	-1.37	4.67	-5.32	0.02722	Beta-lactamase-like (2);	0.000000	0.85682	D	0.000000	D	0.91666	0.7366	H	0.96777	3.88	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.99;1.0	D	0.91960	0.5578	10	0.62326	D	0.03	-16.786	17.6863	0.88257	0.168:0.0:0.832:0.0	.	50;77	B2RCZ7;O95571	.;ETHE1_HUMAN	K	77	ENSP00000292147:N77K	ENSP00000292147:N77K	N	-	3	2	ETHE1	48722337	0.995000	0.38212	0.901000	0.35422	0.992000	0.81027	0.170000	0.16663	-1.038000	0.03279	-0.375000	0.07067	AAT	.	.	.	none		0.637	ETHE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463184.1	NM_014297		T	44030497	A	T	44030497	3	4	230	1	0	0	0	0	1	0	0	0	5274	446	16	5	553	5	ETHE1	19	44030497	Missense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10	24924470	44030497	15098486	78	14004											
NUP62	23636	hgsc.bcm.edu	37	chr19	50411616	50411633	+	In_Frame_Del	DEL	GTCCATGTGCGCATTGAG	GTCCATGTGCGCATTGAG	-																															tggtcgatccactgcagtgaGtccatgtgcgcattgaggat																								rs139913264|rs61751953|rs151075180		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	GTCCATGTGCGCATTGAG	GTCCATGTGCGCATTGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr19:50411616_50411633delGTCCATGTGCGCATTGAG	ENST00000596217.1	-	2	3319_3336	c.1432_1449delCTCAATGCGCACATGGAC	c.(1432-1449)ctcaatgcgcacatggacdel	p.LNAHMD478del	IL4I1_ENST00000341114.3_Intron|NUP62_ENST00000597723.1_In_Frame_Del_p.LNAHMD402del|IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000352066.3_In_Frame_Del_p.LNAHMD478del|NUP62_ENST00000422090.2_In_Frame_Del_p.LNAHMD478del|NUP62_ENST00000600583.1_5'Flank|NUP62_ENST00000597029.1_In_Frame_Del_p.LNAHMD478del|NUP62_ENST00000413454.1_In_Frame_Del_p.LNAHMD478del			P37198	NUP62_HUMAN	nucleoporin 62kDa	478					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)	p.A480A(1)		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)		ACTGCAGTGAGTCCATGTGCGCATTGAGGATCTTGCAG	0.628																																					p.478_484del		Atlas-INDEL	.											.	NUP62	50	.	1	Substitution - coding silent(1)	lung(1)	c.1433_1450del						PASS	.																																			SO:0001651	inframe_deletion	23636	exon3			.	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.1432_1449delCTCAATGCGCACATGGAC	chr19.hg19:g.50411616_50411633delGTCCATGTGCGCATTGAG	ENSP00000471191:p.Leu478_Asp483del	47.0	0.0	0		62.0	17.0	0.274194	NM_153719	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	In_Frame_Del	DEL	ENST00000596217.1	hg19	CCDS12788.1																																																																																			.	.	.	none		0.628	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464991.1	NM_153719		-	50411633	GTCCATGTGCGCATTGAG	-	50411616	7	5	230	1	0	1	0	1	0	0	0	0	10775	1020	36	0	123	0	NUP62	19	50411616	In_Frame_Del	DEL	GTCCATGTGCGCATTGAG	TCGA-P4-A5E7-01A-31D-A28G-10	6381119	50411616	8717367	79	14005											
PRKCG	5582	hgsc.bcm.edu	37	chr19	54401854	54401854	+	Frame_Shift_Del	DEL	C	C	-																															cggccggccccacttcctcaCccagctccactccaccttcc																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr19:54401854delC	ENST00000263431.3	+	11	1535	c.1253delC	c.(1252-1254)accfs	p.T418fs	PRKCG_ENST00000542049.1_Frame_Shift_Del_p.T305fs|PRKCG_ENST00000540413.1_Frame_Shift_Del_p.T418fs	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	418	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cell death (GO:0008219)|chemosensory behavior (GO:0007635)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein ubiquitination (GO:0031397)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of mismatch repair (GO:0032425)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to morphine (GO:0043278)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic membrane (GO:0097060)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(4)|ovary(2)|pancreas(2)|skin(1)	10	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)	Tamoxifen(DB00675)	CACTTCCTCACCCAGCTCCAC	0.662																																					p.T418fs		Atlas-Indel,Pindel	.											.	PRKCG	246	.	0			c.1252delA						PASS	.						12	13	13					19																	54401854		2200	4285	6485	SO:0001589	frameshift_variant	5582	exon11			.	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.1253delC	chr19.hg19:g.54401854delC	ENSP00000263431:p.Thr418fs	52.0	0.0	0		71.0	28.0	0.394366	NM_002739	B7Z8Q0	Frame_Shift_Del	DEL	ENST00000263431.3	hg19	CCDS12867.1																																																																																			.	.	.	none		0.662	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739		-	54401854	C	-	54401854	7	5	230	1	0	1	0	1	0	0	0	0	12522	507	18	0	1295	0	PRKCG	19	54401854	Frame_Shift_Del	DEL	C	TCGA-P4-A5E7-01A-31D-A28G-10	3990238	54401854	4727129	80	14006											
JAG1	182	hgsc.bcm.edu	37	chr20	10653490	10653490	+	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	ccggccgtgacgcgggactgAtactccttgaggcacacttt	7	9	12	13	4	0	3	0	3	0	0	1	4	1	4	3	3	1	1	3	3	1	3			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr20:10653490A>C	ENST00000254958.5	-	2	761	c.246T>G	c.(244-246)taT>taG	p.Y82*	RP11-103J8.1_ENST00000605292.1_RNA	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	82					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						CGCGGGACTGATACTCCTTGA	0.662									Alagille Syndrome																												p.Y82X		Atlas-SNP	.											.	JAG1	213	.	0			c.T246G						PASS	.						51	50	51					20																	10653490		2203	4299	6502	SO:0001587	stop_gained	182	exon2	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	GGACTGATACTCC	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.246T>G	chr20.hg19:g.10653490A>C	ENSP00000254958:p.Tyr82*	49.0	0.0	.		94.0	25.0	.	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Nonsense_Mutation	SNP	ENST00000254958.5	hg19	CCDS13112.1	.	.	.	.	.	.	.	.	.	.	A	41	8.923643	0.99004	.	.	ENSG00000101384	ENST00000254958	.	.	.	5.28	1.45	0.22620	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.9719	0.41759	0.4136:0.0:0.5864:0.0	.	.	.	.	X	82	.	ENSP00000254958:Y82X	Y	-	3	2	JAG1	10601490	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.053000	0.41326	0.554000	0.29061	0.459000	0.35465	TAT	.	.	.	none		0.662	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214		C	10653490	A	C	10653490	4	2	230	1	0	0	0	0	0	1	0	0	7941	340	12	5	3510	5	JAG1	20	10653490	Nonsense_Mutation	SNP	A	TCGA-P4-A5E7-01A-31D-A28G-10		10653490	52372030	81	14007											
C20orf12	55184	hgsc.bcm.edu	37	chr20	18414380	18414380	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgggagtgttcatgggtacCaagcttctgcattctgcaca	9	12	11	9	0	3	0	1	0	2	0	3	1	3	1	1	2	4	5	1	2	2	4			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr20:18414380C>T	ENST00000358866.6	-	8	799	c.777G>A	c.(775-777)ttG>ttA	p.L259L	DZANK1_ENST00000487128.1_5'UTR|DZANK1_ENST00000329494.5_Silent_p.L261L|DZANK1_ENST00000262547.5_Silent_p.L259L|DZANK1_ENST00000357236.4_Silent_p.L145L|RNA5SP476_ENST00000516613.1_RNA			Q9NVP4	DZAN1_HUMAN	double zinc ribbon and ankyrin repeat domains 1	259							zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(10)	19						TCATGGGTACCAAGCTTCTGC	0.458																																					p.L259L		Atlas-SNP	.											.	DZANK1	65	.	0			c.G777A						PASS	.						112	109	110					20																	18414380		2000	4182	6182	SO:0001819	synonymous_variant	55184	exon9			GGGTACCAAGCTT	AK001462	CCDS46582.1	20p11.23	2013-01-11	2011-10-03	2011-10-03	ENSG00000089091	ENSG00000089091		"Ankyrin repeat domain containing"	15858	protein-coding gene	gene with protein product	"ankyrin repeat domain 64"		"chromosome 20 open reading frame 12"	C20orf84, C20orf12			Standard	NM_001099407		Approved	FLJ10600, dJ568F9.2, FLJ30892, bA189K21.8, ANKRD64	uc002wqq.4	Q9NVP4	OTTHUMG00000031968	ENST00000358866.6:c.777G>A	chr20.hg19:g.18414380C>T		68.0	0.0	.		61.0	14.0	.	NM_001099407	B7ZLZ4|Q4F7X1|Q5QPD9|Q5QPE0|Q68DN8|Q6ZMX9|Q96NF0|Q9H1E0|Q9H442	Silent	SNP	ENST00000358866.6	hg19	CCDS46582.1	.	.	.	.	.	.	.	.	.	.	C	0.837	-0.743265	0.03088	.	.	ENSG00000089091	ENST00000358866	.	.	.	4.97	4.02	0.46733	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-0.6738	10.7045	0.45948	0.0:0.9065:0.0:0.0935	.	.	.	.	X	58	.	.	W	-	2	0	C20orf12	18362380	1.000000	0.71417	0.803000	0.32268	0.023000	0.10783	1.732000	0.38146	2.448000	0.82819	0.655000	0.94253	TGG	.	.	.	none		0.458	DZANK1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471926.1	NM_001099407		T	18414380	C	T	18414380	2	4	230	1	0	0	0	0	0	0	0	1	2087	593	21	2		2	C20orf12	20	18414380	Silent	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	7760890	18414380	44611140	82	14008											
PLUNC	51297	hgsc.bcm.edu	37	chr20	31829269	31829269	+	Frame_Shift_Del	DEL	G	G	-																															gtcctgcctgagttggttcaGggcaacgtaagtaggcaagg																										TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr20:31829269delG	ENST00000354297.4	+	6	731	c.660delG	c.(658-660)cagfs	p.Q220fs	BPIFA1_ENST00000375422.2_Frame_Shift_Del_p.Q220fs|BPIFA1_ENST00000375413.4_Frame_Shift_Del_p.Q220fs	NM_130852.2	NP_570913.1	Q9NP55	BPIA1_HUMAN	BPI fold containing family A, member 1	220				Q -> K (in Ref. 1; AAF70860). {ECO:0000305}.	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)										AGTTGGTTCAGGGCAACGTAA	0.512																																					p.Q220fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.659delA						PASS	.						164	158	160					20																	31829269		2203	4300	6503	SO:0001589	frameshift_variant	51297	exon6			.	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.660delG	chr20.hg19:g.31829269delG	ENSP00000346251:p.Gln220fs	115.0	0.0	0		85.0	20.0	0.235294	NM_130852	A8K9R3|E1P5M9|Q9NZT0	Frame_Shift_Del	DEL	ENST00000354297.4	hg19	CCDS13217.1																																																																																			.	.	.	none		0.512	BPIFA1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078667.2	NM_130852		-	31829269	G	-	31829269	7	5	230	1	0	1	0	1	0	0	0	0	12122	991	35	0	678	0	PLUNC	20	31829269	Frame_Shift_Del	DEL	G	TCGA-P4-A5E7-01A-31D-A28G-10	13414889	31829269	31196251	83	14009											
SS18L1	26039	hgsc.bcm.edu	37	chr20	60738629	60738629	+	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	gggcagggcagccaggggagCagcatgatggggcagcggcc	8	2	21	10	1	0	1	0	1	0	0	0	2	0	2	2	7	4	5	2	7	0	0			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr20:60738629C>A	ENST00000331758.3	+	6	698	c.672C>A	c.(670-672)agC>agA	p.S224R	SS18L1_ENST00000421564.1_Missense_Mutation_p.S224R|SS18L1_ENST00000370848.4_Missense_Mutation_p.S227R	NM_198935.1	NP_945173.1	O75177	CREST_HUMAN	synovial sarcoma translocation gene on chromosome 18-like 1	224	Gln-rich.|Methionine-rich intra-molecular domain. {ECO:0000250}.				chromatin modification (GO:0016568)|dendrite development (GO:0016358)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of dendrite development (GO:0050773)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)|kinetochore (GO:0000776)|nuclear body (GO:0016604)|nucleus (GO:0005634)			SS18L1/SSX1(2)	ovary(2)|skin(1)	3	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.92e-08)			GCCAGGGGAGCAGCATGATGG	0.731			T	SSX1	synovial sarcoma																																p.S224R		Atlas-SNP	.		Dom	yes		20	20q13.3	26039	synovial sarcoma translocation gene on chromosome 18-like 1		M	.	SS18L1	37	.	0			c.C672A						PASS	.						23	25	25					20																	60738629		2195	4294	6489	SO:0001583	missense	26039	exon6			GGGGAGCAGCATG	AB014593	CCDS13491.1	20q13.3	2008-07-28			ENSG00000184402	ENSG00000184402			15592	protein-coding gene	gene with protein product		606472					Standard	XM_005260389		Approved	KIAA0693	uc002ycb.3	O75177	OTTHUMG00000032902	ENST00000331758.3:c.672C>A	chr20.hg19:g.60738629C>A	ENSP00000333012:p.Ser224Arg	2.0	0.0	.		98.0	43.0	.	NM_198935	A6NNE3|A8K620|B3KWR8|E1P5H7|Q5JXJ3|Q6MZV9|Q6NTH3|Q6XYD9|Q8NE69|Q9BR55|Q9H4K6	Missense_Mutation	SNP	ENST00000331758.3	hg19	CCDS13491.1	.	.	.	.	.	.	.	.	.	.	C	17.89	3.499248	0.64298	.	.	ENSG00000184402	ENST00000421564;ENST00000331758;ENST00000370848	T;T;T	0.32515	1.45;1.45;1.46	4.99	3.03	0.35002	.	0.269496	0.44483	D	0.000453	T	0.28499	0.0705	L	0.47716	1.5	0.25078	N	0.990947	P;P	0.45902	0.651;0.868	B;B	0.42319	0.198;0.383	T	0.11036	-1.0604	10	0.87932	D	0	-10.1574	11.0441	0.47849	0.0:0.8465:0.0:0.1535	.	224;224	B4DSR7;O75177	.;CREST_HUMAN	R	224;224;227	ENSP00000393999:S224R;ENSP00000333012:S224R;ENSP00000359885:S227R	ENSP00000333012:S224R	S	+	3	2	SS18L1	60172024	1.000000	0.71417	0.766000	0.31476	0.987000	0.75469	1.854000	0.39368	0.498000	0.27948	0.467000	0.42956	AGC	.	.	.	none		0.731	SS18L1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080004.2			A	60738629	C	A	60738629	3	1	230	1	0	0	0	0	1	0	0	0	15188	709	25	4	694	4	SS18L1	20	60738629	Missense_Mutation	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	28909360	60738629	2286891	84	14010											
PWP2	5822	hgsc.bcm.edu	37	chr21	45534138	45534138	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagggctctgtgcacagtgTgtccttctcccctgatggca	6	11	11	13	0	2	1	0	1	2	0	4	1	3	1	3	2	1	3	3	2	1	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr21:45534138T>C	ENST00000291576.7	+	4	432	c.305T>C	c.(304-306)gTg>gCg	p.V102A		NM_005049.2	NP_005040.2	Q15269	PWP2_HUMAN	PWP2 periodic tryptophan protein homolog (yeast)	102					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)		GTGCACAGTGTGTCCTTCTCC	0.652											OREG0026247	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V102A		Atlas-SNP	.											.	PWP2	64	.	0			c.T305C						PASS	.						113	94	100					21																	45534138		2203	4300	6503	SO:0001583	missense	5822	exon4			ACAGTGTGTCCTT		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.305T>C	chr21.hg19:g.45534138T>C	ENSP00000291576:p.Val102Ala	89.0	0.0	.	932	85.0	17.0	.	NM_005049	B2RAG8|Q96A77	Missense_Mutation	SNP	ENST00000291576.7	hg19	CCDS33579.1	.	.	.	.	.	.	.	.	.	.	T	17.88	3.498423	0.64298	.	.	ENSG00000241945	ENST00000291576	T	0.50001	0.76	4.8	4.8	0.61643	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	0.213399	0.38720	N	0.001592	T	0.35451	0.0932	L	0.33624	1.015	0.46131	D	0.998884	B	0.31383	0.321	B	0.25506	0.061	T	0.21999	-1.0229	10	0.42905	T	0.14	-8.6121	12.8724	0.57972	0.0:0.0:0.0:1.0	.	102	Q15269	PWP2_HUMAN	A	102	ENSP00000291576:V102A	ENSP00000291576:V102A	V	+	2	0	PWP2	44358566	0.995000	0.38212	0.948000	0.38648	0.736000	0.42039	5.690000	0.68241	1.929000	0.55896	0.402000	0.26972	GTG	.	.	.	none		0.652	PWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195736.3	NM_005049		C	45534138	T	C	45534138	3	2	230	1	0	0	0	0	1	0	0	0	12857	1696	59	3	319	3	PWP2	21	45534138	Missense_Mutation	SNP	T	TCGA-P4-A5E7-01A-31D-A28G-10		45534138	2595757	85	14011											
C22orf15	150248	hgsc.bcm.edu	37	chr22	24106287	24106287	+	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	tccacagctggctgctcggtGctggtgaacacctcttgcag	6	10	12	13	1	1	1	0	1	1	0	3	1	2	1	2	3	5	5	2	3	1	1			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr22:24106287G>A	ENST00000402217.3	+	2	292	c.39G>A	c.(37-39)gtG>gtA	p.V13V	C22orf15_ENST00000305199.5_Silent_p.V13V|C22orf15_ENST00000382821.3_Silent_p.V13V	NM_182520.2	NP_872326.2	Q8WYQ4	CV015_HUMAN	chromosome 22 open reading frame 15	13										breast(1)|pancreas(1)	2		Medulloblastoma(6;6.27e-05)|all_neural(6;0.00518)				GCTGCTCGGTGCTGGTGAACA	0.602																																					p.V13V		Atlas-SNP	.											.	C22orf15	5	.	0			c.G39A						PASS	.						86	90	89					22																	24106287		692	1591	2283	SO:0001819	synonymous_variant	150248	exon2			CTCGGTGCTGGTG	AB050773	CCDS13814.2	22q11.23	2012-11-13			ENSG00000169314	ENSG00000169314			15558	protein-coding gene	gene with protein product							Standard	NM_182520		Approved	FLJ36561, N27C7-3	uc011aja.2	Q8WYQ4	OTTHUMG00000150740	ENST00000402217.3:c.39G>A	chr22.hg19:g.24106287G>A		95.0	0.0	.		65.0	25.0	.	NM_182520	Q6ICJ7	Silent	SNP	ENST00000402217.3	hg19	CCDS13814.2																																																																																			.	.	.	none		0.602	C22orf15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319887.2	NM_182520		A	24106287	G	A	24106287	2	1	230	1	0	0	0	0	0	0	0	1	2138	1306	46	2		2	C22orf15	22	24106287	Silent	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10		24106287	27198279	86	14012											
GATSL3	652968	hgsc.bcm.edu	37	chr22	30685454	30685454	+	Silent	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	ggacgggcgacgctcagcacCcgcacccggtgttctaggat	7	6	14	14	5	2	0	1	0	1	0	2	3	2	2	2	4	1	4	2	4	1	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr22:30685454C>T	ENST00000407689.3	-	1	162	c.33G>A	c.(31-33)cgG>cgA	p.R11R	GATSL3_ENST00000459785.1_5'Flank|RP1-130H16.18_ENST00000447976.1_Intron|GATSL3_ENST00000404953.3_Silent_p.R11R	NM_001037666.2	NP_001032755.1	Q8WTX7	GATL3_HUMAN	GATS protein-like 3	11										breast(1)|endometrium(1)|lung(1)	3						CGCTCAGCACCCGCACCCGGT	0.741																																					p.R11R		Atlas-SNP	.											.	GATSL3	14	.	0			c.G33A						PASS	.						11	18	16					22																	30685454		1870	4079	5949	SO:0001819	synonymous_variant	652968	exon1			CAGCACCCGCACC		CCDS43001.1	22q12	2010-06-23			ENSG00000239282	ENSG00000239282			34423	protein-coding gene	gene with protein product							Standard	NM_001037666		Approved			Q8WTX7	OTTHUMG00000150929	ENST00000407689.3:c.33G>A	chr22.hg19:g.30685454C>T		8.0	0.0	.		56.0	20.0	.	NM_001037666	O76052|Q96ND9|Q9UIE8	Silent	SNP	ENST00000407689.3	hg19	CCDS43001.1																																																																																			.	.	.	none		0.741	GATSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320581.2	NM_001037666		T	30685454	C	T	30685454	2	4	230	1	0	0	0	0	0	0	0	1	6272	610	22	2		2	GATSL3	22	30685454	Silent	SNP	C	TCGA-P4-A5E7-01A-31D-A28G-10	6579167	30685454	20619112	87	14013											
CBY1	25776	hgsc.bcm.edu	37	chr22	39066951	39066951	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggatccccgactatgaacctGgcagggcaaagcctgaagtt	11	7	12	11	1	0	2	0	2	0	0	1	4	1	3	4	3	2	3	4	3	4	2			TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	g.chr22:39066951G>A	ENST00000216029.3	+	3	275	c.141G>A	c.(139-141)ctG>ctA	p.L47L	RP3-508I15.10_ENST00000423346.1_RNA|RP3-508I15.9_ENST00000431924.2_RNA|RP3-508I15.9_ENST00000444381.1_RNA|RP3-508I15.9_ENST00000422408.2_RNA	NM_015373.3	NP_056188.1	Q9Y3M2	CBY1_HUMAN	chibby homolog 1 (Drosophila)	47					cardiac muscle cell differentiation (GO:0055007)|cilium assembly (GO:0042384)|fat cell differentiation (GO:0045444)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|protein localization (GO:0008104)	ciliary basal body (GO:0036064)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	beta-catenin binding (GO:0008013)|identical protein binding (GO:0042802)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|ovary(1)	4	Melanoma(58;0.04)					CTATGAACCTGGCAGGGCAAA	0.527																																					p.L90L		Atlas-SNP	.											.	CBY1	10	.	0			c.G270A						PASS	.						144	143	143					22																	39066951		2203	4300	6503	SO:0001819	synonymous_variant	25776	exon4			GAACCTGGCAGGG	BK005534	CCDS13974.1, CCDS74861.1	22q12	2014-02-06	2007-01-26	2007-01-26	ENSG00000100211	ENSG00000100211			1307	protein-coding gene	gene with protein product	"chibby CTNNB1-mediated transcription inhibitor"	607757	"chromosome 22 open reading frame 2", "PKD2 interactor, golgi and endoplasmic reticulum associated 1"	C22orf2, PGEA1		10591208, 15194699	Standard	NM_015373		Approved	PIGEA14, PIGEA-14, Chibby, Cby	uc003awb.4	Q9Y3M2	OTTHUMG00000150990	ENST00000216029.3:c.141G>A	chr22.hg19:g.39066951G>A		64.0	0.0	.		67.0	14.0	.	NM_001002880	B2R4S2|Q66GT6|Q9UIK9	Silent	SNP	ENST00000216029.3	hg19	CCDS13974.1																																																																																			.	.	.	none		0.527	CBY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320832.1	NM_015373		A	39066951	G	A	39066951	2	1	230	1	0	0	0	0	0	0	0	1	2727	1335	47	2		2	CBY1	22	39066951	Silent	SNP	G	TCGA-P4-A5E7-01A-31D-A28G-10	8381497	39066951	12237615	88	14014											
EIF4G3	8672	hgsc.bcm.edu	37	chr1	21133827	21133829	+	In_Frame_Del	DEL	CTC	CTC	-																															aagttttagttatcctcagaCtcctcttctgcttcccgcag																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr1:21133827_21133829delCTC	ENST00000264211.8	-	31	4935_4937	c.4741_4743delGAG	c.(4741-4743)gagdel	p.E1581del	EIF4G3_ENST00000400422.1_In_Frame_Del_p.E1581del|EIF4G3_ENST00000374937.3_In_Frame_Del_p.E1587del|EIF4G3_ENST00000374935.3_In_Frame_Del_p.E1301del|EIF4G3_ENST00000536266.1_In_Frame_Del_p.E1185del|EIF4G3_ENST00000537738.1_In_Frame_Del_p.E1071del|EIF4G3_ENST00000602326.1_In_Frame_Del_p.E1587del	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	1581	EIF4A-binding. {ECO:0000250}.|Necessary but not sufficient for MKNK1- binding. {ECO:0000250}.|W2. {ECO:0000255|PROSITE- ProRule:PRU00695}.				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)		TATCCTCAGACTCCTCTTCTGCT	0.438																																					p.1617_1618del		Atlas-Indel,Pindel	.											.	EIF4G3	300	.	0			c.4850_4852del						PASS	.																																			SO:0001651	inframe_deletion	8672	exon35			.	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.4741_4743delGAG	chr1.hg19:g.21133830_21133832delCTC	ENSP00000264211:p.Glu1581del	108.0	0.0	0		99.0	33.0	0.333333	NM_001198801	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	In_Frame_Del	DEL	ENST00000264211.8	hg19	CCDS214.1																																																																																			.	.	.	none		0.438	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760		-	21133829	CTC	-	21133827	7	5	231	1	0	1	0	1	0	0	0	0	5040	564	20	0	18	0	EIF4G3	1	21133827	In_Frame_Del	DEL	CTC	TCGA-P4-A5E8-01A-11D-A28G-10		21133827	228116794	1	14015											
MSH4	4438	hgsc.bcm.edu	37	chr1	76346929	76346934	+	Splice_Site	DEL	TTTCAG	TTTCAG	-																															gtcttaccaaacgtgttttcAggatagtgtgcaaactgctt																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	TTTCAG	TTTCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr1:76346929_76346934delTTTCAG	ENST00000263187.3	+	14	1885_1889	c.1781_1785delTTTCAG	c.(1780-1785)atttca>a	p.IS594del		NM_002440.3	NP_002431.2	O15457	MSH4_HUMAN	mutS homolog 4	594					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|female gamete generation (GO:0007292)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						ACGTGTTTTCAGGATAGTGTGCAAAC	0.306								Mismatch excision repair (MMR)																													.		Pindel	.											.	MSH4	147	.	0			.						PASS	.																																			SO:0001630	splice_region_variant	4438	.			.	U89293	CCDS670.1	1p31	2013-09-12	2013-09-12		ENSG00000057468	ENSG00000057468			7327	protein-coding gene	gene with protein product		602105	"mutS (E. coli) homolog 4", "mutS homolog 4 (E. coli)"			9299235	Standard	NM_002440		Approved		uc001dhd.2	O15457	OTTHUMG00000009788	ENST00000263187.3:c.1782-1TTTCAG>-	chr1.hg19:g.76346929_76346934delTTTCAG		82.0	0.0	.		59.0	11.0	0.186	.	Q5T4U6|Q8NEB3|Q9UNP8	Splice_Site	DEL	ENST00000263187.3	hg19	CCDS670.1																																																																																			.	.	.	none		0.306	MSH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026983.1	NM_002440	In_Frame_Del	-	76346934	TTTCAG	-	76346929	8	5	231	1	0	1	0	1	0	0	1	0	9879	202	7	0	1834	0	MSH4	1	76346929	Splice_Site	DEL	TTTCAG	TCGA-P4-A5E8-01A-11D-A28G-10	55213102	76346929	172903692	2	14016											
LYSMD1	388695	hgsc.bcm.edu	37	chr1	151134570	151134570	+	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	gcggtttgcacgtttaatctGttccatcttaaaaaaaaaag	14	13	7	7	2	2	0	0	0	2	0	3	0	3	0	1	1	1	4	1	1	6	5			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr1:151134570G>T	ENST00000368908.5	-	2	847	c.187C>A	c.(187-189)Cag>Aag	p.Q63K	LYSMD1_ENST00000440902.2_Missense_Mutation_p.Q15K	NM_212551.4	NP_997716.1	Q96S90	LYSM1_HUMAN	LysM, putative peptidoglycan-binding, domain containing 1	63										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)			CGTTTAATCTGTTCCATCTTA	0.378																																					p.Q63K		Atlas-SNP	.											.	LYSMD1	23	.	0			c.C187A						PASS	.						50	51	51					1																	151134570		2203	4300	6503	SO:0001583	missense	388695	exon2			TAATCTGTTCCAT	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.187C>A	chr1.hg19:g.151134570G>T	ENSP00000357904:p.Gln63Lys	69.0	0.0	.		71.0	27.0	.	NM_212551	B4DQA1|Q69YX9	Missense_Mutation	SNP	ENST00000368908.5	hg19	CCDS986.1	.	.	.	.	.	.	.	.	.	.	G	18.50	3.637942	0.67130	.	.	ENSG00000163155	ENST00000368908;ENST00000440902	T;T	0.40225	1.12;1.04	5.66	4.73	0.59995	Peptidoglycan-binding Lysin subgroup (1);Peptidoglycan-binding lysin domain (1);	0.000000	0.85682	D	0.000000	T	0.20210	0.0486	L	0.33189	0.99	0.49915	D	0.99983	P;B	0.41450	0.75;0.235	B;B	0.36766	0.232;0.103	T	0.07520	-1.0768	10	0.87932	D	0	-2.7477	14.7732	0.69696	0.0:0.0:0.8542:0.1457	.	15;63	Q96S90-2;Q96S90	.;LYSM1_HUMAN	K	63;15	ENSP00000357904:Q63K;ENSP00000404059:Q15K	ENSP00000357904:Q63K	Q	-	1	0	LYSMD1	149401194	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.056000	0.93881	1.345000	0.45676	0.467000	0.42956	CAG	.	.	.	none		0.378	LYSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034070.3	NM_212551		T	151134570	G	T	151134570	3	4	231	1	0	0	0	0	1	0	0	0	9131	1386	48	4	504	4	LYSMD1	1	151134570	Missense_Mutation	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	74787641	151134570	98116051	3	14017											
TOR1AIP2	163590	hgsc.bcm.edu	37	chr1	179815212	179815212	+	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	ctctgtgcttagctttagaaAaggcacccctgttcttctat	8	15	7	11	0	3	1	0	0	3	1	3	1	3	1	2	1	2	4	2	1	5	6			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr1:179815212A>C	ENST00000367612.3	-	6	1794	c.1407T>G	c.(1405-1407)ctT>ctG	p.L469L	TOR1AIP2_ENST00000609928.1_Silent_p.L469L	NM_145034.4	NP_659471.1	Q9H496	IFG15_HUMAN	torsin A interacting protein 2	0										cervix(1)|endometrium(3)|large_intestine(1)|lung(10)|ovary(1)|skin(2)	18						AGCTTTAGAAAAGGCACCCCT	0.423																																					p.L469L		Atlas-SNP	.											.	TOR1AIP2	38	.	0			c.T1407G						PASS	.						90	88	89					1																	179815212		2203	4300	6503	SO:0001819	synonymous_variant	163590	exon7			TTAGAAAAGGCAC		CCDS1334.1	1q25.2	2012-02-09			ENSG00000169905	ENSG00000169905			24055	protein-coding gene	gene with protein product		614513				15767459	Standard	NM_145034		Approved	LULL1, NET9, IFRG15	uc001gnk.3	Q8NFQ8	OTTHUMG00000035265	ENST00000367612.3:c.1407T>G	chr1.hg19:g.179815212A>C		118.0	0.0	.		110.0	6.0	.	NM_001199260	Q05BU2	Silent	SNP	ENST00000367612.3	hg19	CCDS1334.1																																																																																			.	.	.	none		0.423	TOR1AIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085304.1	NM_145034		C	179815212	A	C	179815212	2	2	231	1	0	0	0	0	0	0	0	1	16385	1	1	5		5	TOR1AIP2	1	179815212	Silent	SNP	A	TCGA-P4-A5E8-01A-11D-A28G-10	28680642	179815212	69435409	4	14018											
GPR37L1	9283	hgsc.bcm.edu	37	chr1	202097307	202097311	+	Frame_Shift_Del	DEL	CTCAA	CTCAA	-																															acgagcagtgtgagagccagCtcaacagcaccgtggtgggc																								rs76841249	byFrequency	TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	CTCAA	CTCAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr1:202097307_202097311delCTCAA	ENST00000367282.5	+	2	1175_1179	c.1069_1073delCTCAA	c.(1069-1074)ctcaacfs	p.LN357fs		NM_004767.3	NP_004758.3	O60883	ETBR2_HUMAN	G protein-coupled receptor 37 like 1	357					negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	18						TGAGAGCCAGCTCAACAGCACCGTG	0.639																																					p.356_358del		Atlas-Indel,Pindel	.											.	GPR37L1	33	.	0			c.1068_1072del						PASS	.																																			SO:0001589	frameshift_variant	9283	exon2			.	AJ310210	CCDS1420.1	1q32	2012-08-21	2006-02-15		ENSG00000170075	ENSG00000170075		"GPCR / Class A : Orphans"	14923	protein-coding gene	gene with protein product						9539149	Standard	NM_004767		Approved	ETBR-LP-2	uc001gxj.3	O60883	OTTHUMG00000035924	ENST00000367282.5:c.1069_1073delCTCAA	chr1.hg19:g.202097307_202097311delCTCAA	ENSP00000356251:p.Leu357fs	83.0	0.0	0		86.0	37.0	0.430233	NM_004767	B2R7M9|Q5SXP7|Q86VP7	Frame_Shift_Del	DEL	ENST00000367282.5	hg19	CCDS1420.1																																																																																			.	.	.	none		0.639	GPR37L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087496.2	NM_004767		-	202097311	CTCAA	-	202097307	7	5	231	1	0	1	0	1	0	0	0	0	6699	797	28	0	1075	0	GPR37L1	1	202097307	Frame_Shift_Del	DEL	CTCAA	TCGA-P4-A5E8-01A-11D-A28G-10	22282095	202097307	47153314	5	14019											
OR2T4	127074	hgsc.bcm.edu	37	chr1	248525639	248525639	+	Missense_Mutation	SNP	A	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	tttcaagctcctatttactcAtcctcctcaccatccacggg	8	13	4	16	1	3	0	3	0	0	0	7	0	7	0	5	1	2	1	5	1	3	4	rs34079073|rs76878172	byFrequency	TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr1:248525639A>C	ENST00000366475.1	+	1	757	c.757A>C	c.(757-759)Atc>Ctc	p.I253L		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)			CTATTTACTCATCCTCCTCAC	0.522																																					p.I253L		Atlas-SNP	.											OR2T4,brain,glioma,0,1	OR2T4	126	.	0			c.A757C						PASS	.						94	74	81					1																	248525639		2024	3426	5450	SO:0001583	missense	127074	exon1			TTACTCATCCTCC	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.757A>C	chr1.hg19:g.248525639A>C	ENSP00000355431:p.Ile253Leu	668.0	1.0	.		562.0	23.0	.	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	hg19	CCDS31113.1	.	.	.	.	.	.	.	.	.	.	A	13.74	2.326339	0.41197	.	.	ENSG00000196944	ENST00000366475	T	0.00392	7.58	3.09	3.09	0.35607	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000219	T	0.01156	0.0038	H	0.94306	3.52	0.31855	N	0.621781	P	0.50156	0.932	P	0.59948	0.866	T	0.00865	-1.1535	10	0.72032	D	0.01	.	11.1471	0.48436	1.0:0.0:0.0:0.0	.	253	Q8NH00	OR2T4_HUMAN	L	253	ENSP00000355431:I253L	ENSP00000355431:I253L	I	+	1	0	OR2T4	246592262	1.000000	0.71417	0.050000	0.19076	0.010000	0.07245	7.329000	0.79170	1.264000	0.44198	0.477000	0.44152	ATC	.	.	.	alt		0.522	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696		C	248525639	A	C	248525639	3	2	231	1	0	0	0	0	1	0	0	0	11034	217	8	5	759	5	OR2T4	1	248525639	Missense_Mutation	SNP	A	TCGA-P4-A5E8-01A-11D-A28G-10	46428332	248525639	724982	6	14020											
THUMPD2	80745	hgsc.bcm.edu	37	chr2	39964198	39964199	+	Splice_Site	DEL	CT	CT	-																															ggttccgccaacatgaagcaCtctgtgacaaaaaaaaaatg																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr2:39964198_39964199delCT	ENST00000505747.1	-	10	1215_1216	c.1188_1189delAG	c.(1186-1191)agagtg>agtg	p.RV396fs	THUMPD2_ENST00000260619.6_Splice_Site_p.RV366fs	NM_025264.4	NP_079540.2	Q9BTF0	THUM2_HUMAN	THUMP domain containing 2	396							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|skin(1)	17		all_hematologic(82;0.248)				ACATGAAGCACTCTGTGACAAA	0.356																																					p.397_397del		Atlas-Indel,Pindel	.											.	THUMPD2	35	.	0			c.1189_1190del						PASS	.																																			SO:0001630	splice_region_variant	80745	exon10			.	AF380576	CCDS1805.1, CCDS1805.2	2p22.2	2004-06-04	2004-06-04	2004-06-04	ENSG00000138050	ENSG00000138050			14890	protein-coding gene	gene with protein product		611751	"chromosome 2 open reading frame 8"	C2orf8		12063391	Standard	NM_025264		Approved	MGC2454	uc002rru.2	Q9BTF0	OTTHUMG00000102149	ENST00000505747.1:c.1188-1AG>-	chr2.hg19:g.39964200_39964201delCT		94.0	0.0	0		124.0	23.0	0.185484	NM_025264	A8K7I7|Q53TT8|Q53TV0	Frame_Shift_Del	DEL	ENST00000505747.1	hg19	CCDS1805.2																																																																																			.	.	.	none		0.356	THUMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219991.2	NM_025264	Frame_Shift_Del	-	39964199	CT	-	39964198	8	5	231	1	0	1	0	1	0	0	1	0	15895	579	20	0	326	0	THUMPD2	2	39964198	Splice_Site	DEL	CT	TCGA-P4-A5E8-01A-11D-A28G-10		39964198	203235175	7	14021	141	2									
THUMPD2	80745	hgsc.bcm.edu	37	chr2	39964200	39964200	+	Splice_Site	SNP	C	C	G																															ttccgccaacatgaagcactCtgtgacaaaaaaaaaatggt																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr2:39964200C>G	ENST00000505747.1	-	10	1215		c.e10-1		THUMPD2_ENST00000260619.6_Splice_Site	NM_025264.4	NP_079540.2	Q9BTF0	THUM2_HUMAN	THUMP domain containing 2								methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|skin(1)	17		all_hematologic(82;0.248)				ATGAAGCACTCTGTGACAAAA	0.353																																					.		Atlas-SNP	.											.	THUMPD2	35	.	0			c.1188-1G>C						PASS	.						66	62	63					2																	39964200		2203	4300	6503	SO:0001630	splice_region_variant	80745	exon11			AGCACTCTGTGAC	AF380576	CCDS1805.1, CCDS1805.2	2p22.2	2004-06-04	2004-06-04	2004-06-04	ENSG00000138050	ENSG00000138050			14890	protein-coding gene	gene with protein product		611751	"chromosome 2 open reading frame 8"	C2orf8		12063391	Standard	NM_025264		Approved	MGC2454	uc002rru.2	Q9BTF0	OTTHUMG00000102149	ENST00000505747.1:c.1188-1G>C	chr2.hg19:g.39964200C>G		92.0	0.0	.		94.0	8.0	.	NM_025264	A8K7I7|Q53TT8|Q53TV0	Splice_Site	SNP	ENST00000505747.1	hg19	CCDS1805.2	.	.	.	.	.	.	.	.	.	.	C	15.08	2.726690	0.48833	.	.	ENSG00000138050	ENST00000505747;ENST00000260619	.	.	.	5.64	5.64	0.86602	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2156	0.73264	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	THUMPD2	39817704	1.000000	0.71417	1.000000	0.80357	0.548000	0.35241	4.572000	0.60886	2.664000	0.90586	0.655000	0.94253	.	.	.	.	none		0.353	THUMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219991.2	NM_025264	Intron	G	39964200	C	G	39964200	5	3	231	1	0	0	0	0	0	0	1	0	15895	927	32	4	328	4	THUMPD2	2	39964200	Splice_Site	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10	2	39964200	203235173	8	14022	141	2									
TSGA10	80705	hgsc.bcm.edu	37	chr2	99634687	99634687	+	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	ctaatgatcgatctaggcctCggtcaggagatcgatggtga	10	10	13	8	3	2	3	1	2	1	1	5	6	2	3	1	4	0	0	1	4	2	2			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr2:99634687C>T	ENST00000393483.3	-	20	2892	c.2048G>A	c.(2047-2049)cGa>cAa	p.R683Q	TSGA10_ENST00000539964.1_Missense_Mutation_p.R683Q|TSGA10_ENST00000355053.4_Missense_Mutation_p.R683Q|TSGA10_ENST00000410001.1_Missense_Mutation_p.R683Q	NM_025244.2	NP_079520.1	Q9BZW7	TSG10_HUMAN	testis specific, 10	683	Interaction with HIF1A. {ECO:0000250}.				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						ATCTAGGCCTCGGTCAGGAGA	0.383																																					p.R683Q		Atlas-SNP	.											.	TSGA10	81	.	0			c.G2048A						PASS	.						115	109	111					2																	99634687		2203	4300	6503	SO:0001583	missense	80705	exon19			AGGCCTCGGTCAG	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.2048G>A	chr2.hg19:g.99634687C>T	ENSP00000377123:p.Arg683Gln	80.0	0.0	.		87.0	30.0	.	NM_182911	B7Z925|D3DVH7|Q8NEP0|Q9BWX0	Missense_Mutation	SNP	ENST00000393483.3	hg19	CCDS2037.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.604396	0.87157	.	.	ENSG00000135951	ENST00000393483;ENST00000410001;ENST00000355053;ENST00000539964;ENST00000409564;ENST00000393482	T;T;T;T;T;T	0.54071	0.66;0.66;0.66;0.66;0.59;0.72	5.04	4.16	0.48862	.	0.368291	0.23162	N	0.051240	T	0.39384	0.1076	L	0.27053	0.805	0.80722	D	1	B	0.18461	0.028	B	0.10450	0.005	T	0.21827	-1.0234	10	0.39692	T	0.17	-2.5563	12.49	0.55895	0.0:0.9177:0.0:0.0823	.	683	Q9BZW7	TSG10_HUMAN	Q	683;683;683;683;613;683	ENSP00000377123:R683Q;ENSP00000386956:R683Q;ENSP00000347161:R683Q;ENSP00000444419:R683Q;ENSP00000386508:R613Q;ENSP00000377122:R683Q	ENSP00000347161:R683Q	R	-	2	0	TSGA10	99001119	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.166000	0.64965	1.472000	0.48140	0.655000	0.94253	CGA	.	.	.	none		0.383	TSGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253125.1	NM_182911		T	99634687	C	T	99634687	3	4	231	1	0	0	0	0	1	0	0	0	16629	884	31	1	56	1	TSGA10	2	99634687	Missense_Mutation	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10	59670487	99634687	143564686	9	14023											
HOXD10	3236	hgsc.bcm.edu	37	chr2	176981597	176981599	+	In_Frame_Del	DEL	TTT	TTT	-																															agctctcctgctgctaatacTtttttagtagattccttgat																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	TTT	TTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr2:176981597_176981599delTTT	ENST00000249501.4	+	1	291_293	c.36_38delTTT	c.(34-39)actttt>act	p.F13del	HOXD10_ENST00000490088.2_Intron	NM_002148.3	NP_002139.2	P28358	HXD10_HUMAN	homeobox D10	13					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)		CTGCTAATACTTTTTTAGTAGAT	0.453																																					p.12_13del		Atlas-Indel,Pindel	.											.	HOXD10	65	.	0			c.35_37del						PASS	.																																			SO:0001651	inframe_deletion	3236	exon1			.		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.36_38delTTT	chr2.hg19:g.176981600_176981602delTTT	ENSP00000249501:p.Phe13del	80.0	0.0	0		80.0	33.0	0.4125	NM_002148	Q6NT10	In_Frame_Del	DEL	ENST00000249501.4	hg19	CCDS2266.1																																																																																			.	.	.	none		0.453	HOXD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255692.2			-	176981599	TTT	-	176981597	7	5	231	1	0	1	0	1	0	0	0	0	7326	1596	56	0	38	0	HOXD10	2	176981597	In_Frame_Del	DEL	TTT	TCGA-P4-A5E8-01A-11D-A28G-10	77346910	176981597	66217776	10	14024											
GLS	2744	hgsc.bcm.edu	37	chr2	191788697	191788701	+	Frame_Shift_Del	DEL	AAAAG	AAAAG	-																															tttgcaataggatattacttAaaagaaaagaaggtttttaa																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	AAAAG	AAAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr2:191788697_191788701delAAAAG	ENST00000320717.3	+	10	1443_1447	c.1185_1189delAAAAG	c.(1183-1191)ttaaaagaafs	p.KE396fs	GLS_ENST00000338435.4_Frame_Shift_Del_p.KE396fs	NM_014905.4	NP_055720.3	O94925	GLSK_HUMAN	glutaminase	396					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)	GATATTACTTAAAAGAAAAGAAGGT	0.259																																					p.395_396del		Atlas-Indel,Pindel	.											.	GLS	47	.	0			c.1184_1188del						PASS	.																																			SO:0001589	frameshift_variant	2744	exon10			.	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.1185_1189delAAAAG	chr2.hg19:g.191788702_191788706delAAAAG	ENSP00000317379:p.Lys396fs	132.0	0.0	0		120.0	34.0	0.283333	NM_001256310	Q9UL05|Q9UL06|Q9UL07|Q9UN40	Frame_Shift_Del	DEL	ENST00000320717.3	hg19	CCDS2308.1																																																																																			.	.	.	none		0.259	GLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255999.2			-	191788701	AAAAG	-	191788697	7	5	231	1	0	1	0	1	0	0	0	0	6470	359	13	0	1223	0	GLS	2	191788697	Frame_Shift_Del	DEL	AAAAG	TCGA-P4-A5E8-01A-11D-A28G-10	14807100	191788697	51410676	11	14025											
TMEM184C	55751	hgsc.bcm.edu	37	chr4	148545023	148545023	+	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	gcttggtttattgctggaatCtttttgctgttgactattcc	5	20	9	7	0	1	1	0	1	1	0	2	2	2	2	1	2	2	5	1	2	3	9			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr4:148545023C>G	ENST00000296582.3	+	2	736	c.162C>G	c.(160-162)atC>atG	p.I54M	TMEM184C_ENST00000508208.1_Missense_Mutation_p.I54M	NM_018241.2	NP_060711.2	Q9NVA4	T184C_HUMAN	transmembrane protein 184C	54						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(2)|prostate(1)	16						TTGCTGGAATCTTTTTGCTGT	0.333																																					p.I54M		Atlas-SNP	.											.	TMEM184C	25	.	0			c.C162G						PASS	.						137	135	135					4																	148545023		2202	4299	6501	SO:0001583	missense	55751	exon2			TGGAATCTTTTTG	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.162C>G	chr4.hg19:g.148545023C>G	ENSP00000296582:p.Ile54Met	114.0	0.0	.		65.0	37.0	.	NM_018241	D3DP04|Q86X84|Q969I7|Q9NXM2	Missense_Mutation	SNP	ENST00000296582.3	hg19	CCDS3770.1	.	.	.	.	.	.	.	.	.	.	C	13.08	2.130269	0.37630	.	.	ENSG00000164168	ENST00000296582;ENST00000508208	T;T	0.45668	0.89;0.89	5.28	3.47	0.39725	.	0.000000	0.85682	D	0.000000	T	0.45994	0.1370	L	0.60904	1.88	0.50171	D	0.999858	P	0.42456	0.78	P	0.45138	0.471	T	0.45425	-0.9262	10	0.54805	T	0.06	-23.423	13.982	0.64310	0.54:0.46:0.0:0.0	.	54	Q9NVA4	T184C_HUMAN	M	54	ENSP00000296582:I54M;ENSP00000425940:I54M	ENSP00000296582:I54M	I	+	3	3	TMEM184C	148764473	0.945000	0.32115	1.000000	0.80357	0.993000	0.82548	0.073000	0.14640	0.644000	0.30656	0.455000	0.32223	ATC	.	.	.	none		0.333	TMEM184C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364644.1	NM_018241		G	148545023	C	G	148545023	3	3	231	1	0	0	0	0	1	0	0	0	16118	903	32	4	168	4	TMEM184C	4	148545023	Missense_Mutation	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10		148545023	42609253	12	14026											
FAT1	2195	hgsc.bcm.edu	37	chr4	187629210	187629211	+	Frame_Shift_Del	DEL	AC	AC	-																															catctgcatcaatagcagaaAcagtggttatttgctctccc																								rs572691033	byFrequency	TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr4:187629210_187629211delAC	ENST00000441802.2	-	2	1980_1981	c.1771_1772delGT	c.(1771-1773)gttfs	p.V591fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	591	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						AATAGCAGAAACAGTGGTTATT	0.396										HNSCC(5;0.00058)																											p.591_591del	Colon(197;1040 2055 4143 4984 49344)	Atlas-Indel,Pindel	.											.	FAT1	500	.	0			c.1772_1773del						PASS	.																																			SO:0001589	frameshift_variant	2195	exon2			.	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"Cadherins / Cadherin-related"	3595	protein-coding gene	gene with protein product	"cadherin-related family member 8"	600976	"FAT tumor suppressor (Drosophila) homolog", "FAT tumor suppressor homolog 1 (Drosophila)"	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.1771_1772delGT	chr4.hg19:g.187629210_187629211delAC	ENSP00000406229:p.Val591fs	84.0	0.0	0		53.0	25.0	0.471698	NM_005245		Frame_Shift_Del	DEL	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.	.	none		0.396	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		-	187629211	AC	-	187629210	7	5	231	1	0	1	0	1	0	0	0	0	5696	43	2	0	12098	0	FAT1	4	187629210	Frame_Shift_Del	DEL	AC	TCGA-P4-A5E8-01A-11D-A28G-10	39084187	187629210	3525066	13	14027											
NIPBL	25836	hgsc.bcm.edu	37	chr5	36986201	36986204	+	Frame_Shift_Del	DEL	AAAG	AAAG	-																															ggcaatgttactcaggagacAaagaaaatggaaatgaaagg																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	AAAG	AAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr5:36986201_36986204delAAAG	ENST00000282516.8	+	10	3418_3421	c.2919_2922delAAAG	c.(2917-2922)acaaagfs	p.TK973fs	NIPBL_ENST00000448238.2_Frame_Shift_Del_p.TK973fs|NIPBL_ENST00000504430.1_3'UTR	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	973					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)			CTCAGGAGACAAAGAAAATGGAAA	0.373																																					p.973_974del		Atlas-Indel,Pindel	.											.	NIPBL	513	.	0			c.2918_2921del	GRCh37	CD063575	NIPBL	D		PASS	.																																			SO:0001589	frameshift_variant	25836	exon10			.	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.2919_2922delAAAG	chr5.hg19:g.36986201_36986204delAAAG	ENSP00000282516:p.Thr973fs	92.0	0.0	0		80.0	17.0	0.2125	NM_133433	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Frame_Shift_Del	DEL	ENST00000282516.8	hg19	CCDS3920.1																																																																																			.	.	.	none		0.373	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		-	36986204	AAAG	-	36986201	7	5	231	1	0	1	0	1	0	0	0	0	10435	117	5	0	2953	0	NIPBL	5	36986201	Frame_Shift_Del	DEL	AAAG	TCGA-P4-A5E8-01A-11D-A28G-10		36986201	143929059	14	14028											
C5orf35	133383	hgsc.bcm.edu	37	chr5	56210690	56210691	+	Frame_Shift_Del	DEL	AG	AG	-																															tgatgtgcttgttcctagacAgagcagctaatgtctgttat																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr5:56210690_56210691delAG	ENST00000285947.2	+	5	1095_1096	c.709_710delAG	c.(709-711)agafs	p.R237fs	SETD9_ENST00000475908.1_3'UTR|SETD9_ENST00000541720.1_Frame_Shift_Del_p.R237fs	NM_153706.3	NP_714917.2	Q8NE22	SETD9_HUMAN	SET domain containing 9	237	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.						methyltransferase activity (GO:0008168)										GTTCCTAGACAGAGCAGCTAAT	0.356																																					p.236_237del		Atlas-INDEL	.											.	.	.	.	0			c.708_709del						PASS	.																																			SO:0001589	frameshift_variant	133383	exon5			.	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.709_710delAG	chr5.hg19:g.56210692_56210693delAG	ENSP00000285947:p.Arg237fs	86.0	0.0	0		96.0	11.0	0.114583	NM_001171990	F5H713	Frame_Shift_Del	DEL	ENST00000285947.2	hg19	CCDS3972.1																																																																																			.	.	.	none		0.356	SETD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132304.2	NM_153706		-	56210691	AG	-	56210690	7	5	231	1	0	1	0	1	0	0	0	0	2296	180	7	0	727	0	C5orf35	5	56210690	Frame_Shift_Del	DEL	AG	TCGA-P4-A5E8-01A-11D-A28G-10	19224489	56210690	124704570	15	14029											
MAST4	375449	hgsc.bcm.edu	37	chr5	66456396	66456396	+	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	ggtgaggcggagcaagaaatCcaagaagaaagaaagtctcg	17	4	14	6	2	1	5	0	1	1	4	3	6	2	6	1	3	1	1	1	3	6	0			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr5:66456396C>A	ENST00000403625.2	+	27	4056	c.3761C>A	c.(3760-3762)tCc>tAc	p.S1254Y	MAST4_ENST00000261569.7_Missense_Mutation_p.S1060Y|MAST4_ENST00000405643.1_Missense_Mutation_p.S1075Y|MAST4_ENST00000403666.1_Missense_Mutation_p.S1065Y|MAST4_ENST00000404260.3_Missense_Mutation_p.S1257Y	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	1257						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)		AGCAAGAAATCCAAGAAGAAA	0.393																																					p.S1254Y		Atlas-SNP	.											.	MAST4	218	.	0			c.C3761A						PASS	.						104	106	106					5																	66456396		1862	4094	5956	SO:0001583	missense	375449	exon27			AGAAATCCAAGAA	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.3761C>A	chr5.hg19:g.66456396C>A	ENSP00000385727:p.Ser1254Tyr	89.0	0.0	.		76.0	25.0	.	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	hg19	CCDS54861.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.031570	0.75504	.	.	ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569;ENST00000432399	T;T;T;T;T	0.68331	-0.28;-0.28;-0.32;-0.32;-0.28	5.81	4.93	0.64822	.	0.234815	0.43260	D	0.000587	T	0.79106	0.4390	M	0.73217	2.22	0.34416	D	0.696926	D;D	0.69078	0.99;0.997	P;D	0.65443	0.862;0.935	D	0.85389	0.1124	10	0.72032	D	0.01	-19.186	14.3064	0.66386	0.0:0.9294:0.0:0.0706	.	1257;1065	O15021;O15021-3	MAST4_HUMAN;.	Y	1257;1254;1065;1075;1075;1060;993	ENSP00000385048:S1257Y;ENSP00000385727:S1254Y;ENSP00000384313:S1065Y;ENSP00000384099:S1075Y;ENSP00000261569:S1060Y	ENSP00000261569:S1060Y	S	+	2	0	MAST4	66492152	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	3.264000	0.51553	2.736000	0.93811	0.655000	0.94253	TCC	.	.	.	none		0.393	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			A	66456396	C	A	66456396	3	1	231	1	0	0	0	0	1	0	0	0	9334	855	30	4	3997	4	MAST4	5	66456396	Missense_Mutation	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10	10245706	66456396	114458864	16	14030											
EPB41L4A	64097	hgsc.bcm.edu	37	chr5	111506049	111506049	+	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	gttcttcggacaatccggatGgatccacaagttcttttctg	8	14	9	10	2	3	0	0	0	3	0	6	3	5	3	2	3	0	2	2	3	2	5			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr5:111506049G>A	ENST00000261486.5	-	20	1964	c.1688C>T	c.(1687-1689)cCa>cTa	p.P563L	EPB41L4A_ENST00000507810.1_5'UTR	NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	563						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)		CAATCCGGATGGATCCACAAG	0.378																																					p.P563L		Atlas-SNP	.											.	EPB41L4A	130	.	0			c.C1688T						PASS	.						118	111	113					5																	111506049		1832	4086	5918	SO:0001583	missense	64097	exon20			CCGGATGGATCCA	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.1688C>T	chr5.hg19:g.111506049G>A	ENSP00000261486:p.Pro563Leu	71.0	0.0	.		68.0	22.0	.	NM_022140	A4FUI6	Missense_Mutation	SNP	ENST00000261486.5	hg19	CCDS43350.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.543095	0.86022	.	.	ENSG00000129595	ENST00000261486	D	0.84070	-1.8	5.21	5.21	0.72293	.	0.131978	0.51477	D	0.000100	D	0.86703	0.5996	L	0.32530	0.975	0.58432	D	0.999998	D;D	0.89917	0.986;1.0	P;D	0.87578	0.655;0.998	D	0.85851	0.1404	10	0.36615	T	0.2	.	17.5611	0.87908	0.0:0.0:1.0:0.0	.	563;190	Q9HCS5;Q8N8X1	E41LA_HUMAN;.	L	563	ENSP00000261486:P563L	ENSP00000261486:P563L	P	-	2	0	EPB41L4A	111533948	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	7.409000	0.80053	2.415000	0.81967	0.563000	0.77884	CCA	.	.	.	none		0.378	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1			A	111506049	G	A	111506049	3	1	231	1	0	0	0	0	1	0	0	0	5157	1348	47	2	388	2	EPB41L4A	5	111506049	Missense_Mutation	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	45049653	111506049	69409211	17	14031											
DMXL1	1657	hgsc.bcm.edu	37	chr5	118556763	118556765	+	In_Frame_Del	DEL	GAG	GAG	-																															tggtagtacacagactggcaGaggagcatctgtggtatgta																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr5:118556763_118556765delGAG	ENST00000311085.8	+	36	8281_8283	c.8201_8203delGAG	c.(8200-8205)agagga>aga	p.G2735del	DMXL1_ENST00000505312.1_3'UTR|DMXL1_ENST00000539542.1_In_Frame_Del_p.G2756del	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	2735										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)		CAGACTGGCAGAGGAGCATCTGT	0.35																																					p.2734_2734del		Atlas-Indel,Pindel	.											.	DMXL1	268	.	0			c.8200_8202del						PASS	.																																			SO:0001651	inframe_deletion	1657	exon36			.	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.8201_8203delGAG	chr5.hg19:g.118556766_118556768delGAG	ENSP00000309690:p.Gly2735del	385.0	0.0	0		313.0	96.0	0.306709	NM_005509		In_Frame_Del	DEL	ENST00000311085.8	hg19	CCDS4125.1																																																																																			.	.	.	none		0.35	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		-	118556765	GAG	-	118556763	7	5	231	1	0	1	0	1	0	0	0	0	4596	942	33	0	8343	0	DMXL1	5	118556763	In_Frame_Del	DEL	GAG	TCGA-P4-A5E8-01A-11D-A28G-10	7050714	118556763	62358497	18	14032											
TRIM39	56658	hgsc.bcm.edu	37	chr6	30303731	30303752	+	Splice_Site	DEL	GTCAGGCTTCGAGATGCTTAAG	GTCAGGCTTCGAGATGCTTAAG	-																															gtggagggcaagtgcttacaGtcaggcttcgagatgcttaa																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	GTCAGGCTTCGAGATGCTTAAG	GTCAGGCTTCGAGATGCTTAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr6:30303731_30303752delGTCAGGCTTCGAGATGCTTAAG	ENST00000396547.1	+	4	919_940	c.759_780delGTCAGGCTTCGAGATGCTTAAG	c.(757-780)cagtcaggcttcgagatgcttaag>ca	p.QSGFEMLK253fs	TRIM39_ENST00000396551.3_Splice_Site_p.QSGFEMLK253fs|TRIM39_ENST00000376656.4_Splice_Site_p.QSGFEMLK253fs|TRIM39-RPP21_ENST00000513556.1_Splice_Site_p.QSGFEMLK165fs|TRIM39_ENST00000540416.1_Splice_Site_p.QSGFEMLK253fs|TRIM39_ENST00000376659.5_Splice_Site_p.QSGFEMLK253fs|TRIM39_ENST00000396548.1_Splice_Site_p.QSGFEMLK253fs			Q9HCM9	TRI39_HUMAN	tripartite motif containing 39	253					apoptotic process (GO:0006915)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|positive regulation of apoptotic signaling pathway (GO:2001235)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.K260Q(1)		ovary(3)	3						AGTGCTTACAGTCAGGCTTCGAGATGCTTAAGGTTCGACCTT	0.577																																					p.253_260del		Pindel	.											.	TRIM39	56	.	1	Substitution - Missense(1)	lung(1)	c.758_779del						PASS	.																																			SO:0001630	splice_region_variant	56658	exon5			.	BC034985	CCDS34377.1, CCDS34378.1	6p22.1	2013-01-09	2011-01-25	2002-06-07	ENSG00000204599	ENSG00000204599		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10065	protein-coding gene	gene with protein product		605700	"ring finger protein 23", "tripartite motif-containing 39"	RNF23		11006080	Standard	NM_021253		Approved			Q9HCM9	OTTHUMG00000031066	ENST00000396547.1:c.780+1GTCAGGCTTCGAGATGCTTAAG>-	chr6.hg19:g.30303731_30303752delGTCAGGCTTCGAGATGCTTAAG		91.0	0.0	.		40.0	13.0	0.325	NM_172016	Q5STG3|Q5STG4|Q76BL3|Q8IYT9|Q96IB6	Frame_Shift_Del	DEL	ENST00000396547.1	hg19	CCDS34377.1																																																																																			.	.	.	none		0.577	TRIM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076086.2	NM_172016	Frame_Shift_Del	-	30303752	GTCAGGCTTCGAGATGCTTAAG	-	30303731	8	5	231	1	0	1	0	1	0	0	1	0	16525	1020	36	0	769	0	TRIM39	6	30303731	Splice_Site	DEL	GTCAGGCTTCGAGATGCTTAAG	TCGA-P4-A5E8-01A-11D-A28G-10		30303731	140811336	19	14033											
NMBR	4829	hgsc.bcm.edu	37	chr6	142396953	142396953	+	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	ccacagcagagttggctgttGaaatgcctcctgaagctttc	9	11	10	11	0	0	3	0	2	0	1	2	3	1	3	3	1	3	5	3	1	2	3			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr6:142396953G>A	ENST00000258042.1	-	3	1145	c.1005C>T	c.(1003-1005)ttC>ttT	p.F335F	NMBR_ENST00000480652.1_5'UTR	NM_002511.2	NP_002502.2	P28336	NMBR_HUMAN	neuromedin B receptor	335					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)		GTTGGCTGTTGAAATGCCTCC	0.473																																					p.F335F		Atlas-SNP	.											.	NMBR	62	.	0			c.C1005T						PASS	.						109	104	106					6																	142396953		2203	4300	6503	SO:0001819	synonymous_variant	4829	exon3			GCTGTTGAAATGC		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.1005C>T	chr6.hg19:g.142396953G>A		149.0	0.0	.		138.0	8.0	.	NM_002511	E9KL38|Q5VUK8	Silent	SNP	ENST00000258042.1	hg19	CCDS5196.1																																																																																			.	.	.	none		0.473	NMBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042479.1			A	142396953	G	A	142396953	2	1	231	1	0	0	0	0	0	0	0	1	10494	1281	45	2		2	NMBR	6	142396953	Silent	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	112093222	142396953	28718114	20	14034											
MEOX2	4223	hgsc.bcm.edu	37	chr7	15725800	15725800	+	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	tgctgctgatggtggtgatgGtggtggtggtggtggtggtg	2	14	23	2	0	0	2	0	2	0	0	0	2	0	2	0	9	2	2	0	9	0	0	rs113582077	byFrequency	TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr7:15725800G>A	ENST00000262041.5	-	1	637	c.228C>T	c.(226-228)caC>caT	p.H76H	AC005550.4_ENST00000442176.1_lincRNA|AC005550.5_ENST00000438923.1_lincRNA	NM_005924.4	NP_005915.2	P50222	MEOX2_HUMAN	mesenchyme homeobox 2	76	Poly-His.				angiogenesis (GO:0001525)|blood circulation (GO:0008015)|limb development (GO:0060173)|multicellular organismal development (GO:0007275)|neuron death (GO:0070997)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle tissue development (GO:0007519)|somite specification (GO:0001757)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding (GO:0043565)	p.H80delH(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (126;0.0822)		ggtggtgatggtggtggtggt	0.612																																					p.H76H	Esophageal Squamous(140;197 1769 16409 18257 29929)	Atlas-SNP	.											.	MEOX2	68	.	1	Deletion - In frame(1)	stomach(1)	c.C228T						PASS	.						11	13	13					7																	15725800		2192	4293	6485	SO:0001819	synonymous_variant	4223	exon1			GTGATGGTGGTGG		CCDS34605.1	7p22.1-p21.3	2014-07-15	2005-12-22		ENSG00000106511	ENSG00000106511		"Homeoboxes / ANTP class : HOXL subclass"	7014	protein-coding gene	gene with protein product	"growth arrest-specific homeobox"	600535	"mesenchyme homeo box 2 (growth arrest-specific homeo box)", "mesenchyme homeobox 2 (growth arrest-specific homeo box)"	GAX		7713505	Standard	NM_005924		Approved	MOX2	uc003stc.3	P50222	OTTHUMG00000152390	ENST00000262041.5:c.228C>T	chr7.hg19:g.15725800G>A		30.0	0.0	.		32.0	7.0	.	NM_005924	B2R8I7|O75263|Q9UPL6	Silent	SNP	ENST00000262041.5	hg19	CCDS34605.1																																																																																			.	.	.	none		0.612	MEOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326058.2	NM_005924		A	15725800	G	A	15725800	2	1	231	1	0	0	0	0	0	0	0	1	9481	1252	44	2		2	MEOX2	7	15725800	Silent	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10		15725800	143412863	21	14035											
HOXA7	3204	hgsc.bcm.edu	37	chr7	27194707	27194707	+	Missense_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	gaaccagatcttaatctggcGctcggtgaggcagagcgcgt	9	8	14	10	4	2	3	0	1	2	2	3	4	2	3	1	3	2	2	1	3	2	1			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr7:27194707G>A	ENST00000242159.3	-	2	647	c.514C>T	c.(514-516)Cgc>Tgc	p.R172C	RP1-170O19.23_ENST00000498652.1_RNA|HOXA-AS3_ENST00000521197.1_RNA|RP1-170O19.22_ENST00000467897.2_RNA|HOXA-AS3_ENST00000518947.2_RNA|HOXA-AS3_ENST00000524304.1_RNA|HOXA-AS3_ENST00000521231.1_RNA|HOXA7_ENST00000523796.2_5'UTR|HOXA-AS3_ENST00000518848.1_RNA	NM_006896.3	NP_008827.2	P31268	HXA7_HUMAN	homeobox A7	172					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						TTAATCTGGCGCTCGGTGAGG	0.632																																					p.R172C		Atlas-SNP	.											.	HOXA7	34	.	0			c.C514T						PASS	.						87	99	95					7																	27194707		2203	4300	6503	SO:0001583	missense	3204	exon2			TCTGGCGCTCGGT		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.514C>T	chr7.hg19:g.27194707G>A	ENSP00000242159:p.Arg172Cys	111.0	0.0	.		119.0	32.0	.	NM_006896	A4D191|O43368|O43486|O95655|Q9NSC8|Q9UDM1	Missense_Mutation	SNP	ENST00000242159.3	hg19	CCDS5408.1	.	.	.	.	.	.	.	.	.	.	G	17.28	3.349382	0.61183	.	.	ENSG00000122592	ENST00000242159	D	0.96774	-4.12	4.96	3.98	0.46160	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.98365	0.9457	M	0.93854	3.465	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98696	1.0698	10	0.87932	D	0	.	12.334	0.55056	0.0:0.0:0.6713:0.3287	.	172	P31268	HXA7_HUMAN	C	172	ENSP00000242159:R172C	ENSP00000242159:R172C	R	-	1	0	HOXA7	27161232	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.882000	0.39648	2.324000	0.78689	0.456000	0.33151	CGC	.	.	.	none		0.632	HOXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358695.1			A	27194707	G	A	27194707	3	1	231	1	0	0	0	0	1	0	0	0	7304	1087	38	1	182	1	HOXA7	7	27194707	Missense_Mutation	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	11468907	27194707	131943956	22	14036											
SAMD9	54809	hgsc.bcm.edu	37	chr7	92731495	92731495	+	Frame_Shift_Del	DEL	T	T	-																															ttcttctaagagacaaaataTatctacatatttcttaaaat																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr7:92731495delT	ENST00000379958.2	-	3	4185	c.3916delA	c.(3916-3918)atafs	p.I1306fs		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	1306						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)			AGACAAAATATATCTACATAT	0.373																																					p.I1306fs		Atlas-Indel,Pindel	.											.	SAMD9	239	.	0			c.3917delT						PASS	.						73	81	78					7																	92731495		2197	4295	6492	SO:0001589	frameshift_variant	54809	exon2			.	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.3916delA	chr7.hg19:g.92731495delT	ENSP00000369292:p.Ile1306fs	28.0	0.0	0		32.0	12.0	0.375	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Frame_Shift_Del	DEL	ENST00000379958.2	hg19	CCDS34680.1																																																																																			.	.	.	none		0.373	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		-	92731495	T	-	92731495	7	5	231	1	0	1	0	1	0	0	0	0	13839	1406	49	0	857	0	SAMD9	7	92731495	Frame_Shift_Del	DEL	T	TCGA-P4-A5E8-01A-11D-A28G-10	65536788	92731495	66407168	23	14037											
PILRA	29992	hgsc.bcm.edu	37	chr7	99972037	99972037	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcagtccatcgaggggacCaaactctccatcacccaggg	10	6	11	14	1	2	0	1	0	1	0	5	2	3	1	4	4	1	1	4	4	1	0			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr7:99972037C>T	ENST00000198536.2	+	2	647	c.435C>T	c.(433-435)acC>acT	p.T145T	PILRA_ENST00000350573.2_Silent_p.T145T|PILRA_ENST00000453419.1_Silent_p.T145T|PILRA_ENST00000394000.2_Silent_p.T145T|PILRA_ENST00000474013.1_3'UTR	NM_013439.2	NP_038467.2	Q9UKJ1	PILRA_HUMAN	paired immunoglobin-like type 2 receptor alpha	145	Ig-like V-type.				signal transduction (GO:0007165)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	15	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TCGAGGGGACCAAACTCTCCA	0.592																																					p.T145T		Atlas-SNP	.											.	PILRA	28	.	0			c.C435T						PASS	.						76	73	74					7																	99972037		2203	4300	6503	SO:0001819	synonymous_variant	29992	exon2			GGGGACCAAACTC	AF161080	CCDS5691.1, CCDS5692.1, CCDS47660.1	7q22.1	2013-01-11			ENSG00000085514	ENSG00000085514		"Immunoglobulin superfamily / V-set domain containing"	20396	protein-coding gene	gene with protein product		605341				10660620	Standard	NM_178272		Approved	FDF03	uc003uuo.1	Q9UKJ1	OTTHUMG00000155248	ENST00000198536.2:c.435C>T	chr7.hg19:g.99972037C>T		85.0	0.0	.		79.0	21.0	.	NM_013439	Q8NHI1	Silent	SNP	ENST00000198536.2	hg19	CCDS5691.1																																																																																			.	.	.	none		0.592	PILRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339016.1	NM_013439		T	99972037	C	T	99972037	2	4	231	1	0	0	0	0	0	0	0	1	11932	581	21	2		2	PILRA	7	99972037	Silent	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10	7240542	99972037	59166626	24	14038											
KIF13B	23303	hgsc.bcm.edu	37	chr8	28984749	28984749	+	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	taaagtcccagattcctgcaCtgacttcacttcgacttgaa	11	12	6	12	1	1	3	1	2	0	1	4	4	3	3	2	0	1	1	2	0	3	5			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr8:28984749C>G	ENST00000524189.1	-	25	3150	c.3112G>C	c.(3112-3114)Gtg>Ctg	p.V1038L	CTD-2647L4.1_ENST00000523661.1_RNA	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	1038					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)		GATTCCTGCACTGACTTCACT	0.443																																					p.V1038L		Atlas-SNP	.											.	KIF13B	192	.	0			c.G3112C						PASS	.						149	147	148					8																	28984749		1920	4132	6052	SO:0001583	missense	23303	exon25			CCTGCACTGACTT	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.3112G>C	chr8.hg19:g.28984749C>G	ENSP00000427900:p.Val1038Leu	121.0	0.0	.		132.0	9.0	.	NM_015254	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Missense_Mutation	SNP	ENST00000524189.1	hg19	CCDS55217.1	.	.	.	.	.	.	.	.	.	.	C	19.36	3.812352	0.70912	.	.	ENSG00000197892	ENST00000524189	T	0.77620	-1.11	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.77665	0.4164	M	0.66939	2.045	0.80722	D	1	B	0.32620	0.378	B	0.38378	0.272	T	0.78155	-0.2314	10	0.54805	T	0.06	.	12.1601	0.54099	0.0:0.9224:0.0:0.0776	.	1038	F8VPJ2	.	L	1038	ENSP00000427900:V1038L	ENSP00000427900:V1038L	V	-	1	0	KIF13B	29040668	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.510000	0.60455	2.649000	0.89929	0.655000	0.94253	GTG	.	.	.	none		0.443	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1			G	28984749	C	G	28984749	3	3	231	1	0	0	0	0	1	0	0	0	8282	565	20	4	2432	4	KIF13B	8	28984749	Missense_Mutation	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10		28984749	117379273	25	14039											
DCAF13	25879	hgsc.bcm.edu	37	chr8	104432551	104432551	+	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	tcccacgagaatatataagaGctttaaatgctaccaaactg	16	10	6	9	1	0	2	0	0	0	2	1	3	1	2	2	0	4	2	2	0	8	6			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr8:104432551G>T	ENST00000297579.5	+	2	863	c.586G>T	c.(586-588)Gct>Tct	p.A196S	DCAF13_ENST00000521999.1_Intron|DCAF13_ENST00000519682.1_Missense_Mutation_p.A40S|DCAF13_ENST00000521971.1_Missense_Mutation_p.A40S|DCAF13_ENST00000521716.1_Missense_Mutation_p.A40S	NM_015420.6	NP_056235.4	Q9NV06	DCA13_HUMAN	DDB1 and CUL4 associated factor 13	44					protein ubiquitination (GO:0016567)|rRNA processing (GO:0006364)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						ATATATAAGAGCTTTAAATGC	0.388																																					p.A196S		Atlas-SNP	.											.	DCAF13	66	.	0			c.G586T						PASS	.						102	96	98					8																	104432551		2203	4300	6503	SO:0001583	missense	25879	exon2			ATAAGAGCTTTAA	AK074725	CCDS34934.1	8q22.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000164934	ENSG00000164934		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	24535	protein-coding gene	gene with protein product			"WD repeats and SOF1 domain containing"	WDSOF1		11042152	Standard	NM_015420		Approved	DKFZP564O0463, Gm83, HSPC064	uc003yln.3	Q9NV06	OTTHUMG00000164888	ENST00000297579.5:c.586G>T	chr8.hg19:g.104432551G>T	ENSP00000297579:p.Ala196Ser	165.0	0.0	.		135.0	48.0	.	NM_015420	Q3MII9|Q8NCH8|Q8TC51|Q96JY7|Q9NZX3	Missense_Mutation	SNP	ENST00000297579.5	hg19	CCDS34934.1	.	.	.	.	.	.	.	.	.	.	G	33	5.265050	0.95399	.	.	ENSG00000164934	ENST00000297579;ENST00000521716;ENST00000521971;ENST00000388778;ENST00000519682	T;T;T;T	0.01313	5.02;5.02;5.02;5.02	5.2	5.2	0.72013	.	0.050275	0.85682	N	0.000000	T	0.16128	0.0388	H	0.96489	3.83	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.13818	-1.0495	10	0.87932	D	0	-21.6277	18.7279	0.91722	0.0:0.0:1.0:0.0	.	44	B3KME9	.	S	196;40;40;44;40	ENSP00000297579:A196S;ENSP00000430645:A40S;ENSP00000430883:A40S;ENSP00000430411:A40S	ENSP00000297579:A196S	A	+	1	0	DCAF13	104501727	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.260000	0.95568	2.420000	0.82092	0.655000	0.94253	GCT	.	.	.	none		0.388	DCAF13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380797.2	NM_015420		T	104432551	G	T	104432551	3	4	231	1	0	0	0	0	1	0	0	0	4268	971	34	4	592	4	DCAF13	8	104432551	Missense_Mutation	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	75447802	104432551	41931471	26	14040											
C9orf93	203238	hgsc.bcm.edu	37	chr9	15745613	15745613	+	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	tctatggctgaattacaagaCgtcattggtaaagcaggtat	13	12	10	6	1	2	2	1	1	1	1	2	2	2	2	0	3	2	4	0	3	7	5			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr9:15745613C>T	ENST00000380701.3	+	18	2983	c.2655C>T	c.(2653-2655)gaC>gaT	p.D885D	CCDC171_ENST00000297641.3_Silent_p.D885D	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	885								p.D152D(1)|p.D885D(1)									AATTACAAGACGTCATTGGTA	0.363																																					p.D885D		Atlas-SNP	.											C9orf93_ENST00000380689,colon,carcinoma,0,4	.	.	.	2	Substitution - coding silent(2)	lung(2)	c.C2655T						PASS	.						222	221	221					9																	15745613		2203	4300	6503	SO:0001819	synonymous_variant	203238	exon18			ACAAGACGTCATT	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.2655C>T	chr9.hg19:g.15745613C>T		43.0	0.0	.		44.0	16.0	.	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Silent	SNP	ENST00000380701.3	hg19	CCDS6481.1	.	.	.	.	.	.	.	.	.	.	C	0.248	-1.008817	0.02112	.	.	ENSG00000164989	ENST00000449575	.	.	.	5.03	-4.4	0.03600	.	.	.	.	.	T	0.40297	0.1111	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37641	-0.9697	4	.	.	.	-0.9084	3.9218	0.09247	0.3234:0.4014:0.0625:0.2128	.	.	.	.	M	125	.	.	T	+	2	0	C9orf93	15735613	0.998000	0.40836	0.941000	0.38009	0.154000	0.21943	0.535000	0.23114	-0.699000	0.05077	-1.604000	0.00809	ACG	.	.	.	none		0.363	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550		T	15745613	C	T	15745613	2	4	231	1	0	0	0	0	0	0	0	1	2508	535	19	1		1	C9orf93	9	15745613	Silent	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10		15745613	125467818	27	14041											
ITIH5	80760	hgsc.bcm.edu	37	chr10	7621949	7621949	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agacgatgagggacacgctcCggtctccaatgccactgtgg	9	7	13	12	3	1	2	0	1	1	1	3	4	2	3	3	3	1	1	3	3	1	0	rs368004189		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr10:7621949C>T	ENST00000256861.6	-	9	1265	c.1187G>A	c.(1186-1188)cGg>cAg	p.R396Q	ITIH5_ENST00000397145.2_Missense_Mutation_p.R396Q|ITIH5_ENST00000397146.2_Missense_Mutation_p.R396Q|ITIH5_ENST00000446830.2_Missense_Mutation_p.R178Q|ITIH5_ENST00000434980.1_5'UTR|ITIH5_ENST00000298441.6_Missense_Mutation_p.R182Q	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	396	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						GGACACGCTCCGGTCTCCAAT	0.632																																					p.R396Q		Atlas-SNP	.											.	ITIH5	343	.	0			c.G1187A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	79	69	72		1187,1187,545	4.4	1	10		72	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	ITIH5	NM_001001851.2,NM_030569.6,NM_032817.5	43,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	396/703,396/943,182/729	7621949	1,13005	2203	4300	6503	SO:0001583	missense	80760	exon9			ACGCTCCGGTCTC			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.1187G>A	chr10.hg19:g.7621949C>T	ENSP00000256861:p.Arg396Gln	75.0	0.0	.		60.0	33.0	.	NM_001001851	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Missense_Mutation	SNP	ENST00000256861.6	hg19		.	.	.	.	.	.	.	.	.	.	C	14.84	2.656967	0.47467	0.0	1.16E-4	ENSG00000123243	ENST00000256861;ENST00000397146;ENST00000298441;ENST00000446830;ENST00000397145	T;T;T;T;T	0.77750	-1.12;-1.12;-1.12;-1.12;-1.12	5.33	4.41	0.53225	von Willebrand factor, type A (3);	0.152288	0.64402	D	0.000015	D	0.83792	0.5331	.	.	.	0.31433	N	0.672876	P;D;D	0.69078	0.948;0.997;0.997	P;P;P	0.60886	0.745;0.88;0.809	D	0.84790	0.0778	9	0.72032	D	0.01	-30.2968	10.6617	0.45706	0.0:0.8514:0.0:0.1486	.	396;396;182	G5E9D8;Q86UX2;Q86UX2-3	.;ITIH5_HUMAN;.	Q	396;396;182;178;396	ENSP00000256861:R396Q;ENSP00000380333:R396Q;ENSP00000298441:R182Q;ENSP00000387969:R178Q;ENSP00000380332:R396Q	ENSP00000256861:R396Q	R	-	2	0	ITIH5	7661955	1.000000	0.71417	0.994000	0.49952	0.106000	0.19336	2.775000	0.47702	2.491000	0.84063	0.561000	0.74099	CGG	.	.	.	none		0.632	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569		T	7621949	C	T	7621949	3	4	231	1	0	0	0	0	1	0	0	0	7914	652	23	1	1788	1	ITIH5	10	7621949	Missense_Mutation	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10		7621949	127912798	28	14042											
KIAA1217	56243	hgsc.bcm.edu	37	chr10	24832228	24832229	+	Frame_Shift_Del	DEL	AG	AG	-																															gatcaagaggttatcacgacAgattttggccaagttgttct																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr10:24832228_24832229delAG	ENST00000376454.3	+	19	4059_4060	c.4029_4030delAG	c.(4027-4032)acagatfs	p.D1344fs	KIAA1217_ENST00000376451.2_Frame_Shift_Del_p.D1027fs|KIAA1217_ENST00000396445.1_Intron|KIAA1217_ENST00000396446.1_Intron|KIAA1217_ENST00000458595.1_Intron|KIAA1217_ENST00000376462.1_Intron|KIAA1217_ENST00000376452.3_Intron|KIAA1217_ENST00000307544.6_Intron	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1344					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						TTATCACGACAGATTTTGGCCA	0.411																																					p.1343_1343del		Atlas-Indel,Pindel	.											.	KIAA1217	235	.	0			c.4028_4029del						PASS	.																																			SO:0001589	frameshift_variant	56243	exon19			.	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.4029_4030delAG	chr10.hg19:g.24832228_24832229delAG	ENSP00000365637:p.Asp1344fs	304.0	0.0	0		309.0	132.0	0.427184	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Frame_Shift_Del	DEL	ENST00000376454.3	hg19	CCDS31165.1																																																																																			.	.	.	none		0.411	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		-	24832229	AG	-	24832228	7	5	231	1	0	1	0	1	0	0	0	0	8223	175	7	0	4103	0	KIAA1217	10	24832228	Frame_Shift_Del	DEL	AG	TCGA-P4-A5E8-01A-11D-A28G-10	17210279	24832228	110702519	29	14043											
CREB3L1	90993	hgsc.bcm.edu	37	chr11	46342259	46342259	+	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	ctggcctctcttctctctccAggatctgggccccaacacca	6	10	7	18	0	4	0	0	0	4	0	7	1	4	1	5	3	1	0	5	3	1	1	rs79068197|rs386373762|rs386373761		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr11:46342259A>G	ENST00000529193.1	+	12	1974		c.e12-1		CREB3L1_ENST00000288400.3_Splice_Site			Q96BA8	CR3L1_HUMAN	cAMP responsive element binding protein 3-like 1						regulation of bone mineralization (GO:0030500)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)		FUS/CREB3L1(6)	NS(2)|breast(1)|large_intestine(4)|lung(2)|ovary(3)	12				GBM - Glioblastoma multiforme(35;0.0285)		TTCTCTCTCCAGGATCTGGGC	0.577			T	FUS	myxofibrosarcoma																																.	Pancreas(3;159 194 19597 26278 47995)	Atlas-SNP	.		Dom	yes		11	11p11.2	90993	cAMP responsive element binding protein 3-like 1		M	CREB3L1,caecum,carcinoma,0,1	CREB3L1	30	.	0			c.1524-1A>G						PASS	.						89	92	91					11																	46342259		1996	4166	6162	SO:0001630	splice_region_variant	90993	exon12			CTCTCCAGGATCT		CCDS53620.1	11q11	2013-01-10				ENSG00000157613		"basic leucine zipper proteins"	18856	protein-coding gene	gene with protein product	"BBF-2 homolog (drosophila)"						Standard	NM_052854		Approved	OASIS	uc021qil.1	Q96BA8		ENST00000529193.1:c.1524-1A>G	chr11.hg19:g.46342259A>G		149.0	1.0	.		156.0	8.0	.	NM_052854	Q8N2D5|Q96CP0	Splice_Site	SNP	ENST00000529193.1	hg19	CCDS53620.1	.	.	.	.	.	.	.	.	.	.	A	16.47	3.131944	0.56828	.	.	ENSG00000157613	ENST00000529193;ENST00000288400;ENST00000446415	.	.	.	4.08	4.08	0.47627	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.5834	0.39501	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CREB3L1	46298835	1.000000	0.71417	0.998000	0.56505	0.830000	0.47004	3.943000	0.56621	1.837000	0.53436	0.352000	0.21897	.	.	.	.	none		0.577	CREB3L1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389702.1	NM_052854	Intron	G	46342259	A	G	46342259	5	3	231	1	0	0	0	0	0	0	1	0	3858	202	7	3	1569	3	CREB3L1	11	46342259	Splice_Site	SNP	A	TCGA-P4-A5E8-01A-11D-A28G-10		46342259	88664257	30	14044											
ACY3	91703	hgsc.bcm.edu	37	chr11	67413212	67413212	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agacttcgtgggaggacttcGcgattaagcaggtgcccatg	9	9	14	9	3	0	1	0	0	0	1	2	4	0	3	1	3	2	1	1	3	1	3	rs368150084		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr11:67413212G>A	ENST00000255082.3	-	4	553	c.383C>T	c.(382-384)gCg>gTg	p.A128V	ACY3_ENST00000529256.1_Missense_Mutation_p.A7V	NM_080658.1	NP_542389.1	Q96HD9	ACY3_HUMAN	aspartoacylase (aminocyclase) 3	128	Hydrolytic domain. {ECO:0000250}.				viral process (GO:0016032)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	aminoacylase activity (GO:0004046)|hydrolase activity, acting on ester bonds (GO:0016788)|metal ion binding (GO:0046872)			endometrium(1)|lung(5)|prostate(2)	8					L-Aspartic Acid(DB00128)	GGAGGACTTCGCGATTAAGCA	0.642																																					p.A128V	GBM(56;346 1011 27014 29495 46841)	Atlas-SNP	.											.	ACY3	27	.	0			c.C383T						PASS	.	G	VAL/ALA	2,4398	4.2+/-10.8	0,2,2198	170	152	158		383	0.6	0	11		158	0,8588		0,0,4294	no	missense	ACY3	NM_080658.1	64	0,2,6492	AA,AG,GG		0.0,0.0455,0.0154	benign	128/320	67413212	2,12986	2200	4294	6494	SO:0001583	missense	91703	exon4			GACTTCGCGATTA	BC008689	CCDS8175.1	11q13.2	2014-08-08			ENSG00000132744	ENSG00000132744			24104	protein-coding gene	gene with protein product		614413				14656720	Standard	NM_080658		Approved	HCBP1, MGC9740, ACY-3	uc001omq.3	Q96HD9	OTTHUMG00000167283	ENST00000255082.3:c.383C>T	chr11.hg19:g.67413212G>A	ENSP00000255082:p.Ala128Val	195.0	0.0	.		203.0	12.0	.	NM_080658		Missense_Mutation	SNP	ENST00000255082.3	hg19	CCDS8175.1	.	.	.	.	.	.	.	.	.	.	G	1.017	-0.686076	0.03328	4.55E-4	0.0	ENSG00000132744	ENST00000255082;ENST00000529256	D;D	0.97505	-4.41;-4.41	3.79	0.623	0.17654	.	2.785610	0.01103	N	0.005413	D	0.86049	0.5840	N	0.00347	-1.61	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.82808	-0.0274	10	0.22109	T	0.4	.	4.3548	0.11172	0.2931:0.3178:0.3891:0.0	.	128	Q96HD9	ACY3_HUMAN	V	128;7	ENSP00000255082:A128V;ENSP00000434270:A7V	ENSP00000255082:A128V	A	-	2	0	ACY3	67169788	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.470000	0.06639	-0.081000	0.12662	-0.258000	0.10820	GCG	.	.	.	weak		0.642	ACY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394002.1	NM_080658		A	67413212	G	A	67413212	3	1	231	1	0	0	0	0	1	0	0	0	227	1087	38	1	596	1	ACY3	11	67413212	Missense_Mutation	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	21070953	67413212	67593304	31	14045											
POU2AF1	5450	hgsc.bcm.edu	37	chr11	111228192	111228192	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgacattggtgatgagtggcGgagaggcataggtcaacact	11	9	15	6	1	1	4	1	3	0	1	1	5	1	4	0	5	1	1	0	5	2	2			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr11:111228192G>A	ENST00000393067.3	-	4	948	c.434C>T	c.(433-435)cCg>cTg	p.P145L		NM_006235.2	NP_006226.2	Q16633	OBF1_HUMAN	POU class 2 associating factor 1	145					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)		GATGAGTGGCGGAGAGGCATA	0.572			T	BCL6	NHL																																p.P145L		Atlas-SNP	.		Dom	yes		11	11q23.1	5450	"POU domain, class 2, associating factor 1 (OBF1)"		L	.	POU2AF1	23	.	0			c.C434T						PASS	.						81	70	73					11																	111228192		2201	4297	6498	SO:0001583	missense	5450	exon4			AGTGGCGGAGAGG		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.434C>T	chr11.hg19:g.111228192G>A	ENSP00000376786:p.Pro145Leu	370.0	1.0	.		338.0	131.0	.	NM_006235	B2R8Z9|Q14983	Missense_Mutation	SNP	ENST00000393067.3	hg19	CCDS31675.1	.	.	.	.	.	.	.	.	.	.	G	11.34	1.610386	0.28712	.	.	ENSG00000110777	ENST00000393067	T	0.28255	1.62	4.95	3.9	0.45041	.	0.326590	0.29376	N	0.012335	T	0.18718	0.0449	N	0.22421	0.69	0.44937	D	0.997956	B	0.28820	0.224	B	0.22601	0.04	T	0.05007	-1.0912	10	0.27082	T	0.32	-8.7718	10.5839	0.45271	0.0:0.0:0.2373:0.7627	.	145	Q16633	OBF1_HUMAN	L	145	ENSP00000376786:P145L	ENSP00000376786:P145L	P	-	2	0	POU2AF1	110733402	1.000000	0.71417	1.000000	0.80357	0.710000	0.40934	3.360000	0.52299	0.893000	0.36288	0.492000	0.49549	CCG	.	.	.	none		0.572	POU2AF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391002.1	NM_006235		A	111228192	G	A	111228192	3	1	231	1	0	0	0	0	1	0	0	0	12277	1116	39	1	344	1	POU2AF1	11	111228192	Missense_Mutation	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	43814980	111228192	23778324	32	14046											
HTR3A	3359	hgsc.bcm.edu	37	chr11	113846045	113846045	+	5'UTR	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcctatgcttggaaagctcGctatgctgctgtgggtccag	6	12	12	11	1	0	0	0	0	0	0	3	1	2	1	2	2	4	5	2	2	3	3	rs200513646		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr11:113846045G>A	ENST00000504030.2	+	0	443				HTR3A_ENST00000375498.2_Missense_Mutation_p.A6T|HTR3A_ENST00000299961.5_5'Flank|HTR3A_ENST00000355556.2_Missense_Mutation_p.A6T|HTR3A_ENST00000535865.1_5'UTR|HTR3A_ENST00000506841.2_5'UTR			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)	TGGAAAGCTCGCTATGCTGCT	0.632													G|||	1	0.000199681	8e-04	0	5008	,	,		19934	0		0	False		,,,				2504	0				p.A6T		Atlas-SNP	.											.	HTR3A	93	.	0			c.G16A						PASS	.	G	THR/ALA,THR/ALA	4,4398	8.1+/-20.4	0,4,2197	62	55	58		16,16	-5.2	0	11		58	0,8592		0,0,4296	yes	missense,missense	HTR3A	NM_213621.3,NM_000869.5	58,58	0,4,6493	AA,AG,GG		0.0,0.0909,0.0308	benign,benign	6/517,6/485	113846045	4,12990	2201	4296	6497	SO:0001623	5_prime_UTR_variant	3359	exon1			AAGCTCGCTATGC	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.-3G>A	chr11.hg19:g.113846045G>A		53.0	0.0	.		26.0	8.0	.	NM_000869	B4DSY6|G5E986|O60854|Q7KZM7|Q99918|Q9BSZ9	Missense_Mutation	SNP	ENST00000504030.2	hg19		.	.	.	.	.	.	.	.	.	.	G	9.618	1.133138	0.21041	9.09E-4	0.0	ENSG00000166736	ENST00000355556;ENST00000375498	T;T	0.77098	-0.99;-1.07	4.94	-5.23	0.02798	.	.	.	.	.	T	0.54615	0.1869	N	0.08118	0	0.29946	N	0.820675	B;B	0.10296	0.003;0.001	B;B	0.06405	0.002;0.001	T	0.33033	-0.9884	9	0.29301	T	0.29	.	12.1527	0.54059	0.5992:0.0:0.4008:0.0	.	6;6	G5E986;Q7KZM7	.;.	T	6	ENSP00000347754:A6T;ENSP00000364648:A6T	ENSP00000347754:A6T	A	+	1	0	HTR3A	113351255	0.000000	0.05858	0.000000	0.03702	0.240000	0.25518	-1.991000	0.01478	-1.239000	0.02532	-0.119000	0.15052	GCT	.	.	.	weak		0.632	HTR3A-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000360822.2	NM_000869		A	113846045	G	A	113846045	1	1	231	0	1	0	0	0	0	0	0	0	7451	1087	38	1		1	HTR3A	11	113846045	5'UTR	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	2617853	113846045	21160471	33	14047											
IGFBP6	3489	hgsc.bcm.edu	37	chr12	53494509	53494509	+	Frame_Shift_Del	DEL	T	T	-																															cctccagttgcagaggagaaTcctaaggagagtaaacccca																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr12:53494509delT	ENST00000301464.3	+	2	621	c.348delT	c.(346-348)aatfs	p.N116fs	SOAT2_ENST00000301466.3_5'Flank|IGFBP6_ENST00000549628.1_3'UTR|IGFBP6_ENST00000548547.1_Frame_Shift_Del_p.N114fs	NM_002178.2	NP_002169.1	P24592	IBP6_HUMAN	insulin-like growth factor binding protein 6	116					cellular protein metabolic process (GO:0044267)|negative regulation of cell proliferation (GO:0008285)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)				large_intestine(1)|lung(3)|ovary(1)|pancreas(1)	6						CAGAGGAGAATCCTAAGGAGA	0.567																																					p.N116fs	Esophageal Squamous(83;1656 1718 30141 34380)	Atlas-Indel,Pindel	.											.	IGFBP6	16	.	0			c.347delA						PASS	.						95	93	94					12																	53494509		2203	4300	6503	SO:0001589	frameshift_variant	3489	exon2			.		CCDS8846.1	12q13	2008-07-28				ENSG00000167779			5475	protein-coding gene	gene with protein product		146735				1850258, 10087296	Standard	NM_002178		Approved		uc001sbu.1	P24592	OTTHUMG00000169773	ENST00000301464.3:c.348delT	chr12.hg19:g.53494509delT	ENSP00000301464:p.Asn116fs	62.0	0.0	0		71.0	30.0	0.422535	NM_002178	Q14492	Frame_Shift_Del	DEL	ENST00000301464.3	hg19	CCDS8846.1																																																																																			.	.	.	none		0.567	IGFBP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405813.1			-	53494509	T	-	53494509	7	5	231	1	0	1	0	1	0	0	0	0	7590	1432	50	0	354	0	IGFBP6	12	53494509	Frame_Shift_Del	DEL	T	TCGA-P4-A5E8-01A-11D-A28G-10		53494509	80357386	34	14048											
HIF1A	3091	hgsc.bcm.edu	37	chr14	62194216	62194223	+	Frame_Shift_Del	DEL	AACCAACC	AACCAACC	-																															acgtatatgataccaacagtAaccaacctcagtgtgggtat																								rs369217648		TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	AACCAACC	AACCAACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr14:62194216_62194223delAACCAACC	ENST00000337138.4	+	6	881_888	c.616_623delAACCAACC	c.(616-624)aaccaacctfs	p.NQP206fs	HIF1A_ENST00000557538.1_Frame_Shift_Del_p.NQP147fs|HIF1A_ENST00000539097.1_Frame_Shift_Del_p.NQP230fs|HIF1A_ENST00000557206.1_3'UTR|HIF1A_ENST00000394997.1_Frame_Shift_Del_p.NQP207fs|HIF1A-AS2_ENST00000554254.1_lincRNA|HIF1A_ENST00000323441.6_Frame_Shift_Del_p.NQP206fs	NM_001530.3	NP_001521.1	Q16665	HIF1A_HUMAN	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	206	Interaction with TSGA10. {ECO:0000250}.				angiogenesis (GO:0001525)|axon transport of mitochondrion (GO:0019896)|B-1 B cell homeostasis (GO:0001922)|cardiac ventricle morphogenesis (GO:0003208)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cerebral cortex development (GO:0021987)|collagen metabolic process (GO:0032963)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|digestive tract morphogenesis (GO:0048546)|dopaminergic neuron differentiation (GO:0071542)|elastin metabolic process (GO:0051541)|embryonic hemopoiesis (GO:0035162)|embryonic placenta development (GO:0001892)|epithelial cell differentiation involved in mammary gland alveolus development (GO:0061030)|epithelial to mesenchymal transition (GO:0001837)|glucose homeostasis (GO:0042593)|heart looping (GO:0001947)|hemoglobin biosynthetic process (GO:0042541)|intestinal epithelial cell maturation (GO:0060574)|lactate metabolic process (GO:0006089)|lactation (GO:0007595)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of bone mineralization (GO:0030502)|negative regulation of growth (GO:0045926)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of thymocyte apoptotic process (GO:0070244)|negative regulation of TOR signaling (GO:0032007)|neural crest cell migration (GO:0001755)|neural fold elevation formation (GO:0021502)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|oxygen homeostasis (GO:0032364)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine production (GO:0032722)|positive regulation of chemokine-mediated signaling pathway (GO:0070101)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to muscle activity (GO:0014850)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|vascular endothelial growth factor production (GO:0010573)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|Hsp90 protein binding (GO:0051879)|nuclear hormone receptor binding (GO:0035257)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|endometrium(8)|kidney(6)|large_intestine(3)|lung(4)	23				OV - Ovarian serous cystadenocarcinoma(108;1.62e-09)|BRCA - Breast invasive adenocarcinoma(234;0.189)	Carvedilol(DB01136)	TACCAACAGTAACCAACCTCAGTGTGGG	0.385																																					p.229_232del		Atlas-INDEL	.											.	HIF1A	120	.	0			c.687_694del						PASS	.																																			SO:0001589	frameshift_variant	3091	exon6			.	U22431	CCDS9753.1, CCDS9754.1, CCDS58324.1	14q23.2	2013-05-21	2008-12-02		ENSG00000100644	ENSG00000100644		"Basic helix-loop-helix proteins"	4910	protein-coding gene	gene with protein product		603348				8786149, 9079689	Standard	NM_001530		Approved	MOP1, HIF-1alpha, PASD8, HIF1, bHLHe78	uc001xfq.2	Q16665	OTTHUMG00000140344	ENST00000337138.4:c.616_623delAACCAACC	chr14.hg19:g.62194216_62194223delAACCAACC	ENSP00000338018:p.Asn206fs	146.0	0.0	0		93.0	15.0	0.16129	NM_001243084	C0LZJ3|Q53XP6|Q96PT9|Q9UPB1	Frame_Shift_Del	DEL	ENST00000337138.4	hg19	CCDS9753.1																																																																																			.	.	.	none		0.385	HIF1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276977.2	NM_001530		-	62194223	AACCAACC	-	62194216	7	5	231	1	0	1	0	1	0	0	0	0	7110	362	13	0	638	0	HIF1A	14	62194216	Frame_Shift_Del	DEL	AACCAACC	TCGA-P4-A5E8-01A-11D-A28G-10		62194216	45155324	35	14049	142	2									
HIF1A	3091	hgsc.bcm.edu	37	chr14	62194225	62194225	+	Frame_Shift_Del	DEL	C	C	-																															ataccaacagtaaccaacctCagtgtgggtataagaaacca																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr14:62194225delC	ENST00000337138.4	+	6	890	c.625delC	c.(625-627)cagfs	p.Q209fs	HIF1A_ENST00000557538.1_Frame_Shift_Del_p.Q150fs|HIF1A_ENST00000539097.1_Frame_Shift_Del_p.Q233fs|HIF1A_ENST00000557206.1_3'UTR|HIF1A_ENST00000394997.1_Frame_Shift_Del_p.Q210fs|HIF1A-AS2_ENST00000554254.1_lincRNA|HIF1A_ENST00000323441.6_Frame_Shift_Del_p.Q209fs	NM_001530.3	NP_001521.1	Q16665	HIF1A_HUMAN	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	209	Interaction with TSGA10. {ECO:0000250}.				angiogenesis (GO:0001525)|axon transport of mitochondrion (GO:0019896)|B-1 B cell homeostasis (GO:0001922)|cardiac ventricle morphogenesis (GO:0003208)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cerebral cortex development (GO:0021987)|collagen metabolic process (GO:0032963)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|digestive tract morphogenesis (GO:0048546)|dopaminergic neuron differentiation (GO:0071542)|elastin metabolic process (GO:0051541)|embryonic hemopoiesis (GO:0035162)|embryonic placenta development (GO:0001892)|epithelial cell differentiation involved in mammary gland alveolus development (GO:0061030)|epithelial to mesenchymal transition (GO:0001837)|glucose homeostasis (GO:0042593)|heart looping (GO:0001947)|hemoglobin biosynthetic process (GO:0042541)|intestinal epithelial cell maturation (GO:0060574)|lactate metabolic process (GO:0006089)|lactation (GO:0007595)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of bone mineralization (GO:0030502)|negative regulation of growth (GO:0045926)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of thymocyte apoptotic process (GO:0070244)|negative regulation of TOR signaling (GO:0032007)|neural crest cell migration (GO:0001755)|neural fold elevation formation (GO:0021502)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|oxygen homeostasis (GO:0032364)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine production (GO:0032722)|positive regulation of chemokine-mediated signaling pathway (GO:0070101)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to muscle activity (GO:0014850)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|vascular endothelial growth factor production (GO:0010573)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|Hsp90 protein binding (GO:0051879)|nuclear hormone receptor binding (GO:0035257)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|endometrium(8)|kidney(6)|large_intestine(3)|lung(4)	23				OV - Ovarian serous cystadenocarcinoma(108;1.62e-09)|BRCA - Breast invasive adenocarcinoma(234;0.189)	Carvedilol(DB01136)	TAACCAACCTCAGTGTGGGTA	0.383																																					p.P232fs		Atlas-INDEL	.											.	HIF1A	120	.	0			c.696delT						PASS	.						166	142	150					14																	62194225		2203	4300	6503	SO:0001589	frameshift_variant	3091	exon6			.	U22431	CCDS9753.1, CCDS9754.1, CCDS58324.1	14q23.2	2013-05-21	2008-12-02		ENSG00000100644	ENSG00000100644		"Basic helix-loop-helix proteins"	4910	protein-coding gene	gene with protein product		603348				8786149, 9079689	Standard	NM_001530		Approved	MOP1, HIF-1alpha, PASD8, HIF1, bHLHe78	uc001xfq.2	Q16665	OTTHUMG00000140344	ENST00000337138.4:c.625delC	chr14.hg19:g.62194225delC	ENSP00000338018:p.Gln209fs	156.0	0.0	0		98.0	15.0	0.153061	NM_001243084	C0LZJ3|Q53XP6|Q96PT9|Q9UPB1	Frame_Shift_Del	DEL	ENST00000337138.4	hg19	CCDS9753.1																																																																																			.	.	.	none		0.383	HIF1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276977.2	NM_001530		-	62194225	C	-	62194225	7	5	231	1	0	1	0	1	0	0	0	0	7110	827	29	0	647	0	HIF1A	14	62194225	Frame_Shift_Del	DEL	C	TCGA-P4-A5E8-01A-11D-A28G-10	9	62194225	45155315	36	14050	142	2									
TP53BP1	7158	hgsc.bcm.edu	37	chr15	43748237	43748237	+	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	tttctcctgagtttggggctGctgcaactcctggtcaagtc	5	14	11	11	0	2	1	1	1	1	0	5	1	3	1	2	3	3	4	2	3	2	2			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr15:43748237G>A	ENST00000263801.3	-	12	2806	c.2554C>T	c.(2554-2556)Cag>Tag	p.Q852*	TP53BP1_ENST00000605155.1_5'UTR|TP53BP1_ENST00000382044.4_Nonsense_Mutation_p.Q857*|TP53BP1_ENST00000450115.2_Nonsense_Mutation_p.Q857*|TP53BP1_ENST00000382039.3_Nonsense_Mutation_p.Q857*	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	852					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)		GTTTGGGGCTGCTGCAACTCC	0.458								Other conserved DNA damage response genes																													p.Q857X		Atlas-SNP	.											.	TP53BP1	157	.	0			c.C2569T						PASS	.						181	178	179					15																	43748237		2201	4298	6499	SO:0001587	stop_gained	7158	exon12			GGGGCTGCTGCAA	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.2554C>T	chr15.hg19:g.43748237G>A	ENSP00000263801:p.Gln852*	74.0	0.0	.		70.0	26.0	.	NM_001141980	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Nonsense_Mutation	SNP	ENST00000263801.3	hg19	CCDS10096.1	.	.	.	.	.	.	.	.	.	.	G	37	6.362726	0.97507	.	.	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115;ENST00000413546	.	.	.	5.37	4.44	0.53790	.	0.405695	0.25091	N	0.033212	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	-1.0009	12.5477	0.56210	0.0:0.1669:0.833:0.0	.	.	.	.	X	852;857;857;857;857	.	ENSP00000263801:Q852X	Q	-	1	0	TP53BP1	41535529	0.317000	0.24589	0.067000	0.19924	0.006000	0.05464	1.799000	0.38824	1.364000	0.46038	0.650000	0.86243	CAG	.	.	.	none		0.458	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			A	43748237	G	A	43748237	4	1	231	1	0	0	0	0	0	1	0	0	16395	1328	46	2	3432	2	TP53BP1	15	43748237	Nonsense_Mutation	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10		43748237	58783155	37	14051											
ABCC1	4363	hgsc.bcm.edu	37	chr16	16177358	16177358	+	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	gtgccctcctcccagacctgGaaatcctgcccagtggggat	7	8	11	15	0	0	1	0	0	0	1	3	3	3	3	6	3	2	0	6	3	1	0			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr16:16177358G>A	ENST00000399410.3	+	17	2426	c.2251G>A	c.(2251-2253)Gaa>Aaa	p.E751K	ABCC1_ENST00000345148.5_Missense_Mutation_p.E751K|ABCC1_ENST00000346370.5_Missense_Mutation_p.E751K|ABCC1_ENST00000349029.5_Intron|ABCC1_ENST00000399408.2_Missense_Mutation_p.E751K|ABCC1_ENST00000351154.5_Intron	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	751	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)	CCCAGACCTGGAAATCCTGCC	0.517																																					p.E751K		Atlas-SNP	.											.	ABCC1	156	.	0			c.G2251A						PASS	.						82	84	83					16																	16177358		2014	4202	6216	SO:0001583	missense	4363	exon17			GACCTGGAAATCC	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.2251G>A	chr16.hg19:g.16177358G>A	ENSP00000382342:p.Glu751Lys	209.0	0.0	.		253.0	52.0	.	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Missense_Mutation	SNP	ENST00000399410.3	hg19	CCDS42122.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.334110	0.81801	.	.	ENSG00000103222	ENST00000399410;ENST00000399408;ENST00000346370;ENST00000345148;ENST00000536381	D;D;D;D	0.93906	-3.31;-3.31;-2.69;-3.31	5.29	5.29	0.74685	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.045819	0.85682	D	0.000000	D	0.94122	0.8115	N	0.25890	0.77	0.80722	D	1	P;D;P;P	0.71674	0.877;0.998;0.583;0.877	P;D;P;B	0.80764	0.538;0.994;0.455;0.438	D	0.94049	0.7316	10	0.41790	T	0.15	-18.2126	17.9191	0.88961	0.0:0.0:1.0:0.0	.	751;751;751;751	P33527-4;P33527-3;P33527;P33527-9	.;.;MRP1_HUMAN;.	K	751;751;751;751;425	ENSP00000382342:E751K;ENSP00000382340:E751K;ENSP00000263019:E751K;ENSP00000263014:E751K	ENSP00000263014:E751K	E	+	1	0	ABCC1	16084859	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.549000	0.73900	2.484000	0.83849	0.563000	0.77884	GAA	.	.	.	none		0.517	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996		A	16177358	G	A	16177358	3	1	231	1	0	0	0	0	1	0	0	0	49	1175	41	2	2317	2	ABCC1	16	16177358	Missense_Mutation	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10		16177358	74177395	38	14052											
RLTPR	146206	hgsc.bcm.edu	37	chr16	67683208	67683208	+	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	gtccagctcatgcaggacgaCgattgtgtgagttcacggga	9	9	14	9	3	2	1	2	1	0	0	3	5	3	3	1	2	2	3	1	2	0	2			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr16:67683208C>T	ENST00000334583.6	+	19	2068	c.1740C>T	c.(1738-1740)gaC>gaT	p.D580D	RLTPR_ENST00000545661.1_Silent_p.D544D	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	580	Tropomodulin-like.				cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		TGCAGGACGACGATTGTGTGA	0.612																																					p.D580D		Atlas-SNP	.											.	RLTPR	124	.	0			c.C1740T						PASS	.						64	71	69					16																	67683208		2055	4210	6265	SO:0001819	synonymous_variant	146206	exon19			GGACGACGATTGT	AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein", "leucine rich repeat containing 16C"	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.1740C>T	chr16.hg19:g.67683208C>T		40.0	0.0	.		48.0	20.0	.	NM_001013838	B8X2Z3	Silent	SNP	ENST00000334583.6	hg19	CCDS45513.1																																																																																			.	.	.	none		0.612	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838		T	67683208	C	T	67683208	2	4	231	1	0	0	0	0	0	0	0	1	13407	535	19	1		1	RLTPR	16	67683208	Silent	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10	51505850	67683208	22671545	39	14053											
KRTAP4-5	85289	hgsc.bcm.edu	37	chr17	39305774	39305775	+	Missense_Mutation	DNP	CT	CT	GC																															gtggtcctgcagcaggtggtCtggcagcagcaggggcggca																								rs137947981|rs535144703|rs141265645|rs58117746	byFrequency	TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr17:39305774_39305775CT>GC	ENST00000343246.4	-	1	279_280	c.245_246AG>GC	c.(244-246)cAG>cGC	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)		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.Q82H|p.Q82R		Atlas-SNP	.											KRTAP4-5,NS,carcinoma,0,1|KRTAP4-5,NS,carcinoma,+1,1	KRTAP4-5	34	.	1	Substitution - Missense(1)	lung(1)	c.G246C|c.A245G						PASS	.																																			SO:0001583	missense	85289	exon1			GGTGGTCTGGCAG|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.245_246delinsGC	chr17.hg19:g.39305774_39305775delinsGC	ENSP00000340546:p.Gln82Arg	75.0|74.0	0.0	.		83.0|86.0	23.0|26.0	.	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	hg19	CCDS32650.1																																																																																			.	.	.	weak		0.653	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1			GC	39305775	CT	GC	39305774	3	3	231	1	0	0	0	0	1	0	0	0	8561	912	32	4	303	4	KRTAP4-5	17	39305774	Missense_Mutation	DNP	CT	TCGA-P4-A5E8-01A-11D-A28G-10		39305774	41889436	40	14054											
SP6	80320	hgsc.bcm.edu	37	chr17	45925061	45925061	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcttcttcttgcccccatcGggcccacatggagcccccag	5	9	9	18	1	2	0	0	0	2	0	3	1	2	1	5	2	3	1	5	2	0	3			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr17:45925061G>A	ENST00000536300.1	-	2	1066	c.735C>T	c.(733-735)ccC>ccT	p.P245P	SP6_ENST00000342234.2_Silent_p.P245P	NM_001258248.1	NP_001245177.1	Q3SY56	SP6_HUMAN	Sp6 transcription factor	245					positive regulation of cell proliferation (GO:0008284)|regulation of odontogenesis (GO:0042481)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)|lung(5)|prostate(1)|skin(1)	8						TGCCCCCATCGGGCCCACATG	0.672																																					p.P245P		Atlas-SNP	.											.	SP6	26	.	0			c.C735T						PASS	.						21	23	22					17																	45925061		2182	4251	6433	SO:0001819	synonymous_variant	80320	exon2			CCCATCGGGCCCA		CCDS11520.1	17q21.32	2013-01-08			ENSG00000189120	ENSG00000189120		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	14530	protein-coding gene	gene with protein product	"epiprofin"	608613				11087666, 14551215	Standard	NM_001258248		Approved	KLF14, Epfn	uc002img.2	Q3SY56	OTTHUMG00000132067	ENST00000536300.1:c.735C>T	chr17.hg19:g.45925061G>A		101.0	0.0	.		83.0	31.0	.	NM_001258248	B3KXS4	Silent	SNP	ENST00000536300.1	hg19	CCDS11520.1																																																																																			.	.	.	none		0.672	SP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441395.1	NM_199262		A	45925061	G	A	45925061	2	1	231	1	0	0	0	0	0	0	0	1	14981	1103	39	1		1	SP6	17	45925061	Silent	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	6619287	45925061	35270149	41	14055											
DNAI2	64446	hgsc.bcm.edu	37	chr17	72306227	72306227	+	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	atcgcctgcggctcccagctGgggacaaccaccctgctgga	7	6	12	16	2	0	0	0	0	0	0	2	2	1	2	4	4	4	3	4	4	1	0			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr17:72306227G>T	ENST00000311014.6	+	11	1486	c.1419G>T	c.(1417-1419)ctG>ctT	p.L473L	RP11-647F2.2_ENST00000585167.1_RNA|AC103809.1_ENST00000516976.1_RNA|DNAI2_ENST00000307504.5_Silent_p.L330L|DNAI2_ENST00000579490.1_Silent_p.L530L|DNAI2_ENST00000582036.1_Silent_p.L461L|DNAI2_ENST00000446837.2_Silent_p.L473L			Q9GZS0	DNAI2_HUMAN	dynein, axonemal, intermediate chain 2	473					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						GCTCCCAGCTGGGGACAACCA	0.622									Kartagener syndrome																												p.L473L		Atlas-SNP	.											.	DNAI2	102	.	0			c.G1419T						PASS	.						55	51	52					17																	72306227		2203	4300	6503	SO:0001819	synonymous_variant	64446	exon11	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CCAGCTGGGGACA	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.1419G>T	chr17.hg19:g.72306227G>T		96.0	0.0	.		93.0	32.0	.	NM_023036	C9J0S6|Q8IUW4|Q9H179|Q9NT53	Silent	SNP	ENST00000311014.6	hg19	CCDS11697.1																																																																																			.	.	.	none		0.622	DNAI2-001	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442537.1	NM_023036		T	72306227	G	T	72306227	2	4	231	1	0	0	0	0	0	0	0	1	4612	1335	47	4		4	DNAI2	17	72306227	Silent	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	26381166	72306227	8888983	42	14056											
RAB40B	10966	hgsc.bcm.edu	37	chr17	80617514	80617514	+	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	aagaccagcggttcgcaatgTcatagaccaggatcacaccc	13	6	9	13	2	2	2	2	0	0	2	3	3	2	3	3	2	1	2	3	2	3	2			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr17:80617514T>A	ENST00000571995.1	-	4	415	c.284A>T	c.(283-285)gAc>gTc	p.D95V	RAB40B_ENST00000538809.2_Missense_Mutation_p.D95V|RAB40B_ENST00000571880.1_5'Flank|RAB40B_ENST00000269347.6_5'UTR	NM_006822.2	NP_006813.1	Q12829	RB40B_HUMAN	RAB40B, member RAS oncogene family	95					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)			GTTCGCAATGTCATAGACCAG	0.517																																					p.D95V		Atlas-SNP	.											.	RAB40B	24	.	0			c.A284T						PASS	.						149	114	126					17																	80617514		2203	4300	6503	SO:0001583	missense	10966	exon4			GCAATGTCATAGA	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.284A>T	chr17.hg19:g.80617514T>A	ENSP00000461785:p.Asp95Val	138.0	0.0	.		128.0	51.0	.	NM_006822	Q8WVG3	Missense_Mutation	SNP	ENST00000571995.1	hg19	CCDS11816.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.259217	0.80246	.	.	ENSG00000141542	ENST00000269347;ENST00000538809	.	.	.	4.56	4.56	0.56223	Small GTP-binding protein domain (1);	0.000000	0.64402	D	0.000001	D	0.88093	0.6344	H	0.98155	4.16	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.92358	0.5895	9	0.87932	D	0	.	14.2775	0.66189	0.0:0.0:0.0:1.0	.	95	Q12829	RB40B_HUMAN	V	95;129	.	ENSP00000269347:D95V	D	-	2	0	RAB40B	78210803	1.000000	0.71417	0.997000	0.53966	0.803000	0.45373	7.768000	0.85345	1.992000	0.58205	0.533000	0.62120	GAC	.	.	.	none		0.517	RAB40B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439007.1			A	80617514	T	A	80617514	3	1	231	1	0	0	0	0	1	0	0	0	12954	1667	58	5	564	5	RAB40B	17	80617514	Missense_Mutation	SNP	T	TCGA-P4-A5E8-01A-11D-A28G-10	8311287	80617514	577696	43	14057											
MBD1	4152	hgsc.bcm.edu	37	chr18	47802004	47802004	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctggacacatttccactggCgcctgagaccagggcgggga	8	6	15	12	2	0	1	0	1	0	1	1	4	1	3	3	5	0	1	3	5	0	1			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr18:47802004C>T	ENST00000591416.1	-	8	1189	c.758G>A	c.(757-759)cGc>cAc	p.R253H	MBD1_ENST00000588937.1_Missense_Mutation_p.R253H|MBD1_ENST00000590208.1_Missense_Mutation_p.R253H|MBD1_ENST00000585672.1_Missense_Mutation_p.R204H|MBD1_ENST00000349085.2_Missense_Mutation_p.R253H|MBD1_ENST00000591535.1_Missense_Mutation_p.R253H|MBD1_ENST00000382948.5_Missense_Mutation_p.R253H|MBD1_ENST00000424334.2_Missense_Mutation_p.R279H|MBD1_ENST00000398493.1_Missense_Mutation_p.R253H|MBD1_ENST00000339998.6_Missense_Mutation_p.R253H|MBD1_ENST00000587605.1_Missense_Mutation_p.R253H|MBD1_ENST00000353909.3_Missense_Mutation_p.R204H|MBD1_ENST00000585595.1_Missense_Mutation_p.R253H|MBD1_ENST00000347968.3_Missense_Mutation_p.R253H|MBD1_ENST00000457839.2_Missense_Mutation_p.R253H|MBD1_ENST00000398488.1_Missense_Mutation_p.R253H|MBD1_ENST00000398495.2_Missense_Mutation_p.R253H|MBD1_ENST00000269471.5_Missense_Mutation_p.R253H|MBD1_ENST00000436910.1_Missense_Mutation_p.R253H|MBD1_ENST00000269468.5_Missense_Mutation_p.R253H			Q9UIS9	MBD1_HUMAN	methyl-CpG binding domain protein 1	253					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)	p.R253L(4)		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						TTTCCACTGGCGCCTGAGACC	0.602																																					p.R253H		Atlas-SNP	.											.	MBD1	228	.	4	Substitution - Missense(4)	lung(4)	c.G758A						PASS	.						47	47	47					18																	47802004		2203	4300	6503	SO:0001583	missense	4152	exon8			CACTGGCGCCTGA	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.758G>A	chr18.hg19:g.47802004C>T	ENSP00000467017:p.Arg253His	239.0	0.0	.		224.0	74.0	.	NM_001204137	A4UTZ0|B4DXJ5|E9PEC5|K7ELI2|K7EQZ4|K7ESN0|O15248|O95241|Q7Z7B5|Q8N4W4|Q9UNZ6|Q9UNZ7|Q9UNZ8|Q9UNZ9	Missense_Mutation	SNP	ENST00000591416.1	hg19	CCDS11943.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.144536	0.77888	.	.	ENSG00000141644	ENST00000382948;ENST00000353909;ENST00000349085;ENST00000269468;ENST00000347968;ENST00000436910;ENST00000269471;ENST00000424334;ENST00000339998;ENST00000398495;ENST00000457839;ENST00000398493;ENST00000398488	D;D;D;D;D;D;D;D;D;D;D;D;D	0.97232	-4.22;-3.92;-4.04;-4.22;-4.05;-4.18;-4.16;-4.3;-4.17;-4.06;-4.29;-4.05;-4.04	5.29	5.29	0.74685	Zinc finger, CXXC-type (2);	0.000000	0.56097	D	0.000023	D	0.97508	0.9184	L	0.56769	1.78	0.32700	N	0.513027	D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D	0.97110	1.0;0.998;0.999;1.0;0.999;0.997;0.999;0.996;1.0;0.998;1.0;0.998	D	0.97757	1.0218	10	0.52906	T	0.07	-14.4062	10.2988	0.43639	0.0:0.9098:0.0:0.0902	.	253;279;253;253;253;253;204;253;253;253;253;253	B4DUR3;B4DI41;Q9UIS9-8;A8K654;Q9UIS9-6;Q9UIS9-2;Q9UIS9-5;Q9UIS9-4;Q9UIS9;Q9UIS9-7;B4DXJ5;Q9UIS9-3	.;.;.;.;.;.;.;.;MBD1_HUMAN;.;.;.	H	253;204;253;253;253;253;253;279;253;253;253;253;253	ENSP00000372407:R253H;ENSP00000269469:R204H;ENSP00000342531:R253H;ENSP00000269468:R253H;ENSP00000285102:R253H;ENSP00000409561:R253H;ENSP00000269471:R253H;ENSP00000408846:R279H;ENSP00000339546:R253H;ENSP00000381508:R253H;ENSP00000405268:R253H;ENSP00000381506:R253H;ENSP00000381502:R253H	ENSP00000269468:R253H	R	-	2	0	MBD1	46056002	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.576000	0.46033	2.653000	0.90120	0.655000	0.94253	CGC	.	.	.	none		0.602	MBD1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255926.3	NM_015846		T	47802004	C	T	47802004	3	4	231	1	0	0	0	0	1	0	0	0	9349	768	27	1	1289	1	MBD1	18	47802004	Missense_Mutation	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10		47802004	30275244	44	14058											
SPTBN4	57731	hgsc.bcm.edu	37	chr19	41076606	41076606	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcctactgcgcaagcgcgagCtcgacgctaaccgcaagtcg	9	6	11	15	7	0	0	0	0	0	0	3	2	1	0	2	0	5	4	2	0	4	2			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr19:41076606C>T	ENST00000352632.3	+	33	7377	c.7291C>T	c.(7291-7293)Ctc>Ttc	p.L2431F	SPTBN4_ENST00000598249.1_Missense_Mutation_p.L2431F|SPTBN4_ENST00000392025.1_Missense_Mutation_p.L1174F			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	2431	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)			CAAGCGCGAGCTCGACGCTAA	0.711																																					p.L2431F		Atlas-SNP	.											.	SPTBN4	213	.	0			c.C7291T						PASS	.						13	13	13					19																	41076606		2130	4092	6222	SO:0001583	missense	57731	exon33			CGCGAGCTCGACG	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.7291C>T	chr19.hg19:g.41076606C>T	ENSP00000263373:p.Leu2431Phe	68.0	0.0	.		74.0	27.0	.	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Missense_Mutation	SNP	ENST00000352632.3	hg19	CCDS12559.1	.	.	.	.	.	.	.	.	.	.	C	14.31	2.496244	0.44352	.	.	ENSG00000160460	ENST00000428507;ENST00000352632;ENST00000392025	T;T	0.31769	1.48;1.48	4.64	3.59	0.41128	Pleckstrin homology-type (1);Pleckstrin homology domain, spectrin-type (1);Pleckstrin homology domain (3);	0.111049	0.37623	U	0.002018	T	0.36441	0.0967	L	0.42245	1.32	0.80722	D	1	P;P	0.50943	0.94;0.94	P;P	0.51833	0.681;0.681	T	0.08973	-1.0696	10	0.39692	T	0.17	.	13.6768	0.62458	0.0:0.8434:0.1566:0.0	.	1174;2431	C9JY79;Q9H254	.;SPTN4_HUMAN	F	2431;2431;1174	ENSP00000263373:L2431F;ENSP00000375879:L1174F	ENSP00000263373:L2431F	L	+	1	0	SPTBN4	45768446	1.000000	0.71417	1.000000	0.80357	0.028000	0.11728	2.096000	0.41738	1.145000	0.42336	0.491000	0.48974	CTC	.	.	.	none		0.711	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2			T	41076606	C	T	41076606	3	4	231	1	0	0	0	0	1	0	0	0	15133	797	28	2	7511	2	SPTBN4	19	41076606	Missense_Mutation	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10		41076606	18052377	45	14059											
ZNF577	84765	hgsc.bcm.edu	37	chr19	52376124	52376124	+	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	gtctctcttatgtgagttttCtcatgtttaatgaggactga	8	18	9	6	0	3	3	1	3	3	0	5	4	3	4	0	1	0	2	0	1	2	5			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr19:52376124C>A	ENST00000301399.5	-	7	1484	c.1119G>T	c.(1117-1119)gaG>gaT	p.E373D	ZNF577_ENST00000451628.2_Missense_Mutation_p.E314D|ZNF577_ENST00000420592.1_Missense_Mutation_p.E314D|ZNF577_ENST00000412216.1_Intron|ZNF577_ENST00000485702.1_Intron	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	373			E -> K (in dbSNP:rs10407547).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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)		TGTGAGTTTTCTCATGTTTAA	0.448																																					p.E373D		Atlas-SNP	.											ZNF577,NS,carcinoma,0,1	ZNF577	63	.	0			c.G1119T						PASS	.						89	94	92					19																	52376124		2203	4300	6503	SO:0001583	missense	84765	exon7			AGTTTTCTCATGT	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.1119G>T	chr19.hg19:g.52376124C>A	ENSP00000301399:p.Glu373Asp	67.0	0.0	.		84.0	40.0	.	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Missense_Mutation	SNP	ENST00000301399.5	hg19	CCDS12842.2	.	.	.	.	.	.	.	.	.	.	.	7.724	0.697762	0.15106	.	.	ENSG00000161551	ENST00000301399;ENST00000420592;ENST00000451628;ENST00000458390	T;T;T;T	0.50277	0.75;0.75;0.75;0.75	3.06	2.02	0.26589	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.25419	0.0618	N	0.08118	0	0.09310	N	0.999994	B;B	0.25007	0.016;0.116	B;B	0.25884	0.007;0.064	T	0.20840	-1.0263	9	0.87932	D	0	.	4.8679	0.13618	0.0:0.6085:0.0:0.3915	.	373;314	Q9BSK1;Q9BSK1-2	ZN577_HUMAN;.	D	373;314;314;373	ENSP00000301399:E373D;ENSP00000413476:E314D;ENSP00000389652:E314D;ENSP00000404509:E373D	ENSP00000301399:E373D	E	-	3	2	ZNF577	57067936	0.000000	0.05858	0.007000	0.13788	0.327000	0.28475	0.103000	0.15292	0.592000	0.29728	0.655000	0.94253	GAG	.	.	.	none		0.448	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679		A	52376124	C	A	52376124	3	1	231	1	0	0	0	0	1	0	0	0	18021	912	32	4	342	4	ZNF577	19	52376124	Missense_Mutation	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10	11299518	52376124	6752859	46	14060											
EPB41L1	2036	hgsc.bcm.edu	37	chr20	34778710	34778710	+	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	ggtacaccatgtcccgcagcCttgatggaggtatggcccaa	9	8	12	12	1	0	1	0	1	0	0	1	2	1	2	4	4	2	3	4	4	3	3			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr20:34778710C>G	ENST00000338074.2	+	11	1452	c.1291C>G	c.(1291-1293)Ctt>Gtt	p.L431V	EPB41L1_ENST00000373946.3_Missense_Mutation_p.L400V|EPB41L1_ENST00000373950.2_Missense_Mutation_p.L334V|EPB41L1_ENST00000373941.1_Missense_Mutation_p.L431V|EPB41L1_ENST00000441639.1_Missense_Mutation_p.L369V|EPB41L1_ENST00000202028.5_Missense_Mutation_p.L369V	NM_001258329.1|NM_012156.2	NP_001245258.1|NP_036288.2	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	431					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)					GTCCCGCAGCCTTGATGGAGG	0.602																																					p.L431V		Atlas-SNP	.											.	EPB41L1	111	.	0			c.C1291G						PASS	.						47	42	43					20																	34778710		2203	4300	6503	SO:0001583	missense	2036	exon12			CGCAGCCTTGATG	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.1291C>G	chr20.hg19:g.34778710C>G	ENSP00000337168:p.Leu431Val	45.0	0.0	.		38.0	12.0	.	NM_001258329	O15046|Q4VXM6|Q4VXM7|Q4VXM8|Q4VXN4|Q6ZT61|Q8IUU7|Q96CV5|Q96L65	Missense_Mutation	SNP	ENST00000338074.2	hg19	CCDS13271.1	.	.	.	.	.	.	.	.	.	.	C	17.89	3.499624	0.64298	.	.	ENSG00000088367	ENST00000202028;ENST00000373950;ENST00000397315;ENST00000373951;ENST00000441639;ENST00000373946;ENST00000344237;ENST00000338074;ENST00000373941	D;D;D;D;D;D	0.86297	-1.95;-1.92;-1.95;-1.94;-2.1;-2.1	5.48	5.48	0.80851	.	0.292495	0.38005	N	0.001858	D	0.84844	0.5562	N	0.24115	0.695	0.39057	D	0.960441	B;P;P;P;B;P	0.45569	0.249;0.861;0.539;0.794;0.3;0.783	B;P;B;P;B;P	0.47891	0.186;0.471;0.439;0.487;0.13;0.56	D	0.87969	0.2735	10	0.87932	D	0	-4.2264	17.9268	0.88986	0.0:1.0:0.0:0.0	.	431;431;400;334;334;369	B7Z653;Q9H4G0;Q9H4G0-4;Q9H4G0-3;B3KUB6;Q9H4G0-2	.;E41L1_HUMAN;.;.;.;.	V	369;334;431;334;369;400;5;431;431	ENSP00000202028:L369V;ENSP00000363061:L334V;ENSP00000399214:L369V;ENSP00000363057:L400V;ENSP00000337168:L431V;ENSP00000363052:L431V	ENSP00000202028:L369V	L	+	1	0	EPB41L1	34242124	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.048000	0.30379	2.556000	0.86216	0.561000	0.74099	CTT	.	.	.	none		0.602	EPB41L1-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078978.3	NM_012156		G	34778710	C	G	34778710	3	3	231	1	0	0	0	0	1	0	0	0	5154	681	24	4	1329	4	EPB41L1	20	34778710	Missense_Mutation	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10		34778710	28246810	47	14061											
FAM83D	81610	hgsc.bcm.edu	37	chr20	37570604	37570604	+	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	tccctgtttcacctgtaggtGattgcagtggtcatggacgt	6	14	12	9	1	2	1	2	1	0	0	3	2	3	2	2	3	1	3	2	3	1	3			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr20:37570604G>A	ENST00000217429.4	+	2	617	c.576G>A	c.(574-576)gtG>gtA	p.V192V		NM_030919.2	NP_112181.2	Q9H4H8	FA83D_HUMAN	family with sequence similarity 83, member D	162					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)				ACCTGTAGGTGATTGCAGTGG	0.483																																					p.V192V		Atlas-SNP	.											.	FAM83D	60	.	0			c.G576A						PASS	.						149	152	151					20																	37570604		2058	4205	6263	SO:0001819	synonymous_variant	81610	exon2			GTAGGTGATTGCA	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.576G>A	chr20.hg19:g.37570604G>A		155.0	0.0	.		151.0	53.0	.	NM_030919	B4E1I7|Q5THR2|Q68EN1|Q6P457|Q7Z6H0|Q96DF5|Q96N89|Q9BVM8	Silent	SNP	ENST00000217429.4	hg19	CCDS42872.1																																																																																			.	.	.	none		0.483	FAM83D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079211.1			A	37570604	G	A	37570604	2	1	231	1	0	0	0	0	0	0	0	1	5643	1277	45	2		2	FAM83D	20	37570604	Silent	SNP	G	TCGA-P4-A5E8-01A-11D-A28G-10	2791894	37570604	25454916	48	14062											
PLXNB2	23654	hgsc.bcm.edu	37	chr22	50728592	50728593	+	Missense_Mutation	DNP	TT	TT	AC																															cattgctggccacgaaagacTtctccccgctgccgtcctcg																										TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chr22:50728592_50728593TT>AC	ENST00000449103.1	-	3	561_562	c.421_422AA>GT	c.(421-423)AAg>GTg	p.K141V	PLXNB2_ENST00000359337.4_Missense_Mutation_p.K141V			O15031	PLXB2_HUMAN	plexin B2	141	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)		CACGAAAGACTTCTCCCCGCTG	0.644																																					p.K141M|p.K141E		Atlas-SNP	.											.	PLXNB2	172	.	0			c.A422T|c.A421G						PASS	.																																			SO:0001583	missense	23654	exon3			AAAGACTTCTCCC|AAGACTTCTCCCC		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.421_422delinsAC	chr22.hg19:g.50728592_50728593delinsAC	ENSP00000409171:p.Lys141Val	115.0|110.0	0.0	.		113.0	39.0|41.0	.	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Missense_Mutation	SNP	ENST00000449103.1	hg19	CCDS43035.1																																																																																			.	.	.	none		0.644	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401		AC	50728593	TT	AC	50728592	3	1	231	1	0	0	0	0	1	0	0	0	12131	1609	56	5	5234	5	PLXNB2	22	50728592	Missense_Mutation	DNP	TT	TCGA-P4-A5E8-01A-11D-A28G-10		50728592	575974	49	14063											
ARSE	415	hgsc.bcm.edu	37	chrX	2861169	2861169	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgattctctagggaaccgcCgtgatccgacgtaaaataaa	13	10	9	9	4	1	2	0	2	1	0	3	4	2	3	3	1	1	1	3	1	6	5			TCGA-P4-A5E8-01A-11D-A28G-10	TCGA-P4-A5E8-11A-12D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ca2f452-c444-436c-a256-a2e6c6d596d6	98665cdb-4732-42e2-9034-a7b233b8abb2	g.chrX:2861169C>T	ENST00000381134.3	-	8	1129	c.1063G>A	c.(1063-1065)Ggc>Agc	p.G355S	ARSE_ENST00000540563.1_Missense_Mutation_p.G310S|ARSE_ENST00000545496.1_Missense_Mutation_p.G380S	NM_000047.2	NP_000038.2	P51690	ARSE_HUMAN	arylsulfatase E (chondrodysplasia punctata 1)	355					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)				AGGGAACCGCCGTGATCCGAC	0.473																																					p.G355S		Atlas-SNP	.											.	ARSE	43	.	0			c.G1063A						PASS	.						89	83	85					X																	2861169		2203	4300	6503	SO:0001583	missense	415	exon8			AACCGCCGTGATC	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.1063G>A	chrX.hg19:g.2861169C>T	ENSP00000370526:p.Gly355Ser	87.0	0.0	.		91.0	62.0	.	NM_000047	Q53FT2|Q53FU8	Missense_Mutation	SNP	ENST00000381134.3	hg19	CCDS14122.1	.	.	.	.	.	.	.	.	.	.	C	18.74	3.687965	0.68271	.	.	ENSG00000157399	ENST00000540563;ENST00000545496;ENST00000381134	D;D;D	0.99809	-6.86;-6.86;-6.86	3.66	2.8	0.32819	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.109135	0.64402	D	0.000009	D	0.99887	0.9946	H	0.99929	4.97	0.51482	D	0.999923	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.96969	0.9707	10	0.87932	D	0	.	9.8836	0.41249	0.0:0.8911:0.0:0.1089	.	310;380;355	F5H324;F5GYY5;P51690	.;.;ARSE_HUMAN	S	310;380;355	ENSP00000438198:G310S;ENSP00000441417:G380S;ENSP00000370526:G355S	ENSP00000370526:G355S	G	-	1	0	ARSE	2871169	0.999000	0.42202	0.003000	0.11579	0.000000	0.00434	6.039000	0.70972	0.545000	0.28902	-0.191000	0.12829	GGC	.	.	.	none		0.473	ARSE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055643.1	NM_000047		T	2861169	C	T	2861169	3	4	231	1	0	0	0	0	1	0	0	0	990	652	23	1	722	1	ARSE	23	2861169	Missense_Mutation	SNP	C	TCGA-P4-A5E8-01A-11D-A28G-10		2861169	152409391	50	14064											
EPHA2	1969	hgsc.bcm.edu	37	chr1	16459720	16459721	+	Frame_Shift_Ins	INS	-	-	TG																															atgatgttgtggtggctgaaINSctggcccatgatgccggcct																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr1:16459720_16459721insTG	ENST00000358432.5	-	11	2161_2162	c.2007_2008insCA	c.(2005-2010)cagttcfs	p.F670fs		NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	670	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)	TGGTGGCTGAACTGGCCCATGA	0.629																																					p.F670fs		Atlas-Indel,Pindel	.											.	EPHA2	102	.	0			c.2008_2009insCA						PASS	.																																			SO:0001589	frameshift_variant	1969	exon11			.	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.2007_2008insCA	chr1.hg19:g.16459720_16459721insTG	ENSP00000351209:p.Phe670fs	84.0	0.0	0		56.0	13.0	0.232143	NM_004431	B5A968|Q8N3Z2	Frame_Shift_Ins	INS	ENST00000358432.5	hg19	CCDS169.1																																																																																			.	.	.	none		0.629	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431		TG	16459721	-	TG	16459720	7	5	232	1	0	1	1	0	0	0	0	0	5169	43	2	0	950	0	EPHA2	1	16459720	Frame_Shift_Ins	INS	-	TCGA-P4-A5EA-01A-11D-A28G-10		16459720	232790901	1	14065											
MAP3K6	9064	hgsc.bcm.edu	37	chr1	27687435	27687435	+	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	caacatctcccccgcgccctCcgcctcctccgcgggcgccg	3	5	9	24	7	1	0	0	0	1	0	5	0	4	0	8	1	1	0	8	1	1	0			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr1:27687435C>T	ENST00000493901.1	-	15	2136	c.1897G>A	c.(1897-1899)Gag>Aag	p.E633K	MAP3K6_ENST00000357582.2_Missense_Mutation_p.E633K|MAP3K6_ENST00000374040.3_Missense_Mutation_p.E625K	NM_004672.3	NP_004663.3	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase 6	633					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)		CCCGCGCCCTCCGCCTCCTCC	0.736																																					p.E633K		Atlas-SNP	.											.	MAP3K6	134	.	0			c.G1897A						PASS	.						10	14	13					1																	27687435		2139	4246	6385	SO:0001583	missense	9064	exon14			CGCCCTCCGCCTC	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.1897G>A	chr1.hg19:g.27687435C>T	ENSP00000419591:p.Glu633Lys	71.0	0.0	.		102.0	35.0	.	NM_004672	A2ACE8|A2VDG4|A2VDG5|Q59HF4|Q5SSD4|Q75PK3|Q96B75	Missense_Mutation	SNP	ENST00000493901.1	hg19	CCDS299.1	.	.	.	.	.	.	.	.	.	.	C	12.32	1.901459	0.33535	.	.	ENSG00000142733	ENST00000374040;ENST00000493901;ENST00000545447;ENST00000357582	T;T;T	0.68025	-0.3;-0.3;-0.3	4.67	3.73	0.42828	.	.	.	.	.	T	0.61999	0.2392	M	0.62723	1.935	0.09310	N	1	B;B	0.25609	0.13;0.079	B;B	0.24701	0.055;0.025	T	0.54860	-0.8230	9	0.48119	T	0.1	.	8.9619	0.35851	0.0:0.8957:0.0:0.1043	.	625;633	O95382-3;O95382	.;M3K6_HUMAN	K	625;633;356;633	ENSP00000363152:E625K;ENSP00000419591:E633K;ENSP00000350195:E633K	ENSP00000350195:E633K	E	-	1	0	MAP3K6	27560022	0.005000	0.15991	0.073000	0.20177	0.013000	0.08279	1.483000	0.35497	2.433000	0.82419	0.655000	0.94253	GAG	.	.	.	none		0.736	MAP3K6-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013469.2	NM_004672		T	27687435	C	T	27687435	3	4	232	1	0	0	0	0	1	0	0	0	9261	864	30	2	2033	2	MAP3K6	1	27687435	Missense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	11227715	27687435	221563186	2	14066											
NASP	4678	hgsc.bcm.edu	37	chr1	46073053	46073073	+	In_Frame_Del	DEL	CCAAAAAAACAGAAGACAAGT	CCAAAAAAACAGAAGACAAGT	-																															catgggagaaaaagaagaagCcaaaaaaacagaagacaagt																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	CCAAAAAAACAGAAGACAAGT	CCAAAAAAACAGAAGACAAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr1:46073053_46073073delCCAAAAAAACAGAAGACAAGT	ENST00000350030.3	+	6	557_577	c.470_490delCCAAAAAAACAGAAGACAAGT	c.(469-492)gccaaaaaaacagaagacaagtct>gct	p.KKTEDKS158del	NASP_ENST00000351223.3_Intron|NASP_ENST00000402363.3_In_Frame_Del_p.KKTEDKS160del|NASP_ENST00000372052.4_Intron|NASP_ENST00000537798.1_In_Frame_Del_p.KKTEDKS94del	NM_002482.3	NP_002473.2	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein (histone-binding)	158	Glu-rich (acidic).				blastocyst development (GO:0001824)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone exchange (GO:0043486)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	Hsp90 protein binding (GO:0051879)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	17	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)					AAAGAAGAAGCCAAAAAAACAGAAGACAAGTCTTTGGCAAA	0.412																																					p.157_163del		Atlas-INDEL	.											.	NASP	77	.	0			c.469_489del						PASS	.																																			SO:0001651	inframe_deletion	4678	exon6			.	M97856	CCDS524.1, CCDS525.1, CCDS55597.1	1p34.1	2013-01-10			ENSG00000132780	ENSG00000132780		"Tetratricopeptide (TTC) repeat domain containing"	7644	protein-coding gene	gene with protein product		603185				1426632	Standard	NM_002482		Approved	FLB7527, FLJ31599, FLJ35510, MGC19722, MGC20372, MGC2297, DKFZp547F162, PRO1999	uc001coi.2	P49321	OTTHUMG00000007826	ENST00000350030.3:c.470_490delCCAAAAAAACAGAAGACAAGT	chr1.hg19:g.46073053_46073073delCCAAAAAAACAGAAGACAAGT	ENSP00000255120:p.Lys158_Ser164del	222.0	0.0	0		174.0	13.0	0.0747126	NM_002482	A8K6H2|B4DQP3|D3DQ07|F5H3J2|Q53GW5|Q5T622|Q5T625|Q96A69|Q9BTW2	In_Frame_Del	DEL	ENST00000350030.3	hg19	CCDS524.1																																																																																			.	.	.	none		0.412	NASP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021533.2	NM_002482		-	46073073	CCAAAAAAACAGAAGACAAGT	-	46073053	7	5	232	1	0	1	0	1	0	0	0	0	10179	739	26	0	569	0	NASP	1	46073053	In_Frame_Del	DEL	CCAAAAAAACAGAAGACAAGT	TCGA-P4-A5EA-01A-11D-A28G-10	18385618	46073053	203177568	3	14067											
PHTF1	10745	hgsc.bcm.edu	37	chr1	114255942	114255943	+	Frame_Shift_Del	DEL	TT	TT	-																															tgaaaattttgctttctctcTtgtttgccacattctaatct																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr1:114255942_114255943delTT	ENST00000369604.1	-	8	1224_1225	c.741_742delAA	c.(739-744)acaagafs	p.R248fs	PHTF1_ENST00000393357.2_Frame_Shift_Del_p.R248fs|PHTF1_ENST00000369596.2_Frame_Shift_Del_p.R195fs|PHTF1_ENST00000357783.2_Frame_Shift_Del_p.R248fs|PHTF1_ENST00000369600.1_Frame_Shift_Del_p.R195fs|PHTF1_ENST00000474926.1_5'UTR|PHTF1_ENST00000369598.1_Frame_Shift_Del_p.R203fs|PHTF1_ENST00000447664.2_Intron			Q9UMS5	PHTF1_HUMAN	putative homeodomain transcription factor 1	248					transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GCTTTCTCTCTTGTTTGCCACA	0.371																																					p.248_248del		Atlas-Indel,Pindel	.											.	PHTF1	69	.	0			c.742_743del						PASS	.																																			SO:0001589	frameshift_variant	10745	exon7			.	AJ011863	CCDS861.1	1p13-p11	2008-07-18			ENSG00000116793	ENSG00000116793			8939	protein-coding gene	gene with protein product		604950		PHTF		10395808	Standard	NM_006608		Approved		uc009wgp.1	Q9UMS5	OTTHUMG00000011800	ENST00000369604.1:c.741_742delAA	chr1.hg19:g.114255942_114255943delTT	ENSP00000358617:p.Arg248fs	93.0	0.0	0		81.0	20.0	0.246914	NM_006608	Q5VWP7|Q5VWP8|Q9BUP2|Q9H1X8	Frame_Shift_Del	DEL	ENST00000369604.1	hg19	CCDS861.1																																																																																			.	.	.	none		0.371	PHTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032666.1	NM_006608		-	114255943	TT	-	114255942	7	5	232	1	0	1	0	1	0	0	0	0	11869	1617	56	0	1594	0	PHTF1	1	114255942	Frame_Shift_Del	DEL	TT	TCGA-P4-A5EA-01A-11D-A28G-10	68182889	114255942	134994679	4	14068											
TUFT1	7286	hgsc.bcm.edu	37	chr1	151552139	151552139	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgcagctccagaattcaaaAgctgtgatccagtcaaagga	14	9	9	9	0	2	2	2	1	0	1	4	3	4	3	2	1	3	3	2	1	4	2	rs201062061		TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr1:151552139A>G	ENST00000368849.3	+	11	1001	c.939A>G	c.(937-939)aaA>aaG	p.K313K	TUFT1_ENST00000368848.2_Silent_p.K288K|TUFT1_ENST00000392712.3_Silent_p.K258K|TUFT1_ENST00000538902.1_Silent_p.K332K|TUFT1_ENST00000353024.3_Silent_p.K254K	NM_020127.2	NP_064512.1	Q9NNX1	TUFT1_HUMAN	tuftelin 1	313					bone mineralization (GO:0030282)|odontogenesis (GO:0042476)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	structural constituent of tooth enamel (GO:0030345)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)	13	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			AGAATTCAAAAGCTGTGATCC	0.547																																					p.K313K		Atlas-SNP	.											.	TUFT1	32	.	0			c.A939G						PASS	.						58	53	55					1																	151552139		2203	4300	6503	SO:0001819	synonymous_variant	7286	exon11			TTCAAAAGCTGTG	AF254260	CCDS1000.1, CCDS44223.1	1q21	2008-02-05			ENSG00000143367	ENSG00000143367			12422	protein-coding gene	gene with protein product		600087				7919663	Standard	NM_020127		Approved		uc001eyl.3	Q9NNX1	OTTHUMG00000012536	ENST00000368849.3:c.939A>G	chr1.hg19:g.151552139A>G		170.0	0.0	.		138.0	17.0	.	NM_020127	B2RD57|D3DV21|D3DV22|Q5T384|Q5T385|Q9BU28|Q9H5L1	Silent	SNP	ENST00000368849.3	hg19	CCDS1000.1																																																																																			.	.	.	alt		0.547	TUFT1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035022.1	NM_020127		G	151552139	A	G	151552139	2	3	232	1	0	0	0	0	0	0	0	1	16784	69	3	3		3	TUFT1	1	151552139	Silent	SNP	A	TCGA-P4-A5EA-01A-11D-A28G-10	37296197	151552139	97698482	5	14069											
GATAD2B	57459	hgsc.bcm.edu	37	chr1	153792180	153792180	+	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	agacaaaacaatgatgtctgGtgagggagttagccttcctc	12	10	11	8	0	1	3	0	2	1	1	3	4	2	4	2	2	2	1	2	2	4	2			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr1:153792180G>C	ENST00000368655.4	-	3	610	c.367C>G	c.(367-369)Cca>Gca	p.P123A		NM_020699.2	NP_065750.1	Q8WXI9	P66B_HUMAN	GATA zinc finger domain containing 2B	123					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)			ATGATGTCTGGTGAGGGAGTT	0.408																																					p.P123A		Atlas-SNP	.											.	GATAD2B	62	.	0			c.C367G						PASS	.						111	112	112					1																	153792180		2203	4300	6503	SO:0001583	missense	57459	exon3			TGTCTGGTGAGGG	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.367C>G	chr1.hg19:g.153792180G>C	ENSP00000357644:p.Pro123Ala	241.0	0.0	.		193.0	17.0	.	NM_020699	D3DUZ2|Q5VUR2|Q7LG68|Q9ULS0	Missense_Mutation	SNP	ENST00000368655.4	hg19	CCDS1054.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.821458	0.90873	.	.	ENSG00000143614	ENST00000368655	T	0.41400	1.0	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.53029	0.1771	L	0.57536	1.79	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	T	0.42982	-0.9419	10	0.35671	T	0.21	-15.871	17.5737	0.87942	0.0:0.0:1.0:0.0	.	123	Q8WXI9	P66B_HUMAN	A	123	ENSP00000357644:P123A	ENSP00000357644:P123A	P	-	1	0	GATAD2B	152058804	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.086000	0.94088	2.682000	0.91365	0.557000	0.71058	CCA	.	.	.	none		0.408	GATAD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090305.1	NM_020699		C	153792180	G	C	153792180	3	2	232	1	0	0	0	0	1	0	0	0	6268	1261	44	4	1450	4	GATAD2B	1	153792180	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	2240041	153792180	95458441	6	14070											
ASPRV1	151516	hgsc.bcm.edu	37	chr2	70188625	70188626	+	Frame_Shift_Del	DEL	AG	AG	-																															cgccaagaagagaaacccacAgagcagtgtcggcgcaatca																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr2:70188625_70188626delAG	ENST00000320256.4	-	1	771_772	c.195_196delCT	c.(193-198)ctctgtfs	p.C66fs	PCBP1-AS1_ENST00000435880.2_RNA|PCBP1-AS1_ENST00000457076.1_RNA|PCBP1-AS1_ENST00000596259.1_RNA|PCBP1-AS1_ENST00000413436.1_RNA|PCBP1-AS1_ENST00000415222.1_RNA|PCBP1-AS1_ENST00000418564.1_RNA|PCBP1-AS1_ENST00000419542.1_RNA	NM_152792.2	NP_690005.2			aspartic peptidase, retroviral-like 1											endometrium(3)|large_intestine(4)|lung(6)|ovary(1)	14						AGAAACCCACAGAGCAGTGTCG	0.653																																					p.66_66del		Atlas-Indel,Pindel	.											.	ASPRV1	41	.	0			c.196_197del						PASS	.																																			SO:0001589	frameshift_variant	151516	exon1			.	AK055994	CCDS1897.1	2p13.3	2008-02-20			ENSG00000244617	ENSG00000244617			26321	protein-coding gene	gene with protein product	"Skin ASpartic Protease"	611765				16098038, 16565508	Standard	NM_152792		Approved	Taps, SASPase, FLJ25084	uc002sfz.4	Q53RT3	OTTHUMG00000129647	ENST00000320256.4:c.195_196delCT	chr2.hg19:g.70188627_70188628delAG	ENSP00000315383:p.Cys66fs	170.0	0.0	0		162.0	14.0	0.0864198	NM_152792		Frame_Shift_Del	DEL	ENST00000320256.4	hg19	CCDS1897.1																																																																																			.	.	.	none		0.653	ASPRV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334161.1	NM_152792		-	70188626	AG	-	70188625	7	5	232	1	0	1	0	1	0	0	0	0	1058	188	7	0	839	0	ASPRV1	2	70188625	Frame_Shift_Del	DEL	AG	TCGA-P4-A5EA-01A-11D-A28G-10		70188625	173010748	7	14071											
SEMA4C	54910	hgsc.bcm.edu	37	chr2	97526794	97526794	+	Missense_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	ccctttctccagctcttcccGcagccgccggcgcaatgaca	6	8	8	19	4	2	1	0	1	2	0	4	1	3	1	5	1	2	3	5	1	1	2			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr2:97526794G>A	ENST00000305476.5	-	15	2203	c.2071C>T	c.(2071-2073)Cgg>Tgg	p.R691W	ANKRD39_ENST00000393537.4_5'Flank	NM_017789.4	NP_060259.4	Q9C0C4	SEM4C_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C	691					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						AGCTCTTCCCGCAGCCGCCGG	0.687																																					p.R691W		Atlas-SNP	.											.	SEMA4C	56	.	0			c.C2071T						PASS	.						22	27	25					2																	97526794		2200	4287	6487	SO:0001583	missense	54910	exon15			CTTCCCGCAGCCG	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.2071C>T	chr2.hg19:g.97526794G>A	ENSP00000306844:p.Arg691Trp	70.0	0.0	.		100.0	4.0	.	NM_017789	Q32MJ3|Q7Z5X0	Missense_Mutation	SNP	ENST00000305476.5	hg19	CCDS2029.1	.	.	.	.	.	.	.	.	.	.	G	18.78	3.697364	0.68386	.	.	ENSG00000168758	ENST00000305476	T	0.78126	-1.15	4.89	4.89	0.63831	.	0.414868	0.24111	N	0.041444	T	0.73923	0.3649	N	0.08118	0	0.45097	D	0.998111	D;D;D	0.89917	0.997;0.999;1.0	P;P;D	0.67548	0.798;0.874;0.952	T	0.77851	-0.2434	10	0.87932	D	0	.	10.5898	0.45304	0.0:0.0:0.699:0.301	.	691;401;232	Q9C0C4;Q6P5A5;Q71RG3	SEM4C_HUMAN;.;.	W	691	ENSP00000306844:R691W	ENSP00000306844:R691W	R	-	1	2	SEMA4C	96890521	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.946000	0.56644	2.531000	0.85337	0.561000	0.74099	CGG	.	.	.	none		0.687	SEMA4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252957.1	NM_017789		A	97526794	G	A	97526794	3	1	232	1	0	0	0	0	1	0	0	0	14046	1086	38	1	434	1	SEMA4C	2	97526794	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	27338169	97526794	145672579	8	14072											
TTL	150465	hgsc.bcm.edu	37	chr2	113260608	113260609	+	Frame_Shift_Del	DEL	AT	AT	-																															caaaacctgccatttgaccaAtcactgcattcaaaaagagt																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr2:113260608_113260609delAT	ENST00000233336.6	+	5	916_917	c.725_726delAT	c.(724-726)aatfs	p.N242fs		NM_153712.4	NP_714923.1	Q8NG68	TTL_HUMAN	tubulin tyrosine ligase	242	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)|microtubule cytoskeleton organization (GO:0000226)|regulation of axon extension (GO:0030516)		ATP binding (GO:0005524)|tubulin-tyrosine ligase activity (GO:0004835)			breast(1)|large_intestine(2)|ovary(1)	4		Ovarian(717;0.024)		BRCA - Breast invasive adenocarcinoma(221;6.17e-07)|STAD - Stomach adenocarcinoma(1183;0.00644)		CATTTGACCAATCACTGCATTC	0.376			T	ETV6	ALL																																p.242_242del		Atlas-Indel,Pindel	.		Dom	yes		2	2q13	150465	tubulin tyrosine ligase		L	.	TTL	27	.	0			c.724_725del						PASS	.																																			SO:0001589	frameshift_variant	150465	exon5			.		CCDS2096.1	2q13	2010-04-21			ENSG00000114999	ENSG00000114999	6.3.2.25		21586	protein-coding gene	gene with protein product		608291				11431336	Standard	NM_153712		Approved	MGC46235	uc002thu.3	Q8NG68	OTTHUMG00000131316	ENST00000233336.6:c.725_726delAT	chr2.hg19:g.113260608_113260609delAT	ENSP00000233336:p.Asn242fs	130.0	0.0	0		123.0	33.0	0.268293	NM_153712	Q585T3|Q7Z302|Q8N426	Frame_Shift_Del	DEL	ENST00000233336.6	hg19	CCDS2096.1																																																																																			.	.	.	none		0.376	TTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254085.2	NM_153712		-	113260609	AT	-	113260608	7	5	232	1	0	1	0	1	0	0	0	0	16733	101	4	0	743	0	TTL	2	113260608	Frame_Shift_Del	DEL	AT	TCGA-P4-A5EA-01A-11D-A28G-10	15733814	113260608	129938765	9	14073											
GOLGA4	2803	hgsc.bcm.edu	37	chr3	37365077	37365078	+	Splice_Site	DEL	AG	AG	-																															tgcatctgtttttaattaacAgagaattcttgaattggaaa																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr3:37365077_37365078delAG	ENST00000361924.2	+	14	2075		c.e14-1		GOLGA4_ENST00000356847.4_Splice_Site|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4						Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						TTTAATTAACAGAGAATTCTTG	0.307																																					.		Atlas-Indel,Pindel	.											.	GOLGA4	173	.	0			.						PASS	.																																			SO:0001630	splice_region_variant	2803	.			.	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.1702-1AG>-	chr3.hg19:g.37365079_37365080delAG		141.0	0.0	0		128.0	33.0	0.257812	.	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Splice_Site	DEL	ENST00000361924.2	hg19	CCDS2666.1																																																																																			.	.	.	none		0.307	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078	Intron	-	37365078	AG	-	37365077	8	5	232	1	0	1	0	1	0	0	1	0	6562	202	7	0	1824	0	GOLGA4	3	37365077	Splice_Site	DEL	AG	TCGA-P4-A5EA-01A-11D-A28G-10		37365077	160657353	10	14074											
NFKBIZ	64332	hgsc.bcm.edu	37	chr3	101572345	101572345	+	Frame_Shift_Del	DEL	C	C	-																															tcccccgcttatgaaccaaaCctctttgatggtccagaatc																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr3:101572345delC	ENST00000326172.5	+	5	1090	c.975delC	c.(973-975)aacfs	p.N325fs	NFKBIZ_ENST00000394054.2_Frame_Shift_Del_p.N225fs|NFKBIZ_ENST00000326151.5_Intron	NM_031419.3	NP_113607.1	Q9BYH8	IKBZ_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta	325	Required for transcriptional activity. {ECO:0000250}.				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						ATGAACCAAACCTCTTTGATG	0.468																																					p.N325fs		Atlas-Indel,Pindel	.											.	NFKBIZ	55	.	0			c.974delA						PASS	.						128	124	125					3																	101572345		2203	4300	6503	SO:0001589	frameshift_variant	64332	exon5			.	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.975delC	chr3.hg19:g.101572345delC	ENSP00000325663:p.Asn325fs	93.0	0.0	0		91.0	17.0	0.186813	NM_031419	B3KNR2|D3DN54|Q8IUL4|Q8NAZ8	Frame_Shift_Del	DEL	ENST00000326172.5	hg19	CCDS2946.1																																																																																			.	.	.	none		0.468	NFKBIZ-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353793.1	NM_031419		-	101572345	C	-	101572345	7	5	232	1	0	1	0	1	0	0	0	0	10390	506	18	0	993	0	NFKBIZ	3	101572345	Frame_Shift_Del	DEL	C	TCGA-P4-A5EA-01A-11D-A28G-10	64207268	101572345	96450085	11	14075											
CD96	10225	hgsc.bcm.edu	37	chr3	111297955	111297955	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tacttaaagatagagtcaagCttggtacagactacagactc	15	10	8	8	0	1	4	1	0	0	4	2	4	1	4	0	1	4	2	0	1	7	6			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr3:111297955C>T	ENST00000283285.5	+	5	804	c.673C>T	c.(673-675)Ctt>Ttt	p.L225F	CD96_ENST00000438817.2_Missense_Mutation_p.L209F|CD96_ENST00000352690.4_Missense_Mutation_p.L209F	NM_198196.2	NP_937839.1	P40200	TACT_HUMAN	CD96 molecule	225	Ig-like V-type 2.				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						TAGAGTCAAGCTTGGTACAGA	0.423									Opitz Trigonocephaly syndrome																												p.L225F		Atlas-SNP	.											.	CD96	75	.	0			c.C673T						PASS	.						120	108	112					3																	111297955		2203	4300	6503	SO:0001583	missense	10225	exon5	Familial Cancer Database	C syndrome, Trigonocephaly syndrome	GTCAAGCTTGGTA	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.673C>T	chr3.hg19:g.111297955C>T	ENSP00000283285:p.Leu225Phe	178.0	0.0	.		178.0	14.0	.	NM_198196	Q5JPB3	Missense_Mutation	SNP	ENST00000283285.5	hg19	CCDS2959.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	5.734|5.734	0.319968|0.319968	0.10845|0.10845	.|.	.|.	ENSG00000153283|ENSG00000153283	ENST00000465428|ENST00000352690;ENST00000283285;ENST00000438817	.|T;T;T	.|0.73258	.|1.54;-0.73;1.54	5.18|5.18	1.28|1.28	0.21552|0.21552	.|Immunoglobulin subtype (1);	.|0.567715	.|0.14720	.|N	.|0.302408	T|T	0.59702|0.59702	0.2213|0.2213	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	1|1	.|P;P;P;P	.|0.44946	.|0.761;0.846;0.761;0.761	.|B;P;B;B	.|0.46585	.|0.322;0.521;0.443;0.322	T|T	0.50800|0.50800	-0.8785|-0.8785	5|10	.|0.51188	.|T	.|0.08	-0.8167|-0.8167	5.5178|5.5178	0.16916|0.16916	0.2453:0.5587:0.1213:0.0747|0.2453:0.5587:0.1213:0.0747	.|.	.|209;209;225;209	.|E9PEJ1;P40200-2;P40200;Q8WUE2	.|.;.;TACT_HUMAN;.	V|F	50|209;225;209	.|ENSP00000342040:L209F;ENSP00000283285:L225F;ENSP00000389801:L209F	.|ENSP00000283285:L225F	A|L	+|+	2|1	0|0	CD96|CD96	112780645|112780645	0.002000|0.002000	0.14202|0.14202	0.000000|0.000000	0.03702|0.03702	0.017000|0.017000	0.09413|0.09413	0.121000|0.121000	0.15667|0.15667	-0.203000|-0.203000	0.10251|0.10251	-1.886000|-1.886000	0.00541|0.00541	GCT|CTT	.	.	.	none		0.423	CD96-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354312.2			T	111297955	C	T	111297955	3	4	232	1	0	0	0	0	1	0	0	0	3050	797	28	2	691	2	CD96	3	111297955	Missense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	9725610	111297955	86724475	12	14076											
ZIC1	7545	hgsc.bcm.edu	37	chr3	147128794	147128794	+	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	acatccgcgtgcacacgggcGagaagccctttccctgcccc	7	6	10	18	4	0	1	0	0	0	1	2	2	2	1	5	1	3	1	5	1	1	1			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr3:147128794G>T	ENST00000282928.4	+	1	1624	c.895G>T	c.(895-897)Gag>Tag	p.E299*		NM_003412.3	NP_003403.2	Q15915	ZIC1_HUMAN	Zic family member 1	299					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						GCACACGGGCGAGAAGCCCTT	0.562																																					p.E299X		Atlas-SNP	.											.	ZIC1	141	.	0			c.G895T						PASS	.						91	94	93					3																	147128794		2203	4300	6503	SO:0001587	stop_gained	7545	exon1			ACGGGCGAGAAGC	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.895G>T	chr3.hg19:g.147128794G>T	ENSP00000282928:p.Glu299*	169.0	0.0	.		160.0	36.0	.	NM_003412	Q2M3N1	Nonsense_Mutation	SNP	ENST00000282928.4	hg19	CCDS3136.1	.	.	.	.	.	.	.	.	.	.	G	43	9.911065	0.99294	.	.	ENSG00000152977	ENST00000282928	.	.	.	3.89	3.89	0.44902	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.2006	0.82071	0.0:0.0:1.0:0.0	.	.	.	.	X	299	.	ENSP00000282928:E299X	E	+	1	0	ZIC1	148611484	1.000000	0.71417	0.997000	0.53966	0.889000	0.51656	7.528000	0.81941	1.862000	0.54008	0.561000	0.74099	GAG	.	.	.	none		0.562	ZIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355497.1	NM_003412		T	147128794	G	T	147128794	4	4	232	1	0	0	0	0	0	1	0	0	17690	1059	37	4	897	4	ZIC1	3	147128794	Nonsense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	35830839	147128794	50893636	13	14077											
MAEA	10296	hgsc.bcm.edu	37	chr4	1332242	1332242	+	Missense_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	ggaggacggcagctccaagaGccctgactgccctgtgtgca	8	6	14	13	1	0	2	0	1	0	1	1	4	1	4	3	3	4	3	3	3	1	0			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr4:1332242G>A	ENST00000303400.4	+	8	995	c.932G>A	c.(931-933)aGc>aAc	p.S311N	MAEA_ENST00000510794.1_Missense_Mutation_p.S310N|MAEA_ENST00000512289.1_3'UTR|MAEA_ENST00000505177.2_Missense_Mutation_p.S349N|MAEA_ENST00000452175.2_Missense_Mutation_p.S232N|MAEA_ENST00000264750.6_Missense_Mutation_p.S270N|MAEA_ENST00000514708.1_Missense_Mutation_p.S243N|MAEA_ENST00000505839.1_Missense_Mutation_p.S263N	NM_001017405.1	NP_001017405.1	Q7L5Y9	MAEA_HUMAN	macrophage erythroblast attacher	311					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)	AGCTCCAAGAGCCCTGACTGC	0.662																																					p.S311N		Atlas-SNP	.											.	MAEA	39	.	0			c.G932A						PASS	.						61	61	61					4																	1332242		2203	4300	6503	SO:0001583	missense	10296	exon8			CCAAGAGCCCTGA	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.932G>A	chr4.hg19:g.1332242G>A	ENSP00000302830:p.Ser311Asn	76.0	0.0	.		68.0	18.0	.	NM_001017405	O95285|Q5JB54|Q6ZRD6|Q9BQ11|Q9H9V6|Q9H9Z4|Q9NW84	Missense_Mutation	SNP	ENST00000303400.4	hg19	CCDS33936.1	.	.	.	.	.	.	.	.	.	.	G	7.811	0.715683	0.15306	.	.	ENSG00000090316	ENST00000303400;ENST00000505177;ENST00000264750;ENST00000382947;ENST00000539495;ENST00000452175;ENST00000514708;ENST00000510794;ENST00000505839	T;T;T;T;T;T;T	0.10763	2.84;2.84;2.84;2.84;2.84;2.84;2.84	5.41	4.44	0.53790	.	0.178095	0.64402	D	0.000005	T	0.04770	0.0129	N	0.20328	0.56	0.46260	D	0.998958	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.04013	0.0;0.001;0.0;0.001;0.0;0.0	T	0.34254	-0.9836	10	0.05959	T	0.93	-33.7543	3.5266	0.07761	0.3654:0.0:0.6346:0.0	.	310;349;97;243;270;311	B4DVN3;E7ESC7;B3KRN7;D6RIB6;Q7L5Y9-3;Q7L5Y9	.;.;.;.;.;MAEA_HUMAN	N	311;349;270;243;290;232;243;310;263	ENSP00000302830:S311N;ENSP00000422215:S349N;ENSP00000264750:S270N;ENSP00000411415:S232N;ENSP00000427512:S243N;ENSP00000426807:S310N;ENSP00000424436:S263N	ENSP00000264750:S270N	S	+	2	0	MAEA	1322242	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.331000	0.79192	2.531000	0.85337	0.655000	0.94253	AGC	.	.	.	none		0.662	MAEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359511.1	NM_005882		A	1332242	G	A	1332242	3	1	232	1	0	0	0	0	1	0	0	0	9160	971	34	2	962	2	MAEA	4	1332242	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10		1332242	189822034	14	14078											
TLL1	7092	hgsc.bcm.edu	37	chr4	166996130	166996130	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtaatggatttgtgctacaTgacaataaacatgattgcaa	15	12	8	6	1	0	2	0	2	0	0	0	3	0	3	0	1	4	3	0	1	6	5			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr4:166996130T>C	ENST00000061240.2	+	17	2936	c.2289T>C	c.(2287-2289)caT>caC	p.H763H	TLL1_ENST00000507499.1_Silent_p.H786H	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	763	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				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)		TTGTGCTACATGACAATAAAC	0.403																																					p.H763H		Atlas-SNP	.											.	TLL1	194	.	0			c.T2289C						PASS	.						296	244	262					4																	166996130		2203	4300	6503	SO:0001819	synonymous_variant	7092	exon17			GCTACATGACAAT	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.2289T>C	chr4.hg19:g.166996130T>C		223.0	0.0	.		161.0	18.0	.	NM_012464	B2RMU2|Q96AN3|Q9NQS4	Silent	SNP	ENST00000061240.2	hg19	CCDS3811.1																																																																																			.	.	.	none		0.403	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1			C	166996130	T	C	166996130	2	2	232	1	0	0	0	0	0	0	0	1	15957	1461	51	3		3	TLL1	4	166996130	Silent	SNP	T	TCGA-P4-A5EA-01A-11D-A28G-10	165663888	166996130	24158146	15	14079											
MAP3K1	4214	hgsc.bcm.edu	37	chr5	56183244	56183245	+	Frame_Shift_Ins	INS	-	-	TA																															agcactggtcagagactaagINSaattgcagattttggagctg																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr5:56183244_56183245insTA	ENST00000399503.3	+	18	4154_4155	c.4154_4155insTA	c.(4153-4158)agaattfs	p.RI1385fs		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	1385	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		CAGAGACTAAGAATTGCAGATT	0.421																																					p.R1385fs		Atlas-Indel,Pindel	.											.	MAP3K1	355	.	0			c.4154_4155insTA						PASS	.																																			SO:0001589	frameshift_variant	4214	exon18			.	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	Exception_encountered	chr5.hg19:g.56183244_56183245insTA	ENSP00000382423:p.Arg1385fs	130.0	0.0	0		116.0	15.0	0.12931	NM_005921		Frame_Shift_Ins	INS	ENST00000399503.3	hg19	CCDS43318.1																																																																																			.	.	.	none		0.421	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066		TA	56183245	-	TA	56183244	7	5	232	1	0	1	1	0	0	0	0	0	9250	942	33	0	4224	0	MAP3K1	5	56183244	Frame_Shift_Ins	INS	-	TCGA-P4-A5EA-01A-11D-A28G-10		56183244	124732016	16	14080											
FCHO2	115548	hgsc.bcm.edu	37	chr5	72359736	72359736	+	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	ggcctgcttccagaccaaagCttacttcaggcaaactcagt	11	9	8	13	0	2	1	2	0	0	1	3	1	3	1	3	2	4	3	3	2	3	3			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr5:72359736C>A	ENST00000430046.2	+	18	1530	c.1414C>A	c.(1414-1416)Ctt>Att	p.L472I	FCHO2_ENST00000341845.6_Missense_Mutation_p.L472I|FCHO2_ENST00000512348.1_Missense_Mutation_p.L439I	NM_001146032.1|NM_138782.2	NP_001139504.1|NP_620137.2	Q0JRZ9	FCHO2_HUMAN	FCH domain only 2	472	Ser-rich.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|membrane invagination (GO:0010324)|protein localization to plasma membrane (GO:0072659)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	17		Lung NSC(167;0.0465)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;4.6e-53)		CAGACCAAAGCTTACTTCAGG	0.403																																					p.L472I		Atlas-SNP	.											.	FCHO2	96	.	0			c.C1414A						PASS	.						65	61	62					5																	72359736		1850	4087	5937	SO:0001583	missense	115548	exon18			CCAAAGCTTACTT	AL831971	CCDS47230.1, CCDS54868.1	5q13.2	2005-08-15			ENSG00000157107	ENSG00000157107			25180	protein-coding gene	gene with protein product		613438				15254787	Standard	NM_138782		Approved		uc003kcl.3	Q0JRZ9	OTTHUMG00000162413	ENST00000430046.2:c.1414C>A	chr5.hg19:g.72359736C>A	ENSP00000393776:p.Leu472Ile	193.0	0.0	.		139.0	43.0	.	NM_138782	A8K6W7|B2RNQ9|B4DHK0|E9PG79|Q0JTJ3|Q96CF5	Missense_Mutation	SNP	ENST00000430046.2	hg19	CCDS47230.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.967806	0.74131	.	.	ENSG00000157107	ENST00000430046;ENST00000341845;ENST00000512348	T;T;T	0.39056	1.1;1.11;3.55	5.62	5.62	0.85841	.	0.164332	0.40728	N	0.001021	T	0.52933	0.1765	L	0.56769	1.78	0.41260	D	0.986778	D;D	0.67145	0.99;0.996	P;P	0.60415	0.76;0.874	T	0.43956	-0.9359	10	0.18710	T	0.47	-12.133	12.5234	0.56073	0.0:0.8806:0.0:0.1194	.	439;472	E9PG79;Q0JRZ9	.;FCHO2_HUMAN	I	472;472;439	ENSP00000393776:L472I;ENSP00000344034:L472I;ENSP00000427296:L439I	ENSP00000344034:L472I	L	+	1	0	FCHO2	72395492	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.706000	0.47135	2.637000	0.89404	0.650000	0.86243	CTT	.	.	.	none		0.403	FCHO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368795.3	XM_291142		A	72359736	C	A	72359736	3	1	232	1	0	0	0	0	1	0	0	0	5795	797	28	4	1484	4	FCHO2	5	72359736	Missense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	16176492	72359736	108555524	17	14081											
RASA1	5921	hgsc.bcm.edu	37	chr5	86564698	86564699	+	Frame_Shift_Del	DEL	CC	CC	-																															tgccccctcccccttacctgCcccctttgggggcgggcctc																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr5:86564698_86564699delCC	ENST00000274376.6	+	1	994_995	c.430_431delCC	c.(430-432)cccfs	p.P145fs	RASA1_ENST00000506290.1_5'Flank|RASA1_ENST00000456692.2_5'Flank|RASA1_ENST00000512763.1_5'Flank	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	145					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)		CCCTTACCTGCCCCCTTTGGGG	0.624																																					p.143_144del		Atlas-INDEL	.											.	RASA1	213	.	0			c.429_430del						PASS	.																																			SO:0001589	frameshift_variant	5921	exon1			.		CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	9871	protein-coding gene	gene with protein product	"capillary malformation-arteriovenous malformation"	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.430_431delCC	chr5.hg19:g.86564700_86564701delCC	ENSP00000274376:p.Pro145fs	38.0	0.0	0		35.0	12.0	0.342857	NM_002890	B2R6W3|Q9UDI1	Frame_Shift_Del	DEL	ENST00000274376.6	hg19	CCDS34200.1																																																																																			.	.	.	none		0.624	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890		-	86564699	CC	-	86564698	7	5	232	1	0	1	0	1	0	0	0	0	13073	739	26	0	432	0	RASA1	5	86564698	Frame_Shift_Del	DEL	CC	TCGA-P4-A5EA-01A-11D-A28G-10	14204962	86564698	94350562	18	14082											
ANKHD1-EIF4EBP3	8637	hgsc.bcm.edu	37	chr5	139928645	139928646	+	Frame_Shift_Del	DEL	AG	AG	-																															gagctgaaggagcaggagacAgaggaagagatacccggtaa																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr5:139928645_139928646delAG	ENST00000310331.2	+	2	330_331	c.258_259delAG	c.(256-261)acagagfs	p.E89fs	ANKHD1_ENST00000297183.6_Frame_Shift_Del_p.R2612fs|SRA1_ENST00000520427.1_5'Flank|ANKHD1-EIF4EBP3_ENST00000532219.1_Frame_Shift_Del_p.R2612fs	NM_003732.2	NP_003723.1	O60516	4EBP3_HUMAN	eukaryotic translation initiation factor 4E binding protein 3	89					negative regulation of translational initiation (GO:0045947)	eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	translation repressor activity (GO:0030371)			endometrium(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCAGGAGACAGAGGAAGAGAT	0.564																																					p.2611_2612del		Atlas-Indel,Pindel	.											.	ANKHD1-EIF4EBP3	179	.	0			c.7833_7834del						PASS	.																																			SO:0001589	frameshift_variant	404734	exon35			.	AF038869	CCDS4226.1	5q31.3	2007-07-18			ENSG00000243056	ENSG00000243056			3290	protein-coding gene	gene with protein product		603483				9593750	Standard	NM_003732		Approved	4E-BP3	uc003lfy.1	O60516	OTTHUMG00000129498	ENST00000310331.2:c.258_259delAG	chr5.hg19:g.139928647_139928648delAG	ENSP00000308472:p.Glu89fs	124.0	0.0	0		87.0	12.0	0.137931	NM_020690		Frame_Shift_Del	DEL	ENST00000310331.2	hg19	CCDS4226.1																																																																																			.	.	.	none		0.564	EIF4EBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251668.2	NM_003732		-	139928646	AG	-	139928645	7	5	232	1	0	1	0	1	0	0	0	0	629	180	7	0	7972	0	ANKHD1-EIF4EBP3	5	139928645	Frame_Shift_Del	DEL	AG	TCGA-P4-A5EA-01A-11D-A28G-10	53363947	139928645	40986615	19	14083											
PCDHB5	26167	hgsc.bcm.edu	37	chr5	140515133	140515134	+	Frame_Shift_Del	DEL	AG	AG	-																															tattccataccagaagaaacAgaaagtggctattctgtggc																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr5:140515133_140515134delAG	ENST00000231134.5	+	1	334_335	c.117_118delAG	c.(115-120)acagaafs	p.E40fs		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	40	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CAGAAGAAACAGAAAGTGGCTA	0.49																																					p.39_39del		Atlas-INDEL	.											.	PCDHB5	184	.	0			c.116_117del						PASS	.																																			SO:0001589	frameshift_variant	26167	exon1			.	AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"Cadherins / Protocadherins : Clustered"	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.117_118delAG	chr5.hg19:g.140515133_140515134delAG	ENSP00000231134:p.Glu40fs	141.0	0.0	0		102.0	11.0	0.107843	NM_015669	Q549F4|Q9UFU9	Frame_Shift_Del	DEL	ENST00000231134.5	hg19	CCDS4247.1																																																																																			.	.	.	none		0.49	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669		-	140515134	AG	-	140515133	7	5	232	1	0	1	0	1	0	0	0	0	11552	175	7	0	119	0	PCDHB5	5	140515133	Frame_Shift_Del	DEL	AG	TCGA-P4-A5EA-01A-11D-A28G-10	586488	140515133	40400127	20	14084											
MTRF1L	54516	hgsc.bcm.edu	37	chr6	153315714	153315714	+	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	acgcggccttgcttttctgtCtttggcactctttgtactct	3	18	8	12	2	4	0	0	0	4	0	4	0	4	0	1	2	2	3	1	2	1	6			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr6:153315714C>G	ENST00000367233.5	-	4	620	c.621G>C	c.(619-621)aaG>aaC	p.K207N	MTRF1L_ENST00000464135.1_5'UTR|MTRF1L_ENST00000367231.5_Missense_Mutation_p.K207N|MTRF1L_ENST00000367230.1_Missense_Mutation_p.K171N	NM_019041.5	NP_061914.3	Q9UGC7	RF1ML_HUMAN	mitochondrial translational release factor 1-like	207						mitochondrion (GO:0005739)	translation release factor activity, codon specific (GO:0016149)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	10		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.24e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0888)		GCTTTTCTGTCTTTGGCACTC	0.502																																					p.K207N		Atlas-SNP	.											.	MTRF1L	21	.	0			c.G621C						PASS	.						164	143	150					6																	153315714		2203	4300	6503	SO:0001583	missense	54516	exon4			TTCTGTCTTTGGC	BC011873	CCDS5243.1, CCDS47502.1, CCDS75540.1	6q25-q26	2008-02-05			ENSG00000112031	ENSG00000112031			21051	protein-coding gene	gene with protein product		613542					Standard	NM_019041		Approved		uc003qpi.4	Q9UGC7	OTTHUMG00000015857	ENST00000367233.5:c.621G>C	chr6.hg19:g.153315714C>G	ENSP00000356202:p.Lys207Asn	113.0	0.0	.		112.0	14.0	.	NM_019041	B3KTA0|Q3KR06|Q5TF44|Q5TF50|Q96CC5|Q96EX4|Q96K40	Missense_Mutation	SNP	ENST00000367233.5	hg19	CCDS5243.1	.	.	.	.	.	.	.	.	.	.	C	18.15	3.560810	0.65538	.	.	ENSG00000112031	ENST00000367233;ENST00000367231;ENST00000367230;ENST00000414771;ENST00000448966	T;T;T;T;T	0.11604	2.76;2.76;2.76;2.76;2.76	4.97	3.11	0.35812	.	0.096199	0.64402	D	0.000001	T	0.18718	0.0449	M	0.78801	2.425	0.40959	D	0.984603	D;D;D;D	0.89917	0.999;0.999;1.0;1.0	D;D;D;D	0.76071	0.964;0.973;0.987;0.974	T	0.01102	-1.1451	10	0.56958	D	0.05	-12.0679	8.928	0.35652	0.0:0.7454:0.0:0.2546	.	171;207;171;207	B4DMX1;Q9UGC7-2;Q9UGC7-4;Q9UGC7	.;.;.;RF1ML_HUMAN	N	207;207;171;58;71	ENSP00000356202:K207N;ENSP00000356200:K207N;ENSP00000356199:K171N;ENSP00000414383:K58N;ENSP00000415113:K71N	ENSP00000356199:K171N	K	-	3	2	MTRF1L	153357407	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	1.344000	0.33941	0.558000	0.29135	0.585000	0.79938	AAG	.	.	.	none		0.502	MTRF1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042764.1	NM_019041		G	153315714	C	G	153315714	3	3	232	1	0	0	0	0	1	0	0	0	9967	912	32	4	537	4	MTRF1L	6	153315714	Missense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10		153315714	17799353	21	14085											
AUTS2	26053	hgsc.bcm.edu	37	chr7	70231266	70231266	+	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	caccagcacaccttcacgccGttcccccacgccatcccacc	8	5	4	24	3	1	0	1	0	0	0	3	0	3	0	8	0	1	2	8	0	0	2			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr7:70231266G>A	ENST00000342771.4	+	9	1956	c.1635G>A	c.(1633-1635)ccG>ccA	p.P545P	AUTS2_ENST00000406775.2_Silent_p.P545P	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	545	His-rich.									breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		cCTTCACGCCGTTCCCCCACG	0.642																																					p.P545P		Atlas-SNP	.											.	AUTS2	173	.	0			c.G1635A						PASS	.						278	255	263					7																	70231266		2203	4300	6503	SO:0001819	synonymous_variant	26053	exon9			CACGCCGTTCCCC	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.1635G>A	chr7.hg19:g.70231266G>A		63.0	0.0	.		90.0	31.0	.	NM_001127231	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Silent	SNP	ENST00000342771.4	hg19	CCDS5539.1	.	.	.	.	.	.	.	.	.	.	G	10.81	1.455200	0.26161	.	.	ENSG00000158321	ENST00000443672	.	.	.	5.56	-2.87	0.05700	.	.	.	.	.	T	0.50343	0.1610	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45131	-0.9282	4	.	.	.	-11.6373	6.7468	0.23466	0.1273:0.5083:0.2255:0.1389	.	.	.	.	H	87	.	.	R	+	2	0	AUTS2	69869202	0.862000	0.29867	0.976000	0.42696	0.997000	0.91878	-0.056000	0.11787	-0.475000	0.06852	0.561000	0.74099	CGT	.	.	.	none		0.642	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			A	70231266	G	A	70231266	2	1	232	1	0	0	0	0	0	0	0	1	1225	1132	40	1		1	AUTS2	7	70231266	Silent	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10		70231266	88907397	22	14086											
ZNF7	7553	hgsc.bcm.edu	37	chr8	146066868	146066869	+	Frame_Shift_Del	DEL	TC	TC	-																															atcctggctttggagacgttTctgattctgaggtctggtta																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr8:146066868_146066869delTC	ENST00000528372.1	+	5	616_617	c.376_377delTC	c.(376-378)tctfs	p.S126fs	ZNF7_ENST00000532393.1_3'UTR|ZNF7_ENST00000525266.1_Intron|ZNF7_ENST00000325241.6_Frame_Shift_Del_p.S126fs|ZNF7_ENST00000325217.5_Intron|ZNF7_ENST00000544249.1_Frame_Shift_Del_p.S30fs|ZNF7_ENST00000446747.2_Frame_Shift_Del_p.S137fs|ZNF7_ENST00000529819.1_Intron			P17097	ZNF7_HUMAN	zinc finger protein 7	126					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(5)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)		TGGAGACGTTTCTGATTCTGAG	0.485																																					p.125_126del		Atlas-INDEL	.											.	ZNF7	62	.	0			c.375_376del						PASS	.																																			SO:0001589	frameshift_variant	7553	exon5			.	AB209619	CCDS6435.1, CCDS64996.1, CCDS64998.1, CCDS64999.1	8q24	2013-01-08	2006-05-09		ENSG00000147789	ENSG00000147789		"Zinc fingers, C2H2-type", "-"	13139	protein-coding gene	gene with protein product		194531	"zinc finger protein 7 (KOX 4, clone HF.16)"			2106481, 1946370	Standard	NM_003416		Approved	KOX4, HF.16	uc003zeg.4	P17097	OTTHUMG00000165200	ENST00000528372.1:c.376_377delTC	chr8.hg19:g.146066868_146066869delTC	ENSP00000432724:p.Ser126fs	88.0	0.0	0		86.0	10.0	0.116279	NM_003416	B4DT08|D3DWN6|P17015|Q8N8Y4	Frame_Shift_Del	DEL	ENST00000528372.1	hg19	CCDS6435.1																																																																																			.	.	.	none		0.485	ZNF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382660.1	NM_003416		-	146066869	TC	-	146066868	7	5	232	1	0	1	0	1	0	0	0	0	18114	1783	62	0	390	0	ZNF7	8	146066868	Frame_Shift_Del	DEL	TC	TCGA-P4-A5EA-01A-11D-A28G-10		146066868	297154	23	14087											
CAMK1D	57118	hgsc.bcm.edu	37	chr10	12856228	12856228	+	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	ctcctttttatgatgaaaatGactccaagctctttgagcag	11	14	7	9	0	1	4	0	4	1	0	3	4	3	4	2	0	2	2	2	0	4	4			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr10:12856228G>A	ENST00000378847.3	+	7	1013	c.676G>A	c.(676-678)Gac>Aac	p.D226N	CAMK1D_ENST00000378845.1_Missense_Mutation_p.D226N	NM_153498.2	NP_705718.1	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID	226	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				inflammatory response (GO:0006954)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis (GO:0050766)|positive regulation of respiratory burst (GO:0060267)|regulation of dendrite development (GO:0050773)|regulation of granulocyte chemotaxis (GO:0071622)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)	16				GBM - Glioblastoma multiforme(1;3.16e-05)		TGATGAAAATGACTCCAAGCT	0.483																																					p.D226N		Atlas-SNP	.											.	CAMK1D	99	.	0			c.G676A						PASS	.						101	90	94					10																	12856228		2203	4300	6503	SO:0001583	missense	57118	exon7			GAAAATGACTCCA	AF286366	CCDS7091.1, CCDS7092.1	10p13	2003-11-05			ENSG00000183049	ENSG00000183049			19341	protein-coding gene	gene with protein product		607957				11050006	Standard	XM_006717481		Approved	CKLiK	uc001ilo.3	Q8IU85	OTTHUMG00000017683	ENST00000378847.3:c.676G>A	chr10.hg19:g.12856228G>A	ENSP00000368124:p.Asp226Asn	73.0	0.0	.		99.0	10.0	.	NM_153498	B0YIY0|Q9HD31	Missense_Mutation	SNP	ENST00000378847.3	hg19	CCDS7091.1	.	.	.	.	.	.	.	.	.	.	G	31	5.064215	0.93898	.	.	ENSG00000183049	ENST00000378847;ENST00000378845	T;T	0.65364	-0.15;-0.15	5.46	5.46	0.80206	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.70011	0.3175	L	0.35723	1.085	0.80722	D	1	D;B	0.54047	0.964;0.267	D;B	0.63703	0.917;0.344	T	0.68907	-0.5285	10	0.42905	T	0.14	-37.1453	16.7965	0.85603	0.0:0.0:1.0:0.0	.	226;226	Q8IU85;Q5SQQ7	KCC1D_HUMAN;.	N	226	ENSP00000368124:D226N;ENSP00000368122:D226N	ENSP00000368122:D226N	D	+	1	0	CAMK1D	12896234	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.517000	0.98020	2.556000	0.86216	0.555000	0.69702	GAC	.	.	.	none		0.483	CAMK1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046820.1	NM_020397		A	12856228	G	A	12856228	3	1	232	1	0	0	0	0	1	0	0	0	2599	1290	45	2	702	2	CAMK1D	10	12856228	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10		12856228	122678519	24	14088											
KCNQ1	3784	hgsc.bcm.edu	37	chr11	2466535	2466535	+	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	ccccctgcgtccccggccgcGcccgccgcgcccccagttgc	1	4	11	25	7	0	0	0	0	0	0	1	0	1	0	9	1	2	1	9	1	0	1	rs587781009		TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr11:2466535G>T	ENST00000155840.5	+	1	315	c.207G>T	c.(205-207)gcG>gcT	p.A69A		NM_000218.2	NP_000209.2	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 1	69					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)	ccccggccgcgcccgccgcgc	0.811																																					p.A69A		Atlas-SNP	.											.	KCNQ1	60	.	0			c.G207T						PASS	.						3	4	3					11																	2466535		1287	2827	4114	SO:0001819	synonymous_variant	3784	exon1			GGCCGCGCCCGCC	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.207G>T	chr11.hg19:g.2466535G>T		0.0	0.0	.		4.0	4.0	.	NM_000218	O00347|O60607|O94787|Q14D14|Q7Z6G9|Q92960|Q9UMN8|Q9UMN9	Silent	SNP	ENST00000155840.5	hg19	CCDS7736.1																																																																																			.	.	.	none		0.811	KCNQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027382.2	NM_000218		T	2466535	G	T	2466535	2	4	232	1	0	0	0	0	0	0	0	1	8089	1074	38	4		4	KCNQ1	11	2466535	Silent	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10		2466535	132539981	25	14089											
TRIM68	55128	hgsc.bcm.edu	37	chr11	4621750	4621750	+	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	ggtactcatcggtgcctgctCggtactcatttcccttcctc	4	14	8	15	2	2	0	2	0	0	0	7	0	4	0	3	3	4	3	3	3	2	4			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr11:4621750C>T	ENST00000300747.5	-	7	1503	c.1214G>A	c.(1213-1215)cGa>cAa	p.R405Q		NM_018073.6	NP_060543.5	Q6AZZ1	TRI68_HUMAN	tripartite motif containing 68	405	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein autoubiquitination (GO:0051865)|regulation of androgen receptor signaling pathway (GO:0060765)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|histone acetyltransferase binding (GO:0035035)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|urinary_tract(1)	15		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;9.49e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)		GGTGCCTGCTCGGTACTCATT	0.517																																					p.R405Q		Atlas-SNP	.											.	TRIM68	53	.	0			c.G1214A						PASS	.						100	84	89					11																	4621750		2201	4298	6499	SO:0001583	missense	55128	exon7			CCTGCTCGGTACT	AF360739	CCDS31356.1	11p15.4	2013-01-09	2011-01-25	2004-11-17		ENSG00000167333		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	21161	protein-coding gene	gene with protein product		613184	"ring finger protein 137", "tripartite motif-containing 68"	RNF137		11597395	Standard	NM_018073		Approved	SS-56, FLJ10369	uc001lzf.2	Q6AZZ1		ENST00000300747.5:c.1214G>A	chr11.hg19:g.4621750C>T	ENSP00000300747:p.Arg405Gln	196.0	0.0	.		164.0	35.0	.	NM_018073	A6NI19|A8K551|B3KPM5|B4DVK4|Q8WZ70|Q96LE5|Q96PF7|Q9H9C2|Q9NW18	Missense_Mutation	SNP	ENST00000300747.5	hg19	CCDS31356.1	.	.	.	.	.	.	.	.	.	.	C	17.78	3.473848	0.63737	.	.	ENSG00000167333	ENST00000300747;ENST00000544055	T	0.68181	-0.31	4.99	0.918	0.19386	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.160187	0.29932	N	0.010838	T	0.44582	0.1300	L	0.33753	1.03	0.28223	N	0.926426	P	0.34837	0.472	B	0.34824	0.19	T	0.23762	-1.0179	10	0.12766	T	0.61	.	3.2819	0.06918	0.1772:0.4704:0.0:0.3524	.	405	Q6AZZ1	TRI68_HUMAN	Q	405;126	ENSP00000300747:R405Q	ENSP00000300747:R405Q	R	-	2	0	TRIM68	4578326	0.000000	0.05858	0.996000	0.52242	0.995000	0.86356	-0.456000	0.06754	0.351000	0.24027	0.561000	0.74099	CGA	.	.	.	none		0.517	TRIM68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385948.1	NM_018073		T	4621750	C	T	4621750	3	4	232	1	0	0	0	0	1	0	0	0	16553	884	31	1	247	1	TRIM68	11	4621750	Missense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	2155215	4621750	130384766	26	14090											
AHNAK	79026	hgsc.bcm.edu	37	chr11	62285795	62285796	+	Frame_Shift_Del	DEL	AG	AG	-																															cctgcaggcttggtcccctcAgtgtcacatctggtgcccca																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr11:62285795_62285796delAG	ENST00000378024.4	-	5	16367_16368	c.16093_16094delCT	c.(16093-16095)ctgfs	p.L5365fs	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000525875.1_5'Flank	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	5365					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)				TGGTCCCCTCAGTGTCACATCT	0.545																																					p.5365_5365del		Atlas-INDEL	.											.	AHNAK	532	.	0			c.16094_16095del						PASS	.																																			SO:0001589	frameshift_variant	79026	exon5			.	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"desmoyokin"	103390	"AHNAK nucleoprotein (desmoyokin)"			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.16093_16094delCT	chr11.hg19:g.62285795_62285796delAG	ENSP00000367263:p.Leu5365fs	177.0	0.0	0		151.0	16.0	0.10596	NM_001620	A1A586	Frame_Shift_Del	DEL	ENST00000378024.4	hg19	CCDS31584.1																																																																																			.	.	.	none		0.545	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		-	62285796	AG	-	62285795	7	5	232	1	0	1	0	1	0	0	0	0	414	188	7	0	1698	0	AHNAK	11	62285795	Frame_Shift_Del	DEL	AG	TCGA-P4-A5EA-01A-11D-A28G-10	57664045	62285795	72720721	27	14091											
MTA2	9219	hgsc.bcm.edu	37	chr11	62364175	62364176	+	Frame_Shift_Del	DEL	CT	CT	-																															gcctcctcaaatagcatggcCtctgaggctgaccattcctc																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr11:62364175_62364176delCT	ENST00000278823.2	-	9	1204_1205	c.815_816delAG	c.(814-816)gagfs	p.E272fs	MTA2_ENST00000524902.1_Frame_Shift_Del_p.E99fs|MTA2_ENST00000527204.1_Frame_Shift_Del_p.E99fs	NM_004739.3	NP_004730.2	O94776	MTA2_HUMAN	metastasis associated 1 family, member 2	272	SANT. {ECO:0000255|PROSITE- ProRule:PRU00624}.				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						ATAGCATGGCCTCTGAGGCTGA	0.55																																					p.272_273del		Atlas-Indel,Pindel	.											.	MTA2	54	.	0			c.816_817del						PASS	.																																			SO:0001589	frameshift_variant	9219	exon9			.	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.815_816delAG	chr11.hg19:g.62364177_62364178delCT	ENSP00000278823:p.Glu272fs	128.0	0.0	0		134.0	24.0	0.179104	NM_004739	Q68DB1|Q9UQB5	Frame_Shift_Del	DEL	ENST00000278823.2	hg19	CCDS8022.1																																																																																			.	.	.	none		0.55	MTA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395578.1	NM_004739		-	62364176	CT	-	62364175	7	5	232	1	0	1	0	1	0	0	0	0	9916	680	24	0	1230	0	MTA2	11	62364175	Frame_Shift_Del	DEL	CT	TCGA-P4-A5EA-01A-11D-A28G-10	78380	62364175	72642341	28	14092											
ZNHIT2	741	hgsc.bcm.edu	37	chr11	64884755	64884755	+	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	accaccacggccgccatggaGgcagcagccgcccggcctca	8	2	12	19	4	1	0	1	0	0	0	1	1	1	1	7	4	2	2	7	4	0	0	rs200126440		TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr11:64884755G>A	ENST00000310597.4	-	1	415	c.371C>T	c.(370-372)cCt>cTt	p.P124L	AP003068.12_ENST00000527789.1_RNA	NM_014205.2	NP_055020.1	Q9UHR6	ZNHI2_HUMAN	zinc finger, HIT-type containing 2	124							metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(2)|lung(1)|urinary_tract(1)	6						CCGCCATGGAGGCAGCAGCCG	0.731													G|||	1	0.000199681	0	0	5008	,	,		11861	0		0.001	False		,,,				2504	0				p.P124L		Atlas-SNP	.											.	ZNHIT2	12	.	0			c.C371T						PASS	.	G	LEU/PRO	0,3516		0,0,1758	6	8	7		371	4.6	1	11		7	3,7301		0,3,3649	no	missense	ZNHIT2	NM_014205.2	98	0,3,5407	AA,AG,GG		0.0411,0.0,0.0277	probably-damaging	124/404	64884755	3,10817	1758	3652	5410	SO:0001583	missense	741	exon1			CATGGAGGCAGCA		CCDS8094.1	11q13	2012-08-08	2010-09-15	2004-07-14	ENSG00000174276	ENSG00000174276		"Zinc fingers, HIT-type"	1177	protein-coding gene	gene with protein product		604575	"chromosome 11 open reading frame 5", "zinc finger, HIT domain containing 2"	C11orf5			Standard	NM_014205		Approved	FON	uc001ocw.3	Q9UHR6	OTTHUMG00000165604	ENST00000310597.4:c.371C>T	chr11.hg19:g.64884755G>A	ENSP00000308548:p.Pro124Leu	1.0	0.0	.		13.0	8.0	.	NM_014205	Q3SY14|Q8IUV0	Missense_Mutation	SNP	ENST00000310597.4	hg19	CCDS8094.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.129799	0.77549	0.0	4.11E-4	ENSG00000174276	ENST00000310597	T	0.34472	1.36	4.55	4.55	0.56014	.	0.142165	0.47455	U	0.000232	T	0.59959	0.2232	M	0.74881	2.28	0.53005	D	0.999966	D	0.89917	1.0	D	0.83275	0.996	T	0.64757	-0.6332	10	0.72032	D	0.01	-12.5655	14.8345	0.70172	0.0:0.0:1.0:0.0	.	124	Q9UHR6	ZNHI2_HUMAN	L	124	ENSP00000308548:P124L	ENSP00000308548:P124L	P	-	2	0	ZNHIT2	64641331	0.995000	0.38212	0.958000	0.39756	0.786000	0.44442	2.667000	0.46808	2.366000	0.80165	0.561000	0.74099	CCT	.	.	.	weak		0.731	ZNHIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385260.1	NM_014205		A	64884755	G	A	64884755	3	1	232	1	0	0	0	0	1	0	0	0	18219	1000	35	2	844	2	ZNHIT2	11	64884755	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	2520580	64884755	70121761	29	14093											
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117352683	117352683	+	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	ggtgggggtgctcaccttcaGtgtggagacgacctcgtcgc	5	9	16	11	3	2	1	2	0	0	1	4	3	2	1	2	4	1	1	2	4	0	1			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr11:117352683G>C	ENST00000321322.6	-	12	2735	c.2734C>G	c.(2734-2736)Ctg>Gtg	p.L912V	DSCAML1_ENST00000527706.1_Missense_Mutation_p.L642V	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	852	Fibronectin type-III 1. {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)		CTCACCTTCAGTGTGGAGACG	0.622																																					p.L912V		Atlas-SNP	.											.	DSCAML1	286	.	0			c.C2734G						PASS	.						104	73	84					11																	117352683		2201	4296	6497	SO:0001583	missense	57453	exon12			CCTTCAGTGTGGA		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.2734C>G	chr11.hg19:g.117352683G>C	ENSP00000315465:p.Leu912Val	110.0	0.0	.		97.0	33.0	.	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	hg19	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	G	13.98	2.397882	0.42512	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.73681	-0.77;-0.77	3.89	2.97	0.34412	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.85111	0.5622	M	0.83118	2.625	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.85651	0.1282	9	0.62326	D	0.03	.	11.2591	0.49071	0.09:0.0:0.91:0.0	.	852	Q8TD84	DSCL1_HUMAN	V	642;912;619	ENSP00000434335:L642V;ENSP00000315465:L912V	ENSP00000315465:L912V	L	-	1	2	DSCAML1	116857893	1.000000	0.71417	0.934000	0.37439	0.083000	0.17756	4.754000	0.62191	0.844000	0.35094	0.485000	0.47835	CTG	.	.	.	none		0.622	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		C	117352683	G	C	117352683	3	2	232	1	0	0	0	0	1	0	0	0	4771	1020	36	4	3695	4	DSCAML1	11	117352683	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	52467928	117352683	17653833	30	14094											
IL10RA	3587	hgsc.bcm.edu	37	chr11	117869470	117869470	+	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	cttcatcttcatcagccagcGtccctccccagagacccaag	9	8	6	18	1	4	1	3	0	1	1	6	2	6	1	5	0	2	0	5	0	1	2	rs576666901	byFrequency	TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr11:117869470G>T	ENST00000227752.3	+	7	971	c.851G>T	c.(850-852)cGt>cTt	p.R284L	IL10RA_ENST00000545409.1_Missense_Mutation_p.R135L|IL10RA_ENST00000541785.1_Missense_Mutation_p.R264L|IL10RA_ENST00000533700.1_3'UTR	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	284					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)		ATCAGCCAGCGTCCCTCCCCA	0.582																																					p.R284L		Atlas-SNP	.											.	IL10RA	46	.	0			c.G851T						PASS	.						90	73	79					11																	117869470		2200	4296	6496	SO:0001583	missense	3587	exon7			GCCAGCGTCCCTC	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.851G>T	chr11.hg19:g.117869470G>T	ENSP00000227752:p.Arg284Leu	122.0	0.0	.		115.0	18.0	.	NM_001558	A8K6I0|B0YJ27	Missense_Mutation	SNP	ENST00000227752.3	hg19	CCDS8388.1	.	.	.	.	.	.	.	.	.	.	G	8.140	0.784909	0.16189	.	.	ENSG00000110324	ENST00000227752;ENST00000541785;ENST00000545409;ENST00000536858	T;T;T	0.23950	1.88;1.88;1.88	5.26	-3.16	0.05217	.	4.015810	0.00166	N	0.000015	T	0.07052	0.0179	N	0.01267	-0.92	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.20505	-1.0273	10	0.10377	T	0.69	-0.0195	1.5109	0.02496	0.1162:0.2378:0.2516:0.3945	.	264;284	F5GYV8;Q13651	.;I10R1_HUMAN	L	284;264;135;264	ENSP00000227752:R284L;ENSP00000441397:R264L;ENSP00000443019:R135L	ENSP00000227752:R284L	R	+	2	0	IL10RA	117374680	0.000000	0.05858	0.000000	0.03702	0.289000	0.27227	-1.174000	0.03105	-0.149000	0.11215	-0.457000	0.05445	CGT	.	.	.	none		0.582	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1			T	117869470	G	T	117869470	3	4	232	1	0	0	0	0	1	0	0	0	7627	1145	40	4	877	4	IL10RA	11	117869470	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	516787	117869470	17137046	31	14095											
OR8D1	283159	hgsc.bcm.edu	37	chr11	124180084	124180085	+	Frame_Shift_Del	DEL	GT	GT	-																															aaaagtagaagctcattgagGtgtgtgttggagcaggagag																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr11:124180084_124180085delGT	ENST00000357821.2	-	1	648_649	c.578_579delAC	c.(577-579)cacfs	p.H193fs		NM_001002917.1	NP_001002917.1	Q8WZ84	OR8D1_HUMAN	olfactory receptor, family 8, subfamily D, member 1	193						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H193Q(1)		kidney(1)|large_intestine(1)|lung(7)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0528)		GCTCATTGAGGTGTGTGTTGGA	0.46																																					p.193_194del		Atlas-Indel,Pindel	.											.	OR8D1	53	.	1	Substitution - Missense(1)	ovary(1)	c.579_580del						PASS	.																																			SO:0001589	frameshift_variant	283159	exon1			.	AF238489	CCDS31706.1	11q25	2012-08-09			ENSG00000196341	ENSG00000196341		"GPCR / Class A : Olfactory receptors"	8481	protein-coding gene	gene with protein product				OR8D3			Standard	NM_001002917		Approved	OST004	uc010sag.2	Q8WZ84	OTTHUMG00000165977	ENST00000357821.2:c.578_579delAC	chr11.hg19:g.124180090_124180091delGT	ENSP00000350474:p.His193fs	198.0	0.0	0		214.0	45.0	0.21028	NM_001002917	B2RNL4|Q6IEW1|Q8NGH0	Frame_Shift_Del	DEL	ENST00000357821.2	hg19	CCDS31706.1																																																																																			.	.	.	none		0.46	OR8D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387285.1	NM_001002917		-	124180085	GT	-	124180084	7	5	232	1	0	1	0	1	0	0	0	0	11238	1252	44	0	350	0	OR8D1	11	124180084	Frame_Shift_Del	DEL	GT	TCGA-P4-A5EA-01A-11D-A28G-10	6310614	124180084	10826432	32	14096											
LRRK2	120892	hgsc.bcm.edu	37	chr12	40742258	40742261	+	Frame_Shift_Del	DEL	TTAA	TTAA	-																															catggcctatggttgagaaaTtaattaaacagtgtttgaaa																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	TTAA	TTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr12:40742258_40742261delTTAA	ENST00000298910.7	+	43	6386_6389	c.6328_6331delTTAA	c.(6328-6333)ttaattfs	p.LI2110fs		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	2110	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				GGTTGAGAAATTAATTAAACAGTG	0.314																																					p.2109_2110del		Pindel	.											.	LRRK2	763	.	0			c.6327_6330del						PASS	.																																			SO:0001589	frameshift_variant	120892	exon43			.	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.6328_6331delTTAA	chr12.hg19:g.40742262_40742265delTTAA	ENSP00000298910:p.Leu2110fs	200.0	0.0	.		143.0	10.0	0.070	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Frame_Shift_Del	DEL	ENST00000298910.7	hg19	CCDS31774.1																																																																																			.	.	.	none		0.314	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		-	40742261	TTAA	-	40742258	7	5	232	1	0	1	0	1	0	0	0	0	9040	1490	52	0	6498	0	LRRK2	12	40742258	Frame_Shift_Del	DEL	TTAA	TCGA-P4-A5EA-01A-11D-A28G-10		40742258	93109637	33	14097											
UTP20	27340	hgsc.bcm.edu	37	chr12	101720912	101720912	+	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	gagtaaaactcaggggaaatCtgcttcaggcacccgcatgg	12	7	12	10	1	3	0	2	0	1	0	3	2	3	1	1	4	2	4	1	4	3	2			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr12:101720912C>A	ENST00000261637.4	+	26	3269	c.3095C>A	c.(3094-3096)tCt>tAt	p.S1032Y		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	1032					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						CAGGGGAAATCTGCTTCAGGC	0.453																																					p.S1032Y		Atlas-SNP	.											.	UTP20	222	.	0			c.C3095A						PASS	.						103	103	103					12																	101720912		2203	4300	6503	SO:0001583	missense	27340	exon26			GGAAATCTGCTTC	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.3095C>A	chr12.hg19:g.101720912C>A	ENSP00000261637:p.Ser1032Tyr	90.0	0.0	.		82.0	13.0	.	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	hg19	CCDS9081.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.501228	0.85176	.	.	ENSG00000120800	ENST00000261637	T	0.20881	2.04	5.02	5.02	0.67125	Down-regulated-in-metastasis protein (1);Armadillo-type fold (1);	0.112147	0.64402	D	0.000007	T	0.45637	0.1352	M	0.63843	1.955	0.58432	D	0.999997	D	0.89917	1.0	D	0.77557	0.99	T	0.33624	-0.9861	10	0.49607	T	0.09	-16.674	18.7119	0.91661	0.0:1.0:0.0:0.0	.	1032	O75691	UTP20_HUMAN	Y	1032	ENSP00000261637:S1032Y	ENSP00000261637:S1032Y	S	+	2	0	UTP20	100245043	0.999000	0.42202	0.997000	0.53966	0.758000	0.43043	7.357000	0.79456	2.491000	0.84063	0.305000	0.20034	TCT	.	.	.	none		0.453	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		A	101720912	C	A	101720912	3	1	232	1	0	0	0	0	1	0	0	0	17111	913	32	4	3197	4	UTP20	12	101720912	Missense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	60978654	101720912	32130983	34	14098											
C13orf18	80183	hgsc.bcm.edu	37	chr13	46946278	46946278	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggggagaagcgctgccaacGgagtctgtggtatcctcaga	9	8	15	9	2	2	2	1	0	1	2	3	4	3	3	2	4	3	2	2	4	3	1			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr13:46946278G>A	ENST00000429979.1	-	3	937	c.333C>T	c.(331-333)tcC>tcT	p.S111S	KIAA0226L_ENST00000409879.2_Intron|KIAA0226L_ENST00000378781.3_Silent_p.S111S|KIAA0226L_ENST00000480935.1_5'UTR|KIAA0226L_ENST00000389908.3_Silent_p.S111S|KIAA0226L_ENST00000378797.2_Silent_p.S111S|KIAA0226L_ENST00000378787.3_Silent_p.S111S|KIAA0226L_ENST00000534925.1_5'UTR|RNU2-6P_ENST00000411404.1_RNA|KIAA0226L_ENST00000378784.4_Silent_p.S44S|KIAA0226L_ENST00000322896.6_Intron	NM_025113.2	NP_079389.2	Q9H714	K226L_HUMAN	KIAA0226-like	111	Ser-rich.									NS(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|pancreas(1)	26						CGCTGCCAACGGAGTCTGTGG	0.572																																					p.S111S		Atlas-SNP	.											.	KIAA0226L	63	.	0			c.C333T						PASS	.						92	88	89					13																	46946278		2203	4300	6503	SO:0001819	synonymous_variant	80183	exon3			GCCAACGGAGTCT	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.333C>T	chr13.hg19:g.46946278G>A		123.0	0.0	.		122.0	6.0	.	NM_025113	A8KAG9|A8XR19|B3KS87|Q5W051|Q5W053|Q6PJ74|Q6PK94|Q86XH7|Q8N5J6	Silent	SNP	ENST00000429979.1	hg19	CCDS31970.2																																																																																			.	.	.	none		0.572	KIAA0226L-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044809.2	NM_025113		A	46946278	G	A	46946278	2	1	232	1	0	0	0	0	0	0	0	1	1722	1103	39	1		1	C13orf18	13	46946278	Silent	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10		46946278	68223600	35	14099											
TPP2	7174	hgsc.bcm.edu	37	chr13	103328750	103328750	+	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	aaaccaacaaaagaaaactgGaaaaattgtattcaagtaag	23	7	6	5	0	1	1	1	0	0	1	1	2	1	2	1	1	3	2	1	1	11	4			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr13:103328750G>T	ENST00000376065.4	+	28	3681	c.3645G>T	c.(3643-3645)tgG>tgT	p.W1215C	TPP2_ENST00000466153.1_3'UTR|TPP2_ENST00000376052.3_Missense_Mutation_p.W1228C	NM_003291.2	NP_003282.2	P29144	TPP2_HUMAN	tripeptidyl peptidase II	1215					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)					AAGAAAACTGGAAAAATTGTA	0.303																																					p.W1215C		Atlas-SNP	.											.	TPP2	124	.	0			c.G3645T						PASS	.						56	60	58					13																	103328750		2201	4290	6491	SO:0001583	missense	7174	exon28			AAACTGGAAAAAT	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.3645G>T	chr13.hg19:g.103328750G>T	ENSP00000365233:p.Trp1215Cys	137.0	0.0	.		117.0	11.0	.	NM_003291	Q5VZU8	Missense_Mutation	SNP	ENST00000376065.4	hg19	CCDS9502.1	.	.	.	.	.	.	.	.	.	.	G	12.28	1.891078	0.33348	.	.	ENSG00000134900	ENST00000376065;ENST00000376052	.	.	.	5.8	5.8	0.92144	.	0.162876	0.56097	D	0.000022	T	0.39733	0.1089	N	0.22421	0.69	0.80722	D	1	P	0.41748	0.761	B	0.37780	0.258	T	0.28073	-1.0055	9	0.38643	T	0.18	.	15.1747	0.72901	0.0692:0.0:0.9308:0.0	.	1215	P29144	TPP2_HUMAN	C	1215;1228	.	ENSP00000365220:W1228C	W	+	3	0	TPP2	102126751	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.923000	0.70045	2.746000	0.94184	0.563000	0.77884	TGG	.	.	.	none		0.303	TPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045683.2			T	103328750	G	T	103328750	3	4	232	1	0	0	0	0	1	0	0	0	16424	1183	41	4	3755	4	TPP2	13	103328750	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	56382472	103328750	11841128	36	14100											
IRS2	8660	hgsc.bcm.edu	37	chr13	110435073	110435073	+	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	tcccgacacctgctccatgaGgctcagcctcttcacgcccg	6	8	8	19	3	3	1	2	1	1	0	5	2	5	1	5	1	2	2	5	1	0	1			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr13:110435073G>A	ENST00000375856.3	-	1	3842	c.3328C>T	c.(3328-3330)Ctc>Ttc	p.L1110F		NM_003749.2	NP_003740.2	Q9Y4H2	IRS2_HUMAN	insulin receptor substrate 2	1110					brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular response to glucose stimulus (GO:0071333)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid homeostasis (GO:0055088)|mammary gland development (GO:0030879)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of kinase activity (GO:0033673)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mesenchymal cell proliferation (GO:0002053)|regulation of lipid metabolic process (GO:0019216)|response to glucose (GO:0009749)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	19	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)			TGCTCCATGAGGCTCAGCCTC	0.731																																					p.L1110F	Melanoma(100;613 2409 40847)	Atlas-SNP	.											.	IRS2	44	.	0			c.C3328T						PASS	.						5	6	6					13																	110435073		2027	4070	6097	SO:0001583	missense	8660	exon1			CCATGAGGCTCAG	AB000732	CCDS9510.1	13q34	2013-01-10			ENSG00000185950	ENSG00000185950		"Pleckstrin homology (PH) domain containing"	6126	protein-coding gene	gene with protein product		600797				9312143	Standard	NM_003749		Approved		uc001vqv.3	Q9Y4H2	OTTHUMG00000017338	ENST00000375856.3:c.3328C>T	chr13.hg19:g.110435073G>A	ENSP00000365016:p.Leu1110Phe	8.0	0.0	.		54.0	21.0	.	NM_003749	Q96RR2|Q9BZG0|Q9Y6I5	Missense_Mutation	SNP	ENST00000375856.3	hg19	CCDS9510.1	.	.	.	.	.	.	.	.	.	.	G	11.01	1.514438	0.27123	.	.	ENSG00000185950	ENST00000375856	T	0.46063	0.88	3.92	2.96	0.34315	.	0.608901	0.14485	U	0.316713	T	0.58323	0.2114	M	0.64404	1.975	0.36281	D	0.855788	D	0.76494	0.999	D	0.75484	0.986	T	0.62324	-0.6878	10	0.35671	T	0.21	-24.5425	12.0667	0.53592	0.1011:0.0:0.8989:0.0	.	1110	Q9Y4H2	IRS2_HUMAN	F	1110	ENSP00000365016:L1110F	ENSP00000365016:L1110F	L	-	1	0	IRS2	109233074	1.000000	0.71417	0.997000	0.53966	0.010000	0.07245	3.062000	0.49971	2.039000	0.60335	0.644000	0.83932	CTC	.	.	.	none		0.731	IRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045755.1	NM_003749		A	110435073	G	A	110435073	3	1	232	1	0	0	0	0	1	0	0	0	7848	1000	35	2	696	2	IRS2	13	110435073	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	7106323	110435073	4734805	37	14101											
C14orf145	145508	hgsc.bcm.edu	37	chr14	81251281	81251284	+	Frame_Shift_Del	DEL	CTTA	CTTA	-																															tcagcctcactcttttctttCttaaagtgcttcataagctc																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	CTTA	CTTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr14:81251281_81251284delCTTA	ENST00000555265.1	-	15	2541_2544	c.2166_2169delTAAG	c.(2164-2169)tttaagfs	p.FK722fs	CEP128_ENST00000281129.3_Frame_Shift_Del_p.FK722fs			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	722						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						TCTTTTCTTTCTTAAAGTGCTTCA	0.412																																					p.723_724del		Atlas-Indel,Pindel	.											.	CEP128	146	.	0			c.2167_2170del						PASS	.																																			SO:0001589	frameshift_variant	145508	exon14			.	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.2166_2169delTAAG	chr14.hg19:g.81251281_81251284delCTTA	ENSP00000451162:p.Phe722fs	92.0	0.0	0		75.0	25.0	0.333333	NM_152446	B9EK52|Q86X97|Q96ML4	Frame_Shift_Del	DEL	ENST00000555265.1	hg19	CCDS32130.1																																																																																			.	.	.	none		0.412	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446		-	81251284	CTTA	-	81251281	7	5	232	1	0	1	0	1	0	0	0	0	1751	912	32	0	1159	0	C14orf145	14	81251281	Frame_Shift_Del	DEL	CTTA	TCGA-P4-A5EA-01A-11D-A28G-10		81251281	26098259	38	14102											
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94052953	94052953	+	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	tcttcacagcagtaaagaatGataccgaaagaaaattttgc	17	10	7	7	1	2	3	1	1	1	2	2	4	2	3	1	0	3	2	1	0	7	5			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr14:94052953G>C	ENST00000393151.2	+	21	2815	c.2815G>C	c.(2815-2817)Gat>Cat	p.D939H	UNC79_ENST00000553484.1_Missense_Mutation_p.D939H|UNC79_ENST00000256339.4_Missense_Mutation_p.D762H|UNC79_ENST00000555664.1_Missense_Mutation_p.D939H			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	939					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						AGTAAAGAATGATACCGAAAG	0.333																																					p.D762H		Atlas-SNP	.											.	UNC79	366	.	0			c.G2284C						PASS	.						51	51	51					14																	94052953		2202	4299	6501	SO:0001583	missense	57578	exon21			AAGAATGATACCG	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.2815G>C	chr14.hg19:g.94052953G>C	ENSP00000376858:p.Asp939His	24.0	0.0	.		30.0	7.0	.	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	hg19		.	.	.	.	.	.	.	.	.	.	G	19.14	3.769262	0.69992	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.18810	2.2;2.2;2.19;2.2	5.94	5.94	0.96194	.	0.110277	0.64402	D	0.000009	T	0.33235	0.0856	L	0.34521	1.04	0.42647	D	0.99343	D	0.57571	0.98	P	0.55965	0.788	T	0.00860	-1.1537	10	0.51188	T	0.08	-21.7402	20.3736	0.98901	0.0:0.0:1.0:0.0	.	939	C9JQL1	.	H	762;939;939;939;939	ENSP00000256339:D762H;ENSP00000450868:D939H;ENSP00000451360:D939H;ENSP00000376858:D939H	ENSP00000256339:D762H	D	+	1	0	KIAA1409	93122706	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.130000	0.77235	2.820000	0.97059	0.650000	0.86243	GAT	.	.	.	none		0.333	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		C	94052953	G	C	94052953	3	2	232	1	0	0	0	0	1	0	0	0	8237	1290	45	4	2354	4	KIAA1409	14	94052953	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	12801672	94052953	13296587	39	14103											
GLCE	26035	hgsc.bcm.edu	37	chr15	69553563	69553564	+	Frame_Shift_Del	DEL	AG	AG	-																															tatatgaaacagcagaagacAgagacaaaaacaagcctaat																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr15:69553563_69553564delAG	ENST00000261858.2	+	4	952_953	c.724_725delAG	c.(724-726)agafs	p.R242fs	GLCE_ENST00000559500.1_3'UTR|GLCE_ENST00000559420.2_Frame_Shift_Del_p.R178fs	NM_015554.1	NP_056369.1	O94923	GLCE_HUMAN	glucuronic acid epimerase	242					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)	p.R242K(1)		NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	18						AGCAGAAGACAGAGACAAAAAC	0.401																																					p.241_242del		Atlas-Indel,Pindel	.											.	GLCE	48	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.723_724del						PASS	.																																			SO:0001589	frameshift_variant	26035	exon4			.	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.724_725delAG	chr15.hg19:g.69553565_69553566delAG	ENSP00000261858:p.Arg242fs	157.0	0.0	0		105.0	22.0	0.209524	NM_015554	Q6GUQ2	Frame_Shift_Del	DEL	ENST00000261858.2	hg19	CCDS32277.1																																																																																			.	.	.	none		0.401	GLCE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015554		-	69553564	AG	-	69553563	7	5	232	1	0	1	0	1	0	0	0	0	6439	180	7	0	730	0	GLCE	15	69553563	Frame_Shift_Del	DEL	AG	TCGA-P4-A5EA-01A-11D-A28G-10		69553563	32977829	40	14104											
C15orf39	56905	hgsc.bcm.edu	37	chr15	75500838	75500838	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtgcaggggctgctggccAagctgctgtctcagctgcag	5	9	16	11	0	1	0	1	0	1	0	2	0	1	0	1	3	6	7	1	3	1	0			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr15:75500838A>G	ENST00000360639.2	+	2	2769	c.2449A>G	c.(2449-2451)Aag>Gag	p.K817E	C15orf39_ENST00000394987.4_Missense_Mutation_p.K817E|RP11-69H7.3_ENST00000563568.1_RNA|C15orf39_ENST00000567617.1_Missense_Mutation_p.K817E			Q6ZRI6	CO039_HUMAN	chromosome 15 open reading frame 39	817						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16						GCTGCTGGCCAAGCTGCTGTC	0.667																																					p.K817E		Atlas-SNP	.											.	C15orf39	64	.	0			c.A2449G						PASS	.						22	18	19					15																	75500838		2188	4288	6476	SO:0001583	missense	56905	exon2			CTGGCCAAGCTGC	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.2449A>G	chr15.hg19:g.75500838A>G	ENSP00000353854:p.Lys817Glu	22.0	0.0	.		42.0	7.0	.	NM_015492	B3KWI3|C9J888|Q71JB1|Q7L3S0|Q8N3F2|Q96FB6|Q9NTU5	Missense_Mutation	SNP	ENST00000360639.2	hg19	CCDS10276.1	.	.	.	.	.	.	.	.	.	.	A	7.085	0.571051	0.13623	.	.	ENSG00000167173	ENST00000360639;ENST00000394987;ENST00000446981	T;T	0.16324	2.35;2.35	5.07	1.05	0.20165	.	0.591269	0.18433	N	0.141368	T	0.12178	0.0296	L	0.45581	1.43	0.09310	N	0.999999	B;P	0.37370	0.234;0.592	B;B	0.34652	0.14;0.187	T	0.14062	-1.0486	10	0.46703	T	0.11	-8.4875	4.778	0.13189	0.5116:0.3589:0.1295:0.0	.	379;817	Q2VPA3;Q6ZRI6	.;CO039_HUMAN	E	817;817;215	ENSP00000353854:K817E;ENSP00000378438:K817E	ENSP00000353854:K817E	K	+	1	0	C15orf39	73287891	0.993000	0.37304	0.863000	0.33907	0.025000	0.11179	2.862000	0.48388	0.735000	0.32537	0.459000	0.35465	AAG	.	.	.	none		0.667	C15orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286410.1	NM_015492		G	75500838	A	G	75500838	3	3	232	1	0	0	0	0	1	0	0	0	1795	131	5	3	2451	3	C15orf39	15	75500838	Missense_Mutation	SNP	A	TCGA-P4-A5EA-01A-11D-A28G-10	5947275	75500838	27030554	41	14105											
UBE2I	7329	hgsc.bcm.edu	37	chr16	1370453	1370453	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcacagatcctattaggaatAcaggaacttctaaatgaacc	16	9	7	9	0	1	2	0	1	1	1	2	4	2	4	2	2	3	1	2	2	8	5			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr16:1370453A>G	ENST00000355803.4	+	6	899	c.348A>G	c.(346-348)atA>atG	p.I116M	UBE2I_ENST00000325437.5_Missense_Mutation_p.I116M|UBE2I_ENST00000402301.1_Missense_Mutation_p.I116M|UBE2I_ENST00000406620.1_Missense_Mutation_p.I116M|UBE2I_ENST00000397515.2_Missense_Mutation_p.I116M|LA16c-358B7.3_ENST00000567829.1_RNA|UBE2I_ENST00000397514.3_Missense_Mutation_p.I116M|UBE2I_ENST00000403747.2_Missense_Mutation_p.I116M|LA16c-358B7.3_ENST00000568106.1_RNA|UBE2I_ENST00000566587.1_Missense_Mutation_p.I116M	NM_194260.2	NP_919236.1	P63279	UBC9_HUMAN	ubiquitin-conjugating enzyme E2I	116					cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of intracellular steroid hormone receptor signaling pathway (GO:0033145)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-translational protein modification (GO:0043687)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein sumoylation (GO:0016925)|regulation of receptor activity (GO:0010469)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|fibrillar center (GO:0001650)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|synapse (GO:0045202)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RING-like zinc finger domain binding (GO:0071535)|SUMO ligase activity (GO:0019789)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(1)	5		Hepatocellular(780;0.00369)				TATTAGGAATACAGGAACTTC	0.512																																					p.I116M		Atlas-SNP	.											.	UBE2I	15	.	0			c.A348G						PASS	.						96	95	95					16																	1370453		2199	4300	6499	SO:0001583	missense	7329	exon6			AGGAATACAGGAA	D45050	CCDS10433.1	16p13.3	2011-05-19	2011-05-19		ENSG00000103275	ENSG00000103275	6.3.2.19	"Ubiquitin-conjugating enzymes E2"	12485	protein-coding gene	gene with protein product		601661	"ubiquitin-conjugating enzyme E2I (homologous to yeast UBC9)", "ubiquitin-conjugating enzyme E2I (UBC9 homolog, yeast)"			8565643	Standard	NM_003345		Approved	UBC9	uc002cld.2	P63279	OTTHUMG00000047845	ENST00000355803.4:c.348A>G	chr16.hg19:g.1370453A>G	ENSP00000348056:p.Ile116Met	25.0	0.0	.		36.0	5.0	.	NM_003345	D3DU69|P50550|Q15698|Q59GX1|Q86VB3	Missense_Mutation	SNP	ENST00000355803.4	hg19	CCDS10433.1	.	.	.	.	.	.	.	.	.	.	A	16.92	3.254235	0.59212	.	.	ENSG00000103275	ENST00000325437;ENST00000355803;ENST00000397514;ENST00000397515;ENST00000406620;ENST00000403747;ENST00000402301	T;T;T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79;0.79;0.79	5.13	2.85	0.33270	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.85682	D	0.000000	T	0.64427	0.2597	H	0.96805	3.885	0.80722	D	1	P;B	0.49961	0.93;0.326	P;B	0.47827	0.558;0.342	T	0.67856	-0.5562	10	0.87932	D	0	.	6.5449	0.22400	0.686:0.1604:0.0:0.1536	.	116;116	B0QYN7;P63279	.;UBC9_HUMAN	M	116	ENSP00000324897:I116M;ENSP00000348056:I116M;ENSP00000380649:I116M;ENSP00000380650:I116M;ENSP00000384568:I116M;ENSP00000385009:I116M;ENSP00000384361:I116M	ENSP00000324897:I116M	I	+	3	3	UBE2I	1310454	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.052000	0.30429	0.406000	0.25560	0.459000	0.35465	ATA	.	.	.	none		0.512	UBE2I-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250317.2	NM_003345		G	1370453	A	G	1370453	3	3	232	1	0	0	0	0	1	0	0	0	16871	381	14	3	366	3	UBE2I	16	1370453	Missense_Mutation	SNP	A	TCGA-P4-A5EA-01A-11D-A28G-10		1370453	88984300	42	14106											
CREBBP	1387	hgsc.bcm.edu	37	chr16	3817823	3817823	+	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	tttcacttcaggtttcttttCatccacttccattggttctg	5	20	5	11	0	5	0	3	0	2	0	7	0	7	0	2	2	0	2	2	2	0	8			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr16:3817823C>A	ENST00000262367.5	-	16	3957	c.3148G>T	c.(3148-3150)Gaa>Taa	p.E1050*	CREBBP_ENST00000382070.3_Nonsense_Mutation_p.E1012*	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1050					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)		GGTTTCTTTTCATCCACTTCC	0.433			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.E1050X		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.G3148T						PASS	.						250	223	232					16																	3817823		2197	4300	6497	SO:0001587	stop_gained	1387	exon16			TCTTTTCATCCAC	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.3148G>T	chr16.hg19:g.3817823C>A	ENSP00000262367:p.Glu1050*	102.0	0.0	.		110.0	30.0	.	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Nonsense_Mutation	SNP	ENST00000262367.5	hg19	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	C	49	15.549454	0.99837	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	.	.	.	5.61	5.61	0.85477	.	0.069937	0.64402	D	0.000018	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	-12.7639	20.0086	0.97443	0.0:1.0:0.0:0.0	.	.	.	.	X	1050;1080;1012	.	ENSP00000262367:E1050X	E	-	1	0	CREBBP	3757824	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.451000	0.66632	2.808000	0.96608	0.655000	0.94253	GAA	.	.	.	none		0.433	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		A	3817823	C	A	3817823	4	1	232	1	0	0	0	0	0	1	0	0	3863	835	29	4	4244	4	CREBBP	16	3817823	Nonsense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	2447370	3817823	86536930	43	14107											
SRCAP	10847	hgsc.bcm.edu	37	chr16	30744761	30744761	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatggatctactagagttgaAcagagacaggtaacccaggt	14	8	12	7	0	1	3	0	1	1	2	1	6	1	4	1	3	3	2	1	3	4	4			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr16:30744761A>G	ENST00000262518.4	+	28	6673	c.6288A>G	c.(6286-6288)gaA>gaG	p.E2096E	SRCAP_ENST00000395059.2_Silent_p.E2034E|SRCAP_ENST00000344771.4_Silent_p.E1938E	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	2096	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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)			CTAGAGTTGAACAGAGACAGG	0.527																																					p.E2096E		Atlas-SNP	.											.	SRCAP	298	.	0			c.A6288G						PASS	.						82	72	75					16																	30744761		2197	4300	6497	SO:0001819	synonymous_variant	10847	exon28			AGTTGAACAGAGA	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.6288A>G	chr16.hg19:g.30744761A>G		105.0	0.0	.		100.0	25.0	.	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Silent	SNP	ENST00000262518.4	hg19	CCDS10689.2																																																																																			.	.	.	none		0.527	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		G	30744761	A	G	30744761	2	3	232	1	0	0	0	0	0	0	0	1	15147	40	2	3		3	SRCAP	16	30744761	Silent	SNP	A	TCGA-P4-A5EA-01A-11D-A28G-10	26926938	30744761	59609992	44	14108											
CDH8	1006	hgsc.bcm.edu	37	chr16	61823266	61823266	+	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	ttactaatttcagtagcaatGattgttatgttgtgccatac	11	17	7	6	0	1	1	1	1	0	0	1	1	1	1	1	0	4	4	1	0	6	8			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr16:61823266G>C	ENST00000577390.1	-	8	2352	c.1398C>G	c.(1396-1398)atC>atG	p.I466M	CDH8_ENST00000577730.1_Missense_Mutation_p.I466M|CDH8_ENST00000299345.6_Missense_Mutation_p.I466M|CDH8_ENST00000584337.1_Missense_Mutation_p.I466M	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	466	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|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)		CAGTAGCAATGATTGTTATGT	0.403																																					p.I466M		Atlas-SNP	.											.	CDH8	273	.	0			c.C1398G						PASS	.						234	196	209					16																	61823266		2203	4300	6503	SO:0001583	missense	1006	exon8			AGCAATGATTGTT	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.1398C>G	chr16.hg19:g.61823266G>C	ENSP00000462701:p.Ile466Met	154.0	0.0	.		157.0	11.0	.	NM_001796	B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	SNP	ENST00000577390.1	hg19	CCDS10802.1	.	.	.	.	.	.	.	.	.	.	G	12.69	2.012887	0.35511	.	.	ENSG00000150394	ENST00000299345	T	0.68025	-0.3	5.44	5.44	0.79542	Cadherin (4);Cadherin-like (1);	0.056358	0.64402	D	0.000001	T	0.70404	0.3220	M	0.77486	2.375	0.36180	D	0.849374	B;B	0.26845	0.001;0.161	B;B	0.39152	0.01;0.292	T	0.76454	-0.2953	10	0.87932	D	0	.	7.413	0.27027	0.2018:0.0:0.7982:0.0	.	282;466	Q3LID3;P55286	.;CADH8_HUMAN	M	466	ENSP00000299345:I466M	ENSP00000299345:I466M	I	-	3	3	CDH8	60380767	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.084000	0.41625	2.716000	0.92895	0.491000	0.48974	ATC	.	.	.	none		0.403	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		C	61823266	G	C	61823266	3	2	232	1	0	0	0	0	1	0	0	0	3118	1280	45	4	1021	4	CDH8	16	61823266	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	31078505	61823266	28531487	45	14109											
LCAT	3931	hgsc.bcm.edu	37	chr16	67974090	67974091	+	Frame_Shift_Ins	INS	-	-	GGGGG																															gtggtcgtagatgtaggtgcINSggggcgtgggcaggcccacg																								rs202017590|rs368229427		TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr16:67974090_67974091insGGGGG	ENST00000264005.5	-	6	1068_1069	c.1039_1040insCCCCC	c.(1039-1041)cgcfs	p.R347fs		NM_000229.1	NP_000220.1	P04180	LCAT_HUMAN	lecithin-cholesterol acyltransferase	347			R -> C (in FED; results in reduced activity). {ECO:0000269|PubMed:21901787}.		cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|high-density lipoprotein particle remodeling (GO:0034375)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein metabolic process (GO:0042157)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|regulation of high-density lipoprotein particle assembly (GO:0090107)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle remodeling (GO:0034372)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)	apolipoprotein A-I binding (GO:0034186)|phosphatidylcholine-sterol O-acyltransferase activity (GO:0004607)			cervix(4)|endometrium(4)|large_intestine(1)|lung(6)|ovary(1)	16		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00418)|Epithelial(162;0.0183)|all cancers(182;0.12)		GATGTAGGTGCGGGGCGTGGGC	0.619																																					p.R347fs		Atlas-INDEL	.											.	LCAT	31	.	0			c.1040_1041insCCCCC						PASS	.																																			SO:0001589	frameshift_variant	3931	exon6			.		CCDS10854.1	16q22.1	2012-10-02			ENSG00000213398	ENSG00000213398	2.3.1.43		6522	protein-coding gene	gene with protein product		606967					Standard	NM_000229		Approved		uc002euy.1	P04180	OTTHUMG00000137551	ENST00000264005.5:c.1039_1040insCCCCC	chr16.hg19:g.67974090_67974091insGGGGG	ENSP00000264005:p.Arg347fs	124.0	0.0	0		154.0	13.0	0.0844156	NM_000229	Q53XQ3	Frame_Shift_Ins	INS	ENST00000264005.5	hg19	CCDS10854.1																																																																																			.	.	.	none		0.619	LCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268885.3			GGGGG	67974091	-	GGGGG	67974090	7	5	232	1	0	1	1	0	0	0	0	0	8665	768	27	0	286	0	LCAT	16	67974090	Frame_Shift_Ins	INS	-	TCGA-P4-A5EA-01A-11D-A28G-10	6150824	67974090	22380663	46	14110											
SPIRE2	84501	hgsc.bcm.edu	37	chr16	89924825	89924826	+	Frame_Shift_Del	DEL	AG	AG	-																															tgcatcaacctgtcagtcacAgatgctgggggcagcgccca																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr16:89924825_89924826delAG	ENST00000378247.3	+	8	1225_1226	c.1182_1183delAG	c.(1180-1185)acagatfs	p.D395fs	SPIRE2_ENST00000393062.2_Frame_Shift_Del_p.D395fs	NM_032451.1	NP_115827.1	Q8WWL2	SPIR2_HUMAN	spire-type actin nucleation factor 2	395					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)		TGTCAGTCACAGATGCTGGGGG	0.629																																					p.394_394del		Atlas-INDEL	.											.	SPIRE2	63	.	0			c.1181_1182del						PASS	.																																			SO:0001589	frameshift_variant	84501	exon8			.	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.1182_1183delAG	chr16.hg19:g.89924825_89924826delAG	ENSP00000367494:p.Asp395fs	89.0	0.0	0		101.0	12.0	0.118812	NM_032451	A4QPB1|Q2TA98|Q6P433|Q8ND47|Q96JJ5	Frame_Shift_Del	DEL	ENST00000378247.3	hg19	CCDS32516.1																																																																																			.	.	.	none		0.629	SPIRE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421843.1	XM_047462		-	89924826	AG	-	89924825	7	5	232	1	0	1	0	1	0	0	0	0	15084	175	7	0	1212	0	SPIRE2	16	89924825	Frame_Shift_Del	DEL	AG	TCGA-P4-A5EA-01A-11D-A28G-10	21950735	89924825	429928	47	14111											
RPH3AL	9501	hgsc.bcm.edu	37	chr17	131631	131631	+	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	ggggaggcctcgatcccacaTttggtgcagactttctacaa	9	10	11	11	1	1	1	0	0	1	1	3	3	2	2	2	4	2	1	2	4	2	3			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr17:131631T>A	ENST00000331302.7	-	6	673	c.366A>T	c.(364-366)aaA>aaT	p.K122N	RPH3AL_ENST00000323434.8_Intron|RPH3AL_ENST00000576001.1_5'UTR|RPH3AL_ENST00000536489.2_Intron	NM_001190411.1|NM_006987.3	NP_001177340.1|NP_008918.1	Q9UNE2	RPH3L_HUMAN	rabphilin 3A-like (without C2 domains)	122	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				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)		CGATCCCACATTTGGTGCAGA	0.587																																					p.K122N		Atlas-SNP	.											.	RPH3AL	18	.	0			c.A366T						PASS	.						81	81	81					17																	131631		2203	4300	6503	SO:0001583	missense	9501	exon6			CCCACATTTGGTG		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.366A>T	chr17.hg19:g.131631T>A	ENSP00000328977:p.Lys122Asn	211.0	0.0	.		231.0	46.0	.	NM_006987	D3DTG7|Q9BSB3	Missense_Mutation	SNP	ENST00000331302.7	hg19	CCDS10994.1	.	.	.	.	.	.	.	.	.	.	T	15.21	2.767130	0.49574	.	.	ENSG00000181031	ENST00000323434	.	.	.	5.02	-8.63	0.00878	Zinc finger, RING/FYVE/PHD-type (1);Rab-binding domain (1);Zinc finger, FYVE-related (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.64402	D	0.000008	T	0.71426	0.3338	M	0.70903	2.155	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	T	0.82818	-0.0269	9	0.87932	D	0	-14.7906	16.2241	0.82283	0.0:0.5791:0.0:0.4208	.	122	Q9UNE2	RPH3L_HUMAN	N	122	.	ENSP00000319210:K122N	K	-	3	2	RPH3AL	131631	0.328000	0.24687	0.618000	0.29105	0.943000	0.58893	-0.811000	0.04500	-2.189000	0.00758	-1.660000	0.00751	AAA	.	.	.	none		0.587	RPH3AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206597.2	NM_006987		A	131631	T	A	131631	3	1	232	1	0	0	0	0	1	0	0	0	13565	1490	52	5	601	5	RPH3AL	17	131631	Missense_Mutation	SNP	T	TCGA-P4-A5EA-01A-11D-A28G-10		131631	81063579	48	14112											
RPL26	6154	hgsc.bcm.edu	37	chr17	8283223	8283223	+	Missense_Mutation	SNP	A	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	aaacctggactactttgccaAtttgctgacctttatagtgt	10	15	7	9	0	0	1	0	1	0	0	0	2	0	2	3	1	4	1	3	1	5	6			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr17:8283223A>C	ENST00000584164.1	-	3	591	c.200T>G	c.(199-201)aTt>aGt	p.I67S	RPL26_ENST00000583011.1_Missense_Mutation_p.I67S|RPL26_ENST00000578812.1_Missense_Mutation_p.I67S|RPL26_ENST00000585176.1_5'UTR|RPL26_ENST00000293842.5_Missense_Mutation_p.I67S|RP11-849F2.5_ENST00000585181.1_RNA|RPL26_ENST00000582556.1_Missense_Mutation_p.I67S|RP11-849F2.7_ENST00000582471.1_Missense_Mutation_p.I67S|RP11-849F2.5_ENST00000579904.1_RNA			P61254	RL26_HUMAN	ribosomal protein L26	67					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)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			skin(1)|urinary_tract(1)	2						TACTTTGCCAATTTGCTGACC	0.373																																					p.I67S		Atlas-SNP	.											.	RPL26	7	.	0			c.T200G						PASS	.						51	51	51					17																	8283223		2203	4300	6503	SO:0001583	missense	6154	exon3			TTGCCAATTTGCT		CCDS11142.1	17p13	2011-04-06			ENSG00000161970	ENSG00000161970		"L ribosomal proteins"	10327	protein-coding gene	gene with protein product		603704				8479925	Standard	XM_005256749		Approved	L26	uc002glh.1	P61254	OTTHUMG00000108191	ENST00000584164.1:c.200T>G	chr17.hg19:g.8283223A>C	ENSP00000463784:p.Ile67Ser	101.0	0.0	.		117.0	14.0	.	NM_000987	B2R4F0|D3DTR8|Q02877|Q6IPY2	Missense_Mutation	SNP	ENST00000584164.1	hg19	CCDS11142.1	.	.	.	.	.	.	.	.	.	.	A	13.87	2.367500	0.42003	.	.	ENSG00000161970	ENST00000293842	.	.	.	4.7	4.7	0.59300	KOW (2);Translation protein SH3-like (1);Ribosomal protein L24/L26, conserved site (1);Ribosomal protein L24, SH3-like (1);	0.000000	0.85682	D	0.000000	T	0.44582	0.1300	N	0.22421	0.69	0.58432	D	0.999995	B	0.13145	0.007	B	0.25506	0.061	T	0.36016	-0.9765	9	0.37606	T	0.19	-1.2756	12.4268	0.55551	1.0:0.0:0.0:0.0	.	67	P61254	RL26_HUMAN	S	67	.	ENSP00000293842:I67S	I	-	2	0	RPL26	8223948	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	9.239000	0.95389	1.871000	0.54225	0.523000	0.50628	ATT	.	.	.	none		0.373	RPL26-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442322.1	NM_000987		C	8283223	A	C	8283223	3	2	232	1	0	0	0	0	1	0	0	0	13586	101	4	5	245	5	RPL26	17	8283223	Missense_Mutation	SNP	A	TCGA-P4-A5EA-01A-11D-A28G-10	8151592	8283223	72911987	49	14113											
C17orf80	55028	hgsc.bcm.edu	37	chr17	71232036	71232037	+	Frame_Shift_Del	DEL	CA	CA	-																															tccaagaagaaaccaaggctCagttttacgcatcagagaaa																								rs373362252|rs555089459		TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr17:71232036_71232037delCA	ENST00000535032.2	+	2	528_529	c.415_416delCA	c.(415-417)cagfs	p.Q139fs	FAM104A_ENST00000583178.1_Intron|C17orf80_ENST00000359042.2_Frame_Shift_Del_p.Q139fs|C17orf80_ENST00000582793.1_Intron|C17orf80_ENST00000426147.2_Frame_Shift_Del_p.Q139fs|C17orf80_ENST00000577615.1_Frame_Shift_Del_p.Q139fs|C17orf80_ENST00000268942.8_Frame_Shift_Del_p.Q139fs|C17orf80_ENST00000255557.4_Frame_Shift_Del_p.Q139fs			Q9BSJ5	CQ080_HUMAN	chromosome 17 open reading frame 80	139						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(5)|lung(2)|skin(2)|stomach(2)|urinary_tract(2)	14			LUSC - Lung squamous cell carcinoma(166;0.197)			AACCAAGGCTCAGTTTTACGCA	0.381																																					p.138_139del		Atlas-INDEL	.											.	C17orf80	37	.	0			c.414_415del						PASS	.																																			SO:0001589	frameshift_variant	55028	exon3			.	AY163812	CCDS11694.1, CCDS42377.1, CCDS45767.1, CCDS74145.1	17q25.1	2012-02-24	2012-02-24	2012-02-24	ENSG00000141219	ENSG00000141219			29601	protein-coding gene	gene with protein product	"sperm-expressed protein 1", "migration-inducing protein 3"					12477932	Standard	NM_017941		Approved	HLC-8, MIG3, FLJ20721, SPEP1	uc002jjl.4	Q9BSJ5		ENST00000535032.2:c.415_416delCA	chr17.hg19:g.71232036_71232037delCA	ENSP00000440551:p.Gln139fs	137.0	0.0	0		194.0	12.0	0.0618557	NM_001100621	A8K9X3|Q5JB45|Q6YAU3|Q9H0L9|Q9H5E6|Q9NWN5	Frame_Shift_Del	DEL	ENST00000535032.2	hg19	CCDS11694.1																																																																																			.	.	.	none		0.381	C17orf80-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441893.1	NM_017941		-	71232037	CA	-	71232036	7	5	232	1	0	1	0	1	0	0	0	0	1887	827	29	0	417	0	C17orf80	17	71232036	Frame_Shift_Del	DEL	CA	TCGA-P4-A5EA-01A-11D-A28G-10	62948813	71232036	9963174	50	14114											
GGA3	23163	hgsc.bcm.edu	37	chr17	73239164	73239164	+	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	cttggacttctcctcatcatCaaaaacagggtttttgggac	10	13	8	10	0	4	0	3	0	1	0	5	2	4	2	1	3	1	1	1	3	2	4	rs35542883		TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr17:73239164C>G	ENST00000245541.6	-	6	724	c.508G>C	c.(508-510)Gat>Cat	p.D170H	GGA3_ENST00000582717.1_Missense_Mutation_p.D98H|GGA3_ENST00000537686.1_Intron|GGA3_ENST00000538886.1_Missense_Mutation_p.D48H|GGA3_ENST00000578348.1_Missense_Mutation_p.D48H|GGA3_ENST00000351904.7_Missense_Mutation_p.D137H|GGA3_ENST00000579743.1_5'Flank|GGA3_ENST00000582486.1_Missense_Mutation_p.D98H	NM_138619.2	NP_619525.1	Q9NZ52	GGA3_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 3	170	Binds to ARF1 (in long isoform).				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)			TCCTCATCATCAAAAACAGGG	0.547																																					p.D170H		Atlas-SNP	.											.	GGA3	54	.	0			c.G508C						PASS	.						161	149	153					17																	73239164		2203	4300	6503	SO:0001583	missense	23163	exon6			CATCATCAAAAAC	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.508G>C	chr17.hg19:g.73239164C>G	ENSP00000245541:p.Asp170His	240.0	0.0	.		284.0	77.0	.	NM_138619	B7Z7E2|B7Z7M9|J3KRN0|Q15017|Q6IS16|Q9UJY3	Missense_Mutation	SNP	ENST00000245541.6	hg19	CCDS11717.1	.	.	.	.	.	.	.	.	.	.	C	15.59	2.879725	0.51801	.	.	ENSG00000125447	ENST00000245541;ENST00000351904;ENST00000537584;ENST00000538886	T;T	0.52983	2.01;0.64	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.67449	0.2894	M	0.67397	2.05	0.80722	D	1	D;P;D	0.89917	1.0;0.522;1.0	D;P;D	0.72982	0.972;0.729;0.979	T	0.69465	-0.5138	10	0.54805	T	0.06	-21.0362	18.153	0.89682	0.0:1.0:0.0:0.0	.	48;137;170	B7Z7E2;Q9NZ52-2;Q9NZ52	.;.;GGA3_HUMAN	H	170;137;98;48	ENSP00000245541:D170H;ENSP00000326575:D137H	ENSP00000245541:D170H	D	-	1	0	GGA3	70750759	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	7.646000	0.83445	2.505000	0.84491	0.563000	0.77884	GAT	.	.	.	none		0.547	GGA3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446645.1	NM_138619		G	73239164	C	G	73239164	3	3	232	1	0	0	0	0	1	0	0	0	6361	826	29	4	1799	4	GGA3	17	73239164	Missense_Mutation	SNP	C	TCGA-P4-A5EA-01A-11D-A28G-10	2007128	73239164	7956046	51	14115											
MUC16	94025	hgsc.bcm.edu	37	chr19	9058716	9058716	+	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	caggggtcagagatgacattGactctatctcaatccttgta	11	12	9	9	0	3	3	2	2	2	1	5	4	4	3	1	2	0	1	1	2	3	4			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr19:9058716G>C	ENST00000397910.4	-	3	28933	c.28730C>G	c.(28729-28731)tCa>tGa	p.S9577*		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9579	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						AGATGACATTGACTCTATCTC	0.488																																					p.S9577X		Atlas-SNP	.											.	MUC16	4315	.	0			c.C28730G						PASS	.						90	84	86					19																	9058716		2003	4163	6166	SO:0001587	stop_gained	94025	exon3			GACATTGACTCTA	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.28730C>G	chr19.hg19:g.9058716G>C	ENSP00000381008:p.Ser9577*	154.0	0.0	.		155.0	31.0	.	NM_024690	Q6ZQW5|Q96RK2	Nonsense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	60	44.522612	0.99986	.	.	ENSG00000181143	ENST00000397910	.	.	.	2.5	1.41	0.22369	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	6.6673	0.23047	0.0:0.0:0.7208:0.2792	.	.	.	.	X	9577	.	ENSP00000381008:S9577X	S	-	2	0	MUC16	8919716	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-0.009000	0.12765	0.597000	0.29811	0.305000	0.20034	TCA	.	.	.	none		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9058716	G	C	9058716	4	2	232	1	0	0	0	0	0	1	0	0	9980	1294	45	4	15121	4	MUC16	19	9058716	Nonsense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10		9058716	50070267	52	14116											
NF2	4771	hgsc.bcm.edu	37	chr22	30057329	30057329	+	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	tctcgtacagtgacaaggagGtaggacatgtgtgtactgca	11	10	13	7	1	1	1	0	1	1	0	2	3	1	3	0	3	3	4	0	3	4	3			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr22:30057329G>A	ENST00000338641.4	+	8	1251		c.e8+1		NF2_ENST00000334961.7_Splice_Site|NF2_ENST00000347330.5_Splice_Site|NF2_ENST00000361452.4_Splice_Site|NF2_ENST00000397789.3_Splice_Site|NF2_ENST00000413209.2_Intron|NF2_ENST00000361166.4_Splice_Site|NF2_ENST00000403435.1_Splice_Site|NF2_ENST00000353887.4_Splice_Site|NF2_ENST00000403999.3_Splice_Site|NF2_ENST00000361676.4_Splice_Site	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)						actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(5)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						TGACAAGGAGGTAGGACATGT	0.532			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																												.		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	NF2_ENST00000403999,spinal_cord,glioma,0,4	NF2	1312	.	5	Unknown(5)	meninges(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)	c.810+1G>A						PASS	.						117	108	111					22																	30057329		2203	4300	6503	SO:0001630	splice_region_variant	4771	exon8	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	AAGGAGGTAGGAC	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"A-kinase anchor proteins"	7773	protein-coding gene	gene with protein product	"moesin-ezrin-radixin like", "schwannomin"	607379	"neurofibromin 2 (bilateral acoustic neuroma)"			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.810+1G>A	chr22.hg19:g.30057329G>A		68.0	0.0	.		42.0	14.0	.	NM_016418	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Splice_Site	SNP	ENST00000338641.4	hg19	CCDS13861.1	.	.	.	.	.	.	.	.	.	.	G	33	5.287845	0.95517	.	.	ENSG00000186575	ENST00000347330;ENST00000338641;ENST00000403435;ENST00000361452;ENST00000397822;ENST00000403999;ENST00000334961;ENST00000353887;ENST00000397789;ENST00000361676;ENST00000361166	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.0795	0.97766	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NF2	28387329	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.864000	0.99589	2.747000	0.94245	0.650000	0.86243	.	.	.	.	none		0.532	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268	Intron	A	30057329	G	A	30057329	5	1	232	1	0	0	0	0	0	0	1	0	10364	1275	44	2	841	2	NF2	22	30057329	Splice_Site	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10		30057329	21247237	53	14117											
TOM1	10043	hgsc.bcm.edu	37	chr22	35723290	35723290	+	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	aagctgcgcagtgagctggaGatggtgagtgggaacgtgag	10	7	19	5	2	0	4	0	3	0	1	0	6	0	5	0	3	4	3	0	3	2	0			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr22:35723290G>T	ENST00000449058.2	+	7	800	c.675G>T	c.(673-675)gaG>gaT	p.E225D	TOM1_ENST00000436462.2_Missense_Mutation_p.E187D|TOM1_ENST00000425375.1_Missense_Mutation_p.E180D|TOM1_ENST00000411850.1_Missense_Mutation_p.E225D|TOM1_ENST00000382034.5_Missense_Mutation_p.E158D|TOM1_ENST00000447733.1_Missense_Mutation_p.E192D	NM_005488.2	NP_005479.1	O60784	TOM1_HUMAN	target of myb1 (chicken)	225	GAT. {ECO:0000255|PROSITE- ProRule:PRU00373}.				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						GTGAGCTGGAGATGGTGAGTG	0.602																																					p.E225D		Atlas-SNP	.											.	TOM1	43	.	0			c.G675T						PASS	.						187	142	157					22																	35723290		2203	4300	6503	SO:0001583	missense	10043	exon7			GCTGGAGATGGTG	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.675G>T	chr22.hg19:g.35723290G>T	ENSP00000394466:p.Glu225Asp	100.0	0.0	.		73.0	10.0	.	NM_001135732	B4DEL9|B4DNA1|Q5TIJ6|Q86X74	Missense_Mutation	SNP	ENST00000449058.2	hg19	CCDS13913.1	.	.	.	.	.	.	.	.	.	.	G	4.588	0.109203	0.08780	.	.	ENSG00000100284	ENST00000447733;ENST00000456128;ENST00000449058;ENST00000411850;ENST00000425375;ENST00000451197;ENST00000436462;ENST00000382034	T;T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92;0.92	5.39	4.38	0.52667	GAT (2);	0.094349	0.64402	D	0.000001	T	0.12987	0.0315	N	0.01679	-0.765	0.49582	D	0.999809	B;P;B;B;B	0.38827	0.095;0.649;0.002;0.257;0.102	B;B;B;B;B	0.37692	0.023;0.256;0.023;0.103;0.07	T	0.30446	-0.9978	10	0.02654	T	1	-7.1743	6.6853	0.23142	0.3042:0.0:0.6958:0.0	.	180;187;234;225;225	O60784-3;E7EPD0;B4DKQ5;O60784-2;O60784	.;.;.;.;TOM1_HUMAN	D	192;219;225;225;180;234;187;158	ENSP00000398876:E192D;ENSP00000393714:E219D;ENSP00000394466:E225D;ENSP00000413697:E225D;ENSP00000394924:E180D;ENSP00000402556:E187D;ENSP00000371465:E158D	ENSP00000371465:E158D	E	+	3	2	TOM1	34053290	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.774000	0.26675	1.268000	0.44264	0.655000	0.94253	GAG	.	.	.	none		0.602	TOM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320641.1	NM_005488		T	35723290	G	T	35723290	3	4	232	1	0	0	0	0	1	0	0	0	16363	933	33	4	701	4	TOM1	22	35723290	Missense_Mutation	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	5665961	35723290	15581276	54	14118											
C22orf33	339669	hgsc.bcm.edu	37	chr22	37396006	37396008	+	In_Frame_Del	DEL	TCA	TCA	-																															ttttctggccctcgaagactTcatcaatagccttttgagcc																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	TCA	TCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chr22:37396006_37396008delTCA	ENST00000405091.2	-	5	758_760	c.507_509delTGA	c.(505-510)gatgaa>gaa	p.D169del	TEX33_ENST00000402860.3_In_Frame_Del_p.D84del|TEX33_ENST00000381821.1_In_Frame_Del_p.D169del			O43247	TEX33_HUMAN	testis expressed 33	169																	CTCGAAGACTTCATCAATAGCCT	0.542																																					p.170_170del		Atlas-Indel,Pindel	.											.	TEX33	25	.	0			c.508_510del						PASS	.																																			SO:0001651	inframe_deletion	339669	exon4			.	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.507_509delTGA	chr22.hg19:g.37396009_37396011delTCA	ENSP00000386118:p.Asp169del	92.0	0.0	0		88.0	25.0	0.284091	NM_001163857	B1AH46|Q6ICF2|Q8IVQ2|Q9Y4V8	In_Frame_Del	DEL	ENST00000405091.2	hg19	CCDS54524.1																																																																																			.	.	.	none		0.542	TEX33-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318778.2	NM_178552		-	37396008	TCA	-	37396006	7	5	232	1	0	1	0	1	0	0	0	0	2147	1783	62	0	345	0	C22orf33	22	37396006	In_Frame_Del	DEL	TCA	TCGA-P4-A5EA-01A-11D-A28G-10	1672716	37396006	13908560	55	14119											
ZRSR2	8233	hgsc.bcm.edu	37	chrX	15841231	15841236	+	In_Frame_Del	DEL	AGCCGG	AGCCGG	-																															accgcagccggggccggggcAgccggagccggagccggagc																								rs199648317		TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	AGCCGG	AGCCGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chrX:15841231_15841236delAGCCGG	ENST00000307771.7	+	11	1339_1344	c.1315_1320delAGCCGG	c.(1315-1320)agccggdel	p.SR447del		NM_005089.3	NP_005080.1	Q15696	U2AFM_HUMAN	zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2	447	Arg/Ser-rich (RS domain).				mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	U12-type spliceosomal complex (GO:0005689)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|pre-mRNA 3'-splice site binding (GO:0030628)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(38)|kidney(1)|large_intestine(2)|ovary(2)	48	Hepatocellular(33;0.183)					GGGCCGGGGCagccggagccggagcc	0.636			"F, S, Mis"		"MDS, CLL"																																p.438_440del	NSCLC(197;1631 3042 5741 31152)	Atlas-Indel,Pindel	.		Rec	yes		X	Xp22.1	8233	"zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2"		L	.	ZRSR2	78	.	0			c.1314_1319del						PASS	.			17,138,2720		4,1,5,3,32,53,20,1147,368						3	0.1			9	24,75,5168		3,0,9,9,11,35,18,1934,1256	no	codingComplex	ZRSR2	NM_005089.3		7,1,14,12,43,88,38,3081,1624	A1A1,A1A2,A1R,A1,A2A2,A2R,A2,RR,R		1.8796,5.3913,3.1196				41,213,7888				SO:0001651	inframe_deletion	8233	exon11			.	BC050451	CCDS14172.1	Xp22.1	2014-09-17	2006-09-26	2006-09-26	ENSG00000169249	ENSG00000169249		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	23019	protein-coding gene	gene with protein product		300028	"U2(RNU2) small nuclear RNA auxiliary factor 1-like 2", "U2 small nuclear RNA auxiliary factor 1-like 2"	U2AF1L2		8586425, 9237760, 15146077	Standard	NM_005089		Approved	U2AF1-RS2, URP	uc004cxg.4	Q15696	OTTHUMG00000021184	ENST00000307771.7:c.1315_1320delAGCCGG	chrX.hg19:g.15841237_15841242delAGCCGG	ENSP00000303015:p.Ser447_Arg448del	23.0	0.0	0		62.0	19.0	0.306452	NM_005089	Q14D69	In_Frame_Del	DEL	ENST00000307771.7	hg19	CCDS14172.1																																																																																			.	.	.	none		0.636	ZRSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055889.1	NM_005089		-	15841236	AGCCGG	-	15841231	7	5	232	1	0	1	0	1	0	0	0	0	18237	188	7	0	1357	0	ZRSR2	23	15841231	In_Frame_Del	DEL	AGCCGG	TCGA-P4-A5EA-01A-11D-A28G-10		15841231	139429329	56	14120											
BCOR	54880	hgsc.bcm.edu	37	chrX	39913206	39913207	+	Frame_Shift_Del	DEL	AC	AC	-																															ctctgaaaattcaaattcaaAcacatcgctataggcatcgt																										TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chrX:39913206_39913207delAC	ENST00000378444.4	-	14	5136_5137	c.4908_4909delGT	c.(4906-4911)gtgtttfs	p.F1637fs	BCOR_ENST00000378455.4_Frame_Shift_Del_p.F1585fs|BCOR_ENST00000342274.4_Frame_Shift_Del_p.F1603fs|BCOR_ENST00000397354.3_Frame_Shift_Del_p.F1603fs|BCOR_ENST00000378463.1_Frame_Shift_Del_p.F480fs	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	1637	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						TCAAATTCAAACACATCGCTAT	0.465			"F, N, S, T"	RARA	"retinoblastoma, AML, APL(translocation)"		oculo-facio-cardio-dental genetic																														p.1637_1637del		Atlas-Indel,Pindel	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	0			c.4909_4910del						PASS	.																																			SO:0001589	frameshift_variant	54880	exon14			.	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.4908_4909delGT	chrX.hg19:g.39913208_39913209delAC	ENSP00000367705:p.Phe1637fs	260.0	0.0	0		234.0	19.0	0.0811966	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Frame_Shift_Del	DEL	ENST00000378444.4	hg19	CCDS48093.1																																																																																			.	.	.	none		0.465	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		-	39913207	AC	-	39913206	7	5	232	1	0	1	0	1	0	0	0	0	1386	43	2	0	366	0	BCOR	23	39913206	Frame_Shift_Del	DEL	AC	TCGA-P4-A5EA-01A-11D-A28G-10	24071975	39913206	115357354	57	14121											
ZXDB	158586	hgsc.bcm.edu	37	chrX	57619114	57619114	+	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	cccgggtgtctgatcgccccGcaagctgggttcccgcatgc	4	8	13	16	4	1	1	0	1	1	0	3	1	2	1	4	2	2	4	4	2	1	1			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chrX:57619114G>C	ENST00000374888.1	+	1	846	c.633G>C	c.(631-633)ccG>ccC	p.P211P		NM_007157.3	NP_009088.1	P98169	ZXDB_HUMAN	zinc finger, X-linked, duplicated B	211					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)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(2)|skin(6)	27						TGATCGCCCCGCAAGCTGGGT	0.736																																					p.P211P		Atlas-SNP	.											.	ZXDB	51	.	0			c.G633C						PASS	.						9	11	11					X																	57619114		2174	4231	6405	SO:0001819	synonymous_variant	158586	exon1			CGCCCCGCAAGCT	L14788	CCDS35313.1	Xp11.1	2013-01-08			ENSG00000198455	ENSG00000198455		"Zinc fingers, C2H2-type"	13199	protein-coding gene	gene with protein product		300236				8268913	Standard	NM_007157		Approved	ZNF905	uc004dvd.3	P98169	OTTHUMG00000021685	ENST00000374888.1:c.633G>C	chrX.hg19:g.57619114G>C		20.0	0.0	.		117.0	5.0	.	NM_007157	A8K151|Q9UBB3	Silent	SNP	ENST00000374888.1	hg19	CCDS35313.1																																																																																			.	.	.	none		0.736	ZXDB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056922.1	NM_007157		C	57619114	G	C	57619114	2	2	232	1	0	0	0	0	0	0	0	1	18263	1074	38	4		4	ZXDB	23	57619114	Silent	SNP	G	TCGA-P4-A5EA-01A-11D-A28G-10	17705908	57619114	97651446	58	14122											
THOC2	57187	hgsc.bcm.edu	37	chrX	122757675	122757675	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tagatctggcctcttctcttTttcttcttggcagattttgt	4	21	7	9	0	5	2	0	0	5	2	6	2	5	2	1	2	0	1	1	2	1	8			TCGA-P4-A5EA-01A-11D-A28G-10	TCGA-P4-A5EA-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0451b7be-d503-4cad-88a1-322496cffb25	5d70fe2b-81f9-4b9e-8410-3ccf2035292a	g.chrX:122757675T>C	ENST00000245838.8	-	28	3497	c.3466A>G	c.(3466-3468)Aaa>Gaa	p.K1156E	THOC2_ENST00000491737.1_Missense_Mutation_p.K1041E|THOC2_ENST00000355725.4_Missense_Mutation_p.K1156E	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	1156					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						CTCTTCTCTTTTTCTTCTTGG	0.348																																					p.K1156E		Atlas-SNP	.											.	THOC2	310	.	0			c.A3466G						PASS	.						150	119	128					X																	122757675		1809	4080	5889	SO:0001583	missense	57187	exon28			TCTCTTTTTCTTC	AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"THO complex subunits"	19073	protein-coding gene	gene with protein product		300395	"chromosome X open reading frame 3"	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.3466A>G	chrX.hg19:g.122757675T>C	ENSP00000245838:p.Lys1156Glu	67.0	0.0	.		42.0	7.0	.	NM_001081550	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Missense_Mutation	SNP	ENST00000245838.8	hg19	CCDS43988.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.88|19.88	3.909495|3.909495	0.72868|0.72868	.|.	.|.	ENSG00000125676|ENSG00000125676	ENST00000245838;ENST00000355725;ENST00000491737|ENST00000438358	.|.	.|.	.|.	5.9|5.9	5.9|5.9	0.94986|0.94986	THO complex, subunitTHOC2, C-terminal (1);|.	0.000000|0.000000	0.64402|0.64402	D|D	0.000001|0.000001	T|T	0.72661|0.72661	0.3488|0.3488	M|M	0.67625|0.67625	2.065|2.065	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.85130|.	0.997|.	T|T	0.72293|0.72293	-0.4336|-0.4336	9|6	0.13470|.	T|.	0.59|.	-17.2559|-17.2559	15.2657|15.2657	0.73660|0.73660	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1156|.	Q8NI27|.	THOC2_HUMAN|.	E|R	1156;1156;1041|228	.|.	ENSP00000245838:K1156E|.	K|K	-|-	1|2	0|0	THOC2|THOC2	122585356|122585356	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.040000|8.040000	0.89188|0.89188	1.988000|1.988000	0.58038|0.58038	0.481000|0.481000	0.45027|0.45027	AAA|AAA	.	.	.	none		0.348	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3			C	122757675	T	C	122757675	3	2	232	1	0	0	0	0	1	0	0	0	15877	1850	64	3	1359	3	THOC2	23	122757675	Missense_Mutation	SNP	T	TCGA-P4-A5EA-01A-11D-A28G-10	65138561	122757675	32512885	59	14123											
AADACL4	343066	hgsc.bcm.edu	37	chr1	12711237	12711237	+	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	aaaaaggaccctgaacttgtGgtgaccgacctgcgttttgg	10	10	12	9	2	0	2	0	2	0	0	0	4	0	3	3	3	2	1	3	3	3	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:12711237G>T	ENST00000376221.1	+	2	264	c.264G>T	c.(262-264)gtG>gtT	p.V88V		NM_001013630.1	NP_001013652.1	Q5VUY2	ADCL4_HUMAN	arylacetamide deacetylase-like 4	88						integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)	17	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.000937)|all_lung(284;0.00122)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.81e-07)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0384)		CTGAACTTGTGGTGACCGACC	0.498																																					p.V88V		Atlas-SNP	.											.	AADACL4	48	.	0			c.G264T						PASS	.						98	96	97					1																	12711237		2203	4300	6503	SO:0001819	synonymous_variant	343066	exon2			ACTTGTGGTGACC		CCDS30590.1	1p36.21	2010-12-14			ENSG00000204518	ENSG00000204518			32038	protein-coding gene	gene with protein product							Standard	XM_006710608		Approved	OTTHUMG00000001889	uc001auf.3	Q5VUY2	OTTHUMG00000001889	ENST00000376221.1:c.264G>T	chr1.hg19:g.12711237G>T		121.0	0.0	.		120.0	66.0	.	NM_001013630		Silent	SNP	ENST00000376221.1	hg19	CCDS30590.1																																																																																			.	.	.	none		0.498	AADACL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005328.1	NM_001013630		T	12711237	G	T	12711237	2	4	233	1	0	0	0	0	0	0	0	1	13	1335	47	4		4	AADACL4	1	12711237	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10		12711237	236539384	1	14124											
RHD	6007	hgsc.bcm.edu	37	chr1	25628090	25628090	+	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	atcgaaaggaagaatgccgtGttcaacacctactatgctgt	13	10	9	9	2	1	1	1	0	0	1	2	3	1	2	2	1	4	2	2	1	6	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:25628090G>A	ENST00000328664.4	+	5	869	c.714G>A	c.(712-714)gtG>gtA	p.V238V	RHD_ENST00000423810.2_Silent_p.V238V|RHD_ENST00000342055.5_Silent_p.V238V|RHD_ENST00000568195.1_Silent_p.V238V|RHD_ENST00000454452.2_Silent_p.V238V|RHD_ENST00000423253.1_3'UTR|RHD_ENST00000417538.2_Silent_p.V238V|RHD_ENST00000357542.4_Silent_p.V238V	NM_001282867.1|NM_016124.3	NP_001269796.1|NP_057208	Q02161	RHD_HUMAN	Rh blood group, D antigen	238			V -> M (in RhDVa(TO) and RhDVa(TT); dbSNP:rs1053360). {ECO:0000269|Ref.9}.			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)		AGAATGCCGTGTTCAACACCT	0.562																																					p.V238V		Atlas-SNP	.											.	RHD	38	.	0			c.G714A						PASS	.						199	154	171					1																	25628090		2122	3769	5891	SO:0001819	synonymous_variant	6007	exon5			TGCCGTGTTCAAC	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.714G>A	chr1.hg19:g.25628090G>A		87.0	0.0	.		134.0	123.0	.	NM_001127691	Q02162|Q07618|Q16147|Q16235|Q16355|Q5VSK0|Q5XLS9|Q5XLT1|Q5XLT2|Q9NPK0|Q9UQ20|Q9UQ21|Q9UQ22|Q9UQ23	Silent	SNP	ENST00000328664.4	hg19	CCDS262.1																																																																																			.	.	.	none		0.562	RHD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009660.5	NM_016124		A	25628090	G	A	25628090	2	1	233	1	0	0	0	0	0	0	0	1	13340	1364	48	2		2	RHD	1	25628090	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	12916853	25628090	223622531	2	14125											
CSMD2	114784	hgsc.bcm.edu	37	chr1	34015918	34015918	+	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	gtctccagacatctgggagtGaggcggggagcccggatggc	7	6	18	10	2	2	2	0	1	2	1	3	5	2	5	2	6	1	0	2	6	0	0			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:34015918G>T	ENST00000373381.4	-	56	8952	c.8776C>A	c.(8776-8778)Cac>Aac	p.H2926N		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2901	Sushi 21. {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)				ATCTGGGAGTGAGGCGGGGAG	0.572																																					p.H2782N		Atlas-SNP	.											.	CSMD2	946	.	0			c.C8344A						PASS	.						58	57	57					1																	34015918		2203	4300	6503	SO:0001583	missense	114784	exon55			GGGAGTGAGGCGG	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.8776C>A	chr1.hg19:g.34015918G>T	ENSP00000362479:p.His2926Asn	109.0	0.0	.		186.0	106.0	.	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	hg19		.	.	.	.	.	.	.	.	.	.	G	0.673	-0.801317	0.02841	.	.	ENSG00000121904	ENST00000373381	T	0.64618	-0.11	5.71	5.71	0.89125	Complement control module (2);Sushi/SCR/CCP (3);	0.060404	0.64402	D	0.000002	T	0.27241	0.0668	N	0.00661	-1.28	0.80722	D	1	B;B	0.09022	0.002;0.001	B;B	0.14023	0.01;0.01	T	0.43294	-0.9400	10	0.02654	T	1	.	13.8354	0.63406	0.0:0.0:0.8474:0.1526	.	2782;2926	Q7Z408;E7EUA6	CSMD2_HUMAN;.	N	2926	ENSP00000362479:H2926N	ENSP00000241312:H2782N	H	-	1	0	CSMD2	33788505	1.000000	0.71417	0.982000	0.44146	0.320000	0.28249	3.614000	0.54160	2.720000	0.93068	0.650000	0.86243	CAC	.	.	.	none		0.572	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		T	34015918	G	T	34015918	3	4	233	1	0	0	0	0	1	0	0	0	3947	1290	45	4	2179	4	CSMD2	1	34015918	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	8387828	34015918	215234703	3	14126											
MACF1	23499	hgsc.bcm.edu	37	chr1	39853737	39853737	+	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	atctgaggaactttactcagGgtctggtagaagatgcccca	11	10	11	9	0	3	3	1	1	2	2	3	4	3	4	2	3	3	1	2	3	4	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:39853737G>C	ENST00000372915.3	+	57	15325	c.15238G>C	c.(15238-15240)Ggt>Cgt	p.G5080R	MACF1_ENST00000361689.2_Missense_Mutation_p.G3013R|MACF1_ENST00000289893.4_Missense_Mutation_p.G3515R|MACF1_ENST00000564288.1_Missense_Mutation_p.G5075R|MACF1_ENST00000539005.1_Missense_Mutation_p.G2992R|MACF1_ENST00000317713.7_Missense_Mutation_p.G3013R|MACF1_ENST00000567887.1_Missense_Mutation_p.G5112R|MACF1_ENST00000545844.1_Missense_Mutation_p.G3013R			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	5080					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)			CTTTACTCAGGGTCTGGTAGA	0.502																																					p.G3013R		Atlas-SNP	.											.	MACF1	909	.	0			c.G9037C						PASS	.						51	52	52					1																	39853737		2203	4300	6503	SO:0001583	missense	23499	exon54			ACTCAGGGTCTGG	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.15238G>C	chr1.hg19:g.39853737G>C	ENSP00000362006:p.Gly5080Arg	139.0	0.0	.		138.0	42.0	.	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.13|17.13	3.311133|3.311133	0.60414|0.60414	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000372925|ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893	.|T;T;T;T;T;T	.|0.32272	.|1.46;1.46;1.46;1.46;1.46;1.46	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	0.000000|0.000000	0.64402|0.64402	D|D	0.000005|0.000005	T|T	0.55273|0.55273	0.1910|0.1910	L|L	0.58101|0.58101	1.795|1.795	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;0.99;0.991	.|D;D;D	.|0.97110	.|1.0;0.952;0.962	T|T	0.43475|0.43475	-0.9389|-0.9389	6|10	.|0.44086	.|T	.|0.13	.|.	20.5568|20.5568	0.99304|0.99304	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|5080;3013;2957	.|Q9UPN3;F8W8Q1;Q9UPN3-3	.|MACF1_HUMAN;.;.	A|R	2125|3013;5080;3013;3013;2992;3515	.|ENSP00000439537:G3013R;ENSP00000362006:G5080R;ENSP00000354573:G3013R;ENSP00000313438:G3013R;ENSP00000444364:G2992R;ENSP00000289893:G3515R	.|ENSP00000289893:G3515R	G|G	+|+	2|1	0|0	MACF1|MACF1	39626324|39626324	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.947000|0.947000	0.59692|0.59692	9.869000|9.869000	0.99810|0.99810	2.861000|2.861000	0.98227|0.98227	0.655000|0.655000	0.94253|0.94253	GGG|GGT	.	.	.	none		0.502	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		C	39853737	G	C	39853737	3	2	233	1	0	0	0	0	1	0	0	0	9151	1232	43	4	15398	4	MACF1	1	39853737	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	5837819	39853737	209396884	4	14127											
MAST2	23139	hgsc.bcm.edu	37	chr1	46496701	46496702	+	Frame_Shift_Del	DEL	TC	TC	-																															tacggaagcggctgtcggtgTctgagtcatcccacacagag																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:46496701_46496702delTC	ENST00000361297.2	+	23	3014_3015	c.2731_2732delTC	c.(2731-2733)tctfs	p.S911fs	MAST2_ENST00000372009.2_Frame_Shift_Del_p.S841fs	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)					GCTGTCGGTGTCTGAGTCATCC	0.629																																					p.910_911del		Pindel	.											.	MAST2	136	.	0			c.2730_2731del						PASS	.																																			SO:0001589	frameshift_variant	23139	exon23			.	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.2731_2732delTC	chr1.hg19:g.46496701_46496702delTC	ENSP00000354671:p.Ser911fs	111.0	0.0	.		99.0	34.0	0.343	NM_015112		Frame_Shift_Del	DEL	ENST00000361297.2	hg19	CCDS41326.1																																																																																			.	.	.	none		0.629	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112		-	46496702	TC	-	46496701	7	5	233	1	0	1	0	1	0	0	0	0	9332	1667	58	0	2821	0	MAST2	1	46496701	Frame_Shift_Del	DEL	TC	TCGA-P4-A5EB-01A-11D-A28G-10	6642964	46496701	202753920	5	14128											
PCSK9	255738	hgsc.bcm.edu	37	chr1	55529096	55529096	+	Frame_Shift_Del	DEL	G	G	-																															ctggctgcagtgccctccctGggacctcccacgtcctgggg																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:55529096delG	ENST00000302118.5	+	12	2208	c.1918delG	c.(1918-1920)gggfs	p.G640fs	PCSK9_ENST00000543384.1_3'UTR|PCSK9_ENST00000490692.1_3'UTR	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	640	C-terminal domain.				apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|kidney development (GO:0001822)|lipoprotein metabolic process (GO:0042157)|liver development (GO:0001889)|low-density lipoprotein particle receptor catabolic process (GO:0032802)|lysosomal transport (GO:0007041)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor recycling (GO:0001920)|neurogenesis (GO:0022008)|neuron differentiation (GO:0030182)|phospholipid metabolic process (GO:0006644)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of receptor internalization (GO:0002092)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)|regulation of neuron apoptotic process (GO:0043523)|regulation of receptor activity (GO:0010469)|triglyceride metabolic process (GO:0006641)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	apolipoprotein binding (GO:0034185)|apolipoprotein receptor binding (GO:0034190)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein particle receptor binding (GO:0050750)|poly(A) RNA binding (GO:0044822)|protein self-association (GO:0043621)|serine-type endopeptidase activity (GO:0004252)|sodium channel inhibitor activity (GO:0019871)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	32						TGCCCTCCCTGGGACCTCCCA	0.662																																					p.P639fs	Pancreas(137;1454 1827 5886 22361 42375)	Atlas-Indel,Pindel	.											.	PCSK9	76	.	0			c.1917delT						PASS	.						34	34	34					1																	55529096		2203	4300	6503	SO:0001589	frameshift_variant	255738	exon12			.	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.1918delG	chr1.hg19:g.55529096delG	ENSP00000303208:p.Gly640fs	177.0	0.0	0		232.0	129.0	0.556035	NM_174936	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Frame_Shift_Del	DEL	ENST00000302118.5	hg19	CCDS603.1																																																																																			.	.	.	none		0.662	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936		-	55529096	G	-	55529096	7	5	233	1	0	1	0	1	0	0	0	0	11613	1348	47	0	1964	0	PCSK9	1	55529096	Frame_Shift_Del	DEL	G	TCGA-P4-A5EB-01A-11D-A28G-10	9032395	55529096	193721525	6	14129											
ITGB3BP	23421	hgsc.bcm.edu	37	chr1	63974218	63974218	+	Missense_Mutation	SNP	T	T	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	cattttcttctaacagaccaTccaacttcagtgatctttta	11	16	3	11	0	4	2	1	1	3	1	5	2	5	2	2	0	2	0	2	0	3	7			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:63974218T>G	ENST00000271002.10	-	2	110	c.29A>C	c.(28-30)gAt>gCt	p.D10A	ITGB3BP_ENST00000371092.3_Missense_Mutation_p.D49A|ITGB3BP_ENST00000283568.8_Missense_Mutation_p.D10A	NM_014288.4	NP_055103.3	Q13352	CENPR_HUMAN	integrin beta 3 binding protein (beta3-endonexin)	10					apoptotic signaling pathway (GO:0097190)|cell adhesion (GO:0007155)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleosome assembly (GO:0006334)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|signal transducer activity (GO:0004871)	p.D10G(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|upper_aerodigestive_tract(1)	9						TAACAGACCATCCAACTTCAG	0.259																																					p.D49A		Atlas-SNP	.											ITGB3BP,larynx,carcinoma,0,1	ITGB3BP	20	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.A146C						PASS	.						28	28	28					1																	63974218		2149	4215	6364	SO:0001583	missense	23421	exon3			AGACCATCCAACT	U37139	CCDS30736.1, CCDS55603.1	1p31.3	2013-11-05			ENSG00000142856	ENSG00000142856			6157	protein-coding gene	gene with protein product	"centromere protein R"	605494				7593198, 10490654	Standard	NM_014288		Approved	NRIF3, HSU37139, TAP20, CENPR	uc001dbb.2	Q13352	OTTHUMG00000013364	ENST00000271002.10:c.29A>C	chr1.hg19:g.63974218T>G	ENSP00000271002:p.Asp10Ala	292.0	2.0	.		201.0	53.0	.	NM_001206739	B2R7D8|Q13353|Q5RJ42|Q5RJ44|Q5RJ45|Q7KYX2|Q96CD5|Q9UKB6	Missense_Mutation	SNP	ENST00000271002.10	hg19	CCDS30736.1	.	.	.	.	.	.	.	.	.	.	T	3.341	-0.134587	0.06711	.	.	ENSG00000142856	ENST00000271002;ENST00000371092;ENST00000283568	T;T;T	0.67698	-0.27;0.25;-0.28	4.91	3.79	0.43588	.	0.260117	0.25997	N	0.026964	T	0.46073	0.1374	N	0.19112	0.55	0.38496	D	0.948093	P;P;P	0.51537	0.944;0.946;0.78	P;P;B	0.50825	0.651;0.592;0.265	T	0.53947	-0.8366	10	0.66056	D	0.02	-2.1447	10.3835	0.44125	0.0:0.0772:0.0:0.9228	.	10;49;10	Q13352-2;Q13352-5;Q13352	.;.;CENPR_HUMAN	A	10;49;10	ENSP00000271002:D10A;ENSP00000360133:D49A;ENSP00000283568:D10A	ENSP00000271002:D10A	D	-	2	0	ITGB3BP	63746806	1.000000	0.71417	0.469000	0.27204	0.029000	0.11900	5.252000	0.65445	0.732000	0.32470	-0.256000	0.11100	GAT	.	.	.	none		0.259	ITGB3BP-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000037242.2	NM_014288		G	63974218	T	G	63974218	3	3	233	1	0	0	0	0	1	0	0	0	7903	1435	50	5	532	5	ITGB3BP	1	63974218	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	8445122	63974218	185276403	7	14130											
GNG12	55970	hgsc.bcm.edu	37	chr1	68171150	68171150	+	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	tccactataagatgatgcaaGtttttttatccttgaaaggg	12	15	8	6	0	0	3	0	2	0	1	2	3	2	3	2	1	1	2	2	1	5	7			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:68171150G>C	ENST00000370982.3	-	4	402	c.203C>G	c.(202-204)aCt>aGt	p.T68S		NM_018841.5	NP_061329.3	Q9UBI6	GBG12_HUMAN	guanine nucleotide binding protein (G protein), gamma 12	68					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						GATGATGCAAGTTTTTTTATC	0.433																																					p.T68S		Atlas-SNP	.											.,1	GNG12	11	.	0			c.C203G						PASS	.						173	163	167					1																	68171150		2203	4300	6503	SO:0001583	missense	55970	exon4			ATGCAAGTTTTTT	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.203C>G	chr1.hg19:g.68171150G>C	ENSP00000360021:p.Thr68Ser	73.0	0.0	.		89.0	43.0	.	NM_018841	Q69YP5|Q9BRV5	Missense_Mutation	SNP	ENST00000370982.3	hg19	CCDS30749.1	.	.	.	.	.	.	.	.	.	.	G	17.02	3.282741	0.59867	.	.	ENSG00000172380	ENST00000370982	T	0.20200	2.09	5.79	5.79	0.91817	G-protein gamma domain (3);	0.054877	0.85682	D	0.000000	T	0.05502	0.0145	.	.	.	0.41685	D	0.98931	B	0.27625	0.183	B	0.31495	0.131	T	0.08146	-1.0736	9	0.02654	T	1	-5.209	18.8047	0.92032	0.0:0.0:1.0:0.0	.	68	Q9UBI6	GBG12_HUMAN	S	68	ENSP00000360021:T68S	ENSP00000360021:T68S	T	-	2	0	GNG12	67943738	1.000000	0.71417	0.993000	0.49108	0.993000	0.82548	7.072000	0.76777	2.749000	0.94314	0.491000	0.48974	ACT	.	.	.	none		0.433	GNG12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026355.2			C	68171150	G	C	68171150	3	2	233	1	0	0	0	0	1	0	0	0	6532	1029	36	4	19	4	GNG12	1	68171150	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	4196932	68171150	181079471	8	14131											
ZBTB7B	51043	hgsc.bcm.edu	37	chr1	154987232	154987232	+	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	gagcagcgccagctgggccaCctatgtgacctcaccatccg	8	6	11	16	2	1	1	1	1	0	0	2	2	2	1	6	1	3	2	6	1	1	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:154987232C>G	ENST00000368426.3	+	3	233	c.96C>G	c.(94-96)caC>caG	p.H32Q	ZBTB7B_ENST00000535420.1_Missense_Mutation_p.H32Q|ZBTB7B_ENST00000417934.2_Missense_Mutation_p.H66Q|ZBTB7B_ENST00000487542.1_3'UTR|ZBTB7B_ENST00000292176.2_Missense_Mutation_p.H32Q	NM_001256455.1	NP_001243384.1	O15156	ZBT7B_HUMAN	zinc finger and BTB domain containing 7B	32					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)			AGCTGGGCCACCTATGTGACC	0.587																																					p.H66Q		Atlas-SNP	.											.	ZBTB7B	69	.	0			c.C198G						PASS	.						68	69	69					1																	154987232		2203	4300	6503	SO:0001583	missense	51043	exon4			GGGCCACCTATGT	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.96C>G	chr1.hg19:g.154987232C>G	ENSP00000357411:p.His32Gln	77.0	0.0	.		80.0	26.0	.	NM_001252406	B4E3K5|D3DV83|J3KQQ3|Q68DR2|Q96EP2	Missense_Mutation	SNP	ENST00000368426.3	hg19	CCDS1081.1	.	.	.	.	.	.	.	.	.	.	C	10.76	1.439712	0.25900	.	.	ENSG00000160685	ENST00000535420;ENST00000368426;ENST00000417934;ENST00000292176	T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2	3.59	-1.19	0.09585	BTB/POZ (1);BTB/POZ fold (2);	0.413847	0.21695	N	0.070510	T	0.12561	0.0305	N	0.02539	-0.55	0.27857	N	0.940546	B;B;B	0.09022	0.002;0.001;0.002	B;B;B	0.08055	0.003;0.002;0.003	T	0.21075	-1.0256	10	0.66056	D	0.02	.	5.0228	0.14370	0.0:0.4765:0.1713:0.3521	.	32;32;66	A8K6F4;O15156;B4E3K5	.;ZBT7B_HUMAN;.	Q	32;32;66;32	ENSP00000438647:H32Q;ENSP00000357411:H32Q;ENSP00000406286:H66Q;ENSP00000292176:H32Q	ENSP00000292176:H32Q	H	+	3	2	ZBTB7B	153253856	0.762000	0.28451	0.963000	0.40424	0.981000	0.71138	-0.185000	0.09684	-0.072000	0.12864	-0.379000	0.06801	CAC	.	.	.	none		0.587	ZBTB7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091083.1	NM_015872		G	154987232	C	G	154987232	3	3	233	1	0	0	0	0	1	0	0	0	17566	506	18	4	98	4	ZBTB7B	1	154987232	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	86816082	154987232	94263389	9	14132											
RCOR3	55758	hgsc.bcm.edu	37	chr1	211462545	211462545	+	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	tactgaacaacctgtccaaaCtagcaagattggacttggaa	15	9	8	9	0	0	2	0	1	0	1	1	4	1	4	2	2	5	1	2	2	7	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:211462545C>A	ENST00000367005.4	+	7	713	c.572C>A	c.(571-573)aCt>aAt	p.T191N	RCOR3_ENST00000419091.2_Missense_Mutation_p.T249N|RCOR3_ENST00000367006.4_Missense_Mutation_p.T249N|RCOR3_ENST00000452621.2_Missense_Mutation_p.T249N	NM_018254.3	NP_060724.1	Q9P2K3	RCOR3_HUMAN	REST corepressor 3	191					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.00961)|all cancers(67;0.0999)|Epithelial(68;0.171)		CCTGTCCAAACTAGCAAGATT	0.378																																					p.T249N		Atlas-SNP	.											RCOR3,caecum,carcinoma,0,1	RCOR3	51	.	0			c.C746A						PASS	.						127	113	118					1																	211462545		2203	4300	6503	SO:0001583	missense	55758	exon8			TCCAAACTAGCAA	AK001738	CCDS31016.1, CCDS44312.1, CCDS44313.1, CCDS44314.1	1q32.3	2008-02-05			ENSG00000117625	ENSG00000117625			25594	protein-coding gene	gene with protein product						10718198	Standard	NM_018254		Approved	FLJ10876	uc010psw.2	Q9P2K3	OTTHUMG00000036996	ENST00000367005.4:c.572C>A	chr1.hg19:g.211462545C>A	ENSP00000355972:p.Thr191Asn	181.0	0.0	.		244.0	26.0	.	NM_001136223	B3KYA2|B4DYY7|Q5VT47|Q7L9I5|Q8N5U3|Q9NV83	Missense_Mutation	SNP	ENST00000367005.4	hg19	CCDS31016.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.33|13.33	2.205841|2.205841	0.39003|0.39003	.|.	.|.	ENSG00000117625|ENSG00000117625	ENST00000534460|ENST00000367006;ENST00000452621;ENST00000419091;ENST00000367005;ENST00000529763	.|T;T;T;T	.|0.28454	.|1.61;1.61;1.61;1.61	5.62|5.62	4.7|4.7	0.59300|0.59300	.|.	.|0.488580	.|0.25119	.|N	.|0.032996	T|T	0.17874|0.17874	0.0429|0.0429	N|N	0.11201|0.11201	0.11|0.11	0.38814|0.38814	D|D	0.955493|0.955493	.|B;B;B;B	.|0.17268	.|0.002;0.0;0.021;0.018	.|B;B;B;B	.|0.15052	.|0.003;0.001;0.006;0.012	T|T	0.06250|0.06250	-1.0837|-1.0837	5|10	.|0.14252	.|T	.|0.57	-7.2822|-7.2822	16.1088|16.1088	0.81244|0.81244	0.0:0.8548:0.1452:0.0|0.0:0.8548:0.1452:0.0	.|.	.|249;191;249;249	.|Q9P2K3-3;Q9P2K3;Q9P2K3-2;Q9P2K3-4	.|.;RCOR3_HUMAN;.;.	K|N	35|249;249;249;191;9	.|ENSP00000355973:T249N;ENSP00000398558:T249N;ENSP00000413929:T249N;ENSP00000355972:T191N	.|ENSP00000355972:T191N	N|T	+|+	3|2	2|0	RCOR3|RCOR3	209529168|209529168	0.981000|0.981000	0.34729|0.34729	0.995000|0.995000	0.50966|0.50966	0.997000|0.997000	0.91878|0.91878	2.148000|2.148000	0.42235|0.42235	1.335000|1.335000	0.45486|0.45486	0.655000|0.655000	0.94253|0.94253	AAC|ACT	.	.	.	none		0.378	RCOR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089821.1	NM_018254		A	211462545	C	A	211462545	3	1	233	1	0	0	0	0	1	0	0	0	13197	565	20	4	776	4	RCOR3	1	211462545	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	56475313	211462545	37788076	10	14133											
AKT3	10000	hgsc.bcm.edu	37	chr1	243800913	243800913	+	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	aactttaataaatcagttacCtttgcaataatgacttcttt	14	17	3	7	0	2	1	1	1	1	0	2	1	2	1	1	0	3	2	1	0	7	8			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr1:243800913C>T	ENST00000366539.1	-	6	761	c.561G>A	c.(559-561)aaG>aaA	p.K187K	AKT3_ENST00000263826.5_Splice_Site_p.K187K|AKT3_ENST00000366540.1_Splice_Site_p.K187K|AKT3_ENST00000336199.5_Splice_Site_p.K187K			Q9Y243	AKT3_HUMAN	v-akt murine thymoma viral oncogene homolog 3	187	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitochondrial genome maintenance (GO:0000002)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|skin(3)|stomach(1)	26	all_cancers(71;0.000307)|all_epithelial(71;0.000374)|all_lung(81;0.0323)|Ovarian(71;0.0619)|all_neural(11;0.101)|Lung NSC(105;0.168)	all_cancers(173;0.0274)	all cancers(7;4.3e-08)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00196)			AATCAGTTACCTTTGCAATAA	0.328																																					p.K187K		Atlas-SNP	.											.	AKT3	177	.	0			c.G561A						PASS	.						81	81	81					1																	243800913		2202	4295	6497	SO:0001630	splice_region_variant	10000	exon6			AGTTACCTTTGCA	AF124141	CCDS31076.1, CCDS31077.1	1q44	2013-07-09	2013-07-09		ENSG00000117020	ENSG00000117020	2.7.11.1	"Pleckstrin homology (PH) domain containing"	393	protein-coding gene	gene with protein product	"protein kinase B, gamma"	611223				10092583, 10208883	Standard	NM_005465		Approved	PKBG, RAC-gamma, PRKBG	uc001iab.2	Q9Y243	OTTHUMG00000039994	ENST00000366539.1:c.561+1G>A	chr1.hg19:g.243800913C>T		75.0	0.0	.		42.0	6.0	.	NM_001206729	Q0VAA6|Q5VTI1|Q5VTI2|Q96QV3|Q9UFP5	Silent	SNP	ENST00000366539.1	hg19	CCDS31077.1																																																																																			.	.	.	none		0.328	AKT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096479.1	NM_181690	Silent	T	243800913	C	T	243800913	5	4	233	1	0	0	0	0	0	0	1	0	481	695	24	2	962	2	AKT3	1	243800913	Splice_Site	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	32338368	243800913	5449708	11	14134											
KCNS3	3790	hgsc.bcm.edu	37	chr2	18113163	18113163	+	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	cagatcctacggcttatgagGattttccgaattctaaagct	11	13	8	9	2	1	2	0	1	1	1	3	4	3	3	2	2	2	2	2	2	5	6			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:18113163G>C	ENST00000403915.1	+	3	1339	c.888G>C	c.(886-888)agG>agC	p.R296S	KCNS3_ENST00000465292.1_Intron|KCNS3_ENST00000304101.4_Missense_Mutation_p.R296S	NM_001282428.1	NP_001269357.1	Q9BQ31	KCNS3_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3	296					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)			endometrium(5)|kidney(1)|large_intestine(7)|lung(11)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					GGCTTATGAGGATTTTCCGAA	0.502																																					p.R296S		Atlas-SNP	.											.	KCNS3	85	.	0			c.G888C						PASS	.						109	107	108					2																	18113163		2203	4300	6503	SO:0001583	missense	3790	exon3			TATGAGGATTTTC	AF043472	CCDS1692.1	2p24	2011-07-05			ENSG00000170745	ENSG00000170745		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6302	protein-coding gene	gene with protein product		603888				10484328, 16382104	Standard	NM_002252		Approved	Kv9.3	uc002rcw.3	Q9BQ31	OTTHUMG00000044150	ENST00000403915.1:c.888G>C	chr2.hg19:g.18113163G>C	ENSP00000385968:p.Arg296Ser	161.0	0.0	.		220.0	83.0	.	NM_002252	D6W520|O43651|Q4ZFY1|Q96B56	Missense_Mutation	SNP	ENST00000403915.1	hg19	CCDS1692.1	.	.	.	.	.	.	.	.	.	.	G	15.35	2.808968	0.50421	.	.	ENSG00000170745	ENST00000403915;ENST00000304101	D;D	0.99594	-6.25;-6.25	5.86	1.98	0.26296	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99638	0.9867	H	0.96301	3.8	0.52099	D	0.999942	D	0.76494	0.999	D	0.85130	0.997	D	0.99194	1.0871	10	0.87932	D	0	.	6.5286	0.22314	0.2607:0.1183:0.621:0.0	.	296	Q9BQ31	KCNS3_HUMAN	S	296	ENSP00000385968:R296S;ENSP00000305824:R296S	ENSP00000305824:R296S	R	+	3	2	KCNS3	17976644	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.263000	0.33004	0.374000	0.24650	0.655000	0.94253	AGG	.	.	.	none		0.502	KCNS3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323808.1	NM_002252		C	18113163	G	C	18113163	3	2	233	1	0	0	0	0	1	0	0	0	8097	1165	41	4	890	4	KCNS3	2	18113163	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10		18113163	225086210	12	14135											
KHK	3795	hgsc.bcm.edu	37	chr2	27315218	27315218	+	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	aggtgtttgtcccagagatgGcagcgcggaggcaacgcgtc	8	7	16	10	4	0	1	0	0	0	1	2	3	1	2	1	4	2	3	1	4	1	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:27315218G>T	ENST00000260599.6	+	2	624	c.111G>T	c.(109-111)tgG>tgT	p.W37C	KHK_ENST00000260598.5_Missense_Mutation_p.W37C|KHK_ENST00000490823.1_3'UTR	NM_000221.2	NP_000212.1	P50053	KHK_HUMAN	ketohexokinase (fructokinase)	37					carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose catabolic process (GO:0006001)|regulation of glycogen metabolic process (GO:0070873)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ketohexokinase activity (GO:0004454)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCCAGAGATGGCAGCGCGGAG	0.607																																					p.W37C		Atlas-SNP	.											.	KHK	60	.	0			c.G111T						PASS	.						91	80	84					2																	27315218		2203	4300	6503	SO:0001583	missense	3795	exon2			GAGATGGCAGCGC		CCDS1734.1, CCDS1735.1	2p23.3-p23.2	2008-02-05			ENSG00000138030	ENSG00000138030	2.7.1.3		6315	protein-coding gene	gene with protein product		614058				7833921	Standard	NM_000221		Approved		uc002rim.2	P50053	OTTHUMG00000097077	ENST00000260599.6:c.111G>T	chr2.hg19:g.27315218G>T	ENSP00000260599:p.Trp37Cys	32.0	0.0	.		65.0	31.0	.	NM_006488	Q6IBK2|Q99532|Q9BRJ3|Q9UMN1	Missense_Mutation	SNP	ENST00000260599.6	hg19	CCDS1734.1	.	.	.	.	.	.	.	.	.	.	G	15.16	2.750913	0.49257	.	.	ENSG00000138030	ENST00000260599;ENST00000260598;ENST00000429697	T;T;T	0.75938	-0.98;-0.98;-0.98	5.5	5.5	0.81552	Carbohydrate/purine kinase (1);	0.000000	0.85682	D	0.000000	D	0.88377	0.6420	M	0.90082	3.085	0.80722	D	1	D;P;D	0.76494	0.999;0.495;0.999	D;B;D	0.75020	0.985;0.122;0.985	D	0.89208	0.3562	10	0.46703	T	0.11	-18.2402	16.8828	0.86067	0.0:0.0:1.0:0.0	.	37;37;37	Q6IBK2;P50053-2;P50053	.;.;KHK_HUMAN	C	37	ENSP00000260599:W37C;ENSP00000260598:W37C;ENSP00000404741:W37C	ENSP00000260598:W37C	W	+	3	0	KHK	27168722	1.000000	0.71417	1.000000	0.80357	0.325000	0.28411	8.964000	0.93389	2.595000	0.87683	0.462000	0.41574	TGG	.	.	.	none		0.607	KHK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214196.1			T	27315218	G	T	27315218	3	4	233	1	0	0	0	0	1	0	0	0	8156	1212	42	4	117	4	KHK	2	27315218	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	9202055	27315218	215884155	13	14136											
ERLEC1	27248	hgsc.bcm.edu	37	chr2	54028861	54028861	+	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	actgaacaggttcagagcatCtcctgtgaatgacatatttt	12	13	8	8	0	2	4	1	3	1	1	3	4	2	4	1	1	2	2	1	1	3	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:54028861C>A	ENST00000185150.4	+	8	892	c.761C>A	c.(760-762)tCt>tAt	p.S254Y	ERLEC1_ENST00000378239.5_Missense_Mutation_p.S254Y|ERLEC1_ENST00000405123.3_Missense_Mutation_p.S254Y|GPR75-ASB3_ENST00000352846.3_Intron|ASB3_ENST00000498475.2_Intron|ASB3_ENST00000406625.2_Intron	NM_015701.4	NP_056516.2	Q96DZ1	ERLEC_HUMAN	endoplasmic reticulum lectin 1	254					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum lumen (GO:0005788)	glycoprotein binding (GO:0001948)			endometrium(2)|large_intestine(4)|lung(8)|ovary(2)|stomach(1)|urinary_tract(1)	18						TTCAGAGCATCTCCTGTGAAT	0.418																																					p.S254Y		Atlas-SNP	.											.	ERLEC1	32	.	0			c.C761A						PASS	.						102	92	96					2																	54028861		2203	4300	6503	SO:0001583	missense	27248	exon8			GAGCATCTCCTGT	AF131849	CCDS1848.1, CCDS46283.1, CCDS46284.1	2p16	2010-03-19	2009-08-26	2009-08-26	ENSG00000068912	ENSG00000068912			25222	protein-coding gene	gene with protein product	"erlectin 1"	611229	"chromosome 2 open reading frame 30"	C2orf30		9110174, 8619474, 16531414, 18264092	Standard	NM_015701		Approved	CL25084, XTP3TPB, XTP3-B, ERLECTIN	uc002rxl.3	Q96DZ1	OTTHUMG00000129281	ENST00000185150.4:c.761C>A	chr2.hg19:g.54028861C>A	ENSP00000185150:p.Ser254Tyr	122.0	0.0	.		128.0	61.0	.	NM_015701	B2RDB4|B5MC72|O95901|Q6UWN7|Q9NUY7|Q9UQL4	Missense_Mutation	SNP	ENST00000185150.4	hg19	CCDS1848.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.909863	0.92107	.	.	ENSG00000068912	ENST00000405123;ENST00000185150;ENST00000378239	T;T	0.47528	0.84;0.84	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.71350	0.3329	.	.	.	0.80722	D	1	D;P;D	0.71674	0.997;0.756;0.998	D;B;D	0.69479	0.964;0.283;0.931	T	0.72567	-0.4254	9	0.72032	D	0.01	-13.4706	20.4024	0.99000	0.0:1.0:0.0:0.0	.	254;254;254	Q96DZ1-2;B5MC72;Q96DZ1	.;.;ERLEC_HUMAN	Y	254	ENSP00000385629:S254Y;ENSP00000185150:S254Y	ENSP00000185150:S254Y	S	+	2	0	ERLEC1	53882365	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.827000	0.97445	0.650000	0.86243	TCT	.	.	.	none		0.418	ERLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251404.1	NM_015701		A	54028861	C	A	54028861	3	1	233	1	0	0	0	0	1	0	0	0	5233	913	32	4	791	4	ERLEC1	2	54028861	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	26713643	54028861	189170512	14	14137											
NAGK	55577	hgsc.bcm.edu	37	chr2	71304704	71304704	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccaggtcttgttccagggcaAgattggactccccatcctgt	7	11	10	13	0	1	1	0	0	1	1	4	2	4	2	5	3	0	2	5	3	1	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:71304704A>G	ENST00000244204.6	+	9	844	c.782A>G	c.(781-783)aAg>aGg	p.K261R	NAGK_ENST00000443872.2_Missense_Mutation_p.K113R|NAGK_ENST00000455662.2_Missense_Mutation_p.K307R|NAGK_ENST00000443938.2_Missense_Mutation_p.K257R|NAGK_ENST00000418807.3_Missense_Mutation_p.K210R			Q9UJ70	NAGK_HUMAN	N-acetylglucosamine kinase	261					carbohydrate phosphorylation (GO:0046835)|N-acetylglucosamine metabolic process (GO:0006044)|N-acetylmannosamine metabolic process (GO:0006051)|N-acetylneuraminate catabolic process (GO:0019262)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|N-acetylglucosamine kinase activity (GO:0045127)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|urinary_tract(1)	18					N-Acetyl-D-glucosamine(DB00141)	TTCCAGGGCAAGATTGGACTC	0.602																																					p.K307R		Atlas-SNP	.											.	NAGK	34	.	0			c.A920G						PASS	.						66	53	57					2																	71304704		2203	4300	6503	SO:0001583	missense	55577	exon9			AGGGCAAGATTGG	AJ242910	CCDS33220.1, CCDS33220.2	2p24.3-p24.1	2008-02-05			ENSG00000124357	ENSG00000124357	2.7.1.59		17174	protein-coding gene	gene with protein product		606828				10824116	Standard	NM_017567		Approved	GNK	uc002shp.4	Q9UJ70	OTTHUMG00000153239	ENST00000244204.6:c.782A>G	chr2.hg19:g.71304704A>G	ENSP00000244204:p.Lys261Arg	59.0	0.0	.		99.0	38.0	.	NM_017567	B4DLZ5|Q53HD5|Q6IA84|Q9BS29|Q9BVP0|Q9NV37	Missense_Mutation	SNP	ENST00000244204.6	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.73|11.73	1.724892|1.724892	0.30593|0.30593	.|.	.|.	ENSG00000124357|ENSG00000124357	ENST00000244204;ENST00000455662;ENST00000418807|ENST00000443938	T;T;T|.	0.44083|.	1.52;1.49;0.93|.	5.63|5.63	1.85|1.85	0.25348|0.25348	ATPase, BadF/BadG/BcrA/BcrD type (1);|.	0.811995|.	0.11191|.	N|.	0.589950|.	T|T	0.17619|0.17619	0.0423|0.0423	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.18398|0.18398	-1.0338|-1.0338	10|5	0.18276|.	T|.	0.48|.	-17.2471|-17.2471	2.0065|2.0065	0.03478|0.03478	0.4877:0.2795:0.0916:0.1411|0.4877:0.2795:0.0916:0.1411	.|.	261|.	Q9UJ70|.	NAGK_HUMAN|.	R|G	261;307;210|279	ENSP00000244204:K261R;ENSP00000389087:K307R;ENSP00000396070:K210R|.	ENSP00000244204:K261R|.	K|R	+|+	2|1	0|2	NAGK|NAGK	71158212|71158212	0.037000|0.037000	0.19845|0.19845	0.003000|0.003000	0.11579|0.11579	0.043000|0.043000	0.13939|0.13939	1.412000|1.412000	0.34714|0.34714	0.937000|0.937000	0.37394|0.37394	-0.336000|-0.336000	0.08194|0.08194	AAG|AGA	.	.	.	none		0.602	NAGK-032	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471889.1			G	71304704	A	G	71304704	3	3	233	1	0	0	0	0	1	0	0	0	10149	72	3	3	954	3	NAGK	2	71304704	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	17275843	71304704	171894669	15	14138											
UGGT1	56886	hgsc.bcm.edu	37	chr2	128941262	128941262	+	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	tattcagtgcactatatgttGtggatctgaagaagtttagg	11	15	11	4	0	2	2	1	1	1	1	2	3	2	3	0	2	1	3	0	2	6	7			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:128941262G>T	ENST00000259253.6	+	38	4305	c.4258G>T	c.(4258-4260)Gtg>Ttg	p.V1420L	UGGT1_ENST00000375990.3_Missense_Mutation_p.V1396L	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	1420	Glucosyltransferase. {ECO:0000250}.				'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						ACTATATGTTGTGGATCTGAA	0.438																																					p.V1420L		Atlas-SNP	.											.	UGGT1	126	.	0			c.G4258T						PASS	.						107	102	104					2																	128941262		2203	4300	6503	SO:0001583	missense	56886	exon38			TATGTTGTGGATC	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.4258G>T	chr2.hg19:g.128941262G>T	ENSP00000259253:p.Val1420Leu	140.0	0.0	.		141.0	59.0	.	NM_020120	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Missense_Mutation	SNP	ENST00000259253.6	hg19	CCDS2154.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.733269	0.89482	.	.	ENSG00000136731	ENST00000375990;ENST00000259253	T;T	0.37411	1.2;1.2	4.66	4.66	0.58398	.	0.000000	0.85682	D	0.000000	T	0.71978	0.3404	H	0.96175	3.78	0.80722	D	1	D	0.71674	0.998	D	0.69307	0.963	T	0.82600	-0.0377	9	.	.	.	.	18.0955	0.89488	0.0:0.0:1.0:0.0	.	1420	Q9NYU2	UGGG1_HUMAN	L	1396;1420	ENSP00000365158:V1396L;ENSP00000259253:V1420L	.	V	+	1	0	UGGT1	128657732	1.000000	0.71417	0.994000	0.49952	0.844000	0.47949	9.090000	0.94144	2.577000	0.86979	0.563000	0.77884	GTG	.	.	.	none		0.438	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120		T	128941262	G	T	128941262	3	4	233	1	0	0	0	0	1	0	0	0	16953	1377	48	4	4408	4	UGGT1	2	128941262	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	57636558	128941262	114258111	16	14139											
YSK4	80122	hgsc.bcm.edu	37	chr2	135744072	135744072	+	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	ttcatggactgctcaggtgtCtgagccaagttcatgggatg	8	12	13	8	0	4	1	3	1	1	0	4	3	4	3	1	3	2	2	1	3	1	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:135744072C>G	ENST00000375845.3	-	7	2400	c.2370G>C	c.(2368-2370)caG>caC	p.Q790H	MAP3K19_ENST00000392917.3_Intron|MAP3K19_ENST00000392918.3_Intron|MAP3K19_ENST00000392915.1_Missense_Mutation_p.Q807H|MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000375844.3_Intron|MAP3K19_ENST00000358371.4_Missense_Mutation_p.Q677H	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	790							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)										GCTCAGGTGTCTGAGCCAAGT	0.398																																					p.Q790H		Atlas-SNP	.											.	.	.	.	0			c.G2370C						PASS	.						65	65	65					2																	135744072		2203	4300	6503	SO:0001583	missense	80122	exon7			AGGTGTCTGAGCC	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.2370G>C	chr2.hg19:g.135744072C>G	ENSP00000365005:p.Gln790His	80.0	0.0	.		112.0	40.0	.	NM_025052	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	hg19	CCDS2176.2	.	.	.	.	.	.	.	.	.	.	C	0.926	-0.714163	0.03206	.	.	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000392915;ENST00000437365	T;T;T;T	0.72615	-0.53;-0.53;1.83;-0.67	4.61	0.257	0.15574	.	0.519636	0.16240	N	0.223204	T	0.48607	0.1509	N	0.17082	0.46	0.09310	N	0.999998	B;B;B	0.23854	0.023;0.092;0.014	B;B;B	0.22880	0.028;0.042;0.013	T	0.31971	-0.9924	10	0.35671	T	0.21	.	6.5935	0.22659	0.0:0.5532:0.2308:0.2159	.	677;807;790	Q56UN5-3;A8MWG7;Q56UN5	.;.;YSK4_HUMAN	H	790;677;807;180	ENSP00000365005:Q790H;ENSP00000351140:Q677H;ENSP00000376647:Q807H;ENSP00000392827:Q180H	ENSP00000351140:Q677H	Q	-	3	2	YSK4	135460542	0.000000	0.05858	0.005000	0.12908	0.148000	0.21650	-0.294000	0.08309	0.133000	0.18654	0.407000	0.27541	CAG	.	.	.	none		0.398	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052		G	135744072	C	G	135744072	3	3	233	1	0	0	0	0	1	0	0	0	17507	912	32	4	1632	4	YSK4	2	135744072	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	6802810	135744072	107455301	17	14140											
GCA	25801	hgsc.bcm.edu	37	chr2	163208899	163208899	+	Missense_Mutation	SNP	A	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	gatgtttgacacagtctggaAttaatggaacttactctcgt	11	14	9	7	1	2	1	0	1	2	0	3	4	2	3	0	2	2	1	0	2	4	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:163208899A>C	ENST00000437150.2	+	3	405	c.244A>C	c.(244-246)Att>Ctt	p.I82L	GCA_ENST00000233612.4_Missense_Mutation_p.I63L|GCA_ENST00000473240.1_3'UTR|GCA_ENST00000429691.2_Missense_Mutation_p.I63L	NM_012198.3	NP_036330.1	P28676	GRAN_HUMAN	grancalcin, EF-hand calcium binding protein	82	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				membrane fusion (GO:0061025)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|lung(4)|ovary(1)	9						ACAGTCTGGAATTAATGGAAC	0.308																																					p.I82L		Atlas-SNP	.											.	GCA	15	.	0			c.A244C						PASS	.						175	175	175					2																	163208899		2203	4300	6503	SO:0001583	missense	25801	exon3			TCTGGAATTAATG	M81637	CCDS2218.1	2q24.2	2013-01-10	2001-11-28		ENSG00000115271	ENSG00000115271		"EF-hand domain containing"	15990	protein-coding gene	gene with protein product		607030	"grancalcin, EF-hand calcium-binding protein"			1737748, 1530588, 12804766	Standard	NM_012198		Approved	GCL	uc002ucg.3	P28676	OTTHUMG00000132057	ENST00000437150.2:c.244A>C	chr2.hg19:g.163208899A>C	ENSP00000394842:p.Ile82Leu	111.0	0.0	.		119.0	58.0	.	NM_012198	B2R5X3|Q53TB5|Q59EP3	Missense_Mutation	SNP	ENST00000437150.2	hg19	CCDS2218.1	.	.	.	.	.	.	.	.	.	.	A	15.48	2.845886	0.51164	.	.	ENSG00000115271	ENST00000446271;ENST00000429691;ENST00000437150;ENST00000453113;ENST00000233612	T;T;T;T;T	0.75260	-0.92;-0.92;-0.92;-0.92;-0.92	5.19	5.19	0.71726	EF-hand-like domain (1);	0.726139	0.12958	N	0.425264	T	0.77471	0.4135	M	0.72118	2.19	0.52501	D	0.999952	B	0.33940	0.433	B	0.43536	0.423	T	0.69892	-0.5022	10	0.09843	T	0.71	.	14.0628	0.64810	1.0:0.0:0.0:0.0	.	82	P28676	GRAN_HUMAN	L	108;63;82;63;63	ENSP00000393218:I108L;ENSP00000412899:I63L;ENSP00000394842:I82L;ENSP00000403805:I63L;ENSP00000233612:I63L	ENSP00000233612:I63L	I	+	1	0	GCA	162917145	1.000000	0.71417	1.000000	0.80357	0.797000	0.45037	6.473000	0.73572	1.951000	0.56629	0.528000	0.53228	ATT	.	.	.	none		0.308	GCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255080.3	NM_012198		C	163208899	A	C	163208899	3	2	233	1	0	0	0	0	1	0	0	0	6290	101	4	5	254	5	GCA	2	163208899	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	27464827	163208899	79990474	18	14141											
SPC25	57405	hgsc.bcm.edu	37	chr2	169746011	169746011	+	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	tatgcttttatcgaaaagtgCcagttcgtcctctaccatta	10	15	6	10	2	1	0	0	0	1	0	4	1	2	0	3	0	3	2	3	0	6	6			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:169746011C>G	ENST00000282074.2	-	2	160	c.19G>C	c.(19-21)Gca>Cca	p.A7P	SPC25_ENST00000472216.2_5'UTR	NM_020675.3	NP_065726.1	Q9HBM1	SPC25_HUMAN	SPC25, NDC80 kinetochore complex component	7	Interaction with the N-terminus of SPBC24.|Interaction with the NDC80-NUF2 subcomplex.				chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)	condensed chromosome kinetochore (GO:0000777)|cytosol (GO:0005829)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|urinary_tract(1)	9						TCGAAAAGTGCCAGTTCGTCC	0.368																																					p.A7P		Atlas-SNP	.											SPC25,NS,carcinoma,0,1	SPC25	21	.	0			c.G19C						PASS	.						59	55	57					2																	169746011		2203	4300	6503	SO:0001583	missense	57405	exon2			AAAGTGCCAGTTC	AF225416	CCDS2229.1	2q31.1	2013-06-05	2013-06-05	2007-03-02	ENSG00000152253	ENSG00000152253			24031	protein-coding gene	gene with protein product		609395	"spindle pole body component 25 homolog (S. cerevisiae)", "SPC25, NDC80 kinetochore complex component, homolog (S. cerevisiae)"	SPBC25		12477932	Standard	NM_020675		Approved	MGC22228, AD024	uc002uel.3	Q9HBM1	OTTHUMG00000132181	ENST00000282074.2:c.19G>C	chr2.hg19:g.169746011C>G	ENSP00000282074:p.Ala7Pro	59.0	0.0	.		44.0	18.0	.	NM_020675	A8K4X8|D3DPC0	Missense_Mutation	SNP	ENST00000282074.2	hg19	CCDS2229.1	.	.	.	.	.	.	.	.	.	.	C	8.902	0.956561	0.18507	.	.	ENSG00000152253	ENST00000282074;ENST00000451987	.	.	.	6.16	3.38	0.38709	.	0.449522	0.26963	N	0.021614	T	0.18257	0.0438	L	0.27053	0.805	0.26399	N	0.976457	P	0.43169	0.8	B	0.37943	0.261	T	0.08330	-1.0727	9	0.46703	T	0.11	0.0356	6.4946	0.22136	0.0:0.693:0.1487:0.1583	.	7	Q9HBM1	SPC25_HUMAN	P	7	.	ENSP00000282074:A7P	A	-	1	0	SPC25	169454257	0.107000	0.21998	0.161000	0.22692	0.012000	0.07955	0.142000	0.16096	0.469000	0.27268	-0.142000	0.14014	GCA	.	.	.	none		0.368	SPC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255233.2	NM_020675		G	169746011	C	G	169746011	3	3	233	1	0	0	0	0	1	0	0	0	15034	739	26	4	679	4	SPC25	2	169746011	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	6537112	169746011	73453362	19	14142											
METTL5	29081	hgsc.bcm.edu	37	chr2	170677784	170677784	+	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	tgtcaaatccaacacacaacCtataaatacaaaacacatac	21	7	1	12	0	1	0	1	0	0	0	2	0	2	0	2	0	5	0	2	0	10	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:170677784C>A	ENST00000260953.5	-	3	541		c.e3-1		METTL5_ENST00000410097.1_Splice_Site|METTL5_ENST00000409837.1_Splice_Site|METTL5_ENST00000409965.1_Splice_Site|METTL5_ENST00000308099.3_Splice_Site|METTL5_ENST00000409340.1_Intron|METTL5_ENST00000392640.2_Splice_Site	NM_014168.2	NP_054887.2	Q9NRN9	METL5_HUMAN	methyltransferase like 5								methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)			breast(2)|central_nervous_system(1)|large_intestine(5)|lung(1)|prostate(1)	10						AACACACAACCTATAAATACA	0.299																																					.		Atlas-SNP	.											.	METTL5	24	.	0			c.225-1G>T						PASS	.						75	75	75					2																	170677784		2203	4298	6501	SO:0001630	splice_region_variant	29081	exon4			CACAACCTATAAA	AF201938	CCDS33320.1	2q31.1	2011-01-28			ENSG00000138382	ENSG00000138382			25006	protein-coding gene	gene with protein product						11042152	Standard	XM_005246478		Approved	HSPC133	uc002ufn.3	Q9NRN9	OTTHUMG00000154117	ENST00000260953.5:c.225-1G>T	chr2.hg19:g.170677784C>A		82.0	0.0	.		114.0	39.0	.	NM_014168	D3DPC9|Q9NVX1	Splice_Site	SNP	ENST00000260953.5	hg19	CCDS33320.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.065087	0.76187	.	.	ENSG00000138382	ENST00000409837;ENST00000540464;ENST00000260953;ENST00000409965;ENST00000392640;ENST00000308099;ENST00000410097	.	.	.	5.04	5.04	0.67666	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.7542	0.91826	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	METTL5	170386030	1.000000	0.71417	0.932000	0.37286	0.983000	0.72400	7.590000	0.82653	2.490000	0.84030	0.655000	0.94253	.	.	.	.	none		0.299	METTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333957.1	NM_014168	Intron	A	170677784	C	A	170677784	5	1	233	1	0	0	0	0	0	0	1	0	9510	695	24	4	425	4	METTL5	2	170677784	Splice_Site	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	931773	170677784	72521589	20	14143											
RAPH1	65059	hgsc.bcm.edu	37	chr2	204304774	204304775	+	Frame_Shift_Del	DEL	AC	AC	-																															cagaacaggggcttttgctgAcacacacccttgttggagaa																								rs201752703		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:204304774_204304775delAC	ENST00000319170.5	-	14	3437_3438	c.3138_3139delGT	c.(3136-3141)gtgtcafs	p.S1047fs	RAPH1_ENST00000374493.3_Frame_Shift_Del_p.S1099fs|RAPH1_ENST00000457812.1_Intron|ABI2_ENST00000295851.5_3'UTR	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	1047					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						GCTTTTGCTGACACACACCCTT	0.545																																					p.1047_1047del		Atlas-Indel,Pindel	.											.	RAPH1	118	.	0			c.3139_3140del						PASS	.																																			SO:0001589	frameshift_variant	65059	exon14			.	AJ584699	CCDS2359.1, CCDS2360.1	2q33	2013-01-10	2003-11-25	2003-11-26	ENSG00000173166	ENSG00000173166		"Pleckstrin homology (PH) domain containing"	14436	protein-coding gene	gene with protein product	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 18"	609035	"amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 9"	ALS2CR9, ALS2CR18			Standard	NM_203365		Approved	KIAA1681	uc002vad.3	Q70E73	OTTHUMG00000132876	ENST00000319170.5:c.3138_3139delGT	chr2.hg19:g.204304780_204304781delAC	ENSP00000316543:p.Ser1047fs	75.0	0.0	0		79.0	37.0	0.468354	NM_213589	Q96Q37|Q9C0I2	Frame_Shift_Del	DEL	ENST00000319170.5	hg19	CCDS2359.1																																																																																			.	.	.	none		0.545	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252		-	204304775	AC	-	204304774	7	5	233	1	0	1	0	1	0	0	0	0	13063	275	10	0	617	0	RAPH1	2	204304774	Frame_Shift_Del	DEL	AC	TCGA-P4-A5EB-01A-11D-A28G-10	33626990	204304774	38894599	21	14144											
NHEJ1	79840	hgsc.bcm.edu	37	chr2	220022946	220022946	+	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	cacactagtgtccacctgttCatgccacacctgttgaagat	10	11	7	13	0	1	2	1	1	0	1	2	2	2	2	4	0	1	2	4	0	2	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:220022946C>T	ENST00000356853.5	-	2	272	c.139G>A	c.(139-141)Gaa>Aaa	p.E47K	NHEJ1_ENST00000409720.1_Missense_Mutation_p.E47K	NM_024782.2	NP_079058.1	Q9H9Q4	NHEJ1_HUMAN	nonhomologous end-joining factor 1	47	Globular head.				B cell differentiation (GO:0030183)|central nervous system development (GO:0007417)|DNA recombination (GO:0006310)|double-strand break repair via nonhomologous end joining (GO:0006303)|positive regulation of ligase activity (GO:0051351)|response to ionizing radiation (GO:0010212)|T cell differentiation (GO:0030217)	nonhomologous end joining complex (GO:0070419)|nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(2)	12		Renal(207;0.0915)		Epithelial(149;2.15e-06)|all cancers(144;0.000339)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0112)		TCCACCTGTTCATGCCACACC	0.527								Non-homologous end-joining																													p.E47K		Atlas-SNP	.											.	NHEJ1	26	.	0			c.G139A						PASS	.						158	135	143					2																	220022946		2203	4300	6503	SO:0001583	missense	79840	exon2			CCTGTTCATGCCA	AJ972687	CCDS2432.1	2q35	2014-09-17			ENSG00000187736	ENSG00000187736			25737	protein-coding gene	gene with protein product		611290				16439204, 16439205	Standard	NM_024782		Approved	Cernunnos, XLF, FLJ12610	uc002vjp.4	Q9H9Q4	OTTHUMG00000133127	ENST00000356853.5:c.139G>A	chr2.hg19:g.220022946C>T	ENSP00000349313:p.Glu47Lys	76.0	0.0	.		112.0	47.0	.	NM_024782	B8ZZA4|Q4ZFW7|Q6IA64|Q96JS9	Missense_Mutation	SNP	ENST00000356853.5	hg19	CCDS2432.1	.	.	.	.	.	.	.	.	.	.	C	34	5.320702	0.95682	.	.	ENSG00000187736	ENST00000409720;ENST00000356853;ENST00000457600	T;T;T	0.71698	-0.59;-0.59;-0.59	5.7	5.7	0.88788	DNA double-strand break repair and VJ recombination XRCC4, N-terminal (1);	0.000000	0.85682	U	0.000000	D	0.85414	0.5691	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86392	0.1736	10	0.87932	D	0	0.2919	19.8022	0.96513	0.0:1.0:0.0:0.0	.	47	Q9H9Q4	NHEJ1_HUMAN	K	47	ENSP00000387290:E47K;ENSP00000349313:E47K;ENSP00000407201:E47K	ENSP00000349313:E47K	E	-	1	0	NHEJ1	219731190	0.998000	0.40836	1.000000	0.80357	0.994000	0.84299	4.959000	0.63666	2.683000	0.91414	0.655000	0.94253	GAA	.	.	.	none		0.527	NHEJ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256817.2	NM_024782		T	220022946	C	T	220022946	3	4	233	1	0	0	0	0	1	0	0	0	10409	835	29	2	788	2	NHEJ1	2	220022946	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	15718172	220022946	23176427	22	14145											
SPEG	10290	hgsc.bcm.edu	37	chr2	220354060	220354064	+	Frame_Shift_Del	DEL	TCTTC	TCTTC	-																															attttctctctctcttagatTcttcagctgtgccatctgct																								rs78622154	byFrequency	TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	TCTTC	TCTTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr2:220354060_220354064delTCTTC	ENST00000312358.7	+	36	8452_8456	c.8320_8324delTCTTC	c.(8320-8325)tcttcafs	p.SS2774fs	AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2774	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		TCTCTTAGATTCTTCAGCTGTGCCA	0.62																																					p.2773_2775del		Atlas-Indel,Pindel	.											.	SPEG	272	.	0			c.8319_8323del						PASS	.																																			SO:0001589	frameshift_variant	10290	exon36			.	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"Immunoglobulin superfamily / I-set domain containing"	16901	protein-coding gene	gene with protein product		615950	"aortic preferentially expressed gene 1"	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.8320_8324delTCTTC	chr2.hg19:g.220354060_220354064delTCTTC	ENSP00000311684:p.Ser2774fs	54.0	0.0	0		61.0	25.0	0.409836	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Frame_Shift_Del	DEL	ENST00000312358.7	hg19	CCDS42824.1																																																																																			.	.	.	none		0.62	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		-	220354064	TCTTC	-	220354060	7	5	233	1	0	1	0	1	0	0	0	0	15048	1783	62	0	8474	0	SPEG	2	220354060	Frame_Shift_Del	DEL	TCTTC	TCGA-P4-A5EB-01A-11D-A28G-10	331114	220354060	22845313	23	14146											
SETD5	55209	hgsc.bcm.edu	37	chr3	9475587	9475587	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agagcgtgtattccactcatAattatgggaccactcagagg	12	10	10	9	1	2	2	2	0	0	2	3	3	3	3	2	2	1	1	2	2	3	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:9475587A>G	ENST00000406341.1	+	3	320	c.130A>G	c.(130-132)Aat>Gat	p.N44D	SETD5_ENST00000402466.1_5'UTR|SETD5_ENST00000407969.1_Missense_Mutation_p.N44D|SETD5_ENST00000402198.1_Missense_Mutation_p.N44D|SETD5_ENST00000302463.6_5'UTR			Q9C0A6	SETD5_HUMAN	SET domain containing 5	44										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)		TTCCACTCATAATTATGGGAC	0.468																																					p.N44D		Atlas-SNP	.											.	SETD5	210	.	0			c.A130G						PASS	.						204	200	201					3																	9475587		2010	4171	6181	SO:0001583	missense	55209	exon4			ACTCATAATTATG	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.130A>G	chr3.hg19:g.9475587A>G	ENSP00000383939:p.Asn44Asp	168.0	0.0	.		155.0	41.0	.	NM_001080517	Q6AI17|Q8WUB6|Q9H3X4|Q9H6V7|Q9H7S3|Q9NVI9	Missense_Mutation	SNP	ENST00000406341.1	hg19	CCDS46741.1	.	.	.	.	.	.	.	.	.	.	A	11.09	1.537828	0.27475	.	.	ENSG00000168137	ENST00000450326;ENST00000402198;ENST00000406341;ENST00000407969	T;D;D;D	0.90261	1.45;-2.64;-2.64;-2.59	6.07	6.07	0.98685	.	.	.	.	.	D	0.82986	0.5156	L	0.47716	1.5	0.80722	D	1	P	0.38922	0.651	B	0.30401	0.115	T	0.79579	-0.1745	9	0.11485	T	0.65	-13.9018	9.0586	0.36421	0.8937:0.0:0.1063:0.0	.	44	Q9C0A6	SETD5_HUMAN	D	44	ENSP00000413786:N44D;ENSP00000385852:N44D;ENSP00000383939:N44D;ENSP00000384114:N44D	ENSP00000385852:N44D	N	+	1	0	SETD5	9450587	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.856000	0.75450	2.330000	0.79161	0.477000	0.44152	AAT	.	.	.	none		0.468	SETD5-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318425.1	XM_371614		G	9475587	A	G	9475587	3	3	233	1	0	0	0	0	1	0	0	0	14147	362	13	3	136	3	SETD5	3	9475587	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10		9475587	188546843	24	14147											
DNAH1	25981	hgsc.bcm.edu	37	chr3	52428521	52428521	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctgggggctccatctcgaTcatgactgagaatccggcac	8	9	12	12	2	3	2	1	2	2	1	6	4	5	2	2	3	0	2	2	3	1	0			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:52428521T>C	ENST00000420323.2	+	67	10928	c.10667T>C	c.(10666-10668)aTc>aCc	p.I3556T		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	3621					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)		TCCATCTCGATCATGACTGAG	0.622																																					p.I3556T		Atlas-SNP	.											.	DNAH1	534	.	0			c.T10667C						PASS	.						72	79	77					3																	52428521		2065	4195	6260	SO:0001583	missense	25981	exon67			TCTCGATCATGAC	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.10667T>C	chr3.hg19:g.52428521T>C	ENSP00000401514:p.Ile3556Thr	109.0	0.0	.		115.0	58.0	.	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	hg19	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	T	1.598	-0.527373	0.04141	.	.	ENSG00000114841	ENST00000420323;ENST00000273600	D	0.87103	-2.21	5.27	-5.01	0.02991	.	1.697270	0.03317	N	0.191372	T	0.70996	0.3288	N	0.12569	0.235	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.56721	-0.7932	10	0.33141	T	0.24	.	2.3064	0.04175	0.1418:0.4088:0.1794:0.27	.	3556;3621	C9JXH6;Q9P2D7-2	.;.	T	3556;309	ENSP00000401514:I3556T	ENSP00000273600:I309T	I	+	2	0	DNAH1	52403561	0.000000	0.05858	0.000000	0.03702	0.215000	0.24574	-0.451000	0.06795	-0.554000	0.06150	-0.274000	0.10170	ATC	.	.	.	none		0.622	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		C	52428521	T	C	52428521	3	2	233	1	0	0	0	0	1	0	0	0	4599	1435	50	3	10929	3	DNAH1	3	52428521	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	42952934	52428521	145593909	25	14148											
ABHD6	57406	hgsc.bcm.edu	37	chr3	58242370	58242370	+	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	ggcggcacgctggccatcccAatcctggcatttgtggcttc	5	10	12	14	2	0	0	0	0	0	0	3	0	2	0	3	5	0	4	3	5	1	2	rs11544005		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:58242370A>T	ENST00000478253.1	+	3	558	c.57A>T	c.(55-57)ccA>ccT	p.P19P	ABHD6_ENST00000295962.4_Silent_p.P19P			Q9BV23	ABHD6_HUMAN	abhydrolase domain containing 6	19					long term synaptic depression (GO:0060292)|negative regulation of cell migration (GO:0030336)|regulation of endocannabinoid signaling pathway (GO:2000124)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acylglycerol lipase activity (GO:0047372)			NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)	16				BRCA - Breast invasive adenocarcinoma(55;0.000225)|KIRC - Kidney renal clear cell carcinoma(284;0.0471)|Kidney(284;0.0589)|OV - Ovarian serous cystadenocarcinoma(275;0.209)		TGGCCATCCCAATCCTGGCAT	0.463																																					p.P19P		Atlas-SNP	.											.	ABHD6	28	.	0			c.A57T						PASS	.						174	165	168					3																	58242370		2203	4300	6503	SO:0001819	synonymous_variant	57406	exon2			CATCCCAATCCTG	AF225418	CCDS2887.1	3p21.2	2006-03-10			ENSG00000163686	ENSG00000163686		"Abhydrolase domain containing"	21398	protein-coding gene	gene with protein product							Standard	NM_020676		Approved		uc003djs.4	Q9BV23	OTTHUMG00000159150	ENST00000478253.1:c.57A>T	chr3.hg19:g.58242370A>T		106.0	0.0	.		103.0	23.0	.	NM_020676	B2R7Y9|Q6ZMF7	Silent	SNP	ENST00000478253.1	hg19	CCDS2887.1																																																																																			.	.	.	alt		0.463	ABHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353511.1	NM_020676		T	58242370	A	T	58242370	2	4	233	1	0	0	0	0	0	0	0	1	86	117	5	5		5	ABHD6	3	58242370	Silent	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	5813849	58242370	139780060	26	14149											
CBLB	868	hgsc.bcm.edu	37	chr3	105572285	105572285	+	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	gtgactgttcttcatacattCtctccttgccttctttaaag	7	18	5	11	0	4	1	1	1	3	0	6	1	5	1	2	0	2	1	2	0	3	8			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:105572285C>A	ENST00000264122.4	-	3	713	c.392G>T	c.(391-393)aGa>aTa	p.R131I	CBLB_ENST00000394027.3_Missense_Mutation_p.R153I|CBLB_ENST00000403724.1_Missense_Mutation_p.R131I|CBLB_ENST00000405772.1_Missense_Mutation_p.R131I|CBLB_ENST00000545639.1_Missense_Mutation_p.R153I	NM_170662.3	NP_733762.2	Q13191	CBLB_HUMAN	Cbl proto-oncogene B, E3 ubiquitin protein ligase	131	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)			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						TTCATACATTCTCTCCTTGCC	0.343			Mis S		AML																																p.R131I	GBM(93;588 1337 9788 29341 43499)	Atlas-SNP	.		Rec	yes		3	3q13.11	868	Cas-Br-M (murine) ecotropic retroviral transforming sequence b		L	.	CBLB	118	.	0			c.G392T						PASS	.						240	242	241					3																	105572285		2203	4300	6503	SO:0001583	missense	868	exon3			TACATTCTCTCCT	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.392G>T	chr3.hg19:g.105572285C>A	ENSP00000264122:p.Arg131Ile	145.0	0.0	.		135.0	33.0	.	NM_170662	A8K9S7|B7WNM4|Q13192|Q13193|Q3LIC0|Q63Z43|Q8IVC5	Missense_Mutation	SNP	ENST00000264122.4	hg19	CCDS2948.1	.	.	.	.	.	.	.	.	.	.	C	33	5.280158	0.95489	.	.	ENSG00000114423	ENST00000264122;ENST00000394027;ENST00000403724;ENST00000405772;ENST00000545639;ENST00000438603;ENST00000447441;ENST00000443752	T;T;T;T;T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16;-1.16;-1.16;-1.16;-1.16	5.69	5.69	0.88448	Adaptor protein Cbl, N-terminal helical (3);Adaptor protein Cbl, PTB domain (1);	0.000000	0.85682	D	0.000000	D	0.85991	0.5826	L	0.50333	1.59	0.80722	D	1	D;D;D	0.69078	0.997;0.997;0.997	D;D;D	0.74348	0.983;0.972;0.937	D	0.86563	0.1842	10	0.87932	D	0	-13.8454	19.8034	0.96518	0.0:1.0:0.0:0.0	.	153;131;131	E7ENW2;Q13191-3;Q13191	.;.;CBLB_HUMAN	I	131;153;131;131;153;153;131;131	ENSP00000264122:R131I;ENSP00000377595:R153I;ENSP00000384816:R131I;ENSP00000384938:R131I;ENSP00000446116:R153I;ENSP00000409750:R153I;ENSP00000400949:R131I;ENSP00000393906:R131I	ENSP00000264122:R131I	R	-	2	0	CBLB	107054975	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.603000	0.82811	2.669000	0.90835	0.655000	0.94253	AGA	.	.	.	none		0.343	CBLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319417.2	NM_170662		A	105572285	C	A	105572285	3	1	233	1	0	0	0	0	1	0	0	0	2703	913	32	4	2624	4	CBLB	3	105572285	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	47329915	105572285	92450145	27	14150											
EAF2	55840	hgsc.bcm.edu	37	chr3	121554190	121554190	+	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	gcgagcgggttctcaagttaGgggagagtttcgagaagcag	10	8	17	6	3	1	2	1	0	1	2	3	5	1	2	0	3	2	4	0	3	3	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:121554190G>A	ENST00000273668.2	+	1	129	c.58G>A	c.(58-60)Ggg>Agg	p.G20R	EAF2_ENST00000465664.1_3'UTR|EAF2_ENST00000451944.2_Missense_Mutation_p.G20R|IQCB1_ENST00000310864.6_5'Flank|IQCB1_ENST00000349820.6_5'Flank	NM_018456.4	NP_060926.2	Q96CJ1	EAF2_HUMAN	ELL associated factor 2	20	Necessary for interaction with ELL.				apoptotic process (GO:0006915)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	ELL-EAF complex (GO:0032783)|transcription elongation factor complex (GO:0008023)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)	9				GBM - Glioblastoma multiforme(114;0.0972)		TCTCAAGTTAGGGGAGAGTTT	0.592																																					p.G20R	Esophageal Squamous(194;1942 2097 24663 29345 31866)	Atlas-SNP	.											.	EAF2	26	.	0			c.G58A						PASS	.						60	57	58					3																	121554190		2203	4300	6503	SO:0001583	missense	55840	exon1			AAGTTAGGGGAGA	AF517829	CCDS3006.1	3q21.1	2007-08-01			ENSG00000145088	ENSG00000145088			23115	protein-coding gene	gene with protein product		607659				12446457, 12907652	Standard	NM_018456		Approved	BM040, TRAITS, U19	uc003een.3	Q96CJ1	OTTHUMG00000159424	ENST00000273668.2:c.58G>A	chr3.hg19:g.121554190G>A	ENSP00000273668:p.Gly20Arg	75.0	0.0	.		97.0	9.0	.	NM_018456	Q9NZ82	Missense_Mutation	SNP	ENST00000273668.2	hg19	CCDS3006.1	.	.	.	.	.	.	.	.	.	.	G	36	5.612769	0.96637	.	.	ENSG00000145088	ENST00000273668;ENST00000451944	.	.	.	5.95	5.95	0.96441	Transcription elognation factor  Eaf, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.84238	0.5428	M	0.85945	2.785	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.85853	0.1405	9	0.87932	D	0	-12.3041	17.8686	0.88804	0.0:0.0:1.0:0.0	.	20	Q96CJ1	EAF2_HUMAN	R	20	.	ENSP00000273668:G20R	G	+	1	0	EAF2	123036880	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.606000	0.82863	2.817000	0.96982	0.563000	0.77884	GGG	.	.	.	none		0.592	EAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355247.1	NM_018456		A	121554190	G	A	121554190	3	1	233	1	0	0	0	0	1	0	0	0	4878	1000	35	2	60	2	EAF2	3	121554190	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	15981905	121554190	76468240	28	14151											
PARP14	54625	hgsc.bcm.edu	37	chr3	122436993	122436993	+	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	agactttgtccagaaaggatCagcccagtctgtgaaaaaag	15	8	10	8	0	2	3	1	1	1	2	3	4	3	4	2	1	1	0	2	1	4	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:122436993C>G	ENST00000474629.2	+	13	4342	c.4076C>G	c.(4075-4077)tCa>tGa	p.S1359*		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1359	Macro 3. {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)		CAGAAAGGATCAGCCCAGTCT	0.388																																					p.S1359X		Atlas-SNP	.											.	PARP14	242	.	0			c.C4076G						PASS	.						88	82	84					3																	122436993		1860	4108	5968	SO:0001587	stop_gained	54625	exon13			AAGGATCAGCCCA	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.4076C>G	chr3.hg19:g.122436993C>G	ENSP00000418194:p.Ser1359*	165.0	0.0	.		185.0	102.0	.	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Nonsense_Mutation	SNP	ENST00000474629.2	hg19	CCDS46894.1	.	.	.	.	.	.	.	.	.	.	C	40	8.082615	0.98646	.	.	ENSG00000173193	ENST00000474629;ENST00000398162;ENST00000398157	.	.	.	5.28	-1.14	0.09741	.	1.436610	0.04490	N	0.379296	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	.	5.3252	0.15903	0.1259:0.4927:0.0:0.3814	.	.	.	.	X	1359;1278;355	.	ENSP00000381224:S355X	S	+	2	0	PARP14	123919683	0.000000	0.05858	0.000000	0.03702	0.971000	0.66376	0.777000	0.26718	-0.442000	0.07190	0.650000	0.86243	TCA	.	.	.	none		0.388	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		G	122436993	C	G	122436993	4	3	233	1	0	0	0	0	0	1	0	0	11465	838	29	4	4126	4	PARP14	3	122436993	Nonsense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	882803	122436993	75585437	29	14152											
RBP2	5948	hgsc.bcm.edu	37	chr3	139195286	139195286	+	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	ctccatctcccaggttccatTctggtcccttgtcatggtgg	4	14	9	14	0	3	0	1	0	2	0	7	0	6	0	4	4	0	1	4	4	0	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:139195286T>A	ENST00000232217.2	-	1	72	c.16A>T	c.(16-18)Aat>Tat	p.N6Y	RP11-319G6.1_ENST00000515247.1_RNA	NM_004164.2	NP_004155.2	P50120	RET2_HUMAN	retinol binding protein 2, cellular	6					epidermis development (GO:0008544)|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)			breast(1)|large_intestine(1)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	12					Vitamin A(DB00162)	CAGGTTCCATTCTGGTCCCTT	0.537																																					p.N6Y		Atlas-SNP	.											.	RBP2	21	.	0			c.A16T						PASS	.						154	132	139					3																	139195286		2203	4300	6503	SO:0001583	missense	5948	exon1			TTCCATTCTGGTC	U13831	CCDS3109.1	3q23	2013-03-01	2001-11-28		ENSG00000114113	ENSG00000114113		"Fatty acid binding protein family"	9920	protein-coding gene	gene with protein product		180280	"retinol-binding protein 2, cellular"			7657783, 10072590	Standard	NM_004164		Approved	CRBP2, RBPC2, CRBPII, CRABP-II	uc003eth.3	P50120	OTTHUMG00000159956	ENST00000232217.2:c.16A>T	chr3.hg19:g.139195286T>A	ENSP00000232217:p.Asn6Tyr	76.0	0.0	.		74.0	11.0	.	NM_004164	A8K7G3|Q6ISQ9|Q6ISS7	Missense_Mutation	SNP	ENST00000232217.2	hg19	CCDS3109.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.138577	0.77775	.	.	ENSG00000114113	ENST00000232217;ENST00000511956;ENST00000506825	T;T	0.08102	3.13;3.13	5.44	5.44	0.79542	Calycin-like (1);Cytosolic fatty-acid binding (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.550372	0.21049	N	0.081028	T	0.17023	0.0409	L	0.29908	0.895	0.54753	D	0.999987	D	0.76494	0.999	D	0.68039	0.955	T	0.01666	-1.1300	10	0.44086	T	0.13	.	13.5403	0.61671	0.0:0.0:0.0:1.0	.	6	P50120	RET2_HUMAN	Y	6	ENSP00000232217:N6Y;ENSP00000424333:N6Y	ENSP00000232217:N6Y	N	-	1	0	RBP2	140677976	1.000000	0.71417	0.998000	0.56505	0.970000	0.65996	3.604000	0.54081	2.194000	0.70268	0.460000	0.39030	AAT	.	.	.	none		0.537	RBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358490.1	NM_004164		A	139195286	T	A	139195286	3	1	233	1	0	0	0	0	1	0	0	0	13169	1783	62	5	404	5	RBP2	3	139195286	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	16758293	139195286	58827144	30	14153											
ZBTB38	253461	hgsc.bcm.edu	37	chr3	141162052	141162058	+	Frame_Shift_Del	DEL	TTCGGAT	TTCGGAT	-																															acattctccataccacaggaTtcggattcagccacagaaaa																								rs549239683		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	TTCGGAT	TTCGGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:141162052_141162058delTTCGGAT	ENST00000514251.1	+	4	1101_1107	c.822_828delTTCGGAT	c.(820-828)gattcggatfs	p.DSD274fs	ZBTB38_ENST00000441582.2_Frame_Shift_Del_p.DSD274fs|ZBTB38_ENST00000321464.5_Frame_Shift_Del_p.DSD275fs					zinc finger and BTB domain containing 38											breast(3)|cervix(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	41						TACCACAGGATTCGGATTCAGCCACAG	0.459																																					p.274_276del		Atlas-Indel,Pindel	.											.	ZBTB38	92	.	0			c.821_827del						PASS	.																																			SO:0001589	frameshift_variant	253461	exon8			.	BC015444	CCDS43157.1	3q23	2014-06-13			ENSG00000177311	ENSG00000177311		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	26636	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 171"	612218				12477932	Standard	NM_001080412		Approved	FLJ35036, CIBZ, ZNF921, PPP1R171	uc003etw.3	Q8NAP3	OTTHUMG00000160128	ENST00000514251.1:c.822_828delTTCGGAT	chr3.hg19:g.141162052_141162058delTTCGGAT	ENSP00000426387:p.Asp274fs	74.0	0.0	0		65.0	14.0	0.215385	NM_001080412		Frame_Shift_Del	DEL	ENST00000514251.1	hg19	CCDS43157.1																																																																																			.	.	.	none		0.459	ZBTB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359329.2			-	141162058	TTCGGAT	-	141162052	7	5	233	1	0	1	0	1	0	0	0	0	17551	1490	52	0	824	0	ZBTB38	3	141162052	Frame_Shift_Del	DEL	TTCGGAT	TCGA-P4-A5EB-01A-11D-A28G-10	1966766	141162052	56860378	31	14154											
HPS3	84343	hgsc.bcm.edu	37	chr3	148857880	148857881	+	Frame_Shift_Ins	INS	-	-	GT																															taaaaggactgaaaactctcINSgtgtgtgtatccgaatgatt																								rs541164156		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:148857880_148857881insGT	ENST00000296051.2	+	2	447_448	c.307_308insGT	c.(307-309)cgtfs	p.R103fs	HPS3_ENST00000460120.1_Intron	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	103					organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)		p.R103S(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)			TGAAAACTCTCGTGTGTGTATC	0.426									Hermansky-Pudlak syndrome																												p.R103fs		Atlas-Indel,Pindel	.											HPS3,NS,carcinoma,0,1	HPS3	104	.	1	Substitution - Missense(1)	lung(1)	c.307_308insGT						PASS	.																																			SO:0001589	frameshift_variant	84343	exon2	Familial Cancer Database	HPS, HPS1-8	.	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.314_315dupGT	chr3.hg19:g.148857887_148857888dupGT	ENSP00000296051:p.Arg103fs	145.0	0.0	0		131.0	30.0	0.229008	NM_032383	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Frame_Shift_Ins	INS	ENST00000296051.2	hg19	CCDS3140.1																																																																																			.	.	.	none		0.426	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383		GT	148857881	-	GT	148857880	7	5	233	1	0	1	1	0	0	0	0	0	7347	884	31	0	313	0	HPS3	3	148857880	Frame_Shift_Ins	INS	-	TCGA-P4-A5EB-01A-11D-A28G-10	7695828	148857880	49164550	32	14155											
PLD1	5337	hgsc.bcm.edu	37	chr3	171395429	171395429	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcctttccatgccagaatctGgtttccccatgcagctctcc	6	13	6	16	0	2	1	0	0	2	1	6	1	5	1	6	1	3	3	6	1	1	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:171395429G>A	ENST00000351298.4	-	17	2049	c.1923C>T	c.(1921-1923)acC>acT	p.T641T	PLD1_ENST00000356327.5_Silent_p.T603T|PLD1_ENST00000340989.4_Silent_p.T641T|PLD1_ENST00000342215.6_Missense_Mutation_p.P532L	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific	641	Catalytic.				chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	GCCAGAATCTGGTTTCCCCAT	0.498																																					p.T641T	NSCLC(149;2174 3517 34058)	Atlas-SNP	.											.	PLD1	134	.	0			c.C1923T						PASS	.						169	150	157					3																	171395429		2203	4300	6503	SO:0001819	synonymous_variant	5337	exon17			GAATCTGGTTTCC	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.1923C>T	chr3.hg19:g.171395429G>A		141.0	0.0	.		118.0	31.0	.	NM_002662		Silent	SNP	ENST00000351298.4	hg19	CCDS3216.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.196234	0.38806	.	.	ENSG00000075651	ENST00000342215	T	0.34072	1.38	6.16	0.406	0.16366	.	.	.	.	.	T	0.25827	0.0629	.	.	.	0.30550	N	0.765587	.	.	.	.	.	.	T	0.31110	-0.9955	6	0.27785	T	0.31	-24.3912	4.8638	0.13598	0.1371:0.3306:0.4295:0.1029	.	.	.	.	L	532	ENSP00000339936:P532L	ENSP00000339936:P532L	P	-	2	0	PLD1	172878123	0.948000	0.32251	0.748000	0.31131	0.981000	0.71138	0.123000	0.15708	0.117000	0.18138	0.650000	0.86243	CCA	.	.	.	none		0.498	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662		A	171395429	G	A	171395429	2	1	233	1	0	0	0	0	0	0	0	1	12052	1335	47	2		2	PLD1	3	171395429	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	22537549	171395429	26627001	33	14156											
RFC4	5984	hgsc.bcm.edu	37	chr3	186508173	186508173	+	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	gacaggcagcaaatactccaTcaattttctcagctggtatt	12	12	7	10	0	2	0	2	0	1	0	4	1	3	0	1	2	3	4	1	2	4	5			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr3:186508173T>A	ENST00000392481.2	-	9	1105	c.824A>T	c.(823-825)gAt>gTt	p.D275V	RFC4_ENST00000296273.2_Missense_Mutation_p.D275V|RFC4_ENST00000433496.1_Intron|SNORA63_ENST00000363450.1_RNA|SNORA4_ENST00000584302.1_RNA	NM_181573.2	NP_853551.1	P35249	RFC4_HUMAN	replication factor C (activator 1) 4, 37kDa	275					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)	p.D275G(1)		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)		AAATACTCCATCAATTTTCTC	0.428																																					p.D275V		Atlas-SNP	.											RFC4,NS,carcinoma,0,1	RFC4	54	.	1	Substitution - Missense(1)	kidney(1)	c.A824T						PASS	.						112	112	112					3																	186508173		2203	4300	6503	SO:0001583	missense	5984	exon9			ACTCCATCAATTT		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.824A>T	chr3.hg19:g.186508173T>A	ENSP00000376272:p.Asp275Val	182.0	0.0	.		144.0	36.0	.	NM_181573	B4DM41|D3DNV2|Q6FHX7	Missense_Mutation	SNP	ENST00000392481.2	hg19	CCDS3283.1	.	.	.	.	.	.	.	.	.	.	T	11.55	1.670832	0.29693	.	.	ENSG00000163918	ENST00000392481;ENST00000296273;ENST00000417876	T;T;T	0.44083	0.93;0.93;0.93	5.32	2.79	0.32731	Replication factor C (1);DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal (1);	0.428568	0.30538	N	0.009405	T	0.44808	0.1311	M	0.84326	2.69	0.80722	D	1	B	0.18013	0.025	B	0.27887	0.084	T	0.46373	-0.9196	10	0.54805	T	0.06	.	6.9715	0.24652	0.0:0.0842:0.1493:0.7664	.	275	P35249	RFC4_HUMAN	V	275;275;50	ENSP00000376272:D275V;ENSP00000296273:D275V;ENSP00000401429:D50V	ENSP00000296273:D275V	D	-	2	0	RFC4	187990867	0.999000	0.42202	0.697000	0.30258	0.437000	0.31866	2.471000	0.45127	0.970000	0.38263	0.459000	0.35465	GAT	.	.	.	none		0.428	RFC4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344471.1	NM_002916		A	186508173	T	A	186508173	3	1	233	1	0	0	0	0	1	0	0	0	13260	1435	50	5	279	5	RFC4	3	186508173	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	15112744	186508173	11514257	34	14157											
HTT	3064	hgsc.bcm.edu	37	chr4	3162057	3162057	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaagtttggagggtttctcCgctcagccttggatgttctt	7	15	11	8	1	3	0	1	0	2	0	4	2	3	2	2	3	1	4	2	3	2	5			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr4:3162057C>T	ENST00000355072.5	+	29	3947	c.3802C>T	c.(3802-3804)Cgc>Tgc	p.R1268C		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	1268					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)		AGGGTTTCTCCGCTCAGCCTT	0.512																																					p.R1268C		Atlas-SNP	.											.	HTT	221	.	0			c.C3802T						PASS	.																																			SO:0001583	missense	3064	exon29			TTTCTCCGCTCAG	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.3802C>T	chr4.hg19:g.3162057C>T	ENSP00000347184:p.Arg1268Cys	173.0	0.0	.		181.0	67.0	.	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	C	11.56	1.674542	0.29693	.	.	ENSG00000197386	ENST00000355072	T	0.65916	-0.18	4.27	4.27	0.50696	.	0.000000	0.85682	D	0.000000	T	0.57740	0.2074	L	0.52364	1.645	0.80722	D	1	B	0.18166	0.026	B	0.11329	0.006	T	0.57946	-0.7723	10	0.44086	T	0.13	.	16.6252	0.84968	0.0:1.0:0.0:0.0	.	1268	P42858	HD_HUMAN	C	1268	ENSP00000347184:R1268C	ENSP00000347184:R1268C	R	+	1	0	HTT	3131855	1.000000	0.71417	1.000000	0.80357	0.221000	0.24807	4.125000	0.57931	2.069000	0.61940	0.563000	0.77884	CGC	.	.	.	none		0.512	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		T	3162057	C	T	3162057	3	4	233	1	0	0	0	0	1	0	0	0	7464	652	23	1	3916	1	HTT	4	3162057	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10		3162057	187992219	35	14158											
PI4K2B	55300	hgsc.bcm.edu	37	chr4	25235821	25235821	+	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	gagcccgaccggttggcgtcCgcggacggcgggagcccgga	5	3	19	14	8	0	0	0	0	0	0	1	5	1	3	4	6	2	1	4	6	0	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr4:25235821C>A	ENST00000264864.6	+	1	225	c.36C>A	c.(34-36)tcC>tcA	p.S12S	PI4K2B_ENST00000512921.1_Intron	NM_018323.3	NP_060793.2	Q8TCG2	P4K2B_HUMAN	phosphatidylinositol 4-kinase type 2 beta	12					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(3)|skin(3)	15		Breast(46;0.173)				GGTTGGCGTCCGCGGACGGCG	0.731																																					p.S12S		Atlas-SNP	.											.	PI4K2B	42	.	0			c.C36A						PASS	.						3	3	3					4																	25235821		1446	3354	4800	SO:0001819	synonymous_variant	55300	exon1			GGCGTCCGCGGAC	AK001967	CCDS3433.1	4p15.31	2009-05-07			ENSG00000038210	ENSG00000038210			18215	protein-coding gene	gene with protein product		612101				11923287	Standard	NM_018323		Approved	PI4KIIB, FLJ11105, PIK42B	uc003grk.2	Q8TCG2	OTTHUMG00000128564	ENST00000264864.6:c.36C>A	chr4.hg19:g.25235821C>A		7.0	0.0	.		44.0	13.0	.	NM_018323	Q9NUW2	Silent	SNP	ENST00000264864.6	hg19	CCDS3433.1																																																																																			.	.	.	none		0.731	PI4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250415.1	NM_018323		A	25235821	C	A	25235821	2	1	233	1	0	0	0	0	0	0	0	1	11879	639	23	4		4	PI4K2B	4	25235821	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	22073764	25235821	165918455	36	14159											
ARAP2	116984	hgsc.bcm.edu	37	chr4	36152575	36152575	+	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	gccaggcagataacttcattGatattaatggtgccattagg	12	12	10	7	0	1	2	1	1	0	1	1	2	1	2	2	3	2	1	2	3	4	6			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr4:36152575G>T	ENST00000303965.4	-	16	3333	c.2844C>A	c.(2842-2844)atC>atA	p.I948I		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	948	PH 3. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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						TAACTTCATTGATATTAATGG	0.343																																					p.I948I		Atlas-SNP	.											ARAP2,NS,carcinoma,0,1	ARAP2	210	.	0			c.C2844A						PASS	.						169	174	172					4																	36152575		2203	4298	6501	SO:0001819	synonymous_variant	116984	exon16			TTCATTGATATTA	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.2844C>A	chr4.hg19:g.36152575G>T		121.0	1.0	.		115.0	36.0	.	NM_015230	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Silent	SNP	ENST00000303965.4	hg19	CCDS3441.1																																																																																			.	.	.	none		0.343	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230		T	36152575	G	T	36152575	2	4	233	1	0	0	0	0	0	0	0	1	839	1280	45	4		4	ARAP2	4	36152575	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	10916754	36152575	155001701	37	14160											
RCHY1	25898	hgsc.bcm.edu	37	chr4	76416940	76416940	+	Frame_Shift_Del	DEL	A	A	-																															agatgttactttacctatgtAaaagatgtccacatggcaag																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr4:76416940delA	ENST00000324439.5	-	6	901	c.503delT	c.(502-504)ttafs	p.L168fs	RCHY1_ENST00000380840.2_Frame_Shift_Del_p.L128fs|RCHY1_ENST00000512706.1_Frame_Shift_Del_p.L146fs|RCHY1_ENST00000451788.1_Frame_Shift_Del_p.L168fs|RCHY1_ENST00000513257.1_Frame_Shift_Del_p.L168fs|RCHY1_ENST00000514021.1_5'Flank	NM_001278536.1|NM_001278538.1|NM_001278539.1	NP_001265465.1|NP_001265467.1|NP_001265468.1	Q96PM5	ZN363_HUMAN	ring finger and CHY zinc finger domain containing 1, E3 ubiquitin protein ligase	168					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(2)|pancreas(1)	3			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			TTACCTATGTAAAAGATGTCC	0.308																																					p.L168fs		Atlas-Indel,Pindel	.											.	RCHY1	17	.	0			c.504delA						PASS	.						59	59	59					4																	76416940		2203	4297	6500	SO:0001589	frameshift_variant	25898	exon6			.	AF255666	CCDS3567.1, CCDS34012.1, CCDS63990.1, CCDS63991.1, CCDS63992.1	4q21.1-q21.3	2014-02-17	2012-02-23	2004-03-30	ENSG00000163743	ENSG00000163743		"RING-type (C3HC4) zinc fingers"	17479	protein-coding gene	gene with protein product	"androgen-receptor N-terminal-interacting protein", "p53-induced protein with a RING-H2 domain", "zinc finger, CHY-type"	607680	"zinc finger protein 363", "ring finger and CHY zinc finger domain containing 1"	ZNF363		12654245	Standard	NM_015436		Approved	CHIMP, DKFZp586C1620, PRO1996, RNF199, ARNIP, PIRH2, ZCHY	uc003hik.3	Q96PM5	OTTHUMG00000130105	ENST00000324439.5:c.503delT	chr4.hg19:g.76416940delA	ENSP00000321239:p.Leu168fs	282.0	0.0	0		221.0	125.0	0.565611	NM_001008925	B3KRG3|C7E541|C7E542|C7E543|D3YRV2|E7EMC8|E7ETW5|J3KPI0|Q2KN33|Q59GN7|Q86X26|Q96PR5	Frame_Shift_Del	DEL	ENST00000324439.5	hg19	CCDS3567.1																																																																																			.	.	.	none		0.308	RCHY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252411.2	NM_015436		-	76416940	A	-	76416940	7	5	233	1	0	1	0	1	0	0	0	0	13190	372	13	0	298	0	RCHY1	4	76416940	Frame_Shift_Del	DEL	A	TCGA-P4-A5EB-01A-11D-A28G-10	40264365	76416940	114737336	38	14161											
SYNPO2	171024	hgsc.bcm.edu	37	chr4	119952707	119952707	+	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	acctcctcctgtggcctataAtcctatccactcgccgtctt	6	13	5	17	2	1	0	0	0	1	0	6	0	5	0	7	1	0	0	7	1	3	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr4:119952707A>T	ENST00000429713.2	+	4	2959	c.2777A>T	c.(2776-2778)aAt>aTt	p.N926I	SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000434046.2_Missense_Mutation_p.N926I|SYNPO2_ENST00000307142.4_Missense_Mutation_p.N926I	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	926						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						GTGGCCTATAATCCTATCCAC	0.572																																					p.N926I		Atlas-SNP	.											.	SYNPO2	353	.	0			c.A2777T						PASS	.						87	83	84					4																	119952707		2203	4300	6503	SO:0001583	missense	171024	exon4			CCTATAATCCTAT	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.2777A>T	chr4.hg19:g.119952707A>T	ENSP00000395143:p.Asn926Ile	58.0	0.0	.		78.0	11.0	.	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	hg19	CCDS47129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.9|20.9	4.067512|4.067512	0.76301|0.76301	.|.	.|.	ENSG00000172403|ENSG00000172403	ENST00000307142;ENST00000429713;ENST00000434046|ENST00000504178	T;T;T|.	0.14893|.	2.47;2.58;2.47|.	5.66|5.66	5.66|5.66	0.87406|0.87406	.|.	0.000000|.	0.64402|.	D|.	0.000002|.	T|.	0.77239|.	0.4101|.	M|M	0.80982|0.80982	2.52|2.52	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;0.999;0.997|.	D;D;D;D|.	0.91635|.	0.998;0.999;0.997;0.972|.	T|.	0.78874|.	-0.2032|.	9|.	.|.	.|.	.|.	-24.3416|-24.3416	15.8861|15.8861	0.79251|0.79251	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	926;926;926;926|.	B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6|.	.;.;.;SYNP2_HUMAN|.	I|Y	926|877	ENSP00000306015:N926I;ENSP00000395143:N926I;ENSP00000390965:N926I|.	.|.	N|X	+|+	2|3	0|2	SYNPO2|SYNPO2	120172155|120172155	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.914000|0.914000	0.54420|0.54420	9.339000|9.339000	0.96797|0.96797	2.156000|2.156000	0.67533|0.67533	0.533000|0.533000	0.62120|0.62120	AAT|TAA	.	.	.	none		0.572	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1			T	119952707	A	T	119952707	3	4	233	1	0	0	0	0	1	0	0	0	15469	101	4	5	2791	5	SYNPO2	4	119952707	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	43535767	119952707	71201569	39	14162											
SMAD1	4086	hgsc.bcm.edu	37	chr4	146463798	146463798	+	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	acccaggatggctctcagccGatggacacaaacatgatggc	12	6	11	12	1	1	1	1	1	1	0	2	4	1	3	2	4	2	1	2	4	1	0			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr4:146463798G>A	ENST00000515385.1	+	4	1265	c.723G>A	c.(721-723)ccG>ccA	p.P241P	SMAD1_ENST00000302085.4_Silent_p.P241P|SMAD1_ENST00000394092.2_Silent_p.P241P			Q15797	SMAD1_HUMAN	SMAD family member 1	241					BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cardiac muscle cell proliferation (GO:0060038)|cartilage development (GO:0051216)|cellular response to BMP stimulus (GO:0071773)|embryonic pattern specification (GO:0009880)|gamete generation (GO:0007276)|hindbrain development (GO:0030902)|homeostatic process (GO:0042592)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|mesodermal cell fate commitment (GO:0001710)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|negative regulation of muscle cell apoptotic process (GO:0010656)|osteoblast fate commitment (GO:0002051)|positive regulation of cartilage development (GO:0061036)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of gene expression (GO:0010628)|positive regulation of osteoblast differentiation (GO:0045669)|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)|primary miRNA processing (GO:0031053)|protein phosphorylation (GO:0006468)|response to drug (GO:0042493)|response to organonitrogen compound (GO:0010243)|signal transduction (GO:0007165)|SMAD protein complex assembly (GO:0007183)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|mitochondrion (GO:0005739)|nuclear inner membrane (GO:0005637)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	co-SMAD binding (GO:0070410)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)			endometrium(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	17	all_hematologic(180;0.151)					GCTCTCAGCCGATGGACACAA	0.473																																					p.P241P	Pancreas(182;1287 2092 10326 35158 50562)	Atlas-SNP	.											.	SMAD1	48	.	0			c.G723A						PASS	.						65	68	67					4																	146463798		2203	4300	6503	SO:0001819	synonymous_variant	4086	exon4			TCAGCCGATGGAC	U59423	CCDS3765.1	4q31.21	2013-10-22	2006-11-06	2004-05-26	ENSG00000170365	ENSG00000170365		"SMADs"	6767	protein-coding gene	gene with protein product		601595	"MAD, mothers against decapentaplegic homolog 1 (Drosophila)", "SMAD, mothers against DPP homolog 1 (Drosophila)"	MADH1		8653785, 8673135	Standard	NM_005900		Approved	MADR1, JV4-1	uc003ikc.3	Q15797	OTTHUMG00000161592	ENST00000515385.1:c.723G>A	chr4.hg19:g.146463798G>A		89.0	0.0	.		88.0	4.0	.	NM_005900	A8KAJ0|D3DNZ9|Q16636|Q9UFT8	Silent	SNP	ENST00000515385.1	hg19	CCDS3765.1																																																																																			.	.	.	none		0.473	SMAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365467.1	NM_005900		A	146463798	G	A	146463798	2	1	233	1	0	0	0	0	0	0	0	1	14770	1045	37	1		1	SMAD1	4	146463798	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	26511091	146463798	44690478	40	14163											
IQGAP2	10788	hgsc.bcm.edu	37	chr5	75888702	75888702	+	Missense_Mutation	SNP	G	G	A																															aagaaagagatgcttatgaaGaactgctgacacaagcagaa																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr5:75888702G>A	ENST00000274364.6	+	9	1156	c.859G>A	c.(859-861)Gaa>Aaa	p.E287K	IQGAP2_ENST00000379730.3_5'UTR	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	287					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		TGCTTATGAAGAACTGCTGAC	0.323																																					p.E287K		Atlas-SNP	.											.	IQGAP2	186	.	0			c.G859A						PASS	.						138	145	142					5																	75888702		2203	4300	6503	SO:0001583	missense	10788	exon9			TATGAAGAACTGC	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.859G>A	chr5.hg19:g.75888702G>A	ENSP00000274364:p.Glu287Lys	316.0	0.0	.		466.0	78.0	.	NM_006633	A8K4V1|B7Z8A4|J3KR91	Missense_Mutation	SNP	ENST00000274364.6	hg19	CCDS34188.1	.	.	.	.	.	.	.	.	.	.	G	32	5.141279	0.94560	.	.	ENSG00000145703	ENST00000274364;ENST00000514350;ENST00000505766	T;T;T	0.39787	4.12;1.06;4.13	5.83	5.83	0.93111	.	0.100666	0.64402	D	0.000002	T	0.54287	0.1849	M	0.80616	2.505	0.80722	D	1	P	0.42483	0.781	P	0.44732	0.459	T	0.50988	-0.8762	10	0.21540	T	0.41	-17.3562	20.1863	0.98216	0.0:0.0:1.0:0.0	.	287	Q13576	IQGA2_HUMAN	K	287;260;237	ENSP00000274364:E287K;ENSP00000423672:E260K;ENSP00000421097:E237K	ENSP00000274364:E287K	E	+	1	0	IQGAP2	75924458	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	9.798000	0.99111	2.781000	0.95711	0.650000	0.86243	GAA	.	.	.	none		0.323	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		A	75888702	G	A	75888702	3	1	233	1	0	0	0	0	1	0	0	0	7822	943	33	2	893	2	IQGAP2	5	75888702	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10		75888702	105026558	41	14164	143	2									
IQGAP2	10788	hgsc.bcm.edu	37	chr5	75888710	75888710	+	Silent	SNP	G	G	A																															gatgcttatgaagaactgctGacacaagcagaaatccaagg																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr5:75888710G>A	ENST00000274364.6	+	9	1164	c.867G>A	c.(865-867)ctG>ctA	p.L289L	IQGAP2_ENST00000379730.3_5'UTR	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	289					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		AAGAACTGCTGACACAAGCAG	0.333																																					p.L289L		Atlas-SNP	.											.	IQGAP2	186	.	0			c.G867A						PASS	.						145	152	149					5																	75888710		2203	4300	6503	SO:0001819	synonymous_variant	10788	exon9			ACTGCTGACACAA	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.867G>A	chr5.hg19:g.75888710G>A		344.0	0.0	.		484.0	78.0	.	NM_006633	A8K4V1|B7Z8A4|J3KR91	Silent	SNP	ENST00000274364.6	hg19	CCDS34188.1																																																																																			.	.	.	none		0.333	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		A	75888710	G	A	75888710	2	1	233	1	0	0	0	0	0	0	0	1	7822	1277	45	2		2	IQGAP2	5	75888710	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	8	75888710	105026550	42	14165	143	2									
IQGAP2	10788	hgsc.bcm.edu	37	chr5	75973147	75973147	+	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	caaaccagtcatttatatttCaattgaagaaatcatcagca	17	12	4	8	0	4	2	4	1	0	1	4	2	4	2	1	0	2	1	1	0	6	5			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr5:75973147C>T	ENST00000274364.6	+	28	3929	c.3632C>T	c.(3631-3633)tCa>tTa	p.S1211L	IQGAP2_ENST00000502745.1_Missense_Mutation_p.S707L|IQGAP2_ENST00000396234.3_Missense_Mutation_p.S707L|IQGAP2_ENST00000379730.3_Missense_Mutation_p.S713L	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	1211					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		ATTTATATTTCAATTGAAGAA	0.393																																					p.S1211L		Atlas-SNP	.											.	IQGAP2	186	.	0			c.C3632T						PASS	.						65	66	65					5																	75973147		2203	4300	6503	SO:0001583	missense	10788	exon28			ATATTTCAATTGA	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.3632C>T	chr5.hg19:g.75973147C>T	ENSP00000274364:p.Ser1211Leu	88.0	0.0	.		95.0	11.0	.	NM_006633	A8K4V1|B7Z8A4|J3KR91	Missense_Mutation	SNP	ENST00000274364.6	hg19	CCDS34188.1	.	.	.	.	.	.	.	.	.	.	C	32	5.108409	0.94292	.	.	ENSG00000145703	ENST00000274364;ENST00000379730;ENST00000505766;ENST00000396234;ENST00000502745	T;T;T;T;T	0.54071	0.59;0.59;0.59;0.59;0.59	4.98	4.98	0.66077	Rho GTPase activation protein (1);Ras GTPase-activating protein (1);	0.329934	0.33144	N	0.005221	T	0.73094	0.3543	M	0.84326	2.69	0.80722	D	1	D;D;P	0.65815	0.995;0.995;0.792	P;P;B	0.60609	0.877;0.877;0.322	T	0.77910	-0.2411	10	0.72032	D	0.01	-12.9253	18.4229	0.90597	0.0:1.0:0.0:0.0	.	713;707;1211	F5H7S7;Q13576-2;Q13576	.;.;IQGA2_HUMAN	L	1211;713;1161;707;707	ENSP00000274364:S1211L;ENSP00000442313:S713L;ENSP00000421097:S1161L;ENSP00000379535:S707L;ENSP00000426027:S707L	ENSP00000274364:S1211L	S	+	2	0	IQGAP2	76008903	1.000000	0.71417	0.991000	0.47740	0.986000	0.74619	7.557000	0.82243	2.597000	0.87782	0.591000	0.81541	TCA	.	.	.	none		0.393	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		T	75973147	C	T	75973147	3	4	233	1	0	0	0	0	1	0	0	0	7822	838	29	2	3742	2	IQGAP2	5	75973147	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	84437	75973147	104942113	43	14166											
FNIP1	96459	hgsc.bcm.edu	37	chr5	131007961	131007961	+	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	ttttttttccacaaccattcCtgtggatctcattgctttgc	6	19	5	11	0	1	0	1	0	1	0	4	1	3	1	3	1	3	1	3	1	1	7	rs367969091		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr5:131007961C>T	ENST00000510461.1	-	14	2271	c.2176G>A	c.(2176-2178)Gga>Aga	p.G726R	FNIP1_ENST00000307954.8_Missense_Mutation_p.G681R|CTC-432M15.3_ENST00000514667.1_Intron|FNIP1_ENST00000307968.7_Missense_Mutation_p.G698R	NM_133372.2	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1	726					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)		ACAACCATTCCTGTGGATCTC	0.448																																					p.G726R		Atlas-SNP	.											.	FNIP1	104	.	0			c.G2176A						PASS	.	C	ARG/GLY,ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	218	207	211		2092,2176	4.9	1	5		211	0,8600		0,0,4300	no	missense,missense	FNIP1	NM_001008738.2,NM_133372.2	125,125	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	698/1139,726/1167	131007961	1,13005	2203	4300	6503	SO:0001583	missense	96459	exon14			CCATTCCTGTGGA	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.2176G>A	chr5.hg19:g.131007961C>T	ENSP00000421985:p.Gly726Arg	82.0	0.0	.		109.0	63.0	.	NM_133372	D6RJH5|Q86T47|Q9BUT0	Missense_Mutation	SNP	ENST00000510461.1	hg19	CCDS34227.1	.	.	.	.	.	.	.	.	.	.	C	16.76	3.212357	0.58452	2.27E-4	0.0	ENSG00000217128	ENST00000307968;ENST00000307954;ENST00000544351;ENST00000510461	T;T;T	0.42131	0.98;0.98;0.98	5.76	4.89	0.63831	.	.	.	.	.	T	0.45538	0.1347	L	0.43152	1.355	0.80722	D	1	P;P;P	0.46512	0.879;0.879;0.773	P;P;B	0.50708	0.648;0.494;0.414	T	0.31420	-0.9944	9	0.49607	T	0.09	-8.8964	12.306	0.54902	0.0:0.8667:0.0:0.1333	.	726;698;726	A8K8V8;Q8TF40-3;Q8TF40	.;.;FNIP1_HUMAN	R	698;681;478;726	ENSP00000309266:G698R;ENSP00000310453:G681R;ENSP00000421985:G726R	ENSP00000310453:G681R	G	-	1	0	FNIP1	131035860	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.191000	0.58372	2.726000	0.93360	0.655000	0.94253	GGA	.	.	.	weak		0.448	FNIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370077.1	NM_133372		T	131007961	C	T	131007961	3	4	233	1	0	0	0	0	1	0	0	0	5982	690	24	2	1344	2	FNIP1	5	131007961	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	55034814	131007961	49907299	44	14167											
NSD1	64324	hgsc.bcm.edu	37	chr5	176721020	176721020	+	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	aatcctctggaacctggggaGatccgtgagtatgtgcctcc	8	10	12	11	1	1	2	0	1	1	1	4	4	4	3	5	3	2	1	5	3	3	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr5:176721020G>T	ENST00000439151.2	+	23	6696	c.6651G>T	c.(6649-6651)gaG>gaT	p.E2217D	NSD1_ENST00000354179.4_Missense_Mutation_p.E1948D|NSD1_ENST00000361032.4_Missense_Mutation_p.E2114D|NSD1_ENST00000347982.4_Missense_Mutation_p.E1948D	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2217	Pro-rich.				gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		AACCTGGGGAGATCCGTGAGT	0.562			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.E2217D		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.G6651T						PASS	.						81	80	81					5																	176721020		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	TGGGGAGATCCGT	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.6651G>T	chr5.hg19:g.176721020G>T	ENSP00000395929:p.Glu2217Asp	91.0	0.0	.		120.0	46.0	.	NM_022455	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	hg19	CCDS4412.1	.	.	.	.	.	.	.	.	.	.	G	19.51	3.840800	0.71488	.	.	ENSG00000165671	ENST00000354179;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.81996	-1.56;-1.56;-1.56;-1.56	6.17	6.17	0.99709	.	0.000000	0.64402	D	0.000002	D	0.84419	0.5468	L	0.27053	0.805	0.53688	D	0.999975	D;D	0.76494	0.999;0.999	D;D	0.71870	0.975;0.933	D	0.84097	0.0393	10	0.51188	T	0.08	.	11.9775	0.53100	0.1325:0.0:0.8675:0.0	.	1948;2217	Q96L73-2;Q96L73	.;NSD1_HUMAN	D	1948;2217;1948;2114	ENSP00000346111:E1948D;ENSP00000395929:E2217D;ENSP00000343209:E1948D;ENSP00000354310:E2114D	ENSP00000343209:E1948D	E	+	3	2	NSD1	176653626	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.583000	0.53928	2.941000	0.99782	0.655000	0.94253	GAG	.	.	.	none		0.562	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		T	176721020	G	T	176721020	3	4	233	1	0	0	0	0	1	0	0	0	10676	933	33	4	6737	4	NSD1	5	176721020	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	45713059	176721020	4194240	45	14168											
CLK4	57396	hgsc.bcm.edu	37	chr5	178050363	178050363	+	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	tccacgatagctttcatgtcCccagctttctctgctatccc	6	14	5	16	1	2	0	1	0	1	0	6	1	5	0	4	0	3	3	4	0	2	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr5:178050363C>A	ENST00000316308.4	-	2	223	c.55G>T	c.(55-57)Gga>Tga	p.G19*	CLK4_ENST00000520957.1_Nonsense_Mutation_p.G19*	NM_020666.2	NP_065717.1	Q9HAZ1	CLK4_HUMAN	CDC-like kinase 4	19					protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(2)	21	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.235)		CTTTCATGTCCCCAGCTTTCT	0.438																																					p.G19X		Atlas-SNP	.											.	CLK4	103	.	0			c.G55T						PASS	.						207	181	190					5																	178050363		2203	4300	6503	SO:0001587	stop_gained	57396	exon2			CATGTCCCCAGCT	AF294429	CCDS4437.1	5q35	2008-05-02			ENSG00000113240	ENSG00000113240		"CDC-like kinases"	13659	protein-coding gene	gene with protein product		607969				11170754	Standard	NM_020666		Approved		uc003mjf.1	Q9HAZ1	OTTHUMG00000130893	ENST00000316308.4:c.55G>T	chr5.hg19:g.178050363C>A	ENSP00000316948:p.Gly19*	83.0	0.0	.		135.0	60.0	.	NM_020666		Nonsense_Mutation	SNP	ENST00000316308.4	hg19	CCDS4437.1	.	.	.	.	.	.	.	.	.	.	C	38	7.083910	0.98051	.	.	ENSG00000113240	ENST00000316308;ENST00000536763;ENST00000520957	.	.	.	5.83	4.97	0.65823	.	0.325167	0.32548	N	0.005960	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	.	10.8916	0.46998	0.0:0.9136:0.0:0.0864	.	.	.	.	X	19	.	ENSP00000316948:G19X	G	-	1	0	CLK4	177982969	0.989000	0.36119	0.999000	0.59377	0.962000	0.63368	2.363000	0.44178	1.477000	0.48234	0.491000	0.48974	GGA	.	.	.	none		0.438	CLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253479.2			A	178050363	C	A	178050363	4	1	233	1	0	0	0	0	0	1	0	0	3541	632	22	4	1438	4	CLK4	5	178050363	Nonsense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	1329343	178050363	2864897	46	14169											
ZSCAN23	222696	hgsc.bcm.edu	37	chr6	28402345	28402345	+	Missense_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	attcataaggtctctctccaGtgtgaattctctgatgctta	9	16	7	9	0	4	2	1	2	3	0	7	2	4	2	1	1	1	1	1	1	3	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:28402345G>A	ENST00000289788.4	-	4	1212	c.1067C>T	c.(1066-1068)aCt>aTt	p.T356I	ZSCAN23_ENST00000486481.1_5'Flank	NM_001012455.1	NP_001012458.1	Q3MJ62	ZSC23_HUMAN	zinc finger and SCAN domain containing 23	356					transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|prostate(1)|stomach(2)	4						TCTCTCTCCAGTGTGAATTCT	0.448																																					p.T356I		Atlas-SNP	.											.	ZSCAN23	18	.	0			c.C1067T						PASS	.						158	136	142					6																	28402345		692	1591	2283	SO:0001583	missense	222696	exon4			TCTCCAGTGTGAA	AK092117	CCDS47393.1	6p21.33	2013-01-08	2007-02-20	2007-02-20	ENSG00000187987	ENSG00000187987		"-", "Zinc fingers, C2H2-type"	21193	protein-coding gene	gene with protein product			"zinc finger protein 453", "zinc finger protein 390"	ZNF453, ZNF390			Standard	NM_001012455		Approved	dJ29K1.3.1	uc003nli.4	Q3MJ62	OTTHUMG00000016346	ENST00000289788.4:c.1067C>T	chr6.hg19:g.28402345G>A	ENSP00000289788:p.Thr356Ile	99.0	0.0	.		110.0	61.0	.	NM_001012455	Q96KV9	Missense_Mutation	SNP	ENST00000289788.4	hg19	CCDS47393.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.245900	0.80024	.	.	ENSG00000187987	ENST00000289788	T	0.25749	1.78	3.93	3.93	0.45458	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.39909	N	0.001229	T	0.36386	0.0965	M	0.80183	2.485	0.34741	D	0.730734	D	0.55385	0.971	P	0.56788	0.806	T	0.46541	-0.9184	10	0.87932	D	0	.	13.4765	0.61312	0.0:0.0:1.0:0.0	.	356	Q3MJ62	ZSC23_HUMAN	I	356	ENSP00000289788:T356I	ENSP00000289788:T356I	T	-	2	0	ZSCAN23	28510324	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.856000	0.69518	2.007000	0.58848	0.650000	0.86243	ACT	.	.	.	none		0.448	ZSCAN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043751.2	XM_167147		A	28402345	G	A	28402345	3	1	233	1	0	0	0	0	1	0	0	0	18247	1029	36	2	106	2	ZSCAN23	6	28402345	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10		28402345	142712722	47	14170											
DPCR1	135656	hgsc.bcm.edu	37	chr6	30918494	30918494	+	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	gaaaggacagccaatgagaaCaccacaccatccccagcaca	17	2	7	15	0	0	1	0	1	0	1	1	4	1	2	5	1	3	1	5	1	3	0			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:30918494C>G	ENST00000462446.1	+	2	2281	c.2253C>G	c.(2251-2253)aaC>aaG	p.N751K	DPCR1_ENST00000304311.2_5'UTR|HCG21_ENST00000419481.1_RNA			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	315						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						CCAATGAGAACACCACACCAT	0.483																																					p.N751K		Atlas-SNP	.											.	DPCR1	99	.	0			c.C2253G						PASS	.						47	48	48					6																	30918494		692	1591	2283	SO:0001583	missense	135656	exon2			TGAGAACACCACA	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.2253C>G	chr6.hg19:g.30918494C>G	ENSP00000417182:p.Asn751Lys	117.0	0.0	.		113.0	5.0	.	NM_080870	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	hg19	CCDS4692.2	.	.	.	.	.	.	.	.	.	.	-	0.005	-2.134125	0.00338	.	.	ENSG00000168631	ENST00000462446	T	0.42900	0.96	1.63	-3.25	0.05079	.	.	.	.	.	T	0.04770	0.0129	N	0.14661	0.345	0.20196	N	0.999924	B	0.10296	0.003	B	0.04013	0.001	T	0.35375	-0.9791	9	0.05833	T	0.94	.	4.4043	0.11402	0.0:0.2495:0.2493:0.5011	.	751	E9PEI6	.	K	751	ENSP00000417182:N751K	ENSP00000417182:N751K	N	+	3	2	DPCR1	31026473	0.000000	0.05858	0.000000	0.03702	0.072000	0.16883	-0.332000	0.07904	-0.774000	0.04590	0.282000	0.19409	AAC	.	.	.	none		0.483	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870		G	30918494	C	G	30918494	3	3	233	1	0	0	0	0	1	0	0	0	4714	477	17	4	2259	4	DPCR1	6	30918494	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	2516149	30918494	140196573	48	14171											
TNXB	7148	hgsc.bcm.edu	37	chr6	32016288	32016288	+	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	actgcctggggctgcccctgCgcgtccctgtactgtaccag	4	9	12	16	2	0	0	0	0	0	0	1	0	1	0	5	2	5	3	5	2	2	2	rs373655652		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:32016288C>T	ENST00000375244.3	-	29	10098	c.9897G>A	c.(9895-9897)gcG>gcA	p.A3299A	TNXB_ENST00000451343.1_5'Flank|TNXB_ENST00000375247.2_Silent_p.A3297A			P22105	TENX_HUMAN	tenascin XB	3344	Fibronectin type-III 24. {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						GCTGCCCCTGCGCGTCCCTGT	0.687																																					p.A3297A		Atlas-SNP	.											.	TNXB	553	.	0			c.G9891A						PASS	.	C		0,3902		0,0,1951	17	21	19		9891	-7.3	0	6		19	3,8267		0,3,4132	no	coding-synonymous	TNXB	NM_019105.6		0,3,6083	TT,TC,CC		0.0363,0.0,0.0246		3297/4243	32016288	3,12169	1951	4135	6086	SO:0001819	synonymous_variant	7148	exon29			CCCCTGCGCGTCC	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.9897G>A	chr6.hg19:g.32016288C>T		97.0	0.0	.		173.0	105.0	.	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	hg19																																																																																				.	.	.	weak		0.687	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		T	32016288	C	T	32016288	2	4	233	1	0	0	0	0	0	0	0	1	16358	755	27	1		1	TNXB	6	32016288	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	1097794	32016288	139098779	49	14172											
TNXB	7148	hgsc.bcm.edu	37	chr6	32063589	32063589	+	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	ggcgctggctggaggctcttCctgcccgcagtcctcaccgc	3	8	13	17	3	2	0	1	0	1	0	4	1	4	1	4	4	1	4	4	4	0	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:32063589C>G	ENST00000479795.1	-	3	2181	c.2041G>C	c.(2041-2043)Gaa>Caa	p.E681Q	TNXB_ENST00000375244.3_Missense_Mutation_p.E681Q|TNXB_ENST00000375247.2_Missense_Mutation_p.E681Q			P22105	TENX_HUMAN	tenascin XB	681					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						GGAGGCTCTTCCTGCCCGCAG	0.701																																					p.E681Q		Atlas-SNP	.											.	TNXB	553	.	0			c.G2041C						PASS	.						16	20	18					6																	32063589		2114	4231	6345	SO:0001583	missense	7148	exon3			GCTCTTCCTGCCC	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"Fibrinogen C domain containing", "Fibronectin type III domain containing"	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000479795.1:c.2041G>C	chr6.hg19:g.32063589C>G	ENSP00000418248:p.Glu681Gln	109.0	0.0	.		291.0	13.0	.	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000479795.1	hg19		.	.	.	.	.	.	.	.	.	.	C	20.2	3.955354	0.73902	.	.	ENSG00000168477	ENST00000375244;ENST00000375247;ENST00000479795	T;T;T	0.08546	3.08;3.08;3.08	4.78	4.78	0.61160	.	0.000000	0.45126	D	0.000397	T	0.08088	0.0202	L	0.37750	1.13	0.26200	N	0.979459	D	0.65815	0.995	P	0.61477	0.889	T	0.19549	-1.0302	10	0.30078	T	0.28	.	13.3295	0.60479	0.0:1.0:0.0:0.0	.	681	P22105-3	.	Q	681	ENSP00000364393:E681Q;ENSP00000364396:E681Q;ENSP00000418248:E681Q	ENSP00000364393:E681Q	E	-	1	0	TNXB	32171567	0.970000	0.33590	0.850000	0.33497	0.919000	0.55068	0.746000	0.26275	2.198000	0.70561	0.563000	0.77884	GAA	.	.	.	none		0.701	TNXB-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000357059.1	NM_019105		G	32063589	C	G	32063589	3	3	233	1	0	0	0	0	1	0	0	0	16358	864	30	4	12840	4	TNXB	6	32063589	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	47301	32063589	139051478	50	14173											
DNAH8	1769	hgsc.bcm.edu	37	chr6	38818063	38818080	+	In_Frame_Del	DEL	ATAAAAATAATGCAGCGA	ATAAAAATAATGCAGCGA	-																															agaatattgacaagtcttggAtaaaaataatgcagcgagct																								rs200056261|rs201568629|rs547165959		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	ATAAAAATAATGCAGCGA	ATAAAAATAATGCAGCGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:38818063_38818080delATAAAAATAATGCAGCGA	ENST00000359357.3	+	36	4839_4856	c.4585_4602delATAAAAATAATGCAGCGA	c.(4585-4602)ataaaaataatgcagcgadel	p.IKIMQR1529del	DNAH8_ENST00000449981.2_In_Frame_Del_p.IKIMQR1746del|DNAH8_ENST00000441566.1_In_Frame_Del_p.IKIMQR1529del			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1529					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.I1529I(2)		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						CAAGTCTTGGATAAAAATAATGCAGCGAGCTCATGAGA	0.362																																					p.1745_1751del		Atlas-Indel,Pindel	.											.	DNAH8	1239	.	2	Substitution - coding silent(2)	lung(2)	c.5235_5252del						PASS	.																																			SO:0001651	inframe_deletion	1769	exon38			.	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.4585_4602delATAAAAATAATGCAGCGA	chr6.hg19:g.38818063_38818080delATAAAAATAATGCAGCGA	ENSP00000352312:p.Ile1529_Arg1534del	89.0	0.0	0		65.0	25.0	0.384615	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	In_Frame_Del	DEL	ENST00000359357.3	hg19																																																																																				.	.	.	none		0.362	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		-	38818080	ATAAAAATAATGCAGCGA	-	38818063	7	5	233	1	0	1	0	1	0	0	0	0	4609	333	12	0	4719	0	DNAH8	6	38818063	In_Frame_Del	DEL	ATAAAAATAATGCAGCGA	TCGA-P4-A5EB-01A-11D-A28G-10	6754474	38818063	132297004	51	14174											
CUL9	23113	hgsc.bcm.edu	37	chr6	43155541	43155541	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagtagtcgatttgagggcAgcactctcaatgacctgctc	9	11	10	11	1	2	2	2	2	1	0	5	3	2	2	1	1	2	4	1	1	2	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:43155541A>G	ENST00000252050.4	+	7	1756	c.1672A>G	c.(1672-1674)Agc>Ggc	p.S558G	CUL9_ENST00000372647.2_Missense_Mutation_p.S558G|CUL9_ENST00000354495.3_Missense_Mutation_p.S448G	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	558					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						ATTTGAGGGCAGCACTCTCAA	0.517																																					p.S558G		Atlas-SNP	.											.	CUL9	248	.	0			c.A1672G						PASS	.						122	121	121					6																	43155541		2203	4300	6503	SO:0001583	missense	23113	exon7			GAGGGCAGCACTC	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.1672A>G	chr6.hg19:g.43155541A>G	ENSP00000252050:p.Ser558Gly	84.0	0.0	.		84.0	19.0	.	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	hg19	CCDS4890.1	.	.	.	.	.	.	.	.	.	.	A	13.47	2.245727	0.39697	.	.	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.77489	-1.1;-0.91;-1.0	5.5	4.35	0.52113	.	0.665930	0.17251	N	0.181151	T	0.50343	0.1610	L	0.43152	1.355	0.27626	N	0.948198	B;B;B	0.16603	0.018;0.018;0.003	B;B;B	0.16722	0.016;0.016;0.002	T	0.40794	-0.9544	10	0.48119	T	0.1	-13.3974	4.4793	0.11759	0.702:0.0:0.1464:0.1516	.	558;558;558	E9PEZ1;Q8IWT3;Q05C85	.;CUL9_HUMAN;.	G	558;448;558	ENSP00000252050:S558G;ENSP00000346490:S448G;ENSP00000361730:S558G	ENSP00000252050:S558G	S	+	1	0	CUL9	43263519	0.994000	0.37717	1.000000	0.80357	0.943000	0.58893	1.801000	0.38843	2.090000	0.63153	0.383000	0.25322	AGC	.	.	.	none		0.517	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		G	43155541	A	G	43155541	3	3	233	1	0	0	0	0	1	0	0	0	4063	188	7	3	1694	3	CUL9	6	43155541	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	4337478	43155541	127959526	52	14175											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51586795	51586795	+	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	gctcctcctctattctgaaaTcttcaaagcctgctcagtgg	8	13	7	13	0	5	1	2	1	3	0	7	1	7	1	3	1	2	2	3	1	3	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:51586795T>G	ENST00000371117.3	-	60	10432				PKHD1_ENST00000340994.4_Missense_Mutation_p.I3394L	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)						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)					TATTCTGAAATCTTCAAAGCC	0.448																																					p.I3394L		Atlas-SNP	.											.	PKHD1	927	.	0			c.A10180C						PASS	.						71	70	70					6																	51586795		2203	4300	6503	SO:0001627	intron_variant	5314	exon61			CTGAAATCTTCAA	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.10156+22387A>C	chr6.hg19:g.51586795T>G		92.0	0.0	.		76.0	32.0	.	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	T	11.62	1.692382	0.30052	.	.	ENSG00000170927	ENST00000340994	D	0.86627	-2.15	3.72	-0.352	0.12598	.	.	.	.	.	T	0.61949	0.2388	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.54275	-0.8318	8	0.54805	T	0.06	.	4.5853	0.12279	0.0:0.1103:0.3908:0.4988	.	3394	P08F94-2	.	L	3394	ENSP00000341097:I3394L	ENSP00000341097:I3394L	I	-	1	0	PKHD1	51694754	0.000000	0.05858	0.000000	0.03702	0.220000	0.24768	0.004000	0.13106	-0.046000	0.13446	0.379000	0.24179	ATT	.	.	.	none		0.448	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		G	51586795	T	G	51586795	1	3	233	0	1	0	0	0	0	0	0	0	11978	1435	50	5		5	PKHD1	6	51586795	Intron	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	8431254	51586795	119528272	53	14176											
COL21A1	81578	hgsc.bcm.edu	37	chr6	55933890	55933890	+	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	ccatgtatcctggttctcctGgggaacccgttgctcctggt	4	13	11	13	1	1	0	0	0	1	0	4	1	3	1	5	4	2	4	5	4	2	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:55933890G>T	ENST00000244728.5	-	22	2442	c.2045C>A	c.(2044-2046)cCa>cAa	p.P682Q	COL21A1_ENST00000535941.1_Missense_Mutation_p.P682Q|COL21A1_ENST00000370808.2_Missense_Mutation_p.P82Q|COL21A1_ENST00000370819.1_Missense_Mutation_p.P679Q|COL21A1_ENST00000467045.1_5'UTR	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	682	Collagen-like 4.				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)			TGGTTCTCCTGGGGAACCCGT	0.423																																					p.P682Q		Atlas-SNP	.											.	COL21A1	201	.	0			c.C2045A						PASS	.						62	62	62					6																	55933890		1831	4076	5907	SO:0001583	missense	81578	exon22			TCTCCTGGGGAAC	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.2045C>A	chr6.hg19:g.55933890G>T	ENSP00000244728:p.Pro682Gln	84.0	0.0	.		95.0	5.0	.	NM_030820	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Missense_Mutation	SNP	ENST00000244728.5	hg19	CCDS55025.1	.	.	.	.	.	.	.	.	.	.	G	13.12	2.143568	0.37825	.	.	ENSG00000124749	ENST00000244728;ENST00000370819;ENST00000535941;ENST00000370811;ENST00000370808	D;D;D;D	0.97752	-4.52;-4.52;-4.52;-4.52	4.38	3.48	0.39840	.	0.000000	0.49305	U	0.000144	D	0.95968	0.8687	L	0.28192	0.835	0.47407	D	0.999413	P;P;D	0.89917	0.886;0.77;1.0	B;P;D	0.97110	0.381;0.515;1.0	D	0.94500	0.7709	10	0.27785	T	0.31	.	12.3453	0.55118	0.0:0.0:0.8294:0.1705	.	82;682;682	Q96P44-2;B7ZLK3;Q96P44	.;.;COLA1_HUMAN	Q	682;679;682;679;82	ENSP00000244728:P682Q;ENSP00000359855:P679Q;ENSP00000444384:P682Q;ENSP00000359844:P82Q	ENSP00000244728:P682Q	P	-	2	0	COL21A1	56041849	1.000000	0.71417	0.163000	0.22734	0.829000	0.46940	4.396000	0.59684	0.905000	0.36596	0.557000	0.71058	CCA	.	.	.	none		0.423	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2			T	55933890	G	T	55933890	3	4	233	1	0	0	0	0	1	0	0	0	3682	1348	47	4	864	4	COL21A1	6	55933890	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	4347095	55933890	115181177	54	14177											
UBE2CBP	90025	hgsc.bcm.edu	37	chr6	83767555	83767555	+	Missense_Mutation	SNP	T	T	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	tattactcacttgtgcctaaTtttgcttgcgtctgcagtcg	6	17	8	10	2	2	0	1	0	1	0	3	0	2	0	1	0	5	2	1	0	3	7			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:83767555T>G	ENST00000369747.3	-	2	386	c.264A>C	c.(262-264)aaA>aaC	p.K88N		NM_198920.1	NP_944602.1	Q7Z6J8	UBE3D_HUMAN	ubiquitin protein ligase E3D	88					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)										TTGTGCCTAATTTTGCTTGCG	0.443											OREG0017549	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K88N		Atlas-SNP	.											.	.	.	.	0			c.A264C						PASS	.						67	68	68					6																	83767555		2203	4300	6503	SO:0001583	missense	90025	exon2			GCCTAATTTTGCT	AL137544	CCDS34491.1	6q15	2012-02-24	2012-02-24	2012-02-24	ENSG00000118420	ENSG00000118420			21381	protein-coding gene	gene with protein product	"UBCH10 binding protein with a hect-like domain"	612495	"chromosome 6 open reading frame 157", "ubiquitin-conjugating enzyme E2C binding protein"	C6orf157, UBE2CBP		15749827	Standard	NM_198920		Approved	DKFZp434A1520, H10BH, YJR141W	uc003pjp.2	Q7Z6J8	OTTHUMG00000015108	ENST00000369747.3:c.264A>C	chr6.hg19:g.83767555T>G	ENSP00000358762:p.Lys88Asn	83.0	0.0	.	1224	78.0	39.0	.	NM_198920	B4DP63|Q5T4W2|Q6IPR4|Q75UG0|Q9NT42	Missense_Mutation	SNP	ENST00000369747.3	hg19	CCDS34491.1	.	.	.	.	.	.	.	.	.	.	T	10.93	1.490288	0.26686	.	.	ENSG00000118420	ENST00000369747	T	0.30714	1.52	5.27	-10.5	0.00291	.	0.631105	0.16070	N	0.231043	T	0.02767	0.0083	N	0.08118	0	0.09310	N	0.999998	B;B	0.20164	0.042;0.002	B;B	0.18871	0.023;0.002	T	0.20009	-1.0288	10	0.33141	T	0.24	-18.3097	5.2116	0.15320	0.1807:0.4793:0.1961:0.1438	.	88;88	D6RD24;Q7Z6J8	.;UB2CB_HUMAN	N	88	ENSP00000358762:K88N	ENSP00000358762:K88N	K	-	3	2	UBE2CBP	83824274	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.412000	0.02476	-2.085000	0.00864	-0.911000	0.02809	AAA	.	.	.	none		0.443	UBE3D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041347.7	NM_198920		G	83767555	T	G	83767555	3	3	233	1	0	0	0	0	1	0	0	0	16859	1490	52	5	941	5	UBE2CBP	6	83767555	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	27833665	83767555	87347512	55	14178											
COQ3	51805	hgsc.bcm.edu	37	chr6	99823846	99823846	+	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	tgacagcagcactgtaaaaaTgtttctagatcaatcacatg	15	11	7	8	0	3	2	2	1	1	1	3	2	3	2	0	0	2	4	0	0	5	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:99823846T>A	ENST00000254759.3	-	5	723	c.699A>T	c.(697-699)acA>acT	p.T233T	COQ3_ENST00000369240.1_Intron|COQ3_ENST00000479163.1_5'Flank|COQ3_ENST00000369242.1_Intron	NM_017421.3	NP_059117.3	Q9NZJ6	COQ3_HUMAN	coenzyme Q3 methyltransferase	233					glycerol metabolic process (GO:0006071)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity (GO:0008425)|3-demethylubiquinone-9 3-O-methyltransferase activity (GO:0008689)|hexaprenyldihydroxybenzoate methyltransferase activity (GO:0004395)|O-methyltransferase activity (GO:0008171)			cervix(1)|lung(5)|upper_aerodigestive_tract(2)	8		all_cancers(76;1.24e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00716)|Colorectal(196;0.0691)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0625)		ACTGTAAAAATGTTTCTAGAT	0.368																																					p.T233T		Atlas-SNP	.											.	COQ3	19	.	0			c.A699T						PASS	.						154	149	151					6																	99823846		2203	4300	6503	SO:0001819	synonymous_variant	51805	exon5			TAAAAATGTTTCT	AF193016	CCDS5042.1	6q21	2013-05-01	2013-05-01		ENSG00000132423	ENSG00000132423	2.1.1.114		18175	protein-coding gene	gene with protein product	"polyprenyldihydroxybenzoate methyltransferase"	605196	"coenzyme Q3 homolog, methyltransferase (yeast)", "coenzyme Q3 homolog, methyltransferase (S. cerevisiae)"			10777520	Standard	NM_017421		Approved	bA9819.1	uc003ppk.3	Q9NZJ6	OTTHUMG00000015264	ENST00000254759.3:c.699A>T	chr6.hg19:g.99823846T>A		114.0	0.0	.		79.0	26.0	.	NM_017421	B3KPX0|Q5T061|Q6P4F0|Q8IXG6|Q96BG1|Q9H0N1	Silent	SNP	ENST00000254759.3	hg19	CCDS5042.1																																																																																			.	.	.	none		0.368	COQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041602.1	NM_017421		A	99823846	T	A	99823846	2	1	233	1	0	0	0	0	0	0	0	1	3748	1451	51	5		5	COQ3	6	99823846	Silent	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	16056291	99823846	71291221	56	14179											
HECA	51696	hgsc.bcm.edu	37	chr6	139487930	139487930	+	Frame_Shift_Del	DEL	G	G	-																															cagtgggtgccgcagcctacGgtgcccgttcccccggtggc																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:139487930delG	ENST00000367658.2	+	2	1066	c.781delG	c.(781-783)ggtfs	p.G261fs	RP1-225E12.2_ENST00000587577.1_RNA|RP1-225E12.3_ENST00000585874.1_RNA|RP1-225E12.2_ENST00000591102.1_RNA|RP1-225E12.2_ENST00000586229.1_RNA|RP1-225E12.2_ENST00000588638.1_RNA|RP1-225E12.2_ENST00000588529.1_RNA|RP1-225E12.2_ENST00000586266.1_RNA|RP1-225E12.2_ENST00000589192.1_RNA|RP1-225E12.2_ENST00000415194.2_RNA|RP1-225E12.2_ENST00000590679.1_RNA	NM_016217.2	NP_057301.1	Q9UBI9	HDC_HUMAN	headcase homolog (Drosophila)	261					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)		CGCAGCCTACGGTGCCCGTTC	0.682																																					p.Y260X		Atlas-Indel,Pindel	.											.	HECA	45	.	0			c.780delC						PASS	.						15	18	17					6																	139487930		2203	4297	6500	SO:0001589	frameshift_variant	51696	exon2			.	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.781delG	chr6.hg19:g.139487930delG	ENSP00000356630:p.Gly261fs	75.0	0.0	0		66.0	21.0	0.318182	NM_016217		Frame_Shift_Del	DEL	ENST00000367658.2	hg19	CCDS5194.1																																																																																			.	.	.	none		0.682	HECA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042456.1	NM_016217		-	139487930	G	-	139487930	7	5	233	1	0	1	0	1	0	0	0	0	7045	1116	39	0	787	0	HECA	6	139487930	Frame_Shift_Del	DEL	G	TCGA-P4-A5EB-01A-11D-A28G-10	39664084	139487930	31627137	57	14180											
LATS1	9113	hgsc.bcm.edu	37	chr6	149997827	149997827	+	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	catcgacagcttgagggatcCccccattcattactgaaatc	11	10	7	13	1	1	2	1	2	0	0	4	4	2	3	3	1	2	1	3	1	2	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr6:149997827C>G	ENST00000543571.1	-	6	3187	c.2640G>C	c.(2638-2640)ggG>ggC	p.G880G	LATS1_ENST00000253339.5_Silent_p.G880G|LATS1_ENST00000542747.1_5'UTR	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1											central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		TTGAGGGATCCCCCCATTCAT	0.473																																					p.G880G		Atlas-SNP	.											.	LATS1	241	.	0			c.G2640C						PASS	.						73	63	66					6																	149997827		2203	4300	6503	SO:0001819	synonymous_variant	9113	exon6			GGGATCCCCCCAT	AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"LATS (large tumor suppressor, Drosophila) homolog 1", "LATS, large tumor suppressor, homolog 1 (Drosophila)"			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000543571.1:c.2640G>C	chr6.hg19:g.149997827C>G		59.0	0.0	.		71.0	20.0	.	NM_004690		Silent	SNP	ENST00000543571.1	hg19	CCDS34551.1																																																																																			.	.	.	none		0.473	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043923.4	NM_004690		G	149997827	C	G	149997827	2	3	233	1	0	0	0	0	0	0	0	1	8653	610	22	4		4	LATS1	6	149997827	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	10509897	149997827	21117240	58	14181											
RBAK	57786	hgsc.bcm.edu	37	chr7	5104550	5104550	+	Frame_Shift_Del	DEL	G	G	-																															agagaaatcccatgaatgtaGtgaatgtggaaagttctctc																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr7:5104550delG	ENST00000353796.3	+	6	1787	c.1463delG	c.(1462-1464)agtfs	p.S488fs	RBAK-RBAKDN_ENST00000396904.2_Intron|RBAK_ENST00000396912.1_Frame_Shift_Del_p.S488fs|RBAK-RBAKDN_ENST00000407184.1_Intron	NM_001204456.1	NP_001191385.1	Q9NYW8	RBAK_HUMAN	RB-associated KRAB zinc finger	488	Interaction with AR.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(2)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	10		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0916)|OV - Ovarian serous cystadenocarcinoma(56;2.44e-14)		CATGAATGTAGTGAATGTGGA	0.373																																					p.S488fs		Atlas-Indel,Pindel	.											.	RBAK	82	.	0			c.1462delA						PASS	.						64	64	64					7																	5104550		2203	4299	6502	SO:0001589	frameshift_variant	57786	exon5			.	AF226869	CCDS5337.1	7p22.1	2013-01-08			ENSG00000146587	ENSG00000146587		"Zinc fingers, C2H2-type", "-"	17680	protein-coding gene	gene with protein product		608191					Standard	NM_021163		Approved	ZNF769	uc003sns.1	Q9NYW8	OTTHUMG00000121155	ENST00000353796.3:c.1463delG	chr7.hg19:g.5104550delG	ENSP00000275423:p.Ser488fs	114.0	0.0	0		105.0	58.0	0.552381	NM_021163	A6NDF2|A8KAK4|B2RN44|B9EGS1|F8W6M7	Frame_Shift_Del	DEL	ENST00000353796.3	hg19	CCDS5337.1																																																																																			.	.	.	none		0.373	RBAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241640.2	NM_021163		-	5104550	G	-	5104550	7	5	233	1	0	1	0	1	0	0	0	0	13113	1029	36	0	1477	0	RBAK	7	5104550	Frame_Shift_Del	DEL	G	TCGA-P4-A5EB-01A-11D-A28G-10		5104550	154034113	59	14182											
RNF216	54476	hgsc.bcm.edu	37	chr7	5781127	5781127	+	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	agatgatgactttctgctctGatctggggttgacaatgtca	9	14	11	7	0	4	5	1	4	3	1	4	5	4	5	0	2	1	2	0	2	1	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr7:5781127G>C	ENST00000425013.2	-	4	574	c.350C>G	c.(349-351)tCa>tGa	p.S117*	RNF216_ENST00000389902.3_Nonsense_Mutation_p.S174*	NM_207111.3|NM_207116.2	NP_996994.1|NP_996999.1	Q9NWF9	RN216_HUMAN	ring finger protein 216	117					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)		TTTCTGCTCTGATCTGGGGTT	0.463																																					p.S174X		Atlas-SNP	.											.	RNF216	71	.	0			c.C521G						PASS	.						267	250	256					7																	5781127		2203	4300	6503	SO:0001587	stop_gained	54476	exon4			TGCTCTGATCTGG	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.350C>G	chr7.hg19:g.5781127G>C	ENSP00000404602:p.Ser117*	139.0	0.0	.		147.0	74.0	.	NM_207111	Q6Y691|Q75ML7|Q7Z2H7|Q7Z7C1|Q8NHW7|Q9NYT1	Nonsense_Mutation	SNP	ENST00000425013.2	hg19	CCDS34595.1	.	.	.	.	.	.	.	.	.	.	G	18.19	3.567910	0.65651	.	.	ENSG00000011275	ENST00000425013;ENST00000389902	.	.	.	5.97	3.93	0.45458	.	0.519284	0.17997	N	0.155007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.19147	T	0.46	-4.5609	7.8068	0.29206	0.2458:0.0:0.7542:0.0	.	.	.	.	X	117;174	.	ENSP00000374550:S117X	S	-	2	0	RNF216	5747653	0.000000	0.05858	0.995000	0.50966	0.994000	0.84299	0.252000	0.18278	1.509000	0.48786	0.561000	0.74099	TCA	.	.	.	none		0.463	RNF216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340374.1	NM_207111		C	5781127	G	C	5781127	4	2	233	1	0	0	0	0	0	1	0	0	13493	1294	45	4	2306	4	RNF216	7	5781127	Nonsense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	676577	5781127	153357536	60	14183											
VSTM2A	222008	hgsc.bcm.edu	37	chr7	54612346	54612346	+	Frame_Shift_Del	DEL	G	G	-																															gagtttccgcggaacgtgacGgcgaccgaggggcagaatgt																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr7:54612346delG	ENST00000407838.3	+	2	517	c.111delG	c.(109-111)acgfs	p.T37fs	VSTM2A_ENST00000302287.3_Frame_Shift_Del_p.T37fs|VSTM2A_ENST00000402613.3_Frame_Shift_Del_p.T37fs|VSTM2A_ENST00000404951.1_Frame_Shift_Del_p.T37fs|VSTM2A_ENST00000402026.2_Frame_Shift_Del_p.T36fs	NM_182546.2	NP_872352.2	Q8TAG5	VTM2A_HUMAN	V-set and transmembrane domain containing 2A	37	Ig-like V-type.					extracellular region (GO:0005576)				endometrium(1)|large_intestine(2)|lung(12)|prostate(1)	16			STAD - Stomach adenocarcinoma(5;0.0525)			GGAACGTGACGGCGACCGAGG	0.577																																					p.T37fs		Atlas-Indel,Pindel	.											.	VSTM2A	53	.	0			c.110delC						PASS	.						61	60	60					7																	54612346		2203	4300	6503	SO:0001589	frameshift_variant	222008	exon2			.	BC028404	CCDS5512.2, CCDS75604.1	7p11.2	2013-01-11	2007-08-10	2007-08-10	ENSG00000170419	ENSG00000170419		"Immunoglobulin superfamily / V-set domain containing"	28499	protein-coding gene	gene with protein product			"V-set and transmembrane domain containing 2"	VSTM2		12477932	Standard	XM_006715663		Approved	MGC33530	uc010kzf.3	Q8TAG5	OTTHUMG00000129271	ENST00000407838.3:c.111delG	chr7.hg19:g.54612346delG	ENSP00000384967:p.Thr37fs	128.0	0.0	0		167.0	50.0	0.299401	NM_182546	A4D2E9|B5MC94	Frame_Shift_Del	DEL	ENST00000407838.3	hg19	CCDS5512.2																																																																																			.	.	.	none		0.577	VSTM2A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318694.1	NM_182546		-	54612346	G	-	54612346	7	5	233	1	0	1	0	1	0	0	0	0	17241	1103	39	0	117	0	VSTM2A	7	54612346	Frame_Shift_Del	DEL	G	TCGA-P4-A5EB-01A-11D-A28G-10	48831219	54612346	104526317	61	14184											
ZNF655	79027	hgsc.bcm.edu	37	chr7	99158261	99158261	+	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	tggagacccagtctgagtgtCtgtccccagagcctcagttt	7	11	11	12	0	3	3	1	1	2	2	4	4	4	3	4	1	1	1	4	1	0	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr7:99158261C>T	ENST00000394163.2	+	2	262	c.79C>T	c.(79-81)Ctg>Ttg	p.L27L	GS1-259H13.10_ENST00000455905.1_Silent_p.L27L|GS1-259H13.10_ENST00000486324.1_3'UTR|ZNF655_ENST00000449244.1_Silent_p.L27L|ZNF655_ENST00000440391.1_Silent_p.L27L|ZNF655_ENST00000424881.1_Silent_p.L27L|ZNF655_ENST00000493277.1_Silent_p.L27L|ZNF655_ENST00000252713.4_Silent_p.L27L|ZNF655_ENST00000320583.5_Silent_p.L27L|ZNF655_ENST00000454654.1_Silent_p.L27L|ZNF655_ENST00000425063.1_Silent_p.L27L|ZNF655_ENST00000357864.2_Silent_p.L27L	NM_001009960.1|NM_138494.2	NP_001009960.1|NP_612503.1	Q8N720	ZN655_HUMAN	zinc finger protein 655	27					negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|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)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	16	all_epithelial(64;3.19e-09)|Lung NSC(181;0.0066)|all_lung(186;0.011)|Esophageal squamous(72;0.0166)					GTCTGAGTGTCTGTCCCCAGA	0.567																																					p.L27L		Atlas-SNP	.											.	ZNF655	75	.	0			c.C79T						PASS	.						118	113	114					7																	99158261		2203	4300	6503	SO:0001819	synonymous_variant	79027	exon2			GAGTGTCTGTCCC	AY099353	CCDS5669.1, CCDS5670.1, CCDS34695.1, CCDS47655.1	7q22.1	2013-01-08			ENSG00000197343	ENSG00000197343		"Zinc fingers, C2H2-type", "-"	30899	protein-coding gene	gene with protein product						11179890, 15558030	Standard	NM_001083956		Approved	VIK-1, VIK	uc010lgc.3	Q8N720	OTTHUMG00000156637	ENST00000394163.2:c.79C>T	chr7.hg19:g.99158261C>T		69.0	0.0	.		79.0	21.0	.	NM_024061	A4D291|A6NGD3|B4E3M4|B7Z9Q9|D6W5T4|Q8IV00|Q8TA89|Q96EZ3|Q9BQ85	Silent	SNP	ENST00000394163.2	hg19	CCDS5669.1																																																																																			.	.	.	none		0.567	ZNF655-009	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000344929.1	NM_138494		T	99158261	C	T	99158261	2	4	233	1	0	0	0	0	0	0	0	1	18080	912	32	2		2	ZNF655	7	99158261	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	44545915	99158261	59980402	62	14185											
C7orf45	136263	hgsc.bcm.edu	37	chr7	129856036	129856036	+	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	tacggagtatggcagtgaagAgtctaactcagaagcctcct	12	9	11	9	1	2	3	1	1	1	2	3	4	3	4	2	2	3	2	2	2	5	3	rs144099660		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr7:129856036A>T	ENST00000297819.3	+	3	512	c.461A>T	c.(460-462)gAg>gTg	p.E154V		NM_145268.3	NP_660311.1	Q8WWF3	SSMM1_HUMAN	serine-rich single-pass membrane protein 1	154						integral component of membrane (GO:0016021)											GGCAGTGAAGAGTCTAACTCA	0.478																																					p.E154V		Atlas-SNP	.											.	.	.	.	0			c.A461T						PASS	.						98	99	99					7																	129856036		2203	4300	6503	SO:0001583	missense	0	exon3			GTGAAGAGTCTAA	AK097635	CCDS5816.1	7q32.2	2013-03-08	2013-03-08	2013-03-08	ENSG00000165120	ENSG00000165120			29580	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 45"	C7orf45		12477932	Standard	NM_145268		Approved	FLJ40316	uc003vpp.3	Q8WWF3	OTTHUMG00000157844	ENST00000297819.3:c.461A>T	chr7.hg19:g.129856036A>T	ENSP00000297819:p.Glu154Val	171.0	0.0	.		185.0	48.0	.	NM_145268		Missense_Mutation	SNP	ENST00000297819.3	hg19	CCDS5816.1	.	.	.	.	.	.	.	.	.	.	A	15.74	2.921732	0.52653	.	.	ENSG00000165120	ENST00000297819	T	0.55052	0.54	5.56	3.09	0.35607	.	0.365080	0.26103	N	0.026340	T	0.48589	0.1508	M	0.63428	1.95	0.32923	D	0.516117	B	0.20671	0.047	B	0.24541	0.054	T	0.56044	-0.8044	10	0.87932	D	0	-6.405	8.8929	0.35446	0.702:0.0:0.0:0.2979	.	154	Q8WWF3	CG045_HUMAN	V	154	ENSP00000297819:E154V	ENSP00000297819:E154V	E	+	2	0	C7orf45	129643272	0.962000	0.33011	0.961000	0.40146	0.396000	0.30629	2.242000	0.43106	0.352000	0.24053	0.402000	0.26972	GAG	.	A|1.000;C|0.000	.	alt		0.478	SSMEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349768.1	NM_145268		T	129856036	A	T	129856036	3	4	233	1	0	0	0	0	1	0	0	0	2397	304	11	5	471	5	C7orf45	7	129856036	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	30697775	129856036	29282627	63	14186											
HIPK2	28996	hgsc.bcm.edu	37	chr7	139258060	139258060	+	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	ctgttgtgcgggaaggagtaCggagcctgggccatggtggg	6	8	20	7	2	0	0	0	0	0	0	0	3	0	3	2	6	3	2	2	6	2	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr7:139258060C>A	ENST00000406875.3	-	15	3304	c.3210G>T	c.(3208-3210)ccG>ccT	p.P1070P	HIPK2_ENST00000428878.2_Silent_p.P1043P	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	1070	Autoinhibitory domain (AID).				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)			breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					GGAAGGAGTACGGAGCCTGGG	0.682																																					p.P1070P		Atlas-SNP	.											.	HIPK2	192	.	0			c.G3210T						PASS	.						84	104	97					7																	139258060		2181	4276	6457	SO:0001819	synonymous_variant	28996	exon15			GGAGTACGGAGCC	AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"homeodomain-interacting protein kinase 2"			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.3210G>T	chr7.hg19:g.139258060C>A		12.0	0.0	.		37.0	12.0	.	NM_022740	Q75MR7|Q8WWI4|Q9H2Y1	Silent	SNP	ENST00000406875.3	hg19																																																																																				.	.	.	none		0.682	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740		A	139258060	C	A	139258060	2	1	233	1	0	0	0	0	0	0	0	1	7124	523	19	4		4	HIPK2	7	139258060	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	9402024	139258060	19880603	64	14187											
LRRCC1	85444	hgsc.bcm.edu	37	chr8	86057651	86057651	+	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	aaattgaaaaagaaatgcgtGaacttttggaagaaacatgc	19	9	9	4	1	0	4	0	2	0	2	0	5	0	5	0	1	4	0	0	1	7	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr8:86057651G>T	ENST00000360375.3	+	19	3153	c.3004G>T	c.(3004-3006)Gaa>Taa	p.E1002*	LRRCC1_ENST00000414626.2_Nonsense_Mutation_p.E982*	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	1002					mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						AGAAATGCGTGAACTTTTGGA	0.269																																					p.E1002X		Atlas-SNP	.											.	LRRCC1	212	.	0			c.G3004T						PASS	.						49	45	46					8																	86057651		1795	4056	5851	SO:0001587	stop_gained	85444	exon19			ATGCGTGAACTTT	BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"centrosomal leucine-rich repeat and coiled-coil containing protein", "variable number of flagella 1 homolog (Chlamydomonas)"		"leucine rich repeat and coiled-coil domain containing 1"			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.3004G>T	chr8.hg19:g.86057651G>T	ENSP00000353538:p.Glu1002*	335.0	0.0	.		275.0	71.0	.	NM_033402	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Nonsense_Mutation	SNP	ENST00000360375.3	hg19	CCDS43750.1	.	.	.	.	.	.	.	.	.	.	G	38	6.807978	0.97853	.	.	ENSG00000133739	ENST00000360375;ENST00000414626	.	.	.	4.97	4.06	0.47325	.	0.467007	0.15962	N	0.236193	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	-1.6865	14.481	0.67582	0.0:0.2766:0.7234:0.0	.	.	.	.	X	1002;982	.	ENSP00000353538:E1002X	E	+	1	0	LRRCC1	86244903	1.000000	0.71417	0.956000	0.39512	0.626000	0.37791	3.387000	0.52501	2.567000	0.86603	0.491000	0.48974	GAA	.	.	.	none		0.269	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402		T	86057651	G	T	86057651	4	4	233	1	0	0	0	0	0	1	0	0	9033	1291	45	4	3078	4	LRRCC1	8	86057651	Nonsense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10		86057651	60306371	65	14188											
CSMD3	114788	hgsc.bcm.edu	37	chr8	113678545	113678545	+	Missense_Mutation	SNP	T	T	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	tagagtgtccaggttcagctTcaatcacccactcacaattc	11	11	6	13	0	4	1	4	0	0	1	6	1	5	1	2	1	1	2	2	1	3	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr8:113678545T>G	ENST00000297405.5	-	17	3021	c.2777A>C	c.(2776-2778)gAa>gCa	p.E926A	CSMD3_ENST00000352409.3_Missense_Mutation_p.E926A|CSMD3_ENST00000343508.3_Missense_Mutation_p.E886A|CSMD3_ENST00000455883.2_Missense_Mutation_p.E822A	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	926	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						AGGTTCAGCTTCAATCACCCA	0.388										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.E926A		Atlas-SNP	.											.	CSMD3	2325	.	0			c.A2777C						PASS	.						66	64	65					8																	113678545		2203	4300	6503	SO:0001583	missense	114788	exon17			TCAGCTTCAATCA	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.2777A>C	chr8.hg19:g.113678545T>G	ENSP00000297405:p.Glu926Ala	145.0	0.0	.		141.0	90.0	.	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.621461	0.87460	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.18502	2.21;2.21;2.21;2.21;2.21	5.97	5.97	0.96955	CUB (5);	0.000000	0.64402	D	0.000001	T	0.38214	0.1032	L	0.58428	1.81	0.46028	D	0.998827	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.91635	0.997;0.998;0.999	T	0.03374	-1.1043	10	0.25751	T	0.34	.	16.4523	0.83996	0.0:0.0:0.0:1.0	.	822;926;886	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	A	886;926;266;822;926	ENSP00000345799:E886A;ENSP00000297405:E926A;ENSP00000341558:E266A;ENSP00000412263:E822A;ENSP00000343124:E926A	ENSP00000297405:E926A	E	-	2	0	CSMD3	113747721	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.286000	0.76751	0.455000	0.32223	GAA	.	.	.	none		0.388	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		G	113678545	T	G	113678545	3	3	233	1	0	0	0	0	1	0	0	0	3948	1783	62	5	8566	5	CSMD3	8	113678545	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	27620894	113678545	32685477	66	14189											
PLAA	9373	hgsc.bcm.edu	37	chr9	26925951	26925951	+	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	gatctgtcctctgctgttgtCacaaagtctaaaattaatga	12	14	7	8	0	4	1	1	1	3	0	5	2	5	1	1	0	1	2	1	0	4	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:26925951C>A	ENST00000397292.3	-	6	1158	c.741G>T	c.(739-741)gtG>gtT	p.V247V	PLAA_ENST00000520884.1_Silent_p.V247V	NM_001031689.2	NP_001026859.1	Q9Y263	PLAP_HUMAN	phospholipase A2-activating protein	247					inflammatory response (GO:0006954)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)	phospholipase A2 activator activity (GO:0016005)			breast(1)|endometrium(7)|kidney(2)|large_intestine(3)|lung(3)|prostate(1)	17		all_neural(3;3.53e-10)|Glioma(3;2.71e-09)		Lung(218;1.32e-05)|LUSC - Lung squamous cell carcinoma(38;0.00011)		CTGCTGTTGTCACAAAGTCTA	0.373																																					p.V247V	Melanoma(175;2670 2735 14091 35526)	Atlas-SNP	.											.	PLAA	48	.	0			c.G741T						PASS	.						90	80	83					9																	26925951		2203	4300	6503	SO:0001819	synonymous_variant	9373	exon6			TGTTGTCACAAAG	AF083395	CCDS35000.1	9p21	2013-01-10			ENSG00000137055	ENSG00000137055		"WD repeat domain containing"	9043	protein-coding gene	gene with protein product	"DOA1 homolog (S. cerevisiae)"	603873				9931468, 10644453	Standard	NM_001031689		Approved	PLAP, PLA2P, FLJ11281, FLJ12699, DOA1	uc003zqd.3	Q9Y263	OTTHUMG00000019708	ENST00000397292.3:c.741G>T	chr9.hg19:g.26925951C>A		92.0	0.0	.		81.0	48.0	.	NM_001031689	Q53EU5|Q5VY33|Q9NUL8|Q9NVE9|Q9UF53|Q9Y5L1	Silent	SNP	ENST00000397292.3	hg19	CCDS35000.1	.	.	.	.	.	.	.	.	.	.	C	6.836	0.523440	0.13066	.	.	ENSG00000137055	ENST00000523212	.	.	.	4.07	3.16	0.36331	.	.	.	.	.	T	0.47710	0.1460	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35871	-0.9771	4	.	.	.	-2.2178	4.411	0.11432	0.1594:0.5773:0.0:0.2632	.	.	.	.	Y	224	.	.	D	-	1	0	PLAA	26915951	0.997000	0.39634	1.000000	0.80357	0.994000	0.84299	0.336000	0.19823	0.817000	0.34445	0.585000	0.79938	GAC	.	.	.	none		0.373	PLAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051958.2	NM_001031689		A	26925951	C	A	26925951	2	1	233	1	0	0	0	0	0	0	0	1	12018	813	29	4		4	PLAA	9	26925951	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10		26925951	114287480	67	14190											
RUSC2	9853	hgsc.bcm.edu	37	chr9	35547875	35547875	+	Frame_Shift_Del	DEL	G	G	-																															acctattccagaagccagaaGtccagccagaggaacaagaa																								rs375840925		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:35547875delG	ENST00000455600.1	+	2	1926	c.1357delG	c.(1357-1359)gtcfs	p.V453fs		NM_001135999.1	NP_001129471	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	453						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)	Rab GTPase binding (GO:0017137)			NS(1)|breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(4)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)			GAAGCCAGAAGTCCAGCCAGA	0.572																																					p.E452fs		Atlas-Indel,Pindel	.											.	RUSC2	88	.	0			c.1356delA						PASS	.						107	127	120					9																	35547875		2203	4300	6503	SO:0001589	frameshift_variant	9853	exon2			.	AB002373	CCDS35008.1	9p13.2	2003-12-02			ENSG00000198853	ENSG00000198853			23625	protein-coding gene	gene with protein product		611053				9205841	Standard	NM_001135999		Approved	KIAA0375	uc003zww.3	Q8N2Y8	OTTHUMG00000019861	ENST00000455600.1:c.1357delG	chr9.hg19:g.35547875delG	ENSP00000393922:p.Val453fs	76.0	0.0	0		86.0	53.0	0.616279	NM_014806	A2RU62|A7E2A9|O15080|Q5W134|Q641Q6|Q6P1W7	Frame_Shift_Del	DEL	ENST00000455600.1	hg19	CCDS35008.1																																																																																			.	.	.	none		0.572	RUSC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052309.1	XM_048462		-	35547875	G	-	35547875	7	5	233	1	0	1	0	1	0	0	0	0	13764	1029	36	0	1359	0	RUSC2	9	35547875	Frame_Shift_Del	DEL	G	TCGA-P4-A5EB-01A-11D-A28G-10	8621924	35547875	105665556	68	14191											
TLN1	7094	hgsc.bcm.edu	37	chr9	35711276	35711276	+	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	cagctgcagccagctgactcTtgaggttaggggcagcaggg	8	7	16	10	0	1	2	0	2	1	0	1	2	1	2	1	4	5	6	1	4	1	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:35711276T>A	ENST00000314888.9	-	30	4348	c.3995A>T	c.(3994-3996)aAg>aTg	p.K1332M	TLN1_ENST00000540444.1_Missense_Mutation_p.K1332M	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1332	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)			CAGCTGACTCTTGAGGTTAGG	0.562																																					p.K1332M		Atlas-SNP	.											.	TLN1	185	.	0			c.A3995T						PASS	.						51	49	50					9																	35711276		2203	4300	6503	SO:0001583	missense	7094	exon30			TGACTCTTGAGGT	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.3995A>T	chr9.hg19:g.35711276T>A	ENSP00000316029:p.Lys1332Met	61.0	0.0	.		57.0	21.0	.	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	hg19	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.775730	0.90195	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.18810	2.19;2.19	5.82	5.82	0.92795	Vinculin-binding site-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.44138	0.1279	M	0.83953	2.67	0.80722	D	1	P	0.52316	0.952	P	0.53954	0.738	T	0.48234	-0.9053	10	0.62326	D	0.03	-24.4418	16.1778	0.81874	0.0:0.0:0.0:1.0	.	1332	Q9Y490	TLN1_HUMAN	M	1332	ENSP00000316029:K1332M;ENSP00000442981:K1332M	ENSP00000316029:K1332M	K	-	2	0	TLN1	35701276	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	8.040000	0.89188	2.225000	0.72522	0.459000	0.35465	AAG	.	.	.	none		0.562	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		A	35711276	T	A	35711276	3	1	233	1	0	0	0	0	1	0	0	0	15959	1609	56	5	3742	5	TLN1	9	35711276	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	163401	35711276	105502155	69	14192											
TJP2	9414	hgsc.bcm.edu	37	chr9	71869284	71869285	+	Frame_Shift_Ins	INS	-	-	T																															cccgataccgggacacagaaINSttatagatgtctgagcacgg																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:71869284_71869285insT	ENST00000377245.4	+	23	3775_3776	c.3567_3568insT	c.(3568-3570)ttafs	p.L1190fs	TJP2_ENST00000539225.1_Frame_Shift_Ins_p.L1221fs|TJP2_ENST00000535702.1_Frame_Shift_Ins_p.L1157fs|TJP2_ENST00000348208.4_Frame_Shift_Ins_p.L1043fs|TJP2_ENST00000453658.2_Frame_Shift_Ins_p.L1020fs	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	1190	Interaction with SCRIB.				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						GGGACACAGAATTATAGATGTC	0.579																																					p.E1220fs		Atlas-Indel,Pindel	.											.	TJP2	120	.	0			c.3660_3661insT						PASS	.																																			SO:0001589	frameshift_variant	9414	exon23			.	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.3569dupT	chr9.hg19:g.71869286_71869286dupT	ENSP00000366453:p.Leu1190fs	79.0	0.0	0		78.0	21.0	0.269231	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Frame_Shift_Ins	INS	ENST00000377245.4	hg19	CCDS6627.1																																																																																			.	.	.	none		0.579	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629		T	71869285	-	T	71869284	7	5	233	1	0	1	1	0	0	0	0	0	15942	98	4	0	3916	0	TJP2	9	71869284	Frame_Shift_Ins	INS	-	TCGA-P4-A5EB-01A-11D-A28G-10	36158008	71869284	69344147	70	14193											
RNF20	56254	hgsc.bcm.edu	37	chr9	104302538	104302538	+	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	aatcgcaagctggcagaaatGttggatcagcggcaggccat	12	7	13	9	2	1	1	1	0	0	1	2	2	1	2	1	4	2	5	1	4	3	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:104302538G>C	ENST00000389120.3	+	3	273	c.183G>C	c.(181-183)atG>atC	p.M61I	RNF20_ENST00000481046.1_3'UTR	NM_019592.5	NP_062538.5	Q5VTR2	BRE1A_HUMAN	ring finger protein 20, E3 ubiquitin protein ligase	61					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|negative regulation of cell migration (GO:0030336)|positive regulation of histone methylation (GO:0031062)|positive regulation of transcription, DNA-templated (GO:0045893)|protein polyubiquitination (GO:0000209)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(6)|large_intestine(7)|lung(23)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)		TGGCAGAAATGTTGGATCAGC	0.438																																					p.M61I		Atlas-SNP	.											.	RNF20	110	.	0			c.G183C						PASS	.						98	88	92					9																	104302538		2203	4300	6503	SO:0001583	missense	56254	exon3			AGAAATGTTGGAT	AF265230	CCDS35084.1	9q22	2012-02-23	2012-02-23	2008-12-12	ENSG00000155827	ENSG00000155827		"RING-type (C3HC4) zinc fingers"	10062	protein-coding gene	gene with protein product	"BRE1 E3 ubiquitin ligase homolog (S. cerevisiae)"	607699	"ring finger protein 20"			16337599, 12876294, 18832071, 19037095	Standard	NM_019592		Approved	FLJ20382, FLJ11189, KAIA2779, BRE1A, hBRE1, BRE1	uc004bbn.3	Q5VTR2	OTTHUMG00000020385	ENST00000389120.3:c.183G>C	chr9.hg19:g.104302538G>C	ENSP00000373772:p.Met61Ile	92.0	0.0	.		76.0	48.0	.	NM_019592	A7MCT5|Q2TB34|Q69YL5|Q6P527|Q8N3J4|Q96JD3|Q9H9Y7|Q9HA51|Q9NUR4|Q9NWQ3|Q9NX83	Missense_Mutation	SNP	ENST00000389120.3	hg19	CCDS35084.1	.	.	.	.	.	.	.	.	.	.	G	13.05	2.120440	0.37436	.	.	ENSG00000155827	ENST00000389120;ENST00000478347;ENST00000488264;ENST00000374819;ENST00000479306;ENST00000466817	T	0.29655	1.56	4.17	3.28	0.37604	.	0.193183	0.56097	D	0.000035	T	0.21387	0.0515	N	0.22421	0.69	0.36185	D	0.849654	B	0.02656	0.0	B	0.01281	0.0	T	0.16453	-1.0402	10	0.87932	D	0	-19.2966	11.9251	0.52814	0.0866:0.0:0.9134:0.0	.	61	Q5VTR2	BRE1A_HUMAN	I	61;49;47;61;61;61	ENSP00000373772:M61I	ENSP00000363952:M61I	M	+	3	0	RNF20	103342359	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	4.058000	0.57463	1.125000	0.41998	-0.379000	0.06801	ATG	.	.	.	none		0.438	RNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356402.1	NM_019592		C	104302538	G	C	104302538	3	2	233	1	0	0	0	0	1	0	0	0	13486	1377	48	4	189	4	RNF20	9	104302538	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	32433254	104302538	36910893	71	14194											
ABCA1	19	hgsc.bcm.edu	37	chr9	107573100	107573100	+	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	cctgacaaatgtgtactgttCgttgtacatccagggctgaa	10	12	10	9	1	0	2	0	2	0	0	2	2	1	2	2	1	2	5	2	1	4	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:107573100C>G	ENST00000374736.3	-	29	4550	c.4156G>C	c.(4156-4158)Gaa>Caa	p.E1386Q		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	1386					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)	GTGTACTGTTCGTTGTACATC	0.507																																					p.E1386Q		Atlas-SNP	.											.	ABCA1	244	.	0			c.G4156C						PASS	.						198	175	183					9																	107573100		2203	4300	6503	SO:0001583	missense	19	exon29			ACTGTTCGTTGTA	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.4156G>C	chr9.hg19:g.107573100C>G	ENSP00000363868:p.Glu1386Gln	103.0	0.0	.		146.0	24.0	.	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	hg19	CCDS6762.1	.	.	.	.	.	.	.	.	.	.	C	12.90	2.077801	0.36662	.	.	ENSG00000165029	ENST00000374736	D	0.92299	-3.01	5.55	5.55	0.83447	.	0.095616	0.64402	D	0.000001	D	0.88840	0.6546	L	0.37466	1.105	0.80722	D	1	B	0.21309	0.054	B	0.26416	0.069	D	0.83736	0.0201	10	0.15499	T	0.54	.	19.8667	0.96806	0.0:1.0:0.0:0.0	.	1386	O95477	ABCA1_HUMAN	Q	1386	ENSP00000363868:E1386Q	ENSP00000363868:E1386Q	E	-	1	0	ABCA1	106612921	1.000000	0.71417	0.988000	0.46212	0.947000	0.59692	6.015000	0.70791	2.773000	0.95371	0.655000	0.94253	GAA	.	.	.	none		0.507	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		G	107573100	C	G	107573100	3	3	233	1	0	0	0	0	1	0	0	0	28	893	31	4	2717	4	ABCA1	9	107573100	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	3270562	107573100	33640331	72	14195											
RPL7A	6130	hgsc.bcm.edu	37	chr9	136216489	136216489	+	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	tgcagcggcagagagccatcCtctataagcggctgaaagtg	11	7	13	10	2	1	2	0	1	1	1	2	3	2	2	2	2	4	3	2	2	3	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:136216489C>A	ENST00000323345.6	+	3	238	c.208C>A	c.(208-210)Ctc>Atc	p.L70I	MED22_ENST00000471524.1_5'Flank|SNORD36B_ENST00000363961.1_RNA|MED22_ENST00000491289.1_5'Flank|MED22_ENST00000371999.1_5'Flank|SURF1_ENST00000495952.1_5'Flank|RPL7A_ENST00000315731.4_Intron|SNORD36C_ENST00000516733.1_RNA|MED22_ENST00000476080.1_5'Flank|MED22_ENST00000343730.5_5'Flank|SNORD36A_ENST00000362874.1_RNA|SNORD24_ENST00000383884.1_RNA|MED22_ENST00000344469.5_5'Flank|RPL7A_ENST00000463740.1_3'UTR	NM_000972.2	NP_000963.1	P62424	RL7A_HUMAN	ribosomal protein L7a	70					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosome biogenesis (GO:0042254)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(1)|kidney(1)|lung(3)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(145;4.93e-07)|Epithelial(140;4.09e-06)|all cancers(34;3.78e-05)		GAGAGCCATCCTCTATAAGCG	0.552																																					p.L70I		Atlas-SNP	.											.	RPL7A	9	.	0			c.C208A						PASS	.						43	48	46					9																	136216489		2203	4294	6497	SO:0001583	missense	6130	exon3			GCCATCCTCTATA	BC005128	CCDS6965.1	9q34	2011-04-06			ENSG00000148303	ENSG00000148303		"L ribosomal proteins"	10364	protein-coding gene	gene with protein product	"surfeit 3", "PLA-X polypeptide", "surfeit locus protein 3", "60S ribosomal protein L7a", ";", "thyroid hormone receptor uncoupling protein"	185640				2403926, 2966065	Standard	NM_000972		Approved	SURF3, TRUP, L7A	uc004cde.1	P62424	OTTHUMG00000020864	ENST00000323345.6:c.208C>A	chr9.hg19:g.136216489C>A	ENSP00000361076:p.Leu70Ile	80.0	0.0	.		88.0	31.0	.	NM_000972	P11518|Q5T8U4	Missense_Mutation	SNP	ENST00000323345.6	hg19	CCDS6965.1	.	.	.	.	.	.	.	.	.	.	C	16.56	3.158547	0.57368	.	.	ENSG00000148303	ENST00000323345;ENST00000426651	T;T	0.70164	-0.46;-0.13	4.03	4.03	0.46877	.	0.000000	0.85682	D	0.000000	T	0.75539	0.3863	M	0.89287	3.02	0.80722	D	1	B	0.22604	0.072	B	0.34346	0.18	T	0.78841	-0.2045	10	0.66056	D	0.02	.	15.1827	0.72972	0.0:1.0:0.0:0.0	.	70	P62424	RL7A_HUMAN	I	70;97	ENSP00000361076:L70I;ENSP00000416638:L97I	ENSP00000361076:L70I	L	+	1	0	RPL7A	135206310	1.000000	0.71417	0.648000	0.29521	0.115000	0.19883	5.276000	0.65580	1.816000	0.52996	0.313000	0.20887	CTC	.	.	.	none		0.552	RPL7A-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054869.1	NM_000972		A	136216489	C	A	136216489	3	1	233	1	0	0	0	0	1	0	0	0	13613	681	24	4	218	4	RPL7A	9	136216489	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	28643389	136216489	4996942	73	14196											
LHX3	8022	hgsc.bcm.edu	37	chr9	139089398	139089398	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagggaggctctgcggggCggcgggggatggggggacac	5	3	24	9	3	1	0	0	0	1	0	1	3	1	3	1	10	1	1	1	10	0	0			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr9:139089398C>T	ENST00000371748.5	-	6	1063	c.967G>A	c.(967-969)Gcc>Acc	p.A323T	LHX3_ENST00000371746.3_Missense_Mutation_p.A328T	NM_178138.4	NP_835258.1	Q9UBR4	LHX3_HUMAN	LIM homeobox 3	323					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)		CTCTGCGGGGCGGCGGGGGAT	0.736																																					p.A328T		Atlas-SNP	.											.	LHX3	23	.	0			c.G982A						PASS	.						2	2	2					9																	139089398		1495	3217	4712	SO:0001583	missense	8022	exon6			GCGGGGCGGCGGG	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.967G>A	chr9.hg19:g.139089398C>T	ENSP00000360813:p.Ala323Thr	7.0	0.0	.		12.0	6.0	.	NM_014564	Q5TB39|Q5TB40|Q9NZB5|Q9P0I8|Q9P0I9	Missense_Mutation	SNP	ENST00000371748.5	hg19	CCDS6994.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	6.336|6.336	0.430180|0.430180	0.12045|0.12045	.|.	.|.	ENSG00000107187|ENSG00000107187	ENST00000371748;ENST00000371746|ENST00000325195	D;D|.	0.88818|.	-2.27;-2.43|.	4.04|4.04	1.96|1.96	0.26148|0.26148	.|.	0.152719|.	0.45361|.	N|.	0.000361|.	T|T	0.28433|0.28433	0.0703|0.0703	L|L	0.36672|0.36672	1.1|1.1	0.22961|0.22961	N|N	0.998502|0.998502	B;P|.	0.34462|.	0.308;0.454|.	B;B|.	0.29942|.	0.109;0.075|.	T|T	0.20371|0.20371	-1.0277|-1.0277	10|6	0.17369|0.33940	T|T	0.5|0.23	.|.	4.7565|4.7565	0.13086|0.13086	0.3922:0.4882:0.0:0.1196|0.3922:0.4882:0.0:0.1196	.|.	323;328|.	Q9UBR4;F1T0D9|.	LHX3_HUMAN;.|.	T|H	323;328|324	ENSP00000360813:A323T;ENSP00000360811:A328T|.	ENSP00000360811:A328T|ENSP00000319224:R324H	A|R	-|-	1|2	0|0	LHX3|LHX3	138229219|138229219	0.831000|0.831000	0.29352|0.29352	0.042000|0.042000	0.18584|0.18584	0.173000|0.173000	0.22820|0.22820	1.670000|1.670000	0.37502|0.37502	0.891000|0.891000	0.36235|0.36235	0.491000|0.491000	0.48974|0.48974	GCC|CGC	.	.	.	none		0.736	LHX3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055048.3			T	139089398	C	T	139089398	3	4	233	1	0	0	0	0	1	0	0	0	8779	768	27	1	230	1	LHX3	9	139089398	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	2872909	139089398	2124033	74	14197											
OPTN	10133	hgsc.bcm.edu	37	chr10	13160994	13160994	+	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	tgtgcctaagggaagggaatCagaaggtggagagacttgaa	14	7	16	4	0	1	3	1	1	0	2	1	7	1	6	1	4	1	0	1	4	5	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr10:13160994C>T	ENST00000378748.3	+	8	1095	c.733C>T	c.(733-735)Cag>Tag	p.Q245*	OPTN_ENST00000378757.2_Nonsense_Mutation_p.Q245*|OPTN_ENST00000378747.3_Nonsense_Mutation_p.Q245*|OPTN_ENST00000378764.2_Nonsense_Mutation_p.Q239*|OPTN_ENST00000378752.3_Nonsense_Mutation_p.Q239*|OPTN_ENST00000263036.5_Nonsense_Mutation_p.Q245*	NM_001008211.1|NM_001008213.1	NP_001008212|NP_001008214	Q96CV9	OPTN_HUMAN	optineurin	245					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						GGAAGGGAATCAGAAGGTGGA	0.428																																					p.Q245X		Atlas-SNP	.											.	OPTN	57	.	0			c.C733T						PASS	.						93	91	91					10																	13160994		2203	4300	6503	SO:0001587	stop_gained	10133	exon7			GGGAATCAGAAGG	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.733C>T	chr10.hg19:g.13160994C>T	ENSP00000368022:p.Gln245*	199.0	0.0	.		175.0	100.0	.	NM_001008212	B3KP00|D3DRS4|D3DRS8|Q5T672|Q5T673|Q5T674|Q5T675|Q7LDL9|Q8N562|Q9UET9|Q9UEV4|Q9Y218	Nonsense_Mutation	SNP	ENST00000378748.3	hg19	CCDS7094.1	.	.	.	.	.	.	.	.	.	.	C	39	7.381482	0.98248	.	.	ENSG00000123240	ENST00000263036;ENST00000378764;ENST00000378757;ENST00000378752;ENST00000378748;ENST00000378747	.	.	.	6.16	6.16	0.99307	.	0.099240	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	-22.7994	19.6313	0.95704	0.0:1.0:0.0:0.0	.	.	.	.	X	245;239;245;239;245;245	.	ENSP00000263036:Q245X	Q	+	1	0	OPTN	13201000	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	2.672000	0.46850	2.937000	0.99478	0.650000	0.86243	CAG	.	.	.	none		0.428	OPTN-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046834.1	NM_021980		T	13160994	C	T	13160994	4	4	233	1	0	0	0	0	0	1	0	0	10896	827	29	2	751	2	OPTN	10	13160994	Nonsense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10		13160994	122373753	75	14198											
KIAA1462	57608	hgsc.bcm.edu	37	chr10	30336674	30336674	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccccttggggttatcctcgCgtgatgctggggggtctctt	2	13	15	11	2	1	1	0	1	1	0	4	1	2	1	3	5	1	2	3	5	1	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr10:30336674C>T	ENST00000375377.1	-	2	169	c.68G>A	c.(67-69)cGc>cAc	p.R23H		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	23					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						GTTATCCTCGCGTGATGCTGG	0.607																																					p.R23H		Atlas-SNP	.											.	KIAA1462	162	.	0			c.G68A						PASS	.						73	79	77					10																	30336674		2036	4192	6228	SO:0001583	missense	57608	exon2			TCCTCGCGTGATG	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.68G>A	chr10.hg19:g.30336674C>T	ENSP00000364526:p.Arg23His	116.0	0.0	.		128.0	6.0	.	NM_020848	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Missense_Mutation	SNP	ENST00000375377.1	hg19	CCDS41500.1	.	.	.	.	.	.	.	.	.	.	C	7.772	0.707679	0.15239	.	.	ENSG00000165757	ENST00000375377	T	0.11604	2.76	5.3	-1.25	0.09405	.	0.823638	0.10809	N	0.631817	T	0.03434	0.0099	N	0.03115	-0.41	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.46992	-0.9151	10	0.11794	T	0.64	-5.5506	5.0393	0.14451	0.0:0.4095:0.1523:0.4382	.	23	Q9P266	K1462_HUMAN	H	23	ENSP00000364526:R23H	ENSP00000364526:R23H	R	-	2	0	KIAA1462	30376680	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.154000	0.10130	-0.048000	0.13401	-0.373000	0.07131	CGC	.	.	.	none		0.607	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848		T	30336674	C	T	30336674	3	4	233	1	0	0	0	0	1	0	0	0	8241	768	27	1	4023	1	KIAA1462	10	30336674	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	17175680	30336674	105198073	76	14199											
TYSND1	219743	hgsc.bcm.edu	37	chr10	71905802	71905819	+	In_Frame_Del	DEL	CTCTCAGTTGATCCGCCT	CTCTCAGTTGATCCGCCT	-																															cagcgcaaaccagcccagcgCtctcagttgatccgcctcct																								rs370610523|rs572542997|rs562289648|rs553877350	byFrequency	TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	CTCTCAGTTGATCCGCCT	CTCTCAGTTGATCCGCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr10:71905802_71905819delCTCTCAGTTGATCCGCCT	ENST00000287078.6	-	1	523_540	c.524_541delAGGCGGATCAACTGAGAG	c.(523-543)gaggcggatcaactgagagcg>gcg	p.EADQLR175del	TYSND1_ENST00000335494.5_In_Frame_Del_p.EADQLR175del|TYSND1_ENST00000494143.1_5'Flank	NM_173555.2	NP_775826.2	Q2T9J0	TYSD1_HUMAN	trypsin domain containing 1	175					protein homooligomerization (GO:0051260)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of fatty acid beta-oxidation (GO:0031998)	membrane (GO:0016020)|peroxisome (GO:0005777)	identical protein binding (GO:0042802)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(2)|liver(1)|lung(3)|prostate(1)	9						CAGCCCAGCGCTCTCAGTTGATCCGCCTCCTCGTCCTC	0.711														5	0.000998403	8e-04	0	5008	,	,		14648	0.002		0	False		,,,				2504	0.002				p.175_181del		Pindel	.											.	TYSND1	20	.	0			c.525_542del						PASS	.		,	1,4251		0,1,2125					,	3.9	1			26	18,8216		0,18,4099	no	coding,coding	TYSND1	NM_173555.2,NM_001040273.1	,	0,19,6224	A1A1,A1R,RR		0.2186,0.0235,0.1522	,	,		19,12467				SO:0001651	inframe_deletion	219743	exon1			.	BC016840	CCDS31213.1, CCDS31214.1	10q22.1	2009-11-06		2006-09-21	ENSG00000156521	ENSG00000156521			28531	protein-coding gene	gene with protein product		611017				17255948	Standard	NM_173555		Approved	MGC34695, NET41	uc001jqr.4	Q2T9J0	OTTHUMG00000018397	ENST00000287078.6:c.524_541delAGGCGGATCAACTGAGAG	chr10.hg19:g.71905802_71905819delCTCTCAGTTGATCCGCCT	ENSP00000287078:p.Glu175_Arg180del	24.0	0.0	.		112.0	32.0	0.286	NM_001040273	Q5SQT4|Q5SQU1|Q8N6H2|Q96AR5	In_Frame_Del	DEL	ENST00000287078.6	hg19	CCDS31213.1																																																																																			.	.	.	none		0.711	TYSND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048483.1	NM_173555		-	71905819	CTCTCAGTTGATCCGCCT	-	71905802	7	5	233	1	0	1	0	1	0	0	0	0	16829	797	28	0	1175	0	TYSND1	10	71905802	In_Frame_Del	DEL	CTCTCAGTTGATCCGCCT	TCGA-P4-A5EB-01A-11D-A28G-10	41569128	71905802	63628945	77	14200											
KNDC1	85442	hgsc.bcm.edu	37	chr10	135013012	135013012	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctttgccactttctgtggcGccatttccgagaagttctgt	5	15	9	12	2	2	1	0	0	2	1	3	2	3	1	4	1	1	1	4	1	1	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr10:135013012G>A	ENST00000304613.3	+	15	2830	c.2809G>A	c.(2809-2811)Gcc>Acc	p.A937T	KNDC1_ENST00000368572.2_Missense_Mutation_p.A939T|KNDC1_ENST00000368571.2_Missense_Mutation_p.A872T			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	937					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)	p.A937T(1)		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)		TTTCTGTGGCGCCATTTCCGA	0.532																																					p.A937T		Atlas-SNP	.											KNDC1,rectum,carcinoma,0,2	KNDC1	155	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2809A						PASS	.						177	150	159					10																	135013012		2203	4300	6503	SO:0001583	missense	85442	exon15			TGTGGCGCCATTT	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.2809G>A	chr10.hg19:g.135013012G>A	ENSP00000304437:p.Ala937Thr	151.0	0.0	.		192.0	14.0	.	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	hg19	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.244556	0.59103	.	.	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.12984	2.63;2.63;2.63	3.99	3.99	0.46301	.	0.479232	0.18727	N	0.132851	T	0.34571	0.0902	M	0.66939	2.045	0.41003	D	0.984944	D;D;D	0.89917	0.993;1.0;0.997	D;D;P	0.72338	0.919;0.977;0.74	T	0.18116	-1.0347	10	0.72032	D	0.01	-25.397	13.9012	0.63804	0.0:0.0:1.0:0.0	.	937;872;937	Q76NI1-4;Q76NI1-2;Q76NI1	.;.;VKIND_HUMAN	T	937;939;872	ENSP00000304437:A937T;ENSP00000357561:A939T;ENSP00000357560:A872T	ENSP00000304437:A937T	A	+	1	0	KNDC1	134863002	0.937000	0.31787	0.821000	0.32701	0.124000	0.20399	2.706000	0.47135	1.957000	0.56846	0.313000	0.20887	GCC	.	.	.	none		0.532	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		A	135013012	G	A	135013012	3	1	233	1	0	0	0	0	1	0	0	0	8433	1087	38	1	2867	1	KNDC1	10	135013012	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	63107210	135013012	521735	78	14201											
OR51D1	390038	hgsc.bcm.edu	37	chr11	4661643	4661643	+	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	ctgtactgacaccagggtcaAtgtggtttatggactcttca	9	13	10	9	0	3	1	2	1	1	0	3	2	3	2	1	3	1	2	1	3	3	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr11:4661643A>T	ENST00000357605.2	+	1	699	c.623A>T	c.(622-624)aAt>aTt	p.N208I		NM_001004751.2	NP_001004751.1	Q8NGF3	O51D1_HUMAN	olfactory receptor, family 51, subfamily D, member 1	208						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|liver(2)|lung(14)|prostate(1)|skin(2)|urinary_tract(1)	27		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;2.74e-13)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|GBM - Glioblastoma multiforme(2;0.0841)|LUSC - Lung squamous cell carcinoma(625;0.19)		ACCAGGGTCAATGTGGTTTAT	0.468																																					p.N208I		Atlas-SNP	.											.	OR51D1	49	.	0			c.A623T						PASS	.						290	242	259					11																	4661643		2201	4298	6499	SO:0001583	missense	390038	exon1			GGGTCAATGTGGT	AB065855	CCDS31357.1	11p15.4	2012-08-09			ENSG00000197428	ENSG00000197428		"GPCR / Class A : Olfactory receptors"	15193	protein-coding gene	gene with protein product							Standard	NM_001004751		Approved	OR51D1Q	uc010qyk.2	Q8NGF3	OTTHUMG00000165724	ENST00000357605.2:c.623A>T	chr11.hg19:g.4661643A>T	ENSP00000350222:p.Asn208Ile	141.0	0.0	.		172.0	74.0	.	NM_001004751	B9EIK4	Missense_Mutation	SNP	ENST00000357605.2	hg19	CCDS31357.1	.	.	.	.	.	.	.	.	.	.	A	11.92	1.781247	0.31502	.	.	ENSG00000197428	ENST00000357605	T	0.00231	8.49	4.29	3.13	0.36017	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000197	T	0.00580	0.0019	M	0.88906	2.99	0.43330	D	0.995366	P	0.44877	0.845	D	0.63793	0.918	T	0.66272	-0.5965	10	0.87932	D	0	.	9.16	0.37016	0.9102:0.0:0.0898:0.0	.	208	Q8NGF3	O51D1_HUMAN	I	208	ENSP00000350222:N208I	ENSP00000350222:N208I	N	+	2	0	OR51D1	4618219	0.644000	0.27277	0.752000	0.31206	0.008000	0.06430	1.567000	0.36407	0.752000	0.32923	0.460000	0.39030	AAT	.	.	.	none		0.468	OR51D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385956.1	NM_001004751		T	4661643	A	T	4661643	3	4	233	1	0	0	0	0	1	0	0	0	11100	101	4	5	625	5	OR51D1	11	4661643	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10		4661643	130344873	79	14202											
EIF4G2	1982	hgsc.bcm.edu	37	chr11	10820842	10820842	+	Missense_Mutation	SNP	T	T	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	tcaacgtgatcatgaagaaaTttctgcattactggcttgaa	13	13	8	7	1	3	4	2	3	1	1	3	4	3	4	0	1	3	2	0	1	5	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr11:10820842T>G	ENST00000526148.1	-	20	2964	c.2454A>C	c.(2452-2454)aaA>aaC	p.K818N	SNORD97_ENST00000459187.1_RNA|EIF4G2_ENST00000339995.5_Missense_Mutation_p.K818N|RP11-685M7.5_ENST00000532365.1_RNA|EIF4G2_ENST00000525681.1_Missense_Mutation_p.K818N|EIF4G2_ENST00000396525.2_Missense_Mutation_p.K780N	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)		CATGAAGAAATTTCTGCATTA	0.443																																					p.K818N		Atlas-SNP	.											.	EIF4G2	89	.	0			c.A2454C						PASS	.						154	144	148					11																	10820842		2201	4294	6495	SO:0001583	missense	1982	exon20			AAGAAATTTCTGC	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.2454A>C	chr11.hg19:g.10820842T>G	ENSP00000433664:p.Lys818Asn	101.0	0.0	.		120.0	61.0	.	NM_001172705		Missense_Mutation	SNP	ENST00000526148.1	hg19	CCDS31428.1	.	.	.	.	.	.	.	.	.	.	T	19.81	3.896251	0.72639	.	.	ENSG00000110321	ENST00000526148;ENST00000525681;ENST00000339995;ENST00000396525;ENST00000429377;ENST00000528839;ENST00000379653	T;T;T;T	0.22743	1.94;1.94;1.94;1.96	6.07	0.912	0.19349	eIF4-gamma/eIF5/eIF2-epsilon (2);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.000000	0.85682	D	0.000000	T	0.31040	0.0784	M	0.76727	2.345	0.53005	D	0.999965	P;D	0.63880	0.949;0.993	P;P	0.52109	0.493;0.69	T	0.47086	-0.9144	9	0.59425	D	0.04	-9.3023	8.4006	0.32583	0.0:0.5799:0.0:0.4201	.	818;891	P78344;B4DZF2	IF4G2_HUMAN;.	N	818;818;818;780;891;166;200	ENSP00000433664:K818N;ENSP00000433371:K818N;ENSP00000340281:K818N;ENSP00000379778:K780N	ENSP00000340281:K818N	K	-	3	2	EIF4G2	10777418	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	0.781000	0.26774	0.149000	0.19098	0.533000	0.62120	AAA	.	.	.	none		0.443	EIF4G2-006	KNOWN	alternative_5_UTR|non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386603.1	NM_001418		G	10820842	T	G	10820842	3	3	233	1	0	0	0	0	1	0	0	0	5039	1490	52	5	281	5	EIF4G2	11	10820842	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	6159199	10820842	124185674	80	14203											
CKAP5	9793	hgsc.bcm.edu	37	chr11	46799004	46799004	+	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	tttaccttgctgtctccaagGactgtgatgatagggatgcc	8	13	11	9	0	1	2	0	2	1	0	2	4	1	4	3	2	3	1	3	2	3	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr11:46799004G>C	ENST00000529230.1	-	23	2893	c.2847C>G	c.(2845-2847)gtC>gtG	p.V949V	CKAP5_ENST00000312055.5_Silent_p.V949V|CKAP5_ENST00000354558.3_Silent_p.V949V|CKAP5_ENST00000415402.1_Silent_p.V949V			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	949					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						TGTCTCCAAGGACTGTGATGA	0.413																																					p.V949V	Ovarian(4;85 273 2202 4844 13323)	Atlas-SNP	.											.	CKAP5	134	.	0			c.C2847G						PASS	.						137	125	129					11																	46799004		2201	4299	6500	SO:0001819	synonymous_variant	9793	exon23			TCCAAGGACTGTG		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.2847C>G	chr11.hg19:g.46799004G>C		81.0	0.0	.		104.0	43.0	.	NM_001008938	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	Silent	SNP	ENST00000529230.1	hg19	CCDS31477.1																																																																																			.	.	.	none		0.413	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	NM_014756		C	46799004	G	C	46799004	2	2	233	1	0	0	0	0	0	0	0	1	3447	1161	41	4		4	CKAP5	11	46799004	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	35978162	46799004	88207512	81	14204											
NUP160	23279	hgsc.bcm.edu	37	chr11	47837537	47837537	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaacttctttcttcagttcActccaggaaagatccaaatt	12	14	5	10	0	4	1	2	0	2	1	6	2	6	2	2	1	1	2	2	1	3	6			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr11:47837537A>G	ENST00000378460.2	-	12	1522	c.1476T>C	c.(1474-1476)agT>agC	p.S492S	NUP160_ENST00000531016.1_5'UTR|NUP160_ENST00000528501.1_Silent_p.S56S|NUP160_ENST00000528071.1_Silent_p.S378S|NUP160_ENST00000530326.1_Silent_p.S378S	NM_015231.1	NP_056046.1	Q12769	NU160_HUMAN	nucleoporin 160kDa	492					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|biliary_tract(2)|breast(7)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(15)|ovary(6)|prostate(2)|skin(2)|urinary_tract(2)	53						TCTTCAGTTCACTCCAGGAAA	0.363																																					p.S492S		Atlas-SNP	.											.	NUP160	116	.	0			c.T1476C						PASS	.						92	89	90					11																	47837537		2201	4298	6499	SO:0001819	synonymous_variant	23279	exon12			CAGTTCACTCCAG	D83781	CCDS31484.1	11p11.12	2008-07-21	2002-08-29		ENSG00000030066	ENSG00000030066			18017	protein-coding gene	gene with protein product		607614	"nucleoporin 160kD"			11684705	Standard	NM_015231		Approved	KIAA0197, FLJ22583	uc001ngm.3	Q12769	OTTHUMG00000166534	ENST00000378460.2:c.1476T>C	chr11.hg19:g.47837537A>G		264.0	0.0	.		361.0	175.0	.	NM_015231	B4DYE8|B4E2J9|Q08AD3|Q7Z5X6|Q96GB3|Q9H660	Silent	SNP	ENST00000378460.2	hg19	CCDS31484.1																																																																																			.	.	.	none		0.363	NUP160-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390239.2	NM_015231		G	47837537	A	G	47837537	2	3	233	1	0	0	0	0	0	0	0	1	10764	156	6	3		3	NUP160	11	47837537	Silent	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	1038533	47837537	87168979	82	14205											
PTPRJ	5795	hgsc.bcm.edu	37	chr11	48142728	48142728	+	Missense_Mutation	SNP	T	T	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	catggtgtaacatcacaggcTtacgtccagcgacttcatat	11	11	8	11	2	2	0	2	0	0	0	3	1	3	0	1	2	3	2	1	2	3	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr11:48142728T>G	ENST00000418331.2	+	4	878	c.526T>G	c.(526-528)Tta>Gta	p.L176V	PTPRJ_ENST00000440289.2_Missense_Mutation_p.L176V	NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	176	Fibronectin type-III 1. {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						CATCACAGGCTTACGTCCAGC	0.423																																					p.L176V		Atlas-SNP	.											.	PTPRJ	225	.	0			c.T526G						PASS	.						163	147	153					11																	48142728		2201	4298	6499	SO:0001583	missense	5795	exon4			ACAGGCTTACGTC	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.526T>G	chr11.hg19:g.48142728T>G	ENSP00000400010:p.Leu176Val	282.0	1.0	.		323.0	131.0	.	NM_001098503	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	hg19	CCDS7945.1	.	.	.	.	.	.	.	.	.	.	T	16.53	3.149018	0.57151	.	.	ENSG00000149177	ENST00000278456;ENST00000418331;ENST00000440289;ENST00000534219	D;D;D	0.84800	-1.9;-1.9;-1.9	5.41	1.8	0.24995	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	D	0.89894	0.6847	M	0.75615	2.305	0.09310	N	1	D;D	0.71674	0.992;0.998	P;D	0.72338	0.908;0.977	T	0.78858	-0.2038	9	0.72032	D	0.01	.	6.633	0.22867	0.0:0.2796:0.0:0.7204	.	176;176	Q12913;Q6P4H4	PTPRJ_HUMAN;.	V	176;176;176;97	ENSP00000400010:L176V;ENSP00000409733:L176V;ENSP00000432686:L97V	ENSP00000278456:L176V	L	+	1	2	PTPRJ	48099304	0.000000	0.05858	0.014000	0.15608	0.075000	0.17131	-0.197000	0.09518	0.346000	0.23899	0.482000	0.46254	TTA	.	.	.	none		0.423	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1			G	48142728	T	G	48142728	3	3	233	1	0	0	0	0	1	0	0	0	12817	1606	56	5	540	5	PTPRJ	11	48142728	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	305191	48142728	86863788	83	14206											
ANKK1	255239	hgsc.bcm.edu	37	chr11	113265705	113265705	+	Missense_Mutation	SNP	A	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	agtccacccggatgcagtacAtcgagaggtcggctctgcgg	8	7	14	12	4	1	1	0	0	1	1	4	3	2	2	2	4	3	3	2	4	1	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr11:113265705A>C	ENST00000303941.3	+	3	629	c.535A>C	c.(535-537)Atc>Ctc	p.I179L		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	179	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						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)		GATGCAGTACATCGAGAGGTC	0.552																																					p.I179L		Atlas-SNP	.											.	ANKK1	83	.	0			c.A535C						PASS	.						52	51	51					11																	113265705		2003	4170	6173	SO:0001583	missense	255239	exon3			CAGTACATCGAGA	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.535A>C	chr11.hg19:g.113265705A>C	ENSP00000306678:p.Ile179Leu	113.0	0.0	.		192.0	87.0	.	NM_178510		Missense_Mutation	SNP	ENST00000303941.3	hg19	CCDS44734.1	.	.	.	.	.	.	.	.	.	.	A	7.078	0.569692	0.13560	.	.	ENSG00000170209	ENST00000303941	D	0.82167	-1.58	4.25	3.11	0.35812	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.52532	U	0.000079	T	0.76786	0.4036	L	0.27053	0.805	0.42141	D	0.991513	P	0.43231	0.801	P	0.48089	0.566	T	0.72301	-0.4334	10	0.34782	T	0.22	-24.2177	9.4598	0.38778	0.8415:0.0:0.0:0.1585	.	179	Q8NFD2	ANKK1_HUMAN	L	179	ENSP00000306678:I179L	ENSP00000306678:I179L	I	+	1	0	ANKK1	112770915	0.995000	0.38212	0.250000	0.24296	0.020000	0.10135	3.696000	0.54757	0.654000	0.30846	-1.026000	0.02426	ATC	.	.	.	none		0.552	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510		C	113265705	A	C	113265705	3	2	233	1	0	0	0	0	1	0	0	0	631	217	8	5	545	5	ANKK1	11	113265705	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	65122977	113265705	21740811	84	14207											
B4GALNT3	283358	hgsc.bcm.edu	37	chr12	660177	660177	+	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	tggatgggcttcctctgcagCgctaccagggactccggttt	5	11	13	12	2	1	0	0	0	1	0	3	2	3	2	3	4	3	4	3	4	1	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:660177C>T	ENST00000266383.5	+	11	1100	c.1087C>T	c.(1087-1089)Cgc>Tgc	p.R363C		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	363					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)			TCCTCTGCAGCGCTACCAGGG	0.607																																					p.R363C		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.C1087T						PASS	.						172	151	158					12																	660177		2203	4300	6503	SO:0001583	missense	283358	exon11			CTGCAGCGCTACC	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.1087C>T	chr12.hg19:g.660177C>T	ENSP00000266383:p.Arg363Cys	105.0	0.0	.		163.0	37.0	.	NM_173593	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	hg19	CCDS8504.1	.	.	.	.	.	.	.	.	.	.	C	31	5.064455	0.93898	.	.	ENSG00000139044	ENST00000266383;ENST00000322843	T;T	0.72725	-0.68;-0.68	5.22	5.22	0.72569	.	0.107194	0.64402	D	0.000004	D	0.84428	0.5470	M	0.77313	2.365	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.68621	0.959;0.926	D	0.86089	0.1549	10	0.87932	D	0	-22.1916	18.9627	0.92682	0.0:1.0:0.0:0.0	.	265;363	E9PHD9;Q6L9W6	.;B4GN3_HUMAN	C	363;265	ENSP00000266383:R363C;ENSP00000322953:R265C	ENSP00000266383:R363C	R	+	1	0	B4GALNT3	530438	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.267000	0.65530	2.715000	0.92844	0.655000	0.94253	CGC	.	.	.	none		0.607	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593		T	660177	C	T	660177	3	4	233	1	0	0	0	0	1	0	0	0	1268	768	27	1	1129	1	B4GALNT3	12	660177	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10		660177	133191718	85	14208											
LRTM2	654429	hgsc.bcm.edu	37	chr12	1940301	1940301	+	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	tgccaagctgggctttcgccAacctctccagcctgcagcgg	6	8	11	16	2	1	0	0	0	1	0	3	0	1	0	5	2	6	3	5	2	2	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:1940301A>T	ENST00000543818.1	+	4	1110	c.268A>T	c.(268-270)Aac>Tac	p.N90Y	LRTM2_ENST00000299194.1_Missense_Mutation_p.N90Y|CACNA2D4_ENST00000586184.1_Intron|CACNA2D4_ENST00000587995.1_Intron|CACNA2D4_ENST00000585708.1_Intron|CACNA2D4_ENST00000588077.1_Intron|CACNA2D4_ENST00000585732.1_Intron|LRTM2_ENST00000535041.1_Missense_Mutation_p.N90Y|LRTM2_ENST00000543730.1_Intron|CACNA2D4_ENST00000382722.5_Intron	NM_001039029.2|NM_001163925.1|NM_001163926.1	NP_001034118.1|NP_001157397.1|NP_001157398.1	Q8N967	LRTM2_HUMAN	leucine-rich repeats and transmembrane domains 2	90						integral component of membrane (GO:0016021)				NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	20	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000834)			GGCTTTCGCCAACCTCTCCAG	0.617																																					p.N90Y		Atlas-SNP	.											.	LRTM2	43	.	0			c.A268T						PASS	.						57	65	62					12																	1940301		2203	4300	6503	SO:0001583	missense	654429	exon4			TTCGCCAACCTCT	AK095610	CCDS31726.1	12p13.33	2008-02-05				ENSG00000166159			32443	protein-coding gene	gene with protein product							Standard	NM_001039029		Approved		uc010sdx.1	Q8N967		ENST00000543818.1:c.268A>T	chr12.hg19:g.1940301A>T	ENSP00000446278:p.Asn90Tyr	47.0	0.0	.		59.0	30.0	.	NM_001039029	A7E2U6	Missense_Mutation	SNP	ENST00000543818.1	hg19	CCDS31726.1	.	.	.	.	.	.	.	.	.	.	A	17.40	3.379726	0.61845	.	.	ENSG00000166159	ENST00000543818;ENST00000299194;ENST00000535041;ENST00000546167;ENST00000543694	T;T;T;D;D	0.85013	0.52;0.52;0.52;-1.93;-1.93	5.04	3.87	0.44632	.	0.000000	0.85682	D	0.000000	D	0.88224	0.6379	L	0.54323	1.7	0.58432	D	0.999996	D	0.59357	0.985	P	0.61328	0.887	D	0.87459	0.2406	10	0.62326	D	0.03	.	10.9074	0.47088	0.925:0.0:0.075:0.0	.	90	Q8N967	LRTM2_HUMAN	Y	90	ENSP00000446278:N90Y;ENSP00000299194:N90Y;ENSP00000444737:N90Y;ENSP00000438678:N90Y;ENSP00000444104:N90Y	ENSP00000299194:N90Y	N	+	1	0	LRTM2	1810562	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.182000	0.58310	0.748000	0.32831	0.459000	0.35465	AAC	.	.	.	none		0.617	LRTM2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398055.1			T	1940301	A	T	1940301	3	4	233	1	0	0	0	0	1	0	0	0	9052	130	5	5	274	5	LRTM2	12	1940301	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	1280124	1940301	131911594	86	14209											
WBP11	51729	hgsc.bcm.edu	37	chr12	14943406	14943406	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttacctggaggtggaccaggAggaaggcctgtaggtggccc	8	7	17	9	0	0	0	0	0	0	0	0	4	0	4	4	8	1	1	4	8	3	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:14943406A>G	ENST00000261167.2	-	10	1526	c.1293T>C	c.(1291-1293)ccT>ccC	p.P431P		NM_016312.2	NP_057396.1	Q9Y2W2	WBP11_HUMAN	WW domain binding protein 11	431	Pro-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein phosphatase type 1 regulator activity (GO:0008599)|single-stranded DNA binding (GO:0003697)|WW domain binding (GO:0050699)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)	30						GTGGACCAGGAGGAAGGCCTG	0.473																																					p.P431P		Atlas-SNP	.											.	WBP11	66	.	0			c.T1293C						PASS	.						99	103	102					12																	14943406		2203	4300	6503	SO:0001819	synonymous_variant	51729	exon10			ACCAGGAGGAAGG	AB029309	CCDS8666.1	12p12.3	2014-06-13			ENSG00000084463	ENSG00000084463			16461	protein-coding gene	gene with protein product	"splicing factor, PQBP1 and PP1 interacting", "protein phosphatase 1, regulatory subunit 165"					10593949	Standard	NM_016312		Approved	NPWBP, SIPP1, PPP1R165	uc001rci.3	Q9Y2W2	OTTHUMG00000168737	ENST00000261167.2:c.1293T>C	chr12.hg19:g.14943406A>G		97.0	0.0	.		134.0	24.0	.	NM_016312	Q96AY8	Silent	SNP	ENST00000261167.2	hg19	CCDS8666.1																																																																																			.	.	.	none		0.473	WBP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400850.1	NM_016312		G	14943406	A	G	14943406	2	3	233	1	0	0	0	0	0	0	0	1	17270	291	11	3		3	WBP11	12	14943406	Silent	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	13003105	14943406	118908489	87	14210											
KCNH3	23416	hgsc.bcm.edu	37	chr12	49944077	49944077	+	Missense_Mutation	SNP	A	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	tgtctgctctggctccatggAggtgctcaagggtggcaccg	5	10	15	11	1	3	0	1	0	2	0	4	1	4	1	2	5	2	4	2	5	1	0			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:49944077A>C	ENST00000257981.6	+	10	2143	c.1883A>C	c.(1882-1884)gAg>gCg	p.E628A		NM_012284.1	NP_036416.1	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 3	628					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36						GGCTCCATGGAGGTGCTCAAG	0.647																																					p.E628A		Atlas-SNP	.											.	KCNH3	88	.	0			c.A1883C						PASS	.						73	66	68					12																	49944077		2203	4300	6503	SO:0001583	missense	23416	exon10			CCATGGAGGTGCT	AB022696	CCDS8786.1	12q13	2012-07-05				ENSG00000135519		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6252	protein-coding gene	gene with protein product		604527				10455180, 16382104	Standard	NM_012284		Approved	Kv12.2, BEC1, elk2	uc001ruh.1	Q9ULD8	OTTHUMG00000169517	ENST00000257981.6:c.1883A>C	chr12.hg19:g.49944077A>C	ENSP00000257981:p.Glu628Ala	17.0	0.0	.		93.0	48.0	.	NM_012284	Q9UQ06	Missense_Mutation	SNP	ENST00000257981.6	hg19	CCDS8786.1	.	.	.	.	.	.	.	.	.	.	A	31	5.069017	0.93950	.	.	ENSG00000135519	ENST00000257981	D	0.93307	-3.2	5.48	5.48	0.80851	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.000000	0.48767	D	0.000161	D	0.96620	0.8897	M	0.84219	2.685	0.58432	D	0.999997	D	0.76494	0.999	D	0.87578	0.998	D	0.97133	0.9819	10	0.87932	D	0	.	13.8224	0.63331	1.0:0.0:0.0:0.0	.	628	Q9ULD8	KCNH3_HUMAN	A	628	ENSP00000257981:E628A	ENSP00000257981:E628A	E	+	2	0	KCNH3	48230344	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.224000	0.72417	0.533000	0.62120	GAG	.	.	.	none		0.647	KCNH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404571.2	NM_012284		C	49944077	A	C	49944077	3	2	233	1	0	0	0	0	1	0	0	0	8040	304	11	5	1921	5	KCNH3	12	49944077	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	35000671	49944077	83907818	88	14211											
CSAD	51380	hgsc.bcm.edu	37	chr12	53554015	53554015	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggcggccacactgcaccaccTtgtctcccgtgtccagagcc	6	7	10	18	2	1	1	0	0	1	1	3	1	2	1	6	2	2	1	6	2	0	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:53554015T>C	ENST00000444623.1	-	14	1322	c.1055A>G	c.(1054-1056)aAg>aGg	p.K352R	CSAD_ENST00000379846.1_Missense_Mutation_p.K205R|CSAD_ENST00000453446.2_Missense_Mutation_p.K352R|CSAD_ENST00000267085.4_Missense_Mutation_p.K379R|CSAD_ENST00000379843.3_Missense_Mutation_p.K205R|RP11-1136G11.8_ENST00000550908.1_lincRNA	NM_001244705.1	NP_001231634.1	Q9Y600	CSAD_HUMAN	cysteine sulfinic acid decarboxylase	352					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)|taurine biosynthetic process (GO:0042412)		pyridoxal phosphate binding (GO:0030170)|sulfinoalanine decarboxylase activity (GO:0004782)			kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(4)	14					L-Cysteine(DB00151)	CTGCACCACCTTGTCTCCCGT	0.612																																					p.K379R	Ovarian(109;252 1546 16882 28524 44645)	Atlas-SNP	.											.	CSAD	66	.	0			c.A1136G						PASS	.						117	104	108					12																	53554015		2203	4300	6503	SO:0001583	missense	51380	exon14			ACCACCTTGTCTC	AB044561	CCDS8848.2, CCDS58235.1	12q13.11-q14.3	2008-08-04			ENSG00000139631	ENSG00000139631			18966	protein-coding gene	gene with protein product	"P-selectin cytoplasmic tail-associated protein"					15489334	Standard	NM_015989		Approved	PCAP, CSD	uc001sbz.3	Q9Y600	OTTHUMG00000048076	ENST00000444623.1:c.1055A>G	chr12.hg19:g.53554015T>C	ENSP00000415485:p.Lys352Arg	63.0	0.0	.		120.0	60.0	.	NM_015989	A8K0U4|Q4QQH9|Q9UNJ5|Q9Y601	Missense_Mutation	SNP	ENST00000444623.1	hg19	CCDS58235.1	.	.	.	.	.	.	.	.	.	.	T	33	5.207752	0.95033	.	.	ENSG00000139631	ENST00000308926;ENST00000379843;ENST00000267085;ENST00000379846;ENST00000444623;ENST00000398047;ENST00000453446	T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04	4.67	4.67	0.58626	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.047421	0.85682	D	0.000000	T	0.59376	0.2189	L	0.61387	1.9	0.80722	D	1	D;D;P	0.69078	0.997;0.994;0.871	D;D;B	0.68765	0.96;0.96;0.247	T	0.62062	-0.6933	10	0.56958	D	0.05	-26.8125	13.5402	0.61671	0.0:0.0:0.0:1.0	.	379;352;205	Q9Y600-3;Q9Y600;Q9Y600-2	.;CSAD_HUMAN;.	R	441;205;379;205;352;313;352	ENSP00000369172:K205R;ENSP00000267085:K379R;ENSP00000369175:K205R;ENSP00000415485:K352R;ENSP00000410648:K352R	ENSP00000267085:K379R	K	-	2	0	CSAD	51840282	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.430000	0.80321	2.100000	0.63781	0.533000	0.62120	AAG	.	.	.	none		0.612	CSAD-017	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343697.1	NM_015989		C	53554015	T	C	53554015	3	2	233	1	0	0	0	0	1	0	0	0	3927	1609	56	3	442	3	CSAD	12	53554015	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	3609938	53554015	80297880	89	14212											
GPR84	53831	hgsc.bcm.edu	37	chr12	54756649	54756649	+	Silent	SNP	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	aagaaggggatgtagctcagGgcaaagcagaggaacacagc	16	3	15	7	0	1	2	1	0	0	2	1	4	1	4	0	4	4	4	0	4	5	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:54756649G>A	ENST00000551809.1	-	1	1622	c.987C>T	c.(985-987)gcC>gcT	p.A329A	GPR84_ENST00000267015.3_Silent_p.A329A|RP11-753H16.5_ENST00000552785.1_RNA|RP11-753H16.3_ENST00000550474.1_RNA			Q9NQS5	GPR84_HUMAN	G protein-coupled receptor 84	329						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|kidney(2)|large_intestine(6)|lung(5)|skin(1)|urinary_tract(1)	18						TGTAGCTCAGGGCAAAGCAGA	0.537																																					p.A329A		Atlas-SNP	.											.	GPR84	38	.	0			c.C987T						PASS	.						139	138	138					12																	54756649		2203	4300	6503	SO:0001819	synonymous_variant	53831	exon2			GCTCAGGGCAAAG	AF237762	CCDS8878.1	12q13.13	2012-08-20						"GPCR / Class A : Fatty acid receptors"	4535	protein-coding gene	gene with protein product		606383				11273702	Standard	NM_020370		Approved	EX33	uc001sfu.3	Q9NQS5		ENST00000551809.1:c.987C>T	chr12.hg19:g.54756649G>A		153.0	0.0	.		202.0	15.0	.	NM_020370	B6V9G7	Silent	SNP	ENST00000551809.1	hg19	CCDS8878.1																																																																																			.	.	.	none		0.537	GPR84-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406156.1			A	54756649	G	A	54756649	2	1	233	1	0	0	0	0	0	0	0	1	6721	1219	43	2		2	GPR84	12	54756649	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	1202634	54756649	79095246	90	14213											
SMARCC2	6601	hgsc.bcm.edu	37	chr12	56578005	56578005	+	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	tacacaacatgggaggcattGttcttatcctcagtgactgt	10	13	9	9	0	2	1	1	1	1	0	3	2	3	2	1	2	2	2	1	2	3	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:56578005G>T	ENST00000267064.4	-	6	602	c.516C>A	c.(514-516)aaC>aaA	p.N172K	SMARCC2_ENST00000550859.1_5'UTR|SMARCC2_ENST00000347471.4_Missense_Mutation_p.N172K|SMARCC2_ENST00000550164.1_Missense_Mutation_p.N172K|SMARCC2_ENST00000394023.3_Missense_Mutation_p.N172K|RP11-977G19.5_ENST00000553176.1_RNA	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	172					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)			GGGAGGCATTGTTCTTATCCT	0.498																																					p.N172K		Atlas-SNP	.											.	SMARCC2	212	.	0			c.C516A						PASS	.						116	94	101					12																	56578005		2203	4300	6503	SO:0001583	missense	6601	exon6			GGCATTGTTCTTA	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.516C>A	chr12.hg19:g.56578005G>T	ENSP00000267064:p.Asn172Lys	136.0	0.0	.		135.0	55.0	.	NM_139067	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Missense_Mutation	SNP	ENST00000267064.4	hg19	CCDS8907.1	.	.	.	.	.	.	.	.	.	.	G	12.74	2.028067	0.35797	.	.	ENSG00000139613	ENST00000394023;ENST00000550164;ENST00000347471;ENST00000267064	T;T;T;T	0.56941	0.43;0.43;0.43;0.43	5.38	4.49	0.54785	BRCT (1);	0.717108	0.14170	N	0.336810	T	0.28067	0.0692	N	0.04508	-0.205	0.22610	N	0.998937	B;B;B;B;B	0.18310	0.016;0.027;0.016;0.016;0.027	B;B;B;B;B	0.17098	0.007;0.017;0.007;0.007;0.017	T	0.14504	-1.0470	10	0.25751	T	0.34	-3.7705	7.6019	0.28081	0.2492:0.0:0.7508:0.0	.	61;172;177;172;172	B4DF22;F8VTJ5;Q59G16;Q8TAQ2;Q8TAQ2-2	.;.;.;SMRC2_HUMAN;.	K	172	ENSP00000377591:N172K;ENSP00000449396:N172K;ENSP00000302919:N172K;ENSP00000267064:N172K	ENSP00000267064:N172K	N	-	3	2	SMARCC2	54864272	0.956000	0.32656	0.998000	0.56505	0.994000	0.84299	1.519000	0.35888	1.412000	0.46977	0.561000	0.74099	AAC	.	.	.	none		0.498	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1			T	56578005	G	T	56578005	3	4	233	1	0	0	0	0	1	0	0	0	14789	1368	48	4	3317	4	SMARCC2	12	56578005	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	1821356	56578005	77273890	91	14214											
APAF1	317	hgsc.bcm.edu	37	chr12	99093184	99093184	+	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	tttttattactttaattcaaAgctttgggatgcgacatcag	11	17	7	6	1	2	0	2	0	0	0	2	2	2	1	0	1	3	1	0	1	4	8			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:99093184A>C	ENST00000551964.1	+	17	3040		c.e17-1		APAF1_ENST00000333991.1_Intron|APAF1_ENST00000550527.1_Splice_Site|APAF1_ENST00000357310.1_Splice_Site|APAF1_ENST00000549007.1_Splice_Site|APAF1_ENST00000339433.3_Splice_Site|APAF1_ENST00000552268.1_Intron|APAF1_ENST00000359972.2_Splice_Site|APAF1_ENST00000547045.1_Splice_Site	NM_181861.1	NP_863651.1	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway (GO:0097193)|nervous system development (GO:0007399)|neural tube closure (GO:0001843)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|response to G1 DNA damage checkpoint signaling (GO:0072432)	apoptosome (GO:0043293)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(1)	42					Adenosine triphosphate(DB00171)	TTTAATTCAAAGCTTTGGGAT	0.323																																					.		Atlas-SNP	.											.	APAF1	111	.	0			c.2272-2A>C						PASS	.						52	51	51					12																	99093184		2203	4300	6503	SO:0001630	splice_region_variant	317	exon17			ATTCAAAGCTTTG	AF013263	CCDS9069.1, CCDS9070.1, CCDS9071.1, CCDS55862.1, CCDS55863.1	12q23	2013-01-10	2006-10-23			ENSG00000120868		"WD repeat domain containing"	576	protein-coding gene	gene with protein product		602233	"apoptotic protease activating factor", "apoptotic peptidase activating factor"			9267021, 10702682	Standard	NM_181861		Approved	CED4, APAF-1	uc001tfz.3	O14727	OTTHUMG00000170214	ENST00000551964.1:c.2305-1A>C	chr12.hg19:g.99093184A>C		54.0	0.0	.		58.0	22.0	.	NM_001160	B2RMX8|O43297|Q7Z438|Q9BXZ6|Q9UBZ5|Q9UGN8|Q9UGN9|Q9UGP0|Q9UJ58|Q9UJ59|Q9UJ60|Q9UJ61|Q9UJ62|Q9UJ63|Q9UJ64|Q9UJ65|Q9UJ66|Q9UJ67|Q9UNC9	Splice_Site	SNP	ENST00000551964.1	hg19	CCDS9069.1	.	.	.	.	.	.	.	.	.	.	A	14.65	2.598135	0.46318	.	.	ENSG00000120868	ENST00000551964;ENST00000359972;ENST00000357310;ENST00000339433;ENST00000550527;ENST00000547045;ENST00000549007	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5583	0.61773	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	APAF1	97617315	1.000000	0.71417	0.949000	0.38748	0.676000	0.39594	7.031000	0.76491	2.186000	0.69663	0.533000	0.62120	.	.	.	.	none		0.323	APAF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408006.1	NM_181861.1	Intron	C	99093184	A	C	99093184	5	2	233	1	0	0	0	0	0	0	1	0	755	86	3	5	2365	5	APAF1	12	99093184	Splice_Site	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	42515179	99093184	34758711	92	14215											
MLEC	9761	hgsc.bcm.edu	37	chr12	121132908	121132908	+	Frame_Shift_Del	DEL	A	A	-																															cttttcctaggggtactatgAcaatcccaaggtctgtgcac																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr12:121132908delA	ENST00000228506.3	+	4	1030	c.602delA	c.(601-603)gacfs	p.D201fs	MLEC_ENST00000412616.2_Intron|RP11-173P15.3_ENST00000541383.1_RNA	NM_014730.2	NP_055545.1	Q14165	MLEC_HUMAN	malectin	201					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 membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|enzyme binding (GO:0019899)	p.D201G(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)	16						GGGTACTATGACAATCCCAAG	0.498																																					p.D201fs		Atlas-Indel,Pindel	.											.	MLEC	33	.	1	Substitution - Missense(1)	lung(1)	c.601delG						PASS	.						381	352	362					12																	121132908		2203	4300	6503	SO:0001589	frameshift_variant	9761	exon4			.	BC000371	CCDS9206.1	12q24.31	2013-03-06	2008-11-05	2008-11-05	ENSG00000110917	ENSG00000110917			28973	protein-coding gene	gene with protein product	"oligosaccharyltransferase complex subunit (non-catalytic)"	613802	"KIAA0152"	KIAA0152		18524852	Standard	NM_014730		Approved		uc001tyy.1	Q14165	OTTHUMG00000169187	ENST00000228506.3:c.602delA	chr12.hg19:g.121132908delA	ENSP00000228506:p.Asp201fs	123.0	0.0	0		162.0	72.0	0.444444	NM_014730		Frame_Shift_Del	DEL	ENST00000228506.3	hg19	CCDS9206.1																																																																																			.	.	.	none		0.498	MLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402781.2	NM_014730		-	121132908	A	-	121132908	7	5	233	1	0	1	0	1	0	0	0	0	9620	275	10	0	616	0	MLEC	12	121132908	Frame_Shift_Del	DEL	A	TCGA-P4-A5EB-01A-11D-A28G-10	22039724	121132908	12718987	93	14216											
DCLK1	9201	hgsc.bcm.edu	37	chr13	36383187	36383187	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggaaaccacacagcaggatAtaagtgattacacctgctgc	14	7	10	10	0	0	1	0	1	0	0	0	3	0	3	2	2	5	2	2	2	4	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr13:36383187A>G	ENST00000360631.3	-	13	1945	c.1734T>C	c.(1732-1734)taT>taC	p.Y578Y	DCLK1_ENST00000379893.1_Silent_p.Y271Y|DCLK1_ENST00000255448.4_Silent_p.Y578Y			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	578	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		ACAGCAGGATATAAGTGATTA	0.473																																					p.Y578Y		Atlas-SNP	.											.	DCLK1	350	.	0			c.T1734C						PASS	.						101	88	92					13																	36383187		2203	4300	6503	SO:0001819	synonymous_variant	9201	exon13			CAGGATATAAGTG	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.1734T>C	chr13.hg19:g.36383187A>G		93.0	0.0	.		150.0	51.0	.	NM_004734	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Silent	SNP	ENST00000360631.3	hg19																																																																																				.	.	.	none		0.473	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734		G	36383187	A	G	36383187	2	3	233	1	0	0	0	0	0	0	0	1	4293	456	16	3		3	DCLK1	13	36383187	Silent	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10		36383187	78786691	94	14217											
UGGT2	55757	hgsc.bcm.edu	37	chr13	96684163	96684163	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgtttgcttataaattgctAattcttgcacagtttccaaa	11	17	5	8	0	1	0	0	0	1	0	2	0	2	0	1	0	3	5	1	0	5	8			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr13:96684163A>G	ENST00000376747.3	-	2	291	c.221T>C	c.(220-222)tTa>tCa	p.L74S	UGGT2_ENST00000397618.3_Missense_Mutation_p.L74S|UGGT2_ENST00000376714.3_Missense_Mutation_p.L74S|UGGT2_ENST00000376712.4_Missense_Mutation_p.L74S	NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	74					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						ATAAATTGCTAATTCTTGCAC	0.259																																					p.L74S		Atlas-SNP	.											.	UGGT2	127	.	0			c.T221C						PASS	.						59	62	61					13																	96684163		2198	4277	6475	SO:0001583	missense	55757	exon2			ATTGCTAATTCTT	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.221T>C	chr13.hg19:g.96684163A>G	ENSP00000365938:p.Leu74Ser	103.0	0.0	.		102.0	38.0	.	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	hg19	CCDS9480.1	.	.	.	.	.	.	.	.	.	.	A	18.23	3.578856	0.65878	.	.	ENSG00000102595	ENST00000376747;ENST00000376722;ENST00000376714;ENST00000397618;ENST00000376712	T;T	0.32272	3.07;1.46	5.93	5.93	0.95920	.	0.075675	0.56097	D	0.000039	T	0.61565	0.2357	M	0.84683	2.71	0.53688	D	0.999975	D;D;P	0.89917	1.0;1.0;0.937	D;D;P	0.91635	0.999;0.999;0.512	T	0.67772	-0.5584	10	0.87932	D	0	-7.6383	16.3943	0.83563	1.0:0.0:0.0:0.0	.	74;74;74	Q2TAA6;E7EMU6;Q9NYU1	.;.;UGGG2_HUMAN	S	74	ENSP00000365938:L74S;ENSP00000380743:L74S	ENSP00000365902:L74S	L	-	2	0	UGGT2	95482164	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.701000	0.84566	2.281000	0.76405	0.533000	0.62120	TTA	.	.	.	none		0.259	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121		G	96684163	A	G	96684163	3	3	233	1	0	0	0	0	1	0	0	0	16954	372	13	3	4481	3	UGGT2	13	96684163	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	60300976	96684163	18485715	95	14218											
RPGRIP1	57096	hgsc.bcm.edu	37	chr14	21769308	21769308	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccactgcgtcggccctgcCagcccccgccgcgcccagcc	3	5	10	23	5	0	0	0	0	0	0	2	0	1	0	8	1	4	0	8	1	0	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr14:21769308C>T	ENST00000400017.2	+	3	402	c.402C>T	c.(400-402)gcC>gcT	p.A134A	RPGRIP1_ENST00000557771.1_Silent_p.A134A|RPGRIP1_ENST00000206660.6_Silent_p.A134A|RPGRIP1_ENST00000556336.1_Silent_p.A134A	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	134					eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)				breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		TCGGCCCTGCCAGCCCCCGCC	0.682																																					p.A134A		Atlas-SNP	.											.	RPGRIP1	213	.	0			c.C402T						PASS	.						10	14	13					14																	21769308		1990	4127	6117	SO:0001819	synonymous_variant	57096	exon3			CCCTGCCAGCCCC	AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.402C>T	chr14.hg19:g.21769308C>T		114.0	0.0	.		229.0	57.0	.	NM_020366	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Silent	SNP	ENST00000400017.2	hg19	CCDS45080.1																																																																																			.	.	.	none		0.682	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366		T	21769308	C	T	21769308	2	4	233	1	0	0	0	0	0	0	0	1	13562	581	21	2		2	RPGRIP1	14	21769308	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10		21769308	85580232	96	14219											
EFS	10278	hgsc.bcm.edu	37	chr14	23828918	23828918	+	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	gggagcctctggccccagcaGaggcacatcgtagatcccct	8	6	12	15	1	1	2	0	0	1	2	3	3	2	3	5	3	2	3	5	3	1	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr14:23828918G>A	ENST00000216733.3	-	4	1376	c.769C>T	c.(769-771)Ctg>Ttg	p.L257L	EFS_ENST00000429593.2_Intron|RP11-124D2.3_ENST00000554010.1_RNA|EFS_ENST00000351354.3_Silent_p.L164L	NM_005864.2	NP_005855.1	O43281	EFS_HUMAN	embryonal Fyn-associated substrate	257	Pro-rich.				cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			endometrium(2)|kidney(1)|large_intestine(1)|liver(1)|lung(5)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)	16	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00649)		GGCCCCAGCAGAGGCACATCG	0.642																																					p.L257L		Atlas-SNP	.											.	EFS	37	.	0			c.C769T						PASS	.						37	45	42					14																	23828918		2203	4300	6503	SO:0001819	synonymous_variant	10278	exon4			CCAGCAGAGGCAC	AB001466	CCDS9595.1, CCDS9596.1, CCDS61404.1	14q11.2-q12	2011-04-13			ENSG00000100842	ENSG00000100842		"Cas scaffolding proteins"	16898	protein-coding gene	gene with protein product	"Cas scaffolding protein family member 3"	609906				9349509	Standard	NM_005864		Approved	EFS2, EFS1, HEFS, SIN, CASS3	uc001wjo.4	O43281	OTTHUMG00000028741	ENST00000216733.3:c.769C>T	chr14.hg19:g.23828918G>A		50.0	0.0	.		62.0	19.0	.	NM_005864	B2RAJ7|B4DJ56|E9PGU2|O43282	Silent	SNP	ENST00000216733.3	hg19	CCDS9595.1																																																																																			.	.	.	none		0.642	EFS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071770.2			A	23828918	G	A	23828918	2	1	233	1	0	0	0	0	0	0	0	1	4961	933	33	2		2	EFS	14	23828918	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	2059610	23828918	83520622	97	14220											
PPIL5	122769	hgsc.bcm.edu	37	chr14	50081041	50081041	+	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	tggataccgcaaaaatttgtGtttgtggaagattctgtctg	10	15	11	5	1	2	1	0	0	2	1	2	3	2	3	1	2	1	2	1	2	4	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr14:50081041G>T	ENST00000298288.6	+	4	1396	c.1072G>T	c.(1072-1074)Gtt>Ttt	p.V358F	LRR1_ENST00000318317.4_Missense_Mutation_p.C117F	NM_152329.3	NP_689542.2	Q96L50	LLR1_HUMAN	leucine rich repeat protein 1	358					protein ubiquitination (GO:0016567)					kidney(2)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						AAAAATTTGTGTTTGTGGAAG	0.368																																					p.V358F		Atlas-SNP	.											.	LRR1	35	.	0			c.G1072T						PASS	.						117	111	113					14																	50081041		2203	4300	6503	SO:0001583	missense	122769	exon4			ATTTGTGTTTGTG	BC030142	CCDS9686.1, CCDS9687.1	14q21.3	2011-02-02	2011-02-02	2011-02-02	ENSG00000165501	ENSG00000165501			19742	protein-coding gene	gene with protein product	"LRR-repeat protein 1"	609193	"peptidylprolyl isomerase (cyclophilin)-like 5"	PPIL5		11804328, 21074724	Standard	NR_037792		Approved	MGC20689, LRR-1	uc001wwn.3	Q96L50	OTTHUMG00000140273	ENST00000298288.6:c.1072G>T	chr14.hg19:g.50081041G>T	ENSP00000298288:p.Val358Phe	61.0	0.0	.		53.0	11.0	.	NM_152329	A5D6X3|B4DDE0|Q52M24|Q86SZ1|Q8N6H9	Missense_Mutation	SNP	ENST00000298288.6	hg19	CCDS9686.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.98|12.98	2.100514|2.100514	0.37048|0.37048	.|.	.|.	ENSG00000165501|ENSG00000165501	ENST00000318317|ENST00000298288	.|T	.|0.42513	.|0.97	5.55|5.55	3.74|3.74	0.42951|0.42951	.|.	.|0.342603	.|0.30820	.|N	.|0.008808	T|T	0.29850|0.29850	0.0746|0.0746	L|L	0.48642|0.48642	1.525|1.525	0.23050|0.23050	N|N	0.998374|0.998374	P|P	0.48503|0.37864	0.911|0.61	B|B	0.42282|0.30646	0.382|0.118	T|T	0.12785|0.12785	-1.0534|-1.0534	7|10	.|0.33940	.|T	.|0.23	-1.8537|-1.8537	8.4558|8.4558	0.32899|0.32899	0.149:0.1617:0.6893:0.0|0.149:0.1617:0.6893:0.0	.|.	117|358	Q96L50-2|Q96L50	.|LLR1_HUMAN	F|F	117|358	.|ENSP00000298288:V358F	.|ENSP00000298288:V358F	C|V	+|+	2|1	0|0	LRR1|LRR1	49150791|49150791	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.566000|0.566000	0.35808|0.35808	4.799000|4.799000	0.62517|0.62517	0.839000|0.839000	0.34971|0.34971	-0.142000|-0.142000	0.14014|0.14014	TGT|GTT	.	.	.	none		0.368	LRR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410790.1	NM_203467		T	50081041	G	T	50081041	3	4	233	1	0	0	0	0	1	0	0	0	12340	1377	48	4	1086	4	PPIL5	14	50081041	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	26252123	50081041	57268499	98	14221											
PPP2R5E	5529	hgsc.bcm.edu	37	chr14	63881922	63881922	+	Frame_Shift_Del	DEL	A	A	-																															gttggaattcttggctttccAaaaatcgtatgaaaaattca																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr14:63881922delA	ENST00000337537.3	-	5	1087	c.485delT	c.(484-486)ttgfs	p.L162fs	PPP2R5E_ENST00000553266.1_5'UTR|PPP2R5E_ENST00000422769.2_Frame_Shift_Del_p.L86fs|PPP2R5E_ENST00000555899.1_Frame_Shift_Del_p.L162fs	NM_001282179.1|NM_001282180.1|NM_001282181.1|NM_001282182.1|NM_006246.2	NP_001269108.1|NP_001269109.1|NP_001269110.1|NP_001269111.1|NP_006237.1	Q16537	2A5E_HUMAN	protein phosphatase 2, regulatory subunit B', epsilon isoform	162					regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)	15				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)		TTGGCTTTCCAAAAATCGTAT	0.313																																					p.L162fs		Atlas-Indel,Pindel	.											.	PPP2R5E	43	.	0			c.486delG						PASS	.						87	91	90					14																	63881922		2202	4298	6500	SO:0001589	frameshift_variant	5529	exon5			.	L76703	CCDS9758.1, CCDS61467.1, CCDS61468.1	14q23.2	2010-06-18	2007-01-22		ENSG00000154001	ENSG00000154001		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9313	protein-coding gene	gene with protein product		601647	"protein phosphatase 2, regulatory subunit B (B56), epsilon isoform"			7592815	Standard	NM_006246		Approved		uc001xgd.1	Q16537	OTTHUMG00000140341	ENST00000337537.3:c.485delT	chr14.hg19:g.63881922delA	ENSP00000337641:p.Leu162fs	113.0	0.0	0		95.0	51.0	0.536842	NM_006246	A4FU37|B7ZAW5|B7ZKK8|B7ZKK9|J3KQN6|Q52LW4	Frame_Shift_Del	DEL	ENST00000337537.3	hg19	CCDS9758.1																																																																																			.	.	.	none		0.313	PPP2R5E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276973.1	NM_006246		-	63881922	A	-	63881922	7	5	233	1	0	1	0	1	0	0	0	0	12406	131	5	0	958	0	PPP2R5E	14	63881922	Frame_Shift_Del	DEL	A	TCGA-P4-A5EB-01A-11D-A28G-10	13800881	63881922	43467618	99	14222											
FAM164C	79696	hgsc.bcm.edu	37	chr14	75537677	75537677	+	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	ctttacaaagaaacgagttgGagtggaccgggcgttcccat	11	9	12	9	3	0	1	0	0	0	1	1	4	1	3	2	3	2	2	2	3	3	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr14:75537677G>T	ENST00000524913.1	+	2	890	c.401G>T	c.(400-402)gGa>gTa	p.G134V	ZC2HC1C_ENST00000439583.2_Missense_Mutation_p.G134V|ZC2HC1C_ENST00000238686.8_Missense_Mutation_p.G134V|ZC2HC1C_ENST00000526748.1_Intron|ACYP1_ENST00000555463.1_5'Flank	NM_024643.2	NP_078919.2	Q53FD0	ZC21C_HUMAN	zinc finger, C2HC-type containing 1C	134							metal ion binding (GO:0046872)										AAACGAGTTGGAGTGGACCGG	0.522																																					p.G134V		Atlas-SNP	.											.	.	.	.	0			c.G401T						PASS	.						98	96	97					14																	75537677		1869	4100	5969	SO:0001583	missense	79696	exon2			GAGTTGGAGTGGA	AK026746	CCDS41972.1, CCDS45138.1	14q24.3	2013-01-10	2012-02-03	2012-02-03	ENSG00000119703	ENSG00000119703		"Zinc fingers, C2HC-type containing"	20354	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 140", "family with sequence similarity 164, member C"	C14orf140, FAM164C			Standard	XM_005268062		Approved		uc001xrh.3	Q53FD0	OTTHUMG00000167439	ENST00000524913.1:c.401G>T	chr14.hg19:g.75537677G>T	ENSP00000435550:p.Gly134Val	96.0	0.0	.		95.0	31.0	.	NM_024643	E9PJQ0|Q9BTA8|Q9H5S9	Missense_Mutation	SNP	ENST00000524913.1	hg19	CCDS41972.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.02|15.02	2.709290|2.709290	0.48517|0.48517	.|.	.|.	ENSG00000119703|ENSG00000119703	ENST00000532198|ENST00000524913;ENST00000238686;ENST00000554763;ENST00000439583;ENST00000526130	.|T	.|0.76578	.|-1.03	4.53|4.53	4.53|4.53	0.55603|0.55603	.|.	.|0.080328	.|0.49916	.|D	.|0.000121	.|D	.|0.87111	.|0.6096	M|M	0.72118|0.72118	2.19|2.19	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;0.997	.|D	.|0.87264	.|0.2281	.|9	.|.	.|.	.|.	-17.5211|-17.5211	17.4741|17.4741	0.87655|0.87655	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|134;134	.|Q53FD0;E9PJQ0	.|F164C_HUMAN;.	X|V	1|134	.|ENSP00000435550:G134V	.|.	E|G	+|+	1|2	0|0	FAM164C|FAM164C	74607430|74607430	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.325000|0.325000	0.28411|0.28411	6.888000|6.888000	0.75622|0.75622	2.356000|2.356000	0.79943|0.79943	0.557000|0.557000	0.71058|0.71058	GAG|GGA	.	.	.	none		0.522	ZC2HC1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394616.4	NM_001042430		T	75537677	G	T	75537677	3	4	233	1	0	0	0	0	1	0	0	0	5483	1174	41	4	403	4	FAM164C	14	75537677	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	11655755	75537677	31811863	100	14223											
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102478240	102478240	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctctatcagatcacccagaTcaatcatggcctgatgatgg	11	10	9	11	0	5	4	4	2	1	2	5	4	5	4	2	2	0	1	2	2	2	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr14:102478240T>C	ENST00000360184.4	+	33	6811	c.6647T>C	c.(6646-6648)aTc>aCc	p.I2216T		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	2216	AAA 2. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						ATCACCCAGATCAATCATGGC	0.602																																					p.I2216T		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.T6647C						PASS	.						86	74	78					14																	102478240		2203	4300	6503	SO:0001583	missense	1778	exon33			CCCAGATCAATCA	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.6647T>C	chr14.hg19:g.102478240T>C	ENSP00000348965:p.Ile2216Thr	80.0	0.0	.		87.0	27.0	.	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	hg19	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	T	18.82	3.705776	0.68615	.	.	ENSG00000197102	ENST00000360184	T	0.27402	1.67	5.8	5.8	0.92144	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.33265	0.0857	L	0.44542	1.39	0.80722	D	1	P	0.45348	0.856	P	0.44394	0.448	T	0.03423	-1.1038	10	0.40728	T	0.16	.	16.1547	0.81649	0.0:0.0:0.0:1.0	.	2216	Q14204	DYHC1_HUMAN	T	2216	ENSP00000348965:I2216T	ENSP00000348965:I2216T	I	+	2	0	DYNC1H1	101547993	1.000000	0.71417	0.998000	0.56505	0.984000	0.73092	7.991000	0.88244	2.221000	0.72209	0.528000	0.53228	ATC	.	.	.	none		0.602	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		C	102478240	T	C	102478240	3	2	233	1	0	0	0	0	1	0	0	0	4843	1435	50	3	6777	3	DYNC1H1	14	102478240	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	26940563	102478240	4871300	101	14224											
TRIM69	140691	hgsc.bcm.edu	37	chr15	45048565	45048565	+	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	aattctatttgatattcccaGgaggagcttgccatccaaca	12	12	7	10	0	1	1	0	1	1	0	3	3	3	3	3	2	3	1	3	2	4	6			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr15:45048565G>C	ENST00000559390.1	+	4	1411		c.e4-1		TRIM69_ENST00000558173.1_Splice_Site|TRIM69_ENST00000329464.4_Splice_Site|TRIM69_ENST00000558329.1_Splice_Site|TRIM69_ENST00000560442.1_Splice_Site|TRIM69_ENST00000338264.4_Splice_Site|TRIM69_ENST00000561043.1_Splice_Site			Q86WT6	TRI69_HUMAN	tripartite motif containing 69						apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(9)|skin(1)	20		all_cancers(109;2.47e-13)|all_epithelial(112;2.84e-11)|Lung NSC(122;2.23e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;5.5e-19)|GBM - Glioblastoma multiforme(94;1.07e-06)|Colorectal(105;0.138)|COAD - Colon adenocarcinoma(120;0.141)		GATATTCCCAGGAGGAGCTTG	0.488																																					.	Pancreas(84;519 1450 1802 20427 34706)	Atlas-SNP	.											.	TRIM69	47	.	0			c.7-1G>C						PASS	.						41	39	40					15																	45048565		1927	3624	5551	SO:0001630	splice_region_variant	140691	exon2			TTCCCAGGAGGAG	AF302088	CCDS10114.1, CCDS32220.1, CCDS73719.1	15q15-q21	2013-01-09	2011-01-25	2006-09-26	ENSG00000185880	ENSG00000185880		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	17857	protein-coding gene	gene with protein product			"ring finger protein 36", "tripartite motif-containing 69"	RNF36			Standard	XM_005254162		Approved	Trif, TRIMLESS	uc001zug.1	Q86WT6	OTTHUMG00000131246	ENST00000559390.1:c.484-1G>C	chr15.hg19:g.45048565G>C		93.0	0.0	.		130.0	61.0	.	NM_080745	A8MX03|Q309B0|Q4G1A5|Q6W897|Q8IYY3|Q8WY16|Q8WY17	Splice_Site	SNP	ENST00000559390.1	hg19	CCDS32220.1	.	.	.	.	.	.	.	.	.	.	G	10.44	1.350808	0.24512	.	.	ENSG00000185880	ENST00000329464;ENST00000338264	.	.	.	5.34	4.43	0.53597	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.9849	0.53142	0.0847:0.0:0.9153:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TRIM69	42835857	1.000000	0.71417	0.995000	0.50966	0.200000	0.23975	4.849000	0.62882	1.391000	0.46566	0.655000	0.94253	.	.	.	.	none		0.488	TRIM69-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416171.1		Intron	C	45048565	G	C	45048565	5	2	233	1	0	0	0	0	0	0	1	0	16554	1014	35	4	493	4	TRIM69	15	45048565	Splice_Site	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10		45048565	57482827	102	14225											
FBN1	2200	hgsc.bcm.edu	37	chr15	48748937	48748937	+	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	ccattttcacagacccctggGatctcccggcactcatcaat	9	10	6	16	1	4	1	3	0	1	1	5	2	4	2	4	2	0	1	4	2	1	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr15:48748937G>T	ENST00000316623.5	-	44	5774	c.5319C>A	c.(5317-5319)atC>atA	p.I1773I		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1773	EGF-like 29; 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)		AGACCCCTGGGATCTCCCGGC	0.468																																					p.I1773I		Atlas-SNP	.											.	FBN1	310	.	0			c.C5319A						PASS	.						112	99	103					15																	48748937		2198	4296	6494	SO:0001819	synonymous_variant	2200	exon44			CCCTGGGATCTCC	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.5319C>A	chr15.hg19:g.48748937G>T		70.0	0.0	.		112.0	44.0	.	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Silent	SNP	ENST00000316623.5	hg19	CCDS32232.1																																																																																			.	.	.	none		0.468	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			T	48748937	G	T	48748937	2	4	233	1	0	0	0	0	0	0	0	1	5709	1164	41	4		4	FBN1	15	48748937	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	3700372	48748937	53782455	103	14226											
SV2B	9899	hgsc.bcm.edu	37	chr15	91811781	91811781	+	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	gcatgtgtacggcgccacaaTcaacttcacgatggaaaatc	13	8	9	11	3	2	0	2	0	0	0	3	2	2	1	1	2	2	2	1	2	5	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr15:91811781T>A	ENST00000394232.1	+	9	1789	c.1319T>A	c.(1318-1320)aTc>aAc	p.I440N	SV2B_ENST00000545111.2_Missense_Mutation_p.I289N|SV2B_ENST00000330276.4_Missense_Mutation_p.I440N	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	440					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)			GGCGCCACAATCAACTTCACG	0.428																																					p.I440N		Atlas-SNP	.											.	SV2B	98	.	0			c.T1319A						PASS	.						139	136	137					15																	91811781		2198	4298	6496	SO:0001583	missense	9899	exon10			CCACAATCAACTT	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.1319T>A	chr15.hg19:g.91811781T>A	ENSP00000377779:p.Ile440Asn	176.0	0.0	.		271.0	21.0	.	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Missense_Mutation	SNP	ENST00000394232.1	hg19	CCDS10370.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.561903	0.86335	.	.	ENSG00000185518	ENST00000545111;ENST00000394232;ENST00000330276	T;T;T	0.61980	0.06;0.06;0.06	5.49	5.49	0.81192	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.043947	0.85682	D	0.000000	T	0.55273	0.1910	L	0.34521	1.04	0.43761	D	0.99627	P	0.41159	0.74	B	0.43386	0.418	T	0.52260	-0.8599	10	0.24483	T	0.36	-35.1417	14.7146	0.69257	0.0:0.0:0.0:1.0	.	440	Q7L1I2	SV2B_HUMAN	N	289;440;440	ENSP00000443243:I289N;ENSP00000377779:I440N;ENSP00000332818:I440N	ENSP00000332818:I440N	I	+	2	0	SV2B	89612785	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	7.750000	0.85110	2.212000	0.71576	0.533000	0.62120	ATC	.	.	.	none		0.428	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848		A	91811781	T	A	91811781	3	1	233	1	0	0	0	0	1	0	0	0	15430	1435	50	5	1349	5	SV2B	15	91811781	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	43062844	91811781	10719611	104	14227											
RPL3L	6123	hgsc.bcm.edu	37	chr16	1995884	1995884	+	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	gtaccagcaatacaacccttCagcatgacgaagtcgttgtt	12	10	8	11	2	1	1	1	1	0	0	2	2	1	1	2	0	5	5	2	0	5	5			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr16:1995884C>T	ENST00000268661.7	-	8	1093	c.999G>A	c.(997-999)ctG>ctA	p.L333L	MSRB1_ENST00000399753.2_5'Flank|MSRB1_ENST00000361871.3_5'Flank|MSRB1_ENST00000564908.1_5'Flank	NM_005061.2	NP_005052.1	Q92901	RL3L_HUMAN	ribosomal protein L3-like	333					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						TACAACCCTTCAGCATGACGA	0.602																																					p.L333L		Atlas-SNP	.											.	RPL3L	42	.	0			c.G999A						PASS	.						164	138	147					16																	1995884		2199	4300	6499	SO:0001819	synonymous_variant	6123	exon8			ACCCTTCAGCATG	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.999G>A	chr16.hg19:g.1995884C>T		35.0	0.0	.		74.0	5.0	.	NM_005061		Silent	SNP	ENST00000268661.7	hg19	CCDS10450.1																																																																																			.	.	.	none		0.602	RPL3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250582.2	NM_005061		T	1995884	C	T	1995884	2	4	233	1	0	0	0	0	0	0	0	1	13607	813	29	2		2	RPL3L	16	1995884	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10		1995884	88358869	105	14228											
PKMYT1	9088	hgsc.bcm.edu	37	chr16	3025761	3025761	+	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	ggtccttggggccccggaatGgtgacatggaacgctttacc	7	9	14	11	2	0	1	0	1	0	0	1	3	1	3	4	6	2	1	4	6	3	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr16:3025761G>A	ENST00000262300.8	-	4	939	c.431C>T	c.(430-432)cCa>cTa	p.P144L	PKMYT1_ENST00000574385.1_Missense_Mutation_p.P135L|PKMYT1_ENST00000440027.2_Missense_Mutation_p.P144L|PKMYT1_ENST00000573944.1_Missense_Mutation_p.P135L|PKMYT1_ENST00000574730.1_Missense_Mutation_p.P75L|PKMYT1_ENST00000431515.2_Missense_Mutation_p.P144L	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	144	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)			NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	10						GCCCCGGAATGGTGACATGGA	0.667																																					p.P144L		Atlas-SNP	.											.	PKMYT1	23	.	0			c.C431T						PASS	.						25	27	26					16																	3025761		2153	4235	6388	SO:0001583	missense	9088	exon4			CGGAATGGTGACA	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.431C>T	chr16.hg19:g.3025761G>A	ENSP00000262300:p.Pro144Leu	5.0	0.0	.		86.0	33.0	.	NM_182687	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000262300.8	hg19	CCDS10486.1	.	.	.	.	.	.	.	.	.	.	G	15.79	2.938404	0.52972	.	.	ENSG00000127564	ENST00000431515;ENST00000262300;ENST00000440027;ENST00000402679;ENST00000382240	T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15	5.69	5.69	0.88448	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.059815	0.64402	D	0.000002	T	0.47266	0.1436	N	0.11818	0.18	0.80722	D	1	P;P;P;P	0.43701	0.56;0.704;0.56;0.815	B;B;B;B	0.39068	0.217;0.217;0.217;0.289	T	0.56498	-0.7969	10	0.66056	D	0.02	-14.3456	17.2983	0.87175	0.0:0.0:1.0:0.0	.	135;75;144;144	A6NHV6;B4DXD4;Q99640;F8W164	.;.;PMYT1_HUMAN;.	L	144;144;144;144;135	ENSP00000392855:P144L;ENSP00000262300:P144L;ENSP00000397739:P144L;ENSP00000371675:P135L	ENSP00000262300:P144L	P	-	2	0	PKMYT1	2965762	1.000000	0.71417	0.237000	0.24090	0.956000	0.61745	4.915000	0.63355	2.676000	0.91093	0.655000	0.94253	CCA	.	.	.	none		0.667	PKMYT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250963.2	NM_004203		A	3025761	G	A	3025761	3	1	233	1	0	0	0	0	1	0	0	0	11985	1348	47	2	1130	2	PKMYT1	16	3025761	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	1029877	3025761	87328992	106	14229											
NLRC3	197358	hgsc.bcm.edu	37	chr16	3614323	3614323	+	RNA	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	gctgggactgccaccgccagGctgggctccccgacgtgcgg	4	5	16	16	4	0	0	0	0	0	0	1	2	1	1	5	4	2	3	5	4	0	0			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr16:3614323G>C	ENST00000301749.7	-	0	1020				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						CCACCGCCAGGCTGGGCTCCC	0.662																																					p.S205R		Atlas-SNP	.											.	NLRC3	103	.	0			c.C615G						PASS	.						31	37	35					16																	3614323		2003	4170	6173			197358	exon5			CGCCAGGCTGGGC	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		chr16.hg19:g.3614323G>C		57.0	0.0	.		95.0	32.0	.	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	hg19		.	.	.	.	.	.	.	.	.	.	G	1.295	-0.606481	0.03717	.	.	ENSG00000167984	ENST00000419350;ENST00000301749;ENST00000359128;ENST00000448023;ENST00000324659	T;T;T;T	0.79033	-1.23;-1.23;-1.23;-1.23	4.84	0.17	0.15021	.	0.625501	0.16533	N	0.210300	T	0.55625	0.1932	.	.	.	0.09310	N	1	B	0.10296	0.003	B	0.15870	0.014	T	0.32107	-0.9919	9	0.17832	T	0.49	.	4.5952	0.12325	0.0829:0.2788:0.4949:0.1434	.	252	C9JLH9	.	R	205;205;205;252;187	ENSP00000301749:S205R;ENSP00000352039:S205R;ENSP00000414415:S252R;ENSP00000323897:S187R	ENSP00000301749:S205R	S	-	3	2	NLRC3	3554324	0.000000	0.05858	0.004000	0.12327	0.008000	0.06430	0.471000	0.22100	0.074000	0.16767	0.655000	0.94253	AGC	.	.	.	none		0.662	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844		C	3614323	G	C	3614323	1	2	233	0	1	0	0	0	0	0	0	0	10475	1194	42	4		4	NLRC3	16	3614323	RNA	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	588562	3614323	86740430	107	14230											
CREBBP	1387	hgsc.bcm.edu	37	chr16	3779018	3779018	+	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	ggcatgctgggcatgacgggCccgctcacctggttgggtcg	4	8	17	12	3	1	1	1	1	0	0	2	1	1	1	2	5	1	5	2	5	0	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr16:3779018C>T	ENST00000262367.5	-	31	6839	c.6030G>A	c.(6028-6030)ggG>ggA	p.G2010G	CREBBP_ENST00000382070.3_Silent_p.G1972G	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	2010					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)		GCATGACGGGCCCGCTCACCT	0.692			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.G2010G		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.G6030A						PASS	.						12	14	13					16																	3779018		2185	4287	6472	SO:0001819	synonymous_variant	1387	exon31			GACGGGCCCGCTC	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.6030G>A	chr16.hg19:g.3779018C>T		14.0	0.0	.		58.0	18.0	.	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Silent	SNP	ENST00000262367.5	hg19	CCDS10509.1																																																																																			.	.	.	none		0.692	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		T	3779018	C	T	3779018	2	4	233	1	0	0	0	0	0	0	0	1	3863	726	26	2		2	CREBBP	16	3779018	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	164695	3779018	86575735	108	14231											
C16orf68	79091	hgsc.bcm.edu	37	chr16	8736394	8736394	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccacagattgaaaaatgccTgcacagccatactgtcggtg	12	8	9	12	1	0	2	0	1	0	1	1	2	0	2	3	1	4	1	3	1	3	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr16:8736394T>C	ENST00000381920.3	+	9	1240	c.982T>C	c.(982-984)Tgc>Cgc	p.C328R	METTL22_ENST00000561758.1_Missense_Mutation_p.C272R|METTL22_ENST00000568967.1_3'UTR	NM_024109.2	NP_077014.2	Q9BUU2	MET22_HUMAN	methyltransferase like 22	328						nucleus (GO:0005634)	methyltransferase activity (GO:0008168)			large_intestine(5)|lung(4)	9						GAAAAATGCCTGCACAGCCAT	0.532																																					p.C328R		Atlas-SNP	.											.	METTL22	23	.	0			c.T982C						PASS	.						124	139	134					16																	8736394		2055	4190	6245	SO:0001583	missense	79091	exon9			AATGCCTGCACAG	AK022495	CCDS10533.2	16p13.2	2014-07-15	2011-03-03	2011-03-03	ENSG00000067365	ENSG00000067365			28368	protein-coding gene	gene with protein product		615261	"chromosome 16 open reading frame 68"	C16orf68		24140279	Standard	XM_005255570		Approved	FLJ12433,MGC2654	uc002cyz.3	Q9BUU2	OTTHUMG00000129694	ENST00000381920.3:c.982T>C	chr16.hg19:g.8736394T>C	ENSP00000371345:p.Cys328Arg	103.0	0.0	.		157.0	65.0	.	NM_024109	B2RD29|D3DUF2|Q6XYB4|Q9HA03	Missense_Mutation	SNP	ENST00000381920.3	hg19	CCDS10533.2	.	.	.	.	.	.	.	.	.	.	T	10.28	1.307330	0.23821	.	.	ENSG00000067365	ENST00000381920	T	0.40756	1.02	5.18	5.18	0.71444	.	0.177884	0.49305	D	0.000145	T	0.43590	0.1254	L	0.41710	1.295	0.80722	D	1	D;P	0.53462	0.96;0.752	P;P	0.54312	0.748;0.469	T	0.19976	-1.0289	10	0.14252	T	0.57	-39.2838	11.4298	0.50034	0.0:0.0:0.0:1.0	.	103;328	Q9BUU2-3;Q9BUU2	.;MET22_HUMAN	R	328	ENSP00000371345:C328R	ENSP00000371345:C328R	C	+	1	0	METTL22	8643895	1.000000	0.71417	1.000000	0.80357	0.286000	0.27126	2.384000	0.44362	1.956000	0.56807	0.533000	0.62120	TGC	.	.	.	none		0.532	METTL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251901.1	NM_024109		C	8736394	T	C	8736394	3	2	233	1	0	0	0	0	1	0	0	0	1829	1580	55	3	1012	3	C16orf68	16	8736394	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	4957376	8736394	81618359	109	14232											
DHRS7C	201140	hgsc.bcm.edu	37	chr17	9683157	9683157	+	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	gagacctttcgtcaatgtgaTggggccaaagtaattggcat	11	11	12	7	1	1	2	1	1	0	1	2	3	1	2	2	3	0	2	2	3	3	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr17:9683157T>A	ENST00000330255.5	-	3	478	c.466A>T	c.(466-468)Atc>Ttc	p.I156F	DHRS7C_ENST00000571134.1_Missense_Mutation_p.I155F	NM_001105571.2|NM_001220493.1	NP_001099041.1|NP_001207422.1	A6NNS2	DRS7C_HUMAN	dehydrogenase/reductase (SDR family) member 7C	156					regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	extracellular region (GO:0005576)|longitudinal sarcoplasmic reticulum (GO:0014801)|sarcoplasmic reticulum membrane (GO:0033017)	retinol dehydrogenase activity (GO:0004745)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)	15						GTCAATGTGATGGGGCCAAAG	0.478																																					p.I156F		Atlas-SNP	.											.	DHRS7C	34	.	0			c.A466T						PASS	.						49	47	47					17																	9683157		1906	4125	6031	SO:0001583	missense	201140	exon3			ATGTGATGGGGCC		CCDS56020.1, CCDS58517.1	17p13.1	2011-09-20				ENSG00000184544		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	32423	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 32C, member 2"					19027726	Standard	NM_001105571		Approved	SDR32C2	uc010vvb.2	A6NNS2		ENST00000330255.5:c.466A>T	chr17.hg19:g.9683157T>A	ENSP00000327975:p.Ile156Phe	95.0	0.0	.		108.0	8.0	.	NM_001220493	B7ZW74|B9EJH3	Missense_Mutation	SNP	ENST00000330255.5	hg19	CCDS56020.1	.	.	.	.	.	.	.	.	.	.	T	13.39	2.223879	0.39300	.	.	ENSG00000184544	ENST00000330255	D	0.86865	-2.18	5.75	5.75	0.90469	NAD(P)-binding domain (1);	0.045861	0.85682	D	0.000000	D	0.90000	0.6878	L	0.37630	1.12	0.47511	D	0.999443	D;D	0.71674	0.998;0.998	D;D	0.71184	0.972;0.94	D	0.91167	0.4965	10	0.87932	D	0	.	15.0365	0.71751	0.0:0.0:0.0:1.0	.	156;152	A6NNS2;B9EJH3	DRS7C_HUMAN;.	F	156	ENSP00000327975:I156F	ENSP00000327975:I156F	I	-	1	0	DHRS7C	9623882	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.823000	0.69272	2.193000	0.70182	0.533000	0.62120	ATC	.	.	.	none		0.478	DHRS7C-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439863.1	XM_113912		A	9683157	T	A	9683157	3	1	233	1	0	0	0	0	1	0	0	0	4499	1464	51	5	488	5	DHRS7C	17	9683157	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10		9683157	71512053	110	14233											
COX10	1352	hgsc.bcm.edu	37	chr17	13980322	13980322	+	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	ggaaagagatgaagctgcaaGtgtatgatttgccaggaatt	14	10	13	4	0	0	3	0	2	0	1	0	6	0	5	1	2	3	3	1	2	5	3			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr17:13980322G>C	ENST00000261643.3	+	3	525	c.448G>C	c.(448-450)Gtg>Ctg	p.V150L	COX10_ENST00000536205.1_5'UTR|COX10_ENST00000429152.2_Missense_Mutation_p.V150L|COX10_ENST00000537334.1_Intron	NM_001303.3	NP_001294.2	Q12887	COX10_HUMAN	cytochrome c oxidase assembly homolog 10 (yeast)	150					aerobic respiration (GO:0009060)|cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|heme O biosynthetic process (GO:0048034)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|mitochondrial fission (GO:0000266)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	farnesyltranstransferase activity (GO:0004311)|protoheme IX farnesyltransferase activity (GO:0008495)			cervix(1)|endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		GAAGCTGCAAGTGTATGATTT	0.368																																					p.V150L		Atlas-SNP	.											.	COX10	36	.	0			c.G448C						PASS	.						83	88	87					17																	13980322		2203	4300	6503	SO:0001583	missense	1352	exon3			CTGCAAGTGTATG	U09466	CCDS11166.1	17p12	2013-05-24	2012-10-15		ENSG00000006695	ENSG00000006695		"Mitochondrial respiratory chain complex assembly factors"	2260	protein-coding gene	gene with protein product	"heme A: farnesyltransferase", "protoheme IX farnesyltransferase, mitochondrial", "heme O synthase"	602125	"COX10 (yeast) homolog, cytochrome c oxidase assembly protein (heme A: farnesyltransferase)", "COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase (yeast)"			9177788, 12928484	Standard	NM_001303		Approved		uc002gof.4	Q12887	OTTHUMG00000058814	ENST00000261643.3:c.448G>C	chr17.hg19:g.13980322G>C	ENSP00000261643:p.Val150Leu	146.0	0.0	.		161.0	69.0	.	NM_001303	B2R6U5|B4DJ50|O15334|Q969F7	Missense_Mutation	SNP	ENST00000261643.3	hg19	CCDS11166.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.143|0.143	-1.100268|-1.100268	0.01843|0.01843	.|.	.|.	ENSG00000006695|ENSG00000006695	ENST00000429152|ENST00000261643	T|T	0.37235|0.61980	1.21|0.06	5.35|5.35	-6.73|-6.73	0.01749|0.01749	.|.	.|1.554890	.|0.03407	.|N	.|0.204147	T|T	0.36880|0.36880	0.0983|0.0983	N|N	0.25890|0.25890	0.77|0.77	0.34746|0.34746	D|D	0.731242|0.731242	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.49978|0.49978	-0.8881|-0.8881	6|10	.|0.02654	.|T	.|1	0.0067|0.0067	3.698|3.698	0.08372|0.08372	0.2638:0.4606:0.1338:0.1418|0.2638:0.4606:0.1338:0.1418	.|.	.|150	.|Q12887	.|COX10_HUMAN	T|L	110|150	ENSP00000397750:S110T|ENSP00000261643:V150L	.|ENSP00000261643:V150L	S|V	+|+	2|1	0|0	COX10|COX10	13921047|13921047	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.223000|0.223000	0.24884|0.24884	-0.888000|-0.888000	0.04148|0.04148	-0.666000|-0.666000	0.05310|0.05310	0.655000|0.655000	0.94253|0.94253	AGT|GTG	.	.	.	none		0.368	COX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130003.1	NM_001303		C	13980322	G	C	13980322	3	2	233	1	0	0	0	0	1	0	0	0	3764	1029	36	4	458	4	COX10	17	13980322	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	4297165	13980322	67214888	111	14234											
SLFN12L	100506736	hgsc.bcm.edu	37	chr17	33807110	33807110	+	Missense_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	ttctattgttctctccaagaGtgactcttcccacatttaga	9	16	5	11	0	3	3	0	1	3	2	6	3	5	3	2	0	0	1	2	0	3	7			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr17:33807110G>A	ENST00000260908.7	-	2	236	c.119C>T	c.(118-120)aCt>aTt	p.T40I	SLFN12L_ENST00000361112.4_Missense_Mutation_p.T69I|RP11-686D22.9_ENST00000587076.1_RNA|SLFN12L_ENST00000449046.1_Missense_Mutation_p.T71I	NM_001195790.1	NP_001182719.1	Q6IEE8	SN12L_HUMAN	schlafen family member 12-like	40						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)			breast(1)|endometrium(4)|kidney(5)|large_intestine(2)|lung(3)|ovary(1)	16						CTCTCCAAGAGTGACTCTTCC	0.403																																					p.T40I		Atlas-SNP	.											.	SLFN12L	140	.	0			c.C119T						PASS	.						57	44	48					17																	33807110		692	1591	2283	SO:0001583	missense	100506736	exon2			CCAAGAGTGACTC	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.119C>T	chr17.hg19:g.33807110G>A	ENSP00000437635:p.Thr40Ile	74.0	0.0	.		103.0	8.0	.	NM_001195790	F5H6G3	Missense_Mutation	SNP	ENST00000260908.7	hg19	CCDS56026.1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.968021	0.53507	.	.	ENSG00000205045	ENST00000260908;ENST00000361112;ENST00000449046	T;T;T	0.06528	3.32;3.64;3.29	2.72	2.72	0.32119	.	.	.	.	.	T	0.16599	0.0399	L	0.57536	1.79	0.09310	N	1	D	0.65815	0.995	D	0.63703	0.917	T	0.03993	-1.0986	9	0.48119	T	0.1	.	8.9486	0.35773	0.0:0.0:1.0:0.0	.	69	Q6IEE8-2	.	I	40;69;71	ENSP00000437635:T40I;ENSP00000354412:T69I;ENSP00000389348:T71I	ENSP00000437635:T40I	T	-	2	0	SLFN12L	30831223	0.000000	0.05858	0.017000	0.16124	0.662000	0.39071	-0.169000	0.09911	1.504000	0.48704	0.205000	0.17691	ACT	.	.	.	none		0.403	SLFN12L-004	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395748.2	XM_496206		A	33807110	G	A	33807110	3	1	233	1	0	0	0	0	1	0	0	0	14748	1029	36	2	1659	2	SLFN12L	17	33807110	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	19826788	33807110	47388100	112	14235											
KRT38	8687	hgsc.bcm.edu	37	chr17	39596920	39596920	+	Missense_Mutation	SNP	A	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	agattccaatgttgccaggaAtgtggcaggtccctggcaag	10	9	13	9	0	0	1	0	0	0	1	2	2	2	2	3	4	1	3	3	4	3	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr17:39596920A>C	ENST00000246646.3	-	1	253	c.254T>G	c.(253-255)aTt>aGt	p.I85S		NM_006771.3	NP_006762.3	O76015	KRT38_HUMAN	keratin 38	85	Head.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	29		Breast(137;0.000496)				GTTGCCAGGAATGTGGCAGGT	0.607																																					p.I85S		Atlas-SNP	.											.	KRT38	63	.	0			c.T254G						PASS	.						73	68	70					17																	39596920		2203	4300	6503	SO:0001583	missense	8687	exon1			CCAGGAATGTGGC	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.254T>G	chr17.hg19:g.39596920A>C	ENSP00000246646:p.Ile85Ser	109.0	0.0	.		212.0	88.0	.	NM_006771	A2RRM5|Q6A164	Missense_Mutation	SNP	ENST00000246646.3	hg19	CCDS11392.1	.	.	.	.	.	.	.	.	.	.	A	13.77	2.337461	0.41398	.	.	ENSG00000171360	ENST00000246646	D	0.82167	-1.58	4.89	3.82	0.43975	.	0.130125	0.34460	N	0.003941	D	0.84511	0.5488	L	0.50333	1.59	0.09310	N	1	D	0.89917	1.0	D	0.69307	0.963	T	0.72830	-0.4174	10	0.28530	T	0.3	.	5.4631	0.16627	0.6239:0.2845:0.0915:0.0	.	85	O76015	KRT38_HUMAN	S	85	ENSP00000246646:I85S	ENSP00000246646:I85S	I	-	2	0	KRT38	36850446	0.089000	0.21612	0.031000	0.17742	0.359000	0.29487	1.205000	0.32308	0.906000	0.36621	0.528000	0.53228	ATT	.	.	.	none		0.607	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	NM_006771		C	39596920	A	C	39596920	3	2	233	1	0	0	0	0	1	0	0	0	8482	101	4	5	1144	5	KRT38	17	39596920	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	5789810	39596920	41598290	113	14236											
JUP	3728	hgsc.bcm.edu	37	chr17	39925817	39925817	+	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	tgcaggttggtggcctgcccCtccacctgggtggccagcag	4	8	15	14	0	0	0	0	0	0	0	1	0	1	0	6	5	3	3	6	5	0	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr17:39925817C>G	ENST00000393931.3	-	3	439	c.321G>C	c.(319-321)gaG>gaC	p.E107D	JUP_ENST00000393930.1_Missense_Mutation_p.E107D|JUP_ENST00000310706.5_Missense_Mutation_p.E107D|JUP_ENST00000540235.1_Missense_Mutation_p.E107D	NM_002230.2	NP_002221.1	P14923	PLAK_HUMAN	junction plakoglobin	107					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)		TGGCCTGCCCCTCCACCTGGG	0.647																																					p.E107D	Colon(16;42 520 6044 17852 28530)	Atlas-SNP	.											.	JUP	64	.	0			c.G321C						PASS	.						31	29	29					17																	39925817		2201	4297	6498	SO:0001583	missense	3728	exon3			CTGCCCCTCCACC	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.321G>C	chr17.hg19:g.39925817C>G	ENSP00000377508:p.Glu107Asp	67.0	0.0	.		123.0	27.0	.	NM_021991	Q15093|Q15151|Q7L3S5|Q86W21|Q9BWC4|Q9HCX9	Missense_Mutation	SNP	ENST00000393931.3	hg19	CCDS11407.1	.	.	.	.	.	.	.	.	.	.	c	8.550	0.875277	0.17395	.	.	ENSG00000173801	ENST00000540235;ENST00000393930;ENST00000310706;ENST00000393931;ENST00000449889;ENST00000437187;ENST00000420370;ENST00000424457	T;T;T;T;T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06;-0.06;-0.06;-0.06;-0.06	5.52	-7.03	0.01584	.	0.239681	0.42053	D	0.000764	T	0.27454	0.0674	N	0.08118	0	0.22591	N	0.998951	D;B	0.54207	0.965;0.001	B;B	0.43950	0.437;0.003	T	0.51663	-0.8677	10	0.22109	T	0.4	-21.4947	1.588	0.02648	0.2613:0.236:0.089:0.4138	.	107;107	B4DE59;P14923	.;PLAK_HUMAN	D	107	ENSP00000441751:E107D;ENSP00000377507:E107D;ENSP00000311113:E107D;ENSP00000377508:E107D;ENSP00000389886:E107D;ENSP00000394146:E107D;ENSP00000411449:E107D;ENSP00000401034:E107D	ENSP00000311113:E107D	E	-	3	2	JUP	37179343	0.000000	0.05858	0.979000	0.43373	0.992000	0.81027	-4.131000	0.00289	-0.505000	0.06568	0.556000	0.70494	GAG	.	.	.	none		0.647	JUP-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257406.1			G	39925817	C	G	39925817	3	3	233	1	0	0	0	0	1	0	0	0	7979	680	24	4	1964	4	JUP	17	39925817	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	328897	39925817	41269393	114	14237											
HELZ	9931	hgsc.bcm.edu	37	chr17	65105385	65105385	+	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	ctgctccggaattacagcttCtgcaggaggagactgtggcc	8	9	13	11	1	1	1	0	0	1	1	2	4	2	3	2	4	4	3	2	4	2	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr17:65105385C>T	ENST00000358691.5	-	29	4502	c.4336G>A	c.(4336-4338)Gaa>Aaa	p.E1446K	HELZ_ENST00000580168.1_Missense_Mutation_p.E1447K	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	1446						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)					ATTACAGCTTCTGCAGGAGGA	0.547																																					p.E1446K		Atlas-SNP	.											.	HELZ	160	.	0			c.G4336A						PASS	.						65	73	70					17																	65105385		2028	4202	6230	SO:0001583	missense	9931	exon29			CAGCTTCTGCAGG	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.4336G>A	chr17.hg19:g.65105385C>T	ENSP00000351524:p.Glu1446Lys	105.0	0.0	.		111.0	43.0	.	NM_014877	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	hg19	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	C	14.99	2.701438	0.48307	.	.	ENSG00000198265	ENST00000358691	D	0.83419	-1.72	5.9	4.92	0.64577	.	0.199043	0.53938	D	0.000060	T	0.74801	0.3764	N	0.19112	0.55	0.43777	D	0.996308	B;B	0.20261	0.043;0.043	B;B	0.19391	0.025;0.025	T	0.70945	-0.4734	10	0.62326	D	0.03	-11.4842	16.9692	0.86294	0.0:0.8723:0.1277:0.0	.	1447;1446	B7ZLW2;P42694	.;HELZ_HUMAN	K	1446	ENSP00000351524:E1446K	ENSP00000351524:E1446K	E	-	1	0	HELZ	62535847	0.991000	0.36638	0.996000	0.52242	0.966000	0.64601	2.728000	0.47319	1.460000	0.47911	0.549000	0.68633	GAA	.	.	.	none		0.547	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		T	65105385	C	T	65105385	3	4	233	1	0	0	0	0	1	0	0	0	7056	922	32	2	1512	2	HELZ	17	65105385	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	25179568	65105385	16089825	115	14238											
EXOC7	23265	hgsc.bcm.edu	37	chr17	74081440	74081440	+	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	gctcaatgtgctcccggtagGagcgctcagcagtcttctgt	6	11	12	12	2	4	0	2	0	2	0	5	1	5	1	1	2	3	5	1	2	2	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr17:74081440G>A	ENST00000335146.7	-	16	1873	c.1820C>T	c.(1819-1821)tCc>tTc	p.S607F	EXOC7_ENST00000589210.1_Missense_Mutation_p.S556F|EXOC7_ENST00000332065.5_Missense_Mutation_p.S525F|EXOC7_ENST00000467929.2_Missense_Mutation_p.S528F|EXOC7_ENST00000405575.4_Missense_Mutation_p.S579F|EXOC7_ENST00000607838.1_Missense_Mutation_p.S579F|EXOC7_ENST00000411744.2_Missense_Mutation_p.S548F|EXOC7_ENST00000591724.1_5'Flank			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	607					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)			CTCCCGGTAGGAGCGCTCAGC	0.637																																					p.S607F		Atlas-SNP	.											EXOC7,NS,malignant_melanoma,0,1	EXOC7	47	.	0			c.C1820T						PASS	.						57	47	50					17																	74081440		2202	4300	6502	SO:0001583	missense	23265	exon16			CGGTAGGAGCGCT	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.1820C>T	chr17.hg19:g.74081440G>A	ENSP00000334100:p.Ser607Phe	30.0	0.0	.		45.0	4.0	.	NM_001145297	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Missense_Mutation	SNP	ENST00000335146.7	hg19	CCDS45782.1	.	.	.	.	.	.	.	.	.	.	g	11.91	1.778418	0.31502	.	.	ENSG00000182473	ENST00000332065;ENST00000351709;ENST00000405575;ENST00000335146;ENST00000357231;ENST00000425372;ENST00000411744	.	.	.	4.43	4.43	0.53597	Cullin repeat-like-containing domain (1);	0.133958	0.50627	D	0.000114	T	0.54615	0.1869	L	0.40543	1.245	0.80722	D	1	P;B;P;B;P;P;P	0.51653	0.947;0.006;0.844;0.059;0.918;0.809;0.578	B;B;P;B;B;B;B	0.46389	0.283;0.028;0.515;0.028;0.384;0.317;0.129	T	0.54200	-0.8329	9	0.30078	T	0.28	-19.663	17.099	0.86644	0.0:0.0:1.0:0.0	.	548;579;528;493;607;525;556	Q9UPT5-5;Q9UPT5-6;B4DJ07;F5H1P1;Q9UPT5;Q9UPT5-2;Q9UPT5-1	.;.;.;.;EXOC7_HUMAN;.;.	F	525;445;579;607;556;493;548	.	ENSP00000333806:S525F	S	-	2	0	EXOC7	71593035	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	6.700000	0.74619	2.035000	0.60131	0.479000	0.44913	TCC	.	.	.	none		0.637	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219		A	74081440	G	A	74081440	3	1	233	1	0	0	0	0	1	0	0	0	5312	1174	41	2	407	2	EXOC7	17	74081440	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	8976055	74081440	7113770	116	14239											
SETBP1	26040	hgsc.bcm.edu	37	chr18	42533244	42533244	+	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	ggaacgtacagggaaaaggaCatccaagccttcaagatgaa	17	5	11	8	1	1	2	1	1	0	1	2	5	2	5	2	3	3	1	2	3	7	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr18:42533244C>T	ENST00000282030.5	+	4	4235	c.3939C>T	c.(3937-3939)gaC>gaT	p.D1313D		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	1313						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)		GGGAAAAGGACATCCAAGCCT	0.443									Schinzel-Giedion syndrome																												p.D1313D		Atlas-SNP	.											.	SETBP1	577	.	0			c.C3939T						PASS	.						130	120	123					18																	42533244		2203	4300	6503	SO:0001819	synonymous_variant	26040	exon4	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	AAAGGACATCCAA	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.3939C>T	chr18.hg19:g.42533244C>T		158.0	0.0	.		144.0	38.0	.	NM_015559	A6H8W5|Q6P6C3|Q9UEF3	Silent	SNP	ENST00000282030.5	hg19	CCDS11923.2																																																																																			.	.	.	none		0.443	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110		T	42533244	C	T	42533244	2	4	233	1	0	0	0	0	0	0	0	1	14142	477	17	2		2	SETBP1	18	42533244	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10		42533244	35544004	117	14240											
PTPRS	5802	hgsc.bcm.edu	37	chr19	5286082	5286082	+	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	ttctgctgcacagcctccaaCgagcaggaccacaaggaggc	11	5	11	14	1	1	0	0	0	1	0	2	3	2	2	3	3	5	3	3	3	2	1	rs200430287	byFrequency	TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:5286082C>A	ENST00000587303.1	-	1	169	c.70G>T	c.(70-72)Gtt>Ttt	p.V24F	PTPRS_ENST00000353284.2_Missense_Mutation_p.V24F|PTPRS_ENST00000357368.4_Missense_Mutation_p.V24F|PTPRS_ENST00000262963.6_Missense_Mutation_p.V24F|PTPRS_ENST00000588012.1_Missense_Mutation_p.V24F|PTPRS_ENST00000592099.1_Missense_Mutation_p.V24F|PTPRS_ENST00000372412.4_Missense_Mutation_p.V24F|PTPRS_ENST00000348075.2_Missense_Mutation_p.V24F|PTPRS_ENST00000590509.1_Missense_Mutation_p.V24F|PTPRS_ENST00000588552.1_5'UTR			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	24					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)	CAGCCTCCAACGAGCAGGACC	0.617																																					p.V24F		Atlas-SNP	.											.	PTPRS	169	.	0			c.G70T						PASS	.						52	46	48					19																	5286082		2203	4299	6502	SO:0001583	missense	5802	exon2			CTCCAACGAGCAG	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.70G>T	chr19.hg19:g.5286082C>A	ENSP00000467537:p.Val24Phe	150.0	0.0	.		160.0	81.0	.	NM_130854	O75255|O75870|Q15718|Q16341|Q2M3R7	Missense_Mutation	SNP	ENST00000587303.1	hg19	CCDS45930.1	.	.	.	.	.	.	.	.	.	.	C	6.878	0.531372	0.13127	.	.	ENSG00000105426	ENST00000536396;ENST00000372412;ENST00000357368;ENST00000355005;ENST00000356037;ENST00000262963;ENST00000348075;ENST00000355322;ENST00000544524;ENST00000353284	T;T;T;T;T	0.56776	0.62;0.61;0.57;0.44;0.53	4.14	1.83	0.25207	.	1.741500	0.04678	U	0.411808	T	0.32971	0.0847	N	0.08118	0	0.09310	N	0.999997	B;B;B;B;P;B;B	0.34462	0.275;0.207;0.275;0.275;0.454;0.089;0.18	B;B;B;B;B;B;B	0.34138	0.091;0.176;0.091;0.091;0.045;0.017;0.025	T	0.35251	-0.9796	10	0.59425	D	0.04	.	5.1867	0.15187	0.0:0.6502:0.2297:0.1202	.	24;24;24;24;24;24;50	F8W800;Q8NHS7;Q13332-7;F5H2T4;Q13332-6;Q13332;Q59FX6	.;.;.;.;.;PTPRS_HUMAN;.	F	50;24;24;24;24;24;24;24;24;24	ENSP00000361489:V24F;ENSP00000349932:V24F;ENSP00000262963:V24F;ENSP00000269907:V24F;ENSP00000327313:V24F	ENSP00000262963:V24F	V	-	1	0	PTPRS	5237082	0.861000	0.29849	0.878000	0.34440	0.011000	0.07611	1.123000	0.31308	0.973000	0.38340	-0.362000	0.07510	GTT	.	C|0.999;T|0.001	.	alt		0.617	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2			A	5286082	C	A	5286082	3	1	233	1	0	0	0	0	1	0	0	0	12824	536	19	4	5924	4	PTPRS	19	5286082	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10		5286082	53842901	118	14241											
KEAP1	9817	hgsc.bcm.edu	37	chr19	10610178	10610178	+	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	ggcattgctggggtccagctGctgcaccaggaagtcactgc	7	8	14	12	0	1	0	1	0	0	0	2	1	2	1	2	4	5	5	2	4	1	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:10610178G>A	ENST00000171111.5	-	2	1079	c.532C>T	c.(532-534)Cag>Tag	p.Q178*	KEAP1_ENST00000588024.1_5'UTR|KEAP1_ENST00000393623.2_Nonsense_Mutation_p.Q178*	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	178					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)	GGGTCCAGCTGCTGCACCAGG	0.572																																					p.Q178X		Atlas-SNP	.											.	KEAP1	182	.	0			c.C532T						PASS	.						137	109	118					19																	10610178		2203	4300	6503	SO:0001587	stop_gained	9817	exon2			CCAGCTGCTGCAC	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.532C>T	chr19.hg19:g.10610178G>A	ENSP00000171111:p.Gln178*	141.0	1.0	.		104.0	91.0	.	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Nonsense_Mutation	SNP	ENST00000171111.5	hg19	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	G	38	6.966030	0.97967	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	.	.	.	4.81	4.81	0.61882	.	0.116198	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	15.3825	0.74669	0.0:0.0:1.0:0.0	.	.	.	.	X	178	.	ENSP00000171111:Q178X	Q	-	1	0	KEAP1	10471178	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.704000	0.84595	2.232000	0.73038	0.561000	0.74099	CAG	.	.	.	none		0.572	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		A	10610178	G	A	10610178	4	1	233	1	0	0	0	0	0	1	0	0	8148	1328	46	2	1362	2	KEAP1	19	10610178	Nonsense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	5324096	10610178	48518805	119	14242											
SLC7A9	11136	hgsc.bcm.edu	37	chr19	33350841	33350841	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcacgccgtcaccagggggAtcccgatgataatggccaaa	12	5	12	12	3	1	1	1	1	0	0	2	3	2	2	4	3	1	1	4	3	2	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:33350841A>G	ENST00000023064.4	-	8	970	c.779T>C	c.(778-780)aTc>aCc	p.I260T	SLC7A9_ENST00000587772.1_Missense_Mutation_p.I260T|RN7SKP22_ENST00000365097.1_RNA|SLC7A9_ENST00000590341.1_Missense_Mutation_p.I260T	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	260					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)	CACCAGGGGGATCCCGATGAT	0.607																																					p.I260T	GBM(181;1335 2108 9644 44178 46689)	Atlas-SNP	.											.	SLC7A9	78	.	0			c.T779C						PASS	.						100	82	88					19																	33350841		2203	4300	6503	SO:0001583	missense	11136	exon8			AGGGGGATCCCGA	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.779T>C	chr19.hg19:g.33350841A>G	ENSP00000023064:p.Ile260Thr	185.0	0.0	.		210.0	108.0	.	NM_001243036	B2R9A6	Missense_Mutation	SNP	ENST00000023064.4	hg19	CCDS12425.1	.	.	.	.	.	.	.	.	.	.	A	19.17	3.776707	0.70107	.	.	ENSG00000021488	ENST00000023064	D	0.90620	-2.7	5.64	5.64	0.86602	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.95799	0.8633	M	0.87547	2.89	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	D	0.96469	0.9347	10	0.87932	D	0	.	15.8639	0.79047	1.0:0.0:0.0:0.0	.	260;260	Q53FY4;P82251	.;BAT1_HUMAN	T	260	ENSP00000023064:I260T	ENSP00000023064:I260T	I	-	2	0	SLC7A9	38042681	1.000000	0.71417	1.000000	0.80357	0.388000	0.30384	9.192000	0.94947	2.161000	0.67846	0.379000	0.24179	ATC	.	.	.	none		0.607	SLC7A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450585.1			G	33350841	A	G	33350841	3	3	233	1	0	0	0	0	1	0	0	0	14718	333	12	3	708	3	SLC7A9	19	33350841	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	22740663	33350841	25778142	120	14243											
CEBPA	1050	hgsc.bcm.edu	37	chr19	33793108	33793108	+	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	aggaactcgtcgttgaaggcGgccgggtcgatgtaggcgct	7	8	17	9	6	0	1	0	1	0	0	3	3	0	2	1	5	1	3	1	5	3	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:33793108G>T	ENST00000498907.2	-	1	362	c.213C>A	c.(211-213)gcC>gcA	p.A71A	CEBPA-AS1_ENST00000592982.2_RNA|CTD-2540B15.11_ENST00000589932.1_RNA|CTD-2540B15.9_ENST00000593041.1_lincRNA|CTD-2540B15.7_ENST00000587312.1_RNA	NM_004364.3	NP_004355.2	P49715	CEBPA_HUMAN	CCAAT/enhancer binding protein (C/EBP), alpha	71					acute-phase response (GO:0006953)|brown fat cell differentiation (GO:0050873)|cell maturation (GO:0048469)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|cholesterol metabolic process (GO:0008203)|cytokine-mediated signaling pathway (GO:0019221)|embryonic placenta development (GO:0001892)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|liver development (GO:0001889)|lung development (GO:0030324)|macrophage differentiation (GO:0030225)|mitochondrion organization (GO:0007005)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ regeneration (GO:0031100)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|response to glucocorticoid (GO:0051384)|response to vitamin B2 (GO:0033274)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|urea cycle (GO:0000050)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A72fs*89(1)|p.Y7_G130del(1)|p.A72fs*90(1)|p.A72fs*37(1)|p.S61fs*88(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(912)|lung(5)|prostate(1)|stomach(1)	920	Esophageal squamous(110;0.137)					CGTTGAAGGCGGCCGGGTCGA	0.751			"Mis, N, F"		"AML, MDS"				Acute Myeloid Leukemia, Familial, associated with CEBPA germline mutation																												p.A71A		Atlas-SNP	.		Dom	yes		19	19q13.1	1050	"CCAAT/enhancer binding protein (C/EBP), alpha"		L	.,1	CEBPA	986	.	5	Insertion - Frameshift(3)|Deletion - Frameshift(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(5)	c.C213A						PASS	.						4	5	4					19																	33793108		1229	2522	3751	SO:0001819	synonymous_variant	1050	exon1	Familial Cancer Database	Familial AML	GAAGGCGGCCGGG	M37197	CCDS54243.1	19q13.1	2014-09-17				ENSG00000245848		"basic leucine zipper proteins"	1833	protein-coding gene	gene with protein product		116897		CEBP		1535333, 1840554	Standard	NM_004364		Approved	C/EBP-alpha	uc002nun.3	P49715		ENST00000498907.2:c.213C>A	chr19.hg19:g.33793108G>T		26.0	0.0	.		83.0	30.0	.	NM_004364	A7LNP2|P78319|Q05CA4	Silent	SNP	ENST00000498907.2	hg19	CCDS54243.1																																																																																			.	.	.	none		0.751	CEBPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365012.1	NM_004364		T	33793108	G	T	33793108	2	4	233	1	0	0	0	0	0	0	0	1	3201	1103	39	4		4	CEBPA	19	33793108	Silent	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	442267	33793108	25335875	121	14244			1	31		2	2	13	G		5.349263e-05
CEBPA	1050	hgsc.bcm.edu	37	chr19	33793120	33793120	+	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	ttgaaggcggccgggtcgatGtaggcgctgatgtcgatgga	7	9	18	7	5	0	2	0	2	0	0	2	5	0	3	1	5	0	2	1	5	2	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:33793120G>T	ENST00000498907.2	-	1	350	c.201C>A	c.(199-201)taC>taA	p.Y67*	CEBPA-AS1_ENST00000592982.2_RNA|CTD-2540B15.11_ENST00000589932.1_RNA|CTD-2540B15.9_ENST00000593041.1_lincRNA|CTD-2540B15.7_ENST00000587312.1_RNA	NM_004364.3	NP_004355.2	P49715	CEBPA_HUMAN	CCAAT/enhancer binding protein (C/EBP), alpha	67					acute-phase response (GO:0006953)|brown fat cell differentiation (GO:0050873)|cell maturation (GO:0048469)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|cholesterol metabolic process (GO:0008203)|cytokine-mediated signaling pathway (GO:0019221)|embryonic placenta development (GO:0001892)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|liver development (GO:0001889)|lung development (GO:0030324)|macrophage differentiation (GO:0030225)|mitochondrion organization (GO:0007005)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ regeneration (GO:0031100)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|response to glucocorticoid (GO:0051384)|response to vitamin B2 (GO:0033274)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|urea cycle (GO:0000050)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.I68fs*41(4)|p.Y67fs*92(2)|p.S61fs*88(1)|p.Y67fs*95(1)|p.I68fs*39(1)|p.Y7_G130del(1)|p.Y67fs*42(1)|p.Y67fs*37(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(912)|lung(5)|prostate(1)|stomach(1)	920	Esophageal squamous(110;0.137)					CCGGGTCGATGTAGGCGCTGA	0.751			"Mis, N, F"		"AML, MDS"				Acute Myeloid Leukemia, Familial, associated with CEBPA germline mutation																												p.Y67X		Atlas-SNP	.		Dom	yes		19	19q13.1	1050	"CCAAT/enhancer binding protein (C/EBP), alpha"		L	.,2	CEBPA	986	.	12	Insertion - Frameshift(6)|Deletion - Frameshift(5)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(12)	c.C201A						PASS	.						4	5	5					19																	33793120		1255	2546	3801	SO:0001587	stop_gained	1050	exon1	Familial Cancer Database	Familial AML	GTCGATGTAGGCG	M37197	CCDS54243.1	19q13.1	2014-09-17				ENSG00000245848		"basic leucine zipper proteins"	1833	protein-coding gene	gene with protein product		116897		CEBP		1535333, 1840554	Standard	NM_004364		Approved	C/EBP-alpha	uc002nun.3	P49715		ENST00000498907.2:c.201C>A	chr19.hg19:g.33793120G>T	ENSP00000427514:p.Tyr67*	26.0	0.0	.		84.0	29.0	.	NM_004364	A7LNP2|P78319|Q05CA4	Nonsense_Mutation	SNP	ENST00000498907.2	hg19	CCDS54243.1	.	.	.	.	.	.	.	.	.	.	g	33	5.204863	0.95033	.	.	ENSG00000245848	ENST00000498907	.	.	.	3.93	2.89	0.33648	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.1768	0.25749	0.2127:0.0:0.7873:0.0	.	.	.	.	X	67	.	ENSP00000427514:Y67X	Y	-	3	2	CEBPA	38484960	1.000000	0.71417	1.000000	0.80357	0.663000	0.39108	5.273000	0.65564	0.631000	0.30412	0.282000	0.19409	TAC	.	.	.	none		0.751	CEBPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365012.1	NM_004364		T	33793120	G	T	33793120	4	4	233	1	0	0	0	0	0	1	0	0	3201	1372	48	4	879	4	CEBPA	19	33793120	Nonsense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	12	33793120	25335863	122	14245			1	31		2	2	13	G		5.349263e-05
WTIP	126374	hgsc.bcm.edu	37	chr19	34991065	34991065	+	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	gcagctgagcggggaggaggGacgccgttgctatcccctgg	6	6	18	11	3	0	1	0	1	0	0	1	4	1	4	3	5	3	4	3	5	1	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:34991065G>A	ENST00000590071.2	+	8	1521	c.1184G>A	c.(1183-1185)gGa>gAa	p.G395E	WTIP_ENST00000270288.6_Missense_Mutation_p.G619E	NM_001080436.1	NP_001073905.1	A6NIX2	WTIP_HUMAN	Wilms tumor 1 interacting protein	395	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|negative regulation of hippo signaling (GO:0035331)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell morphogenesis (GO:0022604)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(1)	4	all_lung(56;5.94e-07)|Lung NSC(56;9.35e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			GGGGAGGAGGGACGCCGTTGC	0.667																																					p.G395E		Atlas-SNP	.											.	WTIP	12	.	0			c.G1184A						PASS	.						32	40	38					19																	34991065		2142	4235	6377	SO:0001583	missense	126374	exon8			AGGAGGGACGCCG	AK130059	CCDS59375.1	19q13.11	2012-03-16			ENSG00000142279	ENSG00000142279			20964	protein-coding gene	gene with protein product	"WT1-interacting protein"	614790				14736876	Standard	NM_001080436		Approved		uc002nvm.3	A6NIX2		ENST00000590071.2:c.1184G>A	chr19.hg19:g.34991065G>A	ENSP00000466953:p.Gly395Glu	21.0	0.0	.		41.0	20.0	.	NM_001080436		Missense_Mutation	SNP	ENST00000590071.2	hg19	CCDS59375.1	.	.	.	.	.	.	.	.	.	.	G	17.23	3.337153	0.60963	.	.	ENSG00000142279	ENST00000270288	T	0.63580	-0.05	4.35	4.35	0.52113	Zinc finger, LIM-type (4);	0.000000	0.85682	D	0.000000	T	0.72835	0.3510	M	0.76838	2.35	0.80722	D	1	P	0.37370	0.592	P	0.47528	0.549	T	0.77760	-0.2467	10	0.66056	D	0.02	.	15.9833	0.80130	0.0:0.0:1.0:0.0	.	619	A6NIX2	WTIP_HUMAN	E	619	ENSP00000270288:G619E	ENSP00000270288:G619E	G	+	2	0	WTIP	39682905	1.000000	0.71417	0.991000	0.47740	0.294000	0.27393	9.098000	0.94202	2.101000	0.63845	0.305000	0.20034	GGA	.	.	.	none		0.667	WTIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459381.3	XM_059037		A	34991065	G	A	34991065	3	1	233	1	0	0	0	0	1	0	0	0	17422	1174	41	2	1214	2	WTIP	19	34991065	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	1197945	34991065	24137918	123	14246											
LSR	51599	hgsc.bcm.edu	37	chr19	35758028	35758028	+	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	gcagccatgagtgaagtcacCtccctccacgaggacgactg	10	6	11	14	2	1	2	1	2	0	0	3	5	3	3	4	1	1	1	4	1	1	0			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:35758028C>A	ENST00000361790.3	+	9	1464	c.1305C>A	c.(1303-1305)acC>acA	p.T435T	USF2_ENST00000343550.5_5'Flank|LSR_ENST00000347609.4_Silent_p.T377T|USF2_ENST00000222305.3_5'Flank|USF2_ENST00000379134.3_5'Flank|LSR_ENST00000354900.3_Silent_p.T416T|LSR_ENST00000602122.1_Silent_p.T415T|USF2_ENST00000594064.1_5'Flank|LSR_ENST00000360798.3_Silent_p.T367T|USF2_ENST00000595068.1_5'Flank|LSR_ENST00000427250.1_Silent_p.T279T|AD000684.2_ENST00000602262.1_RNA	NM_205834.3	NP_991403.1	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor	435					embryo development (GO:0009790)|liver development (GO:0001889)	chylomicron (GO:0042627)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	13	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			GTGAAGTCACCTCCCTCCACG	0.677																																					p.T435T		Atlas-SNP	.											.	LSR	60	.	0			c.C1305A						PASS	.						31	40	37					19																	35758028		2134	4246	6380	SO:0001819	synonymous_variant	51599	exon9			AGTCACCTCCCTC	AF130366	CCDS12449.1, CCDS12450.1, CCDS12451.1, CCDS59376.1	19q13.12	2013-01-11			ENSG00000105699	ENSG00000105699		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	29572	protein-coding gene	gene with protein product	"lipolysis-stimulated remnant", "immunoglobulin-like domain containing receptor 3"					10224102	Standard	NM_015925		Approved	LISCH7, ILDR3	uc002nyl.3	Q86X29		ENST00000361790.3:c.1305C>A	chr19.hg19:g.35758028C>A		110.0	0.0	.		161.0	93.0	.	NM_205834	A6NDW3|B4DKL4|E9PHD4|O00112|O00426|Q6ZT80|Q8NBM0|Q9BT33|Q9UQL3	Silent	SNP	ENST00000361790.3	hg19	CCDS12450.1																																																																																			.	.	.	none		0.677	LSR-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465513.2	NM_015925		A	35758028	C	A	35758028	2	1	233	1	0	0	0	0	0	0	0	1	9071	668	24	4		4	LSR	19	35758028	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	766963	35758028	23370955	124	14247											
FCGBP	8857	hgsc.bcm.edu	37	chr19	40357745	40357745	+	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	ctcgctgcagtctgaggtcaGcagggaggagtttacctgtg	7	10	15	9	1	2	1	1	1	1	0	3	3	2	3	1	3	3	4	1	3	1	2			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:40357745G>T	ENST00000221347.6	-	34	15575	c.15568C>A	c.(15568-15570)Ctg>Atg	p.L5190M		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	5190	Cys-rich.					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)			TCTGAGGTCAGCAGGGAGGAG	0.577																																					p.L5190M		Atlas-SNP	.											.	FCGBP	416	.	0			c.C15568A						PASS	.						52	48	49					19																	40357745		2203	4300	6503	SO:0001583	missense	8857	exon34			AGGTCAGCAGGGA	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.15568C>A	chr19.hg19:g.40357745G>T	ENSP00000221347:p.Leu5190Met	166.0	0.0	.		199.0	23.0	.	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	hg19	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	G	13.72	2.321017	0.41096	.	.	ENSG00000090920	ENST00000221347	T	0.05649	3.41	4.69	1.09	0.20402	.	0.754197	0.11458	N	0.562013	T	0.07728	0.0194	L	0.28694	0.88	0.22796	N	0.99872	P	0.46395	0.877	P	0.51016	0.656	T	0.39702	-0.9601	10	0.23302	T	0.38	.	7.3143	0.26491	0.0:0.3807:0.4452:0.1741	.	5190	Q9Y6R7	FCGBP_HUMAN	M	5190	ENSP00000221347:L5190M	ENSP00000221347:L5190M	L	-	1	2	FCGBP	45049585	0.892000	0.30473	0.997000	0.53966	0.846000	0.48090	0.111000	0.15458	0.563000	0.29222	0.655000	0.94253	CTG	.	.	.	none		0.577	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		T	40357745	G	T	40357745	3	4	233	1	0	0	0	0	1	0	0	0	5785	962	34	4	661	4	FCGBP	19	40357745	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	4599717	40357745	18771238	125	14248											
HRC	3270	hgsc.bcm.edu	37	chr19	49657889	49657889	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tactcagtggaggcctcctcTtcctcctcctcctcctcctc	3	13	5	20	0	2	0	1	0	1	0	10	1	9	1	8	2	1	0	8	2	1	2	rs57199624|rs147238387|rs551367394|rs542091249		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:49657889T>C	ENST00000252825.4	-	1	792	c.606A>G	c.(604-606)gaA>gaG	p.E202E	HRC_ENST00000595625.1_Silent_p.E202E	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	202	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Glu-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		AGGcctcctcttcctcctcct	0.567																																					p.E202E	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.,1	HRC	85	.	0			c.A606G						PASS	.						122	91	101					19																	49657889		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			CTCCTCTTCCTCC		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.606A>G	chr19.hg19:g.49657889T>C		55.0	0.0	.		58.0	6.0	.	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	hg19	CCDS12759.1																																																																																			.	.	.	none		0.567	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		C	49657889	T	C	49657889	2	2	233	1	0	0	0	0	0	0	0	1	7359	1606	56	3		3	HRC	19	49657889	Silent	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	9300144	49657889	9471094	126	14249											
NUP62	23636	hgsc.bcm.edu	37	chr19	50412996	50412996	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagcaggtgtggttgttgcCgtctttgcagtgccaaacgt	6	13	14	8	2	1	0	0	0	1	0	1	0	1	0	2	2	5	5	2	2	2	4			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:50412996C>T	ENST00000596217.1	-	2	1956	c.69G>A	c.(67-69)acG>acA	p.T23T	NUP62_ENST00000413454.1_Silent_p.T23T|IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000422090.2_Silent_p.T23T|CTC-326K19.6_ENST00000451973.1_3'UTR|NUP62_ENST00000597029.1_Silent_p.T23T|NUP62_ENST00000600583.1_5'UTR|NUP62_ENST00000597723.1_Silent_p.T23T|IL4I1_ENST00000341114.3_Intron|NUP62_ENST00000352066.3_Silent_p.T23T			P37198	NUP62_HUMAN	nucleoporin 62kDa	23	15 X 9 AA approximate repeats.|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)		TGGTTGTTGCCGTCTTTGCAG	0.567																																					p.T23T		Atlas-SNP	.											.	NUP62	50	.	0			c.G69A						PASS	.						48	55	53					19																	50412996		2203	4300	6503	SO:0001819	synonymous_variant	23636	exon3			TGTTGCCGTCTTT	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.69G>A	chr19.hg19:g.50412996C>T		82.0	0.0	.		88.0	50.0	.	NM_153719	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	Silent	SNP	ENST00000596217.1	hg19	CCDS12788.1																																																																																			.	.	.	none		0.567	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464991.1	NM_153719		T	50412996	C	T	50412996	2	4	233	1	0	0	0	0	0	0	0	1	10775	639	23	1		1	NUP62	19	50412996	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	755107	50412996	8715987	127	14250											
MBOAT7	79143	hgsc.bcm.edu	37	chr19	54687463	54687463	+	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	tctccatcagggagggcacgTcgggcagcagccccagggtg	7	5	16	13	2	2	0	1	0	1	0	4	1	2	1	3	4	2	3	3	4	0	0			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:54687463T>A	ENST00000245615.1	-	5	914	c.434A>T	c.(433-435)gAc>gTc	p.D145V	MBOAT7_ENST00000391754.1_Missense_Mutation_p.D145V|MBOAT7_ENST00000474910.1_5'UTR|MBOAT7_ENST00000431666.2_Missense_Mutation_p.D72V|MBOAT7_ENST00000338624.6_Missense_Mutation_p.D72V	NM_024298.3	NP_077274.3	Q96N66	MBOA7_HUMAN	membrane bound O-acyltransferase domain containing 7	145					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)					GGAGGGCACGTCGGGCAGCAG	0.617																																					p.D145V	NSCLC(97;826 2151 10470 22540)	Atlas-SNP	.											.	MBOAT7	37	.	0			c.A434T						PASS	.						105	84	91					19																	54687463		2203	4300	6503	SO:0001583	missense	79143	exon5			GGCACGTCGGGCA	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.434A>T	chr19.hg19:g.54687463T>A	ENSP00000245615:p.Asp145Val	101.0	0.0	.		97.0	52.0	.	NM_001146082	A9C4B6|B0V3I5|B4DQ87|Q05DF0|Q7L5N2|Q99908|Q9BPV2|Q9BRE9	Missense_Mutation	SNP	ENST00000245615.1	hg19	CCDS12883.1	.	.	.	.	.	.	.	.	.	.	T	8.074	0.770996	0.15983	.	.	ENSG00000125505	ENST00000431666;ENST00000338624;ENST00000245615;ENST00000449249;ENST00000391754;ENST00000414665;ENST00000453320	T;T;T;T;T	0.72835	-0.69;-0.69;-0.69;-0.69;-0.69	4.2	1.95	0.26073	.	0.659654	0.15733	N	0.247337	T	0.46718	0.1407	N	0.20685	0.6	0.09310	N	1	B;B;B	0.30973	0.033;0.302;0.033	B;B;B	0.21917	0.023;0.037;0.023	T	0.28650	-1.0037	10	0.40728	T	0.16	-2.1121	4.0508	0.09795	0.0:0.1914:0.1877:0.6209	.	127;72;145	B4DDH8;Q96N66-2;Q96N66	.;.;MBOA7_HUMAN	V	72;72;145;97;145;145;145	ENSP00000410503:D72V;ENSP00000344377:D72V;ENSP00000245615:D145V;ENSP00000375634:D145V;ENSP00000388250:D145V	ENSP00000245615:D145V	D	-	2	0	MBOAT7	59379275	0.001000	0.12720	0.058000	0.19502	0.792000	0.44763	1.025000	0.30090	1.714000	0.51371	0.363000	0.22086	GAC	.	.	.	none		0.617	MBOAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142203.1	NM_024298		A	54687463	T	A	54687463	3	1	233	1	0	0	0	0	1	0	0	0	9365	1667	58	5	1004	5	MBOAT7	19	54687463	Missense_Mutation	SNP	T	TCGA-P4-A5EB-01A-11D-A28G-10	4274467	54687463	4441520	128	14251											
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385280	58385281	+	Frame_Shift_Del	DEL	TG	TG	-																															atttcccacattctccacacTgataaggtctttctccactg																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr19:58385280_58385281delTG	ENST00000435989.2	-	3	1711_1712	c.1477_1478delCA	c.(1477-1479)cagfs	p.Q493fs	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597342.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	493					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						TTCTCCACACTGATAAGGTCTT	0.47																																					p.493_493del		Atlas-INDEL	.											.	ZNF814	93	.	0			c.1478_1479del						PASS	.																																			SO:0001589	frameshift_variant	730051	exon3			.		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.1477_1478delCA	chr19.hg19:g.58385280_58385281delTG	ENSP00000410545:p.Gln493fs	130.0	0.0	0		124.0	12.0	0.0967742	NM_001144989	A6NF35	Frame_Shift_Del	DEL	ENST00000435989.2	hg19	CCDS46212.1																																																																																			.	.	.	none		0.47	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		-	58385281	TG	-	58385280	7	5	233	1	0	1	0	1	0	0	0	0	18188	1580	55	0	1093	0	ZNF814	19	58385280	Frame_Shift_Del	DEL	TG	TCGA-P4-A5EB-01A-11D-A28G-10	3697817	58385280	743703	129	14252											
KCNK15	140730	hgsc.bcm.edu	37	chr20	43378853	43378853	+	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	tgggcatcccgctgacgctgGtcactttccagagcctgggc	5	9	13	14	2	1	2	1	1	0	1	3	2	3	2	3	3	1	3	3	3	0	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr20:43378853G>A	ENST00000372851.3	-	0	5203				KCNK15_ENST00000372861.3_Missense_Mutation_p.V123I	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)				GCTGACGCTGGTCACTTTCCA	0.682																																					p.V123I		Atlas-SNP	.											.	KCNK15	19	.	0			c.G367A						PASS	.						35	31	33					20																	43378853		2203	4300	6503	SO:0001628	intergenic_variant	60598	exon2			ACGCTGGTCACTT		CCDS13338.1, CCDS56191.1	20q13.12	2005-02-03	2003-06-18	2003-06-20	ENSG00000101098	ENSG00000101098			16183	protein-coding gene	gene with protein product		611601	"chromosome 20 open reading frame 190"	C20orf190		12620390	Standard	NM_182970		Approved	dJ781B1.3	uc010ggu.3	Q9H426	OTTHUMG00000032546		chr20.hg19:g.43378853G>A		61.0	0.0	.		136.0	40.0	.	NM_022358	A4FU94|E1P613|Q3MI44|Q5JWT7	Missense_Mutation	SNP	ENST00000372851.3	hg19	CCDS13338.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.418600	0.83559	.	.	ENSG00000124249	ENST00000372861	T	0.28454	1.61	4.08	4.08	0.47627	Ion transport 2 (1);	0.000000	0.64402	U	0.000004	T	0.43100	0.1232	L	0.31578	0.945	0.54753	D	0.999989	D	0.69078	0.997	D	0.72075	0.976	T	0.38351	-0.9665	10	0.45353	T	0.12	.	16.4786	0.84151	0.0:0.0:1.0:0.0	.	123	Q9H427	KCNKF_HUMAN	I	123	ENSP00000361952:V123I	ENSP00000361952:V123I	V	+	1	0	KCNK15	42812267	1.000000	0.71417	0.999000	0.59377	0.904000	0.53231	6.347000	0.73004	2.095000	0.63458	0.655000	0.94253	GTC	.	.	.	none		0.682	RIMS4-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000101027.2	NM_182970		A	43378853	G	A	43378853	1	1	233	0	1	0	0	0	0	0	0	0	8069	1261	44	2		2	KCNK15	20	43378853	IGR	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10		43378853	19646667	130	14253											
LIPI	149998	hgsc.bcm.edu	37	chr21	15554119	15554119	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acatccacaaactttgcatcCgtgtaatctaatctgctata	13	13	4	11	1	2	0	0	0	2	0	4	0	4	0	2	0	3	3	2	0	5	5	rs368826576		TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr21:15554119C>T	ENST00000536861.1	-	4	602	c.603G>A	c.(601-603)acG>acA	p.T201T	LIPI_ENST00000344577.2_Silent_p.T222T			Q6XZB0	LIPI_HUMAN	lipase, member I	201					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		ACTTTGCATCCGTGTAATCTA	0.388																																					p.T222T		Atlas-SNP	.											LIPI,NS,carcinoma,-1,1	LIPI	95	.	0			c.G666A						PASS	.	A		0,4406		0,0,2203	104	98	100		666	-5.4	0.9	21		100	1,8599		0,1,4299	no	coding-synonymous	LIPI	NM_198996.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		222/482	15554119	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	149998	exon4			TGCATCCGTGTAA	BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"membrane-associated phospholipase A1 beta", "cancer/testis antigen 17"	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.603G>A	chr21.hg19:g.15554119C>T		52.0	0.0	.		66.0	18.0	.	NM_198996	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Silent	SNP	ENST00000536861.1	hg19		.	.	.	.	.	.	.	.	.	.	A	8.536	0.872084	0.17322	0.0	1.16E-4	ENSG00000188992	ENST00000400211	.	.	.	5.46	-5.41	0.02648	.	.	.	.	.	T	0.35508	0.0934	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36648	-0.9739	4	.	.	.	.	1.1112	0.01704	0.2909:0.094:0.2357:0.3795	.	.	.	.	R	81	.	.	G	-	1	0	LIPI	14475990	0.021000	0.18746	0.905000	0.35620	0.056000	0.15407	-0.820000	0.04457	-1.108000	0.03000	-4.655000	0.00004	GGA	.	.	.	weak		0.388	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996		T	15554119	C	T	15554119	2	4	233	1	0	0	0	0	0	0	0	1	8832	639	23	1		1	LIPI	21	15554119	Silent	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10		15554119	32575776	131	14254											
NCAM2	4685	hgsc.bcm.edu	37	chr21	22906941	22906941	+	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	cgaagatgggagcccagtaaAtgagccaaatgaaaccacac	17	4	10	10	1	0	3	0	2	0	1	0	5	0	4	3	1	3	1	3	1	5	1			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr21:22906941A>T	ENST00000400546.1	+	17	2615	c.2366A>T	c.(2365-2367)aAt>aTt	p.N789I	NCAM2_ENST00000284894.7_Missense_Mutation_p.N647I	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	789					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)		AGCCCAGTAAATGAGCCAAAT	0.393																																					p.N789I		Atlas-SNP	.											.	NCAM2	220	.	0			c.A2366T						PASS	.						113	108	109					21																	22906941		1920	4124	6044	SO:0001583	missense	4685	exon17			CAGTAAATGAGCC		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.2366A>T	chr21.hg19:g.22906941A>T	ENSP00000383392:p.Asn789Ile	132.0	0.0	.		122.0	35.0	.	NM_004540	A8MQ06|B7Z841|Q7Z7F2	Missense_Mutation	SNP	ENST00000400546.1	hg19	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.935591	0.73442	.	.	ENSG00000154654	ENST00000400546;ENST00000284894	T;T	0.44083	0.93;0.93	5.49	5.49	0.81192	.	0.210687	0.48286	D	0.000186	T	0.49729	0.1574	L	0.41236	1.265	0.80722	D	1	D;D	0.61697	0.99;0.985	P;P	0.56398	0.797;0.724	T	0.49978	-0.8881	10	0.54805	T	0.06	-29.9197	14.4086	0.67101	1.0:0.0:0.0:0.0	.	647;789	B7Z5K2;O15394	.;NCAM2_HUMAN	I	789;647	ENSP00000383392:N789I;ENSP00000284894:N647I	ENSP00000284894:N647I	N	+	2	0	NCAM2	21828812	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.778000	0.75043	2.088000	0.63022	0.377000	0.23210	AAT	.	.	.	none		0.393	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		T	22906941	A	T	22906941	3	4	233	1	0	0	0	0	1	0	0	0	10210	101	4	5	2432	5	NCAM2	21	22906941	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	7352822	22906941	25222954	132	14255											
PLAC4	25825	hgsc.bcm.edu	37	chr21	42551431	42551431	+	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	agggtgaggagtgacggtgtCtggggtgagtgagggtgtcc	6	9	22	4	1	1	4	0	4	1	0	2	5	2	5	1	6	0	0	1	6	0	0			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr21:42551431C>T	ENST00000330333.6	+	1	775				PLAC4_ENST00000430327.2_RNA|PLAC4_ENST00000414699.1_RNA|PLAC4_ENST00000440221.2_RNA|BACE2_ENST00000347667.5_Intron|PLAC4_ENST00000536486.1_RNA|BACE2-IT1_ENST00000433378.1_RNA|BACE2_ENST00000328735.6_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)				GTGACGGTGTCTGGGGTGAGT	0.607																																					p.R42K		Atlas-SNP	.											.	.	.	.	0			c.G125A						PASS	.						125	109	114					21																	42551431		2196	4274	6470	SO:0001627	intron_variant	191585	exon1			CGGTGTCTGGGGT	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+10929C>T	chr21.hg19:g.42551431C>T		137.0	0.0	.		179.0	49.0	.	NM_182832	A8K7P1|Q5DIH8|Q8N2D4|Q9H2V8|Q9NZL1|Q9NZL2|Q9UJT6	Missense_Mutation	SNP	ENST00000330333.6	hg19	CCDS13668.1																																																																																			.	.	.	none		0.607	BACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195056.1			T	42551431	C	T	42551431	1	4	233	0	1	0	0	0	0	0	0	0	12021	913	32	2		2	PLAC4	21	42551431	Intron	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10	19644490	42551431	5578464	133	14256											
SHANK3	85358	hgsc.bcm.edu	37	chr22	51160316	51160316	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accccctgcccctgagtctgCagccgactctggggtggagg	5	7	14	15	1	2	1	0	1	2	0	2	3	2	2	5	4	3	1	5	4	0	0			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chr22:51160316C>T	ENST00000414786.2	+	21	4240	c.4013C>T	c.(4012-4014)gCa>gTa	p.A1338V	SHANK3_ENST00000262795.3_Missense_Mutation_p.A1368V|SHANK3_ENST00000445220.2_Missense_Mutation_p.A1354V			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	1352	Pro-rich.				adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		CCTGAGTCTGCAGCCGACTCT	0.701																																					p.A1338V		Atlas-SNP	.											.	SHANK3	96	.	0			c.C4013T						PASS	.						9	11	10					22																	51160316		1919	4032	5951	SO:0001583	missense	85358	exon21			AGTCTGCAGCCGA	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.4013C>T	chr22.hg19:g.51160316C>T	ENSP00000464552:p.Ala1338Val	30.0	0.0	.		87.0	53.0	.	NM_033517	D7UT47|Q8TET3	Missense_Mutation	SNP	ENST00000414786.2	hg19		.	.	.	.	.	.	.	.	.	.	C	8.474	0.858312	0.17178	.	.	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.13089	2.62;2.62	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.13543	0.0328	N	0.24115	0.695	0.27140	N	0.961671	D;P;D	0.56521	0.97;0.941;0.976	P;B;B	0.51895	0.683;0.43;0.441	T	0.12837	-1.0532	10	0.02654	T	1	.	16.0382	0.80645	0.0:1.0:0.0:0.0	.	1352;1353;1368	D7UT47;Q9BYB0;F2Z3L0	.;SHAN3_HUMAN;.	V	1368;1354	ENSP00000442518:A1368V;ENSP00000446078:A1354V	ENSP00000442518:A1368V	A	+	2	0	SHANK3	49507182	1.000000	0.71417	0.900000	0.35374	0.856000	0.48823	5.501000	0.66950	2.381000	0.81170	0.462000	0.41574	GCA	.	.	.	none		0.701	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420		T	51160316	C	T	51160316	3	4	233	1	0	0	0	0	1	0	0	0	14279	710	25	2	4189	2	SHANK3	22	51160316	Missense_Mutation	SNP	C	TCGA-P4-A5EB-01A-11D-A28G-10		51160316	144250	134	14257											
OFD1	8481	hgsc.bcm.edu	37	chrX	13762547	13762547	+	Frame_Shift_Del	DEL	T	T	-																															tttttaggttttcttatgcaTtttttaaaagaattggcaga																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chrX:13762547delT	ENST00000340096.6	+	6	753	c.426delT	c.(424-426)catfs	p.H142fs	OFD1_ENST00000398395.3_Frame_Shift_Del_p.H142fs|OFD1_ENST00000490265.1_3'UTR|OFD1_ENST00000380550.3_Frame_Shift_Del_p.H142fs|OFD1_ENST00000380567.1_Frame_Shift_Del_p.H2fs	NM_003611.2	NP_003602.1	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1	142					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						TTCTTATGCATTTTTTAAAAG	0.308																																					p.H142fs		Pindel	.											.	OFD1	109	.	0			c.425delA						PASS	.						66	59	61					X																	13762547		2203	4299	6502	SO:0001589	frameshift_variant	8481	exon6			.	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.426delT	chrX.hg19:g.13762547delT	ENSP00000344314:p.His142fs	225.0	0.0	.		290.0	96.0	0.331	NM_003611	B9ZVU5|O75666|Q4VAK4	Frame_Shift_Del	DEL	ENST00000340096.6	hg19	CCDS14157.1																																																																																			.	.	.	none		0.308	OFD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055808.1	NM_003611		-	13762547	T	-	13762547	7	5	233	1	0	1	0	1	0	0	0	0	10845	1490	52	0	448	0	OFD1	23	13762547	Frame_Shift_Del	DEL	T	TCGA-P4-A5EB-01A-11D-A28G-10		13762547	141508013	135	14258											
DMD	1756	hgsc.bcm.edu	37	chrX	32305751	32305751	+	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	caggcgttgcactttgcaatGctgctgtcttcttgctatga	6	15	10	10	1	2	1	0	1	2	0	2	1	2	1	0	1	5	6	0	1	2	5			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chrX:32305751G>T	ENST00000357033.4	-	43	6391	c.6185C>A	c.(6184-6186)gCa>gAa	p.A2062E	DMD_ENST00000378677.2_Missense_Mutation_p.A2058E	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	2062					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)				ACTTTGCAATGCTGCTGTCTT	0.368																																					p.A2062E		Atlas-SNP	.											.	DMD	2127	.	0			c.C6185A						PASS	.						131	105	114					X																	32305751		2202	4300	6502	SO:0001583	missense	1756	exon43			TGCAATGCTGCTG	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.6185C>A	chrX.hg19:g.32305751G>T	ENSP00000354923:p.Ala2062Glu	31.0	0.0	.		29.0	28.0	.	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	G	8.237	0.805865	0.16467	.	.	ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280	T;T	0.35048	1.33;1.33	4.36	2.59	0.31030	.	0.000000	0.36778	U	0.002408	T	0.28830	0.0715	L	0.53249	1.67	0.80722	D	1	B;P;B;B;B	0.38677	0.275;0.642;0.322;0.259;0.44	B;B;B;B;B	0.34418	0.088;0.182;0.144;0.138;0.096	T	0.05835	-1.0861	10	0.72032	D	0.01	.	7.2118	0.25937	0.3674:0.0:0.6326:0.0	.	2054;2062;2058;721;718	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6	.;DMD_HUMAN;.;.;.	E	2054;721;718;2058;2062;2062;1939	ENSP00000367948:A2058E;ENSP00000354923:A2062E	ENSP00000354923:A2062E	A	-	2	0	DMD	32215672	0.996000	0.38824	0.224000	0.23877	0.172000	0.22775	2.060000	0.41394	0.416000	0.25844	-0.191000	0.12829	GCA	.	.	.	none		0.368	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		T	32305751	G	T	32305751	3	4	233	1	0	0	0	0	1	0	0	0	4582	1319	46	4	5168	4	DMD	23	32305751	Missense_Mutation	SNP	G	TCGA-P4-A5EB-01A-11D-A28G-10	18543204	32305751	122964809	136	14259											
BMP15	9210	hgsc.bcm.edu	37	chrX	50658768	50658768	+	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	cttctgcaggtacctggcatAtacagatcctgggctttcct	7	13	9	12	0	1	1	0	0	1	1	3	1	3	1	3	3	3	4	3	3	3	5			TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chrX:50658768A>T	ENST00000252677.3	+	2	340	c.340A>T	c.(340-342)Ata>Tta	p.I114L		NM_005448.2	NP_005439.2	O95972	BMP15_HUMAN	bone morphogenetic protein 15	114					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)					TACCTGGCATATACAGATCCT	0.438																																					p.I114L		Atlas-SNP	.											.	BMP15	62	.	0			c.A340T						PASS	.						95	90	91					X																	50658768		2203	4299	6502	SO:0001583	missense	9210	exon2			TGGCATATACAGA	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.340A>T	chrX.hg19:g.50658768A>T	ENSP00000252677:p.Ile114Leu	81.0	0.0	.		113.0	108.0	.	NM_005448	Q17RM6|Q5JST1|Q9UMS1	Missense_Mutation	SNP	ENST00000252677.3	hg19	CCDS14334.1	.	.	.	.	.	.	.	.	.	.	a	2.291	-0.362548	0.05103	.	.	ENSG00000130385	ENST00000252677	T	0.77489	-1.1	5.42	-3.73	0.04398	.	1.153060	0.05985	N	0.645013	T	0.69006	0.3063	M	0.65975	2.015	0.09310	N	1	B	0.19583	0.037	B	0.16289	0.015	T	0.49214	-0.8963	10	0.10377	T	0.69	.	6.9598	0.24591	0.3592:0.0:0.4995:0.1413	.	114	O95972	BMP15_HUMAN	L	114	ENSP00000252677:I114L	ENSP00000252677:I114L	I	+	1	0	BMP15	50675508	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.129000	0.10515	-0.754000	0.04715	-0.670000	0.03821	ATA	.	.	.	none		0.438	BMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056572.1	NM_005448		T	50658768	A	T	50658768	3	4	233	1	0	0	0	0	1	0	0	0	1458	449	16	5	346	5	BMP15	23	50658768	Missense_Mutation	SNP	A	TCGA-P4-A5EB-01A-11D-A28G-10	18353017	50658768	104611792	137	14260											
UBQLN2	29978	hgsc.bcm.edu	37	chrX	56592091	56592092	+	Frame_Shift_Del	DEL	AA	AA	-																															ctcaacgcaatggggttcttAaaccgtgaagcaaacttgca																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chrX:56592091_56592092delAA	ENST00000338222.5	+	1	2066_2067	c.1785_1786delAA	c.(1783-1788)ttaaacfs	p.N596fs		NM_013444.3	NP_038472.2	Q9UHD9	UBQL2_HUMAN	ubiquilin 2	596	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				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						TGGGGTTCTTAAACCGTGAAGC	0.515																																					p.595_595del	Esophageal Squamous(104;218 1492 6022 10838 28884)	Atlas-Indel,Pindel	.											.	UBQLN2	55	.	0			c.1784_1785del						PASS	.																																			SO:0001589	frameshift_variant	29978	exon1			.	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.1785_1786delAA	chrX.hg19:g.56592091_56592092delAA	ENSP00000345195:p.Asn596fs	106.0	0.0	0		167.0	146.0	0.874251	NM_013444	O94798|Q5D027|Q9H3W6|Q9HAZ4	Frame_Shift_Del	DEL	ENST00000338222.5	hg19	CCDS14374.1																																																																																			.	.	.	none		0.515	UBQLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056891.1	NM_013444		-	56592092	AA	-	56592091	7	5	233	1	0	1	0	1	0	0	0	0	16909	359	13	0	1787	0	UBQLN2	23	56592091	Frame_Shift_Del	DEL	AA	TCGA-P4-A5EB-01A-11D-A28G-10	5933323	56592091	98678469	138	14261											
UPRT	139596	hgsc.bcm.edu	37	chrX	74494317	74494318	+	Frame_Shift_Del	DEL	AG	AG	-																															ggcggctccagcctcaactcAgagggcaacagtggtagtgg																										TCGA-P4-A5EB-01A-11D-A28G-10	TCGA-P4-A5EB-11A-11D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6cf6557-09fb-4516-af87-39037f809609	fa076b69-fed9-4164-af20-7592bff142fd	g.chrX:74494317_74494318delAG	ENST00000373383.4	+	1	395_396	c.228_229delAG	c.(226-231)tcagagfs	p.E77fs	UPRT_ENST00000530743.1_5'Flank|UPRT_ENST00000373379.1_Frame_Shift_Del_p.E77fs|UPRT_ENST00000531704.1_3'UTR	NM_145052.3	NP_659489.1	Q96BW1	UPP_HUMAN	uracil phosphoribosyltransferase (FUR1) homolog (S. cerevisiae)	77					female pregnancy (GO:0007565)|lactation (GO:0007595)|response to insulin (GO:0032868)|UMP biosynthetic process (GO:0006222)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(4)|lung(4)	18						GCCTCAACTCAGAGGGCAACAG	0.639																																					p.76_76del		Pindel	.											.	UPRT	46	.	0			c.227_228del						PASS	.																																			SO:0001589	frameshift_variant	139596	exon1			.	BC015116	CCDS14429.1	Xq13.3	2009-01-14			ENSG00000094841	ENSG00000094841			28334	protein-coding gene	gene with protein product		300656				12477932	Standard	NM_145052		Approved	DKFZp781E1243, MGC23937, FUR1, RP11-311P8.3	uc004ecb.2	Q96BW1	OTTHUMG00000021864	ENST00000373383.4:c.228_229delAG	chrX.hg19:g.74494319_74494320delAG	ENSP00000362481:p.Glu77fs	82.0	0.0	.		146.0	23.0	0.158	NM_145052	Q5JRL1|Q5JRL3|Q68DN0|Q96MW2	Frame_Shift_Del	DEL	ENST00000373383.4	hg19	CCDS14429.1																																																																																			.	.	.	none		0.639	UPRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057278.1	NM_145052		-	74494318	AG	-	74494317	7	5	233	1	0	1	0	1	0	0	0	0	17026	175	7	0	230	0	UPRT	23	74494317	Frame_Shift_Del	DEL	AG	TCGA-P4-A5EB-01A-11D-A28G-10	17902226	74494317	80776243	139	14262											
DCLRE1B	64858	hgsc.bcm.edu	37	chr1	114454514	114454514	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccccactgggattttcagtgCacttaaggtctacagatgag	10	11	10	10	0	2	2	1	1	1	1	2	3	2	3	2	2	2	1	2	2	2	4			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr1:114454514C>T	ENST00000369563.3	+	4	1746	c.1300C>T	c.(1300-1302)Cac>Tac	p.H434Y	DCLRE1B_ENST00000466480.1_Intron	NM_022836.3	NP_073747.1	Q9H816	DCR1B_HUMAN	DNA cross-link repair 1B	434					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|protection from non-homologous end joining at telomere (GO:0031848)|telomere maintenance (GO:0000723)|telomeric 3' overhang formation (GO:0031860)|telomeric loop formation (GO:0031627)	centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)			breast(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(6)|stomach(1)	18	Lung SC(450;0.184)	all_cancers(81;1.46e-05)|all_epithelial(167;2.42e-05)|all_lung(203;0.000353)|Lung NSC(69;0.000518)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		ATTTTCAGTGCACTTAAGGTC	0.473								Other identified genes with known or suspected DNA repair function																													p.H434Y		Atlas-SNP	.											.	DCLRE1B	36	.	0			c.C1300T						PASS	.						168	186	180					1																	114454514		2203	4300	6503	SO:0001583	missense	64858	exon4			TCAGTGCACTTAA	BC029687	CCDS866.1	1p11.1	2010-06-24	2010-06-24		ENSG00000118655	ENSG00000118655			17641	protein-coding gene	gene with protein product	"APOLLO", "PSO2 homolog (S. cerevisiae)"	609683	"DNA cross-link repair 1B (PSO2 homolog, S. cerevisiae)"				Standard	NM_022836		Approved	SNM1B, FLJ12810, FLJ13998	uc001eeg.3	Q9H816	OTTHUMG00000011937	ENST00000369563.3:c.1300C>T	chr1.hg19:g.114454514C>T	ENSP00000358576:p.His434Tyr	135.0	0.0	.		134.0	18.0	.	NM_022836	Q9H9E5	Missense_Mutation	SNP	ENST00000369563.3	hg19	CCDS866.1	.	.	.	.	.	.	.	.	.	.	C	16.27	3.075166	0.55646	.	.	ENSG00000118655	ENST00000369563	T	0.75260	-0.92	5.75	2.18	0.27775	.	1.219440	0.05575	N	0.571775	T	0.42086	0.1187	L	0.27053	0.805	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.42241	-0.9463	10	0.66056	D	0.02	-11.1736	5.1932	0.15220	0.2671:0.6065:0.0:0.1264	.	434	Q9H816	DCR1B_HUMAN	Y	434	ENSP00000358576:H434Y	ENSP00000358576:H434Y	H	+	1	0	DCLRE1B	114256037	0.002000	0.14202	0.004000	0.12327	0.624000	0.37722	0.606000	0.24194	1.186000	0.42985	0.655000	0.94253	CAC	.	.	.	none		0.473	DCLRE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033020.2	NM_022836		T	114454514	C	T	114454514	3	4	234	1	0	0	0	0	1	0	0	0	4297	710	25	2	1314	2	DCLRE1B	1	114454514	Missense_Mutation	SNP	C	TCGA-P4-A5ED-01A-11D-A28G-10		114454514	134796107	1	14263											
MTA3	57504	hgsc.bcm.edu	37	chr2	42886918	42886918	+	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	ttcagtgctgttgggacattCgccagagccctggattgcag	7	11	13	10	1	1	1	1	0	0	1	2	3	1	3	2	2	3	3	2	2	0	4			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr2:42886918C>A	ENST00000405094.1	+	8	618	c.618C>A	c.(616-618)ttC>ttA	p.F206L	MTA3_ENST00000405592.1_Missense_Mutation_p.F150L|MTA3_ENST00000406652.1_Missense_Mutation_p.F150L|MTA3_ENST00000407270.3_Missense_Mutation_p.F206L|MTA3_ENST00000406911.1_Missense_Mutation_p.F206L			Q9BTC8	MTA3_HUMAN	metastasis associated 1 family, member 3	206	ELM2. {ECO:0000255|PROSITE- ProRule:PRU00512}.					intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(9)|ovary(2)|stomach(1)	15						TTGGGACATTCGCCAGAGCCC	0.413																																					p.F206L		Atlas-SNP	.											.	MTA3	39	.	0			c.C618A						PASS	.						78	70	72					2																	42886918		1938	4145	6083	SO:0001583	missense	57504	exon8			GACATTCGCCAGA	AB033092	CCDS46267.1, CCDS62900.1	2p22.1	2013-01-25	2004-12-15		ENSG00000057935	ENSG00000057935		"GATA zinc finger domain containing"	23784	protein-coding gene	gene with protein product		609050	"metastasis associated gene family, member 3"			12705869, 14613024	Standard	NM_001282755		Approved	KIAA1266	uc002rsq.3	Q9BTC8	OTTHUMG00000150452	ENST00000405094.1:c.618C>A	chr2.hg19:g.42886918C>A	ENSP00000385823:p.Phe206Leu	80.0	0.0	.		84.0	5.0	.	NM_020744	Q9NSP2|Q9ULF4	Missense_Mutation	SNP	ENST00000405094.1	hg19		.	.	.	.	.	.	.	.	.	.	C	16.73	3.205367	0.58234	.	.	ENSG00000057935	ENST00000405592;ENST00000406652;ENST00000407270;ENST00000282366;ENST00000406911;ENST00000405094	T;T;T;T;T	0.54866	0.55;0.55;0.61;0.59;0.57	4.96	-7.42	0.01388	.	0.000000	0.85682	D	0.000000	T	0.72645	0.3486	M	0.88105	2.93	0.50171	D	0.999857	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.988;0.994;0.999	T	0.80522	-0.1345	10	0.54805	T	0.06	-18.0256	20.3549	0.98835	0.0:0.0897:0.0:0.9103	.	206;206;150	E7EQY4;Q9BTC8-2;D6W5A2	.;.;.	L	150;150;206;206;206;206	ENSP00000383973:F150L;ENSP00000384249:F150L;ENSP00000385045:F206L;ENSP00000385241:F206L;ENSP00000385823:F206L	ENSP00000282366:F206L	F	+	3	2	MTA3	42740422	0.997000	0.39634	0.147000	0.22382	0.489000	0.33432	0.317000	0.19487	-1.514000	0.01786	-0.252000	0.11476	TTC	.	.	.	none		0.413	MTA3-017	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000318159.1	NM_020744		A	42886918	C	A	42886918	3	1	234	1	0	0	0	0	1	0	0	0	9917	883	31	4	648	4	MTA3	2	42886918	Missense_Mutation	SNP	C	TCGA-P4-A5ED-01A-11D-A28G-10		42886918	200312455	2	14264											
WDSUB1	151525	hgsc.bcm.edu	37	chr2	160139417	160139417	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aacagcagcagtggacagcaTaggtatgaaacttcaatgga	16	7	11	7	0	1	1	1	1	0	0	1	3	1	3	0	3	5	4	0	3	5	3			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr2:160139417T>C	ENST00000409990.3	-	2	420	c.164A>G	c.(163-165)tAt>tGt	p.Y55C	WDSUB1_ENST00000358147.4_Missense_Mutation_p.Y55C|WDSUB1_ENST00000392796.3_Missense_Mutation_p.Y55C|WDSUB1_ENST00000409124.1_Missense_Mutation_p.Y55C|WDSUB1_ENST00000359774.4_Missense_Mutation_p.Y55C	NM_001128213.1	NP_001121685	Q8N9V3	WSDU1_HUMAN	WD repeat, sterile alpha motif and U-box domain containing 1	55							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						GTGGACAGCATAGGTATGAAA	0.443																																					p.Y55C		Atlas-SNP	.											.	WDSUB1	39	.	0			c.A164G						PASS	.						138	135	136					2																	160139417		2203	4300	6503	SO:0001583	missense	151525	exon2			ACAGCATAGGTAT	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.164A>G	chr2.hg19:g.160139417T>C	ENSP00000387078:p.Tyr55Cys	243.0	0.0	.		261.0	27.0	.	NM_152528	Q53TI9|Q8N6N8	Missense_Mutation	SNP	ENST00000409990.3	hg19	CCDS2208.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.360032	0.82353	.	.	ENSG00000196151	ENST00000359774;ENST00000358147;ENST00000392796;ENST00000409990;ENST00000409124	T;T;T;T;T	0.60299	0.2;0.2;0.2;0.2;0.2	5.54	5.54	0.83059	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	0.74359	0.3706	M	0.69185	2.1	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.76353	-0.2990	10	0.56958	D	0.05	.	15.6902	0.77446	0.0:0.0:0.0:1.0	.	55;55;55	Q8N9V3-2;B8ZZF2;Q8N9V3	.;.;WSDU1_HUMAN	C	55	ENSP00000352820:Y55C;ENSP00000350866:Y55C;ENSP00000376545:Y55C;ENSP00000387078:Y55C;ENSP00000386891:Y55C	ENSP00000350866:Y55C	Y	-	2	0	WDSUB1	159847663	1.000000	0.71417	0.989000	0.46669	0.987000	0.75469	7.910000	0.87451	2.115000	0.64714	0.528000	0.53228	TAT	.	.	.	none		0.443	WDSUB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333339.1	NM_152528		C	160139417	T	C	160139417	3	2	234	1	0	0	0	0	1	0	0	0	17353	1406	49	3	1306	3	WDSUB1	2	160139417	Missense_Mutation	SNP	T	TCGA-P4-A5ED-01A-11D-A28G-10	117252499	160139417	83059956	3	14265											
WDFY3	23001	hgsc.bcm.edu	37	chr4	85675021	85675021	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caagatccctcttcttctgaTtgccaaggctgttatgggga	8	13	10	10	0	3	2	0	1	3	1	4	3	4	3	2	3	1	2	2	3	3	4			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr4:85675021T>C	ENST00000295888.4	-	35	5975	c.5568A>G	c.(5566-5568)caA>caG	p.Q1856Q	WDFY3_ENST00000322366.6_Silent_p.Q1856Q	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	1856					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)		CTTCTTCTGATTGCCAAGGCT	0.403																																					p.Q1856Q		Atlas-SNP	.											.	WDFY3	314	.	0			c.A5568G						PASS	.						89	80	83					4																	85675021		2203	4300	6503	SO:0001819	synonymous_variant	23001	exon35			TTCTGATTGCCAA	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.5568A>G	chr4.hg19:g.85675021T>C		127.0	0.0	.		145.0	39.0	.	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Silent	SNP	ENST00000295888.4	hg19	CCDS3609.1																																																																																			.	.	.	none		0.403	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		C	85675021	T	C	85675021	2	2	234	1	0	0	0	0	0	0	0	1	17282	1490	52	3		3	WDFY3	4	85675021	Silent	SNP	T	TCGA-P4-A5ED-01A-11D-A28G-10		85675021	105479255	4	14266											
SNX2	6643	hgsc.bcm.edu	37	chr5	122154607	122154607	+	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	tctagagctttgtctcagctTgcagaggttgaggagaagat	10	12	13	6	0	2	5	1	1	2	4	3	6	2	5	0	2	3	4	0	2	2	4			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr5:122154607T>G	ENST00000379516.2	+	11	1209	c.1101T>G	c.(1099-1101)ctT>ctG	p.L367L	SNX2_ENST00000514949.1_Silent_p.L250L|SNX2_ENST00000510372.1_3'UTR	NM_003100.2	NP_003091.2	O60749	SNX2_HUMAN	sorting nexin 2	367					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)|retromer complex (GO:0030904)	epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|leptin receptor binding (GO:1990460)|phosphatidylinositol binding (GO:0035091)|transferrin receptor binding (GO:1990459)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(2)|prostate(1)|skin(1)	19		all_cancers(142;1.14e-44)|all_lung(232;1.03e-13)|Lung NSC(810;2.5e-13)|Breast(839;0.000812)|Myeloproliferative disorder(839;0.0122)|Prostate(80;0.0235)|all_hematologic(541;0.0592)|all_neural(839;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	all cancers(49;2.13e-24)|Epithelial(69;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(64;5.6e-11)|BRCA - Breast invasive adenocarcinoma(61;0.00013)|GBM - Glioblastoma multiforme(465;0.000357)|COAD - Colon adenocarcinoma(49;0.000887)|Lung(113;0.0109)		TGTCTCAGCTTGCAGAGGTTG	0.393																																					p.L367L		Atlas-SNP	.											.	SNX2	42	.	0			c.T1101G						PASS	.						124	117	119					5																	122154607		2203	4300	6503	SO:0001819	synonymous_variant	6643	exon11			TCAGCTTGCAGAG	AF043453	CCDS34217.1, CCDS64234.1	5q23.2	2011-05-03			ENSG00000205302	ENSG00000205302		"Sorting nexins"	11173	protein-coding gene	gene with protein product		605929				9819414	Standard	NM_003100		Approved		uc003kte.4	O60749	OTTHUMG00000163020	ENST00000379516.2:c.1101T>G	chr5.hg19:g.122154607T>G		100.0	0.0	.		123.0	7.0	.	NM_003100	B3KN44|B4DEK4|B7Z408|O43650|P82862|Q53XK8|Q597H6|Q9BTS8	Silent	SNP	ENST00000379516.2	hg19	CCDS34217.1																																																																																			.	.	.	none		0.393	SNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371392.1	NM_003100		G	122154607	T	G	122154607	2	3	234	1	0	0	0	0	0	0	0	1	14904	1799	63	5		5	SNX2	5	122154607	Silent	SNP	T	TCGA-P4-A5ED-01A-11D-A28G-10		122154607	58760653	5	14267											
SERPINB6	5269	hgsc.bcm.edu	37	chr6	2955761	2955761	+	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	gagcaagtatgacttactgaGaggaaatcacaagacttttc	15	10	9	7	0	1	3	1	2	0	2	2	6	1	4	0	1	2	2	0	1	5	4			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr6:2955761G>C	ENST00000380520.1	-	2	2303	c.309C>G	c.(307-309)ctC>ctG	p.L103L	SERPINB6_ENST00000335686.5_Silent_p.L103L|SERPINB6_ENST00000380539.1_Silent_p.L103L|SERPINB6_ENST00000380524.1_Silent_p.L103L|SERPINB6_ENST00000380529.1_Silent_p.L103L|SERPINB6_ENST00000380546.3_Silent_p.L103L			P35237	SPB6_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 6	103					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)|protein complex (GO:0043234)	protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|stomach(1)|upper_aerodigestive_tract(2)	17	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Drotrecogin alfa(DB00055)	GACTTACTGAGAGGAAATCAC	0.493																																					p.L122L		Atlas-SNP	.											.	SERPINB6	31	.	0			c.C366G						PASS	.						78	78	78					6																	2955761		2203	4300	6503	SO:0001819	synonymous_variant	5269	exon3			TACTGAGAGGAAA	Z22658	CCDS4479.1, CCDS75386.1, CCDS75387.1	6p25.2	2014-02-18	2005-08-18		ENSG00000124570	ENSG00000124570		"Serine (or cysteine) peptidase inhibitors"	8950	protein-coding gene	gene with protein product	"cytoplasmic antiproteinase"	173321	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 6", "deafness, autosomal recessive 91"	PI6, DFNB91		8415716, 9858835, 20451170, 24172014	Standard	NM_004568		Approved	PTI, CAP	uc031smo.1	P35237	OTTHUMG00000016170	ENST00000380520.1:c.309C>G	chr6.hg19:g.2955761G>C		88.0	0.0	.		94.0	9.0	.	NM_001271823	B2RBA8|Q59F97|Q5TD06|Q7Z2Y7|Q96J44|Q9UDI7	Silent	SNP	ENST00000380520.1	hg19	CCDS4479.1																																																																																			.	.	.	none		0.493	SERPINB6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043422.1			C	2955761	G	C	2955761	2	2	234	1	0	0	0	0	0	0	0	1	14118	929	33	4		4	SERPINB6	6	2955761	Silent	SNP	G	TCGA-P4-A5ED-01A-11D-A28G-10		2955761	168159306	6	14268											
NBN	4683	hgsc.bcm.edu	37	chr8	90967743	90967743	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cattctgaatttttgttccaTtttggagactttgatttctt	7	22	6	6	0	2	3	0	2	2	1	3	4	3	3	1	1	0	1	1	1	1	9			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr8:90967743T>C	ENST00000265433.3	-	10	1319	c.1165A>G	c.(1165-1167)Atg>Gtg	p.M389V	NBN_ENST00000409330.1_Missense_Mutation_p.M307V	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	389	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)			TTTTGTTCCATTTTGGAGACT	0.338								Homologous recombination																													p.M389V		Atlas-SNP	.											.	NBN	86	.	0			c.A1165G						PASS	.						104	98	100					8																	90967743		2203	4300	6503	SO:0001583	missense	4683	exon10			GTTCCATTTTGGA	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.1165A>G	chr8.hg19:g.90967743T>C	ENSP00000265433:p.Met389Val	35.0	0.0	.		42.0	14.0	.	NM_002485	B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Missense_Mutation	SNP	ENST00000265433.3	hg19	CCDS6249.1	.	.	.	.	.	.	.	.	.	.	T	0.019	-1.453422	0.01071	.	.	ENSG00000104320	ENST00000265433;ENST00000409330;ENST00000452387	T;T	0.56941	2.1;0.43	5.45	-1.76	0.08006	.	0.952676	0.09006	N	0.862316	T	0.20659	0.0497	N	0.05383	-0.06	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.24119	-1.0169	10	0.02654	T	1	3.3137	1.3277	0.02128	0.1323:0.1639:0.2892:0.4145	.	389;389	A6H8Y5;O60934	.;NBN_HUMAN	V	389;307;389	ENSP00000265433:M389V;ENSP00000386924:M307V	ENSP00000265433:M389V	M	-	1	0	NBN	91036919	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.078000	0.14761	-0.233000	0.09797	-0.321000	0.08615	ATG	.	.	.	none		0.338	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	NM_001024688		C	90967743	T	C	90967743	3	2	234	1	0	0	0	0	1	0	0	0	10198	1493	52	3	1127	3	NBN	8	90967743	Missense_Mutation	SNP	T	TCGA-P4-A5ED-01A-11D-A28G-10		90967743	55396279	7	14269											
TAF1L	138474	hgsc.bcm.edu	37	chr9	32633310	32633310	+	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	tcaagtgcctgcagtaattgGccaggatggagagagcccaa	12	7	13	9	0	1	1	1	0	0	1	1	4	1	3	3	3	3	2	3	3	3	2			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr9:32633310G>A	ENST00000242310.4	-	1	2357	c.2268C>T	c.(2266-2268)ggC>ggT	p.G756G	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	756					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)		GCAGTAATTGGCCAGGATGGA	0.443																																					p.G756G		Atlas-SNP	.											.	TAF1L	382	.	0			c.C2268T						PASS	.						184	180	182					9																	32633310		2203	4300	6503	SO:0001819	synonymous_variant	138474	exon1			TAATTGGCCAGGA	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.2268C>T	chr9.hg19:g.32633310G>A		254.0	0.0	.		254.0	20.0	.	NM_153809	Q0VG57	Silent	SNP	ENST00000242310.4	hg19	CCDS35003.1																																																																																			.	.	.	none		0.443	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			A	32633310	G	A	32633310	2	1	234	1	0	0	0	0	0	0	0	1	15535	1190	42	2		2	TAF1L	9	32633310	Silent	SNP	G	TCGA-P4-A5ED-01A-11D-A28G-10		32633310	108580121	8	14270											
DCAF10	79269	hgsc.bcm.edu	37	chr9	37800965	37800965	+	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	caggcagcagccaccgggccGccctcgccactacatcccgg	7	3	11	20	4	0	0	0	0	0	0	2	0	1	0	6	3	3	2	6	3	1	1	rs373032176		TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr9:37800965G>T	ENST00000377724.3	+	1	467	c.102G>T	c.(100-102)ccG>ccT	p.P34P	DCAF10_ENST00000242323.7_Silent_p.P34P|RP11-613M10.9_ENST00000540557.1_Intron	NM_024345.3	NP_077321.3	Q5QP82	DCA10_HUMAN	DDB1 and CUL4 associated factor 10	34	Pro-rich.				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						CCACCGGGCCGCCCTCGCCAC	0.761													G|||	1	0.000199681	0	0	5008	,	,		10350	0		0.001	False		,,,				2504	0				p.P34P		Atlas-SNP	.											.	DCAF10	31	.	0			c.G102T						PASS	.	G		2,2882		0,2,1440	3	4	3		102	-2.9	0.1	9		3	5,6809		0,5,3402	no	coding-synonymous	DCAF10	NM_024345.3		0,7,4842	TT,TG,GG		0.0734,0.0693,0.0722		34/560	37800965	7,9691	1442	3407	4849	SO:0001819	synonymous_variant	79269	exon1			CGGGCCGCCCTCG	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.102G>T	chr9.hg19:g.37800965G>T		0.0	0.0	.		12.0	8.0	.	NM_024345	A4VCJ5|Q32NE2|Q8N2Q5|Q96ET5|Q9BTQ5|Q9H5P6	Silent	SNP	ENST00000377724.3	hg19	CCDS6613.2																																																																																			.	.	.	weak		0.761	DCAF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052485.2	NM_024345		T	37800965	G	T	37800965	2	4	234	1	0	0	0	0	0	0	0	1	4263	1074	38	4		4	DCAF10	9	37800965	Silent	SNP	G	TCGA-P4-A5ED-01A-11D-A28G-10	5167655	37800965	103412466	9	14271											
B3GNT6	192134	hgsc.bcm.edu	37	chr11	76751497	76751497	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcgcgcggccgcccgccAcaccccgctcttccccatcg	3	5	9	24	7	1	0	0	0	1	0	3	0	2	0	8	1	1	1	8	1	0	1	rs559157215	byFrequency	TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr11:76751497A>G	ENST00000533140.1	+	2	1040	c.902A>G	c.(901-903)cAc>cGc	p.H301R	B3GNT6_ENST00000421061.1_Intron|B3GNT6_ENST00000354301.5_Missense_Mutation_p.H301R			O43505	B3GN1_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6 (core 3 synthase)	0					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|poly-N-acetyllactosamine biosynthetic process (GO:0030311)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity (GO:0008532)			central_nervous_system(1)|kidney(2)|lung(4)|prostate(1)	8						gccgcccgccACACCCCGCTC	0.756													A|||	21	0.00419329	8e-04	0.0288	5008	,	,		10513	0		0	False		,,,				2504	0				p.H301R		Atlas-SNP	.											.	B3GNT6	27	.	0			c.A902G						PASS	.																																			SO:0001583	missense	192134	exon2			CCCGCCACACCCC	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.902A>G	chr11.hg19:g.76751497A>G	ENSP00000435352:p.His301Arg	2.0	0.0	.		8.0	4.0	.	NM_138706	Q4TTN0	Missense_Mutation	SNP	ENST00000533140.1	hg19	CCDS53681.1	.	.	.	.	.	.	.	.	.	.	A	1.535	-0.543236	0.04053	.	.	ENSG00000198488	ENST00000533140;ENST00000354301	T;T	0.44083	0.93;0.93	2.89	0.53	0.17102	.	0.656353	0.15442	N	0.262162	T	0.21921	0.0528	N	0.21097	0.63	0.09310	N	0.999997	B	0.02656	0.0	B	0.09377	0.004	T	0.24368	-1.0162	10	0.11794	T	0.64	.	6.0489	0.19775	0.753:0.0:0.247:0.0	.	301	Q6ZMB0	B3GN6_HUMAN	R	301	ENSP00000435352:H301R;ENSP00000346256:H301R	ENSP00000346256:H301R	H	+	2	0	B3GNT6	76429145	0.000000	0.05858	0.007000	0.13788	0.109000	0.19521	-0.871000	0.04223	0.080000	0.16959	0.374000	0.22700	CAC	.	.	.	none		0.756	B3GNT6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000382740.2	NM_138706		G	76751497	A	G	76751497	3	3	234	1	0	0	0	0	1	0	0	0	1261	159	6	3	904	3	B3GNT6	11	76751497	Missense_Mutation	SNP	A	TCGA-P4-A5ED-01A-11D-A28G-10		76751497	58255019	10	14272											
GRAMD1B	57476	hgsc.bcm.edu	37	chr11	123476178	123476178	+	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	ccacagggagcagtgaggccCccgtctcggtatgggcagtc	7	6	15	13	2	1	1	0	1	1	0	3	2	1	2	3	4	1	3	3	4	1	1			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr11:123476178C>T	ENST00000529750.1	+	9	1213	c.886C>T	c.(886-888)Ccc>Tcc	p.P296S	GRAMD1B_ENST00000450171.2_5'Flank|GRAMD1B_ENST00000456860.2_Missense_Mutation_p.P303S|GRAMD1B_ENST00000322282.7_Missense_Mutation_p.P296S	NM_020716.1	NP_065767.1	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	296						integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)		CAGTGAGGCCCCCGTCTCGGT	0.557																																					p.P296S		Atlas-SNP	.											.	GRAMD1B	122	.	0			c.C886T						PASS	.						142	149	147					11																	123476178		2083	4200	6283	SO:0001583	missense	57476	exon9			GAGGCCCCCGTCT	AB033027	CCDS53720.1, CCDS66253.1, CCDS66254.1	11q24.1	2005-11-02				ENSG00000023171			29214	protein-coding gene	gene with protein product						10574462	Standard	NM_001286564		Approved	KIAA1201	uc001pyx.2	Q3KR37		ENST00000529750.1:c.886C>T	chr11.hg19:g.123476178C>T	ENSP00000436500:p.Pro296Ser	121.0	0.0	.		147.0	45.0	.	NM_020716	Q6UW85|Q9ULL9	Missense_Mutation	SNP	ENST00000529750.1	hg19	CCDS53720.1	.	.	.	.	.	.	.	.	.	.	C	19.90	3.911935	0.72983	.	.	ENSG00000023171	ENST00000539133;ENST00000456860;ENST00000322282;ENST00000529750;ENST00000529432;ENST00000534764	T;T;T;T;T	0.30714	1.92;1.93;1.93;1.92;1.52	5.03	4.11	0.48088	.	0.000000	0.85682	D	0.000000	T	0.31009	0.0783	L	0.34521	1.04	0.58432	D	0.999998	P;P;D;B	0.57899	0.913;0.734;0.981;0.027	B;B;P;B	0.52109	0.424;0.356;0.69;0.065	T	0.02431	-1.1160	10	0.13470	T	0.59	.	13.3208	0.60432	0.0:0.9228:0.0:0.0772	.	256;303;296;303	B7Z4N9;F5H572;Q3KR37;E7EPH8	.;.;GRM1B_HUMAN;.	S	303;303;296;296;256;292	ENSP00000402457:P303S;ENSP00000325628:P296S;ENSP00000436500:P296S;ENSP00000432987:P256S;ENSP00000434214:P292S	ENSP00000325628:P296S	P	+	1	0	GRAMD1B	122981388	0.994000	0.37717	0.842000	0.33263	0.898000	0.52572	3.919000	0.56439	1.112000	0.41740	0.305000	0.20034	CCC	.	.	.	none		0.557	GRAMD1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387404.2	XM_370660		T	123476178	C	T	123476178	3	4	234	1	0	0	0	0	1	0	0	0	6755	623	22	2	920	2	GRAMD1B	11	123476178	Missense_Mutation	SNP	C	TCGA-P4-A5ED-01A-11D-A28G-10	46724681	123476178	11530338	11	14273											
BRAP	8315	hgsc.bcm.edu	37	chr12	112096635	112096635	+	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	tgttttacttgcaaccagtcGatgaacatagttatctacag	12	14	7	8	1	1	1	0	1	1	0	2	2	1	1	1	0	5	3	1	0	6	6			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr12:112096635G>A	ENST00000327551.6	-	9	1176	c.1036C>T	c.(1036-1038)Cga>Tga	p.R346*	BRAP_ENST00000419234.4_Nonsense_Mutation_p.R376*|BRAP_ENST00000539060.1_Nonsense_Mutation_p.R197*			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						GCAACCAGTCGATGAACATAG	0.353																																					p.R376X	Pancreas(146;846 1904 7830 25130 26065)	Atlas-SNP	.											BRAP,NS,carcinoma,0,1	BRAP	42	.	0			c.C1126T						PASS	.						129	119	122					12																	112096635		2203	4300	6503	SO:0001587	stop_gained	8315	exon9			CCAGTCGATGAAC	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.1036C>T	chr12.hg19:g.112096635G>A	ENSP00000330813:p.Arg346*	78.0	0.0	.		80.0	5.0	.	NM_006768	B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Nonsense_Mutation	SNP	ENST00000327551.6	hg19		.	.	.	.	.	.	.	.	.	.	G	36	5.951877	0.97139	.	.	ENSG00000089234	ENST00000419234;ENST00000539060;ENST00000327551;ENST00000547043	.	.	.	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.1227	19.4174	0.94706	0.0:0.0:1.0:0.0	.	.	.	.	X	376;197;346;158	.	ENSP00000330813:R346X	R	-	1	2	BRAP	110581018	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.147000	0.94646	2.606000	0.88127	0.650000	0.86243	CGA	.	.	.	none		0.353	BRAP-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404994.2			A	112096635	G	A	112096635	4	1	234	1	0	0	0	0	0	1	0	0	1499	1066	37	1	668	1	BRAP	12	112096635	Nonsense_Mutation	SNP	G	TCGA-P4-A5ED-01A-11D-A28G-10		112096635	21755260	12	14274											
SEL1L	6400	hgsc.bcm.edu	37	chr14	81969202	81969202	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttggtatggttcatgcttgCtgccttttggagataccgat	6	17	11	7	1	1	1	1	0	0	1	1	3	1	1	2	3	4	4	2	3	2	7			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr14:81969202C>T	ENST00000336735.4	-	6	756	c.640G>A	c.(640-642)Gca>Aca	p.A214T	SEL1L_ENST00000555824.1_Missense_Mutation_p.A214T	NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)	214	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)		TTCATGCTTGCTGCCTTTTGG	0.363																																					p.A214T		Atlas-SNP	.											.	SEL1L	67	.	0			c.G640A						PASS	.						146	139	142					14																	81969202		2203	4300	6503	SO:0001583	missense	6400	exon6			TGCTTGCTGCCTT		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.640G>A	chr14.hg19:g.81969202C>T	ENSP00000337053:p.Ala214Thr	61.0	0.0	.		79.0	22.0	.	NM_001244984	Q6UWT6|Q9P1T9|Q9UHK7	Missense_Mutation	SNP	ENST00000336735.4	hg19	CCDS9876.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.191863	0.78902	.	.	ENSG00000071537	ENST00000336735;ENST00000555824	T;T	0.58940	0.35;0.3	5.45	5.45	0.79879	Tetratricopeptide-like helical (1);	0.104952	0.64402	D	0.000004	T	0.71937	0.3399	M	0.66939	2.045	0.80722	D	1	D;D	0.67145	0.985;0.996	D;D	0.64042	0.92;0.921	T	0.74450	-0.3661	10	0.87932	D	0	.	14.4932	0.67665	0.1468:0.8532:0.0:0.0	.	214;214	Q9UBV2;Q9UBV2-2	SE1L1_HUMAN;.	T	214	ENSP00000337053:A214T;ENSP00000450709:A214T	ENSP00000337053:A214T	A	-	1	0	SEL1L	81038955	1.000000	0.71417	0.999000	0.59377	0.746000	0.42486	4.282000	0.58971	2.719000	0.93026	0.655000	0.94253	GCA	.	.	.	none		0.363	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413325.1	NM_005065		T	81969202	C	T	81969202	3	4	234	1	0	0	0	0	1	0	0	0	14023	797	28	2	1808	2	SEL1L	14	81969202	Missense_Mutation	SNP	C	TCGA-P4-A5ED-01A-11D-A28G-10		81969202	25380338	13	14275											
HS3ST4	9951	hgsc.bcm.edu	37	chr16	26147018	26147018	+	Frame_Shift_Del	DEL	A	A	-																															caaatgaggctcccaagcgcAttcactccatggccaaggac																										TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr16:26147018delA	ENST00000331351.5	+	2	1212	c.820delA	c.(820-822)attfs	p.I274fs	HS3ST4_ENST00000475436.1_3'UTR	NM_006040.2	NP_006031.2	Q9Y661	HS3S4_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	274					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)		TCCCAAGCGCATTCACTCCAT	0.498																																					p.R273fs		Atlas-INDEL	.											.	HS3ST4	120	.	0			c.819delC						PASS	.						122	111	115					16																	26147018		1568	3582	5150	SO:0001589	frameshift_variant	9951	exon2			.	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.820delA	chr16.hg19:g.26147018delA	ENSP00000330606:p.Ile274fs	78.0	0.0	0		112.0	12.0	0.107143	NM_006040	Q5QI42|Q8NDC2	Frame_Shift_Del	DEL	ENST00000331351.5	hg19	CCDS53995.1																																																																																			.	.	.	none		0.498	HS3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133286.2	NM_006040		-	26147018	A	-	26147018	7	5	234	1	0	1	0	1	0	0	0	0	7374	217	8	0	826	0	HS3ST4	16	26147018	Frame_Shift_Del	DEL	A	TCGA-P4-A5ED-01A-11D-A28G-10		26147018	64207735	14	14276	144	3									
HS3ST4	9951	hgsc.bcm.edu	37	chr16	26147021	26147023	+	In_Frame_Del	DEL	CAC	CAC	-																															atgaggctcccaagcgcattCactccatggccaaggacatc																										TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	CAC	CAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr16:26147021_26147023delCAC	ENST00000331351.5	+	2	1215_1217	c.823_825delCAC	c.(823-825)cacdel	p.H275del	HS3ST4_ENST00000475436.1_3'UTR	NM_006040.2	NP_006031.2	Q9Y661	HS3S4_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	275					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)		CAAGCGCATTCACTCCATGGCCA	0.498																																					p.274_275del		Atlas-INDEL	.											.	HS3ST4	120	.	0			c.822_824del						PASS	.																																			SO:0001651	inframe_deletion	9951	exon2			.	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.823_825delCAC	chr16.hg19:g.26147021_26147023delCAC	ENSP00000330606:p.His275del	80.0	0.0	0		115.0	12.0	0.104348	NM_006040	Q5QI42|Q8NDC2	In_Frame_Del	DEL	ENST00000331351.5	hg19	CCDS53995.1																																																																																			.	.	.	none		0.498	HS3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133286.2	NM_006040		-	26147023	CAC	-	26147021	7	5	234	1	0	1	0	1	0	0	0	0	7374	826	29	0	829	0	HS3ST4	16	26147021	In_Frame_Del	DEL	CAC	TCGA-P4-A5ED-01A-11D-A28G-10	3	26147021	64207732	15	14277	144	3									
HS3ST4	9951	hgsc.bcm.edu	37	chr16	26147022	26147025	+	Frame_Shift_Del	DEL	ACTC	ACTC	-																															tgaggctcccaagcgcattcActccatggccaaggacatca																										TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	ACTC	ACTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr16:26147022_26147025delACTC	ENST00000331351.5	+	2	1216_1219	c.824_827delACTC	c.(823-828)cactccfs	p.HS275fs	HS3ST4_ENST00000475436.1_3'UTR	NM_006040.2	NP_006031.2	Q9Y661	HS3S4_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	275					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)		AAGCGCATTCACTCCATGGCCAAG	0.505																																					p.275_276del		Pindel	.											.	HS3ST4	120	.	0			c.823_826del						PASS	.																																			SO:0001589	frameshift_variant	9951	exon2			.	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.824_827delACTC	chr16.hg19:g.26147022_26147025delACTC	ENSP00000330606:p.His275fs	82.0	0.0	.		117.0	10.0	0.085	NM_006040	Q5QI42|Q8NDC2	Frame_Shift_Del	DEL	ENST00000331351.5	hg19	CCDS53995.1																																																																																			.	.	.	none		0.505	HS3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133286.2	NM_006040		-	26147025	ACTC	-	26147022	7	5	234	1	0	1	0	1	0	0	0	0	7374	159	6	0	830	0	HS3ST4	16	26147022	Frame_Shift_Del	DEL	ACTC	TCGA-P4-A5ED-01A-11D-A28G-10	1	26147022	64207731	16	14278	144	3									
NLRP12	91662	hgsc.bcm.edu	37	chr19	54313633	54313633	+	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	ctgcagtggtggtcctggacGtctgtctcaacagcccccca	6	9	11	15	1	2	0	1	0	2	0	4	1	3	1	4	3	3	1	4	3	1	0			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr19:54313633G>T	ENST00000324134.6	-	3	1448	c.1280C>A	c.(1279-1281)aCg>aAg	p.T427K	NLRP12_ENST00000535162.1_Missense_Mutation_p.T427K|NLRP12_ENST00000345770.5_Missense_Mutation_p.T427K|NLRP12_ENST00000391772.1_Missense_Mutation_p.T427K|NLRP12_ENST00000354278.3_Missense_Mutation_p.T427K|NLRP12_ENST00000351894.4_Missense_Mutation_p.T427K|NLRP12_ENST00000391773.1_Missense_Mutation_p.T427K|NLRP12_ENST00000391775.3_Missense_Mutation_p.T427K	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	427	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)		GGTCCTGGACGTCTGTCTCAA	0.642																																					p.T427N		Atlas-SNP	.											NLRP12,colon,carcinoma,0,1	NLRP12	236	.	0			c.C1280A						PASS	.						92	91	92					19																	54313633		2203	4300	6503	SO:0001583	missense	91662	exon3			CTGGACGTCTGTC	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.1280C>A	chr19.hg19:g.54313633G>T	ENSP00000319377:p.Thr427Lys	41.0	0.0	.		49.0	2.0	.	NM_144687	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Missense_Mutation	SNP	ENST00000324134.6	hg19	CCDS12864.1	.	.	.	.	.	.	.	.	.	.	G	13.49	2.253579	0.39797	.	.	ENSG00000142405	ENST00000324134;ENST00000535162;ENST00000351894;ENST00000354278;ENST00000391775;ENST00000391773;ENST00000345770;ENST00000391772	D;D;D;D;D;D;D	0.83914	-1.78;-1.78;-1.78;-1.78;-1.78;-1.78;-1.78	4.77	1.33	0.21861	NACHT nucleoside triphosphatase (1);	0.322809	0.22246	N	0.062616	T	0.77691	0.4168	M	0.77616	2.38	0.09310	N	1	P;P;P;P	0.50443	0.935;0.835;0.835;0.752	B;B;B;B	0.38842	0.264;0.264;0.264;0.283	T	0.70831	-0.4765	10	0.66056	D	0.02	.	5.5314	0.16987	0.1844:0.1613:0.6542:0.0	.	427;427;427;427	F2Z321;A8K407;A8MTQ2;P59046	.;.;.;NAL12_HUMAN	K	427	ENSP00000319377:T427K;ENSP00000438030:T427K;ENSP00000340473:T427K;ENSP00000346231:T427K;ENSP00000375655:T427K;ENSP00000375653:T427K;ENSP00000375652:T427K	ENSP00000319377:T427K	T	-	2	0	NLRP12	59005445	0.000000	0.05858	0.002000	0.10522	0.515000	0.34225	0.072000	0.14617	0.174000	0.19809	-0.344000	0.07964	ACG	.	.	.	none		0.642	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687		T	54313633	G	T	54313633	3	4	234	1	0	0	0	0	1	0	0	0	10481	1145	40	4	2033	4	NLRP12	19	54313633	Missense_Mutation	SNP	G	TCGA-P4-A5ED-01A-11D-A28G-10		54313633	4815350	17	14279											
ZNF628	89887	hgsc.bcm.edu	37	chr19	55993264	55993264	+	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	cgcccccgccccgggtaccgCctccgcggccccgccccccc	1	2	10	28	7	0	0	0	0	0	0	1	0	1	0	12	2	1	1	12	2	1	1			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chr19:55993264C>T	ENST00000598519.1	+	3	1257	c.704C>T	c.(703-705)gCc>gTc	p.A235V	ZNF628_ENST00000391718.2_Missense_Mutation_p.A231V			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	235	Pro-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)		ccgggtaccgcctccgcggcc	0.766																																					p.A235V		Atlas-SNP	.											.	ZNF628	75	.	0			c.C704T						PASS	.						3	4	3					19																	55993264		1658	3351	5009	SO:0001583	missense	89887	exon3			GTACCGCCTCCGC	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.704C>T	chr19.hg19:g.55993264C>T	ENSP00000469591:p.Ala235Val	1.0	0.0	.		7.0	5.0	.	NM_033113	Q86X34	Missense_Mutation	SNP	ENST00000598519.1	hg19	CCDS33116.3	.	.	.	.	.	.	.	.	.	.	.	7.048	0.563911	0.13498	.	.	ENSG00000197483	ENST00000391718	T	0.08807	3.05	3.0	1.93	0.25924	.	.	.	.	.	T	0.06325	0.0163	N	0.19112	0.55	0.09310	N	1	B	0.19445	0.036	B	0.24701	0.055	T	0.35919	-0.9769	9	0.54805	T	0.06	-3.6893	8.11	0.30909	0.0:0.7504:0.2496:0.0	.	231	Q5EBL2	ZN628_HUMAN	V	231	ENSP00000375598:A231V	ENSP00000375598:A231V	A	+	2	0	ZNF628	60685076	0.734000	0.28142	0.009000	0.14445	0.152000	0.21847	0.878000	0.28126	0.836000	0.34901	0.459000	0.35465	GCC	.	.	.	none		0.766	ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317934.2	XM_058964		T	55993264	C	T	55993264	3	4	234	1	0	0	0	0	1	0	0	0	18064	739	26	2	694	2	ZNF628	19	55993264	Missense_Mutation	SNP	C	TCGA-P4-A5ED-01A-11D-A28G-10	1679631	55993264	3135719	18	14280											
KIF4A	24137	hgsc.bcm.edu	37	chrX	69595071	69595071	+	Missense_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	taggttgagtgagcgccgccGcaaacgtctccaggagctgg	8	7	15	11	4	1	2	0	2	1	0	2	3	1	3	3	3	3	3	3	3	2	2			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chrX:69595071G>A	ENST00000374403.3	+	17	1878	c.1796G>A	c.(1795-1797)cGc>cAc	p.R599H	KIF4A_ENST00000374388.3_Missense_Mutation_p.R599H	NM_012310.4	NP_036442.3	O95239	KIF4A_HUMAN	kinesin family member 4A	599					anterograde axon cargo transport (GO:0008089)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle organization (GO:0006996)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(6)|endometrium(9)|kidney(3)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	51						GAGCGCCGCCGCAAACGTCTC	0.468																																					p.R599H		Atlas-SNP	.											.	KIF4A	118	.	0			c.G1796A						PASS	.						67	58	61					X																	69595071		2203	4300	6503	SO:0001583	missense	24137	exon17			GCCGCCGCAAACG	AF179308	CCDS14401.1	Xq13.1	2008-08-11			ENSG00000090889	ENSG00000090889		"Kinesins"	13339	protein-coding gene	gene with protein product	"chromokinesin"	300521				10773663	Standard	NM_012310		Approved	KIF4-G1, KIF4, HSA271784, FLJ12530, FLJ12655, FLJ14204, FLJ20631	uc004dyg.3	O95239	OTTHUMG00000021775	ENST00000374403.3:c.1796G>A	chrX.hg19:g.69595071G>A	ENSP00000363524:p.Arg599His	102.0	0.0	.		120.0	5.0	.	NM_012310	B2R7V5|D3DVU4|Q86TN3|Q86XX7|Q9NNY6|Q9NY24|Q9UMW3	Missense_Mutation	SNP	ENST00000374403.3	hg19	CCDS14401.1	.	.	.	.	.	.	.	.	.	.	G	18.87	3.716466	0.68844	.	.	ENSG00000090889	ENST00000374388;ENST00000374403	T;T	0.70869	2.3;-0.52	5.53	5.53	0.82687	.	0.000000	0.56097	D	0.000035	T	0.76292	0.3967	M	0.83483	2.645	0.80722	D	1	B;B	0.28713	0.143;0.22	B;B	0.33254	0.038;0.16	T	0.76394	-0.2975	10	0.52906	T	0.07	.	17.3242	0.87243	0.0:0.0:1.0:0.0	.	599;599	O95239;O95239-2	KIF4A_HUMAN;.	H	599	ENSP00000363509:R599H;ENSP00000363524:R599H	ENSP00000363509:R599H	R	+	2	0	KIF4A	69511796	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.912000	0.92726	2.562000	0.86427	0.600000	0.82982	CGC	.	.	.	none		0.468	KIF4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057068.1	NM_012310		A	69595071	G	A	69595071	3	1	234	1	0	0	0	0	1	0	0	0	8310	1087	38	1	1858	1	KIF4A	23	69595071	Missense_Mutation	SNP	G	TCGA-P4-A5ED-01A-11D-A28G-10		69595071	85675489	19	14281											
RNF128	79589	hgsc.bcm.edu	37	chrX	106034465	106034465	+	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	ggaacacgtgcagtcaacaaGtaagcatcatactaaaggtt	16	8	9	8	1	2	0	2	0	0	0	2	1	2	1	0	2	5	4	0	2	7	4			TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chrX:106034465G>A	ENST00000255499.2	+	6	1403		c.e6+1		RNF128_ENST00000324342.3_Splice_Site	NM_194463.1	NP_919445.1	Q8TEB7	RN128_HUMAN	ring finger protein 128, E3 ubiquitin protein ligase						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						CAGTCAACAAGTAAGCATCAT	0.453																																					.		Atlas-SNP	.											.	RNF128	74	.	0			c.1075+1G>A						PASS	.						172	148	156					X																	106034465		2203	4300	6503	SO:0001630	splice_region_variant	79589	exon6			CAACAAGTAAGCA	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.1153+1G>A	chrX.hg19:g.106034465G>A		141.0	0.0	.		136.0	33.0	.	NM_024539	A0PJI4|Q6PH80|Q6ZTJ8|Q96RF3|Q9H5E4	Splice_Site	SNP	ENST00000255499.2	hg19	CCDS14521.1	.	.	.	.	.	.	.	.	.	.	G	19.20	3.781964	0.70222	.	.	ENSG00000133135	ENST00000324342;ENST00000255499	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.497	0.67694	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RNF128	105921121	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	6.181000	0.71988	2.165000	0.68154	0.506000	0.49869	.	.	.	.	none		0.453	RNF128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057804.1	NM_024539	Intron	A	106034465	G	A	106034465	5	1	234	1	0	0	0	0	0	0	1	0	13449	1043	36	2	1586	2	RNF128	23	106034465	Splice_Site	SNP	G	TCGA-P4-A5ED-01A-11D-A28G-10	36439394	106034465	49236095	20	14282											
ZIC3	7547	hgsc.bcm.edu	37	chrX	136648984	136648985	+	In_Frame_Ins	INS	-	-	CGC																															cccttcggggactcaacccaINScgccgccgccgccgccgccg																										TCGA-P4-A5ED-01A-11D-A28G-10	TCGA-P4-A5ED-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	79d11c73-74ff-468d-b0e9-b8ddc72de15a	1bc9f60c-2dc6-4bfe-9965-6014f49dc9ac	g.chrX:136648984_136648985insCGC	ENST00000287538.5	+	1	684_685	c.134_135insCGC	c.(133-138)cacgcc>caCGCcgcc	p.55_56insA	RP1-137H15.2_ENST00000456631.1_RNA|RP1-137H15.2_ENST00000442841.1_RNA|ZIC3_ENST00000370606.3_In_Frame_Ins_p.55_56insA	NM_003413.3	NP_003404.1	O60481	ZIC3_HUMAN	Zic family member 3	55	Poly-Ala.				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)					GACTCAACCCAcgccgccgccg	0.718																																					p.H45delinsHA		Atlas-INDEL	.											.	ZIC3	93	.	0			c.134_135insCGC						PASS	.																																			SO:0001652	inframe_insertion	7547	exon1			.	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.159_161dupCGC	chrX.hg19:g.136648991_136648993dupCGC	ENSP00000287538:p.Ala55_Ala55dup	6.0	1.0	0.166667		24.0	10.0	0.416667	NM_003413	B2CNW4|Q14DE5|Q5JY75	In_Frame_Ins	INS	ENST00000287538.5	hg19	CCDS14663.1																																																																																			.	.	.	none		0.718	ZIC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058526.1			CGC	136648985	-	CGC	136648984	7	5	234	1	0	1	1	0	0	0	0	0	17692	159	6	0	136	0	ZIC3	23	136648984	In_Frame_Ins	INS	-	TCGA-P4-A5ED-01A-11D-A28G-10	30614519	136648984	18621576	21	14283											
ACAP3	116983	hgsc.bcm.edu	37	chr1	1235981	1235981	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacctcgtggggccggtgccTcggggcctgggcgttcctca	2	8	16	15	4	1	0	1	0	0	0	4	0	2	0	5	6	1	1	5	6	0	1			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr1:1235981T>C	ENST00000354700.5	-	6	632	c.430A>G	c.(430-432)Agg>Ggg	p.R144G	ACAP3_ENST00000379037.2_5'Flank|ACAP3_ENST00000353662.3_Missense_Mutation_p.R102G	NM_030649.2	NP_085152.2	Q96P50	ACAP3_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 3	144					regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			endometrium(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	14						GGCCGGTGCCTCGGGGCCTGG	0.652																																					p.R144G		Atlas-SNP	.											.	ACAP3	87	.	0			c.A430G						PASS	.						42	45	44					1																	1235981		2198	4296	6494	SO:0001583	missense	116983	exon6			GGTGCCTCGGGGC	AF411981	CCDS19.2	1p36	2013-01-10	2008-09-22	2008-09-22	ENSG00000131584	ENSG00000131584		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16754	protein-coding gene	gene with protein product			"centaurin, beta 5"	CENTB5			Standard	NM_030649		Approved	KIAA1716	uc001aeb.2	Q96P50	OTTHUMG00000002235	ENST00000354700.5:c.430A>G	chr1.hg19:g.1235981T>C	ENSP00000346733:p.Arg144Gly	162.0	0.0	.		156.0	53.0	.	NM_030649	B1AMF5|Q5TA42|Q5TA43|Q86UT3|Q9BSR9|Q9C0E7	Missense_Mutation	SNP	ENST00000354700.5	hg19	CCDS19.2	.	.	.	.	.	.	.	.	.	.	T	13.86	2.362995	0.41902	.	.	ENSG00000131584	ENST00000354700;ENST00000353662	T;T	0.04119	3.7;3.7	4.05	-0.178	0.13303	.	0.063063	0.64402	D	0.000010	T	0.21631	0.0521	M	0.87180	2.865	0.21355	N	0.999713	D;D;D	0.76494	0.999;0.997;0.996	D;P;D	0.77557	0.988;0.889;0.99	T	0.04373	-1.0956	10	0.87932	D	0	.	13.3526	0.60611	0.0:0.0:0.4193:0.5807	.	184;144;102	Q5TA40;Q96P50;Q96P50-1	.;ACAP3_HUMAN;.	G	144;102	ENSP00000346733:R144G;ENSP00000321139:R102G	ENSP00000321139:R102G	R	-	1	2	ACAP3	1225844	0.971000	0.33674	0.507000	0.27676	0.763000	0.43281	1.603000	0.36794	0.182000	0.20032	0.260000	0.18958	AGG	.	.	.	none		0.652	ACAP3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006366.2	NM_030649		C	1235981	T	C	1235981	3	2	235	1	0	0	0	0	1	0	0	0	120	1550	54	3	2150	3	ACAP3	1	1235981	Missense_Mutation	SNP	T	TCGA-P4-AAVL-01A-11D-A42J-10		1235981	248014640	1	14284											
GJB3	2707	hgsc.bcm.edu	37	chr1	35250656	35250656	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcctgcacgtggcctaccGtgaggagcgggagcgccggc	6	5	16	14	5	0	1	0	1	0	0	1	3	1	3	4	4	4	1	4	4	1	1	rs201314683		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr1:35250656G>A	ENST00000373366.2	+	2	908	c.293G>A	c.(292-294)cGt>cAt	p.R98H	GJB3_ENST00000373362.3_Missense_Mutation_p.R98H|RP1-34M23.5_ENST00000542839.1_RNA	NM_024009.2	NP_076872.1	O75712	CXB3_HUMAN	gap junction protein, beta 3, 31kDa	98					cell communication (GO:0007154)|in utero embryonic development (GO:0001701)|placenta development (GO:0001890)|sensory perception of sound (GO:0007605)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	connexon complex (GO:0005922)|cytoplasm (GO:0005737)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)	gap junction channel activity (GO:0005243)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(2)|prostate(3)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				GTGGCCTACCGTGAGGAGCGG	0.632																																					p.R98H		Atlas-SNP	.											GJB3,NS,carcinoma,0,1	GJB3	40	.	0			c.G293A						PASS	.						133	127	129					1																	35250656		2203	4300	6503	SO:0001583	missense	2707	exon2			CCTACCGTGAGGA	BC012918	CCDS384.1	1p34	2008-05-14	2007-01-16		ENSG00000188910	ENSG00000188910		"Ion channels / Gap junction proteins (connexins)"	4285	protein-coding gene	gene with protein product	"connexin 31"	603324	"gap junction protein, beta 3, 31kD (connexin 31)", "gap junction protein, beta 3, 31kDa (connexin 31)", "erythrokeratodermia variabilis"	DFNA2, EKV		9843210, 9704026	Standard	NM_024009		Approved	CX31	uc001bxy.3	O75712	OTTHUMG00000004051	ENST00000373366.2:c.293G>A	chr1.hg19:g.35250656G>A	ENSP00000362464:p.Arg98His	49.0	0.0	.		63.0	26.0	.	NM_001005752	B2R790|Q2TAZ8	Missense_Mutation	SNP	ENST00000373366.2	hg19	CCDS384.1	.	.	.	.	.	.	.	.	.	.	g	23.2	4.390343	0.82902	.	.	ENSG00000188910	ENST00000373366;ENST00000373362;ENST00000543647	D;D	0.99129	-5.46;-5.46	5.85	5.85	0.93711	Connexin, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98782	0.9590	M	0.76328	2.33	0.58432	D	0.99999	D	0.63880	0.993	P	0.53185	0.72	D	0.98959	1.0797	10	0.56958	D	0.05	.	15.6548	0.77124	0.0:0.0:0.8623:0.1377	.	98	O75712	CXB3_HUMAN	H	98	ENSP00000362464:R98H;ENSP00000362460:R98H	ENSP00000362460:R98H	R	+	2	0	GJB3	35023243	1.000000	0.71417	0.966000	0.40874	0.668000	0.39293	7.966000	0.87956	2.771000	0.95319	0.561000	0.74099	CGT	.	G|0.999;A|0.001	0.001	weak		0.632	GJB3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011559.1	NM_024009		A	35250656	G	A	35250656	3	1	235	1	0	0	0	0	1	0	0	0	6416	1145	40	1	295	1	GJB3	1	35250656	Missense_Mutation	SNP	G	TCGA-P4-AAVL-01A-11D-A42J-10	34014675	35250656	213999965	2	14285											
MUTYH	4595	hgsc.bcm.edu	37	chr1	45797447	45797447	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcggctggcctttctggggaAgttgaccactcccagggtct	5	10	14	12	1	2	1	0	1	2	0	3	2	3	2	3	5	0	2	3	5	1	2	rs587781601		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr1:45797447A>G	ENST00000372098.3	-	12	1196	c.1063T>C	c.(1063-1065)Ttc>Ctc	p.F355L	MUTYH_ENST00000372100.5_Missense_Mutation_p.F341L|MUTYH_ENST00000456914.2_Missense_Mutation_p.F330L|MUTYH_ENST00000448481.1_Missense_Mutation_p.F341L|MUTYH_ENST00000372115.3_Missense_Mutation_p.F344L|MUTYH_ENST00000450313.1_Missense_Mutation_p.F358L|MUTYH_ENST00000488731.2_Intron|MUTYH_ENST00000355498.2_Missense_Mutation_p.F330L|MUTYH_ENST00000372110.3_Missense_Mutation_p.F345L|MUTYH_ENST00000531105.1_Intron|MUTYH_ENST00000529984.1_Intron|MUTYH_ENST00000528013.2_Missense_Mutation_p.F344L|MUTYH_ENST00000354383.6_Missense_Mutation_p.F331L|MUTYH_ENST00000372104.1_Missense_Mutation_p.F330L|MUTYH_ENST00000528332.2_Intron			Q9UIF7	MUTYH_HUMAN	mutY homolog	355					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA repair (GO:0006281)|mismatch repair (GO:0006298)	mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|metal ion binding (GO:0046872)|MutSalpha complex binding (GO:0032407)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					TTTCTGGGGAAGTTGACCACT	0.647			Mis			colorectal		Base excision repair (BER), DNA glycosylases	MUTYH-associated polyposis																												p.F358L		Atlas-SNP	.	yes	Rec		Adenomatous polyposis coli	1	1p34.3-1p32.1	4595	mutY homolog (E. coli)		E	.	MUTYH	38	.	0			c.T1072C						PASS	.						20	24	23					1																	45797447		2202	4300	6502	SO:0001583	missense	4595	exon12	Familial Cancer Database	MAP, MYH-associated polyposis	TGGGGAAGTTGAC	U63329	CCDS520.1, CCDS41320.1, CCDS41321.1, CCDS41322.1, CCDS72776.1, CCDS72777.1	1p34.1	2014-09-17	2013-09-12		ENSG00000132781	ENSG00000132781			7527	protein-coding gene	gene with protein product		604933	"mutY (E. coli) homolog", "mutY homolog (E. coli)"			7823963, 10684930	Standard	NM_012222		Approved	MYH	uc009vxp.3	Q9UIF7	OTTHUMG00000007682	ENST00000372098.3:c.1063T>C	chr1.hg19:g.45797447A>G	ENSP00000361170:p.Phe355Leu	46.0	0.0	.		46.0	17.0	.	NM_001128425	D3DPZ4|Q15830|Q9UBP2|Q9UBS7|Q9UIF4|Q9UIF5|Q9UIF6	Missense_Mutation	SNP	ENST00000372098.3	hg19	CCDS520.1	.	.	.	.	.	.	.	.	.	.	A	16.11	3.031555	0.54790	.	.	ENSG00000132781	ENST00000372104;ENST00000448481;ENST00000456914;ENST00000354383;ENST00000355498;ENST00000372098;ENST00000372110;ENST00000372115;ENST00000450313;ENST00000372100;ENST00000525481;ENST00000412971	T;T;T;T;T;T;T;T;T;T;T	0.26660	2.67;2.67;2.67;2.67;2.67;2.66;2.65;2.65;2.64;2.67;1.72	5.5	4.39	0.52855	.	0.047785	0.85682	D	0.000000	T	0.18299	0.0439	N	0.17312	0.475	0.46774	D	0.999199	B;B;B;B;B;B;B	0.27823	0.19;0.001;0.185;0.001;0.19;0.054;0.19	B;B;B;B;B;B;B	0.33799	0.118;0.02;0.17;0.02;0.118;0.046;0.082	T	0.07986	-1.0744	10	0.56958	D	0.05	-13.047	10.8161	0.46575	0.926:0.0:0.074:0.0	.	358;355;345;355;344;238;331	E5KP25;E5KP26;Q9UIF7-2;Q9UIF7;E5KP27;D3DPZ6;E5KP28	.;.;.;MUTYH_HUMAN;.;.;.	L	330;341;330;331;330;355;345;344;358;341;202;202	ENSP00000361176:F330L;ENSP00000409718:F341L;ENSP00000407590:F330L;ENSP00000346354:F331L;ENSP00000347685:F330L;ENSP00000361170:F355L;ENSP00000361182:F345L;ENSP00000361187:F344L;ENSP00000408176:F358L;ENSP00000361172:F341L;ENSP00000410263:F202L	ENSP00000346354:F331L	F	-	1	0	MUTYH	45570034	1.000000	0.71417	1.000000	0.80357	0.767000	0.43475	6.850000	0.75420	2.100000	0.63781	0.533000	0.62120	TTC	.	.	.	none		0.647	MUTYH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020529.1	NM_012222		G	45797447	A	G	45797447	3	3	235	1	0	0	0	0	1	0	0	0	10000	72	3	3	597	3	MUTYH	1	45797447	Missense_Mutation	SNP	A	TCGA-P4-AAVL-01A-11D-A42J-10	10546791	45797447	203453174	3	14286											
CCDC17	149483	hgsc.bcm.edu	37	chr1	46088725	46088725	+	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	agttctcgaatctcctgctcCaggccgaagaggcgggacat	9	8	12	12	3	2	1	0	0	2	1	5	4	3	2	3	3	1	2	3	3	2	1			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr1:46088725C>A	ENST00000528266.1	-	4	705	c.558G>T	c.(556-558)ctG>ctT	p.L186L	CCDC17_ENST00000343901.2_Silent_p.L154L|CCDC17_ENST00000464739.1_5'Flank|CCDC17_ENST00000421127.2_Silent_p.L177L|CCDC17_ENST00000445048.2_Intron			Q96LX7	CCD17_HUMAN	coiled-coil domain containing 17	186										kidney(1)|large_intestine(1)|lung(1)|ovary(2)	5	Acute lymphoblastic leukemia(166;0.155)					TCTCCTGCTCCAGGCCGAAGA	0.667																																					p.L186L		Atlas-SNP	.											.	CCDC17	54	.	0			c.G558T						PASS	.						22	26	25					1																	46088725		2203	4300	6503	SO:0001819	synonymous_variant	149483	exon4			CTGCTCCAGGCCG		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.558G>T	chr1.hg19:g.46088725C>A		58.0	0.0	.		79.0	41.0	.	NM_001114938	A1A4Y7|B4DNX7|B4E1Q5|C9J8L2|Q0P683|Q5T629	Silent	SNP	ENST00000528266.1	hg19	CCDS44131.2																																																																																			.	.	.	none		0.667	CCDC17-008	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386833.1	NM_152500		A	46088725	C	A	46088725	2	1	235	1	0	0	0	0	0	0	0	1	2795	581	21	4		4	CCDC17	1	46088725	Silent	SNP	C	TCGA-P4-AAVL-01A-11D-A42J-10	291278	46088725	203161896	4	14287											
CYP2J2	1573	hgsc.bcm.edu	37	chr1	60370654	60370654	+	Frame_Shift_Del	DEL	G	G	-																															tggatgacagcattggtgtaGggcatggactcccgggcggc																										TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr1:60370654delG	ENST00000371204.3	-	7	1123	c.1080delC	c.(1078-1080)cccfs	p.P360fs	CYP2J2_ENST00000492633.1_5'UTR	NM_000775.2	NP_000766.2	P51589	CP2J2_HUMAN	cytochrome P450, family 2, subfamily J, polypeptide 2	360					arachidonic acid metabolic process (GO:0019369)|epoxygenase P450 pathway (GO:0019373)|icosanoid metabolic process (GO:0006690)|linoleic acid metabolic process (GO:0043651)|regulation of heart contraction (GO:0008016)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	arachidonic acid 11,12-epoxygenase activity (GO:0008405)|arachidonic acid 14,15-epoxygenase activity (GO:0008404)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|linoleic acid epoxygenase activity (GO:0071614)			NS(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|skin(1)	26	all_cancers(7;0.000396)				Apixaban(DB06605)|Astemizole(DB00637)|Cholecalciferol(DB00169)|Levomilnacipran(DB08918)|Masoprocol(DB00179)|Rivaroxaban(DB06228)	CATTGGTGTAGGGCATGGACT	0.542																																					p.Y361fs		Atlas-Indel,Pindel	.											.	CYP2J2	34	.	0			c.1081delT						PASS	.						157	129	139					1																	60370654		2203	4300	6503	SO:0001589	frameshift_variant	1573	exon7			.	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.1080delC	chr1.hg19:g.60370654delG	ENSP00000360247:p.Pro360fs	89.0	0.0	0		76.0	26.0	0.342105	NM_000775	B2RD33|Q8TF13	Frame_Shift_Del	DEL	ENST00000371204.3	hg19	CCDS613.1																																																																																			.	.	.	none		0.542	CYP2J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024940.1	NM_000775		-	60370654	G	-	60370654	7	5	235	1	0	1	0	1	0	0	0	0	4174	987	35	0	440	0	CYP2J2	1	60370654	Frame_Shift_Del	DEL	G	TCGA-P4-AAVL-01A-11D-A42J-10	14281929	60370654	188879967	5	14288											
IL12RB2	3595	hgsc.bcm.edu	37	chr1	67816591	67816592	+	Frame_Shift_Ins	INS	-	-	TA																															caagaggaaaaattctccacINStatcaggtgaccttgcagga																										TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr1:67816591_67816592insTA	ENST00000262345.1	+	9	1717_1718	c.1077_1078insTA	c.(1078-1080)tatfs	p.Y360fs	IL12RB2_ENST00000541374.1_Frame_Shift_Ins_p.Y360fs|IL12RB2_ENST00000544434.1_Frame_Shift_Ins_p.Y360fs|IL12RB2_ENST00000371000.1_Frame_Shift_Ins_p.Y360fs	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	360	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)	p.Y360H(1)		breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						AAATTCTCCACTATCAGGTGAC	0.47																																					p.H359fs		Atlas-Indel,Pindel	.											.	IL12RB2	94	.	1	Substitution - Missense(1)	lung(1)	c.1077_1078insTA						PASS	.																																			SO:0001589	frameshift_variant	3595	exon9			.	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.1078_1079dupTA	chr1.hg19:g.67816592_67816593dupTA	ENSP00000262345:p.Tyr360fs	395.0	0.0	0		381.0	144.0	0.377953	NM_001559	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Frame_Shift_Ins	INS	ENST00000262345.1	hg19	CCDS638.1																																																																																			.	.	.	none		0.47	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559		TA	67816592	-	TA	67816591	7	5	235	1	0	1	1	0	0	0	0	0	7634	564	20	0	1107	0	IL12RB2	1	67816591	Frame_Shift_Ins	INS	-	TCGA-P4-AAVL-01A-11D-A42J-10	7445937	67816591	181434030	6	14289											
ABCD3	5825	hgsc.bcm.edu	37	chr1	94939389	94939389	+	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	acttcatcgctgccatgcctCttgtaagtttaattcattaa	10	16	5	10	1	3	0	2	0	1	0	4	0	3	0	2	0	2	3	2	0	3	7			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr1:94939389C>A	ENST00000370214.4	+	5	427	c.403C>A	c.(403-405)Ctt>Att	p.L135I	ABCD3_ENST00000536817.1_Missense_Mutation_p.L62I|ABCD3_ENST00000315713.5_Missense_Mutation_p.L135I|ABCD3_ENST00000394233.2_Missense_Mutation_p.L135I|ABCD3_ENST00000454898.2_Missense_Mutation_p.L159I	NM_002858.3	NP_002849.1	P28288	ABCD3_HUMAN	ATP-binding cassette, sub-family D (ALD), member 3	135	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.|Interaction with PEX19.				ATP catabolic process (GO:0006200)|fatty acid beta-oxidation (GO:0006635)|peroxisome organization (GO:0007031)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(2)|lung(10)|ovary(1)|pancreas(1)|skin(2)	26		all_lung(203;0.000434)|Lung NSC(277;0.0019)		all cancers(265;0.0261)|Epithelial(280;0.165)		TGCCATGCCTCTTGTAAGTTT	0.328																																					p.L135I		Atlas-SNP	.											.	ABCD3	62	.	0			c.C403A						PASS	.						110	105	107					1																	94939389		2203	4300	6503	SO:0001583	missense	5825	exon5			ATGCCTCTTGTAA	M81182	CCDS749.1, CCDS44175.1	1p21.3	2012-05-16			ENSG00000117528	ENSG00000117528		"ATP binding cassette transporters / subfamily D"	67	protein-coding gene	gene with protein product		170995		PXMP1		1301993, 8449508	Standard	NM_002858		Approved	PMP70, ZWS2	uc001dqn.4	P28288	OTTHUMG00000010717	ENST00000370214.4:c.403C>A	chr1.hg19:g.94939389C>A	ENSP00000359233:p.Leu135Ile	66.0	0.0	.		65.0	23.0	.	NM_002858	D3DT46|Q15271|Q6NUN5|Q96DA3|Q9H529	Missense_Mutation	SNP	ENST00000370214.4	hg19	CCDS749.1	.	.	.	.	.	.	.	.	.	.	C	10.59	1.392782	0.25118	.	.	ENSG00000117528	ENST00000394233;ENST00000454898;ENST00000536817;ENST00000370214;ENST00000315713	D;D;D;D;D	0.99652	-3.5;-3.5;-3.5;-3.5;-6.3	5.78	5.78	0.91487	ABC transporter, N-terminal (1);ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);	0.437369	0.25526	N	0.030069	D	0.96703	0.8924	L	0.31065	0.9	0.27177	N	0.960763	B;B;B;B	0.31680	0.005;0.335;0.001;0.004	B;B;B;B	0.31686	0.014;0.134;0.005;0.01	D	0.92520	0.6024	10	0.12766	T	0.61	-13.3859	14.7668	0.69646	0.0:0.7487:0.2513:0.0	.	159;135;135;135	E7EUE1;P28288-2;P28288;P28288-3	.;.;ABCD3_HUMAN;.	I	135;159;62;135;135	ENSP00000377780:L135I;ENSP00000403357:L159I;ENSP00000440692:L62I;ENSP00000359233:L135I;ENSP00000326880:L135I	ENSP00000326880:L135I	L	+	1	0	ABCD3	94711977	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.930000	0.40124	2.894000	0.99253	0.655000	0.94253	CTT	.	.	.	none		0.328	ABCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029597.1	NM_002858		A	94939389	C	A	94939389	3	1	235	1	0	0	0	0	1	0	0	0	62	913	32	4	421	4	ABCD3	1	94939389	Missense_Mutation	SNP	C	TCGA-P4-AAVL-01A-11D-A42J-10	27122798	94939389	154311232	7	14290											
CSDE1	7812	hgsc.bcm.edu	37	chr1	115280171	115280171	+	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	tactctctaagttgtgaggaAcagcgcacacaacctaccag	13	8	8	12	1	1	1	0	1	1	0	2	2	1	2	2	1	5	2	2	1	5	4			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr1:115280171A>T	ENST00000358528.4	-	5	749	c.323T>A	c.(322-324)gTt>gAt	p.V108D	CSDE1_ENST00000438362.2_Missense_Mutation_p.V154D|CSDE1_ENST00000261443.5_Intron|CSDE1_ENST00000534699.1_Missense_Mutation_p.V108D|CSDE1_ENST00000369530.1_Intron|CSDE1_ENST00000530886.1_Intron|CSDE1_ENST00000339438.6_Intron	NM_001007553.2	NP_001007554.1	O75534	CSDE1_HUMAN	cold shock domain containing E1, RNA-binding	108					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)		GTTGTGAGGAACAGCGCACAC	0.398																																					p.V154D		Atlas-SNP	.											.	CSDE1	145	.	0			c.T461A						PASS	.						64	55	58					1																	115280171		2203	4300	6503	SO:0001583	missense	7812	exon6			TGAGGAACAGCGC		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.323T>A	chr1.hg19:g.115280171A>T	ENSP00000351329:p.Val108Asp	351.0	1.0	.		368.0	148.0	.	NM_001242891	A8K281|E9PGZ0|G5E9Q2|O94961|Q5TF04|Q5TF05|Q68DF1|Q68DI9|Q9Y2S4	Missense_Mutation	SNP	ENST00000358528.4	hg19	CCDS30812.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.041985	0.75732	.	.	ENSG00000009307	ENST00000438362;ENST00000358528;ENST00000534699	.	.	.	5.87	5.87	0.94306	.	.	.	.	.	T	0.50752	0.1634	N	0.22421	0.69	0.80722	D	1	D;D	0.61697	0.971;0.99	P;P	0.58266	0.598;0.836	T	0.56715	-0.7933	8	0.49607	T	0.09	.	16.2631	0.82557	1.0:0.0:0.0:0.0	.	108;154	O75534;G5E9Q2	CSDE1_HUMAN;.	D	154;108;108	.	ENSP00000351329:V108D	V	-	2	0	CSDE1	115081694	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.676000	0.91199	2.239000	0.73571	0.528000	0.53228	GTT	.	.	.	none		0.398	CSDE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033397.1	NM_007158		T	115280171	A	T	115280171	3	4	235	1	0	0	0	0	1	0	0	0	3931	43	2	5	2137	5	CSDE1	1	115280171	Missense_Mutation	SNP	A	TCGA-P4-AAVL-01A-11D-A42J-10	20340782	115280171	133970450	8	14291											
KPRP	448834	hgsc.bcm.edu	37	chr1	152732843	152732843	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagatgccttcctcctcctcGgcggctgcagcttttccccc	3	11	8	19	2	0	1	0	0	0	1	5	1	4	1	6	2	3	3	6	2	0	3			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr1:152732843G>A	ENST00000606109.1	+	1	807	c.779G>A	c.(778-780)cGg>cAg	p.R260Q	KPRP_ENST00000368773.1_Missense_Mutation_p.R260Q			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	260	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)			CCTCCTCCTCGGCGGCTGCAG	0.602																																					p.R260Q		Atlas-SNP	.											.	KPRP	152	.	0			c.G779A						PASS	.						38	44	42					1																	152732843		2203	4300	6503	SO:0001583	missense	448834	exon2			CTCCTCGGCGGCT	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.779G>A	chr1.hg19:g.152732843G>A	ENSP00000475216:p.Arg260Gln	62.0	0.0	.		80.0	4.0	.	NM_001025231		Missense_Mutation	SNP	ENST00000606109.1	hg19	CCDS30862.1	.	.	.	.	.	.	.	.	.	.	G	10.77	1.442856	0.25987	.	.	ENSG00000203786	ENST00000368773	T	0.16073	2.37	5.55	2.56	0.30785	.	0.833462	0.10411	N	0.677910	T	0.05731	0.0150	L	0.29908	0.895	0.09310	N	1	D	0.55385	0.971	P	0.45099	0.469	T	0.25467	-1.0131	10	0.72032	D	0.01	-9.8249	5.4492	0.16552	0.1811:0.1841:0.6347:0.0	.	260	Q5T749	KPRP_HUMAN	Q	260	ENSP00000357762:R260Q	ENSP00000357762:R260Q	R	+	2	0	KPRP	150999467	0.000000	0.05858	0.002000	0.10522	0.023000	0.10783	0.342000	0.19926	0.778000	0.33520	0.563000	0.77884	CGG	.	.	.	none		0.602	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231		A	152732843	G	A	152732843	3	1	235	1	0	0	0	0	1	0	0	0	8443	1116	39	1	781	1	KPRP	1	152732843	Missense_Mutation	SNP	G	TCGA-P4-AAVL-01A-11D-A42J-10	37452672	152732843	96517778	9	14292											
FCRL4	83417	hgsc.bcm.edu	37	chr1	157548316	157548316	+	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	atctcagagtataccaaatcTccctttttggggtgtactgg	9	14	9	9	0	2	1	1	0	2	1	4	1	2	1	2	3	2	2	2	3	4	5			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr1:157548316T>A	ENST00000271532.1	-	10	1512	c.1377A>T	c.(1375-1377)ggA>ggT	p.G459G	FCRL4_ENST00000448509.2_5'UTR	NM_031282.2	NP_112572.1	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4	459					immune system process (GO:0002376)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(20)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	40	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.245)				ATACCAAATCTCCCTTTTTGG	0.423																																					p.G459G		Atlas-SNP	.											.	FCRL4	95	.	0			c.A1377T						PASS	.						102	101	102					1																	157548316		2203	4300	6503	SO:0001819	synonymous_variant	83417	exon10			CAAATCTCCCTTT	AF343661	CCDS1166.1	1q21	2013-01-14			ENSG00000163518	ENSG00000163518		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18507	protein-coding gene	gene with protein product		605876				11290337, 11493702	Standard	NM_031282		Approved	FCRH4, IRTA1, IGFP2, CD307d	uc001fqw.3	Q96PJ5	OTTHUMG00000035488	ENST00000271532.1:c.1377A>T	chr1.hg19:g.157548316T>A		108.0	0.0	.		70.0	32.0	.	NM_031282	Q96PJ3|Q96RE0	Silent	SNP	ENST00000271532.1	hg19	CCDS1166.1																																																																																			.	.	.	none		0.423	FCRL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086180.1	NM_031282		A	157548316	T	A	157548316	2	1	235	1	0	0	0	0	0	0	0	1	5804	1538	54	5		5	FCRL4	1	157548316	Silent	SNP	T	TCGA-P4-AAVL-01A-11D-A42J-10	4815473	157548316	91702305	10	14293											
MYO7B	4648	hgsc.bcm.edu	37	chr2	128389949	128389949	+	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	gaagctgctggcccccgactGcagccgccgaatccagaagg	9	4	13	15	3	0	1	0	0	0	1	1	4	1	1	5	2	4	3	5	2	3	0			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr2:128389949G>C	ENST00000409816.2	+	37	5332	c.5300G>C	c.(5299-5301)tGc>tCc	p.C1767S	MYO7B_ENST00000409090.1_Missense_Mutation_p.C620S|MYO7B_ENST00000389524.4_Missense_Mutation_p.C1768S|MYO7B_ENST00000428314.1_Missense_Mutation_p.C1767S			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1767	MyTH4 2. {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)		GCCCCCGACTGCAGCCGCCGA	0.682																																					p.C1767S		Atlas-SNP	.											.	MYO7B	359	.	0			c.G5300C						PASS	.						34	43	40					2																	128389949		1762	3946	5708	SO:0001583	missense	4648	exon38			CCGACTGCAGCCG		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.5300G>C	chr2.hg19:g.128389949G>C	ENSP00000386461:p.Cys1767Ser	212.0	0.0	.		251.0	112.0	.	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	hg19	CCDS46405.1	.	.	.	.	.	.	.	.	.	.	g	16.39	3.108746	0.56291	.	.	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000272666;ENST00000409816;ENST00000409090	D;D;D;D	0.92495	-3.05;-3.05;-3.05;-3.05	4.84	4.84	0.62591	MyTH4 domain (3);	0.000000	0.85682	D	0.000000	D	0.93746	0.8001	L	0.56396	1.775	0.54753	D	0.999982	D	0.55605	0.972	P	0.56216	0.794	D	0.93035	0.6452	10	0.36615	T	0.2	.	17.9396	0.89023	0.0:0.0:1.0:0.0	.	1767	Q6PIF6	MYO7B_HUMAN	S	1768;1767;863;1767;620	ENSP00000374175:C1768S;ENSP00000415090:C1767S;ENSP00000386461:C1767S;ENSP00000386850:C620S	ENSP00000272666:C863S	C	+	2	0	MYO7B	128106419	1.000000	0.71417	0.996000	0.52242	0.162000	0.22319	6.281000	0.72632	2.229000	0.72834	0.561000	0.74099	TGC	.	.	.	none		0.682	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001		C	128389949	G	C	128389949	3	2	235	1	0	0	0	0	1	0	0	0	10090	1319	46	4	5446	4	MYO7B	2	128389949	Missense_Mutation	SNP	G	TCGA-P4-AAVL-01A-11D-A42J-10		128389949	114809424	11	14294											
LRTM1	57408	hgsc.bcm.edu	37	chr3	54958819	54958819	+	Missense_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	gtatagttaggttctcccaaGtctctcccaaggatgtggga	9	12	11	9	0	2	0	0	0	2	0	5	2	3	2	2	3	0	3	2	3	5	4			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr3:54958819G>A	ENST00000273286.5	-	2	593	c.431C>T	c.(430-432)aCt>aTt	p.T144I	CACNA2D3_ENST00000474759.1_Intron|LRTM1_ENST00000493075.1_Missense_Mutation_p.T68I|CACNA2D3_ENST00000490478.1_Intron|CACNA2D3_ENST00000415676.2_Intron|CACNA2D3_ENST00000288197.5_Intron	NM_020678.2	NP_065729.1	Q9HBL6	LRTM1_HUMAN	leucine-rich repeats and transmembrane domains 1	144						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)		GTTCTCCCAAGTCTCTCCCAA	0.493																																					p.T144I		Atlas-SNP	.											.	LRTM1	52	.	0			c.C431T						PASS	.						95	91	93					3																	54958819		2203	4300	6503	SO:0001583	missense	57408	exon2			TCCCAAGTCTCTC	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.431C>T	chr3.hg19:g.54958819G>A	ENSP00000273286:p.Thr144Ile	107.0	0.0	.		88.0	42.0	.	NM_020678	Q8IUU2	Missense_Mutation	SNP	ENST00000273286.5	hg19	CCDS2876.1	.	.	.	.	.	.	.	.	.	.	G	3.291	-0.144996	0.06627	.	.	ENSG00000144771	ENST00000273286;ENST00000493075	T;D	0.90069	4.29;-2.61	5.96	2.13	0.27403	.	0.822907	0.11590	N	0.548818	T	0.78842	0.4347	L	0.32530	0.975	0.09310	N	1	B	0.28713	0.22	B	0.24848	0.056	T	0.65261	-0.6211	10	0.37606	T	0.19	.	1.0945	0.01670	0.1978:0.2377:0.3423:0.2222	.	144	Q9HBL6	LRTM1_HUMAN	I	144;68	ENSP00000273286:T144I;ENSP00000419772:T68I	ENSP00000273286:T144I	T	-	2	0	LRTM1	54933859	0.009000	0.17119	0.032000	0.17829	0.140000	0.21249	0.516000	0.22817	0.102000	0.17638	-0.126000	0.14955	ACT	.	.	.	none		0.493	LRTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351399.1	NM_020678		A	54958819	G	A	54958819	3	1	235	1	0	0	0	0	1	0	0	0	9051	1029	36	2	614	2	LRTM1	3	54958819	Missense_Mutation	SNP	G	TCGA-P4-AAVL-01A-11D-A42J-10		54958819	143063611	12	14295											
KALRN	8997	hgsc.bcm.edu	37	chr3	124210171	124210171	+	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	aggcatttcctgtctacagaCctcagagctgggtgtgaccg	8	10	12	11	1	2	3	1	1	1	2	3	3	3	3	3	2	2	2	3	2	1	2			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr3:124210171C>T	ENST00000240874.3	+	31	4740	c.4583C>T	c.(4582-4584)aCc>aTc	p.T1528I	KALRN_ENST00000460856.1_Splice_Site_p.T1519I|KALRN_ENST00000360013.3_Splice_Site_p.T1528I	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1528	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						TGTCTACAGACCTCAGAGCTG	0.577																																					p.T1528I		Atlas-SNP	.											.	KALRN	556	.	0			c.C4583T						PASS	.						55	51	52					3																	124210171		2203	4300	6503	SO:0001630	splice_region_variant	8997	exon31			TACAGACCTCAGA	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.4582-1C>T	chr3.hg19:g.124210171C>T		83.0	0.0	.		97.0	51.0	.	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Missense_Mutation	SNP	ENST00000240874.3	hg19	CCDS3027.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.2|25.2	4.610758|4.610758	0.87258|0.87258	.|.	.|.	ENSG00000160145|ENSG00000160145	ENST00000354186|ENST00000460856;ENST00000240874;ENST00000360013	.|T;T;T	.|0.10668	.|2.85;2.85;2.85	5.12|5.12	5.12|5.12	0.69794|0.69794	.|Pleckstrin homology-type (1);Pleckstrin homology domain (2);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.35158|0.35158	0.0922|0.0922	M|M	0.80422|0.80422	2.495|2.495	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.64830	.|0.986;0.994;0.992	.|P;D;P	.|0.67231	.|0.602;0.95;0.776	T|T	0.03354|0.03354	-1.1045|-1.1045	5|10	.|0.34782	.|T	.|0.22	.|.	18.7502|18.7502	0.91810|0.91810	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1519;1528;1528	.|C9IZQ6;O60229;O60229-2	.|.;KALRN_HUMAN;.	S|I	1497|1519;1528;1528	.|ENSP00000418611:T1519I;ENSP00000240874:T1528I;ENSP00000353109:T1528I	.|ENSP00000240874:T1528I	P|T	+|+	1|2	0|0	KALRN|KALRN	125692861|125692861	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.651000|7.651000	0.83577|0.83577	2.664000|2.664000	0.90586|0.90586	0.655000|0.655000	0.94253|0.94253	CCT|ACC	.	.	.	none		0.577	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947	Missense_Mutation	T	124210171	C	T	124210171	5	4	235	1	0	0	0	0	0	0	1	0	7982	521	18	2	4705	2	KALRN	3	124210171	Splice_Site	SNP	C	TCGA-P4-AAVL-01A-11D-A42J-10	69251352	124210171	73812259	13	14296											
IFT122	55764	hgsc.bcm.edu	37	chr3	129185869	129185869	+	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	gtagtgaggcagaggaggaaGaaccagaggaagaggacgac	16	2	18	5	1	0	5	0	1	0	4	0	10	0	9	1	5	1	2	1	5	4	1			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr3:129185869G>A	ENST00000348417.2	+	8	777	c.700G>A	c.(700-702)Gaa>Aaa	p.E234K	IFT122_ENST00000440957.2_Intron|IFT122_ENST00000431818.2_Missense_Mutation_p.E84K|IFT122_ENST00000504021.1_Intron|IFT122_ENST00000347300.2_Intron|IFT122_ENST00000296266.3_Missense_Mutation_p.E285K|IFT122_ENST00000349441.2_Intron|IFT122_ENST00000507564.1_Intron	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	234					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						AGAGGAGGAAGAACCAGAGGA	0.532																																					p.E285K		Atlas-SNP	.											.	IFT122	117	.	0			c.G853A						PASS	.						149	155	153					3																	129185869		2203	4300	6503	SO:0001583	missense	55764	exon9			GAGGAAGAACCAG	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.700G>A	chr3.hg19:g.129185869G>A	ENSP00000324005:p.Glu234Lys	95.0	0.0	.		119.0	28.0	.	NM_052985	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Missense_Mutation	SNP	ENST00000348417.2	hg19	CCDS3061.1	.	.	.	.	.	.	.	.	.	.	G	12.34	1.907475	0.33721	.	.	ENSG00000163913	ENST00000296266;ENST00000431818;ENST00000348417	T;T;T	0.60797	0.16;0.37;0.85	4.64	3.77	0.43336	WD40 repeat-like-containing domain (1);	1.002150	0.08040	N	0.995052	T	0.34193	0.0889	N	0.08118	0	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.001;0.004	T	0.10222	-1.0639	10	0.05959	T	0.93	-10.4607	10.2543	0.43388	0.094:0.0:0.906:0.0	.	234;285	Q9HBG6;G3XAB1	IF122_HUMAN;.	K	285;84;234	ENSP00000296266:E285K;ENSP00000410946:E84K;ENSP00000324005:E234K	ENSP00000296266:E285K	E	+	1	0	IFT122	130668559	1.000000	0.71417	0.999000	0.59377	0.943000	0.58893	2.087000	0.41653	1.190000	0.43042	-0.448000	0.05591	GAA	.	.	.	none		0.532	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262		A	129185869	G	A	129185869	3	1	235	1	0	0	0	0	1	0	0	0	7562	943	33	2	887	2	IFT122	3	129185869	Missense_Mutation	SNP	G	TCGA-P4-AAVL-01A-11D-A42J-10	4975698	129185869	68836561	14	14297											
SEL1L3	23231	hgsc.bcm.edu	37	chr4	25759396	25759396	+	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	ggggctgaaggactcctcgtTactgtggctccagcacctgc	6	9	13	13	1	0	1	0	1	0	0	3	2	2	2	3	4	3	4	3	4	2	1			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr4:25759396T>A	ENST00000399878.3	-	22	3222	c.3100A>T	c.(3100-3102)Aac>Tac	p.N1034Y	SEL1L3_ENST00000502949.1_Missense_Mutation_p.N881Y|SEL1L3_ENST00000264868.5_Missense_Mutation_p.N999Y	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	1034						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						GACTCCTCGTTACTGTGGCTC	0.567																																					p.N1034Y		Atlas-SNP	.											.	SEL1L3	62	.	0			c.A3100T						PASS	.						45	56	52					4																	25759396		2095	4221	6316	SO:0001583	missense	23231	exon22			CCTCGTTACTGTG	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.3100A>T	chr4.hg19:g.25759396T>A	ENSP00000382767:p.Asn1034Tyr	260.0	0.0	.		256.0	92.0	.	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Missense_Mutation	SNP	ENST00000399878.3	hg19	CCDS47037.1	.	.	.	.	.	.	.	.	.	.	T	15.32	2.798546	0.50208	.	.	ENSG00000091490	ENST00000399878;ENST00000264868;ENST00000502949	T;T;T	0.16743	2.53;2.54;2.32	5.61	1.51	0.23008	.	0.645110	0.17263	N	0.180719	T	0.31167	0.0788	L	0.60455	1.87	0.09310	N	1	D;P	0.65815	0.995;0.918	P;P	0.59221	0.854;0.534	T	0.11867	-1.0570	10	0.72032	D	0.01	-0.8083	12.2959	0.54847	0.0:0.0:0.4122:0.5878	.	441;1034	B4DTH5;Q68CR1	.;SE1L3_HUMAN	Y	1034;999;881	ENSP00000382767:N1034Y;ENSP00000264868:N999Y;ENSP00000425438:N881Y	ENSP00000264868:N999Y	N	-	1	0	SEL1L3	25368494	0.040000	0.19996	0.000000	0.03702	0.644000	0.38419	2.343000	0.44001	0.092000	0.17331	0.533000	0.62120	AAC	.	.	.	none		0.567	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187		A	25759396	T	A	25759396	3	1	235	1	0	0	0	0	1	0	0	0	14025	1754	61	5	310	5	SEL1L3	4	25759396	Missense_Mutation	SNP	T	TCGA-P4-AAVL-01A-11D-A42J-10		25759396	165394880	15	14298											
TMPRSS11F	389208	hgsc.bcm.edu	37	chr4	68934461	68934461	+	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	tccccttccatagctgtttcCcttccttggacaattctttg	5	17	5	14	0	1	0	0	0	1	0	5	1	5	1	5	1	1	2	5	1	2	7			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr4:68934461C>A	ENST00000356291.2	-	7	689	c.630G>T	c.(628-630)agG>agT	p.R210S	UBA6-AS1_ENST00000499180.2_RNA|UBA6-AS1_ENST00000511571.1_RNA|UBA6-AS1_ENST00000500538.2_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	210	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						TAGCTGTTTCCCTTCCTTGGA	0.498																																					p.R210S		Atlas-SNP	.											.	TMPRSS11F	79	.	0			c.G630T						PASS	.						120	107	111					4																	68934461		2203	4300	6503	SO:0001583	missense	389208	exon7			TGTTTCCCTTCCT	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.630G>T	chr4.hg19:g.68934461C>A	ENSP00000348639:p.Arg210Ser	104.0	0.0	.		82.0	36.0	.	NM_207407	A8MXX2	Missense_Mutation	SNP	ENST00000356291.2	hg19	CCDS3520.1	.	.	.	.	.	.	.	.	.	.	C	6.884	0.532541	0.13127	.	.	ENSG00000198092	ENST00000356291	D	0.88354	-2.37	5.43	-0.132	0.13489	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.197117	0.34932	N	0.003580	T	0.69351	0.3101	N	0.05574	-0.02	0.09310	N	1	B	0.10296	0.003	B	0.12837	0.008	T	0.54814	-0.8237	10	0.12103	T	0.63	.	3.808	0.08785	0.2927:0.4276:0.0:0.2797	.	210	Q6ZWK6	TM11F_HUMAN	S	210	ENSP00000348639:R210S	ENSP00000348639:R210S	R	-	3	2	TMPRSS11F	68617056	0.000000	0.05858	0.816000	0.32577	0.629000	0.37895	-0.086000	0.11233	0.008000	0.14787	-0.136000	0.14681	AGG	.	.	.	none		0.498	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407		A	68934461	C	A	68934461	3	1	235	1	0	0	0	0	1	0	0	0	16255	622	22	4	702	4	TMPRSS11F	4	68934461	Missense_Mutation	SNP	C	TCGA-P4-AAVL-01A-11D-A42J-10	43175065	68934461	122219815	16	14299											
FNIP2	57600	hgsc.bcm.edu	37	chr4	159812743	159812743	+	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	cctggtctctagtcaggtgtCcagtttgcttcagtccattt	5	16	9	11	0	3	0	2	0	1	0	6	0	5	0	3	2	1	2	3	2	1	4			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr4:159812743C>G	ENST00000264433.6	+	15	3170	c.3095C>G	c.(3094-3096)tCc>tGc	p.S1032C	FNIP2_ENST00000379346.3_Missense_Mutation_p.S1055C|C4orf45_ENST00000508011.1_5'Flank	NM_020840.1	NP_065891.1	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	1032					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)		AGTCAGGTGTCCAGTTTGCTT	0.428																																					p.S1032C		Atlas-SNP	.											.	FNIP2	90	.	0			c.C3095G						PASS	.						150	142	145					4																	159812743		1955	4149	6104	SO:0001583	missense	57600	exon15			AGGTGTCCAGTTT	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.3095C>G	chr4.hg19:g.159812743C>G	ENSP00000264433:p.Ser1032Cys	80.0	0.0	.		61.0	27.0	.	NM_020840	Q05DC3|Q96I31|Q9H994	Missense_Mutation	SNP	ENST00000264433.6	hg19	CCDS47155.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.938238	0.52972	.	.	ENSG00000052795	ENST00000264433;ENST00000379346	T;T	0.30448	1.53;1.53	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.45418	0.1341	M	0.86740	2.835	0.50039	D	0.999849	B	0.22909	0.077	B	0.27170	0.077	T	0.43734	-0.9373	9	.	.	.	.	19.466	0.94939	0.0:1.0:0.0:0.0	.	1032	Q9P278	FNIP2_HUMAN	C	1032;1055	ENSP00000264433:S1032C;ENSP00000368651:S1055C	.	S	+	2	0	FNIP2	160032193	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	3.916000	0.56416	2.607000	0.88179	0.655000	0.94253	TCC	.	.	.	none		0.428	FNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366602.1	NM_020840		G	159812743	C	G	159812743	3	3	235	1	0	0	0	0	1	0	0	0	5983	855	30	4	3153	4	FNIP2	4	159812743	Missense_Mutation	SNP	C	TCGA-P4-AAVL-01A-11D-A42J-10	90878282	159812743	31341533	17	14300											
RAPGEF6	51735	hgsc.bcm.edu	37	chr5	130791652	130791652	+	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	gatgtttctcgtatttgcttGgtaacttttcccaagttcct	6	19	7	9	1	1	0	0	0	1	0	4	1	3	0	2	1	2	5	2	1	3	8			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr5:130791652G>C	ENST00000509018.1	-	20	3123	c.2918C>G	c.(2917-2919)cCa>cGa	p.P973R	CTC-432M15.3_ENST00000514667.1_Missense_Mutation_p.P1023R|RAPGEF6_ENST00000512052.1_Missense_Mutation_p.P688R|RAPGEF6_ENST00000308008.6_Missense_Mutation_p.P973R|RAPGEF6_ENST00000307984.5_Missense_Mutation_p.P978R|RAPGEF6_ENST00000296859.6_Missense_Mutation_p.P973R|RAPGEF6_ENST00000507093.1_Missense_Mutation_p.P973R	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	973	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		GTATTTGCTTGGTAACTTTTC	0.373																																					p.P978R	Melanoma(168;435 1955 13113 13877 23213)	Atlas-SNP	.											.	RAPGEF6	361	.	0			c.C2933G						PASS	.						120	113	116					5																	130791652		2203	4300	6503	SO:0001583	missense	51735	exon21			TTGCTTGGTAACT	AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"PDZ domain containing guanine nucleotide exchange factor (GEF) 2"	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.2918C>G	chr5.hg19:g.130791652G>C	ENSP00000421684:p.Pro973Arg	110.0	0.0	.		100.0	43.0	.	NM_001164387	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Missense_Mutation	SNP	ENST00000509018.1	hg19	CCDS34225.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.634801	0.87760	.	.	ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000217128	ENST00000509018;ENST00000307984;ENST00000507093;ENST00000296859;ENST00000358714;ENST00000512052;ENST00000308008;ENST00000514667	T;T;T;T;T;T;T	0.33654	1.4;1.4;1.4;1.4;1.4;1.4;1.4	5.2	5.2	0.72013	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.69771	0.3148	M	0.91717	3.235	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.991;1.0;1.0;1.0;1.0;0.999	T	0.77504	-0.2563	10	0.87932	D	0	.	19.0931	0.93235	0.0:0.0:1.0:0.0	.	973;973;973;688;1023;978;973	A3KN82;B7ZML2;Q8TEU7-2;D6RE77;E9PCH4;Q8TEU7-3;Q8TEU7	.;.;.;.;.;.;RPGF6_HUMAN	R	973;978;973;973;978;688;973;1023	ENSP00000421684:P973R;ENSP00000309298:P978R;ENSP00000426081:P973R;ENSP00000296859:P973R;ENSP00000426910:P688R;ENSP00000311419:P973R;ENSP00000426948:P1023R	ENSP00000426948:P1023R	P	-	2	0	RAPGEF6;FNIP1	130819551	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.809000	0.99208	2.591000	0.87537	0.591000	0.81541	CCA	.	.	.	none		0.373	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340		C	130791652	G	C	130791652	3	2	235	1	0	0	0	0	1	0	0	0	13061	1348	47	4	2386	4	RAPGEF6	5	130791652	Missense_Mutation	SNP	G	TCGA-P4-AAVL-01A-11D-A42J-10		130791652	50123608	18	14301											
PCDHB3	56132	hgsc.bcm.edu	37	chr5	140482079	140482079	+	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	ccacggagcccgggctgttcGgcgtgtgggcgcacaatggc	5	6	17	13	5	0	0	0	0	0	0	1	1	0	1	2	5	1	3	2	5	1	1			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr5:140482079G>C	ENST00000231130.2	+	1	1846	c.1846G>C	c.(1846-1848)Ggc>Cgc	p.G616R	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	616	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGGGCTGTTCGGCGTGTGGGC	0.687																																					p.G616R		Atlas-SNP	.											.	PCDHB3	208	.	0			c.G1846C						PASS	.						26	28	27					5																	140482079		2076	4062	6138	SO:0001583	missense	56132	exon1			CTGTTCGGCGTGT	AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"Cadherins / Protocadherins : Clustered"	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.1846G>C	chr5.hg19:g.140482079G>C	ENSP00000231130:p.Gly616Arg	31.0	0.0	.		30.0	16.0	.	NM_018937	B2R8P2	Missense_Mutation	SNP	ENST00000231130.2	hg19	CCDS4245.1	.	.	.	.	.	.	.	.	.	.	G	17.04	3.286214	0.59867	.	.	ENSG00000113205	ENST00000231130	T	0.45276	0.9	4.38	-3.96	0.04106	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.23171	0.0560	N	0.00750	-1.22	0.25473	N	0.987806	P	0.51449	0.945	P	0.56916	0.809	T	0.35549	-0.9784	9	0.72032	D	0.01	.	8.1319	0.31033	0.6547:0.233:0.1123:0.0	.	616	Q9Y5E6	PCDB3_HUMAN	R	616	ENSP00000231130:G616R	ENSP00000231130:G616R	G	+	1	0	PCDHB3	140462263	0.000000	0.05858	0.994000	0.49952	0.984000	0.73092	-2.316000	0.01123	-0.517000	0.06461	-0.378000	0.06908	GGC	.	.	.	none		0.687	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937		C	140482079	G	C	140482079	3	2	235	1	0	0	0	0	1	0	0	0	11550	1116	39	4	1848	4	PCDHB3	5	140482079	Missense_Mutation	SNP	G	TCGA-P4-AAVL-01A-11D-A42J-10	9690427	140482079	40433181	19	14302											
KIFC1	3833	hgsc.bcm.edu	37	chr6	33365934	33365934	+	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	cagatggaagatggcctggaGcctgagaaggtgagctgggc	10	6	18	7	0	0	4	0	2	0	3	0	7	0	6	2	5	2	1	2	5	2	0	rs368144446		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr6:33365934G>A	ENST00000428849.2	+	2	591	c.141G>A	c.(139-141)gaG>gaA	p.E47E		NM_002263.3	NP_002254.2	Q9BW19	KIFC1_HUMAN	kinesin family member C1	47					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						ATGGCCTGGAGCCTGAGAAGG	0.537																																					p.E47E		Atlas-SNP	.											.	KIFC1	47	.	0			c.G141A						PASS	.	G		0,4406		0,0,2203	59	62	61		141	3	1	6		61	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KIFC1	NM_002263.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		47/674	33365934	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	3833	exon2			CCTGGAGCCTGAG	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.141G>A	chr6.hg19:g.33365934G>A		119.0	0.0	.		123.0	57.0	.	NM_002263	O60887|Q14834|Q4KMP0|Q5SU09|Q6GMS7|Q6P4A5|Q9UQP7	Silent	SNP	ENST00000428849.2	hg19	CCDS34430.1																																																																																			.	.	.	weak		0.537	KIFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076417.1	NM_002263		A	33365934	G	A	33365934	2	1	235	1	0	0	0	0	0	0	0	1	8319	962	34	2		2	KIFC1	6	33365934	Silent	SNP	G	TCGA-P4-AAVL-01A-11D-A42J-10		33365934	137749133	20	14303											
TULP4	56995	hgsc.bcm.edu	37	chr6	158882608	158882629	+	Frame_Shift_Del	DEL	GTGGTGCACACAGGGGGACTTG	GTGGTGCACACAGGGGGACTTG	-																															gtttcagaggtggtagcccaGtggtgcacacagggggactt																										TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	GTGGTGCACACAGGGGGACTTG	GTGGTGCACACAGGGGGACTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr6:158882608_158882629delGTGGTGCACACAGGGGGACTTG	ENST00000367097.3	+	6	2230_2251	c.873_894delGTGGTGCACACAGGGGGACTTG	c.(871-894)cagtggtgcacacagggggacttgfs	p.QWCTQGDL291fs	TULP4_ENST00000367094.2_Frame_Shift_Del_p.QWCTQGDL291fs	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	291					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)		TGGTAGCCCAGTGGTGCACACAGGGGGACTTGCTGGCAGTCG	0.55																																					p.291_298del		Atlas-Indel,Pindel	.											.	TULP4	137	.	0			c.872_893del						PASS	.																																			SO:0001589	frameshift_variant	56995	exon6			.		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.873_894delGTGGTGCACACAGGGGGACTTG	chr6.hg19:g.158882608_158882629delGTGGTGCACACAGGGGGACTTG	ENSP00000356064:p.Gln291fs	46.0	0.0	0		41.0	15.0	0.365854	NM_001007466	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Frame_Shift_Del	DEL	ENST00000367097.3	hg19	CCDS34561.1																																																																																			.	.	.	none		0.55	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245		-	158882629	GTGGTGCACACAGGGGGACTTG	-	158882608	7	5	235	1	0	1	0	1	0	0	0	0	16788	1020	36	0	895	0	TULP4	6	158882608	Frame_Shift_Del	DEL	GTGGTGCACACAGGGGGACTTG	TCGA-P4-AAVL-01A-11D-A42J-10	125516674	158882608	12232459	21	14304											
TNRC18	84629	hgsc.bcm.edu	37	chr7	5352473	5352476	+	Frame_Shift_Del	DEL	ATCG	ATCG	-																															gtgggggcgggggctgcctcAtcgtccgagctgcaggaaga																										TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	ATCG	ATCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr7:5352473_5352476delATCG	ENST00000430969.1	-	27	8394_8397	c.8046_8049delCGAT	c.(8044-8049)gacgatfs	p.DD2682fs	TNRC18_ENST00000399537.4_Frame_Shift_Del_p.DD2682fs	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2682							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)		GGGCTGCCTCATCGTCCGAGCTGC	0.691																																					p.2683_2684del		Atlas-Indel,Pindel	.											.	TNRC18	311	.	0			c.8047_8050del						PASS	.																																			SO:0001589	frameshift_variant	84629	exon27			.	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"Trinucleotide (CAG) repeat containing"	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.8046_8049delCGAT	chr7.hg19:g.5352473_5352476delATCG	ENSP00000395538:p.Asp2682fs	83.0	0.0	0		101.0	47.0	0.465347	NM_001080495	A8MX41|Q96JH1|Q96K91	Frame_Shift_Del	DEL	ENST00000430969.1	hg19	CCDS47534.1																																																																																			.	.	.	none		0.691	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				-	5352476	ATCG	-	5352473	7	5	235	1	0	1	0	1	0	0	0	0	16351	214	8	0	873	0	TNRC18	7	5352473	Frame_Shift_Del	DEL	ATCG	TCGA-P4-AAVL-01A-11D-A42J-10		5352473	153786190	22	14305											
CALCR	799	hgsc.bcm.edu	37	chr7	93090259	93090259	+	Splice_Site	DEL	C	C	-																															accctttggcagccaaggctCctggaagaaaaagtaacata																										TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr7:93090259delC	ENST00000394441.1	-	7	837	c.522delG	c.(520-522)agg>ag	p.R174fs	CALCR_ENST00000421592.1_Splice_Site_p.L190fs|CALCR_ENST00000426151.1_Splice_Site_p.R174fs|CALCR_ENST00000360249.4_Splice_Site_p.L190fs|CALCR_ENST00000359558.2_Splice_Site_p.L208fs	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor	192					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)	AGCCAAGGCTCCTGGAAGAAA	0.348																																					p.S209fs		Atlas-INDEL	.											.	CALCR	200	.	0			c.625delA						PASS	.						100	100	100					7																	93090259		2203	4300	6503	SO:0001630	splice_region_variant	799	exon10			.	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.522-1G>-	chr7.hg19:g.93090259delC		108.0	0.0	0		168.0	26.0	0.154762	NM_001164737	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Frame_Shift_Del	DEL	ENST00000394441.1	hg19	CCDS5631.1																																																																																			.	.	.	none		0.348	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742	Frame_Shift_Del	-	93090259	C	-	93090259	8	5	235	1	0	1	0	1	0	0	1	0	2581	869	30	0	930	0	CALCR	7	93090259	Splice_Site	DEL	C	TCGA-P4-AAVL-01A-11D-A42J-10	87737786	93090259	66048404	23	14306	145	2									
CALCR	799	hgsc.bcm.edu	37	chr7	93090260	93090267	+	Splice_Site	DEL	CTGGAAGA	CTGGAAGA	-																															ccctttggcagccaaggctcCtggaagaaaaagtaacataa																								rs375917807		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	CTGGAAGA	CTGGAAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr7:93090260_93090267delCTGGAAGA	ENST00000394441.1	-	7	837		c.e7-1		CALCR_ENST00000421592.1_Splice_Site|CALCR_ENST00000426151.1_Splice_Site|CALCR_ENST00000360249.4_Splice_Site|CALCR_ENST00000359558.2_Splice_Site	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor						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)	GCCAAGGCTCCTGGAAGAAAAAGTAACA	0.346																																					p.208_208del		Pindel	.											.,2	CALCR	200	.	0			c.624_624del						PASS	.																																			SO:0001630	splice_region_variant	799	exon10			.	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.522-1TCTTCCAG>-	chr7.hg19:g.93090260_93090267delCTGGAAGA		107.0	0.0	.		163.0	23.0	0.141	NM_001164737	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Frame_Shift_Del	DEL	ENST00000394441.1	hg19	CCDS5631.1																																																																																			.	.	.	none		0.346	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742	Intron	-	93090267	CTGGAAGA	-	93090260	8	5	235	1	0	1	0	1	0	0	1	0	2581	695	24	0	931	0	CALCR	7	93090260	Splice_Site	DEL	CTGGAAGA	TCGA-P4-AAVL-01A-11D-A42J-10	1	93090260	66048403	24	14307	145	2									
ACN9	57001	hgsc.bcm.edu	37	chr7	96810419	96810420	+	Frame_Shift_Ins	INS	-	-	A																															tcctcccagaagaaaaacttINSaatgactttcgtgatgaaca																								rs150372148		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr7:96810419_96810420insA	ENST00000432641.2	+	2	1404_1405	c.270_271insA	c.(271-273)aatfs	p.N91fs	ACN9_ENST00000360382.4_3'UTR|ACN9_ENST00000479853.1_3'UTR	NM_020186.2	NP_064571.1			ACN9 homolog (S. cerevisiae)											large_intestine(1)|lung(4)|ovary(1)|skin(1)|urinary_tract(3)	10	all_cancers(62;2.54e-08)|all_epithelial(64;2.24e-08)|Esophageal squamous(72;0.00507)|all_lung(186;0.154)|Lung NSC(181;0.159)					AAGAAAAACTTAATGACTTTCG	0.391																																					p.L90fs		Atlas-Indel,Pindel	.											.	ACN9	19	.	0			c.270_271insA						PASS	.																																			SO:0001589	frameshift_variant	57001	exon2			.	BC028409	CCDS5648.1	7q22.1	2006-02-09			ENSG00000196636	ENSG00000196636			21752	protein-coding gene	gene with protein product		615773					Standard	NM_020186		Approved	DC11	uc003uoo.4	Q9NRP4	OTTHUMG00000154064	ENST00000432641.2:c.272dupA	chr7.hg19:g.96810421_96810421dupA	ENSP00000414066:p.Asn91fs	410.0	0.0	0		924.0	671.0	0.72619	NM_020186		Frame_Shift_Ins	INS	ENST00000432641.2	hg19	CCDS5648.1																																																																																			.	.	.	none		0.391	ACN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333685.3	NM_020186		A	96810420	-	A	96810419	7	5	235	1	0	1	1	0	0	0	0	0	145	1741	61	0	276	0	ACN9	7	96810419	Frame_Shift_Ins	INS	-	TCGA-P4-AAVL-01A-11D-A42J-10	3720159	96810419	62328244	25	14308											
POP7	10248	hgsc.bcm.edu	37	chr7	100304640	100304640	+	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	tggacggaggggcccggggtCagaacgcgtgctctgagatc	7	6	18	10	4	2	2	1	1	1	2	3	5	2	4	1	6	2	1	1	6	1	0			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr7:100304640C>T	ENST00000303151.4	+	2	449	c.187C>T	c.(187-189)Cag>Tag	p.Q63*		NM_005837.2	NP_005828.2	O75817	POP7_HUMAN	processing of precursor 7, ribonuclease P/MRP subunit (S. cerevisiae)	63					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|nucleolar ribonuclease P complex (GO:0005655)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|ribonuclease P activity (GO:0004526)			endometrium(2)|kidney(1)|ovary(1)	4	Lung NSC(181;0.041)|all_lung(186;0.0581)					GGCCCGGGGTCAGAACGCGTG	0.622																																					p.Q63X		Atlas-SNP	.											.	POP7	8	.	0			c.C187T						PASS	.						89	102	98					7																	100304640		2203	4300	6503	SO:0001587	stop_gained	10248	exon2			CGGGGTCAGAACG	U94316	CCDS5704.1	7q22	2012-05-21	2007-06-26		ENSG00000172336	ENSG00000172336			19949	protein-coding gene	gene with protein product	"ribonuclease P protein subunit p20"	606113	"processing of precursor 7, ribonuclease P subunit (S. cerevisiae)"			9630247	Standard	NM_005837		Approved	RPP20, RPP2	uc003uwh.4	O75817	OTTHUMG00000044311	ENST00000303151.4:c.187C>T	chr7.hg19:g.100304640C>T	ENSP00000304353:p.Gln63*	86.0	0.0	.		230.0	78.0	.	NM_005837	A4D2E0|Q9BV74	Nonsense_Mutation	SNP	ENST00000303151.4	hg19	CCDS5704.1	.	.	.	.	.	.	.	.	.	.	C	33	5.245502	0.95272	.	.	ENSG00000172336	ENST00000303151;ENST00000457480	.	.	.	5.47	4.54	0.55810	.	0.000000	0.45361	D	0.000366	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	-19.7764	11.4012	0.49871	0.0:0.8177:0.1823:0.0	.	.	.	.	X	63	.	ENSP00000304353:Q63X	Q	+	1	0	POP7	100142576	0.998000	0.40836	0.999000	0.59377	0.699000	0.40488	3.263000	0.51546	2.558000	0.86282	0.561000	0.74099	CAG	.	.	.	none		0.622	POP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103070.1	NM_005837		T	100304640	C	T	100304640	4	4	235	1	0	0	0	0	0	1	0	0	12261	827	29	2	189	2	POP7	7	100304640	Nonsense_Mutation	SNP	C	TCGA-P4-AAVL-01A-11D-A42J-10	3494221	100304640	58834023	26	14309											
RELN	5649	hgsc.bcm.edu	37	chr7	103474054	103474054	+	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	gaggttggttgtgggcaggtGactcacgtgagaggctacca	8	9	17	7	1	1	2	1	2	0	1	1	4	1	2	1	5	1	4	1	5	1	3			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr7:103474054G>C	ENST00000428762.1	-	3	562	c.403C>G	c.(403-405)Cac>Gac	p.H135D	RELN_ENST00000424685.2_Missense_Mutation_p.H135D|RELN_ENST00000343529.5_Missense_Mutation_p.H135D	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	135	Reelin. {ECO:0000255|PROSITE- ProRule:PRU00363}.				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)		GTGGGCAGGTGACTCACGTGA	0.483																																					p.H135D	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.C403G						PASS	.						121	106	111					7																	103474054		2203	4300	6503	SO:0001583	missense	5649	exon3			GCAGGTGACTCAC		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.403C>G	chr7.hg19:g.103474054G>C	ENSP00000392423:p.His135Asp	140.0	0.0	.		228.0	39.0	.	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	hg19	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.958642	0.92726	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.21543	2.0;2.0;2.0	5.33	5.33	0.75918	Reeler domain (2);	0.000000	0.85682	D	0.000000	T	0.31857	0.0810	N	0.14661	0.345	0.80722	D	1	D;D	0.62365	0.989;0.991	D;D	0.78314	0.985;0.991	T	0.17167	-1.0378	10	0.42905	T	0.14	.	19.3931	0.94592	0.0:0.0:1.0:0.0	.	135;135	P78509-2;P78509	.;RELN_HUMAN	D	135	ENSP00000392423:H135D;ENSP00000345694:H135D;ENSP00000388446:H135D	ENSP00000345694:H135D	H	-	1	0	RELN	103261290	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.788000	0.91834	2.634000	0.89283	0.650000	0.86243	CAC	.	.	.	none		0.483	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		C	103474054	G	C	103474054	3	2	235	1	0	0	0	0	1	0	0	0	13233	1290	45	4	10231	4	RELN	7	103474054	Missense_Mutation	SNP	G	TCGA-P4-AAVL-01A-11D-A42J-10	3169414	103474054	55664609	27	14310											
SND1	27044	hgsc.bcm.edu	37	chr7	127725765	127725765	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccatgatgccattgcaggtAccgtgcccgagtagagaaag	11	7	12	11	2	0	2	0	1	0	1	0	4	0	2	4	1	4	3	4	1	3	3			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr7:127725765A>G	ENST00000354725.3	+	20	2431	c.2237A>G	c.(2236-2238)tAc>tGc	p.Y746C		NM_014390.2	NP_055205.2	Q7KZF4	SND1_HUMAN	staphylococcal nuclease and tudor domain containing 1	746	Tudor. {ECO:0000255|PROSITE- ProRule:PRU00211}.				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						CATTGCAGGTACCGTGCCCGA	0.572																																					p.Y746C		Atlas-SNP	.											.	SND1	104	.	0			c.A2237G						PASS	.						173	156	162					7																	127725765		2203	4300	6503	SO:0001583	missense	27044	exon20			GCAGGTACCGTGC		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.2237A>G	chr7.hg19:g.127725765A>G	ENSP00000346762:p.Tyr746Cys	53.0	0.0	.		83.0	10.0	.	NM_014390	Q13122|Q96AG0	Missense_Mutation	SNP	ENST00000354725.3	hg19	CCDS34747.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.305315	0.81247	.	.	ENSG00000197157	ENST00000354725;ENST00000438400	T	0.14022	2.54	5.34	5.34	0.76211	Tudor subgroup (1);Staphylococcal nuclease (SNase-like) (1);Staphylococcal nuclease (SNase-like), OB-fold (1);Maternal tudor protein (1);Tudor domain (1);	0.118078	0.64402	D	0.000014	T	0.52370	0.1730	H	0.97540	4.025	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68891	-0.5289	10	0.62326	D	0.03	-15.954	13.5717	0.61851	1.0:0.0:0.0:0.0	.	746	Q7KZF4	SND1_HUMAN	C	746;736	ENSP00000346762:Y746C	ENSP00000346762:Y746C	Y	+	2	0	SND1	127513001	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.540000	0.90641	2.144000	0.66660	0.533000	0.62120	TAC	.	.	.	none		0.572	SND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349148.1	NM_014390		G	127725765	A	G	127725765	3	3	235	1	0	0	0	0	1	0	0	0	14857	391	14	3	2315	3	SND1	7	127725765	Missense_Mutation	SNP	A	TCGA-P4-AAVL-01A-11D-A42J-10	24251711	127725765	31412898	28	14311											
PLXNA4	91584	hgsc.bcm.edu	37	chr7	131864511	131864511	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatctgcagccgcttcagcGtgaggtcactttcgcgggac	6	9	13	13	4	3	1	2	1	1	0	4	2	3	2	1	2	3	3	1	2	0	2			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr7:131864511G>A	ENST00000359827.3	-	20	4771	c.3809C>T	c.(3808-3810)aCg>aTg	p.T1270M	PLXNA4_ENST00000321063.4_Missense_Mutation_p.T1270M			Q9HCM2	PLXA4_HUMAN	plexin A4	1270					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						CCGCTTCAGCGTGAGGTCACT	0.597																																					p.T1270M		Atlas-SNP	.											.	PLXNA4	873	.	0			c.C3809T						PASS	.						55	52	53					7																	131864511		2203	4300	6503	SO:0001583	missense	91584	exon20			TTCAGCGTGAGGT	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.3809C>T	chr7.hg19:g.131864511G>A	ENSP00000352882:p.Thr1270Met	70.0	0.0	.		130.0	25.0	.	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	hg19	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.723727	0.89298	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.00986	5.47;5.47	4.82	4.82	0.62117	.	0.089584	0.85682	D	0.000000	T	0.05777	0.0151	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.18587	-1.0332	10	0.59425	D	0.04	.	18.0686	0.89398	0.0:0.0:1.0:0.0	.	1270	Q9HCM2	PLXA4_HUMAN	M	1270	ENSP00000323194:T1270M;ENSP00000352882:T1270M	ENSP00000323194:T1270M	T	-	2	0	PLXNA4	131515051	1.000000	0.71417	0.924000	0.36721	0.952000	0.60782	9.618000	0.98365	2.524000	0.85096	0.484000	0.47621	ACG	.	.	.	none		0.597	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		A	131864511	G	A	131864511	3	1	235	1	0	0	0	0	1	0	0	0	12129	1145	40	1	1927	1	PLXNA4	7	131864511	Missense_Mutation	SNP	G	TCGA-P4-AAVL-01A-11D-A42J-10	4138746	131864511	27274152	29	14312											
ZNF425	155054	hgsc.bcm.edu	37	chr7	148801369	148801369	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgtcggcggaaactgcggcCgcactcggcgcaggagaacg	8	3	17	13	8	0	1	0	0	0	1	2	3	0	2	1	5	3	2	1	5	2	0			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr7:148801369C>T	ENST00000378061.2	-	4	1726	c.1594G>A	c.(1594-1596)Ggc>Agc	p.G532S		NM_001001661.2	NP_001001661.1	Q6IV72	ZN425_HUMAN	zinc finger protein 425	532					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)			AAACTGCGGCCGCACTCGGCG	0.627																																					p.G532S		Atlas-SNP	.											ZNF425,colon,carcinoma,0,1	ZNF425	99	.	0			c.G1594A						PASS	.						38	34	35					7																	148801369		2203	4300	6503	SO:0001583	missense	155054	exon4			TGCGGCCGCACTC	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.1594G>A	chr7.hg19:g.148801369C>T	ENSP00000367300:p.Gly532Ser	51.0	0.0	.		145.0	31.0	.	NM_001001661	B3KPM1|Q08AG3	Missense_Mutation	SNP	ENST00000378061.2	hg19	CCDS34773.1	.	.	.	.	.	.	.	.	.	.	C	13.55	2.270839	0.40194	.	.	ENSG00000204947	ENST00000378061	T	0.20463	2.07	2.75	-4.16	0.03869	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12135	0.0295	L	0.38175	1.15	0.23704	N	0.997065	P	0.44816	0.844	B	0.29942	0.109	T	0.10613	-1.0622	9	0.87932	D	0	.	11.3998	0.49864	0.0:0.7947:0.0:0.2053	.	532	Q6IV72	ZN425_HUMAN	S	532	ENSP00000367300:G532S	ENSP00000367300:G532S	G	-	1	0	ZNF425	148432302	0.000000	0.05858	0.015000	0.15790	0.114000	0.19823	-0.148000	0.10219	-1.040000	0.03271	-0.768000	0.03414	GGC	.	.	.	none		0.627	ZNF425-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352726.1	XM_088140		T	148801369	C	T	148801369	3	4	235	1	0	0	0	0	1	0	0	0	17911	652	23	1	668	1	ZNF425	7	148801369	Missense_Mutation	SNP	C	TCGA-P4-AAVL-01A-11D-A42J-10	16936858	148801369	10337294	30	14313											
SSPO	23145	hgsc.bcm.edu	37	chr7	149518600	149518600	+	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	cagggcactcgctcccgcacCctgggggacagctggctgca	6	5	14	16	2	0	0	0	0	0	0	2	1	1	1	2	4	2	6	2	4	0	0			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr7:149518600C>T	ENST00000378016.2	+	0	12669							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)			GCTCCCGCACCCTGGGGGACA	0.721																																					p.T4223T		Atlas-SNP	.											.	.	.	.	0			c.C12669T						PASS	.						4	5	5					7																	149518600		1851	3972	5823			23145	exon88			CCGCACCCTGGGG	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149518600C>T		55.0	0.0	.		76.0	31.0	.	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	hg19																																																																																				.	.	.	none		0.721	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				T	149518600	C	T	149518600	1	4	235	0	1	0	0	0	0	0	0	0	15201	610	22	2		2	SSPO	7	149518600	RNA	SNP	C	TCGA-P4-AAVL-01A-11D-A42J-10	717231	149518600	9620063	31	14314											
GPR124	25960	hgsc.bcm.edu	37	chr8	37693093	37693093	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcgtggccctggcctccAtccagctgcccccgagtcta	6	7	10	18	2	1	0	0	0	1	0	3	1	3	0	6	2	3	1	6	2	1	1	rs377757244		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr8:37693093A>G	ENST00000412232.2	+	13	1868	c.1855A>G	c.(1855-1857)Atc>Gtc	p.I619V	GPR124_ENST00000315215.7_Intron	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	619					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)			CCTGGCCTCCATCCAGCTGCC	0.652																																					p.I619V		Atlas-SNP	.											.	GPR124	85	.	0			c.A1855G						PASS	.	A	VAL/ILE	0,4406		0,0,2203	72	87	82		1855	5.2	1	8		82	1,8599	1.2+/-3.3	0,1,4299	no	missense	GPR124	NM_032777.9	29	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	619/1339	37693093	1,13005	2203	4300	6503	SO:0001583	missense	25960	exon13			GCCTCCATCCAGC	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.1855A>G	chr8.hg19:g.37693093A>G	ENSP00000406367:p.Ile619Val	56.0	0.0	.		40.0	15.0	.	NM_032777	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Missense_Mutation	SNP	ENST00000412232.2	hg19	CCDS6097.2	.	.	.	.	.	.	.	.	.	.	A	12.56	1.973999	0.34848	0.0	1.16E-4	ENSG00000020181	ENST00000416514;ENST00000412232	T	0.57907	0.37	5.16	5.16	0.70880	.	0.073105	0.56097	D	0.000031	T	0.35508	0.0934	N	0.12961	0.28	0.45118	D	0.998131	B	0.24963	0.115	B	0.15870	0.014	T	0.14144	-1.0483	10	0.30854	T	0.27	-23.7224	14.9878	0.71362	1.0:0.0:0.0:0.0	.	619	Q96PE1	GP124_HUMAN	V	612;619	ENSP00000406367:I619V	ENSP00000406367:I619V	I	+	1	0	GPR124	37812251	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.170000	0.50816	1.965000	0.57142	0.459000	0.35465	ATC	.	.	.	weak		0.652	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2			G	37693093	A	G	37693093	3	3	235	1	0	0	0	0	1	0	0	0	6645	217	8	3	1884	3	GPR124	8	37693093	Missense_Mutation	SNP	A	TCGA-P4-AAVL-01A-11D-A42J-10		37693093	108670929	32	14315											
NOL6	65083	hgsc.bcm.edu	37	chr9	33467705	33467705	+	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	tcacctctgggactgggggtCgagagtgagccagcaggttc	7	8	16	10	1	2	2	1	1	1	1	4	4	2	3	2	4	2	2	2	4	0	1	rs546933819		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr9:33467705C>T	ENST00000379471.2	-	12	1673	c.1586G>A	c.(1585-1587)cGa>cAa	p.R529Q	NOL6_ENST00000455041.2_Missense_Mutation_p.R477Q|NOL6_ENST00000464829.1_Intron			Q9H6R4	NOL6_HUMAN	nucleolar protein 6 (RNA-associated)	529					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)		GACTGGGGGTCGAGAGTGAGC	0.617																																					p.R529Q		Atlas-SNP	.											.	NOL6	85	.	0			c.G1586A						PASS	.						28	30	29					9																	33467705		2203	4300	6503	SO:0001583	missense	65083	exon12			GGGGGTCGAGAGT	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.1586G>A	chr9.hg19:g.33467705C>T	ENSP00000368784:p.Arg529Gln	60.0	0.0	.		76.0	39.0	.	NM_022917	Q5T5M3|Q5T5M4|Q7L4G6|Q8N6I0|Q8TEY9|Q8TEZ0|Q8TEZ1|Q9H675	Missense_Mutation	SNP	ENST00000379471.2	hg19		.	.	.	.	.	.	.	.	.	.	C	7.723	0.697590	0.15106	.	.	ENSG00000165271	ENST00000353159;ENST00000297990;ENST00000379471;ENST00000541373;ENST00000325914;ENST00000455041	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	5.22	5.22	0.72569	.	0.374443	0.27298	N	0.020004	T	0.32041	0.0816	L	0.58101	1.795	0.34379	D	0.692933	P;P;P;P;P	0.39044	0.646;0.594;0.594;0.656;0.646	B;B;B;B;B	0.30943	0.087;0.052;0.052;0.122;0.087	T	0.39121	-0.9629	10	0.11794	T	0.64	.	11.3263	0.49450	0.2257:0.7743:0.0:0.0	.	477;526;529;529;529	B4DF80;Q9H6R4-4;Q9H6R4-2;Q9H6R4-3;Q9H6R4	.;.;.;.;NOL6_HUMAN	Q	529;529;529;85;529;477	ENSP00000313978:R529Q;ENSP00000297990:R529Q;ENSP00000368784:R529Q;ENSP00000395915:R477Q	ENSP00000297990:R529Q	R	-	2	0	NOL6	33457705	1.000000	0.71417	1.000000	0.80357	0.249000	0.25844	1.842000	0.39250	2.720000	0.93068	0.655000	0.94253	CGA	.	.	.	none		0.617	NOL6-005	NOVEL	non_canonical_TEC|basic	protein_coding	protein_coding	OTTHUMT00000001019.2	NM_022917		T	33467705	C	T	33467705	3	4	235	1	0	0	0	0	1	0	0	0	10532	884	31	1	1914	1	NOL6	9	33467705	Missense_Mutation	SNP	C	TCGA-P4-AAVL-01A-11D-A42J-10		33467705	107745726	33	14316											
PRKACG	5568	hgsc.bcm.edu	37	chr9	71628443	71628443	+	Missense_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	tgcggcccttcacgcgcttgGcgaaaccgaagtccgtcacc	7	7	11	16	6	2	0	2	0	0	0	3	2	3	0	4	2	2	1	4	2	2	2			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr9:71628443G>A	ENST00000377276.2	-	1	596	c.566C>T	c.(565-567)gCc>gTc	p.A189V		NM_002732.3	NP_002723.2	P22612	KAPCG_HUMAN	protein kinase, cAMP-dependent, catalytic, gamma	189	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)|carbohydrate metabolic process (GO:0005975)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|male gonad development (GO:0008584)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						CACGCGCTTGGCGAAACCGAA	0.617																																					p.A189V	Esophageal Squamous(110;2236 2623 32146)	Atlas-SNP	.											.	PRKACG	65	.	0			c.C566T						PASS	.						45	45	45					9																	71628443		2203	4300	6503	SO:0001583	missense	5568	exon1			CGCTTGGCGAAAC	M34182	CCDS6625.1	9q13	2012-10-02			ENSG00000165059	ENSG00000165059	2.7.11.1		9382	protein-coding gene	gene with protein product		176893				2342480, 9598317	Standard	NM_002732		Approved	PKACg	uc004agy.3	P22612	OTTHUMG00000019974	ENST00000377276.2:c.566C>T	chr9.hg19:g.71628443G>A	ENSP00000366488:p.Ala189Val	67.0	0.0	.		79.0	30.0	.	NM_002732	O60850|Q5VZ02|Q86YI1	Missense_Mutation	SNP	ENST00000377276.2	hg19	CCDS6625.1	.	.	.	.	.	.	.	.	.	.	G	18.17	3.565223	0.65651	.	.	ENSG00000165059	ENST00000377276	T	0.75821	-0.97	1.03	1.03	0.20045	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	0.30859	U	0.008721	T	0.75925	0.3916	L	0.56124	1.755	0.33063	D	0.534337	D	0.61697	0.99	P	0.57776	0.827	T	0.79082	-0.1949	10	0.87932	D	0	.	7.4815	0.27408	0.0:0.0:1.0:0.0	.	189	P22612	KAPCG_HUMAN	V	189	ENSP00000366488:A189V	ENSP00000366488:A189V	A	-	2	0	PRKACG	70818263	1.000000	0.71417	0.025000	0.17156	0.026000	0.11368	2.854000	0.48325	0.458000	0.26988	0.467000	0.42956	GCC	.	.	.	none		0.617	PRKACG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052559.1			A	71628443	G	A	71628443	3	1	235	1	0	0	0	0	1	0	0	0	12509	1203	42	2	493	2	PRKACG	9	71628443	Missense_Mutation	SNP	G	TCGA-P4-AAVL-01A-11D-A42J-10	38160738	71628443	69584988	34	14317											
RALGDS	5900	hgsc.bcm.edu	37	chr9	135975749	135975749	+	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	gccttgcggattacagccggAgccttatcttggctggtcac	6	11	12	12	2	2	0	1	0	1	0	2	2	2	2	3	4	4	1	3	4	2	4			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr9:135975749A>C	ENST00000372050.3	-	17	2496	c.2475T>G	c.(2473-2475)gcT>gcG	p.A825A	RALGDS_ENST00000469972.1_5'UTR|RALGDS_ENST00000542690.1_Silent_p.A896A|RALGDS_ENST00000372047.3_Silent_p.A813A|RALGDS_ENST00000393160.3_Silent_p.A770A|RALGDS_ENST00000393157.3_Silent_p.A824A|RALGDS_ENST00000372062.3_Silent_p.A796A	NM_006266.2	NP_006257.1	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator	825	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				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)		TTACAGCCGGAGCCTTATCTT	0.597			T	CIITA	"PMBL, Hodgkin Lymphona, "																																p.A825A	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.T2475G						PASS	.						145	138	140					9																	135975749		2203	4300	6503	SO:0001819	synonymous_variant	5900	exon17			AGCCGGAGCCTTA	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.2475T>G	chr9.hg19:g.135975749A>C		62.0	0.0	.		76.0	29.0	.	NM_006266	B7Z753|E7ER93|E7ERZ0|Q5T7V4|Q6KH11|Q6PCE1|Q6ZSD5|Q9HAX7|Q9HAY1|Q9HCT1|Q9P2N8	Silent	SNP	ENST00000372050.3	hg19	CCDS6959.1																																																																																			.	.	.	none		0.597	RALGDS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054837.1	NM_006266		C	135975749	A	C	135975749	2	2	235	1	0	0	0	0	0	0	0	1	13029	291	11	5		5	RALGDS	9	135975749	Silent	SNP	A	TCGA-P4-AAVL-01A-11D-A42J-10	64347306	135975749	5237682	35	14318											
OPTN	10133	hgsc.bcm.edu	37	chr10	13167963	13167963	+	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	taggtccaaattaactgtgcTacagatgacacacaacaagc	16	8	7	10	0	0	2	0	1	0	1	1	2	1	2	1	1	5	1	1	1	6	3			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr10:13167963T>A	ENST00000378748.3	+	12	1528	c.1166T>A	c.(1165-1167)cTa>cAa	p.L389Q	OPTN_ENST00000378752.3_Missense_Mutation_p.L383Q|OPTN_ENST00000263036.5_Missense_Mutation_p.L389Q|OPTN_ENST00000378747.3_Missense_Mutation_p.L389Q|OPTN_ENST00000378757.2_Missense_Mutation_p.L389Q|OPTN_ENST00000378764.2_Missense_Mutation_p.L383Q	NM_001008211.1|NM_001008213.1	NP_001008212|NP_001008214	Q96CV9	OPTN_HUMAN	optineurin	389					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						TTAACTGTGCTACAGATGACA	0.323																																					p.L389Q		Atlas-SNP	.											.	OPTN	57	.	0			c.T1166A						PASS	.						74	72	73					10																	13167963		2203	4299	6502	SO:0001583	missense	10133	exon11			CTGTGCTACAGAT	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.1166T>A	chr10.hg19:g.13167963T>A	ENSP00000368022:p.Leu389Gln	157.0	0.0	.		139.0	47.0	.	NM_001008212	B3KP00|D3DRS4|D3DRS8|Q5T672|Q5T673|Q5T674|Q5T675|Q7LDL9|Q8N562|Q9UET9|Q9UEV4|Q9Y218	Missense_Mutation	SNP	ENST00000378748.3	hg19	CCDS7094.1	.	.	.	.	.	.	.	.	.	.	T	12.79	2.042827	0.36085	.	.	ENSG00000123240	ENST00000263036;ENST00000378764;ENST00000378757;ENST00000378752;ENST00000378748;ENST00000378747	D;D;D;D;D;D	0.93604	-3.25;-3.23;-3.25;-3.23;-3.25;-3.25	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	D	0.96340	0.8806	M	0.79123	2.44	0.36206	D	0.851028	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99620	1.0983	10	0.87932	D	0	-7.3191	13.5457	0.61702	0.0:0.0:0.0:1.0	.	383;389	Q96CV9-2;Q96CV9	.;OPTN_HUMAN	Q	389;383;389;383;389;389	ENSP00000263036:L389Q;ENSP00000368040:L383Q;ENSP00000368032:L389Q;ENSP00000368027:L383Q;ENSP00000368022:L389Q;ENSP00000368021:L389Q	ENSP00000263036:L389Q	L	+	2	0	OPTN	13207969	0.887000	0.30362	0.150000	0.22450	0.037000	0.13140	4.685000	0.61693	2.239000	0.73571	0.528000	0.53228	CTA	.	.	.	none		0.323	OPTN-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046834.1	NM_021980		A	13167963	T	A	13167963	3	1	235	1	0	0	0	0	1	0	0	0	10896	1522	53	5	1200	5	OPTN	10	13167963	Missense_Mutation	SNP	T	TCGA-P4-AAVL-01A-11D-A42J-10		13167963	122366784	36	14319											
CUBN	8029	hgsc.bcm.edu	37	chr10	17113553	17113554	+	Frame_Shift_Ins	INS	-	-	A																															tctccaggatacacgttaggINSaaaaaaaggcgagcgaatga																										TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr10:17113553_17113554insA	ENST00000377833.4	-	19	2561_2562	c.2496_2497insT	c.(2494-2499)tttcctfs	p.P833fs		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	833	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.P833S(1)		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)	TACACGTTAGGAAAAAAAGGCG	0.416																																					p.P833fs		Atlas-Indel,Pindel	.											CUBN,NS,carcinoma,0,1	CUBN	515	.	1	Substitution - Missense(1)	lung(1)	c.2497_2498insT						PASS	.																																			SO:0001589	frameshift_variant	8029	exon19			.	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.2497dupT	chr10.hg19:g.17113560_17113560dupA	ENSP00000367064:p.Pro833fs	62.0	0.0	0		42.0	11.0	0.261905	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Frame_Shift_Ins	INS	ENST00000377833.4	hg19	CCDS7113.1																																																																																			.	.	.	none		0.416	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		A	17113554	-	A	17113553	7	5	235	1	0	1	1	0	0	0	0	0	4053	1174	41	0	8570	0	CUBN	10	17113553	Frame_Shift_Ins	INS	-	TCGA-P4-AAVL-01A-11D-A42J-10	3945590	17113553	118421194	37	14320											
JMJD1C	221037	hgsc.bcm.edu	37	chr10	64957243	64957243	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccacatttttggcagacccAgtgaatgttaaacaatgttg	12	13	8	8	0	0	2	0	1	0	1	1	2	1	2	2	1	1	3	2	1	4	4			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr10:64957243A>G	ENST00000399262.2	-	13	5790	c.5572T>C	c.(5572-5574)Tgg>Cgg	p.W1858R	JMJD1C_ENST00000399251.1_3'UTR|JMJD1C_ENST00000402544.1_Missense_Mutation_p.W1639R|JMJD1C_ENST00000542921.1_Missense_Mutation_p.W1676R	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	1858					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)					TGGCAGACCCAGTGAATGTTA	0.388																																					p.W1858R		Atlas-SNP	.											.	JMJD1C	347	.	0			c.T5572C						PASS	.						134	125	128					10																	64957243		1918	4150	6068	SO:0001583	missense	221037	exon13			AGACCCAGTGAAT	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.5572T>C	chr10.hg19:g.64957243A>G	ENSP00000382204:p.Trp1858Arg	110.0	0.0	.		90.0	35.0	.	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	hg19	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	A	25.7	4.667939	0.88348	.	.	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000542921	D;T;T	0.89050	-2.46;-0.49;-0.2	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	D	0.95465	0.8527	M	0.89534	3.04	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	0.96187	0.9135	10	0.72032	D	0.01	-4.2633	16.1819	0.81915	1.0:0.0:0.0:0.0	.	1399;1858;1676	A6PW35;Q15652;A0T124	.;JHD2C_HUMAN;.	R	1858;1639;1676	ENSP00000382204:W1858R;ENSP00000384990:W1639R;ENSP00000444682:W1676R	ENSP00000382204:W1858R	W	-	1	0	JMJD1C	64627249	1.000000	0.71417	0.995000	0.50966	0.991000	0.79684	9.255000	0.95524	2.279000	0.76181	0.533000	0.62120	TGG	.	.	.	none		0.388	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		G	64957243	A	G	64957243	3	3	235	1	0	0	0	0	1	0	0	0	7957	188	7	3	2106	3	JMJD1C	10	64957243	Missense_Mutation	SNP	A	TCGA-P4-AAVL-01A-11D-A42J-10	47843690	64957243	70577504	38	14321											
CDH23	64072	hgsc.bcm.edu	37	chr10	73567274	73567274	+	Splice_Site	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	gccatgatcccaccctcagcCggcaacgaagagaagaactt	13	5	9	14	2	1	3	1	1	0	2	2	5	2	3	4	1	3	1	4	1	4	1			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr10:73567274C>G	ENST00000224721.6	+	58	8330	c.8325C>G	c.(8323-8325)gcC>gcG	p.A2775A	CDH23_ENST00000398788.3_Splice_Site_p.A530A|CDH23_ENST00000475158.1_3'UTR	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2770	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)	p.A2775A(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						CACCCTCAGCCGGCAACGAAG	0.607																																					p.A2770A		Atlas-SNP	.											CDH23,colon,carcinoma,0,1	CDH23	365	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C8310G						PASS	.						34	40	38					10																	73567274		2081	4204	6285	SO:0001630	splice_region_variant	64072	exon57			CTCAGCCGGCAAC	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.8324-1C>G	chr10.hg19:g.73567274C>G		55.0	0.0	.		78.0	33.0	.	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	hg19																																																																																				.	.	.	none		0.607	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	Silent	G	73567274	C	G	73567274	5	3	235	1	0	0	0	0	0	0	1	0	3110	666	23	4	8885	4	CDH23	10	73567274	Splice_Site	SNP	C	TCGA-P4-AAVL-01A-11D-A42J-10	8610031	73567274	61967473	39	14322											
ECD	11319	hgsc.bcm.edu	37	chr10	74899240	74899240	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agctgatctggtgagagatcTaaccactggtcatctgaaaa	13	10	10	8	0	4	4	1	3	3	1	4	5	4	4	1	2	2	1	1	2	3	1			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr10:74899240T>C	ENST00000372979.4	-	11	1454	c.1248A>G	c.(1246-1248)ttA>ttG	p.L416L	ECD_ENST00000454759.2_Silent_p.L373L|ECD_ENST00000430082.2_Silent_p.L449L	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	416					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)					GTGAGAGATCTAACCACTGGT	0.443																																					p.L449L		Atlas-SNP	.											.	ECD	50	.	0			c.A1347G						PASS	.						83	86	85					10																	74899240		2203	4300	6503	SO:0001819	synonymous_variant	11319	exon12			GAGATCTAACCAC	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.1248A>G	chr10.hg19:g.74899240T>C		58.0	0.0	.		47.0	20.0	.	NM_001135752	C9JX46|E9PAW8	Silent	SNP	ENST00000372979.4	hg19	CCDS7321.1																																																																																			.	.	.	none		0.443	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265		C	74899240	T	C	74899240	2	2	235	1	0	0	0	0	0	0	0	1	4890	1519	53	3		3	ECD	10	74899240	Silent	SNP	T	TCGA-P4-AAVL-01A-11D-A42J-10	1331966	74899240	60635507	40	14323											
MUC2	4583	hgsc.bcm.edu	37	chr11	1093437	1093437	+	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	cccatcaccaccaccaccacGgtgaccccaaccccgacacc	11	2	4	24	2	1	1	1	1	0	0	1	2	1	1	10	1	1	0	10	1	1	0			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr11:1093437G>C	ENST00000441003.2	+	30	5283	c.5256G>C	c.(5254-5256)acG>acC	p.T1752T	MUC2_ENST00000333592.6_Silent_p.T40T|MUC2_ENST00000359061.5_Silent_p.T1719T|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.T1752T(1)|p.T1719T(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)	ccaccaccacggtgaccccaa	0.632																																					p.T1752T		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	.	2	Substitution - coding silent(2)	kidney(2)	c.G5256C						PASS	.						180	207	198					11																	1093437		2046	4038	6084	SO:0001819	synonymous_variant	4583	exon30			CACCACGGTGACC	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.5256G>C	chr11.hg19:g.1093437G>C		25.0	0.0	.		25.0	3.0	.	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	hg19																																																																																				.	.	.	none		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		C	1093437	G	C	1093437	2	2	235	1	0	0	0	0	0	0	0	1	9982	1103	39	4		4	MUC2	11	1093437	Silent	SNP	G	TCGA-P4-AAVL-01A-11D-A42J-10		1093437	133913079	41	14324											
NUP160	23279	hgsc.bcm.edu	37	chr11	47869930	47869930	+	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	gggccgcgcggtcgccgtcaCttccgggggtggggcgggcg	1	5	22	13	8	1	0	1	0	0	0	3	0	2	0	3	7	0	0	3	7	0	1			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr11:47869930C>T	ENST00000378460.2	-	1	89	c.43G>A	c.(43-45)Gtg>Atg	p.V15M	NUP160_ENST00000526870.1_Missense_Mutation_p.V15M|NUP160_ENST00000530326.1_5'Flank|NUP160_ENST00000532747.1_5'Flank	NM_015231.1	NP_056046.1	Q12769	NU160_HUMAN	nucleoporin 160kDa	15					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|biliary_tract(2)|breast(7)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(15)|ovary(6)|prostate(2)|skin(2)|urinary_tract(2)	53						GTCGCCGTCACTTCCGGGGGT	0.706																																					p.V15M		Atlas-SNP	.											.	NUP160	116	.	0			c.G43A						PASS	.						8	10	9					11																	47869930		2114	4175	6289	SO:0001583	missense	23279	exon1			CCGTCACTTCCGG	D83781	CCDS31484.1	11p11.12	2008-07-21	2002-08-29		ENSG00000030066	ENSG00000030066			18017	protein-coding gene	gene with protein product		607614	"nucleoporin 160kD"			11684705	Standard	NM_015231		Approved	KIAA0197, FLJ22583	uc001ngm.3	Q12769	OTTHUMG00000166534	ENST00000378460.2:c.43G>A	chr11.hg19:g.47869930C>T	ENSP00000367721:p.Val15Met	49.0	0.0	.		45.0	18.0	.	NM_015231	B4DYE8|B4E2J9|Q08AD3|Q7Z5X6|Q96GB3|Q9H660	Missense_Mutation	SNP	ENST00000378460.2	hg19	CCDS31484.1	.	.	.	.	.	.	.	.	.	.	C	16.97	3.269963	0.59540	.	.	ENSG00000030066	ENST00000378460;ENST00000526870	T;T	0.55930	1.37;0.49	4.85	4.85	0.62838	.	0.863746	0.09405	N	0.806618	T	0.55033	0.1895	N	0.08118	0	0.27571	N	0.949872	D;P	0.71674	0.998;0.94	D;P	0.68353	0.957;0.462	T	0.57648	-0.7775	10	0.48119	T	0.1	.	15.2321	0.73398	0.0:1.0:0.0:0.0	.	15;15	Q12769-2;Q12769	.;NU160_HUMAN	M	15	ENSP00000367721:V15M;ENSP00000431495:V15M	ENSP00000367721:V15M	V	-	1	0	NUP160	47826506	1.000000	0.71417	0.999000	0.59377	0.156000	0.22039	1.572000	0.36461	2.404000	0.81709	0.491000	0.48974	GTG	.	.	.	none		0.706	NUP160-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390239.2	NM_015231		T	47869930	C	T	47869930	3	4	235	1	0	0	0	0	1	0	0	0	10764	565	20	2	4411	2	NUP160	11	47869930	Missense_Mutation	SNP	C	TCGA-P4-AAVL-01A-11D-A42J-10	46776493	47869930	87136586	42	14325											
ZBTB3	79842	hgsc.bcm.edu	37	chr11	62520283	62520283	+	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	gggatggaactggagctgagAcaggggctggggctgacgtt	8	7	20	6	1	0	2	0	2	0	1	0	6	0	5	0	7	2	4	0	7	1	1			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr11:62520283A>T	ENST00000394807.3	-	2	1129	c.1004T>A	c.(1003-1005)gTc>gAc	p.V335D		NM_024784.3	NP_079060.1	Q9H5J0	ZBTB3_HUMAN	zinc finger and BTB domain containing 3	335	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)			breast(4)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|ovary(2)|prostate(2)	24						tggagctgagacaggggctgg	0.577																																					p.V335D		Atlas-SNP	.											.	ZBTB3	47	.	0			c.T1004A						PASS	.						42	41	41					11																	62520283		2202	4296	6498	SO:0001583	missense	79842	exon2			GCTGAGACAGGGG	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.1004T>A	chr11.hg19:g.62520283A>T	ENSP00000378286:p.Val335Asp	56.0	0.0	.		65.0	24.0	.	NM_024784		Missense_Mutation	SNP	ENST00000394807.3	hg19	CCDS8034.1	.	.	.	.	.	.	.	.	.	.	A	0.331	-0.955916	0.02267	.	.	ENSG00000185670	ENST00000394807	T	0.11385	2.78	2.63	-3.45	0.04781	.	1.305960	0.05604	U	0.576827	T	0.05181	0.0138	N	0.14661	0.345	0.09310	N	0.999999	B	0.18968	0.032	B	0.20955	0.032	T	0.42275	-0.9461	10	0.12430	T	0.62	.	4.4604	0.11663	0.4401:0.1782:0.3817:0.0	.	335	Q9H5J0	ZBTB3_HUMAN	D	335	ENSP00000378286:V335D	ENSP00000378286:V335D	V	-	2	0	ZBTB3	62276859	0.000000	0.05858	0.027000	0.17364	0.061000	0.15899	-0.163000	0.09997	-0.972000	0.03559	0.459000	0.35465	GTC	.	.	.	none		0.577	ZBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395342.1	NM_024784		T	62520283	A	T	62520283	3	4	235	1	0	0	0	0	1	0	0	0	17546	275	10	5	724	5	ZBTB3	11	62520283	Missense_Mutation	SNP	A	TCGA-P4-AAVL-01A-11D-A42J-10	14650353	62520283	72486233	43	14326											
SLC4A8	9498	hgsc.bcm.edu	37	chr12	51853759	51853759	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	accttcatttcatgaaaaaaAttcctactggggccgaggcc	12	10	8	11	1	2	1	2	1	0	0	3	2	3	1	4	3	1	0	4	3	4	4			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr12:51853759A>G	ENST00000453097.2	+	8	1097	c.880A>G	c.(880-882)Att>Gtt	p.I294V	SLC4A8_ENST00000514353.3_Missense_Mutation_p.I241V|SLC4A8_ENST00000358657.3_Missense_Mutation_p.I321V|SLC4A8_ENST00000535225.2_Missense_Mutation_p.I241V|SLC4A8_ENST00000394856.1_Missense_Mutation_p.I241V	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)		CATGAAAAAAATTCCTACTGG	0.418																																					p.I294V		Atlas-SNP	.											.	SLC4A8	292	.	0			c.A880G						PASS	.						132	138	136					12																	51853759		2203	4300	6503	SO:0001583	missense	9498	exon8			AAAAAAATTCCTA	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.880A>G	chr12.hg19:g.51853759A>G	ENSP00000405812:p.Ile294Val	138.0	0.0	.		138.0	70.0	.	NM_001039960		Missense_Mutation	SNP	ENST00000453097.2	hg19	CCDS44890.1	.	.	.	.	.	.	.	.	.	.	A	17.71	3.456390	0.63401	.	.	ENSG00000050438	ENST00000535225;ENST00000358657;ENST00000453097;ENST00000394856;ENST00000319957;ENST00000514353;ENST00000547697;ENST00000551071	T;T;T;T;T	0.69806	-0.43;-0.43;-0.43;-0.43;-0.43	5.53	5.53	0.82687	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.000000	0.85682	D	0.000000	D	0.83092	0.5179	M	0.85542	2.76	0.80722	D	1	D;B;B;B;B;B;B	0.53151	0.958;0.04;0.018;0.001;0.004;0.002;0.033	D;B;B;B;B;B;B	0.70716	0.97;0.073;0.028;0.077;0.072;0.073;0.036	D	0.85916	0.1443	10	0.87932	D	0	.	14.9425	0.71006	1.0:0.0:0.0:0.0	.	241;321;241;294;294;294;241	E7EML0;Q2Y0W8-2;F5GZ31;Q2Y0W8;Q2Y0W8-3;Q2Y0W8-6;F8VSA8	.;.;.;S4A8_HUMAN;.;.;.	V	241;321;294;241;294;241;241;241	ENSP00000441520:I241V;ENSP00000351483:I321V;ENSP00000405812:I294V;ENSP00000378325:I241V;ENSP00000442561:I241V	ENSP00000315789:I294V	I	+	1	0	SLC4A8	50140026	1.000000	0.71417	0.995000	0.50966	0.865000	0.49528	9.283000	0.95860	2.236000	0.73375	0.482000	0.46254	ATT	.	.	.	none		0.418	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858		G	51853759	A	G	51853759	3	3	235	1	0	0	0	0	1	0	0	0	14672	101	4	3	910	3	SLC4A8	12	51853759	Missense_Mutation	SNP	A	TCGA-P4-AAVL-01A-11D-A42J-10		51853759	81998136	44	14327											
USP15	9958	hgsc.bcm.edu	37	chr12	62777661	62777667	+	Frame_Shift_Del	DEL	AGCAGCA	AGCAGCA	-																															acctcagttctctggatatcAgcagcaagactgtcaagaac																								rs112510834		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	AGCAGCA	AGCAGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr12:62777661_62777667delAGCAGCA	ENST00000280377.5	+	10	1188_1194	c.1130_1136delAGCAGCA	c.(1129-1137)cagcagcaafs	p.QQQ377fs	USP15_ENST00000393654.3_Frame_Shift_Del_p.QQQ352fs|USP15_ENST00000353364.3_Frame_Shift_Del_p.QQQ348fs	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	377	USP.				BMP signaling pathway (GO:0030509)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|protein deubiquitination (GO:0016579)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|identical protein binding (GO:0042802)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(15)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	37			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		TCTGGATATCAGCAGCAAGACTGTCAA	0.353																																					p.377_379del	Melanoma(181;615 2041 39364 49691 50001)	Atlas-Indel,Pindel	.											.	USP15	105	.	0			c.1129_1135del						PASS	.																																			SO:0001589	frameshift_variant	9958	exon10			.	AB011101	CCDS8963.1, CCDS58250.1, CCDS58251.1	12q14	2006-07-18	2005-08-08					"Ubiquitin-specific peptidases"	12613	protein-coding gene	gene with protein product		604731	"ubiquitin specific protease 15"			12838346	Standard	NM_001252078		Approved	KIAA0529, UNPH4	uc001src.2	Q9Y4E8	OTTHUMG00000170186	ENST00000280377.5:c.1130_1136delAGCAGCA	chr12.hg19:g.62777661_62777667delAGCAGCA	ENSP00000280377:p.Gln377fs	88.0	0.0	0		89.0	28.0	0.314607	NM_001252078	Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Frame_Shift_Del	DEL	ENST00000280377.5	hg19	CCDS58251.1																																																																																			.	.	.	none		0.353	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2	NM_006313		-	62777667	AGCAGCA	-	62777661	7	5	235	1	0	1	0	1	0	0	0	0	17058	188	7	0	1077	0	USP15	12	62777661	Frame_Shift_Del	DEL	AGCAGCA	TCGA-P4-AAVL-01A-11D-A42J-10	10923902	62777661	71074234	45	14328											
ANKS1B	56899	hgsc.bcm.edu	37	chr12	99837527	99837527	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aacaatcaggtgttgggcctGttgagctgtttctatggtta	8	15	12	6	0	2	1	1	1	1	0	2	1	2	1	1	3	2	5	1	3	4	5			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr12:99837527G>A	ENST00000547776.2	-	11	1498	c.1499C>T	c.(1498-1500)aCa>aTa	p.T500I	ANKS1B_ENST00000329257.7_Missense_Mutation_p.T500I|ANKS1B_ENST00000547010.1_Missense_Mutation_p.T80I	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	500						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)		TGTTGGGCCTGTTGAGCTGTT	0.433																																					p.T500I		Atlas-SNP	.											.	ANKS1B	180	.	0			c.C1499T						PASS	.						203	196	198					12																	99837527		1901	4130	6031	SO:0001583	missense	56899	exon11			GGGCCTGTTGAGC	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.1499C>T	chr12.hg19:g.99837527G>A	ENSP00000449629:p.Thr500Ile	164.0	1.0	.		209.0	139.0	.	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Missense_Mutation	SNP	ENST00000547776.2	hg19	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.428944	0.83667	.	.	ENSG00000185046	ENST00000547776;ENST00000547010;ENST00000329257;ENST00000538702;ENST00000549866	T;T;T;T	0.69175	0.59;-0.38;0.59;0.42	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.76557	0.4004	L	0.40543	1.245	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.998	D;D;D	0.85130	0.997;0.996;0.987	T	0.72520	-0.4268	9	.	.	.	-11.037	18.7754	0.91910	0.0:0.0:1.0:0.0	.	466;80;500	F8VVQ4;Q7Z6G8-6;Q7Z6G8	.;.;ANS1B_HUMAN	I	500;80;500;79;466	ENSP00000449629:T500I;ENSP00000448512:T80I;ENSP00000331381:T500I;ENSP00000449894:T466I	.	T	-	2	0	ANKS1B	98361658	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	8.328000	0.90014	2.873000	0.98535	0.563000	0.77884	ACA	.	.	.	none		0.433	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140		A	99837527	G	A	99837527	3	1	235	1	0	0	0	0	1	0	0	0	689	1377	48	2	2599	2	ANKS1B	12	99837527	Missense_Mutation	SNP	G	TCGA-P4-AAVL-01A-11D-A42J-10	37059866	99837527	34014368	46	14329											
POLE	5426	hgsc.bcm.edu	37	chr12	133219525	133219525	+	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	agggcccaccttctccaggaGgaggccgtgctctgctgagt	6	8	14	13	1	2	1	0	1	2	0	3	3	2	3	4	4	2	2	4	4	0	1			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr12:133219525G>A	ENST00000320574.5	-	36	4652	c.4609C>T	c.(4609-4611)Ctc>Ttc	p.L1537F	POLE_ENST00000434528.3_5'Flank|POLE_ENST00000535270.1_Missense_Mutation_p.L1510F	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	1537					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)	TTCTCCAGGAGGAGGCCGTGC	0.642								DNA polymerases (catalytic subunits)																													p.L1537F		Atlas-SNP	.											.	POLE	416	.	0			c.C4609T						PASS	.						60	58	59					12																	133219525		2203	4300	6503	SO:0001583	missense	5426	exon36			CCAGGAGGAGGCC		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.4609C>T	chr12.hg19:g.133219525G>A	ENSP00000322570:p.Leu1537Phe	72.0	0.0	.		93.0	38.0	.	NM_006231	Q13533|Q86VH9	Missense_Mutation	SNP	ENST00000320574.5	hg19	CCDS9278.1	.	.	.	.	.	.	.	.	.	.	G	5.595	0.294522	0.10567	.	.	ENSG00000177084	ENST00000320574;ENST00000455752;ENST00000535270	T;T;T	0.24151	1.87;1.87;1.87	5.82	2.89	0.33648	DNA polymerase epsilon, catalytic subunit A, C-terminal (1);	0.063724	0.64402	D	0.000004	T	0.28234	0.0697	M	0.81112	2.525	0.49915	D	0.999831	B	0.30179	0.271	B	0.33121	0.158	T	0.03086	-1.1074	10	0.27785	T	0.31	.	5.8191	0.18518	0.1349:0.0:0.4872:0.3779	.	1537	Q07864	DPOE1_HUMAN	F	1537;1548;1510	ENSP00000322570:L1537F;ENSP00000406383:L1548F;ENSP00000445753:L1510F	ENSP00000322570:L1537F	L	-	1	0	POLE	131729598	0.997000	0.39634	0.986000	0.45419	0.071000	0.16799	2.540000	0.45727	0.322000	0.23283	-1.087000	0.02190	CTC	.	.	.	none		0.642	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231		A	133219525	G	A	133219525	3	1	235	1	0	0	0	0	1	0	0	0	12203	1000	35	2	2307	2	POLE	12	133219525	Missense_Mutation	SNP	G	TCGA-P4-AAVL-01A-11D-A42J-10	33381998	133219525	632370	47	14330											
SACS	26278	hgsc.bcm.edu	37	chr13	23909168	23909168	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagtgtcctttacaacatgAataggggtgttctgtaacac	13	12	9	7	0	1	1	0	1	1	0	2	1	2	1	1	2	3	2	1	2	6	5			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr13:23909168A>G	ENST00000382292.3	-	9	9120	c.8847T>C	c.(8845-8847)atT>atC	p.I2949I	SACS_ENST00000382298.3_Silent_p.I2949I|SACS_ENST00000402364.1_Silent_p.I2199I			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2949					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)		TTACAACATGAATAGGGGTGT	0.348																																					p.I2949I		Atlas-SNP	.											.	SACS	871	.	0			c.T8847C						PASS	.						100	101	101					13																	23909168		2203	4300	6503	SO:0001819	synonymous_variant	26278	exon10			AACATGAATAGGG	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.8847T>C	chr13.hg19:g.23909168A>G		72.0	0.0	.		81.0	37.0	.	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	hg19	CCDS9300.2																																																																																			.	.	.	none		0.348	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		G	23909168	A	G	23909168	2	3	235	1	0	0	0	0	0	0	0	1	13817	242	9	3		3	SACS	13	23909168	Silent	SNP	A	TCGA-P4-AAVL-01A-11D-A42J-10		23909168	91260710	48	14331											
CDK8	1024	hgsc.bcm.edu	37	chr13	26975672	26975672	+	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	acccagggaatcaagacagcAgtcacacacagggacccccg	14	2	10	15	1	2	1	2	0	0	1	2	3	2	3	3	2	1	1	3	2	2	0			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr13:26975672A>T	ENST00000381527.3	+	12	1683	c.1180A>T	c.(1180-1182)Agt>Tgt	p.S394C	CDK8_ENST00000536792.1_3'UTR|CDK8_ENST00000480323.1_3'UTR	NM_001260.1	NP_001251.1	P49336	CDK8_HUMAN	cyclin-dependent kinase 8	394					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	25	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0384)|Epithelial(112;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.188)		TCAAGACAGCAGTCACACACA	0.483																																					p.S394C		Atlas-SNP	.											.	CDK8	61	.	0			c.A1180T						PASS	.						100	93	96					13																	26975672		2203	4300	6503	SO:0001583	missense	1024	exon12			GACAGCAGTCACA	X85753	CCDS9317.1	13q12	2011-11-08			ENSG00000132964	ENSG00000132964		"Cyclin-dependent kinases"	1779	protein-coding gene	gene with protein product		603184				7568034	Standard	NM_001260		Approved	K35	uc001uqr.1	P49336	OTTHUMG00000016617	ENST00000381527.3:c.1180A>T	chr13.hg19:g.26975672A>T	ENSP00000370938:p.Ser394Cys	115.0	0.0	.		118.0	47.0	.	NM_001260	Q5VUF3|Q6ISB5	Missense_Mutation	SNP	ENST00000381527.3	hg19	CCDS9317.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.210803	0.79240	.	.	ENSG00000132964	ENST00000381527	T	0.69806	-0.43	5.58	1.92	0.25849	.	0.070976	0.85682	D	0.000000	T	0.68550	0.3013	L	0.51422	1.61	0.80722	D	1	D;D	0.56968	0.978;0.97	P;P	0.56514	0.8;0.711	T	0.66728	-0.5850	10	0.54805	T	0.06	-1.6909	8.8309	0.35082	0.7859:0.0:0.2141:0.0	.	393;394	P49336-2;P49336	.;CDK8_HUMAN	C	394	ENSP00000370938:S394C	ENSP00000370938:S394C	S	+	1	0	CDK8	25873672	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.426000	0.44731	0.418000	0.25898	0.533000	0.62120	AGT	.	.	.	none		0.483	CDK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044250.1			T	26975672	A	T	26975672	3	4	235	1	0	0	0	0	1	0	0	0	3152	188	7	5	1226	5	CDK8	13	26975672	Missense_Mutation	SNP	A	TCGA-P4-AAVL-01A-11D-A42J-10	3066504	26975672	88194206	49	14332											
FLJ10357	55701	hgsc.bcm.edu	37	chr14	21543506	21543506	+	Frame_Shift_Del	DEL	A	A	-																															tgcaggacacacaggcccagAaggccccctgtctgacactc																										TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr14:21543506delA	ENST00000298694.4	+	4	1593	c.1466delA	c.(1465-1467)gaafs	p.E489fs	ARHGEF40_ENST00000298693.3_Frame_Shift_Del_p.E489fs			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	489						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						ACAGGCCCAGAAGGCCCCCTG	0.552																																					p.E489fs		Atlas-Indel,Pindel	.											.	ARHGEF40	84	.	0			c.1465delG						PASS	.						117	121	120					14																	21543506		2203	4300	6503	SO:0001589	frameshift_variant	55701	exon4			.		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.1466delA	chr14.hg19:g.21543506delA	ENSP00000298694:p.Glu489fs	120.0	0.0	0		128.0	52.0	0.40625	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Frame_Shift_Del	DEL	ENST00000298694.4	hg19	CCDS32041.1																																																																																			.	.	.	none		0.552	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1			-	21543506	A	-	21543506	7	5	235	1	0	1	0	1	0	0	0	0	5933	246	9	0	1480	0	FLJ10357	14	21543506	Frame_Shift_Del	DEL	A	TCGA-P4-AAVL-01A-11D-A42J-10		21543506	85806034	50	14333	146	2									
FLJ10357	55701	hgsc.bcm.edu	37	chr14	21543510	21543510	+	Silent	SNP	C	C	G																															ggacacacaggcccagaaggCcccctgtctgacactccaac																										TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr14:21543510C>G	ENST00000298694.4	+	4	1597	c.1470C>G	c.(1468-1470)ggC>ggG	p.G490G	ARHGEF40_ENST00000298693.3_Silent_p.G490G			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	490						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						GCCCAGAAGGCCCCCTGTCTG	0.557																																					p.G490G		Atlas-SNP	.											.	ARHGEF40	84	.	0			c.C1470G						PASS	.						119	122	121					14																	21543510		2203	4300	6503	SO:0001819	synonymous_variant	55701	exon4			AGAAGGCCCCCTG		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.1470C>G	chr14.hg19:g.21543510C>G		116.0	0.0	.		129.0	51.0	.	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Silent	SNP	ENST00000298694.4	hg19	CCDS32041.1																																																																																			.	.	.	none		0.557	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1			G	21543510	C	G	21543510	2	3	235	1	0	0	0	0	0	0	0	1	5933	726	26	4		4	FLJ10357	14	21543510	Silent	SNP	C	TCGA-P4-AAVL-01A-11D-A42J-10	4	21543510	85806030	51	14334	146	2									
PPP2R3C	55012	hgsc.bcm.edu	37	chr14	35579746	35579746	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttacctgtaattcttcattAtctaacagttctctgctttt	8	20	3	10	0	4	0	1	0	3	0	5	0	4	0	1	0	3	3	1	0	4	9	rs201403377		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr14:35579746A>G	ENST00000261475.5	-	3	629	c.276T>C	c.(274-276)gaT>gaC	p.D92D	PPP2R3C_ENST00000555644.1_Silent_p.D92D	NM_017917.2	NP_060387.2	Q969Q6	P2R3C_HUMAN	protein phosphatase 2, regulatory subunit B'', gamma	92					activation of protein kinase activity (GO:0032147)|B cell homeostasis (GO:0001782)|positive regulation of B cell differentiation (GO:0045579)|regulation of antimicrobial humoral response (GO:0002759)|regulation of mitochondrial depolarization (GO:0051900)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)	15	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;8.62e-06)|LUAD - Lung adenocarcinoma(48;1.42e-05)|Epithelial(34;0.0177)|all cancers(34;0.0491)	GBM - Glioblastoma multiforme(112;0.0803)		ATTCTTCATTATCTAACAGTT	0.348																																					p.D92D		Atlas-SNP	.											.	PPP2R3C	44	.	0			c.T276C						PASS	.						199	184	189					14																	35579746		2203	4299	6502	SO:0001819	synonymous_variant	55012	exon3			TTCATTATCTAAC	AK000651	CCDS9654.1	14q13.2	2010-06-18	2010-06-18	2007-01-22	ENSG00000092020	ENSG00000092020		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	17485	protein-coding gene	gene with protein product		615902	"chromosome 14 open reading frame 10", "protein phosphatase 2 (formerly 2A), regulatory subunit B'', gamma"	C14orf10		12167160, 16129705	Standard	NM_017917		Approved	FLJ20644, G4-1, G5PR	uc001wss.3	Q969Q6	OTTHUMG00000140224	ENST00000261475.5:c.276T>C	chr14.hg19:g.35579746A>G		38.0	0.0	.		43.0	14.0	.	NM_017917	B4DEN7|D3DS97|D3DS98|Q5GJ55|Q5GJ56|Q6P4G2|Q86TZ3|Q9NWR9	Silent	SNP	ENST00000261475.5	hg19	CCDS9654.1	.	.	.	.	.	.	.	.	.	.	A	8.279	0.815077	0.16607	.	.	ENSG00000092020	ENST00000555614	.	.	.	5.8	4.65	0.58169	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-11.4249	8.5736	0.33585	0.7983:0.0:0.2017:0.0	.	.	.	.	Q	31	.	.	X	-	1	0	PPP2R3C	34649497	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.457000	0.35212	2.207000	0.71202	0.528000	0.53228	TAA	.	.	.	alt		0.348	PPP2R3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276687.1	NM_017917		G	35579746	A	G	35579746	2	3	235	1	0	0	0	0	0	0	0	1	12400	446	16	3		3	PPP2R3C	14	35579746	Silent	SNP	A	TCGA-P4-AAVL-01A-11D-A42J-10	14036236	35579746	71769794	52	14335											
GABRB3	2562	hgsc.bcm.edu	37	chr15	26793258	26793258	+	Frame_Shift_Del	DEL	C	C	-																															tgaacttccagcgatgtcaaCagaatatttccatgagcatc																										TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr15:26793258delC	ENST00000311550.5	-	9	1215	c.1104delG	c.(1102-1104)ctgfs	p.L369fs	GABRB3_ENST00000400188.3_Frame_Shift_Del_p.L298fs|GABRB3_ENST00000299267.4_Frame_Shift_Del_p.L369fs|GABRB3_ENST00000545868.1_Frame_Shift_Del_p.L284fs|GABRB3_ENST00000541819.2_Frame_Shift_Del_p.L425fs	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	369					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)	GCGATGTCAACAGAATATTTC	0.448																																					p.L369X		Atlas-Indel,Pindel	.											.	GABRB3	338	.	0			c.1105delT						PASS	.						115	111	112					15																	26793258		2203	4300	6503	SO:0001589	frameshift_variant	2562	exon9			.		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.1104delG	chr15.hg19:g.26793258delC	ENSP00000308725:p.Leu369fs	65.0	0.0	0		55.0	29.0	0.527273	NM_021912	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Frame_Shift_Del	DEL	ENST00000311550.5	hg19	CCDS10019.1																																																																																			.	.	.	none		0.448	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2			-	26793258	C	-	26793258	7	5	235	1	0	1	0	1	0	0	0	0	6175	465	17	0	321	0	GABRB3	15	26793258	Frame_Shift_Del	DEL	C	TCGA-P4-AAVL-01A-11D-A42J-10		26793258	75738134	53	14336											
CHP	11261	hgsc.bcm.edu	37	chr15	41555021	41555022	+	Frame_Shift_Ins	INS	-	-	A																															ccgccccattgaggataatgINSaaaagagcaaagatgtgaat																										TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr15:41555021_41555022insA	ENST00000334660.5	+	4	529_530	c.289_290insA	c.(289-291)gaafs	p.E97fs	CHP1_ENST00000558351.1_3'UTR|CHP1_ENST00000560397.1_Frame_Shift_Ins_p.E97fs	NM_007236.4	NP_009167.1	Q99653	CHP1_HUMAN	calcineurin-like EF-hand protein 1	97	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				calcium ion-dependent exocytosis (GO:0017156)|cellular response to acidic pH (GO:0071468)|cytoplasmic microtubule organization (GO:0031122)|membrane docking (GO:0022406)|membrane fusion (GO:0061025)|membrane organization (GO:0061024)|microtubule bundle formation (GO:0001578)|negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatase activity (GO:0010923)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of protein import into nucleus (GO:0042308)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein ubiquitination (GO:0031397)|positive regulation of protein glycosylation (GO:0060050)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of protein transport (GO:0051222)|positive regulation of sodium:proton antiporter activity (GO:0032417)|potassium ion transport (GO:0006813)|protein export from nucleus (GO:0006611)|protein oligomerization (GO:0051259)|protein stabilization (GO:0050821)|regulation of intracellular pH (GO:0051453)|small GTPase mediated signal transduction (GO:0007264)|transcytosis (GO:0045056)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|kinase binding (GO:0019900)|microtubule binding (GO:0008017)|potassium channel regulator activity (GO:0015459)|protein kinase inhibitor activity (GO:0004860)|transporter activity (GO:0005215)										TGAGGATAATGAAAAGAGCAAA	0.431																																					p.E97fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.289_290insA						PASS	.																																			SO:0001589	frameshift_variant	11261	exon4			.		CCDS10073.1	15q13.3	2013-01-11	2013-01-11		ENSG00000187446	ENSG00000187446		"EF-hand domain containing"	17433	protein-coding gene	gene with protein product	"calcineurin homologous protein"	606988				15987692, 20720019	Standard	NM_007236		Approved	Sid470p, CHP, SLC9A1BP, p22, p24	uc001znl.3	Q99653	OTTHUMG00000130233	ENST00000334660.5:c.293dupA	chr15.hg19:g.41555025_41555025dupA	ENSP00000335632:p.Glu97fs	190.0	0.0	0		236.0	84.0	0.355932	NM_007236	B2R6H9|Q6FHZ9	Frame_Shift_Ins	INS	ENST00000334660.5	hg19	CCDS10073.1																																																																																			.	.	.	none		0.431	CHP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252554.2	NM_007236		A	41555022	-	A	41555021	7	5	235	1	0	1	1	0	0	0	0	0	3368	1291	45	0	303	0	CHP	15	41555021	Frame_Shift_Ins	INS	-	TCGA-P4-AAVL-01A-11D-A42J-10	14761763	41555021	60976371	54	14337											
DUT	1854	hgsc.bcm.edu	37	chr15	48623926	48623926	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaggctgccgcggagccagtAcagtcggggccgctggctgg	6	5	18	12	4	0	0	0	0	0	0	1	1	0	1	3	6	3	4	3	6	2	1			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr15:48623926A>G	ENST00000331200.3	+	1	307	c.214A>G	c.(214-216)Aca>Gca	p.T72A	DUT_ENST00000559540.1_5'Flank|RP11-154J22.1_ENST00000560323.1_RNA|RP11-154J22.1_ENST00000559134.1_RNA|DUT_ENST00000559935.1_Intron|DUT_ENST00000559416.1_Intron|DUT_ENST00000558813.1_Intron|DUT_ENST00000455976.2_5'Flank	NM_001025248.1|NM_001025249.1	NP_001020419.1|NP_001020420.1	P33316	DUT_HUMAN	deoxyuridine triphosphatase	72					DNA replication (GO:0006260)|dUMP biosynthetic process (GO:0006226)|dUTP catabolic process (GO:0046081)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotrimerization (GO:0070207)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|regulation of protein heterodimerization activity (GO:0043497)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dUTP diphosphatase activity (GO:0004170)|poly(A) RNA binding (GO:0044822)|pyrimidine deoxyribonucleotide binding (GO:0032556)|receptor inhibitor activity (GO:0030547)			kidney(2)	2		all_lung(180;0.00265)		all cancers(107;2.66e-09)|GBM - Glioblastoma multiforme(94;6.76e-07)		CGGAGCCAGTACAGTCGGGGC	0.781								Modulation of nucleotide pools																													p.T72A		Atlas-SNP	.											.	DUT	9	.	0			c.A214G						PASS	.						1	1	1					15																	48623926		592	1311	1903	SO:0001583	missense	1854	exon1			GCCAGTACAGTCG	M89913	CCDS32231.1, CCDS45255.1, CCDS45256.1	15q21.1	2010-06-24	2007-12-17		ENSG00000128951	ENSG00000128951	3.6.1.23		3078	protein-coding gene	gene with protein product		601266	"dUTP pyrophosphatase"			1325640, 9070952	Standard	XM_005254211		Approved	dUTPase	uc001zws.3	P33316		ENST00000331200.3:c.214A>G	chr15.hg19:g.48623926A>G	ENSP00000370376:p.Thr72Ala	27.0	0.0	.		29.0	6.0	.	NM_001025248	A8K650|B4DPR5|O14785|Q16708|Q16860|Q6FHN1|Q6NSA3|Q96Q81	Missense_Mutation	SNP	ENST00000331200.3	hg19	CCDS32231.1	.	.	.	.	.	.	.	.	.	.	A	13.01	2.109003	0.37242	.	.	ENSG00000128951	ENST00000331200;ENST00000249783	T	0.45668	0.89	3.42	2.3	0.28687	.	2.177750	0.02159	N	0.058606	T	0.29389	0.0732	N	0.19112	0.55	0.20074	N	0.999933	B	0.14012	0.009	B	0.08055	0.003	T	0.14337	-1.0476	10	0.30078	T	0.28	.	5.3774	0.16172	0.8697:0.0:0.1303:0.0	.	72	P33316	DUT_HUMAN	A	72;70	ENSP00000370376:T72A	ENSP00000249783:T70A	T	+	1	0	DUT	46411218	0.046000	0.20272	0.045000	0.18777	0.277000	0.26821	-0.093000	0.11111	0.686000	0.31488	0.455000	0.32223	ACA	.	.	.	none		0.781	DUT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000417142.2			G	48623926	A	G	48623926	3	3	235	1	0	0	0	0	1	0	0	0	4835	391	14	3	216	3	DUT	15	48623926	Missense_Mutation	SNP	A	TCGA-P4-AAVL-01A-11D-A42J-10	7068905	48623926	53907466	55	14338											
ZNF280D	54816	hgsc.bcm.edu	37	chr15	56935189	56935189	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcctttgcgggagcttctttTtttaatcttgaaaacaagat	10	17	7	7	1	2	2	0	1	2	1	3	3	3	3	1	1	3	1	1	1	4	7			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr15:56935189T>C	ENST00000267807.7	-	20	2436	c.2220A>G	c.(2218-2220)aaA>aaG	p.K740K	ZNF280D_ENST00000559237.1_Silent_p.K727K	NM_017661.2	NP_060131.2	Q6N043	Z280D_HUMAN	zinc finger protein 280D	740					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(4)|large_intestine(7)|lung(12)|ovary(1)|skin(1)	30				all cancers(107;0.0399)|GBM - Glioblastoma multiforme(80;0.0787)		GAGCTTCTTTTTTTAATCTTG	0.274																																					p.K740K		Atlas-SNP	.											.	ZNF280D	82	.	0			c.A2220G						PASS	.						20	19	19					15																	56935189		2154	4168	6322	SO:0001819	synonymous_variant	54816	exon20			TTCTTTTTTTAAT	AB046804	CCDS32245.1, CCDS42041.1, CCDS58364.1	15q21.2	2008-05-02	2007-09-20	2007-09-20					25953	protein-coding gene	gene with protein product			"suppressor of hairy wing homolog 4 (Drosophila)"	SUHW4		10997877	Standard	XM_005254481		Approved	FLJ20086, ZNF634	uc002adu.3	Q6N043		ENST00000267807.7:c.2220A>G	chr15.hg19:g.56935189T>C		405.0	0.0	.		419.0	167.0	.	NM_017661	A1L495|B2RMT6|Q6MZM6|Q6N085|Q6P2R6|Q7Z6J5|Q9H0U5|Q9HCI8|Q9NXS0	Silent	SNP	ENST00000267807.7	hg19	CCDS32245.1																																																																																			.	.	.	none		0.274	ZNF280D-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418891.2	XM_370867		C	56935189	T	C	56935189	2	2	235	1	0	0	0	0	0	0	0	1	17829	1838	64	3		3	ZNF280D	15	56935189	Silent	SNP	T	TCGA-P4-AAVL-01A-11D-A42J-10	8311263	56935189	45596203	56	14339											
MRPL46	26589	hgsc.bcm.edu	37	chr15	89010546	89010546	+	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	cttagactgccggcccagagCctctcgaaccgccgccaacc	8	5	9	19	4	1	2	0	0	1	2	2	3	1	2	7	1	4	0	7	1	3	1	rs540944922		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr15:89010546C>T	ENST00000312475.4	-	1	104	c.63G>A	c.(61-63)agG>agA	p.R21R	MRPS11_ENST00000353598.6_5'Flank|MRPS11_ENST00000325844.4_5'Flank|MRPL46_ENST00000559538.1_5'Flank	NM_022163.3	NP_071446.2	Q9H2W6	RM46_HUMAN	mitochondrial ribosomal protein L46	21						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)			CGGCCCAGAGCCTCTCGAACC	0.672																																					p.R21R		Atlas-SNP	.											.	MRPL46	13	.	0			c.G63A						PASS	.						16	19	18					15																	89010546		2198	4295	6493	SO:0001819	synonymous_variant	26589	exon1			CCAGAGCCTCTCG	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.63G>A	chr15.hg19:g.89010546C>T		114.0	0.0	.		107.0	50.0	.	NM_022163	B2RD75|Q9HBU8	Silent	SNP	ENST00000312475.4	hg19	CCDS10341.1																																																																																			.	.	.	none		0.672	MRPL46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309073.1	NM_022163		T	89010546	C	T	89010546	2	4	235	1	0	0	0	0	0	0	0	1	9817	738	26	2		2	MRPL46	15	89010546	Silent	SNP	C	TCGA-P4-AAVL-01A-11D-A42J-10	32075357	89010546	13520846	57	14340											
LRRK1	79705	hgsc.bcm.edu	37	chr15	101602839	101602839	+	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	ccttaaacacaccccaacagGccttggatactccagctgtc	11	8	6	16	0	0	0	0	0	0	0	2	1	1	1	5	2	4	1	5	2	4	3			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr15:101602839G>T	ENST00000388948.3	+	31	5217	c.4858G>T	c.(4858-4860)Gcc>Tcc	p.A1620S	RP11-505E24.2_ENST00000559857.1_RNA|LRRK1_ENST00000284395.5_Missense_Mutation_p.A1617S	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)			ACCCCAACAGGCCTTGGATAC	0.542																																					p.A1620S		Atlas-SNP	.											.	LRRK1	310	.	0			c.G4858T						PASS	.						155	160	158					15																	101602839		1989	4164	6153	SO:0001583	missense	79705	exon31			CAACAGGCCTTGG	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.4858G>T	chr15.hg19:g.101602839G>T	ENSP00000373600:p.Ala1620Ser	119.0	0.0	.		88.0	34.0	.	NM_024652		Missense_Mutation	SNP	ENST00000388948.3	hg19	CCDS42086.1	.	.	.	.	.	.	.	.	.	.	G	9.469	1.095041	0.20471	.	.	ENSG00000154237	ENST00000388948;ENST00000284395;ENST00000529762;ENST00000542170	T;T	0.69685	-0.42;-0.42	5.29	5.29	0.74685	WD40 repeat-like-containing domain (1);	0.562258	0.19004	N	0.125255	T	0.59770	0.2218	L	0.51422	1.61	0.25804	N	0.984476	B	0.29716	0.255	B	0.22152	0.038	T	0.49969	-0.8882	10	0.11485	T	0.65	.	18.9297	0.92560	0.0:0.0:1.0:0.0	.	1620	Q38SD2	LRRK1_HUMAN	S	1620;1617;311;174	ENSP00000373600:A1620S;ENSP00000284395:A1617S	ENSP00000284395:A1617S	A	+	1	0	LRRK1	99420362	0.998000	0.40836	0.975000	0.42487	0.027000	0.11550	3.003000	0.49505	2.484000	0.83849	0.491000	0.48974	GCC	.	.	.	none		0.542	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		T	101602839	G	T	101602839	3	4	235	1	0	0	0	0	1	0	0	0	9039	1203	42	4	4976	4	LRRK1	15	101602839	Missense_Mutation	SNP	G	TCGA-P4-AAVL-01A-11D-A42J-10	12592293	101602839	928553	58	14341											
PPL	5493	hgsc.bcm.edu	37	chr16	4933991	4933991	+	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	ctcagaaagtctagttccttGgatgacttggagttatggaa	11	13	11	6	0	2	2	1	1	1	1	3	5	3	5	1	3	0	2	1	3	4	5			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr16:4933991G>C	ENST00000345988.2	-	22	4754	c.4665C>G	c.(4663-4665)tcC>tcG	p.S1555S	PPL_ENST00000590782.2_Silent_p.S1553S	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1555					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						CTAGTTCCTTGGATGACTTGG	0.557																																					p.S1555S		Atlas-SNP	.											.	PPL	168	.	0			c.C4665G						PASS	.						102	102	102					16																	4933991		2197	4300	6497	SO:0001819	synonymous_variant	5493	exon22			TTCCTTGGATGAC	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.4665C>G	chr16.hg19:g.4933991G>C		51.0	0.0	.		33.0	16.0	.	NM_002705	O60314|O60454|Q14C98	Silent	SNP	ENST00000345988.2	hg19	CCDS10526.1																																																																																			.	.	.	none		0.557	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705		C	4933991	G	C	4933991	2	2	235	1	0	0	0	0	0	0	0	1	12344	1335	47	4		4	PPL	16	4933991	Silent	SNP	G	TCGA-P4-AAVL-01A-11D-A42J-10		4933991	85420762	59	14342											
C16orf72	29035	hgsc.bcm.edu	37	chr16	9186850	9186850	+	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	agccaccgccgtcaccaatcTctacaaaggtaaagataacc	15	6	6	14	2	2	1	1	0	1	1	3	1	2	1	5	1	3	1	5	1	6	3			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr16:9186850T>A	ENST00000327827.7	+	2	696	c.299T>A	c.(298-300)cTc>cAc	p.L100H		NM_014117.2	NP_054836.2	Q14CZ0	CP072_HUMAN	chromosome 16 open reading frame 72	100										endometrium(4)|large_intestine(2)|lung(2)	8						GTCACCAATCTCTACAAAGGT	0.522																																					p.L100H		Atlas-SNP	.											.	C16orf72	26	.	0			c.T299A						PASS	.						44	40	41					16																	9186850		2197	4300	6497	SO:0001583	missense	29035	exon2			CCAATCTCTACAA	AK123266	CCDS10538.1	16p13.2	2012-11-19			ENSG00000182831	ENSG00000182831			30103	protein-coding gene	gene with protein product						8889548	Standard	NM_014117		Approved	FLJ41272, PRO0149	uc002czm.3	Q14CZ0	OTTHUMG00000178147	ENST00000327827.7:c.299T>A	chr16.hg19:g.9186850T>A	ENSP00000331720:p.Leu100His	131.0	0.0	.		124.0	48.0	.	NM_014117		Missense_Mutation	SNP	ENST00000327827.7	hg19	CCDS10538.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.692171	0.88735	.	.	ENSG00000182831	ENST00000327827	T	0.72167	-0.63	4.09	4.09	0.47781	.	0.065681	0.64402	D	0.000012	D	0.82375	0.5023	M	0.81341	2.54	0.80722	D	1	D	0.76494	0.999	D	0.63703	0.917	D	0.85423	0.1144	10	0.87932	D	0	-16.5797	13.2393	0.59987	0.0:0.0:0.0:1.0	.	100	Q14CZ0	CP072_HUMAN	H	100	ENSP00000331720:L100H	ENSP00000331720:L100H	L	+	2	0	C16orf72	9094351	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.699000	0.84547	1.693000	0.51124	0.533000	0.62120	CTC	.	.	.	none		0.522	C16orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440760.2	NM_014117		A	9186850	T	A	9186850	3	1	235	1	0	0	0	0	1	0	0	0	1833	1551	54	5	305	5	C16orf72	16	9186850	Missense_Mutation	SNP	T	TCGA-P4-AAVL-01A-11D-A42J-10	4252859	9186850	81167903	60	14343											
ZNF423	23090	hgsc.bcm.edu	37	chr16	49672690	49672690	+	Frame_Shift_Del	DEL	G	G	-																															ttcctcctcgccgaggccgaGgtcacaaccatctccgatca																										TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr16:49672690delG	ENST00000561648.1	-	4	426	c.373delC	c.(373-375)ctcfs	p.L125fs	ZNF423_ENST00000562871.1_Frame_Shift_Del_p.L65fs|ZNF423_ENST00000535559.1_Frame_Shift_Del_p.L8fs|ZNF423_ENST00000563137.2_Frame_Shift_Del_p.L65fs|ZNF423_ENST00000562520.1_Frame_Shift_Del_p.L65fs|ZNF423_ENST00000567169.1_Frame_Shift_Del_p.L8fs|ZNF423_ENST00000262383.2_Frame_Shift_Del_p.L125fs	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	125					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)				CCGAGGCCGAGGTCACAACCA	0.602																																					p.L125fs		Atlas-INDEL	.											.	ZNF423	463	.	0			c.374delT						PASS	.						64	60	61					16																	49672690		2198	4300	6498	SO:0001589	frameshift_variant	23090	exon4			.	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.373delC	chr16.hg19:g.49672690delG	ENSP00000455426:p.Leu125fs	59.0	0.0	0		60.0	22.0	0.366667	NM_015069	O94860|Q76N04|Q9NZ13	Frame_Shift_Del	DEL	ENST00000561648.1	hg19	CCDS32445.1																																																																																			.	.	.	none		0.602	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		-	49672690	G	-	49672690	7	5	235	1	0	1	0	1	0	0	0	0	17910	1000	35	0	3501	0	ZNF423	16	49672690	Frame_Shift_Del	DEL	G	TCGA-P4-AAVL-01A-11D-A42J-10	40485840	49672690	40682063	61	14344	147	3									
ZNF423	23090	hgsc.bcm.edu	37	chr16	49672691	49672695	+	Frame_Shift_Del	DEL	GTCAC	GTCAC	-																															tcctcctcgccgaggccgagGtcacaaccatctccgatcat																										TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	GTCAC	GTCAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr16:49672691_49672695delGTCAC	ENST00000561648.1	-	4	421_425	c.368_372delGTGAC	c.(367-372)tgtgacfs	p.CD123fs	ZNF423_ENST00000562871.1_Frame_Shift_Del_p.CD63fs|ZNF423_ENST00000535559.1_Frame_Shift_Del_p.CD6fs|ZNF423_ENST00000563137.2_Frame_Shift_Del_p.CD63fs|ZNF423_ENST00000562520.1_Frame_Shift_Del_p.CD63fs|ZNF423_ENST00000567169.1_Frame_Shift_Del_p.CD6fs|ZNF423_ENST00000262383.2_Frame_Shift_Del_p.CD123fs	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	123					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)				CGAGGCCGAGGTCACAACCATCTCC	0.6																																					p.123_125del		Pindel	.											.	ZNF423	463	.	0			c.369_373del						PASS	.																																			SO:0001589	frameshift_variant	23090	exon4			.	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.368_372delGTGAC	chr16.hg19:g.49672691_49672695delGTCAC	ENSP00000455426:p.Cys123fs	58.0	0.0	.		60.0	20.0	0.333	NM_015069	O94860|Q76N04|Q9NZ13	Frame_Shift_Del	DEL	ENST00000561648.1	hg19	CCDS32445.1																																																																																			.	.	.	none		0.6	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		-	49672695	GTCAC	-	49672691	7	5	235	1	0	1	0	1	0	0	0	0	17910	1252	44	0	3502	0	ZNF423	16	49672691	Frame_Shift_Del	DEL	GTCAC	TCGA-P4-AAVL-01A-11D-A42J-10	1	49672691	40682062	62	14345	147	3									
ZNF423	23090	hgsc.bcm.edu	37	chr16	49672693	49672695	+	In_Frame_Del	DEL	CAC	CAC	-																															ctcctcgccgaggccgaggtCacaaccatctccgatcatct																										TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	CAC	CAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr16:49672693_49672695delCAC	ENST00000561648.1	-	4	421_423	c.368_370delGTG	c.(367-372)tgtgac>tac	p.123_124CD>Y	ZNF423_ENST00000562871.1_In_Frame_Del_p.63_64CD>Y|ZNF423_ENST00000535559.1_In_Frame_Del_p.6_7CD>Y|ZNF423_ENST00000563137.2_In_Frame_Del_p.63_64CD>Y|ZNF423_ENST00000562520.1_In_Frame_Del_p.63_64CD>Y|ZNF423_ENST00000567169.1_In_Frame_Del_p.6_7CD>Y|ZNF423_ENST00000262383.2_In_Frame_Del_p.123_124CD>Y	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	123					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)				AGGCCGAGGTCACAACCATCTCC	0.596																																					p.123_124del		Atlas-INDEL	.											.	ZNF423	463	.	0			c.369_371del						PASS	.																																			SO:0001651	inframe_deletion	23090	exon4			.	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.368_370delGTG	chr16.hg19:g.49672693_49672695delCAC	ENSP00000455426:p.Cys123_Asp124delinsTyr	56.0	0.0	0		58.0	22.0	0.37931	NM_015069	O94860|Q76N04|Q9NZ13	In_Frame_Del	DEL	ENST00000561648.1	hg19	CCDS32445.1																																																																																			.	.	.	none		0.596	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		-	49672695	CAC	-	49672693	7	5	235	1	0	1	0	1	0	0	0	0	17910	826	29	0	3504	0	ZNF423	16	49672693	In_Frame_Del	DEL	CAC	TCGA-P4-AAVL-01A-11D-A42J-10	2	49672693	40682060	63	14346	147	3									
SLC6A2	6530	hgsc.bcm.edu	37	chr16	55719085	55719085	+	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	ctgcaccttcacgagagcagCgggattcatgacatcggcct	9	8	11	13	3	2	2	2	1	0	1	3	4	2	3	2	2	3	2	2	2	0	2			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr16:55719085C>T	ENST00000379906.2	+	4	930	c.675C>T	c.(673-675)agC>agT	p.S225S	SLC6A2_ENST00000414754.3_Silent_p.S225S|SLC6A2_ENST00000566163.1_Silent_p.S225S|SLC6A2_ENST00000567238.1_Silent_p.S120S|SLC6A2_ENST00000561820.1_Silent_p.S225S|SLC6A2_ENST00000219833.8_Silent_p.S225S|SLC6A2_ENST00000568943.1_Silent_p.S225S	NM_001043.3	NP_001034.1	P23975	SC6A2_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 2	225					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)	ACGAGAGCAGCGGGATTCATG	0.587																																					p.S225S		Atlas-SNP	.											.	SLC6A2	189	.	0			c.C675T						PASS	.						118	103	108					16																	55719085		2198	4300	6498	SO:0001819	synonymous_variant	6530	exon5			GAGCAGCGGGATT		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.675C>T	chr16.hg19:g.55719085C>T		46.0	0.0	.		60.0	26.0	.	NM_001172501	B2R707|B4DX48|Q96KH8	Silent	SNP	ENST00000379906.2	hg19	CCDS10754.1																																																																																			.	.	.	none		0.587	SLC6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256922.2			T	55719085	C	T	55719085	2	4	235	1	0	0	0	0	0	0	0	1	14696	767	27	1		1	SLC6A2	16	55719085	Silent	SNP	C	TCGA-P4-AAVL-01A-11D-A42J-10	6046392	55719085	34635668	64	14347											
DPEP1	1800	hgsc.bcm.edu	37	chr16	89704613	89704613	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctcgctcccctggtcctcTgtctgtctctcctgtgaaac	3	13	7	18	1	3	1	0	1	3	0	8	1	6	1	5	1	1	1	5	1	1	0			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr16:89704613T>C	ENST00000393092.3	+	11	1510	c.1219T>C	c.(1219-1221)Tgt>Cgt	p.C407R	DPEP1_ENST00000261615.4_Missense_Mutation_p.C407R|DPEP1_ENST00000421184.1_Missense_Mutation_p.C407R	NM_004413.3	NP_004404.1	P16444	DPEP1_HUMAN	dipeptidase 1 (renal)	407					antibiotic metabolic process (GO:0016999)|arachidonic acid metabolic process (GO:0019369)|cellular lactam catabolic process (GO:0072340)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|cellular response to nitric oxide (GO:0071732)|glutathione metabolic process (GO:0006749)|homocysteine metabolic process (GO:0050667)|leukotriene metabolic process (GO:0006691)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell migration (GO:0030336)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|apical part of cell (GO:0045177)|cell projection (GO:0042995)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|dipeptidyl-peptidase activity (GO:0008239)|GPI anchor binding (GO:0034235)|metallodipeptidase activity (GO:0070573)|metalloexopeptidase activity (GO:0008235)|modified amino acid binding (GO:0072341)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(10)|prostate(1)|urinary_tract(1)	14		all_lung(18;0.0054)|all_hematologic(23;0.094)		BRCA - Breast invasive adenocarcinoma(80;0.0258)	Cilastatin(DB01597)	CCTGGTCCTCTGTCTGTCTCT	0.657																																					p.C407R		Atlas-SNP	.											.	DPEP1	39	.	0			c.T1219C						PASS	.						30	36	34					16																	89704613		2188	4290	6478	SO:0001583	missense	1800	exon11			GTCCTCTGTCTGT		CCDS10982.1	16q24	2011-07-22			ENSG00000015413	ENSG00000015413	3.4.13.19		3002	protein-coding gene	gene with protein product		179780					Standard	NM_004413		Approved		uc002fnr.4	P16444	OTTHUMG00000138052	ENST00000393092.3:c.1219T>C	chr16.hg19:g.89704613T>C	ENSP00000376807:p.Cys407Arg	27.0	0.0	.		33.0	10.0	.	NM_001128141	D3DX80|Q96AK2	Missense_Mutation	SNP	ENST00000393092.3	hg19	CCDS10982.1	.	.	.	.	.	.	.	.	.	.	t	9.017	0.983958	0.18889	.	.	ENSG00000015413	ENST00000421184;ENST00000393092;ENST00000261615	T;T;T	0.20738	2.05;2.05;2.05	5.11	-10.2	0.00374	.	2.970350	0.01127	N	0.005905	T	0.09730	0.0239	N	0.16478	0.41	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.14531	-1.0469	10	0.36615	T	0.2	-6.3644	3.003	0.06019	0.135:0.0879:0.3417:0.4354	.	407	P16444	DPEP1_HUMAN	R	407	ENSP00000397313:C407R;ENSP00000376807:C407R;ENSP00000261615:C407R	ENSP00000261615:C407R	C	+	1	0	DPEP1	88232114	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.591000	0.00899	-2.931000	0.00300	-0.575000	0.04146	TGT	.	.	.	none		0.657	DPEP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000423058.1	NM_001128141		C	89704613	T	C	89704613	3	2	235	1	0	0	0	0	1	0	0	0	4715	1580	55	3	1257	3	DPEP1	16	89704613	Missense_Mutation	SNP	T	TCGA-P4-AAVL-01A-11D-A42J-10	33985528	89704613	650140	65	14348											
SCARF1	8578	hgsc.bcm.edu	37	chr17	1540075	1540075	+	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	aggatcggatgagaaggagtCatcagtggcccagccggcag	11	5	16	9	2	2	1	2	1	0	1	3	5	2	4	2	5	1	1	2	5	1	0			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr17:1540075C>T	ENST00000263071.4	-	10	1610	c.1561G>A	c.(1561-1563)Gac>Aac	p.D521N	SCARF1_ENST00000571272.1_Missense_Mutation_p.M508I|SCARF1_ENST00000348987.3_Missense_Mutation_p.D435N	NM_003693.2|NM_145350.1	NP_003684.2|NP_663325.1	Q14162	SREC_HUMAN	scavenger receptor class F, member 1	521	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)		GAGAAGGAGTCATCAGTGGCC	0.607																																					p.D521N		Atlas-SNP	.											.	SCARF1	46	.	0			c.G1561A						PASS	.						106	108	107					17																	1540075		2203	4300	6503	SO:0001583	missense	8578	exon10			AGGAGTCATCAGT	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.1561G>A	chr17.hg19:g.1540075C>T	ENSP00000263071:p.Asp521Asn	67.0	0.0	.		68.0	31.0	.	NM_003693	A8MQ05|O43701|Q8NHD2|Q8NHD3|Q8NHD4|Q8NHD5	Missense_Mutation	SNP	ENST00000263071.4	hg19	CCDS11007.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	15.34|15.34	2.805426|2.805426	0.50315|0.50315	.|.	.|.	ENSG00000074660|ENSG00000074660	ENST00000263071;ENST00000348987|ENST00000434376	T;T|.	0.33216|.	1.99;1.42|.	5.15|5.15	5.15|5.15	0.70609|0.70609	.|.	0.154024|.	0.31177|.	N|.	0.008101|.	T|T	0.31199|0.31199	0.0789|0.0789	.|.	.|.	.|.	0.31528|0.31528	N|N	0.661541|0.661541	P;B|B	0.45715|0.23249	0.865;0.349|0.082	B;B|B	0.42555|0.21917	0.391;0.122|0.037	T|T	0.23619|0.23619	-1.0183|-1.0183	9|7	0.08179|0.22706	T|T	0.78|0.39	-32.7609|-32.7609	7.8595|7.8595	0.29501|0.29501	0.0:0.8217:0.0:0.1783|0.0:0.8217:0.0:0.1783	.|.	435;521|508	Q14162-2;Q14162|Q14162-3	.;SREC_HUMAN|.	N|I	521;435|508	ENSP00000263071:D521N;ENSP00000323964:D435N|.	ENSP00000263071:D521N|ENSP00000411167:M508I	D|M	-|-	1|3	0|0	SCARF1|SCARF1	1486825|1486825	0.987000|0.987000	0.35691|0.35691	0.959000|0.959000	0.39883|0.39883	0.817000|0.817000	0.46193|0.46193	2.387000|2.387000	0.44389|0.44389	2.580000|2.580000	0.87095|0.87095	0.556000|0.556000	0.70494|0.70494	GAC|ATG	.	.	.	none		0.607	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207081.4	NM_003693		T	1540075	C	T	1540075	3	4	235	1	0	0	0	0	1	0	0	0	13896	826	29	2	939	2	SCARF1	17	1540075	Missense_Mutation	SNP	C	TCGA-P4-AAVL-01A-11D-A42J-10		1540075	79655135	66	14349											
ALOX15B	247	hgsc.bcm.edu	37	chr17	7948885	7948885	+	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	tgctggccaagacctgggtgCgcaatgccgagttctccttc	6	10	12	13	2	1	1	0	0	1	1	3	2	1	1	4	2	3	3	4	2	2	2	rs370434436		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr17:7948885C>T	ENST00000380183.4	+	8	1220	c.1081C>T	c.(1081-1083)Cgc>Tgc	p.R361C	ALOX15B_ENST00000380173.2_Missense_Mutation_p.R361C|ALOX15B_ENST00000573359.1_Missense_Mutation_p.R361C|ALOX15B_ENST00000572022.1_Missense_Mutation_p.R361C	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	361	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						GACCTGGGTGCGCAATGCCGA	0.637													C|||	1	0.000199681	8e-04	0	5008	,	,		17957	0		0	False		,,,				2504	0				p.R361C		Atlas-SNP	.											ALOX15B,NS,carcinoma,0,1	ALOX15B	66	.	0			c.C1081T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG	4,4402	9.9+/-24.2	0,4,2199	108	80	90		1081,1081,1081	1.4	0.8	17		90	0,8600		0,0,4300	no	missense,missense,missense	ALOX15B	NM_001039130.1,NM_001039131.1,NM_001141.2	180,180,180	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	probably-damaging,probably-damaging,probably-damaging	361/648,361/603,361/677	7948885	4,13002	2203	4300	6503	SO:0001583	missense	247	exon8			TGGGTGCGCAATG	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.1081C>T	chr17.hg19:g.7948885C>T	ENSP00000369530:p.Arg361Cys	50.0	0.0	.		41.0	3.0	.	NM_001141	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Missense_Mutation	SNP	ENST00000380183.4	hg19	CCDS11128.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.846791	0.51164	9.08E-4	0.0	ENSG00000179593	ENST00000380173;ENST00000339694;ENST00000380183	D;D	0.90444	-2.67;-2.67	4.53	1.38	0.22167	Lipoxygenase, C-terminal (4);	0.054757	0.64402	D	0.000001	D	0.92509	0.7621	L	0.55103	1.725	0.49299	D	0.999772	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.97110	0.97;1.0;0.999;1.0	D	0.91190	0.4983	10	0.87932	D	0	-29.9769	9.8306	0.40939	0.0:0.7463:0.0:0.2537	.	361;361;361;361	B4DNW8;O15296-2;O15296-4;O15296	.;.;.;LX15B_HUMAN	C	361	ENSP00000369520:R361C;ENSP00000369530:R361C	ENSP00000344337:R361C	R	+	1	0	ALOX15B	7889610	0.511000	0.26179	0.776000	0.31678	0.679000	0.39708	0.972000	0.29409	0.466000	0.27193	-0.244000	0.11960	CGC	.	.	.	weak		0.637	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2			T	7948885	C	T	7948885	3	4	235	1	0	0	0	0	1	0	0	0	539	768	27	1	1111	1	ALOX15B	17	7948885	Missense_Mutation	SNP	C	TCGA-P4-AAVL-01A-11D-A42J-10	6408810	7948885	73246325	67	14350											
MYH10	4628	hgsc.bcm.edu	37	chr17	8448780	8448780	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaatacctcaaaaatttcaaAtccagcaatatccaggattc	17	10	4	10	0	2	0	2	0	0	0	5	2	4	1	3	1	2	1	3	1	7	4			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr17:8448780A>G	ENST00000269243.4	-	12	1525	c.1387T>C	c.(1387-1389)Ttt>Ctt	p.F463L	MYH10_ENST00000360416.3_Missense_Mutation_p.F473L|RN7SL129P_ENST00000479993.2_RNA|MYH10_ENST00000396239.1_Missense_Mutation_p.F463L|MYH10_ENST00000379980.4_Missense_Mutation_p.F479L	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	463	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						AAAATTTCAAATCCAGCAATA	0.433																																					p.F473L		Atlas-SNP	.											.	MYH10	148	.	0			c.T1417C						PASS	.						106	99	102					17																	8448780		2203	4300	6503	SO:0001583	missense	4628	exon13			TTTCAAATCCAGC	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.1387T>C	chr17.hg19:g.8448780A>G	ENSP00000269243:p.Phe463Leu	74.0	0.0	.		69.0	27.0	.	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Missense_Mutation	SNP	ENST00000269243.4	hg19	CCDS11144.1	.	.	.	.	.	.	.	.	.	.	A	32	5.108528	0.94292	.	.	ENSG00000133026	ENST00000269243;ENST00000360416;ENST00000396239;ENST00000379980	D;D;D;D	0.98701	-2.12;-2.12;-5.08;-2.12	5.0	5.0	0.66597	Myosin head, motor domain (3);	0.049358	0.85682	N	0.000000	D	0.99545	0.9837	H	0.99143	4.445	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	0.97669	1.0165	10	0.87932	D	0	.	15.1595	0.72771	1.0:0.0:0.0:0.0	.	472;473;463	B2RWP9;F8VTL3;P35580	.;.;MYH10_HUMAN	L	463;473;463;479	ENSP00000269243:F463L;ENSP00000353590:F473L;ENSP00000379539:F463L;ENSP00000369315:F479L	ENSP00000269243:F463L	F	-	1	0	MYH10	8389505	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.032000	0.93736	2.216000	0.71823	0.533000	0.62120	TTT	.	.	.	none		0.433	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			G	8448780	A	G	8448780	3	3	235	1	0	0	0	0	1	0	0	0	10037	101	4	3	4663	3	MYH10	17	8448780	Missense_Mutation	SNP	A	TCGA-P4-AAVL-01A-11D-A42J-10	499895	8448780	72746430	68	14351											
KRT10	3858	hgsc.bcm.edu	37	chr17	38975316	38975316	+	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	gccgccggaactgccgccgtGgccgccgccgtggccgccgc	2	3	16	20	9	0	0	0	0	0	0	0	1	0	1	9	3	2	0	9	3	1	0			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr17:38975316G>A	ENST00000269576.5	-	7	1480	c.1471C>T	c.(1471-1473)Cac>Tac	p.H491Y	TMEM99_ENST00000301665.3_5'Flank	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	491	Gly-rich.|Ser-rich.|Tail.			Missing (in Ref. 1; AAA60544). {ECO:0000305}.	cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)			NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				ctgccgccgtggccgccgccg	0.801																																					p.H491Y		Atlas-SNP	.											.	KRT10	56	.	0			c.C1471T						PASS	.						1	1	1					17																	38975316		219	517	736	SO:0001583	missense	3858	exon7			CGCCGTGGCCGCC	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"-", "Intermediate filaments type I, keratins (acidic)"	6413	protein-coding gene	gene with protein product	"cytokeratin 10", "epidermolytic hyperkeratosis"	148080	"keratosis palmaris et plantaris"	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.1471C>T	chr17.hg19:g.38975316G>A	ENSP00000269576:p.His491Tyr	44.0	0.0	.		125.0	8.0	.	NM_000421	Q14664|Q8N175	Missense_Mutation	SNP	ENST00000269576.5	hg19	CCDS11377.1	.	.	.	.	.	.	.	.	.	.	g	15.09	2.731363	0.48939	.	.	ENSG00000186395	ENST00000269576	D	0.83591	-1.74	5.21	-9.23	0.00672	.	2.489830	0.01848	N	0.035767	T	0.64724	0.2624	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.59397	-0.7462	10	0.45353	T	0.12	.	9.3977	0.38412	0.3538:0.2897:0.3564:0.0	.	491	P13645	K1C10_HUMAN	Y	491	ENSP00000269576:H491Y	ENSP00000269576:H491Y	H	-	1	0	KRT10	36228842	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-4.792000	0.00185	-2.762000	0.00369	-2.316000	0.00254	CAC	.	.	.	none		0.801	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421		A	38975316	G	A	38975316	3	1	235	1	0	0	0	0	1	0	0	0	8455	1348	47	2	291	2	KRT10	17	38975316	Missense_Mutation	SNP	G	TCGA-P4-AAVL-01A-11D-A42J-10	30526536	38975316	42219894	69	14352											
PLEKHH3	79990	hgsc.bcm.edu	37	chr17	40823573	40823573	+	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	gagtccgggagtgcctgctcGgtcctgggttaggaggaacc	6	8	17	10	2	0	0	0	0	0	0	3	4	2	3	4	5	3	2	4	5	2	1			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr17:40823573G>T	ENST00000591022.1	-	8	1467	c.1080C>A	c.(1078-1080)acC>acA	p.T360T	PLEKHH3_ENST00000456950.2_5'UTR|PLEKHH3_ENST00000293349.6_Silent_p.T360T|PLEKHH3_ENST00000412503.1_Silent_p.T360T	NM_024927.4	NP_079203	Q7Z736	PKHH3_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 3	360	MyTH4. {ECO:0000255|PROSITE- ProRule:PRU00359}.				signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|skin(2)	13		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.14)		GTGCCTGCTCGGTCCTGGGTT	0.592																																					p.T360T		Atlas-SNP	.											.	PLEKHH3	49	.	0			c.C1080A						PASS	.						12	14	13					17																	40823573		2200	4298	6498	SO:0001819	synonymous_variant	79990	exon8			CTGCTCGGTCCTG	BC052978	CCDS11434.1	17q21.2	2013-01-11				ENSG00000068137		"Pleckstrin homology (PH) domain containing"	26105	protein-coding gene	gene with protein product						12477932	Standard	NM_024927		Approved	FLJ21019	uc002iau.3	Q7Z736		ENST00000591022.1:c.1080C>A	chr17.hg19:g.40823573G>T		112.0	0.0	.		152.0	40.0	.	NM_024927	C9JQ76|Q59H20|Q96B28|Q9H7D6|Q9NT18	Silent	SNP	ENST00000591022.1	hg19	CCDS11434.1																																																																																			.	.	.	none		0.592	PLEKHH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452332.1	NM_024927		T	40823573	G	T	40823573	2	4	235	1	0	0	0	0	0	0	0	1	12085	1103	39	4		4	PLEKHH3	17	40823573	Silent	SNP	G	TCGA-P4-AAVL-01A-11D-A42J-10	1848257	40823573	40371637	70	14353											
DHX8	1659	hgsc.bcm.edu	37	chr17	41597598	41597598	+	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	gctgtacacactgggggcccTggatgacgagggcctgctca	7	7	15	12	1	1	1	1	1	0	0	1	3	1	2	2	4	2	3	2	4	1	1			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr17:41597598T>A	ENST00000262415.3	+	19	2972	c.2900T>A	c.(2899-2901)cTg>cAg	p.L967Q	DHX8_ENST00000540306.1_Missense_Mutation_p.L967Q	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	967					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)		CTGGGGGCCCTGGATGACGAG	0.547											OREG0024435	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L967Q	NSCLC(56;1548 1661 49258 49987)	Atlas-SNP	.											.	DHX8	98	.	0			c.T2900A						PASS	.						89	85	86					17																	41597598		2203	4300	6503	SO:0001583	missense	1659	exon19			GGGCCCTGGATGA	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.2900T>A	chr17.hg19:g.41597598T>A	ENSP00000262415:p.Leu967Gln	77.0	0.0	.	902	84.0	22.0	.	NM_004941		Missense_Mutation	SNP	ENST00000262415.3	hg19	CCDS11464.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.905425	0.92107	.	.	ENSG00000067596	ENST00000540306;ENST00000262415	T;T	0.10382	2.88;2.88	5.8	5.8	0.92144	Helicase-associated domain (2);	0.000000	0.64402	D	0.000004	T	0.51517	0.1679	H	0.98664	4.295	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.71573	-0.4552	10	0.87932	D	0	.	15.3296	0.74196	0.0:0.0:0.0:1.0	.	967;967	F5H658;Q14562	.;DHX8_HUMAN	Q	967	ENSP00000437886:L967Q;ENSP00000262415:L967Q	ENSP00000262415:L967Q	L	+	2	0	DHX8	38953124	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.876000	0.87215	2.226000	0.72624	0.459000	0.35465	CTG	.	.	.	none		0.547	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453485.1			A	41597598	T	A	41597598	3	1	235	1	0	0	0	0	1	0	0	0	4517	1580	55	5	2974	5	DHX8	17	41597598	Missense_Mutation	SNP	T	TCGA-P4-AAVL-01A-11D-A42J-10	774025	41597598	39597612	71	14354											
DSG4	147409	hgsc.bcm.edu	37	chr18	28968923	28968923	+	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	gttatggacataaatgataaCgctccagtcttttcgcaaag	13	12	8	8	2	1	1	0	1	1	0	3	2	2	2	1	1	1	3	1	1	5	5			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr18:28968923C>T	ENST00000308128.4	+	5	594	c.459C>T	c.(457-459)aaC>aaT	p.N153N	RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000578477.1_RNA|DSG4_ENST00000359747.4_Silent_p.N153N|RP11-534N16.1_ENST00000581452.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	153	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		Missing (in HYPT6). {ECO:0000269|PubMed:12705872, ECO:0000269|PubMed:15191570}.		anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			TAAATGATAACGCTCCAGTCT	0.413																																					p.N153N		Atlas-SNP	.											.	DSG4	343	.	0			c.C459T						PASS	.						108	104	106					18																	28968923		2203	4299	6502	SO:0001819	synonymous_variant	147409	exon5			TGATAACGCTCCA	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.459C>T	chr18.hg19:g.28968923C>T		77.0	0.0	.		100.0	46.0	.	NM_001134453	A2RUI1|Q6Y9L9|Q8IXV4	Silent	SNP	ENST00000308128.4	hg19	CCDS11897.1																																																																																			.	.	.	none		0.413	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986		T	28968923	C	T	28968923	2	4	235	1	0	0	0	0	0	0	0	1	4781	535	19	1		1	DSG4	18	28968923	Silent	SNP	C	TCGA-P4-AAVL-01A-11D-A42J-10		28968923	49108325	72	14355											
FZR1	51343	hgsc.bcm.edu	37	chr19	3527661	3527661	+	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	ccggtccccccggaaacccaCccgcaagatctccaagatcc	10	4	7	20	3	1	2	0	0	1	2	4	3	3	3	8	2	1	1	8	2	3	0			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr19:3527661C>G	ENST00000395095.3	+	6	503	c.503C>G	c.(502-504)aCc>aGc	p.T168S	FZR1_ENST00000441788.2_Missense_Mutation_p.T168S|FZR1_ENST00000313639.8_Intron	NM_001136198.1	NP_001129670.1	Q9UM11	FZR_HUMAN	fizzy/cell division cycle 20 related 1 (Drosophila)	168					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)		CGGAAACCCACCCGCAAGATC	0.622																																					p.T168S		Atlas-SNP	.											.	FZR1	42	.	0			c.C503G						PASS	.						68	57	61					19																	3527661		2199	4296	6495	SO:0001583	missense	51343	exon6			AACCCACCCGCAA	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.503C>G	chr19.hg19:g.3527661C>G	ENSP00000378529:p.Thr168Ser	41.0	0.0	.		40.0	15.0	.	NM_001136198	O75869|Q86U66|Q96NW8|Q9UI96|Q9ULH8|Q9UM10|Q9UNQ1|Q9Y2T8	Missense_Mutation	SNP	ENST00000395095.3	hg19	CCDS45916.1	.	.	.	.	.	.	.	.	.	.	C	18.68	3.675167	0.67928	.	.	ENSG00000105325	ENST00000441788;ENST00000395095	T;T	0.07327	3.2;3.2	5.14	5.14	0.70334	WD40 repeat-like-containing domain (1);	0.095599	0.64402	D	0.000001	T	0.10809	0.0264	L	0.53249	1.67	0.80722	D	1	B;B	0.09022	0.0;0.002	B;B	0.08055	0.001;0.003	T	0.12708	-1.0537	10	0.18276	T	0.48	-27.132	17.2027	0.86910	0.0:1.0:0.0:0.0	.	168;168	Q9UM11;Q9UM11-2	FZR_HUMAN;.	S	168	ENSP00000410369:T168S;ENSP00000378529:T168S	ENSP00000378529:T168S	T	+	2	0	FZR1	3478661	1.000000	0.71417	0.972000	0.41901	0.989000	0.77384	5.865000	0.69583	2.399000	0.81585	0.655000	0.94253	ACC	.	.	.	none		0.622	FZR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452869.2	NM_016263		G	3527661	C	G	3527661	3	3	235	1	0	0	0	0	1	0	0	0	6145	507	18	4	525	4	FZR1	19	3527661	Missense_Mutation	SNP	C	TCGA-P4-AAVL-01A-11D-A42J-10		3527661	55601322	73	14356											
PLIN4	729359	hgsc.bcm.edu	37	chr19	4512405	4512405	+	Missense_Mutation	SNP	T	T	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	ggttaggacagtcttggtggTgtctacgccggtctggacgg	5	11	17	8	3	3	0	0	0	3	0	3	2	3	2	1	7	1	1	1	7	2	3			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr19:4512405T>G	ENST00000301286.3	-	3	1524	c.1525A>C	c.(1525-1527)Acc>Ccc	p.T509P		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	509	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						GTCTTGGTGGTGTCTACGCCG	0.612																																					p.T509P		Atlas-SNP	.											.	PLIN4	191	.	0			c.A1525C						PASS	.						105	111	109					19																	4512405		2036	4180	6216	SO:0001583	missense	729359	exon3			TGGTGGTGTCTAC	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.1525A>C	chr19.hg19:g.4512405T>G	ENSP00000301286:p.Thr509Pro	81.0	0.0	.		92.0	32.0	.	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	hg19	CCDS45927.1	.	.	.	.	.	.	.	.	.	.	T	14.90	2.674559	0.47781	.	.	ENSG00000167676	ENST00000301286	T	0.06608	3.28	5.43	4.4	0.53042	.	0.131117	0.35040	N	0.003484	T	0.25082	0.0609	M	0.85859	2.78	0.36524	D	0.870345	D	0.89917	1.0	D	0.74348	0.983	T	0.15665	-1.0429	10	0.51188	T	0.08	-21.1732	9.9845	0.41832	0.1518:0.0:0.0:0.8482	.	509	Q96Q06	PLIN4_HUMAN	P	509	ENSP00000301286:T509P	ENSP00000301286:T509P	T	-	1	0	PLIN4	4463405	0.125000	0.22332	0.993000	0.49108	0.030000	0.12068	1.598000	0.36740	0.866000	0.35629	0.459000	0.35465	ACC	.	.	.	none		0.612	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901		G	4512405	T	G	4512405	3	3	235	1	0	0	0	0	1	0	0	0	12099	1696	59	5	2564	5	PLIN4	19	4512405	Missense_Mutation	SNP	T	TCGA-P4-AAVL-01A-11D-A42J-10	984744	4512405	54616578	74	14357											
TNPO2	30000	hgsc.bcm.edu	37	chr19	12816127	12816127	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacgtgaccacccaggcccTcggccaggccgctgagcaga	8	3	12	18	3	0	3	0	2	0	1	1	3	0	3	6	3	1	2	6	3	0	0			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr19:12816127T>C	ENST00000592287.1	-	17	2057	c.1949A>G	c.(1948-1950)gAg>gGg	p.E650G	TNPO2_ENST00000450764.2_Missense_Mutation_p.E650G|TNPO2_ENST00000588216.1_Missense_Mutation_p.E650G|TNPO2_ENST00000425528.1_Missense_Mutation_p.E650G|SNORD41_ENST00000386967.1_RNA|TNPO2_ENST00000441499.1_Missense_Mutation_p.E650G|TNPO2_ENST00000356861.5_Missense_Mutation_p.E650G	NM_001136196.1	NP_001129668.1	O14787	TNPO2_HUMAN	transportin 2	650					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						ACCCAGGCCCTCGGCCAGGCC	0.597																																					p.E650G		Atlas-SNP	.											.	TNPO2	108	.	0			c.A1949G						PASS	.						27	29	28					19																	12816127		2152	4253	6405	SO:0001583	missense	30000	exon17			AGGCCCTCGGCCA	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.1949A>G	chr19.hg19:g.12816127T>C	ENSP00000468434:p.Glu650Gly	58.0	0.0	.		58.0	23.0	.	NM_013433	O14655|Q6IN77	Missense_Mutation	SNP	ENST00000592287.1	hg19	CCDS45991.1	.	.	.	.	.	.	.	.	.	.	T	16.63	3.175437	0.57692	.	.	ENSG00000105576	ENST00000536114;ENST00000425528;ENST00000441499;ENST00000450764;ENST00000356861;ENST00000420511;ENST00000546320	T;T;T;T	0.61158	0.13;0.13;0.13;0.13	5.64	5.64	0.86602	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69504	0.3118	M	0.89353	3.025	0.80722	D	1	P;P	0.49862	0.756;0.929	P;P	0.46339	0.495;0.513	T	0.77702	-0.2489	10	0.87932	D	0	-20.3413	14.8368	0.70190	0.0:0.0:0.0:1.0	.	814;650	Q4LE60;O14787	.;TNPO2_HUMAN	G	814;650;650;650;650;650;650	ENSP00000407182:E650G;ENSP00000389648:E650G;ENSP00000397379:E650G;ENSP00000349321:E650G	ENSP00000349321:E650G	E	-	2	0	TNPO2	12677127	1.000000	0.71417	1.000000	0.80357	0.112000	0.19704	7.671000	0.83941	2.144000	0.66660	0.460000	0.39030	GAG	.	.	.	none		0.597	TNPO2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450785.1	NM_013433		C	12816127	T	C	12816127	3	2	235	1	0	0	0	0	1	0	0	0	16348	1551	54	3	776	3	TNPO2	19	12816127	Missense_Mutation	SNP	T	TCGA-P4-AAVL-01A-11D-A42J-10	8303722	12816127	46312856	75	14358											
NOTCH3	4854	hgsc.bcm.edu	37	chr19	15288556	15288567	+	In_Frame_Del	DEL	TGGCCTGGCAGG	TGGCCTGGCAGG	-																															gcagcgctggtccccgcgctTggcctggcaggcggcgcgcg																										TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	TGGCCTGGCAGG	TGGCCTGGCAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr19:15288556_15288567delTGGCCTGGCAGG	ENST00000263388.2	-	24	4247_4258	c.4172_4183delCCTGCCAGGCCA	c.(4171-4185)gcctgccaggccaag>gag	p.1391_1395ACQAK>E		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	1391					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)			TCCCCGCGCTTGGCCTGGCAGGCGGCGCGCGG	0.778																																					p.1391_1395del		Pindel	.											.	NOTCH3	340	.	0			c.4173_4184del						PASS	.																																			SO:0001651	inframe_deletion	4854	exon24			.	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.4172_4183delCCTGCCAGGCCA	chr19.hg19:g.15288556_15288567delTGGCCTGGCAGG	ENSP00000263388:p.Ala1391_Lys1395delinsGlu	97.0	0.0	.		94.0	21.0	0.223	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	In_Frame_Del	DEL	ENST00000263388.2	hg19	CCDS12326.1																																																																																			.	.	.	none		0.778	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		-	15288567	TGGCCTGGCAGG	-	15288556	7	5	235	1	0	1	0	1	0	0	0	0	10557	1821	63	0	2822	0	NOTCH3	19	15288556	In_Frame_Del	DEL	TGGCCTGGCAGG	TCGA-P4-AAVL-01A-11D-A42J-10	2472429	15288556	43840427	76	14359											
ZNF536	9745	hgsc.bcm.edu	37	chr19	30934626	30934626	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttccccgagctccatcccCggcccaaccccgaggagaag	8	4	9	20	3	0	1	0	0	0	1	3	4	3	1	9	2	2	1	9	2	2	1			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr19:30934626C>T	ENST00000355537.3	+	2	304	c.157C>T	c.(157-159)Cgg>Tgg	p.R53W		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	53					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)					GCTCCATCCCCGGCCCAACCC	0.667																																					p.R53W		Atlas-SNP	.											.	ZNF536	424	.	0			c.C157T						PASS	.						57	59	58					19																	30934626		2203	4300	6503	SO:0001583	missense	9745	exon2			CATCCCCGGCCCA		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.157C>T	chr19.hg19:g.30934626C>T	ENSP00000347730:p.Arg53Trp	89.0	0.0	.		80.0	42.0	.	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	hg19	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	C	12.06	1.824161	0.32237	.	.	ENSG00000198597	ENST00000355537	T	0.09163	3.01	5.37	0.305	0.15801	.	0.059306	0.64402	D	0.000002	T	0.15046	0.0363	L	0.27053	0.805	0.40413	D	0.979763	B;D	0.89917	0.014;1.0	B;P	0.61874	0.003;0.895	T	0.02275	-1.1184	10	0.87932	D	0	-26.6384	10.0943	0.42466	0.4232:0.5051:0.0:0.0716	.	53;53	A7E228;O15090	.;ZN536_HUMAN	W	53	ENSP00000347730:R53W	ENSP00000347730:R53W	R	+	1	2	ZNF536	35626466	0.637000	0.27216	0.761000	0.31378	0.804000	0.45430	1.329000	0.33770	0.302000	0.22762	0.462000	0.41574	CGG	.	.	.	none		0.667	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		T	30934626	C	T	30934626	3	4	235	1	0	0	0	0	1	0	0	0	17986	643	23	1	159	1	ZNF536	19	30934626	Missense_Mutation	SNP	C	TCGA-P4-AAVL-01A-11D-A42J-10	15646070	30934626	28194357	77	14360											
PSG9	5678	hgsc.bcm.edu	37	chr19	43762353	43762353	+	Splice_Site	DEL	C	C	-																															aggatgctgggatccacttaCcagagactttgactgtcatg																										TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr19:43762353delC	ENST00000270077.3	-	5	1340		c.e5+1		PSG9_ENST00000443718.3_Splice_Site|PSG9_ENST00000244293.7_Frame_Shift_Del_p.G322fs|PSG9_ENST00000593948.1_Splice_Site|PSG9_ENST00000291752.5_Splice_Site|PSG9_ENST00000418820.2_Splice_Site|PSG9_ENST00000596730.1_Frame_Shift_Del_p.G229fs	NM_002784.3	NP_002775.3	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9						female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Prostate(69;0.00682)				GATCCACTTACCAGAGACTTT	0.458																																					.		Atlas-Indel,Pindel	.											.	PSG9	77	.	0			c.1243+2G>-						PASS	.						134	157	149					19																	43762353		2139	4280	6419	SO:0001630	splice_region_variant	5678	exon6			.	M34481	CCDS12618.1	19q13.2	2013-01-29			ENSG00000183668	ENSG00000183668		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9526	protein-coding gene	gene with protein product		176398		PSG11		7806221	Standard	XM_005259076		Approved	PSGII	uc002owd.4	Q00887	OTTHUMG00000182826	ENST00000270077.3:c.1243+1G>-	chr19.hg19:g.43762353delC		73.0	0.0	0		110.0	48.0	0.436364	NM_002784	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Splice_Site	DEL	ENST00000270077.3	hg19	CCDS12618.1																																																																																			.	.	.	none		0.458	PSG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323065.1	NM_002784	Intron	-	43762353	C	-	43762353	8	5	235	1	0	1	0	1	0	0	1	0	12672	521	18	0	44	0	PSG9	19	43762353	Splice_Site	DEL	C	TCGA-P4-AAVL-01A-11D-A42J-10	12827727	43762353	15366630	78	14361											
MKKS	8195	hgsc.bcm.edu	37	chr20	10393727	10393727	+	Missense_Mutation	SNP	T	T	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	acaaaggaggatctgagtacTactaaagtccactgggattc	14	9	10	8	0	1	1	0	1	1	0	3	4	2	4	1	3	2	1	1	3	5	4	rs113994195		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr20:10393727T>G	ENST00000347364.3	-	3	1198	c.436A>C	c.(436-438)Agt>Cgt	p.S146R	MKKS_ENST00000399054.2_Missense_Mutation_p.S146R	NM_170784.2	NP_740754.1	Q9NPJ1	MKKS_HUMAN	McKusick-Kaufman syndrome	146					artery smooth muscle contraction (GO:0014824)|brain morphogenesis (GO:0048854)|cartilage development (GO:0051216)|cerebral cortex development (GO:0021987)|chaperone-mediated protein complex assembly (GO:0051131)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|determination of left/right symmetry (GO:0007368)|fat cell differentiation (GO:0045444)|gonad development (GO:0008406)|heart development (GO:0007507)|heart looping (GO:0001947)|hippocampus development (GO:0021766)|intracellular transport (GO:0046907)|melanosome transport (GO:0032402)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of multicellular organism growth (GO:0040018)|protein folding (GO:0006457)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|sensory perception of smell (GO:0007608)|social behavior (GO:0035176)|spermatid development (GO:0007286)|striatum development (GO:0021756)|vasodilation (GO:0042311)|visual perception (GO:0007601)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|motile cilium (GO:0031514)	ATP binding (GO:0005524)|RNA polymerase II repressing transcription factor binding (GO:0001103)|unfolded protein binding (GO:0051082)			kidney(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)|stomach(2)	16						ATCTGAGTACTACTAAAGTCC	0.413																																					p.S146R	Melanoma(79;1979 2212 6640)	Atlas-SNP	.											.	MKKS	35	.	0			c.A436C						PASS	.						93	88	90					20																	10393727		2203	4300	6503	SO:0001583	missense	8195	exon3			GAGTACTACTAAA	AF221993	CCDS13111.1	20p12	2013-01-08			ENSG00000125863	ENSG00000125863		"Heat Shock Proteins / Chaperonins"	7108	protein-coding gene	gene with protein product		604896		BBS6		9467007	Standard	NR_072977		Approved		uc002wnu.2	Q9NPJ1	OTTHUMG00000031868	ENST00000347364.3:c.436A>C	chr20.hg19:g.10393727T>G	ENSP00000246062:p.Ser146Arg	62.0	0.0	.		53.0	24.0	.	NM_170784	A8K7B0|D3DW18	Missense_Mutation	SNP	ENST00000347364.3	hg19	CCDS13111.1	.	.	.	.	.	.	.	.	.	.	T	7.604	0.673385	0.14776	.	.	ENSG00000125863	ENST00000347364;ENST00000399054	D;D	0.87650	-2.28;-2.28	5.63	3.29	0.37713	.	0.254278	0.51477	N	0.000093	T	0.80924	0.4717	L	0.41824	1.3	0.44603	D	0.99757	P	0.35011	0.48	B	0.35413	0.202	T	0.76767	-0.2838	10	0.62326	D	0.03	-36.1867	9.1713	0.37083	0.1233:0.0:0.1295:0.7473	.	146	Q9NPJ1	MKKS_HUMAN	R	146	ENSP00000246062:S146R;ENSP00000382008:S146R	ENSP00000246062:S146R	S	-	1	0	MKKS	10341727	0.997000	0.39634	0.001000	0.08648	0.008000	0.06430	4.565000	0.60836	0.449000	0.26747	0.477000	0.44152	AGT	.	.	.	none		0.413	MKKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077991.3			G	10393727	T	G	10393727	3	3	235	1	0	0	0	0	1	0	0	0	9607	1522	53	5	1292	5	MKKS	20	10393727	Missense_Mutation	SNP	T	TCGA-P4-AAVL-01A-11D-A42J-10		10393727	52631793	79	14362											
ISM1	140862	hgsc.bcm.edu	37	chr20	13273028	13273028	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtctgtgtttaggaattgaAgacacttttaggacagctgc	10	14	11	6	0	1	2	0	1	1	1	1	4	1	4	0	2	2	2	0	2	4	5			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr20:13273028A>G	ENST00000262487.4	+	5	801	c.795A>G	c.(793-795)gaA>gaG	p.E265E	TASP1_ENST00000539805.1_Intron	NM_080826.1	NP_543016.1	B1AKI9	ISM1_HUMAN	isthmin 1, angiogenesis inhibitor	265						extracellular region (GO:0005576)				NS(1)|autonomic_ganglia(1)|endometrium(1)|large_intestine(8)|lung(5)|urinary_tract(1)	17						TAGGAATTGAAGACACTTTTA	0.388																																					p.E265E		Atlas-SNP	.											.	ISM1	41	.	0			c.A795G						PASS	.						85	84	84					20																	13273028		1893	4122	6015	SO:0001819	synonymous_variant	140862	exon5			AATTGAAGACACT	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.795A>G	chr20.hg19:g.13273028A>G		91.0	0.0	.		67.0	27.0	.	NM_080826	Q8WVH9	Silent	SNP	ENST00000262487.4	hg19	CCDS46579.1																																																																																			.	.	.	none		0.388	ISM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078039.2			G	13273028	A	G	13273028	2	3	235	1	0	0	0	0	0	0	0	1	7867	69	3	3		3	ISM1	20	13273028	Silent	SNP	A	TCGA-P4-AAVL-01A-11D-A42J-10	2879301	13273028	49752492	80	14363											
PLXNB2	23654	hgsc.bcm.edu	37	chr22	50721158	50721158	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acctggcaaagcttcgtagcGgctcgaaggctcgcagtacg	9	7	13	12	5	0	0	0	0	0	0	3	1	0	0	1	3	3	7	1	3	4	3			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr22:50721158G>A	ENST00000449103.1	-	18	3109	c.2969C>T	c.(2968-2970)cCg>cTg	p.P990L	PLXNB2_ENST00000496720.1_5'Flank|PLXNB2_ENST00000359337.4_Missense_Mutation_p.P990L			O15031	PLXB2_HUMAN	plexin B2	990	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)	p.P1033R(1)		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)		GCTTCGTAGCGGCTCGAAGGC	0.657																																					p.P990L		Atlas-SNP	.											PLXNB2,NS,carcinoma,0,1	PLXNB2	172	.	1	Substitution - Missense(1)	ovary(1)	c.C2969T						PASS	.						15	22	20					22																	50721158		1975	4135	6110	SO:0001583	missense	23654	exon18			CGTAGCGGCTCGA		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.2969C>T	chr22.hg19:g.50721158G>A	ENSP00000409171:p.Pro990Leu	111.0	0.0	.		121.0	57.0	.	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Missense_Mutation	SNP	ENST00000449103.1	hg19	CCDS43035.1	.	.	.	.	.	.	.	.	.	.	G	16.89	3.246268	0.59103	.	.	ENSG00000196576	ENST00000449103;ENST00000359337;ENST00000427829	D;D	0.89196	-2.48;-2.48	3.66	3.66	0.41972	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.51477	D	0.000082	D	0.93605	0.7958	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.94236	0.7481	10	0.87932	D	0	.	12.8931	0.58082	0.0:0.0:1.0:0.0	.	990	O15031	PLXB2_HUMAN	L	990;990;51	ENSP00000409171:P990L;ENSP00000352288:P990L	ENSP00000352288:P990L	P	-	2	0	PLXNB2	49063285	1.000000	0.71417	0.513000	0.27749	0.186000	0.23388	4.090000	0.57693	1.898000	0.54952	0.313000	0.20887	CCG	.	.	.	none		0.657	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401		A	50721158	G	A	50721158	3	1	235	1	0	0	0	0	1	0	0	0	12131	1116	39	1	2627	1	PLXNB2	22	50721158	Missense_Mutation	SNP	G	TCGA-P4-AAVL-01A-11D-A42J-10		50721158	583408	81	14364											
MAGIX	79917	hgsc.bcm.edu	37	chrX	49022721	49022721	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcgctcaggagatggcagccGgaaggcggagacactgagcc	10	4	16	11	3	1	3	1	1	0	2	2	6	1	4	2	5	2	2	2	5	1	0			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chrX:49022721G>A	ENST00000412696.2	+	6	988	c.988G>A	c.(988-990)Gga>Aga	p.G330R	MAGIX_ENST00000498742.1_3'UTR|MAGIX_ENST00000425661.2_Missense_Mutation_p.G254R|MAGIX_ENST00000376339.1_Missense_Mutation_p.G266R|MAGIX_ENST00000376338.3_Missense_Mutation_p.G271R	NM_024859.2	NP_079135.3	Q9H6Y5	MAGIX_HUMAN	MAGI family member, X-linked	330																	GATGGCAGCCGGAAGGCGGAG	0.711																																					p.G330R		Atlas-SNP	.											.	MAGIX	25	.	0			c.G988A						PASS	.						3	4	4					X																	49022721		1782	3702	5484	SO:0001583	missense	79917	exon6			GCAGCCGGAAGGC	AK025340	CCDS48106.1, CCDS48107.1, CCDS75976.1	Xp11.23	2014-05-06			ENSG00000017621	ENSG00000269313			30006	protein-coding gene	gene with protein product							Standard	XM_005278065		Approved	PDZX, JM10, FLJ21687	uc010nin.1	Q9H6Y5	OTTHUMG00000188218	ENST00000412696.2:c.988G>A	chrX.hg19:g.49022721G>A	ENSP00000387928:p.Gly330Arg	77.0	0.0	.		57.0	10.0	.	NM_024859	A6XND4|A8MSX9|B7WP26|Q14C81	Missense_Mutation	SNP	ENST00000412696.2	hg19	CCDS48106.1	.	.	.	.	.	.	.	.	.	.	.	17.51	3.406473	0.62399	.	.	ENSG00000017621	ENST00000376339;ENST00000425661;ENST00000412696;ENST00000376338	T;T;T;T	0.52754	0.8;1.11;0.66;0.65	4.06	1.19	0.21007	.	.	.	.	.	T	0.50684	0.1630	L	0.32530	0.975	0.24950	N	0.991796	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.79784	0.989;0.983;0.993;0.993	T	0.35895	-0.9770	9	0.87932	D	0	1.7998	3.7223	0.08462	0.2326:0.0:0.5753:0.1921	.	254;330;266;271	F8WCY7;Q9H6Y5;Q9H6Y5-3;Q9H6Y5-2	.;MAGIX_HUMAN;.;.	R	266;254;330;271	ENSP00000365517:G266R;ENSP00000403515:G254R;ENSP00000387928:G330R;ENSP00000365516:G271R	ENSP00000365516:G271R	G	+	1	0	MAGIX	48909665	0.509000	0.26163	0.376000	0.26042	0.719000	0.41307	1.763000	0.38461	-0.009000	0.14296	0.538000	0.68166	GGA	.	.	.	none		0.711	MAGIX-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378832.1	NM_024859		A	49022721	G	A	49022721	3	1	235	1	0	0	0	0	1	0	0	0	9200	1117	39	1	1050	1	MAGIX	23	49022721	Missense_Mutation	SNP	G	TCGA-P4-AAVL-01A-11D-A42J-10		49022721	106247839	82	14365											
GABRQ	55879	hgsc.bcm.edu	37	chrX	151821371	151821371	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcttgagctcggatgagcGccatggccatggccccagtg	7	7	15	12	2	0	2	0	2	0	0	1	4	0	3	4	3	3	2	4	3	0	1			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chrX:151821371G>A	ENST00000370306.2	+	9	1546	c.1526G>A	c.(1525-1527)cGc>cAc	p.R509H		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	509					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)	p.R509H(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TCGGATGAGCGCCATGGCCAT	0.542																																					p.R509H		Atlas-SNP	.											.	GABRQ	131	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1526A						PASS	.						79	68	71					X																	151821371		2203	4300	6503	SO:0001583	missense	55879	exon9			ATGAGCGCCATGG	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.1526G>A	chrX.hg19:g.151821371G>A	ENSP00000359329:p.Arg509His	90.0	0.0	.		97.0	81.0	.	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Missense_Mutation	SNP	ENST00000370306.2	hg19	CCDS14707.1	.	.	.	.	.	.	.	.	.	.	G	9.142	1.013975	0.19277	.	.	ENSG00000147402	ENST00000370306	T	0.78707	-1.2	4.4	-0.308	0.12773	Neurotransmitter-gated ion-channel transmembrane domain (2);	4.416530	0.00424	N	0.000073	T	0.61173	0.2326	N	0.08118	0	0.09310	N	1	B	0.17038	0.02	B	0.09377	0.004	T	0.51585	-0.8687	10	0.44086	T	0.13	.	8.3332	0.32200	0.4021:0.0:0.5979:0.0	.	509	Q9UN88	GBRT_HUMAN	H	509	ENSP00000359329:R509H	ENSP00000359329:R509H	R	+	2	0	GABRQ	151572027	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.804000	0.01738	-0.229000	0.09854	-1.016000	0.02456	CGC	.	.	.	none		0.542	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558		A	151821371	G	A	151821371	3	1	235	1	0	0	0	0	1	0	0	0	6182	1087	38	1	1560	1	GABRQ	23	151821371	Missense_Mutation	SNP	G	TCGA-P4-AAVL-01A-11D-A42J-10	102798650	151821371	3449189	83	14366											
TMEM201	199953	hgsc.bcm.edu	37	chr1	9658629	9658629	+	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	cagaaccgccagctgcgcgcCctgttgctcagccaccagtt	7	7	10	17	3	1	1	1	0	0	1	1	1	1	1	5	0	5	4	5	0	1	2			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr1:9658629C>G	ENST00000340381.6	+	4	561	c.552C>G	c.(550-552)gcC>gcG	p.A184A	TMEM201_ENST00000377376.4_Silent_p.A184A|TMEM201_ENST00000340305.5_Silent_p.A184A	NM_001130924.2	NP_001124396.2	Q5SNT2	TM201_HUMAN	transmembrane protein 201	184					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)		AGCTGCGCGCCCTGTTGCTCA	0.642																																					p.A184A		Atlas-SNP	.											.	TMEM201	63	.	0			c.C552G						PASS	.						55	51	52					1																	9658629		2203	4300	6503	SO:0001819	synonymous_variant	199953	exon4			GCGCGCCCTGTTG		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.552C>G	chr1.hg19:g.9658629C>G		241.0	0.0	.		241.0	82.0	.	NM_001010866	B9EH90|Q5SNT3	Silent	SNP	ENST00000340381.6	hg19	CCDS44055.2	.	.	.	.	.	.	.	.	.	.	C	11.02	1.516596	0.27123	.	.	ENSG00000188807	ENST00000416541	.	.	.	5.4	-0.367	0.12541	.	.	.	.	.	T	0.39172	0.1068	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29088	-1.0023	4	.	.	.	-28.101	0.3087	0.00285	0.2293:0.2578:0.2549:0.258	.	.	.	.	A	94	.	.	P	+	1	0	TMEM201	9581216	0.016000	0.18221	0.995000	0.50966	0.963000	0.63663	-1.022000	0.03611	0.267000	0.21916	-0.304000	0.09214	CCT	.	.	.	none		0.642	TMEM201-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127672.1	NM_001010866		G	9658629	C	G	9658629	2	3	236	1	0	0	0	0	0	0	0	1	16138	610	22	4		4	TMEM201	1	9658629	Silent	SNP	C	TCGA-P4-AAVM-01A-11D-A42J-10		9658629	239591992	1	14367											
KIF1B	23095	hgsc.bcm.edu	37	chr1	10420986	10420986	+	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	ctcttgtctttctgaccttaGgaccttctaccgctttgagg	5	16	8	12	1	4	2	0	2	4	0	4	3	4	3	3	2	1	1	3	2	2	6			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr1:10420986G>A	ENST00000377086.1	+	39	4257		c.e39-1		KIF1B_ENST00000377081.1_Splice_Site|KIF1B_ENST00000263934.6_Splice_Site|KIF1B_ENST00000465635.1_Splice_Site			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)		TCTGACCTTAGGACCTTCTAC	0.468																																					.		Atlas-SNP	.											.	KIF1B	242	.	0			c.3918-1G>A						PASS	.						186	151	163					1																	10420986		2203	4300	6503	SO:0001630	splice_region_variant	23095	exon37			ACCTTAGGACCTT	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.4056-1G>A	chr1.hg19:g.10420986G>A		104.0	0.0	.		126.0	7.0	.	NM_015074	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Splice_Site	SNP	ENST00000377086.1	hg19		.	.	.	.	.	.	.	.	.	.	G	25.9	4.683014	0.88542	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377086;ENST00000377081	.	.	.	4.87	4.87	0.63330	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.355	0.90355	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KIF1B	10343573	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	9.809000	0.99208	2.394000	0.81467	0.491000	0.48974	.	.	.	.	none		0.468	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1		Intron	A	10420986	G	A	10420986	5	1	236	1	0	0	0	0	0	0	1	0	8291	1014	35	2	5548	2	KIF1B	1	10420986	Splice_Site	SNP	G	TCGA-P4-AAVM-01A-11D-A42J-10	762357	10420986	238829635	2	14368											
TMEM39B	55116	hgsc.bcm.edu	37	chr1	32560492	32560492	+	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	ctgcctgccagctactgtgaCctgctgcacaaggccgccgc	6	7	11	17	2	0	1	0	1	0	0	0	1	0	1	5	1	6	3	5	1	2	1			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr1:32560492C>T	ENST00000336294.5	+	7	1181	c.1035C>T	c.(1033-1035)gaC>gaT	p.D345D	TMEM39B_ENST00000373634.4_Silent_p.D146D|TMEM39B_ENST00000487305.1_3'UTR|TMEM39B_ENST00000456834.2_3'UTR|TMEM39B_ENST00000427288.1_Silent_p.D230D	NM_018056.2	NP_060526.2	Q9GZU3	TM39B_HUMAN	transmembrane protein 39B	345						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|lung(5)|ovary(1)|prostate(2)	11		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				GCTACTGTGACCTGCTGCACA	0.607																																					p.D345D		Atlas-SNP	.											.	TMEM39B	66	.	0			c.C1035T						PASS	.						69	59	63					1																	32560492		2203	4300	6503	SO:0001819	synonymous_variant	55116	exon7			CTGTGACCTGCTG	AL136695	CCDS351.2	1p35.1	2008-02-05			ENSG00000121775	ENSG00000121775			25510	protein-coding gene	gene with protein product						12477932	Standard	NM_018056		Approved	FLJ10315	uc010ogv.2	Q9GZU3	OTTHUMG00000004020	ENST00000336294.5:c.1035C>T	chr1.hg19:g.32560492C>T		46.0	0.0	.		46.0	17.0	.	NM_018056	B4DKN8|B4DQE6|B4DTN8|D3DPP4|Q6IA44	Silent	SNP	ENST00000336294.5	hg19	CCDS351.2																																																																																			.	.	.	none		0.607	TMEM39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011489.2	NM_018056		T	32560492	C	T	32560492	2	4	236	1	0	0	0	0	0	0	0	1	16174	506	18	2		2	TMEM39B	1	32560492	Silent	SNP	C	TCGA-P4-AAVM-01A-11D-A42J-10	22139506	32560492	216690129	3	14369											
ALX3	257	hgsc.bcm.edu	37	chr1	110607426	110607426	+	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	gcaggctggccaggcaggggCctggggagccttgcaagtta	7	6	18	10	0	0	0	0	0	0	0	0	1	0	1	3	7	2	5	3	7	2	2			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr1:110607426C>A	ENST00000369792.4	-	2	464	c.377G>T	c.(376-378)gGc>gTc	p.G126V	RP4-773N10.4_ENST00000554749.1_RNA	NM_006492.2	NP_006483.2	O95076	ALX3_HUMAN	ALX homeobox 3	126					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)		CAGGCAGGGGCCTGGGGAGCC	0.637																																					p.G126V		Atlas-SNP	.											.	ALX3	16	.	0			c.G377T						PASS	.						51	59	56					1																	110607426		2203	4300	6503	SO:0001583	missense	257	exon2			CAGGGGCCTGGGG	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.377G>T	chr1.hg19:g.110607426C>A	ENSP00000358807:p.Gly126Val	165.0	0.0	.		135.0	49.0	.	NM_006492	O95075|Q5T8M4	Missense_Mutation	SNP	ENST00000369792.4	hg19	CCDS819.1	.	.	.	.	.	.	.	.	.	.	C	11.89	1.773631	0.31411	.	.	ENSG00000156150	ENST00000369792	D	0.92199	-2.99	4.04	1.77	0.24775	.	0.699687	0.12287	N	0.482336	T	0.71324	0.3326	N	0.19112	0.55	0.47584	D	0.999467	B	0.34372	0.451	B	0.31686	0.134	T	0.66594	-0.5884	10	0.30854	T	0.27	.	4.1379	0.10179	0.0:0.502:0.2576:0.2404	.	126	O95076	ALX3_HUMAN	V	126	ENSP00000358807:G126V	ENSP00000358807:G126V	G	-	2	0	ALX3	110408949	0.002000	0.14202	0.996000	0.52242	0.915000	0.54546	1.144000	0.31565	0.767000	0.33267	0.462000	0.41574	GGC	.	.	.	none		0.637	ALX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032232.2	NM_006492		A	110607426	C	A	110607426	3	1	236	1	0	0	0	0	1	0	0	0	557	739	26	4	666	4	ALX3	1	110607426	Missense_Mutation	SNP	C	TCGA-P4-AAVM-01A-11D-A42J-10	78046934	110607426	138643195	4	14370											
TCHH	7062	hgsc.bcm.edu	37	chr1	152084184	152084185	+	In_Frame_Ins	INS	-	-	CGCCTCTCCTGCTGCTCG																															cccgccttagttgctgctcgINScgcctctcctgctgctcgcg																										TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr1:152084184_152084185insCGCCTCTCCTGCTGCTCG	ENST00000368804.1	-	2	1507_1508	c.1508_1509insCGAGCAGCAGGAGAGGCG	c.(1507-1509)cgc>cgCGAGCAGCAGGAGAGGCGc	p.503_503R>REQQERR		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	503	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)			GTTGCTGCTCGCGCCTCTCCTG	0.663																																					p.R503delinsREQQERR		Atlas-INDEL	.											.	TCHH	275	.	0			c.1509_1510insCGAGCAGCAGGAGAGGCG						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.1491_1508dupCGAGCAGCAGGAGAGGCG	chr1.hg19:g.152084184_152084185insCGCCTCTCCTGCTGCTCG	ENSP00000357794:p.GluGlnGlnGluArgArg503dup	27.0	0.0	0		25.0	10.0	0.4	NM_007113	Q5VUI3	In_Frame_Ins	INS	ENST00000368804.1	hg19	CCDS41396.1																																																																																			.	.	.	none		0.663	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		CGCCTCTCCTGCTGCTCG	152084185	-	CGCCTCTCCTGCTGCTCG	152084184	7	5	236	1	0	1	1	0	0	0	0	0	15712	1074	38	0	4326	0	TCHH	1	152084184	In_Frame_Ins	INS	-	TCGA-P4-AAVM-01A-11D-A42J-10	41476758	152084184	97166437	5	14371											
ASH1L	55870	hgsc.bcm.edu	37	chr1	155308132	155308132	+	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	gggtagagcatcatcctcctGgcccaagtcttttaggggtg	7	11	13	10	0	2	1	1	0	1	1	4	1	4	1	3	4	1	2	3	4	3	3			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr1:155308132G>A	ENST00000368346.3	-	27	9205	c.8566C>T	c.(8566-8568)Cag>Tag	p.Q2856*	ASH1L_ENST00000392403.3_Nonsense_Mutation_p.Q2851*			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	2856					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)			TCATCCTCCTGGCCCAAGTCT	0.517																																					p.Q2851X		Atlas-SNP	.											.	ASH1L	279	.	0			c.C8551T						PASS	.						92	90	90					1																	155308132		2203	4300	6503	SO:0001587	stop_gained	55870	exon27			CCTCCTGGCCCAA	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.8566C>T	chr1.hg19:g.155308132G>A	ENSP00000357330:p.Gln2856*	97.0	0.0	.		124.0	15.0	.	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Nonsense_Mutation	SNP	ENST00000368346.3	hg19		.	.	.	.	.	.	.	.	.	.	G	52	19.235170	0.99916	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	.	.	.	5.5	5.5	0.81552	.	0.135981	0.52532	D	0.000070	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	.	17.348	0.87315	0.0:0.0:1.0:0.0	.	.	.	.	X	2856;2851	.	ENSP00000357330:Q2856X	Q	-	1	0	ASH1L	153574756	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.039000	0.57325	2.861000	0.98227	0.655000	0.94253	CAG	.	.	.	none		0.517	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		A	155308132	G	A	155308132	4	1	236	1	0	0	0	0	0	1	0	0	1041	1357	47	2	351	2	ASH1L	1	155308132	Nonsense_Mutation	SNP	G	TCGA-P4-AAVM-01A-11D-A42J-10	3223948	155308132	93942489	6	14372											
CTSE	1510	hgsc.bcm.edu	37	chr1	206318340	206318340	+	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	caggaggcatccgtccctcaAgaagaagctgcgggcacgga	11	4	14	12	3	1	2	1	0	0	2	3	4	3	4	2	4	2	3	2	4	3	0			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr1:206318340A>T	ENST00000358184.2	+	2	216	c.98A>T	c.(97-99)aAg>aTg	p.K33M	CTSE_ENST00000361052.3_Missense_Mutation_p.K33M|CTSE_ENST00000432969.2_Intron|CTSE_ENST00000360218.2_Missense_Mutation_p.K33M	NM_001910.3	NP_001901.1	P14091	CATE_HUMAN	cathepsin E	33					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)			CCGTCCCTCAAGAAGAAGCTG	0.557																																					p.K33M		Atlas-SNP	.											.	CTSE	72	.	0			c.A98T						PASS	.						56	58	57					1																	206318340		2203	4300	6503	SO:0001583	missense	1510	exon2			CCCTCAAGAAGAA	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.98A>T	chr1.hg19:g.206318340A>T	ENSP00000350911:p.Lys33Met	99.0	0.0	.		53.0	21.0	.	NM_001910	Q5TZ01|Q5TZ02|Q9NY58|Q9UCE3|Q9UCE4	Missense_Mutation	SNP	ENST00000358184.2	hg19	CCDS1462.1	.	.	.	.	.	.	.	.	.	.	A	18.69	3.678705	0.68042	.	.	ENSG00000196188	ENST00000358184;ENST00000361052;ENST00000360218	T;T;T	0.41758	0.99;0.99;0.99	4.57	3.64	0.41730	.	0.213055	0.32503	N	0.006003	T	0.36744	0.0978	L	0.47190	1.495	0.80722	D	1	P;B	0.37864	0.61;0.381	B;B	0.37198	0.243;0.163	T	0.37009	-0.9724	10	0.87932	D	0	.	11.9121	0.52745	0.0883:0.0:0.9117:0.0	.	33;33	P14091-2;P14091-1	.;.	M	33	ENSP00000350911:K33M;ENSP00000354337:K33M;ENSP00000353350:K33M	ENSP00000350911:K33M	K	+	2	0	CTSE	204484963	0.986000	0.35501	1.000000	0.80357	0.735000	0.41995	4.968000	0.63728	1.270000	0.44297	-0.242000	0.12053	AAG	.	.	.	none		0.557	CTSE-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000087998.1	NM_001910		T	206318340	A	T	206318340	3	4	236	1	0	0	0	0	1	0	0	0	4035	72	3	5	104	5	CTSE	1	206318340	Missense_Mutation	SNP	A	TCGA-P4-AAVM-01A-11D-A42J-10	51010208	206318340	42932281	7	14373											
ALMS1	7840	hgsc.bcm.edu	37	chr2	73613036	73613037	+	Missense_Mutation	DNP	GA	GA	CT																															catggccgggcgagctggagGaggaggaggaggaggaggag																								rs61156725|rs72319667|rs3074417	byFrequency	TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr2:73613036_73613037GA>CT	ENST00000264448.6	+	1	151_152	c.40_41GA>CT	c.(40-42)GAg>CTg	p.E14L	ALMS1_ENST00000377715.1_Missense_Mutation_p.E14L|ALMS1_ENST00000409009.1_Missense_Mutation_p.E14L	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	14	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CGAGCTggaggaggaggaggag	0.693																																					p.E14Q|p.E14V		Atlas-SNP	.											.	ALMS1	384	.	1	Deletion - In frame(1)	ovary(1)	c.G40C|c.A41T						PASS	.																																			SO:0001583	missense	7840	exon1			CTGGAGGAGGAGG|TGGAGGAGGAGGA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	Exception_encountered	chr2.hg19:g.73613036_73613037delinsCT	ENSP00000264448:p.Glu14Leu	202.0|200.0	0.0	.		237.0|239.0	13.0|19.0	.	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.	.	none		0.693	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		CT	73613037	GA	CT	73613036	3	2	236	1	0	0	0	0	1	0	0	0	535	1175	41	4	42	4	ALMS1	2	73613036	Missense_Mutation	DNP	GA	TCGA-P4-AAVM-01A-11D-A42J-10		73613036	169586337	8	14374											
CCDC142	84865	hgsc.bcm.edu	37	chr2	74707970	74707970	+	Missense_Mutation	SNP	A	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	cagagctaagctttcctctgAggccaggctatacaaagctt	11	10	9	11	0	1	2	0	1	1	1	2	2	2	2	2	2	4	4	2	2	4	5			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr2:74707970A>C	ENST00000393965.3	-	5	1825	c.1429T>G	c.(1429-1431)Tca>Gca	p.S477A	TTC31_ENST00000410003.1_5'Flank|TTC31_ENST00000233623.5_5'Flank|TTC31_ENST00000442235.2_5'Flank|CCDC142_ENST00000290418.4_Missense_Mutation_p.S470A|CCDC142_ENST00000471713.1_5'UTR	NM_032779.3	NP_116168.3	Q17RM4	CC142_HUMAN	coiled-coil domain containing 142	477										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	16						CTTTCCTCTGAGGCCAGGCTA	0.582																																					p.S470A		Atlas-SNP	.											.	CCDC142	40	.	0			c.T1408G						PASS	.						72	69	70					2																	74707970		2203	4300	6503	SO:0001583	missense	84865	exon5			CCTCTGAGGCCAG	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.1429T>G	chr2.hg19:g.74707970A>C	ENSP00000377537:p.Ser477Ala	114.0	0.0	.		112.0	40.0	.	NM_032779	B7ZKV5|Q8NBJ3|Q8NBV2|Q96KA7	Missense_Mutation	SNP	ENST00000393965.3	hg19		.	.	.	.	.	.	.	.	.	.	A	18.39	3.612677	0.66672	.	.	ENSG00000135637	ENST00000393965;ENST00000290418	T;T	0.44482	0.92;0.92	4.17	4.17	0.49024	.	0.536281	0.15677	N	0.250095	T	0.55465	0.1922	M	0.72118	2.19	0.25148	N	0.990448	D;D;D	0.61697	0.99;0.975;0.99	P;P;P	0.58928	0.848;0.79;0.848	T	0.45381	-0.9265	10	0.37606	T	0.19	-2.1681	9.5608	0.39369	1.0:0.0:0.0:0.0	.	477;470;477	Q17RM4;Q17RM4-2;Q17RM4-3	CC142_HUMAN;.;.	A	477;470	ENSP00000377537:S477A;ENSP00000290418:S470A	ENSP00000290418:S470A	S	-	1	0	CCDC142	74561478	0.997000	0.39634	0.989000	0.46669	0.966000	0.64601	2.551000	0.45820	1.756000	0.51951	0.459000	0.35465	TCA	.	.	.	none		0.582	CCDC142-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000328391.1	NM_032779		C	74707970	A	C	74707970	3	2	236	1	0	0	0	0	1	0	0	0	2778	304	11	5	843	5	CCDC142	2	74707970	Missense_Mutation	SNP	A	TCGA-P4-AAVM-01A-11D-A42J-10	1094934	74707970	168491403	9	14375											
TGOLN2	10618	hgsc.bcm.edu	37	chr2	85554322	85554322	+	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	ccgcacccgacttattagggAcatcttttgtggtctgcgcc	6	12	10	13	3	2	0	0	0	2	0	2	2	2	1	3	2	1	1	3	2	2	4			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr2:85554322A>T	ENST00000409232.3	-	2	594	c.533T>A	c.(532-534)gTc>gAc	p.V178D	TGOLN2_ENST00000282120.2_Missense_Mutation_p.V80D|TGOLN2_ENST00000377386.3_Missense_Mutation_p.V178D|TGOLN2_ENST00000409015.1_Missense_Mutation_p.V178D|TGOLN2_ENST00000398263.2_Missense_Mutation_p.V178D|TGOLN2_ENST00000444342.2_Missense_Mutation_p.V178D			O43493	TGON2_HUMAN	trans-golgi network protein 2	178	14 X 14 AA tandem repeats.					Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)											CTTATTAGGGACATCTTTTGT	0.587																																					p.V178D		Atlas-SNP	.											.	TGOLN2	32	.	0			c.T533A						PASS	.						309	312	311					2																	85554322		1946	4141	6087	SO:0001583	missense	10618	exon2			TTAGGGACATCTT	AF027515	CCDS46351.1, CCDS56126.1, CCDS56127.1	2p11.2	2012-06-25			ENSG00000152291	ENSG00000152291			15450	protein-coding gene	gene with protein product	"trans-Golgi network protein (46, 48, 51kD isoforms)"	603062				9422759, 21994457	Standard	NM_001206840		Approved	TGN51, TGN46, TGN48, TGN38, TTGN2	uc021vjw.1	O43493	OTTHUMG00000153017	ENST00000409232.3:c.533T>A	chr2.hg19:g.85554322A>T	ENSP00000386443:p.Val178Asp	92.0	0.0	.		85.0	38.0	.	NM_001206841	B2R686|B8ZZ88|D6W5K3|F8WBK2|O15282|O43492|O43499|O43500|O43501|Q53G68|Q53GV2|Q6MZV1|Q6ZTM7|Q8N6T8|Q92760|Q96QL2	Missense_Mutation	SNP	ENST00000409232.3	hg19	CCDS56126.1	.	.	.	.	.	.	.	.	.	.	A	0.015	-1.563265	0.00903	.	.	ENSG00000152291	ENST00000377386;ENST00000282120;ENST00000398263;ENST00000409232;ENST00000409015;ENST00000444342	T;T;T;T;T;T	0.11169	2.94;2.86;2.8;2.96;2.95;2.94	2.55	-5.11	0.02901	.	.	.	.	.	T	0.05456	0.0144	L	0.36672	1.1	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;0.0;0.001	T	0.37619	-0.9698	9	0.12430	T	0.62	0.0827	0.495	0.00570	0.3025:0.2571:0.2813:0.1592	.	178;178;178;178	O43493;O43493-5;O43493-4;O43493-2	TGON2_HUMAN;.;.;.	D	178;80;178;178;178;178	ENSP00000366603:V178D;ENSP00000282120:V80D;ENSP00000381312:V178D;ENSP00000386443:V178D;ENSP00000387035:V178D;ENSP00000391190:V178D	ENSP00000282120:V80D	V	-	2	0	TGOLN2	85407833	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-6.946000	0.00048	-3.971000	0.00086	-1.466000	0.01016	GTC	.	.	.	none		0.587	TGOLN2-006	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000329045.2	NM_006464		T	85554322	A	T	85554322	3	4	236	1	0	0	0	0	1	0	0	0	15848	275	10	5	792	5	TGOLN2	2	85554322	Missense_Mutation	SNP	A	TCGA-P4-AAVM-01A-11D-A42J-10	10846352	85554322	157645051	10	14376											
ACTR3	10096	hgsc.bcm.edu	37	chr2	114670788	114670788	+	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	gctggaaatacagaaccacaGtttatcatcccttcctgtaa	13	11	6	11	0	1	1	1	0	0	1	3	2	3	2	3	1	2	3	3	1	5	5			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr2:114670788G>T	ENST00000263238.2	+	2	404	c.84G>T	c.(82-84)caG>caT	p.Q28H	ACTR3_ENST00000535589.2_5'UTR|ACTR3_ENST00000536059.1_Missense_Mutation_p.S8I	NM_001277140.1|NM_005721.3	NP_001264069.1|NP_005712.1	P61158	ARP3_HUMAN	ARP3 actin-related protein 3 homolog (yeast)	28					Arp2/3 complex-mediated actin nucleation (GO:0034314)|asymmetric cell division (GO:0008356)|cellular component movement (GO:0006928)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|meiotic chromosome movement towards spindle pole (GO:0016344)|meiotic cytokinesis (GO:0033206)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of neuron differentiation (GO:0045666)|regulation of myosin II filament organization (GO:0043519)|response to antibiotic (GO:0046677)|response to carbohydrate (GO:0009743)|spindle localization (GO:0051653)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|excitatory synapse (GO:0060076)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|hemidesmosome (GO:0030056)|lamellipodium (GO:0030027)|membrane (GO:0016020)|podosome (GO:0002102)	ATP binding (GO:0005524)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(2)	15						CAGAACCACAGTTTATCATCC	0.289																																					p.Y28Y		Atlas-SNP	.											.	ACTR3	26	.	0			c.T84T						PASS	.						76	79	78					2																	114670788		2203	4296	6499	SO:0001583	missense	10096	exon2			ACCACAGTTTATC	AF006083	CCDS33277.1, CCDS63000.1	2q14.1	2010-07-20	2001-11-28		ENSG00000115091	ENSG00000115091			170	protein-coding gene	gene with protein product		604222	"ARP3 (actin-related protein 3, yeast) homolog"			9230079	Standard	NM_005721		Approved	ARP3	uc002tkx.2	P61158	OTTHUMG00000153497	ENST00000263238.2:c.84G>T	chr2.hg19:g.114670788G>T	ENSP00000263238:p.Gln28His	315.0	1.0	.		288.0	99.0	.	NM_005721	P32391|Q53QM2	Silent	SNP	ENST00000263238.2	hg19	CCDS33277.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.37|13.37	2.217984|2.217984	0.39201|0.39201	.|.	.|.	ENSG00000115091|ENSG00000115091	ENST00000263238|ENST00000536059	D|D	0.94497|0.97575	-3.44|-4.44	4.42|4.42	3.52|3.52	0.40303|0.40303	.|.	0.064264|.	0.64402|.	D|.	0.000005|.	D|D	0.95947|0.95947	0.8680|0.8680	M|M	0.69523|0.69523	2.12|2.12	0.80722|0.80722	D|D	1|1	D|P	0.56521|0.34977	0.976|0.478	D|B	0.63877|0.40636	0.919|0.335	D|D	0.95526|0.95526	0.8599|0.8599	10|9	0.72032|0.72032	D|D	0.01|0.01	.|.	8.005|8.005	0.30319|0.30319	0.2466:0.0:0.7534:0.0|0.2466:0.0:0.7534:0.0	.|.	28|8	P61158|F5H3P5	ARP3_HUMAN|.	H|I	28|8	ENSP00000263238:Q28H|ENSP00000445257:S8I	ENSP00000263238:Q28H|ENSP00000445257:S8I	Q|S	+|+	3|2	2|0	ACTR3|ACTR3	114387258|114387258	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.974000|0.974000	0.67602|0.67602	4.767000|4.767000	0.62286|0.62286	2.290000|2.290000	0.77057|0.77057	0.305000|0.305000	0.20034|0.20034	CAG|AGT	.	.	.	none		0.289	ACTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331366.2	NM_005721		T	114670788	G	T	114670788	3	4	236	1	0	0	0	0	1	0	0	0	212	1020	36	4	90	4	ACTR3	2	114670788	Missense_Mutation	SNP	G	TCGA-P4-AAVM-01A-11D-A42J-10	29116466	114670788	128528585	11	14377											
OLA1	29789	hgsc.bcm.edu	37	chr2	174987981	174987981	+	Missense_Mutation	SNP	A	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	cattggttttgaagtcaaaaAtaagtgtttattcaacactt	14	16	6	5	0	2	1	2	1	0	0	2	1	2	1	0	1	1	2	0	1	6	8			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr2:174987981A>C	ENST00000409546.1	-	7	1345	c.715T>G	c.(715-717)Ttt>Gtt	p.F239V	OLA1_ENST00000284719.3_Missense_Mutation_p.F219V|OLA1_ENST00000428402.2_Missense_Mutation_p.F219V|OLA1_ENST00000392560.2_5'UTR|OLA1_ENST00000344357.5_Missense_Mutation_p.F61V					Obg-like ATPase 1											breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	11						GAAGTCAAAAATAAGTGTTTA	0.308																																					p.F219V		Atlas-SNP	.											.	OLA1	37	.	0			c.T655G						PASS	.						48	49	49					2																	174987981		2201	4296	6497	SO:0001583	missense	29789	exon7			TCAAAAATAAGTG		CCDS2255.1, CCDS42779.1	2q31.1	2014-06-24	2007-07-27	2007-07-27	ENSG00000138430	ENSG00000138430			28833	protein-coding gene	gene with protein product		611175	"GTP-binding protein 9 (putative)"	GTPBP9		17430889, 24486488	Standard	NM_013341		Approved	PTD004	uc002uih.3	Q9NTK5	OTTHUMG00000132335	ENST00000409546.1:c.715T>G	chr2.hg19:g.174987981A>C	ENSP00000386350:p.Phe239Val	46.0	0.0	.		33.0	8.0	.	NM_013341		Missense_Mutation	SNP	ENST00000409546.1	hg19		.	.	.	.	.	.	.	.	.	.	A	21.0	4.083112	0.76642	.	.	ENSG00000138430	ENST00000284719;ENST00000344357;ENST00000428402;ENST00000409546;ENST00000429575	T;T;T;T	0.45668	2.32;2.32;0.89;2.32	5.71	4.52	0.55395	.	0.047967	0.85682	D	0.000000	T	0.63058	0.2479	M	0.85373	2.75	0.80722	D	1	P;P;P;P	0.51791	0.948;0.854;0.885;0.854	P;P;P;P	0.59012	0.786;0.85;0.83;0.85	T	0.68032	-0.5516	10	0.87932	D	0	.	11.9033	0.52697	0.931:0.0:0.069:0.0	.	219;219;61;219	Q9NTK5-3;D7EHM2;Q9NTK5-2;Q9NTK5	.;.;.;OLA1_HUMAN	V	219;61;219;239;61	ENSP00000284719:F219V;ENSP00000340167:F61V;ENSP00000410385:F219V;ENSP00000386350:F239V	ENSP00000284719:F219V	F	-	1	0	OLA1	174696227	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.906000	0.63293	0.944000	0.37579	0.528000	0.53228	TTT	.	.	.	none		0.308	OLA1-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000333877.1	NM_013341		C	174987981	A	C	174987981	3	2	236	1	0	0	0	0	1	0	0	0	10857	101	4	5	555	5	OLA1	2	174987981	Missense_Mutation	SNP	A	TCGA-P4-AAVM-01A-11D-A42J-10	60317193	174987981	68211392	12	14378											
MYO1B	4430	hgsc.bcm.edu	37	chr2	192227007	192227007	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaatagataaacttaagctTgagagggatttcagcaggta	15	11	10	5	0	2	2	2	1	0	2	2	4	2	3	0	2	3	3	0	2	6	6			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr2:192227007T>C	ENST00000392318.3	+	9	922	c.675T>C	c.(673-675)ctT>ctC	p.L225L	MYO1B_ENST00000304164.4_Silent_p.L225L|MYO1B_ENST00000392316.1_Silent_p.L225L|MYO1B_ENST00000339514.4_Silent_p.L225L	NM_001130158.1	NP_001123630.1	O43795	MYO1B_HUMAN	myosin IB	225	Myosin motor.				actin filament bundle assembly (GO:0051017)|actin filament organization (GO:0007015)|actin filament-based movement (GO:0030048)|metabolic process (GO:0008152)|post-Golgi vesicle-mediated transport (GO:0006892)	actin filament (GO:0005884)|brush border (GO:0005903)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			NS(1)|central_nervous_system(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(19)|ovary(1)	55			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			AACTTAAGCTTGAGAGGGATT	0.378																																					p.L225L		Atlas-SNP	.											.	MYO1B	160	.	0			c.T675C						PASS	.						112	111	111					2																	192227007		2203	4300	6503	SO:0001819	synonymous_variant	4430	exon9			TAAGCTTGAGAGG	L29138	CCDS2311.1, CCDS46477.1	2q12-q34	2011-09-27			ENSG00000128641	ENSG00000128641		"Myosins / Myosin superfamily : Class I"	7596	protein-coding gene	gene with protein product		606537				8022818, 8449985	Standard	NM_012223		Approved	myr1	uc010fsg.2	O43795	OTTHUMG00000132718	ENST00000392318.3:c.675T>C	chr2.hg19:g.192227007T>C		143.0	0.0	.		126.0	47.0	.	NM_012223	O43794|Q7Z6L5	Silent	SNP	ENST00000392318.3	hg19	CCDS46477.1																																																																																			.	.	.	none		0.378	MYO1B-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334774.1	NM_012223		C	192227007	T	C	192227007	2	2	236	1	0	0	0	0	0	0	0	1	10076	1799	63	3		3	MYO1B	2	192227007	Silent	SNP	T	TCGA-P4-AAVM-01A-11D-A42J-10	17239026	192227007	50972366	13	14379											
WNT7A	7476	hgsc.bcm.edu	37	chr3	13860792	13860792	+	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	ggctccacgtgaacggcctcGttgtacttgtccttgagcac	6	11	11	13	3	0	2	0	2	0	0	3	2	2	2	3	2	3	4	3	2	2	4			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr3:13860792G>A	ENST00000285018.4	-	4	1003	c.699C>T	c.(697-699)aaC>aaT	p.N233N		NM_004625.3	NP_004616.2	O00755	WNT7A_HUMAN	wingless-type MMTV integration site family, member 7A	233					asymmetric protein localization (GO:0008105)|canonical Wnt signaling pathway (GO:0060070)|cartilage condensation (GO:0001502)|cell fate commitment (GO:0045165)|cell proliferation in forebrain (GO:0021846)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system vasculogenesis (GO:0022009)|cerebellar granule cell differentiation (GO:0021707)|chondrocyte differentiation (GO:0002062)|dorsal/ventral pattern formation (GO:0009953)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment of cell polarity (GO:0030010)|lens fiber cell development (GO:0070307)|negative regulation of apoptotic process (GO:0043066)|negative regulation of neurogenesis (GO:0050768)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|non-canonical Wnt signaling pathway (GO:0035567)|oviduct development (GO:0060066)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|positive regulation of JNK cascade (GO:0046330)|positive regulation of synapse assembly (GO:0051965)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of axon diameter (GO:0031133)|response to estradiol (GO:0032355)|sex differentiation (GO:0007548)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration (GO:0014834)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|stem cell development (GO:0048864)|synapse organization (GO:0050808)|uterus morphogenesis (GO:0061038)|Wnt signaling pathway involved in wound healing, spreading of epidermal cells (GO:0035659)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|receptor binding (GO:0005102)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	24						GAACGGCCTCGTTGTACTTGT	0.612																																					p.N233N		Atlas-SNP	.											.	WNT7A	70	.	0			c.C699T						PASS	.						108	100	103					3																	13860792		2203	4300	6503	SO:0001819	synonymous_variant	7476	exon4			GGCCTCGTTGTAC	D83175	CCDS2616.1	3p25	2008-07-18			ENSG00000154764	ENSG00000154764		"Wingless-type MMTV integration sites"	12786	protein-coding gene	gene with protein product	"proto-oncogene Wnt7a protein"	601570				8893824, 9161407	Standard	NM_004625		Approved		uc003bye.1	O00755	OTTHUMG00000129803	ENST00000285018.4:c.699C>T	chr3.hg19:g.13860792G>A		73.0	0.0	.		120.0	47.0	.	NM_004625	Q96H90|Q9Y560	Silent	SNP	ENST00000285018.4	hg19	CCDS2616.1																																																																																			.	.	.	none		0.612	WNT7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252031.2	NM_004625		A	13860792	G	A	13860792	2	1	236	1	0	0	0	0	0	0	0	1	17406	1136	40	1		1	WNT7A	3	13860792	Silent	SNP	G	TCGA-P4-AAVM-01A-11D-A42J-10		13860792	184161638	14	14380											
ARGFX	503582	hgsc.bcm.edu	37	chr3	121289566	121289566	+	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	cagatttcagaaaccatgagGaacagaatggccccagagaa	17	5	10	9	0	1	5	1	1	0	4	1	7	1	6	3	2	2	0	3	2	4	1			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr3:121289566G>A	ENST00000334384.3	+	1	16	c.6G>A	c.(4-6)agG>agA	p.R2R		NM_001012659.1	NP_001012677.1	A6NJG6	ARGFX_HUMAN	arginine-fifty homeobox	2					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	15				GBM - Glioblastoma multiforme(114;0.152)		AAACCATGAGGAACAGAATGG	0.473																																					p.R2R		Atlas-SNP	.											.	ARGFX	36	.	0			c.G6A						PASS	.						76	77	76					3																	121289566		2203	4300	6503	SO:0001819	synonymous_variant	503582	exon2			CATGAGGAACAGA		CCDS33834.1	3q13.33	2011-06-20			ENSG00000186103	ENSG00000186103		"Homeoboxes / PRD class"	30146	protein-coding gene	gene with protein product		611164					Standard	XM_005247505		Approved		uc003eef.3	A6NJG6	OTTHUMG00000159395	ENST00000334384.3:c.6G>A	chr3.hg19:g.121289566G>A		302.0	1.0	.		404.0	240.0	.	NM_001012659		Silent	SNP	ENST00000334384.3	hg19	CCDS33834.1																																																																																			.	.	.	none		0.473	ARGFX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355096.2	NM_001012659		A	121289566	G	A	121289566	2	1	236	1	0	0	0	0	0	0	0	1	859	1165	41	2		2	ARGFX	3	121289566	Silent	SNP	G	TCGA-P4-AAVM-01A-11D-A42J-10	107428774	121289566	76732864	15	14381											
SI	6476	hgsc.bcm.edu	37	chr3	164783068	164783068	+	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	catcaccaggaagttggtctCgagtaaaaattggccatgtt	12	11	10	8	1	2	0	1	0	1	0	3	2	2	1	2	3	0	3	2	3	4	4	rs143135955		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr3:164783068C>T	ENST00000264382.3	-	7	850	c.788G>A	c.(787-789)cGa>cAa	p.R263Q		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	263	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)	AAGTTGGTCTCGAGTAAAAAT	0.318										HNSCC(35;0.089)																											p.R263Q		Atlas-SNP	.											.	SI	500	.	0			c.G788A						PASS	.	C	GLN/ARG	0,4406		0,0,2203	68	67	67		788	5.9	1	3	dbSNP_134	67	1,8599	1.2+/-3.3	0,1,4299	no	missense	SI	NM_001041.3	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	263/1828	164783068	1,13005	2203	4300	6503	SO:0001583	missense	6476	exon7			TGGTCTCGAGTAA	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.788G>A	chr3.hg19:g.164783068C>T	ENSP00000264382:p.Arg263Gln	221.0	0.0	.		257.0	139.0	.	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	hg19	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	C	33	5.220283	0.95139	0.0	1.16E-4	ENSG00000090402	ENST00000264382	D	0.86164	-2.08	5.9	5.9	0.94986	Glycoside hydrolase-type carbohydrate-binding (1);	0.000000	0.85682	D	0.000000	D	0.95436	0.8518	M	0.92649	3.33	0.54753	D	0.999981	D	0.89917	1.0	D	0.81914	0.995	D	0.95695	0.8744	10	0.87932	D	0	.	20.2789	0.98501	0.0:1.0:0.0:0.0	.	263	P14410	SUIS_HUMAN	Q	263	ENSP00000264382:R263Q	ENSP00000264382:R263Q	R	-	2	0	SI	166265762	1.000000	0.71417	0.994000	0.49952	0.882000	0.50991	5.545000	0.67237	2.788000	0.95919	0.650000	0.86243	CGA	.	C|1.000;T|0.000	0.000	weak		0.318	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		T	164783068	C	T	164783068	3	4	236	1	0	0	0	0	1	0	0	0	14310	884	31	1	4863	1	SI	3	164783068	Missense_Mutation	SNP	C	TCGA-P4-AAVM-01A-11D-A42J-10	43493502	164783068	33239362	16	14382											
SEC24D	9871	hgsc.bcm.edu	37	chr4	119674015	119674015	+	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	atatgtgataaaacccactcGaattgcagacgtctcttctt	12	13	6	10	2	2	2	0	1	2	1	4	3	2	2	1	0	2	1	1	0	4	5			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr4:119674015G>C	ENST00000280551.6	-	12	1688	c.1450C>G	c.(1450-1452)Cga>Gga	p.R484G	SEC24D_ENST00000419654.2_Missense_Mutation_p.R40G|SEC24D_ENST00000505134.1_5'UTR|SEC24D_ENST00000511481.1_Missense_Mutation_p.R115G|SEC24D_ENST00000429811.2_Missense_Mutation_p.R40G|SEC24D_ENST00000379735.5_Missense_Mutation_p.R485G			O94855	SC24D_HUMAN	SEC24 family member D	484					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						AAACCCACTCGAATTGCAGAC	0.373																																					p.R484G		Atlas-SNP	.											.	SEC24D	96	.	0			c.C1450G						PASS	.						73	75	74					4																	119674015		2203	4300	6503	SO:0001583	missense	9871	exon12			CCACTCGAATTGC	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.1450C>G	chr4.hg19:g.119674015G>C	ENSP00000280551:p.Arg484Gly	117.0	0.0	.		119.0	49.0	.	NM_014822	Q8IYI7	Missense_Mutation	SNP	ENST00000280551.6	hg19	CCDS3710.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.683714	0.88639	.	.	ENSG00000150961	ENST00000280551;ENST00000379735;ENST00000429811;ENST00000511481;ENST00000419654	T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63	5.34	5.34	0.76211	Sec23/Sec24, trunk domain (1);	0.061247	0.64402	D	0.000007	T	0.76608	0.4011	M	0.93106	3.38	0.58432	D	0.99999	D;D	0.63880	0.989;0.993	D;D	0.68353	0.91;0.957	T	0.82948	-0.0204	10	0.87932	D	0	-15.9984	19.0321	0.92961	0.0:0.0:1.0:0.0	.	485;484	O94855-2;O94855	.;SC24D_HUMAN	G	484;485;40;115;40	ENSP00000280551:R484G;ENSP00000369059:R485G;ENSP00000409775:R40G;ENSP00000425491:R115G;ENSP00000388324:R40G	ENSP00000280551:R484G	R	-	1	2	SEC24D	119893463	1.000000	0.71417	0.950000	0.38849	0.959000	0.62525	5.727000	0.68523	2.494000	0.84150	0.467000	0.42956	CGA	.	.	.	none		0.373	SEC24D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256514.4			C	119674015	G	C	119674015	3	2	236	1	0	0	0	0	1	0	0	0	14010	1066	37	4	1696	4	SEC24D	4	119674015	Missense_Mutation	SNP	G	TCGA-P4-AAVM-01A-11D-A42J-10		119674015	71480261	17	14383											
UFSP2	55325	hgsc.bcm.edu	37	chr4	186324652	186324652	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaaatggatacttacctttTccaaaataacttgcaggtct	13	15	5	8	0	1	0	0	0	1	0	2	1	2	1	2	2	4	1	2	2	7	7			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr4:186324652T>C	ENST00000264689.6	-	11	1435	c.1319A>G	c.(1318-1320)gAa>gGa	p.E440G		NM_018359.3	NP_060829.2	Q9NUQ7	UFSP2_HUMAN	UFM1-specific peptidase 2	440						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)		ACTTACCTTTTCCAAAATAAC	0.383																																					p.E440G		Atlas-SNP	.											.	UFSP2	33	.	0			c.A1319G						PASS	.						95	88	90					4																	186324652		2203	4300	6503	SO:0001583	missense	55325	exon11			ACCTTTTCCAAAA	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.1319A>G	chr4.hg19:g.186324652T>C	ENSP00000264689:p.Glu440Gly	88.0	0.0	.		65.0	31.0	.	NM_018359	Q6IA77|Q96FS3	Missense_Mutation	SNP	ENST00000264689.6	hg19	CCDS3842.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.38|14.38	2.517213|2.517213	0.44763|0.44763	.|.	.|.	ENSG00000109775|ENSG00000109775	ENST00000264689|ENST00000509180	T|.	0.32988|.	1.43|.	5.92|5.92	4.75|4.75	0.60458|0.60458	.|.	0.190483|.	0.56097|.	N|.	0.000030|.	T|T	0.54695|0.54695	0.1874|0.1874	L|L	0.38953|0.38953	1.18|1.18	0.53688|0.53688	D|D	0.999975|0.999975	B;B|.	0.16396|.	0.003;0.017|.	B;B|.	0.16289|.	0.015;0.007|.	T|T	0.49634|0.49634	-0.8919|-0.8919	10|5	0.45353|.	T|.	0.12|.	-22.9056|-22.9056	11.7184|11.7184	0.51668|0.51668	0.0:0.0684:0.0:0.9316|0.0:0.0684:0.0:0.9316	.|.	440;340|.	Q9NUQ7;B3KRI4|.	UFSP2_HUMAN;.|.	G|E	440|169	ENSP00000264689:E440G|.	ENSP00000264689:E440G|.	E|K	-|-	2|1	0|0	UFSP2|UFSP2	186561646|186561646	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.910000|0.910000	0.53928|0.53928	7.688000|7.688000	0.84153|0.84153	1.073000|1.073000	0.40885|0.40885	0.533000|0.533000	0.62120|0.62120	GAA|AAA	.	.	.	none		0.383	UFSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360589.2	NM_018359		C	186324652	T	C	186324652	3	2	236	1	0	0	0	0	1	0	0	0	16950	1783	62	3	98	3	UFSP2	4	186324652	Missense_Mutation	SNP	T	TCGA-P4-AAVM-01A-11D-A42J-10	66650637	186324652	4829624	18	14384											
ANKRA2	57763	hgsc.bcm.edu	37	chr5	72857114	72857114	+	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	tgtatggatattgcattcagCtaagtgaaaaacaaatgtaa	17	12	8	4	0	1	1	1	1	0	0	1	2	1	2	0	1	3	4	0	1	7	6			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr5:72857114C>T	ENST00000296785.3	-	3	948		c.e3-1			NM_023039.4	NP_075526.1	Q9H9E1	ANRA2_HUMAN	ankyrin repeat, family A (RFXANK-like), 2							cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	low-density lipoprotein particle binding (GO:0030169)			endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)	8		Lung NSC(167;0.0378)|Ovarian(174;0.0908)		OV - Ovarian serous cystadenocarcinoma(47;3.71e-54)		TTGCATTCAGCTAAGTGAAAA	0.358																																					.		Atlas-SNP	.											.	ANKRA2	23	.	0			c.290-1G>A						PASS	.						138	120	126					5																	72857114		2203	4300	6503	SO:0001630	splice_region_variant	57763	exon4			ATTCAGCTAAGTG	AA442702	CCDS4020.1	5q12-q13	2013-01-10			ENSG00000164331	ENSG00000164331		"Ankyrin repeat domain containing"	13208	protein-coding gene	gene with protein product		605787				10965114	Standard	NM_023039		Approved		uc003kcu.2	Q9H9E1	OTTHUMG00000102030	ENST00000296785.3:c.290-1G>A	chr5.hg19:g.72857114C>T		85.0	0.0	.		80.0	29.0	.	NM_023039		Splice_Site	SNP	ENST00000296785.3	hg19	CCDS4020.1	.	.	.	.	.	.	.	.	.	.	C	15.47	2.843321	0.51057	.	.	ENSG00000164331	ENST00000296785	.	.	.	4.84	4.84	0.62591	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.0124	0.89227	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ANKRA2	72892870	1.000000	0.71417	0.998000	0.56505	0.613000	0.37349	7.423000	0.80229	2.246000	0.74042	0.449000	0.29647	.	.	.	.	none		0.358	ANKRA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219814.2	NM_023039	Intron	T	72857114	C	T	72857114	5	4	236	1	0	0	0	0	0	0	1	0	636	811	28	2	680	2	ANKRA2	5	72857114	Splice_Site	SNP	C	TCGA-P4-AAVM-01A-11D-A42J-10		72857114	108058146	19	14385											
ANKRD34B	340120	hgsc.bcm.edu	37	chr5	79854309	79854309	+	Missense_Mutation	SNP	T	T	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	atctcctagaagtttactaaTtgcttaatttgttcagtttg	10	19	6	6	0	2	1	1	0	1	1	3	1	2	1	1	0	2	4	1	0	5	9			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr5:79854309T>G	ENST00000338682.3	-	5	2202	c.1530A>C	c.(1528-1530)caA>caC	p.Q510H		NM_001004441.2	NP_001004441.2	A5PLL1	AN34B_HUMAN	ankyrin repeat domain 34B	510						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)		AGTTTACTAATTGCTTAATTT	0.299																																					p.Q510H		Atlas-SNP	.											.	ANKRD34B	61	.	0			c.A1530C						PASS	.						50	52	51					5																	79854309		2203	4298	6501	SO:0001583	missense	340120	exon5			TACTAATTGCTTA		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.1530A>C	chr5.hg19:g.79854309T>G	ENSP00000339802:p.Gln510His	58.0	0.0	.		89.0	35.0	.	NM_001004441	B2RPH1|Q68D79	Missense_Mutation	SNP	ENST00000338682.3	hg19	CCDS34194.1	.	.	.	.	.	.	.	.	.	.	T	17.15	3.317196	0.60524	.	.	ENSG00000189127	ENST00000338682	T	0.21361	2.01	6.04	-2.62	0.06152	.	0.000000	0.64402	D	0.000004	T	0.42539	0.1207	M	0.77313	2.365	0.47037	D	0.999297	D	0.89917	1.0	D	0.87578	0.998	T	0.46190	-0.9209	10	0.56958	D	0.05	-16.413	14.2293	0.65879	0.0:0.5749:0.0:0.4251	.	510	A5PLL1	AN34B_HUMAN	H	510	ENSP00000339802:Q510H	ENSP00000339802:Q510H	Q	-	3	2	ANKRD34B	79890065	0.773000	0.28580	0.961000	0.40146	0.903000	0.53119	-0.065000	0.11617	-0.344000	0.08338	0.460000	0.39030	CAA	.	.	.	none		0.299	ANKRD34B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369475.1	NM_001004441		G	79854309	T	G	79854309	3	3	236	1	0	0	0	0	1	0	0	0	663	1490	52	5	18	5	ANKRD34B	5	79854309	Missense_Mutation	SNP	T	TCGA-P4-AAVM-01A-11D-A42J-10	6997195	79854309	101060951	20	14386											
PARK2	5071	hgsc.bcm.edu	37	chr6	162864397	162864398	+	Missense_Mutation	DNP	TC	TC	AT																															cgaaaatcacacgcaactggTcagccggaaccccctgtcgc																										TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr6:162864397_162864398TC>AT	ENST00000366898.1	-	2	217_218	c.115_116GA>AT	c.(115-117)GAc>ATc	p.D39I	PARK2_ENST00000366897.1_Missense_Mutation_p.D39I|PARK2_ENST00000366892.1_Missense_Mutation_p.D39I|PARK2_ENST00000366894.1_5'UTR|PARK2_ENST00000338468.3_5'UTR|PARK2_ENST00000366896.1_Missense_Mutation_p.D39I	NM_004562.2	NP_004553.2	O60260	PRKN2_HUMAN	parkin RBR E3 ubiquitin protein ligase	39	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)		ACGCAACTGGTCAGCCGGAACC	0.579																																					p.D39V|p.D39N		Atlas-SNP	.											.	PARK2	96	.	0			c.A116T|c.G115A						PASS	.																																			SO:0001583	missense	5071	exon2			AACTGGTCAGCCG|ACTGGTCAGCCGG		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.115_116delinsAT	chr6.hg19:g.162864397_162864398delinsAT	ENSP00000355865:p.Asp39Ile	79.0	0.0	.		65.0|66.0	28.0|27.0	.	NM_004562	A3FG77|A8K975|D3JZW7|D3K2X0|Q5TFV8|Q5VVX4|Q6Q2I6|Q8NI41|Q8NI43|Q8NI44|Q8WW07	Missense_Mutation	SNP	ENST00000366898.1	hg19	CCDS5281.1																																																																																			.	.	.	none		0.579	PARK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042995.1			AT	162864398	TC	AT	162864397	3	1	236	1	0	0	0	0	1	0	0	0	11456	1667	58	5	1325	5	PARK2	6	162864397	Missense_Mutation	DNP	TC	TCGA-P4-AAVM-01A-11D-A42J-10		162864397	8250670	21	14387											
DBNL	28988	hgsc.bcm.edu	37	chr7	44091488	44091488	+	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	ggaaggtgatgtacgccttcTgcagagtgaaggaccccaac	11	7	13	10	1	1	3	0	2	1	1	1	5	1	5	3	3	3	2	3	3	4	2			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr7:44091488T>A	ENST00000448521.1	+	3	297	c.199T>A	c.(199-201)Tgc>Agc	p.C67S	DBNL_ENST00000440166.1_Intron|DBNL_ENST00000494774.1_Missense_Mutation_p.C67S|DBNL_ENST00000468694.1_Missense_Mutation_p.C67S|DBNL_ENST00000497184.1_3'UTR|DBNL_ENST00000456905.1_Missense_Mutation_p.C67S|DBNL_ENST00000490734.2_Intron|DBNL_ENST00000452943.1_Missense_Mutation_p.C67S	NM_001014436.2	NP_001014436.1	Q9UJU6	DBNL_HUMAN	drebrin-like	67	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|endocytosis (GO:0006897)|immune system process (GO:0002376)|neuron projection morphogenesis (GO:0048812)|podosome assembly (GO:0071800)|Rac protein signal transduction (GO:0016601)|synapse assembly (GO:0007416)	cell cortex (GO:0005938)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|podosome (GO:0002102)|postsynaptic density (GO:0014069)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|enzyme activator activity (GO:0008047)			breast(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|stomach(1)	12						GTACGCCTTCTGCAGAGTGAA	0.562																																					p.C67S	NSCLC(68;573 1327 18604 34760 37992)	Atlas-SNP	.											.	DBNL	26	.	0			c.T199A						PASS	.						181	149	160					7																	44091488		2203	4300	6503	SO:0001583	missense	28988	exon3			GCCTTCTGCAGAG	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.199T>A	chr7.hg19:g.44091488T>A	ENSP00000411701:p.Cys67Ser	95.0	0.0	.		80.0	47.0	.	NM_001122956	A4D2I9|B4DEM2|C9J7P1|P84070|Q6IAI8|Q96F30|Q96K74|Q9HBN8|Q9NR72	Missense_Mutation	SNP	ENST00000448521.1	hg19	CCDS34623.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.931604	0.92389	.	.	ENSG00000136279	ENST00000448521;ENST00000456905;ENST00000452943;ENST00000468694;ENST00000494774	T;T;T;T;T	0.35605	1.3;1.3;1.3;1.3;1.3	5.15	5.15	0.70609	Actin-binding, cofilin/tropomyosin type (3);	0.000000	0.85682	D	0.000000	T	0.64305	0.2586	M	0.84846	2.72	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;0.999;0.999;0.999;1.0;0.999	T	0.71328	-0.4626	10	0.87932	D	0	-34.7951	14.6984	0.69139	0.0:0.0:0.0:1.0	.	15;67;67;67;67;67	B4DXL9;B4DDP6;B4DDD6;Q9UJU6-3;Q9UJU6;Q9UJU6-2	.;.;.;.;DBNL_HUMAN;.	S	67	ENSP00000411701:C67S;ENSP00000416421:C67S;ENSP00000405343:C67S;ENSP00000417653:C67S;ENSP00000419992:C67S	ENSP00000411701:C67S	C	+	1	0	DBNL	44058013	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.864000	0.87037	1.955000	0.56771	0.529000	0.55759	TGC	.	.	.	none		0.562	DBNL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339572.2	NM_014063		A	44091488	T	A	44091488	3	1	236	1	0	0	0	0	1	0	0	0	4257	1580	55	5	209	5	DBNL	7	44091488	Missense_Mutation	SNP	T	TCGA-P4-AAVM-01A-11D-A42J-10		44091488	115047175	22	14388											
TNS3	64759	hgsc.bcm.edu	37	chr7	47342974	47342974	+	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	ctggctgctgggaggcgccaGggagtccggtggctctgcta	4	8	18	11	2	1	0	0	0	1	0	2	2	2	2	2	6	2	4	2	6	1	1			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr7:47342974G>C	ENST00000398879.1	-	22	3397	c.3031C>G	c.(3031-3033)Ctg>Gtg	p.L1011V	TNS3_ENST00000311160.9_Missense_Mutation_p.L1011V|TNS3_ENST00000355730.3_Missense_Mutation_p.L771V			Q68CZ2	TENS3_HUMAN	tensin 3	1011					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						GGAGGCGCCAGGGAGTCCGGT	0.672																																					p.L1011V		Atlas-SNP	.											.	TNS3	140	.	0			c.C3031G						PASS	.						20	24	23					7																	47342974		1966	4140	6106	SO:0001583	missense	64759	exon22			GCGCCAGGGAGTC	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.3031C>G	chr7.hg19:g.47342974G>C	ENSP00000381854:p.Leu1011Val	136.0	0.0	.		102.0	49.0	.	NM_022748	B2RNV1|Q6IPQ2|Q8IZW7|Q8NAD0|Q96PE0|Q96S48	Missense_Mutation	SNP	ENST00000398879.1	hg19	CCDS5506.2	.	.	.	.	.	.	.	.	.	.	G	1.723	-0.496178	0.04291	.	.	ENSG00000136205	ENST00000311160;ENST00000538633;ENST00000398879;ENST00000355730;ENST00000545849;ENST00000457718	D;D;D;D	0.93811	-2.85;-2.85;-3.29;-3.0	5.44	1.6	0.23607	.	0.463335	0.18586	N	0.136878	D	0.84032	0.5383	L	0.34521	1.04	0.09310	N	0.999999	B	0.32573	0.376	B	0.27380	0.079	T	0.70730	-0.4792	10	0.18276	T	0.48	-13.2243	3.4749	0.07581	0.2793:0.0:0.5416:0.1791	.	1011	Q68CZ2	TENS3_HUMAN	V	1011;1121;1011;771;467;1114	ENSP00000312143:L1011V;ENSP00000381854:L1011V;ENSP00000347968:L771V;ENSP00000414358:L1114V	ENSP00000312143:L1011V	L	-	1	2	TNS3	47309499	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	0.334000	0.19787	0.263000	0.21812	0.555000	0.69702	CTG	.	.	.	none		0.672	TNS3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157253.1	NM_022748		C	47342974	G	C	47342974	3	2	236	1	0	0	0	0	1	0	0	0	16356	991	35	4	1346	4	TNS3	7	47342974	Missense_Mutation	SNP	G	TCGA-P4-AAVM-01A-11D-A42J-10	3251486	47342974	111795689	23	14389											
ABCA13	154664	hgsc.bcm.edu	37	chr7	48390271	48390271	+	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	gatgagatgtttaaccatgcAggcgctggacgcttccgttt	8	12	12	9	3	0	1	0	1	0	1	1	4	1	2	2	2	2	5	2	2	1	4			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr7:48390271A>T	ENST00000435803.1	+	30	10260	c.10236A>T	c.(10234-10236)gcA>gcT	p.A3412A		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	3412					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						TTAACCATGCAGGCGCTGGAC	0.522																																					p.A3412A		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A10236T						PASS	.						154	155	154					7																	48390271		2051	4211	6262	SO:0001819	synonymous_variant	154664	exon30			CCATGCAGGCGCT	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.10236A>T	chr7.hg19:g.48390271A>T		107.0	0.0	.		80.0	36.0	.	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	hg19	CCDS47584.1																																																																																			.	.	.	none		0.522	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48390271	A	T	48390271	2	4	236	1	0	0	0	0	0	0	0	1	31	175	7	5		5	ABCA13	7	48390271	Silent	SNP	A	TCGA-P4-AAVM-01A-11D-A42J-10	1047297	48390271	110748392	24	14390											
PPP2CB	5516	hgsc.bcm.edu	37	chr8	30651547	30651547	+	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	ccacgtggtgaaataccccaTccaccacgatcatctggatc	11	8	7	15	2	2	1	1	1	1	0	4	3	3	2	5	2	1	0	5	2	2	1			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr8:30651547T>A	ENST00000221138.4	-	5	1074	c.624A>T	c.(622-624)ggA>ggT	p.G208G	PPP2CB_ENST00000518564.1_Intron	NM_001009552.1	NP_001009552.1	P62714	PP2AB_HUMAN	protein phosphatase 2, catalytic subunit, beta isozyme	208					apoptotic mitochondrial changes (GO:0008637)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of Ras protein signal transduction (GO:0046580)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein dephosphorylation (GO:0006470)|regulation of gene expression (GO:0010468)|response to antibiotic (GO:0046677)|response to endoplasmic reticulum stress (GO:0034976)|response to hydrogen peroxide (GO:0042542)	chromosome, centromeric region (GO:0000775)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	9				KIRC - Kidney renal clear cell carcinoma(542;0.095)|Kidney(114;0.114)	Vitamin E(DB00163)	AAATACCCCATCCACCACGAT	0.438																																					p.G208G		Atlas-SNP	.											.	PPP2CB	27	.	0			c.A624T						PASS	.						72	56	62					8																	30651547		2203	4300	6503	SO:0001819	synonymous_variant	5516	exon5			ACCCCATCCACCA		CCDS6079.1	8p12	2011-05-24	2010-03-05		ENSG00000104695	ENSG00000104695	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9300	protein-coding gene	gene with protein product	"protein phosphatase 2A catalytic subunit, beta isoform"	176916	"protein phosphatase 2 (formerly 2A), catalytic subunit, beta isoform"			8383590	Standard	NM_001009552		Approved	PP2Abeta	uc003xik.3	P62714	OTTHUMG00000163949	ENST00000221138.4:c.624A>T	chr8.hg19:g.30651547T>A		323.0	0.0	.		333.0	32.0	.	NM_001009552	D3DSV4|P11082|Q6FHK5	Silent	SNP	ENST00000221138.4	hg19	CCDS6079.1																																																																																			.	.	.	none		0.438	PPP2CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376527.2	NM_001009552		A	30651547	T	A	30651547	2	1	236	1	0	0	0	0	0	0	0	1	12391	1422	50	5		5	PPP2CB	8	30651547	Silent	SNP	T	TCGA-P4-AAVM-01A-11D-A42J-10		30651547	115712475	25	14391											
PLEKHF2	79666	hgsc.bcm.edu	37	chr8	96167020	96167020	+	Nonstop_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	acgatgatgatagcagtgacTaaggacacatttgggagtat	14	10	12	5	1	0	3	0	3	0	0	0	6	0	5	0	2	1	2	0	2	3	4			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr8:96167020T>A	ENST00000315367.3	+	2	989	c.748T>A	c.(748-750)Taa>Aaa	p.*250K	PLEKHF2_ENST00000519516.1_Nonstop_Mutation_p.*250K	NM_024613.3	NP_078889.1	Q9H8W4	PKHF2_HUMAN	pleckstrin homology domain containing, family F (with FYVE domain) member 2	0					protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|membrane (GO:0016020)|transport vesicle (GO:0030133)	metal ion binding (GO:0046872)			breast(1)|large_intestine(1)|lung(1)|ovary(2)	5	Breast(36;3.18e-05)					TAGCAGTGACTAAGGACACAT	0.428																																					p.X250K		Atlas-SNP	.											.	PLEKHF2	32	.	0			c.T748A						PASS	.						63	61	62					8																	96167020		2203	4300	6503	SO:0001578	stop_lost	79666	exon2			AGTGACTAAGGAC	AF434819	CCDS6267.1	8q22.1	2013-01-10				ENSG00000175895		"Zinc fingers, FYVE domain containing", "Pleckstrin homology (PH) domain containing"	20757	protein-coding gene	gene with protein product		615208					Standard	NM_024613		Approved	ZFYVE18, PHAFIN2, FLJ13187	uc003yhn.2	Q9H8W4		ENST00000315367.3:c.748T>A	chr8.hg19:g.96167020T>A	ENSP00000322373:p.*250Lysext*32	93.0	0.0	.		83.0	12.0	.	NM_024613		Missense_Mutation	SNP	ENST00000315367.3	hg19	CCDS6267.1	.	.	.	.	.	.	.	.	.	.	T	16.74	3.206693	0.58343	.	.	ENSG00000175895	ENST00000315367;ENST00000519516	.	.	.	6.16	6.16	0.99307	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.8061	0.85666	0.0:0.0:0.0:1.0	.	.	.	.	K	250	.	.	X	+	1	0	PLEKHF2	96236196	1.000000	0.71417	0.999000	0.59377	0.770000	0.43624	7.385000	0.79763	2.367000	0.80283	0.528000	0.53228	TAA	.	.	.	none		0.428	PLEKHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379666.1	NM_024613		A	96167020	T	A	96167020	4	1	236	1	0	0	0	0	0	0	0	0	12074	1535	53	5	750	5	PLEKHF2	8	96167020	Nonstop_Mutation	SNP	T	TCGA-P4-AAVM-01A-11D-A42J-10	65515473	96167020	50197002	26	14392											
PLEC	5339	hgsc.bcm.edu	37	chr8	144997632	144997632	+	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	gcctgcttctgccgcagggcCgcctgctccgcctgtgcccg	1	8	13	19	4	1	0	0	0	1	0	2	0	2	0	7	1	4	3	7	1	0	1	rs376957701		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr8:144997632C>G	ENST00000322810.4	-	31	7045	c.6876G>C	c.(6874-6876)gcG>gcC	p.A2292A	PLEC_ENST00000436759.2_Silent_p.A2182A|PLEC_ENST00000345136.3_Silent_p.A2155A|PLEC_ENST00000527096.1_Silent_p.A2178A|PLEC_ENST00000356346.3_Silent_p.A2141A|PLEC_ENST00000354958.2_Silent_p.A2133A|PLEC_ENST00000357649.2_Silent_p.A2159A|PLEC_ENST00000354589.3_Silent_p.A2155A|PLEC_ENST00000398774.2_Silent_p.A2123A	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2292	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						GCCGCAGGGCCGCCTGCTCCG	0.687																																					p.A2292A		Atlas-SNP	.											.	PLEC	1144	.	0			c.G6876C						PASS	.						9	11	11					8																	144997632		2003	4078	6081	SO:0001819	synonymous_variant	5339	exon31			CAGGGCCGCCTGC	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.6876G>C	chr8.hg19:g.144997632C>G		234.0	0.0	.		182.0	76.0	.	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	hg19	CCDS43772.1																																																																																			.	.	.	alt		0.687	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		G	144997632	C	G	144997632	2	3	236	1	0	0	0	0	0	0	0	1	12059	639	23	4		4	PLEC	8	144997632	Silent	SNP	C	TCGA-P4-AAVM-01A-11D-A42J-10	48830612	144997632	1366390	27	14393											
FGD3	89846	hgsc.bcm.edu	37	chr9	95784642	95784642	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccctgtggagcctgtggtgAccaccgaaggcagttcgggt	6	8	16	11	2	0	1	0	1	0	0	1	3	0	2	4	4	1	2	4	4	1	1			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr9:95784642A>G	ENST00000375482.3	+	14	2024	c.1528A>G	c.(1528-1530)Acc>Gcc	p.T510A	FGD3_ENST00000538555.1_Missense_Mutation_p.T113A|FGD3_ENST00000337352.6_Missense_Mutation_p.T510A|FGD3_ENST00000416701.2_Missense_Mutation_p.T510A	NM_001083536.1	NP_001077005.1	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3	510					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						GCCTGTGGTGACCACCGAAGG	0.632																																					p.T510A		Atlas-SNP	.											.	FGD3	116	.	0			c.A1528G						PASS	.						55	58	57					9																	95784642		2036	4171	6207	SO:0001583	missense	89846	exon14			GTGGTGACCACCG	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.1528A>G	chr9.hg19:g.95784642A>G	ENSP00000364631:p.Thr510Ala	44.0	0.0	.		32.0	13.0	.	NM_001083536	F8W7P2|Q4VX84|Q7Z7D9|Q8N5G1	Missense_Mutation	SNP	ENST00000375482.3	hg19	CCDS43849.1	.	.	.	.	.	.	.	.	.	.	A	1.354	-0.590584	0.03799	.	.	ENSG00000127084	ENST00000375482;ENST00000416701;ENST00000337352;ENST00000538555	T;T;T;T	0.71817	-0.5;-0.5;-0.5;-0.6	4.27	2.16	0.27623	Zinc finger, FYVE/PHD-type (1);	1.877530	0.03443	N	0.209516	T	0.39172	0.1068	N	0.00926	-1.1	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.41052	-0.9530	10	0.11182	T	0.66	.	5.0026	0.14271	0.1435:0.2066:0.6499:0.0	.	510;510	F8W7P2;Q5JSP0	.;FGD3_HUMAN	A	510;510;510;113	ENSP00000364631:T510A;ENSP00000413833:T510A;ENSP00000336914:T510A;ENSP00000442560:T113A	ENSP00000336914:T510A	T	+	1	0	FGD3	94824463	0.035000	0.19736	0.001000	0.08648	0.005000	0.04900	2.468000	0.45102	0.387000	0.25024	0.402000	0.26972	ACC	.	.	.	none		0.632	FGD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055493.1	NM_033086		G	95784642	A	G	95784642	3	3	236	1	0	0	0	0	1	0	0	0	5841	275	10	3	1574	3	FGD3	9	95784642	Missense_Mutation	SNP	A	TCGA-P4-AAVM-01A-11D-A42J-10		95784642	45428789	28	14394											
ANKS6	203286	hgsc.bcm.edu	37	chr9	101546300	101546300	+	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	tcctgcttgtcaacatccgcGtgcctctccaccagcagctg	6	10	8	17	2	2	0	1	0	1	0	5	0	4	0	5	0	5	3	5	0	1	1			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr9:101546300G>A	ENST00000353234.4	-	4	1094	c.1047C>T	c.(1045-1047)caC>caT	p.H349H	ANKS6_ENST00000540940.1_Silent_p.H154H|ANKS6_ENST00000375018.1_Silent_p.H349H|ANKS6_ENST00000375019.2_Silent_p.H48H			Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain containing 6	349						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)				CAACATCCGCGTGCCTCTCCA	0.647																																					p.H349H		Atlas-SNP	.											.	ANKS6	59	.	0			c.C1047T						PASS	.						57	63	61					9																	101546300		2177	4270	6447	SO:0001819	synonymous_variant	203286	exon4			ATCCGCGTGCCTC	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.1047C>T	chr9.hg19:g.101546300G>A		26.0	0.0	.		37.0	15.0	.	NM_173551	A0SE62|Q5VSL0|Q5VSL2|Q5VSL3|Q5VSL4|Q68DB8|Q6P2R2|Q8N9L6|Q96D62	Silent	SNP	ENST00000353234.4	hg19	CCDS43856.1																																																																																			.	.	.	none		0.647	ANKS6-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277053.1	NM_173551		A	101546300	G	A	101546300	2	1	236	1	0	0	0	0	0	0	0	1	692	1136	40	1		1	ANKS6	9	101546300	Silent	SNP	G	TCGA-P4-AAVM-01A-11D-A42J-10	5761658	101546300	39667131	29	14395											
ANKS6	203286	hgsc.bcm.edu	37	chr9	101552742	101552742	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagggtggtgatggtccacaAaggcaccggcttccaggagc	10	6	15	10	1	0	1	0	1	0	0	2	2	2	2	3	6	1	2	3	6	2	1			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr9:101552742A>G	ENST00000353234.4	-	2	553	c.506T>C	c.(505-507)tTt>tCt	p.F169S	ANKS6_ENST00000471846.1_5'UTR|ANKS6_ENST00000540940.1_5'UTR|ANKS6_ENST00000375018.1_Missense_Mutation_p.F169S|ANKS6_ENST00000375019.2_Intron			Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain containing 6	169						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)				ATGGTCCACAAAGGCACCGGC	0.647																																					p.F169S		Atlas-SNP	.											.	ANKS6	59	.	0			c.T506C						PASS	.						26	33	31					9																	101552742		2057	4201	6258	SO:0001583	missense	203286	exon2			TCCACAAAGGCAC	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.506T>C	chr9.hg19:g.101552742A>G	ENSP00000297837:p.Phe169Ser	160.0	0.0	.		167.0	65.0	.	NM_173551	A0SE62|Q5VSL0|Q5VSL2|Q5VSL3|Q5VSL4|Q68DB8|Q6P2R2|Q8N9L6|Q96D62	Missense_Mutation	SNP	ENST00000353234.4	hg19	CCDS43856.1	.	.	.	.	.	.	.	.	.	.	A	1.456	-0.563751	0.03939	.	.	ENSG00000165138	ENST00000375018;ENST00000353234	T;T	0.62232	0.04;0.04	5.67	2.06	0.26882	Ankyrin repeat-containing domain (4);	0.555420	0.21506	N	0.073453	T	0.23688	0.0573	N	0.00456	-1.48	0.38197	D	0.940066	B	0.14012	0.009	B	0.21360	0.034	T	0.04454	-1.0950	10	0.17369	T	0.5	-1.109	7.859	0.29499	0.7534:0.0:0.2466:0.0	.	169	Q68DC2	ANKS6_HUMAN	S	169	ENSP00000364158:F169S;ENSP00000297837:F169S	ENSP00000297837:F169S	F	-	2	0	ANKS6	100592563	0.444000	0.25649	0.223000	0.23860	0.040000	0.13550	1.038000	0.30254	0.414000	0.25790	0.459000	0.35465	TTT	.	.	.	none		0.647	ANKS6-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277053.1	NM_173551		G	101552742	A	G	101552742	3	3	236	1	0	0	0	0	1	0	0	0	692	14	1	3	2165	3	ANKS6	9	101552742	Missense_Mutation	SNP	A	TCGA-P4-AAVM-01A-11D-A42J-10	6442	101552742	39660689	30	14396											
LRRC8A	56262	hgsc.bcm.edu	37	chr9	131669737	131669737	+	Missense_Mutation	SNP	G	G	C																															acgggccccacaggcatcaaGtatgacctggaccggcacca																										TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr9:131669737G>C	ENST00000259324.5	+	3	817	c.294G>C	c.(292-294)aaG>aaC	p.K98N	LRRC8A_ENST00000372599.3_Missense_Mutation_p.K98N|LRRC8A_ENST00000372600.4_Missense_Mutation_p.K98N	NM_001127244.1	NP_001120716.1	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member A	98					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						CAGGCATCAAGTATGACCTGG	0.612																																					p.K98N		Atlas-SNP	.											.	LRRC8A	69	.	0			c.G294C						PASS	.						79	78	78					9																	131669737		2203	4300	6503	SO:0001583	missense	56262	exon3			CATCAAGTATGAC	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.294G>C	chr9.hg19:g.131669737G>C	ENSP00000259324:p.Lys98Asn	50.0	0.0	.		44.0	22.0	.	NM_001127244	Q6UXM2|Q8NCI0|Q9P2B1	Missense_Mutation	SNP	ENST00000259324.5	hg19	CCDS35155.1	.	.	.	.	.	.	.	.	.	.	G	13.32	2.203074	0.38905	.	.	ENSG00000136802	ENST00000372600;ENST00000372599;ENST00000259324	T;T;T	0.34472	1.36;1.36;1.36	5.41	3.46	0.39613	Leucine-rich repeat-containing protein 8, N-terminal (1);	0.335130	0.36101	N	0.002800	T	0.25457	0.0619	L	0.38175	1.15	0.36156	D	0.847807	B	0.19706	0.038	B	0.23852	0.049	T	0.24657	-1.0154	10	0.72032	D	0.01	.	4.0417	0.09755	0.2627:0.1813:0.556:0.0	.	98	Q8IWT6	LRC8A_HUMAN	N	98	ENSP00000361682:K98N;ENSP00000361680:K98N;ENSP00000259324:K98N	ENSP00000259324:K98N	K	+	3	2	LRRC8A	130709558	0.997000	0.39634	1.000000	0.80357	0.956000	0.61745	0.459000	0.21908	1.281000	0.44480	0.563000	0.77884	AAG	.	.	.	none		0.612	LRRC8A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054516.2	NM_019594		C	131669737	G	C	131669737	3	2	236	1	0	0	0	0	1	0	0	0	9028	1020	36	4	296	4	LRRC8A	9	131669737	Missense_Mutation	SNP	G	TCGA-P4-AAVM-01A-11D-A42J-10	30116995	131669737	9543694	31	14397	148	2									
LRRC8A	56262	hgsc.bcm.edu	37	chr9	131669746	131669746	+	Silent	SNP	G	G	A																															acaggcatcaagtatgacctGgaccggcaccagtacaacta																										TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr9:131669746G>A	ENST00000259324.5	+	3	826	c.303G>A	c.(301-303)ctG>ctA	p.L101L	LRRC8A_ENST00000372599.3_Silent_p.L101L|LRRC8A_ENST00000372600.4_Silent_p.L101L	NM_001127244.1	NP_001120716.1	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member A	101					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						AGTATGACCTGGACCGGCACC	0.622																																					p.L101L		Atlas-SNP	.											.	LRRC8A	69	.	0			c.G303A						PASS	.						87	85	86					9																	131669746		2203	4300	6503	SO:0001819	synonymous_variant	56262	exon3			TGACCTGGACCGG	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.303G>A	chr9.hg19:g.131669746G>A		53.0	0.0	.		42.0	20.0	.	NM_001127244	Q6UXM2|Q8NCI0|Q9P2B1	Silent	SNP	ENST00000259324.5	hg19	CCDS35155.1																																																																																			.	.	.	none		0.622	LRRC8A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054516.2	NM_019594		A	131669746	G	A	131669746	2	1	236	1	0	0	0	0	0	0	0	1	9028	1335	47	2		2	LRRC8A	9	131669746	Silent	SNP	G	TCGA-P4-AAVM-01A-11D-A42J-10	9	131669746	9543685	32	14398	148	2									
LCN15	389812	hgsc.bcm.edu	37	chr9	139656704	139656705	+	Missense_Mutation	DNP	GG	GG	CC																															gtcgggtagaagtcctggaaGgacttcagagcctggggact																										TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr9:139656704_139656705GG>CC	ENST00000316144.5	-	5	479_480	c.455_456CC>GG	c.(454-456)tCC>tGG	p.S152W	LCN15_ENST00000482511.1_5'UTR	NM_203347.1	NP_976222.1	Q6UWW0	LCN15_HUMAN	lipocalin 15	152			S -> A (in dbSNP:rs2297723).		lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	small molecule binding (GO:0036094)|transporter activity (GO:0005215)			endometrium(1)|lung(1)	2						AGTCCTGGAAGGACTTCAGAGC	0.649																																					p.S152S|p.S152C		Atlas-SNP	.											.	LCN15	11	.	0			c.C456G|c.C455G						PASS	.																																			SO:0001583	missense	389812	exon5			CTGGAAGGACTTC|TGGAAGGACTTCA		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.455_456delinsCC	chr9.hg19:g.139656704_139656705delinsCC	ENSP00000313833:p.Ser152Trp	243.0|242.0	0.0	.		234.0|231.0	105.0|103.0	.	NM_203347		Silent|Missense_Mutation	SNP	ENST00000316144.5	hg19	CCDS7006.1																																																																																			.	.	.	none		0.649	LCN15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055114.2	NM_203347		CC	139656705	GG	CC	139656704	3	2	236	1	0	0	0	0	1	0	0	0	8690	987	35	4	106	4	LCN15	9	139656704	Missense_Mutation	DNP	GG	TCGA-P4-AAVM-01A-11D-A42J-10	7986958	139656704	1556727	33	14399											
ZNF195	7748	hgsc.bcm.edu	37	chr11	3380399	3380399	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtgagaactgggtgaaggcTttgccacacttttcacactt	9	13	10	9	0	1	2	1	2	0	1	1	3	1	2	1	2	2	1	1	2	2	4			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr11:3380399T>C	ENST00000399602.4	-	6	1965	c.1839A>G	c.(1837-1839)aaA>aaG	p.K613K	ZNF195_ENST00000429541.2_Silent_p.K545K|ZNF195_ENST00000354599.6_Silent_p.K541K|ZNF195_ENST00000343338.7_Silent_p.K545K|ZNF195_ENST00000526601.1_Silent_p.K594K|ZNF195_ENST00000005082.9_Silent_p.K590K|ZNF195_ENST00000528796.1_Intron	NM_001130520.2	NP_001123992.1	O14628	ZN195_HUMAN	zinc finger protein 195	613					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)		GGGTGAAGGCTTTGCCACACT	0.378																																					p.K613K		Atlas-SNP	.											.	ZNF195	77	.	0			c.A1839G						PASS	.						63	65	64					11																	3380399		2026	4209	6235	SO:0001819	synonymous_variant	7748	exon6			GAAGGCTTTGCCA		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.1839A>G	chr11.hg19:g.3380399T>C		87.0	0.0	.		68.0	34.0	.	NM_001130520	A8K234|B3KTK2|B4DEL0|C9JLY9|L7MNK2|Q0VAJ6|Q658N8|Q6ZNA9	Silent	SNP	ENST00000399602.4	hg19	CCDS44522.1																																																																																			.	.	.	none		0.378	ZNF195-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032321.2			C	3380399	T	C	3380399	2	2	236	1	0	0	0	0	0	0	0	1	17770	1606	56	3		3	ZNF195	11	3380399	Silent	SNP	T	TCGA-P4-AAVM-01A-11D-A42J-10		3380399	131626117	34	14400											
SMPD1	6609	hgsc.bcm.edu	37	chr11	6411960	6411960	+	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	gcgctggcgctggcgctggcGctggcgctggctctgtctga	1	9	18	13	5	2	1	0	1	2	0	2	1	2	1	0	5	0	6	0	5	0	0			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr11:6411960G>T	ENST00000342245.4	+	1	300	c.132G>T	c.(130-132)gcG>gcT	p.A44A	SMPD1_ENST00000533196.1_3'UTR|SMPD1_ENST00000527275.1_Silent_p.A44A|SMPD1_ENST00000299397.3_Silent_p.A44A|SMPD1_ENST00000356761.2_Silent_p.A44A	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	44					cell death (GO:0008219)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of MAP kinase activity (GO:0043407)|nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein dephosphorylation (GO:0035307)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)|sphingomyelin metabolic process (GO:0006684)|termination of signal transduction (GO:0023021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lamellar body (GO:0042599)|lysosomal lumen (GO:0043202)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(3)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Amlodipine(DB00381)|Chlorpromazine(DB00477)|Desipramine(DB01151)	tggcgctggcgctggcgctgg	0.692																																					p.A44A		Atlas-SNP	.											.	SMPD1	108	.	0			c.G132T						PASS	.						19	22	21					11																	6411960		2199	4295	6494	SO:0001819	synonymous_variant	6609	exon1			GCTGGCGCTGGCG	AB209775	CCDS31409.1, CCDS44531.1, CCDS31409.2	11p15.4-p15.1	2010-04-28	2008-02-04		ENSG00000166311	ENSG00000166311	3.1.4.12		11120	protein-coding gene	gene with protein product	"acid sphingomyelinase"	607608				1711683	Standard	NM_000543		Approved	ASM	uc001mcw.3	P17405	OTTHUMG00000165453	ENST00000342245.4:c.132G>T	chr11.hg19:g.6411960G>T		125.0	0.0	.		87.0	6.0	.	NM_000543	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Silent	SNP	ENST00000342245.4	hg19	CCDS44531.1																																																																																			.	.	.	none		0.692	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543		T	6411960	G	T	6411960	2	4	236	1	0	0	0	0	0	0	0	1	14817	1074	38	4		4	SMPD1	11	6411960	Silent	SNP	G	TCGA-P4-AAVM-01A-11D-A42J-10	3031561	6411960	128594556	35	14401											
NDUFS8	4728	hgsc.bcm.edu	37	chr11	67800585	67800585	+	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	gtgctgcccacaggcctgggCatgaccctgagctacctgtt	6	9	12	14	0	0	2	0	2	0	0	0	2	0	2	4	2	4	4	4	2	1	2			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr11:67800585C>A	ENST00000313468.5	+	5	314	c.207C>A	c.(205-207)ggC>ggA	p.G69G	NDUFS8_ENST00000528492.1_Intron|MIR4691_ENST00000583764.1_RNA|RP5-901A4.1_ENST00000532296.1_RNA	NM_002496.3	NP_002487.1	O00217	NDUS8_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 8, 23kDa (NADH-coenzyme Q reductase)	69					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|mitochondrial respiratory chain complex I assembly (GO:0032981)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			endometrium(1)|kidney(1)|lung(5)|skin(1)	8						CAGGCCTGGGCATGACCCTGA	0.692																																					p.G69G	Colon(116;1205 2770 20054)	Atlas-SNP	.											.	NDUFS8	18	.	0			c.C207A						PASS	.						49	46	47					11																	67800585		2200	4294	6494	SO:0001819	synonymous_variant	4728	exon5			CCTGGGCATGACC	U65579	CCDS8176.1	11q13.2	2011-07-04	2002-08-29		ENSG00000110717	ENSG00000110717	1.6.5.3	"Mitochondrial respiratory chain complex / Complex I"	7715	protein-coding gene	gene with protein product	"complex I 23kDa subunit", "NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial"	602141	"NADH dehydrogenase (ubiquinone) Fe-S protein 8 (23kD) (NADH-coenzyme Q reductase)"			9666055, 9116042	Standard	NM_002496		Approved	TYKY, CI-23k	uc001onc.3	O00217	OTTHUMG00000167331	ENST00000313468.5:c.207C>A	chr11.hg19:g.67800585C>A		152.0	0.0	.		144.0	55.0	.	NM_002496	B2RB86|Q0VDA8	Silent	SNP	ENST00000313468.5	hg19	CCDS8176.1																																																																																			.	.	.	none		0.692	NDUFS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394193.1	NM_002496		A	67800585	C	A	67800585	2	1	236	1	0	0	0	0	0	0	0	1	10305	697	25	4		4	NDUFS8	11	67800585	Silent	SNP	C	TCGA-P4-AAVM-01A-11D-A42J-10	61388625	67800585	67205931	36	14402											
CCDC81	60494	hgsc.bcm.edu	37	chr11	86125892	86125892	+	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	aagaaacacagtgttacaagAgagctttggatgcacaggta	16	8	11	6	0	0	2	0	0	0	2	0	4	0	3	0	2	4	4	0	2	5	3			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr11:86125892A>C	ENST00000445632.2	+	12	1725	c.1453A>C	c.(1453-1455)Aga>Cga	p.R485R	CCDC81_ENST00000278487.3_Silent_p.R220R|CCDC81_ENST00000528728.1_Silent_p.R220R|CCDC81_ENST00000354755.1_Silent_p.R395R	NM_001156474.1	NP_001149946.1	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81	485										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)				GTGTTACAAGAGAGCTTTGGA	0.348																																					p.R485R		Atlas-SNP	.											.	CCDC81	89	.	0			c.A1453C						PASS	.						62	60	61					11																	86125892		2202	4299	6501	SO:0001819	synonymous_variant	60494	exon12			TACAAGAGAGCTT	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.1453A>C	chr11.hg19:g.86125892A>C		123.0	0.0	.		181.0	67.0	.	NM_001156474	A0AVL7|Q53FW3|Q9H5E5	Silent	SNP	ENST00000445632.2	hg19	CCDS53691.1																																																																																			.	.	.	none		0.348	CCDC81-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393756.1	NM_021827		C	86125892	A	C	86125892	2	2	236	1	0	0	0	0	0	0	0	1	2857	296	11	5		5	CCDC81	11	86125892	Silent	SNP	A	TCGA-P4-AAVM-01A-11D-A42J-10	18325307	86125892	48880624	37	14403											
PRICKLE1	144165	hgsc.bcm.edu	37	chr12	42854000	42854000	+	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	atagttatcgggggtgtacaGccgcagtctgtccttgggag	7	11	15	8	2	1	0	0	0	1	0	3	1	2	1	2	3	2	3	2	3	3	4			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr12:42854000G>A	ENST00000455697.1	-	8	2392	c.2107C>T	c.(2107-2109)Ctg>Ttg	p.L703L	PRICKLE1_ENST00000548696.1_Silent_p.L703L|PRICKLE1_ENST00000345127.3_Silent_p.L703L|PRICKLE1_ENST00000445766.2_Silent_p.L703L|RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000552240.1_Silent_p.L703L	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	703					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)		GGGGTGTACAGCCGCAGTCTG	0.493																																					p.L703L		Atlas-SNP	.											.	PRICKLE1	105	.	0			c.C2107T						PASS	.						72	73	73					12																	42854000		2203	4300	6503	SO:0001819	synonymous_variant	144165	exon8			TGTACAGCCGCAG	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.2107C>T	chr12.hg19:g.42854000G>A		113.0	0.0	.		111.0	49.0	.	NM_001144882	Q14C83|Q71QF8|Q96N00	Silent	SNP	ENST00000455697.1	hg19	CCDS8742.1																																																																																			.	.	.	none		0.493	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1			A	42854000	G	A	42854000	2	1	236	1	0	0	0	0	0	0	0	1	12496	962	34	2		2	PRICKLE1	12	42854000	Silent	SNP	G	TCGA-P4-AAVM-01A-11D-A42J-10		42854000	90997895	38	14404											
HOXC8	3224	hgsc.bcm.edu	37	chr12	54403214	54403214	+	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	cggcggctcggcgcccggctTccagcacgcttcgcaccacg	4	5	13	19	8	0	0	0	0	0	0	3	0	1	0	3	4	1	5	3	4	0	2			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr12:54403214T>A	ENST00000040584.4	+	1	383	c.146T>A	c.(145-147)tTc>tAc	p.F49Y	RP11-834C11.12_ENST00000513209.1_Intron	NM_022658.3	NP_073149.1	P31273	HXC8_HUMAN	homeobox C8	49					anterior/posterior pattern specification (GO:0009952)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)	8						GCGCCCGGCTTCCAGCACGCT	0.662																																					p.F49Y	GBM(197;701 2226 7002 18822 41696)	Atlas-SNP	.											.	HOXC8	15	.	0			c.T146A						PASS	.						80	92	88					12																	54403214		2203	4300	6503	SO:0001583	missense	3224	exon1			CCGGCTTCCAGCA	X99680	CCDS8870.1	12q13.13	2011-06-20	2005-12-22			ENSG00000037965		"Homeoboxes / ANTP class : HOXL subclass"	5129	protein-coding gene	gene with protein product		142970	"homeo box C8"	HOX3, HOX3A		1973146, 1358459	Standard	NM_022658		Approved		uc001ser.3	P31273		ENST00000040584.4:c.146T>A	chr12.hg19:g.54403214T>A	ENSP00000040584:p.Phe49Tyr	111.0	0.0	.		78.0	30.0	.	NM_022658	A8K4J4|O15221|O15362	Missense_Mutation	SNP	ENST00000040584.4	hg19	CCDS8870.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.760497	0.89932	.	.	ENSG00000037965	ENST00000040584	T	0.46819	0.86	3.95	3.95	0.45737	.	0.000000	0.85682	D	0.000000	T	0.68375	0.2994	M	0.87456	2.885	0.53688	D	0.999973	D	0.63880	0.993	D	0.67548	0.952	T	0.70784	-0.4778	10	0.34782	T	0.22	.	12.0911	0.53726	0.0:0.0:0.0:1.0	.	49	P31273	HXC8_HUMAN	Y	49	ENSP00000040584:F49Y	ENSP00000040584:F49Y	F	+	2	0	HOXC8	52689481	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.152000	0.58111	1.551000	0.49450	0.379000	0.24179	TTC	.	.	.	none		0.662	HOXC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358957.2			A	54403214	T	A	54403214	3	1	236	1	0	0	0	0	1	0	0	0	7323	1783	62	5	148	5	HOXC8	12	54403214	Missense_Mutation	SNP	T	TCGA-P4-AAVM-01A-11D-A42J-10	11549214	54403214	79448681	39	14405											
BRCA2	675	hgsc.bcm.edu	37	chr13	32907282	32907282	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggaggactccttatgtccaaAtttaattgataatggaagct	13	13	9	6	0	0	1	0	1	0	0	2	4	2	4	2	3	1	1	2	3	5	5			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr13:32907282A>G	ENST00000380152.3	+	10	1900	c.1667A>G	c.(1666-1668)aAt>aGt	p.N556S	BRCA2_ENST00000544455.1_Missense_Mutation_p.N556S			P51587	BRCA2_HUMAN	breast cancer 2, early onset	556					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)		TTATGTCCAAATTTAATTGAT	0.373			"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.N556S	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.A1667G						PASS	.						70	78	76					13																	32907282		2203	4300	6503	SO:0001583	missense	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)	GTCCAAATTTAAT	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.1667A>G	chr13.hg19:g.32907282A>G	ENSP00000369497:p.Asn556Ser	317.0	0.0	.		251.0	104.0	.	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	hg19	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	A	0.003	-2.485706	0.00163	.	.	ENSG00000139618	ENST00000380152;ENST00000544455;ENST00000530893	T;T	0.00664	5.92;5.92	5.5	1.21	0.21127	.	0.434585	0.24740	N	0.035995	T	0.00271	0.0008	N	0.00621	-1.32	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45731	-0.9241	10	0.02654	T	1	.	6.3438	0.21337	0.5377:0.0:0.4623:0.0	.	556;556	P51587;A1YBP1	BRCA2_HUMAN;.	S	556;556;554	ENSP00000369497:N556S;ENSP00000439902:N556S	ENSP00000369497:N556S	N	+	2	0	BRCA2	31805282	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.070000	0.11523	0.362000	0.24319	-0.248000	0.11899	AAT	.	.	.	none		0.373	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		G	32907282	A	G	32907282	3	3	236	1	0	0	0	0	1	0	0	0	1501	101	4	3	1701	3	BRCA2	13	32907282	Missense_Mutation	SNP	A	TCGA-P4-AAVM-01A-11D-A42J-10		32907282	82262596	40	14406											
SNW1	22938	hgsc.bcm.edu	37	chr14	78184510	78184510	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggtcttttagagccaccaTgctgtttggcttcttccaaa	8	14	9	10	0	2	1	0	0	2	1	3	1	3	1	3	2	2	3	3	2	2	5			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr14:78184510T>C	ENST00000261531.7	-	14	1594	c.1532A>G	c.(1531-1533)cAt>cGt	p.H511R	SNW1_ENST00000555761.1_Missense_Mutation_p.M538V|SNW1_ENST00000554775.1_Missense_Mutation_p.H349R|SLIRP_ENST00000557431.1_Intron|SLIRP_ENST00000557623.1_Intron	NM_012245.2	NP_036377.1	Q13573	SNW1_HUMAN	SNW domain containing 1	511					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)		AGAGCCACCATGCTGTTTGGC	0.498																																					p.H511R		Atlas-SNP	.											.	SNW1	44	.	0			c.A1532G						PASS	.						181	184	183					14																	78184510		2203	4300	6503	SO:0001583	missense	22938	exon14			CCACCATGCTGTT	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.1532A>G	chr14.hg19:g.78184510T>C	ENSP00000261531:p.His511Arg	113.0	0.0	.		88.0	34.0	.	NM_012245	A8K8A9|Q13483|Q32N03|Q5D0D6	Missense_Mutation	SNP	ENST00000261531.7	hg19	CCDS9867.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.67|11.67	1.706995|1.706995	0.30232|0.30232	.|.	.|.	ENSG00000100603|ENSG00000100603	ENST00000261531;ENST00000554775|ENST00000555761	.|.	.|.	.|.	5.68|5.68	5.68|5.68	0.88126|0.88126	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.33818|0.33818	0.0876|0.0876	N|N	0.08118|0.08118	0|0	0.33515|0.33515	D|D	0.591654|0.591654	P|B	0.50156|0.06786	0.932|0.001	P|B	0.58520|0.11329	0.84|0.006	T|T	0.37842|0.37842	-0.9688|-0.9688	9|7	0.40728|.	T|.	0.16|.	.|.	15.9314|15.9314	0.79663|0.79663	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	511|538	Q13573|G3V3A4	SNW1_HUMAN|.	R|V	511;349|538	.|.	ENSP00000261531:H511R|.	H|M	-|-	2|1	0|0	SNW1|SNW1	77254263|77254263	1.000000|1.000000	0.71417|0.71417	0.981000|0.981000	0.43875|0.43875	0.989000|0.989000	0.77384|0.77384	7.431000|7.431000	0.80335|0.80335	2.176000|2.176000	0.68965|0.68965	0.383000|0.383000	0.25322|0.25322	CAT|ATG	.	.	.	none		0.498	SNW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413912.1	NM_012245		C	78184510	T	C	78184510	3	2	236	1	0	0	0	0	1	0	0	0	14892	1464	51	3	82	3	SNW1	14	78184510	Missense_Mutation	SNP	T	TCGA-P4-AAVM-01A-11D-A42J-10		78184510	29165030	41	14407											
PML	5371	hgsc.bcm.edu	37	chr15	74315345	74315345	+	Missense_Mutation	SNP	A	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	ctttggcgcggttcacgcgcAgatgcacgcggccgtcggcc	4	7	15	15	8	1	1	1	0	0	1	2	1	1	1	2	4	1	3	2	4	0	2			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr15:74315345A>C	ENST00000268058.3	+	3	875	c.779A>C	c.(778-780)cAg>cCg	p.Q260P	PML_ENST00000436891.3_Missense_Mutation_p.Q260P|PML_ENST00000359928.4_Missense_Mutation_p.Q260P|PML_ENST00000567543.1_Missense_Mutation_p.Q260P|PML_ENST00000395132.2_Missense_Mutation_p.Q260P|PML_ENST00000564428.1_Missense_Mutation_p.Q260P|PML_ENST00000569965.1_Missense_Mutation_p.Q260P|PML_ENST00000354026.6_Missense_Mutation_p.Q260P|PML_ENST00000563500.1_Missense_Mutation_p.Q260P|PML_ENST00000565898.1_Missense_Mutation_p.Q260P|PML_ENST00000395135.3_Missense_Mutation_p.Q260P|PML_ENST00000268059.6_Missense_Mutation_p.Q260P|PML_ENST00000435786.2_Missense_Mutation_p.Q260P|PML_ENST00000569161.1_3'UTR|PML_ENST00000569477.1_Missense_Mutation_p.Q260P	NM_033238.2	NP_150241.2	P29590	PML_HUMAN	promyelocytic leukemia	260					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to interleukin-4 (GO:0071353)|cellular senescence (GO:0090398)|circadian regulation of gene expression (GO:0032922)|common-partner SMAD protein phosphorylation (GO:0007182)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|entrainment of circadian clock by photoperiod (GO:0043153)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|maintenance of protein location in nucleus (GO:0051457)|myeloid cell differentiation (GO:0030099)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation in response to oxidative stress (GO:0032938)|negative regulation of viral release from host cell (GO:1902187)|PML body organization (GO:0030578)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of histone deacetylation (GO:0031065)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)|regulation of calcium ion transport into cytosol (GO:0010522)|regulation of circadian rhythm (GO:0042752)|regulation of double-strand break repair (GO:2000779)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of protein phosphorylation (GO:0001932)|regulation of transcription, DNA-templated (GO:0006355)|response to cytokine (GO:0034097)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|retinoic acid receptor signaling pathway (GO:0048384)|SMAD protein import into nucleus (GO:0007184)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	cobalt ion binding (GO:0050897)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|SUMO binding (GO:0032183)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	31						GTTCACGCGCAGATGCACGCG	0.697			T	"RARA, PAX5"	"APL, ALL"																																p.Q260P		Atlas-SNP	.		Dom	yes		15	15q22	5371	promyelocytic leukemia		L	.	PML	169	.	0			c.A779C						PASS	.						19	17	17					15																	74315345		2189	4289	6478	SO:0001583	missense	5371	exon3			ACGCGCAGATGCA	AB208950	CCDS10255.1, CCDS10256.1, CCDS10257.1, CCDS10258.1, CCDS45297.1, CCDS45298.1, CCDS45299.1, CCDS45300.1, CCDS58386.1	15q24.1	2011-04-21			ENSG00000140464	ENSG00000140464		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	9113	protein-coding gene	gene with protein product		102578					Standard	NM_033244		Approved	MYL, TRIM19, RNF71	uc002awv.3	P29590	OTTHUMG00000137607	ENST00000268058.3:c.779A>C	chr15.hg19:g.74315345A>C	ENSP00000268058:p.Gln260Pro	37.0	0.0	.		48.0	14.0	.	NM_033250	E9PBR7|P29591|P29592|P29593|Q00755|Q15959|Q59FP9|Q8WUA0|Q96S41|Q9BPW2|Q9BWP7|Q9BZX6|Q9BZX7|Q9BZX8|Q9BZX9|Q9BZY0|Q9BZY2|Q9BZY3	Missense_Mutation	SNP	ENST00000268058.3	hg19	CCDS10255.1	.	.	.	.	.	.	.	.	.	.	A	12.18	1.861866	0.32884	.	.	ENSG00000140464	ENST00000395135;ENST00000435786;ENST00000359928;ENST00000436891;ENST00000268058;ENST00000395132;ENST00000268059;ENST00000354026;ENST00000418568	T	0.50277	0.75	4.93	3.81	0.43845	.	0.993173	0.08176	N	0.986262	T	0.60340	0.2261	M	0.61703	1.905	0.09310	N	1	D;P;P;P;P;P;P;D;P;P;P;D;P	0.63880	0.993;0.915;0.91;0.666;0.938;0.727;0.784;0.985;0.89;0.89;0.61;0.993;0.769	P;P;P;B;P;B;P;P;P;P;B;P;P	0.61592	0.843;0.571;0.663;0.348;0.555;0.251;0.478;0.777;0.527;0.628;0.346;0.891;0.46	T	0.42965	-0.9420	10	0.72032	D	0.01	-14.2634	5.078	0.14642	0.7206:0.1838:0.0956:0.0	.	260;210;260;260;260;260;260;260;260;260;260;260;263	P29590-3;Q59GQ8;P29590;P29590-11;P29590-12;P29590-5;E9PBR7;P29590-13;P29590-4;P29590-2;P29590-14;P29590-8;Q59H09	.;.;PML_HUMAN;.;.;.;.;.;.;.;.;.;.	P	260	ENSP00000268058:Q260P	ENSP00000268058:Q260P	Q	+	2	0	PML	72102398	0.018000	0.18449	0.003000	0.11579	0.164000	0.22412	0.479000	0.22228	0.746000	0.32786	0.260000	0.18958	CAG	.	.	.	none		0.697	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269021.3	NM_002675		C	74315345	A	C	74315345	3	2	236	1	0	0	0	0	1	0	0	0	12142	188	7	5	789	5	PML	15	74315345	Missense_Mutation	SNP	A	TCGA-P4-AAVM-01A-11D-A42J-10		74315345	28216047	42	14408											
PDXDC1	23042	hgsc.bcm.edu	37	chr16	15110996	15110996	+	Missense_Mutation	SNP	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	gtgtgaatctggcaacattgGctctgggttatgtctcctca	7	14	11	9	0	4	1	1	1	3	0	5	1	4	1	1	3	1	3	1	3	3	2			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr16:15110996G>A	ENST00000396410.4	+	10	929	c.832G>A	c.(832-834)Gct>Act	p.A278T	PDXDC1_ENST00000455313.2_Missense_Mutation_p.A255T|PDXDC1_ENST00000447912.2_Missense_Mutation_p.A187T|PDXDC1_ENST00000535621.2_Missense_Mutation_p.A278T|PDXDC1_ENST00000563679.1_Missense_Mutation_p.A296T|PDXDC1_ENST00000569715.1_Missense_Mutation_p.A251T|PDXDC1_ENST00000325823.7_Missense_Mutation_p.A263T|RP11-680G24.5_ENST00000565178.1_RNA|PDXDC1_ENST00000450288.2_Missense_Mutation_p.A250T	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	278					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						GGCAACATTGGCTCTGGGTTA	0.373																																					p.A278T		Atlas-SNP	.											.	PDXDC1	59	.	0			c.G832A						PASS	.						300	304	303					16																	15110996		2197	4300	6497	SO:0001583	missense	23042	exon10			ACATTGGCTCTGG	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.832G>A	chr16.hg19:g.15110996G>A	ENSP00000379691:p.Ala278Thr	111.0	0.0	.		142.0	40.0	.	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Missense_Mutation	SNP	ENST00000396410.4	hg19	CCDS32393.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.539966	0.85917	.	.	ENSG00000179889	ENST00000325823;ENST00000447912;ENST00000535621;ENST00000396410;ENST00000450288;ENST00000455313	T;T;T;T;T;T	0.26373	1.74;1.74;1.74;1.74;1.74;1.74	5.45	5.45	0.79879	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.098174	0.64402	D	0.000001	T	0.44159	0.1280	L	0.45698	1.435	0.54753	D	0.999982	D;D;D;D;D;P	0.71674	0.998;0.997;0.986;0.998;0.998;0.55	D;D;P;D;D;B	0.70716	0.966;0.97;0.883;0.966;0.966;0.426	T	0.07177	-1.0786	10	0.27082	T	0.32	-14.2336	18.2726	0.90073	0.0:0.0:1.0:0.0	.	250;187;278;250;278;255	E7EPL4;E7EMH5;Q86XE2;B4DR55;Q6P996;Q6P996-2	.;.;.;.;PDXD1_HUMAN;.	T	263;187;278;278;250;255	ENSP00000322807:A263T;ENSP00000400310:A187T;ENSP00000437835:A278T;ENSP00000379691:A278T;ENSP00000391147:A250T;ENSP00000406703:A255T	ENSP00000322807:A263T	A	+	1	0	PDXDC1	15018497	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.905000	0.87416	2.546000	0.85860	0.542000	0.68232	GCT	.	.	.	none		0.373	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027		A	15110996	G	A	15110996	3	1	236	1	0	0	0	0	1	0	0	0	11703	1203	42	2	870	2	PDXDC1	16	15110996	Missense_Mutation	SNP	G	TCGA-P4-AAVM-01A-11D-A42J-10		15110996	75243757	43	14409											
GLG1	2734	hgsc.bcm.edu	37	chr16	74491772	74491772	+	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	gagtgaacacagagacttacGacgcccgcggccaggggtga	11	4	15	11	4	0	3	0	2	0	1	0	6	0	3	2	3	2	0	2	3	2	1			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr16:74491772G>A	ENST00000422840.2	-	24	3264	c.3265C>T	c.(3265-3267)Caa>Taa	p.Q1089*	RNU6-237P_ENST00000515985.1_RNA|GLG1_ENST00000447066.2_Splice_Site_p.Q1078*|GLG1_ENST00000205061.5_Splice_Site_p.Q1089*	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	1089					blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						AGAGACTTACGACGCCCGCGG	0.517																																					p.Q1089X		Atlas-SNP	.											.	GLG1	106	.	0			c.C3265T						PASS	.						124	113	117					16																	74491772		2198	4300	6498	SO:0001630	splice_region_variant	2734	exon24			ACTTACGACGCCC		CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"golgi apparatus protein 1"			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.3265+1C>T	chr16.hg19:g.74491772G>A		103.0	0.0	.		108.0	66.0	.	NM_001145667	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Nonsense_Mutation	SNP	ENST00000422840.2	hg19	CCDS45527.1	.	.	.	.	.	.	.	.	.	.	G	43	10.072459	0.99330	.	.	ENSG00000090863	ENST00000205061;ENST00000447066;ENST00000422840	.	.	.	5.8	5.8	0.92144	.	0.051884	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-18.3892	20.051	0.97627	0.0:0.0:1.0:0.0	.	.	.	.	X	1089;1078;1089	.	.	Q	-	1	0	GLG1	73049273	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.476000	0.97823	2.740000	0.93945	0.650000	0.86243	CAA	.	.	.	none		0.517	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201	Nonsense_Mutation	A	74491772	G	A	74491772	5	1	236	1	0	0	0	0	0	0	1	0	6443	1072	37	1	366	1	GLG1	16	74491772	Splice_Site	SNP	G	TCGA-P4-AAVM-01A-11D-A42J-10	59380776	74491772	15862981	44	14410											
PLCG2	5336	hgsc.bcm.edu	37	chr16	81965133	81965133	+	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	cagggaaaaaaccagaagtcCtttgtcttcatcctggagcc	12	9	9	11	0	2	1	1	0	1	1	4	3	4	3	4	2	2	0	4	2	4	2			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr16:81965133C>G	ENST00000359376.3	+	25	2827	c.2613C>G	c.(2611-2613)tcC>tcG	p.S871S		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	871					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						ACCAGAAGTCCTTTGTCTTCA	0.527																																					p.S871S		Atlas-SNP	.											.	PLCG2	276	.	0			c.C2613G						PASS	.						72	77	75					16																	81965133		1897	4116	6013	SO:0001819	synonymous_variant	5336	exon25			GAAGTCCTTTGTC		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.2613C>G	chr16.hg19:g.81965133C>G		100.0	0.0	.		118.0	8.0	.	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Silent	SNP	ENST00000359376.3	hg19	CCDS42204.1																																																																																			.	.	.	none		0.527	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1			G	81965133	C	G	81965133	2	3	236	1	0	0	0	0	0	0	0	1	12043	668	24	4		4	PLCG2	16	81965133	Silent	SNP	C	TCGA-P4-AAVM-01A-11D-A42J-10	7473361	81965133	8389620	45	14411											
GPATCH8	23131	hgsc.bcm.edu	37	chr17	42476063	42476063	+	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	cttgggcccaaagtaaccttGtggggggtccttgagcttgg	6	11	15	9	0	0	1	0	1	0	0	1	1	1	1	3	5	2	2	3	5	2	5			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr17:42476063G>A	ENST00000591680.1	-	8	3412	c.3382C>T	c.(3382-3384)Caa>Taa	p.Q1128*	GPATCH8_ENST00000434000.1_Nonsense_Mutation_p.Q1050*	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	1128							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)		AAGTAACCTTGTGGGGGGTCC	0.547																																					p.Q1128X		Atlas-SNP	.											.	GPATCH8	114	.	0			c.C3382T						PASS	.						109	109	109					17																	42476063		2203	4300	6503	SO:0001587	stop_gained	23131	exon8			AACCTTGTGGGGG	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.3382C>T	chr17.hg19:g.42476063G>A	ENSP00000467556:p.Gln1128*	67.0	0.0	.		59.0	28.0	.	NM_001002909	B9EGP9|O60300|Q8TB99	Nonsense_Mutation	SNP	ENST00000591680.1	hg19	CCDS32666.1	.	.	.	.	.	.	.	.	.	.	G	38	7.074636	0.98044	.	.	ENSG00000186566	ENST00000335500;ENST00000434000	.	.	.	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	-16.8599	18.4809	0.90811	0.0:0.0:1.0:0.0	.	.	.	.	X	1128;1050	.	ENSP00000335486:Q1128X	Q	-	1	0	GPATCH8	39831589	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.263000	0.95617	2.602000	0.87976	0.650000	0.86243	CAA	.	.	.	none		0.547	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909		A	42476063	G	A	42476063	4	1	236	1	0	0	0	0	0	1	0	0	6601	1386	48	2	1130	2	GPATCH8	17	42476063	Nonsense_Mutation	SNP	G	TCGA-P4-AAVM-01A-11D-A42J-10		42476063	38719147	46	14412											
MYL4	4635	hgsc.bcm.edu	37	chr17	45299172	45299172	+	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	cgtgtctttgacaaggagagCaatggcacggtcatgggtgc	9	9	15	8	2	2	2	1	1	1	1	2	3	2	2	0	4	2	2	0	4	2	1			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr17:45299172C>T	ENST00000354968.1	+	5	566	c.438C>T	c.(436-438)agC>agT	p.S146S	MYL4_ENST00000393450.1_Silent_p.S146S|snoU13_ENST00000516279.1_RNA|MYL4_ENST00000572316.1_Silent_p.S146S	NM_001002841.1	NP_001002841.1	P12829	MYL4_HUMAN	myosin, light chain 4, alkali; atrial, embryonic	146	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cardiac muscle contraction (GO:0060048)|muscle filament sliding (GO:0030049)|positive regulation of ATPase activity (GO:0032781)|regulation of the force of heart contraction (GO:0002026)	A band (GO:0031672)|cytosol (GO:0005829)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|calcium ion binding (GO:0005509)|myosin II heavy chain binding (GO:0032038)			endometrium(2)|large_intestine(1)|lung(4)|ovary(3)|prostate(1)	11						ACAAGGAGAGCAATGGCACGG	0.587																																					p.S146S		Atlas-SNP	.											.	MYL4	27	.	0			c.C438T						PASS	.						131	101	111					17																	45299172		2203	4300	6503	SO:0001819	synonymous_variant	4635	exon5			GGAGAGCAATGGC		CCDS11510.1	17q21.32	2013-09-19	2006-09-29		ENSG00000198336	ENSG00000198336		"Myosins / Light chain", "EF-hand domain containing"	7585	protein-coding gene	gene with protein product	"myosin, atrial/fetal muscle, light chain"	160770	"myosin, light polypeptide 4, alkali; atrial, embryonic"			3417683	Standard	NM_002476		Approved	ALC1, AMLC, GT1, PRO1957	uc002ilg.3	P12829	OTTHUMG00000178232	ENST00000354968.1:c.438C>T	chr17.hg19:g.45299172C>T		62.0	0.0	.		58.0	18.0	.	NM_001002841	D3DXJ7|P11783	Silent	SNP	ENST00000354968.1	hg19	CCDS11510.1																																																																																			.	.	.	none		0.587	MYL4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441059.1	NM_001002841		T	45299172	C	T	45299172	2	4	236	1	0	0	0	0	0	0	0	1	10056	709	25	2		2	MYL4	17	45299172	Silent	SNP	C	TCGA-P4-AAVM-01A-11D-A42J-10	2823109	45299172	35896038	47	14413											
BPTF	2186	hgsc.bcm.edu	37	chr17	65916183	65916183	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataattaagaggagagatgtTggtccttatggcattcgatc	12	13	11	5	1	0	2	0	0	0	2	3	5	1	3	1	3	0	2	1	3	3	5			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr17:65916183T>C	ENST00000321892.4	+	15	5920	c.5859T>C	c.(5857-5859)gtT>gtC	p.V1953V	BPTF_ENST00000424123.3_Silent_p.V1814V|BPTF_ENST00000335221.5_Silent_p.V1953V|BPTF_ENST00000306378.6_Silent_p.V1827V			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	1953					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)			GGAGAGATGTTGGTCCTTATG	0.323																																					p.V1953V		Atlas-SNP	.											.	BPTF	415	.	0			c.T5859C						PASS	.						138	142	141					17																	65916183		2203	4300	6503	SO:0001819	synonymous_variant	2186	exon15			AGATGTTGGTCCT	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.5859T>C	chr17.hg19:g.65916183T>C		89.0	0.0	.		75.0	25.0	.	NM_004459	Q6NX67|Q7Z7D6|Q9UIG2	Silent	SNP	ENST00000321892.4	hg19																																																																																				.	.	.	none		0.323	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		C	65916183	T	C	65916183	2	2	236	1	0	0	0	0	0	0	0	1	1497	1799	63	3		3	BPTF	17	65916183	Silent	SNP	T	TCGA-P4-AAVM-01A-11D-A42J-10	20617011	65916183	15279027	48	14414											
UBE2O	63893	hgsc.bcm.edu	37	chr17	74449137	74449137	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcgccgggacgggggctgcGgctggggccgggactgcctc	2	4	22	13	5	0	0	0	0	0	0	1	2	0	2	3	8	2	2	3	8	0	0			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr17:74449137G>A	ENST00000319380.7	-	1	151	c.87C>T	c.(85-87)gcC>gcT	p.A29A	AANAT_ENST00000250615.3_5'Flank	NM_022066.3	NP_071349.3	Q9C0C9	UBE2O_HUMAN	ubiquitin-conjugating enzyme E2O	29	Ala-rich.				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						cgggggctgcggctggggccg	0.781																																					p.A29A		Atlas-SNP	.											.	UBE2O	207	.	0			c.C87T						PASS	.						1	1	1					17																	74449137		533	1169	1702	SO:0001819	synonymous_variant	63893	exon1			GGCTGCGGCTGGG	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.87C>T	chr17.hg19:g.74449137G>A		53.0	0.0	.		48.0	23.0	.	NM_022066	A6NDU5|Q69YP4|Q6PIZ2|Q86UA4|Q8N425|Q8TBN1|Q9BSW1|Q9H6E6|Q9H7E4|Q9H9B2	Silent	SNP	ENST00000319380.7	hg19	CCDS32742.1																																																																																			.	.	.	none		0.781	UBE2O-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450123.1	NM_022066		A	74449137	G	A	74449137	2	1	236	1	0	0	0	0	0	0	0	1	16880	1103	39	1		1	UBE2O	17	74449137	Silent	SNP	G	TCGA-P4-AAVM-01A-11D-A42J-10	8532954	74449137	6746073	49	14415											
DENND1C	79958	hgsc.bcm.edu	37	chr19	6468935	6468936	+	Frame_Shift_Ins	INS	-	-	C																															gggctggggccctcagagagINSccccccctctgcaggacaga																										TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr19:6468935_6468936insC	ENST00000381480.2	-	20	1548_1549	c.1436_1437insG	c.(1435-1437)ggcfs	p.G479fs	DENND1C_ENST00000543576.1_Frame_Shift_Ins_p.G435fs	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	479					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						CCCTCAGAGAGCCCCCCCTCTG	0.624																																					p.G479fs		Atlas-Indel,Pindel	.											.	DENND1C	93	.	0			c.1437_1438insG						PASS	.																																			SO:0001589	frameshift_variant	79958	exon20			.	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.1437dupG	chr19.hg19:g.6468942_6468942dupC	ENSP00000370889:p.Gly479fs	47.0	0.0	0		56.0	20.0	0.357143	NM_024898	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Frame_Shift_Ins	INS	ENST00000381480.2	hg19	CCDS45938.1																																																																																			.	.	.	none		0.624	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898		C	6468936	-	C	6468935	7	5	236	1	0	1	1	0	0	0	0	0	4430	958	34	0	984	0	DENND1C	19	6468935	Frame_Shift_Ins	INS	-	TCGA-P4-AAVM-01A-11D-A42J-10		6468935	52660048	50	14416											
SH2D3A	10045	hgsc.bcm.edu	37	chr19	6760717	6760717	+	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	aagctgcgtcgcagaggcccCtgccaagtcacaggcctgga	9	5	13	14	2	1	1	1	0	0	1	2	2	1	2	4	3	3	2	4	3	2	0			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr19:6760717C>A	ENST00000245908.6	-	3	620	c.351G>T	c.(349-351)caG>caT	p.Q117H	SH2D3A_ENST00000437152.3_Intron|SH2D3A_ENST00000599563.1_5'UTR	NM_005490.2	NP_005481.2	Q9BRG2	SH23A_HUMAN	SH2 domain containing 3A	117					JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|urinary_tract(1)	24						GCAGAGGCCCCTGCCAAGTCA	0.602																																					p.Q117H		Atlas-SNP	.											.	SH2D3A	53	.	0			c.G351T						PASS	.						44	43	43					19																	6760717		2203	4300	6503	SO:0001583	missense	10045	exon3			AGGCCCCTGCCAA	AF124249	CCDS12173.1	19p13.3	2013-02-14	2002-01-14			ENSG00000125731		"SH2 domain containing"	16885	protein-coding gene	gene with protein product		604721	"SH2 domain-containing 3A"			10187783	Standard	NM_005490		Approved	NSP1	uc002mft.3	Q9BRG2		ENST00000245908.6:c.351G>T	chr19.hg19:g.6760717C>A	ENSP00000245908:p.Gln117His	98.0	0.0	.		72.0	28.0	.	NM_005490	A8K9R6|B4DRS7|Q9Y2X4	Missense_Mutation	SNP	ENST00000245908.6	hg19	CCDS12173.1	.	.	.	.	.	.	.	.	.	.	C	7.064	0.566967	0.13560	.	.	ENSG00000125731	ENST00000245908	T	0.15256	2.44	4.97	1.25	0.21368	.	0.365819	0.20012	N	0.101107	T	0.10723	0.0262	L	0.39898	1.24	0.09310	N	1	B	0.11235	0.004	B	0.15052	0.012	T	0.23940	-1.0174	10	0.49607	T	0.09	-11.0037	0.6632	0.00846	0.1949:0.3795:0.1695:0.2561	.	117	Q9BRG2	SH23A_HUMAN	H	117	ENSP00000245908:Q117H	ENSP00000245908:Q117H	Q	-	3	2	SH2D3A	6711717	0.000000	0.05858	0.065000	0.19835	0.429000	0.31625	-0.503000	0.06383	0.533000	0.28675	-0.263000	0.10527	CAG	.	.	.	none		0.602	SH2D3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458016.1	NM_005490		A	6760717	C	A	6760717	3	1	236	1	0	0	0	0	1	0	0	0	14246	680	24	4	1411	4	SH2D3A	19	6760717	Missense_Mutation	SNP	C	TCGA-P4-AAVM-01A-11D-A42J-10	291782	6760717	52368266	51	14417											
HSD17B14	51171	hgsc.bcm.edu	37	chr19	49316726	49316726	+	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	cttctacctgggccagcatgCcctctcggattgtggcccta	5	11	10	15	1	2	0	0	0	2	0	3	1	2	1	4	3	3	1	4	3	2	4			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr19:49316726C>G	ENST00000263278.4	-	8	892	c.626G>C	c.(625-627)gGc>gCc	p.G209A	BCAT2_ENST00000598162.1_5'Flank|HSD17B14_ENST00000599157.1_Missense_Mutation_p.G185A|BCAT2_ENST00000316273.6_5'Flank|BCAT2_ENST00000545387.2_5'Flank|BCAT2_ENST00000402551.1_5'Flank|BCAT2_ENST00000601496.1_5'Flank|BCAT2_ENST00000599246.1_5'Flank|BCAT2_ENST00000597011.1_5'Flank	NM_016246.2	NP_057330.2	Q9BPX1	DHB14_HUMAN	hydroxysteroid (17-beta) dehydrogenase 14	209					steroid catabolic process (GO:0006706)	cytosol (GO:0005829)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			large_intestine(3)|lung(1)|skin(1)	5		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;0.000341)|all cancers(93;0.000764)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.0346)		GGCCAGCATGCCCTCTCGGAT	0.607																																					p.G209A		Atlas-SNP	.											.	HSD17B14	25	.	0			c.G626C						PASS	.						76	54	61					19																	49316726		2203	4299	6502	SO:0001583	missense	51171	exon8			AGCATGCCCTCTC	AF126781	CCDS12736.1	19q13.33	2011-09-14	2006-11-22	2006-11-22		ENSG00000087076		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	23238	protein-coding gene	gene with protein product	"retinal short-chain dehydrogenase/reductase 3", "short chain dehydrogenase/reductase family 47C, member 1"	612832	"dehydrogenase/reductase (SDR family) member 10"	DHRS10		10800688, 17067289, 19027726	Standard	XM_005258969		Approved	retSDR3, SDR47C1	uc002pkv.1	Q9BPX1		ENST00000263278.4:c.626G>C	chr19.hg19:g.49316726C>G	ENSP00000263278:p.Gly209Ala	64.0	0.0	.		67.0	20.0	.	NM_016246	Q9UKU3	Missense_Mutation	SNP	ENST00000263278.4	hg19	CCDS12736.1	.	.	.	.	.	.	.	.	.	.	C	14.99	2.700653	0.48307	.	.	ENSG00000087076	ENST00000263278	T	0.20200	2.09	4.43	2.25	0.28309	NAD(P)-binding domain (1);	0.190085	0.43747	N	0.000525	T	0.11707	0.0285	N	0.01197	-0.965	0.47094	D	0.999316	D	0.71674	0.998	P	0.61003	0.882	T	0.18241	-1.0343	10	0.16420	T	0.52	.	7.2282	0.26028	0.0:0.7222:0.1783:0.0996	.	209	Q9BPX1	DHB14_HUMAN	A	209	ENSP00000263278:G209A	ENSP00000263278:G209A	G	-	2	0	HSD17B14	54008538	0.875000	0.30112	0.307000	0.25127	0.408000	0.30992	2.277000	0.43417	1.124000	0.41980	0.462000	0.41574	GGC	.	.	.	none		0.607	HSD17B14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466212.1	NM_016246		G	49316726	C	G	49316726	3	3	236	1	0	0	0	0	1	0	0	0	7390	739	26	4	194	4	HSD17B14	19	49316726	Missense_Mutation	SNP	C	TCGA-P4-AAVM-01A-11D-A42J-10	42556009	49316726	9812257	52	14418											
ZNF836	162962	hgsc.bcm.edu	37	chr19	52663822	52663822	+	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	cctgagagaattctatggctAcatccctgaatgtcaaaggt	12	11	9	9	0	2	3	1	2	1	1	3	4	3	3	2	2	1	1	2	2	5	3			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr19:52663822A>T	ENST00000322146.8	-	4	559	c.38T>A	c.(37-39)gTa>gAa	p.V13E	ZNF836_ENST00000597065.1_Missense_Mutation_p.V13E|CTC-471J1.8_ENST00000594362.1_RNA|ZNF836_ENST00000597252.1_Missense_Mutation_p.V13E	NM_001102657.1	NP_001096127.1	Q6ZNA1	ZN836_HUMAN	zinc finger protein 836	13	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(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						TTCTATGGCTACATCCCTGAA	0.438																																					p.V13E		Atlas-SNP	.											.	ZNF836	158	.	0			c.T38A						PASS	.						89	95	93					19																	52663822		2202	4300	6502	SO:0001583	missense	162962	exon4			ATGGCTACATCCC	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.38T>A	chr19.hg19:g.52663822A>T	ENSP00000325038:p.Val13Glu	71.0	0.0	.		48.0	15.0	.	NM_001102657		Missense_Mutation	SNP	ENST00000322146.8	hg19	CCDS46162.1	.	.	.	.	.	.	.	.	.	.	A	11.56	1.674755	0.29783	.	.	ENSG00000196267	ENST00000322146	T	0.10477	2.87	1.99	1.99	0.26369	Krueppel-associated box (4);	.	.	.	.	T	0.30510	0.0767	H	0.99090	4.425	0.18873	N	0.999988	B	0.30236	0.274	B	0.32805	0.153	T	0.37009	-0.9724	9	0.87932	D	0	.	7.554	0.27814	1.0:0.0:0.0:0.0	.	13	Q6ZNA1	ZN836_HUMAN	E	13	ENSP00000325038:V13E	ENSP00000325038:V13E	V	-	2	0	ZNF836	57355634	0.924000	0.31332	0.451000	0.26982	0.975000	0.68041	1.321000	0.33678	0.897000	0.36392	0.358000	0.22013	GTA	.	.	.	none		0.438	ZNF836-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462456.1	NM_001102657		T	52663822	A	T	52663822	3	4	236	1	0	0	0	0	1	0	0	0	18199	391	14	5	2778	5	ZNF836	19	52663822	Missense_Mutation	SNP	A	TCGA-P4-AAVM-01A-11D-A42J-10	3347096	52663822	6465161	53	14419											
C20orf26	26074	hgsc.bcm.edu	37	chr20	20226857	20226857	+	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	caaaggaaatttttagccagCgagtatgaattgtatttgct	13	14	9	5	1	0	1	0	1	0	0	0	3	0	2	1	1	3	3	1	1	6	7	rs114266049	byFrequency	TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr20:20226857C>T	ENST00000245957.5	+	19	2233	c.2157C>T	c.(2155-2157)agC>agT	p.S719S	C20orf26_ENST00000377293.1_Silent_p.S75S|C20orf26_ENST00000389656.3_Silent_p.S75S|C20orf26_ENST00000377309.2_Silent_p.S75S	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		719										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)		TTTTAGCCAGCGAGTATGAAT	0.358																																					p.S719S		Atlas-SNP	.											.	C20orf26	188	.	0			c.C2157T						PASS	.						75	83	80					20																	20226857		2203	4300	6503	SO:0001819	synonymous_variant	26074	exon19			AGCCAGCGAGTAT																												ENST00000245957.5:c.2157C>T	chr20.hg19:g.20226857C>T		205.0	0.0	.		215.0	66.0	.	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Silent	SNP	ENST00000245957.5	hg19	CCDS33447.1																																																																																			.	C|0.994;A|0.006	.	alt		0.358	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3			T	20226857	C	T	20226857	2	4	236	1	0	0	0	0	0	0	0	1	2108	767	27	1		1	C20orf26	20	20226857	Silent	SNP	C	TCGA-P4-AAVM-01A-11D-A42J-10		20226857	42798663	54	14420											
PPIL2	23759	hgsc.bcm.edu	37	chr22	22024222	22024222	+	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	gtacattacctgtgctgaatAcactcacttttatggtggca	10	14	8	9	0	1	1	1	1	0	0	1	1	1	1	1	2	4	3	1	2	5	5			TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	g.chr22:22024222A>T	ENST00000335025.8	+	2	144	c.53A>T	c.(52-54)tAc>tTc	p.Y18F	PPIL2_ENST00000412327.1_Missense_Mutation_p.Y18F|PPIL2_ENST00000456792.2_Missense_Mutation_p.Y18F|PPIL2_ENST00000492445.2_Missense_Mutation_p.Y18F|PPIL2_ENST00000398831.3_Missense_Mutation_p.Y18F|PPIL2_ENST00000406385.1_Missense_Mutation_p.Y18F					peptidylprolyl isomerase (cyclophilin)-like 2											endometrium(4)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	17	Colorectal(54;0.105)					TGTGCTGAATACACTCACTTT	0.448																																					p.Y18F		Atlas-SNP	.											.	PPIL2	38	.	0			c.A53T						PASS	.						199	161	174					22																	22024222		2203	4300	6503	SO:0001583	missense	23759	exon2			CTGAATACACTCA		CCDS13793.1	22q11.21	2013-01-29			ENSG00000100023	ENSG00000100023		"U-box domain containing"	9261	protein-coding gene	gene with protein product	"U-box domain containing 7"	607588				10591208	Standard	NM_014337		Approved	UBOX7, CYC4, Cyp-60	uc002zvh.4	Q13356	OTTHUMG00000030174	ENST00000335025.8:c.53A>T	chr22.hg19:g.22024222A>T	ENSP00000334553:p.Tyr18Phe	82.0	0.0	.		76.0	39.0	.	NM_014337		Missense_Mutation	SNP	ENST00000335025.8	hg19	CCDS13793.1	.	.	.	.	.	.	.	.	.	.	A	17.87	3.494928	0.64186	.	.	ENSG00000100023	ENST00000412327;ENST00000335025;ENST00000398831;ENST00000492445;ENST00000458567;ENST00000406385;ENST00000456792	T;T;T;T;T;T	0.28454	1.66;1.7;1.7;1.7;1.7;1.61	4.39	4.39	0.52855	.	0.071138	0.64402	D	0.000017	T	0.34890	0.0913	L	0.59436	1.845	0.50632	D	0.999883	P;P;P	0.47409	0.61;0.868;0.895	B;P;B	0.46299	0.219;0.511;0.313	T	0.22591	-1.0212	10	0.87932	D	0	.	10.2502	0.43364	1.0:0.0:0.0:0.0	.	18;18;18	E7EW80;Q13356-2;Q13356	.;.;PPIL2_HUMAN	F	18;18;18;18;49;18;18	ENSP00000390427:Y18F;ENSP00000334553:Y18F;ENSP00000381812:Y18F;ENSP00000445312:Y18F;ENSP00000384299:Y18F;ENSP00000396228:Y18F	ENSP00000334553:Y18F	Y	+	2	0	PPIL2	20354222	1.000000	0.71417	0.999000	0.59377	0.975000	0.68041	4.011000	0.57124	1.974000	0.57490	0.456000	0.33151	TAC	.	.	.	none		0.448	PPIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075028.4			T	22024222	A	T	22024222	3	4	236	1	0	0	0	0	1	0	0	0	12337	391	14	5	59	5	PPIL2	22	22024222	Missense_Mutation	SNP	A	TCGA-P4-AAVM-01A-11D-A42J-10		22024222	29280344	55	14421											
SKI	6497	hgsc.bcm.edu	37	chr1	2238153	2238153	+	Silent	SNP	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	caggaacagctgtggccgcgGgcccgccccgaggctgcggg	5	3	18	15	5	0	0	0	0	0	0	0	2	0	1	4	5	3	2	4	5	1	0			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr1:2238153G>A	ENST00000378536.4	+	7	2208	c.2136G>A	c.(2134-2136)cgG>cgA	p.R712R		NM_003036.3	NP_003027.1	P12755	SKI_HUMAN	SKI proto-oncogene	712					anterior/posterior axis specification (GO:0009948)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell motility (GO:0048870)|cell proliferation (GO:0008283)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|gene expression (GO:0010467)|lens morphogenesis in camera-type eye (GO:0002089)|myelination in peripheral nervous system (GO:0022011)|myotube differentiation (GO:0014902)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neural tube closure (GO:0001843)|nose morphogenesis (GO:0043585)|olfactory bulb development (GO:0021772)|palate development (GO:0060021)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|protein homotrimerization (GO:0070207)|regulation of apoptotic process (GO:0042981)|retina development in camera-type eye (GO:0060041)|skeletal muscle fiber development (GO:0048741)|SMAD protein signal transduction (GO:0060395)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase inhibitor activity (GO:0046811)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|repressing transcription factor binding (GO:0070491)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(2)|lung(5)|prostate(1)|stomach(1)	10	all_cancers(77;0.000139)|all_epithelial(69;4.45e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)			Epithelial(90;2.14e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.72e-29)|GBM - Glioblastoma multiforme(42;2.45e-08)|Colorectal(212;5.33e-05)|COAD - Colon adenocarcinoma(227;0.000228)|Kidney(185;0.00268)|BRCA - Breast invasive adenocarcinoma(365;0.00471)|STAD - Stomach adenocarcinoma(132;0.0147)|KIRC - Kidney renal clear cell carcinoma(229;0.0385)|Lung(427;0.207)		TGTGGCCGCGGGCCCGCCCCG	0.761																																					p.R712R	Ovarian(177;144 1678 13697 20086 27838 40755)	Atlas-SNP	.											.	SKI	33	.	0			c.G2136A						PASS	.						5	6	6					1																	2238153		1501	2825	4326	SO:0001819	synonymous_variant	6497	exon7			GCCGCGGGCCCGC	X15218	CCDS39.1	1p36.33	2014-06-25	2014-06-25		ENSG00000157933	ENSG00000157933		"SKI transcriptional corepressors"	10896	protein-coding gene	gene with protein product		164780	"v-ski avian sarcoma viral oncogene homolog"			2762147	Standard	NM_003036		Approved		uc001aja.4	P12755	OTTHUMG00000001407	ENST00000378536.4:c.2136G>A	chr1.hg19:g.2238153G>A		0.0	0.0	.		26.0	21.0	.	NM_003036	Q5SYT7	Silent	SNP	ENST00000378536.4	hg19	CCDS39.1																																																																																			.	.	.	none		0.761	SKI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004070.1	NM_003036		A	2238153	G	A	2238153	2	1	237	1	0	0	0	0	0	0	0	1	14370	1219	43	2		2	SKI	1	2238153	Silent	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10		2238153	247012468	1	14422											
ARID1A	8289	hgsc.bcm.edu	37	chr1	27101241	27101241	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taatgacatgacctataattAtgccaacaggcagagcacgg	15	8	9	9	1	0	3	0	2	0	1	0	3	0	3	2	2	3	2	2	2	5	4			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr1:27101241A>G	ENST00000324856.7	+	18	4894	c.4523A>G	c.(4522-4524)tAt>tGt	p.Y1508C	ARID1A_ENST00000457599.2_Intron|ARID1A_ENST00000540690.1_Intron|ARID1A_ENST00000374152.2_Missense_Mutation_p.Y1125C	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1508					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)		ACCTATAATTATGCCAACAGG	0.572			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.Y1508C		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.A4523G						PASS	.						68	72	71					1																	27101241		2203	4300	6503	SO:0001583	missense	8289	exon18			ATAATTATGCCAA	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.4523A>G	chr1.hg19:g.27101241A>G	ENSP00000320485:p.Tyr1508Cys	92.0	0.0	.		70.0	20.0	.	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	hg19	CCDS285.1	.	.	.	.	.	.	.	.	.	.	A	18.56	3.650090	0.67472	.	.	ENSG00000117713	ENST00000324856;ENST00000374152	T;T	0.05996	3.53;3.36	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.22666	0.0547	M	0.61703	1.905	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.83275	0.991;0.99;0.996	T	0.00175	-1.1954	10	0.44086	T	0.13	-5.0146	15.8453	0.78883	1.0:0.0:0.0:0.0	.	1125;1508;1161	O14497-3;O14497;Q4LE49	.;ARI1A_HUMAN;.	C	1508;1125	ENSP00000320485:Y1508C;ENSP00000363267:Y1125C	ENSP00000320485:Y1508C	Y	+	2	0	ARID1A	26973828	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	6.707000	0.74654	2.330000	0.79161	0.528000	0.53228	TAT	.	.	.	none		0.572	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		G	27101241	A	G	27101241	3	3	237	1	0	0	0	0	1	0	0	0	913	449	16	3	4593	3	ARID1A	1	27101241	Missense_Mutation	SNP	A	TCGA-PJ-A5Z8-01A-11D-A28G-10	24863088	27101241	222149380	2	14423											
DLGAP3	58512	hgsc.bcm.edu	37	chr1	35331687	35331687	+	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	tgggcgggccggaccggtcaCagcctggtctgggcctcggg	3	6	19	13	4	2	0	1	0	1	0	3	1	2	1	4	7	1	0	4	7	0	0			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr1:35331687C>T	ENST00000373347.1	-	12	3205	c.2937G>A	c.(2935-2937)ctG>ctA	p.L979L	DLGAP3_ENST00000235180.4_Silent_p.L979L			O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated protein 3	979					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)				ggaccggtcacagcctggtct	0.731																																					p.L979L		Atlas-SNP	.											.	DLGAP3	107	.	0			c.G2937A						PASS	.						11	13	12					1																	35331687		2181	4267	6448	SO:0001819	synonymous_variant	58512	exon10			CGGTCACAGCCTG	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.2937G>A	chr1.hg19:g.35331687C>T		1.0	0.0	.		45.0	13.0	.	NM_001080418	Q5TDD5|Q9H3X7	Silent	SNP	ENST00000373347.1	hg19	CCDS30670.1																																																																																			.	.	.	none		0.731	DLGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011554.1	NM_021234		T	35331687	C	T	35331687	2	4	237	1	0	0	0	0	0	0	0	1	4563	465	17	2		2	DLGAP3	1	35331687	Silent	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	8230446	35331687	213918934	3	14424											
ANKRD35	148741	hgsc.bcm.edu	37	chr1	145567075	145567075	+	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	tcatctccacctacaggaatCatctactgaatgctgctcgg	10	11	7	13	1	4	1	2	1	2	0	6	2	4	2	2	2	4	2	2	2	4	2			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr1:145567075C>T	ENST00000355594.4	+	12	3010	c.2923C>T	c.(2923-2925)Cat>Tat	p.H975Y		NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	975										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)					CTACAGGAATCATCTACTGAA	0.473																																					p.H975Y	Melanoma(9;127 754 22988 51047)	Atlas-SNP	.											.	ANKRD35	96	.	0			c.C2923T						PASS	.						168	155	160					1																	145567075		2203	4300	6503	SO:0001583	missense	148741	exon12			AGGAATCATCTAC	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.2923C>T	chr1.hg19:g.145567075C>T	ENSP00000347802:p.His975Tyr	165.0	0.0	.		142.0	38.0	.	NM_144698	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	hg19	CCDS919.1	.	.	.	.	.	.	.	.	.	.	C	15.26	2.780583	0.49891	.	.	ENSG00000198483	ENST00000453670;ENST00000355594	T	0.58652	0.32	5.12	5.12	0.69794	.	0.000000	0.47852	D	0.000209	T	0.69878	0.3160	M	0.74881	2.28	0.80722	D	1	D	0.71674	0.998	D	0.78314	0.991	T	0.73266	-0.4037	10	0.87932	D	0	-3.866	13.9259	0.63961	0.0:1.0:0.0:0.0	.	975	Q8N283	ANR35_HUMAN	Y	884;975	ENSP00000347802:H975Y	ENSP00000347802:H975Y	H	+	1	0	ANKRD35	144278432	0.991000	0.36638	0.888000	0.34837	0.244000	0.25665	2.767000	0.47637	2.679000	0.91253	0.655000	0.94253	CAT	.	.	.	none		0.473	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698		T	145567075	C	T	145567075	3	4	237	1	0	0	0	0	1	0	0	0	664	826	29	2	2969	2	ANKRD35	1	145567075	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	110235388	145567075	103683546	4	14425											
PKP1	5317	hgsc.bcm.edu	37	chr1	201285751	201285751	+	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	tgcagtacctgagctcccagGatgagaaataccaggccatt	12	8	10	11	0	0	2	0	2	0	1	1	4	1	3	4	2	4	3	4	2	3	3			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr1:201285751G>A	ENST00000352845.3	+	4	772	c.772G>A	c.(772-774)Gat>Aat	p.D258N	PKP1_ENST00000367324.3_Missense_Mutation_p.D258N|PKP1_ENST00000475988.1_3'UTR|PKP1_ENST00000263946.3_Missense_Mutation_p.D258N			Q13835	PKP1_HUMAN	plakophilin 1	258					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						GAGCTCCCAGGATGAGAAATA	0.537																																					p.D258N		Atlas-SNP	.											PKP1,NS,carcinoma,0,1	PKP1	127	.	0			c.G772A						PASS	.						83	62	69					1																	201285751		2203	4300	6503	SO:0001583	missense	5317	exon4			TCCCAGGATGAGA	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.772G>A	chr1.hg19:g.201285751G>A	ENSP00000295597:p.Asp258Asn	250.0	1.0	.		207.0	54.0	.	NM_001005337	O00645|Q14CA0|Q15152	Missense_Mutation	SNP	ENST00000352845.3	hg19	CCDS30966.1	.	.	.	.	.	.	.	.	.	.	G	15.47	2.844590	0.51164	.	.	ENSG00000081277	ENST00000367324;ENST00000263946;ENST00000352845	T;T;T	0.55588	0.51;0.51;0.51	4.91	3.96	0.45880	Armadillo-like helical (1);Armadillo-type fold (1);	0.200242	0.51477	D	0.000089	T	0.45397	0.1340	L	0.49778	1.585	0.53688	D	0.99997	P;P	0.49253	0.741;0.921	B;B	0.40940	0.344;0.33	T	0.34428	-0.9829	10	0.19147	T	0.46	-15.2438	14.2686	0.66138	0.0:0.0:0.8497:0.1502	.	258;258	Q13835-2;Q13835	.;PKP1_HUMAN	N	258	ENSP00000356293:D258N;ENSP00000263946:D258N;ENSP00000295597:D258N	ENSP00000263946:D258N	D	+	1	0	PKP1	199552374	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	7.782000	0.85680	1.008000	0.39264	0.591000	0.81541	GAT	.	.	.	none		0.537	PKP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086897.1	NM_000299		A	201285751	G	A	201285751	3	1	237	1	0	0	0	0	1	0	0	0	11991	1174	41	2	786	2	PKP1	1	201285751	Missense_Mutation	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	55718676	201285751	47964870	5	14426											
TAF5L	27097	hgsc.bcm.edu	37	chr1	229730727	229730727	+	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	ccagtatctgatggacatgtCttcagaacaagagagcaacc	14	8	9	10	0	3	3	1	1	2	2	3	5	3	4	2	1	3	2	2	1	4	2			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr1:229730727C>T	ENST00000366676.1	-	4	1086	c.1087G>A	c.(1087-1089)Gac>Aac	p.D363N	TAF5L_ENST00000258281.2_Missense_Mutation_p.D363N			O75529	TAF5L_HUMAN	TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa	363					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)				ATGGACATGTCTTCAGAACAA	0.527																																					p.D363N		Atlas-SNP	.											.	TAF5L	76	.	0			c.G1087A						PASS	.						121	102	108					1																	229730727		2203	4300	6503	SO:0001583	missense	27097	exon5			ACATGTCTTCAGA	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.1087G>A	chr1.hg19:g.229730727C>T	ENSP00000355636:p.Asp363Asn	110.0	0.0	.		85.0	5.0	.	NM_014409	Q5TDI5|Q5TDI6|Q8IW31	Missense_Mutation	SNP	ENST00000366676.1	hg19	CCDS1581.1	.	.	.	.	.	.	.	.	.	.	C	33	5.238803	0.95240	.	.	ENSG00000135801	ENST00000366676;ENST00000258281	D;D	0.88975	-2.45;-2.45	5.88	5.88	0.94601	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	0.96027	0.8706	M	0.91920	3.255	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96166	0.9119	10	0.87932	D	0	-34.0939	20.2422	0.98381	0.0:1.0:0.0:0.0	.	363	O75529	TAF5L_HUMAN	N	363	ENSP00000355636:D363N;ENSP00000258281:D363N	ENSP00000258281:D363N	D	-	1	0	TAF5L	227797350	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.811000	0.86092	2.782000	0.95742	0.655000	0.94253	GAC	.	.	.	none		0.527	TAF5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095229.1	NM_014409		T	229730727	C	T	229730727	3	4	237	1	0	0	0	0	1	0	0	0	15541	913	32	2	686	2	TAF5L	1	229730727	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	28444976	229730727	19519894	6	14427											
HEATR5B	54497	hgsc.bcm.edu	37	chr2	37286106	37286107	+	Frame_Shift_Ins	INS	-	-	A																															ttcagttagtagctcaggacINSaatgtgcaacgaagctcctc																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr2:37286106_37286107insA	ENST00000233099.5	-	13	1968_1969	c.1873_1874insT	c.(1873-1875)tgtfs	p.C625fs	HEATR5B_ENST00000354531.2_Frame_Shift_Ins_p.C625fs	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	625						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)				TAGCTCAGGACAATGTGCAACG	0.347																																					p.C625fs		Atlas-Indel,Pindel	.											.	HEATR5B	185	.	0			c.1874_1875insT						PASS	.																																			SO:0001589	frameshift_variant	54497	exon13			.	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.1874dupT	chr2.hg19:g.37286108_37286108dupA	ENSP00000233099:p.Cys625fs	309.0	0.0	0		284.0	57.0	0.200704	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Frame_Shift_Ins	INS	ENST00000233099.5	hg19	CCDS33181.1																																																																																			.	.	.	none		0.347	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		A	37286107	-	A	37286106	7	5	237	1	0	1	1	0	0	0	0	0	7039	478	17	0	4437	0	HEATR5B	2	37286106	Frame_Shift_Ins	INS	-	TCGA-PJ-A5Z8-01A-11D-A28G-10		37286106	205913267	7	14428											
GKN1	56287	hgsc.bcm.edu	37	chr2	69207170	69207170	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtgtcgtgggattccaacAtacatggctgaggagatgca	11	10	13	7	1	0	2	0	1	0	1	2	4	1	3	1	3	3	2	1	3	2	2			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr2:69207170A>G	ENST00000377938.2	+	5	546	c.483A>G	c.(481-483)acA>acG	p.T161T		NM_019617.3	NP_062563.3	Q9NS71	GKN1_HUMAN	gastrokine 1	161	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.				digestion (GO:0007586)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)	extracellular region (GO:0005576)|secretory granule (GO:0030141)				breast(2)|large_intestine(4)|lung(5)	11						GGATTCCAACATACATGGCTG	0.507																																					p.T161T		Atlas-SNP	.											.	GKN1	24	.	0			c.A483G						PASS	.						156	111	126					2																	69207170		2203	4300	6503	SO:0001819	synonymous_variant	56287	exon5			TCCAACATACATG	AY139182	CCDS1891.2	2p13.3	2012-10-10			ENSG00000169605	ENSG00000169605		"BRICHOS domain containing"	23217	protein-coding gene	gene with protein product	"BRICHOS domain containing 1"	606402				12851218, 11562744	Standard	NM_019617		Approved	AMP18, CA11, BRICD1	uc002sfc.3	Q9NS71	OTTHUMG00000129574	ENST00000377938.2:c.483A>G	chr2.hg19:g.69207170A>G		248.0	0.0	.		207.0	41.0	.	NM_019617	Q8IUA9	Silent	SNP	ENST00000377938.2	hg19	CCDS1891.2																																																																																			.	.	.	none		0.507	GKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251769.2	NM_019617		G	69207170	A	G	69207170	2	3	237	1	0	0	0	0	0	0	0	1	6431	204	8	3		3	GKN1	2	69207170	Silent	SNP	A	TCGA-PJ-A5Z8-01A-11D-A28G-10	31921064	69207170	173992203	8	14429											
POLR1B	84172	hgsc.bcm.edu	37	chr2	113330280	113330285	+	In_Frame_Del	DEL	CCAATG	CCAATG	-																															ggataactatccaattgggaCcaatgccatcgttgctgtga																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	CCAATG	CCAATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr2:113330280_113330285delCCAATG	ENST00000263331.5	+	13	2796_2801	c.2216_2221delCCAATG	c.(2215-2223)accaatgcc>acc	p.NA740del	POLR1B_ENST00000537335.1_In_Frame_Del_p.NA529del|POLR1B_ENST00000417433.2_In_Frame_Del_p.NA684del|POLR1B_ENST00000541869.1_In_Frame_Del_p.NA778del|POLR1B_ENST00000409894.3_In_Frame_Del_p.NA557del	NM_019014.4	NP_061887.2	Q9H9Y6	RPA2_HUMAN	polymerase (RNA) I polypeptide B, 128kDa	740					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						CCAATTGGGACCAATGCCATCGTTGC	0.393																																					p.739_740del	Ovarian(16;256 576 9537 23969 41147)	Pindel	.											.	POLR1B	95	.	0			c.2215_2220del						PASS	.																																			SO:0001651	inframe_deletion	84172	exon13			.	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.2216_2221delCCAATG	chr2.hg19:g.113330280_113330285delCCAATG	ENSP00000263331:p.Asn740_Ala741del	172.0	0.0	.		120.0	10.0	0.083	NM_019014	B7Z6Y7|B7Z823|F5GZX4|F8W898|Q2TAM4|Q585T5|Q6ZRR2|Q9H9D3	In_Frame_Del	DEL	ENST00000263331.5	hg19	CCDS2097.1																																																																																			.	.	.	none		0.393	POLR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254083.1	NM_019014		-	113330285	CCAATG	-	113330280	7	5	237	1	0	1	0	1	0	0	0	0	12217	507	18	0	2266	0	POLR1B	2	113330280	In_Frame_Del	DEL	CCAATG	TCGA-PJ-A5Z8-01A-11D-A28G-10	44123110	113330280	129869093	9	14430											
DCAF17	80067	hgsc.bcm.edu	37	chr2	172333421	172333421	+	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	agttctcagcatcagatctcTgaagattttgtcattttggc	9	16	8	8	0	4	3	3	1	2	2	6	3	4	3	0	1	1	2	0	1	1	5			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr2:172333421T>A	ENST00000375255.3	+	11	1470	c.1143T>A	c.(1141-1143)tcT>tcA	p.S381S	DCAF17_ENST00000468592.1_3'UTR|DCAF17_ENST00000539783.1_Intron	NM_025000.3	NP_079276.2	Q5H9S7	DCA17_HUMAN	DDB1 and CUL4 associated factor 17	381					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|prostate(1)	17						ATCAGATCTCTGAAGATTTTG	0.323																																					p.S381S		Atlas-SNP	.											.	DCAF17	41	.	0			c.T1143A						PASS	.						70	72	71					2																	172333421		2203	4300	6503	SO:0001819	synonymous_variant	80067	exon11			GATCTCTGAAGAT	AK023158	CCDS2243.2, CCDS54419.1	2q31.1	2014-01-28	2009-07-17	2009-07-17	ENSG00000115827	ENSG00000115827		"DDB1 and CUL4 associated factors"	25784	protein-coding gene	gene with protein product	"Woodhouse-Sakati syndrome"	612515	"chromosome 2 open reading frame 37"	C2orf37			Standard	NM_001164821		Approved	FLJ13096	uc002ugx.3	Q5H9S7	OTTHUMG00000132259	ENST00000375255.3:c.1143T>A	chr2.hg19:g.172333421T>A		150.0	0.0	.		144.0	29.0	.	NM_025000	B2RTW5|Q53TN3|Q9H908	Silent	SNP	ENST00000375255.3	hg19	CCDS2243.2	.	.	.	.	.	.	.	.	.	.	T	10.52	1.373792	0.24857	.	.	ENSG00000115827	ENST00000339506;ENST00000431110	.	.	.	5.55	4.37	0.52481	.	.	.	.	.	T	0.46405	0.1391	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43015	-0.9417	4	.	.	.	-6.982	2.2645	0.04075	0.1969:0.0804:0.1334:0.5893	.	.	.	.	Q	132;83	.	.	L	+	2	0	DCAF17	172041667	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.499000	0.35671	0.913000	0.36797	0.472000	0.43445	CTG	.	.	.	none		0.323	DCAF17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255342.2	NM_025000		A	172333421	T	A	172333421	2	1	237	1	0	0	0	0	0	0	0	1	4271	1567	55	5		5	DCAF17	2	172333421	Silent	SNP	T	TCGA-PJ-A5Z8-01A-11D-A28G-10	59003141	172333421	70865952	10	14431											
SLC40A1	30061	hgsc.bcm.edu	37	chr2	190437577	190437577	+	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	tcattgagaacttacgagaaCccatccatggtacatggtca	13	10	8	10	1	2	2	2	1	0	2	3	4	3	2	2	2	4	1	2	2	4	3			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr2:190437577C>A	ENST00000261024.2	-	4	808	c.382G>T	c.(382-384)Gtt>Ttt	p.V128F	SLC40A1_ENST00000418714.1_5'Flank	NM_014585.5	NP_055400.1	Q9NP59	S40A1_HUMAN	solute carrier family 40 (iron-regulated transporter), member 1	128					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)			CTTACGAGAACCCATCCATGG	0.393																																					p.V128F		Atlas-SNP	.											.	SLC40A1	51	.	0			c.G382T						PASS	.						83	78	80					2																	190437577		2203	4300	6503	SO:0001583	missense	30061	exon4			CGAGAACCCATCC	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.382G>T	chr2.hg19:g.190437577C>A	ENSP00000261024:p.Val128Phe	196.0	0.0	.		215.0	42.0	.	NM_014585	Q6FI62|Q7Z4F8|Q8IVB2|Q9NRL0	Missense_Mutation	SNP	ENST00000261024.2	hg19	CCDS2299.1	.	.	.	.	.	.	.	.	.	.	C	12.35	1.911373	0.33721	.	.	ENSG00000138449	ENST00000261024;ENST00000427241	D;D	0.94280	-3.39;-3.39	6.03	1.03	0.20045	Major facilitator superfamily domain, general substrate transporter (1);	0.604283	0.17891	N	0.158506	D	0.83848	0.5343	N	0.17474	0.49	0.42059	D	0.991157	B;B	0.09022	0.002;0.002	B;B	0.14578	0.011;0.011	T	0.70040	-0.4981	10	0.20519	T	0.43	-3.6976	7.1323	0.25508	0.0:0.3425:0.3929:0.2646	.	128;128	A8K7Y1;Q9NP59	.;S40A1_HUMAN	F	128	ENSP00000261024:V128F;ENSP00000390005:V128F	ENSP00000261024:V128F	V	-	1	0	SLC40A1	190145822	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	0.700000	0.25601	0.124000	0.18369	0.655000	0.94253	GTT	.	.	.	none		0.393	SLC40A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255916.2			A	190437577	C	A	190437577	3	1	237	1	0	0	0	0	1	0	0	0	14641	507	18	4	1353	4	SLC40A1	2	190437577	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	18104156	190437577	52761796	11	14432											
GLS	2744	hgsc.bcm.edu	37	chr2	191795284	191795284	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacagtgttaagggaattcActtttgtcacgtaagcatat	13	13	8	7	1	2	0	2	0	0	0	2	1	2	1	0	1	2	3	0	1	5	6			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr2:191795284A>G	ENST00000320717.3	+	13	1805	c.1547A>G	c.(1546-1548)cAc>cGc	p.H516R	GLS_ENST00000409215.1_Missense_Mutation_p.H21R|GLS_ENST00000409626.1_Missense_Mutation_p.H87R|GLS_ENST00000409428.1_Missense_Mutation_p.H21R|GLS_ENST00000338435.4_Missense_Mutation_p.H516R	NM_014905.4	NP_055720.3	O94925	GLSK_HUMAN	glutaminase	516					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)	AAGGGAATTCACTTTTGTCAC	0.383																																					p.H516R		Atlas-SNP	.											.	GLS	47	.	0			c.A1547G						PASS	.						128	119	122					2																	191795284		2203	4300	6503	SO:0001583	missense	2744	exon13			GAATTCACTTTTG	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.1547A>G	chr2.hg19:g.191795284A>G	ENSP00000317379:p.His516Arg	120.0	0.0	.		119.0	31.0	.	NM_014905	Q9UL05|Q9UL06|Q9UL07|Q9UN40	Missense_Mutation	SNP	ENST00000320717.3	hg19	CCDS2308.1	.	.	.	.	.	.	.	.	.	.	A	13.95	2.388942	0.42308	.	.	ENSG00000115419	ENST00000320717;ENST00000338435;ENST00000409626;ENST00000457316;ENST00000409428;ENST00000409215;ENST00000412247	T;T;T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06;1.06;1.06	5.84	5.84	0.93424	Beta-lactamase/transpeptidase-like (1);	0.049755	0.85682	D	0.000000	T	0.26195	0.0639	N	0.10664	0.02	0.54753	D	0.999986	B;B;B;B;B	0.12013	0.003;0.003;0.001;0.003;0.005	B;B;B;B;B	0.12156	0.004;0.006;0.003;0.006;0.007	T	0.06972	-1.0797	10	0.27082	T	0.32	-4.505	16.2233	0.82274	1.0:0.0:0.0:0.0	.	87;516;170;516;516	B7Z2P1;A8K132;Q68D38;O94925;O94925-3	.;.;.;GLSK_HUMAN;.	R	516;516;87;87;21;21;37	ENSP00000317379:H516R;ENSP00000340689:H516R;ENSP00000386417:H87R;ENSP00000395596:H87R;ENSP00000387177:H21R;ENSP00000387135:H21R;ENSP00000403329:H37R	ENSP00000317379:H516R	H	+	2	0	GLS	191503529	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.339000	0.96797	2.243000	0.73865	0.482000	0.46254	CAC	.	.	.	none		0.383	GLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255999.2			G	191795284	A	G	191795284	3	3	237	1	0	0	0	0	1	0	0	0	6470	159	6	3	1597	3	GLS	2	191795284	Missense_Mutation	SNP	A	TCGA-PJ-A5Z8-01A-11D-A28G-10	1357707	191795284	51404089	12	14433											
PGAP1	80055	hgsc.bcm.edu	37	chr2	197791195	197791195	+	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	ggagagggcagaaccttaccTgatactccgggtactcaaac	12	7	11	11	1	1	3	1	1	0	2	2	4	2	3	3	3	5	2	3	3	5	3			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr2:197791195T>A	ENST00000354764.4	-	1	260	c.146A>T	c.(145-147)cAg>cTg	p.Q49L	PGAP1_ENST00000485830.1_Intron|PGAP1_ENST00000409475.1_Splice_Site_p.Q49L|PGAP1_ENST00000409188.1_Intron	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	49					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						GAACCTTACCTGATACTCCGG	0.562																																					p.Q49L		Atlas-SNP	.											.	PGAP1	84	.	0			c.A146T						PASS	.						184	203	197					2																	197791195		2203	4300	6503	SO:0001630	splice_region_variant	80055	exon1			CTTACCTGATACT		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.147+1A>T	chr2.hg19:g.197791195T>A		197.0	0.0	.		220.0	40.0	.	NM_024989	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Missense_Mutation	SNP	ENST00000354764.4	hg19	CCDS2318.1	.	.	.	.	.	.	.	.	.	.	T	14.06	2.422748	0.43020	.	.	ENSG00000197121	ENST00000422382;ENST00000354764;ENST00000409475;ENST00000374738	D	0.83673	-1.75	4.16	4.16	0.48862	.	0.069665	0.64402	D	0.000011	T	0.70745	0.3259	N	0.15975	0.35	0.80722	D	1	B;P	0.48764	0.001;0.915	B;P	0.49361	0.001;0.608	T	0.66284	-0.5962	10	0.11485	T	0.65	-4.6463	6.88	0.24168	0.2059:0.0:0.0:0.7941	.	49;49	Q75T13-3;Q75T13	.;PGAP1_HUMAN	L	49	ENSP00000363870:Q49L	ENSP00000346809:Q49L	Q	-	2	0	PGAP1	197499440	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	2.730000	0.47335	1.752000	0.51891	0.260000	0.18958	CAG	.	.	.	none		0.562	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989	Missense_Mutation	A	197791195	T	A	197791195	5	1	237	1	0	0	0	0	0	0	1	0	11784	1594	55	5	2730	5	PGAP1	2	197791195	Splice_Site	SNP	T	TCGA-PJ-A5Z8-01A-11D-A28G-10	5995911	197791195	45408178	13	14434											
SGOL2	151246	hgsc.bcm.edu	37	chr2	201438489	201438489	+	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	aaggcatttagatctttgtcTgagatacattcacctaacat	13	14	6	8	0	3	2	1	1	2	2	3	3	3	2	1	1	2	1	1	1	4	6			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr2:201438489T>G	ENST00000357799.4	+	7	3518	c.3420T>G	c.(3418-3420)tcT>tcG	p.S1140S		NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	1140					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)				NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						GATCTTTGTCTGAGATACATT	0.343																																					p.S1140S		Atlas-SNP	.											.	SGOL2	126	.	0			c.T3420G						PASS	.						109	101	103					2																	201438489		1844	4087	5931	SO:0001819	synonymous_variant	151246	exon7			TTTGTCTGAGATA	AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.3420T>G	chr2.hg19:g.201438489T>G		80.0	0.0	.		74.0	13.0	.	NM_001160046	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Silent	SNP	ENST00000357799.4	hg19	CCDS42796.1																																																																																			.	.	.	none		0.343	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524		G	201438489	T	G	201438489	2	3	237	1	0	0	0	0	0	0	0	1	14230	1567	55	5		5	SGOL2	2	201438489	Silent	SNP	T	TCGA-PJ-A5Z8-01A-11D-A28G-10	3647294	201438489	41760884	14	14435											
COPG	22820	hgsc.bcm.edu	37	chr3	128993744	128993745	+	Nonsense_Mutation	DNP	GC	GC	TA																															tcatgaaactgaacttcgaaGcagcctgggatgaggtaggg																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr3:128993744_128993745GC>TA	ENST00000314797.6	+	22	2424_2425	c.2320_2321GC>TA	c.(2320-2322)GCa>TAa	p.A774*		NM_016128.3	NP_057212.1	Q9Y678	COPG1_HUMAN	coatomer protein complex, subunit gamma 1	774	Interaction with ZNF289/ARFGAP2.				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)										GAACTTCGAAGCAGCCTGGGAT	0.46																																					p.A774S|p.A774E		Atlas-SNP	.											.	.	.	.	0			c.G2320T|c.C2321A						PASS	.																																			SO:0001587	stop_gained	22820	exon22			TTCGAAGCAGCCT|TCGAAGCAGCCTG	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	Exception_encountered	chr3.hg19:g.128993744_128993745delinsTA	ENSP00000325002:p.Ala774*	279.0|283.0	0.0	.		313.0	63.0|64.0	.	NM_016128	A8K6M8|B3KMF6|Q54AC4	Missense_Mutation	SNP	ENST00000314797.6	hg19	CCDS33851.1																																																																																			.	.	.	none		0.46	COPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355456.1	NM_016128		TA	128993745	GC	TA	128993744	4	4	237	1	0	0	0	0	0	1	0	0	3733	971	34	4	2406	4	COPG	3	128993744	Nonsense_Mutation	DNP	GC	TCGA-PJ-A5Z8-01A-11D-A28G-10		128993744	69028686	15	14436											
HPSE	10855	hgsc.bcm.edu	37	chr4	84240579	84240579	+	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	tagggccattccaaccgtaaCttctcctccacatcaggagg	10	9	8	14	1	2	0	1	0	1	0	5	1	4	1	5	3	2	1	5	3	3	4			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr4:84240579C>G	ENST00000405413.2	-	4	553	c.417G>C	c.(415-417)aaG>aaC	p.K139N	HPSE_ENST00000513463.1_Missense_Mutation_p.K139N|HPSE_ENST00000311412.5_Missense_Mutation_p.K139N|HPSE_ENST00000512196.1_Missense_Mutation_p.K139N	NM_006665.5	NP_006656.2	Q9Y251	HPSE_HUMAN	heparanase	139					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)	CCAACCGTAACTTCTCCTCCA	0.438																																					p.K139N		Atlas-SNP	.											.	HPSE	55	.	0			c.G417C						PASS	.						148	137	141					4																	84240579		2203	4300	6503	SO:0001583	missense	10855	exon3			CCGTAACTTCTCC	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.417G>C	chr4.hg19:g.84240579C>G	ENSP00000384262:p.Lys139Asn	104.0	0.0	.		113.0	17.0	.	NM_001199830	A9JIG7|C7F7I3|C7F7I4|E9PCA9|E9PGR1|Q53GE5|Q9UL39	Missense_Mutation	SNP	ENST00000405413.2	hg19	CCDS3602.1	.	.	.	.	.	.	.	.	.	.	C	2.151	-0.394512	0.04899	.	.	ENSG00000173083	ENST00000311412;ENST00000405413;ENST00000512196;ENST00000513463	T;T;T;T	0.44482	0.94;0.94;0.92;2.02	5.14	0.358	0.16084	Glycoside hydrolase, superfamily (1);	0.691254	0.14121	N	0.340021	T	0.28863	0.0716	L	0.36672	1.1	0.09310	N	1	B;P;P	0.36465	0.0;0.551;0.554	B;B;B	0.40782	0.001;0.34;0.146	T	0.14531	-1.0469	10	0.27082	T	0.32	-4.5686	2.1168	0.03715	0.1217:0.3938:0.1188:0.3657	.	139;139;139	E9PCA9;E9PGR1;Q9Y251	.;.;HPSE_HUMAN	N	139	ENSP00000308107:K139N;ENSP00000384262:K139N;ENSP00000423265:K139N;ENSP00000421365:K139N	ENSP00000308107:K139N	K	-	3	2	HPSE	84459603	0.000000	0.05858	0.002000	0.10522	0.016000	0.09150	-0.862000	0.04263	-0.150000	0.11195	-0.293000	0.09583	AAG	.	.	.	none		0.438	HPSE-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252812.2	NM_006665		G	84240579	C	G	84240579	3	3	237	1	0	0	0	0	1	0	0	0	7351	564	20	4	1254	4	HPSE	4	84240579	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10		84240579	106913697	16	14437											
GRID2	2895	hgsc.bcm.edu	37	chr4	94436380	94436380	+	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	aatcaaggtctctccaggacCtttccaagcaaacagaaatc	15	8	6	12	0	2	1	1	0	1	1	6	2	4	2	3	2	2	1	3	2	5	1			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr4:94436380C>T	ENST00000282020.4	+	13	2269	c.2011C>T	c.(2011-2013)Ctt>Ttt	p.L671F	GRID2_ENST00000510992.1_Missense_Mutation_p.L576F	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	671					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)	p.L671I(1)		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)		TCTCCAGGACCTTTCCAAGCA	0.418																																					p.L671F		Atlas-SNP	.											GRID2,NS,carcinoma,0,1	GRID2	233	.	1	Substitution - Missense(1)	lung(1)	c.C2011T						PASS	.						45	44	44					4																	94436380		2203	4300	6503	SO:0001583	missense	2895	exon13			CAGGACCTTTCCA	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.2011C>T	chr4.hg19:g.94436380C>T	ENSP00000282020:p.Leu671Phe	83.0	0.0	.		81.0	16.0	.	NM_001510	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Missense_Mutation	SNP	ENST00000282020.4	hg19	CCDS3637.1	.	.	.	.	.	.	.	.	.	.	C	19.43	3.826524	0.71143	.	.	ENSG00000152208	ENST00000282020;ENST00000510992	T;T	0.52754	0.65;0.65	4.96	4.96	0.65561	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.062472	0.64402	D	0.000006	T	0.74038	0.3664	M	0.86651	2.83	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.85130	0.992;0.997	T	0.79757	-0.1669	10	0.87932	D	0	.	18.5496	0.91058	0.0:1.0:0.0:0.0	.	576;671	E9PH24;O43424	.;GRID2_HUMAN	F	671;576	ENSP00000282020:L671F;ENSP00000421257:L576F	ENSP00000282020:L671F	L	+	1	0	GRID2	94655403	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.534000	0.45676	2.448000	0.82819	0.585000	0.79938	CTT	.	.	.	none		0.418	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2			T	94436380	C	T	94436380	3	4	237	1	0	0	0	0	1	0	0	0	6779	681	24	2	2061	2	GRID2	4	94436380	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	10195801	94436380	96717896	17	14438											
ADH6	130	hgsc.bcm.edu	37	chr4	100129912	100129912	+	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	acttcttgaatgggtttcttTaagtcctgagggttgaggca	8	15	12	6	0	2	3	0	3	2	0	3	3	3	3	1	3	0	3	1	3	2	6			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr4:100129912T>A	ENST00000237653.7	-	6	1125	c.741A>T	c.(739-741)ttA>ttT	p.L247F	RP11-696N14.1_ENST00000506160.1_RNA|ADH6_ENST00000394899.2_Missense_Mutation_p.L247F|RP11-696N14.1_ENST00000506454.1_RNA|RP11-696N14.1_ENST00000500358.2_RNA|ADH6_ENST00000504257.1_5'UTR|ADH6_ENST00000407820.2_Missense_Mutation_p.L38F|ADH6_ENST00000394897.1_Missense_Mutation_p.L247F	NM_000672.3	NP_000663	P28332	ADH6_HUMAN	alcohol dehydrogenase 6 (class V)	247					ethanol oxidation (GO:0006069)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|ethanol binding (GO:0035276)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(2)	20				OV - Ovarian serous cystadenocarcinoma(123;3.58e-08)	Abacavir(DB01048)	TGGGTTTCTTTAAGTCCTGAG	0.443																																					p.L247F		Atlas-SNP	.											.	ADH6	74	.	0			c.A741T						PASS	.						286	298	294					4																	100129912		2203	4300	6503	SO:0001583	missense	130	exon6			TTTCTTTAAGTCC	AK092768	CCDS3647.1, CCDS43255.1	4q23	2008-02-05			ENSG00000172955	ENSG00000172955	1.1.1.1	"Alcohol dehydrogenases"	255	protein-coding gene	gene with protein product		103735				1881901	Standard	NM_000672		Approved	ADH-5	uc003huo.2	P28332	OTTHUMG00000131024	ENST00000237653.7:c.741A>T	chr4.hg19:g.100129912T>A	ENSP00000237653:p.Leu247Phe	123.0	0.0	.		148.0	39.0	.	NM_000672	B3KS45|Q58F53	Missense_Mutation	SNP	ENST00000237653.7	hg19	CCDS3647.1	.	.	.	.	.	.	.	.	.	.	T	2.163	-0.391751	0.04932	.	.	ENSG00000172955	ENST00000394897;ENST00000394899;ENST00000407820;ENST00000237653;ENST00000508558	T;T;T;T;T	0.04156	3.69;3.69;3.69;3.69;3.69	4.56	-4.66	0.03329	Alcohol dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	0.483471	0.25219	N	0.032258	T	0.01523	0.0049	N	0.11651	0.15	0.22001	N	0.999427	B;B;B;B	0.14012	0.0;0.0;0.0;0.009	B;B;B;B	0.09377	0.004;0.002;0.002;0.004	T	0.42015	-0.9476	10	0.09338	T	0.73	-7.7887	1.7843	0.03038	0.3579:0.2092:0.3238:0.1091	.	124;247;247;247	B4DPD8;E9PBI1;P28332;P28332-2	.;.;ADH6_HUMAN;.	F	247;247;38;247;183	ENSP00000378358:L247F;ENSP00000378359:L247F;ENSP00000384997:L38F;ENSP00000237653:L247F;ENSP00000426187:L183F	ENSP00000237653:L247F	L	-	3	2	ADH6	100348935	0.000000	0.05858	0.004000	0.12327	0.597000	0.36814	0.028000	0.13644	-1.027000	0.03325	-0.294000	0.09567	TTA	.	.	.	none		0.443	ADH6-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253665.1	NM_000672		A	100129912	T	A	100129912	3	1	237	1	0	0	0	0	1	0	0	0	312	1751	61	5	406	5	ADH6	4	100129912	Missense_Mutation	SNP	T	TCGA-PJ-A5Z8-01A-11D-A28G-10	5693532	100129912	91024364	18	14439											
LARP7	51574	hgsc.bcm.edu	37	chr4	113568519	113568519	+	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	agtccactgaaccccaaaagCagtgctcaaagaaaaagaaa	20	4	7	10	0	1	3	1	1	0	2	2	3	2	3	3	0	3	2	3	0	7	0			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr4:113568519C>A	ENST00000344442.5	+	7	1089	c.811C>A	c.(811-813)Cag>Aag	p.Q271K	MIR302D_ENST00000362275.1_RNA|MIR302B_ENST00000509938.1_RNA|MIR302C_ENST00000362232.1_RNA|MIR367_ENST00000362299.1_RNA|MIR302B_ENST00000505215.1_RNA|MIR302B_ENST00000510655.1_RNA|MIR302A_ENST00000385192.1_RNA|MIR302B_ENST00000362188.1_RNA|LARP7_ENST00000509061.1_Missense_Mutation_p.Q278K|LARP7_ENST00000324052.6_Missense_Mutation_p.Q271K	NM_016648.3	NP_057732.2	Q4G0J3	LARP7_HUMAN	La ribonucleoprotein domain family, member 7	271	Lys-rich.				RNA processing (GO:0006396)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	17		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)		ACCCCAAAAGCAGTGCTCAAA	0.448																																					p.Q278K		Atlas-SNP	.											.	LARP7	54	.	0			c.C832A						PASS	.						104	102	102					4																	113568519		1871	4114	5985	SO:0001583	missense	51574	exon9			CAAAAGCAGTGCT	AF068284	CCDS3701.2, CCDS58924.1	4q25	2013-02-12			ENSG00000174720	ENSG00000174720		"La ribonucleoprotein domain containing", "RNA binding motif (RRM) containing"	24912	protein-coding gene	gene with protein product	"P-TEFb-interaction protein for 7SK stability"	612026				18191186, 18249148, 18281698, 22865833, 22488152	Standard	NM_016648		Approved	HDCMA18P, PIP7S, DKFZP564K112	uc003ibb.4	Q4G0J3	OTTHUMG00000132909	ENST00000344442.5:c.811C>A	chr4.hg19:g.113568519C>A	ENSP00000344950:p.Gln271Lys	126.0	0.0	.		147.0	16.0	.	NM_001267039	B2ZHN6|Q3B7A9|Q9P1S7|Q9Y3Z8	Missense_Mutation	SNP	ENST00000344442.5	hg19	CCDS3701.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.204|0.204	-1.041899|-1.041899	0.01997|0.01997	.|.	.|.	ENSG00000174720|ENSG00000174720	ENST00000344442;ENST00000509061;ENST00000505034;ENST00000324052|ENST00000511529	T;T;T;T|.	0.17528|.	2.27;2.27;2.27;2.27|.	5.86|5.86	5.01|5.01	0.66863|0.66863	.|.	0.366809|.	0.30126|.	N|.	0.010347|.	T|T	0.56485|0.56485	0.1988|0.1988	L|L	0.56769|0.56769	1.78|1.78	0.32446|0.32446	N|N	0.546025|0.546025	B;B|.	0.18013|.	0.025;0.025|.	B;B|.	0.18561|.	0.022;0.022|.	T|T	0.65162|0.65162	-0.6235|-0.6235	10|5	0.06236|.	T|.	0.91|.	-6.7457|-6.7457	10.0804|10.0804	0.42386|0.42386	0.0:0.7892:0.1388:0.072|0.0:0.7892:0.1388:0.072	.|.	271;271|.	D6RFF0;Q4G0J3|.	.;LARP7_HUMAN|.	K|R	271;278;271;271|51	ENSP00000344950:Q271K;ENSP00000422626:Q278K;ENSP00000421541:Q271K;ENSP00000314311:Q271K|.	ENSP00000314311:Q271K|.	Q|S	+|+	1|3	0|2	LARP7|LARP7	113787968|113787968	0.865000|0.865000	0.29922|0.29922	0.907000|0.907000	0.35723|0.35723	0.117000|0.117000	0.20001|0.20001	1.026000|1.026000	0.30103|0.30103	1.453000|1.453000	0.47775|0.47775	0.563000|0.563000	0.77884|0.77884	CAG|AGC	.	.	.	none		0.448	LARP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256417.2	NM_016648		A	113568519	C	A	113568519	3	1	237	1	0	0	0	0	1	0	0	0	8640	711	25	4	833	4	LARP7	4	113568519	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	13438607	113568519	77585757	19	14440											
CDH12	1010	hgsc.bcm.edu	37	chr5	21751876	21751876	+	Frame_Shift_Del	DEL	T	T	-																															ttatcagggttataactctcTtcttcgccaaacatgtctgc																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr5:21751876delT	ENST00000382254.1	-	15	3441	c.2355delA	c.(2353-2355)gaafs	p.E786fs	CDH12_ENST00000504376.2_Frame_Shift_Del_p.E786fs|CDH12_ENST00000522262.1_Frame_Shift_Del_p.E746fs|RP11-804N13.1_ENST00000522350.1_RNA|CDH12_ENST00000521384.1_5'UTR	NM_004061.3	NP_004052.2	P55289	CAD12_HUMAN	cadherin 12, type 2 (N-cadherin 2)	786					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)			NS(2)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(19)|lung(75)|ovary(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	120						TATAACTCTCTTCTTCGCCAA	0.428										HNSCC(59;0.17)																											p.E786fs		Atlas-Indel,Pindel	.											.	CDH12	238	.	0			c.2356delG						PASS	.						81	83	82					5																	21751876		2203	4300	6503	SO:0001589	frameshift_variant	1010	exon15			.	L33477	CCDS3890.1	5p14.3	2010-01-26			ENSG00000154162	ENSG00000154162		"Cadherins / Major cadherins"	1751	protein-coding gene	gene with protein product		600562				7731968	Standard	NM_004061		Approved	Br-cadherin, CDHB	uc003jgk.2	P55289	OTTHUMG00000090591	ENST00000382254.1:c.2355delA	chr5.hg19:g.21751876delT	ENSP00000371689:p.Glu786fs	111.0	0.0	0		121.0	33.0	0.272727	NM_004061	B2RBT1|B7Z2U6|Q86UD2	Frame_Shift_Del	DEL	ENST00000382254.1	hg19	CCDS3890.1																																																																																			.	.	.	none		0.428	CDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207139.1	NM_004061		-	21751876	T	-	21751876	7	5	237	1	0	1	0	1	0	0	0	0	3100	1606	56	0	33	0	CDH12	5	21751876	Frame_Shift_Del	DEL	T	TCGA-PJ-A5Z8-01A-11D-A28G-10		21751876	159163384	20	14441											
IQGAP2	10788	hgsc.bcm.edu	37	chr5	75902074	75902074	+	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	aagataacttaagctggaatGaaattcagaattgtattgat	17	13	8	3	0	1	4	1	2	0	2	1	5	1	5	0	1	2	2	0	1	7	6			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr5:75902074G>A	ENST00000274364.6	+	12	1600	c.1303G>A	c.(1303-1305)Gaa>Aaa	p.E435K	IQGAP2_ENST00000379730.3_5'UTR|CTD-2236F14.1_ENST00000511327.1_RNA|IQGAP2_ENST00000502745.1_5'Flank|IQGAP2_ENST00000396234.3_5'Flank	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	435					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		AAGCTGGAATGAAATTCAGAA	0.343																																					p.E435K		Atlas-SNP	.											.	IQGAP2	186	.	0			c.G1303A						PASS	.						100	99	100					5																	75902074		2203	4300	6503	SO:0001583	missense	10788	exon12			TGGAATGAAATTC	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.1303G>A	chr5.hg19:g.75902074G>A	ENSP00000274364:p.Glu435Lys	109.0	0.0	.		122.0	27.0	.	NM_006633	A8K4V1|B7Z8A4|J3KR91	Missense_Mutation	SNP	ENST00000274364.6	hg19	CCDS34188.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.060330	0.76074	.	.	ENSG00000145703	ENST00000274364;ENST00000514350;ENST00000505766	T;T;T	0.06849	3.25;3.25;3.25	5.63	4.76	0.60689	.	0.158913	0.56097	N	0.000036	T	0.11879	0.0289	M	0.68952	2.095	0.80722	D	1	P	0.39404	0.672	B	0.35607	0.206	T	0.02526	-1.1146	10	0.49607	T	0.09	-26.3168	14.1512	0.65387	0.0728:0.0:0.9272:0.0	.	435	Q13576	IQGA2_HUMAN	K	435;408;385	ENSP00000274364:E435K;ENSP00000423672:E408K;ENSP00000421097:E385K	ENSP00000274364:E435K	E	+	1	0	IQGAP2	75937830	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.250000	0.89835	1.370000	0.46153	0.650000	0.86243	GAA	.	.	.	none		0.343	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		A	75902074	G	A	75902074	3	1	237	1	0	0	0	0	1	0	0	0	7822	1291	45	2	1349	2	IQGAP2	5	75902074	Missense_Mutation	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	54150198	75902074	105013186	21	14442											
DDX41	51428	hgsc.bcm.edu	37	chr5	176940458	176940458	+	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	aatcttcttcggcatggtggCactgaagagcagggtctgtc	8	11	13	9	1	3	2	0	1	3	1	5	2	3	2	0	4	1	3	0	4	2	2			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr5:176940458C>G	ENST00000507955.1	-	11	1649	c.1126G>C	c.(1126-1128)Gcc>Ccc	p.A376P	DDX41_ENST00000506965.1_5'Flank	NM_016222.2	NP_057306.2	Q9UJV9	DDX41_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 41	376	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				apoptotic process (GO:0006915)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|multicellular organismal development (GO:0007275)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)|RNA processing (GO:0006396)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)					all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.191)			GGCATGGTGGCACTGAAGAGC	0.612																																					p.A376P		Atlas-SNP	.											.	DDX41	49	.	0			c.G1126C						PASS	.						129	139	136					5																	176940458		2203	4300	6503	SO:0001583	missense	51428	exon11			TGGTGGCACTGAA	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.1126G>C	chr5.hg19:g.176940458C>G	ENSP00000422753:p.Ala376Pro	146.0	0.0	.		135.0	27.0	.	NM_016222	B2RDC8|Q96BK6|Q96K05|Q9NT96|Q9NW04	Missense_Mutation	SNP	ENST00000507955.1	hg19	CCDS4427.1	.	.	.	.	.	.	.	.	.	.	C	34	5.359401	0.95854	.	.	ENSG00000183258	ENST00000330503;ENST00000507955	T;T	0.59772	0.24;0.24	5.25	5.25	0.73442	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.055575	0.64402	D	0.000001	D	0.84705	0.5531	H	0.96777	3.88	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.79108	0.988;0.992	D	0.89650	0.3869	10	0.87932	D	0	-29.9388	19.0273	0.92937	0.0:1.0:0.0:0.0	.	250;376	B3KRK2;Q9UJV9	.;DDX41_HUMAN	P	394;376	ENSP00000330349:A394P;ENSP00000422753:A376P	ENSP00000330349:A394P	A	-	1	0	DDX41	176873064	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.595000	0.82710	2.721000	0.93114	0.655000	0.94253	GCC	.	.	.	none		0.612	DDX41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253432.2	NM_016222		G	176940458	C	G	176940458	3	3	237	1	0	0	0	0	1	0	0	0	4363	710	25	4	770	4	DDX41	5	176940458	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	101038384	176940458	3974802	22	14443											
KDM1B	221656	hgsc.bcm.edu	37	chr6	18218101	18218101	+	Frame_Shift_Del	DEL	C	C	-																															gaagacattcaaggaaccgtCtttttcgctggtgaggtatg																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr6:18218101delC	ENST00000297792.5	+	17	1851	c.1674delC	c.(1672-1674)gtcfs	p.V558fs	KDM1B_ENST00000388870.2_Frame_Shift_Del_p.V791fs|KDM1B_ENST00000397244.1_Frame_Shift_Del_p.V559fs|KDM1B_ENST00000546309.2_Frame_Shift_Del_p.V81fs			Q8NB78	KDM1B_HUMAN	lysine (K)-specific demethylase 1B	790					DNA methylation involved in gamete generation (GO:0043046)|histone H3-K4 demethylation (GO:0034720)|multicellular organismal development (GO:0007275)|regulation of DNA methylation (GO:0044030)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-monomethyl-K4 specific) (GO:0034649)|oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|large_intestine(6)|lung(8)|skin(3)|upper_aerodigestive_tract(1)	25						AAGGAACCGTCTTTTTCGCTG	0.418																																					p.V558fs		Atlas-Indel,Pindel	.											.	KDM1B	58	.	0			c.1673delT						PASS	.						216	181	193					6																	18218101		2203	4300	6503	SO:0001589	frameshift_variant	221656	exon17			.	AK125318	CCDS34343.1	6p22.3	2011-07-01	2009-09-29	2009-09-29	ENSG00000165097	ENSG00000165097		"Chromatin-modifying enzymes / K-demethylases"	21577	protein-coding gene	gene with protein product		613081	"amine oxidase, flavin containing 1", "chromosome 6 open reading frame 193", "amine oxidase (flavin containing) domain 1"	C6orf193, AOF1		19407342, 19727073	Standard	NM_153042		Approved	FLJ34109, FLJ33898, dJ298J15.2, bA204B7.3, FLJ43328, LSD2	uc003ncn.1	Q8NB78	OTTHUMG00000014316	ENST00000297792.5:c.1674delC	chr6.hg19:g.18218101delC	ENSP00000297792:p.Val558fs	95.0	0.0	0		97.0	22.0	0.226804	NM_153042	A2A2C5|A2A2C6|Q5TGV3|Q6AI15|Q6ZUU4|Q8N258|Q96EL7	Frame_Shift_Del	DEL	ENST00000297792.5	hg19	CCDS34343.1																																																																																			.	.	.	none		0.418	KDM1B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277080.1	NM_153042		-	18218101	C	-	18218101	7	5	237	1	0	1	0	1	0	0	0	0	8130	900	32	0	1732	0	KDM1B	6	18218101	Frame_Shift_Del	DEL	C	TCGA-PJ-A5Z8-01A-11D-A28G-10		18218101	152896966	23	14444											
FHL5	9457	hgsc.bcm.edu	37	chr6	97053903	97053904	+	Frame_Shift_Del	DEL	TG	TG	-																															gtggcaattattgtgtgccaTgttttgagaaggagtttgct																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr6:97053903_97053904delTG	ENST00000326771.2	+	5	840_841	c.460_461delTG	c.(460-462)tgtfs	p.C154fs	FHL5_ENST00000541107.1_Frame_Shift_Del_p.C154fs	NM_020482.4	NP_065228.4	Q5TD97	FHL5_HUMAN	four and a half LIM domains 5	154	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|urinary_tract(1)	27		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)		TTGTGTGCCATGTTTTGAGAAG	0.396																																					p.153_154del		Atlas-Indel,Pindel	.											.	FHL5	73	.	0			c.459_460del						PASS	.																																			SO:0001589	frameshift_variant	9457	exon5			.	AF278541	CCDS5035.1	6q16.1-q16.3	2008-02-05			ENSG00000112214	ENSG00000112214			17371	protein-coding gene	gene with protein product		605126					Standard	NM_020482		Approved	FLJ33049, ACT, dJ393D12.2	uc003pot.2	Q5TD97	OTTHUMG00000015239	ENST00000326771.2:c.460_461delTG	chr6.hg19:g.97053903_97053904delTG	ENSP00000326022:p.Cys154fs	146.0	0.0	0		139.0	35.0	0.251799	NM_020482	B2RBD1|E1P526|Q5TD98|Q8WW21|Q9NQU2	Frame_Shift_Del	DEL	ENST00000326771.2	hg19	CCDS5035.1																																																																																			.	.	.	none		0.396	FHL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041559.1	NM_020482		-	97053904	TG	-	97053903	7	5	237	1	0	1	0	1	0	0	0	0	5888	1464	51	0	470	0	FHL5	6	97053903	Frame_Shift_Del	DEL	TG	TCGA-PJ-A5Z8-01A-11D-A28G-10	78835802	97053903	74061164	24	14445											
HECW1	23072	hgsc.bcm.edu	37	chr7	43484075	43484075	+	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	gggcatggtctctgtgggacCtgaaggggctggggagctcc	5	8	19	9	0	1	1	0	1	1	0	3	3	2	3	2	7	1	3	2	7	1	0			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr7:43484075C>A	ENST00000395891.2	+	11	1909	c.1304C>A	c.(1303-1305)cCt>cAt	p.P435H	HECW1_ENST00000453890.1_Missense_Mutation_p.P435H	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	435					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						TCTGTGGGACCTGAAGGGGCT	0.627																																					p.P435H		Atlas-SNP	.											.	HECW1	540	.	0			c.C1304A						PASS	.						22	25	24					7																	43484075		2079	4213	6292	SO:0001583	missense	23072	exon11			TGGGACCTGAAGG	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.1304C>A	chr7.hg19:g.43484075C>A	ENSP00000379228:p.Pro435His	131.0	0.0	.		118.0	23.0	.	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Missense_Mutation	SNP	ENST00000395891.2	hg19	CCDS5469.2	.	.	.	.	.	.	.	.	.	.	C	12.99	2.102929	0.37145	.	.	ENSG00000002746	ENST00000395891;ENST00000453890;ENST00000265522	T;T	0.33654	1.45;1.4	4.77	3.89	0.44902	.	15.800300	0.00906	N	0.002403	T	0.34221	0.0890	L	0.40543	1.245	0.09310	N	1	P;P	0.51791	0.612;0.948	B;B	0.39185	0.219;0.293	T	0.38564	-0.9655	10	0.52906	T	0.07	.	10.3123	0.43716	0.0:0.844:0.0:0.156	.	435;435	B4DH42;Q76N89	.;HECW1_HUMAN	H	435	ENSP00000379228:P435H;ENSP00000407774:P435H	ENSP00000265522:P435H	P	+	2	0	HECW1	43450600	0.000000	0.05858	0.008000	0.14137	0.181000	0.23173	0.250000	0.18235	1.311000	0.45024	0.591000	0.81541	CCT	.	.	.	none		0.627	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		A	43484075	C	A	43484075	3	1	237	1	0	0	0	0	1	0	0	0	7049	681	24	4	1338	4	HECW1	7	43484075	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10		43484075	115654588	25	14446											
ABCA13	154664	hgsc.bcm.edu	37	chr7	48563956	48563956	+	Missense_Mutation	SNP	A	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	gagacattcttgtgttatacAaccttagtaaacattatcga	14	14	6	7	1	1	1	0	0	1	1	2	3	1	1	1	0	3	2	1	0	7	7			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr7:48563956A>C	ENST00000435803.1	+	54	14188	c.14164A>C	c.(14164-14166)Aac>Cac	p.N4722H	ABCA13_ENST00000544596.1_Missense_Mutation_p.N452H	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4722	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TGTGTTATACAACCTTAGTAA	0.363																																					p.N4722H		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A14164C						PASS	.						129	128	128					7																	48563956		1842	4094	5936	SO:0001583	missense	154664	exon54			TTATACAACCTTA	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.14164A>C	chr7.hg19:g.48563956A>C	ENSP00000411096:p.Asn4722His	167.0	0.0	.		138.0	30.0	.	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	A	7.655	0.683805	0.14907	.	.	ENSG00000179869	ENST00000435803;ENST00000411975;ENST00000544596	T;T;T	0.47869	0.83;0.83;0.83	5.59	3.08	0.35506	ABC transporter-like (1);	0.227351	0.30850	N	0.008743	T	0.30448	0.0765	L	0.31526	0.94	0.22127	N	0.999341	B;B;B	0.28760	0.007;0.013;0.221	B;B;B	0.23716	0.017;0.009;0.048	T	0.16070	-1.0415	10	0.45353	T	0.12	.	6.4339	0.21813	0.7623:0.1574:0.0803:0.0	.	452;2424;4722	F5H7B7;Q86UQ4-3;Q86UQ4	.;.;ABCAD_HUMAN	H	4722;495;452	ENSP00000411096:N4722H;ENSP00000391042:N495H;ENSP00000442634:N452H	ENSP00000391042:N495H	N	+	1	0	ABCA13	48534502	0.928000	0.31464	0.072000	0.20136	0.450000	0.32258	2.185000	0.42584	1.050000	0.40346	0.533000	0.62120	AAC	.	.	.	none		0.363	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		C	48563956	A	C	48563956	3	2	237	1	0	0	0	0	1	0	0	0	31	130	5	5	14207	5	ABCA13	7	48563956	Missense_Mutation	SNP	A	TCGA-PJ-A5Z8-01A-11D-A28G-10	5079881	48563956	110574707	26	14447											
LAMB1	3912	hgsc.bcm.edu	37	chr7	107592551	107592555	+	Frame_Shift_Del	DEL	TCACA	TCACA	-																															aggtattgggcgcacagcggTcacagttctgcccgatcaca																								rs376884310		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	TCACA	TCACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr7:107592551_107592555delTCACA	ENST00000222399.6	-	23	3423_3427	c.3193_3197delTGTGA	c.(3193-3198)tgtgacfs	p.CD1065fs	LAMB1_ENST00000393561.1_Frame_Shift_Del_p.CD1089fs	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	1065	Laminin EGF-like 11. {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						CGCACAGCGGTCACAGTTCTGCCCG	0.571																																					p.1065_1066del		Atlas-INDEL	.											.	LAMB1	185	.	0			c.3194_3198del						PASS	.																																			SO:0001589	frameshift_variant	3912	exon23			.	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.3193_3197delTGTGA	chr7.hg19:g.107592551_107592555delTCACA	ENSP00000222399:p.Cys1065fs	240.0	0.0	0		211.0	19.0	0.0900474	NM_002291	Q14D91	Frame_Shift_Del	DEL	ENST00000222399.6	hg19	CCDS5750.1																																																																																			.	.	.	none		0.571	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291		-	107592555	TCACA	-	107592551	7	5	237	1	0	1	0	1	0	0	0	0	8617	1667	58	0	2211	0	LAMB1	7	107592551	Frame_Shift_Del	DEL	TCACA	TCGA-PJ-A5Z8-01A-11D-A28G-10	59028595	107592551	51546112	27	14448	149	2									
LAMB1	3912	hgsc.bcm.edu	37	chr7	107592557	107592562	+	In_Frame_Del	DEL	TTCTGC	TTCTGC	-																															tgggcgcacagcggtcacagTtctgcccgatcacattagga																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	TTCTGC	TTCTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr7:107592557_107592562delTTCTGC	ENST00000222399.6	-	23	3416_3421	c.3186_3191delGCAGAA	c.(3184-3192)gggcagaac>ggc	p.QN1063del	LAMB1_ENST00000393561.1_In_Frame_Del_p.QN1087del	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	1063	Laminin EGF-like 11. {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						GCGGTCACAGTTCTGCCCGATCACAT	0.558																																					p.1063_1064del		Atlas-INDEL	.											.	LAMB1	185	.	0			c.3187_3192del						PASS	.																																			SO:0001651	inframe_deletion	3912	exon23			.	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.3186_3191delGCAGAA	chr7.hg19:g.107592557_107592562delTTCTGC	ENSP00000222399:p.Gln1063_Asn1064del	219.0	0.0	0		200.0	19.0	0.095	NM_002291	Q14D91	In_Frame_Del	DEL	ENST00000222399.6	hg19	CCDS5750.1																																																																																			.	.	.	none		0.558	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291		-	107592562	TTCTGC	-	107592557	7	5	237	1	0	1	0	1	0	0	0	0	8617	1725	60	0	2217	0	LAMB1	7	107592557	In_Frame_Del	DEL	TTCTGC	TCGA-PJ-A5Z8-01A-11D-A28G-10	6	107592557	51546106	28	14449	149	2									
SSPO	23145	hgsc.bcm.edu	37	chr7	149518182	149518182	+	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	agtccctgcagccactcatgCgggcccagagggcagcagag	9	4	14	14	1	1	2	1	0	0	2	2	2	2	2	3	2	4	3	3	2	0	0	rs199773714	byFrequency	TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr7:149518182C>T	ENST00000378016.2	+	0	12525							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)			GCCACTCATGCGGGCCCAGAG	0.692													C|||	2	0.000399361	0	0	5008	,	,		17614	0.002		0	False		,,,				2504	0				p.C4175C		Atlas-SNP	.											.	.	.	.	0			c.C12525T						PASS	.																																					23145	exon87			CTCATGCGGGCCC	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149518182C>T		13.0	0.0	.		37.0	6.0	.	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	hg19																																																																																				.	.	.	weak		0.692	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				T	149518182	C	T	149518182	1	4	237	0	1	0	0	0	0	0	0	0	15201	776	27	1		1	SSPO	7	149518182	RNA	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	41925625	149518182	9620481	29	14450											
MLL3	58508	hgsc.bcm.edu	37	chr7	151919708	151919708	+	Frame_Shift_Del	DEL	T	T	-																															tgctacaatcaaaaccaatgTctgctacattttccacttct																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr7:151919708delT	ENST00000262189.6	-	21	3601	c.3383delA	c.(3382-3384)gacfs	p.D1128fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.D1128fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1128					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)										AAAACCAATGTCTGCTACATT	0.358																																					p.D1128fs		Atlas-Indel,Pindel	.											.	MLL3	1564	.	0			c.3384delC						PASS	.						62	50	54					7																	151919708		2203	4296	6499	SO:0001589	frameshift_variant	58508	exon21			.	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.3383delA	chr7.hg19:g.151919708delT	ENSP00000262189:p.Asp1128fs	343.0	0.0	0		336.0	59.0	0.175595	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	hg19	CCDS5931.1																																																																																			.	.	.	none		0.358	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			-	151919708	T	-	151919708	7	5	237	1	0	1	0	1	0	0	0	0	9629	1667	58	0	11508	0	MLL3	7	151919708	Frame_Shift_Del	DEL	T	TCGA-PJ-A5Z8-01A-11D-A28G-10	2401526	151919708	7218955	30	14451											
OSGIN2	734	hgsc.bcm.edu	37	chr8	90936735	90936736	+	Frame_Shift_Ins	INS	-	-	T																															cttttccttttttaggagccINStaaaaggggatcgagttatg																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr8:90936735_90936736insT	ENST00000297438.2	+	6	848_849	c.493_494insT	c.(493-495)ctafs	p.L165fs	OSGIN2_ENST00000451899.2_Frame_Shift_Ins_p.L209fs	NM_004337.2	NP_004328.1	Q9Y236	OSGI2_HUMAN	oxidative stress induced growth inhibitor family member 2	165					meiotic nuclear division (GO:0007126)					breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|urinary_tract(1)	17			BRCA - Breast invasive adenocarcinoma(11;0.0344)			TTTTAGGAGCCTAAAAGGGGAT	0.322																																					p.L209fs		Atlas-INDEL	.											.	OSGIN2	73	.	0			c.625_626insT						PASS	.																																			SO:0001589	frameshift_variant	734	exon6			.	AF061326	CCDS6248.1, CCDS47888.1	8q21	2006-10-05	2006-10-05	2006-10-05	ENSG00000164823	ENSG00000164823			1355	protein-coding gene	gene with protein product		604598	"chromosome 8 open reading frame 1"	C8orf1		9933573	Standard	NM_004337		Approved	hT41	uc003yeh.3	Q9Y236	OTTHUMG00000163811	ENST00000297438.2:c.494dupT	chr8.hg19:g.90936736_90936736dupT	ENSP00000297438:p.Leu165fs	56.0	0.0	0		83.0	16.0	0.192771	NM_001126111		Frame_Shift_Ins	INS	ENST00000297438.2	hg19	CCDS6248.1																																																																																			.	.	.	none		0.322	OSGIN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375691.1	NM_004337		T	90936736	-	T	90936735	7	5	237	1	0	1	1	0	0	0	0	0	11297	680	24	0	647	0	OSGIN2	8	90936735	Frame_Shift_Ins	INS	-	TCGA-PJ-A5Z8-01A-11D-A28G-10		90936735	55427287	31	14452											
EFR3A	23167	hgsc.bcm.edu	37	chr8	132996502	132996502	+	Missense_Mutation	SNP	T	T	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	ataactattgaactggctaaTgaagaagtagttattgatct	15	14	8	4	0	1	4	0	3	1	1	1	4	1	4	0	1	2	3	0	1	8	7			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr8:132996502T>G	ENST00000254624.5	+	15	1917	c.1692T>G	c.(1690-1692)aaT>aaG	p.N564K	EFR3A_ENST00000519656.1_Missense_Mutation_p.N528K|EFR3A_ENST00000334503.4_Missense_Mutation_p.N564K	NM_015137.4	NP_055952.2	Q14156	EFR3A_HUMAN	EFR3 homolog A (S. cerevisiae)	564						extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|skin(1)|stomach(2)	35	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)			AACTGGCTAATGAAGAAGTAG	0.348																																					p.N564K		Atlas-SNP	.											.	EFR3A	96	.	0			c.T1692G						PASS	.						132	132	132					8																	132996502		2203	4300	6503	SO:0001583	missense	23167	exon15			GGCTAATGAAGAA	D63477	CCDS34942.2	8q24.22	2008-10-23			ENSG00000132294	ENSG00000132294			28970	protein-coding gene	gene with protein product		611798				15363888	Standard	NM_015137		Approved	KIAA0143	uc003yte.3	Q14156	OTTHUMG00000150552	ENST00000254624.5:c.1692T>G	chr8.hg19:g.132996502T>G	ENSP00000254624:p.Asn564Lys	86.0	0.0	.		82.0	15.0	.	NM_015137	A7MD19|Q2VPK2|Q63HL7|Q68DX1|Q6IQ18	Missense_Mutation	SNP	ENST00000254624.5	hg19	CCDS34942.2	.	.	.	.	.	.	.	.	.	.	T	19.05	3.752706	0.69533	.	.	ENSG00000132294	ENST00000254624;ENST00000377917;ENST00000334503;ENST00000519656	T;T;T	0.30182	1.54;1.54;1.54	6.02	3.6	0.41247	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.42698	0.1214	M	0.70275	2.135	0.80722	D	1	P	0.45902	0.868	P	0.51415	0.669	T	0.23084	-1.0198	10	0.51188	T	0.08	-34.8449	10.0781	0.42373	0.0:0.1369:0.0:0.8631	.	564	Q14156	EFR3A_HUMAN	K	564;564;564;528	ENSP00000254624:N564K;ENSP00000334769:N564K;ENSP00000428086:N528K	ENSP00000254624:N564K	N	+	3	2	EFR3A	133065684	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.821000	0.27338	0.491000	0.27793	0.528000	0.53228	AAT	.	.	.	none		0.348	EFR3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318886.1	NM_015137		G	132996502	T	G	132996502	3	3	237	1	0	0	0	0	1	0	0	0	4960	1461	51	5	1750	5	EFR3A	8	132996502	Missense_Mutation	SNP	T	TCGA-PJ-A5Z8-01A-11D-A28G-10	42059767	132996502	13367520	32	14453											
OC90	729330	hgsc.bcm.edu	37	chr8	133041425	133041426	+	Splice_Site	DNP	AC	AC	TT																															gcagtgatgggacaagcagcAcctaagaccaaggaaaaccc																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr8:133041425_133041426AC>TT	ENST00000443356.2	-	14	1166_1167	c.1080_1081GT>AA	c.(1078-1083)agGTgc>agAAgc	p.C361S	OC90_ENST00000603859.1_Splice_Site_p.C345S|OC90_ENST00000254627.3_Splice_Site_p.C345S|OC90_ENST00000262283.5_Splice_Site_p.C557S			Q02509	OC90_HUMAN	otoconin 90	361	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)			GACAAGCAGCACCTAAGACCAA	0.554																																					p.C345S|p.R344R		Atlas-SNP	.											.	OC90	163	.	0			c.T1033A|c.G1032A						PASS	.																																			SO:0001630	splice_region_variant	729330	exon13			AGCAGCACCTAAG|GCAGCACCTAAGA	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.1080_1081delinsTT	chr8.hg19:g.133041425_133041426delinsTT		107.0|105.0	0.0	.		95.0|94.0	15.0|14.0	.	NM_001080399	B4DNG8	Missense_Mutation|Silent	SNP	ENST00000443356.2	hg19																																																																																				.	.	.	none		0.554	OC90-201	KNOWN	basic	protein_coding	protein_coding		NM_001080399	Missense_Mutation	TT	133041426	AC	TT	133041425	5	4	237	1	0	0	0	0	0	0	1	0	10821	173	6	5	408	5	OC90	8	133041425	Splice_Site	DNP	AC	TCGA-PJ-A5Z8-01A-11D-A28G-10	44923	133041425	13322597	33	14454											
ABCA2	20	hgsc.bcm.edu	37	chr9	139907277	139907277	+	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	atctggggcgggtgcccgccCacactgctggggcaggagaa	7	5	17	12	2	1	1	0	0	1	1	1	2	1	1	2	6	2	2	2	6	1	0			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr9:139907277C>G	ENST00000371605.3	-	30	5112	c.4965G>C	c.(4963-4965)gtG>gtC	p.V1655V	ABCA2_ENST00000265662.5_Silent_p.V1656V|ABCA2_ENST00000341511.6_Silent_p.V1656V			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	1655					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)		GGTGCCCGCCCACACTGCTGG	0.677																																					p.V1686V		Atlas-SNP	.											.	ABCA2	113	.	0			c.G5058C						PASS	.						10	14	13					9																	139907277		1886	3995	5881	SO:0001819	synonymous_variant	20	exon31			CCCGCCCACACTG	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.4965G>C	chr9.hg19:g.139907277C>G		59.0	0.0	.		157.0	23.0	.	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Silent	SNP	ENST00000371605.3	hg19		.	.	.	.	.	.	.	.	.	.	C	9.881	1.201473	0.22121	.	.	ENSG00000107331	ENST00000477420	.	.	.	4.15	3.22	0.36961	.	.	.	.	.	T	0.48150	0.1484	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43798	-0.9369	4	.	.	.	.	4.4915	0.11815	0.1537:0.609:0.1497:0.0876	.	.	.	.	R	68	.	.	G	-	1	0	ABCA2	139027098	0.859000	0.29813	1.000000	0.80357	0.989000	0.77384	-0.084000	0.11268	2.142000	0.66516	0.491000	0.48974	GGG	.	.	.	none		0.677	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606		G	139907277	C	G	139907277	2	3	237	1	0	0	0	0	0	0	0	1	32	581	21	4		4	ABCA2	9	139907277	Silent	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10		139907277	1306154	34	14455											
ANK3	288	hgsc.bcm.edu	37	chr10	61833342	61833342	+	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	cttcaatgttttataagagtCatcagatatgagttgagcag	13	14	9	5	0	3	4	3	2	0	2	3	4	3	4	0	0	1	3	0	0	4	6			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr10:61833342C>A	ENST00000280772.2	-	37	7488	c.7297G>T	c.(7297-7299)Gac>Tac	p.D2433Y	ANK3_ENST00000503366.1_Intron|ANK3_ENST00000355288.2_Intron|ANK3_ENST00000373827.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	2433					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						TTATAAGAGTCATCAGATATG	0.418																																					p.D2433Y		Atlas-SNP	.											.	ANK3	703	.	0			c.G7297T						PASS	.						79	80	80					10																	61833342		2203	4300	6503	SO:0001583	missense	288	exon37			AAGAGTCATCAGA	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.7297G>T	chr10.hg19:g.61833342C>A	ENSP00000280772:p.Asp2433Tyr	102.0	0.0	.		111.0	18.0	.	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	hg19	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	C	17.39	3.377882	0.61735	.	.	ENSG00000151150	ENST00000280772	T	0.70986	-0.53	5.8	5.8	0.92144	.	0.000000	0.44688	D	0.000436	T	0.81894	0.4919	L	0.53249	1.67	0.80722	D	1	D	0.89917	1.0	D	0.67231	0.95	T	0.82252	-0.0549	10	0.72032	D	0.01	.	20.0591	0.97667	0.0:1.0:0.0:0.0	.	2433	Q12955	ANK3_HUMAN	Y	2433	ENSP00000280772:D2433Y	ENSP00000280772:D2433Y	D	-	1	0	ANK3	61503348	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.810000	0.86072	2.747000	0.94245	0.462000	0.41574	GAC	.	.	.	none		0.418	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		A	61833342	C	A	61833342	3	1	237	1	0	0	0	0	1	0	0	0	622	826	29	4	6177	4	ANK3	10	61833342	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10		61833342	73701405	35	14456											
ENTPD7	57089	hgsc.bcm.edu	37	chr10	101421214	101421214	+	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	taatttcaggatcagtttttCctacctctgcccagcctcct	7	15	5	14	0	3	0	2	0	1	0	5	1	5	1	5	1	3	1	5	1	2	5			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr10:101421214C>A	ENST00000370489.4	+	3	198	c.20C>A	c.(19-21)tCc>tAc	p.S7Y		NM_020354.3	NP_065087.1	Q9NQZ7	ENTP7_HUMAN	ectonucleoside triphosphate diphosphohydrolase 7	7						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)		ATCAGTTTTTCCTACCTCTGC	0.428																																					p.S7Y		Atlas-SNP	.											.	ENTPD7	44	.	0			c.C20A						PASS	.						133	125	128					10																	101421214		2203	4300	6503	SO:0001583	missense	57089	exon3			GTTTTTCCTACCT	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.20C>A	chr10.hg19:g.101421214C>A	ENSP00000359520:p.Ser7Tyr	71.0	0.0	.		61.0	16.0	.	NM_020354	B2RB83|B3KP21|D3DR64	Missense_Mutation	SNP	ENST00000370489.4	hg19	CCDS7480.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.094777	0.76870	.	.	ENSG00000198018	ENST00000370489	T	0.17691	2.26	5.67	5.67	0.87782	.	0.127291	0.53938	D	0.000047	T	0.21631	0.0521	L	0.32530	0.975	0.48040	D	0.999575	P	0.49696	0.927	P	0.47251	0.542	T	0.00348	-1.1799	10	0.54805	T	0.06	-18.4355	18.5275	0.90978	0.0:1.0:0.0:0.0	.	7	Q9NQZ7	ENTP7_HUMAN	Y	7	ENSP00000359520:S7Y	ENSP00000359520:S7Y	S	+	2	0	ENTPD7	101411204	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.312000	0.59154	2.664000	0.90586	0.555000	0.69702	TCC	.	.	.	none		0.428	ENTPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049809.2	NM_020354		A	101421214	C	A	101421214	3	1	237	1	0	0	0	0	1	0	0	0	5146	855	30	4	26	4	ENTPD7	10	101421214	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	39587872	101421214	34113533	36	14457											
DNMBP	23268	hgsc.bcm.edu	37	chr10	101715503	101715503	+	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	ttaaagtccatgattgaaaaGtggcgtaaaattttatctgg	14	14	9	4	1	1	2	0	2	1	0	2	2	2	2	1	2	0	1	1	2	7	5			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr10:101715503G>T	ENST00000324109.4	-	4	1819	c.1728C>A	c.(1726-1728)caC>caA	p.H576Q	DNMBP-AS1_ENST00000434409.1_RNA|DNMBP_ENST00000342239.3_Missense_Mutation_p.H576Q	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	576					intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		TGATTGAAAAGTGGCGTAAAA	0.507																																					p.H576Q		Atlas-SNP	.											.	DNMBP	173	.	0			c.C1728A						PASS	.						53	57	56					10																	101715503		2203	4300	6503	SO:0001583	missense	23268	exon4			TGAAAAGTGGCGT	AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554		"Rho guanine nucleotide exchange factors"	30373	protein-coding gene	gene with protein product	"scaffold protein TUBA"	611282				10231032, 14506234	Standard	NM_015221		Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.1728C>A	chr10.hg19:g.101715503G>T	ENSP00000315659:p.His576Gln	67.0	0.0	.		55.0	8.0	.	NM_015221	Q8IVY3|Q9Y2L3	Missense_Mutation	SNP	ENST00000324109.4	hg19	CCDS7485.1	.	.	.	.	.	.	.	.	.	.	G	15.85	2.953459	0.53293	.	.	ENSG00000107554	ENST00000342239;ENST00000324109	T;T	0.16897	2.35;2.31	6.04	1.56	0.23342	.	0.248667	0.28647	N	0.014613	T	0.14960	0.0361	M	0.71581	2.175	0.80722	D	1	P	0.43477	0.808	B	0.39419	0.299	T	0.16364	-1.0405	10	0.13108	T	0.6	-7.645	6.0919	0.19999	0.3777:0.1336:0.4887:0.0	.	576	Q6XZF7	DNMBP_HUMAN	Q	576	ENSP00000344914:H576Q;ENSP00000315659:H576Q	ENSP00000315659:H576Q	H	-	3	2	DNMBP	101705493	0.999000	0.42202	1.000000	0.80357	0.974000	0.67602	0.487000	0.22356	0.365000	0.24400	0.561000	0.74099	CAC	.	.	.	none		0.507	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221		T	101715503	G	T	101715503	3	4	237	1	0	0	0	0	1	0	0	0	4676	1020	36	4	3061	4	DNMBP	10	101715503	Missense_Mutation	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	294289	101715503	33819244	37	14458											
CYP17A1	1586	hgsc.bcm.edu	37	chr10	104590667	104590667	+	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	ggatctcacctatacaggagCgaggtcctgctccgaagggc	9	7	13	12	2	1	0	1	0	1	0	4	4	3	2	3	4	3	1	3	4	3	2			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr10:104590667C>T	ENST00000369887.3	-	8	1490	c.1319G>A	c.(1318-1320)cGc>cAc	p.R440H	CYP17A1-AS1_ENST00000369884.4_RNA|CYP17A1_ENST00000489268.1_5'Flank	NM_000102.3	NP_000093.1	P05093	CP17A_HUMAN	cytochrome P450, family 17, subfamily A, polypeptide 1	440			R -> H (in AH5). {ECO:0000269|PubMed:8027220}.		adrenal gland development (GO:0030325)|androgen biosynthetic process (GO:0006702)|biphenyl metabolic process (GO:0018879)|cellular response to antibiotic (GO:0071236)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to lipopolysaccharide (GO:0071222)|dibenzo-p-dioxin metabolic process (GO:0018894)|glucocorticoid biosynthetic process (GO:0006704)|hippocampus development (GO:0021766)|hormone biosynthetic process (GO:0042446)|Leydig cell differentiation (GO:0033327)|ovulation (GO:0030728)|phenol-containing compound metabolic process (GO:0018958)|phthalate metabolic process (GO:0018963)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|progesterone metabolic process (GO:0042448)|response to acetate (GO:0010034)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to fungicide (GO:0060992)|response to herbicide (GO:0009635)|response to insecticide (GO:0017085)|response to ionizing radiation (GO:0010212)|response to methylmercury (GO:0051597)|response to nutrient levels (GO:0031667)|response to retinoic acid (GO:0032526)|response to steroid hormone (GO:0048545)|sex differentiation (GO:0007548)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	axon (GO:0030424)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)	17-alpha-hydroxyprogesterone aldolase activity (GO:0047442)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|steroid 17-alpha-monooxygenase activity (GO:0004508)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)	Abiraterone(DB05812)|Aminophenazone(DB01424)|Dexamethasone(DB01234)|Metoclopramide(DB01233)|Progesterone(DB00396)	TATACAGGAGCGAGGTCCTGC	0.597																																					p.R440H		Atlas-SNP	.											.	CYP17A1	48	.	0			c.G1319A	GRCh37	CM940326	CYP17A1	M		PASS	.						34	28	30					10																	104590667		2203	4299	6502	SO:0001583	missense	1586	exon8			CAGGAGCGAGGTC	M19489	CCDS7541.1	10q24.3	2010-05-04	2003-02-14	2003-02-28	ENSG00000148795	ENSG00000148795	1.14.99.9	"Cytochrome P450s"	2593	protein-coding gene	gene with protein product	"Steroid 17-alpha-monooxygenase"	609300	"cytochrome P450, subfamily XVII (steroid 17-alpha-hydroxylase), adrenal hyperplasia"	CYP17		1347802	Standard	NM_000102		Approved	P450C17, CPT7, S17AH	uc001kwg.3	P05093	OTTHUMG00000018969	ENST00000369887.3:c.1319G>A	chr10.hg19:g.104590667C>T	ENSP00000358903:p.Arg440His	177.0	0.0	.		151.0	31.0	.	NM_000102	Q5TZV7	Missense_Mutation	SNP	ENST00000369887.3	hg19	CCDS7541.1	.	.	.	.	.	.	.	.	.	.	C	35	5.529855	0.96446	.	.	ENSG00000148795	ENST00000369887	D	0.92805	-3.11	5.62	5.62	0.85841	Cytochrome P450, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.97195	0.9083	M	0.92784	3.345	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97779	1.0231	10	0.87932	D	0	.	19.259	0.93959	0.0:1.0:0.0:0.0	.	440	P05093	CP17A_HUMAN	H	440	ENSP00000358903:R440H	ENSP00000358903:R440H	R	-	2	0	CYP17A1	104580657	1.000000	0.71417	0.996000	0.52242	0.970000	0.65996	7.281000	0.78621	2.650000	0.89964	0.555000	0.69702	CGC	.	.	.	none		0.597	CYP17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050101.1	NM_000102		T	104590667	C	T	104590667	3	4	237	1	0	0	0	0	1	0	0	0	4149	768	27	1	211	1	CYP17A1	10	104590667	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	2875164	104590667	30944080	38	14459											
NLRP6	171389	hgsc.bcm.edu	37	chr11	284253	284253	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcccactgcaaactccctgAcgcggtctgccgagaccttt	7	9	9	16	3	1	2	0	1	1	1	3	3	3	2	4	1	3	1	4	1	1	1	rs150530901		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr11:284253A>G	ENST00000312165.5	+	6	2225	c.2225A>G	c.(2224-2226)gAc>gGc	p.D742G	NLRP6_ENST00000534750.1_Missense_Mutation_p.D741G	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	742					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)		AAACTCCCTGACGCGGTCTGC	0.627																																					p.D742G		Atlas-SNP	.											.	NLRP6	4	.	0			c.A2225G						PASS	.	A	GLY/ASP	1,4405	2.1+/-5.4	0,1,2202	43	42	42		2225	1.4	0	11	dbSNP_134	42	0,8600		0,0,4300	no	missense	NLRP6	NM_138329.1	94	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	benign	742/893	284253	1,13005	2203	4300	6503	SO:0001583	missense	171389	exon6			TCCCTGACGCGGT	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.2225A>G	chr11.hg19:g.284253A>G	ENSP00000309767:p.Asp742Gly	60.0	0.0	.		87.0	25.0	.	NM_138329	A8K9F3|E9PJZ8	Missense_Mutation	SNP	ENST00000312165.5	hg19	CCDS7693.1	.	.	.	.	.	.	.	.	.	.	A	3.343	-0.134159	0.06711	2.27E-4	0.0	ENSG00000174885	ENST00000534750;ENST00000312165	T;T	0.57273	0.41;0.41	2.61	1.44	0.22558	.	0.174398	0.23650	U	0.045934	T	0.59018	0.2163	L	0.58354	1.805	0.09310	N	1	D;D	0.63880	0.972;0.993	P;D	0.72338	0.689;0.977	T	0.48222	-0.9054	10	0.19590	T	0.45	.	5.8126	0.18475	0.7241:0.2759:0.0:0.0	.	741;742	E9PJZ8;P59044	.;NALP6_HUMAN	G	741;742	ENSP00000433617:D741G;ENSP00000309767:D742G	ENSP00000309767:D742G	D	+	2	0	NLRP6	274253	0.000000	0.05858	0.013000	0.15412	0.149000	0.21700	0.094000	0.15107	0.419000	0.25927	0.374000	0.22700	GAC	.	A|1.000;G|0.000	0.000	weak		0.627	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329		G	284253	A	G	284253	3	3	237	1	0	0	0	0	1	0	0	0	10488	275	10	3	2247	3	NLRP6	11	284253	Missense_Mutation	SNP	A	TCGA-PJ-A5Z8-01A-11D-A28G-10		284253	134722263	39	14460											
CTSD	1509	hgsc.bcm.edu	37	chr11	1785082	1785082	+	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	cgagcggcagaaggctggagGgctgcatggcggcggcggcc	6	3	21	11	5	0	1	0	0	0	1	0	3	0	2	1	8	2	4	1	8	1	0			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr11:1785082G>A	ENST00000236671.2	-	1	140	c.8C>T	c.(7-9)cCc>cTc	p.P3L	AC068580.5_ENST00000446489.1_RNA|AC068580.1_ENST00000580120.1_RNA|AC068580.6_ENST00000449248.1_RNA	NM_001909.4	NP_001900.1	P07339	CATD_HUMAN	cathepsin D	3					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)"	AAGGCTGGAGGGCTGCATGGC	0.736																																					p.P3L		Atlas-SNP	.											.	CTSD	26	.	0			c.C8T						PASS	.																																			SO:0001583	missense	1509	exon1			CTGGAGGGCTGCA	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.8C>T	chr11.hg19:g.1785082G>A	ENSP00000236671:p.Pro3Leu	0.0	0.0	.		23.0	13.0	.	NM_001909	Q6IB57	Missense_Mutation	SNP	ENST00000236671.2	hg19	CCDS7725.1	.	.	.	.	.	.	.	.	.	.	g	8.700	0.909609	0.17833	.	.	ENSG00000117984	ENST00000236671	T	0.52295	0.67	3.51	1.34	0.21922	.	3.791350	0.01307	N	0.010510	T	0.26231	0.0640	N	0.08118	0	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.19289	-1.0310	10	0.12103	T	0.63	.	4.9541	0.14031	0.122:0.0:0.6694:0.2087	.	3	P07339	CATD_HUMAN	L	3	ENSP00000236671:P3L	ENSP00000236671:P3L	P	-	2	0	CTSD	1741658	0.001000	0.12720	0.258000	0.24420	0.029000	0.11900	0.135000	0.15952	0.769000	0.33313	0.549000	0.68633	CCC	.	.	.	none		0.736	CTSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104272.5	NM_001909		A	1785082	G	A	1785082	3	1	237	1	0	0	0	0	1	0	0	0	4034	1232	43	2	1266	2	CTSD	11	1785082	Missense_Mutation	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	1500829	1785082	133221434	40	14461											
NUP98	4928	hgsc.bcm.edu	37	chr11	3789956	3789956	+	Frame_Shift_Del	DEL	G	G	-																															caaagagaccacctggatttGttccaaatccagttgtacct																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr11:3789956delG	ENST00000324932.7	-	8	1223	c.803delC	c.(802-804)acafs	p.T268fs	NUP98_ENST00000397007.4_Frame_Shift_Del_p.T268fs|NUP98_ENST00000397004.4_Frame_Shift_Del_p.T268fs|NUP98_ENST00000355260.3_Frame_Shift_Del_p.T268fs|NUP98_ENST00000359171.4_Frame_Shift_Del_p.T268fs	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	268	FG repeats 2.|Gly/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		ACCTGGATTTGTTCCAAATCC	0.378			T	"HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"	AML																																p.T268fs		Atlas-INDEL	.		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	NUP98	149	.	0			c.804delA						PASS	.						121	116	118					11																	3789956		2201	4298	6499	SO:0001589	frameshift_variant	4928	exon8			.	AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"nucleoporin 98kD"			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.803delC	chr11.hg19:g.3789956delG	ENSP00000316032:p.Thr268fs	49.0	0.0	0		52.0	12.0	0.230769	NM_016320	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Frame_Shift_Del	DEL	ENST00000324932.7	hg19	CCDS7746.1																																																																																			.	.	.	none		0.378	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320		-	3789956	G	-	3789956	7	5	237	1	0	1	0	1	0	0	0	0	10780	1377	48	0	4775	0	NUP98	11	3789956	Frame_Shift_Del	DEL	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	2004874	3789956	131216560	41	14462											
MRGPRX4	117196	hgsc.bcm.edu	37	chr11	18195097	18195097	+	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	catctcatccgcaaaatcctCgtttctgtgatgacctttcc	8	14	5	14	2	2	2	1	2	2	0	7	2	5	2	4	0	0	2	4	0	2	2	rs267602809		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr11:18195097C>T	ENST00000314254.3	+	1	714	c.294C>T	c.(292-294)ctC>ctT	p.L98L	RP11-113D6.6_ENST00000527671.1_Intron	NM_054032.3	NP_473373.2	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4	98						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						GCAAAATCCTCGTTTCTGTGA	0.527																																					p.L98L		Atlas-SNP	.											MRGPRX4,NS,carcinoma,0,1	MRGPRX4	68	.	0			c.C294T						PASS	.						129	103	112					11																	18195097		2199	4293	6492	SO:0001819	synonymous_variant	117196	exon1			AATCCTCGTTTCT	AY042216	CCDS7831.1	11p15.1	2013-10-10			ENSG00000179817	ENSG00000179817		"GPCR / Class A : Orphans"	17617	protein-coding gene	gene with protein product		607230				11551509	Standard	NM_054032		Approved	MRGX4	uc001mnv.1	Q96LA9	OTTHUMG00000166442	ENST00000314254.3:c.294C>T	chr11.hg19:g.18195097C>T		235.0	1.0	.		187.0	33.0	.	NM_054032	Q3KNU3|Q3KNU4|Q502W0|Q8TDD6|Q8TDD7	Silent	SNP	ENST00000314254.3	hg19	CCDS7831.1																																																																																			.	.	.	none		0.527	MRGPRX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389788.1	NM_054032		T	18195097	C	T	18195097	2	4	237	1	0	0	0	0	0	0	0	1	9776	871	31	1		1	MRGPRX4	11	18195097	Silent	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	14405141	18195097	116811419	42	14463											
LRP5	4041	hgsc.bcm.edu	37	chr11	68181318	68181318	+	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	tccagggccacctggacttcGtgatggacatcctggtgttc	6	11	12	12	1	0	1	0	1	0	0	4	3	2	3	4	4	0	1	4	4	0	2			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr11:68181318G>T	ENST00000294304.7	+	12	2771	c.2665G>T	c.(2665-2667)Gtg>Ttg	p.V889L		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	889	Beta-propeller 3.				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						CCTGGACTTCGTGATGGACAT	0.592																																					p.V889L		Atlas-SNP	.											LRP5,NS,carcinoma,0,1	LRP5	136	.	0			c.G2665T						PASS	.						87	76	79					11																	68181318		2200	4294	6494	SO:0001583	missense	4041	exon12			GACTTCGTGATGG	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.2665G>T	chr11.hg19:g.68181318G>T	ENSP00000294304:p.Val889Leu	59.0	1.0	.		67.0	23.0	.	NM_002335	Q96TD6|Q9UES7|Q9UP66	Missense_Mutation	SNP	ENST00000294304.7	hg19	CCDS8181.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.708228	0.89018	.	.	ENSG00000162337	ENST00000294304	D	0.91407	-2.84	5.02	5.02	0.67125	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.43579	U	0.000546	D	0.88815	0.6539	N	0.25957	0.775	0.58432	D	0.999999	P;P	0.39759	0.687;0.687	P;P	0.48368	0.575;0.575	D	0.86093	0.1551	10	0.21540	T	0.41	.	18.5313	0.90993	0.0:0.0:1.0:0.0	.	889;889	Q9UES7;O75197	.;LRP5_HUMAN	L	889	ENSP00000294304:V889L	ENSP00000294304:V889L	V	+	1	0	LRP5	67937894	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.610000	0.54125	2.601000	0.87937	0.561000	0.74099	GTG	.	.	.	none		0.592	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335		T	68181318	G	T	68181318	3	4	237	1	0	0	0	0	1	0	0	0	8967	1145	40	4	2711	4	LRP5	11	68181318	Missense_Mutation	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	49986221	68181318	66825198	43	14464											
DNAJC14	85406	hgsc.bcm.edu	37	chr12	56217194	56217194	+	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	tctccaacttacatctcataCtcctttcgcttttcagcatt	8	17	2	14	1	3	0	2	0	2	0	7	0	4	0	2	0	4	2	2	0	3	6	rs541345798		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr12:56217194C>G	ENST00000357606.3	-	4	1795	c.1506G>C	c.(1504-1506)gaG>gaC	p.E502D	RP11-762I7.5_ENST00000546837.1_Missense_Mutation_p.V132L|RP11-762I7.5_ENST00000552719.1_5'Flank|DNAJC14_ENST00000317269.3_Missense_Mutation_p.E502D|DNAJC14_ENST00000317287.5_Missense_Mutation_p.E502D			Q6Y2X3	DJC14_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 14	502	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(2)|kidney(1)|large_intestine(8)|lung(7)|ovary(3)|prostate(1)|skin(1)	23						ACATCTCATACTCCTTTCGCT	0.463																																					p.E502D		Atlas-SNP	.											.	DNAJC14	52	.	0			c.G1506C						PASS	.						95	84	87					12																	56217194		2203	4300	6503	SO:0001583	missense	85406	exon3			CTCATACTCCTTT	AF141342	CCDS8894.1	12q12	2011-09-02				ENSG00000135392		"Heat shock proteins / DNAJ (HSP40)"	24581	protein-coding gene	gene with protein product		606092				11331877, 11984006	Standard	NM_032364		Approved	DNAJ, DRIP78, HDJ3, LIP6, FLJ32792	uc001shu.2	Q6Y2X3		ENST00000357606.3:c.1506G>C	chr12.hg19:g.56217194C>G	ENSP00000350223:p.Glu502Asp	76.0	0.0	.		86.0	15.0	.	NM_032364	A5YM67|Q17RY2|Q66K17|Q96N59|Q96T63	Missense_Mutation	SNP	ENST00000357606.3	hg19	CCDS8894.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.64|17.64	3.439259|3.439259	0.63067|0.63067	.|.	.|.	ENSG00000135392|ENSG00000257390	ENST00000357606;ENST00000317269;ENST00000537962;ENST00000317287|ENST00000546837	T;T;T|.	0.32023|.	1.47;1.47;1.47|.	5.85|5.85	4.7|4.7	0.59300|0.59300	Heat shock protein DnaJ, N-terminal (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.45657|0.45657	0.1353|0.1353	L|L	0.35542|0.35542	1.07|1.07	0.49483|0.49483	D|D	0.999795|0.999795	B;B|.	0.29766|.	0.256;0.256|.	P;P|.	0.50231|.	0.635;0.635|.	T|T	0.33240|0.33240	-0.9876|-0.9876	10|5	0.42905|.	T|.	0.14|.	-16.2803|-16.2803	7.9219|7.9219	0.29850|0.29850	0.0:0.1589:0.0:0.8411|0.0:0.1589:0.0:0.8411	.|.	502;502|.	Q6Y2X3;A8K5A7|.	DJC14_HUMAN;.|.	D|L	502;502;212;502|132	ENSP00000350223:E502D;ENSP00000316240:E502D;ENSP00000317500:E502D|.	ENSP00000316240:E502D|.	E|V	-|-	3|1	2|0	DNAJC14|RP11-762I7.5	54503461|54503461	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	2.807000|2.807000	0.47955|0.47955	1.141000|1.141000	0.42275|0.42275	-0.294000|-0.294000	0.09567|0.09567	GAG|GTA	.	.	.	none		0.463	DNAJC14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409095.1	NM_032364		G	56217194	C	G	56217194	3	3	237	1	0	0	0	0	1	0	0	0	4635	564	20	4	622	4	DNAJC14	12	56217194	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10		56217194	77634701	44	14465											
RDH16	8608	hgsc.bcm.edu	37	chr12	57346721	57346721	+	Frame_Shift_Del	DEL	A	A	-																															tactggtcacagcagtcttgAaatagccaggttcaatcata																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr12:57346721delA	ENST00000398138.3	-	3	1482	c.626delT	c.(625-627)ttcfs	p.F209fs	RDH16_ENST00000360752.4_5'UTR	NM_003708.3	NP_003699.3	O75452	RDH16_HUMAN	retinol dehydrogenase 16 (all-trans)	209					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	electron carrier activity (GO:0009055)|retinol dehydrogenase activity (GO:0004745)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)	16						AGCAGTCTTGAAATAGCCAGG	0.507																																					p.F209fs	GBM(179;741 2921 43105 45298)	Atlas-Indel,Pindel	.											.	RDH16	33	.	0			c.627delC						PASS	.						128	124	125					12																	57346721		1873	4112	5985	SO:0001589	frameshift_variant	8608	exon3			.		CCDS41797.1	12q13.3	2011-09-14	2006-05-09			ENSG00000139547		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	29674	protein-coding gene	gene with protein product	"microsomal NAD+ dependent retinol dehydrogenase 4", "short chain dehydrogenase/reductase family 9C, member 8"		"retinol dehydrogenase 16 (all-trans and 13-cis)"			9677409, 10329026, 19027726	Standard	NM_003708		Approved	RODH-4, SDR9C8	uc001smi.4	O75452		ENST00000398138.3:c.626delT	chr12.hg19:g.57346721delA	ENSP00000381206:p.Phe209fs	55.0	0.0	0		90.0	31.0	0.344444	NM_003708	Q9UNV2	Frame_Shift_Del	DEL	ENST00000398138.3	hg19	CCDS41797.1																																																																																			.	.	.	none		0.507	RDH16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410898.1	NM_003708		-	57346721	A	-	57346721	7	5	237	1	0	1	0	1	0	0	0	0	13207	246	9	0	335	0	RDH16	12	57346721	Frame_Shift_Del	DEL	A	TCGA-PJ-A5Z8-01A-11D-A28G-10	1129527	57346721	76505174	45	14466											
MON2	23041	hgsc.bcm.edu	37	chr12	62954348	62954349	+	Frame_Shift_Ins	INS	-	-	T																															caaaaacaatgaagtatctcINStggctgctctgaaaagcttc																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr12:62954348_62954349insT	ENST00000393632.2	+	26	3878_3879	c.3487_3488insT	c.(3487-3489)ctgfs	p.L1163fs	MON2_ENST00000393629.2_Frame_Shift_Ins_p.L1163fs|MON2_ENST00000552738.1_Frame_Shift_Ins_p.L1140fs|MON2_ENST00000393630.3_Frame_Shift_Ins_p.L1164fs|MON2_ENST00000546600.1_Frame_Shift_Ins_p.L1163fs|MON2_ENST00000280379.6_Frame_Shift_Ins_p.L1164fs	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	1163					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)		TGAAGTATCTCTGGCTGCTCTG	0.411																																					p.L1163fs		Atlas-INDEL	.											.	MON2	160	.	0			c.3487_3488insT						PASS	.																																			SO:0001589	frameshift_variant	23041	exon26			.		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.3488dupT	chr12.hg19:g.62954349_62954349dupT	ENSP00000377252:p.Leu1163fs	30.0	0.0	0		43.0	11.0	0.255814	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Frame_Shift_Ins	INS	ENST00000393632.2	hg19	CCDS31849.1																																																																																			.	.	.	none		0.411	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		T	62954349	-	T	62954348	7	5	237	1	0	1	1	0	0	0	0	0	9707	912	32	0	3589	0	MON2	12	62954348	Frame_Shift_Ins	INS	-	TCGA-PJ-A5Z8-01A-11D-A28G-10	5607627	62954348	70897547	46	14467											
DDX54	79039	hgsc.bcm.edu	37	chr12	113610195	113610195	+	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	agtttgcccttggcggggaaGctgtagttgatgacattgtc	7	13	14	7	1	0	2	0	2	0	0	1	3	0	3	1	3	2	4	1	3	2	5			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr12:113610195G>A	ENST00000306014.5	-	11	1269	c.1242C>T	c.(1240-1242)agC>agT	p.S414S	DDX54_ENST00000314045.7_Silent_p.S414S	NM_024072.3	NP_076977.3	Q8TDD1	DDX54_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	414	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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						TGGCGGGGAAGCTGTAGTTGA	0.637																																					p.S414S		Atlas-SNP	.											.	DDX54	73	.	0			c.C1242T						PASS	.						82	67	72					12																	113610195		2203	4300	6503	SO:0001819	synonymous_variant	79039	exon11			GGGGAAGCTGTAG	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.1242C>T	chr12.hg19:g.113610195G>A		175.0	0.0	.		215.0	72.0	.	NM_024072	Q86YT8|Q9BRZ1	Silent	SNP	ENST00000306014.5	hg19	CCDS31907.1																																																																																			.	.	.	none		0.637	DDX54-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405435.1	NM_024072		A	113610195	G	A	113610195	2	1	237	1	0	0	0	0	0	0	0	1	4374	962	34	2		2	DDX54	12	113610195	Silent	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	50655847	113610195	20241700	47	14468											
C14orf106	55320	hgsc.bcm.edu	37	chr14	45693181	45693181	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctgaattaaaccaggtaagCattctaagggatgcctattt	13	12	8	8	0	1	1	0	1	1	0	1	2	1	2	3	2	3	2	3	2	6	6			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr14:45693181C>T	ENST00000310806.4	-	11	3067	c.2609G>A	c.(2608-2610)tGc>tAc	p.C870Y		NM_018353.4	NP_060823.3	Q6P0N0	M18BP_HUMAN	MIS18 binding protein 1	870					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						ACCAGGTAAGCATTCTAAGGG	0.388																																					p.C870Y		Atlas-SNP	.											.	MIS18BP1	92	.	0			c.G2609A						PASS	.						95	90	91					14																	45693181		2203	4300	6503	SO:0001583	missense	55320	exon11			GGTAAGCATTCTA	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.2609G>A	chr14.hg19:g.45693181C>T	ENSP00000309790:p.Cys870Tyr	57.0	0.0	.		50.0	14.0	.	NM_018353	D3DSA7|Q86V14|Q96PY4|Q9NUR5|Q9Y4X9	Missense_Mutation	SNP	ENST00000310806.4	hg19	CCDS9684.1	.	.	.	.	.	.	.	.	.	.	C	0.005	-2.229082	0.00280	.	.	ENSG00000129534	ENST00000310806	T	0.17691	2.26	5.72	2.87	0.33458	Homeodomain-like (1);	0.719999	0.14355	N	0.324833	T	0.12220	0.0297	L	0.57536	1.79	0.09310	N	1	P	0.51351	0.944	B	0.40165	0.321	T	0.10590	-1.0623	10	0.02654	T	1	0.5125	5.2769	0.15655	0.162:0.665:0.0:0.173	.	870	Q6P0N0	M18BP_HUMAN	Y	870	ENSP00000309790:C870Y	ENSP00000309790:C870Y	C	-	2	0	MIS18BP1	44762931	0.000000	0.05858	0.007000	0.13788	0.137000	0.21094	0.035000	0.13797	0.413000	0.25759	0.655000	0.94253	TGC	.	.	.	none		0.388	MIS18BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276795.2			T	45693181	C	T	45693181	3	4	237	1	0	0	0	0	1	0	0	0	1740	710	25	2	817	2	C14orf106	14	45693181	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10		45693181	61656359	48	14469											
ZBTB1	22890	hgsc.bcm.edu	37	chr14	64989255	64989256	+	Frame_Shift_Ins	INS	-	-	T																															actgaaagactttaacattaINSttaaagttactgataaagac																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr14:64989255_64989256insT	ENST00000554015.1	+	4	1464_1465	c.1033_1034insT	c.(1033-1035)attfs	p.I345fs	ZBTB1_ENST00000358738.3_Frame_Shift_Ins_p.I345fs|ZBTB1_ENST00000394712.2_Frame_Shift_Ins_p.I345fs|RP11-973N13.4_ENST00000554918.1_RNA			Q9Y2K1	ZBTB1_HUMAN	zinc finger and BTB domain containing 1	345					B cell differentiation (GO:0030183)|innate immune response (GO:0045087)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of pro-T cell differentiation (GO:2000176)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated immunity (GO:0002711)|protein homooligomerization (GO:0051260)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	13		all_lung(585;0.000567)|Myeloproliferative disorder(585;0.0255)|all_neural(303;0.0294)		UCEC - Uterine corpus endometrioid carcinoma (185;0.0182)|all cancers(60;3.78e-43)|OV - Ovarian serous cystadenocarcinoma(108;1.22e-20)|BRCA - Breast invasive adenocarcinoma(234;6.75e-06)|KIRC - Kidney renal clear cell carcinoma(182;0.00269)|STAD - Stomach adenocarcinoma(64;0.012)		CTTTAACATTATTAAAGTTACT	0.347																																					p.I345fs		Atlas-Indel,Pindel	.											.	ZBTB1	93	.	0			c.1033_1034insT						PASS	.																																			SO:0001589	frameshift_variant	22890	exon2			.	AB023214	CCDS32097.1, CCDS45126.1	14q23.3	2013-01-09			ENSG00000126804	ENSG00000126804		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	20259	protein-coding gene	gene with protein product						10231032	Standard	NM_014950		Approved	KIAA0997, ZNF909	uc010aqg.3	Q9Y2K1		ENST00000554015.1:c.1035dupT	chr14.hg19:g.64989257_64989257dupT	ENSP00000451000:p.Ile345fs	216.0	0.0	0		151.0	36.0	0.238411	NM_001123329	A8K6S8|Q86SW8	Frame_Shift_Ins	INS	ENST00000554015.1	hg19	CCDS45126.1																																																																																			.	.	.	none		0.347	ZBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411912.1			T	64989256	-	T	64989255	7	5	237	1	0	1	1	0	0	0	0	0	17534	449	16	0	1035	0	ZBTB1	14	64989255	Frame_Shift_Ins	INS	-	TCGA-PJ-A5Z8-01A-11D-A28G-10	19296074	64989255	42360285	49	14470											
MTA1	9112	hgsc.bcm.edu	37	chr14	105936238	105936239	+	Frame_Shift_Ins	INS	-	-	G																															caccaaagtgcgcctgatccINSgggggggctccctgccccca																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr14:105936238_105936239insG	ENST00000331320.7	+	20	2120_2121	c.1906_1907insG	c.(1906-1908)cggfs	p.R636fs	MTA1_ENST00000406191.1_Frame_Shift_Ins_p.R624fs|MTA1_ENST00000405646.1_Frame_Shift_Ins_p.R619fs|MTA1_ENST00000435036.2_Frame_Shift_Ins_p.R176fs|RP11-521B24.5_ENST00000552675.1_RNA	NM_001203258.1|NM_004689.3	NP_001190187.1|NP_004680.2	Q13330	MTA1_HUMAN	metastasis associated 1	636					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)		GCGCCTGATCCGGGGGGGCTCC	0.663																																					p.R636fs		Atlas-Indel,Pindel	.											.	MTA1	61	.	0			c.1906_1907insG						PASS	.																																			SO:0001589	frameshift_variant	9112	exon20			.	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.1913dupG	chr14.hg19:g.105936245_105936245dupG	ENSP00000333633:p.Arg636fs	153.0	0.0	0		139.0	28.0	0.201439	NM_004689	A5PLK4|Q86SW2|Q8NFI8|Q96GI8	Frame_Shift_Ins	INS	ENST00000331320.7	hg19	CCDS32169.1																																																																																			.	.	.	none		0.663	MTA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317849.15			G	105936239	-	G	105936238	7	5	237	1	0	1	1	0	0	0	0	0	9915	643	23	0	1984	0	MTA1	14	105936238	Frame_Shift_Ins	INS	-	TCGA-PJ-A5Z8-01A-11D-A28G-10	40946983	105936238	1413302	50	14471											
STOML1	9399	hgsc.bcm.edu	37	chr15	74281093	74281093	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaccgggtcccagatgcgAaactggacatcggctcccac	10	5	11	15	3	0	1	0	0	0	1	3	3	2	2	3	3	3	2	3	3	1	0			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr15:74281093A>G	ENST00000316900.5	-	4	565	c.441T>C	c.(439-441)ttT>ttC	p.F147F	STOML1_ENST00000316911.6_Silent_p.F97F|STOML1_ENST00000561656.1_Silent_p.F60F|STOML1_ENST00000564777.1_Silent_p.F97F|STOML1_ENST00000541638.1_Silent_p.F105F|STOML1_ENST00000359750.4_Silent_p.F147F	NM_001256672.1|NM_001256675.1|NM_001256677.1|NM_004809.4	NP_001243601.1|NP_001243604.1|NP_001243606.1|NP_004800.2	Q9UBI4	STML1_HUMAN	stomatin (EPB72)-like 1	147						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						CCCAGATGCGAAACTGGACAT	0.612																																					p.F147F		Atlas-SNP	.											.	STOML1	22	.	0			c.T441C						PASS	.						108	100	103					15																	74281093		2198	4297	6495	SO:0001819	synonymous_variant	9399	exon4			GATGCGAAACTGG	Y16522	CCDS10254.1, CCDS58381.1, CCDS58382.1, CCDS58383.1, CCDS58384.1, CCDS58385.1	15q24-q25	2008-07-18			ENSG00000067221	ENSG00000067221			14560	protein-coding gene	gene with protein product	"stomatin-like 1", "stomatin (EBP72)-like 1"	608326				9931417	Standard	NM_004809		Approved	hUNC-24, SLP-1, STORP, FLJ36370	uc002awe.4	Q9UBI4	OTTHUMG00000137608	ENST00000316900.5:c.441T>C	chr15.hg19:g.74281093A>G		89.0	0.0	.		71.0	15.0	.	NM_001256672	B3KQN0|B4DUU5|B4DXM9|E7ESC0|H3BRP3|O95675|Q4PNR4|Q6FGL8|Q8WYI7|Q9UMB9|Q9UMC0|Q9Y6H9	Silent	SNP	ENST00000316900.5	hg19	CCDS10254.1																																																																																			.	.	.	none		0.612	STOML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269022.1	NM_004809		G	74281093	A	G	74281093	2	3	237	1	0	0	0	0	0	0	0	1	15325	243	9	3		3	STOML1	15	74281093	Silent	SNP	A	TCGA-PJ-A5Z8-01A-11D-A28G-10		74281093	28250299	51	14472											
LMAN1L	79748	hgsc.bcm.edu	37	chr15	75111060	75111060	+	Splice_Site	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	atgaacaaactgcccacaggGatggagctagccaagggctg	13	5	13	10	0	0	1	0	1	0	0	0	3	0	3	2	3	5	2	2	3	4	1			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr15:75111060G>T	ENST00000309664.5	+	5	638	c.499G>T	c.(499-501)Gat>Tat	p.D167Y	RP11-414J4.2_ENST00000564823.1_RNA|LMAN1L_ENST00000379709.3_Splice_Site_p.D167Y	NM_021819.2	NP_068591.2	Q9HAT1	LMA1L_HUMAN	lectin, mannose-binding, 1 like	167	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						TGCCCACAGGGATGGAGCTAG	0.577																																					p.D167Y		Atlas-SNP	.											.	LMAN1L	43	.	0			c.G499T						PASS	.						38	32	34					15																	75111060		2197	4295	6492	SO:0001630	splice_region_variant	79748	exon5			CACAGGGATGGAG	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.498-1G>T	chr15.hg19:g.75111060G>T		56.0	0.0	.		68.0	24.0	.	NM_021819	Q6UWN2	Missense_Mutation	SNP	ENST00000309664.5	hg19	CCDS10270.1	.	.	.	.	.	.	.	.	.	.	G	9.914	1.210396	0.22289	.	.	ENSG00000140506	ENST00000309664;ENST00000456603;ENST00000379709	T;T	0.69685	-0.42;-0.42	4.89	0.74	0.18330	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.786555	0.11191	N	0.589939	T	0.75752	0.3892	M	0.87456	2.885	0.53005	D	0.999961	B;D;B;B	0.59767	0.009;0.986;0.009;0.271	B;P;B;B	0.54100	0.018;0.742;0.018;0.121	T	0.71790	-0.4486	10	0.87932	D	0	.	5.9881	0.19446	0.1621:0.0:0.5719:0.266	.	59;167;95;167	B4DGW5;Q9HAT1-3;B4DU67;Q9HAT1	.;.;.;LMA1L_HUMAN	Y	167;59;167	ENSP00000310431:D167Y;ENSP00000369031:D167Y	ENSP00000310431:D167Y	D	+	1	0	LMAN1L	72898113	1.000000	0.71417	0.051000	0.19133	0.011000	0.07611	1.479000	0.35453	-0.273000	0.09246	-2.281000	0.00270	GAT	.	.	.	none		0.577	LMAN1L-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286397.4		Missense_Mutation	T	75111060	G	T	75111060	5	4	237	1	0	0	0	0	0	0	1	0	8844	1188	41	4	517	4	LMAN1L	15	75111060	Splice_Site	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	829967	75111060	27420332	52	14473											
ST8SIA2	8128	hgsc.bcm.edu	37	chr15	93007416	93007417	+	Missense_Mutation	DNP	TC	TC	AT																															cacacgtttctgcaaacaaaTctacctctacggcttctggc																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr15:93007416_93007417TC>AT	ENST00000268164.3	+	6	1166_1167	c.929_930TC>AT	c.(928-930)aTC>aAT	p.I310N	ST8SIA2_ENST00000539113.1_Missense_Mutation_p.I289N	NM_006011.3	NP_006002.1	Q92186	SIA8B_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	310					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|ganglioside biosynthetic process (GO:0001574)|N-glycan processing (GO:0006491)|nervous system development (GO:0007399)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	early endosome (GO:0005769)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|recycling endosome (GO:0055037)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			endometrium(2)|large_intestine(6)|lung(9)|skin(2)|urinary_tract(1)	20	Lung NSC(78;0.0893)|all_lung(78;0.125)		BRCA - Breast invasive adenocarcinoma(143;0.0355)|OV - Ovarian serous cystadenocarcinoma(32;0.203)			TGCAAACAAATCTACCTCTACG	0.49																																					p.I310N|p.I310I		Atlas-SNP	.											.	ST8SIA2	41	.	0			c.T929A|c.C930T						PASS	.																																			SO:0001583	missense	8128	exon6			AACAAATCTACCT|ACAAATCTACCTC	U33551	CCDS10372.1	15q26	2013-03-01	2003-01-14	2005-02-07	ENSG00000140557	ENSG00000140557		"Sialyltransferases"	10870	protein-coding gene	gene with protein product		602546	"sialyltransferase 8 (alpha-2, 8-sialytransferase) B"	SIAT8B		7559389	Standard	NM_006011		Approved	STX, ST8SIA-II, HsT19690	uc002bra.3	Q92186	OTTHUMG00000149843	Exception_encountered	chr15.hg19:g.93007416_93007417delinsAT	ENSP00000268164:p.Ile310Asn	119.0	0.0	.		74.0|76.0	18.0|19.0	.	NM_006011	Q4VAZ0|Q92470|Q92746	Missense_Mutation|Silent	SNP	ENST00000268164.3	hg19	CCDS10372.1																																																																																			.	.	.	none		0.49	ST8SIA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313526.1	NM_006011		AT	93007417	TC	AT	93007416	3	1	237	1	0	0	0	0	1	0	0	0	15244	1435	50	5	951	5	ST8SIA2	15	93007416	Missense_Mutation	DNP	TC	TCGA-PJ-A5Z8-01A-11D-A28G-10	17896356	93007416	9523976	53	14474											
MMP15	4324	hgsc.bcm.edu	37	chr16	58079023	58079023	+	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	gacttcatgggctgccaggaGcacgtggagccaggcccccg	7	5	15	14	2	1	0	1	0	0	0	1	3	1	2	4	4	3	2	4	4	0	1			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr16:58079023G>C	ENST00000219271.3	+	10	2468	c.1683G>C	c.(1681-1683)gaG>gaC	p.E561D		NM_002428.2	NP_002419.1	P51511	MMP15_HUMAN	matrix metallopeptidase 15 (membrane-inserted)	561					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)	GCTGCCAGGAGCACGTGGAGC	0.682																																					p.E561D		Atlas-SNP	.											.	MMP15	58	.	0			c.G1683C						PASS	.						15	15	15					16																	58079023		2197	4298	6495	SO:0001583	missense	4324	exon10			CCAGGAGCACGTG	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.1683G>C	chr16.hg19:g.58079023G>C	ENSP00000219271:p.Glu561Asp	50.0	0.0	.		90.0	28.0	.	NM_002428	A0A2U6|Q14111	Missense_Mutation	SNP	ENST00000219271.3	hg19	CCDS10792.1	.	.	.	.	.	.	.	.	.	.	G	10.32	1.316412	0.23908	.	.	ENSG00000102996	ENST00000219271	T	0.15952	2.38	4.5	1.48	0.22813	Hemopexin/matrixin (1);	0.444889	0.25380	N	0.031083	T	0.07324	0.0185	N	0.08118	0	0.36663	D	0.878058	P	0.49185	0.92	P	0.45232	0.474	T	0.41662	-0.9496	10	0.15952	T	0.53	.	3.3205	0.07048	0.2891:0.0:0.5282:0.1827	.	561	P51511	MMP15_HUMAN	D	561	ENSP00000219271:E561D	ENSP00000219271:E561D	E	+	3	2	MMP15	56636524	1.000000	0.71417	0.967000	0.41034	0.905000	0.53344	1.330000	0.33781	0.167000	0.19631	-0.277000	0.10078	GAG	.	.	.	none		0.682	MMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257342.1	NM_002428		C	58079023	G	C	58079023	3	2	237	1	0	0	0	0	1	0	0	0	9661	962	34	4	1721	4	MMP15	16	58079023	Missense_Mutation	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10		58079023	32275730	54	14475											
CLEC18B	497190	hgsc.bcm.edu	37	chr16	74447559	74447559	+	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	cccacagcccagctggcttgAggtggcccacacgagctaca	9	5	11	16	1	0	1	0	1	0	0	0	2	0	1	3	3	4	3	3	3	1	2			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr16:74447559A>T	ENST00000339953.5	-	4	593	c.472T>A	c.(472-474)Tca>Aca	p.S158T		NM_001011880.2	NP_001011880.2	Q6UXF7	CL18B_HUMAN	C-type lectin domain family 18, member B	158	SCP.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			endometrium(3)|kidney(9)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						AGCTGGCTTGAGGTGGCCCAC	0.607																																					p.S158T		Atlas-SNP	.											.	CLEC18B	45	.	0			c.T472A						PASS	.						99	99	99					16																	74447559		2198	4298	6496	SO:0001583	missense	497190	exon4			GGCTTGAGGTGGC	AY358373	CCDS32484.1	16q22.3	2010-04-27	2009-03-10	2009-03-10		ENSG00000140839		"C-type lectin domain containing"	33849	protein-coding gene	gene with protein product							Standard	NM_001011880		Approved		uc002fct.3	Q6UXF7		ENST00000339953.5:c.472T>A	chr16.hg19:g.74447559A>T	ENSP00000341051:p.Ser158Thr	270.0	0.0	.		245.0	21.0	.	NM_001011880	B4DF90	Missense_Mutation	SNP	ENST00000339953.5	hg19	CCDS32484.1	.	.	.	.	.	.	.	.	.	.	a	14.17	2.454450	0.43634	.	.	ENSG00000140839	ENST00000429489;ENST00000339953;ENST00000268492;ENST00000425714	T	0.08807	3.05	3.1	3.1	0.35709	CAP domain (3);	0.000000	0.64402	D	0.000001	T	0.12390	0.0301	N	0.21545	0.675	0.42457	D	0.992777	D;P;D	0.63880	0.993;0.95;0.983	D;P;D	0.77557	0.99;0.871;0.928	T	0.22871	-1.0204	10	0.23891	T	0.37	.	7.6588	0.28392	1.0:0.0:0.0:0.0	.	78;158;158	Q6UXF7-2;C9JSV1;Q6UXF7	.;.;CL18B_HUMAN	T	158;158;158;78	ENSP00000341051:S158T	ENSP00000268492:S158T	S	-	1	0	CLEC18B	73005060	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	6.560000	0.73950	1.286000	0.44565	0.438000	0.28831	TCA	.	.	.	none		0.607	CLEC18B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434697.1	NM_001011880		T	74447559	A	T	74447559	3	4	237	1	0	0	0	0	1	0	0	0	3505	304	11	5	935	5	CLEC18B	16	74447559	Missense_Mutation	SNP	A	TCGA-PJ-A5Z8-01A-11D-A28G-10	16368536	74447559	15907194	55	14476											
DULLARD	23399	hgsc.bcm.edu	37	chr17	7147902	7147902	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcattgggagcaggttgagAagggctgtgtcgctggggtc	7	9	19	6	1	0	1	0	1	0	1	2	3	0	2	0	5	2	5	0	5	1	2			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr17:7147902A>G	ENST00000573600.1	-	8	1063	c.642T>C	c.(640-642)ctT>ctC	p.L214L	GABARAP_ENST00000573928.1_5'Flank|CTDNEP1_ENST00000572043.1_Silent_p.L81L|GABARAP_ENST00000571253.1_5'Flank|GABARAP_ENST00000571129.1_5'Flank|CTD-2545G14.7_ENST00000570760.2_Missense_Mutation_p.F18S|CTDNEP1_ENST00000318988.6_Silent_p.L214L|GABARAP_ENST00000302386.5_5'Flank|GABARAP_ENST00000577035.1_5'Flank|CTDNEP1_ENST00000574322.1_Silent_p.L214L			O95476	CNEP1_HUMAN	CTD nuclear envelope phosphatase 1	214	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.				gamete generation (GO:0007276)|mesoderm development (GO:0007498)|nuclear envelope organization (GO:0006998)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of triglyceride biosynthetic process (GO:0010867)|protein dephosphorylation (GO:0006470)|protein localization to nucleus (GO:0034504)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|Nem1-Spo7 phosphatase complex (GO:0071595)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)	protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(9)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	15						GCAGGTTGAGAAGGGCTGTGT	0.522																																					p.L214L		Atlas-SNP	.											.	CTDNEP1	26	.	0			c.T642C						PASS	.						70	67	68					17																	7147902		2203	4300	6503	SO:0001819	synonymous_variant	23399	exon7			GTTGAGAAGGGCT	AJ011916	CCDS11093.1	17p13	2012-11-27	2010-10-27	2010-10-27	ENSG00000175826	ENSG00000175826		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	19085	protein-coding gene	gene with protein product	"C-terminal domain nuclear envelope phosphatase 1"	610684	"dullard homolog (Xenopus laevis)"	DULLARD		12083771, 17141153	Standard	NM_015343		Approved	HSA011916, NET56	uc002gfd.2	O95476	OTTHUMG00000102180	ENST00000573600.1:c.642T>C	chr17.hg19:g.7147902A>G		63.0	0.0	.		58.0	18.0	.	NM_001143775	D3DTN7|Q96GQ9	Silent	SNP	ENST00000573600.1	hg19	CCDS11093.1																																																																																			.	.	.	none		0.522	CTDNEP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440215.1	NM_015343		G	7147902	A	G	7147902	2	3	237	1	0	0	0	0	0	0	0	1	4801	233	9	3		3	DULLARD	17	7147902	Silent	SNP	A	TCGA-PJ-A5Z8-01A-11D-A28G-10		7147902	74047308	56	14477											
CHD3	1107	hgsc.bcm.edu	37	chr17	7794342	7794342	+	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	tgttctctgaggaggattacCacacgctcaccaactacaaa	13	9	7	12	1	2	1	1	1	1	0	3	3	2	3	2	2	3	2	2	2	4	3			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr17:7794342C>G	ENST00000330494.7	+	4	619	c.469C>G	c.(469-471)Cac>Gac	p.H157D	CHD3_ENST00000380358.4_Missense_Mutation_p.H216D|CHD3_ENST00000358181.4_Missense_Mutation_p.H157D	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	157					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)				GGAGGATTACCACACGCTCAC	0.527																																					p.H216D		Atlas-SNP	.											.	CHD3	169	.	0			c.C646G						PASS	.						166	142	150					17																	7794342		2203	4300	6503	SO:0001583	missense	1107	exon4			GATTACCACACGC	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.469C>G	chr17.hg19:g.7794342C>G	ENSP00000332628:p.His157Asp	184.0	0.0	.		196.0	47.0	.	NM_001005271	D3DTQ9|E9PG89|Q9Y4I0	Missense_Mutation	SNP	ENST00000330494.7	hg19	CCDS32554.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.56|15.56	2.869301|2.869301	0.51588|0.51588	.|.	.|.	ENSG00000170004|ENSG00000170004	ENST00000380358;ENST00000358181;ENST00000330494|ENST00000452447	D;D;D|.	0.89746|.	-2.56;-2.49;-2.49|.	4.54|4.54	4.54|4.54	0.55810|0.55810	High mobility group, HMG1/HMG2 (1);CHD, N-terminal (1);|.	0.000000|.	0.48286|.	D|.	0.000185|.	T|T	0.46833|0.46833	0.1413|0.1413	N|N	0.11427|0.11427	0.14|0.14	0.46061|0.46061	D|D	0.998847|0.998847	P;P;P|.	0.42584|.	0.531;0.586;0.784|.	B;B;P|.	0.45753|.	0.275;0.396;0.492|.	T|T	0.43048|0.43048	-0.9415|-0.9415	10|5	0.33940|.	T|.	0.23|.	-20.7739|-20.7739	17.4864|17.4864	0.87689|0.87689	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	157;157;216|.	Q12873-2;Q12873;E9PG89|.	.;CHD3_HUMAN;.|.	D|R	216;157;157|31	ENSP00000369716:H216D;ENSP00000350907:H157D;ENSP00000332628:H157D|.	ENSP00000332628:H157D|.	H|P	+|+	1|2	0|0	CHD3|CHD3	7735067|7735067	0.997000|0.997000	0.39634|0.39634	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	3.592000|3.592000	0.53993|0.53993	2.349000|2.349000	0.79799|0.79799	0.557000|0.557000	0.71058|0.71058	CAC|CCA	.	.	.	none		0.527	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273		G	7794342	C	G	7794342	3	3	237	1	0	0	0	0	1	0	0	0	3328	594	21	4	764	4	CHD3	17	7794342	Missense_Mutation	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	646440	7794342	73400868	57	14478											
MYH3	4621	hgsc.bcm.edu	37	chr17	10558280	10558281	+	Frame_Shift_Del	DEL	GG	GG	-																															accacgaagcaatacgtcttGgcatcaaagggctggttctg																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr17:10558280_10558281delGG	ENST00000583535.1	-	3	188_189	c.101_102delCC	c.(100-102)gccfs	p.A34fs	MYH3_ENST00000226209.7_Frame_Shift_Del_p.A34fs	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	34					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						AATACGTCTTGGCATCAAAGGG	0.485																																					p.34_35del		Atlas-Indel,Pindel	.											.	MYH3	227	.	0			c.102_103del						PASS	.																																			SO:0001589	frameshift_variant	4621	exon3			.		CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"Myosins / Myosin superfamily : Class II"	7573	protein-coding gene	gene with protein product	"myosin, skeletal, heavy chain, embryonic 1", "muscle embryonic myosin heavy chain 3"	160720	"myosin, heavy polypeptide 3, skeletal muscle, embryonic"			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.101_102delCC	chr17.hg19:g.10558280_10558281delGG	ENSP00000464317:p.Ala34fs	150.0	0.0	0		164.0	38.0	0.231707	NM_002470	Q15492	Frame_Shift_Del	DEL	ENST00000583535.1	hg19	CCDS11157.1																																																																																			.	.	.	none		0.485	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470		-	10558281	GG	-	10558280	7	5	237	1	0	1	0	1	0	0	0	0	10043	1335	47	0	5876	0	MYH3	17	10558280	Frame_Shift_Del	DEL	GG	TCGA-PJ-A5Z8-01A-11D-A28G-10	2763938	10558280	70636930	58	14479											
SLC47A1	55244	hgsc.bcm.edu	37	chr17	19449787	19449787	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcagtgggattcggcttaTcttctgcctgtgacaccctc	5	14	9	13	1	3	1	1	1	3	0	6	2	3	2	2	2	1	1	2	2	1	3			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr17:19449787T>C	ENST00000270570.4	+	3	363	c.277T>C	c.(277-279)Tct>Cct	p.S93P	SLC47A1_ENST00000571335.1_5'UTR|SLC47A1_ENST00000584348.1_3'UTR|SLC47A1_ENST00000575023.1_Missense_Mutation_p.S93P|SLC47A1_ENST00000436810.2_Intron|SLC47A1_ENST00000542886.1_Missense_Mutation_p.S93P|SLC47A1_ENST00000395585.1_Missense_Mutation_p.S93P|SLC47A1_ENST00000457293.1_Missense_Mutation_p.S93P	NM_018242.2	NP_060712.2	Q96FL8	S47A1_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 1	93					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)	ATTCGGCTTATCTTCTGCCTG	0.453																																					p.S93P		Atlas-SNP	.											.	SLC47A1	55	.	0			c.T277C						PASS	.						201	160	174					17																	19449787		2203	4300	6503	SO:0001583	missense	55244	exon3			GGCTTATCTTCTG		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.277T>C	chr17.hg19:g.19449787T>C	ENSP00000270570:p.Ser93Pro	156.0	0.0	.		172.0	36.0	.	NM_018242	Q53HF5|Q6PD77|Q86VL4|Q9NVA3	Missense_Mutation	SNP	ENST00000270570.4	hg19	CCDS11209.1	.	.	.	.	.	.	.	.	.	.	T	15.29	2.790304	0.50102	.	.	ENSG00000142494	ENST00000270570;ENST00000457293;ENST00000542886;ENST00000395585	T;T;T;T	0.35605	1.3;1.3;1.3;1.3	5.32	4.17	0.49024	.	0.175212	0.49305	D	0.000151	T	0.65554	0.2702	M	0.91300	3.195	0.39743	D	0.971774	D;D;D	0.71674	0.998;0.984;0.957	D;D;P	0.76575	0.988;0.944;0.906	T	0.75167	-0.3413	10	0.72032	D	0.01	-17.7724	12.3905	0.55356	0.0:0.0:0.1831:0.8169	.	93;93;93	B4DYV3;Q96FL8;Q96FL8-3	.;S47A1_HUMAN;.	P	93	ENSP00000270570:S93P;ENSP00000415586:S93P;ENSP00000440435:S93P;ENSP00000378951:S93P	ENSP00000270570:S93P	S	+	1	0	SLC47A1	19390379	0.016000	0.18221	1.000000	0.80357	0.472000	0.32918	0.078000	0.14761	2.027000	0.59764	0.454000	0.30748	TCT	.	.	.	none		0.453	SLC47A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132250.1	NM_018242		C	19449787	T	C	19449787	3	2	237	1	0	0	0	0	1	0	0	0	14660	1435	50	3	287	3	SLC47A1	17	19449787	Missense_Mutation	SNP	T	TCGA-PJ-A5Z8-01A-11D-A28G-10	8891507	19449787	61745423	59	14480											
LRRC37A3	374819	hgsc.bcm.edu	37	chr17	62855782	62855782	+	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	aaggtccggataacatgagcAatgagccttctcacattgtt	12	11	9	9	1	1	2	1	2	1	0	3	3	2	3	2	2	3	2	2	2	3	4			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr17:62855782A>T	ENST00000584306.1	-	11	5012	c.4482T>A	c.(4480-4482)atT>atA	p.I1494I	LRRC37A3_ENST00000334962.5_Silent_p.I471I|LRRC37A3_ENST00000319651.5_Silent_p.I1494I|LRRC37A3_ENST00000339474.5_Silent_p.I612I|LRRC37A3_ENST00000400877.3_Silent_p.I532I	NM_199340.2	NP_955372.2	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3	1494						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						TAACATGAGCAATGAGCCTTC	0.522																																					p.I1494I		Atlas-SNP	.											.	LRRC37A3	75	.	0			c.T4482A						PASS	.						186	189	188					17																	62855782		2203	4300	6503	SO:0001819	synonymous_variant	374819	exon11			ATGAGCAATGAGC	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.4482T>A	chr17.hg19:g.62855782A>T		440.0	0.0	.		433.0	90.0	.	NM_199340	Q49A01|Q49A80|Q8NB33	Silent	SNP	ENST00000584306.1	hg19	CCDS32708.1																																																																																			.	.	.	none		0.522	LRRC37A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445377.1	NM_199340		T	62855782	A	T	62855782	2	4	237	1	0	0	0	0	0	0	0	1	9000	126	5	5		5	LRRC37A3	17	62855782	Silent	SNP	A	TCGA-PJ-A5Z8-01A-11D-A28G-10	43405995	62855782	18339428	60	14481											
MC5R	4161	hgsc.bcm.edu	37	chr18	13826448	13826448	+	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	ctgcccggggccagctctgcGcggcagaggaccagcatgca	7	4	15	15	3	1	1	0	0	1	1	1	2	1	2	3	4	5	4	3	4	0	0			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr18:13826448G>A	ENST00000324750.3	+	1	906	c.684G>A	c.(682-684)gcG>gcA	p.A228A	AP001525.1_ENST00000390194.2_RNA	NM_005913.2	NP_005904.1	P33032	MC5R_HUMAN	melanocortin 5 receptor	228				ALPGASSARQRTSM -> LCPGPALRGRGPAW (in Ref. 1). {ECO:0000305}.	G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hormone binding (GO:0042562)|melanocortin receptor activity (GO:0004977)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(23)|ovary(4)|upper_aerodigestive_tract(1)	41						CCAGCTCTGCGCGGCAGAGGA	0.617																																					p.A228A		Atlas-SNP	.											MC5R,NS,carcinoma,0,1	MC5R	83	.	0			c.G684A						PASS	.						210	180	190					18																	13826448		2203	4300	6503	SO:0001819	synonymous_variant	4161	exon1			CTCTGCGCGGCAG	AY268429	CCDS11868.1	18p11.2	2012-08-10			ENSG00000176136	ENSG00000176136		"GPCR / Class A : Melanocortin receptors"	6933	protein-coding gene	gene with protein product		600042				8396929	Standard	NM_005913		Approved		uc010xaf.2	P33032	OTTHUMG00000131720	ENST00000324750.3:c.684G>A	chr18.hg19:g.13826448G>A		45.0	1.0	.		125.0	28.0	.	NM_005913	B0YJ34|Q502V1	Silent	SNP	ENST00000324750.3	hg19	CCDS11868.1																																																																																			.	.	.	none		0.617	MC5R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254638.1	NM_005913		A	13826448	G	A	13826448	2	1	237	1	0	0	0	0	0	0	0	1	9374	1074	38	1		1	MC5R	18	13826448	Silent	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10		13826448	64250800	61	14482											
LAMA3	3909	hgsc.bcm.edu	37	chr18	21508155	21508158	+	Frame_Shift_Del	DEL	GATT	GATT	-																															gaaaaccagtggtgtcgttaGattgaatgatactgtgggag																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	GATT	GATT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr18:21508155_21508158delGATT	ENST00000313654.9	+	63	8487_8490	c.8246_8249delGATT	c.(8245-8250)agattgfs	p.RL2749fs	LAMA3_ENST00000587184.1_Frame_Shift_Del_p.RL1084fs|LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000269217.6_Frame_Shift_Del_p.RL1140fs|LAMA3_ENST00000399516.3_Frame_Shift_Del_p.RL2693fs	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2749	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)					GGTGTCGTTAGATTGAATGATACT	0.436																																					p.2749_2750del		Atlas-Indel,Pindel	.											.	LAMA3	397	.	0			c.8245_8248del						PASS	.																																			SO:0001589	frameshift_variant	3909	exon63			.	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.8246_8249delGATT	chr18.hg19:g.21508155_21508158delGATT	ENSP00000324532:p.Arg2749fs	215.0	0.0	0		208.0	41.0	0.197115	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Frame_Shift_Del	DEL	ENST00000313654.9	hg19	CCDS42419.1																																																																																			.	.	.	none		0.436	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		-	21508158	GATT	-	21508155	7	5	237	1	0	1	0	1	0	0	0	0	8614	942	33	0	8671	0	LAMA3	18	21508155	Frame_Shift_Del	DEL	GATT	TCGA-PJ-A5Z8-01A-11D-A28G-10	7681707	21508155	56569093	62	14483											
ZNF780A	284323	hgsc.bcm.edu	37	chr19	40578806	40578806	+	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	0	0	0	0	0	0	0	0	tacactaaagagagataaccAaatgcaatgcagattctgca	18	8	7	8	0	1	3	0	0	1	3	1	4	1	3	1	0	5	3	1	0	6	4	rs528950544		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr19:40578806A>T	ENST00000595687.2	-	0	3472				ZNF780A_ENST00000414720.2_Missense_Mutation_p.F145L|AC005614.5_ENST00000595508.1_RNA|ZNF780A_ENST00000450241.2_3'UTR	NM_001010880.2	NP_001010880.2	O75290	Z780A_HUMAN	zinc finger protein 780A						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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)					agagataaccaaatgcaatgc	0.353																																					p.F145L		Atlas-SNP	.											.	ZNF780A	156	.	0			c.T435A						PASS	.						112	98	103					19																	40578806		692	1591	2283	SO:0001628	intergenic_variant	284323	exon8			ATAACCAAATGCA	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		chr19.hg19:g.40578806A>T		69.0	0.0	.		59.0	4.0	.	NM_001142579	E9PB48|Q6ZN87	Missense_Mutation	SNP	ENST00000595687.2	hg19	CCDS33026.2	.	.	.	.	.	.	.	.	.	.	A	11.53	1.666731	0.29604	.	.	ENSG00000197782	ENST00000414720	T	0.00620	6.17	0.516	0.516	0.17019	.	.	.	.	.	T	0.00998	0.0033	.	.	.	0.21256	N	0.999747	P	0.46395	0.877	P	0.51866	0.682	T	0.55341	-0.8156	7	0.25751	T	0.34	.	.	.	.	.	145	O75290-2	.	L	145	ENSP00000416294:F145L	ENSP00000416294:F145L	F	-	3	2	ZNF780A	45270646	0.004000	0.15560	0.096000	0.21009	0.182000	0.23217	0.148000	0.16224	0.452000	0.26830	0.254000	0.18369	TTT	.	.	.	none		0.353	ZNF780A-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000470066.1	NM_001010880		T	40578806	A	T	40578806	1	4	237	0	1	0	0	0	0	0	0	0	18164	127	5	5		5	ZNF780A	19	40578806	IGR	SNP	A	TCGA-PJ-A5Z8-01A-11D-A28G-10		40578806	18550177	63	14484											
PRR19	284338	hgsc.bcm.edu	37	chr19	42814045	42814045	+	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	ccaggcagccccacactcccCgccaagccctccccaagccc	8	2	6	25	1	0	0	0	0	0	0	2	0	2	0	10	1	3	1	10	1	2	0	rs78424339		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr19:42814045C>A	ENST00000499536.2	+	1	1120	c.309C>A	c.(307-309)ccC>ccA	p.P103P	PRR19_ENST00000341747.3_Silent_p.P103P|PRR19_ENST00000598490.1_Silent_p.P103P			A6NJB7	PRR19_HUMAN	proline rich 19	103										NS(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	10		Prostate(69;0.00682)				CCACACTCCCCGCCAAGCCCT	0.667																																					p.P103P		Atlas-SNP	.											PRR19,NS,carcinoma,0,1	PRR19	30	.	0			c.C309A						PASS	.						40	51	47					19																	42814045		2203	4300	6503	SO:0001819	synonymous_variant	284338	exon2			ACTCCCCGCCAAG	AK124116	CCDS33036.1	19q13.2	2007-12-17				ENSG00000188368			33728	protein-coding gene	gene with protein product							Standard	NM_199285		Approved	MGC70924	uc002oti.3	A6NJB7		ENST00000499536.2:c.309C>A	chr19.hg19:g.42814045C>A		40.0	1.0	.		61.0	3.0	.	NM_199285	A8K663|B3KW48|Q6P584	Silent	SNP	ENST00000499536.2	hg19	CCDS33036.1																																																																																			.	C|0.500;T|0.500	.	alt		0.667	PRR19-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463735.1	NM_199285		A	42814045	C	A	42814045	2	1	237	1	0	0	0	0	0	0	0	1	12601	639	23	4		4	PRR19	19	42814045	Silent	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10	2235239	42814045	16314938	64	14485											
TRPC4AP	26133	hgsc.bcm.edu	37	chr20	33603843	33603844	+	Frame_Shift_Ins	INS	-	-	AA																															cagttctggttgtgaccatgINSgaggacaagggcagatgctg																										TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr20:33603843_33603844insAA	ENST00000252015.2	-	10	1406_1407	c.1317_1318insTT	c.(1315-1320)ctccatfs	p.H440fs	TRPC4AP_ENST00000451813.2_Frame_Shift_Ins_p.H432fs|TRPC4AP_ENST00000432634.2_Frame_Shift_Ins_p.H401fs|TRPC4AP_ENST00000539834.1_Frame_Shift_Ins_p.H42fs			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein	440					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)			TTGTGACCATGGAGGACAAGGG	0.5																																					p.H440fs		Atlas-Indel,Pindel	.											.	TRPC4AP	64	.	0			c.1318_1319insTT						PASS	.																																			SO:0001589	frameshift_variant	26133	exon10			.	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.1317_1318insTT	chr20.hg19:g.33603843_33603844insAA	ENSP00000252015:p.His440fs	135.0	0.0	0		143.0	32.0	0.223776	NM_015638	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Frame_Shift_Ins	INS	ENST00000252015.2	hg19	CCDS13246.1																																																																																			.	.	.	none		0.5	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638		AA	33603844	-	AA	33603843	7	5	237	1	0	1	1	0	0	0	0	0	16593	1348	47	0	1115	0	TRPC4AP	20	33603843	Frame_Shift_Ins	INS	-	TCGA-PJ-A5Z8-01A-11D-A28G-10		33603843	29421677	65	14486											
DLGAP4	22839	hgsc.bcm.edu	37	chr20	35064566	35064566	+	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	tgctgtccccacgcgagacgGatgccgcggccgagggccct	5	5	15	16	6	0	1	0	0	0	1	1	4	1	2	5	3	2	1	5	3	0	0	rs199988815		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr20:35064566G>A	ENST00000373907.2	+	3	1253	c.1054G>A	c.(1054-1056)Gat>Aat	p.D352N	DLGAP4_ENST00000401952.2_Missense_Mutation_p.D352N|DLGAP4_ENST00000339266.5_Missense_Mutation_p.D352N|DLGAP4_ENST00000373913.3_Missense_Mutation_p.D352N			Q9Y2H0	DLGP4_HUMAN	discs, large (Drosophila) homolog-associated protein 4	352					cell-cell signaling (GO:0007267)	membrane (GO:0016020)|synapse (GO:0045202)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(20)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	37	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				ACGCGAGACGGATGCCGCGGC	0.721																																					p.D352N		Atlas-SNP	.											.	DLGAP4	111	.	0			c.G1054A						PASS	.	G	ASN/ASP	0,4334		0,0,2167	9	11	10		1054	4.2	0.2	20		10	2,8418		0,2,4208	no	missense	DLGAP4	NM_014902.4	23	0,2,6375	AA,AG,GG		0.0238,0.0,0.0157	benign	352/990	35064566	2,12752	2167	4210	6377	SO:0001583	missense	22839	exon3			GAGACGGATGCCG	AF088030	CCDS13274.1, CCDS13275.1	20q11.23	2010-02-05			ENSG00000080845	ENSG00000080845			24476	protein-coding gene	gene with protein product						9115257	Standard	XM_005260329		Approved	DAP4, KIAA0964, SAPAP4	uc010zvp.2	Q9Y2H0	OTTHUMG00000032390	ENST00000373907.2:c.1054G>A	chr20.hg19:g.35064566G>A	ENSP00000363014:p.Asp352Asn	1.0	0.0	.		34.0	21.0	.	NM_014902	E1P5T5|Q5QPG4|Q5T2Y4|Q5T2Y5|Q9H137|Q9H138|Q9H1L7	Missense_Mutation	SNP	ENST00000373907.2	hg19		.	.	.	.	.	.	.	.	.	.	G	15.46	2.840492	0.51057	0.0	2.38E-4	ENSG00000080845	ENST00000373913;ENST00000401952;ENST00000373907;ENST00000339266	T;T;T;T	0.13538	2.58;2.58;2.58;2.58	4.22	4.22	0.49857	.	1.057480	0.07332	N	0.879344	T	0.12178	0.0296	N	0.22421	0.69	0.09310	N	1	B	0.19200	0.034	B	0.18871	0.023	T	0.22591	-1.0212	10	0.27082	T	0.32	.	13.7551	0.62933	0.0:0.0:1.0:0.0	.	352	Q9Y2H0-1	.	N	352	ENSP00000363023:D352N;ENSP00000384954:D352N;ENSP00000363014:D352N;ENSP00000341633:D352N	ENSP00000341633:D352N	D	+	1	0	DLGAP4	34497980	0.998000	0.40836	0.243000	0.24186	0.629000	0.37895	3.978000	0.56881	1.913000	0.55393	0.555000	0.69702	GAT	.	.	.	weak		0.721	DLGAP4-007	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000079025.2	NM_014902		A	35064566	G	A	35064566	3	1	237	1	0	0	0	0	1	0	0	0	4564	1174	41	2	1060	2	DLGAP4	20	35064566	Missense_Mutation	SNP	G	TCGA-PJ-A5Z8-01A-11D-A28G-10	1460723	35064566	27960954	66	14487											
PRDM15	63977	hgsc.bcm.edu	37	chr21	43241557	43241557	+	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	tgcacctccatgatgtgcttCaggtactccttcccccggcc	5	11	8	17	1	1	1	1	1	0	0	4	1	4	1	6	2	3	3	6	2	1	3			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr21:43241557C>T	ENST00000269844.3	-	23	3134	c.3024G>A	c.(3022-3024)ctG>ctA	p.L1008L	PRDM15_ENST00000398548.1_Silent_p.L679L|PRDM15_ENST00000538201.1_Silent_p.L662L|PRDM15_ENST00000447207.2_Silent_p.L642L|PRDM15_ENST00000422911.1_Silent_p.L699L	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	1008					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						TGATGTGCTTCAGGTACTCCT	0.612																																					p.L1008L		Atlas-SNP	.											PRDM15,NS,carcinoma,0,1	PRDM15	110	.	0			c.G3024A						PASS	.						171	113	132					21																	43241557		2203	4300	6503	SO:0001819	synonymous_variant	63977	exon23			GTGCTTCAGGTAC	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.3024G>A	chr21.hg19:g.43241557C>T		115.0	0.0	.		105.0	24.0	.	NM_022115	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Silent	SNP	ENST00000269844.3	hg19	CCDS13676.1																																																																																			.	.	.	none		0.612	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115		T	43241557	C	T	43241557	2	4	237	1	0	0	0	0	0	0	0	1	12466	813	29	2		2	PRDM15	21	43241557	Silent	SNP	C	TCGA-PJ-A5Z8-01A-11D-A28G-10		43241557	4888338	67	14488											
PLXNB2	23654	hgsc.bcm.edu	37	chr22	50716444	50716444	+	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	caaactgctgcagtgtgcccTgtgggggggagggtctcagc	6	8	17	10	0	1	0	1	0	1	0	2	1	1	1	1	4	5	2	1	4	1	0			TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	g.chr22:50716444T>C	ENST00000449103.1	-	32	5028		c.e32-2		PLXNB2_ENST00000359337.4_Splice_Site			O15031	PLXB2_HUMAN	plexin B2						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)		CAGTGTGCCCTGTGGGGGGGA	0.682																																					.		Atlas-SNP	.											.	PLXNB2	172	.	0			c.4888-2A>G						PASS	.						32	37	35					22																	50716444		2093	4223	6316	SO:0001630	splice_region_variant	23654	exon33			GTGCCCTGTGGGG		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.4888-2A>G	chr22.hg19:g.50716444T>C		97.0	0.0	.		124.0	17.0	.	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Splice_Site	SNP	ENST00000449103.1	hg19	CCDS43035.1	.	.	.	.	.	.	.	.	.	.	T	15.43	2.831563	0.50845	.	.	ENSG00000196576	ENST00000449103;ENST00000359337;ENST00000399991;ENST00000399964;ENST00000411680	.	.	.	4.08	4.08	0.47627	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.4923	0.61402	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PLXNB2	49058571	1.000000	0.71417	0.983000	0.44433	0.517000	0.34286	7.524000	0.81866	1.827000	0.53221	0.402000	0.26972	.	.	.	.	none		0.682	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	Intron	C	50716444	T	C	50716444	5	2	237	1	0	0	0	0	0	0	1	0	12131	1594	55	3	654	3	PLXNB2	22	50716444	Splice_Site	SNP	T	TCGA-PJ-A5Z8-01A-11D-A28G-10		50716444	588122	68	14489											
TEKT2	27285	hgsc.bcm.edu	37	chr1	36552574	36552574	+	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	gatgacttcagtcggttcaaCaaggaccgagcggaggctga	11	7	14	9	3	2	2	2	2	0	0	3	6	2	4	1	4	2	2	1	4	2	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:36552574C>T	ENST00000207457.3	+	6	802	c.675C>T	c.(673-675)aaC>aaT	p.N225N	ADPRHL2_ENST00000373178.4_5'Flank	NM_014466.2	NP_055281.2	Q9UIF3	TEKT2_HUMAN	tektin 2 (testicular)	225					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)				GTCGGTTCAACAAGGACCGAG	0.592																																					p.N225N		Atlas-SNP	.											.	TEKT2	32	.	0			c.C675T						PASS	.						58	54	55					1																	36552574		2203	4300	6503	SO:0001819	synonymous_variant	27285	exon6			GTTCAACAAGGAC	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.675C>T	chr1.hg19:g.36552574C>T		65.0	0.0	.		47.0	17.0	.	NM_014466	A6NIS6|O60638	Silent	SNP	ENST00000207457.3	hg19	CCDS401.1																																																																																			.	.	.	none		0.592	TEKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020200.1	NM_014466		T	36552574	C	T	36552574	2	4	238	1	0	0	0	0	0	0	0	1	15765	477	17	2		2	TEKT2	1	36552574	Silent	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10		36552574	212698047	1	14490											
SLC35D1	23169	hgsc.bcm.edu	37	chr1	67519574	67519574	+	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	aagccggcggccagcagcttCagaaacacggtcagcgtttc	10	6	12	13	4	2	1	2	0	0	1	3	1	2	1	2	3	5	3	2	3	2	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:67519574C>A	ENST00000235345.5	-	1	208	c.123G>T	c.(121-123)ctG>ctT	p.L41L	SLC35D1_ENST00000506472.2_5'Flank	NM_015139.2	NP_055954.1	Q9NTN3	S35D1_HUMAN	solute carrier family 35 (UDP-GlcA/UDP-GalNAc transporter), member D1	41					carbohydrate transport (GO:0008643)|cellular glucuronidation (GO:0052695)|chondroitin sulfate biosynthetic process (GO:0030206)|embryonic skeletal system development (GO:0048706)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|UDP-glucuronate biosynthetic process (GO:0006065)|UDP-glucuronic acid transport (GO:0015787)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	UDP-glucuronic acid transmembrane transporter activity (GO:0005461)			endometrium(2)|kidney(1)|large_intestine(3)|lung(4)	10						CCAGCAGCTTCAGAAACACGG	0.612																																					p.L41L		Atlas-SNP	.											.	SLC35D1	22	.	0			c.G123T						PASS	.						47	50	49					1																	67519574		2203	4300	6503	SO:0001819	synonymous_variant	23169	exon1			CAGCTTCAGAAAC	AB044343	CCDS636.1	1p32-p31	2013-07-17	2013-07-17		ENSG00000116704	ENSG00000116704		"Solute carriers"	20800	protein-coding gene	gene with protein product		610804	"solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1"			11322953	Standard	NM_015139		Approved	UGTREL7, KIAA0260	uc001ddk.2	Q9NTN3	OTTHUMG00000009360	ENST00000235345.5:c.123G>T	chr1.hg19:g.67519574C>A		194.0	0.0	.		115.0	35.0	.	NM_015139	A8K185|B7Z3X2|Q52LU5|Q92548	Silent	SNP	ENST00000235345.5	hg19	CCDS636.1																																																																																			.	.	.	none		0.612	SLC35D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025948.1	NM_015139		A	67519574	C	A	67519574	2	1	238	1	0	0	0	0	0	0	0	1	14594	813	29	4		4	SLC35D1	1	67519574	Silent	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	30967000	67519574	181731047	2	14491											
C1orf173	127254	hgsc.bcm.edu	37	chr1	75037280	75037280	+	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	aaaggaggaggctttatttgCtattgttttctcctcggctg	7	16	11	7	1	1	0	0	0	1	0	3	2	1	2	1	4	1	4	1	4	3	7			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:75037280C>A	ENST00000326665.5	-	14	4332	c.4114G>T	c.(4114-4116)Gca>Tca	p.A1372S	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		1372	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						GCTTTATTTGCTATTGTTTTC	0.522																																					p.A1372S		Atlas-SNP	.											.	C1orf173	380	.	0			c.G4114T						PASS	.						130	133	132					1																	75037280		2203	4300	6503	SO:0001583	missense	127254	exon14			TATTTGCTATTGT																												ENST00000326665.5:c.4114G>T	chr1.hg19:g.75037280C>A	ENSP00000322609:p.Ala1372Ser	149.0	0.0	.		97.0	37.0	.	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	hg19	CCDS30755.1	.	.	.	.	.	.	.	.	.	.	C	8.132	0.783370	0.16189	.	.	ENSG00000178965	ENST00000326665	T	0.14516	2.5	5.0	3.1	0.35709	.	.	.	.	.	T	0.02688	0.0081	N	0.24115	0.695	0.09310	N	1	B	0.15473	0.013	B	0.16289	0.015	T	0.45789	-0.9237	9	0.18710	T	0.47	-4.6121	10.2042	0.43103	0.0:0.7597:0.0:0.2403	.	1372	Q5RHP9	CA173_HUMAN	S	1372	ENSP00000322609:A1372S	ENSP00000322609:A1372S	A	-	1	0	C1orf173	74809868	0.148000	0.22702	0.009000	0.14445	0.260000	0.26232	0.903000	0.28475	0.528000	0.28580	-1.134000	0.01955	GCA	.	.	.	none		0.522	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			A	75037280	C	A	75037280	3	1	238	1	0	0	0	0	1	0	0	0	2016	797	28	4	482	4	C1orf173	1	75037280	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	7517706	75037280	174213341	3	14492											
ABCA4	24	hgsc.bcm.edu	37	chr1	94546179	94546179	+	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	ccacacaggaggtcagacagGatgcccatcagctttgtaaa	13	7	10	11	0	2	1	2	0	0	1	2	3	2	3	2	3	2	2	2	3	2	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:94546179G>A	ENST00000370225.3	-	8	1040	c.954C>T	c.(952-954)atC>atT	p.I318I	ABCA4_ENST00000535735.1_Silent_p.I318I	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	318					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)		GGTCAGACAGGATGCCCATCA	0.542																																					p.I318I		Atlas-SNP	.											.	ABCA4	275	.	0			c.C954T						PASS	.						99	91	94					1																	94546179		2203	4300	6503	SO:0001819	synonymous_variant	24	exon8			AGACAGGATGCCC	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.954C>T	chr1.hg19:g.94546179G>A		138.0	0.0	.		97.0	30.0	.	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	hg19	CCDS747.1																																																																																			.	.	.	none		0.542	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		A	94546179	G	A	94546179	2	1	238	1	0	0	0	0	0	0	0	1	34	1164	41	2		2	ABCA4	1	94546179	Silent	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	19508899	94546179	154704442	4	14493											
SLC30A7	148867	hgsc.bcm.edu	37	chr1	101387350	101387350	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaaattttggtctgatgatAgcagatcctatctgttcaat	12	15	7	7	0	3	3	1	2	2	1	4	3	4	3	1	1	1	2	1	1	5	5			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:101387350A>G	ENST00000370112.4	+	8	982	c.795A>G	c.(793-795)atA>atG	p.I265M	SLC30A7_ENST00000357650.4_Missense_Mutation_p.I265M	NM_001144884.1|NM_133496.4	NP_001138356.1|NP_598003.2	Q8NEW0	ZNT7_HUMAN	solute carrier family 30 (zinc transporter), member 7	265					cellular protein metabolic process (GO:0044267)|sequestering of zinc ion (GO:0032119)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	cation transmembrane transporter activity (GO:0008324)			endometrium(3)|large_intestine(2)|lung(10)	15		all_epithelial(167;0.000445)|all_lung(203;0.00645)|Lung NSC(277;0.0119)		Epithelial(280;0.0437)|all cancers(265;0.0498)|COAD - Colon adenocarcinoma(174;0.162)|Colorectal(144;0.19)|Lung(183;0.201)		GTCTGATGATAGCAGATCCTA	0.328																																					p.I265M	NSCLC(91;473 1491 3102 16827 21633)	Atlas-SNP	.											.	SLC30A7	33	.	0			c.A795G						PASS	.						166	157	160					1																	101387350		2202	4299	6501	SO:0001583	missense	148867	exon8			GATGATAGCAGAT	AF233345	CCDS776.1	1p21.1	2013-05-22			ENSG00000162695	ENSG00000162695		"Solute carriers"	19306	protein-coding gene	gene with protein product		611149				12446736	Standard	NM_133496		Approved	ZnTL2, ZNT7	uc001dto.2	Q8NEW0	OTTHUMG00000011815	ENST00000370112.4:c.795A>G	chr1.hg19:g.101387350A>G	ENSP00000359130:p.Ile265Met	59.0	0.0	.		31.0	11.0	.	NM_133496	B2R949|D3DT61|Q8TCH2	Missense_Mutation	SNP	ENST00000370112.4	hg19	CCDS776.1	.	.	.	.	.	.	.	.	.	.	A	18.12	3.552196	0.65311	.	.	ENSG00000162695	ENST00000370112;ENST00000357650	T;T	0.64803	-0.12;-0.12	5.62	4.46	0.54185	.	0.000000	0.85682	D	0.000000	T	0.69477	0.3115	M	0.83692	2.655	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	T	0.72232	-0.4353	10	0.48119	T	0.1	-9.0402	7.9394	0.29950	0.721:0.1427:0.0:0.1363	.	265	Q8NEW0	ZNT7_HUMAN	M	265	ENSP00000359130:I265M;ENSP00000350278:I265M	ENSP00000350278:I265M	I	+	3	3	SLC30A7	101159938	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.388000	0.34442	0.920000	0.36970	0.533000	0.62120	ATA	.	.	.	none		0.328	SLC30A7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032711.1	NM_133496		G	101387350	A	G	101387350	3	3	238	1	0	0	0	0	1	0	0	0	14573	410	15	3	825	3	SLC30A7	1	101387350	Missense_Mutation	SNP	A	TCGA-PJ-A5Z9-01A-11D-A28G-10	6841171	101387350	147863271	5	14494											
HMCN1	83872	hgsc.bcm.edu	37	chr1	186043967	186043967	+	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	agacaccggacgatatacttGtgtagcatctaacattgcag	13	10	9	9	2	1	1	0	0	1	1	1	3	1	2	1	1	4	3	1	1	4	6	rs561957484		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:186043967G>T	ENST00000271588.4	+	53	8463	c.8234G>T	c.(8233-8235)tGt>tTt	p.C2745F	HMCN1_ENST00000367492.2_Missense_Mutation_p.C2745F	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2745	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						CGATATACTTGTGTAGCATCT	0.348																																					p.C2745F		Atlas-SNP	.											.	HMCN1	797	.	0			c.G8234T						PASS	.						130	129	129					1																	186043967		2203	4300	6503	SO:0001583	missense	83872	exon53			ATACTTGTGTAGC	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.8234G>T	chr1.hg19:g.186043967G>T	ENSP00000271588:p.Cys2745Phe	104.0	0.0	.		97.0	4.0	.	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.610506	0.87258	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	D;D	0.89050	-2.46;-2.46	5.47	5.47	0.80525	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.97259	0.9104	H	0.99273	4.495	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.98221	1.0478	10	0.52906	T	0.07	.	19.3239	0.94253	0.0:0.0:1.0:0.0	.	2745	Q96RW7	HMCN1_HUMAN	F	2745	ENSP00000271588:C2745F;ENSP00000356462:C2745F	ENSP00000271588:C2745F	C	+	2	0	HMCN1	184310590	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	9.864000	0.99589	2.558000	0.86282	0.491000	0.48974	TGT	.	.	.	none		0.348	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		T	186043967	G	T	186043967	3	4	238	1	0	0	0	0	1	0	0	0	7227	1377	48	4	8444	4	HMCN1	1	186043967	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	84656617	186043967	63206654	6	14495											
MIA3	375056	hgsc.bcm.edu	37	chr1	222803477	222803477	+	Frame_Shift_Del	DEL	A	A	-																															gagcctgccctataatatggAaaaagtcctagataaggtct																										TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:222803477delA	ENST00000344922.5	+	4	2940	c.2915delA	c.(2914-2916)gaafs	p.E972fs	MIA3_ENST00000344441.6_Frame_Shift_Del_p.E972fs|MIA3_ENST00000344507.1_Intron|MIA3_ENST00000470521.1_3'UTR	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	972					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)		p.V974fs*4(1)		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)		TATAATATGGAAAAAGTCCTA	0.428																																					p.E972fs		Atlas-Indel,Pindel	.											.,1	MIA3	167	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.2914delG						PASS	.						74	72	73					1																	222803477		1967	4169	6136	SO:0001589	frameshift_variant	375056	exon4			.		CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"C219 reactive peptide", "transport and golgi organization"	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.2915delA	chr1.hg19:g.222803477delA	ENSP00000340900:p.Glu972fs	76.0	0.0	0		73.0	32.0	0.438356	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Frame_Shift_Del	DEL	ENST00000344922.5	hg19	CCDS41470.1																																																																																			.	.	.	none		0.428	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551		-	222803477	A	-	222803477	7	5	238	1	0	1	0	1	0	0	0	0	9572	246	9	0	2929	0	MIA3	1	222803477	Frame_Shift_Del	DEL	A	TCGA-PJ-A5Z9-01A-11D-A28G-10	36759510	222803477	26447144	7	14496											
IRF2BP2	359948	hgsc.bcm.edu	37	chr1	234743060	234743060	+	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	tgtctggagcaagggaagcaGaacttgtgcgaagggacgga	12	6	17	6	2	1	1	0	0	1	1	1	6	1	5	0	4	4	2	0	4	4	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:234743060G>A	ENST00000366609.3	-	2	1617	c.1587C>T	c.(1585-1587)ttC>ttT	p.F529F	RP4-781K5.2_ENST00000436039.1_RNA|IRF2BP2_ENST00000366610.3_Silent_p.F513F|IRF2BP2_ENST00000491430.1_5'UTR	NM_182972.2	NP_892017.2	Q7Z5L9	I2BP2_HUMAN	interferon regulatory factor 2 binding protein 2	529	Cys-rich.				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)			AAGGGAAGCAGAACTTGTGCG	0.587																																					p.F529F		Atlas-SNP	.											.	IRF2BP2	37	.	0			c.C1587T						PASS	.						81	87	85					1																	234743060		2203	4300	6503	SO:0001819	synonymous_variant	359948	exon2			GAAGCAGAACTTG	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.1587C>T	chr1.hg19:g.234743060G>A		99.0	0.0	.		99.0	38.0	.	NM_182972	B1AM35|B1AM36|Q6P083|Q7Z5L8|Q8N351|Q8WUH8	Silent	SNP	ENST00000366609.3	hg19	CCDS1602.1																																																																																			.	.	.	none		0.587	IRF2BP2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000092705.1	NM_182972		A	234743060	G	A	234743060	2	1	238	1	0	0	0	0	0	0	0	1	7837	933	33	2		2	IRF2BP2	1	234743060	Silent	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	11939583	234743060	14507561	8	14497											
GRB14	2888	hgsc.bcm.edu	37	chr2	165477654	165477654	+	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	tgcagcacagccgcgggtccCgtccggaaggggcaggagcg	7	3	18	13	5	0	0	0	0	0	0	2	2	2	2	3	5	4	3	3	5	1	0			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr2:165477654C>G	ENST00000263915.3	-	1	704	c.166G>C	c.(166-168)Ggg>Cgg	p.G56R		NM_004490.2	NP_004481.2	Q14449	GRB14_HUMAN	growth factor receptor-bound protein 14	56					blood coagulation (GO:0007596)|leukocyte migration (GO:0050900)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(2)|large_intestine(6)|lung(10)|ovary(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32						CCGCGGGTCCCGTCCGGAAGG	0.771																																					p.G56R		Atlas-SNP	.											.	GRB14	73	.	0			c.G166C						PASS	.						2	3	3					2																	165477654		1387	3094	4481	SO:0001583	missense	2888	exon1			GGGTCCCGTCCGG		CCDS2222.1	2q22-q24	2013-02-14			ENSG00000115290	ENSG00000115290		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	4565	protein-coding gene	gene with protein product		601524				8812444	Standard	XM_005246477		Approved		uc002ucl.3	Q14449	OTTHUMG00000132135	ENST00000263915.3:c.166G>C	chr2.hg19:g.165477654C>G	ENSP00000263915:p.Gly56Arg	2.0	0.0	.		53.0	30.0	.	NM_004490	B7Z7F9|Q7Z6I1	Missense_Mutation	SNP	ENST00000263915.3	hg19	CCDS2222.1	.	.	.	.	.	.	.	.	.	.	C	14.78	2.638721	0.47153	.	.	ENSG00000115290	ENST00000263915	T	0.23552	1.9	3.52	3.52	0.40303	.	0.650759	0.12693	N	0.447067	T	0.14570	0.0352	N	0.08118	0	0.80722	D	1	B	0.28055	0.199	B	0.28139	0.086	T	0.10660	-1.0620	10	0.66056	D	0.02	-0.5305	10.4807	0.44691	0.0:1.0:0.0:0.0	.	56	Q14449	GRB14_HUMAN	R	56	ENSP00000263915:G56R	ENSP00000263915:G56R	G	-	1	0	GRB14	165185900	0.128000	0.22383	0.967000	0.41034	0.993000	0.82548	1.792000	0.38754	1.822000	0.53115	0.585000	0.79938	GGG	.	.	.	none		0.771	GRB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255180.2			G	165477654	C	G	165477654	3	3	238	1	0	0	0	0	1	0	0	0	6764	652	23	4	1512	4	GRB14	2	165477654	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10		165477654	77721719	9	14498											
ATG9A	79065	hgsc.bcm.edu	37	chr2	220085516	220085516	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccgagccctcttcgggcaCgggctcagggtgccttgatg	4	9	14	14	3	2	1	1	1	1	0	4	2	3	1	3	3	2	2	3	3	0	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr2:220085516C>T	ENST00000409618.1	-	15	2906	c.2467G>A	c.(2467-2469)Gtg>Atg	p.V823M	ATG9A_ENST00000396761.2_Missense_Mutation_p.V823M|ABCB6_ENST00000265316.3_5'Flank|ABCB6_ENST00000439002.2_5'Flank|ATG9A_ENST00000361242.4_Missense_Mutation_p.V823M|ATG9A_ENST00000409422.1_Missense_Mutation_p.V762M			Q7Z3C6	ATG9A_HUMAN	autophagy related 9A	823					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)		TCTTCGGGCACGGGCTCAGGG	0.607																																					p.V823M		Atlas-SNP	.											.	ATG9A	50	.	0			c.G2467A						PASS	.						46	47	47					2																	220085516		1899	4124	6023	SO:0001583	missense	79065	exon15			CGGGCACGGGCTC	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.2467G>A	chr2.hg19:g.220085516C>T	ENSP00000386710:p.Val823Met	42.0	0.0	.		73.0	4.0	.	NM_001077198	Q3ZAQ6|Q6P0N7|Q7Z317|Q7Z320|Q8NDK6|Q8WU65|Q9BVL5|Q9H6L1|Q9HAG7	Missense_Mutation	SNP	ENST00000409618.1	hg19	CCDS42820.1	.	.	.	.	.	.	.	.	.	.	C	16.25	3.071397	0.55646	.	.	ENSG00000198925	ENST00000396761;ENST00000409618;ENST00000361242;ENST00000409422	T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68	5.06	5.06	0.68205	.	0.064569	0.64402	D	0.000010	T	0.65984	0.2744	L	0.34521	1.04	0.46874	D	0.999238	D	0.58268	0.982	P	0.44732	0.459	T	0.70722	-0.4794	10	0.56958	D	0.05	-11.0302	18.6114	0.91286	0.0:1.0:0.0:0.0	.	823	Q7Z3C6	ATG9A_HUMAN	M	823;823;823;762	ENSP00000379983:V823M;ENSP00000386710:V823M;ENSP00000355173:V823M;ENSP00000386535:V762M	ENSP00000355173:V823M	V	-	1	0	ATG9A	219793760	0.997000	0.39634	0.956000	0.39512	0.708000	0.40852	3.656000	0.54467	2.627000	0.88993	0.655000	0.94253	GTG	.	.	.	none		0.607	ATG9A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335930.1	NM_024085		T	220085516	C	T	220085516	3	4	238	1	0	0	0	0	1	0	0	0	1102	536	19	1	60	1	ATG9A	2	220085516	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	54607862	220085516	23113857	10	14499											
DES	1674	hgsc.bcm.edu	37	chr2	220283244	220283245	+	Missense_Mutation	DNP	GG	GG	AT																															taccgccgcaccttcggcggGgccccgggcttcccactcgg																								rs1058253		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr2:220283244_220283245GG>AT	ENST00000373960.3	+	1	146_147	c.60_61GG>AT	c.(58-63)ggGGcc>ggATcc	p.A21S		NM_001927.3	NP_001918.3	P17661	DESM_HUMAN	desmin	21	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)		CCTTCGGCGGGGCCCCGGGCTT	0.733																																					p.G20G|p.A21S		Atlas-SNP	.											.	DES	53	.	0			c.G60A|c.G61T						PASS	.																																			SO:0001583	missense	1674	exon1			CGGCGGGGCCCCG|GGCGGGGCCCCGG	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	Exception_encountered	chr2.hg19:g.220283244_220283245delinsAT	ENSP00000363071:p.Ala21Ser	3.0	0.0	.		29.0|31.0	21.0|24.0	.	NM_001927	Q15787|Q549R7|Q549R8|Q549R9|Q8IZR1|Q8IZR6|Q8NES2|Q8NEU6|Q8TAC4|Q8TCX2|Q8TD99|Q9UHN5|Q9UJ80	Silent|Missense_Mutation	SNP	ENST00000373960.3	hg19	CCDS33383.1																																																																																			.	G|1.000;|0.000|.	.	alt|none		0.733	DES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130240.1	NM_001927		AT	220283245	GG	AT	220283244	3	1	238	1	0	0	0	0	1	0	0	0	4451	1219	43	2	62	2	DES	2	220283244	Missense_Mutation	DNP	GG	TCGA-PJ-A5Z9-01A-11D-A28G-10	197728	220283244	22916129	11	14500											
SETD2	29072	hgsc.bcm.edu	37	chr3	47164505	47164505	+	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	cttagaatatgatgaccctcGtcggaatcccagttcattag	11	12	8	10	2	1	3	1	2	0	1	4	4	2	4	2	1	0	1	2	1	5	4			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr3:47164505G>T	ENST00000409792.3	-	3	1663	c.1621C>A	c.(1621-1623)Cga>Aga	p.R541R		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	541					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		GATGACCCTCGTCGGAATCCC	0.358			"N, F, S, Mis"		clear cell renal carcinoma																																p.R541R		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.C1621A						PASS	.						100	100	100					3																	47164505		2200	4292	6492	SO:0001819	synonymous_variant	29072	exon3			ACCCTCGTCGGAA	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.1621C>A	chr3.hg19:g.47164505G>T		42.0	0.0	.		77.0	4.0	.	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Silent	SNP	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.	.	none		0.358	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		T	47164505	G	T	47164505	2	4	238	1	0	0	0	0	0	0	0	1	14144	1153	40	4		4	SETD2	3	47164505	Silent	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10		47164505	150857925	12	14501											
GMPPB	29925	hgsc.bcm.edu	37	chr3	49759370	49759370	+	Intron	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	ggcacactccccgcccctctCcccacccagcccagcccaca	7	3	5	26	1	1	0	0	0	1	0	3	0	2	0	9	1	2	1	9	1	0	0	rs71324991		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr3:49759370C>T	ENST00000480687.1	-	9	1068				GMPPB_ENST00000308375.6_Missense_Mutation_p.E327K|AMIGO3_ENST00000535833.1_Intron|AMIGO3_ENST00000320431.7_5'Flank|GMPPB_ENST00000308388.6_Intron			Q9Y5P6	GMPPB_HUMAN	GDP-mannose pyrophosphorylase B						cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|mannose-1-phosphate guanylyltransferase activity (GO:0004475)			endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CCGCCCCTCTCCCCACCCAGC	0.632																																					p.E327K		Atlas-SNP	.											.	GMPPB	14	.	0			c.G979A						PASS	.						52	52	52					3																	49759370		2203	4300	6503	SO:0001627	intron_variant	29925	exon8			CCCTCTCCCCACC	AF135421	CCDS2802.1, CCDS2803.1	3p21.31	2008-02-05			ENSG00000173540	ENSG00000173540	2.7.7.22		22932	protein-coding gene	gene with protein product		615320					Standard	NM_013334		Approved	KIAA1851	uc003cxl.1	Q9Y5P6	OTTHUMG00000158151	ENST00000480687.1:c.951+27G>A	chr3.hg19:g.49759370C>T		81.0	0.0	.		113.0	67.0	.	NM_013334	A8K6N5|Q9H7U3	Missense_Mutation	SNP	ENST00000480687.1	hg19	CCDS2803.1	.	.	.	.	.	.	.	.	.	.	C	4.938	0.174300	0.09391	.	.	ENSG00000173540	ENST00000308375	T	0.72942	-0.7	4.7	1.73	0.24493	.	1.157320	0.06701	N	0.771475	T	0.53722	0.1814	.	.	.	0.32702	N	0.512756	B	0.02656	0.0	B	0.01281	0.0	T	0.51988	-0.8635	9	0.24483	T	0.36	-2.0563	5.6606	0.17667	0.0:0.442:0.3934:0.1645	.	327	Q9Y5P6-2	.	K	327	ENSP00000309092:E327K	ENSP00000309092:E327K	E	-	1	0	GMPPB	49734374	0.000000	0.05858	0.023000	0.16930	0.167000	0.22549	-0.551000	0.06027	0.524000	0.28502	0.655000	0.94253	GAG	.	C|0.500;T|0.500	0.500	weak		0.632	GMPPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350291.1	NM_013334		T	49759370	C	T	49759370	1	4	238	0	1	0	0	0	0	0	0	0	6502	864	30	2		2	GMPPB	3	49759370	Intron	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	2594865	49759370	148263060	13	14502											
UBA7	7318	hgsc.bcm.edu	37	chr3	49847782	49847782	+	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	tgtgctctgtggtgggatccAgtgggtaggtgagcgggatc	5	11	19	6	1	1	1	0	1	1	0	3	3	2	3	1	5	2	2	1	5	1	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr3:49847782A>T	ENST00000333486.3	-	13	1705	c.1547T>A	c.(1546-1548)cTg>cAg	p.L516Q	UBA7_ENST00000494212.1_5'Flank	NM_003335.2	NP_003326.2	P41226	UBA7_HUMAN	ubiquitin-like modifier activating enzyme 7	516	2 approximate repeats.				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)		GGTGGGATCCAGTGGGTAGGT	0.587																																					p.L516Q		Atlas-SNP	.											.	UBA7	64	.	0			c.T1547A						PASS	.						102	104	103					3																	49847782		2203	4300	6503	SO:0001583	missense	7318	exon13			GGATCCAGTGGGT	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.1547T>A	chr3.hg19:g.49847782A>T	ENSP00000333266:p.Leu516Gln	270.0	0.0	.		254.0	148.0	.	NM_003335	Q9BRB2	Missense_Mutation	SNP	ENST00000333486.3	hg19	CCDS2805.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.249400	0.80024	.	.	ENSG00000182179	ENST00000333486	T	0.67345	-0.26	5.67	5.67	0.87782	UBA/THIF-type NAD/FAD binding fold (1);Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.331674	0.29631	N	0.011601	D	0.86180	0.5871	M	0.93854	3.465	0.52501	D	0.999951	D	0.76494	0.999	D	0.74674	0.984	D	0.89830	0.3995	10	0.87932	D	0	-8.7204	15.9043	0.79412	1.0:0.0:0.0:0.0	.	516	P41226	UBA7_HUMAN	Q	516	ENSP00000333266:L516Q	ENSP00000333266:L516Q	L	-	2	0	UBA7	49822786	1.000000	0.71417	0.352000	0.25734	0.711000	0.40976	8.947000	0.93000	2.169000	0.68431	0.459000	0.35465	CTG	.	.	.	none		0.587	UBA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350503.1	NM_003335		T	49847782	A	T	49847782	3	4	238	1	0	0	0	0	1	0	0	0	16845	188	7	5	1539	5	UBA7	3	49847782	Missense_Mutation	SNP	A	TCGA-PJ-A5Z9-01A-11D-A28G-10	88412	49847782	148174648	14	14503											
IGF2BP2	10644	hgsc.bcm.edu	37	chr3	185542743	185542743	+	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	ttcccgatgtaaagcttgttCatcatccgtctcttccccga	7	14	6	14	3	3	0	2	0	1	0	7	2	6	0	4	0	1	3	4	0	2	5			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr3:185542743C>G	ENST00000382199.2	-	1	101	c.6G>C	c.(4-6)atG>atC	p.M2I	IGF2BP2_ENST00000346192.3_Missense_Mutation_p.M2I|IGF2BP2_ENST00000457616.2_Missense_Mutation_p.M2I	NM_006548.4	NP_006539.3	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding protein 2	2					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)			AAAGCTTGTTCATCATCCGTC	0.706																																					p.M2I		Atlas-SNP	.											.	IGF2BP2	69	.	0			c.G6C						PASS	.						22	24	24					3																	185542743		2202	4300	6502	SO:0001583	missense	10644	exon1			CTTGTTCATCATC	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.6G>C	chr3.hg19:g.185542743C>G	ENSP00000371634:p.Met2Ile	88.0	0.0	.		169.0	34.0	.	NM_001007225	A0A4Z0|B3FTN2|B3FTN3|B3FTN4	Missense_Mutation	SNP	ENST00000382199.2	hg19	CCDS3273.2	.	.	.	.	.	.	.	.	.	.	C	25.2	4.612112	0.87258	.	.	ENSG00000073792	ENST00000382199;ENST00000457616;ENST00000346192	T;T;T	0.20332	2.11;2.31;2.08	2.43	2.43	0.29744	.	0.000000	0.64402	U	0.000001	T	0.47358	0.1441	M	0.85197	2.74	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.998	D;D;D	0.77557	0.978;0.99;0.965	T	0.56914	-0.7900	10	0.87932	D	0	-7.2297	11.9545	0.52974	0.0:1.0:0.0:0.0	.	2;2;2	F8W930;Q9Y6M1-1;Q9Y6M1	.;.;IF2B2_HUMAN	I	2	ENSP00000371634:M2I;ENSP00000410242:M2I;ENSP00000320204:M2I	ENSP00000320204:M2I	M	-	3	0	IGF2BP2	187025437	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.717000	0.74707	1.354000	0.45846	0.393000	0.25936	ATG	.	.	.	none		0.706	IGF2BP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157087.2	NM_006548		G	185542743	C	G	185542743	3	3	238	1	0	0	0	0	1	0	0	0	7581	826	29	4	1857	4	IGF2BP2	3	185542743	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	135694961	185542743	12479687	15	14504											
NKX3-2	579	hgsc.bcm.edu	37	chr4	13545664	13545664	+	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	agctcacagaccggctggccGaggctcaaggatccccccgc	8	4	12	17	3	2	1	2	0	0	1	3	3	3	2	5	4	1	3	5	4	1	0			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr4:13545664G>A	ENST00000382438.5	-	1	1010	c.375C>T	c.(373-375)ctC>ctT	p.L125L	AC006445.8_ENST00000501050.1_lincRNA	NM_001189.3	NP_001180.1	P78367	NKX32_HUMAN	NK3 homeobox 2	125					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						CCGGCTGGCCGAGGCTCAAGG	0.721																																					p.L125L		Atlas-SNP	.											.	NKX3-2	15	.	0			c.C375T						PASS	.						3	4	4					4																	13545664		1713	3631	5344	SO:0001819	synonymous_variant	579	exon1			CTGGCCGAGGCTC	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.375C>T	chr4.hg19:g.13545664G>A		3.0	0.0	.		29.0	18.0	.	NM_001189	Q2M2I7	Silent	SNP	ENST00000382438.5	hg19	CCDS3410.1																																																																																			.	.	.	none		0.721	NKX3-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207317.3			A	13545664	G	A	13545664	2	1	238	1	0	0	0	0	0	0	0	1	10463	1045	37	1		1	NKX3-2	4	13545664	Silent	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10		13545664	177608612	16	14505											
NIPAL1	152519	hgsc.bcm.edu	37	chr4	48037862	48037862	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaggcactggacacctttaaTacctctcttgtgacacccat	11	11	6	13	0	1	1	0	1	1	0	2	2	1	2	3	2	1	1	3	2	3	4			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr4:48037862T>C	ENST00000295461.5	+	6	972	c.906T>C	c.(904-906)aaT>aaC	p.N302N		NM_207330.1	NP_997213.1	Q6NVV3	NIPA3_HUMAN	NIPA-like domain containing 1	302						integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			endometrium(2)|large_intestine(1)|lung(3)|skin(2)	8						ACACCTTTAATACCTCTCTTG	0.423																																					p.N302N		Atlas-SNP	.											.	NIPAL1	29	.	0			c.T906C						PASS	.						138	122	127					4																	48037862		2203	4300	6503	SO:0001819	synonymous_variant	152519	exon6			CTTTAATACCTCT	BC067881	CCDS3479.1	4p12	2009-03-24		2009-03-24	ENSG00000163293	ENSG00000163293			27194	protein-coding gene	gene with protein product				NPAL1			Standard	NM_207330		Approved	DKFZp686A06115	uc003gxw.3	Q6NVV3	OTTHUMG00000128622	ENST00000295461.5:c.906T>C	chr4.hg19:g.48037862T>C		201.0	0.0	.		145.0	58.0	.	NM_207330	B3KTB0|Q68DA9	Silent	SNP	ENST00000295461.5	hg19	CCDS3479.1																																																																																			.	.	.	none		0.423	NIPAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250491.4	NM_207330		C	48037862	T	C	48037862	2	2	238	1	0	0	0	0	0	0	0	1	10431	1403	49	3		3	NIPAL1	4	48037862	Silent	SNP	T	TCGA-PJ-A5Z9-01A-11D-A28G-10	34492198	48037862	143116414	17	14506											
MAP3K1	4214	hgsc.bcm.edu	37	chr5	56170960	56170960	+	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	gatgtcagtggggccctgctGttggcaaatggggagagcac	8	8	17	8	0	1	1	1	0	0	1	1	3	1	1	1	5	2	4	1	5	1	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr5:56170960G>T	ENST00000399503.3	+	10	1788	c.1788G>T	c.(1786-1788)ctG>ctT	p.L596L		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	596					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)		GGGCCCTGCTGTTGGCAAATG	0.552																																					p.L596L		Atlas-SNP	.											.	MAP3K1	355	.	0			c.G1788T						PASS	.						88	87	87					5																	56170960		1908	4114	6022	SO:0001819	synonymous_variant	4214	exon10			CCTGCTGTTGGCA	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.1788G>T	chr5.hg19:g.56170960G>T		96.0	0.0	.		72.0	4.0	.	NM_005921		Silent	SNP	ENST00000399503.3	hg19	CCDS43318.1																																																																																			.	.	.	none		0.552	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066		T	56170960	G	T	56170960	2	4	238	1	0	0	0	0	0	0	0	1	9250	1364	48	4		4	MAP3K1	5	56170960	Silent	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10		56170960	124744300	18	14507											
MSH3	4437	hgsc.bcm.edu	37	chr5	79970928	79970928	+	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	tagggacaaaaaaaagggcaAcatttttattggcattgtgg	15	11	11	4	0	0	0	0	0	0	0	0	1	0	1	0	4	1	2	0	4	7	6			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr5:79970928A>T	ENST00000265081.6	+	7	1234	c.1154A>T	c.(1153-1155)aAc>aTc	p.N385I		NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	385					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)		AAAAAGGGCAACATTTTTATT	0.333								Mismatch excision repair (MMR)																													p.N385I	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											.	MSH3	129	.	0			c.A1154T						PASS	.						148	152	151					5																	79970928		2203	4300	6503	SO:0001583	missense	4437	exon7			AGGGCAACATTTT	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.1154A>T	chr5.hg19:g.79970928A>T	ENSP00000265081:p.Asn385Ile	148.0	0.0	.		98.0	41.0	.	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	hg19	CCDS34195.1	.	.	.	.	.	.	.	.	.	.	A	8.987	0.976749	0.18812	.	.	ENSG00000113318	ENST00000265081;ENST00000535995	D	0.88664	-2.41	5.6	-5.6	0.02497	DNA mismatch repair protein MutS, connector (2);	0.642828	0.16451	N	0.213870	T	0.79405	0.4440	L	0.53249	1.67	0.09310	N	1	B	0.33318	0.408	B	0.34138	0.176	T	0.67783	-0.5581	9	.	.	.	-1.1852	2.0942	0.03664	0.3478:0.3369:0.2064:0.1089	.	385	P20585	MSH3_HUMAN	I	385;376	ENSP00000265081:N385I	.	N	+	2	0	MSH3	80006684	0.010000	0.17322	0.000000	0.03702	0.294000	0.27393	0.093000	0.15086	-0.822000	0.04306	-0.367000	0.07326	AAC	.	.	.	none		0.333	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		T	79970928	A	T	79970928	3	4	238	1	0	0	0	0	1	0	0	0	9878	43	2	5	1180	5	MSH3	5	79970928	Missense_Mutation	SNP	A	TCGA-PJ-A5Z9-01A-11D-A28G-10	23799968	79970928	100944332	19	14508											
KDM3B	51780	hgsc.bcm.edu	37	chr5	137717257	137717257	+	Missense_Mutation	SNP	A	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	aatccatgtgatgctgatggAtaattcagcgcctcaaagcg	12	10	10	9	2	2	2	2	2	0	0	3	3	3	3	2	1	3	1	2	1	3	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr5:137717257A>C	ENST00000314358.5	+	6	958	c.758A>C	c.(757-759)gAt>gCt	p.D253A		NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	253					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						ATGCTGATGGATAATTCAGCG	0.433																																					p.D253A		Atlas-SNP	.											.	KDM3B	177	.	0			c.A758C						PASS	.						134	117	123					5																	137717257		2203	4300	6503	SO:0001583	missense	51780	exon6			TGATGGATAATTC	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.758A>C	chr5.hg19:g.137717257A>C	ENSP00000326563:p.Asp253Ala	87.0	0.0	.		72.0	25.0	.	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Missense_Mutation	SNP	ENST00000314358.5	hg19	CCDS34242.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.253034	0.80135	.	.	ENSG00000120733	ENST00000314358;ENST00000545151	T	0.68025	-0.3	4.79	4.79	0.61399	.	0.104922	0.64402	D	0.000006	T	0.70876	0.3274	N	0.24115	0.695	0.80722	D	1	D	0.71674	0.998	D	0.75484	0.986	T	0.75357	-0.3346	10	0.72032	D	0.01	-8.6271	14.278	0.66194	1.0:0.0:0.0:0.0	.	253	Q7LBC6	KDM3B_HUMAN	A	253;43	ENSP00000326563:D253A	ENSP00000326563:D253A	D	+	2	0	KDM3B	137745156	1.000000	0.71417	0.996000	0.52242	0.876000	0.50452	6.004000	0.70709	1.905000	0.55150	0.460000	0.39030	GAT	.	.	.	none		0.433	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604		C	137717257	A	C	137717257	3	2	238	1	0	0	0	0	1	0	0	0	8134	333	12	5	780	5	KDM3B	5	137717257	Missense_Mutation	SNP	A	TCGA-PJ-A5Z9-01A-11D-A28G-10	57746329	137717257	43198003	20	14509											
CASP8AP2	9994	hgsc.bcm.edu	37	chr6	90573643	90573643	+	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	aaagaaatgataattcagatTattgtggtatttctgaaggt	15	15	9	2	0	2	4	1	2	1	2	2	4	2	4	0	2	0	1	0	2	6	6			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr6:90573643T>C	ENST00000551025.1	+	0	3652									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)		TAATTCAGATTATTGTGGTAT	0.403																																					p.Y739H	Colon(187;1656 2025 17045 31481 39901)	Atlas-SNP	.											.	CASP8AP2	108	.	0			c.T2215C						PASS	.						69	67	67					6																	90573643		1866	4106	5972			9994	exon7			TCAGATTATTGTG	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"FLICE-associated huge protein"	606880	"CASP8 associated protein 2"			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		chr6.hg19:g.90573643T>C		113.0	0.0	.		68.0	5.0	.	NM_001137667		Missense_Mutation	SNP	ENST00000551025.1	hg19																																																																																				.	.	.	none		0.403	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667		C	90573643	T	C	90573643	1	2	238	0	1	0	0	0	0	0	0	0	2680	1754	61	3		3	CASP8AP2	6	90573643	RNA	SNP	T	TCGA-PJ-A5Z9-01A-11D-A28G-10		90573643	80541424	21	14510											
REPS1	85021	hgsc.bcm.edu	37	chr6	139262487	139262487	+	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	cttacctgctgaatcttccaAatcaatcagtttgggcatta	11	14	6	10	0	3	1	2	1	1	0	4	1	4	1	2	1	2	3	2	1	5	4			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr6:139262487A>T	ENST00000450536.2	-	8	1694	c.1120T>A	c.(1120-1122)Ttg>Atg	p.L374M	REPS1_ENST00000415951.2_Missense_Mutation_p.L374M|REPS1_ENST00000409812.2_Missense_Mutation_p.L374M|REPS1_ENST00000367663.4_Missense_Mutation_p.L374M|REPS1_ENST00000258062.5_Missense_Mutation_p.L374M			Q96D71	REPS1_HUMAN	RALBP1 associated Eps domain containing 1	374	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)		GAATCTTCCAAATCAATCAGT	0.388																																					p.L374M		Atlas-SNP	.											.	REPS1	58	.	0			c.T1120A						PASS	.						167	170	169					6																	139262487		2203	4300	6503	SO:0001583	missense	85021	exon8			CTTCCAAATCAAT		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.1120T>A	chr6.hg19:g.139262487A>T	ENSP00000392065:p.Leu374Met	76.0	0.0	.		64.0	12.0	.	NM_001128617	B7ZBZ8|B7ZBZ9|B7ZC00|J3KP76|Q5JWJ5|Q5JWJ6|Q5JWJ7|Q8NDR7|Q8WU62|Q9BXY9	Missense_Mutation	SNP	ENST00000450536.2	hg19		.	.	.	.	.	.	.	.	.	.	A	18.47	3.630297	0.67015	.	.	ENSG00000135597	ENST00000450536;ENST00000367663;ENST00000529597;ENST00000409812;ENST00000258062;ENST00000415951;ENST00000367668	T;T;T;T;T;T	0.35789	1.31;1.35;1.33;1.34;1.29;1.36	5.91	4.76	0.60689	.	0.000000	0.85682	D	0.000000	T	0.23014	0.0556	N	0.08118	0	0.80722	D	1	D;D;D;P;P	0.89917	1.0;1.0;1.0;0.82;0.872	D;D;D;P;B	0.80764	0.992;0.981;0.994;0.451;0.393	T	0.23904	-1.0175	10	0.45353	T	0.12	-6.2792	8.9289	0.35657	0.8584:0.0:0.1416:0.0	.	374;322;374;374;374	Q96D71-3;B2R7D3;Q96D71-2;Q96D71;E9PMG1	.;.;.;REPS1_HUMAN;.	M	374;374;360;374;374;374;322	ENSP00000392065:L374M;ENSP00000356635:L374M;ENSP00000434251:L360M;ENSP00000386699:L374M;ENSP00000258062:L374M;ENSP00000397941:L374M	ENSP00000258062:L374M	L	-	1	2	REPS1	139304180	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.783000	0.47766	1.074000	0.40909	0.533000	0.62120	TTG	.	.	.	none		0.388	REPS1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000042447.3			T	139262487	A	T	139262487	3	4	238	1	0	0	0	0	1	0	0	0	13241	11	1	5	1322	5	REPS1	6	139262487	Missense_Mutation	SNP	A	TCGA-PJ-A5Z9-01A-11D-A28G-10	48688844	139262487	31852580	22	14511											
PDE1C	5137	hgsc.bcm.edu	37	chr7	31862809	31862809	+	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	tcggggcacttccctctgaaCcagaggtcttgacacctgat	8	10	10	13	1	2	4	0	3	2	1	4	4	3	4	3	3	1	1	3	3	1	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr7:31862809C>A	ENST00000396191.1	-	14	1915	c.1460G>T	c.(1459-1461)gGt>gTt	p.G487V	PDE1C_ENST00000396193.1_Missense_Mutation_p.G547V|PDE1C_ENST00000321453.7_Missense_Mutation_p.G487V|PDE1C_ENST00000396184.3_Missense_Mutation_p.G487V|PDE1C_ENST00000479980.1_5'Flank|PDE1C_ENST00000396182.2_Missense_Mutation_p.G487V	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	487	Catalytic. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	TCCCTCTGAACCAGAGGTCTT	0.443																																					p.G547V		Atlas-SNP	.											.	PDE1C	465	.	0			c.G1640T						PASS	.						107	96	100					7																	31862809		2203	4300	6503	SO:0001583	missense	5137	exon15			TCTGAACCAGAGG	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.1460G>T	chr7.hg19:g.31862809C>A	ENSP00000379494:p.Gly487Val	100.0	0.0	.		117.0	38.0	.	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Missense_Mutation	SNP	ENST00000396191.1	hg19	CCDS55099.1	.	.	.	.	.	.	.	.	.	.	C	17.54	3.415990	0.62511	.	.	ENSG00000154678	ENST00000396193;ENST00000396191;ENST00000321453;ENST00000396184;ENST00000396182	T;T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.63;-0.63	5.91	5.91	0.95273	.	0.634852	0.16753	N	0.200964	T	0.76730	0.4028	L	0.29908	0.895	0.80722	D	1	B;B;D	0.65815	0.081;0.23;0.995	B;B;P	0.60949	0.056;0.082;0.881	T	0.76537	-0.2923	10	0.54805	T	0.06	.	19.9003	0.96983	0.0:1.0:0.0:0.0	.	487;547;487	Q14123-2;E9PE92;Q14123	.;.;PDE1C_HUMAN	V	547;487;487;487;487	ENSP00000379496:G547V;ENSP00000379494:G487V;ENSP00000318105:G487V;ENSP00000379487:G487V;ENSP00000379485:G487V	ENSP00000318105:G487V	G	-	2	0	PDE1C	31829334	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.060000	0.76692	2.808000	0.96608	0.655000	0.94253	GGT	.	.	.	none		0.443	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1			A	31862809	C	A	31862809	3	1	238	1	0	0	0	0	1	0	0	0	11642	507	18	4	460	4	PDE1C	7	31862809	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10		31862809	127275854	23	14512											
CSMD1	64478	hgsc.bcm.edu	37	chr8	2824167	2824167	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catgagccctgaggtcttgtAgccttcccagcaggcataga	9	9	11	12	0	1	3	0	2	1	1	2	3	2	3	3	2	3	3	3	2	2	4			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr8:2824167A>G	ENST00000520002.1	-	59	9583	c.9028T>C	c.(9028-9030)Tac>Cac	p.Y3010H	CSMD1_ENST00000602557.1_Missense_Mutation_p.Y3010H|CSMD1_ENST00000400186.3_Intron|CSMD1_ENST00000537824.1_Missense_Mutation_p.Y3009H|CSMD1_ENST00000602723.1_Intron|CSMD1_ENST00000542608.1_Intron			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3010	Sushi 23. {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)		GAGGTCTTGTAGCCTTCCCAG	0.547																																					p.Y3009H		Atlas-SNP	.											.	CSMD1	1469	.	0			c.T9025C						PASS	.						72	76	75					8																	2824167		2071	4221	6292	SO:0001583	missense	64478	exon58			TCTTGTAGCCTTC			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.9028T>C	chr8.hg19:g.2824167A>G	ENSP00000430733:p.Tyr3010His	211.0	0.0	.		122.0	50.0	.	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.86|18.86	3.714217|3.714217	0.68730|0.68730	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000335551|ENST00000520002;ENST00000318252;ENST00000537824	.|T;T	.|0.40756	.|1.02;1.02	5.46|5.46	5.46|5.46	0.80206|0.80206	.|Complement control module (2);Sushi/SCR/CCP (3);	.|0.079141	.|0.53938	.|D	.|0.000060	T|T	0.69495|0.69495	0.3117|0.3117	M|M	0.87827|0.87827	2.91|2.91	0.80722|0.80722	D|D	1|1	.|D;D	.|0.76494	.|0.999;0.999	.|D;D	.|0.83275	.|0.996;0.992	T|T	0.76113|0.76113	-0.3078|-0.3078	5|10	.|0.87932	.|D	.|0	.|.	15.5456|15.5456	0.76097|0.76097	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|3010;3010	.|E5RIG2;Q96PZ7	.|.;CSMD1_HUMAN	P|H	2426|3010;2871;3009	.|ENSP00000430733:Y3010H;ENSP00000441462:Y3009H	.|ENSP00000320445:Y2871H	L|Y	-|-	2|1	0|0	CSMD1|CSMD1	2811574|2811574	1.000000|1.000000	0.71417|0.71417	0.807000|0.807000	0.32361|0.32361	0.329000|0.329000	0.28539|0.28539	9.116000|9.116000	0.94341|0.94341	2.068000|2.068000	0.61886|0.61886	0.533000|0.533000	0.62120|0.62120	CTA|TAC	.	.	.	none		0.547	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		G	2824167	A	G	2824167	3	3	238	1	0	0	0	0	1	0	0	0	3946	420	15	3	1721	3	CSMD1	8	2824167	Missense_Mutation	SNP	A	TCGA-PJ-A5Z9-01A-11D-A28G-10		2824167	143539855	24	14513											
NEFL	4747	hgsc.bcm.edu	37	chr8	24813800	24813800	+	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	tgaggtcgttgctgatggcgGctacctggctcaggtcgagg	5	10	17	9	3	1	2	1	2	0	0	3	3	1	2	1	6	2	4	1	6	1	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr8:24813800G>A	ENST00000221169.5	-	0	824				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)		GCTGATGGCGGCTACCTGGCT	0.637																																					p.A77V		Atlas-SNP	.											.	NEFL	47	.	0			c.C230T						PASS	.						30	33	32					8																	24813800		2172	4272	6444			4747	exon1			ATGGCGGCTACCT		CCDS75712.1	8p21.2	2014-09-17	2008-09-19		ENSG00000104725	ENSG00000277586		"Intermediate filaments type IV"	7739	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 110"	162280	"neurofilament, light polypeptide 68kDa"			17620486, 3145240	Standard	NM_006158		Approved	NFL, CMT1F, CMT2E, NF68, PPP1R110	uc003xee.4	P07196	OTTHUMG00000134284		chr8.hg19:g.24813800G>A		174.0	0.0	.		173.0	13.0	.	NM_006158	B9ZVN2|Q16154|Q8IU72	Missense_Mutation	SNP	ENST00000221169.5	hg19																																																																																				.	.	.	none		0.637	NEFL-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000258943.4	NM_006158		A	24813800	G	A	24813800	1	1	238	0	1	0	0	0	0	0	0	0	10322	1203	42	2		2	NEFL	8	24813800	RNA	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	21989633	24813800	121550222	25	14514											
MATN2	4147	hgsc.bcm.edu	37	chr8	99039960	99039960	+	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	acccaaggagaaggggccagGcccctttccacaagggtgcc	10	4	13	14	0	0	1	0	0	0	1	1	2	1	1	6	5	1	0	6	5	3	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr8:99039960G>T	ENST00000520016.1	+	13	2383	c.2259G>T	c.(2257-2259)agG>agT	p.R753S	MATN2_ENST00000524308.1_Missense_Mutation_p.R712S|MATN2_ENST00000522025.2_Missense_Mutation_p.R469S|MATN2_ENST00000521689.1_Missense_Mutation_p.R753S|RPL30_ENST00000518164.1_Intron|MATN2_ENST00000254898.5_Missense_Mutation_p.R753S			O00339	MATN2_HUMAN	matrilin 2	753	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			AAGGGGCCAGGCCCCTTTCCA	0.562																																					p.R753S		Atlas-SNP	.											.	MATN2	165	.	0			c.G2259T						PASS	.						41	42	42					8																	99039960		1887	4109	5996	SO:0001583	missense	4147	exon14			GGCCAGGCCCCTT	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.2259G>T	chr8.hg19:g.99039960G>T	ENSP00000430487:p.Arg753Ser	124.0	0.0	.		137.0	52.0	.	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Missense_Mutation	SNP	ENST00000520016.1	hg19	CCDS55264.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	18.65|18.65|18.65	3.670245|3.670245|3.670245	0.67814|0.67814|0.67814	.|.|.	.|.|.	ENSG00000132561|ENSG00000132561|ENSG00000132561	ENST00000518154|ENST00000519582|ENST00000521689;ENST00000254898;ENST00000378716;ENST00000524308;ENST00000522025;ENST00000520016	.|.|D;D;D;D;D	.|.|0.87571	.|.|-2.27;-2.27;-2.27;-2.27;-2.27	5.24|5.24|5.24	4.34|4.34|4.34	0.51931|0.51931|0.51931	.|.|von Willebrand factor, type A (3);	.|.|0.000000	.|.|0.64402	.|.|D	.|.|0.000002	D|D|D	0.94548|0.94548|0.94548	0.8244|0.8244|0.8244	H|H|H	0.95187|0.95187|0.95187	3.635|3.635|3.635	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|D;D;D	.|.|0.89917	.|.|1.0;1.0;1.0	.|.|D;D;D	.|.|0.91635	.|.|0.999;0.999;0.999	D|D|D	0.94271|0.94271|0.94271	0.7511|0.7511|0.7511	5|5|10	.|.|0.87932	.|.|D	.|.|0	-23.5915|-23.5915|-23.5915	8.2515|8.2515|8.2515	0.31724|0.31724|0.31724	0.2672:0.0:0.7328:0.0|0.2672:0.0:0.7328:0.0|0.2672:0.0:0.7328:0.0	.|.|.	.|.|753;753;753	.|.|E9PF03;O00339-2;O00339	.|.|.;.;MATN2_HUMAN	S|V|S	536|9|753;753;712;712;469;753	.|.|ENSP00000429977:R753S;ENSP00000254898:R753S;ENSP00000430221:R712S;ENSP00000429010:R469S;ENSP00000430487:R753S	.|.|ENSP00000254898:R753S	A|G|R	+|+|+	1|2|3	0|0|2	MATN2|MATN2|MATN2	99109136|99109136|99109136	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.934000|0.934000|0.934000	0.57294|0.57294|0.57294	3.500000|3.500000|3.500000	0.53318|0.53318|0.53318	1.272000|1.272000|1.272000	0.44329|0.44329|0.44329	0.555000|0.555000|0.555000	0.69702|0.69702|0.69702	GCC|GGC|AGG	.	.	.	none		0.562	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1			T	99039960	G	T	99039960	3	4	238	1	0	0	0	0	1	0	0	0	9341	1194	42	4	2309	4	MATN2	8	99039960	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	74226160	99039960	47324062	26	14515											
PLEC	5339	hgsc.bcm.edu	37	chr8	145024821	145024825	+	Frame_Shift_Del	DEL	CACCT	CACCT	-																															atcacgccctcgcggaagagCacctcatagatggcccgcag																										TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	CACCT	CACCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr8:145024821_145024825delCACCT	ENST00000322810.4	-	1	219_223	c.50_54delAGGTG	c.(49-54)gaggtgfs	p.EV17fs	PLEC_ENST00000436759.2_Intron|PLEC_ENST00000527096.1_Intron|PLEC_ENST00000356346.3_Intron|PLEC_ENST00000354958.2_Intron	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	17	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						CGCGGAAGAGCACCTCATAGATGGC	0.683																																					p.17_19del		Atlas-Indel,Pindel	.											.	PLEC	1144	.	0			c.51_55del						PASS	.																																			SO:0001589	frameshift_variant	5339	exon1			.	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.50_54delAGGTG	chr8.hg19:g.145024821_145024825delCACCT	ENSP00000323856:p.Glu17fs	3.0	0.0	0		46.0	17.0	0.369565	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Frame_Shift_Del	DEL	ENST00000322810.4	hg19	CCDS43772.1																																																																																			.	.	.	none		0.683	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		-	145024825	CACCT	-	145024821	7	5	238	1	0	1	0	1	0	0	0	0	12059	697	25	0	14508	0	PLEC	8	145024821	Frame_Shift_Del	DEL	CACCT	TCGA-PJ-A5Z9-01A-11D-A28G-10	45984861	145024821	1339201	27	14516											
KIAA1797	54914	hgsc.bcm.edu	37	chr9	20988333	20988333	+	Missense_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	atacccttttcatttcaggcGttttgaagagaatggagtgg	10	14	11	6	1	2	2	2	1	0	1	2	4	2	3	1	3	1	1	1	3	3	6			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr9:20988333G>A	ENST00000380249.1	+	43	5273	c.4909G>A	c.(4909-4911)Gtt>Att	p.V1637I	FOCAD_ENST00000338382.6_Missense_Mutation_p.V1637I|FOCAD_ENST00000605086.1_Missense_Mutation_p.V1073I	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	1637						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											CATTTCAGGCGTTTTGAAGAG	0.378																																					p.V1637I		Atlas-SNP	.											.	.	.	.	0			c.G4909A						PASS	.						144	133	137					9																	20988333		2203	4300	6503	SO:0001583	missense	54914	exon43			TCAGGCGTTTTGA	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.4909G>A	chr9.hg19:g.20988333G>A	ENSP00000369599:p.Val1637Ile	103.0	0.0	.		91.0	8.0	.	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	hg19	CCDS34993.1	.	.	.	.	.	.	.	.	.	.	G	17.54	3.415680	0.62511	.	.	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.22945	1.93;1.93	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.52597	0.1744	M	0.72118	2.19	0.80722	D	1	D	0.76494	0.999	D	0.67382	0.951	T	0.36383	-0.9750	10	0.45353	T	0.12	-28.3855	20.8794	0.99867	0.0:0.0:1.0:0.0	.	1637	Q5VW36	K1797_HUMAN	I	1637	ENSP00000369599:V1637I;ENSP00000344307:V1637I	ENSP00000344307:V1637I	V	+	1	0	KIAA1797	20978333	1.000000	0.71417	0.317000	0.25265	0.044000	0.14063	5.911000	0.69939	2.941000	0.99782	0.655000	0.94253	GTT	.	.	.	none		0.378	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		A	20988333	G	A	20988333	3	1	238	1	0	0	0	0	1	0	0	0	8265	1145	40	1	5067	1	KIAA1797	9	20988333	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10		20988333	120225098	28	14517											
TOPORS	10210	hgsc.bcm.edu	37	chr9	32541932	32541932	+	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	aaactatctctacacttaggCtccgggtcttcctttttctc	7	16	5	13	1	3	0	0	0	3	0	7	0	5	0	2	2	2	1	2	2	4	6			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr9:32541932C>T	ENST00000360538.2	-	3	2707	c.2591G>A	c.(2590-2592)aGc>aAc	p.S864N	TOPORS_ENST00000379858.1_Missense_Mutation_p.S799N	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	864	Interaction with TOP1.|Interaction with UBE2I.|Lys-rich.				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)		TACACTTAGGCTCCGGGTCTT	0.358																																					p.S864N		Atlas-SNP	.											.	TOPORS	127	.	0			c.G2591A						PASS	.						203	207	205					9																	32541932		2203	4300	6503	SO:0001583	missense	10210	exon3			CTTAGGCTCCGGG	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.2591G>A	chr9.hg19:g.32541932C>T	ENSP00000353735:p.Ser864Asn	72.0	0.0	.		38.0	11.0	.	NM_005802	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	hg19	CCDS6527.1	.	.	.	.	.	.	.	.	.	.	C	16.72	3.202662	0.58234	.	.	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.34072	1.38;1.44	5.91	5.91	0.95273	.	0.000000	0.64402	D	0.000011	T	0.52468	0.1736	L	0.32530	0.975	0.39310	D	0.965069	D	0.89917	1.0	D	0.83275	0.996	T	0.53982	-0.8361	10	0.87932	D	0	-9.414	19.0572	0.93070	0.0:1.0:0.0:0.0	.	864	Q9NS56	TOPRS_HUMAN	N	864;799	ENSP00000353735:S864N;ENSP00000369187:S799N	ENSP00000353735:S864N	S	-	2	0	TOPORS	32531932	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.479000	0.60236	2.803000	0.96430	0.650000	0.86243	AGC	.	.	.	none		0.358	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		T	32541932	C	T	32541932	3	4	238	1	0	0	0	0	1	0	0	0	16382	797	28	2	550	2	TOPORS	9	32541932	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	11553599	32541932	108671499	29	14518											
FCN2	2220	hgsc.bcm.edu	37	chr9	137777085	137777085	+	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	1	0	0	0	0	0	0	0	0	tccccgggttcccttcccagGcccgcgtacctgcaaggacc	5	7	10	19	3	0	0	0	0	0	0	3	1	3	1	7	3	2	3	7	3	2	3	rs529779645	byFrequency	TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr9:137777085G>T	ENST00000291744.6	+	5	312	c.302G>T	c.(301-303)gGc>gTc	p.G101V	FCN2_ENST00000350339.2_Splice_Site_p.G63V	NM_004108.2	NP_004099.2	Q15485	FCN2_HUMAN	ficolin (collagen/fibrinogen domain containing lectin) 2	101	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)		CCCTTCCCAGGCCCGCGTACC	0.667																																					p.G101V		Atlas-SNP	.											.	FCN2	55	.	0			c.G302T						PASS	.						53	52	52					9																	137777085		2203	4300	6503	SO:0001630	splice_region_variant	2220	exon5			TCCCAGGCCCGCG	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.302-1G>T	chr9.hg19:g.137777085G>T		54.0	0.0	.		45.0	16.0	.	NM_004108	A6NFG7|A8K478|Q6IS69|Q7M4P4|Q9UC57	Missense_Mutation	SNP	ENST00000291744.6	hg19	CCDS6983.1	.	.	.	.	.	.	.	.	.	.	G	6.759	0.508916	0.12883	.	.	ENSG00000160339	ENST00000350339;ENST00000291744	T;T	0.19394	2.15;2.15	3.59	2.66	0.31614	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (3);	.	.	.	.	T	0.40815	0.1132	M	0.89353	3.025	0.30440	N	0.776243	P;P	0.49696	0.927;0.763	P;P	0.51701	0.462;0.677	T	0.48258	-0.9051	8	.	.	.	.	9.7179	0.40284	0.0:0.4147:0.5853:0.0	.	63;101	Q15485-2;Q15485	.;FCN2_HUMAN	V	63;101	ENSP00000291741:G63V;ENSP00000291744:G101V	.	G	+	2	0	FCN2	136916906	0.229000	0.23729	0.063000	0.19743	0.018000	0.09664	0.409000	0.21082	0.444000	0.26612	0.462000	0.41574	GGC	.	.	.	none		0.667	FCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054960.1	NM_004108	Missense_Mutation	T	137777085	G	T	137777085	5	4	238	1	0	0	0	0	0	0	1	0	5799	1217	42	4	320	4	FCN2	9	137777085	Splice_Site	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	105235153	137777085	3436346	30	14519											
KCNT1	402381	hgsc.bcm.edu	37	chr9	138594140	138594140	+	5'Flank	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	ggggcgcggaccccggggggCgtctgccgggaggcgcgcgg	2	2	24	13	8	1	0	0	0	1	0	1	2	1	2	3	9	1	0	3	9	0	0			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr9:138594140C>G	ENST00000298466.5	-	0	0				KCNT1_ENST00000371757.2_Silent_p.G12G|SOHLH1_ENST00000425225.1_5'Flank|KCNT1_ENST00000487664.1_Silent_p.G12G|KCNT1_ENST00000298480.5_Silent_p.G12G	NM_001012415.2	NP_001012415	Q5JUK2	SOLH1_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 1						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)		ccccggggggcgtctgccggg	0.731																																					p.G12G		Atlas-SNP	.											.	KCNT1	139	.	0			c.C36G						PASS	.						12	16	15					9																	138594140		2168	4247	6415	SO:0001631	upstream_gene_variant	57582	exon1			GGGGGGCGTCTGC	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		chr9.hg19:g.138594140C>G	Exception_encountered	1.0	0.0	.		23.0	14.0	.	NM_001272003	C9JG81|Q5EE14|Q5EGC2|Q8NEE3	Silent	SNP	ENST00000298466.5	hg19	CCDS35174.1																																																																																			.	.	.	none		0.731	SOHLH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055018.2	NM_001012415		G	138594140	C	G	138594140	1	3	238	0	1	0	0	0	0	0	0	0	8098	755	27	4		4	KCNT1	9	138594140	5'Flank	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	817055	138594140	2619291	31	14520											
ANK3	288	hgsc.bcm.edu	37	chr10	61829169	61829169	+	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	ttttcctgatgagactttcaCtgggttatctttctctgtgg	5	19	9	8	0	3	2	1	2	2	1	5	3	4	2	1	2	0	1	1	2	1	5			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr10:61829169C>T	ENST00000280772.2	-	37	11661	c.11470G>A	c.(11470-11472)Gtg>Atg	p.V3824M	ANK3_ENST00000503366.1_Intron|ANK3_ENST00000355288.2_Intron|ANK3_ENST00000373827.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3824					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						GAGACTTTCACTGGGTTATCT	0.378																																					p.V3824M		Atlas-SNP	.											.	ANK3	703	.	0			c.G11470A						PASS	.						241	236	238					10																	61829169		2203	4300	6503	SO:0001583	missense	288	exon37			CTTTCACTGGGTT	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.11470G>A	chr10.hg19:g.61829169C>T	ENSP00000280772:p.Val3824Met	76.0	0.0	.		57.0	23.0	.	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	hg19	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	C	12.81	2.048577	0.36181	.	.	ENSG00000151150	ENST00000280772	T	0.43688	0.94	4.99	3.09	0.35607	.	0.226364	0.22221	N	0.062959	T	0.22666	0.0547	N	0.14661	0.345	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.04537	-1.0944	10	0.45353	T	0.12	.	5.5172	0.16914	0.0:0.6224:0.1464:0.2312	.	3824	Q12955	ANK3_HUMAN	M	3824	ENSP00000280772:V3824M	ENSP00000280772:V3824M	V	-	1	0	ANK3	61499175	0.975000	0.34042	1.000000	0.80357	0.979000	0.70002	0.968000	0.29357	0.581000	0.29539	0.650000	0.86243	GTG	.	.	.	none		0.378	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		T	61829169	C	T	61829169	3	4	238	1	0	0	0	0	1	0	0	0	622	565	20	2	2004	2	ANK3	10	61829169	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10		61829169	73705578	32	14521											
MMRN2	79812	hgsc.bcm.edu	37	chr10	88703695	88703695	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agctcctggaagtcagccctGgccacggcactgtcctggac	7	7	12	15	1	1	0	1	0	0	0	3	2	3	2	4	4	2	2	4	4	1	0			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr10:88703695G>A	ENST00000372027.5	-	6	1167	c.846C>T	c.(844-846)gcC>gcT	p.A282A	MMRN2_ENST00000488950.1_5'UTR	NM_024756.2	NP_079032.2	Q9H8L6	MMRN2_HUMAN	multimerin 2	282					angiogenesis (GO:0001525)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|stomach(1)	19						AGTCAGCCCTGGCCACGGCAC	0.602																																					p.A282A		Atlas-SNP	.											.	MMRN2	49	.	0			c.C846T						PASS	.						62	58	59					10																	88703695		2203	4300	6503	SO:0001819	synonymous_variant	79812	exon6			AGCCCTGGCCACG	AK023527	CCDS7379.1	10q23.31	2004-03-10	2004-03-02	2004-03-02	ENSG00000173269	ENSG00000173269		"EMI domain containing"	19888	protein-coding gene	gene with protein product		608925	"elastin microfibril interfacer 3"	EMILIN3		11559704	Standard	NM_024756		Approved	EndoGlyx-1, FLJ13465	uc001kea.3	Q9H8L6	OTTHUMG00000018663	ENST00000372027.5:c.846C>T	chr10.hg19:g.88703695G>A		109.0	0.0	.		89.0	41.0	.	NM_024756	Q504V7|Q6P2N2	Silent	SNP	ENST00000372027.5	hg19	CCDS7379.1																																																																																			.	.	.	none		0.602	MMRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049179.2	NM_024756		A	88703695	G	A	88703695	2	1	238	1	0	0	0	0	0	0	0	1	9678	1335	47	2		2	MMRN2	10	88703695	Silent	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	26874526	88703695	46831052	33	14522											
RRP12	23223	hgsc.bcm.edu	37	chr10	99160073	99160073	+	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	cgcccctacctccttgtgggCagccgagttggactcccaga	6	8	11	16	2	0	1	0	0	0	1	2	3	2	2	6	2	2	2	6	2	1	3			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr10:99160073C>T	ENST00000370992.4	-	2	469	c.358G>A	c.(358-360)Gcc>Acc	p.A120T	RP11-452K12.7_ENST00000422848.1_RNA|RRP12_ENST00000414986.1_Missense_Mutation_p.A120T|RRP12_ENST00000315563.6_Missense_Mutation_p.A120T	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	120						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)		TCCTTGTGGGCAGCCGAGTTG	0.582																																					p.A120T		Atlas-SNP	.											.	RRP12	97	.	0			c.G358A						PASS	.						119	119	119					10																	99160073		2203	4300	6503	SO:0001583	missense	23223	exon2			TGTGGGCAGCCGA		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.358G>A	chr10.hg19:g.99160073C>T	ENSP00000360031:p.Ala120Thr	112.0	0.0	.		75.0	22.0	.	NM_001145114	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Missense_Mutation	SNP	ENST00000370992.4	hg19	CCDS7457.1	.	.	.	.	.	.	.	.	.	.	C	14.00	2.406058	0.42715	.	.	ENSG00000052749	ENST00000370992;ENST00000315563;ENST00000414986	T;T;T	0.64260	-0.09;1.52;1.51	5.7	4.8	0.61643	Armadillo-type fold (1);	0.208574	0.49916	D	0.000127	T	0.51295	0.1666	L	0.40543	1.245	0.80722	D	1	P;P;B	0.45715	0.787;0.865;0.001	B;B;B	0.39503	0.158;0.301;0.005	T	0.48246	-0.9052	10	0.13108	T	0.6	-11.1652	15.9236	0.79592	0.1366:0.8634:0.0:0.0	.	120;120;120	E9PCK7;Q5JTH9-2;Q5JTH9	.;.;RRP12_HUMAN	T	120	ENSP00000360031:A120T;ENSP00000324315:A120T;ENSP00000414863:A120T	ENSP00000324315:A120T	A	-	1	0	RRP12	99150063	0.992000	0.36948	0.983000	0.44433	0.965000	0.64279	3.045000	0.49838	1.429000	0.47314	-0.361000	0.07541	GCC	.	.	.	none		0.582	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179		T	99160073	C	T	99160073	3	4	238	1	0	0	0	0	1	0	0	0	13699	710	25	2	3667	2	RRP12	10	99160073	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	10456378	99160073	36374674	34	14523											
STK32C	282974	hgsc.bcm.edu	37	chr10	134036392	134036392	+	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	acgaagcccggctccaccctCttctcgctcaggtggtccca	6	8	9	18	3	3	0	1	0	2	0	6	1	5	0	4	3	1	2	4	3	1	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr10:134036392C>T	ENST00000368622.1	-	9	1122	c.741G>A	c.(739-741)aaG>aaA	p.K247K	STK32C_ENST00000368625.4_Silent_p.K377K					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)		GCTCCACCCTCTTCTCGCTCA	0.711																																					p.K364K		Atlas-SNP	.											.	STK32C	61	.	0			c.G1092A						PASS	.						20	22	21					10																	134036392		2183	4281	6464	SO:0001819	synonymous_variant	282974	exon9			CACCCTCTTCTCG	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.741G>A	chr10.hg19:g.134036392C>T		2.0	0.0	.		51.0	19.0	.	NM_173575		Silent	SNP	ENST00000368622.1	hg19																																																																																				.	.	.	none		0.711	STK32C-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000051068.2	NM_173575		T	134036392	C	T	134036392	2	4	238	1	0	0	0	0	0	0	0	1	15311	912	32	2		2	STK32C	10	134036392	Silent	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	34876319	134036392	1498355	35	14524											
SLC22A18	5002	hgsc.bcm.edu	37	chr11	2937874	2937874	+	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	ttcagtgcccggccatcctgGctgccctggccaccctcctg	3	9	10	19	1	1	0	1	0	0	0	3	0	3	0	7	3	2	1	7	3	0	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr11:2937874G>T	ENST00000380574.1	+	6	990	c.559G>T	c.(559-561)Gct>Tct	p.A187S	SLC22A18_ENST00000312221.5_Missense_Mutation_p.A187S|SLC22A18_ENST00000449793.2_Missense_Mutation_p.A89S|SLC22A18_ENST00000347936.2_Missense_Mutation_p.A187S			Q96BI1	S22AI_HUMAN	solute carrier family 22, member 18	187					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)		GGCCATCCTGGCTGCCCTGGC	0.687																																					p.A187S		Atlas-SNP	.											.	SLC22A18	20	.	0			c.G559T						PASS	.						41	44	43					11																	2937874		2202	4299	6501	SO:0001583	missense	5002	exon6			ATCCTGGCTGCCC	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.559G>T	chr11.hg19:g.2937874G>T	ENSP00000369948:p.Ala187Ser	57.0	0.0	.		124.0	50.0	.	NM_002555	O14906|O43562|O60485|O60680|Q7LDS5|Q7LGF7	Missense_Mutation	SNP	ENST00000380574.1	hg19	CCDS7740.1	.	.	.	.	.	.	.	.	.	.	G	14.16	2.451570	0.43531	.	.	ENSG00000110628	ENST00000347936;ENST00000312221;ENST00000449793;ENST00000380574	T;T;T;T	0.81163	0.34;0.34;-1.46;0.34	3.77	2.8	0.32819	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.460037	0.20295	N	0.095157	D	0.84316	0.5445	M	0.62723	1.935	0.09310	N	1	D;D	0.59357	0.97;0.985	P;P	0.61070	0.681;0.883	T	0.74343	-0.3696	10	0.59425	D	0.04	-12.6812	8.7536	0.34633	0.0:0.0:0.7726:0.2273	.	89;187	E9PRM7;Q96BI1	.;S22AI_HUMAN	S	187;187;89;187	ENSP00000307859:A187S;ENSP00000311139:A187S;ENSP00000392072:A89S;ENSP00000369948:A187S	ENSP00000311139:A187S	A	+	1	0	SLC22A18	2894450	0.031000	0.19500	0.002000	0.10522	0.012000	0.07955	1.338000	0.33873	0.814000	0.34374	0.491000	0.48974	GCT	.	.	.	none		0.687	SLC22A18-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027770.1	NM_183233		T	2937874	G	T	2937874	3	4	238	1	0	0	0	0	1	0	0	0	14462	1203	42	4	577	4	SLC22A18	11	2937874	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10		2937874	132068642	36	14525											
MARS	4141	hgsc.bcm.edu	37	chr12	57894254	57894254	+	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	tgtggctatgaggaggctcgGggtgaccagtgtgacaagtg	8	9	18	6	1	0	3	0	3	0	0	1	4	0	4	1	5	0	2	1	5	2	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr12:57894254G>C	ENST00000262027.5	+	10	1376	c.1242G>C	c.(1240-1242)cgG>cgC	p.R414R	MARS_ENST00000447721.2_3'UTR|MARS_ENST00000315473.5_Silent_p.R180R	NM_004990.3	NP_004981.2	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	414					gene expression (GO:0010467)|methionyl-tRNA aminoacylation (GO:0006431)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methionine-tRNA ligase activity (GO:0004825)|tRNA binding (GO:0000049)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	33			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)	AGGAGGCTCGGGGTGACCAGT	0.562																																					p.R414R		Atlas-SNP	.											.	MARS	84	.	0			c.G1242C						PASS	.						147	115	126					12																	57894254		2203	4300	6503	SO:0001819	synonymous_variant	4141	exon10			GGCTCGGGGTGAC	X94754	CCDS8942.1	12q13.3	2014-05-06	2007-02-26		ENSG00000166986	ENSG00000166986	6.1.1.10	"Aminoacyl tRNA synthetases / Class I"	6898	protein-coding gene	gene with protein product	"methionine tRNA ligase 1, cytoplasmic"	156560				10448063, 24482476	Standard	NM_004990		Approved	MetRS, SPG70	uc001sog.3	P56192	OTTHUMG00000169996	ENST00000262027.5:c.1242G>C	chr12.hg19:g.57894254G>C		213.0	0.0	.		187.0	44.0	.	NM_004990	B3KVK7|Q14895|Q53H14|Q96A15|Q96BZ0|Q9NSE0	Silent	SNP	ENST00000262027.5	hg19	CCDS8942.1																																																																																			.	.	.	none		0.562	MARS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407014.1	NM_004990		C	57894254	G	C	57894254	2	2	238	1	0	0	0	0	0	0	0	1	9323	1219	43	4		4	MARS	12	57894254	Silent	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10		57894254	75957641	37	14526											
NBEA	26960	hgsc.bcm.edu	37	chr13	35770159	35770159	+	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	cagaattagaaacaagtacaGgccctgatgccatgagtgaa	16	7	10	8	0	0	5	0	3	0	2	0	5	0	5	2	1	3	1	2	1	6	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr13:35770159G>T	ENST00000400445.3	+	31	5620	c.5086G>T	c.(5086-5088)Ggc>Tgc	p.G1696C	NBEA_ENST00000310336.4_Missense_Mutation_p.G1696C|NBEA_ENST00000540320.1_Missense_Mutation_p.G1696C|NBEA_ENST00000379939.2_Missense_Mutation_p.G1693C	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1696					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)		AACAAGTACAGGCCCTGATGC	0.433																																					p.G1696C		Atlas-SNP	.											.	NBEA	340	.	0			c.G5086T						PASS	.						79	78	78					13																	35770159		1906	4130	6036	SO:0001583	missense	26960	exon31			AGTACAGGCCCTG	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.5086G>T	chr13.hg19:g.35770159G>T	ENSP00000383295:p.Gly1696Cys	100.0	0.0	.		111.0	57.0	.	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.376162	0.82682	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518	T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.76688	0.4022	M	0.68317	2.08	0.80722	D	1	D;D	0.89917	0.999;1.0	P;D	0.80764	0.846;0.994	T	0.77742	-0.2474	10	0.72032	D	0.01	.	13.6145	0.62099	0.0706:0.0:0.9294:0.0	.	1696;1693	Q8NFP9;Q5T321	NBEA_HUMAN;.	C	1696;1696;1693;1696;323	ENSP00000440951:G1696C;ENSP00000383295:G1696C;ENSP00000369271:G1693C;ENSP00000308534:G1696C	ENSP00000308534:G1696C	G	+	1	0	NBEA	34668159	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.455000	0.80726	2.843000	0.97960	0.585000	0.79938	GGC	.	.	.	none		0.433	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		T	35770159	G	T	35770159	3	4	238	1	0	0	0	0	1	0	0	0	10194	1000	35	4	5208	4	NBEA	13	35770159	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10		35770159	79399719	38	14527											
FSIP1	161835	hgsc.bcm.edu	37	chr15	40056080	40056080	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttttgtattttccatctcCtctttactttgccaagcttc	5	22	3	11	0	2	0	0	0	2	0	5	0	3	0	3	0	3	2	3	0	3	10			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr15:40056080C>T	ENST00000350221.3	-	5	710	c.501G>A	c.(499-501)gaG>gaA	p.E167E		NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	167										NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		TTTCCATCTCCTCTTTACTTT	0.299																																					p.E167E		Atlas-SNP	.											.	FSIP1	53	.	0			c.G501A						PASS	.						51	57	55					15																	40056080		2201	4293	6494	SO:0001819	synonymous_variant	161835	exon5			CATCTCCTCTTTA	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.501G>A	chr15.hg19:g.40056080C>T		155.0	0.0	.		121.0	49.0	.	NM_152597	Q6X2C8|Q86Y89	Silent	SNP	ENST00000350221.3	hg19	CCDS10050.1																																																																																			.	.	.	none		0.299	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597		T	40056080	C	T	40056080	2	4	238	1	0	0	0	0	0	0	0	1	6081	680	24	2		2	FSIP1	15	40056080	Silent	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10		40056080	62475312	39	14528											
NDUFAF1	51103	hgsc.bcm.edu	37	chr15	41689069	41689069	+	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	tccaaagcaacttctttctgGtgatctccttgcaaatcccc	9	13	5	14	0	3	1	0	1	3	0	6	1	5	1	4	1	3	2	4	1	3	3			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr15:41689069G>A	ENST00000260361.4	-	2	570	c.189C>T	c.(187-189)caC>caT	p.H63H		NM_016013.3	NP_057097.2	Q9Y375	CIA30_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 1	63					mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|mitochondrial respiratory chain complex I (GO:0005747)	unfolded protein binding (GO:0051082)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	12		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;8e-17)|GBM - Glioblastoma multiforme(113;1.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.114)		CTTCTTTCTGGTGATCTCCTT	0.423																																					p.H63H		Atlas-SNP	.											.	NDUFAF1	39	.	0			c.C189T						PASS	.						118	121	120					15																	41689069		2203	4300	6503	SO:0001819	synonymous_variant	51103	exon2			TTTCTGGTGATCT	AF151823	CCDS10075.1	15q11.2-q21.3	2012-10-12	2012-05-08		ENSG00000137806	ENSG00000137806		"Mitochondrial respiratory chain complex assembly factors"	18828	protein-coding gene	gene with protein product		606934				11935339, 10810093	Standard	NM_016013		Approved	CIA30, CGI-65	uc001znx.3	Q9Y375	OTTHUMG00000130340	ENST00000260361.4:c.189C>T	chr15.hg19:g.41689069G>A		77.0	0.0	.		60.0	24.0	.	NM_016013	Q9BVZ5	Silent	SNP	ENST00000260361.4	hg19	CCDS10075.1																																																																																			.	.	.	none		0.423	NDUFAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252692.2	NM_016013		A	41689069	G	A	41689069	2	1	238	1	0	0	0	0	0	0	0	1	10281	1252	44	2		2	NDUFAF1	15	41689069	Silent	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	1632989	41689069	60842323	40	14529											
C15orf42	90381	hgsc.bcm.edu	37	chr15	90167321	90167321	+	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	gcagcagccttcatgggcacGcctcagaatcaaacacacca	13	5	8	15	1	3	1	3	0	0	1	3	1	3	1	3	1	3	3	3	1	2	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr15:90167321G>A	ENST00000268138.7	+	20	3885	c.3780G>A	c.(3778-3780)acG>acA	p.T1260T	KIF7_ENST00000558928.1_Intron|TICRR_ENST00000560985.1_Silent_p.T1259T			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	1260	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)										TCATGGGCACGCCTCAGAATC	0.542																																					p.T1260T		Atlas-SNP	.											.	.	.	.	0			c.G3780A						PASS	.						66	70	69					15																	90167321		2200	4299	6499	SO:0001819	synonymous_variant	90381	exon20			GGGCACGCCTCAG	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.3780G>A	chr15.hg19:g.90167321G>A		49.0	0.0	.		39.0	17.0	.	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Silent	SNP	ENST00000268138.7	hg19	CCDS10352.2																																																																																			.	.	.	none		0.542	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259		A	90167321	G	A	90167321	2	1	238	1	0	0	0	0	0	0	0	1	1798	1074	38	1		1	C15orf42	15	90167321	Silent	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	48478252	90167321	12364071	41	14530											
ANKS3	124401	hgsc.bcm.edu	37	chr16	4748510	4748510	+	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	ctggaggtcctcgcgggcgcGgtcctgctccagcaggcagc	4	6	16	15	4	0	0	0	0	0	0	4	1	3	1	3	5	3	3	3	5	0	0			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr16:4748510G>T	ENST00000304283.4	-	14	1936	c.1642C>A	c.(1642-1644)Cgc>Agc	p.R548S	ANKS3_ENST00000585773.1_Missense_Mutation_p.R475S|ANKS3_ENST00000446014.2_Missense_Mutation_p.R419S	NM_133450.3	NP_597707.1	Q6ZW76	ANKS3_HUMAN	ankyrin repeat and sterile alpha motif domain containing 3	548										endometrium(5)|kidney(4)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	19						TCGCGGGCGCGGTCCTGCTCC	0.736																																					p.R548S		Atlas-SNP	.											.	ANKS3	44	.	0			c.C1642A						PASS	.						6	7	6					16																	4748510		2086	4135	6221	SO:0001583	missense	124401	exon14			GGGCGCGGTCCTG	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.1642C>A	chr16.hg19:g.4748510G>T	ENSP00000304586:p.Arg548Ser	1.0	0.0	.		25.0	17.0	.	NM_133450	B4DWU4|D3DUE2|Q8TF25	Missense_Mutation	SNP	ENST00000304283.4	hg19	CCDS10520.1	.	.	.	.	.	.	.	.	.	.	G	13.71	2.318757	0.41096	.	.	ENSG00000168096	ENST00000304283;ENST00000446014	T;T	0.31510	1.49;3.24	5.46	-6.97	0.01616	.	1.035280	0.07528	N	0.911661	T	0.04815	0.0130	N	0.00289	-1.7	0.09310	N	0.999993	B	0.02656	0.0	B	0.01281	0.0	T	0.30001	-0.9993	10	0.08837	T	0.75	0.351	3.7451	0.08545	0.0874:0.2626:0.181:0.469	.	548	Q6ZW76	ANKS3_HUMAN	S	548;419	ENSP00000304586:R548S;ENSP00000406796:R419S	ENSP00000304586:R548S	R	-	1	0	ANKS3	4688511	0.000000	0.05858	0.001000	0.08648	0.091000	0.18340	-0.450000	0.06803	-1.265000	0.02449	-0.371000	0.07208	CGC	.	.	.	none		0.736	ANKS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251642.3	NM_133450		T	4748510	G	T	4748510	3	4	238	1	0	0	0	0	1	0	0	0	690	1116	39	4	344	4	ANKS3	16	4748510	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10		4748510	85606243	42	14531											
GRIN2A	2903	hgsc.bcm.edu	37	chr16	10273887	10273887	+	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	gatcatagatgcgcccccatGaatgcccaagatggggacga	12	6	12	11	2	1	3	1	1	0	2	1	6	1	4	3	2	2	0	3	2	3	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr16:10273887G>C	ENST00000396573.2	-	3	691	c.382C>G	c.(382-384)Cat>Gat	p.H128D	GRIN2A_ENST00000330684.3_Missense_Mutation_p.H128D|GRIN2A_ENST00000404927.2_Missense_Mutation_p.H128D|GRIN2A_ENST00000562109.1_Missense_Mutation_p.H128D|GRIN2A_ENST00000396575.2_Missense_Mutation_p.H128D	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	128					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)	GCGCCCCCATGAATGCCCAAG	0.597																																					p.H128D		Atlas-SNP	.											.	GRIN2A	366	.	0			c.C382G						PASS	.						56	52	53					16																	10273887		2197	4300	6497	SO:0001583	missense	2903	exon3			CCCCATGAATGCC		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.382C>G	chr16.hg19:g.10273887G>C	ENSP00000379818:p.His128Asp	145.0	0.0	.		158.0	42.0	.	NM_000833	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	hg19	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	G	19.62	3.862300	0.71949	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000330684;ENST00000396575	D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04	4.54	4.54	0.55810	Extracellular ligand-binding receptor (1);	0.062818	0.64402	D	0.000007	D	0.91068	0.7189	M	0.75447	2.3	0.80722	D	1	D;P;P	0.67145	0.996;0.879;0.803	D;P;P	0.64776	0.929;0.677;0.479	D	0.91402	0.5144	9	.	.	.	.	16.2901	0.82747	0.0:0.0:1.0:0.0	.	128;128;128	Q547U9;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	D	128	ENSP00000379818:H128D;ENSP00000385872:H128D;ENSP00000332549:H128D;ENSP00000379820:H128D	.	H	-	1	0	GRIN2A	10181388	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.938000	0.87678	2.088000	0.63022	0.561000	0.74099	CAT	.	.	.	none		0.597	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			C	10273887	G	C	10273887	3	2	238	1	0	0	0	0	1	0	0	0	6786	1290	45	4	4060	4	GRIN2A	16	10273887	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	5525377	10273887	80080866	43	14532											
DBNDD1	79007	hgsc.bcm.edu	37	chr16	90072805	90072805	+	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	gactgtggcctgccgctcggGgtcgcctaggggctgcttct	2	10	16	13	3	1	0	0	0	1	0	3	1	1	0	3	5	2	3	3	5	1	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr16:90072805G>T	ENST00000002501.6	-	4	546	c.415C>A	c.(415-417)Ccc>Acc	p.P139T	DBNDD1_ENST00000568838.1_Missense_Mutation_p.P259T|DBNDD1_ENST00000304733.3_Missense_Mutation_p.P159T|DBNDD1_ENST00000392973.3_Missense_Mutation_p.P145T	NM_001042610.1	NP_001036075.1	Q9H9R9	DBND1_HUMAN	dysbindin (dystrobrevin binding protein 1) domain containing 1	139						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)		TGCCGCTCGGGGTCGCCTAGG	0.677																																					p.P159T		Atlas-SNP	.											.	DBNDD1	9	.	0			c.C475A						PASS	.						35	45	42					16																	90072805		2023	4188	6211	SO:0001583	missense	79007	exon4			GCTCGGGGTCGCC	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.415C>A	chr16.hg19:g.90072805G>T	ENSP00000002501:p.Pro139Thr	38.0	0.0	.		62.0	16.0	.	NM_024043	B4DQS3|Q69YT2|Q9BW25	Missense_Mutation	SNP	ENST00000002501.6	hg19	CCDS42223.1	.	.	.	.	.	.	.	.	.	.	G	12.61	1.990417	0.35131	.	.	ENSG00000003249	ENST00000304733;ENST00000002501;ENST00000392973	T;T	0.30448	1.53;1.53	5.64	0.925	0.19424	.	0.270724	0.37577	N	0.002024	T	0.18002	0.0432	L	0.46157	1.445	0.25250	N	0.989681	B;B	0.20052	0.023;0.041	B;B	0.15052	0.012;0.011	T	0.13098	-1.0522	10	0.16420	T	0.52	-4.1737	1.4458	0.02364	0.2704:0.1553:0.4171:0.1571	.	139;159	Q9H9R9;Q9H9R9-2	DBND1_HUMAN;.	T	159;139;259	ENSP00000306407:P159T;ENSP00000002501:P139T	ENSP00000002501:P139T	P	-	1	0	DBNDD1	88600306	1.000000	0.71417	0.003000	0.11579	0.131000	0.20780	1.604000	0.36804	0.321000	0.23259	0.491000	0.48974	CCC	.	.	.	none		0.677	DBNDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272872.1	NM_024043		T	90072805	G	T	90072805	3	4	238	1	0	0	0	0	1	0	0	0	4255	1232	43	4	65	4	DBNDD1	16	90072805	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	79798918	90072805	281948	44	14533											
DNAH2	146754	hgsc.bcm.edu	37	chr17	7727530	7727530	+	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	cctgctgcagctggcagagcAcatgggcatggcccagcgct	7	6	14	14	1	0	1	0	0	0	1	0	1	0	1	2	3	5	7	2	3	0	0			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr17:7727530A>T	ENST00000572933.1	+	76	13030	c.11570A>T	c.(11569-11571)cAc>cTc	p.H3857L	DNAH2_ENST00000389173.2_Missense_Mutation_p.H3857L			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	3857	AAA 6. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|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)				CTGGCAGAGCACATGGGCATG	0.662																																					p.H3857L		Atlas-SNP	.											.	DNAH2	498	.	0			c.A11570T						PASS	.						63	56	59					17																	7727530		2203	4300	6503	SO:0001583	missense	146754	exon75			CAGAGCACATGGG	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.11570A>T	chr17.hg19:g.7727530A>T	ENSP00000458355:p.His3857Leu	27.0	0.0	.		100.0	56.0	.	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	A	13.72	2.321206	0.41096	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.08193	3.12	4.9	4.9	0.64082	Dynein heavy chain (1);	0.564059	0.19257	N	0.118766	T	0.05731	0.0150	N	0.11201	0.11	0.80722	D	1	B;B	0.14012	0.007;0.009	B;B	0.12156	0.004;0.007	T	0.38802	-0.9644	10	0.40728	T	0.16	.	13.4924	0.61405	1.0:0.0:0.0:0.0	.	3818;3857	Q9P225-2;Q9P225	.;DYH2_HUMAN	L	3818;3857	ENSP00000373825:H3857L	ENSP00000353818:H3818L	H	+	2	0	DNAH2	7668255	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	4.869000	0.63028	1.848000	0.53677	0.334000	0.21626	CAC	.	.	.	none		0.662	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		T	7727530	A	T	7727530	3	4	238	1	0	0	0	0	1	0	0	0	4604	159	6	5	11868	5	DNAH2	17	7727530	Missense_Mutation	SNP	A	TCGA-PJ-A5Z9-01A-11D-A28G-10		7727530	73467680	45	14534											
SPAG5	10615	hgsc.bcm.edu	37	chr17	26912886	26912886	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcctgtcaccttaccgcaTccttgcctctgagagccatt	7	12	7	15	1	2	1	1	1	1	1	3	2	3	1	6	0	4	1	6	0	1	3			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr17:26912886T>C	ENST00000321765.5	-	7	2068	c.1736A>G	c.(1735-1737)gAt>gGt	p.D579G		NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	579	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)					CCTTACCGCATCCTTGCCTCT	0.498																																					p.D579G		Atlas-SNP	.											.	SPAG5	92	.	0			c.A1736G						PASS	.						225	197	206					17																	26912886		2203	4300	6503	SO:0001583	missense	10615	exon7			ACCGCATCCTTGC	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.1736A>G	chr17.hg19:g.26912886T>C	ENSP00000323300:p.Asp579Gly	74.0	0.0	.		79.0	48.0	.	NM_006461	O95213|Q9BWE8|Q9NT17|Q9UFE6	Missense_Mutation	SNP	ENST00000321765.5	hg19	CCDS32594.1	.	.	.	.	.	.	.	.	.	.	T	15.69	2.907625	0.52333	.	.	ENSG00000076382	ENST00000321765;ENST00000536674	.	.	.	5.82	3.52	0.40303	.	0.549745	0.17799	N	0.161643	T	0.25827	0.0629	L	0.29908	0.895	0.22096	N	0.999364	P	0.48294	0.908	B	0.39660	0.306	T	0.05099	-1.0906	9	0.56958	D	0.05	-1.7343	10.252	0.43375	0.0:0.0:0.3183:0.6817	.	579	Q96R06	SPAG5_HUMAN	G	579;76	.	ENSP00000323300:D579G	D	-	2	0	SPAG5	23937013	0.989000	0.36119	0.994000	0.49952	0.917000	0.54804	1.208000	0.32345	0.414000	0.25790	0.533000	0.62120	GAT	.	.	.	none		0.498	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461		C	26912886	T	C	26912886	3	2	238	1	0	0	0	0	1	0	0	0	14994	1435	50	3	1917	3	SPAG5	17	26912886	Missense_Mutation	SNP	T	TCGA-PJ-A5Z9-01A-11D-A28G-10	19185356	26912886	54282324	46	14535											
KRT13	3860	hgsc.bcm.edu	37	chr17	39658844	39658844	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accgtgttctccagccccgcTttctggtggagcgacagaca	7	9	11	14	3	2	1	0	0	2	1	3	3	2	2	4	2	2	2	4	2	0	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr17:39658844T>C	ENST00000246635.3	-	6	1072	c.1026A>G	c.(1024-1026)aaA>aaG	p.K342K	KRT13_ENST00000587544.1_Silent_p.K342K|KRT13_ENST00000587118.1_5'Flank|KRT13_ENST00000336861.3_Silent_p.K342K|AC019349.5_ENST00000411759.1_RNA	NM_153490.2	NP_705694	P13646	K1C13_HUMAN	keratin 13	342	Coil 2.|Rod.				cellular response to retinoic acid (GO:0071300)|cytoskeleton organization (GO:0007010)|response to radiation (GO:0009314)|tongue morphogenesis (GO:0043587)	extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			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)				CCAGCCCCGCTTTCTGGTGGA	0.627																																					p.K342K		Atlas-SNP	.											.	KRT13	72	.	0			c.A1026G						PASS	.						70	66	67					17																	39658844		2203	4300	6503	SO:0001819	synonymous_variant	3860	exon6			CCCCGCTTTCTGG		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.1026A>G	chr17.hg19:g.39658844T>C		67.0	0.0	.		63.0	19.0	.	NM_002274	Q53G54|Q6AZK5|Q8N240	Silent	SNP	ENST00000246635.3	hg19	CCDS11396.1																																																																																			.	.	.	none		0.627	KRT13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257297.1	NM_153490		C	39658844	T	C	39658844	2	2	238	1	0	0	0	0	0	0	0	1	8457	1606	56	3		3	KRT13	17	39658844	Silent	SNP	T	TCGA-PJ-A5Z9-01A-11D-A28G-10	12745958	39658844	41536366	47	14536											
SLC14A1	6563	hgsc.bcm.edu	37	chr18	43316457	43316458	+	Frame_Shift_Ins	INS	-	-	A																															cattgaattccatgctcagcINSaaatgggacctccccgtctt																										TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr18:43316457_43316458insA	ENST00000321925.4	+	6	739_740	c.507_508insA	c.(508-510)aaafs	p.K170fs	SLC14A1_ENST00000535474.1_Frame_Shift_Ins_p.K38fs|SLC14A1_ENST00000586142.1_Frame_Shift_Ins_p.K170fs|RP11-116O18.3_ENST00000589510.1_RNA|SLC14A1_ENST00000402943.2_Frame_Shift_Ins_p.K65fs|SLC14A1_ENST00000415427.3_Frame_Shift_Ins_p.K226fs|RP11-116O18.3_ENST00000586213.1_RNA|SLC14A1_ENST00000589700.1_Frame_Shift_Ins_p.K170fs|SLC14A1_ENST00000591943.1_Intron|SLC14A1_ENST00000436407.3_Frame_Shift_Ins_p.K226fs|SLC14A1_ENST00000502059.2_Frame_Shift_Ins_p.K62fs	NM_001128588.3|NM_001146036.2|NM_015865.6	NP_001122060.3|NP_001139508.2|NP_056949.4	Q13336	UT1_HUMAN	solute carrier family 14 (urea transporter), member 1 (Kidd blood group)	170					transmembrane transport (GO:0055085)|urea transmembrane transport (GO:0071918)|urea transport (GO:0015840)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	urea channel activity (GO:0015265)|urea transmembrane transporter activity (GO:0015204)|water transmembrane transporter activity (GO:0005372)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	21						CCATGCTCAGCAAATGGGACCT	0.455																																					p.S225fs		Atlas-Indel,Pindel	.											.	SLC14A1	84	.	0			c.675_676insA						PASS	.																																			SO:0001589	frameshift_variant	6563	exon5			.	BC040128	CCDS11925.1, CCDS45860.1	18q11-q12	2014-07-19	2014-01-02		ENSG00000141469	ENSG00000141469		"Blood group antigens", "Solute carriers"	10918	protein-coding gene	gene with protein product		613868	"Kidd blood group", "solute carrier family 14 (urea transporter), member 1"	JK		7797558	Standard	NM_001146037		Approved	HsT1341, RACH1, RACH2	uc010dnk.3	Q13336	OTTHUMG00000132617	ENST00000321925.4:c.510dupA	chr18.hg19:g.43316460_43316460dupA	ENSP00000318546:p.Lys170fs	156.0	0.0	0		128.0	51.0	0.398438	NM_001146037	A8K0P3|B3KR62|B3KVX3|C9EHF2|Q86VM5	Frame_Shift_Ins	INS	ENST00000321925.4	hg19	CCDS11925.1																																																																																			.	.	.	none		0.455	SLC14A1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255860.2	NM_015865		A	43316458	-	A	43316457	7	5	238	1	0	1	1	0	0	0	0	0	14409	709	25	0	693	0	SLC14A1	18	43316457	Frame_Shift_Ins	INS	-	TCGA-PJ-A5Z9-01A-11D-A28G-10		43316457	34760791	48	14537											
TMEM149	79713	hgsc.bcm.edu	37	chr19	36230984	36230986	+	In_Frame_Del	DEL	CGG	CGG	-																															cagtgccccttggcagggacCggcctctggggataaggggt																								rs200340760		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	CGG	CGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr19:36230984_36230986delCGG	ENST00000592537.1	-	4	446_448	c.346_348delCCG	c.(346-348)ccgdel	p.P116del	AD000671.6_ENST00000589807.1_3'UTR|IGFLR1_ENST00000587101.1_5'UTR|IGFLR1_ENST00000246532.1_In_Frame_Del_p.P116del|KMT2B_ENST00000607650.1_RNA|IGFLR1_ENST00000588992.1_Intron|IGFLR1_ENST00000592889.1_Intron|IGFLR1_ENST00000344990.3_Intron			Q9H665	IGFR1_HUMAN	IGF-like family receptor 1	116						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(3)|large_intestine(1)|lung(8)|prostate(1)	15						TGGCAGGGACCGGCCTCTGGGGA	0.621																																					p.116_117del		Atlas-INDEL	.											.	IGFLR1	28	.	0			c.347_349del						PASS	.																																			SO:0001651	inframe_deletion	79713	exon4			.	AK026226	CCDS12472.1	19q13.12	2012-10-02	2011-04-04	2011-04-04	ENSG00000126246	ENSG00000126246			23620	protein-coding gene	gene with protein product		614143	"U2(RNU2) small nuclear RNA auxiliary factor 1-like 4", "transmembrane protein 149"	U2AF1L4, TMEM149		21454693	Standard	NM_024660		Approved	FLJ22573	uc002obd.4	Q9H665		ENST00000592537.1:c.346_348delCCG	chr19.hg19:g.36230984_36230986delCGG	ENSP00000466181:p.Pro116del	44.0	0.0	0		34.0	11.0	0.323529	NM_024660	Q8N5X0	In_Frame_Del	DEL	ENST00000592537.1	hg19	CCDS12472.1																																																																																			.	.	.	none		0.621	IGFLR1-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459077.1	NM_024660		-	36230986	CGG	-	36230984	7	5	238	1	0	1	0	1	0	0	0	0	16074	639	23	0	727	0	TMEM149	19	36230984	In_Frame_Del	DEL	CGG	TCGA-PJ-A5Z9-01A-11D-A28G-10		36230984	22897999	49	14538											
TMC2	117532	hgsc.bcm.edu	37	chr20	2592879	2592879	+	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	agaacatcactcactggactCtgtttaactattacaactct	13	13	4	11	0	4	1	2	0	2	1	4	2	4	2	0	1	4	1	0	1	5	4			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr20:2592879C>G	ENST00000358864.1	+	13	1651	c.1636C>G	c.(1636-1638)Ctg>Gtg	p.L546V	TMC2_ENST00000496948.1_3'UTR	NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	546					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						TCACTGGACTCTGTTTAACTA	0.512																																					p.L546V		Atlas-SNP	.											.	TMC2	121	.	0			c.C1636G						PASS	.						155	134	141					20																	2592879		2203	4300	6503	SO:0001583	missense	117532	exon13			TGGACTCTGTTTA	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.1636C>G	chr20.hg19:g.2592879C>G	ENSP00000351732:p.Leu546Val	63.0	0.0	.		78.0	10.0	.	NM_080751	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Missense_Mutation	SNP	ENST00000358864.1	hg19	CCDS13029.2	.	.	.	.	.	.	.	.	.	.	C	14.67	2.603805	0.46423	.	.	ENSG00000149488	ENST00000358864	T	0.66099	-0.19	5.85	5.85	0.93711	.	0.076272	0.53938	D	0.000052	T	0.69540	0.3122	M	0.73962	2.25	0.49051	D	0.999745	B;P;P;P	0.41524	0.382;0.563;0.753;0.638	B;B;P;B	0.46299	0.091;0.139;0.511;0.313	T	0.64609	-0.6367	10	0.22706	T	0.39	-10.7732	18.0364	0.89305	0.0:1.0:0.0:0.0	.	377;378;546;546	B4DFB3;B7ZAE6;Q8TDI7-3;Q8TDI7	.;.;.;TMC2_HUMAN	V	546	ENSP00000351732:L546V	ENSP00000351732:L546V	L	+	1	2	TMC2	2540879	0.933000	0.31639	1.000000	0.80357	0.997000	0.91878	1.970000	0.40520	2.941000	0.99782	0.655000	0.94253	CTG	.	.	.	none		0.512	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2			G	2592879	C	G	2592879	3	3	238	1	0	0	0	0	1	0	0	0	15997	912	32	4	1686	4	TMC2	20	2592879	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10		2592879	60432641	50	14539											
PANK2	80025	hgsc.bcm.edu	37	chr20	3869791	3869791	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccacgcgtccattgggcggCgccgccatcactctcttctg	4	9	10	18	5	3	0	1	0	2	0	5	0	4	0	4	2	0	0	4	2	0	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr20:3869791C>T	ENST00000316562.4	+	1	50	c.44C>T	c.(43-45)gCg>gTg	p.A15V	PANK2_ENST00000497424.1_Intron|RP11-119B16.2_ENST00000451507.1_RNA|PANK2_ENST00000610179.1_5'Flank	NM_153638.2	NP_705902.2	Q9BZ23	PANK2_HUMAN	pantothenate kinase 2	15					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						CATTGGGCGGCGCCGCCATCA	0.701																																					p.A15V		Atlas-SNP	.											.	PANK2	37	.	0			c.C44T						PASS	.						19	14	16					20																	3869791		2183	4282	6465	SO:0001583	missense	80025	exon1			GGGCGGCGCCGCC	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.44C>T	chr20.hg19:g.3869791C>T	ENSP00000313377:p.Ala15Val	85.0	0.0	.		113.0	34.0	.	NM_153638	B1AK33|B2Z3X0|D3DVZ0|Q5T7I2|Q5T7I4|Q7RTX5|Q8N7Q4|Q8TCR5|Q9BYW5|Q9HAF2	Missense_Mutation	SNP	ENST00000316562.4	hg19	CCDS13071.2	.	.	.	.	.	.	.	.	.	.	C	6.152	0.396211	0.11638	.	.	ENSG00000125779	ENST00000316562	D	0.97455	-4.39	4.57	-1.13	0.09775	.	0.546626	0.15407	N	0.263980	D	0.88691	0.6505	N	0.08118	0	0.21933	N	0.99946	B	0.06786	0.001	B	0.04013	0.001	T	0.80320	-0.1432	10	0.30854	T	0.27	-4.0E-4	4.3121	0.10976	0.0:0.4:0.1682:0.4318	.	15	Q9BZ23	PANK2_HUMAN	V	15	ENSP00000313377:A15V	ENSP00000313377:A15V	A	+	2	0	PANK2	3817791	0.959000	0.32827	0.677000	0.29947	0.004000	0.04260	-0.096000	0.11059	-0.135000	0.11495	-0.175000	0.13238	GCG	.	.	.	none		0.701	PANK2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077793.2	NM_024960		T	3869791	C	T	3869791	3	4	238	1	0	0	0	0	1	0	0	0	11424	768	27	1	46	1	PANK2	20	3869791	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10	1276912	3869791	59155729	51	14540											
VAPB	9217	hgsc.bcm.edu	37	chr20	57009683	57009684	+	Frame_Shift_Ins	INS	-	-	C																															tacagcctttcgattatgatINScccaatgagaaaagtaaaca																										TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr20:57009683_57009684insC	ENST00000475243.1	+	3	575_576	c.237_238insC	c.(238-240)cccfs	p.P80fs	VAPB_ENST00000265619.2_Intron|VAPB_ENST00000395802.3_Intron	NM_004738.4	NP_004729.1	O95292	VAPB_HUMAN	VAMP (vesicle-associated membrane protein)-associated protein B and C	80	MSP. {ECO:0000255|PROSITE- ProRule:PRU00132}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|endoplasmic reticulum unfolded protein response (GO:0030968)|modulation by virus of host morphology or physiology (GO:0019048)|positive regulation of viral genome replication (GO:0045070)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-tubulin binding (GO:0048487)|enzyme binding (GO:0019899)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|structural molecule activity (GO:0005198)			kidney(2)|lung(3)|prostate(1)	6	Lung NSC(12;0.000615)|all_lung(29;0.00186)		BRCA - Breast invasive adenocarcinoma(13;6.2e-12)|Epithelial(14;3.7e-08)|all cancers(14;3.88e-07)			TCGATTATGATCCCAATGAGAA	0.361																																					p.D79fs		Atlas-Indel,Pindel	.											.	VAPB	21	.	0			c.237_238insC						PASS	.																																			SO:0001589	frameshift_variant	9217	exon3			.	AF086628	CCDS33498.1, CCDS56198.1	20q13	2014-09-17			ENSG00000124164	ENSG00000124164			12649	protein-coding gene	gene with protein product		605704				9920726	Standard	NM_004738		Approved	VAP-B, VAP-C, ALS8	uc002xza.3	O95292	OTTHUMG00000032840	ENST00000475243.1:c.240dupC	chr20.hg19:g.57009686_57009686dupC	ENSP00000417175:p.Pro80fs	89.0	0.0	0		79.0	21.0	0.265823	NM_004738	A2A2F2|O95293|Q9P0H0	Frame_Shift_Ins	INS	ENST00000475243.1	hg19	CCDS33498.1																																																																																			.	.	.	none		0.361	VAPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079875.2			C	57009684	-	C	57009683	7	5	238	1	0	1	1	0	0	0	0	0	17134	1432	50	0	247	0	VAPB	20	57009683	Frame_Shift_Ins	INS	-	TCGA-PJ-A5Z9-01A-11D-A28G-10	53139892	57009683	6015837	52	14541											
KRTAP19-5	337972	hgsc.bcm.edu	37	chr21	31874285	31874285	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agagccgtatccgtagcctcCgtagccaccgccatagccca	9	6	9	17	4	0	1	0	0	0	1	2	1	2	1	8	0	4	3	8	0	4	4	rs370535457		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr21:31874285C>T	ENST00000334151.2	-	1	150	c.124G>A	c.(124-126)Gga>Aga	p.G42R		NM_181611.1	NP_853642.1	Q3LI72	KR195_HUMAN	keratin associated protein 19-5	42						intermediate filament (GO:0005882)				endometrium(1)|large_intestine(5)|lung(4)|pancreas(1)|prostate(1)	12						CCGTAGCCTCCGTAGCCACCG	0.572													C|||	1	0.000199681	8e-04	0	5008	,	,		17165	0		0	False		,,,				2504	0				p.G42R		Atlas-SNP	.											.	KRTAP19-5	32	.	0			c.G124A						PASS	.	C	ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	128	122	124		124	-0.3	0	21		124	0,8600		0,0,4300	no	missense	KRTAP19-5	NM_181611.1	125	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	42/73	31874285	1,13005	2203	4300	6503	SO:0001583	missense	337972	exon1			AGCCTCCGTAGCC	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.124G>A	chr21.hg19:g.31874285C>T	ENSP00000334985:p.Gly42Arg	172.0	0.0	.		48.0	34.0	.	NM_181611	A4IF22	Missense_Mutation	SNP	ENST00000334151.2	hg19	CCDS13597.1	.	.	.	.	.	.	.	.	.	.	C	12.38	1.920297	0.33908	2.27E-4	0.0	ENSG00000186977	ENST00000334151	T	0.11495	2.77	5.06	-0.26	0.12967	.	0.758211	0.10161	U	0.708309	T	0.07279	0.0184	.	.	.	0.09310	N	0.999999	P	0.48089	0.905	B	0.37480	0.251	T	0.30001	-0.9993	9	0.87932	D	0	-0.8878	4.9837	0.14180	0.0:0.5363:0.1489:0.3148	.	42	Q3LI72	KR195_HUMAN	R	42	ENSP00000334985:G42R	ENSP00000334985:G42R	G	-	1	0	KRTAP19-5	30796156	0.001000	0.12720	0.021000	0.16686	0.458000	0.32498	0.145000	0.16157	0.018000	0.15052	0.591000	0.81541	GGA	.	.	.	weak		0.572	KRTAP19-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128226.2			T	31874285	C	T	31874285	3	4	238	1	0	0	0	0	1	0	0	0	8539	661	23	1	97	1	KRTAP19-5	21	31874285	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10		31874285	16255610	53	14542											
SREBF2	6721	hgsc.bcm.edu	37	chr22	42289217	42289217	+	Frame_Shift_Del	DEL	T	T	-																															gccaccccctgggccagaagTttttcatggagcggagctgg																										TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr22:42289217delT	ENST00000361204.4	+	12	2471	c.2305delT	c.(2305-2307)tttfs	p.F770fs	SREBF2_ENST00000491541.1_3'UTR	NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	770					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						GGGCCAGAAGTTTTTCATGGA	0.582																																					p.K768fs		Atlas-Indel,Pindel	.											.	SREBF2	99	.	0			c.2304delG						PASS	.						55	58	57					22																	42289217		2203	4300	6503	SO:0001589	frameshift_variant	6721	exon12			.	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.2305delT	chr22.hg19:g.42289217delT	ENSP00000354476:p.Phe770fs	97.0	0.0	0		70.0	24.0	0.342857	NM_004599	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Frame_Shift_Del	DEL	ENST00000361204.4	hg19	CCDS14023.1																																																																																			.	.	.	none		0.582	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599		-	42289217	T	-	42289217	7	5	238	1	0	1	0	1	0	0	0	0	15154	1725	60	0	2351	0	SREBF2	22	42289217	Frame_Shift_Del	DEL	T	TCGA-PJ-A5Z9-01A-11D-A28G-10		42289217	9015349	54	14543											
TBL1X	6907	hgsc.bcm.edu	37	chrX	9683003	9683003	+	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	cttcgaggtgtgctggaacgCccgaggagacaaagtgggtg	9	7	17	8	3	0	1	0	0	0	1	1	5	0	2	1	4	2	1	1	4	2	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chrX:9683003C>T	ENST00000217964.7	+	17	2307	c.1667C>T	c.(1666-1668)gCc>gTc	p.A556V	TBL1X_ENST00000407597.2_Missense_Mutation_p.A556V|TBL1X_ENST00000424279.1_Missense_Mutation_p.A505V|TBL1X_ENST00000380961.1_Missense_Mutation_p.A505V|TBL1X_ENST00000536365.1_Missense_Mutation_p.A505V	NM_005647.3	NP_005638.1	O60907	TBL1X_HUMAN	transducin (beta)-like 1X-linked	556					canonical Wnt signaling pathway (GO:0060070)|cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|histone binding (GO:0042393)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|cervix(1)|endometrium(5)|large_intestine(7)|lung(2)|ovary(1)|skin(2)	20		Hepatocellular(5;0.000888)				TGCTGGAACGCCCGAGGAGAC	0.592																																					p.A556V		Atlas-SNP	.											.	TBL1X	103	.	0			c.C1667T						PASS	.						86	62	70					X																	9683003		2203	4300	6503	SO:0001583	missense	6907	exon17			GGAACGCCCGAGG	Y12781	CCDS14133.1, CCDS48078.1	Xp22.3	2013-01-10	2002-05-22	2002-05-24	ENSG00000101849	ENSG00000101849		"WD repeat domain containing"	11585	protein-coding gene	gene with protein product		300196	"transducin (beta)-like 1"	TBL1		10330347	Standard	NM_005647		Approved	EBI	uc004csr.3	O60907	OTTHUMG00000021117	ENST00000217964.7:c.1667C>T	chrX.hg19:g.9683003C>T	ENSP00000217964:p.Ala556Val	272.0	0.0	.		178.0	81.0	.	NM_001139466	A8K044|A8K4J7|Q86UY2	Missense_Mutation	SNP	ENST00000217964.7	hg19	CCDS14133.1	.	.	.	.	.	.	.	.	.	.	C	17.08	3.297142	0.60086	.	.	ENSG00000101849	ENST00000407597;ENST00000424279;ENST00000536365;ENST00000380961;ENST00000217964	T;T;T;T;T	0.81247	-1.47;-1.47;-1.47;-1.47;-1.47	3.8	3.8	0.43715	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.116908	0.56097	D	0.000024	T	0.77994	0.4214	L	0.58101	1.795	0.44852	D	0.997864	B;B	0.29955	0.263;0.263	B;B	0.29598	0.104;0.104	T	0.80054	-0.1543	10	0.72032	D	0.01	.	15.6252	0.76851	0.0:1.0:0.0:0.0	.	519;556	Q59F53;O60907	.;TBL1X_HUMAN	V	556;505;505;505;556	ENSP00000385988:A556V;ENSP00000394097:A505V;ENSP00000445317:A505V;ENSP00000370348:A505V;ENSP00000217964:A556V	ENSP00000217964:A556V	A	+	2	0	TBL1X	9643003	1.000000	0.71417	0.958000	0.39756	0.937000	0.57800	4.399000	0.59703	1.667000	0.50832	0.429000	0.28392	GCC	.	.	.	none		0.592	TBL1X-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055709.1	NM_005647		T	9683003	C	T	9683003	3	4	238	1	0	0	0	0	1	0	0	0	15651	739	26	2	1721	2	TBL1X	23	9683003	Missense_Mutation	SNP	C	TCGA-PJ-A5Z9-01A-11D-A28G-10		9683003	145587557	55	14544											
PHKA1	5255	hgsc.bcm.edu	37	chrX	71802352	71802352	+	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	tgccagcatggtgaggacaaGgatggcttcaaccagcagct	11	7	13	10	0	1	1	1	1	0	0	1	3	1	3	2	4	5	4	2	4	2	1			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chrX:71802352G>A	ENST00000373542.4	-	31	3553	c.3394C>T	c.(3394-3396)Ctt>Ttt	p.L1132F	PHKA1_ENST00000339490.3_Missense_Mutation_p.L1119F|PHKA1_ENST00000541944.1_Missense_Mutation_p.L1060F|PHKA1_ENST00000373539.3_Missense_Mutation_p.L1149F|PHKA1_ENST00000373545.3_Missense_Mutation_p.L1090F	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	1132					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)					GTGAGGACAAGGATGGCTTCA	0.448																																					p.L1132F		Atlas-SNP	.											.	PHKA1	129	.	0			c.C3394T						PASS	.						114	86	96					X																	71802352		2203	4300	6503	SO:0001583	missense	5255	exon31			GGACAAGGATGGC		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.3394C>T	chrX.hg19:g.71802352G>A	ENSP00000362643:p.Leu1132Phe	417.0	1.0	.		293.0	86.0	.	NM_002637	B7ZL05|B7ZL07|Q2M3D7	Missense_Mutation	SNP	ENST00000373542.4	hg19	CCDS14421.1	.	.	.	.	.	.	.	.	.	.	G	15.39	2.819920	0.50633	.	.	ENSG00000067177	ENST00000373545;ENST00000373542;ENST00000541944;ENST00000339490;ENST00000373539	D;D;D;D;D	0.91464	-2.84;-2.85;-2.83;-2.82;-2.83	5.12	5.12	0.69794	.	0.000000	0.64402	D	0.000001	D	0.93216	0.7839	M	0.63428	1.95	0.48901	D	0.999723	D;P;P;D	0.76494	0.999;0.913;0.794;0.975	D;P;P;P	0.87578	0.998;0.459;0.66;0.835	D	0.92493	0.6002	10	0.46703	T	0.11	-11.3305	8.8082	0.34952	0.1046:0.0:0.8954:0.0	.	1060;1090;1119;1132	B7ZL07;A6NIT2;P46020-2;P46020	.;.;.;KPB1_HUMAN	F	1090;1132;1060;1119;1149	ENSP00000362646:L1090F;ENSP00000362643:L1132F;ENSP00000441251:L1060F;ENSP00000342469:L1119F;ENSP00000362640:L1149F	ENSP00000342469:L1119F	L	-	1	0	PHKA1	71719077	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.085000	0.30840	2.132000	0.65825	0.594000	0.82650	CTT	.	.	.	none		0.448	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1			A	71802352	G	A	71802352	3	1	238	1	0	0	0	0	1	0	0	0	11850	1000	35	2	285	2	PHKA1	23	71802352	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	62119349	71802352	83468208	56	14545											
GPR50	9248	hgsc.bcm.edu	37	chrX	150348665	150348665	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgtcctccctctcctcatcGtgggtttctgctacgtgagg	3	14	10	14	3	3	1	1	1	2	0	8	1	5	1	3	2	2	2	3	2	1	2			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chrX:150348665G>A	ENST00000218316.3	+	2	679	c.610G>A	c.(610-612)Gtg>Atg	p.V204M	AF003625.3_ENST00000602313.1_lincRNA|GPR50-AS1_ENST00000454196.1_RNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	204					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)					TCTCCTCATCGTGGGTTTCTG	0.532																																					p.V204M		Atlas-SNP	.											.	GPR50	195	.	0			c.G610A						PASS	.						230	203	212					X																	150348665		2123	4223	6346	SO:0001583	missense	9248	exon2			CTCATCGTGGGTT	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.610G>A	chrX.hg19:g.150348665G>A	ENSP00000218316:p.Val204Met	80.0	0.0	.		43.0	12.0	.	NM_004224	Q0VGG3|Q3ZAR0	Missense_Mutation	SNP	ENST00000218316.3	hg19	CCDS44012.1	.	.	.	.	.	.	.	.	.	.	G	17.71	3.456799	0.63401	.	.	ENSG00000102195	ENST00000535473;ENST00000218316	T	0.35048	1.33	4.33	4.33	0.51752	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.50684	0.1630	L	0.53729	1.69	0.47547	D	0.999454	D;P	0.69078	0.997;0.819	D;P	0.64321	0.924;0.668	T	0.47018	-0.9149	10	0.36615	T	0.2	-12.9108	13.7644	0.62986	0.0:0.0:1.0:0.0	.	157;204	F5H1S3;Q13585	.;MTR1L_HUMAN	M	157;204	ENSP00000218316:V204M	ENSP00000218316:V204M	V	+	1	0	GPR50	150099323	1.000000	0.71417	0.981000	0.43875	0.745000	0.42441	9.754000	0.98908	1.903000	0.55091	0.529000	0.55759	GTG	.	.	.	none		0.532	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060874.1	NM_004224		A	150348665	G	A	150348665	3	1	238	1	0	0	0	0	1	0	0	0	6704	1145	40	1	616	1	GPR50	23	150348665	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	78546313	150348665	4921895	57	14546											
RENBP	5973	hgsc.bcm.edu	37	chrX	153200791	153200791	+	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	cgggggagggggcgggggcgGggcggctcagcagggcgccc	3	1	26	11	5	1	0	1	0	0	0	1	1	1	1	1	10	1	2	1	10	0	0			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chrX:153200791G>T	ENST00000393700.3	-	11	1312	c.1232C>A	c.(1231-1233)cCc>cAc	p.P411H	NAA10_ENST00000370015.4_5'Flank|RENBP_ENST00000369997.3_Missense_Mutation_p.P397H|NAA10_ENST00000370009.1_5'Flank|NAA10_ENST00000393712.3_5'Flank|RENBP_ENST00000412763.1_3'UTR|NAA10_ENST00000393710.3_5'Flank|NAA10_ENST00000464845.1_5'Flank	NM_002910.5	NP_002901.2	P51606	RENBP_HUMAN	renin binding protein	411					N-acetylglucosamine metabolic process (GO:0006044)|N-acetylmannosamine metabolic process (GO:0006051)|N-acetylneuraminate catabolic process (GO:0019262)|regulation of blood pressure (GO:0008217)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|endopeptidase inhibitor activity (GO:0004866)|N-acylglucosamine 2-epimerase activity (GO:0050121)			breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	20	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)				N-Acetyl-D-glucosamine(DB00141)	ggcgggggcggggCGGCTCAG	0.751																																					p.P411H		Atlas-SNP	.											.	RENBP	69	.	0			c.C1232A						PASS	.						2	3	2					X																	153200791		1563	2987	4550	SO:0001583	missense	5973	exon11			GGGGCGGGGCGGC		CCDS14738.2	Xq28	2013-09-23	2001-11-28		ENSG00000102032	ENSG00000102032			9959	protein-coding gene	gene with protein product	"N-acylglucosamine 2-epimerase", "GlcNAc 2-epimerase", "N-acetyl-D-glucosamine 2-epimerase"	312420	"renin-binding protein"			1618798	Standard	NM_002910		Approved	RNBP, RBP	uc004fjo.2	P51606	OTTHUMG00000024224	ENST00000393700.3:c.1232C>A	chrX.hg19:g.153200791G>T	ENSP00000377303:p.Pro411His	0.0	0.0	.		8.0	4.0	.	NM_002910	B4DNZ3|Q96BI6	Missense_Mutation	SNP	ENST00000393700.3	hg19	CCDS14738.2	.	.	.	.	.	.	.	.	.	.	g	13.98	2.398865	0.42512	.	.	ENSG00000102032	ENST00000393700;ENST00000369997;ENST00000451114	T;T	0.32988	1.43;1.43	3.76	-6.35	0.01975	Six-hairpin glycosidase-like (1);	2.963070	0.01364	U	0.012354	T	0.24890	0.0604	L	0.44542	1.39	0.09310	N	0.99999	B	0.02656	0.0	B	0.01281	0.0	T	0.19353	-1.0308	10	0.45353	T	0.12	1.1156	7.9104	0.29787	0.1647:0.1371:0.6982:0.0	.	411	P51606	RENBP_HUMAN	H	411;397;124	ENSP00000377303:P411H;ENSP00000359014:P397H	ENSP00000359014:P397H	P	-	2	0	RENBP	152853985	0.000000	0.05858	0.000000	0.03702	0.698000	0.40448	-1.269000	0.02834	-1.762000	0.01308	0.445000	0.29226	CCC	.	.	.	none		0.751	RENBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061103.3	NM_002910		T	153200791	G	T	153200791	3	4	238	1	0	0	0	0	1	0	0	0	13238	1232	43	4	55	4	RENBP	23	153200791	Missense_Mutation	SNP	G	TCGA-PJ-A5Z9-01A-11D-A28G-10	2852126	153200791	2069769	58	14547											
UBIAD1	29914	hgsc.bcm.edu	37	chr1	11345827	11345827	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcccactggtctatgccaTccccctcgccctcagcaccg	5	9	6	21	2	2	0	1	0	1	0	5	0	4	0	6	1	2	1	6	1	1	2			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr1:11345827T>C	ENST00000376810.5	+	2	982	c.656T>C	c.(655-657)aTc>aCc	p.I219T	UBIAD1_ENST00000376804.2_Intron	NM_013319.2	NP_037451.1	Q9Y5Z9	UBIA1_HUMAN	UbiA prenyltransferase domain containing 1	219					menaquinone biosynthetic process (GO:0009234)|ubiquinone biosynthetic process (GO:0006744)|vitamin K biosynthetic process (GO:0042371)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	antioxidant activity (GO:0016209)|prenyltransferase activity (GO:0004659)			endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|prostate(3)	12	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.000818)|all_lung(284;0.00105)|Colorectal(325;0.0062)|Breast(348;0.012)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.52e-06)|COAD - Colon adenocarcinoma(227;0.000254)|BRCA - Breast invasive adenocarcinoma(304;0.000299)|Kidney(185;0.000754)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0487)		GTCTATGCCATCCCCCTCGCC	0.607																																					p.I219T		Atlas-SNP	.											UBIAD1,caecum,carcinoma,0,1	UBIAD1	27	.	0			c.T656C						PASS	.						170	136	148					1																	11345827		2203	4300	6503	SO:0001583	missense	29914	exon2			ATGCCATCCCCCT		CCDS129.1	1p36.22	2012-05-02			ENSG00000120942	ENSG00000120942			30791	protein-coding gene	gene with protein product	"transitional epithelia response protein"	611632	"Schnyder crystalline corneal dystrophy"	SCCD		20953171, 12497587, 11314041, 17668063, 17962451, 8894705	Standard	NM_013319		Approved	TERE1	uc001asg.3	Q9Y5Z9	OTTHUMG00000002075	ENST00000376810.5:c.656T>C	chr1.hg19:g.11345827T>C	ENSP00000366006:p.Ile219Thr	145.0	0.0	.		107.0	39.0	.	NM_013319	B3KQG3|Q53GX3|Q5THD4	Missense_Mutation	SNP	ENST00000376810.5	hg19	CCDS129.1	.	.	.	.	.	.	.	.	.	.	T	17.95	3.514621	0.64634	.	.	ENSG00000120942	ENST00000376810	D	0.92752	-3.1	5.94	5.94	0.96194	.	0.260438	0.37623	N	0.002007	D	0.90024	0.6885	L	0.52364	1.645	0.80722	D	1	P	0.45768	0.866	B	0.43194	0.411	D	0.89014	0.3430	10	0.33940	T	0.23	-5.3535	14.1354	0.65284	0.0:0.0:0.0:1.0	.	219	Q9Y5Z9	UBIA1_HUMAN	T	219	ENSP00000366006:I219T	ENSP00000366006:I219T	I	+	2	0	UBIAD1	11268414	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.665000	0.83852	2.265000	0.75225	0.482000	0.46254	ATC	.	.	.	none		0.607	UBIAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005773.1	NM_013319		C	11345827	T	C	11345827	3	2	239	1	0	0	0	0	1	0	0	0	16897	1435	50	3	662	3	UBIAD1	1	11345827	Missense_Mutation	SNP	T	TCGA-PJ-A8JU-01A-11D-A35Z-10		11345827	237904794	1	14548											
COL16A1	1307	hgsc.bcm.edu	37	chr1	32151315	32151315	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggccaggcaaggccaccacAcggacatccccatcctgaag	11	3	11	16	1	0	1	0	1	0	0	2	2	2	2	6	4	0	1	6	4	2	0			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr1:32151315A>G	ENST00000373672.3	-	29	2457	c.1941T>C	c.(1939-1941)cgT>cgC	p.R647R	COL16A1_ENST00000373668.3_Silent_p.R647R|COL16A1_ENST00000271069.6_Silent_p.R646R	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	647	Nonhelical region 7 (NC7).				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)		AGGCCACCACACGGACATCCC	0.642																																					p.R647R	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.T1941C						PASS	.						108	116	114					1																	32151315		1933	4136	6069	SO:0001819	synonymous_variant	1307	exon29			CACCACACGGACA	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.1941T>C	chr1.hg19:g.32151315A>G		292.0	0.0	.		270.0	87.0	.	NM_001856	Q16593|Q59F89|Q71RG9	Silent	SNP	ENST00000373672.3	hg19	CCDS41297.1																																																																																			.	.	.	none		0.642	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856		G	32151315	A	G	32151315	2	3	239	1	0	0	0	0	0	0	0	1	3675	146	6	3		3	COL16A1	1	32151315	Silent	SNP	A	TCGA-PJ-A8JU-01A-11D-A35Z-10	20805488	32151315	217099306	2	14549											
C1orf113	79729	hgsc.bcm.edu	37	chr1	36773209	36773209	+	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	gctggacagtgggcccccaaGtgagacctcgactctgtgac	8	7	13	13	1	1	2	0	2	1	1	2	5	1	3	3	2	0	1	3	2	1	0			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr1:36773209G>A	ENST00000426732.2	+	5	373				SH3D21_ENST00000453908.2_Splice_Site|SH3D21_ENST00000505871.1_Splice_Site|SH3D21_ENST00000312808.4_Splice_Site			A4FU49	SH321_HUMAN	SH3 domain containing 21							extracellular vesicular exosome (GO:0070062)				endometrium(1)|large_intestine(6)|lung(4)|pancreas(1)	12						GGGCCCCCAAGTGAGACCTCG	0.577																																					.		Atlas-SNP	.											.	SH3D21	73	.	0			c.436+1G>A						PASS	.						102	107	105					1																	36773209		692	1591	2283	SO:0001627	intron_variant	79729	exon5			CCCCAAGTGAGAC	AK056459	CCDS30674.1, CCDS30674.2	1p34.3	2011-02-21	2011-02-21	2011-02-21	ENSG00000214193	ENSG00000214193			26236	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 113"	C1orf113		12477932	Standard	NM_024676		Approved	FLJ22938	uc010oia.1	A4FU49	OTTHUMG00000007868	ENST00000426732.2:c.89-162G>A	chr1.hg19:g.36773209G>A		144.0	0.0	.		126.0	37.0	.	NM_001162530	B4DLI6|D3DPS6|J3KQM5|Q5VTK7|Q86XZ6|Q8N445|Q96DN4|Q9H5W5	Splice_Site	SNP	ENST00000426732.2	hg19		.	.	.	.	.	.	.	.	.	.	G	23.1	4.379730	0.82682	.	.	ENSG00000214193	ENST00000373139;ENST00000453908;ENST00000505871	.	.	.	5.32	5.32	0.75619	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4867	0.67622	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SH3D21	36545796	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.008000	0.63991	2.491000	0.84063	0.655000	0.94253	.	.	.	.	none		0.577	SH3D21-202	KNOWN	basic	protein_coding	protein_coding		NM_024676		A	36773209	G	A	36773209	1	1	239	0	1	0	0	0	0	0	0	0	1988	1043	36	2		2	C1orf113	1	36773209	Intron	SNP	G	TCGA-PJ-A8JU-01A-11D-A35Z-10	4621894	36773209	212477412	3	14550											
BSND	7809	hgsc.bcm.edu	37	chr1	55472846	55472846	+	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	cagtgatggaggagaaggtgGccctggcgacgttcaggcct	8	7	17	9	2	1	2	1	1	0	1	1	5	1	3	2	6	0	1	2	6	1	1			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr1:55472846G>T	ENST00000371265.4	+	3	703	c.449G>T	c.(448-450)gGc>gTc	p.G150V		NM_057176.2	NP_476517.1	Q8WZ55	BSND_HUMAN	barttin CLCNK-type chloride channel accessory beta subunit	150					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	chloride channel activity (GO:0005254)|chloride channel regulator activity (GO:0017081)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	17						GGAGAAGGTGGCCCTGGCGAC	0.612																																					p.G150V	Ovarian(191;1657 2078 22894 42033 48899)	Atlas-SNP	.											.	BSND	36	.	0			c.G449T						PASS	.						91	82	85					1																	55472846		2203	4300	6503	SO:0001583	missense	7809	exon3			AAGGTGGCCCTGG	AY034632	CCDS602.1	1p32.3	2014-06-17	2014-06-17		ENSG00000162399	ENSG00000162399			16512	protein-coding gene	gene with protein product		606412	"deafness, autosomal recessive 73", "Bartter syndrome, infantile, with sensorineural deafness (Barttin)"	DFNB73		11687798, 11734858, 19646679	Standard	NM_057176		Approved	BART	uc001cye.3	Q8WZ55	OTTHUMG00000008112	ENST00000371265.4:c.449G>T	chr1.hg19:g.55472846G>T	ENSP00000360312:p.Gly150Val	162.0	0.0	.		121.0	40.0	.	NM_057176	Q6NT28	Missense_Mutation	SNP	ENST00000371265.4	hg19	CCDS602.1	.	.	.	.	.	.	.	.	.	.	G	13.70	2.315138	0.40996	.	.	ENSG00000162399	ENST00000371265	T	0.66280	-0.2	3.69	2.76	0.32466	.	0.936787	0.08850	N	0.884550	T	0.63200	0.2491	L	0.57536	1.79	0.19300	N	0.999979	P	0.48016	0.904	P	0.49887	0.625	T	0.53648	-0.8409	10	0.56958	D	0.05	-8.1298	4.0436	0.09763	0.1256:0.0:0.6418:0.2326	.	150	Q8WZ55	BSND_HUMAN	V	150	ENSP00000360312:G150V	ENSP00000360312:G150V	G	+	2	0	BSND	55245434	0.034000	0.19679	0.074000	0.20217	0.134000	0.20937	1.699000	0.37804	1.100000	0.41517	0.478000	0.44815	GGC	.	.	.	none		0.612	BSND-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022213.4	NM_057176		T	55472846	G	T	55472846	3	4	239	1	0	0	0	0	1	0	0	0	1533	1203	42	4	459	4	BSND	1	55472846	Missense_Mutation	SNP	G	TCGA-PJ-A8JU-01A-11D-A35Z-10	18699637	55472846	193777775	4	14551											
PYGO2	90780	hgsc.bcm.edu	37	chr1	154931749	154931749	+	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	agggtccggaccaggaaaggGacttgtgttaggcggcaggc	9	6	18	8	2	0	0	0	0	0	0	1	3	1	3	2	7	0	2	2	7	2	2	rs267598059		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr1:154931749G>A	ENST00000368457.2	-	3	898	c.727C>T	c.(727-729)Ccc>Tcc	p.P243S	PYGO2_ENST00000368456.1_Missense_Mutation_p.P206S|PYGO2_ENST00000483463.1_5'Flank|RP11-307C12.12_ENST00000605085.1_RNA	NM_138300.3	NP_612157.1	Q9BRQ0	PYGO2_HUMAN	pygopus family PHD finger 2	243	Pro-rich.				brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|developmental growth (GO:0048589)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|mammary gland development (GO:0030879)|palate development (GO:0060021)|positive regulation of chromatin binding (GO:0035563)|post-embryonic development (GO:0009791)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|spermatid nucleus differentiation (GO:0007289)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone acetyltransferase regulator activity (GO:0035034)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(3)|skin(2)|urinary_tract(1)	10	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CCAGGAAAGGGACTTGTGTTA	0.612																																					p.P243S	NSCLC(87;357 1460 1955 21029 23522)	Atlas-SNP	.											PYGO2,NS,carcinoma,0,1	PYGO2	32	.	0			c.C727T						PASS	.						22	23	23					1																	154931749		2203	4300	6503	SO:0001583	missense	90780	exon3			GAAAGGGACTTGT	BC006132	CCDS1075.1	1q22	2013-10-09	2013-10-09		ENSG00000163348	ENSG00000163348		"Zinc fingers, PHD-type"	30257	protein-coding gene	gene with protein product		606903	"pygopus homolog 2 (Drosophila)"			11988739	Standard	NM_138300		Approved		uc001fft.3	Q9BRQ0	OTTHUMG00000037370	ENST00000368457.2:c.727C>T	chr1.hg19:g.154931749G>A	ENSP00000357442:p.Pro243Ser	139.0	0.0	.		148.0	38.0	.	NM_138300	Q8WYZ4|Q96CY2	Missense_Mutation	SNP	ENST00000368457.2	hg19	CCDS1075.1	.	.	.	.	.	.	.	.	.	.	G	12.01	1.810294	0.32053	.	.	ENSG00000163348	ENST00000368457;ENST00000368456	T;T	0.52754	0.65;0.71	4.72	4.72	0.59763	.	0.379769	0.24652	N	0.036709	T	0.35128	0.0921	N	0.24115	0.695	0.54753	D	0.999983	D	0.89917	1.0	D	0.79108	0.992	T	0.21348	-1.0248	10	0.02654	T	1	-4.499	14.7378	0.69430	0.0:0.0:1.0:0.0	.	243	Q9BRQ0	PYGO2_HUMAN	S	243;206	ENSP00000357442:P243S;ENSP00000357441:P206S	ENSP00000357441:P206S	P	-	1	0	PYGO2	153198373	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	4.079000	0.57613	2.454000	0.82982	0.462000	0.41574	CCC	.	.	.	none		0.612	PYGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090949.1	NM_138300		A	154931749	G	A	154931749	3	1	239	1	0	0	0	0	1	0	0	0	12877	1174	41	2	497	2	PYGO2	1	154931749	Missense_Mutation	SNP	G	TCGA-PJ-A8JU-01A-11D-A35Z-10	99458903	154931749	94318872	5	14552											
ARHGAP30	257106	hgsc.bcm.edu	37	chr1	161018086	161018086	+	Missense_Mutation	SNP	A	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	aagagaacaggggcatagacAgccgtctggactgggctgcc	11	5	15	10	1	1	2	0	0	1	2	1	4	1	3	2	4	3	2	2	4	3	1			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr1:161018086A>C	ENST00000368013.3	-	12	3045	c.2725T>G	c.(2725-2727)Tgt>Ggt	p.C909G	ARHGAP30_ENST00000368015.1_Missense_Mutation_p.C732G|USF1_ENST00000368021.3_5'Flank|USF1_ENST00000435396.1_5'Flank|ARHGAP30_ENST00000368016.3_Missense_Mutation_p.C698G	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	909					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)			GGGCATAGACAGCCGTCTGGA	0.617																																					p.C909G		Atlas-SNP	.											.	ARHGAP30	105	.	0			c.T2725G						PASS	.						45	41	42					1																	161018086		2203	4300	6503	SO:0001583	missense	257106	exon12			ATAGACAGCCGTC	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.2725T>G	chr1.hg19:g.161018086A>C	ENSP00000356992:p.Cys909Gly	65.0	0.0	.		47.0	17.0	.	NM_001025598	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Missense_Mutation	SNP	ENST00000368013.3	hg19	CCDS30918.1	.	.	.	.	.	.	.	.	.	.	A	4.313	0.057320	0.08339	.	.	ENSG00000186517	ENST00000368016;ENST00000368013;ENST00000368015	T;T;T	0.34859	2.79;2.87;1.34	4.61	3.47	0.39725	.	0.621137	0.14461	N	0.318218	T	0.12475	0.0303	L	0.56769	1.78	0.09310	N	1	B;B	0.30482	0.281;0.0	B;B	0.24701	0.055;0.001	T	0.24048	-1.0171	10	0.14656	T	0.56	.	8.9598	0.35840	0.5893:0.4107:0.0:0.0	.	909;698	Q7Z6I6;Q7Z6I6-2	RHG30_HUMAN;.	G	698;909;732	ENSP00000356995:C698G;ENSP00000356992:C909G;ENSP00000356994:C732G	ENSP00000356992:C909G	C	-	1	0	ARHGAP30	159284710	0.016000	0.18221	0.054000	0.19295	0.338000	0.28826	1.132000	0.31418	0.613000	0.30089	0.374000	0.22700	TGT	.	.	.	none		0.617	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720		C	161018086	A	C	161018086	3	2	239	1	0	0	0	0	1	0	0	0	879	188	7	5	584	5	ARHGAP30	1	161018086	Missense_Mutation	SNP	A	TCGA-PJ-A8JU-01A-11D-A35Z-10	6086337	161018086	88232535	6	14553											
MTR	4548	hgsc.bcm.edu	37	chr1	236979823	236979823	+	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	gagggatttgtcatcagcgtGtctcatggagaaccactctg	9	11	12	9	1	4	1	3	0	2	1	5	4	4	2	1	2	2	0	1	2	1	1			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr1:236979823G>A	ENST00000366577.5	+	8	1138	c.744G>A	c.(742-744)gtG>gtA	p.V248V	MTR_ENST00000418145.2_3'UTR|MTR_ENST00000535889.1_Silent_p.V248V	NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase	248	Hcy-binding. {ECO:0000255|PROSITE- ProRule:PRU00333}.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|methylation (GO:0032259)|nervous system development (GO:0007399)|pteridine-containing compound metabolic process (GO:0042558)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	cobalamin binding (GO:0031419)|methionine synthase activity (GO:0008705)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	67	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	TCATCAGCGTGTCTCATGGAG	0.463																																					p.V248V		Atlas-SNP	.											.	MTR	127	.	0			c.G744A						PASS	.						154	148	150					1																	236979823		2203	4299	6502	SO:0001819	synonymous_variant	4548	exon8			CAGCGTGTCTCAT	U73338	CCDS1614.1, CCDS73054.1	1q43	2011-05-12			ENSG00000116984	ENSG00000116984	2.1.1.13		7468	protein-coding gene	gene with protein product		156570				8968735	Standard	NM_000254		Approved	cblG	uc001hyi.4	Q99707	OTTHUMG00000040060	ENST00000366577.5:c.744G>A	chr1.hg19:g.236979823G>A		85.0	0.0	.		71.0	19.0	.	NM_000254	A1L4N8|A9Z1W4|B9EGF7|Q99713|Q99723	Silent	SNP	ENST00000366577.5	hg19	CCDS1614.1																																																																																			.	.	.	none		0.463	MTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096632.2	NM_000254		A	236979823	G	A	236979823	2	1	239	1	0	0	0	0	0	0	0	1	9965	1364	48	2		2	MTR	1	236979823	Silent	SNP	G	TCGA-PJ-A8JU-01A-11D-A35Z-10	75961737	236979823	12270798	7	14554											
SMC6	79677	hgsc.bcm.edu	37	chr2	17865003	17865003	+	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	actttactatccagatcaagAtaggtctctcttgcttcttg	9	16	6	10	0	4	2	1	0	3	2	6	2	5	2	1	1	2	1	1	1	4	7			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr2:17865003A>C	ENST00000448223.2	-	24	2975	c.2706T>G	c.(2704-2706)taT>taG	p.Y902*	SMC6_ENST00000381272.4_Nonsense_Mutation_p.Y928*|SMC6_ENST00000402989.1_Nonsense_Mutation_p.Y902*|SMC6_ENST00000351948.4_Nonsense_Mutation_p.Y902*	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	902					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					CCAGATCAAGATAGGTCTCTC	0.313																																					p.Y902X		Atlas-SNP	.											.	SMC6	102	.	0			c.T2706G						PASS	.						75	82	79					2																	17865003		2202	4298	6500	SO:0001587	stop_gained	79677	exon24			ATCAAGATAGGTC	AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"Structural maintenance of chromosomes proteins"	20466	protein-coding gene	gene with protein product		609387	"SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.2706T>G	chr2.hg19:g.17865003A>C	ENSP00000404092:p.Tyr902*	289.0	0.0	.		234.0	76.0	.	NM_001142286	A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Nonsense_Mutation	SNP	ENST00000448223.2	hg19	CCDS1690.1	.	.	.	.	.	.	.	.	.	.	A	41	9.120162	0.99071	.	.	ENSG00000163029	ENST00000448223;ENST00000351948;ENST00000381272;ENST00000402989	.	.	.	6.02	-0.274	0.12910	.	0.057067	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08179	T	0.78	.	10.3803	0.44108	0.6665:0.0:0.3335:0.0	.	.	.	.	X	902;902;928;902	.	ENSP00000323439:Y902X	Y	-	3	2	SMC6	17728484	0.997000	0.39634	1.000000	0.80357	0.996000	0.88848	0.364000	0.20325	0.157000	0.19338	0.533000	0.62120	TAT	.	.	.	none		0.313	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207359.1	NM_024624		C	17865003	A	C	17865003	4	2	239	1	0	0	0	0	0	1	0	0	14800	340	12	5	589	5	SMC6	2	17865003	Nonsense_Mutation	SNP	A	TCGA-PJ-A8JU-01A-11D-A35Z-10		17865003	225334370	8	14555											
NCOA1	8648	hgsc.bcm.edu	37	chr2	24930361	24930361	+	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	tctgctaactcttcaggaggTtcttgtccctcttctcatag	6	16	7	12	0	6	0	2	0	5	0	8	1	7	1	1	2	2	2	1	2	2	6			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr2:24930361T>G	ENST00000406961.1	+	13	2674	c.2022T>G	c.(2020-2022)ggT>ggG	p.G674G	NCOA1_ENST00000288599.5_Silent_p.G674G|NCOA1_ENST00000348332.3_Silent_p.G674G|NCOA1_ENST00000407230.1_Silent_p.G523G|NCOA1_ENST00000405141.1_Silent_p.G674G|NCOA1_ENST00000395856.3_Silent_p.G674G|NCOA1_ENST00000538539.1_Silent_p.G674G			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	674	Ser-rich.				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)					CTTCAGGAGGTTCTTGTCCCT	0.493			T	PAX3	alveolar rhadomyosarcoma																																p.G674G		Atlas-SNP	.		Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	NCOA1	210	.	0			c.T2022G						PASS	.						105	104	104					2																	24930361		2203	4300	6503	SO:0001819	synonymous_variant	8648	exon11			AGGAGGTTCTTGT	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.2022T>G	chr2.hg19:g.24930361T>G		145.0	0.0	.		108.0	35.0	.	NM_147223	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Silent	SNP	ENST00000406961.1	hg19	CCDS1712.1																																																																																			.	.	.	none		0.493	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223		G	24930361	T	G	24930361	2	3	239	1	0	0	0	0	0	0	0	1	10235	1712	60	5		5	NCOA1	2	24930361	Silent	SNP	T	TCGA-PJ-A8JU-01A-11D-A35Z-10	7065358	24930361	218269012	9	14556											
NAT8	9027	hgsc.bcm.edu	37	chr2	73868395	73868395	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacaggcagagctcctaccaTgcccaccaccttctcttcag	10	8	6	17	0	2	1	1	0	1	1	4	1	3	1	5	1	4	2	5	1	2	3			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr2:73868395T>C	ENST00000272425.3	-	2	510	c.361A>G	c.(361-363)Atg>Gtg	p.M121V		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						GCTCCTACCATGCCCACCACC	0.537																																					p.M121V		Atlas-SNP	.											.	NAT8	26	.	0			c.A361G						PASS	.						92	90	91					2																	73868395		2203	4300	6503	SO:0001583	missense	9027	exon2			CTACCATGCCCAC	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.361A>G	chr2.hg19:g.73868395T>C	ENSP00000272425:p.Met121Val	101.0	0.0	.		105.0	38.0	.	NM_003960		Missense_Mutation	SNP	ENST00000272425.3	hg19	CCDS1926.1	.	.	.	.	.	.	.	.	.	.	T	4.168	0.029686	0.08101	.	.	ENSG00000144035	ENST00000272425	T	0.21191	2.02	3.86	3.86	0.44501	GCN5-related N-acetyltransferase (GNAT) domain (2);Acyl-CoA N-acyltransferase (2);	0.596637	0.18180	N	0.149173	T	0.15825	0.0381	L	0.33485	1.01	0.26806	N	0.969104	B	0.18610	0.029	B	0.23018	0.043	T	0.15867	-1.0422	10	0.19590	T	0.45	-0.2375	11.3146	0.49383	0.0:0.0:0.0:1.0	.	121	Q9UHE5	NAT8_HUMAN	V	121	ENSP00000272425:M121V	ENSP00000272425:M121V	M	-	1	0	NAT8	73721903	0.986000	0.35501	0.838000	0.33150	0.124000	0.20399	2.187000	0.42602	1.715000	0.51383	0.524000	0.50904	ATG	.	.	.	none		0.537	NAT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327854.1	NM_003960		C	73868395	T	C	73868395	3	2	239	1	0	0	0	0	1	0	0	0	10186	1464	51	3	326	3	NAT8	2	73868395	Missense_Mutation	SNP	T	TCGA-PJ-A8JU-01A-11D-A35Z-10	48938034	73868395	169330978	10	14557											
ACTG2	72	hgsc.bcm.edu	37	chr2	74129580	74129580	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctctcaaataccccattgaaCacggcatcatcaccaactgg	13	8	5	15	1	3	1	3	1	1	0	4	1	3	1	3	2	3	1	3	2	4	2			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr2:74129580C>T	ENST00000409624.1	+	4	863	c.220C>T	c.(220-222)Cac>Tac	p.H74Y	ACTG2_ENST00000409731.3_Intron|ACTG2_ENST00000409918.1_Missense_Mutation_p.H74Y|ACTG2_ENST00000345517.3_Missense_Mutation_p.H74Y			P63267	ACTH_HUMAN	actin, gamma 2, smooth muscle, enteric	74					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						CCCCATTGAACACGGCATCAT	0.493																																					p.H74Y		Atlas-SNP	.											.	ACTG2	37	.	0			c.C220T						PASS	.						145	118	127					2																	74129580		2203	4300	6503	SO:0001583	missense	72	exon3			ATTGAACACGGCA		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.220C>T	chr2.hg19:g.74129580C>T	ENSP00000386857:p.His74Tyr	92.0	0.0	.		76.0	45.0	.	NM_001615	B2R7E7|B4E315|D6W5H8|E9PG30|P12718|Q504R1|Q6FI22	Missense_Mutation	SNP	ENST00000409624.1	hg19	CCDS1930.1	.	.	.	.	.	.	.	.	.	.	C	15.99	2.995682	0.54147	.	.	ENSG00000163017	ENST00000345517;ENST00000409918;ENST00000442912;ENST00000409624	D;D;D;D	0.97404	-4.37;-3.46;-2.56;-4.37	3.84	3.84	0.44239	.	0.000000	0.85682	D	0.000000	D	0.98966	0.9648	H	0.97732	4.065	0.47547	D	0.999456	D;P	0.57571	0.98;0.85	D;D	0.75020	0.985;0.909	D	0.99053	1.0828	10	0.87932	D	0	.	15.0246	0.71659	0.0:1.0:0.0:0.0	.	74;74	B8ZZJ2;P63267	.;ACTH_HUMAN	Y	74	ENSP00000295137:H74Y;ENSP00000387182:H74Y;ENSP00000410020:H74Y;ENSP00000386857:H74Y	ENSP00000295137:H74Y	H	+	1	0	ACTG2	73983088	1.000000	0.71417	0.956000	0.39512	0.795000	0.44927	7.584000	0.82572	2.147000	0.66899	0.563000	0.77884	CAC	.	.	.	none		0.493	ACTG2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328086.1	NM_001615		T	74129580	C	T	74129580	3	4	239	1	0	0	0	0	1	0	0	0	197	478	17	2	226	2	ACTG2	2	74129580	Missense_Mutation	SNP	C	TCGA-PJ-A8JU-01A-11D-A35Z-10	261185	74129580	169069793	11	14558											
FMNL2	114793	hgsc.bcm.edu	37	chr2	153415322	153415322	+	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	agtggaatatctctcatttgCacagtacgcggtaacgtaag	12	11	10	8	3	2	0	1	0	1	0	3	1	2	1	0	2	3	4	0	2	5	5			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr2:153415322C>A	ENST00000288670.9	+	5	795	c.428C>A	c.(427-429)gCa>gAa	p.A143E		NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	143	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						CTCTCATTTGCACAGTACGCG	0.368																																					p.A143E		Atlas-SNP	.											.	FMNL2	75	.	0			c.C428A						PASS	.						115	114	114					2																	153415322		1886	4117	6003	SO:0001583	missense	114793	exon5			CATTTGCACAGTA	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.428C>A	chr2.hg19:g.153415322C>A	ENSP00000288670:p.Ala143Glu	104.0	0.0	.		83.0	24.0	.	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Missense_Mutation	SNP	ENST00000288670.9	hg19	CCDS46429.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.865789	0.91511	.	.	ENSG00000157827	ENST00000288670	D	0.89485	-2.52	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	D	0.94974	0.8374	M	0.84433	2.695	0.80722	D	1	D	0.67145	0.996	D	0.78314	0.991	D	0.95164	0.8284	10	0.52906	T	0.07	.	18.421	0.90590	0.0:1.0:0.0:0.0	.	143	Q96PY5-3	.	E	143	ENSP00000288670:A143E	ENSP00000288670:A143E	A	+	2	0	FMNL2	153123568	1.000000	0.71417	0.987000	0.45799	0.976000	0.68499	7.421000	0.80204	2.335000	0.79485	0.467000	0.42956	GCA	.	.	.	none		0.368	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905		A	153415322	C	A	153415322	3	1	239	1	0	0	0	0	1	0	0	0	5959	710	25	4	446	4	FMNL2	2	153415322	Missense_Mutation	SNP	C	TCGA-PJ-A8JU-01A-11D-A35Z-10	79285742	153415322	89784051	12	14559											
HOXD4	3233	hgsc.bcm.edu	37	chr2	177016768	177016783	+	Frame_Shift_Del	DEL	GGATGAAGAAGGTGCA	GGATGAAGAAGGTGCA	-																															gccggccgtggtctacccctGgatgaagaaggtgcacgtga																								rs547685014		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	GGATGAAGAAGGTGCA	GGATGAAGAAGGTGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr2:177016768_177016783delGGATGAAGAAGGTGCA	ENST00000306324.3	+	1	819_834	c.407_422delGGATGAAGAAGGTGCA	c.(406-423)tggatgaagaaggtgcacfs	p.WMKKVH136fs	HOXD3_ENST00000468418.3_5'UTR|MIR10B_ENST00000385011.1_RNA	NM_014621.2	NP_055436.2	P09016	HXD4_HUMAN	homeobox D4	136					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)		GTCTACCCCTGGATGAAGAAGGTGCACGTGAATTCG	0.671																																					p.136_141del		Atlas-Indel,Pindel	.											.	HOXD4	32	.	0			c.406_421del						PASS	.																																			SO:0001589	frameshift_variant	3233	exon1			.		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.407_422delGGATGAAGAAGGTGCA	chr2.hg19:g.177016768_177016783delGGATGAAGAAGGTGCA	ENSP00000302548:p.Trp136fs	127.0	0.0	0		66.0	14.0	0.212121	NM_014621	B2R9R3|Q96AU0	Frame_Shift_Del	DEL	ENST00000306324.3	hg19	CCDS2269.1																																																																																			.	.	.	none		0.671	HOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255697.2			-	177016783	GGATGAAGAAGGTGCA	-	177016768	7	5	239	1	0	1	0	1	0	0	0	0	7331	1357	47	0	409	0	HOXD4	2	177016768	Frame_Shift_Del	DEL	GGATGAAGAAGGTGCA	TCGA-PJ-A8JU-01A-11D-A35Z-10	23601446	177016768	66182605	13	14560											
TTN	7273	hgsc.bcm.edu	37	chr2	179421832	179421832	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccatgaaaggctgacagagTtctttgaaatatcagtgata	14	11	10	6	0	2	5	1	4	1	1	2	5	2	5	1	1	0	2	1	1	4	4			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr2:179421832T>C	ENST00000591111.1	-	280	83350	c.83126A>G	c.(83125-83127)aAc>aGc	p.N27709S	TTN_ENST00000342992.6_Missense_Mutation_p.N26782S|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.N20477S|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.N20410S|TTN_ENST00000460472.2_Missense_Mutation_p.N20285S|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.N29350S			Q8WZ42	TITIN_HUMAN	titin	27709	Fibronectin type-III 102. {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)			GCTGACAGAGTTCTTTGAAAT	0.433																																					p.N29350S		Atlas-SNP	.											.	TTN	18412	.	0			c.A88049G						PASS	.						59	56	57					2																	179421832		1894	4122	6016	SO:0001583	missense	7273	exon330			ACAGAGTTCTTTG	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.83126A>G	chr2.hg19:g.179421832T>C	ENSP00000465570:p.Asn27709Ser	99.0	0.0	.		47.0	18.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	14.28	2.488456	0.44249	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56444	0.46;0.46;0.46;0.46	5.81	4.59	0.56863	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.38374	0.1038	N	0.17564	0.495	0.38032	D	0.935192	B;B;B;B	0.16603	0.006;0.006;0.006;0.018	B;B;B;B	0.15870	0.014;0.014;0.014;0.014	T	0.41179	-0.9523	9	0.87932	D	0	.	13.5686	0.61832	0.0:0.0:0.1846:0.8154	.	20285;20410;20477;27709	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	S	26782;20285;20477;20410;20282	ENSP00000343764:N26782S;ENSP00000434586:N20285S;ENSP00000340554:N20477S;ENSP00000352154:N20410S	ENSP00000340554:N20477S	N	-	2	0	TTN	179130078	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	4.375000	0.59549	2.343000	0.79666	0.533000	0.62120	AAC	.	.	.	none		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179421832	T	C	179421832	3	2	239	1	0	0	0	0	1	0	0	0	16747	1725	60	3	20062	3	TTN	2	179421832	Missense_Mutation	SNP	T	TCGA-PJ-A8JU-01A-11D-A35Z-10	2405064	179421832	63777541	14	14561											
GLS	2744	hgsc.bcm.edu	37	chr2	191795233	191795233	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccaatgttatgggtatgaTgtgctggtctcctcctctgg	5	14	11	11	0	2	1	0	1	2	0	4	1	3	1	4	3	1	3	4	3	3	2			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr2:191795233T>C	ENST00000320717.3	+	13	1754	c.1496T>C	c.(1495-1497)aTg>aCg	p.M499T	GLS_ENST00000409215.1_Missense_Mutation_p.M4T|GLS_ENST00000409626.1_Missense_Mutation_p.M70T|GLS_ENST00000409428.1_Missense_Mutation_p.M4T|GLS_ENST00000338435.4_Missense_Mutation_p.M499T	NM_014905.4	NP_055720.3	O94925	GLSK_HUMAN	glutaminase	499					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)	ATGGGTATGATGTGCTGGTCT	0.388																																					p.M499T		Atlas-SNP	.											.	GLS	47	.	0			c.T1496C						PASS	.						153	143	146					2																	191795233		2203	4300	6503	SO:0001583	missense	2744	exon13			GTATGATGTGCTG	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.1496T>C	chr2.hg19:g.191795233T>C	ENSP00000317379:p.Met499Thr	123.0	0.0	.		90.0	33.0	.	NM_014905	Q9UL05|Q9UL06|Q9UL07|Q9UN40	Missense_Mutation	SNP	ENST00000320717.3	hg19	CCDS2308.1	.	.	.	.	.	.	.	.	.	.	T	14.94	2.686240	0.47991	.	.	ENSG00000115419	ENST00000320717;ENST00000338435;ENST00000409626;ENST00000457316;ENST00000409428;ENST00000409215;ENST00000412247	T;T;T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01;1.01;1.01	5.84	5.84	0.93424	Beta-lactamase/transpeptidase-like (1);	0.000000	0.85682	D	0.000000	T	0.45856	0.1363	L	0.51422	1.61	0.80722	D	1	B;B;B;B;B	0.33612	0.134;0.419;0.045;0.419;0.145	B;B;B;B;B	0.40101	0.137;0.319;0.097;0.319;0.139	T	0.39563	-0.9608	10	0.45353	T	0.12	-17.0749	16.2233	0.82274	0.0:0.0:0.0:1.0	.	70;499;153;499;499	B7Z2P1;A8K132;Q68D38;O94925;O94925-3	.;.;.;GLSK_HUMAN;.	T	499;499;70;70;4;4;20	ENSP00000317379:M499T;ENSP00000340689:M499T;ENSP00000386417:M70T;ENSP00000395596:M70T;ENSP00000387177:M4T;ENSP00000387135:M4T;ENSP00000403329:M20T	ENSP00000317379:M499T	M	+	2	0	GLS	191503478	1.000000	0.71417	1.000000	0.80357	0.654000	0.38779	8.040000	0.89188	2.243000	0.73865	0.482000	0.46254	ATG	.	.	.	none		0.388	GLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255999.2			C	191795233	T	C	191795233	3	2	239	1	0	0	0	0	1	0	0	0	6470	1464	51	3	1546	3	GLS	2	191795233	Missense_Mutation	SNP	T	TCGA-PJ-A8JU-01A-11D-A35Z-10	12373401	191795233	51404140	15	14562											
PTPRN	5798	hgsc.bcm.edu	37	chr2	220173977	220173977	+	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	ctgcagccccccgggcggctGctcagcagcaggaggcagag	7	3	16	15	2	1	1	1	0	0	1	1	2	1	2	3	4	5	6	3	4	0	0			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr2:220173977G>A	ENST00000295718.2	-	1	318	c.78C>T	c.(76-78)agC>agT	p.S26S	PTPRN_ENST00000409251.3_Silent_p.S26S|PTPRN_ENST00000423636.2_5'Flank	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	26					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)		CCGGGCGGCTGCTCAGCAGCA	0.751																																					p.S26S		Atlas-SNP	.											.	PTPRN	138	.	0			c.C78T						PASS	.						3	4	3					2																	220173977		1857	3826	5683	SO:0001819	synonymous_variant	5798	exon1			GCGGCTGCTCAGC		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.78C>T	chr2.hg19:g.220173977G>A		94.0	0.0	.		95.0	42.0	.	NM_002846	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Silent	SNP	ENST00000295718.2	hg19	CCDS2440.1																																																																																			.	.	.	none		0.751	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2			A	220173977	G	A	220173977	2	1	239	1	0	0	0	0	0	0	0	1	12820	1310	46	2		2	PTPRN	2	220173977	Silent	SNP	G	TCGA-PJ-A8JU-01A-11D-A35Z-10	28378744	220173977	23025396	16	14563											
SERPINE2	5270	hgsc.bcm.edu	37	chr2	224856616	224856616	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctttgtgttctcgggttggaAccgtgatttccacagaccct	6	14	10	11	2	1	2	0	1	1	1	3	3	2	3	3	2	1	2	3	2	1	4			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr2:224856616A>G	ENST00000258405.4	-	4	831	c.589T>C	c.(589-591)Ttc>Ctc	p.F197L	SERPINE2_ENST00000409304.1_Missense_Mutation_p.F197L|SERPINE2_ENST00000447280.2_Missense_Mutation_p.F209L|SERPINE2_ENST00000409840.3_Missense_Mutation_p.F197L	NM_001136528.1|NM_006216.3	NP_001130000.1|NP_006207.1	P07093	GDN_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2	197					blood coagulation (GO:0007596)|cerebellar granular layer morphogenesis (GO:0021683)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|innervation (GO:0060384)|long-term synaptic potentiation (GO:0060291)|mating plug formation (GO:0042628)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of plasminogen activation (GO:0010757)|negative regulation of platelet activation (GO:0010544)|negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein processing (GO:0010955)|negative regulation of proteolysis (GO:0045861)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of sodium ion transport (GO:0010766)|positive regulation of astrocyte differentiation (GO:0048711)|regulation of cell migration (GO:0030334)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of timing of cell differentiation (GO:0048505)|secretion by cell (GO:0032940)|secretory granule organization (GO:0033363)|seminal vesicle epithelium development (GO:0061108)	cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|neuromuscular junction (GO:0031594)|platelet alpha granule (GO:0031091)|vesicle (GO:0031982)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	17		Renal(207;0.025)|all_lung(227;0.0586)|Lung NSC(271;0.0682)|all_hematologic(139;0.0797)		Epithelial(121;5.68e-10)|all cancers(144;1.9e-07)|Lung(261;0.0088)|LUSC - Lung squamous cell carcinoma(224;0.00902)		TCGGGTTGGAACCGTGATTTC	0.517																																					p.F209L		Atlas-SNP	.											.	SERPINE2	103	.	0			c.T625C						PASS	.						160	122	135					2																	224856616		2203	4300	6503	SO:0001583	missense	5270	exon4			GTTGGAACCGTGA	M17783	CCDS2460.1, CCDS46525.1, CCDS46526.1	2q36.1	2014-02-18	2005-08-18		ENSG00000135919	ENSG00000135919		"Serine (or cysteine) peptidase inhibitors"	8951	protein-coding gene	gene with protein product	"glial-derived nexin 1"	177010	"serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2"	PI7		7665170, 24172014	Standard	NM_006216		Approved	PN1, GDN, PNI, nexin	uc002vnu.2	P07093	OTTHUMG00000133163	ENST00000258405.4:c.589T>C	chr2.hg19:g.224856616A>G	ENSP00000258405:p.Phe197Leu	117.0	0.0	.		105.0	32.0	.	NM_001136530	B2R6A4|B4DIF2|Q53S15|Q5D0C4	Missense_Mutation	SNP	ENST00000258405.4	hg19	CCDS2460.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.483952	0.84854	.	.	ENSG00000135919	ENST00000409304;ENST00000258405;ENST00000409840;ENST00000447280;ENST00000432738	T;D;T;T;T	0.94897	-0.02;-3.55;-0.02;-0.02;-0.02	5.8	5.8	0.92144	Serpin domain (3);	0.000000	0.85682	D	0.000000	D	0.96679	0.8916	H	0.95780	3.72	0.80722	D	1	B;B	0.27229	0.172;0.172	B;B	0.35240	0.198;0.198	D	0.96028	0.9014	10	0.87932	D	0	.	16.1506	0.81618	1.0:0.0:0.0:0.0	.	209;197	B4DIF2;P07093	.;GDN_HUMAN	L	197;197;197;209;197	ENSP00000386412:F197L;ENSP00000258405:F197L;ENSP00000386969:F197L;ENSP00000415786:F209L;ENSP00000408452:F197L	ENSP00000258405:F197L	F	-	1	0	SERPINE2	224564860	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	8.890000	0.92477	2.206000	0.71126	0.528000	0.53228	TTC	.	.	.	none		0.517	SERPINE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256865.2	NM_006216		G	224856616	A	G	224856616	3	3	239	1	0	0	0	0	1	0	0	0	14125	43	2	3	631	3	SERPINE2	2	224856616	Missense_Mutation	SNP	A	TCGA-PJ-A8JU-01A-11D-A35Z-10	4682639	224856616	18342757	17	14564											
KBTBD5	131377	hgsc.bcm.edu	37	chr3	42730387	42730387	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctgaacaagatgtgcgtctAtgaccccaagaagtttgagt	12	10	10	9	1	1	5	0	3	1	2	1	5	1	5	3	0	2	1	3	0	5	2			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr3:42730387A>G	ENST00000287777.4	+	4	1548	c.1448A>G	c.(1447-1449)tAt>tGt	p.Y483C		NM_152393.2	NP_689606.2	Q2TBA0	KLH40_HUMAN	kelch-like family member 40	483					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)											ATGTGCGTCTATGACCCCAAG	0.612																																					p.Y483C		Atlas-SNP	.											.	.	.	.	0			c.A1448G						PASS	.						69	71	70					3																	42730387		2203	4300	6503	SO:0001583	missense	131377	exon4			GCGTCTATGACCC	AK056577	CCDS2703.1	3p21.33	2013-07-30	2013-02-22	2013-01-08	ENSG00000157119	ENSG00000157119		"Kelch-like", "BTB/POZ domain containing"	30372	protein-coding gene	gene with protein product	"sarcosynapsin", "nemaline myopathy type 8"	615340	"kelch repeat and BTB (POZ) domain containing 5", "kelch-like 40 (Drosophila)"	KBTBD5		23746549	Standard	NM_152393		Approved	SRYP, NEM8	uc003clv.1	Q2TBA0	OTTHUMG00000133045	ENST00000287777.4:c.1448A>G	chr3.hg19:g.42730387A>G	ENSP00000287777:p.Tyr483Cys	135.0	0.0	.		129.0	25.0	.	NM_152393	Q86SI1|Q96MR2	Missense_Mutation	SNP	ENST00000287777.4	hg19	CCDS2703.1	.	.	.	.	.	.	.	.	.	.	a	19.17	3.775461	0.70107	.	.	ENSG00000157119	ENST00000287777;ENST00000452129	D	0.87966	-2.32	3.81	3.81	0.43845	Kelch-type beta propeller (1);	0.261096	0.39475	N	0.001341	D	0.96012	0.8701	H	0.98786	4.33	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.97162	0.9838	10	0.87932	D	0	.	13.1169	0.59305	1.0:0.0:0.0:0.0	.	483	Q2TBA0	KBTB5_HUMAN	C	483;228	ENSP00000287777:Y483C	ENSP00000287777:Y483C	Y	+	2	0	KBTBD5	42705391	1.000000	0.71417	0.984000	0.44739	0.956000	0.61745	8.989000	0.93506	1.769000	0.52152	0.353000	0.21931	TAT	.	.	.	none		0.612	KLHL40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256651.1	NM_152393		G	42730387	A	G	42730387	3	3	239	1	0	0	0	0	1	0	0	0	8003	449	16	3	1462	3	KBTBD5	3	42730387	Missense_Mutation	SNP	A	TCGA-PJ-A8JU-01A-11D-A35Z-10		42730387	155292043	18	14565											
C3orf54	7318	hgsc.bcm.edu	37	chr3	49841865	49841865	+	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	0	0	0	0	0	0	0	0	0	0	ggcttctcggaggtgtcaggCagcacatggcgagaggaaga	10	6	17	8	2	2	2	1	0	1	2	3	5	2	4	0	6	1	3	0	6	1	1			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr3:49841865C>T	ENST00000333486.3	-	0	3299				MIR5193_ENST00000584510.1_RNA|FAM212A_ENST00000333323.4_Silent_p.G103G	NM_003335.2	NP_003326.2	P41226	UBA7_HUMAN	ubiquitin-like modifier activating enzyme 7						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)		AGGTGTCAGGCAGCACATGGC	0.632																																					p.G103G		Atlas-SNP	.											.	.	.	.	0			c.C309T						PASS	.						93	89	91					3																	49841865		2203	4300	6503	SO:0001628	intergenic_variant	389119	exon2			GTCAGGCAGCACA	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		chr3.hg19:g.49841865C>T		61.0	0.0	.		79.0	17.0	.	NM_203370	Q9BRB2	Silent	SNP	ENST00000333486.3	hg19	CCDS2805.1																																																																																			.	.	.	none		0.632	UBA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350503.1	NM_003335		T	49841865	C	T	49841865	1	4	239	0	1	0	0	0	0	0	0	0	2235	697	25	2		2	C3orf54	3	49841865	IGR	SNP	C	TCGA-PJ-A8JU-01A-11D-A35Z-10	7111478	49841865	148180565	19	14566											
TKT	7086	hgsc.bcm.edu	37	chr3	53264594	53264594	+	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	tgatgcggtcactggcatggCccagcttggccagtgcctgc	5	9	14	13	1	1	1	1	1	0	0	1	1	1	1	3	4	4	2	3	4	0	1			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr3:53264594C>T	ENST00000462138.1	-	8	1074	c.986G>A	c.(985-987)gGc>gAc	p.G329D	TKT_ENST00000423516.1_Missense_Mutation_p.G337D|TKT_ENST00000296289.6_Missense_Mutation_p.G282D|TKT_ENST00000461139.1_5'UTR|TKT_ENST00000423525.2_Missense_Mutation_p.G329D			P29401	TKT_HUMAN	transketolase	329					carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|glyceraldehyde-3-phosphate biosynthetic process (GO:0046166)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|regulation of growth (GO:0040008)|small molecule metabolic process (GO:0044281)|xylulose biosynthetic process (GO:0005999)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|peroxisome (GO:0005777)|vesicle (GO:0031982)	cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|transketolase activity (GO:0004802)	p.K327fs*1(1)		endometrium(5)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17		Prostate(884;0.0959)		BRCA - Breast invasive adenocarcinoma(193;0.000159)|OV - Ovarian serous cystadenocarcinoma(275;0.000314)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)		ACTGGCATGGCCCAGCTTGGC	0.602																																					p.G337D	Colon(133;1506 2347 35238 42177)	Atlas-SNP	.											.	TKT	38	.	1	Deletion - Frameshift(1)	lung(1)	c.G1010A						PASS	.						83	77	79					3																	53264594		2203	4300	6503	SO:0001583	missense	7086	exon9			GCATGGCCCAGCT		CCDS2871.1, CCDS58834.1	3p14.3	2008-07-31	2008-07-31		ENSG00000163931	ENSG00000163931	2.2.1.1		11834	protein-coding gene	gene with protein product	"Wernicke-Korsakoff syndrome"	606781				1567394	Standard	NM_001064		Approved		uc011beq.2	P29401	OTTHUMG00000158192	ENST00000462138.1:c.986G>A	chr3.hg19:g.53264594C>T	ENSP00000417773:p.Gly329Asp	98.0	0.0	.		118.0	67.0	.	NM_001258028	A8K089|B4DE31|E7EPA7|Q8TBA3|Q96HH3	Missense_Mutation	SNP	ENST00000462138.1	hg19	CCDS2871.1	.	.	.	.	.	.	.	.	.	.	C	35	5.464525	0.96257	.	.	ENSG00000163931	ENST00000462138;ENST00000423525;ENST00000423516;ENST00000296289;ENST00000414014	D;D;D;D	0.91792	-2.91;-2.91;-2.91;-2.91	5.69	5.69	0.88448	Transketolase-like, pyrimidine-binding domain (2);	0.000000	0.85682	D	0.000000	D	0.97729	0.9255	H	0.96943	3.91	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98576	1.0648	10	0.87932	D	0	0.4241	19.8045	0.96525	0.0:1.0:0.0:0.0	.	337;246;329	E7EPA7;B3KSI4;P29401	.;.;TKT_HUMAN	D	329;329;337;282;163	ENSP00000417773:G329D;ENSP00000405455:G329D;ENSP00000391481:G337D;ENSP00000296289:G282D	ENSP00000296289:G282D	G	-	2	0	TKT	53239634	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.676000	0.91093	0.655000	0.94253	GGC	.	.	.	none		0.602	TKT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350356.1			T	53264594	C	T	53264594	3	4	239	1	0	0	0	0	1	0	0	0	15946	739	26	2	913	2	TKT	3	53264594	Missense_Mutation	SNP	C	TCGA-PJ-A8JU-01A-11D-A35Z-10	3422729	53264594	144757836	20	14567											
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121417110	121417110	+	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	ttccttcacctgagagagaaGctggtctctttcttcagaca	9	13	8	11	0	4	3	2	1	2	3	6	5	5	3	2	1	1	1	2	1	1	4			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr3:121417110G>C	ENST00000340645.5	-	13	2370	c.2245C>G	c.(2245-2247)Ctt>Gtt	p.L749V	GOLGB1_ENST00000393667.3_Missense_Mutation_p.L754V	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	749					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)		TGAGAGAGAAGCTGGTCTCTT	0.418																																					p.L754V		Atlas-SNP	.											.	GOLGB1	319	.	0			c.C2260G						PASS	.						136	130	132					3																	121417110		2203	4299	6502	SO:0001583	missense	2804	exon13			AGAGAAGCTGGTC	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.2245C>G	chr3.hg19:g.121417110G>C	ENSP00000341848:p.Leu749Val	82.0	0.0	.		95.0	26.0	.	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	hg19	CCDS3004.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.27|11.27	1.587926|1.587926	0.28268|0.28268	.|.	.|.	ENSG00000173230|ENSG00000173230	ENST00000340645;ENST00000393667;ENST00000494517;ENST00000426235|ENST00000489400	T;T;T|.	0.35421|.	1.94;1.94;1.31|.	5.72|5.72	4.83|4.83	0.62350|0.62350	.|.	0.118223|.	0.38436|.	N|.	0.001690|.	T|T	0.57829|0.57829	0.2080|0.2080	M|M	0.69823|0.69823	2.125|2.125	0.21184|0.21184	N|N	0.999765|0.999765	D;B;D;D;D|.	0.76494|.	0.999;0.01;0.998;0.998;0.998|.	D;B;D;D;D|.	0.83275|.	0.991;0.022;0.996;0.99;0.941|.	T|T	0.51741|0.51741	-0.8667|-0.8667	10|5	0.41790|.	T|.	0.15|.	.|.	12.8931|12.8931	0.58082|0.58082	0.0:0.3132:0.6868:0.0|0.0:0.3132:0.6868:0.0	.|.	674;713;754;754;749|.	F1T0J2;E7EU81;E7EP74;B2ZZ91;Q14789|.	.;.;.;.;GOGB1_HUMAN|.	V|R	749;754;713;561|619	ENSP00000341848:L749V;ENSP00000377275:L754V;ENSP00000418231:L713V|.	ENSP00000341848:L749V|.	L|S	-|-	1|3	0|2	GOLGB1|GOLGB1	122899800|122899800	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.805000|0.805000	0.45488|0.45488	3.253000|3.253000	0.51469|0.51469	1.381000|1.381000	0.46364|0.46364	0.655000|0.655000	0.94253|0.94253	CTT|AGC	.	.	.	none		0.418	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		C	121417110	G	C	121417110	3	2	239	1	0	0	0	0	1	0	0	0	6572	971	34	4	7574	4	GOLGB1	3	121417110	Missense_Mutation	SNP	G	TCGA-PJ-A8JU-01A-11D-A35Z-10	68152516	121417110	76605320	21	14568											
STAG1	10274	hgsc.bcm.edu	37	chr3	136096520	136096520	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acctgttctttcactggagtAttaacattagacaggcactg	11	13	8	9	0	2	1	1	0	1	1	2	2	2	2	1	2	1	3	1	2	3	5			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr3:136096520A>G	ENST00000383202.2	-	23	2608	c.2352T>C	c.(2350-2352)aaT>aaC	p.N784N	STAG1_ENST00000236698.5_Silent_p.N784N|STAG1_ENST00000536929.1_Silent_p.N368N|STAG1_ENST00000434713.2_Silent_p.N558N	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	784					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						TCACTGGAGTATTAACATTAG	0.343																																					p.N784N		Atlas-SNP	.											.	STAG1	135	.	0			c.T2352C						PASS	.						70	69	69					3																	136096520		2203	4300	6503	SO:0001819	synonymous_variant	10274	exon23			TGGAGTATTAACA	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.2352T>C	chr3.hg19:g.136096520A>G		55.0	0.0	.		63.0	27.0	.	NM_005862	O00539|Q6P275	Silent	SNP	ENST00000383202.2	hg19	CCDS3090.1																																																																																			.	.	.	none		0.343	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862		G	136096520	A	G	136096520	2	3	239	1	0	0	0	0	0	0	0	1	15254	446	16	3		3	STAG1	3	136096520	Silent	SNP	A	TCGA-PJ-A8JU-01A-11D-A35Z-10	14679410	136096520	61925910	22	14569											
PARL	55486	hgsc.bcm.edu	37	chr3	183560125	183560125	+	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	catgaactgctcttgacccaGaatgttcactatgctggaag	11	11	9	10	0	2	3	1	2	1	1	2	4	2	4	1	1	3	3	1	1	4	3			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr3:183560125G>C	ENST00000317096.4	-	6	778	c.718C>G	c.(718-720)Ctg>Gtg	p.L240V	PARL_ENST00000435888.1_Intron|PARL_ENST00000311101.5_Intron	NM_018622.5	NP_061092.3	Q9H300	PARL_HUMAN	presenilin associated, rhomboid-like	240					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)			TCTTGACCCAGAATGTTCACT	0.423																																					p.L240V		Atlas-SNP	.											.	PARL	32	.	0			c.C718G						PASS	.						166	159	162					3																	183560125		2203	4300	6503	SO:0001583	missense	55486	exon6			GACCCAGAATGTT	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.718C>G	chr3.hg19:g.183560125G>C	ENSP00000325421:p.Leu240Val	72.0	0.0	.		80.0	20.0	.	NM_018622	Q96CQ4|Q9BTJ6|Q9P1E3	Missense_Mutation	SNP	ENST00000317096.4	hg19	CCDS3248.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	17.77|17.77|17.77	3.470034|3.470034|3.470034	0.63625|0.63625|0.63625	.|.|.	.|.|.	ENSG00000175193|ENSG00000175193|ENSG00000175193	ENST00000418450|ENST00000317096;ENST00000450375|ENST00000417784	.|T;T|.	.|0.15718|.	.|2.4;2.4|.	5.32|5.32|5.32	4.43|4.43|4.43	0.53597|0.53597|0.53597	.|Peptidase S54, rhomboid domain (1);|.	.|0.080223|.	.|0.52532|.	.|D|.	.|0.000062|.	T|T|T	0.75583|0.75583|0.75583	0.3869|0.3869|0.3869	M|M|M	0.81802|0.81802|0.81802	2.56|2.56|2.56	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|P|.	.|0.36712|.	.|0.566|.	.|P|.	.|0.51055|.	.|0.657|.	T|T|T	0.76895|0.76895|0.76895	-0.2790|-0.2790|-0.2790	5|10|5	.|0.45353|.	.|T|.	.|0.12|.	-24.5427|-24.5427|-24.5427	13.7302|13.7302|13.7302	0.62783|0.62783|0.62783	0.0744:0.0:0.9256:0.0|0.0744:0.0:0.9256:0.0|0.0744:0.0:0.9256:0.0	.|.|.	.|240|.	.|Q9H300|.	.|PARL_HUMAN|.	L|V|C	6|240;20|31	.|ENSP00000325421:L240V;ENSP00000402689:L20V|.	.|ENSP00000325421:L240V|.	F|L|S	-|-|-	3|1|2	2|2|0	PARL|PARL|PARL	185042819|185042819|185042819	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.989000|0.989000|0.989000	0.77384|0.77384|0.77384	2.485000|2.485000|2.485000	0.45250|0.45250|0.45250	2.653000|2.653000|2.653000	0.90120|0.90120|0.90120	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	TTC|CTG|TCT	.	.	.	none		0.423	PARL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346465.1	NM_018622		C	183560125	G	C	183560125	3	2	239	1	0	0	0	0	1	0	0	0	11458	933	33	4	441	4	PARL	3	183560125	Missense_Mutation	SNP	G	TCGA-PJ-A8JU-01A-11D-A35Z-10	47463605	183560125	14462305	23	14570											
ATOH1	474	hgsc.bcm.edu	37	chr4	94750807	94750807	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accttcgcaccgcggcctccTatgaagggggcgcgggcaac	7	5	14	15	5	0	1	0	1	0	0	2	1	1	1	4	4	1	2	4	4	3	2			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr4:94750807T>C	ENST00000306011.3	+	1	766	c.730T>C	c.(730-732)Tat>Cat	p.Y244H		NM_005172.1	NP_005163.1	Q92858	ATOH1_HUMAN	atonal homolog 1 (Drosophila)	244					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)		CGCGGCCTCCTATGAAGGGGG	0.706																																					p.Y244H		Atlas-SNP	.											.	ATOH1	40	.	0			c.T730C						PASS	.						16	19	18					4																	94750807		2192	4287	6479	SO:0001583	missense	474	exon1			GCCTCCTATGAAG	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.730T>C	chr4.hg19:g.94750807T>C	ENSP00000302216:p.Tyr244His	136.0	0.0	.		105.0	43.0	.	NM_005172	Q14CT9	Missense_Mutation	SNP	ENST00000306011.3	hg19	CCDS3638.1	.	.	.	.	.	.	.	.	.	.	T	12.29	1.894445	0.33442	.	.	ENSG00000172238	ENST00000306011	D	0.97378	-4.36	3.36	3.36	0.38483	.	0.158987	0.29964	N	0.010753	D	0.91150	0.7213	L	0.27053	0.805	0.25583	N	0.986778	B	0.31790	0.34	B	0.28011	0.085	T	0.82269	-0.0541	10	0.16896	T	0.51	-9.6261	6.9541	0.24562	0.0:0.1112:0.0:0.8888	.	244	Q92858	ATOH1_HUMAN	H	244	ENSP00000302216:Y244H	ENSP00000302216:Y244H	Y	+	1	0	ATOH1	94969830	0.585000	0.26774	0.999000	0.59377	0.311000	0.27955	0.000000	0.12993	1.788000	0.52465	0.386000	0.25728	TAT	.	.	.	none		0.706	ATOH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253585.1	NM_005172		C	94750807	T	C	94750807	3	2	239	1	0	0	0	0	1	0	0	0	1112	1522	53	3	732	3	ATOH1	4	94750807	Missense_Mutation	SNP	T	TCGA-PJ-A8JU-01A-11D-A35Z-10		94750807	96403469	24	14571											
ANK2	287	hgsc.bcm.edu	37	chr4	114278777	114278777	+	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	atggaatcccaacaggaaagTaccttgtgggaaatgcaatc	15	8	10	8	0	0	0	0	0	0	0	2	3	1	3	2	3	3	2	2	3	6	2			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr4:114278777T>A	ENST00000357077.4	+	38	9056	c.9003T>A	c.(9001-9003)agT>agA	p.S3001R	ANK2_ENST00000509550.1_Intron|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000510275.2_Intron|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000264366.6_Missense_Mutation_p.S2968R	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	3001					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)		AACAGGAAAGTACCTTGTGGG	0.413																																					p.S3001R		Atlas-SNP	.											.	ANK2	576	.	0			c.T9003A						PASS	.						118	116	117					4																	114278777		2203	4300	6503	SO:0001583	missense	287	exon38			GGAAAGTACCTTG	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.9003T>A	chr4.hg19:g.114278777T>A	ENSP00000349588:p.Ser3001Arg	222.0	0.0	.		144.0	42.0	.	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	hg19	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	T	15.97	2.988836	0.53934	.	.	ENSG00000145362	ENST00000357077;ENST00000264366;ENST00000505342	T;T;D	0.96427	-0.27;-0.29;-4.01	5.72	-3.25	0.05079	.	0.634983	0.15548	N	0.256573	D	0.91506	0.7318	M	0.64997	1.995	0.22266	N	0.999245	B;P	0.42203	0.001;0.773	B;B	0.33521	0.001;0.165	D	0.84583	0.0662	10	0.15499	T	0.54	.	9.5599	0.39362	0.0:0.5174:0.1142:0.3683	.	2968;3001	Q01484;Q01484-4	ANK2_HUMAN;.	R	3001;2968;11	ENSP00000349588:S3001R;ENSP00000264366:S2968R;ENSP00000422498:S11R	ENSP00000264366:S2968R	S	+	3	2	ANK2	114498226	0.000000	0.05858	0.002000	0.10522	0.488000	0.33401	-0.524000	0.06222	-0.771000	0.04608	0.533000	0.62120	AGT	.	.	.	none		0.413	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		A	114278777	T	A	114278777	3	1	239	1	0	0	0	0	1	0	0	0	621	1635	57	5	9218	5	ANK2	4	114278777	Missense_Mutation	SNP	T	TCGA-PJ-A8JU-01A-11D-A35Z-10	19527970	114278777	76875499	25	14572											
ANKRD50	57182	hgsc.bcm.edu	37	chr4	125590179	125590187	+	In_Frame_Del	DEL	TCAGAACCT	TCAGAACCT	-																															ttttatagttgaagctagggTcagaaccttcaatctgaagc																								rs551271977		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	TCAGAACCT	TCAGAACCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr4:125590179_125590187delTCAGAACCT	ENST00000504087.1	-	4	5282_5290	c.4245_4253delAGGTTCTGA	c.(4243-4254)gaaggttctgac>gac	p.EGS1415del	ANKRD50_ENST00000515641.1_In_Frame_Del_p.EGS1236del	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	1415										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						GAAGCTAGGGTCAGAACCTTCAATCTGAA	0.383																																					p.1416_1418del		Atlas-Indel,Pindel	.											.	ANKRD50	136	.	0			c.4246_4254del						PASS	.																																			SO:0001651	inframe_deletion	57182	exon4			.	AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"Ankyrin repeat domain containing"	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.4245_4253delAGGTTCTGA	chr4.hg19:g.125590179_125590187delTCAGAACCT	ENSP00000425658:p.Glu1415_Ser1417del	78.0	0.0	0		66.0	15.0	0.227273	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	In_Frame_Del	DEL	ENST00000504087.1	hg19	CCDS34060.1																																																																																			.	.	.	none		0.383	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337		-	125590187	TCAGAACCT	-	125590179	7	5	239	1	0	1	0	1	0	0	0	0	677	1667	58	0	40	0	ANKRD50	4	125590179	In_Frame_Del	DEL	TCAGAACCT	TCGA-PJ-A8JU-01A-11D-A35Z-10	11311402	125590179	65564097	26	14573											
GPR98	84059	hgsc.bcm.edu	37	chr5	90446037	90446037	+	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	tctcatcggtgctatggaggAggtgtctgcccttgcccttt	4	14	12	11	1	2	0	1	0	2	0	4	2	2	2	2	4	3	1	2	4	1	3			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr5:90446037A>T	ENST00000405460.2	+	88	18719	c.18623A>T	c.(18622-18624)gAg>gTg	p.E6208V	GPR98_ENST00000425867.2_Splice_Site_p.E1869V	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	6208					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)		GCTATGGAGGAGGTGTCTGCC	0.547																																					p.E6208V		Atlas-SNP	.											.	GPR98	605	.	0			c.A18623T						PASS	.						83	85	84					5																	90446037		2027	4182	6209	SO:0001630	splice_region_variant	84059	exon88			TGGAGGAGGTGTC	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.18624+1A>T	chr5.hg19:g.90446037A>T		126.0	0.0	.		85.0	25.0	.	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	19.43	3.825664	0.71143	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.35789	1.32;1.29	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.58509	0.2127	M	0.63428	1.95	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	0.56129	-0.8030	9	.	.	.	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	1869;6208;1869	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	V	6208;6208;1869	ENSP00000384582:E6208V;ENSP00000392618:E1869V	.	E	+	2	0	GPR98	90481793	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	8.730000	0.91510	2.326000	0.78906	0.533000	0.62120	GAG	.	.	.	none		0.547	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	Missense_Mutation	T	90446037	A	T	90446037	5	4	239	1	0	0	0	0	0	0	1	0	6728	318	11	5	18973	5	GPR98	5	90446037	Splice_Site	SNP	A	TCGA-PJ-A8JU-01A-11D-A35Z-10		90446037	90469223	27	14574											
FSTL4	23105	hgsc.bcm.edu	37	chr5	132534854	132534854	+	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	acacctcacaccgcagcgtgTtttgtctcccattgatgagg	8	11	9	13	2	2	2	1	2	1	0	3	2	2	2	3	1	1	2	3	1	0	3			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr5:132534854T>A	ENST00000265342.7	-	16	2711	c.2462A>T	c.(2461-2463)aAc>aTc	p.N821I	CTB-49A3.2_ENST00000509051.1_RNA	NM_015082.1	NP_055897.1	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	821						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(8)|skin(2)|upper_aerodigestive_tract(1)	23		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CCGCAGCGTGTTTTGTCTCCC	0.582																																					p.N821I		Atlas-SNP	.											.	FSTL4	74	.	0			c.A2462T						PASS	.						74	71	72					5																	132534854		2203	4300	6503	SO:0001583	missense	23105	exon16			AGCGTGTTTTGTC	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.2462A>T	chr5.hg19:g.132534854T>A	ENSP00000265342:p.Asn821Ile	70.0	0.0	.		70.0	26.0	.	NM_015082	Q8TBU0|Q9UPU1	Missense_Mutation	SNP	ENST00000265342.7	hg19	CCDS34238.1	.	.	.	.	.	.	.	.	.	.	T	11.27	1.587755	0.28268	.	.	ENSG00000053108	ENST00000265342;ENST00000360575	T	0.60672	0.17	5.15	2.66	0.31614	Immunoglobulin-like (1);	0.265468	0.42548	D	0.000696	T	0.63283	0.2498	M	0.76574	2.34	0.30104	N	0.807186	P;D	0.54601	0.836;0.967	B;P	0.51229	0.366;0.663	T	0.64833	-0.6314	10	0.87932	D	0	-9.6102	8.8288	0.35072	0.0:0.1592:0.0:0.8408	.	821;470	Q6MZW2;B3KPF3	FSTL4_HUMAN;.	I	821;652	ENSP00000265342:N821I	ENSP00000265342:N821I	N	-	2	0	FSTL4	132562753	0.994000	0.37717	0.030000	0.17652	0.231000	0.25187	2.497000	0.45354	0.269000	0.21961	0.477000	0.44152	AAC	.	.	.	none		0.582	FSTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370212.1	XM_048786		A	132534854	T	A	132534854	3	1	239	1	0	0	0	0	1	0	0	0	6086	1725	60	5	70	5	FSTL4	5	132534854	Missense_Mutation	SNP	T	TCGA-PJ-A8JU-01A-11D-A35Z-10	42088817	132534854	48380406	28	14575											
PITX1	5307	hgsc.bcm.edu	37	chr5	134367076	134367076	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tagctcttgcaactgctggcTtgtgaagtgcgtacgttgcc	6	13	12	10	2	1	1	0	1	1	0	1	1	1	1	1	1	7	6	1	1	4	5			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr5:134367076T>C	ENST00000265340.7	-	2	708	c.292A>G	c.(292-294)Agc>Ggc	p.S98G	PITX1_ENST00000506438.1_Missense_Mutation_p.S98G|CTC-349C3.1_ENST00000432382.3_5'Flank	NM_002653.4	NP_002644.4	P78337	PITX1_HUMAN	paired-like homeodomain 1	98					anatomical structure morphogenesis (GO:0009653)|branchiomeric skeletal muscle development (GO:0014707)|cartilage development (GO:0051216)|embryonic hindlimb morphogenesis (GO:0035116)|myoblast fate commitment (GO:0048625)|pituitary gland development (GO:0021983)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)			central_nervous_system(1)|cervix(3)|endometrium(3)|large_intestine(1)|lung(5)|ovary(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	READ - Rectum adenocarcinoma(2;0.0607)		AACTGCTGGCTTGTGAAGTGC	0.647																																					p.S98G		Atlas-SNP	.											.	PITX1	31	.	0			c.A292G						PASS	.						121	93	103					5																	134367076		2203	4300	6503	SO:0001583	missense	5307	exon2			GCTGGCTTGTGAA	AF009648	CCDS4182.1	5q31.1	2011-06-20	2007-07-12		ENSG00000069011	ENSG00000069011		"Homeoboxes / PRD class"	9004	protein-coding gene	gene with protein product		602149	"paired-like homeodomain transcription factor 1"	BFT		9337397, 9070926	Standard	NM_002653		Approved	PTX1, POTX	uc010jea.3	P78337	OTTHUMG00000149983	ENST00000265340.7:c.292A>G	chr5.hg19:g.134367076T>C	ENSP00000265340:p.Ser98Gly	127.0	0.0	.		91.0	25.0	.	NM_002653	A8K3M0|D3DQB0|O14677|O60425|Q9BTI5	Missense_Mutation	SNP	ENST00000265340.7	hg19	CCDS4182.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.559217	0.86335	.	.	ENSG00000069011	ENST00000265340;ENST00000506438;ENST00000507253;ENST00000502676	D;D;D;D	0.96300	-3.97;-3.97;-3.71;-3.71	4.39	4.39	0.52855	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.96303	0.8794	L	0.31371	0.925	0.80722	D	1	D	0.63046	0.992	D	0.76071	0.987	D	0.97051	0.9764	10	0.87932	D	0	.	13.9082	0.63850	0.0:0.0:0.0:1.0	.	98	P78337	PITX1_HUMAN	G	98	ENSP00000265340:S98G;ENSP00000427542:S98G;ENSP00000422908:S98G;ENSP00000423624:S98G	ENSP00000265340:S98G	S	-	1	0	PITX1	134394975	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.199000	0.72112	1.755000	0.51935	0.460000	0.39030	AGC	.	.	.	none		0.647	PITX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251195.3			C	134367076	T	C	134367076	3	2	239	1	0	0	0	0	1	0	0	0	11961	1609	56	3	660	3	PITX1	5	134367076	Missense_Mutation	SNP	T	TCGA-PJ-A8JU-01A-11D-A35Z-10	1832222	134367076	46548184	29	14576											
DPYSL3	1809	hgsc.bcm.edu	37	chr5	146833138	146833138	+	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	ccgcgggatgttcttcttgcCttggtaggacatggtggcgg	4	12	16	9	3	2	0	0	0	2	0	2	2	2	2	2	6	1	2	2	6	1	5			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr5:146833138C>A	ENST00000398514.3	-	1	384	c.13G>T	c.(13-15)Ggc>Tgc	p.G5C	DPYSL3_ENST00000343218.5_Intron|DPYSL3_ENST00000534907.1_Intron	NM_001387.2	NP_001378.1	Q14195	DPYL3_HUMAN	dihydropyrimidinase-like 3	5					actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cell migration (GO:0030336)|negative regulation of neuron projection development (GO:0010977)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron projection development (GO:0010976)|protein homooligomerization (GO:0051260)|pyrimidine nucleobase catabolic process (GO:0006208)|response to axon injury (GO:0048678)	cell body (GO:0044297)|cytosol (GO:0005829)|extracellular space (GO:0005615)|filamentous actin (GO:0031941)|growth cone (GO:0030426)|lamellipodium (GO:0030027)	chondroitin sulfate binding (GO:0035374)|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)|SH3 domain binding (GO:0017124)			breast(2)|endometrium(1)|kidney(4)|large_intestine(6)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCTTCTTGCCTTGGTAGGAC	0.716																																					p.G5C		Atlas-SNP	.											.	DPYSL3	58	.	0			c.G13T						PASS	.						39	52	48					5																	146833138		2088	4144	6232	SO:0001583	missense	1809	exon1			TCTTGCCTTGGTA	D78014	CCDS43381.1, CCDS56387.1	5q32	2008-02-05							3015	protein-coding gene	gene with protein product		601168				8973361, 9115293	Standard	NM_001197294		Approved	DRP-3, ULIP, CRMP4	uc003loo.3	Q14195		ENST00000398514.3:c.13G>T	chr5.hg19:g.146833138C>A	ENSP00000381526:p.Gly5Cys	95.0	0.0	.		101.0	9.0	.	NM_001387	B3SXQ8|Q93012	Missense_Mutation	SNP	ENST00000398514.3	hg19	CCDS43381.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.889019	0.91814	.	.	ENSG00000113657	ENST00000398514;ENST00000512722	D;D	0.86694	-2.04;-2.16	5.22	5.22	0.72569	.	.	.	.	.	D	0.91147	0.7212	M	0.65975	2.015	0.80722	D	1	D	0.60160	0.987	P	0.58077	0.832	D	0.92147	0.5725	9	0.87932	D	0	.	15.7699	0.78162	0.0:1.0:0.0:0.0	.	5	Q14195	DPYL3_HUMAN	C	5	ENSP00000381526:G5C;ENSP00000426720:G5C	ENSP00000381526:G5C	G	-	1	0	DPYSL3	146813331	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.917000	0.56424	2.452000	0.82932	0.558000	0.71614	GGC	.	.	.	none		0.716	DPYSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373421.2	NM_001387		A	146833138	C	A	146833138	3	1	239	1	0	0	0	0	1	0	0	0	4750	681	24	4	1755	4	DPYSL3	5	146833138	Missense_Mutation	SNP	C	TCGA-PJ-A8JU-01A-11D-A35Z-10	12466062	146833138	34082122	30	14577											
CLINT1	9685	hgsc.bcm.edu	37	chr5	157214655	157214655	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgcttcttttacaatctctTatttgctaaaattggcgaaa	11	17	5	8	1	2	0	0	0	2	0	3	1	2	0	0	1	3	2	0	1	6	7			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr5:157214655T>C	ENST00000411809.2	-	12	2081	c.1877A>G	c.(1876-1878)tAa>tGa	p.*626*	CLINT1_ENST00000296951.5_Silent_p.*626*|CLINT1_ENST00000523094.1_Silent_p.*626*|CLINT1_ENST00000530742.1_Silent_p.*626*|CLINT1_ENST00000523908.1_Silent_p.*644*	NM_014666.3	NP_055481.1	Q14677	EPN4_HUMAN	clathrin interactor 1	0					clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)	clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|lipid binding (GO:0008289)			breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|urinary_tract(1)	21	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)			TACAATCTCTTATTTGCTAAA	0.398																																					p.X644X	Colon(22;427 587 2170 6147 14291)	Atlas-SNP	.											.	CLINT1	86	.	0			c.A1931G						PASS	.						153	147	149					5																	157214655		1885	4101	5986	SO:0001819	synonymous_variant	9685	exon12			ATCTCTTATTTGC	AF434813	CCDS47330.1, CCDS56388.1, CCDS56389.1	5q33.3	2006-06-13			ENSG00000113282	ENSG00000113282			23186	protein-coding gene	gene with protein product		607265				12213833, 12429846	Standard	NM_014666		Approved	ENTH, KIAA0171, EPNR, CLINT	uc011ddv.2	Q14677	OTTHUMG00000163527	ENST00000411809.2:c.1877A>G	chr5.hg19:g.157214655T>C		67.0	0.0	.		65.0	7.0	.	NM_001195555	B7Z6F8|D3DQJ6|Q8NAF1|Q96E05	Silent	SNP	ENST00000411809.2	hg19	CCDS47330.1																																																																																			.	.	.	none		0.398	CLINT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374001.1	NM_014666		C	157214655	T	C	157214655	2	2	239	1	0	0	0	0	0	0	0	1	3533	1761	61	3		3	CLINT1	5	157214655	Silent	SNP	T	TCGA-PJ-A8JU-01A-11D-A35Z-10	10381517	157214655	23700605	31	14578											
HTR1B	3351	hgsc.bcm.edu	37	chr6	78172132	78172132	+	Frame_Shift_Del	DEL	A	A	-																															tcactagggagatgatgaagAagggtagccaacacacaata																										TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr6:78172132delA	ENST00000369947.2	-	1	1358	c.989delT	c.(988-990)ttcfs	p.F331fs		NM_000863.1	NP_000854.1	P28222	5HT1B_HUMAN	5-hydroxytryptamine (serotonin) receptor 1B, G protein-coupled	331	Agonist binding.				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)	GATGATGAAGAAGGGTAGCCA	0.512																																					p.F330fs		Atlas-Indel,Pindel	.											.	HTR1B	55	.	0			c.990delC						PASS	.						148	136	140					6																	78172132		2203	4300	6503	SO:0001589	frameshift_variant	3351	exon1			.	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.989delT	chr6.hg19:g.78172132delA	ENSP00000358963:p.Phe331fs	93.0	0.0	0		75.0	32.0	0.426667	NM_000863	Q4VAY7	Frame_Shift_Del	DEL	ENST00000369947.2	hg19	CCDS4986.1																																																																																			.	.	.	none		0.512	HTR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041292.1	NM_000863		-	78172132	A	-	78172132	7	5	239	1	0	1	0	1	0	0	0	0	7444	246	9	0	187	0	HTR1B	6	78172132	Frame_Shift_Del	DEL	A	TCGA-PJ-A8JU-01A-11D-A35Z-10		78172132	92942935	32	14579											
PHIP	55023	hgsc.bcm.edu	37	chr6	79655791	79655791	+	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	gctgaagaagtagatggttgCtcagtgacaactggatctac	12	10	12	7	0	2	4	1	2	1	2	2	5	2	5	0	2	3	4	0	2	5	3			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr6:79655791C>T	ENST00000275034.4	-	38	4724	c.4557G>A	c.(4555-4557)gaG>gaA	p.E1519E	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1519					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)		TAGATGGTTGCTCAGTGACAA	0.408																																					p.E1519E		Atlas-SNP	.											.	PHIP	177	.	0			c.G4557A						PASS	.						146	128	134					6																	79655791		2203	4300	6503	SO:0001819	synonymous_variant	55023	exon38			TGGTTGCTCAGTG	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.4557G>A	chr6.hg19:g.79655791C>T		127.0	0.0	.		109.0	38.0	.	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000275034.4	hg19	CCDS4987.1																																																																																			.	.	.	none		0.408	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			T	79655791	C	T	79655791	2	4	239	1	0	0	0	0	0	0	0	1	11849	796	28	2		2	PHIP	6	79655791	Silent	SNP	C	TCGA-PJ-A8JU-01A-11D-A35Z-10	1483659	79655791	91459276	33	14580											
MUC17	140453	hgsc.bcm.edu	37	chr7	100679990	100679990	+	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	ccacgccggtactcagttctGaggctagcaccctttcagca	8	9	9	15	2	3	1	2	1	1	0	3	1	3	1	3	2	3	5	3	2	2	4			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr7:100679990G>A	ENST00000306151.4	+	3	5357	c.5293G>A	c.(5293-5295)Gag>Aag	p.E1765K		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1765	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)					ACTCAGTTCTGAGGCTAGCAC	0.498																																					p.E1765K		Atlas-SNP	.											.	MUC17	804	.	0			c.G5293A						PASS	.						289	302	298					7																	100679990		2203	4300	6503	SO:0001583	missense	140453	exon3			AGTTCTGAGGCTA	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"Mucins"	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.5293G>A	chr7.hg19:g.100679990G>A	ENSP00000302716:p.Glu1765Lys	76.0	0.0	.		94.0	31.0	.	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	4.090	0.014651	0.07959	.	.	ENSG00000169876	ENST00000306151	T	0.01981	4.52	0.824	0.824	0.18818	.	.	.	.	.	T	0.01222	0.0040	L	0.27053	0.805	0.09310	N	1	P	0.48911	0.917	B	0.35899	0.213	T	0.29305	-1.0016	9	0.06891	T	0.86	.	5.0939	0.14723	0.0:0.0:1.0:0.0	.	1765	Q685J3	MUC17_HUMAN	K	1765	ENSP00000302716:E1765K	ENSP00000302716:E1765K	E	+	1	0	MUC17	100466710	0.000000	0.05858	0.006000	0.13384	0.022000	0.10575	-0.038000	0.12144	0.788000	0.33755	0.134000	0.15878	GAG	.	.	.	none		0.498	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100679990	G	A	100679990	3	1	239	1	0	0	0	0	1	0	0	0	9981	1291	45	2	5303	2	MUC17	7	100679990	Missense_Mutation	SNP	G	TCGA-PJ-A8JU-01A-11D-A35Z-10		100679990	58458673	34	14581											
CUX1	1523	hgsc.bcm.edu	37	chr7	101891788	101891788	+	Silent	SNP	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	ccctcggcccgcagcggccgGgcggcgcccagctcggaggg	3	2	18	18	7	0	0	0	0	0	0	2	1	0	1	4	6	2	2	4	6	0	0			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr7:101891788G>A	ENST00000292535.7	+	24	4022	c.3984G>A	c.(3982-3984)cgG>cgA	p.R1328R	CUX1_ENST00000546411.2_Silent_p.R1226R|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000292538.4_Intron|CUX1_ENST00000556210.1_Silent_p.R1170R|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000360264.3_Silent_p.R1339R|CUX1_ENST00000549414.2_Silent_p.R1306R|CUX1_ENST00000560541.1_Intron|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000550008.2_Silent_p.R1272R	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	1328					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						GCAGCGGCCGGGCGGCGCCCA	0.711																																					p.R1339R		Atlas-SNP	.											.	CUX1	253	.	0			c.G4017A						PASS	.						5	7	6					7																	101891788		2004	3805	5809	SO:0001819	synonymous_variant	1523	exon24			CGGCCGGGCGGCG	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.3984G>A	chr7.hg19:g.101891788G>A		41.0	0.0	.		36.0	18.0	.	NM_001202543	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Silent	SNP	ENST00000292535.7	hg19	CCDS5721.1																																																																																			.	.	.	none		0.711	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913		A	101891788	G	A	101891788	2	1	239	1	0	0	0	0	0	0	0	1	4066	1219	43	2		2	CUX1	7	101891788	Silent	SNP	G	TCGA-PJ-A8JU-01A-11D-A35Z-10	1211798	101891788	57246875	35	14582											
ATP6V1B2	526	hgsc.bcm.edu	37	chr8	20069635	20069635	+	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	aaacatggaaactgcccggtTcttcaaatctgactttgaag	13	11	8	9	1	3	2	1	2	2	0	3	3	3	3	1	2	3	1	1	2	4	3			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr8:20069635T>A	ENST00000276390.2	+	8	768	c.728T>A	c.(727-729)tTc>tAc	p.F243Y		NM_001693.3	NP_001684.2	P21281	VATB2_HUMAN	ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B2	243					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|ruffle (GO:0001726)	ATP binding (GO:0005524)|hydrogen ion transmembrane transporter activity (GO:0015078)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			endometrium(1)|kidney(2)|lung(5)|prostate(1)	9				Colorectal(74;0.0535)|COAD - Colon adenocarcinoma(73;0.211)	Gallium nitrate(DB05260)	ACTGCCCGGTTCTTCAAATCT	0.373																																					p.F243Y	Pancreas(119;1230 1726 3901 4036 31644)	Atlas-SNP	.											.	ATP6V1B2	34	.	0			c.T728A						PASS	.						83	81	82					8																	20069635		2203	4300	6503	SO:0001583	missense	526	exon8			CCCGGTTCTTCAA	L35249	CCDS6014.1	8p21.3	2010-04-21	2006-01-13	2002-05-10	ENSG00000147416	ENSG00000147416	3.6.3.14	"ATPases / V-type"	854	protein-coding gene	gene with protein product		606939	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), beta polypeptide, 56/58kD, isoform 2", "ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B, isoform 2"	VPP3, ATP6B2		2145275, 14580332	Standard	NM_001693		Approved	VATB, Vma2, HO57	uc003wzp.3	P21281	OTTHUMG00000131073	ENST00000276390.2:c.728T>A	chr8.hg19:g.20069635T>A	ENSP00000276390:p.Phe243Tyr	97.0	0.0	.		88.0	36.0	.	NM_001693	B2R5Z3|D3DSQ5|Q14544|Q15859|Q96IR0	Missense_Mutation	SNP	ENST00000276390.2	hg19	CCDS6014.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.632303	0.87660	.	.	ENSG00000147416	ENST00000276390;ENST00000542368	T	0.81415	-1.49	4.35	4.35	0.52113	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain (1);	0.097712	0.64402	D	0.000001	T	0.79627	0.4478	L	0.52126	1.63	0.80722	D	1	P	0.35872	0.525	B	0.43575	0.424	T	0.79988	-0.1571	10	0.46703	T	0.11	-15.7153	12.8046	0.57605	0.0:0.0:0.0:1.0	.	243	P21281	VATB2_HUMAN	Y	243;117	ENSP00000276390:F243Y	ENSP00000276390:F243Y	F	+	2	0	ATP6V1B2	20113915	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.790000	0.85794	1.947000	0.56498	0.533000	0.62120	TTC	.	.	.	none		0.373	ATP6V1B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253732.1	NM_001693		A	20069635	T	A	20069635	3	1	239	1	0	0	0	0	1	0	0	0	1179	1783	62	5	758	5	ATP6V1B2	8	20069635	Missense_Mutation	SNP	T	TCGA-PJ-A8JU-01A-11D-A35Z-10		20069635	126294387	36	14583											
MYBL1	4603	hgsc.bcm.edu	37	chr8	67514696	67514696	+	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	tgttccagagtttcttcagtCctttttgttgtggtacttca	5	20	8	8	0	3	1	2	0	1	1	5	1	5	1	2	1	1	4	2	1	1	8			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr8:67514696C>T	ENST00000522677.3	-	2	493	c.83G>A	c.(82-84)gGa>gAa	p.G28E	MYBL1_ENST00000517885.1_Missense_Mutation_p.G28E|MYBL1_ENST00000524176.2_Missense_Mutation_p.G28E	NM_001080416.2|NM_001144755.1	NP_001073885.1|NP_001138227.1	P10243	MYBA_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 1	28					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)			TTTCTTCAGTCCTTTTTGTTG	0.343																																					p.G28E		Atlas-SNP	.											.	MYBL1	73	.	0			c.G83A						PASS	.						172	162	166					8																	67514696		1848	4099	5947	SO:0001583	missense	4603	exon2			TTCAGTCCTTTTT	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.83G>A	chr8.hg19:g.67514696C>T	ENSP00000429633:p.Gly28Glu	96.0	0.0	.		78.0	27.0	.	NM_001080416	E7EW29|Q495F9	Missense_Mutation	SNP	ENST00000522677.3	hg19	CCDS47867.1	.	.	.	.	.	.	.	.	.	.	C	12.41	1.928320	0.34002	.	.	ENSG00000185697	ENST00000522677;ENST00000517885;ENST00000524176	T;T;T	0.17054	2.81;2.33;2.3	5.55	4.67	0.58626	.	0.265955	0.41500	D	0.000876	T	0.18257	0.0438	L	0.43152	1.355	0.38359	D	0.944558	B;D;B	0.59767	0.049;0.986;0.126	B;P;B	0.48304	0.027;0.573;0.04	T	0.03673	-1.1014	10	0.02654	T	1	-9.9575	15.9114	0.79475	0.1363:0.8637:0.0:0.0	.	28;28;28	Q495F9;Q495G0;P10243	.;.;MYBA_HUMAN	E	28	ENSP00000429633:G28E;ENSP00000428265:G28E;ENSP00000428011:G28E	ENSP00000428265:G28E	G	-	2	0	MYBL1	67677250	0.974000	0.33945	1.000000	0.80357	0.995000	0.86356	2.102000	0.41796	1.314000	0.45095	0.655000	0.94253	GGA	.	.	.	none		0.343	MYBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379221.3	XM_034274		T	67514696	C	T	67514696	3	4	239	1	0	0	0	0	1	0	0	0	10016	855	30	2	2235	2	MYBL1	8	67514696	Missense_Mutation	SNP	C	TCGA-PJ-A8JU-01A-11D-A35Z-10	47445061	67514696	78849326	37	14584											
NCOA2	10499	hgsc.bcm.edu	37	chr8	71056986	71056986	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgtttctgattggtgggaaAggtccagcaccagttgggct	7	12	14	8	0	1	1	0	1	1	0	2	2	2	2	2	4	1	4	2	4	1	3			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr8:71056986A>G	ENST00000452400.2	-	13	2884	c.2703T>C	c.(2701-2703)ccT>ccC	p.P901P	NCOA2_ENST00000267974.4_Intron	NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	901					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)			TTGGTGGGAAAGGTCCAGCAC	0.458			T	"RUNXBP2, HEY1"	"AML, Chondrosarcoma"																																p.P901P		Atlas-SNP	.		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	.	NCOA2	147	.	0			c.T2703C						PASS	.						204	190	195					8																	71056986		1925	4138	6063	SO:0001819	synonymous_variant	10499	exon13			TGGGAAAGGTCCA	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.2703T>C	chr8.hg19:g.71056986A>G		181.0	0.0	.		155.0	45.0	.	NM_006540	Q14CD2	Silent	SNP	ENST00000452400.2	hg19	CCDS47872.1																																																																																			.	.	.	none		0.458	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1			G	71056986	A	G	71056986	2	3	239	1	0	0	0	0	0	0	0	1	10236	59	3	3		3	NCOA2	8	71056986	Silent	SNP	A	TCGA-PJ-A8JU-01A-11D-A35Z-10	3542290	71056986	75307036	38	14585											
TP53INP1	94241	hgsc.bcm.edu	37	chr8	95952262	95952262	+	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	ctgcagtaaaacatgggggtGgggtgataaaccagctctcc	11	8	13	9	0	1	1	0	1	1	0	2	1	1	1	2	4	4	3	2	4	4	2			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr8:95952262G>T	ENST00000342697.4	-	3	706	c.299C>A	c.(298-300)cCa>cAa	p.P100Q	NDUFAF6_ENST00000396113.1_Intron|TP53INP1_ENST00000378776.4_Missense_Mutation_p.P100Q|TP53INP1_ENST00000448464.2_Missense_Mutation_p.P100Q	NM_033285.3	NP_150601.1	Q96A56	T53I1_HUMAN	tumor protein p53 inducible nuclear protein 1	100					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)					ACATGGGGGTGGGGTGATAAA	0.463																																					p.P100Q		Atlas-SNP	.											.	TP53INP1	22	.	0			c.C299A						PASS	.						123	115	118					8																	95952262		2203	4300	6503	SO:0001583	missense	94241	exon3			GGGGGTGGGGTGA	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.299C>A	chr8.hg19:g.95952262G>T	ENSP00000344215:p.Pro100Gln	153.0	0.0	.		133.0	51.0	.	NM_001135733	B2RCE5|Q969R9	Missense_Mutation	SNP	ENST00000342697.4	hg19	CCDS6265.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.434936	0.83885	.	.	ENSG00000164938	ENST00000448464;ENST00000342697;ENST00000378776	T;T;T	0.79653	-1.29;-1.29;-1.29	6.17	5.3	0.74995	.	0.045488	0.85682	D	0.000000	D	0.89938	0.6860	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.983;0.999	D	0.91385	0.5130	10	0.87932	D	0	-22.1295	15.699	0.77528	0.0652:0.0:0.9348:0.0	.	100;100	Q96A56-2;Q96A56	.;T53I1_HUMAN	Q	100	ENSP00000390063:P100Q;ENSP00000344215:P100Q;ENSP00000368052:P100Q	ENSP00000344215:P100Q	P	-	2	0	TP53INP1	96021438	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	9.323000	0.96364	1.630000	0.50440	0.655000	0.94253	CCA	.	.	.	none		0.463	TP53INP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379818.1			T	95952262	G	T	95952262	3	4	239	1	0	0	0	0	1	0	0	0	16400	1348	47	4	457	4	TP53INP1	8	95952262	Missense_Mutation	SNP	G	TCGA-PJ-A8JU-01A-11D-A35Z-10	24895276	95952262	50411760	39	14586											
PABPC1	26986	hgsc.bcm.edu	37	chr8	101717893	101717893	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttcctgaccttgtacatgAacagcaggctagacagaaaa	14	8	10	9	0	0	4	0	2	0	2	1	4	1	4	2	2	3	4	2	2	5	4			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr8:101717893A>G	ENST00000318607.5	-	12	2739	c.1611T>C	c.(1609-1611)gtT>gtC	p.V537V	PABPC1_ENST00000519596.1_5'Flank|AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000519004.1_Silent_p.V492V|PABPC1_ENST00000522387.1_Silent_p.V505V	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	537					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)			CTTGTACATGAACAGCAGGCT	0.433																																					p.V537V		Atlas-SNP	.											.	PABPC1	76	.	0			c.T1611C						PASS	.						58	50	53					8																	101717893		2203	4300	6503	SO:0001819	synonymous_variant	26986	exon12			TACATGAACAGCA	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.1611T>C	chr8.hg19:g.101717893A>G		244.0	0.0	.		252.0	86.0	.	NM_002568	Q15097|Q93004	Silent	SNP	ENST00000318607.5	hg19	CCDS6289.1	.	.	.	.	.	.	.	.	.	.	A	15.34	2.804600	0.50315	.	.	ENSG00000070756	ENST00000520868	.	.	.	5.75	3.37	0.38596	.	.	.	.	.	T	0.54565	0.1866	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50030	-0.8875	4	.	.	.	.	5.8593	0.18736	0.6593:0.0:0.3407:0.0	.	.	.	.	S	70	.	.	F	-	2	0	PABPC1	101787069	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.676000	0.25247	1.106000	0.41623	0.533000	0.62120	TTC	.	.	.	none		0.433	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568		G	101717893	A	G	101717893	2	3	239	1	0	0	0	0	0	0	0	1	11370	233	9	3		3	PABPC1	8	101717893	Silent	SNP	A	TCGA-PJ-A8JU-01A-11D-A35Z-10	5765631	101717893	44646129	40	14587											
OR13C2	392376	hgsc.bcm.edu	37	chr9	107367111	107367111	+	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	aagtcatccgaattaagtgtCtctttagacttgggcttcat	10	15	8	8	1	3	1	2	0	1	1	5	2	4	1	1	1	0	1	1	1	4	5	rs75116810		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr9:107367111C>A	ENST00000542196.1	-	1	840	c.798G>T	c.(796-798)gaG>gaT	p.E266D		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	266						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(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						AATTAAGTGTCTCTTTAGACT	0.418																																					p.E266D		Atlas-SNP	.											.	OR13C2	46	.	0			c.G798T						PASS	.						148	132	137					9																	107367111		2201	4300	6501	SO:0001583	missense	392376	exon1			AAGTGTCTCTTTA		CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119		"GPCR / Class A : Olfactory receptors"	14701	protein-coding gene	gene with protein product							Standard	NM_001004481		Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.798G>T	chr9.hg19:g.107367111C>A	ENSP00000438815:p.Glu266Asp	148.0	0.0	.		109.0	44.0	.	NM_001004481	B9EGV8|Q6IF54	Missense_Mutation	SNP	ENST00000542196.1	hg19	CCDS35092.1	.	.	.	.	.	.	.	.	.	.	C	0.001	-3.250712	0.00022	.	.	ENSG00000257019	ENST00000542196	T	0.00164	8.64	3.08	-3.79	0.04320	GPCR, rhodopsin-like superfamily (1);	0.448415	0.16003	U	0.234188	T	0.00039	0.0001	N	0.01824	-0.7	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.36792	-0.9733	10	0.02654	T	1	.	4.0407	0.09750	0.1362:0.2057:0.5389:0.1192	.	266	Q8NGS9	O13C2_HUMAN	D	266	ENSP00000438815:E266D	ENSP00000438815:E266D	E	-	3	2	OR13C2	106406932	0.004000	0.15560	0.000000	0.03702	0.004000	0.04260	-0.422000	0.07043	-0.512000	0.06505	-0.657000	0.03884	GAG	.	.	.	weak		0.418	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481		A	107367111	C	A	107367111	3	1	239	1	0	0	0	0	1	0	0	0	10941	912	32	4	161	4	OR13C2	9	107367111	Missense_Mutation	SNP	C	TCGA-PJ-A8JU-01A-11D-A35Z-10		107367111	33846320	41	14588											
CDK5RAP2	55755	hgsc.bcm.edu	37	chr9	123287316	123287316	+	Missense_Mutation	SNP	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	cctctctggctttagcaaagGcagcactgagcttttcaatt	9	13	8	11	0	2	1	1	1	1	0	3	1	2	1	1	2	3	5	1	2	3	5			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr9:123287316G>A	ENST00000349780.4	-	11	1219	c.1040C>T	c.(1039-1041)gCc>gTc	p.A347V	CDK5RAP2_ENST00000360822.3_Missense_Mutation_p.A347V|CDK5RAP2_ENST00000359309.3_Missense_Mutation_p.A347V|CDK5RAP2_ENST00000360190.4_Missense_Mutation_p.A347V	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	347					brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)			breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						TTTAGCAAAGGCAGCACTGAG	0.468																																					p.A347V		Atlas-SNP	.											.	CDK5RAP2	157	.	0			c.C1040T						PASS	.						125	105	112					9																	123287316		2203	4300	6503	SO:0001583	missense	55755	exon11			GCAAAGGCAGCAC	BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"centrosomin"	608201	"microcephaly, primary autosomal recessive 3"	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.1040C>T	chr9.hg19:g.123287316G>A	ENSP00000343818:p.Ala347Val	102.0	0.0	.		83.0	30.0	.	NM_018249	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Missense_Mutation	SNP	ENST00000349780.4	hg19	CCDS6823.1	.	.	.	.	.	.	.	.	.	.	G	18.41	3.617235	0.66672	.	.	ENSG00000136861	ENST00000360822;ENST00000359309;ENST00000349780;ENST00000360190;ENST00000345313;ENST00000482047	T;T;T;T;T	0.42900	3.84;3.75;3.84;3.75;0.96	5.51	4.59	0.56863	.	0.432373	0.21888	N	0.067631	T	0.46268	0.1384	L	0.56769	1.78	0.09310	N	0.999996	P;P;B;P	0.46142	0.86;0.873;0.078;0.799	P;B;B;B	0.47075	0.536;0.306;0.127;0.162	T	0.34725	-0.9817	10	0.29301	T	0.29	.	13.6699	0.62418	0.0:0.0:0.8403:0.1597	.	148;347;347;347	Q6MZT4;Q96SN8-2;Q96SN8-4;Q96SN8	.;.;.;CK5P2_HUMAN	V	347;347;347;347;349;101	ENSP00000354065:A347V;ENSP00000352258:A347V;ENSP00000343818:A347V;ENSP00000353317:A347V;ENSP00000419640:A101V	ENSP00000341695:A349V	A	-	2	0	CDK5RAP2	122327137	1.000000	0.71417	0.019000	0.16419	0.844000	0.47949	5.391000	0.66266	1.290000	0.44636	0.555000	0.69702	GCC	.	.	.	none		0.468	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249		A	123287316	G	A	123287316	3	1	239	1	0	0	0	0	1	0	0	0	3148	1203	42	2	4753	2	CDK5RAP2	9	123287316	Missense_Mutation	SNP	G	TCGA-PJ-A8JU-01A-11D-A35Z-10	15920205	123287316	17926115	42	14589											
STOX1	219736	hgsc.bcm.edu	37	chr10	70645490	70645490	+	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	agtctgccatcacgaggtgcCtccttttcagaccgaacacc	9	9	8	15	2	3	1	2	0	1	1	4	3	4	1	5	1	3	0	5	1	1	2			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr10:70645490C>A	ENST00000298596.6	+	3	2021	c.1938C>A	c.(1936-1938)gcC>gcA	p.A646A	STOX1_ENST00000399165.4_Intron|STOX1_ENST00000421961.2_Silent_p.A536A|STOX1_ENST00000399162.2_Intron|STOX1_ENST00000399169.4_Silent_p.A646A	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	646						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						CACGAGGTGCCTCCTTTTCAG	0.448																																					p.A646A		Atlas-SNP	.											.	STOX1	75	.	0			c.C1938A						PASS	.						128	121	123					10																	70645490		1926	4138	6064	SO:0001819	synonymous_variant	219736	exon3			AGGTGCCTCCTTT	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.1938C>A	chr10.hg19:g.70645490C>A		78.0	0.0	.		64.0	46.0	.	NM_152709	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Silent	SNP	ENST00000298596.6	hg19	CCDS41535.1																																																																																			.	.	.	none		0.448	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709		A	70645490	C	A	70645490	2	1	239	1	0	0	0	0	0	0	0	1	15331	668	24	4		4	STOX1	10	70645490	Silent	SNP	C	TCGA-PJ-A8JU-01A-11D-A35Z-10		70645490	64889257	43	14590											
FUT11	170384	hgsc.bcm.edu	37	chr10	75535419	75535419	+	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	tgggattacctacatgaaatCttcatgaagaggcaacatct	14	11	8	8	0	3	3	1	2	2	1	3	4	3	4	1	2	3	1	1	2	5	3			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr10:75535419C>A	ENST00000372841.3	+	3	1498	c.1455C>A	c.(1453-1455)atC>atA	p.I485I	RMRPP1_ENST00000517236.1_RNA	NM_173540.2	NP_775811.2	Q495W5	FUT11_HUMAN	fucosyltransferase 11 (alpha (1,3) fucosyltransferase)	485					protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	7	Prostate(51;0.0112)					TACATGAAATCTTCATGAAGA	0.453																																					p.I485I		Atlas-SNP	.											.	FUT11	30	.	0			c.C1455A						PASS	.						110	99	103					10																	75535419		2203	4300	6503	SO:0001819	synonymous_variant	170384	exon3			TGAAATCTTCATG	BC036037	CCDS7333.1, CCDS60558.1	10q22.3	2014-01-02			ENSG00000196968	ENSG00000196968		"Fucosyltransferases"	19233	protein-coding gene	gene with protein product						11698403, 24318988	Standard	NM_173540		Approved	MGC33202	uc001jva.3	Q495W5	OTTHUMG00000018483	ENST00000372841.3:c.1455C>A	chr10.hg19:g.75535419C>A		116.0	0.0	.		80.0	51.0	.	NM_173540	Q495W7|Q8IYE4	Silent	SNP	ENST00000372841.3	hg19	CCDS7333.1																																																																																			.	.	.	none		0.453	FUT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048689.1	NM_173540		A	75535419	C	A	75535419	2	1	239	1	0	0	0	0	0	0	0	1	6110	903	32	4		4	FUT11	10	75535419	Silent	SNP	C	TCGA-PJ-A8JU-01A-11D-A35Z-10	4889929	75535419	59999328	44	14591											
PTEN	5728	hgsc.bcm.edu	37	chr10	89720833	89720833	+	Frame_Shift_Del	DEL	A	A	-																															aaaaatgatcttgacaaagcAaataaagacaaagccaaccg																								rs587782304		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr10:89720833delA	ENST00000371953.3	+	8	2341	c.984delA	c.(982-984)gcafs	p.A328fs	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	328	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.T319_K332del(1)|p.G165_*404del(1)|p.A328fs*15(1)|p.W274_F341del(1)|p.A328fs*1(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)		TTGACAAAGCAAATAAAGACA	0.328		31	"D, Mis, N, F, S"		"glioma,  prostate, endometrial"	"harmartoma, glioma,  prostate, endometrial"			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.A328fs		Pindel	.	yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	.	PTEN	3652	.	54	Whole gene deletion(37)|Deletion - Frameshift(11)|Deletion - In frame(4)|Unknown(2)	prostate(16)|central_nervous_system(13)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|endometrium(3)|breast(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)	c.983delC						PASS	.						73	76	75					10																	89720833		2203	4297	6500	SO:0001589	frameshift_variant	5728	exon8	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.984delA	chr10.hg19:g.89720833delA	ENSP00000361021:p.Ala328fs	416.0	0.0	.		270.0	97.0	0.359	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Frame_Shift_Del	DEL	ENST00000371953.3	hg19	CCDS31238.1																																																																																			.	.	.	none		0.328	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		-	89720833	A	-	89720833	7	5	239	1	0	1	0	1	0	0	0	0	12748	117	5	0	1014	0	PTEN	10	89720833	Frame_Shift_Del	DEL	A	TCGA-PJ-A8JU-01A-11D-A35Z-10	14185414	89720833	45813914	45	14592	150	2									
PTEN	5728	hgsc.bcm.edu	37	chr10	89720837	89720837	+	Nonsense_Mutation	SNP	A	A	T																															atgatcttgacaaagcaaatAaagacaaagccaaccgatac																										TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr10:89720837A>T	ENST00000371953.3	+	8	2345	c.988A>T	c.(988-990)Aaa>Taa	p.K330*	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	330	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.N329fs*14(3)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.T319_K332del(1)|p.G165_*404del(1)|p.W274_F341del(1)|p.N329fs*12(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)		CAAAGCAAATAAAGACAAAGC	0.323		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.K330X		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	3652	.	56	Whole gene deletion(37)|Deletion - Frameshift(13)|Deletion - In frame(4)|Unknown(2)	prostate(16)|central_nervous_system(13)|skin(6)|endometrium(4)|lung(4)|breast(4)|haematopoietic_and_lymphoid_tissue(3)|ovary(3)|urinary_tract(2)|soft_tissue(1)	c.A988T						PASS	.						71	73	72					10																	89720837		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.	GCAAATAAAGACA	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.988A>T	chr10.hg19:g.89720837A>T	ENSP00000361021:p.Lys330*	398.0	1.0	.		271.0	186.0	.	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Nonsense_Mutation	SNP	ENST00000371953.3	hg19	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	A	49	15.016191	0.99819	.	.	ENSG00000171862	ENST00000371953	.	.	.	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-12.5629	15.3536	0.74409	1.0:0.0:0.0:0.0	.	.	.	.	X	330	.	.	K	+	1	0	PTEN	89710817	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.861000	0.92277	2.034000	0.60081	0.482000	0.46254	AAA	.	.	.	none		0.323	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		T	89720837	A	T	89720837	4	4	239	1	0	0	0	0	0	1	0	0	12748	363	13	5	1018	5	PTEN	10	89720837	Nonsense_Mutation	SNP	A	TCGA-PJ-A8JU-01A-11D-A35Z-10	4	89720837	45813910	46	14593	150	2									
AMBRA1	55626	hgsc.bcm.edu	37	chr11	46563838	46563838	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcgcagggtatcgttgttgaAggtcaggagattgtggcaag	9	10	17	5	2	1	2	1	1	0	1	2	3	1	2	0	4	0	5	0	4	3	4			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr11:46563838A>G	ENST00000458649.2	-	7	2147	c.1729T>C	c.(1729-1731)Ttc>Ctc	p.F577L	AMBRA1_ENST00000533727.1_Missense_Mutation_p.F487L|AMBRA1_ENST00000298834.3_Missense_Mutation_p.F577L|AMBRA1_ENST00000528950.1_Missense_Mutation_p.F577L|AMBRA1_ENST00000534300.1_Missense_Mutation_p.F577L|AMBRA1_ENST00000314845.3_Missense_Mutation_p.F487L|AMBRA1_ENST00000426438.1_Missense_Mutation_p.F577L			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	577					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)		TCGTTGTTGAAGGTCAGGAGA	0.582																																					p.F487L		Atlas-SNP	.											.	AMBRA1	201	.	0			c.T1459C						PASS	.						121	99	106					11																	46563838		2201	4299	6500	SO:0001583	missense	55626	exon8			TGTTGAAGGTCAG	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.1729T>C	chr11.hg19:g.46563838A>G	ENSP00000415327:p.Phe577Leu	54.0	0.0	.		40.0	15.0	.	NM_001267783	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Missense_Mutation	SNP	ENST00000458649.2	hg19		.	.	.	.	.	.	.	.	.	.	A	17.64	3.440069	0.63067	.	.	ENSG00000110497	ENST00000314845;ENST00000533727;ENST00000534300;ENST00000426438;ENST00000298834;ENST00000314823;ENST00000458649;ENST00000528950	T;T;T;T;T;T;T	0.80824	-1.02;-1.42;-0.83;-0.96;-0.83;-0.84;-0.96	5.73	5.73	0.89815	.	0.044861	0.85682	D	0.000000	D	0.84097	0.5397	L	0.29908	0.895	0.80722	D	1	P;D;D;D;D;D	0.71674	0.953;0.998;0.998;0.974;0.99;0.974	B;D;D;D;D;D	0.76071	0.294;0.987;0.987;0.969;0.979;0.969	D	0.84535	0.0635	10	0.44086	T	0.13	.	16.0234	0.80516	1.0:0.0:0.0:0.0	.	577;577;577;487;487;487	Q9C0C7;Q9C0C7-3;Q9C0C7-2;G3V193;Q9C0C7-5;Q9C0C7-4	AMRA1_HUMAN;.;.;.;.;.	L	487;487;577;577;577;487;577;577	ENSP00000318313:F487L;ENSP00000433372:F487L;ENSP00000431926:F577L;ENSP00000410899:F577L;ENSP00000298834:F577L;ENSP00000415327:F577L;ENSP00000433945:F577L	ENSP00000298834:F577L	F	-	1	0	AMBRA1	46520414	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.935000	0.92923	2.172000	0.68678	0.533000	0.62120	TTC	.	.	.	none		0.582	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749		G	46563838	A	G	46563838	3	3	239	1	0	0	0	0	1	0	0	0	565	72	3	3	2215	3	AMBRA1	11	46563838	Missense_Mutation	SNP	A	TCGA-PJ-A8JU-01A-11D-A35Z-10		46563838	88442678	47	14594											
AMBRA1	55626	hgsc.bcm.edu	37	chr11	46569397	46569397	+	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	tgaaggccaataagaaggtaGagcgtggactatccggcagt	13	7	14	7	2	0	3	0	1	0	2	1	4	1	4	2	4	1	2	2	4	6	3			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr11:46569397G>T	ENST00000458649.2	-	3	582	c.164C>A	c.(163-165)tCt>tAt	p.S55Y	AMBRA1_ENST00000533727.1_Missense_Mutation_p.S55Y|AMBRA1_ENST00000298834.3_Missense_Mutation_p.S55Y|AMBRA1_ENST00000528950.1_Missense_Mutation_p.S55Y|AMBRA1_ENST00000534300.1_Missense_Mutation_p.S55Y|AMBRA1_ENST00000314845.3_Missense_Mutation_p.S55Y|AMBRA1_ENST00000426438.1_Missense_Mutation_p.S55Y			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	55					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)		TAAGAAGGTAGAGCGTGGACT	0.383																																					p.S55Y		Atlas-SNP	.											.	AMBRA1	201	.	0			c.C164A						PASS	.						53	54	54					11																	46569397		2201	4299	6500	SO:0001583	missense	55626	exon3			AAGGTAGAGCGTG	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.164C>A	chr11.hg19:g.46569397G>T	ENSP00000415327:p.Ser55Tyr	65.0	0.0	.		53.0	16.0	.	NM_001267783	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Missense_Mutation	SNP	ENST00000458649.2	hg19		.	.	.	.	.	.	.	.	.	.	G	19.58	3.853645	0.71719	.	.	ENSG00000110497	ENST00000314845;ENST00000533727;ENST00000534300;ENST00000426438;ENST00000298834;ENST00000314823;ENST00000458649;ENST00000528950	T;T;T;T;T;T;T	0.72282	-0.48;-0.64;-0.34;-0.45;-0.34;-0.43;-0.45	6.04	6.04	0.98038	WD40/YVTN repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.84188	0.5417	M	0.67397	2.05	0.80722	D	1	D;D;D;D;D;D	0.89917	0.998;1.0;1.0;0.999;0.999;0.999	D;D;D;D;D;D	0.87578	0.991;0.998;0.998;0.996;0.996;0.996	T	0.83247	-0.0055	10	0.56958	D	0.05	.	20.5792	0.99380	0.0:0.0:1.0:0.0	.	55;55;55;55;55;55	Q9C0C7;Q9C0C7-3;Q9C0C7-2;G3V193;Q9C0C7-5;Q9C0C7-4	AMRA1_HUMAN;.;.;.;.;.	Y	55	ENSP00000318313:S55Y;ENSP00000433372:S55Y;ENSP00000431926:S55Y;ENSP00000410899:S55Y;ENSP00000298834:S55Y;ENSP00000415327:S55Y;ENSP00000433945:S55Y	ENSP00000298834:S55Y	S	-	2	0	AMBRA1	46525973	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.659000	0.98597	2.873000	0.98535	0.561000	0.74099	TCT	.	.	.	none		0.383	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749		T	46569397	G	T	46569397	3	4	239	1	0	0	0	0	1	0	0	0	565	942	33	4	3530	4	AMBRA1	11	46569397	Missense_Mutation	SNP	G	TCGA-PJ-A8JU-01A-11D-A35Z-10	5559	46569397	88437119	48	14595											
NXF1	10482	hgsc.bcm.edu	37	chr11	62561809	62561809	+	Missense_Mutation	SNP	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	ctgctctggagagagggtggGcaccgggctggaggaaggcg	7	5	21	8	2	1	1	0	0	1	1	1	5	1	4	1	7	1	3	1	7	1	0	rs546919784		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr11:62561809G>A	ENST00000532297.1	-	20	2310	c.1681C>T	c.(1681-1683)Ccc>Tcc	p.P561S	NXF1_ENST00000294172.2_Missense_Mutation_p.P561S|TMEM223_ENST00000527073.1_5'Flank|TMEM223_ENST00000525631.1_5'Flank|NXF1_ENST00000533048.1_5'UTR|NXF1_ENST00000531709.2_3'UTR|TMEM223_ENST00000307366.7_5'Flank			Q9UBU9	NXF1_HUMAN	nuclear RNA export factor 1	561	Pro-rich.				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						GAGAGGGTGGGCACCGGGCTG	0.537													G|||	1	0.000199681	0	0	5008	,	,		17580	0		0	False		,,,				2504	0.001				p.P561S		Atlas-SNP	.											.	NXF1	67	.	0			c.C1681T						PASS	.						103	95	98					11																	62561809		2201	4299	6500	SO:0001583	missense	10482	exon19			GGGTGGGCACCGG	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.1681C>T	chr11.hg19:g.62561809G>A	ENSP00000436679:p.Pro561Ser	123.0	0.0	.		127.0	6.0	.	NM_006362	B4E269|Q99799|Q9UQL2	Missense_Mutation	SNP	ENST00000532297.1	hg19	CCDS8037.1	.	.	.	.	.	.	.	.	.	.	G	19.02	3.745384	0.69418	.	.	ENSG00000162231	ENST00000294172;ENST00000532297	T;T	0.52295	0.67;0.67	5.38	4.43	0.53597	TAP, C-terminal (1);UBA-like (1);	0.000000	0.85682	D	0.000000	T	0.44746	0.1308	M	0.70842	2.15	0.80722	D	1	P	0.44734	0.842	B	0.37601	0.254	T	0.46816	-0.9164	10	0.29301	T	0.29	-18.3515	13.9834	0.64319	0.0:0.1517:0.8483:0.0	.	561	Q9UBU9	NXF1_HUMAN	S	561	ENSP00000294172:P561S;ENSP00000436679:P561S	ENSP00000294172:P561S	P	-	1	0	NXF1	62318385	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.633000	0.83260	2.526000	0.85167	0.462000	0.41574	CCC	.	.	.	none		0.537	NXF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395365.2	NM_006362		A	62561809	G	A	62561809	3	1	239	1	0	0	0	0	1	0	0	0	10789	1203	42	2	190	2	NXF1	11	62561809	Missense_Mutation	SNP	G	TCGA-PJ-A8JU-01A-11D-A35Z-10	15992412	62561809	72444707	49	14596											
PCF11	51585	hgsc.bcm.edu	37	chr11	82877708	82877708	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaatgtagaaaactggcaaaGttccaagtctgccaaaagat	17	8	9	7	0	1	2	0	0	1	2	2	3	2	2	2	1	2	3	2	1	8	2			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr11:82877708G>A	ENST00000298281.4	+	5	2221	c.1769G>A	c.(1768-1770)aGt>aAt	p.S590N		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	590					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						AACTGGCAAAGTTCCAAGTCT	0.368																																					p.S590N		Atlas-SNP	.											.	PCF11	220	.	0			c.G1769A						PASS	.						70	70	70					11																	82877708		1802	3980	5782	SO:0001583	missense	51585	exon5			GGCAAAGTTCCAA	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.1769G>A	chr11.hg19:g.82877708G>A	ENSP00000298281:p.Ser590Asn	291.0	0.0	.		277.0	83.0	.	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	hg19	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	G	7.024	0.559350	0.13436	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.45276	1.9;0.9;0.9	6.07	4.18	0.49190	.	0.165679	0.43747	D	0.000537	T	0.27278	0.0669	N	0.19112	0.55	0.24915	N	0.992017	B;B	0.19583	0.037;0.0	B;B	0.19391	0.025;0.003	T	0.14615	-1.0466	9	.	.	.	.	11.9702	0.53060	0.0652:0.1224:0.8124:0.0	.	590;590	E9PQ01;O94913	.;PCF11_HUMAN	N	590	ENSP00000298281:S590N;ENSP00000434540:S590N;ENSP00000431567:S590N	.	S	+	2	0	PCF11	82555356	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.554000	0.53720	0.869000	0.35703	0.655000	0.94253	AGT	.	.	.	none		0.368	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		A	82877708	G	A	82877708	3	1	239	1	0	0	0	0	1	0	0	0	11580	1029	36	2	1787	2	PCF11	11	82877708	Missense_Mutation	SNP	G	TCGA-PJ-A8JU-01A-11D-A35Z-10	20315899	82877708	52128808	50	14597											
CREBZF	58487	hgsc.bcm.edu	37	chr11	85375427	85375427	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tccgataccgtttaacagccTttgcagcaggtcagagaagc	11	9	10	11	2	1	1	1	0	0	1	2	3	2	1	3	1	6	3	3	1	3	4			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr11:85375427T>C	ENST00000527447.1	-	1	719	c.493A>G	c.(493-495)Agg>Ggg	p.R165G	CREBZF_ENST00000398294.2_Missense_Mutation_p.R83G|CREBZF_ENST00000531515.1_Intron|CREBZF_ENST00000534224.1_Intron	NM_001039618.2	NP_001034707.1	Q9NS37	ZHANG_HUMAN	CREB/ATF bZIP transcription factor	165					negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)				TTTAACAGCCTTTGCAGCAGG	0.647											OREG0021274	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R165G	NSCLC(172;674 2044 9050 18334 41735)	Atlas-SNP	.											.	CREBZF	26	.	0			c.A493G						PASS	.						20	23	22					11																	85375427		2044	4204	6248	SO:0001583	missense	58487	exon1			ACAGCCTTTGCAG	AF039942	CCDS41697.1	11q14.1	2013-01-10			ENSG00000137504	ENSG00000137504		"basic leucine zipper proteins"	24905	protein-coding gene	gene with protein product	"Zhangfei"	606444				10871379	Standard	NM_001039618		Approved	ZF	uc001pas.2	Q9NS37	OTTHUMG00000133648	ENST00000527447.1:c.493A>G	chr11.hg19:g.85375427T>C	ENSP00000433459:p.Arg165Gly	89.0	0.0	.	1236	67.0	20.0	.	NM_001039618	B2R8Q9|Q0P5U9|Q52LT3	Missense_Mutation	SNP	ENST00000527447.1	hg19	CCDS41697.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.279731	0.80692	.	.	ENSG00000137504	ENST00000398294;ENST00000527447	.	.	.	4.46	4.46	0.54185	.	0.219310	0.30879	N	0.008690	T	0.41026	0.1141	N	0.04508	-0.205	0.35343	D	0.78664	D	0.57899	0.981	D	0.67231	0.95	T	0.50955	-0.8766	8	.	.	.	-19.5129	10.3281	0.43805	0.0:0.0:0.0:1.0	.	165	Q9NS37	ZHANG_HUMAN	G	83;165	.	.	R	-	1	2	CREBZF	85053075	0.997000	0.39634	1.000000	0.80357	0.990000	0.78478	0.977000	0.29475	2.003000	0.58678	0.459000	0.35465	AGG	.	.	.	none		0.647	CREBZF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390191.2	NM_001039618		C	85375427	T	C	85375427	3	2	239	1	0	0	0	0	1	0	0	0	3865	1608	56	3	575	3	CREBZF	11	85375427	Missense_Mutation	SNP	T	TCGA-PJ-A8JU-01A-11D-A35Z-10	2497719	85375427	49631089	51	14598											
DDX10	1662	hgsc.bcm.edu	37	chr11	108562631	108562631	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctgtaccgagtgttttgccGgctacgtcctggtgtttcta	4	16	11	10	3	2	0	0	0	2	0	3	1	3	0	3	2	3	4	3	2	3	6			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr11:108562631G>A	ENST00000322536.3	+	8	1133	c.1004G>A	c.(1003-1005)cGg>cAg	p.R335Q	DDX10_ENST00000526794.1_Missense_Mutation_p.R335Q	NM_004398.2	NP_004389.2	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	335	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				metabolic process (GO:0008152)		ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			breast(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|prostate(2)	27		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		GTGTTTTGCCGGCTACGTCCT	0.448			T	NUP98	AML*																																p.R335Q		Atlas-SNP	.		Dom	yes		11	11q22-q23	1662	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10		L	.	DDX10	70	.	0			c.G1004A						PASS	.						159	132	141					11																	108562631		2201	4298	6499	SO:0001583	missense	1662	exon8			TTTGCCGGCTACG	U28042	CCDS8342.1	11q22-q23	2005-10-11	2003-06-13		ENSG00000178105	ENSG00000178105		"DEAD-boxes"	2735	protein-coding gene	gene with protein product		601235	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 10 (RNA helicase)"			8660968	Standard	NM_004398		Approved	HRH-J8	uc001pkm.3	Q13206	OTTHUMG00000166540	ENST00000322536.3:c.1004G>A	chr11.hg19:g.108562631G>A	ENSP00000314348:p.Arg335Gln	104.0	0.0	.		100.0	29.0	.	NM_004398	B2RCQ3|Q5BJD8	Missense_Mutation	SNP	ENST00000322536.3	hg19	CCDS8342.1	.	.	.	.	.	.	.	.	.	.	G	19.44	3.827186	0.71143	.	.	ENSG00000178105	ENST00000322536;ENST00000456020;ENST00000526794	T;T	0.04706	3.57;3.57	5.48	4.57	0.56435	Helicase, C-terminal (2);	0.051708	0.64402	D	0.000001	T	0.07413	0.0187	N	0.19112	0.55	0.46356	D	0.999001	D;D	0.60575	0.988;0.979	P;P	0.55112	0.74;0.769	T	0.39375	-0.9617	10	0.48119	T	0.1	-12.4144	11.2003	0.48736	0.1599:0.0:0.8401:0.0	.	335;335	Q13206;E9PIF2	DDX10_HUMAN;.	Q	335;241;335	ENSP00000314348:R335Q;ENSP00000432032:R335Q	ENSP00000314348:R335Q	R	+	2	0	DDX10	108067841	1.000000	0.71417	0.955000	0.39395	0.226000	0.24999	6.285000	0.72658	1.309000	0.44985	0.591000	0.81541	CGG	.	.	.	none		0.448	DDX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390343.1	NM_004398		A	108562631	G	A	108562631	3	1	239	1	0	0	0	0	1	0	0	0	4344	1116	39	1	1034	1	DDX10	11	108562631	Missense_Mutation	SNP	G	TCGA-PJ-A8JU-01A-11D-A35Z-10	23187204	108562631	26443885	52	14599											
ARHGAP9	64333	hgsc.bcm.edu	37	chr12	57872506	57872506	+	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	ctgcttgggagggcctgagaCaactcctccagggaaccatg	9	7	13	12	0	0	1	0	1	0	1	2	4	2	3	4	3	3	1	4	3	2	1	rs368912616		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr12:57872506C>G	ENST00000356411.2	-	3	489	c.351G>C	c.(349-351)ttG>ttC	p.L117F	ARHGAP9_ENST00000430041.2_5'Flank|ARHGAP9_ENST00000550288.1_Missense_Mutation_p.L196F|ARHGAP9_ENST00000424809.2_Missense_Mutation_p.L117F|ARHGAP9_ENST00000393797.2_Missense_Mutation_p.L188F|ARHGAP9_ENST00000550454.1_5'Flank|ARHGAP9_ENST00000393791.3_Missense_Mutation_p.L117F			Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9	117					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)			GGGCCTGAGACAACTCCTCCA	0.577																																					p.L117F		Atlas-SNP	.											.	ARHGAP9	79	.	0			c.G351C						PASS	.						59	56	57					12																	57872506		2203	4300	6503	SO:0001583	missense	64333	exon2			CTGAGACAACTCC	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.351G>C	chr12.hg19:g.57872506C>G	ENSP00000348782:p.Leu117Phe	59.0	0.0	.		53.0	32.0	.	NM_001080157	B4DVI3|E9PDX9|Q8NAF3|Q8TCJ3|Q8WYR0|Q96EZ2|Q96S74	Missense_Mutation	SNP	ENST00000356411.2	hg19		.	.	.	.	.	.	.	.	.	.	c	2.790	-0.251593	0.05867	.	.	ENSG00000123329	ENST00000393791;ENST00000356411;ENST00000424809;ENST00000393797;ENST00000340423;ENST00000552249	T;T;T;T;T	0.61742	2.86;2.86;1.5;2.75;0.08	3.96	0.0109	0.14085	.	0.959081	0.08578	N	0.925035	T	0.53142	0.1778	L	0.48642	1.525	0.09310	N	1	D;P;B;P;B	0.61697	0.99;0.745;0.001;0.527;0.392	P;B;B;B;B	0.51806	0.68;0.161;0.001;0.158;0.076	T	0.43261	-0.9402	10	0.51188	T	0.08	.	1.2457	0.01972	0.1714:0.4464:0.1797:0.2026	.	117;196;117;117;117	B4E248;Q6ZN13;Q9BRR9;Q9BRR9-2;E9PDX9	.;.;RHG09_HUMAN;.;.	F	117;117;117;188;166;35	ENSP00000377380:L117F;ENSP00000348782:L117F;ENSP00000394307:L117F;ENSP00000377386:L188F;ENSP00000448358:L35F	ENSP00000344852:L166F	L	-	3	2	ARHGAP9	56158773	0.000000	0.05858	0.003000	0.11579	0.020000	0.10135	-0.013000	0.12678	0.003000	0.14656	-1.776000	0.00657	TTG	.	.	.	alt		0.577	ARHGAP9-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_032496		G	57872506	C	G	57872506	3	3	239	1	0	0	0	0	1	0	0	0	889	477	17	4	1908	4	ARHGAP9	12	57872506	Missense_Mutation	SNP	C	TCGA-PJ-A8JU-01A-11D-A35Z-10		57872506	75979389	53	14600											
TRHDE	29953	hgsc.bcm.edu	37	chr12	72962372	72962372	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgtggcagattccattaacTattgtggtaggaaatagaag	13	12	11	5	0	0	2	0	0	0	2	1	3	1	3	1	3	1	2	1	3	6	6			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr12:72962372T>C	ENST00000261180.4	+	10	2028	c.1932T>C	c.(1930-1932)acT>acC	p.T644T	TRHDE_ENST00000549138.1_3'UTR	NM_013381.2	NP_037513.1	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	644					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						TTCCATTAACTATTGTGGTAG	0.348																																					p.T644T		Atlas-SNP	.											.	TRHDE	194	.	0			c.T1932C						PASS	.						112	111	111					12																	72962372		2203	4300	6503	SO:0001819	synonymous_variant	29953	exon10			ATTAACTATTGTG	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.1932T>C	chr12.hg19:g.72962372T>C		108.0	0.0	.		133.0	70.0	.	NM_013381	A5PL19|Q6UWJ4	Silent	SNP	ENST00000261180.4	hg19	CCDS9004.1																																																																																			.	.	.	none		0.348	TRHDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405380.1	NM_013381		C	72962372	T	C	72962372	2	2	239	1	0	0	0	0	0	0	0	1	16491	1509	53	3		3	TRHDE	12	72962372	Silent	SNP	T	TCGA-PJ-A8JU-01A-11D-A35Z-10	15089866	72962372	60889523	54	14601											
TUBGCP3	10426	hgsc.bcm.edu	37	chr13	113212595	113212596	+	Frame_Shift_Ins	INS	-	-	G																															ccactgctgcccacgctgccINSggagctctgggctgactggg																								rs9324311	byFrequency	TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr13:113212595_113212596insG	ENST00000261965.3	-	5	648_649	c.462_463insC	c.(460-465)tccggcfs	p.G155fs	TUBGCP3_ENST00000375669.3_Frame_Shift_Ins_p.G155fs	NM_006322.4	NP_006313.1	Q96CW5	GCP3_HUMAN	tubulin, gamma complex associated protein 3	155					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)					CCCACGCTGCCGGAGCTCTGGG	0.624																																					p.G155fs		Atlas-Indel,Pindel	.											TUBGCP3,NS,carcinoma,0,1	TUBGCP3	74	.	0			c.463_464insC						PASS	.																																			SO:0001589	frameshift_variant	10426	exon5			.	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.463dupC	chr13.hg19:g.113212597_113212597dupG	ENSP00000261965:p.Gly155fs	97.0	0.0	0		79.0	30.0	0.379747	NM_006322	O43631|O60852|O60853|Q5T8L2|Q7Z4K1|Q96I79	Frame_Shift_Ins	INS	ENST00000261965.3	hg19	CCDS9525.1																																																																																			.	.	.	none		0.624	TUBGCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045825.2	NM_006322		G	113212596	-	G	113212595	7	5	239	1	0	1	1	0	0	0	0	0	16779	652	23	0	2332	0	TUBGCP3	13	113212595	Frame_Shift_Ins	INS	-	TCGA-PJ-A8JU-01A-11D-A35Z-10		113212595	1957283	55	14602											
CMA1	1215	hgsc.bcm.edu	37	chr14	24976587	24976588	+	Missense_Mutation	DNP	GC	GC	CA																															tgcacaatgagcagccgtcaGcacaaagttccgtcttataa																										TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr14:24976587_24976588GC>CA	ENST00000250378.3	-	2	212_213	c.183_184GC>TG	c.(181-186)gtGCtg>gtTGtg	p.L62V	CMA1_ENST00000206446.4_Intron|RP11-80A15.1_ENST00000555109.1_Intron	NM_001836.3	NP_001827.1	P23946	CMA1_HUMAN	chymase 1, mast cell	62	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)		GCAGCCGTCAGCACAAAGTTCC	0.48																																					p.L62V|p.V61V		Atlas-SNP	.											.	CMA1	21	.	0			c.C184G|c.G183T						PASS	.																																			SO:0001583	missense	1215	exon2			CCGTCAGCACAAA|CGTCAGCACAAAG		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.183_184delinsCA	chr14.hg19:g.24976587_24976588delinsCA	ENSP00000250378:p.Leu62Val	146.0|148.0	0.0	.		94.0|98.0	24.0|26.0	.	NM_001836	B5BUM8|Q16018|Q3SY36|Q3SY37|Q9UDH5	Missense_Mutation|Silent	SNP	ENST00000250378.3	hg19	CCDS9630.1																																																																																			.	.	.	none		0.48	CMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276535.2			CA	24976588	GC	CA	24976587	3	2	239	1	0	0	0	0	1	0	0	0	3576	962	34	4	575	4	CMA1	14	24976587	Missense_Mutation	DNP	GC	TCGA-PJ-A8JU-01A-11D-A35Z-10		24976587	82372953	56	14603											
ARG2	384	hgsc.bcm.edu	37	chr14	68113700	68113700	+	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	agatattgatcgacttggtaTccagaaggtcatggaacgaa	14	10	11	6	2	1	3	1	1	0	2	3	6	2	4	1	3	1	1	1	3	5	4			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr14:68113700T>A	ENST00000261783.3	+	6	860	c.680T>A	c.(679-681)aTc>aAc	p.I227N		NM_001172.3	NP_001163.1	P78540	ARGI2_HUMAN	arginase 2	227					arginine metabolic process (GO:0006525)|cellular nitrogen compound metabolic process (GO:0034641)|nitric oxide biosynthetic process (GO:0006809)|small molecule metabolic process (GO:0044281)|striated muscle contraction (GO:0006941)|urea cycle (GO:0000050)|ureteric bud development (GO:0001657)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	arginase activity (GO:0004053)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|ovary(1)|prostate(1)	11				all cancers(60;0.000582)|OV - Ovarian serous cystadenocarcinoma(108;0.00392)|BRCA - Breast invasive adenocarcinoma(234;0.00928)	L-Arginine(DB00125)|L-Ornithine(DB00129)	CGACTTGGTATCCAGAAGGTC	0.378																																					p.I227N		Atlas-SNP	.											.	ARG2	20	.	0			c.T680A						PASS	.						108	104	105					14																	68113700		2203	4300	6503	SO:0001583	missense	384	exon6			TTGGTATCCAGAA	D86724	CCDS9785.1	14q24.1	2013-05-01	2013-05-01			ENSG00000081181			664	protein-coding gene	gene with protein product		107830	"arginase, type II"			8954792, 8898077	Standard	NM_001172		Approved		uc001xjs.3	P78540		ENST00000261783.3:c.680T>A	chr14.hg19:g.68113700T>A	ENSP00000261783:p.Ile227Asn	60.0	0.0	.		59.0	25.0	.	NM_001172	B2R690|Q6FHY8	Missense_Mutation	SNP	ENST00000261783.3	hg19	CCDS9785.1	.	.	.	.	.	.	.	.	.	.	T	31	5.095241	0.94197	.	.	ENSG00000081181	ENST00000261783	D	0.85955	-2.05	6.17	6.17	0.99709	Ureohydrolase domain (1);	0.044090	0.85682	D	0.000000	D	0.95446	0.8521	H	0.97365	3.99	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.96930	0.9680	10	0.87932	D	0	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	227	P78540	ARGI2_HUMAN	N	227	ENSP00000261783:I227N	ENSP00000261783:I227N	I	+	2	0	ARG2	67183453	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.371000	0.80710	0.533000	0.62120	ATC	.	.	.	none		0.378	ARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415190.2	NM_001172		A	68113700	T	A	68113700	3	1	239	1	0	0	0	0	1	0	0	0	858	1435	50	5	702	5	ARG2	14	68113700	Missense_Mutation	SNP	T	TCGA-PJ-A8JU-01A-11D-A35Z-10	43137113	68113700	39235840	57	14604											
SNURF	8926	hgsc.bcm.edu	37	chr15	25207341	25207341	+	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	caaacgcagaaggactgcctCactgagcaaccaagagtgag	15	4	11	11	1	1	4	1	2	0	2	1	5	1	5	2	1	4	2	2	1	4	0			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr15:25207341C>A	ENST00000577949.1	+	2	158	c.95C>A	c.(94-96)tCa>tAa	p.S32*	SNRPN_ENST00000400100.1_5'UTR|SNURF_ENST00000551312.2_Nonsense_Mutation_p.S32*|SNRPN_ENST00000400098.1_5'UTR|SNRPN_ENST00000553597.1_3'UTR|SNRPN_ENST00000400097.1_5'UTR|SNRPN_ENST00000390687.4_5'UTR|SNURF_ENST00000338094.6_Nonsense_Mutation_p.S32*|SNRPN_ENST00000346403.6_5'UTR|SNURF_ENST00000338327.4_Nonsense_Mutation_p.S32*|SNRPN_ENST00000577565.1_5'UTR|SNRPN_ENST00000554227.2_5'UTR			Q9Y675	SNURF_HUMAN	SNRPN upstream reading frame	32						nucleus (GO:0005634)				breast(2)|large_intestine(2)|lung(1)	5		all_cancers(20;1.4e-21)|Breast(32;0.000625)		all cancers(64;3.48e-07)|Epithelial(43;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0142)		AGGACTGCCTCACTGAGCAAC	0.453																																					p.S32X		Atlas-SNP	.											.	SNURF	17	.	0			c.C95A						PASS	.						137	104	115					15																	25207341		2203	4300	6503	SO:0001587	stop_gained	8926	exon2			CTGCCTCACTGAG		CCDS10016.1	15q11.2	2013-08-27			ENSG00000214265	ENSG00000214265			11171	protein-coding gene	gene with protein product						10318933	Standard	NM_022804		Approved		uc001ywu.3	Q9Y675	OTTHUMG00000129181	ENST00000577949.1:c.95C>A	chr15.hg19:g.25207341C>A	ENSP00000463201:p.Ser32*	131.0	0.0	.		94.0	36.0	.	NM_005678	A6NCW2	Nonsense_Mutation	SNP	ENST00000577949.1	hg19	CCDS10016.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.359258	0.82353	.	.	ENSG00000214265	ENST00000338094;ENST00000338327	.	.	.	3.76	3.76	0.43208	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.4824	11.3845	0.49776	0.0:1.0:0.0:0.0	.	.	.	.	X	32	.	ENSP00000336543:S32X	S	+	2	0	SNURF	22758434	0.993000	0.37304	0.937000	0.37676	0.838000	0.47535	2.269000	0.43346	2.412000	0.81896	0.655000	0.94253	TCA	.	.	.	none		0.453	SNURF-005	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446300.1	NM_005678		A	25207341	C	A	25207341	4	1	239	1	0	0	0	0	0	1	0	0	14891	838	29	4	101	4	SNURF	15	25207341	Nonsense_Mutation	SNP	C	TCGA-PJ-A8JU-01A-11D-A35Z-10		25207341	77324051	58	14605											
GLCE	26035	hgsc.bcm.edu	37	chr15	69548297	69548297	+	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	tagtggcttcagagtggatgGgtttgaaaaaagagcagcag	13	9	15	4	0	1	3	1	1	0	2	1	4	1	4	0	3	2	4	0	3	4	3			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr15:69548297G>A	ENST00000261858.2	+	3	380	c.152G>A	c.(151-153)gGg>gAg	p.G51E	GLCE_ENST00000559420.2_5'UTR	NM_015554.1	NP_056369.1	O94923	GLCE_HUMAN	glucuronic acid epimerase	51					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						AGAGTGGATGGGTTTGAAAAA	0.463																																					p.G51E		Atlas-SNP	.											.	GLCE	48	.	0			c.G152A						PASS	.						90	87	88					15																	69548297		2200	4298	6498	SO:0001583	missense	26035	exon3			TGGATGGGTTTGA	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.152G>A	chr15.hg19:g.69548297G>A	ENSP00000261858:p.Gly51Glu	178.0	0.0	.		155.0	49.0	.	NM_015554	Q6GUQ2	Missense_Mutation	SNP	ENST00000261858.2	hg19	CCDS32277.1	.	.	.	.	.	.	.	.	.	.	G	12.76	2.034619	0.35893	.	.	ENSG00000138604	ENST00000261858	T	0.32753	1.44	5.3	3.42	0.39159	.	0.261099	0.38164	N	0.001783	T	0.21962	0.0529	L	0.36672	1.1	0.33073	D	0.535579	B	0.33694	0.421	B	0.27500	0.08	T	0.29088	-1.0023	10	0.62326	D	0.03	-2.6096	10.3667	0.44028	0.0:0.1541:0.699:0.1469	.	51	O94923	GLCE_HUMAN	E	51	ENSP00000261858:G51E	ENSP00000261858:G51E	G	+	2	0	GLCE	67335351	1.000000	0.71417	0.914000	0.36105	0.752000	0.42762	5.519000	0.67074	0.722000	0.32252	0.655000	0.94253	GGG	.	.	.	none		0.463	GLCE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015554		A	69548297	G	A	69548297	3	1	239	1	0	0	0	0	1	0	0	0	6439	1232	43	2	154	2	GLCE	15	69548297	Missense_Mutation	SNP	G	TCGA-PJ-A8JU-01A-11D-A35Z-10	44340956	69548297	32983095	59	14606											
GOLGA6B	55889	hgsc.bcm.edu	37	chr15	72947139	72947139	+	Frame_Shift_Del	DEL	A	A	-																															tagaagaatctcgacagaatAaattggcagcagccaagaaa																										TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr15:72947139delA	ENST00000421285.3	+	1	61	c.61delA	c.(61-63)aaafs	p.K21fs		NM_018652.4	NP_061122.4	A6NDN3	GOG6B_HUMAN	golgin A6 family, member B	21						Golgi apparatus (GO:0005794)				NS(1)|breast(1)|endometrium(1)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	16						TCGACAGAATAAATTGGCAGC	0.522																																					p.N20fs		Pindel	.											.	GOLGA6B	30	.	0			c.60delT						PASS	.																																			SO:0001589	frameshift_variant	55889	exon1			.		CCDS10245.2	15q24.1	2011-10-25	2010-02-12		ENSG00000215186	ENSG00000215186			32205	protein-coding gene	gene with protein product			"golgi autoantigen, golgin subfamily a, 6B"				Standard	XM_006720604		Approved		uc010uks.1	A6NDN3	OTTHUMG00000133511	ENST00000421285.3:c.61delA	chr15.hg19:g.72947139delA	ENSP00000408132:p.Lys21fs	703.0	0.0	.		621.0	33.0	0.053	NM_018652	A8MYY7	Frame_Shift_Del	DEL	ENST00000421285.3	hg19	CCDS10245.2																																																																																			.	.	.	none		0.522	GOLGA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257474.4	NM_018652		-	72947139	A	-	72947139	7	5	239	1	0	1	0	1	0	0	0	0	6565	363	13	0	63	0	GOLGA6B	15	72947139	Frame_Shift_Del	DEL	A	TCGA-PJ-A8JU-01A-11D-A35Z-10	3398842	72947139	29584253	60	14607											
CYP1A2	1544	hgsc.bcm.edu	37	chr15	75042653	75042653	+	Missense_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	acttcgacccttacaatcagGtggtggtgtcagtggccaac	9	10	11	11	1	2	0	2	0	0	0	3	1	2	0	2	4	2	0	2	4	3	2			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr15:75042653G>A	ENST00000343932.4	+	2	637	c.574G>A	c.(574-576)Gtg>Atg	p.V192M		NM_000761.3	NP_000752.2	P05177	CP1A2_HUMAN	cytochrome P450, family 1, subfamily A, polypeptide 2	192					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)"	TTACAATCAGGTGGTGGTGTC	0.567																																					p.V192M		Atlas-SNP	.											.	CYP1A2	70	.	0			c.G574A						PASS	.						244	192	210					15																	75042653		2197	4296	6493	SO:0001583	missense	1544	exon2			AATCAGGTGGTGG	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.574G>A	chr15.hg19:g.75042653G>A	ENSP00000342007:p.Val192Met	68.0	0.0	.		51.0	24.0	.	NM_000761	Q16754|Q6NWU5|Q9BXX7|Q9UK49	Missense_Mutation	SNP	ENST00000343932.4	hg19	CCDS32293.1	.	.	.	.	.	.	.	.	.	.	G	10.79	1.450299	0.26074	.	.	ENSG00000140505	ENST00000343932	T	0.70631	-0.5	4.98	-3.32	0.04973	.	0.338015	0.32593	N	0.005883	T	0.72946	0.3524	M	0.64080	1.96	0.26746	N	0.970298	D	0.62365	0.991	P	0.60286	0.872	T	0.67837	-0.5567	10	0.62326	D	0.03	.	8.2501	0.31712	0.3197:0.4156:0.2647:0.0	.	192	P05177-2	.	M	192	ENSP00000342007:V192M	ENSP00000342007:V192M	V	+	1	0	CYP1A2	72829706	0.028000	0.19301	0.002000	0.10522	0.002000	0.02628	0.368000	0.20399	-0.525000	0.06391	-0.254000	0.11334	GTG	.	.	.	none		0.567	CYP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421263.2	NM_000761		A	75042653	G	A	75042653	3	1	239	1	0	0	0	0	1	0	0	0	4152	1261	44	2	576	2	CYP1A2	15	75042653	Missense_Mutation	SNP	G	TCGA-PJ-A8JU-01A-11D-A35Z-10	2095514	75042653	27488739	61	14608											
GOLGA6C	653641	hgsc.bcm.edu	37	chr15	75562489	75562489	+	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	gagggttctccccatgacaaCcccccggtacagcagatcgt	9	7	10	15	2	1	2	0	1	1	1	3	3	1	2	5	2	3	3	5	2	2	2			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr15:75562489C>T	ENST00000300576.5	+	18	2031	c.2031C>T	c.(2029-2031)aaC>aaT	p.N677N	RN7SL489P_ENST00000486185.2_RNA	NM_001164404.1	NP_001157876.1	A6NDK9	GOG6C_HUMAN	golgin A6 family, member C	677						Golgi apparatus (GO:0005794)				ovary(1)	1						CCCATGACAACCCCCCGGTAC	0.602																																					p.N677N		Atlas-SNP	.											.	GOLGA6C	12	.	0			c.C2031T						PASS	.						50	62	58					15																	75562489		665	1575	2240	SO:0001819	synonymous_variant	653641	exon18			TGACAACCCCCCG		CCDS58388.1	15q24.2	2014-02-12	2010-02-12		ENSG00000167195	ENSG00000167195			32206	protein-coding gene	gene with protein product			"golgi autoantigen, golgin subfamily a, 6C"				Standard	NM_001164404		Approved		uc002azs.2	A6NDK9	OTTHUMG00000172671	ENST00000300576.5:c.2031C>T	chr15.hg19:g.75562489C>T		542.0	0.0	.		441.0	55.0	.	NM_001164404		Silent	SNP	ENST00000300576.5	hg19	CCDS58388.1																																																																																			.	.	.	none		0.602	GOLGA6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419797.1	NM_001164404		T	75562489	C	T	75562489	2	4	239	1	0	0	0	0	0	0	0	1	6566	506	18	2		2	GOLGA6C	15	75562489	Silent	SNP	C	TCGA-PJ-A8JU-01A-11D-A35Z-10	519836	75562489	26968903	62	14609											
NR2F2	7026	hgsc.bcm.edu	37	chr15	96880778	96880778	+	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	ccgtttggtaggtaaaacccCcatcgaaaccctcatccggg	10	8	9	14	3	1	0	1	0	0	0	3	1	2	0	5	3	2	3	5	3	4	3			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr15:96880778C>A	ENST00000394166.3	+	3	2561	c.1172C>A	c.(1171-1173)cCc>cAc	p.P391H	NR2F2_ENST00000453270.2_Missense_Mutation_p.P238H|NR2F2_ENST00000394171.2_Missense_Mutation_p.P238H|NR2F2_ENST00000421109.2_Missense_Mutation_p.P258H	NM_021005.3	NP_066285.1	P24468	COT2_HUMAN	nuclear receptor subfamily 2, group F, member 2	391	Important for dimerization.|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)			GGTAAAACCCCCATCGAAACC	0.463																																					p.P391H		Atlas-SNP	.											.	NR2F2	35	.	0			c.C1172A						PASS	.						151	147	148					15																	96880778		2197	4298	6495	SO:0001583	missense	7026	exon3			AAACCCCCATCGA	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.1172C>A	chr15.hg19:g.96880778C>A	ENSP00000377721:p.Pro391His	155.0	0.0	.		129.0	45.0	.	NM_021005	B4DQJ2|B6ZGU1|Q03754|Q3KQR7	Missense_Mutation	SNP	ENST00000394166.3	hg19	CCDS10375.1	.	.	.	.	.	.	.	.	.	.	C	18.16	3.562655	0.65538	.	.	ENSG00000185551	ENST00000421109;ENST00000394166;ENST00000394171;ENST00000453270	T;T;D;D	0.95137	0.5;0.5;-3.62;-3.62	5.44	5.44	0.79542	Nuclear hormone receptor, ligand-binding (2);	0.000000	0.85682	D	0.000000	D	0.97300	0.9117	M	0.78285	2.405	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.987	D	0.97614	1.0131	10	0.87932	D	0	.	19.6189	0.95647	0.0:1.0:0.0:0.0	.	391;258	P24468;Q3KQR7	COT2_HUMAN;.	H	258;391;238;238	ENSP00000401674:P258H;ENSP00000377721:P391H;ENSP00000377726:P238H;ENSP00000389853:P238H	ENSP00000377721:P391H	P	+	2	0	NR2F2	94681782	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.776000	0.85560	2.698000	0.92095	0.650000	0.86243	CCC	.	.	.	none		0.463	NR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313534.1			A	96880778	C	A	96880778	3	1	239	1	0	0	0	0	1	0	0	0	10635	623	22	4	1229	4	NR2F2	15	96880778	Missense_Mutation	SNP	C	TCGA-PJ-A8JU-01A-11D-A35Z-10	21318289	96880778	5650614	63	14610											
ZG16B	124220	hgsc.bcm.edu	37	chr16	2880794	2880794	+	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	tgtaggtcttctcctggtgaAaaggtgagtagggctatggt	8	13	15	5	0	2	2	0	2	2	0	3	2	2	2	1	5	0	3	1	5	5	4			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr16:2880794A>T	ENST00000382280.3	+	3	339	c.260A>T	c.(259-261)aAa>aTa	p.K87I	ZG16B_ENST00000572863.1_Missense_Mutation_p.K57I	NM_145252.2	NP_660295.2	Q96DA0	ZG16B_HUMAN	zymogen granule protein 16B	87					retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|lung(2)|ovary(1)|prostate(1)	5						CTCCTGGTGAAAAGGTGAGTA	0.562																																					p.K87I		Atlas-SNP	.											.	ZG16B	16	.	0			c.A260T						PASS	.						139	147	144					16																	2880794		2015	4157	6172	SO:0001583	missense	124220	exon3			TGGTGAAAAGGTG	BC009722	CCDS10479.2	16p13.3	2014-02-12	2012-12-07		ENSG00000162078	ENSG00000162078			30456	protein-coding gene	gene with protein product	"jacalin-like lectin domain containing 2"		"zymogen granule protein 16 homolog B (rat)"			12477932	Standard	NM_145252		Approved	HRPE773, PRO1567, JCLN2	uc002cru.3	Q96DA0	OTTHUMG00000128933	ENST00000382280.3:c.260A>T	chr16.hg19:g.2880794A>T	ENSP00000371715:p.Lys87Ile	97.0	0.0	.		140.0	76.0	.	NM_145252	A6NIY1|B2R4F6|Q6UW28	Missense_Mutation	SNP	ENST00000382280.3	hg19	CCDS10479.2	.	.	.	.	.	.	.	.	.	.	a	12.20	1.866528	0.32977	.	.	ENSG00000162078	ENST00000382280	T	0.30981	1.51	3.4	-1.96	0.07525	Mannose-binding lectin (3);	2.708630	0.01864	N	0.036792	T	0.30008	0.0751	N	0.14661	0.345	0.09310	N	0.999999	D	0.67145	0.996	D	0.66716	0.946	T	0.15983	-1.0418	10	0.33141	T	0.24	-8.9085	0.1357	0.00078	0.3502:0.1732:0.2343:0.2422	.	87	Q96DA0	ZG16B_HUMAN	I	87	ENSP00000371715:K87I	ENSP00000371715:K87I	K	+	2	0	ZG16B	2820795	0.002000	0.14202	0.006000	0.13384	0.005000	0.04900	0.180000	0.16860	-0.466000	0.06943	-0.295000	0.09555	AAA	.	.	.	none		0.562	ZG16B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250912.1	NM_145252		T	2880794	A	T	2880794	3	4	239	1	0	0	0	0	1	0	0	0	17684	14	1	5	270	5	ZG16B	16	2880794	Missense_Mutation	SNP	A	TCGA-PJ-A8JU-01A-11D-A35Z-10		2880794	87473959	64	14611											
IL32	9235	hgsc.bcm.edu	37	chr16	3119166	3119166	+	Frame_Shift_Del	DEL	T	T	-																															gcagacctggtggcacggggTtctggcctgggtgaaggaga																										TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr16:3119166delT	ENST00000534507.1	+	6	726	c.515delT	c.(514-516)gttfs	p.V172fs	IL32_ENST00000552356.1_Frame_Shift_Del_p.V106fs|IL32_ENST00000530890.1_Frame_Shift_Del_p.V106fs|RNU1-125P_ENST00000516752.1_RNA|IL32_ENST00000552936.1_Frame_Shift_Del_p.V150fs|IL32_ENST00000325568.5_Frame_Shift_Del_p.V126fs|IL32_ENST00000529699.1_Frame_Shift_Del_p.V106fs|IL32_ENST00000008180.9_Frame_Shift_Del_p.V106fs|IL32_ENST00000552664.1_Frame_Shift_Del_p.V126fs|IL32_ENST00000551122.1_Intron|IL32_ENST00000440815.3_Frame_Shift_Del_p.V126fs|IL32_ENST00000533097.2_Frame_Shift_Del_p.V126fs|IL32_ENST00000549213.1_Intron|IL32_ENST00000548476.1_Frame_Shift_Del_p.V172fs|IL32_ENST00000396887.3_Intron|IL32_ENST00000444393.3_Frame_Shift_Del_p.V126fs|IL32_ENST00000382213.3_Frame_Shift_Del_p.V117fs|IL32_ENST00000530538.2_Frame_Shift_Del_p.V126fs|IL32_ENST00000548246.1_Frame_Shift_Del_p.V86fs|IL32_ENST00000548652.1_Frame_Shift_Del_p.V117fs|IL32_ENST00000396890.2_Frame_Shift_Del_p.V172fs|IL32_ENST00000526464.2_Frame_Shift_Del_p.V126fs|IL32_ENST00000529550.1_Frame_Shift_Del_p.V126fs|IL32_ENST00000531965.1_Frame_Shift_Del_p.V116fs|IL32_ENST00000551513.1_Frame_Shift_Del_p.V163fs|IL32_ENST00000525643.2_Frame_Shift_Del_p.V126fs|IL32_ENST00000528163.2_Frame_Shift_Del_p.V126fs			P24001	IL32_HUMAN	interleukin 32	172					cell adhesion (GO:0007155)|defense response (GO:0006952)|immune response (GO:0006955)	extracellular space (GO:0005615)|membrane (GO:0016020)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	15						TGGCACGGGGTTCTGGCCTGG	0.602																																					p.V126fs		Atlas-Indel,Pindel	.											.	IL32	32	.	0			c.376delG						PASS	.						21	25	24					16																	3119166		2192	4276	6468	SO:0001589	frameshift_variant	9235	exon7			.	M59807	CCDS32377.1, CCDS32378.1, CCDS32379.1, CCDS45394.1	16p13.3	2011-07-21			ENSG00000008517	ENSG00000008517		"Interleukins and interleukin receptors"	16830	protein-coding gene	gene with protein product	"natural killer cell transcript 4"	606001				1729377, 9653642	Standard	XM_005255686		Approved	NK4, TAIF, TAIFb, TAIFd	uc002ctn.3	P24001	OTTHUMG00000167498	ENST00000534507.1:c.515delT	chr16.hg19:g.3119166delT	ENSP00000431775:p.Val172fs	267.0	0.0	0		317.0	117.0	0.369085	NM_004221	A6NNM0|A8MPX0|B4DJM1|B8Q191|D3DUB0|D3DUB2|Q5VFH7|Q5VFH8|Q8WV38|Q96GK9	Frame_Shift_Del	DEL	ENST00000534507.1	hg19																																																																																				.	.	.	none		0.602	IL32-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000394812.2	NM_004221		-	3119166	T	-	3119166	7	5	239	1	0	1	0	1	0	0	0	0	7699	1725	60	0	399	0	IL32	16	3119166	Frame_Shift_Del	DEL	T	TCGA-PJ-A8JU-01A-11D-A35Z-10	238372	3119166	87235587	65	14612											
SETD1A	9739	hgsc.bcm.edu	37	chr16	30976438	30976439	+	Frame_Shift_Ins	INS	-	-	C																															gagagaagaagttcggacttINSccccccgcccagcctcccct																										TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr16:30976438_30976439insC	ENST00000262519.8	+	7	2061_2062	c.1375_1376insC	c.(1375-1377)tccfs	p.S459fs		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	459	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						AGTTCGGACTTCCCCCCGCCCA	0.698																																					p.S459fs		Atlas-Indel,Pindel	.											.	SETD1A	143	.	0			c.1375_1376insC						PASS	.																																			SO:0001589	frameshift_variant	9739	exon7			.	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.1381dupC	chr16.hg19:g.30976444_30976444dupC	ENSP00000262519:p.Ser459fs	51.0	0.0	0		66.0	14.0	0.212121	NM_014712	A6NP62|Q6PIF3|Q8TAJ6	Frame_Shift_Ins	INS	ENST00000262519.8	hg19	CCDS32435.1																																																																																			.	.	.	none		0.698	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712		C	30976439	-	C	30976438	7	5	239	1	0	1	1	0	0	0	0	0	14143	1783	62	0	1397	0	SETD1A	16	30976438	Frame_Shift_Ins	INS	-	TCGA-PJ-A8JU-01A-11D-A35Z-10	27857272	30976438	59378315	66	14613											
GOT2	2806	hgsc.bcm.edu	37	chr16	58742096	58742096	+	Frame_Shift_Del	DEL	G	G	-																															tacttggtgacctggtgaatGgcatgggcaaggtagcccac																										TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr16:58742096delG	ENST00000245206.5	-	10	1400	c.1272delC	c.(1270-1272)gccfs	p.A424fs	GOT2_ENST00000434819.2_Frame_Shift_Del_p.A381fs	NM_002080.2	NP_002071.2	P00505	AATM_HUMAN	glutamic-oxaloacetic transaminase 2, mitochondrial	424					2-oxoglutarate metabolic process (GO:0006103)|4-hydroxyproline catabolic process (GO:0019470)|aspartate biosynthetic process (GO:0006532)|aspartate catabolic process (GO:0006533)|aspartate metabolic process (GO:0006531)|carbohydrate metabolic process (GO:0005975)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|fatty acid transport (GO:0015908)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glutamate catabolic process to 2-oxoglutarate (GO:0019551)|glutamate catabolic process to aspartate (GO:0019550)|glutamate metabolic process (GO:0006536)|oxaloacetate metabolic process (GO:0006107)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	kynurenine-oxoglutarate transaminase activity (GO:0016212)|L-aspartate:2-oxoglutarate aminotransferase activity (GO:0004069)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|poly(A) RNA binding (GO:0044822)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|prostate(2)|skin(1)	22					L-Aspartic Acid(DB00128)	CCTGGTGAATGGCATGGGCAA	0.527																																					p.I425fs		Atlas-Indel,Pindel	.											.	GOT2	42	.	0			c.1273delA						PASS	.						74	67	70					16																	58742096		2198	4300	6498	SO:0001589	frameshift_variant	2806	exon10			.		CCDS10801.1, CCDS67045.1	16q21	2013-05-29	2013-05-29		ENSG00000125166	ENSG00000125166	2.6.1.1		4433	protein-coding gene	gene with protein product	"kynurenine aminotransferase IV", "aspartate aminotransferase 2", "aspartate transaminase 2"	138150	"glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2)"			17442055	Standard	NM_002080		Approved	mitAAT, KATIV, KAT4	uc002eof.1	P00505	OTTHUMG00000133769	ENST00000245206.5:c.1272delC	chr16.hg19:g.58742096delG	ENSP00000245206:p.Ala424fs	47.0	0.0	0		53.0	28.0	0.528302	NM_002080	B4DJA6|E7ERW2|Q53FL3|Q9BWA3	Frame_Shift_Del	DEL	ENST00000245206.5	hg19	CCDS10801.1																																																																																			.	.	.	none		0.527	GOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258289.3			-	58742096	G	-	58742096	7	5	239	1	0	1	0	1	0	0	0	0	6588	1335	47	0	24	0	GOT2	16	58742096	Frame_Shift_Del	DEL	G	TCGA-PJ-A8JU-01A-11D-A35Z-10	27765658	58742096	31612657	67	14614											
CES8	283848	hgsc.bcm.edu	37	chr16	67038021	67038021	+	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	gagccctgtggtggatggtgTggtgatcccagatgaccctt	6	11	15	9	0	0	3	0	2	0	1	1	5	1	4	3	4	1	0	3	4	0	1	rs3859072		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr16:67038021T>A	ENST00000326686.5	+	9	974	c.974T>A	c.(973-975)gTg>gAg	p.V325E	CES4A_ENST00000540947.2_Missense_Mutation_p.V325E|CES4A_ENST00000535696.1_Missense_Mutation_p.V231E|CES4A_ENST00000398354.1_Missense_Mutation_p.V325E|CES4A_ENST00000541479.1_Missense_Mutation_p.V348E|CES4A_ENST00000338718.4_Missense_Mutation_p.V348E|CES4A_ENST00000540579.1_Missense_Mutation_p.V227E			Q5XG92	EST4A_HUMAN	carboxylesterase 4A	325						extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)			large_intestine(2)|liver(2)|lung(4)|ovary(1)	9						GTGGATGGTGTGGTGATCCCA	0.532																																					p.V325E		Atlas-SNP	.											.	CES4A	24	.	0			c.T974A						PASS	.						231	234	233					16																	67038021		2056	4189	6245	SO:0001583	missense	283848	exon9			ATGGTGTGGTGAT	AK094783	CCDS42174.1, CCDS42174.2, CCDS54024.1, CCDS54025.1, CCDS42174.3	16q22.1	2011-10-25	2010-10-12	2010-10-12	ENSG00000172824	ENSG00000172824		"Carboxylesterases"	26741	protein-coding gene	gene with protein product			"carboxylesterase 8 (putative)"	CES8		12975309, 17364878, 20931200	Standard	NM_001190201		Approved	FLJ37464	uc010vix.2	Q5XG92		ENST00000326686.5:c.974T>A	chr16.hg19:g.67038021T>A	ENSP00000314145:p.Val325Glu	139.0	0.0	.		142.0	30.0	.	NM_173815	A8KAJ6|B7Z349|B7Z3L2|B7Z6R3|Q6UX55|Q8N9F4	Missense_Mutation	SNP	ENST00000326686.5	hg19		.	.	.	.	.	.	.	.	.	.	t	8.048	0.765292	0.15914	.	.	ENSG00000172824	ENST00000540947;ENST00000541479;ENST00000338718;ENST00000398354;ENST00000326686;ENST00000538199;ENST00000540579;ENST00000535696	T;T;T;T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18	4.63	3.51	0.40186	Carboxylesterase, type B (1);	0.321128	0.21974	N	0.066417	T	0.43144	0.1234	N	0.21324	0.655	0.37145	D	0.901879	P;P;B;B	0.38370	0.628;0.496;0.001;0.049	B;B;B;B	0.34489	0.137;0.184;0.029;0.029	T	0.43196	-0.9406	10	0.39692	T	0.17	.	8.757	0.34652	0.1697:0.0:0.0:0.8303	.	231;348;325;348	Q5XG92-7;F8WEE9;Q5XG92;F5H5S4	.;.;EST4A_HUMAN;.	E	325;348;348;325;325;288;227;231	ENSP00000444052:V325E;ENSP00000443175:V348E;ENSP00000340714:V348E;ENSP00000381397:V325E;ENSP00000314145:V325E;ENSP00000441103:V288E;ENSP00000441907:V227E;ENSP00000441644:V231E	ENSP00000314145:V325E	V	+	2	0	CES4A	65595522	0.833000	0.29383	0.102000	0.21198	0.070000	0.16714	1.730000	0.38125	0.612000	0.30071	0.398000	0.26397	GTG	.	T|1.000;|0.000	.	alt		0.532	CES4A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173815		A	67038021	T	A	67038021	3	1	239	1	0	0	0	0	1	0	0	0	3275	1696	59	5	1089	5	CES8	16	67038021	Missense_Mutation	SNP	T	TCGA-PJ-A8JU-01A-11D-A35Z-10	8295925	67038021	23316732	68	14615											
OR1A1	8383	hgsc.bcm.edu	37	chr17	3119721	3119721	+	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	accaattatagcctaaaagaCgcagtgatcactgtaatgta	16	10	7	8	1	1	2	1	1	0	1	1	2	1	2	2	0	1	3	2	0	7	5			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr17:3119721C>T	ENST00000304094.1	+	1	807	c.807C>T	c.(805-807)gaC>gaT	p.D269D		NM_014565.2	NP_055380.2	Q9P1Q5	OR1A1_HUMAN	olfactory receptor, family 1, subfamily A, member 1	269						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	23						GCCTAAAAGACGCAGTGATCA	0.478																																					p.D269D		Atlas-SNP	.											OR1A1,NS,carcinoma,0,1	OR1A1	54	.	0			c.C807T						PASS	.						153	135	141					17																	3119721		2203	4300	6503	SO:0001819	synonymous_variant	8383	exon1			AAAAGACGCAGTG	AF087918	CCDS11022.1	17p13.3	2012-08-09			ENSG00000172146	ENSG00000172146		"GPCR / Class A : Olfactory receptors"	8179	protein-coding gene	gene with protein product						10673334	Standard	NM_014565		Approved	OR17-7	uc010vrc.2	Q9P1Q5	OTTHUMG00000090637	ENST00000304094.1:c.807C>T	chr17.hg19:g.3119721C>T		135.0	0.0	.		112.0	38.0	.	NM_014565	A5D914|Q6IFM1|Q6NTA9|Q96R87	Silent	SNP	ENST00000304094.1	hg19	CCDS11022.1																																																																																			.	.	.	none		0.478	OR1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207292.1	NM_014565		T	3119721	C	T	3119721	2	4	239	1	0	0	0	0	0	0	0	1	10956	535	19	1		1	OR1A1	17	3119721	Silent	SNP	C	TCGA-PJ-A8JU-01A-11D-A35Z-10		3119721	78075489	69	14616											
MYH1	4619	hgsc.bcm.edu	37	chr17	10404016	10404016	+	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	tgctgctcctcttccttggtCttaatttcactcagttgatc	5	18	6	12	0	4	1	2	1	2	0	7	1	6	1	2	1	2	3	2	1	1	5			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr17:10404016C>G	ENST00000226207.5	-	28	3886	c.3792G>C	c.(3790-3792)aaG>aaC	p.K1264N	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1264					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						CTTCCTTGGTCTTAATTTCAC	0.493																																					p.K1264N		Atlas-SNP	.											.	MYH1	403	.	0			c.G3792C						PASS	.						164	143	150					17																	10404016		2203	4300	6503	SO:0001583	missense	4619	exon28			CTTGGTCTTAATT		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.3792G>C	chr17.hg19:g.10404016C>G	ENSP00000226207:p.Lys1264Asn	74.0	0.0	.		77.0	23.0	.	NM_005963	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	hg19	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.144571	0.77888	.	.	ENSG00000109061	ENST00000226207	D	0.83673	-1.75	5.45	4.26	0.50523	Myosin tail (1);	0.000000	0.45126	U	0.000393	T	0.76248	0.3961	L	0.49513	1.565	0.42767	D	0.993824	B	0.12630	0.006	B	0.20577	0.03	T	0.68401	-0.5418	10	0.18710	T	0.47	.	10.9761	0.47467	0.0:0.8405:0.0:0.1595	.	1264	P12882	MYH1_HUMAN	N	1264	ENSP00000226207:K1264N	ENSP00000226207:K1264N	K	-	3	2	MYH1	10344741	0.916000	0.31088	1.000000	0.80357	0.996000	0.88848	0.626000	0.24492	2.716000	0.92895	0.650000	0.86243	AAG	.	.	.	none		0.493	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		G	10404016	C	G	10404016	3	3	239	1	0	0	0	0	1	0	0	0	10036	912	32	4	2079	4	MYH1	17	10404016	Missense_Mutation	SNP	C	TCGA-PJ-A8JU-01A-11D-A35Z-10	7284295	10404016	70791194	70	14617											
GRB7	2886	hgsc.bcm.edu	37	chr17	37903002	37903002	+	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	caccccctttactgtaccccAgagcgaggaggagggccgcc	8	5	12	16	2	0	1	0	0	0	1	0	4	0	3	6	3	3	1	6	3	2	3			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr17:37903002A>C	ENST00000309156.4	+	15	1709		c.e15-1		GRB7_ENST00000394209.2_Splice_Site|GRB7_ENST00000394204.1_Splice_Site|GRB7_ENST00000394211.3_Splice_Site|GRB7_ENST00000445327.2_Splice_Site|GRB7_ENST00000309185.3_Splice_Site	NM_005310.3	NP_005301.2	Q14451	GRB7_HUMAN	growth factor receptor-bound protein 7						blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|leukocyte migration (GO:0050900)|negative regulation of translation (GO:0017148)|positive regulation of cell migration (GO:0030335)|positive regulation of signal transduction (GO:0009967)|stress granule assembly (GO:0034063)	cell projection (GO:0042995)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;6.86e-60)|all cancers(3;1.65e-53)|BRCA - Breast invasive adenocarcinoma(8;2.03e-43)|STAD - Stomach adenocarcinoma(3;1.43e-12)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			ACTGTACCCCAGAGCGAGGAG	0.602																																					.		Atlas-SNP	.											.	GRB7	48	.	0			c.1453-2A>C						PASS	.						73	70	71					17																	37903002		2203	4300	6503	SO:0001630	splice_region_variant	2886	exon15			TACCCCAGAGCGA	D43772	CCDS11345.1, CCDS56028.1	17q12	2013-02-14			ENSG00000141738	ENSG00000141738		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	4567	protein-coding gene	gene with protein product		601522					Standard	NM_005310		Approved		uc021twu.1	Q14451	OTTHUMG00000133253	ENST00000309156.4:c.1453-1A>C	chr17.hg19:g.37903002A>C		65.0	0.0	.		59.0	20.0	.	NM_005310	B2RAV1|B3KNL0|B3KWP9|B7WP75|J3KQM4|Q53YD3|Q92568|Q96DF9|Q9Y220	Splice_Site	SNP	ENST00000309156.4	hg19	CCDS11345.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.106122	0.77096	.	.	ENSG00000141738	ENST00000309156;ENST00000394211;ENST00000394209;ENST00000445327	.	.	.	4.8	4.8	0.61643	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.4461	0.61142	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GRB7	35156528	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	8.595000	0.90840	2.017000	0.59298	0.482000	0.46254	.	.	.	.	none		0.602	GRB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257024.2	NM_005310	Intron	C	37903002	A	C	37903002	5	2	239	1	0	0	0	0	0	0	1	0	6766	202	7	5	1505	5	GRB7	17	37903002	Splice_Site	SNP	A	TCGA-PJ-A8JU-01A-11D-A35Z-10	27498986	37903002	43292208	71	14618											
KRT28	162605	hgsc.bcm.edu	37	chr17	38955927	38955927	+	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	cccccttcgcttccagcaaaGccaatacaagcagcatttcc	11	8	5	17	1	0	0	0	0	0	0	3	0	2	0	5	0	5	4	5	0	4	4			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr17:38955927G>A	ENST00000306658.7	-	1	284	c.219C>T	c.(217-219)ggC>ggT	p.G73G		NM_181535.3	NP_853513.2			keratin 28											NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30		Breast(137;0.000301)				TTCCAGCAAAGCCAATACAAG	0.532																																					p.G73G	Melanoma(19;789 869 15380 26882 39836)	Atlas-SNP	.											.	KRT28	65	.	0			c.C219T						PASS	.						78	77	77					17																	38955927		2203	4300	6503	SO:0001819	synonymous_variant	162605	exon1			AGCAAAGCCAATA	AK129827	CCDS11376.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000173908	ENSG00000173908		"-", "Intermediate filaments type I, keratins (acidic)"	30842	protein-coding gene	gene with protein product			"keratin 25D"	KRT25D		16831889	Standard	NM_181535		Approved		uc002hvh.1	Q7Z3Y7	OTTHUMG00000133365	ENST00000306658.7:c.219C>T	chr17.hg19:g.38955927G>A		93.0	0.0	.		90.0	32.0	.	NM_181535		Silent	SNP	ENST00000306658.7	hg19	CCDS11376.1																																																																																			.	.	.	none		0.532	KRT28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257201.2	NM_181535		A	38955927	G	A	38955927	2	1	239	1	0	0	0	0	0	0	0	1	8472	958	34	2		2	KRT28	17	38955927	Silent	SNP	G	TCGA-PJ-A8JU-01A-11D-A35Z-10	1052925	38955927	42239283	72	14619											
KRT33B	3884	hgsc.bcm.edu	37	chr17	39521769	39521769	+	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	agcgtccacctccacgttgaGgcggtctccaagctggcagc	7	7	12	15	3	1	1	0	1	1	0	4	1	3	1	4	3	3	3	4	3	1	1			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr17:39521769G>T	ENST00000251646.3	-	4	674	c.625C>A	c.(625-627)Ctc>Atc	p.L209I		NM_002279.4	NP_002270.1	Q14525	KT33B_HUMAN	keratin 33B	209	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)				TCCACGTTGAGGCGGTCTCCA	0.527																																					p.L209I		Atlas-SNP	.											.	KRT33B	46	.	0			c.C625A						PASS	.						58	58	58					17																	39521769		2191	4300	6491	SO:0001583	missense	3884	exon4			CGTTGAGGCGGTC	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.625C>A	chr17.hg19:g.39521769G>T	ENSP00000251646:p.Leu209Ile	159.0	0.0	.		136.0	6.0	.	NM_002279	O76010	Missense_Mutation	SNP	ENST00000251646.3	hg19	CCDS11389.1	.	.	.	.	.	.	.	.	.	.	g	19.30	3.800219	0.70567	.	.	ENSG00000131738	ENST00000251646	D	0.88741	-2.42	4.51	4.51	0.55191	Filament (1);	0.000000	0.56097	D	0.000035	D	0.91061	0.7187	L	0.52126	1.63	0.34950	D	0.751156	P	0.49961	0.93	D	0.63877	0.919	D	0.92304	0.5852	10	0.38643	T	0.18	.	11.734	0.51755	0.0:0.2947:0.7053:0.0	.	209	Q14525	KT33B_HUMAN	I	209	ENSP00000251646:L209I	ENSP00000251646:L209I	L	-	1	0	KRT33B	36775295	0.942000	0.31987	1.000000	0.80357	0.961000	0.63080	2.329000	0.43876	2.474000	0.83562	0.650000	0.86243	CTC	.	.	.	none		0.527	KRT33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257292.1	NM_002279		T	39521769	G	T	39521769	3	4	239	1	0	0	0	0	1	0	0	0	8477	1000	35	4	605	4	KRT33B	17	39521769	Missense_Mutation	SNP	G	TCGA-PJ-A8JU-01A-11D-A35Z-10	565842	39521769	41673441	73	14620											
C17orf57	124989	hgsc.bcm.edu	37	chr17	45452288	45452311	+	In_Frame_Del	DEL	AAAAACAGGTTTCGTCTACGGAAA	AAAAACAGGTTTCGTCTACGGAAA	-																															aagaaagcattccagtctccAaaaacaggtttcgtctacgg																								rs370066816|rs377193277|rs377629904|rs554788706|rs144496511|rs536593341	byFrequency	TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	AAAAACAGGTTTCGTCTACGGAAA	AAAAACAGGTTTCGTCTACGGAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr17:45452288_45452311delAAAAACAGGTTTCGTCTACGGAAA	ENST00000331493.2	+	12	1739_1762	c.1328_1351delAAAAACAGGTTTCGTCTACGGAAA	c.(1327-1353)caaaaacaggtttcgtctacggaaaaa>caa	p.KQVSSTEK444del	EFCAB13_ENST00000517484.1_In_Frame_Del_p.KQVSSTEK348del	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	444						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.T449M(1)									TCCAGTCTCCAAAAACAGGTTTCGTCTACGGAAAAAACTGCAAT	0.357																																					p.443_450del		Atlas-Indel,Pindel	.											.	.	.	.	1	Substitution - Missense(1)	lung(1)	c.1327_1350del						PASS	.																																			SO:0001651	inframe_deletion	124989	exon12			.	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.1328_1351delAAAAACAGGTTTCGTCTACGGAAA	chr17.hg19:g.45452288_45452311delAAAAACAGGTTTCGTCTACGGAAA	ENSP00000332111:p.Lys444_Lys451del	248.0	0.0	0		168.0	23.0	0.136905	NM_152347	G3V128|Q49AG9	In_Frame_Del	DEL	ENST00000331493.2	hg19	CCDS11512.1																																																																																			.	.	.	none		0.357	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347		-	45452311	AAAAACAGGTTTCGTCTACGGAAA	-	45452288	7	5	239	1	0	1	0	1	0	0	0	0	1867	130	5	0	1362	0	C17orf57	17	45452288	In_Frame_Del	DEL	AAAAACAGGTTTCGTCTACGGAAA	TCGA-PJ-A8JU-01A-11D-A35Z-10	5930519	45452288	35742922	74	14621											
KPNB1	3837	hgsc.bcm.edu	37	chr17	45735997	45735997	+	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	atgcactcctgaactcattgGagttcaccaaagcaaacttt	13	11	6	11	0	2	1	2	1	0	0	3	2	3	2	2	1	4	3	2	1	3	3			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr17:45735997G>A	ENST00000290158.4	+	5	1014	c.607G>A	c.(607-609)Gag>Aag	p.E203K	KPNB1_ENST00000537679.1_Missense_Mutation_p.E58K|KPNB1_ENST00000540627.1_Missense_Mutation_p.E58K|KPNB1_ENST00000535458.2_Missense_Mutation_p.E58K|KPNB1_ENST00000577918.1_3'UTR	NM_001276453.1|NM_002265.4	NP_001263382.1|NP_002256.2	Q14974	IMB1_HUMAN	karyopherin (importin) beta 1	203					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						GAACTCATTGGAGTTCACCAA	0.378																																					p.T203T		Atlas-SNP	.											.	KPNB1	58	.	0			c.A607A						PASS	.						80	77	78					17																	45735997		2203	4300	6503	SO:0001583	missense	3837	exon5			TCATTGGAGTTCA	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.607G>A	chr17.hg19:g.45735997G>A	ENSP00000290158:p.Glu203Lys	62.0	0.0	.		49.0	20.0	.	NM_002265	B7ZAV6|D3DTT3|Q14637|Q53XN2|Q96J27	Silent	SNP	ENST00000290158.4	hg19	CCDS11513.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.097962	0.76870	.	.	ENSG00000108424	ENST00000535458;ENST00000290158;ENST00000540627;ENST00000537679	T;T;T;T	0.68903	-0.36;-0.36;-0.36;-0.36	6.02	6.02	0.97574	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.86272	0.5893	M	0.91818	3.245	0.47037	D	0.999291	D;D	0.89917	0.969;1.0	P;D	0.87578	0.89;0.998	D	0.85203	0.1016	9	0.36615	T	0.2	-3.7334	20.5407	0.99260	0.0:0.0:1.0:0.0	.	58;203	F5H4R7;Q14974	.;IMB1_HUMAN	K	58;203;58;58	ENSP00000438253:E58K;ENSP00000290158:E203K;ENSP00000438964:E58K;ENSP00000445006:E58K	ENSP00000290158:E203K	E	+	1	0	KPNB1	43090996	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.866000	0.99616	2.865000	0.98341	0.655000	0.94253	GAG	.	.	.	none		0.378	KPNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089755.2	NM_002265		A	45735997	G	A	45735997	3	1	239	1	0	0	0	0	1	0	0	0	8442	1175	41	2	625	2	KPNB1	17	45735997	Missense_Mutation	SNP	G	TCGA-PJ-A8JU-01A-11D-A35Z-10	283709	45735997	35459213	75	14622											
HOXB13	10481	hgsc.bcm.edu	37	chr17	46805780	46805780	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgggtggcattgctttggcGgctccgccgagcctggcaga	5	9	16	11	3	0	1	0	0	0	1	1	2	1	1	3	5	2	4	3	5	0	2			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr17:46805780G>A	ENST00000290295.7	-	1	760	c.176C>T	c.(175-177)cCg>cTg	p.P59L	PRAC2_ENST00000422730.2_RNA	NM_006361.5	NP_006352.2	Q92826	HXB13_HUMAN	homeobox B13	59					angiogenesis (GO:0001525)|epidermis development (GO:0008544)|epithelial cell maturation involved in prostate gland development (GO:0060743)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|response to testosterone (GO:0033574)|response to wounding (GO:0009611)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(2)|lung(6)|prostate(1)	11						TTGCTTTGGCGGCTCCGCCGA	0.652																																					p.P59L		Atlas-SNP	.											.	HOXB13	28	.	0			c.C176T						PASS	.						42	50	48					17																	46805780		2201	4296	6497	SO:0001583	missense	10481	exon1			TTTGGCGGCTCCG	U57052	CCDS11536.1	17q21.32	2014-09-17	2005-12-22		ENSG00000159184	ENSG00000159184		"Homeoboxes / ANTP class : HOXL subclass"	5112	protein-coding gene	gene with protein product		604607	"homeo box B13"			8756292, 9665387	Standard	NM_006361		Approved		uc002ioa.3	Q92826	OTTHUMG00000159900	ENST00000290295.7:c.176C>T	chr17.hg19:g.46805780G>A	ENSP00000290295:p.Pro59Leu	71.0	0.0	.		59.0	21.0	.	NM_006361	B2R878|Q96QM4|Q99810	Missense_Mutation	SNP	ENST00000290295.7	hg19	CCDS11536.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.230315	0.79688	.	.	ENSG00000159184	ENST00000290295	T	0.52295	0.67	4.9	4.9	0.64082	.	0.191648	0.48286	D	0.000197	T	0.53302	0.1788	M	0.66939	2.045	0.54753	D	0.999989	D	0.54047	0.964	P	0.45712	0.491	T	0.62201	-0.6904	10	0.87932	D	0	.	16.7972	0.85605	0.0:0.0:1.0:0.0	.	59	Q92826	HXB13_HUMAN	L	59	ENSP00000290295:P59L	ENSP00000290295:P59L	P	-	2	0	HOXB13	44160779	0.923000	0.31300	0.854000	0.33618	0.824000	0.46624	4.091000	0.57700	2.544000	0.85801	0.462000	0.41574	CCG	.	.	.	none		0.652	HOXB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358087.3	NM_006361		A	46805780	G	A	46805780	3	1	239	1	0	0	0	0	1	0	0	0	7307	1116	39	1	686	1	HOXB13	17	46805780	Missense_Mutation	SNP	G	TCGA-PJ-A8JU-01A-11D-A35Z-10	1069783	46805780	34389430	76	14623											
DLX3	1747	hgsc.bcm.edu	37	chr17	48072155	48072155	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctgcaagcccattgagatTgaattggtggtggtaggtgt	8	12	15	6	0	0	2	0	2	0	1	0	3	0	2	2	4	2	2	2	4	3	4			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr17:48072155T>C	ENST00000434704.2	-	1	433	c.208A>G	c.(208-210)Aat>Gat	p.N70D	DLX3_ENST00000512495.2_5'Flank|RP11-1094H24.3_ENST00000511867.1_lincRNA	NM_005220.2	NP_005211.1	O60479	DLX3_HUMAN	distal-less homeobox 3	70					blood vessel development (GO:0001568)|odontoblast differentiation (GO:0071895)|odontogenesis of dentin-containing tooth (GO:0042475)|placenta development (GO:0001890)	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	12						CCATTGAGATTGAATTGGTGG	0.597																																					p.N70D		Atlas-SNP	.											.	DLX3	28	.	0			c.A208G						PASS	.						101	106	104					17																	48072155		2203	4300	6503	SO:0001583	missense	1747	exon1			TGAGATTGAATTG		CCDS11556.1	17q21.33	2011-06-20	2005-12-22			ENSG00000064195		"Homeoboxes / ANTP class : NKL subclass"	2916	protein-coding gene	gene with protein product		600525	"distal-less homeo box 3"			7613049	Standard	NM_005220		Approved		uc002ipy.3	O60479		ENST00000434704.2:c.208A>G	chr17.hg19:g.48072155T>C	ENSP00000389870:p.Asn70Asp	109.0	0.0	.		73.0	28.0	.	NM_005220	B3KQL6	Missense_Mutation	SNP	ENST00000434704.2	hg19	CCDS11556.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.319787	0.81469	.	.	ENSG00000064195	ENST00000434704	D	0.90324	-2.65	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	D	0.92711	0.7683	M	0.77103	2.36	0.80722	D	1	D	0.57257	0.979	P	0.55508	0.777	D	0.90896	0.4765	10	0.19590	T	0.45	-21.8499	12.7113	0.57092	0.0:0.0:0.0:1.0	.	70	O60479	DLX3_HUMAN	D	70	ENSP00000389870:N70D	ENSP00000389870:N70D	N	-	1	0	DLX3	45427154	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.584000	0.67490	2.115000	0.64714	0.402000	0.26972	AAT	.	.	.	none		0.597	DLX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366307.1			C	48072155	T	C	48072155	3	2	239	1	0	0	0	0	1	0	0	0	4574	1812	63	3	667	3	DLX3	17	48072155	Missense_Mutation	SNP	T	TCGA-PJ-A8JU-01A-11D-A35Z-10	1266375	48072155	33123055	77	14624											
USP32	84669	hgsc.bcm.edu	37	chr17	58262881	58262881	+	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	gctaagcagtgggtcttacaCttggaacagtagtacatctc	11	11	10	9	0	2	0	0	0	2	0	3	1	2	1	0	2	4	4	0	2	5	5			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr17:58262881C>A	ENST00000300896.4	-	30	3968	c.3774G>T	c.(3772-3774)aaG>aaT	p.K1258N	USP32_ENST00000592339.1_Missense_Mutation_p.K928N	NM_032582.3	NP_115971.2	Q8NFA0	UBP32_HUMAN	ubiquitin specific peptidase 32	1258	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			NS(3)|breast(5)|endometrium(5)|kidney(4)|large_intestine(12)|liver(1)|lung(24)|pancreas(1)|prostate(3)|skin(3)|urinary_tract(1)	62	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			GGGTCTTACACTTGGAACAGT	0.537																																					p.K1258N		Atlas-SNP	.											.	USP32	128	.	0			c.G3774T						PASS	.						121	111	114					17																	58262881		2203	4298	6501	SO:0001583	missense	84669	exon30			CTTACACTTGGAA	AF533230	CCDS32697.1	17q23.3	2013-01-10	2005-08-08		ENSG00000170832	ENSG00000170832		"Ubiquitin-specific peptidases", "EF-hand domain containing"	19143	protein-coding gene	gene with protein product		607740	"ubiquitin specific protease 32"			12838346	Standard	NM_032582		Approved	NY-REN-60, USP10	uc002iyo.1	Q8NFA0		ENST00000300896.4:c.3774G>T	chr17.hg19:g.58262881C>A	ENSP00000300896:p.Lys1258Asn	203.0	0.0	.		180.0	65.0	.	NM_032582	Q7Z5T3|Q9BX85|Q9Y591	Missense_Mutation	SNP	ENST00000300896.4	hg19	CCDS32697.1	.	.	.	.	.	.	.	.	.	.	C	18.62	3.662725	0.67700	.	.	ENSG00000170832	ENST00000300896	T	0.31510	1.49	5.6	2.37	0.29283	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.37073	0.0990	L	0.28556	0.865	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.03148	-1.1067	10	0.24483	T	0.36	.	9.4228	0.38561	0.0:0.6358:0.0:0.3642	.	1258	Q8NFA0	UBP32_HUMAN	N	1258	ENSP00000300896:K1258N	ENSP00000300896:K1258N	K	-	3	2	USP32	55617663	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.057000	0.30492	0.253000	0.21552	0.650000	0.86243	AAG	.	.	.	none		0.537	USP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449235.2	NM_032582		A	58262881	C	A	58262881	3	1	239	1	0	0	0	0	1	0	0	0	17075	564	20	4	1060	4	USP32	17	58262881	Missense_Mutation	SNP	C	TCGA-PJ-A8JU-01A-11D-A35Z-10	10190726	58262881	22932329	78	14625											
MED13	9969	hgsc.bcm.edu	37	chr17	60039087	60039087	+	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	gattttaaatgctggggataGatttctctatcttcatgctt	9	18	8	6	0	3	1	1	0	2	1	4	3	3	2	0	2	2	2	0	2	4	7			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr17:60039087G>T	ENST00000397786.2	-	22	5194	c.5118C>A	c.(5116-5118)atC>atA	p.I1706I		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1706					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.I1706I(1)		breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						GCTGGGGATAGATTTCTCTAT	0.403																																					p.I1706I		Atlas-SNP	.											MED13,colon,carcinoma,0,1	MED13	181	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C5118A						PASS	.						138	138	138					17																	60039087		1824	4076	5900	SO:0001819	synonymous_variant	9969	exon22			GGGATAGATTTCT	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.5118C>A	chr17.hg19:g.60039087G>T		109.0	0.0	.		82.0	19.0	.	NM_005121	B2RU05|O60334	Silent	SNP	ENST00000397786.2	hg19	CCDS42366.1																																																																																			.	.	.	none		0.403	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		T	60039087	G	T	60039087	2	4	239	1	0	0	0	0	0	0	0	1	9437	932	33	4		4	MED13	17	60039087	Silent	SNP	G	TCGA-PJ-A8JU-01A-11D-A35Z-10	1776206	60039087	21156123	79	14626											
MRC2	9902	hgsc.bcm.edu	37	chr17	60743875	60743875	+	Frame_Shift_Del	DEL	A	A	-																															ctgacagctgctaccagtttAacttccagtccacgctgtcg																										TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr17:60743875delA	ENST00000303375.5	+	4	1156	c.754delA	c.(754-756)aacfs	p.N252fs		NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	252	C-type lectin 1. {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						CTACCAGTTTAACTTCCAGTC	0.617																																					p.F251fs		Atlas-INDEL	.											.	MRC2	126	.	0			c.753delT						PASS	.						57	60	59					17																	60743875		2203	4300	6503	SO:0001589	frameshift_variant	9902	exon4			.	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.754delA	chr17.hg19:g.60743875delA	ENSP00000307513:p.Asn252fs	78.0	0.0	0		47.0	15.0	0.319149	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Frame_Shift_Del	DEL	ENST00000303375.5	hg19	CCDS11634.1																																																																																			.	.	.	none		0.617	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1			-	60743875	A	-	60743875	7	5	239	1	0	1	0	1	0	0	0	0	9765	362	13	0	768	0	MRC2	17	60743875	Frame_Shift_Del	DEL	A	TCGA-PJ-A8JU-01A-11D-A35Z-10	704788	60743875	20451335	80	14627											
ACE	1636	hgsc.bcm.edu	37	chr17	61558530	61558530	+	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	caagcccaacctcgatgtcaCcagtactatgctgcagcagg	11	7	9	14	1	1	0	1	0	0	0	2	1	1	0	3	1	6	4	3	1	4	2			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr17:61558530C>G	ENST00000290866.4	+	6	950	c.926C>G	c.(925-927)aCc>aGc	p.T309S	ACE_ENST00000428043.1_Missense_Mutation_p.T309S|ACE_ENST00000538928.1_Missense_Mutation_p.T309S|ACE_ENST00000584529.1_3'UTR	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	309	Peptidase M2 1.				angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|arachidonic acid secretion (GO:0050482)|blood vessel remodeling (GO:0001974)|cellular protein metabolic process (GO:0044267)|hematopoietic stem cell differentiation (GO:0060218)|hormone catabolic process (GO:0042447)|kidney development (GO:0001822)|mononuclear cell proliferation (GO:0032943)|peptide catabolic process (GO:0043171)|regulation of blood pressure (GO:0008217)|regulation of renal output by angiotensin (GO:0002019)|regulation of smooth muscle cell migration (GO:0014910)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|bradykinin receptor binding (GO:0031711)|carboxypeptidase activity (GO:0004180)|chloride ion binding (GO:0031404)|drug binding (GO:0008144)|endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(3)|lung(22)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	51					Benazepril(DB00542)|Candoxatril(DB00616)|Captopril(DB01197)|Cilazapril(DB01340)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	CTCGATGTCACCAGTACTATG	0.587																																					p.T309S		Atlas-SNP	.											.	ACE	187	.	0			c.C926G						PASS	.						104	90	95					17																	61558530		2203	4300	6503	SO:0001583	missense	1636	exon6			ATGTCACCAGTAC	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.926C>G	chr17.hg19:g.61558530C>G	ENSP00000290866:p.Thr309Ser	148.0	0.0	.		128.0	42.0	.	NM_000789	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Missense_Mutation	SNP	ENST00000290866.4	hg19	CCDS11637.1	.	.	.	.	.	.	.	.	.	.	C	17.38	3.375723	0.61735	.	.	ENSG00000159640	ENST00000538928;ENST00000290866;ENST00000428043	T;T;T	0.40476	1.03;1.03;1.03	4.21	4.21	0.49690	.	0.000000	0.85682	D	0.000000	T	0.62073	0.2398	M	0.65677	2.01	0.80722	D	1	D;D;B	0.71674	0.998;0.996;0.162	D;D;B	0.75020	0.985;0.977;0.245	T	0.64343	-0.6430	10	0.45353	T	0.12	-36.2495	16.7665	0.85525	0.0:1.0:0.0:0.0	.	309;309;309	F5H1K1;P12821-2;P12821	.;.;ACE_HUMAN	S	309	ENSP00000439591:T309S;ENSP00000290866:T309S;ENSP00000397593:T309S	ENSP00000290866:T309S	T	+	2	0	ACE	58912262	1.000000	0.71417	0.397000	0.26308	0.867000	0.49689	4.748000	0.62148	2.180000	0.69256	0.561000	0.74099	ACC	.	.	.	none		0.587	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2			G	61558530	C	G	61558530	3	3	239	1	0	0	0	0	1	0	0	0	136	507	18	4	948	4	ACE	17	61558530	Missense_Mutation	SNP	C	TCGA-PJ-A8JU-01A-11D-A35Z-10	814655	61558530	19636680	81	14628											
SOCS3	9021	hgsc.bcm.edu	37	chr17	76355088	76355088	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgttcaccaccagctggtacTcgctcttggagctgaaggtc	7	10	11	13	2	2	1	1	1	1	0	4	2	2	2	2	3	3	5	2	3	2	3			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr17:76355088T>C	ENST00000330871.2	-	2	504	c.89A>G	c.(88-90)gAg>gGg	p.E30G	RP11-806H10.4_ENST00000592569.1_lincRNA	NM_003955.3	NP_003946.3	O14543	SOCS3_HUMAN	suppressor of cytokine signaling 3	30	Kinase inhibitory region (KIR).				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)			CAGCTGGTACTCGCTCTTGGA	0.667																																					p.E30G		Atlas-SNP	.											.	SOCS3	16	.	0			c.A89G						PASS	.						13	12	12					17																	76355088		2183	4290	6473	SO:0001583	missense	9021	exon2			TGGTACTCGCTCT	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.89A>G	chr17.hg19:g.76355088T>C	ENSP00000330341:p.Glu30Gly	129.0	0.0	.		90.0	32.0	.	NM_003955	O14509	Missense_Mutation	SNP	ENST00000330871.2	hg19	CCDS11756.1	.	.	.	.	.	.	.	.	.	.	T	13.69	2.311224	0.40895	.	.	ENSG00000184557	ENST00000330871	T	0.47869	0.83	4.16	4.16	0.48862	SH2 motif (1);	0.123969	0.53938	D	0.000044	T	0.37705	0.1013	L	0.44542	1.39	0.43808	D	0.996369	P	0.48764	0.915	B	0.36922	0.236	T	0.43294	-0.9400	10	0.72032	D	0.01	-18.8506	13.1915	0.59713	0.0:0.0:0.0:1.0	.	30	O14543	SOCS3_HUMAN	G	30	ENSP00000330341:E30G	ENSP00000330341:E30G	E	-	2	0	SOCS3	73866683	1.000000	0.71417	1.000000	0.80357	0.595000	0.36748	5.546000	0.67243	1.514000	0.48869	0.383000	0.25322	GAG	.	.	.	none		0.667	SOCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437300.1			C	76355088	T	C	76355088	3	2	239	1	0	0	0	0	1	0	0	0	14928	1551	54	3	592	3	SOCS3	17	76355088	Missense_Mutation	SNP	T	TCGA-PJ-A8JU-01A-11D-A35Z-10	14796558	76355088	4840122	82	14629											
FAM38B	63895	hgsc.bcm.edu	37	chr18	10680336	10680336	+	Silent	SNP	T	T	C																															tctgctactgttatgtcttcTttttcataattttccagaaa																										TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr18:10680336T>C	ENST00000503781.3	-	48	7472	c.7473A>G	c.(7471-7473)aaA>aaG	p.K2491K	PIEZO2_ENST00000580640.1_Silent_p.K2516K|PIEZO2_ENST00000302079.6_Silent_p.K2428K|PIEZO2_ENST00000581680.1_5'UTR|PIEZO2_ENST00000285141.4_Silent_p.K283K|PIEZO2_ENST00000538948.1_Silent_p.K448K	NM_022068.2	NP_071351.2	Q9H5I5	PIEZ2_HUMAN	piezo-type mechanosensitive ion channel component 2	2491					cation transport (GO:0006812)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|regulation of membrane potential (GO:0042391)|response to mechanical stimulus (GO:0009612)	integral component of membrane (GO:0016021)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)										TTATGTCTTCTTTTTCATAAT	0.398																																					p.K2491K		Atlas-SNP	.											.,2	.	.	.	0			c.A7473G						PASS	.						142	138	139					18																	10680336		2203	4300	6503	SO:0001819	synonymous_variant	63895	exon48			GTCTTCTTTTTCA	AK027056		18p11.21	2012-11-19	2011-08-31	2011-08-31	ENSG00000154864	ENSG00000154864			26270	protein-coding gene	gene with protein product		613629	"chromosome 18 open reading frame 30", "chromosome 18 open reading frame 58", "family with sequence similarity 38, member B"	FAM38B2, C18orf30, C18orf58, FAM38B		20813920, 21056836, 21299953	Standard	NM_022068		Approved	FLJ23403, FLJ23144, HsT748, HsT771, FLJ34907	uc002kos.2	Q9H5I5	OTTHUMG00000178507	ENST00000503781.3:c.7473A>G	chr18.hg19:g.10680336T>C		73.0	0.0	.		64.0	28.0	.	NM_022068	B7Z812|M4GPJ9|Q6ZS91|Q8N787|Q8NAR6|Q9H5R4	Silent	SNP	ENST00000503781.3	hg19																																																																																				.	.	.	none		0.398	PIEZO2-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442385.4	NM_022068		C	10680336	T	C	10680336	2	2	239	1	0	0	0	0	0	0	0	1	5562	1606	56	3		3	FAM38B	18	10680336	Silent	SNP	T	TCGA-PJ-A8JU-01A-11D-A35Z-10		10680336	67396912	83	14630	151	2									
FAM38B	63895	hgsc.bcm.edu	37	chr18	10680342	10680342	+	Nonsense_Mutation	SNP	A	A	T																															actgttatgtcttctttttcAtaattttccagaaattgcat																										TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr18:10680342A>T	ENST00000503781.3	-	48	7466	c.7467T>A	c.(7465-7467)taT>taA	p.Y2489*	PIEZO2_ENST00000580640.1_Nonsense_Mutation_p.Y2514*|PIEZO2_ENST00000302079.6_Nonsense_Mutation_p.Y2426*|PIEZO2_ENST00000581680.1_5'UTR|PIEZO2_ENST00000285141.4_Nonsense_Mutation_p.Y281*|PIEZO2_ENST00000538948.1_Nonsense_Mutation_p.Y446*	NM_022068.2	NP_071351.2	Q9H5I5	PIEZ2_HUMAN	piezo-type mechanosensitive ion channel component 2	2489					cation transport (GO:0006812)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|regulation of membrane potential (GO:0042391)|response to mechanical stimulus (GO:0009612)	integral component of membrane (GO:0016021)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)										CTTCTTTTTCATAATTTTCCA	0.393																																					p.Y2489X		Atlas-SNP	.											.	.	.	.	0			c.T7467A						PASS	.						141	137	138					18																	10680342		2203	4300	6503	SO:0001587	stop_gained	63895	exon48			TTTTTCATAATTT	AK027056		18p11.21	2012-11-19	2011-08-31	2011-08-31	ENSG00000154864	ENSG00000154864			26270	protein-coding gene	gene with protein product		613629	"chromosome 18 open reading frame 30", "chromosome 18 open reading frame 58", "family with sequence similarity 38, member B"	FAM38B2, C18orf30, C18orf58, FAM38B		20813920, 21056836, 21299953	Standard	NM_022068		Approved	FLJ23403, FLJ23144, HsT748, HsT771, FLJ34907	uc002kos.2	Q9H5I5	OTTHUMG00000178507	ENST00000503781.3:c.7467T>A	chr18.hg19:g.10680342A>T	ENSP00000421377:p.Tyr2489*	63.0	0.0	.		60.0	27.0	.	NM_022068	B7Z812|M4GPJ9|Q6ZS91|Q8N787|Q8NAR6|Q9H5R4	Nonsense_Mutation	SNP	ENST00000503781.3	hg19		.	.	.	.	.	.	.	.	.	.	A	43	10.389114	0.99396	.	.	ENSG00000154864	ENST00000503781;ENST00000302079;ENST00000538948;ENST00000285141	.	.	.	5.92	4.77	0.60923	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.7631	0.51914	0.9317:0.0:0.0683:0.0	.	.	.	.	X	383;2489;446;281	.	ENSP00000285141:Y281X	Y	-	3	2	FAM38B	10670342	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.634000	0.54302	1.075000	0.40932	0.533000	0.62120	TAT	.	.	.	none		0.393	PIEZO2-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442385.4	NM_022068		T	10680342	A	T	10680342	4	4	239	1	0	0	0	0	0	1	0	0	5562	224	8	5	811	5	FAM38B	18	10680342	Nonsense_Mutation	SNP	A	TCGA-PJ-A8JU-01A-11D-A35Z-10	6	10680342	67396906	84	14631	151	2									
FUT5	2527	hgsc.bcm.edu	37	chr19	5867537	5867537	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggtgggcaggggtcgccatgCtgtcctggcagcgggaccca	5	6	18	12	2	0	0	0	0	0	0	2	1	1	1	3	6	2	3	3	6	0	0			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr19:5867537C>T	ENST00000588525.1	-	2	287	c.200G>A	c.(199-201)aGc>aAc	p.S67N	FUT5_ENST00000252675.5_Missense_Mutation_p.S67N	NM_002034.2	NP_002025.2	Q11128	FUT5_HUMAN	fucosyltransferase 5 (alpha (1,3) fucosyltransferase)	67					carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12						GGTCGCCATGCTGTCCTGGCA	0.657																																					p.S67N		Atlas-SNP	.											.	FUT5	29	.	0			c.G200A						PASS	.						38	39	38					19																	5867537		2203	4300	6503	SO:0001583	missense	2527	exon2			GCCATGCTGTCCT		CCDS12154.1	19p13.3	2013-02-26				ENSG00000130383	2.4.1.65	"Fucosyltransferases"	4016	protein-coding gene	gene with protein product		136835				1740457	Standard	NM_002034		Approved	FUC-TV	uc002mdo.4	Q11128	OTTHUMG00000180616	ENST00000588525.1:c.200G>A	chr19.hg19:g.5867537C>T	ENSP00000466880:p.Ser67Asn	93.0	0.0	.		80.0	33.0	.	NM_002034	A8K4X2	Missense_Mutation	SNP	ENST00000588525.1	hg19	CCDS12154.1	.	.	.	.	.	.	.	.	.	.	C	6.711	0.499852	0.12762	.	.	ENSG00000130383	ENST00000252675	T	0.28454	1.61	1.74	-3.05	0.05396	.	.	.	.	.	T	0.17874	0.0429	L	0.36672	1.1	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.28808	-1.0032	9	0.22706	T	0.39	.	4.3455	0.11131	0.1716:0.4677:0.3607:0.0	.	67	Q11128	FUT5_HUMAN	N	67	ENSP00000252675:S67N	ENSP00000252675:S67N	S	-	2	0	FUT5	5818537	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.184000	0.16939	-0.600000	0.05790	-0.693000	0.03709	AGC	.	.	.	none		0.657	FUT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452213.1	NM_002034		T	5867537	C	T	5867537	3	4	239	1	0	0	0	0	1	0	0	0	6114	797	28	2	928	2	FUT5	19	5867537	Missense_Mutation	SNP	C	TCGA-PJ-A8JU-01A-11D-A35Z-10		5867537	53261446	85	14632											
CRB3	92359	hgsc.bcm.edu	37	chr19	6466490	6466490	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgcagcgtccagaagccaTcactgctatcatcgtggtct	8	11	9	13	2	4	1	2	0	2	1	6	1	5	1	2	1	4	2	2	1	2	1			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr19:6466490T>C	ENST00000598494.1	+	4	701	c.170T>C	c.(169-171)aTc>aCc	p.I57T	CRB3_ENST00000356762.3_Missense_Mutation_p.I57T|CRB3_ENST00000308243.7_Missense_Mutation_p.I57T|CRB3_ENST00000600229.1_Missense_Mutation_p.I57T			Q9BUF7	CRUM3_HUMAN	crumbs family member 3	57					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|protein localization to plasma membrane (GO:0072659)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	protein domain specific binding (GO:0019904)|SH3 domain binding (GO:0017124)			endometrium(1)|large_intestine(1)|lung(1)	3						CCAGAAGCCATCACTGCTATC	0.612																																					p.I57T		Atlas-SNP	.											.	CRB3	8	.	0			c.T170C						PASS	.						190	166	174					19																	6466490		2203	4300	6503	SO:0001583	missense	92359	exon4			AAGCCATCACTGC	AF503290	CCDS12166.1, CCDS12167.1	19p13.3	2014-02-06	2014-02-06		ENSG00000130545	ENSG00000130545			20237	protein-coding gene	gene with protein product		609737	"crumbs homolog 3 (Drosophila)"				Standard	XM_005259680		Approved	MGC17303	uc002mez.3	Q9BUF7	OTTHUMG00000181828	ENST00000598494.1:c.170T>C	chr19.hg19:g.6466490T>C	ENSP00000469707:p.Ile57Thr	39.0	0.0	.		34.0	7.0	.	NM_174881	A8KA91|D6W643|Q8N0V8|Q8WVA0	Missense_Mutation	SNP	ENST00000598494.1	hg19	CCDS12167.1	.	.	.	.	.	.	.	.	.	.	T	9.135	1.012505	0.19277	.	.	ENSG00000130545	ENST00000356762;ENST00000308243	.	.	.	4.72	1.11	0.20524	.	0.394099	0.19507	N	0.112599	T	0.36744	0.0978	L	0.46885	1.475	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	T	0.24190	-1.0167	9	0.42905	T	0.14	-6.2219	8.2264	0.31570	0.0:0.3766:0.0:0.6234	.	57;57	Q9BUF7-2;Q9BUF7	.;CRUM3_HUMAN	T	57	.	ENSP00000310123:I57T	I	+	2	0	CRB3	6417490	0.006000	0.16342	0.026000	0.17262	0.892000	0.51952	0.507000	0.22675	-0.059000	0.13154	0.477000	0.44152	ATC	.	.	.	none		0.612	CRB3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457837.1			C	6466490	T	C	6466490	3	2	239	1	0	0	0	0	1	0	0	0	3852	1435	50	3	180	3	CRB3	19	6466490	Missense_Mutation	SNP	T	TCGA-PJ-A8JU-01A-11D-A35Z-10	598953	6466490	52662493	86	14633											
MUC16	94025	hgsc.bcm.edu	37	chr19	9074427	9074427	+	Frame_Shift_Del	DEL	A	A	-																															aagtggcttgtgtcttggtgAcatgagtagtagcatcacca																										TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr19:9074427delA	ENST00000397910.4	-	3	13222	c.13019delT	c.(13018-13020)gtcfs	p.V4340fs		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4342	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						TGTCTTGGTGACATGAGTAGT	0.488																																					p.V4340fs		Atlas-Indel,Pindel	.											.	MUC16	4315	.	0			c.13020delC						PASS	.						109	114	112					19																	9074427		2096	4210	6306	SO:0001589	frameshift_variant	94025	exon3			.	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"Mucins"	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.13019delT	chr19.hg19:g.9074427delA	ENSP00000381008:p.Val4340fs	78.0	0.0	0		78.0	36.0	0.461538	NM_024690	Q6ZQW5|Q96RK2	Frame_Shift_Del	DEL	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.	.	none		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		-	9074427	A	-	9074427	7	5	239	1	0	1	0	1	0	0	0	0	9980	275	10	0	30832	0	MUC16	19	9074427	Frame_Shift_Del	DEL	A	TCGA-PJ-A8JU-01A-11D-A35Z-10	2607937	9074427	50054556	87	14634											
ZGLP1	100125288	hgsc.bcm.edu	37	chr19	10418909	10418909	+	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	agtccggctttatctgaaacTtcagagtcaccccctcgaac	10	10	7	14	2	3	2	2	1	1	1	5	3	4	2	3	1	2	1	3	1	3	3			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr19:10418909T>A	ENST00000403903.3	-	1	1647	c.449A>T	c.(448-450)aAg>aTg	p.K150M	CTD-2369P2.10_ENST00000452032.2_3'UTR|ZGLP1_ENST00000403352.1_Missense_Mutation_p.K66M|FDX1L_ENST00000492239.1_5'Flank|FDX1L_ENST00000541276.1_3'UTR	NM_001103167.1	NP_001096637.1	P0C6A0	ZGLP1_HUMAN	zinc finger, GATA-like protein 1	150					multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oocyte development (GO:0048599)|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)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(2)|ovary(1)	6						TATCTGAAACTTCAGAGTCAC	0.642																																					p.K150M		Atlas-SNP	.											.	ZGLP1	18	.	0			c.A449T						PASS	.						39	43	42					19																	10418909		1930	4133	6063	SO:0001583	missense	100125288	exon1			TGAAACTTCAGAG	AK096830	CCDS45959.1	19p13.2	2013-01-25			ENSG00000220201	ENSG00000220201		"GATA zinc finger domain containing"	37245	protein-coding gene	gene with protein product	"GATA like protein 1", "GATA zinc finger domain containing 3"	611639				16982049	Standard	NM_001103167		Approved	GLP1, GLP-1, GATAD3	uc002mnw.4	P0C6A0	OTTHUMG00000152114	ENST00000403903.3:c.449A>T	chr19.hg19:g.10418909T>A	ENSP00000384434:p.Lys150Met	29.0	0.0	.		30.0	12.0	.	NM_001103167		Missense_Mutation	SNP	ENST00000403903.3	hg19	CCDS45959.1	.	.	.	.	.	.	.	.	.	.	T	10.64	1.406851	0.25378	.	.	ENSG00000220201	ENST00000403903;ENST00000403352	D;D	0.98296	-4.85;-4.76	4.65	-1.45	0.08828	.	.	.	.	.	D	0.93684	0.7982	N	0.24115	0.695	0.20873	N	0.999839	B	0.32918	0.39	B	0.30179	0.112	D	0.87717	0.2570	9	0.66056	D	0.02	-7.2845	6.175	0.20439	0.0:0.1636:0.3897:0.4467	.	150	P0C6A0	ZGLP1_HUMAN	M	150;66	ENSP00000384434:K150M;ENSP00000385403:K66M	ENSP00000385403:K66M	K	-	2	0	ZGLP1	10279909	0.180000	0.23148	0.439000	0.26833	0.595000	0.36748	-0.563000	0.05943	-0.708000	0.05015	-2.944000	0.00085	AAG	.	.	.	none		0.642	ZGLP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325278.1	NM_001103167		A	10418909	T	A	10418909	3	1	239	1	0	0	0	0	1	0	0	0	17685	1609	56	5	382	5	ZGLP1	19	10418909	Missense_Mutation	SNP	T	TCGA-PJ-A8JU-01A-11D-A35Z-10	1344482	10418909	48710074	88	14635											
GCDH	2639	hgsc.bcm.edu	37	chr19	13010540	13010540	+	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	1	0	0	0	0	0	0	0	agatgtgttccttaaaaagaAgatggaattctctgtagagc	14	12	10	5	0	1	4	0	0	1	4	3	5	2	5	1	1	1	2	1	1	6	4	rs376334735		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr19:13010540A>G	ENST00000222214.5	+	0	1713				SYCE2_ENST00000293695.7_Intron|GCDH_ENST00000457854.1_Missense_Mutation_p.R424G|GCDH_ENST00000588242.2_3'UTR|GCDH_ENST00000422947.2_3'UTR|GCDH_ENST00000591470.1_3'UTR			Q92947	GCDH_HUMAN	glutaryl-CoA dehydrogenase						cellular nitrogen compound metabolic process (GO:0034641)|fatty acid oxidation (GO:0019395)|fatty-acyl-CoA biosynthetic process (GO:0046949)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tryptophan metabolic process (GO:0006568)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|glutaryl-CoA dehydrogenase activity (GO:0004361)			autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)	19					Flavin adenine dinucleotide(DB03147)	CTTAAAAAGAAGATGGAATTC	0.423																																					p.T424A	GBM(123;875 1636 7726 16444 26754)	Atlas-SNP	.											.	GCDH	76	.	0			c.A1270G						PASS	.						75	86	82					19																	13010540		2076	4215	6291	SO:0001624	3_prime_UTR_variant	2639	exon12			AAAAGAAGATGGA	AF012342	CCDS12286.1	19p13.2	2010-04-30	2010-04-30			ENSG00000105607	1.3.99.7		4189	protein-coding gene	gene with protein product		608801	"glutaryl-Coenzyme A dehydrogenase"			1438360, 8088809	Standard	NM_000159		Approved	ACAD5	uc002mvq.4	Q92947		ENST00000222214.5:c.*185A>G	chr19.hg19:g.13010540A>G		174.0	0.0	.		136.0	36.0	.	NM_013976	A8K2Z2|O14719	Missense_Mutation	SNP	ENST00000222214.5	hg19	CCDS12286.1	.	.	.	.	.	.	.	.	.	.	A	16.79	3.220902	0.58560	.	.	ENSG00000105607	ENST00000457854	D	0.97505	-4.41	4.81	0.392	0.16288	.	.	.	.	.	D	0.87799	0.6268	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.78505	-0.2178	8	0.02654	T	1	.	3.8177	0.08822	0.5063:0.1922:0.3015:0.0	.	424	Q92947-2	.	G	424	ENSP00000394872:R424G	ENSP00000394872:R424G	R	+	1	2	GCDH	12871540	0.004000	0.15560	0.000000	0.03702	0.892000	0.51952	-0.302000	0.08221	0.093000	0.17368	0.460000	0.39030	AGA	.	.	.	weak		0.423	GCDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451897.1			G	13010540	A	G	13010540	1	3	239	0	1	0	0	0	0	0	0	0	6294	64	3	3		3	GCDH	19	13010540	3'UTR	SNP	A	TCGA-PJ-A8JU-01A-11D-A35Z-10	2591631	13010540	46118443	89	14636											
GDF15	9518	hgsc.bcm.edu	37	chr19	18496998	18497015	+	Start_Codon_Del	DEL	AACCTGCACAGCCATGCC	AACCTGCACAGCCATGCC	-																															cagagccgcaacctgcacagCcatgcccgggcaagaactca																								rs201445214|rs373073926|rs573590688		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	AACCTGCACAGCCATGCC	AACCTGCACAGCCATGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr19:18496998_18497015delAACCTGCACAGCCATGCC	ENST00000252809.3	+	0	31_48				MIR3189_ENST00000578735.1_RNA	NM_004864.2	NP_004855.2	Q99988	GDF15_HUMAN	growth differentiation factor 15						cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)	p.P2H(1)		kidney(2)|large_intestine(1)|liver(1)|lung(5)|prostate(2)|skin(1)	12						ACCTGCACAGCCATGCCCGGGCAAGAACTCAGGACGGT	0.661																																					.		Pindel	.											.	GDF15	31	.	1	Substitution - Missense(1)	large_intestine(1)	.						PASS	.																																			SO:0001582	initiator_codon_variant	9518	wholegene			.	BC008962	CCDS12376.1	19p13.11	2008-05-14				ENSG00000130513			30142	protein-coding gene	gene with protein product	"prostate differentiation factor"	605312				11895857, 9593718	Standard	NM_004864		Approved	PLAB, MIC-1, PDF, MIC1, NAG-1, PTGFB	uc002niv.2	Q99988			chr19.hg19:g.18496998_18497015delAACCTGCACAGCCATGCC		62.0	0.0	.		48.0	11.0	0.229	NM_004864	O14629|P78360|Q9BWA0|Q9NRT0	Frame_Shift_Del	DEL	ENST00000252809.3	hg19	CCDS12376.1																																																																																			.	.	.	none		0.661	GDF15-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466340.2	NM_004864		-	18497015	AACCTGCACAGCCATGCC	-	18496998	7	5	239	1	0	1	0	1	0	0	0	0	6320	754	26	0	1	0	GDF15	19	18496998	Start_Codon_Del	DEL	AACCTGCACAGCCATGCC	TCGA-PJ-A8JU-01A-11D-A35Z-10	5486458	18496998	40631985	90	14637	152	2									
GDF15	9518	hgsc.bcm.edu	37	chr19	18497000	18497001	+	Start_Codon_Del	DEL	AT	AT	-																															gagccgcaacctgcacagccAtgcccgggcaagaactcagg																										TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr19:18497000_18497001delAT	ENST00000252809.3	+	0	33_34				MIR3189_ENST00000578735.1_RNA	NM_004864.2	NP_004855.2	Q99988	GDF15_HUMAN	growth differentiation factor 15						cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)			kidney(2)|large_intestine(1)|liver(1)|lung(5)|prostate(2)|skin(1)	12						CTGCACAGCCATGCCCGGGCAA	0.649																																					.		Atlas-INDEL	.											.	GDF15	31	.	0			.						PASS	.																																			SO:0001582	initiator_codon_variant	9518	wholegene			.	BC008962	CCDS12376.1	19p13.11	2008-05-14				ENSG00000130513			30142	protein-coding gene	gene with protein product	"prostate differentiation factor"	605312				11895857, 9593718	Standard	NM_004864		Approved	PLAB, MIC-1, PDF, MIC1, NAG-1, PTGFB	uc002niv.2	Q99988			chr19.hg19:g.18497000_18497001delAT		66.0	0.0	0		48.0	11.0	0.229167	NM_004864	O14629|P78360|Q9BWA0|Q9NRT0	Frame_Shift_Del	DEL	ENST00000252809.3	hg19	CCDS12376.1																																																																																			.	.	.	none		0.649	GDF15-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466340.2	NM_004864		-	18497001	AT	-	18497000	7	5	239	1	0	1	0	1	0	0	0	0	6320	217	8	0	3	0	GDF15	19	18497000	Start_Codon_Del	DEL	AT	TCGA-PJ-A8JU-01A-11D-A35Z-10	2	18497000	40631983	91	14638	152	2									
CILP2	148113	hgsc.bcm.edu	37	chr19	19655554	19655554	+	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	tcaatctggacgtgcctgagCgccgccgctgcttcgtgaag	6	9	13	13	5	2	2	1	2	1	0	3	3	2	3	3	1	3	2	3	1	2	1			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr19:19655554C>T	ENST00000291495.5	+	8	2285	c.2200C>T	c.(2200-2202)Cgc>Tgc	p.R734C	CILP2_ENST00000586018.1_Missense_Mutation_p.R740C	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	734						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						CGTGCCTGAGCGCCGCCGCTG	0.697																																					p.R734C		Atlas-SNP	.											CILP2,caecum,carcinoma,0,1	CILP2	84	.	0			c.C2200T						PASS	.						14	16	15					19																	19655554		2197	4288	6485	SO:0001583	missense	148113	exon8			CCTGAGCGCCGCC	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.2200C>T	chr19.hg19:g.19655554C>T	ENSP00000291495:p.Arg734Cys	80.0	0.0	.		70.0	27.0	.	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Missense_Mutation	SNP	ENST00000291495.5	hg19	CCDS12405.1	.	.	.	.	.	.	.	.	.	.	C	17.11	3.305389	0.60305	.	.	ENSG00000160161	ENST00000291495	T	0.51574	0.7	4.89	2.58	0.30949	.	0.477682	0.22795	N	0.055552	T	0.39733	0.1089	L	0.40543	1.245	0.43803	D	0.996357	D;D	0.65815	0.995;0.995	P;P	0.48677	0.586;0.586	T	0.29971	-0.9994	10	0.59425	D	0.04	-23.0496	3.694	0.08357	0.1728:0.568:0.1673:0.0919	.	734;734	B2RAJ0;Q8IUL8	.;CILP2_HUMAN	C	734	ENSP00000291495:R734C	ENSP00000291495:R734C	R	+	1	0	CILP2	19516554	0.991000	0.36638	1.000000	0.80357	0.997000	0.91878	1.880000	0.39628	1.016000	0.39470	0.555000	0.69702	CGC	.	.	.	none		0.697	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221		T	19655554	C	T	19655554	3	4	239	1	0	0	0	0	1	0	0	0	3432	768	27	1	2230	1	CILP2	19	19655554	Missense_Mutation	SNP	C	TCGA-PJ-A8JU-01A-11D-A35Z-10	1158554	19655554	39473429	92	14639											
ZNF527	84503	hgsc.bcm.edu	37	chr19	37879856	37879856	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcacagtggagaaaaaccatAtgcatgcaatgactgtggaa	16	8	10	7	0	1	2	1	1	0	1	1	4	1	3	1	2	3	2	1	2	5	1			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr19:37879856A>G	ENST00000436120.2	+	5	1012	c.905A>G	c.(904-906)tAt>tGt	p.Y302C	ZNF527_ENST00000587349.1_Intron	NM_032453.1	NP_115829.1	Q8NB42	ZN527_HUMAN	zinc finger protein 527	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)	p.Y302>?(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	33			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GAAAAACCATATGCATGCAAT	0.393																																					p.Y302C		Atlas-SNP	.											.,1	ZNF527	78	.	1	Complex(1)	lung(1)	c.A905G						PASS	.						105	96	99					19																	37879856		2093	4241	6334	SO:0001583	missense	84503	exon5			AACCATATGCATG	AB058732, AK091585	CCDS42559.1	19q13.1	2013-01-08			ENSG00000189164	ENSG00000189164		"Zinc fingers, C2H2-type", "-"	29385	protein-coding gene	gene with protein product						11347906	Standard	NM_032453		Approved	KIAA1829	uc010efk.1	Q8NB42	OTTHUMG00000048173	ENST00000436120.2:c.905A>G	chr19.hg19:g.37879856A>G	ENSP00000390179:p.Tyr302Cys	63.0	2.0	.		85.0	5.0	.	NM_032453	B4DVL5	Missense_Mutation	SNP	ENST00000436120.2	hg19	CCDS42559.1	.	.	.	.	.	.	.	.	.	.	A	2.120	-0.401673	0.04865	.	.	ENSG00000189164	ENST00000356178;ENST00000317566;ENST00000436120	.	.	.	4.19	2.11	0.27256	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.557068	0.13635	N	0.373399	T	0.49983	0.1589	M	0.88704	2.975	0.09310	N	0.999999	B;B	0.17038	0.02;0.016	B;B	0.16722	0.016;0.009	T	0.53704	-0.8401	9	0.72032	D	0.01	.	3.9384	0.09316	0.6603:0.0:0.1838:0.1559	.	302;270	Q8NB42;Q8NB42-2	ZN527_HUMAN;.	C	302;270;250	.	ENSP00000325231:Y270C	Y	+	2	0	ZNF527	42571696	0.000000	0.05858	0.042000	0.18584	0.284000	0.27059	-0.422000	0.07043	0.193000	0.20303	-0.274000	0.10170	TAT	.	.	.	none		0.393	ZNF527-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458434.1	NM_032453		G	37879856	A	G	37879856	3	3	239	1	0	0	0	0	1	0	0	0	17980	449	16	3	919	3	ZNF527	19	37879856	Missense_Mutation	SNP	A	TCGA-PJ-A8JU-01A-11D-A35Z-10	18224302	37879856	21249127	93	14640											
PRKD2	25865	hgsc.bcm.edu	37	chr19	47181737	47181737	+	Missense_Mutation	SNP	T	T	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	attgatgtcctcatcctcgtTgaaagggaaggtgccgctga	9	11	12	9	2	1	3	1	3	0	0	4	4	3	4	3	2	1	2	3	2	2	2			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr19:47181737T>G	ENST00000291281.4	-	16	2479	c.2254A>C	c.(2254-2256)Aac>Cac	p.N752H	PRKD2_ENST00000433867.1_Missense_Mutation_p.N752H|PRKD2_ENST00000600194.1_Missense_Mutation_p.N595H|PRKD2_ENST00000593492.1_5'Flank|PRKD2_ENST00000595515.1_Missense_Mutation_p.N752H|PRKD2_ENST00000601806.1_Missense_Mutation_p.N595H|DACT3-AS1_ENST00000525008.1_RNA			Q9BZL6	KPCD2_HUMAN	protein kinase D2	752	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		TCATCCTCGTTGAAAGGGAAG	0.627																																					p.N752H		Atlas-SNP	.											.	PRKD2	94	.	0			c.A2254C						PASS	.						163	123	136					19																	47181737		2203	4300	6503	SO:0001583	missense	25865	exon16			CCTCGTTGAAAGG	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.2254A>C	chr19.hg19:g.47181737T>G	ENSP00000291281:p.Asn752His	109.0	0.0	.		100.0	34.0	.	NM_016457	Q8TB08|Q9P0T6|Q9Y3X8	Missense_Mutation	SNP	ENST00000291281.4	hg19	CCDS12689.1	.	.	.	.	.	.	.	.	.	.	T	28.8	4.949602	0.92660	.	.	ENSG00000105287	ENST00000291281;ENST00000433867	T;T	0.65732	-0.17;-0.17	4.65	4.65	0.58169	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	U	0.000002	T	0.67748	0.2926	N	0.26092	0.79	0.58432	D	0.999999	P;D;D	0.89917	0.87;1.0;1.0	P;D;D	0.97110	0.867;0.999;1.0	T	0.71626	-0.4536	10	0.66056	D	0.02	-41.8641	13.3949	0.60846	0.0:0.0:0.0:1.0	.	752;237;752	E7ER94;A0JLT6;Q9BZL6	.;.;KPCD2_HUMAN	H	752	ENSP00000291281:N752H;ENSP00000393978:N752H	ENSP00000291281:N752H	N	-	1	0	PRKD2	51873577	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.956000	0.87863	1.872000	0.54250	0.460000	0.39030	AAC	.	.	.	none		0.627	PRKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466591.1	NM_016457		G	47181737	T	G	47181737	3	3	239	1	0	0	0	0	1	0	0	0	12529	1812	63	5	394	5	PRKD2	19	47181737	Missense_Mutation	SNP	T	TCGA-PJ-A8JU-01A-11D-A35Z-10	9301881	47181737	11947246	94	14641											
CRX	1406	hgsc.bcm.edu	37	chr19	48342911	48342911	+	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	cccctatgccatgacctacgCcccggcctccgctttctgct	4	10	7	20	3	1	1	0	1	1	0	2	1	2	1	8	1	3	2	8	1	2	3	rs61748454		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr19:48342911C>T	ENST00000221996.7	+	4	793	c.587C>T	c.(586-588)gCc>gTc	p.A196V	TPRX2P_ENST00000535362.1_Intron|CRX_ENST00000539067.1_Missense_Mutation_p.A196V	NM_000554.4	NP_000545.1	O43186	CRX_HUMAN	cone-rod homeobox	196					circadian rhythm (GO:0007623)|organ morphogenesis (GO:0009887)|positive regulation of photoreceptor cell differentiation (GO:0046534)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|leucine zipper domain binding (GO:0043522)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II core promoter 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)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|urinary_tract(1)	23		all_cancers(25;2.76e-09)|all_epithelial(76;7.01e-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;0.000266)|all cancers(93;0.000788)|Epithelial(262;0.0226)|GBM - Glioblastoma multiforme(486;0.0521)		ATGACCTACGCCCCGGCCTCC	0.662																																					p.A196V	Pancreas(57;461 1196 22201 40716 47188)	Atlas-SNP	.											.	CRX	52	.	0			c.C587T	GRCh37	CD972156	CRX	D	rs61748454	PASS	.						58	60	60					19																	48342911		2203	4300	6503	SO:0001583	missense	1406	exon4			CCTACGCCCCGGC	AF024711	CCDS12706.1	19q13.3	2013-01-08				ENSG00000105392		"Homeoboxes / PRD class"	2383	protein-coding gene	gene with protein product	"orthodenticle homeobox 3"	602225		CORD2		9390563, 9537410	Standard	NM_000554		Approved	CRD, LCA7, OTX3	uc002phq.4	O43186		ENST00000221996.7:c.587C>T	chr19.hg19:g.48342911C>T	ENSP00000221996:p.Ala196Val	50.0	0.0	.		66.0	29.0	.	NM_000554	Q0QD45	Missense_Mutation	SNP	ENST00000221996.7	hg19	CCDS12706.1	.	.	.	.	.	.	.	.	.	.	C	12.74	2.029682	0.35797	.	.	ENSG00000105392	ENST00000221996;ENST00000539067	D;D	0.86366	-2.11;-2.11	4.36	3.24	0.37175	Transcription factor Otx, C-terminal (1);	0.215353	0.37669	N	0.001989	T	0.80204	0.4580	L	0.46157	1.445	0.25471	N	0.987827	P	0.43826	0.818	B	0.39562	0.303	T	0.70267	-0.4919	10	0.21540	T	0.41	-11.5606	10.1228	0.42632	0.0:0.6446:0.3554:0.0	.	196	O43186	CRX_HUMAN	V	196	ENSP00000221996:A196V;ENSP00000445565:A196V	ENSP00000221996:A196V	A	+	2	0	CRX	53034723	0.958000	0.32768	0.986000	0.45419	0.310000	0.27922	0.591000	0.23969	1.975000	0.57531	0.467000	0.42956	GCC	.	.	.	none		0.662	CRX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409812.4	NM_000554		T	48342911	C	T	48342911	3	4	239	1	0	0	0	0	1	0	0	0	3904	739	26	2	597	2	CRX	19	48342911	Missense_Mutation	SNP	C	TCGA-PJ-A8JU-01A-11D-A35Z-10	1161174	48342911	10786072	95	14642											
HRC	3270	hgsc.bcm.edu	37	chr19	49656860	49656860	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcctctcctcgtcttcttcCtcctcctcctcctccttgtc	0	17	2	22	1	3	0	0	0	3	0	13	0	10	0	8	0	0	0	8	0	0	3			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr19:49656860C>T	ENST00000252825.4	-	1	1821	c.1635G>A	c.(1633-1635)gaG>gaA	p.E545E	HRC_ENST00000595625.1_Silent_p.E545E	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	545					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)		cgtcttcttcctcctcctcct	0.622																																					p.E545E	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											HRC,NS,carcinoma,0,1	HRC	85	.	0			c.G1635A						PASS	.						58	29	39					19																	49656860		2202	4300	6502	SO:0001819	synonymous_variant	3270	exon1			TTCTTCCTCCTCC		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.1635G>A	chr19.hg19:g.49656860C>T		38.0	1.0	.		25.0	3.0	.	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	hg19	CCDS12759.1																																																																																			.	.	.	none		0.622	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		T	49656860	C	T	49656860	2	4	239	1	0	0	0	0	0	0	0	1	7359	680	24	2		2	HRC	19	49656860	Silent	SNP	C	TCGA-PJ-A8JU-01A-11D-A35Z-10	1313949	49656860	9472123	96	14643											
KLK3	354	hgsc.bcm.edu	37	chr19	51361852	51361853	+	Splice_Site	INS	-	-	TTT																															gggcaaaagcacctgctcggINStgagtcatccctactcccaa																										TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr19:51361852_51361853insTTT	ENST00000326003.2	+	4	671		c.e4+1		KLK3_ENST00000595952.1_Splice_Site|KLK3_ENST00000593997.1_In_Frame_Ins_p.211_212insL|KLK3_ENST00000360617.3_Splice_Site|KLK3_ENST00000597483.1_Splice_Site	NM_001030047.1|NM_001030048.1|NM_001648.2	NP_001025218.1|NP_001025219.1|NP_001639.1	P07288	KLK3_HUMAN	kallikrein-related peptidase 3						cellular protein metabolic process (GO:0044267)|negative regulation of angiogenesis (GO:0016525)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|cervix(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00763)|GBM - Glioblastoma multiforme(134;0.0144)		CACCTGCTCGGTGAGTCATCCC	0.554																																					.	Colon(185;1767 2023 13025 30120 37630)	Atlas-Indel,Pindel	.											.	KLK3	76	.	0			c.630+1->TTT						PASS	.																																			SO:0001630	splice_region_variant	354	exon4			.	X14810	CCDS12807.1, CCDS33083.1, CCDS46155.1	19q13.41	2012-10-02	2006-10-27			ENSG00000142515		"Kallikreins"	6364	protein-coding gene	gene with protein product		176820	"kallikrein 3, (prostate specific antigen)"	APS		2456523, 2436946, 16800724, 16800723	Standard	NM_001648		Approved	PSA	uc021uyi.1	P07288		ENST00000326003.2:c.630+1->TTT	chr19.hg19:g.51361852_51361853insTTT		77.0	0.0	0		59.0	18.0	0.305085	NM_001030047	C9JXH3|G3V0H4|G3XAE3|Q15096|Q16272|Q86TG8|Q8IXI4	Splice_Site	INS	ENST00000326003.2	hg19	CCDS12807.1																																																																																			.	.	.	none		0.554	KLK3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464067.1	NM_145864	Intron	TTT	51361853	-	TTT	51361852	8	5	239	1	0	1	1	0	0	0	1	0	8412	1275	44	0	649	0	KLK3	19	51361852	Splice_Site	INS	-	TCGA-PJ-A8JU-01A-11D-A35Z-10	1704992	51361852	7767131	97	14644											
ZNF71	58491	hgsc.bcm.edu	37	chr19	57133451	57133451	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcaccagcgcacgcacaccGgggagaagccgtacgtgtgc	9	4	14	14	5	0	1	0	0	0	1	0	2	0	1	3	2	5	4	3	2	2	1			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr19:57133451G>A	ENST00000328070.6	+	3	1030	c.796G>A	c.(796-798)Ggg>Agg	p.G266R		NM_021216.4	NP_067039.1	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	266					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|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)		CACGCACACCGGGGAGAAGCC	0.677																																					p.G266R		Atlas-SNP	.											.	ZNF71	69	.	0			c.G796A						PASS	.						50	53	52					19																	57133451		2203	4300	6503	SO:0001583	missense	58491	exon3			CACACCGGGGAGA	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.796G>A	chr19.hg19:g.57133451G>A	ENSP00000328245:p.Gly266Arg	180.0	0.0	.		186.0	66.0	.	NM_021216	Q15919|Q9UC09|Q9UQD3	Missense_Mutation	SNP	ENST00000328070.6	hg19	CCDS12947.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.049854	0.75846	.	.	ENSG00000197951	ENST00000328070	T	0.26223	1.75	3.82	3.82	0.43975	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.46425	0.1392	M	0.64997	1.995	0.37570	D	0.919396	D	0.89917	1.0	D	0.68765	0.96	T	0.56335	-0.7996	9	0.62326	D	0.03	.	14.6514	0.68800	0.0:0.0:1.0:0.0	.	266	Q9NQZ8	ZNF71_HUMAN	R	266	ENSP00000328245:G266R	ENSP00000328245:G266R	G	+	1	0	ZNF71	61825263	0.999000	0.42202	0.614000	0.29051	0.963000	0.63663	4.418000	0.59828	1.958000	0.56883	0.561000	0.74099	GGG	.	.	.	none		0.677	ZNF71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459798.2	NM_021216		A	57133451	G	A	57133451	3	1	239	1	0	0	0	0	1	0	0	0	18126	1116	39	1	798	1	ZNF71	19	57133451	Missense_Mutation	SNP	G	TCGA-PJ-A8JU-01A-11D-A35Z-10	5771599	57133451	1995532	98	14645											
ZNF419	79744	hgsc.bcm.edu	37	chr19	58004676	58004676	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccaacctttttatacaccaaAtagttcacactggagaaagg	15	10	6	10	0	1	1	1	0	0	1	1	2	1	1	3	2	2	1	3	2	6	6			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr19:58004676A>G	ENST00000221735.7	+	5	937	c.751A>G	c.(751-753)Ata>Gta	p.I251V	ZNF419_ENST00000426954.2_Missense_Mutation_p.I239V|ZNF419_ENST00000347466.6_Missense_Mutation_p.I219V|AC003005.4_ENST00000601674.1_Intron|ZNF419_ENST00000415379.2_Missense_Mutation_p.I205V|ZNF419_ENST00000442920.2_Missense_Mutation_p.I238V|ZNF419_ENST00000424930.2_Missense_Mutation_p.I252V|ZNF419_ENST00000354197.4_Missense_Mutation_p.I239V			Q96HQ0	ZN419_HUMAN	zinc finger protein 419	251					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0252)|Lung(386;0.171)		TATACACCAAATAGTTCACAC	0.423																																					p.I252V		Atlas-SNP	.											.	ZNF419	134	.	0			c.A754G						PASS	.						71	73	72					19																	58004676		2203	4300	6503	SO:0001583	missense	79744	exon5			CACCAAATAGTTC	AK026886	CCDS42637.1, CCDS46211.1, CCDS54325.1, CCDS54326.1, CCDS54327.1, CCDS54328.1	19q13.43	2013-01-08	2006-12-15	2006-12-15	ENSG00000105136	ENSG00000105136		"Zinc fingers, C2H2-type", "-"	20648	protein-coding gene	gene with protein product			"zinc finger protein 419A"	ZNF419A			Standard	NM_001098492		Approved		uc010ety.1	Q96HQ0	OTTHUMG00000037073	ENST00000221735.7:c.751A>G	chr19.hg19:g.58004676A>G	ENSP00000221735:p.Ile251Val	105.0	0.0	.		92.0	33.0	.	NM_001098491	B4DXU7|B4E348|B7ZA41|E9PCP4|E9PED0|E9PET3|E9PFX9|Q9H5P0	Missense_Mutation	SNP	ENST00000221735.7	hg19	CCDS54326.1	.	.	.	.	.	.	.	.	.	.	A	16.17	3.046280	0.55110	.	.	ENSG00000105136	ENST00000424930;ENST00000426954;ENST00000354197;ENST00000427558;ENST00000442920;ENST00000517598;ENST00000347466;ENST00000415379;ENST00000221735	T;T;T;T;T;T;T	0.18338	2.22;2.22;2.22;2.22;2.22;2.22;2.22	1.69	0.633	0.17712	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.24509	0.0594	L	0.31845	0.965	0.09310	N	0.999999	P;P;D;P;P;D;P	0.56968	0.699;0.898;0.958;0.898;0.771;0.978;0.771	P;D;D;D;B;P;B	0.70716	0.768;0.956;0.97;0.956;0.276;0.608;0.276	T	0.10776	-1.0615	9	0.72032	D	0.01	.	5.1817	0.15163	0.6777:0.0:0.3223:0.0	.	205;205;238;239;252;219;251	E9PFX9;B4DXU7;E9PCP4;E9PET3;E9PED0;Q96HQ0-2;Q96HQ0	.;.;.;.;.;.;ZN419_HUMAN	V	252;239;239;122;238;252;219;205;251	ENSP00000388864:I252V;ENSP00000390916:I239V;ENSP00000346136:I239V;ENSP00000414709:I238V;ENSP00000299860:I219V;ENSP00000392129:I205V;ENSP00000221735:I251V	ENSP00000221735:I251V	I	+	1	0	ZNF419	62696488	0.000000	0.05858	0.008000	0.14137	0.589000	0.36550	-0.691000	0.05133	0.119000	0.18210	0.172000	0.16884	ATA	.	.	.	none		0.423	ZNF419-006	KNOWN	NAGNAG_splice_site|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378506.1	NM_024691		G	58004676	A	G	58004676	3	3	239	1	0	0	0	0	1	0	0	0	17908	101	4	3	772	3	ZNF419	19	58004676	Missense_Mutation	SNP	A	TCGA-PJ-A8JU-01A-11D-A35Z-10	871225	58004676	1124307	99	14646											
SOX12	6666	hgsc.bcm.edu	37	chr20	306671	306679	+	In_Frame_Del	DEL	ACCCCGAGC	ACCCCGAGC	-																															gcgagcccggctggtgcaagAccccgagcggccacatcaag																								rs375905724|rs369922526		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	ACCCCGAGC	ACCCCGAGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr20:306671_306679delACCCCGAGC	ENST00000342665.2	+	1	433_441	c.103_111delACCCCGAGC	c.(103-111)accccgagcdel	p.TPS35del	RP5-1103G7.4_ENST00000414676.1_RNA|SOX12_ENST00000544632.1_In_Frame_Del_p.TPS35del|RP5-1103G7.4_ENST00000442637.1_RNA	NM_006943.2	NP_008874.2	O15370	SOX12_HUMAN	SRY (sex determining region Y)-box 12	35					cell fate commitment (GO:0045165)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein-DNA complex assembly (GO:0065004)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spinal cord development (GO:0021510)	nucleus (GO:0005634)|protein-DNA complex (GO:0032993)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2		all_cancers(10;0.000331)|Lung NSC(37;0.0496)|all_lung(30;0.0831)|all_epithelial(17;0.0868)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			cTGGTGCAAGACCCCGAGCGGCCACATCA	0.722																																					p.34_37del		Atlas-Indel,Pindel	.											.	SOX12	8	.	0			c.102_110del						PASS	.																																			SO:0001651	inframe_deletion	6666	exon1			.	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.103_111delACCCCGAGC	chr20.hg19:g.306671_306679delACCCCGAGC	ENSP00000347646:p.Thr35_Ser37del	95.0	0.0	0		71.0	15.0	0.211268	NM_006943	Q5D038|Q9NUD4	In_Frame_Del	DEL	ENST00000342665.2	hg19	CCDS12995.1																																																																																			.	.	.	none		0.722	SOX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077435.2	NM_006943		-	306679	ACCCCGAGC	-	306671	7	5	239	1	0	1	0	1	0	0	0	0	14956	275	10	0	105	0	SOX12	20	306671	In_Frame_Del	DEL	ACCCCGAGC	TCGA-PJ-A8JU-01A-11D-A35Z-10		306671	62718849	100	14647											
STAU1	6780	hgsc.bcm.edu	37	chr20	47732330	47732330	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcactcacacagacattggTccgtttcctgttcttggcat	7	14	8	12	1	2	1	1	0	1	1	4	1	4	1	2	2	1	4	2	2	0	4			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr20:47732330T>C	ENST00000371856.2	-	13	2117	c.1707A>G	c.(1705-1707)ggA>ggG	p.G569G	STAU1_ENST00000347458.5_Silent_p.G488G|STAU1_ENST00000371792.1_Silent_p.G486G|STAU1_ENST00000371802.1_Silent_p.G494G|STAU1_ENST00000340954.7_Silent_p.G488G|STAU1_ENST00000371828.3_Silent_p.G494G|STAU1_ENST00000360426.4_Silent_p.G488G	NM_017453.2	NP_059347.2	O95793	STAU1_HUMAN	staufen double-stranded RNA binding protein 1	569					intracellular mRNA localization (GO:0008298)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|rough endoplasmic reticulum (GO:0005791)	double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|liver(1)|lung(6)|ovary(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	23			BRCA - Breast invasive adenocarcinoma(12;0.000644)|Colorectal(8;0.198)			CAGACATTGGTCCGTTTCCTG	0.507																																					p.G569G		Atlas-SNP	.											.	STAU1	54	.	0			c.A1707G						PASS	.						263	209	227					20																	47732330		2203	4300	6503	SO:0001819	synonymous_variant	6780	exon13			CATTGGTCCGTTT		CCDS13414.1, CCDS13415.1, CCDS33481.1	20q13.1	2014-06-13	2013-06-05	2005-11-04	ENSG00000124214	ENSG00000124214			11370	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 150"	601716	"staufen (Drosophila, RNA-binding protein)", "staufen, RNA binding protein (Drosophila)", "staufen, RNA binding protein, homolog 1 (Drosophila)"	STAU		8884277, 15680326	Standard	XM_005260524		Approved	PPP1R150	uc002xud.3	O95793	OTTHUMG00000032691	ENST00000371856.2:c.1707A>G	chr20.hg19:g.47732330T>C		54.0	0.0	.		51.0	15.0	.	NM_017453	A8K9Z4|E1P5Y1|E1P608|Q5JW29|Q6GTM4|Q9H5B4|Q9H5B5|Q9Y3Q2	Silent	SNP	ENST00000371856.2	hg19	CCDS13414.1																																																																																			.	.	.	none		0.507	STAU1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079633.1	NM_017453		C	47732330	T	C	47732330	2	2	239	1	0	0	0	0	0	0	0	1	15284	1654	58	3		3	STAU1	20	47732330	Silent	SNP	T	TCGA-PJ-A8JU-01A-11D-A35Z-10	47425659	47732330	15293190	101	14648											
BRWD1	54014	hgsc.bcm.edu	37	chr21	40670471	40670471	+	Missense_Mutation	SNP	A	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	cgatgcgctggcagatttgcAaaagatgatcaggagccaca	13	7	12	9	2	1	3	1	1	0	2	1	5	1	4	1	2	3	3	1	2	2	1			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr21:40670471A>C	ENST00000333229.2	-	5	563	c.236T>G	c.(235-237)tTg>tGg	p.L79W	BRWD1_ENST00000380800.3_Missense_Mutation_p.L79W|BRWD1_ENST00000342449.3_Missense_Mutation_p.L79W|BRWD1_ENST00000470108.1_5'UTR|BRWD1_ENST00000341322.4_Missense_Mutation_p.L79W	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	79					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)				GCAGATTTGCAAAAGATGATC	0.388																																					p.L79W	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.T236G						PASS	.						115	120	118					21																	40670471		2203	4300	6503	SO:0001583	missense	54014	exon5			ATTTGCAAAAGAT	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.236T>G	chr21.hg19:g.40670471A>C	ENSP00000330753:p.Leu79Trp	301.0	0.0	.		323.0	91.0	.	NM_001007246	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	hg19	CCDS13662.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.796583	0.90453	.	.	ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800;ENST00000341322	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	5.55	5.55	0.83447	.	0.000000	0.50627	D	0.000103	T	0.69611	0.3130	M	0.87682	2.9	0.50313	D	0.999863	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	T	0.76091	-0.3086	10	0.87932	D	0	-4.6002	15.6873	0.77421	1.0:0.0:0.0:0.0	.	79;79;79	Q6P2D1;Q9NSI6-2;Q9NSI6	.;.;BRWD1_HUMAN	W	79	ENSP00000330753:L79W;ENSP00000344333:L79W;ENSP00000370178:L79W;ENSP00000342106:L79W	ENSP00000330753:L79W	L	-	2	0	BRWD1	39592341	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.850000	0.92190	2.119000	0.64992	0.383000	0.25322	TTG	.	.	.	none		0.388	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		C	40670471	A	C	40670471	3	2	239	1	0	0	0	0	1	0	0	0	1527	131	5	5	7131	5	BRWD1	21	40670471	Missense_Mutation	SNP	A	TCGA-PJ-A8JU-01A-11D-A35Z-10		40670471	7459424	102	14649											
MN1	4330	hgsc.bcm.edu	37	chr22	28193970	28193970	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcagtttcctcttgccctcTggcgggttcttcttgttgaa	3	17	9	12	1	5	1	1	1	4	0	6	1	6	1	2	2	1	3	2	2	1	6			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr22:28193970T>C	ENST00000302326.4	-	1	3516	c.2562A>G	c.(2560-2562)ccA>ccG	p.P854P		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	854					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						TCTTGCCCTCTGGCGGGTTCT	0.657			T	ETV6	"AML, meningioma"																																p.P854P		Atlas-SNP	.		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"L, O"	.	MN1	122	.	0			c.A2562G						PASS	.						71	78	76					22																	28193970		1886	4093	5979	SO:0001819	synonymous_variant	4330	exon1			GCCCTCTGGCGGG	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.2562A>G	chr22.hg19:g.28193970T>C		38.0	0.0	.		28.0	12.0	.	NM_002430	A9Z1V9	Silent	SNP	ENST00000302326.4	hg19	CCDS42998.1																																																																																			.	.	.	none		0.657	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430		C	28193970	T	C	28193970	2	2	239	1	0	0	0	0	0	0	0	1	9680	1567	55	3		3	MN1	22	28193970	Silent	SNP	T	TCGA-PJ-A8JU-01A-11D-A35Z-10		28193970	23110596	103	14650											
RNF185	91445	hgsc.bcm.edu	37	chr22	31583132	31583132	+	Frame_Shift_Del	DEL	G	G	-																															ctcctgagaactccagtgcaGgggggcccagtgggagcagc																										TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr22:31583132delG	ENST00000326132.6	+	2	211	c.52delG	c.(52-54)gggfs	p.G19fs	RNF185_ENST00000266252.7_Frame_Shift_Del_p.G19fs|RNF185_ENST00000426256.2_5'UTR	NM_152267.3	NP_689480.2	Q96GF1	RN185_HUMAN	ring finger protein 185	19					autophagy (GO:0006914)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(3)|skin(1)	6						CTCCAGTGCAGGGGGGCCCAG	0.607																																					p.A17fs		Atlas-Indel,Pindel	.											.	RNF185	14	.	0			c.51delA						PASS	.						71	73	72					22																	31583132		2203	4300	6503	SO:0001589	frameshift_variant	91445	exon2			.		CCDS13890.1, CCDS46689.1	22q12.2	2013-01-09			ENSG00000138942	ENSG00000138942		"RING-type (C3HC4) zinc fingers"	26783	protein-coding gene	gene with protein product	"hypothetical protein FLJ38628"					12477932	Standard	NM_152267		Approved	FLJ38628	uc003akb.3	Q96GF1	OTTHUMG00000151253	ENST00000326132.6:c.52delG	chr22.hg19:g.31583132delG	ENSP00000320508:p.Gly19fs	184.0	0.0	0		102.0	47.0	0.460784	NM_152267	A8K5C1|A9X3T8|Q8N900	Frame_Shift_Del	DEL	ENST00000326132.6	hg19	CCDS13890.1																																																																																			.	.	.	none		0.607	RNF185-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321927.2	NM_152267		-	31583132	G	-	31583132	7	5	239	1	0	1	0	1	0	0	0	0	13481	1000	35	0	54	0	RNF185	22	31583132	Frame_Shift_Del	DEL	G	TCGA-PJ-A8JU-01A-11D-A35Z-10	3389162	31583132	19721434	104	14651											
ATF4	468	hgsc.bcm.edu	37	chr22	39918544	39918544	+	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	gattccctggccaaggagatCcagtacctgaaagatttgat	12	10	10	9	0	0	4	0	2	0	2	2	6	2	4	4	2	1	1	4	2	3	3	rs189922789		TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chr22:39918544C>A	ENST00000337304.2	+	2	1875	c.993C>A	c.(991-993)atC>atA	p.I331I	ATF4_ENST00000396680.1_Silent_p.I331I|ATF4_ENST00000404241.2_Silent_p.I331I	NM_001675.2	NP_001666.2	P18848	ATF4_HUMAN	activating transcription factor 4	331	Interaction with GABBR1. {ECO:0000250}.|Leucine-zipper. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.			KEI -> REK (in Ref. 5; no nucleotide entry). {ECO:0000305}.	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)	CCAAGGAGATCCAGTACCTGA	0.512																																					p.I331I		Atlas-SNP	.											.	ATF4	27	.	0			c.C993A						PASS	.						19	22	21					22																	39918544		2195	4289	6484	SO:0001819	synonymous_variant	468	exon2			GGAGATCCAGTAC	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.993C>A	chr22.hg19:g.39918544C>A		210.0	0.0	.		122.0	64.0	.	NM_001675	Q9UH31	Silent	SNP	ENST00000337304.2	hg19	CCDS13996.1																																																																																			.	C|1.000;G|0.000	.	alt		0.512	ATF4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321305.1	NM_001675		A	39918544	C	A	39918544	2	1	239	1	0	0	0	0	0	0	0	1	1082	845	30	4		4	ATF4	22	39918544	Silent	SNP	C	TCGA-PJ-A8JU-01A-11D-A35Z-10	8335412	39918544	11386022	105	14652											
RGAG1	57529	hgsc.bcm.edu	37	chrX	109694814	109694814	+	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	tctgaagtaatgtccacaccGctactgtcagtcccagatgc	10	10	8	13	1	2	2	1	1	1	1	4	2	4	2	3	0	2	2	3	0	3	2			TCGA-PJ-A8JU-01A-11D-A35Z-10	TCGA-PJ-A8JU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	13034367-8ee9-4a37-b910-2798632c44fe	d0b1cf4a-51b3-49a9-9a97-c719fa400826	g.chrX:109694814G>A	ENST00000465301.2	+	3	1215	c.969G>A	c.(967-969)ccG>ccA	p.P323P	RGAG1_ENST00000540313.1_Silent_p.P323P	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	323										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						TGTCCACACCGCTACTGTCAG	0.502													G|||	1	0.000264901	0	0	3775	,	,		16677	0.001		0	False		,,,				2504	0				p.P323P		Atlas-SNP	.											.	RGAG1	168	.	0			c.G969A						PASS	.						257	235	242					X																	109694814		2203	4300	6503	SO:0001819	synonymous_variant	57529	exon3			CACACCGCTACTG	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.969G>A	chrX.hg19:g.109694814G>A		148.0	0.0	.		69.0	5.0	.	NM_020769	Q9P2M8	Silent	SNP	ENST00000465301.2	hg19	CCDS14552.1																																																																																			.	.	.	none		0.502	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		A	109694814	G	A	109694814	2	1	239	1	0	0	0	0	0	0	0	1	13287	1074	38	1		1	RGAG1	23	109694814	Silent	SNP	G	TCGA-PJ-A8JU-01A-11D-A35Z-10		109694814	45575746	106	14653											
RERE	473	hgsc.bcm.edu	37	chr1	8419867	8419868	+	Missense_Mutation	DNP	CG	CG	TT																															cccgctctcgctcccgctccCgctccttctccttctccttc																								rs538667090|rs147985313|rs557606465	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C|G	C|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr1:8419867_8419868CG>TT	ENST00000337907.3	-	20	4208_4209	c.3574_3575CG>AA	c.(3574-3576)CGg>AAg	p.R1192K	RERE_ENST00000377464.1_Missense_Mutation_p.R924K|RERE_ENST00000400907.2_Intron|RERE_ENST00000476556.1_Missense_Mutation_p.R638K|RERE_ENST00000400908.2_Missense_Mutation_p.R1192K	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	1192	Arg/Glu-rich (mixed charge).				chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.E1191_R1192insKE(1)		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)		ctcccgctcccgctccttctcc	0.683																																					p.R1192Q|p.R1192R		Atlas-SNP	.											RERE,NS,carcinoma,-1,1|RERE,NS,carcinoma,0,1	RERE	129	.	1	Insertion - In frame(1)	ovary(1)	c.G3575A|c.C3574A						PASS	.																																			SO:0001583	missense	473	exon20			CGCTCCCGCTCCT|GCTCCCGCTCCTT	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.3574_3575delinsTT	chr1.hg19:g.8419867_8419868delinsTT	ENSP00000338629:p.Arg1192Lys	15.0	0.0	.		46.0|45.0	4.0	.	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Missense_Mutation|Silent	SNP	ENST00000337907.3	hg19	CCDS95.1																																																																																			.	.	.	none		0.683	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1			TT	8419868	CG	TT	8419867	3	4	240	1	0	0	0	0	1	0	0	0	13244	652	23	1	1145	1	RERE	1	8419867	Missense_Mutation	DNP	CG	TCGA-Q2-A5QZ-01A-11D-A28G-10		8419867	240830754	1	14654											
NSUN4	387338	hgsc.bcm.edu	37	chr1	46818626	46818626	+	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	atgtgcctgaagagatcaggGatggaaatcaagttcgagtt	13	10	13	5	1	2	2	2	1	0	1	3	6	2	4	1	2	1	2	1	2	3	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr1:46818626G>T	ENST00000474844.1	+	4	1329	c.679G>T	c.(679-681)Gat>Tat	p.D227Y	NSUN4_ENST00000498008.1_3'UTR|NSUN4_ENST00000537428.1_Missense_Mutation_p.D178Y|NSUN4_ENST00000536062.1_Missense_Mutation_p.D178Y	NM_199044.3	NP_950245.2	Q96CB9	NSUN4_HUMAN	NOP2/Sun domain family, member 4	227					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)					AGAGATCAGGGATGGAAATCA	0.488																																					p.D227Y		Atlas-SNP	.											.	NSUN4	26	.	0			c.G679T						PASS	.						146	132	137					1																	46818626		2203	4300	6503	SO:0001583	missense	387338	exon4			ATCAGGGATGGAA	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.679G>T	chr1.hg19:g.46818626G>T	ENSP00000419740:p.Asp227Tyr	53.0	0.0	.		95.0	4.0	.	NM_199044	A8K6S6|B3KQ50|B4DHA4|Q5TDF7|Q96AN8|Q9HAJ8	Missense_Mutation	SNP	ENST00000474844.1	hg19	CCDS534.1	.	.	.	.	.	.	.	.	.	.	G	18.78	3.696993	0.68386	.	.	ENSG00000117481	ENST00000474844;ENST00000536062;ENST00000537428	T;T;T	0.22336	1.96;1.96;1.96	5.33	3.36	0.38483	Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p (1);	0.525534	0.23606	N	0.046396	T	0.21674	0.0522	L	0.40543	1.245	0.35335	D	0.785985	P;B	0.49253	0.921;0.355	P;B	0.48368	0.575;0.393	T	0.25467	-1.0131	10	0.72032	D	0.01	-3.2295	7.9929	0.30250	0.1399:0.0:0.7295:0.1306	.	94;227	B3KUM0;Q96CB9	.;NSUN4_HUMAN	Y	227;178;178	ENSP00000419740:D227Y;ENSP00000438912:D178Y;ENSP00000437758:D178Y	ENSP00000419740:D227Y	D	+	1	0	NSUN4	46591213	0.997000	0.39634	0.990000	0.47175	0.980000	0.70556	1.385000	0.34408	1.458000	0.47871	0.591000	0.81541	GAT	.	.	.	none		0.488	NSUN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021427.1	NM_199044		T	46818626	G	T	46818626	3	4	240	1	0	0	0	0	1	0	0	0	10687	1174	41	4	693	4	NSUN4	1	46818626	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	38398759	46818626	202431995	2	14655											
CLCA1	1179	hgsc.bcm.edu	37	chr1	86934706	86934706	+	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	tgattcttcaccttctagaaGgggccctgagtaattcactc	9	13	8	11	0	4	3	2	2	2	1	5	3	4	3	2	2	0	1	2	2	3	6	rs377703691		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr1:86934706G>A	ENST00000234701.3	+	2	403	c.52G>A	c.(52-54)Ggg>Agg	p.G18R	CLCA1_ENST00000394711.1_Missense_Mutation_p.G18R			A8K7I4	CLCA1_HUMAN	chloride channel accessory 1	18					calcium ion transport (GO:0006816)|cellular response to hypoxia (GO:0071456)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|zymogen granule membrane (GO:0042589)	chloride channel activity (GO:0005254)			NS(1)|breast(3)|endometrium(1)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		CCTTCTAGAAGGGGCCCTGAG	0.443																																					p.G18R		Atlas-SNP	.											.	CLCA1	109	.	0			c.G52A						PASS	.	G	ARG/GLY	0,4406		0,0,2203	139	134	136		52	6	0.8	1		136	1,8599	1.2+/-3.3	0,1,4299	no	missense	CLCA1	NM_001285.3	125	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	18/915	86934706	1,13005	2203	4300	6503	SO:0001583	missense	1179	exon1			CTAGAAGGGGCCC		CCDS709.1	1p22.3	2012-02-26	2009-01-29		ENSG00000016490	ENSG00000016490			2015	protein-coding gene	gene with protein product		603906	"chloride channel, calcium activated, family member 1", "chloride channel regulator 1"			9828122	Standard	NM_001285		Approved	CaCC, CLCRG1	uc001dlt.3	A8K7I4	OTTHUMG00000010254	ENST00000234701.3:c.52G>A	chr1.hg19:g.86934706G>A	ENSP00000234701:p.Gly18Arg	68.0	0.0	.		87.0	41.0	.	NM_001285	B2RAV5|O95151|Q5TDF4|Q9UNF6|Q9UPC6	Missense_Mutation	SNP	ENST00000234701.3	hg19	CCDS709.1	.	.	.	.	.	.	.	.	.	.	G	18.23	3.577478	0.65878	0.0	1.16E-4	ENSG00000016490	ENST00000234701;ENST00000394711	T;T	0.11821	2.74;2.74	5.96	5.96	0.96718	Chloride channel calcium-activated (1);	0.298342	0.31415	N	0.007685	T	0.28995	0.0720	M	0.77486	2.375	0.36444	D	0.865661	D	0.89917	1.0	D	0.81914	0.995	T	0.02307	-1.1179	10	0.25106	T	0.35	-15.6633	17.336	0.87281	0.0:0.0:1.0:0.0	.	18	A8K7I4	CLCA1_HUMAN	R	18	ENSP00000234701:G18R;ENSP00000378200:G18R	ENSP00000234701:G18R	G	+	1	0	CLCA1	86707294	0.978000	0.34361	0.836000	0.33094	0.545000	0.35147	2.435000	0.44811	2.831000	0.97527	0.650000	0.86243	GGG	.	.	.	none		0.443	CLCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028277.1	NM_001285		A	86934706	G	A	86934706	3	1	240	1	0	0	0	0	1	0	0	0	3459	1000	35	2	54	2	CLCA1	1	86934706	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	40116080	86934706	162315915	3	14656											
LCE1C	353133	hgsc.bcm.edu	37	chr1	152777877	152777877	+	Silent	SNP	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	cactttgggggacactttggGgtggggcacttgggagggca	6	9	19	7	0	0	0	0	0	0	0	0	2	0	2	0	8	0	2	0	8	0	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	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	chr1.hg19:g.152777877G>A		50.0	0.0	.		198.0	18.0	.	NM_178351		Silent	SNP	ENST00000607093.1	hg19	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	240	1	0	0	0	0	0	0	0	1	8668	1219	43	2		2	LCE1C	1	152777877	Silent	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	65843171	152777877	96472744	4	14657											
SPRR2D	6703	hgsc.bcm.edu	37	chr1	153012642	153012642	+	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	acactttggctggcagggtgGggaaggtgtcacaggaggat	9	8	18	6	0	1	0	1	0	0	0	1	3	1	3	0	8	0	2	0	8	1	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr1:153012642G>T	ENST00000368757.1	-	2	461	c.181C>A	c.(181-183)Cca>Aca	p.P61T	SPRR2D_ENST00000368756.1_Missense_Mutation_p.P61T|SPRR2D_ENST00000368758.3_Missense_Mutation_p.P61T|SPRR2D_ENST00000360379.3_Missense_Mutation_p.P61T			P22532	SPR2D_HUMAN	small proline-rich protein 2D	61					epidermis development (GO:0008544)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)				endometrium(1)|skin(1)	2	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)			TGGCAGGGTGGGGAAGGTGTC	0.562																																					p.P61T		Atlas-SNP	.											.	SPRR2D	9	.	0			c.C181A						PASS	.						228	212	217					1																	153012642		2203	4298	6501	SO:0001583	missense	6703	exon2			AGGGTGGGGAAGG	AF333954	CCDS30864.1	1q21-q22	2008-02-05			ENSG00000163216	ENSG00000163216			11264	protein-coding gene	gene with protein product						8325635	Standard	NM_006945		Approved		uc001fbb.2	P22532	OTTHUMG00000014396	ENST00000368757.1:c.181C>A	chr1.hg19:g.153012642G>T	ENSP00000357746:p.Pro61Thr	93.0	0.0	.		342.0	16.0	.	NM_006945	A4QN03|A8K5K2|D3DV33|Q5T523|Q96RM3	Missense_Mutation	SNP	ENST00000368757.1	hg19	CCDS30864.1	.	.	.	.	.	.	.	.	.	.	G	0.024	-1.388841	0.01185	.	.	ENSG00000163216	ENST00000360379;ENST00000368758;ENST00000368757;ENST00000368756	T;T;T;T	0.35048	1.33;1.33;1.33;1.33	3.62	0.403	0.16350	.	1.027660	0.07812	N	0.958367	T	0.09423	0.0232	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.37753	-0.9692	9	0.87932	D	0	.	2.2809	0.04114	0.1152:0.1919:0.4957:0.1972	.	61	P22532	SPR2D_HUMAN	T	61	ENSP00000353542:P61T;ENSP00000357747:P61T;ENSP00000357746:P61T;ENSP00000357745:P61T	ENSP00000353542:P61T	P	-	1	0	SPRR2D	151279266	0.003000	0.15002	0.000000	0.03702	0.016000	0.09150	0.726000	0.25984	-0.130000	0.11599	-0.535000	0.04281	CCA	.	.	.	none		0.562	SPRR2D-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040051.1			T	153012642	G	T	153012642	3	4	240	1	0	0	0	0	1	0	0	0	15111	1232	43	4	41	4	SPRR2D	1	153012642	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	234765	153012642	96237979	5	14658											
DUSP23	54935	hgsc.bcm.edu	37	chr1	159751066	159751066	+	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	ctgccccggcctcaccctgcAccgcctgcgcatccccgact	4	6	8	23	4	1	0	1	0	0	0	2	1	2	0	8	1	3	2	8	1	0	0	rs141314838		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr1:159751066A>T	ENST00000368107.1	+	1	274	c.176A>T	c.(175-177)cAc>cTc	p.H59L	DUSP23_ENST00000368108.3_Missense_Mutation_p.H59L|DUSP23_ENST00000368109.1_Missense_Mutation_p.H59L			Q9BVJ7	DUS23_HUMAN	dual specificity phosphatase 23	59						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			lung(1)	1	all_hematologic(112;0.0537)					CTCACCCTGCACCGCCTGCGC	0.716																																					p.H59L		Atlas-SNP	.											.	DUSP23	9	.	0			c.A176T						PASS	.						4	4	4					1																	159751066		1795	3557	5352	SO:0001583	missense	54935	exon2			CCCTGCACCGCCT		CCDS1187.1	1q23.1	2011-06-09			ENSG00000158716	ENSG00000158716		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	21480	protein-coding gene	gene with protein product						15147733	Standard	XM_005245289		Approved	FLJ20442, DUSP25	uc001ftz.1	Q9BVJ7	OTTHUMG00000022795	ENST00000368107.1:c.176A>T	chr1.hg19:g.159751066A>T	ENSP00000357087:p.His59Leu	3.0	0.0	.		183.0	78.0	.	NM_017823	Q9NX48	Missense_Mutation	SNP	ENST00000368107.1	hg19	CCDS1187.1	.	.	.	.	.	.	.	.	.	.	A	9.461	1.093071	0.20471	.	.	ENSG00000158716	ENST00000368109;ENST00000368108;ENST00000368107	D;D;D	0.82711	-1.64;-1.64;-1.64	4.89	3.76	0.43208	Dual specificity phosphatase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.56062	0.1960	L	0.48935	1.535	0.58432	D	0.999997	B	0.24186	0.099	B	0.17433	0.018	T	0.53521	-0.8427	10	0.07644	T	0.81	-38.779	8.8034	0.34923	0.9101:0.0:0.0899:0.0	.	59	Q9BVJ7	DUS23_HUMAN	L	59	ENSP00000357089:H59L;ENSP00000357088:H59L;ENSP00000357087:H59L	ENSP00000357087:H59L	H	+	2	0	DUSP23	158017690	1.000000	0.71417	0.997000	0.53966	0.010000	0.07245	8.405000	0.90213	0.877000	0.35895	-0.441000	0.05720	CAC	.	.	.	none		0.716	DUSP23-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085552.1	NM_017823		T	159751066	A	T	159751066	3	4	240	1	0	0	0	0	1	0	0	0	4824	159	6	5	178	5	DUSP23	1	159751066	Missense_Mutation	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	6738424	159751066	89499555	6	14659											
FAM5B	57795	hgsc.bcm.edu	37	chr1	177242681	177242690	+	Frame_Shift_Del	DEL	GTCAGTTCTG	GTCAGTTCTG	-																															actatgacaatctggactcaGtcagttctgtcttggtacag																								rs138487282		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	GTCAGTTCTG	GTCAGTTCTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr1:177242681_177242690delGTCAGTTCTG	ENST00000361539.4	+	5	1039_1048	c.727_736delGTCAGTTCTG	c.(727-738)gtcagttctgtcfs	p.VSSV243fs	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	243	MACPF.				cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)											TCTGGACTCAGTCAGTTCTGTCTTGGTACA	0.443																																					p.242_245del		Atlas-Indel,Pindel	.											.	FAM5B	191	.	0			c.726_735del						PASS	.																																			SO:0001589	frameshift_variant	57795	exon5			.		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.727_736delGTCAGTTCTG	chr1.hg19:g.177242681_177242690delGTCAGTTCTG	ENSP00000354481:p.Val243fs	126.0	0.0	0		181.0	18.0	0.0994475	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Frame_Shift_Del	DEL	ENST00000361539.4	hg19	CCDS1320.1																																																																																			.	.	.	none		0.443	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165		-	177242690	GTCAGTTCTG	-	177242681	7	5	240	1	0	1	0	1	0	0	0	0	5600	1029	36	0	741	0	FAM5B	1	177242681	Frame_Shift_Del	DEL	GTCAGTTCTG	TCGA-Q2-A5QZ-01A-11D-A28G-10	17491615	177242681	72007940	7	14660											
NFASC	23114	hgsc.bcm.edu	37	chr1	204985554	204985554	+	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	gtggcgagggtcagttcaatGaagacggctccttcatcggc	8	9	14	10	3	3	2	3	1	0	1	5	3	4	2	1	4	0	2	1	4	2	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr1:204985554G>T	ENST00000401399.1	+	29	3809	c.3610G>T	c.(3610-3612)Gaa>Taa	p.E1204*	NFASC_ENST00000360049.4_Nonsense_Mutation_p.E1133*|NFASC_ENST00000404076.1_Nonsense_Mutation_p.E1121*|NFASC_ENST00000367172.4_Nonsense_Mutation_p.E1311*|NFASC_ENST00000539706.1_Nonsense_Mutation_p.E1138*|NFASC_ENST00000513543.1_Nonsense_Mutation_p.E1133*|NFASC_ENST00000495396.1_3'UTR|NFASC_ENST00000404907.1_Nonsense_Mutation_p.E1138*|NFASC_ENST00000339876.6_Nonsense_Mutation_p.E1204*|NFASC_ENST00000367171.4_Nonsense_Mutation_p.E1296*|NFASC_ENST00000367170.4_Nonsense_Mutation_p.E1232*|NFASC_ENST00000338515.6_Nonsense_Mutation_p.E1221*|NFASC_ENST00000338586.6_Nonsense_Mutation_p.E1188*|NFASC_ENST00000367169.4_Nonsense_Mutation_p.E1035*			O94856	NFASC_HUMAN	neurofascin	1311	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			TCAGTTCAATGAAGACGGCTC	0.562																																					p.E1204X		Atlas-SNP	.											.	NFASC	396	.	0			c.G3610T						PASS	.						197	175	182					1																	204985554		2203	4300	6503	SO:0001587	stop_gained	23114	exon30			TTCAATGAAGACG	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.3610G>T	chr1.hg19:g.204985554G>T	ENSP00000385637:p.Glu1204*	89.0	0.0	.		310.0	34.0	.	NM_001005388	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Nonsense_Mutation	SNP	ENST00000401399.1	hg19	CCDS53460.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	45|45	11.626230|11.626230	0.99583|0.99583	.|.	.|.	ENSG00000163531|ENSG00000163531	ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000404076;ENST00000401399;ENST00000404907;ENST00000513543;ENST00000430393;ENST00000447819|ENST00000367173;ENST00000425360	.|.	.|.	.|.	5.34|5.34	5.34|5.34	0.76211|0.76211	.|.	0.000000|.	0.51477|.	D|.	0.000096|.	.|T	.|0.74718	.|0.3753	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.73553	.|-0.3946	.|4	0.87932|.	D|.	0|.	.|.	18.6493|18.6493	0.91425|0.91425	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|I	1311;1296;1232;1221;1204;1188;1153;1138;1133;1035;1121;1204;1138;1133;1129;182|1004;261	.|.	ENSP00000295776:E1153X|.	E|M	+|+	1|3	0|0	NFASC|NFASC	203252177|203252177	1.000000|1.000000	0.71417|0.71417	0.966000|0.966000	0.40874|0.40874	0.941000|0.941000	0.58515|0.58515	9.835000|9.835000	0.99442|0.99442	2.484000|2.484000	0.83849|0.83849	0.563000|0.563000	0.77884|0.77884	GAA|ATG	.	.	.	none		0.562	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388		T	204985554	G	T	204985554	4	4	240	1	0	0	0	0	0	1	0	0	10366	1291	45	4	4133	4	NFASC	1	204985554	Nonsense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	27742873	204985554	44265067	8	14661											
NRXN1	9378	hgsc.bcm.edu	37	chr2	50850682	50850682	+	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	tatttcatcactgctgctttGaatggggttttgagacaagt	9	16	10	6	0	2	2	2	2	0	1	2	3	2	2	0	2	2	3	0	2	3	5			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr2:50850682G>T	ENST00000406316.2	-	6	2380	c.904C>A	c.(904-906)Caa>Aaa	p.Q302K	NRXN1_ENST00000405472.3_Missense_Mutation_p.Q302K|NRXN1_ENST00000404971.1_Missense_Mutation_p.Q335K|NRXN1_ENST00000406859.3_Missense_Mutation_p.Q302K|NRXN1_ENST00000402717.3_Missense_Mutation_p.Q302K|NRXN1_ENST00000401669.2_Missense_Mutation_p.Q302K|NRXN1_ENST00000331040.5_5'UTR	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	302	Laminin G-like 2. {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)			CTGCTGCTTTGAATGGGGTTT	0.393																																					p.Q335K		Atlas-SNP	.											.	NRXN1	1118	.	0			c.C1003A						PASS	.						138	129	132					2																	50850682		1869	4095	5964	SO:0001583	missense	9378	exon7			TGCTTTGAATGGG	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.904C>A	chr2.hg19:g.50850682G>T	ENSP00000384311:p.Gln302Lys	66.0	0.0	.		79.0	34.0	.	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	ENST00000406316.2	hg19	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	G	17.39	3.378078	0.61735	.	.	ENSG00000179915	ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859	T;T;T;T;T;T	0.79141	-1.24;-1.24;-1.19;-1.24;-1.19;-1.24	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.81545	0.4845	L	0.38175	1.15	0.49389	D	0.999783	D;P	0.56035	0.974;0.946	P;D	0.68353	0.793;0.957	T	0.73933	-0.3826	10	0.09084	T	0.74	.	19.2231	0.93806	0.0:0.0:1.0:0.0	.	335;302	Q9ULB1-3;F8WB18	.;.	K	335;302;302;302;336;302;302	ENSP00000385142:Q335K;ENSP00000384311:Q302K;ENSP00000434015:Q302K;ENSP00000385017:Q302K;ENSP00000385434:Q302K;ENSP00000385681:Q302K	ENSP00000385017:Q302K	Q	-	1	0	NRXN1	50704186	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.657000	0.98554	2.776000	0.95493	0.650000	0.86243	CAA	.	.	.	none		0.393	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			T	50850682	G	T	50850682	3	4	240	1	0	0	0	0	1	0	0	0	10672	1299	45	4	3975	4	NRXN1	2	50850682	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10		50850682	192348691	9	14662											
SPOPL	339745	hgsc.bcm.edu	37	chr2	139322375	139322375	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttgtccttgcagatttgcAcagtgcagaacagttgaaag	11	11	10	9	0	0	3	0	1	0	2	1	3	1	3	2	0	4	4	2	0	2	4			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr2:139322375A>G	ENST00000280098.4	+	9	1314	c.935A>G	c.(934-936)cAc>cGc	p.H312R		NM_001001664.2	NP_001001664.1	Q6IQ16	SPOPL_HUMAN	speckle-type POZ protein-like	312					negative regulation of protein ubiquitination (GO:0031397)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nucleus (GO:0005634)				breast(2)|cervix(2)|endometrium(2)|large_intestine(2)|lung(11)|skin(2)	21				BRCA - Breast invasive adenocarcinoma(221;0.0296)		GCAGATTTGCACAGTGCAGAA	0.413																																					p.H312R		Atlas-SNP	.											.	SPOPL	54	.	0			c.A935G						PASS	.						170	161	164					2																	139322375		2203	4300	6503	SO:0001583	missense	339745	exon9			ATTTGCACAGTGC		CCDS33298.1	2q22.1	2013-01-09			ENSG00000144228	ENSG00000144228		"BTB/POZ domain containing"	27934	protein-coding gene	gene with protein product	"HIB homolog 2", "roadkill homolog 2"						Standard	NM_001001664		Approved	BTBD33	uc002tvh.3	Q6IQ16	OTTHUMG00000153635	ENST00000280098.4:c.935A>G	chr2.hg19:g.139322375A>G	ENSP00000280098:p.His312Arg	80.0	0.0	.		176.0	29.0	.	NM_001001664		Missense_Mutation	SNP	ENST00000280098.4	hg19	CCDS33298.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.545679	0.86022	.	.	ENSG00000144228	ENST00000280098	T	0.76316	-1.01	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	D	0.88749	0.6521	M	0.89353	3.025	0.80722	D	1	D	0.71674	0.998	P	0.62813	0.907	D	0.90622	0.4560	9	.	.	.	-9.3536	15.6521	0.77104	1.0:0.0:0.0:0.0	.	312	Q6IQ16	SPOPL_HUMAN	R	312	ENSP00000280098:H312R	.	H	+	2	0	SPOPL	139038845	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.287000	0.95975	2.161000	0.67846	0.533000	0.62120	CAC	.	.	.	none		0.413	SPOPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331897.1			G	139322375	A	G	139322375	3	3	240	1	0	0	0	0	1	0	0	0	15097	159	6	3	965	3	SPOPL	2	139322375	Missense_Mutation	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	88471693	139322375	103876998	10	14663											
SCN9A	6335	hgsc.bcm.edu	37	chr2	167055820	167055820	+	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	atagaacatctcaaagtcatCctcactcagaggttcagtac	14	10	6	11	0	5	2	5	0	1	2	7	2	6	2	1	1	2	2	1	1	4	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr2:167055820C>T	ENST00000409435.1	-	26	5328	c.5329G>A	c.(5329-5331)Gat>Aat	p.D1777N	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Missense_Mutation_p.D1778N|SCN9A_ENST00000409672.1_Missense_Mutation_p.D1766N|SCN9A_ENST00000375387.4_Missense_Mutation_p.D1778N			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	1777					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)	TCAAAGTCATCCTCACTCAGA	0.428																																					p.D1766N		Atlas-SNP	.											.	SCN9A	296	.	0			c.G5296A						PASS	.						121	125	123					2																	167055820		2203	4300	6503	SO:0001583	missense	6335	exon27			AGTCATCCTCACT	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.5329G>A	chr2.hg19:g.167055820C>T	ENSP00000386330:p.Asp1777Asn	142.0	0.0	.		189.0	10.0	.	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Missense_Mutation	SNP	ENST00000409435.1	hg19	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.837192	0.91117	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435	T;T;T;T	0.10005	2.92;2.92;2.92;2.92	5.86	5.86	0.93980	.	0.000000	0.64402	D	0.000006	T	0.48169	0.1485	H	0.94847	3.59	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	T	0.61028	-0.7145	10	0.87932	D	0	.	20.1802	0.98196	0.0:1.0:0.0:0.0	.	1766	E7EUN6	.	N	1766;1778;1778;1777	ENSP00000386306:D1766N;ENSP00000364536:D1778N;ENSP00000304748:D1778N;ENSP00000386330:D1777N	ENSP00000304748:D1778N	D	-	1	0	SCN9A	166764066	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.689000	0.84165	2.777000	0.95525	0.655000	0.94253	GAT	.	.	.	none		0.428	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		T	167055820	C	T	167055820	3	4	240	1	0	0	0	0	1	0	0	0	13938	855	30	2	641	2	SCN9A	2	167055820	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	27733445	167055820	76143553	11	14664											
GIGYF2	26058	hgsc.bcm.edu	37	chr2	233671361	233671361	+	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	ccaggtccagctccccctccTcatatggtaagtacctttca	8	11	6	16	0	2	0	2	0	0	0	5	0	5	0	6	2	2	3	6	2	3	4			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr2:233671361T>A	ENST00000409547.1	+	17	2111	c.1800T>A	c.(1798-1800)ccT>ccA	p.P600P	GIGYF2_ENST00000409196.3_Silent_p.P594P|GIGYF2_ENST00000409451.3_Silent_p.P621P|GIGYF2_ENST00000373563.4_Silent_p.P600P|GIGYF2_ENST00000373566.3_Silent_p.P622P|GIGYF2_ENST00000409480.1_Silent_p.P622P|GIGYF2_ENST00000452341.2_Silent_p.P431P	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	600					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)		CTCCCCCTCCTCATATGGTAA	0.433																																					p.P621P		Atlas-SNP	.											.	GIGYF2	288	.	0			c.T1863A						PASS	.						111	108	109					2																	233671361		2203	4300	6503	SO:0001819	synonymous_variant	26058	exon17			CCCTCCTCATATG	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.1800T>A	chr2.hg19:g.233671361T>A		39.0	0.0	.		54.0	35.0	.	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Silent	SNP	ENST00000409547.1	hg19	CCDS33401.1																																																																																			.	.	.	none		0.433	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		A	233671361	T	A	233671361	2	1	240	1	0	0	0	0	0	0	0	1	6385	1538	54	5		5	GIGYF2	2	233671361	Silent	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	66615541	233671361	9528012	12	14665											
IQCA1	79781	hgsc.bcm.edu	37	chr2	237272540	237272540	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcggtgcagatggcatggacCagcattttcttccctacccc	7	11	9	14	1	1	1	0	0	1	1	3	2	2	2	4	3	3	3	4	3	1	4			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr2:237272540C>T	ENST00000409907.3	-	15	2026	c.1752G>A	c.(1750-1752)ctG>ctA	p.L584L	IQCA1_ENST00000309507.5_Silent_p.L581L|IQCA1_ENST00000431676.2_Silent_p.L543L	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	584							ATP binding (GO:0005524)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						TGGCATGGACCAGCATTTTCT	0.512																																					p.L592L		Atlas-SNP	.											IQCA1_ENST00000409907,NS,carcinoma,0,2	IQCA1	170	.	0			c.G1776A						PASS	.						167	165	166					2																	237272540		1994	4155	6149	SO:0001819	synonymous_variant	79781	exon15			ATGGACCAGCATT	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.1752G>A	chr2.hg19:g.237272540C>T		94.0	1.0	.		187.0	100.0	.	NM_001270585	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	Silent	SNP	ENST00000409907.3	hg19	CCDS46549.1																																																																																			.	.	.	none		0.512	IQCA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329266.1	NM_024726		T	237272540	C	T	237272540	2	4	240	1	0	0	0	0	0	0	0	1	7809	581	21	2		2	IQCA1	2	237272540	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	3601179	237272540	5926833	13	14666											
PTPRG	5793	hgsc.bcm.edu	37	chr3	62189090	62189090	+	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	ggcccacgcgcctcccgacgGccgcctcagccagcaagcag	7	2	12	20	5	1	0	1	0	0	0	2	1	2	0	6	2	3	2	6	2	1	0			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr3:62189090G>C	ENST00000474889.1	+	12	1998	c.1621G>C	c.(1621-1623)Gcc>Ccc	p.A541P	PTPRG_ENST00000295874.10_Missense_Mutation_p.A541P	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	541					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)		CCTCCCGACGGCCGCCTCAGC	0.687																																					p.A541P		Atlas-SNP	.											.	PTPRG	153	.	0			c.G1621C						PASS	.						17	15	16					3																	62189090		2203	4297	6500	SO:0001583	missense	5793	exon12			CCGACGGCCGCCT	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.1621G>C	chr3.hg19:g.62189090G>C	ENSP00000418112:p.Ala541Pro	32.0	0.0	.		99.0	67.0	.	NM_002841	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Missense_Mutation	SNP	ENST00000474889.1	hg19	CCDS2895.1	.	.	.	.	.	.	.	.	.	.	G	9.459	1.092688	0.20471	.	.	ENSG00000144724	ENST00000474889;ENST00000295874	T;T	0.55760	0.57;0.5	4.39	3.51	0.40186	.	0.179080	0.48286	D	0.000192	T	0.58836	0.2150	L	0.57536	1.79	0.09310	N	1	D;P	0.61080	0.989;0.93	P;P	0.58266	0.836;0.462	T	0.50750	-0.8791	10	0.59425	D	0.04	.	6.385	0.21556	0.0862:0.0:0.5861:0.3277	.	541;541	P23470-2;P23470	.;PTPRG_HUMAN	P	541	ENSP00000418112:A541P;ENSP00000295874:A541P	ENSP00000295874:A541P	A	+	1	0	PTPRG	62164130	0.995000	0.38212	0.010000	0.14722	0.036000	0.12997	4.014000	0.57145	0.959000	0.37980	0.591000	0.81541	GCC	.	.	.	none		0.687	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841		C	62189090	G	C	62189090	3	2	240	1	0	0	0	0	1	0	0	0	12815	1203	42	4	1667	4	PTPRG	3	62189090	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10		62189090	135833340	14	14667											
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113376122	113376122	+	Silent	SNP	C	C	T																															tgttgctgttgctgctgctgCtgctgctgctgctgctgctg																										TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr3:113376122C>T	ENST00000478658.1	-	5	4424	c.4407G>A	c.(4405-4407)caG>caA	p.Q1469Q	KIAA2018_ENST00000316407.4_Silent_p.Q1469Q|KIAA2018_ENST00000491165.1_Intron			Q68DE3	K2018_HUMAN	KIAA2018	1469	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						gctgctgctgctgctgctgct	0.498																																					p.Q1469Q		Atlas-SNP	.											.	KIAA2018	180	.	0			c.G4407A						PASS	.						55	66	62					3																	113376122		2188	4278	6466	SO:0001819	synonymous_variant	205717	exon7			CTGCTGCTGCTGC	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.4407G>A	chr3.hg19:g.113376122C>T		24.0	0.0	.		98.0	17.0	.	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	hg19	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	113376122	C	T	113376122	2	4	240	1	0	0	0	0	0	0	0	1	8275	796	28	2		2	KIAA2018	3	113376122	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	51187032	113376122	84646308	15	14668	153	2									
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113376128	113376128	+	Silent	SNP	C	C	T																															tgttgctgctgctgctgctgCtgctgctgctgctgctgctt																										TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr3:113376128C>T	ENST00000478658.1	-	5	4418	c.4401G>A	c.(4399-4401)caG>caA	p.Q1467Q	KIAA2018_ENST00000316407.4_Silent_p.Q1467Q|KIAA2018_ENST00000491165.1_Intron			Q68DE3	K2018_HUMAN	KIAA2018	1467	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						gctgctgctgctgctgctgct	0.493																																					p.Q1467Q		Atlas-SNP	.											.	KIAA2018	180	.	0			c.G4401A						PASS	.						52	61	58					3																	113376128		2177	4283	6460	SO:0001819	synonymous_variant	205717	exon7			CTGCTGCTGCTGC	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.4401G>A	chr3.hg19:g.113376128C>T		21.0	0.0	.		93.0	22.0	.	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	hg19	CCDS43133.1																																																																																			.	.	.	none		0.493	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		T	113376128	C	T	113376128	2	4	240	1	0	0	0	0	0	0	0	1	8275	796	28	2		2	KIAA2018	3	113376128	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	6	113376128	84646302	16	14669	153	2									
ROPN1B	152015	hgsc.bcm.edu	37	chr3	125690910	125690910	+	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	accaatcaatggctcagacaGataagccaacatgcatcccg	15	6	7	13	1	2	2	2	0	0	2	3	2	3	2	3	1	3	2	3	1	4	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr3:125690910G>T	ENST00000514116.1	+	3	328	c.13G>T	c.(13-15)Gat>Tat	p.D5Y	ROPN1B_ENST00000251776.4_Missense_Mutation_p.D5Y|ROPN1B_ENST00000504401.1_Missense_Mutation_p.D5Y|ROPN1B_ENST00000511862.1_3'UTR			Q9BZX4	ROP1B_HUMAN	rhophilin associated tail protein 1B	5					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)		GGCTCAGACAGATAAGCCAAC	0.517																																					p.D5Y		Atlas-SNP	.											.	ROPN1B	16	.	0			c.G13T						PASS	.						54	56	56					3																	125690910		2203	4300	6503	SO:0001583	missense	152015	exon2			CAGACAGATAAGC	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.13G>T	chr3.hg19:g.125690910G>T	ENSP00000426271:p.Asp5Tyr	30.0	0.0	.		86.0	26.0	.	NM_001012337	D3DNA6|Q96BM7	Missense_Mutation	SNP	ENST00000514116.1	hg19	CCDS33841.1	.	.	.	.	.	.	.	.	.	.	G	12.60	1.986274	0.35036	.	.	ENSG00000114547	ENST00000514116;ENST00000251776;ENST00000504401;ENST00000513830;ENST00000508088;ENST00000509879	T;T;T;T	0.50548	1.7;1.7;1.3;0.74	3.37	2.48	0.30137	cAMP-dependent protein kinase, regulatory subunit, type I/II alpha/beta (1);	0.169791	0.40222	N	0.001160	T	0.59224	0.2178	L	0.60455	1.87	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.995;0.998	T	0.57900	-0.7731	10	0.87932	D	0	-2.9193	7.0352	0.24989	0.1362:0.0:0.8638:0.0	.	5;5	B7Z7H1;Q9BZX4	.;ROP1B_HUMAN	Y	5	ENSP00000426271:D5Y;ENSP00000251776:D5Y;ENSP00000425548:D5Y;ENSP00000423058:D5Y	ENSP00000251776:D5Y	D	+	1	0	ROPN1B	127173600	0.992000	0.36948	0.966000	0.40874	0.278000	0.26855	2.272000	0.43373	0.510000	0.28216	0.305000	0.20034	GAT	.	.	.	none		0.517	ROPN1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369931.1	NM_001012337		T	125690910	G	T	125690910	3	4	240	1	0	0	0	0	1	0	0	0	13537	942	33	4	15	4	ROPN1B	3	125690910	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	12314782	125690910	72331520	17	14670											
PPP2R3A	5523	hgsc.bcm.edu	37	chr3	135825108	135825108	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gactgggaccggtttgccgcTgaggagtatgagacgcttgt	7	10	16	8	3	0	2	0	2	0	1	0	6	0	4	2	3	1	4	2	3	1	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr3:135825108T>C	ENST00000264977.3	+	13	3890	c.3273T>C	c.(3271-3273)gcT>gcC	p.A1091A	PPP2R3A_ENST00000334546.2_Silent_p.A470A|PPP2R3A_ENST00000490467.1_Silent_p.A355A|PPP2R3A_ENST00000469270.1_3'UTR	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	1091					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						GGTTTGCCGCTGAGGAGTATG	0.453																																					p.A1091A		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.T3273C						PASS	.						74	76	75					3																	135825108		2203	4300	6503	SO:0001819	synonymous_variant	5523	exon13			TGCCGCTGAGGAG	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.3273T>C	chr3.hg19:g.135825108T>C		69.0	0.0	.		126.0	41.0	.	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Silent	SNP	ENST00000264977.3	hg19	CCDS3087.1																																																																																			.	.	.	none		0.453	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718		C	135825108	T	C	135825108	2	2	240	1	0	0	0	0	0	0	0	1	12398	1567	55	3		3	PPP2R3A	3	135825108	Silent	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	10134198	135825108	62197322	18	14671											
MFSD1	64747	hgsc.bcm.edu	37	chr3	158519842	158519842	+	5'Flank	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	gggcgtcacgtgagctcccgGagtcatgtgaccgccgtctt	5	9	14	13	5	3	2	2	2	1	0	4	3	4	3	3	2	1	1	3	2	0	1	rs569538342	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr3:158519842G>A	ENST00000264266.8	+	0	0				RP11-379F4.9_ENST00000607044.1_RNA|MFSD1_ENST00000415822.2_Silent_p.R16R|MFSD1_ENST00000392813.4_Silent_p.R16R			Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing 1						transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	26			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)			TGAGCTCCCGGAGTCATGTGA	0.677													G|||	3	0.000599042	0.0023	0	5008	,	,		14763	0		0	False		,,,				2504	0				p.R16R	Pancreas(62;1186 1654 36636 37908)	Atlas-SNP	.											.	MFSD1	88	.	0			c.G48A						PASS	.						29	32	31					3																	158519842		692	1591	2283	SO:0001631	upstream_gene_variant	64747	exon1			CTCCCGGAGTCAT	BC017661	CCDS3185.1, CCDS3185.2, CCDS54666.1	3q25.32	2005-11-17			ENSG00000118855	ENSG00000118855			25874	protein-coding gene	gene with protein product							Standard	NM_022736		Approved	FLJ14153, UG0581B09	uc003fcl.2	Q9H3U5	OTTHUMG00000158835		chr3.hg19:g.158519842G>A	Exception_encountered	0.0	0.0	.		15.0	9.0	.	NM_022736	B4DGJ8|B4DMR8|B4DU49|B4DWU1|C9JS94|J3KQL7|Q05C07|Q5XKJ1|Q8IVS1|Q8IXG4|Q9H7X1	Silent	SNP	ENST00000264266.8	hg19																																																																																				.	.	.	none		0.677	MFSD1-018	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470730.1	NM_022736		A	158519842	G	A	158519842	1	1	240	0	1	0	0	0	0	0	0	0	9534	1161	41	2		2	MFSD1	3	158519842	5'Flank	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	22694734	158519842	39502588	19	14672											
YEATS2	55689	hgsc.bcm.edu	37	chr3	183525842	183525842	+	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	ggatcaccctgcagcccgtgGcactccacaggaacgtgtat	9	7	11	14	2	1	0	1	0	0	0	2	2	2	2	3	3	3	3	3	3	2	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr3:183525842G>T	ENST00000305135.5	+	29	4231	c.4036G>T	c.(4036-4038)Gca>Tca	p.A1346S	YEATS2-AS1_ENST00000425008.3_RNA|YEATS2-AS1_ENST00000609195.1_RNA|YEATS2-AS1_ENST00000609871.1_RNA	NM_018023.4	NP_060493.3	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	1346					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686)	TBP-class protein binding (GO:0017025)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			GCAGCCCGTGGCACTCCACAG	0.572																																					p.A1346S		Atlas-SNP	.											.	YEATS2	111	.	0			c.G4036T						PASS	.						44	46	45					3																	183525842		2006	4162	6168	SO:0001583	missense	55689	exon29			CCCGTGGCACTCC	AB033023	CCDS43175.1	3q27.3	2004-08-18			ENSG00000163872	ENSG00000163872			25489	protein-coding gene	gene with protein product		613373				10574462	Standard	NM_018023		Approved	FLJ10201, FLJ12841, FLJ13308, KIAA1197	uc003fly.2	Q9ULM3	OTTHUMG00000156898	ENST00000305135.5:c.4036G>T	chr3.hg19:g.183525842G>T	ENSP00000306983:p.Ala1346Ser	42.0	0.0	.		140.0	6.0	.	NM_018023	A7E2B9|D3DNS9|Q641P6|Q9NW96	Missense_Mutation	SNP	ENST00000305135.5	hg19	CCDS43175.1	.	.	.	.	.	.	.	.	.	.	G	18.95	3.732056	0.69189	.	.	ENSG00000163872	ENST00000421660;ENST00000305135	T	0.22134	1.97	5.53	4.63	0.57726	.	0.290196	0.31347	N	0.007819	T	0.12817	0.0311	N	0.08118	0	0.32028	N	0.599863	B	0.20368	0.044	B	0.15870	0.014	T	0.04991	-1.0913	10	0.59425	D	0.04	-14.0042	15.0579	0.71930	0.0:0.1431:0.8569:0.0	.	1346	Q9ULM3	YETS2_HUMAN	S	1346	ENSP00000306983:A1346S	ENSP00000306983:A1346S	A	+	1	0	YEATS2	185008536	1.000000	0.71417	0.918000	0.36340	0.889000	0.51656	5.256000	0.65468	1.291000	0.44653	0.561000	0.74099	GCA	.	.	.	none		0.572	YEATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346507.2	NM_018023		T	183525842	G	T	183525842	3	4	240	1	0	0	0	0	1	0	0	0	17484	1203	42	4	4146	4	YEATS2	3	183525842	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	25006000	183525842	14496588	20	14673											
DGKG	1608	hgsc.bcm.edu	37	chr3	185960324	185960324	+	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	tttttcaggatgtttctctcTcatcacatggaatctgtgtg	7	18	8	8	0	5	0	3	0	3	0	7	2	5	2	0	2	0	1	0	2	1	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr3:185960324T>A	ENST00000265022.3	-	20	2334	c.1795A>T	c.(1795-1797)Aga>Tga	p.R599*	DGKG_ENST00000382164.4_Nonsense_Mutation_p.R560*|DGKG_ENST00000344484.4_Nonsense_Mutation_p.R574*|DGKG_ENST00000544847.1_Nonsense_Mutation_p.R540*	NM_001080744.1|NM_001080745.1|NM_001346.2	NP_001074213.1|NP_001074214.1|NP_001337.2	P49619	DGKG_HUMAN	diacylglycerol kinase, gamma 90kDa	599					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|neuron development (GO:0048666)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	42	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	TGTTTCTCTCTCATCACATGG	0.547											OREG0015965	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R599X		Atlas-SNP	.											.	DGKG	98	.	0			c.A1795T						PASS	.						100	87	92					3																	185960324		2203	4300	6503	SO:0001587	stop_gained	1608	exon20			TCTCTCTCATCAC	AF020945	CCDS3274.1, CCDS43181.1, CCDS43182.1	3q27-q28	2013-01-10	2002-08-29		ENSG00000058866	ENSG00000058866	2.7.1.107	"EF-hand domain containing"	2853	protein-coding gene	gene with protein product		601854	"diacylglycerol kinase, gamma (90kD)"	DAGK3		8034597	Standard	NM_001080744		Approved		uc003fqa.3	P49619	OTTHUMG00000156617	ENST00000265022.3:c.1795A>T	chr3.hg19:g.185960324T>A	ENSP00000265022:p.Arg599*	27.0	0.0	.	2003	111.0	31.0	.	NM_001346	B2RAH4|Q2M1H4|Q5FWG1	Nonsense_Mutation	SNP	ENST00000265022.3	hg19	CCDS3274.1	.	.	.	.	.	.	.	.	.	.	T	46	12.295792	0.99654	.	.	ENSG00000058866	ENST00000265022;ENST00000344484;ENST00000382164;ENST00000544847;ENST00000538691	.	.	.	5.38	-0.167	0.13347	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.3395	0.66617	0.0:0.0:0.4781:0.5218	.	.	.	.	X	599;574;560;540;563	.	ENSP00000265022:R599X	R	-	1	2	DGKG	187443018	0.993000	0.37304	1.000000	0.80357	0.992000	0.81027	0.192000	0.17096	0.099000	0.17552	0.533000	0.62120	AGA	.	.	.	none		0.547	DGKG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344800.3			A	185960324	T	A	185960324	4	1	240	1	0	0	0	0	0	1	0	0	4471	1559	54	5	604	5	DGKG	3	185960324	Nonsense_Mutation	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	2434482	185960324	12062106	21	14674											
CRIPAK	285464	hgsc.bcm.edu	37	chr4	1388661	1388665	+	Frame_Shift_Del	DEL	CGATG	CGATG	-																															gcccgcctgctcacacgtgcCgatgcggagtgcccgcctgc																								rs199774688|rs150559021|rs9762106	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	CGATG	CGATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr4:1388661_1388665delCGATG	ENST00000324803.4	+	1	3322_3326	c.362_366delCGATG	c.(361-366)ccgatgfs	p.PM121fs		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	121					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)			TCACACGTGCCGATGCGGAGTGCCC	0.678																																					p.121_122del		Atlas-INDEL	.											.	CRIPAK	185	.	0			c.361_365del						PASS	.																																			SO:0001589	frameshift_variant	285464	exon1			.	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.362_366delCGATG	chr4.hg19:g.1388661_1388665delCGATG	ENSP00000323978:p.Pro121fs	11.0	0.0	0		98.0	11.0	0.112245	NM_175918	Q8NB03	Frame_Shift_Del	DEL	ENST00000324803.4	hg19	CCDS3349.1																																																																																			.	.	.	none		0.678	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918		-	1388665	CGATG	-	1388661	7	5	240	1	0	1	0	1	0	0	0	0	3879	652	23	0	364	0	CRIPAK	4	1388661	Frame_Shift_Del	DEL	CGATG	TCGA-Q2-A5QZ-01A-11D-A28G-10		1388661	189765615	22	14675											
PPP2R2C	5522	hgsc.bcm.edu	37	chr4	6335365	6335365	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtagtcccgggtgagcatgTagcggccgctgtggctgaac	6	8	17	10	3	0	2	0	2	0	0	1	2	1	2	2	4	3	5	2	4	3	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr4:6335365T>C	ENST00000382599.4	-	7	1100	c.884A>G	c.(883-885)tAc>tGc	p.Y295C	PPP2R2C_ENST00000335585.5_Missense_Mutation_p.Y295C|PPP2R2C_ENST00000515571.1_Missense_Mutation_p.Y278C|PPP2R2C_ENST00000507294.1_Missense_Mutation_p.Y288C|PPP2R2C_ENST00000506140.1_Missense_Mutation_p.Y288C			Q9Y2T4	2ABG_HUMAN	protein phosphatase 2, regulatory subunit B, gamma	295					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						GGTGAGCATGTAGCGGCCGCT	0.572											OREG0016071	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y295C		Atlas-SNP	.											.	PPP2R2C	63	.	0			c.A884G						PASS	.						110	105	107					4																	6335365		2203	4300	6503	SO:0001583	missense	5522	exon7			AGCATGTAGCGGC	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.884A>G	chr4.hg19:g.6335365T>C	ENSP00000372042:p.Tyr295Cys	59.0	0.0	.	633	128.0	77.0	.	NM_181876	A8MSY7|B7Z3Y1|Q7Z4V7|Q8NEC4|Q9H3G7	Missense_Mutation	SNP	ENST00000382599.4	hg19		.	.	.	.	.	.	.	.	.	.	T	16.16	3.044169	0.55110	.	.	ENSG00000074211	ENST00000335585;ENST00000506140;ENST00000515571;ENST00000382599;ENST00000507294	T;T;T;T;T	0.32753	1.44;1.44;1.44;1.44;1.44	4.11	1.24	0.21308	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.286388	0.35320	N	0.003299	T	0.59636	0.2208	H	0.94222	3.51	0.80722	D	1	D;D;D;D	0.67145	0.994;0.987;0.996;0.977	D;D;D;P	0.67900	0.933;0.926;0.954;0.87	T	0.66228	-0.5976	10	0.87932	D	0	.	9.1465	0.36937	0.3036:0.0:0.0:0.6964	.	288;295;278;295	B7Z3Y1;Q9Y2T4;Q9Y2T4-3;Q9Y2T4-2	.;2ABG_HUMAN;.;.	C	295;288;278;295;288	ENSP00000335083:Y295C;ENSP00000423649:Y288C;ENSP00000422374:Y278C;ENSP00000372042:Y295C;ENSP00000425247:Y288C	ENSP00000335083:Y295C	Y	-	2	0	PPP2R2C	6386266	1.000000	0.71417	0.995000	0.50966	0.715000	0.41141	5.431000	0.66507	0.586000	0.29626	0.402000	0.26972	TAC	.	.	.	none		0.572	PPP2R2C-001	NOVEL	overlapping_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206889.2	NM_181876		C	6335365	T	C	6335365	3	2	240	1	0	0	0	0	1	0	0	0	12396	1638	57	3	471	3	PPP2R2C	4	6335365	Missense_Mutation	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	4946704	6335365	184818911	23	14676											
ATP10D	57205	hgsc.bcm.edu	37	chr4	47593174	47593174	+	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	ctctcaagaagtggagagggGctggaaagatgaatcaagtg	14	7	15	5	0	2	4	2	1	1	3	3	6	2	5	0	4	0	1	0	4	5	0			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr4:47593174G>T	ENST00000273859.3	+	23	4326	c.4057G>T	c.(4057-4059)Gct>Tct	p.A1353S		NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	1353					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						GTGGAGAGGGGCTGGAAAGAT	0.468																																					p.A1353S		Atlas-SNP	.											.	ATP10D	168	.	0			c.G4057T						PASS	.						107	108	108					4																	47593174		2203	4300	6503	SO:0001583	missense	57205	exon23			AGAGGGGCTGGAA	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.4057G>T	chr4.hg19:g.47593174G>T	ENSP00000273859:p.Ala1353Ser	77.0	0.0	.		90.0	4.0	.	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	hg19	CCDS3476.1	.	.	.	.	.	.	.	.	.	.	G	13.67	2.305821	0.40795	.	.	ENSG00000145246	ENST00000273859	T	0.38401	1.14	4.62	-2.03	0.07365	.	0.657993	0.13943	N	0.352047	T	0.20981	0.0505	L	0.51422	1.61	0.19775	N	0.999953	B	0.13145	0.007	B	0.08055	0.003	T	0.34576	-0.9823	10	0.09590	T	0.72	-0.9921	1.5641	0.02601	0.337:0.1313:0.3977:0.1341	.	1353	Q9P241	AT10D_HUMAN	S	1353	ENSP00000273859:A1353S	ENSP00000273859:A1353S	A	+	1	0	ATP10D	47287931	0.000000	0.05858	0.000000	0.03702	0.410000	0.31052	-0.016000	0.12613	-0.789000	0.04498	0.460000	0.39030	GCT	.	.	.	none		0.468	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453		T	47593174	G	T	47593174	3	4	240	1	0	0	0	0	1	0	0	0	1118	1203	42	4	4143	4	ATP10D	4	47593174	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	41257809	47593174	143561102	24	14677											
DSPP	1834	hgsc.bcm.edu	37	chr4	88536436	88536436	+	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	agcgatagcagtgacagcagCaacagcagtgacagcagtga	15	4	13	9	1	0	3	0	3	0	0	0	4	0	3	0	0	7	5	0	0	2	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr4:88536436C>T	ENST00000282478.7	+	4	2655	c.2622C>T	c.(2620-2622)agC>agT	p.S874S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S874S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	874	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gtgacagcagcaacagcagtg	0.502																																					p.S874S		Atlas-SNP	.											.	DSPP	174	.	0			c.C2622T						PASS	.						70	85	79					4																	88536436		1641	2936	4577	SO:0001819	synonymous_variant	1834	exon5			CAGCAGCAACAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2622C>T	chr4.hg19:g.88536436C>T		131.0	0.0	.		371.0	30.0	.	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	hg19	CCDS43248.1																																																																																			.	.	.	none		0.502	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		T	88536436	C	T	88536436	2	4	240	1	0	0	0	0	0	0	0	1	4784	709	25	2		2	DSPP	4	88536436	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	40943262	88536436	102617840	25	14678											
TLX3	30012	hgsc.bcm.edu	37	chr5	170736390	170736390	+	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	atggaggcgcccgccagcgcGcagaccccgcacccgcacga	8	1	13	19	7	0	1	0	0	0	1	0	3	0	2	5	2	1	3	5	2	0	0	rs537348276		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr5:170736390G>A	ENST00000296921.5	+	1	103	c.21G>A	c.(19-21)gcG>gcA	p.A7A		NM_021025.2	NP_066305.2	O43711	TLX3_HUMAN	T-cell leukemia homeobox 3	7					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)			CCGCCAGCGCGCAGACCCCGC	0.771			T	BCL11B	T-ALL																																p.A7A	Esophageal Squamous(33;43 807 3116 3348 30094)	Atlas-SNP	.		Dom	yes		5	5q35.1	30012	"T-cell leukemia, homeobox 3 (HOX11L2)"		L	.	TLX3	23	.	0			c.G21A						PASS	.						11	13	12					5																	170736390		2176	4263	6439	SO:0001819	synonymous_variant	30012	exon1			CAGCGCGCAGACC	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.21G>A	chr5.hg19:g.170736390G>A		0.0	0.0	.		45.0	21.0	.	NM_021025	Q96AD3	Silent	SNP	ENST00000296921.5	hg19	CCDS34288.1																																																																																			.	.	.	none		0.771	TLX3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372076.3			A	170736390	G	A	170736390	2	1	240	1	0	0	0	0	0	0	0	1	15974	1074	38	1		1	TLX3	5	170736390	Silent	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10		170736390	10178870	26	14679											
OR10C1	442194	hgsc.bcm.edu	37	chr6	29408232	29408232	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctacagctagctgggtcggCgtgggcctgtggggtgctgg	3	10	19	9	2	1	0	0	0	1	0	2	0	1	0	1	6	4	3	1	6	2	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr6:29408232C>T	ENST00000444197.2	+	1	1150	c.440C>T	c.(439-441)gCg>gTg	p.A147V	OR11A1_ENST00000377149.1_Intron	NM_013941.3	NP_039229.3	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C, member 1 (gene/pseudogene)	147						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						GCTGGGTCGGCGTGGGCCTGT	0.622																																					p.A147V		Atlas-SNP	.											.	OR10C1	58	.	0			c.C440T						PASS	.						80	91	87					6																	29408232		1509	2709	4218	SO:0001583	missense	442194	exon1			GGTCGGCGTGGGC		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.440C>T	chr6.hg19:g.29408232C>T	ENSP00000419119:p.Ala147Val	26.0	0.0	.		61.0	4.0	.	NM_013941	Q5SUN7|Q96R18	Missense_Mutation	SNP	ENST00000444197.2	hg19	CCDS34364.1	.	.	.	.	.	.	.	.	.	.	C	14.10	2.434952	0.43224	.	.	ENSG00000206474	ENST00000444197	T	0.34859	1.34	3.53	3.53	0.40419	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38897	N	0.001526	T	0.29028	0.0721	N	0.16708	0.43	0.09310	N	1	D	0.67145	0.996	D	0.67725	0.953	T	0.18650	-1.0330	10	0.87932	D	0	.	14.9009	0.70678	0.0:1.0:0.0:0.0	.	147	Q96KK4	O10C1_HUMAN	V	147	ENSP00000419119:A147V	ENSP00000419119:A147V	A	+	2	0	OR10C1	29516211	0.000000	0.05858	0.027000	0.17364	0.033000	0.12548	-1.281000	0.02802	1.805000	0.52779	0.508000	0.49915	GCG	.	.	.	none		0.622	OR10C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076415.2			T	29408232	C	T	29408232	3	4	240	1	0	0	0	0	1	0	0	0	10905	768	27	1	442	1	OR10C1	6	29408232	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10		29408232	141706835	27	14680											
HLA-C	3107	hgsc.bcm.edu	37	chr6	31239552	31239552	+	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	cgctgtcgaaccgcacgaacTgcgtgtcgtccacgtagccc	7	7	11	16	7	0	0	0	0	0	0	3	2	1	0	3	0	4	3	3	0	3	1	rs41545521		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr6:31239552T>A	ENST00000376228.5	-	2	181	c.167A>T	c.(166-168)cAg>cTg	p.Q56L	HLA-C_ENST00000383329.3_Missense_Mutation_p.Q56L	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	56	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						CCGCACGAACTGCGTGTCGTC	0.701																																					p.Q56L		Atlas-SNP	.											HLA-C_ENST00000383329,colon,carcinoma,0,2	HLA-C	92	.	0			c.A167T						PASS	.						40	38	38					6																	31239552		1511	2707	4218	SO:0001583	missense	3107	exon2			ACGAACTGCGTGT	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.167A>T	chr6.hg19:g.31239552T>A	ENSP00000365402:p.Gln56Leu	14.0	1.0	.		174.0	11.0	.	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	hg19	CCDS34393.1	.	.	.	.	.	.	.	.	.	.	-	12.33	1.906500	0.33628	.	.	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.00014	9.2;9.2	2.81	2.81	0.32909	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	1.195700	0.06728	N	0.776207	T	0.00178	0.0005	M	0.90542	3.125	0.26353	N	0.977175	D;D;D;D	0.67145	0.978;0.978;0.978;0.996	D;D;D;D	0.79108	0.98;0.98;0.98;0.992	T	0.41592	-0.9500	10	0.66056	D	0.02	.	7.4347	0.27148	0.0:0.0:0.0:1.0	.	56;56;56;56	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	L	56;56;56;93	ENSP00000365402:Q56L;ENSP00000372819:Q56L	ENSP00000365402:Q56L	Q	-	2	0	HLA-C	31347531	0.000000	0.05858	1.000000	0.80357	0.175000	0.22909	-0.001000	0.12947	1.536000	0.49237	0.254000	0.18369	CAG	.	.	.	alt		0.701	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117		A	31239552	T	A	31239552	3	1	240	1	0	0	0	0	1	0	0	0	7204	1580	55	5	961	5	HLA-C	6	31239552	Missense_Mutation	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	1831320	31239552	139875515	28	14681											
CD2AP	23607	hgsc.bcm.edu	37	chr6	47471115	47471115	+	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	tgtgaaaaagctacaggaggAagggtggctggaaggagaac	15	5	17	4	0	0	2	0	1	0	1	0	6	0	5	0	6	3	2	0	6	6	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr6:47471115A>T	ENST00000359314.5	+	2	560	c.104A>T	c.(103-105)gAa>gTa	p.E35V		NM_012120.2	NP_036252.1	Q9Y5K6	CD2AP_HUMAN	CD2-associated protein	35	Interaction with ANLN and localization to the midbody.|SH3 1; truncated. {ECO:0000255|PROSITE- ProRule:PRU00192}.				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)			CTACAGGAGGAAGGGTGGCTG	0.378																																					p.E35V		Atlas-SNP	.											CD2AP,NS,carcinoma,0,1	CD2AP	43	.	0			c.A104T						PASS	.						139	134	135					6																	47471115		2203	4300	6503	SO:0001583	missense	23607	exon2			AGGAGGAAGGGTG	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.104A>T	chr6.hg19:g.47471115A>T	ENSP00000352264:p.Glu35Val	51.0	0.0	.		384.0	30.0	.	NM_012120	A6NL34|Q5VYA3|Q9UG97	Missense_Mutation	SNP	ENST00000359314.5	hg19	CCDS34472.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.024553	0.75390	.	.	ENSG00000198087	ENST00000359314	T	0.54071	0.59	4.68	4.68	0.58851	Src homology-3 domain (4);	0.560263	0.21123	N	0.079786	T	0.63698	0.2533	M	0.75264	2.295	0.48452	D	0.999652	D	0.89917	1.0	D	0.83275	0.996	T	0.64935	-0.6290	10	0.38643	T	0.18	-17.8438	14.1476	0.65360	1.0:0.0:0.0:0.0	.	35	Q9Y5K6	CD2AP_HUMAN	V	35	ENSP00000352264:E35V	ENSP00000352264:E35V	E	+	2	0	CD2AP	47579074	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.530000	0.73816	1.735000	0.51646	0.533000	0.62120	GAA	.	.	.	none		0.378	CD2AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040817.2			T	47471115	A	T	47471115	3	4	240	1	0	0	0	0	1	0	0	0	2996	246	9	5	110	5	CD2AP	6	47471115	Missense_Mutation	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	16231563	47471115	123643952	29	14682											
C6orf138	442213	hgsc.bcm.edu	37	chr6	48036108	48036108	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagctggcttttggactggTccagggggaaaaggctgctg	8	9	17	7	0	0	1	0	0	0	1	1	3	1	3	1	6	2	4	1	6	2	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr6:48036108T>C	ENST00000339488.4	-	1	317	c.284A>G	c.(283-285)gAc>gGc	p.D95G	PTCHD4_ENST00000543600.1_Missense_Mutation_p.D78G	NM_001013732.3	NP_001013754.3	Q6ZW05	PTHD4_HUMAN	patched domain containing 4	95						integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)										TTTGGACTGGTCCAGGGGGAA	0.627																																					p.D95G		Atlas-SNP	.											.	.	.	.	0			c.A284G						PASS	.						72	79	77					6																	48036108		1946	4139	6085	SO:0001583	missense	442213	exon1			GACTGGTCCAGGG		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.284A>G	chr6.hg19:g.48036108T>C	ENSP00000341914:p.Asp95Gly	41.0	0.0	.		377.0	19.0	.	NM_001013732	B0QZ29|B4DRK3|Q5T884	Missense_Mutation	SNP	ENST00000339488.4	hg19	CCDS34473.2	.	.	.	.	.	.	.	.	.	.	T	18.19	3.569479	0.65765	.	.	ENSG00000244694	ENST00000339488;ENST00000543600	D;T	0.92397	-3.03;0.62	4.88	4.88	0.63580	.	0.103230	0.64402	D	0.000006	D	0.91088	0.7195	L	0.51422	1.61	0.80722	D	1	P;D	0.67145	0.826;0.996	B;P	0.57620	0.438;0.824	D	0.90227	0.4276	10	0.34782	T	0.22	.	14.4665	0.67488	0.0:0.0:0.0:1.0	.	95;78	Q6ZW05;B0QZ29	CF138_HUMAN;.	G	95;78	ENSP00000341914:D95G;ENSP00000439864:D78G	ENSP00000341914:D95G	D	-	2	0	C6orf138	48144067	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.602000	0.82796	1.813000	0.52934	0.460000	0.39030	GAC	.	.	.	none		0.627	PTCHD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317987.2	NM_001013732		C	48036108	T	C	48036108	3	2	240	1	0	0	0	0	1	0	0	0	2334	1667	58	3	2268	3	C6orf138	6	48036108	Missense_Mutation	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	564993	48036108	123078959	30	14683											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51890186	51890186	+	Frame_Shift_Del	DEL	C	C	-																															cttatgaaaagagtgcaattCccctgacactcgctggttag																										TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr6:51890186delC	ENST00000371117.3	-	32	4697	c.4422delG	c.(4420-4422)gggfs	p.G1474fs	PKHD1_ENST00000340994.4_Frame_Shift_Del_p.G1474fs	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1474	IPT/TIG 9.				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)					GAGTGCAATTCCCCTGACACT	0.542																																					p.N1475fs		Atlas-Indel,Pindel	.											.	PKHD1	927	.	0			c.4423delA						PASS	.						57	52	54					6																	51890186		2203	4300	6503	SO:0001589	frameshift_variant	5314	exon32			.	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.4422delG	chr6.hg19:g.51890186delC	ENSP00000360158:p.Gly1474fs	40.0	0.0	0		239.0	53.0	0.221757	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Frame_Shift_Del	DEL	ENST00000371117.3	hg19	CCDS4935.1																																																																																			.	.	.	none		0.542	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		-	51890186	C	-	51890186	7	5	240	1	0	1	0	1	0	0	0	0	11978	842	30	0	7985	0	PKHD1	6	51890186	Frame_Shift_Del	DEL	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	3854078	51890186	119224881	31	14684											
LRRC1	55227	hgsc.bcm.edu	37	chr6	53764574	53764575	+	Frame_Shift_Del	DEL	TT	TT	-																															aatctgaagaacctgctgtgTttagatgtctctgaaaacag																								rs550591899		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr6:53764574_53764575delTT	ENST00000370888.1	+	8	949_950	c.672_673delTT	c.(670-675)tgtttafs	p.L225fs		NM_018214.4	NP_060684.4	Q9BTT6	LRRC1_HUMAN	leucine rich repeat containing 1	225						cytoplasm (GO:0005737)|membrane (GO:0016020)				cervix(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)		ACCTGCTGTGTTTAGATGTCTC	0.391																																					p.224_224del		Atlas-Indel,Pindel	.											.	LRRC1	59	.	0			c.671_672del						PASS	.																																			SO:0001589	frameshift_variant	55227	exon8			.	AF332199	CCDS4953.2	6p12.2	2014-07-30	2003-11-19		ENSG00000137269	ENSG00000137269			14307	protein-coding gene	gene with protein product		608195	"leucine-rich repeat-containing 1"				Standard	NM_018214		Approved	dJ523E19.1, LANO, FLJ10775, FLJ11834	uc003pcd.1	Q9BTT6	OTTHUMG00000014885	ENST00000370888.1:c.672_673delTT	chr6.hg19:g.53764574_53764575delTT	ENSP00000359925:p.Leu225fs	83.0	0.0	0		409.0	32.0	0.0782396	NM_018214	Q5TGN3|Q9HAC0|Q9NVF1	Frame_Shift_Del	DEL	ENST00000370888.1	hg19	CCDS4953.2																																																																																			.	.	.	none		0.391	LRRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040970.2	NM_025168		-	53764575	TT	-	53764574	7	5	240	1	0	1	0	1	0	0	0	0	8973	1731	60	0	702	0	LRRC1	6	53764574	Frame_Shift_Del	DEL	TT	TCGA-Q2-A5QZ-01A-11D-A28G-10	1874388	53764574	117350493	32	14685											
ZNF451	26036	hgsc.bcm.edu	37	chr6	56989656	56989656	+	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	agagaagaatagagcattcaGagtatgtgctattttaattg	15	13	10	3	0	1	4	1	0	0	4	1	5	1	4	0	0	2	3	0	0	6	7			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr6:56989656G>A	ENST00000370706.4	+	4	555	c.311G>A	c.(310-312)aGa>aAa	p.R104K	RP11-203B9.4_ENST00000592038.1_RNA|RP11-203B9.4_ENST00000588811.1_RNA|RP11-203B9.4_ENST00000416069.2_RNA|RP11-203B9.4_ENST00000585792.1_RNA|RP11-203B9.4_ENST00000592500.1_RNA|RP11-203B9.4_ENST00000591553.1_RNA|RP11-203B9.4_ENST00000587815.1_RNA|ZNF451_ENST00000491832.2_Splice_Site_p.R104K|ZNF451_ENST00000357489.3_Splice_Site_p.R104K|RP11-203B9.4_ENST00000586432.1_RNA|RP11-203B9.4_ENST00000586668.1_RNA|RP11-203B9.4_ENST00000586053.1_RNA	NM_001031623.2	NP_001026794.1	Q9Y4E5	ZN451_HUMAN	zinc finger protein 451	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)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			AGAGCATTCAGAGTATGTGCT	0.289																																					p.R104K		Atlas-SNP	.											.	ZNF451	181	.	0			c.G311A						PASS	.						35	33	34					6																	56989656		2203	4298	6501	SO:0001630	splice_region_variant	26036	exon4			CATTCAGAGTATG	AB011148	CCDS4960.1, CCDS43477.1, CCDS59026.1	6p12.1	2012-08-08			ENSG00000112200	ENSG00000112200		"Zinc fingers, C2H2-type"	21091	protein-coding gene	gene with protein product		615708				9628581	Standard	NM_001031623		Approved	KIAA0576, COASTER, dJ417I1.1, KIAA1702	uc003pdm.2	Q9Y4E5	OTTHUMG00000014916	ENST00000370706.4:c.312+1G>A	chr6.hg19:g.56989656G>A		102.0	0.0	.		253.0	16.0	.	NM_001031623	Q5VVE9|Q5VVF1|Q86YE4|Q8N380|Q8TD15|Q9C0G1|Q9NQM1	Missense_Mutation	SNP	ENST00000370706.4	hg19	CCDS43477.1	.	.	.	.	.	.	.	.	.	.	G	10.81	1.456326	0.26161	.	.	ENSG00000112200	ENST00000510483;ENST00000370706;ENST00000357489;ENST00000491832	T;T;T;T	0.05996	3.36;3.36;3.36;3.36	5.37	5.37	0.77165	.	0.061002	0.64402	D	0.000003	T	0.01156	0.0038	N	0.17082	0.46	0.80722	D	1	B;B;B;B	0.20887	0.049;0.037;0.027;0.037	B;B;B;B	0.15484	0.013;0.008;0.008;0.008	T	0.43360	-0.9396	10	0.06625	T	0.88	-16.7164	7.7021	0.28630	0.2013:0.0:0.7987:0.0	.	104;104;104;104	Q9Y4E5-2;Q9Y4E5;E9PH99;Q4KMR5	.;ZN451_HUMAN;.;.	K	76;104;104;104	ENSP00000427558:R76K;ENSP00000359740:R104K;ENSP00000350083:R104K;ENSP00000421645:R104K	ENSP00000350083:R104K	R	+	2	0	ZNF451	57097615	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	4.870000	0.63035	2.665000	0.90641	0.655000	0.94253	AGA	.	.	.	none		0.289	ZNF451-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041035.2	NM_015555	Missense_Mutation	A	56989656	G	A	56989656	5	1	240	1	0	0	0	0	0	0	1	0	17934	956	33	2	325	2	ZNF451	6	56989656	Splice_Site	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	3225082	56989656	114125411	33	14686											
PHF3	23469	hgsc.bcm.edu	37	chr6	64394128	64394128	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgggaagactgtatctactGctaaagcaggagtgaaacaa	15	8	11	7	0	1	2	0	1	1	1	1	4	1	4	0	2	4	3	0	2	7	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr6:64394128G>A	ENST00000262043.3	+	4	845	c.505G>A	c.(505-507)Gct>Act	p.A169T	PHF3_ENST00000509330.1_Missense_Mutation_p.A169T|PHF3_ENST00000393387.1_Missense_Mutation_p.A169T			Q92576	PHF3_HUMAN	PHD finger protein 3	169					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)			TGTATCTACTGCTAAAGCAGG	0.418																																					p.A169T	GBM(135;136 1820 29512 34071 46235)	Atlas-SNP	.											.	PHF3	191	.	0			c.G505A						PASS	.						176	182	180					6																	64394128		2203	4300	6503	SO:0001583	missense	23469	exon3			TCTACTGCTAAAG	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.505G>A	chr6.hg19:g.64394128G>A	ENSP00000262043:p.Ala169Thr	139.0	0.0	.		233.0	92.0	.	NM_015153	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Missense_Mutation	SNP	ENST00000262043.3	hg19	CCDS4966.1	.	.	.	.	.	.	.	.	.	.	G	7.135	0.580718	0.13686	.	.	ENSG00000118482	ENST00000481385;ENST00000262043;ENST00000494284;ENST00000509330;ENST00000393387;ENST00000514822	T;T;T;T;T	0.41758	2.0;2.31;1.99;0.99;2.31	5.92	2.2	0.27929	.	1.243890	0.06006	N	0.648726	T	0.05686	0.0149	N	0.03608	-0.345	0.09310	N	0.999998	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29941	-0.9995	10	0.21540	T	0.41	-2.6584	2.9393	0.05825	0.1274:0.5534:0.1251:0.1941	.	169;169	Q92576;D6R9X2	PHF3_HUMAN;.	T	81;169;122;169;169;99	ENSP00000425227:A81T;ENSP00000262043:A169T;ENSP00000424078:A122T;ENSP00000422841:A169T;ENSP00000377048:A169T	ENSP00000262043:A169T	A	+	1	0	PHF3	64452087	0.066000	0.20996	0.643000	0.29450	0.707000	0.40811	0.935000	0.28924	0.120000	0.18254	-0.139000	0.14373	GCT	.	.	.	none		0.418	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2			A	64394128	G	A	64394128	3	1	240	1	0	0	0	0	1	0	0	0	11843	1319	46	2	515	2	PHF3	6	64394128	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	7404472	64394128	106720939	34	14687											
UNC93A	54346	hgsc.bcm.edu	37	chr6	167709627	167709627	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaacacacatgcagagaaggCgggaaagcgtggcaaagaca	18	2	13	8	2	0	2	0	0	0	2	0	4	0	3	0	3	3	2	0	3	4	0	rs538293568		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr6:167709627C>T	ENST00000230256.3	+	3	552	c.377C>T	c.(376-378)gCg>gTg	p.A126V	UNC93A_ENST00000366830.2_3'UTR|UNC93A_ENST00000366829.2_Missense_Mutation_p.A126V	NM_018974.3	NP_061847.2	Q86WB7	UN93A_HUMAN	unc-93 homolog A (C. elegans)	126						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	40		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		GCAGAGAAGGCGGGAAAGCGT	0.547													C|||	1	0.000199681	0	0	5008	,	,		22340	0.001		0	False		,,,				2504	0				p.A126V		Atlas-SNP	.											.	UNC93A	66	.	0			c.C377T						PASS	.						224	203	210					6																	167709627		2203	4300	6503	SO:0001583	missense	54346	exon3			AGAAGGCGGGAAA	AJ508812	CCDS5300.1, CCDS47515.1	6q27	2014-05-16	2001-11-28		ENSG00000112494	ENSG00000112494			12570	protein-coding gene	gene with protein product		607995	"unc93 (C.elegans) homolog A"			12381271	Standard	NM_001143947		Approved	dJ366N23.2, dJ366N23.1	uc003qvq.3	Q86WB7	OTTHUMG00000016021	ENST00000230256.3:c.377C>T	chr6.hg19:g.167709627C>T	ENSP00000230256:p.Ala126Val	105.0	0.0	.		270.0	109.0	.	NM_018974	B3KRP5|Q4QQJ4|Q5JZD6	Missense_Mutation	SNP	ENST00000230256.3	hg19	CCDS5300.1	.	.	.	.	.	.	.	.	.	.	C	5.524	0.281564	0.10458	.	.	ENSG00000112494	ENST00000503433;ENST00000230256;ENST00000366829	T;T;T	0.30981	1.51;3.54;3.52	5.53	-3.43	0.04810	Major facilitator superfamily domain, general substrate transporter (1);	1.006790	0.07968	N	0.983528	T	0.04634	0.0126	N	0.17723	0.515	0.09310	N	1	B;B	0.16166	0.016;0.006	B;B	0.13407	0.009;0.009	T	0.37244	-0.9714	10	0.25106	T	0.35	-1.2474	4.3328	0.11071	0.3325:0.2722:0.0:0.3953	.	126;126	Q4QQJ4;Q86WB7	.;UN93A_HUMAN	V	126	ENSP00000421484:A126V;ENSP00000230256:A126V;ENSP00000355794:A126V	ENSP00000230256:A126V	A	+	2	0	UNC93A	167629617	0.020000	0.18652	0.000000	0.03702	0.018000	0.09664	1.103000	0.31062	-1.274000	0.02421	-0.890000	0.02929	GCG	.	.	.	none		0.547	UNC93A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043125.2	NM_018974		T	167709627	C	T	167709627	3	4	240	1	0	0	0	0	1	0	0	0	17008	768	27	1	387	1	UNC93A	6	167709627	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	103315499	167709627	3405440	35	14688											
TRA2A	29896	hgsc.bcm.edu	37	chr7	23547073	23547073	+	Missense_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	catgtagatgcctggtgttgGtgtgtgcgctctcttggtta	4	16	14	7	1	1	1	0	0	1	1	2	1	1	1	1	3	2	4	1	3	2	4			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr7:23547073G>A	ENST00000297071.4	-	5	823	c.607C>T	c.(607-609)Cca>Tca	p.P203S	TRA2A_ENST00000474586.1_5'UTR|TRA2A_ENST00000538367.1_Missense_Mutation_p.P102S|TRA2A_ENST00000392502.4_Missense_Mutation_p.P102S	NM_013293.3	NP_037425.1	Q13595	TRA2A_HUMAN	transformer 2 alpha homolog (Drosophila)	203	Linker.				mRNA splicing, via spliceosome (GO:0000398)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	10						CCTGGTGTTGGTGTGTGCGCT	0.413																																					p.P203S	Pancreas(121;2137 2973 46590)	Atlas-SNP	.											.	TRA2A	29	.	0			c.C607T						PASS	.						249	237	241					7																	23547073		2203	4300	6503	SO:0001583	missense	29896	exon5			GTGTTGGTGTGTG	U53209	CCDS5383.1, CCDS64609.1, CCDS75569.1	7p15.3	2014-02-12			ENSG00000164548	ENSG00000164548		"RNA binding motif (RRM) containing"	16645	protein-coding gene	gene with protein product		602718				8799144, 9546399	Standard	XM_005249725		Approved	htra-2-alpha, tra2a, AWMS1	uc003swi.3	Q13595	OTTHUMG00000128459	ENST00000297071.4:c.607C>T	chr7.hg19:g.23547073G>A	ENSP00000297071:p.Pro203Ser	40.0	0.0	.		102.0	37.0	.	NM_013293	B4DUA9	Missense_Mutation	SNP	ENST00000297071.4	hg19	CCDS5383.1	.	.	.	.	.	.	.	.	.	.	G	34	5.300909	0.95601	.	.	ENSG00000164548	ENST00000297071;ENST00000392502;ENST00000538367	T;T;T	0.74106	-0.81;-0.81;-0.81	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.87293	0.6141	M	0.88906	2.99	0.80722	D	1	D	0.55800	0.973	P	0.58577	0.841	D	0.88826	0.3302	10	0.59425	D	0.04	-12.1484	19.5178	0.95171	0.0:0.0:1.0:0.0	.	203	Q13595	TRA2A_HUMAN	S	203;102;102	ENSP00000297071:P203S;ENSP00000376290:P102S;ENSP00000441116:P102S	ENSP00000297071:P203S	P	-	1	0	TRA2A	23513598	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.831000	0.99420	2.615000	0.88500	0.650000	0.86243	CCA	.	.	.	none		0.413	TRA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250257.1	NM_013293		A	23547073	G	A	23547073	3	1	240	1	0	0	0	0	1	0	0	0	16445	1261	44	2	257	2	TRA2A	7	23547073	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10		23547073	135591590	36	14689											
KIAA1324L	222223	hgsc.bcm.edu	37	chr7	86577110	86577110	+	Frame_Shift_Del	DEL	A	A	-																															catgaatgttgcgatgttagAaaatcctgccggcaattcat																								rs536741266		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr7:86577110delA	ENST00000450689.2	-	3	624	c.439delT	c.(439-441)tctfs	p.S147fs	KIAA1324L_ENST00000444627.1_Frame_Shift_Del_p.S147fs|KIAA1324L_ENST00000416314.1_Intron	NM_001142749.2	NP_001136221.1	A8MWY0	K132L_HUMAN	KIAA1324-like	147						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(14)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44	Esophageal squamous(14;0.0058)					GCGATGTTAGAAAATCCTGCC	0.473																																					p.S147fs		Atlas-Indel,Pindel	.											.	KIAA1324L	225	.	0			c.440delC						PASS	.						124	101	108					7																	86577110		692	1591	2283	SO:0001589	frameshift_variant	222223	exon3			.	AK055902	CCDS34677.1, CCDS47632.1, CCDS34677.2	7q21.12	2008-09-18			ENSG00000164659	ENSG00000164659			21945	protein-coding gene	gene with protein product	"EIG121-like"	614048					Standard	NM_001142749		Approved	FLJ31340, EIG121L	uc011kha.2	A8MWY0	OTTHUMG00000153995	ENST00000450689.2:c.439delT	chr7.hg19:g.86577110delA	ENSP00000413445:p.Ser147fs	73.0	0.0	0		178.0	64.0	0.359551	NM_001142749	A4D1C9|B4DJV3|Q17RI6|Q96DP2	Frame_Shift_Del	DEL	ENST00000450689.2	hg19	CCDS47632.1																																																																																			.	.	.	none		0.473	KIAA1324L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333372.3	NM_152748		-	86577110	A	-	86577110	7	5	240	1	0	1	0	1	0	0	0	0	8231	246	9	0	2730	0	KIAA1324L	7	86577110	Frame_Shift_Del	DEL	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	63030037	86577110	72561553	37	14690											
ARPC1B	10095	hgsc.bcm.edu	37	chr7	98990335	98990335	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgttcacctatgacgccgcCgcggggatgctgagcttcgg	5	9	14	13	5	1	2	1	2	0	0	2	3	1	3	3	3	2	3	3	3	1	3	rs530272604	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr7:98990335C>T	ENST00000451682.1	+	10	1134	c.825C>T	c.(823-825)gcC>gcT	p.A275A	ARPC1B_ENST00000252725.5_Silent_p.A275A|PDAP1_ENST00000496335.1_5'UTR			O15143	ARC1B_HUMAN	actin related protein 2/3 complex, subunit 1B, 41kDa	275					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(2)|lung(1)	11	all_cancers(62;3.49e-09)|all_epithelial(64;2.57e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			ATGACGCCGCCGCGGGGATGC	0.697													C|||	4	0.000798722	0.003	0	5008	,	,		13061	0		0	False		,,,				2504	0				p.A275A		Atlas-SNP	.											.	ARPC1B	41	.	0			c.C825T						PASS	.						4	5	4					7																	98990335		1777	3378	5155	SO:0001819	synonymous_variant	10095	exon8			CGCCGCCGCGGGG	AF006084	CCDS5661.1	7q22.1	2013-03-14	2002-08-29		ENSG00000130429	ENSG00000130429		"Actin related protein 2/3 complex subunits", "WD repeat domain containing"	704	protein-coding gene	gene with protein product	"ARP2/3 protein complex subunit p41", "actin related protein 2/3 complex, subunit 1A (41 kD)"	604223	"actin related protein 2/3 complex, subunit 1B (41 kD)"			9230079, 9359840	Standard	NM_005720		Approved	ARC41, p40-ARC, p41-ARC	uc003upz.3	O15143	OTTHUMG00000154552	ENST00000451682.1:c.825C>T	chr7.hg19:g.98990335C>T		5.0	0.0	.		147.0	84.0	.	NM_005720	Q9BU00	Silent	SNP	ENST00000451682.1	hg19	CCDS5661.1																																																																																			.	.	.	none		0.697	ARPC1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335894.1	NM_005720		T	98990335	C	T	98990335	2	4	240	1	0	0	0	0	0	0	0	1	970	639	23	1		1	ARPC1B	7	98990335	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	12413225	98990335	60148328	38	14691											
OPN1SW	611	hgsc.bcm.edu	37	chr7	128415147	128415147	+	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	aagcggaagttgccgaagggCttacagatgacaatgtagcg	13	7	14	7	3	0	2	0	1	0	1	0	4	0	3	1	2	4	3	1	2	6	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr7:128415147C>T	ENST00000249389.2	-	2	413	c.414G>A	c.(412-414)aaG>aaA	p.K138K		NM_001708.2	NP_001699.1	P03999	OPSB_HUMAN	opsin 1 (cone pigments), short-wave-sensitive	138					phototransduction (GO:0007602)|phototransduction, visible light (GO:0007603)|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)|receptor activity (GO:0004872)			NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|stomach(1)	19						TGCCGAAGGGCTTACAGATGA	0.547																																					p.K138K		Atlas-SNP	.											.	OPN1SW	52	.	0			c.G414A						PASS	.						96	75	82					7																	128415147		2203	4300	6503	SO:0001819	synonymous_variant	611	exon2			GAAGGGCTTACAG	U53874	CCDS5806.1	7q31.3-q32	2013-01-08	2008-04-16		ENSG00000128617	ENSG00000128617		"GPCR / Class A : Opsin receptors"	1012	protein-coding gene	gene with protein product	"color blindness, tritan", "blue-sensitive opsin"	613522	"blue cone photoreceptor pigment"	BCP		2937147, 8270261	Standard	NM_001708		Approved	BOP, CBT	uc003vnt.4	P03999	OTTHUMG00000158311	ENST00000249389.2:c.414G>A	chr7.hg19:g.128415147C>T		62.0	0.0	.		197.0	54.0	.	NM_001708	Q13877	Silent	SNP	ENST00000249389.2	hg19	CCDS5806.1																																																																																			.	.	.	none		0.547	OPN1SW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350655.1	NM_001708		T	128415147	C	T	128415147	2	4	240	1	0	0	0	0	0	0	0	1	10887	796	28	2		2	OPN1SW	7	128415147	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	29424812	128415147	30723516	39	14692											
AGAP3	116988	hgsc.bcm.edu	37	chr7	150839014	150839014	+	Missense_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	agtcgtttgaatttgtggtgGtgtccctcactgggcagacg	6	13	14	8	2	1	2	1	1	0	1	3	2	2	2	1	3	0	2	1	3	1	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr7:150839014G>A	ENST00000463381.1	+	12	1337	c.841G>A	c.(841-843)Gtg>Atg	p.V281M	AGAP3_ENST00000397238.2_Missense_Mutation_p.V612M	NM_001281300.1	NP_001268229.1	Q96P47	AGAP3_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 3	576	Small GTPase-like.				cellular response to reactive oxygen species (GO:0034614)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein import into nucleus, translocation (GO:0000060)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|liver(2)|lung(9)|ovary(2)|prostate(3)|urinary_tract(1)	28						ATTTGTGGTGGTGTCCCTCAC	0.612																																					p.V612M		Atlas-SNP	.											.	AGAP3	121	.	0			c.G1834A						PASS	.						94	112	106					7																	150839014		2150	4240	6390	SO:0001583	missense	116988	exon14			GTGGTGGTGTCCC	AF413079	CCDS43681.1, CCDS55185.1, CCDS64802.1	7q36.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000133612	ENSG00000133612		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16923	protein-coding gene	gene with protein product			"centaurin, gamma 3"	CENTG3			Standard	NM_001042535		Approved		uc003wjg.1	Q96P47	OTTHUMG00000158724	ENST00000463381.1:c.841G>A	chr7.hg19:g.150839014G>A	ENSP00000418016:p.Val281Met	88.0	0.0	.		327.0	124.0	.	NM_031946	B3KNZ8|E9PAL8|Q59EN0|Q96RK3	Missense_Mutation	SNP	ENST00000463381.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.6|24.6	4.553104|4.553104	0.86127|0.86127	.|.	.|.	ENSG00000133612|ENSG00000133612	ENST00000463381;ENST00000397232;ENST00000397238;ENST00000335355|ENST00000461065	T;T|.	0.19394|.	2.15;2.15|.	4.24|4.24	4.24|4.24	0.50183|0.50183	Pleckstrin homology-type (1);Pleckstrin homology domain (3);|.	0.000000|.	0.64402|.	D|.	0.000008|.	T|.	0.74558|.	0.3732|.	M|M	0.75085|0.75085	2.285|2.285	0.80722|0.80722	D|D	1|1	D;D;D;P|.	0.89917|.	1.0;0.999;0.999;0.95|.	D;D;D;P|.	0.97110|.	1.0;0.981;0.964;0.755|.	T|.	0.75977|.	-0.3127|.	10|.	0.72032|.	D|.	0.01|.	.|.	16.1835|16.1835	0.81929|0.81929	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	576;111;612;281|.	Q96P47;E7ETI2;Q96P47-4;B3KNZ8|.	AGAP3_HUMAN;.;.;.|.	M|X	281;111;612;576|104	ENSP00000418016:V281M;ENSP00000380413:V612M|.	ENSP00000334157:V576M|.	V|W	+|+	1|3	0|0	AGAP3|AGAP3	150469947|150469947	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	7.458000|7.458000	0.80787|0.80787	2.346000|2.346000	0.79739|0.79739	0.655000|0.655000	0.94253|0.94253	GTG|TGG	.	.	.	none		0.612	AGAP3-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000351909.2	NM_031946		A	150839014	G	A	150839014	3	1	240	1	0	0	0	0	1	0	0	0	369	1261	44	2	1955	2	AGAP3	7	150839014	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	22423867	150839014	8299649	40	14693											
RHEB	6009	hgsc.bcm.edu	37	chr7	151188050	151188050	+	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	gttttctatggttggatcgtAggagtccacaaattggcctt	8	15	11	7	1	1	0	0	0	1	0	3	2	2	2	2	4	0	3	2	4	3	7			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr7:151188050A>T	ENST00000262187.5	-	2	515	c.103T>A	c.(103-105)Tac>Aac	p.Y35N	RHEB_ENST00000496004.1_5'UTR|RHEB_ENST00000472642.1_5'UTR	NM_005614.3	NP_005605.1	Q15382	RHEB_HUMAN	Ras homolog enriched in brain	35					cell cycle arrest (GO:0007050)|insulin receptor signaling pathway (GO:0008286)|positive regulation of TOR signaling (GO:0032008)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|spliceosomal complex (GO:0005681)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)	p.Y35N(1)		breast(3)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)	14			OV - Ovarian serous cystadenocarcinoma(82;0.00306)	UCEC - Uterine corpus endometrioid carcinoma (81;0.174)		GTTGGATCGTAGGAGTCCACA	0.358																																					p.Y35N	Pancreas(98;671 892 8111 15140 36556 39178 39939 44184)	Atlas-SNP	.											RHEB,NS,carcinoma,0,3	RHEB	30	.	1	Substitution - Missense(1)	kidney(1)	c.T103A						PASS	.						103	100	101					7																	151188050		2203	4300	6503	SO:0001583	missense	6009	exon2			GATCGTAGGAGTC	D78132	CCDS5927.1	7q36	2014-05-09	2003-07-14	2003-07-14	ENSG00000106615	ENSG00000106615			10011	protein-coding gene	gene with protein product		601293	"Ras homolog enriched in brain 2"	RHEB2		8661031	Standard	NM_005614		Approved		uc003wkh.1	Q15382	OTTHUMG00000157330	ENST00000262187.5:c.103T>A	chr7.hg19:g.151188050A>T	ENSP00000262187:p.Tyr35Asn	48.0	0.0	.		87.0	5.0	.	NM_005614	B3KWN6|D3DX13|Q53Y56|Q99444	Missense_Mutation	SNP	ENST00000262187.5	hg19	CCDS5927.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.708820	0.89018	.	.	ENSG00000106615	ENST00000262187	T	0.81247	-1.47	5.42	5.42	0.78866	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.91841	0.7418	M	0.93283	3.4	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93659	0.6980	10	0.87932	D	0	.	13.3975	0.60863	1.0:0.0:0.0:0.0	.	35	Q15382	RHEB_HUMAN	N	35	ENSP00000262187:Y35N	ENSP00000262187:Y35N	Y	-	1	0	RHEB	150818983	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.143000	0.89621	2.051000	0.60960	0.533000	0.62120	TAC	.	.	.	none		0.358	RHEB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348468.2	NM_005614		T	151188050	A	T	151188050	3	4	240	1	0	0	0	0	1	0	0	0	13341	420	15	5	479	5	RHEB	7	151188050	Missense_Mutation	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	349036	151188050	7950613	41	14694											
MLL3	58508	hgsc.bcm.edu	37	chr7	152012386	152012386	+	Frame_Shift_Del	DEL	T	T	-																															gtctccttgtcctaaggaacTtttttccccacagtaacaaa																										TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr7:152012386delT	ENST00000262189.6	-	4	645	c.427delA	c.(427-429)agtfs	p.S144fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.S144fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	144					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)										CCTAAGGAACTTTTTTCCCCA	0.378																																					p.S143fs		Atlas-Indel,Pindel	.											.	MLL3	1564	.	0			c.428delG						PASS	.						136	126	129					7																	152012386		2203	4300	6503	SO:0001589	frameshift_variant	58508	exon4			.	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.427delA	chr7.hg19:g.152012386delT	ENSP00000262189:p.Ser144fs	87.0	0.0	0		144.0	52.0	0.361111	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	hg19	CCDS5931.1																																																																																			.	.	.	none		0.378	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			-	152012386	T	-	152012386	7	5	240	1	0	1	0	1	0	0	0	0	9629	1609	56	0	14532	0	MLL3	7	152012386	Frame_Shift_Del	DEL	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	824336	152012386	7126277	42	14695											
TRAPPC9	83696	hgsc.bcm.edu	37	chr8	140744445	140744445	+	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	gctgtccgtccaccagcacaTctgtaagggacacgagactg	10	7	11	13	2	1	1	0	0	1	1	3	3	3	2	3	1	1	3	3	1	1	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr8:140744445T>G	ENST00000438773.2	-	22	3189	c.3056A>C	c.(3055-3057)gAt>gCt	p.D1019A	TRAPPC9_ENST00000389328.4_Splice_Site_p.D1117A|TRAPPC9_ENST00000389327.3_Splice_Site_p.D1010A|TRAPPC9_ENST00000522504.1_5'UTR	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	1019					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						CACCAGCACATCTGTAAGGGA	0.677																																					p.D1117A		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.A3350C						PASS	.						13	15	14					8																	140744445		2197	4283	6480	SO:0001630	splice_region_variant	83696	exon22			AGCACATCTGTAA	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.3056-1A>C	chr8.hg19:g.140744445T>G		0.0	0.0	.		27.0	12.0	.	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Missense_Mutation	SNP	ENST00000438773.2	hg19	CCDS55278.1	.	.	.	.	.	.	.	.	.	.	T	17.56	3.420212	0.62622	.	.	ENSG00000167632	ENST00000389328;ENST00000389327;ENST00000438773	.	.	.	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.64360	0.2591	L	0.29908	0.895	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.83275	0.995;0.996	T	0.64241	-0.6454	9	0.39692	T	0.17	.	13.8481	0.63479	0.0:0.0:0.0:1.0	.	1019;1117	Q96Q05;Q96Q05-2	TPPC9_HUMAN;.	A	1117;1010;1019	.	ENSP00000373978:D1010A	D	-	2	0	TRAPPC9	140813627	1.000000	0.71417	0.999000	0.59377	0.853000	0.48598	7.220000	0.78008	1.911000	0.55334	0.533000	0.62120	GAT	.	.	.	none		0.677	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466	Missense_Mutation	G	140744445	T	G	140744445	5	3	240	1	0	0	0	0	0	0	1	0	16477	1449	50	5	398	5	TRAPPC9	8	140744445	Splice_Site	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10		140744445	5619577	43	14696											
FRMPD1	22844	hgsc.bcm.edu	37	chr9	37745145	37745145	+	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	actaaataatgtctctcaagGagacacactagagctccagt	15	9	7	10	0	2	2	1	0	1	2	4	3	3	2	1	1	1	1	1	1	5	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr9:37745145G>A	ENST00000539465.1	+	16	3709	c.3116G>A	c.(3115-3117)gGa>gAa	p.G1039E	FRMPD1_ENST00000377765.3_Missense_Mutation_p.G1039E|RP11-613M10.9_ENST00000540557.1_Intron			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	1039						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)		GTCTCTCAAGGAGACACACTA	0.488																																					p.G1039E		Atlas-SNP	.											.	FRMPD1	237	.	0			c.G3116A						PASS	.						75	81	79					9																	37745145		2202	4299	6501	SO:0001583	missense	22844	exon16			CTCAAGGAGACAC	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.3116G>A	chr9.hg19:g.37745145G>A	ENSP00000444411:p.Gly1039Glu	33.0	0.0	.		47.0	18.0	.	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	hg19	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	G	18.81	3.702580	0.68501	.	.	ENSG00000070601	ENST00000377765;ENST00000539465	T;T	0.07908	3.15;3.15	5.17	3.32	0.38043	.	3.748350	0.00496	N	0.000156	T	0.08358	0.0208	N	0.24115	0.695	0.80722	D	1	B	0.12630	0.006	B	0.15052	0.012	T	0.17592	-1.0364	10	0.46703	T	0.11	-5.6669	7.1991	0.25871	0.0943:0.1842:0.7215:0.0	.	1039	Q5SYB0	FRPD1_HUMAN	E	1039	ENSP00000366995:G1039E;ENSP00000444411:G1039E	ENSP00000366995:G1039E	G	+	2	0	FRMPD1	37735145	0.009000	0.17119	0.861000	0.33841	0.973000	0.67179	0.191000	0.17076	0.557000	0.29117	0.462000	0.41574	GGA	.	.	.	none		0.488	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		A	37745145	G	A	37745145	3	1	240	1	0	0	0	0	1	0	0	0	6064	1174	41	2	3174	2	FRMPD1	9	37745145	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10		37745145	103468286	44	14697											
PRKACG	5568	hgsc.bcm.edu	37	chr9	71628295	71628295	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgggctggtcggcgtagaaGggtgggaagcccacggccat	8	6	18	9	3	0	1	0	0	0	1	1	2	0	2	2	6	1	2	2	6	3	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr9:71628295G>A	ENST00000377276.2	-	1	744	c.714C>T	c.(712-714)ccC>ccT	p.P238P		NM_002732.3	NP_002723.2	P22612	KAPCG_HUMAN	protein kinase, cAMP-dependent, catalytic, gamma	238	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)|carbohydrate metabolic process (GO:0005975)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|male gonad development (GO:0008584)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						CGGCGTAGAAGGGTGGGAAGC	0.597																																					p.P238P	Esophageal Squamous(110;2236 2623 32146)	Atlas-SNP	.											.	PRKACG	65	.	0			c.C714T						PASS	.						70	68	69					9																	71628295		2203	4300	6503	SO:0001819	synonymous_variant	5568	exon1			GTAGAAGGGTGGG	M34182	CCDS6625.1	9q13	2012-10-02			ENSG00000165059	ENSG00000165059	2.7.11.1		9382	protein-coding gene	gene with protein product		176893				2342480, 9598317	Standard	NM_002732		Approved	PKACg	uc004agy.3	P22612	OTTHUMG00000019974	ENST00000377276.2:c.714C>T	chr9.hg19:g.71628295G>A		35.0	0.0	.		96.0	34.0	.	NM_002732	O60850|Q5VZ02|Q86YI1	Silent	SNP	ENST00000377276.2	hg19	CCDS6625.1																																																																																			.	.	.	none		0.597	PRKACG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052559.1			A	71628295	G	A	71628295	2	1	240	1	0	0	0	0	0	0	0	1	12509	987	35	2		2	PRKACG	9	71628295	Silent	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	33883150	71628295	69585136	45	14698											
NIPSNAP3A	25934	hgsc.bcm.edu	37	chr9	107521616	107521616	+	Missense_Mutation	SNP	A	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	acatcgttttcaccactgaaAtagttttctactgaaataca	14	14	4	9	1	2	2	1	2	1	0	3	2	2	2	1	0	2	2	1	0	5	7	rs546236502	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr9:107521616A>C	ENST00000374767.4	+	6	846	c.741A>C	c.(739-741)aaA>aaC	p.K247N		NM_015469.1	NP_056284.1	Q9UFN0	NPS3A_HUMAN	nipsnap homolog 3A (C. elegans)	247						cytoplasm (GO:0005737)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(1)|large_intestine(3)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	8						CACCACTGAAATAGTTTTCTA	0.358																																					p.K247N		Atlas-SNP	.											.	NIPSNAP3A	18	.	0			c.A741C						PASS	.						105	97	100					9																	107521616		2203	4300	6503	SO:0001583	missense	25934	exon6			ACTGAAATAGTTT	BC005935	CCDS6760.1	9q31.3	2003-11-27			ENSG00000136783	ENSG00000136783			23619	protein-coding gene	gene with protein product		608871				12477932	Standard	NM_015469		Approved	DKFZp564D177, FLJ13953, HSPC299, MGC14553		Q9UFN0	OTTHUMG00000020413	ENST00000374767.4:c.741A>C	chr9.hg19:g.107521616A>C	ENSP00000363899:p.Lys247Asn	63.0	0.0	.		85.0	24.0	.	NM_015469	A6NM55|Q5VX32|Q9BRV7|Q9H843|Q9P083	Missense_Mutation	SNP	ENST00000374767.4	hg19	CCDS6760.1	.	.	.	.	.	.	.	.	.	.	A	17.18	3.325054	0.60634	.	.	ENSG00000136783	ENST00000374767	T	0.73047	-0.71	3.97	2.82	0.32997	Dimeric alpha-beta barrel (1);	0.047557	0.85682	D	0.000000	T	0.80166	0.4573	M	0.81239	2.535	0.37125	D	0.901004	D	0.76494	0.999	D	0.71656	0.974	T	0.80739	-0.1248	10	0.87932	D	0	.	4.8972	0.13757	0.6882:0.0:0.3118:0.0	.	247	Q9UFN0	NPS3A_HUMAN	N	247	ENSP00000363899:K247N	ENSP00000363899:K247N	K	+	3	2	NIPSNAP3A	106561437	0.997000	0.39634	1.000000	0.80357	0.978000	0.69477	0.441000	0.21611	0.697000	0.31718	0.482000	0.46254	AAA	.	.	.	none		0.358	NIPSNAP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053484.1	NM_015469		C	107521616	A	C	107521616	3	2	240	1	0	0	0	0	1	0	0	0	10437	98	4	5	763	5	NIPSNAP3A	9	107521616	Missense_Mutation	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	35893321	107521616	33691815	46	14699											
SVEP1	79987	hgsc.bcm.edu	37	chr9	113233740	113233740	+	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	ggctataagtatttctgatgCaagctgaaaggaatacatgg	14	11	11	5	0	1	2	0	2	1	0	1	3	1	3	0	3	3	4	0	3	7	5			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr9:113233740C>A	ENST00000401783.2	-	16	3238	c.2902G>T	c.(2902-2904)Gca>Tca	p.A968S	SVEP1_ENST00000374469.1_Missense_Mutation_p.A945S|SVEP1_ENST00000302728.8_Missense_Mutation_p.A968S|SVEP1_ENST00000467821.1_5'UTR	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	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						ATTTCTGATGCAAGCTGAAAG	0.428																																					p.A968S		Atlas-SNP	.											.	SVEP1	326	.	0			c.G2902T						PASS	.						122	112	115					9																	113233740		1855	4107	5962	SO:0001583	missense	79987	exon16			CTGATGCAAGCTG	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.2902G>T	chr9.hg19:g.113233740C>A	ENSP00000384917:p.Ala968Ser	88.0	0.0	.		152.0	16.0	.	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	C	7.630	0.678635	0.14841	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728	T;T;T	0.78246	-1.01;-1.02;-1.16	5.49	5.49	0.81192	.	0.158375	0.56097	D	0.000024	T	0.56834	0.2012	N	0.08118	0	0.27524	N	0.951309	B;B	0.17268	0.021;0.012	B;B	0.15052	0.012;0.012	T	0.37033	-0.9723	10	0.10902	T	0.67	.	12.9639	0.58473	0.283:0.717:0.0:0.0	.	968;968	E9PBN8;Q4LDE5	.;SVEP1_HUMAN	S	968;945;968	ENSP00000384917:A968S;ENSP00000363593:A945S;ENSP00000304118:A968S	ENSP00000304118:A968S	A	-	1	0	SVEP1	112273561	1.000000	0.71417	0.854000	0.33618	0.607000	0.37147	2.741000	0.47426	2.583000	0.87209	0.650000	0.86243	GCA	.	.	.	none		0.428	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	113233740	C	A	113233740	3	1	240	1	0	0	0	0	1	0	0	0	15432	710	25	4	7945	4	SVEP1	9	113233740	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	5712124	113233740	27979691	47	14700											
CIZ1	25792	hgsc.bcm.edu	37	chr9	130947865	130947865	+	Frame_Shift_Del	DEL	T	T	-																															gaggaggaggtccgggcctgTttctgggggttccgtcctga																										TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr9:130947865delT	ENST00000393608.1	-	5	751	c.549delA	c.(547-549)aaafs	p.K183fs	CIZ1_ENST00000538431.1_Frame_Shift_Del_p.K183fs|CIZ1_ENST00000372938.5_Frame_Shift_Del_p.K183fs|CIZ1_ENST00000325721.8_Frame_Shift_Del_p.K159fs|CIZ1_ENST00000357558.5_Frame_Shift_Del_p.K183fs|CIZ1_ENST00000372948.3_Frame_Shift_Del_p.K183fs|CIZ1_ENST00000372954.1_Frame_Shift_Del_p.K159fs|CIZ1_ENST00000277465.4_Frame_Shift_Del_p.K183fs|CIZ1_ENST00000541172.1_Frame_Shift_Del_p.K82fs|CIZ1_ENST00000476727.2_5'UTR	NM_012127.2	NP_036259.2	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1	183					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						TCCGGGCCTGTTTCTGGGGGT	0.637																																					p.Q214fs		Atlas-Indel,Pindel	.											.	CIZ1	75	.	0			c.640delC						PASS	.						67	68	68					9																	130947865		2203	4300	6503	SO:0001589	frameshift_variant	25792	exon5			.	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.549delA	chr9.hg19:g.130947865delT	ENSP00000377232:p.Lys183fs	45.0	0.0	0		118.0	36.0	0.305085	NM_001257975	A8K9J8|B4E131|B7ZAS8|Q5SYW3|Q5SYW5|Q8WU72|Q9H868|Q9NYM8|Q9UHK4|Q9Y3F9|Q9Y3G0	Frame_Shift_Del	DEL	ENST00000393608.1	hg19	CCDS6894.1																																																																																			.	.	.	none		0.637	CIZ1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054399.1	NM_012127		-	130947865	T	-	130947865	7	5	240	1	0	1	0	1	0	0	0	0	3443	1722	60	0	2199	0	CIZ1	9	130947865	Frame_Shift_Del	DEL	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	17714125	130947865	10265566	48	14701											
SDCCAG3	10807	hgsc.bcm.edu	37	chr9	139302279	139302279	+	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	cacagtgccgtggatttaccTttgcataaattctgctggcc	8	13	9	11	1	1	0	0	0	1	0	1	1	1	1	3	2	4	2	3	2	3	5			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr9:139302279T>G	ENST00000357365.3	-	4	530	c.401A>C	c.(400-402)aAg>aCg	p.K134T	SDCCAG3_ENST00000298537.7_Splice_Site_p.K111T|PMPCA_ENST00000371720.1_5'Flank|SDCCAG3_ENST00000371725.3_Splice_Site_p.K61T|PMPCA_ENST00000399219.3_5'Flank|SDCCAG3_ENST00000461693.1_5'Flank|PMPCA_ENST00000371717.3_5'Flank	NM_001039707.1	NP_001034796.1	Q96C92	SDCG3_HUMAN	serologically defined colon cancer antigen 3	134						cytoplasm (GO:0005737)				NS(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)	16		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.18e-06)|Epithelial(140;9.31e-06)		TGGATTTACCTTTGCATAAAT	0.522																																					p.K134T		Atlas-SNP	.											.	SDCCAG3	41	.	0			c.A401C						PASS	.						117	127	124					9																	139302279		1996	4158	6154	SO:0001630	splice_region_variant	10807	exon4			TTTACCTTTGCAT	AF039688	CCDS6999.2, CCDS43903.1, CCDS43904.1	9q34.3	2010-10-27			ENSG00000165689	ENSG00000165689			10667	protein-coding gene	gene with protein product						9610721	Standard	XM_005266050		Approved	NY-CO-3	uc004chi.3	Q96C92	OTTHUMG00000020928	ENST00000357365.3:c.402+1A>C	chr9.hg19:g.139302279T>G		28.0	0.0	.		43.0	11.0	.	NM_001039707	A6NCP1|O60525|Q5SXN1|Q5SXN2|Q5SXN3|Q5SXN4|Q5SXN8|Q6V704|Q9NVY5	Missense_Mutation	SNP	ENST00000357365.3	hg19	CCDS43904.1	.	.	.	.	.	.	.	.	.	.	T	14.76	2.632253	0.46944	.	.	ENSG00000165689	ENST00000357365;ENST00000298537;ENST00000371725;ENST00000371723	T;T;T;T	0.39406	2.24;2.31;2.29;1.08	5.34	5.34	0.76211	.	0.221148	0.38837	N	0.001555	T	0.58366	0.2117	M	0.63843	1.955	0.42845	D	0.994066	D;D;D	0.76494	0.99;0.997;0.999	P;D;D	0.68353	0.864;0.928;0.957	T	0.59627	-0.7419	10	0.45353	T	0.12	-23.4229	11.7031	0.51581	0.0:0.0:0.0:1.0	.	61;111;134	Q96C92-4;Q96C92-2;Q96C92	.;.;SDCG3_HUMAN	T	134;111;61;84	ENSP00000349929:K134T;ENSP00000298537:K111T;ENSP00000360790:K61T;ENSP00000360788:K84T	ENSP00000298537:K111T	K	-	2	0	SDCCAG3	138422100	1.000000	0.71417	0.628000	0.29241	0.117000	0.20001	4.054000	0.57434	2.012000	0.59069	0.528000	0.53228	AAG	.	.	.	none		0.522	SDCCAG3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055060.2	NM_006643	Missense_Mutation	G	139302279	T	G	139302279	5	3	240	1	0	0	0	0	0	0	1	0	13971	1623	56	5	934	5	SDCCAG3	9	139302279	Splice_Site	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	8354414	139302279	1911152	49	14702											
CUL2	8453	hgsc.bcm.edu	37	chr10	35360197	35360197	+	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	ggcttttattgtcgtcaaaaGtttgttccatgtttcatcaa	9	18	7	7	1	3	0	3	0	0	0	5	0	4	0	1	1	0	4	1	1	4	6			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr10:35360197G>C	ENST00000374748.1	-	3	362	c.49C>G	c.(49-51)Ctt>Gtt	p.L17V	CUL2_ENST00000602371.1_5'UTR|CUL2_ENST00000374742.1_Missense_Mutation_p.L17V|CUL2_ENST00000478044.1_5'UTR|CUL2_ENST00000374749.3_Missense_Mutation_p.L17V|CUL2_ENST00000374751.3_Missense_Mutation_p.L17V|CUL2_ENST00000537177.1_Missense_Mutation_p.L36V|CUL2_ENST00000374746.1_Missense_Mutation_p.L17V			Q13617	CUL2_HUMAN	cullin 2	17					cell cycle arrest (GO:0007050)|cellular response to hypoxia (GO:0071456)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	Cul2-RING ubiquitin ligase complex (GO:0031462)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|VCB complex (GO:0030891)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|prostate(2)|skin(1)|urinary_tract(2)	31						GTCGTCAAAAGTTTGTTCCAT	0.358																																					p.L36V		Atlas-SNP	.											.	CUL2	63	.	0			c.C106G						PASS	.						148	122	131					10																	35360197		2203	4300	6503	SO:0001583	missense	8453	exon2			TCAAAAGTTTGTT	U83410	CCDS7179.1, CCDS73086.1	10p11.2	2011-05-24			ENSG00000108094	ENSG00000108094			2552	protein-coding gene	gene with protein product		603135				8681378	Standard	NM_003591		Approved		uc021ppa.1	Q13617	OTTHUMG00000017950	ENST00000374748.1:c.49C>G	chr10.hg19:g.35360197G>C	ENSP00000363880:p.Leu17Val	116.0	0.0	.		173.0	41.0	.	NM_001198778	B3KT95|B7Z6K8|D3DRY6|G3V1S2|O00200|Q5T2B6|Q9UNF9	Missense_Mutation	SNP	ENST00000374748.1	hg19	CCDS7179.1	.	.	.	.	.	.	.	.	.	.	G	18.26	3.585575	0.66105	.	.	ENSG00000108094	ENST00000374751;ENST00000374748;ENST00000374746;ENST00000374749;ENST00000374742;ENST00000537177;ENST00000421317	T;T;T;T;T;T;T	0.55052	0.54;0.54;0.54;0.54;0.54;0.54;0.54	5.92	4.06	0.47325	Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	0.058793	0.64402	N	0.000001	T	0.65491	0.2696	L	0.58101	1.795	0.80722	D	1	D;D;D	0.71674	0.998;0.997;0.998	D;P;D	0.66497	0.944;0.875;0.923	T	0.67150	-0.5743	10	0.87932	D	0	-7.8946	11.7589	0.51890	0.0663:0.1241:0.8097:0.0	.	17;36;17	Q5T2B5;G3V1S2;Q13617	.;.;CUL2_HUMAN	V	17;17;17;17;17;36;17	ENSP00000363883:L17V;ENSP00000363880:L17V;ENSP00000363878:L17V;ENSP00000363881:L17V;ENSP00000363874:L17V;ENSP00000444856:L36V;ENSP00000414095:L17V	ENSP00000363874:L17V	L	-	1	0	CUL2	35400203	1.000000	0.71417	0.282000	0.24776	0.833000	0.47200	6.391000	0.73208	0.824000	0.34613	0.655000	0.94253	CTT	.	.	.	none		0.358	CUL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047538.1	NM_003591		C	35360197	G	C	35360197	3	2	240	1	0	0	0	0	1	0	0	0	4057	1029	36	4	2268	4	CUL2	10	35360197	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10		35360197	100174550	50	14703											
TET1	80312	hgsc.bcm.edu	37	chr10	70404893	70404893	+	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	acactgcaaaccataaaaacGctatgagctctgttgctact	14	10	6	11	1	1	1	0	1	1	0	1	1	1	1	1	0	6	5	1	0	6	4			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr10:70404893G>T	ENST00000373644.4	+	4	2616	c.2407G>T	c.(2407-2409)Gct>Tct	p.A803S		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	803					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)	p.A803T(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						CCATAAAAACGCTATGAGCTC	0.353																																					p.A803S		Atlas-SNP	.											TET1_ENST00000373644,NS,carcinoma,0,1	TET1	255	.	1	Substitution - Missense(1)	endometrium(1)	c.G2407T						PASS	.						100	100	100					10																	70404893		2203	4300	6503	SO:0001583	missense	80312	exon4			AAAAACGCTATGA	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.2407G>T	chr10.hg19:g.70404893G>T	ENSP00000362748:p.Ala803Ser	102.0	0.0	.		84.0	10.0	.	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	hg19	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	G	14.69	2.609899	0.46527	.	.	ENSG00000138336	ENST00000373644	T	0.08458	3.09	5.92	4.93	0.64822	.	0.759080	0.12137	N	0.496237	T	0.05318	0.0141	L	0.27053	0.805	0.27338	N	0.956599	P	0.44429	0.835	B	0.38056	0.264	T	0.21449	-1.0245	10	0.24483	T	0.36	.	4.6605	0.12639	0.2192:0.0:0.7808:0.0	.	803	Q8NFU7	TET1_HUMAN	S	803	ENSP00000362748:A803S	ENSP00000362748:A803S	A	+	1	0	TET1	70074899	1.000000	0.71417	1.000000	0.80357	0.721000	0.41392	1.045000	0.30341	2.822000	0.97130	0.650000	0.86243	GCT	.	.	.	none		0.353	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		T	70404893	G	T	70404893	3	4	240	1	0	0	0	0	1	0	0	0	15781	1087	38	4	2417	4	TET1	10	70404893	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	35044696	70404893	65129854	51	14704											
C10orf129	142827	hgsc.bcm.edu	37	chr10	96967018	96967018	+	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	ctgccaagaaaattcgctatCaattacgcatgtctaaggcc	13	10	7	11	2	2	1	1	0	1	1	3	1	2	1	2	1	2	2	2	1	7	4			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr10:96967018C>A	ENST00000394005.3	+	3	466	c.457C>A	c.(457-459)Caa>Aaa	p.Q153K	C10orf129_ENST00000341686.3_Missense_Mutation_p.Q153K|C10orf129_ENST00000430183.1_5'UTR			Q6P461	ACSM6_HUMAN		153					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			breast(1)|kidney(2)|lung(1)|pancreas(1)|prostate(1)|skin(1)	7		Colorectal(252;0.083)		Epithelial(162;1.64e-06)|all cancers(201;3.71e-05)		AATTCGCTATCAATTACGCAT	0.468																																					p.Q153K		Atlas-SNP	.											C10orf129_ENST00000341686,NS,carcinoma,0,1	C10orf129	52	.	0			c.C457A						PASS	.						82	76	78					10																	96967018		2203	4300	6503	SO:0001583	missense	142827	exon4			CGCTATCAATTAC																												ENST00000394005.3:c.457C>A	chr10.hg19:g.96967018C>A	ENSP00000377573:p.Gln153Lys	53.0	0.0	.		94.0	20.0	.	NM_207321	A4FU95|A4IF38|Q5VZX2|Q6ZTX1	Missense_Mutation	SNP	ENST00000394005.3	hg19	CCDS7440.2	.	.	.	.	.	.	.	.	.	.	C	6.282	0.420077	0.11928	.	.	ENSG00000173124	ENST00000539707;ENST00000341686;ENST00000394005	T;T	0.41065	1.01;1.01	1.2	0.259	0.15583	AMP-dependent synthetase/ligase (1);	.	.	.	.	T	0.23249	0.0562	N	0.14661	0.345	0.09310	N	0.999999	B	0.02656	0.0	B	0.09377	0.004	T	0.21586	-1.0241	9	0.87932	D	0	.	5.4913	0.16777	0.0:0.7911:0.0:0.2089	.	153	Q6P461	ACSM6_HUMAN	K	179;153;153	ENSP00000340296:Q153K;ENSP00000377573:Q153K	ENSP00000340296:Q153K	Q	+	1	0	C10orf129	96957008	0.001000	0.12720	0.001000	0.08648	0.002000	0.02628	-1.319000	0.02702	0.134000	0.18681	0.579000	0.79373	CAA	.	.	.	none		0.468	C10orf129-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049506.2			A	96967018	C	A	96967018	3	1	240	1	0	0	0	0	1	0	0	0	1595	827	29	4	467	4	C10orf129	10	96967018	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	26562125	96967018	38567729	52	14705											
PDZD7	79955	hgsc.bcm.edu	37	chr10	102783355	102783355	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatcttgtcccccacgcacAggccagcccgctctgcacca	7	7	8	19	2	2	1	0	1	2	0	3	1	3	1	5	1	2	3	5	1	0	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr10:102783355A>G	ENST00000370215.3	-	4	605	c.380T>C	c.(379-381)cTg>cCg	p.L127P	PDZD7_ENST00000470414.1_Missense_Mutation_p.L127P	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)		CCCCACGCACAGGCCAGCCCG	0.657																																					p.L127P		Atlas-SNP	.											.	PDZD7	101	.	0			c.T380C						PASS	.						62	54	57					10																	102783355		2203	4300	6503	SO:0001583	missense	79955	exon4			ACGCACAGGCCAG	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.380T>C	chr10.hg19:g.102783355A>G	ENSP00000359234:p.Leu127Pro	13.0	0.0	.		31.0	13.0	.	NM_001195263	D5FJ77|Q8N321	Missense_Mutation	SNP	ENST00000370215.3	hg19	CCDS31269.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.403886	0.83230	.	.	ENSG00000186862	ENST00000393462;ENST00000370215	T	0.50548	0.74	5.05	5.05	0.67936	PDZ/DHR/GLGF (4);	0.000000	0.64402	D	0.000001	T	0.79581	0.4470	H	0.97315	3.98	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.961	D	0.87162	0.2215	10	0.87932	D	0	.	14.7786	0.69749	1.0:0.0:0.0:0.0	.	127;127	Q9H5P4;Q9H5P4-2	PDZD7_HUMAN;.	P	127	ENSP00000359234:L127P	ENSP00000359234:L127P	L	-	2	0	PDZD7	102773345	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.224000	0.95209	1.893000	0.54813	0.459000	0.35465	CTG	.	.	.	none		0.657	PDZD7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049883.1	NM_024895		G	102783355	A	G	102783355	3	3	240	1	0	0	0	0	1	0	0	0	11711	188	7	3	1201	3	PDZD7	10	102783355	Missense_Mutation	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	5816337	102783355	32751392	53	14706											
MUC2	4583	hgsc.bcm.edu	37	chr11	1078339	1078339	+	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	cgatgtggtgtgtgaggatcCcgaggaggaggtggcccccg	6	7	19	9	3	0	1	0	1	0	0	1	6	1	4	3	6	0	0	3	6	0	0			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr11:1078339C>T	ENST00000441003.2	+	5	653	c.626C>T	c.(625-627)cCc>cTc	p.P209L	MUC2_ENST00000359061.5_Missense_Mutation_p.P209L	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	209	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	TGTGAGGATCCCGAGGAGGAG	0.642																																					p.P209L		Atlas-SNP	.											.	MUC2	614	.	0			c.C626T						PASS	.						76	90	86					11																	1078339		2086	4194	6280	SO:0001583	missense	4583	exon5			AGGATCCCGAGGA	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.626C>T	chr11.hg19:g.1078339C>T	ENSP00000415183:p.Pro209Leu	73.0	0.0	.		224.0	60.0	.	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	C	12.34	1.909914	0.33721	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.14766	2.54;2.48	4.08	4.08	0.47627	.	0.567974	0.14666	U	0.305646	T	0.21881	0.0527	L	0.53729	1.69	0.45554	D	0.998508	P	0.37525	0.598	B	0.43386	0.418	T	0.04454	-1.0950	10	0.48119	T	0.1	.	16.2743	0.82636	0.0:1.0:0.0:0.0	.	209	E7EUV1	.	L	209	ENSP00000415183:P209L;ENSP00000351956:P209L	ENSP00000351956:P209L	P	+	2	0	MUC2	1068339	0.995000	0.38212	0.394000	0.26270	0.046000	0.14306	2.838000	0.48199	1.818000	0.53035	0.561000	0.74099	CCC	.	.	.	none		0.642	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1078339	C	T	1078339	3	4	240	1	0	0	0	0	1	0	0	0	9982	623	22	2	644	2	MUC2	11	1078339	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10		1078339	133928177	54	14707											
OR10A2	341276	hgsc.bcm.edu	37	chr11	6891503	6891503	+	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	tgacagcccacctgtgctgaGgctggtctgtgcagacacag	8	8	13	12	0	1	3	0	2	1	1	1	3	1	3	2	2	3	3	2	2	0	0			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr11:6891503G>A	ENST00000307322.4	+	1	580	c.518G>A	c.(517-519)aGg>aAg	p.R173K		NM_001004460.1	NP_001004460.1	Q9H208	O10A2_HUMAN	olfactory receptor, family 10, subfamily A, member 2	173				R -> K (in Ref. 4; AAK95109). {ECO:0000305}.		integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(12)|urinary_tract(1)	24		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.89e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		CCTGTGCTGAGGCTGGTCTGT	0.507																																					p.R173K		Atlas-SNP	.											OR10A2,right_upper_lobe,carcinoma,0,1	OR10A2	55	.	0			c.G518A						PASS	.						191	158	169					11																	6891503		2201	4296	6497	SO:0001583	missense	341276	exon1			TGCTGAGGCTGGT	BK004293	CCDS31415.1	11p15.4	2012-08-09		2004-03-10	ENSG00000170790	ENSG00000170790		"GPCR / Class A : Olfactory receptors"	8161	protein-coding gene	gene with protein product				OR10A2P			Standard	NM_001004460		Approved	OST363	uc001meu.1	Q9H208	OTTHUMG00000165739	ENST00000307322.4:c.518G>A	chr11.hg19:g.6891503G>A	ENSP00000303862:p.Arg173Lys	87.0	1.0	.		248.0	12.0	.	NM_001004460	B2RNL9|Q6IFG9	Missense_Mutation	SNP	ENST00000307322.4	hg19	CCDS31415.1	.	.	.	.	.	.	.	.	.	.	g	0.888	-0.726545	0.03158	.	.	ENSG00000170790	ENST00000307322	T	0.00016	9.13	4.14	-2.4	0.06583	GPCR, rhodopsin-like superfamily (1);	0.386873	0.25280	N	0.031805	T	0.00039	0.0001	N	0.00815	-1.16	0.22620	N	0.998928	B	0.02656	0.0	B	0.04013	0.001	T	0.40040	-0.9584	10	0.02654	T	1	.	9.7558	0.40502	0.6387:0.0:0.3613:0.0	.	173	Q9H208	O10A2_HUMAN	K	173	ENSP00000303862:R173K	ENSP00000303862:R173K	R	+	2	0	OR10A2	6848079	0.000000	0.05858	0.986000	0.45419	0.922000	0.55478	-0.974000	0.03794	-0.362000	0.08113	-0.201000	0.12746	AGG	.	.	.	none		0.507	OR10A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385984.1	NM_001004460		A	6891503	G	A	6891503	3	1	240	1	0	0	0	0	1	0	0	0	10897	1000	35	2	520	2	OR10A2	11	6891503	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	5813164	6891503	128115013	55	14708											
PDE3B	5140	hgsc.bcm.edu	37	chr11	14666027	14666027	+	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	tcttcttcctcacctgcttcCtcacccggaccaagcgggga	6	10	8	17	2	4	0	2	0	2	0	6	2	6	2	5	3	2	1	5	3	1	3	rs373522381	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr11:14666027C>G	ENST00000282096.4	+	1	759	c.406C>G	c.(406-408)Ctc>Gtc	p.L136V	PSMA1_ENST00000418988.2_5'Flank|PDE3B_ENST00000534317.1_3'UTR|PDE3B_ENST00000455098.2_Missense_Mutation_p.L136V	NM_000922.3	NP_000913.2	Q13370	PDE3B_HUMAN	phosphodiesterase 3B, cGMP-inhibited	136					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of lipid catabolic process (GO:0050995)|regulation of insulin secretion (GO:0050796)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)|protein kinase B binding (GO:0043422)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39					Caffeine(DB00201)	CACCTGCTTCCTCACCCGGAC	0.692													C|||	2	0.000399361	0.0015	0	5008	,	,		14055	0		0	False		,,,				2504	0				p.L136V		Atlas-SNP	.											.	PDE3B	98	.	0			c.C406G						PASS	.						29	32	31					11																	14666027		2199	4294	6493	SO:0001583	missense	5140	exon1			TGCTTCCTCACCC	U38178	CCDS7817.1	11p15.2	2008-03-18			ENSG00000152270	ENSG00000152270	3.1.4.17	"Phosphodiesterases"	8779	protein-coding gene	gene with protein product		602047				8884271, 16395595	Standard	NM_000922		Approved	HcGIP1	uc001mln.3	Q13370	OTTHUMG00000165898	ENST00000282096.4:c.406C>G	chr11.hg19:g.14666027C>G	ENSP00000282096:p.Leu136Val	10.0	0.0	.		146.0	52.0	.	NM_000922	B7ZM37|O00639|Q14408|Q6SEI4	Missense_Mutation	SNP	ENST00000282096.4	hg19	CCDS7817.1	.	.	.	.	.	.	.	.	.	.	C	16.61	3.170982	0.57584	.	.	ENSG00000152270	ENST00000282096;ENST00000455098	T;T	0.74842	-0.72;-0.88	3.78	0.801	0.18679	.	8.111930	0.00166	N	0.000000	T	0.73953	0.3653	L	0.40543	1.245	0.31630	N	0.649153	P;P;P	0.52842	0.884;0.884;0.956	B;B;P	0.50659	0.358;0.358;0.647	T	0.62058	-0.6934	10	0.45353	T	0.12	.	6.7026	0.23232	0.0:0.5775:0.0:0.4225	.	136;136;136	B7ZM37;Q13370;A7E2E5	.;PDE3B_HUMAN;.	V	136	ENSP00000282096:L136V;ENSP00000388644:L136V	ENSP00000282096:L136V	L	+	1	0	PDE3B	14622603	1.000000	0.71417	0.998000	0.56505	0.834000	0.47266	1.686000	0.37669	0.130000	0.18549	0.313000	0.20887	CTC	.	.	.	alt		0.692	PDE3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386974.1	NM_000922		G	14666027	C	G	14666027	3	3	240	1	0	0	0	0	1	0	0	0	11645	681	24	4	408	4	PDE3B	11	14666027	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	7774524	14666027	120340489	56	14709											
OR4X1	390113	hgsc.bcm.edu	37	chr11	48285602	48285602	+	Missense_Mutation	SNP	T	T	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	tgtatttctttctcagctacTtatcctttgtggagatctgc	6	19	7	9	0	3	1	1	0	3	1	5	2	4	1	1	1	3	2	1	1	3	6			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr11:48285602T>G	ENST00000320048.1	+	1	190	c.190T>G	c.(190-192)Tta>Gta	p.L64V		NM_001004726.1	NP_001004726.1	Q8NH49	OR4X1_HUMAN	olfactory receptor, family 4, subfamily X, member 1 (gene/pseudogene)	64						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						TCTCAGCTACTTATCCTTTGT	0.493																																					p.L64V		Atlas-SNP	.											.	OR4X1	75	.	0			c.T190G						PASS	.						148	135	139					11																	48285602		2201	4298	6499	SO:0001583	missense	390113	exon1			AGCTACTTATCCT	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.190T>G	chr11.hg19:g.48285602T>G	ENSP00000321506:p.Leu64Val	66.0	0.0	.		156.0	18.0	.	NM_001004726	Q6IF74	Missense_Mutation	SNP	ENST00000320048.1	hg19	CCDS31487.1	.	.	.	.	.	.	.	.	.	.	T	10.30	1.313474	0.23908	.	.	ENSG00000176567	ENST00000320048	T	0.00507	6.92	4.29	-3.51	0.04696	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.01976	0.0062	H	0.97540	4.025	0.20403	N	0.999903	D	0.57571	0.98	P	0.56960	0.81	T	0.01084	-1.1457	9	0.87932	D	0	.	8.1735	0.31268	0.0:0.4875:0.1294:0.3831	.	64	Q8NH49	OR4X1_HUMAN	V	64	ENSP00000321506:L64V	ENSP00000321506:L64V	L	+	1	2	OR4X1	48242178	0.000000	0.05858	0.901000	0.35422	0.022000	0.10575	-2.554000	0.00926	-1.009000	0.03400	-2.821000	0.00108	TTA	.	.	.	none		0.493	OR4X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383373.1	NM_001004726		G	48285602	T	G	48285602	3	3	240	1	0	0	0	0	1	0	0	0	11091	1606	56	5	192	5	OR4X1	11	48285602	Missense_Mutation	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	33619575	48285602	86720914	57	14710											
MLL	4297	hgsc.bcm.edu	37	chr11	118373932	118373932	+	Missense_Mutation	SNP	A	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	ctgtaaagaaactttcaaagAaaagcattccagtaaatctt	18	11	5	7	0	2	2	1	0	1	2	3	2	3	2	1	0	2	3	1	0	8	5			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr11:118373932A>C	ENST00000389506.5	+	27	7316	c.7316A>C	c.(7315-7317)gAa>gCa	p.E2439A	KMT2A_ENST00000534358.1_Missense_Mutation_p.E2442A|KMT2A_ENST00000354520.4_Missense_Mutation_p.E2401A			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	2439					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)										ACTTTCAAAGAAAAGCATTCC	0.403																																					p.E2442A		Atlas-SNP	.											.	MLL	548	.	0			c.A7325C						PASS	.						62	65	64					11																	118373932		2199	4296	6495	SO:0001583	missense	4297	exon27			TCAAAGAAAAGCA	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.7316A>C	chr11.hg19:g.118373932A>C	ENSP00000374157:p.Glu2439Ala	96.0	0.0	.		87.0	34.0	.	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	hg19	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	A	11.96	1.794138	0.31777	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	D;D;D	0.83591	-1.74;-1.74;-1.71	5.85	5.85	0.93711	.	0.109676	0.64402	D	0.000008	T	0.70064	0.3181	N	0.19112	0.55	0.49915	D	0.999833	P;P	0.49090	0.919;0.919	B;B	0.33339	0.162;0.162	T	0.76889	-0.2792	10	0.72032	D	0.01	.	16.2303	0.82332	1.0:0.0:0.0:0.0	.	2442;2439	E9PQG7;Q03164	.;MLL1_HUMAN	A	2442;2439;2401;1349	ENSP00000436786:E2442A;ENSP00000374157:E2439A;ENSP00000346516:E2401A	ENSP00000346516:E2401A	E	+	2	0	MLL	117879142	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.414000	0.73318	2.233000	0.73108	0.533000	0.62120	GAA	.	.	.	none		0.403	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		C	118373932	A	C	118373932	3	2	240	1	0	0	0	0	1	0	0	0	9627	246	9	5	7422	5	MLL	11	118373932	Missense_Mutation	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	70088330	118373932	16632584	58	14711											
SCNN1A	6337	hgsc.bcm.edu	37	chr12	6457064	6457064	+	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	gcccccccagaggacaggtgGaggaactggcccctgcagag	9	3	15	14	0	0	2	0	0	0	2	0	5	0	5	5	5	2	1	5	5	1	0			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr12:6457064G>A	ENST00000228916.2	-	13	2083	c.1985C>T	c.(1984-1986)tCc>tTc	p.S662F	SCNN1A_ENST00000543768.1_Missense_Mutation_p.S685F|SCNN1A_ENST00000360168.3_Missense_Mutation_p.S721F|SCNN1A_ENST00000540037.1_Missense_Mutation_p.S362F|SCNN1A_ENST00000396966.2_3'UTR|SCNN1A_ENST00000358945.3_Missense_Mutation_p.S684F	NM_001038.5	NP_001029.1	P37088	SCNNA_HUMAN	sodium channel, non-voltage-gated 1 alpha subunit	662					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)	AGGACAGGTGGAGGAACTGGC	0.672																																					p.S721F		Atlas-SNP	.											.	SCNN1A	54	.	0			c.C2162T						PASS	.						7	8	7					12																	6457064		2098	4115	6213	SO:0001583	missense	6337	exon12			CAGGTGGAGGAAC	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.1985C>T	chr12.hg19:g.6457064G>A	ENSP00000228916:p.Ser662Phe	34.0	0.0	.		95.0	31.0	.	NM_001159576	A5X2U9|B4E2Q5|C5HTZ0|O43271|Q6GSQ6|Q9UM64	Missense_Mutation	SNP	ENST00000228916.2	hg19	CCDS8543.1	.	.	.	.	.	.	.	.	.	.	G	13.93	2.383587	0.42207	.	.	ENSG00000111319	ENST00000360168;ENST00000358945;ENST00000540037;ENST00000228916;ENST00000543768	T;T;T;T;T	0.73258	-0.73;-0.69;-0.44;-0.63;-0.67	3.95	1.82	0.25136	.	1.972990	0.02819	N	0.125281	T	0.70090	0.3184	M	0.63428	1.95	0.09310	N	1	B;B;B	0.32693	0.38;0.38;0.226	B;B;B	0.29267	0.085;0.085;0.1	T	0.60627	-0.7226	10	0.72032	D	0.01	-0.3348	11.2996	0.49298	0.0:0.3534:0.6466:0.0	.	685;662;721	B4E2Q5;P37088;P37088-2	.;SCNNA_HUMAN;.	F	721;684;362;662;685	ENSP00000353292:S721F;ENSP00000351825:S684F;ENSP00000440876:S362F;ENSP00000228916:S662F;ENSP00000438739:S685F	ENSP00000228916:S662F	S	-	2	0	SCNN1A	6327325	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.471000	0.22100	0.933000	0.37291	0.555000	0.69702	TCC	.	.	.	none		0.672	SCNN1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399055.1			A	6457064	G	A	6457064	3	1	240	1	0	0	0	0	1	0	0	0	13940	1174	41	2	28	2	SCNN1A	12	6457064	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10		6457064	127394831	59	14712											
KLRK1	22914	hgsc.bcm.edu	37	chr12	10539523	10539523	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attttctctacatttgctttTgactactggacatctttgct	7	20	5	9	0	2	1	0	1	2	0	3	2	2	2	0	1	4	2	0	1	2	8			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr12:10539523T>C	ENST00000240618.6	-	3	267	c.127A>G	c.(127-129)Aaa>Gaa	p.K43E	KLRC4-KLRK1_ENST00000539300.1_3'UTR|RP11-277P12.20_ENST00000500682.1_RNA|KLRK1_ENST00000540818.1_Missense_Mutation_p.K43E	NM_001199805.1|NM_007360.3	NP_001186734.1|NP_031386.2	P26718	NKG2D_HUMAN	killer cell lectin-like receptor subfamily K, member 1	43					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						CATTTGCTTTTGACTACTGGA	0.323																																					p.K43E		Atlas-SNP	.											.	.	.	.	0			c.A127G						PASS	.						207	186	193					12																	10539523		2203	4298	6501	SO:0001583	missense	0	exon8			TGCTTTTGACTAC	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.127A>G	chr12.hg19:g.10539523T>C	ENSP00000240618:p.Lys43Glu	47.0	0.0	.		85.0	32.0	.	NM_001199805	A8K7K5|A8K7P4|Q9NR41	Missense_Mutation	SNP	ENST00000240618.6	hg19	CCDS8623.1	.	.	.	.	.	.	.	.	.	.	T	10.78	1.445773	0.25987	.	.	ENSG00000213809	ENST00000240618;ENST00000540818	T;T	0.01474	4.85;4.85	4.24	1.81	0.25067	.	0.304503	0.23859	N	0.043877	T	0.01661	0.0053	L	0.36672	1.1	0.09310	N	1	B;B;B	0.26775	0.056;0.159;0.081	B;B;B	0.29524	0.029;0.103;0.028	T	0.46527	-0.9185	10	0.34782	T	0.22	.	4.666	0.12666	0.1788:0.0:0.2431:0.5781	.	43;24;43	Q8WZ67;Q1HEA1;P26718	.;.;NKG2D_HUMAN	E	43	ENSP00000240618:K43E;ENSP00000446003:K43E	ENSP00000240618:K43E	K	-	1	0	KLRK1	10430790	0.005000	0.15991	0.001000	0.08648	0.025000	0.11179	0.895000	0.28363	0.250000	0.21479	0.455000	0.32223	AAA	.	.	.	none		0.323	KLRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400269.1	NM_007360		C	10539523	T	C	10539523	3	2	240	1	0	0	0	0	1	0	0	0	8430	1821	63	3	547	3	KLRK1	12	10539523	Missense_Mutation	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	4082459	10539523	123312372	60	14713											
PTPRO	5800	hgsc.bcm.edu	37	chr12	15673198	15673198	+	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	ttaccatggtgacgtggggaGatccagaattgagctgctgt	9	11	14	7	1	0	4	0	2	0	2	1	5	1	4	2	3	3	2	2	3	2	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr12:15673198G>A	ENST00000281171.4	+	10	2173	c.1843G>A	c.(1843-1845)Gat>Aat	p.D615N	PTPRO_ENST00000348962.2_Missense_Mutation_p.D615N	NM_030667.2	NP_109592.1	Q16827	PTPRO_HUMAN	protein tyrosine phosphatase, receptor type, O	615	Fibronectin type-III 6. {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)				GACGTGGGGAGATCCAGAATT	0.478																																					p.D615N		Atlas-SNP	.											.	PTPRO	148	.	0			c.G1843A						PASS	.						138	124	129					12																	15673198		2203	4300	6503	SO:0001583	missense	5800	exon10			TGGGGAGATCCAG	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.1843G>A	chr12.hg19:g.15673198G>A	ENSP00000281171:p.Asp615Asn	96.0	0.0	.		262.0	78.0	.	NM_002848	A0AV39|Q13101|Q8IYG3|Q9UBF0|Q9UBT5	Missense_Mutation	SNP	ENST00000281171.4	hg19	CCDS8675.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.956744	0.92726	.	.	ENSG00000151490	ENST00000281171;ENST00000348962	T;T	0.53640	3.8;0.61	5.2	5.2	0.72013	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.249218	0.27922	N	0.017316	T	0.41558	0.1164	N	0.19112	0.55	0.80722	D	1	P;P	0.41188	0.741;0.624	B;B	0.43658	0.426;0.245	T	0.44952	-0.9294	10	0.72032	D	0.01	.	17.0929	0.86627	0.0:0.0:1.0:0.0	.	615;615	Q16827-2;Q16827	.;PTPRO_HUMAN	N	615	ENSP00000281171:D615N;ENSP00000343434:D615N	ENSP00000281171:D615N	D	+	1	0	PTPRO	15564465	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.851000	0.92205	2.689000	0.91719	0.655000	0.94253	GAT	.	.	.	none		0.478	PTPRO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401079.1			A	15673198	G	A	15673198	3	1	240	1	0	0	0	0	1	0	0	0	12822	942	33	2	1881	2	PTPRO	12	15673198	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	5133675	15673198	118178697	61	14714											
DDN	23109	hgsc.bcm.edu	37	chr12	49391677	49391677	+	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	ttggggatggctgtcgctacCactgttcaggtcagcagcag	7	10	14	10	1	2	0	2	0	0	0	3	1	2	1	1	4	3	5	1	4	1	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr12:49391677C>T	ENST00000421952.2	-	2	1003	c.982G>A	c.(982-984)Ggt>Agt	p.G328S	RP11-386G11.3_ENST00000549516.1_RNA|RP11-386G11.5_ENST00000547395.1_RNA|RP11-386G11.5_ENST00000552284.1_RNA|RP11-386G11.5_ENST00000552933.1_RNA|RP11-386G11.5_ENST00000547866.1_RNA	NM_015086.1	NP_055901.2	O94850	DEND_HUMAN	dendrin	328						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						CTGTCGCTACCACTGTTCAGG	0.677																																					p.G328S		Atlas-SNP	.											.	DDN	54	.	0			c.G982A						PASS	.						46	53	51					12																	49391677		2203	4299	6502	SO:0001583	missense	23109	exon2			CGCTACCACTGTT	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.982G>A	chr12.hg19:g.49391677C>T	ENSP00000390590:p.Gly328Ser	20.0	0.0	.		53.0	11.0	.	NM_015086		Missense_Mutation	SNP	ENST00000421952.2	hg19	CCDS31791.2	.	.	.	.	.	.	.	.	.	.	C	18.60	3.658359	0.67586	.	.	ENSG00000181418	ENST00000421952	T	0.44881	0.91	3.88	2.05	0.26809	.	0.148751	0.31601	N	0.007378	T	0.21387	0.0515	N	0.24115	0.695	0.09310	N	1	P	0.40909	0.732	B	0.31191	0.125	T	0.10776	-1.0615	10	0.42905	T	0.14	-3.234	7.9639	0.30087	0.0:0.798:0.0:0.202	.	328	O94850	DEND_HUMAN	S	328	ENSP00000390590:G328S	ENSP00000390590:G328S	G	-	1	0	DDN	47677944	0.000000	0.05858	0.001000	0.08648	0.743000	0.42351	0.617000	0.24359	0.617000	0.30160	0.561000	0.74099	GGT	.	.	.	none		0.677	DDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343335.1			T	49391677	C	T	49391677	3	4	240	1	0	0	0	0	1	0	0	0	4335	594	21	2	1157	2	DDN	12	49391677	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	33718479	49391677	84460218	62	14715											
C12orf24	29902	hgsc.bcm.edu	37	chr12	110906786	110906786	+	Missense_Mutation	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	agcgtagctcttctgcagagCcgcccgctgtggccgggacc	5	7	14	15	4	2	1	0	0	2	1	2	2	2	2	4	2	4	4	4	2	1	2	rs202079205	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr12:110906786C>T	ENST00000377673.5	+	1	618	c.106C>T	c.(106-108)Ccg>Tcg	p.P36S	GPN3_ENST00000537466.2_5'Flank|GPN3_ENST00000228827.3_5'Flank|GPN3_ENST00000552180.1_5'UTR|GPN3_ENST00000543199.1_5'Flank	NM_013300.2	NP_037432.2	Q8WUB2	F216A_HUMAN	family with sequence similarity 216, member A	36																	TTCTGCAGAGCCGCCCGCTGT	0.771													C|||	12	0.00239617	0.0091	0	5008	,	,		13111	0		0	False		,,,				2504	0				p.P36S		Atlas-SNP	.											.	.	.	.	0			c.C106T						PASS	.	C	SER/PRO	24,3054		0,24,1515	2	2	2		106	3.3	0.1	12		2	0,6186		0,0,3093	yes	missense	C12orf24	NM_013300.2	74	0,24,4608	TT,TC,CC		0.0,0.7797,0.2591	probably-damaging	36/274	110906786	24,9240	1539	3093	4632	SO:0001583	missense	29902	exon1			GCAGAGCCGCCCG	U79274	CCDS31899.1	12q24.11	2012-02-07	2012-02-07	2012-02-07	ENSG00000204856	ENSG00000204856			30180	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 24"	C12orf24			Standard	NM_013300		Approved	HSU79274	uc001tqu.4	Q8WUB2	OTTHUMG00000169526	ENST00000377673.5:c.106C>T	chr12.hg19:g.110906786C>T	ENSP00000366901:p.Pro36Ser	1.0	0.0	.		25.0	12.0	.	NM_013300	A6NH30|Q99776	Missense_Mutation	SNP	ENST00000377673.5	hg19	CCDS31899.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.171608	0.78452	0.007797	0.0	ENSG00000204856	ENST00000377673;ENST00000538285	T	0.51071	0.72	4.16	3.27	0.37495	.	0.000000	0.39544	N	0.001336	T	0.32645	0.0836	L	0.56769	1.78	0.27811	N	0.942126	B;B	0.30709	0.291;0.129	B;B	0.26693	0.072;0.031	T	0.41645	-0.9497	10	0.87932	D	0	-0.6948	9.2806	0.37727	0.0:0.8974:0.0:0.1026	.	36;36	F5GZE4;Q8WUB2	.;CL024_HUMAN	S	36	ENSP00000366901:P36S	ENSP00000366901:P36S	P	+	1	0	C12orf24	109391169	0.943000	0.32029	0.132000	0.22025	0.895000	0.52256	2.944000	0.49034	1.096000	0.41439	0.462000	0.41574	CCG	.	.	.	weak		0.771	FAM216A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404616.1	NM_013300		T	110906786	C	T	110906786	3	4	240	1	0	0	0	0	1	0	0	0	1680	739	26	2	108	2	C12orf24	12	110906786	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	61515109	110906786	22945109	63	14716											
RAD9B	160760	hgsc.bcm.edu	37	chr12	110969392	110969392	+	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	1	0	0	0	0	0	0	0	tttgcagtgtgctgcaggaaAgaatttaatggaagtgatgc	12	12	13	4	0	0	2	0	1	0	1	0	4	0	4	0	2	4	3	0	2	4	3	rs139110749	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr12:110969392A>G	ENST00000354300.3	-	0	6653				RAD9B_ENST00000409778.3_Missense_Mutation_p.K311R|RAD9B_ENST00000409300.1_3'UTR|RAD9B_ENST00000409425.1_3'UTR|RAD9B_ENST00000409246.1_3'UTR|RAD9B_ENST00000392672.4_Silent_p.K416K	NM_139283.1	NP_644812.1	Q8NI37	PPTC7_HUMAN	PTC7 protein phosphatase homolog (S. cerevisiae)							mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			endometrium(1)|large_intestine(2)|lung(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	9						GCTGCAGGAAAGAATTTAATG	0.353																																					p.K416K		Atlas-SNP	.											.	RAD9B	50	.	0			c.A1248G						PASS	.						94	83	87					12																	110969392		1566	3582	5148	SO:0001624	3_prime_UTR_variant	144715	exon12			CAGGAAAGAATTT	AF385435	CCDS9149.1	12q24.11	2009-11-05				ENSG00000196850			30695	protein-coding gene	gene with protein product	"T cell activation protein phosphatase 2C"	609668				15177553	Standard	NM_139283		Approved	TA-PP2C	uc001trh.1	Q8NI37	OTTHUMG00000169529	ENST00000354300.3:c.*5450T>C	chr12.hg19:g.110969392A>G		12.0	0.0	.		27.0	9.0	.	NM_152442	B3KWC5|Q68DZ7|Q6UY82	Silent	SNP	ENST00000354300.3	hg19	CCDS9149.1	.	.	.	.	.	.	.	.	.	.	A	13.82	2.352501	0.41700	.	.	ENSG00000151164	ENST00000409778	T	0.19250	2.16	4.49	2.08	0.27032	.	155.184000	0.02530	U	0.093532	T	0.15609	0.0376	.	.	.	0.09310	N	1	B	0.26635	0.155	B	0.23574	0.047	T	0.21211	-1.0252	9	0.40728	T	0.16	14.2473	4.9792	0.14157	0.6246:0.1916:0.0:0.1837	.	311	B4DYM6	.	R	311	ENSP00000386697:K311R	ENSP00000386697:K311R	K	+	2	0	RAD9B	109453775	0.009000	0.17119	0.001000	0.08648	0.372000	0.29890	1.856000	0.39389	0.343000	0.23821	0.397000	0.26171	AAG	.	.	.	none		0.353	PPTC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404635.1	NM_139283		G	110969392	A	G	110969392	1	3	240	0	1	0	0	0	0	0	0	0	13009	69	3	3		3	RAD9B	12	110969392	3'UTR	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	62606	110969392	22882503	64	14717											
CUX2	23316	hgsc.bcm.edu	37	chr12	111785758	111785759	+	Frame_Shift_Ins	INS	-	-	A																															ctgtccctcacttcatccccINSaacaggagagtgaggccggg																										TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr12:111785758_111785759insA	ENST00000261726.6	+	22	4244_4245	c.4090_4091insA	c.(4090-4092)caafs	p.Q1364fs		NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	1364	Pro-rich.				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						ACTTCATCCCCAACAGGAGAGT	0.604																																					p.Q1364fs		Atlas-Indel,Pindel	.											.	CUX2	145	.	0			c.4090_4091insA						PASS	.																																			SO:0001589	frameshift_variant	23316	exon22			.	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.4092dupA	chr12.hg19:g.111785760_111785760dupA	ENSP00000261726:p.Gln1364fs	40.0	0.0	0		69.0	24.0	0.347826	NM_015267	A7E2Y4	Frame_Shift_Ins	INS	ENST00000261726.6	hg19	CCDS41837.1																																																																																			.	.	.	none		0.604	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267		A	111785759	-	A	111785758	7	5	240	1	0	1	1	0	0	0	0	0	4067	595	21	0	4176	0	CUX2	12	111785758	Frame_Shift_Ins	INS	-	TCGA-Q2-A5QZ-01A-11D-A28G-10	816366	111785758	22066137	65	14718											
RBM19	9904	hgsc.bcm.edu	37	chr12	114385205	114385205	+	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	tcagggaacatgaaggtgatGaatgcaaaacccttgggttt	13	10	12	6	0	1	3	1	3	0	0	1	4	1	4	1	3	3	2	1	3	5	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr12:114385205G>A	ENST00000545145.2	-	11	1419	c.1341C>T	c.(1339-1341)ttC>ttT	p.F447F	RBM19_ENST00000392561.3_Silent_p.F447F|RBM19_ENST00000261741.5_Silent_p.F447F	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	447	RRM 3. {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)					TGAAGGTGATGAATGCAAAAC	0.602																																					p.F447F		Atlas-SNP	.											.	RBM19	117	.	0			c.C1341T						PASS	.						144	122	130					12																	114385205		2203	4300	6503	SO:0001819	synonymous_variant	9904	exon11			GGTGATGAATGCA	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.1341C>T	chr12.hg19:g.114385205G>A		73.0	0.0	.		278.0	64.0	.	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	hg19	CCDS9172.1																																																																																			.	.	.	none		0.602	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196		A	114385205	G	A	114385205	2	1	240	1	0	0	0	0	0	0	0	1	13134	1281	45	2		2	RBM19	12	114385205	Silent	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	2599447	114385205	19466690	66	14719											
BRI3BP	140707	hgsc.bcm.edu	37	chr12	125509640	125509640	+	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	ctggcctactggttcttgtcCctgaccctgggcttcacttt	3	15	9	14	0	2	1	1	1	1	0	3	1	3	1	3	3	1	2	3	3	1	5			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr12:125509640C>A	ENST00000341446.8	+	3	511	c.420C>A	c.(418-420)tcC>tcA	p.S140S		NM_080626.5	NP_542193.3			BRI3 binding protein											large_intestine(1)|lung(8)|ovary(1)	10	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.35e-05)|Epithelial(86;0.000426)|all cancers(50;0.00576)		GGTTCTTGTCCCTGACCCTGG	0.632																																					p.S140S		Atlas-SNP	.											.	BRI3BP	18	.	0			c.C420A						PASS	.						100	83	89					12																	125509640		2203	4300	6503	SO:0001819	synonymous_variant	140707	exon3			CTTGTCCCTGACC	AF284094	CCDS9262.1	12q24.1	2008-08-04			ENSG00000184992	ENSG00000184992			14251	protein-coding gene	gene with protein product		615627				11860200, 17765869	Standard	NM_080626		Approved	BNAS1, KG19, HCCR-2	uc001uha.1	Q8WY22	OTTHUMG00000168548	ENST00000341446.8:c.420C>A	chr12.hg19:g.125509640C>A		25.0	0.0	.		85.0	32.0	.	NM_080626		Silent	SNP	ENST00000341446.8	hg19	CCDS9262.1																																																																																			.	.	.	none		0.632	BRI3BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400200.2	NM_080626		A	125509640	C	A	125509640	2	1	240	1	0	0	0	0	0	0	0	1	1515	610	22	4		4	BRI3BP	12	125509640	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	11124435	125509640	8342255	67	14720											
N6AMT2	221143	hgsc.bcm.edu	37	chr13	21306119	21306119	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attctttcgggtaagtccaaTggattattgtaatcatagaa	13	15	8	5	1	2	1	1	0	1	1	4	2	3	2	1	2	0	2	1	2	6	7			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr13:21306119T>C	ENST00000382758.1	-	4	416	c.369A>G	c.(367-369)ccA>ccG	p.P123P	N6AMT2_ENST00000382754.4_Silent_p.P123P			Q8WVE0	N6MT2_HUMAN	N-6 adenine-specific DNA methyltransferase 2 (putative)	123						extracellular vesicular exosome (GO:0070062)	methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(3)|lung(3)	7		all_cancers(29;5.91e-19)|all_epithelial(30;1.42e-15)|all_lung(29;5.9e-14)|Lung SC(185;0.0367)		all cancers(112;0.000234)|Epithelial(112;0.000471)|OV - Ovarian serous cystadenocarcinoma(117;0.0111)|Lung(94;0.0161)|LUSC - Lung squamous cell carcinoma(192;0.0431)		GTAAGTCCAATGGATTATTGT	0.378																																					p.P123P		Atlas-SNP	.											.	N6AMT2	26	.	0			c.A369G						PASS	.						121	116	118					13																	21306119		2203	4300	6503	SO:0001819	synonymous_variant	221143	exon4			GTCCAATGGATTA	AK055408	CCDS9293.1	13q12.11	2006-12-14			ENSG00000150456	ENSG00000150456			27351	protein-coding gene	gene with protein product						12477932	Standard	NM_174928		Approved		uc001uno.1	Q8WVE0	OTTHUMG00000016519	ENST00000382758.1:c.369A>G	chr13.hg19:g.21306119T>C		83.0	0.0	.		82.0	37.0	.	NM_174928	B5G4V1	Silent	SNP	ENST00000382758.1	hg19	CCDS9293.1																																																																																			.	.	.	none		0.378	N6AMT2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044083.1	NM_174928		C	21306119	T	C	21306119	2	2	240	1	0	0	0	0	0	0	0	1	10122	1451	51	3		3	N6AMT2	13	21306119	Silent	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10		21306119	93863759	68	14721											
FARP1	10160	hgsc.bcm.edu	37	chr13	99092299	99092299	+	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	ccatcatcgtggccgccaggTaactcgggagcccgcccctt	6	7	11	17	4	1	0	1	0	0	0	3	1	1	1	6	3	2	1	6	3	1	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr13:99092299T>A	ENST00000319562.6	+	22	2781		c.e22+2		FARP1_ENST00000595437.1_Splice_Site|FARP1_ENST00000376586.2_Splice_Site	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)						dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			GGCCGCCAGGTAACTCGGGAG	0.627																																					.		Atlas-SNP	.											.	FARP1	207	.	0			c.2516+2T>A						PASS	.						103	116	112					13																	99092299		2203	4300	6503	SO:0001630	splice_region_variant	10160	exon22			GCCAGGTAACTCG	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.2516+2T>A	chr13.hg19:g.99092299T>A		27.0	0.0	.		70.0	13.0	.	NM_005766	Q5JVI9|Q6IQ29	Splice_Site	SNP	ENST00000319562.6	hg19	CCDS9487.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.843475	0.91197	.	.	ENSG00000152767	ENST00000376586;ENST00000319562	.	.	.	5.07	5.07	0.68467	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0308	0.64615	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	FARP1	97890300	1.000000	0.71417	0.999000	0.59377	0.910000	0.53928	5.986000	0.70563	1.917000	0.55516	0.533000	0.62120	.	.	.	.	none		0.627	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766	Intron	A	99092299	T	A	99092299	5	1	240	1	0	0	0	0	0	0	1	0	5683	1652	57	5	2823	5	FARP1	13	99092299	Splice_Site	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	77786180	99092299	16077579	69	14722											
FLJ10357	55701	hgsc.bcm.edu	37	chr14	21543565	21543565	+	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	ctgtgcaggaaggaaaagggGacaacattccagaagaggcc	15	4	14	8	0	0	2	0	0	0	2	1	5	1	5	2	5	2	1	2	5	5	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr14:21543565G>C	ENST00000298694.4	+	4	1652	c.1525G>C	c.(1525-1527)Gac>Cac	p.D509H	ARHGEF40_ENST00000298693.3_Missense_Mutation_p.D509H			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	509						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						AGGAAAAGGGGACAACATTCC	0.557																																					p.D509H		Atlas-SNP	.											.	ARHGEF40	84	.	0			c.G1525C						PASS	.						131	127	128					14																	21543565		2203	4300	6503	SO:0001583	missense	55701	exon4			AAAGGGGACAACA		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.1525G>C	chr14.hg19:g.21543565G>C	ENSP00000298694:p.Asp509His	108.0	0.0	.		227.0	62.0	.	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Missense_Mutation	SNP	ENST00000298694.4	hg19	CCDS32041.1	.	.	.	.	.	.	.	.	.	.	G	0.307	-0.970175	0.02232	.	.	ENSG00000165801	ENST00000298694;ENST00000555038;ENST00000298693	T;T	0.02472	4.34;4.28	5.12	2.29	0.28610	.	0.113584	0.39210	N	0.001427	T	0.02230	0.0069	N	0.22421	0.69	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.09377	0.002;0.004	T	0.44329	-0.9335	10	0.40728	T	0.16	.	7.8371	0.29376	0.0851:0.308:0.6069:0.0	.	509;509	Q8TER5;G3V3N2	ARH40_HUMAN;.	H	509	ENSP00000298694:D509H;ENSP00000298693:D509H	ENSP00000298693:D509H	D	+	1	0	ARHGEF40	20613405	0.142000	0.22610	0.001000	0.08648	0.002000	0.02628	1.389000	0.34453	0.272000	0.22027	-0.225000	0.12378	GAC	.	.	.	none		0.557	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1			C	21543565	G	C	21543565	3	2	240	1	0	0	0	0	1	0	0	0	5933	1174	41	4	1539	4	FLJ10357	14	21543565	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10		21543565	85805975	70	14723											
KIAA1737	85457	hgsc.bcm.edu	37	chr14	77580238	77580238	+	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	aaagctcccagtctgaccttCgcttcccccgccagtcctgt	6	10	7	18	2	1	1	0	1	1	0	5	1	4	1	6	0	1	2	6	0	1	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr14:77580238C>T	ENST00000361786.2	+	4	1094	c.777C>T	c.(775-777)ttC>ttT	p.F259F	RP11-463C8.4_ENST00000557752.1_Intron	NM_033426.2	NP_219494.2	Q9C0C6	CIPC_HUMAN		259					negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(2)|lung(4)|prostate(3)	9			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0284)		GTCTGACCTTCGCTTCCCCCG	0.572																																					p.F259F		Atlas-SNP	.											KIAA1737,NS,carcinoma,0,1	KIAA1737	26	.	0			c.C777T						PASS	.						84	68	74					14																	77580238		2203	4300	6503	SO:0001819	synonymous_variant	85457	exon4			GACCTTCGCTTCC																												ENST00000361786.2:c.777C>T	chr14.hg19:g.77580238C>T		26.0	0.0	.		48.0	24.0	.	NM_033426	B2RCI1|Q8N389|Q8NDZ1	Silent	SNP	ENST00000361786.2	hg19	CCDS9855.1																																																																																			.	.	.	none		0.572	KIAA1737-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414278.1			T	77580238	C	T	77580238	2	4	240	1	0	0	0	0	0	0	0	1	8262	883	31	1		1	KIAA1737	14	77580238	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	56036673	77580238	29769302	71	14724											
ITPK1	3705	hgsc.bcm.edu	37	chr14	93408017	93408017	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagcttggcggtgccgccCgcgtcggcctcagccttcca	3	7	14	17	5	1	0	1	0	0	0	3	0	2	0	5	4	3	2	5	4	0	2	rs563090061	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr14:93408017C>T	ENST00000267615.6	-	11	1307	c.1134G>A	c.(1132-1134)gcG>gcA	p.A378A	ITPK1_ENST00000556603.2_Silent_p.A378A|ITPK1_ENST00000555495.1_Silent_p.A259A|ITPK1_ENST00000354313.3_Intron			Q13572	ITPK1_HUMAN	inositol-tetrakisphosphate 1-kinase	378					blood coagulation (GO:0007596)|dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|inositol trisphosphate metabolic process (GO:0032957)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|inositol tetrakisphosphate 1-kinase activity (GO:0047325)|inositol-1,3,4,5,6-pentakisphosphate 1-phosphatase activity (GO:0052825)|inositol-1,3,4,6-tetrakisphosphate 1-phosphatase activity (GO:0052831)|inositol-1,3,4,6-tetrakisphosphate 6-phosphatase activity (GO:0052830)|inositol-1,3,4-trisphosphate 5-kinase activity (GO:0052726)|inositol-1,3,4-trisphosphate 6-kinase activity (GO:0052725)|inositol-3,4,6-trisphosphate 1-kinase activity (GO:0052835)|isomerase activity (GO:0016853)|magnesium ion binding (GO:0000287)			endometrium(1)|large_intestine(3)|lung(6)|ovary(1)	11		all_cancers(154;0.077)|all_epithelial(191;0.247)		Epithelial(152;0.124)|all cancers(159;0.169)		CGGTGCCGCCCGCGTCGGCCT	0.736													C|||	4	0.000798722	8e-04	0.0014	5008	,	,		13386	0.001		0	False		,,,				2504	0.001				p.A378A		Atlas-SNP	.											.	ITPK1	53	.	0			c.G1134A						PASS	.						3	3	3					14																	93408017		1665	3314	4979	SO:0001819	synonymous_variant	3705	exon11			GCCGCCCGCGTCG	U51336	CCDS9907.1, CCDS45157.1	14q32.12	2012-08-16	2011-04-28		ENSG00000100605	ENSG00000100605	2.7.1.134		6177	protein-coding gene	gene with protein product		601838	"inositol 1,3,4-triphosphate 5/6 kinase"			8662638, 11042108	Standard	NM_014216		Approved		uc001ybh.3	Q13572	OTTHUMG00000171226	ENST00000267615.6:c.1134G>A	chr14.hg19:g.93408017C>T		0.0	0.0	.		14.0	12.0	.	NM_001142593	Q9BTL6|Q9H2E7	Silent	SNP	ENST00000267615.6	hg19	CCDS9907.1																																																																																			.	.	.	none		0.736	ITPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412421.2	NM_014216		T	93408017	C	T	93408017	2	4	240	1	0	0	0	0	0	0	0	1	7923	639	23	1		1	ITPK1	14	93408017	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	15827779	93408017	13941523	72	14725											
CASC5	57082	hgsc.bcm.edu	37	chr15	40915310	40915310	+	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	tagtgtttgtagataatcatGttgaactagaaatgacagag	15	13	10	3	0	1	5	1	2	0	3	1	5	1	5	0	0	1	3	0	0	6	6			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr15:40915310G>T	ENST00000346991.5	+	11	3316	c.2926G>T	c.(2926-2928)Gtt>Ttt	p.V976F	CASC5_ENST00000527044.1_3'UTR|CASC5_ENST00000399668.2_Missense_Mutation_p.V950F			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	976	2 X 104 AA approximate repeats.				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)		AGATAATCATGTTGAACTAGA	0.378																																					p.V976F		Atlas-SNP	.											.	CASC5	269	.	0			c.G2926T						PASS	.						92	86	88					15																	40915310		1860	4104	5964	SO:0001583	missense	57082	exon11			AATCATGTTGAAC	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.2926G>T	chr15.hg19:g.40915310G>T	ENSP00000335463:p.Val976Phe	58.0	0.0	.		88.0	21.0	.	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Missense_Mutation	SNP	ENST00000346991.5	hg19	CCDS42023.1	.	.	.	.	.	.	.	.	.	.	G	11.84	1.757693	0.31137	.	.	ENSG00000137812	ENST00000346991;ENST00000260369;ENST00000399668	T;T	0.16897	2.31;2.31	4.64	0.322	0.15888	.	0.547984	0.17535	N	0.170730	T	0.07503	0.0189	N	0.08118	0	0.09310	N	1	B;B;P	0.39352	0.101;0.009;0.669	B;B;B	0.34652	0.053;0.001;0.187	T	0.24621	-1.0155	10	0.62326	D	0.03	.	9.0014	0.36083	0.436:0.0:0.564:0.0	.	950;976;950	Q8NG31-2;Q8NG31;Q8NG31-4	.;CASC5_HUMAN;.	F	976;950;950	ENSP00000335463:V976F;ENSP00000382576:V950F	ENSP00000260369:V950F	V	+	1	0	CASC5	38702602	0.000000	0.05858	0.020000	0.16555	0.900000	0.52787	-0.061000	0.11693	0.051000	0.15978	0.557000	0.71058	GTT	.	.	.	none		0.378	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		T	40915310	G	T	40915310	3	4	240	1	0	0	0	0	1	0	0	0	2665	1377	48	4	2964	4	CASC5	15	40915310	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10		40915310	61616082	73	14726											
TGM7	116179	hgsc.bcm.edu	37	chr15	43585144	43585145	+	Missense_Mutation	DNP	GC	GC	TT																															ggtccccagcagctctgacgGcttgggtcctgtgtaggaga																								rs267604217		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr15:43585144_43585145GC>TT	ENST00000452443.2	-	3	205_206	c.201_202GC>AA	c.(199-204)aaGCcg>aaAAcg	p.P68T		NM_052955.2	NP_443187.1	Q96PF1	TGM7_HUMAN	transglutaminase 7	68					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)	AGCTCTGACGGCTTGGGTCCTG	0.559																																					p.P68T|p.K67K		Atlas-SNP	.											.	TGM7	86	.	0			c.C202A|c.G201A						PASS	.																																			SO:0001583	missense	116179	exon3			CTGACGGCTTGGG|TGACGGCTTGGGT	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.201_202delinsTT	chr15.hg19:g.43585144_43585145delinsTT	ENSP00000389466:p.Pro68Thr	44.0	0.0	.		65.0|62.0	14.0	.	NM_052955		Missense_Mutation|Silent	SNP	ENST00000452443.2	hg19	CCDS32213.1																																																																																			.	.	.	none		0.559	TGM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432489.1	NM_052955		TT	43585145	GC	TT	43585144	3	4	240	1	0	0	0	0	1	0	0	0	15847	1203	42	4	1974	4	TGM7	15	43585144	Missense_Mutation	DNP	GC	TCGA-Q2-A5QZ-01A-11D-A28G-10	2669834	43585144	58946248	74	14727											
HDC	3067	hgsc.bcm.edu	37	chr15	50535435	50535435	+	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	ttcaaaatatttagccatttCagtaccctggaattgcaagt	13	14	6	8	0	2	0	2	0	0	0	2	1	2	1	2	1	3	2	2	1	7	7			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr15:50535435C>T	ENST00000267845.3	-	11	1549	c.1147G>A	c.(1147-1149)Gaa>Aaa	p.E383K	HDC_ENST00000543581.1_Missense_Mutation_p.E350K|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)		TTAGCCATTTCAGTACCCTGG	0.403																																					p.E383K	GBM(95;1627 1936 6910 9570)	Atlas-SNP	.											.	HDC	86	.	0			c.G1147A						PASS	.						65	65	65					15																	50535435		2196	4295	6491	SO:0001583	missense	3067	exon11			CCATTTCAGTACC		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.1147G>A	chr15.hg19:g.50535435C>T	ENSP00000267845:p.Glu383Lys	106.0	0.0	.		155.0	62.0	.	NM_002112		Missense_Mutation	SNP	ENST00000267845.3	hg19	CCDS10134.1	.	.	.	.	.	.	.	.	.	.	C	16.16	3.043666	0.55003	.	.	ENSG00000140287	ENST00000267845;ENST00000543581	T;T	0.39592	1.07;1.07	5.82	4.9	0.64082	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.280579	0.41605	N	0.000857	T	0.37972	0.1023	L	0.28694	0.88	0.58432	D	0.999998	P;P	0.35894	0.526;0.526	B;B	0.43508	0.422;0.307	T	0.10200	-1.0640	10	0.18276	T	0.48	-10.5182	14.7799	0.69756	0.0:0.9307:0.0:0.0693	.	350;383	B7ZM01;P19113	.;DCHS_HUMAN	K	383;350	ENSP00000267845:E383K;ENSP00000440252:E350K	ENSP00000267845:E383K	E	-	1	0	HDC	48322727	0.999000	0.42202	0.897000	0.35233	0.970000	0.65996	3.899000	0.56288	1.462000	0.47948	0.467000	0.42956	GAA	.	.	.	none		0.403	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1			T	50535435	C	T	50535435	3	4	240	1	0	0	0	0	1	0	0	0	7022	835	29	2	849	2	HDC	15	50535435	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	6950291	50535435	51995957	75	14728											
MYO5C	55930	hgsc.bcm.edu	37	chr15	52500781	52500781	+	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	ctgtactgcttcaggcaattGagaaaatgacaagtgttgga	13	11	11	6	0	1	2	1	2	0	1	1	4	1	3	0	2	2	4	0	2	5	4			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr15:52500781G>T	ENST00000261839.7	-	36	4517	c.4356C>A	c.(4354-4356)ctC>ctA	p.L1452L	RP11-430B1.2_ENST00000560518.1_lincRNA	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	1452	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)		TCAGGCAATTGAGAAAATGAC	0.438											OREG0023129	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L1452L		Atlas-SNP	.											.	MYO5C	162	.	0			c.C4356A						PASS	.						105	107	106					15																	52500781		1889	4099	5988	SO:0001819	synonymous_variant	55930	exon36			GCAATTGAGAAAA	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.4356C>A	chr15.hg19:g.52500781G>T		58.0	0.0	.	985	108.0	9.0	.	NM_018728	Q6P1W8	Silent	SNP	ENST00000261839.7	hg19	CCDS42036.1																																																																																			.	.	.	none		0.438	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728		T	52500781	G	T	52500781	2	4	240	1	0	0	0	0	0	0	0	1	10087	1277	45	4		4	MYO5C	15	52500781	Silent	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	1965346	52500781	50030611	76	14729											
CSPG4	1464	hgsc.bcm.edu	37	chr15	75982866	75982866	+	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	tcgggggtcagaggccggagGaggctgcggccattgagggt	6	6	21	8	3	1	2	1	1	0	1	2	4	1	4	2	8	1	1	2	8	0	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr15:75982866G>C	ENST00000308508.5	-	3	632	c.540C>G	c.(538-540)ctC>ctG	p.L180L		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	180	Globular or compact configuration stabilized by disulfide bonds.|Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						GAGGCCGGAGGAGGCTGCGGC	0.647																																					p.L180L		Atlas-SNP	.											.	CSPG4	175	.	0			c.C540G						PASS	.						35	40	38					15																	75982866		2147	4173	6320	SO:0001819	synonymous_variant	1464	exon3			CCGGAGGAGGCTG	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.540C>G	chr15.hg19:g.75982866G>C		43.0	0.0	.		62.0	20.0	.	NM_001897	D3DW77|Q92675	Silent	SNP	ENST00000308508.5	hg19	CCDS10284.1																																																																																			.	.	.	none		0.647	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		C	75982866	G	C	75982866	2	2	240	1	0	0	0	0	0	0	0	1	3962	1161	41	4		4	CSPG4	15	75982866	Silent	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	23482085	75982866	26548526	77	14730											
HMOX2	3163	hgsc.bcm.edu	37	chr16	4557977	4557977	+	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	gtggcccatgcatacacccgCtacatgggggatctctcggg	7	8	13	13	2	1	0	0	0	1	0	3	1	1	1	2	4	3	2	2	4	2	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr16:4557977C>T	ENST00000570646.1	+	4	1073	c.468C>T	c.(466-468)cgC>cgT	p.R156R	HMOX2_ENST00000575120.1_Silent_p.R127R|HMOX2_ENST00000414777.1_Silent_p.R156R|HMOX2_ENST00000406590.2_Silent_p.R156R|HMOX2_ENST00000458134.3_Silent_p.R156R|HMOX2_ENST00000219700.6_Silent_p.R156R|HMOX2_ENST00000398595.3_Silent_p.R156R	NM_002134.3	NP_002125.3	P30519	HMOX2_HUMAN	heme oxygenase (decycling) 2	156					cellular iron ion homeostasis (GO:0006879)|heme catabolic process (GO:0042167)|heme oxidation (GO:0006788)|porphyrin-containing compound metabolic process (GO:0006778)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heme oxygenase (decyclizing) activity (GO:0004392)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	8						CATACACCCGCTACATGGGGG	0.617																																					p.R156R		Atlas-SNP	.											.	HMOX2	22	.	0			c.C468T						PASS	.						39	43	41					16																	4557977		2197	4300	6497	SO:0001819	synonymous_variant	3163	exon4			CACCCGCTACATG		CCDS10517.1, CCDS66931.1, CCDS73818.1	16p13.3	2008-02-05			ENSG00000103415	ENSG00000103415	1.14.99.3		5014	protein-coding gene	gene with protein product		141251				1575508	Standard	NM_002134		Approved	HO-2	uc002cwq.4	P30519	OTTHUMG00000129473	ENST00000570646.1:c.468C>T	chr16.hg19:g.4557977C>T		80.0	0.0	.		216.0	85.0	.	NM_001127205	A8MT35|D3DUD5|I3L430|O60605	Silent	SNP	ENST00000570646.1	hg19	CCDS10517.1																																																																																			.	.	.	none		0.617	HMOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251636.2			T	4557977	C	T	4557977	2	4	240	1	0	0	0	0	0	0	0	1	7251	784	28	2		2	HMOX2	16	4557977	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10		4557977	85796776	78	14731											
LAT	27040	hgsc.bcm.edu	37	chr16	28996234	28996234	+	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	1	0	0	0	0	0	0	0	0	ctgtccccgtcttgggggggGccagcagacccttggtgagt	4	9	16	12	1	1	2	0	1	1	1	2	2	2	2	4	5	1	1	4	5	0	2	rs572112079	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr16:28996234G>A	ENST00000360872.5	+	0	0				LAT_ENST00000454369.2_5'Flank|LAT_ENST00000354453.4_5'Flank|RP11-264B17.3_ENST00000569969.1_RNA|LAT_ENST00000395461.3_Missense_Mutation_p.A18T|LAT_ENST00000395456.2_5'Flank|LAT_ENST00000564277.1_5'Flank|LAT_ENST00000566177.1_5'Flank			O43561	LAT_HUMAN	linker for activation of T cells						blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|gene expression (GO:0010467)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|lymphocyte homeostasis (GO:0002260)|mast cell degranulation (GO:0043303)|platelet activation (GO:0030168)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|regulation of T cell activation (GO:0050863)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|immunological synapse (GO:0001772)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|SH3/SH2 adaptor activity (GO:0005070)			large_intestine(2)|lung(3)|urinary_tract(1)	6		Hepatocellular(780;0.244)				CTTGGGGGGGGCCAGCAGACC	0.731																																					p.A18T		Atlas-SNP	.											.	LAT	22	.	0			c.G52A						PASS	.						7	8	8					16																	28996234		690	1584	2274	SO:0001631	upstream_gene_variant	27040	exon1			GGGGGGGCCAGCA	AF036905	CCDS10647.1, CCDS32425.1, CCDS45455.1, CCDS53999.1	16q13	2011-11-01			ENSG00000213658	ENSG00000213658			18874	protein-coding gene	gene with protein product	"linker for activation of T cells, transmembrane adaptor"	602354				9489702	Standard	NM_014387		Approved	LAT1	uc010vdj.2	O43561	OTTHUMG00000131761		chr16.hg19:g.28996234G>A	Exception_encountered	16.0	0.0	.		91.0	29.0	.	NM_001014989	B7WPI0|C7C5T6|G5E9K3|O43919	Missense_Mutation	SNP	ENST00000360872.5	hg19	CCDS10647.1	.	.	.	.	.	.	.	.	.	.	G	10.06	1.247385	0.22880	.	.	ENSG00000213658	ENST00000395461	.	.	.	2.5	-1.56	0.08532	.	.	.	.	.	T	0.16128	0.0388	N	0.08118	0	0.19300	N	0.999973	B	0.02656	0.0	B	0.01281	0.0	T	0.21655	-1.0239	8	0.87932	D	0	-0.7971	3.9972	0.09564	0.1852:0.4888:0.326:0.0	.	18	B7WPI0	.	T	18	.	ENSP00000378845:A18T	A	+	1	0	LAT	28903735	0.000000	0.05858	0.002000	0.10522	0.036000	0.12997	-0.751000	0.04803	-0.063000	0.13065	-0.264000	0.10439	GCC	.	.	.	none		0.731	LAT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254688.2			A	28996234	G	A	28996234	1	1	240	0	1	0	0	0	0	0	0	0	8651	1203	42	2		2	LAT	16	28996234	5'Flank	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	24438257	28996234	61358519	79	14732											
PRRT2	112476	hgsc.bcm.edu	37	chr16	29825753	29825753	+	Missense_Mutation	SNP	A	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	cgctggtggggggagtcctcAtcatcatcgcctcctgcgtc	4	10	13	14	3	3	0	3	0	0	0	7	1	5	1	3	4	1	1	3	4	0	0			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr16:29825753A>C	ENST00000358758.7	+	3	1262	c.979A>C	c.(979-981)Atc>Ctc	p.I327L	AC009133.20_ENST00000569039.1_RNA|PAGR1_ENST00000609618.1_5'Flank|PRRT2_ENST00000567659.1_Missense_Mutation_p.I327L|PAGR1_ENST00000320330.6_5'Flank|AC009133.14_ENST00000569981.1_RNA|PRRT2_ENST00000300797.6_3'UTR	NM_001256442.1|NM_001256443.1|NM_145239.2	NP_001243371.1|NP_001243372.1|NP_660282.2	Q7Z6L0	PRRT2_HUMAN	proline-rich transmembrane protein 2	327					neuromuscular process controlling posture (GO:0050884)|response to biotic stimulus (GO:0009607)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	8						GGGAGTCCTCATCATCATCGC	0.642																																					p.I327L		Atlas-SNP	.											.	PRRT2	28	.	0			c.A979C						PASS	.						73	81	78					16																	29825753		2197	4300	6497	SO:0001583	missense	112476	exon3			GTCCTCATCATCA	BC011405	CCDS10654.1, CCDS58445.1, CCDS58446.1	16p11.2	2014-02-03			ENSG00000167371	ENSG00000167371		"Proline-rich transmembrane proteins"	30500	protein-coding gene	gene with protein product	"interferon induced transmembrane protein domain containing 1"	614386	"infantile convulsions and paroxysmal choreoathetosis"	ICCA		22101681, 22243967	Standard	NM_145239		Approved	FLJ25513, DKFZp547J199, IFITMD1, FICCA	uc002dud.3	Q7Z6L0	OTTHUMG00000177142	ENST00000358758.7:c.979A>C	chr16.hg19:g.29825753A>C	ENSP00000351608:p.Ile327Leu	18.0	0.0	.		59.0	18.0	.	NM_001256442	A8K8M8|Q8N2N8|Q8NAQ7|Q8ND36|Q96FA8	Missense_Mutation	SNP	ENST00000358758.7	hg19	CCDS10654.1	.	.	.	.	.	.	.	.	.	.	A	19.38	3.815687	0.70912	.	.	ENSG00000167371	ENST00000358758	D	0.85339	-1.97	3.71	3.71	0.42584	.	0.745808	0.12408	N	0.471504	D	0.86410	0.5926	N	0.25380	0.74	0.80722	D	1	D;D	0.63046	0.992;0.99	D;D	0.76071	0.987;0.978	T	0.82796	-0.0280	10	0.40728	T	0.16	-8.8013	10.7234	0.46052	1.0:0.0:0.0:0.0	.	327;327	Q7Z6L0;Q7Z6L0-2	PRRT2_HUMAN;.	L	327	ENSP00000351608:I327L	ENSP00000351608:I327L	I	+	1	0	PRRT2	29733254	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.922000	0.48860	1.481000	0.48307	0.372000	0.22366	ATC	.	.	.	none		0.642	PRRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255161.3	NM_145239		C	29825753	A	C	29825753	3	2	240	1	0	0	0	0	1	0	0	0	12620	217	8	5	985	5	PRRT2	16	29825753	Missense_Mutation	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	829519	29825753	60529000	80	14733											
DHX38	9785	hgsc.bcm.edu	37	chr16	72141342	72141342	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgctgctgctcaagtccctcGgggtgcaggacctgctgcag	5	9	14	13	1	1	0	1	0	0	0	3	1	2	1	2	3	6	6	2	3	1	0	rs374391366		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr16:72141342G>A	ENST00000268482.3	+	20	3213	c.2704G>A	c.(2704-2706)Ggg>Agg	p.G902R	DHX38_ENST00000536867.1_Missense_Mutation_p.G214R	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	902	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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)				CAAGTCCCTCGGGGTGCAGGA	0.597																																					p.G902R	Melanoma(97;711 1442 7855 13832 28836)	Atlas-SNP	.											.	DHX38	91	.	0			c.G2704A						PASS	.	G	ARG/GLY	2,4394	4.2+/-10.8	0,2,2196	42	37	38		2704	5.3	1	16		38	0,8600		0,0,4300	no	missense	DHX38	NM_014003.3	125	0,2,6496	AA,AG,GG		0.0,0.0455,0.0154	possibly-damaging	902/1228	72141342	2,12994	2198	4300	6498	SO:0001583	missense	9785	exon20			TCCCTCGGGGTGC	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.2704G>A	chr16.hg19:g.72141342G>A	ENSP00000268482:p.Gly902Arg	25.0	0.0	.		118.0	5.0	.	NM_014003	B4DVG8|D3DWS7|O75212|Q96HN7	Missense_Mutation	SNP	ENST00000268482.3	hg19	CCDS10907.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.651253	0.88056	4.55E-4	0.0	ENSG00000140829	ENST00000268482;ENST00000536867	T;T	0.04156	3.69;3.69	5.28	5.28	0.74379	Helicase, C-terminal (1);	0.125696	0.52532	D	0.000067	T	0.14743	0.0356	M	0.85462	2.755	0.80722	D	1	D;P	0.53885	0.963;0.936	B;P	0.45449	0.429;0.481	T	0.01604	-1.1314	10	0.72032	D	0.01	.	18.7055	0.91637	0.0:0.0:1.0:0.0	.	214;902	B4DVG8;Q92620	.;PRP16_HUMAN	R	902;214	ENSP00000268482:G902R;ENSP00000437898:G214R	ENSP00000268482:G902R	G	+	1	0	DHX38	70698843	1.000000	0.71417	0.966000	0.40874	0.973000	0.67179	9.190000	0.94934	2.745000	0.94114	0.655000	0.94253	GGG	.	.	.	weak		0.597	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003		A	72141342	G	A	72141342	3	1	240	1	0	0	0	0	1	0	0	0	4513	1116	39	1	2778	1	DHX38	16	72141342	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	42315589	72141342	18213411	81	14734											
ZFHX3	463	hgsc.bcm.edu	37	chr16	72923790	72923790	+	Frame_Shift_Del	DEL	G	G	-																															aggttgagcttggccttggtGgagtagttgcacagaacgca																										TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr16:72923790delG	ENST00000268489.5	-	4	3960	c.3288delC	c.(3286-3288)tccfs	p.S1096fs	ZFHX3_ENST00000397992.5_Frame_Shift_Del_p.S182fs	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	1096					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)				TGGCCTTGGTGGAGTAGTTGC	0.557																																					p.T1097fs		Atlas-Indel,Pindel	.											.	ZFHX3	404	.	0			c.3289delA						PASS	.						107	75	86					16																	72923790		2198	4300	6498	SO:0001589	frameshift_variant	463	exon4			.	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.3288delC	chr16.hg19:g.72923790delG	ENSP00000268489:p.Ser1096fs	16.0	0.0	0		42.0	14.0	0.333333	NM_006885	D3DWS8|O15101|Q13719	Frame_Shift_Del	DEL	ENST00000268489.5	hg19	CCDS10908.1																																																																																			.	.	.	none		0.557	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		-	72923790	G	-	72923790	7	5	240	1	0	1	0	1	0	0	0	0	17646	1335	47	0	7851	0	ZFHX3	16	72923790	Frame_Shift_Del	DEL	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	782448	72923790	17430963	82	14735											
MYO1D	4642	hgsc.bcm.edu	37	chr17	31098169	31098169	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgagctcccacatgaatatAgttgtaggatgaaagggatt	13	12	11	5	0	0	3	0	3	0	0	1	5	1	5	1	2	1	3	1	2	5	6			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr17:31098169A>G	ENST00000318217.5	-	6	992	c.688T>C	c.(688-690)Tat>Cat	p.Y230H	MYO1D_ENST00000579584.1_Missense_Mutation_p.Y230H|MYO1D_ENST00000583621.1_Missense_Mutation_p.Y230H|MYO1D_ENST00000394649.4_Missense_Mutation_p.Y142H	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID	230	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)			ACATGAATATAGTTGTAGGAT	0.348																																					p.Y230H		Atlas-SNP	.											.	MYO1D	93	.	0			c.T688C						PASS	.						104	105	105					17																	31098169		2203	4300	6503	SO:0001583	missense	4642	exon6			GAATATAGTTGTA	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.688T>C	chr17.hg19:g.31098169A>G	ENSP00000324527:p.Tyr230His	64.0	0.0	.		87.0	4.0	.	NM_015194	A6H8V3|Q8NHP9	Missense_Mutation	SNP	ENST00000318217.5	hg19	CCDS32615.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.637013	0.87760	.	.	ENSG00000176658	ENST00000318217	D	0.91124	-2.79	5.82	5.82	0.92795	Myosin head, motor domain (2);	0.000000	0.36134	U	0.002776	D	0.96941	0.9001	H	0.97265	3.97	0.58432	D	0.999999	D;D	0.67145	0.996;0.993	D;D	0.71870	0.966;0.975	D	0.98122	1.0426	10	0.87932	D	0	.	14.1486	0.65367	1.0:0.0:0.0:0.0	.	141;230	Q7Z3N6;O94832	.;MYO1D_HUMAN	H	230	ENSP00000324527:Y230H	ENSP00000324527:Y230H	Y	-	1	0	MYO1D	28122282	1.000000	0.71417	0.999000	0.59377	0.921000	0.55340	8.730000	0.91510	2.232000	0.73038	0.528000	0.53228	TAT	.	.	.	none		0.348	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1			G	31098169	A	G	31098169	3	3	240	1	0	0	0	0	1	0	0	0	10078	420	15	3	2400	3	MYO1D	17	31098169	Missense_Mutation	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10		31098169	50097041	83	14736											
LYZL6	57151	hgsc.bcm.edu	37	chr17	34263772	34263772	+	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	tcctcaccagttgttcatccCccgtgctccggacacaatcc	7	10	6	18	2	2	0	2	0	0	0	6	1	6	1	6	1	1	3	6	1	1	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr17:34263772C>G	ENST00000585556.1	-	4	698	c.364G>C	c.(364-366)Ggg>Cgg	p.G122R	LYZL6_ENST00000492340.2_5'UTR|LYZL6_ENST00000394523.3_Missense_Mutation_p.G122R|LYZL6_ENST00000293274.4_Missense_Mutation_p.G122R			O75951	LYZL6_HUMAN	lysozyme-like 6	122					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)			breast(1)|endometrium(1)|large_intestine(1)|lung(8)|stomach(1)	12				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TTGTTCATCCCCCGTGCTCCG	0.572																																					p.G122R		Atlas-SNP	.											.	LYZL6	18	.	0			c.G364C						PASS	.						114	103	107					17																	34263772		2203	4300	6503	SO:0001583	missense	57151	exon3			TCATCCCCCGTGC	AF088219, AY742214	CCDS11302.1	17q11.2	2014-04-10			ENSG00000161572	ENSG00000275722			29614	protein-coding gene	gene with protein product		612751				10213461	Standard	NM_020426		Approved	LYC1, PRO1485, TKAL754	uc002hkj.2	O75951	OTTHUMG00000188400	ENST00000585556.1:c.364G>C	chr17.hg19:g.34263772C>G	ENSP00000468094:p.Gly122Arg	20.0	0.0	.		115.0	61.0	.	NM_020426	Q6UW30	Missense_Mutation	SNP	ENST00000585556.1	hg19	CCDS11302.1	.	.	.	.	.	.	.	.	.	.	C	11.76	1.733915	0.30684	.	.	ENSG00000161572	ENST00000293274;ENST00000394523	T;T	0.75589	-0.95;-0.95	4.89	3.9	0.45041	Lysozyme-like domain (1);	0.000000	0.64402	D	0.000001	D	0.88273	0.6392	M	0.93462	3.42	0.09310	N	0.999991	D	0.89917	1.0	D	0.97110	1.0	T	0.81048	-0.1109	10	0.87932	D	0	-6.5656	10.8134	0.46559	0.1893:0.8107:0.0:0.0	.	122	O75951	LYZL6_HUMAN	R	122	ENSP00000293274:G122R;ENSP00000378031:G122R	ENSP00000293274:G122R	G	-	1	0	LYZL6	31287885	0.102000	0.21896	0.008000	0.14137	0.071000	0.16799	1.597000	0.36729	1.168000	0.42723	0.561000	0.74099	GGG	.	.	.	none		0.572	LYZL6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256578.2	NM_020426		G	34263772	C	G	34263772	3	3	240	1	0	0	0	0	1	0	0	0	9141	623	22	4	90	4	LYZL6	17	34263772	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	3165603	34263772	46931438	84	14737											
KRTAP4-11	653240	hgsc.bcm.edu	37	chr17	39274238	39274238	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacacacagcagctggggcgAcagcagctggagatgcagca	12	3	15	11	1	0	1	0	0	0	1	0	4	0	1	0	3	6	6	0	3	0	0			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr17:39274238A>G	ENST00000391413.2	-	1	368	c.330T>C	c.(328-330)tgT>tgC	p.C110C		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	110	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)			agctggggcgacagcagctgg	0.652																																					p.C110C		Atlas-SNP	.											.	KRTAP4-11	94	.	0			c.T330C						PASS	.						5	9	8					17																	39274238		657	1550	2207	SO:0001819	synonymous_variant	653240	exon1			GGGGCGACAGCAG	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.330T>C	chr17.hg19:g.39274238A>G		27.0	0.0	.		116.0	14.0	.	NM_033059	A0AUY2	Silent	SNP	ENST00000391413.2	hg19	CCDS45675.1																																																																																			.	.	.	none		0.652	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1			G	39274238	A	G	39274238	2	3	240	1	0	0	0	0	0	0	0	1	8556	273	10	3		3	KRTAP4-11	17	39274238	Silent	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	5010466	39274238	41920972	85	14738											
KRTAP4-12	83755	hgsc.bcm.edu	37	chr17	39280069	39280069	+	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	gtggtctgacagcagctgggGcggcagcaggtgggctggca	6	6	20	9	1	1	1	0	1	1	0	1	1	1	1	0	7	3	6	0	7	0	0	rs374262239		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr17:39280069G>A	ENST00000394014.1	-	1	350	c.306C>T	c.(304-306)cgC>cgT	p.R102R		NM_031854.2	NP_114060.1	Q9BQ66	KR412_HUMAN	keratin associated protein 4-12	102	31 X 5 AA repeats of C-C-[GRQVIL]-[SPTR]- [VSTQPC].					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)			AGCAGCTGGGGCGGCAGCAGG	0.667																																					p.R102R		Atlas-SNP	.											.	KRTAP4-12	32	.	0			c.C306T						PASS	.	G		44,4314		0,44,2135	38	44	42		306	-2.5	0	17		42	0,8532		0,0,4266	no	coding-synonymous	KRTAP4-12	NM_031854.2		0,44,6401	AA,AG,GG		0.0,1.0096,0.3413		102/202	39280069	44,12846	2179	4266	6445	SO:0001819	synonymous_variant	83755	exon1			GCTGGGGCGGCAG	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.306C>T	chr17.hg19:g.39280069G>A		13.0	0.0	.		197.0	20.0	.	NM_031854	A3KMC5|Q495I0	Silent	SNP	ENST00000394014.1	hg19	CCDS32649.1																																																																																			.	.	.	weak		0.667	KRTAP4-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257777.1			A	39280069	G	A	39280069	2	1	240	1	0	0	0	0	0	0	0	1	8557	1190	42	2		2	KRTAP4-12	17	39280069	Silent	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	5831	39280069	41915141	86	14739											
TUBG1	7283	hgsc.bcm.edu	37	chr17	40765685	40765685	+	Silent	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	gtggtgctggacaacacagcCctgaaccggattgccacaga	11	6	12	12	1	0	2	0	1	0	1	0	4	0	4	3	3	5	1	3	3	2	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr17:40765685C>T	ENST00000251413.3	+	7	689	c.627C>T	c.(625-627)gcC>gcT	p.A209A		NM_001070.4	NP_001061.2	P23258	TBG1_HUMAN	tubulin, gamma 1	209					cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|meiotic spindle organization (GO:0000212)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	apical part of cell (GO:0045177)|cell leading edge (GO:0031252)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|gamma-tubulin complex (GO:0000930)|nonmotile primary cilium (GO:0031513)|pericentriolar material (GO:0000242)|polar microtubule (GO:0005827)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.A209A(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.129)	Vinblastine(DB00570)	ACAACACAGCCCTGAACCGGA	0.562																																					p.A209A	Colon(20;114 698 11420 22864)	Atlas-SNP	.											TUBG1,colon,carcinoma,0,1	TUBG1	25	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C627T						PASS	.						176	166	169					17																	40765685		2203	4300	6503	SO:0001819	synonymous_variant	7283	exon7			CACAGCCCTGAAC	BC000619	CCDS11433.1	17q21.31	2010-03-15	2000-01-20		ENSG00000131462	ENSG00000131462		"Tubulins"	12417	protein-coding gene	gene with protein product		191135	"tubulin, gamma polypeptide"	TUBG		1904010	Standard	NM_001070		Approved	TUBGCP1	uc002ian.3	P23258		ENST00000251413.3:c.627C>T	chr17.hg19:g.40765685C>T		65.0	0.0	.		200.0	8.0	.	NM_001070	Q53X79|Q9BW59	Silent	SNP	ENST00000251413.3	hg19	CCDS11433.1																																																																																			.	.	.	none		0.562	TUBG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450548.1	NM_001070		T	40765685	C	T	40765685	2	4	240	1	0	0	0	0	0	0	0	1	16776	610	22	2		2	TUBG1	17	40765685	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	1485616	40765685	40429525	87	14740											
SOST	50964	hgsc.bcm.edu	37	chr17	41835944	41835944	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgttctccgcccggttcaTggtcttgttgttctccagct	2	16	9	14	3	4	0	1	0	3	0	7	0	5	0	4	2	1	5	4	2	0	5			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr17:41835944T>C	ENST00000301691.2	-	1	212	c.166A>G	c.(166-168)Atg>Gtg	p.M56V		NM_025237.2	NP_079513.1	Q9BQB4	SOST_HUMAN	sclerostin	56					cellular response to parathyroid hormone stimulus (GO:0071374)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000054)|ossification (GO:0001503)|positive regulation of transcription, DNA-templated (GO:0045893)|response to mechanical stimulus (GO:0009612)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|transcription factor binding (GO:0008134)			large_intestine(2)|lung(3)|prostate(1)	6		Breast(137;0.00725)		UCEC - Uterine corpus endometrioid carcinoma (308;0.177)|BRCA - Breast invasive adenocarcinoma(366;0.0741)		GCCCGGTTCATGGTCTTGTTG	0.597																																					p.M56V		Atlas-SNP	.											.	SOST	19	.	0			c.A166G						PASS	.						57	54	55					17																	41835944		2203	4300	6503	SO:0001583	missense	50964	exon1			GGTTCATGGTCTT	AF326736	CCDS11468.1	17q12-q21	2014-06-28	2010-04-28			ENSG00000167941			13771	protein-coding gene	gene with protein product		605740	"sclerosteosis"			11179006, 11181578	Standard	NM_025237		Approved	VBCH	uc002iec.1	Q9BQB4		ENST00000301691.2:c.166A>G	chr17.hg19:g.41835944T>C	ENSP00000301691:p.Met56Val	22.0	0.0	.		87.0	26.0	.	NM_025237	Q495N9	Missense_Mutation	SNP	ENST00000301691.2	hg19	CCDS11468.1	.	.	.	.	.	.	.	.	.	.	T	16.55	3.155167	0.57259	.	.	ENSG00000167941	ENST00000301691	T	0.76578	-1.03	4.26	3.15	0.36227	.	0.404445	0.25642	N	0.029277	T	0.67702	0.2921	L	0.55481	1.735	0.35701	D	0.815622	B	0.33171	0.4	B	0.24394	0.053	T	0.69756	-0.5059	10	0.48119	T	0.1	-0.6649	8.7222	0.34447	0.1693:0.0:0.0:0.8307	.	56	Q9BQB4	SOST_HUMAN	V	56	ENSP00000301691:M56V	ENSP00000301691:M56V	M	-	1	0	SOST	39191470	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.993000	0.49425	0.648000	0.30732	0.454000	0.30748	ATG	.	.	.	none		0.597	SOST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453502.1	NM_025237		C	41835944	T	C	41835944	3	2	240	1	0	0	0	0	1	0	0	0	14951	1464	51	3	483	3	SOST	17	41835944	Missense_Mutation	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	1070259	41835944	39359266	88	14741											
HDAC5	10014	hgsc.bcm.edu	37	chr17	42171119	42171119	+	Missense_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	agagcccaccagagccccccGtagctccacagggctggggc	8	3	13	17	1	0	2	0	0	0	2	1	2	1	2	6	3	3	3	6	3	1	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr17:42171119G>A	ENST00000393622.2	-	4	509	c.178C>T	c.(178-180)Cgg>Tgg	p.R60W	HDAC5_ENST00000586802.1_Missense_Mutation_p.R60W|HDAC5_ENST00000336057.5_Missense_Mutation_p.R60W|HDAC5_ENST00000225983.6_Missense_Mutation_p.R61W	NM_001015053.1|NM_005474.4	NP_001015053.1|NP_005465.2	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5	60					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|chromatin silencing (GO:0006342)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|inflammatory response (GO:0006954)|multicellular organismal response to stress (GO:0033555)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|osteoblast development (GO:0002076)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression, epigenetic (GO:0040029)|regulation of myotube differentiation (GO:0010830)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|histone deacetylase complex (GO:0000118)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	21		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		AGAGCCCCCCGTAGCTCCACA	0.667																																					p.R61W		Atlas-SNP	.											HDAC5,NS,carcinoma,0,1	HDAC5	67	.	0			c.C181T						PASS	.						13	15	15					17																	42171119		2197	4295	6492	SO:0001583	missense	10014	exon4			CCCCCCGTAGCTC	AF249731	CCDS32663.1, CCDS45696.1	17q21	2008-07-18					3.5.1.98		14068	protein-coding gene	gene with protein product		605315				10220385, 9610721	Standard	XM_005256905		Approved	KIAA0600, NY-CO-9, FLJ90614	uc002iff.1	Q9UQL6		ENST00000393622.2:c.178C>T	chr17.hg19:g.42171119G>A	ENSP00000377244:p.Arg60Trp	26.0	0.0	.		156.0	73.0	.	NM_001015053	C9JFV9|O60340|O60528|Q96DY4	Missense_Mutation	SNP	ENST00000393622.2	hg19	CCDS45696.1	.	.	.	.	.	.	.	.	.	.	G	18.35	3.604577	0.66445	.	.	ENSG00000108840	ENST00000225983;ENST00000393622;ENST00000336057	T;T;T	0.50001	0.78;0.78;0.76	4.14	4.14	0.48551	.	0.240511	0.26859	N	0.022121	T	0.56891	0.2016	L	0.32530	0.975	0.42561	D	0.993142	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.69654	0.965;0.924;0.965;0.924	T	0.63189	-0.6693	10	0.87932	D	0	-23.2017	15.156	0.72743	0.0:0.0:1.0:0.0	.	60;60;61;60	Q9UQL6-2;B4DGT4;Q9UQL6-3;Q9UQL6	.;.;.;HDAC5_HUMAN	W	61;60;60	ENSP00000225983:R61W;ENSP00000377244:R60W;ENSP00000337290:R60W	ENSP00000225983:R61W	R	-	1	2	HDAC5	39526645	0.996000	0.38824	0.992000	0.48379	0.875000	0.50365	3.362000	0.52314	1.858000	0.53909	0.462000	0.41574	CGG	.	.	.	none		0.667	HDAC5-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457686.1	NM_001015053		A	42171119	G	A	42171119	3	1	240	1	0	0	0	0	1	0	0	0	7017	1144	40	1	3286	1	HDAC5	17	42171119	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	335175	42171119	39024091	89	14742											
RALBP1	10928	hgsc.bcm.edu	37	chr18	9524725	9524725	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacgctgccagagacccaggCgggcatcaaggaggagatca	12	3	14	12	2	2	2	2	0	0	2	2	5	2	3	2	4	1	2	2	4	1	0			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr18:9524725C>T	ENST00000019317.4	+	5	1410	c.1187C>T	c.(1186-1188)gCg>gTg	p.A396V	RALBP1_ENST00000383432.3_Missense_Mutation_p.A396V			Q15311	RBP1_HUMAN	ralA binding protein 1	396					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)	GAGACCCAGGCGGGCATCAAG	0.557																																					p.A396V		Atlas-SNP	.											RALBP1,NS,neuroblastoma,0,1	RALBP1	48	.	0			c.C1187T						PASS	.						42	36	38					18																	9524725		2203	4300	6503	SO:0001583	missense	10928	exon5			CCCAGGCGGGCAT	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.1187C>T	chr18.hg19:g.9524725C>T	ENSP00000019317:p.Ala396Val	64.0	1.0	.		73.0	6.0	.	NM_006788	D3DUI0	Missense_Mutation	SNP	ENST00000019317.4	hg19	CCDS11845.1	.	.	.	.	.	.	.	.	.	.	C	14.23	2.472202	0.43942	.	.	ENSG00000017797	ENST00000019317;ENST00000383432	T;T	0.10763	2.84;2.84	5.51	3.42	0.39159	.	0.141251	0.64402	D	0.000006	T	0.06142	0.0159	N	0.14661	0.345	0.41488	D	0.988201	B	0.23650	0.089	B	0.18871	0.023	T	0.32079	-0.9920	10	0.51188	T	0.08	0.7672	7.3696	0.26794	0.6491:0.2443:0.0:0.1066	.	396	Q15311	RBP1_HUMAN	V	396	ENSP00000019317:A396V;ENSP00000372924:A396V	ENSP00000019317:A396V	A	+	2	0	RALBP1	9514725	1.000000	0.71417	0.749000	0.31150	0.410000	0.31052	6.100000	0.71473	0.640000	0.30582	-0.140000	0.14226	GCG	.	.	.	none		0.557	RALBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254479.1	NM_006788		T	9524725	C	T	9524725	3	4	240	1	0	0	0	0	1	0	0	0	13025	768	27	1	1201	1	RALBP1	18	9524725	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10		9524725	68552523	90	14743											
OR7E24	26648	hgsc.bcm.edu	37	chr19	9362181	9362181	+	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	ctgcactaccgaatcatcatGaacccacgcctctgtggctt	9	10	7	15	2	3	1	2	1	1	0	3	2	3	1	3	1	3	2	3	1	3	2			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr19:9362181G>C	ENST00000456448.1	+	1	576	c.462G>C	c.(460-462)atG>atC	p.M154I		NM_001079935.1	NP_001073404.1	Q6IFN5	O7E24_HUMAN	olfactory receptor, family 7, subfamily E, member 24	154						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)	16						GAATCATCATGAACCCACGCC	0.443																																					p.M154I		Atlas-SNP	.											.	OR7E24	48	.	0			c.G462C						PASS	.						130	144	139					19																	9362181		2193	4296	6489	SO:0001583	missense	26648	exon1			CATCATGAACCCA	Y10529	CCDS45955.1	19p13.2	2012-08-09	2004-03-04	2004-03-05		ENSG00000237521		"GPCR / Class A : Olfactory receptors"	8396	protein-coding gene	gene with protein product			"olfactory receptor, family 7, subfamily E, member 24 pseudogene"	OR7E24P		9268701	Standard	NM_001079935		Approved	OR19-8, HSHT2, OR7E24Q	uc002mlb.1	Q6IFN5		ENST00000456448.1:c.462G>C	chr19.hg19:g.9362181G>C	ENSP00000387523:p.Met154Ile	51.0	0.0	.		124.0	36.0	.	NM_001079935	B9EJD9|Q9UPJ1	Missense_Mutation	SNP	ENST00000456448.1	hg19	CCDS45955.1	.	.	.	.	.	.	.	.	.	.	g	10.46	1.356506	0.24598	.	.	ENSG00000237521	ENST00000456448	T	0.00551	6.65	2.39	2.39	0.29439	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00906	0.0030	M	0.80847	2.515	0.28275	N	0.924234	B	0.19706	0.038	B	0.16289	0.015	T	0.12293	-1.0553	9	0.66056	D	0.02	.	11.6917	0.51519	0.0:0.0:1.0:0.0	.	154	Q6IFN5	O7E24_HUMAN	I	154	ENSP00000387523:M154I	ENSP00000387523:M154I	M	+	3	0	OR7E24	9223181	0.999000	0.42202	0.492000	0.27490	0.028000	0.11728	2.571000	0.45990	1.353000	0.45828	0.436000	0.28706	ATG	.	.	.	none		0.443	OR7E24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449006.1			C	9362181	G	C	9362181	3	2	240	1	0	0	0	0	1	0	0	0	11228	1290	45	4	464	4	OR7E24	19	9362181	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10		9362181	49766802	91	14744											
MAN2B1	4125	hgsc.bcm.edu	37	chr19	12760979	12760979	+	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	ccgctgtcctgggtacaggcGaaccacctgggaacaccaag	10	5	12	14	2	0	0	0	0	0	0	1	2	1	1	5	3	3	2	5	3	4	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr19:12760979G>A	ENST00000456935.2	-	17	2144	c.2104C>T	c.(2104-2106)Cgc>Tgc	p.R702C	CTD-2192J16.22_ENST00000597692.1_5'Flank|MAN2B1_ENST00000221363.4_Missense_Mutation_p.R701C	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	702					cellular protein modification process (GO:0006464)|mannose metabolic process (GO:0006013)|protein deglycosylation (GO:0006517)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						GGGTACAGGCGAACCACCTGG	0.627																																					p.R702C		Atlas-SNP	.											.	MAN2B1	91	.	0			c.C2104T						PASS	.						132	111	118					19																	12760979		2203	4300	6503	SO:0001583	missense	4125	exon17			ACAGGCGAACCAC		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.2104C>T	chr19.hg19:g.12760979G>A	ENSP00000395473:p.Arg702Cys	43.0	0.0	.		166.0	8.0	.	NM_000528	G5E928|O15330|Q16680|Q93094|Q9BW13	Missense_Mutation	SNP	ENST00000456935.2	hg19	CCDS32919.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.667589	0.88348	.	.	ENSG00000104774	ENST00000456935;ENST00000536796;ENST00000221363	D;D	0.86097	-2.07;-2.07	4.91	4.91	0.64330	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	0.000000	0.45126	D	0.000392	D	0.94565	0.8249	H	0.95328	3.655	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95872	0.8892	10	0.87932	D	0	-28.1246	15.638	0.76970	0.0:0.0:1.0:0.0	.	701;702	G5E928;O00754	.;MA2B1_HUMAN	C	702;641;701	ENSP00000395473:R702C;ENSP00000221363:R701C	ENSP00000221363:R701C	R	-	1	0	MAN2B1	12621979	1.000000	0.71417	0.999000	0.59377	0.834000	0.47266	7.042000	0.76565	2.564000	0.86499	0.555000	0.69702	CGC	.	.	.	none		0.627	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344062.1			A	12760979	G	A	12760979	3	1	240	1	0	0	0	0	1	0	0	0	9223	1058	37	1	963	1	MAN2B1	19	12760979	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	3398798	12760979	46368004	92	14745											
ZNF571	51276	hgsc.bcm.edu	37	chr19	38056037	38056037	+	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	tgatgttcactaagttgtttGccacaaataaaggcctttcc	11	14	7	9	0	1	1	1	1	0	0	2	1	2	1	3	1	1	3	3	1	4	6			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr19:38056037G>A	ENST00000328550.2	-	4	1392	c.1293C>T	c.(1291-1293)ggC>ggT	p.G431G	ZNF571-AS1_ENST00000589802.1_RNA|ZNF571-AS1_ENST00000592392.1_RNA|ZNF571-AS1_ENST00000590838.1_RNA|ZNF571-AS1_ENST00000586139.1_RNA|ZNF540_ENST00000592533.1_Intron|ZNF571-AS1_ENST00000585578.1_RNA|ZNF571-AS1_ENST00000586013.1_RNA|ZNF571_ENST00000590751.1_Intron|ZNF571-AS1_ENST00000587121.1_RNA|ZNF571_ENST00000451802.2_Silent_p.G431G|ZNF571_ENST00000593133.1_Silent_p.G431G|ZNF571_ENST00000358744.3_Silent_p.G431G|ZNF571-AS1_ENST00000589750.1_RNA|ZNF571-AS1_ENST00000591430.1_RNA			Q7Z3V5	ZN571_HUMAN	zinc finger protein 571	431					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	25			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TAAGTTGTTTGCCACAAATAA	0.363																																					p.G431G		Atlas-SNP	.											.	ZNF571	54	.	0			c.C1293T						PASS	.						48	52	51					19																	38056037		2203	4299	6502	SO:0001819	synonymous_variant	51276	exon4			TTGTTTGCCACAA	AF161544	CCDS12505.1	19q13.12	2013-09-20			ENSG00000180479	ENSG00000180479		"Zinc fingers, C2H2-type", "-"	25000	protein-coding gene	gene with protein product						11042152	Standard	XM_005258977		Approved	HSPC059	uc002ogt.3	Q7Z3V5	OTTHUMG00000182016	ENST00000328550.2:c.1293C>T	chr19.hg19:g.38056037G>A		66.0	0.0	.		34.0	20.0	.	NM_016536	Q2HIY0|Q3ZCU3|Q9NZX7	Silent	SNP	ENST00000328550.2	hg19	CCDS12505.1																																																																																			.	.	.	none		0.363	ZNF571-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458669.1	NM_016536		A	38056037	G	A	38056037	2	1	240	1	0	0	0	0	0	0	0	1	18015	1306	46	2		2	ZNF571	19	38056037	Silent	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	25295058	38056037	21072946	93	14746											
B9D2	80776	hgsc.bcm.edu	37	chr19	41869392	41869392	+	Frame_Shift_Del	DEL	T	T	-																															tccgagaaaccgctggccccTatgatctgcccgatcacgtg																								rs2241714	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr19:41869392delT	ENST00000243578.3	-	2	252	c.33delA	c.(31-33)atafs	p.I11fs	TMEM91_ENST00000604123.1_Intron|TMEM91_ENST00000539627.1_Intron|B9D2_ENST00000601597.1_5'UTR|TMEM91_ENST00000413014.2_5'Flank|CTC-435M10.3_ENST00000604424.1_Intron	NM_030578.3	NP_085055.2	Q9BPU9	B9D2_HUMAN	B9 protein domain 2	11	B9. {ECO:0000255|PROSITE- ProRule:PRU00713}.		I -> M (in dbSNP:rs2241714). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		cilium assembly (GO:0042384)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|TCTN-B9D complex (GO:0036038)	gamma-tubulin binding (GO:0043015)			large_intestine(1)|ovary(1)	2						CGCTGGCCCCTATGATCTGCC	0.537																																					p.G12fs		Atlas-Indel,Pindel	.											.	B9D2	9	.	0			c.34delG						PASS	.						69	58	62					19																	41869392		2203	4300	6503	SO:0001589	frameshift_variant	80776	exon2			.	BC004157	CCDS12579.1	19q13.2	2014-01-28				ENSG00000123810			28636	protein-coding gene	gene with protein product		611951				21763481	Standard	NM_030578		Approved	MGC4093, MKS10	uc002oqj.2	Q9BPU9		ENST00000243578.3:c.33delA	chr19.hg19:g.41869392delT	ENSP00000243578:p.Ile11fs	72.0	0.0	0		124.0	67.0	0.540323	NM_030578		Frame_Shift_Del	DEL	ENST00000243578.3	hg19	CCDS12579.1																																																																																			.	.	.	none		0.537	B9D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463489.1	NM_030578		-	41869392	T	-	41869392	7	5	240	1	0	1	0	1	0	0	0	0	1278	1512	53	0	506	0	B9D2	19	41869392	Frame_Shift_Del	DEL	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	3813355	41869392	17259591	94	14747											
GLTSCR1	29998	hgsc.bcm.edu	37	chr19	48183862	48183862	+	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	tcctactgcctggcgccccgGcggtccagctcccgcagcag	4	6	12	19	4	0	0	0	0	0	0	3	0	3	0	6	3	4	3	6	3	1	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr19:48183862G>C	ENST00000396720.3	+	6	1629	c.1435G>C	c.(1435-1437)Gcg>Ccg	p.A479P	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	479										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)		TGGCGCCCCGGCGGTCCAGCT	0.692																																					p.A479P		Atlas-SNP	.											.	GLTSCR1	79	.	0			c.G1435C						PASS	.						16	21	19					19																	48183862		2061	4175	6236	SO:0001583	missense	29998	exon6			GCCCCGGCGGTCC	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.1435G>C	chr19.hg19:g.48183862G>C	ENSP00000379946:p.Ala479Pro	1.0	0.0	.		44.0	12.0	.	NM_015711	A8MW01	Missense_Mutation	SNP	ENST00000396720.3	hg19	CCDS46134.1	.	.	.	.	.	.	.	.	.	.	G	2.717	-0.267452	0.05754	.	.	ENSG00000063169	ENST00000396720	T	0.38722	1.12	4.7	-0.598	0.11649	.	.	.	.	.	T	0.40862	0.1134	L	0.38531	1.155	0.27198	N	0.960237	D	0.53885	0.963	P	0.56042	0.79	T	0.32295	-0.9912	9	0.31617	T	0.26	.	6.572	0.22543	0.2611:0.0:0.6073:0.1316	.	479	Q9NZM4	GSCR1_HUMAN	P	479	ENSP00000379946:A479P	ENSP00000379946:A479P	A	+	1	0	GLTSCR1	52875674	0.160000	0.22878	0.002000	0.10522	0.054000	0.15201	0.417000	0.21214	0.077000	0.16863	0.491000	0.48974	GCG	.	.	.	none		0.692	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711		C	48183862	G	C	48183862	3	2	240	1	0	0	0	0	1	0	0	0	6481	1203	42	4	1449	4	GLTSCR1	19	48183862	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	6314470	48183862	10945121	95	14748											
PRR12	57479	hgsc.bcm.edu	37	chr19	50100554	50100554	+	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	cccccggcccccctgcttatGatccctatgggccctactgt	4	10	8	19	1	0	1	0	1	0	0	1	1	1	1	7	2	2	1	7	2	3	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr19:50100554G>A	ENST00000418929.2	+	4	2974	c.2962G>A	c.(2962-2964)Gat>Aat	p.D988N		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	0							DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		CCCTGCTTATGATCCCTATGG	0.736																																					p.D988N		Atlas-SNP	.											.	PRR12	157	.	0			c.G2962A						PASS	.						3	4	4					19																	50100554		1585	3699	5284	SO:0001583	missense	57479	exon4			GCTTATGATCCCT	AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"KIAA1205"	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.2962G>A	chr19.hg19:g.50100554G>A	ENSP00000394510:p.Asp988Asn	0.0	0.0	.		36.0	26.0	.	NM_020719	E9PB06|Q8N4J6	Missense_Mutation	SNP	ENST00000418929.2	hg19	CCDS46143.1	.	.	.	.	.	.	.	.	.	.	G	13.42	2.231566	0.39399	.	.	ENSG00000126464	ENST00000418929;ENST00000246798;ENST00000314734	T	0.24350	1.86	4.79	4.79	0.61399	.	0.000000	0.45126	D	0.000382	T	0.37571	0.1008	L	0.38175	1.15	0.45690	D	0.998604	D	0.89917	1.0	D	0.87578	0.998	T	0.03473	-1.1033	10	0.13108	T	0.6	-21.245	14.8476	0.70272	0.0:0.0:1.0:0.0	.	988	Q9ULL5-3	.	N	988;168;168	ENSP00000394510:D988N	ENSP00000246798:D168N	D	+	1	0	PRR12	54792366	0.986000	0.35501	0.979000	0.43373	0.599000	0.36880	2.157000	0.42320	2.476000	0.83614	0.491000	0.48974	GAT	.	.	.	none		0.736	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719		A	50100554	G	A	50100554	3	1	240	1	0	0	0	0	1	0	0	0	12594	1290	45	2	2976	2	PRR12	19	50100554	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	1916692	50100554	9028429	96	14749											
GPR32	2854	hgsc.bcm.edu	37	chr19	51274070	51274070	+	Silent	SNP	T	T	C																															ctgtggatgactgtcttccgTatggcacgcacggtctccac																										TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr19:51274070T>C	ENST00000270590.4	+	1	350	c.213T>C	c.(211-213)cgT>cgC	p.R71R		NM_001506.1	NP_001497.1	O75388	GPR32_HUMAN	G protein-coupled receptor 32	71					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(4)|endometrium(4)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	29		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		CTGTCTTCCGTATGGCACGCA	0.572																																					p.R71R	Esophageal Squamous(113;152 1581 5732 15840 44398)	Atlas-SNP	.											.	GPR32	68	.	0			c.T213C						PASS	.						225	169	188					19																	51274070		2203	4300	6503	SO:0001819	synonymous_variant	2854	exon1			CTTCCGTATGGCA	AF045764	CCDS12801.1	19q13.33	2012-08-20			ENSG00000142511	ENSG00000142511		"GPCR / Class A : Resolvin receptors"	4487	protein-coding gene	gene with protein product	"resolvin D1 receptor"	603195				9653656	Standard	NM_001506		Approved	RVDR1	uc010ycf.3	O75388		ENST00000270590.4:c.213T>C	chr19.hg19:g.51274070T>C		57.0	0.0	.		158.0	8.0	.	NM_001506	Q502U7|Q6NWS5	Silent	SNP	ENST00000270590.4	hg19	CCDS12801.1																																																																																			.	.	.	none		0.572	GPR32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465016.1			C	51274070	T	C	51274070	2	2	240	1	0	0	0	0	0	0	0	1	6695	1625	57	3		3	GPR32	19	51274070	Silent	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	1173516	51274070	7854913	97	14750	154	2									
GPR32	2854	hgsc.bcm.edu	37	chr19	51274076	51274076	+	Silent	SNP	A	A	C																															atgactgtcttccgtatggcAcgcacggtctccaccgtctg																										TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr19:51274076A>C	ENST00000270590.4	+	1	356	c.219A>C	c.(217-219)gcA>gcC	p.A73A		NM_001506.1	NP_001497.1	O75388	GPR32_HUMAN	G protein-coupled receptor 32	73					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(4)|endometrium(4)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	29		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		TCCGTATGGCACGCACGGTCT	0.572																																					p.A73A	Esophageal Squamous(113;152 1581 5732 15840 44398)	Atlas-SNP	.											.	GPR32	68	.	0			c.A219C						PASS	.						215	162	180					19																	51274076		2203	4300	6503	SO:0001819	synonymous_variant	2854	exon1			TATGGCACGCACG	AF045764	CCDS12801.1	19q13.33	2012-08-20			ENSG00000142511	ENSG00000142511		"GPCR / Class A : Resolvin receptors"	4487	protein-coding gene	gene with protein product	"resolvin D1 receptor"	603195				9653656	Standard	NM_001506		Approved	RVDR1	uc010ycf.3	O75388		ENST00000270590.4:c.219A>C	chr19.hg19:g.51274076A>C		55.0	0.0	.		164.0	10.0	.	NM_001506	Q502U7|Q6NWS5	Silent	SNP	ENST00000270590.4	hg19	CCDS12801.1																																																																																			.	.	.	none		0.572	GPR32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465016.1			C	51274076	A	C	51274076	2	2	240	1	0	0	0	0	0	0	0	1	6695	146	6	5		5	GPR32	19	51274076	Silent	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10	6	51274076	7854907	98	14751	154	2									
GPR32	2854	hgsc.bcm.edu	37	chr19	51274184	51274184	+	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	gtctccaggcagtggctcctCggagagtgggcctgcaaact	7	8	14	12	1	1	1	0	0	1	1	4	2	2	1	3	4	2	3	3	4	1	0			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr19:51274184C>T	ENST00000270590.4	+	1	464	c.327C>T	c.(325-327)ctC>ctT	p.L109L		NM_001506.1	NP_001497.1	O75388	GPR32_HUMAN	G protein-coupled receptor 32	109					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(4)|endometrium(4)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	29		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		AGTGGCTCCTCGGAGAGTGGG	0.527																																					p.L109L	Esophageal Squamous(113;152 1581 5732 15840 44398)	Atlas-SNP	.											.	GPR32	68	.	0			c.C327T						PASS	.						135	123	127					19																	51274184		2203	4300	6503	SO:0001819	synonymous_variant	2854	exon1			GCTCCTCGGAGAG	AF045764	CCDS12801.1	19q13.33	2012-08-20			ENSG00000142511	ENSG00000142511		"GPCR / Class A : Resolvin receptors"	4487	protein-coding gene	gene with protein product	"resolvin D1 receptor"	603195				9653656	Standard	NM_001506		Approved	RVDR1	uc010ycf.3	O75388		ENST00000270590.4:c.327C>T	chr19.hg19:g.51274184C>T		44.0	0.0	.		129.0	6.0	.	NM_001506	Q502U7|Q6NWS5	Silent	SNP	ENST00000270590.4	hg19	CCDS12801.1																																																																																			.	.	.	none		0.527	GPR32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465016.1			T	51274184	C	T	51274184	2	4	240	1	0	0	0	0	0	0	0	1	6695	871	31	1		1	GPR32	19	51274184	Silent	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	108	51274184	7854799	99	14752											
LRRN4	164312	hgsc.bcm.edu	37	chr20	6033147	6033147	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagggtcagcacctgcagcTgctccaggtggccgagctcg	6	6	15	14	2	1	0	1	0	0	0	3	1	2	0	3	3	5	6	3	3	0	0			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr20:6033147T>C	ENST00000378858.4	-	2	523	c.299A>G	c.(298-300)cAg>cGg	p.Q100R		NM_152611.4	NP_689824.2	Q8WUT4	LRRN4_HUMAN	leucine rich repeat neuronal 4	100					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						CACCTGCAGCTGCTCCAGGTG	0.731																																					p.Q100R		Atlas-SNP	.											.	LRRN4	54	.	0			c.A299G						PASS	.						6	8	7					20																	6033147		2113	4185	6298	SO:0001583	missense	164312	exon2			TGCAGCTGCTCCA	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.299A>G	chr20.hg19:g.6033147T>C	ENSP00000368135:p.Gln100Arg	0.0	0.0	.		31.0	13.0	.	NM_152611	A8K258|Q5JWV6|Q9H419	Missense_Mutation	SNP	ENST00000378858.4	hg19	CCDS13097.1	.	.	.	.	.	.	.	.	.	.	T	1.702	-0.501239	0.04261	.	.	ENSG00000125872	ENST00000378858	T	0.04406	3.63	5.37	0.364	0.16124	.	0.918843	0.09178	N	0.837822	T	0.02970	0.0088	N	0.16233	0.39	0.18873	N	0.999982	B;B	0.06786	0.001;0.001	B;B	0.04013	0.0;0.001	T	0.48399	-0.9039	10	0.25751	T	0.34	-6.0721	4.5538	0.12126	0.2133:0.256:0.0:0.5307	.	100;100	Q6ZMD1;Q8WUT4	.;LRRN4_HUMAN	R	100	ENSP00000368135:Q100R	ENSP00000368135:Q100R	Q	-	2	0	LRRN4	5981147	0.002000	0.14202	0.402000	0.26371	0.002000	0.02628	-0.227000	0.09126	-0.136000	0.11475	-0.516000	0.04426	CAG	.	.	.	none		0.731	LRRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077907.2	NM_152611		C	6033147	T	C	6033147	3	2	240	1	0	0	0	0	1	0	0	0	9044	1580	55	3	1939	3	LRRN4	20	6033147	Missense_Mutation	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10		6033147	56992373	100	14753											
ARFGAP1	55738	hgsc.bcm.edu	37	chr20	61918934	61918934	+	Missense_Mutation	SNP	T	T	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	agcccctcggagggccacagTtatcagaacagcggtctgga	10	6	13	12	2	2	1	1	0	1	1	3	3	2	3	3	4	3	1	3	4	2	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr20:61918934T>G	ENST00000370283.4	+	13	1070	c.930T>G	c.(928-930)agT>agG	p.S310R	ARFGAP1_ENST00000353546.3_Missense_Mutation_p.S318R|ARFGAP1_ENST00000519604.1_Missense_Mutation_p.S265R|ARFGAP1_ENST00000519273.2_Missense_Mutation_p.S197R|ARFGAP1_ENST00000370275.4_Missense_Mutation_p.V390G|ARFGAP1_ENST00000547204.1_Missense_Mutation_p.S244R|MIR4326_ENST00000582203.1_RNA|ARFGAP1_ENST00000518794.2_3'UTR	NM_018209.2	NP_060679.1	Q8N6T3	ARFG1_HUMAN	ADP-ribosylation factor GTPase activating protein 1	310					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)					AGGGCCACAGTTATCAGAACA	0.542																																					p.S318R		Atlas-SNP	.											.	ARFGAP1	38	.	0			c.T954G						PASS	.						44	45	44					20																	61918934		2201	4299	6500	SO:0001583	missense	55738	exon14			CCACAGTTATCAG	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.930T>G	chr20.hg19:g.61918934T>G	ENSP00000359306:p.Ser310Arg	35.0	0.0	.		76.0	26.0	.	NM_175609	B7Z3U0|B7Z8H8|B7ZBI3|E1P5I9|E7EV62|Q6PK71|Q96KC4|Q96T02|Q9NSU3|Q9NVF6|Q9UIL0	Missense_Mutation	SNP	ENST00000370283.4	hg19	CCDS13515.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.23|13.23	2.173905|2.173905	0.38413|0.38413	.|.	.|.	ENSG00000101199|ENSG00000101199	ENST00000370283;ENST00000547204;ENST00000549047;ENST00000523460;ENST00000519604;ENST00000519273;ENST00000353546|ENST00000370275	T;T;T;T;T;T|T	0.50001|0.38560	1.39;0.77;0.85;0.78;0.76;1.41|1.13	4.81|4.81	-0.361|-0.361	0.12564|0.12564	.|.	0.782541|.	0.12772|.	N|.	0.440467|.	T|T	0.36663|0.36663	0.0975|0.0975	L|L	0.60455|0.60455	1.87|1.87	0.49798|0.49798	D|D	0.999824|0.999824	D;D;P;P|B	0.60160|0.26318	0.958;0.987;0.859;0.913|0.146	P;P;P;P|B	0.57960|0.24974	0.663;0.83;0.556;0.742|0.057	T|T	0.33548|0.33548	-0.9864|-0.9864	10|9	0.32370|0.87932	T|D	0.25|0	-9.8078|-9.8078	9.7438|9.7438	0.40435|0.40435	0.0:0.6144:0.0:0.3856|0.0:0.6144:0.0:0.3856	.|.	197;265;310;318|390	B7Z8H8;E7EV62;Q8N6T3;Q8N6T3-2|B7ZBI2	.;.;ARFG1_HUMAN;.|.	R|G	310;244;236;66;265;197;318|390	ENSP00000359306:S310R;ENSP00000449800:S244R;ENSP00000447037:S236R;ENSP00000430500:S265R;ENSP00000443716:S197R;ENSP00000314615:S318R|ENSP00000359298:V390G	ENSP00000314615:S318R|ENSP00000359298:V390G	S|V	+|+	3|2	2|0	ARFGAP1|ARFGAP1	61389379|61389379	1.000000|1.000000	0.71417|0.71417	0.316000|0.316000	0.25252|0.25252	0.180000|0.180000	0.23129|0.23129	1.634000|1.634000	0.37123|0.37123	0.106000|0.106000	0.17784|0.17784	0.379000|0.379000	0.24179|0.24179	AGT|GTT	.	.	.	none		0.542	ARFGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080134.3	NM_018209		G	61918934	T	G	61918934	3	3	240	1	0	0	0	0	1	0	0	0	849	1722	60	5	1010	5	ARFGAP1	20	61918934	Missense_Mutation	SNP	T	TCGA-Q2-A5QZ-01A-11D-A28G-10	55885787	61918934	1106586	101	14754											
PRIC285	85441	hgsc.bcm.edu	37	chr20	62197379	62197379	+	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	tgccgctccacgcactcacgGatgaagctctcccagagctt	8	8	9	16	3	2	2	1	1	1	1	4	3	3	3	3	1	3	4	3	1	1	1			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr20:62197379G>A	ENST00000467148.1	-	8	2865	c.2796C>T	c.(2794-2796)atC>atT	p.I932I	HELZ2_ENST00000427522.2_Silent_p.I363I	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	932	Interaction with THRAP3.				cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										CGCACTCACGGATGAAGCTCT	0.701																																					p.I932I		Atlas-SNP	.											.	.	.	.	0			c.C2796T						PASS	.						16	16	16					20																	62197379		2174	4285	6459	SO:0001819	synonymous_variant	85441	exon9			CTCACGGATGAAG	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.2796C>T	chr20.hg19:g.62197379G>A		5.0	0.0	.		78.0	32.0	.	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	hg19	CCDS33508.1																																																																																			.	.	.	none		0.701	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		A	62197379	G	A	62197379	2	1	240	1	0	0	0	0	0	0	0	1	12495	1164	41	2		2	PRIC285	20	62197379	Silent	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	278445	62197379	828141	102	14755											
ADAMTS5	11096	hgsc.bcm.edu	37	chr21	28338045	28338045	+	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	ctcgggttgctgtgcgccggAgcatgctcgtgggcctccgg	2	9	17	13	5	0	0	0	0	0	0	3	1	1	1	3	4	4	4	3	4	0	1	rs369445782	byFrequency	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr21:28338045A>T	ENST00000284987.5	-	1	787	c.666T>A	c.(664-666)gcT>gcA	p.A222A		NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	222					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						TGTGCGCCGGAGCATGCTCGT	0.716													A|||	4	0.000798722	0.0023	0	5008	,	,		14660	0		0.001	False		,,,				2504	0				p.A222A	Esophageal Squamous(53;683 1080 10100 14424 45938)	Atlas-SNP	.											.	ADAMTS5	184	.	0			c.T666A						PASS	.	A		15,4337		0,15,2161	9	12	11		666	-4.4	0	21		11	2,8476		0,2,4237	no	coding-synonymous	ADAMTS5	NM_007038.3		0,17,6398	TT,TA,AA		0.0236,0.3447,0.1325		222/931	28338045	17,12813	2176	4239	6415	SO:0001819	synonymous_variant	11096	exon1			CGCCGGAGCATGC	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.666T>A	chr21.hg19:g.28338045A>T		0.0	0.0	.		73.0	33.0	.	NM_007038	Q52LV4|Q9UKP2	Silent	SNP	ENST00000284987.5	hg19	CCDS13579.1																																																																																			.	.	.	weak		0.716	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1			T	28338045	A	T	28338045	2	4	240	1	0	0	0	0	0	0	0	1	269	291	11	5		5	ADAMTS5	21	28338045	Silent	SNP	A	TCGA-Q2-A5QZ-01A-11D-A28G-10		28338045	19791850	103	14756											
TTC3	7267	hgsc.bcm.edu	37	chr21	38519809	38519809	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agagaaatttgttgaagaatGcaagttccctccagtgccag	13	10	10	8	0	0	3	0	1	0	2	2	4	2	3	3	0	2	3	3	0	4	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr21:38519809G>A	ENST00000399017.2	+	22	4669	c.1922G>A	c.(1921-1923)tGc>tAc	p.C641Y	TTC3_ENST00000540756.1_Missense_Mutation_p.C331Y|TTC3_ENST00000355666.1_Missense_Mutation_p.C641Y|TTC3_ENST00000354749.2_Missense_Mutation_p.C641Y|TTC3_ENST00000479930.1_3'UTR	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	641					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)				GTTGAAGAATGCAAGTTCCCT	0.323																																					p.C641Y	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.G1922A						PASS	.						111	108	109					21																	38519809		2203	4300	6503	SO:0001583	missense	7267	exon22			AAGAATGCAAGTT	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.1922G>A	chr21.hg19:g.38519809G>A	ENSP00000381981:p.Cys641Tyr	38.0	0.0	.		56.0	4.0	.	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	hg19	CCDS13651.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.0|20.0	3.930568|3.930568	0.73327|0.73327	.|.	.|.	ENSG00000182670|ENSG00000182670	ENST00000414818|ENST00000418766;ENST00000450533;ENST00000438055;ENST00000355666;ENST00000540756;ENST00000399017;ENST00000354749	.|T;T;T;T;T;T;T	.|0.53640	.|2.42;0.66;2.43;2.72;0.61;2.72;2.72	4.88|4.88	4.88|4.88	0.63580|0.63580	.|.	.|0.294582	.|0.30020	.|N	.|0.010617	T|T	0.57227|0.57227	0.2039|0.2039	N|N	0.20986|0.20986	0.625|0.625	0.58432|0.58432	D|D	0.999993|0.999993	.|D;D	.|0.76494	.|0.998;0.999	.|D;D	.|0.83275	.|0.994;0.996	T|T	0.63589|0.63589	-0.6603|-0.6603	5|10	.|0.87932	.|D	.|0	-11.1008|-11.1008	17.997|17.997	0.89187|0.89187	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|331;641	.|B4DSZ9;P53804	.|.;TTC3_HUMAN	T|Y	39|641;641;623;641;331;641;641	.|ENSP00000403943:C641Y;ENSP00000408456:C641Y;ENSP00000391891:C623Y;ENSP00000347889:C641Y;ENSP00000442875:C331Y;ENSP00000381981:C641Y;ENSP00000346791:C641Y	.|ENSP00000346791:C641Y	A|C	+|+	1|2	0|0	TTC3|TTC3	37441679|37441679	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.969000|0.969000	0.65631|0.65631	7.912000|7.912000	0.87465|0.87465	2.409000|2.409000	0.81822|0.81822	0.650000|0.650000	0.86243|0.86243	GCA|TGC	.	.	.	none		0.323	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			A	38519809	G	A	38519809	3	1	240	1	0	0	0	0	1	0	0	0	16709	1319	46	2	2004	2	TTC3	21	38519809	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	10181764	38519809	9610086	104	14757											
PRDM15	63977	hgsc.bcm.edu	37	chr21	43221434	43221434	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgctgctgctgctgctccGcctgcacctggggctgggcc	1	10	14	16	1	1	0	0	0	1	0	2	0	2	0	4	3	6	7	4	3	0	0	rs147616045		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chr21:43221434G>A	ENST00000269844.3	-	31	4600	c.4490C>T	c.(4489-4491)gCg>gTg	p.A1497V	PRDM15_ENST00000398548.1_Missense_Mutation_p.A1168V|PRDM15_ENST00000447207.2_Missense_Mutation_p.A1131V|PRDM15_ENST00000538201.1_Missense_Mutation_p.A1151V|PRDM15_ENST00000470586.1_5'UTR|PRDM15_ENST00000422911.1_Missense_Mutation_p.A1188V	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	1497					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						CTGCTGCTCCGCCTGCACCTG	0.637													g|||	1	0.000199681	8e-04	0	5008	,	,		15122	0		0	False		,,,				2504	0				p.A1497V		Atlas-SNP	.											.	PRDM15	110	.	0			c.C4490T						PASS	.		VAL/ALA,VAL/ALA	5,4369		0,5,2182	33	38	36		3503,4490	3.7	0	21	dbSNP_134	36	2,8498		0,2,4248	yes	missense,missense	PRDM15	NM_001040424.1,NM_022115.3	64,64	0,7,6430	AA,AG,GG		0.0235,0.1143,0.0544	possibly-damaging,possibly-damaging	1168/1179,1497/1508	43221434	7,12867	2187	4250	6437	SO:0001583	missense	63977	exon31			TGCTCCGCCTGCA	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.4490C>T	chr21.hg19:g.43221434G>A	ENSP00000269844:p.Ala1497Val	0.0	0.0	.		24.0	10.0	.	NM_022115	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Missense_Mutation	SNP	ENST00000269844.3	hg19	CCDS13676.1	.	.	.	.	.	.	.	.	.	.	g	13.53	2.264687	0.40095	0.001143	2.35E-4	ENSG00000141956	ENST00000422911;ENST00000398548;ENST00000538201;ENST00000447207;ENST00000269844	T;T;T;T;T	0.08546	3.16;3.17;3.17;3.16;3.08	4.56	3.65	0.41850	.	.	.	.	.	T	0.04952	0.0133	N	0.14661	0.345	0.09310	N	1	P;B;B	0.35226	0.491;0.043;0.043	B;B;B	0.22753	0.041;0.012;0.007	T	0.33420	-0.9869	9	0.72032	D	0.01	-4.2914	10.8161	0.46575	0.0:0.0:0.6437:0.3563	.	1497;1188;1168	P57071;E9PDJ6;E9PF37	PRD15_HUMAN;.;.	V	1188;1168;1151;1131;1497	ENSP00000408592:A1188V;ENSP00000381556:A1168V;ENSP00000444044:A1151V;ENSP00000390245:A1131V;ENSP00000269844:A1497V	ENSP00000269844:A1497V	A	-	2	0	PRDM15	42094503	0.050000	0.20438	0.003000	0.11579	0.735000	0.41995	2.502000	0.45398	0.847000	0.35167	0.558000	0.71614	GCG	.	G|1.000;A|0.000	0.000	weak		0.637	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115		A	43221434	G	A	43221434	3	1	240	1	0	0	0	0	1	0	0	0	12466	1087	38	1	37	1	PRDM15	21	43221434	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	4701625	43221434	4908461	105	14758											
PRPS2	5634	hgsc.bcm.edu	37	chrX	12840843	12840843	+	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	gtcattgacatttccatgatCttggccgaagcaatccgaag	11	11	9	10	2	2	2	1	2	1	0	4	4	4	2	3	1	1	1	3	1	3	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chrX:12840843C>G	ENST00000380668.5	+	7	1013	c.885C>G	c.(883-885)atC>atG	p.I295M	PRPS2_ENST00000398491.2_Missense_Mutation_p.I298M	NM_001039091.2|NM_002765.4	NP_001034180.1|NP_002756.1	P11908	PRPS2_HUMAN	phosphoribosyl pyrophosphate synthetase 2	295					5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|AMP biosynthetic process (GO:0006167)|nucleobase-containing compound metabolic process (GO:0006139)|organ regeneration (GO:0031100)	extracellular vesicular exosome (GO:0070062)|ribose phosphate diphosphokinase complex (GO:0002189)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|ATP binding (GO:0005524)|carbohydrate binding (GO:0030246)|GDP binding (GO:0019003)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)|ribose phosphate diphosphokinase activity (GO:0004749)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|urinary_tract(1)	16						TTTCCATGATCTTGGCCGAAG	0.453																																					p.I298M		Atlas-SNP	.											.	PRPS2	41	.	0			c.C894G						PASS	.						174	117	136					X																	12840843		2203	4300	6503	SO:0001583	missense	5634	exon7			CATGATCTTGGCC	Y00971	CCDS14150.1, CCDS43918.1	Xp22.2	2012-10-02			ENSG00000101911	ENSG00000101911	2.7.6.1		9465	protein-coding gene	gene with protein product	"PRS II", "ribose-phosphate diphosphokinase 2"	311860				1962753	Standard	NM_002765		Approved		uc004cva.3	P11908	OTTHUMG00000021139	ENST00000380668.5:c.885C>G	chrX.hg19:g.12840843C>G	ENSP00000370043:p.Ile295Met	90.0	0.0	.		232.0	69.0	.	NM_001039091	Q0VDH9|Q0VDI0|Q15245|Q2TAK7	Missense_Mutation	SNP	ENST00000380668.5	hg19	CCDS14150.1	.	.	.	.	.	.	.	.	.	.	C	11.17	1.559940	0.27827	.	.	ENSG00000101911	ENST00000380668;ENST00000398491;ENST00000461630;ENST00000460220	T;T;T	0.73363	-0.74;-0.74;-0.74	5.12	-0.0434	0.13859	.	0.000000	0.85682	D	0.000000	T	0.58018	0.2093	N	0.25485	0.75	0.80722	D	1	B;B	0.20164	0.042;0.012	B;B	0.37451	0.25;0.238	T	0.21586	-1.0241	10	0.12103	T	0.63	-23.1539	4.2961	0.10902	0.2341:0.3845:0.0:0.3814	.	295;298	P11908;P11908-2	PRPS2_HUMAN;.	M	295;298;150;127	ENSP00000370043:I295M;ENSP00000381504:I298M;ENSP00000418911:I150M	ENSP00000370043:I295M	I	+	3	3	PRPS2	12750764	0.945000	0.32115	0.987000	0.45799	0.993000	0.82548	0.139000	0.16036	0.131000	0.18576	0.513000	0.50165	ATC	.	.	.	none		0.453	PRPS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055772.2	NM_002765		G	12840843	C	G	12840843	3	3	240	1	0	0	0	0	1	0	0	0	12590	903	32	4	920	4	PRPS2	23	12840843	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10		12840843	142429717	106	14759											
PHKA2	5256	hgsc.bcm.edu	37	chrX	18919658	18919658	+	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	tcctctcagttttggtgactCcggtatggcccacctcgtgg	4	13	11	13	2	1	1	1	1	1	0	5	1	3	1	4	4	0	2	4	4	1	3			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chrX:18919658C>A	ENST00000379942.4	-	27	3637	c.2972G>T	c.(2971-2973)gGa>gTa	p.G991V		NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	991					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61	Hepatocellular(33;0.183)					TTTGGTGACTCCGGTATGGCC	0.547																																					p.G991V		Atlas-SNP	.											.	PHKA2	122	.	0			c.G2972T						PASS	.						180	139	153					X																	18919658		2203	4300	6503	SO:0001583	missense	5256	exon27			GTGACTCCGGTAT		CCDS14190.1	Xp22.2-p22.1	2009-07-10			ENSG00000044446	ENSG00000044446	2.7.11.19		8926	protein-coding gene	gene with protein product		300798		PHK, PYK		2387090	Standard	NM_000292		Approved		uc004cyv.4	P46019	OTTHUMG00000021222	ENST00000379942.4:c.2972G>T	chrX.hg19:g.18919658C>A	ENSP00000369274:p.Gly991Val	53.0	0.0	.		186.0	65.0	.	NM_000292	A8K1T1|Q6LAJ5|Q7Z6W0|Q96CR3|Q9UDA1	Missense_Mutation	SNP	ENST00000379942.4	hg19	CCDS14190.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.573963	0.86542	.	.	ENSG00000044446	ENST00000379942	D	0.90955	-2.76	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.94798	0.8320	M	0.67953	2.075	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	D	0.93740	0.7049	10	0.41790	T	0.15	-16.0545	19.5104	0.95139	0.0:1.0:0.0:0.0	.	991	P46019	KPB2_HUMAN	V	991	ENSP00000369274:G991V	ENSP00000369274:G991V	G	-	2	0	PHKA2	18829579	1.000000	0.71417	0.996000	0.52242	0.959000	0.62525	7.400000	0.79949	2.562000	0.86427	0.600000	0.82982	GGA	.	.	.	none		0.547	PHKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055960.1	NM_000292		A	18919658	C	A	18919658	3	1	240	1	0	0	0	0	1	0	0	0	11851	855	30	4	763	4	PHKA2	23	18919658	Missense_Mutation	SNP	C	TCGA-Q2-A5QZ-01A-11D-A28G-10	6078815	18919658	136350902	107	14760											
BRWD3	254065	hgsc.bcm.edu	37	chrX	80001213	80001213	+	Missense_Mutation	SNP	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	tacagccggttaattgcctgGcagaggtgatattcactgaa	11	11	11	8	1	1	3	1	2	0	1	1	3	1	3	2	3	3	2	2	3	4	5			TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chrX:80001213G>A	ENST00000373275.4	-	7	662	c.446C>T	c.(445-447)gCc>gTc	p.A149V		NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	149					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						TAATTGCCTGGCAGAGGTGAT	0.343																																					p.A149V		Atlas-SNP	.											.	BRWD3	251	.	0			c.C446T						PASS	.						36	33	34					X																	80001213		2203	4298	6501	SO:0001583	missense	254065	exon7			TGCCTGGCAGAGG		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.446C>T	chrX.hg19:g.80001213G>A	ENSP00000362372:p.Ala149Val	204.0	0.0	.		303.0	98.0	.	NM_153252	C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Missense_Mutation	SNP	ENST00000373275.4	hg19	CCDS14447.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.873392	0.91664	.	.	ENSG00000165288	ENST00000373275	T	0.29397	1.57	4.96	4.08	0.47627	.	0.065291	0.64402	D	0.000010	T	0.46580	0.1400	M	0.64997	1.995	0.49798	D	0.999826	D	0.67145	0.996	P	0.57911	0.829	T	0.42832	-0.9428	9	.	.	.	-1.3369	14.4752	0.67541	0.0:0.144:0.856:0.0	.	149	Q6RI45	BRWD3_HUMAN	V	149	ENSP00000362372:A149V	.	A	-	2	0	BRWD3	79887869	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.170000	0.64990	1.065000	0.40693	0.544000	0.68410	GCC	.	.	.	none		0.343	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252		A	80001213	G	A	80001213	3	1	240	1	0	0	0	0	1	0	0	0	1528	1203	42	2	5102	2	BRWD3	23	80001213	Missense_Mutation	SNP	G	TCGA-Q2-A5QZ-01A-11D-A28G-10	61081555	80001213	75269347	108	14761											
GPR112	139378	hgsc.bcm.edu	37	chrX	135475736	135475737	+	Frame_Shift_Ins	INS	-	-	AAAAT																															cttttgggattttgagaataINSatagtaagtatttttgttag																										TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chrX:135475736_135475737insAAAAT	ENST00000394143.1	+	18	8368_8369	c.8077_8078insAAAAT	c.(8077-8079)aatfs	p.-2692fs	GPR112_ENST00000370652.1_Frame_Shift_Ins_p.-2692fs|GPR112_ENST00000412101.1_Frame_Shift_Ins_p.-2487fs|GPR112_ENST00000287534.4_Frame_Shift_Ins_p.-2445fs|GPR112_ENST00000394141.1_Frame_Shift_Ins_p.-2487fs	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112						G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					TTTTGAGAATAATAGTAAGTAT	0.371																																					p.N2693fs		Atlas-Indel,Pindel	.											.	GPR112	459	.	0			c.8077_8078insAAAAT						PASS	.																																			SO:0001589	frameshift_variant	139378	exon18			.	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"-", "GPCR / Class B : Orphans"	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	Exception_encountered	chrX.hg19:g.135475736_135475737insAAAAT	ENSP00000377699:p.Asn2692fs	52.0	0.0	0		58.0	16.0	0.275862	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Frame_Shift_Ins	INS	ENST00000394143.1	hg19	CCDS35409.1																																																																																			.	.	.	none		0.371	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			AAAAT	135475737	-	AAAAT	135475736	7	5	240	1	0	1	1	0	0	0	0	0	6636	362	13	0	8135	0	GPR112	23	135475736	Frame_Shift_Ins	INS	-	TCGA-Q2-A5QZ-01A-11D-A28G-10	55474523	135475736	19794824	109	14762											
GABRQ	55879	hgsc.bcm.edu	37	chrX	151808889	151808890	+	Frame_Shift_Del	DEL	TG	TG	-																															aaagattttggacagggtgcTgtcaagatacgatgtccgcc																										TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	g.chrX:151808889_151808890delTG	ENST00000370306.2	+	2	220_221	c.200_201delTG	c.(199-201)ctgfs	p.L67fs		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	67					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)	GACAGGGTGCTGTCAAGATACG	0.47																																					p.67_67del		Atlas-Indel,Pindel	.											.	GABRQ	131	.	0			c.199_200del						PASS	.																																			SO:0001589	frameshift_variant	55879	exon2			.	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.200_201delTG	chrX.hg19:g.151808889_151808890delTG	ENSP00000359329:p.Leu67fs	70.0	0.0	0		159.0	56.0	0.352201	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Frame_Shift_Del	DEL	ENST00000370306.2	hg19	CCDS14707.1																																																																																			.	.	.	none		0.47	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558		-	151808890	TG	-	151808889	7	5	240	1	0	1	0	1	0	0	0	0	6182	1580	55	0	206	0	GABRQ	23	151808889	Frame_Shift_Del	DEL	TG	TCGA-Q2-A5QZ-01A-11D-A28G-10	16333153	151808889	3461671	110	14763											
MASP2	10747	hgsc.bcm.edu	37	chr1	11090277	11090277	+	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	tttctcctttggagctcgtcCagaatccatcagcctcacac	8	12	6	15	1	3	1	2	0	1	1	7	2	5	2	4	1	2	1	4	1	1	2			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr1:11090277C>G	ENST00000400897.3	-	10	1268	c.1253G>C	c.(1252-1254)tGg>tCg	p.W418S	RP4-635E18.8_ENST00000607145.1_RNA	NM_006610.3	NP_006601.2	O00187	MASP2_HUMAN	mannan-binding lectin serine peptidase 2	418	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				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)		GGAGCTCGTCCAGAATCCATC	0.408																																					p.W418S	GBM(35;611 746 20780 22741 36496)	Atlas-SNP	.											.	MASP2	71	.	0			c.G1253C						PASS	.						131	126	128					1																	11090277		2203	4300	6503	SO:0001583	missense	10747	exon10			CTCGTCCAGAATC	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.1253G>C	chr1.hg19:g.11090277C>G	ENSP00000383690:p.Trp418Ser	87.0	0.0	.		69.0	27.0	.	NM_006610	A8K458|A8MWJ2|O75754|Q5TEQ5|Q5TER0|Q96QG4|Q9BZH0|Q9H498|Q9H499|Q9UBP3|Q9UC48|Q9ULC7|Q9UMV3|Q9Y270	Missense_Mutation	SNP	ENST00000400897.3	hg19	CCDS123.1	.	.	.	.	.	.	.	.	.	.	C	19.15	3.771585	0.69992	.	.	ENSG00000009724	ENST00000400897	D	0.91068	-2.78	5.63	5.63	0.86233	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000001	D	0.97111	0.9056	H	0.96048	3.76	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	D	0.97998	1.0358	10	0.87932	D	0	.	19.2809	0.94052	0.0:1.0:0.0:0.0	.	418	O00187	MASP2_HUMAN	S	418	ENSP00000383690:W418S	ENSP00000383690:W418S	W	-	2	0	MASP2	11012864	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.095000	0.64529	2.660000	0.90430	0.655000	0.94253	TGG	.	.	.	none		0.408	MASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006072.1	NM_006610		G	11090277	C	G	11090277	3	3	241	1	0	0	0	0	1	0	0	0	9330	595	21	4	815	4	MASP2	1	11090277	Missense_Mutation	SNP	C	TCGA-SX-A71R-01A-12D-A33Q-10		11090277	238160344	1	14764											
CACNA1E	777	hgsc.bcm.edu	37	chr1	181695257	181695258	+	Frame_Shift_Ins	INS	-	-	GAGGTCA																															atgcactgcagaaggccaagINSgaggtcagcccgatgtctgc																										TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr1:181695257_181695258insGAGGTCA	ENST00000367573.2	+	18	2199_2200	c.2199_2200insGAGGTCA	c.(2200-2202)gagfs	p.-734fs	CACNA1E_ENST00000526775.1_Frame_Shift_Ins_p.-734fs|CACNA1E_ENST00000357570.5_Frame_Shift_Ins_p.-685fs|CACNA1E_ENST00000367570.1_Frame_Shift_Ins_p.-734fs|CACNA1E_ENST00000367567.4_Frame_Shift_Ins_p.-341fs|CACNA1E_ENST00000360108.3_Frame_Shift_Ins_p.-734fs|CACNA1E_ENST00000358338.5_Frame_Shift_Ins_p.-685fs	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit						calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						AGAAGGCCAAGGAGGTCAGCCC	0.54																																					p.K733fs		Atlas-Indel,Pindel	.											.	CACNA1E	778	.	0			c.2199_2200insGAGGTCA						PASS	.																																			SO:0001589	frameshift_variant	777	exon18			.	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.2200_2206dupGAGGTCA	chr1.hg19:g.181695258_181695264dupGAGGTCA	ENSP00000356545:p.Glu734fs	101.0	0.0	0		78.0	23.0	0.294872	NM_000721	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Frame_Shift_Ins	INS	ENST00000367573.2	hg19	CCDS55664.1																																																																																			.	.	.	none		0.54	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		GAGGTCA	181695258	-	GAGGTCA	181695257	7	5	241	1	0	1	1	0	0	0	0	0	2544	991	35	0	2269	0	CACNA1E	1	181695257	Frame_Shift_Ins	INS	-	TCGA-SX-A71R-01A-12D-A33Q-10	170604980	181695257	67555364	2	14765											
KCNT2	343450	hgsc.bcm.edu	37	chr1	196288615	196288615	+	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	caaagattttgtcacctactTgtcaatagagcccaccatgt	12	12	6	11	0	2	2	2	0	0	2	2	2	2	2	3	0	2	0	3	0	4	5			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr1:196288615T>G	ENST00000294725.9	-	20	3262	c.2347A>C	c.(2347-2349)Aac>Cac	p.N783H	KCNT2_ENST00000451324.2_Intron|KCNT2_ENST00000498426.1_Intron|KCNT2_ENST00000367431.4_Intron|KCNT2_ENST00000609185.1_Intron|KCNT2_ENST00000367433.5_Intron			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	783					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						GTCACCTACTTGTCAATAGAG	0.418																																					p.N783H		Atlas-SNP	.											.	KCNT2	243	.	0			c.A2347C						PASS	.						136	120	125					1																	196288615		2203	4300	6503	SO:0001630	splice_region_variant	343450	exon20			CCTACTTGTCAAT	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.2348+1A>C	chr1.hg19:g.196288615T>G		108.0	0.0	.		77.0	34.0	.	NM_198503	Q3SY59|Q5VTN1|Q6ZMT3	Missense_Mutation	SNP	ENST00000294725.9	hg19	CCDS1384.1	.	.	.	.	.	.	.	.	.	.	T	18.02	3.530130	0.64860	.	.	ENSG00000162687	ENST00000294725	T	0.75704	-0.96	5.83	5.83	0.93111	.	0.000000	0.64402	D	0.000002	D	0.83589	0.5287	M	0.72118	2.19	0.80722	D	1	D	0.65815	0.995	P	0.61800	0.894	T	0.83023	-0.0166	10	0.37606	T	0.19	-21.4942	16.1894	0.81975	0.0:0.0:0.0:1.0	.	783	Q6UVM3	KCNT2_HUMAN	H	783	ENSP00000294725:N783H	ENSP00000294725:N783H	N	-	1	0	KCNT2	194555238	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.826000	0.86716	2.222000	0.72286	0.477000	0.44152	AAC	.	.	.	none		0.418	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503	Missense_Mutation	G	196288615	T	G	196288615	5	3	241	1	0	0	0	0	0	0	1	0	8099	1826	63	5	1096	5	KCNT2	1	196288615	Splice_Site	SNP	T	TCGA-SX-A71R-01A-12D-A33Q-10	14593358	196288615	52962006	3	14766											
DENND1B	163486	hgsc.bcm.edu	37	chr1	197479793	197479793	+	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	aagcagatcatctgaaatctGgcttagtgtttccctctttt	9	16	7	9	0	4	2	1	1	3	1	5	2	5	2	1	1	1	3	1	1	3	4			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr1:197479793G>A								CRB1 (32208 upstream) : DENND1B (41591 downstream)																							TCTGAAATCTGGCTTAGTGTT	0.448																																					p.Q709X		Atlas-SNP	.											.	DENND1B	108	.	0			c.C2125T						PASS	.						142	127	132					1																	197479793		2203	4300	6503	SO:0001628	intergenic_variant	163486	exon23			AAATCTGGCTTAG																													chr1.hg19:g.197479793G>A		139.0	0.0	.		137.0	56.0	.	NM_001195215		Nonsense_Mutation	SNP		hg19		.	.	.	.	.	.	.	.	.	.	G	11.20	1.569014	0.28003	.	.	ENSG00000213047	ENST00000391979;ENST00000542760;ENST00000450419	.	.	.	5.43	4.49	0.54785	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	.	9.2796	0.37720	0.0:0.1314:0.6622:0.2063	.	.	.	.	X	349;709;689	.	ENSP00000375839:Q349X	Q	-	1	0	DENND1B	195746416	1.000000	0.71417	0.378000	0.26068	0.024000	0.10985	2.407000	0.44565	1.377000	0.46286	0.563000	0.77884	CAG	.	.	.	none	0	0.448									A	197479793	G	A	197479793	1	1	241	0	1	0	0	0	0	0	0	0	4429	1357	47	2		2	DENND1B	1	197479793	IGR	SNP	G	TCGA-SX-A71R-01A-12D-A33Q-10	1191178	197479793	51770828	4	14767											
NRXN1	9378	hgsc.bcm.edu	37	chr2	50280612	50280612	+	Missense_Mutation	SNP	T	T	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	atcgttttcggctgccatatTcagaactttcaagccattgt	9	15	7	10	2	2	1	2	0	0	1	4	1	2	1	2	1	3	2	2	1	3	6	rs201877761		TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr2:50280612T>G	ENST00000406316.2	-	20	5311	c.3835A>C	c.(3835-3837)Aat>Cat	p.N1279H	NRXN1_ENST00000406859.3_Missense_Mutation_p.N1279H|NRXN1_ENST00000401710.1_Missense_Mutation_p.N297H|NRXN1_ENST00000405472.3_Missense_Mutation_p.N1301H|NRXN1_ENST00000404971.1_Missense_Mutation_p.N1349H|NRXN1_ENST00000401669.2_Missense_Mutation_p.N1309H|NRXN1_ENST00000342183.5_Missense_Mutation_p.N244H|NRXN1_ENST00000402717.3_Missense_Mutation_p.N1301H	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	1279	Laminin G-like 6. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			GCTGCCATATTCAGAACTTTC	0.507																																					p.N1349H		Atlas-SNP	.											.	NRXN1	1118	.	0			c.A4045C						PASS	.						97	89	92					2																	50280612		2203	4300	6503	SO:0001583	missense	9378	exon22			CCATATTCAGAAC	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.3835A>C	chr2.hg19:g.50280612T>G	ENSP00000384311:p.Asn1279His	104.0	0.0	.		57.0	26.0	.	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	ENST00000406316.2	hg19	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	T	14.56	2.572415	0.45798	.	.	ENSG00000179915	ENST00000342183;ENST00000536347;ENST00000401710;ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859	T;T;T;T;T;T;T;T	0.71579	0.89;2.14;0.13;0.11;-0.58;-0.46;-0.17;-0.03	5.65	5.65	0.86999	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.093114	0.39687	U	0.001295	T	0.79822	0.4512	M	0.73962	2.25	0.39056	D	0.960425	B;D;P;P	0.59357	0.367;0.985;0.566;0.502	B;P;P;B	0.53518	0.246;0.712;0.728;0.261	D	0.84151	0.0423	10	0.87932	D	0	.	15.8691	0.79098	0.0:0.0:0.0:1.0	.	1349;244;1279;1301	Q9ULB1-3;P58400;F8WB18;A7E294	.;NRX1B_HUMAN;.;.	H	244;198;297;1349;1279;1301;1309;1350;1301;1279	ENSP00000341184:N244H;ENSP00000385580:N297H;ENSP00000385142:N1349H;ENSP00000384311:N1279H;ENSP00000434015:N1301H;ENSP00000385017:N1309H;ENSP00000385434:N1301H;ENSP00000385681:N1279H	ENSP00000341184:N244H	N	-	1	0	NRXN1	50134116	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.186000	0.72026	2.151000	0.67156	0.533000	0.62120	AAT	.	T|0.999;C|0.001	.	alt		0.507	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			G	50280612	T	G	50280612	3	3	241	1	0	0	0	0	1	0	0	0	10672	1783	62	5	610	5	NRXN1	2	50280612	Missense_Mutation	SNP	T	TCGA-SX-A71R-01A-12D-A33Q-10		50280612	192918761	5	14768											
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54884994	54884994	+	Frame_Shift_Del	DEL	G	G	-																															gtaccctgtgcagttctggaGgtccatcagttctcaagaga																										TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr2:54884994delG	ENST00000356805.4	+	30	6335	c.6054delG	c.(6052-6054)gagfs	p.E2018fs	SPTBN1_ENST00000333896.5_Frame_Shift_Del_p.E2005fs	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	2018	Interaction with ANK2.				actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			CAGTTCTGGAGGTCCATCAGT	0.592											OREG0014619	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E2018fs		Atlas-Indel,Pindel	.											.	SPTBN1	378	.	0			c.6053delA						PASS	.						67	61	63					2																	54884994		2203	4300	6503	SO:0001589	frameshift_variant	6711	exon30			.		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.6054delG	chr2.hg19:g.54884994delG	ENSP00000349259:p.Glu2018fs	99.0	0.0	0	1003	67.0	31.0	0.462687	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Frame_Shift_Del	DEL	ENST00000356805.4	hg19	CCDS33198.1																																																																																			.	.	.	none		0.592	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			-	54884994	G	-	54884994	7	5	241	1	0	1	0	1	0	0	0	0	15131	991	35	0	6281	0	SPTBN1	2	54884994	Frame_Shift_Del	DEL	G	TCGA-SX-A71R-01A-12D-A33Q-10	4604382	54884994	188314379	6	14769											
KCNH8	131096	hgsc.bcm.edu	37	chr3	19479828	19479828	+	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	acagatgcagaaaagatcttCtccatctgcaccatgctgat	13	10	7	11	0	3	4	0	1	3	3	4	4	3	4	2	0	3	3	2	0	2	1			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr3:19479828C>T	ENST00000328405.2	+	8	1616	c.1350C>T	c.(1348-1350)ttC>ttT	p.F450F	KCNH8_ENST00000537696.1_Silent_p.F91F	NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	450					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						AAAAGATCTTCTCCATCTGCA	0.473																																					p.F450F	NSCLC(124;1625 1765 8018 24930 42026)	Atlas-SNP	.											.	KCNH8	189	.	0			c.C1350T						PASS	.						74	66	69					3																	19479828		2203	4300	6503	SO:0001819	synonymous_variant	131096	exon8			GATCTTCTCCATC	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.1350C>T	chr3.hg19:g.19479828C>T		129.0	0.0	.		110.0	52.0	.	NM_144633	B7Z2I7|Q59GQ6	Silent	SNP	ENST00000328405.2	hg19	CCDS2632.1																																																																																			.	.	.	none		0.473	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633		T	19479828	C	T	19479828	2	4	241	1	0	0	0	0	0	0	0	1	8045	912	32	2		2	KCNH8	3	19479828	Silent	SNP	C	TCGA-SX-A71R-01A-12D-A33Q-10		19479828	178542602	7	14770											
SLC4A7	9497	hgsc.bcm.edu	37	chr3	27477880	27477880	+	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	aaagtcagtttactataaccTgctatttcatctagagtgct	12	15	6	8	0	3	1	2	0	1	1	3	1	3	1	1	0	4	3	1	0	6	7			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr3:27477880T>C	ENST00000295736.5	-	5	631	c.561A>G	c.(559-561)gcA>gcG	p.A187A	SLC4A7_ENST00000435667.2_Splice_Site_p.A196A|SLC4A7_ENST00000437179.1_Splice_Site_p.A192A|SLC4A7_ENST00000446700.1_Splice_Site_p.A192A|SLC4A7_ENST00000440156.1_Splice_Site_p.A196A|SLC4A7_ENST00000445684.1_Splice_Site_p.A196A|SLC4A7_ENST00000425128.2_Splice_Site_p.A192A|SLC4A7_ENST00000454389.1_Splice_Site_p.A196A|SLC4A7_ENST00000428386.1_Splice_Site_p.A187A|SLC4A7_ENST00000455077.1_Splice_Site_p.A192A|SLC4A7_ENST00000388777.4_5'UTR	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	187					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)	TACTATAACCTGCTATTTCAT	0.373																																					p.A192A		Atlas-SNP	.											.	SLC4A7	119	.	0			c.A576G						PASS	.						76	74	74					3																	27477880		2203	4300	6503	SO:0001630	splice_region_variant	9497	exon5			ATAACCTGCTATT	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.562+1A>G	chr3.hg19:g.27477880T>C		98.0	0.0	.		80.0	40.0	.	NM_001258379	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Silent	SNP	ENST00000295736.5	hg19	CCDS33721.1																																																																																			.	.	.	none		0.373	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	Silent	C	27477880	T	C	27477880	5	2	241	1	0	0	0	0	0	0	1	0	14671	1594	55	3	3167	3	SLC4A7	3	27477880	Splice_Site	SNP	T	TCGA-SX-A71R-01A-12D-A33Q-10	7998052	27477880	170544550	8	14771											
VEPH1	79674	hgsc.bcm.edu	37	chr3	157081265	157081265	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tagagcttatcttggtattcTataggacttgcagttgtctc	8	17	9	7	0	3	1	0	0	3	1	4	2	3	2	0	2	2	4	0	2	5	9			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr3:157081265T>C	ENST00000362010.2	-	9	1930	c.1623A>G	c.(1621-1623)atA>atG	p.I541M	VEPH1_ENST00000392833.2_Missense_Mutation_p.I541M|VEPH1_ENST00000543418.1_Missense_Mutation_p.I541M|RP11-550I24.2_ENST00000487238.1_RNA|VEPH1_ENST00000392832.2_Missense_Mutation_p.I541M	NM_001167912.1	NP_001161384.1	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain-containing 1	541						plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|cervix(1)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|pancreas(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			CTTGGTATTCTATAGGACTTG	0.363																																					p.I541M		Atlas-SNP	.											.	VEPH1	129	.	0			c.A1623G						PASS	.						152	159	157					3																	157081265		2203	4300	6503	SO:0001583	missense	79674	exon9			GTATTCTATAGGA	AL713656	CCDS3179.1, CCDS54661.1, CCDS54662.1, CCDS54663.1	3q24-q25	2013-01-10	2012-12-10		ENSG00000197415	ENSG00000197415		"Pleckstrin homology (PH) domain containing"	25735	protein-coding gene	gene with protein product		609594	"ventricular zone expressed PH domain homolog 1 (zebrafish)"			11214970, 15388229	Standard	NM_024621		Approved	FLJ12604, KIAA1692	uc003fbk.2	Q14D04	OTTHUMG00000158711	ENST00000362010.2:c.1623A>G	chr3.hg19:g.157081265T>C	ENSP00000354919:p.Ile541Met	185.0	0.0	.		189.0	73.0	.	NM_001167911	D3DNL0|F5GZ91|Q2TAA9|Q3MIX2|Q6PEL3|Q86TL5|Q8TCR3|Q96SP7|Q9C0H1|Q9H9Q7	Missense_Mutation	SNP	ENST00000362010.2	hg19	CCDS3179.1	.	.	.	.	.	.	.	.	.	.	T	10.23	1.291609	0.23564	.	.	ENSG00000197415	ENST00000392833;ENST00000362010;ENST00000543418;ENST00000392832	T;T;T;T	0.08458	3.09;3.09;3.09;3.09	5.5	-4.25	0.03766	.	1.486880	0.03948	N	0.287996	T	0.05456	0.0144	N	0.14661	0.345	0.43708	D	0.996171	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	T	0.23511	-1.0186	10	0.44086	T	0.13	-14.1107	8.4805	0.33040	0.1087:0.5:0.0:0.3913	.	541;541	Q14D04-2;Q14D04	.;MELT_HUMAN	M	541	ENSP00000376578:I541M;ENSP00000354919:I541M;ENSP00000446258:I541M;ENSP00000376577:I541M	ENSP00000354919:I541M	I	-	3	3	VEPH1	158563959	0.000000	0.05858	0.016000	0.15963	0.611000	0.37282	-0.300000	0.08243	-0.666000	0.05310	0.533000	0.62120	ATA	.	.	.	none		0.363	VEPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351845.3	NM_024621		C	157081265	T	C	157081265	3	2	241	1	0	0	0	0	1	0	0	0	17166	1512	53	3	902	3	VEPH1	3	157081265	Missense_Mutation	SNP	T	TCGA-SX-A71R-01A-12D-A33Q-10	129603385	157081265	40941165	9	14772											
HNRNPD	3184	hgsc.bcm.edu	37	chr4	83279841	83279841	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accaccaaagtactcccttaTtttctcttcaggtgtatctg	9	15	5	12	0	3	0	1	0	2	0	5	0	4	0	3	1	1	2	3	1	4	6			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr4:83279841T>C	ENST00000313899.7	-	4	869	c.592A>G	c.(592-594)Ata>Gta	p.I198V	HNRNPD_ENST00000541060.1_Missense_Mutation_p.I44V|HNRNPD_ENST00000543098.1_Missense_Mutation_p.I146V|HNRNPD_ENST00000353341.4_Missense_Mutation_p.I198V|HNRNPD_ENST00000508119.1_5'Flank|HNRNPD_ENST00000352301.4_Missense_Mutation_p.I179V	NM_031370.2	NP_112738.1	Q14103	HNRPD_HUMAN	heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37kDa)	198	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				circadian regulation of translation (GO:0097167)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|regulation of circadian rhythm (GO:0042752)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(1)	7						TACTCCCTTATTTTCTCTTCA	0.378																																					p.I198V		Atlas-SNP	.											.	HNRNPD	23	.	0			c.A592G						PASS	.						89	94	92					4																	83279841		2203	4300	6503	SO:0001583	missense	3184	exon4			CCCTTATTTTCTC	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.592A>G	chr4.hg19:g.83279841T>C	ENSP00000313199:p.Ile198Val	139.0	0.0	.		113.0	55.0	.	NM_031370	A8K9J2|P07029|Q01858|Q14100|Q14101|Q14102|Q4W5A1|Q9UCE8|Q9UCE9	Missense_Mutation	SNP	ENST00000313899.7	hg19	CCDS3592.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.992|8.992	0.977861|0.977861	0.18812|0.18812	.|.	.|.	ENSG00000138668|ENSG00000138668	ENST00000313899;ENST00000353341;ENST00000352301;ENST00000543098;ENST00000307213;ENST00000541060;ENST00000509263;ENST00000507010;ENST00000515432|ENST00000514671	T;T;T;T;T;T;T;T|.	0.18502|.	2.21;2.21;2.21;2.21;2.21;2.21;2.21;2.21|.	6.07|6.07	6.07|6.07	0.98685|0.98685	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);|.	0.042341|.	0.85682|.	D|.	0.000000|.	T|T	0.59838|0.59838	0.2223|0.2223	L|L	0.37630|0.37630	1.12|1.12	0.50467|0.50467	D|D	0.99987|0.99987	P;P;B;B|.	0.39964|.	0.697;0.697;0.112;0.136|.	B;B;B;B|.	0.44085|.	0.44;0.44;0.108;0.173|.	T|T	0.55425|0.55425	-0.8143|-0.8143	10|5	0.26408|.	T|.	0.33|.	.|.	16.6407|16.6407	0.85098|0.85098	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	179;198;179;198|.	Q14103-4;Q14103-3;Q14103-2;Q14103|.	.;.;.;HNRPD_HUMAN|.	V|S	198;198;179;146;173;44;131;198;100|101	ENSP00000313199:I198V;ENSP00000313327:I198V;ENSP00000305860:I179V;ENSP00000439380:I146V;ENSP00000437416:I44V;ENSP00000420926:I131V;ENSP00000421952:I198V;ENSP00000426666:I100V|.	ENSP00000307544:I173V|.	I|N	-|-	1|2	0|0	HNRNPD|HNRNPD	83498865|83498865	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.309000|0.309000	0.27889|0.27889	4.737000|4.737000	0.62066|0.62066	2.326000|2.326000	0.78906|0.78906	0.533000|0.533000	0.62120|0.62120	ATA|AAT	.	.	.	none		0.378	HNRNPD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252630.2	NM_031370		C	83279841	T	C	83279841	3	2	241	1	0	0	0	0	1	0	0	0	7271	1493	52	3	495	3	HNRNPD	4	83279841	Missense_Mutation	SNP	T	TCGA-SX-A71R-01A-12D-A33Q-10		83279841	107874435	10	14773											
HERC6	55008	hgsc.bcm.edu	37	chr4	89361148	89361148	+	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	gatacttagacatttctaccCtgaagaactaatgacagcaa	16	10	6	9	0	1	4	0	2	1	2	1	5	1	4	1	0	4	1	1	0	7	5			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr4:89361148C>A	ENST00000264346.7	+	21	2737	c.2678C>A	c.(2677-2679)cCt>cAt	p.P893H	HERC6_ENST00000380265.5_Missense_Mutation_p.P857H	NM_017912.3	NP_060382.3	Q8IVU3	HERC6_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6	893	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				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)		CATTTCTACCCTGAAGAACTA	0.363																																					p.P893H		Atlas-SNP	.											.	HERC6	104	.	0			c.C2678A						PASS	.						70	64	66					4																	89361148		1828	4104	5932	SO:0001583	missense	55008	exon21			TCTACCCTGAAGA	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.2678C>A	chr4.hg19:g.89361148C>A	ENSP00000264346:p.Pro893His	169.0	0.0	.		131.0	58.0	.	NM_017912	B4DIY5|Q5GC90|Q5GRH3|Q5HYM6|Q5JPB6|Q6PIF4|Q8NAN3|Q9NWS4	Missense_Mutation	SNP	ENST00000264346.7	hg19	CCDS47098.1	.	.	.	.	.	.	.	.	.	.	C	15.20	2.763291	0.49574	.	.	ENSG00000138642	ENST00000380265;ENST00000264346	T;T	0.50548	0.74;0.74	4.66	4.66	0.58398	HECT (4);	0.000000	0.64402	D	0.000012	T	0.72252	0.3437	M	0.86097	2.795	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.77734	-0.2477	10	0.87932	D	0	.	16.8302	0.85942	0.0:1.0:0.0:0.0	.	857;893	Q8IVU3-2;Q8IVU3	.;HERC6_HUMAN	H	857;893	ENSP00000369617:P857H;ENSP00000264346:P893H	ENSP00000264346:P893H	P	+	2	0	HERC6	89580171	1.000000	0.71417	0.891000	0.34965	0.024000	0.10985	6.932000	0.75869	2.581000	0.87130	0.585000	0.79938	CCT	.	.	.	none		0.363	HERC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363259.2			A	89361148	C	A	89361148	3	1	241	1	0	0	0	0	1	0	0	0	7069	681	24	4	2557	4	HERC6	4	89361148	Missense_Mutation	SNP	C	TCGA-SX-A71R-01A-12D-A33Q-10	6081307	89361148	101793128	11	14774											
DNAJC18	202052	hgsc.bcm.edu	37	chr5	138758461	138758461	+	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	agtaatgacagatataatcaCaatcacaagaactggaagta	20	8	7	6	0	2	3	2	1	0	2	2	4	2	4	0	1	1	2	0	1	8	4			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr5:138758461C>A	ENST00000302060.5	-	6	795	c.715G>T	c.(715-717)Gtg>Ttg	p.V239L		NM_152686.3	NP_689899.1	Q9H819	DJC18_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 18	239						integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GATATAATCACAATCACAAGA	0.318																																					p.V239L		Atlas-SNP	.											.	DNAJC18	30	.	0			c.G715T						PASS	.						85	87	86					5																	138758461		2203	4300	6503	SO:0001583	missense	202052	exon6			TAATCACAATCAC	AK024054	CCDS4214.1	5q31.2	2011-09-02		2005-08-09	ENSG00000170464	ENSG00000170464		"Heat shock proteins / DNAJ (HSP40)"	28429	protein-coding gene	gene with protein product							Standard	NM_152686		Approved	MGC29463	uc003len.3	Q9H819	OTTHUMG00000129225	ENST00000302060.5:c.715G>T	chr5.hg19:g.138758461C>A	ENSP00000302843:p.Val239Leu	250.0	0.0	.		230.0	89.0	.	NM_152686		Missense_Mutation	SNP	ENST00000302060.5	hg19	CCDS4214.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.10|18.10	3.547400|3.547400	0.65311|0.65311	.|.	.|.	ENSG00000170464|ENSG00000170464	ENST00000514052|ENST00000302060;ENST00000508445	.|T;T	.|0.55760	.|0.5;1.07	5.87|5.87	5.87|5.87	0.94306|0.94306	.|.	.|0.064922	.|0.64402	.|D	.|0.000004	T|T	0.30039|0.30039	0.0752|0.0752	N|N	0.25332|0.25332	0.735|0.735	0.52099|0.52099	D|D	0.999946|0.999946	.|P	.|0.43431	.|0.807	.|B	.|0.31495	.|0.131	T|T	0.12167|0.12167	-1.0558|-1.0558	5|10	.|0.12766	.|T	.|0.61	-13.8827|-13.8827	9.4781|9.4781	0.38884|0.38884	0.0:0.8512:0.0:0.1488|0.0:0.8512:0.0:0.1488	.|.	.|239	.|Q9H819	.|DJC18_HUMAN	F|L	30|239;72	.|ENSP00000302843:V239L;ENSP00000426338:V72L	.|ENSP00000302843:V239L	L|V	-|-	3|1	2|0	DNAJC18|DNAJC18	138786360|138786360	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.740000|3.740000	0.55082|0.55082	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	TTG|GTG	.	.	.	none		0.318	DNAJC18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374191.1	NM_152686		A	138758461	C	A	138758461	3	1	241	1	0	0	0	0	1	0	0	0	4639	478	17	4	373	4	DNAJC18	5	138758461	Missense_Mutation	SNP	C	TCGA-SX-A71R-01A-12D-A33Q-10		138758461	42156799	12	14775											
PCDHGA4	56111	hgsc.bcm.edu	37	chr5	140736033	140736033	+	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	tcagaatataacatcactgtAactgccactgaccagggaac	15	8	7	11	0	2	2	2	1	0	1	2	3	2	3	2	1	4	1	2	1	5	3			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr5:140736033A>T	ENST00000571252.1	+	1	1266	c.1266A>T	c.(1264-1266)gtA>gtT	p.V422V	PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	422	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACATCACTGTAACTGCCACTG	0.433																																					p.V422V		Atlas-SNP	.											.	PCDHGA4	150	.	0			c.A1266T						PASS	.						55	57	57					5																	140736033		2042	4208	6250	SO:0001819	synonymous_variant	56111	exon1			CACTGTAACTGCC	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.1266A>T	chr5.hg19:g.140736033A>T		95.0	0.0	.		70.0	32.0	.	NM_018917	Q9Y5D3	Silent	SNP	ENST00000571252.1	hg19	CCDS58979.1																																																																																			.	.	.	none		0.433	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917		T	140736033	A	T	140736033	2	4	241	1	0	0	0	0	0	0	0	1	11563	349	13	5		5	PCDHGA4	5	140736033	Silent	SNP	A	TCGA-SX-A71R-01A-12D-A33Q-10	1977572	140736033	40179227	13	14776											
SKIV2L	6499	hgsc.bcm.edu	37	chr6	31932058	31932058	+	Missense_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	cggcctgggtgtgcaccataGcggcatcctgcccatcctca	6	8	11	16	2	1	0	1	0	0	0	3	0	3	0	5	3	3	2	5	3	1	1			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr6:31932058G>A	ENST00000375394.2	+	17	2023	c.1910G>A	c.(1909-1911)aGc>aAc	p.S637N	SKIV2L_ENST00000544581.1_Missense_Mutation_p.S444N	NM_006929.4	NP_008860.4	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like (S. cerevisiae)	637	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)	nucleus (GO:0005634)|Ski complex (GO:0055087)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|large_intestine(1)|ovary(1)	4						GTGCACCATAGCGGCATCCTG	0.597																																					p.S637N		Atlas-SNP	.											.	SKIV2L	97	.	0			c.G1910A						PASS	.						115	87	97					6																	31932058		1511	2708	4219	SO:0001583	missense	6499	exon17			ACCATAGCGGCAT		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.1910G>A	chr6.hg19:g.31932058G>A	ENSP00000364543:p.Ser637Asn	81.0	0.0	.		62.0	26.0	.	NM_006929	O15005|Q12902|Q15476|Q5ST66	Missense_Mutation	SNP	ENST00000375394.2	hg19	CCDS4731.1	.	.	.	.	.	.	.	.	.	.	G	33	5.219357	0.95139	.	.	ENSG00000204351	ENST00000375394;ENST00000433155;ENST00000544581	T;T	0.43294	0.95;0.95	5.95	5.95	0.96441	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.66665	0.2812	M	0.86805	2.84	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.70662	-0.4810	10	0.72032	D	0.01	-16.4781	19.1568	0.93514	0.0:0.0:1.0:0.0	.	637	Q15477	SKIV2_HUMAN	N	637;479;444	ENSP00000364543:S637N;ENSP00000442645:S444N	ENSP00000364543:S637N	S	+	2	0	SKIV2L	32040037	1.000000	0.71417	0.979000	0.43373	0.967000	0.64934	8.574000	0.90763	2.825000	0.97269	0.655000	0.94253	AGC	.	.	.	none		0.597	SKIV2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076264.3			A	31932058	G	A	31932058	3	1	241	1	0	0	0	0	1	0	0	0	14372	971	34	2	1976	2	SKIV2L	6	31932058	Missense_Mutation	SNP	G	TCGA-SX-A71R-01A-12D-A33Q-10		31932058	139183009	14	14777											
GSTA1	2938	hgsc.bcm.edu	37	chr6	52656735	52656735	+	Missense_Mutation	SNP	A	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	ttgggctgccaggctgtagaAacttcttcactgtgggcagg	7	11	14	9	0	2	1	1	0	1	1	2	1	2	1	1	4	2	4	1	4	2	4			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr6:52656735A>C	ENST00000334575.5	-	7	745	c.590T>G	c.(589-591)tTt>tGt	p.F197C	GSTA1_ENST00000493331.1_5'UTR	NM_145740.3	NP_665683.1	P08263	GSTA1_HUMAN	glutathione S-transferase alpha 1	197	GST C-terminal.				epithelial cell differentiation (GO:0030855)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|metabolic process (GO:0008152)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)			large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	12	Lung NSC(77;0.118)				Azathioprine(DB00993)|Busulfan(DB01008)|Glutathione(DB00143)	AGGCTGTAGAAACTTCTTCAC	0.473																																					p.F197C		Atlas-SNP	.											.	GSTA1	40	.	0			c.T590G						PASS	.						128	127	127					6																	52656735		2203	4300	6503	SO:0001583	missense	2938	exon7			TGTAGAAACTTCT		CCDS4945.1	6p12.2	2012-06-21	2008-11-26		ENSG00000243955	ENSG00000243955	2.5.1.18	"Glutathione S-transferases / Soluble"	4626	protein-coding gene	gene with protein product		138359	"glutathione S-transferase A1"			9503014	Standard	NM_145740		Approved		uc003paz.3	P08263	OTTHUMG00000014861	ENST00000334575.5:c.590T>G	chr6.hg19:g.52656735A>C	ENSP00000335620:p.Phe197Cys	93.0	0.0	.		75.0	41.0	.	NM_145740	Q14750|Q5GHF8|Q5SZC1	Missense_Mutation	SNP	ENST00000334575.5	hg19	CCDS4945.1	.	.	.	.	.	.	.	.	.	.	.	11.55	1.671100	0.29693	.	.	ENSG00000243955	ENST00000334575	T	0.11712	2.75	2.44	2.44	0.29823	Glutathione S-transferase, C-terminal-like (1);Glutathione S-transferase/chloride channel, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.30198	0.0757	H	0.94503	3.545	0.49582	D	0.999806	D	0.89917	1.0	D	0.97110	1.0	T	0.36359	-0.9751	10	0.87932	D	0	.	10.0672	0.42311	1.0:0.0:0.0:0.0	.	197	P08263	GSTA1_HUMAN	C	197	ENSP00000335620:F197C	ENSP00000335620:F197C	F	-	2	0	GSTA1	52764694	1.000000	0.71417	0.986000	0.45419	0.165000	0.22458	5.795000	0.69074	0.868000	0.35678	0.172000	0.16884	TTT	.	.	.	none		0.473	GSTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040922.1			C	52656735	A	C	52656735	3	2	241	1	0	0	0	0	1	0	0	0	6837	14	1	5	82	5	GSTA1	6	52656735	Missense_Mutation	SNP	A	TCGA-SX-A71R-01A-12D-A33Q-10	20724677	52656735	118458332	15	14778											
HBS1L	10767	hgsc.bcm.edu	37	chr6	135358073	135358073	+	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	tgatggagcaatggatgggtCtactacaggctttggaacaa	12	10	13	6	0	1	1	0	1	1	0	1	4	1	4	0	5	4	2	0	5	5	3			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr6:135358073C>T	ENST00000367837.5	-	4	637				HBS1L_ENST00000367826.2_Intron|HBS1L_ENST00000314674.3_Intron|HBS1L_ENST00000415177.2_Intron|HBS1L_ENST00000367824.4_Intron|HBS1L_ENST00000367822.5_Missense_Mutation_p.D508N|HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000367820.2_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)		ATGGATGGGTCTACTACAGGC	0.368																																					p.D508N		Atlas-SNP	.											.	HBS1L	75	.	0			c.G1522A						PASS	.						52	48	49					6																	135358073		692	1591	2283	SO:0001627	intron_variant	10767	exon5			ATGGGTCTACTAC	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+2637G>A	chr6.hg19:g.135358073C>T		159.0	0.0	.		128.0	55.0	.	NM_001145207	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Missense_Mutation	SNP	ENST00000367837.5	hg19	CCDS5173.1	.	.	.	.	.	.	.	.	.	.	C	3.012	-0.203760	0.06180	.	.	ENSG00000112339	ENST00000367822	.	.	.	5.32	3.5	0.40072	.	.	.	.	.	T	0.21674	0.0522	.	.	.	0.24288	N	0.995175	B	0.12013	0.005	B	0.09377	0.004	T	0.32693	-0.9897	7	0.66056	D	0.02	.	12.4456	0.55649	0.0:0.8558:0.0:0.1442	.	508	Q9Y450-2	.	N	508	.	ENSP00000356796:D508N	D	-	1	0	HBS1L	135399766	0.002000	0.14202	0.020000	0.16555	0.158000	0.22134	0.745000	0.26259	1.373000	0.46208	0.655000	0.94253	GAC	.	.	.	none		0.368	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2			T	135358073	C	T	135358073	1	4	241	0	1	0	0	0	0	0	0	0	6994	913	32	2		2	HBS1L	6	135358073	Intron	SNP	C	TCGA-SX-A71R-01A-12D-A33Q-10	82701338	135358073	35756994	16	14779											
MRPL32	64983	hgsc.bcm.edu	37	chr7	42974719	42974719	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taggagaagaaatccgcagaAgcttattaaagttaaggtaa	18	9	10	4	1	0	3	0	0	0	3	1	4	1	3	1	2	1	4	1	2	9	5			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr7:42974719A>G	ENST00000223324.2	+	2	483	c.296A>G	c.(295-297)aAg>aGg	p.K99R	MRPL32_ENST00000496564.1_3'UTR|PSMA2_ENST00000538645.1_5'Flank|PSMA2_ENST00000442788.1_5'Flank|PSMA2_ENST00000445517.1_5'Flank|PSMA2_ENST00000223321.4_5'Flank	NM_031903.2	NP_114109.1	Q9BYC8	RM32_HUMAN	mitochondrial ribosomal protein L32	99					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						AATCCGCAGAAGCTTATTAAA	0.403																																					p.K99R		Atlas-SNP	.											.	MRPL32	25	.	0			c.A296G						PASS	.						75	72	73					7																	42974719		2203	4300	6503	SO:0001583	missense	64983	exon2			CGCAGAAGCTTAT	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.296A>G	chr7.hg19:g.42974719A>G	ENSP00000223324:p.Lys99Arg	129.0	0.0	.		210.0	56.0	.	NM_031903	Q96Q68|Q9P098	Missense_Mutation	SNP	ENST00000223324.2	hg19	CCDS5468.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.249005	0.80024	.	.	ENSG00000106591	ENST00000223324	.	.	.	5.33	5.33	0.75918	.	0.181632	0.64402	D	0.000020	T	0.79233	0.4411	M	0.77712	2.385	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.81870	-0.0734	9	0.62326	D	0.03	-29.9723	15.3359	0.74255	1.0:0.0:0.0:0.0	.	99	Q9BYC8	RM32_HUMAN	R	99	.	ENSP00000223324:K99R	K	+	2	0	MRPL32	42941244	1.000000	0.71417	0.793000	0.32043	0.740000	0.42216	9.300000	0.96151	2.000000	0.58554	0.528000	0.53228	AAG	.	.	.	none		0.403	MRPL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338669.1	NM_031903		G	42974719	A	G	42974719	3	3	241	1	0	0	0	0	1	0	0	0	9802	72	3	3	302	3	MRPL32	7	42974719	Missense_Mutation	SNP	A	TCGA-SX-A71R-01A-12D-A33Q-10		42974719	116163944	17	14780											
EPHB6	2051	hgsc.bcm.edu	37	chr7	142562102	142562102	+	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	cctctgcagcgtgggctgtgGgaccccacggggctgggcag	4	6	18	13	2	1	0	0	0	1	0	1	1	1	1	3	5	2	4	3	5	0	0			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr7:142562102G>A	ENST00000392957.2	+	7	1331	c.544G>A	c.(544-546)Gga>Aga	p.G182R	EPHB6_ENST00000411471.2_Intron|EPHB6_ENST00000442129.1_Missense_Mutation_p.G182R	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	182	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)					GTGGGCTGTGGGACCCCACGG	0.622																																					p.G182R		Atlas-SNP	.											.	EPHB6	168	.	0			c.G544A						PASS	.						106	126	119					7																	142562102		2201	4293	6494	SO:0001583	missense	2051	exon7			GCTGTGGGACCCC	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.544G>A	chr7.hg19:g.142562102G>A	ENSP00000376684:p.Gly182Arg	98.0	0.0	.		115.0	82.0	.	NM_004445	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Missense_Mutation	SNP	ENST00000392957.2	hg19	CCDS5873.2	.	.	.	.	.	.	.	.	.	.	G	16.30	3.084918	0.55861	.	.	ENSG00000106123	ENST00000392957;ENST00000442129	T;T	0.70045	-0.45;-0.45	5.24	5.24	0.73138	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.40302	N	0.001135	T	0.58807	0.2148	N	0.08118	0	0.80722	D	1	P	0.45672	0.864	P	0.52554	0.702	T	0.61535	-0.7043	10	0.39692	T	0.17	.	15.0592	0.71939	0.0:0.0:1.0:0.0	.	182	O15197	EPHB6_HUMAN	R	182	ENSP00000376684:G182R;ENSP00000410789:G182R	ENSP00000376684:G182R	G	+	1	0	EPHB6	142272224	0.903000	0.30736	0.871000	0.34182	0.427000	0.31564	0.820000	0.27323	2.837000	0.97791	0.655000	0.94253	GGA	.	.	.	none		0.622	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			A	142562102	G	A	142562102	3	1	241	1	0	0	0	0	1	0	0	0	5180	1233	43	2	554	2	EPHB6	7	142562102	Missense_Mutation	SNP	G	TCGA-SX-A71R-01A-12D-A33Q-10	99587383	142562102	16576561	18	14781											
RRAGA	54801	hgsc.bcm.edu	37	chr9	19050301	19050301	+	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	agctacattcttggttatttCccactaccagtgcaaagagc	11	12	7	11	0	1	1	0	0	1	1	2	1	2	1	2	1	5	3	2	1	4	6			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr9:19050301C>T	ENST00000380502.3	-	0	6536				RRAGA_ENST00000380527.1_Missense_Mutation_p.S215F	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6						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						TTGGTTATTTCCCACTACCAG	0.488																																					p.S215F		Atlas-SNP	.											.	RRAGA	17	.	0			c.C644T						PASS	.						130	122	125					9																	19050301		2203	4300	6503	SO:0001628	intergenic_variant	10670	exon1			TTATTTCCCACTA	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		chr9.hg19:g.19050301C>T		100.0	0.0	.		95.0	40.0	.	NM_006570	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Missense_Mutation	SNP	ENST00000380502.3	hg19	CCDS6489.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.970361	0.74246	.	.	ENSG00000155876	ENST00000380527	T	0.67171	-0.25	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	D	0.83894	0.5353	M	0.89095	3.005	0.80722	D	1	D	0.61080	0.989	D	0.71870	0.975	D	0.86791	0.1985	10	0.87932	D	0	-11.9386	16.0156	0.80439	0.0:1.0:0.0:0.0	.	215	Q7L523	RRAGA_HUMAN	F	215	ENSP00000369899:S215F	ENSP00000369899:S215F	S	+	2	0	RRAGA	19040301	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.104000	0.77024	2.735000	0.93741	0.655000	0.94253	TCC	.	.	.	none		0.488	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645		T	19050301	C	T	19050301	1	4	241	0	1	0	0	0	0	0	0	0	13685	855	30	2		2	RRAGA	9	19050301	IGR	SNP	C	TCGA-SX-A71R-01A-12D-A33Q-10		19050301	122163130	19	14782											
FBP2	8789	hgsc.bcm.edu	37	chr9	97329630	97329630	+	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	tagccctcattcaggctgtaAatctttcctttcttcttaat	8	18	4	11	0	5	0	2	0	3	0	6	0	6	0	2	1	1	2	2	1	4	7			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr9:97329630A>T	ENST00000375337.3	-	5	693	c.627T>A	c.(625-627)atT>atA	p.I209I	PCAT7_ENST00000452148.2_RNA	NM_003837.2	NP_003828.2	O00757	F16P2_HUMAN	fructose-1,6-bisphosphatase 2	209					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)				TCAGGCTGTAAATCTTTCCTT	0.443																																					p.I209I		Atlas-SNP	.											.	FBP2	26	.	0			c.T627A						PASS	.						164	164	164					9																	97329630		2203	4300	6503	SO:0001819	synonymous_variant	8789	exon5			GCTGTAAATCTTT	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.627T>A	chr9.hg19:g.97329630A>T		74.0	0.0	.		65.0	26.0	.	NM_003837	Q17R39|Q6FI53	Silent	SNP	ENST00000375337.3	hg19	CCDS6711.1																																																																																			.	.	.	none		0.443	FBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053189.1	NM_003837		T	97329630	A	T	97329630	2	4	241	1	0	0	0	0	0	0	0	1	5713	10	1	5		5	FBP2	9	97329630	Silent	SNP	A	TCGA-SX-A71R-01A-12D-A33Q-10	78279329	97329630	43883801	20	14783											
SWAP70	23075	hgsc.bcm.edu	37	chr11	9746244	9746244	+	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	agcttacagaagctatgggaGgaggttggcagcaagaacaa	15	6	14	6	0	0	2	0	0	0	2	0	4	0	4	0	4	5	5	0	4	6	3			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr11:9746244G>A	ENST00000318950.6	+	4	557	c.454G>A	c.(454-456)Gga>Aga	p.G152R	SWAP70_ENST00000447399.2_Missense_Mutation_p.G94R	NM_015055.2	NP_055870.2	Q9UH65	SWP70_HUMAN	SWAP switching B-cell complex 70kDa subunit	152					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)		AGCTATGGGAGGAGGTTGGCA	0.318																																					p.G152R		Atlas-SNP	.											.	SWAP70	40	.	0			c.G454A						PASS	.						71	69	70					11																	9746244		2201	4294	6495	SO:0001583	missense	23075	exon4			ATGGGAGGAGGTT	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.454G>A	chr11.hg19:g.9746244G>A	ENSP00000315630:p.Gly152Arg	121.0	0.0	.		108.0	56.0	.	NM_015055	D3DQV1|O75135|Q7LCY6|Q9P061|Q9P0Z8	Missense_Mutation	SNP	ENST00000318950.6	hg19	CCDS31426.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.920223	0.33908	.	.	ENSG00000133789	ENST00000447399;ENST00000318950;ENST00000534662	T;T;T	0.11930	2.73;2.73;3.18	5.51	4.59	0.56863	.	0.108656	0.64402	D	0.000007	T	0.12390	0.0301	L	0.43152	1.355	0.40606	D	0.981623	P;P;P	0.39964	0.697;0.664;0.612	B;B;B	0.38655	0.276;0.278;0.091	T	0.10200	-1.0640	10	0.32370	T	0.25	-6.8811	9.8943	0.41309	0.0725:0.0:0.7885:0.139	.	94;152;94	E7EMB1;Q9UH65;B3KUB9	.;SWP70_HUMAN;.	R	94;152;3	ENSP00000399056:G94R;ENSP00000315630:G152R;ENSP00000435587:G3R	ENSP00000315630:G152R	G	+	1	0	SWAP70	9702820	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.623000	0.54224	1.313000	0.45069	0.467000	0.42956	GGA	.	.	.	none		0.318	SWAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386766.2	NM_015055		A	9746244	G	A	9746244	3	1	241	1	0	0	0	0	1	0	0	0	15437	1001	35	2	468	2	SWAP70	11	9746244	Missense_Mutation	SNP	G	TCGA-SX-A71R-01A-12D-A33Q-10		9746244	125260272	21	14784											
ARHGEF17	9828	hgsc.bcm.edu	37	chr11	73021391	73021391	+	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	ctctgaagtccagctcctccGagctcctgctcacaggccct	6	9	8	18	1	2	1	1	1	1	0	6	2	6	1	5	1	3	3	5	1	1	0			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr11:73021391G>A	ENST00000263674.3	+	1	2058	c.1708G>A	c.(1708-1710)Gag>Aag	p.E570K	RP11-800A3.7_ENST00000546324.1_RNA	NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	570					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						CAGCTCCTCCGAGCTCCTGCT	0.622																																					p.E570K		Atlas-SNP	.											.	ARHGEF17	117	.	0			c.G1708A						PASS	.						37	40	39					11																	73021391		2200	4293	6493	SO:0001583	missense	9828	exon1			TCCTCCGAGCTCC	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.1708G>A	chr11.hg19:g.73021391G>A	ENSP00000263674:p.Glu570Lys	84.0	0.0	.		54.0	25.0	.	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Missense_Mutation	SNP	ENST00000263674.3	hg19	CCDS8221.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.419170	0.83559	.	.	ENSG00000110237	ENST00000263674	T	0.62364	0.03	4.62	4.62	0.57501	.	0.082023	0.49305	D	0.000152	T	0.68412	0.2998	L	0.29908	0.895	0.41778	D	0.989808	D	0.89917	1.0	D	0.66351	0.943	T	0.73404	-0.3993	10	0.87932	D	0	-17.8299	16.1961	0.82025	0.0:0.0:1.0:0.0	.	570	Q96PE2	ARHGH_HUMAN	K	570	ENSP00000263674:E570K	ENSP00000263674:E570K	E	+	1	0	ARHGEF17	72699039	1.000000	0.71417	0.997000	0.53966	0.641000	0.38312	9.074000	0.93998	2.384000	0.81235	0.561000	0.74099	GAG	.	.	.	none		0.622	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		A	73021391	G	A	73021391	3	1	241	1	0	0	0	0	1	0	0	0	900	1059	37	1	1710	1	ARHGEF17	11	73021391	Missense_Mutation	SNP	G	TCGA-SX-A71R-01A-12D-A33Q-10	63275147	73021391	61985125	22	14785											
XRRA1	143570	hgsc.bcm.edu	37	chr11	74563097	74563097	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcagagagatgggaagagagCtactggtaggacagcatcct	13	6	15	7	0	0	3	0	0	0	3	1	7	1	5	1	3	3	4	1	3	3	2			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr11:74563097C>T	ENST00000340360.6	-	13	1508	c.1177G>A	c.(1177-1179)Gct>Act	p.A393T	XRRA1_ENST00000321448.8_Missense_Mutation_p.A118T|XRRA1_ENST00000527087.1_Intron	NM_182969.2	NP_892014.1			X-ray radiation resistance associated 1											breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(3)	20						GGGAAGAGAGCTACTGGTAGG	0.537																																					p.A393T		Atlas-SNP	.											.	XRRA1	46	.	0			c.G1177A						PASS	.						137	140	139					11																	74563097		2057	4183	6240	SO:0001583	missense	143570	exon13			AGAGAGCTACTGG	AK074152	CCDS44680.1, CCDS58159.1, CCDS58160.1	11q13.4	2010-03-19			ENSG00000166435	ENSG00000166435			18868	protein-coding gene	gene with protein product		609788				12908878, 17295261	Standard	NM_182969		Approved	FLJ00225	uc009yub.3	Q6P2D8		ENST00000340360.6:c.1177G>A	chr11.hg19:g.74563097C>T	ENSP00000339918:p.Ala393Thr	117.0	0.0	.		73.0	26.0	.	NM_182969		Missense_Mutation	SNP	ENST00000340360.6	hg19	CCDS44680.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.908003	0.92107	.	.	ENSG00000166435	ENST00000340360;ENST00000321448;ENST00000344880;ENST00000398418	T;T	0.51817	1.83;0.69	6.07	6.07	0.98685	.	.	.	.	.	T	0.63558	0.2521	L	0.46614	1.455	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;0.999	D;D;D;D	0.87578	0.996;0.986;0.998;0.986	T	0.63363	-0.6654	9	0.87932	D	0	-7.6097	16.1526	0.81632	0.0:1.0:0.0:0.0	.	393;337;18;379	Q6P2D8;Q6P2D8-4;Q8TEH2;Q6P2D8-3	XRRA1_HUMAN;.;.;.	T	393;118;379;337	ENSP00000339918:A393T;ENSP00000319303:A118T	ENSP00000319303:A118T	A	-	1	0	XRRA1	74240745	1.000000	0.71417	0.988000	0.46212	0.716000	0.41182	4.186000	0.58337	2.890000	0.99128	0.585000	0.79938	GCT	.	.	.	none		0.537	XRRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384715.1	NM_182969		T	74563097	C	T	74563097	3	4	241	1	0	0	0	0	1	0	0	0	17473	797	28	2	1229	2	XRRA1	11	74563097	Missense_Mutation	SNP	C	TCGA-SX-A71R-01A-12D-A33Q-10	1541706	74563097	60443419	23	14786											
MAML2	84441	hgsc.bcm.edu	37	chr11	95826617	95826617	+	Frame_Shift_Del	DEL	T	T	-																															atgagttgtccacaaagccaTtgggtcgcttgctgttggca																										TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr11:95826617delT	ENST00000524717.1	-	2	1862	c.578delA	c.(577-579)aatfs	p.N193fs		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	193					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)				CACAAAGCCATTGGGTCGCTT	0.418			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.N193fs		Atlas-Indel,Pindel	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2	94	.	0			c.579delT						PASS	.						106	100	102					11																	95826617		1855	4114	5969	SO:0001589	frameshift_variant	84441	exon2			.	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.578delA	chr11.hg19:g.95826617delT	ENSP00000434552:p.Asn193fs	167.0	0.0	0		138.0	63.0	0.456522	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Frame_Shift_Del	DEL	ENST00000524717.1	hg19	CCDS44714.1																																																																																			.	.	.	none		0.418	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			-	95826617	T	-	95826617	7	5	241	1	0	1	0	1	0	0	0	0	9213	1493	52	0	2908	0	MAML2	11	95826617	Frame_Shift_Del	DEL	T	TCGA-SX-A71R-01A-12D-A33Q-10	21263520	95826617	39179899	24	14787											
PCSK7	9159	hgsc.bcm.edu	37	chr11	117097999	117097999	+	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	atccgggtggggcatggggtCagggtcattagagttgaggt	7	10	19	5	1	2	2	2	1	0	1	3	2	3	2	1	7	0	2	1	7	1	2			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr11:117097999C>T	ENST00000320934.3	-	5	1273	c.643G>A	c.(643-645)Gac>Aac	p.D215N		NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	215	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)		GGCATGGGGTCAGGGTCATTA	0.567			T	IGH@	MLCLS																																p.D215N		Atlas-SNP	.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	.	PCSK7	59	.	0			c.G643A						PASS	.						111	109	110					11																	117097999		2201	4296	6497	SO:0001583	missense	9159	exon5			TGGGGTCAGGGTC	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.643G>A	chr11.hg19:g.117097999C>T	ENSP00000325917:p.Asp215Asn	99.0	0.0	.		58.0	27.0	.	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Missense_Mutation	SNP	ENST00000320934.3	hg19	CCDS8382.1	.	.	.	.	.	.	.	.	.	.	C	36	5.694404	0.96793	.	.	ENSG00000160613	ENST00000320934;ENST00000543900;ENST00000525027	D;D	0.87103	-2.21;-2.21	5.61	5.61	0.85477	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.000000	0.85682	D	0.000000	D	0.87621	0.6223	L	0.52126	1.63	0.80722	D	1	P	0.44139	0.827	P	0.45856	0.495	D	0.88316	0.2959	10	0.59425	D	0.04	-34.5595	18.6171	0.91306	0.0:1.0:0.0:0.0	.	215	Q16549	PCSK7_HUMAN	N	215	ENSP00000325917:D215N;ENSP00000431181:D215N	ENSP00000325917:D215N	D	-	1	0	PCSK7	116603209	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.633000	0.89246	0.655000	0.94253	GAC	.	.	.	none		0.567	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716		T	117097999	C	T	117097999	3	4	241	1	0	0	0	0	1	0	0	0	11612	826	29	2	1766	2	PCSK7	11	117097999	Missense_Mutation	SNP	C	TCGA-SX-A71R-01A-12D-A33Q-10	21271382	117097999	17908517	25	14788											
BCDIN3D	144233	hgsc.bcm.edu	37	chr12	50232321	50232321	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catgccatgatcctgggtcaAgatctgcacaatctgattgg	10	11	10	10	0	3	3	1	2	2	1	4	3	4	3	2	2	2	1	2	2	2	1			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr12:50232321A>G	ENST00000333924.4	-	2	753	c.712T>C	c.(712-714)Ttg>Ctg	p.L238L	BCDIN3D-AS1_ENST00000548872.1_RNA|BCDIN3D-AS1_ENST00000549124.1_RNA	NM_181708.2	NP_859059.1	Q7Z5W3	BN3D2_HUMAN	BCDIN3 domain containing	238	Bin3-type SAM. {ECO:0000255|PROSITE- ProRule:PRU00848}.				miRNA metabolic process (GO:0010586)|negative regulation of pre-miRNA processing (GO:2000632)|RNA methylation (GO:0001510)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	O-methyltransferase activity (GO:0008171)|RNA methyltransferase activity (GO:0008173)			endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)|stomach(1)	9						TCCTGGGTCAAGATCTGCACA	0.502																																					p.L238L		Atlas-SNP	.											.	BCDIN3D	20	.	0			c.T712C						PASS	.						130	121	124					12																	50232321		2203	4300	6503	SO:0001819	synonymous_variant	144233	exon2			GGGTCAAGATCTG		CCDS8790.1	12q13.13	2008-03-12				ENSG00000186666			27050	protein-coding gene	gene with protein product							Standard	NM_181708		Approved		uc001rvh.3	Q7Z5W3	OTTHUMG00000169807	ENST00000333924.4:c.712T>C	chr12.hg19:g.50232321A>G		84.0	0.0	.		64.0	36.0	.	NM_181708	A8K829	Silent	SNP	ENST00000333924.4	hg19	CCDS8790.1																																																																																			.	.	.	none		0.502	BCDIN3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405982.1	NM_181708		G	50232321	A	G	50232321	2	3	241	1	0	0	0	0	0	0	0	1	1357	69	3	3		3	BCDIN3D	12	50232321	Silent	SNP	A	TCGA-SX-A71R-01A-12D-A33Q-10		50232321	83619574	26	14789											
CCDC59	29080	hgsc.bcm.edu	37	chr12	82752072	82752072	+	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	ttctgtctcacattcttattCctgtacccgacagtggaaac	9	14	6	12	1	3	0	1	0	3	0	5	2	4	1	2	1	2	1	2	1	3	5			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr12:82752072C>T	ENST00000256151.7	-	1	495	c.84G>A	c.(82-84)agG>agA	p.R28R	METTL25_ENST00000248306.3_5'Flank|CCDC59_ENST00000548126.1_Intron	NM_014167.4	NP_054886.2	Q9P031	TAP26_HUMAN	coiled-coil domain containing 59	28					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)	5						CATTCTTATTCCTGTACCCGA	0.587											OREG0022008	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R28R		Atlas-SNP	.											.	CCDC59	17	.	0			c.G84A						PASS	.						69	63	65					12																	82752072		2203	4300	6503	SO:0001819	synonymous_variant	29080	exon1			CTTATTCCTGTAC	AF213377	CCDS9023.1	12q21.31	2007-10-17				ENSG00000133773			25005	protein-coding gene	gene with protein product						16630564, 12882447	Standard	NM_014167		Approved	HSPC128, TAP26, BR22	uc001szp.4	Q9P031		ENST00000256151.7:c.84G>A	chr12.hg19:g.82752072C>T		76.0	0.0	.	1216	81.0	29.0	.	NM_014167	Q9H2V5|Q9NW62	Silent	SNP	ENST00000256151.7	hg19	CCDS9023.1																																																																																			.	.	.	none		0.587	CCDC59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408186.1	NM_014167		T	82752072	C	T	82752072	2	4	241	1	0	0	0	0	0	0	0	1	2831	854	30	2		2	CCDC59	12	82752072	Silent	SNP	C	TCGA-SX-A71R-01A-12D-A33Q-10	32519751	82752072	51099823	27	14790											
RAN	5901	hgsc.bcm.edu	37	chr12	131360202	131360202	+	Missense_Mutation	SNP	T	T	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	actacaactttgaaaagcccTtcctctggcttgctaggaag	11	11	8	11	0	1	1	0	1	1	0	2	2	2	2	2	2	4	2	2	2	6	5			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr12:131360202T>G	ENST00000543796.1	+	6	739	c.481T>G	c.(481-483)Ttc>Gtc	p.F161V	RAN_ENST00000254675.3_Missense_Mutation_p.F73V|RAN_ENST00000392369.2_Missense_Mutation_p.F161V|RAN_ENST00000541630.1_Missense_Mutation_p.F73V|RAN_ENST00000392367.3_Missense_Mutation_p.F178V			P62826	RAN_HUMAN	RAN, member RAS oncogene family	161					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)		TGAAAAGCCCTTCCTCTGGCT	0.408																																					p.F161V		Atlas-SNP	.											.	RAN	18	.	0			c.T481G						PASS	.						52	53	53					12																	131360202		2203	4300	6503	SO:0001583	missense	5901	exon6			AAGCCCTTCCTCT	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.481T>G	chr12.hg19:g.131360202T>G	ENSP00000446215:p.Phe161Val	126.0	0.0	.		117.0	58.0	.	NM_006325	A8K3Z8|P17080|P28746|P28747|Q6IPB2|Q86V08|Q8NI90|Q9CSP3|Q9CWI7|Q9CZA2|Q9UDJ5|Q9UEU9	Missense_Mutation	SNP	ENST00000543796.1	hg19	CCDS9271.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.415702	0.83449	.	.	ENSG00000132341	ENST00000543796;ENST00000448750;ENST00000541630;ENST00000392369;ENST00000254675;ENST00000535090;ENST00000392367	D;D;D;D;D;D;D	0.83419	-1.72;-1.72;-1.72;-1.72;-1.72;-1.72;-1.72	3.94	3.94	0.45596	.	0.000000	0.85682	D	0.000000	D	0.92136	0.7507	M	0.93594	3.435	0.80722	D	1	D;D	0.59767	0.986;0.986	D;D	0.66497	0.944;0.944	D	0.93640	0.6964	10	0.87932	D	0	-8.6508	12.2939	0.54833	0.0:0.0:0.0:1.0	.	161;161	A8K3Z8;P62826	.;RAN_HUMAN	V	161;179;73;161;73;157;178	ENSP00000446215:F161V;ENSP00000396127:F179V;ENSP00000441210:F73V;ENSP00000376176:F161V;ENSP00000254675:F73V;ENSP00000444042:F157V;ENSP00000376174:F178V	ENSP00000254675:F73V	F	+	1	0	RAN	129926155	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.590000	0.82653	1.554000	0.49487	0.460000	0.39030	TTC	.	.	.	none		0.408	RAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259441.2	NM_006325		G	131360202	T	G	131360202	3	3	241	1	0	0	0	0	1	0	0	0	13037	1609	56	5	499	5	RAN	12	131360202	Missense_Mutation	SNP	T	TCGA-SX-A71R-01A-12D-A33Q-10	48608130	131360202	2491693	28	14791											
CENPJ	55835	hgsc.bcm.edu	37	chr13	25486722	25486722	+	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	ggccaaatcctattgtacctGttcaagttttttaaaaagtg	12	15	7	7	0	1	0	1	0	0	0	2	0	2	0	3	1	1	3	3	1	7	7			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr13:25486722G>A	ENST00000381884.4	-	2	627	c.442C>T	c.(442-444)Cag>Tag	p.Q148*	CENPJ_ENST00000545981.1_Nonsense_Mutation_p.Q148*	NM_018451.4	NP_060921.3	Q9HC77	CENPJ_HUMAN	centromere protein J	148					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)		TATTGTACCTGTTCAAGTTTT	0.368																																					p.Q148X		Atlas-SNP	.											.	CENPJ	116	.	0			c.C442T						PASS	.						68	70	69					13																	25486722		2203	4300	6503	SO:0001587	stop_gained	55835	exon2			GTACCTGTTCAAG	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.442C>T	chr13.hg19:g.25486722G>A	ENSP00000371308:p.Gln148*	91.0	0.0	.		57.0	30.0	.	NM_018451	Q2KHM6|Q5JPD5|Q5T6R5|Q96KS5|Q9C067	Nonsense_Mutation	SNP	ENST00000381884.4	hg19	CCDS9310.1	.	.	.	.	.	.	.	.	.	.	G	38	6.752924	0.97813	.	.	ENSG00000151849	ENST00000381884;ENST00000545981;ENST00000445729	.	.	.	5.9	5.9	0.94986	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	.	17.1723	0.86833	0.0:0.0:1.0:0.0	.	.	.	.	X	148	.	ENSP00000371308:Q148X	Q	-	1	0	CENPJ	24384722	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	6.301000	0.72782	2.791000	0.96007	0.655000	0.94253	CAG	.	.	.	none		0.368	CENPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044209.1	NM_018451		A	25486722	G	A	25486722	4	1	241	1	0	0	0	0	0	1	0	0	3236	1386	48	2	3638	2	CENPJ	13	25486722	Nonsense_Mutation	SNP	G	TCGA-SX-A71R-01A-12D-A33Q-10		25486722	89683156	29	14792											
CHD8	57680	hgsc.bcm.edu	37	chr14	21862288	21862288	+	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	agcgccgaagcaattctataCggtagagagtccgtgaggct	11	8	13	9	4	1	2	0	1	1	1	2	4	2	2	2	2	3	3	2	2	5	4			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr14:21862288C>T	ENST00000557364.1	-	32	5929	c.5666G>A	c.(5665-5667)cGt>cAt	p.R1889H	CHD8_ENST00000555962.1_5'Flank|CHD8_ENST00000430710.3_Missense_Mutation_p.R1610H|CHD8_ENST00000399982.2_Missense_Mutation_p.R1889H|SNORD9_ENST00000362566.1_RNA			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1889					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)		CAATTCTATACGGTAGAGAGT	0.512																																					p.R1889H		Atlas-SNP	.											.	CHD8	339	.	0			c.G5666A						PASS	.						51	50	50					14																	21862288		1868	4106	5974	SO:0001583	missense	57680	exon31			TCTATACGGTAGA	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.5666G>A	chr14.hg19:g.21862288C>T	ENSP00000451601:p.Arg1889His	30.0	0.0	.		35.0	15.0	.	NM_001170629	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Missense_Mutation	SNP	ENST00000557364.1	hg19	CCDS53885.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.382302	0.82792	.	.	ENSG00000100888	ENST00000430710;ENST00000399982;ENST00000262707;ENST00000557364	D;D;D	0.83335	-1.71;-1.71;-1.71	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	D	0.91868	0.7426	M	0.83774	2.66	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92496	0.6004	10	0.87932	D	0	-13.5033	18.1345	0.89614	0.0:1.0:0.0:0.0	.	1610	Q9HCK8-2	.	H	1610;1889;1609;1889	ENSP00000406288:R1610H;ENSP00000382863:R1889H;ENSP00000451601:R1889H	ENSP00000262707:R1609H	R	-	2	0	CHD8	20932128	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	7.651000	0.83577	2.816000	0.96949	0.563000	0.77884	CGT	.	.	.	none		0.512	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920		T	21862288	C	T	21862288	3	4	241	1	0	0	0	0	1	0	0	0	3333	536	19	1	2107	1	CHD8	14	21862288	Missense_Mutation	SNP	C	TCGA-SX-A71R-01A-12D-A33Q-10		21862288	85487252	30	14793											
STRN3	29966	hgsc.bcm.edu	37	chr14	31382758	31382758	+	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	tatagtctgcatcatttgttAccgtcaagtctgcaaggtct	9	15	8	9	1	5	0	2	0	3	0	5	0	5	0	1	1	3	3	1	1	5	4			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr14:31382758A>T	ENST00000357479.5	-	10	1542	c.1346T>A	c.(1345-1347)gTa>gAa	p.V449E	STRN3_ENST00000366206.2_Intron|STRN3_ENST00000355683.5_Missense_Mutation_p.V365E	NM_001083893.1	NP_001077362.1	Q13033	STRN3_HUMAN	striatin, calmodulin binding protein 3	449					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)		ATCATTTGTTACCGTCAAGTC	0.343																																					p.V449E		Atlas-SNP	.											.	STRN3	117	.	0			c.T1346A						PASS	.						96	89	91					14																	31382758		2203	4300	6503	SO:0001583	missense	29966	exon10			TTTGTTACCGTCA		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.1346T>A	chr14.hg19:g.31382758A>T	ENSP00000350071:p.Val449Glu	104.0	0.0	.		102.0	49.0	.	NM_001083893	A2RTX7|A6NHZ7|Q9NRA5	Missense_Mutation	SNP	ENST00000357479.5	hg19	CCDS41938.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.099076	0.76983	.	.	ENSG00000196792	ENST00000355683;ENST00000357479;ENST00000554991	T;T	0.64438	-0.1;2.37	5.97	4.84	0.62591	WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.78591	0.4307	M	0.81682	2.555	0.80722	D	1	D;P	0.89917	1.0;0.931	D;B	0.77004	0.989;0.444	T	0.80756	-0.1240	10	0.87932	D	0	-15.1617	11.8795	0.52566	0.9324:0.0:0.0676:0.0	.	365;449	Q13033-2;Q13033	.;STRN3_HUMAN	E	365;449;130	ENSP00000347909:V365E;ENSP00000350071:V449E	ENSP00000347909:V365E	V	-	2	0	STRN3	30452509	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.639000	0.91023	1.097000	0.41459	0.533000	0.62120	GTA	.	.	.	none		0.343	STRN3-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409713.1	NM_014574		T	31382758	A	T	31382758	3	4	241	1	0	0	0	0	1	0	0	0	15342	391	14	5	1083	5	STRN3	14	31382758	Missense_Mutation	SNP	A	TCGA-SX-A71R-01A-12D-A33Q-10	9520470	31382758	75966782	31	14794											
TRPM1	4308	hgsc.bcm.edu	37	chr15	31327765	31327765	+	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	ccacctctcgtatcttctctAacgccaggctcacgatgtag	8	11	7	15	3	4	0	1	0	3	0	6	1	4	0	3	1	1	3	3	1	3	4			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr15:31327765A>T	ENST00000256552.6	-	21	2831	c.2684T>A	c.(2683-2685)tTa>tAa	p.L895*	RP11-348B17.1_ENST00000558755.1_RNA|RP11-348B17.1_ENST00000561299.1_RNA|TRPM1_ENST00000397795.2_Nonsense_Mutation_p.L873*|TRPM1_ENST00000542188.1_Nonsense_Mutation_p.L912*	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)		TATCTTCTCTAACGCCAGGCT	0.542																																					p.L912X		Atlas-SNP	.											.	TRPM1	183	.	0			c.T2735A						PASS	.						80	81	80					15																	31327765		2047	4192	6239	SO:0001587	stop_gained	4308	exon20			TTCTCTAACGCCA	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.2684T>A	chr15.hg19:g.31327765A>T	ENSP00000256552:p.Leu895*	79.0	0.0	.		72.0	39.0	.	NM_001252020		Nonsense_Mutation	SNP	ENST00000256552.6	hg19	CCDS58346.1	.	.	.	.	.	.	.	.	.	.	A	37	6.205158	0.97376	.	.	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	.	.	.	5.57	5.57	0.84162	.	0.157867	0.42682	D	0.000679	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15952	T	0.53	-13.7367	15.7279	0.77777	1.0:0.0:0.0:0.0	.	.	.	.	X	873;912;895;873	.	ENSP00000256552:L895X	L	-	2	0	TRPM1	29115057	0.009000	0.17119	0.004000	0.12327	0.180000	0.23129	2.643000	0.46604	2.124000	0.65301	0.533000	0.62120	TTA	.	.	.	none		0.542	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420		T	31327765	A	T	31327765	4	4	241	1	0	0	0	0	0	1	0	0	16597	372	13	5	2225	5	TRPM1	15	31327765	Nonsense_Mutation	SNP	A	TCGA-SX-A71R-01A-12D-A33Q-10		31327765	71203627	32	14795											
SLC7A5	8140	hgsc.bcm.edu	37	chr16	87902587	87902587	+	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	ggtggcgaagaccagggccaCgatgtactgcgatgaaggcc	10	5	16	10	3	0	2	0	1	0	1	0	5	0	2	3	4	2	1	3	4	3	1			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr16:87902587C>A	ENST00000261622.4	-	1	507	c.442G>T	c.(442-444)Gtg>Ttg	p.V148L		NM_003486.5	NP_003477.4	Q01650	LAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 5	148					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)	ACCAGGGCCACGATGTACTGC	0.652																																					p.V148L		Atlas-SNP	.											.	SLC7A5	28	.	0			c.G442T						PASS	.						15	13	13					16																	87902587		2119	4119	6238	SO:0001583	missense	8140	exon1			GGGCCACGATGTA	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.442G>T	chr16.hg19:g.87902587C>A	ENSP00000261622:p.Val148Leu	190.0	0.0	.		195.0	61.0	.	NM_003486	Q8IV97|Q9UBN8|Q9UP15|Q9UQC0	Missense_Mutation	SNP	ENST00000261622.4	hg19	CCDS10964.1	.	.	.	.	.	.	.	.	.	.	c	35	5.508315	0.96386	.	.	ENSG00000103257	ENST00000261622	D	0.89196	-2.48	4.34	4.34	0.51931	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.89904	0.6850	L	0.33137	0.985	0.80722	D	1	D	0.64830	0.994	P	0.59761	0.863	D	0.91451	0.5181	10	0.72032	D	0.01	.	15.8578	0.78994	0.0:1.0:0.0:0.0	.	148	Q01650	LAT1_HUMAN	L	148	ENSP00000261622:V148L	ENSP00000261622:V148L	V	-	1	0	SLC7A5	86460088	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	3.077000	0.50089	1.972000	0.57404	0.400000	0.26472	GTG	.	.	.	none		0.652	SLC7A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269110.2	NM_003486		A	87902587	C	A	87902587	3	1	241	1	0	0	0	0	1	0	0	0	14713	536	19	4	1121	4	SLC7A5	16	87902587	Missense_Mutation	SNP	C	TCGA-SX-A71R-01A-12D-A33Q-10		87902587	2452166	33	14796											
ALKBH5	54890	hgsc.bcm.edu	37	chr17	18088007	18088007	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctgcagaagcgcgggccCggccaggagcgcctctaccc	7	3	14	17	4	1	1	0	0	1	1	1	2	1	2	4	3	5	2	4	3	2	1			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr17:18088007C>T	ENST00000399138.4	+	1	455	c.450C>T	c.(448-450)ccC>ccT	p.P150P	ALKBH5_ENST00000541285.1_Intron|RP11-258F1.1_ENST00000583062.1_RNA|RP11-258F1.1_ENST00000577847.1_RNA	NM_017758.3	NP_060228.3	Q6P6C2	ALKB5_HUMAN	AlkB family member 5, RNA demethylase	150					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|oxidative single-stranded RNA demethylation (GO:0035553)|response to hypoxia (GO:0001666)|spermatogenesis (GO:0007283)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|oxidative RNA demethylase activity (GO:0035515)|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)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|skin(1)	10	all_neural(463;0.228)					AGCGCGGGCCCGGCCAGGAGC	0.672																																					p.P150P	Ovarian(166;154 1953 40235 46283 46309)	Atlas-SNP	.											.	ALKBH5	24	.	0			c.C450T						PASS	.						26	31	30					17																	18088007		1901	4074	5975	SO:0001819	synonymous_variant	54890	exon1			CGGGCCCGGCCAG	AK000315	CCDS42272.1	17p11.2	2014-07-23	2014-07-23	2006-02-09	ENSG00000091542	ENSG00000091542	1.14.11.-	"Alkylation repair homologs"	25996	protein-coding gene	gene with protein product		613303	"oxoglutarate and iron-dependent oxygenase domain containing", "alkB, alkylation repair homolog 5 (E. coli)"	OFOXD1		11997338, 24778178	Standard	NM_017758		Approved	FLJ20308	uc010cpw.3	Q6P6C2	OTTHUMG00000059397	ENST00000399138.4:c.450C>T	chr17.hg19:g.18088007C>T		115.0	0.0	.		137.0	40.0	.	NM_017758	B4DVJ4|D3DXC6|Q9NXD6	Silent	SNP	ENST00000399138.4	hg19	CCDS42272.1																																																																																			.	.	.	none		0.672	ALKBH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132069.3	NM_017758		T	18088007	C	T	18088007	2	4	241	1	0	0	0	0	0	0	0	1	530	639	23	1		1	ALKBH5	17	18088007	Silent	SNP	C	TCGA-SX-A71R-01A-12D-A33Q-10		18088007	63107203	34	14797											
EVPLL	645027	hgsc.bcm.edu	37	chr17	18284974	18284974	+	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	gcggagtactgtgccctgtaCgagaagatggtgctgccgcc	7	8	15	11	3	0	2	0	0	0	2	0	4	0	3	3	2	5	3	3	2	3	2	rs567752730		TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr17:18284974C>G	ENST00000399134.4	+	4	634	c.276C>G	c.(274-276)taC>taG	p.Y92*	RP1-37N7.1_ENST00000579352.1_RNA	NM_001145127.1	NP_001138599.1	A8MZ36	EVPLL_HUMAN	envoplakin-like	92										NS(1)|endometrium(1)|large_intestine(1)|lung(2)	5						GTGCCCTGTACGAGAAGATGG	0.627																																					p.Y92X		Atlas-SNP	.											.	EVPLL	10	.	0			c.C276G						PASS	.						134	123	126					17																	18284974		692	1591	2283	SO:0001587	stop_gained	645027	exon4			CCTGTACGAGAAG		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.276C>G	chr17.hg19:g.18284974C>G	ENSP00000382086:p.Tyr92*	124.0	0.0	.		112.0	35.0	.	NM_001145127	B4DPD4	Nonsense_Mutation	SNP	ENST00000399134.4	hg19	CCDS45626.1	.	.	.	.	.	.	.	.	.	.	.	16.41	3.116101	0.56505	.	.	ENSG00000214860	ENST00000399134	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	2.8319	0.05503	0.0:0.5931:0.0:0.4069	.	.	.	.	X	92	.	ENSP00000382086:Y92X	Y	+	3	2	EVPLL	18225699	0.225000	0.23685	0.990000	0.47175	0.206000	0.24218	-1.410000	0.02480	0.432000	0.26286	0.074000	0.15403	TAC	.	.	.	none		0.627	EVPLL-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130836.2	NM_001145127		G	18284974	C	G	18284974	4	3	241	1	0	0	0	0	0	1	0	0	5295	547	19	4	286	4	EVPLL	17	18284974	Nonsense_Mutation	SNP	C	TCGA-SX-A71R-01A-12D-A33Q-10	196967	18284974	62910236	35	14798											
EVI2B	2124	hgsc.bcm.edu	37	chr17	29632360	29632360	+	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	agtatgtgcttctggtttttCagaagaggtatagacagctg	10	14	12	5	0	2	3	1	0	1	3	2	3	2	3	0	2	2	5	0	2	4	6			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr17:29632360C>G	ENST00000330927.4	-	2	422	c.268G>C	c.(268-270)Gaa>Caa	p.E90Q	EVI2B_ENST00000544462.1_Missense_Mutation_p.E105Q|EVI2B_ENST00000577894.1_Missense_Mutation_p.E90Q|NF1_ENST00000356175.3_Intron|NF1_ENST00000358273.4_Intron|CTD-2370N5.3_ENST00000578584.1_3'UTR	NM_006495.3	NP_006486.3	P34910	EVI2B_HUMAN	ecotropic viral integration site 2B	90						integral component of plasma membrane (GO:0005887)		p.0?(8)|p.?(3)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|urinary_tract(1)	12		all_cancers(10;6.97e-11)|all_epithelial(10;0.0051)|all_hematologic(16;0.0149)|Breast(31;0.0155)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|all_lung(9;0.0468)|Lung NSC(157;0.094)		UCEC - Uterine corpus endometrioid carcinoma (4;6.64e-05)|all cancers(4;6.88e-13)|Epithelial(4;8.95e-12)|OV - Ovarian serous cystadenocarcinoma(4;1.01e-11)|GBM - Glioblastoma multiforme(4;0.184)		TCTGGTTTTTCAGAAGAGGTA	0.478																																					p.E90Q		Atlas-SNP	.											.	EVI2B	33	.	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	c.G268C						PASS	.						379	306	331					17																	29632360		2203	4300	6503	SO:0001583	missense	2124	exon2			GTTTTTCAGAAGA		CCDS11266.1	17q11.2	2011-08-11			ENSG00000185862	ENSG00000185862		"CD molecules"	3500	protein-coding gene	gene with protein product		158381				1903357	Standard	NM_006495		Approved	D17S376, EVDB, CD361	uc002hgk.2	P34910	OTTHUMG00000132869	ENST00000330927.4:c.268G>C	chr17.hg19:g.29632360C>G	ENSP00000333779:p.Glu90Gln	268.0	0.0	.		275.0	98.0	.	NM_006495	B7Z4A7	Missense_Mutation	SNP	ENST00000330927.4	hg19	CCDS11266.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.233965	0.39498	.	.	ENSG00000185862	ENST00000330927;ENST00000544462	T;T	0.46819	0.87;0.86	5.04	4.06	0.47325	.	0.894418	0.09273	N	0.824825	T	0.39009	0.1062	L	0.44542	1.39	0.80722	D	1	P;P	0.42296	0.775;0.775	B;B	0.40825	0.341;0.341	T	0.09509	-1.0671	10	0.15499	T	0.54	-17.1445	8.413	0.32655	0.0:0.8949:0.0:0.1051	.	105;90	B7Z4A7;P34910	.;EVI2B_HUMAN	Q	90;105	ENSP00000333779:E90Q;ENSP00000439738:E105Q	ENSP00000333779:E90Q	E	-	1	0	EVI2B	26656486	0.456000	0.25744	0.876000	0.34364	0.015000	0.08874	0.763000	0.26517	2.348000	0.79779	0.561000	0.74099	GAA	.	.	.	none		0.478	EVI2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256349.2	NM_006495		G	29632360	C	G	29632360	3	3	241	1	0	0	0	0	1	0	0	0	5290	835	29	4	1082	4	EVI2B	17	29632360	Missense_Mutation	SNP	C	TCGA-SX-A71R-01A-12D-A33Q-10	11347386	29632360	51562850	36	14799											
NAT9	26151	hgsc.bcm.edu	37	chr17	72768111	72768111	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atccttacctgctcaaagtgAagtttctggaacatccggat	11	12	8	10	1	2	1	1	1	1	0	4	3	4	3	3	2	3	2	3	2	4	2			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr17:72768111A>G	ENST00000357814.3	-	6	550	c.477T>C	c.(475-477)ctT>ctC	p.L159L	NAT9_ENST00000580301.1_Silent_p.L158L|NAT9_ENST00000582524.1_Intron|NAT9_ENST00000578822.1_Silent_p.L164L|NAT9_ENST00000582870.1_Silent_p.L163L|NAT9_ENST00000580632.1_Silent_p.L159L|NAT9_ENST00000583476.1_Missense_Mutation_p.S134P|NAT9_ENST00000581136.1_Silent_p.L154L|NAT9_ENST00000583757.1_Intron|NAT9_ENST00000580216.1_5'Flank	NM_015654.3	NP_056469.2	Q9BTE0	NAT9_HUMAN	N-acetyltransferase 9 (GCN5-related, putative)	159	N-acetyltransferase.					protein complex (GO:0043234)	N-acetyltransferase activity (GO:0008080)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)	8						GCTCAAAGTGAAGTTTCTGGA	0.512																																					p.L159L		Atlas-SNP	.											.	NAT9	16	.	0			c.T477C						PASS	.						158	153	155					17																	72768111		2203	4300	6503	SO:0001819	synonymous_variant	26151	exon6			AAAGTGAAGTTTC	AK123115	CCDS11706.1	17q25.2	2011-11-25	2008-09-24		ENSG00000109065	ENSG00000109065			23133	protein-coding gene	gene with protein product			"N-acetyltransferase 9"			14608357	Standard	NM_015654		Approved	DKFZP564C103	uc002jlq.3	Q9BTE0		ENST00000357814.3:c.477T>C	chr17.hg19:g.72768111A>G		151.0	0.0	.		182.0	110.0	.	NM_015654	B2R7F0|Q9BTD0|Q9Y3T3	Silent	SNP	ENST00000357814.3	hg19	CCDS11706.1																																																																																			.	.	.	none		0.512	NAT9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000443700.1	NM_015654		G	72768111	A	G	72768111	2	3	241	1	0	0	0	0	0	0	0	1	10189	233	9	3		3	NAT9	17	72768111	Silent	SNP	A	TCGA-SX-A71R-01A-12D-A33Q-10	43135751	72768111	8427099	37	14800											
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11144020	11144020	+	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	ggcagcagaacgaggtgcgtGtgctccgcctctgcaccgtc	6	7	14	14	4	1	1	0	0	1	1	3	2	2	1	3	2	5	4	3	2	1	0			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr19:11144020G>C	ENST00000429416.3	+	27	3882	c.3601G>C	c.(3601-3603)Gtg>Ctg	p.V1201L	SMARCA4_ENST00000444061.3_Missense_Mutation_p.V1201L|SMARCA4_ENST00000413806.3_Missense_Mutation_p.V1201L|SMARCA4_ENST00000344626.4_Missense_Mutation_p.V1201L|SMARCA4_ENST00000590574.1_Missense_Mutation_p.V1201L|SMARCA4_ENST00000358026.2_Missense_Mutation_p.V1201L|SMARCA4_ENST00000541122.2_Missense_Mutation_p.V1201L|SMARCA4_ENST00000450717.3_Missense_Mutation_p.V1201L|SMARCA4_ENST00000589677.1_Missense_Mutation_p.V1201L	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1201	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CGAGGTGCGTGTGCTCCGCCT	0.622			"F, N, Mis"		NSCLC																																p.V1201L		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.G3601C						PASS	.						86	82	83					19																	11144020		2203	4300	6503	SO:0001583	missense	6597	exon26			GTGCGTGTGCTCC	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.3601G>C	chr19.hg19:g.11144020G>C	ENSP00000395654:p.Val1201Leu	216.0	0.0	.		164.0	83.0	.	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.549924	0.86127	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	T;T;T;T;T;T;T	0.79749	-1.3;-1.3;-1.3;-1.3;-1.3;-1.3;-1.3	4.74	4.74	0.60224	Helicase, C-terminal (1);	0.146662	0.44902	D	0.000416	D	0.90827	0.7119	H	0.95365	3.66	0.58432	D	0.999996	P;P;P;B;P;D;B	0.55605	0.887;0.887;0.887;0.139;0.589;0.972;0.139	P;P;P;B;B;P;B	0.54590	0.656;0.723;0.723;0.139;0.239;0.756;0.139	D	0.93705	0.7019	10	0.87932	D	0	-33.2279	16.7067	0.85374	0.0:0.0:1.0:0.0	.	1201;1201;1201;1201;1201;421;1201	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	L	1201;1201;1265;1201;1201;1201;1201;1201	ENSP00000395654:V1201L;ENSP00000350720:V1201L;ENSP00000343896:V1201L;ENSP00000445036:V1201L;ENSP00000392837:V1201L;ENSP00000397783:V1201L;ENSP00000414727:V1201L	ENSP00000343896:V1201L	V	+	1	0	SMARCA4	11005020	1.000000	0.71417	0.963000	0.40424	0.961000	0.63080	9.319000	0.96338	2.488000	0.83962	0.558000	0.71614	GTG	.	.	.	none		0.622	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		C	11144020	G	C	11144020	3	2	241	1	0	0	0	0	1	0	0	0	14783	1377	48	4	3699	4	SMARCA4	19	11144020	Missense_Mutation	SNP	G	TCGA-SX-A71R-01A-12D-A33Q-10		11144020	47984963	38	14801											
CYP4F3	4051	hgsc.bcm.edu	37	chr19	15752326	15752326	+	Missense_Mutation	SNP	T	T	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	ctcctggctcctggcccgcaTcctggcctggacctatacct	4	10	9	18	1	0	0	0	0	0	0	3	1	3	1	7	4	1	2	7	4	2	2			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr19:15752326T>G	ENST00000221307.8	+	2	148	c.101T>G	c.(100-102)aTc>aGc	p.I34S	CYP4F3_ENST00000591058.1_Missense_Mutation_p.I34S|CYP4F3_ENST00000586182.2_Missense_Mutation_p.I34S|CYP4F3_ENST00000585846.1_Missense_Mutation_p.I34S	NM_000896.2	NP_000887.2	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 3	34					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						CTGGCCCGCATCCTGGCCTGG	0.637																																					p.I34S		Atlas-SNP	.											.	CYP4F3	69	.	0			c.T101G						PASS	.						60	63	62					19																	15752326		2203	4300	6503	SO:0001583	missense	4051	exon2			CCCGCATCCTGGC	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.101T>G	chr19.hg19:g.15752326T>G	ENSP00000221307:p.Ile34Ser	150.0	0.0	.		98.0	39.0	.	NM_001199209	B7Z8Z3|O60634|Q5U740	Missense_Mutation	SNP	ENST00000221307.8	hg19	CCDS12332.1	.	.	.	.	.	.	.	.	.	.	.	9.352	1.065809	0.20067	.	.	ENSG00000186529	ENST00000221307	D	0.90069	-2.61	3.9	0.0418	0.14214	.	1.091210	0.07176	U	0.853302	D	0.85877	0.5799	L	0.48642	1.525	0.09310	N	1	B;B	0.26363	0.147;0.147	B;B	0.31337	0.128;0.128	T	0.74711	-0.3573	10	0.62326	D	0.03	.	9.4966	0.38993	0.0:0.0:0.5539:0.4461	.	34;34	B7Z8Z3;Q08477	.;CP4F3_HUMAN	S	34	ENSP00000221307:I34S	ENSP00000221307:I34S	I	+	2	0	CYP4F3	15613326	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.096000	0.15147	-0.033000	0.13736	-0.811000	0.03165	ATC	.	.	.	none		0.637	CYP4F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460819.3	NM_000896		G	15752326	T	G	15752326	3	3	241	1	0	0	0	0	1	0	0	0	4192	1435	50	5	103	5	CYP4F3	19	15752326	Missense_Mutation	SNP	T	TCGA-SX-A71R-01A-12D-A33Q-10	4608306	15752326	43376657	39	14802											
TTC3	7267	hgsc.bcm.edu	37	chr21	38494269	38494269	+	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	aagttacaaaaacaaatagaAgacctacaaggtatttcacc	20	8	5	8	0	1	2	1	0	0	2	1	2	1	2	2	1	3	2	2	1	10	5			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr21:38494269A>T	ENST00000399017.2	+	12	3800	c.1053A>T	c.(1051-1053)gaA>gaT	p.E351D	TTC3_ENST00000540756.1_Missense_Mutation_p.E41D|TTC3_ENST00000355666.1_Missense_Mutation_p.E351D|TTC3_ENST00000354749.2_Missense_Mutation_p.E351D|TTC3_ENST00000479930.1_3'UTR	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	351					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)				AACAAATAGAAGACCTACAAG	0.373																																					p.E351D	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.A1053T						PASS	.						64	65	65					21																	38494269		2203	4300	6503	SO:0001583	missense	7267	exon12			AATAGAAGACCTA	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.1053A>T	chr21.hg19:g.38494269A>T	ENSP00000381981:p.Glu351Asp	267.0	0.0	.		205.0	92.0	.	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	hg19	CCDS13651.1	.	.	.	.	.	.	.	.	.	.	A	14.03	2.413394	0.42817	.	.	ENSG00000182670	ENST00000418766;ENST00000450533;ENST00000438055;ENST00000355666;ENST00000540756;ENST00000399017;ENST00000354749	T;T;T;T;T;T;T	0.48836	1.03;1.03;1.03;2.93;0.8;2.93;2.93	5.41	4.26	0.50523	Tetratricopeptide-like helical (1);	0.000000	0.56097	D	0.000032	T	0.34048	0.0884	L	0.27053	0.805	0.32047	N	0.597515	B;B	0.21753	0.009;0.06	B;B	0.17433	0.007;0.018	T	0.39035	-0.9633	10	0.56958	D	0.05	-16.3909	10.2565	0.43401	0.8212:0.1788:0.0:0.0	.	41;351	B4DSZ9;P53804	.;TTC3_HUMAN	D	351;351;333;351;41;351;351	ENSP00000403943:E351D;ENSP00000408456:E351D;ENSP00000391891:E333D;ENSP00000347889:E351D;ENSP00000442875:E41D;ENSP00000381981:E351D;ENSP00000346791:E351D	ENSP00000346791:E351D	E	+	3	2	TTC3	37416139	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.903000	0.28475	0.895000	0.36342	0.528000	0.53228	GAA	.	.	.	none		0.373	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			T	38494269	A	T	38494269	3	4	241	1	0	0	0	0	1	0	0	0	16709	69	3	5	1095	5	TTC3	21	38494269	Missense_Mutation	SNP	A	TCGA-SX-A71R-01A-12D-A33Q-10		38494269	9635626	40	14803											
MTM1	4534	hgsc.bcm.edu	37	chrX	149767104	149767104	+	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	caatggccccattaagggaaGagtttacatcacaaattatc	15	10	7	9	0	1	1	1	0	0	1	2	2	1	2	2	2	1	1	2	2	6	4			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chrX:149767104G>T	ENST00000370396.2	+	4	239	c.185G>T	c.(184-186)aGa>aTa	p.R62I	MTM1_ENST00000542741.1_Intron|MTM1_ENST00000306167.7_3'UTR|MTM1_ENST00000543350.1_Intron|MTM1_ENST00000413012.2_Missense_Mutation_p.R62I	NM_000252.2	NP_000243.1	Q13496	MTM1_HUMAN	myotubularin 1	62	GRAM.				endosome to lysosome transport (GO:0008333)|intermediate filament organization (GO:0045109)|mitochondrion distribution (GO:0048311)|mitochondrion morphogenesis (GO:0070584)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|protein transport (GO:0015031)|regulation of vacuole organization (GO:0044088)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	intermediate filament binding (GO:0019215)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Acute lymphoblastic leukemia(192;6.56e-05)					ATTAAGGGAAGAGTTTACATC	0.299																																					p.R62I		Atlas-SNP	.											.	MTM1	89	.	0			c.G185T						PASS	.						72	71	71					X																	149767104		2202	4295	6497	SO:0001583	missense	4534	exon4			AGGGAAGAGTTTA	U46024	CCDS14694.1	Xq27.3-q28	2014-09-17			ENSG00000171100	ENSG00000171100		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7448	protein-coding gene	gene with protein product		300415	"myotubular myopathy 1"				Standard	NM_000252		Approved		uc004fef.4	Q13496	OTTHUMG00000024158	ENST00000370396.2:c.185G>T	chrX.hg19:g.149767104G>T	ENSP00000359423:p.Arg62Ile	356.0	1.0	.		297.0	272.0	.	NM_000252	A6NDB1|B7Z491|F2Z330|Q8NEL1	Missense_Mutation	SNP	ENST00000370396.2	hg19	CCDS14694.1	.	.	.	.	.	.	.	.	.	.	G	14.82	2.650071	0.47362	.	.	ENSG00000171100	ENST00000370396;ENST00000424519;ENST00000413012	D;D;D	0.88818	-2.43;-2.43;-2.43	5.62	4.75	0.60458	GRAM (2);	0.096235	0.64402	D	0.000001	D	0.84115	0.5401	L	0.43923	1.385	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.19666	0.026;0.026	T	0.79200	-0.1901	10	0.30854	T	0.27	.	11.9192	0.52783	0.0872:0.0:0.9128:0.0	.	62;62	B7Z491;Q13496	.;MTM1_HUMAN	I	62	ENSP00000359423:R62I;ENSP00000400699:R62I;ENSP00000389157:R62I	ENSP00000359423:R62I	R	+	2	0	MTM1	149517762	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.671000	0.54576	2.363000	0.80096	0.600000	0.82982	AGA	.	.	.	none		0.299	MTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060847.3	NM_000252		T	149767104	G	T	149767104	3	4	241	1	0	0	0	0	1	0	0	0	9944	942	33	4	195	4	MTM1	23	149767104	Missense_Mutation	SNP	G	TCGA-SX-A71R-01A-12D-A33Q-10		149767104	5503456	41	14804											
MASP2	10747	hgsc.bcm.edu	37	chr1	11105002	11105002	+	Intron	DEL	G	G	-																															gagctccaggggaggctagaGgctctgctctggaagagaga																										TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr1:11105002delG	ENST00000400897.3	-	4	560				MASP2_ENST00000400898.3_Frame_Shift_Del_p.L185fs	NM_006610.3	NP_006601.2	O00187	MASP2_HUMAN	mannan-binding lectin serine peptidase 2						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)		GGAGGCTAGAGGCTCTGCTCT	0.667																																					p.L185fs	GBM(35;611 746 20780 22741 36496)	Atlas-Indel,Pindel	.											.	MASP2	71	.	0			c.554delT						PASS	.						22	24	23					1																	11105002		2201	4299	6500	SO:0001627	intron_variant	10747	exon5			.	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.544+462C>-	chr1.hg19:g.11105002delG		142.0	0.0	0		119.0	56.0	0.470588	NM_139208	A8K458|A8MWJ2|O75754|Q5TEQ5|Q5TER0|Q96QG4|Q9BZH0|Q9H498|Q9H499|Q9UBP3|Q9UC48|Q9ULC7|Q9UMV3|Q9Y270	Frame_Shift_Del	DEL	ENST00000400897.3	hg19	CCDS123.1																																																																																			.	.	.	none		0.667	MASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006072.1	NM_006610		-	11105002	G	-	11105002	6	5	242	0	1	1	0	1	0	0	0	0	9330	1000	35	0		0	MASP2	1	11105002	Intron	DEL	G	TCGA-SX-A71S-01A-11D-A33Q-10		11105002	238145619	1	14805											
TNFRSF8	943	hgsc.bcm.edu	37	chr1	12170173	12170173	+	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	agcaccatgcctgtaagaggGggcacccgcctcgcccagga	9	4	13	15	2	0	1	0	0	0	1	1	2	0	2	5	3	2	3	5	3	1	1			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr1:12170173G>T	ENST00000263932.2	+	6	810	c.588G>T	c.(586-588)ggG>ggT	p.G196G	TNFRSF8_ENST00000417814.2_Silent_p.G85G	NM_001243.3|NM_001281430.1	NP_001234.2|NP_001268359.1	P28908	TNR8_HUMAN	tumor necrosis factor receptor superfamily, member 8	196					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)	CTGTAAGAGGGGGCACCCGCC	0.627																																					p.G196G		Atlas-SNP	.											.	TNFRSF8	70	.	0			c.G588T						PASS	.						50	48	49					1																	12170173		2203	4300	6503	SO:0001819	synonymous_variant	943	exon6			AAGAGGGGGCACC	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.588G>T	chr1.hg19:g.12170173G>T		110.0	0.0	.		135.0	69.0	.	NM_001243	B1AN79|B9EGD9|D3YTD8|Q6P4D9	Silent	SNP	ENST00000263932.2	hg19	CCDS144.1																																																																																			.	.	.	none		0.627	TNFRSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005130.1			T	12170173	G	T	12170173	2	4	242	1	0	0	0	0	0	0	0	1	16311	1219	43	4		4	TNFRSF8	1	12170173	Silent	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	1065171	12170173	237080448	2	14806											
PAX7	5081	hgsc.bcm.edu	37	chr1	18961677	18961677	+	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	acccaggcatgttcagctggGagatccgggacaggctgctg	8	7	15	11	1	1	1	1	0	0	1	2	3	2	2	2	4	2	5	2	4	0	1			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr1:18961677G>A	ENST00000375375.3	+	3	992	c.394G>A	c.(394-396)Gag>Aag	p.E132K	PAX7_ENST00000400661.3_Missense_Mutation_p.E132K|PAX7_ENST00000420770.2_Missense_Mutation_p.E132K	NM_002584.2|NM_013945.2	NP_002575.1|NP_039236.1	P23759	PAX7_HUMAN	paired box 7	132	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.|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)		GTTCAGCTGGGAGATCCGGGA	0.587			T	FOXO1A	alveolar rhabdomyosarcoma																																p.E132K		Atlas-SNP	.		Dom	yes		1	1p36.2-p36.12	5081	paired box gene 7		M	.	PAX7	127	.	0			c.G394A						PASS	.						81	75	77					1																	18961677		2203	4300	6503	SO:0001583	missense	5081	exon3			AGCTGGGAGATCC	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.394G>A	chr1.hg19:g.18961677G>A	ENSP00000364524:p.Glu132Lys	224.0	0.0	.		193.0	85.0	.	NM_002584	E9PFV9|Q0VA99|Q2PJS5	Missense_Mutation	SNP	ENST00000375375.3	hg19	CCDS186.1	.	.	.	.	.	.	.	.	.	.	G	34	5.375541	0.95923	.	.	ENSG00000009709	ENST00000375375;ENST00000420770;ENST00000400661	D;D;D	0.99598	-6.26;-6.26;-6.26	5.14	5.14	0.70334	Paired box protein, N-terminal (3);Winged helix-turn-helix transcription repressor DNA-binding (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99796	0.9913	H	0.97540	4.025	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.983	D;D;D	0.85130	0.997;0.995;0.94	D	0.96972	0.9709	10	0.87932	D	0	.	17.337	0.87285	0.0:0.0:1.0:0.0	.	132;132;132	E9PFV9;P23759-2;P23759	.;.;PAX7_HUMAN	K	132	ENSP00000364524:E132K;ENSP00000403389:E132K;ENSP00000383502:E132K	ENSP00000364524:E132K	E	+	1	0	PAX7	18834264	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.558000	0.98132	2.686000	0.91538	0.561000	0.74099	GAG	.	.	.	none		0.587	PAX7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000006928.1	NM_002584		A	18961677	G	A	18961677	3	1	242	1	0	0	0	0	1	0	0	0	11491	1175	41	2	404	2	PAX7	1	18961677	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	6791504	18961677	230288944	3	14807											
GPN2	63906	hgsc.bcm.edu	37	chr1	27216294	27216294	+	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	tggccgcggagggggtcgagCttggcacgcagccagtccag	6	5	18	12	4	0	0	0	0	0	0	2	2	1	1	3	5	2	3	3	5	0	1			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr1:27216294C>T	ENST00000361720.5	-	0	2123				GPN2_ENST00000374135.4_Silent_p.K98K|GPN2_ENST00000461282.1_5'Flank	NM_022078.2	NP_071361.2	Q96I76	GPTC3_HUMAN	G patch domain containing 3								nucleic acid binding (GO:0003676)			endometrium(2)|large_intestine(1)|lung(11)|skin(1)	15		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.97e-51)|OV - Ovarian serous cystadenocarcinoma(117;9.55e-30)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|STAD - Stomach adenocarcinoma(196;0.000595)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|READ - Rectum adenocarcinoma(331;0.0419)		GGGGGTCGAGCTTGGCACGCA	0.667																																					p.K98K		Atlas-SNP	.											.	GPN2	18	.	0			c.G294A						PASS	.						59	55	56					1																	27216294		2203	4300	6503	SO:0001628	intergenic_variant	54707	exon1			GTCGAGCTTGGCA	BC007767	CCDS290.1	1p35.3-p35.1	2013-01-28		2006-12-13	ENSG00000198746	ENSG00000198746		"G patch domain containing"	25720	protein-coding gene	gene with protein product				GPATC3			Standard	NM_022078		Approved	FLJ12455	uc001bne.3	Q96I76	OTTHUMG00000004229		chr1.hg19:g.27216294C>T		80.0	0.0	.		100.0	50.0	.	NM_018066	Q5JYH2|Q8NDJ2|Q9H9Z3	Silent	SNP	ENST00000361720.5	hg19	CCDS290.1																																																																																			.	.	.	none		0.667	GPATCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012181.1	NM_022078		T	27216294	C	T	27216294	1	4	242	0	1	0	0	0	0	0	0	0	6625	796	28	2		2	GPN2	1	27216294	IGR	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10	8254617	27216294	222034327	4	14808											
MACF1	23499	hgsc.bcm.edu	37	chr1	39824842	39824842	+	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	gaggaattggctgagcaccaAgtacctgtggaaaaactcca	14	7	11	9	0	0	1	0	1	0	0	1	4	1	3	3	3	3	3	3	3	5	2			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr1:39824842A>T	ENST00000372915.3	+	46	12252	c.12165A>T	c.(12163-12165)caA>caT	p.Q4055H	MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000539005.1_Missense_Mutation_p.Q1988H|MACF1_ENST00000567887.1_Missense_Mutation_p.Q4087H|MACF1_ENST00000564288.1_Missense_Mutation_p.Q4050H|MACF1_ENST00000317713.7_Missense_Mutation_p.Q1988H|MACF1_ENST00000545844.1_Missense_Mutation_p.Q1988H|MACF1_ENST00000289893.4_Missense_Mutation_p.Q2490H|MACF1_ENST00000361689.2_Missense_Mutation_p.Q1988H			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	4055					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)			CTGAGCACCAAGTACCTGTGG	0.423																																					p.Q1988H		Atlas-SNP	.											.	MACF1	909	.	0			c.A5964T						PASS	.						71	70	70					1																	39824842		2203	4300	6503	SO:0001583	missense	23499	exon43			GCACCAAGTACCT	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.12165A>T	chr1.hg19:g.39824842A>T	ENSP00000362006:p.Gln4055His	272.0	1.0	.		308.0	146.0	.	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.8|22.8	4.339791|4.339791	0.81911|0.81911	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893|ENST00000372925	T;T;T;T;T;T|.	0.55760|.	0.5;0.5;0.5;0.5;0.5;0.5|.	5.35|5.35	4.21|4.21	0.49690|0.49690	.|.	0.000000|.	0.64402|.	D|.	0.000012|.	T|T	0.63355|0.63355	0.2504|0.2504	M|M	0.74881|0.74881	2.28|2.28	0.80722|0.80722	D|D	1|1	P;B;D;D|.	0.63880|.	0.86;0.067;0.993;0.975|.	P;B;D;P|.	0.65443|.	0.797;0.103;0.935;0.796|.	T|T	0.64689|0.64689	-0.6348|-0.6348	10|5	0.72032|.	D|.	0.01|.	.|.	5.0785|5.0785	0.14644|0.14644	0.8019:0.0:0.1981:0.0|0.8019:0.0:0.1981:0.0	.|.	4055;1988;1988;1953|.	Q9UPN3;F8W8Q1;Q9UPN3-2;Q9UPN3-3|.	MACF1_HUMAN;.;.;.|.	H|C	1988;4055;1988;1988;1988;2490|1122	ENSP00000439537:Q1988H;ENSP00000362006:Q4055H;ENSP00000354573:Q1988H;ENSP00000313438:Q1988H;ENSP00000444364:Q1988H;ENSP00000289893:Q2490H|.	ENSP00000289893:Q2490H|.	Q|S	+|+	3|1	2|0	MACF1|MACF1	39597429|39597429	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	2.308000|2.308000	0.43690|0.43690	2.149000|2.149000	0.67028|0.67028	0.460000|0.460000	0.39030|0.39030	CAA|AGT	.	.	.	none		0.423	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		T	39824842	A	T	39824842	3	4	242	1	0	0	0	0	1	0	0	0	9151	69	3	5	12281	5	MACF1	1	39824842	Missense_Mutation	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10	12608548	39824842	209425779	5	14809											
RLF	6018	hgsc.bcm.edu	37	chr1	40704556	40704556	+	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	aacctagaccatattgaagaGcctaaagtactttccgaagc	15	9	7	10	1	0	3	0	1	0	2	1	4	1	3	4	0	4	1	4	0	8	6			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr1:40704556G>C	ENST00000372771.4	+	8	4209	c.4182G>C	c.(4180-4182)gaG>gaC	p.E1394D		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	1394					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)			ATATTGAAGAGCCTAAAGTAC	0.403																																					p.E1394D		Atlas-SNP	.											.	RLF	152	.	0			c.G4182C						PASS	.						80	79	79					1																	40704556		2203	4300	6503	SO:0001583	missense	6018	exon8			TGAAGAGCCTAAA		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.4182G>C	chr1.hg19:g.40704556G>C	ENSP00000361857:p.Glu1394Asp	127.0	0.0	.		159.0	75.0	.	NM_012421	Q14CQ1|Q9NU60	Missense_Mutation	SNP	ENST00000372771.4	hg19	CCDS448.1	.	.	.	.	.	.	.	.	.	.	G	10.54	1.379214	0.24944	.	.	ENSG00000117000	ENST00000372771;ENST00000535839	T	0.15139	2.45	5.91	4.92	0.64577	.	0.305702	0.34507	N	0.003918	T	0.04272	0.0118	N	0.00707	-1.245	0.39572	D	0.969296	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	T	0.39643	-0.9604	10	0.23891	T	0.37	-13.2144	5.5377	0.17021	0.078:0.1073:0.6082:0.2065	.	1087;1394	F5H2M5;Q13129	.;RLF_HUMAN	D	1394;1087	ENSP00000361857:E1394D	ENSP00000361857:E1394D	E	+	3	2	RLF	40477143	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	1.454000	0.35178	2.793000	0.96121	0.655000	0.94253	GAG	.	.	.	none		0.403	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421		C	40704556	G	C	40704556	3	2	242	1	0	0	0	0	1	0	0	0	13402	962	34	4	4212	4	RLF	1	40704556	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	879714	40704556	208546065	6	14810											
TTC39A	22996	hgsc.bcm.edu	37	chr1	51777848	51777848	+	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	gctgctgaaggaatctgttaCagaagacttcctccggtgcc	9	10	11	11	1	1	3	0	1	1	2	3	4	3	4	3	2	3	3	3	2	4	2			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr1:51777848C>A	ENST00000447632.2	-	4	349	c.301G>T	c.(301-303)Gta>Tta	p.V101L	TTC39A_ENST00000262675.7_Missense_Mutation_p.V73L|TTC39A_ENST00000371750.5_Missense_Mutation_p.V101L|TTC39A_ENST00000413473.2_Missense_Mutation_p.V104L|TTC39A_ENST00000451380.1_Missense_Mutation_p.V100L|TTC39A_ENST00000371747.3_Missense_Mutation_p.V100L|TTC39A_ENST00000262676.5_Missense_Mutation_p.V97L			Q5SRH9	TT39A_HUMAN	tetratricopeptide repeat domain 39A	101								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						GAATCTGTTACAGAAGACTTC	0.552																																					p.V104L		Atlas-SNP	.											.	TTC39A	40	.	2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)	c.G310T						PASS	.						43	45	44					1																	51777848		1893	4104	5997	SO:0001583	missense	22996	exon4			CTGTTACAGAAGA	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.301G>T	chr1.hg19:g.51777848C>A	ENSP00000393952:p.Val101Leu	50.0	0.0	.		50.0	28.0	.	NM_001144832	B7Z782|E7EQY9|G3XAF8|O43417|O75040|Q5SRH5|Q5SRH6|Q5SRH7|Q5SRH8|Q5SRI0|Q5SRI1|Q5SRI2|Q5T7S1|Q6PIU8|Q9BT24	Missense_Mutation	SNP	ENST00000447632.2	hg19		.	.	.	.	.	.	.	.	.	.	C	6.034	0.374693	0.11409	.	.	ENSG00000085831	ENST00000447632;ENST00000413473;ENST00000262675;ENST00000451380;ENST00000371750;ENST00000371747;ENST00000262676;ENST00000411642;ENST00000439482;ENST00000422925;ENST00000380849;ENST00000401051;ENST00000532836;ENST00000527205	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96	3.55	2.6	0.31112	.	0.459723	0.22016	N	0.065781	T	0.18718	0.0449	N	0.10685	0.025	0.31602	N	0.652598	B;B;B;B;B;B;B	0.13594	0.0;0.0;0.003;0.008;0.001;0.0;0.002	B;B;B;B;B;B;B	0.18871	0.001;0.002;0.02;0.023;0.012;0.004;0.011	T	0.25467	-1.0131	10	0.07325	T	0.83	-1.0752	9.2988	0.37833	0.0:0.8868:0.0:0.1132	.	104;100;73;97;100;101;101	Q5SRH9-4;E7EQY9;D3DQ30;Q5SRH9-3;B7Z782;Q5SRH9;G3XAF8	.;.;.;.;.;TT39A_HUMAN;.	L	101;104;73;100;101;100;97;73;100;73;73;104;73;128	ENSP00000393952:V101L;ENSP00000406144:V104L;ENSP00000262675:V73L;ENSP00000397207:V100L;ENSP00000360815:V101L;ENSP00000360812:V100L;ENSP00000262676:V97L;ENSP00000408532:V73L;ENSP00000405803:V100L;ENSP00000388995:V73L;ENSP00000370230:V73L;ENSP00000383830:V104L;ENSP00000434483:V73L;ENSP00000432453:V128L	ENSP00000262675:V73L	V	-	1	0	TTC39A	51550436	0.436000	0.25586	0.967000	0.41034	0.601000	0.36947	1.159000	0.31749	0.798000	0.33994	0.313000	0.20887	GTA	.	.	.	none		0.552	TTC39A-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000022434.2			A	51777848	C	A	51777848	3	1	242	1	0	0	0	0	1	0	0	0	16719	478	17	4	1495	4	TTC39A	1	51777848	Missense_Mutation	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10	11073292	51777848	197472773	7	14811											
RABGGTB	5876	hgsc.bcm.edu	37	chr1	76257870	76257871	+	Frame_Shift_Ins	INS	-	-	TT																															tgtctgtaattttagatctaINSttgttgcacaggatttctgg																										TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr1:76257870_76257871insTT	ENST00000319942.3	+	7	655_656	c.584_585insTT	c.(583-588)tattgtfs	p.C196fs	SNORD45B_ENST00000364617.1_RNA|RABGGTB_ENST00000496055.1_3'UTR|RABGGTB_ENST00000535300.1_Frame_Shift_Ins_p.C22fs	NM_004582.3	NP_004573.2	P53611	PGTB2_HUMAN	Rab geranylgeranyltransferase, beta subunit	196					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						TTTTAGATCTATTGTTGCACAG	0.327																																					p.Y195fs		Atlas-Indel,Pindel	.											.	RABGGTB	37	.	0			c.584_585insTT						PASS	.																																			SO:0001589	frameshift_variant	5876	exon7			.	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.585_586dupTT	chr1.hg19:g.76257871_76257872dupTT	ENSP00000317473:p.Cys196fs	52.0	0.0	0		55.0	16.0	0.290909	NM_004582	Q92697	Frame_Shift_Ins	INS	ENST00000319942.3	hg19	CCDS669.1																																																																																			.	.	.	none		0.327	RABGGTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026972.1	NM_004582		TT	76257871	-	TT	76257870	7	5	242	1	0	1	1	0	0	0	0	0	12981	449	16	0	610	0	RABGGTB	1	76257870	Frame_Shift_Ins	INS	-	TCGA-SX-A71S-01A-11D-A33Q-10	24480022	76257870	172992751	8	14812											
GLMN	11146	hgsc.bcm.edu	37	chr1	92731987	92731988	+	Frame_Shift_Ins	INS	-	-	T																															atacatacctaaataatgtaINStatttgccttgtgaatccaa																										TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr1:92731987_92731988insT	ENST00000370360.3	-	13	1283_1284	c.1202_1203insA	c.(1201-1203)tatfs	p.Y401fs	GLMN_ENST00000534881.1_Frame_Shift_Ins_p.Y387fs	NM_053274.2	NP_444504.1	Q92990	GLMN_HUMAN	glomulin, FKBP associated protein	401					muscle cell differentiation (GO:0042692)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of T cell proliferation (GO:0042130)|neural tube closure (GO:0001843)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of phosphorylation (GO:0042327)|regulation of gene expression, epigenetic (GO:0040029)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|vasculogenesis (GO:0001570)	Cul2-RING ubiquitin ligase complex (GO:0031462)|Cul3-RING ubiquitin ligase complex (GO:0031463)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|cullin-RING ubiquitin ligase complex (GO:0031461)|intracellular (GO:0005622)	hepatocyte growth factor receptor binding (GO:0005171)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase inhibitor activity (GO:0055105)			endometrium(5)|kidney(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)	17		all_lung(203;0.00827)|Lung NSC(277;0.0295)		all cancers(265;0.00702)|GBM - Glioblastoma multiforme(16;0.0381)|Epithelial(280;0.0989)		TAAATAATGTATATTTGCCTTG	0.302									Multiple Glomus Tumors (of the Skin), Familial																												p.Y401_T402delinsX		Atlas-Indel,Pindel	.											GLMN,colon,carcinoma,0,1	GLMN	37	.	0			c.1203_1204insA						PASS	.																																			SO:0001589	frameshift_variant	11146	exon13	Familial Cancer Database	Multiple Familial Glomangiomas, Hereditary Multiple Glomus Tumors, Familial Multiple Glomangiomatosis, Inherited Cutaneous Venous Anomalies, incl. Familial Multiple Glomangiomyoma	.	U73704	CCDS738.1	1p22.1	2008-02-05	2004-07-01		ENSG00000174842	ENSG00000174842			14373	protein-coding gene	gene with protein product		601749	"venous malformation with glomus cells"	VMGLOM		8955134	Standard	XM_005270400		Approved	FAP48, GLML, GVM, FKBPAP	uc001dor.3	Q92990	OTTHUMG00000010283	ENST00000370360.3:c.1203dupA	chr1.hg19:g.92731988_92731988dupT	ENSP00000359385:p.Tyr401fs	199.0	0.0	0		196.0	79.0	0.403061	NM_053274	Q5VVC3|Q9BVE8	Frame_Shift_Ins	INS	ENST00000370360.3	hg19	CCDS738.1																																																																																			.	.	.	none		0.302	GLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028358.1	NM_007070		T	92731988	-	T	92731987	7	5	242	1	0	1	1	0	0	0	0	0	6455	456	16	0	609	0	GLMN	1	92731987	Frame_Shift_Ins	INS	-	TCGA-SX-A71S-01A-11D-A33Q-10	16474117	92731987	156518634	9	14813											
TRIM33	51592	hgsc.bcm.edu	37	chr1	115006036	115006036	+	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	acaatgcatctatcttacctGagacatcttctttcttcctg	9	16	4	12	0	5	1	0	1	5	1	6	2	6	1	2	0	2	1	2	0	3	5			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr1:115006036G>T	ENST00000358465.2	-	3	871	c.788C>A	c.(787-789)tCa>tAa	p.S263*	TRIM33_ENST00000450349.2_5'UTR|TRIM33_ENST00000369543.2_Nonsense_Mutation_p.S263*	NM_015906.3	NP_056990.3	Q9UPN9	TRI33_HUMAN	tripartite motif containing 33	263					gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	48	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TATCTTACCTGAGACATCTTC	0.333			T	RET	papillary thyroid																																p.S263X		Atlas-SNP	.		Dom	yes		1	1p13	51592	" tripartite motif-containing 33 (PTC7,TIF1G)"		E	.	TRIM33	115	.	0			c.C788A						PASS	.						152	135	141					1																	115006036		2203	4299	6502	SO:0001587	stop_gained	51592	exon3			TTACCTGAGACAT	AF220136	CCDS872.1, CCDS873.1	1p13.1	2014-02-17	2011-01-25		ENSG00000197323	ENSG00000197323		"Tripartite motif containing / Tripartite motif containing", "Zinc fingers, PHD-type", "RING-type (C3HC4) zinc fingers"	16290	protein-coding gene	gene with protein product	"transcriptional intermediary factor 1 gamma", "ret-fused gene 7"	605769	"tripartite motif-containing 33"			11331580, 10022127	Standard	XM_005270936		Approved	TIF1GAMMA, FLJ11429, KIAA1113, TIFGAMMA, RFG7, TF1G, TIF1G, PTC7	uc001eew.3	Q9UPN9	OTTHUMG00000011891	ENST00000358465.2:c.788C>A	chr1.hg19:g.115006036G>T	ENSP00000351250:p.Ser263*	137.0	0.0	.		123.0	45.0	.	NM_033020	O95855|Q5TG72|Q5TG73|Q5TG74|Q9C017|Q9UJ79	Nonsense_Mutation	SNP	ENST00000358465.2	hg19	CCDS872.1	.	.	.	.	.	.	.	.	.	.	G	39	7.889202	0.98545	.	.	ENSG00000197323	ENST00000358465;ENST00000369543	.	.	.	5.67	5.67	0.87782	.	0.174270	0.51477	D	0.000096	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.1834	19.7863	0.96440	0.0:0.0:1.0:0.0	.	.	.	.	X	263	.	ENSP00000351250:S263X	S	-	2	0	TRIM33	114807559	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	9.352000	0.97076	2.665000	0.90641	0.655000	0.94253	TCA	.	.	.	none		0.333	TRIM33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032854.1	NM_015906		T	115006036	G	T	115006036	4	4	242	1	0	0	0	0	0	1	0	0	16519	1294	45	4	2667	4	TRIM33	1	115006036	Nonsense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	22274049	115006036	134244585	10	14814											
NRAS	4893	hgsc.bcm.edu	37	chr1	115251231	115251231	+	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	ttgagttttttcattcggtaCtggcgtatttctcttaccag	6	19	8	8	2	2	1	1	1	1	0	4	1	2	1	1	2	2	3	1	2	3	9			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr1:115251231C>A	ENST00000369535.4	-	5	748	c.495G>T	c.(493-495)caG>caT	p.Q165H		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	165					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)			NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCATTCGGTACTGGCGTATTT	0.413		50	Mis		"melanoma, MM, AML, thyroid"				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																											p.Q165H		Atlas-SNP	.		Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"L, E"	.	NRAS	3766	.	0			c.G495T						PASS	.						293	247	263					1																	115251231		2203	4300	6503	SO:0001583	missense	4893	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	TCGGTACTGGCGT	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.495G>T	chr1.hg19:g.115251231C>A	ENSP00000358548:p.Gln165His	136.0	0.0	.		130.0	50.0	.	NM_002524	Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	hg19	CCDS877.1	.	.	.	.	.	.	.	.	.	.	C	16.19	3.053902	0.55218	.	.	ENSG00000213281	ENST00000369535	T	0.69040	-0.37	5.86	4.95	0.65309	.	0.125967	0.33040	U	0.005343	T	0.43743	0.1261	L	0.40543	1.245	0.51767	D	0.999937	B	0.02656	0.0	B	0.06405	0.002	T	0.51301	-0.8723	10	0.66056	D	0.02	.	12.4792	0.55831	0.0:0.8651:0.0:0.1349	.	165	P01111	RASN_HUMAN	H	165	ENSP00000358548:Q165H	ENSP00000358548:Q165H	Q	-	3	2	NRAS	115052754	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.426000	0.34870	1.623000	0.50342	0.650000	0.86243	CAG	.	.	.	none		0.413	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524		A	115251231	C	A	115251231	3	1	242	1	0	0	0	0	1	0	0	0	10647	564	20	4	78	4	NRAS	1	115251231	Missense_Mutation	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10	245195	115251231	133999390	11	14815											
ZNF687	57592	hgsc.bcm.edu	37	chr1	151260816	151260816	+	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	gagtgcaaggaacagtgccgGgacaaggctggcatggcagc	11	4	17	9	1	0	0	0	0	0	0	0	3	0	2	1	5	4	4	1	5	3	0			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr1:151260816G>T	ENST00000368879.2	+	2	2147	c.2049G>T	c.(2047-2049)cgG>cgT	p.R683R		NM_020832.1	NP_065883.1	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	683					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	32	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			AACAGTGCCGGGACAAGGCTG	0.652																																					p.R683R		Atlas-SNP	.											.	ZNF687	94	.	0			c.G2049T						PASS	.						20	21	20					1																	151260816		2201	4297	6498	SO:0001819	synonymous_variant	57592	exon2			GTGCCGGGACAAG		CCDS992.1	1q21.2	2008-05-02			ENSG00000143373	ENSG00000143373			29277	protein-coding gene	gene with protein product		610568				10718198	Standard	NM_020832		Approved	KIAA1441	uc001exq.3	Q8N1G0	OTTHUMG00000012347	ENST00000368879.2:c.2049G>T	chr1.hg19:g.151260816G>T		39.0	0.0	.		47.0	25.0	.	NM_020832	D3DV17|Q68DQ8|Q9H937|Q9P2A7	Silent	SNP	ENST00000368879.2	hg19		.	.	.	.	.	.	.	.	.	.	G	10.30	1.313509	0.23908	.	.	ENSG00000143373	ENST00000426871	.	.	.	4.96	-0.935	0.10423	.	.	.	.	.	T	0.45074	0.1324	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49093	-0.8975	4	.	.	.	.	11.7294	0.51728	0.0763:0.4559:0.4678:0.0	.	.	.	.	V	286	.	.	G	+	2	0	ZNF687	149527440	0.982000	0.34865	0.998000	0.56505	0.998000	0.95712	0.117000	0.15583	-0.015000	0.14150	0.561000	0.74099	GGG	.	.	.	none		0.652	ZNF687-201	KNOWN	basic	protein_coding	protein_coding		NM_020832		T	151260816	G	T	151260816	2	4	242	1	0	0	0	0	0	0	0	1	18104	1219	43	4		4	ZNF687	1	151260816	Silent	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	36009585	151260816	97989805	12	14816											
SNX27	81609	hgsc.bcm.edu	37	chr1	151665956	151665956	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgcgagctcaagtggagaaaAgaggtaattctgaacagtcc	14	8	12	7	1	2	3	1	1	1	2	3	5	3	3	1	2	3	2	1	2	5	2			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr1:151665956A>G	ENST00000458013.2	+	11	1695	c.1575A>G	c.(1573-1575)aaA>aaG	p.K525K	SNX27_ENST00000368838.1_Silent_p.K432K|SNX27_ENST00000368843.3_Silent_p.K525K			Q96L92	SNX27_HUMAN	sorting nexin family member 27	525	FERM-like region F3.				endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|establishment of natural killer cell polarity (GO:0001770)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to plasma membrane (GO:1990126)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|immunological synapse (GO:0001772)|nucleus (GO:0005634)	phosphatidylinositol-3-phosphate binding (GO:0032266)			central_nervous_system(1)|large_intestine(2)|ovary(2)	5	Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			AGTGGAGAAAAGAGGTAATTC	0.423																																					p.K525K	Colon(46;291 966 40145 41237 41888)	Atlas-SNP	.											.	SNX27	44	.	0			c.A1575G						PASS	.						186	174	178					1																	151665956		2203	4300	6503	SO:0001819	synonymous_variant	81609	exon11			GAGAAAAGAGGTA	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.1575A>G	chr1.hg19:g.151665956A>G		83.0	0.0	.		81.0	38.0	.	NM_030918	Q32Q36|Q4AEJ5|Q5VWB0|Q5VWB1|Q5VWB2|Q6IPP6|Q86UB1|Q96D79|Q9H3K8	Silent	SNP	ENST00000458013.2	hg19																																																																																				.	.	.	none		0.423	SNX27-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000036624.3	NM_030918		G	151665956	A	G	151665956	2	3	242	1	0	0	0	0	0	0	0	1	14910	69	3	3		3	SNX27	1	151665956	Silent	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10	405140	151665956	97584665	13	14817											
HDGF	3068	hgsc.bcm.edu	37	chr1	156713487	156713487	+	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	ggcctcagcatcttccttggTagcctcttcctcttcatcct	4	15	6	16	0	5	0	2	0	3	0	8	0	8	0	5	2	2	2	5	2	1	5			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr1:156713487T>A	ENST00000357325.5	-	5	987	c.673A>T	c.(673-675)Acc>Tcc	p.T225S	HDGF_ENST00000416666.2_Missense_Mutation_p.T193S|HDGF_ENST00000537739.1_Missense_Mutation_p.T225S|HDGF_ENST00000368206.5_Missense_Mutation_p.T241S|MRPL24_ENST00000361531.2_5'Flank|HDGF_ENST00000368209.5_Missense_Mutation_p.T218S|HDGF_ENST00000465180.1_5'UTR|MRPL24_ENST00000368211.4_5'Flank	NM_004494.2	NP_004485.1	P51858	HDGF_HUMAN	hepatoma-derived growth factor	225	Glu-rich.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription corepressor binding (GO:0001222)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9	all_hematologic(923;0.088)|Hepatocellular(266;0.158)	Breast(1374;0.198)		Colorectal(1306;0.018)		TCTTCCTTGGTAGcctcttcc	0.617																																					p.T241S		Atlas-SNP	.											.	HDGF	60	.	0			c.A721T						PASS	.						58	63	61					1																	156713487		2202	4300	6502	SO:0001583	missense	3068	exon5			CCTTGGTAGCCTC	D16431	CCDS1156.1, CCDS44247.1, CCDS44248.1	1q23.1	2013-10-14	2010-03-19		ENSG00000143321	ENSG00000143321			4856	protein-coding gene	gene with protein product	"high-mobility group protein 1-like"	600339	"hepatoma-derived growth factor (high-mobility group protein 1-like)"			8833162	Standard	NM_004494		Approved	HMG1L2	uc001fpy.4	P51858	OTTHUMG00000041295	ENST00000357325.5:c.673A>T	chr1.hg19:g.156713487T>A	ENSP00000349878:p.Thr225Ser	49.0	0.0	.		45.0	15.0	.	NM_001126050	B3KU21|D3DVC9|Q5SZ07|Q5SZ08|Q5SZ09	Missense_Mutation	SNP	ENST00000357325.5	hg19	CCDS1156.1	.	.	.	.	.	.	.	.	.	.	T	6.574	0.474156	0.12521	.	.	ENSG00000143321	ENST00000357325;ENST00000368209;ENST00000537739;ENST00000416666;ENST00000368206;ENST00000406805	T;T;T;T;T	0.30448	1.99;1.54;1.99;1.57;1.53	4.51	-1.35	0.09114	.	1.112620	0.07019	U	0.826534	T	0.03695	0.0105	N	0.08118	0	0.20873	N	0.99984	B;B;B;B	0.16603	0.018;0.018;0.018;0.001	B;B;B;B	0.14578	0.011;0.011;0.007;0.003	T	0.40534	-0.9558	10	0.19147	T	0.46	-1.4395	4.2504	0.10691	0.0:0.3977:0.1699:0.4324	.	200;241;218;225	B7Z958;Q5SZ07;Q5SZ08;P51858	.;.;.;HDGF_HUMAN	S	225;218;225;193;241;248	ENSP00000349878:T225S;ENSP00000357192:T218S;ENSP00000443120:T225S;ENSP00000416752:T193S;ENSP00000357189:T241S	ENSP00000349878:T225S	T	-	1	0	HDGF	154980111	0.103000	0.21917	0.809000	0.32408	0.771000	0.43674	-0.486000	0.06513	-0.407000	0.07576	-0.602000	0.04101	ACC	.	.	.	none		0.617	HDGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098946.1	NM_004494		A	156713487	T	A	156713487	3	1	242	1	0	0	0	0	1	0	0	0	7025	1638	57	5	57	5	HDGF	1	156713487	Missense_Mutation	SNP	T	TCGA-SX-A71S-01A-11D-A33Q-10	5047531	156713487	92537134	14	14818											
PLEKHA6	22874	hgsc.bcm.edu	37	chr1	204237388	204237388	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcattggggttccgcttcAtggagtgtgagcgcttgcca	5	12	15	9	2	1	1	1	1	0	0	2	2	2	2	2	3	3	4	2	3	0	4			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr1:204237388A>G	ENST00000272203.3	-	4	471	c.155T>C	c.(154-156)aTg>aCg	p.M52T	PLEKHA6_ENST00000414478.1_Missense_Mutation_p.M52T	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	52										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)			GTTCCGCTTCATGGAGTGTGA	0.622																																					p.M52T		Atlas-SNP	.											.	PLEKHA6	115	.	0			c.T155C						PASS	.						117	98	104					1																	204237388		2203	4300	6503	SO:0001583	missense	22874	exon4			CGCTTCATGGAGT	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.155T>C	chr1.hg19:g.204237388A>G	ENSP00000272203:p.Met52Thr	54.0	0.0	.		56.0	23.0	.	NM_014935	A7MD51|Q5VTI6	Missense_Mutation	SNP	ENST00000272203.3	hg19	CCDS1444.1	.	.	.	.	.	.	.	.	.	.	A	17.34	3.364816	0.61513	.	.	ENSG00000143850	ENST00000272203;ENST00000414478	T;T	0.11385	2.78;2.78	5.67	5.67	0.87782	.	0.042149	0.85682	D	0.000000	T	0.17874	0.0429	M	0.72479	2.2	0.54753	D	0.999986	B	0.14805	0.011	B	0.21708	0.036	T	0.01345	-1.1379	10	0.72032	D	0.01	-31.4344	15.5746	0.76365	1.0:0.0:0.0:0.0	.	52	Q9Y2H5	PKHA6_HUMAN	T	52	ENSP00000272203:M52T;ENSP00000402046:M52T	ENSP00000272203:M52T	M	-	2	0	PLEKHA6	202504011	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.693000	0.84214	2.148000	0.66965	0.533000	0.62120	ATG	.	.	.	none		0.622	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935		G	204237388	A	G	204237388	3	3	242	1	0	0	0	0	1	0	0	0	12067	217	8	3	3067	3	PLEKHA6	1	204237388	Missense_Mutation	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10	47523901	204237388	45013233	15	14819											
NENF	29937	hgsc.bcm.edu	37	chr1	212617777	212617777	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatcctgcagacctcacccAtgacactgtgagccagatta	11	8	9	13	0	1	4	1	2	0	2	2	5	2	5	4	1	2	1	4	1	1	1			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr1:212617777A>G	ENST00000366988.3	+	3	392	c.335A>G	c.(334-336)cAt>cGt	p.H112R	NENF_ENST00000473900.1_3'UTR	NM_013349.4	NP_037481.1	Q9UMX5	NENF_HUMAN	neudesin neurotrophic factor	112	Cytochrome b5 heme-binding.				positive regulation of MAPK cascade (GO:0043410)	extracellular space (GO:0005615)	heme binding (GO:0020037)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(2)	4				all cancers(67;0.00967)|OV - Ovarian serous cystadenocarcinoma(81;0.0108)|GBM - Glioblastoma multiforme(131;0.0325)|Epithelial(68;0.132)		GACCTCACCCATGACACTGTG	0.478																																					p.H112R		Atlas-SNP	.											.	NENF	11	.	0			c.A335G						PASS	.						85	76	79					1																	212617777		2203	4300	6503	SO:0001583	missense	29937	exon3			TCACCCATGACAC		CCDS1505.1	1q32.3	2011-07-05	2011-07-05		ENSG00000117691	ENSG00000117691			30384	protein-coding gene	gene with protein product	"neudesin"	611874	"neuron derived neurotrophic factor"			9771976, 15605373	Standard	NM_013349		Approved	CIR2, SCIRP10, SPUF	uc001hjd.3	Q9UMX5	OTTHUMG00000036744	ENST00000366988.3:c.335A>G	chr1.hg19:g.212617777A>G	ENSP00000355955:p.His112Arg	118.0	0.0	.		117.0	46.0	.	NM_013349	A1KYQ8|Q53FZ6|Q5TM90	Missense_Mutation	SNP	ENST00000366988.3	hg19	CCDS1505.1	.	.	.	.	.	.	.	.	.	.	A	12.23	1.874425	0.33069	.	.	ENSG00000117691	ENST00000366988	T	0.76060	-0.99	5.2	5.2	0.72013	Cytochrome b5 (3);	0.229621	0.45361	D	0.000377	T	0.71484	0.3345	M	0.64997	1.995	0.41696	D	0.989376	P	0.39601	0.68	B	0.36378	0.223	T	0.75614	-0.3257	10	0.54805	T	0.06	-17.1208	15.0799	0.72106	1.0:0.0:0.0:0.0	.	112	Q9UMX5	NENF_HUMAN	R	112	ENSP00000355955:H112R	ENSP00000355955:H112R	H	+	2	0	NENF	210684400	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.415000	0.66411	1.965000	0.57142	0.491000	0.48974	CAT	.	.	.	none		0.478	NENF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089291.1	NM_013349		G	212617777	A	G	212617777	3	3	242	1	0	0	0	0	1	0	0	0	10342	217	8	3	345	3	NENF	1	212617777	Missense_Mutation	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10	8380389	212617777	36632844	16	14820											
EPRS	2058	hgsc.bcm.edu	37	chr1	220160681	220160681	+	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	gacacaggcttatactctacTcctatcaaagacttgtactg	12	12	6	11	0	2	1	1	0	1	1	3	2	3	1	1	1	3	2	1	1	6	6			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr1:220160681T>A	ENST00000366923.3	-	20	3110	c.2841A>T	c.(2839-2841)ggA>ggT	p.G947G	snoU13_ENST00000459217.1_RNA	NM_004446.2	NP_004437.2	P07814	SYEP_HUMAN	glutamyl-prolyl-tRNA synthetase	947	3 X 57 AA approximate repeats.|WHEP-TRS 3.				cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|negative regulation of translation (GO:0017148)|prolyl-tRNA aminoacylation (GO:0006433)|protein complex assembly (GO:0006461)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|GAIT complex (GO:0097452)|membrane (GO:0016020)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|proline-tRNA ligase activity (GO:0004827)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(11)|kidney(2)|large_intestine(13)|lung(24)|ovary(1)|prostate(3)|skin(2)|stomach(2)|urinary_tract(3)	63				GBM - Glioblastoma multiforme(131;0.0735)	L-Proline(DB00172)	TATACTCTACTCCTATCAAAG	0.378																																					p.G947G		Atlas-SNP	.											.	EPRS	140	.	0			c.A2841T						PASS	.						82	81	82					1																	220160681		2203	4300	6503	SO:0001819	synonymous_variant	2058	exon20			CTCTACTCCTATC	X54326	CCDS31027.1	1q41	2011-07-01			ENSG00000136628	ENSG00000136628	6.1.1.15, 6.1.1.17	"Aminoacyl tRNA synthetases / Class I", "Aminoacyl tRNA synthetases / Class II"	3418	protein-coding gene	gene with protein product	"glutamate tRNA ligase", "proline tRNA ligase"	138295		QPRS, QARS		1988429	Standard	NM_004446		Approved	EARS, PARS, GLUPRORS	uc001hly.1	P07814	OTTHUMG00000037433	ENST00000366923.3:c.2841A>T	chr1.hg19:g.220160681T>A		84.0	0.0	.		123.0	53.0	.	NM_004446	A0AVA9|B9EGH3|Q05BP6|Q05DF8|Q5DSM1|Q5H9S5|Q6PD57|Q86X73	Silent	SNP	ENST00000366923.3	hg19	CCDS31027.1																																																																																			.	.	.	none		0.378	EPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091133.2	NM_004446		A	220160681	T	A	220160681	2	1	242	1	0	0	0	0	0	0	0	1	5193	1538	54	5		5	EPRS	1	220160681	Silent	SNP	T	TCGA-SX-A71S-01A-11D-A33Q-10	7542904	220160681	29089940	17	14821											
C1orf69	200205	hgsc.bcm.edu	37	chr1	228362451	228362451	+	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	agtgtgacagctcggtgcagGgcgcgctgcagaagcacctc	8	6	15	12	3	0	2	0	1	0	1	2	2	0	2	1	2	4	5	1	2	1	0			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr1:228362451G>A	ENST00000366711.3	+	2	402	c.400G>A	c.(400-402)Ggc>Agc	p.G134S	IBA57_ENST00000546123.1_5'UTR|IBA57_ENST00000484749.1_3'UTR	NM_001010867.2	NP_001010867.1	Q5T440	CAF17_HUMAN	IBA57, iron-sulfur cluster assembly homolog (S. cerevisiae)	134					glycine catabolic process (GO:0006546)|heme biosynthetic process (GO:0006783)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|prostate(1)	11						CTCGGTGCAGGGCGCGCTGCA	0.662																																					p.G134S		Atlas-SNP	.											.	IBA57	22	.	0			c.G400A						PASS	.						24	24	24					1																	228362451		2200	4297	6497	SO:0001583	missense	200205	exon2			GTGCAGGGCGCGC	AK022796	CCDS31046.1	1q42.13	2011-03-11	2011-03-11	2011-03-11	ENSG00000181873	ENSG00000181873			27302	protein-coding gene	gene with protein product	"iron-sulfur cluster assembly factor for biotin synthase- and aconitase-like mitochondrial proteins, with a mass of 57kDa"	615316	"chromosome 1 open reading frame 69"	C1orf69			Standard	NM_001010867		Approved	FLJ12734	uc001hsl.4	Q5T440	OTTHUMG00000039769	ENST00000366711.3:c.400G>A	chr1.hg19:g.228362451G>A	ENSP00000355672:p.Gly134Ser	32.0	0.0	.		25.0	11.0	.	NM_001010867		Missense_Mutation	SNP	ENST00000366711.3	hg19	CCDS31046.1	.	.	.	.	.	.	.	.	.	.	G	8.657	0.899594	0.17686	.	.	ENSG00000181873	ENST00000366711	T	0.41065	1.01	4.65	2.75	0.32379	Glycine cleavage T-protein, N-terminal (1);	0.474372	0.24368	N	0.039124	T	0.26376	0.0644	N	0.21373	0.66	0.80722	D	1	B	0.12013	0.005	B	0.20384	0.029	T	0.04565	-1.0942	10	0.18276	T	0.48	-1.4742	10.0048	0.41951	0.076:0.1384:0.7856:0.0	.	134	Q5T440	CAF17_HUMAN	S	134	ENSP00000355672:G134S	ENSP00000355672:G134S	G	+	1	0	IBA57	226429074	0.998000	0.40836	0.000000	0.03702	0.095000	0.18619	4.116000	0.57871	0.562000	0.29204	0.655000	0.94253	GGC	.	.	.	none		0.662	IBA57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095980.1	NM_001010867		A	228362451	G	A	228362451	3	1	242	1	0	0	0	0	1	0	0	0	2059	1232	43	2	406	2	C1orf69	1	228362451	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	8201770	228362451	20888170	18	14822											
NCOA1	8648	hgsc.bcm.edu	37	chr2	24896243	24896243	+	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	tctttattatagagaaatcaAcaactgatgacgatgtacag	16	12	7	6	1	2	3	1	2	1	1	2	5	2	3	0	0	3	1	0	0	7	5			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr2:24896243A>T	ENST00000406961.1	+	7	917	c.265A>T	c.(265-267)Aca>Tca	p.T89S	NCOA1_ENST00000405141.1_Missense_Mutation_p.T89S|NCOA1_ENST00000348332.3_Missense_Mutation_p.T89S|NCOA1_ENST00000288599.5_Missense_Mutation_p.T89S|NCOA1_ENST00000407230.1_5'UTR|NCOA1_ENST00000395856.3_Missense_Mutation_p.T89S|RNU6-936P_ENST00000384005.1_RNA|NCOA1_ENST00000538539.1_Missense_Mutation_p.T89S			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	89					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)					AGAGAAATCAACAACTGATGA	0.343			T	PAX3	alveolar rhadomyosarcoma																																p.T89S		Atlas-SNP	.		Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	NCOA1	210	.	0			c.A265T						PASS	.						79	82	81					2																	24896243		2203	4300	6503	SO:0001583	missense	8648	exon5			AAATCAACAACTG	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.265A>T	chr2.hg19:g.24896243A>T	ENSP00000385216:p.Thr89Ser	160.0	0.0	.		172.0	67.0	.	NM_147223	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Missense_Mutation	SNP	ENST00000406961.1	hg19	CCDS1712.1	.	.	.	.	.	.	.	.	.	.	A	7.169	0.587162	0.13812	.	.	ENSG00000084676	ENST00000406961;ENST00000405141;ENST00000538539;ENST00000348332;ENST00000288599;ENST00000395856	T;T;T;T;T;T	0.01629	4.72;4.72;4.72;4.72;4.72;4.72	4.84	3.68	0.42216	Helix-loop-helix DNA-binding (2);	0.320508	0.31612	N	0.007353	T	0.00580	0.0019	N	0.00446	-1.495	0.29426	N	0.860201	B;B;B	0.09022	0.002;0.001;0.002	B;B;B	0.14023	0.01;0.005;0.004	T	0.42816	-0.9429	10	0.18276	T	0.48	.	5.8454	0.18663	0.7718:0.0:0.2282:0.0	.	89;89;89	Q15788-3;Q15788;Q15788-2	.;NCOA1_HUMAN;.	S	89	ENSP00000385216:T89S;ENSP00000385097:T89S;ENSP00000444039:T89S;ENSP00000320940:T89S;ENSP00000288599:T89S;ENSP00000379197:T89S	ENSP00000288599:T89S	T	+	1	0	NCOA1	24749747	0.998000	0.40836	1.000000	0.80357	0.977000	0.68977	1.262000	0.32992	2.022000	0.59522	0.459000	0.35465	ACA	.	.	.	none		0.343	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223		T	24896243	A	T	24896243	3	4	242	1	0	0	0	0	1	0	0	0	10235	43	2	5	275	5	NCOA1	2	24896243	Missense_Mutation	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10		24896243	218303130	19	14823											
C2orf71	388939	hgsc.bcm.edu	37	chr2	29295391	29295391	+	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	ctcctgctgccacttaccgtGctaggtcttggggggaccac	5	10	12	14	1	1	0	0	0	1	0	2	1	2	1	4	4	4	2	4	4	2	3			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr2:29295391G>A	ENST00000331664.5	-	1	1736	c.1737C>T	c.(1735-1737)agC>agT	p.S579S		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	579					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						CACTTACCGTGCTAGGTCTTG	0.612																																					p.S579S		Atlas-SNP	.											.	C2orf71	146	.	0			c.C1737T						PASS	.						41	45	43					2																	29295391		2078	4215	6293	SO:0001819	synonymous_variant	388939	exon1			TACCGTGCTAGGT		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.1737C>T	chr2.hg19:g.29295391G>A		63.0	0.0	.		67.0	30.0	.	NM_001029883		Silent	SNP	ENST00000331664.5	hg19	CCDS42669.1																																																																																			.	.	.	none		0.612	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		A	29295391	G	A	29295391	2	1	242	1	0	0	0	0	0	0	0	1	2193	1310	46	2		2	C2orf71	2	29295391	Silent	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	4399148	29295391	213903982	20	14824											
SP3	6670	hgsc.bcm.edu	37	chr2	174820133	174820133	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgactggatataatttccCtgaagatctgaagaatgaac	14	10	10	7	1	1	5	0	3	1	2	2	7	2	6	1	2	1	0	1	2	6	3			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr2:174820133C>T	ENST00000310015.6	-	4	1637	c.1107G>A	c.(1105-1107)caG>caA	p.Q369Q	SP3_ENST00000483084.1_5'Flank|SP3_ENST00000455789.2_Silent_p.Q316Q|SP3_ENST00000418194.2_Silent_p.Q301Q	NM_001172712.1|NM_003111.4	NP_001166183.1|NP_003102.1	Q02447	SP3_HUMAN	Sp3 transcription factor	369	Transactivation domain (Gln-rich).				B cell differentiation (GO:0030183)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|embryonic skeletal system development (GO:0048706)|enucleate erythrocyte differentiation (GO:0043353)|granulocyte differentiation (GO:0030851)|liver development (GO:0001889)|lung development (GO:0030324)|megakaryocyte differentiation (GO:0030219)|monocyte differentiation (GO:0030224)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|T cell differentiation (GO:0030217)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)		EWSR1/SP3(3)	NS(2)|large_intestine(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.185)			TATAATTTCCCTGAAGATCTG	0.408																																					p.Q369Q		Atlas-SNP	.											.	SP3	82	.	0			c.G1107A						PASS	.						79	76	77					2																	174820133		2203	4300	6503	SO:0001819	synonymous_variant	6670	exon4			ATTTCCCTGAAGA	M97191	CCDS2254.1, CCDS46452.1	2q31	2013-01-08			ENSG00000172845	ENSG00000172845		"Specificity protein transcription factors", "Zinc fingers, C2H2-type"	11208	protein-coding gene	gene with protein product		601804				1341900, 1454515	Standard	NM_003111		Approved	SPR-2	uc002uig.3	Q02447	OTTHUMG00000132333	ENST00000310015.6:c.1107G>A	chr2.hg19:g.174820133C>T		68.0	0.0	.		62.0	28.0	.	NM_003111	A0AVL9|B4E2B7|Q69B26|Q69B27|Q8TD56|Q8WWU4|Q9BQR1	Silent	SNP	ENST00000310015.6	hg19	CCDS2254.1	.	.	.	.	.	.	.	.	.	.	C	2.337	-0.351976	0.05173	.	.	ENSG00000172845	ENST00000416195	.	.	.	5.69	5.69	0.88448	.	.	.	.	.	T	0.70937	0.3281	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69072	-0.5242	4	.	.	.	.	14.6237	0.68605	0.1457:0.8543:0.0:0.0	.	.	.	.	K	326	.	.	R	-	2	0	SP3	174528379	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.488000	0.45276	2.670000	0.90874	0.563000	0.77884	AGG	.	.	.	none		0.408	SP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255452.1	NM_003111		T	174820133	C	T	174820133	2	4	242	1	0	0	0	0	0	0	0	1	14978	680	24	2		2	SP3	2	174820133	Silent	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10	145524742	174820133	68379240	21	14825											
TTN	7273	hgsc.bcm.edu	37	chr2	179403955	179403955	+	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	tacatcgagtacttctggagGattgcttggaggttctggag	8	13	14	6	1	2	0	0	0	2	0	3	5	2	4	0	5	3	3	0	5	2	6			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr2:179403955G>C	ENST00000591111.1	-	303	94008	c.93784C>G	c.(93784-93786)Cct>Gct	p.P31262A	TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.P30335A|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P23963A|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.P23838A|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.P32903A|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P24030A|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000588257.1_RNA|RP11-65L3.4_ENST00000604692.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	31262	Fibronectin type-III 128. {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)			ACTTCTGGAGGATTGCTTGGA	0.423																																					p.P32903A		Atlas-SNP	.											.	TTN	18412	.	0			c.C98707G						PASS	.						97	88	91					2																	179403955		1895	4108	6003	SO:0001583	missense	7273	exon353			CTGGAGGATTGCT	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.93784C>G	chr2.hg19:g.179403955G>C	ENSP00000465570:p.Pro31262Ala	71.0	0.0	.		99.0	43.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	17.73	3.461654	0.63513	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.55930	0.49;0.49;0.49;0.49	6.04	5.17	0.71159	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.63570	0.2522	L	0.56340	1.77	0.58432	D	0.999996	D;D;D;D	0.58970	0.984;0.984;0.984;0.984	P;P;P;P	0.56612	0.802;0.802;0.802;0.802	T	0.67699	-0.5603	9	0.87932	D	0	.	15.4494	0.75262	0.0663:0.0:0.9337:0.0	.	23838;23963;24030;31262	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	A	30335;23838;24030;23963;23835	ENSP00000343764:P30335A;ENSP00000434586:P23838A;ENSP00000340554:P24030A;ENSP00000352154:P23963A	ENSP00000340554:P24030A	P	-	1	0	TTN	179112201	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.869000	0.99810	1.571000	0.49722	0.563000	0.77884	CCT	.	.	.	none		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179403955	G	C	179403955	3	2	242	1	0	0	0	0	1	0	0	0	16747	1174	41	4	9312	4	TTN	2	179403955	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	4583822	179403955	63795418	22	14826											
TTN	7273	hgsc.bcm.edu	37	chr2	179480386	179480388	+	In_Frame_Del	DEL	TTA	TTA	-																															acttgcaggagttgacatatTtacaggttcatcaacatatg																										TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	TTA	TTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr2:179480386_179480388delTTA	ENST00000591111.1	-	208	43741_43743	c.43517_43519delTAA	c.(43516-43521)gtaaat>gat	p.14506_14507VN>D	TTN_ENST00000342992.6_In_Frame_Del_p.13579_13580VN>D|RP11-171I2.4_ENST00000605334.1_lincRNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000359218.5_In_Frame_Del_p.7207_7208VN>D|TTN_ENST00000460472.2_In_Frame_Del_p.7082_7083VN>D|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_In_Frame_Del_p.16147_16148VN>D|TTN_ENST00000342175.6_In_Frame_Del_p.7274_7275VN>D|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	14506	Fibronectin type-III 4. {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)			GTTGACATATTTACAGGTTCATC	0.384																																					p.16147_16148del		Pindel	.											.	TTN	18412	.	0			c.48441_48443del						PASS	.																																			SO:0001651	inframe_deletion	7273	exon258			.	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.43517_43519delTAA	chr2.hg19:g.179480386_179480388delTTA	ENSP00000465570:p.Val14506_Asn14507delinsAsp	177.0	0.0	.		167.0	49.0	0.293	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	In_Frame_Del	DEL	ENST00000591111.1	hg19																																																																																				.	.	.	none		0.384	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		-	179480388	TTA	-	179480386	7	5	242	1	0	1	0	1	0	0	0	0	16747	1841	64	0	59671	0	TTN	2	179480386	In_Frame_Del	DEL	TTA	TCGA-SX-A71S-01A-11D-A33Q-10	76431	179480386	63718987	23	14827											
PARD3B	117583	hgsc.bcm.edu	37	chr2	206058030	206058030	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aattaatttgaaagcctcgaAgagcatggaccttggtaagc	14	10	10	7	1	0	2	0	1	0	1	1	4	0	3	2	2	3	2	2	2	5	4			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr2:206058030A>G	ENST00000406610.2	+	15	2333	c.2126A>G	c.(2125-2127)aAg>aGg	p.K709R	PARD3B_ENST00000351153.1_Missense_Mutation_p.K709R|PARD3B_ENST00000358768.2_Missense_Mutation_p.K647R|PARD3B_ENST00000349953.3_Missense_Mutation_p.K709R|PARD3B_ENST00000462231.1_Missense_Mutation_p.K709R	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	709					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)		AAAGCCTCGAAGAGCATGGAC	0.478																																					p.K709R		Atlas-SNP	.											.	PARD3B	314	.	0			c.A2126G						PASS	.						63	62	62					2																	206058030		1957	4155	6112	SO:0001583	missense	117583	exon15			CCTCGAAGAGCAT	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.2126A>G	chr2.hg19:g.206058030A>G	ENSP00000385848:p.Lys709Arg	274.0	0.0	.		257.0	126.0	.	NM_205863	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	Missense_Mutation	SNP	ENST00000406610.2	hg19		.	.	.	.	.	.	.	.	.	.	A	20.4	3.982851	0.74474	.	.	ENSG00000116117	ENST00000406610;ENST00000358768;ENST00000351153;ENST00000349953	T;T;T;T	0.17370	2.54;2.28;2.71;2.61	5.54	5.54	0.83059	.	0.129926	0.51477	D	0.000098	T	0.32255	0.0823	L	0.58428	1.81	0.43841	D	0.996422	P;D;P;D;P	0.54964	0.669;0.969;0.897;0.958;0.864	B;P;P;P;P	0.56163	0.19;0.585;0.574;0.793;0.523	T	0.01810	-1.1269	10	0.52906	T	0.07	.	14.5322	0.67934	1.0:0.0:0.0:0.0	.	709;709;709;647;709	Q8TEW8-3;Q8TEW8;E9PE87;Q8TEW8-2;Q8TEW8-5	.;PAR3L_HUMAN;.;.;.	R	709;647;709;709	ENSP00000385848:K709R;ENSP00000351618:K647R;ENSP00000317261:K709R;ENSP00000340280:K709R	ENSP00000340280:K709R	K	+	2	0	PARD3B	205766275	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	5.958000	0.70330	2.231000	0.72958	0.397000	0.26171	AAG	.	.	.	none		0.478	PARD3B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000335992.1	NM_057177		G	206058030	A	G	206058030	3	3	242	1	0	0	0	0	1	0	0	0	11451	72	3	3	2184	3	PARD3B	2	206058030	Missense_Mutation	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10	26577644	206058030	37141343	24	14828											
UGT1A5	54579	hgsc.bcm.edu	37	chr2	234622434	234622434	+	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	ggactttgtgatggattaccCcaggccgatcatgcccaaca	10	9	10	12	1	1	1	1	1	0	0	1	4	1	3	4	3	3	0	4	3	2	2			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr2:234622434C>G	ENST00000373414.3	+	1	797	c.797C>G	c.(796-798)cCc>cGc	p.P266R	UGT1A9_ENST00000354728.4_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A1_ENST00000608381.1_Missense_Mutation_p.P266R|UGT1A6_ENST00000373424.1_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000344644.5_Intron			P35504	UD15_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A5	266						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			cervix(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|urinary_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;4.51e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000523)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.00645)		ATGGATTACCCCAGGCCGATC	0.517																																					p.P266R		Atlas-SNP	.											.	UGT1A5	66	.	0			c.C797G						PASS	.						109	124	119					2																	234622434		2201	4295	6496	SO:0001583	missense	54579	exon1			ATTACCCCAGGCC	M84129	CCDS33404.1	2q37	2010-03-05	2005-07-20		ENSG00000240224	ENSG00000240224		"UDP glucuronosyltransferases"	12537	other	complex locus constituent		606430	"UDP glycosyltransferase 1 family, polypeptide A5"			9295054, 1339448	Standard	NM_019078		Approved	UGT1E		P35504	OTTHUMG00000059120	ENST00000373414.3:c.797C>G	chr2.hg19:g.234622434C>G	ENSP00000362513:p.Pro266Arg	103.0	0.0	.		73.0	38.0	.	NM_019078	B8K294	Missense_Mutation	SNP	ENST00000373414.3	hg19	CCDS33404.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.028709	0.75504	.	.	ENSG00000240224	ENST00000373414	T	0.80994	-1.44	4.73	4.73	0.59995	.	0.000000	0.85682	D	0.000000	D	0.93884	0.8043	H	0.98559	4.265	0.58432	D	0.999999	D;D	0.67145	0.996;0.996	D;D	0.72625	0.978;0.978	D	0.96616	0.9456	10	0.87932	D	0	.	17.7257	0.88364	0.0:1.0:0.0:0.0	.	266;266	Q5DSZ9;P35504	.;UD15_HUMAN	R	266	ENSP00000362513:P266R	ENSP00000362513:P266R	P	+	2	0	UGT1A5	234287173	1.000000	0.71417	0.987000	0.45799	0.594000	0.36715	7.529000	0.81952	2.189000	0.69895	0.561000	0.74099	CCC	.	.	.	none		0.517	UGT1A5-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130985.1	NM_019078		G	234622434	C	G	234622434	3	3	242	1	0	0	0	0	1	0	0	0	16960	623	22	4	799	4	UGT1A5	2	234622434	Missense_Mutation	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10	28564404	234622434	8576939	25	14829											
MYEOV2	150678	hgsc.bcm.edu	37	chr2	241073396	241073396	+	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	ttttcattggctgccaagtcCatcaagagcccggtgctgcc	7	11	10	13	1	2	1	2	0	0	1	3	1	3	1	4	2	4	2	4	2	2	3			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr2:241073396C>A	ENST00000607357.1	-	2	108	c.90G>T	c.(88-90)atG>atT	p.M30I	MYEOV2_ENST00000307266.3_Missense_Mutation_p.M61I|MYEOV2_ENST00000489698.1_5'UTR	NM_001163424.1	NP_001156896.1	Q8WXC6	MYOV2_HUMAN	myeloma overexpressed 2	30										breast(1)|lung(5)|pancreas(1)	7		all_epithelial(40;1.56e-11)|Breast(86;0.0002)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;3.81e-30)|all cancers(36;1.1e-27)|OV - Ovarian serous cystadenocarcinoma(60;2.74e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;8.54e-06)|Lung(119;0.00361)|LUSC - Lung squamous cell carcinoma(224;0.0153)|Colorectal(34;0.0202)|COAD - Colon adenocarcinoma(134;0.143)		CTGCCAAGTCCATCAAGAGCC	0.488																																					p.M61I		Atlas-SNP	.											.	MYEOV2	20	.	0			c.G183T						PASS	.						106	112	110					2																	241073396		2203	4300	6503	SO:0001583	missense	150678	exon2			CAAGTCCATCAAG	AF453951	CCDS2532.1, CCDS63183.1	2q37.3	2008-02-05			ENSG00000172428	ENSG00000172428			21314	protein-coding gene	gene with protein product							Standard	NM_138336		Approved		uc002vyu.1	Q8WXC6	OTTHUMG00000133352	ENST00000607357.1:c.90G>T	chr2.hg19:g.241073396C>A	ENSP00000475979:p.Met30Ile	88.0	0.0	.		70.0	31.0	.	NM_138336	Q8N110	Missense_Mutation	SNP	ENST00000607357.1	hg19		.	.	.	.	.	.	.	.	.	.	C	18.15	3.558987	0.65538	.	.	ENSG00000172428	ENST00000307266;ENST00000403160	.	.	.	4.55	4.55	0.56014	.	0.000000	0.85682	U	0.000000	T	0.73705	0.3621	.	.	.	0.80722	D	1	B;P	0.44281	0.393;0.831	P;P	0.54664	0.584;0.758	T	0.77120	-0.2705	8	0.62326	D	0.03	-13.8025	15.1841	0.72986	0.0:1.0:0.0:0.0	.	30;61	Q8WXC6;Q8WXC6-1	MYOV2_HUMAN;.	I	61;51	.	ENSP00000304147:M61I	M	-	3	0	MYEOV2	240722069	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.087000	0.71362	2.240000	0.73641	0.650000	0.86243	ATG	.	.	.	none		0.488	MYEOV2-005	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470698.1	NM_138336		A	241073396	C	A	241073396	3	1	242	1	0	0	0	0	1	0	0	0	10033	594	21	4	595	4	MYEOV2	2	241073396	Missense_Mutation	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10	6450962	241073396	2125977	26	14830											
GOLGA4	2803	hgsc.bcm.edu	37	chr3	37366995	37366995	+	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	gaggacaagagcttggaattTaaaaaactgtctgaggaact	16	9	11	5	0	1	2	0	1	1	1	1	6	1	5	0	3	3	1	0	3	6	3			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr3:37366995T>A	ENST00000361924.2	+	14	3992	c.3618T>A	c.(3616-3618)ttT>ttA	p.F1206L	GOLGA4_ENST00000356847.4_Missense_Mutation_p.F1228L|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1206	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						GCTTGGAATTTAAAAAACTGT	0.348																																					p.F1228L		Atlas-SNP	.											.	GOLGA4	173	.	0			c.T3684A						PASS	.						40	42	41					3																	37366995		2203	4299	6502	SO:0001583	missense	2803	exon15			GGAATTTAAAAAA	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.3618T>A	chr3.hg19:g.37366995T>A	ENSP00000354486:p.Phe1206Leu	243.0	1.0	.		222.0	92.0	.	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	hg19	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	T	3.525	-0.096941	0.07010	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000437131	T;T;T	0.22134	1.98;1.97;1.97	5.53	2.29	0.28610	.	0.211412	0.24120	N	0.041370	T	0.12646	0.0307	L	0.47190	1.495	0.09310	N	1	B;B;B;B	0.15141	0.012;0.002;0.002;0.007	B;B;B;B	0.14578	0.011;0.003;0.006;0.01	T	0.37979	-0.9682	10	0.02654	T	1	.	4.6894	0.12772	0.0:0.4299:0.161:0.4091	.	1206;1206;1228;1206	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	L	1206;1228;1077	ENSP00000354486:F1206L;ENSP00000349305:F1228L;ENSP00000405842:F1077L	ENSP00000349305:F1228L	F	+	3	2	GOLGA4	37341999	0.022000	0.18835	0.785000	0.31869	0.667000	0.39255	0.082000	0.14847	0.686000	0.31488	-0.468000	0.05107	TTT	.	.	.	none		0.348	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		A	37366995	T	A	37366995	3	1	242	1	0	0	0	0	1	0	0	0	6562	1751	61	5	3742	5	GOLGA4	3	37366995	Missense_Mutation	SNP	T	TCGA-SX-A71S-01A-11D-A33Q-10		37366995	160655435	27	14831											
PLCD1	5333	hgsc.bcm.edu	37	chr3	38053124	38053124	+	Frame_Shift_Del	DEL	C	C	-																															cttgaagctcatcttgttgtCcttgtttttgtcagcttttc																										TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr3:38053124delC	ENST00000334661.4	-	4	691	c.469delG	c.(469-471)gacfs	p.D157fs	Y_RNA_ENST00000363709.1_RNA|PLCD1_ENST00000479619.1_5'UTR|PLCD1_ENST00000463876.1_Frame_Shift_Del_p.D178fs	NM_006225.3	NP_006216.2	P51178	PLCD1_HUMAN	phospholipase C, delta 1	157	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				angiogenesis (GO:0001525)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|labyrinthine layer blood vessel development (GO:0060716)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTPase activating protein binding (GO:0032794)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol phosphate binding (GO:1901981)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylserine binding (GO:0001786)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		ATCTTGTTGTCCTTGTTTTTG	0.522																																					p.D178fs		Atlas-Indel,Pindel	.											.	PLCD1	87	.	0			c.533delA						PASS	.						147	136	140					3																	38053124		2203	4300	6503	SO:0001589	frameshift_variant	5333	exon4			.		CCDS2671.1, CCDS46793.1	3p22-p21.3	2013-01-10			ENSG00000187091	ENSG00000187091	3.1.4.11	"EF-hand domain containing"	9060	protein-coding gene	gene with protein product		602142				9345909	Standard	NM_001130964		Approved		uc003chm.3	P51178	OTTHUMG00000130813	ENST00000334661.4:c.469delG	chr3.hg19:g.38053124delC	ENSP00000335600:p.Asp157fs	134.0	0.0	0		111.0	49.0	0.441441	NM_001130964	B3KR14|Q86VN8	Frame_Shift_Del	DEL	ENST00000334661.4	hg19	CCDS2671.1																																																																																			.	.	.	none		0.522	PLCD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253359.2			-	38053124	C	-	38053124	7	5	242	1	0	1	0	1	0	0	0	0	12038	855	30	0	1849	0	PLCD1	3	38053124	Frame_Shift_Del	DEL	C	TCGA-SX-A71S-01A-11D-A33Q-10	686129	38053124	159969306	28	14832											
CCR9	10803	hgsc.bcm.edu	37	chr3	45942619	45942619	+	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	gctgctgctgaccagtggaaGttccagaccttcatgtgcaa	9	10	11	11	0	1	2	1	1	0	1	2	3	2	3	3	1	3	5	3	1	2	2			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr3:45942619G>T	ENST00000357632.2	+	3	519	c.339G>T	c.(337-339)aaG>aaT	p.K113N	CCR9_ENST00000355983.2_Missense_Mutation_p.K101N|LZTFL1_ENST00000536047.1_Intron|Y_RNA_ENST00000364765.1_RNA|CCR9_ENST00000395963.2_Missense_Mutation_p.K101N|LZTFL1_ENST00000539217.1_Intron|CCR9_ENST00000422395.1_3'UTR	NM_001256369.1|NM_031200.2	NP_001243298.1|NP_112477.1	P51686	CCR9_HUMAN	chemokine (C-C motif) receptor 9	113					cellular defense response (GO:0006968)|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)	cell surface (GO:0009986)|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(4)|large_intestine(8)|lung(2)|ovary(2)|prostate(2)|skin(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.00118)|KIRC - Kidney renal clear cell carcinoma(197;0.0182)|Kidney(197;0.0214)		ACCAGTGGAAGTTCCAGACCT	0.483																																					p.K113N		Atlas-SNP	.											.	CCR9	45	.	0			c.G339T						PASS	.						200	188	192					3																	45942619		2203	4300	6503	SO:0001583	missense	10803	exon3			GTGGAAGTTCCAG	AJ132337	CCDS2732.1, CCDS2733.1	3p21.31	2012-09-20			ENSG00000173585	ENSG00000173585		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1610	protein-coding gene	gene with protein product		604738		GPR28		10229797	Standard	NM_006641		Approved	GPR-9-6, CDw199	uc003coz.2	P51686	OTTHUMG00000133450	ENST00000357632.2:c.339G>T	chr3.hg19:g.45942619G>T	ENSP00000350256:p.Lys113Asn	89.0	0.0	.		82.0	34.0	.	NM_031200	Q4VBM3|Q549E0|Q9UQQ6	Missense_Mutation	SNP	ENST00000357632.2	hg19	CCDS2732.1	.	.	.	.	.	.	.	.	.	.	G	4.329	0.060379	0.08339	.	.	ENSG00000173585	ENST00000357632;ENST00000395963;ENST00000355983	T;T;T	0.37058	1.22;1.22;1.22	4.96	-3.74	0.04385	GPCR, rhodopsin-like superfamily (1);	0.949681	0.08862	N	0.882804	T	0.18299	0.0439	N	0.20685	0.6	0.09310	N	0.999997	B	0.14438	0.01	B	0.16722	0.016	T	0.28459	-1.0043	10	0.21014	T	0.42	.	5.4602	0.16612	0.1717:0.1145:0.5256:0.1882	.	113	P51686	CCR9_HUMAN	N	113;101;101	ENSP00000350256:K113N;ENSP00000379292:K101N;ENSP00000348260:K101N	ENSP00000348260:K101N	K	+	3	2	CCR9	45917623	0.000000	0.05858	0.343000	0.25615	0.801000	0.45260	-0.482000	0.06544	-0.736000	0.04831	-1.166000	0.01754	AAG	.	.	.	none		0.483	CCR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257323.2			T	45942619	G	T	45942619	3	4	242	1	0	0	0	0	1	0	0	0	2950	1020	36	4	345	4	CCR9	3	45942619	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	7889495	45942619	152079811	29	14833											
C3orf45	132228	hgsc.bcm.edu	37	chr3	50324199	50324199	+	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	ctgtgtgcccaggctggctgCagccctgtgtacagacgagg	6	8	15	12	1	0	1	0	0	0	1	0	2	0	1	2	3	4	4	2	3	1	1			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr3:50324199C>T	ENST00000316436.3	+	3	354	c.267C>T	c.(265-267)tgC>tgT	p.C89C		NM_153215.1	NP_694947.1	Q8N112	LSME2_HUMAN	leucine-rich single-pass membrane protein 2	89						integral component of membrane (GO:0016021)											AGGCTGGCTGCAGCCCTGTGT	0.632																																					p.C89C		Atlas-SNP	.											.	.	.	.	0			c.C267T						PASS	.						78	76	76					3																	50324199		2203	4300	6503	SO:0001819	synonymous_variant	0	exon3			TGGCTGCAGCCCT	AK095927	CCDS2814.1	3p21.31	2013-03-08	2013-03-08	2013-03-08	ENSG00000179564	ENSG00000179564			26781	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 45"	C3orf45			Standard	NM_153215		Approved	FLJ38608	uc003cyz.3	Q8N112	OTTHUMG00000156938	ENST00000316436.3:c.267C>T	chr3.hg19:g.50324199C>T		67.0	0.0	.		38.0	19.0	.	NM_153215		Silent	SNP	ENST00000316436.3	hg19	CCDS2814.1																																																																																			.	.	.	none		0.632	LSMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346671.1	NM_153215		T	50324199	C	T	50324199	2	4	242	1	0	0	0	0	0	0	0	1	2233	718	25	2		2	C3orf45	3	50324199	Silent	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10	4381580	50324199	147698231	30	14834											
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113376476	113376476	+	Silent	SNP	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	gacatactttcaagcctgagGggggctggctgacagtgctt	8	10	14	9	0	1	2	1	2	0	0	1	3	1	2	1	4	3	3	1	4	2	3			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr3:113376476G>A	ENST00000478658.1	-	5	4070	c.4053C>T	c.(4051-4053)ccC>ccT	p.P1351P	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Silent_p.P1351P			Q68DE3	K2018_HUMAN	KIAA2018	1351						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						CAAGCCTGAGGGGGGCTGGCT	0.473																																					p.P1351P		Atlas-SNP	.											.	KIAA2018	180	.	0			c.C4053T						PASS	.						99	97	98					3																	113376476		1966	4162	6128	SO:0001819	synonymous_variant	205717	exon7			CCTGAGGGGGGCT	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.4053C>T	chr3.hg19:g.113376476G>A		60.0	0.0	.		50.0	27.0	.	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	hg19	CCDS43133.1																																																																																			.	.	.	none		0.473	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		A	113376476	G	A	113376476	2	1	242	1	0	0	0	0	0	0	0	1	8275	1219	43	2		2	KIAA2018	3	113376476	Silent	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	63052277	113376476	84645954	31	14835											
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121413729	121413729	+	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	accatcctttgttgatatctGactcagtaaggtatttttct	9	18	6	8	0	3	2	1	2	2	0	4	2	4	2	2	1	0	3	2	1	3	7			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr3:121413729G>T	ENST00000340645.5	-	13	5751	c.5626C>A	c.(5626-5628)Cag>Aag	p.Q1876K	GOLGB1_ENST00000393667.3_Missense_Mutation_p.Q1881K	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	1876					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)		GTTGATATCTGACTCAGTAAG	0.368																																					p.Q1881K		Atlas-SNP	.											.	GOLGB1	319	.	0			c.C5641A						PASS	.						133	150	144					3																	121413729		2203	4300	6503	SO:0001583	missense	2804	exon13			ATATCTGACTCAG	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.5626C>A	chr3.hg19:g.121413729G>T	ENSP00000341848:p.Gln1876Lys	98.0	0.0	.		102.0	38.0	.	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	hg19	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	G	6.523	0.464725	0.12402	.	.	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.15952	2.38;2.38	5.92	5.04	0.67666	.	0.129584	0.35407	N	0.003230	T	0.33411	0.0862	M	0.65975	2.015	0.35168	D	0.771267	D;B;B;D	0.67145	0.996;0.112;0.112;0.988	D;B;B;P	0.72982	0.979;0.032;0.032;0.794	T	0.44421	-0.9329	10	0.19590	T	0.45	.	8.3617	0.32363	0.0812:0.1576:0.7612:0.0	.	1801;1881;1881;1876	F1T0J2;E7EP74;B2ZZ91;Q14789	.;.;.;GOGB1_HUMAN	K	1876;1881	ENSP00000341848:Q1876K;ENSP00000377275:Q1881K	ENSP00000341848:Q1876K	Q	-	1	0	GOLGB1	122896419	0.004000	0.15560	0.986000	0.45419	0.247000	0.25773	0.789000	0.26886	1.459000	0.47892	0.650000	0.86243	CAG	.	.	.	none		0.368	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		T	121413729	G	T	121413729	3	4	242	1	0	0	0	0	1	0	0	0	6572	1299	45	4	4193	4	GOLGB1	3	121413729	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	8037253	121413729	76608701	32	14836											
MAGEF1	64110	hgsc.bcm.edu	37	chr3	184428920	184428920	+	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	tattctggtggattggtgtgAggcacccgcctgtaactgag	7	12	14	8	1	1	2	0	2	1	0	1	3	1	3	2	4	1	2	2	4	2	4			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr3:184428920A>C	ENST00000317897.3	-	1	916	c.690T>G	c.(688-690)ccT>ccG	p.P230P		NM_022149.4	NP_071432.2	Q9HAY2	MAGF1_HUMAN	melanoma antigen family F, 1	230	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.					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)			GATTGGTGTGAGGCACCCGCC	0.488																																					p.P230P		Atlas-SNP	.											.	MAGEF1	27	.	0			c.T690G						PASS	.						53	60	58					3																	184428920		2203	4300	6503	SO:0001819	synonymous_variant	64110	exon1			GGTGTGAGGCACC	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.690T>G	chr3.hg19:g.184428920A>C		104.0	0.0	.		91.0	46.0	.	NM_022149	Q9H215	Silent	SNP	ENST00000317897.3	hg19	CCDS3269.1																																																																																			.	.	.	none		0.488	MAGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345417.1	NM_022149		C	184428920	A	C	184428920	2	2	242	1	0	0	0	0	0	0	0	1	9194	291	11	5		5	MAGEF1	3	184428920	Silent	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10	63015191	184428920	13593510	33	14837											
DGKG	1608	hgsc.bcm.edu	37	chr3	185969621	185969621	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttccacttcctctctggggAtgacttccagatgccagcgg	6	12	10	13	1	1	2	0	1	1	1	5	3	4	3	4	3	2	0	4	3	0	3			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr3:185969621A>G	ENST00000265022.3	-	19	2227	c.1688T>C	c.(1687-1689)aTc>aCc	p.I563T	DGKG_ENST00000344484.4_Missense_Mutation_p.I538T|DGKG_ENST00000544847.1_Missense_Mutation_p.I504T|DGKG_ENST00000382164.4_Missense_Mutation_p.I524T	NM_001080744.1|NM_001080745.1|NM_001346.2	NP_001074213.1|NP_001074214.1|NP_001337.2	P49619	DGKG_HUMAN	diacylglycerol kinase, gamma 90kDa	563	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|neuron development (GO:0048666)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	42	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	CTCTCTGGGGATGACTTCCAG	0.507																																					p.I563T		Atlas-SNP	.											.	DGKG	98	.	0			c.T1688C						PASS	.						183	170	174					3																	185969621		2203	4300	6503	SO:0001583	missense	1608	exon19			CTGGGGATGACTT	AF020945	CCDS3274.1, CCDS43181.1, CCDS43182.1	3q27-q28	2013-01-10	2002-08-29		ENSG00000058866	ENSG00000058866	2.7.1.107	"EF-hand domain containing"	2853	protein-coding gene	gene with protein product		601854	"diacylglycerol kinase, gamma (90kD)"	DAGK3		8034597	Standard	NM_001080744		Approved		uc003fqa.3	P49619	OTTHUMG00000156617	ENST00000265022.3:c.1688T>C	chr3.hg19:g.185969621A>G	ENSP00000265022:p.Ile563Thr	101.0	0.0	.		97.0	4.0	.	NM_001346	B2RAH4|Q2M1H4|Q5FWG1	Missense_Mutation	SNP	ENST00000265022.3	hg19	CCDS3274.1	.	.	.	.	.	.	.	.	.	.	A	7.945	0.743641	0.15642	.	.	ENSG00000058866	ENST00000265022;ENST00000344484;ENST00000382164;ENST00000544847;ENST00000538691	D;D;D;T	0.83075	-1.5;-1.51;-1.68;-1.35	5.06	-0.278	0.12894	Diacylglycerol kinase, catalytic domain (1);	0.549028	0.18794	N	0.130972	T	0.56702	0.2003	N	0.04335	-0.225	0.34056	D	0.656773	B;B;B;B	0.06786	0.001;0.001;0.001;0.001	B;B;B;B	0.12837	0.004;0.008;0.004;0.002	T	0.47861	-0.9084	10	0.11485	T	0.65	.	5.7195	0.17978	0.5853:0.2645:0.1503:0.0	.	504;538;524;563	F5GX27;P49619-2;P49619-3;P49619	.;.;.;DGKG_HUMAN	T	563;538;524;504;527	ENSP00000265022:I563T;ENSP00000339777:I538T;ENSP00000371599:I524T;ENSP00000440507:I504T	ENSP00000265022:I563T	I	-	2	0	DGKG	187452315	0.998000	0.40836	0.994000	0.49952	0.996000	0.88848	1.589000	0.36644	0.065000	0.16485	0.383000	0.25322	ATC	.	.	.	none		0.507	DGKG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344800.3			G	185969621	A	G	185969621	3	3	242	1	0	0	0	0	1	0	0	0	4471	333	12	3	715	3	DGKG	3	185969621	Missense_Mutation	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10	1540701	185969621	12052809	34	14838											
PCDH10	57575	hgsc.bcm.edu	37	chr4	134072496	134072496	+	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	agtgcgagctactgggagacGtgcctttccgcctcaagtct	7	10	12	12	3	2	1	1	0	1	1	3	3	3	1	3	1	4	1	3	1	2	2			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr4:134072496G>T	ENST00000264360.5	+	1	2027	c.1201G>T	c.(1201-1203)Gtg>Ttg	p.V401L	RP11-9G1.3_ENST00000505289.1_lincRNA	NM_032961.1	NP_116586.1	Q9P2E7	PCD10_HUMAN	protocadherin 10	401	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(30)|liver(1)|lung(72)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(2)	136				LUSC - Lung squamous cell carcinoma(193;0.227)		ACTGGGAGACGTGCCTTTCCG	0.607																																					p.V401L		Atlas-SNP	.											.	PCDH10	290	.	0			c.G1201T						PASS	.						139	140	140					4																	134072496		2203	4300	6503	SO:0001583	missense	57575	exon1			GGAGACGTGCCTT	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.1201G>T	chr4.hg19:g.134072496G>T	ENSP00000264360:p.Val401Leu	72.0	0.0	.		66.0	29.0	.	NM_032961	Q4W5F6|Q96SF0	Missense_Mutation	SNP	ENST00000264360.5	hg19	CCDS34063.1	.	.	.	.	.	.	.	.	.	.	G	9.624	1.134716	0.21123	.	.	ENSG00000138650	ENST00000264360;ENST00000394248	T	0.51071	0.72	4.68	4.68	0.58851	Cadherin (4);Cadherin-like (1);	0.000000	0.40818	N	0.001004	T	0.44685	0.1305	L	0.35487	1.065	0.52501	D	0.999955	P;B	0.36354	0.549;0.004	P;B	0.46659	0.523;0.018	T	0.18429	-1.0337	10	0.05721	T	0.95	.	17.3997	0.87456	0.0:0.0:1.0:0.0	.	401;401	Q9P2E7;Q96SF0	PCD10_HUMAN;.	L	401	ENSP00000264360:V401L	ENSP00000264360:V401L	V	+	1	0	PCDH10	134291946	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.674000	0.83992	2.423000	0.82170	0.561000	0.74099	GTG	.	.	.	none		0.607	PCDH10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000364457.2	NM_032961		T	134072496	G	T	134072496	3	4	242	1	0	0	0	0	1	0	0	0	11514	1145	40	4	1203	4	PCDH10	4	134072496	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10		134072496	57081780	35	14839											
GPM6A	2823	hgsc.bcm.edu	37	chr4	176556203	176556203	+	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	gcagacagaaccataaggtaGtgaacctaatcaaagagaaa	20	5	9	7	0	1	4	1	1	0	3	1	5	1	4	2	1	2	2	2	1	7	3			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr4:176556203G>T	ENST00000280187.7	-	8	735	c.690C>A	c.(688-690)caC>caA	p.H230Q	GPM6A_ENST00000393658.2_Missense_Mutation_p.H230Q|GPM6A_ENST00000515090.1_Missense_Mutation_p.H223Q|GPM6A_ENST00000506894.1_Missense_Mutation_p.H219Q|GPM6A_ENST00000506219.1_5'UTR	NM_005277.4	NP_005268.1	P51674	GPM6A_HUMAN	glycoprotein M6A	230					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)		CCATAAGGTAGTGAACCTAAT	0.403																																					p.H230Q		Atlas-SNP	.											.	GPM6A	70	.	0			c.C690A						PASS	.						61	59	59					4																	176556203		2203	4300	6503	SO:0001583	missense	2823	exon7			AAGGTAGTGAACC		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.690C>A	chr4.hg19:g.176556203G>T	ENSP00000280187:p.His230Gln	38.0	0.0	.		28.0	11.0	.	NM_201591	B7Z642|E9PHI5|Q92602	Missense_Mutation	SNP	ENST00000280187.7	hg19	CCDS3824.1	.	.	.	.	.	.	.	.	.	.	G	18.86	3.714211	0.68730	.	.	ENSG00000150625	ENST00000280187;ENST00000393658;ENST00000506894;ENST00000515090	D;D;D;D	0.99176	-5.52;-5.52;-5.52;-5.52	5.77	4.92	0.64577	.	0.000000	0.85682	D	0.000000	D	0.98651	0.9548	L	0.55990	1.75	0.80722	D	1	D;D;D	0.69078	0.997;0.997;0.997	D;D;D	0.81914	0.995;0.995;0.995	D	0.96785	0.9578	10	0.26408	T	0.33	-20.0308	10.7457	0.46179	0.1426:0.0:0.8574:0.0	.	223;219;230	B7Z642;E9PHI5;P51674	.;.;GPM6A_HUMAN	Q	230;230;219;223	ENSP00000280187:H230Q;ENSP00000377268:H230Q;ENSP00000421578:H219Q;ENSP00000423984:H223Q	ENSP00000280187:H230Q	H	-	3	2	GPM6A	176793197	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.806000	0.38892	2.885000	0.99019	0.655000	0.94253	CAC	.	.	.	none		0.403	GPM6A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362163.1			T	176556203	G	T	176556203	3	4	242	1	0	0	0	0	1	0	0	0	6622	1020	36	4	150	4	GPM6A	4	176556203	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	42483707	176556203	14598073	36	14840											
WDR17	116966	hgsc.bcm.edu	37	chr4	177098622	177098622	+	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	gatatctgttgaaaatatagAtcattagaagactctccgta	15	13	7	6	1	3	4	1	1	2	3	4	5	3	4	1	0	0	2	1	0	8	6			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr4:177098622A>G	ENST00000280190.4	+	30	3822	c.3666A>G	c.(3664-3666)agA>agG	p.R1222R	WDR17_ENST00000393643.2_Splice_Site_p.R1198R|WDR17_ENST00000507824.2_Splice_Site_p.R1197R|WDR17_ENST00000508596.1_Splice_Site_p.R1183R			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	1222										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)		GAAAATATAGATCATTAGAAG	0.299																																					p.R1222R		Atlas-SNP	.											.	WDR17	198	.	0			c.A3666G						PASS	.						60	69	66					4																	177098622		2201	4296	6497	SO:0001630	splice_region_variant	116966	exon30			ATATAGATCATTA	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.3666-1A>G	chr4.hg19:g.177098622A>G		124.0	0.0	.		100.0	40.0	.	NM_170710	E7EQX0|Q0QD35	Silent	SNP	ENST00000280190.4	hg19	CCDS3825.1	.	.	.	.	.	.	.	.	.	.	A	9.886	1.202950	0.22121	.	.	ENSG00000150627	ENST00000443118	.	.	.	5.6	0.312	0.15837	.	.	.	.	.	T	0.51483	0.1677	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36915	-0.9728	4	.	.	.	.	5.914	0.19045	0.5729:0.2349:0.1922:0.0	.	.	.	.	V	457	.	.	I	+	1	0	WDR17	177335616	0.984000	0.35163	0.979000	0.43373	0.803000	0.45373	0.955000	0.29188	-0.046000	0.13446	0.524000	0.50904	ATC	.	.	.	none		0.299	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2		Silent	G	177098622	A	G	177098622	5	3	242	1	0	0	0	0	0	0	1	0	17289	347	12	3	3780	3	WDR17	4	177098622	Splice_Site	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10	542419	177098622	14055654	37	14841											
PLEKHG4B	153478	hgsc.bcm.edu	37	chr5	163420	163421	+	Missense_Mutation	DNP	AA	AA	TT																															caggaaacatccccagaagaAaatgataaagaaaacgcaaa																										TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr5:163420_163421AA>TT	ENST00000283426.6	+	11	2215_2216	c.2165_2166AA>TT	c.(2164-2166)aAA>aTT	p.K722I		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	722							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)		CCCCAGAAGAAAATGATAAAGA	0.609																																					p.K722I|p.K722N		Atlas-SNP	.											.	PLEKHG4B	167	.	0			c.A2165T|c.A2166T						PASS	.																																			SO:0001583	missense	153478	exon11			AGAAGAAAATGAT|GAAGAAAATGATA	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	Exception_encountered	chr5.hg19:g.163420_163421delinsTT	ENSP00000283426:p.Lys722Ile	133.0|132.0	0.0	.		86.0	38.0|39.0	.	NM_052909		Missense_Mutation	SNP	ENST00000283426.6	hg19	CCDS34124.1																																																																																			.	.	.	none		0.609	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		TT	163421	AA	TT	163420	3	4	242	1	0	0	0	0	1	0	0	0	12079	14	1	5	2207	5	PLEKHG4B	5	163420	Missense_Mutation	DNP	AA	TCGA-SX-A71S-01A-11D-A33Q-10		163420	180751840	38	14842											
NIPBL	25836	hgsc.bcm.edu	37	chr5	37049326	37049326	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcttgaggcattttttcacAcccagtcaagtgtacgccac	9	12	8	12	1	2	1	2	1	0	0	2	1	2	1	2	1	2	3	2	1	2	5			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr5:37049326A>G	ENST00000282516.8	+	40	7376	c.6877A>G	c.(6877-6879)Acc>Gcc	p.T2293A	NIPBL_ENST00000448238.2_Missense_Mutation_p.T2293A	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	2293					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)			ATTTTTTCACACCCAGTCAAG	0.413																																					p.T2293A		Atlas-SNP	.											.	NIPBL	513	.	0			c.A6877G						PASS	.						224	213	216					5																	37049326		2203	4300	6503	SO:0001583	missense	25836	exon40			TTTCACACCCAGT	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.6877A>G	chr5.hg19:g.37049326A>G	ENSP00000282516:p.Thr2293Ala	72.0	0.0	.		75.0	39.0	.	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	ENST00000282516.8	hg19	CCDS3920.1	.	.	.	.	.	.	.	.	.	.	A	7.931	0.740748	0.15642	.	.	ENSG00000164190	ENST00000282516;ENST00000448238	D;D	0.95307	-3.67;-3.67	5.55	5.55	0.83447	Armadillo-like helical (1);Armadillo-type fold (1);	0.052442	0.64402	D	0.000001	D	0.88194	0.6371	N	0.11560	0.145	0.40370	D	0.979331	B;B	0.25486	0.127;0.104	B;B	0.33960	0.173;0.084	D	0.84616	0.0681	10	0.07990	T	0.79	-4.9512	15.6935	0.77473	1.0:0.0:0.0:0.0	.	2293;2293	Q6KC79;Q6KC79-2	NIPBL_HUMAN;.	A	2293	ENSP00000282516:T2293A;ENSP00000406266:T2293A	ENSP00000282516:T2293A	T	+	1	0	NIPBL	37085083	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.929000	0.70096	2.109000	0.64355	0.477000	0.44152	ACC	.	.	.	none		0.413	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		G	37049326	A	G	37049326	3	3	242	1	0	0	0	0	1	0	0	0	10435	159	6	3	7031	3	NIPBL	5	37049326	Missense_Mutation	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10	36885906	37049326	143865934	39	14843											
MAST4	375449	hgsc.bcm.edu	37	chr5	66461904	66461904	+	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	cggcccctggaggtgctggaGaagcctgtgcatttgccaag	7	8	15	11	1	0	1	0	0	0	1	0	3	0	2	4	4	4	2	4	4	2	1			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr5:66461904G>A	ENST00000403625.2	+	29	7192	c.6897G>A	c.(6895-6897)gaG>gaA	p.E2299E	MAST4_ENST00000405643.1_Silent_p.E2120E|MAST4_ENST00000261569.7_Silent_p.E2105E|MAST4_ENST00000403666.1_Silent_p.E2110E|MAST4_ENST00000404260.3_Silent_p.E2302E	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	2302						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)		AGGTGCTGGAGAAGCCTGTGC	0.622											OREG0016638	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E2299E		Atlas-SNP	.											.	MAST4	218	.	0			c.G6897A						PASS	.						21	27	25					5																	66461904		1916	4110	6026	SO:0001819	synonymous_variant	375449	exon29			GCTGGAGAAGCCT	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.6897G>A	chr5.hg19:g.66461904G>A		92.0	0.0	.	1092	65.0	21.0	.	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Silent	SNP	ENST00000403625.2	hg19	CCDS54861.1	.	.	.	.	.	.	.	.	.	.	G	2.764	-0.257184	0.05791	.	.	ENSG00000069020	ENST00000443808	T	0.04862	3.54	4.27	1.4	0.22301	.	0.737317	0.12126	N	0.497250	T	0.08447	0.0210	.	.	.	0.19300	N	0.99998	.	.	.	.	.	.	T	0.30679	-0.9970	7	0.66056	D	0.02	-8.1738	6.124	0.20170	0.1728:0.293:0.5342:0.0	.	.	.	.	K	1356	ENSP00000400551:E1356K	ENSP00000400551:E1356K	E	+	1	0	MAST4	66497660	0.738000	0.28186	0.006000	0.13384	0.014000	0.08584	0.180000	0.16860	0.511000	0.28236	0.462000	0.41574	GAA	.	.	.	none		0.622	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			A	66461904	G	A	66461904	2	1	242	1	0	0	0	0	0	0	0	1	9334	933	33	2		2	MAST4	5	66461904	Silent	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	29412578	66461904	114453356	40	14844											
CD180	4064	hgsc.bcm.edu	37	chr5	66479076	66479076	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatcaatgctgtcgcatgtcAggctgttgtggcttaagtct	8	14	11	8	1	3	0	2	0	1	0	4	0	3	0	0	2	1	5	0	2	3	2			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr5:66479076A>G	ENST00000256447.4	-	3	1752	c.1595T>C	c.(1594-1596)cTg>cCg	p.L532P	CTD-2306M10.1_ENST00000602471.1_lincRNA	NM_005582.2	NP_005573.2	Q99467	CD180_HUMAN	CD180 molecule	532					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)		GTCGCATGTCAGGCTGTTGTG	0.473																																					p.L532P		Atlas-SNP	.											.	CD180	78	.	0			c.T1595C						PASS	.						87	59	68					5																	66479076		2203	4300	6503	SO:0001583	missense	4064	exon3			CATGTCAGGCTGT	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.1595T>C	chr5.hg19:g.66479076A>G	ENSP00000256447:p.Leu532Pro	117.0	0.0	.		104.0	37.0	.	NM_005582	B2R7Z7|Q32MM5	Missense_Mutation	SNP	ENST00000256447.4	hg19	CCDS3992.1	.	.	.	.	.	.	.	.	.	.	A	15.88	2.962783	0.53507	.	.	ENSG00000134061	ENST00000256447	T	0.69435	-0.4	4.95	4.95	0.65309	.	0.117810	0.35378	N	0.003258	D	0.87148	0.6105	H	0.96301	3.8	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.91268	0.5042	10	0.87932	D	0	.	14.7906	0.69841	1.0:0.0:0.0:0.0	.	532	Q99467	CD180_HUMAN	P	532	ENSP00000256447:L532P	ENSP00000256447:L532P	L	-	2	0	CD180	66514832	0.728000	0.28080	0.946000	0.38457	0.663000	0.39108	6.357000	0.73051	2.076000	0.62316	0.460000	0.39030	CTG	.	.	.	none		0.473	CD180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253973.2	NM_005582		G	66479076	A	G	66479076	3	3	242	1	0	0	0	0	1	0	0	0	2974	188	7	3	394	3	CD180	5	66479076	Missense_Mutation	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10	17172	66479076	114436184	41	14845											
NRG2	9542	hgsc.bcm.edu	37	chr5	139422438	139422438	+	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	ccgggctgcggggctgcgggGctgcggctgttgctgcggcc	0	7	21	13	5	0	0	0	0	0	0	0	0	0	0	2	7	5	6	2	7	0	1			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr5:139422438G>T	ENST00000361474.1	-	1	441	c.217C>A	c.(217-219)Ccc>Acc	p.P73T	NRG2_ENST00000541337.1_Missense_Mutation_p.P73T|NRG2_ENST00000289409.4_Missense_Mutation_p.P73T|NRG2_ENST00000394770.1_Missense_Mutation_p.P73T|NRG2_ENST00000545385.1_Missense_Mutation_p.P73T|NRG2_ENST00000289422.7_Missense_Mutation_p.P73T|NRG2_ENST00000358522.3_Missense_Mutation_p.P73T	NM_004883.2	NP_004874.1	O14511	NRG2_HUMAN	neuregulin 2	73					embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	25			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			gggctgcggggctgcggCTGT	0.746																																					p.P73T		Atlas-SNP	.											.	NRG2	69	.	0			c.C217A						PASS	.						1	2	1					5																	139422438		838	1656	2494	SO:0001583	missense	9542	exon1			TGCGGGGCTGCGG		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.217C>A	chr5.hg19:g.139422438G>T	ENSP00000354910:p.Pro73Thr	3.0	0.0	.		6.0	4.0	.	NM_013982		Missense_Mutation	SNP	ENST00000361474.1	hg19	CCDS4217.1	.	.	.	.	.	.	.	.	.	.	G	13.05	2.122733	0.37436	.	.	ENSG00000158458	ENST00000541337;ENST00000289422;ENST00000361474;ENST00000446269;ENST00000545385;ENST00000394770;ENST00000289409;ENST00000358522;ENST00000378238	T;T;T;T;T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32;-1.32;-1.32;-1.32;-1.32	4.1	4.1	0.47936	.	1.266670	0.05928	N	0.634708	T	0.66025	0.2748	N	0.08118	0	0.38024	D	0.934932	B;B;B;B	0.33103	0.397;0.276;0.397;0.397	B;B;B;B	0.31614	0.133;0.037;0.133;0.08	T	0.51076	-0.8751	10	0.15066	T	0.55	-6.9595	14.2466	0.65993	0.0:0.0:1.0:0.0	.	73;73;73;73	O14511-2;O14511;O14511-4;O14511-3	.;NRG2_HUMAN;.;.	T	73	ENSP00000444235:P73T;ENSP00000289422:P73T;ENSP00000354910:P73T;ENSP00000438753:P73T;ENSP00000378251:P73T;ENSP00000289409:P73T;ENSP00000351323:P73T;ENSP00000367483:P73T	ENSP00000289409:P73T	P	-	1	0	NRG2	139402622	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	6.579000	0.74036	2.133000	0.65898	0.491000	0.48974	CCC	.	.	.	none		0.746	NRG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251340.1	NM_013982		T	139422438	G	T	139422438	3	4	242	1	0	0	0	0	1	0	0	0	10655	1203	42	4	2466	4	NRG2	5	139422438	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	72943362	139422438	41492822	42	14846											
PCDHGC3	5098	hgsc.bcm.edu	37	chr5	140857046	140857046	+	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	ccgacatcaatgacaaccctCcacaatcttctcaatcttcc	12	10	2	17	1	4	1	2	1	3	0	7	2	6	1	4	0	1	0	4	0	4	2			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr5:140857046C>T	ENST00000308177.3	+	1	1467	c.1363C>T	c.(1363-1365)Cca>Tca	p.P455S	PCDHGA12_ENST00000252085.3_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA11_ENST00000398587.2_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGB1_ENST00000523390.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB6_ENST00000520790.1_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	455	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			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)			TGACAACCCTCCACAATCTTC	0.527																																					p.P455S		Atlas-SNP	.											.	PCDHGC3	173	.	0			c.C1363T						PASS	.						146	149	148					5																	140857046		2203	4300	6503	SO:0001583	missense	5098	exon1			AACCCTCCACAAT	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.1363C>T	chr5.hg19:g.140857046C>T	ENSP00000312070:p.Pro455Ser	243.0	0.0	.		211.0	14.0	.	NM_032402	O60622|Q08192|Q9Y5C4	Missense_Mutation	SNP	ENST00000308177.3	hg19	CCDS4261.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.050852	0.75960	.	.	ENSG00000240184	ENST00000308177	D	0.84800	-1.9	5.19	5.19	0.71726	Cadherin (5);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	D	0.96821	0.8962	H	0.99948	5.02	0.46586	D	0.999111	D;D	0.89917	1.0;1.0	D;D	0.97110	0.996;1.0	D	0.98483	1.0606	9	0.87932	D	0	.	19.2755	0.94030	0.0:1.0:0.0:0.0	.	455;455	Q9UN70;Q9UN70-2	PCDGK_HUMAN;.	S	455	ENSP00000312070:P455S	ENSP00000312070:P455S	P	+	1	0	PCDHGC3	140837230	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	7.575000	0.82447	2.865000	0.98341	0.655000	0.94253	CCA	.	.	.	none		0.527	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588		T	140857046	C	T	140857046	3	4	242	1	0	0	0	0	1	0	0	0	11576	855	30	2	1365	2	PCDHGC3	5	140857046	Missense_Mutation	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10	1434608	140857046	40058214	43	14847											
SLC36A2	153201	hgsc.bcm.edu	37	chr5	150726918	150726918	+	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	gactttcatccaagaatgtaGagtccttgttctccaacttc	10	14	6	11	0	2	2	1	0	1	2	6	3	4	2	3	0	1	2	3	0	4	5			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr5:150726918G>C	ENST00000335244.4	-	1	233	c.104C>G	c.(103-105)tCt>tGt	p.S35C	SLC36A2_ENST00000521967.1_Missense_Mutation_p.S35C	NM_181776.2	NP_861441.2	Q495M3	S36A2_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 2	35					amino acid transport (GO:0006865)|ion transport (GO:0006811)|proline transmembrane transport (GO:0035524)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine transmembrane transporter activity (GO:0015187)|hydrogen:amino acid symporter activity (GO:0005280)|L-alanine transmembrane transporter activity (GO:0015180)|L-proline transmembrane transporter activity (GO:0015193)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(14)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Cycloserine(DB00260)	CAAGAATGTAGAGTCCTTGTT	0.478																																					p.S35C		Atlas-SNP	.											.	SLC36A2	71	.	0			c.C104G						PASS	.						206	200	202					5																	150726918		2203	4300	6503	SO:0001583	missense	153201	exon1			AATGTAGAGTCCT	AY162214	CCDS4315.1	5q33.1	2013-05-22			ENSG00000186335	ENSG00000186335		"Solute carriers"	18762	protein-coding gene	gene with protein product		608331				11959859	Standard	NM_181776		Approved	PAT2, tramdorin, TRAMD1	uc003lty.3	Q495M3	OTTHUMG00000130129	ENST00000335244.4:c.104C>G	chr5.hg19:g.150726918G>C	ENSP00000334223:p.Ser35Cys	164.0	0.0	.		141.0	61.0	.	NM_181776	Q495M4|Q495M6|Q6ZWK5|Q7Z6B5	Missense_Mutation	SNP	ENST00000335244.4	hg19	CCDS4315.1	.	.	.	.	.	.	.	.	.	.	G	10.73	1.432660	0.25813	.	.	ENSG00000186335	ENST00000335244;ENST00000521967	T;T	0.10960	3.63;2.82	4.87	2.96	0.34315	.	0.318730	0.31188	N	0.008086	T	0.11965	0.0291	N	0.24115	0.695	0.09310	N	0.999999	D;D;P	0.69078	0.997;0.969;0.829	P;P;P	0.56865	0.808;0.682;0.502	T	0.05550	-1.0878	10	0.52906	T	0.07	-9.6566	5.61	0.17400	0.0989:0.0:0.7072:0.1939	.	35;35;35	B4DMY0;E5RJJ5;Q495M3	.;.;S36A2_HUMAN	C	35	ENSP00000334223:S35C;ENSP00000430535:S35C	ENSP00000334223:S35C	S	-	2	0	SLC36A2	150707111	0.031000	0.19500	0.015000	0.15790	0.074000	0.17049	1.709000	0.37909	1.405000	0.46838	0.655000	0.94253	TCT	.	.	.	none		0.478	SLC36A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252437.1			C	150726918	G	C	150726918	3	2	242	1	0	0	0	0	1	0	0	0	14607	942	33	4	1387	4	SLC36A2	5	150726918	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	9869872	150726918	30188342	44	14848											
UIMC1	51720	hgsc.bcm.edu	37	chr5	176395811	176395811	+	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	tccccaaaaccttttttattAaggagctgcctctgagccat	10	13	6	12	0	1	1	0	1	1	0	2	2	2	2	5	1	4	1	5	1	4	4			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr5:176395811A>T	ENST00000377227.4	-	6	1077	c.945T>A	c.(943-945)ctT>ctA	p.L315L	UIMC1_ENST00000511320.1_Silent_p.L315L|UIMC1_ENST00000377219.2_Silent_p.L315L|UIMC1_ENST00000503273.1_5'UTR|UIMC1_ENST00000506128.1_Intron			Q96RL1	UIMC1_HUMAN	ubiquitin interaction motif containing 1	315	AIR.				double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)	BRCA1-A complex (GO:0070531)|nucleus (GO:0005634)	histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)			NS(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	21	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTTTTTTATTAAGGAGCTGCC	0.458																																					p.L315L		Atlas-SNP	.											.	UIMC1	55	.	0			c.T945A						PASS	.						59	60	60					5																	176395811		2203	4300	6503	SO:0001819	synonymous_variant	51720	exon6			TTTATTAAGGAGC	AF349313	CCDS4408.1	5q35.2	2008-02-05			ENSG00000087206	ENSG00000087206			30298	protein-coding gene	gene with protein product	"receptor associated protein 80"	609433				12080054	Standard	NM_001199297		Approved	RAP80	uc021yin.1	Q96RL1	OTTHUMG00000130852	ENST00000377227.4:c.945T>A	chr5.hg19:g.176395811A>T		89.0	0.0	.		92.0	39.0	.	NM_016290	A8MSA1|B3KMZ1|B4E3N2|Q5XKQ1|Q7Z3W7|Q8N5B9|Q9BZR1|Q9BZR5|Q9UHX7	Silent	SNP	ENST00000377227.4	hg19	CCDS4408.1																																																																																			.	.	.	none		0.458	UIMC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253422.1	NM_016290		T	176395811	A	T	176395811	2	4	242	1	0	0	0	0	0	0	0	1	16983	349	13	5		5	UIMC1	5	176395811	Silent	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10	25668893	176395811	4519449	45	14849											
C6orf27	80737	hgsc.bcm.edu	37	chr6	31744458	31744458	+	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	ggggcagccagcaggctccaGatgttggggaagaaggcaga	11	4	18	8	0	0	3	0	0	0	3	1	4	1	4	2	6	2	5	2	6	2	1			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr6:31744458G>C	ENST00000375688.4	-	2	299	c.99C>G	c.(97-99)atC>atG	p.I33M	VWA7_ENST00000467576.1_5'UTR|VWA7_ENST00000375686.3_Missense_Mutation_p.I33M|Y_RNA_ENST00000364685.1_RNA|VWA7_ENST00000447450.1_Missense_Mutation_p.I33M			Q9Y334	VWA7_HUMAN	von Willebrand factor A domain containing 7	33						extracellular region (GO:0005576)											GCAGGCTCCAGATGTTGGGGA	0.652																																					p.I33M		Atlas-SNP	.											.	.	.	.	0			c.C99G						PASS	.						11	6	8					6																	31744458		1433	2570	4003	SO:0001583	missense	80737	exon2			GCTCCAGATGTTG		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.99C>G	chr6.hg19:g.31744458G>C	ENSP00000364840:p.Ile33Met	120.0	0.0	.		80.0	45.0	.	NM_025258	A2BEX8|A6NHR6|B0V041|Q5SSR5|Q96QC8|Q9UMP9	Missense_Mutation	SNP	ENST00000375688.4	hg19	CCDS4721.2	.	.	.	.	.	.	.	.	.	.	G	17.62	3.433786	0.62955	.	.	ENSG00000204396	ENST00000375688;ENST00000375686;ENST00000447450	T;T;T	0.14893	2.47;2.47;2.47	5.07	5.07	0.68467	.	0.189670	0.43747	D	0.000529	T	0.11452	0.0279	L	0.36672	1.1	0.31565	N	0.657011	P	0.41131	0.739	P	0.44518	0.452	T	0.01675	-1.1298	10	0.72032	D	0.01	-11.1767	15.9908	0.80202	0.0:0.0:1.0:0.0	.	33	Q9Y334	G7C_HUMAN	M	33	ENSP00000364840:I33M;ENSP00000364838:I33M;ENSP00000390554:I33M	ENSP00000364838:I33M	I	-	3	3	C6orf27	31852437	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.076000	0.41548	2.646000	0.89796	0.557000	0.71058	ATC	.	.	.	none		0.652	VWA7-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076233.2	NM_025258		C	31744458	G	C	31744458	3	2	242	1	0	0	0	0	1	0	0	0	2364	932	33	4	2639	4	C6orf27	6	31744458	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10		31744458	139370609	46	14850											
PPT2	9374	hgsc.bcm.edu	37	chr6	32122818	32122818	+	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	ttcccacagacacaccccggGactgtggtgacagtgctcga	9	7	11	14	2	0	2	0	1	0	1	2	4	1	3	3	2	1	1	3	2	0	1			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr6:32122818G>T	ENST00000324816.6	+	3	763	c.195G>T	c.(193-195)ggG>ggT	p.G65G	PPT2-EGFL8_ENST00000453656.2_3'UTR|PRRT1_ENST00000375152.2_5'Flank|PPT2_ENST00000375137.2_Silent_p.G65G|PPT2_ENST00000375143.2_Silent_p.G65G|PRRT1_ENST00000375150.2_5'Flank|PPT2_ENST00000395523.1_Silent_p.G65G|PPT2_ENST00000493548.1_3'UTR|PPT2_ENST00000437001.2_Intron|PPT2_ENST00000361568.2_Silent_p.G71G|PPT2_ENST00000445576.2_Silent_p.G65G|PPT2-EGFL8_ENST00000422437.1_Silent_p.G65G			Q9UMR5	PPT2_HUMAN	palmitoyl-protein thioesterase 2	65					cellular protein modification process (GO:0006464)|macromolecule depalmitoylation (GO:0098734)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	palmitoyl hydrolase activity (GO:0098599)|palmitoyl-(protein) hydrolase activity (GO:0008474)|thiolester hydrolase activity (GO:0016790)			NS(1)|endometrium(2)|large_intestine(2)|lung(10)|prostate(1)|urinary_tract(1)	17						CACACCCCGGGACTGTGGTGA	0.622																																					p.G71G		Atlas-SNP	.											.	PPT2	19	.	0			c.G213T						PASS	.						75	72	73					6																	32122818		1509	2708	4217	SO:0001819	synonymous_variant	9374	exon3			CCCCGGGACTGTG	AF020543	CCDS4740.1, CCDS4742.1	6p21.3	2012-07-02			ENSG00000221988	ENSG00000221988	3.1.2.22		9326	protein-coding gene	gene with protein product		603298				9341199, 10051407	Standard	NM_138717		Approved		uc003nzw.3	Q9UMR5	OTTHUMG00000031257	ENST00000324816.6:c.195G>T	chr6.hg19:g.32122818G>T		96.0	0.0	.		93.0	48.0	.	NM_138717	A2ABC9|A2ABD1|A2ARM7|A2BFH7|A2BFH9|A2BFI2|A8K9L4|B0S868|G8JLE1|O14799|Q0P6K0|Q5JP13|Q5JP14|Q5JQF0|Q5SSX4|Q5SSX5|Q5SSX6|Q5STJ4|Q5STJ5|Q5STJ6|Q6FI80|Q99945	Silent	SNP	ENST00000324816.6	hg19	CCDS4742.1																																																																																			.	.	.	none		0.622	PPT2-207	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076552.4	NM_138717		T	32122818	G	T	32122818	2	4	242	1	0	0	0	0	0	0	0	1	12422	1161	41	4		4	PPT2	6	32122818	Silent	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	378360	32122818	138992249	47	14851											
TRERF1	55809	hgsc.bcm.edu	37	chr6	42204006	42204006	+	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	tggcccagggcctgcaggggCggcccctccgtgggagccag	4	4	18	15	2	0	0	0	0	0	0	1	1	1	1	6	6	2	1	6	6	0	0			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr6:42204006C>A	ENST00000372922.4	-	16	3565	c.3003G>T	c.(3001-3003)ccG>ccT	p.P1001P	TRERF1_ENST00000354325.2_Silent_p.P918P|TRERF1_ENST00000541110.1_Silent_p.P1021P|TRERF1_ENST00000340840.2_Silent_p.P918P|TRERF1_ENST00000372917.4_Silent_p.P918P	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	1001	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)			CCTGCAGGGGCGGCCCCTCCG	0.617																																					p.P1001P		Atlas-SNP	.											.	TRERF1	124	.	0			c.G3003T						PASS	.						44	50	48					6																	42204006		2203	4300	6503	SO:0001819	synonymous_variant	55809	exon16			CAGGGGCGGCCCC	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.3003G>T	chr6.hg19:g.42204006C>A		107.0	0.0	.		82.0	33.0	.	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Silent	SNP	ENST00000372922.4	hg19	CCDS4867.1																																																																																			.	.	.	none		0.617	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502		A	42204006	C	A	42204006	2	1	242	1	0	0	0	0	0	0	0	1	16487	755	27	4		4	TRERF1	6	42204006	Silent	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10	10081188	42204006	128911061	48	14852											
EYS	346007	hgsc.bcm.edu	37	chr6	65301559	65301559	+	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	ttgtgtaggaaaaataaaatCtgacattaaggaagacatga	19	10	9	3	0	1	3	0	2	1	1	1	5	1	5	0	2	0	1	0	2	7	4			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr6:65301559C>A	ENST00000370621.3	-	26	4727	c.4201G>T	c.(4201-4203)Gat>Tat	p.D1401Y	EYS_ENST00000370616.2_Missense_Mutation_p.D1401Y|EYS_ENST00000503581.1_Missense_Mutation_p.D1401Y			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1401					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						AAAATAAAATCTGACATTAAG	0.398																																					p.D1401Y		Atlas-SNP	.											.	EYS	527	.	0			c.G4201T						PASS	.						71	67	68					6																	65301559		692	1591	2283	SO:0001583	missense	346007	exon26			TAAAATCTGACAT		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.4201G>T	chr6.hg19:g.65301559C>A	ENSP00000359655:p.Asp1401Tyr	77.0	0.0	.		81.0	31.0	.	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	hg19		.	.	.	.	.	.	.	.	.	.	C	12.58	1.980085	0.34942	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	D;D;D	0.85258	-1.96;-1.94;-1.94	5.74	2.61	0.31194	.	.	.	.	.	T	0.70631	0.3246	N	0.08118	0	0.80722	D	1	D;D	0.65815	0.995;0.976	P;P	0.61201	0.885;0.556	T	0.73375	-0.4002	9	0.66056	D	0.02	.	5.5222	0.16939	0.0:0.6394:0.1555:0.2051	.	1401;1401	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	Y	1401	ENSP00000424243:D1401Y;ENSP00000359655:D1401Y;ENSP00000359650:D1401Y	ENSP00000359650:D1401Y	D	-	1	0	EYS	65358280	0.961000	0.32948	0.110000	0.21437	0.785000	0.44390	-0.091000	0.11146	0.206000	0.20587	0.591000	0.81541	GAT	.	.	.	none		0.398	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		A	65301559	C	A	65301559	3	1	242	1	0	0	0	0	1	0	0	0	5334	913	32	4	5150	4	EYS	6	65301559	Missense_Mutation	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10	23097553	65301559	105813508	49	14853											
KPNA5	3841	hgsc.bcm.edu	37	chr6	117043373	117043373	+	Missense_Mutation	SNP	T	T	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	acgtgtgttgggccctttctTatctctccgatggacccaat	6	14	9	12	2	2	0	0	0	2	0	4	2	3	1	3	2	0	1	3	2	2	3			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr6:117043373T>G	ENST00000368564.1	+	9	989	c.841T>G	c.(841-843)Tat>Gat	p.Y281D	KPNA5_ENST00000356348.1_Missense_Mutation_p.Y281D			O15131	IMA6_HUMAN	karyopherin alpha 5 (importin alpha 6)	278					cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)	protein transporter activity (GO:0008565)			breast(6)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0298)|all cancers(137;0.0461)|OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.212)		GGCCCTTTCTTATCTCTCCGA	0.413																																					p.Y281D		Atlas-SNP	.											.	KPNA5	57	.	0			c.T841G						PASS	.						151	132	138					6																	117043373		2203	4300	6503	SO:0001583	missense	3841	exon9			CTTTCTTATCTCT	AF005361	CCDS5111.1	6q22.2	2013-02-14			ENSG00000196911	ENSG00000196911		"Importins", "Armadillo repeat containing"	6398	protein-coding gene	gene with protein product		604545				9395085	Standard	NM_002269		Approved	SRP6, IPOA6	uc003pxh.3	O15131	OTTHUMG00000015448	ENST00000368564.1:c.841T>G	chr6.hg19:g.117043373T>G	ENSP00000357552:p.Tyr281Asp	84.0	0.0	.		79.0	36.0	.	NM_002269	B2RAI5|Q86X23	Missense_Mutation	SNP	ENST00000368564.1	hg19	CCDS5111.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.855264	0.91355	.	.	ENSG00000196911	ENST00000368564;ENST00000356348	T;T	0.70282	-0.47;-0.47	5.81	5.81	0.92471	Armadillo-like helical (1);Armadillo-type fold (1);	0.077905	0.52532	D	0.000062	D	0.85999	0.5828	M	0.92970	3.365	0.54753	D	0.999981	D	0.89917	1.0	D	0.91635	0.999	D	0.89578	0.3818	10	0.87932	D	0	.	16.1671	0.81777	0.0:0.0:0.0:1.0	.	278	O15131	IMA5_HUMAN	D	281	ENSP00000357552:Y281D;ENSP00000348704:Y281D	ENSP00000348704:Y281D	Y	+	1	0	KPNA5	117150066	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.414000	0.80117	2.224000	0.72417	0.528000	0.53228	TAT	.	.	.	none		0.413	KPNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041967.1	NM_002269		G	117043373	T	G	117043373	3	3	242	1	0	0	0	0	1	0	0	0	8440	1754	61	5	875	5	KPNA5	6	117043373	Missense_Mutation	SNP	T	TCGA-SX-A71S-01A-11D-A33Q-10	51741814	117043373	54071694	50	14854											
GPRC6A	222545	hgsc.bcm.edu	37	chr6	117127768	117127768	+	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	gactcaaatcagtgtccttgAcatatgcgcaggcagataaa	14	9	9	9	1	2	2	2	1	0	1	3	3	3	2	1	1	1	2	1	1	4	3			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr6:117127768A>T	ENST00000310357.3	-	3	1121	c.1100T>A	c.(1099-1101)gTc>gAc	p.V367D	GPRC6A_ENST00000368549.3_Missense_Mutation_p.V367D|GPRC6A_ENST00000530250.1_Intron	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	367					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)		AGTGTCCTTGACATATGCGCA	0.403																																					p.V367D		Atlas-SNP	.											.	GPRC6A	152	.	0			c.T1100A						PASS	.						103	93	96					6																	117127768		2203	4299	6502	SO:0001583	missense	222545	exon3			TCCTTGACATATG	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.1100T>A	chr6.hg19:g.117127768A>T	ENSP00000309493:p.Val367Asp	61.0	0.0	.		84.0	37.0	.	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Missense_Mutation	SNP	ENST00000310357.3	hg19	CCDS5112.1	.	.	.	.	.	.	.	.	.	.	A	10.68	1.417587	0.25552	.	.	ENSG00000173612	ENST00000310357;ENST00000368549	D;D	0.85556	-2.0;-2.0	5.18	0.0122	0.14090	Extracellular ligand-binding receptor (1);	0.459032	0.18165	N	0.149641	T	0.60444	0.2269	N	0.25647	0.755	0.09310	N	1	P;P	0.44946	0.846;0.794	P;P	0.46629	0.466;0.522	T	0.62969	-0.6741	10	0.12430	T	0.62	.	9.2807	0.37727	0.7229:0.0:0.2771:0.0	.	367;367	Q5T6X5-3;Q5T6X5	.;GPC6A_HUMAN	D	367	ENSP00000309493:V367D;ENSP00000357537:V367D	ENSP00000309493:V367D	V	-	2	0	GPRC6A	117234461	0.000000	0.05858	0.058000	0.19502	0.605000	0.37080	0.342000	0.19926	-0.057000	0.13199	0.528000	0.53228	GTC	.	.	.	none		0.403	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2			T	117127768	A	T	117127768	3	4	242	1	0	0	0	0	1	0	0	0	6735	275	10	5	1696	5	GPRC6A	6	117127768	Missense_Mutation	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10	84395	117127768	53987299	51	14855											
GPR126	57211	hgsc.bcm.edu	37	chr6	142691326	142691326	+	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	gttgccgtgtccttaaggaaTcaaaaggtcattttacccca	11	12	8	10	1	2	0	2	0	0	0	3	1	3	1	4	2	2	1	4	2	5	4			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr6:142691326T>A	ENST00000230173.6	+	4	941	c.465T>A	c.(463-465)aaT>aaA	p.N155K	GPR126_ENST00000545477.1_3'UTR|GPR126_ENST00000367608.2_Missense_Mutation_p.N155K|GPR126_ENST00000367609.3_Missense_Mutation_p.N155K|GPR126_ENST00000296932.8_Missense_Mutation_p.N155K	NM_020455.5	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126	155	Pentaxin.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(12)|lung(10)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		CCTTAAGGAATCAAAAGGTCA	0.408																																					p.N155K		Atlas-SNP	.											.	GPR126	192	.	0			c.T465A						PASS	.						108	96	100					6																	142691326		1894	4119	6013	SO:0001583	missense	57211	exon4			AAGGAATCAAAAG	AK027843	CCDS47489.1, CCDS47490.1, CCDS47491.1, CCDS55064.1	6q23.1-q24.3	2014-08-08			ENSG00000112414	ENSG00000112414		"-", "GPCR / Class B : Orphans"	13841	protein-coding gene	gene with protein product		612243				12565841	Standard	NM_001032395		Approved	FLJ14937	uc010khe.3	Q86SQ4	OTTHUMG00000015709	ENST00000230173.6:c.465T>A	chr6.hg19:g.142691326T>A	ENSP00000230173:p.Asn155Lys	108.0	0.0	.		79.0	33.0	.	NM_198569	Q5TGN7|Q6DHZ4|Q6F3F5|Q6F3F6|Q6F3F7|Q6F3F8|Q6MZU7|Q8IXA4|Q8NC14|Q96JW0	Missense_Mutation	SNP	ENST00000230173.6	hg19	CCDS47490.1	.	.	.	.	.	.	.	.	.	.	T	19.73	3.882482	0.72294	.	.	ENSG00000112414	ENST00000230173;ENST00000367608;ENST00000296932;ENST00000367609;ENST00000541199	T;T;T;T;T	0.60040	0.22;0.22;0.22;0.22;1.96	5.66	4.49	0.54785	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.080775	0.52532	D	0.000061	T	0.65207	0.2669	M	0.71581	2.175	0.43372	D	0.995461	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.992	D;D;D;D;P	0.91635	0.999;0.999;0.999;0.998;0.856	T	0.70249	-0.4924	10	0.72032	D	0.01	.	10.8928	0.47004	0.0:0.0763:0.0:0.9237	.	155;155;155;155;154	Q86SQ4-4;Q86SQ4-3;Q86SQ4-2;Q86SQ4;F5H2L1	.;.;.;GP126_HUMAN;.	K	155;155;155;155;154	ENSP00000230173:N155K;ENSP00000356580:N155K;ENSP00000296932:N155K;ENSP00000356581:N155K;ENSP00000446287:N154K	ENSP00000230173:N155K	N	+	3	2	GPR126	142733019	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.705000	0.47127	0.971000	0.38288	0.528000	0.53228	AAT	.	.	.	none		0.408	GPR126-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042487.2			A	142691326	T	A	142691326	3	1	242	1	0	0	0	0	1	0	0	0	6647	1432	50	5	479	5	GPR126	6	142691326	Missense_Mutation	SNP	T	TCGA-SX-A71S-01A-11D-A33Q-10	25563558	142691326	28423741	52	14856											
WBSCR28	135886	hgsc.bcm.edu	37	chr7	73280192	73280192	+	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	ttttgccagagcaagaaactCccagagaataaatgtatccc	15	9	7	10	0	0	3	0	0	0	3	2	4	2	3	3	0	3	2	3	0	6	4			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr7:73280192C>T	ENST00000320531.2	+	3	823	c.787C>T	c.(787-789)Ccc>Tcc	p.P263S		NM_182504.3	NP_872310.2	Q6UE05	WBS28_HUMAN	Williams-Beuren syndrome chromosome region 28	263						integral component of membrane (GO:0016021)				breast(2)|kidney(2)|lung(6)|skin(1)	11		Lung NSC(55;0.159)				GCAAGAAACTCCCAGAGAATA	0.542																																					p.P263S		Atlas-SNP	.											.	WBSCR28	24	.	0			c.C787T						PASS	.						84	93	90					7																	73280192		1999	4170	6169	SO:0001583	missense	135886	exon3			GAAACTCCCAGAG	BC030643	CCDS43597.1	7q11.23	2006-07-04			ENSG00000175877	ENSG00000175877			23018	protein-coding gene	gene with protein product		612547				8812460	Standard	NM_182504		Approved	MGC26719	uc003tzk.2	Q6UE05	OTTHUMG00000157243	ENST00000320531.2:c.787C>T	chr7.hg19:g.73280192C>T	ENSP00000316775:p.Pro263Ser	28.0	0.0	.		31.0	13.0	.	NM_182504	Q6UE04|Q8NHP4	Missense_Mutation	SNP	ENST00000320531.2	hg19	CCDS43597.1	.	.	.	.	.	.	.	.	.	.	C	12.06	1.824780	0.32237	.	.	ENSG00000175877	ENST00000320531	T	0.34072	1.38	3.55	3.55	0.40652	.	0.000000	0.40064	N	0.001182	T	0.45013	0.1321	L	0.34521	1.04	0.22975	N	0.998486	D	0.76494	0.999	D	0.71656	0.974	T	0.17018	-1.0383	10	0.87932	D	0	-3.4254	11.0008	0.47604	0.0:1.0:0.0:0.0	.	263	Q6UE05	WBS28_HUMAN	S	263	ENSP00000316775:P263S	ENSP00000316775:P263S	P	+	1	0	WBSCR28	72918128	0.004000	0.15560	0.662000	0.29724	0.009000	0.06853	0.329000	0.19698	2.302000	0.77476	0.644000	0.83932	CCC	.	.	.	none		0.542	WBSCR28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348130.1	NM_182504		T	73280192	C	T	73280192	3	4	242	1	0	0	0	0	1	0	0	0	17279	855	30	2	797	2	WBSCR28	7	73280192	Missense_Mutation	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10		73280192	85858471	53	14857											
PCLO	27445	hgsc.bcm.edu	37	chr7	82582455	82582455	+	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	ctttggagggtgatcccaagGgccaactggtaattgcttga	9	11	13	8	0	0	2	0	2	0	0	1	3	1	3	2	4	2	2	2	4	3	4			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr7:82582455G>A	ENST00000333891.9	-	5	8151	c.7814C>T	c.(7813-7815)cCc>cTc	p.P2605L	PCLO_ENST00000437081.1_5'Flank|PCLO_ENST00000423517.2_Missense_Mutation_p.P2605L	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						TGATCCCAAGGGCCAACTGGT	0.428																																					p.P2605L		Atlas-SNP	.											.	PCLO	1506	.	0			c.C7814T						PASS	.						144	136	138					7																	82582455		1852	4102	5954	SO:0001583	missense	27445	exon5			CCCAAGGGCCAAC	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.7814C>T	chr7.hg19:g.82582455G>A	ENSP00000334319:p.Pro2605Leu	112.0	0.0	.		164.0	108.0	.	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	6.685	0.495051	0.12762	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.17528	2.27;2.28	5.04	4.16	0.48862	.	.	.	.	.	T	0.19485	0.0468	L	0.54323	1.7	0.80722	D	1	B;B	0.18461	0.028;0.028	B;B	0.19946	0.027;0.027	T	0.03000	-1.1084	9	0.87932	D	0	.	12.8617	0.57918	0.0805:0.0:0.9195:0.0	.	2605;2605	Q9Y6V0-5;Q9Y6V0-6	.;.	L	2536;2605;2605	ENSP00000334319:P2605L;ENSP00000388393:P2605L	ENSP00000334319:P2605L	P	-	2	0	PCLO	82420391	1.000000	0.71417	0.968000	0.41197	0.748000	0.42578	3.224000	0.51238	1.116000	0.41820	0.591000	0.81541	CCC	.	.	.	none		0.428	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82582455	G	A	82582455	3	1	242	1	0	0	0	0	1	0	0	0	11590	1232	43	2	7715	2	PCLO	7	82582455	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	9302263	82582455	76556208	54	14858											
MET	4233	hgsc.bcm.edu	37	chr7	116423414	116423414	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggtcttgccagagacatgtAtgataaagaatactatagtg	14	12	10	5	0	1	3	0	1	1	2	1	4	1	3	1	1	2	1	1	1	7	6	rs121913246		TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr7:116423414A>G	ENST00000318493.6	+	19	3930	c.3743A>G	c.(3742-3744)tAt>tGt	p.Y1248C	MET_ENST00000539704.1_Missense_Mutation_p.Y100C|MET_ENST00000397752.3_Missense_Mutation_p.Y1230C			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.Y1248C(8)		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)			AGAGACATGTATGATAAAGAA	0.393			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.Y1248C		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,rectum,carcinoma,-1,9	MET	412	.	8	Substitution - Missense(8)	upper_aerodigestive_tract(7)|kidney(1)	c.A3743G	GRCh37	CM970947	MET	M	rs121913246	PASS	.						105	99	101					7																	116423414		1843	4094	5937	SO:0001583	missense	4233	exon19	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	ACATGTATGATAA	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.3743A>G	chr7.hg19:g.116423414A>G	ENSP00000317272:p.Tyr1248Cys	119.0	0.0	.		133.0	87.0	.	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	A	17.26	3.345049	0.61073	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000539704	D;D;D	0.83250	-1.7;-1.7;-1.7	5.46	5.46	0.80206	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.91270	0.7248	M	0.82132	2.575	0.58432	A	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92475	0.5988	9	0.87932	D	0	.	15.824	0.78683	1.0:0.0:0.0:0.0	.	1248;1230	P08581-2;P08581	.;MET_HUMAN	C	1230;1248;100	ENSP00000380860:Y1230C;ENSP00000317272:Y1248C;ENSP00000445020:Y100C	ENSP00000317272:Y1248C	Y	+	2	0	MET	116210650	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.960000	0.70348	2.197000	0.70478	0.460000	0.39030	TAT	.	.	.	weak		0.393	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			G	116423414	A	G	116423414	3	3	242	1	0	0	0	0	1	0	0	0	9492	449	16	3	3813	3	MET	7	116423414	Missense_Mutation	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10	33840959	116423414	42715249	55	14859											
CCDC136	64753	hgsc.bcm.edu	37	chr7	128441373	128441373	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcaagcagcagaggattcCgcaactgaacatgagagtga	14	5	13	9	2	0	4	0	3	0	2	1	6	1	5	1	2	4	4	1	2	3	1			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr7:128441373C>T	ENST00000297788.4	+	4	847	c.480C>T	c.(478-480)tcC>tcT	p.S160S	CCDC136_ENST00000464832.1_Silent_p.S210S|CCDC136_ENST00000378685.4_Silent_p.S210S|CCDC136_ENST00000487361.1_Silent_p.S160S	NM_022742.4	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	160	Glu-rich.					integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)	24						CAGAGGATTCCGCAACTGAAC	0.483																																					p.S210S		Atlas-SNP	.											.	CCDC136	170	.	0			c.C630T						PASS	.						63	66	65					7																	128441373		2037	4186	6223	SO:0001819	synonymous_variant	64753	exon5			GGATTCCGCAACT		CCDS47704.1, CCDS56510.1	7q33	2007-08-01			ENSG00000128596	ENSG00000128596			22225	protein-coding gene	gene with protein product		611902				15112360	Standard	NM_022742		Approved	KIAA1793, NAG6, DKFZP434G156	uc003vnv.2	Q96JN2	OTTHUMG00000158310	ENST00000297788.4:c.480C>T	chr7.hg19:g.128441373C>T		68.0	0.0	.		115.0	41.0	.	NM_001201372	A4D1K1|A7MCY7|A8MYA7|Q6ZVK7|Q9H8M3|Q9UFE1	Silent	SNP	ENST00000297788.4	hg19	CCDS47704.1	.	.	.	.	.	.	.	.	.	.	T	2.942	-0.218780	0.06101	.	.	ENSG00000128596	ENST00000494552	.	.	.	5.65	-11.3	0.00108	.	.	.	.	.	T	0.39279	0.1072	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46527	-0.9185	4	.	.	.	-8.6599	4.439	0.11564	0.2265:0.4454:0.1525:0.1756	.	.	.	.	L	37	.	.	P	+	2	0	CCDC136	128228609	0.000000	0.05858	0.011000	0.14972	0.310000	0.27922	-4.697000	0.00197	-2.356000	0.00613	-1.213000	0.01624	CCG	.	.	.	none		0.483	CCDC136-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350641.1	NM_022742		T	128441373	C	T	128441373	2	4	242	1	0	0	0	0	0	0	0	1	2772	639	23	1		1	CCDC136	7	128441373	Silent	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10	12017959	128441373	30697290	56	14860											
CPA1	1357	hgsc.bcm.edu	37	chr7	130022030	130022030	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggcaacacctatgaagggCgtcccatttacgtgctgaag	10	10	11	10	2	0	2	0	2	0	0	1	2	1	2	2	2	3	2	2	2	5	4			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr7:130022030C>T	ENST00000011292.3	+	4	613	c.463C>T	c.(463-465)Cgt>Tgt	p.R155C	CPA1_ENST00000484324.1_Missense_Mutation_p.R67C	NM_001868.2	NP_001859.1	P15085	CBPA1_HUMAN	carboxypeptidase A1 (pancreatic)	155					proteolysis (GO:0006508)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)	21	Melanoma(18;0.0435)					CTATGAAGGGCGTCCCATTTA	0.557																																					p.R155C		Atlas-SNP	.											.	CPA1	73	.	0			c.C463T						PASS	.						130	101	111					7																	130022030		2203	4300	6503	SO:0001583	missense	1357	exon4			GAAGGGCGTCCCA		CCDS5820.1	7q32	2012-02-10			ENSG00000091704	ENSG00000091704	3.4.17.1		2296	protein-coding gene	gene with protein product	"pancreatic carboxypeptidase A"	114850		CPA			Standard	NM_001868		Approved		uc003vpx.3	P15085	OTTHUMG00000157826	ENST00000011292.3:c.463C>T	chr7.hg19:g.130022030C>T	ENSP00000011292:p.Arg155Cys	77.0	0.0	.		108.0	6.0	.	NM_001868	A4D1M1|Q53XU0|Q9BS67|Q9UCF2	Missense_Mutation	SNP	ENST00000011292.3	hg19	CCDS5820.1	.	.	.	.	.	.	.	.	.	.	C	16.17	3.048277	0.55110	.	.	ENSG00000091704	ENST00000481342;ENST00000011292;ENST00000476062;ENST00000484324	T;T;T;T	0.28895	1.59;1.59;1.59;1.59	5.46	5.46	0.80206	Peptidase M14, carboxypeptidase A (3);	0.046442	0.85682	D	0.000000	T	0.75265	0.3826	H	0.99619	4.66	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.996	D	0.86816	0.2001	10	0.87932	D	0	.	16.4592	0.84031	0.0:1.0:0.0:0.0	.	67;155	B4DDW9;P15085	.;CBPA1_HUMAN	C	67;155;67;67	ENSP00000420218:R67C;ENSP00000011292:R155C;ENSP00000419408:R67C;ENSP00000419497:R67C	ENSP00000011292:R155C	R	+	1	0	CPA1	129809266	0.992000	0.36948	0.143000	0.22291	0.163000	0.22366	3.032000	0.49736	2.576000	0.86940	0.561000	0.74099	CGT	.	.	.	none		0.557	CPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349736.2	NM_001868		T	130022030	C	T	130022030	3	4	242	1	0	0	0	0	1	0	0	0	3791	768	27	1	477	1	CPA1	7	130022030	Missense_Mutation	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10	1580657	130022030	29116633	57	14861											
HEY1	23462	hgsc.bcm.edu	37	chr8	80677948	80677948	+	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	taacgcgcaacttctgccagGcattcccgaaatcccaaact	12	8	6	15	3	1	0	0	0	1	0	3	1	3	0	3	1	4	2	3	1	4	3			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr8:80677948G>C	ENST00000354724.3	-	5	589	c.390C>G	c.(388-390)tgC>tgG	p.C130W	RP11-27N21.3_ENST00000607172.1_lincRNA|HEY1_ENST00000523976.1_Missense_Mutation_p.C40W|HEY1_ENST00000337919.5_Missense_Mutation_p.C134W|HEY1_ENST00000435063.2_5'UTR	NM_012258.3	NP_036390.3	Q9Y5J3	HEY1_HUMAN	hes-related family bHLH transcription factor with YRPW motif 1	130	Orange. {ECO:0000255|PROSITE- ProRule:PRU00380}.				angiogenesis (GO:0001525)|anterior/posterior axis specification (GO:0009948)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular valve formation (GO:0003190)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac septum morphogenesis (GO:0060411)|cardiac ventricle morphogenesis (GO:0003208)|cellular response to glucocorticoid stimulus (GO:0071385)|dorsal aorta morphogenesis (GO:0035912)|endocardial cushion morphogenesis (GO:0003203)|endocardial cushion to mesenchymal transition involved in heart valve formation (GO:0003199)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|heart trabecula formation (GO:0060347)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000820)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|osteoblast development (GO:0002076)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary valve morphogenesis (GO:0003184)|regulation of vasculogenesis (GO:2001212)|transcription from RNA polymerase II promoter (GO:0006366)|umbilical cord morphogenesis (GO:0036304)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	microsatellite binding (GO:0035939)|protein binding transcription factor activity (GO:0000988)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)		HEY1/NCOA2(10)	cervix(1)|kidney(2)|large_intestine(5)|lung(14)	22	all_lung(9;5.1e-05)		Epithelial(68;0.076)|all cancers(69;0.179)			CTTCTGCCAGGCATTCCCGAA	0.498			T	NCOA2	mesenchymal chondrosarcoma						OREG0018837	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C134W		Atlas-SNP	.		Dom	yes		8	8q21	23462	hairy/enhancer-of-split related with YRPW motif 1		M	.	HEY1	51	.	0			c.C402G						PASS	.						61	64	63					8																	80677948		2203	4300	6503	SO:0001583	missense	23462	exon5			TGCCAGGCATTCC	AF151522	CCDS6225.1, CCDS43749.1, CCDS64915.1	8q21	2013-10-17	2013-10-17					"Basic helix-loop-helix proteins"	4880	protein-coding gene	gene with protein product		602953	"hairy/enhancer-of-split related with YRPW motif 1"			10415358, 10403790	Standard	NM_001040708		Approved	HESR-1, CHF2, HESR1, HRT-1, CHF-2, HERP2, BHLHb31	uc003ybl.3	Q9Y5J3		ENST00000354724.3:c.390C>G	chr8.hg19:g.80677948G>C	ENSP00000346761:p.Cys130Trp	144.0	0.0	.	1200	116.0	45.0	.	NM_001040708	B2R883|Q5TZS3|Q8NAM2|Q9NYP4	Missense_Mutation	SNP	ENST00000354724.3	hg19	CCDS6225.1	.	.	.	.	.	.	.	.	.	.	G	16.37	3.104243	0.56291	.	.	ENSG00000164683	ENST00000354724;ENST00000542205;ENST00000337919;ENST00000523976;ENST00000518733	D;D;D;D	0.89050	-2.46;-2.46;-2.46;-2.46	4.98	4.98	0.66077	Orange subgroup (1);Orange (2);	0.000000	0.85682	D	0.000000	D	0.96234	0.8772	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	0.97377	0.9980	10	0.87932	D	0	-1.6691	18.6141	0.91296	0.0:0.0:1.0:0.0	.	130;134	Q9Y5J3;Q9Y5J3-2	HEY1_HUMAN;.	W	130;134;134;40;92	ENSP00000346761:C130W;ENSP00000338272:C134W;ENSP00000429792:C40W;ENSP00000429705:C92W	ENSP00000338272:C134W	C	-	3	2	HEY1	80840503	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.614000	0.46359	2.456000	0.83038	0.561000	0.74099	TGC	.	.	.	none		0.498	HEY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000379516.1	NM_012258		C	80677948	G	C	80677948	3	2	242	1	0	0	0	0	1	0	0	0	7085	1195	42	4	528	4	HEY1	8	80677948	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10		80677948	65686074	58	14862											
FAM135B	51059	hgsc.bcm.edu	37	chr8	139165353	139165353	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagacaaggtcttccctaaaAgataaattgctatttaccat	16	12	5	8	0	1	2	0	0	1	2	2	2	2	2	2	1	2	1	2	1	8	7			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr8:139165353A>G	ENST00000395297.1	-	13	1535	c.1365T>C	c.(1363-1365)tcT>tcC	p.S455S		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	455										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)			CTTCCCTAAAAGATAAATTGC	0.378										HNSCC(54;0.14)																											p.S455S		Atlas-SNP	.											.	FAM135B	423	.	0			c.T1365C						PASS	.						73	70	71					8																	139165353		1881	4106	5987	SO:0001819	synonymous_variant	51059	exon13			CCTAAAAGATAAA	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.1365T>C	chr8.hg19:g.139165353A>G		203.0	0.0	.		191.0	76.0	.	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Silent	SNP	ENST00000395297.1	hg19	CCDS6375.2																																																																																			.	.	.	none		0.378	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		G	139165353	A	G	139165353	2	3	242	1	0	0	0	0	0	0	0	1	5453	59	3	3		3	FAM135B	8	139165353	Silent	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10	58487405	139165353	7198669	59	14863											
ZNF16	7564	hgsc.bcm.edu	37	chr8	146156157	146156157	+	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	tgaatcaactggtgtttgatCaactttgatcgctggctgaa	10	14	10	7	1	2	4	2	4	0	0	3	4	2	4	0	2	2	3	0	2	4	2			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr8:146156157C>A	ENST00000276816.4	-	4	2202	c.2016G>T	c.(2014-2016)ttG>ttT	p.L672F	ZNF16_ENST00000394909.2_Missense_Mutation_p.L672F	NM_001029976.2	NP_001025147.2	P17020	ZNF16_HUMAN	zinc finger protein 16	672					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)		GGTGTTTGATCAACTTTGATC	0.527																																					p.L672F		Atlas-SNP	.											.	ZNF16	80	.	0			c.G2016T						PASS	.						177	165	169					8																	146156157		2203	4300	6503	SO:0001583	missense	7564	exon3			TTTGATCAACTTT	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.2016G>T	chr8.hg19:g.146156157C>A	ENSP00000276816:p.Leu672Phe	48.0	0.0	.		37.0	15.0	.	NM_006958	B3KXM4|D3DWP2|Q45SH7|Q96FG0|Q9NRA4	Missense_Mutation	SNP	ENST00000276816.4	hg19	CCDS6437.1	.	.	.	.	.	.	.	.	.	.	C	11.87	1.768564	0.31320	.	.	ENSG00000170631	ENST00000276816;ENST00000394909	T;T	0.68624	-0.34;-0.34	4.03	3.09	0.35607	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.76485	0.3994	M	0.69185	2.1	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.62374	-0.6868	9	0.62326	D	0.03	.	6.346	0.21349	0.0:0.5505:0.3465:0.1029	.	672	P17020	ZNF16_HUMAN	F	672	ENSP00000276816:L672F;ENSP00000378369:L672F	ENSP00000276816:L672F	L	-	3	2	ZNF16	146126961	0.000000	0.05858	0.711000	0.30485	0.594000	0.36715	-1.750000	0.01822	2.081000	0.62600	0.462000	0.41574	TTG	.	.	.	none		0.527	ZNF16-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000382978.1	NM_006958		A	146156157	C	A	146156157	3	1	242	1	0	0	0	0	1	0	0	0	17750	825	29	4	36	4	ZNF16	8	146156157	Missense_Mutation	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10	6990804	146156157	207865	60	14864											
HAUS6	54801	hgsc.bcm.edu	37	chr9	19080609	19080609	+	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	tcaccttcaagacttcatttAataactgaataactgttaag	15	14	4	8	0	3	2	3	1	0	1	3	2	3	2	1	0	2	1	1	0	6	7			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr9:19080609A>T	ENST00000380502.3	-	9	1399	c.932T>A	c.(931-933)tTa>tAa	p.L311*	HAUS6_ENST00000380496.1_Nonsense_Mutation_p.L175*	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	311					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						GACTTCATTTAATAACTGAAT	0.368																																					p.L311X		Atlas-SNP	.											.	HAUS6	66	.	0			c.T932A						PASS	.						56	53	54					9																	19080609		2201	4297	6498	SO:0001587	stop_gained	54801	exon9			TCATTTAATAACT	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.932T>A	chr9.hg19:g.19080609A>T	ENSP00000369871:p.Leu311*	228.0	0.0	.		194.0	70.0	.	NM_017645	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Nonsense_Mutation	SNP	ENST00000380502.3	hg19	CCDS6489.1	.	.	.	.	.	.	.	.	.	.	A	36	5.706308	0.96821	.	.	ENSG00000147874	ENST00000380502;ENST00000380496	.	.	.	5.49	5.49	0.81192	.	0.142736	0.46758	D	0.000268	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.7991	13.5326	0.61631	1.0:0.0:0.0:0.0	.	.	.	.	X	311;175	.	ENSP00000369865:L175X	L	-	2	0	HAUS6	19070609	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.947000	0.70242	2.089000	0.63090	0.482000	0.46254	TTA	.	.	.	none		0.368	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645		T	19080609	A	T	19080609	4	4	242	1	0	0	0	0	0	1	0	0	6977	372	13	5	1971	5	HAUS6	9	19080609	Nonsense_Mutation	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10		19080609	122132822	61	14865											
GBA2	57704	hgsc.bcm.edu	37	chr9	35741770	35741770	+	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	ggctcggggatagagggcatGgtagaaagcaaagtacccac	13	5	15	8	1	0	2	0	0	0	2	1	3	0	3	1	5	2	5	1	5	5	3			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr9:35741770G>A	ENST00000378103.3	-	4	1208	c.685C>T	c.(685-687)Cat>Tat	p.H229Y	GBA2_ENST00000378094.4_Missense_Mutation_p.H229Y|GBA2_ENST00000467252.1_5'UTR|GBA2_ENST00000545786.1_Missense_Mutation_p.H235Y	NM_020944.2	NP_065995.1	Q9HCG7	GBA2_HUMAN	glucosidase, beta (bile acid) 2	229					bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|central nervous system neuron development (GO:0021954)|glucosylceramide catabolic process (GO:0006680)|glycoside catabolic process (GO:0016139)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)	beta-glucosidase activity (GO:0008422)|glucosylceramidase activity (GO:0004348)			NS(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(4)|skin(3)	21	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TAGAGGGCATGGTAGAAAGCA	0.587																																					p.H229Y		Atlas-SNP	.											.	GBA2	77	.	0			c.C685T						PASS	.						130	123	125					9																	35741770		2203	4300	6503	SO:0001583	missense	57704	exon4			GGGCATGGTAGAA	AJ309567	CCDS6589.1	9p13.2	2013-09-11			ENSG00000070610	ENSG00000070610			18986	protein-coding gene	gene with protein product	"bile acid beta-glucosidase", "non-lysosomal glucosylceramidase"	609471	"spastic paraplegia 46 (autosomal recessive)"	SPG46		11489889, 23332916, 23332917	Standard	NM_020944		Approved	KIAA1605, AD035, DKFZp762K054	uc003zxw.3	Q9HCG7	OTTHUMG00000021024	ENST00000378103.3:c.685C>T	chr9.hg19:g.35741770G>A	ENSP00000367343:p.His229Tyr	82.0	0.0	.		72.0	27.0	.	NM_020944	D3DRP2|Q5TCV6|Q96A51|Q96LY1|Q96SJ2|Q9H2L8	Missense_Mutation	SNP	ENST00000378103.3	hg19	CCDS6589.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.017890	0.93404	.	.	ENSG00000070610	ENST00000378103;ENST00000378094;ENST00000545786	.	.	.	5.37	5.37	0.77165	Beta-glucosidase, GBA2 type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.77191	0.4094	M	0.71296	2.17	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.975;0.998	T	0.70757	-0.4785	9	0.11485	T	0.65	-22.5324	19.4817	0.95013	0.0:0.0:1.0:0.0	.	235;229;229	F5H7P6;Q9HCG7-2;Q9HCG7	.;.;GBA2_HUMAN	Y	229;229;235	.	ENSP00000367334:H229Y	H	-	1	0	GBA2	35731770	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.686000	0.98664	2.673000	0.90976	0.557000	0.71058	CAT	.	.	.	none		0.587	GBA2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055456.1	NM_020944		A	35741770	G	A	35741770	3	1	242	1	0	0	0	0	1	0	0	0	6274	1348	47	2	2154	2	GBA2	9	35741770	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	16661161	35741770	105471661	62	14866											
CNTNAP3	79937	hgsc.bcm.edu	37	chr9	39144299	39144299	+	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	cacaggagaaggtgtcccacGactgggaacactcgccccca	11	4	11	15	2	0	1	0	0	0	1	2	4	1	2	3	3	1	0	3	3	2	0			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr9:39144299G>A	ENST00000297668.6	-	11	1767	c.1694C>T	c.(1693-1695)tCg>tTg	p.S565L	CNTNAP3_ENST00000377656.2_Missense_Mutation_p.S565L|CNTNAP3_ENST00000358144.2_Missense_Mutation_p.S477L|CNTNAP3_ENST00000323947.7_Intron|CNTNAP3_ENST00000377659.1_Missense_Mutation_p.S565L	NM_033655.3	NP_387504.2	Q9BZ76	CNTP3_HUMAN	contactin associated protein-like 3	565	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)		GGTGTCCCACGACTGGGAACA	0.502																																					p.S565L		Atlas-SNP	.											.	CNTNAP3	82	.	0			c.C1694T						PASS	.						9	6	7					9																	39144299		2038	3953	5991	SO:0001583	missense	79937	exon11			TCCCACGACTGGG	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.1694C>T	chr9.hg19:g.39144299G>A	ENSP00000297668:p.Ser565Leu	630.0	0.0	.		632.0	235.0	.	NM_033655	B1AMA0|Q9C0E9	Missense_Mutation	SNP	ENST00000297668.6	hg19	CCDS6616.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.186331	0.78789	.	.	ENSG00000106714	ENST00000297668;ENST00000377656;ENST00000358144;ENST00000377659	T;T;T;T	0.17854	2.25;2.25;2.25;2.25	3.04	3.04	0.35103	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.23492	0.0568	L	0.47078	1.49	0.80722	D	1	D;P;P	0.62365	0.991;0.807;0.801	P;B;B	0.50590	0.645;0.266;0.14	T	0.05733	-1.0867	9	0.66056	D	0.02	.	13.1565	0.59520	0.0:0.0:1.0:0.0	.	565;565;565	Q9BZ76-2;A6NC89;Q9BZ76	.;.;CNTP3_HUMAN	L	565;565;477;565	ENSP00000297668:S565L;ENSP00000366884:S565L;ENSP00000350863:S477L;ENSP00000366887:S565L	ENSP00000297668:S565L	S	-	2	0	CNTNAP3	39134299	1.000000	0.71417	0.997000	0.53966	0.949000	0.60115	5.316000	0.65815	1.691000	0.51100	0.306000	0.20318	TCG	.	.	.	none		0.502	CNTNAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052511.1	NM_033655		A	39144299	G	A	39144299	3	1	242	1	0	0	0	0	1	0	0	0	3650	1059	37	1	2228	1	CNTNAP3	9	39144299	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	3402529	39144299	102069132	63	14867											
C9orf47	286223	hgsc.bcm.edu	37	chr9	91606554	91606554	+	Missense_Mutation	SNP	A	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	gcaggaccgggcgccccggcAccgccgcgcgccacccgcta	5	1	14	21	8	0	0	0	0	0	0	0	1	0	1	7	3	0	3	7	3	1	1			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr9:91606554A>C	ENST00000334490.5	+	2	484	c.416A>C	c.(415-417)cAc>cCc	p.H139P	S1PR3_ENST00000358157.2_5'UTR|C9orf47_ENST00000375850.3_Missense_Mutation_p.H120P|C9orf47_ENST00000375851.2_Missense_Mutation_p.H120P			Q6ZRZ4	CI047_HUMAN	chromosome 9 open reading frame 47	139						extracellular region (GO:0005576)				endometrium(1)|large_intestine(1)|liver(1)|lung(1)	4						GCGCCCCGGCACCGCCGCGCG	0.781																																					p.H139P		Atlas-SNP	.											.	C9orf47	9	.	0			c.A416C						PASS	.						2	2	2					9																	91606554		1448	2974	4422	SO:0001583	missense	286223	exon2			CCCGGCACCGCCG	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.416A>C	chr9.hg19:g.91606554A>C	ENSP00000335616:p.His139Pro	18.0	0.0	.		19.0	12.0	.	NM_001001938	B7ZMC7|Q5SQD7|Q7Z568|Q8N1V4	Missense_Mutation	SNP	ENST00000334490.5	hg19	CCDS35062.1	.	.	.	.	.	.	.	.	.	.	A	10.64	1.407244	0.25378	.	.	ENSG00000186354	ENST00000375851;ENST00000375850;ENST00000334490	.	.	.	1.58	-1.41	0.08941	.	.	.	.	.	T	0.11707	0.0285	N	0.08118	0	0.09310	N	0.999995	D;D	0.58268	0.982;0.982	P;P	0.44422	0.449;0.449	T	0.13229	-1.0517	8	0.87932	D	0	.	2.3629	0.04312	0.3788:0.3701:0.0:0.2511	.	139;120	Q6ZRZ4;Q6ZRZ4-2	CI047_HUMAN;.	P	120;120;139	.	ENSP00000335616:H139P	H	+	2	0	C9orf47	90796374	0.002000	0.14202	0.000000	0.03702	0.044000	0.14063	-0.122000	0.10627	-0.403000	0.07622	0.454000	0.30748	CAC	.	.	.	none		0.781	C9orf47-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355972.1	NM_182599		C	91606554	A	C	91606554	3	2	242	1	0	0	0	0	1	0	0	0	2487	159	6	5	422	5	C9orf47	9	91606554	Missense_Mutation	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10	52462255	91606554	49606877	64	14868											
ALG2	85365	hgsc.bcm.edu	37	chr9	101980479	101980480	+	Frame_Shift_Ins	INS	-	-	A																															tacatggcttccagagggacINSaatgccaaagtgctcattgc																										TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr9:101980479_101980480insA	ENST00000476832.1	-	2	1048_1049	c.987_988insT	c.(985-990)attgtcfs	p.V330fs	ALG2_ENST00000319033.6_Frame_Shift_Ins_p.V237fs	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)				TCCAGAGGGACAATGCCAAAGT	0.495																																					p.V330fs		Atlas-Indel,Pindel	.											.	ALG2	37	.	0			c.988_989insT						PASS	.																																			SO:0001589	frameshift_variant	85365	exon2			.	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.988dupT	chr9.hg19:g.101980481_101980481dupA	ENSP00000417764:p.Val330fs	171.0	0.0	0		145.0	68.0	0.468966	NM_033087	B2RD16|E7ESR3|Q2YDC2|Q5TZS0	Frame_Shift_Ins	INS	ENST00000476832.1	hg19	CCDS6739.1																																																																																			.	.	.	none		0.495	ALG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215080.1	NM_033087		A	101980480	-	A	101980479	7	5	242	1	0	1	1	0	0	0	0	0	519	478	17	0	266	0	ALG2	9	101980479	Frame_Shift_Ins	INS	-	TCGA-SX-A71S-01A-11D-A33Q-10	10373925	101980479	39232952	65	14869											
RNF20	56254	hgsc.bcm.edu	37	chr9	104302568	104302568	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cggcaggccattgaagatgaActtcgtgagcacattgaaaa	14	8	11	8	2	0	5	0	4	0	1	1	5	0	5	1	2	2	2	1	2	4	3	rs150763272		TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr9:104302568A>G	ENST00000389120.3	+	3	303	c.213A>G	c.(211-213)gaA>gaG	p.E71E		NM_019592.5	NP_062538.5	Q5VTR2	BRE1A_HUMAN	ring finger protein 20, E3 ubiquitin protein ligase	71					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|negative regulation of cell migration (GO:0030336)|positive regulation of histone methylation (GO:0031062)|positive regulation of transcription, DNA-templated (GO:0045893)|protein polyubiquitination (GO:0000209)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(6)|large_intestine(7)|lung(23)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)		TTGAAGATGAACTTCGTGAGC	0.453																																					p.E71E		Atlas-SNP	.											.	RNF20	110	.	0			c.A213G						PASS	.	A		4,4402	8.1+/-20.4	0,4,2199	134	119	124		213	-0.6	1	9	dbSNP_134	124	0,8600		0,0,4300	no	coding-synonymous	RNF20	NM_019592.5		0,4,6499	GG,GA,AA		0.0,0.0908,0.0308		71/976	104302568	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	56254	exon3			AGATGAACTTCGT	AF265230	CCDS35084.1	9q22	2012-02-23	2012-02-23	2008-12-12	ENSG00000155827	ENSG00000155827		"RING-type (C3HC4) zinc fingers"	10062	protein-coding gene	gene with protein product	"BRE1 E3 ubiquitin ligase homolog (S. cerevisiae)"	607699	"ring finger protein 20"			16337599, 12876294, 18832071, 19037095	Standard	NM_019592		Approved	FLJ20382, FLJ11189, KAIA2779, BRE1A, hBRE1, BRE1	uc004bbn.3	Q5VTR2	OTTHUMG00000020385	ENST00000389120.3:c.213A>G	chr9.hg19:g.104302568A>G		112.0	0.0	.		106.0	60.0	.	NM_019592	A7MCT5|Q2TB34|Q69YL5|Q6P527|Q8N3J4|Q96JD3|Q9H9Y7|Q9HA51|Q9NUR4|Q9NWQ3|Q9NX83	Silent	SNP	ENST00000389120.3	hg19	CCDS35084.1																																																																																			.	A|1.000;G|0.000	0.000	weak		0.453	RNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356402.1	NM_019592		G	104302568	A	G	104302568	2	3	242	1	0	0	0	0	0	0	0	1	13486	40	2	3		3	RNF20	9	104302568	Silent	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10	2322089	104302568	36910863	66	14870											
TSC1	7248	hgsc.bcm.edu	37	chr9	135787825	135787825	+	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	acactcgatcacaacatcatGagtttctaatctcttccacc	12	12	3	14	1	4	1	2	1	2	0	7	2	5	1	2	0	1	1	2	0	2	3			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr9:135787825G>T	ENST00000298552.3	-	9	978	c.757C>A	c.(757-759)Cat>Aat	p.H253N	TSC1_ENST00000403810.1_Missense_Mutation_p.H253N|TSC1_ENST00000440111.2_Missense_Mutation_p.H253N|TSC1_ENST00000545250.1_Missense_Mutation_p.H202N	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	253					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)		ACAACATCATGAGTTTCTAAT	0.418			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.H253N		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"E, O"	.	TSC1	167	.	1	Unknown(1)	bone(1)	c.C757A						PASS	.						123	105	111					9																	135787825		2203	4300	6503	SO:0001583	missense	7248	exon9	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	CATCATGAGTTTC	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.757C>A	chr9.hg19:g.135787825G>T	ENSP00000298552:p.His253Asn	50.0	0.0	.		40.0	15.0	.	NM_000368	B7Z897|Q5VVN5	Missense_Mutation	SNP	ENST00000298552.3	hg19	CCDS6956.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.859483	0.91433	.	.	ENSG00000165699	ENST00000298552;ENST00000440111;ENST00000545250;ENST00000537172;ENST00000424271;ENST00000403810	D;D;D;D;D	0.88896	-2.44;-2.44;-2.44;-2.44;-2.44	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.95046	0.8396	M	0.83603	2.65	0.80722	D	1	D;D;P;D;P;D	0.76494	0.999;0.989;0.852;0.981;0.956;0.976	D;D;P;P;D;D	0.87578	0.998;0.944;0.539;0.852;0.955;0.924	D	0.95026	0.8165	10	0.66056	D	0.02	-14.9842	18.9865	0.92773	0.0:0.0:1.0:0.0	.	132;202;253;253;253;253	B7Z604;B7Z897;Q86WV8;Q59IT9;Q32NF0;Q92574	.;.;.;.;.;TSC1_HUMAN	N	253;253;202;132;132;253	ENSP00000298552:H253N;ENSP00000394524:H253N;ENSP00000444017:H202N;ENSP00000438099:H132N;ENSP00000386093:H253N	ENSP00000298552:H253N	H	-	1	0	TSC1	134777646	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.869000	0.99810	2.724000	0.93272	0.561000	0.74099	CAT	.	.	.	none		0.418	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1			T	135787825	G	T	135787825	3	4	242	1	0	0	0	0	1	0	0	0	16617	1290	45	4	2797	4	TSC1	9	135787825	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	31485257	135787825	5425606	67	14871											
PRPF18	8559	hgsc.bcm.edu	37	chr10	13658405	13658405	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actttcctttcaggcaaatgAtgcttatcttcagatggcca	10	14	7	10	0	3	2	2	1	1	1	4	2	4	2	2	2	1	2	2	2	2	4			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr10:13658405A>G	ENST00000378572.3	+	9	960	c.800A>G	c.(799-801)gAt>gGt	p.D267G		NM_003675.3	NP_003666.1	Q99633	PRP18_HUMAN	pre-mRNA processing factor 18	267					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						CAGGCAAATGATGCTTATCTT	0.413																																					p.D267G		Atlas-SNP	.											.	PRPF18	32	.	0			c.A800G						PASS	.						143	134	137					10																	13658405		2203	4300	6503	SO:0001583	missense	8559	exon9			CAAATGATGCTTA	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.800A>G	chr10.hg19:g.13658405A>G	ENSP00000367835:p.Asp267Gly	49.0	0.0	.		58.0	22.0	.	NM_003675	Q5T9P9|Q9BUI9	Missense_Mutation	SNP	ENST00000378572.3	hg19	CCDS7100.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.309778	0.81247	.	.	ENSG00000165630	ENST00000378572;ENST00000298451	.	.	.	5.3	5.3	0.74995	Prp18 (3);	0.000000	0.85682	D	0.000000	D	0.84460	0.5477	M	0.91768	3.24	0.80722	D	1	D	0.63046	0.992	D	0.65987	0.94	D	0.88339	0.2973	9	0.87932	D	0	-32.6043	15.2507	0.73542	1.0:0.0:0.0:0.0	.	267	Q99633	PRP18_HUMAN	G	267;29	.	ENSP00000298451:D29G	D	+	2	0	PRPF18	13698411	1.000000	0.71417	1.000000	0.80357	0.670000	0.39368	9.320000	0.96346	2.006000	0.58801	0.528000	0.53228	GAT	.	.	.	none		0.413	PRPF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046879.1			G	13658405	A	G	13658405	3	3	242	1	0	0	0	0	1	0	0	0	12573	333	12	3	834	3	PRPF18	10	13658405	Missense_Mutation	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10		13658405	121876342	68	14872											
SVIL	6840	hgsc.bcm.edu	37	chr10	29769500	29769500	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgaacttccacttgaccacAtaggcatccccctcatggaa	12	9	6	14	0	1	2	1	2	0	0	3	3	3	3	4	2	1	1	4	2	3	3			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr10:29769500A>G	ENST00000355867.4	-	29	6095	c.5343T>C	c.(5341-5343)taT>taC	p.Y1781Y	SVIL_ENST00000375398.2_Silent_p.Y1781Y|PTCHD3P1_ENST00000423223.1_RNA|SVIL_ENST00000535393.1_Silent_p.Y695Y|PTCHD3P1_ENST00000446807.1_RNA|SVIL_ENST00000460007.1_5'UTR|SVIL_ENST00000538146.1_Silent_p.Y573Y|SVIL_ENST00000375400.3_Silent_p.Y1355Y|PTCHD3P1_ENST00000413405.1_RNA|PTCHD3P1_ENST00000414457.1_RNA	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1781					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)				ACTTGACCACATAGGCATCCC	0.567																																					p.Y1781Y		Atlas-SNP	.											.	SVIL	226	.	0			c.T5343C						PASS	.						104	95	98					10																	29769500		2203	4300	6503	SO:0001819	synonymous_variant	6840	exon29			GACCACATAGGCA	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.5343T>C	chr10.hg19:g.29769500A>G		106.0	0.0	.		96.0	44.0	.	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	hg19	CCDS7164.1																																																																																			.	.	.	none		0.567	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			G	29769500	A	G	29769500	2	3	242	1	0	0	0	0	0	0	0	1	15433	224	8	3		3	SVIL	10	29769500	Silent	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10	16111095	29769500	105765247	69	14873											
ANKRD30A	91074	hgsc.bcm.edu	37	chr10	37508624	37508625	+	Frame_Shift_Ins	INS	-	-	A																															aattatttcaactacaaagcINSaaaaatatgtggcttcaaca																										TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr10:37508624_37508625insA	ENST00000602533.1	+	34	3915_3916	c.3816_3817insA	c.(3817-3819)aaafs	p.K1273fs	ANKRD30A_ENST00000361713.1_Frame_Shift_Ins_p.K1273fs|ANKRD30A_ENST00000374660.1_Frame_Shift_Ins_p.K1392fs			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1329					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						AACTACAAAGCAAAAATATGTG	0.342																																					p.S1272fs		Atlas-Indel,Pindel	.											.	ANKRD30A	448	.	0			c.3816_3817insA						PASS	.																																			SO:0001589	frameshift_variant	91074	exon34			.	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"Ankyrin repeat domain containing"	17234	protein-coding gene	gene with protein product	"breast cancer antigen NY-BR-1"	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.3821dupA	chr10.hg19:g.37508629_37508629dupA	ENSP00000473551:p.Lys1273fs	186.0	0.0	0		203.0	92.0	0.453202	NM_052997	Q5W025	Frame_Shift_Ins	INS	ENST00000602533.1	hg19																																																																																				.	.	.	none		0.342	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		A	37508625	-	A	37508624	7	5	242	1	0	1	1	0	0	0	0	0	658	709	25	0	3950	0	ANKRD30A	10	37508624	Frame_Shift_Ins	INS	-	TCGA-SX-A71S-01A-11D-A33Q-10	7739124	37508624	98026123	70	14874											
SLC16A12	387700	hgsc.bcm.edu	37	chr10	91203518	91203518	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaagtaatactcaccacagAgcatggtcacacaatctaca	16	8	6	11	0	3	1	2	0	1	1	3	1	3	1	1	1	3	3	1	1	5	4			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr10:91203518A>G	ENST00000341233.4	-	4	599	c.209T>C	c.(208-210)cTc>cCc	p.L70P	SLC16A12_ENST00000371790.4_Missense_Mutation_p.L100P	NM_213606.3	NP_998771.3	Q6ZSM3	MOT12_HUMAN	solute carrier family 16, member 12	70						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						CTCACCACAGAGCATGGTCAC	0.393																																					p.L100P		Atlas-SNP	.											.	SLC16A12	40	.	0			c.T299C						PASS	.						107	93	98					10																	91203518		2203	4300	6503	SO:0001583	missense	387700	exon4			CCACAGAGCATGG		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.209T>C	chr10.hg19:g.91203518A>G	ENSP00000343022:p.Leu70Pro	77.0	0.0	.		80.0	31.0	.	NM_213606	Q5M9M9|Q5T7J2|Q6ZV76	Missense_Mutation	SNP	ENST00000341233.4	hg19		.	.	.	.	.	.	.	.	.	.	A	24.7	4.555001	0.86231	.	.	ENSG00000152779	ENST00000341233;ENST00000371790	T;T	0.60797	0.16;0.16	5.62	5.62	0.85841	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.118609	0.64402	D	0.000016	T	0.77572	0.4150	M	0.85373	2.75	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	T	0.79215	-0.1895	10	0.41790	T	0.15	.	15.0059	0.71513	1.0:0.0:0.0:0.0	.	70	Q6ZSM3	MOT12_HUMAN	P	70;100	ENSP00000343022:L70P;ENSP00000360855:L100P	ENSP00000343022:L70P	L	-	2	0	SLC16A12	91193498	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	9.339000	0.96797	2.151000	0.67156	0.482000	0.46254	CTC	.	.	.	none		0.393	SLC16A12-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_213606		G	91203518	A	G	91203518	3	3	242	1	0	0	0	0	1	0	0	0	14418	304	11	3	1271	3	SLC16A12	10	91203518	Missense_Mutation	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10	53694894	91203518	44331229	71	14875											
MGEA5	10724	hgsc.bcm.edu	37	chr10	103577714	103577714	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcgatgcccccgcagaggcGgcagggttggagctgagctc	7	5	17	12	3	0	2	0	1	0	1	1	4	0	3	2	4	4	5	2	4	0	1			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr10:103577714G>A	ENST00000361464.3	-	1	461	c.66C>T	c.(64-66)gcC>gcT	p.A22A	KCNIP2-AS1_ENST00000412353.1_RNA|MGEA5_ENST00000370094.3_Silent_p.A22A|MGEA5_ENST00000419011.2_Silent_p.A22A|MGEA5_ENST00000439817.1_Silent_p.A22A|MGEA5_ENST00000357797.5_Silent_p.A22A	NM_012215.3	NP_036347.1	O60502	OGA_HUMAN	meningioma expressed antigen 5 (hyaluronidase)	22					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)		CCGCAGAGGCGGCAGGGTTGG	0.736																																					p.A22A		Atlas-SNP	.											.	MGEA5	53	.	0			c.C66T						PASS	.						9	10	10					10																	103577714		2166	4258	6424	SO:0001819	synonymous_variant	10724	exon1			AGAGGCGGCAGGG	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.66C>T	chr10.hg19:g.103577714G>A		25.0	0.0	.		39.0	16.0	.	NM_001142434	B7WPB9|D3DR79|E9PGF9|O75166|Q86WV0|Q8IV98|Q9BVA5|Q9HAR0	Silent	SNP	ENST00000361464.3	hg19	CCDS7520.1																																																																																			.	.	.	none		0.736	MGEA5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049987.1	NM_012215		A	103577714	G	A	103577714	2	1	242	1	0	0	0	0	0	0	0	1	9562	1103	39	1		1	MGEA5	10	103577714	Silent	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	12374196	103577714	31957033	72	14876											
PHRF1	57661	hgsc.bcm.edu	37	chr11	598434	598434	+	Missense_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	catcgaggctgtggcgactgGcctgagcactgccgtgtatc	6	9	14	12	3	0	1	0	1	0	0	2	3	0	1	2	3	2	3	2	3	1	1			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr11:598434G>A	ENST00000264555.5	+	9	1084	c.956G>A	c.(955-957)gGc>gAc	p.G319D	PHRF1_ENST00000533464.1_Missense_Mutation_p.G315D|PHRF1_ENST00000416188.2_Missense_Mutation_p.G319D|PHRF1_ENST00000413872.2_Missense_Mutation_p.G318D	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	319	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						GTGGCGACTGGCCTGAGCACT	0.657																																					p.G319D		Atlas-SNP	.											.	PHRF1	188	.	0			c.G956A						PASS	.						29	37	34					11																	598434		2125	4237	6362	SO:0001583	missense	57661	exon9			CGACTGGCCTGAG	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.956G>A	chr11.hg19:g.598434G>A	ENSP00000264555:p.Gly319Asp	31.0	0.0	.		24.0	8.0	.	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Missense_Mutation	SNP	ENST00000264555.5	hg19		.	.	.	.	.	.	.	.	.	.	G	17.75	3.465596	0.63513	.	.	ENSG00000070047	ENST00000264555;ENST00000413872;ENST00000416188;ENST00000533464	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	4.64	4.64	0.57946	.	0.000000	0.42420	D	0.000719	T	0.62368	0.2422	M	0.66939	2.045	0.51233	D	0.999914	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.999;0.999;0.998	T	0.66582	-0.5887	10	0.72032	D	0.01	-24.5391	14.6641	0.68893	0.0:0.0:1.0:0.0	.	315;318;319;319	E9PJ24;F8WEF5;Q9P1Y6-3;Q9P1Y6	.;.;.;PHRF1_HUMAN	D	319;318;319;315	ENSP00000264555:G319D;ENSP00000388589:G318D;ENSP00000410626:G319D;ENSP00000431870:G315D	ENSP00000264555:G319D	G	+	2	0	PHRF1	588434	1.000000	0.71417	0.651000	0.29564	0.079000	0.17450	7.543000	0.82106	2.134000	0.65973	0.491000	0.48974	GGC	.	.	.	none		0.657	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901		A	598434	G	A	598434	3	1	242	1	0	0	0	0	1	0	0	0	11868	1203	42	2	986	2	PHRF1	11	598434	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10		598434	134408082	73	14877											
EPS8L2	64787	hgsc.bcm.edu	37	chr11	721127	721127	+	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	cctccccagggcccggcgccCatccccttccagcaccgcgg	4	4	10	23	4	0	0	0	0	0	0	3	0	3	0	9	3	1	1	9	3	0	1			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr11:721127C>A	ENST00000533256.1	+	9	996	c.621C>A	c.(619-621)ccC>ccA	p.P207P	AP006621.9_ENST00000527021.2_RNA|EPS8L2_ENST00000318562.8_Silent_p.P207P|EPS8L2_ENST00000526198.1_Silent_p.P223P|EPS8L2_ENST00000530636.1_Silent_p.P207P			Q9H6S3	ES8L2_HUMAN	EPS8-like 2	207					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)		GCCCGGCGCCCATCCCCTTCC	0.736																																					p.P207P		Atlas-SNP	.											.	EPS8L2	42	.	0			c.C621A						PASS	.						9	11	10					11																	721127		2060	4086	6146	SO:0001819	synonymous_variant	64787	exon8			GGCGCCCATCCCC	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.621C>A	chr11.hg19:g.721127C>A		16.0	0.0	.		13.0	6.0	.	NM_022772	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Silent	SNP	ENST00000533256.1	hg19	CCDS31328.1																																																																																			.	.	.	none		0.736	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772		A	721127	C	A	721127	2	1	242	1	0	0	0	0	0	0	0	1	5198	581	21	4		4	EPS8L2	11	721127	Silent	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10	122693	721127	134285389	74	14878											
OR52M1	119772	hgsc.bcm.edu	37	chr11	4566635	4566636	+	Frame_Shift_Ins	INS	-	-	C																															tgcatgttggctgccattgaINScctggttctgtctacttcca																										TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr11:4566635_4566636insC	ENST00000360213.1	+	1	215_216	c.215_216insC	c.(214-219)gacctgfs	p.L73fs		NM_001004137.1	NP_001004137.1	Q8NGK5	O52M1_HUMAN	olfactory receptor, family 52, subfamily M, 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)			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)		GCTGCCATTGACCTGGTTCTGT	0.515																																					p.D72fs		Atlas-Indel,Pindel	.											.	OR52M1	53	.	0			c.215_216insC						PASS	.																																			SO:0001589	frameshift_variant	119772	exon1			.	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.217dupC	chr11.hg19:g.4566637_4566637dupC	ENSP00000353343:p.Leu73fs	95.0	0.0	0		98.0	40.0	0.408163	NM_001004137		Frame_Shift_Ins	INS	ENST00000360213.1	hg19	CCDS31353.1																																																																																			.	.	.	none		0.515	OR52M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385847.1	NM_001004137		C	4566636	-	C	4566635	7	5	242	1	0	1	1	0	0	0	0	0	11133	275	10	0	217	0	OR52M1	11	4566635	Frame_Shift_Ins	INS	-	TCGA-SX-A71S-01A-11D-A33Q-10	3845508	4566635	130439881	75	14879											
OR51D1	390038	hgsc.bcm.edu	37	chr11	4661416	4661416	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctgtcctgctggccatggcTtttgaccgctttgtggccat	3	14	12	12	1	0	1	0	1	0	0	1	1	1	1	4	3	1	4	4	3	0	3			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr11:4661416T>C	ENST00000357605.2	+	1	472	c.396T>C	c.(394-396)gcT>gcC	p.A132A		NM_001004751.2	NP_001004751.1	Q8NGF3	O51D1_HUMAN	olfactory receptor, family 51, subfamily D, 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)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|liver(2)|lung(14)|prostate(1)|skin(2)|urinary_tract(1)	27		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;2.74e-13)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|GBM - Glioblastoma multiforme(2;0.0841)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGGCCATGGCTTTTGACCGCT	0.557																																					p.A132A		Atlas-SNP	.											.	OR51D1	49	.	0			c.T396C						PASS	.						135	111	119					11																	4661416		2201	4298	6499	SO:0001819	synonymous_variant	390038	exon1			CATGGCTTTTGAC	AB065855	CCDS31357.1	11p15.4	2012-08-09			ENSG00000197428	ENSG00000197428		"GPCR / Class A : Olfactory receptors"	15193	protein-coding gene	gene with protein product							Standard	NM_001004751		Approved	OR51D1Q	uc010qyk.2	Q8NGF3	OTTHUMG00000165724	ENST00000357605.2:c.396T>C	chr11.hg19:g.4661416T>C		104.0	0.0	.		91.0	31.0	.	NM_001004751	B9EIK4	Silent	SNP	ENST00000357605.2	hg19	CCDS31357.1																																																																																			.	.	.	none		0.557	OR51D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385956.1	NM_001004751		C	4661416	T	C	4661416	2	2	242	1	0	0	0	0	0	0	0	1	11100	1596	56	3		3	OR51D1	11	4661416	Silent	SNP	T	TCGA-SX-A71S-01A-11D-A33Q-10	94781	4661416	130345100	76	14880											
FERMT3	83706	hgsc.bcm.edu	37	chr11	63978141	63978141	+	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	gaacagaagaggcagtggctGctgcagacccactggacact	12	5	13	11	0	0	3	0	0	0	3	0	5	0	4	1	3	3	4	1	3	2	0			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr11:63978141G>A	ENST00000279227.5	+	3	314	c.219G>A	c.(217-219)ctG>ctA	p.L73L	FERMT3_ENST00000345728.5_Silent_p.L73L	NM_178443.2	NP_848537.1	Q86UX7	URP2_HUMAN	fermitin family member 3	73					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						GGCAGTGGCTGCTGCAGACCC	0.622																																					p.L73L		Atlas-SNP	.											.	FERMT3	51	.	0			c.G219A						PASS	.						127	117	120					11																	63978141		2201	4297	6498	SO:0001819	synonymous_variant	83706	exon3			GTGGCTGCTGCAG	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.219G>A	chr11.hg19:g.63978141G>A		144.0	0.0	.		138.0	55.0	.	NM_031471	Q8IUA1|Q8N207|Q9BT48	Silent	SNP	ENST00000279227.5	hg19	CCDS8060.1																																																																																			.	.	.	none		0.622	FERMT3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396297.1	NM_031471		A	63978141	G	A	63978141	2	1	242	1	0	0	0	0	0	0	0	1	5826	1306	46	2		2	FERMT3	11	63978141	Silent	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	59316725	63978141	71028375	77	14881											
C11orf80	79703	hgsc.bcm.edu	37	chr11	66610424	66610425	+	Frame_Shift_Ins	INS	-	-	C																															cccgagcccgtcagaggccgINSccccgcgccgcccggaagcc																										TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr11:66610424_66610425insC	ENST00000360962.4	+	16	1859_1860	c.1852_1853insC	c.(1852-1854)gccfs	p.A618fs	C11orf80_ENST00000525449.2_Frame_Shift_Ins_p.A426fs|RCE1_ENST00000525356.1_5'Flank|RCE1_ENST00000524506.1_5'Flank|C11orf80_ENST00000532565.2_Frame_Shift_Ins_p.A400fs|C11orf80_ENST00000346672.4_Frame_Shift_Ins_p.A427fs|C11orf80_ENST00000527634.1_Frame_Shift_Ins_p.A401fs|C11orf80_ENST00000540737.1_Frame_Shift_Ins_p.A452fs|RCE1_ENST00000309657.3_5'Flank	NM_024650.3	NP_078926.3	Q8N6T0	CK080_HUMAN	chromosome 11 open reading frame 80	618										autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	14						GTCAGAGGCCGCCCCGCGCCGC	0.733																																					p.A618fs		Atlas-Indel,Pindel	.											.	C11orf80	31	.	0			c.1852_1853insC						PASS	.																																			SO:0001589	frameshift_variant	79703	exon16			.			11q13.2	2012-05-30			ENSG00000173715	ENSG00000173715			26197	protein-coding gene	gene with protein product						18160775	Standard	NM_024650		Approved	FLJ22531	uc021qmd.1	Q8N6T0	OTTHUMG00000167164	ENST00000360962.4:c.1856dupC	chr11.hg19:g.66610428_66610428dupC	ENSP00000354227:p.Ala618fs	47.0	0.0	0		43.0	19.0	0.44186	NM_024650	Q9H677	Frame_Shift_Ins	INS	ENST00000360962.4	hg19	CCDS53664.1																																																																																			.	.	.	none		0.733	C11orf80-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_024650		C	66610425	-	C	66610424	7	5	242	1	0	1	1	0	0	0	0	0	1666	1087	38	0	1914	0	C11orf80	11	66610424	Frame_Shift_Ins	INS	-	TCGA-SX-A71S-01A-11D-A33Q-10	2632283	66610424	68396092	78	14882											
ANKRD13D	338692	hgsc.bcm.edu	37	chr11	67057877	67057877	+	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	ctaccagagggccacgcagaGgctggcgggcattccggaac	9	4	15	13	3	0	2	0	0	0	2	1	3	1	3	3	5	2	3	3	5	2	2			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr11:67057877G>A	ENST00000447274.2	+	3	1225	c.50G>A	c.(49-51)aGg>aAg	p.R17K	ANKRD13D_ENST00000511455.2_Missense_Mutation_p.R104K|ANKRD13D_ENST00000308440.6_Missense_Mutation_p.R17K|ANKRD13D_ENST00000514166.1_Missense_Mutation_p.R17K			Q6ZTN6	AN13D_HUMAN	ankyrin repeat domain 13 family, member D	17						endosome (GO:0005768)|plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			GCCACGCAGAGGCTGGCGGGC	0.627																																					p.R104K		Atlas-SNP	.											.	ANKRD13D	71	.	0			c.G311A						PASS	.						76	47	57					11																	67057877		2193	4291	6484	SO:0001583	missense	338692	exon3			CGCAGAGGCTGGC	AK027313	CCDS31616.1, CCDS31616.2	11q13.2	2013-01-11		2005-08-09	ENSG00000172932	ENSG00000172932		"Ankyrin repeat domain containing"	27880	protein-coding gene	gene with protein product		615126					Standard	NM_207354		Approved		uc001okd.2	Q6ZTN6	OTTHUMG00000162929	ENST00000447274.2:c.50G>A	chr11.hg19:g.67057877G>A	ENSP00000402616:p.Arg17Lys	93.0	0.0	.		96.0	27.0	.	NM_207354	D6RCN6|Q0VAK0|Q0VGC3|Q6ZVD0|Q86SU1	Missense_Mutation	SNP	ENST00000447274.2	hg19		.	.	.	.	.	.	.	.	.	.	G	34	5.342333	0.95783	.	.	ENSG00000172932	ENST00000447274;ENST00000511455;ENST00000308440;ENST00000514166	T;T;T;T	0.31769	1.48;1.67;1.48;1.48	3.52	3.52	0.40303	.	0.058843	0.64402	D	0.000004	T	0.50240	0.1604	M	0.77103	2.36	0.58432	D	0.999996	D;P	0.76494	0.999;0.757	D;B	0.71656	0.974;0.397	T	0.52162	-0.8612	10	0.07990	T	0.79	-28.4454	15.0538	0.71897	0.0:0.0:1.0:0.0	.	104;17	Q6ZTN6-3;Q6ZTN6	.;AN13D_HUMAN	K	17;104;17;17	ENSP00000402616:R17K;ENSP00000427130:R104K;ENSP00000310874:R17K;ENSP00000444404:R17K	ENSP00000310874:R17K	R	+	2	0	ANKRD13D	66814453	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	6.544000	0.73878	2.265000	0.75225	0.655000	0.94253	AGG	.	.	.	none		0.627	ANKRD13D-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000371067.2	NM_207354		A	67057877	G	A	67057877	3	1	242	1	0	0	0	0	1	0	0	0	644	1000	35	2	321	2	ANKRD13D	11	67057877	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	447453	67057877	67948639	79	14883											
PAK1	5058	hgsc.bcm.edu	37	chr11	77103498	77103498	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttgctgccggctccaatcAtagtgctggtatttctcatc	6	15	8	12	1	2	0	2	0	1	0	5	0	3	0	2	2	3	4	2	2	3	4			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr11:77103498A>G	ENST00000356341.3	-	2	599	c.68T>C	c.(67-69)aTg>aCg	p.M23T	PAK1_ENST00000528203.1_Intron|PAK1_ENST00000530617.1_Missense_Mutation_p.M23T|PAK1_ENST00000278568.4_Missense_Mutation_p.M23T	NM_002576.4	NP_002567.3	Q13153	PAK1_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 1	23					actin cytoskeleton reorganization (GO:0031532)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cellular response to insulin stimulus (GO:0032869)|dendrite development (GO:0016358)|exocytosis (GO:0006887)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor clustering (GO:0043113)|response to hypoxia (GO:0001666)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|wound healing (GO:0042060)	axon (GO:0030424)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|intercalated disc (GO:0014704)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|Z disc (GO:0030018)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(13)|skin(2)|stomach(1)	29	all_cancers(14;1.75e-18)					GGCTCCAATCATAGTGCTGGT	0.483																																					p.M23T		Atlas-SNP	.											.	PAK1	89	.	0			c.T68C						PASS	.						110	103	105					11																	77103498		2200	4292	6492	SO:0001583	missense	5058	exon2			CCAATCATAGTGC	U51120	CCDS8250.1, CCDS44687.1	11q13-q14	2008-06-17	2008-06-17						8590	protein-coding gene	gene with protein product	"STE20 homolog, yeast"	602590	"p21/Cdc42/Rac1-activated kinase 1 (yeast Ste20-related)", "p21/Cdc42/Rac1-activated kinase 1 (STE20 homolog, yeast)"			8805275, 9533029	Standard	NM_002576		Approved		uc001oyg.4	Q13153		ENST00000356341.3:c.68T>C	chr11.hg19:g.77103498A>G	ENSP00000348696:p.Met23Thr	76.0	0.0	.		78.0	37.0	.	NM_001128620	O75561|Q13567|Q32M53|Q32M54|Q86W79	Missense_Mutation	SNP	ENST00000356341.3	hg19	CCDS8250.1	.	.	.	.	.	.	.	.	.	.	A	15.36	2.809226	0.50421	.	.	ENSG00000149269	ENST00000356341;ENST00000530617;ENST00000278568;ENST00000529248;ENST00000524847;ENST00000528592;ENST00000528633;ENST00000526968	T;T;T	0.69806	-0.4;-0.43;-0.43	6.17	6.17	0.99709	.	0.034131	0.85682	D	0.000000	T	0.61837	0.2379	L	0.43152	1.355	0.80722	D	1	B;B;B	0.23185	0.025;0.081;0.034	B;B;B	0.31390	0.045;0.129;0.062	T	0.56511	-0.7967	10	0.19590	T	0.45	.	15.3933	0.74767	1.0:0.0:0.0:0.0	.	23;23;23	B3KNX7;Q13153;Q13153-2	.;PAK1_HUMAN;.	T	23	ENSP00000348696:M23T;ENSP00000433423:M23T;ENSP00000278568:M23T	ENSP00000278568:M23T	M	-	2	0	PAK1	76781146	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.074000	0.89500	2.371000	0.80710	0.533000	0.62120	ATG	.	.	.	none		0.483	PAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382083.2	NM_002576		G	77103498	A	G	77103498	3	3	242	1	0	0	0	0	1	0	0	0	11406	217	8	3	1678	3	PAK1	11	77103498	Missense_Mutation	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10	10045621	77103498	57903018	80	14884											
MLL	4297	hgsc.bcm.edu	37	chr11	118366483	118366483	+	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	ttatgctcagtggcaggagcGagaggaaaacagccacactg	13	6	13	9	1	1	1	1	0	0	1	1	4	1	3	1	3	4	2	1	3	3	1			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr11:118366483G>A	ENST00000389506.5	+	19	5423	c.5423G>A	c.(5422-5424)cGa>cAa	p.R1808Q	KMT2A_ENST00000354520.4_Missense_Mutation_p.R1770Q|KMT2A_ENST00000534358.1_Missense_Mutation_p.R1811Q			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	1808					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)										TGGCAGGAGCGAGAGGAAAAC	0.458																																					p.R1811Q		Atlas-SNP	.											.	MLL	548	.	0			c.G5432A						PASS	.						111	112	112					11																	118366483		2200	4296	6496	SO:0001583	missense	4297	exon19			AGGAGCGAGAGGA	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.5423G>A	chr11.hg19:g.118366483G>A	ENSP00000374157:p.Arg1808Gln	184.0	0.0	.		153.0	68.0	.	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	hg19	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.941101	0.92526	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	D;D;D	0.84800	-1.89;-1.9;-1.81	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	D	0.88115	0.6350	L	0.31664	0.95	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.79108	0.919;0.992	D	0.86200	0.1618	10	0.33141	T	0.24	.	18.2774	0.90087	0.0:0.0:1.0:0.0	.	1811;1808	E9PQG7;Q03164	.;MLL1_HUMAN	Q	1811;1808;1770;718	ENSP00000436786:R1811Q;ENSP00000374157:R1808Q;ENSP00000346516:R1770Q	ENSP00000346516:R1770Q	R	+	2	0	MLL	117871693	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.411000	0.80078	2.830000	0.97506	0.585000	0.79938	CGA	.	.	.	none		0.458	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		A	118366483	G	A	118366483	3	1	242	1	0	0	0	0	1	0	0	0	9627	1058	37	1	5497	1	MLL	11	118366483	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	41262985	118366483	16640033	81	14885											
VWF	7450	hgsc.bcm.edu	37	chr12	6120943	6120943	+	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	gtgtggcactggtctggcaaGgtccagacgtccccgggctg	5	8	16	12	2	1	1	0	0	1	1	3	1	3	1	3	5	0	3	3	5	1	0			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr12:6120943G>C	ENST00000261405.5	-	34	5936	c.5682C>G	c.(5680-5682)acC>acG	p.T1894T		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	1894					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)	GGTCTGGCAAGGTCCAGACGT	0.582																																					p.T1894T		Atlas-SNP	.											.	VWF	338	.	0			c.C5682G						PASS	.						11	13	13					12																	6120943		2190	4266	6456	SO:0001819	synonymous_variant	7450	exon34			TGGCAAGGTCCAG		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.5682C>G	chr12.hg19:g.6120943G>C		245.0	0.0	.		249.0	110.0	.	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	hg19	CCDS8539.1																																																																																			.	.	.	none		0.582	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		C	6120943	G	C	6120943	2	2	242	1	0	0	0	0	0	0	0	1	17258	987	35	4		4	VWF	12	6120943	Silent	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10		6120943	127730952	82	14886											
CLEC4D	338339	hgsc.bcm.edu	37	chr12	8672900	8672900	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaatgccaaaggtcagtggCgttgggtggaccagacgcca	11	6	15	9	2	1	2	1	0	0	2	1	3	1	3	3	4	1	1	3	4	2	1			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr12:8672900C>T	ENST00000299665.2	+	5	656	c.463C>T	c.(463-465)Cgt>Tgt	p.R155C		NM_080387.4	NP_525126.2	Q8WXI8	CLC4D_HUMAN	C-type lectin domain family 4, member D	155	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				innate immune response (GO:0045087)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.R155C(1)		large_intestine(4)|lung(6)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Lung SC(5;0.184)					AGGTCAGTGGCGTTGGGTGGA	0.403																																					p.R155C		Atlas-SNP	.											CLEC4D,NS,carcinoma,0,1	CLEC4D	46	.	1	Substitution - Missense(1)	lung(1)	c.C463T						PASS	.						97	98	98					12																	8672900		2203	4300	6503	SO:0001583	missense	338339	exon5			CAGTGGCGTTGGG	AF411850	CCDS8593.1	12p13.31	2005-09-21	2005-02-09	2005-02-11		ENSG00000166527		"C-type lectin domain containing"	14554	protein-coding gene	gene with protein product		609964	"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 8"	CLECSF8			Standard	NM_080387		Approved	Mpcl	uc001qun.3	Q8WXI8		ENST00000299665.2:c.463C>T	chr12.hg19:g.8672900C>T	ENSP00000299665:p.Arg155Cys	86.0	0.0	.		71.0	5.0	.	NM_080387	Q8N5J5	Missense_Mutation	SNP	ENST00000299665.2	hg19	CCDS8593.1	.	.	.	.	.	.	.	.	.	.	C	15.95	2.983050	0.53827	.	.	ENSG00000166527	ENST00000299665	T	0.18502	2.21	4.67	1.48	0.22813	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	.	.	.	.	T	0.17238	0.0414	M	0.76727	2.345	0.27413	N	0.954503	B	0.10296	0.003	B	0.09377	0.004	T	0.23976	-1.0173	8	.	.	.	.	3.4237	0.07402	0.1972:0.5788:0.0:0.224	.	155	Q8WXI8	CLC4D_HUMAN	C	155	ENSP00000299665:R155C	.	R	+	1	0	CLEC4D	8564167	0.099000	0.21834	0.689000	0.30133	0.721000	0.41392	0.074000	0.14662	0.606000	0.29965	-0.135000	0.14842	CGT	.	.	.	none		0.403	CLEC4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400565.1	NM_080387		T	8672900	C	T	8672900	3	4	242	1	0	0	0	0	1	0	0	0	3516	768	27	1	481	1	CLEC4D	12	8672900	Missense_Mutation	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10	2551957	8672900	125178995	83	14887											
MAGOHB	55110	hgsc.bcm.edu	37	chr12	10762497	10762497	+	Missense_Mutation	SNP	A	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	ttgtaatttcactgtcatcaAtaattctcttcagttcttcc	9	19	3	10	0	6	0	4	0	2	0	8	0	7	0	1	0	0	2	1	0	3	8			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr12:10762497A>C	ENST00000320756.2	-	3	287	c.197T>G	c.(196-198)aTt>aGt	p.I66S	MAGOHB_ENST00000381881.2_Intron|MAGOHB_ENST00000539554.1_Missense_Mutation_p.I20S	NM_018048.3	NP_060518.1	Q96A72	MGN2_HUMAN	mago-nashi homolog B (Drosophila)	66					mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|large_intestine(2)	4						ACTGTCATCAATAATTCTCTT	0.368																																					p.I66S		Atlas-SNP	.											.	MAGOHB	17	.	0			c.T197G						PASS	.						128	127	127					12																	10762497		2203	4300	6503	SO:0001583	missense	55110	exon3			TCATCAATAATTC		CCDS8628.1	12p13.2	2014-02-12	2008-01-24		ENSG00000111196	ENSG00000111196			25504	protein-coding gene	gene with protein product							Standard	NM_018048		Approved	FLJ10292, MGN2	uc001qyq.2	Q96A72	OTTHUMG00000168407	ENST00000320756.2:c.197T>G	chr12.hg19:g.10762497A>C	ENSP00000319240:p.Ile66Ser	57.0	0.0	.		60.0	32.0	.	NM_018048		Missense_Mutation	SNP	ENST00000320756.2	hg19	CCDS8628.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.153073	0.78001	.	.	ENSG00000111196	ENST00000539554;ENST00000320756	.	.	.	4.61	4.61	0.57282	.	0.000000	0.85682	U	0.000000	D	0.84982	0.5593	M	0.93420	3.415	0.80722	D	1	D	0.69078	0.997	D	0.75484	0.986	D	0.88474	0.3064	9	0.87932	D	0	.	12.6083	0.56535	1.0:0.0:0.0:0.0	.	66	Q96A72	MGN2_HUMAN	S	20;66	.	ENSP00000319240:I66S	I	-	2	0	MAGOHB	10653764	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.162000	0.89657	2.293000	0.77203	0.482000	0.46254	ATT	.	.	.	none		0.368	MAGOHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399616.1	NM_018048		C	10762497	A	C	10762497	3	2	242	1	0	0	0	0	1	0	0	0	9202	101	4	5	261	5	MAGOHB	12	10762497	Missense_Mutation	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10	2089597	10762497	123089398	84	14888											
LIMA1	51474	hgsc.bcm.edu	37	chr12	50571335	50571336	+	Frame_Shift_Ins	INS	-	-	A																															ctcttgacagaggtgctttgINSaaatgaagctgctacagtga																										TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr12:50571335_50571336insA	ENST00000341247.4	-	11	1940_1941	c.1791_1792insT	c.(1789-1794)tttcaafs	p.Q598fs	LIMA1_ENST00000552909.1_Frame_Shift_Ins_p.Q437fs|LIMA1_ENST00000552783.1_Frame_Shift_Ins_p.Q439fs|LIMA1_ENST00000394943.3_Frame_Shift_Ins_p.Q599fs|LIMA1_ENST00000552823.1_Frame_Shift_Ins_p.Q438fs|LIMA1_ENST00000547825.1_Frame_Shift_Ins_p.Q296fs|LIMA1_ENST00000552491.1_Frame_Shift_Ins_p.Q295fs	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	598					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)	p.Q598E(1)		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						GAGGTGCTTTGAAATGAAGCTG	0.495																																					p.Q599fs		Atlas-Indel,Pindel	.											LIMA1,NS,carcinoma,0,1	LIMA1	67	.	1	Substitution - Missense(1)	lung(1)	c.1795_1796insT						PASS	.																																			SO:0001589	frameshift_variant	51474	exon11			.	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.1792dupT	chr12.hg19:g.50571338_50571338dupA	ENSP00000340184:p.Gln598fs	65.0	0.0	0		50.0	22.0	0.44	NM_001113546	B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Frame_Shift_Ins	INS	ENST00000341247.4	hg19	CCDS8802.1																																																																																			.	.	.	none		0.495	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357		A	50571336	-	A	50571335	7	5	242	1	0	1	1	0	0	0	0	0	8803	1299	45	0	491	0	LIMA1	12	50571335	Frame_Shift_Ins	INS	-	TCGA-SX-A71S-01A-11D-A33Q-10	39808838	50571335	83280560	85	14889											
PTPRR	5801	hgsc.bcm.edu	37	chr12	71155251	71155251	+	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	tgtttcgtgcaacaacatacCtcaggagagacttctgtaat	12	12	8	9	1	2	1	1	0	1	1	3	3	2	2	1	1	4	3	1	1	4	4			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr12:71155251C>A	ENST00000283228.2	-	4	1079	c.627G>T	c.(625-627)gaG>gaT	p.E209D	PTPRR_ENST00000342084.4_Splice_Site_p.E97D	NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	209					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)		AACAACATACCTCAGGAGAGA	0.373																																					p.E209D		Atlas-SNP	.											.	PTPRR	109	.	0			c.G627T						PASS	.						124	127	126					12																	71155251		2203	4300	6503	SO:0001630	splice_region_variant	5801	exon4			ACATACCTCAGGA	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.627+1G>T	chr12.hg19:g.71155251C>A		73.0	0.0	.		83.0	37.0	.	NM_002849	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Missense_Mutation	SNP	ENST00000283228.2	hg19	CCDS8998.1	.	.	.	.	.	.	.	.	.	.	C	15.46	2.839074	0.51057	.	.	ENSG00000153233	ENST00000283228;ENST00000342084	T;T	0.35421	1.31;1.31	5.68	5.68	0.88126	.	0.121494	0.36234	U	0.002712	T	0.52403	0.1732	L	0.57536	1.79	0.80722	D	1	D;D	0.55605	0.967;0.972	P;P	0.55391	0.775;0.675	T	0.41431	-0.9509	9	.	.	.	-17.9149	19.7965	0.96487	0.0:1.0:0.0:0.0	.	97;209	F5GXR7;Q15256	.;PTPRR_HUMAN	D	209;97	ENSP00000283228:E209D;ENSP00000339605:E97D	.	E	-	3	2	PTPRR	69441518	1.000000	0.71417	1.000000	0.80357	0.128000	0.20619	6.292000	0.72725	2.686000	0.91538	0.448000	0.29417	GAG	.	.	.	none		0.373	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849	Missense_Mutation	A	71155251	C	A	71155251	5	1	242	1	0	0	0	0	0	0	1	0	12823	695	24	4	1390	4	PTPRR	12	71155251	Splice_Site	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10	20583916	71155251	62696644	86	14890											
APAF1	317	hgsc.bcm.edu	37	chr12	99109218	99109218	+	Frame_Shift_Del	DEL	T	T	-																															tttgaagattttagaacttgTaaacaatagaatcttccagt																										TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr12:99109218delT	ENST00000551964.1	+	22	3708	c.2972delT	c.(2971-2973)gtafs	p.V991fs	APAF1_ENST00000550527.1_Frame_Shift_Del_p.V980fs|APAF1_ENST00000547045.1_Frame_Shift_Del_p.V948fs|APAF1_ENST00000552268.1_Intron|APAF1_ENST00000357310.1_Frame_Shift_Del_p.V948fs|APAF1_ENST00000339433.3_Frame_Shift_Del_p.V948fs|APAF1_ENST00000359972.2_Frame_Shift_Del_p.V937fs|APAF1_ENST00000333991.1_Intron|APAF1_ENST00000549007.1_Frame_Shift_Del_p.V948fs	NM_181861.1	NP_863651.1	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1	991					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway (GO:0097193)|nervous system development (GO:0007399)|neural tube closure (GO:0001843)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|response to G1 DNA damage checkpoint signaling (GO:0072432)	apoptosome (GO:0043293)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(1)	42					Adenosine triphosphate(DB00171)	TTAGAACTTGTAAACAATAGA	0.343																																					p.V991X		Atlas-Indel,Pindel	.											.	APAF1	111	.	0			c.2971delG						PASS	.						62	60	60					12																	99109218		2203	4300	6503	SO:0001589	frameshift_variant	317	exon22			.	AF013263	CCDS9069.1, CCDS9070.1, CCDS9071.1, CCDS55862.1, CCDS55863.1	12q23	2013-01-10	2006-10-23			ENSG00000120868		"WD repeat domain containing"	576	protein-coding gene	gene with protein product		602233	"apoptotic protease activating factor", "apoptotic peptidase activating factor"			9267021, 10702682	Standard	NM_181861		Approved	CED4, APAF-1	uc001tfz.3	O14727	OTTHUMG00000170214	ENST00000551964.1:c.2972delT	chr12.hg19:g.99109218delT	ENSP00000448165:p.Val991fs	44.0	0.0	0		40.0	16.0	0.4	NM_181861	B2RMX8|O43297|Q7Z438|Q9BXZ6|Q9UBZ5|Q9UGN8|Q9UGN9|Q9UGP0|Q9UJ58|Q9UJ59|Q9UJ60|Q9UJ61|Q9UJ62|Q9UJ63|Q9UJ64|Q9UJ65|Q9UJ66|Q9UJ67|Q9UNC9	Frame_Shift_Del	DEL	ENST00000551964.1	hg19	CCDS9069.1																																																																																			.	.	.	none		0.343	APAF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408006.1	NM_181861.1		-	99109218	T	-	99109218	7	5	242	1	0	1	0	1	0	0	0	0	755	1638	57	0	3054	0	APAF1	12	99109218	Frame_Shift_Del	DEL	T	TCGA-SX-A71S-01A-11D-A33Q-10	27953967	99109218	34742677	87	14891											
DTX1	1840	hgsc.bcm.edu	37	chr12	113531444	113531444	+	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	cccgtgagcaagagcgacgtGaagcccgtgcctggcgtgcc	7	5	15	14	5	0	3	0	2	0	1	0	4	0	3	4	1	5	1	4	1	2	0			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr12:113531444G>T	ENST00000257600.3	+	4	1607	c.1104G>T	c.(1102-1104)gtG>gtT	p.V368V	DTX1_ENST00000547974.1_3'UTR	NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN	deltex 1, E3 ubiquitin ligase	368	Pro-rich.				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						AGAGCGACGTGAAGCCCGTGC	0.677																																					p.V368V		Atlas-SNP	.											.	DTX1	83	.	0			c.G1104T						PASS	.						22	28	26					12																	113531444		2203	4299	6502	SO:0001819	synonymous_variant	1840	exon4			CGACGTGAAGCCC	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.1104G>T	chr12.hg19:g.113531444G>T		56.0	0.0	.		42.0	21.0	.	NM_004416	O60630|Q9BS04	Silent	SNP	ENST00000257600.3	hg19	CCDS9164.1																																																																																			.	.	.	none		0.677	DTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405045.2			T	113531444	G	T	113531444	2	4	242	1	0	0	0	0	0	0	0	1	4795	1277	45	4		4	DTX1	12	113531444	Silent	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	14422226	113531444	20320451	88	14892											
KCTD12	115207	hgsc.bcm.edu	37	chr13	77459491	77459491	+	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	gtaatagcgcgaggtgtagcGctccgggggacggtcggggt	6	7	20	8	6	0	0	0	0	0	0	2	2	1	1	1	6	2	3	1	6	3	3			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr13:77459491G>C	ENST00000377474.2	-	1	1034	c.793C>G	c.(793-795)Cgc>Ggc	p.R265G	AC000403.1_ENST00000579275.1_RNA|KCTD12_ENST00000317765.2_Missense_Mutation_p.R265G	NM_138444.3	NP_612453.1	Q96CX2	KCD12_HUMAN	potassium channel tetramerization domain containing 12	265					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(1)|lung(1)|ovary(1)	4		Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.0499)		GAGGTGTAGCGCTCCGGGGGA	0.637											OREG0022449	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R265G		Atlas-SNP	.											.	KCTD12	11	.	0			c.C793G						PASS	.						38	33	35					13																	77459491		2203	4300	6503	SO:0001583	missense	115207	exon1			TGTAGCGCTCCGG	AF359381	CCDS9455.1	13q21	2013-06-20	2013-06-20	2003-11-26	ENSG00000178695	ENSG00000178695			14678	protein-coding gene	gene with protein product	"predominantly fetal expressed T1 domain"	610521	"chromosome 13 open reading frame 2", "potassium channel tetramerisation domain containing 12"	C13orf2		15357420	Standard	NM_138444		Approved	KIAA1778, PFET1	uc010aeu.1	Q96CX2	OTTHUMG00000017096	ENST00000377474.2:c.793C>G	chr13.hg19:g.77459491G>C	ENSP00000366694:p.Arg265Gly	48.0	0.0	.	1175	40.0	11.0	.	NM_138444		Missense_Mutation	SNP	ENST00000377474.2	hg19	CCDS9455.1	.	.	.	.	.	.	.	.	.	.	G	16.70	3.197163	0.58126	.	.	ENSG00000178695	ENST00000377474;ENST00000317765	T;T	0.55588	0.51;0.51	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.52240	0.1722	M	0.68952	2.095	0.80722	D	1	P	0.44578	0.838	B	0.41088	0.347	T	0.59343	-0.7472	10	0.56958	D	0.05	.	12.9674	0.58492	0.0:0.0:0.838:0.162	.	265	Q96CX2	KCD12_HUMAN	G	265	ENSP00000366694:R265G;ENSP00000317141:R265G	ENSP00000317141:R265G	R	-	1	0	KCTD12	76357492	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.246000	0.32803	2.399000	0.81585	0.462000	0.41574	CGC	.	.	.	none		0.637	KCTD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045309.2	NM_138444		C	77459491	G	C	77459491	3	2	242	1	0	0	0	0	1	0	0	0	8106	1087	38	4	188	4	KCTD12	13	77459491	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10		77459491	37710387	89	14893											
CPNE6	9362	hgsc.bcm.edu	37	chr14	24546923	24546923	+	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	ctgcacactggctacgactcCcagccctagcccgtgactgc	7	7	9	18	2	0	1	0	1	0	0	1	2	1	1	3	1	5	2	3	1	2	2			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr14:24546923C>A	ENST00000397016.2	+	17	1969	c.1658C>A	c.(1657-1659)cCc>cAc	p.P553H	CPNE6_ENST00000216775.2_Missense_Mutation_p.P553H|CPNE6_ENST00000537691.1_Missense_Mutation_p.P608H	NM_001280558.1	NP_001267487.1	O95741	CPNE6_HUMAN	copine VI (neuronal)	553					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)		GCTACGACTCCCAGCCCTAGC	0.652																																					p.P553H		Atlas-SNP	.											.	CPNE6	40	.	0			c.C1658A						PASS	.						32	34	33					14																	24546923		2200	4300	6500	SO:0001583	missense	9362	exon16			CGACTCCCAGCCC	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.1658C>A	chr14.hg19:g.24546923C>A	ENSP00000380211:p.Pro553His	51.0	0.0	.		45.0	18.0	.	NM_006032	B2RAG6|B7Z1M3|D3DS55|F5GXN1|Q53HA6|Q8WVG1	Missense_Mutation	SNP	ENST00000397016.2	hg19	CCDS9607.1	.	.	.	.	.	.	.	.	.	.	C	15.50	2.851144	0.51270	.	.	ENSG00000100884	ENST00000537691;ENST00000397016;ENST00000216775	T;T;T	0.07567	3.18;3.22;3.22	5.3	5.3	0.74995	.	0.000000	0.47455	D	0.000232	T	0.11495	0.0280	L	0.53249	1.67	0.40964	D	0.98464	P;B	0.41569	0.755;0.036	B;B	0.42386	0.386;0.063	T	0.01136	-1.1440	10	0.66056	D	0.02	-1.2104	9.9851	0.41837	0.0:0.9081:0.0:0.0919	.	608;553	F5GXN1;O95741	.;CPNE6_HUMAN	H	608;553;553	ENSP00000440077:P608H;ENSP00000380211:P553H;ENSP00000216775:P553H	ENSP00000216775:P553H	P	+	2	0	CPNE6	23616763	0.873000	0.30073	0.996000	0.52242	0.727000	0.41649	1.078000	0.30754	2.467000	0.83353	0.561000	0.74099	CCC	.	.	.	none		0.652	CPNE6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071869.5			A	24546923	C	A	24546923	3	1	242	1	0	0	0	0	1	0	0	0	3818	623	22	4	1716	4	CPNE6	14	24546923	Missense_Mutation	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10		24546923	82802617	90	14894											
TXNDC16	57544	hgsc.bcm.edu	37	chr14	52899033	52899033	+	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	cctataaaattagttcacttTtgagcatcctaactctttat	12	17	3	9	0	2	1	1	1	1	0	3	1	3	1	2	0	2	2	2	0	6	9			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr14:52899033T>A	ENST00000281741.4	-	21	2838	c.2467A>T	c.(2467-2469)Aaa>Taa	p.K823*		NM_001160047.1|NM_020784.2	NP_001153519.1|NP_065835.2	Q9P2K2	TXD16_HUMAN	thioredoxin domain containing 16	823					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)					TAGTTCACTTTTGAGCATCCT	0.289																																					p.K823X		Atlas-SNP	.											.	TXNDC16	59	.	0			c.A2467T						PASS	.						72	67	69					14																	52899033		2203	4299	6502	SO:0001587	stop_gained	57544	exon21			TCACTTTTGAGCA	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.2467A>T	chr14.hg19:g.52899033T>A	ENSP00000281741:p.Lys823*	67.0	0.0	.		56.0	27.0	.	NM_020784	A5PKW9|A7E260|A7MD07|B9EH67|Q9H9W7	Nonsense_Mutation	SNP	ENST00000281741.4	hg19	CCDS32083.1	.	.	.	.	.	.	.	.	.	.	T	38	6.750790	0.97813	.	.	ENSG00000087301	ENST00000281741	.	.	.	5.07	-0.183	0.13284	.	1.550970	0.04296	N	0.346487	.	.	.	.	.	.	0.09310	N	0.999997	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.9709	7.2863	0.26342	0.0:0.0915:0.5545:0.3539	.	.	.	.	X	823	.	ENSP00000281741:K823X	K	-	1	0	TXNDC16	51968783	0.041000	0.20044	0.012000	0.15200	0.006000	0.05464	0.206000	0.17375	0.019000	0.15079	-0.340000	0.08031	AAA	.	.	.	none		0.289	TXNDC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411681.1	XM_051699		A	52899033	T	A	52899033	4	1	242	1	0	0	0	0	0	1	0	0	16807	1850	64	5	14	5	TXNDC16	14	52899033	Nonsense_Mutation	SNP	T	TCGA-SX-A71S-01A-11D-A33Q-10	28352110	52899033	54450507	91	14895											
YLPM1	56252	hgsc.bcm.edu	37	chr14	75265567	75265567	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatcaccgggatgagcctccTagggctccatggaaccatgg	9	8	12	12	1	1	1	1	1	0	0	3	3	3	3	5	4	2	1	5	4	3	2			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr14:75265567T>C	ENST00000325680.7	+	5	3691	c.3567T>C	c.(3565-3567)ccT>ccC	p.P1189P	YLPM1_ENST00000552421.1_Intron|YLPM1_ENST00000238571.3_Silent_p.P994P	NM_019589.2	NP_062535.2	P49750	YLPM1_HUMAN	YLP motif containing 1	994	Arg-rich.				regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		ATGAGCCTCCTAGGGCTCCAT	0.483																																					p.P1189P		Atlas-SNP	.											.	YLPM1	298	.	0			c.T3567C						PASS	.						60	58	58					14																	75265567		1899	4114	6013	SO:0001819	synonymous_variant	56252	exon5			GCCTCCTAGGGCT	AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 169"		"chromosome 14 open reading frame 170"	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000325680.7:c.3567T>C	chr14.hg19:g.75265567T>C		92.0	0.0	.		62.0	32.0	.	NM_019589	P49752|Q96I64|Q9P1V7	Silent	SNP	ENST00000325680.7	hg19	CCDS45135.1																																																																																			.	.	.	none		0.483	YLPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404451.1	NM_019589		C	75265567	T	C	75265567	2	2	242	1	0	0	0	0	0	0	0	1	17498	1509	53	3		3	YLPM1	14	75265567	Silent	SNP	T	TCGA-SX-A71S-01A-11D-A33Q-10	22366534	75265567	32083973	92	14896											
C14orf159	80017	hgsc.bcm.edu	37	chr14	91642285	91642285	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttccatctgcagaactgttGggaatcaaagagctttccaa	12	12	8	9	0	2	2	1	0	1	2	4	3	4	3	2	1	3	3	2	1	4	3			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr14:91642285G>A	ENST00000523771.1	+	7	1203	c.600G>A	c.(598-600)ttG>ttA	p.L200L	C14orf159_ENST00000522322.1_Silent_p.L200L|C14orf159_ENST00000428926.2_Silent_p.L200L|C14orf159_ENST00000518868.1_Silent_p.L205L|C14orf159_ENST00000520328.1_Silent_p.L188L|C14orf159_ENST00000521077.2_Silent_p.L205L|C14orf159_ENST00000523816.1_Silent_p.L200L|C14orf159_ENST00000412671.2_Silent_p.L205L|C14orf159_ENST00000256324.10_Silent_p.L205L|C14orf159_ENST00000525393.2_Silent_p.L76L			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	200						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)		CAGAACTGTTGGGAATCAAAG	0.483																																					p.L205L		Atlas-SNP	.											.	C14orf159	57	.	0			c.G615A						PASS	.						105	99	101					14																	91642285		2203	4300	6503	SO:0001819	synonymous_variant	80017	exon7			ACTGTTGGGAATC	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.600G>A	chr14.hg19:g.91642285G>A		107.0	0.0	.		81.0	34.0	.	NM_001102368	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Silent	SNP	ENST00000523771.1	hg19	CCDS32141.1																																																																																			.	.	.	none		0.483	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952		A	91642285	G	A	91642285	2	1	242	1	0	0	0	0	0	0	0	1	1757	1339	47	2		2	C14orf159	14	91642285	Silent	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	16376718	91642285	15707255	93	14897											
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102514292	102514292	+	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	ctggatgcggacactgcacaCcaccgcgtccaactggctgc	8	6	11	16	3	0	0	0	0	0	0	1	2	1	2	3	3	4	2	3	3	1	0			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr14:102514292C>G	ENST00000360184.4	+	73	13309	c.13145C>G	c.(13144-13146)aCc>aGc	p.T4382S	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	4382					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						ACACTGCACACCACCGCGTCC	0.642																																					p.T4382S		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.C13145G						PASS	.						118	73	88					14																	102514292		2203	4300	6503	SO:0001583	missense	1778	exon73			TGCACACCACCGC	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.13145C>G	chr14.hg19:g.102514292C>G	ENSP00000348965:p.Thr4382Ser	22.0	0.0	.		29.0	14.0	.	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	hg19	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	C	11.14	1.550260	0.27652	.	.	ENSG00000197102	ENST00000360184	T	0.08193	3.12	5.37	5.37	0.77165	Dynein heavy chain (1);	0.160376	0.56097	D	0.000033	T	0.06005	0.0156	N	0.20766	0.605	0.49130	D	0.999759	B	0.02656	0.0	B	0.06405	0.002	T	0.41484	-0.9506	10	0.18710	T	0.47	.	12.4528	0.55686	0.0:0.9233:0.0:0.0767	.	4382	Q14204	DYHC1_HUMAN	S	4382	ENSP00000348965:T4382S	ENSP00000348965:T4382S	T	+	2	0	DYNC1H1	101584045	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	3.949000	0.56668	2.509000	0.84616	0.655000	0.94253	ACC	.	.	.	none		0.642	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		G	102514292	C	G	102514292	3	3	242	1	0	0	0	0	1	0	0	0	4843	507	18	4	13435	4	DYNC1H1	14	102514292	Missense_Mutation	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10	10872007	102514292	4835248	94	14898											
HERC2	8924	hgsc.bcm.edu	37	chr15	28457714	28457714	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggcaggttgttcacattaaAggccacggcagggagctgga	10	7	16	8	1	1	0	1	0	0	0	1	2	1	2	1	6	1	5	1	6	2	3			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr15:28457714A>G	ENST00000261609.7	-	43	6910	c.6802T>C	c.(6802-6804)Ttt>Ctt	p.F2268L		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)		TTCACATTAAAGGCCACGGCA	0.478																																					p.F2268L		Atlas-SNP	.											.	HERC2	501	.	0			c.T6802C						PASS	.						12	12	12					15																	28457714		2161	4231	6392	SO:0001583	missense	8924	exon43			CATTAAAGGCCAC	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.6802T>C	chr15.hg19:g.28457714A>G	ENSP00000261609:p.Phe2268Leu	219.0	0.0	.		178.0	70.0	.	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	A	15.66	2.900211	0.52227	.	.	ENSG00000128731	ENST00000261609	T	0.48522	0.81	4.57	4.57	0.56435	.	0.000000	0.85682	D	0.000000	T	0.67183	0.2866	M	0.80422	2.495	0.80722	D	1	P	0.49447	0.924	P	0.60682	0.878	T	0.72766	-0.4194	10	0.72032	D	0.01	.	14.0923	0.65000	1.0:0.0:0.0:0.0	.	2268	O95714	HERC2_HUMAN	L	2268	ENSP00000261609:F2268L	ENSP00000261609:F2268L	F	-	1	0	HERC2	26131309	1.000000	0.71417	0.179000	0.23059	0.494000	0.33585	9.125000	0.94402	1.906000	0.55180	0.254000	0.18369	TTT	.	.	.	none		0.478	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		G	28457714	A	G	28457714	3	3	242	1	0	0	0	0	1	0	0	0	7065	72	3	3	7906	3	HERC2	15	28457714	Missense_Mutation	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10		28457714	74073678	95	14899											
CALML4	91860	hgsc.bcm.edu	37	chr15	68489951	68489951	+	Missense_Mutation	SNP	A	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	tcagaaaagtggagaaatccAgctctccatttccgtctagg	12	10	9	10	1	3	2	1	0	2	2	6	3	5	2	3	2	1	1	3	2	4	2			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr15:68489951A>C	ENST00000467889.1	-	4	504	c.320T>G	c.(319-321)cTg>cGg	p.L107R	CALML4_ENST00000448060.2_Missense_Mutation_p.L60R|RP11-315D16.2_ENST00000562767.1_Silent_p.A33A|CALML4_ENST00000395465.3_Intron|CALML4_ENST00000540479.1_Missense_Mutation_p.L31R	NM_033429.2	NP_219501.2	Q96GE6	CALL4_HUMAN	calmodulin-like 4	107	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)			large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	4						GGAGAAATCCAGCTCTCCATT	0.478																																					p.L107R		Atlas-SNP	.											.	CALML4	16	.	0			c.T320G						PASS	.						104	95	98					15																	68489951		1887	4129	6016	SO:0001583	missense	91860	exon4			AAATCCAGCTCTC	AF308287	CCDS10226.2, CCDS42052.1, CCDS66808.1	15q22.31	2013-01-10			ENSG00000129007	ENSG00000129007		"EF-hand domain containing"	18445	protein-coding gene	gene with protein product							Standard	NM_033429		Approved	MGC4809, NY-BR-20	uc002arb.3	Q96GE6	OTTHUMG00000133287	ENST00000467889.1:c.320T>G	chr15.hg19:g.68489951A>C	ENSP00000419081:p.Leu107Arg	40.0	0.0	.		52.0	15.0	.	NM_033429	B4DL15|F8W6Y4|Q6MZY3|Q6N048|Q9H286	Missense_Mutation	SNP	ENST00000467889.1	hg19	CCDS10226.2	.	.	.	.	.	.	.	.	.	.	A	21.1	4.101169	0.76983	.	.	ENSG00000129007	ENST00000448060;ENST00000540479;ENST00000467889	T;T;T	0.80738	-1.41;0.68;-1.18	5.0	5.0	0.66597	EF-hand-like domain (1);	0.073080	0.56097	D	0.000024	D	0.91422	0.7293	M	0.91561	3.22	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.994;0.997	D	0.93345	0.6713	10	0.87932	D	0	-21.1778	14.6621	0.68879	1.0:0.0:0.0:0.0	.	60;107	F8W6Y4;Q96GE6	.;CALL4_HUMAN	R	60;31;107	ENSP00000400755:L60R;ENSP00000438177:L31R;ENSP00000419081:L107R	ENSP00000400755:L60R	L	-	2	0	CALML4	66277005	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	8.844000	0.92147	2.002000	0.58637	0.402000	0.26972	CTG	.	.	.	none		0.478	CALML4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257067.3	NM_033429		C	68489951	A	C	68489951	3	2	242	1	0	0	0	0	1	0	0	0	2590	188	7	5	278	5	CALML4	15	68489951	Missense_Mutation	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10	40032237	68489951	34041441	96	14900											
ADAMTS17	170691	hgsc.bcm.edu	37	chr15	100882071	100882071	+	Frame_Shift_Del	DEL	G	G	-																															cagcagcagcagcacgggcaGgacgagcggaggcagcaggg																										TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr15:100882071delG	ENST00000268070.4	-	1	139	c.34delC	c.(34-36)ctgfs	p.L12fs	SPATA41_ENST00000560282.1_lincRNA	NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	12						proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)	50	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		AGCACGGGCAGGACGAGCGGA	0.741																																					p.L12fs		Atlas-Indel,Pindel	.											.	ADAMTS17	127	.	0			c.35delT						PASS	.						23	23	23					15																	100882071		2092	4138	6230	SO:0001589	frameshift_variant	170691	exon1			.	AJ315735	CCDS10383.1	15q24	2014-01-28	2005-08-19		ENSG00000140470	ENSG00000140470		"ADAM metallopeptidases with thrombospondin type 1 motif"	17109	protein-coding gene	gene with protein product		607511	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17"			11867212	Standard	NM_139057		Approved	FLJ32769, FLJ16363	uc002bvv.1	Q8TE56	OTTHUMG00000149867	ENST00000268070.4:c.34delC	chr15.hg19:g.100882071delG	ENSP00000268070:p.Leu12fs	85.0	0.0	0		74.0	23.0	0.310811	NM_139057	Q2I7G4|Q6ZN75	Frame_Shift_Del	DEL	ENST00000268070.4	hg19	CCDS10383.1																																																																																			.	.	.	none		0.741	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1	NM_139057		-	100882071	G	-	100882071	7	5	242	1	0	1	0	1	0	0	0	0	262	991	35	0	3341	0	ADAMTS17	15	100882071	Frame_Shift_Del	DEL	G	TCGA-SX-A71S-01A-11D-A33Q-10	32392120	100882071	1649321	97	14901											
LINS1	55180	hgsc.bcm.edu	37	chr15	101120996	101120997	+	Frame_Shift_Ins	INS	-	-	A																															tcattttcaagtgtggctccINSaagaagtaccttcttgtata																								rs141782332	byFrequency	TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr15:101120996_101120997insA	ENST00000314742.8	-	2	273_274	c.51_52insT	c.(49-54)cttggafs	p.G18fs	LINS_ENST00000560133.1_Intron|LINS_ENST00000559149.1_5'UTR|LINS_ENST00000561308.1_Frame_Shift_Ins_p.G18fs	NM_001040616.2	NP_001035706	Q8NG48	LINES_HUMAN	lines homolog (Drosophila)	18										central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(4)	21						AGTGTGGCTCCAAGAAGTACCT	0.371																																					p.G18fs		Atlas-Indel,Pindel	.											.	LINS	62	.	0			c.52_53insT						PASS	.																																			SO:0001589	frameshift_variant	55180	exon2			.	AK095448	CCDS10385.1	15q26.3	2010-09-08	2010-09-08	2010-09-08	ENSG00000140471	ENSG00000140471			30922	protein-coding gene	gene with protein product		610350	"lines homolog 1 (Drosophila)"	LINS1		12119551, 8889548	Standard	NM_001040616		Approved	WINS1	uc002bwg.3	Q8NG48	OTTHUMG00000149865	ENST00000314742.8:c.52dupT	chr15.hg19:g.101120998_101120998dupA	ENSP00000318423:p.Gly18fs	93.0	0.0	0		80.0	42.0	0.525	NM_001040616	Q96FW2|Q9NVQ3	Frame_Shift_Ins	INS	ENST00000314742.8	hg19	CCDS10385.1																																																																																			.	.	.	none		0.371	LINS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313592.1	NM_018148		A	101120997	-	A	101120996	7	5	242	1	0	1	1	0	0	0	0	0	8825	603	21	0	2245	0	LINS1	15	101120996	Frame_Shift_Ins	INS	-	TCGA-SX-A71S-01A-11D-A33Q-10	238925	101120996	1410396	98	14902											
DNAJA3	9093	hgsc.bcm.edu	37	chr16	4504895	4504895	+	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	agggattcctttccaaacttAagaaaatgtttacctcatga	14	13	6	8	0	1	2	1	1	0	1	3	3	3	3	3	1	2	1	3	1	5	5			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr16:4504895A>T	ENST00000262375.6	+	11	1500	c.1423A>T	c.(1423-1425)Aag>Tag	p.K475*	DNAJA3_ENST00000355296.4_Intron|DNAJA3_ENST00000431375.2_Intron	NM_005147.5	NP_005138.3	Q96EY1	DNJA3_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 3	475					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation-induced cell death of T cells (GO:0006924)|cell aging (GO:0007569)|mitochondrial DNA replication (GO:0006264)|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 I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of programmed cell death (GO:0043069)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell proliferation (GO:0042102)|protein folding (GO:0006457)|protein stabilization (GO:0050821)|response to heat (GO:0009408)|response to interferon-gamma (GO:0034341)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|small GTPase mediated signal transduction (GO:0007264)|T cell differentiation in thymus (GO:0033077)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of plasma membrane (GO:0019897)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|interferon-gamma receptor binding (GO:0005133)|metal ion binding (GO:0046872)|NF-kappaB binding (GO:0051059)|protein kinase binding (GO:0019901)|small GTPase regulator activity (GO:0005083)|transcription factor binding (GO:0008134)			NS(1)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|upper_aerodigestive_tract(2)	15						TTCCAAACTTAAGAAAATGTT	0.502																																					p.K475X		Atlas-SNP	.											.	DNAJA3	52	.	0			c.A1423T						PASS	.						78	75	76					16																	4504895		2197	4300	6497	SO:0001587	stop_gained	9093	exon11			AAACTTAAGAAAA	AF061749	CCDS10515.1, CCDS45400.1, CCDS66930.1	16p13.3	2011-09-02			ENSG00000103423	ENSG00000103423		"Heat shock proteins / DNAJ (HSP40)"	11808	protein-coding gene	gene with protein product		608382		TID1		9683573	Standard	NM_005147		Approved	hTid-1	uc002cwk.3	Q96EY1	OTTHUMG00000129470	ENST00000262375.6:c.1423A>T	chr16.hg19:g.4504895A>T	ENSP00000262375:p.Lys475*	111.0	0.0	.		87.0	40.0	.	NM_005147	B2RAJ5|B4DI33|E7ES32|O75472|Q8WUJ6|Q8WXJ3|Q96D76|Q96IV1|Q9NYH8	Nonsense_Mutation	SNP	ENST00000262375.6	hg19	CCDS10515.1	.	.	.	.	.	.	.	.	.	.	A	38	7.066242	0.98040	.	.	ENSG00000103423	ENST00000262375	.	.	.	5.49	5.49	0.81192	.	0.152909	0.41938	D	0.000786	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-22.0755	14.7634	0.69621	1.0:0.0:0.0:0.0	.	.	.	.	X	475	.	ENSP00000262375:K475X	K	+	1	0	DNAJA3	4444896	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.482000	0.81143	2.085000	0.62840	0.482000	0.46254	AAG	.	.	.	none		0.502	DNAJA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251633.1			T	4504895	A	T	4504895	4	4	242	1	0	0	0	0	0	1	0	0	4615	363	13	5	1465	5	DNAJA3	16	4504895	Nonsense_Mutation	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10		4504895	85849858	99	14903											
ITGAX	3687	hgsc.bcm.edu	37	chr16	31391906	31391908	+	In_Frame_Del	DEL	CTC	CTC	-																															acgttcgacacatccgtgtaCtcccagcttccaggacagga																										TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr16:31391906_31391908delCTC	ENST00000268296.4	+	28	3358_3360	c.3237_3239delCTC	c.(3235-3240)tactcc>tac	p.S1080del	ITGAX_ENST00000562522.1_In_Frame_Del_p.S1080del	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	1080					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						CATCCGTGTACTCCCAGCTTCCA	0.547																																					p.1079_1080del		Atlas-Indel,Pindel	.											.	ITGAX	198	.	0			c.3236_3238del						PASS	.																																			SO:0001651	inframe_deletion	3687	exon28			.	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.3237_3239delCTC	chr16.hg19:g.31391906_31391908delCTC	ENSP00000268296:p.Ser1080del	95.0	0.0	0		95.0	36.0	0.378947	NM_000887	Q8IVA6	In_Frame_Del	DEL	ENST00000268296.4	hg19	CCDS10711.1																																																																																			.	.	.	none		0.547	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887		-	31391908	CTC	-	31391906	7	5	242	1	0	1	0	1	0	0	0	0	7896	576	20	0	3347	0	ITGAX	16	31391906	In_Frame_Del	DEL	CTC	TCGA-SX-A71S-01A-11D-A33Q-10	26887011	31391906	58962847	100	14904											
NT5M	56953	hgsc.bcm.edu	37	chr17	17248204	17248204	+	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	ctgctgaccttctcatagacGaccggccggacatcacaggc	9	7	10	15	3	2	2	2	1	1	1	3	4	2	3	3	3	1	1	3	3	1	2			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr17:17248204G>A	ENST00000389022.4	+	4	742	c.526G>A	c.(526-528)Gac>Aac	p.D176N	NT5M_ENST00000582909.1_3'UTR	NM_020201.3	NP_064586.1	Q9NPB1	NT5M_HUMAN	5',3'-nucleotidase, mitochondrial	176					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						TCTCATAGACGACCGGCCGGA	0.602																																					p.D176N		Atlas-SNP	.											.	NT5M	17	.	0			c.G526A						PASS	.						122	102	109					17																	17248204		2203	4300	6503	SO:0001583	missense	56953	exon4			ATAGACGACCGGC	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.526G>A	chr17.hg19:g.17248204G>A	ENSP00000373674:p.Asp176Asn	73.0	0.0	.		96.0	55.0	.	NM_020201		Missense_Mutation	SNP	ENST00000389022.4	hg19	CCDS32581.1	.	.	.	.	.	.	.	.	.	.	G	31	5.099176	0.94197	.	.	ENSG00000205309	ENST00000446264;ENST00000389022	D	0.82167	-1.58	5.78	4.81	0.61882	HAD-like domain (2);	0.000000	0.85682	D	0.000000	D	0.91402	0.7287	M	0.86268	2.805	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;0.998	D	0.92515	0.6020	10	0.72032	D	0.01	-42.4803	13.7786	0.63069	0.0746:0.0:0.9254:0.0	.	176;176;176	Q2I378;Q9NPB1;F6S3X3	.;NT5M_HUMAN;.	N	176	ENSP00000373674:D176N	ENSP00000373674:D176N	D	+	1	0	NT5M	17188929	1.000000	0.71417	0.958000	0.39756	0.960000	0.62799	8.533000	0.90617	1.434000	0.47414	0.655000	0.94253	GAC	.	.	.	none		0.602	NT5M-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446045.1			A	17248204	G	A	17248204	3	1	242	1	0	0	0	0	1	0	0	0	10701	1058	37	1	540	1	NT5M	17	17248204	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10		17248204	63947006	101	14905											
FLII	2314	hgsc.bcm.edu	37	chr17	18160230	18160230	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaacccccttaccagcttcTgcagggcggccagctcctcg	7	7	9	18	2	1	0	0	0	1	0	3	0	2	0	5	2	5	3	5	2	2	2			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr17:18160230T>C	ENST00000327031.4	-	2	392	c.167A>G	c.(166-168)cAg>cGg	p.Q56R	FLII_ENST00000545457.2_Missense_Mutation_p.Q56R|FLII_ENST00000584444.1_5'UTR|FLII_ENST00000579294.1_Missense_Mutation_p.Q45R|FLII_ENST00000578558.1_Missense_Mutation_p.Q56R|FLII_ENST00000379450.4_Missense_Mutation_p.Q25R	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	56	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)					TACCAGCTTCTGCAGGGCGGC	0.637																																					p.Q56R		Atlas-SNP	.											.	FLII	79	.	0			c.A167G						PASS	.						18	19	19					17																	18160230		2200	4299	6499	SO:0001583	missense	2314	exon2			AGCTTCTGCAGGG	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.167A>G	chr17.hg19:g.18160230T>C	ENSP00000324573:p.Gln56Arg	34.0	0.0	.		57.0	18.0	.	NM_001256265	B4DIL0|F5H407|J3QLG3	Missense_Mutation	SNP	ENST00000327031.4	hg19	CCDS11192.1	.	.	.	.	.	.	.	.	.	.	T	15.75	2.924494	0.52653	.	.	ENSG00000177731	ENST00000327031;ENST00000545457;ENST00000379450	T;T;T	0.36157	1.27;1.86;1.9	5.12	5.12	0.69794	.	0.054847	0.85682	D	0.000000	T	0.28134	0.0694	L	0.47716	1.5	0.58432	D	0.999999	B;B;P;B	0.42248	0.009;0.009;0.774;0.024	B;B;B;B	0.32928	0.013;0.013;0.155;0.042	T	0.07083	-1.0791	10	0.20519	T	0.43	-31.848	14.9182	0.70815	0.0:0.0:0.0:1.0	.	25;25;56;56	E7EPM0;B4DIL0;F5H407;Q13045	.;.;.;FLII_HUMAN	R	56;56;25	ENSP00000324573:Q56R;ENSP00000438536:Q56R;ENSP00000368763:Q25R	ENSP00000324573:Q56R	Q	-	2	0	FLII	18100955	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.887000	0.87295	1.924000	0.55735	0.418000	0.28097	CAG	.	.	.	none		0.637	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018		C	18160230	T	C	18160230	3	2	242	1	0	0	0	0	1	0	0	0	5932	1580	55	3	3758	3	FLII	17	18160230	Missense_Mutation	SNP	T	TCGA-SX-A71S-01A-11D-A33Q-10	912026	18160230	63034980	102	14906											
FOXN1	8456	hgsc.bcm.edu	37	chr17	26861931	26861932	+	Frame_Shift_Del	DEL	CC	CC	-																															acctacttatggggcacacaCcctcctgctatgggcagaca																										TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr17:26861931_26861932delCC	ENST00000226247.2	+	7	1371_1372	c.1342_1343delCC	c.(1342-1344)cccfs	p.P448fs	FOXN1_ENST00000579795.1_Frame_Shift_Del_p.P448fs	NM_003593.2	NP_003584.2	O15353	FOXN1_HUMAN	forkhead box N1	448					defense response (GO:0006952)|epidermis development (GO:0008544)|epithelial cell proliferation (GO:0050673)|hair follicle development (GO:0001942)|keratinocyte differentiation (GO:0030216)|lymphocyte homeostasis (GO:0002260)|nail development (GO:0035878)|organ morphogenesis (GO:0009887)|regulation of T cell differentiation in thymus (GO:0033081)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(8)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Lung NSC(42;0.00431)					GGGGCACACACCCTCCTGCTAT	0.649																																					p.447_448del		Atlas-Indel,Pindel	.											.	FOXN1	51	.	0			c.1341_1342del						PASS	.																																			SO:0001589	frameshift_variant	8456	exon7			.	Y11739	CCDS11232.1	17q11-q12	2014-09-17	2003-06-12	2003-06-13	ENSG00000109101	ENSG00000109101		"Forkhead boxes"	12765	protein-coding gene	gene with protein product		600838	"winged-helix nude", "Rowett nude"	WHN, RONU		9321431	Standard	NM_003593		Approved	FKHL20	uc002hbj.3	O15353	OTTHUMG00000132603	ENST00000226247.2:c.1342_1343delCC	chr17.hg19:g.26861931_26861932delCC	ENSP00000226247:p.Pro448fs	160.0	0.0	0		188.0	42.0	0.223404	NM_003593	B2R9Q7|O15352	Frame_Shift_Del	DEL	ENST00000226247.2	hg19	CCDS11232.1																																																																																			.	.	.	none		0.649	FOXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255832.1			-	26861932	CC	-	26861931	7	5	242	1	0	1	0	1	0	0	0	0	6026	507	18	0	1368	0	FOXN1	17	26861931	Frame_Shift_Del	DEL	CC	TCGA-SX-A71S-01A-11D-A33Q-10	8701701	26861931	54333279	103	14907											
SLFN5	162394	hgsc.bcm.edu	37	chr17	33588032	33588032	+	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	ggttctccagttgagtttgtCatctgccacgccccgcagca	6	11	10	14	2	3	1	1	1	2	0	4	1	3	1	4	1	2	5	4	1	0	3			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr17:33588032C>A	ENST00000299977.4	+	3	1203	c.1055C>A	c.(1054-1056)tCa>tAa	p.S352*	SLFN5_ENST00000542451.1_Nonsense_Mutation_p.S352*	NM_144975.3	NP_659412.3	Q08AF3	SLFN5_HUMAN	schlafen family member 5	352					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)		TTGAGTTTGTCATCTGCCACG	0.468																																					p.S352X		Atlas-SNP	.											.	SLFN5	92	.	0			c.C1055A						PASS	.						191	176	181					17																	33588032		2203	4300	6503	SO:0001587	stop_gained	162394	exon3			GTTTGTCATCTGC	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.1055C>A	chr17.hg19:g.33588032C>A	ENSP00000299977:p.Ser352*	150.0	0.0	.		170.0	108.0	.	NM_144975	Q08AF2|Q8WU54|Q96A82	Nonsense_Mutation	SNP	ENST00000299977.4	hg19	CCDS32619.1	.	.	.	.	.	.	.	.	.	.	C	19.82	3.898751	0.72639	.	.	ENSG00000166750	ENST00000299977;ENST00000542451	.	.	.	3.25	0.959	0.19624	.	1.010410	0.07984	N	0.986128	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	2.8337	0.05507	0.2761:0.563:0.0:0.1609	.	.	.	.	X	352	.	ENSP00000299977:S352X	S	+	2	0	SLFN5	30612145	0.000000	0.05858	0.087000	0.20705	0.209000	0.24338	-0.092000	0.11129	0.682000	0.31407	0.591000	0.81541	TCA	.	.	.	none		0.468	SLFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448649.2	NM_144975		A	33588032	C	A	33588032	4	1	242	1	0	0	0	0	0	1	0	0	14750	838	29	4	1061	4	SLFN5	17	33588032	Nonsense_Mutation	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10	6726101	33588032	47607178	104	14908											
PGAP3	93210	hgsc.bcm.edu	37	chr17	37829901	37829901	+	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	ctgggtgctgcagccccacgGtcctgccccaccgtccaggg	4	6	13	18	2	0	0	0	0	0	0	2	0	2	0	7	3	4	2	7	3	0	0			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr17:37829901G>T	ENST00000300658.4	-	6	652	c.560C>A	c.(559-561)aCc>aAc	p.T187N	PGAP3_ENST00000579146.1_Intron|PGAP3_ENST00000429199.2_Missense_Mutation_p.T166N|PGAP3_ENST00000378011.4_Missense_Mutation_p.T136N	NM_033419.3	NP_219487.3	Q96FM1	PGAP3_HUMAN	post-GPI attachment to proteins 3	187					GPI anchor biosynthetic process (GO:0006506)|GPI anchor metabolic process (GO:0006505)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	hydrolase activity, acting on ester bonds (GO:0016788)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12						CAGCCCCACGGTCCTGCCCCA	0.652																																					p.T187N		Atlas-SNP	.											.	PGAP3	37	.	0			c.C560A						PASS	.						68	65	66					17																	37829901		2203	4300	6503	SO:0001583	missense	93210	exon6			CCCACGGTCCTGC	AB088396	CCDS32641.1	17q21.2	2009-06-02	2009-06-02	2009-06-02		ENSG00000161395			23719	protein-coding gene	gene with protein product	"post-GPI attachment to proteins 3"	611801	"per1-like domain containing 1"	PERLD1		15010812, 17021251, 17314402	Standard	NM_001291728		Approved	MGC9753, CAB2, PP1498, PER1	uc002hsj.3	Q96FM1		ENST00000300658.4:c.560C>A	chr17.hg19:g.37829901G>T	ENSP00000300658:p.Thr187Asn	52.0	0.0	.		64.0	39.0	.	NM_033419	B4DGK7|Q86Z03|Q8NBJ8	Missense_Mutation	SNP	ENST00000300658.4	hg19	CCDS32641.1	.	.	.	.	.	.	.	.	.	.	G	17.44	3.389718	0.61956	.	.	ENSG00000161395	ENST00000300658;ENST00000378011;ENST00000309862;ENST00000429199	.	.	.	4.65	3.67	0.42095	.	0.224770	0.45126	D	0.000394	T	0.58206	0.2106	L	0.54323	1.7	0.80722	D	1	P;P;P	0.46706	0.841;0.883;0.841	P;P;P	0.50136	0.632;0.576;0.632	T	0.54682	-0.8257	9	0.27082	T	0.32	-14.3119	11.0755	0.48030	0.0932:0.0:0.9068:0.0	.	166;136;187	B4DGK7;Q96FM1-2;Q96FM1	.;.;PGAP3_HUMAN	N	187;136;131;166	.	ENSP00000300658:T187N	T	-	2	0	PGAP3	35083427	1.000000	0.71417	0.999000	0.59377	0.754000	0.42855	7.571000	0.82399	2.113000	0.64589	0.655000	0.94253	ACC	.	.	.	none		0.652	PGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444825.2	NM_033419		T	37829901	G	T	37829901	3	4	242	1	0	0	0	0	1	0	0	0	11786	1261	44	4	414	4	PGAP3	17	37829901	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	4241869	37829901	43365309	105	14909											
GSDMA	284110	hgsc.bcm.edu	37	chr17	38122087	38122087	+	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	aggaagagcacgctcttctgGggggcccggtacgtccgcac	7	6	15	13	4	2	1	0	0	2	1	3	2	3	2	2	5	2	4	2	5	2	2			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr17:38122087G>T	ENST00000301659.4	+	2	265	c.147G>T	c.(145-147)tgG>tgT	p.W49C		NM_178171.4	NP_835465.2	Q96QA5	GSDMA_HUMAN	gasdermin A	49					apoptotic process (GO:0006915)	perinuclear region of cytoplasm (GO:0048471)				NS(1)|endometrium(2)|large_intestine(3)|lung(1)	7						CGCTCTTCTGGGGGGCCCGGT	0.622																																					p.W49C		Atlas-SNP	.											.	GSDMA	26	.	0			c.G147T						PASS	.						32	37	35					17																	38122087		1984	4138	6122	SO:0001583	missense	284110	exon2			CTTCTGGGGGGCC	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.147G>T	chr17.hg19:g.38122087G>T	ENSP00000301659:p.Trp49Cys	73.0	0.0	.		101.0	68.0	.	NM_178171	Q32MC5|Q86VE7|Q8N1M6	Missense_Mutation	SNP	ENST00000301659.4	hg19	CCDS45669.1	.	.	.	.	.	.	.	.	.	.	G	10.68	1.418683	0.25552	.	.	ENSG00000167914	ENST00000301659	T	0.41758	0.99	5.51	4.54	0.55810	.	0.338661	0.26176	N	0.025884	T	0.65668	0.2713	M	0.85630	2.765	0.52099	D	0.999946	D	0.89917	1.0	D	0.91635	0.999	T	0.70051	-0.4978	10	0.87932	D	0	-3.0E-4	10.2534	0.43383	0.0914:0.0:0.9086:0.0	.	49	Q96QA5	GSDMA_HUMAN	C	49	ENSP00000301659:W49C	ENSP00000301659:W49C	W	+	3	0	GSDMA	35375613	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	3.268000	0.51585	1.337000	0.45525	0.462000	0.41574	TGG	.	.	.	none		0.622	GSDMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446847.1	NM_178171		T	38122087	G	T	38122087	3	4	242	1	0	0	0	0	1	0	0	0	6823	1241	43	4	149	4	GSDMA	17	38122087	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	292186	38122087	43073123	106	14910											
ACLY	47	hgsc.bcm.edu	37	chr17	40049362	40049362	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagtccagcatgccttgcaCggcccgggtctgcatgcccc	7	7	11	16	2	1	0	0	0	1	0	2	0	2	0	5	2	5	3	5	2	1	1			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr17:40049362C>T	ENST00000352035.2	-	15	1655	c.1525G>A	c.(1525-1527)Gtg>Atg	p.V509M	ACLY_ENST00000393896.2_Missense_Mutation_p.V499M|ACLY_ENST00000590151.1_Missense_Mutation_p.V509M|ACLY_ENST00000537919.1_Missense_Mutation_p.V238M|ACLY_ENST00000353196.1_Missense_Mutation_p.V499M	NM_001096.2	NP_001087.2	P53396	ACLY_HUMAN	ATP citrate lyase	509					ATP catabolic process (GO:0006200)|cellular carbohydrate metabolic process (GO:0044262)|cellular lipid metabolic process (GO:0044255)|citrate metabolic process (GO:0006101)|coenzyme A metabolic process (GO:0015936)|energy reserve metabolic process (GO:0006112)|lipid biosynthetic process (GO:0008610)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	citrate lyase complex (GO:0009346)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)		NTN1/ACLY(2)	breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	28		Breast(137;0.000143)				ATGCCTTGCACGGCCCGGGTC	0.592																																					p.V509M	Colon(64;807 1396 15971 30971)	Atlas-SNP	.											.	ACLY	85	.	0			c.G1525A						PASS	.						105	99	101					17																	40049362		2203	4300	6503	SO:0001583	missense	47	exon15			CTTGCACGGCCCG	X64330	CCDS11412.1, CCDS11413.1	17q21.2	2010-04-27			ENSG00000131473	ENSG00000131473	2.3.3.8		115	protein-coding gene	gene with protein product	"ATP citrate synthase"	108728				1371749, 8088842	Standard	NM_001096		Approved	ATPCL, CLATP, ACL	uc002hyg.3	P53396	OTTHUMG00000133507	ENST00000352035.2:c.1525G>A	chr17.hg19:g.40049362C>T	ENSP00000253792:p.Val509Met	87.0	0.0	.		100.0	4.0	.	NM_001096	B4DIM0|B4E3P0|Q13037|Q9BRL0	Missense_Mutation	SNP	ENST00000352035.2	hg19	CCDS11412.1	.	.	.	.	.	.	.	.	.	.	C	34	5.389813	0.95988	.	.	ENSG00000131473	ENST00000352035;ENST00000401700;ENST00000353196;ENST00000537919;ENST00000393896	D;D;D;D	0.82711	-1.64;-1.64;-1.64;-1.64	5.88	5.88	0.94601	CoA-binding (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.93726	0.7995	M	0.92367	3.3	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.998;0.995;0.994	D	0.94345	0.7574	10	0.87932	D	0	.	20.2228	0.98330	0.0:1.0:0.0:0.0	.	238;553;563;499;509	B4E3P0;B4DIM0;E7ENH9;G3XAI4;P53396	.;.;.;.;ACLY_HUMAN	M	509;563;499;238;499	ENSP00000253792:V509M;ENSP00000345398:V499M;ENSP00000445349:V238M;ENSP00000377474:V499M	ENSP00000253792:V509M	V	-	1	0	ACLY	37302888	1.000000	0.71417	0.989000	0.46669	0.997000	0.91878	7.610000	0.82949	2.789000	0.95967	0.655000	0.94253	GTG	.	.	.	none		0.592	ACLY-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257465.1	NM_001096		T	40049362	C	T	40049362	3	4	242	1	0	0	0	0	1	0	0	0	143	536	19	1	1840	1	ACLY	17	40049362	Missense_Mutation	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10	1927275	40049362	41145848	107	14911											
BRCA1	672	hgsc.bcm.edu	37	chr17	41243848	41243848	+	Frame_Shift_Del	DEL	C	C	-																															ctgagaaggtatattgtttaCtttaccaaataacaagtgtt																								rs80357873|rs80357609		TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr17:41243848delC	ENST00000357654.3	-	10	3818	c.3700delG	c.(3700-3702)gtafs	p.V1234fs	BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000346315.3_Frame_Shift_Del_p.V1234fs|BRCA1_ENST00000309486.4_Frame_Shift_Del_p.V938fs|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000493795.1_Frame_Shift_Del_p.V1187fs|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000354071.3_Frame_Shift_Del_p.V1234fs|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000471181.2_Frame_Shift_Del_p.V1234fs|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000468300.1_Intron	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	1234					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)		ATATTGTTTACTTTACCAAAT	0.413			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.V1234fs		Atlas-Indel,Pindel	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.3701delT						PASS	.						98	94	96					17																	41243848		2203	4300	6503	SO:0001589	frameshift_variant	672	exon10	Familial Cancer Database		.	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.3700delG	chr17.hg19:g.41243848delC	ENSP00000350283:p.Val1234fs	132.0	0.0	0		139.0	78.0	0.561151	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Frame_Shift_Del	DEL	ENST00000357654.3	hg19	CCDS11453.1																																																																																			.	.	.	none		0.413	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		-	41243848	C	-	41243848	7	5	242	1	0	1	0	1	0	0	0	0	1500	565	20	0	2017	0	BRCA1	17	41243848	Frame_Shift_Del	DEL	C	TCGA-SX-A71S-01A-11D-A33Q-10	1194486	41243848	39951362	108	14912											
INTS2	57508	hgsc.bcm.edu	37	chr17	59952339	59952339	+	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	atcaggtcattctgagtataCttttgttgtcgtacaaactt	10	17	7	7	1	3	1	2	1	1	0	4	1	3	1	0	1	3	3	0	1	4	8			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr17:59952339C>T	ENST00000444766.3	-	19	2616	c.2541G>A	c.(2539-2541)aaG>aaA	p.K847K	INTS2_ENST00000251334.6_Silent_p.K839K|Y_RNA_ENST00000365491.1_RNA	NM_020748.2	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	847					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020)				NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	38						TCTGAGTATACTTTTGTTGTC	0.348																																					p.K847K		Atlas-SNP	.											INTS2,NS,carcinoma,0,1	INTS2	89	.	0			c.G2541A						PASS	.						57	55	56					17																	59952339		1869	4102	5971	SO:0001819	synonymous_variant	57508	exon19			AGTATACTTTTGT	AB033113	CCDS45750.1	17q23.2	2006-04-26	2006-03-15	2006-03-15		ENSG00000108506			29241	protein-coding gene	gene with protein product		611346	"KIAA1287"	KIAA1287		16239144	Standard	NR_026641		Approved	INT2	uc002izn.3	Q9H0H0		ENST00000444766.3:c.2541G>A	chr17.hg19:g.59952339C>T		107.0	0.0	.		124.0	38.0	.	NM_020748	Q9ULD3	Silent	SNP	ENST00000444766.3	hg19	CCDS45750.1																																																																																			.	.	.	none		0.348	INTS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000445368.1	NM_020748		T	59952339	C	T	59952339	2	4	242	1	0	0	0	0	0	0	0	1	7785	564	20	2		2	INTS2	17	59952339	Silent	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10	18708491	59952339	21242871	109	14913											
TBC1D16	125058	hgsc.bcm.edu	37	chr17	77923648	77923648	+	Missense_Mutation	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	cgcggattgacacatcaataCcgccaaagaaaatggcctgg	14	6	10	11	3	1	2	1	1	0	1	1	3	1	3	3	3	1	0	3	3	5	2			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr17:77923648C>T	ENST00000310924.2	-	7	1389	c.1274G>A	c.(1273-1275)gGt>gAt	p.G425D	TBC1D16_ENST00000340848.7_Missense_Mutation_p.G63D|TBC1D16_ENST00000570373.1_Missense_Mutation_p.G64D|TBC1D16_ENST00000572862.1_Missense_Mutation_p.G63D|TBC1D16_ENST00000576768.1_Intron	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	425	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(3)	28	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)			CACATCAATACCGCCAAAGAA	0.577																																					p.G425D	Ovarian(14;397 562 4850 31922 49378)	Atlas-SNP	.											.	TBC1D16	48	.	0			c.G1274A						PASS	.						27	31	30					17																	77923648		2202	4300	6502	SO:0001583	missense	125058	exon7			TCAATACCGCCAA	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.1274G>A	chr17.hg19:g.77923648C>T	ENSP00000309794:p.Gly425Asp	84.0	0.0	.		131.0	43.0	.	NM_019020	B9A6L7|I3L1E0|I3L4U2|Q8N3Z4|Q96DH7	Missense_Mutation	SNP	ENST00000310924.2	hg19	CCDS11766.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.767431	0.90020	.	.	ENSG00000167291	ENST00000340848;ENST00000310924	T;T	0.11385	2.78;2.78	4.79	4.79	0.61399	Rab-GAP/TBC domain (3);	0.231325	0.44688	D	0.000440	T	0.50034	0.1592	H	0.97564	4.03	0.80722	D	1	D;D;D	0.89917	1.0;0.997;0.999	D;D;D	0.77004	0.989;0.964;0.972	T	0.71441	-0.4592	10	0.87932	D	0	-39.6362	17.8354	0.88694	0.0:1.0:0.0:0.0	.	85;425;63	Q96DH7;Q8TBP0;Q8N3Z4	.;TBC16_HUMAN;.	D	63;425	ENSP00000341517:G63D;ENSP00000309794:G425D	ENSP00000309794:G425D	G	-	2	0	TBC1D16	75538243	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.649000	0.83500	2.192000	0.70111	0.585000	0.79938	GGT	.	.	.	none		0.577	TBC1D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437145.1	NM_019020		T	77923648	C	T	77923648	3	4	242	1	0	0	0	0	1	0	0	0	15617	507	18	2	1053	2	TBC1D16	17	77923648	Missense_Mutation	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10	17971309	77923648	3271562	110	14914											
TNFRSF11A	8792	hgsc.bcm.edu	37	chr18	60052147	60052147	+	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	caggaggagaccctggcgcgCcgagactccttcgcggggaa	8	4	16	13	5	0	2	0	0	0	2	2	6	1	4	3	5	0	0	3	5	1	1			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr18:60052147C>T	ENST00000586569.1	+	10	1769	c.1731C>T	c.(1729-1731)cgC>cgT	p.R577R	TNFRSF11A_ENST00000269485.7_Silent_p.R260R	NM_001270949.1|NM_003839.3	NP_001257878.1|NP_003830.1	Q9Y6Q6	TNR11_HUMAN	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	577					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)				CCCTGGCGCGCCGAGACTCCT	0.761																																					p.R577R		Atlas-SNP	.											.	TNFRSF11A	51	.	0			c.C1731T						PASS	.						7	8	8					18																	60052147		2099	3994	6093	SO:0001819	synonymous_variant	8792	exon10			GGCGCGCCGAGAC	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.1731C>T	chr18.hg19:g.60052147C>T		17.0	0.0	.		27.0	12.0	.	NM_003839	I4EC36|I4EC38|I4EC39|I7JE63|N0GVH0|Q59EP9	Silent	SNP	ENST00000586569.1	hg19	CCDS11980.1																																																																																			.	.	.	none		0.761	TNFRSF11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256186.2			T	60052147	C	T	60052147	2	4	242	1	0	0	0	0	0	0	0	1	16296	726	26	2		2	TNFRSF11A	18	60052147	Silent	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10		60052147	18025101	111	14915											
CHAF1A	10036	hgsc.bcm.edu	37	chr19	4433229	4433229	+	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	cacccccacccccagcgaggAtgccgccatcccctctaagt	8	5	7	21	2	1	0	0	0	1	0	2	2	2	1	8	1	2	0	8	1	1	1			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr19:4433229A>T	ENST00000301280.5	+	13	2467	c.2366A>T	c.(2365-2367)gAt>gTt	p.D789V	CTB-50L17.5_ENST00000590159.1_RNA|CHAF1A_ENST00000587368.1_3'UTR	NM_005483.2	NP_005474	Q13111	CAF1A_HUMAN	chromatin assembly factor 1, subunit A (p150)	789	Binds to p60.				cell cycle (GO:0007049)|chromatin assembly (GO:0031497)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|identical protein binding (GO:0042802)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	27		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCAGCGAGGATGCCGCCATC	0.652								Chromatin Structure																													p.D789V		Atlas-SNP	.											.	CHAF1A	69	.	0			c.A2366T						PASS	.						69	71	70					19																	4433229		2203	4300	6503	SO:0001583	missense	10036	exon13			GCGAGGATGCCGC	U20979	CCDS32875.1	19p13.3	2008-07-16				ENSG00000167670			1910	protein-coding gene	gene with protein product	"chromatin assembly factor I (150 kDa)"	601246				7600578	Standard	NM_005483		Approved	CAF1P150, CAF1B, CAF-1, CAF1, P150, MGC71229	uc002mal.3	Q13111		ENST00000301280.5:c.2366A>T	chr19.hg19:g.4433229A>T	ENSP00000301280:p.Asp789Val	65.0	0.0	.		71.0	30.0	.	NM_005483	Q6NXG5|Q7Z7K3|Q9UJY8	Missense_Mutation	SNP	ENST00000301280.5	hg19	CCDS32875.1	.	.	.	.	.	.	.	.	.	.	A	9.618	1.132969	0.21041	.	.	ENSG00000167670	ENST00000301280	T	0.26373	1.74	5.65	4.61	0.57282	.	.	.	.	.	T	0.21022	0.0506	L	0.47716	1.5	0.58432	D	0.99999	P	0.40398	0.716	B	0.34873	0.191	T	0.01925	-1.1246	8	.	.	.	-21.8765	11.8638	0.52482	0.8154:0.1846:0.0:0.0	.	789	Q13111	CAF1A_HUMAN	V	789	ENSP00000301280:D789V	.	D	+	2	0	CHAF1A	4384229	1.000000	0.71417	0.039000	0.18376	0.005000	0.04900	3.819000	0.55686	0.966000	0.38159	0.533000	0.62120	GAT	.	.	.	none		0.652	CHAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458310.2	NM_005483		T	4433229	A	T	4433229	3	4	242	1	0	0	0	0	1	0	0	0	3313	333	12	5	2416	5	CHAF1A	19	4433229	Missense_Mutation	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10		4433229	54695754	112	14916											
ZNF491	126069	hgsc.bcm.edu	37	chr19	11917180	11917180	+	Frame_Shift_Del	DEL	A	A	-																															ataaatgtaagttttgtgggAaagccttggattgtctcagt																										TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr19:11917180delA	ENST00000323169.5	+	3	743	c.412delA	c.(412-414)aaafs	p.K138fs	ZNF491_ENST00000492230.1_Intron	NM_152356.3	NP_689569.2	Q8N8L2	ZN491_HUMAN	zinc finger protein 491	138					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(14)|lung(6)|ovary(2)|skin(1)	26						GTTTTGTGGGAAAGCCTTGGA	0.388																																					p.G137fs		Atlas-Indel,Pindel	.											.	ZNF491	61	.	0			c.411delG						PASS	.						99	99	99					19																	11917180		2203	4300	6503	SO:0001589	frameshift_variant	126069	exon3			.	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.412delA	chr19.hg19:g.11917180delA	ENSP00000313443:p.Lys138fs	76.0	0.0	0		88.0	35.0	0.397727	NM_152356	Q3MJ35|Q8NAT8	Frame_Shift_Del	DEL	ENST00000323169.5	hg19	CCDS12267.1																																																																																			.	.	.	none		0.388	ZNF491-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344518.1	NM_152356		-	11917180	A	-	11917180	7	5	242	1	0	1	0	1	0	0	0	0	17954	247	9	0	414	0	ZNF491	19	11917180	Frame_Shift_Del	DEL	A	TCGA-SX-A71S-01A-11D-A33Q-10	7483951	11917180	47211803	113	14917											
FARSA	2193	hgsc.bcm.edu	37	chr19	13035292	13035292	+	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	agctgaacacctccatgctgGgctctgtgtatgggttgtag	7	12	13	9	0	1	1	0	1	1	0	2	1	2	1	2	2	3	6	2	2	3	3			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr19:13035292G>A	ENST00000314606.4	-	11	1262	c.1244C>T	c.(1243-1245)cCc>cTc	p.P415L	FARSA_ENST00000588025.1_Missense_Mutation_p.P455L|FARSA_ENST00000423140.2_Missense_Mutation_p.P384L	NM_004461.2	NP_004452.1	Q9Y285	SYFA_HUMAN	phenylalanyl-tRNA synthetase, alpha subunit	415					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)	CTCCATGCTGGGCTCTGTGTA	0.607																																					p.P415L		Atlas-SNP	.											.	FARSA	46	.	0			c.C1244T						PASS	.						105	86	93					19																	13035292		2203	4300	6503	SO:0001583	missense	2193	exon11			ATGCTGGGCTCTG	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.1244C>T	chr19.hg19:g.13035292G>A	ENSP00000320309:p.Pro415Leu	25.0	0.0	.		30.0	13.0	.	NM_004461	B4E363|Q9NSD8|Q9Y4W8	Missense_Mutation	SNP	ENST00000314606.4	hg19	CCDS12287.1	.	.	.	.	.	.	.	.	.	.	G	31	5.075764	0.94000	.	.	ENSG00000179115	ENST00000314606;ENST00000423140	D;D	0.81739	-1.53;-1.53	5.11	5.11	0.69529	Aminoacyl-tRNA synthetase, class II (1);Phenylalanyl-tRNA synthetase (1);	0.000000	0.85682	D	0.000000	D	0.92873	0.7733	H	0.95437	3.67	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	0.94955	0.8103	10	0.87932	D	0	-16.8972	17.3314	0.87265	0.0:0.0:1.0:0.0	.	384;415;415	B4E363;Q6IBR2;Q9Y285	.;.;SYFA_HUMAN	L	415;384	ENSP00000320309:P415L;ENSP00000396548:P384L	ENSP00000320309:P415L	P	-	2	0	FARSA	12896292	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.200000	0.95010	2.388000	0.81334	0.561000	0.74099	CCC	.	.	.	none		0.607	FARSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451935.1	NM_004461		A	13035292	G	A	13035292	3	1	242	1	0	0	0	0	1	0	0	0	5686	1232	43	2	294	2	FARSA	19	13035292	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	1118112	13035292	46093691	114	14918			1	32		2	2	15	G		5.743339e-05
FARSA	2193	hgsc.bcm.edu	37	chr19	13035306	13035306	+	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	atgctgggctctgtgtatggGttgtaggctggcttgaagcg	5	13	17	6	1	1	1	0	1	1	0	1	1	1	1	0	4	2	7	0	4	3	4			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr19:13035306G>T	ENST00000314606.4	-	11	1248	c.1230C>A	c.(1228-1230)aaC>aaA	p.N410K	FARSA_ENST00000588025.1_Missense_Mutation_p.N450K|FARSA_ENST00000423140.2_Missense_Mutation_p.N379K	NM_004461.2	NP_004452.1	Q9Y285	SYFA_HUMAN	phenylalanyl-tRNA synthetase, alpha subunit	410					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)	CTGTGTATGGGTTGTAGGCTG	0.587																																					p.N410K		Atlas-SNP	.											.	FARSA	46	.	0			c.C1230A						PASS	.						109	89	96					19																	13035306		2203	4300	6503	SO:0001583	missense	2193	exon11			GTATGGGTTGTAG	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.1230C>A	chr19.hg19:g.13035306G>T	ENSP00000320309:p.Asn410Lys	26.0	0.0	.		32.0	13.0	.	NM_004461	B4E363|Q9NSD8|Q9Y4W8	Missense_Mutation	SNP	ENST00000314606.4	hg19	CCDS12287.1	.	.	.	.	.	.	.	.	.	.	G	19.04	3.750860	0.69533	.	.	ENSG00000179115	ENST00000314606;ENST00000423140	T;T	0.63744	-0.06;-0.06	5.11	2.94	0.34122	Aminoacyl-tRNA synthetase, class II (1);Phenylalanyl-tRNA synthetase (1);	0.000000	0.85682	D	0.000000	D	0.83613	0.5292	H	0.97103	3.94	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	0.86119	0.1567	10	0.87932	D	0	-22.818	9.606	0.39634	0.2346:0.0:0.7654:0.0	.	379;410;410	B4E363;Q6IBR2;Q9Y285	.;.;SYFA_HUMAN	K	410;379	ENSP00000320309:N410K;ENSP00000396548:N379K	ENSP00000320309:N410K	N	-	3	2	FARSA	12896306	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.984000	0.40658	1.162000	0.42619	0.561000	0.74099	AAC	.	.	.	none		0.587	FARSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451935.1	NM_004461		T	13035306	G	T	13035306	3	4	242	1	0	0	0	0	1	0	0	0	5686	1252	44	4	308	4	FARSA	19	13035306	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	14	13035306	46093677	115	14919			1	32		2	2	15	G		5.743339e-05
ZNF552	79818	hgsc.bcm.edu	37	chr19	58319468	58319468	+	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	agtgaagagatttgcctaaaTtttttttcacattcactgca	12	16	6	7	0	2	2	2	1	0	1	2	3	2	2	1	0	2	1	1	0	3	7			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr19:58319468T>A	ENST00000391701.1	-	3	1333	c.1164A>T	c.(1162-1164)aaA>aaT	p.K388N	ZNF586_ENST00000599802.1_Intron|ZNF586_ENST00000598885.1_Intron	NM_024762.3	NP_079038.2	Q9H707	ZN552_HUMAN	zinc finger protein 552	388					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	11		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0259)		TTTGCCTAAATTTTTTTTCAC	0.413																																					p.K388N		Atlas-SNP	.											ZNF552,NS,carcinoma,0,1	ZNF552	32	.	0			c.A1164T						PASS	.						147	143	144					19																	58319468		2203	4300	6503	SO:0001583	missense	79818	exon3			CCTAAATTTTTTT	AK097041	CCDS12963.1	19q13.43	2013-09-20			ENSG00000178935	ENSG00000178935		"Zinc fingers, C2H2-type", "-"	26135	protein-coding gene	gene with protein product							Standard	XM_005259267		Approved	FLJ21603	uc002qqg.3	Q9H707	OTTHUMG00000183478	ENST00000391701.1:c.1164A>T	chr19.hg19:g.58319468T>A	ENSP00000375582:p.Lys388Asn	127.0	0.0	.		115.0	54.0	.	NM_024762	B3KUE9|Q6P5A6	Missense_Mutation	SNP	ENST00000391701.1	hg19	CCDS12963.1	.	.	.	.	.	.	.	.	.	.	T	7.935	0.741520	0.15642	.	.	ENSG00000178935	ENST00000391701	T	0.20200	2.09	1.96	-3.92	0.04155	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08088	0.0202	N	0.11427	0.14	0.09310	N	1	B;B	0.28820	0.224;0.124	B;B	0.26094	0.066;0.026	T	0.16100	-1.0414	9	0.51188	T	0.08	.	0.9994	0.01474	0.473:0.1394:0.1527:0.2349	.	384;388	B7Z1H1;Q9H707	.;ZN552_HUMAN	N	388	ENSP00000375582:K388N	ENSP00000375582:K388N	K	-	3	2	ZNF552	63011280	0.000000	0.05858	0.000000	0.03702	0.322000	0.28314	-4.686000	0.00198	-2.729000	0.00385	-1.256000	0.01477	AAA	.	.	.	none		0.413	ZNF552-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466829.1	NM_024762		A	58319468	T	A	58319468	3	1	242	1	0	0	0	0	1	0	0	0	17996	1490	52	5	63	5	ZNF552	19	58319468	Missense_Mutation	SNP	T	TCGA-SX-A71S-01A-11D-A33Q-10	45284162	58319468	809515	116	14920											
LPIN3	64900	hgsc.bcm.edu	37	chr20	39978760	39978760	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagctggggcaacctctccTcctcggggaggacccagcac	8	5	13	15	1	1	1	0	0	1	1	4	3	2	3	4	5	3	3	4	5	1	0			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr20:39978760T>C	ENST00000373257.3	+	7	916	c.825T>C	c.(823-825)ccT>ccC	p.P275P		NM_022896.1	NP_075047.1	Q9BQK8	LPIN3_HUMAN	lipin 3	275					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)				CAACCTCTCCTCCTCGGGGAG	0.622																																					p.P275P		Atlas-SNP	.											.	LPIN3	69	.	0			c.T825C						PASS	.						29	22	24					20																	39978760		2202	4299	6501	SO:0001819	synonymous_variant	64900	exon7			CTCTCCTCCTCGG	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.825T>C	chr20.hg19:g.39978760T>C		94.0	0.0	.		91.0	51.0	.	NM_022896	B2RTT5|Q5TDB9|Q9NPY8|Q9UJE5	Silent	SNP	ENST00000373257.3	hg19	CCDS33469.1																																																																																			.	.	.	none		0.622	LPIN3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080393.1	NM_022896		C	39978760	T	C	39978760	2	2	242	1	0	0	0	0	0	0	0	1	8927	1538	54	3		3	LPIN3	20	39978760	Silent	SNP	T	TCGA-SX-A71S-01A-11D-A33Q-10		39978760	23046760	117	14921											
PREX1	57580	hgsc.bcm.edu	37	chr20	47261019	47261023	+	Frame_Shift_Del	DEL	GATTG	GATTG	-																															gtaggacaggaccgagtctcGattgctgttacactcgctgc																										TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	GATTG	GATTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr20:47261019_47261023delGATTG	ENST00000371941.3	-	27	3547_3551	c.3525_3529delCAATC	c.(3523-3531)agcaatcgafs	p.SN1175fs	PREX1_ENST00000396220.1_Frame_Shift_Del_p.SN1175fs|PREX1_ENST00000496915.1_5'Flank	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	1175					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)			ACCGAGTCTCGATTGCTGTTACACT	0.585																																					p.1176_1177del		Atlas-INDEL	.											.	PREX1	441	.	0			c.3526_3530del						PASS	.																																			SO:0001589	frameshift_variant	57580	exon27			.	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.3525_3529delCAATC	chr20.hg19:g.47261019_47261023delGATTG	ENSP00000361009:p.Ser1175fs	94.0	0.0	0		61.0	14.0	0.229508	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Frame_Shift_Del	DEL	ENST00000371941.3	hg19	CCDS13410.1																																																																																			.	.	.	none		0.585	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		-	47261023	GATTG	-	47261019	7	5	242	1	0	1	0	1	0	0	0	0	12486	1066	37	0	1506	0	PREX1	20	47261019	Frame_Shift_Del	DEL	GATTG	TCGA-SX-A71S-01A-11D-A33Q-10	7282259	47261019	15764501	118	14922	155	2									
PREX1	57580	hgsc.bcm.edu	37	chr20	47261025	47261033	+	In_Frame_Del	DEL	TGTTACACT	TGTTACACT	-																															caggaccgagtctcgattgcTgttacactcgctgcaaaggg																										TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	TGTTACACT	TGTTACACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr20:47261025_47261033delTGTTACACT	ENST00000371941.3	-	27	3537_3545	c.3515_3523delAGTGTAACA	c.(3514-3525)gagtgtaacagc>ggc	p.1172_1175ECNS>G	PREX1_ENST00000396220.1_In_Frame_Del_p.1172_1175ECNS>G|PREX1_ENST00000496915.1_5'Flank	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	1172					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)			TCTCGATTGCTGTTACACTCGCTGCAAAG	0.579																																					p.1172_1175del		Atlas-INDEL	.											.	PREX1	441	.	0			c.3516_3524del						PASS	.																																			SO:0001651	inframe_deletion	57580	exon27			.	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.3515_3523delAGTGTAACA	chr20.hg19:g.47261025_47261033delTGTTACACT	ENSP00000361009:p.Glu1172_Ser1175delinsGly	94.0	0.0	0		57.0	14.0	0.245614	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	In_Frame_Del	DEL	ENST00000371941.3	hg19	CCDS13410.1																																																																																			.	.	.	none		0.579	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		-	47261033	TGTTACACT	-	47261025	7	5	242	1	0	1	0	1	0	0	0	0	12486	1580	55	0	1512	0	PREX1	20	47261025	In_Frame_Del	DEL	TGTTACACT	TCGA-SX-A71S-01A-11D-A33Q-10	6	47261025	15764495	119	14923	155	2									
COL20A1	57642	hgsc.bcm.edu	37	chr20	61940011	61940011	+	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	gtcccaggacgatgtgcacaCtgctgcccgtgtcctcaagg	7	8	12	14	2	1	0	1	0	0	0	3	2	3	1	3	2	3	2	3	2	1	0			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr20:61940011C>T	ENST00000358894.6	+	8	993	c.893C>T	c.(892-894)aCt>aTt	p.T298I	COL20A1_ENST00000422202.1_Missense_Mutation_p.T305I|COL20A1_ENST00000326996.6_Missense_Mutation_p.T298I|COL20A1_ENST00000435874.1_Missense_Mutation_p.T305I	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	298	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					GATGTGCACACTGCTGCCCGT	0.667																																					p.T298I		Atlas-SNP	.											.	COL20A1	137	.	0			c.C893T						PASS	.						26	32	30					20																	61940011		2120	4220	6340	SO:0001583	missense	57642	exon8			TGCACACTGCTGC	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.893C>T	chr20.hg19:g.61940011C>T	ENSP00000351767:p.Thr298Ile	90.0	0.0	.		67.0	37.0	.	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Missense_Mutation	SNP	ENST00000358894.6	hg19	CCDS46628.1	.	.	.	.	.	.	.	.	.	.	C	8.261	0.811242	0.16537	.	.	ENSG00000101203	ENST00000358894;ENST00000326996;ENST00000435874;ENST00000422202	D;D;D;D	0.83506	-1.73;-1.73;-1.73;-1.73	4.07	3.1	0.35709	von Willebrand factor, type A (3);	0.727564	0.12360	N	0.475743	T	0.75975	0.3923	L	0.35793	1.09	0.09310	N	1	P;P	0.36027	0.478;0.533	B;B	0.37451	0.174;0.25	T	0.66862	-0.5816	10	0.42905	T	0.14	.	10.6662	0.45732	0.0:0.8393:0.0:0.1607	.	305;298	Q9P218-2;Q9P218	.;COKA1_HUMAN	I	298;298;305;305	ENSP00000351767:T298I;ENSP00000323077:T298I;ENSP00000408690:T305I;ENSP00000414753:T305I	ENSP00000323077:T298I	T	+	2	0	COL20A1	61410456	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	0.134000	0.15932	1.982000	0.57802	0.467000	0.42956	ACT	.	.	.	none		0.667	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882		T	61940011	C	T	61940011	3	4	242	1	0	0	0	0	1	0	0	0	3681	565	20	2	919	2	COL20A1	20	61940011	Missense_Mutation	SNP	C	TCGA-SX-A71S-01A-11D-A33Q-10	14678986	61940011	1085509	120	14924											
USP25	29761	hgsc.bcm.edu	37	chr21	17172133	17172133	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgaattacaagcctccatcaAatgctcaagatttaccccga	14	10	5	12	1	2	2	2	1	0	1	3	3	3	2	4	0	4	1	4	0	6	3			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr21:17172133A>G	ENST00000285679.6	+	6	982	c.613A>G	c.(613-615)Aat>Gat	p.N205D	USP25_ENST00000285681.2_Missense_Mutation_p.N205D|USP25_ENST00000547201.1_3'UTR|USP25_ENST00000351097.5_Missense_Mutation_p.N205D|USP25_ENST00000400183.2_Missense_Mutation_p.N205D	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	205	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)		GCCTCCATCAAATGCTCAAGA	0.289																																					p.N205D		Atlas-SNP	.											.	USP25	156	.	0			c.A613G						PASS	.						80	80	80					21																	17172133		2203	4294	6497	SO:0001583	missense	29761	exon6			CCATCAAATGCTC	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.613A>G	chr21.hg19:g.17172133A>G	ENSP00000285679:p.Asn205Asp	184.0	0.0	.		171.0	67.0	.	NM_013396	C0LSZ0|Q6DHZ9|Q9H9W1	Missense_Mutation	SNP	ENST00000285679.6	hg19	CCDS33515.1	.	.	.	.	.	.	.	.	.	.	A	12.64	1.999424	0.35320	.	.	ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000351097;ENST00000400183	T;T;T;T	0.30182	1.54;1.54;1.54;1.54	5.03	2.6	0.31112	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.221075	0.44688	D	0.000432	T	0.14787	0.0357	N	0.10916	0.065	0.25753	N	0.985036	P;B;B;B	0.35139	0.486;0.08;0.222;0.009	B;B;B;B	0.32624	0.149;0.018;0.096;0.016	T	0.17592	-1.0364	10	0.18710	T	0.47	.	12.1748	0.54180	0.7294:0.2706:0.0:0.0	.	205;205;205;205	Q9UHP3-3;Q96B65;Q9UHP3-1;Q9UHP3	.;.;.;UBP25_HUMAN	D	205	ENSP00000285681:N205D;ENSP00000285679:N205D;ENSP00000299574:N205D;ENSP00000383044:N205D	ENSP00000285679:N205D	N	+	1	0	USP25	16094004	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.993000	0.40747	0.324000	0.23333	0.528000	0.53228	AAT	.	.	.	none		0.289	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			G	17172133	A	G	17172133	3	3	242	1	0	0	0	0	1	0	0	0	17068	14	1	3	635	3	USP25	21	17172133	Missense_Mutation	SNP	A	TCGA-SX-A71S-01A-11D-A33Q-10		17172133	30957762	121	14925											
BACH1	571	hgsc.bcm.edu	37	chr21	30715024	30715024	+	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	cagtgagcctggctacgcgcGagggcaggagtcccagcaga	9	4	16	12	3	0	2	0	1	0	1	1	4	1	3	2	3	3	3	2	3	1	1	rs377002114		TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr21:30715024G>A	ENST00000399921.1	+	5	2324	c.2081G>A	c.(2080-2082)cGa>cAa	p.R694Q	BACH1_ENST00000286800.3_Missense_Mutation_p.R694Q	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						GGCTACGCGCGAGGGCAGGAG	0.577													G|||	1	0.000199681	0	0	5008	,	,		18154	0.001		0	False		,,,				2504	0				p.R694Q		Atlas-SNP	.											BACH1,NS,carcinoma,0,1	BACH1	66	.	0			c.G2081A						PASS	.	G	GLN/ARG,GLN/ARG	0,4406		0,0,2203	49	51	50		2081,2081	-10.2	0	21		50	1,8599		0,1,4299	no	missense,missense	BACH1	NM_001186.2,NM_206866.1	43,43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	694/737,694/737	30715024	1,13005	2203	4300	6503	SO:0001583	missense	571	exon5			ACGCGCGAGGGCA	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.2081G>A	chr21.hg19:g.30715024G>A	ENSP00000382805:p.Arg694Gln	87.0	0.0	.		69.0	36.0	.	NM_206866	Q3MJE2|Q8NCI5	Missense_Mutation	SNP	ENST00000399921.1	hg19	CCDS13585.1	.	.	.	.	.	.	.	.	.	.	G	5.245	0.230686	0.09969	0.0	1.16E-4	ENSG00000156273	ENST00000286800;ENST00000399921	T;T	0.70399	-0.48;-0.48	5.18	-10.2	0.00374	.	1.645150	0.03069	N	0.156896	T	0.37812	0.1017	N	0.11427	0.14	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.37197	-0.9716	10	0.10902	T	0.67	5.0905	0.5012	0.00580	0.3585:0.218:0.1401:0.2834	.	694	O14867	BACH1_HUMAN	Q	694	ENSP00000286800:R694Q;ENSP00000382805:R694Q	ENSP00000286800:R694Q	R	+	2	0	BACH1	29636895	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.738000	0.01842	-2.180000	0.00766	-0.355000	0.07637	CGA	.	.	.	weak		0.577	BACH1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171974.1	NM_206866		A	30715024	G	A	30715024	3	1	242	1	0	0	0	0	1	0	0	0	1283	1058	37	1	2095	1	BACH1	21	30715024	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	13542891	30715024	17414871	122	14926											
SIM2	6493	hgsc.bcm.edu	37	chr21	38084911	38084911	+	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	agaccgcttctgtccatttaGgcttatcccaggtgggtatt	7	14	10	10	1	1	1	0	0	1	1	3	1	3	1	3	3	0	3	3	3	3	6			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr21:38084911G>T	ENST00000290399.6	+	3	950	c.337G>T	c.(337-339)Ggc>Tgc	p.G113C	SIM2_ENST00000430056.3_Missense_Mutation_p.G113C	NM_005069.3	NP_005060.1	Q14190	SIM2_HUMAN	single-minded family bHLH transcription factor 2	113	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				cell differentiation (GO:0030154)|embryonic pattern specification (GO:0009880)|lung development (GO:0030324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(6)|prostate(1)|skin(2)	16						TGTCCATTTAGGCTTATCCCA	0.388																																					p.G113C		Atlas-SNP	.											.	SIM2	55	.	0			c.G337T						PASS	.						155	136	142					21																	38084911		2203	4300	6503	SO:0001583	missense	6493	exon3			CATTTAGGCTTAT		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.337G>T	chr21.hg19:g.38084911G>T	ENSP00000290399:p.Gly113Cys	45.0	0.0	.		59.0	26.0	.	NM_005069	O60766|Q15470|Q15471|Q15472|Q15473|Q16532|Q2TBD8	Missense_Mutation	SNP	ENST00000290399.6	hg19	CCDS13646.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.5|24.5	4.541391|4.541391	0.85917|0.85917	.|.	.|.	ENSG00000159263|ENSG00000159263	ENST00000290399;ENST00000430056|ENST00000431229	T;T|.	0.39056|.	1.1;1.1|.	5.42|5.42	5.42|5.42	0.78866|0.78866	PAS (2);PAS fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.90717|0.90717	0.7087|0.7087	H|H	0.98199|0.98199	4.17|4.17	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	0.94002|0.94002	0.7276|0.7276	10|5	0.87932|.	D|.	0|.	.|.	19.2521|19.2521	0.93929|0.93929	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	113;113|.	Q14190;Q14190-2|.	SIM2_HUMAN;.|.	C|M	113|50	ENSP00000290399:G113C;ENSP00000404176:G113C|.	ENSP00000290399:G113C|.	G|R	+|+	1|2	0|0	SIM2|SIM2	37006781|37006781	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.904000|0.904000	0.53231|0.53231	9.287000|9.287000	0.95975|0.95975	2.542000|2.542000	0.85734|0.85734	0.655000|0.655000	0.94253|0.94253	GGC|AGG	.	.	.	none		0.388	SIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194692.1	NM_009586		T	38084911	G	T	38084911	3	4	242	1	0	0	0	0	1	0	0	0	14337	1000	35	4	347	4	SIM2	21	38084911	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	7369887	38084911	10044984	123	14927											
DSCAM	1826	hgsc.bcm.edu	37	chr21	41559859	41559859	+	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	ttccacggtcctccccataaGaattaatagcatggcaggaa	13	9	8	11	1	0	1	0	0	0	1	3	2	3	2	4	3	1	2	4	3	5	4			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr21:41559859G>A	ENST00000400454.1	-	13	3086	c.2609C>T	c.(2608-2610)tCt>tTt	p.S870F		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	870	Ig-like C2-type 9.				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)				CTCCCCATAAGAATTAATAGC	0.403																																					p.S870F	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.C2609T						PASS	.						113	102	105					21																	41559859		1859	4104	5963	SO:0001583	missense	1826	exon13			CCATAAGAATTAA	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.2609C>T	chr21.hg19:g.41559859G>A	ENSP00000383303:p.Ser870Phe	94.0	0.0	.		57.0	22.0	.	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	hg19	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.580605	0.86645	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.70399	-0.48;-0.48	4.74	4.74	0.60224	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.86678	0.5990	M	0.89287	3.02	0.58432	D	0.999996	D	0.76494	0.999	D	0.87578	0.998	D	0.88729	0.3235	10	0.52906	T	0.07	.	18.0962	0.89490	0.0:0.0:1.0:0.0	.	870	O60469	DSCAM_HUMAN	F	870;622	ENSP00000383303:S870F;ENSP00000385342:S622F	ENSP00000383303:S870F	S	-	2	0	DSCAM	40481729	1.000000	0.71417	0.992000	0.48379	0.985000	0.73830	9.679000	0.98649	2.309000	0.77851	0.561000	0.74099	TCT	.	.	.	none		0.403	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		A	41559859	G	A	41559859	3	1	242	1	0	0	0	0	1	0	0	0	4770	942	33	2	3513	2	DSCAM	21	41559859	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	3474948	41559859	6570036	124	14928											
COL18A1	80781	hgsc.bcm.edu	37	chr21	46875847	46875847	+	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	ggaatgacactgtccccactGagagcttggccagggcggaa	10	6	14	11	1	0	2	0	2	0	1	1	5	1	4	3	4	1	1	3	4	2	1			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr21:46875847G>A	ENST00000359759.4	+	1	424	c.403G>A	c.(403-405)Gag>Aag	p.E135K	COL18A1_ENST00000400337.2_Intron|COL18A1_ENST00000355480.5_Missense_Mutation_p.E135K			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	135					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)		TGTCCCCACTGAGAGCTTGGC	0.642																																					p.E135K		Atlas-SNP	.											.	COL18A1	129	.	0			c.G403A						PASS	.						34	40	38					21																	46875847		2089	4179	6268	SO:0001583	missense	80781	exon1			CCCACTGAGAGCT		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.403G>A	chr21.hg19:g.46875847G>A	ENSP00000352798:p.Glu135Lys	131.0	0.0	.		130.0	61.0	.	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	hg19		.	.	.	.	.	.	.	.	.	.	G	12.33	1.906637	0.33628	.	.	ENSG00000182871	ENST00000355480;ENST00000359759;ENST00000539645	T;T	0.31769	1.48;1.48	3.11	-0.0648	0.13771	Domain of unknown function DUF959, collagen XVIII, N-terminal (1);	0.988177	0.08216	N	0.979979	T	0.28764	0.0713	L	0.53249	1.67	0.09310	N	1	B;B	0.25441	0.126;0.103	B;B	0.28916	0.096;0.039	T	0.37888	-0.9686	10	0.52906	T	0.07	.	6.3553	0.21398	0.1093:0.3523:0.5383:0.0	.	135;135	P39060;P39060-1	COIA1_HUMAN;.	K	135	ENSP00000347665:E135K;ENSP00000352798:E135K	ENSP00000347665:E135K	E	+	1	0	COL18A1	45700275	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.939000	0.01545	-0.007000	0.14345	-0.479000	0.04858	GAG	.	.	.	none		0.642	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			A	46875847	G	A	46875847	3	1	242	1	0	0	0	0	1	0	0	0	3677	1291	45	2	519	2	COL18A1	21	46875847	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10	5315988	46875847	1254048	125	14929											
SREBF2	6721	hgsc.bcm.edu	37	chr22	42281013	42281013	+	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	gaggcaagctgggcttcctgGccgtgagtacccttcggttc	5	10	14	12	2	0	1	0	1	0	0	3	2	1	1	3	4	2	5	3	4	2	4			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chr22:42281013G>T	ENST00000361204.4	+	11	2372	c.2206G>T	c.(2206-2208)Gcc>Tcc	p.A736S		NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	736					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						GGGCTTCCTGGCCGTGAGTAC	0.562																																					p.A736S		Atlas-SNP	.											.	SREBF2	99	.	0			c.G2206T						PASS	.						101	78	86					22																	42281013		2203	4300	6503	SO:0001583	missense	6721	exon11			TTCCTGGCCGTGA	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.2206G>T	chr22.hg19:g.42281013G>T	ENSP00000354476:p.Ala736Ser	104.0	0.0	.		79.0	41.0	.	NM_004599	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Missense_Mutation	SNP	ENST00000361204.4	hg19	CCDS14023.1	.	.	.	.	.	.	.	.	.	.	G	12.89	2.073508	0.36566	.	.	ENSG00000198911	ENST00000361204;ENST00000457567	T	0.08458	3.09	5.13	5.13	0.70059	.	0.101356	0.64402	D	0.000002	T	0.06325	0.0163	L	0.32530	0.975	0.51482	D	0.999926	B	0.31581	0.329	B	0.27170	0.077	T	0.36187	-0.9758	10	0.11485	T	0.65	-16.1308	11.9942	0.53191	0.0796:0.0:0.9204:0.0	.	736	Q12772	SRBP2_HUMAN	S	736	ENSP00000354476:A736S	ENSP00000354476:A736S	A	+	1	0	SREBF2	40610959	1.000000	0.71417	1.000000	0.80357	0.694000	0.40290	4.372000	0.59530	2.412000	0.81896	0.491000	0.48974	GCC	.	.	.	none		0.562	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599		T	42281013	G	T	42281013	3	4	242	1	0	0	0	0	1	0	0	0	15154	1203	42	4	2248	4	SREBF2	22	42281013	Missense_Mutation	SNP	G	TCGA-SX-A71S-01A-11D-A33Q-10		42281013	9023553	126	14930											
DACH2	117154	hgsc.bcm.edu	37	chrX	85906115	85906115	+	Frame_Shift_Del	DEL	A	A	-																															gctatgaacactcttcagggAaatggaagccaaaatgggac																										TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chrX:85906115delA	ENST00000373125.4	+	4	717	c.717delA	c.(715-717)ggafs	p.G239fs	DACH2_ENST00000510272.1_Frame_Shift_Del_p.G20fs|DACH2_ENST00000373131.1_Frame_Shift_Del_p.G226fs|DACH2_ENST00000508860.1_Frame_Shift_Del_p.G72fs	NM_053281.3	NP_444511.1	Q96NX9	DACH2_HUMAN	dachshund family transcription factor 2	239					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						CTCTTCAGGGAAATGGAAGCC	0.433																																					p.G239fs		Atlas-Indel,Pindel	.											.	DACH2	263	.	0			c.716delG						PASS	.						99	78	85					X																	85906115		2203	4299	6502	SO:0001589	frameshift_variant	117154	exon4			.	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.717delA	chrX.hg19:g.85906115delA	ENSP00000362217:p.Gly239fs	228.0	0.0	0		237.0	106.0	0.447257	NM_053281	B1AJV3|B4DQG3|Q8NAY3|Q8ND17|Q96N55	Frame_Shift_Del	DEL	ENST00000373125.4	hg19	CCDS14455.1																																																																																			.	.	.	none		0.433	DACH2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359266.1	NM_053281		-	85906115	A	-	85906115	7	5	242	1	0	1	0	1	0	0	0	0	4223	233	9	0	731	0	DACH2	23	85906115	Frame_Shift_Del	DEL	A	TCGA-SX-A71S-01A-11D-A33Q-10		85906115	69364445	127	14931											
FMR1	2332	hgsc.bcm.edu	37	chrX	147014033	147014033	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attggtactcatggtgctaaTattcagcaagctagaaaagt	14	12	9	6	0	2	1	2	0	0	1	2	1	2	1	0	2	4	4	0	2	7	6			TCGA-SX-A71S-01A-11D-A33Q-10	TCGA-SX-A71S-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	158b7380-c848-4b01-a581-e79ff31ca48f	0175a079-c143-46a1-975c-4d940bd28bc4	g.chrX:147014033T>C	ENST00000370475.4	+	8	848	c.720T>C	c.(718-720)aaT>aaC	p.N240N	FMR1_ENST00000370470.1_Silent_p.N240N|FMR1_ENST00000370477.1_Silent_p.N240N|FMR1_ENST00000218200.8_Silent_p.N240N|FMR1_ENST00000370471.3_Silent_p.N240N|FMR1_ENST00000334557.6_Silent_p.N240N|FMR1_ENST00000440235.2_5'UTR|FMR1_ENST00000439526.2_Silent_p.N240N	NM_002024.5	NP_002015.1	Q06787	FMR1_HUMAN	fragile X mental retardation 1	240	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				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)					ATGGTGCTAATATTCAGCAAG	0.388									Fragile X syndrome																												p.N240N		Atlas-SNP	.											.	FMR1	93	.	0			c.T720C						PASS	.						176	164	168					X																	147014033		2203	4300	6503	SO:0001819	synonymous_variant	2332	exon8	Familial Cancer Database	Martin-Bell syndrome, FRAXA syndrome	TGCTAATATTCAG	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.720T>C	chrX.hg19:g.147014033T>C		364.0	0.0	.		328.0	141.0	.	NM_002024	A6NNH4|D3DWT0|D3DWT1|D3DWT2|G8JL90|Q16578|Q5PQZ6|Q99054	Silent	SNP	ENST00000370475.4	hg19	CCDS14682.1																																																																																			.	.	.	none		0.388	FMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058655.1	NM_002024		C	147014033	T	C	147014033	2	2	242	1	0	0	0	0	0	0	0	1	5967	1403	49	3		3	FMR1	23	147014033	Silent	SNP	T	TCGA-SX-A71S-01A-11D-A33Q-10	61107918	147014033	8256527	128	14932											
PTCHD2	57540	hgsc.bcm.edu	37	chr1	11561256	11561256	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accctgggctgggccttcacCaatccgtgctgtgctgggct	4	10	13	14	1	1	0	1	0	0	0	2	0	2	0	4	3	2	4	4	3	1	1			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr1:11561256C>T	ENST00000294484.6	+	2	345	c.207C>T	c.(205-207)acC>acT	p.T69T	PTCHD2_ENST00000389575.3_Silent_p.T69T	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	69					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)		GGGCCTTCACCAATCCGTGCT	0.642																																					p.T69T		Atlas-SNP	.											.	PTCHD2	193	.	0			c.C207T						PASS	.						72	74	73					1																	11561256		2068	4188	6256	SO:0001819	synonymous_variant	57540	exon2			CTTCACCAATCCG	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.207C>T	chr1.hg19:g.11561256C>T		76.0	0.0	.		75.0	29.0	.	NM_020780	Q5VTU9|Q9UJD6	Silent	SNP	ENST00000294484.6	hg19	CCDS41247.1																																																																																			.	.	.	none		0.642	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561		T	11561256	C	T	11561256	2	4	243	1	0	0	0	0	0	0	0	1	12743	581	21	2		2	PTCHD2	1	11561256	Silent	SNP	C	TCGA-SX-A71U-01A-12D-A33Q-10		11561256	237689365	1	14933											
KLHDC7A	127707	hgsc.bcm.edu	37	chr1	18808064	18808064	+	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	acagtaaaccccgtgagcatCcaggactggggcaactagaa	14	5	11	11	1	0	2	0	1	0	1	1	3	1	3	3	3	3	3	3	3	5	2			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr1:18808064C>T	ENST00000400664.1	+	1	641	c.589C>T	c.(589-591)Cca>Tca	p.P197S		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	197						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)		CCGTGAGCATCCAGGACTGGG	0.602																																					p.P197S		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.C589T						PASS	.						45	47	46					1																	18808064		2203	4300	6503	SO:0001583	missense	127707	exon1			GAGCATCCAGGAC	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.589C>T	chr1.hg19:g.18808064C>T	ENSP00000383505:p.Pro197Ser	37.0	0.0	.		27.0	6.0	.	NM_152375	Q8N8W6	Missense_Mutation	SNP	ENST00000400664.1	hg19	CCDS185.2	.	.	.	.	.	.	.	.	.	.	C	12.19	1.864315	0.32977	.	.	ENSG00000179023	ENST00000400664;ENST00000540290	T	0.72394	-0.65	5.7	3.79	0.43588	.	1.829710	0.03990	U	0.294708	T	0.54367	0.1854	N	0.14661	0.345	0.09310	N	1	B	0.21905	0.062	B	0.20577	0.03	T	0.42015	-0.9476	10	0.14656	T	0.56	.	7.7248	0.28753	0.1675:0.7492:0.0:0.0834	.	197	Q5VTJ3	KLD7A_HUMAN	S	197;134	ENSP00000383505:P197S	ENSP00000383505:P197S	P	+	1	0	KLHDC7A	18680651	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	0.281000	0.18810	0.710000	0.31997	0.591000	0.81541	CCA	.	.	.	none		0.602	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375		T	18808064	C	T	18808064	3	4	243	1	0	0	0	0	1	0	0	0	8367	855	30	2	591	2	KLHDC7A	1	18808064	Missense_Mutation	SNP	C	TCGA-SX-A71U-01A-12D-A33Q-10	7246808	18808064	230442557	2	14934											
SNRNP40	9410	hgsc.bcm.edu	37	chr1	31744229	31744229	+	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	ttcctttccaaagttacctgTattgtccattgcattggaca	9	16	6	10	0	0	0	0	0	0	0	3	1	3	1	4	1	2	3	4	1	3	7			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr1:31744229T>A	ENST00000263694.4	-	6	790	c.772A>T	c.(772-774)Aca>Tca	p.T258S	SNRNP40_ENST00000446633.2_Missense_Mutation_p.T258S|SNRNP40_ENST00000373720.3_5'Flank|SNRNP40_ENST00000489853.1_5'UTR	NM_004814.2	NP_004805.2	Q96DI7	SNR40_HUMAN	small nuclear ribonucleoprotein 40kDa (U5)	258					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nucleolar ribonucleoprotein complex (GO:0005732)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	7						AAGTTACCTGTATTGTCCATT	0.423																																					p.T258S		Atlas-SNP	.											.	SNRNP40	18	.	0			c.A772T						PASS	.						74	76	76					1																	31744229		2203	4300	6503	SO:0001583	missense	9410	exon6			TACCTGTATTGTC	AF090988	CCDS340.1	1p35.2	2013-01-09	2008-10-29	2008-10-29	ENSG00000060688	ENSG00000060688		"WD repeat domain containing"	30857	protein-coding gene	gene with protein product		607797	"WD repeat domain 57 (U5 snRNP specific)"	WDR57		9774689, 9731529, 10788320	Standard	NM_004814		Approved	PRP8BP, SPF38, PRPF8BP, HPRP8BP	uc009vtt.3	Q96DI7	OTTHUMG00000003790	ENST00000263694.4:c.772A>T	chr1.hg19:g.31744229T>A	ENSP00000263694:p.Thr258Ser	29.0	0.0	.		31.0	7.0	.	NM_004814	B4DQJ1|O75938|O95320	Missense_Mutation	SNP	ENST00000263694.4	hg19	CCDS340.1	.	.	.	.	.	.	.	.	.	.	T	16.61	3.169851	0.57584	.	.	ENSG00000060688	ENST00000263694;ENST00000446633	T;T	0.66638	-0.22;-0.22	5.52	5.52	0.82312	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.044686	0.85682	D	0.000000	T	0.65165	0.2665	L	0.50333	1.59	0.58432	D	0.999999	B;B	0.19935	0.04;0.022	B;B	0.31101	0.122;0.124	T	0.61792	-0.6990	10	0.39692	T	0.17	.	15.6465	0.77061	0.0:0.0:0.0:1.0	.	258;258	B4DQJ1;Q96DI7	.;SNR40_HUMAN	S	258	ENSP00000263694:T258S;ENSP00000406841:T258S	ENSP00000263694:T258S	T	-	1	0	SNRNP40	31516816	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.895000	0.69814	2.091000	0.63221	0.460000	0.39030	ACA	.	.	.	none		0.423	SNRNP40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010657.1	NM_004814		A	31744229	T	A	31744229	3	1	243	1	0	0	0	0	1	0	0	0	14869	1638	57	5	321	5	SNRNP40	1	31744229	Missense_Mutation	SNP	T	TCGA-SX-A71U-01A-12D-A33Q-10	12936165	31744229	217506392	3	14935											
WDR65	149465	hgsc.bcm.edu	37	chr1	43649431	43649431	+	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	tgacaagattgtcgttggcaCtgacacaggcaaactcttcc	11	10	9	11	1	1	3	0	2	1	1	3	3	2	3	1	2	1	3	1	2	2	3			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr1:43649431C>A	ENST00000372492.4	+	4	968	c.644C>A	c.(643-645)aCt>aAt	p.T215N	WDR65_ENST00000528956.1_Missense_Mutation_p.T215N	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		215										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)				GTCGTTGGCACTGACACAGGC	0.502																																					p.T215N		Atlas-SNP	.											.	WDR65	76	.	0			c.C644A						PASS	.						142	133	136					1																	43649431		2203	4300	6503	SO:0001583	missense	149465	exon4			TTGGCACTGACAC																												ENST00000372492.4:c.644C>A	chr1.hg19:g.43649431C>A	ENSP00000361570:p.Thr215Asn	112.0	0.0	.		95.0	36.0	.	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Missense_Mutation	SNP	ENST00000372492.4	hg19		.	.	.	.	.	.	.	.	.	.	C	27.8	4.865019	0.91511	.	.	ENSG00000243710	ENST00000372492;ENST00000528956	T;T	0.48201	0.82;0.82	6.07	6.07	0.98685	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.67268	0.2875	M	0.80982	2.52	0.80722	D	1	P;P	0.51653	0.947;0.845	P;P	0.54100	0.742;0.731	T	0.68473	-0.5399	10	0.59425	D	0.04	.	20.6593	0.99626	0.0:1.0:0.0:0.0	.	215;215	Q96MR6;Q96MR6-2	WDR65_HUMAN;.	N	215	ENSP00000361570:T215N;ENSP00000435310:T215N	ENSP00000361570:T215N	T	+	2	0	WDR65	43422018	1.000000	0.71417	0.997000	0.53966	0.910000	0.53928	4.461000	0.60115	2.885000	0.99019	0.655000	0.94253	ACT	.	.	.	none		0.502	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1			A	43649431	C	A	43649431	3	1	243	1	0	0	0	0	1	0	0	0	17328	565	20	4	654	4	WDR65	1	43649431	Missense_Mutation	SNP	C	TCGA-SX-A71U-01A-12D-A33Q-10	11905202	43649431	205601190	4	14936											
HIPK1	204851	hgsc.bcm.edu	37	chr1	114483624	114483626	+	In_Frame_Del	DEL	TGC	TGC	-																															catttggacaggtggctaagTgctggaagaggagcaccaag																										TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	TGC	TGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr1:114483624_114483626delTGC	ENST00000369558.1	+	2	851_853	c.619_621delTGC	c.(619-621)tgcdel	p.C207del	HIPK1_ENST00000369555.2_In_Frame_Del_p.C207del|HIPK1_ENST00000369561.4_In_Frame_Del_p.C207del|HIPK1_ENST00000426820.2_In_Frame_Del_p.C207del|HIPK1_ENST00000369554.2_In_Frame_Del_p.C207del|HIPK1_ENST00000369559.4_In_Frame_Del_p.C207del			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1	207	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)		GGTGGCTAAGTGCTGGAAGAGGA	0.498																																					p.206_207del		Atlas-INDEL	.											.	HIPK1	195	.	0			c.618_620del						PASS	.																																			SO:0001651	inframe_deletion	204851	exon2			.	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.619_621delTGC	chr1.hg19:g.114483624_114483626delTGC	ENSP00000358571:p.Cys207del	55.0	0.0	0		35.0	10.0	0.285714	NM_152696	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	In_Frame_Del	DEL	ENST00000369558.1	hg19	CCDS867.1																																																																																			.	.	.	none		0.498	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033127.1	NM_198268		-	114483626	TGC	-	114483624	7	5	243	1	0	1	0	1	0	0	0	0	7123	1696	59	0	621	0	HIPK1	1	114483624	In_Frame_Del	DEL	TGC	TCGA-SX-A71U-01A-12D-A33Q-10	70834193	114483624	134766997	5	14937											
HMGCS2	3158	hgsc.bcm.edu	37	chr1	120300026	120300026	+	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	tgtatgaaagatcatgtactGtaaatcgtcaagggtgaagg	14	11	12	4	1	2	3	2	2	0	1	3	3	2	3	0	2	1	3	0	2	7	3			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr1:120300026G>A	ENST00000369406.3	-	5	935	c.886C>T	c.(886-888)Cag>Tag	p.Q296*	HMGCS2_ENST00000476640.1_5'UTR|HMGCS2_ENST00000544913.2_Nonsense_Mutation_p.Q254*	NM_005518.3	NP_005509.1	P54868	HMCS2_HUMAN	3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)	296					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)		ATCATGTACTGTAAATCGTCA	0.517																																					p.Q296X		Atlas-SNP	.											.	HMGCS2	58	.	0			c.C886T						PASS	.						95	85	88					1																	120300026		2203	4300	6503	SO:0001587	stop_gained	3158	exon5			TGTACTGTAAATC	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.886C>T	chr1.hg19:g.120300026G>A	ENSP00000358414:p.Gln296*	92.0	0.0	.		74.0	20.0	.	NM_005518	B7Z8R3|D3Y5K6|Q5SZU2|Q6IBF4	Nonsense_Mutation	SNP	ENST00000369406.3	hg19	CCDS905.1	.	.	.	.	.	.	.	.	.	.	G	35	5.588598	0.96590	.	.	ENSG00000134240	ENST00000369406;ENST00000544913	.	.	.	5.33	4.36	0.52297	.	0.195185	0.36303	N	0.002662	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-1.6266	8.8144	0.34987	0.0:0.2688:0.5824:0.1487	.	.	.	.	X	296;254	.	ENSP00000358414:Q296X	Q	-	1	0	HMGCS2	120101549	0.983000	0.35010	0.944000	0.38274	0.855000	0.48748	1.916000	0.39986	2.646000	0.89796	0.655000	0.94253	CAG	.	.	.	none		0.517	HMGCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033469.2	NM_005518		A	120300026	G	A	120300026	4	1	243	1	0	0	0	0	0	1	0	0	7240	1386	48	2	660	2	HMGCS2	1	120300026	Nonsense_Mutation	SNP	G	TCGA-SX-A71U-01A-12D-A33Q-10	5816402	120300026	128950595	6	14938											
PEAR1	375033	hgsc.bcm.edu	37	chr1	156876561	156876561	+	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	cccgaactgccttcagccctGtacccctggctactatggcc	6	9	8	18	1	1	0	1	0	0	0	1	1	1	0	6	2	5	2	6	2	4	4			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr1:156876561G>T	ENST00000338302.3	+	7	758	c.533G>T	c.(532-534)tGt>tTt	p.C178F	PEAR1_ENST00000292357.7_Missense_Mutation_p.C178F			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	178					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)					CTTCAGCCCTGTACCCCTGGC	0.632																																					p.C178F		Atlas-SNP	.											.	PEAR1	118	.	0			c.G533T						PASS	.						119	104	109					1																	156876561		2203	4300	6503	SO:0001583	missense	375033	exon6			AGCCCTGTACCCC	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.533G>T	chr1.hg19:g.156876561G>T	ENSP00000344465:p.Cys178Phe	132.0	0.0	.		101.0	39.0	.	NM_001080471	Q8TEK2	Missense_Mutation	SNP	ENST00000338302.3	hg19	CCDS30892.1	.	.	.	.	.	.	.	.	.	.	G	17.99	3.523741	0.64747	.	.	ENSG00000187800	ENST00000338302;ENST00000292357	T;T	0.72835	-0.69;-0.69	4.81	4.81	0.61882	.	0.000000	0.53938	D	0.000045	D	0.90170	0.6928	H	0.99732	4.735	0.58432	D	0.999999	D	0.71674	0.998	D	0.68621	0.959	D	0.94083	0.7346	9	.	.	.	.	15.4054	0.74874	0.0:0.0:1.0:0.0	.	178	Q5VY43	PEAR1_HUMAN	F	178	ENSP00000344465:C178F;ENSP00000292357:C178F	.	C	+	2	0	PEAR1	155143185	1.000000	0.71417	0.632000	0.29296	0.378000	0.30076	8.189000	0.89712	2.497000	0.84241	0.561000	0.74099	TGT	.	.	.	none		0.632	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471		T	156876561	G	T	156876561	3	4	243	1	0	0	0	0	1	0	0	0	11719	1377	48	4	551	4	PEAR1	1	156876561	Missense_Mutation	SNP	G	TCGA-SX-A71U-01A-12D-A33Q-10	36576535	156876561	92374060	7	14939											
TADA1	117143	hgsc.bcm.edu	37	chr1	166838685	166838685	+	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	tatttccactcccttacctgGtgtagaaaccaaaatctgac	12	12	5	12	0	1	2	0	1	1	1	3	2	3	2	4	1	2	1	4	1	6	4			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr1:166838685G>C	ENST00000367874.4	-	3	322	c.229C>G	c.(229-231)Cca>Gca	p.P77A		NM_053053.3	NP_444281.1	Q96BN2	TADA1_HUMAN	transcriptional adaptor 1	77					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	11						CCCTTACCTGGTGTAGAAACC	0.398																																					p.P77A		Atlas-SNP	.											.	TADA1	32	.	0			c.C229G						PASS	.						75	64	67					1																	166838685		2203	4300	6503	SO:0001583	missense	117143	exon3			TACCTGGTGTAGA	BC015401	CCDS1255.1	1q24.1	2009-10-02	2009-10-02	2009-10-02	ENSG00000152382	ENSG00000152382			30631	protein-coding gene	gene with protein product		612763	"transcriptional adaptor 1 (HFI1 homolog, yeast)-like", "transcriptional adaptor 1 (HFI1 homolog, yeast)"	TADA1L		11564863	Standard	NM_053053		Approved	STAF42, ADA1, hADA1, HFI1	uc001gdw.3	Q96BN2	OTTHUMG00000034321	ENST00000367874.4:c.229C>G	chr1.hg19:g.166838685G>C	ENSP00000356848:p.Pro77Ala	77.0	0.0	.		60.0	25.0	.	NM_053053	A8K4J9	Missense_Mutation	SNP	ENST00000367874.4	hg19	CCDS1255.1	.	.	.	.	.	.	.	.	.	.	G	17.23	3.336601	0.60963	.	.	ENSG00000152382	ENST00000367874	T	0.50548	0.74	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.21145	0.0509	N	0.08118	0	0.47153	D	0.999336	B;P	0.37708	0.149;0.606	B;B	0.43018	0.196;0.405	T	0.11446	-1.0587	9	0.17832	T	0.49	.	17.4199	0.87512	0.0:0.0:1.0:0.0	.	77;77	A8K4J9;Q96BN2	.;TADA1_HUMAN	A	77	ENSP00000356848:P77A	ENSP00000356848:P77A	P	-	1	0	TADA1	165105309	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.289000	0.78701	2.707000	0.92482	0.655000	0.94253	CCA	.	.	.	none		0.398	TADA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082881.1	NM_053053		C	166838685	G	C	166838685	3	2	243	1	0	0	0	0	1	0	0	0	15521	1261	44	4	802	4	TADA1	1	166838685	Missense_Mutation	SNP	G	TCGA-SX-A71U-01A-12D-A33Q-10	9962124	166838685	82411936	8	14940											
ADCY10	55811	hgsc.bcm.edu	37	chr1	167871039	167871039	+	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	ctccacagggctagcagtgcAtcaccttcagagagagacat	12	7	10	12	0	2	2	2	0	0	2	3	4	3	2	2	1	2	3	2	1	1	2			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr1:167871039A>T	ENST00000367851.4	-	5	481	c.297T>A	c.(295-297)gaT>gaA	p.D99E	ADCY10_ENST00000545172.1_Intron|ADCY10_ENST00000367848.1_Missense_Mutation_p.D7E	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	99	Guanylate cyclase 1. {ECO:0000255|PROSITE-ProRule:PRU00099}.				cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						CTAGCAGTGCATCACCTTCAG	0.463																																					p.D99E		Atlas-SNP	.											.	ADCY10	175	.	0			c.T297A						PASS	.						126	130	129					1																	167871039		2203	4300	6503	SO:0001583	missense	55811	exon5			CAGTGCATCACCT	AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	4.6.1.1	"Adenylate cyclases"	21285	protein-coding gene	gene with protein product	"soluble adenylyl cyclase", "Hypercalciuria, absorptive, 2"	605205					Standard	XM_006711449		Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.297T>A	chr1.hg19:g.167871039A>T	ENSP00000356825:p.Asp99Glu	59.0	0.0	.		62.0	18.0	.	NM_018417	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Missense_Mutation	SNP	ENST00000367851.4	hg19	CCDS1265.1	.	.	.	.	.	.	.	.	.	.	A	17.68	3.448680	0.63178	.	.	ENSG00000143199	ENST00000367851;ENST00000367848	D;T	0.87256	-2.23;0.04	5.78	-9.57	0.00562	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.64402	D	0.000003	D	0.90137	0.6918	M	0.85373	2.75	0.35082	D	0.763464	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.93979	0.7256	9	0.87932	D	0	-29.5589	18.8216	0.92099	0.2805:0.0:0.7195:0.0	.	7;99	Q96PN6-2;Q96PN6	.;ADCYA_HUMAN	E	99;7	ENSP00000356825:D99E;ENSP00000356822:D7E	ENSP00000356822:D7E	D	-	3	2	ADCY10	166137663	0.626000	0.27120	0.019000	0.16419	0.642000	0.38348	-0.516000	0.06282	-2.105000	0.00842	-0.468000	0.05107	GAT	.	.	.	none		0.463	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417		T	167871039	A	T	167871039	3	4	243	1	0	0	0	0	1	0	0	0	293	214	8	5	4651	5	ADCY10	1	167871039	Missense_Mutation	SNP	A	TCGA-SX-A71U-01A-12D-A33Q-10	1032354	167871039	81379582	9	14941											
BAT2L2	23215	hgsc.bcm.edu	37	chr1	171526383	171526383	+	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	ccgttaattttttaaggtctGgaacaaaaagaatgcaaatg	16	12	8	5	1	1	1	0	0	1	1	1	2	1	2	1	2	2	2	1	2	7	4			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr1:171526383G>T	ENST00000338920.4	+	19	5363	c.5126G>T	c.(5125-5127)tGg>tTg	p.W1709L	PRRC2C_ENST00000367742.3_Missense_Mutation_p.W1711L|PRRC2C_ENST00000392078.3_Missense_Mutation_p.W1711L|PRRC2C_ENST00000426496.2_Missense_Mutation_p.W1709L	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	1709					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										TTTAAGGTCTGGAACAAAAAG	0.398																																					p.W1709L		Atlas-SNP	.											.	.	.	.	0			c.G5126T						PASS	.						28	32	31					1																	171526383		1620	2828	4448	SO:0001583	missense	23215	exon19			AGGTCTGGAACAA	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.5126G>T	chr1.hg19:g.171526383G>T	ENSP00000343629:p.Trp1709Leu	119.0	0.0	.		71.0	22.0	.	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	hg19	CCDS1296.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.42|14.42	2.530678|2.530678	0.45073|0.45073	.|.	.|.	ENSG00000117523|ENSG00000117523	ENST00000495585|ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080	.|T;T;T;T	.|0.01838	.|4.62;4.61;4.61;4.62	5.89|5.89	5.89|5.89	0.94794|0.94794	.|.	.|0.000000	.|0.44285	.|D	.|0.000468	.|T	.|0.07413	.|0.0187	L|L	0.56769|0.56769	1.78|1.78	0.53688|0.53688	D|D	0.999979|0.999979	.|D	.|0.76494	.|0.999	.|D	.|0.69479	.|0.964	.|T	.|0.11743	.|-1.0575	.|10	.|0.87932	.|D	.|0	.|.	20.3242|20.3242	0.98691|0.98691	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1709	.|Q9Y520-4	.|.	X|L	257|1711;1710;1709;1711;1709;1466	.|ENSP00000375928:W1711L;ENSP00000410219:W1709L;ENSP00000356716:W1711L;ENSP00000343629:W1709L	.|ENSP00000343629:W1709L	G|W	+|+	1|2	0|0	PRRC2C|PRRC2C	169793007|169793007	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	6.908000|6.908000	0.75730|0.75730	2.817000|2.817000	0.96982|0.96982	0.549000|0.549000	0.68633|0.68633	GGA|TGG	.	.	.	none		0.398	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		T	171526383	G	T	171526383	3	4	243	1	0	0	0	0	1	0	0	0	1321	1357	47	4	5196	4	BAT2L2	1	171526383	Missense_Mutation	SNP	G	TCGA-SX-A71U-01A-12D-A33Q-10	3655344	171526383	77724238	10	14942											
ARPC5	10092	hgsc.bcm.edu	37	chr1	183604774	183604774	+	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	accttccggaagcgggccgaCgacactgtgttcttcgacat	8	9	11	13	5	1	0	0	0	1	0	3	4	2	1	3	2	1	1	3	2	1	3			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr1:183604774C>A	ENST00000359856.6	-	1	87	c.21G>T	c.(19-21)tcG>tcT	p.S7S	RGL1_ENST00000304685.4_5'Flank|RGL1_ENST00000536277.1_5'Flank|ARPC5_ENST00000294742.6_Silent_p.S7S|ARPC5_ENST00000462965.1_5'Flank|ARPC5_ENST00000367534.1_Silent_p.S7S	NM_005717.3	NP_005708.1	O15511	ARPC5_HUMAN	actin related protein 2/3 complex, subunit 5, 16kDa	7					actin cytoskeleton organization (GO:0030036)|Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	structural constituent of cytoskeleton (GO:0005200)			cervix(1)|large_intestine(1)|lung(2)	4						AGCGGGCCGACGACACTGTGT	0.632																																					p.S7S	Melanoma(136;1596 1789 3041 4830 41075)	Atlas-SNP	.											.	ARPC5	6	.	0			c.G21T						PASS	.						85	68	74					1																	183604774		2203	4300	6503	SO:0001819	synonymous_variant	10092	exon1			GGCCGACGACACT	AF017807	CCDS1357.1, CCDS58050.1	1q	2011-07-06	2002-08-29		ENSG00000162704	ENSG00000162704		"Actin related protein 2/3 complex subunits"	708	protein-coding gene	gene with protein product	"Arp2/3 protein complex subunit p16"	604227	"actin related protein 2/3 complex, subunit 5 (16 kD)"			9359840, 9230079	Standard	NM_005717		Approved	p16-Arc, ARC16, dJ127C7.3	uc021pgb.2	O15511	OTTHUMG00000035326	ENST00000359856.6:c.21G>T	chr1.hg19:g.183604774C>A		69.0	0.0	.		71.0	20.0	.	NM_005717	A6NEC4|Q6PG42	Silent	SNP	ENST00000359856.6	hg19	CCDS1357.1																																																																																			.	.	.	none		0.632	ARPC5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000085477.1	NM_005717		A	183604774	C	A	183604774	2	1	243	1	0	0	0	0	0	0	0	1	974	523	19	4		4	ARPC5	1	183604774	Silent	SNP	C	TCGA-SX-A71U-01A-12D-A33Q-10	12078391	183604774	65645847	11	14943											
HMCN1	83872	hgsc.bcm.edu	37	chr1	186101461	186101461	+	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	acgctgcttatttccatagaAtgaagatgccggtgactata	12	12	9	8	2	0	4	0	2	0	2	1	4	1	4	2	1	2	2	2	1	6	5			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr1:186101461A>C	ENST00000271588.4	+	86	13461	c.13232A>C	c.(13231-13233)aAt>aCt	p.N4411T	HMCN1_ENST00000367492.2_Splice_Site_p.N4411T	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4411	Ig-like C2-type 43.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TTTCCATAGAATGAAGATGCC	0.403																																					p.N4411T		Atlas-SNP	.											.	HMCN1	797	.	0			c.A13232C						PASS	.						87	84	85					1																	186101461		2203	4300	6503	SO:0001630	splice_region_variant	83872	exon86			CATAGAATGAAGA	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.13231-1A>C	chr1.hg19:g.186101461A>C		73.0	0.0	.		61.0	18.0	.	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	A	9.020	0.984732	0.18889	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.71579	1.63;-0.58	5.46	5.46	0.80206	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.125941	0.64402	D	0.000001	T	0.67050	0.2852	N	0.11870	0.19	0.37850	D	0.929355	D	0.69078	0.997	D	0.81914	0.995	T	0.65471	-0.6160	10	0.14252	T	0.57	.	10.7243	0.46059	0.8578:0.0:0.0:0.1422	.	4411	Q96RW7	HMCN1_HUMAN	T	4411	ENSP00000271588:N4411T;ENSP00000356462:N4411T	ENSP00000271588:N4411T	N	+	2	0	HMCN1	184368084	1.000000	0.71417	1.000000	0.80357	0.721000	0.41392	4.620000	0.61226	2.186000	0.69663	0.533000	0.62120	AAT	.	.	.	none		0.403	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	Missense_Mutation	C	186101461	A	C	186101461	5	2	243	1	0	0	0	0	0	0	1	0	7227	115	4	5	13574	5	HMCN1	1	186101461	Splice_Site	SNP	A	TCGA-SX-A71U-01A-12D-A33Q-10	2496687	186101461	63149160	12	14944											
TMCC2	9911	hgsc.bcm.edu	37	chr1	205211011	205211011	+	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	agccccagcgtggcagccctCacctgctgcgcaaggccccc	6	4	11	20	2	1	0	1	0	0	0	1	0	1	0	6	2	5	3	6	2	1	0			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr1:205211011C>A	ENST00000358024.3	+	2	975	c.586C>A	c.(586-588)Cac>Aac	p.H196N	TMCC2_ENST00000545499.1_Missense_Mutation_p.H118N|TMCC2_ENST00000495538.1_3'UTR	NM_014858.3	NP_055673.2	O75069	TMCC2_HUMAN	transmembrane and coiled-coil domain family 2	196						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)			TGGCAGCCCTCACCTGCTGCG	0.721																																					p.H196N		Atlas-SNP	.											.	TMCC2	89	.	0			c.C586A						PASS	.						11	11	11					1																	205211011		2168	4246	6414	SO:0001583	missense	9911	exon2			AGCCCTCACCTGC	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.586C>A	chr1.hg19:g.205211011C>A	ENSP00000350718:p.His196Asn	32.0	0.0	.		25.0	12.0	.	NM_014858	A2RRH3|B7Z1P7|Q6ZN09	Missense_Mutation	SNP	ENST00000358024.3	hg19	CCDS30984.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.265906	0.80358	.	.	ENSG00000133069	ENST00000358024;ENST00000545499	T;T	0.32272	1.46;1.5	4.95	4.95	0.65309	.	0.095820	0.45867	D	0.000324	T	0.25044	0.0608	N	0.24115	0.695	0.50813	D	0.999895	B	0.23058	0.079	B	0.18263	0.021	T	0.06881	-1.0802	10	0.87932	D	0	.	17.7809	0.88523	0.0:1.0:0.0:0.0	.	196	O75069	TMCC2_HUMAN	N	196;118	ENSP00000350718:H196N;ENSP00000437943:H118N	ENSP00000350718:H196N	H	+	1	0	TMCC2	203477634	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.465000	0.73538	2.273000	0.75805	0.462000	0.41574	CAC	.	.	.	none		0.721	TMCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090383.1	NM_014858		A	205211011	C	A	205211011	3	1	243	1	0	0	0	0	1	0	0	0	16005	826	29	4	592	4	TMCC2	1	205211011	Missense_Mutation	SNP	C	TCGA-SX-A71U-01A-12D-A33Q-10	19109550	205211011	44039610	13	14945											
TSPYL6	388951	hgsc.bcm.edu	37	chr2	54482228	54482228	+	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	ctggaaggctgtggtctgaaAaccaggtgaagaagctgcag	12	7	15	7	0	1	3	0	2	1	1	1	4	1	4	1	4	3	3	1	4	5	0			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr2:54482228A>T	ENST00000317802.7	-	1	1181	c.1061T>A	c.(1060-1062)tTt>tAt	p.F354Y	ACYP2_ENST00000607452.1_Intron|ACYP2_ENST00000394666.3_Intron|ACYP2_ENST00000303536.4_Intron|ACYP2_ENST00000606865.1_Intron	NM_001003937.2	NP_001003937.2	Q8N831	TSYL6_HUMAN	TSPY-like 6	354					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						GTGGTCTGAAAACCAGGTGAA	0.512																																					p.F354Y		Atlas-SNP	.											.	TSPYL6	54	.	0			c.T1061A						PASS	.						76	82	80					2																	54482228		2148	4284	6432	SO:0001583	missense	388951	exon1			TCTGAAAACCAGG	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.1061T>A	chr2.hg19:g.54482228A>T	ENSP00000417919:p.Phe354Tyr	87.0	0.0	.		73.0	25.0	.	NM_001003937	Q6NUJ3	Missense_Mutation	SNP	ENST00000317802.7	hg19	CCDS42682.1	.	.	.	.	.	.	.	.	.	.	A	18.98	3.737596	0.69304	.	.	ENSG00000178021	ENST00000317802	T	0.61158	0.13	1.67	1.67	0.24075	.	.	.	.	.	T	0.77916	0.4202	M	0.93854	3.465	0.42947	D	0.99436	D	0.89917	1.0	D	0.91635	0.999	T	0.79050	-0.1962	9	0.87932	D	0	.	7.3612	0.26748	1.0:0.0:0.0:0.0	.	354	Q8N831	TSYL6_HUMAN	Y	354	ENSP00000417919:F354Y	ENSP00000417919:F354Y	F	-	2	0	TSPYL6	54335732	1.000000	0.71417	0.766000	0.31476	0.265000	0.26407	3.776000	0.55356	1.022000	0.39626	0.383000	0.25322	TTT	.	.	.	none		0.512	TSPYL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324069.3	XM_371494		T	54482228	A	T	54482228	3	4	243	1	0	0	0	0	1	0	0	0	16675	14	1	5	175	5	TSPYL6	2	54482228	Missense_Mutation	SNP	A	TCGA-SX-A71U-01A-12D-A33Q-10		54482228	188717145	14	14946											
FANCL	55120	hgsc.bcm.edu	37	chr2	58425781	58425781	+	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	gaaaatccacaaaataatctGgtgattctgcaggatactat	16	11	7	7	0	2	1	0	1	2	0	3	3	3	2	1	2	2	1	1	2	7	4			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr2:58425781G>A	ENST00000233741.4	-	7	524	c.488C>T	c.(487-489)cCa>cTa	p.P163L	FANCL_ENST00000403295.3_Missense_Mutation_p.P163L|FANCL_ENST00000402135.3_Missense_Mutation_p.P163L|FANCL_ENST00000540646.1_Intron|FANCL_ENST00000403676.1_Missense_Mutation_p.P46L	NM_018062.3	NP_060532.2	Q9NW38	FANCL_HUMAN	Fanconi anemia, complementation group L	163	UBC-RWD region (URD).				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						AAAATAATCTGGTGATTCTGC	0.313								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.P163L		Atlas-SNP	.											.	FANCL	35	.	0			c.C488T						PASS	.						58	60	59					2																	58425781		2203	4300	6503	SO:0001583	missense	55120	exon7	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TAATCTGGTGATT	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.488C>T	chr2.hg19:g.58425781G>A	ENSP00000233741:p.Pro163Leu	207.0	0.0	.		181.0	51.0	.	NM_018062	Q6GU60	Missense_Mutation	SNP	ENST00000233741.4	hg19	CCDS1860.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.418254	0.83449	.	.	ENSG00000115392	ENST00000403295;ENST00000233741;ENST00000402135;ENST00000403676;ENST00000449070;ENST00000417361	T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96	5.54	5.54	0.83059	Fanconi anemia complex, subunit FancL, WD-repeat containing domain (1);	0.100460	0.64402	D	0.000001	T	0.71239	0.3316	M	0.87269	2.87	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;0.997;0.998	D;D;D;D	0.79784	0.993;0.991;0.934;0.947	T	0.75733	-0.3214	10	0.87932	D	0	-29.5995	19.8426	0.96695	0.0:0.0:1.0:0.0	.	104;163;163;163	C9JZA9;B5MC31;Q9NW38-2;Q9NW38	.;.;.;FANCL_HUMAN	L	163;163;163;46;104;46	ENSP00000386097:P163L;ENSP00000233741:P163L;ENSP00000385021:P163L;ENSP00000384046:P46L;ENSP00000401280:P104L;ENSP00000389448:P46L	ENSP00000233741:P163L	P	-	2	0	FANCL	58279285	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.706000	0.74649	2.759000	0.94783	0.563000	0.77884	CCA	.	.	.	none		0.313	FANCL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251497.1	NM_018062		A	58425781	G	A	58425781	3	1	243	1	0	0	0	0	1	0	0	0	5677	1348	47	2	686	2	FANCL	2	58425781	Missense_Mutation	SNP	G	TCGA-SX-A71U-01A-12D-A33Q-10	3943553	58425781	184773592	15	14947											
EHBP1	23301	hgsc.bcm.edu	37	chr2	63175859	63175859	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtctcagcagagctctggAaggacttcaggatctgatga	12	9	12	8	0	4	3	2	2	3	1	5	6	4	6	0	3	2	2	0	3	2	1			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr2:63175859A>G	ENST00000263991.5	+	14	2465	c.1983A>G	c.(1981-1983)ggA>ggG	p.G661G	EHBP1_ENST00000405015.3_Silent_p.G626G|EHBP1_ENST00000431489.1_Silent_p.G626G|EHBP1_ENST00000354487.3_Silent_p.G626G|EHBP1_ENST00000405289.1_Silent_p.G626G	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	661						cytoplasm (GO:0005737)|membrane (GO:0016020)				biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			AGAGCTCTGGAAGGACTTCAG	0.458																																					p.G661G		Atlas-SNP	.											.	EHBP1	127	.	0			c.A1983G						PASS	.						55	56	55					2																	63175859		2203	4300	6503	SO:0001819	synonymous_variant	23301	exon14			CTCTGGAAGGACT	AL833968	CCDS1872.1, CCDS46299.1, CCDS46300.1	2p15	2008-02-05			ENSG00000115504	ENSG00000115504			29144	protein-coding gene	gene with protein product		609922				10048485	Standard	NM_015252		Approved	KIAA0903, NACSIN	uc002sby.3	Q8NDI1	OTTHUMG00000129453	ENST00000263991.5:c.1983A>G	chr2.hg19:g.63175859A>G		105.0	0.0	.		87.0	24.0	.	NM_015252	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Silent	SNP	ENST00000263991.5	hg19	CCDS1872.1																																																																																			.	.	.	none		0.458	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252		G	63175859	A	G	63175859	2	3	243	1	0	0	0	0	0	0	0	1	4977	233	9	3		3	EHBP1	2	63175859	Silent	SNP	A	TCGA-SX-A71U-01A-12D-A33Q-10	4750078	63175859	180023514	16	14948											
RNF181	51255	hgsc.bcm.edu	37	chr2	85823986	85823987	+	Missense_Mutation	DNP	GA	GA	AC																															ttttggaatttgaggaggagGagactgccattgagatgcct																										TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr2:85823986_85823987GA>AC	ENST00000306368.4	+	3	289_290	c.259_260GA>AC	c.(259-261)GAg>ACg	p.E87T	RNF181_ENST00000441634.1_Missense_Mutation_p.E87T	NM_016494.3	NP_057578.1	Q9P0P0	RN181_HUMAN	ring finger protein 181	87					protein autoubiquitination (GO:0051865)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			lung(1)|stomach(1)	2						TGAGGAGGAGGAGACTGCCATT	0.535																																					p.E87K|p.E87A		Atlas-SNP	.											.	RNF181	10	.	0			c.G259A|c.A260C						PASS	.																																			SO:0001583	missense	51255	exon3			GAGGAGGAGACTG|AGGAGGAGACTGC	AF151072	CCDS1981.1	2p11.2	2013-01-09			ENSG00000168894	ENSG00000168894		"RING-type (C3HC4) zinc fingers"	28037	protein-coding gene	gene with protein product		612490				11042152	Standard	XM_005264359		Approved	HSPC238	uc002spv.1	Q9P0P0	OTTHUMG00000130182	Exception_encountered	chr2.hg19:g.85823986_85823987delinsAC	ENSP00000306906:p.Glu87Thr	92.0	0.0	.		46.0	14.0	.	NM_016494	Q53H81	Missense_Mutation	SNP	ENST00000306368.4	hg19	CCDS1981.1																																																																																			.	.	.	none		0.535	RNF181-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252500.1	NM_016494		AC	85823987	GA	AC	85823986	3	1	243	1	0	0	0	0	1	0	0	0	13478	1175	41	2	269	2	RNF181	2	85823986	Missense_Mutation	DNP	GA	TCGA-SX-A71U-01A-12D-A33Q-10	22648127	85823986	157375387	17	14949											
TTN	7273	hgsc.bcm.edu	37	chr2	179426840	179426840	+	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	agaagaaacattgactctagTtgtctctttaagagtctgac	13	13	8	7	0	3	5	0	2	3	3	4	5	3	5	0	0	1	1	0	0	4	5			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr2:179426840T>A	ENST00000591111.1	-	276	79320	c.79096A>T	c.(79096-79098)Act>Tct	p.T26366S	TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.T25439S|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T19067S|TTN_ENST00000460472.2_Missense_Mutation_p.T18942S|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.T28007S|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T19134S			Q8WZ42	TITIN_HUMAN	titin	26366	Ig-like 127.				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)			TTGACTCTAGTTGTCTCTTTA	0.363																																					p.T28007S		Atlas-SNP	.											.	TTN	18412	.	0			c.A84019T						PASS	.						45	47	46					2																	179426840		1883	4112	5995	SO:0001583	missense	7273	exon326			CTCTAGTTGTCTC	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.79096A>T	chr2.hg19:g.179426840T>A	ENSP00000465570:p.Thr26366Ser	90.0	0.0	.		85.0	21.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	13.09	2.134735	0.37728	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.38560	1.13;1.13;1.13;1.13	6.05	4.88	0.63580	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	0.42877	0.1222	N	0.20445	0.575	0.49582	D	0.999808	D;D;D;D	0.56746	0.977;0.977;0.977;0.958	P;P;P;P	0.55011	0.766;0.766;0.766;0.689	T	0.44787	-0.9305	9	0.87932	D	0	.	13.6782	0.62467	0.0:0.0:0.1285:0.8715	.	18942;19067;19134;26366	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	S	25439;18942;19134;19067;18940	ENSP00000343764:T25439S;ENSP00000434586:T18942S;ENSP00000340554:T19134S;ENSP00000352154:T19067S	ENSP00000340554:T19134S	T	-	1	0	TTN	179135086	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	6.190000	0.72057	1.076000	0.40961	0.528000	0.53228	ACT	.	.	.	none		0.363	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179426840	T	A	179426840	3	1	243	1	0	0	0	0	1	0	0	0	16747	1725	60	5	24108	5	TTN	2	179426840	Missense_Mutation	SNP	T	TCGA-SX-A71U-01A-12D-A33Q-10	93602854	179426840	63772533	18	14950											
PMS1	5378	hgsc.bcm.edu	37	chr2	190717495	190717495	+	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	gaccagtacatcaaaaagatAtcttaaaggtagtatgcttt	16	12	7	6	0	2	1	1	0	1	1	2	2	2	1	1	1	2	4	1	1	8	6	rs375164425		TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr2:190717495A>T	ENST00000441310.2	+	7	1047	c.814A>T	c.(814-816)Atc>Ttc	p.I272F	PMS1_ENST00000409823.3_Missense_Mutation_p.I233F|PMS1_ENST00000447232.2_Missense_Mutation_p.I272F|PMS1_ENST00000432292.3_Missense_Mutation_p.I96F|PMS1_ENST00000421722.1_3'UTR|PMS1_ENST00000418224.3_Missense_Mutation_p.I96F	NM_000534.4	NP_000525.1	P54277	PMS1_HUMAN	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)	272					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)			TCAAAAAGATATCTTAAAGGT	0.313			"Mis, N"			"colorectal, endometrial, ovarian"		Direct reversal of damage;Mismatch excision repair (MMR)																													p.I272F		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.A814T						PASS	.						56	58	57					2																	190717495		2203	4299	6502	SO:0001583	missense	5378	exon7			AAAGATATCTTAA		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.814A>T	chr2.hg19:g.190717495A>T	ENSP00000406490:p.Ile272Phe	226.0	0.0	.		190.0	69.0	.	NM_001128144	D3DPI1|Q4VAL4|Q5FBZ3|Q5FBZ6|Q5FBZ8	Missense_Mutation	SNP	ENST00000441310.2	hg19	CCDS2302.1	.	.	.	.	.	.	.	.	.	.	A	18.12	3.553094	0.65425	.	.	ENSG00000064933	ENST00000392338;ENST00000441310;ENST00000418224;ENST00000409823;ENST00000447232;ENST00000432292;ENST00000424307;ENST00000409593	D;D;D;D;D;D;D	0.85773	-2.03;-2.03;-2.03;-2.03;-2.03;-2.03;-2.03	5.39	5.39	0.77823	Ribosomal protein S5 domain 2-type fold (1);DNA mismatch repair protein, N-terminal (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);DNA mismatch repair protein, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.92750	0.7695	M	0.85630	2.765	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.986;1.0;1.0;0.994;0.987;0.986;0.986	D;D;D;D;D;D;D	0.87578	0.952;0.998;0.998;0.979;0.952;0.952;0.952	D	0.92936	0.6368	10	0.45353	T	0.12	-13.672	15.6976	0.77512	1.0:0.0:0.0:0.0	.	272;233;233;57;233;272;272	Q4VAL4;B4DMF4;Q5FBZ9;Q5FBZ6;Q5FBZ3;Q5FBZ8;P54277	.;.;.;.;.;.;PMS1_HUMAN	F	96;272;96;233;272;96;211;57	ENSP00000406490:I272F;ENSP00000404492:I96F;ENSP00000387125:I233F;ENSP00000401064:I272F;ENSP00000398378:I96F;ENSP00000389938:I211F;ENSP00000387169:I57F	ENSP00000376149:I96F	I	+	1	0	PMS1	190425740	1.000000	0.71417	1.000000	0.80357	0.366000	0.29705	4.548000	0.60718	2.168000	0.68352	0.397000	0.26171	ATC	.	.	.	alt		0.313	PMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255918.2			T	190717495	A	T	190717495	3	4	243	1	0	0	0	0	1	0	0	0	12149	449	16	5	836	5	PMS1	2	190717495	Missense_Mutation	SNP	A	TCGA-SX-A71U-01A-12D-A33Q-10	11290655	190717495	52481878	19	14951											
STAT1	6772	hgsc.bcm.edu	37	chr2	191873805	191873805	+	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	gtcatgaaaacggatggtggCaaatgaaacatcattggcag	15	8	12	6	1	2	2	2	2	0	0	2	3	2	3	0	4	2	2	0	4	4	1			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr2:191873805C>G	ENST00000361099.3	-	4	544	c.157G>C	c.(157-159)Gcc>Ccc	p.A53P	STAT1_ENST00000392323.2_Missense_Mutation_p.A55P|STAT1_ENST00000392322.3_Missense_Mutation_p.A53P|STAT1_ENST00000540176.1_Missense_Mutation_p.A53P|STAT1_ENST00000409465.1_Missense_Mutation_p.A53P	NM_007315.3	NP_009330.1	P42224	STAT1_HUMAN	signal transducer and activator of transcription 1, 91kDa	53					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)			CGGATGGTGGCAAATGAAACA	0.373																																					p.A53P		Atlas-SNP	.											.	STAT1	93	.	0			c.G157C						PASS	.						113	106	108					2																	191873805		2203	4300	6503	SO:0001583	missense	6772	exon4			TGGTGGCAAATGA		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.157G>C	chr2.hg19:g.191873805C>G	ENSP00000354394:p.Ala53Pro	78.0	0.0	.		69.0	16.0	.	NM_007315	A8K989|B2RCA0|D2KFR8|D3DPI7|Q53S88|Q53XW4|Q68D00|Q9UDL5	Missense_Mutation	SNP	ENST00000361099.3	hg19	CCDS2309.1	.	.	.	.	.	.	.	.	.	.	C	34	5.300702	0.95601	.	.	ENSG00000115415	ENST00000361099;ENST00000409465;ENST00000540176;ENST00000392322;ENST00000392323;ENST00000424722;ENST00000454414;ENST00000432058	T;T;T;T;T;T;T;T	0.60424	0.19;0.19;0.19;0.19;0.19;0.19;0.19;0.19	5.52	5.52	0.82312	STAT transcription factor, protein interaction (4);	0.000000	0.85682	D	0.000000	T	0.80308	0.4599	M	0.86953	2.85	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.83341	-0.0008	10	0.72032	D	0.01	-28.6958	18.4444	0.90678	0.0:1.0:0.0:0.0	.	53;53	P42224-2;P42224	.;STAT1_HUMAN	P	53;53;53;53;55;53;53;53	ENSP00000354394:A53P;ENSP00000386244:A53P;ENSP00000438703:A53P;ENSP00000376136:A53P;ENSP00000376137:A55P;ENSP00000402548:A53P;ENSP00000411398:A53P;ENSP00000416019:A53P	ENSP00000354394:A53P	A	-	1	0	STAT1	191582050	1.000000	0.71417	0.977000	0.42913	0.863000	0.49368	7.818000	0.86416	2.602000	0.87976	0.557000	0.71058	GCC	.	.	.	none		0.373	STAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255997.3	NM_007315		G	191873805	C	G	191873805	3	3	243	1	0	0	0	0	1	0	0	0	15276	710	25	4	2187	4	STAT1	2	191873805	Missense_Mutation	SNP	C	TCGA-SX-A71U-01A-12D-A33Q-10	1156310	191873805	51325568	20	14952											
DNPEP	23549	hgsc.bcm.edu	37	chr2	220251040	220251040	+	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	gcgtccagccagagtcaggtCacggtcaaaccaggtgctcc	9	6	12	14	2	3	1	3	0	0	1	5	1	5	1	4	3	3	1	4	3	1	0			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr2:220251040C>T	ENST00000273075.4	-	5	647	c.427G>A	c.(427-429)Gac>Aac	p.D143N	DNPEP_ENST00000373972.1_Missense_Mutation_p.D68N|DNPEP_ENST00000523282.1_Missense_Mutation_p.D151N|AC053503.4_ENST00000420563.1_RNA	NM_012100.2	NP_036232	Q9ULA0	DNPEP_HUMAN	aspartyl aminopeptidase	133					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)		AGAGTCAGGTCACGGTCAAAC	0.612																																					p.D143N		Atlas-SNP	.											.	DNPEP	40	.	0			c.G427A						PASS	.						109	114	112					2																	220251040		2112	4221	6333	SO:0001583	missense	23549	exon5			TCAGGTCACGGTC		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.427G>A	chr2.hg19:g.220251040C>T	ENSP00000273075:p.Asp143Asn	79.0	0.0	.		85.0	21.0	.	NM_012100	Q9BW44|Q9NUV5	Missense_Mutation	SNP	ENST00000273075.4	hg19	CCDS42823.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.902953	0.92035	.	.	ENSG00000123992	ENST00000273075;ENST00000337010;ENST00000373972;ENST00000523282;ENST00000535056;ENST00000457935;ENST00000429013;ENST00000521459;ENST00000322176;ENST00000434339;ENST00000430206	.	.	.	5.25	4.38	0.52667	Peptidase M18, domain 2 (1);	0.000000	0.85682	D	0.000000	D	0.87204	0.6119	H	0.97158	3.95	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.998;0.999;1.0;0.999	D	0.90886	0.4757	9	0.87932	D	0	-5.5253	13.5776	0.61883	0.0:0.9251:0.0:0.0749	.	151;143;151;133;143	E7ETB3;B7Z822;B7Z7F0;Q9ULA0;Q53SB6	.;.;.;DNPEP_HUMAN;.	N	143;143;68;151;36;151;129;143;143;68;68	.	ENSP00000273075:D143N	D	-	1	0	DNPEP	219959284	1.000000	0.71417	0.934000	0.37439	0.798000	0.45092	7.422000	0.80217	1.217000	0.43442	0.561000	0.74099	GAC	.	.	.	none		0.612	DNPEP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000130212.1	NM_012100		T	220251040	C	T	220251040	3	4	243	1	0	0	0	0	1	0	0	0	4681	826	29	2	1074	2	DNPEP	2	220251040	Missense_Mutation	SNP	C	TCGA-SX-A71U-01A-12D-A33Q-10	28377235	220251040	22948333	21	14953											
SLC19A3	80704	hgsc.bcm.edu	37	chr2	228566972	228566972	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atcatggagaaaaaaccaaaTaagcagaggatcacagtggg	19	5	11	6	0	2	2	2	0	0	2	2	4	2	3	1	3	2	1	1	3	5	1			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr2:228566972T>C	ENST00000258403.3	-	2	134	c.63A>G	c.(61-63)ttA>ttG	p.L21L	SLC19A3_ENST00000409287.1_Silent_p.L21L|SLC19A3_ENST00000541617.1_5'UTR	NM_025243.3	NP_079519.1	Q9BZV2	S19A3_HUMAN	solute carrier family 19 (thiamine transporter), member 3	21					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)	AAAAACCAAATAAGCAGAGGA	0.393																																					p.L21L		Atlas-SNP	.											.	SLC19A3	62	.	0			c.A63G						PASS	.						114	120	118					2																	228566972		2203	4300	6503	SO:0001819	synonymous_variant	80704	exon2			ACCAAATAAGCAG	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.63A>G	chr2.hg19:g.228566972T>C		59.0	0.0	.		77.0	27.0	.	NM_025243		Silent	SNP	ENST00000258403.3	hg19	CCDS2468.1																																																																																			.	.	.	none		0.393	SLC19A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256894.1			C	228566972	T	C	228566972	2	2	243	1	0	0	0	0	0	0	0	1	14443	1403	49	3		3	SLC19A3	2	228566972	Silent	SNP	T	TCGA-SX-A71U-01A-12D-A33Q-10	8315932	228566972	14632401	22	14954											
UGT1A5	54579	hgsc.bcm.edu	37	chr2	234622288	234622288	+	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	gtcaagaacatgctctacccTctggccctgtcctacctttg	7	12	7	15	0	3	1	1	0	2	1	4	1	4	1	4	1	4	1	4	1	4	3			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr2:234622288T>G	ENST00000373414.3	+	1	651	c.651T>G	c.(649-651)ccT>ccG	p.P217P	UGT1A6_ENST00000373424.1_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000608381.1_Silent_p.P217P|UGT1A1_ENST00000373450.4_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A6_ENST00000480628.1_Intron			P35504	UD15_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A5	217						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			cervix(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|urinary_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;4.51e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000523)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.00645)		TGCTCTACCCTCTGGCCCTGT	0.493																																					p.P217P		Atlas-SNP	.											.	UGT1A5	66	.	0			c.T651G						PASS	.						219	205	210					2																	234622288		2203	4300	6503	SO:0001819	synonymous_variant	54579	exon1			CTACCCTCTGGCC	M84129	CCDS33404.1	2q37	2010-03-05	2005-07-20		ENSG00000240224	ENSG00000240224		"UDP glucuronosyltransferases"	12537	other	complex locus constituent		606430	"UDP glycosyltransferase 1 family, polypeptide A5"			9295054, 1339448	Standard	NM_019078		Approved	UGT1E		P35504	OTTHUMG00000059120	ENST00000373414.3:c.651T>G	chr2.hg19:g.234622288T>G		108.0	0.0	.		102.0	39.0	.	NM_019078	B8K294	Silent	SNP	ENST00000373414.3	hg19	CCDS33404.1																																																																																			.	.	.	none		0.493	UGT1A5-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130985.1	NM_019078		G	234622288	T	G	234622288	2	3	243	1	0	0	0	0	0	0	0	1	16960	1538	54	5		5	UGT1A5	2	234622288	Silent	SNP	T	TCGA-SX-A71U-01A-12D-A33Q-10	6055316	234622288	8577085	23	14955											
CNTN6	27255	hgsc.bcm.edu	37	chr3	1337389	1337389	+	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	acttgtacattgccaaagtgGaaccatcagatgtgggcaac	13	9	10	9	0	1	1	1	0	0	1	1	2	1	2	2	2	4	2	2	2	4	3			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr3:1337389G>C	ENST00000446702.2	+	6	1186	c.559G>C	c.(559-561)Gaa>Caa	p.E187Q	CNTN6_ENST00000350110.2_Missense_Mutation_p.E187Q|CNTN6_ENST00000539053.1_Missense_Mutation_p.E115Q			Q9UQ52	CNTN6_HUMAN	contactin 6	187	Ig-like C2-type 2.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		TGCCAAAGTGGAACCATCAGA	0.453																																					p.E187Q		Atlas-SNP	.											.	CNTN6	245	.	0			c.G559C						PASS	.						102	93	96					3																	1337389		2203	4300	6503	SO:0001583	missense	27255	exon6			AAAGTGGAACCAT	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	2176	protein-coding gene	gene with protein product	"neural adhesion molecule"	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.559G>C	chr3.hg19:g.1337389G>C	ENSP00000407822:p.Glu187Gln	120.0	0.0	.		116.0	39.0	.	NM_014461	Q2KHM2	Missense_Mutation	SNP	ENST00000446702.2	hg19	CCDS2557.1	.	.	.	.	.	.	.	.	.	.	G	16.90	3.251401	0.59212	.	.	ENSG00000134115	ENST00000446702;ENST00000539053;ENST00000350110	T;T;T	0.67523	-0.27;-0.27;-0.27	5.79	4.91	0.64330	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.101551	0.42821	N	0.000649	T	0.54498	0.1862	L	0.31371	0.925	0.58432	D	0.999998	B;B	0.31274	0.019;0.317	B;B	0.26094	0.015;0.066	T	0.51076	-0.8751	10	0.30078	T	0.28	.	16.6803	0.85290	0.0:0.1297:0.8703:0.0	.	115;187	B4DGV0;Q9UQ52	.;CNTN6_HUMAN	Q	187;115;187	ENSP00000407822:E187Q;ENSP00000442791:E115Q;ENSP00000341882:E187Q	ENSP00000341882:E187Q	E	+	1	0	CNTN6	1312389	1.000000	0.71417	0.993000	0.49108	0.996000	0.88848	6.506000	0.73712	1.419000	0.47118	0.655000	0.94253	GAA	.	.	.	none		0.453	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461		C	1337389	G	C	1337389	3	2	243	1	0	0	0	0	1	0	0	0	3647	1175	41	4	577	4	CNTN6	3	1337389	Missense_Mutation	SNP	G	TCGA-SX-A71U-01A-12D-A33Q-10		1337389	196685041	24	14956											
PLXNB1	5364	hgsc.bcm.edu	37	chr3	48463585	48463585	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgcacagtccaggtgctgAgcacaggaagccacaggaac	13	4	13	11	0	0	1	0	1	0	0	1	4	1	3	2	3	5	3	2	3	2	0			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr3:48463585A>G	ENST00000358536.4	-	6	1718	c.1449T>C	c.(1447-1449)gcT>gcC	p.A483A	PLXNB1_ENST00000448774.2_Intron|PLXNB1_ENST00000358459.4_Silent_p.A483A|PLXNB1_ENST00000456774.1_Silent_p.A483A|PLXNB1_ENST00000296440.6_Silent_p.A483A	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	483					axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CCAGGTGCTGAGCACAGGAAG	0.587																																					p.A483A		Atlas-SNP	.											.	PLXNB1	150	.	0			c.T1449C						PASS	.						66	60	62					3																	48463585		2203	4300	6503	SO:0001819	synonymous_variant	5364	exon6			GTGCTGAGCACAG	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"Plexins"	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.1449T>C	chr3.hg19:g.48463585A>G		71.0	0.0	.		65.0	26.0	.	NM_001130082	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Silent	SNP	ENST00000358536.4	hg19	CCDS2765.1																																																																																			.	.	.	none		0.587	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673		G	48463585	A	G	48463585	2	3	243	1	0	0	0	0	0	0	0	1	12130	291	11	3		3	PLXNB1	3	48463585	Silent	SNP	A	TCGA-SX-A71U-01A-12D-A33Q-10	47126196	48463585	149558845	25	14957											
ROBO2	6092	hgsc.bcm.edu	37	chr3	77626674	77626674	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accacagtctgtcactgtacTgacagttggaagctacaata	13	10	8	10	0	2	1	1	1	1	0	2	2	2	2	1	1	3	3	1	1	5	4			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr3:77626674T>C	ENST00000461745.1	+	15	3137	c.2237T>C	c.(2236-2238)cTg>cCg	p.L746P	ROBO2_ENST00000332191.8_Missense_Mutation_p.L746P|ROBO2_ENST00000487694.3_Missense_Mutation_p.L762P	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	746	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		GTCACTGTACTGACAGTTGGA	0.448																																					p.L746P		Atlas-SNP	.											.	ROBO2	527	.	0			c.T2237C						PASS	.						92	93	92					3																	77626674		1901	4119	6020	SO:0001583	missense	6092	exon15			CTGTACTGACAGT	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.2237T>C	chr3.hg19:g.77626674T>C	ENSP00000417164:p.Leu746Pro	202.0	0.0	.		216.0	77.0	.	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	hg19	CCDS43109.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.008858	0.75046	.	.	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191;ENST00000398467	T;T;T	0.57752	0.38;0.38;0.38	5.66	5.66	0.87406	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.36002	N	0.002843	T	0.59715	0.2214	L	0.41632	1.29	0.37584	D	0.919925	D;D;D	0.60160	0.984;0.97;0.987	P;P;P	0.57846	0.828;0.786;0.828	T	0.62374	-0.6868	9	0.35671	T	0.21	.	15.8956	0.79333	0.0:0.0:0.0:1.0	.	762;746;746	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	P	762;762;766;746;746;467	ENSP00000417335:L762P;ENSP00000417164:L746P;ENSP00000327536:L746P	ENSP00000327536:L746P	L	+	2	0	ROBO2	77709364	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	6.139000	0.71728	2.154000	0.67381	0.402000	0.26972	CTG	.	.	.	none		0.448	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		C	77626674	T	C	77626674	3	2	243	1	0	0	0	0	1	0	0	0	13527	1580	55	3	2297	3	ROBO2	3	77626674	Missense_Mutation	SNP	T	TCGA-SX-A71U-01A-12D-A33Q-10	29163089	77626674	120395756	26	14958											
ABCC5	10057	hgsc.bcm.edu	37	chr3	183639163	183639163	+	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	gaactgtcgttggacagaagGaccgatggggtgtcaaactc	11	8	14	8	2	1	1	1	0	0	1	3	5	1	3	1	4	2	1	1	4	3	1			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr3:183639163G>C	ENST00000334444.6	-	30	4479	c.4239C>G	c.(4237-4239)gtC>gtG	p.V1413V	ABCC5_ENST00000265586.6_Silent_p.V1370V	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	1413	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	TGGACAGAAGGACCGATGGGG	0.547																																					p.V1413V		Atlas-SNP	.											.	ABCC5	142	.	0			c.C4239G						PASS	.						99	108	105					3																	183639163		2112	4243	6355	SO:0001819	synonymous_variant	10057	exon30			CAGAAGGACCGAT	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.4239C>G	chr3.hg19:g.183639163G>C		206.0	0.0	.		160.0	55.0	.	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Silent	SNP	ENST00000334444.6	hg19	CCDS43176.1																																																																																			.	.	.	none		0.547	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688		C	183639163	G	C	183639163	2	2	243	1	0	0	0	0	0	0	0	1	56	1161	41	4		4	ABCC5	3	183639163	Silent	SNP	G	TCGA-SX-A71U-01A-12D-A33Q-10	106012489	183639163	14383267	27	14959											
HGFAC	3083	hgsc.bcm.edu	37	chr4	3447058	3447058	+	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	agcgcgctctcctgggagtaCtgccgcctggaggcctgcgg	4	7	16	14	4	1	0	0	0	1	0	2	2	1	2	4	4	4	2	4	4	1	1			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr4:3447058C>A	ENST00000382774.3	+	9	1198	c.1083C>A	c.(1081-1083)taC>taA	p.Y361*	HGFAC_ENST00000511533.1_Nonsense_Mutation_p.Y361*	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	361	Kringle. {ECO:0000255|PROSITE- ProRule:PRU00121}.				proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		CCTGGGAGTACTGCCGCCTGG	0.677																																					p.Y361X		Atlas-SNP	.											.	HGFAC	69	.	0			c.C1083A						PASS	.						38	28	31					4																	3447058		2179	4288	6467	SO:0001587	stop_gained	3083	exon9			GGAGTACTGCCGC	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.1083C>A	chr4.hg19:g.3447058C>A	ENSP00000372224:p.Tyr361*	107.0	0.0	.		91.0	38.0	.	NM_001528	Q14726|Q2M1W7|Q53X47	Nonsense_Mutation	SNP	ENST00000382774.3	hg19	CCDS3369.1	.	.	.	.	.	.	.	.	.	.	C	36	5.967662	0.97156	.	.	ENSG00000109758	ENST00000382774;ENST00000511533	.	.	.	3.49	1.7	0.24286	.	0.250171	0.34110	U	0.004254	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.8091	0.23794	0.0:0.7478:0.0:0.2522	.	.	.	.	X	361	.	ENSP00000372224:Y361X	Y	+	3	2	HGFAC	3416856	1.000000	0.71417	1.000000	0.80357	0.582000	0.36321	0.700000	0.25601	0.167000	0.19631	-0.448000	0.05591	TAC	.	.	.	none		0.677	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3			A	3447058	C	A	3447058	4	1	243	1	0	0	0	0	0	1	0	0	7093	576	20	4	1117	4	HGFAC	4	3447058	Nonsense_Mutation	SNP	C	TCGA-SX-A71U-01A-12D-A33Q-10		3447058	187707218	28	14960											
RBM47	54502	hgsc.bcm.edu	37	chr4	40440004	40440004	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgagccctccagctcagtgcCgttgaggttgttcatggcat	6	11	12	12	2	2	1	2	1	0	0	3	2	3	1	3	2	3	5	3	2	0	3			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr4:40440004C>T	ENST00000381793.2	-	3	1303	c.907G>A	c.(907-909)Ggc>Agc	p.G303S	RBM47_ENST00000515809.1_Intron|RBM47_ENST00000295971.7_Missense_Mutation_p.G303S|RBM47_ENST00000381795.6_Missense_Mutation_p.G303S|RBM47_ENST00000319592.4_Missense_Mutation_p.G303S|RBM47_ENST00000514014.1_Missense_Mutation_p.G265S			A0AV96	RBM47_HUMAN	RNA binding motif protein 47	303	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				hematopoietic progenitor cell differentiation (GO:0002244)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(5)|endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	29						AGCTCAGTGCCGTTGAGGTTG	0.662																																					p.G303S		Atlas-SNP	.											.	RBM47	146	.	0			c.G907A						PASS	.						48	42	44					4																	40440004		2203	4300	6503	SO:0001583	missense	54502	exon4			CAGTGCCGTTGAG	AK000280	CCDS3460.1, CCDS43223.1	4p14	2013-02-12			ENSG00000163694	ENSG00000163694		"RNA binding motif (RRM) containing"	30358	protein-coding gene	gene with protein product							Standard	NM_019027		Approved	FLJ20273, NET18	uc003gvc.2	A0AV96	OTTHUMG00000128598	ENST00000381793.2:c.907G>A	chr4.hg19:g.40440004C>T	ENSP00000371212:p.Gly303Ser	49.0	0.0	.		44.0	21.0	.	NM_001098634	A0PJK2|B5MED4|Q8NI52|Q8NI53|Q9NXG3	Missense_Mutation	SNP	ENST00000381793.2	hg19	CCDS43223.1	.	.	.	.	.	.	.	.	.	.	C	16.21	3.059780	0.55325	.	.	ENSG00000163694	ENST00000319592;ENST00000381793;ENST00000381795;ENST00000295971;ENST00000514014	D;D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54;-1.54	5.58	4.71	0.59529	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	D	0.85195	0.5641	M	0.72576	2.205	0.80722	D	1	D;P	0.71674	0.998;0.828	P;P	0.57776	0.827;0.507	D	0.86236	0.1640	10	0.87932	D	0	-31.4629	10.2085	0.43126	0.1366:0.7926:0.0:0.0708	.	303;303	A0AV96-2;A0AV96	.;RBM47_HUMAN	S	303;303;303;303;265	ENSP00000320108:G303S;ENSP00000371212:G303S;ENSP00000371214:G303S;ENSP00000295971:G303S;ENSP00000423243:G265S	ENSP00000295971:G303S	G	-	1	0	RBM47	40134761	1.000000	0.71417	0.997000	0.53966	0.090000	0.18270	5.721000	0.68477	2.630000	0.89119	0.462000	0.41574	GGC	.	.	.	none		0.662	RBM47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250456.2	NM_019027		T	40440004	C	T	40440004	3	4	243	1	0	0	0	0	1	0	0	0	13154	652	23	1	890	1	RBM47	4	40440004	Missense_Mutation	SNP	C	TCGA-SX-A71U-01A-12D-A33Q-10	36992946	40440004	150714272	29	14961											
KLHL8	57563	hgsc.bcm.edu	37	chr4	88091657	88091657	+	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	tcattggtgccactgtactcCactgatcagattctatgtca	9	14	7	11	0	4	2	3	1	1	1	5	2	5	2	2	1	2	1	2	1	2	4			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr4:88091657C>A	ENST00000273963.5	-	7	1660	c.1319G>T	c.(1318-1320)tGg>tTg	p.W440L	KLHL8_ENST00000512111.1_Missense_Mutation_p.W440L|KLHL8_ENST00000545252.1_Missense_Mutation_p.W89L|KLHL8_ENST00000498875.2_Missense_Mutation_p.W364L|KLHL8_ENST00000425278.2_Missense_Mutation_p.W257L	NM_020803.3	NP_065854.3	Q9P2G9	KLHL8_HUMAN	kelch-like family member 8	440					protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nucleus (GO:0005634)				breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)	17		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)		CACTGTACTCCACTGATCAGA	0.423																																					p.W440L		Atlas-SNP	.											.	KLHL8	51	.	0			c.G1319T						PASS	.						120	109	113					4																	88091657		2203	4300	6503	SO:0001583	missense	57563	exon7			GTACTCCACTGAT	AB037799	CCDS3617.1, CCDS75163.1	4q21.3	2013-01-30	2013-01-30		ENSG00000145332	ENSG00000145332		"Kelch-like", "BTB/POZ domain containing"	18644	protein-coding gene	gene with protein product		611967	"kelch-like 8 (Drosophila)"				Standard	XM_005263153		Approved	KIAA1378	uc003hql.1	Q9P2G9	OTTHUMG00000130593	ENST00000273963.5:c.1319G>T	chr4.hg19:g.88091657C>A	ENSP00000273963:p.Trp440Leu	358.0	0.0	.		337.0	82.0	.	NM_020803	Q53XA3|Q6N018	Missense_Mutation	SNP	ENST00000273963.5	hg19	CCDS3617.1	.	.	.	.	.	.	.	.	.	.	C	32	5.140373	0.94560	.	.	ENSG00000145332	ENST00000273963;ENST00000498875;ENST00000425278;ENST00000545252;ENST00000512111	D;D;D;D;D	0.96940	-4.18;-4.18;-4.18;-4.18;-4.18	5.54	5.54	0.83059	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	D	0.98957	0.9645	H	0.97214	3.96	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.99316	1.0905	10	0.87932	D	0	.	19.4987	0.95085	0.0:1.0:0.0:0.0	.	257;364;440	Q68DU9;Q6N018;Q9P2G9	.;.;KLHL8_HUMAN	L	440;364;257;89;440	ENSP00000273963:W440L;ENSP00000426451:W364L;ENSP00000408854:W257L;ENSP00000439514:W89L;ENSP00000424131:W440L	ENSP00000273963:W440L	W	-	2	0	KLHL8	88310681	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.401000	0.79962	2.609000	0.88269	0.460000	0.39030	TGG	.	.	.	none		0.423	KLHL8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253040.1			A	88091657	C	A	88091657	3	1	243	1	0	0	0	0	1	0	0	0	8402	595	21	4	559	4	KLHL8	4	88091657	Missense_Mutation	SNP	C	TCGA-SX-A71U-01A-12D-A33Q-10	47651653	88091657	103062619	30	14962											
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123277058	123277059	+	Frame_Shift_Ins	INS	-	-	A																															aggttctagctacaaccatgINSaaacagagactatctttgca																										TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr4:123277058_123277059insA	ENST00000264501.4	+	83	14786_14787	c.14413_14414insA	c.(14413-14415)gaafs	p.E4805fs	KIAA1109_ENST00000388738.3_Frame_Shift_Ins_p.E4805fs			Q2LD37	K1109_HUMAN	KIAA1109	4805					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CTACAACCATGAAACAGAGACT	0.396																																					p.E4805fs		Atlas-Indel,Pindel	.											.	KIAA1109	424	.	0			c.14413_14414insA						PASS	.																																			SO:0001589	frameshift_variant	84162	exon81			.	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.14416dupA	chr4.hg19:g.123277061_123277061dupA	ENSP00000264501:p.Glu4805fs	101.0	0.0	0		92.0	35.0	0.380435	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Frame_Shift_Ins	INS	ENST00000264501.4	hg19	CCDS43267.1																																																																																			.	.	.	none		0.396	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		A	123277059	-	A	123277058	7	5	243	1	0	1	1	0	0	0	0	0	8215	1291	45	0	14735	0	KIAA1109	4	123277058	Frame_Shift_Ins	INS	-	TCGA-SX-A71U-01A-12D-A33Q-10	35185401	123277058	67877218	31	14963											
ETFDH	2110	hgsc.bcm.edu	37	chr4	159627888	159627888	+	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	tgtcatctgtggctctgagtGgtactaatcatgaacatgac	10	13	10	8	0	4	3	2	3	2	0	4	3	4	3	0	2	2	2	0	2	3	2			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr4:159627888G>T	ENST00000511912.1	+	12	1908	c.1576G>T	c.(1576-1578)Ggt>Tgt	p.G526C	ETFDH_ENST00000307738.5_Missense_Mutation_p.G479C	NM_001281738.1|NM_004453.2	NP_001268667.1|NP_004444.2	Q16134	ETFD_HUMAN	electron-transferring-flavoprotein dehydrogenase	526					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)		GGCTCTGAGTGGTACTAATCA	0.468																																					p.G526C		Atlas-SNP	.											.	ETFDH	57	.	0			c.G1576T						PASS	.						170	162	164					4																	159627888		2203	4300	6503	SO:0001583	missense	2110	exon12			CTGAGTGGTACTA	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.1576G>T	chr4.hg19:g.159627888G>T	ENSP00000426638:p.Gly526Cys	63.0	0.0	.		60.0	18.0	.	NM_004453	B4E3R9|J3KND9|Q7Z347	Missense_Mutation	SNP	ENST00000511912.1	hg19	CCDS3800.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.348293	0.82132	.	.	ENSG00000171503	ENST00000511912;ENST00000307738	D;D	0.91577	-2.87;-2.87	5.64	4.8	0.61643	.	0.000000	0.85682	D	0.000000	D	0.96895	0.8986	H	0.96805	3.885	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	0.97943	1.0327	10	0.87932	D	0	0.4172	14.4099	0.67109	0.0711:0.0:0.9289:0.0	.	479;465;526	B4E3R9;B4DEQ0;Q16134	.;.;ETFD_HUMAN	C	526;479	ENSP00000426638:G526C;ENSP00000303552:G479C	ENSP00000303552:G479C	G	+	1	0	ETFDH	159847338	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.869000	0.99810	1.380000	0.46344	0.591000	0.81541	GGT	.	.	.	none		0.468	ETFDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365718.2			T	159627888	G	T	159627888	3	4	243	1	0	0	0	0	1	0	0	0	5273	1348	47	4	1622	4	ETFDH	4	159627888	Missense_Mutation	SNP	G	TCGA-SX-A71U-01A-12D-A33Q-10	36350830	159627888	31526388	32	14964											
GALNT7	51809	hgsc.bcm.edu	37	chr4	174213365	174213365	+	Missense_Mutation	SNP	A	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	gaacagtccacagtgtaattAaaaggactccaaggaaatat	18	8	8	7	0	0	0	0	0	0	0	2	3	2	2	2	2	1	1	2	2	7	3			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr4:174213365A>C	ENST00000265000.4	+	3	777	c.694A>C	c.(694-696)Aaa>Caa	p.K232Q	GALNT7_ENST00000512285.1_Missense_Mutation_p.K232Q|GALNT7_ENST00000502407.1_3'UTR	NM_017423.2	NP_059119.2	Q86SF2	GALT7_HUMAN	polypeptide N-acetylgalactosaminyltransferase 7	232	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 (GO:0006493)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			central_nervous_system(1)|kidney(3)|large_intestine(5)|liver(1)|lung(9)	19		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;1.87e-18)|Epithelial(43;3.44e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-09)|STAD - Stomach adenocarcinoma(60;0.0019)|GBM - Glioblastoma multiforme(59;0.0119)|LUSC - Lung squamous cell carcinoma(193;0.0199)		CAGTGTAATTAAAAGGACTCC	0.353																																					p.K232Q		Atlas-SNP	.											.	GALNT7	61	.	0			c.A694C						PASS	.						87	93	91					4																	174213365		2203	4300	6503	SO:0001583	missense	51809	exon3			GTAATTAAAAGGA	AJ002744	CCDS3815.1	4q31.1	2014-03-13	2014-03-13		ENSG00000109586	ENSG00000109586		"Glycosyltransferase family 2 domain containing"	4129	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 7"	605005	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7)"			10544240	Standard	NM_017423		Approved	GALNAC-T7	uc003isz.4	Q86SF2	OTTHUMG00000160817	ENST00000265000.4:c.694A>C	chr4.hg19:g.174213365A>C	ENSP00000265000:p.Lys232Gln	176.0	0.0	.		151.0	53.0	.	NM_017423	B3KQU3|Q7Z5W7|Q9UJ28	Missense_Mutation	SNP	ENST00000265000.4	hg19	CCDS3815.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	26.3|26.3	4.724413|4.724413	0.89298|0.89298	.|.	.|.	ENSG00000109586|ENSG00000109586	ENST00000265000;ENST00000512285;ENST00000458613|ENST00000505308	T;T|.	0.61980|.	0.06;0.06|.	5.77|5.77	5.77|5.77	0.91146|0.91146	Glycosyl transferase, family 2 (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.59459|0.59459	0.2195|0.2195	L|L	0.37897|0.37897	1.145|1.145	0.80722|0.80722	D|D	1|1	D;D|.	0.71674|.	0.971;0.998|.	P;D|.	0.68621|.	0.893;0.959|.	T|T	0.55289|0.55289	-0.8164|-0.8164	10|5	0.54805|.	T|.	0.06|.	.|.	16.3948|16.3948	0.83586|0.83586	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	9;232|.	B4DIB4;Q86SF2|.	.;GALT7_HUMAN|.	Q|F	232;232;9|28	ENSP00000265000:K232Q;ENSP00000427050:K232Q|.	ENSP00000265000:K232Q|.	K|L	+|+	1|3	0|2	GALNT7|GALNT7	174449940|174449940	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	9.339000|9.339000	0.96797|0.96797	2.326000|2.326000	0.78906|0.78906	0.533000|0.533000	0.62120|0.62120	AAA|TTA	.	.	.	none		0.353	GALNT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362456.2	NM_017423		C	174213365	A	C	174213365	3	2	243	1	0	0	0	0	1	0	0	0	6225	363	13	5	704	5	GALNT7	4	174213365	Missense_Mutation	SNP	A	TCGA-SX-A71U-01A-12D-A33Q-10	14585477	174213365	16940911	33	14965											
NIPBL	25836	hgsc.bcm.edu	37	chr5	37024711	37024728	+	In_Frame_Del	DEL	AGAGTAATAAAGATTCTC	AGAGTAATAAAGATTCTC	-																															ctggtatcagtgtcaggaaaAgagtaataaagattctcaga																										TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	AGAGTAATAAAGATTCTC	AGAGTAATAAAGATTCTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr5:37024711_37024728delAGAGTAATAAAGATTCTC	ENST00000282516.8	+	30	6098_6115	c.5599_5616delAGAGTAATAAAGATTCTC	c.(5599-5616)agagtaataaagattctcdel	p.RVIKIL1867del	NIPBL_ENST00000448238.2_In_Frame_Del_p.RVIKIL1867del	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	1867					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)			TGTCAGGAAAAGAGTAATAAAGATTCTCAGAGACATTT	0.326																																					p.1866_1872del		Atlas-Indel,Pindel	.											.	NIPBL	513	.	0			c.5598_5615del	GRCh37	CM073229	NIPBL	M		PASS	.																																			SO:0001651	inframe_deletion	25836	exon30			.	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.5599_5616delAGAGTAATAAAGATTCTC	chr5.hg19:g.37024711_37024728delAGAGTAATAAAGATTCTC	ENSP00000282516:p.Arg1867_Leu1872del	235.0	0.0	0		168.0	24.0	0.142857	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	In_Frame_Del	DEL	ENST00000282516.8	hg19	CCDS3920.1																																																																																			.	.	.	none		0.326	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		-	37024728	AGAGTAATAAAGATTCTC	-	37024711	7	5	243	1	0	1	0	1	0	0	0	0	10435	64	3	0	5713	0	NIPBL	5	37024711	In_Frame_Del	DEL	AGAGTAATAAAGATTCTC	TCGA-SX-A71U-01A-12D-A33Q-10		37024711	143890549	34	14966											
PPIP5K2	23262	hgsc.bcm.edu	37	chr5	102509564	102509564	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtctgcttctaattttaggtAttctagaggtgttctgtctc	6	19	9	7	0	5	1	0	0	5	1	6	1	5	1	0	2	1	3	0	2	4	8			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr5:102509564A>G	ENST00000358359.3	+	21	2926	c.2417A>G	c.(2416-2418)tAt>tGt	p.Y806C	PPIP5K2_ENST00000513500.1_3'UTR|PPIP5K2_ENST00000321521.9_Missense_Mutation_p.Y806C|PPIP5K2_ENST00000414217.1_Missense_Mutation_p.Y806C	NM_001276277.1	NP_001263206.1	O43314	VIP2_HUMAN	diphosphoinositol pentakisphosphate kinase 2	806					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						AATTTTAGGTATTCTAGAGGT	0.303																																					p.Y806C		Atlas-SNP	.											.	PPIP5K2	98	.	0			c.A2417G						PASS	.						131	126	128					5																	102509564		2202	4299	6501	SO:0001583	missense	23262	exon20			TTAGGTATTCTAG	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.2417A>G	chr5.hg19:g.102509564A>G	ENSP00000351126:p.Tyr806Cys	38.0	0.0	.		36.0	12.0	.	NM_015216	A1NI53|A6NGS8|Q8TB50	Missense_Mutation	SNP	ENST00000358359.3	hg19		.	.	.	.	.	.	.	.	.	.	A	22.0	4.224670	0.79576	.	.	ENSG00000145725	ENST00000321521;ENST00000358359;ENST00000451606;ENST00000414217;ENST00000509597	T;T;T;T	0.27256	2.35;2.34;2.35;1.68	6.05	6.05	0.98169	.	0.000000	0.64402	D	0.000003	T	0.57007	0.2024	M	0.84948	2.725	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.79108	0.992;0.973;0.984	T	0.63198	-0.6691	10	0.72032	D	0.01	.	16.5993	0.84807	1.0:0.0:0.0:0.0	.	806;806;806	E9PGM8;O43314-2;O43314	.;.;VIP2_HUMAN	C	806;806;806;806;80	ENSP00000313070:Y806C;ENSP00000351126:Y806C;ENSP00000416016:Y806C;ENSP00000424948:Y80C	ENSP00000313070:Y806C	Y	+	2	0	PPIP5K2	102537463	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	9.335000	0.96500	2.311000	0.77944	0.528000	0.53228	TAT	.	.	.	none		0.303	PPIP5K2-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000370487.1	NM_015216		G	102509564	A	G	102509564	3	3	243	1	0	0	0	0	1	0	0	0	12343	449	16	3	2495	3	PPIP5K2	5	102509564	Missense_Mutation	SNP	A	TCGA-SX-A71U-01A-12D-A33Q-10	65484853	102509564	78405696	35	14967											
IK	3550	hgsc.bcm.edu	37	chr5	140034273	140034273	+	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	tttgtcttttcaggaaagatGaggatcctgaaaataaaatt	15	14	8	4	0	2	3	1	2	1	1	3	5	3	5	1	2	0	0	1	2	5	5			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr5:140034273G>T	ENST00000417647.2	+	8	737	c.598G>T	c.(598-600)Gag>Tag	p.E200*		NM_006083.3	NP_006074.2	Q13123	RED_HUMAN	IK cytokine, down-regulator of HLA II	200					cell-cell signaling (GO:0007267)|immune response (GO:0006955)	extracellular space (GO:0005615)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			large_intestine(1)	1		all_hematologic(541;4.8e-07)|all_lung(500;0.000434)|Lung NSC(810;0.00161)|Breast(839;0.128)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGGAAAGATGAGGATCCTGA	0.318																																					p.E200X		Atlas-SNP	.											.	IK	46	.	0			c.G598T						PASS	.						47	45	46					5																	140034273		1814	4070	5884	SO:0001587	stop_gained	3550	exon8			AAAGATGAGGATC	BC051295	CCDS47280.1	5q31.3	2008-08-07			ENSG00000113141	ENSG00000113141			5958	protein-coding gene	gene with protein product		600549				7970704	Standard	NM_006083		Approved		uc003lgq.3	Q13123	OTTHUMG00000163374	ENST00000417647.2:c.598G>T	chr5.hg19:g.140034273G>T	ENSP00000396301:p.Glu200*	362.0	1.0	.		277.0	105.0	.	NM_006083	Q6IPD8	Nonsense_Mutation	SNP	ENST00000417647.2	hg19	CCDS47280.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.300878	0.81136	.	.	ENSG00000113141	ENST00000417647;ENST00000508301;ENST00000261812;ENST00000502899	.	.	.	5.92	5.92	0.95590	.	0.044646	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	.	19.9276	0.97108	0.0:0.0:1.0:0.0	.	.	.	.	X	200	.	ENSP00000261812:E200X	E	+	1	0	IK	140014457	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.605000	0.98321	2.805000	0.96524	0.655000	0.94253	GAG	.	.	.	none		0.318	IK-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372897.1	NM_006083		T	140034273	G	T	140034273	4	4	243	1	0	0	0	0	0	1	0	0	7615	1291	45	4	628	4	IK	5	140034273	Nonsense_Mutation	SNP	G	TCGA-SX-A71U-01A-12D-A33Q-10	37524709	140034273	40880987	36	14968											
HIVEP1	3096	hgsc.bcm.edu	37	chr6	12125716	12125716	+	Frame_Shift_Del	DEL	G	G	-																															gacaataaccaagaaaggaaGtctccaggggttaaaaatca																										TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr6:12125716delG	ENST00000379388.2	+	4	6020	c.5688delG	c.(5686-5688)aagfs	p.K1896fs	HIVEP1_ENST00000541134.1_5'Flank	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	1896					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)				AAGAAAGGAAGTCTCCAGGGG	0.398																																					p.K1896fs		Atlas-Indel,Pindel	.											.	HIVEP1	242	.	0			c.5687delA						PASS	.						55	52	53					6																	12125716		1848	4081	5929	SO:0001589	frameshift_variant	3096	exon4			.	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"Zinc fingers, C2H2-type"	4920	protein-coding gene	gene with protein product		194540	"human immunodeficiency virus type I enhancer-binding protein 1", "zinc finger protein 40"	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.5688delG	chr6.hg19:g.12125716delG	ENSP00000368698:p.Lys1896fs	62.0	0.0	0		58.0	16.0	0.275862	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Frame_Shift_Del	DEL	ENST00000379388.2	hg19	CCDS43426.1																																																																																			.	.	.	none		0.398	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114		-	12125716	G	-	12125716	7	5	243	1	0	1	0	1	0	0	0	0	7193	1020	36	0	5698	0	HIVEP1	6	12125716	Frame_Shift_Del	DEL	G	TCGA-SX-A71U-01A-12D-A33Q-10		12125716	158989351	37	14969											
RANBP9	10048	hgsc.bcm.edu	37	chr6	13639868	13639868	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatggctggggctcatactTggactactaaaaggtcgagg	10	9	13	9	1	1	0	1	0	0	0	2	2	1	1	1	6	2	2	1	6	4	4			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr6:13639868T>C	ENST00000011619.3	-	9	1510	c.1452A>G	c.(1450-1452)ccA>ccG	p.P484P	RANBP9_ENST00000539980.1_Silent_p.P255P	NM_005493.2	NP_005484.2	Q96S59	RANB9_HUMAN	RAN binding protein 9	484					axon guidance (GO:0007411)|microtubule nucleation (GO:0007020)|protein complex assembly (GO:0006461)	cytosol (GO:0005829)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|Ran GTPase binding (GO:0008536)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	16	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.223)			GGCTCATACTTGGACTACTAA	0.413																																					p.P484P		Atlas-SNP	.											.	RANBP9	42	.	0			c.A1452G						PASS	.						140	126	131					6																	13639868		2203	4300	6503	SO:0001819	synonymous_variant	10048	exon9			CATACTTGGACTA	AB008515	CCDS4529.1	6p23	2010-05-25			ENSG00000010017	ENSG00000010017			13727	protein-coding gene	gene with protein product	"Ran Binding Protein in the Microtubule organizing center"	603854				9817760	Standard	NM_005493		Approved	RanBPM	uc003nbb.3	Q96S59	OTTHUMG00000015642	ENST00000011619.3:c.1452A>G	chr6.hg19:g.13639868T>C		97.0	0.0	.		86.0	36.0	.	NM_005493	A0PJA2|B2R8E1|O94764|Q6P3T7|Q7LBR2|Q7Z7F9	Silent	SNP	ENST00000011619.3	hg19	CCDS4529.1																																																																																			.	.	.	none		0.413	RANBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042373.1			C	13639868	T	C	13639868	2	2	243	1	0	0	0	0	0	0	0	1	13045	1799	63	3		3	RANBP9	6	13639868	Silent	SNP	T	TCGA-SX-A71U-01A-12D-A33Q-10	1514152	13639868	157475199	38	14970											
FAM8A1	51439	hgsc.bcm.edu	37	chr6	17601243	17601243	+	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	acccctgctccagtcgcgggCctgggaccccgggctcctca	4	6	12	19	3	1	0	1	0	0	0	4	1	3	1	7	3	1	2	7	3	0	0			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr6:17601243C>A	ENST00000259963.3	+	1	658	c.603C>A	c.(601-603)ggC>ggA	p.G201G		NM_016255.2	NP_057339.1	Q9UBU6	FA8A1_HUMAN	family with sequence similarity 8, member A1	201						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(3)	6	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.143)	all cancers(50;0.176)|Epithelial(50;0.204)			CAGTCGCGGGCCTGGGACCCC	0.716																																					p.G201G		Atlas-SNP	.											.	FAM8A1	26	.	0			c.C603A						PASS	.						4	5	5					6																	17601243		1915	3803	5718	SO:0001819	synonymous_variant	51439	exon1			CGCGGGCCTGGGA	AF097027	CCDS4540.1	6p23	2010-11-22			ENSG00000137414	ENSG00000137414			16372	protein-coding gene	gene with protein product						11707071	Standard	NM_016255		Approved	AHCP	uc003ncc.3	Q9UBU6	OTTHUMG00000014309	ENST00000259963.3:c.603C>A	chr6.hg19:g.17601243C>A		21.0	0.0	.		23.0	8.0	.	NM_016255	B2R725	Silent	SNP	ENST00000259963.3	hg19	CCDS4540.1																																																																																			.	.	.	none		0.716	FAM8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039950.1			A	17601243	C	A	17601243	2	1	243	1	0	0	0	0	0	0	0	1	5656	726	26	4		4	FAM8A1	6	17601243	Silent	SNP	C	TCGA-SX-A71U-01A-12D-A33Q-10	3961375	17601243	153513824	39	14971											
KDM1B	221656	hgsc.bcm.edu	37	chr6	18166565	18166565	+	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	ctagcaatggcaaaaccgaaCctagtcccaaagctttcatg	14	8	7	12	1	1	0	1	0	0	0	2	1	2	0	3	1	4	3	3	1	7	3			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr6:18166565C>G	ENST00000297792.5	+	6	550	c.373C>G	c.(373-375)Cct>Gct	p.P125A	KDM1B_ENST00000388870.2_Missense_Mutation_p.P125A|KDM1B_ENST00000397244.1_Missense_Mutation_p.P125A|KDM1B_ENST00000546309.2_Intron			Q8NB78	KDM1B_HUMAN	lysine (K)-specific demethylase 1B	125					DNA methylation involved in gamete generation (GO:0043046)|histone H3-K4 demethylation (GO:0034720)|multicellular organismal development (GO:0007275)|regulation of DNA methylation (GO:0044030)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-monomethyl-K4 specific) (GO:0034649)|oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|large_intestine(6)|lung(8)|skin(3)|upper_aerodigestive_tract(1)	25						CAAAACCGAACCTAGTCCCAA	0.398																																					p.P125A		Atlas-SNP	.											.	KDM1B	58	.	0			c.C373G						PASS	.						108	103	105					6																	18166565		2203	4300	6503	SO:0001583	missense	221656	exon6			ACCGAACCTAGTC	AK125318	CCDS34343.1	6p22.3	2011-07-01	2009-09-29	2009-09-29	ENSG00000165097	ENSG00000165097		"Chromatin-modifying enzymes / K-demethylases"	21577	protein-coding gene	gene with protein product		613081	"amine oxidase, flavin containing 1", "chromosome 6 open reading frame 193", "amine oxidase (flavin containing) domain 1"	C6orf193, AOF1		19407342, 19727073	Standard	NM_153042		Approved	FLJ34109, FLJ33898, dJ298J15.2, bA204B7.3, FLJ43328, LSD2	uc003ncn.1	Q8NB78	OTTHUMG00000014316	ENST00000297792.5:c.373C>G	chr6.hg19:g.18166565C>G	ENSP00000297792:p.Pro125Ala	132.0	0.0	.		124.0	50.0	.	NM_153042	A2A2C5|A2A2C6|Q5TGV3|Q6AI15|Q6ZUU4|Q8N258|Q96EL7	Missense_Mutation	SNP	ENST00000297792.5	hg19	CCDS34343.1	.	.	.	.	.	.	.	.	.	.	C	15.08	2.726252	0.48833	.	.	ENSG00000165097	ENST00000388870;ENST00000397244;ENST00000297792;ENST00000388869	T;T;T	0.40225	1.38;1.04;1.04	5.66	5.66	0.87406	.	0.000000	0.56097	U	0.000024	T	0.47948	0.1473	L	0.35723	1.085	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.14980	-1.0453	10	0.29301	T	0.29	-3.916	20.1253	0.97977	0.0:1.0:0.0:0.0	.	125	A2A2C6	.	A	125	ENSP00000373522:P125A;ENSP00000380419:P125A;ENSP00000297792:P125A	ENSP00000297792:P125A	P	+	1	0	KDM1B	18274544	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	7.152000	0.77419	2.832000	0.97577	0.655000	0.94253	CCT	.	.	.	none		0.398	KDM1B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277080.1	NM_153042		G	18166565	C	G	18166565	3	3	243	1	0	0	0	0	1	0	0	0	8130	507	18	4	387	4	KDM1B	6	18166565	Missense_Mutation	SNP	C	TCGA-SX-A71U-01A-12D-A33Q-10	565322	18166565	152948502	40	14972											
HIST1H2BB	3018	hgsc.bcm.edu	37	chr6	26043884	26043884	+	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	cagacttagagggttcaggcAttgctattcctaaacagaat	13	11	9	8	0	1	3	1	0	0	3	2	3	2	3	1	2	2	3	1	2	5	6			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr6:26043884A>G	ENST00000357905.2	-	1	1	c.2T>C	c.(1-3)aTg>aCg	p.M1T	HIST1H3C_ENST00000540144.1_5'Flank	NM_021062.2	NP_066406.1	P33778	H2B1B_HUMAN	histone cluster 1, H2bb	1					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	7						GGGTTCAGGCATTGCTATTCC	0.453																																					p.M1T		Atlas-SNP	.											.	HIST1H2BB	20	.	0			c.T2C						PASS	.						50	51	50					6																	26043884		2203	4300	6503	SO:0001630	splice_region_variant	3018	exon1			TCAGGCATTGCTA	AF531285	CCDS4575.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000196226			"Histones / Replication-dependent"	4751	protein-coding gene	gene with protein product		602803	"H2B histone family, member F", "histone 1, H2bb"	H2BFF		8227173, 12408966	Standard	NM_021062		Approved	H2B/f	uc003nfu.3	P33778	OTTHUMG00000014421	ENST00000357905.2:c.0-1T>C	chr6.hg19:g.26043884A>G		40.0	0.0	.		34.0	15.0	.	NM_021062	Q4KN36	Missense_Mutation	SNP	ENST00000357905.2	hg19	CCDS4575.1	.	.	.	.	.	.	.	.	.	.	A	11.00	1.510401	0.27036	.	.	ENSG00000196226	ENST00000357905	T	0.18960	2.18	5.34	5.34	0.76211	.	0.000000	0.64402	U	0.000001	T	0.34861	0.0912	.	.	.	0.80722	D	1	D	0.55800	0.973	P	0.61201	0.885	T	0.22034	-1.0228	9	0.87932	D	0	.	14.7798	0.69756	1.0:0.0:0.0:0.0	.	1	P33778	H2B1B_HUMAN	T	1	ENSP00000350580:M1T	ENSP00000350580:M1T	M	-	2	0	HIST1H2BB	26151863	1.000000	0.71417	0.975000	0.42487	0.004000	0.04260	7.131000	0.77243	2.126000	0.65437	0.533000	0.62120	ATG	.	.	.	none		0.453	HIST1H2BB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040083.1	NM_021062	Missense_Mutation	G	26043884	A	G	26043884	5	3	243	1	0	0	0	0	0	0	1	0	7148	231	8	3	382	3	HIST1H2BB	6	26043884	Splice_Site	SNP	A	TCGA-SX-A71U-01A-12D-A33Q-10	7877319	26043884	145071183	41	14973											
ZNF391	346157	hgsc.bcm.edu	37	chr6	27368767	27368767	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaagcctttagccgaagcacTaaccttagtcagcatcagcg	13	8	8	12	2	2	0	2	0	0	0	2	1	2	0	3	0	6	2	3	0	5	4			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr6:27368767T>C	ENST00000244576.4	+	3	1163	c.618T>C	c.(616-618)acT>acC	p.T206T		NM_001076781.1	NP_001070249.1	Q9UJN7	ZN391_HUMAN	zinc finger protein 391	206					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(6)|lung(7)|pancreas(2)|skin(3)|upper_aerodigestive_tract(1)	21						GCCGAAGCACTAACCTTAGTC	0.423																																					p.T206T		Atlas-SNP	.											.	ZNF391	90	.	0			c.T618C						PASS	.						71	75	73					6																	27368767		2193	4298	6491	SO:0001819	synonymous_variant	346157	exon3			AAGCACTAACCTT	BC132797	CCDS43429.1	6p21	2013-01-08			ENSG00000124613	ENSG00000124613		"Zinc fingers, C2H2-type"	18779	protein-coding gene	gene with protein product							Standard	NM_001076781		Approved	dJ153G14.3	uc003njf.1	Q9UJN7	OTTHUMG00000014477	ENST00000244576.4:c.618T>C	chr6.hg19:g.27368767T>C		61.0	0.0	.		48.0	20.0	.	NM_001076781	B4DH77	Silent	SNP	ENST00000244576.4	hg19	CCDS43429.1																																																																																			.	.	.	none		0.423	ZNF391-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040145.2	NM_001076781		C	27368767	T	C	27368767	2	2	243	1	0	0	0	0	0	0	0	1	17891	1509	53	3		3	ZNF391	6	27368767	Silent	SNP	T	TCGA-SX-A71U-01A-12D-A33Q-10	1324883	27368767	143746300	42	14974											
SLC22A7	10864	hgsc.bcm.edu	37	chr6	43266308	43266308	+	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	gctggaggcccatcttccccGggagcctgatggcacgctca	6	7	13	15	2	2	1	1	1	1	0	3	3	3	3	4	4	1	3	4	4	0	1			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr6:43266308G>T	ENST00000372585.5	+	1	307	c.212G>T	c.(211-213)cGg>cTg	p.R71L	SLC22A7_ENST00000487175.1_Intron|SLC22A7_ENST00000372574.3_Missense_Mutation_p.R71L|SLC22A7_ENST00000372589.3_Missense_Mutation_p.R71L	NM_153320.2	NP_696961.2	Q9Y694	S22A7_HUMAN	solute carrier family 22 (organic anion transporter), member 7	71					organic anion transport (GO:0015711)|response to stilbenoid (GO:0035634)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)	p.R71Q(1)		NS(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(3)	26			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)		Acetylsalicylic acid(DB00945)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Cimetidine(DB00501)|Clarithromycin(DB01211)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Docetaxel(DB01248)|Enalapril(DB00584)|Erythromycin(DB00199)|Fluorouracil(DB00544)|Ganciclovir(DB01004)|Glyburide(DB01016)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Oxtriphylline(DB01303)|Oxytetracycline(DB00595)|Pravastatin(DB00175)|Probenecid(DB01032)|Rifampicin(DB01045)|Salicylic acid(DB00936)|Testosterone(DB00624)|Tetracycline(DB00759)|Theophylline(DB00277)|Valproic Acid(DB00313)|Zalcitabine(DB00943)|Zidovudine(DB00495)	CATCTTCCCCGGGAGCCTGAT	0.662																																					p.R71L		Atlas-SNP	.											SLC22A7,NS,carcinoma,0,1	SLC22A7	69	.	1	Substitution - Missense(1)	lung(1)	c.G212T						PASS	.						45	42	43					6																	43266308		2203	4300	6503	SO:0001583	missense	10864	exon1			TTCCCCGGGAGCC	AF097518	CCDS4892.1, CCDS4893.2	6p21.1	2013-05-22			ENSG00000137204	ENSG00000137204		"Solute carriers"	10971	protein-coding gene	gene with protein product		604995				9650585, 10773670	Standard	XM_006714970		Approved	NLT, OAT2	uc003out.3	Q9Y694	OTTHUMG00000014726	ENST00000372585.5:c.212G>T	chr6.hg19:g.43266308G>T	ENSP00000361666:p.Arg71Leu	46.0	0.0	.		24.0	11.0	.	NM_006672	B2CZX6|Q5T046|Q5T048|Q5T050|Q9H2W5	Missense_Mutation	SNP	ENST00000372585.5	hg19	CCDS4893.2	.	.	.	.	.	.	.	.	.	.	G	9.154	1.017095	0.19355	.	.	ENSG00000137204	ENST00000449231;ENST00000372589;ENST00000372585;ENST00000372574	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	5.63	0.872	0.19113	.	0.276047	0.36409	N	0.002603	T	0.12475	0.0303	L	0.28115	0.83	0.36271	D	0.855183	B;B;B	0.14438	0.006;0.01;0.01	B;B;B	0.18263	0.016;0.021;0.021	T	0.32719	-0.9896	10	0.02654	T	1	.	8.7559	0.34645	0.4671:0.0:0.5329:0.0	.	71;71;71	Q9Y694;Q9Y694-2;Q9Y694-3	S22A7_HUMAN;.;.	L	71	ENSP00000411818:R71L;ENSP00000361670:R71L;ENSP00000361666:R71L;ENSP00000361655:R71L	ENSP00000361655:R71L	R	+	2	0	SLC22A7	43374286	0.000000	0.05858	0.848000	0.33437	0.486000	0.33341	-0.458000	0.06737	-0.127000	0.11661	-0.253000	0.11424	CGG	.	.	.	none		0.662	SLC22A7-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040588.1			T	43266308	G	T	43266308	3	4	243	1	0	0	0	0	1	0	0	0	14472	1116	39	4	214	4	SLC22A7	6	43266308	Missense_Mutation	SNP	G	TCGA-SX-A71U-01A-12D-A33Q-10	15897541	43266308	127848759	43	14975											
DDO	8528	hgsc.bcm.edu	37	chr6	110726039	110726039	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggttgtaaaagcctgaccAaacacatactgggggaattt	14	9	11	7	0	0	1	0	1	0	0	0	2	0	2	2	3	3	2	2	3	5	4			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr6:110726039A>G	ENST00000368924.3	-	4	495	c.480T>C	c.(478-480)ttT>ttC	p.F160F	DDO_ENST00000368923.3_Intron	NM_003649.2	NP_003640.2	Q99489	OXDD_HUMAN	D-aspartate oxidase	132					aspartate catabolic process (GO:0006533)|aspartate metabolic process (GO:0006531)|D-amino acid catabolic process (GO:0019478)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insemination (GO:0007320)|oxidation-reduction process (GO:0055114)	peroxisome (GO:0005777)	cofactor binding (GO:0048037)|D-aspartate oxidase activity (GO:0008445)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|pancreas(1)|skin(3)	24		all_cancers(87;3.47e-21)|all_epithelial(87;9.03e-20)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_lung(197;2.98e-05)|Lung NSC(302;3.25e-05)|Colorectal(196;3.46e-05)|Ovarian(999;0.00327)		all cancers(137;2.54e-48)|Epithelial(106;3.11e-44)|OV - Ovarian serous cystadenocarcinoma(136;2.08e-24)|BRCA - Breast invasive adenocarcinoma(108;0.000141)|GBM - Glioblastoma multiforme(226;0.00046)		AAGCCTGACCAAACACATACT	0.483																																					p.F160F		Atlas-SNP	.											.	DDO	51	.	0			c.T480C						PASS	.						99	88	91					6																	110726039		2203	4300	6503	SO:0001819	synonymous_variant	8528	exon4			CTGACCAAACACA	D89858	CCDS5082.1, CCDS5083.1	6q22.1	2008-02-05			ENSG00000203797	ENSG00000203797	1.4.3.1		2727	protein-coding gene	gene with protein product		124450				9163533	Standard	NM_003649		Approved		uc003puc.3	Q99489	OTTHUMG00000015360	ENST00000368924.3:c.480T>C	chr6.hg19:g.110726039A>G		145.0	0.0	.		105.0	47.0	.	NM_003649	A8KAG4|Q5JXM4|Q5JXM5|Q5JXM6|Q8N552	Silent	SNP	ENST00000368924.3	hg19	CCDS5082.1																																																																																			.	.	.	none		0.483	DDO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041796.1			G	110726039	A	G	110726039	2	3	243	1	0	0	0	0	0	0	0	1	4336	127	5	3		3	DDO	6	110726039	Silent	SNP	A	TCGA-SX-A71U-01A-12D-A33Q-10	67459731	110726039	60389028	44	14976											
NUP43	348995	hgsc.bcm.edu	37	chr6	150059828	150059828	+	Frame_Shift_Del	DEL	T	T	-																															ttgttgtctgaaatcccataTtttcaactgtccaattgaat																										TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr6:150059828delT	ENST00000340413.2	-	5	665	c.589delA	c.(589-591)atafs	p.I197fs	NUP43_ENST00000460354.2_Frame_Shift_Del_p.I197fs|NUP43_ENST00000367403.3_Intron|NUP43_ENST00000367404.4_Intron	NM_198887.1	NP_942590.1	Q8NFH3	NUP43_HUMAN	nucleoporin 43kDa	197					carbohydrate metabolic process (GO:0005975)|chromosome segregation (GO:0007059)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)				breast(1)|large_intestine(2)|lung(8)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	18		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;4.71e-13)|GBM - Glioblastoma multiforme(68;0.101)		AAATCCCATATTTTCAACTGT	0.323																																					p.I197fs		Atlas-Indel,Pindel	.											.	NUP43	32	.	0			c.590delT						PASS	.						127	119	122					6																	150059828		2203	4297	6500	SO:0001589	frameshift_variant	348995	exon5			.	AF514997	CCDS5218.1	6q25.1	2013-01-10			ENSG00000120253	ENSG00000120253		"WD repeat domain containing"	21182	protein-coding gene	gene with protein product		608141				12196509	Standard	XM_005266961		Approved	bA350J20.1, FLJ13287	uc003qmz.3	Q8NFH3	OTTHUMG00000015795	ENST00000340413.2:c.589delA	chr6.hg19:g.150059828delT	ENSP00000342262:p.Ile197fs	51.0	0.0	0		76.0	30.0	0.394737	NM_198887	B4E2F0|Q9H8S0	Frame_Shift_Del	DEL	ENST00000340413.2	hg19	CCDS5218.1																																																																																			.	.	.	none		0.323	NUP43-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396947.1	NM_198887		-	150059828	T	-	150059828	7	5	243	1	0	1	0	1	0	0	0	0	10772	1493	52	0	569	0	NUP43	6	150059828	Frame_Shift_Del	DEL	T	TCGA-SX-A71U-01A-12D-A33Q-10	39333789	150059828	21055239	45	14977											
C6orf97	80129	hgsc.bcm.edu	37	chr6	151907203	151907203	+	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	ggaggtgttttgcgagacaaCttgaattttgagaaacaaaa	15	11	11	4	1	0	3	0	2	0	2	0	6	0	4	0	2	3	1	0	2	5	5			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr6:151907203C>T	ENST00000239374.7	+	7	1371	c.1272C>T	c.(1270-1272)aaC>aaT	p.N424N	CCDC170_ENST00000367290.5_Silent_p.N424N	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	424																	TGCGAGACAACTTGAATTTTG	0.433																																					p.N424N		Atlas-SNP	.											.	.	.	.	0			c.C1272T						PASS	.						60	60	60					6																	151907203		1880	4125	6005	SO:0001819	synonymous_variant	80129	exon7			AGACAACTTGAAT	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.1272C>T	chr6.hg19:g.151907203C>T		72.0	0.0	.		66.0	24.0	.	NM_025059	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Silent	SNP	ENST00000239374.7	hg19	CCDS43515.1																																																																																			.	.	.	none		0.433	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059		T	151907203	C	T	151907203	2	4	243	1	0	0	0	0	0	0	0	1	2376	564	20	2		2	C6orf97	6	151907203	Silent	SNP	C	TCGA-SX-A71U-01A-12D-A33Q-10	1847375	151907203	19207864	46	14978											
MAS1	4142	hgsc.bcm.edu	37	chr6	160328746	160328746	+	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	ctttacctgctgtactatgaGtattggtcgacctttgggaa	8	15	10	8	1	0	1	0	1	0	0	1	3	0	2	2	2	3	3	2	2	5	7			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr6:160328746G>T	ENST00000252660.4	+	1	773	c.759G>T	c.(757-759)gaG>gaT	p.E253D		NM_002377.2	NP_002368.1	P04201	MAS_HUMAN	MAS1 proto-oncogene, G protein-coupled receptor	253					activation of NF-kappaB-inducing kinase activity (GO:0007250)|anatomical structure morphogenesis (GO:0009653)|cell proliferation (GO:0008283)|cellular response to peptide hormone stimulus (GO:0071375)|G-protein coupled receptor signaling pathway (GO:0007186)|hippocampus development (GO:0021766)|male gonad development (GO:0008584)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of inositol phosphate biosynthetic process (GO:0060732)|protein kinase C signaling (GO:0070528)|regulation of inflammatory response (GO:0050727)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	angiotensin receptor activity (GO:0001595)|angiotensin type II receptor activity (GO:0004945)|G-protein coupled receptor activity (GO:0004930)|peptide binding (GO:0042277)|peptide hormone binding (GO:0017046)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	23		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.44e-18)|BRCA - Breast invasive adenocarcinoma(81;5.6e-06)		TGTACTATGAGTATTGGTCGA	0.448																																					p.E253D		Atlas-SNP	.											.	MAS1	42	.	0			c.G759T						PASS	.						133	123	126					6																	160328746		2203	4300	6503	SO:0001583	missense	4142	exon1			CTATGAGTATTGG	M13150	CCDS5272.1	6q24-q27	2014-06-26	2014-06-26		ENSG00000130368	ENSG00000130368		"GPCR / Class A : Orphans"	6899	protein-coding gene	gene with protein product		165180	"MAS1 oncogene"				Standard	NM_002377		Approved		uc003qsz.3	P04201	OTTHUMG00000015944	ENST00000252660.4:c.759G>T	chr6.hg19:g.160328746G>T	ENSP00000252660:p.Glu253Asp	110.0	0.0	.		110.0	47.0	.	NM_002377	E1P5B3|Q2TBC9|Q6FG47	Missense_Mutation	SNP	ENST00000252660.4	hg19	CCDS5272.1	.	.	.	.	.	.	.	.	.	.	G	12.12	1.843115	0.32606	.	.	ENSG00000130368	ENST00000252660	T	0.37058	1.22	5.2	5.2	0.72013	GPCR, rhodopsin-like superfamily (1);	0.272836	0.26103	N	0.026338	T	0.17238	0.0414	L	0.39898	1.24	0.34753	D	0.731961	P	0.34615	0.459	B	0.34590	0.186	T	0.08432	-1.0722	10	0.35671	T	0.21	.	12.3072	0.54908	0.0:0.1845:0.8155:0.0	.	253	P04201	MAS_HUMAN	D	253	ENSP00000252660:E253D	ENSP00000252660:E253D	E	+	3	2	MAS1	160248736	0.678000	0.27586	0.981000	0.43875	0.612000	0.37316	0.732000	0.26072	2.407000	0.81776	0.655000	0.94253	GAG	.	.	.	none		0.448	MAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042930.2	NM_002377		T	160328746	G	T	160328746	3	4	243	1	0	0	0	0	1	0	0	0	9327	1020	36	4	761	4	MAS1	6	160328746	Missense_Mutation	SNP	G	TCGA-SX-A71U-01A-12D-A33Q-10	8421543	160328746	10786321	47	14979											
IGF2BP3	10643	hgsc.bcm.edu	37	chr7	23352352	23352353	+	Splice_Site	DNP	GC	GC	AT																															gcttattttagagcccacttGcctggcaagcatagaagtga																										TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr7:23352352_23352353GC>AT	ENST00000258729.3	-	14	1998		c.e14+1			NM_006547.2	NP_006538.2	O00425	IF2B3_HUMAN	insulin-like growth factor 2 mRNA binding protein 3						anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation regulator activity (GO:0045182)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(2)|prostate(2)|skin(4)|stomach(1)	34						GAGCCCACTTGCCTGGCAAGCA	0.431																																					.		Atlas-SNP	.											.	IGF2BP3	71	.	0			c.1641+2C>T|c.1641+1G>A						PASS	.																																			SO:0001630	splice_region_variant	10643	exon15			CCACTTGCCTGGC|CACTTGCCTGGCA	AF117108	CCDS5382.1	7p15.3	2014-02-19			ENSG00000136231	ENSG00000136231		"RNA binding motif (RRM) containing"	28868	protein-coding gene	gene with protein product	"IGF II mRNA binding protein 3", "cancer/testis antigen 98"	608259				9891060, 9178771	Standard	NM_006547		Approved	IMP-3, CT98, IMP3	uc003swg.3	O00425	OTTHUMG00000128445	ENST00000258729.3:c.1642_1642delinsAT	chr7.hg19:g.23352352_23352353delinsAT		185.0|184.0	0.0	.		237.0	117.0|120.0	.	NM_006547	A0A4Z5|Q63HM0|Q6MZZ2|Q86VB1	Splice_Site	SNP	ENST00000258729.3	hg19	CCDS5382.1																																																																																			.	.	.	none		0.431	IGF2BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250243.2	NM_006547	Intron	AT	23352353	GC	AT	23352352	5	1	243	1	0	0	0	0	0	0	1	0	7582	1333	46	2	104	2	IGF2BP3	7	23352352	Splice_Site	DNP	GC	TCGA-SX-A71U-01A-12D-A33Q-10		23352352	135786311	48	14980											
GATS	352954	hgsc.bcm.edu	37	chr7	99821281	99821281	+	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	acaggatggtgaactctgatGacaacgtgtgggtgacaaag	13	8	14	6	1	1	4	0	4	1	0	1	5	1	5	0	3	2	0	0	3	3	0			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr7:99821281G>A	ENST00000436886.2	-	4	700	c.452C>T	c.(451-453)tCa>tTa	p.S151L	GATS_ENST00000543273.1_RNA	NM_178831.6	NP_849153.3	Q8NAP1	GATS_HUMAN	GATS, stromal antigen 3 opposite strand	151										endometrium(2)|large_intestine(2)|lung(4)	8	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GAACTCTGATGACAACGTGTG	0.607																																					p.S151L		Atlas-SNP	.											.	GATS	18	.	0			c.C452T						PASS	.						205	216	212					7																	99821281		2134	4232	6366	SO:0001583	missense	352954	exon4			TCTGATGACAACG	AK095056	CCDS43621.1	7q22.1	2014-08-13	2009-04-08	2009-04-08	ENSG00000160844	ENSG00000239521			29954	protein-coding gene	gene with protein product	"stromal antigen 3 opposite strand"					12477932	Standard	NM_178831		Approved	DKFZp686B07267, STAG3OS	uc003uua.4	Q8NAP1	OTTHUMG00000155289	ENST00000436886.2:c.452C>T	chr7.hg19:g.99821281G>A	ENSP00000389760:p.Ser151Leu	378.0	0.0	.		408.0	90.0	.	NM_178831	D6W5V0|Q68D93|Q6P198|Q6PII7|Q7Z720|Q86UK9	Missense_Mutation	SNP	ENST00000436886.2	hg19	CCDS43621.1	.	.	.	.	.	.	.	.	.	.	g	13.87	2.367175	0.41902	.	.	ENSG00000160844	ENST00000436886	.	.	.	1.56	1.56	0.23342	.	0.216774	0.39687	N	0.001293	T	0.31136	0.0787	N	0.12182	0.205	0.35791	D	0.822377	B	0.17038	0.02	B	0.22152	0.038	T	0.23332	-1.0191	9	0.37606	T	0.19	.	9.1169	0.36764	0.0:0.0:1.0:0.0	.	151	Q8NAP1	GATS_HUMAN	L	151	.	ENSP00000389760:S151L	S	-	2	0	GATS	99659217	1.000000	0.71417	0.999000	0.59377	0.322000	0.28314	7.487000	0.81328	0.787000	0.33731	0.173000	0.16961	TCA	.	.	.	none		0.607	GATS-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178831		A	99821281	G	A	99821281	3	1	243	1	0	0	0	0	1	0	0	0	6271	1294	45	2	43	2	GATS	7	99821281	Missense_Mutation	SNP	G	TCGA-SX-A71U-01A-12D-A33Q-10	76468929	99821281	59317382	49	14981											
SRRT	51593	hgsc.bcm.edu	37	chr7	100482162	100482162	+	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	acaaggatgagaagaaggaaGacggcaagcaggtccgagcc	16	2	15	8	2	0	3	0	1	0	3	1	7	1	5	2	4	2	2	2	4	5	0			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr7:100482162G>A	ENST00000347433.4	+	7	1089	c.931G>A	c.(931-933)Gac>Aac	p.D311N	SRRT_ENST00000432932.1_Missense_Mutation_p.D311N|SRRT_ENST00000457580.2_Missense_Mutation_p.D311N|SRRT_ENST00000388793.4_Missense_Mutation_p.D311N			Q9BXP5	SRRT_HUMAN	serrate, RNA effector molecule	311	Glu-rich.			D -> Y (in Ref. 4; BAG64018). {ECO:0000305}.	cell proliferation (GO:0008283)|neuronal stem cell maintenance (GO:0097150)|primary miRNA processing (GO:0031053)|regulation of transcription, DNA-templated (GO:0006355)|response to arsenic-containing substance (GO:0046685)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						GAAGAAGGAAGACGGCAAGCA	0.627																																					p.D311N		Atlas-SNP	.											.	SRRT	108	.	0			c.G931A						PASS	.						47	48	48					7																	100482162		2198	4300	6498	SO:0001583	missense	51593	exon7			AAGGAAGACGGCA		CCDS34709.1, CCDS47665.1, CCDS47666.1, CCDS47667.1	7q21	2014-04-14	2014-04-14		ENSG00000087087	ENSG00000087087			24101	protein-coding gene	gene with protein product	"arsenite resistance protein"	614469	"serrate RNA effector molecule homolog (Arabidopsis)"			11239002, 11230166	Standard	NM_015908		Approved	Asr2, serrate, ARS2	uc003uwy.2	Q9BXP5	OTTHUMG00000157031	ENST00000347433.4:c.931G>A	chr7.hg19:g.100482162G>A	ENSP00000314491:p.Asp311Asn	163.0	0.0	.		234.0	62.0	.	NM_001128853	A4D2E5|A4D2E6|A6NK22|B4DJL4|B4DZA6|O95808|Q32MI4|Q6NT74|Q8TDQ5|Q9BWP6|Q9BXP4|Q9Y4S4	Missense_Mutation	SNP	ENST00000347433.4	hg19	CCDS34709.1	.	.	.	.	.	.	.	.	.	.	G	14.03	2.414782	0.42817	.	.	ENSG00000087087	ENST00000457580;ENST00000388793;ENST00000432932;ENST00000347433	T;T	0.16597	2.33;2.33	3.91	3.91	0.45181	.	0.380247	0.27031	N	0.021263	T	0.07413	0.0187	N	0.08118	0	0.45567	D	0.998511	P;P;P;B	0.36535	0.557;0.557;0.557;0.421	B;B;B;B	0.30855	0.121;0.121;0.121;0.057	T	0.38824	-0.9643	10	0.21014	T	0.42	.	11.5862	0.50920	0.0:0.0:1.0:0.0	.	311;311;311;311	Q9BXP5-3;Q9BXP5-4;Q9BXP5-2;Q9BXP5	.;.;.;SRRT_HUMAN	N	311	ENSP00000416553:D311N;ENSP00000314491:D311N	ENSP00000314491:D311N	D	+	1	0	SRRT	100320098	1.000000	0.71417	0.972000	0.41901	0.015000	0.08874	3.933000	0.56545	2.203000	0.70933	0.491000	0.48974	GAC	.	.	.	none		0.627	SRRT-004	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347168.1	NM_015908		A	100482162	G	A	100482162	3	1	243	1	0	0	0	0	1	0	0	0	15184	942	33	2	953	2	SRRT	7	100482162	Missense_Mutation	SNP	G	TCGA-SX-A71U-01A-12D-A33Q-10	660881	100482162	58656501	50	14982											
C7orf58	79974	hgsc.bcm.edu	37	chr7	120935571	120935571	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatcatatcatgggaagataTttcagcaatcaaagcaaact	18	10	6	7	0	4	1	4	0	0	1	4	2	4	2	0	1	3	2	0	1	7	3			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr7:120935571T>C	ENST00000310396.5	+	23	3413	c.2946T>C	c.(2944-2946)taT>taC	p.Y982Y		NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	982						endoplasmic reticulum (GO:0005783)											TGGGAAGATATTTCAGCAATC	0.323																																					p.Y982Y		Atlas-SNP	.											.	.	.	.	0			c.T2946C						PASS	.						82	78	79					7																	120935571		2203	4300	6503	SO:0001819	synonymous_variant	79974	exon23			AAGATATTTCAGC		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.2946T>C	chr7.hg19:g.120935571T>C		114.0	0.0	.		117.0	31.0	.	NM_024913	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Silent	SNP	ENST00000310396.5	hg19	CCDS34739.1																																																																																			.	.	.	none		0.323	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913		C	120935571	T	C	120935571	2	2	243	1	0	0	0	0	0	0	0	1	2407	1500	52	3		3	C7orf58	7	120935571	Silent	SNP	T	TCGA-SX-A71U-01A-12D-A33Q-10	20453409	120935571	38203092	51	14983											
DLGAP2	9228	hgsc.bcm.edu	37	chr8	1626467	1626467	+	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	ttcccaggccacatcaccacGgaggacaaaggccttcagtt	11	7	9	14	1	2	0	2	0	0	0	3	2	3	2	4	4	0	1	4	4	1	3	rs149482724		TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr8:1626467G>T	ENST00000421627.2	+	9	2270	c.2136G>T	c.(2134-2136)acG>acT	p.T712T	DLGAP2_ENST00000524065.1_3'UTR	NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	791					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)		ACATCACCACGGAGGACAAAG	0.622																																					p.T712T		Atlas-SNP	.											.	DLGAP2	292	.	0			c.G2136T						PASS	.						58	66	63					8																	1626467		2124	4221	6345	SO:0001819	synonymous_variant	9228	exon9			CACCACGGAGGAC	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.2136G>T	chr8.hg19:g.1626467G>T		96.0	0.0	.		98.0	9.0	.	NM_004745	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	Silent	SNP	ENST00000421627.2	hg19	CCDS47760.1	.	.	.	.	.	.	.	.	.	.	G	7.146	0.582724	0.13749	.	.	ENSG00000198010	ENST00000520901	.	.	.	5.09	2.26	0.28386	.	.	.	.	.	T	0.54447	0.1859	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42275	-0.9461	4	.	.	.	-7.5861	6.5711	0.22539	0.0714:0.1308:0.662:0.1358	.	.	.	.	L	715	.	.	R	+	2	0	DLGAP2	1613874	1.000000	0.71417	0.267000	0.24556	0.686000	0.39977	3.695000	0.54749	0.159000	0.19401	-0.321000	0.08615	CGG	.	G|0.999;A|0.001	.	alt		0.622	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374478.1	NM_004745		T	1626467	G	T	1626467	2	4	243	1	0	0	0	0	0	0	0	1	4562	1103	39	4		4	DLGAP2	8	1626467	Silent	SNP	G	TCGA-SX-A71U-01A-12D-A33Q-10		1626467	144737555	52	14984											
SPAG11B	10407	hgsc.bcm.edu	37	chr8	7308713	7308713	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcgagcctcccggtgagAgatgtgcactagaaggaaac	11	7	12	11	2	0	3	0	1	0	2	3	6	2	4	3	2	3	1	3	2	3	1			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr8:7308713A>G	ENST00000297498.2	-	3	389	c.223T>C	c.(223-225)Tct>Cct	p.S75P	SPAG11B_ENST00000528168.1_Missense_Mutation_p.S22P|SPAG11B_ENST00000361111.2_Intron|SPAG11B_ENST00000359758.5_Intron|SPAG11B_ENST00000398462.2_Intron|SPAG11B_ENST00000458665.1_Intron	NM_016512.3	NP_057596.1	Q08648	SG11B_HUMAN	sperm associated antigen 11B	75					spermatogenesis (GO:0007283)	extracellular region (GO:0005576)				large_intestine(2)|lung(3)|urinary_tract(1)	6				COAD - Colon adenocarcinoma(149;0.0162)|READ - Rectum adenocarcinoma(644;0.236)		TCCCGGTGAGAGATGTGCACT	0.458																																					p.S75P		Atlas-SNP	.											.	SPAG11B	32	.	0			c.T223C						PASS	.						63	77	72					8																	7308713		2080	4188	6268	SO:0001583	missense	10407	exon3			GGTGAGAGATGTG	AF168616	CCDS5964.1, CCDS5965.1, CCDS5966.1, CCDS5967.1, CCDS47774.1	8p23.1	2014-02-21	2007-03-15	2007-03-15	ENSG00000164871	ENSG00000164871			14534	protein-coding gene	gene with protein product	"epididymal protein 2B"	606560				8167223, 1693137	Standard	NM_058200		Approved	HE2, EP2, EP2C, EP2D, EDDM2B	uc003wrl.3	Q08648	OTTHUMG00000129219	ENST00000297498.2:c.223T>C	chr8.hg19:g.7308713A>G	ENSP00000297498:p.Ser75Pro	420.0	0.0	.		507.0	146.0	.	NM_016512	E9PFH0|Q546A0|Q6ZYB2|Q9H4P8|Q9H4P9|Q9H4Q0|Q9H4Q1|Q9H4Q2|Q9NRT3|Q9NRV4|Q9NRV5|Q9NRV6|Q9NRV7|Q9NRV8	Missense_Mutation	SNP	ENST00000297498.2	hg19	CCDS5966.1	.	.	.	.	.	.	.	.	.	.	A	9.682	1.149439	0.21288	.	.	ENSG00000164871	ENST00000297498;ENST00000528168	T;T	0.51071	1.18;0.72	2.69	-2.8	0.05823	.	.	.	.	.	T	0.22126	0.0533	N	0.12746	0.255	0.09310	N	1	B;B	0.16603	0.018;0.003	B;B	0.17433	0.018;0.006	T	0.17048	-1.0382	9	0.23891	T	0.37	.	3.1877	0.06607	0.378:0.0:0.4097:0.2123	.	75;22	Q08648;Q08648-2	SG11B_HUMAN;.	P	75;22	ENSP00000297498:S75P;ENSP00000431230:S22P	ENSP00000297498:S75P	S	-	1	0	SPAG11B	7296123	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.320000	0.08028	-0.619000	0.05648	0.373000	0.22412	TCT	.	.	.	none		0.458	SPAG11B-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251390.2	NM_058202, NM_058200, NM_058201, NM_016512, NM_058203, NM_058206, NM_058207		G	7308713	A	G	7308713	3	3	243	1	0	0	0	0	1	0	0	0	14990	304	11	3	301	3	SPAG11B	8	7308713	Missense_Mutation	SNP	A	TCGA-SX-A71U-01A-12D-A33Q-10	5682246	7308713	139055309	53	14985											
ENTPD4	9583	hgsc.bcm.edu	37	chr8	23305329	23305329	+	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	ccactgctaccacagtccacCacgatcccatagttcacatt	11	9	4	17	1	1	0	1	0	0	0	3	1	3	0	5	0	2	2	5	0	2	4			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr8:23305329C>G	ENST00000358689.4	-	4	511	c.276G>C	c.(274-276)gtG>gtC	p.V92V	ENTPD4_ENST00000356206.6_Silent_p.V92V|ENTPD4_ENST00000417069.2_Silent_p.V92V	NM_001128930.2|NM_004901.4	NP_001122402.1|NP_004892.1	Q9Y227	ENTP4_HUMAN	ectonucleoside triphosphate diphosphohydrolase 4	92					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)		CACAGTCCACCACGATCCCAT	0.453																																					p.V92V		Atlas-SNP	.											.	ENTPD4	56	.	0			c.G276C						PASS	.						259	200	220					8																	23305329		2203	4300	6503	SO:0001819	synonymous_variant	9583	exon4			GTCCACCACGATC	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.276G>C	chr8.hg19:g.23305329C>G		110.0	0.0	.		153.0	77.0	.	NM_004901	D3DSS3|O15092	Silent	SNP	ENST00000358689.4	hg19	CCDS6041.1																																																																																			.	.	.	none		0.453	ENTPD4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215142.1	NM_004901		G	23305329	C	G	23305329	2	3	243	1	0	0	0	0	0	0	0	1	5143	581	21	4		4	ENTPD4	8	23305329	Silent	SNP	C	TCGA-SX-A71U-01A-12D-A33Q-10	15996616	23305329	123058693	54	14986											
ZNF395	55893	hgsc.bcm.edu	37	chr8	28206326	28206326	+	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	ccatacaccttgcggcacttCttagcctcccctcgggcttt	5	12	7	17	2	1	0	0	0	1	0	3	0	2	0	5	2	3	2	5	2	2	5			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr8:28206326C>G	ENST00000344423.5	-	10	1583	c.1452G>C	c.(1450-1452)aaG>aaC	p.K484N	ZNF395_ENST00000523095.1_Missense_Mutation_p.K484N|ZNF395_ENST00000523202.1_Missense_Mutation_p.K484N	NM_018660.2	NP_061130.1	Q9H8N7	ZN395_HUMAN	zinc finger protein 395	484					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(5)|large_intestine(6)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.102)|Kidney(114;0.123)|Colorectal(74;0.142)		TGCGGCACTTCTTAGCCTCCC	0.627																																					p.K484N		Atlas-SNP	.											.	ZNF395	54	.	0			c.G1452C						PASS	.						63	60	61					8																	28206326		2203	4300	6503	SO:0001583	missense	55893	exon10			GCACTTCTTAGCC	AB044750	CCDS6067.1	8p21	2008-05-02			ENSG00000186918	ENSG00000186918		"Zinc fingers, C2H2-type"	18737	protein-coding gene	gene with protein product		609494				14625278	Standard	NM_018660		Approved	PRF-1, HDBP2, PBF, DKFZp434K1210	uc003xgr.3	Q9H8N7	OTTHUMG00000102137	ENST00000344423.5:c.1452G>C	chr8.hg19:g.28206326C>G	ENSP00000340494:p.Lys484Asn	86.0	0.0	.		82.0	21.0	.	NM_018660	B3KUY7|D3DST4|Q6F6H2|Q9BY72|Q9NPB2|Q9NS57|Q9NS58|Q9NS59	Missense_Mutation	SNP	ENST00000344423.5	hg19	CCDS6067.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.885180	0.91814	.	.	ENSG00000186918	ENST00000344423;ENST00000523202;ENST00000523095	T;T;T	0.38560	1.13;1.13;1.13	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.69387	0.3105	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.74216	-0.3737	10	0.87932	D	0	-24.8941	17.1137	0.86683	0.0:1.0:0.0:0.0	.	484	Q9H8N7	ZN395_HUMAN	N	484	ENSP00000340494:K484N;ENSP00000429640:K484N;ENSP00000428452:K484N	ENSP00000340494:K484N	K	-	3	2	ZNF395	28262245	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.488000	0.45276	2.633000	0.89246	0.650000	0.86243	AAG	.	.	.	none		0.627	ZNF395-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219976.1			G	28206326	C	G	28206326	3	3	243	1	0	0	0	0	1	0	0	0	17893	912	32	4	93	4	ZNF395	8	28206326	Missense_Mutation	SNP	C	TCGA-SX-A71U-01A-12D-A33Q-10	4900997	28206326	118157696	55	14987											
ADAM32	203102	hgsc.bcm.edu	37	chr8	39080665	39080665	+	Missense_Mutation	SNP	T	T	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	tggtcctgacataactttaaTcaatggactttcatgcaaaa	14	13	6	8	0	2	1	2	1	0	0	3	2	3	2	1	2	2	1	1	2	5	4			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr8:39080665T>G	ENST00000379907.4	+	14	1560	c.1433T>G	c.(1432-1434)aTc>aGc	p.I478S	ADAM32_ENST00000519315.1_Missense_Mutation_p.I372S|ADAM32_ENST00000437682.2_Missense_Mutation_p.I379S	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	478	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.					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)			ATAACTTTAATCAATGGACTT	0.393																																					p.I478S		Atlas-SNP	.											.	ADAM32	70	.	0			c.T1433G						PASS	.						64	62	62					8																	39080665		1893	4113	6006	SO:0001583	missense	203102	exon14			CTTTAATCAATGG	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.1433T>G	chr8.hg19:g.39080665T>G	ENSP00000369238:p.Ile478Ser	66.0	0.0	.		87.0	27.0	.	NM_145004	Q8TC42	Missense_Mutation	SNP	ENST00000379907.4	hg19	CCDS47846.1	.	.	.	.	.	.	.	.	.	.	T	7.793	0.711971	0.15306	.	.	ENSG00000197140	ENST00000437682;ENST00000519315;ENST00000379907	T;T;T	0.03004	4.08;4.16;4.47	5.55	-11.1	0.00147	ADAM, cysteine-rich (1);Blood coagulation inhibitor, Disintegrin (2);	2.794810	0.02236	N	0.065318	T	0.02610	0.0079	N	0.20574	0.59	0.09310	N	1	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.09377	0.0;0.001;0.004	T	0.26883	-1.0090	10	0.16420	T	0.52	.	13.9077	0.63845	0.1274:0.0861:0.0:0.7864	.	379;372;478	E7EPX8;E7ER82;Q8TC27	.;.;ADA32_HUMAN	S	379;372;478	ENSP00000405978:I379S;ENSP00000429422:I372S;ENSP00000369238:I478S	ENSP00000369238:I478S	I	+	2	0	ADAM32	39199822	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.629000	0.02029	-2.184000	0.00762	-0.339000	0.08088	ATC	.	.	.	none		0.393	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004		G	39080665	T	G	39080665	3	3	243	1	0	0	0	0	1	0	0	0	249	1435	50	5	1487	5	ADAM32	8	39080665	Missense_Mutation	SNP	T	TCGA-SX-A71U-01A-12D-A33Q-10	10874339	39080665	107283357	56	14988											
C9orf152	401546	hgsc.bcm.edu	37	chr9	112963539	112963539	+	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	cttgcccctatgatgtacttGatgactggtgtcctgggggg	5	13	14	9	0	0	3	0	3	0	0	1	3	1	3	3	4	2	1	3	4	2	4			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr9:112963539G>A	ENST00000400613.4	-	2	1018	c.409C>T	c.(409-411)Caa>Taa	p.Q137*	C9orf152_ENST00000473442.1_Intron	NM_001012993.2	NP_001013011.2	Q5JTZ5	CI152_HUMAN	chromosome 9 open reading frame 152	137										NS(1)|endometrium(1)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						TGATGTACTTGATGACTGGTG	0.547																																					p.Q137X		Atlas-SNP	.											.	C9orf152	20	.	0			c.C409T						PASS	.						169	154	159					9																	112963539		2203	4300	6503	SO:0001587	stop_gained	401546	exon2			GTACTTGATGACT	BX648620	CCDS35102.2	9q31.3	2012-04-03			ENSG00000188959	ENSG00000188959			31455	protein-coding gene	gene with protein product							Standard	NM_001012993		Approved	bA470J20.2	uc011lwk.2	Q5JTZ5	OTTHUMG00000020478	ENST00000400613.4:c.409C>T	chr9.hg19:g.112963539G>A	ENSP00000383456:p.Gln137*	62.0	0.0	.		30.0	11.0	.	NM_001012993	A8MWT6	Nonsense_Mutation	SNP	ENST00000400613.4	hg19	CCDS35102.2	.	.	.	.	.	.	.	.	.	.	G	38	6.959087	0.97964	.	.	ENSG00000188959	ENST00000400613	.	.	.	4.16	2.19	0.27852	.	0.833553	0.10475	N	0.670329	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	-0.2823	12.1388	0.53986	0.0:0.3309:0.6691:0.0	.	.	.	.	X	137	.	ENSP00000383456:Q137X	Q	-	1	0	C9orf152	112003360	0.002000	0.14202	0.023000	0.16930	0.171000	0.22731	0.763000	0.26517	0.632000	0.30432	0.655000	0.94253	CAA	.	.	.	none		0.547	C9orf152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053602.2	NM_001012993		A	112963539	G	A	112963539	4	1	243	1	0	0	0	0	0	1	0	0	2465	1299	45	2	314	2	C9orf152	9	112963539	Nonsense_Mutation	SNP	G	TCGA-SX-A71U-01A-12D-A33Q-10		112963539	28249892	57	14989											
OR1L1	26737	hgsc.bcm.edu	37	chr9	125424669	125424669	+	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	ttaagaatcctcatcactgtTctgaagattccttcagctgc	10	14	6	11	0	4	3	3	1	1	2	6	3	6	3	2	0	2	2	2	0	3	4			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr9:125424669T>G	ENST00000373686.1	+	1	825	c.825T>G	c.(823-825)gtT>gtG	p.V275V	OR1L1_ENST00000309623.1_Silent_p.V225V			Q8NH94	OR1L1_HUMAN	olfactory receptor, family 1, subfamily L, member 1	275						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)	17						TCATCACTGTTCTGAAGATTC	0.408																																					p.V225V		Atlas-SNP	.											.	OR1L1	54	.	0			c.T675G						PASS	.						169	169	169					9																	125424669		2203	4300	6503	SO:0001819	synonymous_variant	26737	exon1			CACTGTTCTGAAG		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.825T>G	chr9.hg19:g.125424669T>G		113.0	0.0	.		80.0	31.0	.	NM_001005236	Q5T7Z3|Q6IFN2	Silent	SNP	ENST00000373686.1	hg19																																																																																				.	.	.	none		0.408	OR1L1-201	KNOWN	basic	protein_coding	protein_coding				G	125424669	T	G	125424669	2	3	243	1	0	0	0	0	0	0	0	1	10970	1770	62	5		5	OR1L1	9	125424669	Silent	SNP	T	TCGA-SX-A71U-01A-12D-A33Q-10	12461130	125424669	15788762	58	14990											
PHYHD1	254295	hgsc.bcm.edu	37	chr9	131702760	131702760	+	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	aacggctgtctctggttcatCcctggctcccacaccagtga	7	10	9	15	1	2	1	1	1	1	0	5	1	4	1	3	3	1	3	3	3	1	1			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr9:131702760C>A	ENST00000372592.3	+	10	1503	c.570C>A	c.(568-570)atC>atA	p.I190I	PHYHD1_ENST00000487504.1_3'UTR|PHYHD1_ENST00000353176.5_Silent_p.I169I|RP11-101E3.5_ENST00000482796.1_5'Flank|PHYHD1_ENST00000308941.5_Missense_Mutation_p.S183Y|PHYHD1_ENST00000421063.2_Silent_p.I169I	NM_001100876.1	NP_001094346.1	Q5SRE7	PHYD1_HUMAN	phytanoyl-CoA dioxygenase domain containing 1	190							dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|skin(1)|stomach(3)	10						TCTGGTTCATCCCTGGCTCCC	0.627																																					p.S183Y		Atlas-SNP	.											.	PHYHD1	29	.	0			c.C548A						PASS	.						90	95	93					9																	131702760		2203	4300	6503	SO:0001819	synonymous_variant	254295	exon9			GTTCATCCCTGGC	BC051300	CCDS6914.1, CCDS43885.1, CCDS43886.1	9q34.13	2010-08-13			ENSG00000175287	ENSG00000175287			23396	protein-coding gene	gene with protein product						12477932	Standard	NM_174933		Approved	MGC16638	uc004bwp.2	Q5SRE7	OTTHUMG00000020764	ENST00000372592.3:c.570C>A	chr9.hg19:g.131702760C>A		58.0	0.0	.		61.0	26.0	.	NM_174933	A6PWN9|A6PWP0|B3KT57|B4E3X8|Q5SRE9|Q5SRF0|Q7Z623|Q7Z7P9|Q96GM4	Missense_Mutation	SNP	ENST00000372592.3	hg19	CCDS43885.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.941654	0.73557	.	.	ENSG00000175287	ENST00000308941;ENST00000419872	.	.	.	5.25	5.25	0.73442	.	0.956782	0.08660	N	0.912562	T	0.65354	0.2683	.	.	.	0.80722	D	1	D	0.63046	0.992	P	0.62560	0.904	T	0.50583	-0.8811	8	0.16896	T	0.51	-13.1688	9.684	0.40087	0.0:0.84:0.0:0.16	.	183	Q5SRE7-3	.	Y	183;48	.	ENSP00000309515:S183Y	S	+	2	0	PHYHD1	130742581	0.911000	0.30947	1.000000	0.80357	0.998000	0.95712	0.063000	0.14410	2.470000	0.83445	0.555000	0.69702	TCC	.	.	.	none		0.627	PHYHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054506.2	NM_174933		A	131702760	C	A	131702760	2	1	243	1	0	0	0	0	0	0	0	1	11872	855	30	4		4	PHYHD1	9	131702760	Silent	SNP	C	TCGA-SX-A71U-01A-12D-A33Q-10	6278091	131702760	9510671	59	14991											
DIP2C	22982	hgsc.bcm.edu	37	chr10	459927	459927	+	Frame_Shift_Del	DEL	C	C	-																															gcgccttgggcgagatggtgCcccacctctgcagtgcggcc																										TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr10:459927delC	ENST00000280886.6	-	8	1070	c.983delG	c.(982-984)ggcfs	p.G328fs	DIP2C_ENST00000381496.3_Frame_Shift_Del_p.G221fs	NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	328						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)		CGAGATGGTGCCCCACCTCTG	0.672																																					p.G328fs		Atlas-Indel,Pindel	.											.	DIP2C	195	.	0			c.984delC						PASS	.						63	63	63					10																	459927		2203	4300	6503	SO:0001589	frameshift_variant	22982	exon8			.	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"KIAA0934"	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.983delG	chr10.hg19:g.459927delC	ENSP00000280886:p.Gly328fs	40.0	0.0	0		39.0	14.0	0.358974	NM_014974	B4DPI5|Q5SS78	Frame_Shift_Del	DEL	ENST00000280886.6	hg19	CCDS7054.1																																																																																			.	.	.	none		0.672	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974		-	459927	C	-	459927	7	5	243	1	0	1	0	1	0	0	0	0	4531	739	26	0	3807	0	DIP2C	10	459927	Frame_Shift_Del	DEL	C	TCGA-SX-A71U-01A-12D-A33Q-10		459927	135074820	60	14992											
ZNF22	7570	hgsc.bcm.edu	37	chr10	45499114	45499114	+	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	ttcagagttctaatctcattCagcatcgacggatccatacg	11	12	7	11	3	4	1	3	0	2	1	7	3	5	2	1	1	2	2	1	1	2	5			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr10:45499114C>T	ENST00000298299.3	+	2	891	c.298C>T	c.(298-300)Cag>Tag	p.Q100*	C10orf25_ENST00000298298.1_5'Flank|CEP164P1_ENST00000456938.2_RNA	NM_006963.4	NP_008894.2	P17026	ZNF22_HUMAN	zinc finger protein 22	100					odontogenesis (GO:0042476)|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(2)|endometrium(1)|kidney(2)|lung(2)	8		Prostate(175;0.0352)|all_neural(218;0.202)				TAATCTCATTCAGCATCGACG	0.413																																					p.Q100X		Atlas-SNP	.											.	ZNF22	28	.	0			c.C298T						PASS	.						57	56	56					10																	45499114		2203	4300	6503	SO:0001587	stop_gained	7570	exon2			CTCATTCAGCATC	BC041139	CCDS7211.1	10q11	2013-01-08	2012-07-12		ENSG00000165512	ENSG00000165512		"Zinc fingers, C2H2-type"	13012	protein-coding gene	gene with protein product		194529					Standard	NM_006963		Approved	KOX15, HKR-T1, ZNF422, Zfp422	uc001jbw.3	P17026	OTTHUMG00000018064	ENST00000298299.3:c.298C>T	chr10.hg19:g.45499114C>T	ENSP00000298299:p.Gln100*	42.0	0.0	.		32.0	8.0	.	NM_006963	Q5T741|Q96FM4	Nonsense_Mutation	SNP	ENST00000298299.3	hg19	CCDS7211.1	.	.	.	.	.	.	.	.	.	.	C	40	8.366025	0.98779	.	.	ENSG00000165512	ENST00000298299	.	.	.	5.02	5.02	0.67125	.	0.000000	0.46758	D	0.000280	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.14656	T	0.56	-16.5608	10.8467	0.46746	0.1881:0.8119:0.0:0.0	.	.	.	.	X	100	.	ENSP00000298299:Q100X	Q	+	1	0	ZNF22	44819120	0.000000	0.05858	1.000000	0.80357	0.946000	0.59487	-0.103000	0.10940	2.583000	0.87209	0.655000	0.94253	CAG	.	.	.	none		0.413	ZNF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047761.1	NM_006963		T	45499114	C	T	45499114	4	4	243	1	0	0	0	0	0	1	0	0	17786	827	29	2	300	2	ZNF22	10	45499114	Nonsense_Mutation	SNP	C	TCGA-SX-A71U-01A-12D-A33Q-10	45039187	45499114	90035633	61	14993											
ADK	132	hgsc.bcm.edu	37	chr10	75911070	75911070	+	Missense_Mutation	SNP	A	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	aggaggagccgaagcccaaaAagctgaaggtggaggcgccg	13	2	17	9	3	0	1	0	1	0	0	0	5	0	4	3	5	3	1	3	5	4	0			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr10:75911070A>C	ENST00000286621.2	+	1	84	c.34A>C	c.(34-36)Aag>Cag	p.K12Q	ADK_ENST00000539909.1_Missense_Mutation_p.K12Q|AP3M1_ENST00000372745.1_5'Flank|AP3M1_ENST00000487653.1_5'Flank|AP3M1_ENST00000355264.4_5'Flank	NM_006721.3	NP_006712.2	P55263	ADK_HUMAN	adenosine kinase	12					adenosine metabolic process (GO:0046085)|AMP salvage (GO:0044209)|circadian regulation of gene expression (GO:0032922)|dATP biosynthetic process (GO:0006175)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of T cell proliferation (GO:0042102)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|ribonucleoside monophosphate biosynthetic process (GO:0009156)|small molecule metabolic process (GO:0044281)|type B pancreatic cell proliferation (GO:0044342)	cytosol (GO:0005829)|nucleus (GO:0005634)	adenosine kinase activity (GO:0004001)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)|poly(A) RNA binding (GO:0044822)			breast(1)|large_intestine(2)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	8	Prostate(51;0.0112)|Ovarian(15;0.148)				Abacavir(DB01048)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Adenosine(DB00640)|Ribavirin(DB00811)	GAAGCCCAAAAAGCTGAAGGT	0.672																																					p.K12Q		Atlas-SNP	.											.	ADK	28	.	0			c.A34C						PASS	.						51	47	49					10																	75911070		1959	3758	5717	SO:0001583	missense	132	exon1			CCCAAAAAGCTGA	U50196	CCDS7343.1, CCDS7344.1, CCDS55716.1, CCDS55717.1	10q22.2	2006-02-21			ENSG00000156110	ENSG00000156110	2.7.1.20		257	protein-coding gene	gene with protein product	"adenosine 5'-phosphotransferase"	102750				8577746	Standard	NM_001123		Approved	AK	uc001jwi.3	P55263	OTTHUMG00000018506	ENST00000286621.2:c.34A>C	chr10.hg19:g.75911070A>C	ENSP00000286621:p.Lys12Gln	81.0	0.0	.		105.0	32.0	.	NM_001202450	B7Z783|B7Z800|O00741|O00742|Q16710|Q5JQ10|Q5JQ11|Q9BTN2	Missense_Mutation	SNP	ENST00000286621.2	hg19	CCDS7343.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.243859	0.79912	.	.	ENSG00000156110	ENST00000539909;ENST00000286621	.	.	.	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.54695	0.1874	L	0.48362	1.52	0.80722	D	1	P;P	0.48162	0.906;0.906	B;B	0.44224	0.444;0.444	T	0.56842	-0.7912	9	0.45353	T	0.12	-10.7025	13.8494	0.63487	1.0:0.0:0.0:0.0	.	12;12	B7Z783;P55263	.;ADK_HUMAN	Q	12	.	ENSP00000286621:K12Q	K	+	1	0	ADK	75581076	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.757000	0.47557	2.292000	0.77174	0.533000	0.62120	AAG	.	.	.	none		0.672	ADK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048763.1	NM_001123, NM_006721		C	75911070	A	C	75911070	3	2	243	1	0	0	0	0	1	0	0	0	320	15	1	5	36	5	ADK	10	75911070	Missense_Mutation	SNP	A	TCGA-SX-A71U-01A-12D-A33Q-10	30411956	75911070	59623677	62	14994											
FAM190B	54462	hgsc.bcm.edu	37	chr10	86185593	86185593	+	Missense_Mutation	SNP	T	T	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	aggtggagtggacaggagcaTtaccacctcagccaccctga	11	6	12	12	0	1	1	1	1	0	0	1	4	1	4	4	4	3	1	4	4	1	1			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr10:86185593T>G	ENST00000224756.8	+	5	1997	c.1812T>G	c.(1810-1812)caT>caG	p.H604Q	CCSER2_ENST00000494144.1_3'UTR|CCSER2_ENST00000543283.1_Missense_Mutation_p.H31Q|CCSER2_ENST00000372088.2_Missense_Mutation_p.H604Q	NM_001284243.1|NM_018999.2	NP_001271172.1|NP_061872.2	Q9H7U1	CCSE2_HUMAN	coiled-coil serine-rich protein 2	604	His-rich.				microtubule bundle formation (GO:0001578)	microtubule cytoskeleton (GO:0015630)											GACAGGAGCATTACCACCTCA	0.478																																					p.H604Q		Atlas-SNP	.											.	CCSER2	7	.	0			c.T1812G						PASS	.						136	115	122					10																	86185593		2203	4300	6503	SO:0001583	missense	54462	exon5			GGAGCATTACCAC		CCDS31235.1, CCDS60582.1, CCDS60583.1, CCDS73159.1	10q23.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000107771	ENSG00000107771			29197	protein-coding gene	gene with protein product			"KIAA1128", "family with sequence similarity 190, member B"	KIAA1128, FAM190B		10574461	Standard	XM_005269905		Approved		uc001kdh.1	Q9H7U1	OTTHUMG00000018641	ENST00000224756.8:c.1812T>G	chr10.hg19:g.86185593T>G	ENSP00000224756:p.His604Gln	100.0	0.0	.		60.0	19.0	.	NM_018999	B4DFY4|B4DQU9|B7WPE8|D3DWE2|Q8N6E9|Q9H2S0|Q9ULU1	Missense_Mutation	SNP	ENST00000224756.8	hg19	CCDS31235.1	.	.	.	.	.	.	.	.	.	.	T	13.11	2.139604	0.37728	.	.	ENSG00000107771	ENST00000224756;ENST00000372088;ENST00000543283	T;T;T	0.29917	1.93;1.91;1.55	6.07	2.64	0.31445	.	0.000000	0.85682	D	0.000000	T	0.18923	0.0454	L	0.33485	1.01	0.48762	D	0.999706	B;B	0.17667	0.023;0.005	B;B	0.14578	0.011;0.005	T	0.08027	-1.0742	10	0.36615	T	0.2	-13.8603	4.0095	0.09616	0.0:0.2881:0.3875:0.3244	.	604;604	Q9H7U1-3;Q9H7U1	.;F190B_HUMAN	Q	604;604;31	ENSP00000224756:H604Q;ENSP00000361160:H604Q;ENSP00000439944:H31Q	ENSP00000224756:H604Q	H	+	3	2	FAM190B	86175573	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	0.712000	0.25779	0.133000	0.18654	0.528000	0.53228	CAT	.	.	.	none		0.478	CCSER2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049132.2	NM_018999		G	86185593	T	G	86185593	3	3	243	1	0	0	0	0	1	0	0	0	5526	1490	52	5	1826	5	FAM190B	10	86185593	Missense_Mutation	SNP	T	TCGA-SX-A71U-01A-12D-A33Q-10	10274523	86185593	49349154	63	14995											
MRPL23	6150	hgsc.bcm.edu	37	chr11	1972132	1972133	+	Frame_Shift_Del	DEL	CC	CC	-																															caatctcttctgtacaggtaCcccctgtaccggctgggtgg																										TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr11:1972132_1972133delCC	ENST00000397298.3	+	2	106_107	c.21_22delCC	c.(19-24)taccccfs	p.P8fs	MRPL23_ENST00000486931.1_3'UTR|MRPL23_ENST00000397294.3_Frame_Shift_Del_p.P8fs|MRPL23_ENST00000381519.1_Frame_Shift_Del_p.P8fs|MRPL23_ENST00000397297.3_Frame_Shift_Del_p.P8fs|MRPL23_ENST00000381514.3_Frame_Shift_Del_p.P8fs	NM_021134.3	NP_066957.3	Q16540	RM23_HUMAN	mitochondrial ribosomal protein L23	8					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)		TGTACAGGTACCCCCTGTACCG	0.609																																					p.7_7del		Atlas-Indel,Pindel	.											.	MRPL23	14	.	0			c.20_21del						PASS	.																																			SO:0001589	frameshift_variant	6150	exon2			.	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.21_22delCC	chr11.hg19:g.1972134_1972135delCC	ENSP00000380466:p.Pro8fs	51.0	0.0	0		51.0	14.0	0.27451	NM_021134	A8MT29|Q96Q71	Frame_Shift_Del	DEL	ENST00000397298.3	hg19	CCDS31336.1																																																																																			.	.	.	none		0.609	MRPL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034765.2	NM_021134		-	1972133	CC	-	1972132	7	5	243	1	0	1	0	1	0	0	0	0	9796	518	18	0	27	0	MRPL23	11	1972132	Frame_Shift_Del	DEL	CC	TCGA-SX-A71U-01A-12D-A33Q-10		1972132	133034384	64	14996											
FCHSD2	9873	hgsc.bcm.edu	37	chr11	72552500	72552500	+	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	tgcccaggagaacccttaccGtttgctgaaggagaccgggg	9	7	14	11	2	0	3	0	1	0	2	0	5	0	3	4	4	4	2	4	4	3	2	rs201269620	byFrequency	TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr11:72552500G>A	ENST00000409418.4	-	18	2438	c.2055C>T	c.(2053-2055)aaC>aaT	p.N685N	FCHSD2_ENST00000409263.1_Splice_Site_p.N46N|FCHSD2_ENST00000311172.7_Splice_Site_p.N629N|FCHSD2_ENST00000409314.1_Splice_Site_p.N709N|ATG16L2_ENST00000534905.1_Intron|FCHSD2_ENST00000458644.2_Splice_Site_p.N549N	NM_014824.2	NP_055639.2	O94868	FCSD2_HUMAN	FCH and double SH3 domains 2	685										endometrium(2)|large_intestine(11)|lung(5)|ovary(2)|prostate(1)|skin(1)	22			BRCA - Breast invasive adenocarcinoma(5;3.3e-05)			AACCCTTACCGTTTGCTGAAG	0.507													G|||	2	0.000399361	0	0	5008	,	,		17201	0.001		0	False		,,,				2504	0.001				p.N685N		Atlas-SNP	.											FCHSD2_ENST00000409418,NS,carcinoma,0,6	FCHSD2	106	.	0			c.C2055T						PASS	.						46	40	42					11																	72552500		2200	4293	6493	SO:0001630	splice_region_variant	9873	exon18			CTTACCGTTTGCT	AB018312	CCDS8218.2	11q13.3	2008-02-05	2004-04-14	2004-04-16	ENSG00000137478	ENSG00000137478			29114	protein-coding gene	gene with protein product			"SH3 multiple domains 3"	SH3MD3		9872452, 15067381	Standard	NM_014824		Approved	KIAA0769	uc009ytl.3	O94868	OTTHUMG00000153082	ENST00000409418.4:c.2056+1C>T	chr11.hg19:g.72552500G>A		100.0	0.0	.		78.0	32.0	.	NM_014824	B4DNI3|Q7L8J9|Q8WVM2|Q96FV7|Q9UF77	Silent	SNP	ENST00000409418.4	hg19	CCDS8218.2																																																																																			.	G|0.998;A|0.002	0.002	weak		0.507	FCHSD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329429.2	NM_014824	Silent	A	72552500	G	A	72552500	5	1	243	1	0	0	0	0	0	0	1	0	5797	1159	40	1	179	1	FCHSD2	11	72552500	Splice_Site	SNP	G	TCGA-SX-A71U-01A-12D-A33Q-10	70580368	72552500	62454016	65	14997											
PCF11	51585	hgsc.bcm.edu	37	chr11	82877707	82877707	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaatgtagaaaactggcaaAgttccaagtctgccaaaaga	18	7	9	7	0	1	3	0	0	1	3	2	3	2	3	2	1	2	3	2	1	8	2			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr11:82877707A>G	ENST00000298281.4	+	5	2220	c.1768A>G	c.(1768-1770)Agt>Ggt	p.S590G		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	590					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						AAACTGGCAAAGTTCCAAGTC	0.373																																					p.S590G		Atlas-SNP	.											PCF11_ENST00000298281,NS,carcinoma,0,2	PCF11	220	.	0			c.A1768G						PASS	.						69	70	70					11																	82877707		1801	3982	5783	SO:0001583	missense	51585	exon5			TGGCAAAGTTCCA	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.1768A>G	chr11.hg19:g.82877707A>G	ENSP00000298281:p.Ser590Gly	192.0	0.0	.		159.0	38.0	.	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	hg19	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	A	3.378	-0.127022	0.06795	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.42900	2.0;0.96;0.99	6.07	4.96	0.65561	.	0.165679	0.43747	D	0.000537	T	0.17916	0.0430	N	0.04880	-0.145	0.25814	N	0.984368	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.0	T	0.11421	-1.0588	9	.	.	.	.	4.9308	0.13916	0.7534:0.0:0.2466:0.0	.	590;590	E9PQ01;O94913	.;PCF11_HUMAN	G	590	ENSP00000298281:S590G;ENSP00000434540:S590G;ENSP00000431567:S590G	.	S	+	1	0	PCF11	82555355	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.144000	0.64832	2.326000	0.78906	0.533000	0.62120	AGT	.	.	.	none		0.373	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		G	82877707	A	G	82877707	3	3	243	1	0	0	0	0	1	0	0	0	11580	72	3	3	1786	3	PCF11	11	82877707	Missense_Mutation	SNP	A	TCGA-SX-A71U-01A-12D-A33Q-10	10325207	82877707	52128809	66	14998											
VAMP1	6843	hgsc.bcm.edu	37	chr12	6574108	6574108	+	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	gctcccagcatgatcatcatCtgaggaaacatggacaaaaa	16	7	8	10	0	3	2	2	2	1	0	4	4	4	4	1	2	2	2	1	2	3	0			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr12:6574108C>T	ENST00000396308.3	-	4	434		c.e4-1		VAMP1_ENST00000361716.3_Splice_Site|TAPBPL_ENST00000545700.1_Intron|VAMP1_ENST00000544432.1_Splice_Site|VAMP1_ENST00000400911.3_Splice_Site|VAMP1_ENST00000535180.1_Splice_Site	NM_014231.3|NM_199245.1	NP_055046.1|NP_954740.1	P23763	VAMP1_HUMAN	vesicle-associated membrane protein 1 (synaptobrevin 1)						neurotransmitter secretion (GO:0007269)|SNARE complex assembly (GO:0035493)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell surface (GO:0009986)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuron projection (GO:0043005)|synapse (GO:0045202)				endometrium(1)|large_intestine(1)|prostate(1)	3					Botulinum Toxin Type B(DB00042)	TGATCATCATCTGAGGAAACA	0.463																																					.		Atlas-SNP	.											VAMP1,NS,carcinoma,0,1	VAMP1	6	.	0			c.289-1G>A						PASS	.						181	159	167					12																	6574108		2203	4300	6503	SO:0001630	splice_region_variant	6843	exon5			CATCATCTGAGGA		CCDS31731.1, CCDS41740.1, CCDS44809.1, CCDS73422.1	12p	2013-02-13			ENSG00000139190	ENSG00000139190		"Vesicle-associated membrane proteins"	12642	protein-coding gene	gene with protein product		185880		SYB1		1976629	Standard	XM_006719011		Approved	VAMP-1	uc001qok.3	P23763	OTTHUMG00000168269	ENST00000396308.3:c.289-1G>A	chr12.hg19:g.6574108C>T		35.0	0.0	.		30.0	12.0	.	NM_016830	A8MVP3|D3DUR3|O75468|Q15857|Q6FG94|Q8IVC9	Splice_Site	SNP	ENST00000396308.3	hg19	CCDS41740.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.696389	0.88830	.	.	ENSG00000139190	ENST00000400911;ENST00000361716;ENST00000535180;ENST00000355479;ENST00000396308;ENST00000396943	.	.	.	5.73	5.73	0.89815	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8991	0.96978	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	VAMP1	6444369	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.818000	0.86416	2.708000	0.92522	0.655000	0.94253	.	.	.	.	none		0.463	VAMP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399078.1		Intron	T	6574108	C	T	6574108	5	4	243	1	0	0	0	0	0	0	1	0	17124	927	32	2	105	2	VAMP1	12	6574108	Splice_Site	SNP	C	TCGA-SX-A71U-01A-12D-A33Q-10		6574108	127277787	67	14999											
ATF7IP	55729	hgsc.bcm.edu	37	chr12	14577946	14577946	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgttcagatcgacctcctgAaaatgaaaagaaggtagagg	15	9	11	6	1	1	5	1	2	0	3	3	6	2	5	2	2	0	2	2	2	6	3			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr12:14577946A>G	ENST00000540793.1	+	1	1252	c.1097A>G	c.(1096-1098)gAa>gGa	p.E366G	ATF7IP_ENST00000544627.1_Missense_Mutation_p.E374G|ATF7IP_ENST00000261168.4_Missense_Mutation_p.E366G|ATF7IP_ENST00000541654.1_3'UTR|ATF7IP_ENST00000543189.1_Missense_Mutation_p.E366G|ATF7IP_ENST00000536444.1_Missense_Mutation_p.E366G			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	366	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						CGACCTCCTGAAAATGAAAAG	0.343																																					p.E366G		Atlas-SNP	.											.	ATF7IP	136	.	0			c.A1097G						PASS	.						77	86	83					12																	14577946		2203	4299	6502	SO:0001583	missense	55729	exon2			CTCCTGAAAATGA	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.1097A>G	chr12.hg19:g.14577946A>G	ENSP00000444589:p.Glu366Gly	56.0	0.0	.		58.0	33.0	.	NM_018179	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Missense_Mutation	SNP	ENST00000540793.1	hg19	CCDS8663.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.982845	0.74474	.	.	ENSG00000171681	ENST00000261168;ENST00000543189;ENST00000536444;ENST00000544627;ENST00000396279;ENST00000540793	T;T;T;T;T;T	0.35421	1.69;1.68;1.69;1.69;1.31;1.69	5.1	3.95	0.45737	.	0.000000	0.64402	D	0.000017	T	0.38852	0.1056	L	0.50333	1.59	0.34100	D	0.661804	P;B;B;B;B	0.44946	0.846;0.011;0.015;0.015;0.001	P;B;B;B;B	0.47470	0.548;0.01;0.027;0.027;0.007	T	0.57757	-0.7756	10	0.87932	D	0	-12.7544	10.2279	0.43236	0.9202:0.0:0.0798:0.0	.	374;366;366;366;366	B4E2A2;B4DRL6;G3V1U0;Q6VMQ6;Q6VMQ6-2	.;.;.;MCAF1_HUMAN;.	G	366;366;366;374;366;366	ENSP00000261168:E366G;ENSP00000443179:E366G;ENSP00000445955:E366G;ENSP00000440440:E374G;ENSP00000379575:E366G;ENSP00000444589:E366G	ENSP00000261168:E366G	E	+	2	0	ATF7IP	14469213	1.000000	0.71417	0.995000	0.50966	0.862000	0.49288	3.175000	0.50855	2.038000	0.60285	0.482000	0.46254	GAA	.	.	.	none		0.343	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179		G	14577946	A	G	14577946	3	3	243	1	0	0	0	0	1	0	0	0	1087	246	9	3	1099	3	ATF7IP	12	14577946	Missense_Mutation	SNP	A	TCGA-SX-A71U-01A-12D-A33Q-10	8003838	14577946	119273949	68	15000											
PDZRN4	29951	hgsc.bcm.edu	37	chr12	41967250	41967250	+	Missense_Mutation	SNP	A	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	agagcccaagatggaatggaAggtgaaaattaggagcgacg	16	5	15	5	2	0	3	0	1	0	2	0	7	0	6	1	4	2	0	1	4	6	1			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr12:41967250A>C	ENST00000402685.2	+	10	2677	c.2669A>C	c.(2668-2670)aAg>aCg	p.K890T	PDZRN4_ENST00000298919.7_Missense_Mutation_p.K630T|PDZRN4_ENST00000539469.2_Missense_Mutation_p.K632T	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	890							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)				ATGGAATGGAAGGTGAAAATT	0.498																																					p.K890T		Atlas-SNP	.											.	PDZRN4	346	.	0			c.A2669C						PASS	.						114	104	107					12																	41967250		2203	4300	6503	SO:0001583	missense	29951	exon10			AATGGAAGGTGAA	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.2669A>C	chr12.hg19:g.41967250A>C	ENSP00000384197:p.Lys890Thr	37.0	0.0	.		51.0	31.0	.	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Missense_Mutation	SNP	ENST00000402685.2	hg19	CCDS53777.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.091044	0.76756	.	.	ENSG00000165966	ENST00000402685;ENST00000539469;ENST00000298919	T;T;T	0.65732	-0.17;-0.17;-0.17	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.81273	0.4788	M	0.85373	2.75	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;1.0;1.0	D	0.84706	0.0731	10	0.87932	D	0	-49.9998	15.8245	0.78686	1.0:0.0:0.0:0.0	.	890;630;632	Q6ZMN7;Q6ZMN7-4;Q6ZMN7-2	PZRN4_HUMAN;.;.	T	890;632;630	ENSP00000384197:K890T;ENSP00000439990:K632T;ENSP00000298919:K630T	ENSP00000298919:K630T	K	+	2	0	PDZRN4	40253517	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.287000	0.95975	2.274000	0.75844	0.528000	0.53228	AAG	.	.	.	none		0.498	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377		C	41967250	A	C	41967250	3	2	243	1	0	0	0	0	1	0	0	0	11717	72	3	5	2780	5	PDZRN4	12	41967250	Missense_Mutation	SNP	A	TCGA-SX-A71U-01A-12D-A33Q-10	27389304	41967250	91884645	69	15001											
PPHLN1	51535	hgsc.bcm.edu	37	chr12	42768782	42768782	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcacctgttggccgaaaggaTtctccacacagcagatctgg	10	9	10	12	1	3	1	1	0	2	1	4	3	3	2	3	3	1	2	3	3	1	2			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr12:42768782T>C	ENST00000395568.2	+	5	501	c.417T>C	c.(415-417)gaT>gaC	p.D139D	PPHLN1_ENST00000432191.2_Silent_p.D84D|PPHLN1_ENST00000552761.1_Silent_p.D91D|PPHLN1_ENST00000395580.3_Silent_p.D146D|PPHLN1_ENST00000358314.7_Silent_p.D139D|PPHLN1_ENST00000317560.9_Silent_p.D91D|PPHLN1_ENST00000256678.8_Silent_p.D38D|PPHLN1_ENST00000449194.2_Silent_p.D139D|PPHLN1_ENST00000549190.1_Silent_p.D157D|PPHLN1_ENST00000337898.6_Silent_p.D84D	NM_016488.6	NP_057572.5	Q8NEY8	PPHLN_HUMAN	periphilin 1	139					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)		GCCGAAAGGATTCTCCACACA	0.418																																					p.D146D		Atlas-SNP	.											.	PPHLN1	101	.	0			c.T438C						PASS	.						100	95	97					12																	42768782		2203	4300	6503	SO:0001819	synonymous_variant	51535	exon6			AAAGGATTCTCCA	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.417T>C	chr12.hg19:g.42768782T>C		152.0	0.0	.		201.0	108.0	.	NM_201515	E9PAX8|Q86YT2|Q8IXN3|Q8TB09|Q96NB9|Q9NXL4|Q9P0P6|Q9P0R9	Silent	SNP	ENST00000395568.2	hg19	CCDS31777.1																																																																																			.	.	.	none		0.418	PPHLN1-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404047.1	NM_201515		C	42768782	T	C	42768782	2	2	243	1	0	0	0	0	0	0	0	1	12322	1490	52	3		3	PPHLN1	12	42768782	Silent	SNP	T	TCGA-SX-A71U-01A-12D-A33Q-10	801532	42768782	91083113	70	15002											
SLC38A2	54407	hgsc.bcm.edu	37	chr12	46756297	46756297	+	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	caataaaaccaaagatatccCtaatagttgggacaaagatg	19	8	7	7	0	0	2	0	0	0	2	1	3	1	3	2	1	1	1	2	1	8	5			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr12:46756297C>G	ENST00000256689.5	-	14	1748	c.1304G>C	c.(1303-1305)aGg>aCg	p.R435T	SLC38A2_ENST00000551374.1_Missense_Mutation_p.R273T|SLC38A2_ENST00000547252.1_5'Flank	NM_018976.4	NP_061849.2	Q96QD8	S38A2_HUMAN	solute carrier family 38, member 2	435					amino acid transport (GO:0006865)|glutamate secretion (GO:0014047)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|sodium ion transport (GO:0006814)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|symporter activity (GO:0015293)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	18	Lung SC(27;0.192)|Renal(347;0.236)		OV - Ovarian serous cystadenocarcinoma(5;0.0048)|Epithelial(2;0.0374)	GBM - Glioblastoma multiforme(48;0.226)		AAAGATATCCCTAATAGTTGG	0.348																																					p.R435T	Ovarian(9;448 492 8335 28722 40361)	Atlas-SNP	.											.	SLC38A2	36	.	0			c.G1304C						PASS	.						78	74	75					12																	46756297		2202	4298	6500	SO:0001583	missense	54407	exon14			ATATCCCTAATAG	AB037803	CCDS8749.1	12q13.11	2014-08-12			ENSG00000134294	ENSG00000134294		"Solute carriers"	13448	protein-coding gene	gene with protein product		605180				10747860, 17237199	Standard	NM_018976		Approved	SAT2, ATA2, KIAA1382, SNAT2	uc001rpg.3	Q96QD8	OTTHUMG00000169471	ENST00000256689.5:c.1304G>C	chr12.hg19:g.46756297C>G	ENSP00000256689:p.Arg435Thr	157.0	0.0	.		210.0	55.0	.	NM_018976	Q6IA88|Q6ZMG2|Q9HAV3|Q9NVA8|Q9P2G5	Missense_Mutation	SNP	ENST00000256689.5	hg19	CCDS8749.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.620493	0.87460	.	.	ENSG00000134294	ENST00000256689;ENST00000551374	T;T	0.02216	4.39;4.39	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.11196	0.0273	M	0.78637	2.42	0.58432	D	0.999999	B;P;D	0.58970	0.367;0.954;0.984	B;P;P	0.58928	0.217;0.848;0.834	T	0.19647	-1.0299	10	0.21540	T	0.41	-17.7125	20.0916	0.97822	0.0:1.0:0.0:0.0	.	273;335;435	F8VQW8;Q96QD8-2;Q96QD8	.;.;S38A2_HUMAN	T	435;273	ENSP00000256689:R435T;ENSP00000450406:R273T	ENSP00000256689:R435T	R	-	2	0	SLC38A2	45042564	1.000000	0.71417	0.997000	0.53966	0.951000	0.60555	3.058000	0.49939	2.737000	0.93849	0.650000	0.86243	AGG	.	.	.	none		0.348	SLC38A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404226.1			G	46756297	C	G	46756297	3	3	243	1	0	0	0	0	1	0	0	0	14617	681	24	4	228	4	SLC38A2	12	46756297	Missense_Mutation	SNP	C	TCGA-SX-A71U-01A-12D-A33Q-10	3987515	46756297	87095598	71	15003											
TBC1D15	64786	hgsc.bcm.edu	37	chr12	72274296	72274296	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggccccaaaagaaagaggTcatcgaggatcagaacatct	16	5	10	10	1	3	3	2	0	1	3	4	5	3	4	2	3	1	0	2	3	4	0			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr12:72274296T>C	ENST00000550746.1	+	4	316	c.252T>C	c.(250-252)ggT>ggC	p.G84G	TBC1D15_ENST00000319106.8_Silent_p.G92G|TBC1D15_ENST00000393309.3_5'UTR|TBC1D15_ENST00000485960.2_Silent_p.G84G	NM_001146213.1|NM_022771.4	NP_001139685.2|NP_073608.4	Q8TC07	TBC15_HUMAN	TBC1 domain family, member 15	84					positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab GTPase activity (GO:0032313)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	Rab GTPase activator activity (GO:0005097)			NS(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						AAGAAAGAGGTCATCGAGGAT	0.333																																					p.G92G		Atlas-SNP	.											.	TBC1D15	99	.	0			c.T276C						PASS	.						48	42	44					12																	72274296		2203	4300	6503	SO:0001819	synonymous_variant	64786	exon5			AAGAGGTCATCGA	AL157464	CCDS31858.1, CCDS53814.1, CCDS55849.1	12q15	2013-07-09			ENSG00000121749	ENSG00000121749			25694	protein-coding gene	gene with protein product		612662				16055087	Standard	NM_022771		Approved	FLJ12085, DKFZp761D0223	uc001swu.3	Q8TC07	OTTHUMG00000158553	ENST00000550746.1:c.252T>C	chr12.hg19:g.72274296T>C		158.0	0.0	.		224.0	111.0	.	NM_001146214	B4DMT9|B9A6L6|J3KNI9|Q9HA83	Silent	SNP	ENST00000550746.1	hg19	CCDS31858.1																																																																																			.	.	.	none		0.333	TBC1D15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351266.2	NM_022771		C	72274296	T	C	72274296	2	2	243	1	0	0	0	0	0	0	0	1	15616	1654	58	3		3	TBC1D15	12	72274296	Silent	SNP	T	TCGA-SX-A71U-01A-12D-A33Q-10	25517999	72274296	61577599	72	15004											
MED13L	23389	hgsc.bcm.edu	37	chr12	116418708	116418709	+	Frame_Shift_Ins	INS	-	-	T																															tgtagaaaacttgctcatccINSttcattgtctgcagcatgta																								rs376850639		TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr12:116418708_116418709insT	ENST00000281928.3	-	23	5416_5417	c.5210_5211insA	c.(5209-5211)aagfs	p.K1737fs		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1737						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)		CTTGCTCATCCTTCATTGTCTG	0.396																																					p.K1737fs		Atlas-Indel,Pindel	.											.	MED13L	193	.	0			c.5211_5212insA						PASS	.																																			SO:0001589	frameshift_variant	23389	exon23			.	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.5211dupA	chr12.hg19:g.116418710_116418710dupT	ENSP00000281928:p.Lys1737fs	53.0	0.0	0		93.0	18.0	0.193548	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Frame_Shift_Ins	INS	ENST00000281928.3	hg19	CCDS9177.1																																																																																			.	.	.	none		0.396	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3			T	116418709	-	T	116418708	7	5	243	1	0	1	1	0	0	0	0	0	9438	680	24	0	1457	0	MED13L	12	116418708	Frame_Shift_Ins	INS	-	TCGA-SX-A71U-01A-12D-A33Q-10	44144412	116418708	17433187	73	15005											
COL4A2	1284	hgsc.bcm.edu	37	chr13	111090980	111090980	+	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	cctagggcatttccttgaagGgagaagaaggaatcatgggc	12	8	14	7	0	1	3	1	1	0	2	2	5	2	4	2	4	0	1	2	4	5	3			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr13:111090980G>A	ENST00000360467.5	+	15	1183	c.877G>A	c.(877-879)Gga>Aga	p.G293R		NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	293	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)	p.G293*(1)		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)			TTCCTTGAAGGGAGAAGAAGG	0.542																																					p.G293R		Atlas-SNP	.											COL4A2,NS,carcinoma,0,1	COL4A2	178	.	1	Substitution - Nonsense(1)	lung(1)	c.G877A						PASS	.						148	150	149					13																	111090980		1894	4127	6021	SO:0001583	missense	1284	exon15			TTGAAGGGAGAAG	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.877G>A	chr13.hg19:g.111090980G>A	ENSP00000353654:p.Gly293Arg	83.0	0.0	.		66.0	20.0	.	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Missense_Mutation	SNP	ENST00000360467.5	hg19	CCDS41907.1	.	.	.	.	.	.	.	.	.	.	G	12.31	1.900715	0.33535	.	.	ENSG00000134871	ENST00000360467;ENST00000257309	D	0.99353	-5.77	4.52	4.52	0.55395	.	0.000000	0.50627	D	0.000108	D	0.99507	0.9824	M	0.94101	3.495	0.53688	D	0.999975	D	0.89917	1.0	D	0.97110	1.0	D	0.98190	1.0462	10	0.72032	D	0.01	.	13.127	0.59360	0.0:0.0:1.0:0.0	.	293	P08572	CO4A2_HUMAN	R	293	ENSP00000353654:G293R	ENSP00000257309:G293R	G	+	1	0	COL4A2	109888981	1.000000	0.71417	0.997000	0.53966	0.321000	0.28281	4.562000	0.60816	2.226000	0.72624	0.557000	0.71058	GGA	.	.	.	none		0.542	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846		A	111090980	G	A	111090980	3	1	243	1	0	0	0	0	1	0	0	0	3692	1233	43	2	931	2	COL4A2	13	111090980	Missense_Mutation	SNP	G	TCGA-SX-A71U-01A-12D-A33Q-10		111090980	4078898	74	15006											
KIAA0586	9786	hgsc.bcm.edu	37	chr14	58965662	58965663	+	Frame_Shift_Ins	INS	-	-	T																															ctaaaccattatctcggcaaINStttgacacagtttcaggtag																										TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr14:58965662_58965663insT	ENST00000556134.1	+	28	4381_4382	c.4107_4108insT	c.(4108-4110)tttfs	p.F1370fs	KIAA0586_ENST00000261244.5_Frame_Shift_Ins_p.F1309fs|KIAA0586_ENST00000354386.6_Frame_Shift_Ins_p.F1438fs|KIAA0586_ENST00000423743.3_Frame_Shift_Ins_p.F1341fs|KIAA0586_ENST00000538571.2_3'UTR	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	1370					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|regulation of establishment of protein localization (GO:0070201)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				endometrium(4)|kidney(6)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TATCTCGGCAATTTGACACAGT	0.376																																					p.Q1437fs		Atlas-Indel,Pindel	.											.	KIAA0586	180	.	0			c.4311_4312insT						PASS	.																																			SO:0001589	frameshift_variant	9786	exon29			.	AB011158	CCDS45115.1, CCDS58320.1, CCDS58321.1, CCDS58322.1, CCDS73639.1	14q23.1	2012-12-06			ENSG00000100578	ENSG00000100578			19960	protein-coding gene	gene with protein product		610178				16702409	Standard	NM_014749		Approved	Talpid3	uc010trr.2	Q9BVV6	OTTHUMG00000171141	ENST00000556134.1:c.4110dupT	chr14.hg19:g.58965665_58965665dupT	ENSP00000452351:p.Phe1370fs	66.0	0.0	0		60.0	26.0	0.433333	NM_001244189	B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	Frame_Shift_Ins	INS	ENST00000556134.1	hg19	CCDS58321.1																																																																																			.	.	.	none		0.376	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1	NM_014749		T	58965663	-	T	58965662	7	5	243	1	0	1	1	0	0	0	0	0	8193	98	4	0	4026	0	KIAA0586	14	58965662	Frame_Shift_Ins	INS	-	TCGA-SX-A71U-01A-12D-A33Q-10		58965662	48383878	75	15007											
ATG2B	55102	hgsc.bcm.edu	37	chr14	96783528	96783528	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atccatgattaatattcagaAgaactgagagaaaactctga	18	10	7	6	0	2	6	1	3	1	3	3	7	3	6	1	0	2	0	1	0	6	3			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr14:96783528A>G	ENST00000359933.4	-	20	4057	c.3164T>C	c.(3163-3165)cTt>cCt	p.L1055P		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	1055					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)		AATATTCAGAAGAACTGAGAG	0.333																																					p.L1055P		Atlas-SNP	.											.	ATG2B	169	.	0			c.T3164C						PASS	.						78	79	79					14																	96783528		1796	4078	5874	SO:0001583	missense	55102	exon20			TTCAGAAGAACTG	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.3164T>C	chr14.hg19:g.96783528A>G	ENSP00000353010:p.Leu1055Pro	108.0	0.0	.		97.0	41.0	.	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	hg19	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	A	22.5	4.304738	0.81247	.	.	ENSG00000066739	ENST00000359933	T	0.10573	2.86	5.56	5.56	0.83823	.	0.604497	0.14732	U	0.301693	T	0.17109	0.0411	L	0.53249	1.67	0.58432	D	0.999999	P	0.47409	0.895	P	0.47470	0.548	T	0.01238	-1.1409	10	0.34782	T	0.22	.	12.2792	0.54755	0.8732:0.0:0.0:0.1268	.	1055	Q96BY7	ATG2B_HUMAN	P	1055	ENSP00000353010:L1055P	ENSP00000353010:L1055P	L	-	2	0	ATG2B	95853281	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.464000	0.66719	2.239000	0.73571	0.528000	0.53228	CTT	.	.	.	none		0.333	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		G	96783528	A	G	96783528	3	3	243	1	0	0	0	0	1	0	0	0	1094	72	3	3	3164	3	ATG2B	14	96783528	Missense_Mutation	SNP	A	TCGA-SX-A71U-01A-12D-A33Q-10	37817866	96783528	10566012	76	15008											
TMEM85	51234	hgsc.bcm.edu	37	chr15	34519983	34519983	+	Frame_Shift_Del	DEL	C	C	-																															ggcaatactatctccatcttCcctactatgatggtgtgtat																										TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr15:34519983delC	ENST00000267750.4	+	3	407	c.291delC	c.(289-291)ttcfs	p.F97fs	EMC4_ENST00000559421.1_Intron|EMC4_ENST00000249209.4_Frame_Shift_Del_p.F97fs|EMC4_ENST00000559078.1_Frame_Shift_Del_p.F97fs|EMC4_ENST00000557879.1_Intron	NM_016454.2	NP_057538.1	Q5J8M3	EMC4_HUMAN	ER membrane protein complex subunit 4	97					apoptotic process (GO:0006915)	ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)											TCTCCATCTTCCCTACTATGA	0.453																																					p.F97fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.290delT						PASS	.						180	154	163					15																	34519983		2201	4298	6499	SO:0001589	frameshift_variant	51234	exon3			.	BC016348	CCDS10035.1, CCDS66732.1	15q14	2012-05-23	2012-05-23	2012-05-23	ENSG00000128463	ENSG00000128463			28032	protein-coding gene	gene with protein product			"transmembrane protein 85"	TMEM85		18586032, 22119785	Standard	NM_001286420		Approved	FLJ90746, MGC24415, PIG17	uc001zhq.3	Q5J8M3	OTTHUMG00000129411	ENST00000267750.4:c.291delC	chr15.hg19:g.34519983delC	ENSP00000267750:p.Phe97fs	98.0	0.0	0		84.0	21.0	0.25	NM_016454	A8K3A9|B4DJQ4|Q96KX9|Q9BUI5|Q9P0T9	Frame_Shift_Del	DEL	ENST00000267750.4	hg19	CCDS10035.1																																																																																			.	.	.	none		0.453	EMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251568.1	NM_016454		-	34519983	C	-	34519983	7	5	243	1	0	1	0	1	0	0	0	0	16219	854	30	0	301	0	TMEM85	15	34519983	Frame_Shift_Del	DEL	C	TCGA-SX-A71U-01A-12D-A33Q-10		34519983	68011409	77	15009											
EID1	399694	hgsc.bcm.edu	37	chr15	49170567	49170567	+	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	0	0	0	0	0	0	0	0	0	0	ggaggaggaggaggcccagcCaatggcggcgccagagggga	10	1	21	9	2	0	1	0	0	0	1	0	6	0	6	3	9	1	0	3	9	1	0			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr15:49170567C>A	ENST00000332408.4	-	4	1269				SHC4_ENST00000396535.3_5'Flank|EID1_ENST00000558295.1_Intron|EID1_ENST00000530028.2_Missense_Mutation_p.P65Q|EID1_ENST00000560490.1_Missense_Mutation_p.P43Q|SHC4_ENST00000537958.1_5'Flank	NM_203349.3	NP_976224.3	Q6S5L8	SHC4_HUMAN	SHC (Src homology 2 domain containing) family, member 4						apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of cell proliferation (GO:0008284)|regulation of gene expression (GO:0010468)|stem cell differentiation (GO:0048863)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(2)|large_intestine(8)|lung(11)|ovary(3)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	29		all_lung(180;0.00466)		all cancers(107;9.4e-08)|GBM - Glioblastoma multiforme(94;5.94e-07)		GAGGCCCAGCCAATGGCGGCG	0.701																																					p.P65Q		Atlas-SNP	.											.	EID1	16	.	0			c.C194A						PASS	.						16	20	19					15																	49170567		2001	4147	6148	SO:0001627	intron_variant	23741	exon1			CCCAGCCAATGGC	AY358250	CCDS10130.1	15q21.1-q21.2	2013-02-14			ENSG00000185634	ENSG00000185634		"SH2 domain containing"	16743	protein-coding gene	gene with protein product	"rai-like protein"						Standard	NM_203349		Approved	RaLP	uc001zxb.1	Q6S5L8	OTTHUMG00000131513	ENST00000332408.4:c.840+5877G>T	chr15.hg19:g.49170567C>A		60.0	0.0	.		49.0	14.0	.	NM_014335	Q6UXQ3|Q8IYW3	Missense_Mutation	SNP	ENST00000332408.4	hg19	CCDS10130.1	.	.	.	.	.	.	.	.	.	.	C	9.230	1.035638	0.19590	.	.	ENSG00000255302	ENST00000530028	T	0.54279	0.58	4.04	4.04	0.47022	.	.	.	.	.	T	0.50684	0.1630	L	0.36672	1.1	0.54753	D	0.999982	P	0.48503	0.911	P	0.49421	0.61	T	0.54357	-0.8306	9	0.72032	D	0.01	.	12.0069	0.53265	0.0:1.0:0.0:0.0	.	65	Q9Y6B2	EID1_HUMAN	Q	65	ENSP00000431162:P65Q	ENSP00000431162:P65Q	P	+	2	0	EID1	46957859	0.015000	0.18098	0.110000	0.21437	0.061000	0.15899	0.095000	0.15127	2.530000	0.85305	0.650000	0.86243	CCA	.	.	.	none		0.701	SHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254371.1	NM_203349		A	49170567	C	A	49170567	1	1	243	0	1	0	0	0	0	0	0	0	4988	594	21	4		4	EID1	15	49170567	Intron	SNP	C	TCGA-SX-A71U-01A-12D-A33Q-10	14650584	49170567	53360825	78	15010											
MYO5C	55930	hgsc.bcm.edu	37	chr15	52517329	52517329	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgtttggtgatctctgacAtcttttctgaaagggaaagg	9	15	12	5	0	3	3	0	3	3	0	4	4	3	4	0	3	0	2	0	3	2	4			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr15:52517329A>G	ENST00000261839.7	-	27	3469	c.3308T>C	c.(3307-3309)aTg>aCg	p.M1103T		NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	1103						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)		GATCTCTGACATCTTTTCTGA	0.358																																					p.M1103T		Atlas-SNP	.											.	MYO5C	162	.	0			c.T3308C						PASS	.						102	89	93					15																	52517329		1846	4102	5948	SO:0001583	missense	55930	exon27			TCTGACATCTTTT	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.3308T>C	chr15.hg19:g.52517329A>G	ENSP00000261839:p.Met1103Thr	70.0	0.0	.		45.0	17.0	.	NM_018728	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	hg19	CCDS42036.1	.	.	.	.	.	.	.	.	.	.	A	12.19	1.864189	0.32977	.	.	ENSG00000128833	ENST00000261839	T	0.19669	2.13	5.89	5.89	0.94794	.	0.046494	0.85682	D	0.000000	T	0.16642	0.0400	N	0.22421	0.69	0.80722	D	1	P	0.36789	0.57	B	0.38264	0.269	T	0.08700	-1.0709	10	0.15066	T	0.55	.	16.3127	0.82898	1.0:0.0:0.0:0.0	.	1103	Q9NQX4	MYO5C_HUMAN	T	1103	ENSP00000261839:M1103T	ENSP00000261839:M1103T	M	-	2	0	MYO5C	50304621	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.863000	0.75489	2.246000	0.74042	0.533000	0.62120	ATG	.	.	.	none		0.358	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728		G	52517329	A	G	52517329	3	3	243	1	0	0	0	0	1	0	0	0	10087	217	8	3	1980	3	MYO5C	15	52517329	Missense_Mutation	SNP	A	TCGA-SX-A71U-01A-12D-A33Q-10	3346762	52517329	50014063	79	15011											
NEDD4	4734	hgsc.bcm.edu	37	chr15	56207818	56207818	+	Frame_Shift_Del	DEL	A	A	-																															tctgaatcagaattaagcttAatttctgacatttctggttt																										TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr15:56207818delA	ENST00000508342.1	-	1	1511	c.1212delT	c.(1210-1212)attfs	p.I404fs	NEDD4_ENST00000338963.2_Frame_Shift_Del_p.I404fs|NEDD4_ENST00000435532.3_Intron|NEDD4_ENST00000506154.1_Frame_Shift_Del_p.I404fs	NM_001284338.1	NP_001271267.1	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	404					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)		AATTAAGCTTAATTTCTGACA	0.353																																					p.K405fs		Atlas-Indel,Pindel	.											.	NEDD4	167	.	0			c.1213delA						PASS	.						58	58	58					15																	56207818		2193	4292	6485	SO:0001589	frameshift_variant	4734	exon1			.	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.1212delT	chr15.hg19:g.56207818delA	ENSP00000424827:p.Ile404fs	119.0	0.0	0		98.0	37.0	0.377551	NM_198400	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Frame_Shift_Del	DEL	ENST00000508342.1	hg19																																																																																				.	.	.	none		0.353	NEDD4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000359817.1	NM_198400		-	56207818	A	-	56207818	7	5	243	1	0	1	0	1	0	0	0	0	10317	358	13	0	2847	0	NEDD4	15	56207818	Frame_Shift_Del	DEL	A	TCGA-SX-A71U-01A-12D-A33Q-10	3690489	56207818	46323574	80	15012											
CCDC64B	146439	hgsc.bcm.edu	37	chr16	3078253	3078253	+	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	ctgtgagcgcagctgctgccCgatcaccacctgcatgtcgt	6	9	11	15	3	1	1	1	1	0	0	2	2	1	1	3	0	5	4	3	0	0	0			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr16:3078253C>G	ENST00000572449.1	-	10	1443	c.1381G>C	c.(1381-1383)Ggg>Cgg	p.G461R	CCDC64B_ENST00000389347.4_Missense_Mutation_p.G461R|CCDC64B_ENST00000573514.1_Missense_Mutation_p.G254R			A1A5D9	BICR2_HUMAN	coiled-coil domain containing 64B	461										breast(1)|endometrium(2)|large_intestine(1)	4						AGCTGCTGCCCGATCACCACC	0.771																																					p.G461R		Atlas-SNP	.											.	CCDC64B	19	.	0			c.G1381C						PASS	.						8	9	9					16																	3078253		1914	3952	5866	SO:0001583	missense	146439	exon9			GCTGCCCGATCAC	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.1381G>C	chr16.hg19:g.3078253C>G	ENSP00000459043:p.Gly461Arg	0.0	0.0	.		10.0	6.0	.	NM_001103175	Q658L9	Missense_Mutation	SNP	ENST00000572449.1	hg19	CCDS45393.1	.	.	.	.	.	.	.	.	.	.	c	17.50	3.405799	0.62288	.	.	ENSG00000162069	ENST00000389347	T	0.30714	1.52	4.97	4.02	0.46733	.	0.230323	0.33040	N	0.005353	T	0.44074	0.1276	L	0.50333	1.59	0.09310	N	0.999998	D	0.89917	1.0	D	0.75484	0.986	T	0.17837	-1.0356	10	0.46703	T	0.11	-47.1987	7.3929	0.26919	0.0:0.8046:0.0:0.1954	.	461	A1A5D9	BICR2_HUMAN	R	461	ENSP00000373998:G461R	ENSP00000373998:G461R	G	-	1	0	CCDC64B	3018254	0.043000	0.20138	0.936000	0.37596	0.459000	0.32528	0.772000	0.26647	1.099000	0.41499	0.556000	0.70494	GGG	.	.	.	none		0.771	CCDC64B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436991.1			G	3078253	C	G	3078253	3	3	243	1	0	0	0	0	1	0	0	0	2838	652	23	4	149	4	CCDC64B	16	3078253	Missense_Mutation	SNP	C	TCGA-SX-A71U-01A-12D-A33Q-10		3078253	87276500	81	15013											
SPIRE2	84501	hgsc.bcm.edu	37	chr16	89929899	89929899	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctaggagttcagccaccccGtggagagcctggcgctgact	7	7	13	14	2	1	2	1	1	0	1	1	4	1	3	5	3	2	2	5	3	1	2			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr16:89929899G>A	ENST00000378247.3	+	11	1634	c.1591G>A	c.(1591-1593)Gtg>Atg	p.V531M	SPIRE2_ENST00000393062.2_Missense_Mutation_p.V531M	NM_032451.1	NP_115827.1	Q8WWL2	SPIR2_HUMAN	spire-type actin nucleation factor 2	531					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)		CAGCCACCCCGTGGAGAGCCT	0.582																																					p.V531M		Atlas-SNP	.											.	SPIRE2	63	.	0			c.G1591A						PASS	.						53	51	51					16																	89929899		2198	4300	6498	SO:0001583	missense	84501	exon11			CACCCCGTGGAGA	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.1591G>A	chr16.hg19:g.89929899G>A	ENSP00000367494:p.Val531Met	40.0	0.0	.		39.0	23.0	.	NM_032451	A4QPB1|Q2TA98|Q6P433|Q8ND47|Q96JJ5	Missense_Mutation	SNP	ENST00000378247.3	hg19	CCDS32516.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.421999	0.83559	.	.	ENSG00000204991	ENST00000378247;ENST00000393062	T;T	0.52754	0.65;0.72	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.73369	0.3578	M	0.85710	2.77	0.80722	D	1	D;P;D;D	0.89917	0.998;0.8;0.999;1.0	D;B;D;D	0.91635	0.917;0.303;0.917;0.999	T	0.75625	-0.3253	10	0.52906	T	0.07	-45.1084	18.6856	0.91562	0.0:0.0:1.0:0.0	.	398;531;483;531	Q8WWL2-4;Q8WWL2-2;Q8WWL2-3;Q8WWL2	.;.;.;SPIR2_HUMAN	M	531	ENSP00000367494:V531M;ENSP00000376782:V531M	ENSP00000367494:V531M	V	+	1	0	SPIRE2	88457400	1.000000	0.71417	0.962000	0.40283	0.527000	0.34593	7.430000	0.80321	2.660000	0.90430	0.467000	0.42956	GTG	.	.	.	none		0.582	SPIRE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421843.1	XM_047462		A	89929899	G	A	89929899	3	1	243	1	0	0	0	0	1	0	0	0	15084	1145	40	1	1633	1	SPIRE2	16	89929899	Missense_Mutation	SNP	G	TCGA-SX-A71U-01A-12D-A33Q-10	86851646	89929899	424854	82	15014											
DHRS13	147015	hgsc.bcm.edu	37	chr17	27229847	27229847	+	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	cgcactcacccgtgaccacgGccgtgcggccccgcaggttg	5	5	13	18	6	1	1	1	1	0	0	1	1	1	1	5	3	1	3	5	3	0	1			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr17:27229847G>C	ENST00000378895.4	-	1	242	c.116C>G	c.(115-117)gCc>gGc	p.A39G	DHRS13_ENST00000394901.3_5'UTR|DHRS13_ENST00000426464.2_Missense_Mutation_p.A39G	NM_144683.3	NP_653284.2	Q6UX07	DHR13_HUMAN	dehydrogenase/reductase (SDR family) member 13	39						extracellular region (GO:0005576)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	9	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)		Epithelial(11;1.59e-06)|all cancers(11;9.27e-06)|BRCA - Breast invasive adenocarcinoma(11;5.78e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.0602)			CGTGACCACGGCCGTGCGGCC	0.751																																					p.A39G		Atlas-SNP	.											.	DHRS13	22	.	0			c.C116G						PASS	.						6	7	7					17																	27229847		1759	3831	5590	SO:0001583	missense	147015	exon1			ACCACGGCCGTGC	BC015582	CCDS11246.2	17q11.2	2011-09-14			ENSG00000167536	ENSG00000167536	1.1.-.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	28326	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 7C, member 5"					12975309, 19027726	Standard	NM_144683		Approved	MGC23280, SDR7C5	uc002hde.4	Q6UX07	OTTHUMG00000132678	ENST00000378895.4:c.116C>G	chr17.hg19:g.27229847G>C	ENSP00000368173:p.Ala39Gly	2.0	0.0	.		6.0	5.0	.	NM_144683	Q96BH7	Missense_Mutation	SNP	ENST00000378895.4	hg19	CCDS11246.2	.	.	.	.	.	.	.	.	.	.	g	14.25	2.478736	0.44044	.	.	ENSG00000167536	ENST00000378895;ENST00000426464	D;D	0.89050	-2.46;-1.82	4.4	1.28	0.21552	NAD(P)-binding domain (1);	0.658530	0.15142	N	0.278221	D	0.89805	0.6821	H	0.94542	3.55	0.09310	N	1	B;B	0.12013	0.005;0.001	B;B	0.10450	0.002;0.005	D	0.83708	0.0186	10	0.87932	D	0	.	4.2743	0.10800	0.2818:0.1707:0.5476:0.0	.	39;39	B4DJC5;Q6UX07	.;DHR13_HUMAN	G	39	ENSP00000368173:A39G;ENSP00000412826:A39G	ENSP00000368173:A39G	A	-	2	0	DHRS13	24253973	0.316000	0.24580	0.300000	0.25030	0.071000	0.16799	0.744000	0.26245	0.146000	0.19002	0.306000	0.20318	GCC	.	.	.	none		0.751	DHRS13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255952.1	NM_144683		C	27229847	G	C	27229847	3	2	243	1	0	0	0	0	1	0	0	0	4491	1203	42	4	1037	4	DHRS13	17	27229847	Missense_Mutation	SNP	G	TCGA-SX-A71U-01A-12D-A33Q-10		27229847	53965363	83	15015											
HGS	9146	hgsc.bcm.edu	37	chr17	79663907	79663907	+	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	taccagccctcgggaccagcCagcttccccagcaccttcag	8	6	8	19	1	1	0	1	0	0	0	3	1	2	1	7	1	5	2	7	1	1	3			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr17:79663907C>A	ENST00000329138.4	+	18	1896	c.1761C>A	c.(1759-1761)gcC>gcA	p.A587A		NM_004712.4	NP_004703.1	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine kinase substrate	587	Gln-rich.|Interaction with NF2.				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)			CGGGACCAGCCAGCTTCCCCA	0.682																																					p.A587A		Atlas-SNP	.											.	HGS	54	.	0			c.C1761A						PASS	.						40	49	46					17																	79663907		2202	4296	6498	SO:0001819	synonymous_variant	9146	exon18			ACCAGCCAGCTTC	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.1761C>A	chr17.hg19:g.79663907C>A		29.0	0.0	.		43.0	15.0	.	NM_004712	Q9NR36	Silent	SNP	ENST00000329138.4	hg19	CCDS11784.1																																																																																			.	.	.	none		0.682	HGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440541.1	NM_004712		A	79663907	C	A	79663907	2	1	243	1	0	0	0	0	0	0	0	1	7094	581	21	4		4	HGS	17	79663907	Silent	SNP	C	TCGA-SX-A71U-01A-12D-A33Q-10	52434060	79663907	1531303	84	15016											
ARHGDIA	396	hgsc.bcm.edu	37	chr17	79827786	79827786	+	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	atctgggccagctgctcggcTgtgggctcctgctcagccat	4	10	13	14	1	2	0	1	0	1	0	4	0	3	0	3	3	4	5	3	3	0	0			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr17:79827786T>G	ENST00000269321.7	-	2	156	c.21A>C	c.(19-21)acA>acC	p.T7T	ARHGDIA_ENST00000541078.2_Silent_p.T7T|RP11-498C9.3_ENST00000576554.1_RNA|ARHGDIA_ENST00000582520.1_5'Flank|ARHGDIA_ENST00000580685.1_Silent_p.T7T|ARHGDIA_ENST00000581876.1_Silent_p.T7T|RP11-498C9.3_ENST00000576021.1_RNA|ARHGDIA_ENST00000584461.1_Silent_p.T7T|ARHGDIA_ENST00000400721.4_Silent_p.T7T	NM_001185078.1|NM_004309.4	NP_001172007.1|NP_004300.1	P52565	GDIR1_HUMAN	Rho GDP dissociation inhibitor (GDI) alpha	7					cellular component movement (GO:0006928)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell adhesion (GO:0007162)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of axonogenesis (GO:0050772)|regulation of axonogenesis (GO:0050770)|regulation of protein localization (GO:0032880)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|semaphorin-plexin signaling pathway (GO:0071526)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)	GTPase activator activity (GO:0005096)|Rho GDP-dissociation inhibitor activity (GO:0005094)			endometrium(1)|lung(1)|prostate(1)	3	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			GCTGCTCGGCTGTGGGCTCCT	0.647																																					p.T7T		Atlas-SNP	.											.	ARHGDIA	14	.	0			c.A21C						PASS	.						67	57	60					17																	79827786		2203	4300	6503	SO:0001819	synonymous_variant	396	exon2			CTCGGCTGTGGGC	BC028333	CCDS11788.1, CCDS58609.1	17q25.3	2005-12-20				ENSG00000141522			678	protein-coding gene	gene with protein product		601925		GDIA1		9186513	Standard	NM_001185077		Approved	RHOGDI	uc002kbq.3	P52565		ENST00000269321.7:c.21A>C	chr17.hg19:g.79827786T>G		45.0	0.0	.		50.0	14.0	.	NM_004309	A8MXW0|B2R5X1|B4DDD3|B4DUV9|Q6IBM5	Silent	SNP	ENST00000269321.7	hg19	CCDS11788.1																																																																																			.	.	.	none		0.647	ARHGDIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441679.2	NM_004309		G	79827786	T	G	79827786	2	3	243	1	0	0	0	0	0	0	0	1	890	1567	55	5		5	ARHGDIA	17	79827786	Silent	SNP	T	TCGA-SX-A71U-01A-12D-A33Q-10	163879	79827786	1367424	85	15017											
TEX19	400629	hgsc.bcm.edu	37	chr17	80320408	80320408	+	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	ccactgaactatggcctcagGaggctgtgcccctgggcctg	6	8	13	14	0	1	1	1	1	0	0	1	2	1	2	5	4	2	1	5	4	2	1			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr17:80320408G>T	ENST00000333437.4	+	2	692	c.382G>T	c.(382-384)Gag>Tag	p.E128*		NM_207459.3	NP_997342.1	Q8NA77	TEX19_HUMAN	testis expressed 19	128					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						ATGGCCTCAGGAGGCTGTGCC	0.617																																					p.E128X		Atlas-SNP	.											.	TEX19	17	.	0			c.G382T						PASS	.						74	73	74					17																	80320408		2203	4300	6503	SO:0001587	stop_gained	400629	exon2			CCTCAGGAGGCTG	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.382G>T	chr17.hg19:g.80320408G>T	ENSP00000331500:p.Glu128*	77.0	0.0	.		91.0	37.0	.	NM_207459		Nonsense_Mutation	SNP	ENST00000333437.4	hg19	CCDS11809.1	.	.	.	.	.	.	.	.	.	.	G	17.05	3.290355	0.59976	.	.	ENSG00000182459	ENST00000333437	.	.	.	3.79	1.79	0.24919	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999993	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-12.0754	6.2075	0.20610	0.2189:0.0:0.7811:0.0	.	.	.	.	X	128	.	ENSP00000331500:E128X	E	+	1	0	TEX19	77913697	0.004000	0.15560	0.106000	0.21319	0.007000	0.05969	0.207000	0.17395	0.560000	0.29169	0.563000	0.77884	GAG	.	.	.	none		0.617	TEX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256331.1	NM_207459		T	80320408	G	T	80320408	4	4	243	1	0	0	0	0	0	1	0	0	15792	1175	41	4	384	4	TEX19	17	80320408	Nonsense_Mutation	SNP	G	TCGA-SX-A71U-01A-12D-A33Q-10	492622	80320408	874802	86	15018											
NEDD4L	23327	hgsc.bcm.edu	37	chr18	56050535	56050535	+	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	taatggtcacaaatgaaaacAaaagggaatatatcgagtat	20	9	8	4	1	1	1	1	1	0	0	2	3	1	2	0	2	1	1	0	2	10	4			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr18:56050535A>T	ENST00000400345.3	+	25	2693	c.2410A>T	c.(2410-2412)Aaa>Taa	p.K804*	NEDD4L_ENST00000431212.2_Nonsense_Mutation_p.K683*|NEDD4L_ENST00000357895.5_Nonsense_Mutation_p.K796*|NEDD4L_ENST00000586263.1_Nonsense_Mutation_p.K776*|NEDD4L_ENST00000256830.9_Nonsense_Mutation_p.K700*|NEDD4L_ENST00000435432.2_Nonsense_Mutation_p.K663*|NEDD4L_ENST00000456173.2_Nonsense_Mutation_p.K663*|NEDD4L_ENST00000382850.4_Nonsense_Mutation_p.K784*|NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000456986.1_Nonsense_Mutation_p.K683*|NEDD4L_ENST00000356462.6_Nonsense_Mutation_p.K740*|NEDD4L_ENST00000256832.7_Nonsense_Mutation_p.K664*	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	804	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						AAATGAAAACAAAAGGGAATA	0.343																																					p.K804X		Atlas-SNP	.											.	NEDD4L	126	.	0			c.A2410T						PASS	.						112	103	106					18																	56050535		1845	4049	5894	SO:0001587	stop_gained	23327	exon25			GAAAACAAAAGGG	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.2410A>T	chr18.hg19:g.56050535A>T	ENSP00000383199:p.Lys804*	61.0	0.0	.		62.0	22.0	.	NM_001144967	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Nonsense_Mutation	SNP	ENST00000400345.3	hg19	CCDS45872.1	.	.	.	.	.	.	.	.	.	.	A	45	11.885282	0.99613	.	.	ENSG00000049759	ENST00000400345;ENST00000382850;ENST00000356462;ENST00000256830;ENST00000256832;ENST00000456986;ENST00000357895;ENST00000435432;ENST00000456173;ENST00000431212	.	.	.	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.9462	0.79796	1.0:0.0:0.0:0.0	.	.	.	.	X	804;784;740;700;664;683;796;663;663;683	.	ENSP00000256830:K700X	K	+	1	0	NEDD4L	54201515	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.681000	0.91228	2.242000	0.73789	0.528000	0.53228	AAA	.	.	.	none		0.343	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1			T	56050535	A	T	56050535	4	4	243	1	0	0	0	0	0	1	0	0	10318	131	5	5	2536	5	NEDD4L	18	56050535	Nonsense_Mutation	SNP	A	TCGA-SX-A71U-01A-12D-A33Q-10		56050535	22026713	87	15019											
ARRDC5	645432	hgsc.bcm.edu	37	chr19	4891365	4891365	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctgtccagccgagaccgcCgctctgcactgggcgtgaag	6	7	14	14	4	1	2	0	1	1	1	2	3	2	2	4	1	3	3	4	1	1	0			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr19:4891365C>T	ENST00000381781.2	-	3	721	c.722G>A	c.(721-723)cGg>cAg	p.R241Q	AC027319.1_ENST00000408608.1_RNA	NM_001080523.1	NP_001073992.1	A6NEK1	ARRD5_HUMAN	arrestin domain containing 5	241										endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0257)		CCGAGACCGCCGCTCTGCACT	0.587																																					p.R241Q		Atlas-SNP	.											.	ARRDC5	19	.	0			c.G722A						PASS	.						62	72	68					19																	4891365		2088	4212	6300	SO:0001583	missense	645432	exon3			GACCGCCGCTCTG		CCDS45929.1	19p13.3	2007-10-05				ENSG00000205784			31407	protein-coding gene	gene with protein product						12886014	Standard	NM_001080523		Approved		uc002mbm.3	A6NEK1		ENST00000381781.2:c.722G>A	chr19.hg19:g.4891365C>T	ENSP00000371200:p.Arg241Gln	21.0	0.0	.		24.0	9.0	.	NM_001080523		Missense_Mutation	SNP	ENST00000381781.2	hg19	CCDS45929.1	.	.	.	.	.	.	.	.	.	.	C	11.90	1.777714	0.31502	.	.	ENSG00000205784	ENST00000381781	T	0.18960	2.18	4.92	1.6	0.23607	Immunoglobulin E-set (1);Arrestin-like, C-terminal (1);	1.356790	0.05157	N	0.497009	T	0.15609	0.0376	L	0.29908	0.895	0.19300	N	0.999972	B	0.32396	0.369	B	0.23419	0.046	T	0.28933	-1.0028	10	0.44086	T	0.13	-14.9505	8.5502	0.33447	0.0:0.7431:0.0:0.2569	.	241	A6NEK1	ARRD5_HUMAN	Q	241	ENSP00000371200:R241Q	ENSP00000371200:R241Q	R	-	2	0	ARRDC5	4842365	0.028000	0.19301	0.021000	0.16686	0.004000	0.04260	-0.061000	0.11693	0.339000	0.23719	-0.140000	0.14226	CGG	.	.	.	none		0.587	ARRDC5-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450443.1	XM_292803		T	4891365	C	T	4891365	3	4	243	1	0	0	0	0	1	0	0	0	986	652	23	1	310	1	ARRDC5	19	4891365	Missense_Mutation	SNP	C	TCGA-SX-A71U-01A-12D-A33Q-10		4891365	54237618	88	15020											
TSSK6	51079	hgsc.bcm.edu	37	chr19	19625679	19625679	+	5'Flank	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	tacttcttggggtcgtagggGatgcccaggagcacctcggg	6	9	16	10	2	1	0	0	0	1	0	3	2	1	2	2	6	3	2	2	6	2	4			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr19:19625679G>T	ENST00000507754.4	+	0	0				NDUFA13_ENST00000252576.5_5'Flank|NDUFA13_ENST00000428459.2_5'Flank|CTC-260F20.3_ENST00000555938.1_5'Flank|TSSK6_ENST00000360913.3_Silent_p.I186I|TSSK6_ENST00000585580.3_Silent_p.I186I|NDUFA13_ENST00000503283.1_5'Flank|YJEFN3_ENST00000608404.1_5'Flank|NDUFA13_ENST00000512771.3_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						GGTCGTAGGGGATGCCCAGGA	0.662																																					p.I186I		Atlas-SNP	.											.	TSSK6	32	.	0			c.C558A						PASS	.						50	37	42					19																	19625679		2203	4300	6503	SO:0001631	upstream_gene_variant	83983	exon1			GTAGGGGATGCCC	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		chr19.hg19:g.19625679G>T	Exception_encountered	14.0	0.0	.		21.0	7.0	.	NM_032037	B4DF76|K7EK58|Q6PKI0|Q9H2L3|Q9Y327	Silent	SNP	ENST00000507754.4	hg19	CCDS12404.2																																																																																			.	.	.	none		0.662	NDUFA13-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367916.6	NM_015965		T	19625679	G	T	19625679	1	4	243	0	1	0	0	0	0	0	0	0	16684	1164	41	4		4	TSSK6	19	19625679	5'Flank	SNP	G	TCGA-SX-A71U-01A-12D-A33Q-10	14734314	19625679	39503304	89	15021											
ZNF681	148213	hgsc.bcm.edu	37	chr19	23927682	23927682	+	Missense_Mutation	SNP	T	T	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	ttcttcacatatgtacgattTctctccaatatgaattcttt	10	19	3	9	1	4	1	1	1	3	0	6	2	5	1	1	0	1	1	1	0	5	8			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr19:23927682T>G	ENST00000402377.3	-	4	811	c.670A>C	c.(670-672)Aaa>Caa	p.K224Q	ZNF681_ENST00000395385.3_Missense_Mutation_p.K155Q	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	224				K -> R (in Ref. 1; BAG53769). {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)|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)				ATGTACGATTTCTCTCCAATA	0.323																																					p.K224Q		Atlas-SNP	.											.	ZNF681	76	.	0			c.A670C						PASS	.						48	47	47					19																	23927682		2203	4299	6502	SO:0001583	missense	148213	exon4			ACGATTTCTCTCC	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.670A>C	chr19.hg19:g.23927682T>G	ENSP00000384000:p.Lys224Gln	34.0	0.0	.		31.0	13.0	.	NM_138286	B3KVF7	Missense_Mutation	SNP	ENST00000402377.3	hg19	CCDS12414.2	.	.	.	.	.	.	.	.	.	.	.	14.55	2.569056	0.45798	.	.	ENSG00000196172	ENST00000402377;ENST00000395385	T;T	0.54071	0.59;2.06	1.62	1.62	0.23740	Zinc finger, C2H2 (1);	.	.	.	.	T	0.69513	0.3119	M	0.88906	2.99	0.22305	N	0.999218	D	0.71674	0.998	D	0.67103	0.949	T	0.56817	-0.7916	9	0.87932	D	0	.	3.4119	0.07361	0.0:0.235:0.0:0.765	.	224	Q96N22	ZN681_HUMAN	Q	224;155	ENSP00000384000:K224Q;ENSP00000378783:K155Q	ENSP00000378783:K155Q	K	-	1	0	ZNF681	23719522	0.841000	0.29509	0.004000	0.12327	0.011000	0.07611	2.723000	0.47277	0.722000	0.32252	0.372000	0.22366	AAA	.	.	.	none		0.323	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286		G	23927682	T	G	23927682	3	3	243	1	0	0	0	0	1	0	0	0	18100	1792	62	5	1271	5	ZNF681	19	23927682	Missense_Mutation	SNP	T	TCGA-SX-A71U-01A-12D-A33Q-10	4302003	23927682	35201301	90	15022											
CD3EAP	10849	hgsc.bcm.edu	37	chr19	45912507	45912507	+	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	accaagaagaagaagaagaaGaaagagagaggtcacacagt	22	2	12	5	0	1	8	1	0	0	8	1	9	1	8	1	1	0	0	1	1	7	0	rs200430601		TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr19:45912507G>A	ENST00000309424.3	+	3	1769	c.1281G>A	c.(1279-1281)aaG>aaA	p.K427K	ERCC1_ENST00000300853.3_3'UTR|ERCC1_ENST00000588738.1_5'Flank|PPP1R13L_ENST00000418234.2_5'Flank|CD3EAP_ENST00000589804.1_Silent_p.K429K|ERCC1_ENST00000423698.2_3'UTR	NM_012099.1	NP_036231.1	O15446	RPA34_HUMAN	CD3e molecule, epsilon associated protein	427	Poly-Lys.				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)		agaagaagaagaaagagaGAG	0.582																																					p.K427K		Atlas-SNP	.											.	CD3EAP	27	.	0			c.G1281A						PASS	.						41	49	46					19																	45912507		2201	4296	6497	SO:0001819	synonymous_variant	10849	exon3			GAAGAAGAAAGAG	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.1281G>A	chr19.hg19:g.45912507G>A		90.0	0.0	.		85.0	30.0	.	NM_012099	Q32N11|Q7Z5U2|Q9UPF6	Silent	SNP	ENST00000309424.3	hg19	CCDS12661.1																																																																																			.	.	.	none		0.582	CD3EAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459538.1	NM_012099		A	45912507	G	A	45912507	2	1	243	1	0	0	0	0	0	0	0	1	3014	933	33	2		2	CD3EAP	19	45912507	Silent	SNP	G	TCGA-SX-A71U-01A-12D-A33Q-10	21984825	45912507	13216476	91	15023											
ZFP64	55734	hgsc.bcm.edu	37	chr20	50701317	50701318	+	Frame_Shift_Ins	INS	-	-	G																															gccctctgcgtcacgatcttINSggccacgtgctgggagctgc																										TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr20:50701317_50701318insG	ENST00000361387.2	-	9	1776_1777	c.1716_1717insC	c.(1714-1719)gccaagfs	p.K573fs	ZFP64_ENST00000371523.4_Frame_Shift_Ins_p.K354fs|ZFP64_ENST00000371518.2_Intron	NM_199427.2	NP_955459.2	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	418					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						GTCACGATCTTGGCCACGTGCT	0.629																																					p.K573fs		Atlas-INDEL	.											.	ZFP64	240	.	0			c.1717_1718insC						PASS	.																																			SO:0001589	frameshift_variant	55734	exon9			.	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"Zinc fingers, C2H2-type"	15940	protein-coding gene	gene with protein product			"zinc finger protein 338", "zinc finger protein 64 homolog (mouse)", "zinc finger protein 64"	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000361387.2:c.1717dupC	chr20.hg19:g.50701319_50701319dupG	ENSP00000355179:p.Lys573fs	52.0	0.0	0		27.0	12.0	0.444444	NM_199427	Q9NTS7|Q9NVH4	Frame_Shift_Ins	INS	ENST00000361387.2	hg19	CCDS13439.1																																																																																			.	.	.	none		0.629	ZFP64-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079743.2	NM_018197		G	50701318	-	G	50701317	7	5	243	1	0	1	1	0	0	0	0	0	17664	1821	63	0	224	0	ZFP64	20	50701317	Frame_Shift_Ins	INS	-	TCGA-SX-A71U-01A-12D-A33Q-10		50701317	12324203	92	15024											
NFAM1	150372	hgsc.bcm.edu	37	chr22	42781205	42781205	+	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	caggttaagttcgccatcatCttcgaatctatgcggtctct	8	14	8	11	3	4	0	1	0	3	0	7	1	4	0	1	2	1	2	1	2	3	4			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chr22:42781205C>A	ENST00000329021.5	-	6	812	c.775G>T	c.(775-777)Gat>Tat	p.D259Y		NM_145912.5	NP_666017.1	Q8NET5	NFAM1_HUMAN	NFAT activating protein with ITAM motif 1	259					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						TCGCCATCATCTTCGAATCTA	0.493																																					p.D259Y		Atlas-SNP	.											.	NFAM1	12	.	0			c.G775T						PASS	.						121	127	125					22																	42781205		2203	4300	6503	SO:0001583	missense	150372	exon6			CATCATCTTCGAA	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.775G>T	chr22.hg19:g.42781205C>A	ENSP00000333680:p.Asp259Tyr	62.0	0.0	.		37.0	14.0	.	NM_145912	B0QYD0|Q20WL2|Q5JZ96|Q8IUY8|Q8TEM8	Missense_Mutation	SNP	ENST00000329021.5	hg19	CCDS14034.1	.	.	.	.	.	.	.	.	.	.	C	14.10	2.434821	0.43224	.	.	ENSG00000235568	ENST00000329021	T	0.46819	0.86	4.38	2.25	0.28309	.	0.629307	0.12632	U	0.452079	T	0.57489	0.2057	L	0.50333	1.59	0.09310	N	1	D	0.76494	0.999	D	0.66979	0.948	T	0.42599	-0.9442	10	0.72032	D	0.01	-1.9549	7.6212	0.28187	0.0:0.7942:0.0:0.2058	.	259	Q8NET5	NFAM1_HUMAN	Y	259	ENSP00000333680:D259Y	ENSP00000333680:D259Y	D	-	1	0	NFAM1	41111149	0.000000	0.05858	0.005000	0.12908	0.002000	0.02628	0.206000	0.17375	0.554000	0.29061	0.561000	0.74099	GAT	.	.	.	none		0.493	NFAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320541.1	NM_145912		A	42781205	C	A	42781205	3	1	243	1	0	0	0	0	1	0	0	0	10365	913	32	4	41	4	NFAM1	22	42781205	Missense_Mutation	SNP	C	TCGA-SX-A71U-01A-12D-A33Q-10		42781205	8523361	93	15025											
CXorf22	170063	hgsc.bcm.edu	37	chrX	35994031	35994032	+	Splice_Site	INS	-	-	T																															tctatttgtccagctaaaggINStaacagtttattgtttgttt																										TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chrX:35994031_35994032insT	ENST00000297866.5	+	15	2779		c.e15+1			NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22											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						CCAGCTAAAGGTAACAGTTTAT	0.332																																					.		Pindel	.											.	CXorf22	272	.	0			c.2713+1->T						PASS	.																																			SO:0001630	splice_region_variant	170063	exon15			.	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.2713+1->T	chrX.hg19:g.35994032_35994032dupT		39.0	0.0	.		35.0	18.0	0.514	NM_152632	Q5JRM8|Q8N6X8	Splice_Site	INS	ENST00000297866.5	hg19	CCDS14237.2																																																																																			.	.	.	none		0.332	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056216.2	NM_152632	Intron	T	35994032	-	T	35994031	8	5	243	1	0	1	1	0	0	0	1	0	4104	1275	44	0	2772	0	CXorf22	23	35994031	Splice_Site	INS	-	TCGA-SX-A71U-01A-12D-A33Q-10		35994031	119276529	94	15026											
CXorf38	159013	hgsc.bcm.edu	37	chrX	40496278	40496278	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctgttctattctggagtatActgccacaatctctgggatg	8	14	9	10	0	3	0	0	0	3	0	4	2	3	2	2	2	2	2	2	2	4	5			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chrX:40496278A>G	ENST00000327877.5	-	4	628	c.602T>C	c.(601-603)gTa>gCa	p.V201A	CXorf38_ENST00000378426.1_Missense_Mutation_p.V82A|CXorf38_ENST00000378421.1_Missense_Mutation_p.V82A|CXorf38_ENST00000440784.2_Missense_Mutation_p.V116A	NM_144970.2	NP_659407.1	Q8TB03	CX038_HUMAN	chromosome X open reading frame 38	201										NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	12						TCTGGAGTATACTGCCACAAT	0.353																																					p.V201A		Atlas-SNP	.											.	CXorf38	29	.	0			c.T602C						PASS	.						78	73	75					X																	40496278		2202	4300	6502	SO:0001583	missense	159013	exon4			GAGTATACTGCCA	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.602T>C	chrX.hg19:g.40496278A>G	ENSP00000330488:p.Val201Ala	98.0	0.0	.		86.0	66.0	.	NM_144970	B3KW28|D3DWB5|Q5JPF5|Q8N941	Missense_Mutation	SNP	ENST00000327877.5	hg19	CCDS14253.1	.	.	.	.	.	.	.	.	.	.	A	3.196	-0.164851	0.06502	.	.	ENSG00000185753	ENST00000378426;ENST00000327877;ENST00000378421;ENST00000440784	T;T;T;T	0.39056	1.1;1.1;1.1;1.1	4.84	-0.221	0.13126	.	0.908091	0.09387	N	0.809142	T	0.22399	0.0540	N	0.22421	0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.28459	-1.0043	10	0.11182	T	0.66	-0.1447	4.6716	0.12692	0.3284:0.0:0.4847:0.1869	.	116;201	E7EN46;Q8TB03	.;CX038_HUMAN	A	82;201;82;116	ENSP00000367683:V82A;ENSP00000330488:V201A;ENSP00000367677:V82A;ENSP00000400019:V116A	ENSP00000330488:V201A	V	-	2	0	CXorf38	40381222	0.001000	0.12720	0.010000	0.14722	0.944000	0.59088	1.064000	0.30579	-0.051000	0.13334	0.345000	0.21793	GTA	.	.	.	none		0.353	CXorf38-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060685.3	NM_144970		G	40496278	A	G	40496278	3	3	243	1	0	0	0	0	1	0	0	0	4109	391	14	3	369	3	CXorf38	23	40496278	Missense_Mutation	SNP	A	TCGA-SX-A71U-01A-12D-A33Q-10	4502247	40496278	114774282	95	15027											
TSPYL2	64061	hgsc.bcm.edu	37	chrX	53112145	53112145	+	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	tgtagcgcagtggggtgggcGccccagaggttagttgaccc	6	8	17	10	2	0	2	0	1	0	1	0	2	0	2	3	4	1	4	3	4	2	3			TCGA-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chrX:53112145G>C	ENST00000375442.4	+	1	597	c.465G>C	c.(463-465)gcG>gcC	p.A155A		NM_022117.3	NP_071400.1	Q9H2G4	TSYL2_HUMAN	TSPY-like 2	155					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						TGGGGTGGGCGCCCCAGAGGT	0.582																																					p.A155A		Atlas-SNP	.											.	TSPYL2	53	.	0			c.G465C						PASS	.						25	24	24					X																	53112145		2202	4299	6501	SO:0001819	synonymous_variant	64061	exon1			GTGGGCGCCCCAG	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.465G>C	chrX.hg19:g.53112145G>C		77.0	0.0	.		54.0	43.0	.	NM_022117	O94799|Q96DG7|Q9BZW6	Silent	SNP	ENST00000375442.4	hg19	CCDS14350.1																																																																																			.	.	.	none		0.582	TSPYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056718.1	NM_022117		C	53112145	G	C	53112145	2	2	243	1	0	0	0	0	0	0	0	1	16672	1074	38	4		4	TSPYL2	23	53112145	Silent	SNP	G	TCGA-SX-A71U-01A-12D-A33Q-10	12615867	53112145	102158415	96	15028											
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-SX-A71U-01A-12D-A33Q-10	TCGA-SX-A71U-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3d451356-8c58-451d-a6cf-223e76cae191	2c6bb397-d986-49b1-b1dc-1151c8aae19f	g.chrX:66765164A>T	ENST00000374690.3	+	1	700	c.176A>T	c.(175-177)cAg>cTg	p.Q59L	AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.Q59L|AR_ENST00000504326.1_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	chrX.hg19:g.66765164A>T	ENSP00000363822:p.Gln59Leu	71.0	0.0	.		66.0	13.0	.	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	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	243	1	0	0	0	0	1	0	0	0	836	188	7	5	178	5	AR	23	66765164	Missense_Mutation	SNP	A	TCGA-SX-A71U-01A-12D-A33Q-10	13653019	66765164	88505396	97	15029											
NIPAL3	57185	hgsc.bcm.edu	37	chr1	24768627	24768627	+	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	atggtggctgggcctgttccTgatgcttctgggcgagctgg	3	12	17	9	1	1	1	0	1	1	0	2	2	2	1	2	5	2	4	2	5	0	2			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr1:24768627T>A	ENST00000374399.4	+	4	613	c.245T>A	c.(244-246)cTg>cAg	p.L82Q	NIPAL3_ENST00000358028.4_Missense_Mutation_p.L82Q|NIPAL3_ENST00000428131.1_Missense_Mutation_p.L82Q|NIPAL3_ENST00000003912.3_5'UTR|NIPAL3_ENST00000339255.2_Missense_Mutation_p.L82Q	NM_020448.4	NP_065181.1	Q6P499	NPAL3_HUMAN	NIPA-like domain containing 3	82						integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|skin(1)	14						GGCCTGTTCCTGATGCTTCTG	0.582																																					p.L82Q		Atlas-SNP	.											.	NIPAL3	36	.	0			c.T245A						PASS	.						125	113	117					1																	24768627		2203	4300	6503	SO:0001583	missense	57185	exon4			TGTTCCTGATGCT	BX640883	CCDS30631.1	1p36.12-p35.1	2009-03-24		2009-03-24	ENSG00000001461	ENSG00000001461			25233	protein-coding gene	gene with protein product				NPAL3		8619474, 9110174	Standard	NM_020448		Approved	DJ462O23.2	uc001bjh.3	Q6P499	OTTHUMG00000003299	ENST00000374399.4:c.245T>A	chr1.hg19:g.24768627T>A	ENSP00000363520:p.Leu82Gln	56.0	0.0	.		51.0	16.0	.	NM_020448	A2A298|Q6MZT9|Q9BVE6	Missense_Mutation	SNP	ENST00000374399.4	hg19	CCDS30631.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.499788	0.85176	.	.	ENSG00000001461	ENST00000374399;ENST00000358028;ENST00000339255;ENST00000428131	T;T;T;T	0.71222	-0.55;-0.55;-0.55;-0.55	5.22	4.09	0.47781	.	0.139109	0.49305	D	0.000159	D	0.85435	0.5696	M	0.89601	3.045	0.54753	D	0.999985	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.86798	0.1990	10	0.72032	D	0.01	-13.663	11.2516	0.49028	0.0:0.0724:0.0:0.9276	.	82;82;82	Q6P499-3;Q6P499;A6NN97	.;NPAL3_HUMAN;.	Q	82	ENSP00000363520:L82Q;ENSP00000350722:L82Q;ENSP00000343549:L82Q;ENSP00000406509:L82Q	ENSP00000343549:L82Q	L	+	2	0	NIPAL3	24641214	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.253000	0.78320	0.911000	0.36747	0.533000	0.62120	CTG	.	.	.	none		0.582	NIPAL3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276996.1	NM_020448		A	24768627	T	A	24768627	3	1	244	1	0	0	0	0	1	0	0	0	10433	1580	55	5	255	5	NIPAL3	1	24768627	Missense_Mutation	SNP	T	TCGA-SX-A71V-01A-11D-A33Q-10		24768627	224481994	1	15030											
TNNI3K	100526835	hgsc.bcm.edu	37	chr1	74808658	74808658	+	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	tgttaatatctatggagataCccccttacacctgtgagtat	11	14	7	9	0	1	2	0	1	1	1	1	3	1	2	3	1	2	2	3	1	6	6			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr1:74808658C>A	ENST00000370899.3	+	10	1155	c.1118C>A	c.(1117-1119)aCc>aAc	p.T373N	TNNI3K_ENST00000326637.3_Missense_Mutation_p.T272N|FPGT-TNNI3K_ENST00000370895.1_Missense_Mutation_p.T373N|FPGT-TNNI3K_ENST00000557284.2_Missense_Mutation_p.T386N|TNNI3K_ENST00000370891.2_Missense_Mutation_p.T373N|RP11-439H8.4_ENST00000415549.2_RNA	NM_001199327.1	NP_001186256			FPGT-TNNI3K readthrough																		TATGGAGATACCCCCTTACAC	0.363																																					p.T373N		Atlas-SNP	.											.,1	.	.	.	0			c.C1118A						PASS	.						171	158	162					1																	74808658		2203	4300	6503	SO:0001583	missense	100526835	exon10			GAGATACCCCCTT			1p31.3	2014-03-14			ENSG00000259030	ENSG00000259030			42952	other	readthrough							Standard	NM_001112808		Approved		uc001dge.2		OTTHUMG00000166281	ENST00000370899.3:c.1118C>A	chr1.hg19:g.74808658C>A	ENSP00000359936:p.Thr373Asn	183.0	0.0	.		140.0	55.0	.	NM_001199327		Missense_Mutation	SNP	ENST00000370899.3	hg19		.	.	.	.	.	.	.	.	.	.	C	22.9	4.352277	0.82132	.	.	ENSG00000259030;ENSG00000259030;ENSG00000259030;ENSG00000116783;ENSG00000116783	ENST00000370899;ENST00000370895;ENST00000557284;ENST00000370891;ENST00000326637	T;T;T;T;T	0.75050	-0.83;-0.83;-0.9;-0.9;-0.83	5.77	5.77	0.91146	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	D	0.88396	0.6425	M	0.89785	3.06	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;0.999;0.996	D	0.89504	0.3766	10	0.72032	D	0.01	.	19.9928	0.97374	0.0:1.0:0.0:0.0	.	272;373;373;373	Q59H18;Q59H18-1;Q59H18-4;Q59H18-3	TNI3K_HUMAN;.;.;.	N	373;373;373;373;272	ENSP00000359936:T373N;ENSP00000359932:T373N;ENSP00000450895:T373N;ENSP00000359928:T373N;ENSP00000322251:T272N	ENSP00000322251:T272N	T	+	2	0	RP11-653A5.2;AC093158.1	74581246	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	5.551000	0.67274	2.745000	0.94114	0.650000	0.86243	ACC	.	.	.	none		0.363	FPGT-TNNI3K-003	NOVEL	basic|appris_candidate|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000026438.3			A	74808658	C	A	74808658	3	1	244	1	0	0	0	0	1	0	0	0	16341	507	18	4	1200	4	TNNI3K	1	74808658	Missense_Mutation	SNP	C	TCGA-SX-A71V-01A-11D-A33Q-10	50040031	74808658	174441963	2	15031											
WNT2B	7482	hgsc.bcm.edu	37	chr1	113058824	113058824	+	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	gggtagtccacgctattactCgcgcctgtagccagggtgaa	8	9	13	11	3	0	1	0	1	0	0	2	1	1	1	3	2	2	3	3	2	5	4			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr1:113058824C>A	ENST00000369684.4	+	3	951	c.466C>A	c.(466-468)Cgc>Agc	p.R156S	WNT2B_ENST00000256640.5_Missense_Mutation_p.R64S|WNT2B_ENST00000478360.1_3'UTR|RP4-671G15.2_ENST00000608357.1_RNA|WNT2B_ENST00000369686.5_Missense_Mutation_p.R137S	NM_024494.2	NP_078613.1	Q93097	WNT2B_HUMAN	wingless-type MMTV integration site family, member 2B	156					canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cellular response to starvation (GO:0009267)|chondrocyte differentiation (GO:0002062)|cornea development in camera-type eye (GO:0061303)|forebrain regionalization (GO:0021871)|hematopoietic stem cell proliferation (GO:0071425)|iris morphogenesis (GO:0061072)|lens development in camera-type eye (GO:0002088)|lung induction (GO:0060492)|male gonad development (GO:0008584)|mesenchymal-epithelial cell signaling (GO:0060638)|neuron differentiation (GO:0030182)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(4)|ovary(2)|skin(1)|stomach(1)	18	Lung SC(450;0.246)	all_cancers(81;7.31e-07)|all_epithelial(167;4.59e-06)|all_lung(203;2.56e-05)|Lung NSC(69;4.38e-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)		CGCTATTACTCGCGCCTGTAG	0.562																																					p.R156S		Atlas-SNP	.											.	WNT2B	51	.	0			c.C466A						PASS	.						137	126	130					1																	113058824		2203	4300	6503	SO:0001583	missense	7482	exon3			ATTACTCGCGCCT	AB045116	CCDS847.1, CCDS846.1	1p13	2008-07-18			ENSG00000134245	ENSG00000134245		"Wingless-type MMTV integration sites"	12781	protein-coding gene	gene with protein product	"XWNT2, Xenopus, homolog of", "wingless-type MMTV integration site family, member 13"	601968		WNT13		8761309, 10944466	Standard	NM_024494		Approved	XWNT2	uc001ecb.3	Q93097	OTTHUMG00000011157	ENST00000369684.4:c.466C>A	chr1.hg19:g.113058824C>A	ENSP00000358698:p.Arg156Ser	169.0	0.0	.		132.0	46.0	.	NM_024494	O14903|Q5TEH9|Q5TEI2|Q9HDC1|Q9HDC2	Missense_Mutation	SNP	ENST00000369684.4	hg19	CCDS847.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.562764	0.86335	.	.	ENSG00000134245	ENST00000256640;ENST00000369686;ENST00000369684	T;T;T	0.77358	-1.09;-1.09;-1.09	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.89504	0.6734	M	0.90309	3.105	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.987	D	0.90387	0.4392	10	0.59425	D	0.04	.	19.2708	0.94008	0.0:1.0:0.0:0.0	.	156;137	Q93097;Q93097-2	WNT2B_HUMAN;.	S	64;137;156	ENSP00000256640:R64S;ENSP00000358700:R137S;ENSP00000358698:R156S	ENSP00000256640:R64S	R	+	1	0	WNT2B	112860347	0.939000	0.31865	0.998000	0.56505	0.953000	0.61014	2.076000	0.41548	2.644000	0.89710	0.561000	0.74099	CGC	.	.	.	none		0.562	WNT2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030692.1	NM_004185		A	113058824	C	A	113058824	3	1	244	1	0	0	0	0	1	0	0	0	17399	884	31	4	609	4	WNT2B	1	113058824	Missense_Mutation	SNP	C	TCGA-SX-A71V-01A-11D-A33Q-10	38250166	113058824	136191797	3	15032											
PGLYRP3	114771	hgsc.bcm.edu	37	chr1	153283087	153283087	+	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	tgcaagtaaataaaacttacCccaagcctggagacccagaa	17	6	7	11	0	0	2	0	0	0	2	0	3	0	2	4	1	4	2	4	1	8	3	rs375220818		TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr1:153283087C>T	ENST00000290722.1	-	1	107	c.55G>A	c.(55-57)Gat>Aat	p.D19N		NM_052891.1	NP_443123.1	Q96LB9	PGRP3_HUMAN	peptidoglycan recognition protein 3	19					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(1)|liver(1)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	28	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			TAAAACTTACCCCAAGCCTGG	0.493																																					p.D19N		Atlas-SNP	.											.	PGLYRP3	55	.	0			c.G55A						PASS	.						149	154	152					1																	153283087		2203	4300	6503	SO:0001630	splice_region_variant	114771	exon1			ACTTACCCCAAGC	AY035376	CCDS1035.1	1q21	2008-02-05			ENSG00000159527	ENSG00000159527			30014	protein-coding gene	gene with protein product	"peptidoglycan recognition protein I alpha precursor"	608197				11461926	Standard	NM_052891		Approved	PGRPIA, PGLYRPIalpha, PGRP-Ialpha	uc001fbn.1	Q96LB9	OTTHUMG00000014044	ENST00000290722.1:c.55+1G>A	chr1.hg19:g.153283087C>T		196.0	0.0	.		129.0	47.0	.	NM_052891	A1A4U8|Q5SY65	Missense_Mutation	SNP	ENST00000290722.1	hg19	CCDS1035.1	.	.	.	.	.	.	.	.	.	.	C	11.31	1.601956	0.28534	.	.	ENSG00000159527	ENST00000290722	T	0.07444	3.19	3.22	1.35	0.21983	N-acetylmuramoyl-L-alanine amidase domain (1);	0.794118	0.10474	N	0.670413	T	0.02380	0.0073	L	0.48642	1.525	0.21445	N	0.999685	P	0.37688	0.605	B	0.35413	0.202	T	0.44559	-0.9320	9	.	.	.	.	5.3598	0.16081	0.0:0.735:0.0:0.265	.	19	Q96LB9	PGRP3_HUMAN	N	19	ENSP00000290722:D19N	.	D	-	1	0	PGLYRP3	151549711	0.958000	0.32768	0.703000	0.30354	0.007000	0.05969	2.781000	0.47750	0.374000	0.24650	-0.136000	0.14681	GAT	.	.	.	none		0.493	PGLYRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039488.1	NM_052891	Missense_Mutation	T	153283087	C	T	153283087	5	4	244	1	0	0	0	0	0	0	1	0	11802	637	22	2	998	2	PGLYRP3	1	153283087	Splice_Site	SNP	C	TCGA-SX-A71V-01A-11D-A33Q-10	40224263	153283087	95967534	4	15033											
NUP210L	91181	hgsc.bcm.edu	37	chr1	153974267	153974267	+	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	tcttatctccccgatatcttGtttgtggctaagaaccaatt	9	16	6	10	1	3	1	0	0	3	1	4	2	3	1	3	1	1	2	3	1	5	6			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr1:153974267G>C	ENST00000368559.3	-	36	5196	c.5125C>G	c.(5125-5127)Caa>Gaa	p.Q1709E	NUP210L_ENST00000368553.1_Intron|NUP210L_ENST00000271854.3_Intron	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	1709					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)			CCGATATCTTGTTTGTGGCTA	0.413																																					p.Q1709E		Atlas-SNP	.											.	NUP210L	181	.	0			c.C5125G						PASS	.						238	220	225					1																	153974267		1876	4114	5990	SO:0001583	missense	91181	exon36			TATCTTGTTTGTG	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.5125C>G	chr1.hg19:g.153974267G>C	ENSP00000357547:p.Gln1709Glu	146.0	0.0	.		99.0	30.0	.	NM_207308	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Missense_Mutation	SNP	ENST00000368559.3	hg19	CCDS41399.1	.	.	.	.	.	.	.	.	.	.	G	1.526	-0.545710	0.04024	.	.	ENSG00000143552	ENST00000368559	T	0.04917	3.53	4.28	-0.146	0.13432	.	0.968910	0.08488	N	0.938435	T	0.01765	0.0056	L	0.44542	1.39	0.09310	N	1	B	0.13594	0.008	B	0.14578	0.011	T	0.46652	-0.9176	10	0.28530	T	0.3	-35.7249	7.2674	0.26237	0.0:0.2873:0.3793:0.3334	.	1709	Q5VU65	P210L_HUMAN	E	1709	ENSP00000357547:Q1709E	ENSP00000357547:Q1709E	Q	-	1	0	NUP210L	152240891	0.768000	0.28519	0.000000	0.03702	0.250000	0.25880	1.989000	0.40707	-0.207000	0.10187	0.561000	0.74099	CAA	.	.	.	none		0.413	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308		C	153974267	G	C	153974267	3	2	244	1	0	0	0	0	1	0	0	0	10768	1386	48	4	561	4	NUP210L	1	153974267	Missense_Mutation	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	691180	153974267	95276354	5	15034											
HAX1	10456	hgsc.bcm.edu	37	chr1	154247707	154247707	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatcctatttcaagagcatcTctgtgaccaagatcactaaa	15	11	5	10	0	3	3	2	1	1	2	5	3	4	3	2	0	1	1	2	0	6	3			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr1:154247707T>C	ENST00000328703.7	+	5	847	c.634T>C	c.(634-636)Tct>Cct	p.S212P	HAX1_ENST00000532105.1_Missense_Mutation_p.S84P|HAX1_ENST00000483970.2_Missense_Mutation_p.S220P|HAX1_ENST00000457918.2_Missense_Mutation_p.S164P	NM_006118.3	NP_006109.2	O00165	HAX1_HUMAN	HCLS1 associated protein X-1	212	Involved in ATP2A2 binding.|Involved in GNA13 binding.|Involved in HCLS1 binding.|Involved in PKD2 binding.|Involved in PLN binding.|Required for localization in sarcoplasmic reticulum. {ECO:0000250}.				cellular response to cytokine stimulus (GO:0071345)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of actin filament polymerization (GO:0030833)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrion degradation (GO:1903146)|regulation of protein targeting to mitochondrion (GO:1903214)	actin cytoskeleton (GO:0015629)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|lamellipodium (GO:0030027)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|sarcoplasmic reticulum (GO:0016529)|transcription factor complex (GO:0005667)	interleukin-1 binding (GO:0019966)|protein N-terminus binding (GO:0047485)			cervix(1)|endometrium(2)|large_intestine(2)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	15	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			CAAGAGCATCTCTGTGACCAA	0.488									Kostmann syndrome																												p.S212P		Atlas-SNP	.											.	HAX1	25	.	0			c.T634C						PASS	.						71	72	72					1																	154247707		2203	4300	6503	SO:0001583	missense	10456	exon5	Familial Cancer Database	Kostmann Infantile Agranulocytosis, Severe Congenital Neutropenia, Congenital Agranulocytosis	AGCATCTCTGTGA	U68566	CCDS1064.1, CCDS44230.1	1q21.3	2014-09-17			ENSG00000143575	ENSG00000143575			16915	protein-coding gene	gene with protein product	"HCLS1 (and PKD2) associated protein"	605998				9058808, 10760273	Standard	NM_006118		Approved	HS1BP1, HCLSBP1	uc001fes.3	O00165	OTTHUMG00000035978	ENST00000328703.7:c.634T>C	chr1.hg19:g.154247707T>C	ENSP00000329002:p.Ser212Pro	124.0	0.0	.		100.0	37.0	.	NM_006118	A8W4W9|A8W4X0|B4DUJ7|Q5VYD5|Q5VYD7|Q96AU4|Q9BS80	Missense_Mutation	SNP	ENST00000328703.7	hg19	CCDS1064.1	.	.	.	.	.	.	.	.	.	.	T	18.40	3.614964	0.66672	.	.	ENSG00000143575	ENST00000328703;ENST00000457918;ENST00000483970;ENST00000435087;ENST00000532105	T;T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19;-0.19	5.6	4.46	0.54185	.	0.415528	0.25233	N	0.032160	T	0.68860	0.3047	M	0.80183	2.485	0.41243	D	0.98665	D;D;D;D	0.67145	0.984;0.996;0.996;0.992	P;D;D;P	0.63703	0.828;0.917;0.917;0.882	T	0.73949	-0.3821	10	0.87932	D	0	-19.8327	9.6673	0.39992	0.1554:0.0:0.0:0.8446	.	220;186;164;212	O00165-2;O00165-3;O00165-5;O00165	.;.;.;HAX1_HUMAN	P	212;164;220;216;84	ENSP00000329002:S212P;ENSP00000411448:S164P;ENSP00000435088:S220P;ENSP00000394920:S216P;ENSP00000433951:S84P	ENSP00000329002:S212P	S	+	1	0	HAX1	152514331	1.000000	0.71417	0.996000	0.52242	0.962000	0.63368	1.873000	0.39558	0.918000	0.36919	0.460000	0.39030	TCT	.	.	.	none		0.488	HAX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087650.1	NM_006118		C	154247707	T	C	154247707	3	2	244	1	0	0	0	0	1	0	0	0	6982	1551	54	3	652	3	HAX1	1	154247707	Missense_Mutation	SNP	T	TCGA-SX-A71V-01A-11D-A33Q-10	273440	154247707	95002914	6	15035											
KIAA1614	57710	hgsc.bcm.edu	37	chr1	180910417	180910417	+	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	cccatcgttacaatccctgcAcccggtgagtccaggggccc	7	7	10	17	2	0	1	0	1	0	0	3	1	2	1	5	3	2	2	5	3	2	1			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr1:180910417A>T	ENST00000367588.4	+	7	3210	c.3155A>T	c.(3154-3156)cAc>cTc	p.H1052L	KIAA1614_ENST00000367587.1_Missense_Mutation_p.H673L|KIAA1614_ENST00000461346.1_3'UTR|RP11-46A10.5_ENST00000358073.2_RNA	NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	1052	Ser-rich.									NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						CAATCCCTGCACCCGGTGAGT	0.627																																					p.H1052L		Atlas-SNP	.											.	KIAA1614	75	.	0			c.A3155T						PASS	.						28	33	31					1																	180910417		1953	4131	6084	SO:0001583	missense	57710	exon7			CCCTGCACCCGGT	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.3155A>T	chr1.hg19:g.180910417A>T	ENSP00000356560:p.His1052Leu	154.0	0.0	.		146.0	49.0	.	NM_020950	Q5VZ45|Q9HCF8	Missense_Mutation	SNP	ENST00000367588.4	hg19	CCDS41442.1	.	.	.	.	.	.	.	.	.	.	A	13.91	2.377776	0.42105	.	.	ENSG00000135835	ENST00000367588;ENST00000367587	T;T	0.25414	2.38;1.8	5.21	-1.02	0.10135	.	0.919516	0.09186	N	0.836801	T	0.21103	0.0508	L	0.44542	1.39	0.36487	D	0.868171	B;P	0.36535	0.403;0.557	B;B	0.36186	0.12;0.219	T	0.29941	-0.9995	9	0.46703	T	0.11	0.0845	9.023	0.36211	0.582:0.0:0.418:0.0	.	673;1052	Q5VZ46-2;Q5VZ46	.;K1614_HUMAN	L	1052;673	ENSP00000356560:H1052L;ENSP00000356559:H673L	ENSP00000356559:H673L	H	+	2	0	KIAA1614	179177040	0.007000	0.16637	0.097000	0.21041	0.888000	0.51559	-0.051000	0.11885	-0.214000	0.10078	0.459000	0.35465	CAC	.	.	.	none		0.627	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531		T	180910417	A	T	180910417	3	4	244	1	0	0	0	0	1	0	0	0	8255	159	6	5	3181	5	KIAA1614	1	180910417	Missense_Mutation	SNP	A	TCGA-SX-A71V-01A-11D-A33Q-10	26662710	180910417	68340204	7	15036											
CACNA1E	777	hgsc.bcm.edu	37	chr1	181452978	181452978	+	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	aggaacccccgtgccggcctCggggcaggcggccgcctaca	6	3	15	17	5	0	0	0	0	0	0	1	1	0	1	6	6	3	1	6	6	2	1			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr1:181452978C>G	ENST00000367573.2	+	1	98	c.98C>G	c.(97-99)tCg>tGg	p.S33W	CACNA1E_ENST00000358338.5_5'UTR|CACNA1E_ENST00000367567.4_5'UTR|CACNA1E_ENST00000526775.1_Missense_Mutation_p.S33W|CACNA1E_ENST00000360108.3_Missense_Mutation_p.S33W|CACNA1E_ENST00000357570.5_5'UTR|CACNA1E_ENST00000367570.1_Missense_Mutation_p.S33W	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	33					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						GTGCCGGCCTCGGGGCAGGCG	0.662																																					p.S33W		Atlas-SNP	.											.	CACNA1E	778	.	0			c.C98G						PASS	.						44	52	49					1																	181452978		1866	4078	5944	SO:0001583	missense	777	exon1			CGGCCTCGGGGCA	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.98C>G	chr1.hg19:g.181452978C>G	ENSP00000356545:p.Ser33Trp	138.0	0.0	.		139.0	44.0	.	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	C	14.90	2.672842	0.47781	.	.	ENSG00000198216	ENST00000524607;ENST00000367570;ENST00000526775;ENST00000360108;ENST00000367573	D;D;D;D;D	0.97328	-4.34;-3.97;-3.93;-3.93;-3.97	5.67	5.67	0.87782	.	0.487945	0.18345	N	0.144056	D	0.94833	0.8331	L	0.29908	0.895	0.80722	D	1	D	0.55605	0.972	P	0.47134	0.539	D	0.94502	0.7710	10	0.87932	D	0	.	11.9558	0.52981	0.0:0.9198:0.0:0.0802	.	33	Q15878-3	.	W	33	ENSP00000432038:S33W;ENSP00000356542:S33W;ENSP00000434814:S33W;ENSP00000353222:S33W;ENSP00000356545:S33W	ENSP00000353222:S33W	S	+	2	0	CACNA1E	179719601	0.414000	0.25408	1.000000	0.80357	0.984000	0.73092	0.778000	0.26732	2.667000	0.90743	0.561000	0.74099	TCG	.	.	.	none		0.662	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		G	181452978	C	G	181452978	3	3	244	1	0	0	0	0	1	0	0	0	2544	893	31	4	100	4	CACNA1E	1	181452978	Missense_Mutation	SNP	C	TCGA-SX-A71V-01A-11D-A33Q-10	542561	181452978	67797643	8	15037											
KCNT2	343450	hgsc.bcm.edu	37	chr1	196303029	196303029	+	Frame_Shift_Del	DEL	C	C	-																															agtttcatcttctgattggtCacttagaagatcacatgttt																										TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr1:196303029delC	ENST00000294725.9	-	17	2860	c.1945delG	c.(1945-1947)gacfs	p.D649fs	KCNT2_ENST00000609185.1_Frame_Shift_Del_p.D599fs|KCNT2_ENST00000367431.4_Frame_Shift_Del_p.D599fs|KCNT2_ENST00000367433.5_Frame_Shift_Del_p.D649fs|KCNT2_ENST00000498426.1_5'UTR|KCNT2_ENST00000451324.2_Frame_Shift_Del_p.D260fs			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	649					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						TCTGATTGGTCACTTAGAAGA	0.373																																					p.D649fs		Atlas-Indel,Pindel	.											.	KCNT2	243	.	0			c.1946delA						PASS	.						144	134	137					1																	196303029		2203	4300	6503	SO:0001589	frameshift_variant	343450	exon17			.	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.1945delG	chr1.hg19:g.196303029delC	ENSP00000294725:p.Asp649fs	68.0	0.0	0		55.0	21.0	0.381818	NM_198503	Q3SY59|Q5VTN1|Q6ZMT3	Frame_Shift_Del	DEL	ENST00000294725.9	hg19	CCDS1384.1																																																																																			.	.	.	none		0.373	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503		-	196303029	C	-	196303029	7	5	244	1	0	1	0	1	0	0	0	0	8099	826	29	0	1510	0	KCNT2	1	196303029	Frame_Shift_Del	DEL	C	TCGA-SX-A71V-01A-11D-A33Q-10	14850051	196303029	52947592	9	15038											
CR1	1378	hgsc.bcm.edu	37	chr1	207715843	207715848	+	In_Frame_Del	DEL	TGGCTT	TGGCTT	-																															gtggagtttaggtgtcagccTggctttgtcatgaaaggacc																										TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	TGGCTT	TGGCTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr1:207715843_207715848delTGGCTT	ENST00000367049.4	+	13	2154_2159	c.2154_2159delTGGCTT	c.(2152-2160)cctggcttt>cct	p.GF719del	CR1_ENST00000367052.1_In_Frame_Del_p.GF719del|CR1_ENST00000367053.1_Intron|CR1_ENST00000400960.2_In_Frame_Del_p.GF719del|CR1_ENST00000367050.4_Intron|CR1_ENST00000367051.1_In_Frame_Del_p.GF269del	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	269	Sushi 11. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						GGTGTCAGCCTGGCTTTGTCATGAAA	0.49																																					p.718_720del		Pindel	.											.	CR1	354	.	0			c.2153_2158del						PASS	.																																			SO:0001651	inframe_deletion	1378	exon13			.	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.2154_2159delTGGCTT	chr1.hg19:g.207715843_207715848delTGGCTT	ENSP00000356016:p.Gly719_Phe720del	194.0	0.0	.		140.0	16.0	0.114	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	In_Frame_Del	DEL	ENST00000367049.4	hg19	CCDS44308.1																																																																																			.	.	.	none		0.49	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573		-	207715848	TGGCTT	-	207715843	7	5	244	1	0	1	0	1	0	0	0	0	3842	1567	55	0	2204	0	CR1	1	207715843	In_Frame_Del	DEL	TGGCTT	TCGA-SX-A71V-01A-11D-A33Q-10	11412814	207715843	41534778	10	15039											
CR1	1378	hgsc.bcm.edu	37	chr1	207734400	207734405	+	In_Frame_Del	DEL	TGGCTT	TGGCTT	-																															gtggagtttaggtgtcagccTggctttgtcatgaaaggacc																										TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	TGGCTT	TGGCTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr1:207734400_207734405delTGGCTT	ENST00000367049.4	+	21	3504_3509	c.3504_3509delTGGCTT	c.(3502-3510)cctggcttt>cct	p.GF1169del	CR1_ENST00000367052.1_Intron|CR1_ENST00000367053.1_In_Frame_Del_p.GF719del|CR1_ENST00000400960.2_Intron|RP11-78B10.2_ENST00000597497.1_RNA|CR1_ENST00000367051.1_In_Frame_Del_p.GF719del	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	719	Sushi 18. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						GGTGTCAGCCTGGCTTTGTCATGAAA	0.49																																					p.1168_1170del		Pindel	.											.	CR1	354	.	0			c.3503_3508del						PASS	.																																			SO:0001651	inframe_deletion	1378	exon21			.	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.3504_3509delTGGCTT	chr1.hg19:g.207734400_207734405delTGGCTT	ENSP00000356016:p.Gly1169_Phe1170del	174.0	0.0	.		119.0	20.0	0.168	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	In_Frame_Del	DEL	ENST00000367049.4	hg19	CCDS44308.1																																																																																			.	.	.	none		0.49	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573		-	207734405	TGGCTT	-	207734400	7	5	244	1	0	1	0	1	0	0	0	0	3842	1567	55	0	3586	0	CR1	1	207734400	In_Frame_Del	DEL	TGGCTT	TCGA-SX-A71V-01A-11D-A33Q-10	18557	207734400	41516221	11	15040											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228521014	228521017	+	Frame_Shift_Del	DEL	CAAG	CAAG	-																															cgcctggccaagttccagctCaaggtgaaaggtgagaagga																										TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	CAAG	CAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr1:228521014_228521017delCAAG	ENST00000422127.1	+	58	15890_15893	c.15846_15849delCAAG	c.(15844-15849)ctcaagfs	p.LK5282fs	OBSCN_ENST00000284548.11_Frame_Shift_Del_p.LK5282fs|OBSCN_ENST00000570156.2_Frame_Shift_Del_p.LK6239fs|OBSCN_ENST00000366709.4_Frame_Shift_Del_p.LK2401fs|OBSCN_ENST00000366707.4_Frame_Shift_Del_p.LK2916fs	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5282	Ig-like 50.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AGTTCCAGCTCAAGGTGAAAGGTG	0.613																																					p.6239_6240del		Atlas-Indel,Pindel	.											.	OBSCN	2142	.	0			c.18716_18719del						PASS	.																																			SO:0001589	frameshift_variant	84033	exon69			.	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.15846_15849delCAAG	chr1.hg19:g.228521014_228521017delCAAG	ENSP00000409493:p.Leu5282fs	99.0	0.0	0		81.0	34.0	0.419753	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Frame_Shift_Del	DEL	ENST00000422127.1	hg19	CCDS58065.1																																																																																			.	.	.	none		0.613	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		-	228521017	CAAG	-	228521014	7	5	244	1	0	1	0	1	0	0	0	0	10819	813	29	0	16072	0	OBSCN	1	228521014	Frame_Shift_Del	DEL	CAAG	TCGA-SX-A71V-01A-11D-A33Q-10	20786614	228521014	20729607	12	15041											
SIPA1L2	57568	hgsc.bcm.edu	37	chr1	232615472	232615472	+	Missense_Mutation	SNP	A	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	agagagtgcgtgcccgtggaAtcagctgaaaacaaagatga	15	6	13	7	2	1	4	1	2	0	2	1	6	1	5	1	1	4	1	1	1	4	0			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr1:232615472A>C	ENST00000366630.1	-	6	2344	c.1986T>G	c.(1984-1986)gaT>gaG	p.D662E	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.D662E			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	662	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				TGCCCGTGGAATCAGCTGAAA	0.408																																					p.D662E		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.T1986G						PASS	.						134	144	141					1																	232615472		2082	4252	6334	SO:0001583	missense	57568	exon5			CGTGGAATCAGCT	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.1986T>G	chr1.hg19:g.232615472A>C	ENSP00000355589:p.Asp662Glu	42.0	0.0	.		40.0	12.0	.	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	hg19	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.609252	0.87258	.	.	ENSG00000116991	ENST00000366630;ENST00000262861	D;D	0.94232	-3.38;-3.38	5.54	0.415	0.16411	Rap/ran-GAP (2);	0.000000	0.85682	D	0.000000	D	0.95843	0.8647	M	0.85859	2.78	0.47341	D	0.999394	D	0.69078	0.997	D	0.72075	0.976	D	0.94353	0.7581	10	0.87932	D	0	-29.4799	9.2931	0.37800	0.7007:0.0:0.2993:0.0	.	662	Q9P2F8	SI1L2_HUMAN	E	662	ENSP00000355589:D662E;ENSP00000262861:D662E	ENSP00000262861:D662E	D	-	3	2	SIPA1L2	230682095	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.660000	0.37397	0.100000	0.17581	0.533000	0.62120	GAT	.	.	.	none		0.408	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		C	232615472	A	C	232615472	3	2	244	1	0	0	0	0	1	0	0	0	14343	98	4	5	3250	5	SIPA1L2	1	232615472	Missense_Mutation	SNP	A	TCGA-SX-A71V-01A-11D-A33Q-10	4094458	232615472	16635149	13	15042											
APLF	200558	hgsc.bcm.edu	37	chr2	68740321	68740322	+	Frame_Shift_Ins	INS	-	-	A																															acaactggaaggaagcacagINSaaatagccaagacccagatg																										TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr2:68740321_68740322insA	ENST00000303795.4	+	4	622_623	c.451_452insA	c.(451-453)gaafs	p.E151fs		NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	151					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						AGGAAGCACAGAAATAGCCAAG	0.376																																					p.E151fs		Atlas-Indel,Pindel	.											.	APLF	69	.	0			c.451_452insA						PASS	.																																			SO:0001589	frameshift_variant	200558	exon4			.	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.454dupA	chr2.hg19:g.68740324_68740324dupA	ENSP00000307004:p.Glu151fs	113.0	0.0	0		127.0	35.0	0.275591	NM_173545	A8K476|Q53P47|Q53PB9|Q53QU0	Frame_Shift_Ins	INS	ENST00000303795.4	hg19	CCDS1888.1																																																																																			.	.	.	none		0.376	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545		A	68740322	-	A	68740321	7	5	244	1	0	1	1	0	0	0	0	0	776	943	33	0	465	0	APLF	2	68740321	Frame_Shift_Ins	INS	-	TCGA-SX-A71V-01A-11D-A33Q-10		68740321	174459052	14	15043											
C2orf78	388960	hgsc.bcm.edu	37	chr2	74043598	74043598	+	Missense_Mutation	SNP	T	T	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	cacgtaggcctgctgtggctTaccctgctcgacctgattct	5	12	10	14	2	1	1	0	1	1	0	2	2	1	1	3	2	3	4	3	2	2	3			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr2:74043598T>G	ENST00000409561.1	+	3	2369	c.2248T>G	c.(2248-2250)Tac>Gac	p.Y750D		NM_001080474.1	NP_001073943.1	A6NCI8	CB078_HUMAN	chromosome 2 open reading frame 78	750										cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|soft_tissue(1)|urinary_tract(1)	34						TGCTGTGGCTTACCCTGCTCG	0.537																																					p.Y750D		Atlas-SNP	.											.	C2orf78	150	.	0			c.T2248G						PASS	.						159	166	164					2																	74043598		2116	4225	6341	SO:0001583	missense	388960	exon3			GTGGCTTACCCTG	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.2248T>G	chr2.hg19:g.74043598T>G	ENSP00000387124:p.Tyr750Asp	214.0	0.0	.		236.0	56.0	.	NM_001080474		Missense_Mutation	SNP	ENST00000409561.1	hg19	CCDS46338.1	.	.	.	.	.	.	.	.	.	.	T	1.402	-0.577786	0.03854	.	.	ENSG00000187833	ENST00000409561;ENST00000342345	T	0.45668	0.89	5.08	-10.2	0.00374	.	1.247370	0.05957	N	0.639954	T	0.16769	0.0403	N	0.16130	0.375	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.12041	-1.0563	10	0.32370	T	0.25	1.7364	1.4355	0.02342	0.4555:0.2176:0.1839:0.143	.	750	A6NCI8	CB078_HUMAN	D	750;720	ENSP00000387124:Y750D	ENSP00000340692:Y720D	Y	+	1	0	C2orf78	73897106	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-1.317000	0.02707	-2.190000	0.00757	-0.490000	0.04691	TAC	.	.	.	none		0.537	C2orf78-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000328083.1	NM_001080474		G	74043598	T	G	74043598	3	3	244	1	0	0	0	0	1	0	0	0	2197	1754	61	5	2258	5	C2orf78	2	74043598	Missense_Mutation	SNP	T	TCGA-SX-A71V-01A-11D-A33Q-10	5303277	74043598	169155775	15	15044											
ATF2	1386	hgsc.bcm.edu	37	chr2	175945471	175945471	+	Missense_Mutation	SNP	T	T	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	gtttcagctgtgccacttcaTttctcagcagggtgacttca	7	14	9	11	0	4	1	4	1	1	0	5	1	4	1	1	1	3	3	1	1	0	4			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr2:175945471T>G	ENST00000264110.2	-	13	1506	c.1208A>C	c.(1207-1209)aAt>aCt	p.N403T	ATF2_ENST00000409499.1_Missense_Mutation_p.N42T|ATF2_ENST00000426833.3_Missense_Mutation_p.N385T|ATF2_ENST00000538946.1_3'UTR|ATF2_ENST00000487334.2_3'UTR|ATF2_ENST00000409437.1_Missense_Mutation_p.N287T|ATF2_ENST00000345739.5_Missense_Mutation_p.N345T|ATF2_ENST00000392544.1_Missense_Mutation_p.N403T|ATF2_ENST00000409635.1_Missense_Mutation_p.N345T|ATF2_ENST00000392543.2_Missense_Mutation_p.N24T	NM_001256090.1|NM_001256091.1|NM_001880.3	NP_001243019.1|NP_001243020.1|NP_001871.2	P15336	ATF2_HUMAN	activating transcription factor 2	403	Leucine-zipper. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				adipose tissue development (GO:0060612)|cellular response to DNA damage stimulus (GO:0006974)|chromatin organization (GO:0006325)|fat cell differentiation (GO:0045444)|histone acetylation (GO:0016573)|innate immune response (GO:0045087)|intra-S DNA damage checkpoint (GO:0031573)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|outflow tract morphogenesis (GO:0003151)|positive regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902110)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta2 production (GO:0032915)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to osmotic stress (GO:0006970)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	cAMP response element binding (GO:0035497)|cAMP response element binding protein binding (GO:0008140)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|pancreas(1)|skin(1)	17			OV - Ovarian serous cystadenocarcinoma(117;0.125)		Pseudoephedrine(DB00852)	TGCCACTTCATTTCTCAGCAG	0.388																																					p.N403T	Pancreas(17;87 705 4534 15538 30988)	Atlas-SNP	.											.	ATF2	52	.	0			c.A1208C						PASS	.						156	153	154					2																	175945471		2203	4300	6503	SO:0001583	missense	1386	exon13			ACTTCATTTCTCA	X15875	CCDS2262.1, CCDS58737.1, CCDS58738.1, CCDS58739.1	2q32	2013-01-10			ENSG00000115966	ENSG00000115966		"basic leucine zipper proteins"	784	protein-coding gene	gene with protein product		123811	"cAMP responsive element binding protein 2"	CREB2		1833307, 1838349	Standard	NM_001880		Approved	TREB7, CRE-BP1, HB16	uc002ujl.4	P15336	OTTHUMG00000132424	ENST00000264110.2:c.1208A>C	chr2.hg19:g.175945471T>G	ENSP00000264110:p.Asn403Thr	53.0	0.0	.		59.0	26.0	.	NM_001880	A1L3Z2|A4D7U4|A4D7U5|A4D7V1|D3DPE9|G8JLM5|Q13000|Q3B7B7|Q4ZFU9|Q53RY2|Q8TAR1|Q96JT8	Missense_Mutation	SNP	ENST00000264110.2	hg19	CCDS2262.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.620506	0.87460	.	.	ENSG00000115966	ENST00000264110;ENST00000345739;ENST00000542046;ENST00000409437;ENST00000409635;ENST00000392544;ENST00000409499;ENST00000426833;ENST00000392543	T;T;T;T;T;T	0.56103	0.48;0.48;0.48;0.48;0.48;0.48	5.91	5.91	0.95273	Basic-leucine zipper (bZIP) transcription factor (2);bZIP transcription factor, bZIP-1 (1);	0.000000	0.85682	D	0.000000	T	0.60907	0.2305	L	0.28192	0.835	0.80722	D	1	D;P;D;B;B	0.76494	0.997;0.854;0.999;0.41;0.288	D;P;D;P;B	0.79108	0.992;0.505;0.972;0.475;0.103	T	0.60031	-0.7342	10	0.36615	T	0.2	-42.5065	16.3453	0.83126	0.0:0.0:0.0:1.0	.	385;380;42;345;403	A4D7U4;B3KY57;Q96JT8;Q3B7B7;P15336	.;.;.;.;ATF2_HUMAN	T	403;345;380;287;345;403;42;385;24	ENSP00000264110:N403T;ENSP00000340576:N345T;ENSP00000386326:N287T;ENSP00000387093:N345T;ENSP00000376327:N403T;ENSP00000407911:N385T	ENSP00000264110:N403T	N	-	2	0	ATF2	175653717	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.909000	0.69923	2.261000	0.74972	0.533000	0.62120	AAT	.	.	.	none		0.388	ATF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255562.1	NM_001880		G	175945471	T	G	175945471	3	3	244	1	0	0	0	0	1	0	0	0	1080	1493	52	5	317	5	ATF2	2	175945471	Missense_Mutation	SNP	T	TCGA-SX-A71V-01A-11D-A33Q-10	101901873	175945471	67253902	16	15045											
TTN	7273	hgsc.bcm.edu	37	chr2	179398278	179398278	+	Frame_Shift_Del	DEL	G	G	-																															ttaaggtactatctgttggaGgtgggtgtagggttactgtc																										TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr2:179398278delG	ENST00000591111.1	-	308	98365	c.98141delC	c.(98140-98142)cctfs	p.P32715fs	TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342175.6_Frame_Shift_Del_p.P25483fs|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN_ENST00000589042.1_Frame_Shift_Del_p.P34356fs|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000359218.5_Frame_Shift_Del_p.P25416fs|TTN-AS1_ENST00000585358.1_RNA|TTN_ENST00000460472.2_Frame_Shift_Del_p.P25291fs|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000342992.6_Frame_Shift_Del_p.P31788fs|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000591867.1_RNA			Q8WZ42	TITIN_HUMAN	titin	32715					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)			ATCTGTTGGAGGTGGGTGTAG	0.448																																					p.P34355fs		Atlas-Indel,Pindel	.											.	TTN	18412	.	0			c.103065delT						PASS	.						110	97	101					2																	179398278		1962	4174	6136	SO:0001589	frameshift_variant	7273	exon358			.	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.98141delC	chr2.hg19:g.179398278delG	ENSP00000465570:p.Pro32715fs	83.0	0.0	0		90.0	52.0	0.577778	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Frame_Shift_Del	DEL	ENST00000591111.1	hg19																																																																																				.	.	.	none		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		-	179398278	G	-	179398278	7	5	244	1	0	1	0	1	0	0	0	0	16747	1000	35	0	4935	0	TTN	2	179398278	Frame_Shift_Del	DEL	G	TCGA-SX-A71V-01A-11D-A33Q-10	3452807	179398278	63801095	17	15046											
TTN	7273	hgsc.bcm.edu	37	chr2	179575930	179575930	+	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	aaatgatgtttgtacatttgGgctgtctttcaatggcttgc	8	17	10	6	0	2	1	1	1	1	0	2	1	2	1	0	2	2	4	0	2	3	5			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr2:179575930G>C	ENST00000591111.1	-	95	27306	c.27082C>G	c.(27082-27084)Cca>Gca	p.P9028A	TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.P9345A|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.P8101A|TTN-AS1_ENST00000431752.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13166	Ig-like 73.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGTACATTTGGGCTGTCTTTC	0.428																																					p.P9345A		Atlas-SNP	.											.	TTN	18412	.	0			c.C28033G						PASS	.						212	209	210					2																	179575930		1869	4109	5978	SO:0001583	missense	7273	exon97			CATTTGGGCTGTC	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.27082C>G	chr2.hg19:g.179575930G>C	ENSP00000465570:p.Pro9028Ala	142.0	0.0	.		176.0	93.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	8.880	0.951423	0.18431	.	.	ENSG00000155657	ENST00000342992	T	0.41400	1.0	5.76	0.755	0.18415	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.21881	0.0527	N	0.16307	0.4	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.26155	-1.0111	9	0.87932	D	0	.	0.6363	0.00802	0.308:0.1208:0.3244:0.2469	.	9028	Q8WZ42	TITIN_HUMAN	A	8101	ENSP00000343764:P8101A	ENSP00000343764:P8101A	P	-	1	0	TTN	179284175	0.913000	0.31002	0.693000	0.30195	0.889000	0.51656	0.482000	0.22276	-0.064000	0.13043	-0.169000	0.13324	CCA	.	.	.	none		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179575930	G	C	179575930	3	2	244	1	0	0	0	0	1	0	0	0	16747	1232	43	4	76560	4	TTN	2	179575930	Missense_Mutation	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	177652	179575930	63623443	18	15047											
SLC40A1	30061	hgsc.bcm.edu	37	chr2	190428539	190428539	+	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	agggggcttccaggcatgaaTacagagatcacacacaagat	15	6	11	9	0	1	3	1	1	0	2	2	4	2	3	1	3	1	2	1	3	3	2			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr2:190428539T>A	ENST00000261024.2	-	7	1599	c.1173A>T	c.(1171-1173)gtA>gtT	p.V391V		NM_014585.5	NP_055400.1	Q9NP59	S40A1_HUMAN	solute carrier family 40 (iron-regulated transporter), member 1	391					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)			CAGGCATGAATACAGAGATCA	0.453																																					p.V391V		Atlas-SNP	.											.	SLC40A1	51	.	0			c.A1173T						PASS	.						84	78	80					2																	190428539		2203	4300	6503	SO:0001819	synonymous_variant	30061	exon7			CATGAATACAGAG	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.1173A>T	chr2.hg19:g.190428539T>A		119.0	0.0	.		117.0	25.0	.	NM_014585	Q6FI62|Q7Z4F8|Q8IVB2|Q9NRL0	Silent	SNP	ENST00000261024.2	hg19	CCDS2299.1																																																																																			.	.	.	none		0.453	SLC40A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255916.2			A	190428539	T	A	190428539	2	1	244	1	0	0	0	0	0	0	0	1	14641	1393	49	5		5	SLC40A1	2	190428539	Silent	SNP	T	TCGA-SX-A71V-01A-11D-A33Q-10	10852609	190428539	52770834	19	15048											
FGD5	152273	hgsc.bcm.edu	37	chr3	14861143	14861143	+	Missense_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	ggccttgggctggagaggggGtcttccagagcgacctcctc	5	8	16	12	1	1	2	0	0	1	2	4	4	3	2	4	5	1	1	4	5	0	2			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr3:14861143G>A	ENST00000285046.5	+	1	675	c.565G>A	c.(565-567)Gtc>Atc	p.V189I	FGD5_ENST00000543601.1_5'UTR	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	189	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						TGGAGAGGGGGTCTTCCAGAG	0.637																																					p.V189I		Atlas-SNP	.											.	FGD5	248	.	0			c.G565A						PASS	.						32	41	38					3																	14861143		692	1591	2283	SO:0001583	missense	152273	exon1			GAGGGGGTCTTCC	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.565G>A	chr3.hg19:g.14861143G>A	ENSP00000285046:p.Val189Ile	101.0	0.0	.		125.0	51.0	.	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Missense_Mutation	SNP	ENST00000285046.5	hg19	CCDS46767.1	.	.	.	.	.	.	.	.	.	.	G	9.096	1.003024	0.19121	.	.	ENSG00000154783	ENST00000285046	T	0.75260	-0.92	5.21	-1.04	0.10068	.	2.198090	0.02044	N	0.049557	T	0.53061	0.1773	N	0.12182	0.205	0.09310	N	0.999997	B	0.02656	0.0	B	0.04013	0.001	T	0.29822	-0.9999	10	0.33940	T	0.23	-4.0	1.0228	0.01521	0.3558:0.155:0.3405:0.1487	.	189	Q6ZNL6	FGD5_HUMAN	I	189	ENSP00000285046:V189I	ENSP00000285046:V189I	V	+	1	0	FGD5	14836147	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.344000	0.19962	-0.288000	0.09051	0.591000	0.81541	GTC	.	.	.	none		0.637	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536		A	14861143	G	A	14861143	3	1	244	1	0	0	0	0	1	0	0	0	5843	1261	44	2	567	2	FGD5	3	14861143	Missense_Mutation	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10		14861143	183161287	20	15049											
TRANK1	9881	hgsc.bcm.edu	37	chr3	36898563	36898563	+	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	ttcgaagagctggatgcttcCtttcaggtgcttcagtcgct	6	14	11	10	2	2	1	2	0	0	1	5	3	3	2	1	2	3	4	1	2	1	4			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr3:36898563C>G	ENST00000429976.2	-	12	2765	c.2518G>C	c.(2518-2520)Gga>Cga	p.G840R	TRANK1_ENST00000428977.2_Missense_Mutation_p.G290R|TRANK1_ENST00000301807.6_Missense_Mutation_p.G290R	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	840							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						TGGATGCTTCCTTTCAGGTGC	0.537																																					p.G840R		Atlas-SNP	.											.	TRANK1	398	.	0			c.G2518C						PASS	.						60	59	59					3																	36898563		1986	4166	6152	SO:0001583	missense	9881	exon12			TGCTTCCTTTCAG	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.2518G>C	chr3.hg19:g.36898563C>G	ENSP00000416168:p.Gly840Arg	80.0	0.0	.		62.0	22.0	.	NM_014831	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	hg19	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	C	18.26	3.584939	0.65992	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.30182	1.54;1.95;1.54	5.51	5.51	0.81932	.	0.099482	0.44688	D	0.000427	T	0.38348	0.1037	N	0.24115	0.695	0.39623	D	0.970059	D	0.71674	0.998	D	0.66716	0.946	T	0.07673	-1.0760	10	0.25106	T	0.35	.	14.6176	0.68560	0.1457:0.8542:0.0:0.0	.	840	O15050	TRNK1_HUMAN	R	290;840;290	ENSP00000416826:G290R;ENSP00000416168:G840R;ENSP00000301807:G290R	ENSP00000301807:G290R	G	-	1	0	TRANK1	36873567	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	2.438000	0.44837	2.768000	0.95171	0.561000	0.74099	GGA	.	.	.	none		0.537	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		G	36898563	C	G	36898563	3	3	244	1	0	0	0	0	1	0	0	0	16466	690	24	4	6307	4	TRANK1	3	36898563	Missense_Mutation	SNP	C	TCGA-SX-A71V-01A-11D-A33Q-10	22037420	36898563	161123867	21	15050											
DNAH1	25981	hgsc.bcm.edu	37	chr3	52422336	52422336	+	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	accactttgtggccaaggccGtggagcccaagcgggtgagg	8	6	16	11	2	0	1	0	1	0	0	0	2	0	2	4	5	2	0	4	5	2	1			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr3:52422336G>C	ENST00000420323.2	+	57	9418	c.9157G>C	c.(9157-9159)Gtg>Ctg	p.V3053L		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	3053	Stalk. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GGCCAAGGCCGTGGAGCCCAA	0.652																																					p.V3053L		Atlas-SNP	.											.	DNAH1	534	.	0			c.G9157C						PASS	.						39	42	41					3																	52422336		2070	4193	6263	SO:0001583	missense	25981	exon57			AAGGCCGTGGAGC	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.9157G>C	chr3.hg19:g.52422336G>C	ENSP00000401514:p.Val3053Leu	80.0	0.0	.		91.0	40.0	.	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	hg19	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.163685	0.78226	.	.	ENSG00000114841	ENST00000420323	T	0.79454	-1.27	4.29	4.29	0.51040	.	0.000000	0.56097	D	0.000038	D	0.90577	0.7046	M	0.93808	3.46	0.53688	D	0.999974	D	0.71674	0.998	D	0.68943	0.961	D	0.93448	0.6799	10	0.87932	D	0	.	16.9513	0.86246	0.0:0.0:1.0:0.0	.	3053	C9JXH6	.	L	3053	ENSP00000401514:V3053L	ENSP00000401514:V3053L	V	+	1	0	DNAH1	52397376	1.000000	0.71417	0.996000	0.52242	0.906000	0.53458	6.903000	0.75703	2.229000	0.72834	0.561000	0.74099	GTG	.	.	.	none		0.652	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		C	52422336	G	C	52422336	3	2	244	1	0	0	0	0	1	0	0	0	4599	1145	40	4	9379	4	DNAH1	3	52422336	Missense_Mutation	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	15523773	52422336	145600094	22	15051											
OSBPL11	114885	hgsc.bcm.edu	37	chr3	125266348	125266348	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgactttgccacccagttcTacccaaggaacagtcaaaat	13	9	6	13	0	2	1	1	1	1	0	2	2	2	2	3	1	3	1	3	1	5	3			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr3:125266348T>C	ENST00000296220.5	-	10	2032	c.1743A>G	c.(1741-1743)gtA>gtG	p.V581V		NM_022776.4	NP_073613.2	Q9BXB4	OSB11_HUMAN	oxysterol binding protein-like 11	581					fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|positive regulation of sequestering of triglyceride (GO:0010890)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)			NS(1)|breast(1)|cervix(1)|kidney(2)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	27						CACCCAGTTCTACCCAAGGAA	0.438																																					p.V581V		Atlas-SNP	.											.	OSBPL11	64	.	0			c.A1743G						PASS	.						137	125	129					3																	125266348		2203	4300	6503	SO:0001819	synonymous_variant	114885	exon10			CAGTTCTACCCAA	AF392454	CCDS3033.1	3q21	2013-01-10			ENSG00000144909	ENSG00000144909		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16397	protein-coding gene	gene with protein product		606739					Standard	NM_022776		Approved	ORP-11, ORP11, FLJ13012, FLJ13164	uc003eic.3	Q9BXB4	OTTHUMG00000159571	ENST00000296220.5:c.1743A>G	chr3.hg19:g.125266348T>C		136.0	0.0	.		129.0	67.0	.	NM_022776	A8K9I7	Silent	SNP	ENST00000296220.5	hg19	CCDS3033.1																																																																																			.	.	.	none		0.438	OSBPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356295.1	NM_022776		C	125266348	T	C	125266348	2	2	244	1	0	0	0	0	0	0	0	1	11283	1509	53	3		3	OSBPL11	3	125266348	Silent	SNP	T	TCGA-SX-A71V-01A-11D-A33Q-10	72844012	125266348	72756082	23	15052											
TRIM42	287015	hgsc.bcm.edu	37	chr3	140397260	140397260	+	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	tgttctgagagccccaactgCcattggtgttgctgctcttg	5	14	11	11	0	2	1	0	1	2	1	2	2	2	1	3	1	5	4	3	1	1	4			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr3:140397260C>T	ENST00000286349.3	+	1	380	c.189C>T	c.(187-189)tgC>tgT	p.C63C		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	63	Cys-rich.					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						GCCCCAACTGCCATTGGTGTT	0.557																																					p.C63C		Atlas-SNP	.											.	TRIM42	143	.	0			c.C189T						PASS	.						134	110	118					3																	140397260		2203	4300	6503	SO:0001819	synonymous_variant	287015	exon1			CAACTGCCATTGG	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.189C>T	chr3.hg19:g.140397260C>T		82.0	0.0	.		109.0	51.0	.	NM_152616	A1L4B4|Q8N832|Q8NDL3	Silent	SNP	ENST00000286349.3	hg19	CCDS3113.1																																																																																			.	.	.	none		0.557	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616		T	140397260	C	T	140397260	2	4	244	1	0	0	0	0	0	0	0	1	16529	747	26	2		2	TRIM42	3	140397260	Silent	SNP	C	TCGA-SX-A71V-01A-11D-A33Q-10	15130912	140397260	57625170	24	15053											
PLD1	5337	hgsc.bcm.edu	37	chr3	171362716	171362716	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacctgtagttgaagtgcaTgattgcctgtagagcatttc	9	13	11	8	0	0	3	0	2	0	1	1	3	0	3	2	0	3	6	2	0	3	5			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr3:171362716T>C	ENST00000351298.4	-	22	2653	c.2527A>G	c.(2527-2529)Atg>Gtg	p.M843V	PLD1_ENST00000340989.4_Missense_Mutation_p.M843V|PLD1_ENST00000356327.5_Missense_Mutation_p.M805V|PLD1_ENST00000342215.6_3'UTR	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific	843	Catalytic.				chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	TTGAAGTGCATGATTGCCTGT	0.463																																					p.M843V	NSCLC(149;2174 3517 34058)	Atlas-SNP	.											.	PLD1	134	.	0			c.A2527G						PASS	.						124	113	117					3																	171362716		2203	4300	6503	SO:0001583	missense	5337	exon22			AGTGCATGATTGC	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.2527A>G	chr3.hg19:g.171362716T>C	ENSP00000342793:p.Met843Val	75.0	0.0	.		86.0	19.0	.	NM_002662		Missense_Mutation	SNP	ENST00000351298.4	hg19	CCDS3216.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.279208	0.80692	.	.	ENSG00000075651	ENST00000356327;ENST00000351298;ENST00000340989	T;T;T	0.34859	1.34;1.34;1.34	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.56202	0.1969	M	0.64567	1.98	0.80722	D	1	P;P;P	0.50819	0.855;0.937;0.939	P;P;D	0.64877	0.644;0.864;0.93	T	0.55995	-0.8052	10	0.51188	T	0.08	-36.3673	15.0031	0.71489	0.0:0.0:0.0:1.0	.	843;828;843	Q13393-4;Q59EA4;Q13393	.;.;PLD1_HUMAN	V	805;843;843	ENSP00000348681:M805V;ENSP00000342793:M843V;ENSP00000340326:M843V	ENSP00000340326:M843V	M	-	1	0	PLD1	172845410	1.000000	0.71417	0.992000	0.48379	0.983000	0.72400	7.609000	0.82925	2.194000	0.70268	0.533000	0.62120	ATG	.	.	.	none		0.463	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662		C	171362716	T	C	171362716	3	2	244	1	0	0	0	0	1	0	0	0	12052	1464	51	3	721	3	PLD1	3	171362716	Missense_Mutation	SNP	T	TCGA-SX-A71V-01A-11D-A33Q-10	30965456	171362716	26659714	25	15054											
MUC20	200958	hgsc.bcm.edu	37	chr3	195453023	195453023	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgacagcacccggggccacgAccctcagtggagctctggtc	7	6	13	15	2	2	1	1	1	1	0	3	3	2	2	3	4	2	2	3	4	0	0			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr3:195453023A>G	ENST00000447234.2	+	2	1675	c.1549A>G	c.(1549-1551)Acc>Gcc	p.T517A	MUC20_ENST00000436408.1_Missense_Mutation_p.T517A|MUC20_ENST00000320736.6_Missense_Mutation_p.T346A|MUC20_ENST00000445522.2_Missense_Mutation_p.T482A	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	517	Involved in oligomerization.		Missing. {ECO:0000269|PubMed:14702039}.		activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		CGGGGCCACGACCCTCAGTGG	0.582																																					p.T346A		Atlas-SNP	.											.	MUC20	84	.	0			c.A1036G						PASS	.						56	53	54					3																	195453023		2122	4218	6340	SO:0001583	missense	200958	exon3			GCCACGACCCTCA	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.1549A>G	chr3.hg19:g.195453023A>G	ENSP00000414350:p.Thr517Ala	234.0	0.0	.		283.0	109.0	.	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	hg19		.	.	.	.	.	.	.	.	.	.	A	12.67	2.008608	0.35415	.	.	ENSG00000176945	ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	T;T;T;T	0.13778	2.98;2.98;3.15;2.56	3.97	-3.15	0.05233	.	0.867446	0.09841	N	0.748862	T	0.07954	0.0199	L	0.34521	1.04	0.09310	N	1	P	0.35507	0.506	B	0.31812	0.136	T	0.23119	-1.0197	10	0.48119	T	0.1	0.2299	4.3567	0.11181	0.4003:0.0:0.4259:0.1738	.	346	E9PH32	.	A	517;346;517;482	ENSP00000414350:T517A;ENSP00000325431:T346A;ENSP00000396774:T517A;ENSP00000405629:T482A	ENSP00000325431:T346A	T	+	1	0	MUC20	196938694	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	-1.788000	0.01763	-0.716000	0.04962	0.421000	0.28195	ACC	.	.	.	none		0.582	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673		G	195453023	A	G	195453023	3	3	244	1	0	0	0	0	1	0	0	0	9983	275	10	3	1046	3	MUC20	3	195453023	Missense_Mutation	SNP	A	TCGA-SX-A71V-01A-11D-A33Q-10	24090307	195453023	2569407	26	15055											
TADA2B	93624	hgsc.bcm.edu	37	chr4	7056602	7056602	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaaggtgctctgcagctctTtaaacttgagtccagcccgc	9	10	10	12	1	2	2	0	1	2	1	3	2	3	2	2	1	5	3	2	1	3	3			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr4:7056602T>C	ENST00000310074.7	+	2	1273	c.1084T>C	c.(1084-1086)Tta>Cta	p.L362L	TADA2B_ENST00000512388.1_Silent_p.L287L|TADA2B_ENST00000515646.1_Silent_p.L270L	NM_152293.2	NP_689506.2	Q86TJ2	TAD2B_HUMAN	transcriptional adaptor 2B	362					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						CTGCAGCTCTTTAAACTTGAG	0.537																																					p.L362L		Atlas-SNP	.											.	TADA2B	29	.	0			c.T1084C						PASS	.						70	74	73					4																	7056602		1944	4140	6084	SO:0001819	synonymous_variant	93624	exon2			AGCTCTTTAAACT	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.1084T>C	chr4.hg19:g.7056602T>C		132.0	0.0	.		102.0	44.0	.	NM_152293	A0AUJ8|A4QMR7|B3KSN0|B3KU86|Q6MZG9	Silent	SNP	ENST00000310074.7	hg19	CCDS47007.1																																																																																			.	.	.	none		0.537	TADA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358687.2	NM_152293		C	7056602	T	C	7056602	2	2	244	1	0	0	0	0	0	0	0	1	15523	1838	64	3		3	TADA2B	4	7056602	Silent	SNP	T	TCGA-SX-A71V-01A-11D-A33Q-10		7056602	184097674	27	15056											
MOBKL1A	92597	hgsc.bcm.edu	37	chr4	71768265	71768265	+	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	gcggccaacatgagcttcttGttgtgagtagccaggccccg	7	9	13	12	2	1	2	0	2	1	0	1	2	1	2	4	2	3	3	4	2	2	4			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr4:71768265G>T	ENST00000309395.2	+	1	213	c.12G>T	c.(10-12)ttG>ttT	p.L4F	MOB1B_ENST00000396051.2_5'UTR|MOB1B_ENST00000511449.1_3'UTR	NM_001244766.1|NM_173468.3	NP_001231695.1|NP_775739.1	Q7L9L4	MOB1B_HUMAN	MOB kinase activator 1B	4					hippo signaling (GO:0035329)|positive regulation of phosphorylation (GO:0042327)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	kinase activator activity (GO:0019209)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)										TGAGCTTCTTGTTGTGAGTAG	0.726																																					p.L4F		Atlas-SNP	.											.	.	.	.	0			c.G12T						PASS	.						9	10	10					4																	71768265		2154	4235	6389	SO:0001583	missense	92597	exon1			CTTCTTGTTGTGA	BC038112	CCDS34002.1, CCDS58903.1	4q13.3	2011-09-28	2011-09-28	2011-09-27	ENSG00000173542	ENSG00000173542		"MOB kinase activators"	29801	protein-coding gene	gene with protein product	"Mob4A protein"	609282	"MOB1, Mps One Binder kinase activator-like 1A (yeast)", "MOB1 Mps One Binder homolog B (yeast)"	MOBKL1A		15067004	Standard	NM_173468		Approved	MOB4A	uc003hfw.3	Q7L9L4	OTTHUMG00000160844	ENST00000309395.2:c.12G>T	chr4.hg19:g.71768265G>T	ENSP00000310189:p.Leu4Phe	52.0	0.0	.		36.0	10.0	.	NM_001244767	B2R8U6|B4DRY3|Q8IY23	Missense_Mutation	SNP	ENST00000309395.2	hg19	CCDS34002.1	.	.	.	.	.	.	.	.	.	.	G	9.947	1.219208	0.22373	.	.	ENSG00000173542	ENST00000309395	.	.	.	3.97	2.23	0.28157	.	0.780131	0.11880	N	0.520563	T	0.16642	0.0400	N	0.01228	-0.945	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.12837	0.008;0.001	T	0.10451	-1.0629	9	0.11182	T	0.66	.	6.3657	0.21453	0.2295:0.0:0.7705:0.0	.	4;4	Q7L9L4;B3KSH6	MOB1B_HUMAN;.	F	4	.	ENSP00000310189:L4F	L	+	3	2	MOBKL1A	71987129	1.000000	0.71417	1.000000	0.80357	0.329000	0.28539	0.824000	0.27379	0.450000	0.26774	0.491000	0.48974	TTG	.	.	.	none		0.726	MOB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362634.1	NM_173468		T	71768265	G	T	71768265	3	4	244	1	0	0	0	0	1	0	0	0	9689	1368	48	4	14	4	MOBKL1A	4	71768265	Missense_Mutation	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	64711663	71768265	119386011	28	15057											
PRDM5	11107	hgsc.bcm.edu	37	chr4	121702315	121702315	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tactttcttatgacttctaaGcactgaaggtgtaacaaagg	13	13	8	7	0	2	2	0	2	2	0	2	2	2	2	0	2	3	2	0	2	6	6			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr4:121702315G>A	ENST00000264808.3	-	12	1666	c.1426C>T	c.(1426-1428)Ctt>Ttt	p.L476F	PRDM5_ENST00000428209.2_Missense_Mutation_p.L445F|PRDM5_ENST00000515109.1_Missense_Mutation_p.L445F	NM_018699.2	NP_061169.2	Q9NQX1	PRDM5_HUMAN	PR domain containing 5	476					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						TGACTTCTAAGCACTGAAGGT	0.353																																					p.L476F		Atlas-SNP	.											.	PRDM5	76	.	0			c.C1426T						PASS	.						157	137	143					4																	121702315		2203	4300	6503	SO:0001583	missense	11107	exon12			TTCTAAGCACTGA	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.1426C>T	chr4.hg19:g.121702315G>A	ENSP00000264808:p.Leu476Phe	94.0	0.0	.		89.0	22.0	.	NM_018699	Q0VAI9|Q0VAJ0|Q6NXQ7	Missense_Mutation	SNP	ENST00000264808.3	hg19	CCDS3716.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.762993	0.89932	.	.	ENSG00000138738	ENST00000264808;ENST00000515109;ENST00000428209	T;T;T	0.52057	0.68;0.68;0.68	5.9	5.9	0.94986	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	0.71384	0.3333	M	0.75264	2.295	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.997	T	0.71991	-0.4425	10	0.66056	D	0.02	-23.0771	20.2704	0.98474	0.0:0.0:1.0:0.0	.	445;445;476	Q0VAI9;Q9NQX1-2;Q9NQX1	.;.;PRDM5_HUMAN	F	476;445;445	ENSP00000264808:L476F;ENSP00000422309:L445F;ENSP00000404832:L445F	ENSP00000264808:L476F	L	-	1	0	PRDM5	121921765	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	9.675000	0.98638	2.793000	0.96121	0.591000	0.81541	CTT	.	.	.	none		0.353	PRDM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256528.2			A	121702315	G	A	121702315	3	1	244	1	0	0	0	0	1	0	0	0	12470	971	34	2	486	2	PRDM5	4	121702315	Missense_Mutation	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	49934050	121702315	69451961	29	15058											
ZNF622	90441	hgsc.bcm.edu	37	chr5	16463272	16463272	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atcgccatctgtgaagagctTacagtggcttttgtcattca	9	14	9	9	1	3	2	2	1	1	1	4	2	3	2	1	1	2	2	1	1	2	4			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr5:16463272T>C	ENST00000308683.2	-	3	1120	c.994A>G	c.(994-996)Aag>Gag	p.K332E		NM_033414.2	NP_219482.1	Q969S3	ZN622_HUMAN	zinc finger protein 622	332					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						GTGAAGAGCTTACAGTGGCTT	0.413																																					p.K332E		Atlas-SNP	.											.	ZNF622	49	.	0			c.A994G						PASS	.						185	186	186					5																	16463272		2203	4300	6503	SO:0001583	missense	90441	exon3			AGAGCTTACAGTG	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.994A>G	chr5.hg19:g.16463272T>C	ENSP00000310042:p.Lys332Glu	287.0	0.0	.		253.0	84.0	.	NM_033414		Missense_Mutation	SNP	ENST00000308683.2	hg19	CCDS3886.1	.	.	.	.	.	.	.	.	.	.	T	32	5.118738	0.94385	.	.	ENSG00000173545	ENST00000308683	T	0.46451	0.87	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.73179	0.3554	M	0.92691	3.335	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.80386	-0.1404	10	0.72032	D	0.01	-5.2815	16.2879	0.82732	0.0:0.0:0.0:1.0	.	332	Q969S3	ZN622_HUMAN	E	332	ENSP00000310042:K332E	ENSP00000310042:K332E	K	-	1	0	ZNF622	16516272	1.000000	0.71417	0.994000	0.49952	0.992000	0.81027	7.988000	0.88194	2.242000	0.73789	0.533000	0.62120	AAG	.	.	.	none		0.413	ZNF622-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207105.1	NM_033414		C	16463272	T	C	16463272	3	2	244	1	0	0	0	0	1	0	0	0	18058	1763	61	3	455	3	ZNF622	5	16463272	Missense_Mutation	SNP	T	TCGA-SX-A71V-01A-11D-A33Q-10		16463272	164451988	30	15059											
MAN2A1	4124	hgsc.bcm.edu	37	chr5	109155930	109155930	+	Missense_Mutation	SNP	A	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	ttaatctttagcaaatgatgActaaagaagatggtaaacac	18	11	7	5	0	1	4	0	2	1	2	1	4	1	4	0	1	2	2	0	1	8	5			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr5:109155930A>C	ENST00000261483.4	+	15	3390	c.2338A>C	c.(2338-2340)Act>Cct	p.T780P		NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	780					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		GCAAATGATGACTAAAGAAGA	0.313																																					p.T780P		Atlas-SNP	.											.	MAN2A1	136	.	0			c.A2338C						PASS	.						57	56	56					5																	109155930		2202	4300	6502	SO:0001583	missense	4124	exon15			ATGATGACTAAAG		CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"golgi integral membrane protein 7"	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.2338A>C	chr5.hg19:g.109155930A>C	ENSP00000261483:p.Thr780Pro	50.0	0.0	.		43.0	19.0	.	NM_002372	Q16767	Missense_Mutation	SNP	ENST00000261483.4	hg19	CCDS34209.1	.	.	.	.	.	.	.	.	.	.	A	10.27	1.303856	0.23736	.	.	ENSG00000112893	ENST00000261483	T	0.78707	-1.2	5.97	3.56	0.40772	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	0.633028	0.16350	N	0.218261	T	0.72260	0.3438	M	0.61703	1.905	0.09310	N	1	B	0.11235	0.004	B	0.18263	0.021	T	0.58999	-0.7536	10	0.30078	T	0.28	-7.0965	8.6679	0.34132	0.8031:0.1298:0.067:0.0	.	780	Q16706	MA2A1_HUMAN	P	780	ENSP00000261483:T780P	ENSP00000261483:T780P	T	+	1	0	MAN2A1	109183829	0.010000	0.17322	0.110000	0.21437	0.981000	0.71138	2.300000	0.43620	0.495000	0.27882	-0.256000	0.11100	ACT	.	.	.	none		0.313	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1			C	109155930	A	C	109155930	3	2	244	1	0	0	0	0	1	0	0	0	9221	275	10	5	2396	5	MAN2A1	5	109155930	Missense_Mutation	SNP	A	TCGA-SX-A71V-01A-11D-A33Q-10	92692658	109155930	71759330	31	15060											
SNCAIP	9627	hgsc.bcm.edu	37	chr5	121758736	121758736	+	Missense_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	atgaccaaaagaaccagaaaGtggttgagtaccagaaaggg	18	5	12	6	0	0	5	0	2	0	3	0	5	0	5	3	2	2	2	3	2	6	2			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr5:121758736G>A	ENST00000261368.8	+	4	566	c.304G>A	c.(304-306)Gtg>Atg	p.V102M	SNCAIP_ENST00000542191.1_Intron|SNCAIP_ENST00000379538.3_Intron|SNCAIP_ENST00000503116.2_Missense_Mutation_p.V149M|SNCAIP_ENST00000379533.2_Missense_Mutation_p.V149M|SNCAIP_ENST00000504884.2_Intron|SNCAIP_ENST00000261367.7_Missense_Mutation_p.V149M|SNCAIP_ENST00000379536.2_Missense_Mutation_p.V102M|SNCAIP_ENST00000414317.2_Intron	NM_005460.2	NP_005451.2	Q9Y6H5	SNCAP_HUMAN	synuclein, alpha interacting protein	102					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)		GAACCAGAAAGTGGTTGAGTA	0.552																																					p.V102M		Atlas-SNP	.											.	SNCAIP	308	.	0			c.G304A						PASS	.						55	60	58					5																	121758736		2203	4300	6503	SO:0001583	missense	9627	exon4			CAGAAAGTGGTTG	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.304G>A	chr5.hg19:g.121758736G>A	ENSP00000261368:p.Val102Met	224.0	0.0	.		186.0	62.0	.	NM_005460	D3DSZ1|Q05BS1|Q1PSC2|Q49AC6|Q504U9|Q6L984|Q6L985|Q6L986|Q9HC59	Missense_Mutation	SNP	ENST00000261368.8	hg19	CCDS4131.1	.	.	.	.	.	.	.	.	.	.	G	17.01	3.280488	0.59758	.	.	ENSG00000064692	ENST00000514467;ENST00000506272;ENST00000509154;ENST00000261368;ENST00000379533;ENST00000379536;ENST00000261367;ENST00000503116	T;T;T;T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52	5.53	2.75	0.32379	.	0.885835	0.09030	U	0.858812	T	0.23094	0.0558	N	0.24115	0.695	0.58432	D	0.999994	B;B;B;B	0.32526	0.257;0.374;0.374;0.257	B;B;B;B	0.33521	0.049;0.165;0.165;0.049	T	0.02320	-1.1177	10	0.66056	D	0.02	.	8.6976	0.34305	0.1371:0.1257:0.7373:0.0	.	102;149;149;102	D6R9G8;Q9Y6H5-6;Q9Y6H5-3;Q9Y6H5	.;.;.;SNCAP_HUMAN	M	102;149;102;102;149;102;149;149	ENSP00000427090:V102M;ENSP00000426551:V149M;ENSP00000422106:V102M;ENSP00000261368:V102M;ENSP00000368848:V149M;ENSP00000368851:V102M;ENSP00000261367:V149M;ENSP00000423199:V149M	ENSP00000261367:V149M	V	+	1	0	SNCAIP	121786635	0.996000	0.38824	0.051000	0.19133	0.975000	0.68041	3.922000	0.56462	0.294000	0.22547	0.561000	0.74099	GTG	.	.	.	none		0.552	SNCAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250888.1			A	121758736	G	A	121758736	3	1	244	1	0	0	0	0	1	0	0	0	14854	1029	36	2	314	2	SNCAIP	5	121758736	Missense_Mutation	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	12602806	121758736	59156524	32	15061											
SIL1	64374	hgsc.bcm.edu	37	chr5	138378379	138378379	+	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	gtgcactcttgagatcctgaGatgtgtaggtgttggtgttg	6	15	15	5	0	1	2	0	2	1	2	2	4	2	2	1	2	1	4	1	2	1	4	rs55660322		TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr5:138378379G>T	ENST00000394817.2	-	5	522	c.383C>A	c.(382-384)tCt>tAt	p.S128Y	CTB-46B19.2_ENST00000512875.2_RNA|SIL1_ENST00000265195.5_Missense_Mutation_p.S128Y|SIL1_ENST00000509534.1_Missense_Mutation_p.S135Y	NM_022464.4	NP_071909.1	Q9H173	SIL1_HUMAN	SIL1 nucleotide exchange factor	128	Interaction with HSPA5 and localization to the endoplasmic reticulum. {ECO:0000250}.				intracellular protein transport (GO:0006886)|protein folding (GO:0006457)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GAGATCCTGAGATGTGTAGGT	0.463									Marinesco-Sjgren syndrome																												p.S128Y		Atlas-SNP	.											.	SIL1	31	.	0			c.C383A						PASS	.						221	200	207					5																	138378379		2203	4300	6503	SO:0001583	missense	64374	exon6	Familial Cancer Database	Marinesco-Sjogren syndrome	TCCTGAGATGTGT	AK075177	CCDS4209.1	5q31	2013-08-21	2013-08-21		ENSG00000120725	ENSG00000120725			24624	protein-coding gene	gene with protein product		608005	"Marinesco-Sjogren syndrome", "SIL1 homolog, endoplasmic reticulum chaperone (S. cerevisiae)"	MSS		11101517, 12356756, 16282977	Standard	XM_006714671		Approved	BAP, ULG5	uc003ldp.3	Q9H173	OTTHUMG00000129226	ENST00000394817.2:c.383C>A	chr5.hg19:g.138378379G>T	ENSP00000378294:p.Ser128Tyr	60.0	0.0	.		62.0	23.0	.	NM_001037633	D3DQC2|Q8N2L3	Missense_Mutation	SNP	ENST00000394817.2	hg19	CCDS4209.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.943178	0.73672	.	.	ENSG00000120725	ENST00000394817;ENST00000265195;ENST00000537511;ENST00000509534;ENST00000508639	T;T;T;T	0.72051	-0.61;-0.61;-0.62;-0.22	4.97	4.97	0.65823	.	0.265230	0.39759	N	0.001272	T	0.76292	0.3967	L	0.56769	1.78	0.42774	D	0.993843	D;D	0.62365	0.991;0.991	P;P	0.54544	0.755;0.676	T	0.78695	-0.2104	10	0.66056	D	0.02	-14.7438	13.924	0.63950	0.0:0.0:1.0:0.0	.	135;128	D6REA1;Q9H173	.;SIL1_HUMAN	Y	128;128;107;135;128	ENSP00000378294:S128Y;ENSP00000265195:S128Y;ENSP00000426858:S135Y;ENSP00000427371:S128Y	ENSP00000265195:S128Y	S	-	2	0	SIL1	138406278	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	5.244000	0.65400	2.746000	0.94184	0.555000	0.69702	TCT	.	.	.	alt		0.463	SIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251319.1	NM_022464		T	138378379	G	T	138378379	3	4	244	1	0	0	0	0	1	0	0	0	14334	942	33	4	1026	4	SIL1	5	138378379	Missense_Mutation	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	16619643	138378379	42536881	33	15062											
PCDHGA2	56113	hgsc.bcm.edu	37	chr5	140720354	140720354	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccagaacgcctggctgtctTaccacctgctcaaggccagc	8	7	10	16	1	2	1	1	0	1	1	2	1	2	1	5	2	4	2	5	2	3	1			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr5:140720354T>C	ENST00000394576.2	+	1	1816	c.1816T>C	c.(1816-1818)Tac>Cac	p.Y606H	PCDHGA1_ENST00000517417.1_Intron	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	606	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(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)			CTGGCTGTCTTACCACCTGCT	0.692																																					p.Y606H		Atlas-SNP	.											.	PCDHGA2	205	.	0			c.T1816C						PASS	.						60	70	66					5																	140720354		2203	4299	6502	SO:0001583	missense	56113	exon1			CTGTCTTACCACC	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.1816T>C	chr5.hg19:g.140720354T>C	ENSP00000378077:p.Tyr606His	56.0	0.0	.		67.0	19.0	.	NM_018915	Q52LL6|Q9Y5D5	Missense_Mutation	SNP	ENST00000394576.2	hg19	CCDS47289.1	.	.	.	.	.	.	.	.	.	.	.	15.58	2.874786	0.51695	.	.	ENSG00000081853	ENST00000394576	T	0.62941	-0.01	5.14	5.14	0.70334	Cadherin (4);Cadherin-like (1);	0.000000	0.37669	U	0.001992	D	0.88581	0.6475	H	0.99609	4.655	0.33366	D	0.573012	D;D	0.89917	1.0;1.0	D;D	0.87578	0.994;0.998	D	0.95385	0.8476	10	0.87932	D	0	.	14.99	0.71381	0.0:0.0:0.0:1.0	.	606;606	Q9Y5H1-2;Q9Y5H1	.;PCDG2_HUMAN	H	606	ENSP00000378077:Y606H	ENSP00000378077:Y606H	Y	+	1	0	PCDHGA2	140700538	1.000000	0.71417	1.000000	0.80357	0.038000	0.13279	7.952000	0.87827	2.093000	0.63338	0.397000	0.26171	TAC	.	.	.	none		0.692	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374738.1	NM_018915		C	140720354	T	C	140720354	3	2	244	1	0	0	0	0	1	0	0	0	11561	1754	61	3	1818	3	PCDHGA2	5	140720354	Missense_Mutation	SNP	T	TCGA-SX-A71V-01A-11D-A33Q-10	2341975	140720354	40194906	34	15063											
POU4F3	5459	hgsc.bcm.edu	37	chr5	145719332	145719332	+	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	caccacgccgtgcaccagggCctcgaaggcgacctgctgga	8	4	13	16	4	0	0	0	0	0	0	1	3	0	1	5	3	2	2	5	3	1	0			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr5:145719332C>T	ENST00000230732.4	+	2	431	c.342C>T	c.(340-342)ggC>ggT	p.G114G	CTC-359M8.1_ENST00000515598.1_RNA	NM_002700.2	NP_002691.1	Q15319	PO4F3_HUMAN	POU class 4 homeobox 3	114					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)			TGCACCAGGGCCTCGAAGGCG	0.662																																					p.G114G		Atlas-SNP	.											.	POU4F3	47	.	0			c.C342T						PASS	.						113	99	104					5																	145719332		2203	4299	6502	SO:0001819	synonymous_variant	5459	exon2			CCAGGGCCTCGAA	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.342C>T	chr5.hg19:g.145719332C>T		50.0	0.0	.		46.0	21.0	.	NM_002700	O60557|Q2M3F8	Silent	SNP	ENST00000230732.4	hg19	CCDS4281.1																																																																																			.	.	.	none		0.662	POU4F3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251887.2	NM_002700		T	145719332	C	T	145719332	2	4	244	1	0	0	0	0	0	0	0	1	12287	726	26	2		2	POU4F3	5	145719332	Silent	SNP	C	TCGA-SX-A71V-01A-11D-A33Q-10	4998978	145719332	35195928	35	15064											
CCDC99	54908	hgsc.bcm.edu	37	chr5	169018070	169018071	+	Frame_Shift_Ins	INS	-	-	G																															gagttatgaacaagaaaaatINSatacccttcaaagagaagtt																								rs535922596		TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr5:169018070_169018071insG	ENST00000265295.4	+	3	457_458	c.178_179insG	c.(178-180)tatfs	p.Y60fs	SPDL1_ENST00000510751.1_3'UTR	NM_017785.4	NP_060255.3			spindle apparatus coiled-coil protein 1																		ACAAGAAAAATATACCCTTCAA	0.312																																					p.Y60_T61delinsX		Atlas-Indel,Pindel	.											.	.	.	.	0			c.178_179insG						PASS	.																																			SO:0001589	frameshift_variant	54908	exon3			.	BC012568	CCDS4370.1	5q35.1	2012-09-27	2012-09-27	2012-09-27	ENSG00000040275	ENSG00000040275			26010	protein-coding gene	gene with protein product	"spindly homolog (Drosophila)"		"coiled-coil domain containing 99"	CCDC99		20427577	Standard	NM_017785		Approved	FLJ20364, hSpindly	uc003mae.4	Q96EA4	OTTHUMG00000130438	Exception_encountered	chr5.hg19:g.169018070_169018071insG	ENSP00000265295:p.Tyr60fs	194.0	0.0	0		146.0	59.0	0.40411	NM_017785		Frame_Shift_Ins	INS	ENST00000265295.4	hg19	CCDS4370.1																																																																																			.	.	.	none		0.312	SPDL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252829.2	NM_017785		G	169018071	-	G	169018070	7	5	244	1	0	1	1	0	0	0	0	0	2878	1406	49	0	184	0	CCDC99	5	169018070	Frame_Shift_Ins	INS	-	TCGA-SX-A71V-01A-11D-A33Q-10	23298738	169018070	11897190	36	15065											
DUSP1	1843	hgsc.bcm.edu	37	chr5	172196606	172196606	+	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	tcaatggcctcgttgaaccaGgagctgatgtctgccttgtg	7	12	12	10	1	2	2	1	2	1	0	3	3	2	3	3	2	3	2	3	2	2	2			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr5:172196606G>T	ENST00000239223.3	-	3	947	c.705C>A	c.(703-705)tcC>tcA	p.S235S	RP11-779O18.3_ENST00000523005.1_RNA	NM_004417.3	NP_004408.1	P28562	DUS1_HUMAN	dual specificity phosphatase 1	235	Tyrosine-protein phosphatase.				cellular response to hormone stimulus (GO:0032870)|endoderm formation (GO:0001706)|inactivation of MAPK activity (GO:0000188)|intracellular signal transduction (GO:0035556)|mitotic cell cycle arrest (GO:0071850)|negative regulation of apoptotic process (GO:0043066)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of meiotic cell cycle (GO:0051447)|peptidyl-threonine dephosphorylation (GO:0035970)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of apoptotic process (GO:0043065)|protein dephosphorylation (GO:0006470)|regulation of apoptotic process (GO:0042981)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to light stimulus (GO:0009416)|response to oxidative stress (GO:0006979)|response to retinoic acid (GO:0032526)|response to testosterone (GO:0033574)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|protein tyrosine/threonine phosphatase activity (GO:0008330)			NS(1)|breast(2)|endometrium(1)|large_intestine(1)|liver(1)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	10	Renal(175;0.000159)|Lung NSC(126;0.00431)|all_lung(126;0.00729)	all_hematologic(541;4.11e-18)|Breast(839;0.00637)|Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.15)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)	GBM - Glioblastoma multiforme(465;0.0103)		CGTTGAACCAGGAGCTGATGT	0.493																																					p.S235S		Atlas-SNP	.											.	DUSP1	27	.	0			c.C705A						PASS	.						217	196	203					5																	172196606		2203	4300	6503	SO:0001819	synonymous_variant	1843	exon3			GAACCAGGAGCTG	X68277	CCDS4380.1	5q35.1	2011-06-09			ENSG00000120129	ENSG00000120129		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3064	protein-coding gene	gene with protein product		600714		PTPN10		1406996, 7806236	Standard	NM_004417		Approved	HVH1, CL100, MKP-1	uc003mbv.2	P28562	OTTHUMG00000130523	ENST00000239223.3:c.705C>A	chr5.hg19:g.172196606G>T		92.0	0.0	.		53.0	18.0	.	NM_004417	D3DQL9|Q2V508	Silent	SNP	ENST00000239223.3	hg19	CCDS4380.1																																																																																			.	.	.	none		0.493	DUSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252943.3	NM_004417		T	172196606	G	T	172196606	2	4	244	1	0	0	0	0	0	0	0	1	4811	987	35	4		4	DUSP1	5	172196606	Silent	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	3178536	172196606	8718654	37	15066											
MOG	4340	hgsc.bcm.edu	37	chr6	29634002	29634002	+	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	gtgctcctcctgcagatcacTgttggcctcatcttcctctg	4	14	8	15	0	4	1	2	0	2	1	7	1	7	1	4	1	2	3	4	1	0	2			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr6:29634002T>G	ENST00000376917.3	+	3	739	c.510T>G	c.(508-510)acT>acG	p.T170T	MOG_ENST00000396701.2_Silent_p.T170T|MOG_ENST00000396704.3_Silent_p.T170T|MOG_ENST00000416766.2_Intron|MOG_ENST00000483013.1_Silent_p.T54T|MOG_ENST00000533330.2_3'UTR|MOG_ENST00000490427.1_Silent_p.T54T|MOG_ENST00000376894.4_Silent_p.T170T|MOG_ENST00000494692.1_Silent_p.T170T|MOG_ENST00000376898.3_Silent_p.T170T|MOG_ENST00000376902.3_3'UTR|MOG_ENST00000376888.2_Silent_p.T54T|MOG_ENST00000376891.4_Silent_p.T170T|MOG_ENST00000431798.2_Silent_p.T170T	NM_002433.4|NM_206809.3	NP_002424.3|NP_996532.2	Q16653	MOG_HUMAN	myelin oligodendrocyte glycoprotein	170					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						TGCAGATCACTGTTGGCCTCA	0.542																																					p.T170T		Atlas-SNP	.											.	MOG	47	.	0			c.T510G						PASS	.						256	224	236					6																	29634002		1511	2709	4220	SO:0001819	synonymous_variant	4340	exon3			GATCACTGTTGGC		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.510T>G	chr6.hg19:g.29634002T>G		56.0	0.0	.		46.0	20.0	.	NM_001008229	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	hg19	CCDS34370.1																																																																																			.	.	.	none		0.542	MOG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076160.3	NM_002433		G	29634002	T	G	29634002	2	3	244	1	0	0	0	0	0	0	0	1	9700	1567	55	5		5	MOG	6	29634002	Silent	SNP	T	TCGA-SX-A71V-01A-11D-A33Q-10		29634002	141481065	38	15067											
MDC1	9656	hgsc.bcm.edu	37	chr6	30681674	30681674	+	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	tctactgtcagagggccccgGgagacaaagggcagagagac	12	4	15	10	1	2	4	1	0	1	4	2	6	2	4	2	3	1	1	2	3	2	1			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr6:30681674G>C	ENST00000376406.3	-	3	1070	c.423C>G	c.(421-423)tcC>tcG	p.S141S	MDC1_ENST00000494654.1_5'Flank|MDC1_ENST00000376405.2_Silent_p.S141S|MDC1-AS1_ENST00000442150.1_RNA	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	141	Interaction with CHEK2.|Interaction with the MRN complex.				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						GAGGGCCCCGGGAGACAAAGG	0.562								Other conserved DNA damage response genes																													p.S141S		Atlas-SNP	.											.	MDC1	218	.	0			c.C423G						PASS	.						65	75	72					6																	30681674		1511	2709	4220	SO:0001819	synonymous_variant	9656	exon3			GCCCCGGGAGACA	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.423C>G	chr6.hg19:g.30681674G>C		144.0	0.0	.		109.0	47.0	.	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Silent	SNP	ENST00000376406.3	hg19	CCDS34384.1																																																																																			.	.	.	none		0.562	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641		C	30681674	G	C	30681674	2	2	244	1	0	0	0	0	0	0	0	1	9410	1219	43	4		4	MDC1	6	30681674	Silent	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	1047672	30681674	140433393	39	15068											
MAPK14	1432	hgsc.bcm.edu	37	chr6	36027090	36027091	+	Missense_Mutation	DNP	AC	AC	CA																															ttggtctgttggacgtttttAcacctgcaaggtctctggag																										TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr6:36027090_36027091AC>CA	ENST00000229794.4	+	3	659_660	c.271_272AC>CA	c.(271-273)ACa>CAa	p.T91Q	MAPK14_ENST00000229795.3_Missense_Mutation_p.T91Q|MAPK14_ENST00000468133.1_Missense_Mutation_p.T14Q|MAPK14_ENST00000310795.4_Missense_Mutation_p.T91Q	NM_139012.2|NM_139014.2	NP_620581.1|NP_620583.1	Q16539	MK14_HUMAN	mitogen-activated protein kinase 14	91	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cartilage condensation (GO:0001502)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to ionizing radiation (GO:0071479)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|chemotaxis (GO:0006935)|chondrocyte differentiation (GO:0002062)|DNA damage checkpoint (GO:0000077)|fatty acid oxidation (GO:0019395)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mRNA metabolic process (GO:0016071)|muscle cell differentiation (GO:0042692)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myoblast differentiation involved in skeletal muscle regeneration (GO:0014835)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neurotrophin TRK receptor signaling pathway (GO:0048011)|osteoclast differentiation (GO:0030316)|p38MAPK cascade (GO:0038066)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myoblast fusion (GO:1901741)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Ras protein signal transduction (GO:0007265)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to muramyl dipeptide (GO:0032495)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|signal transduction in response to DNA damage (GO:0042770)|skeletal muscle tissue development (GO:0007519)|stress-activated MAPK cascade (GO:0051403)|stress-induced premature senescence (GO:0090400)|striated muscle cell differentiation (GO:0051146)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|MAP kinase kinase activity (GO:0004708)|NFAT protein binding (GO:0051525)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|stomach(1)	16						GGACGTTTTTACACCTGCAAGG	0.337																																					p.T91P|p.T91K	Pancreas(20;8 363 26997 32430 36377 43317 49243 50560 51947)|Colon(176;951 1093 20177 30266 32328 34418 35271 44052 51610)	Atlas-SNP	.											.	MAPK14	75	.	0			c.A271C|c.C272A						PASS	.																																			SO:0001583	missense	1432	exon3			GTTTTTACACCTG|TTTTTACACCTGC	L35263	CCDS4815.1, CCDS4816.1, CCDS4817.1	6p21.3-p21.2	2011-06-09			ENSG00000112062	ENSG00000112062		"Mitogen-activated protein kinase cascade / Kinases"	6876	protein-coding gene	gene with protein product	"p38 MAP kinase"	600289		CSPB1, CSBP1, CSBP2		7997261	Standard	NM_139012		Approved	PRKM14, p38, Mxi2, PRKM15	uc003olq.3	Q16539	OTTHUMG00000159806	Exception_encountered	chr6.hg19:g.36027090_36027091delinsCA	ENSP00000229794:p.Thr91Gln	22.0	0.0	.		21.0	10.0	.	NM_139012	A6ZJ92|A8K6P4|B0LPH0|B5TY32|O60776|Q13083|Q14084|Q8TDX0	Missense_Mutation	SNP	ENST00000229794.4	hg19	CCDS4816.1																																																																																			.	.	.	none		0.337	MAPK14-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357450.1	NM_001315		CA	36027091	AC	CA	36027090	3	2	244	1	0	0	0	0	1	0	0	0	9283	391	14	5	281	5	MAPK14	6	36027090	Missense_Mutation	DNP	AC	TCGA-SX-A71V-01A-11D-A33Q-10	5345416	36027090	135087977	40	15069											
PPIL1	51645	hgsc.bcm.edu	37	chr6	36823708	36823708	+	Frame_Shift_Del	DEL	T	T	-																															ctgacacactcggccaaaaaTggtgtgtttgccgtcaagcc																										TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr6:36823708delT	ENST00000373699.5	-	4	633	c.382delA	c.(382-384)attfs	p.I128fs	PPIL1_ENST00000483552.1_5'UTR	NM_016059.4	NP_057143.1	Q9Y3C6	PPIL1_HUMAN	peptidylprolyl isomerase (cyclophilin)-like 1	128	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			lung(1)|ovary(1)	2						CGGCCAAAAATGGTGTGTTTG	0.552																																					p.I128fs		Atlas-Indel,Pindel	.											.	PPIL1	6	.	0			c.383delT						PASS	.						90	79	83					6																	36823708		2203	4300	6503	SO:0001589	frameshift_variant	51645	exon4			.	AF090992	CCDS4826.1	6p21.1	2008-08-29			ENSG00000137168	ENSG00000137168			9260	protein-coding gene	gene with protein product		601301				10072585, 8978786	Standard	NM_016059		Approved	CYPL1	uc003omu.2	Q9Y3C6	OTTHUMG00000014612	ENST00000373699.5:c.382delA	chr6.hg19:g.36823708delT	ENSP00000362803:p.Ile128fs	106.0	0.0	0		78.0	27.0	0.346154	NM_016059	O15001|Q5TDC9	Frame_Shift_Del	DEL	ENST00000373699.5	hg19	CCDS4826.1																																																																																			.	.	.	none		0.552	PPIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040382.1			-	36823708	T	-	36823708	7	5	244	1	0	1	0	1	0	0	0	0	12336	1464	51	0	122	0	PPIL1	6	36823708	Frame_Shift_Del	DEL	T	TCGA-SX-A71V-01A-11D-A33Q-10	796618	36823708	134291359	41	15070											
ZNF292	23036	hgsc.bcm.edu	37	chr6	87967887	87967887	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaatgctttctcatgtttcaAcaggttgtgtctctgatgca	9	16	8	8	0	3	1	2	1	2	0	5	1	3	1	0	1	3	4	0	1	2	3			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr6:87967887A>G	ENST00000369577.3	+	8	4583	c.4540A>G	c.(4540-4542)Aca>Gca	p.T1514A	ZNF292_ENST00000339907.4_Missense_Mutation_p.T1509A	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	1514						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		TCATGTTTCAACAGGTTGTGT	0.448																																					p.T1514A		Atlas-SNP	.											.	ZNF292	479	.	0			c.A4540G						PASS	.						41	41	41					6																	87967887		1995	4156	6151	SO:0001583	missense	23036	exon8			GTTTCAACAGGTT	AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"Zinc fingers, C2H2-type"	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.4540A>G	chr6.hg19:g.87967887A>G	ENSP00000358590:p.Thr1514Ala	104.0	0.0	.		57.0	19.0	.	NM_015021	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	hg19	CCDS47457.1	.	.	.	.	.	.	.	.	.	.	A	7.769	0.707088	0.15239	.	.	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.07114	3.22;3.23	5.87	-8.87	0.00792	.	0.913634	0.09402	N	0.806994	T	0.01061	0.0035	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47761	-0.9092	10	0.54805	T	0.06	.	1.7259	0.02921	0.22:0.2477:0.3344:0.1979	.	1514	O60281	ZN292_HUMAN	A	1514;1509	ENSP00000358590:T1514A;ENSP00000342847:T1509A	ENSP00000342847:T1509A	T	+	1	0	ZNF292	88024606	0.000000	0.05858	0.004000	0.12327	0.911000	0.54048	-0.943000	0.03917	-1.272000	0.02427	-0.250000	0.11733	ACA	.	.	.	none		0.448	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021		G	87967887	A	G	87967887	3	3	244	1	0	0	0	0	1	0	0	0	17838	43	2	3	4570	3	ZNF292	6	87967887	Missense_Mutation	SNP	A	TCGA-SX-A71V-01A-11D-A33Q-10	51144179	87967887	83147180	42	15071											
CASP8AP2	9994	hgsc.bcm.edu	37	chr6	90575693	90575693	+	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	0	0	0	0	0	0	0	0	0	0	tgtgtttttaccaaattcagCtcattctacctctaagagtc	10	16	5	10	0	4	1	2	0	2	1	5	1	4	1	2	0	3	2	2	0	4	7			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr6:90575693C>G	ENST00000551025.1	+	0	4121									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)		CCAAATTCAGCTCATTCTACC	0.289																																					p.A895G	Colon(187;1656 2025 17045 31481 39901)	Atlas-SNP	.											.	CASP8AP2	108	.	0			c.C2684G						PASS	.						16	15	16					6																	90575693		1803	4056	5859			9994	exon8			ATTCAGCTCATTC	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"FLICE-associated huge protein"	606880	"CASP8 associated protein 2"			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		chr6.hg19:g.90575693C>G		199.0	0.0	.		173.0	50.0	.	NM_001137667		Missense_Mutation	SNP	ENST00000551025.1	hg19																																																																																				.	.	.	none		0.289	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667		G	90575693	C	G	90575693	1	3	244	0	1	0	0	0	0	0	0	0	2680	797	28	4		4	CASP8AP2	6	90575693	RNA	SNP	C	TCGA-SX-A71V-01A-11D-A33Q-10	2607806	90575693	80539374	43	15072											
HOXA7	3204	hgsc.bcm.edu	37	chr7	27194784	27194784	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttgaagtggaactccttcTccagctccagcgtctggtag	7	11	12	11	1	2	1	0	1	2	0	5	2	4	2	3	3	3	3	3	3	3	3			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr7:27194784T>C	ENST00000242159.3	-	2	570	c.437A>G	c.(436-438)gAg>gGg	p.E146G	HOXA7_ENST00000523796.2_5'UTR|HOXA-AS3_ENST00000524304.1_RNA|RP1-170O19.22_ENST00000467897.2_RNA|HOXA-AS3_ENST00000518947.2_RNA|HOXA-AS3_ENST00000521231.1_RNA|RP1-170O19.23_ENST00000498652.1_RNA|HOXA-AS3_ENST00000518848.1_RNA|HOXA-AS3_ENST00000521197.1_RNA	NM_006896.3	NP_008827.2	P31268	HXA7_HUMAN	homeobox A7	146					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						GAACTCCTTCTCCAGCTCCAG	0.597																																					p.E146G		Atlas-SNP	.											.	HOXA7	34	.	0			c.A437G						PASS	.						100	98	98					7																	27194784		2203	4300	6503	SO:0001583	missense	3204	exon2			TCCTTCTCCAGCT		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.437A>G	chr7.hg19:g.27194784T>C	ENSP00000242159:p.Glu146Gly	66.0	0.0	.		72.0	23.0	.	NM_006896	A4D191|O43368|O43486|O95655|Q9NSC8|Q9UDM1	Missense_Mutation	SNP	ENST00000242159.3	hg19	CCDS5408.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.440700	0.83993	.	.	ENSG00000122592	ENST00000242159	D	0.97831	-4.56	5.0	5.0	0.66597	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99127	0.9699	H	0.97186	3.955	0.80722	D	1	D	0.54207	0.965	D	0.69142	0.962	D	0.99078	1.0836	10	0.72032	D	0.01	.	14.697	0.69129	0.0:0.0:0.0:1.0	.	146	P31268	HXA7_HUMAN	G	146	ENSP00000242159:E146G	ENSP00000242159:E146G	E	-	2	0	HOXA7	27161309	1.000000	0.71417	0.999000	0.59377	0.957000	0.61999	7.904000	0.87408	1.887000	0.54652	0.379000	0.24179	GAG	.	.	.	none		0.597	HOXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358695.1			C	27194784	T	C	27194784	3	2	244	1	0	0	0	0	1	0	0	0	7304	1551	54	3	259	3	HOXA7	7	27194784	Missense_Mutation	SNP	T	TCGA-SX-A71V-01A-11D-A33Q-10		27194784	131943879	44	15073											
PCLO	27445	hgsc.bcm.edu	37	chr7	82545774	82545774	+	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	gactttctattcgggttggtCttgtgctactcacttcactg	5	17	9	10	1	4	0	2	0	2	0	5	1	4	0	0	2	2	2	0	2	2	7			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr7:82545774C>T	ENST00000333891.9	-	7	11865	c.11528G>A	c.(11527-11529)aGa>aAa	p.R3843K	PCLO_ENST00000423517.2_Missense_Mutation_p.R3843K|PCLO_ENST00000437081.1_Missense_Mutation_p.R563K	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						TCGGGTTGGTCTTGTGCTACT	0.473																																					p.R3843K		Atlas-SNP	.											.	PCLO	1506	.	0			c.G11528A						PASS	.						303	287	292					7																	82545774		2036	4183	6219	SO:0001583	missense	27445	exon7			GTTGGTCTTGTGC	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.11528G>A	chr7.hg19:g.82545774C>T	ENSP00000334319:p.Arg3843Lys	171.0	0.0	.		204.0	42.0	.	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	16.21	3.060110	0.55432	.	.	ENSG00000186472	ENST00000333891;ENST00000423517;ENST00000437081	T;T	0.31769	1.48;1.5	5.67	5.67	0.87782	.	.	.	.	.	T	0.59390	0.2190	M	0.73962	2.25	0.58432	D	0.99999	D;D;D	0.89917	0.997;1.0;1.0	D;D;D	0.83275	0.978;0.996;0.996	T	0.61417	-0.7067	9	0.87932	D	0	.	19.7691	0.96356	0.0:1.0:0.0:0.0	.	3774;3843;3843	Q9Y6V0;Q9Y6V0-5;Q9Y6V0-6	PCLO_HUMAN;.;.	K	3843;3843;563	ENSP00000334319:R3843K;ENSP00000388393:R3843K	ENSP00000334319:R3843K	R	-	2	0	PCLO	82383710	1.000000	0.71417	0.896000	0.35187	0.120000	0.20174	7.818000	0.86416	2.689000	0.91719	0.462000	0.41574	AGA	.	.	.	none		0.473	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82545774	C	T	82545774	3	4	244	1	0	0	0	0	1	0	0	0	11590	913	32	2	3993	2	PCLO	7	82545774	Missense_Mutation	SNP	C	TCGA-SX-A71V-01A-11D-A33Q-10	55350990	82545774	76592889	45	15074											
UBN2	254048	hgsc.bcm.edu	37	chr7	138943310	138943310	+	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	cactggcactctacagtttcGccaagcttcagatactgaag	11	10	8	12	1	2	2	1	1	1	1	3	2	2	2	1	1	3	3	1	1	4	4			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr7:138943310G>T	ENST00000473989.3	+	4	740	c.740G>T	c.(739-741)cGc>cTc	p.R247L	UBN2_ENST00000288561.8_Missense_Mutation_p.R164L	NM_173569.3	NP_775840.3	Q6ZU65	UBN2_HUMAN	ubinuclein 2	247						extracellular space (GO:0005615)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	42						CTACAGTTTCGCCAAGCTTCA	0.363																																					p.R247L		Atlas-SNP	.											.	UBN2	90	.	0			c.G740T						PASS	.						103	93	96					7																	138943310		1854	4090	5944	SO:0001583	missense	254048	exon4			AGTTTCGCCAAGC	AK098644	CCDS43655.1, CCDS43655.2	7q34	2008-12-08			ENSG00000157741	ENSG00000157741			21931	protein-coding gene	gene with protein product		613841				19029251	Standard	NM_173569		Approved	FLJ25778, KIAA2030	uc011kqr.2	Q6ZU65	OTTHUMG00000157623	ENST00000473989.3:c.740G>T	chr7.hg19:g.138943310G>T	ENSP00000418648:p.Arg247Leu	83.0	0.0	.		76.0	38.0	.	NM_173569	A4D1S2|Q2YDY4|Q6P1K0|Q86XN9|Q8N7D1	Missense_Mutation	SNP	ENST00000473989.3	hg19	CCDS43655.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	35|35	5.450349|5.450349	0.96205|0.96205	.|.	.|.	ENSG00000157741|ENSG00000157741	ENST00000483726|ENST00000486663;ENST00000473989;ENST00000288561	.|T;T;T	.|0.27256	.|1.68;1.68;1.68	5.27|5.27	5.27|5.27	0.74061|0.74061	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.54175|0.54175	0.1842|0.1842	M|M	0.76328|0.76328	2.33|2.33	0.80722|0.80722	D|D	1|1	.|D	.|0.76494	.|0.999	.|D	.|0.85130	.|0.997	T|T	0.56986|0.56986	-0.7888|-0.7888	5|10	.|0.72032	.|D	.|0.01	-7.8458|-7.8458	19.2541|19.2541	0.93938|0.93938	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|247	.|Q6ZU65	.|UBN2_HUMAN	S|L	16|70;247;164	.|ENSP00000417849:R70L;ENSP00000418648:R247L;ENSP00000288561:R164L	.|ENSP00000288561:R164L	A|R	+|+	1|2	0|0	UBN2|UBN2	138593850|138593850	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	9.713000|9.713000	0.98740|0.98740	2.628000|2.628000	0.89032|0.89032	0.460000|0.460000	0.39030|0.39030	GCC|CGC	.	.	.	none		0.363	UBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349272.3	NM_173569		T	138943310	G	T	138943310	3	4	244	1	0	0	0	0	1	0	0	0	16905	1087	38	4	754	4	UBN2	7	138943310	Missense_Mutation	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	56397536	138943310	20195353	46	15075											
GIMAP8	155038	hgsc.bcm.edu	37	chr7	150171317	150171317	+	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	agaaaaaagaaagtttcgatCattgatgctccggacatctc	15	10	8	8	2	2	3	1	1	1	2	5	5	3	4	1	1	1	2	1	1	4	2			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr7:150171317C>T	ENST00000307271.3	+	4	1474	c.900C>T	c.(898-900)atC>atT	p.I300I		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	300	AIG1-type G 2.					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)		AAGTTTCGATCATTGATGCTC	0.478																																					p.I300I		Atlas-SNP	.											.	GIMAP8	136	.	0			c.C900T						PASS	.						81	89	87					7																	150171317		2203	4300	6503	SO:0001819	synonymous_variant	155038	exon4			TTCGATCATTGAT	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.900C>T	chr7.hg19:g.150171317C>T		118.0	0.0	.		159.0	40.0	.	NM_175571		Silent	SNP	ENST00000307271.3	hg19	CCDS34777.1																																																																																			.	.	.	none		0.478	GIMAP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350701.1	NM_175571		T	150171317	C	T	150171317	2	4	244	1	0	0	0	0	0	0	0	1	6392	816	29	2		2	GIMAP8	7	150171317	Silent	SNP	C	TCGA-SX-A71V-01A-11D-A33Q-10	11228007	150171317	8967346	47	15076											
AGPAT6	137964	hgsc.bcm.edu	37	chr8	41476269	41476269	+	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	ggatggtgacgtacctgctgCgaatgatgaccagctgggcc	8	8	15	10	2	0	3	0	3	0	0	0	5	0	4	3	3	4	3	3	3	2	1			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr8:41476269C>A	ENST00000396987.3	+	11	2047	c.1120C>A	c.(1120-1122)Cga>Aga	p.R374R	RP11-360L9.8_ENST00000581909.1_RNA	NM_178819.3	NP_848934.1	Q86UL3	GPAT4_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 6	374					acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|diacylglycerol metabolic process (GO:0046339)|fatty acid metabolic process (GO:0006631)|glandular epithelial cell maturation (GO:0002071)|glycerophospholipid biosynthetic process (GO:0046474)|lactation (GO:0007595)|lipid biosynthetic process (GO:0008610)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			endometrium(3)|kidney(2)|large_intestine(3)|lung(6)	14	Ovarian(28;0.00769)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	OV - Ovarian serous cystadenocarcinoma(14;0.00126)|Colorectal(10;0.0014)|Lung(22;0.00177)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0147)			GTACCTGCTGCGAATGATGAC	0.547																																					p.R374R		Atlas-SNP	.											.	AGPAT6	32	.	0			c.C1120A						PASS	.						204	178	187					8																	41476269		2203	4300	6503	SO:0001819	synonymous_variant	137964	exon11			CTGCTGCGAATGA	AF406612	CCDS6117.1	8p11.21	2013-02-05	2013-02-05			ENSG00000158669	2.3.1.15	"1-acylglycerol-3-phosphate O-acyltransferases"	20880	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, zeta"	608143	"1-acylglycerol-3-phosphate O-acyltransferase 6 (lysophosphatidic acid acyltransferase, zeta)"			12938015	Standard	NM_178819		Approved	DKFZp586M1819, LPAAT-zeta	uc003xnz.2	Q86UL3		ENST00000396987.3:c.1120C>A	chr8.hg19:g.41476269C>A		70.0	0.0	.		66.0	25.0	.	NM_178819	Q86V89	Silent	SNP	ENST00000396987.3	hg19	CCDS6117.1																																																																																			.	.	.	none		0.547	AGPAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377158.1	NM_178819		A	41476269	C	A	41476269	2	1	244	1	0	0	0	0	0	0	0	1	391	760	27	4		4	AGPAT6	8	41476269	Silent	SNP	C	TCGA-SX-A71V-01A-11D-A33Q-10		41476269	104887753	48	15077											
OXR1	55074	hgsc.bcm.edu	37	chr8	107719085	107719085	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acagcacaagtataaaaggtAattcagaccaggattctttt	16	11	7	7	0	2	1	1	0	1	1	2	2	2	2	1	2	1	3	1	2	5	7			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr8:107719085A>G	ENST00000442977.2	+	8	1438	c.1339A>G	c.(1339-1341)Aat>Gat	p.N447D	OXR1_ENST00000497705.1_Missense_Mutation_p.N379D|OXR1_ENST00000517566.2_Missense_Mutation_p.N446D|OXR1_ENST00000312046.6_Missense_Mutation_p.N439D|OXR1_ENST00000531443.1_Missense_Mutation_p.N446D|OXR1_ENST00000445937.1_Missense_Mutation_p.N446D|OXR1_ENST00000452423.2_5'UTR	NM_001198532.1	NP_001185461.1	Q8N573	OXR1_HUMAN	oxidation resistance 1	447					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)			TATAAAAGGTAATTCAGACCA	0.338																																					p.N447D		Atlas-SNP	.											.	OXR1	190	.	0			c.A1339G						PASS	.						70	71	70					8																	107719085		2203	4300	6503	SO:0001583	missense	55074	exon8			AAAGGTAATTCAG	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.1339A>G	chr8.hg19:g.107719085A>G	ENSP00000405424:p.Asn447Asp	140.0	0.0	.		139.0	59.0	.	NM_001198532	A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7	Missense_Mutation	SNP	ENST00000442977.2	hg19	CCDS56548.1	.	.	.	.	.	.	.	.	.	.	A	3.501	-0.101859	0.06967	.	.	ENSG00000164830	ENST00000445937;ENST00000531443;ENST00000517566;ENST00000442977;ENST00000497705;ENST00000312046	T;T;T;T;T;T	0.22743	2.78;2.78;2.78;2.78;1.94;2.77	5.29	0.47	0.16747	.	1.123310	0.06446	N	0.726853	T	0.14098	0.0341	L	0.29908	0.895	0.09310	N	0.999999	B;B;B;B;B	0.23249	0.0;0.001;0.0;0.003;0.082	B;B;B;B;B	0.20767	0.003;0.001;0.001;0.004;0.031	T	0.35599	-0.9782	10	0.22109	T	0.4	-12.2398	5.566	0.17170	0.4857:0.1807:0.3335:0.0	.	439;447;446;379;446	Q8N573-2;Q8N573;D3HIS6;Q8N573-3;Q8N573-5	.;OXR1_HUMAN;.;.;.	D	446;446;446;447;379;439	ENSP00000402918:N446D;ENSP00000431966:N446D;ENSP00000429205:N446D;ENSP00000405424:N447D;ENSP00000431014:N379D;ENSP00000311026:N439D	ENSP00000311026:N439D	N	+	1	0	OXR1	107788261	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	0.254000	0.18314	0.128000	0.18479	0.482000	0.46254	AAT	.	.	.	none		0.338	OXR1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_181354		G	107719085	A	G	107719085	3	3	244	1	0	0	0	0	1	0	0	0	11341	362	13	3	1569	3	OXR1	8	107719085	Missense_Mutation	SNP	A	TCGA-SX-A71V-01A-11D-A33Q-10	66242816	107719085	38644937	49	15078											
FAM83A	84985	hgsc.bcm.edu	37	chr8	124195568	124195569	+	Missense_Mutation	DNP	AC	AC	CT																															tccgccgctgcatcacccggActagccaggtaccgatggca																										TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr8:124195568_124195569AC>CT	ENST00000518448.1	+	2	2486_2487	c.472_473AC>CT	c.(472-474)ACt>CTt	p.T158L	FAM83A_ENST00000546351.1_Missense_Mutation_p.T158L|FAM83A_ENST00000522648.1_Missense_Mutation_p.T158L|FAM83A_ENST00000276699.6_Missense_Mutation_p.T158L|U3_ENST00000408534.1_RNA|FAM83A_ENST00000318462.6_Missense_Mutation_p.T158L|FAM83A_ENST00000536633.1_Missense_Mutation_p.T158L|RP11-539E17.5_ENST00000522383.1_RNA			Q86UY5	FA83A_HUMAN	family with sequence similarity 83, member A	158										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(2)|skin(1)	17	Lung NSC(37;1.55e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			CATCACCCGGACTAGCCAGGTA	0.594																																					p.T158P|p.T158I		Atlas-SNP	.											.	FAM83A	64	.	0			c.A472C|c.C473T						PASS	.																																			SO:0001583	missense	84985	exon1			ACCCGGACTAGCC|CCCGGACTAGCCA	BC052300	CCDS6339.1, CCDS6340.1, CCDS75784.1	8q24.13	2014-03-13			ENSG00000147689	ENSG00000147689			28210	protein-coding gene	gene with protein product						22886303	Standard	XM_005251087		Approved	MGC14128, BJ-TSA-9	uc003ypx.3	Q86UY5	OTTHUMG00000165083	Exception_encountered	chr8.hg19:g.124195568_124195569delinsCT	ENSP00000428876:p.Thr158Leu	50.0|48.0	0.0	.		43.0|45.0	14.0	.	NM_032899	Q71HL2|Q8N7I1|Q96I47	Missense_Mutation	SNP	ENST00000518448.1	hg19	CCDS6340.1																																																																																			.	.	.	none		0.594	FAM83A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381737.1	NM_032899		CT	124195569	AC	CT	124195568	3	2	244	1	0	0	0	0	1	0	0	0	5640	275	10	5	474	5	FAM83A	8	124195568	Missense_Mutation	DNP	AC	TCGA-SX-A71V-01A-11D-A33Q-10	16476483	124195568	22168454	50	15079											
EIF2C2	27161	hgsc.bcm.edu	37	chr8	141554392	141554393	+	Frame_Shift_Del	DEL	AC	AC	-																															aaagatgacgggctgctggaAcaccggcggcctgcggagag																										TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr8:141554392_141554393delAC	ENST00000220592.5	-	14	1870_1871	c.1758_1759delGT	c.(1756-1761)gtgttcfs	p.F587fs	AGO2_ENST00000519980.1_Frame_Shift_Del_p.F587fs	NM_012154.3	NP_036286.2	Q9UKV8	AGO2_HUMAN	argonaute RISC catalytic component 2	587	Interaction with GW182 family members. {ECO:0000255}.|Piwi. {ECO:0000255|HAMAP-Rule:MF_03031}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|regulation of transcription, DNA-templated (GO:0006355)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|mRNA cap binding complex (GO:0005845)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|RISC complex (GO:0016442)	endoribonuclease activity (GO:0004521)|endoribonuclease activity, cleaving siRNA-paired mRNA (GO:0070551)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA 7-methylguanosine cap binding (GO:0000340)|siRNA binding (GO:0035197)|translation initiation factor activity (GO:0003743)										GGCTGCTGGAACACCGGCGGCC	0.653																																					p.587_587del		Atlas-Indel,Pindel	.											.	.	.	.	0			c.1759_1760del						PASS	.																																			SO:0001589	frameshift_variant	27161	exon14			.	AF121255	CCDS6380.1, CCDS55279.1	8q24.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000123908	ENSG00000123908		"Argonaute/PIWI family"	3263	protein-coding gene	gene with protein product	"argonaute 2"	606229	"eukaryotic translation initiation factor 2C, 2"	EIF2C2		10534406, 12906857	Standard	NM_012154		Approved	hAGO2, Q10	uc003yvn.3	Q9UKV8	OTTHUMG00000164232	ENST00000220592.5:c.1758_1759delGT	chr8.hg19:g.141554394_141554395delAC	ENSP00000220592:p.Phe587fs	42.0	0.0	0		38.0	12.0	0.315789	NM_012154	Q8TCZ5|Q8WV58|Q96ID1	Frame_Shift_Del	DEL	ENST00000220592.5	hg19	CCDS6380.1																																																																																			.	.	.	none		0.653	AGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377866.4			-	141554393	AC	-	141554392	7	5	244	1	0	1	0	1	0	0	0	0	5008	43	2	0	844	0	EIF2C2	8	141554392	Frame_Shift_Del	DEL	AC	TCGA-SX-A71V-01A-11D-A33Q-10	17358824	141554392	4809630	51	15080											
PKN3	29941	hgsc.bcm.edu	37	chr9	131477477	131477477	+	Missense_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	ccctcggcttcaggacttccGctgcttagctgtgctgggcc	3	11	12	15	2	1	0	1	0	0	0	3	1	2	1	3	3	3	5	3	3	1	3			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr9:131477477G>A	ENST00000291906.4	+	14	2072	c.1679G>A	c.(1678-1680)cGc>cAc	p.R560H	PKN3_ENST00000485301.1_3'UTR	NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	560	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						CAGGACTTCCGCTGCTTAGCT	0.612																																					p.R560H		Atlas-SNP	.											PKN3,colon,carcinoma,0,1	PKN3	62	.	0			c.G1679A						PASS	.						58	62	61					9																	131477477		2203	4300	6503	SO:0001583	missense	29941	exon14			ACTTCCGCTGCTT	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.1679G>A	chr9.hg19:g.131477477G>A	ENSP00000291906:p.Arg560His	146.0	0.0	.		108.0	38.0	.	NM_013355	Q9UM03	Missense_Mutation	SNP	ENST00000291906.4	hg19	CCDS6908.1	.	.	.	.	.	.	.	.	.	.	G	14.89	2.671151	0.47781	.	.	ENSG00000160447	ENST00000291906	T	0.66280	-0.2	5.33	4.43	0.53597	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	0.50752	0.1634	L	0.35723	1.085	0.39701	D	0.97118	B	0.17268	0.021	B	0.17722	0.019	T	0.49969	-0.8882	9	0.48119	T	0.1	.	9.7494	0.40466	0.0949:0.0:0.9051:0.0	.	560	Q6P5Z2	PKN3_HUMAN	H	560	ENSP00000291906:R560H	ENSP00000291906:R560H	R	+	2	0	PKN3	130517298	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	1.236000	0.32683	1.255000	0.44051	0.557000	0.71058	CGC	.	.	.	none		0.612	PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054487.1	NM_013355		A	131477477	G	A	131477477	3	1	244	1	0	0	0	0	1	0	0	0	11988	1087	38	1	1733	1	PKN3	9	131477477	Missense_Mutation	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10		131477477	9735954	52	15081											
RXRA	6256	hgsc.bcm.edu	37	chr9	137325968	137325968	+	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	actccaaggggctctcgaacCcggccgaggtggaggcgctg	7	5	16	13	4	1	0	0	0	1	0	3	3	2	1	3	6	1	2	3	6	2	0			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr9:137325968C>T	ENST00000481739.1	+	9	1208	c.1156C>T	c.(1156-1158)Ccg>Tcg	p.P386S	RXRA_ENST00000540193.1_Missense_Mutation_p.P289S|RXRA_ENST00000356384.4_3'UTR	NM_002957.4	NP_002948.1	P19793	RXRA_HUMAN	retinoid X receptor, alpha	386	Ligand-binding.				camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|cellular lipid metabolic process (GO:0044255)|cholesterol metabolic process (GO:0008203)|embryo implantation (GO:0007566)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|response to retinoic acid (GO:0032526)|retinoic acid receptor signaling pathway (GO:0048384)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|vitamin metabolic process (GO:0006766)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein heterodimerization activity (GO:0046982)|retinoic acid receptor activity (GO:0003708)|retinoic acid-responsive element binding (GO:0044323)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|vitamin D receptor binding (GO:0042809)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19				OV - Ovarian serous cystadenocarcinoma(145;4.66e-08)|Epithelial(140;6.72e-08)|all cancers(34;2.22e-07)	Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Etodolac(DB00749)	GCTCTCGAACCCGGCCGAGGT	0.652																																					p.P386S		Atlas-SNP	.											.	RXRA	52	.	0			c.C1156T						PASS	.						53	56	55					9																	137325968		2203	4300	6503	SO:0001583	missense	6256	exon9			TCGAACCCGGCCG	X52773	CCDS35172.1	9q34	2013-01-16			ENSG00000186350	ENSG00000186350		"Nuclear hormone receptors"	10477	protein-coding gene	gene with protein product	"nuclear receptor subfamily 2 group B member 1"	180245				2159111	Standard	XM_005263409		Approved	NR2B1	uc004cfa.1	P19793	OTTHUMG00000020887	ENST00000481739.1:c.1156C>T	chr9.hg19:g.137325968C>T	ENSP00000419692:p.Pro386Ser	46.0	0.0	.		59.0	21.0	.	NM_002957	B3KY83|Q2NL52|Q2V504	Missense_Mutation	SNP	ENST00000481739.1	hg19	CCDS35172.1	.	.	.	.	.	.	.	.	.	.	C	13.70	2.315159	0.40996	.	.	ENSG00000186350	ENST00000481739;ENST00000540193	D;D	0.96265	-3.96;-3.96	4.3	4.3	0.51218	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.91556	0.7333	N	0.15975	0.35	0.80722	D	1	B	0.17667	0.023	B	0.10450	0.005	D	0.87989	0.2748	10	0.33940	T	0.23	.	17.1165	0.86690	0.0:1.0:0.0:0.0	.	386	P19793	RXRA_HUMAN	S	386;289	ENSP00000419692:P386S;ENSP00000442123:P289S	ENSP00000419692:P386S	P	+	1	0	RXRA	136465789	1.000000	0.71417	0.985000	0.45067	0.978000	0.69477	7.443000	0.80521	2.102000	0.63906	0.491000	0.48974	CCG	.	.	.	none		0.652	RXRA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054949.1	NM_002957		T	137325968	C	T	137325968	3	4	244	1	0	0	0	0	1	0	0	0	13776	623	22	2	1190	2	RXRA	9	137325968	Missense_Mutation	SNP	C	TCGA-SX-A71V-01A-11D-A33Q-10	5848491	137325968	3887463	53	15082											
SVIL	6840	hgsc.bcm.edu	37	chr10	29756744	29756744	+	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	aatccgagtggctcggagccTtcatcacactcgtgtattgt	8	12	10	11	3	2	0	2	0	0	0	5	2	3	1	2	2	1	2	2	2	2	3			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr10:29756744T>A	ENST00000355867.4	-	33	6656	c.5904A>T	c.(5902-5904)gaA>gaT	p.E1968D	PTCHD3P1_ENST00000414457.1_RNA|PTCHD3P1_ENST00000413405.1_RNA|SVIL_ENST00000375400.3_Missense_Mutation_p.E1542D|SVIL_ENST00000375398.2_Missense_Mutation_p.E1968D|PTCHD3P1_ENST00000446807.1_RNA|PTCHD3P1_ENST00000445521.1_RNA|PTCHD3P1_ENST00000455774.1_RNA|SVIL_ENST00000535393.1_Missense_Mutation_p.E882D|PTCHD3P1_ENST00000423223.1_RNA	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1968					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)				GCTCGGAGCCTTCATCACACT	0.498																																					p.E1968D		Atlas-SNP	.											.	SVIL	226	.	0			c.A5904T						PASS	.						128	111	117					10																	29756744		2203	4300	6503	SO:0001583	missense	6840	exon33			GGAGCCTTCATCA	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.5904A>T	chr10.hg19:g.29756744T>A	ENSP00000348128:p.Glu1968Asp	73.0	0.0	.		66.0	23.0	.	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	hg19	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	T	17.37	3.371683	0.61624	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867;ENST00000535393	T;T;T;T	0.54479	0.57;0.57;0.57;0.57	5.42	-2.88	0.05682	.	0.000000	0.85682	D	0.000000	T	0.74068	0.3668	M	0.93763	3.455	0.80722	D	1	D;D;D	0.89917	1.0;0.992;0.997	D;D;D	0.97110	1.0;0.985;0.972	T	0.76119	-0.3076	10	0.72032	D	0.01	-19.859	11.3269	0.49454	0.0:0.3744:0.0:0.6256	.	882;1542;1968	F5H2Q5;O95425-2;O95425	.;.;SVIL_HUMAN	D	1542;1968;1968;882	ENSP00000364549:E1542D;ENSP00000364547:E1968D;ENSP00000348128:E1968D;ENSP00000445472:E882D	ENSP00000348128:E1968D	E	-	3	2	SVIL	29796750	0.996000	0.38824	0.332000	0.25469	0.295000	0.27426	0.336000	0.19823	-0.671000	0.05274	-0.256000	0.11100	GAA	.	.	.	none		0.498	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			A	29756744	T	A	29756744	3	1	244	1	0	0	0	0	1	0	0	0	15433	1606	56	5	764	5	SVIL	10	29756744	Missense_Mutation	SNP	T	TCGA-SX-A71V-01A-11D-A33Q-10		29756744	105778003	54	15083											
TET1	80312	hgsc.bcm.edu	37	chr10	70451029	70451029	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagaccttgcctcttctccaAtggaagaagatgagcagcat	13	9	9	10	0	2	4	0	1	2	3	3	5	2	5	3	1	3	2	3	1	4	2	rs147755307		TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr10:70451029A>G	ENST00000373644.4	+	12	6078	c.5869A>G	c.(5869-5871)Atg>Gtg	p.M1957V		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1957					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						CTCTTCTCCAATGGAAGAAGA	0.542																																					p.M1957V		Atlas-SNP	.											.	TET1	255	.	0			c.A5869G						PASS	.	A	VAL/MET	0,4406		0,0,2203	116	102	107		5869	-1.6	0	10	dbSNP_134	107	1,8599	1.2+/-3.3	0,1,4299	no	missense	TET1	NM_030625.2	21	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	1957/2137	70451029	1,13005	2203	4300	6503	SO:0001583	missense	80312	exon12			TCTCCAATGGAAG	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.5869A>G	chr10.hg19:g.70451029A>G	ENSP00000362748:p.Met1957Val	102.0	0.0	.		85.0	4.0	.	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	hg19	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	A	0.003	-2.433229	0.00182	0.0	1.16E-4	ENSG00000138336	ENST00000373644	T	0.05580	3.42	5.53	-1.65	0.08291	Methylcytosine dioxygenase TET, double-stranded beta helix fold domain (1);	2.646000	0.01051	N	0.004474	T	0.01835	0.0058	N	0.00879	-1.12	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.40478	-0.9561	10	0.06236	T	0.91	.	4.764	0.13123	0.364:0.2719:0.3641:0.0	.	1957	Q8NFU7	TET1_HUMAN	V	1957	ENSP00000362748:M1957V	ENSP00000362748:M1957V	M	+	1	0	TET1	70121035	0.000000	0.05858	0.000000	0.03702	0.104000	0.19210	0.332000	0.19751	-0.345000	0.08325	-0.313000	0.08912	ATG	.	A|1.000;G|0.000	0.000	weak		0.542	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		G	70451029	A	G	70451029	3	3	244	1	0	0	0	0	1	0	0	0	15781	101	4	3	5911	3	TET1	10	70451029	Missense_Mutation	SNP	A	TCGA-SX-A71V-01A-11D-A33Q-10	40694285	70451029	65083718	55	15084											
LRRC20	55222	hgsc.bcm.edu	37	chr10	72083705	72083705	+	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	agtcctggaactggttccggGacaggtcaatggccttgagg	8	9	15	9	1	1	1	1	1	0	0	3	3	3	3	3	6	1	1	3	6	2	2			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr10:72083705G>C	ENST00000355790.4	-	4	791	c.314C>G	c.(313-315)tCc>tGc	p.S105C	LRRC20_ENST00000395011.1_Missense_Mutation_p.S55C|LRRC20_ENST00000373224.1_Missense_Mutation_p.S105C|LRRC20_ENST00000395010.1_Intron|LRRC20_ENST00000358141.2_Missense_Mutation_p.S55C	NM_001278212.1|NM_001278214.1|NM_207119.1	NP_001265141.1|NP_001265143.1|NP_997002.1	Q8TCA0	LRC20_HUMAN	leucine rich repeat containing 20	105										endometrium(2)|large_intestine(4)|lung(2)|urinary_tract(1)	9						CTGGTTCCGGGACAGGTCAAT	0.637																																					p.S105C		Atlas-SNP	.											.	LRRC20	19	.	0			c.C314G						PASS	.						97	83	88					10																	72083705		2203	4300	6503	SO:0001583	missense	55222	exon4			TTCCGGGACAGGT	BC024001	CCDS7300.1, CCDS7301.1, CCDS7302.1, CCDS73145.1	10q22.2	2004-04-15			ENSG00000172731	ENSG00000172731			23421	protein-coding gene	gene with protein product							Standard	NM_207119		Approved	FLJ10751, FLJ10844	uc031pvr.1	Q8TCA0	OTTHUMG00000018407	ENST00000355790.4:c.314C>G	chr10.hg19:g.72083705G>C	ENSP00000348043:p.Ser105Cys	98.0	0.0	.		96.0	45.0	.	NM_207119	Q5T6D4|Q5T6D6|Q9NVA6|Q9NVG3	Missense_Mutation	SNP	ENST00000355790.4	hg19	CCDS7302.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.430343	0.83776	.	.	ENSG00000172731	ENST00000373224;ENST00000355790;ENST00000395011;ENST00000358141;ENST00000446961	T;T;T;T;T	0.59502	0.26;0.26;1.53;1.53;0.26	5.37	5.37	0.77165	.	0.114590	0.64402	D	0.000012	T	0.76550	0.4003	M	0.77486	2.375	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.71870	0.971;0.975	T	0.78352	-0.2237	10	0.54805	T	0.06	-36.6006	17.6721	0.88221	0.0:0.0:1.0:0.0	.	55;105	Q8TCA0-2;Q8TCA0	.;LRC20_HUMAN	C	105;105;55;55;105	ENSP00000362321:S105C;ENSP00000348043:S105C;ENSP00000378458:S55C;ENSP00000350860:S55C;ENSP00000413745:S105C	ENSP00000348043:S105C	S	-	2	0	LRRC20	71753711	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.513000	0.81739	2.514000	0.84764	0.563000	0.77884	TCC	.	.	.	none		0.637	LRRC20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048510.1	NM_018239		C	72083705	G	C	72083705	3	2	244	1	0	0	0	0	1	0	0	0	8984	1174	41	4	248	4	LRRC20	10	72083705	Missense_Mutation	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	1632676	72083705	63451042	56	15085											
CDH23	64072	hgsc.bcm.edu	37	chr10	73550921	73550921	+	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	tgaggtcaggtgtcatcattGaccgggaggcattctcgcca	8	10	13	10	2	4	2	3	2	1	0	5	3	4	3	2	4	0	1	2	4	0	2			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr10:73550921G>A	ENST00000224721.6	+	46	6102	c.6097G>A	c.(6097-6099)Gac>Aac	p.D2033N		NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2028	Cadherin 19. {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						TGTCATCATTGACCGGGAGGC	0.622																																					p.D2028N		Atlas-SNP	.											.	CDH23	365	.	0			c.G6082A						PASS	.						44	49	47					10																	73550921		2189	4288	6477	SO:0001583	missense	64072	exon45			ATCATTGACCGGG	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.6097G>A	chr10.hg19:g.73550921G>A	ENSP00000224721:p.Asp2033Asn	44.0	0.0	.		38.0	15.0	.	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	hg19		.	.	.	.	.	.	.	.	.	.	G	35	5.558045	0.96514	.	.	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721	.	.	.	5.91	5.91	0.95273	Cadherin (3);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.85208	0.5644	M	0.86343	2.81	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85488	0.1183	9	0.52906	T	0.07	.	20.2985	0.98592	0.0:0.0:1.0:0.0	.	2028	Q9H251	CAD23_HUMAN	N	2033;2028;2031	.	ENSP00000224721:D2033N	D	+	1	0	CDH23	73220927	1.000000	0.71417	1.000000	0.80357	0.754000	0.42855	9.132000	0.94455	2.793000	0.96121	0.655000	0.94253	GAC	.	.	.	none		0.622	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		A	73550921	G	A	73550921	3	1	244	1	0	0	0	0	1	0	0	0	3110	1290	45	2	6609	2	CDH23	10	73550921	Missense_Mutation	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	1467216	73550921	61983826	57	15086											
SLC16A12	387700	hgsc.bcm.edu	37	chr10	91195920	91195920	+	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	actatctctgtggtcactacTgggatcaaagtcacataggc	11	11	9	10	0	4	0	3	0	1	0	5	1	4	1	0	3	1	0	0	3	4	3			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr10:91195920T>A	ENST00000341233.4	-	7	1485	c.1095A>T	c.(1093-1095)ccA>ccT	p.P365P	SLC16A12_ENST00000371790.4_Silent_p.P395P	NM_213606.3	NP_998771.3	Q6ZSM3	MOT12_HUMAN	solute carrier family 16, member 12	365						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						TGGTCACTACTGGGATCAAAG	0.512																																					p.P395P		Atlas-SNP	.											.	SLC16A12	40	.	0			c.A1185T						PASS	.						129	101	110					10																	91195920		2203	4300	6503	SO:0001819	synonymous_variant	387700	exon7			CACTACTGGGATC		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.1095A>T	chr10.hg19:g.91195920T>A		109.0	0.0	.		102.0	37.0	.	NM_213606	Q5M9M9|Q5T7J2|Q6ZV76	Silent	SNP	ENST00000341233.4	hg19																																																																																				.	.	.	none		0.512	SLC16A12-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_213606		A	91195920	T	A	91195920	2	1	244	1	0	0	0	0	0	0	0	1	14418	1567	55	5		5	SLC16A12	10	91195920	Silent	SNP	T	TCGA-SX-A71V-01A-11D-A33Q-10	17644999	91195920	44338827	58	15087											
SLIT1	6585	hgsc.bcm.edu	37	chr10	98803147	98803147	+	Silent	SNP	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	agtgtggagagggactggagGgtgtcgaaggctcctgggga	8	7	21	5	1	0	1	0	0	0	1	2	6	1	4	1	7	0	1	1	7	1	0			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr10:98803147G>A	ENST00000266058.4	-	19	2222	c.1977C>T	c.(1975-1977)acC>acT	p.T659T	ARHGAP19-SLIT1_ENST00000453547.2_3'UTR|SLIT1_ENST00000371070.4_Silent_p.T659T	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	659					axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		GGGACTGGAGGGTGTCGAAGG	0.642																																					p.T659T		Atlas-SNP	.											.	SLIT1	154	.	0			c.C1977T						PASS	.						204	207	206					10																	98803147		2203	4300	6503	SO:0001819	synonymous_variant	6585	exon19			CTGGAGGGTGTCG	AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"slit (Drosophila) homolog 1"	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.1977C>T	chr10.hg19:g.98803147G>A		110.0	0.0	.		106.0	36.0	.	NM_003061	Q5T0V1|Q8WWZ2|Q9UIL7	Silent	SNP	ENST00000266058.4	hg19	CCDS7453.1																																																																																			.	.	.	none		0.642	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061		A	98803147	G	A	98803147	2	1	244	1	0	0	0	0	0	0	0	1	14752	1219	43	2		2	SLIT1	10	98803147	Silent	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	7607227	98803147	36731600	59	15088											
TIAL1	7073	hgsc.bcm.edu	37	chr10	121339523	121339523	+	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	ctttaactacccgggcatccCtgtgaaaagaagcacagcta	13	8	8	12	1	0	2	0	1	0	1	1	2	1	2	2	1	4	3	2	1	6	4			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr10:121339523C>G	ENST00000436547.2	-	6	416		c.e6-1		TIAL1_ENST00000463089.2_5'Flank|TIAL1_ENST00000369092.4_Splice_Site|TIAL1_ENST00000369093.2_Splice_Site	NM_003252.3	NP_003243.1	Q01085	TIAR_HUMAN	TIA1 cytotoxic granule-associated RNA binding protein-like 1						apoptotic process (GO:0006915)|defense response (GO:0006952)|germ cell development (GO:0007281)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell division (GO:0017145)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(3)|ovary(1)	13		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00239)|BRCA - Breast invasive adenocarcinoma(275;0.0932)		CCGGGCATCCCTGTGAAAAGA	0.368																																					.		Atlas-SNP	.											.	TIAL1	47	.	0			c.423-1G>C						PASS	.						52	52	52					10																	121339523		2203	4300	6503	SO:0001630	splice_region_variant	7073	exon7			GCATCCCTGTGAA	AL833106	CCDS7613.1, CCDS31295.1	10q	2013-02-12	2001-11-28		ENSG00000151923	ENSG00000151923		"RNA binding motif (RRM) containing"	11804	protein-coding gene	gene with protein product		603413	"TIA1 cytotoxic granule-associated RNA-binding protein-like 1"			1326761	Standard	XM_005270108		Approved	TIAR	uc001lej.1	Q01085	OTTHUMG00000019156	ENST00000436547.2:c.372-1G>C	chr10.hg19:g.121339523C>G		78.0	0.0	.		63.0	26.0	.	NM_001033925	A8K3T0|A8K4L9	Splice_Site	SNP	ENST00000436547.2	hg19	CCDS7613.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.410918	0.83340	.	.	ENSG00000151923	ENST00000369093;ENST00000369092;ENST00000436547;ENST00000412524	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4345	0.94786	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TIAL1	121329513	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.717000	0.84732	2.587000	0.87381	0.563000	0.77884	.	.	.	.	none		0.368	TIAL1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050672.2	NM_022333, NM_003252	Intron	G	121339523	C	G	121339523	5	3	244	1	0	0	0	0	0	0	1	0	15901	695	24	4	784	4	TIAL1	10	121339523	Splice_Site	SNP	C	TCGA-SX-A71V-01A-11D-A33Q-10	22536376	121339523	14195224	60	15089											
RIC8A	60626	hgsc.bcm.edu	37	chr11	209726	209726	+	Missense_Mutation	SNP	A	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	cacagagcgtgtggggctgtAccgtgagaggagcttccccc	7	7	15	12	2	0	2	0	1	0	2	1	4	1	3	3	3	3	3	3	3	1	2			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr11:209726A>C	ENST00000526104.1	+	3	1796	c.452A>C	c.(451-453)tAc>tCc	p.Y151S	BET1L_ENST00000529614.2_5'Flank|BET1L_ENST00000410108.1_5'Flank|RIC8A_ENST00000325207.5_Missense_Mutation_p.Y151S|BET1L_ENST00000382762.3_5'Flank|BET1L_ENST00000332865.6_5'Flank|RIC8A_ENST00000527696.1_Missense_Mutation_p.Y145S|BET1L_ENST00000325147.9_5'Flank|BET1L_ENST00000486280.1_5'Flank			Q9NPQ8	RIC8A_HUMAN	RIC8 guanine nucleotide exchange factor A	151					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)		GTGGGGCTGTACCGTGAGAGG	0.612																																					p.Y151S		Atlas-SNP	.											.	RIC8A	45	.	0			c.A452C						PASS	.						58	51	54					11																	209726		2203	4300	6503	SO:0001583	missense	60626	exon3			GGCTGTACCGTGA	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.452A>C	chr11.hg19:g.209726A>C	ENSP00000432008:p.Tyr151Ser	63.0	0.0	.		55.0	15.0	.	NM_021932	Q0P508|Q2T9J1|Q7Z352|Q96EZ1|Q96SZ2|Q9H064|Q9H5H3|Q9H9E7	Missense_Mutation	SNP	ENST00000526104.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	8.422|8.422	0.846586|0.846586	0.16963|0.16963	.|.	.|.	ENSG00000177963|ENSG00000177963	ENST00000527728|ENST00000526104;ENST00000325207;ENST00000528357;ENST00000530889;ENST00000527696;ENST00000527468	.|.	.|.	.|.	4.45|4.45	-1.06|-1.06	0.10002|0.10002	.|Armadillo-type fold (1);	.|0.377347	.|0.30667	.|N	.|0.009138	T|T	0.21468|0.21468	0.0517|0.0517	N|N	0.21194|0.21194	0.64|0.64	0.09310|0.09310	N|N	0.999995|0.999995	.|B;B;B	.|0.17852	.|0.004;0.024;0.019	.|B;B;B	.|0.17979	.|0.005;0.02;0.011	T|T	0.13442|0.13442	-1.0509|-1.0509	5|9	.|0.22109	.|T	.|0.4	-1.5871|-1.5871	5.6898|5.6898	0.17823|0.17823	0.6387:0.1321:0.2291:0.0|0.6387:0.1321:0.2291:0.0	.|.	.|145;151;151	.|Q9NPQ8-2;Q9NPQ8;Q9NPQ8-3	.|.;RIC8A_HUMAN;.	P|S	33|151;151;127;155;145;41	.|.	.|ENSP00000325941:Y151S	T|Y	+|+	1|2	0|0	RIC8A|RIC8A	199726|199726	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.694000|0.694000	0.40290|0.40290	0.532000|0.532000	0.23067|0.23067	-0.289000|-0.289000	0.09038|0.09038	0.459000|0.459000	0.35465|0.35465	ACC|TAC	.	.	.	none		0.612	RIC8A-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000384761.1	NM_021932		C	209726	A	C	209726	3	2	244	1	0	0	0	0	1	0	0	0	13368	391	14	5	462	5	RIC8A	11	209726	Missense_Mutation	SNP	A	TCGA-SX-A71V-01A-11D-A33Q-10		209726	134796790	61	15090											
KCNQ1	3784	hgsc.bcm.edu	37	chr11	2799217	2799217	+	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	cccccatagaaaagagcaagGatcgcggcagcaacacgatc	15	3	10	13	3	0	2	0	0	0	2	2	4	0	3	2	2	3	3	2	2	5	1			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr11:2799217G>C	ENST00000155840.5	+	15	1852	c.1744G>C	c.(1744-1746)Gat>Cat	p.D582H	KCNQ1_ENST00000526095.1_3'UTR|KCNQ1_ENST00000335475.5_Missense_Mutation_p.D455H	NM_000218.2	NP_000209.2	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 1	582					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)	AAAGAGCAAGGATCGCGGCAG	0.637																																					p.D582H		Atlas-SNP	.											.	KCNQ1	60	.	0			c.G1744C						PASS	.						69	69	69					11																	2799217		2202	4299	6501	SO:0001583	missense	3784	exon15			AGCAAGGATCGCG	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.1744G>C	chr11.hg19:g.2799217G>C	ENSP00000155840:p.Asp582His	39.0	0.0	.		39.0	19.0	.	NM_000218	O00347|O60607|O94787|Q14D14|Q7Z6G9|Q92960|Q9UMN8|Q9UMN9	Missense_Mutation	SNP	ENST00000155840.5	hg19	CCDS7736.1	.	.	.	.	.	.	.	.	.	.	G	13.98	2.397789	0.42512	.	.	ENSG00000053918	ENST00000155840;ENST00000335475	D;D	0.99671	-6.35;-6.35	3.11	3.11	0.35812	Potassium channel, voltage dependent, KCNQ, C-terminal (1);	0.071471	0.52532	D	0.000063	D	0.99438	0.9801	M	0.78049	2.395	0.48762	D	0.999707	P;P;D	0.63046	0.511;0.567;0.992	B;B;D	0.67900	0.18;0.275;0.954	D	0.97889	1.0296	10	0.59425	D	0.04	-30.827	12.4561	0.55706	0.0:0.0:1.0:0.0	.	455;455;582	P51787-2;Q14D14;P51787	.;.;KCNQ1_HUMAN	H	582;455	ENSP00000155840:D582H;ENSP00000334497:D455H	ENSP00000155840:D582H	D	+	1	0	KCNQ1	2755793	1.000000	0.71417	1.000000	0.80357	0.220000	0.24768	7.172000	0.77604	2.043000	0.60533	0.313000	0.20887	GAT	.	.	.	none		0.637	KCNQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027382.2	NM_000218		C	2799217	G	C	2799217	3	2	244	1	0	0	0	0	1	0	0	0	8089	1174	41	4	1811	4	KCNQ1	11	2799217	Missense_Mutation	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	2589491	2799217	132207299	62	15091											
C11orf58	10944	hgsc.bcm.edu	37	chr11	16776551	16776551	+	Missense_Mutation	SNP	T	T	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	agaagaatctgctgaagaacTccaagctgctgagcaccctg	13	7	10	11	0	1	5	0	2	1	3	2	5	2	5	2	0	5	4	2	0	5	0			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr11:16776551T>G	ENST00000228136.4	+	5	830	c.452T>G	c.(451-453)cTc>cGc	p.L151R	C11orf58_ENST00000525684.1_3'UTR|C11orf58_ENST00000422258.2_Missense_Mutation_p.L107R			O00193	SMAP_HUMAN	chromosome 11 open reading frame 58	151										NS(1)|endometrium(1)|lung(3)|prostate(1)|skin(1)	7						GCTGAAGAACTCCAAGCTGCT	0.393																																					p.L151R		Atlas-SNP	.											.	C11orf58	14	.	0			c.T452G						PASS	.						72	77	75					11																	16776551		2200	4294	6494	SO:0001583	missense	10944	exon5			AAGAACTCCAAGC	BC007103	CCDS7822.1	11p15.1	2012-05-30			ENSG00000110696	ENSG00000110696			16990	protein-coding gene	gene with protein product	"small acidic protein"					9263035	Standard	NM_014267		Approved	SMAP	uc001mmk.2	O00193	OTTHUMG00000165910	ENST00000228136.4:c.452T>G	chr11.hg19:g.16776551T>G	ENSP00000228136:p.Leu151Arg	148.0	0.0	.		102.0	34.0	.	NM_014267	B2RD28	Missense_Mutation	SNP	ENST00000228136.4	hg19	CCDS7822.1	.	.	.	.	.	.	.	.	.	.	T	8.393	0.840219	0.16891	.	.	ENSG00000110696	ENST00000228136;ENST00000422258	.	.	.	5.21	5.21	0.72293	.	0.639834	0.16310	N	0.220024	T	0.32704	0.0838	L	0.29908	0.895	0.37202	D	0.904438	B	0.25312	0.123	B	0.16289	0.015	T	0.20706	-1.0267	9	0.07030	T	0.85	.	6.5732	0.22551	0.0:0.0785:0.1566:0.7649	.	151	O00193	SMAP_HUMAN	R	151;107	.	ENSP00000228136:L151R	L	+	2	0	C11orf58	16733127	0.978000	0.34361	0.989000	0.46669	0.994000	0.84299	2.518000	0.45537	1.951000	0.56629	0.528000	0.53228	CTC	.	.	.	none		0.393	C11orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387023.2	NM_014267		G	16776551	T	G	16776551	3	3	244	1	0	0	0	0	1	0	0	0	1653	1551	54	5	470	5	C11orf58	11	16776551	Missense_Mutation	SNP	T	TCGA-SX-A71V-01A-11D-A33Q-10	13977334	16776551	118229965	63	15092											
RSF1	51773	hgsc.bcm.edu	37	chr11	77378053	77378054	+	Frame_Shift_Ins	INS	-	-	CA																															tggtgctcctgcctcctgccINScaccacttgtcccattggag																										TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr11:77378053_77378054insCA	ENST00000308488.6	-	16	4536_4537	c.4234_4235insTG	c.(4234-4236)gggfs	p.G1412fs	RSF1_ENST00000360355.2_Frame_Shift_Ins_p.G1381fs|RSF1_ENST00000480887.1_Frame_Shift_Ins_p.G1160fs			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	1412					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)			TGCCTCCTGCCCACCACTTGTC	0.485																																					p.G1412fs		Atlas-Indel,Pindel	.											.	RSF1	105	.	0			c.4235_4236insTG						PASS	.																																			SO:0001589	frameshift_variant	51773	exon16			.	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.4233_4234dupTG	chr11.hg19:g.77378054_77378055dupCA	ENSP00000311513:p.Gly1412fs	76.0	0.0	0		103.0	30.0	0.291262	NM_016578	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Frame_Shift_Ins	INS	ENST00000308488.6	hg19	CCDS8253.1																																																																																			.	.	.	none		0.485	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578		CA	77378054	-	CA	77378053	7	5	244	1	0	1	1	0	0	0	0	0	13712	623	22	0	94	0	RSF1	11	77378053	Frame_Shift_Ins	INS	-	TCGA-SX-A71V-01A-11D-A33Q-10	60601502	77378053	57628463	64	15093											
HSPB2	3316	hgsc.bcm.edu	37	chr11	111784216	111784216	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actctaccatggctactatgTccggcctcgggccgccccag	6	8	10	17	3	1	0	0	0	1	0	3	0	2	0	6	3	2	1	6	3	3	3			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr11:111784216T>C	ENST00000304298.3	+	2	734	c.146T>C	c.(145-147)gTc>gCc	p.V49A	CRYAB_ENST00000526180.1_5'Flank|CRYAB_ENST00000527950.1_Intron|CRYAB_ENST00000525823.1_5'Flank|CRYAB_ENST00000227251.3_5'Flank|CRYAB_ENST00000533280.1_5'Flank|HSPB2-C11orf52_ENST00000534100.1_Intron|CRYAB_ENST00000531198.1_5'Flank|HSPB2_ENST00000537382.1_Missense_Mutation_p.V49A|CRYAB_ENST00000533475.1_Intron|CRYAB_ENST00000533971.1_5'Flank	NM_001541.3	NP_001532.1	Q16082	HSPB2_HUMAN	heat shock 27kDa protein 2	49					positive regulation of catalytic activity (GO:0043085)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)			large_intestine(2)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		all_cancers(61;3.75e-11)|all_epithelial(67;2.33e-06)|Melanoma(852;9.42e-06)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0512)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)		Epithelial(105;3.57e-07)|BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|all cancers(92;6.57e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.051)		GGCTACTATGTCCGGCCTCGG	0.627																																					p.V49A		Atlas-SNP	.											.	HSPB2	20	.	0			c.T146C						PASS	.						136	147	144					11																	111784216		2201	4297	6498	SO:0001583	missense	3316	exon2			ACTATGTCCGGCC	U75898	CCDS8352.1	11q22-q23	2011-09-02	2002-08-29			ENSG00000170276		"Heat shock proteins / HSPB"	5247	protein-coding gene	gene with protein product		602179	"heat shock 27kD protein 2"			9344664, 9490724	Standard	NM_001541		Approved	Hs.78846, MKBP	uc001pmg.2	Q16082		ENST00000304298.3:c.146T>C	chr11.hg19:g.111784216T>C	ENSP00000302476:p.Val49Ala	38.0	0.0	.		27.0	10.0	.	NM_001541	Q6I9U7	Missense_Mutation	SNP	ENST00000304298.3	hg19	CCDS8352.1	.	.	.	.	.	.	.	.	.	.	T	13.66	2.304473	0.40795	.	.	ENSG00000170276	ENST00000304298;ENST00000537382	D;D	0.90004	-2.6;-2.6	4.86	4.86	0.63082	.	0.429389	0.21511	N	0.073367	T	0.79621	0.4477	N	0.14661	0.345	0.35008	D	0.756652	B	0.14438	0.01	B	0.11329	0.006	T	0.77550	-0.2546	10	0.17369	T	0.5	-25.4453	14.9188	0.70818	0.0:0.0:0.0:1.0	.	49	Q16082	HSPB2_HUMAN	A	49	ENSP00000302476:V49A;ENSP00000445585:V49A	ENSP00000302476:V49A	V	+	2	0	HSPB2	111289426	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.167000	0.71902	2.177000	0.69029	0.455000	0.32223	GTC	.	.	.	none		0.627	HSPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391669.1			C	111784216	T	C	111784216	3	2	244	1	0	0	0	0	1	0	0	0	7427	1667	58	3	152	3	HSPB2	11	111784216	Missense_Mutation	SNP	T	TCGA-SX-A71V-01A-11D-A33Q-10	34406163	111784216	23222300	65	15094											
BCL9L	283149	hgsc.bcm.edu	37	chr11	118771955	118771955	+	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	tgaaggcatcagcatcttctGcgggccgcccatcacgccac	8	7	10	16	3	4	1	2	1	2	0	4	1	4	1	3	2	2	2	3	2	1	1			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr11:118771955G>C	ENST00000334801.3	-	6	3461	c.2497C>G	c.(2497-2499)Cag>Gag	p.Q833E	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	833	Met-rich.				canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		AGCATCTTCTGCGGGCCGCCC	0.647																																					p.Q833E		Atlas-SNP	.											.	BCL9L	254	.	0			c.C2497G						PASS	.						65	64	64					11																	118771955		2200	4295	6495	SO:0001583	missense	283149	exon6			TCTTCTGCGGGCC	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.2497C>G	chr11.hg19:g.118771955G>C	ENSP00000335320:p.Gln833Glu	75.0	0.0	.		62.0	20.0	.	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Missense_Mutation	SNP	ENST00000334801.3	hg19	CCDS8403.1	.	.	.	.	.	.	.	.	.	.	G	15.44	2.833281	0.50951	.	.	ENSG00000186174	ENST00000334801;ENST00000526143;ENST00000525300;ENST00000392849;ENST00000431085	T	0.79653	-1.29	5.21	4.23	0.50019	.	0.000000	0.48286	D	0.000188	D	0.83843	0.5342	L	0.53249	1.67	0.33316	D	0.566665	P;P	0.49783	0.928;0.882	P;P	0.54856	0.762;0.582	D	0.88896	0.3349	10	0.66056	D	0.02	-11.7031	14.8728	0.70471	0.0:0.1441:0.8559:0.0	.	828;833	Q86UU0-2;Q86UU0	.;BCL9L_HUMAN	E	833;796;126;833;833	ENSP00000335320:Q833E	ENSP00000335320:Q833E	Q	-	1	0	BCL9L	118277165	1.000000	0.71417	0.982000	0.44146	0.880000	0.50808	6.524000	0.73791	2.415000	0.81967	0.655000	0.94253	CAG	.	.	.	none		0.647	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557		C	118771955	G	C	118771955	3	2	244	1	0	0	0	0	1	0	0	0	1382	1328	46	4	2014	4	BCL9L	11	118771955	Missense_Mutation	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	6987739	118771955	16234561	66	15095											
ARHGAP32	9743	hgsc.bcm.edu	37	chr11	129034246	129034246	+	Missense_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	agtttcttcccaatcaggccGctctcgagggtgtacatttc	7	13	9	12	2	3	0	1	0	2	0	6	1	4	0	2	2	1	3	2	2	2	4			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr11:129034246G>A	ENST00000310343.9	-	2	192	c.193C>T	c.(193-195)Cgg>Tgg	p.R65W	ARHGAP32_ENST00000524655.1_5'Flank	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	65					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						CAATCAGGCCGCTCTCGAGGG	0.343																																					p.R65W		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.C193T						PASS	.						74	63	67					11																	129034246		1566	3578	5144	SO:0001583	missense	9743	exon2			CAGGCCGCTCTCG	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.193C>T	chr11.hg19:g.129034246G>A	ENSP00000310561:p.Arg65Trp	60.0	0.0	.		57.0	14.0	.	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Missense_Mutation	SNP	ENST00000310343.9	hg19	CCDS44769.1	.	.	.	.	.	.	.	.	.	.	G	18.76	3.692891	0.68271	.	.	ENSG00000134909	ENST00000310343;ENST00000525234	T;T	0.33216	1.42;1.42	5.02	5.02	0.67125	.	.	.	.	.	T	0.44222	0.1283	L	0.39898	1.24	0.80722	D	1	D	0.89917	1.0	D	0.72075	0.976	T	0.35822	-0.9773	9	0.87932	D	0	.	11.3313	0.49477	0.0:0.0:0.8182:0.1818	.	65	A7KAX9	RHG32_HUMAN	W	65;25	ENSP00000310561:R65W;ENSP00000432303:R25W	ENSP00000310561:R65W	R	-	1	2	ARHGAP32	128539456	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	1.936000	0.40183	2.492000	0.84095	0.655000	0.94253	CGG	.	.	.	none		0.343	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		A	129034246	G	A	129034246	3	1	244	1	0	0	0	0	1	0	0	0	881	1086	38	1	6154	1	ARHGAP32	11	129034246	Missense_Mutation	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	10262291	129034246	5972270	67	15096											
TMTC1	83857	hgsc.bcm.edu	37	chr12	29908774	29908774	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcaagaagaagggagacAccgtggaagggaaacttccc	15	3	14	9	1	0	3	0	0	0	3	1	6	1	5	2	3	2	2	2	3	5	1			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr12:29908774A>G	ENST00000539277.1	-	4	657	c.599T>C	c.(598-600)gTg>gCg	p.V200A	TMTC1_ENST00000551659.1_Missense_Mutation_p.V200A|TMTC1_ENST00000256062.5_Missense_Mutation_p.V92A|TMTC1_ENST00000381224.2_Missense_Mutation_p.V92A|TMTC1_ENST00000552618.1_Missense_Mutation_p.V200A	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	200						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.V92A(1)		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)					GAAGGGAGACACCGTGGAAGG	0.468																																					p.V200A		Atlas-SNP	.											TMTC1,NS,carcinoma,0,1	TMTC1	147	.	1	Substitution - Missense(1)	lung(1)	c.T599C						PASS	.						95	88	90					12																	29908774		2203	4300	6503	SO:0001583	missense	83857	exon4			GGAGACACCGTGG		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.599T>C	chr12.hg19:g.29908774A>G	ENSP00000442046:p.Val200Ala	150.0	0.0	.		172.0	37.0	.	NM_001193451	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Missense_Mutation	SNP	ENST00000539277.1	hg19	CCDS53772.1	.	.	.	.	.	.	.	.	.	.	A	4.340	0.062471	0.08388	.	.	ENSG00000133687	ENST00000256062;ENST00000551659;ENST00000552618;ENST00000539277;ENST00000381224	T;T;T;T;T	0.68624	-0.34;-0.11;-0.34;-0.2;1.5	5.45	1.58	0.23477	.	0.896727	0.09708	N	0.766111	T	0.37237	0.0996	N	0.02357	-0.585	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.21518	-1.0243	9	.	.	.	0.1217	8.5489	0.33440	0.3291:0.0:0.6709:0.0	.	92;200	Q8IUR5-3;Q8IUR5	.;TMTC1_HUMAN	A	92;200;200;200;92	ENSP00000256062:V92A;ENSP00000448112:V200A;ENSP00000449043:V200A;ENSP00000442046:V200A;ENSP00000370622:V92A	.	V	-	2	0	TMTC1	29800041	0.698000	0.27777	0.516000	0.27786	0.771000	0.43674	2.015000	0.40961	0.266000	0.21894	-0.468000	0.05107	GTG	.	.	.	none		0.468	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403509.1	NM_031920		G	29908774	A	G	29908774	3	3	244	1	0	0	0	0	1	0	0	0	16272	159	6	3	2109	3	TMTC1	12	29908774	Missense_Mutation	SNP	A	TCGA-SX-A71V-01A-11D-A33Q-10		29908774	103943121	68	15097											
IFNG	3458	hgsc.bcm.edu	37	chr12	68552039	68552039	+	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	tacatctgaatgacctgcatTctaaaaaaaaaaaaagaaaa	23	8	4	6	0	2	3	0	2	2	1	2	3	2	3	1	0	2	1	1	0	11	3			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr12:68552039T>G	ENST00000229135.3	-	2	246	c.115A>C	c.(115-117)Aat>Cat	p.N39H	IFNG-AS1_ENST00000536914.1_RNA	NM_000619.2	NP_000610.2	P01579	IFNG_HUMAN	interferon, gamma	39					adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|apoptotic process (GO:0006915)|CD8-positive, alpha-beta T cell differentiation involved in immune response (GO:0002302)|cell cycle arrest (GO:0007050)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to interleukin-18 (GO:0071351)|cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endoplasmic reticulum unfolded protein response (GO:0030968)|extrinsic apoptotic signaling pathway (GO:0097191)|humoral immune response (GO:0006959)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of myelination (GO:0031642)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neutrophil apoptotic process (GO:0001781)|neutrophil chemotaxis (GO:0030593)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity (GO:0060550)|positive regulation of fructose 1,6-bisphosphate metabolic process (GO:0060552)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-23 production (GO:0032747)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000309)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of vitamin D biosynthetic process (GO:0060557)|protein import into nucleus, translocation (GO:0000060)|regulation of insulin secretion (GO:0050796)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of the force of heart contraction (GO:0002026)|response to drug (GO:0042493)|response to virus (GO:0009615)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|interferon-gamma receptor binding (GO:0005133)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000829)	Glucosamine(DB01296)|Olsalazine(DB01250)	TGACCTGCATTCTAAAAAAAA	0.303																																					p.N39H		Atlas-SNP	.											.	IFNG	38	.	0			c.A115C						PASS	.						45	46	46					12																	68552039		2202	4299	6501	SO:0001630	splice_region_variant	3458	exon2			CTGCATTCTAAAA		CCDS8980.1	12q14	2007-10-17			ENSG00000111537	ENSG00000111537		"Interferons"	5438	protein-coding gene	gene with protein product		147570					Standard	NM_000619		Approved		uc001stw.1	P01579	OTTHUMG00000169113	ENST00000229135.3:c.115-1A>C	chr12.hg19:g.68552039T>G		50.0	0.0	.		63.0	31.0	.	NM_000619	B5BU88|Q53ZV4	Missense_Mutation	SNP	ENST00000229135.3	hg19	CCDS8980.1	.	.	.	.	.	.	.	.	.	.	T	11.67	1.709060	0.30322	.	.	ENSG00000111537	ENST00000229135	T	0.52983	0.64	5.2	4.06	0.47325	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.171430	0.49916	D	0.000123	T	0.66247	0.2770	M	0.85710	2.77	0.42308	D	0.992201	D	0.69078	0.997	D	0.65987	0.94	T	0.68269	-0.5453	9	.	.	.	-28.2407	7.9531	0.30027	0.0:0.0934:0.0:0.9066	.	39	P01579	IFNG_HUMAN	H	39	ENSP00000229135:N39H	.	N	-	1	0	IFNG	66838306	1.000000	0.71417	0.924000	0.36721	0.002000	0.02628	2.660000	0.46749	0.932000	0.37266	-0.250000	0.11733	AAT	.	.	.	none		0.303	IFNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402301.1		Missense_Mutation	G	68552039	T	G	68552039	5	3	244	1	0	0	0	0	0	0	1	0	7555	1797	62	5	397	5	IFNG	12	68552039	Splice_Site	SNP	T	TCGA-SX-A71V-01A-11D-A33Q-10	38643265	68552039	65299856	69	15098											
AKAP11	11215	hgsc.bcm.edu	37	chr13	42882690	42882690	+	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	ctggtagctggtccaatttaAgttttgaagatgaacaccaa	13	12	9	7	0	0	3	0	2	0	1	1	3	1	3	2	2	2	3	2	2	6	5			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr13:42882690A>T	ENST00000025301.2	+	9	5393	c.5218A>T	c.(5218-5220)Agt>Tgt	p.S1740C		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	1740	Ser-rich.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		GTCCAATTTAAGTTTTGAAGA	0.388																																					p.S1740C		Atlas-SNP	.											.	AKAP11	146	.	0			c.A5218T						PASS	.						116	108	110					13																	42882690		2203	4300	6503	SO:0001583	missense	11215	exon9			AATTTAAGTTTTG	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.5218A>T	chr13.hg19:g.42882690A>T	ENSP00000025301:p.Ser1740Cys	72.0	0.0	.		47.0	26.0	.	NM_016248	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	hg19	CCDS9383.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.783681	0.90282	.	.	ENSG00000023516	ENST00000025301	T	0.20463	2.07	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.46718	0.1407	M	0.72894	2.215	0.58432	D	0.999994	D	0.89917	1.0	D	0.91635	0.999	T	0.43637	-0.9379	10	0.54805	T	0.06	.	15.7898	0.78345	1.0:0.0:0.0:0.0	.	1740	Q9UKA4	AKA11_HUMAN	C	1740	ENSP00000025301:S1740C	ENSP00000025301:S1740C	S	+	1	0	AKAP11	41780690	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.815000	0.91973	2.187000	0.69744	0.528000	0.53228	AGT	.	.	.	none		0.388	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248		T	42882690	A	T	42882690	3	4	244	1	0	0	0	0	1	0	0	0	447	72	3	5	5244	5	AKAP11	13	42882690	Missense_Mutation	SNP	A	TCGA-SX-A71V-01A-11D-A33Q-10		42882690	72287188	70	15099											
TBC1D4	9882	hgsc.bcm.edu	37	chr13	75869072	75869072	+	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	gcagcataaagactggggctGatttcattttcttcaaggtg	10	13	11	7	0	3	2	2	1	1	1	3	2	3	2	0	3	1	3	0	3	3	5			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr13:75869072G>T	ENST00000377636.3	-	18	3580	c.3234C>A	c.(3232-3234)atC>atA	p.I1078I	TBC1D4_ENST00000377625.2_Silent_p.I1015I|TBC1D4_ENST00000478591.1_5'UTR|TBC1D4_ENST00000431480.2_Silent_p.I1070I|TBC1D4_ENST00000425511.1_Silent_p.I242I	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	1078	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				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)		GACTGGGGCTGATTTCATTTT	0.403																																					p.I1078I		Atlas-SNP	.											.	TBC1D4	142	.	0			c.C3234A						PASS	.						82	81	81					13																	75869072		1916	4169	6085	SO:0001819	synonymous_variant	9882	exon18			GGGGCTGATTTCA	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.3234C>A	chr13.hg19:g.75869072G>T		117.0	0.0	.		75.0	21.0	.	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Silent	SNP	ENST00000377636.3	hg19	CCDS41901.1																																																																																			.	.	.	none		0.403	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832		T	75869072	G	T	75869072	2	4	244	1	0	0	0	0	0	0	0	1	15634	1280	45	4		4	TBC1D4	13	75869072	Silent	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	32986382	75869072	39300806	71	15100											
OXA1L	9056	hgsc.bcm.edu	37	chr14	23240288	23240288	+	IGR	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	ggtccaagtatcctgtctccGgattccagcagtacgcactg	8	10	10	13	2	1	0	0	0	1	0	5	1	4	1	4	2	2	4	4	2	3	3			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr14:23240288G>T	ENST00000397532.3	-	0	2447				OXA1L_ENST00000358043.5_Missense_Mutation_p.R318L|OXA1L_ENST00000412791.1_Missense_Mutation_p.R334L|SLC7A7_ENST00000554061.1_5'Flank|OXA1L_ENST00000285848.5_Missense_Mutation_p.R394L|OXA1L_ENST00000604262.1_Missense_Mutation_p.R334L			Q9UM01	YLAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, y+L system), member 7						amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(2)	20	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.00741)		TCCTGTCTCCGGATTCCAGCA	0.483																																					p.R394L		Atlas-SNP	.											.	OXA1L	49	.	0			c.G1181T						PASS	.						137	121	127					14																	23240288		2203	4300	6503	SO:0001628	intergenic_variant	5018	exon8			GTCTCCGGATTCC	AF092032	CCDS9574.1	14q11.2	2014-09-17	2011-07-12		ENSG00000155465	ENSG00000155465		"Solute carriers"	11065	protein-coding gene	gene with protein product		603593		LPI		9829974	Standard	NM_001126106		Approved	y+LAT-1	uc001wgs.4	Q9UM01	OTTHUMG00000028692		chr14.hg19:g.23240288G>T		120.0	0.0	.		89.0	4.0	.	NM_005015	B2RAU0|D3DS26|O95984|Q53XC1|Q86U07|Q9P2V5	Missense_Mutation	SNP	ENST00000397532.3	hg19	CCDS9574.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.756988	0.69648	.	.	ENSG00000155463	ENST00000285848;ENST00000412791;ENST00000358043	T;T;T	0.39592	1.07;1.15;1.07	5.71	4.63	0.57726	.	0.048408	0.85682	D	0.000000	T	0.64659	0.2618	M	0.80746	2.51	0.80722	D	1	D;D;D	0.69078	0.988;0.989;0.997	D;D;D	0.68483	0.913;0.958;0.95	T	0.69087	-0.5238	10	0.72032	D	0.01	-22.9462	14.5012	0.67722	0.085:0.0:0.915:0.0	.	334;334;394	E7EVY0;Q15070;Q2M1J6	.;OXA1L_HUMAN;.	L	394;334;318	ENSP00000285848:R394L;ENSP00000387601:R334L;ENSP00000350740:R318L	ENSP00000285848:R394L	R	+	2	0	OXA1L	22310128	1.000000	0.71417	1.000000	0.80357	0.426000	0.31534	6.148000	0.71788	2.677000	0.91161	0.609000	0.83330	CGG	.	.	.	none		0.483	SLC7A7-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071636.3			T	23240288	G	T	23240288	1	4	244	0	1	0	0	0	0	0	0	0	11335	1116	39	4		4	OXA1L	14	23240288	IGR	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10		23240288	84109252	72	15101											
LRP10	26020	hgsc.bcm.edu	37	chr14	23344406	23344406	+	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	ccatcacttacagctatgctGgggccagagcacccatgggc	9	7	11	14	0	1	1	1	0	0	1	1	1	1	1	3	3	4	3	3	3	2	2			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr14:23344406G>A	ENST00000359591.4	+	4	1049	c.358G>A	c.(358-360)Ggg>Agg	p.G120R	LRP10_ENST00000546834.1_Missense_Mutation_p.G120R	NM_014045.3	NP_054764.2	Q7Z4F1	LRP10_HUMAN	low density lipoprotein receptor-related protein 10	120	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				endocytosis (GO:0006897)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(2)	32	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.00549)		CAGCTATGCTGGGGCCAGAGC	0.632																																					p.G120R		Atlas-SNP	.											.	LRP10	72	.	0			c.G358A						PASS	.						44	41	42					14																	23344406		2203	4300	6503	SO:0001583	missense	26020	exon4			TATGCTGGGGCCA	AF131760	CCDS9578.1	14q11.2	2013-05-29			ENSG00000197324	ENSG00000197324		"Low density lipoprotein receptors"	14553	protein-coding gene	gene with protein product		609921				11123907	Standard	XM_005267510		Approved	DKFZP564C1940, MGC8675, LRP9, MST087, MSTP087	uc001whd.3	Q7Z4F1	OTTHUMG00000028705	ENST00000359591.4:c.358G>A	chr14.hg19:g.23344406G>A	ENSP00000352601:p.Gly120Arg	65.0	0.0	.		67.0	14.0	.	NM_014045	A8K4R5|D3DS31|O95882|Q14CK7|Q86T02|Q8NCZ4|Q9HC42|Q9UG33	Missense_Mutation	SNP	ENST00000359591.4	hg19	CCDS9578.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.04|17.04	3.287260|3.287260	0.59867|0.59867	.|.	.|.	ENSG00000197324|ENSG00000197324	ENST00000359591;ENST00000546834|ENST00000551466	T;T|.	0.28666|.	1.6;1.6|.	5.4|5.4	5.4|5.4	0.78164|0.78164	CUB (3);|.	0.122018|.	0.56097|.	D|.	0.000023|.	T|.	0.46367|.	0.1389|.	L|L	0.27053|0.27053	0.805|0.805	0.36299|0.36299	D|D	0.856899|0.856899	D|.	0.76494|.	0.999|.	D|.	0.66716|.	0.946|.	T|.	0.51585|.	-0.8687|.	10|.	0.24483|.	T|.	0.36|.	-20.6468|-20.6468	11.7283|11.7283	0.51722|0.51722	0.0:0.0:0.8237:0.1763|0.0:0.0:0.8237:0.1763	.|.	120|.	Q7Z4F1|.	LRP10_HUMAN|.	R|X	120|21	ENSP00000352601:G120R;ENSP00000447559:G120R|.	ENSP00000352601:G120R|.	G|W	+|+	1|2	0|0	LRP10|LRP10	22414246|22414246	0.992000|0.992000	0.36948|0.36948	0.992000|0.992000	0.48379|0.48379	0.961000|0.961000	0.63080|0.63080	2.281000|2.281000	0.43452|0.43452	2.547000|2.547000	0.85894|0.85894	0.563000|0.563000	0.77884|0.77884	GGG|TGG	.	.	.	none		0.632	LRP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071663.3			A	23344406	G	A	23344406	3	1	244	1	0	0	0	0	1	0	0	0	8959	1348	47	2	372	2	LRP10	14	23344406	Missense_Mutation	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	104118	23344406	84005134	73	15102											
LRP10	26020	hgsc.bcm.edu	37	chr14	23344686	23344686	+	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	atgaagcaggttgcagctcaGaccccttccctggcctgacc	8	8	10	15	0	1	3	1	2	0	1	2	3	2	3	5	2	3	4	5	2	1	2			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr14:23344686G>C	ENST00000359591.4	+	5	1220	c.529G>C	c.(529-531)Gac>Cac	p.D177H	LRP10_ENST00000546834.1_Missense_Mutation_p.D177H	NM_014045.3	NP_054764.2	Q7Z4F1	LRP10_HUMAN	low density lipoprotein receptor-related protein 10	177					endocytosis (GO:0006897)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(2)	32	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.00549)		TTGCAGCTCAGACCCCTTCCC	0.572																																					p.D177H		Atlas-SNP	.											.	LRP10	72	.	0			c.G529C						PASS	.						136	111	119					14																	23344686		2203	4300	6503	SO:0001583	missense	26020	exon5			AGCTCAGACCCCT	AF131760	CCDS9578.1	14q11.2	2013-05-29			ENSG00000197324	ENSG00000197324		"Low density lipoprotein receptors"	14553	protein-coding gene	gene with protein product		609921				11123907	Standard	XM_005267510		Approved	DKFZP564C1940, MGC8675, LRP9, MST087, MSTP087	uc001whd.3	Q7Z4F1	OTTHUMG00000028705	ENST00000359591.4:c.529G>C	chr14.hg19:g.23344686G>C	ENSP00000352601:p.Asp177His	112.0	0.0	.		83.0	23.0	.	NM_014045	A8K4R5|D3DS31|O95882|Q14CK7|Q86T02|Q8NCZ4|Q9HC42|Q9UG33	Missense_Mutation	SNP	ENST00000359591.4	hg19	CCDS9578.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.854|9.854	1.194470|1.194470	0.22037|0.22037	.|.	.|.	ENSG00000197324|ENSG00000197324	ENST00000359591;ENST00000546834|ENST00000551466	D;D|.	0.94330|.	-3.2;-3.4|.	5.2|5.2	3.22|3.22	0.36961|0.36961	.|.	0.294917|.	0.36665|.	N|.	0.002472|.	T|T	0.34948|0.34948	0.0915|0.0915	N|N	0.25380|0.25380	0.74|0.74	0.32900|0.32900	D|D	0.51306|0.51306	B|.	0.09022|.	0.002|.	B|.	0.06405|.	0.002|.	T|T	0.43048|0.43048	-0.9415|-0.9415	10|5	0.32370|.	T|.	0.25|.	-15.981|-15.981	6.461|6.461	0.21956|0.21956	0.0985:0.359:0.5425:0.0|0.0985:0.359:0.5425:0.0	.|.	177|.	Q7Z4F1|.	LRP10_HUMAN|.	H|T	177|78	ENSP00000352601:D177H;ENSP00000447559:D177H|.	ENSP00000352601:D177H|.	D|R	+|+	1|2	0|0	LRP10|LRP10	22414526|22414526	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.857000|0.857000	0.48899|0.48899	1.419000|1.419000	0.34793|0.34793	1.424000|1.424000	0.47217|0.47217	0.655000|0.655000	0.94253|0.94253	GAC|AGA	.	.	.	none		0.572	LRP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071663.3			C	23344686	G	C	23344686	3	2	244	1	0	0	0	0	1	0	0	0	8959	942	33	4	547	4	LRP10	14	23344686	Missense_Mutation	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	280	23344686	84004854	74	15103											
SLC7A8	23428	hgsc.bcm.edu	37	chr14	23634563	23634563	+	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	ggtggggaagagcggctgcaGcacgtagttggagaaggtga	10	6	20	5	2	0	3	0	1	0	2	0	5	0	4	0	6	3	5	0	6	3	2			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr14:23634563G>A	ENST00000316902.7	-	3	1164	c.439C>T	c.(439-441)Ctg>Ttg	p.L147L	SLC7A8_ENST00000469263.1_Silent_p.L147L	NM_012244.3	NP_036376.2	Q9UHI5	LAT2_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 8	147					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|metal ion homeostasis (GO:0055065)|neutral amino acid transport (GO:0015804)|organic cation transport (GO:0015695)|response to toxic substance (GO:0009636)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|organic cation transmembrane transporter activity (GO:0015101)|peptide antigen binding (GO:0042605)|toxin transporter activity (GO:0019534)			autonomic_ganglia(1)|endometrium(6)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|skin(1)	24	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00809)	L-Alanine(DB00160)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	AGCGGCTGCAGCACGTAGTTG	0.582																																					p.L147L		Atlas-SNP	.											.	SLC7A8	54	.	0			c.C439T						PASS	.						57	44	48					14																	23634563		2203	4300	6503	SO:0001819	synonymous_variant	23428	exon3			GCTGCAGCACGTA	Y18483	CCDS9590.1, CCDS41924.1, CCDS58304.1, CCDS58305.1	14q11.2	2013-05-22	2011-07-12		ENSG00000092068	ENSG00000092068		"Solute carriers"	11066	protein-coding gene	gene with protein product		604235				10080183, 10391915	Standard	NM_001267036		Approved	LPI-PC1, LAT2	uc001wiz.4	Q9UHI5	OTTHUMG00000028720	ENST00000316902.7:c.439C>T	chr14.hg19:g.23634563G>A		87.0	0.0	.		67.0	21.0	.	NM_012244	B2R8Q4|B4DKT4|B4DTV6|D3DS46|F2Z2J4|Q86U05|Q9UKQ6|Q9UKQ7|Q9UKQ8|Q9Y445	Silent	SNP	ENST00000316902.7	hg19	CCDS9590.1																																																																																			.	.	.	none		0.582	SLC7A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071718.3			A	23634563	G	A	23634563	2	1	244	1	0	0	0	0	0	0	0	1	14717	962	34	2		2	SLC7A8	14	23634563	Silent	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	289877	23634563	83714977	75	15104											
HOMEZ	57594	hgsc.bcm.edu	37	chr14	23744802	23744802	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcagtcttgtatgatcacAtcatcatcatcatcatcatc	12	14	3	12	0	9	1	8	1	1	0	10	1	9	1	0	0	0	1	0	0	1	2	rs148005528		TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr14:23744802A>G	ENST00000357460.5	-	2	1799	c.1635T>C	c.(1633-1635)gaT>gaC	p.D545D	HOMEZ_ENST00000431326.2_Silent_p.D547D|HOMEZ_ENST00000561013.1_Silent_p.D547D	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	545					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)		GTATGatcacatcatcatcat	0.443																																					p.D545D		Atlas-SNP	.											.	HOMEZ	80	.	0			c.T1635C						PASS	.						30	32	31					14																	23744802		2079	4051	6130	SO:0001819	synonymous_variant	57594	exon2			GATCACATCATCA	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.1635T>C	chr14.hg19:g.23744802A>G		110.0	0.0	.		115.0	58.0	.	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Silent	SNP	ENST00000357460.5	hg19	CCDS45085.1																																																																																			.	.	.	none		0.443	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834		G	23744802	A	G	23744802	2	3	244	1	0	0	0	0	0	0	0	1	7288	214	8	3		3	HOMEZ	14	23744802	Silent	SNP	A	TCGA-SX-A71V-01A-11D-A33Q-10	110239	23744802	83604738	76	15105											
RDH12	145226	hgsc.bcm.edu	37	chr14	68192868	68192868	+	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	acccacctgggagtcaaccaCctgggtaagtatctttgggt	9	10	11	11	0	2	0	1	0	1	0	2	1	2	1	4	3	1	2	4	3	3	3			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr14:68192868C>A	ENST00000551171.1	+	6	768	c.444C>A	c.(442-444)caC>caA	p.H148Q	RDH12_ENST00000267502.3_Missense_Mutation_p.H148Q|RDH12_ENST00000539142.1_Missense_Mutation_p.H148Q	NM_152443.2	NP_689656.2	Q96NR8	RDH12_HUMAN	retinol dehydrogenase 12 (all-trans/9-cis/11-cis)	148					photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	intracellular (GO:0005622)|photoreceptor inner segment membrane (GO:0060342)	retinol dehydrogenase activity (GO:0004745)			large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(4)	12				all cancers(60;0.000704)|OV - Ovarian serous cystadenocarcinoma(108;0.00161)|BRCA - Breast invasive adenocarcinoma(234;0.00953)	Vitamin A(DB00162)	GAGTCAACCACCTGGGTAAGT	0.443																																					p.H148Q		Atlas-SNP	.											.	RDH12	43	.	0			c.C444A						PASS	.						114	114	114					14																	68192868		2203	4300	6503	SO:0001583	missense	145226	exon6			CAACCACCTGGGT	AK054835	CCDS9787.1	14q24.1	2013-02-14	2006-05-09		ENSG00000139988	ENSG00000139988	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	19977	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 7C, member 2"	608830	"retinol dehydrogenase 12 (all-trans and 9-cis)"			12226107, 19027726	Standard	NM_152443		Approved	FLJ30273, SDR7C2, LCA13, RP53	uc001xjz.4	Q96NR8		ENST00000551171.1:c.444C>A	chr14.hg19:g.68192868C>A	ENSP00000449079:p.His148Gln	90.0	0.0	.		86.0	38.0	.	NM_152443	B2RDA2|Q8TAW6	Missense_Mutation	SNP	ENST00000551171.1	hg19	CCDS9787.1	.	.	.	.	.	.	.	.	.	.	C	17.57	3.422880	0.62733	.	.	ENSG00000139988	ENST00000551171;ENST00000267502;ENST00000539142	D;D;D	0.87256	-2.23;-2.23;-2.23	6.04	3.28	0.37604	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.92954	0.7758	M	0.89214	3.015	0.53005	D	0.999962	D	0.67145	0.996	D	0.74023	0.982	D	0.92340	0.5881	10	0.87932	D	0	.	8.3376	0.32224	0.0:0.6449:0.0:0.3551	.	148	Q96NR8	RDH12_HUMAN	Q	148	ENSP00000449079:H148Q;ENSP00000267502:H148Q;ENSP00000438715:H148Q	ENSP00000267502:H148Q	H	+	3	2	RDH12	67262621	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	0.886000	0.28241	0.914000	0.36822	-0.217000	0.12591	CAC	.	.	.	none		0.443	RDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406918.1			A	68192868	C	A	68192868	3	1	244	1	0	0	0	0	1	0	0	0	13204	506	18	4	458	4	RDH12	14	68192868	Missense_Mutation	SNP	C	TCGA-SX-A71V-01A-11D-A33Q-10	44448066	68192868	39156672	77	15106											
PPP2R5C	5527	hgsc.bcm.edu	37	chr14	102368158	102368158	+	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	tagatgtcattgaaccatcaGaatttgtgaagatcatggaa	15	12	9	5	0	3	5	3	2	0	3	3	6	3	6	1	1	1	0	1	1	5	3			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr14:102368158G>C	ENST00000334743.5	+	9	1003	c.955G>C	c.(955-957)Gaa>Caa	p.E319Q	PPP2R5C_ENST00000422945.2_Missense_Mutation_p.E350Q|PPP2R5C_ENST00000557095.1_Missense_Mutation_p.E319Q|PPP2R5C_ENST00000445439.3_Missense_Mutation_p.E319Q|PPP2R5C_ENST00000350249.3_Missense_Mutation_p.E319Q|PPP2R5C_ENST00000328724.5_Missense_Mutation_p.E374Q	NM_002719.3	NP_002710.2	Q13362	2A5G_HUMAN	protein phosphatase 2, regulatory subunit B', gamma	319					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of cell proliferation (GO:0008285)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20						TGAACCATCAGAATTTGTGAA	0.443																																					p.E374Q		Atlas-SNP	.											.	PPP2R5C	74	.	0			c.G1120C						PASS	.						94	95	95					14																	102368158		2203	4300	6503	SO:0001583	missense	5527	exon11			CCATCAGAATTTG	L42375	CCDS9964.1, CCDS9965.1, CCDS45163.1, CCDS53911.1, CCDS53912.1	14q32.31	2010-06-18	2010-04-14		ENSG00000078304	ENSG00000078304		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9311	protein-coding gene	gene with protein product		601645	"protein phosphatase 2, regulatory subunit B (B56), gamma isoform", "protein phosphatase 2, regulatory subunit B', gamma isoform"			7592815	Standard	NM_002719		Approved	B56G, PR61G	uc001ykk.3	Q13362		ENST00000334743.5:c.955G>C	chr14.hg19:g.102368158G>C	ENSP00000333905:p.Glu319Gln	82.0	0.0	.		90.0	35.0	.	NM_001161726	B4DYJ8|B5BUA5|F5GWP3|Q14391|Q15060|Q15174|Q6ZN33	Missense_Mutation	SNP	ENST00000334743.5	hg19	CCDS9964.1	.	.	.	.	.	.	.	.	.	.	G	14.40	2.523143	0.44866	.	.	ENSG00000078304	ENST00000422945;ENST00000328724;ENST00000557268;ENST00000350249;ENST00000334756;ENST00000445439;ENST00000334743;ENST00000557095;ENST00000557716	T;T;T;T;T	0.51071	0.72;0.78;0.72;0.82;0.73	5.3	5.3	0.74995	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.66954	0.2842	M	0.69358	2.11	0.80722	D	1	P;P;D;P;B;P	0.60575	0.826;0.531;0.988;0.856;0.049;0.847	B;B;D;P;B;D	0.70716	0.422;0.294;0.97;0.557;0.216;0.923	T	0.63129	-0.6706	10	0.30854	T	0.27	-11.4511	18.9542	0.92653	0.0:0.0:1.0:0.0	.	350;217;319;319;319;374	F5GWP3;E9PHN5;Q13362-3;Q13362;Q13362-2;Q6ZN33	.;.;.;2A5G_HUMAN;.;.	Q	350;374;348;319;217;319;319;319;115	ENSP00000412324:E350Q;ENSP00000329009:E374Q;ENSP00000450931:E348Q;ENSP00000262239:E319Q;ENSP00000333905:E319Q	ENSP00000329009:E374Q	E	+	1	0	PPP2R5C	101437911	1.000000	0.71417	0.142000	0.22268	0.959000	0.62525	7.799000	0.85936	2.490000	0.84030	0.655000	0.94253	GAA	.	.	.	none		0.443	PPP2R5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414373.2	NM_002719		C	102368158	G	C	102368158	3	2	244	1	0	0	0	0	1	0	0	0	12404	943	33	4	1358	4	PPP2R5C	14	102368158	Missense_Mutation	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	34175290	102368158	4981382	78	15107											
TRPM1	4308	hgsc.bcm.edu	37	chr15	31294200	31294200	+	Frame_Shift_Del	DEL	G	G	-																															aactttttgacctgagagatGggaatcccaaagtttgatct																										TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr15:31294200delG	ENST00000256552.6	-	28	4850	c.4703delC	c.(4702-4704)ccafs	p.P1568fs	TRPM1_ENST00000542188.1_Frame_Shift_Del_p.P1585fs|RP11-348B17.1_ENST00000561299.1_RNA|TRPM1_ENST00000397795.2_Frame_Shift_Del_p.P1546fs	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)		CCTGAGAGATGGGAATCCCAA	0.433																																					p.P1585fs		Atlas-Indel,Pindel	.											.	TRPM1	183	.	0			c.4755delA						PASS	.						205	187	193					15																	31294200		1890	4112	6002	SO:0001589	frameshift_variant	4308	exon27			.	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.4703delC	chr15.hg19:g.31294200delG	ENSP00000256552:p.Pro1568fs	84.0	0.0	0		74.0	20.0	0.27027	NM_001252020		Frame_Shift_Del	DEL	ENST00000256552.6	hg19	CCDS58346.1																																																																																			.	.	.	none		0.433	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420		-	31294200	G	-	31294200	7	5	244	1	0	1	0	1	0	0	0	0	16597	1348	47	0	178	0	TRPM1	15	31294200	Frame_Shift_Del	DEL	G	TCGA-SX-A71V-01A-11D-A33Q-10		31294200	71237192	79	15108											
GATM	2628	hgsc.bcm.edu	37	chr15	45668863	45668863	+	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	tgcccactatcacttcctctAaggggtcccattcgttgtaa	8	13	7	13	1	2	0	1	0	1	0	5	0	4	0	3	2	1	2	3	2	3	6			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr15:45668863A>C	ENST00000396659.3	-	2	563	c.224T>G	c.(223-225)tTa>tGa	p.L75*	GATM_ENST00000558336.1_Nonsense_Mutation_p.L75*|GATM_ENST00000458245.5_5'Flank	NM_001482.2	NP_001473.1	P50440	GATM_HUMAN	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	75					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)	CACTTCCTCTAAGGGGTCCCA	0.542																																					p.L75X		Atlas-SNP	.											.	GATM	34	.	0			c.T224G						PASS	.						135	127	129					15																	45668863		2198	4298	6496	SO:0001587	stop_gained	2628	exon2			TCCTCTAAGGGGT	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.224T>G	chr15.hg19:g.45668863A>C	ENSP00000379895:p.Leu75*	57.0	0.0	.		73.0	31.0	.	NM_001482	B4DH99|B4DPI3|Q53EQ4	Nonsense_Mutation	SNP	ENST00000396659.3	hg19	CCDS10122.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.405479	0.83230	.	.	ENSG00000171766	ENST00000396659	.	.	.	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.5014	14.1188	0.65172	1.0:0.0:0.0:0.0	.	.	.	.	X	75	.	ENSP00000379895:L75X	L	-	2	0	GATM	43456155	1.000000	0.71417	0.962000	0.40283	0.993000	0.82548	8.884000	0.92432	2.210000	0.71456	0.533000	0.62120	TTA	.	.	.	none		0.542	GATM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254220.2	NM_001482		C	45668863	A	C	45668863	4	2	244	1	0	0	0	0	0	1	0	0	6270	372	13	5	1079	5	GATM	15	45668863	Nonsense_Mutation	SNP	A	TCGA-SX-A71V-01A-11D-A33Q-10	14374663	45668863	56862529	80	15109											
FGF7	2252	hgsc.bcm.edu	37	chr15	49716529	49716529	+	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	actgacatggatcctgccaaCtttgctctacagatcatgct	10	12	7	12	0	2	2	1	1	1	1	3	3	3	3	2	1	5	2	2	1	2	2			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr15:49716529C>G	ENST00000267843.4	+	2	646	c.35C>G	c.(34-36)aCt>aGt	p.T12S	FAM227B_ENST00000561064.1_Intron|FAM227B_ENST00000299338.6_Intron|FGF7_ENST00000560270.1_Missense_Mutation_p.T12S	NM_002009.3	NP_002000.1	P21781	FGF7_HUMAN	fibroblast growth factor 7	12					actin cytoskeleton reorganization (GO:0031532)|branching involved in salivary gland morphogenesis (GO:0060445)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis development (GO:0008544)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle morphogenesis (GO:0031069)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|mesenchymal cell proliferation (GO:0010463)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein localization to cell surface (GO:0034394)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)|response to wounding (GO:0009611)|secretion by lung epithelial cell involved in lung growth (GO:0061033)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)	chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)			kidney(1)|large_intestine(1)|lung(2)|prostate(1)	5		all_lung(180;0.00391)		all cancers(107;3.61e-08)|GBM - Glioblastoma multiforme(94;4.06e-05)		ATCCTGCCAACTTTGCTCTAC	0.383																																					p.T12S		Atlas-SNP	.											.	FGF7	21	.	0			c.C35G						PASS	.						192	168	176					15																	49716529		2196	4295	6491	SO:0001583	missense	2252	exon2			TGCCAACTTTGCT	M60828	CCDS10131.1	15q21.2	2014-01-30	2010-08-18		ENSG00000140285	ENSG00000140285		"Endogenous ligands"	3685	protein-coding gene	gene with protein product	"keratinocyte growth factor"	148180	"fibroblast growth factor 7 (keratinocyte growth factor)"			7749227, 1409637	Standard	NM_002009		Approved	KGF	uc001zxn.3	P21781	OTTHUMG00000131517	ENST00000267843.4:c.35C>G	chr15.hg19:g.49716529C>G	ENSP00000267843:p.Thr12Ser	87.0	0.0	.		53.0	22.0	.	NM_002009	H0YNY5|Q6FGV5|Q96FG5	Missense_Mutation	SNP	ENST00000267843.4	hg19	CCDS10131.1	.	.	.	.	.	.	.	.	.	.	C	7.769	0.706993	0.15239	.	.	ENSG00000140285	ENST00000267843	T	0.23348	1.91	5.7	3.72	0.42706	.	0.719107	0.14365	N	0.324213	T	0.17450	0.0419	.	.	.	0.31782	N	0.630781	B	0.10296	0.003	B	0.06405	0.002	T	0.10894	-1.0610	9	0.29301	T	0.29	.	9.8033	0.40777	0.0:0.6371:0.2844:0.0784	.	12	P21781	FGF7_HUMAN	S	12	ENSP00000267843:T12S	ENSP00000267843:T12S	T	+	2	0	FGF7	47503821	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.034000	0.41145	1.425000	0.47237	0.655000	0.94253	ACT	.	.	.	none		0.383	FGF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254374.3	NM_002009		G	49716529	C	G	49716529	3	3	244	1	0	0	0	0	1	0	0	0	5864	565	20	4	37	4	FGF7	15	49716529	Missense_Mutation	SNP	C	TCGA-SX-A71V-01A-11D-A33Q-10	4047666	49716529	52814863	81	15110											
SETD1A	9739	hgsc.bcm.edu	37	chr16	30982956	30982956	+	Missense_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	cagtgcccacgccagcacctGtggaggtgccagtgccggaa	8	5	14	14	2	0	0	0	0	0	0	0	2	0	2	5	3	4	1	5	3	1	0			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr16:30982956G>A	ENST00000262519.8	+	13	3960	c.3274G>A	c.(3274-3276)Gtg>Atg	p.V1092M		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	1092	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						GCCAGCACCTGTGGAGGTGCC	0.662																																					p.V1092M		Atlas-SNP	.											.	SETD1A	143	.	0			c.G3274A						PASS	.						35	38	37					16																	30982956		2197	4299	6496	SO:0001583	missense	9739	exon13			GCACCTGTGGAGG	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.3274G>A	chr16.hg19:g.30982956G>A	ENSP00000262519:p.Val1092Met	61.0	0.0	.		67.0	14.0	.	NM_014712	A6NP62|Q6PIF3|Q8TAJ6	Missense_Mutation	SNP	ENST00000262519.8	hg19	CCDS32435.1	.	.	.	.	.	.	.	.	.	.	G	10.45	1.353357	0.24512	.	.	ENSG00000099381	ENST00000262519	D	0.94897	-3.55	5.81	5.81	0.92471	.	0.788898	0.11531	N	0.554670	D	0.93262	0.7853	L	0.46157	1.445	0.20821	N	0.999847	B	0.22480	0.07	B	0.31016	0.123	D	0.86220	0.1630	10	0.51188	T	0.08	.	15.5798	0.76425	0.0:0.0:1.0:0.0	.	1092	O15047	SET1A_HUMAN	M	1092	ENSP00000262519:V1092M	ENSP00000262519:V1092M	V	+	1	0	SETD1A	30890457	0.274000	0.24191	0.181000	0.23098	0.366000	0.29705	1.028000	0.30128	2.752000	0.94435	0.467000	0.42956	GTG	.	.	.	none		0.662	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712		A	30982956	G	A	30982956	3	1	244	1	0	0	0	0	1	0	0	0	14143	1377	48	2	3320	2	SETD1A	16	30982956	Missense_Mutation	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10		30982956	59371797	82	15111											
NKD1	85407	hgsc.bcm.edu	37	chr16	50583410	50583410	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggagacagcgctgcccgggcGgtgtctcgggaccccgacag	6	4	17	14	5	1	1	0	0	1	1	2	4	1	2	3	4	2	1	3	4	0	0			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr16:50583410G>A	ENST00000268459.3	+	3	360	c.136G>A	c.(136-138)Ggt>Agt	p.G46S	NKD1_ENST00000564336.1_3'UTR|RP11-401P9.1_ENST00000569940.2_RNA	NM_033119.4	NP_149110.1	Q969G9	NKD1_HUMAN	naked cuticle homolog 1 (Drosophila)	46					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)		CTGCCCGGGCGGTGTCTCGGG	0.687																																					p.G46S		Atlas-SNP	.											.	NKD1	43	.	0			c.G136A						PASS	.						24	26	25					16																	50583410		2195	4298	6493	SO:0001583	missense	85407	exon3			CCGGGCGGTGTCT	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.136G>A	chr16.hg19:g.50583410G>A	ENSP00000268459:p.Gly46Ser	52.0	0.0	.		70.0	38.0	.	NM_033119	B2RC39|Q8WZ08	Missense_Mutation	SNP	ENST00000268459.3	hg19	CCDS10743.1	.	.	.	.	.	.	.	.	.	.	G	6.267	0.417444	0.11870	.	.	ENSG00000140807	ENST00000268459	T	0.62232	0.04	4.15	1.98	0.26296	.	0.774566	0.12349	N	0.476745	T	0.28699	0.0711	N	0.02011	-0.69	0.09310	N	1	B	0.14438	0.01	B	0.12837	0.008	T	0.23404	-1.0189	10	0.06494	T	0.89	-5.2334	8.1969	0.31402	0.2365:0.0:0.7635:0.0	.	46	Q969G9	NKD1_HUMAN	S	46	ENSP00000268459:G46S	ENSP00000268459:G46S	G	+	1	0	NKD1	49140911	0.996000	0.38824	0.078000	0.20375	0.659000	0.38960	1.536000	0.36072	0.941000	0.37499	0.313000	0.20887	GGT	.	.	.	none		0.687	NKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256873.1			A	50583410	G	A	50583410	3	1	244	1	0	0	0	0	1	0	0	0	10448	1116	39	1	146	1	NKD1	16	50583410	Missense_Mutation	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	19600454	50583410	39771343	83	15112											
DDX28	55794	hgsc.bcm.edu	37	chr16	68057034	68057034	+	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	tcgtcgggactgcggaccgtGaggccccgtcgcggcgccag	4	5	17	15	8	0	1	0	1	0	0	3	3	0	3	4	4	1	0	4	4	0	0			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr16:68057034G>A	ENST00000332395.5	-	1	736	c.72C>T	c.(70-72)ctC>ctT	p.L24L	DUS2_ENST00000432752.1_5'Flank|DUS2_ENST00000565263.1_5'UTR|DUS2_ENST00000358896.6_5'Flank	NM_018380.3	NP_060850.2	Q9NUL7	DDX28_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 28	24						mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	13		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0116)|Epithelial(162;0.0474)|all cancers(182;0.233)		TGCGGACCGTGAGGCCCCGTC	0.672																																					p.L24L		Atlas-SNP	.											.	DDX28	29	.	0			c.C72T						PASS	.						15	17	16					16																	68057034		2175	4253	6428	SO:0001819	synonymous_variant	55794	exon1			GACCGTGAGGCCC	AF329821	CCDS10858.1	16q22.1-q22.3	2008-02-05	2003-06-13		ENSG00000182810	ENSG00000182810		"DEAD-boxes"	17330	protein-coding gene	gene with protein product		607618	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 28"			10493829, 11350955	Standard	NM_018380		Approved	MDDX28, FLJ11282	uc002evh.2	Q9NUL7	OTTHUMG00000137549	ENST00000332395.5:c.72C>T	chr16.hg19:g.68057034G>A		11.0	0.0	.		25.0	15.0	.	NM_018380		Silent	SNP	ENST00000332395.5	hg19	CCDS10858.1																																																																																			.	.	.	none		0.672	DDX28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268883.1	NM_018380		A	68057034	G	A	68057034	2	1	244	1	0	0	0	0	0	0	0	1	4357	1277	45	2		2	DDX28	16	68057034	Silent	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	17473624	68057034	22297719	84	15113											
WWP2	11060	hgsc.bcm.edu	37	chr16	69820957	69820957	+	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	ggcaggagtggccctgccttTtgagaagtctcagctcactt	7	11	12	11	0	2	1	2	1	1	1	3	3	2	2	2	3	2	2	2	3	1	3			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr16:69820957T>A	ENST00000359154.2	+	2	145	c.44T>A	c.(43-45)tTt>tAt	p.F15Y	WWP2_ENST00000569174.1_Missense_Mutation_p.F15Y|WWP2_ENST00000448661.1_Missense_Mutation_p.F15Y|SNORA62_ENST00000516634.1_RNA|WWP2_ENST00000356003.2_Missense_Mutation_p.F15Y	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	15					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						GCCCTGCCTTTTGAGAAGTCT	0.468																																					p.F15Y		Atlas-SNP	.											.	WWP2	88	.	0			c.T44A						PASS	.						118	98	105					16																	69820957		2198	4300	6498	SO:0001583	missense	11060	exon2			TGCCTTTTGAGAA	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.44T>A	chr16.hg19:g.69820957T>A	ENSP00000352069:p.Phe15Tyr	73.0	0.0	.		83.0	19.0	.	NM_001270454	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Missense_Mutation	SNP	ENST00000359154.2	hg19	CCDS10885.1	.	.	.	.	.	.	.	.	.	.	T	9.974	1.226372	0.22542	.	.	ENSG00000198373	ENST00000359154;ENST00000448661;ENST00000356003	T;T;T	0.29397	1.57;1.57;1.57	5.29	4.19	0.49359	C2 calcium/lipid-binding domain, CaLB (1);	0.560166	0.20039	N	0.100552	T	0.14527	0.0351	N	0.14661	0.345	0.80722	D	1	B	0.29909	0.261	B	0.25759	0.063	T	0.10019	-1.0648	9	.	.	.	.	5.4691	0.16660	0.0:0.0909:0.1754:0.7337	.	15	O00308	WWP2_HUMAN	Y	15	ENSP00000352069:F15Y;ENSP00000396871:F15Y;ENSP00000348283:F15Y	.	F	+	2	0	WWP2	68378458	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.190000	0.42630	0.859000	0.35456	0.460000	0.39030	TTT	.	.	.	none		0.468	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014		A	69820957	T	A	69820957	3	1	244	1	0	0	0	0	1	0	0	0	17428	1841	64	5	46	5	WWP2	16	69820957	Missense_Mutation	SNP	T	TCGA-SX-A71V-01A-11D-A33Q-10	1763923	69820957	20533796	85	15114											
MINK1	100130311	hgsc.bcm.edu	37	chr17	4799846	4799846	+	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	tacgggcgcatcattaaggaTgtggtgctgcagtgggggga	8	9	18	6	2	1	0	1	0	0	0	1	2	1	2	0	6	3	3	0	6	2	2	rs372981603		TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr17:4799846T>C	ENST00000381365.3	+	0	0				C17orf107_ENST00000521575.1_5'Flank|MINK1_ENST00000453408.3_Silent_p.D1226D|MINK1_ENST00000355280.6_Silent_p.D1246D|MINK1_ENST00000347992.7_Silent_p.D1217D	NM_001145536.1	NP_001139008.1	Q6ZR85	CQ107_HUMAN	chromosome 17 open reading frame 107											endometrium(2)	2						TCATTAAGGATGTGGTGCTGC	0.622																																					p.D1246D		Atlas-SNP	.											.	MINK1	110	.	0			c.T3738C						PASS	.						94	101	99					17																	4799846		2183	4270	6453	SO:0001631	upstream_gene_variant	50488	exon30			TAAGGATGTGGTG	AK128415	CCDS45591.1	17p13.2	2009-09-30			ENSG00000205710	ENSG00000205710			37238	protein-coding gene	gene with protein product							Standard	NM_001145536		Approved		uc002fzl.3	Q6ZR85	OTTHUMG00000164838		chr17.hg19:g.4799846T>C	Exception_encountered	67.0	0.0	.		107.0	34.0	.	NM_153827		Silent	SNP	ENST00000381365.3	hg19	CCDS45591.1																																																																																			.	.	.	alt		0.622	C17orf107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380556.1	NM_001145536		C	4799846	T	C	4799846	1	2	244	0	1	0	0	0	0	0	0	0	9594	1461	51	3		3	MINK1	17	4799846	5'Flank	SNP	T	TCGA-SX-A71V-01A-11D-A33Q-10		4799846	76395364	86	15115											
COX10	1352	hgsc.bcm.edu	37	chr17	14110151	14110151	+	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	atttctcctgggaggaatccTctactcctggcagtttcctc	6	14	8	13	0	2	0	0	0	2	0	7	2	5	2	4	3	1	2	4	3	2	3			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr17:14110151T>A	ENST00000261643.3	+	7	1030	c.953T>A	c.(952-954)cTc>cAc	p.L318H	COX10_ENST00000537334.1_Missense_Mutation_p.L101H|COX10_ENST00000536205.1_Missense_Mutation_p.L126H	NM_001303.3	NP_001294.2	Q12887	COX10_HUMAN	cytochrome c oxidase assembly homolog 10 (yeast)	318					aerobic respiration (GO:0009060)|cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|heme O biosynthetic process (GO:0048034)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|mitochondrial fission (GO:0000266)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	farnesyltranstransferase activity (GO:0004311)|protoheme IX farnesyltransferase activity (GO:0008495)			cervix(1)|endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		GGAGGAATCCTCTACTCCTGG	0.587																																					p.L318H		Atlas-SNP	.											.	COX10	36	.	0			c.T953A						PASS	.						61	68	66					17																	14110151		2203	4300	6503	SO:0001583	missense	1352	exon7			GAATCCTCTACTC	U09466	CCDS11166.1	17p12	2013-05-24	2012-10-15		ENSG00000006695	ENSG00000006695		"Mitochondrial respiratory chain complex assembly factors"	2260	protein-coding gene	gene with protein product	"heme A: farnesyltransferase", "protoheme IX farnesyltransferase, mitochondrial", "heme O synthase"	602125	"COX10 (yeast) homolog, cytochrome c oxidase assembly protein (heme A: farnesyltransferase)", "COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase (yeast)"			9177788, 12928484	Standard	NM_001303		Approved		uc002gof.4	Q12887	OTTHUMG00000058814	ENST00000261643.3:c.953T>A	chr17.hg19:g.14110151T>A	ENSP00000261643:p.Leu318His	66.0	0.0	.		91.0	45.0	.	NM_001303	B2R6U5|B4DJ50|O15334|Q969F7	Missense_Mutation	SNP	ENST00000261643.3	hg19	CCDS11166.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.647456	0.87958	.	.	ENSG00000006695	ENST00000261643;ENST00000536205;ENST00000537334	D;D;D	0.93906	-3.31;-3.31;-3.31	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	D	0.97829	0.9287	H	0.97158	3.95	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.99257	1.0889	10	0.87932	D	0	-10.0897	14.9423	0.71003	0.0:0.0:0.0:1.0	.	126;318	B4DJ50;Q12887	.;COX10_HUMAN	H	318;126;101	ENSP00000261643:L318H;ENSP00000439494:L126H;ENSP00000443354:L101H	ENSP00000261643:L318H	L	+	2	0	COX10	14050876	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.577000	0.82486	2.005000	0.58758	0.533000	0.62120	CTC	.	.	.	none		0.587	COX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130003.1	NM_001303		A	14110151	T	A	14110151	3	1	244	1	0	0	0	0	1	0	0	0	3764	1551	54	5	979	5	COX10	17	14110151	Missense_Mutation	SNP	T	TCGA-SX-A71V-01A-11D-A33Q-10	9310305	14110151	67085059	87	15116											
FLII	2314	hgsc.bcm.edu	37	chr17	18151250	18151250	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcatctcttaccagccgcAttcttggcatcagctccacc	7	11	6	17	1	3	0	1	0	2	0	5	0	4	0	4	1	4	4	4	1	1	3			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr17:18151250A>G	ENST00000327031.4	-	19	2513	c.2288T>C	c.(2287-2289)aTg>aCg	p.M763T	FLII_ENST00000379450.4_Missense_Mutation_p.M677T|FLII_ENST00000579294.1_Missense_Mutation_p.M752T|FLII_ENST00000545457.2_Missense_Mutation_p.M708T|FLII_ENST00000578558.1_Intron	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	763	Interaction with ACTL6A.				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)					TACCAGCCGCATTCTTGGCAT	0.622																																					p.M763T		Atlas-SNP	.											.	FLII	79	.	0			c.T2288C						PASS	.						117	106	110					17																	18151250		2203	4300	6503	SO:0001583	missense	2314	exon19			AGCCGCATTCTTG	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.2288T>C	chr17.hg19:g.18151250A>G	ENSP00000324573:p.Met763Thr	78.0	0.0	.		78.0	39.0	.	NM_002018	B4DIL0|F5H407|J3QLG3	Missense_Mutation	SNP	ENST00000327031.4	hg19	CCDS11192.1	.	.	.	.	.	.	.	.	.	.	A	13.33	2.204846	0.38905	.	.	ENSG00000177731	ENST00000327031;ENST00000379450	T;T	0.53640	0.61;0.61	5.21	5.21	0.72293	Gelsolin domain (1);	0.136494	0.64402	D	0.000003	T	0.37625	0.1010	N	0.22421	0.69	0.47009	D	0.999288	B;B;B;B	0.30563	0.189;0.189;0.02;0.285	B;B;B;B	0.33846	0.113;0.113;0.103;0.171	T	0.22521	-1.0214	10	0.36615	T	0.2	-36.048	15.0785	0.72096	1.0:0.0:0.0:0.0	.	677;677;763;732	E7EPM0;B4DIL0;Q13045;B4DIX0	.;.;FLII_HUMAN;.	T	763;677	ENSP00000324573:M763T;ENSP00000368763:M677T	ENSP00000324573:M763T	M	-	2	0	FLII	18091975	1.000000	0.71417	0.990000	0.47175	0.800000	0.45204	6.897000	0.75671	1.971000	0.57363	0.379000	0.24179	ATG	.	.	.	none		0.622	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018		G	18151250	A	G	18151250	3	3	244	1	0	0	0	0	1	0	0	0	5932	217	8	3	1569	3	FLII	17	18151250	Missense_Mutation	SNP	A	TCGA-SX-A71V-01A-11D-A33Q-10	4041099	18151250	63043960	88	15117											
HSD17B1	3292	hgsc.bcm.edu	37	chr17	40706580	40706580	+	Frame_Shift_Del	DEL	A	A	-																															tctttcgcgaggcggcgcagAaccctgaggaggtggcggag																										TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr17:40706580delA	ENST00000585807.1	+	5	4417	c.697delA	c.(697-699)aacfs	p.N233fs	RP11-400F19.8_ENST00000585572.1_RNA|HSD17B1_ENST00000225929.5_Frame_Shift_Del_p.N234fs|RP11-400F19.6_ENST00000590513.1_RNA	NM_000413.2	NP_000404.2	P14061	DHB1_HUMAN	hydroxysteroid (17-beta) dehydrogenase 1	233					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)	GGCGGCGCAGAACCCTGAGGA	0.692																																					p.Q232fs		Atlas-Indel,Pindel	.											.	HSD17B1	24	.	0			c.696delG						PASS	.						47	37	40					17																	40706580		2203	4300	6503	SO:0001589	frameshift_variant	3292	exon5			.		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.697delA	chr17.hg19:g.40706580delA	ENSP00000466799:p.Asn233fs	68.0	0.0	0		80.0	18.0	0.225	NM_000413	B3KXS1|Q2M2L8	Frame_Shift_Del	DEL	ENST00000585807.1	hg19	CCDS11428.1																																																																																			.	.	.	none		0.692	HSD17B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450392.1	NM_000413		-	40706580	A	-	40706580	7	5	244	1	0	1	0	1	0	0	0	0	7385	246	9	0	715	0	HSD17B1	17	40706580	Frame_Shift_Del	DEL	A	TCGA-SX-A71V-01A-11D-A33Q-10	22555330	40706580	40488630	89	15118											
TRIM65	201292	hgsc.bcm.edu	37	chr17	73887171	73887171	+	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	gcagggtccccggccaatgtTgtctgtgtggggccccagcc	4	8	15	14	1	1	0	0	0	1	0	2	0	2	0	6	4	1	2	6	4	1	1			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr17:73887171T>A	ENST00000269383.3	-	6	1308	c.1243A>T	c.(1243-1245)Aac>Tac	p.N415Y		NM_001256124.1|NM_173547.3	NP_001243053.1|NP_775818.2	Q6PJ69	TRI65_HUMAN	tripartite motif containing 65	415	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)			CGGCCAATGTTGTCTGTGTGG	0.697																																					p.N415Y		Atlas-SNP	.											.	TRIM65	23	.	0			c.A1243T						PASS	.						30	31	30					17																	73887171		2202	4296	6498	SO:0001583	missense	201292	exon6			CAATGTTGTCTGT	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.1243A>T	chr17.hg19:g.73887171T>A	ENSP00000269383:p.Asn415Tyr	23.0	0.0	.		20.0	8.0	.	NM_173547	Q4G0F0|Q6DKJ6|Q9BRP6	Missense_Mutation	SNP	ENST00000269383.3	hg19	CCDS11732.1	.	.	.	.	.	.	.	.	.	.	T	16.83	3.230594	0.58777	.	.	ENSG00000141569	ENST00000269383	T	0.68331	-0.32	5.33	5.33	0.75918	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.56097	D	0.000025	T	0.57066	0.2028	L	0.28458	0.855	0.37276	D	0.907619	B	0.28400	0.21	B	0.38921	0.285	T	0.54330	-0.8310	10	0.02654	T	1	.	15.2933	0.73882	0.0:0.0:0.0:1.0	.	415	Q6PJ69	TRI65_HUMAN	Y	415	ENSP00000269383:N415Y	ENSP00000269383:N415Y	N	-	1	0	TRIM65	71398766	1.000000	0.71417	1.000000	0.80357	0.466000	0.32739	3.892000	0.56235	2.030000	0.59900	0.448000	0.29417	AAC	.	.	.	none		0.697	TRIM65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255170.2	NM_173547		A	73887171	T	A	73887171	3	1	244	1	0	0	0	0	1	0	0	0	16551	1812	63	5	314	5	TRIM65	17	73887171	Missense_Mutation	SNP	T	TCGA-SX-A71V-01A-11D-A33Q-10	33180591	73887171	7308039	90	15119											
USP14	9097	hgsc.bcm.edu	37	chr18	192871	192871	+	Frame_Shift_Del	DEL	A	A	-																															tgccttgagagcttcaggggAaatggcttcagcgcagtata																										TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr18:192871delA	ENST00000261601.7	+	6	525	c.434delA	c.(433-435)gaafs	p.E145fs	USP14_ENST00000383589.2_Frame_Shift_Del_p.E99fs|USP14_ENST00000582707.1_Frame_Shift_Del_p.E110fs|USP14_ENST00000400266.3_Frame_Shift_Del_p.E134fs	NM_005151.3	NP_005142.1	P54578	UBP14_HUMAN	ubiquitin specific peptidase 14 (tRNA-guanine transglycosylase)	145	USP.				negative regulation of endopeptidase activity (GO:0010951)|protein deubiquitination (GO:0016579)|regulation of chemotaxis (GO:0050920)|regulation of proteasomal protein catabolic process (GO:0061136)|synaptic transmission (GO:0007268)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)|synapse (GO:0045202)	cysteine-type endopeptidase activity (GO:0004197)|endopeptidase inhibitor activity (GO:0004866)|proteasome binding (GO:0070628)|tRNA guanylyltransferase activity (GO:0008193)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|skin(2)	11		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)				GCTTCAGGGGAAATGGCTTCA	0.378																																					p.E145fs		Atlas-Indel,Pindel	.											.	USP14	41	.	0			c.433delG						PASS	.						179	176	177					18																	192871		2203	4300	6503	SO:0001589	frameshift_variant	9097	exon6			.	U30888	CCDS32780.1, CCDS32781.1	18p11.32	2006-10-06	2005-08-08			ENSG00000101557		"Ubiquitin-specific peptidases"	12612	protein-coding gene	gene with protein product		607274	"ubiquitin specific protease 14 (tRNA-guanine transglycosylase)"			12838346	Standard	NM_001037334		Approved	TGT	uc002kkf.1	P54578		ENST00000261601.7:c.434delA	chr18.hg19:g.192871delA	ENSP00000261601:p.Glu145fs	79.0	0.0	0		77.0	34.0	0.441558	NM_005151	J3QRZ5|Q53XY5	Frame_Shift_Del	DEL	ENST00000261601.7	hg19	CCDS32780.1																																																																																			.	.	.	none		0.378	USP14-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440305.3	NM_005151		-	192871	A	-	192871	7	5	244	1	0	1	0	1	0	0	0	0	17057	246	9	0	456	0	USP14	18	192871	Frame_Shift_Del	DEL	A	TCGA-SX-A71V-01A-11D-A33Q-10		192871	77884377	91	15120											
CTAGE1	64693	hgsc.bcm.edu	37	chr18	19995661	19995661	+	5'Flank	DEL	G	G	-																															gacctgggacatcccttggaGaaaaataatctggagaagct																										TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr18:19995661delG	ENST00000525417.1	-	0	0				CTAGE1_ENST00000391403.2_Frame_Shift_Del_p.S705fs			Q9HC47	CTGE1_HUMAN	cutaneous T-cell lymphoma-associated antigen 1							integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(19)|ovary(1)	27	all_cancers(21;0.000361)|all_epithelial(16;9.61e-06)|Colorectal(14;0.0533)|Lung NSC(20;0.0605)|Ovarian(2;0.116)|all_lung(20;0.135)					ATCCCTTGGAGAAAAATAATC	0.493																																					p.S705fs		Atlas-Indel,Pindel	.											.	CTAGE1	146	.	0			c.2115delT						PASS	.						54	60	58					18																	19995661		2125	4239	6364	SO:0001631	upstream_gene_variant	64693	exon1			.	AF177229	CCDS45837.1	18q11.2	2010-05-26			ENSG00000212710	ENSG00000212710			24346	protein-coding gene	gene with protein product	"cutaneous T-cell lymphoma-associated antigen 1", "cutaneous T-cell lymphoma-associated antigen 2", "cancer/testis antigen family 21, member 1", "cancer/testis antigen family 21, member 2"	608856				11149944, 12839582	Standard	NM_172241		Approved	cTAGE-1, cTAGE-2, CTAGE, CT21.1, CT21.2	uc002ktv.1	Q96RT6			chr18.hg19:g.19995661delG	Exception_encountered	114.0	0.0	0		109.0	33.0	0.302752	NM_172241	B0YIZ3	Frame_Shift_Del	DEL	ENST00000525417.1	hg19																																																																																				.	.	.	none		0.493	CTAGE1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000386767.1	NM_022663, NM_172241		-	19995661	G	-	19995661	6	5	244	0	1	1	0	1	0	0	0	0	3994	942	33	0		0	CTAGE1	18	19995661	5'Flank	DEL	G	TCGA-SX-A71V-01A-11D-A33Q-10	19802790	19995661	58081587	92	15121											
MCART2	147407	hgsc.bcm.edu	37	chr18	29340393	29340393	+	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	gattccacgatacaaatttcGaaatccatcccttctcaact	13	12	3	13	2	1	0	1	0	1	0	6	3	4	0	3	0	2	0	3	0	4	4			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr18:29340393G>A	ENST00000579441.2	-	1	231	c.232C>T	c.(232-234)Cga>Tga	p.R78*	SLC25A52_ENST00000269205.5_Nonsense_Mutation_p.R88*			Q3SY17	S2552_HUMAN	solute carrier family 25, member 52	78					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)											TACAAATTTCGAAATCCATCC	0.463																																					p.R88X		Atlas-SNP	.											.	.	.	.	0			c.C262T						PASS	.						120	107	112					18																	29340393		2203	4300	6503	SO:0001587	stop_gained	147407	exon1			AATTTCGAAATCC		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.232C>T	chr18.hg19:g.29340393G>A	ENSP00000462754:p.Arg78*	132.0	0.0	.		118.0	36.0	.	NM_001034172		Nonsense_Mutation	SNP	ENST00000579441.2	hg19		.	.	.	.	.	.	.	.	.	.	G	36	5.905485	0.97087	.	.	ENSG00000141437	ENST00000269205;ENST00000535708	.	.	.	1.03	1.03	0.20045	.	0.259609	0.30538	N	0.009404	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	.	7.9599	0.30066	0.0:0.0:1.0:0.0	.	.	.	.	X	88;78	.	ENSP00000372612:R88X	R	-	1	2	MCART2	27594391	0.991000	0.36638	0.295000	0.24960	0.834000	0.47266	0.956000	0.29202	0.877000	0.35895	0.505000	0.49811	CGA	.	.	.	none		0.463	SLC25A52-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_084000		A	29340393	G	A	29340393	4	1	244	1	0	0	0	0	0	1	0	0	9377	1066	37	1	665	1	MCART2	18	29340393	Nonsense_Mutation	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	9344732	29340393	48736855	93	15122											
CACNA1A	773	hgsc.bcm.edu	37	chr19	13372413	13372413	+	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	ttaagtgagttcaccacacaGtcaaacacagcctgtggggt	12	9	10	10	0	2	1	2	1	0	0	2	1	2	1	2	2	2	1	2	2	2	2			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr19:13372413G>A	ENST00000360228.5	-	26	4100	c.4101C>T	c.(4099-4101)gaC>gaT	p.D1367D	CACNA1A_ENST00000573710.2_Silent_p.D1368D	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	1368					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)	TCACCACACAGTCAAACACAG	0.522																																					p.D1368D		Atlas-SNP	.											.	CACNA1A	715	.	0			c.C4104T						PASS	.						48	46	47					19																	13372413		2040	4201	6241	SO:0001819	synonymous_variant	773	exon26			CACACAGTCAAAC	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.4101C>T	chr19.hg19:g.13372413G>A		51.0	0.0	.		68.0	27.0	.	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	hg19	CCDS45998.1																																																																																			.	.	.	none		0.522	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		A	13372413	G	A	13372413	2	1	244	1	0	0	0	0	0	0	0	1	2540	1020	36	2		2	CACNA1A	19	13372413	Silent	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10		13372413	45756570	94	15123											
ARHGAP33	115703	hgsc.bcm.edu	37	chr19	36279024	36279024	+	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	ctcacctgcctcttcctcctCctcttcccctcctgcccacc	2	12	2	25	0	3	0	1	0	2	0	8	0	8	0	10	0	2	0	10	0	0	2			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr19:36279024C>T	ENST00000007510.4	+	21	3701	c.3557C>T	c.(3556-3558)tCc>tTc	p.S1186F	ARHGAP33_ENST00000314737.5_Missense_Mutation_p.S1025F|AC002398.5_ENST00000433059.1_lincRNA|ARHGAP33_ENST00000378944.5_Missense_Mutation_p.S1022F			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	1186	Poly-Ser.				protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|Rac GTPase activator activity (GO:0030675)			endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						TCTTCCTCCTCCTCTTCCCCT	0.692																																					p.S1025F		Atlas-SNP	.											.	ARHGAP33	102	.	0			c.C3074T						PASS	.						30	34	33					19																	36279024		2193	4287	6480	SO:0001583	missense	115703	exon21			CCTCCTCCTCTTC	AY044864	CCDS12477.1, CCDS54254.1	19q13.13	2011-06-29	2010-02-19	2010-02-19		ENSG00000004777		"Rho GTPase activating proteins"	23085	protein-coding gene	gene with protein product		614902	"sorting nexin 26"	SNX26		12297274, 12461558	Standard	NM_052948		Approved	FLJ39019, TCGAP	uc002obs.2	O14559		ENST00000007510.4:c.3557C>T	chr19.hg19:g.36279024C>T	ENSP00000007510:p.Ser1186Phe	168.0	0.0	.		114.0	36.0	.	NM_052948	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	Missense_Mutation	SNP	ENST00000007510.4	hg19		.	.	.	.	.	.	.	.	.	.	c	15.16	2.750938	0.49257	.	.	ENSG00000004777	ENST00000007510;ENST00000314737;ENST00000378944	T;T;T	0.21543	2.63;2.0;2.33	4.68	3.55	0.40652	.	0.000000	0.44285	D	0.000469	T	0.22126	0.0533	N	0.19112	0.55	0.24977	N	0.991621	D;D	0.64830	0.994;0.994	P;P	0.56865	0.808;0.808	T	0.02345	-1.1173	10	0.66056	D	0.02	.	8.8936	0.35449	0.1653:0.6739:0.1608:0.0	.	1022;1025	O14559-10;O14559-11	.;.	F	1186;1025;1022	ENSP00000007510:S1186F;ENSP00000320038:S1025F;ENSP00000368227:S1022F	ENSP00000007510:S1186F	S	+	2	0	ARHGAP33	40970864	0.014000	0.17966	0.999000	0.59377	0.889000	0.51656	0.825000	0.27393	2.325000	0.78763	0.401000	0.26515	TCC	.	.	.	none		0.692	ARHGAP33-201	KNOWN	basic	protein_coding	protein_coding		NM_052948		T	36279024	C	T	36279024	3	4	244	1	0	0	0	0	1	0	0	0	882	855	30	2	3639	2	ARHGAP33	19	36279024	Missense_Mutation	SNP	C	TCGA-SX-A71V-01A-11D-A33Q-10	22906611	36279024	22849959	95	15124											
SARS2	54938	hgsc.bcm.edu	37	chr19	39409424	39409424	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaaacactgctccgcggagAaggtctggcaccgtcatggg	10	6	13	12	3	2	1	1	0	1	1	3	2	3	1	2	4	2	2	2	4	2	0			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr19:39409424A>G	ENST00000221431.6	-	8	948	c.789T>C	c.(787-789)ctT>ctC	p.L263L	CTC-360G5.8_ENST00000599996.1_Missense_Mutation_p.S333P|SARS2_ENST00000600042.1_Silent_p.L265L|SARS2_ENST00000430193.3_Silent_p.L263L|SARS2_ENST00000598831.1_5'Flank|SARS2_ENST00000448145.2_Silent_p.L263L|SARS2_ENST00000594171.1_Silent_p.L73L	NM_017827.3	NP_060297.1	Q9NP81	SYSM_HUMAN	seryl-tRNA synthetase 2, mitochondrial	263					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)			CTCCGCGGAGAAGGTCTGGCA	0.647																																					p.L265L		Atlas-SNP	.											.	SARS2	33	.	0			c.T795C						PASS	.						58	40	46					19																	39409424		2187	4267	6454	SO:0001819	synonymous_variant	54938	exon9			GCGGAGAAGGTCT	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.789T>C	chr19.hg19:g.39409424A>G		71.0	0.0	.		40.0	14.0	.	NM_001145901	A6NHW7|B4DE10|Q9BVP3	Silent	SNP	ENST00000221431.6	hg19	CCDS33017.1																																																																																			.	.	.	none		0.647	SARS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463139.1	NM_017827		G	39409424	A	G	39409424	2	3	244	1	0	0	0	0	0	0	0	1	13858	233	9	3		3	SARS2	19	39409424	Silent	SNP	A	TCGA-SX-A71V-01A-11D-A33Q-10	3130400	39409424	19719559	96	15125											
DKKL1	27120	hgsc.bcm.edu	37	chr19	49868766	49868766	+	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	agtccctcctccggccccagGgtaacctgcttcggggcata	6	8	11	16	2	0	0	0	0	0	0	4	0	3	0	6	4	2	3	6	4	2	3			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr19:49868766G>T	ENST00000221498.2	+	3	589	c.184G>T	c.(184-186)Ggt>Tgt	p.G62C	DKKL1_ENST00000594268.1_Intron	NM_014419.3	NP_055234.1	Q9UK85	DKKL1_HUMAN	dickkopf-like 1	62					anatomical structure morphogenesis (GO:0009653)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	signal transducer activity (GO:0004871)			large_intestine(2)|upper_aerodigestive_tract(1)	3		all_lung(116;1.66e-06)|Lung NSC(112;5.89e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0456)		CCGGCCCCAGGGTAACCTGCT	0.617																																					p.G62C		Atlas-SNP	.											.	DKKL1	23	.	0			c.G184T						PASS	.						45	44	44					19																	49868766		2203	4300	6503	SO:0001630	splice_region_variant	27120	exon3			CCCCAGGGTAACC	AB047816	CCDS12762.1	19q13.3	2010-10-12	2010-10-12		ENSG00000104901	ENSG00000104901			16528	protein-coding gene	gene with protein product	"cancer/testis antigen 34", "soggy"	605418	"dickkopf-like 1 (soggy)"			10570958	Standard	NM_001197301		Approved	SGY-1, CT34	uc002pnk.3	Q9UK85		ENST00000221498.2:c.184-1G>T	chr19.hg19:g.49868766G>T		55.0	0.0	.		35.0	11.0	.	NM_014419		Missense_Mutation	SNP	ENST00000221498.2	hg19	CCDS12762.1	.	.	.	.	.	.	.	.	.	.	G	13.83	2.353860	0.41700	.	.	ENSG00000104901	ENST00000221498	T	0.12255	2.7	4.72	3.68	0.42216	.	0.570475	0.14682	N	0.304666	T	0.07638	0.0192	N	0.08118	0	0.30619	N	0.758645	D	0.53619	0.961	B	0.43950	0.437	T	0.08743	-1.0707	9	.	.	.	-3.2024	8.3814	0.32474	0.1131:0.0:0.8869:0.0	.	62	Q9UK85	DKKL1_HUMAN	C	62	ENSP00000221498:G62C	.	G	+	1	0	DKKL1	54560578	1.000000	0.71417	1.000000	0.80357	0.319000	0.28217	2.193000	0.42658	1.091000	0.41335	0.462000	0.41574	GGT	.	.	.	none		0.617	DKKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465454.2	NM_014419	Missense_Mutation	T	49868766	G	T	49868766	5	4	244	1	0	0	0	0	0	0	1	0	4550	1246	43	4	194	4	DKKL1	19	49868766	Splice_Site	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	10459342	49868766	9260217	97	15126											
CASS4	57091	hgsc.bcm.edu	37	chr20	55026927	55026927	+	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	cttaagaagaggcggttacaGcacattaccaaatcctcaga	15	8	8	10	1	1	3	1	0	0	3	2	3	2	3	2	2	3	2	2	2	5	3			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr20:55026927G>T	ENST00000360314.3	+	6	920	c.695G>T	c.(694-696)aGc>aTc	p.S232I	CASS4_ENST00000371336.3_Missense_Mutation_p.S232I|CASS4_ENST00000434344.1_Intron	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	232					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						GGCGGTTACAGCACATTACCA	0.502																																					p.S232I		Atlas-SNP	.											.	CASS4	121	.	0			c.G695T						PASS	.						62	58	60					20																	55026927		2203	4300	6503	SO:0001583	missense	57091	exon5			GTTACAGCACATT	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.695G>T	chr20.hg19:g.55026927G>T	ENSP00000353462:p.Ser232Ile	184.0	0.0	.		195.0	47.0	.	NM_020356	E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Missense_Mutation	SNP	ENST00000360314.3	hg19	CCDS33492.1	.	.	.	.	.	.	.	.	.	.	G	13.35	2.210183	0.39003	.	.	ENSG00000087589	ENST00000360314;ENST00000371336	T;T	0.14022	2.54;2.54	5.23	-1.56	0.08532	.	0.840559	0.11112	N	0.598507	T	0.08802	0.0218	N	0.22421	0.69	0.22903	N	0.998584	B;B;B	0.26081	0.052;0.141;0.087	B;B;B	0.31547	0.033;0.132;0.046	T	0.38564	-0.9655	10	0.40728	T	0.16	-6.211	6.0264	0.19658	0.5951:0.125:0.2799:0.0	.	178;232;232	B4DII4;Q9NQ75-2;Q9NQ75	.;.;CASS4_HUMAN	I	232	ENSP00000353462:S232I;ENSP00000360387:S232I	ENSP00000353462:S232I	S	+	2	0	CASS4	54460334	0.006000	0.16342	0.001000	0.08648	0.046000	0.14306	0.119000	0.15626	-0.277000	0.09193	-0.253000	0.11424	AGC	.	.	.	none		0.502	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079789.2	NM_020356		T	55026927	G	T	55026927	3	4	244	1	0	0	0	0	1	0	0	0	2685	971	34	4	713	4	CASS4	20	55026927	Missense_Mutation	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10		55026927	7998593	98	15127											
LSM14B	149986	hgsc.bcm.edu	37	chr20	60704972	60704972	+	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	ccacagggacgcagctcaacGgtcgtcaggcccagccgagc	9	3	13	16	4	2	0	2	0	0	0	3	2	2	1	3	3	4	2	3	3	1	0	rs139247673	byFrequency	TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr20:60704972G>C	ENST00000279068.6	+	4	719	c.559G>C	c.(559-561)Ggt>Cgt	p.G187R	LSM14B_ENST00000253001.4_Intron	NM_144703.2	NP_653304.2	Q9BX40	LS14B_HUMAN	LSM14B, SCD6 homolog B (S. cerevisiae)	187					multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)	ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|lung(4)	8	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.28e-07)			GCAGCTCAACGGTCGTCAGGC	0.552																																					p.G187R		Atlas-SNP	.											.	LSM14B	62	.	0			c.G559C						PASS	.						32	35	34					20																	60704972		2076	4203	6279	SO:0001583	missense	149986	exon4			CTCAACGGTCGTC	AF172328	CCDS46626.1	20q13.33	2010-01-27	2006-12-21	2006-01-24	ENSG00000149657	ENSG00000149657			15887	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 40", "family with sequence similarity 61, member B", "LSM14 homolog B (SCD6, S. cerevisiae)"	C20orf40, FAM61B			Standard	NM_144703		Approved	FT005, bA11M20.3, FLJ25473, LSM13, RAP55B	uc010gjy.1	Q9BX40	OTTHUMG00000032901	ENST00000279068.6:c.559G>C	chr20.hg19:g.60704972G>C	ENSP00000279068:p.Gly187Arg	115.0	0.0	.		139.0	32.0	.	NM_144703	Q6PFW8|Q96LH8	Missense_Mutation	SNP	ENST00000279068.6	hg19	CCDS46626.1	.	.	.	.	.	.	.	.	.	.	G	10.62	1.400557	0.25291	.	.	ENSG00000149657	ENST00000279068;ENST00000444156;ENST00000400318;ENST00000279069;ENST00000370906;ENST00000361670	T;T;T	0.47528	0.86;0.84;0.85	5.59	2.61	0.31194	.	.	.	.	.	T	0.60560	0.2278	M	0.67953	2.075	0.23966	N	0.996323	P;D;P;P	0.89917	0.955;1.0;0.955;0.954	P;D;B;P	0.97110	0.513;1.0;0.416;0.62	T	0.51818	-0.8657	9	0.13470	T	0.59	.	9.7243	0.40322	0.271:0.0:0.729:0.0	.	107;143;187;213	E9PG81;C9J454;Q9BX40;Q5TBQ0	.;.;LS14B_HUMAN;.	R	187;143;213;187;143;107	ENSP00000279068:G187R;ENSP00000383172:G213R;ENSP00000355209:G107R	ENSP00000279068:G187R	G	+	1	0	LSM14B	60138367	0.931000	0.31567	0.462000	0.27118	0.111000	0.19643	2.157000	0.42320	0.321000	0.23259	0.555000	0.69702	GGT	.	G|0.990;A|0.010	.	alt		0.552	LSM14B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079996.4	NM_144703		C	60704972	G	C	60704972	3	2	244	1	0	0	0	0	1	0	0	0	9062	1116	39	4	573	4	LSM14B	20	60704972	Missense_Mutation	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10	5678045	60704972	2320548	99	15128											
COL6A2	1292	hgsc.bcm.edu	37	chr21	47544599	47544599	+	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	ccctggtgagccaggccctcGggggccaagaggagtcccag	7	4	16	14	1	0	2	0	1	0	1	2	3	1	3	5	5	1	0	5	5	1	0	rs147158850	byFrequency	TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr21:47544599G>T	ENST00000300527.4	+	22	1810	c.1706G>T	c.(1705-1707)cGg>cTg	p.R569L	COL6A2_ENST00000310645.5_Missense_Mutation_p.R569L|COL6A2_ENST00000357838.4_Missense_Mutation_p.R569L|COL6A2_ENST00000397763.1_Missense_Mutation_p.R569L|COL6A2_ENST00000409416.1_Missense_Mutation_p.R569L	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	569	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)		CCAGGCCCTCGGGGGCCAAGA	0.667																																					p.R569L		Atlas-SNP	.											.	COL6A2	351	.	0			c.G1706T						PASS	.						44	52	49					21																	47544599		2201	4300	6501	SO:0001583	missense	1292	exon22			GCCCTCGGGGGCC	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.1706G>T	chr21.hg19:g.47544599G>T	ENSP00000300527:p.Arg569Leu	110.0	0.0	.		72.0	28.0	.	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Missense_Mutation	SNP	ENST00000300527.4	hg19	CCDS13728.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.814804	0.90790	.	.	ENSG00000142173	ENST00000300527;ENST00000357838;ENST00000310645;ENST00000409416;ENST00000397763;ENST00000413758	D;D;D;D;D;D	0.94576	-3.46;-3.46;-3.46;-3.46;-3.46;-3.21	4.08	4.08	0.47627	.	0.110157	0.64402	D	0.000015	D	0.96473	0.8849	M	0.64567	1.98	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.997	D	0.96914	0.9669	10	0.59425	D	0.04	-5.6344	16.3469	0.83138	0.0:0.0:1.0:0.0	.	569;569;569	P12110;P12110-2;P12110-3	CO6A2_HUMAN;.;.	L	569;569;569;569;569;110	ENSP00000300527:R569L;ENSP00000350497:R569L;ENSP00000312529:R569L;ENSP00000387115:R569L;ENSP00000380870:R569L;ENSP00000395751:R110L	ENSP00000300527:R569L	R	+	2	0	COL6A2	46369027	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	6.434000	0.73408	1.852000	0.53769	0.585000	0.79938	CGG	.	G|0.999;A|0.001	.	alt		0.667	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1			T	47544599	G	T	47544599	3	4	244	1	0	0	0	0	1	0	0	0	3702	1116	39	4	1788	4	COL6A2	21	47544599	Missense_Mutation	SNP	G	TCGA-SX-A71V-01A-11D-A33Q-10		47544599	585296	100	15129											
NEFH	4744	hgsc.bcm.edu	37	chr22	29885584	29885585	+	In_Frame_Ins	INS	-	-	CAAGTCCCCTGAGAAGGC																															gcaaagtcccctgagaaggcINScaagtccccagagaaggaag																								rs200984527|rs267607533		TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr22:29885584_29885585insCAAGTCCCCTGAGAAGGC	ENST00000310624.6	+	4	1988_1989	c.1955_1956insCAAGTCCCCTGAGAAGGC	c.(1954-1959)gccaag>gcCAAGTCCCCTGAGAAGGCcaag	p.652_653AK>AKSPEKAK		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	658	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.			Missing (in Ref. 1; CAA33366 and 5; AC000035). {ECO:0000305}.	axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						CCTGAGAAGGCCAAGTCCCCAG	0.559																																					p.A652delinsAKSPEKA		Atlas-INDEL	.											.,1	NEFH	178	.	0			c.1955_1956insCAAGTCCCCTGAGAAGGC						PASS	.																																			SO:0001652	inframe_insertion	4744	exon4			.		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	Exception_encountered	chr22.hg19:g.29885584_29885585insCAAGTCCCCTGAGAAGGC	ENSP00000311997:p.Lys647_Ala652dup	138.0	0.0	0		158.0	39.0	0.246835	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.	.	none		0.559	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		CAAGTCCCCTGAGAAGGC	29885585	-	CAAGTCCCCTGAGAAGGC	29885584	7	5	244	1	0	1	1	0	0	0	0	0	10321	739	26	0	1969	0	NEFH	22	29885584	In_Frame_Ins	INS	-	TCGA-SX-A71V-01A-11D-A33Q-10		29885584	21418982	101	15130											
SHANK3	85358	hgsc.bcm.edu	37	chr22	51160753	51160753	+	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	caactgtgatcagtgagctcAgctcccgcctgcagcagctg	8	8	11	14	1	2	2	2	2	0	0	3	2	3	2	2	0	6	5	2	0	1	0			TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chr22:51160753A>T	ENST00000414786.2	+	21	4677	c.4450A>T	c.(4450-4452)Agc>Tgc	p.S1484C	SHANK3_ENST00000262795.3_Missense_Mutation_p.S1514C|SHANK3_ENST00000445220.2_Missense_Mutation_p.S1500C			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	1498					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)		CAGTGAGCTCAGCTCCCGCCT	0.632																																					p.S1484C		Atlas-SNP	.											.	SHANK3	96	.	0			c.A4450T						PASS	.						25	29	28					22																	51160753		1937	4003	5940	SO:0001583	missense	85358	exon21			GAGCTCAGCTCCC	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.4450A>T	chr22.hg19:g.51160753A>T	ENSP00000464552:p.Ser1484Cys	182.0	0.0	.		148.0	53.0	.	NM_033517	D7UT47|Q8TET3	Missense_Mutation	SNP	ENST00000414786.2	hg19		.	.	.	.	.	.	.	.	.	.	A	17.99	3.522943	0.64747	.	.	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.54479	0.57;0.69	5.43	4.4	0.53042	.	0.045054	0.85682	D	0.000000	T	0.66626	0.2808	M	0.68952	2.095	0.29241	N	0.872645	D;D;D	0.89917	0.996;0.999;1.0	P;D;D	0.77557	0.819;0.99;0.956	T	0.63708	-0.6576	10	0.72032	D	0.01	.	8.8082	0.34952	0.9114:0.0:0.0886:0.0	.	1498;1499;1514	D7UT47;Q9BYB0;F2Z3L0	.;SHAN3_HUMAN;.	C	1514;1500	ENSP00000442518:S1514C;ENSP00000446078:S1500C	ENSP00000442518:S1514C	S	+	1	0	SHANK3	49507619	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.406000	0.73276	2.064000	0.61679	0.460000	0.39030	AGC	.	.	.	none		0.632	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420		T	51160753	A	T	51160753	3	4	244	1	0	0	0	0	1	0	0	0	14279	188	7	5	4626	5	SHANK3	22	51160753	Missense_Mutation	SNP	A	TCGA-SX-A71V-01A-11D-A33Q-10	21275169	51160753	143813	102	15131											
MAGEC1	9947	hgsc.bcm.edu	37	chrX	140993981	140994085	+	In_Frame_Del	DEL	CCCAGTCTTCTCTCCAGATTCCTGTGAGCCCCTCCTTCTCCTCCACTTTAGTGAGTCTTTTCCAGAGTTCCCCTGAGAGAACTCAGAGTACTTTTGAGGGTTTTC	CCCAGTCTTCTCTCCAGATTCCTGTGAGCCCCTCCTTCTCCTCCACTTTAGTGAGTCTTTTCCAGAGTTCCCCTGAGAGAACTCAGAGTACTTTTGAGGGTTTTC	-																															gagtacttttgagggttttgCccagtcttctctccagattc																								rs144495362|rs77648555|rs146798989|rs143600642|rs138695129|rs150017439|rs176043|rs176045|rs176044|rs146036055|rs386828015|rs112112998|rs80051600|rs78189215|rs150327147|rs75148863|rs176046|rs140075882|rs200821167|rs149195933|rs141817885	byFrequency	TCGA-SX-A71V-01A-11D-A33Q-10	TCGA-SX-A71V-10A-01D-A33Q-10	CCCAGTCTTCTCTCCAGATTCCTGTGAGCCCCTCCTTCTCCTCCACTTTAGTGAGTCTTTTCCAGAGTTCCCCTGAGAGAACTCAGAGTACTTTTGAGGGTTTTC	CCCAGTCTTCTCTCCAGATTCCTGTGAGCCCCTCCTTCTCCTCCACTTTAGTGAGTCTTTTCCAGAGTTCCCCTGAGAGAACTCAGAGTACTTTTGAGGGTTTTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7879708e-a807-4002-9d4d-efc84d51a4e5	af4acae0-89a6-4004-ad5b-149db143f98b	g.chrX:140993981_140994085delCCCAGTCTTCTCTCCAGATTCCTGTGAGCCCCTCCTTCTCCTCCACTTTAGTGAGTCTTTTCCAGAGTTCCCCTGAGAGAACTCAGAGTACTTTTGAGGGTTTTC	ENST00000285879.4	+	4	1077_1181	c.791_895delCCCAGTCTTCTCTCCAGATTCCTGTGAGCCCCTCCTTCTCCTCCACTTTAGTGAGTCTTTTCCAGAGTTCCCCTGAGAGAACTCAGAGTACTTTTGAGGGTTTTC	c.(790-897)gcccagtcttctctccagattcctgtgagcccctccttctcctccactttagtgagtcttttccagagttcccctgagagaactcagagtacttttgagggttttccc>gcc	p.QSSLQIPVSPSFSSTLVSLFQSSPERTQSTFEGFP265del	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	265								p.Q265K(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)					GAGGGTTTTGCCCAGTCTTCTCTCCAGATTCCTGTGAGCCCCTCCTTCTCCTCCACTTTAGTGAGTCTTTTCCAGAGTTCCCCTGAGAGAACTCAGAGTACTTTTGAGGGTTTTCCCCAGTCTCC	0.495										HNSCC(15;0.026)																											p.264_298del		Pindel	.											.	MAGEC1	317	.	1	Substitution - Missense(1)	lung(1)	c.790_894del						PASS	.																																			SO:0001651	inframe_deletion	9947	exon4			.	AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"cancer/testis antigen family 7, member 1"	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.791_895delCCCAGTCTTCTCTCCAGATTCCTGTGAGCCCCTCCTTCTCCTCCACTTTAGTGAGTCTTTTCCAGAGTTCCCCTGAGAGAACTCAGAGTACTTTTGAGGGTTTTC	chrX.hg19:g.140993981_140994085delCCCAGTCTTCTCTCCAGATTCCTGTGAGCCCCTCCTTCTCCTCCACTTTAGTGAGTCTTTTCCAGAGTTCCCCTGAGAGAACTCAGAGTACTTTTGAGGGTTTTC	ENSP00000285879:p.Gln265_Pro299del	273.0	0.0	.		251.0	19.0	0.076	NM_005462	A0PK03|O75451|Q8TCV4	In_Frame_Del	DEL	ENST00000285879.4	hg19	CCDS35417.1																																																																																			.	.	.	none		0.495	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462		-	140994085	CCCAGTCTTCTCTCCAGATTCCTGTGAGCCCCTCCTTCTCCTCCACTTTAGTGAGTCTTTTCCAGAGTTCCCCTGAGAGAACTCAGAGTACTTTTGAGGGTTTTC	-	140993981	7	5	244	1	0	1	0	1	0	0	0	0	9187	739	26	0	797	0	MAGEC1	23	140993981	In_Frame_Del	DEL	CCCAGTCTTCTCTCCAGATTCCTGTGAGCCCCTCCTTCTCCTCCACTTTAGTGAGTCTTTTCCAGAGTTCCCCTGAGAGAACTCAGAGTACTTTTGAGGGTTTTC	TCGA-SX-A71V-01A-11D-A33Q-10		140993981	14276579	103	15132											
LRPPRC	10128	hgsc.bcm.edu	37	chr2	44139609	44139609	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttgtgtaaaataatcttcTgacatcagtaatttaatgag	14	15	7	5	0	3	2	1	2	2	0	3	2	3	2	0	0	0	3	0	0	5	7			TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr2:44139609T>C	ENST00000260665.7	-	30	3294	c.3237A>G	c.(3235-3237)tcA>tcG	p.S1079S		NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	1079					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)				AATAATCTTCTGACATCAGTA	0.328																																					p.S1079S		Atlas-SNP	.											.	LRPPRC	105	.	0			c.A3237G						PASS	.						117	113	114					2																	44139609		2202	4297	6499	SO:0001819	synonymous_variant	10128	exon30			ATCTTCTGACATC	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.3237A>G	chr2.hg19:g.44139609T>C		363.0	0.0	.		210.0	80.0	.	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Silent	SNP	ENST00000260665.7	hg19	CCDS33189.1																																																																																			.	.	.	none		0.328	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259		C	44139609	T	C	44139609	2	2	245	1	0	0	0	0	0	0	0	1	8972	1567	55	3		3	LRPPRC	2	44139609	Silent	SNP	T	TCGA-SX-A71W-01A-12D-A34Z-10		44139609	199059764	1	15133											
SMEK2	57223	hgsc.bcm.edu	37	chr2	55805411	55805411	+	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	atggaggaagagggggtagaAtgggaatgggaatgtgaagg	14	6	21	0	0	0	3	0	1	0	2	0	7	0	7	0	7	0	1	0	7	6	1			TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr2:55805411A>T	ENST00000345102.5	-	10	1837	c.1536T>A	c.(1534-1536)caT>caA	p.H512Q	SMEK2_ENST00000272313.5_Intron|SMEK2_ENST00000407823.3_Intron	NM_001122964.1	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	512					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)			agggggtagaatgggaatggg	0.323																																					p.H512Q		Atlas-SNP	.											.	SMEK2	86	.	0			c.T1536A						PASS	.						111	113	112					2																	55805411		692	1591	2283	SO:0001583	missense	57223	exon10			GGTAGAATGGGAA	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.1536T>A	chr2.hg19:g.55805411A>T	ENSP00000339769:p.His512Gln	189.0	0.0	.		119.0	55.0	.	NM_001122964	Q6P9B0|Q86XB8|Q9BQJ0|Q9BRK2|Q9H913|Q9P2G0	Missense_Mutation	SNP	ENST00000345102.5	hg19	CCDS46289.1	.	.	.	.	.	.	.	.	.	.	A	3.267	-0.149862	0.06585	.	.	ENSG00000138041	ENST00000345102	T	0.40225	1.04	1.84	0.645	0.17782	Armadillo-type fold (1);	1.447810	0.05139	U	0.493933	T	0.20577	0.0495	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18085	-1.0348	10	0.18710	T	0.47	.	3.6958	0.08364	0.7972:0.0:0.2028:0.0	.	512	Q5MIZ7	P4R3B_HUMAN	Q	512	ENSP00000339769:H512Q	ENSP00000339769:H512Q	H	-	3	2	SMEK2	55658915	0.000000	0.05858	0.001000	0.08648	0.024000	0.10985	0.114000	0.15520	0.187000	0.20147	0.383000	0.25322	CAT	.	.	.	none		0.323	SMEK2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251483.1	NM_020463		T	55805411	A	T	55805411	3	4	245	1	0	0	0	0	1	0	0	0	14807	98	4	5	1045	5	SMEK2	2	55805411	Missense_Mutation	SNP	A	TCGA-SX-A71W-01A-12D-A34Z-10	11665802	55805411	187393962	2	15134											
DPP10	57628	hgsc.bcm.edu	37	chr2	116497451	116497451	+	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	gcgttgtatcccaaaggaaaGcagtatccgtatcctaaggt	12	10	10	9	2	0	0	0	0	0	0	3	1	3	1	3	2	1	5	3	2	6	5	rs541980291		TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr2:116497451G>A	ENST00000410059.1	+	9	1314	c.834G>A	c.(832-834)aaG>aaA	p.K278K	DPP10_ENST00000310323.8_Silent_p.K271K|DPP10_ENST00000409163.1_Silent_p.K228K|DPP10_ENST00000393147.2_Silent_p.K282K	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	278						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						CCAAAGGAAAGCAGTATCCGT	0.433													G|||	1	0.000199681	0	0	5008	,	,		20710	0		0	False		,,,				2504	0.001				p.K282K		Atlas-SNP	.											.	DPP10	415	.	0			c.G846A						PASS	.						222	197	205					2																	116497451		2203	4300	6503	SO:0001819	synonymous_variant	57628	exon9			AGGAAAGCAGTAT	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.834G>A	chr2.hg19:g.116497451G>A		175.0	0.0	.		87.0	7.0	.	NM_001178034	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Silent	SNP	ENST00000410059.1	hg19	CCDS46400.1																																																																																			.	.	.	none		0.433	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		A	116497451	G	A	116497451	2	1	245	1	0	0	0	0	0	0	0	1	4729	962	34	2		2	DPP10	2	116497451	Silent	SNP	G	TCGA-SX-A71W-01A-12D-A34Z-10	60692040	116497451	126701922	3	15135											
GPR148	344561	hgsc.bcm.edu	37	chr2	131487490	131487490	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caggcatctgggggcagggcTattcccgggccaggggcacc	6	5	17	13	1	1	0	0	0	1	0	2	0	2	0	3	7	0	4	3	7	1	2			TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr2:131487490T>C	ENST00000309926.4	+	1	848	c.766T>C	c.(766-768)Tat>Cat	p.Y256H		NM_207364.2	NP_997247.2	Q8TDV2	GP148_HUMAN	G protein-coupled receptor 148	256						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)					GGGGCAGGGCTATTCCCGGGC	0.567																																					p.Y256H		Atlas-SNP	.											.	GPR148	54	.	0			c.T766C						PASS	.						122	116	118					2																	131487490		2203	4300	6503	SO:0001583	missense	344561	exon1			CAGGGCTATTCCC	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.766T>C	chr2.hg19:g.131487490T>C	ENSP00000308908:p.Tyr256His	66.0	0.0	.		39.0	17.0	.	NM_207364	Q2M369|Q86SP7|Q86U87	Missense_Mutation	SNP	ENST00000309926.4	hg19	CCDS2163.1	.	.	.	.	.	.	.	.	.	.	.	14.59	2.581074	0.46006	.	.	ENSG00000173302	ENST00000309926	T	0.36340	1.26	2.87	2.87	0.33458	GPCR, rhodopsin-like superfamily (1);	0.119947	0.34932	U	0.003580	T	0.31734	0.0806	N	0.19112	0.55	0.27290	N	0.957872	D	0.55385	0.971	P	0.55161	0.77	T	0.08330	-1.0727	10	0.23302	T	0.38	-0.0036	9.4681	0.38824	0.0:0.0:0.0:1.0	.	256	Q8TDV2	GP148_HUMAN	H	256	ENSP00000308908:Y256H	ENSP00000308908:Y256H	Y	+	1	0	GPR148	131203960	0.837000	0.29446	0.200000	0.23457	0.707000	0.40811	3.721000	0.54941	1.276000	0.44395	0.379000	0.24179	TAT	.	.	.	none		0.567	GPR148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254552.3	XM_293092		C	131487490	T	C	131487490	3	2	245	1	0	0	0	0	1	0	0	0	6660	1522	53	3	768	3	GPR148	2	131487490	Missense_Mutation	SNP	T	TCGA-SX-A71W-01A-12D-A34Z-10	14990039	131487490	111711883	4	15136											
SGOL2	151246	hgsc.bcm.edu	37	chr2	201436485	201436485	+	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	caggtgaatgaactaaagaaAatgacccttcaaactggctt	16	9	8	8	0	1	4	1	3	0	1	1	4	1	4	1	2	2	1	1	2	7	3			TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr2:201436485A>T	ENST00000357799.4	+	7	1514	c.1416A>T	c.(1414-1416)aaA>aaT	p.K472N		NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	472					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)				NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						AACTAAAGAAAATGACCCTTC	0.388																																					p.K472N		Atlas-SNP	.											.	SGOL2	126	.	0			c.A1416T						PASS	.						151	151	151					2																	201436485		1827	4081	5908	SO:0001583	missense	151246	exon7			AAAGAAAATGACC	AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.1416A>T	chr2.hg19:g.201436485A>T	ENSP00000350447:p.Lys472Asn	130.0	0.0	.		87.0	46.0	.	NM_001160046	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Missense_Mutation	SNP	ENST00000357799.4	hg19	CCDS42796.1	.	.	.	.	.	.	.	.	.	.	A	11.53	1.667269	0.29604	.	.	ENSG00000163535	ENST00000357799	T	0.49720	0.77	5.15	3.92	0.45320	.	0.504521	0.19999	N	0.101377	T	0.40886	0.1135	L	0.50333	1.59	0.23371	N	0.997817	P;P;P	0.40431	0.717;0.717;0.717	B;B;B	0.37198	0.243;0.243;0.243	T	0.45818	-0.9235	10	0.72032	D	0.01	-6.3242	11.4245	0.50003	0.8502:0.1498:0.0:0.0	.	472;472;472	B7Z7S9;Q562F6-2;Q562F6	.;.;SGOL2_HUMAN	N	472	ENSP00000350447:K472N	ENSP00000350447:K472N	K	+	3	2	SGOL2	201144730	0.018000	0.18449	0.053000	0.19242	0.163000	0.22366	0.469000	0.22067	2.285000	0.76669	0.477000	0.44152	AAA	.	.	.	none		0.388	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524		T	201436485	A	T	201436485	3	4	245	1	0	0	0	0	1	0	0	0	14230	11	1	5	1438	5	SGOL2	2	201436485	Missense_Mutation	SNP	A	TCGA-SX-A71W-01A-12D-A34Z-10	69948995	201436485	41762888	5	15137											
UGT1A4	54657	hgsc.bcm.edu	37	chr2	234627924	234627924	+	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	tgatgtggttttaacagaccCcgttaacctctgtggggcgg	7	12	13	9	2	1	2	0	1	1	1	1	2	1	2	3	4	2	2	3	4	2	3			TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr2:234627924C>G	ENST00000373409.3	+	1	501	c.458C>G	c.(457-459)cCc>cGc	p.P153R	UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A10_ENST00000344644.5_Intron	NM_007120.2	NP_009051.1	P22310	UD14_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A4	153					cellular glucuronidation (GO:0052695)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|skin(2)|urinary_tract(1)	26		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;3.49e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000504)|Lung(119;0.0026)|LUSC - Lung squamous cell carcinoma(224;0.00624)	Asenapine(DB06216)|Clozapine(DB00363)|Ezogabine(DB04953)|Lamotrigine(DB00555)|Midazolam(DB00683)|Paricalcitol(DB00910)|Tamoxifen(DB00675)|Trifluoperazine(DB00831)|Valproic Acid(DB00313)	TTAACAGACCCCGTTAACCTC	0.483																																					p.P153R	Melanoma(99;1011 1962 13201 26492)	Atlas-SNP	.											.	UGT1A4	63	.	0			c.C458G						PASS	.						186	187	186					2																	234627924		2203	4300	6503	SO:0001583	missense	54657	exon1			CAGACCCCGTTAA	M84128	CCDS33405.1	2q37.1	2014-01-10	2005-07-20		ENSG00000244474	ENSG00000244474		"UDP glucuronosyltransferases"	12536	other	complex locus constituent		606429	"UDP glycosyltransferase 1 family, polypeptide A4"			9295054, 1339448	Standard	NM_007120		Approved	HUG-BR2, UGT1D	uc002vux.3	P22310	OTTHUMG00000059119	ENST00000373409.3:c.458C>G	chr2.hg19:g.234627924C>G	ENSP00000362508:p.Pro153Arg	303.0	0.0	.		174.0	57.0	.	NM_007120	B2R937|B8K288|Q5DT00	Missense_Mutation	SNP	ENST00000373409.3	hg19	CCDS33405.1	.	.	.	.	.	.	.	.	.	.	C	17.51	3.408615	0.62399	.	.	ENSG00000244474	ENST00000373409	T	0.64085	-0.08	4.31	3.41	0.39046	.	.	.	.	.	D	0.82323	0.5012	M	0.92026	3.265	0.39588	D	0.96953	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.86763	0.1968	9	0.87932	D	0	.	14.1475	0.65360	0.0:0.8489:0.1511:0.0	.	153;153	B8K288;P22310	.;UD14_HUMAN	R	153	ENSP00000362508:P153R	ENSP00000362508:P153R	P	+	2	0	UGT1A4	234292663	0.664000	0.27457	0.002000	0.10522	0.002000	0.02628	3.930000	0.56522	0.764000	0.33197	0.491000	0.48974	CCC	.	.	.	none		0.483	UGT1A4-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130984.1	NM_007120		G	234627924	C	G	234627924	3	3	245	1	0	0	0	0	1	0	0	0	16959	623	22	4	460	4	UGT1A4	2	234627924	Missense_Mutation	SNP	C	TCGA-SX-A71W-01A-12D-A34Z-10	33191439	234627924	8571449	6	15138											
SH3BP5	9467	hgsc.bcm.edu	37	chr3	15298489	15298489	+	Missense_Mutation	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	caggctgccaggcctcacaaCcgcagggaactggtcaggca	10	4	13	14	1	2	0	2	0	0	0	2	1	2	1	3	5	3	3	3	5	2	0			TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr3:15298489C>T	ENST00000383791.3	-	8	1241	c.1021G>A	c.(1021-1023)Gtt>Att	p.V341I	SH3BP5-AS1_ENST00000413977.1_RNA|SH3BP5-AS1_ENST00000420195.1_RNA|SH3BP5-AS1_ENST00000436602.1_RNA|SH3BP5_ENST00000253688.5_Missense_Mutation_p.V184I|SH3BP5_ENST00000426925.1_Missense_Mutation_p.V184I|SH3BP5_ENST00000408919.3_Missense_Mutation_p.V184I	NM_004844.4	NP_004835.2	O60239	3BP5_HUMAN	SH3-domain binding protein 5 (BTK-associated)	341	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						GGCCTCACAACCGCAGGGAAC	0.572																																					p.V341I		Atlas-SNP	.											.	SH3BP5	32	.	0			c.G1021A						PASS	.						79	68	71					3																	15298489		2203	4300	6503	SO:0001583	missense	9467	exon8			TCACAACCGCAGG	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.1021G>A	chr3.hg19:g.15298489C>T	ENSP00000373301:p.Val341Ile	92.0	0.0	.		63.0	20.0	.	NM_004844	B3KQW6|Q5JWV9	Missense_Mutation	SNP	ENST00000383791.3	hg19	CCDS2625.2	.	.	.	.	.	.	.	.	.	.	C	11.98	1.800873	0.31869	.	.	ENSG00000131370	ENST00000383791;ENST00000426925;ENST00000253688;ENST00000408919	.	.	.	5.43	4.56	0.56223	.	0.475884	0.23055	N	0.052451	T	0.41073	0.1143	L	0.40543	1.245	0.26692	N	0.971326	B	0.12630	0.006	B	0.11329	0.006	T	0.38650	-0.9651	9	0.56958	D	0.05	-13.6705	13.829	0.63368	0.0:0.9254:0.0:0.0746	.	341	O60239	3BP5_HUMAN	I	341;184;184;184	.	ENSP00000253688:V184I	V	-	1	0	SH3BP5	15273493	0.048000	0.20356	0.036000	0.18154	0.411000	0.31082	3.448000	0.52943	1.314000	0.45095	0.456000	0.33151	GTT	.	.	.	none		0.572	SH3BP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340740.2	NM_004844		T	15298489	C	T	15298489	3	4	245	1	0	0	0	0	1	0	0	0	14260	507	18	2	354	2	SH3BP5	3	15298489	Missense_Mutation	SNP	C	TCGA-SX-A71W-01A-12D-A34Z-10		15298489	182723941	7	15139											
KIAA0232	9778	hgsc.bcm.edu	37	chr4	6865878	6865878	+	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	gtcagtttcctgcttatgaaGataatccagtttcttcggga	9	15	9	8	1	2	2	1	1	1	1	5	3	4	3	2	1	1	3	2	1	3	5			TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr4:6865878G>T	ENST00000307659.5	+	7	4224	c.3769G>T	c.(3769-3771)Gat>Tat	p.D1257Y	KIAA0232_ENST00000425103.1_Missense_Mutation_p.D1257Y	NM_014743.2	NP_055558.2	Q92628	K0232_HUMAN	KIAA0232	1257							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						TGCTTATGAAGATAATCCAGT	0.393																																					p.D1257Y		Atlas-SNP	.											.	KIAA0232	102	.	0			c.G3769T						PASS	.						84	76	78					4																	6865878		1863	4110	5973	SO:0001583	missense	9778	exon7			TATGAAGATAATC	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.3769G>T	chr4.hg19:g.6865878G>T	ENSP00000303928:p.Asp1257Tyr	141.0	0.0	.		91.0	34.0	.	NM_014743	A7E2D2	Missense_Mutation	SNP	ENST00000307659.5	hg19	CCDS43209.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.289279	0.80914	.	.	ENSG00000170871	ENST00000425103;ENST00000307659	.	.	.	5.43	5.43	0.79202	.	0.200580	0.43919	D	0.000507	T	0.63438	0.2511	N	0.24115	0.695	0.52501	D	0.999958	D	0.63046	0.992	P	0.60473	0.875	T	0.67628	-0.5622	9	0.87932	D	0	-33.6837	19.1974	0.93695	0.0:0.0:1.0:0.0	.	1257	Q92628	K0232_HUMAN	Y	1257	.	ENSP00000303928:D1257Y	D	+	1	0	KIAA0232	6916779	1.000000	0.71417	0.994000	0.49952	0.977000	0.68977	4.717000	0.61923	2.708000	0.92522	0.655000	0.94253	GAT	.	.	.	none		0.393	KIAA0232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359102.2	NM_014743		T	6865878	G	T	6865878	3	4	245	1	0	0	0	0	1	0	0	0	8170	942	33	4	3787	4	KIAA0232	4	6865878	Missense_Mutation	SNP	G	TCGA-SX-A71W-01A-12D-A34Z-10		6865878	184288398	8	15140											
ALB	213	hgsc.bcm.edu	37	chr4	74277773	74277773	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttgcagaagtttccaagttAgtgacagatcttaccaaagt	13	13	8	7	0	1	3	0	1	1	2	2	3	2	3	2	0	2	3	2	0	5	4			TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr4:74277773A>G	ENST00000503124.1	+	5	531	c.324A>G	c.(322-324)ttA>ttG	p.L108L	ALB_ENST00000295897.4_Silent_p.L258L|ALB_ENST00000415165.2_Silent_p.L66L|ALB_ENST00000401494.3_Silent_p.L143L|ALB_ENST00000509063.1_Silent_p.L258L|ALB_ENST00000505649.1_3'UTR			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TTTCCAAGTTAGTGACAGATC	0.448																																					p.L258L		Atlas-SNP	.											.	ALB	132	.	0			c.A774G						PASS	.						163	154	157					4																	74277773		2203	4300	6503	SO:0001819	synonymous_variant	213	exon7			CAAGTTAGTGACA	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.324A>G	chr4.hg19:g.74277773A>G		131.0	0.0	.		78.0	29.0	.	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000503124.1	hg19		.	.	.	.	.	.	.	.	.	.	A	5.075	0.199470	0.09652	.	.	ENSG00000163631	ENST00000511370	.	.	.	6.02	-2.56	0.06268	.	.	.	.	.	T	0.18635	0.0447	.	.	.	0.23320	N	0.997914	.	.	.	.	.	.	T	0.26292	-1.0107	4	.	.	.	-0.2498	1.6874	0.02845	0.2818:0.1219:0.3593:0.237	.	.	.	.	G	103	.	.	S	+	1	0	ALB	74496637	0.041000	0.20044	0.019000	0.16419	0.625000	0.37756	-0.401000	0.07232	-0.286000	0.09076	0.533000	0.62120	AGT	.	.	.	none		0.448	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		G	74277773	A	G	74277773	2	3	245	1	0	0	0	0	0	0	0	1	486	417	15	3		3	ALB	4	74277773	Silent	SNP	A	TCGA-SX-A71W-01A-12D-A34Z-10	67411895	74277773	116876503	9	15141											
ITGA1	3672	hgsc.bcm.edu	37	chr5	52235508	52235508	+	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	atcaactgaccatctcaaacGaggcacaattctggtaaatt	15	10	6	10	1	3	1	2	1	2	0	4	2	3	1	1	2	2	2	1	2	5	3			TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr5:52235508G>A	ENST00000282588.6	+	25	3625	c.3167G>A	c.(3166-3168)cGa>cAa	p.R1056Q	CTD-2175A23.1_ENST00000505701.1_RNA|CTD-2175A23.1_ENST00000503559.1_RNA	NM_181501.1	NP_852478.1	P56199	ITA1_HUMAN	integrin, alpha 1	1056					activation of MAPK activity (GO:0000187)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular extravasation (GO:0045123)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neutrophil chemotaxis (GO:0030593)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|vasodilation (GO:0042311)	acrosomal vesicle (GO:0001669)|basal part of cell (GO:0045178)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha1-beta1 complex (GO:0034665)|integrin complex (GO:0008305)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|protein phosphatase binding (GO:0019903)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(19)|ovary(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				CATCTCAAACGAGGCACAATT	0.333																																					p.R1056Q		Atlas-SNP	.											.	ITGA1	112	.	0			c.G3167A						PASS	.						73	71	72					5																	52235508		2203	4300	6503	SO:0001583	missense	3672	exon25			TCAAACGAGGCAC	X68742	CCDS3955.1	5q11.1	2010-03-23			ENSG00000213949	ENSG00000213949		"CD molecules", "Integrins"	6134	protein-coding gene	gene with protein product		192968				8428973, 11937138	Standard	NM_181501		Approved	VLA1, CD49a	uc003jou.3	P56199	OTTHUMG00000131163	ENST00000282588.6:c.3167G>A	chr5.hg19:g.52235508G>A	ENSP00000282588:p.Arg1056Gln	186.0	0.0	.		108.0	7.0	.	NM_181501	B2RNU0	Missense_Mutation	SNP	ENST00000282588.6	hg19	CCDS3955.1	.	.	.	.	.	.	.	.	.	.	G	8.692	0.907639	0.17833	.	.	ENSG00000213949	ENST00000282588	T	0.46819	0.86	6.05	2.19	0.27852	.	0.307081	0.26553	N	0.023732	T	0.35941	0.0949	L	0.40543	1.245	0.26987	N	0.965229	B	0.22276	0.067	B	0.24541	0.054	T	0.24440	-1.0160	10	0.40728	T	0.16	.	8.7957	0.34878	0.1521:0.1263:0.7215:0.0	.	1056	P56199	ITA1_HUMAN	Q	1056	ENSP00000282588:R1056Q	ENSP00000282588:R1056Q	R	+	2	0	ITGA1	52271265	0.253000	0.23982	1.000000	0.80357	0.146000	0.21551	-0.082000	0.11304	0.449000	0.26747	-0.961000	0.02630	CGA	.	.	.	none		0.333	ITGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253855.3	NM_181501		A	52235508	G	A	52235508	3	1	245	1	0	0	0	0	1	0	0	0	7879	1058	37	1	3265	1	ITGA1	5	52235508	Missense_Mutation	SNP	G	TCGA-SX-A71W-01A-12D-A34Z-10		52235508	128679752	10	15142											
GCNT2	2651	hgsc.bcm.edu	37	chr6	10529942	10529942	+	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	atttactttggcacggcctaCgtggctctcacaagggactt	8	12	10	11	2	1	0	1	0	1	0	2	1	1	1	1	4	2	2	1	4	3	5	rs377397535		TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr6:10529942C>G	ENST00000379597.3	+	1	1354	c.798C>G	c.(796-798)taC>taG	p.Y266*	GCNT2_ENST00000397423.2_Intron|GCNT2_ENST00000410107.1_Intron|GCNT2_ENST00000495262.1_Nonsense_Mutation_p.Y266*			Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)	266					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)		GCACGGCCTACGTGGCTCTCA	0.458																																					p.Y266X		Atlas-SNP	.											.	GCNT2	123	.	0			c.C798G						PASS	.						135	128	130					6																	10529942		2203	4300	6503	SO:0001587	stop_gained	2651	exon3			GGCCTACGTGGCT	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.798C>G	chr6.hg19:g.10529942C>G	ENSP00000368917:p.Tyr266*	95.0	0.0	.		35.0	11.0	.	NM_145649		Nonsense_Mutation	SNP	ENST00000379597.3	hg19	CCDS34338.1	.	.	.	.	.	.	.	.	.	.	C	40	8.527037	0.98850	.	.	ENSG00000111846	ENST00000495262;ENST00000379597	.	.	.	5.7	-2.52	0.06346	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-18.0933	13.3481	0.60587	0.0:0.4988:0.0:0.5012	.	.	.	.	X	266	.	ENSP00000368917:Y266X	Y	+	3	2	GCNT2	10637928	0.061000	0.20836	0.972000	0.41901	0.910000	0.53928	-0.622000	0.05553	-0.685000	0.05177	-1.072000	0.02254	TAC	.	.	.	alt		0.458	GCNT2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327912.3	NM_145649		G	10529942	C	G	10529942	4	3	245	1	0	0	0	0	0	1	0	0	6308	547	19	4	800	4	GCNT2	6	10529942	Nonsense_Mutation	SNP	C	TCGA-SX-A71W-01A-12D-A34Z-10		10529942	160585125	11	15143											
MRPS18A	55168	hgsc.bcm.edu	37	chr6	43646267	43646267	+	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	agactcacgtcatagttataCttgtgcttcaggttccaacg	10	13	8	10	2	3	1	3	0	0	1	4	1	4	1	1	1	3	3	1	1	4	6	rs568509997		TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr6:43646267C>T	ENST00000372133.3	-	3	251	c.240G>A	c.(238-240)aaG>aaA	p.K80K	MRPS18A_ENST00000372116.1_Silent_p.K80K	NM_018135.3	NP_060605.1	Q9NVS2	RT18A_HUMAN	mitochondrial ribosomal protein S18A	80					translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)	structural constituent of ribosome (GO:0003735)			kidney(3)|large_intestine(1)	4	all_cancers(18;6.56e-06)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000479)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0102)|OV - Ovarian serous cystadenocarcinoma(102;0.137)			CATAGTTATACTTGTGCTTCA	0.527													C|||	1	0.000199681	8e-04	0	5008	,	,		20679	0		0	False		,,,				2504	0				p.K80K		Atlas-SNP	.											.	MRPS18A	14	.	0			c.G240A						PASS	.						114	96	102					6																	43646267		2203	4300	6503	SO:0001819	synonymous_variant	55168	exon3			GTTATACTTGTGC	AB049952	CCDS4906.1, CCDS55006.1	6p21.3	2012-09-13			ENSG00000096080	ENSG00000096080		"Mitochondrial ribosomal proteins / small subunits"	14515	protein-coding gene	gene with protein product		611981				11279123, 11543634	Standard	NM_018135		Approved	FLJ10548, MRPS18-3	uc003ovy.2	Q9NVS2	OTTHUMG00000014750	ENST00000372133.3:c.240G>A	chr6.hg19:g.43646267C>T		86.0	0.0	.		57.0	21.0	.	NM_001193343	A6XND3|Q5QPA4	Silent	SNP	ENST00000372133.3	hg19	CCDS4906.1																																																																																			.	.	.	none		0.527	MRPS18A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040697.1	NM_018135		T	43646267	C	T	43646267	2	4	245	1	0	0	0	0	0	0	0	1	9835	564	20	2		2	MRPS18A	6	43646267	Silent	SNP	C	TCGA-SX-A71W-01A-12D-A34Z-10	33116325	43646267	127468800	12	15144											
CFTR	1080	hgsc.bcm.edu	37	chr7	117232346	117232346	+	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	tcaatccaatcaactctataCgaaaattttccattgtgcaa	15	13	3	10	1	3	0	2	0	1	0	5	1	5	0	2	0	3	1	2	0	8	5	rs121908760|rs35722447		TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr7:117232346C>A	ENST00000003084.6	+	14	2257	c.2125C>A	c.(2125-2127)Cga>Aga	p.R709R	CFTR_ENST00000454343.1_Silent_p.R648R	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	709					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)	CAACTCTATACGAAAATTTTC	0.383									Cystic Fibrosis																												p.R709R		Atlas-SNP	.											.	CFTR	171	.	0			c.C2125A	GRCh37	CM950248	CFTR	M	rs121908760	PASS	.						42	43	43					7																	117232346		2203	4300	6503	SO:0001819	synonymous_variant	1080	exon14	Familial Cancer Database	CF	TCTATACGAAAAT	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.2125C>A	chr7.hg19:g.117232346C>A		78.0	0.0	.		66.0	17.0	.	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Silent	SNP	ENST00000003084.6	hg19	CCDS5773.1																																																																																			.	.	.	alt		0.383	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492		A	117232346	C	A	117232346	2	1	245	1	0	0	0	0	0	0	0	1	3296	528	19	4		4	CFTR	7	117232346	Silent	SNP	C	TCGA-SX-A71W-01A-12D-A34Z-10		117232346	41906317	13	15145											
SPAG11B	10407	hgsc.bcm.edu	37	chr8	7320361	7320361	+	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	ctcagtggctgagtggttcaCatgtctggcttgagacgatc	7	12	13	9	1	3	2	2	2	1	1	4	4	3	2	0	3	0	3	0	3	0	2			TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr8:7320361C>T	ENST00000297498.2	-	2	248	c.82G>A	c.(82-84)Gtg>Atg	p.V28M	SPAG11B_ENST00000361111.2_Missense_Mutation_p.V28M|SPAG11B_ENST00000359758.5_Missense_Mutation_p.V28M|SPAG11B_ENST00000317900.5_Missense_Mutation_p.V28M|SPAG11B_ENST00000398462.2_Missense_Mutation_p.V28M	NM_016512.3	NP_057596.1	Q08648	SG11B_HUMAN	sperm associated antigen 11B	28					spermatogenesis (GO:0007283)	extracellular region (GO:0005576)				large_intestine(2)|lung(3)|urinary_tract(1)	6				COAD - Colon adenocarcinoma(149;0.0162)|READ - Rectum adenocarcinoma(644;0.236)		GAGTGGTTCACATGTCTGGCT	0.587																																					p.V28M		Atlas-SNP	.											SPAG11B_ENST00000398462,NS,carcinoma,0,3	SPAG11B	32	.	0			c.G82A						PASS	.						94	103	100					8																	7320361		2201	4295	6496	SO:0001583	missense	10407	exon2			GGTTCACATGTCT	AF168616	CCDS5964.1, CCDS5965.1, CCDS5966.1, CCDS5967.1, CCDS47774.1	8p23.1	2014-02-21	2007-03-15	2007-03-15	ENSG00000164871	ENSG00000164871			14534	protein-coding gene	gene with protein product	"epididymal protein 2B"	606560				8167223, 1693137	Standard	NM_058200		Approved	HE2, EP2, EP2C, EP2D, EDDM2B	uc003wrl.3	Q08648	OTTHUMG00000129219	ENST00000297498.2:c.82G>A	chr8.hg19:g.7320361C>T	ENSP00000297498:p.Val28Met	755.0	0.0	.		447.0	66.0	.	NM_016512	E9PFH0|Q546A0|Q6ZYB2|Q9H4P8|Q9H4P9|Q9H4Q0|Q9H4Q1|Q9H4Q2|Q9NRT3|Q9NRV4|Q9NRV5|Q9NRV6|Q9NRV7|Q9NRV8	Missense_Mutation	SNP	ENST00000297498.2	hg19	CCDS5966.1	.	.	.	.	.	.	.	.	.	.	C	12.20	1.866049	0.32977	.	.	ENSG00000164871	ENST00000528943;ENST00000359758;ENST00000361111;ENST00000297498;ENST00000398462;ENST00000317900	T;T;T	0.54279	1.17;0.58;1.18	2.59	-1.72	0.08107	.	.	.	.	.	T	0.56645	0.1999	L	0.43152	1.355	0.09310	N	1	P;D;D;D;D	0.89917	0.926;0.97;0.996;0.994;1.0	P;P;D;D;D	0.91635	0.628;0.744;0.992;0.986;0.999	T	0.47598	-0.9105	9	0.72032	D	0.01	.	3.3012	0.06984	0.0:0.3248:0.2202:0.455	.	28;28;28;28;28	Q08648-3;A8MZA0;Q08648;Q6PDA7-3;E9PAK7	.;.;SG11B_HUMAN;.;.	M	11;28;28;28;28;28	ENSP00000437154:V11M;ENSP00000354411:V28M;ENSP00000297498:V28M	ENSP00000297498:V28M	V	-	1	0	SPAG11B	7307771	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.299000	0.08254	-0.461000	0.06993	0.461000	0.40582	GTG	.	.	.	none		0.587	SPAG11B-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251390.2	NM_058202, NM_058200, NM_058201, NM_016512, NM_058203, NM_058206, NM_058207		T	7320361	C	T	7320361	3	4	245	1	0	0	0	0	1	0	0	0	14990	478	17	2	637	2	SPAG11B	8	7320361	Missense_Mutation	SNP	C	TCGA-SX-A71W-01A-12D-A34Z-10		7320361	139043661	14	15146											
GNE	10020	hgsc.bcm.edu	37	chr9	36246171	36246171	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcactgcgggtgcagcacAcatgataatgagccagtttt	10	10	11	10	1	0	2	0	2	0	0	0	2	0	2	1	1	5	4	1	1	1	3			TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr9:36246171A>G	ENST00000539815.1	-	2	513	c.473T>C	c.(472-474)gTg>gCg	p.V158A	GNE_ENST00000539208.1_Missense_Mutation_p.V99A|GNE_ENST00000396594.3_Missense_Mutation_p.V189A|GNE_ENST00000543356.2_Missense_Mutation_p.V153A|GNE_ENST00000377902.5_Missense_Mutation_p.V158A|GNE_ENST00000447283.2_Missense_Mutation_p.V158A			Q9Y223	GLCNE_HUMAN	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	158					carbohydrate phosphorylation (GO:0046835)|cell adhesion (GO:0007155)|N-acetylglucosamine biosynthetic process (GO:0006045)|N-acetylneuraminate metabolic process (GO:0006054)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|metal ion binding (GO:0046872)|N-acylmannosamine kinase activity (GO:0009384)|UDP-N-acetylglucosamine 2-epimerase activity (GO:0008761)			endometrium(8)|kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	19			STAD - Stomach adenocarcinoma(86;0.228)			GGTGCAGCACACATGATAATG	0.483																																					p.V189A	GBM(184;106 2118 20004 35750 50727)	Atlas-SNP	.											.	GNE	141	.	0			c.T566C						PASS	.						189	151	164					9																	36246171		2203	4300	6503	SO:0001583	missense	10020	exon3			CAGCACACATGAT	AF051852	CCDS6602.1, CCDS47965.1, CCDS55308.1, CCDS55309.1, CCDS55310.1	9p13.1	2008-02-05	2003-12-01		ENSG00000159921	ENSG00000159921			23657	protein-coding gene	gene with protein product		603824	"UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase"	IBM2		9305887, 9305888	Standard	NM_005476		Approved	Uae1	uc010mli.3	Q9Y223	OTTHUMG00000019899	ENST00000539815.1:c.473T>C	chr9.hg19:g.36246171A>G	ENSP00000439155:p.Val158Ala	86.0	0.0	.		52.0	20.0	.	NM_001128227	A6PZH2|A6PZH3|A7UNU7|B2R6E1|B7Z372|B7Z428|D3DRP7|F5H499|H0YFA7|Q0VA94	Missense_Mutation	SNP	ENST00000539815.1	hg19	CCDS6602.1	.	.	.	.	.	.	.	.	.	.	A	11.94	1.787539	0.31593	.	.	ENSG00000159921	ENST00000377902;ENST00000396594;ENST00000339267;ENST00000539815;ENST00000543356;ENST00000539208;ENST00000447283	D;D;D;D;D	0.99207	-5.56;-5.56;-5.56;-5.56;-5.56	5.77	5.77	0.91146	.	0.054309	0.64402	D	0.000001	D	0.93077	0.7796	N	0.00347	-1.61	0.41973	D	0.990766	B;B;B;B;B	0.11235	0.0;0.0;0.0;0.0;0.004	B;B;B;B;B	0.14023	0.001;0.001;0.001;0.001;0.01	D	0.89903	0.4046	10	0.36615	T	0.2	0.989	8.5662	0.33540	0.9149:0.0:0.0851:0.0	.	99;117;189;158;158	F5H499;Q9Y223-3;Q9Y223-2;Q9Y223;A7UNU7	.;.;.;GLCNE_HUMAN;.	A	158;189;153;158;130;99;158	ENSP00000367134:V158A;ENSP00000379839:V189A;ENSP00000439155:V158A;ENSP00000445117:V99A;ENSP00000414760:V158A	ENSP00000340770:V153A	V	-	2	0	GNE	36236171	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.584000	0.67490	2.204000	0.70986	0.383000	0.25322	GTG	.	.	.	none		0.483	GNE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052412.4	NM_005476		G	36246171	A	G	36246171	3	3	245	1	0	0	0	0	1	0	0	0	6529	159	6	3	1735	3	GNE	9	36246171	Missense_Mutation	SNP	A	TCGA-SX-A71W-01A-12D-A34Z-10		36246171	104967260	15	15147											
ZBTB5	9925	hgsc.bcm.edu	37	chr9	37442187	37442187	+	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	gagacatgggcagcgtccttGtcgttaagtaatgtttacat	10	13	11	7	2	0	1	0	0	0	1	2	2	1	1	1	1	2	4	1	1	3	5			TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr9:37442187G>T	ENST00000307750.4	-	2	550	c.362C>A	c.(361-363)aCa>aAa	p.T121K		NM_014872.2	NP_055687.1	O15062	ZBTB5_HUMAN	zinc finger and BTB domain containing 5	121					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.T121K(1)		NS(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	8				GBM - Glioblastoma multiforme(29;0.00733)|Lung(182;0.226)		CAGCGTCCTTGTCGTTAAGTA	0.532																																					p.T121K		Atlas-SNP	.											ZBTB5,NS,carcinoma,0,1	ZBTB5	43	.	1	Substitution - Missense(1)	ovary(1)	c.C362A						PASS	.						97	89	92					9																	37442187		2203	4300	6503	SO:0001583	missense	9925	exon2			GTCCTTGTCGTTA	AB002352	CCDS6610.1	9p13.1	2013-01-09			ENSG00000168795	ENSG00000168795		"-", "BTB/POZ domain containing", "Zinc fingers, C2H2-type"	23836	protein-coding gene	gene with protein product						9205841	Standard	NM_014872		Approved	KIAA0354	uc003zzx.3	O15062	OTTHUMG00000019918	ENST00000307750.4:c.362C>A	chr9.hg19:g.37442187G>T	ENSP00000307604:p.Thr121Lys	75.0	0.0	.		45.0	17.0	.	NM_014872		Missense_Mutation	SNP	ENST00000307750.4	hg19	CCDS6610.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.935859	0.73442	.	.	ENSG00000168795	ENST00000307750	T	0.65916	-0.18	5.54	5.54	0.83059	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.62925	0.2468	N	0.11427	0.14	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.57642	-0.7776	10	0.11794	T	0.64	.	19.6787	0.95950	0.0:0.0:1.0:0.0	.	121	O15062	ZBTB5_HUMAN	K	121	ENSP00000307604:T121K	ENSP00000307604:T121K	T	-	2	0	ZBTB5	37432187	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	7.211000	0.77933	2.884000	0.98904	0.655000	0.94253	ACA	.	.	.	none		0.532	ZBTB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052462.1	NM_014872		T	37442187	G	T	37442187	3	4	245	1	0	0	0	0	1	0	0	0	17563	1377	48	4	1675	4	ZBTB5	9	37442187	Missense_Mutation	SNP	G	TCGA-SX-A71W-01A-12D-A34Z-10	1196016	37442187	103771244	16	15148											
COL15A1	1306	hgsc.bcm.edu	37	chr9	101806896	101806896	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgacagaggacattcctcTggaaaggctgatggggaaaa	13	7	13	8	0	1	3	0	2	1	1	2	6	2	6	2	5	0	1	2	5	3	1			TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr9:101806896T>C	ENST00000375001.3	+	25	3044	c.2621T>C	c.(2620-2622)cTg>cCg	p.L874P		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	874	Nonhelical region 5 (NC5).				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)				GACATTCCTCTGGAAAGGCTG	0.512																																					p.L874P		Atlas-SNP	.											.	COL15A1	211	.	0			c.T2621C						PASS	.						108	101	103					9																	101806896		2203	4300	6503	SO:0001583	missense	1306	exon25			TTCCTCTGGAAAG	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.2621T>C	chr9.hg19:g.101806896T>C	ENSP00000364140:p.Leu874Pro	87.0	0.0	.		53.0	20.0	.	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	hg19	CCDS35081.1	.	.	.	.	.	.	.	.	.	.	T	12.61	1.991071	0.35131	.	.	ENSG00000204291	ENST00000375001	T	0.34472	1.36	4.99	4.99	0.66335	C-type lectin fold (1);	0.658378	0.14535	N	0.313620	T	0.39600	0.1084	N	0.12831	0.26	0.80722	D	1	D	0.71674	0.998	D	0.81914	0.995	T	0.13361	-1.0512	10	0.29301	T	0.29	-5.7456	11.3753	0.49724	0.0:0.0:0.0:1.0	.	874	P39059	COFA1_HUMAN	P	874	ENSP00000364140:L874P	ENSP00000364140:L874P	L	+	2	0	COL15A1	100846717	1.000000	0.71417	0.909000	0.35828	0.577000	0.36160	4.646000	0.61411	2.005000	0.58758	0.402000	0.26972	CTG	.	.	.	none		0.512	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855		C	101806896	T	C	101806896	3	2	245	1	0	0	0	0	1	0	0	0	3674	1580	55	3	2719	3	COL15A1	9	101806896	Missense_Mutation	SNP	T	TCGA-SX-A71W-01A-12D-A34Z-10	64364709	101806896	39406535	17	15149											
HK1	3098	hgsc.bcm.edu	37	chr10	71160778	71160778	+	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	tcatgcaccagacggtgaagGaactgtcaccaaaatgtaac	15	7	9	10	1	2	2	2	1	0	1	2	3	2	3	2	2	3	2	2	2	5	1			TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr10:71160778G>A	ENST00000359426.6	+	18	2745	c.2641G>A	c.(2641-2643)Gaa>Aaa	p.E881K	HK1_ENST00000448642.2_Missense_Mutation_p.E916K|HK1_ENST00000360289.2_Missense_Mutation_p.E869K|HK1_ENST00000404387.2_Missense_Mutation_p.E885K|HK1_ENST00000298649.3_Missense_Mutation_p.E880K	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	881	Catalytic.|Hexokinase type-2 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						GACGGTGAAGGAACTGTCACC	0.557																																					p.E885K		Atlas-SNP	.											.	HK1	170	.	0			c.G2653A						PASS	.						92	84	87					10																	71160778		2203	4300	6503	SO:0001583	missense	3098	exon21			GTGAAGGAACTGT	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.2641G>A	chr10.hg19:g.71160778G>A	ENSP00000352398:p.Glu881Lys	105.0	0.0	.		46.0	16.0	.	NM_033498	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Missense_Mutation	SNP	ENST00000359426.6	hg19	CCDS7292.1	.	.	.	.	.	.	.	.	.	.	G	15.49	2.850351	0.51270	.	.	ENSG00000156515	ENST00000360289;ENST00000448642;ENST00000404387;ENST00000298649;ENST00000359426;ENST00000405407	D;D;D;D;D	0.96396	-4.0;-4.0;-4.0;-4.0;-4.0	5.78	5.78	0.91487	Hexokinase, C-terminal (1);	0.132704	0.64402	D	0.000002	D	0.93598	0.7956	L	0.33668	1.02	0.58432	D	0.999999	B;B;B;B;B	0.10296	0.001;0.0;0.003;0.001;0.003	B;B;B;B;B	0.11329	0.005;0.003;0.006;0.005;0.002	D	0.88826	0.3302	10	0.23891	T	0.37	-29.3498	20.3681	0.98887	0.0:0.0:1.0:0.0	.	881;880;916;885;869	P19367;P19367-2;E7ENR4;P19367-3;P19367-4	HXK1_HUMAN;.;.;.;.	K	869;916;885;880;881;881	ENSP00000353433:E869K;ENSP00000402103:E916K;ENSP00000384774:E885K;ENSP00000298649:E880K;ENSP00000352398:E881K	ENSP00000298649:E880K	E	+	1	0	HK1	70830784	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.336000	0.65935	2.890000	0.99128	0.655000	0.94253	GAA	.	.	.	none		0.557	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048429.2	NM_000188		A	71160778	G	A	71160778	3	1	245	1	0	0	0	0	1	0	0	0	7197	1175	41	2	2889	2	HK1	10	71160778	Missense_Mutation	SNP	G	TCGA-SX-A71W-01A-12D-A34Z-10		71160778	64373969	18	15150											
C11orf24	53838	hgsc.bcm.edu	37	chr11	68030090	68030107	+	In_Frame_Del	DEL	TGGAGGCCGCAGTCGTAA	TGGAGGCCGCAGTCGTAA	-																															actggaggccacagtcatacTggaggccgcagtcgtaatgg																								rs199576193|rs201174414|rs201655090|rs373234316		TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	TGGAGGCCGCAGTCGTAA	TGGAGGCCGCAGTCGTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr11:68030090_68030107delTGGAGGCCGCAGTCGTAA	ENST00000304271.6	-	4	758_775	c.356_373delTTACGACTGCGGCCTCCA	c.(355-375)attacgactgcggcctccagt>agt	p.ITTAAS119del	C11orf24_ENST00000530166.1_5'UTR|C11orf24_ENST00000533310.1_Intron	NM_022338.3	NP_071733.1	Q96F05	CK024_HUMAN	chromosome 11 open reading frame 24	119						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						ACAGTCATACTGGAGGCCGCAGTCGTAATGGAGGCCGC	0.601																																					p.119_125del	NSCLC(21;855 905 4198 36694)	Atlas-INDEL	.											C11orf24,NS,carcinoma,0,1	C11orf24	35	.	0			c.357_374del						PASS	.																																			SO:0001651	inframe_deletion	53838	exon4			.	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.356_373delTTACGACTGCGGCCTCCA	chr11.hg19:g.68030090_68030107delTGGAGGCCGCAGTCGTAA	ENSP00000307264:p.Ile119_Ser124del	92.0	0.0	0		63.0	15.0	0.238095	NM_022338	Q9H2K4	In_Frame_Del	DEL	ENST00000304271.6	hg19	CCDS8180.1																																																																																			.	.	.	none		0.601	C11orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394750.1	NM_022338		-	68030107	TGGAGGCCGCAGTCGTAA	-	68030090	7	5	245	1	0	1	0	1	0	0	0	0	1637	1580	55	0	980	0	C11orf24	11	68030090	In_Frame_Del	DEL	TGGAGGCCGCAGTCGTAA	TCGA-SX-A71W-01A-12D-A34Z-10		68030090	66976426	19	15151											
ZNF641	121274	hgsc.bcm.edu	37	chr12	48736774	48736774	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcaaaagacagatgttccTctgtcccagctgttccgggg	8	12	10	11	1	2	2	1	0	1	2	5	2	5	2	3	2	1	3	3	2	2	3			TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr12:48736774T>C	ENST00000544117.2	-	6	2007	c.1299A>G	c.(1297-1299)agA>agG	p.R433R	ZNF641_ENST00000448928.3_Silent_p.R410R|ZNF641_ENST00000547026.1_Silent_p.R419R|ZNF641_ENST00000301042.3_Silent_p.R433R			Q96N77	ZN641_HUMAN	zinc finger protein 641	433					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|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(2)|kidney(3)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	12						CAGATGTTCCTCTGTCCCAGC	0.552																																					p.R433R		Atlas-SNP	.											.	ZNF641	28	.	0			c.A1299G						PASS	.						61	56	58					12																	48736774		2203	4300	6503	SO:0001819	synonymous_variant	121274	exon7			TGTTCCTCTGTCC	BC018090	CCDS8763.1, CCDS53787.1, CCDS53788.1	12q13.11	2013-01-08				ENSG00000167528		"Zinc fingers, C2H2-type", "-"	31834	protein-coding gene	gene with protein product		613906					Standard	NM_152320		Approved	FLJ31295	uc001rro.2	Q96N77		ENST00000544117.2:c.1299A>G	chr12.hg19:g.48736774T>C		58.0	0.0	.		49.0	34.0	.	NM_152320	B3KS43|B4DNU5|Q8TCQ7|Q8WVE1	Silent	SNP	ENST00000544117.2	hg19	CCDS8763.1																																																																																			.	.	.	none		0.552	ZNF641-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000406518.1	NM_152320		C	48736774	T	C	48736774	2	2	245	1	0	0	0	0	0	0	0	1	18069	1548	54	3		3	ZNF641	12	48736774	Silent	SNP	T	TCGA-SX-A71W-01A-12D-A34Z-10		48736774	85115121	20	15152											
GEFT	115557	hgsc.bcm.edu	37	chr12	58009666	58009666	+	Missense_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	cctccaaggtgacccttgccGctttgcactgacctccagag	7	9	9	16	1	0	3	0	2	0	1	2	3	2	3	6	1	2	2	6	1	1	2			TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr12:58009666G>A	ENST00000286494.4	+	13	1746	c.1286G>A	c.(1285-1287)cGc>cAc	p.R429H	ARHGEF25_ENST00000333972.7_Missense_Mutation_p.R468H|AC025165.8_ENST00000610219.1_RNA|AC025165.8_ENST00000593846.1_RNA|AC025165.8_ENST00000356672.3_RNA|AC025165.8_ENST00000444467.1_RNA	NM_182947.3	NP_891992	Q86VW2	ARHGP_HUMAN	Rho guanine nucleotide exchange factor (GEF) 25	429	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cytosol (GO:0005829)|myofibril (GO:0030016)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	28						GACCCTTGCCGCTTTGCACTG	0.617																																					p.R468H		Atlas-SNP	.											.	ARHGEF25	111	.	0			c.G1403A						PASS	.						88	85	87					12																	58009666		2203	4300	6503	SO:0001583	missense	115557	exon14			CTTGCCGCTTTGC		CCDS8947.1, CCDS44931.1	12q13.3	2011-11-16			ENSG00000240771	ENSG00000240771		"Rho guanine nucleotide exchange factors"	30275	protein-coding gene	gene with protein product	"RAC/CDC42 exchange factor"	610215				12547822	Standard	NM_182947		Approved	GEFT, p63RhoGEF	uc009zpy.4	Q86VW2	OTTHUMG00000152516	ENST00000286494.4:c.1286G>A	chr12.hg19:g.58009666G>A	ENSP00000286494:p.Arg429His	91.0	0.0	.		63.0	22.0	.	NM_001111270	A6NJH5|A9CQZ6|F8W7Z4|Q8WV84|Q96E63	Missense_Mutation	SNP	ENST00000286494.4	hg19	CCDS8947.1	.	.	.	.	.	.	.	.	.	.	g	15.84	2.951692	0.53186	.	.	ENSG00000240771	ENST00000333972;ENST00000286494	T;T	0.25414	1.8;1.8	4.91	4.91	0.64330	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.38111	N	0.001820	T	0.25457	0.0619	M	0.75447	2.3	0.54753	D	0.999988	P;P	0.51537	0.946;0.627	B;B	0.36666	0.23;0.116	T	0.13548	-1.0505	10	0.87932	D	0	.	9.3708	0.38252	0.0951:0.0:0.9049:0.0	.	468;429	F8W7Z4;Q86VW2	.;ARHGP_HUMAN	H	468;429	ENSP00000335560:R468H;ENSP00000286494:R429H	ENSP00000286494:R429H	R	+	2	0	ARHGEF25	56295933	0.993000	0.37304	1.000000	0.80357	0.997000	0.91878	2.702000	0.47102	2.724000	0.93272	0.561000	0.74099	CGC	.	.	.	none		0.617	ARHGEF25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000326561.1	NM_133483		A	58009666	G	A	58009666	3	1	245	1	0	0	0	0	1	0	0	0	6335	1087	38	1	1558	1	GEFT	12	58009666	Missense_Mutation	SNP	G	TCGA-SX-A71W-01A-12D-A34Z-10	9272892	58009666	75842229	21	15153											
GRIP1	23426	hgsc.bcm.edu	37	chr12	66935595	66935595	+	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	tttccccaagaggcagttacCtagcagcaattcctccttgc	9	11	7	14	0	0	1	0	0	0	1	3	1	3	1	5	1	4	4	5	1	4	5			TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr12:66935595C>T	ENST00000398016.3	-	3	340	c.272G>A	c.(271-273)aGa>aAa	p.R91K	GRIP1_ENST00000286445.7_Splice_Site_p.R91K|GRIP1_ENST00000359742.4_Splice_Site_p.R91K	NM_021150.3	NP_066973.2	Q96DT0	LEG12_HUMAN	glutamate receptor interacting protein 1	0	Galectin 1. {ECO:0000255|PROSITE- ProRule:PRU00639}.				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)		AGGCAGTTACCTAGCAGCAAT	0.428																																					p.R91K		Atlas-SNP	.											.	GRIP1	106	.	0			c.G272A						PASS	.						216	218	217					12																	66935595		1891	4124	6015	SO:0001630	splice_region_variant	23426	exon3			AGTTACCTAGCAG	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.272+1G>A	chr12.hg19:g.66935595C>T		205.0	0.0	.		127.0	80.0	.	NM_001178074	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Missense_Mutation	SNP	ENST00000398016.3	hg19	CCDS41807.1	.	.	.	.	.	.	.	.	.	.	C	36	5.600611	0.96614	.	.	ENSG00000155974	ENST00000398016;ENST00000359742;ENST00000286445;ENST00000538211;ENST00000540433;ENST00000536215;ENST00000545666;ENST00000542309;ENST00000539540;ENST00000541947	T;T;T;T;T;T;T;T;T;T	0.27256	1.68;1.68;1.68;1.68;1.68;1.68;1.68;1.68;1.68;1.68	5.36	5.36	0.76844	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.45397	0.1340	L	0.44542	1.39	0.80722	D	1	D;D;D	0.76494	0.994;0.999;0.994	D;D;D	0.87578	0.945;0.998;0.945	T	0.11155	-1.0599	9	.	.	.	-18.0174	19.4655	0.94935	0.0:1.0:0.0:0.0	.	91;91;91	F5H4N6;Q9Y3R0;Q9Y3R0-3	.;GRIP1_HUMAN;.	K	91;91;91;91;35;35;64;35;35;117	ENSP00000381098:R91K;ENSP00000352780:R91K;ENSP00000286445:R91K;ENSP00000446047:R91K;ENSP00000446024:R35K;ENSP00000446011:R35K;ENSP00000439124:R64K;ENSP00000438500:R35K;ENSP00000443392:R35K;ENSP00000438921:R117K	.	R	-	2	0	GRIP1	65221862	1.000000	0.71417	0.997000	0.53966	0.854000	0.48673	7.782000	0.85680	2.698000	0.92095	0.655000	0.94253	AGA	.	.	.	none		0.428	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2		Missense_Mutation	T	66935595	C	T	66935595	5	4	245	1	0	0	0	0	0	0	1	0	6794	695	24	2	3046	2	GRIP1	12	66935595	Splice_Site	SNP	C	TCGA-SX-A71W-01A-12D-A34Z-10	8925929	66935595	66916300	22	15154											
C14orf4	64207	hgsc.bcm.edu	37	chr14	77494080	77494080	+	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	tggcccagggcatgcggggcAggtcgcacaggtagcaagat	9	5	17	10	2	0	1	0	0	0	1	1	1	0	1	1	6	2	5	1	6	2	1			TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr14:77494080A>T	ENST00000238647.3	-	1	954	c.56T>A	c.(55-57)cTg>cAg	p.L19Q		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	19					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						CATGCGGGGCAGGTCGCACAG	0.652																																					p.L19Q		Atlas-SNP	.											.	IRF2BPL	40	.	0			c.T56A						PASS	.						30	32	31					14																	77494080		2203	4298	6501	SO:0001583	missense	64207	exon1			CGGGGCAGGTCGC	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.56T>A	chr14.hg19:g.77494080A>T	ENSP00000238647:p.Leu19Gln	60.0	0.0	.		38.0	18.0	.	NM_024496	Q8NDQ2|Q96JG2|Q9H3I7	Missense_Mutation	SNP	ENST00000238647.3	hg19	CCDS9854.1	.	.	.	.	.	.	.	.	.	.	A	17.31	3.356823	0.61293	.	.	ENSG00000119669	ENST00000238647	T	0.63913	-0.07	4.08	4.08	0.47627	Interferon regulatory factor 2-binding protein 1 &amp (1); 2, zinc finger (1);	0.116341	0.35615	U	0.003086	T	0.77465	0.4134	M	0.76328	2.33	0.54753	D	0.999988	D	0.89917	1.0	D	0.91635	0.999	T	0.80839	-0.1203	10	0.87932	D	0	-13.394	13.2324	0.59951	1.0:0.0:0.0:0.0	.	19	Q9H1B7	I2BPL_HUMAN	Q	19	ENSP00000238647:L19Q	ENSP00000238647:L19Q	L	-	2	0	IRF2BPL	76563833	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	8.305000	0.89960	1.708000	0.51301	0.260000	0.18958	CTG	.	.	.	none		0.652	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496		T	77494080	A	T	77494080	3	4	245	1	0	0	0	0	1	0	0	0	1775	188	7	5	2338	5	C14orf4	14	77494080	Missense_Mutation	SNP	A	TCGA-SX-A71W-01A-12D-A34Z-10		77494080	29855460	23	15155											
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94060077	94060077	+	Frame_Shift_Del	DEL	C	C	-																															cagctgtcttccctggcagtCcctcttctcctccatgccct																										TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr14:94060077delC	ENST00000393151.2	+	23	3084	c.3084delC	c.(3082-3084)gtcfs	p.V1028fs	UNC79_ENST00000555664.1_Frame_Shift_Del_p.V1028fs|UNC79_ENST00000553484.1_Frame_Shift_Del_p.V1028fs|UNC79_ENST00000256339.4_Frame_Shift_Del_p.V851fs			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1028					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						CCCTGGCAGTCCCTCTTCTCC	0.483																																					p.V851fs		Atlas-Indel,Pindel	.											.	UNC79	366	.	0			c.2552delT						PASS	.						253	214	228					14																	94060077		2203	4300	6503	SO:0001589	frameshift_variant	57578	exon23			.	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.3084delC	chr14.hg19:g.94060077delC	ENSP00000376858:p.Val1028fs	335.0	0.0	0		207.0	87.0	0.42029	NM_020818	B5MDL6|Q6ZUT7	Frame_Shift_Del	DEL	ENST00000393151.2	hg19																																																																																				.	.	.	none		0.483	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		-	94060077	C	-	94060077	7	5	245	1	0	1	0	1	0	0	0	0	8237	842	30	0	2631	0	KIAA1409	14	94060077	Frame_Shift_Del	DEL	C	TCGA-SX-A71W-01A-12D-A34Z-10	16565997	94060077	13289463	24	15156											
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94125586	94125586	+	Frame_Shift_Del	DEL	C	C	-																															atgatttgcctcttgaagatCccttctaccaatgctacaag																										TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr14:94125586delC	ENST00000393151.2	+	40	6621	c.6621delC	c.(6619-6621)atcfs	p.I2207fs	UNC79_ENST00000555664.1_Frame_Shift_Del_p.I2168fs|UNC79_ENST00000553484.1_Frame_Shift_Del_p.I2229fs|UNC79_ENST00000256339.4_Frame_Shift_Del_p.I2030fs			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	2207					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						TCTTGAAGATCCCTTCTACCA	0.299																																					p.I2030fs		Atlas-Indel,Pindel	.											.	UNC79	366	.	0			c.6089delT						PASS	.						64	66	66					14																	94125586		2202	4298	6500	SO:0001589	frameshift_variant	57578	exon40			.	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.6621delC	chr14.hg19:g.94125586delC	ENSP00000376858:p.Ile2207fs	137.0	0.0	0		80.0	30.0	0.375	NM_020818	B5MDL6|Q6ZUT7	Frame_Shift_Del	DEL	ENST00000393151.2	hg19																																																																																				.	.	.	none		0.299	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		-	94125586	C	-	94125586	7	5	245	1	0	1	0	1	0	0	0	0	8237	845	30	0	6236	0	KIAA1409	14	94125586	Frame_Shift_Del	DEL	C	TCGA-SX-A71W-01A-12D-A34Z-10	65509	94125586	13223954	25	15157											
HHIPL1	84439	hgsc.bcm.edu	37	chr14	100118913	100118913	+	Frame_Shift_Del	DEL	G	G	-																															cgtggccatggtccatgccaGggatggcacccaccgcttct																										TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr14:100118913delG	ENST00000330710.5	+	2	706	c.608delG	c.(607-609)aggfs	p.R203fs	HHIPL1_ENST00000357223.2_Frame_Shift_Del_p.R203fs	NM_001127258.1	NP_001120730.1	Q96JK4	HIPL1_HUMAN	HHIP-like 1	203					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)|membrane (GO:0016020)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)|scavenger receptor activity (GO:0005044)			breast(1)|endometrium(2)|large_intestine(2)|lung(8)|skin(2)	15		Melanoma(154;0.128)				GTCCATGCCAGGGATGGCACC	0.677																																					p.R203fs		Atlas-INDEL	.											.	HHIPL1	86	.	0			c.607delA						PASS	.						49	41	44					14																	100118913		2202	4299	6501	SO:0001589	frameshift_variant	84439	exon2			.	AB058725	CCDS9953.1, CCDS45162.1	14q32	2008-01-16	2008-01-16	2008-01-16		ENSG00000182218			19710	protein-coding gene	gene with protein product			"KIAA1822"	KIAA1822			Standard	NM_032425		Approved		uc010avs.3	Q96JK4		ENST00000330710.5:c.608delG	chr14.hg19:g.100118913delG	ENSP00000330601:p.Arg203fs	69.0	0.0	0		23.0	10.0	0.434783	NM_032425	A2RUF8|B2RN09|Q6UXX2	Frame_Shift_Del	DEL	ENST00000330710.5	hg19	CCDS45162.1																																																																																			.	.	.	none		0.677	HHIPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413811.1	XM_041566		-	100118913	G	-	100118913	7	5	245	1	0	1	0	1	0	0	0	0	7100	1000	35	0	614	0	HHIPL1	14	100118913	Frame_Shift_Del	DEL	G	TCGA-SX-A71W-01A-12D-A34Z-10	5993327	100118913	7230627	26	15158											
GAA	2548	hgsc.bcm.edu	37	chr17	78085901	78085901	+	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	aagccatcgcctcccacaggTgagggccacgtcccgcccca	8	4	10	19	3	0	1	0	1	0	0	3	1	2	1	7	2	1	0	7	2	1	0			TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr17:78085901T>G	ENST00000302262.3	+	12	1973		c.e12+2		GAA_ENST00000390015.3_Splice_Site	NM_000152.3	NP_000143.2	P10253	LYAG_HUMAN	glucosidase, alpha; acid						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)	CTCCCACAGGTGAGGGCCACG	0.652																																					.		Atlas-SNP	.											.	GAA	66	.	0			c.1754+2T>G						PASS	.						101	85	90					17																	78085901		2203	4300	6503	SO:0001630	splice_region_variant	2548	exon12			CACAGGTGAGGGC		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.1754+2T>G	chr17.hg19:g.78085901T>G		47.0	0.0	.		30.0	20.0	.	NM_000152	Q09GN4|Q14351|Q16302|Q8IWE7	Splice_Site	SNP	ENST00000302262.3	hg19	CCDS32760.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.996347	0.74818	.	.	ENSG00000171298	ENST00000302262;ENST00000390015	.	.	.	4.65	4.65	0.58169	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.7205	0.62723	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	GAA	75700496	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	7.203000	0.77864	1.716000	0.51395	0.533000	0.62120	.	.	.	.	none		0.652	GAA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437441.1		Intron	G	78085901	T	G	78085901	5	3	245	1	0	0	0	0	0	0	1	0	6154	1710	59	5	1798	5	GAA	17	78085901	Splice_Site	SNP	T	TCGA-SX-A71W-01A-12D-A34Z-10		78085901	3109309	27	15159											
INO80C	125476	hgsc.bcm.edu	37	chr18	33077699	33077699	+	Missense_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	gtacctgcgcaaagctggaaGcggacgcttttttcttctta	8	13	10	10	3	2	0	0	0	2	0	2	2	2	2	1	2	4	4	1	2	4	6			TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr18:33077699G>A	ENST00000334598.7	-	1	256	c.140C>T	c.(139-141)gCt>gTt	p.A47V	INO80C_ENST00000590757.1_Missense_Mutation_p.A47V|INO80C_ENST00000592173.1_Missense_Mutation_p.A47V|RP11-322E11.6_ENST00000589258.1_Missense_Mutation_p.A47V|INO80C_ENST00000586489.1_5'Flank|INO80C_ENST00000441607.2_Missense_Mutation_p.A47V	NM_194281.3	NP_919257.2	Q6PI98	IN80C_HUMAN	INO80 complex subunit C	47					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						AAAGCTGGAAGCGGACGCTTT	0.667																																					p.A47V		Atlas-SNP	.											.	INO80C	18	.	0			c.C140T						PASS	.						22	23	23					18																	33077699		2203	4300	6503	SO:0001583	missense	125476	exon1			CTGGAAGCGGACG		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.140C>T	chr18.hg19:g.33077699G>A	ENSP00000334473:p.Ala47Val	97.0	0.0	.		47.0	16.0	.	NM_194281	B4DUI4|E9PCS7|Q86WR1|Q8N994	Missense_Mutation	SNP	ENST00000334598.7	hg19	CCDS11914.1	.	.	.	.	.	.	.	.	.	.	G	13.82	2.351758	0.41700	.	.	ENSG00000153391	ENST00000283410;ENST00000441607;ENST00000334598	.	.	.	4.37	0.0571	0.14322	.	0.677038	0.15251	N	0.272331	T	0.25494	0.0620	L	0.36672	1.1	0.09310	N	0.999995	B;B;B	0.32829	0.267;0.004;0.386	B;B;B	0.25140	0.041;0.015;0.058	T	0.22138	-1.0225	9	0.05620	T	0.96	.	13.8549	0.63519	0.0:0.6381:0.3619:0.0	.	47;47;47	E9PCS7;Q6PI98;Q6PI98-3	.;IN80C_HUMAN;.	V	47	.	ENSP00000283410:A47V	A	-	2	0	INO80C	31331697	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	0.555000	0.23422	-0.088000	0.12506	0.555000	0.69702	GCT	.	.	.	none		0.667	INO80C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255768.1	NM_194281		A	33077699	G	A	33077699	3	1	245	1	0	0	0	0	1	0	0	0	7755	971	34	2	574	2	INO80C	18	33077699	Missense_Mutation	SNP	G	TCGA-SX-A71W-01A-12D-A34Z-10		33077699	44999549	28	15160											
CNDP2	55748	hgsc.bcm.edu	37	chr18	72185851	72185851	+	Missense_Mutation	SNP	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	tcagtcaccctcattacctgGctgggagaagagccatgaag	11	8	11	11	0	3	3	3	1	0	2	3	4	3	3	3	2	2	1	3	2	3	1			TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr18:72185851G>A	ENST00000324262.4	+	10	1502	c.1186G>A	c.(1186-1188)Gct>Act	p.A396T	CNDP2_ENST00000579847.1_Missense_Mutation_p.A396T|CNDP2_ENST00000324301.8_Missense_Mutation_p.A312T	NM_018235.2	NP_060705.2	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2 (metallopeptidase M20 family)	396					cellular nitrogen compound metabolic process (GO:0034641)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)			breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(5)|ovary(2)|skin(2)|stomach(3)	24		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)		TCATTACCTGGCTGGGAGAAG	0.572																																					p.A396T		Atlas-SNP	.											.	CNDP2	55	.	0			c.G1186A						PASS	.						105	99	101					18																	72185851		2203	4300	6503	SO:0001583	missense	55748	exon10			TACCTGGCTGGGA	AK001692	CCDS12006.1, CCDS54190.1	18q22.3	2014-07-14	2004-07-12		ENSG00000133313	ENSG00000133313	3.4.13.18		24437	protein-coding gene	gene with protein product	"cytosolic nonspecific dipeptidase"	169800	"peptidase A"	PEPA		12473676	Standard	NM_018235		Approved	FLJ10830, CN2, HsT2298, CPGL	uc002llm.2	Q96KP4	OTTHUMG00000132853	ENST00000324262.4:c.1186G>A	chr18.hg19:g.72185851G>A	ENSP00000325548:p.Ala396Thr	92.0	0.0	.		47.0	18.0	.	NM_018235	B3KUG4|Q8WY59|Q9BQ94|Q9NVB4	Missense_Mutation	SNP	ENST00000324262.4	hg19	CCDS12006.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.337023	0.81801	.	.	ENSG00000133313	ENST00000324262;ENST00000324301	T;T	0.56941	0.43;0.43	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.77745	0.4176	M	0.86740	2.835	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.76575	0.988;0.967	T	0.81488	-0.0910	10	0.87932	D	0	-18.9123	19.4462	0.94847	0.0:0.0:1.0:0.0	.	312;396	Q96KP4-2;Q96KP4	.;CNDP2_HUMAN	T	396;312	ENSP00000325548:A396T;ENSP00000325756:A312T	ENSP00000325548:A396T	A	+	1	0	CNDP2	70336831	1.000000	0.71417	0.710000	0.30468	0.041000	0.13682	9.618000	0.98365	2.595000	0.87683	0.650000	0.86243	GCT	.	.	.	none		0.572	CNDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256327.1	NM_018235		A	72185851	G	A	72185851	3	1	245	1	0	0	0	0	1	0	0	0	3596	1203	42	2	1220	2	CNDP2	18	72185851	Missense_Mutation	SNP	G	TCGA-SX-A71W-01A-12D-A34Z-10	39108152	72185851	5891397	29	15161											
FBXO46	23403	hgsc.bcm.edu	37	chr19	46216657	46216658	+	Missense_Mutation	DNP	TG	TG	CT																															ctcagggcaggctgatggctTgagggccgcagaaggcgggc																										TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr19:46216657_46216658TG>CT	ENST00000317683.3	-	2	229_230	c.96_97CA>AG	c.(94-99)ctCAag>ctAGag	p.K33E		NM_001080469.1	NP_001073938.1	Q6PJ61	FBX46_HUMAN	F-box protein 46	33										breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(2)|skin(1)	15		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00568)|GBM - Glioblastoma multiforme(486;0.0844)|Epithelial(262;0.201)		GCTGATGGCTTGAGGGCCGCAG	0.683																																					p.K33E|p.L32L		Atlas-SNP	.											.	FBXO46	34	.	0			c.A97G|c.C96A						PASS	.																																			SO:0001583	missense	23403	exon2			ATGGCTTGAGGGC|TGGCTTGAGGGCC	BC021978	CCDS46116.1	19q13.3	2008-02-05	2004-06-15	2004-06-16		ENSG00000177051		"F-boxes /  "other""	25069	protein-coding gene	gene with protein product		609117	"F-box only protein 34-like"	FBXO34L		9585442	Standard	NM_001080469		Approved	20D7-FC4, Fbx46	uc002pcz.3	Q6PJ61		ENST00000317683.3:c.96_97delinsCT	chr19.hg19:g.46216657_46216658delinsCT	ENSP00000410007:p.Lys33Glu	42.0|41.0	0.0	.		29.0	11.0	.	NM_001080469		Missense_Mutation|Silent	SNP	ENST00000317683.3	hg19	CCDS46116.1																																																																																			.	.	.	none		0.683	FBXO46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459661.1	XM_371179		CT	46216658	TG	CT	46216657	3	2	245	1	0	0	0	0	1	0	0	0	5762	1821	63	3	1718	3	FBXO46	19	46216657	Missense_Mutation	DNP	TG	TCGA-SX-A71W-01A-12D-A34Z-10		46216657	12912326	30	15162											
IRF2BP1	26145	hgsc.bcm.edu	37	chr19	46387535	46387535	+	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	gcacagggtacagcacagggGggccccaggggtcgccccag	8	2	17	14	1	0	0	0	0	0	0	1	0	0	0	4	6	2	3	4	6	1	1			TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chr19:46387535G>C	ENST00000302165.3	-	1	1841	c.1498C>G	c.(1498-1500)Ccc>Gcc	p.P500A		NM_015649.1	NP_056464.1	Q8IU81	I2BP1_HUMAN	interferon regulatory factor 2 binding protein 1	500					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)			cervix(1)|kidney(1)|lung(2)	4		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00442)|GBM - Glioblastoma multiforme(486;0.0402)|Epithelial(262;0.231)		CAGCACAGGGGGGCCCCAGGG	0.687																																					p.P500A		Atlas-SNP	.											.	IRF2BP1	23	.	0			c.C1498G						PASS	.						12	14	13					19																	46387535		2179	4270	6449	SO:0001583	missense	26145	exon1			ACAGGGGGGCCCC	AY278022	CCDS12678.1	19q13.32	2008-02-05							21728	protein-coding gene	gene with protein product		615331				12799427	Standard	NM_015649		Approved	DKFZP434M154, IRF-2BP1	uc002pds.1	Q8IU81		ENST00000302165.3:c.1498C>G	chr19.hg19:g.46387535G>C	ENSP00000307265:p.Pro500Ala	67.0	0.0	.		42.0	13.0	.	NM_015649	Q53EL7|Q6DC95|Q9BRZ9|Q9Y4P4	Missense_Mutation	SNP	ENST00000302165.3	hg19	CCDS12678.1	.	.	.	.	.	.	.	.	.	.	G	7.291	0.611129	0.14066	.	.	ENSG00000170604	ENST00000302165	T	0.47869	0.83	4.71	3.68	0.42216	.	0.199902	0.32343	N	0.006230	T	0.25344	0.0616	N	0.08118	0	0.40030	D	0.975524	B	0.29862	0.259	B	0.19666	0.026	T	0.14008	-1.0488	10	0.56958	D	0.05	.	10.6802	0.45811	0.0937:0.0:0.9063:0.0	.	500	Q8IU81	I2BP1_HUMAN	A	500	ENSP00000307265:P500A	ENSP00000307265:P500A	P	-	1	0	IRF2BP1	51079375	1.000000	0.71417	0.987000	0.45799	0.119000	0.20118	5.061000	0.64319	1.199000	0.43173	-0.140000	0.14226	CCC	.	.	.	none		0.687	IRF2BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461683.1	NM_015649		C	46387535	G	C	46387535	3	2	245	1	0	0	0	0	1	0	0	0	7836	1232	43	4	260	4	IRF2BP1	19	46387535	Missense_Mutation	SNP	G	TCGA-SX-A71W-01A-12D-A34Z-10	170878	46387535	12741448	31	15163											
HUWE1	10075	hgsc.bcm.edu	37	chrX	53565885	53565885	+	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	gggagaagaatgggtcaaggGaggaaggcgtggctggggtt	10	6	22	3	1	1	2	1	0	0	2	1	5	1	4	0	8	0	2	0	8	4	1			TCGA-SX-A71W-01A-12D-A34Z-10	TCGA-SX-A71W-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	39d5e130-8dd3-4884-81ca-045c8ae54290	365767f7-d1f9-4779-86a3-9b5ad8bbe963	g.chrX:53565885G>A	ENST00000342160.3	-	75	12246	c.11789C>T	c.(11788-11790)tCc>tTc	p.S3930F	HUWE1_ENST00000262854.6_Missense_Mutation_p.S3930F			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	3930					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						TGGGTCAAGGGAGGAAGGCGT	0.602																																					p.S3930F		Atlas-SNP	.											.	HUWE1	724	.	0			c.C11789T						PASS	.						75	52	60					X																	53565885		2203	4300	6503	SO:0001583	missense	10075	exon76			TCAAGGGAGGAAG	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.11789C>T	chrX.hg19:g.53565885G>A	ENSP00000340648:p.Ser3930Phe	59.0	0.0	.		53.0	46.0	.	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	hg19	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	G	14.23	2.472928	0.43942	.	.	ENSG00000086758	ENST00000342160;ENST00000262854	T;T	0.39592	1.07;1.07	5.62	5.62	0.85841	.	0.135606	0.51477	D	0.000092	T	0.51736	0.1692	L	0.43152	1.355	0.80722	D	1	B;P;D	0.57899	0.055;0.936;0.981	B;P;P	0.54706	0.031;0.578;0.759	T	0.54241	-0.8323	10	0.87932	D	0	.	17.2701	0.87098	0.0:0.0:1.0:0.0	.	752;3930;3914	Q5H935;Q7Z6Z7;Q7Z6Z7-2	.;HUWE1_HUMAN;.	F	3930	ENSP00000340648:S3930F;ENSP00000262854:S3930F	ENSP00000262854:S3930F	S	-	2	0	HUWE1	53582610	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.788000	0.91834	2.344000	0.79699	0.600000	0.82982	TCC	.	.	.	none		0.602	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		A	53565885	G	A	53565885	3	1	245	1	0	0	0	0	1	0	0	0	7468	1174	41	2	1371	2	HUWE1	23	53565885	Missense_Mutation	SNP	G	TCGA-SX-A71W-01A-12D-A34Z-10		53565885	101704675	32	15164											
TMEM52	339456	hgsc.bcm.edu	37	chr1	1849559	1849559	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtccagctccccaaagggcAggggcaaccgcatgcccagt	9	4	13	15	1	0	0	0	0	0	0	2	0	2	0	5	4	3	4	5	4	2	0			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr1:1849559A>G	ENST00000310991.3	-	5	399	c.392T>C	c.(391-393)cTg>cCg	p.L131P	TMEM52_ENST00000378602.3_Missense_Mutation_p.L116P	NM_178545.3	NP_848640.1	Q8NDY8	TMM52_HUMAN	transmembrane protein 52	131						integral component of membrane (GO:0016021)				NS(1)|prostate(1)|stomach(1)	3	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)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.82e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.75e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		CCCAAAGGGCAGGGGCAACCG	0.637																																					p.L131P		Atlas-SNP	.											.	TMEM52	21	.	0			c.T392C						PASS	.						70	70	70					1																	1849559		2203	4300	6503	SO:0001583	missense	339456	exon5			AAGGGCAGGGGCA	AJ278736	CCDS35.1	1p36.33	2008-02-05			ENSG00000178821	ENSG00000178821			27916	protein-coding gene	gene with protein product							Standard	NM_178545		Approved		uc001aij.2	Q8NDY8	OTTHUMG00000000944	ENST00000310991.3:c.392T>C	chr1.hg19:g.1849559A>G	ENSP00000311122:p.Leu131Pro	90.0	0.0	.		78.0	39.0	.	NM_178545	Q4VXS6|Q6UX25	Missense_Mutation	SNP	ENST00000310991.3	hg19	CCDS35.1	.	.	.	.	.	.	.	.	.	.	.	11.55	1.671700	0.29693	.	.	ENSG00000178821	ENST00000378602;ENST00000310991	T;T	0.35789	1.29;1.29	3.12	3.12	0.35913	.	0.416227	0.16370	N	0.217372	T	0.46737	0.1408	L	0.44542	1.39	0.31254	N	0.693716	D;P	0.69078	0.997;0.772	D;P	0.66351	0.943;0.632	T	0.49133	-0.8971	10	0.51188	T	0.08	-0.8967	9.9579	0.41678	1.0:0.0:0.0:0.0	.	131;116	Q8NDY8;Q8NDY8-2	TMM52_HUMAN;.	P	116;131	ENSP00000367865:L116P;ENSP00000311122:L131P	ENSP00000311122:L131P	L	-	2	0	TMEM52	1839419	0.012000	0.17670	0.490000	0.27465	0.016000	0.09150	1.648000	0.37271	1.669000	0.50854	0.418000	0.28097	CTG	.	.	.	none		0.637	TMEM52-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000002781.1	NM_178545		G	1849559	A	G	1849559	3	3	246	1	0	0	0	0	1	0	0	0	16190	188	7	3	241	3	TMEM52	1	1849559	Missense_Mutation	SNP	A	TCGA-SX-A7SL-01A-11D-A34Z-10		1849559	247401062	1	15165											
EPHA8	2046	hgsc.bcm.edu	37	chr1	22903066	22903066	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaacacggaggtgcgcagTgtgggtcccctcagcaagcg	8	6	14	13	3	2	0	2	0	0	0	3	1	3	1	2	3	4	2	2	3	2	0	rs570237058		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr1:22903066T>C	ENST00000166244.3	+	3	588	c.516T>C	c.(514-516)agT>agC	p.S172S	EPHA8_ENST00000538803.1_Silent_p.S172S|EPHA8_ENST00000374644.4_Silent_p.S172S	NM_020526.3	NP_065387.1	P29322	EPHA8_HUMAN	EPH receptor A8	172	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|ephrin receptor signaling pathway (GO:0048013)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell adhesion mediated by integrin (GO:0033628)|substrate-dependent cell migration (GO:0006929)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(6)|lung(22)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		AGGTGCGCAGTGTGGGTCCCC	0.592													T|||	1	0.000199681	0	0.0014	5008	,	,		17796	0		0	False		,,,				2504	0				p.S172S		Atlas-SNP	.											.	EPHA8	221	.	0			c.T516C						PASS	.						90	79	83					1																	22903066		2203	4300	6503	SO:0001819	synonymous_variant	2046	exon3			GCGCAGTGTGGGT	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.516T>C	chr1.hg19:g.22903066T>C		99.0	0.0	.		69.0	35.0	.	NM_020526	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Silent	SNP	ENST00000166244.3	hg19	CCDS225.1																																																																																			.	.	.	none		0.592	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526		C	22903066	T	C	22903066	2	2	246	1	0	0	0	0	0	0	0	1	5175	1693	59	3		3	EPHA8	1	22903066	Silent	SNP	T	TCGA-SX-A7SL-01A-11D-A34Z-10	21053507	22903066	226347555	2	15166											
CDCP2	200008	hgsc.bcm.edu	37	chr1	54605763	54605763	+	Frame_Shift_Del	DEL	T	T	-																															ttgccccgcatggccatgtaTacctcctggcattctcctgg																										TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr1:54605763delT	ENST00000371330.1	-	4	1627	c.780delA	c.(778-780)gtafs	p.V260fs	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	260	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						TGGCCATGTATACCTCCTGGC	0.612																																					p.Y261fs		Atlas-Indel,Pindel	.											.	CDCP2	52	.	0			c.781delT						PASS	.						41	32	35					1																	54605763		2143	4212	6355	SO:0001589	frameshift_variant	200008	exon4			.		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.780delA	chr1.hg19:g.54605763delT	ENSP00000360381:p.Val260fs	85.0	0.0	0		61.0	34.0	0.557377	NM_201546	Q6ZWJ3	Frame_Shift_Del	DEL	ENST00000371330.1	hg19	CCDS588.2																																																																																			.	.	.	none		0.612	CDCP2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000022209.2	NM_201546		-	54605763	T	-	54605763	7	5	246	1	0	1	0	1	0	0	0	0	3096	1393	49	0	573	0	CDCP2	1	54605763	Frame_Shift_Del	DEL	T	TCGA-SX-A7SL-01A-11D-A34Z-10	31702697	54605763	194644858	3	15167											
PEX11B	8799	hgsc.bcm.edu	37	chr1	145522603	145522603	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agagtcttctgcttgtagccGgcgactgaaaggttctggag	8	11	14	8	2	3	2	0	1	3	1	3	4	3	3	1	3	2	3	1	3	2	4	rs369527712		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr1:145522603G>A	ENST00000369306.3	+	4	613	c.464G>A	c.(463-465)cGg>cAg	p.R155Q	ITGA10_ENST00000538811.1_5'Flank|ITGA10_ENST00000539363.1_5'Flank|PEX11B_ENST00000537888.1_Missense_Mutation_p.R141Q|ITGA10_ENST00000369304.3_5'Flank	NM_003846.2	NP_003837.1	O96011	PX11B_HUMAN	peroxisomal biogenesis factor 11 beta	155					peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|protein homooligomerization (GO:0051260)|regulation of peroxisome size (GO:0044375)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)	7	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GCTTGTAGCCGGCGACTGAAA	0.532													G|||	1	0.000199681	0	0	5008	,	,		17434	0.001		0	False		,,,				2504	0				p.R155Q		Atlas-SNP	.											.	PEX11B	26	.	0			c.G464A						PASS	.	G	GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	93	90	91		422,464	4.3	1	1		91	0,8600		0,0,4300	no	missense,missense	PEX11B	NM_001184795.1,NM_003846.2	43,43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign	141/246,155/260	145522603	1,13005	2203	4300	6503	SO:0001583	missense	8799	exon4			GTAGCCGGCGACT	AF093670	CCDS72870.1, CCDS72871.1	1q21	2008-08-26	2008-08-26		ENSG00000131779	ENSG00000131779			8853	protein-coding gene	gene with protein product		603867	"peroxisomal biogenesis factor 11B"			9792670	Standard	NM_003846		Approved		uc001eny.2	O96011	OTTHUMG00000013756	ENST00000369306.3:c.464G>A	chr1.hg19:g.145522603G>A	ENSP00000358312:p.Arg155Gln	103.0	0.0	.		85.0	26.0	.	NM_003846	B3KN85|B4DXH9|Q96ET2	Missense_Mutation	SNP	ENST00000369306.3	hg19	CCDS917.1	.	.	.	.	.	.	.	.	.	.	G	15.80	2.939499	0.52972	2.27E-4	0.0	ENSG00000131779	ENST00000369306;ENST00000537888	T;T	0.41400	1.0;1.0	5.23	4.31	0.51392	.	0.261053	0.36932	N	0.002331	T	0.08223	0.0205	N	0.12182	0.205	0.33147	D	0.545202	P;P	0.47604	0.826;0.898	B;B	0.32533	0.142;0.147	T	0.07986	-1.0744	10	0.15952	T	0.53	-15.2013	12.9098	0.58173	0.0:0.0:0.8365:0.1635	.	141;155	B4DXH9;O96011	.;PX11B_HUMAN	Q	155;141	ENSP00000358312:R155Q;ENSP00000437510:R141Q	ENSP00000358312:R155Q	R	+	2	0	PEX11B	144233960	0.998000	0.40836	0.978000	0.43139	0.985000	0.73830	1.788000	0.38714	1.408000	0.46895	0.591000	0.81541	CGG	.	.	.	none		0.532	PEX11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038549.1	NM_003846		A	145522603	G	A	145522603	3	1	246	1	0	0	0	0	1	0	0	0	11745	1116	39	1	496	1	PEX11B	1	145522603	Missense_Mutation	SNP	G	TCGA-SX-A7SL-01A-11D-A34Z-10	90916840	145522603	103728018	4	15168											
LYST	1130	hgsc.bcm.edu	37	chr1	235904811	235904811	+	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	ttgctttctctcttgtgcagCgtgggctggcgacaaaatat	7	14	11	9	2	2	0	0	0	2	0	3	1	2	0	0	2	3	3	0	2	3	4			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr1:235904811C>T	ENST00000389794.3	-	31	8443	c.8269G>A	c.(8269-8271)Gct>Act	p.A2757T	LYST_ENST00000389793.2_Missense_Mutation_p.A2757T			Q99698	LYST_HUMAN	lysosomal trafficking regulator	2757					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)			TCTTGTGCAGCGTGGGCTGGC	0.438																																					p.A2757T		Atlas-SNP	.											.	LYST	370	.	0			c.G8269A						PASS	.						175	154	161					1																	235904811		2203	4300	6503	SO:0001583	missense	1130	exon31			GTGCAGCGTGGGC	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.8269G>A	chr1.hg19:g.235904811C>T	ENSP00000374444:p.Ala2757Thr	220.0	0.0	.		170.0	57.0	.	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	hg19	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	c	6.807	0.517876	0.13005	.	.	ENSG00000143669	ENST00000389794;ENST00000389793	T;T	0.60920	0.15;0.15	5.63	-3.34	0.04943	.	0.354203	0.36972	N	0.002306	T	0.16342	0.0393	N	0.02011	-0.69	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34725	-0.9817	10	0.02654	T	1	.	1.3225	0.02119	0.3033:0.0855:0.2092:0.4021	.	2757	Q99698	LYST_HUMAN	T	2757	ENSP00000374444:A2757T;ENSP00000374443:A2757T	ENSP00000374443:A2757T	A	-	1	0	LYST	233971434	0.822000	0.29219	0.952000	0.39060	0.141000	0.21300	0.448000	0.21726	-0.670000	0.05282	-1.158000	0.01797	GCT	.	.	.	none		0.438	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			T	235904811	C	T	235904811	3	4	246	1	0	0	0	0	1	0	0	0	9135	768	27	1	3228	1	LYST	1	235904811	Missense_Mutation	SNP	C	TCGA-SX-A7SL-01A-11D-A34Z-10	90382208	235904811	13345810	5	15169											
OR2M4	26245	hgsc.bcm.edu	37	chr1	248402822	248402822	+	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	aaacatctgcatttgaaagaCtacttgtcatttgttgtgtg	11	16	8	6	0	2	2	1	1	1	1	2	2	2	2	0	0	3	2	0	0	3	5			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr1:248402822C>G	ENST00000306687.1	+	1	592	c.592C>G	c.(592-594)Cta>Gta	p.L198V		NM_017504.1	NP_059974.1	Q96R27	OR2M4_HUMAN	olfactory receptor, family 2, subfamily M, member 4	198					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(27)|skin(3)|upper_aerodigestive_tract(2)	50	all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			ATTTGAAAGACTACTTGTCAT	0.418																																					p.L198V		Atlas-SNP	.											.	OR2M4	111	.	0			c.C592G						PASS	.						126	125	125					1																	248402822		2203	4300	6503	SO:0001583	missense	26245	exon1			GAAAGACTACTTG	X64992	CCDS31108.1	1q44	2012-08-09			ENSG00000171180	ENSG00000171180		"GPCR / Class A : Olfactory receptors"	8270	protein-coding gene	gene with protein product						1370859, 9119360	Standard	NM_017504		Approved	HTPCRX18, TPCR100, HSHTPCRX18, OST710	uc010pzh.2	Q96R27	OTTHUMG00000040456	ENST00000306687.1:c.592C>G	chr1.hg19:g.248402822C>G	ENSP00000306688:p.Leu198Val	312.0	0.0	.		295.0	18.0	.	NM_017504	Q15611|Q8NG82	Missense_Mutation	SNP	ENST00000306687.1	hg19	CCDS31108.1	.	.	.	.	.	.	.	.	.	.	c	0.004	-2.358263	0.00214	.	.	ENSG00000171180	ENST00000306687	T	0.37915	1.17	3.34	-3.45	0.04781	GPCR, rhodopsin-like superfamily (1);	5.055650	0.00963	N	0.003125	T	0.13970	0.0338	N	0.05619	-0.005	0.09310	N	1	B	0.13594	0.008	B	0.23150	0.044	T	0.16837	-1.0389	10	0.05351	T	0.99	.	0.5132	0.00599	0.3604:0.1921:0.2485:0.199	.	198	Q96R27	OR2M4_HUMAN	V	198	ENSP00000306688:L198V	ENSP00000306688:L198V	L	+	1	2	OR2M4	246469445	0.000000	0.05858	0.001000	0.08648	0.512000	0.34134	-2.918000	0.00695	-0.440000	0.07211	0.543000	0.68304	CTA	.	.	.	none		0.418	OR2M4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097352.1	NM_017504		G	248402822	C	G	248402822	3	3	246	1	0	0	0	0	1	0	0	0	11019	564	20	4	594	4	OR2M4	1	248402822	Missense_Mutation	SNP	C	TCGA-SX-A7SL-01A-11D-A34Z-10	12498011	248402822	847799	6	15170											
PXDN	7837	hgsc.bcm.edu	37	chr2	1687921	1687921	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctatctgattaaagtgcaggTatctagaggagttaaaagaa	16	11	10	4	0	2	3	0	1	2	2	2	4	2	4	0	2	1	3	0	2	8	5			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr2:1687921T>C	ENST00000252804.4	-	5	469	c.419A>G	c.(418-420)tAc>tGc	p.Y140C		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	140					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)		AAAGTGCAGGTATCTAGAGGA	0.363																																					p.Y140C		Atlas-SNP	.											.	PXDN	255	.	0			c.A419G						PASS	.						37	38	38					2																	1687921		1825	4074	5899	SO:0001583	missense	7837	exon5			TGCAGGTATCTAG	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.419A>G	chr2.hg19:g.1687921T>C	ENSP00000252804:p.Tyr140Cys	43.0	0.0	.		43.0	22.0	.	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	hg19	CCDS46221.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	19.69|19.69|19.69	3.873824|3.873824|3.873824	0.72180|0.72180|0.72180	.|.|.	.|.|.	ENSG00000130508|ENSG00000130508|ENSG00000130508	ENST00000447941|ENST00000433670|ENST00000252804;ENST00000425171	.|.|T;T	.|.|0.58506	.|.|0.33;0.99	5.72|5.72|5.72	5.72|5.72|5.72	0.89469|0.89469|0.89469	.|.|.	.|.|0.000000	.|.|0.85682	.|.|D	.|.|0.000000	T|T|T	0.73822|0.73822|0.73822	0.3636|0.3636|0.3636	M|M|M	0.64404|0.64404|0.64404	1.975|1.975|1.975	0.54753|0.54753|0.54753	D|D|D	0.999988|0.999988|0.999988	.|.|D;D	.|.|0.76494	.|.|0.999;0.995	.|.|D;D	.|.|0.76575	.|.|0.988;0.972	T|T|T	0.76637|0.76637|0.76637	-0.2886|-0.2886|-0.2886	5|5|10	.|.|0.87932	.|.|D	.|.|0	-57.8067|-57.8067|-57.8067	15.9741|15.9741|15.9741	0.80044|0.80044|0.80044	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.|.	.|.|140;140	.|.|Q92626-2;Q92626	.|.|.;PXDN_HUMAN	M|A|C	63|136|140;116	.|.|ENSP00000252804:Y140C;ENSP00000398363:Y116C	.|.|ENSP00000252804:Y140C	I|T|Y	-|-|-	3|1|2	3|0|0	PXDN|PXDN|PXDN	1666928|1666928|1666928	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.704000|0.704000|0.704000	0.40688|0.40688|0.40688	7.883000|7.883000|7.883000	0.87264|0.87264|0.87264	2.169000|2.169000|2.169000	0.68431|0.68431|0.68431	0.460000|0.460000|0.460000	0.39030|0.39030|0.39030	ATA|ACC|TAC	.	.	.	none		0.363	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		C	1687921	T	C	1687921	3	2	246	1	0	0	0	0	1	0	0	0	12860	1638	57	3	4096	3	PXDN	2	1687921	Missense_Mutation	SNP	T	TCGA-SX-A7SL-01A-11D-A34Z-10		1687921	241511452	7	15171											
WDR35	57539	hgsc.bcm.edu	37	chr2	20113904	20113904	+	Frame_Shift_Del	DEL	G	G	-																															ctgtttctgttctgaactgaGggtctctaaagatttaagtt																										TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr2:20113904delG	ENST00000345530.3	-	27	3404	c.3289delC	c.(3289-3291)ctcfs	p.L1097fs	WDR35_ENST00000416055.2_Intron|WDR35_ENST00000281405.4_Frame_Shift_Del_p.L1086fs	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN	WD repeat domain 35	1097					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)				breast(1)|endometrium(5)|kidney(8)|large_intestine(8)|lung(16)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCTGAACTGAGGGTCTCTAAA	0.413																																					p.L1097fs		Atlas-Indel,Pindel	.											.	WDR35	92	.	0			c.3290delT						PASS	.						120	121	121					2																	20113904		2203	4300	6503	SO:0001589	frameshift_variant	57539	exon27			.	AB037757	CCDS1695.1, CCDS33152.1	2p24.3	2014-02-21			ENSG00000118965	ENSG00000118965		"WD repeat domain containing", "Intraflagellar transport homologs"	29250	protein-coding gene	gene with protein product		613602				10718198	Standard	NM_001006657		Approved	MGC33196, KIAA1336, IFT121, IFTA1	uc002rdi.3	Q9P2L0	OTTHUMG00000090737	ENST00000345530.3:c.3289delC	chr2.hg19:g.20113904delG	ENSP00000314444:p.Leu1097fs	256.0	0.0	0		230.0	95.0	0.413043	NM_001006657	B3KVI5|Q4ZG01|Q8NE11	Frame_Shift_Del	DEL	ENST00000345530.3	hg19	CCDS33152.1																																																																																			.	.	.	none		0.413	WDR35-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207472.2	NM_020779		-	20113904	G	-	20113904	7	5	246	1	0	1	0	1	0	0	0	0	17301	1000	35	0	264	0	WDR35	2	20113904	Frame_Shift_Del	DEL	G	TCGA-SX-A7SL-01A-11D-A34Z-10	18425983	20113904	223085469	8	15172											
PUM2	23369	hgsc.bcm.edu	37	chr2	20483190	20483190	+	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	ggccagtccttgctccagggCcaaccactaaggcaccagtc	9	6	10	16	0	0	0	0	0	0	0	3	0	2	0	6	3	2	2	6	3	2	2			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr2:20483190C>T	ENST00000361078.2	-	10	1371	c.1349G>A	c.(1348-1350)gGc>gAc	p.G450D	PUM2_ENST00000403432.1_Missense_Mutation_p.G450D|PUM2_ENST00000338086.5_Missense_Mutation_p.G450D|PUM2_ENST00000319801.5_Missense_Mutation_p.G450D|PUM2_ENST00000536417.1_Missense_Mutation_p.G394D			Q8TB72	PUM2_HUMAN	pumilio RNA-binding family member 2	450	Ala-rich.				regulation of translation (GO:0006417)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear membrane (GO:0031965)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(7)|lung(13)|ovary(2)|prostate(4)|urinary_tract(3)	42	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGCTCCAGGGCCAACCACTAA	0.428																																					p.G450D		Atlas-SNP	.											.	PUM2	91	.	0			c.G1349A						PASS	.						92	91	92					2																	20483190		2203	4300	6503	SO:0001583	missense	23369	exon10			CCAGGGCCAACCA	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.1349G>A	chr2.hg19:g.20483190C>T	ENSP00000354370:p.Gly450Asp	149.0	0.0	.		114.0	10.0	.	NM_015317	B3KSL0|B4E2B6|D6W527|O00234|Q53TV7|Q8WY43|Q9HAN2	Missense_Mutation	SNP	ENST00000361078.2	hg19		.	.	.	.	.	.	.	.	.	.	C	25.8	4.679173	0.88542	.	.	ENSG00000055917	ENST00000338086;ENST00000361078;ENST00000319801;ENST00000440577;ENST00000403432;ENST00000536417	T;T;T;T;T;T	0.24908	1.84;2.11;2.18;1.92;1.84;1.83	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.36608	0.0973	L	0.55481	1.735	0.80722	D	1	P;P;P	0.50066	0.752;0.931;0.721	P;P;P	0.47673	0.507;0.554;0.46	T	0.00768	-1.1574	10	0.34782	T	0.22	-7.7954	20.8598	0.99761	0.0:1.0:0.0:0.0	.	394;450;450	B4E2B6;B7ZL34;Q8TB72-3	.;.;.	D	450;450;450;341;450;394	ENSP00000338173:G450D;ENSP00000354370:G450D;ENSP00000326746:G450D;ENSP00000409905:G341D;ENSP00000385992:G450D;ENSP00000440093:G394D	ENSP00000326746:G450D	G	-	2	0	PUM2	20346671	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.927000	0.63440	2.937000	0.99478	0.650000	0.86243	GGC	.	.	.	none		0.428	PUM2-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015317		T	20483190	C	T	20483190	3	4	246	1	0	0	0	0	1	0	0	0	12839	739	26	2	1889	2	PUM2	2	20483190	Missense_Mutation	SNP	C	TCGA-SX-A7SL-01A-11D-A34Z-10	369286	20483190	222716183	9	15173											
PPM1G	5496	hgsc.bcm.edu	37	chr2	27604506	27604506	+	Frame_Shift_Del	DEL	T	T	-																															tcttcttgtcgctgttgccaTtttcttcagccccctcagta																										TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr2:27604506delT	ENST00000344034.4	-	10	1865	c.1601delA	c.(1600-1602)aatfs	p.N534fs	ZNF513_ENST00000323703.6_5'Flank|ZNF513_ENST00000491924.1_5'Flank|PPM1G_ENST00000350803.4_Frame_Shift_Del_p.N534fs|ZNF513_ENST00000407879.1_5'Flank	NM_177983.2	NP_817092.1	O15355	PPM1G_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1G	534					cell cycle arrest (GO:0007050)|peptidyl-threonine dephosphorylation (GO:0035970)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	19	Acute lymphoblastic leukemia(172;0.155)					GCTGTTGCCATTTTCTTCAGC	0.537																																					p.N534fs		Atlas-Indel,Pindel	.											.	PPM1G	42	.	0			c.1602delT						PASS	.						250	237	241					2																	27604506		2203	4300	6503	SO:0001589	frameshift_variant	5496	exon10			.	Y13936	CCDS1752.1	2p23.3	2012-04-17	2010-03-05		ENSG00000115241	ENSG00000115241	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	9278	protein-coding gene	gene with protein product	"PP2C, gamma", "protein phosphatase 2C, gamma isoform"	605119	"protein phosphatase 1G (formerly 2C), magnesium-dependent, gamma isoform"			9276438	Standard	NM_177983		Approved	PP2CG, PP2Cgamma	uc002rkl.4	O15355	OTTHUMG00000097788	ENST00000344034.4:c.1601delA	chr2.hg19:g.27604506delT	ENSP00000342778:p.Asn534fs	231.0	0.0	0		218.0	101.0	0.463303	NM_177983		Frame_Shift_Del	DEL	ENST00000344034.4	hg19	CCDS1752.1																																																																																			.	.	.	none		0.537	PPM1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215032.1	NM_002707		-	27604506	T	-	27604506	7	5	246	1	0	1	0	1	0	0	0	0	12350	1493	52	0	43	0	PPM1G	2	27604506	Frame_Shift_Del	DEL	T	TCGA-SX-A7SL-01A-11D-A34Z-10	7121316	27604506	215594867	10	15174											
CLIP4	79745	hgsc.bcm.edu	37	chr2	29404714	29404714	+	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	gttcgaccgagcagagtgacCtatcggggaattaatgggtc	10	9	14	8	3	0	2	0	1	0	1	3	5	0	3	2	3	1	2	2	3	3	3			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr2:29404714C>A	ENST00000320081.5	+	16	2328	c.2073C>A	c.(2071-2073)acC>acA	p.T691T	CLIP4_ENST00000404424.1_Silent_p.T691T|CLIP4_ENST00000401617.2_Intron	NM_024692.4	NP_078968.3	Q8N3C7	CLIP4_HUMAN	CAP-GLY domain containing linker protein family, member 4	691										endometrium(4)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(1)	26	Acute lymphoblastic leukemia(172;0.155)					GCAGAGTGACCTATCGGGGAA	0.403																																					p.T691T		Atlas-SNP	.											.	CLIP4	69	.	0			c.C2073A						PASS	.						99	100	100					2																	29404714		2203	4300	6503	SO:0001819	synonymous_variant	79745	exon16			AGTGACCTATCGG	AK024722	CCDS1770.1, CCDS74502.1	2p23	2013-01-10	2007-01-04	2007-01-04	ENSG00000115295	ENSG00000115295		"Ankyrin repeat domain containing"	26108	protein-coding gene	gene with protein product			"restin-like 2"	RSNL2			Standard	XM_005264562		Approved	FLJ21069	uc002rmv.3	Q8N3C7	OTTHUMG00000097837	ENST00000320081.5:c.2073C>A	chr2.hg19:g.29404714C>A		124.0	0.0	.		106.0	47.0	.	NM_024692	A0AV10|B2RMQ3|B7Z7N8|Q7Z4U3|Q96BR7|Q96MA5|Q9H7C0	Silent	SNP	ENST00000320081.5	hg19	CCDS1770.1																																																																																			.	.	.	none		0.403	CLIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215123.2	NM_024692		A	29404714	C	A	29404714	2	1	246	1	0	0	0	0	0	0	0	1	3537	668	24	4		4	CLIP4	2	29404714	Silent	SNP	C	TCGA-SX-A7SL-01A-11D-A34Z-10	1800208	29404714	213794659	11	15175											
BIRC6	57448	hgsc.bcm.edu	37	chr2	32640306	32640306	+	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	ggaaagatcttttcacagatGaacaatattatgagtaaaag	18	11	8	4	0	2	4	1	2	1	2	2	5	2	5	0	1	1	1	0	1	7	5			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr2:32640306G>T	ENST00000421745.2	+	10	2081	c.1947G>T	c.(1945-1947)atG>atT	p.M649I		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	649					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)	p.M649I(1)|p.M621I(1)		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)					TTTCACAGATGAACAATATTA	0.378																																					p.M649I	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											BIRC6_ENST00000421745,NS,carcinoma,0,2	BIRC6	838	.	2	Substitution - Missense(2)	lung(2)	c.G1947T						PASS	.						75	74	74					2																	32640306		2203	4300	6503	SO:0001583	missense	57448	exon10			ACAGATGAACAAT	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.1947G>T	chr2.hg19:g.32640306G>T	ENSP00000393596:p.Met649Ile	105.0	0.0	.		101.0	54.0	.	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	hg19	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	G	15.54	2.862687	0.51482	.	.	ENSG00000115760	ENST00000421745	T	0.74737	-0.87	5.56	5.56	0.83823	.	0.087525	0.85682	D	0.000000	T	0.64461	0.2600	N	0.24115	0.695	0.58432	D	0.999999	B	0.06786	0.001	B	0.08055	0.003	T	0.56571	-0.7957	10	0.26408	T	0.33	.	19.8856	0.96911	0.0:0.0:1.0:0.0	.	649	Q9NR09	BIRC6_HUMAN	I	649	ENSP00000393596:M649I	ENSP00000393596:M649I	M	+	3	0	BIRC6	32493810	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.506000	0.97992	2.771000	0.95319	0.650000	0.86243	ATG	.	.	.	none		0.378	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		T	32640306	G	T	32640306	3	4	246	1	0	0	0	0	1	0	0	0	1438	1290	45	4	1985	4	BIRC6	2	32640306	Missense_Mutation	SNP	G	TCGA-SX-A7SL-01A-11D-A34Z-10	3235592	32640306	210559067	12	15176											
C2orf3	6936	hgsc.bcm.edu	37	chr2	75907421	75907421	+	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	tgtgaggttgacaaaggatcCcaaaggaattctacaaagtc	15	9	10	7	0	1	2	0	2	1	0	3	4	2	4	1	3	1	1	1	3	5	3			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr2:75907421C>A	ENST00000321027.3	-	12	1843	c.1710G>T	c.(1708-1710)tgG>tgT	p.W570C	GCFC2_ENST00000541687.1_3'UTR|MRPL19_ENST00000358788.6_Intron|GCFC2_ENST00000409857.3_Missense_Mutation_p.W532C	NM_001201334.1|NM_003203.4	NP_001188263.1|NP_003194.3	P16383	GCFC2_HUMAN	GC-rich sequence DNA-binding factor 2	570					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)|U2-type post-mRNA release spliceosomal complex (GO:0071008)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)										ACAAAGGATCCCAAAGGAATT	0.323																																					p.W570C		Atlas-SNP	.											.	.	.	.	0			c.G1710T						PASS	.						102	106	104					2																	75907421		2203	4299	6502	SO:0001583	missense	6936	exon12			AGGATCCCAAAGG	AB026911	CCDS1961.1, CCDS62943.1	2p12	2014-01-17	2011-11-24	2011-11-24	ENSG00000005436	ENSG00000005436			1317	protein-coding gene	gene with protein product	"GC binding factor"	189901	"transcription factor 9 (binds GC-rich sequences)", "chromosome 2 open reading frame 3"	TCF9, C2orf3		1370479, 2556218, 17309879, 24304693	Standard	NM_003203		Approved	DNABF, GCF	uc002sno.3	P16383	OTTHUMG00000129989	ENST00000321027.3:c.1710G>T	chr2.hg19:g.75907421C>A	ENSP00000318690:p.Trp570Cys	124.0	0.0	.		109.0	52.0	.	NM_003203	A4UHQ8|O95032|Q53TY0|Q6P2F2	Missense_Mutation	SNP	ENST00000321027.3	hg19	CCDS1961.1	.	.	.	.	.	.	.	.	.	.	C	19.32	3.804904	0.70682	.	.	ENSG00000005436	ENST00000321027;ENST00000409857	T;T	0.68479	-0.33;-0.33	5.42	5.42	0.78866	GC-rich sequence DNA-binding factor domain (1);	0.000000	0.85682	D	0.000000	D	0.84772	0.5546	M	0.88310	2.945	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.87287	0.2296	10	0.87932	D	0	-7.8026	17.0811	0.86599	0.0:1.0:0.0:0.0	.	570	P16383	GCF_HUMAN	C	570;532	ENSP00000318690:W570C;ENSP00000386552:W532C	ENSP00000318690:W570C	W	-	3	0	C2orf3	75760929	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.129000	0.71657	2.722000	0.93159	0.650000	0.86243	TGG	.	.	.	none		0.323	GCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252255.2	NM_003203		A	75907421	C	A	75907421	3	1	246	1	0	0	0	0	1	0	0	0	2164	624	22	4	659	4	C2orf3	2	75907421	Missense_Mutation	SNP	C	TCGA-SX-A7SL-01A-11D-A34Z-10	43267115	75907421	167291952	13	15177											
CCDC141	285025	hgsc.bcm.edu	37	chr2	179720165	179720165	+	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	agtcatccacatgtttttgcAaatccttcatgacttccaaa	12	14	4	11	0	2	1	2	1	0	0	5	1	5	1	3	0	1	2	3	0	2	4			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr2:179720165A>T	ENST00000420890.2	-	19	3086	c.2969T>A	c.(2968-2970)tTg>tAg	p.L990*	CCDC141_ENST00000295723.5_Nonsense_Mutation_p.L415*	NM_173648.3	NP_775919.3	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	990										NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(37)|ovary(8)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)	78			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			ATGTTTTTGCAAATCCTTCAT	0.338																																					p.L990X		Atlas-SNP	.											.	CCDC141	362	.	0			c.T2969A						PASS	.						123	120	121					2																	179720165		2203	4300	6503	SO:0001587	stop_gained	285025	exon19			TTTTGCAAATCCT	AK096821		2q31.2	2013-01-14			ENSG00000163492	ENSG00000163492		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26821	protein-coding gene	gene with protein product	"coiled-coil protein associated with myosin II and DISC1"					20956536	Standard	NM_173648		Approved	FLJ39502, CAMDI	uc002une.2	Q6ZP82	OTTHUMG00000132578	ENST00000420890.2:c.2969T>A	chr2.hg19:g.179720165A>T	ENSP00000395995:p.Leu990*	384.0	0.0	.		325.0	144.0	.	NM_173648	H7C0P1|J3KNW6|Q8N8H3	Nonsense_Mutation	SNP	ENST00000420890.2	hg19		.	.	.	.	.	.	.	.	.	.	A	36	5.972060	0.97162	.	.	ENSG00000163492	ENST00000420890;ENST00000343876;ENST00000295723	.	.	.	4.99	4.99	0.66335	.	0.000000	0.41712	D	0.000821	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.431	15.0074	0.71524	1.0:0.0:0.0:0.0	.	.	.	.	X	990;434;415	.	ENSP00000295723:L415X	L	-	2	0	CCDC141	179428410	1.000000	0.71417	0.990000	0.47175	0.209000	0.24338	7.831000	0.86748	1.993000	0.58246	0.533000	0.62120	TTG	.	.	.	none		0.338	CCDC141-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173648		T	179720165	A	T	179720165	4	4	246	1	0	0	0	0	0	1	0	0	2777	131	5	5	1403	5	CCDC141	2	179720165	Nonsense_Mutation	SNP	A	TCGA-SX-A7SL-01A-11D-A34Z-10	103812744	179720165	63479208	14	15178											
ABI2	10152	hgsc.bcm.edu	37	chr2	204267454	204267454	+	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	gacctttttatagccagaatCcaggttagtttttttgtttt	8	20	7	6	0	0	1	0	0	0	1	1	2	1	1	3	1	1	3	3	1	4	10			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr2:204267454C>G	ENST00000422511.2	+	9	1121	c.1090C>G	c.(1090-1092)Cca>Gca	p.P364A	ABI2_ENST00000261018.7_Missense_Mutation_p.P183A|ABI2_ENST00000261016.6_Missense_Mutation_p.P285A|RAPH1_ENST00000457812.1_Intron|ABI2_ENST00000424558.1_Missense_Mutation_p.P391A|ABI2_ENST00000295851.5_Missense_Mutation_p.P397A|ABI2_ENST00000261017.5_Missense_Mutation_p.P330A|ABI2_ENST00000430574.1_3'UTR|ABI2_ENST00000430418.1_Missense_Mutation_p.P342A			Q9NYB9	ABI2_HUMAN	abl-interactor 2	397	Pro-rich.				actin polymerization or depolymerization (GO:0008154)|cell migration (GO:0016477)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|Rac protein signal transduction (GO:0016601)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|SCAR complex (GO:0031209)	cytoskeletal adaptor activity (GO:0008093)|DNA binding (GO:0003677)|kinase binding (GO:0019900)|proline-rich region binding (GO:0070064)|protein complex binding (GO:0032403)|SH3 domain binding (GO:0017124)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(3)|large_intestine(1)|liver(2)|lung(4)|prostate(2)|skin(1)|urinary_tract(1)	15						TAGCCAGAATCCAGGTTAGTT	0.368																																					p.P330A		Atlas-SNP	.											.	ABI2	44	.	0			c.C988G						PASS	.						98	96	97					2																	204267454		2203	4300	6503	SO:0001583	missense	10152	exon7			CAGAATCCAGGTT	AF260261	CCDS2358.1, CCDS63093.1, CCDS63094.1, CCDS74634.1	2q33	2010-09-20	2009-07-23		ENSG00000138443	ENSG00000138443			24011	protein-coding gene	gene with protein product		606442				7590236, 10964520	Standard	XM_005246217		Approved	ABI-2, AIP-1, ABI2B, AblBP3, argBPIA, SSH3BP2	uc002uzz.3	Q9NYB9	OTTHUMG00000132879	ENST00000422511.2:c.1090C>G	chr2.hg19:g.204267454C>G	ENSP00000396249:p.Pro364Ala	148.0	0.0	.		145.0	9.0	.	NM_005759	B4DSN1|Q13147|Q13249|Q13801|Q9BV70	Missense_Mutation	SNP	ENST00000422511.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.94|18.94	3.730696|3.730696	0.69074|0.69074	.|.	.|.	ENSG00000138443|ENSG00000138443	ENST00000451591;ENST00000454023|ENST00000295851;ENST00000261017;ENST00000430418;ENST00000424558;ENST00000261016;ENST00000417864;ENST00000422511;ENST00000261018	.|T;T;T;T;T;T;T;T	.|0.41400	.|1.2;1.22;1.35;1.21;1.03;1.51;1.18;1.0	5.6|5.6	5.6|5.6	0.85130|0.85130	.|.	.|0.203600	.|0.52532	.|D	.|0.000061	T|T	0.22003|0.22003	0.0530|0.0530	N|N	0.02539|0.02539	-0.55|-0.55	0.80722|0.80722	D|D	1|1	.|B;P;P;B;P;P;P;B;B	.|0.41131	.|0.439;0.58;0.524;0.212;0.525;0.646;0.739;0.39;0.051	.|B;B;B;B;B;B;B;B;B	.|0.36666	.|0.23;0.184;0.095;0.094;0.115;0.124;0.225;0.054;0.097	T|T	0.25882|0.25882	-1.0119|-1.0119	5|10	.|0.49607	.|T	.|0.09	-8.0595|-8.0595	17.8057|17.8057	0.88600|0.88600	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|183;232;122;274;391;342;285;397;330	.|B7Z5L1;B7Z612;B4DMM5;B7Z836;Q9NYB9-4;E9PEZ7;Q9NYB9-3;Q9NYB9;Q9NYB9-2	.|.;.;.;.;.;.;.;ABI2_HUMAN;.	M|A	200;176|397;330;342;391;285;397;364;183	.|ENSP00000295851:P397A;ENSP00000261017:P330A;ENSP00000408898:P342A;ENSP00000391433:P391A;ENSP00000261016:P285A;ENSP00000414703:P397A;ENSP00000396249:P364A;ENSP00000261018:P183A	.|ENSP00000261016:P285A	I|P	+|+	3|1	3|0	ABI2|ABI2	203975699|203975699	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	7.263000|7.263000	0.78421|0.78421	2.636000|2.636000	0.89361|0.89361	0.655000|0.655000	0.94253|0.94253	ATC|CCA	.	.	.	none		0.368	ABI2-007	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000336179.2	NM_005759		G	204267454	C	G	204267454	3	3	246	1	0	0	0	0	1	0	0	0	89	855	30	4	1014	4	ABI2	2	204267454	Missense_Mutation	SNP	C	TCGA-SX-A7SL-01A-11D-A34Z-10	24547289	204267454	38931919	15	15179											
MTMR14	64419	hgsc.bcm.edu	37	chr3	9730673	9730673	+	Frame_Shift_Del	DEL	C	C	-																															cagccttggcagcgacttctCcctggtcatggagagttccc																										TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr3:9730673delC	ENST00000296003.4	+	16	1462	c.1340delC	c.(1339-1341)tccfs	p.S447fs	MTMR14_ENST00000353332.5_Frame_Shift_Del_p.S447fs|MTMR14_ENST00000351233.5_Frame_Shift_Del_p.S447fs|MTMR14_ENST00000420925.1_Frame_Shift_Del_p.S201fs	NM_001077525.2	NP_001070993.1	Q8NCE2	MTMRE_HUMAN	myotubularin related protein 14	447					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)					AGCGACTTCTCCCTGGTCATG	0.602																																					p.S447fs		Atlas-INDEL	.											.	MTMR14	43	.	0			c.1339delT						PASS	.						48	53	51					3																	9730673		2079	4221	6300	SO:0001589	frameshift_variant	64419	exon16			.	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.1340delC	chr3.hg19:g.9730673delC	ENSP00000296003:p.Ser447fs	39.0	0.0	0		21.0	11.0	0.52381	NM_001077525	Q0JTH5|Q0JU83|Q6PIZ4|Q6QE21|Q86VK9|Q8IYK1|Q8TCM7|Q9H6C0	Frame_Shift_Del	DEL	ENST00000296003.4	hg19	CCDS43043.1																																																																																			.	.	.	none		0.602	MTMR14-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338435.1	NM_022485		-	9730673	C	-	9730673	7	5	246	1	0	1	0	1	0	0	0	0	9949	855	30	0	1402	0	MTMR14	3	9730673	Frame_Shift_Del	DEL	C	TCGA-SX-A7SL-01A-11D-A34Z-10		9730673	188291757	16	15180											
ATP2B2	491	hgsc.bcm.edu	37	chr3	10400378	10400378	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggccctggggcctacctcTggccgcaccgggtcctcgat	3	8	13	17	3	1	0	0	0	1	0	3	1	2	0	6	5	1	1	6	5	1	1			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr3:10400378T>C	ENST00000352432.4	-	13	2202	c.2133A>G	c.(2131-2133)ccA>ccG	p.P711P	ATP2B2_ENST00000360273.2_Silent_p.P711P|ATP2B2_ENST00000343816.4_Silent_p.P697P|ATP2B2_ENST00000383800.4_Silent_p.P666P|ATP2B2_ENST00000397077.1_Silent_p.P666P			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	711					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						GGCCTACCTCTGGCCGCACCG	0.622																																					p.P711P	Ovarian(125;1619 1709 15675 19819 38835)	Atlas-SNP	.											.	ATP2B2	304	.	0			c.A2133G						PASS	.						34	27	30					3																	10400378		2203	4300	6503	SO:0001819	synonymous_variant	491	exon14			TACCTCTGGCCGC	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"ATPases / P-type"	815	protein-coding gene	gene with protein product	"plasma membrane Ca2+ pump 2", "plasma membrane calcium-transporting ATPase 2"	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.2133A>G	chr3.hg19:g.10400378T>C		61.0	0.0	.		66.0	30.0	.	NM_001001331	O00766|Q12994|Q16818	Silent	SNP	ENST00000352432.4	hg19	CCDS33701.1																																																																																			.	.	.	none		0.622	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683		C	10400378	T	C	10400378	2	2	246	1	0	0	0	0	0	0	0	1	1140	1567	55	3		3	ATP2B2	3	10400378	Silent	SNP	T	TCGA-SX-A7SL-01A-11D-A34Z-10	669705	10400378	187622052	17	15181											
LRRC58	116064	hgsc.bcm.edu	37	chr3	120050190	120050190	+	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	acacaagtagtgcatcagtgGgaggcgatacttcccacaga	13	7	11	10	1	1	1	1	0	0	1	2	3	2	2	1	2	2	2	1	2	3	3			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr3:120050190G>A	ENST00000295628.3	-	4	1068	c.973C>T	c.(973-975)Cca>Tca	p.P325S		NM_001099678.1	NP_001093148.1	Q96CX6	LRC58_HUMAN	leucine rich repeat containing 58	325										large_intestine(2)|lung(5)	7				GBM - Glioblastoma multiforme(114;0.147)		TGCATCAGTGGGAGGCGATAC	0.438																																					p.P325S		Atlas-SNP	.											.	LRRC58	18	.	0			c.C973T						PASS	.						83	83	83					3																	120050190		1928	4134	6062	SO:0001583	missense	116064	exon4			TCAGTGGGAGGCG	BC013757	CCDS46892.1	3q13.33	2006-01-06			ENSG00000163428	ENSG00000163428			26968	protein-coding gene	gene with protein product							Standard	NM_001099678		Approved		uc003edr.2	Q96CX6	OTTHUMG00000159407	ENST00000295628.3:c.973C>T	chr3.hg19:g.120050190G>A	ENSP00000295628:p.Pro325Ser	276.0	0.0	.		237.0	119.0	.	NM_001099678		Missense_Mutation	SNP	ENST00000295628.3	hg19	CCDS46892.1	.	.	.	.	.	.	.	.	.	.	G	32	5.106531	0.94292	.	.	ENSG00000163428	ENST00000295628	T	0.55052	0.54	5.61	5.61	0.85477	.	0.047934	0.85682	D	0.000000	T	0.74397	0.3711	M	0.88377	2.95	0.80722	D	1	D	0.71674	0.998	P	0.57425	0.82	T	0.79999	-0.1566	10	0.87932	D	0	-10.0529	18.612	0.91288	0.0:0.0:1.0:0.0	.	325	Q96CX6	LRC58_HUMAN	S	325	ENSP00000295628:P325S	ENSP00000295628:P325S	P	-	1	0	LRRC58	121532880	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.768000	0.98965	2.638000	0.89438	0.655000	0.94253	CCA	.	.	.	none		0.438	LRRC58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355142.1	XM_057296		A	120050190	G	A	120050190	3	1	246	1	0	0	0	0	1	0	0	0	9021	1232	43	2	146	2	LRRC58	3	120050190	Missense_Mutation	SNP	G	TCGA-SX-A7SL-01A-11D-A34Z-10	109649812	120050190	77972240	18	15182											
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121435943	121435943	+	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	tttccacagtgttcctcaaaGtattatgctcagcttccatc	9	15	5	12	0	2	0	2	0	0	0	6	0	5	0	3	0	2	4	3	0	3	5			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr3:121435943G>T	ENST00000340645.5	-	9	1039	c.914C>A	c.(913-915)aCt>aAt	p.T305N	GOLGB1_ENST00000393667.3_Missense_Mutation_p.T310N	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	305					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)		GTTCCTCAAAGTATTATGCTC	0.378																																					p.T310N		Atlas-SNP	.											.	GOLGB1	319	.	0			c.C929A						PASS	.						76	75	75					3																	121435943		2203	4300	6503	SO:0001583	missense	2804	exon9			CTCAAAGTATTAT	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.914C>A	chr3.hg19:g.121435943G>T	ENSP00000341848:p.Thr305Asn	156.0	0.0	.		150.0	62.0	.	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	hg19	CCDS3004.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.33|10.33	1.320829|1.320829	0.23994|0.23994	.|.	.|.	ENSG00000173230|ENSG00000173230	ENST00000489400|ENST00000340645;ENST00000393667;ENST00000494517;ENST00000426235	.|T;T;T	.|0.23552	.|2.53;2.53;1.9	5.93|5.93	2.19|2.19	0.27852|0.27852	.|.	.|0.485196	.|0.20990	.|N	.|0.082042	T|T	0.30634|0.30634	0.0771|0.0771	L|L	0.45137|0.45137	1.4|1.4	0.24072|0.24072	N|N	0.995973|0.995973	.|D;D;D;D;D	.|0.67145	.|0.996;0.988;0.996;0.988;0.978	.|P;P;P;P;P	.|0.58266	.|0.834;0.836;0.834;0.756;0.675	T|T	0.11891|0.11891	-1.0569|-1.0569	5|10	.|0.20046	.|T	.|0.44	.|.	8.3021|8.3021	0.32021|0.32021	0.3197:0.0:0.6803:0.0|0.3197:0.0:0.6803:0.0	.|.	.|230;269;310;310;305	.|F1T0J2;E7EU81;E7EP74;B2ZZ91;Q14789	.|.;.;.;.;GOGB1_HUMAN	I|N	176|305;310;269;117	.|ENSP00000341848:T305N;ENSP00000377275:T310N;ENSP00000418231:T269N	.|ENSP00000341848:T305N	L|T	-|-	1|2	0|0	GOLGB1|GOLGB1	122918633|122918633	0.797000|0.797000	0.28877|0.28877	0.838000|0.838000	0.33150|0.33150	0.211000|0.211000	0.24417|0.24417	1.008000|1.008000	0.29872|0.29872	0.440000|0.440000	0.26502|0.26502	0.555000|0.555000	0.69702|0.69702	CTT|ACT	.	.	.	none		0.378	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		T	121435943	G	T	121435943	3	4	246	1	0	0	0	0	1	0	0	0	6572	1029	36	4	8921	4	GOLGB1	3	121435943	Missense_Mutation	SNP	G	TCGA-SX-A7SL-01A-11D-A34Z-10	1385753	121435943	76586487	19	15183											
PDIA5	10954	hgsc.bcm.edu	37	chr3	122880182	122880182	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctagattgcctgtgccgcTgttgactgtgtcaaagacaa	9	12	10	10	1	1	3	1	1	0	2	2	3	2	3	3	0	2	2	3	0	3	3			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr3:122880182T>C	ENST00000316218.7	+	16	1454	c.1359T>C	c.(1357-1359)gcT>gcC	p.A453A	PDIA5_ENST00000467157.1_3'UTR	NM_006810.3	NP_006801.1	Q14554	PDIA5_HUMAN	protein disulfide isomerase family A, member 5	453	Thioredoxin 3. {ECO:0000255|PROSITE- ProRule:PRU00691}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|oxidation-reduction process (GO:0055114)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	oxidoreductase activity (GO:0016491)|protein disulfide isomerase activity (GO:0003756)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	21				GBM - Glioblastoma multiforme(114;0.0427)		CCTGTGCCGCTGTTGACTGTG	0.547																																					p.A453A		Atlas-SNP	.											.	PDIA5	66	.	0			c.T1359C						PASS	.						100	88	92					3																	122880182		2203	4300	6503	SO:0001819	synonymous_variant	10954	exon16			TGCCGCTGTTGAC	AK054963	CCDS3020.1	3q21.1	2009-11-20	2005-06-29		ENSG00000065485	ENSG00000065485	5.3.4.1	"Protein disulfide isomerases"	24811	protein-coding gene	gene with protein product			"protein disulfide isomerase-associated 5"			7556671	Standard	NM_006810		Approved	PDIR, FLJ30401	uc003egc.2	Q14554	OTTHUMG00000159558	ENST00000316218.7:c.1359T>C	chr3.hg19:g.122880182T>C		54.0	0.0	.		45.0	32.0	.	NM_006810	D3DN95|Q9BV43	Silent	SNP	ENST00000316218.7	hg19	CCDS3020.1																																																																																			.	.	.	none		0.547	PDIA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356192.1	NM_006810		C	122880182	T	C	122880182	2	2	246	1	0	0	0	0	0	0	0	1	11678	1567	55	3		3	PDIA5	3	122880182	Silent	SNP	T	TCGA-SX-A7SL-01A-11D-A34Z-10	1444239	122880182	75142248	20	15184											
PLOD2	5352	hgsc.bcm.edu	37	chr3	145824360	145824360	+	Missense_Mutation	SNP	G	G	T																															aactttagtgtaaaagagctGatcatcatcattatcctgga																										TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr3:145824360G>T	ENST00000360060.3	-	5	751	c.574C>A	c.(574-576)Cag>Aag	p.Q192K	PLOD2_ENST00000494950.1_Missense_Mutation_p.Q137K|RP11-274H2.2_ENST00000480247.1_RNA|PLOD2_ENST00000282903.5_Missense_Mutation_p.Q192K	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	192					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)	TAAAAGAGCTGATCATCATCA	0.348																																					p.Q192K		Atlas-SNP	.											.	PLOD2	81	.	0			c.C574A						PASS	.						160	158	159					3																	145824360		2203	4300	6503	SO:0001583	missense	5352	exon5			AGAGCTGATCATC	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.574C>A	chr3.hg19:g.145824360G>T	ENSP00000353170:p.Gln192Lys	134.0	0.0	.		89.0	35.0	.	NM_182943	B3KWS3|Q59ED2|Q8N170	Missense_Mutation	SNP	ENST00000360060.3	hg19	CCDS3131.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.002651	0.93227	.	.	ENSG00000152952	ENST00000282903;ENST00000360060;ENST00000494950;ENST00000469350	T;T;T;T	0.39592	1.07;1.07;1.07;1.07	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.73984	0.3657	M	0.92169	3.28	0.80722	D	1	D;D;D	0.89917	0.994;0.998;1.0	D;D;D	0.91635	0.965;0.996;0.999	T	0.81437	-0.0933	10	0.87932	D	0	-34.5777	18.8329	0.92148	0.0:0.0:1.0:0.0	.	137;192;192	E7ETU9;O00469;O00469-2	.;PLOD2_HUMAN;.	K	192;192;137;164	ENSP00000282903:Q192K;ENSP00000353170:Q192K;ENSP00000420094:Q137K;ENSP00000419963:Q164K	ENSP00000282903:Q192K	Q	-	1	0	PLOD2	147307050	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.444000	0.97578	2.442000	0.82660	0.655000	0.94253	CAG	.	.	.	none		0.348	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935		T	145824360	G	T	145824360	3	4	246	1	0	0	0	0	1	0	0	0	12109	1299	45	4	1766	4	PLOD2	3	145824360	Missense_Mutation	SNP	G	TCGA-SX-A7SL-01A-11D-A34Z-10	22944178	145824360	52198070	21	15185	156	2									
PLOD2	5352	hgsc.bcm.edu	37	chr3	145824369	145824369	+	Missense_Mutation	SNP	C	C	T																															gtaaaagagctgatcatcatCattatcctggagattccatt																										TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr3:145824369C>T	ENST00000360060.3	-	5	742	c.565G>A	c.(565-567)Gat>Aat	p.D189N	PLOD2_ENST00000494950.1_Missense_Mutation_p.D134N|RP11-274H2.2_ENST00000480247.1_RNA|PLOD2_ENST00000282903.5_Missense_Mutation_p.D189N	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	189					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)	TGATCATCATCATTATCCTGG	0.348																																					p.D189N		Atlas-SNP	.											.	PLOD2	81	.	0			c.G565A						PASS	.						158	157	157					3																	145824369		2203	4300	6503	SO:0001583	missense	5352	exon5			CATCATCATTATC	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.565G>A	chr3.hg19:g.145824369C>T	ENSP00000353170:p.Asp189Asn	140.0	0.0	.		92.0	36.0	.	NM_182943	B3KWS3|Q59ED2|Q8N170	Missense_Mutation	SNP	ENST00000360060.3	hg19	CCDS3131.1	.	.	.	.	.	.	.	.	.	.	C	33	5.214470	0.95104	.	.	ENSG00000152952	ENST00000282903;ENST00000360060;ENST00000494950;ENST00000469350	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.63034	0.2477	M	0.86343	2.81	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.997;1.0;0.995	T	0.68614	-0.5362	10	0.54805	T	0.06	-38.5898	18.8329	0.92148	0.0:1.0:0.0:0.0	.	134;189;189	E7ETU9;O00469;O00469-2	.;PLOD2_HUMAN;.	N	189;189;134;161	ENSP00000282903:D189N;ENSP00000353170:D189N;ENSP00000420094:D134N;ENSP00000419963:D161N	ENSP00000282903:D189N	D	-	1	0	PLOD2	147307059	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.463000	0.80869	2.442000	0.82660	0.655000	0.94253	GAT	.	.	.	none		0.348	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935		T	145824369	C	T	145824369	3	4	246	1	0	0	0	0	1	0	0	0	12109	826	29	2	1775	2	PLOD2	3	145824369	Missense_Mutation	SNP	C	TCGA-SX-A7SL-01A-11D-A34Z-10	9	145824369	52198061	22	15186	156	2									
GFM1	85476	hgsc.bcm.edu	37	chr3	158362456	158362456	+	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	ggagctgcagccgtcgcggcTctggggcgcggaagggcccc	4	4	19	14	5	1	0	0	0	1	0	2	2	1	2	3	6	3	3	3	6	1	0			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr3:158362456T>G	ENST00000486715.1	+	1	390	c.33T>G	c.(31-33)gcT>gcG	p.A11A	GFM1_ENST00000264263.5_Silent_p.A11A|GFM1_ENST00000478576.1_Silent_p.A11A	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)			CCGTCGCGGCTCTGGGGCGCG	0.667											OREG0015898	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A11A		Atlas-SNP	.											.	GFM1	83	.	0			c.T33G						PASS	.						6	8	7					3																	158362456		2165	4239	6404	SO:0001819	synonymous_variant	85476	exon1			CGCGGCTCTGGGG	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.33T>G	chr3.hg19:g.158362456T>G		153.0	0.0	.	1793	140.0	68.0	.	NM_024996		Silent	SNP	ENST00000486715.1	hg19	CCDS33885.1																																																																																			.	.	.	none		0.667	GFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352271.1	NM_024996		G	158362456	T	G	158362456	2	3	246	1	0	0	0	0	0	0	0	1	6348	1538	54	5		5	GFM1	3	158362456	Silent	SNP	T	TCGA-SX-A7SL-01A-11D-A34Z-10	12538087	158362456	39659974	23	15187											
ATP8A1	10396	hgsc.bcm.edu	37	chr4	42457327	42457327	+	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	gtcctaccttggtgttgaagTccagggcattctgagatgtt	7	14	12	8	0	1	2	0	2	1	1	3	3	3	2	3	2	1	3	3	2	2	5			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr4:42457327T>A	ENST00000381668.5	-	29	3035	c.2804A>T	c.(2803-2805)gAc>gTc	p.D935V	ATP8A1_ENST00000264449.10_Missense_Mutation_p.D920V	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	935					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)	GGTGTTGAAGTCCAGGGCATT	0.443																																					p.D935V		Atlas-SNP	.											.	ATP8A1	206	.	0			c.A2804T						PASS	.						166	139	148					4																	42457327		2203	4300	6503	SO:0001583	missense	10396	exon29			TTGAAGTCCAGGG	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.2804A>T	chr4.hg19:g.42457327T>A	ENSP00000371084:p.Asp935Val	182.0	0.0	.		140.0	67.0	.	NM_006095	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Missense_Mutation	SNP	ENST00000381668.5	hg19	CCDS3466.1	.	.	.	.	.	.	.	.	.	.	T	10.20	1.284164	0.23392	.	.	ENSG00000124406	ENST00000381668;ENST00000264449	T;T	0.71341	-0.56;-0.56	5.09	5.09	0.68999	.	0.069887	0.56097	D	0.000023	T	0.59335	0.2186	L	0.28115	0.83	0.80722	D	1	B;B;B	0.11235	0.004;0.004;0.004	B;B;B	0.14023	0.01;0.007;0.007	T	0.55309	-0.8161	10	0.36615	T	0.2	.	15.1662	0.72828	0.0:0.0:0.0:1.0	.	920;935;927	Q32M35;Q9Y2Q0;E7EUK4	.;AT8A1_HUMAN;.	V	935;920	ENSP00000371084:D935V;ENSP00000264449:D920V	ENSP00000264449:D920V	D	-	2	0	ATP8A1	42152084	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.734000	0.62043	2.030000	0.59900	0.455000	0.32223	GAC	.	.	.	none		0.443	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095		A	42457327	T	A	42457327	3	1	246	1	0	0	0	0	1	0	0	0	1192	1667	58	5	726	5	ATP8A1	4	42457327	Missense_Mutation	SNP	T	TCGA-SX-A7SL-01A-11D-A34Z-10		42457327	148696949	24	15188											
UGT2A1	10941	hgsc.bcm.edu	37	chr4	70512663	70512663	+	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	catacctaaagctttactatAgtatgaatcccatgatttcc	13	14	4	10	0	0	2	0	2	0	0	2	2	2	2	3	0	3	2	3	0	8	8			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr4:70512663A>T	ENST00000503640.1	-	1	755	c.700T>A	c.(700-702)Tat>Aat	p.Y234N	UGT2A1_ENST00000286604.4_Missense_Mutation_p.Y234N|UGT2A1_ENST00000512704.1_Missense_Mutation_p.Y234N|UGT2A1_ENST00000514019.1_Missense_Mutation_p.Y234N	NM_006798.3	NP_006789.2	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A1, complex locus	234					cellular glucuronidation (GO:0052695)|detection of chemical stimulus (GO:0009593)|metabolic process (GO:0008152)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						GCTTTACTATAGTATGAATCC	0.338																																					p.Y234N		Atlas-SNP	.											.	UGT2A1	131	.	0			c.T700A						PASS	.						56	56	56					4																	70512663		2200	4298	6498	SO:0001583	missense	10941	exon2			TACTATAGTATGA	AJ006054	CCDS3529.1, CCDS58901.1, CCDS58902.1	4q13	2013-03-28	2010-12-02					"UDP glucuronosyltransferases"	12542	protein-coding gene	gene with protein product		604716	"UDP glycosyltransferase 2 family, polypeptide A1", "UDP glucuronosyltransferase 2 family, polypeptide A1"			10359671	Standard	NM_001252274		Approved		uc011caq.2	Q9Y4X1	OTTHUMG00000184942	ENST00000503640.1:c.700T>A	chr4.hg19:g.70512663A>T	ENSP00000424478:p.Tyr234Asn	75.0	0.0	.		76.0	28.0	.	NM_001252274	B4E2F4|D3GER1|D3GER2|E9PDM7|J3KNA3	Missense_Mutation	SNP	ENST00000503640.1	hg19	CCDS3529.1	.	.	.	.	.	.	.	.	.	.	A	18.05	3.538159	0.65085	.	.	ENSG00000173610	ENST00000503640;ENST00000512704;ENST00000514019;ENST00000286604	T;T;T;T	0.62232	0.08;0.04;0.08;0.08	5.78	5.78	0.91487	.	0.127268	0.56097	D	0.000040	T	0.80869	0.4706	M	0.84846	2.72	.	.	.	D;D;D;D	0.89917	1.0;1.0;0.994;0.994	D;D;D;D	0.97110	1.0;1.0;0.93;0.93	D	0.85603	0.1253	9	0.66056	D	0.02	.	14.0552	0.64764	1.0:0.0:0.0:0.0	.	234;234;234;234	E9PDM7;B4E2F4;D6RFW5;Q9Y4X1	.;.;.;UD2A1_HUMAN	N	234	ENSP00000424478:Y234N;ENSP00000421432:Y234N;ENSP00000425497:Y234N;ENSP00000286604:Y234N	ENSP00000286604:Y234N	Y	-	1	0	UGT2A1	70547252	1.000000	0.71417	0.994000	0.49952	0.733000	0.41908	7.912000	0.87465	2.215000	0.71742	0.482000	0.46254	TAT	.	.	.	none		0.338	UGT2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251554.3	NM_006798		T	70512663	A	T	70512663	3	4	246	1	0	0	0	0	1	0	0	0	16965	420	15	5	907	5	UGT2A1	4	70512663	Missense_Mutation	SNP	A	TCGA-SX-A7SL-01A-11D-A34Z-10	28055336	70512663	120641613	25	15189											
PCDH10	57575	hgsc.bcm.edu	37	chr4	134072787	134072787	+	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	atgagggcgccaacgcccagCttgcctactctatcctcgag	8	8	10	15	3	1	1	0	1	1	0	3	2	2	1	4	1	4	1	4	1	3	3			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr4:134072787C>G	ENST00000264360.5	+	1	2318	c.1492C>G	c.(1492-1494)Ctt>Gtt	p.L498V	RP11-9G1.3_ENST00000505289.1_lincRNA	NM_032961.1	NP_116586.1	Q9P2E7	PCD10_HUMAN	protocadherin 10	498	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(30)|liver(1)|lung(72)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(2)	136				LUSC - Lung squamous cell carcinoma(193;0.227)		CAACGCCCAGCTTGCCTACTC	0.587																																					p.L498V		Atlas-SNP	.											.	PCDH10	290	.	0			c.C1492G						PASS	.						59	61	60					4																	134072787		2203	4299	6502	SO:0001583	missense	57575	exon1			GCCCAGCTTGCCT	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.1492C>G	chr4.hg19:g.134072787C>G	ENSP00000264360:p.Leu498Val	125.0	0.0	.		71.0	25.0	.	NM_032961	Q4W5F6|Q96SF0	Missense_Mutation	SNP	ENST00000264360.5	hg19	CCDS34063.1	.	.	.	.	.	.	.	.	.	.	C	8.080	0.772215	0.16051	.	.	ENSG00000138650	ENST00000264360;ENST00000394248	T	0.48836	0.8	4.51	1.71	0.24356	Cadherin (4);Cadherin-like (1);	0.000000	0.35179	N	0.003395	T	0.22666	0.0547	N	0.12611	0.24	0.32518	N	0.536591	B;B	0.14012	0.007;0.009	B;B	0.23574	0.004;0.047	T	0.16958	-1.0385	10	0.13470	T	0.59	.	4.0843	0.09940	0.3205:0.4962:0.0:0.1832	.	498;498	Q9P2E7;Q96SF0	PCD10_HUMAN;.	V	498	ENSP00000264360:L498V	ENSP00000264360:L498V	L	+	1	0	PCDH10	134292237	0.927000	0.31430	0.858000	0.33744	0.998000	0.95712	1.899000	0.39818	0.127000	0.18452	0.655000	0.94253	CTT	.	.	.	none		0.587	PCDH10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000364457.2	NM_032961		G	134072787	C	G	134072787	3	3	246	1	0	0	0	0	1	0	0	0	11514	797	28	4	1494	4	PCDH10	4	134072787	Missense_Mutation	SNP	C	TCGA-SX-A7SL-01A-11D-A34Z-10	63560124	134072787	57081489	26	15190											
MAML3	55534	hgsc.bcm.edu	37	chr4	140640884	140640884	+	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	gactgactggctcagtccctGtgggaagtgctgcttggtca	6	11	14	10	0	2	1	2	1	0	0	3	3	3	2	1	3	2	3	1	3	1	1			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr4:140640884G>C	ENST00000509479.2	-	5	3866	c.3010C>G	c.(3010-3012)Cag>Gag	p.Q1004E	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)					CTCAGTCCCTGTGGGAAGTGC	0.602																																					p.Q1000E		Atlas-SNP	.											.	MAML3	192	.	0			c.C2998G						PASS	.						45	47	47					4																	140640884		2103	4232	6335	SO:0001583	missense	55534	exon6			GTCCCTGTGGGAA	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.3010C>G	chr4.hg19:g.140640884G>C	ENSP00000421180:p.Gln1004Glu	77.0	0.0	.		45.0	19.0	.	NM_018717		Missense_Mutation	SNP	ENST00000509479.2	hg19	CCDS54805.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.089751	0.76756	.	.	ENSG00000196782	ENST00000509479;ENST00000538400	T	0.38240	1.15	4.86	4.86	0.63082	.	0.147180	0.45126	D	0.000383	T	0.61223	0.2330	M	0.81942	2.565	0.80722	D	1	D;D	0.54207	0.965;0.965	P;P	0.61201	0.885;0.885	T	0.66196	-0.5984	10	0.56958	D	0.05	.	18.3673	0.90396	0.0:0.0:1.0:0.0	.	1004;1000	E7EVW8;Q96JK9	.;MAML3_HUMAN	E	1004;311	ENSP00000421180:Q1004E	ENSP00000421180:Q1004E	Q	-	1	0	MAML3	140860334	1.000000	0.71417	0.979000	0.43373	0.959000	0.62525	7.904000	0.87408	2.401000	0.81631	0.591000	0.81541	CAG	.	.	.	none		0.602	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			C	140640884	G	C	140640884	3	2	246	1	0	0	0	0	1	0	0	0	9214	1386	48	4	410	4	MAML3	4	140640884	Missense_Mutation	SNP	G	TCGA-SX-A7SL-01A-11D-A34Z-10	6568097	140640884	50513392	27	15191											
SRPK1	6732	hgsc.bcm.edu	37	chr6	35803124	35803125	+	Missense_Mutation	DNP	GC	GC	AT																															ggagacactcggcggcagtgGctctcttctcagggatcagc																										TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr6:35803124_35803125GC>AT	ENST00000373825.2	-	16	2209_2210	c.1924_1925GC>AT	c.(1924-1926)GCc>ATc	p.A642I	SRPK1_ENST00000423325.2_Missense_Mutation_p.A626I|SRPK1_ENST00000373822.1_Missense_Mutation_p.A534I					SRSF protein kinase 1											endometrium(2)|large_intestine(10)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21						GGCGGCAGTGGCTCTCTTCTCA	0.564																																					p.A642V|p.A642T	NSCLC(31;67 978 16289 24856 26454)	Atlas-SNP	.											.	SRPK1	61	.	0			c.C1925T|c.G1924A						PASS	.																																			SO:0001583	missense	6732	exon16			GCAGTGGCTCTCT|CAGTGGCTCTCTT	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.1924_1925delinsAT	chr6.hg19:g.35803124_35803125delinsAT	ENSP00000362931:p.Ala642Ile	93.0|94.0	0.0	.		25.0	23.0	.	NM_003137		Missense_Mutation	SNP	ENST00000373825.2	hg19	CCDS47415.1																																																																																			.	.	.	none		0.564	SRPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040319.3	NM_003137		AT	35803125	GC	AT	35803124	3	1	246	1	0	0	0	0	1	0	0	0	15171	1203	42	2	46	2	SRPK1	6	35803124	Missense_Mutation	DNP	GC	TCGA-SX-A7SL-01A-11D-A34Z-10		35803124	135311943	28	15192											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51913390	51913390	+	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	accaggaccagtccagatccCtcttctgttccttcagtggg	7	11	9	14	0	3	1	1	0	2	1	6	2	6	2	5	2	0	1	5	2	0	3			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr6:51913390C>G	ENST00000371117.3	-	23	2582	c.2307G>C	c.(2305-2307)gaG>gaC	p.E769D	PKHD1_ENST00000340994.4_Missense_Mutation_p.E769D	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	769					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)					GTCCAGATCCCTCTTCTGTTC	0.522																																					p.E769D		Atlas-SNP	.											PKHD1_ENST00000340994,NS,carcinoma,0,2	PKHD1	927	.	0			c.G2307C						PASS	.						114	95	101					6																	51913390		2203	4300	6503	SO:0001583	missense	5314	exon23			AGATCCCTCTTCT	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.2307G>C	chr6.hg19:g.51913390C>G	ENSP00000360158:p.Glu769Asp	70.0	0.0	.		34.0	26.0	.	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	11.80	1.746328	0.30955	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.87571	-2.06;-2.27	5.65	0.145	0.14829	.	0.742423	0.12926	N	0.427779	T	0.56202	0.1969	L	0.37850	1.14	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.001	T	0.39482	-0.9612	10	0.19590	T	0.45	.	1.7503	0.02970	0.2806:0.0806:0.1461:0.4928	.	769;769	P08F94-2;P08F94	.;PKHD1_HUMAN	D	769	ENSP00000360158:E769D;ENSP00000341097:E769D	ENSP00000341097:E769D	E	-	3	2	PKHD1	52021349	0.002000	0.14202	0.000000	0.03702	0.349000	0.29174	0.845000	0.27668	-0.198000	0.10333	-0.302000	0.09304	GAG	.	.	.	none		0.522	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		G	51913390	C	G	51913390	3	3	246	1	0	0	0	0	1	0	0	0	11978	680	24	4	10136	4	PKHD1	6	51913390	Missense_Mutation	SNP	C	TCGA-SX-A7SL-01A-11D-A34Z-10	16110266	51913390	119201677	29	15193											
CD164	8763	hgsc.bcm.edu	37	chr6	109699166	109699166	+	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	tgttgagttatgtgaacaatAgctctcatctgttggggggc	8	14	13	6	0	2	2	1	2	2	0	3	2	2	2	0	3	2	4	0	3	4	4			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr6:109699166A>T	ENST00000310786.4	-	3	333	c.268T>A	c.(268-270)Tat>Aat	p.Y90N	CD164_ENST00000275080.7_Missense_Mutation_p.Y90N|CD164_ENST00000506649.1_5'UTR|CD164_ENST00000368961.5_Missense_Mutation_p.Y90N|CD164_ENST00000413644.2_Missense_Mutation_p.Y90N|CD164_ENST00000504373.1_Missense_Mutation_p.Y56N|CD164_ENST00000324953.5_Missense_Mutation_p.Y90N|CD164_ENST00000512821.1_Missense_Mutation_p.Y90N	NM_001142404.1|NM_006016.4	NP_001135876.1|NP_006007.2	Q04900	MUC24_HUMAN	CD164 molecule, sialomucin	90					cell adhesion (GO:0007155)|hemopoiesis (GO:0030097)|heterophilic cell-cell adhesion (GO:0007157)|immune response (GO:0006955)|multicellular organismal development (GO:0007275)|muscle organ development (GO:0007517)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|plasma membrane (GO:0005886)				breast(1)|lung(2)	3		all_cancers(87;4.65e-22)|all_epithelial(87;2.54e-20)|all_lung(197;1.6e-05)|Lung NSC(302;2.92e-05)|Colorectal(196;3.46e-05)|Ovarian(999;0.0175)		Epithelial(106;7.83e-46)|all cancers(137;1.15e-45)|OV - Ovarian serous cystadenocarcinoma(136;2.89e-26)|BRCA - Breast invasive adenocarcinoma(108;0.00128)|GBM - Glioblastoma multiforme(226;0.16)		TGTGAACAATAGCTCTCATCT	0.443																																					p.Y90N		Atlas-SNP	.											.	CD164	10	.	0			c.T268A						PASS	.						115	104	108					6																	109699166		2203	4300	6503	SO:0001583	missense	8763	exon3			AACAATAGCTCTC	AF106518	CCDS5073.1, CCDS47462.1, CCDS47463.1, CCDS47464.1, CCDS47465.1	6q21	2014-09-05	2006-03-28		ENSG00000135535	ENSG00000135535		"CD molecules"	1632	protein-coding gene	gene with protein product		603356	"CD164 antigen, sialomucin"			9680353, 9763543	Standard	NM_006016		Approved	MUC-24, MGC-24	uc003pte.3	Q04900	OTTHUMG00000015339	ENST00000310786.4:c.268T>A	chr6.hg19:g.109699166A>T	ENSP00000309376:p.Tyr90Asn	34.0	0.0	.		17.0	12.0	.	NM_006016	B4DQ85|E1P5E7|E1P5E8|E1P5E9|O95413|Q5JSU6|Q9BPV0|Q9NR26	Missense_Mutation	SNP	ENST00000310786.4	hg19	CCDS5073.1	.	.	.	.	.	.	.	.	.	.	A	17.89	3.498712	0.64298	.	.	ENSG00000135535	ENST00000413644;ENST00000368961;ENST00000324953;ENST00000310786;ENST00000275080;ENST00000512821;ENST00000504373	T;T;T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86;0.86;0.86	4.65	1.74	0.24563	.	0.788335	0.11567	N	0.551169	T	0.30759	0.0775	L	0.52573	1.65	0.29687	N	0.841213	P;P;P;P;P	0.46512	0.739;0.741;0.879;0.78;0.739	P;P;P;P;B	0.50708	0.63;0.528;0.648;0.511;0.377	T	0.16305	-1.0407	10	0.62326	D	0.03	-6.0273	3.4508	0.07498	0.6908:0.0:0.1178:0.1914	.	90;90;90;90;90	Q04900-5;Q04900-3;Q04900-4;Q04900;Q04900-2	.;.;.;MUC24_HUMAN;.	N	90;90;90;90;90;90;56	ENSP00000402237:Y90N;ENSP00000357957:Y90N;ENSP00000314177:Y90N;ENSP00000309376:Y90N;ENSP00000275080:Y90N;ENSP00000427546:Y90N;ENSP00000422999:Y56N	ENSP00000275080:Y90N	Y	-	1	0	CD164	109805859	0.903000	0.30736	0.976000	0.42696	0.351000	0.29236	0.322000	0.19576	0.786000	0.33708	0.460000	0.39030	TAT	.	.	.	none		0.443	CD164-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041742.1	NM_006016		T	109699166	A	T	109699166	3	4	246	1	0	0	0	0	1	0	0	0	2971	420	15	5	392	5	CD164	6	109699166	Missense_Mutation	SNP	A	TCGA-SX-A7SL-01A-11D-A34Z-10	57785776	109699166	61415901	30	15194											
MIOS	54468	hgsc.bcm.edu	37	chr7	7612994	7612994	+	Frame_Shift_Del	DEL	T	T	-																															agtaatattattagattgtaTgatatgcagcatacacccac																										TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr7:7612994delT	ENST00000340080.4	+	4	1309	c.888delT	c.(886-888)tatfs	p.Y296fs	MIOS_ENST00000405785.1_Frame_Shift_Del_p.Y296fs	NM_019005.3	NP_061878.3	Q9NXC5	MIO_HUMAN	missing oocyte, meiosis regulator, homolog (Drosophila)	296						lysosomal membrane (GO:0005765)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TTAGATTGTATGATATGCAGC	0.408																																					p.Y296fs		Atlas-Indel,Pindel	.											.	MIOS	68	.	0			c.887delA						PASS	.						101	96	98					7																	7612994		1907	4106	6013	SO:0001589	frameshift_variant	54468	exon4			.		CCDS43554.1	7p21.3	2011-09-12			ENSG00000164654	ENSG00000164654			21905	protein-coding gene	gene with protein product	"WD repeat-containing protein mio"	615359				14973288	Standard	NM_019005		Approved	FLJ20323	uc003srf.3	Q9NXC5	OTTHUMG00000152440	ENST00000340080.4:c.888delT	chr7.hg19:g.7612994delT	ENSP00000339881:p.Tyr296fs	104.0	0.0	0		103.0	41.0	0.398058	NM_019005	B2RTV6|O75216|Q7L551|Q9H092	Frame_Shift_Del	DEL	ENST00000340080.4	hg19	CCDS43554.1																																																																																			.	.	.	none		0.408	MIOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326218.1	NM_019005		-	7612994	T	-	7612994	7	5	246	1	0	1	0	1	0	0	0	0	9596	1471	51	0	890	0	MIOS	7	7612994	Frame_Shift_Del	DEL	T	TCGA-SX-A7SL-01A-11D-A34Z-10		7612994	151525669	31	15195											
ABCA13	154664	hgsc.bcm.edu	37	chr7	48431545	48431545	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgacggggctccaccctccCacttctggaaccatcatcat	8	10	7	16	1	3	1	2	1	1	0	5	2	5	2	4	3	1	1	4	3	1	2	rs189672968	byFrequency	TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr7:48431545C>T	ENST00000435803.1	+	38	11706	c.11682C>T	c.(11680-11682)ccC>ccT	p.P3894P		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	3894	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TCCACCCTCCCACTTCTGGAA	0.522																																					p.P3894P		Atlas-SNP	.											.	ABCA13	1192	.	0			c.C11682T						PASS	.						78	78	78					7																	48431545		2002	4160	6162	SO:0001819	synonymous_variant	154664	exon38			CCCTCCCACTTCT	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.11682C>T	chr7.hg19:g.48431545C>T		123.0	0.0	.		88.0	8.0	.	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	hg19	CCDS47584.1																																																																																			.	C|0.999;G|0.001	.	alt		0.522	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48431545	C	T	48431545	2	4	246	1	0	0	0	0	0	0	0	1	31	581	21	2		2	ABCA13	7	48431545	Silent	SNP	C	TCGA-SX-A7SL-01A-11D-A34Z-10	40818551	48431545	110707118	32	15196											
MCPH1	79648	hgsc.bcm.edu	37	chr8	6266814	6266814	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tttcagatgtagtggcctatGttgaagtgtggtcatccaat	9	15	11	6	0	2	2	2	1	0	1	3	2	3	2	2	2	0	2	2	2	4	4			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr8:6266814G>A	ENST00000344683.5	+	2	113	c.37G>A	c.(37-39)Gtt>Att	p.V13I	RP11-115C21.2_ENST00000500118.2_RNA|MCPH1_ENST00000522905.1_Missense_Mutation_p.V13I|RP11-115C21.2_ENST00000523225.1_RNA|MCPH1_ENST00000519480.1_Missense_Mutation_p.V13I|RP11-115C21.2_ENST00000606853.1_RNA	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	13	BRCT 1. {ECO:0000255|PROSITE- ProRule:PRU00033}.				cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)		AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		AGTGGCCTATGTTGAAGTGTG	0.363																																					p.V13I	Colon(95;1448 1467 8277 34473 35819)	Atlas-SNP	.											.	MCPH1	65	.	0			c.G37A						PASS	.						170	158	162					8																	6266814		1898	4124	6022	SO:0001583	missense	79648	exon2			GCCTATGTTGAAG	AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"BRCT-repeat inhibitor of TERT expression 1"	607117	"microcephaly, primary autosomal recessive 1"			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.37G>A	chr8.hg19:g.6266814G>A	ENSP00000342924:p.Val13Ile	251.0	0.0	.		199.0	81.0	.	NM_001172575	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Missense_Mutation	SNP	ENST00000344683.5	hg19	CCDS43689.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.856648	0.91433	.	.	ENSG00000147316	ENST00000344683;ENST00000519480;ENST00000522905	D;D;D	0.84370	-1.84;-1.84;-1.84	5.33	5.33	0.75918	BRCT (3);	0.000000	0.64402	D	0.000004	D	0.92011	0.7469	M	0.74881	2.28	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.985;0.998;0.985	D	0.92820	0.6271	10	0.87932	D	0	-22.1517	16.5324	0.84365	0.0:0.0:1.0:0.0	.	13;13;13	E9PH63;Q8NEM0;E9PGU5	.;MCPH1_HUMAN;.	I	13	ENSP00000342924:V13I;ENSP00000430962:V13I;ENSP00000430768:V13I	ENSP00000342924:V13I	V	+	1	0	MCPH1	6254222	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.390000	0.73204	2.488000	0.83962	0.591000	0.81541	GTT	.	.	.	none		0.363	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596		A	6266814	G	A	6266814	3	1	246	1	0	0	0	0	1	0	0	0	9405	1377	48	2	43	2	MCPH1	8	6266814	Missense_Mutation	SNP	G	TCGA-SX-A7SL-01A-11D-A34Z-10		6266814	140097208	33	15197											
WWP1	11059	hgsc.bcm.edu	37	chr8	87410646	87410646	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acaaactggtgaattgacagTtgtgcttgatggattggtga	11	13	13	4	0	0	4	0	4	0	0	0	5	0	5	0	3	2	2	0	3	2	4			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr8:87410646T>C	ENST00000517970.1	+	6	717	c.410T>C	c.(409-411)gTt>gCt	p.V137A	WWP1_ENST00000349423.2_Intron|WWP1_ENST00000341922.2_Intron|WWP1_ENST00000265428.4_Missense_Mutation_p.V137A	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	137					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						GAATTGACAGTTGTGCTTGAT	0.328																																					p.V137A		Atlas-SNP	.											.	WWP1	97	.	0			c.T410C						PASS	.						79	84	82					8																	87410646		2203	4299	6502	SO:0001583	missense	11059	exon6			TGACAGTTGTGCT	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.410T>C	chr8.hg19:g.87410646T>C	ENSP00000427793:p.Val137Ala	234.0	0.0	.		204.0	109.0	.	NM_007013	O00307|Q5YLC1|Q96BP4	Missense_Mutation	SNP	ENST00000517970.1	hg19	CCDS6242.1	.	.	.	.	.	.	.	.	.	.	T	18.88	3.718480	0.68844	.	.	ENSG00000123124	ENST00000517970;ENST00000265428	T;T	0.68765	-0.35;-0.35	5.69	5.69	0.88448	C2 calcium/lipid-binding domain, CaLB (1);	0.487699	0.21187	N	0.078705	T	0.68393	0.2996	L	0.58101	1.795	0.80722	D	1	P	0.51351	0.944	P	0.46850	0.529	T	0.66736	-0.5848	10	0.28530	T	0.3	.	15.9391	0.79739	0.0:0.0:0.0:1.0	.	137	Q9H0M0	WWP1_HUMAN	A	137	ENSP00000427793:V137A;ENSP00000265428:V137A	ENSP00000265428:V137A	V	+	2	0	WWP1	87479762	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.829000	0.69316	2.165000	0.68154	0.528000	0.53228	GTT	.	.	.	none		0.328	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013		C	87410646	T	C	87410646	3	2	246	1	0	0	0	0	1	0	0	0	17427	1725	60	3	424	3	WWP1	8	87410646	Missense_Mutation	SNP	T	TCGA-SX-A7SL-01A-11D-A34Z-10	81143832	87410646	58953376	34	15198											
PARP10	84875	hgsc.bcm.edu	37	chr8	145057194	145057194	+	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	cggtgttctctgccagacgcTccaggttgttccagggcccc	4	10	12	15	2	1	1	0	0	1	1	4	1	3	1	5	3	1	4	5	3	0	3			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr8:145057194T>A	ENST00000313028.7	-	9	2556	c.2462A>T	c.(2461-2463)gAg>gTg	p.E821V	PARP10_ENST00000525773.1_Missense_Mutation_p.E833V|PARP10_ENST00000524918.1_Missense_Mutation_p.E812V|PARP10_ENST00000533665.1_5'Flank	NM_032789.3	NP_116178.2	Q53GL7	PAR10_HUMAN	poly (ADP-ribose) polymerase family, member 10	821	Myc binding.|PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of gene expression (GO:0010629)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of protein K63-linked ubiquitination (GO:1900045)|negative regulation of viral genome replication (GO:0045071)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein poly-ADP-ribosylation (GO:0070212)|regulation of chromatin assembly (GO:0010847)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(2)	27	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;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TGCCAGACGCTCCAGGTTGTT	0.657																																					p.E821V		Atlas-SNP	.											.	PARP10	57	.	0			c.A2462T						PASS	.						56	60	59					8																	145057194		2203	4300	6503	SO:0001583	missense	84875	exon9			AGACGCTCCAGGT	AK027370	CCDS34960.1	8q24	2010-02-16				ENSG00000178685		"Poly (ADP-ribose) polymerases"	25895	protein-coding gene	gene with protein product		609564				15273990	Standard	NM_032789		Approved	FLJ14464	uc003zal.4	Q53GL7		ENST00000313028.7:c.2462A>T	chr8.hg19:g.145057194T>A	ENSP00000325618:p.Glu821Val	36.0	0.0	.		27.0	11.0	.	NM_032789	Q8N2I0|Q8WV05|Q96CH7|Q96K72	Missense_Mutation	SNP	ENST00000313028.7	hg19	CCDS34960.1	.	.	.	.	.	.	.	.	.	.	T	14.26	2.483160	0.44147	.	.	ENSG00000178685	ENST00000524918;ENST00000534861;ENST00000313028;ENST00000525773	T;T;T	0.15834	2.39;2.39;2.39	5.09	3.92	0.45320	Poly(ADP-ribose) polymerase, catalytic domain (2);	0.118179	0.37955	N	0.001871	T	0.21387	0.0515	N	0.17631	0.505	0.33963	D	0.645837	D;D	0.65815	0.995;0.995	D;D	0.68943	0.961;0.961	T	0.22521	-1.0214	10	0.23891	T	0.37	.	9.28	0.37722	0.0:0.0:0.1818:0.8182	.	833;821	E9PNI7;Q53GL7	.;PAR10_HUMAN	V	812;527;821;833	ENSP00000431620:E812V;ENSP00000325618:E821V;ENSP00000434776:E833V	ENSP00000325618:E821V	E	-	2	0	PARP10	145129182	0.009000	0.17119	0.729000	0.30791	0.249000	0.25844	0.114000	0.15520	0.871000	0.35750	0.451000	0.29950	GAG	.	.	.	none		0.657	PARP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383866.1	NM_032789		A	145057194	T	A	145057194	3	1	246	1	0	0	0	0	1	0	0	0	11462	1551	54	5	627	5	PARP10	8	145057194	Missense_Mutation	SNP	T	TCGA-SX-A7SL-01A-11D-A34Z-10	57646548	145057194	1306828	35	15199											
DAPK1	1612	hgsc.bcm.edu	37	chr9	90312114	90312114	+	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	ccttgtcccagttgaagaacCcataggtgagctaagtccct	10	10	9	12	0	0	3	0	2	0	1	2	3	2	3	4	1	2	2	4	1	4	4			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr9:90312114C>G	ENST00000408954.3	+	22	2941	c.2606C>G	c.(2605-2607)cCc>cGc	p.P869R	DAPK1_ENST00000491893.1_Intron|DAPK1_ENST00000472284.1_Missense_Mutation_p.P869R|DAPK1_ENST00000469640.2_Missense_Mutation_p.P869R|DAPK1_ENST00000358077.5_Missense_Mutation_p.P869R	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	869					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						GTTGAAGAACCCATAGGTGAG	0.527									Chronic Lymphocytic Leukemia, Familial Clustering of																												p.P869R		Atlas-SNP	.											.	DAPK1	329	.	0			c.C2606G						PASS	.						82	78	79					9																	90312114		1995	4162	6157	SO:0001583	missense	1612	exon22	Familial Cancer Database	Familial CLL	AAGAACCCATAGG	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.2606C>G	chr9.hg19:g.90312114C>G	ENSP00000386135:p.Pro869Arg	234.0	0.0	.		180.0	85.0	.	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	hg19	CCDS43842.1	.	.	.	.	.	.	.	.	.	.	C	13.63	2.294346	0.40594	.	.	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954	T;T;T;T	0.70516	-0.29;-0.29;-0.49;-0.29	5.5	4.61	0.57282	.	0.000000	0.52532	D	0.000080	T	0.62109	0.2401	L	0.46157	1.445	0.40576	D	0.981348	B	0.23650	0.089	B	0.17098	0.017	T	0.63620	-0.6596	10	0.72032	D	0.01	.	9.8246	0.40903	0.1396:0.7875:0.0:0.0729	.	869	P53355	DAPK1_HUMAN	R	869	ENSP00000350785:P869R;ENSP00000417076:P869R;ENSP00000418885:P869R;ENSP00000386135:P869R	ENSP00000350785:P869R	P	+	2	0	DAPK1	89501934	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.045000	0.41250	1.559000	0.49555	0.655000	0.94253	CCC	.	.	.	none		0.527	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938		G	90312114	C	G	90312114	3	3	246	1	0	0	0	0	1	0	0	0	4237	623	22	4	2688	4	DAPK1	9	90312114	Missense_Mutation	SNP	C	TCGA-SX-A7SL-01A-11D-A34Z-10		90312114	50901317	36	15200											
LMX1B	4010	hgsc.bcm.edu	37	chr9	129456044	129456044	+	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	gatgaagaagctggcgcggcGgcaccagcagcagcaggagc	11	2	17	11	3	0	2	0	1	0	1	0	4	0	3	1	4	5	5	1	4	2	0			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr9:129456044G>C	ENST00000373474.4	+	6	846	c.839G>C	c.(838-840)cGg>cCg	p.R280P	LMX1B_ENST00000425646.2_Missense_Mutation_p.R257P|LMX1B_ENST00000526117.1_Missense_Mutation_p.R280P|LMX1B_ENST00000561065.1_Missense_Mutation_p.R257P|LMX1B_ENST00000355497.5_Missense_Mutation_p.R280P			O60663	LMX1B_HUMAN	LIM homeobox transcription factor 1, beta	280					cell proliferation (GO:0008283)|central nervous system neuron development (GO:0021954)|cerebellum morphogenesis (GO:0021587)|collagen fibril organization (GO:0030199)|dopaminergic neuron differentiation (GO:0071542)|dorsal/ventral pattern formation (GO:0009953)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|midbrain development (GO:0030901)|multicellular organismal development (GO:0007275)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|organ growth (GO:0035265)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|trabecular meshwork development (GO:0002930)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	15						CTGGCGCGGCGGCACCAGCAG	0.741									Nail-Patella Syndrome																												p.R280P	Pancreas(110;1796 2278 18357 20466)	Atlas-SNP	.											.	LMX1B	86	.	0			c.G839C						PASS	.						4	4	4					9																	129456044		1996	3909	5905	SO:0001583	missense	4010	exon6	Familial Cancer Database	Osteo-Onychodysplasia, Turner-Kieser syndrome, Fong disease	CGCGGCGGCACCA	U77457	CCDS6866.1, CCDS6866.2, CCDS55342.1, CCDS55343.1	9q33.3	2011-06-20			ENSG00000136944	ENSG00000136944		"Homeoboxes / LIM class"	6654	protein-coding gene	gene with protein product		602575		NPS1		9441763, 9590287	Standard	NM_002316		Approved		uc004bqj.3	O60663	OTTHUMG00000020692	ENST00000373474.4:c.839G>C	chr9.hg19:g.129456044G>C	ENSP00000362573:p.Arg280Pro	16.0	0.0	.		21.0	13.0	.	NM_001174146	F8W7W6|O75463|Q5JU95|Q6ISC9	Missense_Mutation	SNP	ENST00000373474.4	hg19	CCDS55342.1	.	.	.	.	.	.	.	.	.	.	G	17.97	3.517624	0.64634	.	.	ENSG00000136944	ENST00000526117;ENST00000373474;ENST00000355497;ENST00000425646	T;T;T;T	0.78246	-1.16;-1.16;-1.07;-1.16	4.56	3.65	0.41850	Homeobox (1);	0.000000	0.85682	D	0.000000	T	0.76543	0.4002	M	0.66939	2.045	0.80722	D	1	P;B;P	0.37015	0.578;0.369;0.502	B;B;B	0.39068	0.289;0.112;0.224	T	0.77167	-0.2687	10	0.62326	D	0.03	.	12.7907	0.57533	0.0:0.0:0.8352:0.1648	.	257;257;280	B7ZLH2;O60663;F8VYP0	.;LMX1B_HUMAN;.	P	280;280;280;257	ENSP00000436930:R280P;ENSP00000362573:R280P;ENSP00000347684:R280P;ENSP00000390923:R257P	ENSP00000347684:R280P	R	+	2	0	LMX1B	128495865	1.000000	0.71417	0.532000	0.27989	0.961000	0.63080	6.065000	0.71176	0.867000	0.35654	0.561000	0.74099	CGG	.	.	.	none		0.741	LMX1B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054123.2			C	129456044	G	C	129456044	3	2	246	1	0	0	0	0	1	0	0	0	8869	1116	39	4	861	4	LMX1B	9	129456044	Missense_Mutation	SNP	G	TCGA-SX-A7SL-01A-11D-A34Z-10	39143930	129456044	11757387	37	15201											
SEC16A	9919	hgsc.bcm.edu	37	chr9	139360854	139360854	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctctgtgcggatcggggtcAtcgtcaaaactccccgtgaa	8	10	11	12	4	3	1	2	1	1	0	7	2	4	2	2	3	2	0	2	3	3	0			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr9:139360854A>G	ENST00000371706.3	-	5	3489	c.3456T>C	c.(3454-3456)gaT>gaC	p.D1152D	SEC16A_ENST00000290037.6_Silent_p.D1152D|SEC16A_ENST00000313050.7_Silent_p.D1330D|SEC16A_ENST00000431893.2_Silent_p.D1152D			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	1152	Required for endoplasmic reticulum localization.				COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		GATCGGGGTCATCGTCAAAAC	0.627																																					p.D1330D		Atlas-SNP	.											.	SEC16A	249	.	0			c.T3990C						PASS	.						24	30	28					9																	139360854		2163	4267	6430	SO:0001819	synonymous_variant	9919	exon7			GGGGTCATCGTCA	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.3456T>C	chr9.hg19:g.139360854A>G		79.0	0.0	.		73.0	28.0	.	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Silent	SNP	ENST00000371706.3	hg19		.	.	.	.	.	.	.	.	.	.	A	3.831	-0.035868	0.07497	.	.	ENSG00000148396	ENST00000433860	.	.	.	5.69	-11.4	0.00090	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-16.346	10.1481	0.42776	0.2182:0.2055:0.5134:0.0629	.	.	.	.	R	27	.	.	X	-	1	0	SEC16A	138480675	0.000000	0.05858	0.010000	0.14722	0.419000	0.31324	-1.735000	0.01847	-4.404000	0.00051	-1.139000	0.01908	TGA	.	.	.	none		0.627	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459		G	139360854	A	G	139360854	2	3	246	1	0	0	0	0	0	0	0	1	13999	214	8	3		3	SEC16A	9	139360854	Silent	SNP	A	TCGA-SX-A7SL-01A-11D-A34Z-10	9904810	139360854	1852577	38	15202											
ZMYND19	116225	hgsc.bcm.edu	37	chr9	140477471	140477471	+	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	gtgcagggagggtagtggcaCtcatagtaggtgcaagagtt	10	9	17	5	0	1	1	1	0	0	1	1	2	1	2	0	4	2	6	0	4	4	4			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr9:140477471C>A	ENST00000298585.2	-	5	730	c.504G>T	c.(502-504)gaG>gaT	p.E168D		NM_138462.2	NP_612471.1	Q96E35	ZMY19_HUMAN	zinc finger, MYND-type containing 19	168						cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|synapse (GO:0045202)	metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	13	all_cancers(76;0.106)			OV - Ovarian serous cystadenocarcinoma(145;0.000275)|Epithelial(140;0.00047)		GGTAGTGGCACTCATAGTAGG	0.537																																					p.E168D		Atlas-SNP	.											.	ZMYND19	16	.	0			c.G504T						PASS	.						256	205	222					9																	140477471		2203	4300	6503	SO:0001583	missense	116225	exon5			GTGGCACTCATAG	BC012948	CCDS7048.1	9q34.3	2008-02-05			ENSG00000165724	ENSG00000165724		"Zinc fingers, MYND-type"	21146	protein-coding gene	gene with protein product		611424					Standard	NM_138462		Approved	MIZIP	uc004cno.1	Q96E35	OTTHUMG00000020992	ENST00000298585.2:c.504G>T	chr9.hg19:g.140477471C>A	ENSP00000298585:p.Glu168Asp	81.0	0.0	.		43.0	19.0	.	NM_138462	Q5T366	Missense_Mutation	SNP	ENST00000298585.2	hg19	CCDS7048.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.308524	0.81247	.	.	ENSG00000165724	ENST00000298585	.	.	.	5.29	3.2	0.36748	.	0.048852	0.85682	D	0.000000	T	0.69223	0.3087	M	0.68317	2.08	0.49483	D	0.999792	D	0.63046	0.992	D	0.77004	0.989	T	0.70234	-0.4928	9	0.87932	D	0	-33.5417	7.342	0.26641	0.0:0.7433:0.0:0.2567	.	168	Q96E35	ZMY19_HUMAN	D	168	.	ENSP00000298585:E168D	E	-	3	2	ZMYND19	139597292	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	2.044000	0.41241	1.239000	0.43787	0.561000	0.74099	GAG	.	.	.	none		0.537	ZMYND19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055356.1	NM_138462		A	140477471	C	A	140477471	3	1	246	1	0	0	0	0	1	0	0	0	17722	564	20	4	187	4	ZMYND19	9	140477471	Missense_Mutation	SNP	C	TCGA-SX-A7SL-01A-11D-A34Z-10	1116617	140477471	735960	39	15203											
FRMD4A	55691	hgsc.bcm.edu	37	chr10	13803654	13803654	+	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	attgtaaacttacctagaaaAatctccctttgcctcctgta	12	14	4	11	0	1	1	0	0	1	1	3	1	2	1	4	0	3	2	4	0	7	6			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr10:13803654A>T	ENST00000357447.2	-	8	825	c.457T>A	c.(457-459)Ttt>Att	p.F153I	FRMD4A_ENST00000342409.2_Missense_Mutation_p.F169I|FRMD4A_ENST00000378503.1_Missense_Mutation_p.F153I|FRMD4A_ENST00000358621.4_Missense_Mutation_p.F138I	NM_018027.3	NP_060497.3	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A	153	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						TACCTAGAAAAATCTCCCTTT	0.333																																					p.F153I		Atlas-SNP	.											.	FRMD4A	108	.	0			c.T457A						PASS	.						104	107	106					10																	13803654		2203	4300	6503	SO:0001583	missense	55691	exon8			TAGAAAAATCTCC	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.457T>A	chr10.hg19:g.13803654A>T	ENSP00000350032:p.Phe153Ile	194.0	0.0	.		144.0	65.0	.	NM_018027	A7E2Y3|Q5T377	Missense_Mutation	SNP	ENST00000357447.2	hg19	CCDS7101.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.440458	0.83993	.	.	ENSG00000151474	ENST00000358621;ENST00000357447;ENST00000378503;ENST00000264546;ENST00000342409	T;T;T;T;T	0.31510	1.49;1.49;1.49;1.49;1.49	5.04	5.04	0.67666	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	T	0.44726	0.1307	M	0.62723	1.935	0.58432	D	0.999997	P;P;P	0.51933	0.831;0.902;0.949	P;P;P	0.55222	0.716;0.598;0.771	T	0.45056	-0.9287	10	0.87932	D	0	-11.814	11.4873	0.50361	1.0:0.0:0.0:0.0	.	169;186;153	Q5T378;Q5T376;Q9P2Q2	.;.;FRM4A_HUMAN	I	138;153;153;186;169	ENSP00000351438:F138I;ENSP00000350032:F153I;ENSP00000367764:F153I;ENSP00000264546:F186I;ENSP00000344237:F169I	ENSP00000264546:F186I	F	-	1	0	FRMD4A	13843660	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.129000	0.64739	2.003000	0.58678	0.533000	0.62120	TTT	.	.	.	none		0.333	FRMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046889.1	NM_018027		T	13803654	A	T	13803654	3	4	246	1	0	0	0	0	1	0	0	0	6058	14	1	5	2730	5	FRMD4A	10	13803654	Missense_Mutation	SNP	A	TCGA-SX-A7SL-01A-11D-A34Z-10		13803654	121731093	40	15204											
KIAA1279	26128	hgsc.bcm.edu	37	chr10	70748678	70748678	+	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	ctgcataaaaatccggagaaGgaaccatacaagtccaaata	19	6	7	9	1	0	1	0	0	0	1	2	3	2	2	3	2	3	1	3	2	9	3			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr10:70748678G>C	ENST00000361983.4	+	1	192	c.90G>C	c.(88-90)aaG>aaC	p.K30N		NM_015634.3	NP_056449.1	Q96EK5	KBP_HUMAN	KIAA1279	30					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						ATCCGGAGAAGGAACCATACA	0.622											OREG0020215	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K30N		Atlas-SNP	.											.	KIAA1279	35	.	0			c.G90C						PASS	.						65	74	71					10																	70748678		2203	4300	6503	SO:0001583	missense	26128	exon1			GGAGAAGGAACCA	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.90G>C	chr10.hg19:g.70748678G>C	ENSP00000354848:p.Lys30Asn	164.0	0.0	.	1124	158.0	70.0	.	NM_015634	A8K5M8|Q9BR89|Q9ULE1|Q9Y428	Missense_Mutation	SNP	ENST00000361983.4	hg19	CCDS7284.1	.	.	.	.	.	.	.	.	.	.	G	11.31	1.601804	0.28534	.	.	ENSG00000198954	ENST00000361983	T	0.42900	0.96	5.73	2.82	0.32997	.	0.102956	0.64402	D	0.000002	T	0.17534	0.0421	N	0.05441	-0.05	0.31545	N	0.659403	B	0.02656	0.0	B	0.01281	0.0	T	0.27297	-1.0078	10	0.06099	T	0.92	-12.8014	8.5315	0.33337	0.1689:0.2585:0.5727:0.0	.	30	Q96EK5	KBP_HUMAN	N	30	ENSP00000354848:K30N	ENSP00000354848:K30N	K	+	3	2	KIAA1279	70418684	0.922000	0.31269	1.000000	0.80357	0.992000	0.81027	-0.005000	0.12855	0.781000	0.33589	0.650000	0.86243	AAG	.	.	.	none		0.622	KIAA1279-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048370.1	NM_015634		C	70748678	G	C	70748678	3	2	246	1	0	0	0	0	1	0	0	0	8228	991	35	4	92	4	KIAA1279	10	70748678	Missense_Mutation	SNP	G	TCGA-SX-A7SL-01A-11D-A34Z-10	56945024	70748678	64786069	41	15205											
OR4C13	283092	hgsc.bcm.edu	37	chr11	49974862	49974862	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctcaaatgaaaaatgccatTaggaaattgtgtagtaggaa	17	10	10	4	0	1	1	1	1	0	0	1	3	1	3	1	2	1	3	1	2	8	4			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr11:49974862T>C	ENST00000555099.1	+	1	920	c.888T>C	c.(886-888)atT>atC	p.I296I		NM_001001955.2	NP_001001955.2	Q8NGP0	OR4CD_HUMAN	olfactory receptor, family 4, subfamily C, member 13	296						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						AAAATGCCATTAGGAAATTGT	0.378																																					p.I296I		Atlas-SNP	.											.	OR4C13	96	.	0			c.T888C						PASS	.						42	42	42					11																	49974862		2192	4292	6484	SO:0001819	synonymous_variant	283092	exon1			TGCCATTAGGAAA	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.888T>C	chr11.hg19:g.49974862T>C		43.0	0.0	.		27.0	12.0	.	NM_001001955	A6NJJ3|B9EH30|Q6IF48|Q96R68	Silent	SNP	ENST00000555099.1	hg19	CCDS31495.1																																																																																			.	.	.	none		0.378	OR4C13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391103.1	NM_001001955		C	49974862	T	C	49974862	2	2	246	1	0	0	0	0	0	0	0	1	11054	1742	61	3		3	OR4C13	11	49974862	Silent	SNP	T	TCGA-SX-A7SL-01A-11D-A34Z-10		49974862	85031654	42	15206											
CASP4	837	hgsc.bcm.edu	37	chr11	104819264	104819264	+	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	actgaaagatacatacgtggCgttgaagagcagaaagcaat	17	7	11	6	2	0	5	0	2	0	3	0	5	0	5	0	1	4	3	0	1	6	3	rs552187293		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr11:104819264C>T	ENST00000444739.2	-	6	1831	c.921G>A	c.(919-921)acG>acA	p.T307T	CASP4_ENST00000393150.3_Silent_p.T251T|CASP4_ENST00000531333.1_5'Flank	NM_001225.3	NP_001216.1	P49662	CASP4_HUMAN	caspase 4, apoptosis-related cysteine peptidase	307					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)	p.T307T(1)		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)		ACATACGTGGCGTTGAAGAGC	0.448													c|||	1	0.000199681	0	0	5008	,	,		20358	0		0	False		,,,				2504	0.001				p.T307T		Atlas-SNP	.											CASP4,NS,carcinoma,0,2	CASP4	57	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G921A						PASS	.						133	97	109					11																	104819264		2202	4299	6501	SO:0001819	synonymous_variant	837	exon6			ACGTGGCGTTGAA	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.921G>A	chr11.hg19:g.104819264C>T		77.0	0.0	.		62.0	23.0	.	NM_001225	A2NHL8|A2NHM0	Silent	SNP	ENST00000444739.2	hg19	CCDS8327.1																																																																																			.	.	.	none		0.448	CASP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387751.1	NM_001225		T	104819264	C	T	104819264	2	4	246	1	0	0	0	0	0	0	0	1	2675	755	27	1		1	CASP4	11	104819264	Silent	SNP	C	TCGA-SX-A7SL-01A-11D-A34Z-10	54844402	104819264	30187252	43	15207											
NCAPD3	23310	hgsc.bcm.edu	37	chr11	134023240	134023240	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aactgacccctgctccaaacGtgacatcactgatgctctct	10	10	6	15	1	2	3	1	3	1	0	4	3	3	3	3	0	4	2	3	0	2	0			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr11:134023240G>A	ENST00000534548.2	-	33	4335	c.4271C>T	c.(4270-4272)aCg>aTg	p.T1424M	NCAPD3_ENST00000526787.2_5'UTR	NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	1424					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)		TGCTCCAAACGTGACATCACT	0.542																																					p.T1424M		Atlas-SNP	.											.	NCAPD3	141	.	0			c.C4271T						PASS	.						212	176	188					11																	134023240		2201	4297	6498	SO:0001583	missense	23310	exon33			CCAAACGTGACAT	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.4271C>T	chr11.hg19:g.134023240G>A	ENSP00000433681:p.Thr1424Met	126.0	0.0	.		83.0	35.0	.	NM_015261	A6NFS2|Q4KMQ9	Missense_Mutation	SNP	ENST00000534548.2	hg19	CCDS31723.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.140591	0.77775	.	.	ENSG00000151503	ENST00000534548	T	0.48522	0.81	5.44	5.44	0.79542	.	0.052095	0.85682	D	0.000000	T	0.68091	0.2963	M	0.65498	2.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.69142	0.962;0.948	T	0.70204	-0.4936	10	0.87932	D	0	-18.9547	19.206	0.93730	0.0:0.0:1.0:0.0	.	1424;484	P42695;Q96FA6	CNDD3_HUMAN;.	M	1424	ENSP00000433681:T1424M	ENSP00000433681:T1424M	T	-	2	0	NCAPD3	133528450	1.000000	0.71417	0.914000	0.36105	0.773000	0.43773	6.493000	0.73658	2.712000	0.92718	0.561000	0.74099	ACG	.	.	.	none		0.542	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261		A	134023240	G	A	134023240	3	1	246	1	0	0	0	0	1	0	0	0	10213	1145	40	1	237	1	NCAPD3	11	134023240	Missense_Mutation	SNP	G	TCGA-SX-A7SL-01A-11D-A34Z-10	29203976	134023240	983276	44	15208											
CLEC1A	51267	hgsc.bcm.edu	37	chr12	10251473	10251480	+	Frame_Shift_Del	DEL	CCCCATCA	CCCCATCA	-																															atgcaggctcatggtggtgtCcccatcatcatccagcatgt																								rs553428572		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	CCCCATCA	CCCCATCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr12:10251473_10251480delCCCCATCA	ENST00000315330.4	-	1	104_111	c.42_49delTGATGGGG	c.(40-51)gatgatggggacfs	p.DDGD14fs	CLEC1A_ENST00000420265.2_Frame_Shift_Del_p.DDGD14fs|CLEC1A_ENST00000457018.2_Frame_Shift_Del_p.DDGD14fs	NM_016511.2	NP_057595.2	Q8NC01	CLC1A_HUMAN	C-type lectin domain family 1, member A	14					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	23						ATGGTGGTGTCCCCATCATCATCCAGCA	0.591																																					p.15_17del		Atlas-Indel,Pindel	.											.	CLEC1A	48	.	0			c.43_50del						PASS	.																																			SO:0001589	frameshift_variant	51267	exon1			.	AY358587	CCDS8612.1, CCDS73443.1	12p13.31	2005-02-09				ENSG00000150048		"C-type lectin domain containing"	24355	protein-coding gene	gene with protein product		606782				10671229, 11745369	Standard	XM_005253383		Approved	CLEC1, MGC34328	uc001qxb.3	Q8NC01		ENST00000315330.4:c.42_49delTGATGGGG	chr12.hg19:g.10251473_10251480delCCCCATCA	ENSP00000326407:p.Asp14fs	175.0	0.0	0		100.0	34.0	0.34	NM_016511	Q8IUW7|Q9NZH3	Frame_Shift_Del	DEL	ENST00000315330.4	hg19	CCDS8612.1																																																																																			.	.	.	none		0.591	CLEC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399924.1	NM_016511		-	10251480	CCCCATCA	-	10251473	7	5	246	1	0	1	0	1	0	0	0	0	3507	855	30	0	817	0	CLEC1A	12	10251473	Frame_Shift_Del	DEL	CCCCATCA	TCGA-SX-A7SL-01A-11D-A34Z-10		10251473	123600422	45	15209											
BCDIN3D	144233	hgsc.bcm.edu	37	chr12	50232203	50232203	+	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	tttctttccctttttctatcAgtgattcagggattggatga	7	19	8	7	0	4	2	2	2	2	0	5	4	5	4	1	2	0	0	1	2	1	7			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr12:50232203A>T	ENST00000333924.4	-	2	871	c.830T>A	c.(829-831)cTg>cAg	p.L277Q	BCDIN3D-AS1_ENST00000548872.1_RNA|BCDIN3D-AS1_ENST00000549124.1_RNA	NM_181708.2	NP_859059.1	Q7Z5W3	BN3D2_HUMAN	BCDIN3 domain containing	277					miRNA metabolic process (GO:0010586)|negative regulation of pre-miRNA processing (GO:2000632)|RNA methylation (GO:0001510)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	O-methyltransferase activity (GO:0008171)|RNA methyltransferase activity (GO:0008173)			endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)|stomach(1)	9						TTTTTCTATCAGTGATTCAGG	0.403																																					p.L277Q		Atlas-SNP	.											.	BCDIN3D	20	.	0			c.T830A						PASS	.						140	137	138					12																	50232203		2203	4300	6503	SO:0001583	missense	144233	exon2			TCTATCAGTGATT		CCDS8790.1	12q13.13	2008-03-12				ENSG00000186666			27050	protein-coding gene	gene with protein product							Standard	NM_181708		Approved		uc001rvh.3	Q7Z5W3	OTTHUMG00000169807	ENST00000333924.4:c.830T>A	chr12.hg19:g.50232203A>T	ENSP00000335201:p.Leu277Gln	24.0	0.0	.		22.0	7.0	.	NM_181708	A8K829	Missense_Mutation	SNP	ENST00000333924.4	hg19	CCDS8790.1	.	.	.	.	.	.	.	.	.	.	A	11.25	1.583428	0.28268	.	.	ENSG00000186666	ENST00000333924	T	0.50277	0.75	4.35	0.717	0.18196	.	1.385570	0.04949	N	0.460066	T	0.29256	0.0728	N	0.14661	0.345	0.09310	N	1	B	0.13145	0.007	B	0.14578	0.011	T	0.26430	-1.0103	10	0.59425	D	0.04	-17.2455	2.4992	0.04629	0.5719:0.0:0.2253:0.2029	.	277	Q7Z5W3	BN3D2_HUMAN	Q	277	ENSP00000335201:L277Q	ENSP00000335201:L277Q	L	-	2	0	BCDIN3D	48518470	0.000000	0.05858	0.006000	0.13384	0.768000	0.43524	0.590000	0.23954	0.117000	0.18138	0.402000	0.26972	CTG	.	.	.	none		0.403	BCDIN3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405982.1	NM_181708		T	50232203	A	T	50232203	3	4	246	1	0	0	0	0	1	0	0	0	1357	188	7	5	52	5	BCDIN3D	12	50232203	Missense_Mutation	SNP	A	TCGA-SX-A7SL-01A-11D-A34Z-10	39980730	50232203	83619692	46	15210											
OBFC2B	79035	hgsc.bcm.edu	37	chr12	56619250	56619250	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatctctgtctgggacgatgTtggcaatctgatccagcctg	7	13	11	10	1	3	1	0	1	3	0	5	3	4	2	2	2	1	2	2	2	2	2			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr12:56619250T>C	ENST00000380198.2	+	2	671	c.173T>C	c.(172-174)gTt>gCt	p.V58A	NABP2_ENST00000267023.4_Missense_Mutation_p.V58A|NABP2_ENST00000341463.5_Missense_Mutation_p.V58A			Q9BQ15	SOSB1_HUMAN	nucleic acid binding protein 2	58					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)|SOSS complex (GO:0070876)	single-stranded DNA binding (GO:0003697)										TGGGACGATGTTGGCAATCTG	0.537																																					p.V58A		Atlas-SNP	.											.	.	.	.	0			c.T173C						PASS	.						180	154	163					12																	56619250		2203	4300	6503	SO:0001583	missense	79035	exon3			ACGATGTTGGCAA	BC006171	CCDS8911.1	12q13.3	2012-06-19	2012-06-19	2012-06-19	ENSG00000139579	ENSG00000139579			28412	protein-coding gene	gene with protein product	"single strand DNA-binding protein 1", "sensor of single-strand DNA complex subunit B1"	612104	"oligonucleotide/oligosaccharide-binding fold containing 2B"	OBFC2B			Standard	NM_024068		Approved	MGC2731, SSB1, hSSB1, SOSS-B1	uc001ski.3	Q9BQ15	OTTHUMG00000152527	ENST00000380198.2:c.173T>C	chr12.hg19:g.56619250T>C	ENSP00000369545:p.Val58Ala	137.0	0.0	.		83.0	40.0	.	NM_024068	A6NDF8|Q6XYC8	Missense_Mutation	SNP	ENST00000380198.2	hg19	CCDS8911.1	.	.	.	.	.	.	.	.	.	.	T	11.40	1.628069	0.28978	.	.	ENSG00000139579	ENST00000447747;ENST00000399713;ENST00000267023;ENST00000380198;ENST00000341463	T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62	4.59	3.44	0.39384	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);Nucleic acid binding, OB-fold, tRNA/helicase-type (1);	0.096640	0.39759	N	0.001268	T	0.16896	0.0406	N	0.14661	0.345	0.40726	D	0.982701	B;B;B	0.21452	0.056;0.034;0.014	B;B;B	0.25759	0.026;0.044;0.063	T	0.07927	-1.0747	10	0.25751	T	0.34	-14.59	8.9473	0.35767	0.0:0.0914:0.0:0.9086	.	58;58;58	C9JT95;C9JMP5;Q9BQ15	.;.;SOSB1_HUMAN	A	58	ENSP00000413902:V58A;ENSP00000408616:V58A;ENSP00000267023:V58A;ENSP00000369545:V58A;ENSP00000368862:V58A	ENSP00000267023:V58A	V	+	2	0	OBFC2B	54905517	1.000000	0.71417	0.987000	0.45799	0.757000	0.42996	6.043000	0.71004	1.852000	0.53769	0.374000	0.22700	GTT	.	.	.	none		0.537	NABP2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326610.1	NM_024068		C	56619250	T	C	56619250	3	2	246	1	0	0	0	0	1	0	0	0	10816	1725	60	3	179	3	OBFC2B	12	56619250	Missense_Mutation	SNP	T	TCGA-SX-A7SL-01A-11D-A34Z-10	6387047	56619250	77232645	47	15211											
NXPH4	11247	hgsc.bcm.edu	37	chr12	57619136	57619140	+	Frame_Shift_Del	DEL	CTACG	CTACG	-																															tgtcccccaccctctgcagtCtacgctcgccctggaggggg																										TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	CTACG	CTACG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr12:57619136_57619140delCTACG	ENST00000349394.5	+	2	708_712	c.533_537delCTACG	c.(532-537)tctacgfs	p.ST178fs	NXPH4_ENST00000555154.1_3'UTR|Y_RNA_ENST00000365197.1_RNA	NM_007224.3	NP_009155.1	O95158	NXPH4_HUMAN	neurexophilin 4	178	IV (linker domain).				neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)	10						CCTCTGCAGTCTACGCTCGCCCTGG	0.732																																					p.178_179del		Atlas-INDEL	.											.	NXPH4	40	.	0			c.532_536del						PASS	.																																			SO:0001589	frameshift_variant	11247	exon2			.	AF043469	CCDS8933.1	12q13.3	2014-09-04			ENSG00000182379	ENSG00000182379			8078	protein-coding gene	gene with protein product		604637				9570794	Standard	NM_007224		Approved	NPH4	uc009zpj.4	O95158	OTTHUMG00000171241	ENST00000349394.5:c.533_537delCTACG	chr12.hg19:g.57619136_57619140delCTACG	ENSP00000333593:p.Ser178fs	51.0	0.0	0		25.0	14.0	0.56	NM_007224	A8K4I4|Q7Z6L3|Q8N462	Frame_Shift_Del	DEL	ENST00000349394.5	hg19	CCDS8933.1																																																																																			.	.	.	none		0.732	NXPH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412474.1	NM_007224		-	57619140	CTACG	-	57619136	7	5	246	1	0	1	0	1	0	0	0	0	10800	913	32	0	539	0	NXPH4	12	57619136	Frame_Shift_Del	DEL	CTACG	TCGA-SX-A7SL-01A-11D-A34Z-10	999886	57619136	76232759	48	15212											
KIF5A	3798	hgsc.bcm.edu	37	chr12	57963875	57963875	+	Missense_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	caactcatccatcgtggtgcGcatcgcgcccgaggagcggc	7	6	13	15	6	1	0	1	0	0	0	4	2	2	1	2	3	3	1	2	3	1	0			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr12:57963875G>A	ENST00000455537.2	+	12	1497	c.1223G>A	c.(1222-1224)cGc>cAc	p.R408H	KIF5A_ENST00000286452.5_Missense_Mutation_p.R319H	NM_004984.2	NP_004975.2	Q12840	KIF5A_HUMAN	kinesin family member 5A	408					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein localization (GO:0008104)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(32)|ovary(2)|prostate(2)|skin(2)	62						ATCGTGGTGCGCATCGCGCCC	0.627																																					p.R408H		Atlas-SNP	.											.	KIF5A	143	.	0			c.G1223A						PASS	.						57	45	49					12																	57963875		2203	4300	6503	SO:0001583	missense	3798	exon12			TGGTGCGCATCGC	U06698	CCDS8945.1	12q13.13	2011-07-15	2004-02-13			ENSG00000155980		"Kinesins"	6323	protein-coding gene	gene with protein product		602821	"spastic paraplegia 10 (autosomal dominant)"	SPG10		9858832, 10441583, 16489470	Standard	NM_004984		Approved	D12S1889, NKHC, MY050	uc001sor.1	Q12840	OTTHUMG00000170143	ENST00000455537.2:c.1223G>A	chr12.hg19:g.57963875G>A	ENSP00000408979:p.Arg408His	65.0	0.0	.		47.0	21.0	.	NM_004984	A6H8M5|Q4LE26	Missense_Mutation	SNP	ENST00000455537.2	hg19	CCDS8945.1	.	.	.	.	.	.	.	.	.	.	G	10.95	1.496792	0.26861	.	.	ENSG00000155980	ENST00000455537;ENST00000286452	T;T	0.76968	-1.06;-1.06	4.79	4.79	0.61399	.	0.000000	0.85682	D	0.000000	T	0.67933	0.2946	N	0.25890	0.77	0.58432	D	0.999996	B;B	0.15719	0.007;0.014	B;B	0.08055	0.003;0.003	T	0.63332	-0.6661	10	0.40728	T	0.16	.	17.1515	0.86779	0.0:0.0:1.0:0.0	.	319;408	B7Z2M7;Q12840	.;KIF5A_HUMAN	H	408;319	ENSP00000408979:R408H;ENSP00000286452:R319H	ENSP00000286452:R319H	R	+	2	0	KIF5A	56250142	1.000000	0.71417	0.999000	0.59377	0.062000	0.15995	4.074000	0.57577	2.667000	0.90743	0.655000	0.94253	CGC	.	.	.	none		0.627	KIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407634.1	NM_004984		A	57963875	G	A	57963875	3	1	246	1	0	0	0	0	1	0	0	0	8312	1087	38	1	1269	1	KIF5A	12	57963875	Missense_Mutation	SNP	G	TCGA-SX-A7SL-01A-11D-A34Z-10	344739	57963875	75888020	49	15213											
FICD	11153	hgsc.bcm.edu	37	chr12	108913231	108913231	+	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	aaccactctgggttcaaggaGacgcttcctgtgaagcccta	10	9	10	12	1	2	2	1	1	1	1	3	3	3	2	3	2	2	2	3	2	4	3			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr12:108913231G>C	ENST00000552695.1	+	3	1591	c.1356G>C	c.(1354-1356)gaG>gaC	p.E452D	FICD_ENST00000361549.2_3'UTR	NM_007076.2	NP_009007.2	Q9BVA6	FICD_HUMAN	FIC domain containing	452					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						GGTTCAAGGAGACGCTTCCTG	0.498																																					p.E452D		Atlas-SNP	.											.	FICD	35	.	0			c.G1356C						PASS	.						48	40	43					12																	108913231		2203	4300	6503	SO:0001583	missense	11153	exon3			CAAGGAGACGCTT	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.1356G>C	chr12.hg19:g.108913231G>C	ENSP00000446479:p.Glu452Asp	42.0	0.0	.		34.0	11.0	.	NM_007076	O75406	Missense_Mutation	SNP	ENST00000552695.1	hg19	CCDS9116.1	.	.	.	.	.	.	.	.	.	.	G	13.88	2.369148	0.42003	.	.	ENSG00000198855	ENST00000552695	.	.	.	6.02	4.21	0.49690	.	0.212676	0.50627	D	0.000109	T	0.29652	0.0740	N	0.08118	0	0.80722	D	1	B	0.27791	0.189	B	0.22386	0.039	T	0.09314	-1.0680	9	0.48119	T	0.1	-14.3343	8.8477	0.35181	0.2969:0.0:0.7031:0.0	.	452	Q9BVA6	FICD_HUMAN	D	452	.	ENSP00000446479:E452D	E	+	3	2	FICD	107437361	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.997000	0.40786	0.891000	0.36235	-0.136000	0.14681	GAG	.	.	.	none		0.498	FICD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404842.1	NM_007076		C	108913231	G	C	108913231	3	2	246	1	0	0	0	0	1	0	0	0	5894	933	33	4	1362	4	FICD	12	108913231	Missense_Mutation	SNP	G	TCGA-SX-A7SL-01A-11D-A34Z-10	50949356	108913231	24938664	50	15214											
ZNF828	283489	hgsc.bcm.edu	37	chr13	115091586	115091586	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aatctctccttaaaaatcatGtagcagcccatgggcaaagt	14	10	7	10	0	2	0	1	0	1	0	4	0	3	0	2	1	2	3	2	1	6	2			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr13:115091586G>A	ENST00000361283.1	+	3	2578	c.2269G>A	c.(2269-2271)Gta>Ata	p.V757I		NM_001164144.1|NM_001164145.1|NM_032436.2	NP_001157616.1|NP_001157617.1|NP_115812.1	Q96JM3	CHAP1_HUMAN	chromosome alignment maintaining phosphoprotein 1	757	Mediates localization to the chromosome and the spindle and negatively regulates chromosome alignment.				attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|protein localization to kinetochore (GO:0034501)|protein localization to microtubule (GO:0035372)|sister chromatid biorientation (GO:0031134)	condensed chromosome (GO:0000793)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)										TAAAAATCATGTAGCAGCCCA	0.348																																					p.V757I		Atlas-SNP	.											.	.	.	.	0			c.G2269A						PASS	.						69	71	70					13																	115091586		2203	4300	6503	SO:0001583	missense	283489	exon3			AATCATGTAGCAG	AK074894	CCDS9545.1	13q34	2013-01-07	2011-10-07	2011-10-07	ENSG00000198824	ENSG00000198824		"Zinc fingers, C2H2-type"	20311	protein-coding gene	gene with protein product	"chromosome alignment-maintaining phosphoprotein"		"chromosome 13 open reading frame 8", "zinc finger protein 828"	C13orf8, ZNF828		21063390	Standard	NM_032436		Approved	CAMP, CHAMP	uc010ahb.3	Q96JM3	OTTHUMG00000017404	ENST00000361283.1:c.2269G>A	chr13.hg19:g.115091586G>A	ENSP00000354730:p.Val757Ile	139.0	0.0	.		97.0	45.0	.	NM_001164144	B3KU06|Q6P181|Q8NC88|Q9BST0	Missense_Mutation	SNP	ENST00000361283.1	hg19	CCDS9545.1	.	.	.	.	.	.	.	.	.	.	g	16.10	3.026411	0.54683	.	.	ENSG00000198824	ENST00000361283	T	0.41400	1.0	5.81	4.96	0.65561	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.53938	D	0.000057	T	0.37073	0.0990	L	0.31845	0.965	0.29635	N	0.845125	D	0.55605	0.972	P	0.48334	0.574	T	0.25882	-1.0119	9	.	.	.	-10.4679	10.7799	0.46371	0.0695:0.1292:0.8013:0.0	.	757	Q96JM3	ZN828_HUMAN	I	757	ENSP00000354730:V757I	.	V	+	1	0	ZNF828	114109688	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.615000	0.46368	2.746000	0.94184	0.655000	0.94253	GTA	.	.	.	none		0.348	CHAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045977.2	NM_032436		A	115091586	G	A	115091586	3	1	246	1	0	0	0	0	1	0	0	0	18193	1377	48	2	2271	2	ZNF828	13	115091586	Missense_Mutation	SNP	G	TCGA-SX-A7SL-01A-11D-A34Z-10		115091586	78292	51	15215											
C14orf102	55051	hgsc.bcm.edu	37	chr14	90755068	90755068	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacagctgtcacccaaacagTcctgcagtgcgtgctcataa	11	8	8	14	1	2	0	2	0	0	0	3	0	3	0	2	0	5	3	2	0	2	1			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr14:90755068T>C	ENST00000354366.3	-	11	2883	c.2651A>G	c.(2650-2652)gAc>gGc	p.D884G	NRDE2_ENST00000357904.3_Missense_Mutation_p.D653G	NM_017970.3	NP_060440.2	Q9H7Z3	NRDE2_HUMAN	NRDE-2, necessary for RNA interference, domain containing	884																	ACCCAAACAGTCCTGCAGTGC	0.527																																					p.D884G		Atlas-SNP	.											.	.	.	.	0			c.A2651G						PASS	.						61	60	60					14																	90755068		2203	4300	6503	SO:0001583	missense	55051	exon11			AAACAGTCCTGCA	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.2651A>G	chr14.hg19:g.90755068T>C	ENSP00000346335:p.Asp884Gly	61.0	0.0	.		78.0	42.0	.	NM_017970	B4DH71|Q4G0A7|Q9NWH6	Missense_Mutation	SNP	ENST00000354366.3	hg19	CCDS9890.1	.	.	.	.	.	.	.	.	.	.	T	9.884	1.202458	0.22121	.	.	ENSG00000119720	ENST00000354366;ENST00000357904	T;T	0.32515	1.85;1.45	5.1	3.91	0.45181	.	0.183302	0.46442	D	0.000284	T	0.27731	0.0682	M	0.72118	2.19	0.42839	D	0.994042	P;P	0.40144	0.704;0.495	B;B	0.30401	0.115;0.106	T	0.08207	-1.0733	10	0.25751	T	0.34	-33.9301	11.8658	0.52493	0.0:0.0:0.1464:0.8536	.	653;884	E9PBK4;Q9H7Z3	.;CN102_HUMAN	G	884;653	ENSP00000346335:D884G;ENSP00000350579:D653G	ENSP00000346335:D884G	D	-	2	0	C14orf102	89824821	1.000000	0.71417	0.979000	0.43373	0.044000	0.14063	1.437000	0.34991	0.916000	0.36871	0.528000	0.53228	GAC	.	.	.	none		0.527	NRDE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411264.1	NM_017970		C	90755068	T	C	90755068	3	2	246	1	0	0	0	0	1	0	0	0	1737	1667	58	3	859	3	C14orf102	14	90755068	Missense_Mutation	SNP	T	TCGA-SX-A7SL-01A-11D-A34Z-10		90755068	16594472	52	15216											
MAPK6	5597	hgsc.bcm.edu	37	chr15	52357196	52357196	+	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	cattctgaaacatctgaactAaaacactcagcagacattta	17	10	4	10	0	3	3	1	2	2	1	3	3	3	3	0	0	4	1	0	0	5	4			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr15:52357196A>T	ENST00000261845.5	+	6	2972	c.2165A>T	c.(2164-2166)tAa>tTa	p.*722L	CTD-2184D3.5_ENST00000558607.1_RNA	NM_002748.3	NP_002739.1	Q16659	MK06_HUMAN	mitogen-activated protein kinase 6	0					cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	20				all cancers(107;0.0028)		CATCTGAACTAAAACACTCAG	0.338																																					p.X722L		Atlas-SNP	.											.	MAPK6	70	.	0			c.A2165T						PASS	.						36	38	38					15																	52357196		2135	4102	6237	SO:0001578	stop_lost	5597	exon6			TGAACTAAAACAC	L77964	CCDS10147.1	15q21	2011-06-10			ENSG00000069956	ENSG00000069956		"Mitogen-activated protein kinase cascade / Kinases"	6879	protein-coding gene	gene with protein product		602904		PRKM6		8875998	Standard	NM_002748		Approved	ERK3, p97MAPK, HsT17250	uc002abp.3	Q16659	OTTHUMG00000131891	ENST00000261845.5:c.2165A>T	chr15.hg19:g.52357196A>T	ENSP00000261845:p.*722Leuext*24	131.0	0.0	.		112.0	44.0	.	NM_002748	B2R945|B5BU65|Q68DH4|Q8IYN8	Missense_Mutation	SNP	ENST00000261845.5	hg19	CCDS10147.1	.	.	.	.	.	.	.	.	.	.	A	11.66	1.706321	0.30232	.	.	ENSG00000069956	ENST00000261845	.	.	.	4.46	4.46	0.54185	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8766	0.63655	1.0:0.0:0.0:0.0	.	.	.	.	L	722	.	.	X	+	2	2	MAPK6	50144488	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.522000	0.53480	1.709000	0.51313	0.444000	0.29173	TAA	.	.	.	none		0.338	MAPK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254841.2	NM_002748		T	52357196	A	T	52357196	4	4	246	1	0	0	0	0	0	0	0	0	9288	369	13	5	2183	5	MAPK6	15	52357196	Nonstop_Mutation	SNP	A	TCGA-SX-A7SL-01A-11D-A34Z-10		52357196	50174196	53	15217											
DET1	55070	hgsc.bcm.edu	37	chr15	89074206	89074214	+	In_Frame_Del	DEL	ACCTGGAAG	ACCTGGAAG	-																															tgaaagtgccttcaggagtcAcctggaagacatggatggtc																										TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	ACCTGGAAG	ACCTGGAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr15:89074206_89074214delACCTGGAAG	ENST00000268148.8	-	2	868_876	c.723_731delCTTCCAGGT	c.(721-732)gtcttccaggtg>gtg	p.241_244VFQV>V	DET1_ENST00000559656.1_5'Flank|DET1_ENST00000564406.1_In_Frame_Del_p.252_255VFQV>V|DET1_ENST00000444300.1_In_Frame_Del_p.252_255VFQV>V|DET1_ENST00000558413.1_Splice_Site_p.A92del	NM_001144074.1	NP_001137546.1	Q7L5Y6	DET1_HUMAN	de-etiolated homolog 1 (Arabidopsis)	241						nucleus (GO:0005634)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(10)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	Lung NSC(78;0.105)|all_lung(78;0.182)		BRCA - Breast invasive adenocarcinoma(143;0.188)			TTCAGGAGTCACCTGGAAGACATGGATGG	0.502																																					p.253_255del		Atlas-Indel,Pindel	.											.	DET1	55	.	0			c.757_765del						PASS	.																																			SO:0001651	inframe_deletion	55070	exon3			.	BC001242	CCDS45343.1, CCDS45344.1	15q25.3	2004-12-13				ENSG00000140543			25477	protein-coding gene	gene with protein product		608727				14739464	Standard	NM_001144074		Approved	FLJ10103	uc002bmq.2	Q7L5Y6		ENST00000268148.8:c.723_731delCTTCCAGGT	chr15.hg19:g.89074206_89074214delACCTGGAAG	ENSP00000268148:p.Val241_Gln243del	105.0	0.0	0		54.0	11.0	0.203704	NM_017996	B3KNN6|Q2VPC0|Q9NWD5	In_Frame_Del	DEL	ENST00000268148.8	hg19	CCDS45344.1																																																																																			.	.	.	none		0.502	DET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415442.2	NM_017996		-	89074214	ACCTGGAAG	-	89074206	7	5	246	1	0	1	0	1	0	0	0	0	4452	159	6	0	937	0	DET1	15	89074206	In_Frame_Del	DEL	ACCTGGAAG	TCGA-SX-A7SL-01A-11D-A34Z-10	36717010	89074206	13457186	54	15218											
MPG	4350	hgsc.bcm.edu	37	chr16	135675	135675	+	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	cagcccgggtgggcgtcggcCatgcaggggagtgggcccgg	4	4	21	12	4	0	0	0	0	0	0	1	1	0	1	3	7	2	1	3	7	0	0			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr16:135675C>A	ENST00000219431.4	+	5	1027	c.796C>A	c.(796-798)Cat>Aat	p.H266N	MPG_ENST00000397817.1_Missense_Mutation_p.H249N|NPRL3_ENST00000405960.3_5'Flank	NM_002434.3	NP_002425.2	P29372	3MG_HUMAN	N-methylpurine-DNA glycosylase	266					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA repair (GO:0006281)	mitochondrial nucleoid (GO:0042645)|nucleoplasm (GO:0005654)	alkylbase DNA N-glycosylase activity (GO:0003905)|damaged DNA binding (GO:0003684)|DNA-3-methyladenine glycosylase activity (GO:0008725)|DNA-3-methylguanine glycosylase activity (GO:0052822)|DNA-7-methyladenine glycosylase activity (GO:0052821)|DNA-7-methylguanine glycosylase activity (GO:0043916)			endometrium(4)|kidney(1)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9		all_cancers(16;9.01e-08)|all_epithelial(16;7.64e-07)|Hepatocellular(780;0.000325)|Lung NSC(18;0.0104)|all_lung(18;0.0239)				GGGCGTCGGCCATGCAGGGGA	0.677								Base excision repair (BER), DNA glycosylases																													p.H266N		Atlas-SNP	.											.	MPG	26	.	0			c.C796A						PASS	.						19	22	21					16																	135675		2201	4299	6500	SO:0001583	missense	4350	exon5			GTCGGCCATGCAG		CCDS32345.1, CCDS32346.1, CCDS42087.1	16p13.3	2008-07-29			ENSG00000103152	ENSG00000103152	3.2.2.21		7211	protein-coding gene	gene with protein product	"alkyladenine DNA glycosylase"	156565				1874728	Standard	NM_002434		Approved	MDG	uc002cfo.4	P29372	OTTHUMG00000047887	ENST00000219431.4:c.796C>A	chr16.hg19:g.135675C>A	ENSP00000219431:p.His266Asn	91.0	0.0	.		95.0	58.0	.	NM_002434	G5E9E2|Q13770|Q15275|Q15961|Q5J9I4|Q96BZ6|Q96S33|Q9NNX5	Missense_Mutation	SNP	ENST00000219431.4	hg19	CCDS32346.1	.	.	.	.	.	.	.	.	.	.	C	4.676	0.125740	0.08931	.	.	ENSG00000103152	ENST00000436333;ENST00000397817;ENST00000356432;ENST00000219431	T;T;T;T	0.15718	2.4;2.4;2.4;2.4	5.39	-10.8	0.00216	Formyl transferase, C-terminal-like (1);	0.916781	0.09550	N	0.787006	T	0.03178	0.0093	N	0.01729	-0.75	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.25047	-1.0143	10	0.15066	T	0.55	-18.2344	1.8122	0.03092	0.3214:0.2239:0.0751:0.3795	.	261;266	Q5J9I4;P29372	.;3MG_HUMAN	N	249;249;261;266	ENSP00000388097:H249N;ENSP00000380918:H249N;ENSP00000348809:H261N;ENSP00000219431:H266N	ENSP00000219431:H266N	H	+	1	0	MPG	75675	0.000000	0.05858	0.000000	0.03702	0.265000	0.26407	-0.133000	0.10451	-2.198000	0.00749	-0.505000	0.04504	CAT	.	.	.	none		0.677	MPG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109121.4			A	135675	C	A	135675	3	1	246	1	0	0	0	0	1	0	0	0	9731	594	21	4	838	4	MPG	16	135675	Missense_Mutation	SNP	C	TCGA-SX-A7SL-01A-11D-A34Z-10		135675	90219078	55	15219											
CRAMP1L	57585	hgsc.bcm.edu	37	chr16	1717963	1717963	+	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	aaatacctgtctcccagcagGgctcatctgttctctcctta	8	13	6	14	0	4	0	1	0	3	0	7	0	5	0	3	1	2	3	3	1	3	3			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr16:1717963G>A	ENST00000397412.3	+	18	3202	c.3103G>A	c.(3103-3105)Ggc>Agc	p.G1035S	CRAMP1L_ENST00000436138.3_Splice_Site_p.G1032S|CRAMP1L_ENST00000293925.5_Splice_Site_p.G1035S|LA16c-431H6.6_ENST00000454337.1_3'UTR|CRAMP1L_ENST00000262317.4_Splice_Site_p.G413S			Q96RY5	CRML_HUMAN	Crm, cramped-like (Drosophila)	1035						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						CTCCCAGCAGGGCTCATCTGT	0.537																																					p.G1035S		Atlas-SNP	.											.	CRAMP1L	60	.	0			c.G3103A						PASS	.						49	45	46					16																	1717963		2008	4186	6194	SO:0001630	splice_region_variant	57585	exon17			CAGCAGGGCTCAT	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.3103-1G>A	chr16.hg19:g.1717963G>A		103.0	0.0	.		122.0	65.0	.	NM_020825	A8MZL1|B1AJY1|Q8NDN1|Q9P2C1	Missense_Mutation	SNP	ENST00000397412.3	hg19	CCDS10440.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.636|9.636	1.137722|1.137722	0.21123|0.21123	.|.	.|.	ENSG00000007545|ENSG00000007545	ENST00000415022|ENST00000397412;ENST00000293925;ENST00000436138;ENST00000262317	.|.	.|.	.|.	5.86|5.86	3.88|3.88	0.44766|0.44766	.|.	0.761849|0.761849	0.12840|0.12840	N|N	0.434905|0.434905	T|T	0.44180|0.44180	0.1281|0.1281	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	.|B	.|0.23249	.|0.082	.|B	.|0.28011	.|0.085	T|T	0.12708|0.12708	-1.0537|-1.0537	6|8	.|.	.|.	.|.	-3.5501|-3.5501	9.7444|9.7444	0.40437|0.40437	0.0756:0.1391:0.7853:0.0|0.0756:0.1391:0.7853:0.0	.|.	.|1035	.|Q96RY5	.|CRML_HUMAN	E|S	135|1035;1035;1032;413	.|.	.|.	G|G	+|+	2|1	0|0	CRAMP1L|CRAMP1L	1657964|1657964	0.995000|0.995000	0.38212|0.38212	0.655000|0.655000	0.29622|0.29622	0.263000|0.263000	0.26337|0.26337	2.508000|2.508000	0.45450|0.45450	0.786000|0.786000	0.33708|0.33708	0.650000|0.650000	0.86243|0.86243	GGG|GGC	.	.	.	none		0.537	CRAMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157297.4		Missense_Mutation	A	1717963	G	A	1717963	5	1	246	1	0	0	0	0	0	0	1	0	3848	1246	43	2	3169	2	CRAMP1L	16	1717963	Splice_Site	SNP	G	TCGA-SX-A7SL-01A-11D-A34Z-10	1582288	1717963	88636790	56	15220											
HN1L	90861	hgsc.bcm.edu	37	chr16	1735486	1735486	+	Frame_Shift_Del	DEL	C	C	-																															cgagcaatctttttggaagtCcagaagaagctactccttcc																										TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr16:1735486delC	ENST00000248098.3	+	2	148	c.91delC	c.(91-93)ccafs	p.P31fs	LA16c-431H6.6_ENST00000454337.1_3'UTR|HN1L_ENST00000382710.4_Frame_Shift_Del_p.P19fs|HN1L_ENST00000561516.1_Frame_Shift_Del_p.P31fs|HN1L_ENST00000562684.1_Frame_Shift_Del_p.P59fs|HN1L_ENST00000569765.1_Frame_Shift_Del_p.P59fs|HN1L_ENST00000382711.5_Frame_Shift_Del_p.P15fs|HN1L_ENST00000569256.1_Intron	NM_144570.2	NP_653171.1	Q9H910	HN1L_HUMAN	hematological and neurological expressed 1-like	31						cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|kidney(2)|lung(3)|upper_aerodigestive_tract(1)	9						TTTTGGAAGTCCAGAAGAAGC	0.478																																					p.S30fs		Atlas-Indel,Pindel	.											.	HN1L	17	.	0			c.90delT						PASS	.						89	86	87					16																	1735486		2199	4300	6499	SO:0001589	frameshift_variant	90861	exon2			.	AK023154	CCDS10441.1	16p13.3	2006-12-13	2006-12-13	2006-12-13	ENSG00000206053	ENSG00000206053			14137	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 34"	C16orf34		15094197	Standard	NM_144570		Approved	FLJ13092, L11, KIAA1426	uc002cmg.3	Q9H910	OTTHUMG00000047859	ENST00000248098.3:c.91delC	chr16.hg19:g.1735486delC	ENSP00000248098:p.Pro31fs	79.0	0.0	0		73.0	48.0	0.657534	NM_144570	B1AJY2|Q6EIC7	Frame_Shift_Del	DEL	ENST00000248098.3	hg19	CCDS10441.1																																																																																			.	.	.	none		0.478	HN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109086.2	NM_144570		-	1735486	C	-	1735486	7	5	246	1	0	1	0	1	0	0	0	0	7257	855	30	0	97	0	HN1L	16	1735486	Frame_Shift_Del	DEL	C	TCGA-SX-A7SL-01A-11D-A34Z-10	17523	1735486	88619267	57	15221											
RPGRIP1L	23322	hgsc.bcm.edu	37	chr16	53674983	53674984	+	Frame_Shift_Ins	INS	-	-	A																															atatccacgaaagataccttINScttatctacaggtgttaaac																										TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr16:53674983_53674984insA	ENST00000379925.3	-	19	2969_2970	c.2919_2920insT	c.(2917-2922)aagaagfs	p.K974fs	RPGRIP1L_ENST00000563746.1_Frame_Shift_Ins_p.K974fs|RPGRIP1L_ENST00000564374.1_Frame_Shift_Ins_p.K974fs|RPGRIP1L_ENST00000568009.1_5'Flank|RPGRIP1L_ENST00000262135.4_Frame_Shift_Ins_p.K974fs	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	974					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)				AAAGATACCTTCTTATCTACAG	0.337																																					p.K974_V975delinsX		Atlas-Indel,Pindel	.											.	RPGRIP1L	118	.	0			c.2920_2921insT						PASS	.																																			SO:0001589	frameshift_variant	23322	exon19			.		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.2919_2920insT	chr16.hg19:g.53674983_53674984insA	ENSP00000369257:p.Lys974fs	130.0	0.0	0		152.0	92.0	0.605263	NM_001127897	A0PJ88|Q9Y2K8	Frame_Shift_Ins	INS	ENST00000379925.3	hg19	CCDS32447.1																																																																																			.	.	.	none		0.337	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272		A	53674984	-	A	53674983	7	5	246	1	0	1	1	0	0	0	0	0	13563	1792	62	0	1063	0	RPGRIP1L	16	53674983	Frame_Shift_Ins	INS	-	TCGA-SX-A7SL-01A-11D-A34Z-10	51939497	53674983	36679770	58	15222											
WDR81	124997	hgsc.bcm.edu	37	chr17	1634163	1634164	+	Frame_Shift_Ins	INS	-	-	A																															gtgtcagggcctgtgctcagINSctgcctcctccacatcgccc																										TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr17:1634163_1634164insA	ENST00000409644.1	+	3	3890_3891	c.3890_3891insA	c.(3889-3894)agctgcfs	p.SC1297fs	RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000446363.1_De_novo_Start_OutOfFrame|WDR81_ENST00000437219.2_Frame_Shift_Ins_p.SC94fs|WDR81_ENST00000545662.1_De_novo_Start_OutOfFrame|WDR81_ENST00000419248.1_Frame_Shift_Ins_p.SC70fs|WDR81_ENST00000309182.5_Frame_Shift_Ins_p.SC246fs	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1297					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)		CCTGTGCTCAGCTGCCTCCTCC	0.639																																					p.S1297fs		Atlas-INDEL	.											.	WDR81	180	.	0			c.3890_3891insA						PASS	.																																			SO:0001589	frameshift_variant	124997	exon3			.	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	Exception_encountered	chr17.hg19:g.1634163_1634164insA	ENSP00000386609:p.Ser1297fs	53.0	0.0	0		34.0	16.0	0.470588	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Frame_Shift_Ins	INS	ENST00000409644.1	hg19	CCDS54062.1																																																																																			.	.	.	none		0.639	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348		A	1634164	-	A	1634163	7	5	246	1	0	1	1	0	0	0	0	0	17342	971	34	0	3962	0	WDR81	17	1634163	Frame_Shift_Ins	INS	-	TCGA-SX-A7SL-01A-11D-A34Z-10		1634163	79561047	59	15223											
SGSM2	9905	hgsc.bcm.edu	37	chr17	2278871	2278878	+	Frame_Shift_Del	DEL	CCGGGACT	CCGGGACT	-																															acctgagcaggaagcaggacCcgggactccgggcaccgccg																								rs61739394	byFrequency	TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	CCGGGACT	CCGGGACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr17:2278871_2278878delCCGGGACT	ENST00000426855.2	+	17	2226_2233	c.2051_2058delCCGGGACT	c.(2050-2058)cccgggactfs	p.PGT687fs	RP1-59D14.5_ENST00000573007.1_RNA|RP1-59D14.5_ENST00000574290.1_RNA|SGSM2_ENST00000574563.1_Frame_Shift_Del_p.PGT687fs|SGSM2_ENST00000268989.3_Frame_Shift_Del_p.PGT732fs	NM_001098509.1	NP_001091979.1	O43147	SGSM2_HUMAN	small G protein signaling modulator 2	687	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				late endosome to Golgi transport (GO:0034499)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)	p.G730W(1)		biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)		GAAGCAGGACCCGGGACTCCGGGCACCG	0.615																																					p.729_731del		Atlas-Indel,Pindel	.											.	SGSM2	60	.	1	Substitution - Missense(1)	kidney(1)	c.2185_2192del						PASS	.																																			SO:0001589	frameshift_variant	9905	exon18			.	BC039204	CCDS32526.1, CCDS45570.1	17p13.3	2013-07-10	2007-08-14	2007-08-14		ENSG00000141258		"Small G protein signaling modulators"	29026	protein-coding gene	gene with protein product		611418	"RUN and TBC1 domain containing 1"	RUTBC1		9455477, 17509819, 21808068	Standard	NM_014853		Approved	KIAA0397	uc002fum.4	O43147		ENST00000426855.2:c.2051_2058delCCGGGACT	chr17.hg19:g.2278871_2278878delCCGGGACT	ENSP00000415107:p.Pro687fs	49.0	0.0	0		38.0	15.0	0.394737	NM_014853	A5LGW2|B4DH69|Q49AC2|Q6ZUY2|Q8IXU4	Frame_Shift_Del	DEL	ENST00000426855.2	hg19	CCDS45570.1																																																																																			.	.	.	none		0.615	SGSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438186.1	NM_014853		-	2278878	CCGGGACT	-	2278871	7	5	246	1	0	1	0	1	0	0	0	0	14236	623	22	0	2256	0	SGSM2	17	2278871	Frame_Shift_Del	DEL	CCGGGACT	TCGA-SX-A7SL-01A-11D-A34Z-10	644708	2278871	78916339	60	15224											
SGSM2	9905	hgsc.bcm.edu	37	chr17	2282478	2282480	+	In_Frame_Del	DEL	CAT	CAT	-																															aacaacatggacttcactgaCatcatcaagtttttcaatgg																								rs143690160		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	CAT	CAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr17:2282478_2282480delCAT	ENST00000426855.2	+	22	3088_3090	c.2913_2915delCAT	c.(2911-2916)gacatc>gac	p.I973del	RP1-59D14.5_ENST00000573007.1_RNA|RP1-59D14.5_ENST00000574290.1_RNA|SGSM2_ENST00000574563.1_In_Frame_Del_p.I973del|SGSM2_ENST00000268989.3_In_Frame_Del_p.I1018del	NM_001098509.1	NP_001091979.1	O43147	SGSM2_HUMAN	small G protein signaling modulator 2	973					late endosome to Golgi transport (GO:0034499)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)	p.I1018delI(1)		biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)		ACTTCACTGACATCATCAAGTTT	0.581																																					p.1016_1017del		Atlas-Indel,Pindel	.											.	SGSM2	60	.	1	Deletion - In frame(1)	large_intestine(1)	c.3047_3049del						PASS	.																																			SO:0001651	inframe_deletion	9905	exon23			.	BC039204	CCDS32526.1, CCDS45570.1	17p13.3	2013-07-10	2007-08-14	2007-08-14		ENSG00000141258		"Small G protein signaling modulators"	29026	protein-coding gene	gene with protein product		611418	"RUN and TBC1 domain containing 1"	RUTBC1		9455477, 17509819, 21808068	Standard	NM_014853		Approved	KIAA0397	uc002fum.4	O43147		ENST00000426855.2:c.2913_2915delCAT	chr17.hg19:g.2282481_2282483delCAT	ENSP00000415107:p.Ile973del	124.0	0.0	0		93.0	32.0	0.344086	NM_014853	A5LGW2|B4DH69|Q49AC2|Q6ZUY2|Q8IXU4	In_Frame_Del	DEL	ENST00000426855.2	hg19	CCDS45570.1																																																																																			.	.	.	none		0.581	SGSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438186.1	NM_014853		-	2282480	CAT	-	2282478	7	5	246	1	0	1	0	1	0	0	0	0	14236	477	17	0	3138	0	SGSM2	17	2282478	In_Frame_Del	DEL	CAT	TCGA-SX-A7SL-01A-11D-A34Z-10	3607	2282478	78912732	61	15225											
ANKFY1	51479	hgsc.bcm.edu	37	chr17	4087143	4087143	+	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	gcccagcacagtctggtctcGggaatctttgaggctgaagt	8	10	13	10	1	3	2	0	2	3	0	4	3	3	3	1	3	1	2	1	3	2	1			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr17:4087143G>A	ENST00000341657.4	-	13	1797	c.1762C>T	c.(1762-1764)Cga>Tga	p.R588*	ANKFY1_ENST00000574367.1_Nonsense_Mutation_p.R588*|CYB5D2_ENST00000573984.1_Intron|ANKFY1_ENST00000573722.1_5'Flank|Y_RNA_ENST00000516003.1_RNA|ANKFY1_ENST00000570535.1_Nonsense_Mutation_p.R630*	NM_016376.3	NP_057460.3	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	588					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						GTCTGGTCTCGGGAATCTTTG	0.527																																					p.R630X		Atlas-SNP	.											.	ANKFY1	81	.	0			c.C1888T						PASS	.						130	134	133					17																	4087143		1936	4146	6082	SO:0001587	stop_gained	51479	exon13			GGTCTCGGGAATC	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.1762C>T	chr17.hg19:g.4087143G>A	ENSP00000343362:p.Arg588*	68.0	0.0	.		35.0	9.0	.	NM_001257999	A8KA65|Q5RKV4|Q9ULG5	Nonsense_Mutation	SNP	ENST00000341657.4	hg19		.	.	.	.	.	.	.	.	.	.	G	36	5.646460	0.96704	.	.	ENSG00000185722	ENST00000341657;ENST00000535427	.	.	.	4.81	-0.265	0.12946	.	0.197229	0.41001	D	0.000965	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	-0.3118	7.3258	0.26555	0.0923:0.0:0.3819:0.5258	.	.	.	.	X	588;529	.	ENSP00000343362:R588X	R	-	1	2	ANKFY1	4033892	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.230000	0.32612	0.388000	0.25054	0.467000	0.42956	CGA	.	.	.	none		0.527	ANKFY1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000438702.1	NM_016376		A	4087143	G	A	4087143	4	1	246	1	0	0	0	0	0	1	0	0	626	1124	39	1	1802	1	ANKFY1	17	4087143	Nonsense_Mutation	SNP	G	TCGA-SX-A7SL-01A-11D-A34Z-10	1804665	4087143	77108067	62	15226											
MYO18A	399687	hgsc.bcm.edu	37	chr17	27441098	27441098	+	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	gggggttccaagtcgtcaaaCgccagctcgatgttctcctg	7	10	12	12	3	2	0	1	0	1	0	6	1	3	0	3	2	2	3	3	2	2	2			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr17:27441098C>A	ENST00000527372.1	-	15	2709	c.2529G>T	c.(2527-2529)gcG>gcT	p.A843A	MYO18A_ENST00000354329.4_Silent_p.A843A|MYO18A_ENST00000533112.1_Silent_p.A843A|MYO18A_ENST00000531253.1_Silent_p.A843A	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	843	Myosin motor.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			AGTCGTCAAACGCCAGCTCGA	0.607																																					p.A843A	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.G2529T						PASS	.						39	47	45					17																	27441098		1988	4160	6148	SO:0001819	synonymous_variant	399687	exon15			GTCAAACGCCAGC	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.2529G>T	chr17.hg19:g.27441098C>A		23.0	0.0	.		24.0	6.0	.	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Silent	SNP	ENST00000527372.1	hg19	CCDS45642.1																																																																																			.	.	.	none		0.607	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		A	27441098	C	A	27441098	2	1	246	1	0	0	0	0	0	0	0	1	10072	523	19	4		4	MYO18A	17	27441098	Silent	SNP	C	TCGA-SX-A7SL-01A-11D-A34Z-10	23353955	27441098	53754112	63	15227											
TMEM106A	113277	hgsc.bcm.edu	37	chr17	41365867	41365867	+	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	agctggagaagcagttggtgGctctcattccctatggggac	8	10	14	9	0	1	1	1	0	1	1	3	3	2	2	1	5	2	4	1	5	2	3			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr17:41365867G>T	ENST00000331615.3	+	4	469	c.232G>T	c.(232-234)Gct>Tct	p.A78S	TMEM106A_ENST00000541594.1_Missense_Mutation_p.A30S|TMEM106A_ENST00000536052.1_Missense_Mutation_p.A78S|TMEM106A_ENST00000592564.1_3'UTR|TMEM106A_ENST00000588659.1_Missense_Mutation_p.A78S	NM_145041.1	NP_659478.1	Q96A25	T106A_HUMAN	transmembrane protein 106A	78						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)	11		Breast(137;0.0164)		BRCA - Breast invasive adenocarcinoma(366;0.0917)		GCAGTTGGTGGCTCTCATTCC	0.572																																					p.A78S		Atlas-SNP	.											.	TMEM106A	20	.	0			c.G232T						PASS	.						103	80	88					17																	41365867		2203	4296	6499	SO:0001583	missense	113277	exon4			TTGGTGGCTCTCA	AK056132	CCDS11462.1, CCDS74073.1	17q21.31	2012-01-23			ENSG00000184988	ENSG00000184988			28288	protein-coding gene	gene with protein product							Standard	XM_006721658		Approved	MGC20235	uc002idn.1	Q96A25		ENST00000331615.3:c.232G>T	chr17.hg19:g.41365867G>T	ENSP00000330774:p.Ala78Ser	50.0	0.0	.		22.0	9.0	.	NM_145041	A8K2X2|B7Z698	Missense_Mutation	SNP	ENST00000331615.3	hg19	CCDS11462.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.040236	0.93630	.	.	ENSG00000184988	ENST00000331615;ENST00000536052;ENST00000541594	T;T;T	0.38401	1.14;1.14;1.14	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.65481	0.2695	M	0.86028	2.79	0.54753	D	0.999982	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	T	0.70439	-0.4871	10	0.87932	D	0	-19.9634	16.644	0.85172	0.0:0.0:1.0:0.0	.	78;30;78	B7Z779;B7Z698;Q96A25	.;.;T106A_HUMAN	S	78;78;30	ENSP00000330774:A78S;ENSP00000439835:A78S;ENSP00000439844:A30S	ENSP00000330774:A78S	A	+	1	0	TMEM106A	38721393	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.837000	0.75354	2.646000	0.89796	0.655000	0.94253	GCT	.	.	.	none		0.572	TMEM106A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453470.2	NM_145041		T	41365867	G	T	41365867	3	4	246	1	0	0	0	0	1	0	0	0	16032	1203	42	4	238	4	TMEM106A	17	41365867	Missense_Mutation	SNP	G	TCGA-SX-A7SL-01A-11D-A34Z-10	13924769	41365867	39829343	64	15228											
MED13	9969	hgsc.bcm.edu	37	chr17	60038289	60038289	+	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	ttctccatatagatctgtgcAagatgcaagaatccaccttt	12	13	6	10	0	2	3	0	0	2	3	4	3	3	3	3	0	2	2	3	0	5	4			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr17:60038289A>T	ENST00000397786.2	-	23	5495	c.5419T>A	c.(5419-5421)Tgc>Agc	p.C1807S		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1807					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						AGATCTGTGCAAGATGCAAGA	0.333																																					p.C1807S		Atlas-SNP	.											.	MED13	181	.	0			c.T5419A						PASS	.						120	110	113					17																	60038289		1841	4094	5935	SO:0001583	missense	9969	exon23			CTGTGCAAGATGC	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.5419T>A	chr17.hg19:g.60038289A>T	ENSP00000380888:p.Cys1807Ser	166.0	0.0	.		180.0	106.0	.	NM_005121	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	hg19	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.798802	0.90538	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	D	0.82711	-1.64	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	D	0.90511	0.7027	M	0.75447	2.3	0.80722	D	1	D	0.62365	0.991	D	0.78314	0.991	D	0.91619	0.5309	10	0.72032	D	0.01	-7.5787	15.3239	0.74144	1.0:0.0:0.0:0.0	.	1807	Q9UHV7	MED13_HUMAN	S	1807;1806	ENSP00000380888:C1807S	ENSP00000262436:C1806S	C	-	1	0	MED13	57393071	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.842000	0.92136	2.016000	0.59253	0.519000	0.50382	TGC	.	.	.	none		0.333	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		T	60038289	A	T	60038289	3	4	246	1	0	0	0	0	1	0	0	0	9437	130	5	5	1137	5	MED13	17	60038289	Missense_Mutation	SNP	A	TCGA-SX-A7SL-01A-11D-A34Z-10	18672422	60038289	21156921	65	15229											
PSMC5	5705	hgsc.bcm.edu	37	chr17	61909160	61909160	+	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	tcaggaggactttgagatggCagtagccaaggtataggcct	11	9	14	7	0	1	1	1	1	0	1	1	4	1	3	2	5	1	3	2	5	4	4			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr17:61909160C>T	ENST00000310144.6	+	11	1465	c.1157C>T	c.(1156-1158)gCa>gTa	p.A386V	PSMC5_ENST00000375812.4_Missense_Mutation_p.A378V|FTSJ3_ENST00000580295.1_5'Flank|PSMC5_ENST00000580864.1_Missense_Mutation_p.A378V|PSMC5_ENST00000581882.1_Missense_Mutation_p.A378V	NM_002805.5	NP_002796.4	P62195	PRS8_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 5	386	May mediate interaction with PRPF9. {ECO:0000250|UniProtKB:P62196}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of inclusion body assembly (GO:0090261)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|nuclear proteasome complex (GO:0031595)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|thyrotropin-releasing hormone receptor binding (GO:0031531)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(2)|large_intestine(8)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	20						TTTGAGATGGCAGTAGCCAAG	0.527																																					p.A386V		Atlas-SNP	.											.	PSMC5	41	.	0			c.C1157T						PASS	.						111	87	95					17																	61909160		2203	4300	6503	SO:0001583	missense	5705	exon11			AGATGGCAGTAGC	L38810	CCDS11645.1, CCDS56043.1	17q23.3	2010-04-21			ENSG00000087191	ENSG00000087191		"Proteasome (prosome, macropain) subunits", "ATPases / AAA-type"	9552	protein-coding gene	gene with protein product		601681				9473509, 9048938	Standard	NM_002805		Approved	SUG1, p45/SUG, TBP10, p45, S8, TRIP1, SUG-1	uc002jcb.3	P62195		ENST00000310144.6:c.1157C>T	chr17.hg19:g.61909160C>T	ENSP00000310572:p.Ala386Val	118.0	0.0	.		142.0	46.0	.	NM_002805	A8K3Z3|A8K763|O35051|O43208|P47210|P52915|P52916	Missense_Mutation	SNP	ENST00000310144.6	hg19	CCDS11645.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.557777	0.86231	.	.	ENSG00000087191	ENST00000310144;ENST00000375812	T;T	0.80653	-1.4;-1.4	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.90256	0.6953	M	0.86864	2.845	0.80722	D	1	D;D	0.89917	0.996;1.0	P;D	0.63703	0.763;0.917	D	0.91405	0.5146	10	0.87932	D	0	.	16.9624	0.86275	0.0:1.0:0.0:0.0	.	378;386	A8K3Z3;P62195	.;PRS8_HUMAN	V	386;378	ENSP00000310572:A386V;ENSP00000364970:A378V	ENSP00000310572:A386V	A	+	2	0	PSMC5	59262892	1.000000	0.71417	0.999000	0.59377	0.962000	0.63368	5.877000	0.69675	2.873000	0.98535	0.561000	0.74099	GCA	.	.	.	none		0.527	PSMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444404.1	NM_002805		T	61909160	C	T	61909160	3	4	246	1	0	0	0	0	1	0	0	0	12700	710	25	2	1199	2	PSMC5	17	61909160	Missense_Mutation	SNP	C	TCGA-SX-A7SL-01A-11D-A34Z-10	1870871	61909160	19286050	66	15230											
TRIM65	201292	hgsc.bcm.edu	37	chr17	73887900	73887901	+	Frame_Shift_Del	DEL	AG	AG	-																															aacggcctccttactctgccAgagtttcctcctcagtggac																								rs372788583		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr17:73887900_73887901delAG	ENST00000269383.3	-	5	1043_1044	c.978_979delCT	c.(976-981)ctctggfs	p.W327fs		NM_001256124.1|NM_173547.3	NP_001243053.1|NP_775818.2	Q6PJ69	TRI65_HUMAN	tripartite motif containing 65	327	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)			TTACTCTGCCAGAGTTTCCTCC	0.574																																					p.327_327del		Atlas-Indel,Pindel	.											.	TRIM65	23	.	0			c.979_980del						PASS	.			5,4259		0,5,2127						3.4	1			113	14,8240		6,2,4119	no	frameshift	TRIM65	NM_173547.2		6,7,6246	A1A1,A1R,RR		0.1696,0.1173,0.1518				19,12499				SO:0001589	frameshift_variant	201292	exon5			.	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.978_979delCT	chr17.hg19:g.73887902_73887903delAG	ENSP00000269383:p.Trp327fs	72.0	0.0	0		68.0	41.0	0.602941	NM_173547	Q4G0F0|Q6DKJ6|Q9BRP6	Frame_Shift_Del	DEL	ENST00000269383.3	hg19	CCDS11732.1																																																																																			.	.	.	weak		0.574	TRIM65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255170.2	NM_173547		-	73887901	AG	-	73887900	7	5	246	1	0	1	0	1	0	0	0	0	16551	188	7	0	582	0	TRIM65	17	73887900	Frame_Shift_Del	DEL	AG	TCGA-SX-A7SL-01A-11D-A34Z-10	11978740	73887900	7307310	67	15231											
ABHD3	171586	hgsc.bcm.edu	37	chr18	19283591	19283591	+	Frame_Shift_Del	DEL	G	G	-																															agtgatgaaaggtctaagcaGggtctgtcctcgaccctccc																										TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr18:19283591delG	ENST00000289119.2	-	2	419	c.280delC	c.(280-282)ctgfs	p.L95fs	ABHD3_ENST00000579875.1_5'UTR|ABHD3_ENST00000578270.1_5'UTR|ABHD3_ENST00000580981.1_Frame_Shift_Del_p.L95fs	NM_138340.4	NP_612213.2	Q8WU67	ABHD3_HUMAN	abhydrolase domain containing 3	95						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						GGTCTAAGCAGGGTCTGTCCT	0.517																																					p.L94fs		Atlas-Indel,Pindel	.											.	ABHD3	32	.	0			c.281delT						PASS	.						97	86	89					18																	19283591		2203	4300	6503	SO:0001589	frameshift_variant	171586	exon2			.	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.280delC	chr18.hg19:g.19283591delG	ENSP00000289119:p.Leu95fs	73.0	0.0	0		59.0	20.0	0.338983	NM_138340	B0YIV0|B7Z5C2|O43411	Frame_Shift_Del	DEL	ENST00000289119.2	hg19	CCDS32802.1																																																																																			.	.	.	none		0.517	ABHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444757.1			-	19283591	G	-	19283591	7	5	246	1	0	1	0	1	0	0	0	0	83	991	35	0	981	0	ABHD3	18	19283591	Frame_Shift_Del	DEL	G	TCGA-SX-A7SL-01A-11D-A34Z-10		19283591	58793657	68	15232											
PPAN	56342	hgsc.bcm.edu	37	chr19	10218531	10218531	+	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	tgaccttccaggtcaagaagGtgagaggggtggaggtggta	10	8	18	5	0	1	3	1	2	0	2	2	5	2	4	2	7	0	1	2	7	3	2			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr19:10218531G>C	ENST00000253107.7	+	4	448		c.e4+1		PPAN_ENST00000556468.1_Splice_Site|PPAN-P2RY11_ENST00000393796.4_Splice_Site|PPAN_ENST00000393793.1_Splice_Site|PPAN-P2RY11_ENST00000428358.1_Splice_Site|SNORD105_ENST00000386910.1_RNA|SNORD105B_ENST00000458770.1_RNA	NM_020230.5	NP_064615.3	Q9NQ55	SSF1_HUMAN	peter pan homolog (Drosophila)						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)			GGTCAAGAAGGTGAGAGGGGT	0.597																																					.		Atlas-SNP	.											.	PPAN	43	.	0			c.342+1G>C						PASS	.						76	90	85					19																	10218531		2203	4299	6502	SO:0001630	splice_region_variant	56342	exon4			AAGAAGGTGAGAG	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.342+1G>C	chr19.hg19:g.10218531G>C		43.0	0.0	.		57.0	25.0	.	NM_020230	C9J3F9|Q9BW97|Q9H170	Splice_Site	SNP	ENST00000253107.7	hg19	CCDS12225.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.989428	0.53934	.	.	ENSG00000243207;ENSG00000243207;ENSG00000130810;ENSG00000130810;ENSG00000130810;ENSG00000130810;ENSG00000130810;ENSG00000130810	ENST00000428358;ENST00000393796;ENST00000253107;ENST00000556468;ENST00000342696;ENST00000393793;ENST00000446223;ENST00000430370	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.1466	0.89659	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PPAN;PPAN-P2RY11	10079531	1.000000	0.71417	0.984000	0.44739	0.522000	0.34438	7.352000	0.79404	2.586000	0.87340	0.561000	0.74099	.	.	.	.	none		0.597	PPAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316658.1	NM_020230	Intron	C	10218531	G	C	10218531	5	2	246	1	0	0	0	0	0	0	1	0	12295	1275	44	4	357	4	PPAN	19	10218531	Splice_Site	SNP	G	TCGA-SX-A7SL-01A-11D-A34Z-10		10218531	48910452	69	15233											
COX7A1	1346	hgsc.bcm.edu	37	chr19	36641914	36641914	+	Silent	SNP	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	gggaaggaggcccagccaagGgagtacaagctgtagacagt	13	4	16	8	0	0	1	0	0	0	1	0	4	0	4	2	4	3	3	2	4	5	2			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr19:36641914G>A	ENST00000292907.3	-	4	671	c.210C>T	c.(208-210)tcC>tcT	p.S70S	COX7A1_ENST00000437291.2_Silent_p.S14S|AD001527.7_ENST00000604228.1_RNA	NM_001864.2	NP_001855.1	P24310	CX7A1_HUMAN	cytochrome c oxidase subunit VIIa polypeptide 1 (muscle)	70					generation of precursor metabolites and energy (GO:0006091)|hydrogen ion transmembrane transport (GO:1902600)	integral component of membrane (GO:0016021)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)			endometrium(2)|large_intestine(1)	3	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			CCCAGCCAAGGGAGTACAAGC	0.542																																					p.S70S		Atlas-SNP	.											.	COX7A1	9	.	0			c.C210T						PASS	.						135	116	122					19																	36641914		2203	4300	6503	SO:0001819	synonymous_variant	1346	exon4			GCCAAGGGAGTAC	BC002757	CCDS12490.1	19q13.1	2011-07-04			ENSG00000161281	ENSG00000161281	1.9.3.1	"Mitochondrial respiratory chain complex / Complex IV"	2287	protein-coding gene	gene with protein product		123995		COX7A		1327965, 2550906	Standard	NM_001864		Approved	COX7AH	uc002odm.1	P24310	OTTHUMG00000048144	ENST00000292907.3:c.210C>T	chr19.hg19:g.36641914G>A		109.0	0.0	.		74.0	35.0	.	NM_001864		Silent	SNP	ENST00000292907.3	hg19	CCDS12490.1	.	.	.	.	.	.	.	.	.	.	g	7.112	0.576232	0.13686	.	.	ENSG00000161281	ENST00000437291	.	.	.	4.54	3.51	0.40186	.	.	.	.	.	T	0.58395	0.2119	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54503	-0.8284	4	.	.	.	-14.8375	8.4726	0.32995	0.1061:0.0:0.8939:0.0	.	.	.	.	L	100	.	.	P	-	2	0	COX7A1	41333754	1.000000	0.71417	0.991000	0.47740	0.585000	0.36419	2.050000	0.41297	1.121000	0.41925	0.643000	0.83706	CCC	.	.	.	none		0.542	COX7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109545.2	NM_001864		A	36641914	G	A	36641914	2	1	246	1	0	0	0	0	0	0	0	1	3781	1219	43	2		2	COX7A1	19	36641914	Silent	SNP	G	TCGA-SX-A7SL-01A-11D-A34Z-10	26423383	36641914	22487069	70	15234											
FIZ1	84922	hgsc.bcm.edu	37	chr19	56109104	56109104	+	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	gcttgagcgctgtgtgccggGcaaagtggcgccgcaggtct	5	8	17	11	4	1	1	0	1	1	0	1	1	1	1	2	3	2	4	2	3	1	1			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr19:56109104G>T	ENST00000221665.3	-	2	217	c.128C>A	c.(127-129)gCc>gAc	p.A43D	FIZ1_ENST00000592585.1_Missense_Mutation_p.A43D|ZNF524_ENST00000301073.3_5'Flank	NM_032836.2	NP_116225.2	Q96SL8	FIZ1_HUMAN	FLT3-interacting zinc finger 1	43					positive regulation of protein phosphorylation (GO:0001934)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)	11			BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		TGTGTGCCGGGCAAAGTGGCG	0.672																																					p.A43D		Atlas-SNP	.											FIZ1,NS,carcinoma,0,1	FIZ1	29	.	0			c.C128A						PASS	.						50	46	48					19																	56109104		2203	4299	6502	SO:0001583	missense	84922	exon2			TGCCGGGCAAAGT	AK027674	CCDS12928.1	19q13.42	2013-01-08				ENSG00000179943		"Zinc fingers, C2H2-type"	25917	protein-coding gene	gene with protein product		609133				12566383	Standard	NM_032836		Approved	FLJ14768, ZNF798	uc002qli.4	Q96SL8		ENST00000221665.3:c.128C>A	chr19.hg19:g.56109104G>T	ENSP00000221665:p.Ala43Asp	109.0	0.0	.		77.0	33.0	.	NM_032836	A2RU72|Q6ZMJ7	Missense_Mutation	SNP	ENST00000221665.3	hg19	CCDS12928.1	.	.	.	.	.	.	.	.	.	.	G	11.91	1.779874	0.31502	.	.	ENSG00000179943	ENST00000221665	T	0.18810	2.19	3.57	3.57	0.40892	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17238	0.0414	N	0.21282	0.65	0.09310	N	1	B	0.25850	0.136	B	0.33196	0.159	T	0.20207	-1.0282	9	0.72032	D	0.01	-17.8725	9.9577	0.41678	0.0:0.0:0.7965:0.2035	.	43	Q96SL8	FIZ1_HUMAN	D	43	ENSP00000221665:A43D	ENSP00000221665:A43D	A	-	2	0	FIZ1	60800916	0.000000	0.05858	0.988000	0.46212	0.756000	0.42949	0.243000	0.18106	2.017000	0.59298	0.462000	0.41574	GCC	.	.	.	none		0.672	FIZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453350.1	NM_032836		T	56109104	G	T	56109104	3	4	246	1	0	0	0	0	1	0	0	0	5907	1203	42	4	1370	4	FIZ1	19	56109104	Missense_Mutation	SNP	G	TCGA-SX-A7SL-01A-11D-A34Z-10	19467190	56109104	3019879	71	15235											
SNRPB2	6629	hgsc.bcm.edu	37	chr20	16719517	16719517	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaactccaaattcagctaaTacccaaggaaattcaacacc	17	7	5	12	0	2	0	2	0	0	0	3	2	3	2	3	2	4	1	3	2	7	4			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr20:16719517T>C	ENST00000246071.6	+	5	615	c.399T>C	c.(397-399)aaT>aaC	p.N133N	SNRPB2_ENST00000377943.5_Silent_p.N133N	NM_003092.4	NP_003083.1	P08579	RU2B_HUMAN	small nuclear ribonucleoprotein polypeptide B	133					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U2 snRNP (GO:0005686)	nucleotide binding (GO:0000166)|snRNA binding (GO:0017069)			large_intestine(2)|lung(2)|urinary_tract(1)	5						ATTCAGCTAATACCCAAGGAA	0.323																																					p.N133N		Atlas-SNP	.											.	SNRPB2	12	.	0			c.T399C						PASS	.						65	66	66					20																	16719517		2203	4298	6501	SO:0001819	synonymous_variant	6629	exon5			AGCTAATACCCAA		CCDS13123.1	20p12.1	2013-02-12	2010-07-07		ENSG00000125870	ENSG00000125870		"RNA binding motif (RRM) containing"	11155	protein-coding gene	gene with protein product		603520	"small nuclear ribonucleoprotein polypeptide B2", "small nuclear ribonucleoprotein polypeptide B''"			2951739	Standard	NM_198220		Approved	Msl1	uc002wpi.2	P08579	OTTHUMG00000031933	ENST00000246071.6:c.399T>C	chr20.hg19:g.16719517T>C		166.0	0.0	.		210.0	131.0	.	NM_003092	B2R7J3|D3DW21|Q9UJD4	Silent	SNP	ENST00000246071.6	hg19	CCDS13123.1																																																																																			.	.	.	none		0.323	SNRPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078110.1	NM_003092		C	16719517	T	C	16719517	2	2	246	1	0	0	0	0	0	0	0	1	14875	1403	49	3		3	SNRPB2	20	16719517	Silent	SNP	T	TCGA-SX-A7SL-01A-11D-A34Z-10		16719517	46306003	72	15236											
SYS1	90196	hgsc.bcm.edu	37	chr20	43995569	43995569	+	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	aagcagtgtctggatttcacTgtcactgtccatttctttca	8	16	7	10	0	5	0	3	0	2	0	6	1	6	1	1	1	1	1	1	1	1	3	rs564852027		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr20:43995569T>A	ENST00000243918.5	+	4	576	c.285T>A	c.(283-285)acT>acA	p.T95T	SYS1_ENST00000414310.1_Silent_p.T74T|SYS1-DBNDD2_ENST00000452133.1_Intron|SYS1_ENST00000372727.1_Silent_p.T95T|SYS1-DBNDD2_ENST00000475242.1_Intron|SYS1_ENST00000426004.1_Intron|SYS1_ENST00000479779.1_3'UTR	NM_033542.3	NP_291020.1	Q8N2H4	SYS1_HUMAN	Sys1 golgi trafficking protein	95					protein transport (GO:0015031)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|large_intestine(2)|prostate(1)|skin(1)	7		Myeloproliferative disorder(115;0.0122)				TGGATTTCACTGTCACTGTCC	0.587																																					p.T95T		Atlas-SNP	.											.	SYS1	15	.	0			c.T285A						PASS	.						161	137	145					20																	43995569		2203	4300	6503	SO:0001819	synonymous_variant	90196	exon5			TTTCACTGTCACT	AL021578	CCDS13351.1, CCDS56192.1	20q13.12	2014-05-07	2014-05-07	2006-11-06	ENSG00000204070	ENSG00000204070			16162	protein-coding gene	gene with protein product		612979	"chromosome 20 open reading frame 169", "SYS1 Golgi-localized integral membrane protein homolog (S. cerevisiae)"	C20orf169		15077113	Standard	NM_001197129		Approved	dJ453C12.4	uc002xnv.3	Q8N2H4	OTTHUMG00000032579	ENST00000243918.5:c.285T>A	chr20.hg19:g.43995569T>A		135.0	0.0	.		145.0	47.0	.	NM_001197129	C9JFB3|E1P620|Q5QPU7|Q96SD8|Q9BQZ2|Q9BQZ4|Q9H1F7	Silent	SNP	ENST00000243918.5	hg19	CCDS13351.1																																																																																			.	.	.	none		0.587	SYS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079453.2	NM_033542		A	43995569	T	A	43995569	2	1	246	1	0	0	0	0	0	0	0	1	15476	1567	55	5		5	SYS1	20	43995569	Silent	SNP	T	TCGA-SX-A7SL-01A-11D-A34Z-10	27276052	43995569	19029951	73	15237											
CDH22	64405	hgsc.bcm.edu	37	chr20	44806794	44806794	+	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	agaacacgtcctgctcctgcCggttgaagcccacgtgctgc	7	8	11	15	3	0	2	0	1	0	1	2	2	2	2	4	1	6	3	4	1	2	1			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr20:44806794C>A	ENST00000372262.3	-	10	2106	c.1706G>T	c.(1705-1707)cGg>cTg	p.R569L	CDH22_ENST00000537909.1_Missense_Mutation_p.R569L	NM_021248.1	NP_067071.1	Q9UJ99	CAD22_HUMAN	cadherin 22, type 2	569	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	44		Myeloproliferative disorder(115;0.0122)				CTGCTCCTGCCGGTTGAAGCC	0.642																																					p.R569L		Atlas-SNP	.											.	CDH22	112	.	0			c.G1706T						PASS	.						75	57	63					20																	44806794		2203	4300	6503	SO:0001583	missense	64405	exon11			TCCTGCCGGTTGA	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.1706G>T	chr20.hg19:g.44806794C>A	ENSP00000361336:p.Arg569Leu	74.0	0.0	.		69.0	37.0	.	NM_021248	B9EGK7|O43205	Missense_Mutation	SNP	ENST00000372262.3	hg19	CCDS13395.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.711454	0.89112	.	.	ENSG00000149654	ENST00000372262;ENST00000537909	T;T	0.59638	0.25;0.25	4.36	4.36	0.52297	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.66713	0.2817	M	0.76328	2.33	0.58432	D	0.999997	D	0.54964	0.969	P	0.50708	0.648	T	0.71094	-0.4692	10	0.46703	T	0.11	.	15.618	0.76784	0.0:1.0:0.0:0.0	.	569	Q9UJ99	CAD22_HUMAN	L	569	ENSP00000361336:R569L;ENSP00000437790:R569L	ENSP00000361336:R569L	R	-	2	0	CDH22	44240201	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.586000	0.60984	2.263000	0.75096	0.650000	0.86243	CGG	.	.	.	none		0.642	CDH22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080491.1	NM_021248		A	44806794	C	A	44806794	3	1	246	1	0	0	0	0	1	0	0	0	3109	652	23	4	788	4	CDH22	20	44806794	Missense_Mutation	SNP	C	TCGA-SX-A7SL-01A-11D-A34Z-10	811225	44806794	18218726	74	15238											
MYT1	4661	hgsc.bcm.edu	37	chr20	62843457	62843457	+	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	ctcctggctgcacaggccagGgtcacgtgaacagcaaccgc	9	5	12	15	2	1	1	1	1	0	0	2	1	2	1	3	3	4	3	3	3	2	0			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr20:62843457G>A	ENST00000328439.1	+	9	1847	c.1483G>A	c.(1483-1485)Ggt>Agt	p.G495S	MYT1_ENST00000360149.4_Missense_Mutation_p.G197S|MYT1_ENST00000536311.1_Missense_Mutation_p.G495S	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0	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)			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)					CACAGGCCAGGGTCACGTGAA	0.637																																					p.G495S	GBM(59;481 1041 20555 21139 33705)	Atlas-SNP	.											.	MYT1	152	.	0			c.G1483A						PASS	.						136	126	129					20																	62843457		2203	4300	6503	SO:0001583	missense	4661	exon9			GGCCAGGGTCACG	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.1483G>A	chr20.hg19:g.62843457G>A	ENSP00000327465:p.Gly495Ser	25.0	0.0	.		29.0	21.0	.	NM_004535	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000328439.1	hg19	CCDS13558.1	.	.	.	.	.	.	.	.	.	.	G	19.41	3.822666	0.71028	.	.	ENSG00000196132	ENST00000360149;ENST00000328439;ENST00000536311	T;T;T	0.72505	-0.66;-0.61;1.74	4.46	4.46	0.54185	.	0.000000	0.85682	D	0.000000	D	0.87442	0.6178	M	0.91818	3.245	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.997;0.999	D	0.90880	0.4753	10	0.87932	D	0	-27.2192	17.4965	0.87719	0.0:0.0:1.0:0.0	.	495;495;197	F5H7M8;Q01538;Q6P6D5	.;MYT1_HUMAN;.	S	197;495;495	ENSP00000353269:G197S;ENSP00000327465:G495S;ENSP00000442412:G495S	ENSP00000327465:G495S	G	+	1	0	MYT1	62313901	1.000000	0.71417	0.997000	0.53966	0.689000	0.40095	9.725000	0.98778	2.187000	0.69744	0.557000	0.71058	GGT	.	.	.	none		0.637	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535		A	62843457	G	A	62843457	3	1	246	1	0	0	0	0	1	0	0	0	10113	1232	43	2	1509	2	MYT1	20	62843457	Missense_Mutation	SNP	G	TCGA-SX-A7SL-01A-11D-A34Z-10	18036663	62843457	182063	75	15239											
TIAM1	7074	hgsc.bcm.edu	37	chr21	32638851	32638851	+	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	gtataggaatgctgcctcctGcctccctcagccaaatatgt	9	11	8	13	0	1	0	1	0	0	0	3	1	3	1	5	1	4	2	5	1	5	3			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr21:32638851G>A	ENST00000286827.3	-	5	909	c.438C>T	c.(436-438)ggC>ggT	p.G146G	TIAM1_ENST00000541036.1_Silent_p.G146G|TIAM1_ENST00000469412.1_Intron	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	146					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						GCTGCCTCCTGCCTCCCTCAG	0.547																																					p.G146G		Atlas-SNP	.											.	TIAM1	522	.	0			c.C438T						PASS	.						106	94	98					21																	32638851		2203	4300	6503	SO:0001819	synonymous_variant	7074	exon5			CCTCCTGCCTCCC		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.438C>T	chr21.hg19:g.32638851G>A		52.0	0.0	.		62.0	30.0	.	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Silent	SNP	ENST00000286827.3	hg19	CCDS13609.1																																																																																			.	.	.	none		0.547	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		A	32638851	G	A	32638851	2	1	246	1	0	0	0	0	0	0	0	1	15902	1306	46	2		2	TIAM1	21	32638851	Silent	SNP	G	TCGA-SX-A7SL-01A-11D-A34Z-10		32638851	15491044	76	15240											
RANBP1	5902	hgsc.bcm.edu	37	chr22	20109843	20109843	+	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	tctcccagaatggaaggagcGaggcactggtgacgtcaagc	11	6	14	10	2	2	2	1	1	1	1	3	5	2	4	1	4	2	1	1	4	3	0			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr22:20109843G>A	ENST00000331821.3	+	3	311	c.209G>A	c.(208-210)cGa>cAa	p.R70Q	RANBP1_ENST00000430524.1_5'UTR|RANBP1_ENST00000402752.1_Missense_Mutation_p.R70Q	NM_002882.2	NP_002873.1	P43487	RANG_HUMAN	RAN binding protein 1	70	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)					TGGAAGGAGCGAGGCACTGGT	0.562																																					p.R70Q		Atlas-SNP	.											.	RANBP1	19	.	0			c.G209A						PASS	.						75	67	70					22																	20109843		2203	4300	6503	SO:0001583	missense	5902	exon3			AGGAGCGAGGCAC	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.209G>A	chr22.hg19:g.20109843G>A	ENSP00000327583:p.Arg70Gln	101.0	0.0	.		62.0	10.0	.	NM_002882	Q53EY3	Missense_Mutation	SNP	ENST00000331821.3	hg19	CCDS13775.1	.	.	.	.	.	.	.	.	.	.	G	36	5.878801	0.97055	.	.	ENSG00000099901	ENST00000432879;ENST00000402752;ENST00000447917;ENST00000331821;ENST00000411892;ENST00000416427;ENST00000421656;ENST00000423859;ENST00000418705	T;T;T;T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18	5.53	5.53	0.82687	Pleckstrin homology-type (1);Ran binding protein 1 (3);	0.000000	0.85682	D	0.000000	D	0.85133	0.5627	M	0.93808	3.46	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.80764	0.994;0.952;0.986	D	0.88552	0.3117	10	0.72032	D	0.01	-3.2042	19.4537	0.94878	0.0:0.0:1.0:0.0	.	70;70;70	B4DE76;Q53EY3;P43487	.;.;RANG_HUMAN	Q	147;70;70;70;70;20;20;20;20	ENSP00000404724:R147Q;ENSP00000384925:R70Q;ENSP00000327583:R70Q;ENSP00000395472:R70Q;ENSP00000404126:R20Q;ENSP00000400940:R20Q;ENSP00000404298:R20Q;ENSP00000413502:R20Q	ENSP00000327583:R70Q	R	+	2	0	RANBP1	18489843	1.000000	0.71417	0.999000	0.59377	0.859000	0.49053	9.618000	0.98365	2.606000	0.88127	0.563000	0.77884	CGA	.	.	.	none		0.562	RANBP1-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343733.1	NM_002882		A	20109843	G	A	20109843	3	1	246	1	0	0	0	0	1	0	0	0	13038	1058	37	1	219	1	RANBP1	22	20109843	Missense_Mutation	SNP	G	TCGA-SX-A7SL-01A-11D-A34Z-10		20109843	31194723	77	15241											
NEFH	4744	hgsc.bcm.edu	37	chr22	29885585	29885586	+	In_Frame_Ins	INS	-	-	AAGTCCCCTGAGAAGGCC																															caaagtcccctgagaaggccINSaagtccccagagaaggaaga																								rs200984527|rs267607533		TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr22:29885585_29885586insAAGTCCCCTGAGAAGGCC	ENST00000310624.6	+	4	1989_1990	c.1956_1957insAAGTCCCCTGAGAAGGCC	c.(1957-1959)aag>AAGTCCCCTGAGAAGGCCaag	p.653_653K>KSPEKAK		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	659	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						CTGAGAAGGCCAAGTCCCCAGA	0.564																																					p.A652delinsAKSPEKA		Atlas-INDEL	.											.,1	NEFH	178	.	0			c.1956_1957insAAGTCCCCTGAGAAGGCC						PASS	.																																			SO:0001652	inframe_insertion	4744	exon4			.		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1939_1956dupAAGTCCCCTGAGAAGGCC	chr22.hg19:g.29885585_29885586insAAGTCCCCTGAGAAGGCC	ENSP00000311997:p.SerProGluLysAlaLys653dup	43.0	0.0	0		38.0	19.0	0.5	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.	.	none		0.564	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		AAGTCCCCTGAGAAGGCC	29885586	-	AAGTCCCCTGAGAAGGCC	29885585	7	5	246	1	0	1	1	0	0	0	0	0	10321	581	21	0	1970	0	NEFH	22	29885585	In_Frame_Ins	INS	-	TCGA-SX-A7SL-01A-11D-A34Z-10	9775742	29885585	21418981	78	15242											
NF2	4771	hgsc.bcm.edu	37	chr22	30050649	30050649	+	Frame_Shift_Del	DEL	G	G	-																															ccctttcttctttccagtatGgtgactacgaccccagtgtt																										TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr22:30050649delG	ENST00000338641.4	+	5	892	c.451delG	c.(451-453)ggtfs	p.G151fs	NF2_ENST00000361452.4_Frame_Shift_Del_p.G110fs|NF2_ENST00000403435.1_Frame_Shift_Del_p.G151fs|NF2_ENST00000353887.4_Frame_Shift_Del_p.G68fs|NF2_ENST00000347330.5_Intron|NF2_ENST00000403999.3_Frame_Shift_Del_p.G151fs|NF2_ENST00000334961.7_Frame_Shift_Del_p.G68fs|NF2_ENST00000413209.2_Intron|NF2_ENST00000361166.4_Frame_Shift_Del_p.G151fs|NF2_ENST00000397789.3_Frame_Shift_Del_p.G151fs|NF2_ENST00000361676.4_Frame_Shift_Del_p.G109fs	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	151	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(4)|p.Y150fs*46(1)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						TTTCCAGTATGGTGACTACGA	0.463			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																												p.Y150X		Atlas-Indel,Pindel	.	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	.	NF2	1312	.	5	Unknown(4)|Deletion - Frameshift(1)	meninges(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)	c.450delT						PASS	.						163	165	164					22																	30050649		2203	4300	6503	SO:0001589	frameshift_variant	4771	exon5	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	.	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"A-kinase anchor proteins"	7773	protein-coding gene	gene with protein product	"moesin-ezrin-radixin like", "schwannomin"	607379	"neurofibromin 2 (bilateral acoustic neuroma)"			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.451delG	chr22.hg19:g.30050649delG	ENSP00000344666:p.Gly151fs	156.0	0.0	0		105.0	98.0	0.933333	NM_181832	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Frame_Shift_Del	DEL	ENST00000338641.4	hg19	CCDS13861.1																																																																																			.	.	.	none		0.463	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268		-	30050649	G	-	30050649	7	5	246	1	0	1	0	1	0	0	0	0	10364	1348	47	0	469	0	NF2	22	30050649	Frame_Shift_Del	DEL	G	TCGA-SX-A7SL-01A-11D-A34Z-10	165064	30050649	21253917	79	15243											
SGSM3	57591	hgsc.bcm.edu	37	chr22	40803843	40803843	+	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	gtgggggagctcaacggcctGcgaggtggggtccttggtct	4	9	19	9	2	2	0	1	0	1	0	3	2	3	1	2	7	3	1	2	7	1	1			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chr22:40803843G>A	ENST00000355630.3	-	0	4496				SGSM3_ENST00000248929.9_Silent_p.L525L|SGSM3_ENST00000454798.2_Silent_p.L458L	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1						negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						TCAACGGCCTGCGAGGTGGGG	0.627			T	RBM15	acute megakaryocytic leukemia																																p.L525L		Atlas-SNP	.		Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	.	SGSM3	48	.	0			c.G1575A						PASS	.						50	53	52					22																	40803843		2203	4300	6503	SO:0001628	intergenic_variant	27352	exon14			CGGCCTGCGAGGT	AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588			14334	protein-coding gene	gene with protein product	"megakaryocytic acute leukemia", "myocardin-related transcription factor A", "basic, SAP and coiled-coil domain"	606078				11431691, 12019265, 14970199	Standard	XM_005261692		Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146		chr22.hg19:g.40803843G>A		81.0	0.0	.		44.0	41.0	.	NM_015705	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Silent	SNP	ENST00000355630.3	hg19	CCDS14003.1																																																																																			.	.	.	none		0.627	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831		A	40803843	G	A	40803843	1	1	246	0	1	0	0	0	0	0	0	0	14237	1306	46	2		2	SGSM3	22	40803843	IGR	SNP	G	TCGA-SX-A7SL-01A-11D-A34Z-10	10753194	40803843	10500723	80	15244											
GPR173	54328	hgsc.bcm.edu	37	chrX	53106377	53106377	+	Missense_Mutation	SNP	A	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	acacgctgggcttcatgcttAtgttggctgtgctcatggca	6	13	12	10	1	2	0	2	0	0	0	2	0	2	0	0	3	2	7	0	3	1	3			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chrX:53106377A>C	ENST00000332582.4	+	2	1065	c.574A>C	c.(574-576)Atg>Ctg	p.M192L		NM_018969.5	NP_061842.1	Q9NS66	GP173_HUMAN	G protein-coupled receptor 173	192					negative regulation of neuron migration (GO:2001223)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|gonadotropin-releasing hormone receptor activity (GO:0004968)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)	16						CTTCATGCTTATGTTGGCTGT	0.537																																					p.M192L		Atlas-SNP	.											.	GPR173	66	.	0			c.A574C						PASS	.						39	37	38					X																	53106377		2200	4299	6499	SO:0001583	missense	54328	exon2			ATGCTTATGTTGG	AB040801	CCDS14349.1	Xp11	2012-08-21	2006-02-15		ENSG00000184194	ENSG00000184194		"GPCR / Class A : Orphans"	18186	protein-coding gene	gene with protein product		300253	"G-protein coupled receptor 173", "G protein coupled receptor 173"			10833454	Standard	NM_018969		Approved	SREB3	uc004dru.3	Q9NS66	OTTHUMG00000021596	ENST00000332582.4:c.574A>C	chrX.hg19:g.53106377A>C	ENSP00000331600:p.Met192Leu	46.0	0.0	.		31.0	31.0	.	NM_018969	B1B0A5	Missense_Mutation	SNP	ENST00000332582.4	hg19	CCDS14349.1	.	.	.	.	.	.	.	.	.	.	A	3.370	-0.128697	0.06753	.	.	ENSG00000184194	ENST00000332582	T	0.70516	-0.49	4.85	4.85	0.62838	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.53433	0.1796	L	0.28400	0.85	0.58432	D	0.999999	B	0.11235	0.004	B	0.18871	0.023	T	0.47182	-0.9137	10	0.02654	T	1	-11.4851	11.4995	0.50428	1.0:0.0:0.0:0.0	.	192	Q9NS66	GP173_HUMAN	L	192	ENSP00000331600:M192L	ENSP00000331600:M192L	M	+	1	0	GPR173	53123102	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.287000	0.72671	1.614000	0.50241	0.430000	0.28490	ATG	.	.	.	none		0.537	GPR173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056717.2	NM_018969		C	53106377	A	C	53106377	3	2	246	1	0	0	0	0	1	0	0	0	6678	449	16	5	576	5	GPR173	23	53106377	Missense_Mutation	SNP	A	TCGA-SX-A7SL-01A-11D-A34Z-10		53106377	102164183	81	15245											
PAK3	5063	hgsc.bcm.edu	37	chrX	110385396	110385396	+	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	tgagcatacgattcatgtggGgtttgatgcagtcaccgggg	8	11	15	7	2	2	2	2	2	0	0	2	3	2	2	1	4	3	3	1	4	1	3			TCGA-SX-A7SL-01A-11D-A34Z-10	TCGA-SX-A7SL-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e274845c-65ec-4db0-89f9-7d502ac2e427	e96052fd-169c-4e27-bd82-a5b6c796da53	g.chrX:110385396G>A	ENST00000372010.1	+	6	690	c.248G>A	c.(247-249)gGg>gAg	p.G83E	PAK3_ENST00000425146.1_Missense_Mutation_p.G83E|PAK3_ENST00000519681.1_Missense_Mutation_p.G83E|PAK3_ENST00000372007.5_Missense_Mutation_p.G83E|PAK3_ENST00000262836.4_Missense_Mutation_p.G83E|PAK3_ENST00000518291.1_Missense_Mutation_p.G83E|PAK3_ENST00000446737.1_Missense_Mutation_p.G83E|PAK3_ENST00000417227.1_Missense_Mutation_p.G83E|PAK3_ENST00000360648.4_Missense_Mutation_p.G83E			O75914	PAK3_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 3	83	Autoregulatory region. {ECO:0000250}.|CRIB. {ECO:0000255|PROSITE- ProRule:PRU00057}.|GTPase-binding. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|dendritic spine morphogenesis (GO:0060997)|MAPK cascade (GO:0000165)|regulation of actin filament polymerization (GO:0030833)|synapse organization (GO:0050808)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(15)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	41						ATTCATGTGGGGTTTGATGCA	0.393										TSP Lung(19;0.15)																											p.G83E		Atlas-SNP	.											.	PAK3	179	.	0			c.G248A						PASS	.						195	193	194					X																	110385396		2203	4300	6503	SO:0001583	missense	5063	exon4			ATGTGGGGTTTGA	AF068864	CCDS14554.1, CCDS48151.1, CCDS48152.1, CCDS48153.1	Xq22.3	2008-06-17	2008-06-17		ENSG00000077264	ENSG00000077264			8592	protein-coding gene	gene with protein product		300142	"mental retardation, X-linked 47", "p21 (CDKN1A)-activated kinase 3"	MRX30, MRX47		8826460, 9731525	Standard	NM_002578		Approved	hPAK3, bPAK	uc010npv.1	O75914	OTTHUMG00000022202	ENST00000372010.1:c.248G>A	chrX.hg19:g.110385396G>A	ENSP00000361080:p.Gly83Glu	78.0	0.0	.		51.0	48.0	.	NM_001128166	A8K389|B1GX77|B1GX78|B1GX79|Q5JWX1|Q5JWX2|Q7Z2D6|Q7Z2E4|Q7Z3Z8|Q8WWK5|Q8WX23|Q9P0J8	Missense_Mutation	SNP	ENST00000372010.1	hg19	CCDS48153.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.502816	0.85176	.	.	ENSG00000077264	ENST00000446737;ENST00000425146;ENST00000372010;ENST00000519681;ENST00000372007;ENST00000518291;ENST00000429193;ENST00000360648;ENST00000417227;ENST00000262836	D;D;D;D;D;D;D;D;D;D	0.94280	-3.39;-3.39;-3.39;-3.39;-3.39;-3.39;-3.39;-3.39;-3.39;-3.39	5.96	5.09	0.68999	PAK-box/P21-Rho-binding (3);	0.110129	0.64402	D	0.000007	D	0.97123	0.9060	M	0.88031	2.925	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.999;0.999	D;D;D;D	0.85130	0.996;0.997;0.994;0.987	D	0.97620	1.0135	10	0.87932	D	0	.	15.638	0.76970	0.0:0.0:0.8618:0.1382	.	83;83;83;83	O75914-4;O75914-3;O75914;O75914-2	.;.;PAK3_HUMAN;.	E	83	ENSP00000410853:G83E;ENSP00000401982:G83E;ENSP00000361080:G83E;ENSP00000429113:G83E;ENSP00000361077:G83E;ENSP00000428921:G83E;ENSP00000405642:G83E;ENSP00000353864:G83E;ENSP00000389172:G83E;ENSP00000262836:G83E	ENSP00000262836:G83E	G	+	2	0	PAK3	110272052	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.476000	0.97823	1.251000	0.43983	0.600000	0.82982	GGG	.	.	.	none		0.393	PAK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057918.1	NM_002578		A	110385396	G	A	110385396	3	1	246	1	0	0	0	0	1	0	0	0	11409	1232	43	2	254	2	PAK3	23	110385396	Missense_Mutation	SNP	G	TCGA-SX-A7SL-01A-11D-A34Z-10	57279019	110385396	44885164	82	15246											
CELA2A	63036	hgsc.bcm.edu	37	chr1	15789342	15789342	+	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	cacaaggactggaactccaaCcaaatctccaaagggttcgt	14	7	8	12	1	1	0	0	0	1	0	4	2	2	2	3	3	2	1	3	3	5	1			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr1:15789342C>A	ENST00000359621.4	+	4	367	c.342C>A	c.(340-342)aaC>aaA	p.N114K		NM_033440.2	NP_254275.1	P08217	CEL2A_HUMAN	chymotrypsin-like elastase family, member 2A	114	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|keratohyalin granule (GO:0036457)	serine hydrolase activity (GO:0017171)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)|ovary(2)|prostate(1)	16						GGAACTCCAACCAAATCTCCA	0.582																																					p.N114K		Atlas-SNP	.											.	CELA2A	32	.	0			c.C342A						PASS	.						121	125	124					1																	15789342		2203	4300	6503	SO:0001583	missense	63036	exon4			CTCCAACCAAATC		CCDS157.1	1p36.21	2009-07-09			ENSG00000142615	ENSG00000142615	3.4.21.71		24609	protein-coding gene	gene with protein product	"elastase 2A"	609443				3646943, 2834346	Standard	NM_033440		Approved	ELA2A	uc001awk.3	P08217	OTTHUMG00000002258	ENST00000359621.4:c.342C>A	chr1.hg19:g.15789342C>A	ENSP00000352639:p.Asn114Lys	111.0	0.0	.		72.0	21.0	.	NM_033440	B2R5I4|Q14243	Missense_Mutation	SNP	ENST00000359621.4	hg19	CCDS157.1	.	.	.	.	.	.	.	.	.	.	C	6.323	0.427644	0.11987	.	.	ENSG00000142615	ENST00000359621	D	0.88277	-2.36	4.12	3.16	0.36331	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.565730	0.03988	N	0.294417	T	0.75133	0.3808	N	0.02539	-0.55	0.09310	N	1	B	0.18741	0.03	B	0.22386	0.039	T	0.64330	-0.6433	10	0.13470	T	0.59	.	8.2539	0.31743	0.1825:0.653:0.1645:0.0	.	114	P08217	CEL2A_HUMAN	K	114	ENSP00000352639:N114K	ENSP00000352639:N114K	N	+	3	2	CELA2A	15661929	0.000000	0.05858	0.003000	0.11579	0.019000	0.09904	0.083000	0.14871	0.666000	0.31087	0.281000	0.19383	AAC	.	.	.	none		0.582	CELA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006445.1	NM_033440		A	15789342	C	A	15789342	3	1	247	1	0	0	0	0	1	0	0	0	3213	506	18	4	356	4	CELA2A	1	15789342	Missense_Mutation	SNP	C	TCGA-SX-A7SM-01A-11D-A34Z-10		15789342	233461279	1	15247											
MAN1C1	57134	hgsc.bcm.edu	37	chr1	26109142	26109142	+	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	aagacgtgtacagtagcaccCccaaccacgacaacaagcag	16	3	8	14	2	0	1	0	0	0	1	0	2	0	1	3	0	5	4	3	0	6	2			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr1:26109142C>G	ENST00000374332.4	+	11	2047	c.1717C>G	c.(1717-1719)Ccc>Gcc	p.P573A	MAN1C1_ENST00000263979.3_Missense_Mutation_p.P393A|MAN1C1_ENST00000374329.1_Missense_Mutation_p.P344A	NM_020379.2	NP_065112.1	Q9NR34	MA1C1_HUMAN	mannosidase, alpha, class 1C, member 1	573					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)		CAGTAGCACCCCCAACCACGA	0.542																																					p.P573A		Atlas-SNP	.											.	MAN1C1	48	.	0			c.C1717G						PASS	.						157	142	147					1																	26109142		2203	4300	6503	SO:0001583	missense	57134	exon11			AGCACCCCCAACC	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.1717C>G	chr1.hg19:g.26109142C>G	ENSP00000363452:p.Pro573Ala	83.0	0.0	.		62.0	28.0	.	NM_020379	A6NNE2|B2RNP2|Q9Y545	Missense_Mutation	SNP	ENST00000374332.4	hg19	CCDS265.1	.	.	.	.	.	.	.	.	.	.	C	12.67	2.006504	0.35415	.	.	ENSG00000117643	ENST00000374332;ENST00000263979;ENST00000374329	T;T;T	0.72051	-0.62;-0.62;-0.62	5.0	5.0	0.66597	.	0.205916	0.44097	D	0.000492	T	0.73210	0.3558	M	0.65677	2.01	0.47511	D	0.999445	P	0.36354	0.549	B	0.40444	0.329	T	0.73357	-0.4008	10	0.36615	T	0.2	.	18.2971	0.90150	0.0:1.0:0.0:0.0	.	573	Q9NR34	MA1C1_HUMAN	A	573;393;344	ENSP00000363452:P573A;ENSP00000263979:P393A;ENSP00000363449:P344A	ENSP00000263979:P393A	P	+	1	0	MAN1C1	25981729	0.997000	0.39634	0.930000	0.37139	0.679000	0.39708	3.736000	0.55052	2.319000	0.78375	0.561000	0.74099	CCC	.	.	.	none		0.542	MAN1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012828.3	NM_020379		G	26109142	C	G	26109142	3	3	247	1	0	0	0	0	1	0	0	0	9220	623	22	4	1759	4	MAN1C1	1	26109142	Missense_Mutation	SNP	C	TCGA-SX-A7SM-01A-11D-A34Z-10	10319800	26109142	223141479	2	15248											
AIM1L	55057	hgsc.bcm.edu	37	chr1	26664849	26664849	+	Frame_Shift_Del	DEL	A	A	-																															ccctgttctttaccaatctcAtgggcttcagggagcccacg																										TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr1:26664849delA	ENST00000308182.5	-	6	758	c.329delT	c.(328-330)atgfs	p.M110fs	AIM1L_ENST00000522993.1_5'UTR|AIM1L_ENST00000527815.1_Frame_Shift_Del_p.M281fs			Q8N1P7	AIM1L_HUMAN	absent in melanoma 1-like	110	Beta/gamma crystallin 'Greek key' 2. {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)		TACCAATCTCATGGGCTTCAG	0.607																																					p.M1155fs		Atlas-INDEL	.											.	AIM1L	98	.	0			c.3465delG						PASS	.						70	69	70					1																	26664849		2203	4300	6503	SO:0001589	frameshift_variant	55057	exon7			.			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.329delT	chr1.hg19:g.26664849delA	ENSP00000310435:p.Met110fs	45.0	0.0	0		44.0	10.0	0.227273	NM_001039775	B2RNG3|Q5T137|Q5T150	Frame_Shift_Del	DEL	ENST00000308182.5	hg19																																																																																				.	.	.	none		0.607	AIM1L-201	KNOWN	basic	protein_coding	protein_coding		NM_001039775.2		-	26664849	A	-	26664849	7	5	247	1	0	1	0	1	0	0	0	0	431	217	8	0	1577	0	AIM1L	1	26664849	Frame_Shift_Del	DEL	A	TCGA-SX-A7SM-01A-11D-A34Z-10	555707	26664849	222585772	3	15249											
PPP1R8	5511	hgsc.bcm.edu	37	chr1	28157385	28157385	+	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	0	0	0	0	0	0	0	0	0	tccggctctagcctcccgctGttcgactgcccaacctggtg	4	10	10	17	3	1	0	0	0	1	0	4	1	3	0	5	2	3	3	5	2	2	2			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr1:28157385G>C	ENST00000311772.5	+	1	97	c.39G>C	c.(37-39)ctG>ctC	p.L13L	PPP1R8_ENST00000373931.4_5'UTR|PPP1R8_ENST00000236412.7_5'UTR	NM_014110.4	NP_054829.2	Q12972	PP1R8_HUMAN	protein phosphatase 1, regulatory subunit 8	13	Interaction with CDC5L, SF3B1 and MELK.				cell proliferation (GO:0008283)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|regulation of transcription, DNA-templated (GO:0006355)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|protein phosphatase type 1 regulator activity (GO:0008599)|protein serine/threonine phosphatase inhibitor activity (GO:0004865)|ribonuclease E activity (GO:0008995)|RNA binding (GO:0003723)			breast(2)|cervix(1)|endometrium(2)|lung(2)|upper_aerodigestive_tract(1)	8		Colorectal(325;3.46e-05)|all_lung(284;0.000129)|Lung NSC(340;0.000259)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;2.76e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00248)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0649)		GCCTCCCGCTGTTCGACTGCC	0.652																																					p.L13L		Atlas-SNP	.											.	PPP1R8	17	.	0			c.G39C						PASS	.						6	6	6					1																	28157385		2096	4160	6256	SO:0001819	synonymous_variant	5511	exon1			CCCGCTGTTCGAC	AF061959	CCDS311.1, CCDS312.1, CCDS313.1	1p35.3	2012-04-17	2011-10-04		ENSG00000117751	ENSG00000117751		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9296	protein-coding gene	gene with protein product	"RNase E", "nuclear subunit of PP-1", "nuclear inhibitor of protein phosphatase-1", "activator of RNA decay", "protein phosphatase 1 regulatory subunit 8"	602636	"protein phosphatase 1, regulatory (inhibitor) subunit 8"			7524097, 8473324	Standard	NM_014110		Approved	ard-1, NIPP-1, PRO2047, ARD1, NIPP1	uc001bov.2	Q12972	OTTHUMG00000003734	ENST00000311772.5:c.39G>C	chr1.hg19:g.28157385G>C		81.0	0.0	.		65.0	19.0	.	NM_014110	Q5TEJ2|Q5TEJ4|Q5TIF2|Q6PKF6|Q9UBH1|Q9UBZ0	Silent	SNP	ENST00000311772.5	hg19	CCDS311.1																																																																																			.	.	.	none		0.652	PPP1R8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010528.1	NM_014110		C	28157385	G	C	28157385	2	2	247	1	0	0	0	0	0	0	0	1	12387	1364	48	4		4	PPP1R8	1	28157385	Silent	SNP	G	TCGA-SX-A7SM-01A-11D-A34Z-10	1492536	28157385	221093236	4	15250											
GNL2	29889	hgsc.bcm.edu	37	chr1	38039944	38039951	+	Splice_Site	DEL	CTGGGGGG	CTGGGGGG	-																															tgggcccaccctgctcttacCtggggggccacaagtggctc																										TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	CTGGGGGG	CTGGGGGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr1:38039944_38039951delCTGGGGGG	ENST00000373062.3	-	12	1507_1514	c.1409_1416delCCCCCCAG	c.(1408-1416)gccccccag>g	p.APQ470fs		NM_013285.2	NP_037417.1	Q13823	NOG2_HUMAN	guanine nucleotide binding protein-like 2 (nucleolar)	470					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)				CTGCTCTTACCTGGGGGGCCACAAGTGG	0.553																																					p.470_472del		Atlas-Indel,Pindel	.											.	GNL2	58	.	0			c.1410_1416del						PASS	.																																			SO:0001630	splice_region_variant	29889	exon12			.	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.1416+1CCCCCCAG>-	chr1.hg19:g.38039944_38039951delCTGGGGGG		45.0	0.0	0		44.0	16.0	0.363636	NM_013285	Q9BWN7	Frame_Shift_Del	DEL	ENST00000373062.3	hg19	CCDS421.1																																																																																			.	.	.	none		0.553	GNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012478.1	NM_013285	Frame_Shift_Del	-	38039951	CTGGGGGG	-	38039944	8	5	247	1	0	1	0	1	0	0	1	0	6543	695	24	0	799	0	GNL2	1	38039944	Splice_Site	DEL	CTGGGGGG	TCGA-SX-A7SM-01A-11D-A34Z-10	9882559	38039944	211210677	5	15251											
C1orf190	541468	hgsc.bcm.edu	37	chr1	46685818	46685818	+	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	gaccacctgagtcaccagagGatgagagtgccaagctgggc	11	5	14	11	0	1	3	1	2	0	2	1	6	1	4	4	2	2	1	4	2	1	0			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr1:46685818G>A	ENST00000371980.3	+	2	739	c.646G>A	c.(646-648)Gat>Aat	p.D216N	POMGNT1_ENST00000371992.1_5'UTR|POMGNT1_ENST00000396420.3_5'UTR	NM_001013615.2	NP_001013633.1	Q96LR2	LURA1_HUMAN	leucine rich adaptor protein 1	216					actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)											GTCACCAGAGGATGAGAGTGC	0.567																																					p.D216N		Atlas-SNP	.											.	.	.	.	0			c.G646A						PASS	.						51	52	52					1																	46685818		2203	4300	6503	SO:0001583	missense	541468	exon2			CCAGAGGATGAGA	AK057892	CCDS30703.1	1p34.1	2012-02-01	2012-02-01	2012-02-01	ENSG00000171357	ENSG00000171357			32327	protein-coding gene	gene with protein product	"leucine repeat adaptor protein 35a"		"chromosome 1 open reading frame 190"	C1orf190		21048106	Standard	NM_001013615		Approved	FLJ25163, LRAP35a	uc010oma.2	Q96LR2	OTTHUMG00000007605	ENST00000371980.3:c.646G>A	chr1.hg19:g.46685818G>A	ENSP00000361048:p.Asp216Asn	30.0	0.0	.		35.0	13.0	.	NM_001013615		Missense_Mutation	SNP	ENST00000371980.3	hg19	CCDS30703.1	.	.	.	.	.	.	.	.	.	.	G	11.75	1.731556	0.30684	.	.	ENSG00000171357	ENST00000371980	.	.	.	5.33	4.36	0.52297	.	0.898838	0.09783	N	0.756440	T	0.27205	0.0667	N	0.24115	0.695	0.26481	N	0.975106	B	0.10296	0.003	B	0.11329	0.006	T	0.07443	-1.0772	9	0.30078	T	0.28	-15.8251	5.1771	0.15141	0.0803:0.145:0.6247:0.15	.	216	Q96LR2	LP35A_HUMAN	N	216	.	ENSP00000361048:D216N	D	+	1	0	C1orf190	46458405	0.992000	0.36948	0.996000	0.52242	0.954000	0.61252	1.980000	0.40618	2.503000	0.84419	0.557000	0.71058	GAT	.	.	.	none		0.567	LURAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020154.1	NM_001013615		A	46685818	G	A	46685818	3	1	247	1	0	0	0	0	1	0	0	0	2025	1174	41	2	652	2	C1orf190	1	46685818	Missense_Mutation	SNP	G	TCGA-SX-A7SM-01A-11D-A34Z-10	8645874	46685818	202564803	6	15252											
SSX2IP	117178	hgsc.bcm.edu	37	chr1	85116084	85116084	+	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	aacgtgtctggcaaaagtctGaagtggaaggtgaagcagga	14	7	15	5	1	2	2	0	2	2	0	2	4	2	4	0	4	2	2	0	4	6	0			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr1:85116084G>A	ENST00000342203.3	-	13	1894	c.1631C>T	c.(1630-1632)tCa>tTa	p.S544L	SSX2IP_ENST00000370612.4_Missense_Mutation_p.S544L|SSX2IP_ENST00000603677.1_Missense_Mutation_p.S63L|SSX2IP_ENST00000437941.2_Missense_Mutation_p.S517L|SSX2IP_ENST00000605755.1_Missense_Mutation_p.S517L	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	544					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)		GCAAAAGTCTGAAGTGGAAGG	0.423																																					p.S544L		Atlas-SNP	.											.	SSX2IP	53	.	0			c.C1631T						PASS	.						157	158	158					1																	85116084		2203	4300	6503	SO:0001583	missense	117178	exon14			AAGTCTGAAGTGG		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.1631C>T	chr1.hg19:g.85116084G>A	ENSP00000340279:p.Ser544Leu	99.0	0.0	.		103.0	6.0	.	NM_001166417	A8K8W0|B4DFE3|D3DT13|J3KR02|Q6P2P8|Q6ULS1|Q7L168|Q9UIX0	Missense_Mutation	SNP	ENST00000342203.3	hg19	CCDS699.1	.	.	.	.	.	.	.	.	.	.	G	16.81	3.225873	0.58668	.	.	ENSG00000117155	ENST00000342203;ENST00000437941;ENST00000370612	T;T	0.49139	0.8;0.79	5.37	4.46	0.54185	.	0.488922	0.21259	N	0.077513	T	0.19406	0.0466	L	0.44542	1.39	0.29393	N	0.862506	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.09862	-1.0655	10	0.29301	T	0.29	-27.8433	9.8504	0.41053	0.0948:0.0:0.9052:0.0	.	544;544;517	Q9Y2D8-2;Q9Y2D8;B4DFE3	.;ADIP_HUMAN;.	L	544;517;544	ENSP00000340279:S544L;ENSP00000412781:S517L	ENSP00000340279:S544L	S	-	2	0	SSX2IP	84888672	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.321000	0.51999	1.255000	0.44051	0.655000	0.94253	TCA	.	.	.	none		0.423	SSX2IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027469.1	NM_014021		A	85116084	G	A	85116084	3	1	247	1	0	0	0	0	1	0	0	0	15216	1294	45	2	221	2	SSX2IP	1	85116084	Missense_Mutation	SNP	G	TCGA-SX-A7SM-01A-11D-A34Z-10	38430266	85116084	164134537	7	15253											
DNTTIP2	30836	hgsc.bcm.edu	37	chr1	94341887	94341887	+	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	actcatcttcattttcgtcaTggtctgatgaatcttcttca	8	18	5	10	1	8	2	4	2	4	0	9	2	8	2	0	1	0	0	0	1	1	5			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr1:94341887T>A	ENST00000436063.2	-	2	1661	c.1604A>T	c.(1603-1605)cAt>cTt	p.H535L	DNTTIP2_ENST00000460191.1_5'UTR	NM_014597.4	NP_055412.2	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 2	535					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	38		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		ATTTTCGTCATGGTCTGATGA	0.338																																					p.H535L		Atlas-SNP	.											.	DNTTIP2	59	.	0			c.A1604T						PASS	.						144	128	133					1																	94341887		1826	3969	5795	SO:0001583	missense	30836	exon2			TCGTCATGGTCTG	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.1604A>T	chr1.hg19:g.94341887T>A	ENSP00000411010:p.His535Leu	294.0	0.0	.		265.0	73.0	.	NM_014597	Q12987|Q53H59|Q5TFJ4|Q6TLI0|Q76MJ8|Q86WX9	Missense_Mutation	SNP	ENST00000436063.2	hg19	CCDS44174.1	.	.	.	.	.	.	.	.	.	.	T	2.905	-0.226532	0.06022	.	.	ENSG00000067334	ENST00000436063	T	0.14144	2.53	5.44	-0.376	0.12505	.	1.507750	0.04004	N	0.297049	T	0.03220	0.0094	L	0.57536	1.79	0.09310	N	1	B	0.29716	0.255	B	0.23275	0.045	T	0.37454	-0.9705	10	0.10902	T	0.67	.	4.1395	0.10186	0.2885:0.2841:0.0:0.4275	.	535	Q5QJE6	TDIF2_HUMAN	L	535	ENSP00000411010:H535L	ENSP00000352137:H535L	H	-	2	0	DNTTIP2	94114475	0.000000	0.05858	0.003000	0.11579	0.065000	0.16274	0.473000	0.22132	-0.194000	0.10399	0.533000	0.62120	CAT	.	.	.	none		0.338	DNTTIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028317.2	NM_014597		A	94341887	T	A	94341887	3	1	247	1	0	0	0	0	1	0	0	0	4684	1464	51	5	690	5	DNTTIP2	1	94341887	Missense_Mutation	SNP	T	TCGA-SX-A7SM-01A-11D-A34Z-10	9225803	94341887	154908734	8	15254											
HAO2	51179	hgsc.bcm.edu	37	chr1	119925589	119925589	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtctgaggtggacaccagAaccacaatccaaggggagga	13	5	14	9	0	1	2	0	1	1	1	2	5	2	5	3	5	1	0	3	5	3	0	rs199672779		TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr1:119925589A>G	ENST00000325945.3	+	3	256	c.183A>G	c.(181-183)agA>agG	p.R61R	HAO2_ENST00000361035.4_Silent_p.R74R	NM_001005783.1|NM_016527.2	NP_001005783.1|NP_057611.1	Q9NYQ3	HAOX2_HUMAN	hydroxyacid oxidase 2 (long chain)	61	FMN hydroxy acid dehydrogenase. {ECO:0000255|PROSITE-ProRule:PRU00683}.				fatty acid oxidation (GO:0019395)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	(S)-2-hydroxy-acid oxidase activity (GO:0003973)|FMN binding (GO:0010181)|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(6)|kidney(2)|large_intestine(5)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)		Lung(183;0.0155)|LUSC - Lung squamous cell carcinoma(189;0.0856)		TGGACACCAGAACCACAATCC	0.542																																					p.R61R		Atlas-SNP	.											.	HAO2	62	.	0			c.A183G						PASS	.						121	94	103					1																	119925589		2203	4300	6503	SO:0001819	synonymous_variant	51179	exon4			CACCAGAACCACA	AF231917	CCDS901.1	1p13.3-p13.1	2008-07-18			ENSG00000116882	ENSG00000116882	1.1.3.15		4810	protein-coding gene	gene with protein product	"(S)-2-hydroxy-acid oxidase", "glycolate oxidase", "long-chain L-2-hydroxy acid oxidase", "growth-inhibiting protein 16"	605176				10777549	Standard	XM_005270913		Approved	HAOX2, GIG16	uc001ehr.1	Q9NYQ3	OTTHUMG00000012410	ENST00000325945.3:c.183A>G	chr1.hg19:g.119925589A>G		32.0	0.0	.		43.0	4.0	.	NM_001005783	Q2TU86|Q5QP00|Q9UJS6	Silent	SNP	ENST00000325945.3	hg19	CCDS901.1																																																																																			.	A|0.999;C|0.001	.	alt		0.542	HAO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034984.1	NM_001005783		G	119925589	A	G	119925589	2	3	247	1	0	0	0	0	0	0	0	1	6959	243	9	3		3	HAO2	1	119925589	Silent	SNP	A	TCGA-SX-A7SM-01A-11D-A34Z-10	25583702	119925589	129325032	9	15255											
PGLYRP4	57115	hgsc.bcm.edu	37	chr1	153320386	153320386	+	Frame_Shift_Del	DEL	A	A	-																															cctggatacccagagcagagAagacaagaagccacggcagc																										TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr1:153320386delA	ENST00000359650.5	-	2	87	c.23delT	c.(22-24)ttcfs	p.F8fs	PGLYRP4_ENST00000368739.3_Frame_Shift_Del_p.F8fs|PGLYRP4_ENST00000490266.1_5'UTR	NM_020393.2	NP_065126.2	Q96LB8	PGRP4_HUMAN	peptidoglycan recognition protein 4	8					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	23	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			CAGAGCAGAGAAGACAAGAAG	0.502																																					p.F8fs		Atlas-Indel,Pindel	.											.	PGLYRP4	45	.	0			c.24delC						PASS	.						51	52	52					1																	153320386		2203	4300	6503	SO:0001589	frameshift_variant	57115	exon2			.	AF242518	CCDS30871.1	1q21	2008-02-05			ENSG00000163218	ENSG00000163218			30015	protein-coding gene	gene with protein product	"peptidoglycan recognition protein I beta precursor"	608198				11461926	Standard	XR_241090		Approved	SBBI67, PGRPIB, PGLYRPIbeta, PGRP-Ibeta	uc001fbo.3	Q96LB8	OTTHUMG00000037057	ENST00000359650.5:c.23delT	chr1.hg19:g.153320386delA	ENSP00000352672:p.Phe8fs	117.0	0.0	0		96.0	40.0	0.416667	NM_020393	A8K838|Q3B822|Q3B823|Q5SY63|Q5SY64|Q9HD75	Frame_Shift_Del	DEL	ENST00000359650.5	hg19	CCDS30871.1																																																																																			.	.	.	none		0.502	PGLYRP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089978.1	NM_020393		-	153320386	A	-	153320386	7	5	247	1	0	1	0	1	0	0	0	0	11803	246	9	0	1130	0	PGLYRP4	1	153320386	Frame_Shift_Del	DEL	A	TCGA-SX-A7SM-01A-11D-A34Z-10	33394797	153320386	95930235	10	15256											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228558813	228558813	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gacagcccctccctcggcgtAgcccggcacctctgcaggga	6	5	12	18	3	1	0	0	0	1	0	3	2	2	1	5	3	3	3	5	3	1	1			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr1:228558813A>G	ENST00000422127.1	+	94	20378	c.20334A>G	c.(20332-20334)gtA>gtG	p.V6778V	OBSCN_ENST00000366707.4_Silent_p.V4412V|OBSCN_ENST00000570156.2_Silent_p.V7735V	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6778					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)				CCCTCGGCGTAGCCCGGCACC	0.652																																					p.V7735V		Atlas-SNP	.											.	OBSCN	2142	.	0			c.A23205G						PASS	.						30	34	33					1																	228558813		2071	4205	6276	SO:0001819	synonymous_variant	84033	exon105			CGGCGTAGCCCGG	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.20334A>G	chr1.hg19:g.228558813A>G		76.0	0.0	.		56.0	20.0	.	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	a	8.379	0.837015	0.16891	.	.	ENSG00000154358	ENST00000441106	.	.	.	4.79	0.632	0.17705	.	.	.	.	.	T	0.45094	0.1325	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.22347	-1.0219	4	.	.	.	.	3.6268	0.08116	0.093:0.251:0.4623:0.1937	.	.	.	.	G	1395	.	.	S	+	1	0	OBSCN	226625436	0.584000	0.26766	0.857000	0.33713	0.037000	0.13140	-0.174000	0.09839	-0.032000	0.13758	-0.253000	0.11424	AGC	.	.	.	none		0.652	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		G	228558813	A	G	228558813	2	3	247	1	0	0	0	0	0	0	0	1	10819	407	15	3		3	OBSCN	1	228558813	Silent	SNP	A	TCGA-SX-A7SM-01A-11D-A34Z-10	75238427	228558813	20691808	11	15257											
HEATR5B	54497	hgsc.bcm.edu	37	chr2	37255868	37255868	+	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	tacaaagcattagccaatgaGaaagtttttctactgccagc	14	11	7	9	0	1	1	0	1	1	1	1	2	1	1	2	0	6	2	2	0	6	5			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr2:37255868G>C	ENST00000233099.5	-	23	3652	c.3557C>G	c.(3556-3558)tCt>tGt	p.S1186C	HEATR5B_ENST00000354531.2_Missense_Mutation_p.S1186C	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1186						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)				TAGCCAATGAGAAAGTTTTTC	0.358																																					p.S1186C		Atlas-SNP	.											HEATR5B,NS,carcinoma,0,1	HEATR5B	185	.	0			c.C3557G						PASS	.						77	78	78					2																	37255868		2203	4300	6503	SO:0001583	missense	54497	exon23			CAATGAGAAAGTT	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.3557C>G	chr2.hg19:g.37255868G>C	ENSP00000233099:p.Ser1186Cys	177.0	0.0	.		154.0	53.0	.	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Missense_Mutation	SNP	ENST00000233099.5	hg19	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	G	19.80	3.894573	0.72639	.	.	ENSG00000008869	ENST00000233099;ENST00000354531	T;T	0.60171	0.21;0.21	4.68	4.68	0.58851	Armadillo-like helical (1);Armadillo-type fold (1);	0.104740	0.64402	D	0.000002	T	0.76456	0.3990	M	0.77616	2.38	0.58432	D	0.999999	D	0.89917	1.0	D	0.72075	0.976	T	0.79626	-0.1725	10	0.54805	T	0.06	-7.9536	17.6029	0.88030	0.0:0.0:1.0:0.0	.	1186	Q9P2D3	HTR5B_HUMAN	C	1186	ENSP00000233099:S1186C;ENSP00000346531:S1186C	ENSP00000233099:S1186C	S	-	2	0	HEATR5B	37109372	1.000000	0.71417	0.997000	0.53966	0.964000	0.63967	7.935000	0.87658	2.143000	0.66587	0.655000	0.94253	TCT	.	.	.	none		0.358	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		C	37255868	G	C	37255868	3	2	247	1	0	0	0	0	1	0	0	0	7039	942	33	4	2714	4	HEATR5B	2	37255868	Missense_Mutation	SNP	G	TCGA-SX-A7SM-01A-11D-A34Z-10		37255868	205943505	12	15258											
POLR2D	5433	hgsc.bcm.edu	37	chr2	128610641	128610642	+	Frame_Shift_Ins	INS	-	-	A																															cgatgttccagaagcatatgINSaacttctgaatttagaagtg																										TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr2:128610641_128610642insA	ENST00000272645.4	-	2	167_168	c.111_112insT	c.(109-114)gttcatfs	p.H38fs	POLR2D_ENST00000487079.1_Intron|POLR2D_ENST00000409698.1_5'UTR|POLR2D_ENST00000409955.1_Frame_Shift_Ins_p.H38fs	NM_004805.3	NP_004796.1	O15514	RPB4_HUMAN	polymerase (RNA) II (DNA directed) polypeptide D	38					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus in response to heat stress (GO:0031990)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nucleotide-excision repair (GO:0006289)|positive regulation of translational initiation (GO:0045948)|positive regulation of viral transcription (GO:0050434)|recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex (GO:0034402)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	cytoplasmic mRNA processing body (GO:0000932)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)|nucleotide binding (GO:0000166)|translation initiation factor binding (GO:0031369)			large_intestine(1)|lung(4)|urinary_tract(1)	6	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0675)		AGAAGCATATGAACTTCTGAAT	0.386																																					p.H38fs		Atlas-Indel,Pindel	.											.	POLR2D	13	.	0			c.112_113insT						PASS	.																																			SO:0001589	frameshift_variant	5433	exon2			.	U85510	CCDS2151.1	2q21	2013-01-21			ENSG00000144231	ENSG00000144231		"RNA polymerase subunits"	9191	protein-coding gene	gene with protein product	"RNA polymerase II subunit hsRBP4"	606017				9528765	Standard	NM_004805		Approved	RBP4	uc002tpj.3	O15514	OTTHUMG00000131531	ENST00000272645.4:c.112dupT	chr2.hg19:g.128610643_128610643dupA	ENSP00000272645:p.His38fs	127.0	0.0	0		116.0	46.0	0.396552	NM_004805	Q52LT4	Frame_Shift_Ins	INS	ENST00000272645.4	hg19	CCDS2151.1																																																																																			.	.	.	none		0.386	POLR2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254388.3	NM_004805		A	128610642	-	A	128610641	7	5	247	1	0	1	1	0	0	0	0	0	12224	1290	45	0	328	0	POLR2D	2	128610641	Frame_Shift_Ins	INS	-	TCGA-SX-A7SM-01A-11D-A34Z-10	91354773	128610641	114588732	13	15259											
YSK4	80122	hgsc.bcm.edu	37	chr2	135744888	135744888	+	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	tcttggtgtacaggtatgttGacactatggttgttatgaat	9	17	11	4	0	1	2	0	2	1	0	1	2	1	2	0	3	1	5	0	3	5	7			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr2:135744888G>A	ENST00000375845.3	-	7	1584	c.1554C>T	c.(1552-1554)gtC>gtT	p.V518V	MAP3K19_ENST00000392918.3_Intron|MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000375844.3_Intron|MAP3K19_ENST00000392915.1_Silent_p.V535V|MAP3K19_ENST00000392917.3_Intron|MAP3K19_ENST00000358371.4_Silent_p.V405V	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	518							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)										CAGGTATGTTGACACTATGGT	0.428																																					p.V518V		Atlas-SNP	.											.	.	.	.	0			c.C1554T						PASS	.						193	180	184					2																	135744888		2203	4300	6503	SO:0001819	synonymous_variant	80122	exon7			TATGTTGACACTA	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.1554C>T	chr2.hg19:g.135744888G>A		295.0	0.0	.		233.0	89.0	.	NM_025052	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Silent	SNP	ENST00000375845.3	hg19	CCDS2176.2																																																																																			.	.	.	none		0.428	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052		A	135744888	G	A	135744888	2	1	247	1	0	0	0	0	0	0	0	1	17507	1277	45	2		2	YSK4	2	135744888	Silent	SNP	G	TCGA-SX-A7SM-01A-11D-A34Z-10	7134247	135744888	107454485	14	15260											
TTN	7273	hgsc.bcm.edu	37	chr2	179615537	179615537	+	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	0	0	0	0	0	0	0	0	0	0	attttcaggagtctcatataCttcctccttctcacatacat	10	16	3	12	0	3	0	3	0	2	0	7	1	5	1	2	1	2	0	2	1	3	7			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr2:179615537C>A	ENST00000591111.1	-	45	10585				TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.V3864L|TTN_ENST00000589042.1_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTCTCATATACTTCCTCCTTC	0.383																																					p.V3864L		Atlas-SNP	.											.	TTN	18412	.	0			c.G11590T						PASS	.						89	87	88					2																	179615537		2203	4299	6502	SO:0001627	intron_variant	7273	exon46			CATATACTTCCTC	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+2313G>T	chr2.hg19:g.179615537C>A		167.0	0.0	.		138.0	47.0	.	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	15.21	2.767157	0.49574	.	.	ENSG00000155657	ENST00000360870	T	0.57595	0.39	5.55	-1.34	0.09143	.	.	.	.	.	T	0.24890	0.0604	N	0.08118	0	0.24042	N	0.99608	B	0.02656	0.0	B	0.08055	0.003	T	0.26883	-1.0090	9	0.07030	T	0.85	.	8.6105	0.33800	0.0:0.55:0.1411:0.3089	.	3864	Q8WZ42-6	.	L	3864	ENSP00000354117:V3864L	ENSP00000354117:V3864L	V	-	1	0	TTN	179323782	0.142000	0.22610	0.007000	0.13788	0.428000	0.31595	0.002000	0.13061	-0.365000	0.08076	0.655000	0.94253	GTA	.	.	.	none		0.383	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179615537	C	A	179615537	1	1	247	0	1	0	0	0	0	0	0	0	16747	565	20	4		4	TTN	2	179615537	Intron	SNP	C	TCGA-SX-A7SM-01A-11D-A34Z-10	43870649	179615537	63583836	15	15261											
STAT1	6772	hgsc.bcm.edu	37	chr2	191874648	191874649	+	Frame_Shift_Del	DEL	TG	TG	-																															caggtactgtctgatttccaTgggaaaactgtcatcataaa																										TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr2:191874648_191874649delTG	ENST00000361099.3	-	3	468_469	c.81_82delCA	c.(79-84)cccatgfs	p.M28fs	STAT1_ENST00000392322.3_Frame_Shift_Del_p.M28fs|STAT1_ENST00000409465.1_Frame_Shift_Del_p.M28fs|STAT1_ENST00000540176.1_Frame_Shift_Del_p.M28fs|STAT1_ENST00000392323.2_Frame_Shift_Del_p.M30fs	NM_007315.3	NP_009330.1	P42224	STAT1_HUMAN	signal transducer and activator of transcription 1, 91kDa	28					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)			CTGATTTCCATGGGAAAACTGT	0.406																																					p.28_28del		Atlas-Indel,Pindel	.											.	STAT1	93	.	0			c.82_83del						PASS	.																																			SO:0001589	frameshift_variant	6772	exon3			.		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.81_82delCA	chr2.hg19:g.191874648_191874649delTG	ENSP00000354394:p.Met28fs	208.0	0.0	0		186.0	68.0	0.365591	NM_007315	A8K989|B2RCA0|D2KFR8|D3DPI7|Q53S88|Q53XW4|Q68D00|Q9UDL5	Frame_Shift_Del	DEL	ENST00000361099.3	hg19	CCDS2309.1																																																																																			.	.	.	none		0.406	STAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255997.3	NM_007315		-	191874649	TG	-	191874648	7	5	247	1	0	1	0	1	0	0	0	0	15276	1464	51	0	2266	0	STAT1	2	191874648	Frame_Shift_Del	DEL	TG	TCGA-SX-A7SM-01A-11D-A34Z-10	12259111	191874648	51324725	16	15262											
ANKMY1	51281	hgsc.bcm.edu	37	chr2	241463492	241463492	+	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	ctcagcactgcacagactgcCccggtctgtgtttcccaaca	8	9	8	16	1	2	1	1	0	1	1	3	1	3	1	3	1	4	3	3	1	1	1			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr2:241463492C>A	ENST00000272972.3	-	7	1589	c.1375G>T	c.(1375-1377)Ggc>Tgc	p.G459C	ANKMY1_ENST00000536462.1_Missense_Mutation_p.G271C|ANKMY1_ENST00000406958.1_Intron|ANKMY1_ENST00000405002.1_Missense_Mutation_p.G229C|ANKMY1_ENST00000462004.1_5'Flank|ANKMY1_ENST00000373318.2_Missense_Mutation_p.G318C|ANKMY1_ENST00000401804.1_Missense_Mutation_p.G548C|ANKMY1_ENST00000391987.1_Missense_Mutation_p.G459C|ANKMY1_ENST00000373320.4_Missense_Mutation_p.G229C|ANKMY1_ENST00000405523.3_Missense_Mutation_p.G318C|ANKMY1_ENST00000361678.4_Missense_Mutation_p.G318C|ANKMY1_ENST00000403283.1_Missense_Mutation_p.G397C	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	459							metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	30		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		CACAGACTGCCCCGGTCTGTG	0.597																																					p.G459C		Atlas-SNP	.											.	ANKMY1	112	.	0			c.G1375T						PASS	.						120	107	111					2																	241463492		2203	4300	6503	SO:0001583	missense	51281	exon7			GACTGCCCCGGTC	AB034636	CCDS2535.1, CCDS2536.1, CCDS63184.1, CCDS63185.1, CCDS74681.1	2q37.3	2013-01-10			ENSG00000144504	ENSG00000144504		"Zinc fingers, MYND-type", "Ankyrin repeat domain containing"	20987	protein-coding gene	gene with protein product							Standard	XM_005247020		Approved	FLJ20499, ZMYND13	uc002vyz.1	Q9P2S6	OTTHUMG00000133355	ENST00000272972.3:c.1375G>T	chr2.hg19:g.241463492C>A	ENSP00000272972:p.Gly459Cys	42.0	0.0	.		39.0	13.0	.	NM_016552	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Missense_Mutation	SNP	ENST00000272972.3	hg19	CCDS2536.1	.	.	.	.	.	.	.	.	.	.	C	6.247	0.413729	0.11812	.	.	ENSG00000144504	ENST00000373318;ENST00000272972;ENST00000361678;ENST00000391987;ENST00000373320;ENST00000403283;ENST00000401804;ENST00000536462;ENST00000405523;ENST00000405002	T;T;T;T;T;T;T;T;T;T	0.54479	2.98;0.59;2.31;0.59;4.46;2.54;0.57;2.37;2.3;2.63	4.06	-8.12	0.01078	Ankyrin repeat-containing domain (1);	2.746800	0.00846	N	0.001781	T	0.25975	0.0633	N	0.03608	-0.345	0.09310	N	1	B;B;B;B;B;B	0.11235	0.0;0.004;0.0;0.001;0.0;0.0	B;B;B;B;B;B	0.08055	0.0;0.003;0.001;0.001;0.001;0.0	T	0.27536	-1.0071	10	0.49607	T	0.09	-18.3189	6.7555	0.23512	0.6542:0.2072:0.0:0.1386	.	459;271;229;318;318;459	Q4ZFV3;F5H558;Q9P2S6-4;Q6GPI0;Q9P2S6-2;Q9P2S6	.;.;.;.;.;ANKY1_HUMAN	C	318;459;318;459;229;397;548;271;318;229	ENSP00000362415:G318C;ENSP00000272972:G459C;ENSP00000355097:G318C;ENSP00000375847:G459C;ENSP00000362417:G229C;ENSP00000383968:G397C;ENSP00000385887:G548C;ENSP00000444707:G271C;ENSP00000385635:G318C;ENSP00000385145:G229C	ENSP00000272972:G459C	G	-	1	0	ANKMY1	241112165	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.025000	0.00640	-2.201000	0.00746	-1.337000	0.01257	GGC	.	.	.	none		0.597	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2	NM_017844		A	241463492	C	A	241463492	3	1	247	1	0	0	0	0	1	0	0	0	634	623	22	4	1494	4	ANKMY1	2	241463492	Missense_Mutation	SNP	C	TCGA-SX-A7SM-01A-11D-A34Z-10	49588844	241463492	1735881	17	15263											
SETD2	29072	hgsc.bcm.edu	37	chr3	47165283	47165286	+	Frame_Shift_Del	DEL	TTTT	TTTT	-																															ttcccaatatgggaatcttcTttttttgaggaaatatctgc																										TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	TTTT	TTTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr3:47165283_47165286delTTTT	ENST00000409792.3	-	3	882_885	c.840_843delAAAA	c.(838-843)aaaaaafs	p.KK280fs		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	280					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		GGGAATCTTCTTTTTTTGAGGAAA	0.338			"N, F, S, Mis"		clear cell renal carcinoma																																p.281_282del		Atlas-Indel,Pindel	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.841_844del						PASS	.																																			SO:0001589	frameshift_variant	29072	exon3			.	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"Chromatin-modifying enzymes / K-methyltransferases"	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.840_843delAAAA	chr3.hg19:g.47165283_47165286delTTTT	ENSP00000386759:p.Lys280fs	162.0	0.0	0		166.0	109.0	0.656627	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Frame_Shift_Del	DEL	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.	.	none		0.338	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159		-	47165286	TTTT	-	47165283	7	5	247	1	0	1	0	1	0	0	0	0	14144	1606	56	0	6927	0	SETD2	3	47165283	Frame_Shift_Del	DEL	TTTT	TCGA-SX-A7SM-01A-11D-A34Z-10		47165283	150857147	18	15264											
ZFYVE28	57732	hgsc.bcm.edu	37	chr4	2337512	2337512	+	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	tcctgagtcaggtacccgaaGtccagggccctgtccgggga	7	7	14	13	2	1	1	1	1	0	0	4	3	4	2	5	4	1	1	5	4	2	1			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr4:2337512G>C	ENST00000290974.2	-	6	960	c.621C>G	c.(619-621)gaC>gaG	p.D207E	ZFYVE28_ENST00000515169.1_Missense_Mutation_p.D137E|ZFYVE28_ENST00000511071.1_Intron|ZFYVE28_ENST00000515312.1_Missense_Mutation_p.D137E|ZFYVE28_ENST00000509171.1_Intron|ZFYVE28_ENST00000503000.1_Missense_Mutation_p.D207E	NM_020972.2	NP_066023.2	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28	207					negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	31						GGTACCCGAAGTCCAGGGCCC	0.632																																					p.D207E		Atlas-SNP	.											.	ZFYVE28	79	.	0			c.C621G						PASS	.						93	74	80					4																	2337512		2184	4275	6459	SO:0001583	missense	57732	exon6			CCCGAAGTCCAGG	AK126692	CCDS33942.1, CCDS54708.1, CCDS54709.1, CCDS54710.1, CCDS54711.1, CCDS54712.1	4p16.3	2008-05-02			ENSG00000159733	ENSG00000159733		"Zinc fingers, FYVE domain containing"	29334	protein-coding gene	gene with protein product		614176				10997877	Standard	NM_020972		Approved	KIAA1643	uc003gex.2	Q9HCC9	OTTHUMG00000160292	ENST00000290974.2:c.621C>G	chr4.hg19:g.2337512G>C	ENSP00000290974:p.Asp207Glu	32.0	0.0	.		40.0	15.0	.	NM_020972	B2RP83|B3KX50|B7Z1Q7|B7Z2G9|B7Z2M2|B7ZB19|E9PB54|E9PB64|E9PG77|Q7Z6J3	Missense_Mutation	SNP	ENST00000290974.2	hg19	CCDS33942.1	.	.	.	.	.	.	.	.	.	.	G	10.19	1.282949	0.23392	.	.	ENSG00000159733	ENST00000290974;ENST00000515312;ENST00000515169;ENST00000503000	T;T;T;T	0.28255	1.62;1.62;2.7;1.62	4.81	0.466	0.16716	.	0.344757	0.32218	N	0.006401	T	0.10380	0.0254	N	0.03608	-0.345	0.23492	N	0.997569	B	0.09022	0.002	B	0.08055	0.003	T	0.22277	-1.0221	10	0.25106	T	0.35	.	5.0301	0.14405	0.0942:0.5179:0.2697:0.1182	.	207	Q9HCC9	LST2_HUMAN	E	207;137;137;207	ENSP00000290974:D207E;ENSP00000426299:D137E;ENSP00000425766:D137E;ENSP00000423694:D207E	ENSP00000290974:D207E	D	-	3	2	ZFYVE28	2307310	1.000000	0.71417	0.828000	0.32881	0.980000	0.70556	2.009000	0.40903	0.447000	0.26695	0.533000	0.62120	GAC	.	.	.	none		0.632	ZFYVE28-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360078.1	XM_035371		C	2337512	G	C	2337512	3	2	247	1	0	0	0	0	1	0	0	0	17682	1020	36	4	2294	4	ZFYVE28	4	2337512	Missense_Mutation	SNP	G	TCGA-SX-A7SM-01A-11D-A34Z-10		2337512	188816764	19	15265											
NOP14	8602	hgsc.bcm.edu	37	chr4	2946954	2946954	+	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	ccagtgattttcaaataaatGagctggaaagaaagtgttac	16	11	9	5	0	1	3	1	2	0	1	1	4	1	4	1	1	2	2	1	1	6	4			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr4:2946954G>A	ENST00000314262.6	-	12	1686	c.1638C>T	c.(1636-1638)ctC>ctT	p.L546L	NOP14_ENST00000502735.1_Silent_p.L546L|NOP14-AS1_ENST00000515194.1_RNA|NOP14-AS1_ENST00000505731.1_RNA|NOP14_ENST00000416614.2_Silent_p.L546L|NOP14_ENST00000398071.4_Silent_p.L546L|NOP14-AS1_ENST00000503709.1_RNA|NOP14-AS1_ENST00000507702.1_RNA	NM_003703.1	NP_003694.1	P78316	NOP14_HUMAN	NOP14 nucleolar protein	546					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						TCAAATAAATGAGCTGGAAAG	0.512																																					p.L546L		Atlas-SNP	.											.	NOP14	69	.	0			c.C1638T						PASS	.						31	29	30					4																	2946954		2198	4289	6487	SO:0001819	synonymous_variant	8602	exon12			ATAAATGAGCTGG	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.1638C>T	chr4.hg19:g.2946954G>A		51.0	0.0	.		45.0	20.0	.	NM_003703	D3DVR6|Q7LGI5|Q7Z6K0|Q8TBR6	Silent	SNP	ENST00000314262.6	hg19	CCDS33945.1																																																																																			.	.	.	none		0.512	NOP14-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358135.2	NM_003703		A	2946954	G	A	2946954	2	1	247	1	0	0	0	0	0	0	0	1	10543	1277	45	2		2	NOP14	4	2946954	Silent	SNP	G	TCGA-SX-A7SM-01A-11D-A34Z-10	609442	2946954	188207322	20	15266											
FNIP2	57600	hgsc.bcm.edu	37	chr4	159812799	159812800	+	Splice_Site	INS	-	-	T																															tcacctccctgctgattttgINStaagtactggttcttatatc																										TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr4:159812799_159812800insT	ENST00000264433.6	+	15	3225		c.e15+1		FNIP2_ENST00000379346.3_Splice_Site|C4orf45_ENST00000508011.1_5'Flank	NM_020840.1	NP_065891.1	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2						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)		TGCTGATTTTGTAAGTACTGGT	0.347																																					.		Pindel	.											.	FNIP2	90	.	0			c.3150+1->T						PASS	.																																			SO:0001630	splice_region_variant	57600	exon15			.	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.3150+1->T	chr4.hg19:g.159812800_159812800dupT		93.0	0.0	.		90.0	20.0	0.222	NM_020840	Q05DC3|Q96I31|Q9H994	Splice_Site	INS	ENST00000264433.6	hg19	CCDS47155.1																																																																																			.	.	.	none		0.347	FNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366602.1	NM_020840	Intron	T	159812800	-	T	159812799	8	5	247	1	0	1	1	0	0	0	1	0	5983	1391	48	0	3209	0	FNIP2	4	159812799	Splice_Site	INS	-	TCGA-SX-A7SM-01A-11D-A34Z-10	156865845	159812799	31341477	21	15267											
BHMT2	23743	hgsc.bcm.edu	37	chr5	78375253	78375253	+	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	gtcatgcagacttttaccttTtctgccagtgaggacaatat	10	14	8	9	0	2	2	1	1	1	1	2	3	2	3	2	1	3	1	2	1	3	5			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr5:78375253T>A	ENST00000255192.3	+	3	294	c.228T>A	c.(226-228)ttT>ttA	p.F76L	BHMT2_ENST00000521567.1_Missense_Mutation_p.F76L|DMGDH_ENST00000520388.1_Intron	NM_017614.4	NP_060084.2	Q9H2M3	BHMT2_HUMAN	betaine--homocysteine S-methyltransferase 2	76	Hcy-binding. {ECO:0000255|PROSITE- ProRule:PRU00333}.				L-methionine salvage (GO:0071267)|S-adenosylmethionine metabolic process (GO:0046500)|S-methylmethionine metabolic process (GO:0033477)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|S-methylmethionine-homocysteine S-methyltransferase activity (GO:0061627)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(8)|lung(2)|ovary(1)|skin(1)|urinary_tract(1)	15		all_lung(232;0.00063)|Lung NSC(167;0.00171)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;2.09e-45)|Epithelial(54;9.3e-41)|all cancers(79;4.09e-36)	L-Methionine(DB00134)	CTTTTACCTTTTCTGCCAGTG	0.398																																					p.F76L		Atlas-SNP	.											.	BHMT2	44	.	0			c.T228A						PASS	.						87	83	84					5																	78375253		2203	4300	6503	SO:0001583	missense	23743	exon3			TACCTTTTCTGCC		CCDS4045.1, CCDS54871.1	5q13	2010-04-28	2010-04-28		ENSG00000132840	ENSG00000132840	2.1.1.5		1048	protein-coding gene	gene with protein product		605932				11087663, 18230605	Standard	NM_017614		Approved		uc003kft.3	Q9H2M3	OTTHUMG00000108158	ENST00000255192.3:c.228T>A	chr5.hg19:g.78375253T>A	ENSP00000255192:p.Phe76Leu	40.0	0.0	.		49.0	14.0	.	NM_017614	B7Z516|Q9NXX7	Missense_Mutation	SNP	ENST00000255192.3	hg19	CCDS4045.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.814416	0.90790	.	.	ENSG00000132840	ENST00000255192;ENST00000521567;ENST00000518666	T;T;T	0.21191	2.02;2.02;2.02	5.72	3.33	0.38152	Homocysteine S-methyltransferase (4);	0.000000	0.85682	D	0.000000	T	0.50786	0.1636	M	0.92923	3.36	0.26429	N	0.975969	D;P	0.76494	0.999;0.853	D;P	0.79108	0.992;0.5	T	0.48692	-0.9013	10	0.87932	D	0	-16.3792	8.4267	0.32733	0.0:0.2141:0.0:0.7859	.	76;76	B7Z516;Q9H2M3	.;BHMT2_HUMAN	L	76;76;16	ENSP00000255192:F76L;ENSP00000430278:F76L;ENSP00000428640:F16L	ENSP00000255192:F76L	F	+	3	2	BHMT2	78411009	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.584000	0.36589	1.012000	0.39366	0.533000	0.62120	TTT	.	.	.	none		0.398	BHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226962.2	NM_017614		A	78375253	T	A	78375253	3	1	247	1	0	0	0	0	1	0	0	0	1426	1838	64	5	238	5	BHMT2	5	78375253	Missense_Mutation	SNP	T	TCGA-SX-A7SM-01A-11D-A34Z-10		78375253	102540007	22	15268											
FEM1C	56929	hgsc.bcm.edu	37	chr5	114860849	114860849	+	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	tatatctaatatagtaagagGtatcaggatgagaaggacca	17	10	10	4	0	2	2	1	1	1	2	2	5	2	4	1	3	0	2	1	3	8	7			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr5:114860849G>C	ENST00000274457.3	-	3	1571	c.1010C>G	c.(1009-1011)aCc>aGc	p.T337S		NM_020177.2	NP_064562.1	Q96JP0	FEM1C_HUMAN	fem-1 homolog c (C. elegans)	337					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(5)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	18		all_cancers(142;0.000575)|all_epithelial(76;9.98e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;2.5e-07)|Epithelial(69;2.66e-07)|all cancers(49;1.39e-05)		ATAGTAAGAGGTATCAGGATG	0.418																																					p.T337S		Atlas-SNP	.											.	FEM1C	50	.	0			c.C1010G						PASS	.						113	116	115					5																	114860849		2202	4300	6502	SO:0001583	missense	56929	exon3			TAAGAGGTATCAG		CCDS4118.1	5q22	2013-01-10	2006-11-08		ENSG00000145780	ENSG00000145780		"Ankyrin repeat domain containing"	16933	protein-coding gene	gene with protein product		608767				14527725, 11733146	Standard	NM_020177		Approved	KIAA1785, EUROIMAGE686608, EUROIMAGE783647, FEM1A	uc003krb.1	Q96JP0	OTTHUMG00000128895	ENST00000274457.3:c.1010C>G	chr5.hg19:g.114860849G>C	ENSP00000274457:p.Thr337Ser	114.0	0.0	.		84.0	32.0	.	NM_020177	B2RE47|Q8N3V8|Q9H704|Q9NPL6|Q9NPL9	Missense_Mutation	SNP	ENST00000274457.3	hg19	CCDS4118.1	.	.	.	.	.	.	.	.	.	.	G	18.55	3.647404	0.67358	.	.	ENSG00000145780	ENST00000274457	T	0.72835	-0.69	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.75874	0.3909	M	0.82517	2.595	0.58432	D	0.999999	P	0.44241	0.829	B	0.40256	0.324	T	0.80826	-0.1209	10	0.62326	D	0.03	-21.2018	19.502	0.95098	0.0:0.0:1.0:0.0	.	337	Q96JP0	FEM1C_HUMAN	S	337	ENSP00000274457:T337S	ENSP00000274457:T337S	T	-	2	0	FEM1C	114888748	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.809000	0.99208	2.602000	0.87976	0.655000	0.94253	ACC	.	.	.	none		0.418	FEM1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250857.3	NM_020177		C	114860849	G	C	114860849	3	2	247	1	0	0	0	0	1	0	0	0	5818	1261	44	4	847	4	FEM1C	5	114860849	Missense_Mutation	SNP	G	TCGA-SX-A7SM-01A-11D-A34Z-10	36485596	114860849	66054411	23	15269											
GRAMD3	65983	hgsc.bcm.edu	37	chr5	125807996	125807996	+	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	cggaggaaccactgaagcaaAgtaagttctgacctgtttga	13	9	11	8	1	1	3	0	3	1	0	1	5	1	5	2	2	2	4	2	2	4	3			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr5:125807996A>G	ENST00000285689.3	+	4	843	c.382A>G	c.(382-384)Agc>Ggc	p.S128G	GRAMD3_ENST00000502348.1_Splice_Site_p.S19G|GRAMD3_ENST00000542322.1_Splice_Site_p.S136G|GRAMD3_ENST00000515200.1_Splice_Site_p.S105G|GRAMD3_ENST00000513040.1_Splice_Site_p.S143G|GRAMD3_ENST00000511134.1_Splice_Site_p.S112G|GRAMD3_ENST00000514932.1_3'UTR|GRAMD3_ENST00000543198.1_Splice_Site_p.S105G|GRAMD3_ENST00000544396.1_Splice_Site_p.S24G|RP11-517I3.1_ENST00000515808.1_RNA	NM_023927.2	NP_076416.2	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3	128	GRAM.					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)		ACTGAAGCAAAGTAAGTTCTG	0.388																																					p.S143G		Atlas-SNP	.											.	GRAMD3	30	.	0			c.A427G						PASS	.						159	146	150					5																	125807996		2203	4300	6503	SO:0001630	splice_region_variant	65983	exon4			AAGCAAAGTAAGT	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.382+1A>G	chr5.hg19:g.125807996A>G		106.0	0.0	.		102.0	39.0	.	NM_001146319	B7Z1F2|B7Z3R1|B7Z6D8|B7Z8T2|D3DSZ3|Q9H753	Missense_Mutation	SNP	ENST00000285689.3	hg19	CCDS4136.1	.	.	.	.	.	.	.	.	.	.	A	19.31	3.802280	0.70682	.	.	ENSG00000155324	ENST00000513040;ENST00000506445;ENST00000543367;ENST00000285689;ENST00000515200;ENST00000542322;ENST00000544396;ENST00000543198;ENST00000502348;ENST00000511134	D;D;D;D;D;D;D;D;D	0.87809	-2.3;-2.3;-2.3;-2.3;-2.3;-2.3;-2.3;-2.3;-2.3	5.87	4.72	0.59763	GRAM (2);	0.111914	0.85682	N	0.000000	D	0.92166	0.7516	M	0.74546	2.27	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.995;0.997;0.991;0.999	D;D;D;P;D	0.72338	0.958;0.923;0.977;0.892;0.958	D	0.92000	0.5610	10	0.56958	D	0.05	.	11.7093	0.51616	0.9307:0.0:0.0693:0.0	.	112;24;136;143;128	B7Z8T2;B7Z1F2;B7Z3R1;B7Z6D8;Q96HH9	.;.;.;.;GRAM3_HUMAN	G	143;142;112;128;105;136;24;105;19;112	ENSP00000426120:S143G;ENSP00000424985:S142G;ENSP00000285689:S128G;ENSP00000426143:S105G;ENSP00000441876:S136G;ENSP00000444049:S24G;ENSP00000442902:S105G;ENSP00000427596:S19G;ENSP00000426088:S112G	ENSP00000285689:S128G	S	+	1	0	GRAMD3	125835895	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	7.449000	0.80643	1.166000	0.42689	0.533000	0.62120	AGC	.	.	.	none		0.388	GRAMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250922.2	NM_023927	Missense_Mutation	G	125807996	A	G	125807996	5	3	247	1	0	0	0	0	0	0	1	0	6758	86	3	3	610	3	GRAMD3	5	125807996	Splice_Site	SNP	A	TCGA-SX-A7SM-01A-11D-A34Z-10	10947147	125807996	55107264	24	15270											
PCDHGA1	56114	hgsc.bcm.edu	37	chr5	140710446	140710446	+	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	ctggcagatggcggagtccgCatcgtctccagaggtaggat	8	8	15	10	3	1	2	0	0	1	2	4	4	2	4	2	5	0	3	2	5	1	1			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr5:140710446C>G	ENST00000517417.1	+	1	195	c.195C>G	c.(193-195)cgC>cgG	p.R65R	AC005618.6_ENST00000606901.1_lincRNA|PCDHGA1_ENST00000378105.3_Silent_p.R65R	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	65	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(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)			GCGGAGTCCGCATCGTCTCCA	0.587																																					p.R65R		Atlas-SNP	.											.	PCDHGA1	397	.	0			c.C195G						PASS	.						108	115	113					5																	140710446		2203	4300	6503	SO:0001819	synonymous_variant	56114	exon1			AGTCCGCATCGTC	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.195C>G	chr5.hg19:g.140710446C>G		62.0	0.0	.		74.0	27.0	.	NM_018912	Q2M273|Q9Y5D6	Silent	SNP	ENST00000517417.1	hg19	CCDS54922.1																																																																																			.	.	.	none		0.587	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		G	140710446	C	G	140710446	2	3	247	1	0	0	0	0	0	0	0	1	11557	697	25	4		4	PCDHGA1	5	140710446	Silent	SNP	C	TCGA-SX-A7SM-01A-11D-A34Z-10	14902450	140710446	40204814	25	15271											
CLK4	57396	hgsc.bcm.edu	37	chr5	178032332	178032332	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaatcatgtgttgtggtaTgggtcctaatattcgttcca	8	16	10	7	1	1	1	1	1	0	0	4	1	3	1	2	2	0	3	2	2	4	6			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr5:178032332T>C	ENST00000316308.4	-	11	1354	c.1186A>G	c.(1186-1188)Ata>Gta	p.I396V		NM_020666.2	NP_065717.1	Q9HAZ1	CLK4_HUMAN	CDC-like kinase 4	396	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(2)	21	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.235)		TGTTGTGGTATGGGTCCTAAT	0.343																																					p.I396V		Atlas-SNP	.											.	CLK4	103	.	0			c.A1186G						PASS	.						164	148	153					5																	178032332		2203	4299	6502	SO:0001583	missense	57396	exon11			GTGGTATGGGTCC	AF294429	CCDS4437.1	5q35	2008-05-02			ENSG00000113240	ENSG00000113240		"CDC-like kinases"	13659	protein-coding gene	gene with protein product		607969				11170754	Standard	NM_020666		Approved		uc003mjf.1	Q9HAZ1	OTTHUMG00000130893	ENST00000316308.4:c.1186A>G	chr5.hg19:g.178032332T>C	ENSP00000316948:p.Ile396Val	137.0	0.0	.		105.0	29.0	.	NM_020666		Missense_Mutation	SNP	ENST00000316308.4	hg19	CCDS4437.1	.	.	.	.	.	.	.	.	.	.	T	13.56	2.273315	0.40194	.	.	ENSG00000113240	ENST00000316308	T	0.19938	2.11	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);	0.145745	0.64402	D	0.000013	T	0.19846	0.0477	L	0.37697	1.125	0.80722	D	1	B;B	0.21225	0.053;0.053	B;B	0.34991	0.193;0.193	T	0.09574	-1.0668	10	0.30854	T	0.27	.	8.8995	0.35485	0.1663:0.0:0.0:0.8337	.	396;396	B9EG64;Q9HAZ1	.;CLK4_HUMAN	V	396	ENSP00000316948:I396V	ENSP00000316948:I396V	I	-	1	0	CLK4	177964938	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	2.255000	0.43222	2.061000	0.61500	0.477000	0.44152	ATA	.	.	.	none		0.343	CLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253479.2			C	178032332	T	C	178032332	3	2	247	1	0	0	0	0	1	0	0	0	3541	1464	51	3	271	3	CLK4	5	178032332	Missense_Mutation	SNP	T	TCGA-SX-A7SM-01A-11D-A34Z-10	37321886	178032332	2882928	26	15272											
GFPT2	9945	hgsc.bcm.edu	37	chr5	179743447	179743447	+	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	ggaagctcagtcagttcctcCaaaacttgccgcgtctgaag	10	9	10	12	2	3	1	2	1	1	0	5	2	5	2	3	1	3	2	3	1	4	2			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr5:179743447C>A	ENST00000253778.8	-	13	1336	c.1167G>T	c.(1165-1167)ttG>ttT	p.L389F	GFPT2_ENST00000520165.1_5'Flank	NM_005110.2	NP_005101.1	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2	389	SIS 1. {ECO:0000255|PROSITE- ProRule:PRU00797}.				carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|energy reserve metabolic process (GO:0006112)|fructose 6-phosphate metabolic process (GO:0006002)|glutamine metabolic process (GO:0006541)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)	carbohydrate binding (GO:0030246)|glutamine-fructose-6-phosphate transaminase (isomerizing) activity (GO:0004360)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)	TCAGTTCCTCCAAAACTTGCC	0.507																																					p.L389F		Atlas-SNP	.											.	GFPT2	74	.	0			c.G1167T						PASS	.						85	82	83					5																	179743447		2029	4213	6242	SO:0001583	missense	9945	exon13			TTCCTCCAAAACT	AB016789	CCDS43411.1	5q	2008-07-18			ENSG00000131459	ENSG00000131459			4242	protein-coding gene	gene with protein product	"glutamine: fructose-6-phosphate aminotransferase 2"	603865				10198162	Standard	NM_005110		Approved	GFAT2	uc003mlw.1	O94808	OTTHUMG00000163442	ENST00000253778.8:c.1167G>T	chr5.hg19:g.179743447C>A	ENSP00000253778:p.Leu389Phe	72.0	0.0	.		96.0	49.0	.	NM_005110	Q53XM2|Q9BWS4	Missense_Mutation	SNP	ENST00000253778.8	hg19	CCDS43411.1	.	.	.	.	.	.	.	.	.	.	C	8.577	0.881520	0.17467	.	.	ENSG00000131459	ENST00000253778	T	0.66815	-0.23	5.89	2.61	0.31194	Sugar isomerase (SIS) (2);	0.000000	0.85682	D	0.000000	T	0.54159	0.1841	N	0.01686	-0.76	0.80722	D	1	D	0.71674	0.998	D	0.72075	0.976	T	0.53258	-0.8464	9	.	.	.	-19.7846	10.2944	0.43616	0.0:0.7537:0.0:0.2463	.	389	O94808	GFPT2_HUMAN	F	389	ENSP00000253778:L389F	.	L	-	3	2	GFPT2	179676053	0.999000	0.42202	0.955000	0.39395	0.945000	0.59286	0.747000	0.26290	0.570000	0.29347	0.561000	0.74099	TTG	.	.	.	none		0.507	GFPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373444.4	NM_005110		A	179743447	C	A	179743447	3	1	247	1	0	0	0	0	1	0	0	0	6353	593	21	4	909	4	GFPT2	5	179743447	Missense_Mutation	SNP	C	TCGA-SX-A7SM-01A-11D-A34Z-10	1711115	179743447	1171813	27	15273											
GLI3	2737	hgsc.bcm.edu	37	chr7	42187973	42187973	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcactcgatgttgaaggttcCtcactgactttgctgagccc	7	13	9	12	1	2	3	2	3	0	0	4	4	3	3	2	1	2	3	2	1	1	3			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr7:42187973C>T	ENST00000395925.3	-	3	303	c.219G>A	c.(217-219)gaG>gaA	p.E73E	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	73					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						TTGAAGGTTCCTCACTGACTT	0.532									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																												p.E73E		Atlas-SNP	.											.	GLI3	312	.	0			c.G219A						PASS	.						150	121	131					7																	42187973		2203	4300	6503	SO:0001819	synonymous_variant	2737	exon3	Familial Cancer Database	;	AGGTTCCTCACTG		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.219G>A	chr7.hg19:g.42187973C>T		196.0	0.0	.		201.0	84.0	.	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Silent	SNP	ENST00000395925.3	hg19	CCDS5465.1																																																																																			.	.	.	none		0.532	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		T	42187973	C	T	42187973	2	4	247	1	0	0	0	0	0	0	0	1	6446	680	24	2		2	GLI3	7	42187973	Silent	SNP	C	TCGA-SX-A7SM-01A-11D-A34Z-10		42187973	116950690	28	15274											
DBF4	10926	hgsc.bcm.edu	37	chr7	87530188	87530188	+	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	tgcagaaatatgaagatctaGaaactgtaaatgtgatttta	17	13	8	3	0	1	5	0	2	1	3	1	5	1	5	0	0	2	2	0	0	8	5			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr7:87530188G>A	ENST00000265728.1	+	10	1423	c.919G>A	c.(919-921)Gaa>Aaa	p.E307K		NM_006716.3	NP_006707.1	Q9UBU7	DBF4A_HUMAN	DBF4 zinc finger	307					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)				TGAAGATCTAGAAACTGTAAA	0.318																																					p.E307K		Atlas-SNP	.											.	DBF4	67	.	0			c.G919A						PASS	.						111	125	120					7																	87530188		2203	4300	6503	SO:0001583	missense	10926	exon10			GATCTAGAAACTG	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.919G>A	chr7.hg19:g.87530188G>A	ENSP00000265728:p.Glu307Lys	52.0	0.0	.		58.0	27.0	.	NM_006716	A4D1D8|A8K954|O75226|Q75MS6|Q75N01|Q9Y2M6	Missense_Mutation	SNP	ENST00000265728.1	hg19	CCDS5611.1	.	.	.	.	.	.	.	.	.	.	G	16.20	3.054701	0.55325	.	.	ENSG00000006634	ENST00000265728	T	0.32272	1.46	4.93	3.97	0.46021	Zinc finger, DBF-type (3);	0.496290	0.22384	N	0.060764	T	0.25082	0.0609	L	0.36672	1.1	0.36946	D	0.892611	B;B	0.32031	0.304;0.352	B;B	0.34242	0.068;0.178	T	0.17228	-1.0376	10	0.40728	T	0.16	-16.1246	11.2252	0.48880	0.0:0.2654:0.7346:0.0	.	83;307	B7Z8C6;Q9UBU7	.;DBF4A_HUMAN	K	307	ENSP00000265728:E307K	ENSP00000265728:E307K	E	+	1	0	DBF4	87368124	0.975000	0.34042	0.896000	0.35187	0.979000	0.70002	1.952000	0.40343	2.663000	0.90544	0.591000	0.81541	GAA	.	.	.	none		0.318	DBF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253678.1	NM_006716		A	87530188	G	A	87530188	3	1	247	1	0	0	0	0	1	0	0	0	4250	943	33	2	957	2	DBF4	7	87530188	Missense_Mutation	SNP	G	TCGA-SX-A7SM-01A-11D-A34Z-10	45342215	87530188	71608475	29	15275											
MUC17	140453	hgsc.bcm.edu	37	chr7	100674406	100674406	+	Missense_Mutation	SNP	A	A	T																															ctttgtctctttcagacctcAgtgtgaacagggctgtgtgg																										TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr7:100674406A>T	ENST00000306151.4	+	2	152	c.88A>T	c.(88-90)Agt>Tgt	p.S30C		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	30					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)					TTCAGACCTCAGTGTGAACAG	0.532																																					p.S30C		Atlas-SNP	.											.	MUC17	804	.	0			c.A88T						PASS	.						191	167	175					7																	100674406		2203	4300	6503	SO:0001583	missense	140453	exon2			GACCTCAGTGTGA	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.88A>T	chr7.hg19:g.100674406A>T	ENSP00000302716:p.Ser30Cys	171.0	0.0	.		125.0	43.0	.	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	4.680	0.126381	0.08931	.	.	ENSG00000169876	ENST00000306151	T	0.02682	4.2	1.9	-0.636	0.11508	.	.	.	.	.	T	0.02156	0.0067	N	0.08118	0	0.09310	N	1	D	0.57899	0.981	P	0.49477	0.612	T	0.45249	-0.9274	9	0.87932	D	0	.	2.6293	0.04939	0.4862:0.3252:0.1887:0.0	.	30	Q685J3	MUC17_HUMAN	C	30	ENSP00000302716:S30C	ENSP00000302716:S30C	S	+	1	0	MUC17	100461126	0.000000	0.05858	0.001000	0.08648	0.190000	0.23558	0.102000	0.15272	-0.154000	0.11118	0.411000	0.27672	AGT	.	.	.	none		0.532	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		T	100674406	A	T	100674406	3	4	247	1	0	0	0	0	1	0	0	0	9981	188	7	5	94	5	MUC17	7	100674406	Missense_Mutation	SNP	A	TCGA-SX-A7SM-01A-11D-A34Z-10	13144218	100674406	58464257	30	15276	157	2									
MUC17	140453	hgsc.bcm.edu	37	chr7	100674408	100674408	+	Frame_Shift_Del	DEL	T	T	-																															ttgtctctttcagacctcagTgtgaacagggctgtgtggga																										TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr7:100674408delT	ENST00000306151.4	+	2	154	c.90delT	c.(88-90)agtfs	p.S30fs		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	30					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)					CAGACCTCAGTGTGAACAGGG	0.532																																					p.S30fs		Atlas-INDEL	.											.	MUC17	804	.	0			c.89delG						PASS	.						194	169	177					7																	100674408		2203	4300	6503	SO:0001589	frameshift_variant	140453	exon2			.	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.90delT	chr7.hg19:g.100674408delT	ENSP00000302716:p.Ser30fs	169.0	0.0	0		124.0	44.0	0.354839	NM_001040105	O14761|Q685J2|Q8TDH7	Frame_Shift_Del	DEL	ENST00000306151.4	hg19	CCDS34711.1																																																																																			.	.	.	none		0.532	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		-	100674408	T	-	100674408	7	5	247	1	0	1	0	1	0	0	0	0	9981	1693	59	0	96	0	MUC17	7	100674408	Frame_Shift_Del	DEL	T	TCGA-SX-A7SM-01A-11D-A34Z-10	2	100674408	58464255	31	15277	157	2									
VPS37A	137492	hgsc.bcm.edu	37	chr8	17142073	17142073	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tattgcagaagacttcttggAgggaaagatggaaatagatg	15	10	13	3	0	1	4	0	0	1	4	1	7	1	7	0	3	1	1	0	3	5	5			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr8:17142073A>G	ENST00000324849.4	+	10	1735	c.1061A>G	c.(1060-1062)gAg>gGg	p.E354G	VPS37A_ENST00000521829.1_Missense_Mutation_p.E329G	NM_001145152.1|NM_152415.2	NP_001138624.1|NP_689628.2	Q8NEZ2	VP37A_HUMAN	vacuolar protein sorting 37 homolog A (S. cerevisiae)	354	VPS37 C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00646}.				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)		GACTTCTTGGAGGGAAAGATG	0.393																																					p.E354G		Atlas-SNP	.											.	VPS37A	22	.	0			c.A1061G						PASS	.						108	109	108					8																	17142073		2203	4300	6503	SO:0001583	missense	137492	exon10			TCTTGGAGGGAAA		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.1061A>G	chr8.hg19:g.17142073A>G	ENSP00000318629:p.Glu354Gly	117.0	0.0	.		116.0	42.0	.	NM_152415	Q336D5|Q6NW27|Q8N3D7|Q8TBL7|Q96DL9	Missense_Mutation	SNP	ENST00000324849.4	hg19	CCDS6001.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.307807	0.81247	.	.	ENSG00000155975	ENST00000324849;ENST00000521829;ENST00000521976	T;T;T	0.78707	-1.2;-1.2;-1.2	5.31	5.31	0.75309	Modifier of rudimentary, Modr (2);	0.000000	0.85682	D	0.000000	D	0.84593	0.5506	L	0.55834	1.745	0.80722	D	1	D;D;D	0.76494	0.99;0.997;0.999	D;D;D	0.78314	0.921;0.954;0.991	T	0.82313	-0.0519	10	0.27785	T	0.31	-11.7351	15.9692	0.79998	1.0:0.0:0.0:0.0	.	125;329;354	B3KW95;Q8NEZ2-2;Q8NEZ2	.;.;VP37A_HUMAN	G	354;329;127	ENSP00000318629:E354G;ENSP00000429680:E329G;ENSP00000429858:E127G	ENSP00000318629:E354G	E	+	2	0	VPS37A	17186444	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	8.962000	0.93254	2.302000	0.77476	0.533000	0.62120	GAG	.	.	.	none		0.393	VPS37A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253301.2	NM_152415		G	17142073	A	G	17142073	3	3	247	1	0	0	0	0	1	0	0	0	17217	304	11	3	1099	3	VPS37A	8	17142073	Missense_Mutation	SNP	A	TCGA-SX-A7SM-01A-11D-A34Z-10		17142073	129221949	32	15278											
KIF13B	23303	hgsc.bcm.edu	37	chr8	28980929	28980929	+	Missense_Mutation	SNP	T	T	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	actgccagcagaggggaccaTcaccgcgttcctctcctcag	8	7	10	16	2	3	1	2	0	1	1	5	2	4	2	5	2	2	2	5	2	0	1			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr8:28980929T>G	ENST00000524189.1	-	28	3471	c.3433A>C	c.(3433-3435)Atg>Ctg	p.M1145L	CTD-2647L4.1_ENST00000523661.1_RNA	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	1145					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)		GAGGGGACCATCACCGCGTTC	0.552																																					p.M1145L		Atlas-SNP	.											.	KIF13B	192	.	0			c.A3433C						PASS	.						99	100	100					8																	28980929		1965	4150	6115	SO:0001583	missense	23303	exon28			GGACCATCACCGC	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.3433A>C	chr8.hg19:g.28980929T>G	ENSP00000427900:p.Met1145Leu	30.0	0.0	.		36.0	9.0	.	NM_015254	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Missense_Mutation	SNP	ENST00000524189.1	hg19	CCDS55217.1	.	.	.	.	.	.	.	.	.	.	T	3.369	-0.128796	0.06753	.	.	ENSG00000197892	ENST00000524189	T	0.73047	-0.71	4.63	4.63	0.57726	.	0.038546	0.85682	D	0.000000	T	0.41396	0.1157	N	0.02225	-0.63	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.46665	-0.9175	10	0.02654	T	1	.	14.2118	0.65769	0.0:0.0:0.0:1.0	.	1145	F8VPJ2	.	L	1145	ENSP00000427900:M1145L	ENSP00000427900:M1145L	M	-	1	0	KIF13B	29036848	0.991000	0.36638	0.896000	0.35187	0.838000	0.47535	2.211000	0.42825	1.929000	0.55896	0.533000	0.62120	ATG	.	.	.	none		0.552	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1			G	28980929	T	G	28980929	3	3	247	1	0	0	0	0	1	0	0	0	8282	1435	50	5	2099	5	KIF13B	8	28980929	Missense_Mutation	SNP	T	TCGA-SX-A7SM-01A-11D-A34Z-10	11838856	28980929	117383093	33	15279											
PHF20L1	51105	hgsc.bcm.edu	37	chr8	133851799	133851799	+	Frame_Shift_Del	DEL	G	G	-																															gtgttacagaagtgctacacGggctacagctgaagattgga																										TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr8:133851799delG	ENST00000395386.2	+	18	2658	c.2359delG	c.(2359-2361)gggfs	p.G787fs	PHF20L1_ENST00000220847.7_Frame_Shift_Del_p.G174fs|AF230666.2_ENST00000608375.1_RNA|PHF20L1_ENST00000395390.2_Frame_Shift_Del_p.G762fs|AF230666.2_ENST00000429151.1_RNA	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	787							zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			AGTGCTACACGGGCTACAGCT	0.403																																					p.H786fs		Atlas-Indel,Pindel	.											.	PHF20L1	129	.	0			c.2358delC						PASS	.						106	96	99					8																	133851799		1892	4120	6012	SO:0001589	frameshift_variant	51105	exon18			.	AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"Tudor domain containing", "Zinc fingers, PHD-type"	24280	protein-coding gene	gene with protein product	"tudor domain containing 20B"					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.2359delG	chr8.hg19:g.133851799delG	ENSP00000378784:p.Gly787fs	50.0	0.0	0		54.0	21.0	0.388889	NM_016018	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Frame_Shift_Del	DEL	ENST00000395386.2	hg19	CCDS6367.2																																																																																			.	.	.	none		0.403	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018		-	133851799	G	-	133851799	7	5	247	1	0	1	0	1	0	0	0	0	11839	1116	39	0	2521	0	PHF20L1	8	133851799	Frame_Shift_Del	DEL	G	TCGA-SX-A7SM-01A-11D-A34Z-10	104870870	133851799	12512223	34	15280											
VPS13A	23230	hgsc.bcm.edu	37	chr9	79955390	79955390	+	Frame_Shift_Del	DEL	T	T	-																															atttacccctttttatatgaTtaaaaacaaaagcaaatacc																								rs370606167		TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr9:79955390delT	ENST00000360280.3	+	50	7210	c.6950delT	c.(6949-6951)attfs	p.I2317fs	VPS13A_ENST00000376634.4_Frame_Shift_Del_p.I2317fs|VPS13A_ENST00000376636.3_Frame_Shift_Del_p.I2278fs|VPS13A_ENST00000357409.5_Frame_Shift_Del_p.I2317fs	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	2317					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						TTTTATATGATTAAAAACAAA	0.323																																					p.I2317fs		Atlas-Indel,Pindel	.											.	VPS13A	735	.	0			c.6949delA						PASS	.						77	81	80					9																	79955390		2203	4296	6499	SO:0001589	frameshift_variant	23230	exon50			.	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.6950delT	chr9.hg19:g.79955390delT	ENSP00000353422:p.Ile2317fs	198.0	0.0	0		190.0	67.0	0.352632	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Frame_Shift_Del	DEL	ENST00000360280.3	hg19	CCDS6655.1																																																																																			.	.	.	none		0.323	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		-	79955390	T	-	79955390	7	5	247	1	0	1	0	1	0	0	0	0	17201	1493	52	0	7148	0	VPS13A	9	79955390	Frame_Shift_Del	DEL	T	TCGA-SX-A7SM-01A-11D-A34Z-10		79955390	61258041	35	15281											
C9orf5	23731	hgsc.bcm.edu	37	chr9	111819564	111819564	+	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	ctattctgacgactgacatgCaacttctgtcctttgtgcct	7	15	7	12	1	2	2	0	2	2	0	3	3	3	2	2	0	3	1	2	0	2	4	rs201566707		TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr9:111819564C>T	ENST00000374586.3	-	12	1792	c.1761G>A	c.(1759-1761)ttG>ttA	p.L587L		NM_032012.3	NP_114401.2	Q9H330	TM245_HUMAN	transmembrane protein 245	587						integral component of membrane (GO:0016021)											GACTGACATGCAACTTCTGTC	0.398																																					p.L587L		Atlas-SNP	.											.	.	.	.	0			c.G1761A						PASS	.						81	78	79					9																	111819564		1899	4129	6028	SO:0001819	synonymous_variant	23731	exon12			GACATGCAACTTC	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.1761G>A	chr9.hg19:g.111819564C>T		105.0	0.0	.		81.0	34.0	.	NM_032012	B4DSW7|Q5JTQ5|Q5SS43|Q6ZME3|Q8NDJ5|Q96CG6	Silent	SNP	ENST00000374586.3	hg19	CCDS43858.1	.	.	.	.	.	.	.	.	.	.	C	8.570	0.879929	0.17467	.	.	ENSG00000106771	ENST00000413712	.	.	.	5.47	4.56	0.56223	.	.	.	.	.	T	0.70753	0.3260	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.70197	-0.4938	4	.	.	.	-9.3841	15.3007	0.73949	0.0:0.735:0.265:0.0	.	.	.	.	T	180	.	.	A	-	1	0	C9orf5	110859385	1.000000	0.71417	0.998000	0.56505	0.845000	0.48019	1.986000	0.40677	1.272000	0.44329	0.655000	0.94253	GCA	.	C|0.999;A|0.001	.	alt		0.398	TMEM245-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053587.2	NM_032012		T	111819564	C	T	111819564	2	4	247	1	0	0	0	0	0	0	0	1	2488	709	25	2		2	C9orf5	9	111819564	Silent	SNP	C	TCGA-SX-A7SM-01A-11D-A34Z-10	31864174	111819564	29393867	36	15282											
USP20	10868	hgsc.bcm.edu	37	chr9	132638511	132638511	+	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	aggatcgagatcgacaccttCatcaaggtgcgtgcggcgag	10	7	14	10	5	2	1	2	0	0	1	4	5	2	2	1	3	2	0	1	3	1	1			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr9:132638511C>T	ENST00000315480.4	+	22	2561	c.2403C>T	c.(2401-2403)ttC>ttT	p.F801F	USP20_ENST00000358355.1_Silent_p.F801F|USP20_ENST00000372429.3_Silent_p.F801F			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	801	DUSP 2. {ECO:0000255|PROSITE- ProRule:PRU00613}.				endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				TCGACACCTTCATCAAGGTGC	0.667																																					p.F801F		Atlas-SNP	.											.	USP20	186	.	0			c.C2403T						PASS	.						23	25	24					9																	132638511		2073	4199	6272	SO:0001819	synonymous_variant	10868	exon22			CACCTTCATCAAG	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"Ubiquitin-specific peptidases"	12619	protein-coding gene	gene with protein product		615143	"ubiquitin specific protease 20"			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.2403C>T	chr9.hg19:g.132638511C>T		65.0	0.0	.		62.0	25.0	.	NM_001008563	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Silent	SNP	ENST00000315480.4	hg19	CCDS43892.1																																																																																			.	.	.	none		0.667	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2			T	132638511	C	T	132638511	2	4	247	1	0	0	0	0	0	0	0	1	17064	825	29	2		2	USP20	9	132638511	Silent	SNP	C	TCGA-SX-A7SM-01A-11D-A34Z-10	20818947	132638511	8574920	37	15283											
TUBAL3	79861	hgsc.bcm.edu	37	chr10	5443030	5443030	+	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	tggatgccagcttgaccgatGtggatggaaaggcactccct	9	9	13	10	1	0	1	0	1	0	0	1	5	1	4	3	4	2	2	3	4	1	1			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr10:5443030G>T	ENST00000380419.3	-	2	61	c.24C>A	c.(22-24)caC>caA	p.H8Q	TUBAL3_ENST00000479328.1_Intron	NM_024803.2	NP_079079.1	A6NHL2	TBAL3_HUMAN	tubulin, alpha-like 3	8					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(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(7)|prostate(2)|skin(3)	25						CTTGACCGATGTGGATGGAAA	0.488																																					p.H8Q		Atlas-SNP	.											.	TUBAL3	54	.	0			c.C24A						PASS	.						89	85	86					10																	5443030		2203	4300	6503	SO:0001583	missense	79861	exon2			ACCGATGTGGATG	AK025318	CCDS7066.2, CCDS53491.1	10p15.1	2007-03-15			ENSG00000178462	ENSG00000178462		"Tubulins"	23534	protein-coding gene	gene with protein product							Standard	NM_024803		Approved	FLJ21665	uc001ihy.3	A6NHL2	OTTHUMG00000017595	ENST00000380419.3:c.24C>A	chr10.hg19:g.5443030G>T	ENSP00000369784:p.His8Gln	54.0	0.0	.		48.0	17.0	.	NM_024803	B4DKL2|Q4QQJ5|Q9H6Z0	Missense_Mutation	SNP	ENST00000380419.3	hg19	CCDS7066.2	.	.	.	.	.	.	.	.	.	.	G	12.39	1.922227	0.33908	.	.	ENSG00000178462	ENST00000380419	T	0.63255	-0.03	4.06	2.19	0.27852	Tubulin/FtsZ, GTPase domain (3);	0.168717	0.28647	N	0.014618	T	0.60274	0.2256	N	0.16833	0.445	0.80722	D	1	D	0.67145	0.996	D	0.75484	0.986	T	0.60616	-0.7228	10	0.87932	D	0	.	7.209	0.25923	0.2913:0.0:0.7087:0.0	.	8	A6NHL2	TBAL3_HUMAN	Q	8	ENSP00000369784:H8Q	ENSP00000369784:H8Q	H	-	3	2	TUBAL3	5433030	0.810000	0.29049	0.715000	0.30552	0.060000	0.15804	0.327000	0.19663	0.449000	0.26747	-0.136000	0.14681	CAC	.	.	.	none		0.488	TUBAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046548.2	NM_024803		T	5443030	G	T	5443030	3	4	247	1	0	0	0	0	1	0	0	0	16763	1368	48	4	1328	4	TUBAL3	10	5443030	Missense_Mutation	SNP	G	TCGA-SX-A7SM-01A-11D-A34Z-10		5443030	130091717	38	15284											
KIAA1274	27143	hgsc.bcm.edu	37	chr10	72324203	72324203	+	Missense_Mutation	SNP	T	T	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	gagcgctatgtctgcctgatTctcttcaacgcgtacctcca	7	12	8	14	3	3	1	1	1	2	0	5	2	4	1	3	0	4	2	3	0	3	4			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr10:72324203T>G	ENST00000263563.6	+	19	2614	c.2346T>G	c.(2344-2346)atT>atG	p.I782M		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	782						cytosol (GO:0005829)											TCTGCCTGATTCTCTTCAACG	0.632																																					p.I782M		Atlas-SNP	.											KIAA1274,NS,haematopoietic_neoplasm,0,3	.	.	.	0			c.T2346G						PASS	.						122	117	119					10																	72324203		2203	4300	6503	SO:0001583	missense	27143	exon19			CCTGATTCTCTTC	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.2346T>G	chr10.hg19:g.72324203T>G	ENSP00000263563:p.Ile782Met	86.0	0.0	.		99.0	40.0	.	NM_014431	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Missense_Mutation	SNP	ENST00000263563.6	hg19	CCDS31215.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.20|15.20	2.763695|2.763695	0.49574|0.49574	.|.	.|.	ENSG00000107719|ENSG00000107719	ENST00000263563;ENST00000373214|ENST00000426268	T|.	0.29917|.	1.55|.	5.12|5.12	-1.85|-1.85	0.07784|0.07784	.|.	0.120287|.	0.56097|.	D|.	0.000040|.	T|T	0.67571|0.67571	0.2907|0.2907	M|M	0.79011|0.79011	2.435|2.435	0.49798|0.49798	D|D	0.999823|0.999823	P|.	0.52463|.	0.953|.	D|.	0.63597|.	0.916|.	T|T	0.65776|0.65776	-0.6086|-0.6086	10|5	0.87932|.	D|.	0|.	-9.6058|-9.6058	7.9563|7.9563	0.30045|0.30045	0.0:0.5989:0.151:0.2501|0.0:0.5989:0.151:0.2501	.|.	782|.	Q9ULE6|.	PALD_HUMAN|.	M|A	782;758|163	ENSP00000263563:I782M|.	ENSP00000263563:I782M|.	I|S	+|+	3|1	3|0	KIAA1274|KIAA1274	71994209|71994209	0.997000|0.997000	0.39634|0.39634	0.994000|0.994000	0.49952|0.49952	0.268000|0.268000	0.26511|0.26511	0.541000|0.541000	0.23207|0.23207	-0.223000|-0.223000	0.09943|0.09943	-0.425000|-0.425000	0.05940|0.05940	ATT|TCT	.	.	.	none		0.632	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431		G	72324203	T	G	72324203	3	3	247	1	0	0	0	0	1	0	0	0	8227	1771	62	5	2416	5	KIAA1274	10	72324203	Missense_Mutation	SNP	T	TCGA-SX-A7SM-01A-11D-A34Z-10	66881173	72324203	63210544	39	15285											
MYST4	23522	hgsc.bcm.edu	37	chr10	76788653	76788653	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggaagaggaagaggaggaGgaggaggaagaggaagaaga	19	0	22	0	0	0	5	0	0	0	5	0	14	0	13	0	8	0	0	0	8	5	0			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr10:76788653G>A	ENST00000287239.4	+	18	4560	c.4071G>A	c.(4069-4071)gaG>gaA	p.E1357E	KAT6B_ENST00000372725.1_Silent_p.E1065E|KAT6B_ENST00000372711.1_Silent_p.E1174E|KAT6B_ENST00000372724.1_Silent_p.E1065E|KAT6B_ENST00000372714.1_Silent_p.E1065E	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1357	Poly-Glu.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										aagaggaggaggaggaggaag	0.453																																					p.E1357E		Atlas-SNP	.											.	.	.	.	0			c.G4071A						PASS	.						41	42	41					10																	76788653		2203	4300	6503	SO:0001819	synonymous_variant	23522	exon18			GGAGGAGGAGGAG	AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.4071G>A	chr10.hg19:g.76788653G>A		33.0	0.0	.		24.0	5.0	.	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Silent	SNP	ENST00000287239.4	hg19	CCDS7345.1																																																																																			.	.	.	none		0.453	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		A	76788653	G	A	76788653	2	1	247	1	0	0	0	0	0	0	0	1	10112	991	35	2		2	MYST4	10	76788653	Silent	SNP	G	TCGA-SX-A7SM-01A-11D-A34Z-10	4464450	76788653	58746094	40	15286											
KIF20B	9585	hgsc.bcm.edu	37	chr10	91479191	91479191	+	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	aacaggtttgtgtcccagacActttaaattcctctcaagag	12	12	7	10	0	1	2	1	0	1	2	4	2	3	2	2	1	1	1	2	1	4	4			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr10:91479191A>T	ENST00000371728.3	+	13	1515	c.1450A>T	c.(1450-1452)Act>Tct	p.T484S	KIF20B_ENST00000260753.4_Missense_Mutation_p.T484S|KIF20B_ENST00000394289.2_Missense_Mutation_p.T484S|KIF20B_ENST00000416354.1_Missense_Mutation_p.T484S	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	484					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						TGTCCCAGACACTTTAAATTC	0.279																																					p.T484S		Atlas-SNP	.											.	KIF20B	191	.	0			c.A1450T						PASS	.						35	39	38					10																	91479191		2153	4287	6440	SO:0001583	missense	9585	exon13			CCAGACACTTTAA	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.1450A>T	chr10.hg19:g.91479191A>T	ENSP00000360793:p.Thr484Ser	132.0	0.0	.		91.0	37.0	.	NM_016195	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Missense_Mutation	SNP	ENST00000371728.3	hg19		.	.	.	.	.	.	.	.	.	.	A	7.315	0.615724	0.14129	.	.	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	T;T;T;T	0.72394	-0.65;-0.65;-0.65;-0.65	5.63	1.83	0.25207	Kinesin, motor domain (1);	0.370049	0.23367	N	0.048955	T	0.47581	0.1453	L	0.28274	0.84	0.09310	N	1	B;B	0.11235	0.002;0.004	B;B	0.13407	0.006;0.009	T	0.13202	-1.0518	10	0.19590	T	0.45	-0.0742	1.5376	0.02548	0.5113:0.1337:0.2256:0.1293	.	484;484	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	S	484	ENSP00000260753:T484S;ENSP00000411545:T484S;ENSP00000377830:T484S;ENSP00000360793:T484S	ENSP00000260753:T484S	T	+	1	0	KIF20B	91469171	0.000000	0.05858	0.478000	0.27316	0.794000	0.44872	-0.552000	0.06020	0.421000	0.25980	0.377000	0.23210	ACT	.	.	.	none		0.279	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195		T	91479191	A	T	91479191	3	4	247	1	0	0	0	0	1	0	0	0	8294	159	6	5	1496	5	KIF20B	10	91479191	Missense_Mutation	SNP	A	TCGA-SX-A7SM-01A-11D-A34Z-10	14690538	91479191	44055556	41	15287											
CD151	977	hgsc.bcm.edu	37	chr11	836827	836827	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catcgctggtatcctcgcctAcgcctactaccagcaggtga	8	9	9	15	3	0	1	0	1	0	0	3	1	1	1	4	2	4	3	4	2	4	4			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr11:836827A>G	ENST00000397420.3	+	5	584	c.335A>G	c.(334-336)tAc>tGc	p.Y112C	CD151_ENST00000397421.1_Missense_Mutation_p.Y112C|CD151_ENST00000528011.1_Missense_Mutation_p.Y112C|CD151_ENST00000322008.4_Missense_Mutation_p.Y112C			P48509	CD151_HUMAN	CD151 molecule (Raph blood group)	112					cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|T cell proliferation (GO:0042098)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	3		all_cancers(49;2.31e-08)|all_epithelial(84;3.72e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.179)|all_lung(207;0.227)		all cancers(45;1.54e-25)|Epithelial(43;1.22e-24)|OV - Ovarian serous cystadenocarcinoma(40;6.91e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		ATCCTCGCCTACGCCTACTAC	0.607																																					p.Y112C	Esophageal Squamous(14;501 559 15826 37823 38305)	Atlas-SNP	.											.	CD151	7	.	0			c.A335G						PASS	.						72	60	64					11																	836827		2198	4294	6492	SO:0001583	missense	977	exon4			TCGCCTACGCCTA	AL161965, BC013302, D29963	CCDS7719.1	11p15.5	2014-07-18	2006-03-28		ENSG00000177697	ENSG00000177697		"CD molecules", "Blood group antigens", "Tetraspanins"	1630	protein-coding gene	gene with protein product		602243	"CD151 antigen", "CD151 antigen (Raph blood group)"			9070943	Standard	NM_004357		Approved	SFA-1, PETA-3, TSPAN24, RAPH	uc001lsb.3	P48509	OTTHUMG00000133311	ENST00000397420.3:c.335A>G	chr11.hg19:g.836827A>G	ENSP00000380565:p.Tyr112Cys	98.0	0.0	.		63.0	25.0	.	NM_139030	A8KAK8|E9PI15|Q14826|Q86U54|Q96TE3	Missense_Mutation	SNP	ENST00000397420.3	hg19	CCDS7719.1	.	.	.	.	.	.	.	.	.	.	A	15.50	2.852392	0.51270	.	.	ENSG00000177697	ENST00000397420;ENST00000322008;ENST00000397421;ENST00000526693;ENST00000524748;ENST00000527341;ENST00000530320;ENST00000528011	D;D;D;D;D;D;D;D	0.89939	-2.59;-2.59;-2.59;-2.59;-2.59;-2.59;-2.59;-2.59	4.74	4.74	0.60224	Tetraspanin, EC2 domain (1);	0.000000	0.85682	D	0.000000	D	0.95472	0.8529	M	0.92784	3.345	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.96508	0.9376	10	0.87932	D	0	.	14.3849	0.66938	1.0:0.0:0.0:0.0	.	112	P48509	CD151_HUMAN	C	112	ENSP00000380565:Y112C;ENSP00000324101:Y112C;ENSP00000380566:Y112C;ENSP00000435054:Y112C;ENSP00000431403:Y112C;ENSP00000436591:Y112C;ENSP00000433787:Y112C;ENSP00000432990:Y112C	ENSP00000324101:Y112C	Y	+	2	0	CD151	826827	1.000000	0.71417	0.982000	0.44146	0.092000	0.18411	6.692000	0.74578	1.992000	0.58205	0.459000	0.35465	TAC	.	.	.	none		0.607	CD151-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257108.1	NM_004357		G	836827	A	G	836827	3	3	247	1	0	0	0	0	1	0	0	0	2967	391	14	3	345	3	CD151	11	836827	Missense_Mutation	SNP	A	TCGA-SX-A7SM-01A-11D-A34Z-10		836827	134169689	42	15288											
ARFIP2	23647	hgsc.bcm.edu	37	chr11	6500088	6500088	+	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	agctgcaggacactctcataCttgcgcttcgtctcacgcag	8	10	9	14	3	2	0	2	0	2	0	5	1	2	1	0	1	4	4	0	1	1	3			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr11:6500088C>A	ENST00000254584.2	-	5	500	c.417G>T	c.(415-417)aaG>aaT	p.K139N	ARFIP2_ENST00000423813.2_Missense_Mutation_p.K101N|ARFIP2_ENST00000396777.3_Missense_Mutation_p.K139N|TIMM10B_ENST00000472836.1_5'Flank|ARFIP2_ENST00000445086.2_Missense_Mutation_p.K54N|TIMM10B_ENST00000530751.1_5'Flank|TIMM10B_ENST00000254616.6_5'Flank|ARFIP2_ENST00000525235.1_Missense_Mutation_p.K139N	NM_012402.3	NP_036534.1	P53365	ARFP2_HUMAN	ADP-ribosylation factor interacting protein 2	139	AH. {ECO:0000255|PROSITE- ProRule:PRU00294}.				actin cytoskeleton organization (GO:0030036)|cellular component movement (GO:0006928)|lamellipodium assembly (GO:0030032)|ruffle organization (GO:0031529)|small GTPase mediated signal transduction (GO:0007264)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	GTP binding (GO:0005525)|GTP-dependent protein binding (GO:0030742)|Rac GTPase binding (GO:0048365)			endometrium(2)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|skin(2)	15		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;3.41e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CACTCTCATACTTGCGCTTCG	0.577																																					p.K172N	Melanoma(119;796 1674 9049 20480 24794)	Atlas-SNP	.											.	ARFIP2	23	.	0			c.G516T						PASS	.						84	60	68					11																	6500088		2201	4296	6497	SO:0001583	missense	23647	exon5			CTCATACTTGCGC	BC000392	CCDS7765.1, CCDS55739.1, CCDS55740.1, CCDS73250.1	11p15	2008-08-01	2008-08-01		ENSG00000132254	ENSG00000132254			17160	protein-coding gene	gene with protein product	"arfaptin 2"	601638				8670882, 9038142	Standard	NM_012402		Approved	POR1	uc010ran.2	P53365	OTTHUMG00000133406	ENST00000254584.2:c.417G>T	chr11.hg19:g.6500088C>A	ENSP00000254584:p.Lys139Asn	53.0	0.0	.		70.0	30.0	.	NM_001242854	B4DX86|B4E306|D3DQT5	Missense_Mutation	SNP	ENST00000254584.2	hg19	CCDS7765.1	.	.	.	.	.	.	.	.	.	.	C	16.58	3.163707	0.57476	.	.	ENSG00000132254	ENST00000254584;ENST00000396777;ENST00000445086;ENST00000423813;ENST00000525235	T;T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13;-1.13	5.67	3.81	0.43845	Arfaptin-like (3);	0.000000	0.85682	D	0.000000	D	0.86834	0.6028	M	0.79693	2.465	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.995;0.999	D	0.87256	0.2276	10	0.52906	T	0.07	.	11.391	0.49815	0.0:0.8534:0.0:0.1466	.	172;54;139	B4DUZ3;B4E306;P53365	.;.;ARFP2_HUMAN	N	139;139;54;101;139	ENSP00000254584:K139N;ENSP00000379998:K139N;ENSP00000391427:K54N;ENSP00000398375:K101N;ENSP00000434124:K139N	ENSP00000254584:K139N	K	-	3	2	ARFIP2	6456664	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.141000	0.42168	1.408000	0.46895	0.561000	0.74099	AAG	.	.	.	none		0.577	ARFIP2-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387044.1	NM_012402		A	6500088	C	A	6500088	3	1	247	1	0	0	0	0	1	0	0	0	855	564	20	4	624	4	ARFIP2	11	6500088	Missense_Mutation	SNP	C	TCGA-SX-A7SM-01A-11D-A34Z-10	5663261	6500088	128506428	43	15289											
SIK3	23387	hgsc.bcm.edu	37	chr11	116729011	116729011	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtattcttgctgttgctgcTgttgctgctgctgctgccgt	1	17	13	10	1	1	0	0	0	1	0	1	0	1	0	1	1	8	10	1	1	1	5	rs537893827	byFrequency	TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr11:116729011T>C	ENST00000292055.4	-	20	2887	c.2852A>G	c.(2851-2853)cAg>cGg	p.Q951R	SIK3_ENST00000542607.1_Missense_Mutation_p.Q891R|SIK3_ENST00000446921.2_Missense_Mutation_p.Q949R|SIK3_ENST00000434315.2_Missense_Mutation_p.Q790R|AP006216.12_ENST00000444200.1_RNA|SIK3_ENST00000488337.1_5'UTR|SIK3_ENST00000375288.1_Missense_Mutation_p.Q286R|SIK3_ENST00000375300.1_Missense_Mutation_p.Q1009R	NM_025164.3	NP_079440.3	Q9Y2K2	SIK3_HUMAN	SIK family kinase 3	951	Gln-rich.				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						ctgttgctgctgttgctgctg	0.592																																					p.Q951R		Atlas-SNP	.											.	SIK3	112	.	0			c.A2852G						PASS	.						40	39	39					11																	116729011		2201	4296	6497	SO:0001583	missense	23387	exon20			TGCTGCTGTTGCT	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.2852A>G	chr11.hg19:g.116729011T>C	ENSP00000292055:p.Gln951Arg	89.0	0.0	.		96.0	18.0	.	NM_025164	A1A5A8|Q59FY2|Q5M9N1|Q6P3R6|Q8IYM8|Q9HA50	Missense_Mutation	SNP	ENST00000292055.4	hg19	CCDS8379.1	.	.	.	.	.	.	.	.	.	.	T	8.339	0.828231	0.16749	.	.	ENSG00000160584	ENST00000375300;ENST00000292055;ENST00000375288;ENST00000542607;ENST00000434315	T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56	5.22	2.87	0.33458	.	0.213574	0.23076	U	0.052215	T	0.16257	0.0391	N	0.12182	0.205	0.44168	D	0.996977	B;B;B;B;B	0.11235	0.004;0.001;0.0;0.001;0.0	B;B;B;B;B	0.10450	0.005;0.001;0.001;0.002;0.002	T	0.05053	-1.0909	10	0.72032	D	0.01	.	6.9418	0.24496	0.0:0.1912:0.0:0.8088	.	951;891;790;951;286	Q9Y2K2-3;A1A5A8;A1A5A9;Q9Y2K2;Q9Y2K2-2	.;.;.;SIK3_HUMAN;.	R	1009;951;286;891;790	ENSP00000364449:Q1009R;ENSP00000292055:Q951R;ENSP00000364437:Q286R;ENSP00000438108:Q891R;ENSP00000415873:Q790R	ENSP00000292055:Q951R	Q	-	2	0	SIK3	116234221	1.000000	0.71417	0.995000	0.50966	0.191000	0.23601	3.827000	0.55745	0.821000	0.34540	0.533000	0.62120	CAG	.	.	.	none		0.592	SIK3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_025164		C	116729011	T	C	116729011	3	2	247	1	0	0	0	0	1	0	0	0	14332	1580	55	3	955	3	SIK3	11	116729011	Missense_Mutation	SNP	T	TCGA-SX-A7SM-01A-11D-A34Z-10	110228923	116729011	18277505	44	15290											
PLEKHA5	54477	hgsc.bcm.edu	37	chr12	19408098	19408100	+	Splice_Site	DEL	GAG	GAG	-																															tccaatgagccctgtaggcaGagtaagttattttgctttat																										TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr12:19408098_19408100delGAG	ENST00000299275.6	+	5	437_438	c.431_432delGAG	c.(430-432)aga>a	p.R144del	PLEKHA5_ENST00000543806.1_Splice_Site_p.R36del|PLEKHA5_ENST00000538714.1_Splice_Site_p.R144del|PLEKHA5_ENST00000539256.1_5'UTR|PLEKHA5_ENST00000359180.3_Splice_Site_p.R144del|PLEKHA5_ENST00000309364.4_Splice_Site_p.R144del|PLEKHA5_ENST00000424268.1_Splice_Site_p.R36del|PLEKHA5_ENST00000429027.2_Splice_Site_p.R144del|PLEKHA5_ENST00000317589.4_Splice_Site_p.R144del|PLEKHA5_ENST00000355397.3_Splice_Site_p.R144del	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	144					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)					CCTGTAGGCAGAGTAAGTTATTT	0.31																																					p.144_144del	Pancreas(196;329 2193 11246 14234 19524)	Atlas-Indel,Pindel	.											.	PLEKHA5	198	.	0			c.430_432del						PASS	.																																			SO:0001630	splice_region_variant	54477	exon5			.	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.432+1GAG>-	chr12.hg19:g.19408098_19408100delGAG		37.0	0.0	0		54.0	14.0	0.259259	NM_001256470	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	In_Frame_Del	DEL	ENST00000299275.6	hg19	CCDS8682.1																																																																																			.	.	.	none		0.31	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012	In_Frame_Del	-	19408100	GAG	-	19408098	8	5	247	1	0	1	0	1	0	0	1	0	12066	956	33	0	449	0	PLEKHA5	12	19408098	Splice_Site	DEL	GAG	TCGA-SX-A7SM-01A-11D-A34Z-10		19408098	114443797	45	15291											
ARID2	196528	hgsc.bcm.edu	37	chr12	46244757	46244758	+	Frame_Shift_Del	DEL	CC	CC	-																															accaaattgttcttgctaatCcagcagctcttccagctggt																										TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr12:46244757_46244758delCC	ENST00000334344.6	+	15	3023_3024	c.2851_2852delCC	c.(2851-2853)ccafs	p.P951fs	ARID2_ENST00000444670.1_Frame_Shift_Del_p.P561fs|ARID2_ENST00000457135.1_5'Flank|ARID2_ENST00000422737.1_Frame_Shift_Del_p.P802fs|ARID2_ENST00000479608.1_3'UTR	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	951	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)		TCTTGCTAATCCAGCAGCTCTT	0.47			"N, S, F"		hepatocellular carcinoma																																p.950_951del		Atlas-Indel,Pindel	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.2850_2851del						PASS	.																																			SO:0001589	frameshift_variant	196528	exon15			.		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"-"	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.2851_2852delCC	chr12.hg19:g.46244757_46244758delCC	ENSP00000335044:p.Pro951fs	75.0	0.0	0		115.0	21.0	0.182609	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Frame_Shift_Del	DEL	ENST00000334344.6	hg19	CCDS31783.1																																																																																			.	.	.	none		0.47	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		-	46244758	CC	-	46244757	7	5	247	1	0	1	0	1	0	0	0	0	915	855	30	0	2909	0	ARID2	12	46244757	Frame_Shift_Del	DEL	CC	TCGA-SX-A7SM-01A-11D-A34Z-10	26836659	46244757	87607138	46	15292											
PRPF40B	25766	hgsc.bcm.edu	37	chr12	50025231	50025231	+	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	tttcctccgatggggctaccCcccatgagtcagagaccacc	8	8	9	16	1	1	2	1	1	0	1	3	4	3	2	7	2	1	1	7	2	1	2			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr12:50025231C>G	ENST00000380281.1	+	2	130	c.66C>G	c.(64-66)ccC>ccG	p.P22P	PRPF40B_ENST00000548825.2_Silent_p.P44P|PRPF40B_ENST00000261897.1_Silent_p.P16P			Q6NWY9	PR40B_HUMAN	PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae)	22	Pro-rich.				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						TGGGGCTACCCCCCATGAGTC	0.597																																					p.P44P		Atlas-SNP	.											.	PRPF40B	83	.	0			c.C132G						PASS	.						100	102	101					12																	50025231		2203	4300	6503	SO:0001819	synonymous_variant	25766	exon3			GCTACCCCCCATG	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.66C>G	chr12.hg19:g.50025231C>G		143.0	0.0	.		161.0	40.0	.	NM_001031698	O75401|Q6PI09|Q6ZWB3|Q8NCZ1|Q9H5G4|Q9NT95	Silent	SNP	ENST00000380281.1	hg19																																																																																				.	.	.	none		0.597	PRPF40B-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000404838.1	NM_012272		G	50025231	C	G	50025231	2	3	247	1	0	0	0	0	0	0	0	1	12582	610	22	4		4	PRPF40B	12	50025231	Silent	SNP	C	TCGA-SX-A7SM-01A-11D-A34Z-10	3780474	50025231	83826664	47	15293											
UNG	7374	hgsc.bcm.edu	37	chr12	109536367	109536367	+	Missense_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	cctgctcagactcgcggcccGcaacgtgcccgtgggctttg	4	8	13	16	5	1	1	1	0	0	1	2	1	1	1	3	2	3	3	3	2	1	1			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr12:109536367G>A	ENST00000242576.2	+	2	369	c.263G>A	c.(262-264)cGc>cAc	p.R88H	UNG_ENST00000336865.2_Missense_Mutation_p.R79H	NM_080911.2	NP_550433.1			uracil-DNA glycosylase											central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	9						CTCGCGGCCCGCAACGTGCCC	0.617								Base excision repair (BER), DNA glycosylases	Immune Deficiency with Hyper-IgM																												p.R88H		Atlas-SNP	.											.	UNG	30	.	0			c.G263A						PASS	.						39	46	44					12																	109536367		2202	4287	6489	SO:0001583	missense	7374	exon2	Familial Cancer Database	Hypogammaglobulinemia with Hyper-IgM, HIGM type I-V, XLHIGM	CGGCCCGCAACGT	A64377	CCDS9124.1, CCDS9125.1	12q23-q24.1	2014-09-17			ENSG00000076248	ENSG00000076248	3.2.2.27		12572	protein-coding gene	gene with protein product	"uracil-DNA glycosylase 1, uracil-DNA glycosylase 2"	191525		DGU		1923798, 17101234	Standard	NM_080911		Approved	UDG, UNG1, UNG2, HIGM4	uc001tnz.2	P13051	OTTHUMG00000169247	ENST00000242576.2:c.263G>A	chr12.hg19:g.109536367G>A	ENSP00000242576:p.Arg88His	110.0	0.0	.		119.0	67.0	.	NM_080911		Missense_Mutation	SNP	ENST00000242576.2	hg19	CCDS9124.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.776487	0.90195	.	.	ENSG00000076248	ENST00000242576;ENST00000336865;ENST00000537518	T;T	0.77750	-0.11;-1.12	4.21	4.21	0.49690	.	0.201019	0.43919	D	0.000502	T	0.80576	0.4649	M	0.64404	1.975	0.49213	D	0.999761	D;D	0.61697	0.99;0.987	P;P	0.49999	0.628;0.467	D	0.84208	0.0454	10	0.87932	D	0	-18.7494	15.3137	0.74056	0.0:0.0:1.0:0.0	.	79;88	E5KTA6;P13051	.;UNG_HUMAN	H	88;79;45	ENSP00000242576:R88H;ENSP00000337398:R79H	ENSP00000242576:R88H	R	+	2	0	UNG	108020750	1.000000	0.71417	0.998000	0.56505	0.938000	0.57974	3.714000	0.54889	2.182000	0.69389	0.455000	0.32223	CGC	.	.	.	none		0.617	UNG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403067.1	NM_080911		A	109536367	G	A	109536367	3	1	247	1	0	0	0	0	1	0	0	0	17011	1087	38	1	374	1	UNG	12	109536367	Missense_Mutation	SNP	G	TCGA-SX-A7SM-01A-11D-A34Z-10	59511136	109536367	24315528	48	15294											
C12orf51	283450	hgsc.bcm.edu	37	chr12	112622150	112622150	+	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	cccaggctgccggtgctgcaCagggaaatgtccaggctttc	7	8	13	13	1	0	0	0	0	0	0	2	1	1	1	3	4	3	4	3	4	1	1			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr12:112622150C>G	ENST00000430131.2	-	60	10499	c.9354G>C	c.(9352-9354)ctG>ctC	p.L3118L	HECTD4_ENST00000550722.1_Silent_p.L3394L|HECTD4_ENST00000377560.5_Silent_p.L3368L			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3118					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)										cGGTGCTGCACAGGGAAATGT	0.672																																					p.L3406L		Atlas-SNP	.											.	.	.	.	0			c.G10218C						PASS	.						20	26	24					12																	112622150		1997	4171	6168	SO:0001819	synonymous_variant	283450	exon61			GCTGCACAGGGAA	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.9354G>C	chr12.hg19:g.112622150C>G		30.0	0.0	.		41.0	21.0	.	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	hg19																																																																																				.	.	.	none		0.672	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		G	112622150	C	G	112622150	2	3	247	1	0	0	0	0	0	0	0	1	1698	465	17	4		4	C12orf51	12	112622150	Silent	SNP	C	TCGA-SX-A7SM-01A-11D-A34Z-10	3085783	112622150	21229745	49	15295											
RILPL1	353116	hgsc.bcm.edu	37	chr12	124017929	124017929	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgctcgaactcgtggcccAcaagcgacgcgatgtcgtac	8	6	11	16	7	0	0	0	0	0	0	3	3	0	0	2	1	3	2	2	1	3	1			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr12:124017929A>G	ENST00000376874.4	-	1	336	c.101T>C	c.(100-102)gTg>gCg	p.V34A		NM_178314.3	NP_847884.2	Q5EBL4	RIPL1_HUMAN	Rab interacting lysosomal protein-like 1	34					epithelial cell morphogenesis (GO:0003382)|intracellular protein transport (GO:0006886)|regulation of neuron death (GO:1901214)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)				endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.00067)|all cancers(50;0.00836)|BRCA - Breast invasive adenocarcinoma(302;0.197)		CTCGTGGCCCACAAGCGACGC	0.677																																					p.V34A		Atlas-SNP	.											.	RILPL1	23	.	0			c.T101C						PASS	.						8	11	10					12																	124017929		2117	4182	6299	SO:0001583	missense	353116	exon1			TGGCCCACAAGCG	AK097550	CCDS45006.1	12q24.31	2007-11-27			ENSG00000188026	ENSG00000188026			26814	protein-coding gene	gene with protein product		614092				14668488	Standard	NM_178314		Approved	FLJ39378	uc001ufe.2	Q5EBL4	OTTHUMG00000168686	ENST00000376874.4:c.101T>C	chr12.hg19:g.124017929A>G	ENSP00000366070:p.Val34Ala	52.0	0.0	.		50.0	29.0	.	NM_178314	Q66K36|Q8N1M0	Missense_Mutation	SNP	ENST00000376874.4	hg19	CCDS45006.1	.	.	.	.	.	.	.	.	.	.	A	33	5.253266	0.95336	.	.	ENSG00000188026	ENST00000376874	T	0.53423	0.62	4.59	4.59	0.56863	JNK/Rab-associated protein-1, N-terminal (1);	0.000000	0.64402	D	0.000007	T	0.52677	0.1749	L	0.53249	1.67	0.80722	D	1	P;D	0.53619	0.792;0.961	B;P	0.50082	0.415;0.63	T	0.58929	-0.7549	10	0.87932	D	0	18.0805	13.6685	0.62409	1.0:0.0:0.0:0.0	.	10;34	Q5EBL4-2;Q5EBL4	.;RIPL1_HUMAN	A	34	ENSP00000366070:V34A	ENSP00000366070:V34A	V	-	2	0	RILPL1	122583882	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.114000	0.77103	1.726000	0.51525	0.486000	0.48141	GTG	.	.	.	none		0.677	RILPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400595.1	NM_178314		G	124017929	A	G	124017929	3	3	247	1	0	0	0	0	1	0	0	0	13374	159	6	3	1138	3	RILPL1	12	124017929	Missense_Mutation	SNP	A	TCGA-SX-A7SM-01A-11D-A34Z-10	11395779	124017929	9833966	50	15296											
COG3	83548	hgsc.bcm.edu	37	chr13	46054390	46054390	+	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	tgtccaataagacaggaaccCtacatgaagcctgtgaacag	15	7	9	10	0	0	3	0	2	0	1	1	4	1	4	3	1	4	0	3	1	6	2			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr13:46054390C>G	ENST00000349995.5	+	4	626	c.514C>G	c.(514-516)Cta>Gta	p.L172V		NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	172					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)		GACAGGAACCCTACATGAAGC	0.363																																					p.L172V	Ovarian(150;1048 1859 18083 21577 42700)	Atlas-SNP	.											.	COG3	52	.	0			c.C514G						PASS	.						101	101	101					13																	46054390		2203	4300	6503	SO:0001583	missense	83548	exon4			GGAACCCTACATG	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.514C>G	chr13.hg19:g.46054390C>G	ENSP00000258654:p.Leu172Val	100.0	0.0	.		123.0	37.0	.	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Missense_Mutation	SNP	ENST00000349995.5	hg19	CCDS9398.1	.	.	.	.	.	.	.	.	.	.	C	17.83	3.485022	0.63962	.	.	ENSG00000136152	ENST00000349995	T	0.59638	0.25	5.98	3.26	0.37387	.	0.000000	0.64402	D	0.000001	T	0.75982	0.3924	M	0.87097	2.86	0.58432	D	0.999999	D;D;D	0.89917	0.999;1.0;0.996	D;D;P	0.87578	0.997;0.998;0.865	T	0.77448	-0.2584	10	0.66056	D	0.02	-7.9329	9.7147	0.40268	0.0:0.7711:0.0:0.2289	.	9;172;172	B4E2F3;Q96JB2;Q96JB2-2	.;COG3_HUMAN;.	V	172	ENSP00000258654:L172V	ENSP00000258654:L172V	L	+	1	2	COG3	44952391	0.999000	0.42202	1.000000	0.80357	0.995000	0.86356	2.857000	0.48349	0.822000	0.34565	-0.229000	0.12294	CTA	.	.	.	none		0.363	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2			G	46054390	C	G	46054390	3	3	247	1	0	0	0	0	1	0	0	0	3661	680	24	4	528	4	COG3	13	46054390	Missense_Mutation	SNP	C	TCGA-SX-A7SM-01A-11D-A34Z-10		46054390	69115488	51	15297											
NALCN	259232	hgsc.bcm.edu	37	chr13	101760142	101760142	+	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	atctcactgtattggaatgcTagaaataaattaacaggggg	15	11	10	5	0	1	1	1	0	1	1	2	2	1	2	0	3	2	2	0	3	7	5			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr13:101760142T>C	ENST00000251127.6	-	21	2446		c.e21-2			NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective						calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					ATTGGAATGCTAGAAATAAAT	0.318																																					.		Atlas-SNP	.											.	NALCN	431	.	0			c.2365-2A>G						PASS	.						107	97	100					13																	101760142		2202	4300	6502	SO:0001630	splice_region_variant	259232	exon22			GAATGCTAGAAAT	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"Ion channels / Sodium leak channels, non-selective"	19082	protein-coding gene	gene with protein product		611549	"voltage gated channel like 1"	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.2365-2A>G	chr13.hg19:g.101760142T>C		222.0	0.0	.		217.0	94.0	.	NM_052867	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Splice_Site	SNP	ENST00000251127.6	hg19	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	T	17.72	3.459576	0.63401	.	.	ENSG00000102452	ENST00000251127	.	.	.	5.55	5.55	0.83447	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6931	0.77469	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	NALCN	100558143	1.000000	0.71417	0.945000	0.38365	0.630000	0.37929	5.847000	0.69451	2.097000	0.63578	0.528000	0.53228	.	.	.	.	none		0.318	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867	Intron	C	101760142	T	C	101760142	5	2	247	1	0	0	0	0	0	0	1	0	10155	1536	53	3	2949	3	NALCN	13	101760142	Splice_Site	SNP	T	TCGA-SX-A7SM-01A-11D-A34Z-10	55705752	101760142	13409736	52	15298											
NIN	51199	hgsc.bcm.edu	37	chr14	51273464	51273464	+	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	agtgaccttacctggttcttGaaagtgttcttcatttgaca	9	16	8	8	0	3	3	1	3	2	0	3	3	3	3	2	1	1	2	2	1	2	6			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr14:51273464G>C	ENST00000382041.3	-	4	446	c.256C>G	c.(256-258)Caa>Gaa	p.Q86E	NIN_ENST00000324330.9_Missense_Mutation_p.Q86E|NIN_ENST00000389868.3_Missense_Mutation_p.Q86E|NIN_ENST00000382043.4_Missense_Mutation_p.Q86E|NIN_ENST00000453196.1_Missense_Mutation_p.Q86E|NIN_ENST00000245441.5_Missense_Mutation_p.Q86E|NIN_ENST00000530997.2_Missense_Mutation_p.Q86E	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	86					centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					CCTGGTTCTTGAAAGTGTTCT	0.363			T	PDGFRB	MPD																																p.Q86E		Atlas-SNP	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN	475	.	0			c.C256G						PASS	.						114	111	112					14																	51273464		2203	4300	6503	SO:0001583	missense	51199	exon4			GTTCTTGAAAGTG	AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"EF-hand domain containing"	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.256C>G	chr14.hg19:g.51273464G>C	ENSP00000371472:p.Gln86Glu	63.0	0.0	.		39.0	14.0	.	NM_020921	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Missense_Mutation	SNP	ENST00000382041.3	hg19	CCDS32079.1	.	.	.	.	.	.	.	.	.	.	G	2.935	-0.220218	0.06061	.	.	ENSG00000100503	ENST00000245441;ENST00000311149;ENST00000389868;ENST00000382043;ENST00000324292;ENST00000382041;ENST00000324330;ENST00000453196;ENST00000453401;ENST00000496749	T;T;T;T;T;T;T;T	0.23147	1.92;1.92;1.92;1.92;1.92;1.92;1.92;1.92	5.51	1.21	0.21127	.	0.499688	0.21964	N	0.066546	T	0.12263	0.0298	N	0.11023	0.085	0.25242	N	0.989742	B;B;B;B;B	0.13145	0.007;0.003;0.001;0.0;0.0	B;B;B;B;B	0.13407	0.009;0.006;0.002;0.002;0.002	T	0.28459	-1.0043	10	0.19590	T	0.45	-4.0393	11.4578	0.50191	0.0:0.3593:0.5227:0.118	.	92;86;86;86;86	Q8N4C6-5;C9J066;Q8N4C6;Q5BKU3;Q8N4C6-7	.;.;NIN_HUMAN;.;.	E	86;86;86;86;92;86;86;86;48;86	ENSP00000245441:Q86E;ENSP00000374518:Q86E;ENSP00000371474:Q86E;ENSP00000371472:Q86E;ENSP00000324210:Q86E;ENSP00000412391:Q86E;ENSP00000398641:Q48E;ENSP00000431826:Q86E	ENSP00000245441:Q86E	Q	-	1	0	NIN	50343214	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	0.799000	0.27028	0.642000	0.30620	0.491000	0.48974	CAA	.	.	.	none		0.363	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946		C	51273464	G	C	51273464	3	2	247	1	0	0	0	0	1	0	0	0	10424	1299	45	4	6405	4	NIN	14	51273464	Missense_Mutation	SNP	G	TCGA-SX-A7SM-01A-11D-A34Z-10		51273464	56076076	53	15299											
HIF1A	3091	hgsc.bcm.edu	37	chr14	62207303	62207303	+	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	ttggaattggtagaaaaactTtttgctgaagacacagaagc	15	11	10	5	0	0	4	0	1	0	3	0	5	0	5	0	2	3	2	0	2	6	5			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr14:62207303T>G	ENST00000337138.4	+	11	1882	c.1617T>G	c.(1615-1617)ctT>ctG	p.L539L	HIF1A_ENST00000323441.6_Silent_p.L539L|HIF1A-AS2_ENST00000554254.1_lincRNA|RP11-618G20.1_ENST00000555937.1_RNA|HIF1A_ENST00000394997.1_Silent_p.L540L|HIF1A_ENST00000557538.1_Silent_p.L480L|HIF1A_ENST00000539097.1_Silent_p.L563L	NM_001530.3	NP_001521.1	Q16665	HIF1A_HUMAN	hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)	539	NTAD.|ODD.				angiogenesis (GO:0001525)|axon transport of mitochondrion (GO:0019896)|B-1 B cell homeostasis (GO:0001922)|cardiac ventricle morphogenesis (GO:0003208)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cerebral cortex development (GO:0021987)|collagen metabolic process (GO:0032963)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|digestive tract morphogenesis (GO:0048546)|dopaminergic neuron differentiation (GO:0071542)|elastin metabolic process (GO:0051541)|embryonic hemopoiesis (GO:0035162)|embryonic placenta development (GO:0001892)|epithelial cell differentiation involved in mammary gland alveolus development (GO:0061030)|epithelial to mesenchymal transition (GO:0001837)|glucose homeostasis (GO:0042593)|heart looping (GO:0001947)|hemoglobin biosynthetic process (GO:0042541)|intestinal epithelial cell maturation (GO:0060574)|lactate metabolic process (GO:0006089)|lactation (GO:0007595)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of bone mineralization (GO:0030502)|negative regulation of growth (GO:0045926)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of thymocyte apoptotic process (GO:0070244)|negative regulation of TOR signaling (GO:0032007)|neural crest cell migration (GO:0001755)|neural fold elevation formation (GO:0021502)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|oxygen homeostasis (GO:0032364)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine production (GO:0032722)|positive regulation of chemokine-mediated signaling pathway (GO:0070101)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to muscle activity (GO:0014850)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|vascular endothelial growth factor production (GO:0010573)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|Hsp90 protein binding (GO:0051879)|nuclear hormone receptor binding (GO:0035257)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|endometrium(8)|kidney(6)|large_intestine(3)|lung(4)	23				OV - Ovarian serous cystadenocarcinoma(108;1.62e-09)|BRCA - Breast invasive adenocarcinoma(234;0.189)	Carvedilol(DB01136)	TAGAAAAACTTTTTGCTGAAG	0.289																																					p.L563L		Atlas-SNP	.											.	HIF1A	120	.	0			c.T1689G						PASS	.						95	95	95					14																	62207303		2203	4300	6503	SO:0001819	synonymous_variant	3091	exon11			AAAACTTTTTGCT	U22431	CCDS9753.1, CCDS9754.1, CCDS58324.1	14q23.2	2013-05-21	2008-12-02		ENSG00000100644	ENSG00000100644		"Basic helix-loop-helix proteins"	4910	protein-coding gene	gene with protein product		603348				8786149, 9079689	Standard	NM_001530		Approved	MOP1, HIF-1alpha, PASD8, HIF1, bHLHe78	uc001xfq.2	Q16665	OTTHUMG00000140344	ENST00000337138.4:c.1617T>G	chr14.hg19:g.62207303T>G		84.0	0.0	.		101.0	36.0	.	NM_001243084	C0LZJ3|Q53XP6|Q96PT9|Q9UPB1	Silent	SNP	ENST00000337138.4	hg19	CCDS9753.1																																																																																			.	.	.	none		0.289	HIF1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276977.2	NM_001530		G	62207303	T	G	62207303	2	3	247	1	0	0	0	0	0	0	0	1	7110	1828	64	5		5	HIF1A	14	62207303	Silent	SNP	T	TCGA-SX-A7SM-01A-11D-A34Z-10	10933839	62207303	45142237	54	15300											
C15orf57	90416	hgsc.bcm.edu	37	chr15	40846226	40846226	+	Missense_Mutation	SNP	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	tggctcgtcctcggccactgGcttctcaacctgtgactctg	4	12	10	15	2	2	1	1	1	2	0	6	1	3	1	3	3	1	2	3	3	1	1			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr15:40846226G>A	ENST00000358005.3	-	4	775	c.502C>T	c.(502-504)Cca>Tca	p.P168S	C15orf57_ENST00000558750.1_Missense_Mutation_p.P177S|RP11-111A22.1_ENST00000561460.1_RNA|C15orf57_ENST00000559911.1_Intron|C15orf57_ENST00000560305.1_Intron|RP11-111A22.1_ENST00000561039.1_RNA|C15orf57_ENST00000561011.1_Intron|C15orf57_ENST00000558113.1_Intron|C15orf57_ENST00000416810.2_Missense_Mutation_p.P168S	NM_001080791.1|NM_052849.2	NP_001074260.1|NP_443081.1	Q9BV29	CO057_HUMAN	chromosome 15 open reading frame 57	168										endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	9						TCGGCCACTGGCTTCTCAACC	0.537																																					p.P177S		Atlas-SNP	.											.	C15orf57	20	.	0			c.C529T						PASS	.						65	57	60					15																	40846226		2203	4300	6503	SO:0001583	missense	90416	exon4			CCACTGGCTTCTC	BC012189	CCDS10060.1, CCDS42022.1, CCDS73706.1	15q15.1	2008-05-30	2008-05-30	2008-05-30	ENSG00000128891	ENSG00000128891			28295	protein-coding gene	gene with protein product			"coiled-coil domain containing 32"	CCDC32		12477932	Standard	NM_001080791		Approved	MGC20481	uc001zma.1	Q9BV29	OTTHUMG00000129993	ENST00000358005.3:c.502C>T	chr15.hg19:g.40846226G>A	ENSP00000350695:p.Pro168Ser	84.0	0.0	.		94.0	41.0	.	NM_001080791	A8KAL4|Q86TC4|Q8N788|Q8NAR7	Missense_Mutation	SNP	ENST00000358005.3	hg19	CCDS10060.1	.	.	.	.	.	.	.	.	.	.	G	12.20	1.867941	0.32977	.	.	ENSG00000128891	ENST00000358005;ENST00000416810	T	0.42900	0.96	5.35	4.44	0.53790	.	0.298703	0.31821	N	0.007006	T	0.29093	0.0723	L	0.40543	1.245	0.29718	N	0.838855	B;B	0.29988	0.112;0.264	B;B	0.24701	0.032;0.055	T	0.17440	-1.0369	10	0.13108	T	0.6	-15.494	9.8807	0.41231	0.0728:0.1386:0.7886:0.0	.	168;177	Q9BV29;Q9BV29-2	CO057_HUMAN;.	S	168;177	ENSP00000350695:P168S	ENSP00000350695:P168S	P	-	1	0	C15orf57	38633518	1.000000	0.71417	0.996000	0.52242	0.669000	0.39330	1.577000	0.36515	1.487000	0.48415	0.655000	0.94253	CCA	.	.	.	none		0.537	C15orf57-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252259.2	NM_052849		A	40846226	G	A	40846226	3	1	247	1	0	0	0	0	1	0	0	0	1807	1203	42	2	59	2	C15orf57	15	40846226	Missense_Mutation	SNP	G	TCGA-SX-A7SM-01A-11D-A34Z-10		40846226	61685166	55	15301											
TLN2	83660	hgsc.bcm.edu	37	chr15	63073341	63073341	+	Frame_Shift_Del	DEL	G	G	-																															ttttcctctcctctgtagctGgatgaaggcactcctccaga																										TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr15:63073341delG	ENST00000561311.1	+	43	5747	c.5517delG	c.(5515-5517)ctgfs	p.L1839fs	TLN2_ENST00000472902.1_Frame_Shift_Del_p.L232fs|TLN2_ENST00000306829.6_Frame_Shift_Del_p.L1839fs			Q9Y4G6	TLN2_HUMAN	talin 2	1839					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						CTCTGTAGCTGGATGAAGGCA	0.453																																					p.L1839fs		Atlas-Indel,Pindel	.											.	TLN2	253	.	0			c.5516delT						PASS	.						60	59	59					15																	63073341		2203	4300	6503	SO:0001589	frameshift_variant	83660	exon41			.	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.5517delG	chr15.hg19:g.63073341delG	ENSP00000453508:p.Leu1839fs	54.0	0.0	0		36.0	14.0	0.388889	NM_015059	A6NLB8	Frame_Shift_Del	DEL	ENST00000561311.1	hg19	CCDS32261.1																																																																																			.	.	.	none		0.453	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			-	63073341	G	-	63073341	7	5	247	1	0	1	0	1	0	0	0	0	15960	1335	47	0	5679	0	TLN2	15	63073341	Frame_Shift_Del	DEL	G	TCGA-SX-A7SM-01A-11D-A34Z-10	22227115	63073341	39458051	56	15302											
TRIP4	9325	hgsc.bcm.edu	37	chr15	64710865	64710867	+	In_Frame_Del	DEL	TGG	TGG	-																															gaatttcaggaaggctttgaTggtggctggtgcctctctgt																										TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	TGG	TGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr15:64710865_64710867delTGG	ENST00000261884.3	+	9	1356_1358	c.1296_1298delTGG	c.(1294-1299)gatggt>gat	p.G434del	RN7SL707P_ENST00000582206.1_RNA	NM_016213.4	NP_057297.2	Q15650	TRIP4_HUMAN	thyroid hormone receptor interactor 4	434					positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21						AAGGCTTTGATGGTGGCTGGTGC	0.453																																					p.432_433del		Atlas-Indel,Pindel	.											.	TRIP4	43	.	0			c.1295_1297del						PASS	.																																			SO:0001651	inframe_deletion	9325	exon9			.	L40371	CCDS10194.1	15q22.1	2014-02-17			ENSG00000103671	ENSG00000103671		"-"	12310	protein-coding gene	gene with protein product	"zinc finger, C2HC5-type"	604501				7776974	Standard	NM_016213		Approved	HsT17391, ZC2HC5	uc002anm.3	Q15650	OTTHUMG00000133033	ENST00000261884.3:c.1296_1298delTGG	chr15.hg19:g.64710868_64710870delTGG	ENSP00000261884:p.Gly434del	99.0	0.0	0		104.0	34.0	0.326923	NM_016213	B2RAS0|Q96ED7|Q9UKH0	In_Frame_Del	DEL	ENST00000261884.3	hg19	CCDS10194.1																																																																																			.	.	.	none		0.453	TRIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256635.2	NM_016213		-	64710867	TGG	-	64710865	7	5	247	1	0	1	0	1	0	0	0	0	16570	1461	51	0	1330	0	TRIP4	15	64710865	In_Frame_Del	DEL	TGG	TCGA-SX-A7SM-01A-11D-A34Z-10	1637524	64710865	37820527	57	15303											
RPL4	6124	hgsc.bcm.edu	37	chr15	66791910	66791910	+	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	ttacctaccacaggcttcttGcctgcaaccgccgccttctc	6	11	6	18	2	2	0	0	0	2	0	3	0	2	0	6	1	5	2	6	1	3	5			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr15:66791910G>T	ENST00000307961.6	-	10	1211	c.1119C>A	c.(1117-1119)ggC>ggA	p.G373G	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|MIR4512_ENST00000583257.1_RNA|RPL4_ENST00000568588.1_Silent_p.G279G|SNAPC5_ENST00000566658.1_5'Flank	NM_000968.3	NP_000959.2	P36578	RL4_HUMAN	ribosomal protein L4	373	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						CAGGCTTCTTGCCTGCAACCG	0.517																																					p.G373G		Atlas-SNP	.											.	RPL4	29	.	0			c.C1119A						PASS	.						36	39	38					15																	66791910		2198	4294	6492	SO:0001819	synonymous_variant	6124	exon10			CTTCTTGCCTGCA	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.1119C>A	chr15.hg19:g.66791910G>T		107.0	0.0	.		105.0	40.0	.	NM_000968	A8K502|P39029|Q4VBR0|Q969Z9	Silent	SNP	ENST00000307961.6	hg19	CCDS10218.1																																																																																			.	.	.	none		0.517	RPL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256903.2	NM_000968		T	66791910	G	T	66791910	2	4	247	1	0	0	0	0	0	0	0	1	13608	1306	46	4		4	RPL4	15	66791910	Silent	SNP	G	TCGA-SX-A7SM-01A-11D-A34Z-10	2081045	66791910	35739482	58	15304											
DNAJA4	55466	hgsc.bcm.edu	37	chr15	78566592	78566592	+	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	gcccgctgtgcaaggggcggGggatgcagatccacatccag	8	5	16	12	2	0	1	0	0	0	1	2	2	2	2	3	4	2	3	3	4	1	0			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr15:78566592G>T	ENST00000394852.3	+	4	662	c.472G>T	c.(472-474)Ggg>Tgg	p.G158W	DNAJA4_ENST00000446172.2_Missense_Mutation_p.G131W|DNAJA4_ENST00000343789.3_Missense_Mutation_p.G158W|DNAJA4_ENST00000394855.3_Missense_Mutation_p.G187W	NM_001130182.1	NP_001123654.1	Q8WW22	DNJA4_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 4	158					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						CAAGGGGCGGGGGATGCAGAT	0.622																																					p.G187W		Atlas-SNP	.											.	DNAJA4	63	.	0			c.G559T						PASS	.						65	52	57					15																	78566592		2196	4293	6489	SO:0001583	missense	55466	exon5			GGGCGGGGGATGC	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.472G>T	chr15.hg19:g.78566592G>T	ENSP00000378321:p.Gly158Trp	50.0	0.0	.		53.0	20.0	.	NM_018602	E9PDM9|Q6AW87|Q8N5Z4|Q8N7P2	Missense_Mutation	SNP	ENST00000394852.3	hg19	CCDS45316.1	.	.	.	.	.	.	.	.	.	.	G	33	5.220515	0.95139	.	.	ENSG00000140403	ENST00000394855;ENST00000343789;ENST00000394852;ENST00000446172	T;T;T;D	0.85339	-1.47;-1.39;-1.39;-1.97	5.91	5.91	0.95273	HSP40/DnaJ peptide-binding (1);Heat shock protein DnaJ, cysteine-rich domain (4);	0.000000	0.85682	D	0.000000	D	0.96892	0.8985	H	0.99942	5.005	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	0.98616	1.0665	10	0.87932	D	0	-14.2943	19.2867	0.94077	0.0:0.0:1.0:0.0	.	73;131;158;187	Q9P1H1;E9PDM9;Q8WW22;Q8WW22-2	.;.;DNJA4_HUMAN;.	W	187;158;158;131	ENSP00000378324:G187W;ENSP00000339581:G158W;ENSP00000378321:G158W;ENSP00000413499:G131W	ENSP00000339581:G158W	G	+	1	0	DNAJA4	76353647	1.000000	0.71417	0.832000	0.32986	0.990000	0.78478	9.658000	0.98594	2.793000	0.96121	0.655000	0.94253	GGG	.	.	.	none		0.622	DNAJA4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289801.1	NM_018602		T	78566592	G	T	78566592	3	4	247	1	0	0	0	0	1	0	0	0	4616	1232	43	4	632	4	DNAJA4	15	78566592	Missense_Mutation	SNP	G	TCGA-SX-A7SM-01A-11D-A34Z-10	11774682	78566592	23964800	59	15305											
EME2	197342	hgsc.bcm.edu	37	chr16	1823269	1823269	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagggcgggggtctcttgccAgggccggggccggggacggg	3	4	24	10	4	1	0	0	0	1	0	2	2	1	1	3	9	1	0	3	9	0	1	rs372940829	byFrequency	TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr16:1823269A>G	ENST00000568449.1	+	1	62	c.41A>G	c.(40-42)cAg>cGg	p.Q14R	MRPS34_ENST00000177742.3_5'Flank|NME3_ENST00000219302.3_5'Flank|MRPS34_ENST00000397375.2_5'Flank|NME3_ENST00000563498.1_5'Flank|EME2_ENST00000307394.7_Missense_Mutation_p.Q14R	NM_001257370.1	NP_001244299.1	A4GXA9	EME2_HUMAN	essential meiotic structure-specific endonuclease subunit 2	14					DNA recombination (GO:0006310)|DNA repair (GO:0006281)	nucleus (GO:0005634)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)			central_nervous_system(1)|kidney(2)|lung(5)|pancreas(1)	9						GTCTCTTGCCAGGGCCGGGGC	0.736								Direct reversal of damage;Homologous recombination					a|||	4	0.000798722	0.003	0	5008	,	,		10624	0		0	False		,,,				2504	0				p.Q14R		Atlas-SNP	.											.	EME2	40	.	0			c.A41G						PASS	.	A	ARG/GLN	2,3076		0,2,1537	3	5	4		41	-0.3	0	16		4	0,6824		0,0,3412	no	missense	EME2	NM_001010865.1	43	0,2,4949	GG,GA,AA		0.0,0.065,0.0202	benign	14/445	1823269	2,9900	1539	3412	4951	SO:0001583	missense	197342	exon1			CTTGCCAGGGCCG	AK074080	CCDS58404.1	16p13.3	2013-07-03	2013-07-03			ENSG00000197774			27289	protein-coding gene	gene with protein product	"SLX2 structure-specific endonuclease subunit homolog B (S. cerevisiae)"	610886	"essential meiotic endonuclease 1 homolog 2 (S. pombe)"			12721304	Standard	NM_001257370		Approved	FLJ00151, SLX2B	uc010brw.1	A4GXA9		ENST00000568449.1:c.41A>G	chr16.hg19:g.1823269A>G	ENSP00000457353:p.Gln14Arg	5.0	0.0	.		13.0	6.0	.	NM_001257370	Q8TEP2|Q96RY3	Missense_Mutation	SNP	ENST00000568449.1	hg19	CCDS58404.1	.	.	.	.	.	.	.	.	.	.	a	1.144	-0.648714	0.03506	6.5E-4	0.0	ENSG00000197774	ENST00000307394;ENST00000454910	.	.	.	3.03	-0.341	0.12639	.	0.834282	0.09836	N	0.749571	T	0.15998	0.0385	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32903	-0.9889	8	0.06891	T	0.86	1.3716	8.4242	0.32718	0.1085:0.0:0.7482:0.1433	.	14	A4GXA9	EME2_HUMAN	R	14	.	ENSP00000303779:Q14R	Q	+	2	0	EME2	1763270	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.801000	0.04550	-0.678000	0.05224	-2.469000	0.00203	CAG	.	.	.	weak		0.736	EME2-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433185.2	NM_001010865		G	1823269	A	G	1823269	3	3	247	1	0	0	0	0	1	0	0	0	5091	188	7	3	43	3	EME2	16	1823269	Missense_Mutation	SNP	A	TCGA-SX-A7SM-01A-11D-A34Z-10		1823269	88531484	60	15306											
MYLK3	91807	hgsc.bcm.edu	37	chr16	46771758	46771758	+	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	cagggtcaggcctgctggacGatgctccttgtcctgcacct	5	10	12	14	1	1	0	1	0	0	0	3	2	3	1	4	3	3	3	4	3	0	1	rs374905189		TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr16:46771758G>A	ENST00000394809.4	-	3	981	c.866C>T	c.(865-867)tCg>tTg	p.S289L	MYLK3_ENST00000536476.1_Intron	NM_182493.2	NP_872299.2	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3	289					cardiac myofibril assembly (GO:0055003)|cellular response to interleukin-1 (GO:0071347)|positive regulation of sarcomere organization (GO:0060298)|protein phosphorylation (GO:0006468)|regulation of vascular permeability involved in acute inflammatory response (GO:0002528)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(5)|stomach(3)	37		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				CCTGCTGGACGATGCTCCTTG	0.667																																					p.S289L		Atlas-SNP	.											.	MYLK3	82	.	0			c.C866T						PASS	.	G	LEU/SER	0,4406		0,0,2203	81	80	80		866	-0.4	0	16		80	1,8599	1.2+/-3.3	0,1,4299	no	missense	MYLK3	NM_182493.2	145	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	289/820	46771758	1,13005	2203	4300	6503	SO:0001583	missense	91807	exon3			CTGGACGATGCTC	AJ247087	CCDS10723.2	16q11.2	2008-10-23			ENSG00000140795	ENSG00000140795			29826	protein-coding gene	gene with protein product	"MLC kinase"	612147				17885681	Standard	NM_182493		Approved	caMLCK, MLCK	uc002eei.4	Q32MK0	OTTHUMG00000132543	ENST00000394809.4:c.866C>T	chr16.hg19:g.46771758G>A	ENSP00000378288:p.Ser289Leu	48.0	0.0	.		34.0	8.0	.	NM_182493	B5BUL9|B7Z5U8|Q32MK1|Q96DV1	Missense_Mutation	SNP	ENST00000394809.4	hg19	CCDS10723.2	.	.	.	.	.	.	.	.	.	.	G	12.29	1.893498	0.33442	0.0	1.16E-4	ENSG00000140795	ENST00000394809	T	0.69435	-0.4	4.94	-0.448	0.12230	.	0.616301	0.12413	N	0.471152	T	0.45094	0.1325	N	0.19112	0.55	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	T	0.22591	-1.0212	10	0.24483	T	0.36	.	7.4858	0.27432	0.6492:0.0:0.3508:0.0	.	289	Q32MK0	MYLK3_HUMAN	L	289	ENSP00000378288:S289L	ENSP00000378288:S289L	S	-	2	0	MYLK3	45329259	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.096000	0.15147	-0.029000	0.13827	0.655000	0.94253	TCG	.	.	.	weak		0.667	MYLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255743.2	NM_182493		A	46771758	G	A	46771758	3	1	247	1	0	0	0	0	1	0	0	0	10065	1059	37	1	1637	1	MYLK3	16	46771758	Missense_Mutation	SNP	G	TCGA-SX-A7SM-01A-11D-A34Z-10	44948489	46771758	43582995	61	15307											
CNOT1	23019	hgsc.bcm.edu	37	chr16	58608632	58608633	+	Frame_Shift_Ins	INS	-	-	A																															tagaaggacaccgtctctttINSaaaaaagtcatacacgcctg																										TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr16:58608632_58608633insA	ENST00000317147.5	-	16	2191_2192	c.1859_1860insT	c.(1858-1860)ttafs	p.L620fs	CNOT1_ENST00000441024.2_Frame_Shift_Ins_p.L620fs|CNOT1_ENST00000569240.1_Frame_Shift_Ins_p.L620fs	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	620					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)		ACCGTCTCTTTAAAAAAGTCAT	0.396																																					p.L620fs		Atlas-INDEL	.											.	CNOT1	359	.	0			c.1860_1861insT						PASS	.																																			SO:0001589	frameshift_variant	23019	exon16			.	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.1860dupT	chr16.hg19:g.58608638_58608638dupA	ENSP00000320949:p.Leu620fs	55.0	0.0	0		44.0	12.0	0.272727	NM_001265612	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Frame_Shift_Ins	INS	ENST00000317147.5	hg19	CCDS10799.1																																																																																			.	.	.	none		0.396	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		A	58608633	-	A	58608632	7	5	247	1	0	1	1	0	0	0	0	0	3619	1751	61	0	5628	0	CNOT1	16	58608632	Frame_Shift_Ins	INS	-	TCGA-SX-A7SM-01A-11D-A34Z-10	11836874	58608632	31746121	62	15308											
KCTD19	146212	hgsc.bcm.edu	37	chr16	67337132	67337132	+	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	ggttgtcttcagtcactaggCtgggatatttggccaccagg	7	12	13	9	0	3	0	2	0	1	0	3	1	3	1	2	5	0	2	2	5	2	5			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr16:67337132C>A	ENST00000304372.5	-	4	615	c.560G>T	c.(559-561)aGc>aTc	p.S187I	KCTD19_ENST00000562860.1_5'UTR	NM_001100915.1	NP_001094385.1	Q17RG1	KCD19_HUMAN	potassium channel tetramerization domain containing 19	187					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)		AGTCACTAGGCTGGGATATTT	0.577																																					p.S187I		Atlas-SNP	.											.	KCTD19	82	.	0			c.G560T						PASS	.						79	83	81					16																	67337132		2093	4215	6308	SO:0001583	missense	146212	exon4			ACTAGGCTGGGAT	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.560G>T	chr16.hg19:g.67337132C>A	ENSP00000305702:p.Ser187Ile	80.0	0.0	.		51.0	21.0	.	NM_001100915	B4DZ49|Q8N804	Missense_Mutation	SNP	ENST00000304372.5	hg19	CCDS42179.1	.	.	.	.	.	.	.	.	.	.	C	14.66	2.601465	0.46423	.	.	ENSG00000168676	ENST00000304372	T	0.60424	0.19	5.82	3.83	0.44106	.	0.366488	0.29980	N	0.010709	T	0.33933	0.0880	N	0.14661	0.345	0.28909	N	0.892832	B	0.17038	0.02	B	0.14023	0.01	T	0.11916	-1.0568	10	0.40728	T	0.16	-11.966	3.7416	0.08532	0.1448:0.5549:0.2088:0.0915	.	187	Q17RG1	KCD19_HUMAN	I	187	ENSP00000305702:S187I	ENSP00000305702:S187I	S	-	2	0	KCTD19	65894633	0.995000	0.38212	1.000000	0.80357	0.984000	0.73092	1.566000	0.36396	1.479000	0.48272	0.655000	0.94253	AGC	.	.	.	none		0.577	KCTD19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422061.1	XM_085367		A	67337132	C	A	67337132	3	1	247	1	0	0	0	0	1	0	0	0	8113	797	28	4	2272	4	KCTD19	16	67337132	Missense_Mutation	SNP	C	TCGA-SX-A7SM-01A-11D-A34Z-10	8728500	67337132	23017621	63	15309											
ESRP2	80004	hgsc.bcm.edu	37	chr16	68265766	68265766	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atcgcttacccagcatgcccTtgtgcctgcgcagtgcagcc	6	9	10	16	2	0	0	0	0	0	0	1	0	0	0	4	0	7	4	4	0	1	2			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr16:68265766T>C	ENST00000565858.1	-	10	1354	c.1268A>G	c.(1267-1269)aAg>aGg	p.K423R	RP11-96D1.11_ENST00000571197.1_RNA|ESRP2_ENST00000473183.2_Missense_Mutation_p.K413R	NM_024939.2	NP_079215.2	Q9H6T0	ESRP2_HUMAN	epithelial splicing regulatory protein 2	423	RRM 2.				mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	16						CAGCATGCCCTTGTGCCTGCG	0.617																																					p.K413R		Atlas-SNP	.											.	ESRP2	118	.	0			c.A1238G						PASS	.						52	47	49					16																	68265766		2198	4300	6498	SO:0001583	missense	80004	exon10			ATGCCCTTGTGCC	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.1268A>G	chr16.hg19:g.68265766T>C	ENSP00000454554:p.Lys423Arg	85.0	0.0	.		63.0	26.0	.	NM_024939	Q8N6H8|Q8WZ15|Q9H6I4	Missense_Mutation	SNP	ENST00000565858.1	hg19		.	.	.	.	.	.	.	.	.	.	T	12.90	2.075230	0.36662	.	.	ENSG00000103067	ENST00000473183	T	0.29917	1.55	5.93	5.93	0.95920	RNA recognition motif domain (1);	0.000000	0.85682	D	0.000000	T	0.23210	0.0561	N	0.11845	0.185	0.58432	D	0.999998	B;B	0.27068	0.167;0.002	B;B	0.37508	0.252;0.046	T	0.11891	-1.0569	10	0.11794	T	0.64	-15.5772	16.3829	0.83481	0.0:0.0:0.0:1.0	.	423;413	Q9H6T0;Q9H6T0-2	ESRP2_HUMAN;.	R	413	ENSP00000418748:K413R	ENSP00000418748:K413R	K	-	2	0	ESRP2	66823267	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.243000	0.72384	2.271000	0.75665	0.459000	0.35465	AAG	.	.	.	none		0.617	ESRP2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000433083.1	NM_024939		C	68265766	T	C	68265766	3	2	247	1	0	0	0	0	1	0	0	0	5261	1609	56	3	939	3	ESRP2	16	68265766	Missense_Mutation	SNP	T	TCGA-SX-A7SM-01A-11D-A34Z-10	928634	68265766	22088987	64	15310											
FXR2	9513	hgsc.bcm.edu	37	chr17	7506290	7506290	+	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	ttggctcccagggctttcttGaactctttatggacgttttc	5	17	9	10	1	2	1	0	1	2	0	4	2	3	2	1	3	1	3	1	3	2	7			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr17:7506290G>T	ENST00000250113.7	-	6	814	c.480C>A	c.(478-480)ttC>ttA	p.F160L		NM_004860.3	NP_004851.2	P51116	FXR2_HUMAN	fragile X mental retardation, autosomal homolog 2	160						cytoplasm (GO:0005737)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.?(1)		NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)	26				READ - Rectum adenocarcinoma(115;0.17)		GGGCTTTCTTGAACTCTTTAT	0.463																																					p.F160L		Atlas-SNP	.											.	FXR2	44	.	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.C480A						PASS	.						88	83	85					17																	7506290		1857	4103	5960	SO:0001583	missense	9513	exon6			TTTCTTGAACTCT	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.480C>A	chr17.hg19:g.7506290G>T	ENSP00000250113:p.Phe160Leu	82.0	0.0	.		52.0	17.0	.	NM_004860	B2R9M2|D3DTQ1|Q86V09|Q8WUM2	Missense_Mutation	SNP	ENST00000250113.7	hg19	CCDS45604.1	.	.	.	.	.	.	.	.	.	.	G	17.57	3.423205	0.62733	.	.	ENSG00000129245	ENST00000250113	T	0.56941	0.43	6.03	3.02	0.34903	.	0.050013	0.85682	D	0.000000	T	0.45796	0.1360	L	0.49455	1.56	0.48395	D	0.999643	B;B	0.20550	0.046;0.046	B;B	0.24006	0.05;0.05	T	0.39354	-0.9618	10	0.62326	D	0.03	2.3364	9.635	0.39802	0.2243:0.0:0.7757:0.0	.	160;160	Q86V09;P51116	.;FXR2_HUMAN	L	160	ENSP00000250113:F160L	ENSP00000250113:F160L	F	-	3	2	FXR2	7447015	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.970000	0.29383	0.457000	0.26962	0.655000	0.94253	TTC	.	.	.	none		0.463	FXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441084.1			T	7506290	G	T	7506290	3	4	247	1	0	0	0	0	1	0	0	0	6123	1281	45	4	1489	4	FXR2	17	7506290	Missense_Mutation	SNP	G	TCGA-SX-A7SM-01A-11D-A34Z-10		7506290	73688920	65	15311											
TBCD	6904	hgsc.bcm.edu	37	chr17	80858535	80858535	+	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	tgtcttttccagtgtgtttaTtgccggctttcctgagtaca	5	18	9	9	1	1	1	0	1	1	0	3	1	3	1	3	1	2	3	3	1	2	7			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr17:80858535T>A	ENST00000355528.4	+	18	1788	c.1658T>A	c.(1657-1659)aTt>aAt	p.I553N	TBCD_ENST00000397466.2_Missense_Mutation_p.I167N|TBCD_ENST00000539345.2_Missense_Mutation_p.I553N	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	553					'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)			AGTGTGTTTATTGCCGGCTTT	0.478																																					p.I553N		Atlas-SNP	.											.	TBCD	94	.	0			c.T1658A						PASS	.						143	141	142					17																	80858535		2017	4169	6186	SO:0001583	missense	6904	exon18			TGTTTATTGCCGG	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.1658T>A	chr17.hg19:g.80858535T>A	ENSP00000347719:p.Ile553Asn	233.0	0.0	.		166.0	70.0	.	NM_005993	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Missense_Mutation	SNP	ENST00000355528.4	hg19	CCDS45818.1	.	.	.	.	.	.	.	.	.	.	T	14.04	2.417097	0.42918	.	.	ENSG00000141556	ENST00000355528;ENST00000334614;ENST00000397466;ENST00000536182	T;T	0.69561	-0.41;-0.41	5.23	5.23	0.72850	Armadillo-like helical (1);Armadillo-type fold (1);	0.067842	0.56097	D	0.000032	D	0.84786	0.5549	M	0.92219	3.285	0.50171	D	0.99985	D;D;D	0.89917	1.0;0.999;0.991	D;D;D	0.74348	0.976;0.983;0.92	D	0.88364	0.2990	9	.	.	.	.	13.0491	0.58944	0.0:0.0:0.0:1.0	.	553;553;553	Q9BTW9;Q9BTW9-4;F5H8C7	TBCD_HUMAN;.;.	N	553;304;167;553	ENSP00000347719:I553N;ENSP00000380608:I167N	.	I	+	2	0	TBCD	78451824	1.000000	0.71417	0.310000	0.25168	0.011000	0.07611	5.948000	0.70249	1.982000	0.57802	0.533000	0.62120	ATT	.	.	.	none		0.478	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993		A	80858535	T	A	80858535	3	1	247	1	0	0	0	0	1	0	0	0	15645	1493	52	5	1728	5	TBCD	17	80858535	Missense_Mutation	SNP	T	TCGA-SX-A7SM-01A-11D-A34Z-10	73352245	80858535	336675	66	15312											
MIER2	54531	hgsc.bcm.edu	37	chr19	327981	327981	+	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	agcagctcatcaaagggcatGtcgttgctctgagttgggga	9	10	14	8	1	3	1	2	1	1	0	4	2	3	2	0	3	3	6	0	3	1	2			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr19:327981G>T	ENST00000264819.4	-	4	262	c.252C>A	c.(250-252)gaC>gaA	p.D84E	MIER2_ENST00000592722.1_5'UTR	NM_017550.1	NP_060020.1	Q8N344	MIER2_HUMAN	mesoderm induction early response 1, family member 2	84					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)		CAAAGGGCATGTCGTTGCTCT	0.617																																					p.D84E		Atlas-SNP	.											.	MIER2	51	.	0			c.C252A						PASS	.						98	75	83					19																	327981		2203	4300	6503	SO:0001583	missense	54531	exon4			GGGCATGTCGTTG	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.252C>A	chr19.hg19:g.327981G>T	ENSP00000264819:p.Asp84Glu	57.0	0.0	.		40.0	9.0	.	NM_017550	Q9ULM7	Missense_Mutation	SNP	ENST00000264819.4	hg19	CCDS32855.1	.	.	.	.	.	.	.	.	.	.	.	12.28	1.891165	0.33348	.	.	ENSG00000105556	ENST00000264819	T	0.20881	2.04	5.01	5.01	0.66863	.	0.131175	0.34223	N	0.004142	T	0.14270	0.0345	N	0.26042	0.785	0.36198	D	0.85053	B	0.18166	0.026	B	0.12837	0.008	T	0.15350	-1.0440	10	0.22706	T	0.39	-26.9904	11.1838	0.48644	0.0:0.0:0.8034:0.1966	.	84	Q8N344	MIER2_HUMAN	E	84	ENSP00000264819:D84E	ENSP00000264819:D84E	D	-	3	2	MIER2	278981	1.000000	0.71417	1.000000	0.80357	0.748000	0.42578	2.566000	0.45948	2.328000	0.79073	0.563000	0.77884	GAC	.	.	.	none		0.617	MIER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451784.1	XM_041843		T	327981	G	T	327981	3	4	247	1	0	0	0	0	1	0	0	0	9588	1368	48	4	1429	4	MIER2	19	327981	Missense_Mutation	SNP	G	TCGA-SX-A7SM-01A-11D-A34Z-10		327981	58801002	67	15313											
ZNF442	79973	hgsc.bcm.edu	37	chr19	12460640	12460640	+	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	agttttttcatgtcctcgaaGgaaacgagaacgagtgaagg	13	10	12	6	3	1	2	1	1	0	1	3	6	2	3	1	2	2	1	1	2	4	3			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr19:12460640G>A	ENST00000242804.4	-	6	2341	c.1759C>T	c.(1759-1761)Ctt>Ttt	p.L587F	CTD-3105H18.13_ENST00000563695.2_lincRNA|ZNF442_ENST00000438182.1_Missense_Mutation_p.L518F	NM_030824.2	NP_110451.1	Q9H7R0	ZN442_HUMAN	zinc finger protein 442	587					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						TGTCCTCGAAGGAAACGAGAA	0.423																																					p.L587F		Atlas-SNP	.											.	ZNF442	102	.	0			c.C1759T						PASS	.						122	108	112					19																	12460640		2203	4300	6503	SO:0001583	missense	79973	exon6			CTCGAAGGAAACG	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.1759C>T	chr19.hg19:g.12460640G>A	ENSP00000242804:p.Leu587Phe	133.0	0.0	.		98.0	37.0	.	NM_030824	B4DJ48	Missense_Mutation	SNP	ENST00000242804.4	hg19	CCDS12271.1	.	.	.	.	.	.	.	.	.	.	G	9.506	1.104614	0.20632	.	.	ENSG00000198342	ENST00000242804;ENST00000438182	T;T	0.52057	0.68;0.68	0.792	-0.362	0.12560	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.33876	0.0878	L	0.48174	1.505	0.09310	N	1	B	0.31274	0.317	B	0.26969	0.075	T	0.18335	-1.0340	9	0.42905	T	0.14	.	5.0248	0.14379	0.2454:0.0:0.7546:0.0	.	587	Q9H7R0	ZN442_HUMAN	F	587;518	ENSP00000242804:L587F;ENSP00000388634:L518F	ENSP00000242804:L587F	L	-	1	0	ZNF442	12321640	0.004000	0.15560	0.001000	0.08648	0.030000	0.12068	-0.320000	0.08028	-0.075000	0.12798	0.306000	0.20318	CTT	.	.	.	none		0.423	ZNF442-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344109.1	NM_030824		A	12460640	G	A	12460640	3	1	247	1	0	0	0	0	1	0	0	0	17927	1000	35	2	128	2	ZNF442	19	12460640	Missense_Mutation	SNP	G	TCGA-SX-A7SM-01A-11D-A34Z-10	12132659	12460640	46668343	68	15314											
EPHX3	79852	hgsc.bcm.edu	37	chr19	15342598	15342598	+	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	cagacgtaccagttctcaggGaagccgtgcagaaacagcat	13	6	11	11	2	1	2	1	0	1	2	2	3	1	3	2	1	5	4	2	1	3	2			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr19:15342598G>A	ENST00000221730.3	-	2	538	c.318C>T	c.(316-318)ttC>ttT	p.F106F	EPHX3_ENST00000602233.1_Silent_p.F106F|EPHX3_ENST00000435261.1_Silent_p.F106F	NM_024794.2	NP_079070.1	Q9H6B9	EPHX3_HUMAN	epoxide hydrolase 3	106						extracellular region (GO:0005576)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)|skin(1)	7						AGTTCTCAGGGAAGCCGTGCA	0.657																																					p.F106F		Atlas-SNP	.											.	EPHX3	22	.	0			c.C318T						PASS	.						64	67	66					19																	15342598		2203	4300	6503	SO:0001819	synonymous_variant	79852	exon3			CTCAGGGAAGCCG	AK026061	CCDS12327.1	19p13.13	2011-10-05	2009-04-06	2009-04-06	ENSG00000105131	ENSG00000105131		"Abhydrolase domain containing"	23760	protein-coding gene	gene with protein product			"abhydrolase domain containing 9"	ABHD9			Standard	NM_024794		Approved	FLJ22408	uc002nap.3	Q9H6B9		ENST00000221730.3:c.318C>T	chr19.hg19:g.15342598G>A		40.0	0.0	.		46.0	21.0	.	NM_001142886	A3KMR3	Silent	SNP	ENST00000221730.3	hg19	CCDS12327.1																																																																																			.	.	.	none		0.657	EPHX3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465797.1	NM_024794		A	15342598	G	A	15342598	2	1	247	1	0	0	0	0	0	0	0	1	5183	1165	41	2		2	EPHX3	19	15342598	Silent	SNP	G	TCGA-SX-A7SM-01A-11D-A34Z-10	2881958	15342598	43786385	69	15315											
RABAC1	10567	hgsc.bcm.edu	37	chr19	42461049	42461049	+	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	tccacagcctcaatctggtgGaaggcagcgtgggagccgat	9	7	14	11	2	2	0	1	0	1	0	3	3	3	2	3	4	3	1	3	4	2	0			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr19:42461049G>C	ENST00000222008.6	-	5	604	c.507C>G	c.(505-507)ttC>ttG	p.F169L	RABAC1_ENST00000601891.1_Missense_Mutation_p.F135L|RABAC1_ENST00000601078.1_Missense_Mutation_p.F75L	NM_006423.2	NP_006414.2	Q9UI14	PRAF1_HUMAN	Rab acceptor 1 (prenylated)	169	Required for interaction with GDI1. {ECO:0000250}.					cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|synapse (GO:0045202)	identical protein binding (GO:0042802)			central_nervous_system(1)|kidney(1)|prostate(1)	3						CAATCTGGTGGAAGGCAGCGT	0.682																																					p.F169L		Atlas-SNP	.											.	RABAC1	6	.	0			c.C507G						PASS	.						42	39	40					19																	42461049		2202	4297	6499	SO:0001583	missense	10567	exon5			CTGGTGGAAGGCA	AJ133534	CCDS12593.1	19q13.2	2012-09-20			ENSG00000105404	ENSG00000105404			9794	protein-coding gene	gene with protein product	"PRA1 domain family 1", "prenylated Rab acceptor 1"	604925				10329441, 10751420	Standard	NM_006423		Approved	PRA1, PRAF1, YIP3	uc002osf.3	Q9UI14		ENST00000222008.6:c.507C>G	chr19.hg19:g.42461049G>C	ENSP00000222008:p.Phe169Leu	96.0	0.0	.		91.0	39.0	.	NM_006423	Q7Z4Y2|Q9Y3R1	Missense_Mutation	SNP	ENST00000222008.6	hg19	CCDS12593.1	.	.	.	.	.	.	.	.	.	.	G	15.44	2.834121	0.50951	.	.	ENSG00000105404	ENST00000222008	T	0.38401	1.14	4.65	2.45	0.29901	.	0.000000	0.85682	D	0.000000	T	0.32496	0.0831	L	0.45698	1.435	0.58432	D	0.999996	P	0.47841	0.901	P	0.48598	0.583	T	0.05289	-1.0894	10	0.27785	T	0.31	-25.6508	5.0709	0.14606	0.1909:0.1743:0.6348:0.0	.	169	Q9UI14	PRAF1_HUMAN	L	169	ENSP00000222008:F169L	ENSP00000222008:F169L	F	-	3	2	RABAC1	47152889	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	1.693000	0.37742	0.495000	0.27882	0.563000	0.77884	TTC	.	.	.	none		0.682	RABAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463388.1	NM_006423		C	42461049	G	C	42461049	3	2	247	1	0	0	0	0	1	0	0	0	12973	1165	41	4	54	4	RABAC1	19	42461049	Missense_Mutation	SNP	G	TCGA-SX-A7SM-01A-11D-A34Z-10	27118451	42461049	16667934	70	15316											
TPRX1	284355	hgsc.bcm.edu	37	chr19	48305603	48305603	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgggattgggcctgggatcGggcctgggtttgggcctgag	3	10	20	8	1	0	1	0	1	0	0	1	3	0	3	3	6	0	1	3	6	0	2	rs199739873		TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr19:48305603G>A	ENST00000322175.3	-	2	820	c.665C>T	c.(664-666)cCg>cTg	p.P222L	TPRX1_ENST00000543508.1_Missense_Mutation_p.P212L|TPRX1_ENST00000535759.1_Missense_Mutation_p.P319L	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	222	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P222L(1)		endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		gcctgggatcgggcctgggtt	0.667																																					p.P222L	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											TPRX1,NS,carcinoma,0,1	TPRX1	46	.	1	Substitution - Missense(1)	prostate(1)	c.C665T						PASS	.						12	10	10					19																	48305603		1907	3812	5719	SO:0001583	missense	284355	exon2			GGGATCGGGCCTG		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.665C>T	chr19.hg19:g.48305603G>A	ENSP00000323455:p.Pro222Leu	52.0	0.0	.		42.0	21.0	.	NM_198479	A5D8Y3|B2RPL5	Missense_Mutation	SNP	ENST00000322175.3	hg19	CCDS33066.1	.	.	.	.	.	.	.	.	.	.	g	4.957	0.177797	0.09443	.	.	ENSG00000178928	ENST00000322175;ENST00000535759;ENST00000543508	D;D;T	0.93659	-2.02;-3.26;-0.19	0.401	-0.802	0.10889	.	.	.	.	.	D	0.83727	0.5317	N	0.14661	0.345	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.70901	-0.4746	8	0.56958	D	0.05	.	.	.	.	.	222	Q8N7U7	TPRX1_HUMAN	L	222;319;212	ENSP00000323455:P222L;ENSP00000438832:P319L;ENSP00000438712:P212L	ENSP00000323455:P222L	P	-	2	0	TPRX1	52997415	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.050000	0.03510	-0.453000	0.07076	-0.462000	0.05337	CCG	.	.	.	weak		0.667	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479		A	48305603	G	A	48305603	3	1	247	1	0	0	0	0	1	0	0	0	16434	1116	39	1	574	1	TPRX1	19	48305603	Missense_Mutation	SNP	G	TCGA-SX-A7SM-01A-11D-A34Z-10	5844554	48305603	10823380	71	15317											
RRBP1	6238	hgsc.bcm.edu	37	chr20	17602147	17602148	+	Frame_Shift_Del	DEL	GT	GT	-																															ctggtcacactcggcctgcaGtgtgctctgcgtctcctcgg																										TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr20:17602147_17602148delGT	ENST00000377813.1	-	16	3672_3673	c.3369_3370delAC	c.(3367-3372)acactgfs	p.L1124fs	RRBP1_ENST00000360807.4_Frame_Shift_Del_p.L691fs|RRBP1_ENST00000470422.1_5'UTR|RRBP1_ENST00000455029.2_Frame_Shift_Del_p.L465fs|RRBP1_ENST00000377807.2_Frame_Shift_Del_p.L691fs|RRBP1_ENST00000246043.4_Frame_Shift_Del_p.L1124fs			Q9P2E9	RRBP1_HUMAN	ribosome binding protein 1	1124					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						TCGGCCTGCAGTGTGCTCTGCG	0.594																																					p.691_691del		Atlas-INDEL	.											.	RRBP1	157	.	0			c.2071_2072del						PASS	.																																			SO:0001589	frameshift_variant	6238	exon17			.	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.3369_3370delAC	chr20.hg19:g.17602149_17602150delGT	ENSP00000367044:p.Leu1124fs	28.0	0.0	0		26.0	10.0	0.384615	NM_001042576	A2A2S6|A6NCN6|O75300|O75301|Q5W165|Q96SB2|Q9BWP1|Q9H476	Frame_Shift_Del	DEL	ENST00000377813.1	hg19																																																																																				.	.	.	none		0.594	RRBP1-002	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000078125.1	NM_001042576		-	17602148	GT	-	17602147	7	5	247	1	0	1	0	1	0	0	0	0	13691	1020	36	0	902	0	RRBP1	20	17602147	Frame_Shift_Del	DEL	GT	TCGA-SX-A7SM-01A-11D-A34Z-10		17602147	45423373	72	15318											
SLC12A5	57468	hgsc.bcm.edu	37	chr20	44670004	44670004	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaccgcacgctgtctcgccaTggctttgatgtctgtgccaa	7	11	10	13	3	2	1	0	1	2	0	3	1	2	1	3	1	2	3	3	1	2	1			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr20:44670004T>C	ENST00000454036.2	+	8	1009	c.960T>C	c.(958-960)caT>caC	p.H320H	SLC12A5_ENST00000243964.3_Silent_p.H297H	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5	320					cellular ion homeostasis (GO:0006873)|chloride transmembrane transport (GO:1902476)|ion transport (GO:0006811)|learning (GO:0007612)|multicellular organism growth (GO:0035264)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|thermosensory behavior (GO:0040040)|transmembrane transport (GO:0055085)|transport (GO:0006810)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(1)|lung(38)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	80		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	TGTCTCGCCATGGCTTTGATG	0.572																																					p.H320H		Atlas-SNP	.											.	SLC12A5	181	.	0			c.T960C						PASS	.						104	92	96					20																	44670004		2203	4300	6503	SO:0001819	synonymous_variant	57468	exon8			TCGCCATGGCTTT	AB033002	CCDS13391.1, CCDS46610.1	20q13.12	2013-05-22	2010-04-20		ENSG00000124140	ENSG00000124140		"Solute carriers"	13818	protein-coding gene	gene with protein product		606726					Standard	NM_020708		Approved	KIAA1176, KCC2	uc010zxl.1	Q9H2X9	OTTHUMG00000032638	ENST00000454036.2:c.960T>C	chr20.hg19:g.44670004T>C		75.0	0.0	.		77.0	17.0	.	NM_001134771	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Silent	SNP	ENST00000454036.2	hg19	CCDS46610.1																																																																																			.	.	.	none		0.572	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1			C	44670004	T	C	44670004	2	2	247	1	0	0	0	0	0	0	0	1	14399	1461	51	3		3	SLC12A5	20	44670004	Silent	SNP	T	TCGA-SX-A7SM-01A-11D-A34Z-10	27067857	44670004	18355516	73	15319											
DNAJC5	80331	hgsc.bcm.edu	37	chr20	62560863	62560863	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aacacctacttcgtgctgtcCagctggtgggccaaggtgag	8	9	13	11	1	0	1	0	1	0	0	2	1	1	1	3	3	4	2	3	3	3	2			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr20:62560863C>T	ENST00000360864.4	+	3	459	c.306C>T	c.(304-306)tcC>tcT	p.S102S	DNAJC5_ENST00000369911.2_Silent_p.S102S	NM_025219.2	NP_079495.1	Q9H3Z4	DNJC5_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 5	102					cell death (GO:0008219)|exocytosis (GO:0006887)|negative regulation of neuron apoptotic process (GO:0043524)|neurotransmitter secretion (GO:0007269)|regulated secretory pathway (GO:0045055)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)				cervix(1)|endometrium(1)|lung(1)|pancreas(1)|upper_aerodigestive_tract(1)	5	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					TCGTGCTGTCCAGCTGGTGGG	0.642																																					p.S102S		Atlas-SNP	.											.	DNAJC5	16	.	0			c.C306T						PASS	.						118	94	102					20																	62560863		2203	4300	6503	SO:0001819	synonymous_variant	80331	exon3			GCTGTCCAGCTGG		CCDS13546.1	20q13.33	2014-09-17			ENSG00000101152	ENSG00000101152		"Heat shock proteins / DNAJ (HSP40)"	16235	protein-coding gene	gene with protein product		611203	"ceroid-lipofuscinosis, neuronal 4 (Kufs disease)"	CLN4			Standard	NM_025219		Approved	FLJ00118, FLJ13070, DNAJC5A	uc002yhf.3	Q9H3Z4	OTTHUMG00000033007	ENST00000360864.4:c.306C>T	chr20.hg19:g.62560863C>T		25.0	0.0	.		21.0	9.0	.	NM_025219	A8K0M0|B3KY68|E1P5G8|Q9H3Z5|Q9H7H2	Silent	SNP	ENST00000360864.4	hg19	CCDS13546.1																																																																																			.	.	.	none		0.642	DNAJC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080244.1	NM_025219		T	62560863	C	T	62560863	2	4	247	1	0	0	0	0	0	0	0	1	4652	581	21	2		2	DNAJC5	20	62560863	Silent	SNP	C	TCGA-SX-A7SM-01A-11D-A34Z-10	17890859	62560863	464657	74	15320											
SOX18	54345	hgsc.bcm.edu	37	chr20	62680619	62680619	+	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	cgttcatgggccgccggatgCgcgactcgtctgccgcctgg	3	8	15	15	7	2	0	1	0	1	0	3	2	2	1	4	3	2	1	4	3	0	1			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr20:62680619C>T	ENST00000340356.7	-	1	375	c.251G>A	c.(250-252)cGc>cAc	p.R84H	ZNF512B_ENST00000450537.1_5'Flank	NM_018419.2	NP_060889.1	P35713	SOX18_HUMAN	SRY (sex determining region Y)-box 18	84					angiogenesis (GO:0001525)|blood vessel endothelial cell migration (GO:0043534)|cell maturation (GO:0048469)|embryonic heart tube development (GO:0035050)|endocardial cell differentiation (GO:0060956)|endocardium formation (GO:0060214)|establishment of endothelial barrier (GO:0061028)|hair cycle process (GO:0022405)|hair follicle development (GO:0001942)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|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 transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of stem cell proliferation (GO:0072091)|stem cell fate specification (GO:0048866)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)	nuclear chromatin (GO:0000790)|nuclear transcription factor complex (GO:0044798)|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)|transcription regulatory region DNA binding (GO:0044212)			lung(3)	3	all_cancers(38;3.45e-11)|all_epithelial(29;9.12e-13)|Lung NSC(23;2e-09)|all_lung(23;6.77e-09)					CCGCCGGATGCGCGACTCGTC	0.736																																					p.R84H	GBM(27;64 690 17108 39708)	Atlas-SNP	.											.	SOX18	5	.	0			c.G251A						PASS	.						24	27	26					20																	62680619		2194	4289	6483	SO:0001583	missense	54345	exon1			CGGATGCGCGACT	AB033888	CCDS13552.1	20q13.33	2008-07-28			ENSG00000203883	ENSG00000203883		"SRY (sex determining region Y)-boxes"	11194	protein-coding gene	gene with protein product		601618				10807548	Standard	NM_018419		Approved		uc002yhs.3	P35713	OTTHUMG00000033017	ENST00000340356.7:c.251G>A	chr20.hg19:g.62680619C>T	ENSP00000341815:p.Arg84His	41.0	0.0	.		39.0	19.0	.	NM_018419	Q0VGA9|Q9NPH8	Missense_Mutation	SNP	ENST00000340356.7	hg19	CCDS13552.1	.	.	.	.	.	.	.	.	.	.	c	22.7	4.321194	0.81580	.	.	ENSG00000203883	ENST00000340356	D	0.93906	-3.31	2.44	2.44	0.29823	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (2);	0.000000	0.64402	U	0.000006	D	0.92522	0.7625	N	0.20445	0.575	0.48341	D	0.999631	D	0.89917	1.0	D	0.87578	0.998	D	0.91194	0.4986	10	0.38643	T	0.18	.	12.5069	0.55986	0.0:1.0:0.0:0.0	.	84	P35713	SOX18_HUMAN	H	84	ENSP00000341815:R84H	ENSP00000341815:R84H	R	-	2	0	SOX18	62151063	1.000000	0.71417	1.000000	0.80357	0.767000	0.43475	2.710000	0.47169	1.197000	0.43143	0.187000	0.17357	CGC	.	.	.	none		0.736	SOX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080265.1			T	62680619	C	T	62680619	3	4	247	1	0	0	0	0	1	0	0	0	14961	768	27	1	911	1	SOX18	20	62680619	Missense_Mutation	SNP	C	TCGA-SX-A7SM-01A-11D-A34Z-10	119756	62680619	344901	75	15321											
MCM3AP	8888	hgsc.bcm.edu	37	chr21	47665020	47665020	+	Missense_Mutation	SNP	A	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	ggccactaaactcatggccaAtcccgtcttcgacgtactga	10	9	8	14	3	2	1	1	1	1	0	4	2	3	1	3	2	2	1	3	2	4	3			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chr21:47665020A>C	ENST00000397708.1	-	24	4993	c.4739T>G	c.(4738-4740)aTt>aGt	p.I1580S	MCM3AP-AS1_ENST00000444998.1_RNA|MCM3AP_ENST00000467026.1_5'UTR|MCM3AP_ENST00000291688.1_Missense_Mutation_p.I1580S|MCM3AP-AS1_ENST00000588753.1_RNA|MCM3AP-AS1_ENST00000432735.1_RNA|MCM3AP-AS1_ENST00000591223.1_RNA|MCM3AP-AS1_ENST00000421927.1_RNA|AP001469.7_ENST00000444966.1_RNA|MCM3AP-AS1_ENST00000414659.1_RNA|MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP-AS1_ENST00000455567.1_RNA			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1580					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)					CTCATGGCCAATCCCGTCTTC	0.542																																					p.I1580S		Atlas-SNP	.											.	MCM3AP	146	.	0			c.T4739G						PASS	.						63	65	64					21																	47665020		2203	4300	6503	SO:0001583	missense	8888	exon23			TGGCCAATCCCGT	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.4739T>G	chr21.hg19:g.47665020A>C	ENSP00000380820:p.Ile1580Ser	58.0	0.0	.		60.0	22.0	.	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Missense_Mutation	SNP	ENST00000397708.1	hg19	CCDS13734.1	.	.	.	.	.	.	.	.	.	.	A	12.96	2.094267	0.36952	.	.	ENSG00000160294	ENST00000397708;ENST00000291688;ENST00000539647	T;T	0.03831	3.79;3.79	5.31	5.31	0.75309	.	0.754197	0.12852	N	0.433865	T	0.07908	0.0198	L	0.44542	1.39	0.18873	N	0.999984	B;P	0.36909	0.181;0.573	B;B	0.37833	0.057;0.259	T	0.20672	-1.0268	10	0.87932	D	0	-2.8064	15.2629	0.73637	1.0:0.0:0.0:0.0	.	1580;75	O60318;B3KT88	MCM3A_HUMAN;.	S	1580;1580;75	ENSP00000380820:I1580S;ENSP00000291688:I1580S	ENSP00000291688:I1580S	I	-	2	0	MCM3AP	46489448	0.863000	0.29885	0.041000	0.18516	0.496000	0.33645	7.945000	0.87732	2.003000	0.58678	0.459000	0.35465	ATT	.	.	.	none		0.542	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906		C	47665020	A	C	47665020	3	2	247	1	0	0	0	0	1	0	0	0	9395	101	4	5	1227	5	MCM3AP	21	47665020	Missense_Mutation	SNP	A	TCGA-SX-A7SM-01A-11D-A34Z-10		47665020	464875	76	15322											
CLCN5	1184	hgsc.bcm.edu	37	chrX	49851346	49851347	+	In_Frame_Ins	INS	-	-	TAA																															gagctcatttctgagctgttINStaatgactgtggccttctgg																										TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chrX:49851346_49851347insTAA	ENST00000307367.2	+	8	1457_1458	c.1166_1167insTAA	c.(1165-1170)tttaat>ttTAAtaat	p.390_391insN	CLCN5_ENST00000376091.3_In_Frame_Ins_p.460_461insN|CLCN5_ENST00000376108.3_In_Frame_Ins_p.390_391insN|CLCN5_ENST00000376088.3_In_Frame_Ins_p.460_461insN			P51795	CLCN5_HUMAN	chloride channel, voltage-sensitive 5	390					chloride transmembrane transport (GO:1902476)|endocytosis (GO:0006897)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)	30	Ovarian(276;0.236)					TCTGAGCTGTTTAATGACTGTG	0.515																																					p.F459delinsFN		Atlas-Indel,Pindel	.											.	CLCN5	137	.	0			c.1376_1377insTAA						PASS	.																																			SO:0001652	inframe_insertion	1184	exon11			.	X91906	CCDS14328.1, CCDS48115.1, CCDS69763.1	Xp11.23-p11.22	2012-09-26	2012-02-23		ENSG00000171365	ENSG00000171365		"Ion channels / Chloride channels : Voltage-sensitive"	2023	protein-coding gene	gene with protein product	"Dent disease"	300008	"nephrolithiasis 2, X-linked", "nephrolithiasis 1 (X-linked)", "chloride channel 5"	NPHL2, NPHL1		7874126, 8111383, 8099916, 8559248, 9602200	Standard	NM_001272102		Approved	DENTS, XLRH, hClC-K2, hCIC-K2, CLC5, XRN, ClC-5	uc004doq.1	P51795	OTTHUMG00000021514	ENST00000307367.2:c.1167_1169dupTAA	chrX.hg19:g.49851347_49851349dupTAA	ENSP00000304257:p.Asn390_Asn390dup	75.0	0.0	0		58.0	38.0	0.655172	NM_001127898	A1L475|B3KPN6|Q5JQD5|Q7RTN8	In_Frame_Ins	INS	ENST00000307367.2	hg19	CCDS14328.1																																																																																			.	.	.	none		0.515	CLCN5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056544.1			TAA	49851347	-	TAA	49851346	7	5	247	1	0	1	1	0	0	0	0	0	3468	1841	64	0	1410	0	CLCN5	23	49851346	In_Frame_Ins	INS	-	TCGA-SX-A7SM-01A-11D-A34Z-10		49851346	105419214	77	15323											
CENPI	2491	hgsc.bcm.edu	37	chrX	100402791	100402791	+	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	gccgcaaagaaaaatgagttGgtacaaaaggtatgaatgag	18	7	12	4	1	0	4	0	3	0	1	0	4	0	4	1	2	1	4	1	2	8	3			TCGA-SX-A7SM-01A-11D-A34Z-10	TCGA-SX-A7SM-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e	bab99f69-b881-4371-88d4-ffdd35a761fd	g.chrX:100402791G>T	ENST00000372927.1	+	18	2143	c.1866G>T	c.(1864-1866)ttG>ttT	p.L622F	CENPI_ENST00000423383.1_Missense_Mutation_p.L622F|CENPI_ENST00000218507.5_Missense_Mutation_p.L622F	NM_006733.2	NP_006724.2	Q92674	CENPI_HUMAN	centromere protein I	622					CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)|sex differentiation (GO:0007548)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)				breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(19)|prostate(1)|skin(2)	30						AAAATGAGTTGGTACAAAAGG	0.318																																					p.L622F		Atlas-SNP	.											.	CENPI	70	.	0			c.G1866T						PASS	.						62	53	56					X																	100402791		2203	4297	6500	SO:0001583	missense	2491	exon18			TGAGTTGGTACAA	X97249	CCDS14479.1	Xq22.1	2013-11-05	2006-06-15	2006-06-15	ENSG00000102384	ENSG00000102384			3968	protein-coding gene	gene with protein product		300065	"FSH primary response (LRPR1, rat) homolog 1", "FSH primary response (LRPR1 homolog, rat) 1"	FSHPRH1		16622420	Standard	NM_006733		Approved	LRPR1, CENP-I, Mis6	uc004egx.3	Q92674	OTTHUMG00000022018	ENST00000372927.1:c.1866G>T	chrX.hg19:g.100402791G>T	ENSP00000362018:p.Leu622Phe	162.0	0.0	.		136.0	90.0	.	NM_006733	Q5JWZ9|Q96ED0	Missense_Mutation	SNP	ENST00000372927.1	hg19	CCDS14479.1	.	.	.	.	.	.	.	.	.	.	G	4.054	0.007761	0.07866	.	.	ENSG00000102384	ENST00000423383;ENST00000218507;ENST00000372927	.	.	.	5.12	1.06	0.20224	.	1.201730	0.05831	N	0.617505	T	0.25938	0.0632	L	0.27053	0.805	0.09310	N	1	B;B	0.17038	0.02;0.02	B;B	0.14578	0.011;0.011	T	0.20042	-1.0287	9	0.10111	T	0.7	0.5429	4.4124	0.11439	0.1768:0.0:0.3555:0.4677	.	622;622	B4DZL4;Q92674	.;CENPI_HUMAN	F	622	.	ENSP00000218507:L622F	L	+	3	2	CENPI	100289447	0.000000	0.05858	0.000000	0.03702	0.282000	0.26991	0.391000	0.20784	-0.148000	0.11234	0.462000	0.41574	TTG	.	.	.	none		0.318	CENPI-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057519.1	NM_006733		T	100402791	G	T	100402791	3	4	247	1	0	0	0	0	1	0	0	0	3235	1339	47	4	1932	4	CENPI	23	100402791	Missense_Mutation	SNP	G	TCGA-SX-A7SM-01A-11D-A34Z-10	50551445	100402791	54867769	78	15324											
EBNA1BP2	10969	hgsc.bcm.edu	37	chr1	43637311	43637311	+	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	ttgaattctgccaaacattgCttcaggccattctaggaaat	12	13	7	9	0	3	1	1	1	2	0	3	2	3	2	2	2	3	1	2	2	4	6			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr1:43637311C>T	ENST00000236051.2	-	3	303	c.162G>A	c.(160-162)aaG>aaA	p.K54K	WDR65_ENST00000528956.1_5'Flank|WDR65_ENST00000372492.4_5'Flank|EBNA1BP2_ENST00000472982.1_5'UTR|EBNA1BP2_ENST00000431635.2_Silent_p.K109K	NM_006824.2	NP_006815.2	Q99848	EBP2_HUMAN	EBNA1 binding protein 2	54					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)				CCAAACATTGCTTCAGGCCAT	0.527																																					p.K109K		Atlas-SNP	.											.	EBNA1BP2	37	.	0			c.G327A						PASS	.						143	142	143					1																	43637311		2203	4300	6503	SO:0001819	synonymous_variant	10969	exon4			ACATTGCTTCAGG	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.162G>A	chr1.hg19:g.43637311C>T		75.0	0.0	.		101.0	37.0	.	NM_001159936	Q96A66	Silent	SNP	ENST00000236051.2	hg19	CCDS478.1																																																																																			.	.	.	none		0.527	EBNA1BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019015.1			T	43637311	C	T	43637311	2	4	248	1	0	0	0	0	0	0	0	1	4887	796	28	2		2	EBNA1BP2	1	43637311	Silent	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10		43637311	205613310	1	15325											
NRD1	4898	hgsc.bcm.edu	37	chr1	52277743	52277743	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctgcatgttctcacacaTgttttccacatactcaactg	10	13	5	13	0	2	0	2	0	1	0	4	0	3	0	1	0	4	4	1	0	2	4			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr1:52277743T>C	ENST00000354831.7	-	17	2095	c.1906A>G	c.(1906-1908)Atg>Gtg	p.M636V	NRD1_ENST00000485608.1_5'UTR|NRD1_ENST00000544028.1_Missense_Mutation_p.M436V|NRD1_ENST00000539524.1_Missense_Mutation_p.M504V|NRD1_ENST00000352171.7_Missense_Mutation_p.M568V	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	567					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						TTCTCACACATGTTTTCCACA	0.368																																					p.M636V		Atlas-SNP	.											.	NRD1	89	.	0			c.A1906G						PASS	.						140	127	131					1																	52277743		2203	4300	6503	SO:0001583	missense	4898	exon17			CACACATGTTTTC	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.1906A>G	chr1.hg19:g.52277743T>C	ENSP00000346890:p.Met636Val	85.0	0.0	.		89.0	31.0	.	NM_002525	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Missense_Mutation	SNP	ENST00000354831.7	hg19	CCDS559.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.945|8.945	0.966856|0.966856	0.18659|0.18659	.|.	.|.	ENSG00000078618|ENSG00000078618	ENST00000440943|ENST00000352171;ENST00000354831;ENST00000539524;ENST00000371665;ENST00000546169;ENST00000544028	.|T;T;T;T	.|0.27720	.|1.65;1.66;1.66;1.66	5.98|5.98	4.85|4.85	0.62838|0.62838	.|Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	.|0.175165	.|0.64402	.|D	.|0.000009	T|T	0.12050|0.12050	0.0293|0.0293	N|N	0.01297|0.01297	-0.9|-0.9	0.35327|0.35327	D|D	0.785267|0.785267	.|B;B;B	.|0.13145	.|0.004;0.003;0.007	.|B;B;B	.|0.06405	.|0.002;0.001;0.001	T|T	0.09907|0.09907	-1.0653|-1.0653	5|10	.|0.30854	.|T	.|0.27	-5.3765|-5.3765	12.8858|12.8858	0.58042|0.58042	0.0:0.0:0.3186:0.6814|0.0:0.0:0.3186:0.6814	.|.	.|568;567;636	.|F5H6R2;O43847;B1AKJ5	.|.;NRDC_HUMAN;.	R|V	22|568;636;504;38;568;436	.|ENSP00000262679:M568V;ENSP00000346890:M636V;ENSP00000444416:M504V;ENSP00000442262:M436V	.|ENSP00000262679:M568V	H|M	-|-	2|1	0|0	NRD1|NRD1	52050331|52050331	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	2.668000|2.668000	0.46816|0.46816	1.068000|1.068000	0.40764|0.40764	0.528000|0.528000	0.53228|0.53228	CAT|ATG	.	.	.	none		0.368	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525		C	52277743	T	C	52277743	3	2	248	1	0	0	0	0	1	0	0	0	10652	1464	51	3	1821	3	NRD1	1	52277743	Missense_Mutation	SNP	T	TCGA-SX-A7SN-01A-11D-A34Z-10	8640432	52277743	196972878	2	15326											
C1orf173	127254	hgsc.bcm.edu	37	chr1	75072484	75072484	+	Frame_Shift_Del	DEL	T	T	-																															tactctctctctttcctcacTttcccctcagccttcttcag																										TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr1:75072484delT	ENST00000326665.5	-	10	1508	c.1290delA	c.(1288-1290)aaafs	p.K430fs	RP4-612J11.1_ENST00000416017.1_RNA|C1orf173_ENST00000420661.2_Frame_Shift_Del_p.K233fs	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		430	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						CTTTCCTCACTTTCCCCTCAG	0.403																																					p.V431X		Atlas-Indel,Pindel	.											.	C1orf173	380	.	0			c.1291delG						PASS	.						150	144	146					1																	75072484		2203	4298	6501	SO:0001589	frameshift_variant	127254	exon10			.																												ENST00000326665.5:c.1290delA	chr1.hg19:g.75072484delT	ENSP00000322609:p.Lys430fs	334.0	0.0	0		424.0	157.0	0.370283	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Frame_Shift_Del	DEL	ENST00000326665.5	hg19	CCDS30755.1																																																																																			.	.	.	none		0.403	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			-	75072484	T	-	75072484	7	5	248	1	0	1	0	1	0	0	0	0	2016	1606	56	0	3322	0	C1orf173	1	75072484	Frame_Shift_Del	DEL	T	TCGA-SX-A7SN-01A-11D-A34Z-10	22794741	75072484	174178137	3	15327											
LRRC8D	55144	hgsc.bcm.edu	37	chr1	90399387	90399387	+	Missense_Mutation	SNP	A	A	C																															ccagtgccagtacaccaatgAtcaataaaactggctttaaa																										TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr1:90399387A>C	ENST00000337338.5	+	3	1167	c.760A>C	c.(760-762)Atc>Ctc	p.I254L	LRRC8D_ENST00000394593.3_Missense_Mutation_p.I254L	NM_001134479.1	NP_001127951.1	Q7L1W4	LRC8D_HUMAN	leucine rich repeat containing 8 family, member D	254					ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(2)|skin(1)	29		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)		TACACCAATGATCAATAAAAC	0.463																																					p.I254L		Atlas-SNP	.											.	LRRC8D	78	.	0			c.A760C						PASS	.						49	47	48					1																	90399387		2203	4300	6503	SO:0001583	missense	55144	exon3			CCAATGATCAATA	AK001332	CCDS726.1	1p22.2	2008-02-05	2005-06-29	2005-06-29	ENSG00000171492	ENSG00000171492			16992	protein-coding gene	gene with protein product		612890	"leucine rich repeat containing 5"	LRRC5			Standard	NM_018103		Approved	FLJ10470	uc001dnn.3	Q7L1W4	OTTHUMG00000010583	ENST00000337338.5:c.760A>C	chr1.hg19:g.90399387A>C	ENSP00000338887:p.Ile254Leu	48.0	0.0	.		52.0	20.0	.	NM_018103	D3DT29|Q6UWB2|Q9NVW3	Missense_Mutation	SNP	ENST00000337338.5	hg19	CCDS726.1	.	.	.	.	.	.	.	.	.	.	A	0.018	-1.467060	0.01053	.	.	ENSG00000171492	ENST00000337338;ENST00000394593;ENST00000441269	T;T;T	0.39229	1.67;1.67;1.09	5.88	5.88	0.94601	.	0.132704	0.47093	D	0.000259	T	0.04679	0.0127	N	0.00186	-1.895	0.40496	D	0.980591	B	0.02656	0.0	B	0.01281	0.0	T	0.34750	-0.9816	9	.	.	.	.	16.3009	0.82811	1.0:0.0:0.0:0.0	.	254	Q7L1W4	LRC8D_HUMAN	L	254	ENSP00000338887:I254L;ENSP00000378093:I254L;ENSP00000405784:I254L	.	I	+	1	0	LRRC8D	90171975	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	3.832000	0.55783	2.246000	0.74042	0.533000	0.62120	ATC	.	.	.	none		0.463	LRRC8D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029203.2	NM_018103		C	90399387	A	C	90399387	3	2	248	1	0	0	0	0	1	0	0	0	9031	333	12	5	762	5	LRRC8D	1	90399387	Missense_Mutation	SNP	A	TCGA-SX-A7SN-01A-11D-A34Z-10	15326903	90399387	158851234	4	15328	158	2									
LRRC8D	55144	hgsc.bcm.edu	37	chr1	90399389	90399389	+	Frame_Shift_Del	DEL	C	C	-																															agtgccagtacaccaatgatCaataaaactggctttaaatt																										TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr1:90399389delC	ENST00000337338.5	+	3	1169	c.762delC	c.(760-762)atcfs	p.I254fs	LRRC8D_ENST00000394593.3_Frame_Shift_Del_p.I254fs	NM_001134479.1	NP_001127951.1	Q7L1W4	LRC8D_HUMAN	leucine rich repeat containing 8 family, member D	254					ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(2)|skin(1)	29		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)		CACCAATGATCAATAAAACTG	0.463																																					p.I254fs		Atlas-INDEL	.											.	LRRC8D	78	.	0			c.761delT						PASS	.						48	46	47					1																	90399389		2203	4300	6503	SO:0001589	frameshift_variant	55144	exon3			.	AK001332	CCDS726.1	1p22.2	2008-02-05	2005-06-29	2005-06-29	ENSG00000171492	ENSG00000171492			16992	protein-coding gene	gene with protein product		612890	"leucine rich repeat containing 5"	LRRC5			Standard	NM_018103		Approved	FLJ10470	uc001dnn.3	Q7L1W4	OTTHUMG00000010583	ENST00000337338.5:c.762delC	chr1.hg19:g.90399389delC	ENSP00000338887:p.Ile254fs	47.0	0.0	0		51.0	19.0	0.372549	NM_018103	D3DT29|Q6UWB2|Q9NVW3	Frame_Shift_Del	DEL	ENST00000337338.5	hg19	CCDS726.1																																																																																			.	.	.	none		0.463	LRRC8D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029203.2	NM_018103		-	90399389	C	-	90399389	7	5	248	1	0	1	0	1	0	0	0	0	9031	816	29	0	764	0	LRRC8D	1	90399389	Frame_Shift_Del	DEL	C	TCGA-SX-A7SN-01A-11D-A34Z-10	2	90399389	158851232	5	15329	158	2									
PTBP2	58155	hgsc.bcm.edu	37	chr1	97278858	97278858	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaaatggctcttcttcagaTggcaacagtggaagaagcta	14	9	10	8	0	3	2	1	0	2	2	3	3	3	3	0	3	2	3	0	3	6	3			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr1:97278858T>C	ENST00000426398.2	+	14	1536	c.1493T>C	c.(1492-1494)aTg>aCg	p.M498T	PTBP2_ENST00000370197.1_Missense_Mutation_p.M504T|PTBP2_ENST00000609116.1_Missense_Mutation_p.M499T|PTBP2_ENST00000482253.1_3'UTR|PTBP2_ENST00000370198.1_Missense_Mutation_p.M503T|PTBP2_ENST00000394184.3_Missense_Mutation_p.M515T|PTBP2_ENST00000541987.1_3'UTR	NM_021190.2	NP_067013.1	Q9UKA9	PTBP2_HUMAN	polypyrimidine tract binding protein 2	498	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA splice site selection (GO:0006376)|negative regulation of RNA splicing (GO:0033119)|regulation of neural precursor cell proliferation (GO:2000177)	spliceosomal complex (GO:0005681)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|skin(1)	26		all_epithelial(167;2.95e-05)|all_lung(203;0.000396)|Lung NSC(277;0.00171)		all cancers(265;0.0582)|Epithelial(280;0.0716)|Colorectal(170;0.0879)|KIRC - Kidney renal clear cell carcinoma(1967;0.202)		CTTCTTCAGATGGCAACAGTG	0.338																																					p.M498T		Atlas-SNP	.											.	PTBP2	62	.	0			c.T1493C						PASS	.						69	77	75					1																	97278858		2203	4300	6503	SO:0001583	missense	58155	exon14			TTCAGATGGCAAC	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.1493T>C	chr1.hg19:g.97278858T>C	ENSP00000412788:p.Met498Thr	251.0	0.0	.		247.0	79.0	.	NM_021190	Q8N0Z1|Q8N160|Q8NFB0|Q8NFB1|Q969N9|Q96Q76	Missense_Mutation	SNP	ENST00000426398.2	hg19	CCDS754.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.282184	0.80692	.	.	ENSG00000117569	ENST00000236228;ENST00000543738;ENST00000370198;ENST00000370197;ENST00000426398;ENST00000394184	T;T;T;T;T	0.09538	2.97;2.97;2.97;2.97;2.97	5.5	5.5	0.81552	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.38983	0.1061	H	0.95745	3.715	0.80722	D	1	P;P;P;P;B;B;P	0.48694	0.891;0.914;0.66;0.894;0.354;0.059;0.868	D;D;D;D;P;P;D	0.70716	0.966;0.97;0.933;0.949;0.772;0.732;0.93	T	0.54827	-0.8235	10	0.87932	D	0	-4.0584	15.8942	0.79323	0.0:0.0:0.0:1.0	.	507;515;171;503;498;499;504	B4DSU5;B4DSS8;B4DSI2;Q9UKA9-4;Q9UKA9;Q9UKA9-2;Q9UKA9-3	.;.;.;.;PTBP2_HUMAN;.;.	T	499;171;503;504;498;515	ENSP00000236228:M499T;ENSP00000359217:M503T;ENSP00000359216:M504T;ENSP00000412788:M498T;ENSP00000377738:M515T	ENSP00000236228:M499T	M	+	2	0	PTBP2	97051446	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.993000	0.88291	2.206000	0.71126	0.528000	0.53228	ATG	.	.	.	none		0.338	PTBP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029453.1			C	97278858	T	C	97278858	3	2	248	1	0	0	0	0	1	0	0	0	12736	1464	51	3	1547	3	PTBP2	1	97278858	Missense_Mutation	SNP	T	TCGA-SX-A7SN-01A-11D-A34Z-10	6879469	97278858	151971763	6	15330											
MAGI3	260425	hgsc.bcm.edu	37	chr1	114184618	114184618	+	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	atgtttcaattggtacctgtCaatcagtatgtaaacctcac	12	14	6	9	0	4	0	4	0	0	0	4	0	4	0	2	1	2	4	2	1	6	5			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr1:114184618C>T	ENST00000307546.9	+	10	1521	c.1446C>T	c.(1444-1446)gtC>gtT	p.V482V	MAGI3_ENST00000369615.1_Silent_p.V482V|MAGI3_ENST00000369617.4_Silent_p.V507V|MAGI3_ENST00000369611.4_Silent_p.V482V	NM_001142782.1	NP_001136254.1	Q5TCQ9	MAGI3_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 3	507	Interaction with PTEN.|PDZ 2. {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)		TGGTACCTGTCAATCAGTATG	0.428																																					p.V482V		Atlas-SNP	.											.	MAGI3	181	.	0			c.C1446T						PASS	.						218	189	199					1																	114184618		2203	4300	6503	SO:0001819	synonymous_variant	260425	exon10			ACCTGTCAATCAG	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.1446C>T	chr1.hg19:g.114184618C>T		69.0	0.0	.		79.0	29.0	.	NM_152900	Q5TCQ8|Q5TCR0|Q9H2V6|Q9H5Y8|Q9HBC4|Q9HCD8	Silent	SNP	ENST00000307546.9	hg19	CCDS44196.1																																																																																			.	.	.	none		0.428	MAGI3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000032429.1	NM_152900		T	114184618	C	T	114184618	2	4	248	1	0	0	0	0	0	0	0	1	9199	813	29	2		2	MAGI3	1	114184618	Silent	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10	16905760	114184618	135066003	7	15331											
SPAG17	200162	hgsc.bcm.edu	37	chr1	118509280	118509281	+	Frame_Shift_Ins	INS	-	-	A																															tgctctgtcataatctcgatINSattgtgagagatgtgtgctg																										TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr1:118509280_118509281insA	ENST00000336338.5	-	47	6548_6549	c.6483_6484insT	c.(6481-6486)aatatcfs	p.I2162fs		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	2162						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)		ATAATCTCGATATTGTGAGAGA	0.421																																					p.I2162fs		Atlas-Indel,Pindel	.											.	SPAG17	263	.	0			c.6484_6485insT						PASS	.																																			SO:0001589	frameshift_variant	200162	exon47			.		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.6484dupT	chr1.hg19:g.118509281_118509281dupA	ENSP00000337804:p.Ile2162fs	115.0	0.0	0		148.0	58.0	0.391892	NM_206996	Q8NAZ1|Q9NT21	Frame_Shift_Ins	INS	ENST00000336338.5	hg19	CCDS899.1																																																																																			.	.	.	none		0.421	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		A	118509281	-	A	118509280	7	5	248	1	0	1	1	0	0	0	0	0	14992	1406	49	0	195	0	SPAG17	1	118509280	Frame_Shift_Ins	INS	-	TCGA-SX-A7SN-01A-11D-A34Z-10	4324662	118509280	130741341	8	15332											
ITGA10	8515	hgsc.bcm.edu	37	chr1	145525111	145525111	+	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	tgttcttgcccctggtgttcCtgacaggtgagggaagttaa	7	13	13	8	0	1	2	0	2	1	0	2	3	2	3	3	3	1	3	3	3	2	4			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr1:145525111C>A	ENST00000369304.3	+	1	221	c.46C>A	c.(46-48)Ctg>Atg	p.L16M	ITGA10_ENST00000539363.1_Missense_Mutation_p.L16M|ITGA10_ENST00000538811.1_5'UTR	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	16					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)					CCTGGTGTTCCTGACAGGTGA	0.468											OREG0013749	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L16M		Atlas-SNP	.											.	ITGA10	131	.	0			c.C46A						PASS	.						221	186	197					1																	145525111		2203	4300	6503	SO:0001583	missense	8515	exon1			GTGTTCCTGACAG	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.46C>A	chr1.hg19:g.145525111C>A	ENSP00000358310:p.Leu16Met	105.0	0.0	.	1695	109.0	24.0	.	NM_003637	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Missense_Mutation	SNP	ENST00000369304.3	hg19	CCDS918.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.077591	0.76528	.	.	ENSG00000143127	ENST00000369304;ENST00000539363	T;T	0.61274	0.12;0.29	5.43	5.43	0.79202	.	0.210074	0.29956	N	0.010776	T	0.65270	0.2675	L	0.55990	1.75	0.80722	D	1	D;B;D	0.76494	0.998;0.074;0.999	D;B;D	0.85130	0.994;0.031;0.997	T	0.63501	-0.6623	10	0.46703	T	0.11	.	14.599	0.68427	0.0:1.0:0.0:0.0	.	16;16;16	B2RTV5;O75578;O75578-2	.;ITA10_HUMAN;.	M	16	ENSP00000358310:L16M;ENSP00000439894:L16M	ENSP00000358310:L16M	L	+	1	2	ITGA10	144236468	0.999000	0.42202	0.998000	0.56505	0.899000	0.52679	1.993000	0.40747	2.825000	0.97269	0.655000	0.94253	CTG	.	.	.	none		0.468	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637		A	145525111	C	A	145525111	3	1	248	1	0	0	0	0	1	0	0	0	7880	680	24	4	48	4	ITGA10	1	145525111	Missense_Mutation	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10	27015831	145525111	103725510	9	15333											
SNX27	81609	hgsc.bcm.edu	37	chr1	151611491	151611491	+	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	cagataacctagatcccagtGacgactcgttgggacaatca	13	8	9	11	2	1	3	1	1	0	2	3	5	2	4	2	1	1	1	2	1	3	3			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr1:151611491G>C	ENST00000458013.2	+	2	559	c.439G>C	c.(439-441)Gac>Cac	p.D147H	SNX27_ENST00000368838.1_Missense_Mutation_p.D54H|SNX27_ENST00000368843.3_Missense_Mutation_p.D147H			Q96L92	SNX27_HUMAN	sorting nexin family member 27	147					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)			AGATCCCAGTGACGACTCGTT	0.468																																					p.D147H	Colon(46;291 966 40145 41237 41888)	Atlas-SNP	.											.	SNX27	44	.	0			c.G439C						PASS	.						134	118	124					1																	151611491		2203	4300	6503	SO:0001583	missense	81609	exon2			CCCAGTGACGACT	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.439G>C	chr1.hg19:g.151611491G>C	ENSP00000400333:p.Asp147His	62.0	0.0	.		84.0	30.0	.	NM_030918	Q32Q36|Q4AEJ5|Q5VWB0|Q5VWB1|Q5VWB2|Q6IPP6|Q86UB1|Q96D79|Q9H3K8	Missense_Mutation	SNP	ENST00000458013.2	hg19		.	.	.	.	.	.	.	.	.	.	G	21.4	4.140324	0.77775	.	.	ENSG00000143376	ENST00000458013;ENST00000368843;ENST00000368838	T;T;T	0.53640	0.61;0.62;0.81	4.49	4.49	0.54785	Phox homologous domain (1);PDZ/DHR/GLGF (1);	0.000000	0.85682	D	0.000000	T	0.55353	0.1915	M	0.64404	1.975	0.80722	D	1	D;D	0.69078	0.989;0.997	P;P	0.61477	0.838;0.889	T	0.60505	-0.7250	10	0.66056	D	0.02	.	15.8961	0.79336	0.0:0.0:1.0:0.0	.	147;147	Q96L92;Q96L92-3	SNX27_HUMAN;.	H	147;147;54	ENSP00000400333:D147H;ENSP00000357836:D147H;ENSP00000357831:D54H	ENSP00000357831:D54H	D	+	1	0	SNX27	149878115	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.235000	0.95353	2.331000	0.79229	0.591000	0.81541	GAC	.	.	.	none		0.468	SNX27-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000036624.3	NM_030918		C	151611491	G	C	151611491	3	2	248	1	0	0	0	0	1	0	0	0	14910	1290	45	4	445	4	SNX27	1	151611491	Missense_Mutation	SNP	G	TCGA-SX-A7SN-01A-11D-A34Z-10	6086380	151611491	97639130	10	15334											
TDRD10	126668	hgsc.bcm.edu	37	chr1	154520167	154520167	+	3'UTR	SNP	A	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	cttccagttgcacatcctaaAgtttgaagagtctaaataac	14	12	6	9	0	1	2	0	1	1	1	3	2	3	2	2	0	2	3	2	0	6	6			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr1:154520167A>T	ENST00000368480.3	+	0	1320				TDRD10_ENST00000368482.4_Missense_Mutation_p.K346M|TDRD10_ENST00000479937.1_3'UTR			Q5VZ19	TDR10_HUMAN	tudor domain containing 10								nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			CACATCCTAAAGTTTGAAGAG	0.527																																					p.K346M		Atlas-SNP	.											.	TDRD10	48	.	0			c.A1037T						PASS	.						107	103	104					1																	154520167		2203	4300	6503	SO:0001624	3_prime_UTR_variant	126668	exon13			TCCTAAAGTTTGA	AL713777	CCDS30878.2, CCDS41406.1	1q21.3	2013-02-12			ENSG00000163239	ENSG00000163239		"Tudor domain containing", "RNA binding motif (RRM) containing"	25316	protein-coding gene	gene with protein product						12975309	Standard	NM_182499		Approved	DKFZp434M202	uc009wow.3	Q5VZ19	OTTHUMG00000037264	ENST00000368480.3:c.*134A>T	chr1.hg19:g.154520167A>T		148.0	0.0	.		173.0	68.0	.	NM_182499	A4FU09|B0QZ53|B4DXV4|Q3ZCP1|Q3ZCS7|Q5SXY7|Q6UXV2|Q8TCN3	Missense_Mutation	SNP	ENST00000368480.3	hg19	CCDS41406.1	.	.	.	.	.	.	.	.	.	.	A	15.17	2.753359	0.49362	.	.	ENSG00000163239	ENST00000368482	T	0.31769	1.48	4.9	1.07	0.20283	.	.	.	.	.	T	0.08403	0.0209	.	.	.	0.26631	N	0.972462	P	0.37955	0.612	B	0.37692	0.256	T	0.22208	-1.0223	8	0.35671	T	0.21	.	5.9611	0.19301	0.5122:0.3295:0.0:0.1583	.	346	Q5VZ19-2	.	M	346	ENSP00000357467:K346M	ENSP00000357467:K346M	K	+	2	0	TDRD10	152786791	0.022000	0.18835	0.030000	0.17652	0.002000	0.02628	0.010000	0.13242	0.068000	0.16574	-0.313000	0.08912	AAG	.	.	.	none		0.527	TDRD10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090700.2	NM_182499		T	154520167	A	T	154520167	1	4	248	0	1	0	0	0	0	0	0	0	15743	72	3	5		5	TDRD10	1	154520167	3'UTR	SNP	A	TCGA-SX-A7SN-01A-11D-A34Z-10	2908676	154520167	94730454	11	15335											
C1orf107	27042	hgsc.bcm.edu	37	chr1	210010373	210010380	+	Frame_Shift_Del	DEL	CTACCCGG	CTACCCGG	-																															aattcttaccgggacctgttCtacccggaaaggactgctct																								rs200536666		TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	CTACCCGG	CTACCCGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr1:210010373_210010380delCTACCCGG	ENST00000491415.2	+	6	936_943	c.879_886delCTACCCGG	c.(877-888)ttctacccggaafs	p.FYPE293fs		NM_014388.6	NP_055203.4	Q68CQ4	DIEXF_HUMAN	digestive organ expansion factor homolog (zebrafish)	293					multicellular organismal development (GO:0007275)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(15)|large_intestine(7)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(2)	53						GGGACCTGTTCTACCCGGAAAGGACTGC	0.49																																					p.293_295del		Atlas-Indel,Pindel	.											.	DIEXF	97	.	0			c.878_885del						PASS	.																																			SO:0001589	frameshift_variant	27042	exon6			.	BC022964	CCDS1493.1	1q32.2	2011-08-12	2011-02-16	2011-02-16	ENSG00000117597	ENSG00000117597			28440	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 107"	C1orf107		16322560	Standard	NM_014388		Approved	MGC29875, DEF, UTP25	uc001hhr.2	Q68CQ4	OTTHUMG00000036654	ENST00000491415.2:c.879_886delCTACCCGG	chr1.hg19:g.210010373_210010380delCTACCCGG	ENSP00000419005:p.Phe293fs	77.0	0.0	0		65.0	28.0	0.430769	NM_014388	O75992|Q4VY00|Q63HL9	Frame_Shift_Del	DEL	ENST00000491415.2	hg19	CCDS1493.1																																																																																			.	.	.	none		0.49	DIEXF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089127.2	NM_014388		-	210010380	CTACCCGG	-	210010373	7	5	248	1	0	1	0	1	0	0	0	0	1983	912	32	0	901	0	C1orf107	1	210010373	Frame_Shift_Del	DEL	CTACCCGG	TCGA-SX-A7SN-01A-11D-A34Z-10	55490206	210010373	39240248	12	15336											
SLC30A1	7779	hgsc.bcm.edu	37	chr1	211751453	211751453	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcgctgctcccggggcgggTgctcttaacgcgaggcccct	3	8	15	15	5	1	0	0	0	1	0	3	1	2	0	3	4	3	3	3	4	1	1			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr1:211751453T>C	ENST00000367001.4	-	1	631	c.502A>G	c.(502-504)Acc>Gcc	p.T168A		NM_021194.2	NP_067017.2	Q9Y6M5	ZNT1_HUMAN	solute carrier family 30 (zinc transporter), member 1	168					cadmium ion transmembrane transport (GO:0070574)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|cellular zinc ion homeostasis (GO:0006882)|detoxification of cadmium ion (GO:0071585)|in utero embryonic development (GO:0001701)|negative regulation of calcium ion import (GO:0090281)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of zinc ion transmembrane import (GO:0071584)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	calcium channel inhibitor activity (GO:0019855)|zinc ion transmembrane transporter activity (GO:0005385)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(3)|prostate(1)	11				OV - Ovarian serous cystadenocarcinoma(81;0.00535)|GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.0604)|Epithelial(68;0.0978)		CCGGGGCGGGTGCTCTTAACG	0.701																																					p.T168A		Atlas-SNP	.											.	SLC30A1	27	.	0			c.A502G						PASS	.						17	20	19					1																	211751453		2198	4295	6493	SO:0001583	missense	7779	exon1			GGCGGGTGCTCTT	AF323590	CCDS1499.1	1q32.3	2013-05-22			ENSG00000170385	ENSG00000170385		"Solute carriers"	11012	protein-coding gene	gene with protein product		609521		ZNT1			Standard	NM_021194		Approved	ZRC1	uc001hio.1	Q9Y6M5	OTTHUMG00000036995	ENST00000367001.4:c.502A>G	chr1.hg19:g.211751453T>C	ENSP00000355968:p.Thr168Ala	34.0	0.0	.		43.0	18.0	.	NM_021194	Q0VAK9|Q9BZF6	Missense_Mutation	SNP	ENST00000367001.4	hg19	CCDS1499.1	.	.	.	.	.	.	.	.	.	.	T	7.932	0.740859	0.15642	.	.	ENSG00000170385	ENST00000367001	T	0.63255	-0.03	4.13	-5.39	0.02664	.	3.281300	0.00751	N	0.001077	T	0.28732	0.0712	N	0.01242	-0.935	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39860	-0.9593	10	0.08837	T	0.75	1.0089	9.0099	0.36135	0.0:0.5305:0.2346:0.2349	.	168	Q9Y6M5	ZNT1_HUMAN	A	168	ENSP00000355968:T168A	ENSP00000355968:T168A	T	-	1	0	SLC30A1	209818076	0.000000	0.05858	0.004000	0.12327	0.024000	0.10985	-1.009000	0.03660	-0.892000	0.03935	-0.624000	0.04008	ACC	.	.	.	none		0.701	SLC30A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104738.2			C	211751453	T	C	211751453	3	2	248	1	0	0	0	0	1	0	0	0	14566	1696	59	3	1029	3	SLC30A1	1	211751453	Missense_Mutation	SNP	T	TCGA-SX-A7SN-01A-11D-A34Z-10	1741080	211751453	37499168	13	15337											
NSL1	25936	hgsc.bcm.edu	37	chr1	212960912	212960912	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtcacatacccataaaacaaTtatctgaagcttcctgccat	14	11	4	12	0	2	1	1	1	1	0	3	1	3	1	3	0	4	1	3	0	6	4			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr1:212960912T>C	ENST00000366977.3	-	2	320	c.302A>G	c.(301-303)aAt>aGt	p.N101S	NSL1_ENST00000366975.6_Missense_Mutation_p.N101S|NSL1_ENST00000366976.1_Missense_Mutation_p.N101S|NSL1_ENST00000473995.1_5'UTR|NSL1_ENST00000422588.2_Missense_Mutation_p.N101S|NSL1_ENST00000366978.1_5'UTR	NM_015471.3	NP_056286.3	Q96IY1	NSL1_HUMAN	NSL1, MIS12 kinetochore complex component	101					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|MIS12/MIND type complex (GO:0000444)|nucleus (GO:0005634)				breast(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	9				OV - Ovarian serous cystadenocarcinoma(81;0.00597)|all cancers(67;0.00893)|GBM - Glioblastoma multiforme(131;0.0514)|Epithelial(68;0.102)		CATAAAACAATTATCTGAAGC	0.328																																					p.N101S		Atlas-SNP	.											.	NSL1	24	.	0			c.A302G						PASS	.						86	84	85					1																	212960912		2203	4300	6503	SO:0001583	missense	25936	exon2			AAACAATTATCTG	AF255793	CCDS1509.1, CCDS73025.1	1q41	2013-07-03	2013-07-03	2006-11-07	ENSG00000117697	ENSG00000117697			24548	protein-coding gene	gene with protein product		609174	"chromosome 1 open reading frame 48", "NSL1, MIND kinetochore complex component, homolog (S. cerevisiae)"	C1orf48		20819937	Standard	NM_015471		Approved	DC8, DKFZP566O1646, MIS14	uc001hjn.3	Q96IY1	OTTHUMG00000036806	ENST00000366977.3:c.302A>G	chr1.hg19:g.212960912T>C	ENSP00000355944:p.Asn101Ser	219.0	0.0	.		272.0	92.0	.	NM_015471	E7ETD5|Q5SY75|Q9H2M5|Q9NRN8|Q9Y415	Missense_Mutation	SNP	ENST00000366977.3	hg19	CCDS1509.1	.	.	.	.	.	.	.	.	.	.	T	2.442	-0.328274	0.05314	.	.	ENSG00000117697	ENST00000366977;ENST00000422588;ENST00000366975;ENST00000366976	T;T;T;T	0.43688	1.56;0.94;1.61;0.97	4.7	2.37	0.29283	.	0.833602	0.11159	N	0.593288	T	0.18509	0.0444	N	0.03115	-0.41	0.09310	N	1	B;B;B	0.14438	0.003;0.003;0.01	B;B;B	0.17098	0.008;0.008;0.017	T	0.29027	-1.0025	10	0.21014	T	0.42	-0.3034	6.3421	0.21328	0.0:0.2038:0.0:0.7962	.	101;101;101	B4E071;Q96IY1;E7ETD5	.;NSL1_HUMAN;.	S	101	ENSP00000355944:N101S;ENSP00000388406:N101S;ENSP00000355942:N101S;ENSP00000355943:N101S	ENSP00000355942:N101S	N	-	2	0	NSL1	211027535	0.000000	0.05858	0.002000	0.10522	0.953000	0.61014	-0.221000	0.09202	0.263000	0.21812	0.533000	0.62120	AAT	.	.	.	none		0.328	NSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089398.2	NM_015471		C	212960912	T	C	212960912	3	2	248	1	0	0	0	0	1	0	0	0	10680	1493	52	3	652	3	NSL1	1	212960912	Missense_Mutation	SNP	T	TCGA-SX-A7SN-01A-11D-A34Z-10	1209459	212960912	36289709	14	15338											
GRHL1	29841	hgsc.bcm.edu	37	chr2	10140748	10140748	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgaacatggacgacaacatTgtgaagcattactccaatga	15	9	9	8	1	0	3	0	3	0	0	1	5	1	4	1	1	4	1	1	1	5	2			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr2:10140748T>C	ENST00000324907.9	+	16	1906	c.1770T>C	c.(1768-1770)atT>atC	p.I590I	GRHL1_ENST00000324883.5_Silent_p.I401I|GRHL1_ENST00000480736.1_Silent_p.I44I|AC010969.1_ENST00000340444.1_RNA|GRHL1_ENST00000405379.2_Silent_p.I590I	NM_198182.2	NP_937825.2	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1 (Drosophila)	590					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)		ACGACAACATTGTGAAGCATT	0.542																																					p.I590I		Atlas-SNP	.											.	GRHL1	95	.	0			c.T1770C						PASS	.						209	212	211					2																	10140748		2203	4300	6503	SO:0001819	synonymous_variant	29841	exon16			CAACATTGTGAAG	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.1770T>C	chr2.hg19:g.10140748T>C		45.0	0.0	.		52.0	22.0	.	NM_198182	A6NLA4|B2R7E4|B5MEC2|Q53T93|Q6NWN7|Q6NWN8|Q6NWN9|Q8NI33	Silent	SNP	ENST00000324907.9	hg19	CCDS33144.2																																																																																			.	.	.	none		0.542	GRHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323543.2	NM_014552		C	10140748	T	C	10140748	2	2	248	1	0	0	0	0	0	0	0	1	6770	1800	63	3		3	GRHL1	2	10140748	Silent	SNP	T	TCGA-SX-A7SN-01A-11D-A34Z-10		10140748	233058625	15	15339											
NBAS	51594	hgsc.bcm.edu	37	chr2	15415752	15415752	+	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	gggacttgtttaatgagatgAgggtctccagtccagaacaa	12	10	12	7	0	1	3	0	2	1	2	3	5	2	4	2	2	1	1	2	2	3	3			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr2:15415752A>T	ENST00000281513.5	-	44	5605	c.5580T>A	c.(5578-5580)ccT>ccA	p.P1860P	NBAS_ENST00000441750.1_Silent_p.P1740P	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	1860					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)		p.P1860P(1)		NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						TAATGAGATGAGGGTCTCCAG	0.483																																					p.P1860P		Atlas-SNP	.											NBAS,rectum,NS,0,1	NBAS	246	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T5580A						PASS	.						109	107	108					2																	15415752		2203	4300	6503	SO:0001819	synonymous_variant	51594	exon44			GAGATGAGGGTCT	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.5580T>A	chr2.hg19:g.15415752A>T		84.0	1.0	.		93.0	43.0	.	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Silent	SNP	ENST00000281513.5	hg19	CCDS1685.1	.	.	.	.	.	.	.	.	.	.	A	10.35	1.327219	0.24080	.	.	ENSG00000151779	ENST00000442506	.	.	.	5.57	1.78	0.24846	.	.	.	.	.	T	0.53867	0.1823	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44050	-0.9353	4	.	.	.	.	6.1768	0.20449	0.574:0.3101:0.1159:0.0	.	.	.	.	H	908	.	.	L	-	2	0	NBAS	15333203	0.802000	0.28943	1.000000	0.80357	0.972000	0.66771	-0.088000	0.11198	0.457000	0.26962	0.482000	0.46254	CTC	.	.	.	none		0.483	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		T	15415752	A	T	15415752	2	4	248	1	0	0	0	0	0	0	0	1	10193	291	11	5		5	NBAS	2	15415752	Silent	SNP	A	TCGA-SX-A7SN-01A-11D-A34Z-10	5275004	15415752	227783621	16	15340											
SMC6	79677	hgsc.bcm.edu	37	chr2	17881504	17881504	+	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	gtctgctagctccgatagttGattaattttgaatttaattg	10	18	8	5	1	1	2	0	2	1	0	2	3	2	2	1	0	2	3	1	0	5	9			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr2:17881504G>A	ENST00000448223.2	-	21	2634	c.2365C>T	c.(2365-2367)Caa>Taa	p.Q789*	SMC6_ENST00000351948.4_Nonsense_Mutation_p.Q789*|SMC6_ENST00000402989.1_Nonsense_Mutation_p.Q789*|SMC6_ENST00000381272.4_Nonsense_Mutation_p.Q815*	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	789					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TCCGATAGTTGATTAATTTTG	0.303																																					p.Q789X		Atlas-SNP	.											.	SMC6	102	.	0			c.C2365T						PASS	.						144	140	141					2																	17881504		2202	4296	6498	SO:0001587	stop_gained	79677	exon21			ATAGTTGATTAAT	AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"Structural maintenance of chromosomes proteins"	20466	protein-coding gene	gene with protein product		609387	"SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.2365C>T	chr2.hg19:g.17881504G>A	ENSP00000404092:p.Gln789*	279.0	1.0	.		290.0	123.0	.	NM_001142286	A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Nonsense_Mutation	SNP	ENST00000448223.2	hg19	CCDS1690.1	.	.	.	.	.	.	.	.	.	.	G	41	8.532883	0.98852	.	.	ENSG00000163029	ENST00000448223;ENST00000351948;ENST00000381272;ENST00000402989	.	.	.	5.0	5.0	0.66597	.	0.577318	0.18021	N	0.154256	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	11.8172	0.52218	0.0818:0.0:0.9182:0.0	.	.	.	.	X	789;789;815;789	.	ENSP00000323439:Q789X	Q	-	1	0	SMC6	17744985	1.000000	0.71417	0.987000	0.45799	0.865000	0.49528	4.865000	0.62998	2.520000	0.84964	0.585000	0.79938	CAA	.	.	.	none		0.303	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207359.1	NM_024624		A	17881504	G	A	17881504	4	1	248	1	0	0	0	0	0	1	0	0	14800	1299	45	2	942	2	SMC6	2	17881504	Nonsense_Mutation	SNP	G	TCGA-SX-A7SN-01A-11D-A34Z-10	2465752	17881504	225317869	17	15341											
SRBD1	55133	hgsc.bcm.edu	37	chr2	45645662	45645662	+	Missense_Mutation	SNP	A	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	atatttttggccctgttggcAttgagtcctgcaatatgcct	7	16	9	9	0	0	1	0	1	0	0	1	1	1	1	3	2	2	3	3	2	3	6			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr2:45645662A>C	ENST00000263736.4	-	18	2237	c.2175T>G	c.(2173-2175)aaT>aaG	p.N725K	SRBD1_ENST00000490133.1_5'UTR|SRBD1_ENST00000535761.1_Missense_Mutation_p.N244K	NM_018079.4	NP_060549.4	Q8N5C6	SRBD1_HUMAN	S1 RNA binding domain 1	725					nucleobase-containing compound metabolic process (GO:0006139)		hydrolase activity, acting on ester bonds (GO:0016788)|RNA binding (GO:0003723)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(13)|large_intestine(8)|lung(15)|skin(2)|stomach(1)|urinary_tract(1)	49		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)			CCCTGTTGGCATTGAGTCCTG	0.363																																					p.N725K		Atlas-SNP	.											.	SRBD1	107	.	0			c.T2175G						PASS	.						153	110	125					2																	45645662		2203	4300	6503	SO:0001583	missense	55133	exon18			GTTGGCATTGAGT	AK056536	CCDS1823.1	2p21	2008-02-05			ENSG00000068784	ENSG00000068784			25521	protein-coding gene	gene with protein product						12477932	Standard	NM_018079		Approved	FLJ10379	uc002rus.3	Q8N5C6	OTTHUMG00000128814	ENST00000263736.4:c.2175T>G	chr2.hg19:g.45645662A>C	ENSP00000263736:p.Asn725Lys	93.0	0.0	.		140.0	54.0	.	NM_018079	Q53T56|Q96TA4|Q9NW11	Missense_Mutation	SNP	ENST00000263736.4	hg19	CCDS1823.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.073946	0.76415	.	.	ENSG00000068784	ENST00000263736;ENST00000535761	T;T	0.32515	1.78;1.45	5.86	3.53	0.40419	Tex RuvX-like domain (1);	0.000000	0.85682	D	0.000000	T	0.40839	0.1133	L	0.49699	1.58	0.54753	D	0.999984	D	0.54397	0.966	P	0.56865	0.808	T	0.28522	-1.0041	10	0.87932	D	0	.	9.8085	0.40808	0.8618:0.0:0.1382:0.0	.	725	Q8N5C6	SRBD1_HUMAN	K	725;244	ENSP00000263736:N725K;ENSP00000441272:N244K	ENSP00000263736:N725K	N	-	3	2	SRBD1	45499166	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.102000	0.57776	1.061000	0.40601	0.524000	0.50904	AAT	.	.	.	none		0.363	SRBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250747.3	NM_018079		C	45645662	A	C	45645662	3	2	248	1	0	0	0	0	1	0	0	0	15145	214	8	5	828	5	SRBD1	2	45645662	Missense_Mutation	SNP	A	TCGA-SX-A7SN-01A-11D-A34Z-10	27764158	45645662	197553711	18	15342											
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54874386	54874386	+	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	ccgggccctggtggccgacaGccatcctgaaaggtgagcgc	7	5	15	14	3	0	2	0	2	0	0	1	3	1	2	5	4	2	0	5	4	1	0	rs200274009		TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr2:54874386G>C	ENST00000356805.4	+	24	5266	c.4985G>C	c.(4984-4986)aGc>aCc	p.S1662T	SPTBN1_ENST00000333896.5_Missense_Mutation_p.S1649T	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1662	Interaction with ANK2.				actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			GTGGCCGACAGCCATCCTGAA	0.542																																					p.S1662T		Atlas-SNP	.											.	SPTBN1	378	.	0			c.G4985C						PASS	.						77	79	78					2																	54874386		2203	4300	6503	SO:0001583	missense	6711	exon24			CCGACAGCCATCC		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.4985G>C	chr2.hg19:g.54874386G>C	ENSP00000349259:p.Ser1662Thr	23.0	0.0	.		31.0	14.0	.	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	hg19	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	G	15.64	2.893188	0.52121	.	.	ENSG00000115306	ENST00000356805;ENST00000333896	T;T	0.67523	-0.27;0.71	5.66	4.68	0.58851	.	0.333582	0.36167	N	0.002746	T	0.49830	0.1580	N	0.24115	0.695	0.28355	N	0.920718	B;B	0.19935	0.032;0.04	B;B	0.25614	0.062;0.045	T	0.42799	-0.9430	10	0.52906	T	0.07	.	6.8223	0.23864	0.2001:0.0:0.7999:0.0	.	1649;1662	Q01082-3;Q01082	.;SPTB2_HUMAN	T	1662;1649	ENSP00000349259:S1662T;ENSP00000334156:S1649T	ENSP00000334156:S1649T	S	+	2	0	SPTBN1	54727890	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.003000	0.49505	2.689000	0.91719	0.591000	0.81541	AGC	.	G|1.000;A|0.000	.	alt		0.542	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			C	54874386	G	C	54874386	3	2	248	1	0	0	0	0	1	0	0	0	15131	971	34	4	5188	4	SPTBN1	2	54874386	Missense_Mutation	SNP	G	TCGA-SX-A7SN-01A-11D-A34Z-10	9228724	54874386	188324987	19	15343											
SLC9A4	389015	hgsc.bcm.edu	37	chr2	103120119	103120119	+	Frame_Shift_Del	DEL	T	T	-																															atcgtcttcatgttcagctaTttgtcttacttagctgctga																										TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr2:103120119delT	ENST00000295269.4	+	3	1390	c.933delT	c.(931-933)tatfs	p.Y311fs		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	311					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						TGTTCAGCTATTTGTCTTACT	0.393																																					p.Y311fs		Atlas-Indel,Pindel	.											.	SLC9A4	115	.	0			c.932delA						PASS	.						199	186	190					2																	103120119		2203	4300	6503	SO:0001589	frameshift_variant	389015	exon3			.		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.933delT	chr2.hg19:g.103120119delT	ENSP00000295269:p.Tyr311fs	211.0	0.0	0		227.0	68.0	0.299559	NM_001011552	Q69YK0	Frame_Shift_Del	DEL	ENST00000295269.4	hg19	CCDS33264.1																																																																																			.	.	.	none		0.393	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3		-	103120119	T	-	103120119	7	5	248	1	0	1	0	1	0	0	0	0	14729	1500	52	0	943	0	SLC9A4	2	103120119	Frame_Shift_Del	DEL	T	TCGA-SX-A7SN-01A-11D-A34Z-10	48245733	103120119	140079254	20	15344											
FAM128B	80097	hgsc.bcm.edu	37	chr2	130948157	130948157	+	Frame_Shift_Del	DEL	G	G	-																															agcgctaccaggctgcccaaGgggggcgggcctgggaagag																								rs543965632	byFrequency	TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr2:130948157delG	ENST00000281871.6	+	3	790	c.435delG	c.(433-435)aagfs	p.K145fs	MZT2B_ENST00000409255.1_Frame_Shift_Del_p.K205fs	NM_025029.3	NP_079305.2	Q6NZ67	MZT2B_HUMAN	mitotic spindle organizing protein 2B	145						centrosome (GO:0005813)|gamma-tubulin ring complex (GO:0008274)|spindle (GO:0005819)				lung(1)	1						GGCTGCCCAAGGGGGGCGGGC	0.657																																					p.K145fs		Pindel	.											.	MZT2B	5	.	0			c.434delA						PASS	.						35	41	39					2																	130948157		2192	4293	6485	SO:0001589	frameshift_variant	80097	exon3			.	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	ENST00000281871.6:c.435delG	chr2.hg19:g.130948157delG	ENSP00000281871:p.Lys145fs	115.0	0.0	.		132.0	36.0	0.273	NM_025029	Q96CG4	Frame_Shift_Del	DEL	ENST00000281871.6	hg19	CCDS2157.1																																																																																			.	.	.	none		0.657	MZT2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254518.1	NM_025029		-	130948157	G	-	130948157	7	5	248	1	0	1	0	1	0	0	0	0	5439	991	35	0	445	0	FAM128B	2	130948157	Frame_Shift_Del	DEL	G	TCGA-SX-A7SN-01A-11D-A34Z-10	27828038	130948157	112251216	21	15345											
ITGA6	3655	hgsc.bcm.edu	37	chr2	173349951	173349951	+	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	attcacttccagaagttcttCcaattctgaattcagatgaa	13	14	5	9	0	4	4	2	2	2	2	6	4	6	4	2	0	0	1	2	0	4	6			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr2:173349951C>T	ENST00000264106.6	+	14	2133	c.1930C>T	c.(1930-1932)Cca>Tca	p.P644S	ITGA6_ENST00000375221.2_Missense_Mutation_p.P644S|AC093818.1_ENST00000442417.1_RNA|ITGA6_ENST00000409532.1_Missense_Mutation_p.P486S|ITGA6_ENST00000343713.4_Missense_Mutation_p.P600S|ITGA6_ENST00000409080.1_Missense_Mutation_p.P605S|ITGA6_ENST00000264107.7_Missense_Mutation_p.P605S			P23229	ITA6_HUMAN	integrin, alpha 6	644					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)			AGAAGTTCTTCCAATTCTGAA	0.403																																					p.P605S		Atlas-SNP	.											.	ITGA6	171	.	0			c.C1813T						PASS	.						95	96	96					2																	173349951		2203	4300	6503	SO:0001583	missense	3655	exon13			GTTCTTCCAATTC		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.1930C>T	chr2.hg19:g.173349951C>T	ENSP00000264106:p.Pro644Ser	154.0	0.0	.		157.0	68.0	.	NM_000210	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Missense_Mutation	SNP	ENST00000264106.6	hg19		.	.	.	.	.	.	.	.	.	.	C	26.4	4.729408	0.89390	.	.	ENSG00000091409	ENST00000409532;ENST00000264107;ENST00000264106;ENST00000375221;ENST00000343713;ENST00000409080;ENST00000442250;ENST00000458358	T;T;T;T;T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	D	0.90504	0.7025	M	0.89904	3.07	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	0.92409	0.5936	10	0.87932	D	0	.	18.4111	0.90550	0.0:1.0:0.0:0.0	.	600;644;605;605	P23229-4;P23229-9;G5E9H1;P23229-2	.;.;.;.	S	486;605;644;644;600;605;644;600	ENSP00000386614:P486S;ENSP00000264107:P605S;ENSP00000264106:P644S;ENSP00000364369:P644S;ENSP00000341078:P600S;ENSP00000386896:P605S;ENSP00000406694:P644S;ENSP00000394169:P600S	ENSP00000264106:P644S	P	+	1	0	ITGA6	173058197	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.497000	0.73674	2.437000	0.82529	0.655000	0.94253	CCA	.	.	.	none		0.403	ITGA6-201	KNOWN	basic	protein_coding	protein_coding				T	173349951	C	T	173349951	3	4	248	1	0	0	0	0	1	0	0	0	7887	855	30	2	1863	2	ITGA6	2	173349951	Missense_Mutation	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10	42401794	173349951	69849422	22	15346											
NAB1	4664	hgsc.bcm.edu	37	chr2	191524460	191524460	+	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	tcccccgcgtccccaaaggaGagcagtgaggcgctggatgc	8	5	14	14	3	0	2	0	1	0	1	2	4	2	3	4	3	2	2	4	3	1	0			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr2:191524460G>T	ENST00000337386.5	+	4	1019	c.558G>T	c.(556-558)gaG>gaT	p.E186D	NAB1_ENST00000357215.5_Missense_Mutation_p.E186D|NAB1_ENST00000409581.1_Missense_Mutation_p.E186D|NAB1_ENST00000545490.1_5'Flank|NAB1_ENST00000409641.1_Missense_Mutation_p.E186D	NM_005966.3	NP_005957.2	Q13506	NAB1_HUMAN	NGFI-A binding protein 1 (EGR1 binding protein 1)	186					endochondral ossification (GO:0001958)|myelination (GO:0042552)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of epidermis development (GO:0045682)|regulation of transcription, DNA-templated (GO:0006355)|Schwann cell differentiation (GO:0014037)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				kidney(2)|large_intestine(2)|lung(1)|prostate(1)|skin(1)	7			OV - Ovarian serous cystadenocarcinoma(117;0.00318)|Epithelial(96;0.0405)|all cancers(119;0.109)			CCCCAAAGGAGAGCAGTGAGG	0.607																																					p.E186D		Atlas-SNP	.											.	NAB1	31	.	0			c.G558T						PASS	.						32	33	33					2																	191524460		2203	4300	6503	SO:0001583	missense	4664	exon4			AAAGGAGAGCAGT		CCDS2307.1	2q32.3-q33	2008-05-23			ENSG00000138386	ENSG00000138386			7626	protein-coding gene	gene with protein product	"EGR1 binding protein 1"	600800				7624335, 8668170, 9418898	Standard	XM_005246579		Approved		uc002usb.3	Q13506	OTTHUMG00000132689	ENST00000337386.5:c.558G>T	chr2.hg19:g.191524460G>T	ENSP00000336894:p.Glu186Asp	79.0	0.0	.		77.0	33.0	.	NM_005966	O75383|O75384|Q6GTU1|Q9UEV1	Missense_Mutation	SNP	ENST00000337386.5	hg19	CCDS2307.1	.	.	.	.	.	.	.	.	.	.	G	6.327	0.428405	0.11987	.	.	ENSG00000138386	ENST00000409581;ENST00000337386;ENST00000357215;ENST00000409641	.	.	.	5.51	-7.42	0.01388	NAB co-repressor, domain (1);	0.097440	0.64402	N	0.000001	T	0.12603	0.0306	N	0.01800	-0.715	0.80722	D	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.10450	0.004;0.005;0.005	T	0.20706	-1.0267	9	0.12766	T	0.61	-13.235	6.2518	0.20850	0.2258:0.0931:0.4985:0.1826	.	186;186;186	F8W8J7;B8ZZS2;Q13506	.;.;NAB1_HUMAN	D	186	.	ENSP00000336894:E186D	E	+	3	2	NAB1	191232705	0.012000	0.17670	0.740000	0.30986	0.983000	0.72400	-0.752000	0.04797	-1.363000	0.02164	-0.367000	0.07326	GAG	.	.	.	none		0.607	NAB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255986.1	NM_005966		T	191524460	G	T	191524460	3	4	248	1	0	0	0	0	1	0	0	0	10138	933	33	4	560	4	NAB1	2	191524460	Missense_Mutation	SNP	G	TCGA-SX-A7SN-01A-11D-A34Z-10	18174509	191524460	51674913	23	15347											
TMBIM1	64114	hgsc.bcm.edu	37	chr2	219140208	219140208	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcttgctccttaattgcgaTcccccatcagctgcagcaca	8	10	8	15	1	1	0	1	0	0	0	3	1	3	0	3	1	5	5	3	1	1	3			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr2:219140208T>C	ENST00000444881.1	-	13	1651	c.926A>G	c.(925-927)gAt>gGt	p.D309G	PNKD_ENST00000273077.4_Intron|TMBIM1_ENST00000396809.2_Missense_Mutation_p.D309G|TMBIM1_ENST00000445635.1_Missense_Mutation_p.D135G|PNKD_ENST00000472650.1_Intron|TMBIM1_ENST00000258412.3_Missense_Mutation_p.D309G			Q969X1	LFG3_HUMAN	transmembrane BAX inhibitor motif containing 1	309					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of Fas signaling pathway (GO:1902045)|negative regulation of metalloenzyme activity (GO:0048553)|positive regulation of blood vessel remodeling (GO:2000504)	endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	death receptor binding (GO:0005123)			NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(2)	9		Renal(207;0.0474)		Epithelial(149;8.56e-07)|all cancers(144;0.000154)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TTAATTGCGATCCCCCATCAG	0.567																																					p.D309G		Atlas-SNP	.											.	TMBIM1	20	.	0			c.A926G						PASS	.						141	127	132					2																	219140208		2203	4300	6503	SO:0001583	missense	64114	exon12			TTGCGATCCCCCA	BN000408	CCDS2412.1	2q35	2010-03-18			ENSG00000135926	ENSG00000135926			23410	protein-coding gene	gene with protein product		610364				12477932	Standard	NM_022152		Approved	PP1201, RECS1, LFG3	uc002vhp.1	Q969X1	OTTHUMG00000133105	ENST00000444881.1:c.926A>G	chr2.hg19:g.219140208T>C	ENSP00000409738:p.Asp309Gly	25.0	0.0	.		36.0	14.0	.	NM_022152	B3KQY6|Q8N1R3|Q8TAM3|Q96K13	Missense_Mutation	SNP	ENST00000444881.1	hg19	CCDS2412.1	.	.	.	.	.	.	.	.	.	.	T	13.44	2.238335	0.39598	.	.	ENSG00000135926	ENST00000258412;ENST00000444881;ENST00000396809;ENST00000445635;ENST00000543441	T;T;T	0.22945	1.93;1.93;1.93	5.28	-0.281	0.12882	.	1.212450	0.05241	N	0.512237	T	0.12603	0.0306	N	0.04787	-0.16	0.09310	N	1	B;B	0.17465	0.022;0.001	B;B	0.14023	0.01;0.001	T	0.29427	-1.0012	10	0.33141	T	0.24	-0.4623	6.4147	0.21710	0.0:0.4821:0.1591:0.3587	.	247;309	B4DNZ1;Q969X1	.;TMBI1_HUMAN	G	309;309;309;135;247	ENSP00000258412:D309G;ENSP00000409738:D309G;ENSP00000380025:D309G	ENSP00000258412:D309G	D	-	2	0	TMBIM1	218848452	0.000000	0.05858	0.003000	0.11579	0.968000	0.65278	-0.049000	0.11924	-0.168000	0.10853	0.533000	0.62120	GAT	.	.	.	none		0.567	TMBIM1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338559.1	NM_022152		C	219140208	T	C	219140208	3	2	248	1	0	0	0	0	1	0	0	0	15993	1435	50	3	13	3	TMBIM1	2	219140208	Missense_Mutation	SNP	T	TCGA-SX-A7SN-01A-11D-A34Z-10	27615748	219140208	24059165	24	15348											
TRIP12	9320	hgsc.bcm.edu	37	chr2	230659907	230659907	+	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	gtccttacctgcctcctgtcCcatttccactagggaaatca	8	12	6	15	0	1	0	1	0	0	0	5	1	5	1	6	1	2	0	6	1	3	3			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr2:230659907C>T	ENST00000283943.5	-	25	3909	c.3731G>A	c.(3730-3732)gGg>gAg	p.G1244E	TRIP12_ENST00000389044.4_Missense_Mutation_p.G1292E|TRIP12_ENST00000389045.3_Missense_Mutation_p.G974E	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1244					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		GCCTCCTGTCCCATTTCCACT	0.448																																					p.G1244E		Atlas-SNP	.											.	TRIP12	207	.	0			c.G3731A						PASS	.						126	113	118					2																	230659907		2203	4300	6503	SO:0001583	missense	9320	exon25			CCTGTCCCATTTC	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.3731G>A	chr2.hg19:g.230659907C>T	ENSP00000283943:p.Gly1244Glu	71.0	0.0	.		55.0	16.0	.	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Missense_Mutation	SNP	ENST00000283943.5	hg19	CCDS33391.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.034386	0.93575	.	.	ENSG00000153827	ENST00000283943;ENST00000389045;ENST00000389044	T;T;T	0.50277	0.76;1.12;0.75	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.67144	0.2862	L	0.54323	1.7	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.963;0.996	T	0.67356	-0.5691	10	0.72032	D	0.01	.	19.9433	0.97172	0.0:1.0:0.0:0.0	.	974;1292;1244	Q14CF1;Q14CA3;Q14669	.;.;TRIPC_HUMAN	E	1244;974;1292	ENSP00000283943:G1244E;ENSP00000373697:G974E;ENSP00000373696:G1292E	ENSP00000283943:G1244E	G	-	2	0	TRIP12	230368151	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.365000	0.79537	2.716000	0.92895	0.655000	0.94253	GGG	.	.	.	none		0.448	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		T	230659907	C	T	230659907	3	4	248	1	0	0	0	0	1	0	0	0	16568	623	22	2	2315	2	TRIP12	2	230659907	Missense_Mutation	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10	11519699	230659907	12539466	25	15349											
KLHL30	377007	hgsc.bcm.edu	37	chr2	239057702	239057702	+	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	caagtacctgtcctcgcctcGctgtgctgcactgcacgggg	5	9	12	15	3	0	0	0	0	0	0	3	0	1	0	3	2	4	5	3	2	2	1			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr2:239057702G>C	ENST00000409223.1	+	7	1501	c.1394G>C	c.(1393-1395)cGc>cCc	p.R465P	KLHL30_ENST00000305959.4_Missense_Mutation_p.R447P			Q0D2K2	KLH30_HUMAN	kelch-like family member 30	465										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)		TCCTCGCCTCGCTGTGCTGCA	0.652																																					p.R465P		Atlas-SNP	.											KLHL30_ENST00000409223,right_upper_lobe,carcinoma,0,2	KLHL30	79	.	0			c.G1394C						PASS	.						74	89	84					2																	239057702		2165	4251	6416	SO:0001583	missense	377007	exon7			CGCCTCGCTGTGC		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.1394G>C	chr2.hg19:g.239057702G>C	ENSP00000386389:p.Arg465Pro	15.0	0.0	.		29.0	13.0	.	NM_198582	Q6ZUS1	Missense_Mutation	SNP	ENST00000409223.1	hg19	CCDS46555.2	.	.	.	.	.	.	.	.	.	.	G	17.74	3.464502	0.63513	.	.	ENSG00000168427	ENST00000409223;ENST00000305959	T;T	0.65549	-0.16;-0.16	4.49	4.49	0.54785	Kelch-type beta propeller (1);	0.059738	0.64402	D	0.000002	T	0.70307	0.3209	L	0.38531	1.155	0.54753	D	0.999985	D	0.76494	0.999	D	0.68353	0.957	T	0.73861	-0.3849	10	0.66056	D	0.02	.	16.0887	0.81076	0.0:0.0:1.0:0.0	.	465	Q0D2K2	KLH30_HUMAN	P	465;447	ENSP00000386389:R465P;ENSP00000302386:R447P	ENSP00000302386:R447P	R	+	2	0	KLHL30	238722441	1.000000	0.71417	0.988000	0.46212	0.189000	0.23516	9.102000	0.94226	2.327000	0.79052	0.491000	0.48974	CGC	.	.	.	none		0.652	KLHL30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328518.1	NM_198582		C	239057702	G	C	239057702	3	2	248	1	0	0	0	0	1	0	0	0	8391	1087	38	4	1416	4	KLHL30	2	239057702	Missense_Mutation	SNP	G	TCGA-SX-A7SN-01A-11D-A34Z-10	8397795	239057702	4141671	26	15350											
XYLB	9942	hgsc.bcm.edu	37	chr3	38408332	38408332	+	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	accaaattgcaaaaatttacCagcagaaccccgaggcctac	16	6	6	13	1	0	1	0	0	0	1	0	2	0	1	5	1	5	2	5	1	6	4			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr3:38408332C>A	ENST00000207870.3	+	7	631	c.541C>A	c.(541-543)Cag>Aag	p.Q181K	XYLB_ENST00000542835.1_Missense_Mutation_p.Q44K	NM_005108.3	NP_005099.2	O75191	XYLB_HUMAN	xylulokinase homolog (H. influenzae)	181					carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|D-xylose metabolic process (GO:0042732)|generation of precursor metabolites and energy (GO:0006091)|xylulose catabolic process (GO:0005998)|xylulose metabolic process (GO:0005997)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|xylulokinase activity (GO:0004856)			endometrium(3)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(1)|prostate(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.00372)|Kidney(284;0.00405)		AAAAATTTACCAGCAGAACCC	0.368																																					p.Q181K		Atlas-SNP	.											.	XYLB	50	.	0			c.C541A						PASS	.						85	86	86					3																	38408332		2203	4300	6503	SO:0001583	missense	9942	exon7			ATTTACCAGCAGA	AB015046	CCDS2678.1	3p22-p21.3	2006-12-18	2001-12-04		ENSG00000093217	ENSG00000093217			12839	protein-coding gene	gene with protein product		604049	"xylulokinase (H. influenzae) homolog"			9763671	Standard	NM_005108		Approved	FLJ10343, FLJ12539	uc003cic.2	O75191	OTTHUMG00000131294	ENST00000207870.3:c.541C>A	chr3.hg19:g.38408332C>A	ENSP00000207870:p.Gln181Lys	32.0	0.0	.		61.0	22.0	.	NM_005108	B2RAW4|B4DDT2|B9EH64	Missense_Mutation	SNP	ENST00000207870.3	hg19	CCDS2678.1	.	.	.	.	.	.	.	.	.	.	c	14.24	2.475111	0.43942	.	.	ENSG00000093217	ENST00000207870;ENST00000542835	T;T	0.16073	2.37;2.37	5.43	4.44	0.53790	Carbohydrate kinase, FGGY, N-terminal (1);	0.472911	0.23189	N	0.050929	T	0.11537	0.0281	N	0.21194	0.64	0.25694	N	0.98565	B;B	0.14012	0.009;0.0	B;B	0.21151	0.033;0.02	T	0.19516	-1.0303	10	0.15066	T	0.55	.	12.751	0.57308	0.1976:0.8024:0.0:0.0	.	44;181	B4DDT2;O75191	.;XYLB_HUMAN	K	181;44	ENSP00000207870:Q181K;ENSP00000443659:Q44K	ENSP00000207870:Q181K	Q	+	1	0	XYLB	38383336	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.763000	0.38461	2.727000	0.93392	0.550000	0.68814	CAG	.	.	.	none		0.368	XYLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254062.2	NM_005108		A	38408332	C	A	38408332	3	1	248	1	0	0	0	0	1	0	0	0	17474	595	21	4	567	4	XYLB	3	38408332	Missense_Mutation	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10		38408332	159614098	27	15351											
QRICH1	54870	hgsc.bcm.edu	37	chr3	49114324	49114324	+	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	ggctgtctgctggaactcctGaagggcttctggccccttag	5	11	13	12	0	2	1	0	1	2	0	3	2	3	2	3	4	2	3	3	4	3	2			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr3:49114324G>A	ENST00000395443.2	-	2	599	c.127C>T	c.(127-129)Cag>Tag	p.Q43*	QRICH1_ENST00000424300.1_Nonsense_Mutation_p.Q43*|QRICH1_ENST00000357496.2_Nonsense_Mutation_p.Q43*	NM_198880.1	NP_942581.1	Q2TAL8	QRIC1_HUMAN	glutamine-rich 1	43	CARD.					nucleus (GO:0005634)				breast(2)|endometrium(5)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(193;8.88e-05)|Kidney(197;0.00239)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		TGGAACTCCTGAAGGGCTTCT	0.527																																					p.Q43X		Atlas-SNP	.											.	QRICH1	48	.	0			c.C127T						PASS	.						124	115	118					3																	49114324		2203	4300	6503	SO:0001587	stop_gained	54870	exon2			ACTCCTGAAGGGC		CCDS2787.1	3p21.31	2011-06-03			ENSG00000198218	ENSG00000198218			24713	protein-coding gene	gene with protein product						12477932	Standard	NM_017730		Approved	FLJ20259	uc003cvv.3	Q2TAL8	OTTHUMG00000156772	ENST00000395443.2:c.127C>T	chr3.hg19:g.49114324G>A	ENSP00000378830:p.Gln43*	75.0	0.0	.		87.0	34.0	.	NM_198880	Q4G0F7|Q7L621|Q8TEA5	Nonsense_Mutation	SNP	ENST00000395443.2	hg19	CCDS2787.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.708717	0.68615	.	.	ENSG00000198218	ENST00000395443;ENST00000357496;ENST00000424300;ENST00000437939;ENST00000450685;ENST00000411682;ENST00000430979	.	.	.	5.62	5.62	0.85841	.	0.055405	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-2.293	19.653	0.95825	0.0:0.0:1.0:0.0	.	.	.	.	X	43	.	ENSP00000350094:Q43X	Q	-	1	0	QRICH1	49089328	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.476000	0.97823	2.658000	0.90341	0.655000	0.94253	CAG	.	.	.	none		0.527	QRICH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345669.1	NM_017730		A	49114324	G	A	49114324	4	1	248	1	0	0	0	0	0	1	0	0	12892	1299	45	2	2239	2	QRICH1	3	49114324	Nonsense_Mutation	SNP	G	TCGA-SX-A7SN-01A-11D-A34Z-10	10705992	49114324	148908106	28	15352											
CHST13	166012	hgsc.bcm.edu	37	chr3	126260730	126260730	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcctgctctactgctacgTgcccaaggtggcctgcacca	6	9	11	15	1	1	0	0	0	1	0	1	0	1	0	4	3	6	3	4	3	3	2			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr3:126260730T>C	ENST00000319340.2	+	3	385	c.335T>C	c.(334-336)gTg>gCg	p.V112A		NM_152889.2	NP_690849.1	Q8NET6	CHSTD_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 13	112					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)		TACTGCTACGTGCCCAAGGTG	0.721																																					p.V112A		Atlas-SNP	.											.	CHST13	21	.	0			c.T335C						PASS	.						28	20	22					3																	126260730		2194	4286	6480	SO:0001583	missense	166012	exon3			GCTACGTGCCCAA	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.335T>C	chr3.hg19:g.126260730T>C	ENSP00000317404:p.Val112Ala	108.0	0.0	.		67.0	22.0	.	NM_152889	Q3SYA3|Q3SYA5	Missense_Mutation	SNP	ENST00000319340.2	hg19	CCDS3039.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.770907	0.90108	.	.	ENSG00000180767	ENST00000319340;ENST00000383575	D	0.82344	-1.6	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	D	0.92635	0.7660	M	0.93854	3.465	0.80722	D	1	D	0.71674	0.998	D	0.76575	0.988	D	0.93994	0.7269	10	0.72032	D	0.01	-9.0677	12.3582	0.55188	0.0:0.0:0.0:1.0	.	112	Q8NET6	CHSTD_HUMAN	A	112	ENSP00000317404:V112A	ENSP00000317404:V112A	V	+	2	0	CHST13	127743420	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.670000	0.83925	1.806000	0.52798	0.402000	0.26972	GTG	.	.	.	none		0.721	CHST13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370201.2	NM_152889		C	126260730	T	C	126260730	3	2	248	1	0	0	0	0	1	0	0	0	3403	1696	59	3	345	3	CHST13	3	126260730	Missense_Mutation	SNP	T	TCGA-SX-A7SN-01A-11D-A34Z-10	77146406	126260730	71761700	29	15353											
WDFY3	23001	hgsc.bcm.edu	37	chr4	85758174	85758174	+	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	ctcaggcacatgtggaaggtCaaaaaacagatataaacatt	18	8	8	7	0	2	1	2	0	0	1	2	2	2	2	0	3	2	1	0	3	7	3			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr4:85758174C>G	ENST00000295888.4	-	7	891	c.484G>C	c.(484-486)Gac>Cac	p.D162H	WDFY3_ENST00000322366.6_Missense_Mutation_p.D162H	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	162					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)		TGTGGAAGGTCAAAAAACAGA	0.428																																					p.D162H		Atlas-SNP	.											.	WDFY3	314	.	0			c.G484C						PASS	.						87	78	81					4																	85758174		2203	4300	6503	SO:0001583	missense	23001	exon7			GAAGGTCAAAAAA	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.484G>C	chr4.hg19:g.85758174C>G	ENSP00000295888:p.Asp162His	213.0	0.0	.		239.0	88.0	.	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	hg19	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.579583	0.86645	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.27104	1.69;1.69	5.76	4.91	0.64330	.	0.193997	0.52532	D	0.000064	T	0.53465	0.1798	M	0.78637	2.42	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.60500	-0.7251	10	0.87932	D	0	.	16.1206	0.81351	0.1349:0.8651:0.0:0.0	.	162;162	E2QRK8;Q8IZQ1	.;WDFY3_HUMAN	H	162	ENSP00000318466:D162H;ENSP00000295888:D162H	ENSP00000295888:D162H	D	-	1	0	WDFY3	85977198	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.666000	0.83877	1.406000	0.46857	0.455000	0.32223	GAC	.	.	.	none		0.428	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		G	85758174	C	G	85758174	3	3	248	1	0	0	0	0	1	0	0	0	17282	826	29	4	10387	4	WDFY3	4	85758174	Missense_Mutation	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10		85758174	105396102	30	15354											
FHDC1	85462	hgsc.bcm.edu	37	chr4	153897841	153897841	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaggactccagtcggaccaCgctggggagaatcctcaatc	11	6	12	12	2	1	1	1	0	0	1	5	5	3	3	3	4	0	1	3	4	3	0			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr4:153897841C>T	ENST00000511601.1	+	12	3586	c.3398C>T	c.(3397-3399)aCg>aTg	p.T1133M	FHDC1_ENST00000260008.3_Missense_Mutation_p.T1133M			Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	1133									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)					AGTCGGACCACGCTGGGGAGA	0.627																																					p.T1133M		Atlas-SNP	.											.	FHDC1	102	.	0			c.C3398T						PASS	.						15	13	13					4																	153897841		2191	4282	6473	SO:0001583	missense	85462	exon11			GGACCACGCTGGG	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.3398C>T	chr4.hg19:g.153897841C>T	ENSP00000427567:p.Thr1133Met	39.0	0.0	.		38.0	14.0	.	NM_033393		Missense_Mutation	SNP	ENST00000511601.1	hg19	CCDS34081.1	.	.	.	.	.	.	.	.	.	.	C	19.21	3.784330	0.70222	.	.	ENSG00000137460	ENST00000511601;ENST00000260008	T;T	0.41758	0.99;0.99	5.39	5.39	0.77823	.	0.362675	0.26727	N	0.022801	T	0.49389	0.1554	L	0.29908	0.895	0.09310	N	0.999998	D	0.76494	0.999	P	0.56088	0.791	T	0.48055	-0.9068	10	0.87932	D	0	.	19.1456	0.93467	0.0:1.0:0.0:0.0	.	1133	Q9C0D6	FHDC1_HUMAN	M	1133	ENSP00000427567:T1133M;ENSP00000260008:T1133M	ENSP00000260008:T1133M	T	+	2	0	FHDC1	154117291	0.102000	0.21896	0.005000	0.12908	0.004000	0.04260	4.146000	0.58072	2.534000	0.85438	0.655000	0.94253	ACG	.	.	.	none		0.627	FHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364981.2	NM_033393		T	153897841	C	T	153897841	3	4	248	1	0	0	0	0	1	0	0	0	5883	536	19	1	3440	1	FHDC1	4	153897841	Missense_Mutation	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10	68139667	153897841	37256435	31	15355											
IQGAP2	10788	hgsc.bcm.edu	37	chr5	75970433	75970433	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaacttaggatcagtggcCaaggttcttcagcacgcagc	12	8	11	10	1	3	1	2	0	1	1	3	2	3	2	1	3	3	3	1	3	3	3			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr5:75970433C>T	ENST00000274364.6	+	27	3723	c.3426C>T	c.(3424-3426)gcC>gcT	p.A1142A	IQGAP2_ENST00000502745.1_Silent_p.A638A|IQGAP2_ENST00000379730.3_Silent_p.A644A|IQGAP2_ENST00000396234.3_Silent_p.A638A	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	1142	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		GATCAGTGGCCAAGGTTCTTC	0.428																																					p.A1142A		Atlas-SNP	.											.	IQGAP2	186	.	0			c.C3426T						PASS	.						95	89	91					5																	75970433		2203	4300	6503	SO:0001819	synonymous_variant	10788	exon27			AGTGGCCAAGGTT	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.3426C>T	chr5.hg19:g.75970433C>T		78.0	0.0	.		99.0	37.0	.	NM_006633	A8K4V1|B7Z8A4|J3KR91	Silent	SNP	ENST00000274364.6	hg19	CCDS34188.1																																																																																			.	.	.	none		0.428	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633		T	75970433	C	T	75970433	2	4	248	1	0	0	0	0	0	0	0	1	7822	581	21	2		2	IQGAP2	5	75970433	Silent	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10		75970433	104944827	32	15356											
FEM1C	56929	hgsc.bcm.edu	37	chr5	114860103	114860103	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acgagcagcaagacactgcaAtgtggtatgatttataggct	13	10	11	7	1	0	2	0	1	0	1	0	3	0	2	0	2	3	5	0	2	5	4			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr5:114860103A>G	ENST00000274457.3	-	3	2317	c.1756T>C	c.(1756-1758)Ttg>Ctg	p.L586L		NM_020177.2	NP_064562.1	Q96JP0	FEM1C_HUMAN	fem-1 homolog c (C. elegans)	586					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(5)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	18		all_cancers(142;0.000575)|all_epithelial(76;9.98e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;2.5e-07)|Epithelial(69;2.66e-07)|all cancers(49;1.39e-05)		AGACACTGCAATGTGGTATGA	0.363																																					p.L586L		Atlas-SNP	.											.	FEM1C	50	.	0			c.T1756C						PASS	.						98	100	99					5																	114860103		2202	4300	6502	SO:0001819	synonymous_variant	56929	exon3			ACTGCAATGTGGT		CCDS4118.1	5q22	2013-01-10	2006-11-08		ENSG00000145780	ENSG00000145780		"Ankyrin repeat domain containing"	16933	protein-coding gene	gene with protein product		608767				14527725, 11733146	Standard	NM_020177		Approved	KIAA1785, EUROIMAGE686608, EUROIMAGE783647, FEM1A	uc003krb.1	Q96JP0	OTTHUMG00000128895	ENST00000274457.3:c.1756T>C	chr5.hg19:g.114860103A>G		102.0	0.0	.		147.0	57.0	.	NM_020177	B2RE47|Q8N3V8|Q9H704|Q9NPL6|Q9NPL9	Silent	SNP	ENST00000274457.3	hg19	CCDS4118.1																																																																																			.	.	.	none		0.363	FEM1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250857.3	NM_020177		G	114860103	A	G	114860103	2	3	248	1	0	0	0	0	0	0	0	1	5818	98	4	3		3	FEM1C	5	114860103	Silent	SNP	A	TCGA-SX-A7SN-01A-11D-A34Z-10	38889670	114860103	66055157	33	15357											
PCDHA13	56136	hgsc.bcm.edu	37	chr5	140263609	140263609	+	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	agctgatgccgcggtcggtgGgtgcaggccacgtggtggcg	4	7	20	10	5	0	1	0	1	0	0	1	1	0	1	2	6	3	2	2	6	0	0			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr5:140263609G>T	ENST00000289272.2	+	1	1756	c.1756G>T	c.(1756-1758)Ggt>Tgt	p.G586C	PCDHA6_ENST00000527624.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA13_ENST00000409494.1_Missense_Mutation_p.G586C|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA9_ENST00000532602.1_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	586	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			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)			GCGGTCGGTGGGTGCAGGCCA	0.697																																					p.G586C	Melanoma(147;1739 1852 5500 27947 37288)	Atlas-SNP	.											PCDHA13,NS,carcinoma,0,1	PCDHA13	213	.	0			c.G1756T						PASS	.						57	63	61					5																	140263609		2202	4298	6500	SO:0001583	missense	56136	exon1			TCGGTGGGTGCAG	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.1756G>T	chr5.hg19:g.140263609G>T	ENSP00000289272:p.Gly586Cys	54.0	0.0	.		59.0	20.0	.	NM_031865	O75277	Missense_Mutation	SNP	ENST00000289272.2	hg19	CCDS4240.1	.	.	.	.	.	.	.	.	.	.	G	11.44	1.640074	0.29157	.	.	ENSG00000239389	ENST00000409494;ENST00000289272	T;T	0.20463	2.07;2.07	4.21	4.21	0.49690	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.47229	0.1434	M	0.89414	3.03	0.22947	N	0.998528	D;D;D	0.71674	0.998;0.995;0.994	P;D;D	0.71870	0.886;0.944;0.975	T	0.43245	-0.9403	9	0.72032	D	0.01	.	5.8955	0.18937	0.1033:0.1979:0.6988:0.0	.	586;586;586	Q9Y5I0;C9JA99;Q9Y5I0-2	PCDAD_HUMAN;.;.	C	586	ENSP00000386821:G586C;ENSP00000289272:G586C	ENSP00000289272:G586C	G	+	1	0	PCDHA13	140243793	0.000000	0.05858	0.457000	0.27056	0.048000	0.14542	0.017000	0.13399	2.144000	0.66660	0.655000	0.94253	GGT	.	.	.	none		0.697	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		T	140263609	G	T	140263609	3	4	248	1	0	0	0	0	1	0	0	0	11530	1232	43	4	1758	4	PCDHA13	5	140263609	Missense_Mutation	SNP	G	TCGA-SX-A7SN-01A-11D-A34Z-10	25403506	140263609	40651651	34	15358											
HNRNPAB	85007	hgsc.bcm.edu	37	chr5	177632987	177632988	+	IGR	INS	-	-	A																															ggtttgggtttatcctgttcINSaaagatgcagccagtgtgga																										TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr5:177632987_177632988insA	ENST00000308158.5	-	0	2038				HNRNPAB_ENST00000515193.1_Frame_Shift_Ins_p.K119fs|HNRNPAB_ENST00000504898.1_Frame_Shift_Ins_p.K119fs|HNRNPAB_ENST00000506339.1_Frame_Shift_Ins_p.K119fs|PHYKPL_ENST00000481811.1_5'Flank|HNRNPAB_ENST00000355836.5_Frame_Shift_Ins_p.K119fs|HNRNPAB_ENST00000514633.1_Frame_Shift_Ins_p.K119fs|HNRNPAB_ENST00000506259.1_Frame_Shift_Ins_p.K119fs|HNRNPAB_ENST00000358344.3_Frame_Shift_Ins_p.K119fs	NM_153373.2	NP_699204.1	Q8IUZ5	AT2L2_HUMAN	5-phosphohydroxy-L-lysine phospho-lyase							mitochondrion (GO:0005739)	lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)									L-Alanine(DB00160)	TTATCCTGTTCAAAGATGCAGC	0.406																																					p.F118fs		Atlas-Indel,Pindel	.											.	HNRNPAB	24	.	0			c.354_355insA						PASS	.																																			SO:0001628	intergenic_variant	3182	exon3			.	BC037567	CCDS4434.1	5q35.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000175309	ENSG00000175309	4.2.3.134		28249	protein-coding gene	gene with protein product	"5-phosphonooxy-L-lysine phospho-lyase"	614683	"alanine-glyoxylate aminotransferase 2-like 2"	AGXT2L2		22241472	Standard	NM_153373		Approved	MGC15875	uc003miz.3	Q8IUZ5	OTTHUMG00000130892		chr5.hg19:g.177632990_177632990dupA		124.0	0.0	0		124.0	54.0	0.435484	NM_004499	A8K7P6|B3KN36|D3DWP9|Q8WYS6|Q96HW8	Frame_Shift_Ins	INS	ENST00000308158.5	hg19	CCDS4434.1																																																																																			.	.	.	none		0.406	PHYKPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253477.1	NM_032921		A	177632988	-	A	177632987	6	5	248	0	1	1	1	0	0	0	0	0	7268	825	29	0		0	HNRNPAB	5	177632987	IGR	INS	-	TCGA-SX-A7SN-01A-11D-A34Z-10	37369378	177632987	3282273	35	15359											
CLK4	57396	hgsc.bcm.edu	37	chr5	178045754	178045754	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcccgataatctcgctcatTcaaggaccttgcttctaaat	10	13	6	12	2	4	0	2	0	2	0	6	2	5	1	2	1	1	2	2	1	4	5			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr5:178045754T>C	ENST00000316308.4	-	3	355	c.187A>G	c.(187-189)Aat>Gat	p.N63D	RN7SKP70_ENST00000516655.1_RNA|CLK4_ENST00000522749.1_5'UTR	NM_020666.2	NP_065717.1	Q9HAZ1	CLK4_HUMAN	CDC-like kinase 4	63					protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(2)	21	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.235)		TCTCGCTCATTCAAGGACCTT	0.368																																					p.N63D		Atlas-SNP	.											.	CLK4	103	.	0			c.A187G						PASS	.						102	95	97					5																	178045754		2203	4300	6503	SO:0001583	missense	57396	exon3			GCTCATTCAAGGA	AF294429	CCDS4437.1	5q35	2008-05-02			ENSG00000113240	ENSG00000113240		"CDC-like kinases"	13659	protein-coding gene	gene with protein product		607969				11170754	Standard	NM_020666		Approved		uc003mjf.1	Q9HAZ1	OTTHUMG00000130893	ENST00000316308.4:c.187A>G	chr5.hg19:g.178045754T>C	ENSP00000316948:p.Asn63Asp	67.0	0.0	.		65.0	26.0	.	NM_020666		Missense_Mutation	SNP	ENST00000316308.4	hg19	CCDS4437.1	.	.	.	.	.	.	.	.	.	.	T	15.38	2.817846	0.50633	.	.	ENSG00000113240	ENST00000316308;ENST00000536763	T	0.08008	3.14	5.87	4.67	0.58626	.	0.200770	0.51477	D	0.000085	T	0.21761	0.0524	M	0.75447	2.3	0.80722	D	1	P;D;P;D;D	0.69078	0.718;0.997;0.879;0.997;0.997	B;D;P;D;D	0.73380	0.107;0.98;0.482;0.98;0.98	T	0.13019	-1.0525	10	0.18710	T	0.47	.	6.6902	0.23167	0.153:0.0:0.1597:0.6873	.	63;63;63;63;63	B7Z990;B7ZL31;Q4G0Z5;B9EG64;Q9HAZ1	.;.;.;.;CLK4_HUMAN	D	63	ENSP00000316948:N63D	ENSP00000316948:N63D	N	-	1	0	CLK4	177978360	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	2.188000	0.42612	0.996000	0.38943	0.482000	0.46254	AAT	.	.	.	none		0.368	CLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253479.2			C	178045754	T	C	178045754	3	2	248	1	0	0	0	0	1	0	0	0	3541	1783	62	3	1302	3	CLK4	5	178045754	Missense_Mutation	SNP	T	TCGA-SX-A7SN-01A-11D-A34Z-10	412767	178045754	2869506	36	15360											
VPS52	6293	hgsc.bcm.edu	37	chr6	33231610	33231610	+	Frame_Shift_Del	DEL	G	G	-																															acacaagctgctccttccttGaggagaactcagctgccact																										TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr6:33231610delG	ENST00000445902.2	-	16	1885	c.1667delC	c.(1666-1668)tcafs	p.S556fs	VPS52_ENST00000436044.2_Frame_Shift_Del_p.S431fs|VPS52_ENST00000478934.1_5'UTR|VPS52_ENST00000482399.1_3'UTR	NM_022553.4	NP_072047.4	Q8N1B4	VPS52_HUMAN	vacuolar protein sorting 52 homolog (S. cerevisiae)	556					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						CTCCTTCCTTGAGGAGAACTC	0.512																																					p.S556fs		Atlas-Indel,Pindel	.											.	VPS52	56	.	0			c.1668delA						PASS	.						75	65	68					6																	33231610		2203	4300	6503	SO:0001589	frameshift_variant	6293	exon16			.	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.1667delC	chr6.hg19:g.33231610delG	ENSP00000409952:p.Ser556fs	55.0	0.0	0		70.0	22.0	0.314286	NM_022553	A2BF38|B0UZZ4|B4DNI9|Q53GR4|Q5JPA0|Q5SQW1|Q8IUN6|Q9NPT5	Frame_Shift_Del	DEL	ENST00000445902.2	hg19	CCDS4770.2																																																																																			.	.	.	none		0.512	VPS52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076598.2	NM_022553		-	33231610	G	-	33231610	7	5	248	1	0	1	0	1	0	0	0	0	17226	1294	45	0	524	0	VPS52	6	33231610	Frame_Shift_Del	DEL	G	TCGA-SX-A7SN-01A-11D-A34Z-10		33231610	137883457	37	15361											
SLC22A7	10864	hgsc.bcm.edu	37	chr6	43269967	43269967	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaacttctcctattacggccTgagtctggatgtgtcggggc	6	12	13	10	2	2	1	0	1	2	0	4	3	2	2	2	4	2	0	2	4	3	3			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr6:43269967T>C	ENST00000372585.5	+	8	1186	c.1091T>C	c.(1090-1092)cTg>cCg	p.L364P	SLC22A7_ENST00000372574.3_Missense_Mutation_p.L362P|SLC22A7_ENST00000372589.3_Missense_Mutation_p.L362P	NM_153320.2	NP_696961.2	Q9Y694	S22A7_HUMAN	solute carrier family 22 (organic anion transporter), member 7	364					organic anion transport (GO:0015711)|response to stilbenoid (GO:0035634)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			NS(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(3)	26			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)		Acetylsalicylic acid(DB00945)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Cimetidine(DB00501)|Clarithromycin(DB01211)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Docetaxel(DB01248)|Enalapril(DB00584)|Erythromycin(DB00199)|Fluorouracil(DB00544)|Ganciclovir(DB01004)|Glyburide(DB01016)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Oxtriphylline(DB01303)|Oxytetracycline(DB00595)|Pravastatin(DB00175)|Probenecid(DB01032)|Rifampicin(DB01045)|Salicylic acid(DB00936)|Testosterone(DB00624)|Tetracycline(DB00759)|Theophylline(DB00277)|Valproic Acid(DB00313)|Zalcitabine(DB00943)|Zidovudine(DB00495)	TATTACGGCCTGAGTCTGGAT	0.572																																					p.L364P		Atlas-SNP	.											.	SLC22A7	69	.	0			c.T1091C						PASS	.						125	115	118					6																	43269967		2203	4300	6503	SO:0001583	missense	10864	exon7			ACGGCCTGAGTCT	AF097518	CCDS4892.1, CCDS4893.2	6p21.1	2013-05-22			ENSG00000137204	ENSG00000137204		"Solute carriers"	10971	protein-coding gene	gene with protein product		604995				9650585, 10773670	Standard	XM_006714970		Approved	NLT, OAT2	uc003out.3	Q9Y694	OTTHUMG00000014726	ENST00000372585.5:c.1091T>C	chr6.hg19:g.43269967T>C	ENSP00000361666:p.Leu364Pro	50.0	0.0	.		56.0	18.0	.	NM_153320	B2CZX6|Q5T046|Q5T048|Q5T050|Q9H2W5	Missense_Mutation	SNP	ENST00000372585.5	hg19	CCDS4893.2	.	.	.	.	.	.	.	.	.	.	T	20.4	3.987683	0.74589	.	.	ENSG00000137204	ENST00000372589;ENST00000372585;ENST00000372574;ENST00000436107	T;T;T;T	0.70282	-0.08;-0.08;-0.08;-0.47	5.27	4.08	0.47627	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.280243	0.33092	N	0.005292	T	0.78886	0.4354	M	0.93062	3.375	0.80722	D	1	P;P;P	0.46621	0.881;0.855;0.855	P;P;P	0.56398	0.797;0.694;0.694	T	0.81929	-0.0708	10	0.87932	D	0	.	8.9149	0.35576	0.1813:0.0:0.0:0.8187	.	364;362;362	Q9Y694;Q9Y694-2;Q9Y694-3	S22A7_HUMAN;.;.	P	362;364;362;57	ENSP00000361670:L362P;ENSP00000361666:L364P;ENSP00000361655:L362P;ENSP00000393836:L57P	ENSP00000361655:L362P	L	+	2	0	SLC22A7	43377945	0.987000	0.35691	0.994000	0.49952	0.888000	0.51559	4.148000	0.58085	0.804000	0.34136	0.379000	0.24179	CTG	.	.	.	none		0.572	SLC22A7-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040588.1			C	43269967	T	C	43269967	3	2	248	1	0	0	0	0	1	0	0	0	14472	1580	55	3	1117	3	SLC22A7	6	43269967	Missense_Mutation	SNP	T	TCGA-SX-A7SN-01A-11D-A34Z-10	10038357	43269967	127845100	38	15362											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51924726	51924726	+	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	aatgagaagacagtgaatacCttagtccttggttcctctga	12	12	9	8	0	1	4	0	3	1	2	3	5	3	4	3	1	1	1	3	1	5	4			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr6:51924726C>A	ENST00000371117.3	-	15	1508	c.1233G>T	c.(1231-1233)aaG>aaT	p.K411N	PKHD1_ENST00000340994.4_Splice_Site_p.K411N|AL590391.1_ENST00000408630.2_RNA	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	411					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)					CAGTGAATACCTTAGTCCTTG	0.408																																					p.K411N		Atlas-SNP	.											.	PKHD1	927	.	0			c.G1233T						PASS	.						104	86	92					6																	51924726		2203	4300	6503	SO:0001630	splice_region_variant	5314	exon15			GAATACCTTAGTC	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.1233+1G>T	chr6.hg19:g.51924726C>A		33.0	0.0	.		33.0	8.0	.	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	hg19	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.017046	0.75161	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.88354	-2.37;-2.37	5.47	5.47	0.80525	.	0.074122	0.56097	D	0.000033	D	0.94351	0.8184	M	0.82823	2.61	0.42116	D	0.991401	D;D	0.89917	1.0;1.0	D;D	0.85130	0.996;0.997	D	0.93787	0.7089	9	.	.	.	.	18.6748	0.91525	0.0:1.0:0.0:0.0	.	411;411	P08F94-2;P08F94	.;PKHD1_HUMAN	N	411	ENSP00000360158:K411N;ENSP00000341097:K411N	.	K	-	3	2	PKHD1	52032685	1.000000	0.71417	1.000000	0.80357	0.609000	0.37215	5.100000	0.64560	2.723000	0.93209	0.655000	0.94253	AAG	.	.	.	none		0.408	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	Missense_Mutation	A	51924726	C	A	51924726	5	1	248	1	0	0	0	0	0	0	1	0	11978	695	24	4	11242	4	PKHD1	6	51924726	Splice_Site	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10	8654759	51924726	119190341	39	15363											
SMAP1	60682	hgsc.bcm.edu	37	chr6	71377783	71377783	+	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	ctgaacgagcagcaccagctCatcctatccaagcttctgag	11	8	8	14	1	2	2	1	2	1	0	4	3	4	2	3	0	5	4	3	0	3	2			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr6:71377783C>A	ENST00000370455.3	+	1	305	c.57C>A	c.(55-57)ctC>ctA	p.L19L	SMAP1_ENST00000422334.2_Silent_p.L19L|SMAP1_ENST00000370452.3_Silent_p.L19L|SMAP1_ENST00000316999.5_Silent_p.L19L	NM_001044305.1|NM_001281440.1	NP_001037770.1|NP_001268369.1	Q8IYB5	SMAP1_HUMAN	small ArfGAP 1	19	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				positive regulation of erythrocyte differentiation (GO:0045648)|regulation of ARF GTPase activity (GO:0032312)|regulation of clathrin-mediated endocytosis (GO:2000369)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(1)|urinary_tract(1)	15						AGCACCAGCTCATCCTATCCA	0.667																																					p.L19L		Atlas-SNP	.											SMAP1_ENST00000370455,NS,carcinoma,0,2	SMAP1	77	.	0			c.C57A						PASS	.						67	57	60					6																	71377783		2203	4300	6503	SO:0001819	synonymous_variant	60682	exon1			CCAGCTCATCCTA	AK023221	CCDS4973.1, CCDS43478.1, CCDS64459.1, CCDS75478.1	6q12-q13	2009-11-30	2008-09-05		ENSG00000112305	ENSG00000112305		"ADP-ribosylation factor GTPase activating proteins"	19651	protein-coding gene	gene with protein product		611372	"stromal membrane-associated protein 1", "stromal membrane-associated GTPase-activating protein 1"			9644265, 12119110	Standard	NM_001044305		Approved	FLJ13159, SMAP-1	uc003pfr.3	Q8IYB5	OTTHUMG00000014996	ENST00000370455.3:c.57C>A	chr6.hg19:g.71377783C>A		71.0	0.0	.		81.0	35.0	.	NM_001044305	Q53H70|Q5SYQ2|Q6PK24|Q8NDH4|Q96L38|Q96L39|Q9H8X4	Silent	SNP	ENST00000370455.3	hg19	CCDS43478.1																																																																																			.	.	.	none		0.667	SMAP1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041149.1	NM_001044305		A	71377783	C	A	71377783	2	1	248	1	0	0	0	0	0	0	0	1	14779	813	29	4		4	SMAP1	6	71377783	Silent	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10	19453057	71377783	99737284	40	15364											
EEF1A1	1915	hgsc.bcm.edu	37	chr6	74228567	74228567	+	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	ctttccatcccttgaaccaaGgcatctgaaacacaagcatg	13	9	6	13	0	1	2	0	2	1	0	3	2	3	2	3	1	3	2	3	1	4	2			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr6:74228567G>T	ENST00000316292.9	-	4	1617	c.626C>A	c.(625-627)cCt>cAt	p.P209H	EEF1A1_ENST00000331523.2_Missense_Mutation_p.P209H|EEF1A1_ENST00000309268.6_Missense_Mutation_p.P209H|EEF1A1_ENST00000491404.1_Intron	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1	209	tr-type G.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation elongation factor activity (GO:0003746)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						CTTGAACCAAGGCATCTGAAA	0.488											OREG0003891|OREG0003895	type=REGULATORY REGION|Gene=D16891|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay|type=REGULATORY REGION|Gene=EEF1A1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.P209H		Atlas-SNP	.											.	EEF1A1	56	.	0			c.C626A						PASS	.						94	87	90					6																	74228567		2203	4300	6503	SO:0001583	missense	1915	exon5			AACCAAGGCATCT	BC019669	CCDS4980.1	6q14.1	2010-06-30	2004-11-19		ENSG00000156508	ENSG00000156508			3189	protein-coding gene	gene with protein product		130590	"leukocyte receptor cluster (LRC) member 7"	EF1A, EEF1A, LENG7		8812466, 10941842	Standard	NM_001402		Approved	EE1A1	uc003phj.3	P68104	OTTHUMG00000015031	ENST00000316292.9:c.626C>A	chr6.hg19:g.74228567G>T	ENSP00000339063:p.Pro209His	86.0	0.0	.	1151	85.0	38.0	.	NM_001402	P04719|P04720|Q6IQ15	Missense_Mutation	SNP	ENST00000316292.9	hg19	CCDS4980.1	.	.	.	.	.	.	.	.	.	.	G	19.33	3.806766	0.70682	.	.	ENSG00000156508	ENST00000316292;ENST00000358190;ENST00000309268;ENST00000331523;ENST00000391977	T;T;T	0.44881	0.91;0.91;0.91	4.31	4.31	0.51392	Protein synthesis factor, GTP-binding (2);	0.209202	0.40385	U	0.001106	T	0.58637	0.2136	M	0.87038	2.855	0.53688	D	0.999975	P;P;P;P	0.46952	0.887;0.887;0.887;0.887	P;P;P;P	0.56343	0.796;0.796;0.796;0.796	T	0.69079	-0.5240	10	0.87932	D	0	.	17.2248	0.86966	0.0:0.0:1.0:0.0	.	209;209;209;209	P68104;Q53HR5;Q6IPS9;Q5VTE0	EF1A1_HUMAN;.;.;EF1A3_HUMAN	H	209;209;209;209;188	ENSP00000339063:P209H;ENSP00000339053:P209H;ENSP00000330054:P209H	ENSP00000339053:P209H	P	-	2	0	EEF1A1	74285288	1.000000	0.71417	0.994000	0.49952	0.986000	0.74619	7.413000	0.80104	2.115000	0.64714	0.549000	0.68633	CCT	.	.	.	none		0.488	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041210.2	NM_001402		T	74228567	G	T	74228567	3	4	248	1	0	0	0	0	1	0	0	0	4925	1000	35	4	778	4	EEF1A1	6	74228567	Missense_Mutation	SNP	G	TCGA-SX-A7SN-01A-11D-A34Z-10	2850784	74228567	96886500	41	15365											
QRSL1	55278	hgsc.bcm.edu	37	chr6	107111042	107111042	+	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	cccaggatgatatttttacaCaagctgtaaatatggcaggt	13	12	9	7	0	0	1	0	1	0	0	0	2	0	2	1	3	2	3	1	3	6	6			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr6:107111042C>A	ENST00000369046.4	+	10	1452	c.1348C>A	c.(1348-1350)Caa>Aaa	p.Q450K		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)		TATTTTTACACAAGCTGTAAA	0.433																																					p.Q450K	NSCLC(192;2127 2142 11668 26277 49545)	Atlas-SNP	.											.	QRSL1	30	.	0			c.C1348A						PASS	.						64	63	63					6																	107111042		2203	4300	6503	SO:0001583	missense	55278	exon10			TTTACACAAGCTG	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.1348C>A	chr6.hg19:g.107111042C>A	ENSP00000358042:p.Gln450Lys	57.0	0.0	.		59.0	13.0	.	NM_018292		Missense_Mutation	SNP	ENST00000369046.4	hg19	CCDS5057.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.782043	0.90282	.	.	ENSG00000130348	ENST00000369046	T	0.54479	0.57	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.60209	0.2251	L	0.39898	1.24	0.80722	D	1	D	0.69078	0.997	D	0.74023	0.982	T	0.63791	-0.6557	10	0.87932	D	0	-9.5878	19.2883	0.94087	0.0:1.0:0.0:0.0	.	450	Q9H0R6	GATA_HUMAN	K	450	ENSP00000358042:Q450K	ENSP00000358042:Q450K	Q	+	1	0	QRSL1	107217735	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.487000	0.81328	2.578000	0.87016	0.484000	0.47621	CAA	.	.	.	none		0.433	QRSL1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041667.1	NM_018292		A	107111042	C	A	107111042	3	1	248	1	0	0	0	0	1	0	0	0	12894	479	17	4	1386	4	QRSL1	6	107111042	Missense_Mutation	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10	32882475	107111042	64004025	42	15366											
RAET1E	135250	hgsc.bcm.edu	37	chr6	150211134	150211134	+	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	tggtggcatataccttcttcCccaggaggcccagaggtttg	7	11	12	11	0	1	1	0	0	1	1	2	2	2	2	4	5	1	2	4	5	2	5			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr6:150211134C>T	ENST00000357183.4	-	2	365	c.233G>A	c.(232-234)gGg>gAg	p.G78E	RAET1E-AS1_ENST00000446954.2_RNA|RAET1E_ENST00000532335.1_Missense_Mutation_p.G78E|RAET1E_ENST00000529948.1_Missense_Mutation_p.G78E|RAET1E_ENST00000367363.3_Missense_Mutation_p.G42E|RAET1E-AS1_ENST00000605899.1_RNA|RP11-244K5.8_ENST00000606915.1_RNA	NM_139165.2	NP_631904.1	Q8TD07	N2DL4_HUMAN	retinoic acid early transcript 1E	78	MHC class I alpha-1 like.				antigen processing and presentation (GO:0019882)|natural killer cell mediated cytotoxicity (GO:0042267)|regulation of immune response (GO:0050776)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	natural killer cell lectin-like receptor binding (GO:0046703)			cervix(1)|kidney(2)|large_intestine(3)|lung(3)|skin(1)	10		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.58e-12)		TACCTTCTTCCCCAGGAGGCC	0.517																																					p.G78E		Atlas-SNP	.											.	RAET1E	20	.	0			c.G233A						PASS	.						100	92	95					6																	150211134		2203	4300	6503	SO:0001583	missense	135250	exon2			TTCTTCCCCAGGA	AF359243	CCDS5221.1, CCDS59042.1, CCDS59043.1, CCDS59044.1	6q24.3	2011-02-09			ENSG00000164520	ENSG00000164520			16793	protein-coding gene	gene with protein product		609243				11827464	Standard	NM_139165		Approved	LETAL, bA350J20.7, ULBP4	uc003qnl.1	Q8TD07	OTTHUMG00000015796	ENST00000357183.4:c.233G>A	chr6.hg19:g.150211134C>T	ENSP00000349709:p.Gly78Glu	100.0	0.0	.		133.0	45.0	.	NM_139165	A6YF59|Q5VYB7|Q5VYB8|Q8TEZ2|Q96L41	Missense_Mutation	SNP	ENST00000357183.4	hg19	CCDS5221.1	.	.	.	.	.	.	.	.	.	.	C	14.11	2.438330	0.43326	.	.	ENSG00000164520	ENST00000532335;ENST00000357183;ENST00000367363;ENST00000529948;ENST00000531073	T;T;T;T;T	0.24723	1.84;1.84;5.83;1.84;3.29	3.85	-0.0414	0.13868	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.619520	0.14505	N	0.315517	T	0.25082	0.0609	L	0.61036	1.89	0.09310	N	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.04481	-1.0948	10	0.87932	D	0	-12.1253	4.4654	0.11687	0.0:0.4291:0.3606:0.2102	.	78;42;78	Q8TD07;Q8TD07-2;Q8TD07-3	N2DL4_HUMAN;.;.	E	78;78;42;78;78	ENSP00000437067:G78E;ENSP00000349709:G78E;ENSP00000356332:G42E;ENSP00000432366:G78E;ENSP00000433489:G78E	ENSP00000349709:G78E	G	-	2	0	RAET1E	150252827	0.000000	0.05858	0.000000	0.03702	0.091000	0.18340	-0.538000	0.06120	-0.033000	0.13736	0.591000	0.81541	GGG	.	.	.	none		0.517	RAET1E-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042659.1	NM_139165		T	150211134	C	T	150211134	3	4	248	1	0	0	0	0	1	0	0	0	13012	623	22	2	570	2	RAET1E	6	150211134	Missense_Mutation	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10	43100092	150211134	20903933	43	15367											
MLXIPL	51085	hgsc.bcm.edu	37	chr7	73038696	73038696	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgtggatgacctgcgagcGgagcaagccgcccgcgctgc	6	5	16	14	5	0	1	0	1	0	0	0	4	0	3	3	2	5	3	3	2	1	0			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr7:73038696G>A	ENST00000313375.3	-	1	174	c.127C>T	c.(127-129)Cgc>Tgc	p.R43C	MLXIPL_ENST00000429400.2_Missense_Mutation_p.R43C|MLXIPL_ENST00000354613.1_Missense_Mutation_p.R43C|MLXIPL_ENST00000434326.1_Missense_Mutation_p.R43C|MLXIPL_ENST00000414749.2_Missense_Mutation_p.R43C|MLXIPL_ENST00000395189.1_Missense_Mutation_p.R43C	NM_032951.2|NM_032953.2	NP_116569.1|NP_116571.1	Q9NP71	MLXPL_HUMAN	MLX interacting protein-like	43					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)				ACCTGCGAGCGGAGCAAGCCG	0.736																																					p.R43C		Atlas-SNP	.											.	MLXIPL	54	.	0			c.C127T						PASS	.						7	8	8					7																	73038696		2141	4188	6329	SO:0001583	missense	51085	exon1			GCGAGCGGAGCAA	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.127C>T	chr7.hg19:g.73038696G>A	ENSP00000320886:p.Arg43Cys	20.0	0.0	.		49.0	20.0	.	NM_032954	C5HU02|C5HU03|C5HU04|Q96E48|Q9BY03|Q9BY04|Q9BY05|Q9BY06|Q9Y2P3	Missense_Mutation	SNP	ENST00000313375.3	hg19	CCDS5553.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.458986	0.84317	.	.	ENSG00000009950	ENST00000414749;ENST00000429400;ENST00000313375;ENST00000354613;ENST00000395189;ENST00000434326;ENST00000453275	T;T;T;T;T;T	0.33216	1.97;1.99;1.98;1.99;1.42;1.42	4.24	4.24	0.50183	.	0.353680	0.21200	N	0.078499	T	0.43765	0.1262	M	0.63843	1.955	0.45056	D	0.998073	D;D;D;D;D	0.76494	0.996;0.998;0.999;0.999;0.999	P;P;P;P;P	0.54924	0.648;0.585;0.764;0.764;0.764	T	0.44907	-0.9297	10	0.87932	D	0	-17.4128	11.9628	0.53017	0.0:0.0:1.0:0.0	.	43;43;43;43;43	Q9NP71-6;Q9NP71;Q9NP71-2;Q9NP71-3;Q9NP71-4	.;MLXPL_HUMAN;.;.;.	C	43	ENSP00000412330:R43C;ENSP00000406296:R43C;ENSP00000320886:R43C;ENSP00000346629:R43C;ENSP00000378616:R43C;ENSP00000392636:R43C	ENSP00000320886:R43C	R	-	1	0	MLXIPL	72676632	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	5.668000	0.68074	2.170000	0.68504	0.491000	0.48974	CGC	.	.	.	none		0.736	MLXIPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252262.1	NM_032951		A	73038696	G	A	73038696	3	1	248	1	0	0	0	0	1	0	0	0	9644	1116	39	1	2499	1	MLXIPL	7	73038696	Missense_Mutation	SNP	G	TCGA-SX-A7SN-01A-11D-A34Z-10		73038696	86099967	44	15368											
TRRAP	8295	hgsc.bcm.edu	37	chr7	98506430	98506430	+	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	tcagcgacctctccctcgccGtccagctcttcgccaagaac	7	8	7	19	4	3	1	1	0	2	1	7	2	4	1	5	0	3	1	5	0	2	1			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr7:98506430G>C	ENST00000359863.4	+	14	1404	c.1195G>C	c.(1195-1197)Gtc>Ctc	p.V399L	TRRAP_ENST00000446306.3_Missense_Mutation_p.V399L|TRRAP_ENST00000355540.3_Missense_Mutation_p.V399L	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	399					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)	p.V399I(2)		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)			CTCCCTCGCCGTCCAGCTCTT	0.647																																					p.V399L		Atlas-SNP	.											TRRAP_ENST00000359863,NS,carcinoma,0,4	TRRAP	863	.	2	Substitution - Missense(2)	lung(2)	c.G1195C						PASS	.						77	50	59					7																	98506430		2203	4300	6503	SO:0001583	missense	8295	exon14			CTCGCCGTCCAGC	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.1195G>C	chr7.hg19:g.98506430G>C	ENSP00000352925:p.Val399Leu	49.0	0.0	.		97.0	42.0	.	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Missense_Mutation	SNP	ENST00000359863.4	hg19	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.796795	0.90453	.	.	ENSG00000196367	ENST00000359863;ENST00000355540;ENST00000446306	T;T	0.59772	3.92;0.24	5.84	5.84	0.93424	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000001	T	0.78394	0.4276	M	0.81179	2.53	0.80722	D	1	D;P;P	0.53312	0.959;0.931;0.931	D;P;P	0.65987	0.94;0.872;0.872	T	0.79557	-0.1754	10	0.72032	D	0.01	.	20.1551	0.98106	0.0:0.0:1.0:0.0	.	399;113;399	Q9Y4A5-2;Q59FH1;Q9Y4A5	.;.;TRRAP_HUMAN	L	399	ENSP00000352925:V399L;ENSP00000347733:V399L	ENSP00000347733:V399L	V	+	1	0	TRRAP	98344366	1.000000	0.71417	0.994000	0.49952	0.998000	0.95712	9.625000	0.98406	2.760000	0.94817	0.655000	0.94253	GTC	.	.	.	none		0.647	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		C	98506430	G	C	98506430	3	2	248	1	0	0	0	0	1	0	0	0	16613	1145	40	4	1245	4	TRRAP	7	98506430	Missense_Mutation	SNP	G	TCGA-SX-A7SN-01A-11D-A34Z-10	25467734	98506430	60632233	45	15369											
ZKSCAN5	23660	hgsc.bcm.edu	37	chr7	99117529	99117529	+	Silent	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	tcacttctctcaactgggtcCcaggtgagctggtgcccctt	5	12	10	14	0	3	1	2	1	1	0	5	1	4	1	3	3	3	1	3	3	1	2			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr7:99117529C>T	ENST00000394170.2	+	4	884	c.633C>T	c.(631-633)tcC>tcT	p.S211S	ZKSCAN5_ENST00000326775.5_Silent_p.S211S|ZKSCAN5_ENST00000451158.1_Silent_p.S211S	NM_014569.3	NP_055384.1	Q9Y2L8	ZKSC5_HUMAN	zinc finger with KRAB and SCAN domains 5	211					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)					CAACTGGGTCCCAGGTGAGCT	0.547																																					p.S211S		Atlas-SNP	.											.	ZKSCAN5	63	.	0			c.C633T						PASS	.						82	74	77					7																	99117529		2203	4300	6503	SO:0001819	synonymous_variant	23660	exon4			TGGGTCCCAGGTG	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.633C>T	chr7.hg19:g.99117529C>T		39.0	0.0	.		67.0	35.0	.	NM_145102	A4D280|D6W5S9	Silent	SNP	ENST00000394170.2	hg19	CCDS5667.1																																																																																			.	.	.	none		0.547	ZKSCAN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345597.1	NM_014569		T	99117529	C	T	99117529	2	4	248	1	0	0	0	0	0	0	0	1	17702	610	22	2		2	ZKSCAN5	7	99117529	Silent	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10	611099	99117529	60021134	46	15370											
ZNF282	8427	hgsc.bcm.edu	37	chr7	148892698	148892698	+	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	caggatgcagtttgtgtcaaCacggccgcagcctcagcagc	9	7	12	13	2	2	0	2	0	0	0	2	1	2	1	2	2	5	4	2	2	1	1			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr7:148892698C>A	ENST00000262085.3	+	1	122	c.17C>A	c.(16-18)aCa>aAa	p.T6K	ZNF282_ENST00000479907.1_Missense_Mutation_p.T6K	NM_003575.2	NP_003566.1	Q9UDV7	ZN282_HUMAN	zinc finger protein 282	6					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(3)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	17	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)	Lung(243;0.145)		TTTGTGTCAACACGGCCGCAG	0.687																																					p.T6K		Atlas-SNP	.											.	ZNF282	42	.	0			c.C17A						PASS	.						17	18	18					7																	148892698		2201	4297	6498	SO:0001583	missense	8427	exon1			TGTCAACACGGCC	D30612	CCDS5895.1	7q36.1	2013-01-08			ENSG00000170265	ENSG00000170265		"Zinc fingers, C2H2-type", "-"	13076	protein-coding gene	gene with protein product		603397				9396811	Standard	NM_003575		Approved	HUB1	uc003wfm.3	Q9UDV7	OTTHUMG00000158974	ENST00000262085.3:c.17C>A	chr7.hg19:g.148892698C>A	ENSP00000262085:p.Thr6Lys	27.0	0.0	.		54.0	22.0	.	NM_003575	B4DRI5|O43691|Q6DKK0	Missense_Mutation	SNP	ENST00000262085.3	hg19	CCDS5895.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.383155	0.82792	.	.	ENSG00000170265	ENST00000262085;ENST00000479907	T;T	0.07567	3.18;4.93	4.52	4.52	0.55395	.	0.000000	0.42821	D	0.000660	T	0.13970	0.0338	N	0.14661	0.345	0.37992	D	0.933934	D;D	0.71674	0.998;0.981	D;D	0.73708	0.981;0.95	T	0.18178	-1.0345	10	0.87932	D	0	-10.484	12.7526	0.57316	0.0:1.0:0.0:0.0	.	6;6	B4DRI5;Q9UDV7	.;ZN282_HUMAN	K	6	ENSP00000262085:T6K;ENSP00000418840:T6K	ENSP00000262085:T6K	T	+	2	0	ZNF282	148523631	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.024000	0.41049	2.024000	0.59613	0.313000	0.20887	ACA	.	.	.	none		0.687	ZNF282-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352746.1	NM_003575		A	148892698	C	A	148892698	3	1	248	1	0	0	0	0	1	0	0	0	17831	478	17	4	19	4	ZNF282	7	148892698	Missense_Mutation	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10	49775169	148892698	10245965	47	15371											
RP1	6101	hgsc.bcm.edu	37	chr8	55537660	55537660	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caagagggcagtttggcagaGgagataaacattcaaatgac	16	7	12	6	0	1	4	1	1	0	3	1	5	1	4	0	3	1	3	0	3	4	3			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr8:55537660G>A	ENST00000220676.1	+	4	1366	c.1218G>A	c.(1216-1218)gaG>gaA	p.E406E		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	406					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.E406D(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)			GTTTGGCAGAGGAGATAAACA	0.448																																					p.E406E	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											RP1,colon,carcinoma,0,1	RP1	429	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1218A						PASS	.						94	93	93					8																	55537660		2203	4300	6503	SO:0001819	synonymous_variant	6101	exon4			GGCAGAGGAGATA	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.1218G>A	chr8.hg19:g.55537660G>A		86.0	0.0	.		93.0	35.0	.	NM_006269		Silent	SNP	ENST00000220676.1	hg19	CCDS6160.1																																																																																			.	.	.	none		0.448	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		A	55537660	G	A	55537660	2	1	248	1	0	0	0	0	0	0	0	1	13545	991	35	2		2	RP1	8	55537660	Silent	SNP	G	TCGA-SX-A7SN-01A-11D-A34Z-10		55537660	90826362	48	15372											
ARFGEF1	10565	hgsc.bcm.edu	37	chr8	68200291	68200291	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgtcatataacacttcatttTtagataatgctttaaaagaa	16	15	4	6	1	2	2	2	0	0	2	2	2	2	2	0	0	2	1	0	0	7	9			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr8:68200291T>C	ENST00000262215.3	-	7	1315	c.926A>G	c.(925-927)aAa>aGa	p.K309R		NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	309					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)			CACTTCATTTTTAGATAATGC	0.294																																					p.K309R		Atlas-SNP	.											.	ARFGEF1	196	.	0			c.A926G						PASS	.						143	139	141					8																	68200291		2203	4299	6502	SO:0001583	missense	10565	exon7			TCATTTTTAGATA	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.926A>G	chr8.hg19:g.68200291T>C	ENSP00000262215:p.Lys309Arg	82.0	0.0	.		101.0	38.0	.	NM_006421	Q9NV46|Q9UFV2|Q9UNL0	Missense_Mutation	SNP	ENST00000262215.3	hg19	CCDS6199.1	.	.	.	.	.	.	.	.	.	.	T	8.851	0.944495	0.18356	.	.	ENSG00000066777	ENST00000262215	T	0.20200	2.09	5.39	5.39	0.77823	Armadillo-type fold (1);	0.222812	0.46758	D	0.000280	T	0.15392	0.0371	N	0.22421	0.69	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.08006	-1.0743	10	0.18710	T	0.47	.	15.6988	0.77521	0.0:0.0:0.0:1.0	.	309	Q9Y6D6	BIG1_HUMAN	R	309	ENSP00000262215:K309R	ENSP00000262215:K309R	K	-	2	0	ARFGEF1	68362845	1.000000	0.71417	1.000000	0.80357	0.549000	0.35272	5.052000	0.64263	2.171000	0.68590	0.377000	0.23210	AAA	.	.	.	none		0.294	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421		C	68200291	T	C	68200291	3	2	248	1	0	0	0	0	1	0	0	0	852	1841	64	3	4755	3	ARFGEF1	8	68200291	Missense_Mutation	SNP	T	TCGA-SX-A7SN-01A-11D-A34Z-10	12662631	68200291	78163731	49	15373											
CLTA	1211	hgsc.bcm.edu	37	chr9	36204095	36204095	+	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	tcggaagcaagaagcagagtGgaaagaaaaggcaataaagg	20	3	14	4	1	0	3	0	0	0	3	1	5	0	5	0	4	2	3	0	4	9	1			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr9:36204095G>A	ENST00000242285.6	+	4	524	c.404G>A	c.(403-405)tGg>tAg	p.W135*	CLTA_ENST00000433436.2_Nonsense_Mutation_p.W135*|CLTA_ENST00000540080.1_Nonsense_Mutation_p.W83*|CLTA_ENST00000466396.1_Nonsense_Mutation_p.W83*|CLTA_ENST00000345519.5_Nonsense_Mutation_p.W135*|CLTA_ENST00000396603.2_Nonsense_Mutation_p.W135*|CLTA_ENST00000538225.1_Nonsense_Mutation_p.W135*|CLTA_ENST00000470744.1_Nonsense_Mutation_p.W135*			P09496	CLCA_HUMAN	clathrin, light chain A	135	Involved in binding clathrin heavy chain.				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)			GAAGCAGAGTGGAAAGAAAAG	0.418																																					p.W135X		Atlas-SNP	.											.	CLTA	18	.	0			c.G404A						PASS	.						134	106	115					9																	36204095		2203	4300	6503	SO:0001587	stop_gained	1211	exon4			CAGAGTGGAAAGA		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.404G>A	chr9.hg19:g.36204095G>A	ENSP00000242285:p.Trp135*	59.0	0.0	.		66.0	21.0	.	NM_001184761	A8K4W3|B4DIN1|F5H6N3|Q2XPN5|Q53XZ1	Nonsense_Mutation	SNP	ENST00000242285.6	hg19	CCDS6601.1	.	.	.	.	.	.	.	.	.	.	G	34	5.323721	0.95708	.	.	ENSG00000122705	ENST00000433436;ENST00000538225;ENST00000540080;ENST00000345519;ENST00000470744;ENST00000242285;ENST00000466396;ENST00000396603	.	.	.	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07482	T	0.82	-8.2768	17.8186	0.88643	0.0:0.0:1.0:0.0	.	.	.	.	X	135;135;83;135;135;135;83;135	.	ENSP00000242285:W135X	W	+	2	0	CLTA	36194095	1.000000	0.71417	1.000000	0.80357	0.608000	0.37181	9.078000	0.94023	2.818000	0.97014	0.655000	0.94253	TGG	.	.	.	none		0.418	CLTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052405.1	NM_007096		A	36204095	G	A	36204095	4	1	248	1	0	0	0	0	0	1	0	0	3566	1357	47	2	418	2	CLTA	9	36204095	Nonsense_Mutation	SNP	G	TCGA-SX-A7SN-01A-11D-A34Z-10		36204095	105009336	50	15374											
KIF27	55582	hgsc.bcm.edu	37	chr9	86518501	86518501	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cacatgtgatcatgacagtcTtagcactgcctcccagagaa	12	9	8	12	0	2	3	1	2	1	1	3	4	3	3	2	0	2	1	2	0	2	1			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr9:86518501T>C	ENST00000297814.2	-	4	1075	c.932A>G	c.(931-933)aAg>aGg	p.K311R	KIF27_ENST00000334204.2_Missense_Mutation_p.K311R|KIF27_ENST00000413982.1_Missense_Mutation_p.K311R	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	311	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						CATGACAGTCTTAGCACTGCC	0.448																																					p.K311R		Atlas-SNP	.											.	KIF27	103	.	0			c.A932G						PASS	.						77	79	79					9																	86518501		2203	4300	6503	SO:0001583	missense	55582	exon4			ACAGTCTTAGCAC	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.932A>G	chr9.hg19:g.86518501T>C	ENSP00000297814:p.Lys311Arg	143.0	0.0	.		130.0	49.0	.	NM_017576	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Missense_Mutation	SNP	ENST00000297814.2	hg19	CCDS6665.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.076262	0.76415	.	.	ENSG00000165115	ENST00000297814;ENST00000413982;ENST00000334204	T;T;T	0.77098	-1.07;-1.07;-1.07	5.8	5.8	0.92144	Kinesin, motor domain (4);	0.000000	0.64402	D	0.000012	T	0.75708	0.3886	N	0.04355	-0.22	0.47009	D	0.999284	D;P;D	0.89917	1.0;0.885;1.0	D;P;D	0.91635	0.988;0.482;0.999	T	0.79574	-0.1747	10	0.35671	T	0.21	.	16.1596	0.81693	0.0:0.0:0.0:1.0	.	311;311;311	Q86VH2-3;Q86VH2-2;Q86VH2	.;.;KIF27_HUMAN	R	311	ENSP00000297814:K311R;ENSP00000401688:K311R;ENSP00000333928:K311R	ENSP00000297814:K311R	K	-	2	0	KIF27	85708321	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.179000	0.65043	2.216000	0.71823	0.533000	0.62120	AAG	.	.	.	none		0.448	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576		C	86518501	T	C	86518501	3	2	248	1	0	0	0	0	1	0	0	0	8303	1609	56	3	3333	3	KIF27	9	86518501	Missense_Mutation	SNP	T	TCGA-SX-A7SN-01A-11D-A34Z-10	50314406	86518501	54694930	51	15375											
ANKS6	203286	hgsc.bcm.edu	37	chr9	101498890	101498890	+	Missense_Mutation	SNP	T	T	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	gtgaatggtttcctgtaaaaTttgtctctcgcgtccctgtg	6	16	10	9	2	1	1	0	1	1	0	5	1	3	1	2	1	0	2	2	1	3	3			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr9:101498890T>G	ENST00000353234.4	-	15	2574	c.2527A>C	c.(2527-2529)Att>Ctt	p.I843L	ANKS6_ENST00000375019.2_Missense_Mutation_p.I542L|ANKS6_ENST00000540940.1_Missense_Mutation_p.I648L|ANKS6_ENST00000375018.1_Missense_Mutation_p.I844L			Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain containing 6	843						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)				TCCTGTAAAATTTGTCTCTCG	0.448																																					p.I843L		Atlas-SNP	.											.	ANKS6	59	.	0			c.A2527C						PASS	.						80	83	82					9																	101498890		1910	4119	6029	SO:0001583	missense	203286	exon15			GTAAAATTTGTCT	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.2527A>C	chr9.hg19:g.101498890T>G	ENSP00000297837:p.Ile843Leu	55.0	0.0	.		59.0	11.0	.	NM_173551	A0SE62|Q5VSL0|Q5VSL2|Q5VSL3|Q5VSL4|Q68DB8|Q6P2R2|Q8N9L6|Q96D62	Missense_Mutation	SNP	ENST00000353234.4	hg19	CCDS43856.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.6|21.6	4.180089|4.180089	0.78564|0.78564	.|.	.|.	ENSG00000165138|ENSG00000165138	ENST00000375019;ENST00000375018;ENST00000353234;ENST00000540940|ENST00000444472	T;T;T;T|.	0.67698|.	1.89;-0.28;-0.26;2.16|.	5.31|5.31	5.31|5.31	0.75309|0.75309	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.52075|0.52075	0.1712|0.1712	L|L	0.27053|0.27053	0.805|0.805	0.38043|0.38043	D|D	0.935529|0.935529	D;D|.	0.58268|.	0.982;0.97|.	D;P|.	0.69307|.	0.963;0.804|.	T|T	0.54268|0.54268	-0.8319|-0.8319	10|5	0.62326|.	D|.	0.03|.	-17.0533|-17.0533	13.5089|13.5089	0.61499|0.61499	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	844;843|.	Q68DC2-4;Q68DC2|.	.;ANKS6_HUMAN|.	L|T	542;844;843;648|312	ENSP00000364159:I542L;ENSP00000364158:I844L;ENSP00000297837:I843L;ENSP00000442189:I648L|.	ENSP00000297837:I843L|.	I|N	-|-	1|2	0|0	ANKS6|ANKS6	100538711|100538711	1.000000|1.000000	0.71417|0.71417	0.528000|0.528000	0.27938|0.27938	0.996000|0.996000	0.88848|0.88848	4.077000|4.077000	0.57598|0.57598	2.134000|2.134000	0.65973|0.65973	0.533000|0.533000	0.62120|0.62120	ATT|AAT	.	.	.	none		0.448	ANKS6-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277053.1	NM_173551		G	101498890	T	G	101498890	3	3	248	1	0	0	0	0	1	0	0	0	692	1493	52	5	92	5	ANKS6	9	101498890	Missense_Mutation	SNP	T	TCGA-SX-A7SN-01A-11D-A34Z-10	14980389	101498890	39714541	52	15376											
STX17	55014	hgsc.bcm.edu	37	chr9	102730737	102730737	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgcaaaatacaagctggcaGctctgcctgtggcaggtgca	10	8	12	11	0	1	0	0	0	1	0	1	0	1	0	1	3	6	6	1	3	4	1			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr9:102730737G>A	ENST00000259400.6	+	8	827	c.691G>A	c.(691-693)Gct>Act	p.A231T	STX17_ENST00000525640.1_Missense_Mutation_p.A231T|STX17_ENST00000534052.1_Missense_Mutation_p.A231T|STX17_ENST00000525847.1_3'UTR	NM_017919.2	NP_060389.2	P56962	STX17_HUMAN	syntaxin 17	231	Necessary and sufficient for localization to autophagosome.				autophagic vacuole fusion (GO:0000046)|endoplasmic reticulum-Golgi intermediate compartment organization (GO:0097111)|ER to Golgi vesicle-mediated transport (GO:0006888)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|protein localization to pre-autophagosomal structure (GO:0034497)	autophagic vacuole membrane (GO:0000421)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|ER to Golgi transport vesicle (GO:0030134)|ER-mitochondrion membrane contact site (GO:0044233)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|smooth endoplasmic reticulum membrane (GO:0030868)|SNARE complex (GO:0031201)	protein phosphatase binding (GO:0019903)|SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			endometrium(2)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189)				CAAGCTGGCAGCTCTGCCTGT	0.473																																					p.A231T		Atlas-SNP	.											.	STX17	17	.	0			c.G691A						PASS	.						26	30	29					9																	102730737		2112	4179	6291	SO:0001583	missense	55014	exon8			CTGGCAGCTCTGC	AL834371	CCDS6745.1	9q31.1	2008-02-05			ENSG00000136874	ENSG00000136874			11432	protein-coding gene	gene with protein product		604204				9852078	Standard	NM_017919		Approved	FLJ20651	uc004bal.4	P56962	OTTHUMG00000020359	ENST00000259400.6:c.691G>A	chr9.hg19:g.102730737G>A	ENSP00000259400:p.Ala231Thr	52.0	0.0	.		61.0	22.0	.	NM_017919	Q4VXC2	Missense_Mutation	SNP	ENST00000259400.6	hg19	CCDS6745.1	.	.	.	.	.	.	.	.	.	.	G	11.82	1.753782	0.31046	.	.	ENSG00000136874	ENST00000259400;ENST00000525640;ENST00000534052	.	.	.	5.52	3.65	0.41850	.	0.258408	0.38720	N	0.001584	T	0.43743	0.1261	L	0.36672	1.1	0.40216	D	0.977689	B	0.19817	0.039	B	0.15870	0.014	T	0.25882	-1.0119	9	0.31617	T	0.26	-8.1716	8.8801	0.35370	0.0748:0.0:0.777:0.1481	.	231	P56962	STX17_HUMAN	T	231	.	ENSP00000259400:A231T	A	+	1	0	STX17	101770558	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.513000	0.67037	0.660000	0.30964	0.655000	0.94253	GCT	.	.	.	none		0.473	STX17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053398.3	NM_017919		A	102730737	G	A	102730737	3	1	248	1	0	0	0	0	1	0	0	0	15352	971	34	2	717	2	STX17	9	102730737	Missense_Mutation	SNP	G	TCGA-SX-A7SN-01A-11D-A34Z-10	1231847	102730737	38482694	53	15377											
ENTPD8	377841	hgsc.bcm.edu	37	chr9	140332422	140332422	+	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	cagaacagcccactaaccttCcacctggcaggccagggcct	10	5	9	17	0	0	1	0	0	0	1	1	1	1	1	6	3	3	1	6	3	2	2			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr9:140332422C>A	ENST00000472938.1	-	2	257	c.241G>T	c.(241-243)Gaa>Taa	p.E81*	ENTPD8_ENST00000344119.2_Nonsense_Mutation_p.E81*|ENTPD8_ENST00000371506.2_Nonsense_Mutation_p.E81*			Q5MY95	ENTP8_HUMAN	ectonucleoside triphosphate diphosphohydrolase 8	81					nucleoside diphosphate biosynthetic process (GO:0009133)|nucleoside monophosphate biosynthetic process (GO:0009124)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			biliary_tract(1)|lung(4)|prostate(1)|skin(1)	7	all_cancers(76;0.0926)			OV - Ovarian serous cystadenocarcinoma(145;0.000224)|Epithelial(140;0.000898)		CACTAACCTTCCACCTGGCAG	0.622																																					p.E81X		Atlas-SNP	.											.	ENTPD8	53	.	0			c.G241T						PASS	.						54	58	56					9																	140332422		2202	4300	6502	SO:0001587	stop_gained	377841	exon3			AACCTTCCACCTG	AY359088	CCDS7043.1, CCDS43913.1	9q34.3	2013-09-20			ENSG00000188833	ENSG00000188833			24860	protein-coding gene	gene with protein product	"GLSR2492"					12975309	Standard	NM_198585		Approved	UNQ2492, NTPDase-8	uc004cmw.3	Q5MY95	OTTHUMG00000131831	ENST00000472938.1:c.241G>T	chr9.hg19:g.140332422C>A	ENSP00000420531:p.Glu81*	31.0	0.0	.		20.0	10.0	.	NM_198585	A2BG17|Q6UVZ0	Nonsense_Mutation	SNP	ENST00000472938.1	hg19	CCDS43913.1	.	.	.	.	.	.	.	.	.	.	C	37	6.173688	0.97348	.	.	ENSG00000188833	ENST00000344119;ENST00000371506;ENST00000472938;ENST00000493135	.	.	.	4.3	0.708	0.18144	.	0.719465	0.12972	N	0.424026	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.9216	0.19086	0.0:0.5815:0.2643:0.1542	.	.	.	.	X	81;81;81;68	.	ENSP00000344089:E81X	E	-	1	0	ENTPD8	139452243	0.000000	0.05858	0.975000	0.42487	0.957000	0.61999	-4.003000	0.00316	0.289000	0.22422	0.561000	0.74099	GAA	.	.	.	none		0.622	ENTPD8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355991.1	NM_198585		A	140332422	C	A	140332422	4	1	248	1	0	0	0	0	0	1	0	0	5147	864	30	4	1278	4	ENTPD8	9	140332422	Nonsense_Mutation	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10	37601685	140332422	881009	54	15378											
DIP2C	22982	hgsc.bcm.edu	37	chr10	375429	375429	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcacagctccatcacggagtAggagcaaaacgtgtctcgga	12	6	12	11	3	2	0	1	0	1	0	4	3	3	3	1	3	3	4	1	3	3	1			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr10:375429A>G	ENST00000280886.6	-	30	3784	c.3697T>C	c.(3697-3699)Tac>Cac	p.Y1233H		NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1233						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)		ATCACGGAGTAGGAGCAAAAC	0.597																																					p.Y1233H		Atlas-SNP	.											.	DIP2C	195	.	0			c.T3697C						PASS	.						63	53	57					10																	375429		2203	4300	6503	SO:0001583	missense	22982	exon30			CGGAGTAGGAGCA	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.3697T>C	chr10.hg19:g.375429A>G	ENSP00000280886:p.Tyr1233His	35.0	0.0	.		24.0	8.0	.	NM_014974	B4DPI5|Q5SS78	Missense_Mutation	SNP	ENST00000280886.6	hg19	CCDS7054.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.1|20.1	3.932482|3.932482	0.73442|0.73442	.|.	.|.	ENSG00000151240|ENSG00000151240	ENST00000434695|ENST00000280886;ENST00000535541;ENST00000381503	.|T	.|0.10477	.|2.87	5.84|5.84	5.84|5.84	0.93424|0.93424	.|AMP-dependent synthetase/ligase (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.15522|0.15522	0.0374|0.0374	L|L	0.56769|0.56769	1.78|1.78	0.80722|0.80722	D|D	1|1	.|B	.|0.32382	.|0.368	.|B	.|0.37346	.|0.247	T|T	0.06588|0.06588	-1.0818|-1.0818	5|10	.|0.15952	.|T	.|0.53	-25.606|-25.606	16.2141|16.2141	0.82191|0.82191	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|1233	.|Q9Y2E4	.|DIP2C_HUMAN	P|H	38|1233;158;82	.|ENSP00000280886:Y1233H	.|ENSP00000280886:Y1233H	L|Y	-|-	2|1	0|0	DIP2C|DIP2C	365429|365429	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.978000|0.978000	0.69477|0.69477	9.339000|9.339000	0.96797|0.96797	2.230000|2.230000	0.72887|0.72887	0.528000|0.528000	0.53228|0.53228	CTA|TAC	.	.	.	none		0.597	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974		G	375429	A	G	375429	3	3	248	1	0	0	0	0	1	0	0	0	4531	420	15	3	1005	3	DIP2C	10	375429	Missense_Mutation	SNP	A	TCGA-SX-A7SN-01A-11D-A34Z-10		375429	135159318	55	15379											
ASB13	79754	hgsc.bcm.edu	37	chr10	5683908	5683908	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagtctcatgaagctttgcCgcattcacgttggcccctgg	6	11	11	13	2	2	1	2	1	1	0	3	1	2	1	3	2	2	4	3	2	1	3			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr10:5683908C>T	ENST00000357700.6	-	5	560	c.534G>A	c.(532-534)gcG>gcA	p.A178A	ASB13_ENST00000479033.1_5'UTR	NM_024701.3	NP_078977.2	Q8WXK3	ASB13_HUMAN	ankyrin repeat and SOCS box containing 13	178					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					NS(1)|endometrium(3)|lung(3)|ovary(1)	8				GBM - Glioblastoma multiforme(2;9.59e-09)		GAAGCTTTGCCGCATTCACGT	0.537																																					p.A178A		Atlas-SNP	.											.	ASB13	26	.	0			c.G534A						PASS	.						108	88	95					10																	5683908		2203	4300	6503	SO:0001819	synonymous_variant	79754	exon5			CTTTGCCGCATTC	AK091935	CCDS7070.1	10p15.1	2013-01-10	2011-01-25		ENSG00000196372	ENSG00000196372		"Ankyrin repeat domain containing"	19765	protein-coding gene	gene with protein product		615055	"ankyrin repeat and SOCS box-containing 13"			12076535	Standard	NM_024701		Approved	FLJ13134, MGC19879	uc001iig.2	Q8WXK3	OTTHUMG00000017603	ENST00000357700.6:c.534G>A	chr10.hg19:g.5683908C>T		78.0	0.0	.		84.0	28.0	.	NM_024701	A8K7Q6|D3DRR2|Q96EP7|Q9H8Z1	Silent	SNP	ENST00000357700.6	hg19	CCDS7070.1																																																																																			.	.	.	none		0.537	ASB13-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046564.1			T	5683908	C	T	5683908	2	4	248	1	0	0	0	0	0	0	0	1	1017	639	23	1		1	ASB13	10	5683908	Silent	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10	5308479	5683908	129850839	56	15380											
IPMK	253430	hgsc.bcm.edu	37	chr10	59986850	59986850	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgccataatattttggcaaAtattttcgtagctctagaag	13	15	7	6	1	1	1	0	0	1	1	2	1	1	1	1	1	2	3	1	1	7	9			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr10:59986850A>G	ENST00000373935.3	-	3	649	c.327T>C	c.(325-327)taT>taC	p.Y109Y		NM_152230.4	NP_689416.1	Q8NFU5	IPMK_HUMAN	inositol polyphosphate multikinase	109					inositol phosphate biosynthetic process (GO:0032958)|inositol phosphate metabolic process (GO:0043647)|neural tube formation (GO:0001841)|small molecule metabolic process (GO:0044281)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol tetrakisphosphate 3-kinase activity (GO:0000824)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)|inositol-1,4,5-trisphosphate 6-kinase activity (GO:0000823)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)	22						ATTTTGGCAAATATTTTCGTA	0.348																																					p.Y109Y		Atlas-SNP	.											.	IPMK	45	.	0			c.T327C						PASS	.						103	104	104					10																	59986850		2203	4300	6503	SO:0001819	synonymous_variant	253430	exon3			TGGCAAATATTTT	AF432853	CCDS7250.1	10q21.1	2010-11-29		2004-07-22	ENSG00000151151	ENSG00000151151			20739	protein-coding gene	gene with protein product		609851				12223481, 12027805	Standard	NM_152230		Approved		uc001jkb.3	Q8NFU5	OTTHUMG00000018268	ENST00000373935.3:c.327T>C	chr10.hg19:g.59986850A>G		52.0	0.0	.		49.0	15.0	.	NM_152230		Silent	SNP	ENST00000373935.3	hg19	CCDS7250.1																																																																																			.	.	.	none		0.348	IPMK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048142.1	NM_152230		G	59986850	A	G	59986850	2	3	248	1	0	0	0	0	0	0	0	1	7799	108	4	3		3	IPMK	10	59986850	Silent	SNP	A	TCGA-SX-A7SN-01A-11D-A34Z-10	54302942	59986850	75547897	57	15381											
CCAR1	55749	hgsc.bcm.edu	37	chr10	70547942	70547942	+	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	accaacagtaaagcaggaatCaaaggatgtggaagaaaatg	20	5	11	5	0	1	1	1	0	0	1	1	4	1	4	1	3	2	2	1	3	8	1			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr10:70547942C>T	ENST00000265872.6	+	23	3163	c.3044C>T	c.(3043-3045)tCa>tTa	p.S1015L	CCAR1_ENST00000543719.1_Missense_Mutation_p.S1000L|CCAR1_ENST00000535016.1_Missense_Mutation_p.S1000L	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	1015					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						AAGCAGGAATCAAAGGATGTG	0.318																																					p.S1015L		Atlas-SNP	.											.	CCAR1	118	.	0			c.C3044T						PASS	.						115	114	114					10																	70547942		2203	4300	6503	SO:0001583	missense	55749	exon23			AGGAATCAAAGGA	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.3044C>T	chr10.hg19:g.70547942C>T	ENSP00000265872:p.Ser1015Leu	241.0	0.0	.		290.0	118.0	.	NM_018237	A0JLT7|A1L4P7|A8K9D4|B4DNP8|B4DRK8|Q32NE3|Q5EBM3|Q5VUP6|Q6PIZ0|Q6X935|Q9H8N4|Q9NVA7|Q9NVQ0|Q9NWM6	Missense_Mutation	SNP	ENST00000265872.6	hg19	CCDS7282.1	.	.	.	.	.	.	.	.	.	.	C	11.89	1.773748	0.31411	.	.	ENSG00000060339	ENST00000265872;ENST00000535016;ENST00000543719;ENST00000539539	T;T;T;T	0.00316	8.13;8.13;8.13;8.13	5.0	1.92	0.25849	.	0.653955	0.14932	N	0.290013	T	0.00109	0.0003	N	0.12182	0.205	0.18873	N	0.999989	B	0.02656	0.0	B	0.01281	0.0	T	0.07888	-1.0749	10	0.28530	T	0.3	-2.6089	7.6308	0.28238	0.0:0.5156:0.3318:0.1526	.	1015	Q8IX12	CCAR1_HUMAN	L	1015;1000;1000;1000	ENSP00000265872:S1015L;ENSP00000441820:S1000L;ENSP00000445254:S1000L;ENSP00000439252:S1000L	ENSP00000265872:S1015L	S	+	2	0	CCAR1	70217948	0.002000	0.14202	0.997000	0.53966	0.996000	0.88848	0.130000	0.15850	0.511000	0.28236	0.558000	0.71614	TCA	.	.	.	none		0.318	CCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048356.2	NM_018237		T	70547942	C	T	70547942	3	4	248	1	0	0	0	0	1	0	0	0	2732	838	29	2	3130	2	CCAR1	10	70547942	Missense_Mutation	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10	10561092	70547942	64986805	58	15382											
SEC24C	9632	hgsc.bcm.edu	37	chr10	75529171	75529171	+	Missense_Mutation	SNP	T	T	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	tccataatctggccctgaacTgctgcacccagctggctgat	8	10	9	14	0	1	2	0	2	1	0	2	2	2	2	3	2	4	4	3	2	2	1			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr10:75529171T>G	ENST00000339365.2	+	19	2653	c.2491T>G	c.(2491-2493)Tgc>Ggc	p.C831G	FUT11_ENST00000372841.3_5'Flank|FUT11_ENST00000394790.1_5'Flank|SEC24C_ENST00000411652.2_Missense_Mutation_p.C712G|SEC24C_ENST00000540668.1_Missense_Mutation_p.C79G|SEC24C_ENST00000496827.1_3'UTR|SEC24C_ENST00000535742.1_Missense_Mutation_p.C79G|SEC24C_ENST00000345254.4_Missense_Mutation_p.C831G	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	831					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)					GGCCCTGAACTGCTGCACCCA	0.567																																					p.C831G		Atlas-SNP	.											.	SEC24C	86	.	0			c.T2491G						PASS	.						53	48	50					10																	75529171		2203	4300	6503	SO:0001583	missense	9632	exon18			CTGAACTGCTGCA	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.2491T>G	chr10.hg19:g.75529171T>G	ENSP00000343405:p.Cys831Gly	85.0	0.0	.		95.0	45.0	.	NM_198597	B4DZT4|Q8WV25	Missense_Mutation	SNP	ENST00000339365.2	hg19	CCDS7332.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.435280	0.83885	.	.	ENSG00000176986	ENST00000535742;ENST00000345254;ENST00000540668;ENST00000339365;ENST00000411652	T;T;T;T;T	0.74209	-0.82;-0.82;-0.82;-0.82;-0.82	5.57	5.57	0.84162	Sec23/Sec24 beta-sandwich (1);	0.000000	0.85682	D	0.000000	D	0.87581	0.6213	M	0.84683	2.71	0.80722	D	1	P;D	0.61080	0.952;0.989	D;D	0.85130	0.975;0.997	D	0.89605	0.3837	10	0.87932	D	0	-10.2796	15.7123	0.77641	0.0:0.0:0.0:1.0	.	712;831	E7EP00;P53992	.;SC24C_HUMAN	G	79;831;79;831;712	ENSP00000446174:C79G;ENSP00000321845:C831G;ENSP00000445023:C79G;ENSP00000343405:C831G;ENSP00000402913:C712G	ENSP00000343405:C831G	C	+	1	0	SEC24C	75199177	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.994000	0.88315	2.123000	0.65237	0.260000	0.18958	TGC	.	.	.	none		0.567	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1			G	75529171	T	G	75529171	3	3	248	1	0	0	0	0	1	0	0	0	14009	1580	55	5	2557	5	SEC24C	10	75529171	Missense_Mutation	SNP	T	TCGA-SX-A7SN-01A-11D-A34Z-10	4981229	75529171	60005576	59	15383											
AFAP1L2	84632	hgsc.bcm.edu	37	chr10	116062118	116062118	+	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	aagagagagtttttggccgcActcacaatacaggagaccct	13	8	10	10	1	1	3	1	0	0	3	1	5	1	3	2	2	1	2	2	2	3	3			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr10:116062118A>T	ENST00000304129.4	-	12	1439	c.1410T>A	c.(1408-1410)agT>agA	p.S470R	AFAP1L2_ENST00000369271.3_Missense_Mutation_p.S470R|AFAP1L2_ENST00000545353.1_Missense_Mutation_p.S523R|AFAP1L2_ENST00000491814.1_5'Flank			Q8N4X5	AF1L2_HUMAN	actin filament associated protein 1-like 2	470					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)		TTTTGGCCGCACTCACAATAC	0.542																																					p.S470R		Atlas-SNP	.											.	AFAP1L2	90	.	0			c.T1410A						PASS	.						154	170	165					10																	116062118		2203	4300	6503	SO:0001583	missense	84632	exon12			GGCCGCACTCACA	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.1410T>A	chr10.hg19:g.116062118A>T	ENSP00000303042:p.Ser470Arg	56.0	0.0	.		48.0	4.0	.	NM_032550	A8K6P7|B3KVQ8|Q2UZW3|Q8TB54|Q96PX4|Q96SY5	Missense_Mutation	SNP	ENST00000304129.4	hg19	CCDS31286.1	.	.	.	.	.	.	.	.	.	.	A	19.72	3.880627	0.72294	.	.	ENSG00000169129	ENST00000369271;ENST00000304129;ENST00000392974;ENST00000545353	T;T;T	0.17854	2.25;2.25;2.25	5.67	-5.88	0.02290	.	0.233607	0.50627	D	0.000118	T	0.27798	0.0684	M	0.73598	2.24	0.29591	N	0.848408	P;P;P;B;P;P	0.52463	0.953;0.928;0.922;0.249;0.953;0.921	P;P;P;B;P;B	0.53401	0.725;0.494;0.535;0.444;0.615;0.411	T	0.20438	-1.0275	10	0.31617	T	0.26	-8.7309	17.5452	0.87859	0.3705:0.0:0.6295:0.0	.	523;36;524;498;470;470	F5GZE1;B7Z363;B7Z2Q0;Q8N4X5-4;Q8N4X5-2;Q8N4X5	.;.;.;.;.;AF1L2_HUMAN	R	470;470;497;523	ENSP00000358276:S470R;ENSP00000303042:S470R;ENSP00000444511:S523R	ENSP00000303042:S470R	S	-	3	2	AFAP1L2	116052108	0.151000	0.22747	0.270000	0.24601	0.994000	0.84299	-0.307000	0.08167	-1.227000	0.02571	0.533000	0.62120	AGT	.	.	.	none		0.542	AFAP1L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050462.1	NM_032550		T	116062118	A	T	116062118	3	4	248	1	0	0	0	0	1	0	0	0	355	156	6	5	1078	5	AFAP1L2	10	116062118	Missense_Mutation	SNP	A	TCGA-SX-A7SN-01A-11D-A34Z-10	40532947	116062118	19472629	60	15384											
BCCIP	56647	hgsc.bcm.edu	37	chr10	127515167	127515167	+	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	gtgttatttacaggaagtgaAtattgaatttgaagcttatt	13	17	9	2	0	0	3	0	3	0	0	0	4	0	4	0	1	2	2	0	1	8	8			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr10:127515167A>T	ENST00000278100.6	+	2	185	c.173A>T	c.(172-174)aAt>aTt	p.N58I	BCCIP_ENST00000478798.1_3'UTR|BCCIP_ENST00000368759.5_Missense_Mutation_p.N58I|BCCIP_ENST00000299130.3_Missense_Mutation_p.N58I|BCCIP_ENST00000429863.2_Missense_Mutation_p.N58I	NM_078468.2	NP_510868.1	Q9P287	BCCIP_HUMAN	BRCA2 and CDKN1A interacting protein	58					cell cycle (GO:0007049)|DNA repair (GO:0006281)|neuroendocrine cell differentiation (GO:0061101)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nucleus (GO:0005634)	kinase regulator activity (GO:0019207)|poly(A) RNA binding (GO:0044822)			breast(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(1)	8		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				CAGGAAGTGAATATTGAATTT	0.308																																					p.N58I		Atlas-SNP	.											.	BCCIP	48	.	0			c.A173T						PASS	.						81	83	82					10																	127515167		2202	4299	6501	SO:0001583	missense	56647	exon2			AAGTGAATATTGA	AB040451	CCDS7649.1, CCDS7650.1, CCDS7651.1	10q26.2	2008-05-14	2001-11-29		ENSG00000107949	ENSG00000107949			978	protein-coding gene	gene with protein product		611883	"BRCA2 and CDKN1A-interacting protein"			11313963, 10878006	Standard	NM_016567		Approved	BCCIPalpha, TOK-1	uc001ljd.4	Q9P287	OTTHUMG00000019237	ENST00000278100.6:c.173A>T	chr10.hg19:g.127515167A>T	ENSP00000278100:p.Asn58Ile	72.0	0.0	.		78.0	16.0	.	NM_016567	B3KP45|Q8ND15|Q96GC4|Q9P288	Missense_Mutation	SNP	ENST00000278100.6	hg19	CCDS7651.1	.	.	.	.	.	.	.	.	.	.	A	15.78	2.934472	0.52866	.	.	ENSG00000107949	ENST00000278100;ENST00000299130;ENST00000368759;ENST00000429863;ENST00000392718	T;T;T;T	0.51071	0.72;0.72;0.72;0.72	5.09	2.58	0.30949	.	0.364353	0.31257	N	0.007978	T	0.31670	0.0804	L	0.41027	1.25	0.58432	D	0.999998	B;B;B;B;B	0.30068	0.267;0.267;0.225;0.225;0.065	B;B;B;B;B	0.27380	0.079;0.079;0.047;0.047;0.054	T	0.04796	-1.0926	10	0.12766	T	0.61	-32.3549	8.2271	0.31575	0.7938:0.1334:0.0728:0.0	.	58;58;58;58;58	B4E318;B4DUS0;Q9P287-2;Q9P287-4;Q9P287	.;.;.;.;BCCIP_HUMAN	I	58	ENSP00000278100:N58I;ENSP00000299130:N58I;ENSP00000357748:N58I;ENSP00000394758:N58I	ENSP00000278100:N58I	N	+	2	0	BCCIP	127505157	0.972000	0.33761	0.995000	0.50966	0.992000	0.81027	2.162000	0.42367	0.895000	0.36342	0.533000	0.62120	AAT	.	.	.	none		0.308	BCCIP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050941.1			T	127515167	A	T	127515167	3	4	248	1	0	0	0	0	1	0	0	0	1356	101	4	5	179	5	BCCIP	10	127515167	Missense_Mutation	SNP	A	TCGA-SX-A7SN-01A-11D-A34Z-10	11453049	127515167	8019580	61	15385											
NAV2	89797	hgsc.bcm.edu	37	chr11	20065595	20065595	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgatgatgtcaagaaatcAgacggaggctcagacagcgg	13	6	15	7	2	3	5	3	2	0	3	3	6	3	6	0	4	1	1	0	4	2	0			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr11:20065595A>G	ENST00000396087.3	+	14	3144	c.3045A>G	c.(3043-3045)tcA>tcG	p.S1015S	NAV2_ENST00000396085.1_Silent_p.S992S|NAV2_ENST00000533917.1_Silent_p.S78S|NAV2_ENST00000527559.2_Silent_p.S944S|NAV2_ENST00000360655.4_Silent_p.S928S|NAV2_ENST00000540292.1_Silent_p.S946S|NAV2-AS2_ENST00000533767.1_RNA|NAV2_ENST00000349880.4_Silent_p.S992S|NAV2_ENST00000311043.8_Silent_p.S78S	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	1015					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						TCAAGAAATCAGACGGAGGCT	0.517																																					p.S1015S		Atlas-SNP	.											.	NAV2	255	.	0			c.A3045G						PASS	.						99	99	99					11																	20065595		2203	4300	6503	SO:0001819	synonymous_variant	89797	exon14			GAAATCAGACGGA	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.3045A>G	chr11.hg19:g.20065595A>G		33.0	0.0	.		50.0	17.0	.	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	hg19	CCDS58126.1																																																																																			.	.	.	none		0.517	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		G	20065595	A	G	20065595	2	3	248	1	0	0	0	0	0	0	0	1	10191	175	7	3		3	NAV2	11	20065595	Silent	SNP	A	TCGA-SX-A7SN-01A-11D-A34Z-10		20065595	114940921	62	15386											
SLC5A12	159963	hgsc.bcm.edu	37	chr11	26720062	26720062	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagaatgatccagagacccAgcaagttaaaatacaaggca	18	5	8	10	0	0	3	0	1	0	2	1	4	1	3	3	1	2	3	3	1	6	2			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr11:26720062A>G	ENST00000396005.3	-	7	1151	c.842T>C	c.(841-843)cTg>cCg	p.L281P	SLC5A12_ENST00000280467.6_Missense_Mutation_p.L281P	NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	281					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						CCAGAGACCCAGCAAGTTAAA	0.448																																					p.L281P		Atlas-SNP	.											.	SLC5A12	134	.	0			c.T842C						PASS	.						116	105	109					11																	26720062		2203	4299	6502	SO:0001583	missense	159963	exon7			AGACCCAGCAAGT	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.842T>C	chr11.hg19:g.26720062A>G	ENSP00000379326:p.Leu281Pro	55.0	0.0	.		76.0	34.0	.	NM_178498	Q86UC7	Missense_Mutation	SNP	ENST00000396005.3	hg19	CCDS7860.2	.	.	.	.	.	.	.	.	.	.	A	25.0	4.593547	0.86953	.	.	ENSG00000148942	ENST00000396005;ENST00000280467;ENST00000533617	D;D;D	0.87334	-2.24;-2.24;-2.24	6.07	6.07	0.98685	.	0.268718	0.27951	N	0.017189	D	0.86439	0.5933	N	0.11064	0.09	0.80722	D	1	P;D	0.69078	0.942;0.997	P;D	0.73708	0.771;0.981	D	0.85491	0.1185	10	0.22706	T	0.39	.	16.6277	0.84984	1.0:0.0:0.0:0.0	.	281;281	Q1EHB4-2;Q1EHB4	.;SC5AC_HUMAN	P	281;281;93	ENSP00000379326:L281P;ENSP00000280467:L281P;ENSP00000435053:L93P	ENSP00000280467:L281P	L	-	2	0	SLC5A12	26676638	1.000000	0.71417	0.936000	0.37596	0.825000	0.46686	9.154000	0.94694	2.330000	0.79161	0.528000	0.53228	CTG	.	.	.	none		0.448	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498		G	26720062	A	G	26720062	3	3	248	1	0	0	0	0	1	0	0	0	14677	188	7	3	1050	3	SLC5A12	11	26720062	Missense_Mutation	SNP	A	TCGA-SX-A7SN-01A-11D-A34Z-10	6654467	26720062	108286454	63	15387											
ZNF408	79797	hgsc.bcm.edu	37	chr11	46724728	46724728	+	Missense_Mutation	SNP	A	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	agctgtagcagtggtgacagAagtggagtctgctgtacagc	10	9	15	7	0	1	2	0	1	1	1	1	3	1	3	0	2	5	5	0	2	3	2	rs376220307|rs148055528	byFrequency	TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr11:46724728A>C	ENST00000311764.2	+	4	817	c.587A>C	c.(586-588)gAa>gCa	p.E196A	ARHGAP1_ENST00000311956.4_5'Flank	NM_001184751.1|NM_024741.2	NP_001171680.1|NP_079017.1	Q9H9D4	ZN408_HUMAN	zinc finger protein 408	196					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GTGGTGACAGAAGTGGAGTCT	0.567																																					p.E196A	Pancreas(79;698 1390 6545 18745 34127)|Esophageal Squamous(120;1014 1625 12837 24601 49525)	Atlas-SNP	.											ZNF408,caecum,carcinoma,0,1	ZNF408	70	.	0			c.A587C						PASS	.	A	ALA/GLU,ALA/GLU	4,4398		0,4,2197	46	39	42		563,587	0.5	0.6	11		42	36,8500		10,16,4242	no	missense,missense	ZNF408	NM_001184751.1,NM_024741.2	107,107	10,20,6439	CC,CA,AA		0.4217,0.0909,0.3092	benign,benign	188/713,196/721	46724728	40,12898	2201	4268	6469	SO:0001583	missense	79797	exon4			TGACAGAAGTGGA	AF346626	CCDS7923.1	11p11.2	2008-02-05			ENSG00000175213	ENSG00000175213		"Zinc fingers, C2H2-type"	20041	protein-coding gene	gene with protein product						15231747	Standard	NM_024741		Approved	FLJ12827	uc010rgw.2	Q9H9D4	OTTHUMG00000166568	ENST00000311764.2:c.587A>C	chr11.hg19:g.46724728A>C	ENSP00000309606:p.Glu196Ala	31.0	0.0	.		37.0	4.0	.	NM_024741		Missense_Mutation	SNP	ENST00000311764.2	hg19	CCDS7923.1	.	.	.	.	.	.	.	.	.	.	A	16.30	3.083402	0.55861	9.09E-4	0.004217	ENSG00000175213	ENST00000311764	T	0.10477	2.87	5.66	0.47	0.16747	.	0.900334	0.09183	N	0.837160	T	0.07593	0.0191	L	0.32530	0.975	0.09310	N	1	B;B	0.31680	0.335;0.335	B;B	0.25140	0.058;0.058	T	0.40590	-0.9555	10	0.19590	T	0.45	-0.378	9.3275	0.38001	0.6254:0.0:0.3746:0.0	.	188;196	B4DXY4;Q9H9D4	.;ZN408_HUMAN	A	196	ENSP00000309606:E196A	ENSP00000309606:E196A	E	+	2	0	ZNF408	46681304	0.229000	0.23729	0.610000	0.28997	0.457000	0.32468	-0.129000	0.10515	0.078000	0.16900	0.533000	0.62120	GAA	.	.	.	weak		0.567	ZNF408-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390485.2	NM_024741		C	46724728	A	C	46724728	3	2	248	1	0	0	0	0	1	0	0	0	17900	246	9	5	633	5	ZNF408	11	46724728	Missense_Mutation	SNP	A	TCGA-SX-A7SN-01A-11D-A34Z-10	20004666	46724728	88281788	64	15388											
C11orf73	51501	hgsc.bcm.edu	37	chr11	86048421	86048421	+	Splice_Site	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	catatgttaatttcttgcagGagaaggaagccaacatcctt	13	12	8	8	0	1	1	0	0	1	1	2	3	2	2	2	2	3	2	2	2	5	5			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr11:86048421G>C	ENST00000278483.3	+	3	495	c.269G>C	c.(268-270)gGa>gCa	p.G90A	C11orf73_ENST00000530208.1_3'UTR|C11orf73_ENST00000533986.1_Splice_Site_p.G90A	NM_016401.3	NP_057485.2	Q53FT3	HIKES_HUMAN	chromosome 11 open reading frame 73	90					cellular response to heat (GO:0034605)|Golgi organization (GO:0007030)|lung development (GO:0030324)|protein import into nucleus (GO:0006606)|protein transport (GO:0015031)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	Hsp70 protein binding (GO:0030544)|protein transporter activity (GO:0008565)			kidney(1)|large_intestine(1)|urinary_tract(1)	3		Acute lymphoblastic leukemia(157;1.17e-07)|all_hematologic(158;0.000556)				TTTCTTGCAGGAGAAGGAAGC	0.338																																					p.G90A		Atlas-SNP	.											.	C11orf73	9	.	0			c.G269C						PASS	.						150	142	144					11																	86048421		2202	4299	6501	SO:0001630	splice_region_variant	51501	exon3			TTGCAGGAGAAGG	BC015991	CCDS8275.1	11q14.2	2013-03-12			ENSG00000149196	ENSG00000149196			26938	protein-coding gene	gene with protein product		614908				11042152, 22541429	Standard	NM_016401		Approved	HSPC138, HSPC179, Hikeshi, OPI10	uc001pbu.3	Q53FT3	OTTHUMG00000167212	ENST00000278483.3:c.269-1G>C	chr11.hg19:g.86048421G>C		76.0	0.0	.		90.0	32.0	.	NM_016401	Q8WVE8|Q9NVQ2|Q9NZZ1|Q9P022|Q9P0N1	Missense_Mutation	SNP	ENST00000278483.3	hg19	CCDS8275.1	.	.	.	.	.	.	.	.	.	.	G	13.81	2.348862	0.41599	.	.	ENSG00000149196	ENST00000533986;ENST00000278483	T;T	0.41400	1.0;1.0	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.53142	0.1778	M	0.63428	1.95	0.80722	D	1	B;P	0.45348	0.106;0.856	B;P	0.49887	0.179;0.625	T	0.50541	-0.8816	9	.	.	.	.	18.5985	0.91239	0.0:0.0:1.0:0.0	.	90;90	Q53FT3;E9PPG8	CK073_HUMAN;.	A	90	ENSP00000432699:G90A;ENSP00000278483:G90A	.	G	+	2	0	C11orf73	85726069	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	6.629000	0.74267	2.566000	0.86566	0.555000	0.69702	GGA	.	.	.	none		0.338	C11orf73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393747.1	NM_016401	Missense_Mutation	C	86048421	G	C	86048421	5	2	248	1	0	0	0	0	0	0	1	0	1663	1188	41	4	279	4	C11orf73	11	86048421	Splice_Site	SNP	G	TCGA-SX-A7SN-01A-11D-A34Z-10	39323693	86048421	48958095	65	15389											
GUCY2C	2984	hgsc.bcm.edu	37	chr12	14822676	14822676	+	Frame_Shift_Del	DEL	G	G	-																															cccggcctgtaatatcattaGgaagtttagagttcttccaa																										TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr12:14822676delG	ENST00000261170.3	-	10	1398	c.1262delC	c.(1261-1263)cctfs	p.P421fs	RP11-174G6.1_ENST00000501178.2_RNA	NM_004963.3	NP_004954.2	P25092	GUC2C_HUMAN	guanylate cyclase 2C (heat stable enterotoxin receptor)	421					intracellular signal transduction (GO:0035556)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of cell proliferation (GO:0042127)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|toxic substance binding (GO:0015643)			breast(3)|endometrium(7)|kidney(3)|large_intestine(9)|lung(17)|ovary(4)|skin(7)|urinary_tract(1)	51					Linaclotide(DB08890)	AATATCATTAGGAAGTTTAGA	0.383																																					p.P421fs		Atlas-Indel,Pindel	.											.	GUCY2C	126	.	0			c.1263delT						PASS	.						113	109	111					12																	14822676		2203	4300	6503	SO:0001589	frameshift_variant	2984	exon10			.		CCDS8664.1	12p12	2008-08-18			ENSG00000070019	ENSG00000070019			4688	protein-coding gene	gene with protein product		601330		GUC2C		8661067	Standard	NM_004963		Approved	STAR	uc001rcd.3	P25092	OTTHUMG00000168732	ENST00000261170.3:c.1262delC	chr12.hg19:g.14822676delG	ENSP00000261170:p.Pro421fs	58.0	0.0	0		62.0	20.0	0.322581	NM_004963	B2RMY6	Frame_Shift_Del	DEL	ENST00000261170.3	hg19	CCDS8664.1																																																																																			.	.	.	none		0.383	GUCY2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400835.1			-	14822676	G	-	14822676	7	5	248	1	0	1	0	1	0	0	0	0	6903	1000	35	0	2031	0	GUCY2C	12	14822676	Frame_Shift_Del	DEL	G	TCGA-SX-A7SN-01A-11D-A34Z-10		14822676	119029219	66	15390											
ITPR2	3709	hgsc.bcm.edu	37	chr12	26810815	26810815	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catggggttgtctgcttgcaTtgagaccacccttcaaataa	10	12	9	10	0	2	1	1	1	1	1	2	2	2	1	2	2	2	3	2	2	2	5			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr12:26810815T>C	ENST00000381340.3	-	18	2433	c.2017A>G	c.(2017-2019)Atg>Gtg	p.M673V		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	673					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)	TCTGCTTGCATTGAGACCACC	0.378																																					p.M673V		Atlas-SNP	.											.	ITPR2	270	.	0			c.A2017G						PASS	.						99	90	93					12																	26810815		1858	4096	5954	SO:0001583	missense	3709	exon18			CTTGCATTGAGAC	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.2017A>G	chr12.hg19:g.26810815T>C	ENSP00000370744:p.Met673Val	126.0	0.0	.		132.0	50.0	.	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	hg19	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	T	0.151	-1.091885	0.01858	.	.	ENSG00000123104	ENST00000381340	D	0.95103	-3.61	4.4	4.4	0.53042	Intracellular calcium-release channel (1);	0.287733	0.43260	D	0.000583	D	0.85283	0.5661	N	0.08118	0	0.80722	D	1	B	0.11235	0.004	B	0.18263	0.021	T	0.79529	-0.1766	10	0.16896	T	0.51	.	9.5261	0.39165	0.157:0.0:0.0:0.843	.	673	Q14571	ITPR2_HUMAN	V	673	ENSP00000370744:M673V	ENSP00000370744:M673V	M	-	1	0	ITPR2	26702082	1.000000	0.71417	0.882000	0.34594	0.934000	0.57294	4.236000	0.58675	1.983000	0.57843	0.533000	0.62120	ATG	.	.	.	none		0.378	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		C	26810815	T	C	26810815	3	2	248	1	0	0	0	0	1	0	0	0	7928	1493	52	3	6248	3	ITPR2	12	26810815	Missense_Mutation	SNP	T	TCGA-SX-A7SN-01A-11D-A34Z-10	11988139	26810815	107041080	67	15391											
MLL2	8085	hgsc.bcm.edu	37	chr12	49445630	49445630	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggaaaggggagactcctcAggtggaggggacagaggaga	12	3	21	5	0	1	3	1	0	0	3	2	8	2	6	1	9	0	0	1	9	1	0			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr12:49445630A>G	ENST00000301067.7	-	10	1835	c.1836T>C	c.(1834-1836)ccT>ccC	p.P612P		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	612	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)										GAGACTCCTCAGGTGGAGGGG	0.597																																					p.P612P		Atlas-SNP	.											.	MLL2	1173	.	0			c.T1836C						PASS	.						76	79	78					12																	49445630		2092	4211	6303	SO:0001819	synonymous_variant	8085	exon10			CTCCTCAGGTGGA	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.1836T>C	chr12.hg19:g.49445630A>G		39.0	0.0	.		45.0	14.0	.	NM_003482	O14687	Silent	SNP	ENST00000301067.7	hg19	CCDS44873.1																																																																																			.	.	.	none		0.597	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			G	49445630	A	G	49445630	2	3	248	1	0	0	0	0	0	0	0	1	9628	175	7	3		3	MLL2	12	49445630	Silent	SNP	A	TCGA-SX-A7SN-01A-11D-A34Z-10	22634815	49445630	84406265	68	15392											
KERA	11081	hgsc.bcm.edu	37	chr12	91445296	91445296	+	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	tattacagagacattcacacCtacagtgacaaagagaatag	18	8	7	8	0	1	3	1	1	0	2	1	5	1	3	1	0	2	0	1	0	6	5			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr12:91445296C>T	ENST00000266719.3	-	3	1134		c.e3-1			NM_007035.3	NP_008966.1	O60938	KERA_HUMAN	keratocan						carbohydrate metabolic process (GO:0005975)|cornea development in camera-type eye (GO:0061303)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|response to stimulus (GO:0050896)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)				breast(2)|large_intestine(8)|lung(5)|prostate(2)|skin(2)	19						ACATTCACACCTACAGTGACA	0.458																																					.		Atlas-SNP	.											.	KERA	62	.	0			c.887-1G>A						PASS	.						71	61	64					12																	91445296		2203	4299	6502	SO:0001630	splice_region_variant	11081	exon4			TCACACCTACAGT	AF063301	CCDS9037.1	12q21.3-q22	2014-09-17				ENSG00000139330		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	6309	protein-coding gene	gene with protein product	"keratocan proteoglycan"	603288		CNA2		10565548, 10802664	Standard	NM_007035		Approved	SLRR2B	uc001tbl.3	O60938		ENST00000266719.3:c.887-1G>A	chr12.hg19:g.91445296C>T		23.0	0.0	.		26.0	12.0	.	NM_007035		Splice_Site	SNP	ENST00000266719.3	hg19	CCDS9037.1	.	.	.	.	.	.	.	.	.	.	C	12.83	2.054257	0.36277	.	.	ENSG00000139330	ENST00000266719	.	.	.	5.62	5.62	0.85841	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.2611	0.93968	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KERA	89969427	1.000000	0.71417	0.917000	0.36280	0.020000	0.10135	7.378000	0.79679	2.655000	0.90218	0.655000	0.94253	.	.	.	.	none		0.458	KERA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407149.2	NM_007035	Intron	T	91445296	C	T	91445296	5	4	248	1	0	0	0	0	0	0	1	0	8150	695	24	2	176	2	KERA	12	91445296	Splice_Site	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10	41999666	91445296	42406599	69	15393											
MTERFD3	80298	hgsc.bcm.edu	37	chr12	107371849	107371849	+	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	ttaacaaaataaatgggtttTggcttaacaattttagtagc	15	15	7	4	0	0	0	0	0	0	0	0	0	0	0	0	2	3	3	0	2	9	8			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr12:107371849T>A	ENST00000552029.1	-	2	2712	c.644A>T	c.(643-645)cAa>cTa	p.Q215L	C12orf23_ENST00000551237.1_Intron|MTERFD3_ENST00000240050.4_Missense_Mutation_p.Q215L|MTERFD3_ENST00000392830.2_Missense_Mutation_p.Q215L			Q49AM1	MTEF2_HUMAN		215					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)	transcription regulatory region DNA binding (GO:0044212)			breast(1)|kidney(1)|large_intestine(2)|lung(3)	7						AAATGGGTTTTGGCTTAACAA	0.378																																					p.Q215L		Atlas-SNP	.											.	MTERFD3	32	.	0			c.A644T						PASS	.						44	49	48					12																	107371849		2201	4299	6500	SO:0001583	missense	80298	exon3			GGGTTTTGGCTTA																												ENST00000552029.1:c.644A>T	chr12.hg19:g.107371849T>A	ENSP00000447651:p.Gln215Leu	79.0	0.0	.		102.0	38.0	.	NM_001033050	Q53HM2|Q9H4L6|Q9H7Y9	Missense_Mutation	SNP	ENST00000552029.1	hg19	CCDS9111.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.403428	0.83230	.	.	ENSG00000120832	ENST00000392830;ENST00000240050;ENST00000552029	T;T;T	0.08984	3.03;3.03;3.03	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.28962	0.0719	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00677	-1.1614	10	0.44086	T	0.13	-0.2116	16.1777	0.81874	0.0:0.0:0.0:1.0	.	215	Q49AM1	MTER3_HUMAN	L	215	ENSP00000376575:Q215L;ENSP00000240050:Q215L;ENSP00000447651:Q215L	ENSP00000240050:Q215L	Q	-	2	0	MTERFD3	105895979	1.000000	0.71417	0.997000	0.53966	0.986000	0.74619	7.698000	0.84413	2.222000	0.72286	0.383000	0.25322	CAA	.	.	.	none		0.378	MTERFD3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406835.1			A	107371849	T	A	107371849	3	1	248	1	0	0	0	0	1	0	0	0	9928	1812	63	5	517	5	MTERFD3	12	107371849	Missense_Mutation	SNP	T	TCGA-SX-A7SN-01A-11D-A34Z-10	15926553	107371849	26480046	70	15394											
ALDH2	217	hgsc.bcm.edu	37	chr12	112220989	112220990	+	Missense_Mutation	DNP	GC	GC	AA																															tggacaaggcagtgaaggccGcccgggccgccttccagctg																								rs375845001		TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr12:112220989_112220990GC>AA	ENST00000261733.2	+	3	308_309	c.247_248GC>AA	c.(247-249)GCc>AAc	p.A83N	RP11-162P23.2_ENST00000546840.2_Missense_Mutation_p.P80T|ALDH2_ENST00000416293.3_Intron	NM_000690.3	NP_000681.2	P05091	ALDH2_HUMAN	aldehyde dehydrogenase 2 family (mitochondrial)	83				VKAARA -> REGRPG (in Ref. 1; CAA28990). {ECO:0000305}.	alcohol metabolic process (GO:0006066)|carbohydrate metabolic process (GO:0005975)|ethanol catabolic process (GO:0006068)|ethanol oxidation (GO:0006069)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|electron carrier activity (GO:0009055)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|stomach(1)	22					Amyl Nitrite(DB01612)|Benzyl alcohol(DB06770)|Disulfiram(DB00822)|Guanidine(DB00536)|Nitric Oxide(DB00435)|Nitroglycerin(DB00727)	AGTGAAGGCCGCCCGGGCCGCC	0.594			T	HMGA2	leiomyoma																																p.A83T|p.A83D		Atlas-SNP	.		Dom	yes		12	12q24.2	217	aldehyde dehydrogenase 2 family (mitochondrial)		M	.	ALDH2	91	.	0			c.G247A|c.C248A						PASS	.																																			SO:0001583	missense	217	exon3			AAGGCCGCCCGGG|AGGCCGCCCGGGC	M26760	CCDS9155.1, CCDS55885.1	12q24.12	2007-12-14				ENSG00000111275	1.2.1.3	"Aldehyde dehydrogenases"	404	protein-coding gene	gene with protein product		100650				4015823, 2987944	Standard	NM_000690		Approved		uc001tst.3	P05091	OTTHUMG00000169603	Exception_encountered	chr12.hg19:g.112220989_112220990delinsAA	ENSP00000261733:p.Ala83Asn	31.0|32.0	0.0	.		36.0	14.0	.	NM_000690	B4DW54|E7EUE5|Q03639|Q6IB13|Q6IV71	Missense_Mutation	SNP	ENST00000261733.2	hg19	CCDS9155.1																																																																																			.	.	.	weak|none		0.594	ALDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405008.1	NM_000690		AA	112220990	GC	AA	112220989	3	1	248	1	0	0	0	0	1	0	0	0	496	1087	38	1	257	1	ALDH2	12	112220989	Missense_Mutation	DNP	GC	TCGA-SX-A7SN-01A-11D-A34Z-10	4849140	112220989	21630906	71	15395											
C12orf43	64897	hgsc.bcm.edu	37	chr12	121441960	121441960	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgcccatggctgggttcagTttgcaggtatagctgtagca	7	12	14	8	0	1	0	1	0	0	0	1	0	1	0	1	3	4	8	1	3	3	5			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr12:121441960T>C	ENST00000288757.3	-	6	807	c.785A>G	c.(784-786)aAc>aGc	p.N262S	C12orf43_ENST00000366211.2_Missense_Mutation_p.N221S|C12orf43_ENST00000536407.2_3'UTR|RP11-216P16.2_ENST00000606238.1_RNA|C12orf43_ENST00000537817.1_Missense_Mutation_p.N263S|C12orf43_ENST00000539736.1_Missense_Mutation_p.N252S|C12orf43_ENST00000445832.3_Missense_Mutation_p.N232S	NM_022895.1	NP_075046.1	Q96C57	CL043_HUMAN	chromosome 12 open reading frame 43	262										cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CTGGGTTCAGTTTGCAGGTAT	0.572																																					p.N262S		Atlas-SNP	.											.	C12orf43	30	.	0			c.A785G						PASS	.						184	182	183					12																	121441960		2203	4300	6503	SO:0001583	missense	64897	exon6			GTTCAGTTTGCAG	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.785A>G	chr12.hg19:g.121441960T>C	ENSP00000288757:p.Asn262Ser	96.0	0.0	.		121.0	38.0	.	NM_022895	Q53HF0|Q9H9Z7	Missense_Mutation	SNP	ENST00000288757.3	hg19	CCDS9210.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.02|15.02	2.708809|2.708809	0.48517|0.48517	.|.	.|.	ENSG00000157895|ENSG00000157895	ENST00000445832;ENST00000288757;ENST00000537817;ENST00000536407;ENST00000366211;ENST00000539736|ENST00000546272	T;T;T;T|.	0.52983|.	0.67;0.66;0.66;0.64|.	5.5|5.5	1.86|1.86	0.25419|0.25419	.|.	1.121610|.	0.06531|.	N|.	0.741551|.	T|T	0.37919|0.37919	0.1021|0.1021	L|L	0.53249|0.53249	1.67|1.67	0.09310|0.09310	N|N	1|1	B;B;D;B;B|.	0.61697|.	0.102;0.047;0.99;0.021;0.102|.	B;B;P;B;B|.	0.49597|.	0.037;0.013;0.616;0.022;0.037|.	T|T	0.30387|0.30387	-0.9980|-0.9980	10|5	0.66056|.	D|.	0.02|.	.|.	3.2634|3.2634	0.06856|0.06856	0.1723:0.1815:0.0:0.6462|0.1723:0.1815:0.0:0.6462	.|.	252;221;263;252;262|.	G5EA44;F6TFQ5;F5H7W8;B4DWJ9;Q96C57|.	.;.;.;.;CL043_HUMAN|.	S|A	232;262;263;160;221;252|216	ENSP00000409788:N232S;ENSP00000288757:N262S;ENSP00000442224:N263S;ENSP00000437803:N252S|.	ENSP00000288757:N262S|.	N|T	-|-	2|1	0|0	C12orf43|C12orf43	119926343|119926343	0.438000|0.438000	0.25602|0.25602	0.014000|0.014000	0.15608|0.15608	0.014000|0.014000	0.08584|0.08584	0.673000|0.673000	0.25203|0.25203	0.451000|0.451000	0.26802|0.26802	0.533000|0.533000	0.62120|0.62120	AAC|ACT	.	.	.	none		0.572	C12orf43-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022895		C	121441960	T	C	121441960	3	2	248	1	0	0	0	0	1	0	0	0	1691	1725	60	3	7	3	C12orf43	12	121441960	Missense_Mutation	SNP	T	TCGA-SX-A7SN-01A-11D-A34Z-10	9220971	121441960	12409935	72	15396											
KNTC1	9735	hgsc.bcm.edu	37	chr12	123089162	123089163	+	Missense_Mutation	DNP	GG	GG	AT																															cctttatttagctgagagatGgctacagaatatcccatcgc																										TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr12:123089162_123089163GG>AT	ENST00000333479.7	+	49	5330_5331	c.5153_5154GG>AT	c.(5152-5154)tGG>tAT	p.W1718Y	KNTC1_ENST00000450485.2_Intron|KNTC1_ENST00000436959.3_5'UTR|KNTC1_ENST00000537348.1_Missense_Mutation_p.W143Y	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	1718					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)		GCTGAGAGATGGCTACAGAATA	0.337																																					p.W1718X|p.W1718C		Atlas-SNP	.											.	KNTC1	182	.	0			c.G5153A|c.G5154T						PASS	.																																			SO:0001583	missense	9735	exon49			AGAGATGGCTACA|GAGATGGCTACAG		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	Exception_encountered	chr12.hg19:g.123089162_123089163delinsAT	ENSP00000328236:p.Trp1718Tyr	88.0	0.0	.		77.0	23.0	.	NM_014708	A7E2C4|B3KSG2	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000333479.7	hg19	CCDS45002.1																																																																																			.	.	.	none		0.337	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2			AT	123089163	GG	AT	123089162	3	1	248	1	0	0	0	0	1	0	0	0	8435	1357	47	2	5343	2	KNTC1	12	123089162	Missense_Mutation	DNP	GG	TCGA-SX-A7SN-01A-11D-A34Z-10	1647202	123089162	10762733	73	15397											
CCDC62	84660	hgsc.bcm.edu	37	chr12	123285813	123285813	+	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	ggtcagacaagagctcttgcGatgaatgcaaagagaagaaa	17	6	12	6	1	2	5	1	1	1	4	2	7	2	5	0	1	3	2	0	1	5	1			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr12:123285813G>A	ENST00000253079.6	+	9	1464	c.1120G>A	c.(1120-1122)Gat>Aat	p.D374N	CCDC62_ENST00000392441.4_Missense_Mutation_p.D374N|CCDC62_ENST00000392440.2_Missense_Mutation_p.D135N|CCDC62_ENST00000537566.1_Missense_Mutation_p.D135N	NM_201435.4	NP_958843.2	Q6P9F0	CCD62_HUMAN	coiled-coil domain containing 62	374					cellular response to estradiol stimulus (GO:0071392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(1)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.51e-06)|Epithelial(86;2.65e-05)|BRCA - Breast invasive adenocarcinoma(302;0.206)		GAGCTCTTGCGATGAATGCAA	0.383																																					p.D374N		Atlas-SNP	.											.	CCDC62	119	.	0			c.G1120A						PASS	.						97	91	93					12																	123285813		2203	4300	6503	SO:0001583	missense	84660	exon9			TCTTGCGATGAAT		CCDS9238.1	12q24.31	2009-08-18			ENSG00000130783	ENSG00000130783			30723	protein-coding gene	gene with protein product	"cancer/testis antigen 109"	613481				18563714, 19126643	Standard	NM_201435		Approved	TSP-NY, FLJ40344, CT109, ERAP75	uc001udc.3	Q6P9F0	OTTHUMG00000168764	ENST00000253079.6:c.1120G>A	chr12.hg19:g.123285813G>A	ENSP00000253079:p.Asp374Asn	101.0	0.0	.		122.0	46.0	.	NM_201435	A8K8V1|B3KUP3|Q6ZVF2|Q86VJ0|Q9BYZ5	Missense_Mutation	SNP	ENST00000253079.6	hg19	CCDS9238.1	.	.	.	.	.	.	.	.	.	.	G	18.64	3.668017	0.67814	.	.	ENSG00000130783	ENST00000253079;ENST00000392441;ENST00000537566;ENST00000392440	T;T;T;T	0.59364	0.92;0.91;0.27;0.27	5.62	2.84	0.33178	.	0.538297	0.16861	N	0.196523	T	0.46249	0.1383	L	0.59436	1.845	0.09310	N	1	B;P;B	0.44281	0.212;0.831;0.066	B;B;B	0.33042	0.029;0.157;0.011	T	0.41592	-0.9500	10	0.87932	D	0	-2.9694	7.8178	0.29269	0.2517:0.0:0.7483:0.0	.	374;135;374	Q6P9F0-2;Q6P9F0-3;Q6P9F0	.;.;CCD62_HUMAN	N	374;374;135;135	ENSP00000253079:D374N;ENSP00000376236:D374N;ENSP00000445045:D135N;ENSP00000376235:D135N	ENSP00000253079:D374N	D	+	1	0	CCDC62	121851766	0.519000	0.26242	0.000000	0.03702	0.010000	0.07245	2.499000	0.45372	0.344000	0.23847	0.655000	0.94253	GAT	.	.	.	none		0.383	CCDC62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400930.1	NM_032573		A	123285813	G	A	123285813	3	1	248	1	0	0	0	0	1	0	0	0	2835	1058	37	1	1154	1	CCDC62	12	123285813	Missense_Mutation	SNP	G	TCGA-SX-A7SN-01A-11D-A34Z-10	196651	123285813	10566082	74	15398											
PCDH20	64881	hgsc.bcm.edu	37	chr13	61986120	61986120	+	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	cacaaagtataggagctttgCtgctctctgtccaaagagac	12	10	9	10	0	1	1	0	0	1	1	3	3	2	2	1	1	3	4	1	1	4	3			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr13:61986120C>T	ENST00000409186.1	-	5	4217	c.2112G>A	c.(2110-2112)caG>caA	p.Q704Q	PCDH20_ENST00000409204.4_Silent_p.Q704Q			Q8N6Y1	PCD20_HUMAN	protocadherin 20	704	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)|poly(A) RNA binding (GO:0044822)	p.Q704H(1)|p.Q677H(1)		breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(14)|liver(1)|lung(23)|ovary(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	58		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		AGGAGCTTTGCTGCTCTCTGT	0.463																																					p.Q704Q		Atlas-SNP	.											PCDH20_ENST00000409186,NS,carcinoma,0,2	PCDH20	265	.	2	Substitution - Missense(2)	lung(2)	c.G2112A						PASS	.						96	103	101					13																	61986120		2203	4299	6502	SO:0001819	synonymous_variant	64881	exon2			GCTTTGCTGCTCT	AF169693	CCDS9442.2	13q21	2010-01-26			ENSG00000197991	ENSG00000197991		"Cadherins / Protocadherins : Non-clustered"	14257	protein-coding gene	gene with protein product		614449					Standard	NM_022843		Approved	PCDH13, FLJ22218	uc001vid.4	Q8N6Y1	OTTHUMG00000017012	ENST00000409186.1:c.2112G>A	chr13.hg19:g.61986120C>T		82.0	0.0	.		85.0	25.0	.	NM_022843	A8K1K9|B1AQU2|Q8NDN4|Q9NRT9	Silent	SNP	ENST00000409186.1	hg19	CCDS9442.2																																																																																			.	.	.	none		0.463	PCDH20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333054.2	NM_022843		T	61986120	C	T	61986120	2	4	248	1	0	0	0	0	0	0	0	1	11522	796	28	2		2	PCDH20	13	61986120	Silent	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10		61986120	53183758	75	15399											
RAB20	55647	hgsc.bcm.edu	37	chr13	111213813	111213813	+	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	taccgctgcagcagcgacgtCttccccacgttcatgtcccc	6	9	8	18	4	2	0	1	0	1	0	4	1	4	0	5	0	4	4	5	0	1	3			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr13:111213813C>G	ENST00000267328.3	-	1	267	c.54G>C	c.(52-54)aaG>aaC	p.K18N		NM_017817.1	NP_060287.1	Q9NX57	RAB20_HUMAN	RAB20, member RAS oncogene family	18					phagosome acidification (GO:0090383)|phagosome-lysosome fusion (GO:0090385)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|phagocytic vesicle (GO:0045335)	GTP binding (GO:0005525)			endometrium(2)|large_intestine(2)|lung(3)	7	all_cancers(4;1.54e-11)|all_epithelial(4;1.22e-06)|all_lung(23;1e-05)|Lung NSC(43;0.000453)|Colorectal(4;0.00323)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.197)			GCAGCGACGTCTTCCCCACGT	0.652																																					p.K18N		Atlas-SNP	.											.	RAB20	34	.	0			c.G54C						PASS	.						62	57	59					13																	111213813		2203	4300	6503	SO:0001583	missense	55647	exon1			CGACGTCTTCCCC	AK000436	CCDS9512.1	13q34	2008-07-18			ENSG00000139832	ENSG00000139832		"RAB, member RAS oncogene"	18260	protein-coding gene	gene with protein product						11697911	Standard	NM_017817		Approved	FLJ20429	uc001vqy.3	Q9NX57	OTTHUMG00000017343	ENST00000267328.3:c.54G>C	chr13.hg19:g.111213813C>G	ENSP00000267328:p.Lys18Asn	61.0	0.0	.		107.0	22.0	.	NM_017817	Q5T9X5|Q9NX49	Missense_Mutation	SNP	ENST00000267328.3	hg19	CCDS9512.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.620006	0.87460	.	.	ENSG00000139832	ENST00000267328	D	0.94232	-3.38	4.06	2.23	0.28157	Small GTP-binding protein domain (1);	0.049143	0.85682	D	0.000000	D	0.96778	0.8948	M	0.92077	3.27	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96147	0.9105	10	0.87932	D	0	1.1772	9.4073	0.38469	0.0:0.8181:0.0:0.1819	.	18	Q9NX57	RAB20_HUMAN	N	18	ENSP00000267328:K18N	ENSP00000267328:K18N	K	-	3	2	RAB20	110011814	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.658000	0.46733	0.897000	0.36392	0.561000	0.74099	AAG	.	.	.	none		0.652	RAB20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045760.2	NM_017817		G	111213813	C	G	111213813	3	3	248	1	0	0	0	0	1	0	0	0	12920	912	32	4	658	4	RAB20	13	111213813	Missense_Mutation	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10	49227693	111213813	3956065	76	15400											
CEBPE	1053	hgsc.bcm.edu	37	chr14	23586764	23586764	+	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	ctggcggaagaggttgcggaGggtgtctagctcctgggtga	6	9	19	7	2	1	2	0	1	1	1	2	4	2	4	1	6	2	2	1	6	2	2			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr14:23586764G>A	ENST00000206513.5	-	2	1302	c.778C>T	c.(778-780)Ctc>Ttc	p.L260F		NM_001805.3	NP_001796.2	Q15744	CEBPE_HUMAN	CCAAT/enhancer binding protein (C/EBP), epsilon	260	bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				cellular response to lipopolysaccharide (GO:0071222)|cytokine biosynthetic process (GO:0042089)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|macrophage differentiation (GO:0030225)|phagocytosis (GO:0006909)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			large_intestine(2)|lung(3)|ovary(2)|prostate(1)|skin(1)	9	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.0064)		AGGTTGCGGAGGGTGTCTAGC	0.647																																					p.L260F	NSCLC(63;1230 1818 14565 22565)	Atlas-SNP	.											.	CEBPE	34	.	0			c.C778T						PASS	.						62	48	53					14																	23586764		2203	4300	6503	SO:0001583	missense	1053	exon2			TGCGGAGGGTGTC		CCDS9589.1	14q11.2	2014-09-17			ENSG00000092067	ENSG00000092067		"basic leucine zipper proteins"	1836	protein-coding gene	gene with protein product		600749				8661101	Standard	NM_001805		Approved	CRP1	uc001wiv.2	Q15744	OTTHUMG00000028719	ENST00000206513.5:c.778C>T	chr14.hg19:g.23586764G>A	ENSP00000206513:p.Leu260Phe	36.0	0.0	.		39.0	16.0	.	NM_001805	Q15745|Q8IYI2|Q99803	Missense_Mutation	SNP	ENST00000206513.5	hg19	CCDS9589.1	.	.	.	.	.	.	.	.	.	.	G	19.51	3.840809	0.71488	.	.	ENSG00000092067	ENST00000206513	T	0.52295	0.67	5.38	4.48	0.54585	Basic-leucine zipper (bZIP) transcription factor (2);	0.000000	0.85682	D	0.000000	T	0.67021	0.2849	M	0.81239	2.535	0.45899	D	0.998748	D	0.89917	1.0	D	0.83275	0.996	T	0.70479	-0.4860	10	0.87932	D	0	-21.9209	9.8241	0.40901	0.1613:0.0:0.8387:0.0	.	260	Q15744	CEBPE_HUMAN	F	260	ENSP00000206513:L260F	ENSP00000206513:L260F	L	-	1	0	CEBPE	22656604	1.000000	0.71417	0.850000	0.33497	0.996000	0.88848	3.362000	0.52314	2.532000	0.85374	0.655000	0.94253	CTC	.	.	.	none		0.647	CEBPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071716.2	NM_001805		A	23586764	G	A	23586764	3	1	248	1	0	0	0	0	1	0	0	0	3204	1000	35	2	71	2	CEBPE	14	23586764	Missense_Mutation	SNP	G	TCGA-SX-A7SN-01A-11D-A34Z-10		23586764	83762776	77	15401											
SDR39U1	23351	hgsc.bcm.edu	37	chr14	24911432	24911432	+	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	0	0	0	0	0	0	0	cggccaggttgacggcggcaTcgcagctcggcagccccgat	6	5	15	15	6	0	1	0	1	0	0	2	2	0	1	3	5	2	5	3	5	0	1	rs201052867		TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr14:24911432T>C	ENST00000251343.5	+	0	6225				SDR39U1_ENST00000399390.1_5'Flank|SDR39U1_ENST00000538105.2_Missense_Mutation_p.M12V|SDR39U1_ENST00000555561.1_5'Flank|SDR39U1_ENST00000399395.3_Missense_Mutation_p.D53G|SDR39U1_ENST00000553930.1_5'UTR|SDR39U1_ENST00000555365.1_Intron|SDR39U1_ENST00000554698.1_5'UTR			O15037	KHNYN_HUMAN	KH and NYN domain containing								RNA binding (GO:0003723)			kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(3)	24						GACGGCGGCATCGCAGCTCGG	0.667																																					p.D53G		Atlas-SNP	.											.	SDR39U1	19	.	0			c.A158G						PASS	.						26	30	29					14																	24911432		2010	4170	6180	SO:0001628	intergenic_variant	56948	exon3			GCGGCATCGCAGC	AB002321	CCDS32058.1	14q11.2	2010-11-23	2009-10-14	2009-10-14	ENSG00000100441	ENSG00000100441			20166	protein-coding gene	gene with protein product			"KIAA0323"	KIAA0323		17114934	Standard	NM_015299		Approved		uc001wph.4	O15037			chr14.hg19:g.24911432T>C		34.0	0.0	.		35.0	17.0	.	NM_020195	Q86TZ6|Q8IUQ2|Q96BA9	Missense_Mutation	SNP	ENST00000251343.5	hg19	CCDS32058.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.24|14.24	2.476759|2.476759	0.44044|0.44044	.|.	.|.	ENSG00000100445|ENSG00000100445	ENST00000399395;ENST00000336353|ENST00000538105	D|T	0.95853|0.21191	-3.83|2.02	5.24|5.24	5.24|5.24	0.73138|0.73138	.|.	0.207799|.	0.49305|.	N|.	0.000144|.	T|T	0.23492|0.23492	0.0568|0.0568	M|M	0.66297|0.66297	2.02|2.02	0.80722|0.80722	D|D	1|1	P|B	0.35272|0.11235	0.493|0.004	B|B	0.32289|0.12837	0.143|0.008	T|T	0.03278|0.03278	-1.1053|-1.1053	10|8	0.72032|.	D|.	0.01|.	-20.9366|-20.9366	11.7055|11.7055	0.51595|0.51595	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	53|12	Q9NRG7-2|F6RWC2	.|.	G|V	53;79|12	ENSP00000382327:D53G|ENSP00000446077:M12V	ENSP00000336854:D79G|.	D|M	-|-	2|1	0|0	SDR39U1|SDR39U1	23981272|23981272	1.000000|1.000000	0.71417|0.71417	0.968000|0.968000	0.41197|0.41197	0.642000|0.642000	0.38348|0.38348	4.911000|4.911000	0.63328|0.63328	2.330000|2.330000	0.79161|0.79161	0.528000|0.528000	0.53228|0.53228	GAT|ATG	.	.	.	alt		0.667	KHNYN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412928.1			C	24911432	T	C	24911432	1	2	248	0	1	0	0	0	0	0	0	0	13985	1435	50	3		3	SDR39U1	14	24911432	IGR	SNP	T	TCGA-SX-A7SN-01A-11D-A34Z-10	1324668	24911432	82438108	78	15402											
SERPINA3	12	hgsc.bcm.edu	37	chr14	95089993	95089993	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tatttgaggagggcacagaaGcatctgctgccacagcagtc	11	8	12	10	0	1	2	0	1	1	1	2	3	1	3	1	2	4	4	1	2	2	2			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr14:95089993G>A	ENST00000467132.1	+	5	2262	c.1114G>A	c.(1114-1116)Gca>Aca	p.A372T	SERPINA3_ENST00000482740.1_Missense_Mutation_p.A154T|SERPINA3_ENST00000393078.3_Missense_Mutation_p.A372T|RP11-986E7.7_ENST00000553947.1_3'UTR|SERPINA3_ENST00000393080.4_Missense_Mutation_p.A372T			P01011	AACT_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3	372	RCL.				acute-phase response (GO:0006953)|inflammatory response (GO:0006954)|maintenance of gastrointestinal epithelium (GO:0030277)|negative regulation of endopeptidase activity (GO:0010951)|regulation of lipid metabolic process (GO:0019216)|regulation of proteolysis (GO:0030162)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	DNA binding (GO:0003677)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(17)|ovary(2)|pancreas(1)|skin(3)|stomach(1)	40		all_cancers(154;0.0525)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.212)|Epithelial(152;0.228)		GGGCACAGAAGCATCTGCTGC	0.512																																					p.A372T		Atlas-SNP	.											.	SERPINA3	78	.	0			c.G1114A						PASS	.						163	140	148					14																	95089993		2203	4300	6503	SO:0001583	missense	12	exon5			ACAGAAGCATCTG	K01500	CCDS32150.1	14q32.1	2014-06-03	2005-08-18		ENSG00000196136	ENSG00000196136		"Serine (or cysteine) peptidase inhibitors"	16	protein-coding gene	gene with protein product		107280	"alpha-1-antichymotrypsin", "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3"	AACT		3260956, 24172014	Standard	NM_001085		Approved	ACT, alpha-1-antichymotrypsin	uc001ydp.3	P01011	OTTHUMG00000029851	ENST00000467132.1:c.1114G>A	chr14.hg19:g.95089993G>A	ENSP00000450540:p.Ala372Thr	98.0	0.0	.		86.0	24.0	.	NM_001085	B3KVQ7|Q13703|Q2TU87|Q2TU88|Q59GP9|Q6LBY8|Q6LDT7|Q6NSC9|Q8N177|Q96DW8|Q9UC47|Q9UNU9	Missense_Mutation	SNP	ENST00000467132.1	hg19	CCDS32150.1	.	.	.	.	.	.	.	.	.	.	G	34	5.396546	0.96009	.	.	ENSG00000196136	ENST00000553947;ENST00000393078;ENST00000393080;ENST00000467132;ENST00000482740	D;D;D;D;D	0.91124	-2.79;-2.79;-2.79;-2.79;-2.79	4.95	4.03	0.46877	Serpin domain (3);	0.088586	0.47093	D	0.000244	D	0.93265	0.7854	M	0.92555	3.32	0.45962	D	0.998783	P;P	0.48503	0.656;0.911	P;B	0.44673	0.457;0.44	D	0.94127	0.7385	10	0.87932	D	0	.	14.1908	0.65637	0.0:0.1511:0.8489:0.0	.	372;397	P01011;G3V5I3	AACT_HUMAN;.	T	397;372;372;372;154	ENSP00000452367:A397T;ENSP00000376793:A372T;ENSP00000376795:A372T;ENSP00000450540:A372T;ENSP00000451119:A154T	ENSP00000376793:A372T	A	+	1	0	SERPINA3	94159746	1.000000	0.71417	0.482000	0.27366	0.560000	0.35617	9.300000	0.96151	1.161000	0.42604	0.557000	0.71058	GCA	.	.	.	none		0.512	SERPINA3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268080.3	NM_001085		A	95089993	G	A	95089993	3	1	248	1	0	0	0	0	1	0	0	0	14103	971	34	2	1128	2	SERPINA3	14	95089993	Missense_Mutation	SNP	G	TCGA-SX-A7SN-01A-11D-A34Z-10	70178561	95089993	12259547	79	15403											
C14orf49	161176	hgsc.bcm.edu	37	chr14	95942145	95942145	+	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	tcctgtcaaagtcgtcctggGgctgctgagtcatggcacct	6	11	12	12	1	2	1	2	1	0	0	5	1	4	1	3	3	1	3	3	3	1	0			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr14:95942145G>A	ENST00000334258.5	-	1	28	c.14C>T	c.(13-15)cCc>cTc	p.P5L	SYNE3_ENST00000557275.1_Missense_Mutation_p.P5L|SYNE3_ENST00000553340.1_Missense_Mutation_p.P5L	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	5					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						GTCGTCCTGGGGCTGCTGAGT	0.617																																					p.P5L		Atlas-SNP	.											.	SYNE3	130	.	0			c.C14T						PASS	.																																			SO:0001583	missense	161176	exon1			TCCTGGGGCTGCT	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.14C>T	chr14.hg19:g.95942145G>A	ENSP00000334308:p.Pro5Leu	29.0	0.0	.		32.0	12.0	.	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	hg19	CCDS9935.1	.	.	.	.	.	.	.	.	.	.	G	12.65	2.003039	0.35320	.	.	ENSG00000176438	ENST00000334258;ENST00000557275;ENST00000553340	T;T;T	0.09723	3.53;3.52;2.95	5.05	4.15	0.48705	.	0.837651	0.09723	N	0.764118	T	0.08313	0.0207	N	0.20685	0.6	0.46203	D	0.998922	B;B;B	0.12013	0.005;0.005;0.003	B;B;B	0.11329	0.006;0.006;0.003	T	0.16748	-1.0392	10	0.29301	T	0.29	-13.6362	10.1912	0.43028	0.1754:0.0:0.8246:0.0	.	5;5;5	Q6ZMZ3-2;Q6ZMZ3-3;Q6ZMZ3	.;.;SYNE3_HUMAN	L	5	ENSP00000334308:P5L;ENSP00000450562:P5L;ENSP00000450774:P5L	ENSP00000334308:P5L	P	-	2	0	C14orf49	95011898	1.000000	0.71417	0.996000	0.52242	0.984000	0.73092	3.235000	0.51328	1.115000	0.41800	0.462000	0.41574	CCC	.	.	.	none		0.617	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592		A	95942145	G	A	95942145	3	1	248	1	0	0	0	0	1	0	0	0	1778	1232	43	2	2981	2	C14orf49	14	95942145	Missense_Mutation	SNP	G	TCGA-SX-A7SN-01A-11D-A34Z-10	852152	95942145	11407395	80	15404											
NARG2	79664	hgsc.bcm.edu	37	chr15	60741577	60741577	+	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	catgtaatatatctatagtcAtatcatttttattagaagtt	14	19	4	4	0	3	1	2	0	1	1	3	1	3	1	0	0	0	2	0	0	9	11			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr15:60741577A>T	ENST00000261520.4	-	10	1823	c.1589T>A	c.(1588-1590)aTg>aAg	p.M530K	NARG2_ENST00000439632.1_Missense_Mutation_p.M393K	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						ATCTATAGTCATATCATTTTT	0.328																																					p.M530K		Atlas-SNP	.											.	NARG2	82	.	0			c.T1589A						PASS	.						52	54	53					15																	60741577		2203	4297	6500	SO:0001583	missense	79664	exon10			ATAGTCATATCAT																												ENST00000261520.4:c.1589T>A	chr15.hg19:g.60741577A>T	ENSP00000261520:p.Met530Lys	87.0	0.0	.		93.0	38.0	.	NM_024611		Missense_Mutation	SNP	ENST00000261520.4	hg19	CCDS10176.1	.	.	.	.	.	.	.	.	.	.	A	0.372	-0.933198	0.02359	.	.	ENSG00000128915	ENST00000261520;ENST00000439632	.	.	.	5.06	0.943	0.19531	.	0.776640	0.12418	N	0.470660	T	0.25865	0.0630	N	0.19112	0.55	0.09310	N	1	B;B	0.26400	0.148;0.016	B;B	0.24848	0.056;0.01	T	0.19257	-1.0311	9	0.28530	T	0.3	-0.0038	9.6349	0.39802	0.7606:0.0:0.2394:0.0	.	198;530	B3KXT2;Q659A1	.;NARG2_HUMAN	K	530;393	.	ENSP00000261520:M530K	M	-	2	0	NARG2	58528869	0.003000	0.15002	0.001000	0.08648	0.005000	0.04900	1.397000	0.34543	0.268000	0.21939	0.528000	0.53228	ATG	.	.	.	none		0.328	NARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256136.1			T	60741577	A	T	60741577	3	4	248	1	0	0	0	0	1	0	0	0	10176	217	8	5	1387	5	NARG2	15	60741577	Missense_Mutation	SNP	A	TCGA-SX-A7SN-01A-11D-A34Z-10		60741577	41789815	81	15405											
RORA	6095	hgsc.bcm.edu	37	chr15	60803577	60803577	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggggaaggctgtatgtccAggtagaagctgctgacggcg	8	8	17	8	2	0	2	0	1	0	1	1	3	1	3	1	5	2	5	1	5	4	2			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr15:60803577A>G	ENST00000335670.6	-	5	768	c.668T>C	c.(667-669)cTg>cCg	p.L223P	RORA_ENST00000261523.5_Missense_Mutation_p.L256P|RP11-219B17.1_ENST00000501579.2_RNA|RP11-219B17.1_ENST00000558235.1_RNA|RORA_ENST00000449337.2_Missense_Mutation_p.L168P|RP11-219B17.1_ENST00000558140.1_RNA|RORA_ENST00000560004.1_5'Flank|RP11-219B17.1_ENST00000559824.1_RNA|RP11-219B17.1_ENST00000559902.1_RNA|RORA_ENST00000309157.4_Missense_Mutation_p.L248P	NM_134261.2	NP_599023.1	P35398	RORA_HUMAN	RAR-related orphan receptor A	223	Hinge.				angiogenesis (GO:0001525)|cellular response to hypoxia (GO:0071456)|cellular response to sterol (GO:0036315)|cerebellar granule cell precursor proliferation (GO:0021930)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|circadian regulation of gene expression (GO:0032922)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|muscle cell differentiation (GO:0042692)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of cholesterol homeostasis (GO:2000188)|regulation of glucose metabolic process (GO:0010906)|regulation of macrophage activation (GO:0043030)|regulation of smoothened signaling pathway (GO:0008589)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription involved in cell fate commitment (GO:0060850)|regulation of transcription, DNA-templated (GO:0006355)|T-helper 17 cell differentiation (GO:0072539)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	direct ligand regulated sequence-specific DNA binding transcription factor activity (GO:0098531)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|oxysterol binding (GO:0008142)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator binding (GO:0001223)|transcription corepressor binding (GO:0001222)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	21						CTGTATGTCCAGGTAGAAGCT	0.532																																					p.L256P		Atlas-SNP	.											.	RORA	114	.	0			c.T767C						PASS	.						193	148	163					15																	60803577		2203	4300	6503	SO:0001583	missense	6095	exon6			ATGTCCAGGTAGA	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.668T>C	chr15.hg19:g.60803577A>G	ENSP00000335087:p.Leu223Pro	148.0	0.0	.		207.0	73.0	.	NM_134260	P35397|P35399|P45445|Q495X4|Q96H83	Missense_Mutation	SNP	ENST00000335670.6	hg19	CCDS10177.1	.	.	.	.	.	.	.	.	.	.	A	16.23	3.063733	0.55432	.	.	ENSG00000069667	ENST00000335670;ENST00000449337;ENST00000309157;ENST00000261523	D;D;D;D	0.95001	-3.53;-3.52;-3.58;-3.49	5.9	5.9	0.94986	.	0.065297	0.64402	D	0.000006	D	0.92854	0.7727	L	0.38838	1.175	0.80722	D	1	B;B;D;B	0.54207	0.006;0.005;0.965;0.024	B;B;P;B	0.48488	0.012;0.023;0.579;0.038	D	0.91956	0.5575	10	0.31617	T	0.26	.	16.3322	0.83039	1.0:0.0:0.0:0.0	.	223;248;256;168	P35398-2;P35398-3;P35398;P35398-4	.;.;RORA_HUMAN;.	P	223;168;248;256	ENSP00000335087:L223P;ENSP00000402971:L168P;ENSP00000309753:L248P;ENSP00000261523:L256P	ENSP00000261523:L256P	L	-	2	0	RORA	58590869	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.948000	0.93006	2.251000	0.74343	0.528000	0.53228	CTG	.	.	.	none		0.532	RORA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256142.2			G	60803577	A	G	60803577	3	3	248	1	0	0	0	0	1	0	0	0	13541	188	7	3	931	3	RORA	15	60803577	Missense_Mutation	SNP	A	TCGA-SX-A7SN-01A-11D-A34Z-10	62000	60803577	41727815	82	15406											
AKAP13	11214	hgsc.bcm.edu	37	chr15	86122646	86122646	+	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	gatgctgtgcttcagagagaCttggtcatggagccaggcac	9	9	14	9	0	2	2	2	0	0	2	2	5	2	3	1	3	3	3	1	3	0	2			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr15:86122646C>T	ENST00000394518.2	+	7	1442	c.1347C>T	c.(1345-1347)gaC>gaT	p.D449D	AKAP13_ENST00000361243.2_Silent_p.D449D|RP11-815J21.2_ENST00000561409.1_RNA	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	449					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						TTCAGAGAGACTTGGTCATGG	0.512																																					p.D449D	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.C1347T						PASS	.						63	67	66					15																	86122646		2202	4299	6501	SO:0001819	synonymous_variant	11214	exon7			GAGAGACTTGGTC	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.1347C>T	chr15.hg19:g.86122646C>T		78.0	0.0	.		79.0	31.0	.	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Silent	SNP	ENST00000394518.2	hg19	CCDS32319.1																																																																																			.	.	.	none		0.512	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		T	86122646	C	T	86122646	2	4	248	1	0	0	0	0	0	0	0	1	449	564	20	2		2	AKAP13	15	86122646	Silent	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10	25319069	86122646	16408746	83	15407											
HMOX2	3163	hgsc.bcm.edu	37	chr16	4557964	4557964	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccggagctactggtggcccAtgcatacacccgctacatgg	8	7	12	14	2	0	0	0	0	0	0	0	1	0	1	3	4	5	3	3	4	3	3			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr16:4557964A>G	ENST00000570646.1	+	4	1060	c.455A>G	c.(454-456)cAt>cGt	p.H152R	HMOX2_ENST00000414777.1_Missense_Mutation_p.H152R|HMOX2_ENST00000575120.1_Missense_Mutation_p.H123R|HMOX2_ENST00000398595.3_Missense_Mutation_p.H152R|HMOX2_ENST00000406590.2_Missense_Mutation_p.H152R|HMOX2_ENST00000458134.3_Missense_Mutation_p.H152R|HMOX2_ENST00000219700.6_Missense_Mutation_p.H152R	NM_002134.3	NP_002125.3	P30519	HMOX2_HUMAN	heme oxygenase (decycling) 2	152					cellular iron ion homeostasis (GO:0006879)|heme catabolic process (GO:0042167)|heme oxidation (GO:0006788)|porphyrin-containing compound metabolic process (GO:0006778)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heme oxygenase (decyclizing) activity (GO:0004392)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	8						CTGGTGGCCCATGCATACACC	0.627																																					p.H152R		Atlas-SNP	.											.	HMOX2	22	.	0			c.A455G						PASS	.						43	45	45					16																	4557964		2197	4300	6497	SO:0001583	missense	3163	exon4			TGGCCCATGCATA		CCDS10517.1, CCDS66931.1, CCDS73818.1	16p13.3	2008-02-05			ENSG00000103415	ENSG00000103415	1.14.99.3		5014	protein-coding gene	gene with protein product		141251				1575508	Standard	NM_002134		Approved	HO-2	uc002cwq.4	P30519	OTTHUMG00000129473	ENST00000570646.1:c.455A>G	chr16.hg19:g.4557964A>G	ENSP00000459214:p.His152Arg	50.0	0.0	.		90.0	41.0	.	NM_001127205	A8MT35|D3DUD5|I3L430|O60605	Missense_Mutation	SNP	ENST00000570646.1	hg19	CCDS10517.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.618349	0.87359	.	.	ENSG00000103415	ENST00000406590;ENST00000458134;ENST00000219700;ENST00000414777;ENST00000398595	T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53	5.62	5.62	0.85841	Haem oxygenase conserved site (1);Haem oxygenase-like, multi-helical (2);	0.000000	0.85682	D	0.000000	T	0.68357	0.2992	H	0.95917	3.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.79468	-0.1791	10	0.87932	D	0	-17.4632	14.6409	0.68723	1.0:0.0:0.0:0.0	.	152;152	B3KSE0;P30519	.;HMOX2_HUMAN	R	152	ENSP00000385100:H152R;ENSP00000394103:H152R;ENSP00000219700:H152R;ENSP00000391637:H152R;ENSP00000381595:H152R	ENSP00000219700:H152R	H	+	2	0	HMOX2	4497965	1.000000	0.71417	0.997000	0.53966	0.972000	0.66771	9.339000	0.96797	2.142000	0.66516	0.459000	0.35465	CAT	.	.	.	none		0.627	HMOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251636.2			G	4557964	A	G	4557964	3	3	248	1	0	0	0	0	1	0	0	0	7251	217	8	3	465	3	HMOX2	16	4557964	Missense_Mutation	SNP	A	TCGA-SX-A7SN-01A-11D-A34Z-10		4557964	85796789	84	15408											
CES1	1066	hgsc.bcm.edu	37	chr16	55846940	55846940	+	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	catcccatcaatcacagtgcCcagaaggggttgactctggg	10	8	11	12	0	3	2	2	1	1	1	4	2	4	2	2	3	1	1	2	3	2	1	rs138161688		TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr16:55846940C>T	ENST00000361503.4	-	9	1088	c.958G>A	c.(958-960)Ggc>Agc	p.G320S	CES1_ENST00000422046.2_Missense_Mutation_p.G320S|CES1_ENST00000360526.3_Missense_Mutation_p.G321S			P23141	EST1_HUMAN	carboxylesterase 1	320					epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)								all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	ATCACAGTGCCCAGAAGGGGT	0.532																																					p.G321S	NSCLC(162;1801 2756 42904 52896)	Atlas-SNP	.											.	CES1	78	.	0			c.G961A						PASS	.	G	SER/GLY,SER/GLY,SER/GLY	0,4396		0,0,2198	104	100	101		958,961,958	-7.7	0	16	dbSNP_134	101	1,8599		0,1,4299	no	missense,missense,missense	CES1	NM_001025194.1,NM_001025195.1,NM_001266.4	56,56,56	0,1,6497	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	320/568,321/569,320/567	55846940	1,12995	2198	4300	6498	SO:0001583	missense	1066	exon9			CAGTGCCCAGAAG	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"Carboxylesterases"	1863	protein-coding gene	gene with protein product	"human monocyte/macrophage serine esterase 1"	114835	"carboxylesterase 1 (monocyte/macrophage serine esterase 1)"			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.958G>A	chr16.hg19:g.55846940C>T	ENSP00000355193:p.Gly320Ser	32.0	0.0	.		48.0	30.0	.	NM_001025195	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Missense_Mutation	SNP	ENST00000361503.4	hg19	CCDS45488.1	.	.	.	.	.	.	.	.	.	.	.	6.832	0.522731	0.13066	0.0	1.16E-4	ENSG00000198848	ENST00000360526;ENST00000361503;ENST00000422046;ENST00000426667	T;T;T	0.08634	3.22;3.22;3.07	3.85	-7.71	0.01254	Carboxylesterase, type B (1);	1.383420	0.04583	N	0.395340	T	0.02533	0.0077	N	0.02412	-0.56	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.15052	0.012;0.012;0.007	T	0.42344	-0.9457	10	0.32370	T	0.25	.	2.9914	0.05984	0.1197:0.3586:0.3581:0.1636	.	320;320;321	E9PAU8;P23141;P23141-2	.;EST1_HUMAN;.	S	321;320;320;185	ENSP00000353720:G321S;ENSP00000355193:G320S;ENSP00000390492:G320S	ENSP00000353720:G321S	G	-	1	0	CES1	54404441	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.577000	0.02127	-1.091000	0.03065	-1.907000	0.00523	GGC	.	C|1.000;T|0.000	0.000	weak		0.532	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266		T	55846940	C	T	55846940	3	4	248	1	0	0	0	0	1	0	0	0	3271	623	22	2	769	2	CES1	16	55846940	Missense_Mutation	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10	51288976	55846940	34507813	85	15409											
E2F4	1874	hgsc.bcm.edu	37	chr16	67226690	67226690	+	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	gacaccctagctgtacgccaGaagcggcggatttacgacat	11	7	11	12	4	0	1	0	0	0	1	0	4	0	2	2	2	4	2	2	2	4	4	rs143700278		TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr16:67226690G>A	ENST00000379378.3	+	2	221	c.162G>A	c.(160-162)caG>caA	p.Q54Q	EXOC3L1_ENST00000314586.6_5'Flank|E2F4_ENST00000564718.1_3'UTR|EXOC3L1_ENST00000562887.1_5'Flank	NM_001950.3	NP_001941.2	Q16254	E2F4_HUMAN	E2F transcription factor 4, p107/p130-binding	54	Leucine-zipper.				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)		CTGTACGCCAGAAGCGGCGGA	0.547																																					p.Q54Q		Atlas-SNP	.											.	E2F4	25	.	0			c.G162A						PASS	.	G		0,4394		0,0,2197	44	38	40		162	4.8	1	16	dbSNP_134	40	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	E2F4	NM_001950.3		0,2,6495	AA,AG,GG		0.0233,0.0,0.0154		54/414	67226690	2,12992	2197	4300	6497	SO:0001819	synonymous_variant	1874	exon2			ACGCCAGAAGCGG	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.162G>A	chr16.hg19:g.67226690G>A		63.0	0.0	.		72.0	37.0	.	NM_001950	A6NGR8|B5BU56|Q12991|Q15328	Silent	SNP	ENST00000379378.3	hg19	CCDS32464.1																																																																																			.	G|1.000;A|0.000	0.000	weak		0.547	E2F4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421565.1	NM_001950		A	67226690	G	A	67226690	2	1	248	1	0	0	0	0	0	0	0	1	4871	933	33	2		2	E2F4	16	67226690	Silent	SNP	G	TCGA-SX-A7SN-01A-11D-A34Z-10	11379750	67226690	23128063	86	15410											
AARS	16	hgsc.bcm.edu	37	chr16	70316587	70316587	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgggatggtggcagacgagTgaacatacgtatgctcgttc	10	10	14	7	3	0	2	0	1	0	1	2	4	0	3	0	3	3	4	0	3	3	3	rs77753666		TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr16:70316587T>C	ENST00000261772.8	-	2	223	c.80A>G	c.(79-81)cAc>cGc	p.H27R		NM_001605.2	NP_001596.2			alanyl-tRNA synthetase											breast(3)|cervix(2)|endometrium(5)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)		GGCAGACGAGTGAACATACGT	0.448																																					p.H27R		Atlas-SNP	.											.	AARS	62	.	0			c.A80G						PASS	.						175	164	168					16																	70316587		2198	4300	6498	SO:0001583	missense	16	exon2			GACGAGTGAACAT	D32050	CCDS32474.1	16q22.1	2014-09-17			ENSG00000090861	ENSG00000090861	6.1.1.7	"Aminoacyl tRNA synthetases / Class II"	20	protein-coding gene	gene with protein product	"alanine tRNA ligase 1, cytoplasmic"	601065				8595897	Standard	NM_001605		Approved		uc002eyn.1	P49588	OTTHUMG00000177042	ENST00000261772.8:c.80A>G	chr16.hg19:g.70316587T>C	ENSP00000261772:p.His27Arg	74.0	0.0	.		100.0	60.0	.	NM_001605		Missense_Mutation	SNP	ENST00000261772.8	hg19	CCDS32474.1	.	.	.	.	.	.	.	.	.	.	T	5.294	0.239679	0.10023	.	.	ENSG00000090861	ENST00000261772	D	0.81739	-1.53	5.56	5.56	0.83823	Alanyl-tRNA synthetase, class IIc, core domain (1);Alanyl-tRNA synthetase, class IIc, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.84561	0.5499	L	0.42487	1.325	0.80722	D	1	D	0.67145	0.996	D	0.75020	0.985	T	0.82372	-0.0490	10	0.27082	T	0.32	-19.0749	13.6719	0.62430	0.0:0.0:0.0:1.0	.	27	P49588	SYAC_HUMAN	R	27	ENSP00000261772:H27R	ENSP00000261772:H27R	H	-	2	0	AARS	68874088	1.000000	0.71417	1.000000	0.80357	0.174000	0.22865	7.799000	0.85936	2.108000	0.64289	0.482000	0.46254	CAC	.	.	.	alt		0.448	AARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435021.2	NM_001605		C	70316587	T	C	70316587	3	2	248	1	0	0	0	0	1	0	0	0	19	1696	59	3	2906	3	AARS	16	70316587	Missense_Mutation	SNP	T	TCGA-SX-A7SN-01A-11D-A34Z-10	3089897	70316587	20038166	87	15411											
FAM92B	339145	hgsc.bcm.edu	37	chr16	85144008	85144008	+	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	ggccagcagcgagcagaactGcccaaagtacttctcggtgt	10	7	12	12	2	1	1	0	0	1	1	2	2	1	1	2	2	6	3	2	2	3	2			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr16:85144008G>C	ENST00000539556.1	-	2	234	c.79C>G	c.(79-81)Cag>Gag	p.Q27E		NM_198491.1	NP_940893.1	Q6ZTR7	FA92B_HUMAN	family with sequence similarity 92, member B	27										breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	16						GAGCAGAACTGCCCAAAGTAC	0.627																																					p.Q27E		Atlas-SNP	.											.	FAM92B	29	.	0			c.C79G						PASS	.						58	58	58					16																	85144008		2198	4300	6498	SO:0001583	missense	339145	exon2			AGAACTGCCCAAA		CCDS32500.1	16q24.1	2005-09-22				ENSG00000153789			24781	protein-coding gene	gene with protein product						12477932	Standard	NM_198491		Approved	FLJ44299	uc021tlz.1	Q6ZTR7		ENST00000539556.1:c.79C>G	chr16.hg19:g.85144008G>C	ENSP00000443411:p.Gln27Glu	60.0	0.0	.		78.0	23.0	.	NM_198491		Missense_Mutation	SNP	ENST00000539556.1	hg19	CCDS32500.1	.	.	.	.	.	.	.	.	.	.	G	6.166	0.398907	0.11696	.	.	ENSG00000153789	ENST00000393246;ENST00000539556	T	0.27256	1.68	5.12	4.15	0.48705	.	0.216981	0.31936	N	0.006838	T	0.16342	0.0393	L	0.31578	0.945	0.28775	N	0.900143	B	0.32939	0.391	B	0.33799	0.17	T	0.15521	-1.0434	10	0.02654	T	1	-29.3987	12.675	0.56889	0.0:0.0:0.8335:0.1665	.	27	Q6ZTR7	FA92B_HUMAN	E	27	ENSP00000443411:Q27E	ENSP00000376937:Q27E	Q	-	1	0	FAM92B	83701509	1.000000	0.71417	0.986000	0.45419	0.959000	0.62525	2.336000	0.43938	1.116000	0.41820	0.561000	0.74099	CAG	.	.	.	none		0.627	FAM92B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_198491		C	85144008	G	C	85144008	3	2	248	1	0	0	0	0	1	0	0	0	5660	1328	46	4	863	4	FAM92B	16	85144008	Missense_Mutation	SNP	G	TCGA-SX-A7SN-01A-11D-A34Z-10	14827421	85144008	5210745	88	15412											
PIK3R5	23533	hgsc.bcm.edu	37	chr17	8794161	8794161	+	Missense_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	tgtgaggcgagtgtccgggcGtactcagcttattggctaca	7	11	14	9	3	1	1	1	1	0	0	2	2	2	1	1	3	3	3	1	3	3	4			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr17:8794161G>A	ENST00000447110.1	-	7	675	c.551C>T	c.(550-552)aCg>aTg	p.T184M	PIK3R5_ENST00000581552.1_Missense_Mutation_p.T184M|PIK3R5_ENST00000584803.1_Missense_Mutation_p.T184M	NM_001142633.2|NM_001251851.1|NM_001251852.1|NM_001251853.1|NM_001251855.1	NP_001136105.1|NP_001238780.1|NP_001238781.1|NP_001238782.1|NP_001238784.1	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5	184					blood coagulation (GO:0007596)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|small molecule metabolic process (GO:0044281)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|G-protein beta/gamma-subunit complex binding (GO:0031683)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(14)|prostate(3)|skin(4)|urinary_tract(1)	34						GTGTCCGGGCGTACTCAGCTT	0.647																																					p.T184M	NSCLC(18;589 615 7696 20311 50332)	Atlas-SNP	.											.	PIK3R5	79	.	0			c.C551T						PASS	.						153	116	129					17																	8794161		2203	4300	6503	SO:0001583	missense	23533	exon7			CCGGGCGTACTCA	AF128881	CCDS11147.1, CCDS73986.1	17p13.1	2011-10-13	2008-02-04		ENSG00000141506	ENSG00000141506			30035	protein-coding gene	gene with protein product		611317				12507995	Standard	NM_014308		Approved	P101-PI3K, p101	uc002glt.3	Q8WYR1	OTTHUMG00000108197	ENST00000447110.1:c.551C>T	chr17.hg19:g.8794161G>A	ENSP00000392812:p.Thr184Met	35.0	0.0	.		48.0	23.0	.	NM_001142633	B0LPH4|D3DTS3|Q5G936|Q5G938|Q5G939|Q8IZ23|Q9Y2Y2	Missense_Mutation	SNP	ENST00000447110.1	hg19	CCDS11147.1	.	.	.	.	.	.	.	.	.	.	G	1.328	-0.597516	0.03771	.	.	ENSG00000141506	ENST00000269300;ENST00000447110	T	0.77620	-1.11	5.24	4.06	0.47325	.	0.930217	0.09115	N	0.846548	T	0.71048	0.3294	N	0.19112	0.55	0.09310	N	1	P	0.43542	0.81	P	0.50109	0.631	T	0.60089	-0.7331	10	0.44086	T	0.13	-6.0E-4	6.061	0.19839	0.0865:0.1349:0.6404:0.1381	.	184	Q8WYR1	PI3R5_HUMAN	M	184	ENSP00000392812:T184M	ENSP00000269300:T184M	T	-	2	0	PIK3R5	8734886	0.002000	0.14202	0.004000	0.12327	0.019000	0.09904	1.078000	0.30754	2.433000	0.82419	0.555000	0.69702	ACG	.	.	.	none		0.647	PIK3R5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000227003.2	NM_014308		A	8794161	G	A	8794161	3	1	248	1	0	0	0	0	1	0	0	0	11929	1145	40	1	2143	1	PIK3R5	17	8794161	Missense_Mutation	SNP	G	TCGA-SX-A7SN-01A-11D-A34Z-10		8794161	72401049	89	15413											
SMCR8	140775	hgsc.bcm.edu	37	chr17	18220521	18220521	+	Frame_Shift_Del	DEL	A	A	-																															cagcagtggtgaaagtattgAagttttgggcacggagaaat																										TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr17:18220521delA	ENST00000406438.3	+	1	1898	c.1418delA	c.(1417-1419)gaafs	p.E473fs	TOP3A_ENST00000582230.1_5'Flank|TOP3A_ENST00000321105.5_5'Flank|TOP3A_ENST00000542570.1_5'Flank	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	473						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						GAAAGTATTGAAGTTTTGGGC	0.502																																					p.E473fs		Atlas-Indel,Pindel	.											.	SMCR8	62	.	0			c.1417delG						PASS	.						68	69	69					17																	18220521		2203	4300	6503	SO:0001589	frameshift_variant	140775	exon1			.	AF467440	CCDS11195.2	17p11.2	2014-06-12			ENSG00000176994	ENSG00000176994			17921	protein-coding gene	gene with protein product						11997338, 23248642	Standard	NM_144775		Approved	FLJ34716	uc002gsy.4	Q8TEV9	OTTHUMG00000059394	ENST00000406438.3:c.1418delA	chr17.hg19:g.18220521delA	ENSP00000385025:p.Glu473fs	49.0	0.0	0		51.0	15.0	0.294118	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Frame_Shift_Del	DEL	ENST00000406438.3	hg19	CCDS11195.2																																																																																			.	.	.	none		0.502	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775		-	18220521	A	-	18220521	7	5	248	1	0	1	0	1	0	0	0	0	14805	246	9	0	1420	0	SMCR8	17	18220521	Frame_Shift_Del	DEL	A	TCGA-SX-A7SN-01A-11D-A34Z-10	9426360	18220521	62974689	90	15414			1	33		2	2	13	N	C_A	3.915066e-05
SMCR8	140775	hgsc.bcm.edu	37	chr17	18220533	18220533	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtattgaagttttgggcaCggagaaatccacctccgtgc	11	10	11	9	2	0	2	0	1	0	1	2	3	2	2	3	2	1	3	3	2	4	4	rs571482412	byFrequency	TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr17:18220533C>T	ENST00000406438.3	+	1	1910	c.1430C>T	c.(1429-1431)aCg>aTg	p.T477M	TOP3A_ENST00000582230.1_5'Flank|TOP3A_ENST00000321105.5_5'Flank|TOP3A_ENST00000542570.1_5'Flank	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	477						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						GTTTTGGGCACGGAGAAATCC	0.512													C|||	2	0.000399361	0.0015	0	5008	,	,		19889	0		0	False		,,,				2504	0				p.T477M		Atlas-SNP	.											.	SMCR8	62	.	0			c.C1430T						PASS	.						63	65	64					17																	18220533		2203	4300	6503	SO:0001583	missense	140775	exon1			TGGGCACGGAGAA	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.1430C>T	chr17.hg19:g.18220533C>T	ENSP00000385025:p.Thr477Met	39.0	0.0	.		52.0	14.0	.	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Missense_Mutation	SNP	ENST00000406438.3	hg19	CCDS11195.2	.	.	.	.	.	.	.	.	.	.	C	13.09	2.131979	0.37630	.	.	ENSG00000176994	ENST00000406438	T	0.34859	1.34	5.73	4.76	0.60689	.	0.269349	0.37012	N	0.002284	T	0.49201	0.1543	L	0.34521	1.04	0.39220	D	0.963485	D	0.89917	1.0	D	0.78314	0.991	T	0.55088	-0.8195	10	0.62326	D	0.03	-23.1601	15.0297	0.71696	0.0:0.9319:0.0:0.0681	.	477	Q8TEV9	SMCR8_HUMAN	M	477	ENSP00000385025:T477M	ENSP00000385025:T477M	T	+	2	0	SMCR8	18161258	0.990000	0.36364	0.882000	0.34594	0.535000	0.34838	2.896000	0.48656	1.437000	0.47472	-0.122000	0.15005	ACG	.	.	.	none		0.512	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775		T	18220533	C	T	18220533	3	4	248	1	0	0	0	0	1	0	0	0	14805	536	19	1	1432	1	SMCR8	17	18220533	Missense_Mutation	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10	12	18220533	62974677	91	15415			1	33		2	2	13	N	C_A	3.915066e-05
KSR1	8844	hgsc.bcm.edu	37	chr17	25919618	25919618	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacagagcagccgaaccccAttttggaaccctccccaaag	12	5	9	15	1	0	1	0	0	0	1	1	4	1	3	6	2	4	1	6	2	3	2			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr17:25919618A>G	ENST00000319524.6	+	9	1265	c.1265A>G	c.(1264-1266)cAt>cGt	p.H422R	KSR1_ENST00000509603.2_Missense_Mutation_p.H422R|KSR1_ENST00000398988.3_Missense_Mutation_p.H285R|KSR1_ENST00000268763.6_Missense_Mutation_p.H285R|KSR1_ENST00000581975.1_3'UTR			Q8IVT5	KSR1_HUMAN	kinase suppressor of ras 1	422					Ras protein signal transduction (GO:0007265)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(12)|prostate(2)|urinary_tract(1)	28	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		GCCGAACCCCATTTTGGAACC	0.547																																					p.H285R	Esophageal Squamous(88;1120 1336 6324 10502 16832)	Atlas-SNP	.											.	KSR1	151	.	0			c.A854G						PASS	.						71	70	71					17																	25919618		1910	4120	6030	SO:0001583	missense	8844	exon9			AACCCCATTTTGG	U43586	CCDS58532.1	17q11.2	2012-05-23	2005-12-14	2005-12-14	ENSG00000141068	ENSG00000141068			6465	protein-coding gene	gene with protein product		601132	"kinase suppressor of ras"	KSR		8521512	Standard	XM_006722151		Approved	RSU2	uc031qzj.1	Q8IVT5	OTTHUMG00000132051	ENST00000319524.6:c.1265A>G	chr17.hg19:g.25919618A>G	ENSP00000323178:p.His422Arg	68.0	0.0	.		91.0	34.0	.	NM_014238	F8WEA9|H7BYU0|Q13476	Missense_Mutation	SNP	ENST00000319524.6	hg19		.	.	.	.	.	.	.	.	.	.	A	16.91	3.251807	0.59212	.	.	ENSG00000141068	ENST00000319524;ENST00000509603;ENST00000268763;ENST00000398982	T;T;T	0.80738	-1.41;-1.34;-1.41	5.14	5.14	0.70334	.	0.463486	0.26136	N	0.026130	T	0.75568	0.3867	L	0.58810	1.83	0.32224	N	0.574889	P;P	0.43826	0.544;0.818	B;B	0.39840	0.162;0.311	T	0.77308	-0.2636	10	0.14252	T	0.57	.	14.1401	0.65313	1.0:0.0:0.0:0.0	.	420;422	Q8IVT5;F5H0K8	KSR1_HUMAN;.	R	422;422;285;285	ENSP00000323178:H422R;ENSP00000438795:H422R;ENSP00000268763:H285R	ENSP00000268763:H285R	H	+	2	0	KSR1	22943745	1.000000	0.71417	0.997000	0.53966	0.966000	0.64601	6.933000	0.75874	1.951000	0.56629	0.482000	0.46254	CAT	.	.	.	none		0.547	KSR1-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_014238		G	25919618	A	G	25919618	3	3	248	1	0	0	0	0	1	0	0	0	8588	217	8	3	876	3	KSR1	17	25919618	Missense_Mutation	SNP	A	TCGA-SX-A7SN-01A-11D-A34Z-10	7699085	25919618	55275592	92	15416											
NR1D1	9572	hgsc.bcm.edu	37	chr17	38249443	38249443	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtgaagcgggaagtctccaAgggccggttcttcagcacca	9	7	14	11	2	3	1	1	1	2	0	4	2	3	2	3	4	2	2	3	4	3	2			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr17:38249443A>G	ENST00000246672.3	-	8	2368	c.1738T>C	c.(1738-1740)Ttg>Ctg	p.L580L	THRA_ENST00000584985.1_Silent_p.Q388Q|THRA_ENST00000394121.4_Silent_p.Q427Q|THRA_ENST00000264637.4_Silent_p.Q427Q	NM_021724.3	NP_068370.1	P20393	NR1D1_HUMAN	nuclear receptor subfamily 1, group D, member 1	580	Ligand-binding.				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)					GAAGTCTCCAAGGGCCGGTTC	0.637																																					p.L580L		Atlas-SNP	.											.	NR1D1	45	.	0			c.T1738C						PASS	.						44	46	45					17																	38249443		2203	4300	6503	SO:0001819	synonymous_variant	9572	exon8			TCTCCAAGGGCCG	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.1738T>C	chr17.hg19:g.38249443A>G		60.0	0.0	.		81.0	57.0	.	NM_021724	Q0P5Z4|Q15304	Silent	SNP	ENST00000246672.3	hg19	CCDS11361.1																																																																																			.	.	.	none		0.637	NR1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257135.1			G	38249443	A	G	38249443	2	3	248	1	0	0	0	0	0	0	0	1	10622	69	3	3		3	NR1D1	17	38249443	Silent	SNP	A	TCGA-SX-A7SN-01A-11D-A34Z-10	12329825	38249443	42945767	93	15417											
AZI1	22994	hgsc.bcm.edu	37	chr17	79166382	79166382	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcctcagctcttccagcTccgcccgctgcctgcggcca	3	8	10	20	3	2	0	1	0	1	0	4	0	4	0	6	1	5	4	6	1	0	1			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr17:79166382T>C	ENST00000269392.4	-	20	2697	c.2450A>G	c.(2449-2451)gAg>gGg	p.E817G	AZI1_ENST00000374782.3_Missense_Mutation_p.E778G|AZI1_ENST00000450824.2_Missense_Mutation_p.E814G|AZI1_ENST00000575907.1_Missense_Mutation_p.E781G	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		817					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)			CTCTTCCAGCTCCGCCCGCTG	0.682																																					p.E814G		Atlas-SNP	.											.	AZI1	145	.	0			c.A2441G						PASS	.						22	21	21					17																	79166382		2187	4289	6476	SO:0001583	missense	22994	exon20			TCCAGCTCCGCCC																												ENST00000269392.4:c.2450A>G	chr17.hg19:g.79166382T>C	ENSP00000269392:p.Glu817Gly	54.0	0.0	.		64.0	18.0	.	NM_014984	A6NHI8|B2RN11|Q96F50	Missense_Mutation	SNP	ENST00000269392.4	hg19		.	.	.	.	.	.	.	.	.	.	T	18.92	3.725194	0.68959	.	.	ENSG00000141577	ENST00000450824;ENST00000374782;ENST00000269392	T;T;T	0.18174	2.23;2.24;2.23	3.28	3.28	0.37604	.	0.064317	0.64402	D	0.000012	T	0.37544	0.1007	M	0.66939	2.045	0.53688	D	0.999972	D;D;D;D	0.89917	1.0;1.0;0.998;0.998	D;D;D;D	0.87578	0.998;0.998;0.948;0.948	T	0.22417	-1.0217	10	0.72032	D	0.01	-15.5695	11.7935	0.52084	0.0:0.0:0.0:1.0	.	814;817;778;814	B2RN10;Q9UPN4;Q9UPN4-3;Q9UPN4-2	.;AZI1_HUMAN;.;.	G	814;778;817	ENSP00000393583:E814G;ENSP00000363914:E778G;ENSP00000269392:E817G	ENSP00000269392:E817G	E	-	2	0	AZI1	76780977	1.000000	0.71417	0.904000	0.35570	0.561000	0.35649	5.333000	0.65917	1.368000	0.46115	0.260000	0.18958	GAG	.	.	.	none		0.682	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1			C	79166382	T	C	79166382	3	2	248	1	0	0	0	0	1	0	0	0	1240	1551	54	3	829	3	AZI1	17	79166382	Missense_Mutation	SNP	T	TCGA-SX-A7SN-01A-11D-A34Z-10	40916939	79166382	2028828	94	15418											
TGIF1	7050	hgsc.bcm.edu	37	chr18	3457644	3457644	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgtccatcagtgatctgccaTaccactgtgactgcattgaa	10	11	8	12	1	2	3	1	3	1	0	3	3	3	3	3	0	3	1	3	0	2	2			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr18:3457644T>C	ENST00000330513.5	+	3	1215	c.912T>C	c.(910-912)caT>caC	p.H304H	TGIF1_ENST00000551541.1_Silent_p.H155H|TGIF1_ENST00000401449.1_Silent_p.H155H|TGIF1_ENST00000472042.1_Silent_p.H155H|TGIF1_ENST00000407501.2_Silent_p.H175H|TGIF1_ENST00000405385.3_Silent_p.H155H|TGIF1_ENST00000343820.5_Silent_p.H175H|TGIF1_ENST00000345133.5_Silent_p.H155H|TGIF1_ENST00000548489.2_Silent_p.H189H|TGIF1_ENST00000400167.2_Silent_p.H155H	NM_170695.2	NP_733796.2	Q15583	TGIF1_HUMAN	TGFB-induced factor homeobox 1	304					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)				TGATCTGCCATACCACTGTGA	0.522																																					p.H304H		Atlas-SNP	.											.	TGIF1	41	.	0			c.T912C						PASS	.						79	69	72					18																	3457644		2203	4300	6503	SO:0001819	synonymous_variant	7050	exon3			CTGCCATACCACT	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.912T>C	chr18.hg19:g.3457644T>C		85.0	0.0	.		81.0	25.0	.	NM_170695	A6NE42|A6NLU7|F8VZB6|Q6ICR0|Q8N5X9|Q9NRS0	Silent	SNP	ENST00000330513.5	hg19	CCDS11834.1																																																																																			.	.	.	none		0.522	TGIF1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254368.4	NM_170695		C	3457644	T	C	3457644	2	2	248	1	0	0	0	0	0	0	0	1	15837	1403	49	3		3	TGIF1	18	3457644	Silent	SNP	T	TCGA-SX-A7SN-01A-11D-A34Z-10		3457644	74619604	95	15419											
GADD45B	4616	hgsc.bcm.edu	37	chr19	2477521	2477521	+	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	gcctggaagagccacggcttGgtggaggtggccagctactg	7	7	17	10	1	0	1	0	0	0	1	0	3	0	3	3	6	3	2	3	6	2	2			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr19:2477521G>C	ENST00000215631.4	+	4	637	c.405G>C	c.(403-405)ttG>ttC	p.L135F		NM_015675.3	NP_056490.2	O75293	GA45B_HUMAN	growth arrest and DNA-damage-inducible, beta	135					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)		GCCACGGCTTGGTGGAGGTGG	0.607																																					p.L135F		Atlas-SNP	.											.	GADD45B	6	.	0			c.G405C						PASS	.						45	43	44					19																	2477521		2203	4300	6503	SO:0001583	missense	4616	exon4			CGGCTTGGTGGAG	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.405G>C	chr19.hg19:g.2477521G>C	ENSP00000215631:p.Leu135Phe	20.0	0.0	.		35.0	17.0	.	NM_015675	A8KAM2|O75960|Q17R46	Missense_Mutation	SNP	ENST00000215631.4	hg19	CCDS32868.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.697218	0.88830	.	.	ENSG00000099860	ENST00000215631	T	0.55413	0.52	4.66	4.66	0.58398	.	0.076693	0.53938	D	0.000053	T	0.71484	0.3345	M	0.84082	2.675	0.80722	D	1	D	0.71674	0.998	P	0.62089	0.898	T	0.75852	-0.3171	10	0.51188	T	0.08	.	15.0579	0.71930	0.0:0.0:1.0:0.0	.	135	O75293	GA45B_HUMAN	F	135	ENSP00000215631:L135F	ENSP00000215631:L135F	L	+	3	2	GADD45B	2428521	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.014000	0.57145	2.126000	0.65437	0.542000	0.68232	TTG	.	.	.	none		0.607	GADD45B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451337.1	NM_015675		C	2477521	G	C	2477521	3	2	248	1	0	0	0	0	1	0	0	0	6189	1339	47	4	419	4	GADD45B	19	2477521	Missense_Mutation	SNP	G	TCGA-SX-A7SN-01A-11D-A34Z-10		2477521	56651462	96	15420											
ZNF283	284349	hgsc.bcm.edu	37	chr19	44341266	44341266	+	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	ggaggagtgggaatgcctggAccctgctcagagggacttgt	8	8	17	8	0	1	1	1	0	0	1	1	6	1	6	2	5	2	1	2	5	1	1			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr19:44341266A>T	ENST00000324461.7	+	6	569	c.272A>T	c.(271-273)gAc>gTc	p.D91V	ZNF283_ENST00000588797.1_Intron|ZNF283_ENST00000586976.1_3'UTR|ZNF283_ENST00000590950.1_Missense_Mutation_p.D66V|ZNF283_ENST00000310738.8_Missense_Mutation_p.D55V|ZNF283_ENST00000593164.1_Missense_Mutation_p.D66V|ZNF283_ENST00000593268.1_Missense_Mutation_p.D91V	NM_181845.1	NP_862828.1	Q8N7M2	ZN283_HUMAN	zinc finger protein 283	91	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(4)	8		Prostate(69;0.0352)				GAATGCCTGGACCCTGCTCAG	0.453																																					p.D91V		Atlas-SNP	.											.	ZNF283	83	.	0			c.A272T						PASS	.						166	180	175					19																	44341266		2203	4300	6503	SO:0001583	missense	284349	exon6			GCCTGGACCCTGC	AK098175	CCDS46097.1, CCDS74387.1	19q13.31	2013-01-08			ENSG00000167637	ENSG00000167637		"Zinc fingers, C2H2-type", "-"	13077	protein-coding gene	gene with protein product						12743021	Standard	NM_181845		Approved		uc002oxr.4	Q8N7M2		ENST00000324461.7:c.272A>T	chr19.hg19:g.44341266A>T	ENSP00000327314:p.Asp91Val	82.0	0.0	.		92.0	33.0	.	NM_181845	B4DGZ5|B7WP04|Q6RFR9|Q86WM6	Missense_Mutation	SNP	ENST00000324461.7	hg19	CCDS46097.1	.	.	.	.	.	.	.	.	.	.	A	16.64	3.178962	0.57692	.	.	ENSG00000167637	ENST00000324461;ENST00000310738	T;T	0.02837	4.14;4.14	4.08	1.91	0.25777	Krueppel-associated box (4);	.	.	.	.	T	0.14356	0.0347	H	0.95504	3.68	0.34818	D	0.738409	D	0.56521	0.976	P	0.58172	0.834	T	0.04708	-1.0932	9	0.87932	D	0	.	4.0098	0.09618	0.6729:0.2131:0.114:0.0	.	91	Q8N7M2	ZN283_HUMAN	V	91;55	ENSP00000327314:D91V;ENSP00000312519:D55V	ENSP00000312519:D55V	D	+	2	0	ZNF283	49033106	0.087000	0.21565	0.991000	0.47740	0.997000	0.91878	0.216000	0.17585	0.142000	0.18901	0.477000	0.44152	GAC	.	.	.	none		0.453	ZNF283-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459909.1	NM_181845		T	44341266	A	T	44341266	3	4	248	1	0	0	0	0	1	0	0	0	17832	275	10	5	282	5	ZNF283	19	44341266	Missense_Mutation	SNP	A	TCGA-SX-A7SN-01A-11D-A34Z-10	41863745	44341266	14787717	97	15421											
SYMPK	8189	hgsc.bcm.edu	37	chr19	46355636	46355636	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acttgtctgcttggaatgcgAtgatctcctgccaatgttag	8	14	10	9	1	2	1	0	1	2	0	3	3	2	2	2	1	3	2	2	1	3	3			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr19:46355636A>G	ENST00000245934.7	-	5	477	c.233T>C	c.(232-234)aTc>aCc	p.I78T		NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	78	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)		TTGGAATGCGATGATCTCCTG	0.527																																					p.I78T		Atlas-SNP	.											.	SYMPK	104	.	0			c.T233C						PASS	.						174	172	173					19																	46355636		2048	4195	6243	SO:0001583	missense	8189	exon5			AATGCGATGATCT	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.233T>C	chr19.hg19:g.46355636A>G	ENSP00000245934:p.Ile78Thr	112.0	0.0	.		101.0	37.0	.	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Missense_Mutation	SNP	ENST00000245934.7	hg19	CCDS12676.2	.	.	.	.	.	.	.	.	.	.	A	17.00	3.276339	0.59649	.	.	ENSG00000125755	ENST00000245934;ENST00000340643	T	0.34072	1.38	4.81	4.81	0.61882	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.30008	0.0751	L	0.38838	1.175	0.80722	D	1	P;P	0.36874	0.572;0.519	B;B	0.36030	0.216;0.177	T	0.12915	-1.0529	10	0.54805	T	0.06	.	12.6398	0.56702	1.0:0.0:0.0:0.0	.	93;78	Q4LE61;Q92797	.;SYMPK_HUMAN	T	78;82	ENSP00000245934:I78T	ENSP00000245934:I78T	I	-	2	0	SYMPK	51047476	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.581000	0.90788	1.929000	0.55896	0.459000	0.35465	ATC	.	.	.	none		0.527	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819		G	46355636	A	G	46355636	3	3	248	1	0	0	0	0	1	0	0	0	15451	333	12	3	3683	3	SYMPK	19	46355636	Missense_Mutation	SNP	A	TCGA-SX-A7SN-01A-11D-A34Z-10	2014370	46355636	12773347	98	15422											
ZNF649	65251	hgsc.bcm.edu	37	chr19	52394350	52394350	+	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	cttgccacagtcaatgcatcCataaggtttctctccagtgt	9	13	7	12	0	2	0	1	0	1	0	5	0	4	0	3	1	2	2	3	1	2	3			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr19:52394350C>A	ENST00000354957.3	-	5	1323	c.1039G>T	c.(1039-1041)Gga>Tga	p.G347*	CTC-429C10.2_ENST00000600329.1_RNA|ZNF649_ENST00000600738.1_Nonsense_Mutation_p.G319*	NM_023074.3	NP_075562.2	Q9BS31	ZN649_HUMAN	zinc finger protein 649	347					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)		TCAATGCATCCATAAGGTTTC	0.453																																					p.G347X		Atlas-SNP	.											.	ZNF649	72	.	0			c.G1039T						PASS	.						146	116	126					19																	52394350		2203	4300	6503	SO:0001587	stop_gained	65251	exon5			TGCATCCATAAGG	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.1039G>T	chr19.hg19:g.52394350C>A	ENSP00000347043:p.Gly347*	71.0	0.0	.		79.0	30.0	.	NM_023074	A8MYJ5|B2RDC4|Q9H9N2	Nonsense_Mutation	SNP	ENST00000354957.3	hg19	CCDS12843.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.380873	0.82792	.	.	ENSG00000198093	ENST00000354957	.	.	.	2.52	1.47	0.22746	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	.	1.3017	0.02080	0.2192:0.4244:0.2154:0.141	.	.	.	.	X	347	.	ENSP00000347043:G347X	G	-	1	0	ZNF649	57086162	0.000000	0.05858	0.219000	0.23793	0.013000	0.08279	-2.196000	0.01241	0.273000	0.22049	0.404000	0.27445	GGA	.	.	.	none		0.453	ZNF649-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461097.1	NM_023074		A	52394350	C	A	52394350	4	1	248	1	0	0	0	0	0	1	0	0	18076	603	21	4	482	4	ZNF649	19	52394350	Nonsense_Mutation	SNP	C	TCGA-SX-A7SN-01A-11D-A34Z-10	6038714	52394350	6734633	99	15423											
EPS8L1	54869	hgsc.bcm.edu	37	chr19	55593489	55593489	+	Frame_Shift_Del	DEL	C	C	-																															tgacgctgcgggccaagccgCcctcggaggccgagtacacc																								rs148596546		TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr19:55593489delC	ENST00000201647.6	+	10	987	c.931delC	c.(931-933)cccfs	p.P311fs	EPS8L1_ENST00000592824.1_3'UTR|EPS8L1_ENST00000540810.1_Frame_Shift_Del_p.P247fs|EPS8L1_ENST00000588359.1_Intron|EPS8L1_ENST00000245618.5_Frame_Shift_Del_p.P184fs|EPS8L1_ENST00000586329.1_Frame_Shift_Del_p.P293fs	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1	311					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)		GGCCAAGCCGCCCTCGGAGGC	0.721																																					p.P310fs	Ovarian(149;255 1863 3636 27051 29647)	Atlas-Indel,Pindel	.											.	EPS8L1	122	.	0			c.930delG						PASS	.						12	13	13					19																	55593489		2185	4270	6455	SO:0001589	frameshift_variant	54869	exon10			.	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.931delC	chr19.hg19:g.55593489delC	ENSP00000201647:p.Pro311fs	111.0	0.0	0		109.0	42.0	0.385321	NM_133180	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	Frame_Shift_Del	DEL	ENST00000201647.6	hg19	CCDS12914.1																																																																																			.	.	.	none		0.721	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451713.1	NM_017729		-	55593489	C	-	55593489	7	5	248	1	0	1	0	1	0	0	0	0	5197	739	26	0	1017	0	EPS8L1	19	55593489	Frame_Shift_Del	DEL	C	TCGA-SX-A7SN-01A-11D-A34Z-10	3199139	55593489	3535494	100	15424											
CTCFL	140690	hgsc.bcm.edu	37	chr20	56098332	56098332	+	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	ttcttctcctgctcttcctcGagctaataaacaacaaatat	12	14	3	12	1	3	0	0	0	3	0	6	1	4	0	2	0	4	2	2	0	6	6			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chr20:56098332G>A	ENST00000608263.1	-	2	1207	c.546C>T	c.(544-546)ctC>ctT	p.L182L	CTCFL_ENST00000371196.2_Silent_p.L182L|CTCFL_ENST00000502686.2_Intron|CTCFL_ENST00000423479.3_Silent_p.L182L|CTCFL_ENST00000608158.1_Silent_p.L182L|CTCFL_ENST00000608425.1_Silent_p.L182L|CTCFL_ENST00000608858.1_Intron|CTCFL_ENST00000609232.1_Silent_p.L182L|CTCFL_ENST00000539382.1_5'UTR|CTCFL_ENST00000433949.3_5'UTR|CTCFL_ENST00000481655.2_Silent_p.L182L|CTCFL_ENST00000429804.3_Silent_p.L182L|CTCFL_ENST00000608440.1_Silent_p.L182L|CTCFL_ENST00000608903.1_Intron|CTCFL_ENST00000422869.2_Silent_p.L182L|CTCFL_ENST00000243914.3_Silent_p.L182L|CTCFL_ENST00000432255.2_Silent_p.L182L	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	182					cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			GCTCTTCCTCGAGCTAATAAA	0.353																																					p.L182L		Atlas-SNP	.											.	CTCFL	97	.	0			c.C546T						PASS	.						85	83	84					20																	56098332		2202	4300	6502	SO:0001819	synonymous_variant	140690	exon2			TTCCTCGAGCTAA		CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"Zinc fingers, C2H2-type"	16234	protein-coding gene	gene with protein product	"cancer/testis antigen 27"	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.546C>T	chr20.hg19:g.56098332G>A		146.0	0.0	.		163.0	67.0	.	NM_001269044	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Silent	SNP	ENST00000608263.1	hg19	CCDS13459.1																																																																																			.	.	.	none		0.353	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618		A	56098332	G	A	56098332	2	1	248	1	0	0	0	0	0	0	0	1	4003	1045	37	1		1	CTCFL	20	56098332	Silent	SNP	G	TCGA-SX-A7SN-01A-11D-A34Z-10		56098332	6927188	101	15425											
THOC2	57187	hgsc.bcm.edu	37	chrX	122766884	122766884	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtttctgatctgaccaaaaTaaccaccctgcacaagggaa	14	9	7	11	0	2	2	0	2	2	0	2	3	2	3	3	1	2	2	3	1	5	2			TCGA-SX-A7SN-01A-11D-A34Z-10	TCGA-SX-A7SN-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d71c98f8-db62-494f-8677-8997e476ee98	7b35d4fc-dac8-427e-b9c4-1acb0a501501	g.chrX:122766884T>C	ENST00000245838.8	-	21	2175	c.2144A>G	c.(2143-2145)tAt>tGt	p.Y715C	THOC2_ENST00000355725.4_Missense_Mutation_p.Y715C|THOC2_ENST00000491737.1_Missense_Mutation_p.Y600C	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	715					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						CTGACCAAAATAACCACCCTG	0.388																																					p.Y715C		Atlas-SNP	.											.	THOC2	310	.	0			c.A2144G						PASS	.						120	97	104					X																	122766884		1842	4081	5923	SO:0001583	missense	57187	exon21			CCAAAATAACCAC	AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"THO complex subunits"	19073	protein-coding gene	gene with protein product		300395	"chromosome X open reading frame 3"	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.2144A>G	chrX.hg19:g.122766884T>C	ENSP00000245838:p.Tyr715Cys	59.0	0.0	.		64.0	49.0	.	NM_001081550	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Missense_Mutation	SNP	ENST00000245838.8	hg19	CCDS43988.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.074453	0.76415	.	.	ENSG00000125676	ENST00000245838;ENST00000355725;ENST00000491737;ENST00000408933	.	.	.	5.73	5.73	0.89815	.	0.000000	0.64402	D	0.000010	T	0.78046	0.4222	M	0.80982	2.52	0.80722	D	1	D;D	0.71674	0.998;0.996	D;D	0.63033	0.91;0.91	T	0.79647	-0.1716	9	0.45353	T	0.12	-12.6621	15.0184	0.71605	0.0:0.0:0.0:1.0	.	640;715	B4DKZ6;Q8NI27	.;THOC2_HUMAN	C	715;715;600;640	.	ENSP00000245838:Y715C	Y	-	2	0	THOC2	122594565	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	8.024000	0.88770	1.929000	0.55896	0.437000	0.28790	TAT	.	.	.	none		0.388	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3			C	122766884	T	C	122766884	3	2	248	1	0	0	0	0	1	0	0	0	15877	1406	49	3	2709	3	THOC2	23	122766884	Missense_Mutation	SNP	T	TCGA-SX-A7SN-01A-11D-A34Z-10		122766884	32503676	102	15426											
LOC440563	0	hgsc.bcm.edu	37	chr1	13183800	13183800	+	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	agatttcttgacaacaagagTgttgagattcccaatgaaca	15	11	8	7	0	1	5	0	3	1	3	2	6	2	5	1	0	2	1	1	0	4	4			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr1:13183800T>A								RP13-221M14.3 (19332 upstream) : PRAMEF26 (32555 downstream)																							ACAACAAGAGTGTTGAGATTC	0.443																																					p.T25S		Atlas-SNP	.											.	.	.	.	0			c.A73T						PASS	.						62	46	51					1																	13183800		691	1591	2282	SO:0001628	intergenic_variant	0	exon2			CAAGAGTGTTGAG																													chr1.hg19:g.13183800T>A		81.0	0.0	.		91.0	48.0	.	NM_001136561		Missense_Mutation	SNP		hg19																																																																																				.	.	.	none	0	0.443									A	13183800	T	A	13183800	1	1	249	0	1	0	0	0	0	0	0	0	8886	1696	59	5		5	LOC440563	1	13183800	IGR	SNP	T	TCGA-SX-A7SO-01A-11D-A34Z-10		13183800	236066821	1	15427											
EIF4G3	8672	hgsc.bcm.edu	37	chr1	21155712	21155712	+	Missense_Mutation	SNP	A	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	gttcagcaaggtacaaccaaAtatggggaatatcaatggcc	15	8	10	8	0	2	0	2	0	0	0	2	1	2	1	2	4	3	3	2	4	8	4			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr1:21155712A>C	ENST00000264211.8	-	25	4141	c.3947T>G	c.(3946-3948)aTt>aGt	p.I1316S	EIF4G3_ENST00000536266.1_Missense_Mutation_p.I920S|EIF4G3_ENST00000537738.1_Missense_Mutation_p.I806S|EIF4G3_ENST00000602326.1_Missense_Mutation_p.I1322S|EIF4G3_ENST00000374937.3_Missense_Mutation_p.I1322S|EIF4G3_ENST00000374935.3_Missense_Mutation_p.I1036S|EIF4G3_ENST00000400422.1_Missense_Mutation_p.I1316S	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	1316	MI. {ECO:0000255|PROSITE- ProRule:PRU00698}.				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)		GTACAACCAAATATGGGGAAT	0.373																																					p.I1352S		Atlas-SNP	.											.	EIF4G3	300	.	0			c.T4055G						PASS	.						90	93	92					1																	21155712		2203	4300	6503	SO:0001583	missense	8672	exon29			AACCAAATATGGG	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.3947T>G	chr1.hg19:g.21155712A>C	ENSP00000264211:p.Ile1316Ser	114.0	0.0	.		157.0	58.0	.	NM_001198801	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Missense_Mutation	SNP	ENST00000264211.8	hg19	CCDS214.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.813791	0.90790	.	.	ENSG00000075151	ENST00000264211;ENST00000400415;ENST00000400422;ENST00000374935;ENST00000537738;ENST00000374937;ENST00000536266;ENST00000435383	T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91	5.78	5.78	0.91487	Initiation factor eIF-4 gamma, MA3 (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.66674	0.2813	M	0.79475	2.455	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;0.999;1.0;0.999	D;D;D;D;D	0.91635	0.999;0.988;0.986;0.998;0.98	T	0.71069	-0.4699	10	0.87932	D	0	-13.8129	16.1095	0.81250	1.0:0.0:0.0:0.0	.	1511;1036;920;1322;1316	Q59GJ0;Q504Z1;F5H564;B9EGQ7;O43432	.;.;.;.;IF4G3_HUMAN	S	1316;1512;1316;1036;806;1322;920;82	ENSP00000264211:I1316S;ENSP00000383274:I1316S;ENSP00000364071:I1036S;ENSP00000442010:I806S;ENSP00000364073:I1322S;ENSP00000444693:I920S	ENSP00000264211:I1316S	I	-	2	0	EIF4G3	21028299	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.887000	0.92456	2.210000	0.71456	0.482000	0.46254	ATT	.	.	.	none		0.373	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760		C	21155712	A	C	21155712	3	2	249	1	0	0	0	0	1	0	0	0	5040	101	4	5	838	5	EIF4G3	1	21155712	Missense_Mutation	SNP	A	TCGA-SX-A7SO-01A-11D-A34Z-10	7971912	21155712	228094909	2	15428											
C1orf173	127254	hgsc.bcm.edu	37	chr1	75114960	75114960	+	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	gtattgttaaaatacccagcCaggtgtttatccataaggct	12	13	8	8	0	0	0	0	0	0	0	1	0	1	0	3	2	2	4	3	2	6	7			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr1:75114960C>A	ENST00000326665.5	-	2	281	c.63G>T	c.(61-63)ctG>ctT	p.L21L		NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		21										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						AATACCCAGCCAGGTGTTTAT	0.353																																					p.L21L		Atlas-SNP	.											.	C1orf173	380	.	0			c.G63T						PASS	.						110	109	109					1																	75114960		2203	4300	6503	SO:0001819	synonymous_variant	127254	exon2			CCCAGCCAGGTGT																												ENST00000326665.5:c.63G>T	chr1.hg19:g.75114960C>A		39.0	0.0	.		61.0	27.0	.	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Silent	SNP	ENST00000326665.5	hg19	CCDS30755.1																																																																																			.	.	.	none		0.353	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			A	75114960	C	A	75114960	2	1	249	1	0	0	0	0	0	0	0	1	2016	581	21	4		4	C1orf173	1	75114960	Silent	SNP	C	TCGA-SX-A7SO-01A-11D-A34Z-10	53959248	75114960	174135661	3	15429											
BCAR3	8412	hgsc.bcm.edu	37	chr1	94049639	94049639	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcttctgtcctgcatgtgAtccaggcaggcgggctggct	4	11	14	12	1	2	1	0	1	2	0	4	1	4	1	2	4	1	5	2	4	0	1			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr1:94049639A>G	ENST00000370244.1	-	8	1257	c.969T>C	c.(967-969)gaT>gaC	p.D323D	BCAR3_ENST00000260502.6_Silent_p.D323D|BCAR3_ENST00000539242.1_5'UTR|BCAR3_ENST00000370247.3_Silent_p.D232D|BCAR3_ENST00000466632.1_5'UTR|BCAR3_ENST00000370243.1_Silent_p.D323D	NM_001261408.1	NP_001248337.1	O75815	BCAR3_HUMAN	breast cancer anti-estrogen resistance 3	323					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)		CCTGCATGTGATCCAGGCAGG	0.463																																					p.D323D		Atlas-SNP	.											.	BCAR3	62	.	0			c.T969C						PASS	.						104	100	102					1																	94049639		2203	4300	6503	SO:0001819	synonymous_variant	8412	exon6			CATGTGATCCAGG	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.969T>C	chr1.hg19:g.94049639A>G		116.0	0.0	.		141.0	45.0	.	NM_001261409	D3DT43|Q5TEW3|Q6UW40|Q9BR50	Silent	SNP	ENST00000370244.1	hg19	CCDS745.1																																																																																			.	.	.	none		0.463	BCAR3-003	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028420.1			G	94049639	A	G	94049639	2	3	249	1	0	0	0	0	0	0	0	1	1349	330	12	3		3	BCAR3	1	94049639	Silent	SNP	A	TCGA-SX-A7SO-01A-11D-A34Z-10	18934679	94049639	155200982	4	15430											
IGSF3	3321	hgsc.bcm.edu	37	chr1	117156796	117156796	+	Splice_Site	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	gtctgcagggagtctgggatCactgcaacacagaaatgtcc	11	8	12	10	0	3	1	1	0	2	1	4	3	4	3	1	2	3	2	1	2	2	0			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr1:117156796C>T	ENST00000369486.3	-	4	1188	c.423G>A	c.(421-423)gtG>gtA	p.V141V	IGSF3_ENST00000369483.1_Splice_Site_p.V141V|IGSF3_ENST00000318837.6_Splice_Site_p.V141V	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	141					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)		AGTCTGGGATCACTGCAACAC	0.582																																					p.V141V		Atlas-SNP	.											.	IGSF3	294	.	0			c.G423A						PASS	.						28	28	28					1																	117156796		2201	4293	6494	SO:0001630	splice_region_variant	3321	exon4			TGGGATCACTGCA	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.422-1G>A	chr1.hg19:g.117156796C>T		87.0	0.0	.		99.0	53.0	.	NM_001542	A6NJZ6|A6NMC7	Silent	SNP	ENST00000369486.3	hg19	CCDS30813.1																																																																																			.	.	.	none		0.582	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542	Silent	T	117156796	C	T	117156796	5	4	249	1	0	0	0	0	0	0	1	0	7608	840	29	2	3257	2	IGSF3	1	117156796	Splice_Site	SNP	C	TCGA-SX-A7SO-01A-11D-A34Z-10	23107157	117156796	132093825	5	15431											
LCE4A	199834	hgsc.bcm.edu	37	chr1	152681689	152681689	+	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	tgctgtggctccagctctggGggctgtggttgctgcagctc	2	12	16	11	0	1	0	0	0	1	0	3	0	2	0	1	4	5	8	1	4	0	1	rs200223098	byFrequency	TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr1:152681689G>C	ENST00000368777.1	+	2	394	c.138G>C	c.(136-138)ggG>ggC	p.G46G	LCE4A_ENST00000335535.3_Silent_p.G46G			Q5TA78	LCE4A_HUMAN	late cornified envelope 4A	46	Cys-rich.				keratinization (GO:0031424)					endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.116)			CCAGCTCTGGGGGCTGTGGTT	0.577													G|||	245	0.0489217	0.003	0.0821	5008	,	,		16464	0.129		0.0109	False		,,,				2504	0.044				p.G46G		Atlas-SNP	.											.,2	LCE4A	37	.	0			c.G138C						PASS	.						81	94	90					1																	152681689		2203	4300	6503	SO:0001819	synonymous_variant	199834	exon1			CTCTGGGGGCTGT	BI670517	CCDS1022.1	1q22	2008-02-05	2004-10-11	2004-10-15	ENSG00000187170	ENSG00000187170		"Late cornified envelopes"	16613	protein-coding gene	gene with protein product		612618	"small proline rich-like (epidermal differentiation complex) 4A"	SPRL4A		11698679	Standard	NM_178356		Approved	LEP8	uc001fak.2	Q5TA78	OTTHUMG00000014394	ENST00000368777.1:c.138G>C	chr1.hg19:g.152681689G>C		78.0	0.0	.		97.0	31.0	.	NM_178356	Q14D97	Silent	SNP	ENST00000368777.1	hg19	CCDS1022.1																																																																																			.	G|0.999;C|0.001	0.001	weak		0.577	LCE4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040048.1	NM_178356		C	152681689	G	C	152681689	2	2	249	1	0	0	0	0	0	0	0	1	8681	1219	43	4		4	LCE4A	1	152681689	Silent	SNP	G	TCGA-SX-A7SO-01A-11D-A34Z-10	35524893	152681689	96568932	6	15432											
HMCN1	83872	hgsc.bcm.edu	37	chr1	186026523	186026524	+	Frame_Shift_Ins	INS	-	-	ATTCTTTCAGGTA																															gccttagcaattctgtgaggINSattctttcaggtattagaaa																										TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr1:186026523_186026524insATTCTTTCAGGTA	ENST00000271588.4	+	46	7531_7532	c.7302_7303insATTCTTTCAGGTA	c.(7303-7305)attfs	p.-2435fs	HMCN1_ENST00000367492.2_Frame_Shift_Ins_p.-2435fs	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1						response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.R2434S(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						ATTCTGTGAGGATTCTTTCAGG	0.391																																					p.R2434fs		Pindel	.											HMCN1,NS,carcinoma,0,1	HMCN1	797	.	1	Substitution - Missense(1)	lung(1)	c.7302_7303insATTCTTTCAGGTA						PASS	.																																			SO:0001589	frameshift_variant	83872	exon46			.	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	Exception_encountered	chr1.hg19:g.186026523_186026524insATTCTTTCAGGTA	ENSP00000271588:p.Ile2435fs	58.0	0.0	.		60.0	14.0	0.233	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Frame_Shift_Ins	INS	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.	.	none		0.391	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		ATTCTTTCAGGTA	186026524	-	ATTCTTTCAGGTA	186026523	7	5	249	1	0	1	1	0	0	0	0	0	7227	1165	41	0	7484	0	HMCN1	1	186026523	Frame_Shift_Ins	INS	-	TCGA-SX-A7SO-01A-11D-A34Z-10	33344834	186026523	63224098	7	15433											
RYR2	6262	hgsc.bcm.edu	37	chr1	237758908	237758908	+	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	tgtggtggatgctgccagcgGgctgctcacattcattgcca	6	11	13	11	1	2	0	2	0	0	0	2	1	2	1	2	3	5	3	2	3	0	2			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr1:237758908G>A	ENST00000366574.2	+	34	4864	c.4547G>A	c.(4546-4548)gGg>gAg	p.G1516E	RYR2_ENST00000542537.1_Missense_Mutation_p.G1500E|RYR2_ENST00000360064.6_Missense_Mutation_p.G1514E	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1516	4 X approximate repeats.|B30.2/SPRY 3. {ECO:0000255|PROSITE- ProRule:PRU00548}.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GCTGCCAGCGGGCTGCTCACA	0.522																																					p.G1516E		Atlas-SNP	.											.	RYR2	1273	.	0			c.G4547A						PASS	.						71	80	77					1																	237758908		2103	4237	6340	SO:0001583	missense	6262	exon34			CCAGCGGGCTGCT	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.4547G>A	chr1.hg19:g.237758908G>A	ENSP00000355533:p.Gly1516Glu	56.0	0.0	.		92.0	48.0	.	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	hg19	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.958439	0.92726	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	T;T;T	0.72051	-0.62;-0.62;-0.62	5.72	5.72	0.89469	SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.64402	D	0.000004	D	0.85881	0.5800	M	0.80982	2.52	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86888	0.2046	10	0.87932	D	0	.	19.8805	0.96895	0.0:0.0:1.0:0.0	.	1516	Q92736	RYR2_HUMAN	E	1516;1514;1500	ENSP00000355533:G1516E;ENSP00000353174:G1514E;ENSP00000443798:G1500E	ENSP00000353174:G1514E	G	+	2	0	RYR2	235825531	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.822000	0.99363	2.704000	0.92352	0.655000	0.94253	GGG	.	.	.	none		0.522	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237758908	G	A	237758908	3	1	249	1	0	0	0	0	1	0	0	0	13782	1232	43	2	4681	2	RYR2	1	237758908	Missense_Mutation	SNP	G	TCGA-SX-A7SO-01A-11D-A34Z-10	51732385	237758908	11491713	8	15434											
DNAH6	1768	hgsc.bcm.edu	37	chr2	84774641	84774641	+	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	agaacgcctaggagaatttcGaaatgaggcaaaatatgtag	17	8	11	5	2	0	3	0	1	0	2	1	5	0	3	1	2	1	2	1	2	8	4			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr2:84774641G>A	ENST00000237449.6	+	6	1099	c.1091G>A	c.(1090-1092)cGa>cAa	p.R364Q	DNAH6_ENST00000389394.3_Missense_Mutation_p.R364Q|DNAH6_ENST00000398278.2_Missense_Mutation_p.R364Q			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	364	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			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						GGAGAATTTCGAAATGAGGCA	0.393																																					p.R364Q		Atlas-SNP	.											.	DNAH6	194	.	0			c.G1091A						PASS	.						244	208	219					2																	84774641		692	1591	2283	SO:0001583	missense	1768	exon7			AATTTCGAAATGA	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.1091G>A	chr2.hg19:g.84774641G>A	ENSP00000237449:p.Arg364Gln	176.0	0.0	.		187.0	35.0	.	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	hg19	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.969191	0.92855	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.25414	1.8;1.93;1.8	5.35	5.35	0.76521	.	.	.	.	.	T	0.31638	0.0803	M	0.76002	2.32	0.37615	D	0.921094	P	0.40083	0.702	B	0.34038	0.174	T	0.45454	-0.9260	9	0.62326	D	0.03	.	17.8272	0.88669	0.0:0.0:1.0:0.0	.	364	Q9C0G6	DYH6_HUMAN	Q	364	ENSP00000374045:R364Q;ENSP00000381326:R364Q;ENSP00000237449:R364Q	ENSP00000237449:R364Q	R	+	2	0	DNAH6	84628152	1.000000	0.71417	0.344000	0.25628	0.767000	0.43475	6.769000	0.74985	2.501000	0.84356	0.591000	0.81541	CGA	.	.	.	none		0.393	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		A	84774641	G	A	84774641	3	1	249	1	0	0	0	0	1	0	0	0	4607	1058	37	1	1113	1	DNAH6	2	84774641	Missense_Mutation	SNP	G	TCGA-SX-A7SO-01A-11D-A34Z-10		84774641	158424732	9	15435											
ITPR1	3708	hgsc.bcm.edu	37	chr3	4741539	4741539	+	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	ggaaacatgcagactcgattTtggagaagtatgtcaccgaa	14	9	11	7	2	1	2	1	0	0	2	2	6	1	3	1	2	2	2	1	2	4	3			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr3:4741539T>A	ENST00000443694.2	+	32	4405	c.4405T>A	c.(4405-4407)Ttg>Atg	p.L1469M	ITPR1_ENST00000423119.2_Missense_Mutation_p.L1475M|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000354582.6_Missense_Mutation_p.L1484M|ITPR1_ENST00000302640.8_Missense_Mutation_p.L1469M|ITPR1_ENST00000357086.4_Missense_Mutation_p.L1475M|ITPR1_ENST00000456211.2_Missense_Mutation_p.L1460M			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	1484					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)	AGACTCGATTTTGGAGAAGTA	0.413																																					p.L1475M		Atlas-SNP	.											.	ITPR1	659	.	0			c.T4423A						PASS	.						174	161	166					3																	4741539		1946	4134	6080	SO:0001583	missense	3708	exon35			TCGATTTTGGAGA	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.4405T>A	chr3.hg19:g.4741539T>A	ENSP00000401671:p.Leu1469Met	68.0	0.0	.		80.0	33.0	.	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	hg19	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	T	16.55	3.155209	0.57259	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	T;T;T;T;T;T	0.78924	-1.22;-1.22;-1.22;-1.22;-1.22;-1.22	5.7	-3.64	0.04515	.	0.000000	0.64402	D	0.000001	D	0.87398	0.6167	M	0.85197	2.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.996	D	0.86486	0.1794	10	0.51188	T	0.08	.	18.2794	0.90092	0.0:0.6888:0.0:0.3112	.	1484;1475	Q14643;G5E9P1	ITPR1_HUMAN;.	M	1484;1469;1484;1475;1475;1460;1469	ENSP00000306253:L1469M;ENSP00000346595:L1484M;ENSP00000405934:L1475M;ENSP00000349597:L1475M;ENSP00000397885:L1460M;ENSP00000401671:L1469M	ENSP00000306253:L1469M	L	+	1	2	ITPR1	4716539	0.002000	0.14202	0.003000	0.11579	0.784000	0.44337	0.017000	0.13399	-0.994000	0.03463	0.477000	0.44152	TTG	.	.	.	none		0.413	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		A	4741539	T	A	4741539	3	1	249	1	0	0	0	0	1	0	0	0	7927	1838	64	5	4580	5	ITPR1	3	4741539	Missense_Mutation	SNP	T	TCGA-SX-A7SO-01A-11D-A34Z-10		4741539	193280891	10	15436											
C3orf62	375341	hgsc.bcm.edu	37	chr3	49308828	49308828	+	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	catgtggttcaattcgttttCaaattctatttttccagcca	9	18	5	9	1	3	0	2	0	1	0	5	0	4	0	2	1	1	2	2	1	3	8			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr3:49308828C>A	ENST00000343010.3	-	3	1625	c.589G>T	c.(589-591)Gaa>Taa	p.E197*	MIR4271_ENST00000582451.1_RNA|Y_RNA_ENST00000362676.1_RNA	NM_198562.2	NP_940964.1	Q6ZUJ4	CC062_HUMAN	chromosome 3 open reading frame 62	197										breast(1)|kidney(1)|large_intestine(1)|lung(3)	6				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		AATTCGTTTTCAAATTCTATT	0.423																																					p.E197X		Atlas-SNP	.											C3orf62,bladder,carcinoma,0,1	C3orf62	23	.	0			c.G589T						PASS	.						72	76	75					3																	49308828		2203	4300	6503	SO:0001587	stop_gained	375341	exon3			CGTTTTCAAATTC	AK125642	CCDS2792.1	3p21.31	2006-02-11			ENSG00000188315	ENSG00000188315			24771	protein-coding gene	gene with protein product						12477932	Standard	NM_198562		Approved	FLJ43654	uc003cwn.2	Q6ZUJ4	OTTHUMG00000156819	ENST00000343010.3:c.589G>T	chr3.hg19:g.49308828C>A	ENSP00000341139:p.Glu197*	189.0	1.0	.		208.0	76.0	.	NM_198562	Q6P7E9|Q7Z3X6	Nonsense_Mutation	SNP	ENST00000343010.3	hg19	CCDS2792.1	.	.	.	.	.	.	.	.	.	.	C	42	9.581914	0.99211	.	.	ENSG00000188315	ENST00000343010	.	.	.	5.3	5.3	0.74995	.	0.000000	0.50627	D	0.000115	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-23.8339	14.3179	0.66465	0.0:1.0:0.0:0.0	.	.	.	.	X	197	.	ENSP00000341139:E197X	E	-	1	0	C3orf62	49283832	1.000000	0.71417	1.000000	0.80357	0.599000	0.36880	2.613000	0.46351	2.745000	0.94114	0.585000	0.79938	GAA	.	.	.	none		0.423	C3orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345990.1	NM_198562		A	49308828	C	A	49308828	4	1	249	1	0	0	0	0	0	1	0	0	2240	835	29	4	218	4	C3orf62	3	49308828	Nonsense_Mutation	SNP	C	TCGA-SX-A7SO-01A-11D-A34Z-10	44567289	49308828	148713602	11	15437											
AMIGO3	29925	hgsc.bcm.edu	37	chr3	49756686	49756686	+	3'UTR	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggcgcaggcgctggagcgcGttgtggctcaggtcgaggtc	4	7	20	10	5	1	0	1	0	0	0	3	2	1	1	0	6	1	4	0	6	0	1			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr3:49756686G>A	ENST00000480687.1	-	0	3698				RNF123_ENST00000327697.6_Intron|RNF123_ENST00000433785.1_Intron|RNF123_ENST00000497099.1_Intron|AMIGO3_ENST00000535833.1_Silent_p.N71N|AMIGO3_ENST00000320431.7_Silent_p.N71N			Q9Y5P6	GMPPB_HUMAN	GDP-mannose pyrophosphorylase B						cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|mannose-1-phosphate guanylyltransferase activity (GO:0004475)			endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GCTGGAGCGCGTTGTGGCTCA	0.677											OREG0015572	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N71N		Atlas-SNP	.											.	AMIGO3	40	.	0			c.C213T						PASS	.						41	47	45					3																	49756686		2203	4299	6502	SO:0001624	3_prime_UTR_variant	386724	exon1			GAGCGCGTTGTGG	AF135421	CCDS2802.1, CCDS2803.1	3p21.31	2008-02-05			ENSG00000173540	ENSG00000173540	2.7.7.22		22932	protein-coding gene	gene with protein product		615320					Standard	NM_013334		Approved	KIAA1851	uc003cxl.1	Q9Y5P6	OTTHUMG00000158151	ENST00000480687.1:c.*2499C>T	chr3.hg19:g.49756686G>A		67.0	0.0	.	964	67.0	30.0	.	NM_198722	A8K6N5|Q9H7U3	Silent	SNP	ENST00000480687.1	hg19	CCDS2803.1																																																																																			.	.	.	none		0.677	GMPPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350291.1	NM_013334		A	49756686	G	A	49756686	1	1	249	0	1	0	0	0	0	0	0	0	577	1136	40	1		1	AMIGO3	3	49756686	3'UTR	SNP	G	TCGA-SX-A7SO-01A-11D-A34Z-10	447858	49756686	148265744	12	15438											
PLA1A	51365	hgsc.bcm.edu	37	chr3	119347690	119347690	+	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	ttattgggaagttctgcactGcccttttgcctgtcaatgac	7	15	9	10	0	2	1	1	1	1	0	2	2	2	2	2	1	3	2	2	1	3	5			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr3:119347690G>C	ENST00000273371.4	+	10	1336	c.1264G>C	c.(1264-1266)Gcc>Ccc	p.A422P	PLA1A_ENST00000495992.1_Missense_Mutation_p.A406P|PLA1A_ENST00000488919.1_Missense_Mutation_p.A249P|PLA1A_ENST00000494440.1_Missense_Mutation_p.A406P	NM_015900.3	NP_056984.1	Q53H76	PLA1A_HUMAN	phospholipase A1 member A	422	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						GTTCTGCACTGCCCTTTTGCC	0.463																																					p.A422P		Atlas-SNP	.											.	PLA1A	65	.	0			c.G1264C						PASS	.						118	116	117					3																	119347690		2203	4300	6503	SO:0001583	missense	51365	exon10			TGCACTGCCCTTT	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.1264G>C	chr3.hg19:g.119347690G>C	ENSP00000273371:p.Ala422Pro	41.0	0.0	.		53.0	26.0	.	NM_015900	B2R8V2|B4DXA2|O95991|Q86WX6|Q9UPD2	Missense_Mutation	SNP	ENST00000273371.4	hg19	CCDS2991.1	.	.	.	.	.	.	.	.	.	.	G	12.17	1.856610	0.32791	.	.	ENSG00000144837	ENST00000273371;ENST00000488919;ENST00000495992;ENST00000494440	D;D;D;D	0.93763	-2.69;-3.28;-2.68;-2.78	5.39	2.05	0.26809	.	0.525301	0.20420	N	0.092687	D	0.89181	0.6642	L	0.34521	1.04	0.09310	N	1	D;P	0.53885	0.963;0.938	P;B	0.48270	0.572;0.368	T	0.81669	-0.0828	10	0.52906	T	0.07	-11.9479	6.4226	0.21752	0.1844:0.0:0.6528:0.1627	.	406;422	Q53H76-3;Q53H76	.;PLA1A_HUMAN	P	422;249;406;406	ENSP00000273371:A422P;ENSP00000420625:A249P;ENSP00000417326:A406P;ENSP00000418793:A406P	ENSP00000273371:A422P	A	+	1	0	PLA1A	120830380	0.025000	0.19082	0.399000	0.26333	0.198000	0.23893	1.027000	0.30115	0.599000	0.29845	0.561000	0.74099	GCC	.	.	.	none		0.463	PLA1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355252.2			C	119347690	G	C	119347690	3	2	249	1	0	0	0	0	1	0	0	0	11995	1319	46	4	1302	4	PLA1A	3	119347690	Missense_Mutation	SNP	G	TCGA-SX-A7SO-01A-11D-A34Z-10	69591004	119347690	78674740	13	15439											
PARP9	83666	hgsc.bcm.edu	37	chr3	122274833	122274833	+	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	tgttgccttcctgaactggaGagaccagggtagagatacag	11	9	13	8	0	0	3	0	1	0	2	1	6	1	4	3	2	3	2	3	2	3	4			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr3:122274833G>A	ENST00000360356.2	-	4	517	c.290C>T	c.(289-291)tCt>tTt	p.S97F	PARP9_ENST00000492382.1_Intron|PARP9_ENST00000471785.1_Missense_Mutation_p.S62F|PARP9_ENST00000477522.2_Missense_Mutation_p.S62F|PARP9_ENST00000462315.1_Missense_Mutation_p.S62F	NM_001146102.1|NM_031458.2	NP_001139574.1|NP_113646.2	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	97					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)		CTGAACTGGAGAGACCAGGGT	0.413																																					p.S97F		Atlas-SNP	.											.	PARP9	72	.	0			c.C290T						PASS	.						72	67	69					3																	122274833		2203	4300	6503	SO:0001583	missense	83666	exon4			ACTGGAGAGACCA	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.290C>T	chr3.hg19:g.122274833G>A	ENSP00000353512:p.Ser97Phe	66.0	0.0	.		74.0	37.0	.	NM_031458	A8KA94|B2R8S9|E9PFM7|Q8TCP3|Q9BZL8|Q9BZL9	Missense_Mutation	SNP	ENST00000360356.2	hg19	CCDS3014.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.11|10.11	1.261631|1.261631	0.23051|0.23051	.|.	.|.	ENSG00000138496|ENSG00000138496	ENST00000452457|ENST00000360356;ENST00000477522;ENST00000471785;ENST00000462315;ENST00000466126	.|T;T;T;T	.|0.19250	.|3.17;3.02;3.02;2.16	4.54|4.54	0.716|0.716	0.18191|0.18191	.|.	.|0.491451	.|0.17733	.|N	.|0.163823	T|T	0.10723|0.10723	0.0262|0.0262	L|L	0.27053|0.27053	0.805|0.805	0.09310|0.09310	N|N	1|1	.|P;B;P	.|0.45078	.|0.841;0.062;0.85	.|B;B;B	.|0.43445	.|0.253;0.039;0.42	T|T	0.11275|0.11275	-1.0594|-1.0594	5|10	.|0.10636	.|T	.|0.68	.|.	1.4955|1.4955	0.02465|0.02465	0.1893:0.167:0.4713:0.1724|0.1893:0.167:0.4713:0.1724	.|.	.|62;97;62	.|E9PFM7;Q8IXQ6;Q8IXQ6-2	.|.;PARP9_HUMAN;.	F|F	21|97;62;62;62;75	.|ENSP00000353512:S97F;ENSP00000419506:S62F;ENSP00000419001:S62F;ENSP00000418894:S62F	.|ENSP00000353512:S97F	L|S	-|-	1|2	0|0	PARP9|PARP9	123757523|123757523	0.449000|0.449000	0.25689|0.25689	0.245000|0.245000	0.24217|0.24217	0.362000|0.362000	0.29581|0.29581	-0.156000|-0.156000	0.10100|0.10100	0.119000|0.119000	0.18210|0.18210	0.655000|0.655000	0.94253|0.94253	CTC|TCT	.	.	.	none		0.413	PARP9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355957.1	NM_031458		A	122274833	G	A	122274833	3	1	249	1	0	0	0	0	1	0	0	0	11473	942	33	2	2359	2	PARP9	3	122274833	Missense_Mutation	SNP	G	TCGA-SX-A7SO-01A-11D-A34Z-10	2927143	122274833	75747597	14	15440											
STX18	53407	hgsc.bcm.edu	37	chr4	4436549	4436549	+	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	cgcctttgccatctccccacGttcccaattcaggttgtgtt	5	14	7	15	2	2	0	1	0	1	0	4	0	3	0	5	1	1	3	5	1	1	5			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr4:4436549G>C	ENST00000306200.2	-	7	713	c.650C>G	c.(649-651)aCg>aGg	p.T217R	STX18_ENST00000505286.1_Missense_Mutation_p.T217R	NM_016930.2	NP_058626.1	Q9P2W9	STX18_HUMAN	syntaxin 18	217					ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.0534)		ATCTCCCCACGTTCCCAATTC	0.333																																					p.T217R		Atlas-SNP	.											.	STX18	16	.	0			c.C650G						PASS	.						102	102	102					4																	4436549		2203	4300	6503	SO:0001583	missense	53407	exon7			CCCCACGTTCCCA	AB028741	CCDS3377.1	4p16.3-p16.2	2013-09-23			ENSG00000168818	ENSG00000168818			15942	protein-coding gene	gene with protein product		606046				10788491	Standard	NM_016930		Approved	Ufe1	uc003gic.3	Q9P2W9	OTTHUMG00000090331	ENST00000306200.2:c.650C>G	chr4.hg19:g.4436549G>C	ENSP00000305810:p.Thr217Arg	46.0	0.0	.		54.0	31.0	.	NM_016930	Q596L3|Q5TZP5	Missense_Mutation	SNP	ENST00000306200.2	hg19	CCDS3377.1	.	.	.	.	.	.	.	.	.	.	G	10.08	1.252631	0.22880	.	.	ENSG00000168818	ENST00000505286;ENST00000306200;ENST00000512195;ENST00000507908	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	5.19	-0.775	0.10988	.	0.508381	0.19111	N	0.122452	T	0.25938	0.0632	L	0.34521	1.04	0.09310	N	1	B	0.21753	0.06	B	0.23852	0.049	T	0.24548	-1.0157	10	0.16420	T	0.52	-1.8989	8.4572	0.32906	0.1241:0.6685:0.2073:0.0	.	217	Q9P2W9	STX18_HUMAN	R	217;217;136;136	ENSP00000426648:T217R;ENSP00000305810:T217R;ENSP00000425483:T136R;ENSP00000422376:T136R	ENSP00000305810:T217R	T	-	2	0	STX18	4487450	0.000000	0.05858	0.016000	0.15963	0.922000	0.55478	0.387000	0.20718	-0.061000	0.13110	0.655000	0.94253	ACG	.	.	.	none		0.333	STX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206696.1			C	4436549	G	C	4436549	3	2	249	1	0	0	0	0	1	0	0	0	15353	1145	40	4	377	4	STX18	4	4436549	Missense_Mutation	SNP	G	TCGA-SX-A7SO-01A-11D-A34Z-10		4436549	186717727	15	15441											
PKD2L2	27039	hgsc.bcm.edu	37	chr5	137244511	137244511	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgtcatcaaccttgtccCgttgtgttaaagacatagta	11	13	8	9	1	2	1	2	0	0	1	3	1	3	1	2	0	2	4	2	0	5	5			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr5:137244511C>T	ENST00000508883.1	+	8	1230	c.1204C>T	c.(1204-1206)Cgt>Tgt	p.R402C	PKD2L2_ENST00000508638.1_Intron|PKD2L2_ENST00000290431.5_Missense_Mutation_p.R402C|PKD2L2_ENST00000350250.4_Missense_Mutation_p.R368C|PKD2L2_ENST00000502810.1_Missense_Mutation_p.R380C			Q9NZM6	PK2L2_HUMAN	polycystic kidney disease 2-like 2	402					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)			AACCTTGTCCCGTTGTGTTAA	0.318																																					p.R402C		Atlas-SNP	.											.	PKD2L2	68	.	0			c.C1204T						PASS	.						103	92	96					5																	137244511		1828	4083	5911	SO:0001583	missense	27039	exon8			TTGTCCCGTTGTG	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.1204C>T	chr5.hg19:g.137244511C>T	ENSP00000424725:p.Arg402Cys	189.0	0.0	.		254.0	103.0	.	NM_014386	A6NK98|B4DXD2|E9PC91|E9PDG4|Q86YB4|Q9UNJ0	Missense_Mutation	SNP	ENST00000508883.1	hg19		.	.	.	.	.	.	.	.	.	.	C	13.90	2.374343	0.42105	.	.	ENSG00000078795	ENST00000350250;ENST00000502810;ENST00000508883;ENST00000290431	T;T;T;T	0.72394	-0.65;-0.65;-0.65;-0.65	5.82	4.95	0.65309	Polycystin cation channel, PKD1/PKD2 (1);	0.091705	0.48767	N	0.000179	T	0.79009	0.4374	M	0.85373	2.75	0.80722	D	1	P;P	0.47841	0.834;0.901	P;B	0.47705	0.555;0.232	T	0.83180	-0.0089	10	0.87932	D	0	-0.9502	14.562	0.68148	0.0:0.9293:0.0:0.0707	.	402;402	Q9NZM6;Q9NZM6-5	PK2L2_HUMAN;.	C	368;380;402;402	ENSP00000344177:R368C;ENSP00000425513:R380C;ENSP00000424725:R402C;ENSP00000290431:R402C	ENSP00000290431:R402C	R	+	1	0	PKD2L2	137272410	0.994000	0.37717	0.983000	0.44433	0.515000	0.34225	2.672000	0.46850	1.468000	0.48064	0.561000	0.74099	CGT	.	.	.	none		0.318	PKD2L2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372521.1	NM_014386		T	137244511	C	T	137244511	3	4	249	1	0	0	0	0	1	0	0	0	11975	652	23	1	1234	1	PKD2L2	5	137244511	Missense_Mutation	SNP	C	TCGA-SX-A7SO-01A-11D-A34Z-10		137244511	43670749	16	15442											
COL9A1	1297	hgsc.bcm.edu	37	chr6	70970367	70970367	+	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	atcaccatcttactttttccCctttgtccccaactatgccg	7	15	3	16	1	2	0	1	0	1	0	4	0	4	0	6	0	3	0	6	0	3	5			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr6:70970367C>T	ENST00000357250.6	-	20	1600	c.1442G>A	c.(1441-1443)gGg>gAg	p.G481E	COL9A1_ENST00000320755.7_Missense_Mutation_p.G238E|COL9A1_ENST00000489611.1_5'UTR|COL9A1_ENST00000370499.4_Missense_Mutation_p.G238E	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	481	Collagen-like 5.|Triple-helical region (COL2).				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)	p.G481V(1)		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						TACTTTTTCCCCTTTGTCCCC	0.333																																					p.G481E		Atlas-SNP	.											COL9A1,NS,carcinoma,0,1	COL9A1	228	.	1	Substitution - Missense(1)	ovary(1)	c.G1442A						PASS	.						62	62	62					6																	70970367		2203	4300	6503	SO:0001583	missense	1297	exon20			TTTTCCCCTTTGT		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.1442G>A	chr6.hg19:g.70970367C>T	ENSP00000349790:p.Gly481Glu	128.0	0.0	.		145.0	51.0	.	NM_001851	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Missense_Mutation	SNP	ENST00000357250.6	hg19	CCDS4971.1	.	.	.	.	.	.	.	.	.	.	C	16.86	3.239425	0.58995	.	.	ENSG00000112280	ENST00000357250;ENST00000320755;ENST00000370499	D;D;D	0.99488	-6.0;-6.0;-5.77	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	D	0.99837	0.9926	H	0.99415	4.555	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.96750	0.9553	10	0.87932	D	0	.	17.1033	0.86655	0.0:1.0:0.0:0.0	.	481;238;54	P20849;P20849-2;B3KWS8	CO9A1_HUMAN;.;.	E	481;238;238	ENSP00000349790:G481E;ENSP00000315252:G238E;ENSP00000359530:G238E	ENSP00000315252:G238E	G	-	2	0	COL9A1	71027088	0.998000	0.40836	0.967000	0.41034	0.935000	0.57460	5.054000	0.64275	2.775000	0.95449	0.655000	0.94253	GGG	.	.	.	none		0.333	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2			T	70970367	C	T	70970367	3	4	249	1	0	0	0	0	1	0	0	0	3709	623	22	2	1399	2	COL9A1	6	70970367	Missense_Mutation	SNP	C	TCGA-SX-A7SO-01A-11D-A34Z-10		70970367	100144700	17	15443											
ZNF398	57541	hgsc.bcm.edu	37	chr7	148851297	148851297	+	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	gggaaccagctggagggcaaGtgggccgtgctgggaaccct	8	5	18	10	1	0	0	0	0	0	0	0	3	0	3	3	5	4	3	3	5	3	0			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr7:148851297G>A	ENST00000475153.1	+	2	552	c.285G>A	c.(283-285)aaG>aaA	p.K95K	ZNF398_ENST00000485111.1_3'UTR|ZNF398_ENST00000540950.1_Silent_p.K100K|ZNF398_ENST00000335901.4_5'UTR|ZNF398_ENST00000420008.2_5'UTR|ZNF398_ENST00000491174.1_5'UTR|ZNF398_ENST00000483892.1_5'UTR|ZNF398_ENST00000426851.2_5'UTR			Q8TD17	ZN398_HUMAN	zinc finger protein 398	95					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)|metal ion binding (GO:0046872)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)	25	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00143)			TGGAGGGCAAGTGGGCCGTGC	0.597																																					p.K95K		Atlas-SNP	.											.	ZNF398	54	.	0			c.G285A						PASS	.						64	66	65					7																	148851297		2203	4300	6503	SO:0001819	synonymous_variant	57541	exon2			GGGCAAGTGGGCC	AB037760	CCDS5894.1, CCDS47739.1	7q35	2013-01-08			ENSG00000197024	ENSG00000197024		"Zinc fingers, C2H2-type", "-"	18373	protein-coding gene	gene with protein product						11779858	Standard	NM_170686		Approved	ZER6, KIAA1339, P51, P71	uc003wfl.3	Q8TD17	OTTHUMG00000158970	ENST00000475153.1:c.285G>A	chr7.hg19:g.148851297G>A		39.0	0.0	.		29.0	11.0	.	NM_170686	A8K384|B4E377|Q8TD18|Q9P2K7|Q9UDV8	Silent	SNP	ENST00000475153.1	hg19	CCDS5894.1																																																																																			.	.	.	none		0.597	ZNF398-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352722.2			A	148851297	G	A	148851297	2	1	249	1	0	0	0	0	0	0	0	1	17897	1020	36	2		2	ZNF398	7	148851297	Silent	SNP	G	TCGA-SX-A7SO-01A-11D-A34Z-10		148851297	10287366	18	15444											
CELF2	10659	hgsc.bcm.edu	37	chr10	11308581	11308581	+	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	gctgtgcgtttgtcacatttTctacaagggcaatggcacag	9	12	11	9	1	2	0	1	0	1	0	2	0	2	0	0	2	2	4	0	2	3	4			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr10:11308581T>A	ENST00000379261.4	+	6	630	c.538T>A	c.(538-540)Tct>Act	p.S180T	CELF2_ENST00000608830.1_Missense_Mutation_p.S156T|CELF2_ENST00000354440.2_Missense_Mutation_p.S156T|CELF2_ENST00000416382.2_Missense_Mutation_p.S180T|CELF2_ENST00000427450.1_Missense_Mutation_p.S156T|CELF2_ENST00000315874.4_Missense_Mutation_p.S156T|CELF2_ENST00000609692.1_Missense_Mutation_p.S156T|CELF2_ENST00000354897.3_Missense_Mutation_p.S156T|CELF2_ENST00000417956.2_Missense_Mutation_p.S156T|CELF2_ENST00000399850.3_Missense_Mutation_p.S156T|CELF2_ENST00000542579.1_Missense_Mutation_p.S187T|CELF2_ENST00000537122.1_Missense_Mutation_p.S69T|CELF2_ENST00000450189.1_Missense_Mutation_p.S187T	NM_001025077.2	NP_001020248.1	O95319	CELF2_HUMAN	CUGBP, Elav-like family member 2	180	Necessary for RNA-binding, TNNT2 exon 5 and NMDA R1 exon 21 inclusion.|RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|regulation of heart contraction (GO:0008016)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	16						TGTCACATTTTCTACAAGGGC	0.448																																					p.S187T		Atlas-SNP	.											.	CELF2	78	.	0			c.T559A						PASS	.						173	159	164					10																	11308581		1983	4172	6155	SO:0001583	missense	10659	exon6			ACATTTTCTACAA	U69546	CCDS41488.1, CCDS44354.1, CCDS44355.1, CCDS44356.1	10p13	2013-02-12	2010-02-19	2010-02-19	ENSG00000048740	ENSG00000048740		"RNA binding motif (RRM) containing"	2550	protein-coding gene	gene with protein product		602538	"CUG triplet repeat, RNA-binding protein 2", "CUG triplet repeat, RNA binding protein 2"	CUGBP2		7869393, 9887331	Standard	NM_006561		Approved	Etr-3, NAPOR-2, BRUNOL3	uc001ikl.4	O95319	OTTHUMG00000017668	ENST00000379261.4:c.538T>A	chr10.hg19:g.11308581T>A	ENSP00000368563:p.Ser180Thr	121.0	0.0	.		166.0	70.0	.	NM_006561	B7ZAN9|Q7KYU4|Q8N499|Q92950|Q96NW9|Q96RQ5|Q96RQ6|Q9UL67	Missense_Mutation	SNP	ENST00000379261.4	hg19	CCDS44354.1	.	.	.	.	.	.	.	.	.	.	T	2.328	-0.354040	0.05173	.	.	ENSG00000048740	ENST00000379261;ENST00000416382;ENST00000450189;ENST00000542579;ENST00000399850;ENST00000417956;ENST00000315874;ENST00000354440;ENST00000354897;ENST00000427450;ENST00000537122	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	5.96	5.96	0.96718	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.049275	0.85682	D	0.000000	T	0.11750	0.0286	N	0.25031	0.7	0.80722	D	1	B;B;P;B;B;B	0.39576	0.002;0.006;0.679;0.081;0.028;0.003	B;B;B;B;B;B	0.35182	0.016;0.016;0.197;0.097;0.044;0.016	T	0.16958	-1.0385	10	0.12103	T	0.63	-14.4969	16.4338	0.83864	0.0:0.0:0.0:1.0	.	164;180;175;187;175;180	B4DDE7;B4DS31;B2RA86;E9PC62;O95319-3;O95319	.;.;.;.;.;CELF2_HUMAN	T	180;180;187;187;156;156;156;156;156;156;69	ENSP00000368563:S180T;ENSP00000406451:S180T;ENSP00000389951:S187T;ENSP00000443926:S187T;ENSP00000382743:S156T;ENSP00000404834:S156T;ENSP00000315328:S156T;ENSP00000346426:S156T;ENSP00000388530:S156T;ENSP00000438884:S69T	ENSP00000315328:S156T	S	+	1	0	CELF2	11348587	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.889000	0.56212	2.270000	0.75569	0.533000	0.62120	TCT	.	.	.	none		0.448	CELF2-201	KNOWN	basic|CCDS	protein_coding	protein_coding				A	11308581	T	A	11308581	3	1	249	1	0	0	0	0	1	0	0	0	3218	1783	62	5	638	5	CELF2	10	11308581	Missense_Mutation	SNP	T	TCGA-SX-A7SO-01A-11D-A34Z-10		11308581	124226166	19	15445											
C10orf68	79741	hgsc.bcm.edu	37	chr10	33123784	33123786	+	In_Frame_Del	DEL	ATA	ATA	-																															aaggtgttaatggaaaagatAtaataaagcatctaatcaac																										TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	ATA	ATA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr10:33123784_33123786delATA	ENST00000375030.2	+	15	1618_1620	c.1000_1002delATA	c.(1000-1002)atadel	p.I335del	C10orf68_ENST00000375025.4_In_Frame_Del_p.I412del|C10orf68_ENST00000375028.3_In_Frame_Del_p.I352del			Q9H943	CJ068_HUMAN		376										breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(4)	29						TGGAAAAGATATAATAAAGCATC	0.305																																					p.374_375del		Atlas-Indel,Pindel	.											.	C10orf68	75	.	0			c.1122_1124del						PASS	.																																			SO:0001651	inframe_deletion	79741	exon14			.																												ENST00000375030.2:c.1000_1002delATA	chr10.hg19:g.33123787_33123789delATA	ENSP00000364170:p.Ile335del	165.0	0.0	0		211.0	80.0	0.379147	NM_024688	B0QZ71|Q08AN7|Q8N7T7	In_Frame_Del	DEL	ENST00000375030.2	hg19																																																																																				.	.	.	none		0.305	C10orf68-001	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000313999.2			-	33123786	ATA	-	33123784	7	5	249	1	0	1	0	1	0	0	0	0	1615	449	16	0	1169	0	C10orf68	10	33123784	In_Frame_Del	DEL	ATA	TCGA-SX-A7SO-01A-11D-A34Z-10	21815203	33123784	102410963	20	15446											
NUDT13	25961	hgsc.bcm.edu	37	chr10	74884008	74884008	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgaaatggagacagagctcaAggggtctttcattgagctga	12	10	13	6	0	3	5	2	3	1	2	3	6	3	5	0	3	2	2	0	3	2	2			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr10:74884008A>G	ENST00000357321.4	+	5	513	c.395A>G	c.(394-396)aAg>aGg	p.K132R	NUDT13_ENST00000537969.1_Intron|NUDT13_ENST00000544879.1_Missense_Mutation_p.K6R|NUDT13_ENST00000488223.1_3'UTR|NUDT13_ENST00000372997.3_Missense_Mutation_p.K132R|RP11-152N13.16_ENST00000608444.1_RNA|NUDT13_ENST00000349051.5_Missense_Mutation_p.K132R|SNORA11_ENST00000408237.1_RNA	NM_001283016.1|NM_015901.4	NP_001269945.1|NP_056985.3			nudix (nucleoside diphosphate linked moiety X)-type motif 13											large_intestine(2)|lung(5)	7	Prostate(51;0.0119)					ACAGAGCTCAAGGGGTCTTTC	0.423																																					p.K132R		Atlas-SNP	.											.	NUDT13	16	.	0			c.A395G						PASS	.						89	89	89					10																	74884008		2203	4300	6503	SO:0001583	missense	25961	exon5			AGCTCAAGGGGTC	AL050114	CCDS31220.1, CCDS60551.1, CCDS60552.1, CCDS60553.1, CCDS73148.1	10q22.3	2014-04-24			ENSG00000166321	ENSG00000166321		"Nudix motif containing"	18827	protein-coding gene	gene with protein product		609233				15164054	Standard	NM_001283019		Approved	DKFZp586P2219	uc001jtj.3	Q86X67	OTTHUMG00000018453	ENST00000357321.4:c.395A>G	chr10.hg19:g.74884008A>G	ENSP00000349874:p.Lys132Arg	35.0	0.0	.		38.0	17.0	.	NM_015901		Missense_Mutation	SNP	ENST00000357321.4	hg19	CCDS31220.1	.	.	.	.	.	.	.	.	.	.	A	12.91	2.080125	0.36662	.	.	ENSG00000166321	ENST00000357321;ENST00000349051;ENST00000544879;ENST00000372997	T;T;T;T	0.29655	1.56;1.56;1.56;1.56	5.78	0.0152	0.14103	NADH pyrophosphatase-like, N-terminal (1);	1.129060	0.06171	N	0.677690	T	0.18635	0.0447	L	0.29908	0.895	0.31085	N	0.711441	B;B;B	0.27140	0.169;0.046;0.012	B;B;B	0.20767	0.031;0.029;0.011	T	0.35051	-0.9804	10	0.15952	T	0.53	.	5.0363	0.14436	0.5681:0.1459:0.286:0.0	.	132;132;132	Q86X67-2;Q5SQM6;Q86X67	.;.;NUD13_HUMAN	R	132;132;6;132	ENSP00000349874:K132R;ENSP00000335326:K132R;ENSP00000440760:K6R;ENSP00000362088:K132R	ENSP00000335326:K132R	K	+	2	0	NUDT13	74554014	0.553000	0.26513	0.515000	0.27774	0.985000	0.73830	1.094000	0.30951	-0.157000	0.11059	0.533000	0.62120	AAG	.	.	.	none		0.423	NUDT13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048614.1	NM_015901		G	74884008	A	G	74884008	3	3	249	1	0	0	0	0	1	0	0	0	10736	72	3	3	409	3	NUDT13	10	74884008	Missense_Mutation	SNP	A	TCGA-SX-A7SO-01A-11D-A34Z-10	41760224	74884008	60650739	21	15447											
LRIT1	26103	hgsc.bcm.edu	37	chr10	85997255	85997255	+	Missense_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	ccgcaggcgtcgcaggccccGcagcatgagggcgttgagct	6	5	16	14	5	0	2	0	2	0	0	1	2	0	2	3	3	2	6	3	3	0	1			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr10:85997255G>A	ENST00000372105.3	-	2	331	c.310C>T	c.(310-312)Cgg>Tgg	p.R104W		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	104						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						CGCAGGCCCCGCAGCATGAGG	0.731																																					p.R104W		Atlas-SNP	.											.	LRIT1	73	.	0			c.C310T						PASS	.						7	9	8					10																	85997255		2119	4164	6283	SO:0001583	missense	26103	exon2			GGCCCCGCAGCAT	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.310C>T	chr10.hg19:g.85997255G>A	ENSP00000361177:p.Arg104Trp	19.0	0.0	.		13.0	8.0	.	NM_015613	Q0QD41|Q9Y4N7	Missense_Mutation	SNP	ENST00000372105.3	hg19	CCDS7373.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.199249	0.79015	.	.	ENSG00000148602	ENST00000372105	T	0.52983	0.64	4.93	1.89	0.25635	.	0.142637	0.46145	D	0.000317	T	0.56863	0.2014	M	0.76170	2.325	0.39900	D	0.973881	D	0.69078	0.997	P	0.52343	0.696	T	0.63274	-0.6674	10	0.72032	D	0.01	.	12.1	0.53778	0.0:0.0:0.3369:0.6631	.	104	Q9P2V4	LRIT1_HUMAN	W	104	ENSP00000361177:R104W	ENSP00000361177:R104W	R	-	1	2	LRIT1	85987235	0.612000	0.27000	0.796000	0.32109	0.989000	0.77384	1.233000	0.32648	0.202000	0.20498	0.655000	0.94253	CGG	.	.	.	none		0.731	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613		A	85997255	G	A	85997255	3	1	249	1	0	0	0	0	1	0	0	0	8954	1086	38	1	1573	1	LRIT1	10	85997255	Missense_Mutation	SNP	G	TCGA-SX-A7SO-01A-11D-A34Z-10	11113247	85997255	49537492	22	15448											
LRDD	79751	hgsc.bcm.edu	37	chr11	799527	799527	+	5'Flank	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	cagcctggcgctcagcccagGagaagagcatgtgacggatc	10	5	14	12	2	1	3	1	1	0	2	2	5	1	4	2	3	3	2	2	3	1	0			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr11:799527G>C	ENST00000531214.1	-	0	0				PIDD_ENST00000347755.5_Missense_Mutation_p.S838C|PIDD_ENST00000411829.2_Missense_Mutation_p.S821C	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)		CTCAGCCCAGGAGAAGAGCAT	0.672																																					p.S838C	Colon(93;848 1468 3270 23355 49636)	Atlas-SNP	.											.	PIDD	76	.	0			c.C2513G						PASS	.						32	30	31					11																	799527		2199	4290	6489	SO:0001631	upstream_gene_variant	55367	exon16			GCCCAGGAGAAGA	AJ428202	CCDS7715.1	11p15.5	2013-05-22			ENSG00000177542	ENSG00000177542		"Solute carriers"	19954	protein-coding gene	gene with protein product		609302				11897791	Standard	NM_024698		Approved	GC1, FLJ13044, NET44, EIEE3	uc001lrj.3	Q9H936	OTTHUMG00000133310		chr11.hg19:g.799527G>C	Exception_encountered	31.0	0.0	.		33.0	13.0	.	NM_145886	A8K366|C9J1H6|E9PJD3|E9PKB2|E9PL68|E9PN26|E9PNQ3|E9PP01|E9PR97|Q8TBU8	Missense_Mutation	SNP	ENST00000531214.1	hg19	CCDS7715.1	.	.	.	.	.	.	.	.	.	.	G	18.63	3.664457	0.67700	.	.	ENSG00000177595	ENST00000411829;ENST00000347755	D;D	0.85702	-2.02;-2.02	4.74	4.74	0.60224	Death (3);DEATH-like (2);	0.143577	0.49305	D	0.000148	D	0.89832	0.6829	L	0.46157	1.445	0.37083	D	0.899066	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.995;0.998;0.988	D	0.90731	0.4642	10	0.39692	T	0.17	.	18.0695	0.89402	0.0:0.0:1.0:0.0	.	838;681;821	Q9HB75;Q9HB75-3;Q9HB75-2	PIDD_HUMAN;.;.	C	821;838	ENSP00000416801:S821C;ENSP00000337797:S838C	ENSP00000337797:S838C	S	-	2	0	PIDD	789527	1.000000	0.71417	1.000000	0.80357	0.731000	0.41821	5.070000	0.64376	2.338000	0.79540	0.448000	0.29417	TCC	.	.	.	none		0.672	SLC25A22-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384124.1			C	799527	G	C	799527	1	2	249	0	1	0	0	0	0	0	0	0	8943	1174	41	4		4	LRDD	11	799527	5'Flank	SNP	G	TCGA-SX-A7SO-01A-11D-A34Z-10		799527	134206989	23	15449											
OR51G2	81282	hgsc.bcm.edu	37	chr11	4936639	4936639	+	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	acccaaaagatgcccaggacTgtagggagagtgcaaaggga	15	4	14	8	0	0	2	0	0	0	2	0	5	0	4	2	3	2	2	2	3	4	1			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr11:4936639T>A	ENST00000322013.3	-	1	283	c.255A>T	c.(253-255)acA>acT	p.T85T	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	85						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)		TGCCCAGGACTGTAGGGAGAG	0.483																																					p.T85T		Atlas-SNP	.											.	OR51G2	70	.	0			c.A255T						PASS	.						83	74	77					11																	4936639		2201	4298	6499	SO:0001819	synonymous_variant	81282	exon1			CAGGACTGTAGGG	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.255A>T	chr11.hg19:g.4936639T>A		45.0	0.0	.		66.0	31.0	.	NM_001005238	Q6IFH7	Silent	SNP	ENST00000322013.3	hg19	CCDS31365.1																																																																																			.	.	.	none		0.483	OR51G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142174.1	NM_001005238		A	4936639	T	A	4936639	2	1	249	1	0	0	0	0	0	0	0	1	11106	1567	55	5		5	OR51G2	11	4936639	Silent	SNP	T	TCGA-SX-A7SO-01A-11D-A34Z-10	4137112	4936639	130069877	24	15450											
SLC5A12	159963	hgsc.bcm.edu	37	chr11	26743093	26743093	+	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	tgacatgaagctggctgtcaGagacaagccgacagggccaa	13	5	13	10	1	1	3	1	2	0	1	1	5	1	3	2	2	2	2	2	2	3	0			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr11:26743093G>C	ENST00000396005.3	-	1	478	c.169C>G	c.(169-171)Ctg>Gtg	p.L57V	SLC5A12_ENST00000280467.6_Missense_Mutation_p.L57V	NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	57					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						CTGGCTGTCAGAGACAAGCCG	0.512																																					p.L57V		Atlas-SNP	.											.	SLC5A12	134	.	0			c.C169G						PASS	.						67	68	68					11																	26743093		2203	4299	6502	SO:0001583	missense	159963	exon1			CTGTCAGAGACAA	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.169C>G	chr11.hg19:g.26743093G>C	ENSP00000379326:p.Leu57Val	101.0	0.0	.		129.0	61.0	.	NM_178498	Q86UC7	Missense_Mutation	SNP	ENST00000396005.3	hg19	CCDS7860.2	.	.	.	.	.	.	.	.	.	.	G	21.3	4.123364	0.77436	.	.	ENSG00000148942	ENST00000396005;ENST00000280467	D;D	0.89343	-2.5;-2.5	5.59	4.49	0.54785	.	0.000000	0.64402	D	0.000011	D	0.94837	0.8332	M	0.86573	2.825	0.53005	D	0.999963	D;D	0.89917	0.997;1.0	D;D	0.97110	0.976;1.0	D	0.95388	0.8479	10	0.87932	D	0	.	15.3594	0.74460	0.0783:0.0:0.9217:0.0	.	57;57	Q1EHB4-2;Q1EHB4	.;SC5AC_HUMAN	V	57	ENSP00000379326:L57V;ENSP00000280467:L57V	ENSP00000280467:L57V	L	-	1	2	SLC5A12	26699669	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	6.698000	0.74608	2.643000	0.89663	0.585000	0.79938	CTG	.	.	.	none		0.512	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498		C	26743093	G	C	26743093	3	2	249	1	0	0	0	0	1	0	0	0	14677	933	33	4	1747	4	SLC5A12	11	26743093	Missense_Mutation	SNP	G	TCGA-SX-A7SO-01A-11D-A34Z-10	21806454	26743093	108263423	25	15451											
OR8K3	219473	hgsc.bcm.edu	37	chr11	56086707	56086707	+	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	ggacatggaataacttatgtAatatttttgtttaaattttg	13	19	7	2	0	0	0	0	0	0	0	0	2	0	2	0	2	1	2	0	2	7	10			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr11:56086707A>T	ENST00000312711.1	+	1	925	c.925A>T	c.(925-927)Aat>Tat	p.N309Y		NM_001005202.1	NP_001005202.1	Q8NH51	OR8K3_HUMAN	olfactory receptor, family 8, subfamily K, member 3	309						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(2)|endometrium(3)|large_intestine(6)|liver(2)|lung(15)|ovary(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	40	Esophageal squamous(21;0.00448)					TAACTTATGTAATATTTTTGT	0.318																																					p.N309Y		Atlas-SNP	.											.	OR8K3	92	.	0			c.A925T						PASS	.						29	29	29					11																	56086707		2200	4295	6495	SO:0001583	missense	219473	exon1			TTATGTAATATTT	AB065541	CCDS31527.1	11q11	2012-08-09			ENSG00000181689	ENSG00000181689		"GPCR / Class A : Olfactory receptors"	15313	protein-coding gene	gene with protein product							Standard	NM_001005202		Approved		uc010rjf.2	Q8NH51	OTTHUMG00000166855	ENST00000312711.1:c.925A>T	chr11.hg19:g.56086707A>T	ENSP00000323555:p.Asn309Tyr	67.0	0.0	.		75.0	38.0	.	NM_001005202	Q6IFC4	Missense_Mutation	SNP	ENST00000312711.1	hg19	CCDS31527.1	.	.	.	.	.	.	.	.	.	.	A	11.01	1.513383	0.27123	.	.	ENSG00000181689	ENST00000312711	T	0.00004	9.8	3.9	2.76	0.32466	.	1.533820	0.03744	N	0.255508	T	0.00073	0.0002	N	0.08118	0	0.09310	N	1	P	0.37612	0.602	P	0.47744	0.556	T	0.17715	-1.0360	10	0.33141	T	0.24	.	5.9741	0.19369	0.8777:0.0:0.1223:0.0	.	309	Q8NH51	OR8K3_HUMAN	Y	309	ENSP00000323555:N309Y	ENSP00000323555:N309Y	N	+	1	0	OR8K3	55843283	0.001000	0.12720	0.001000	0.08648	0.002000	0.02628	1.242000	0.32755	0.659000	0.30945	0.386000	0.25728	AAT	.	.	.	none		0.318	OR8K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391602.1	NM_001005202		T	56086707	A	T	56086707	3	4	249	1	0	0	0	0	1	0	0	0	11251	362	13	5	927	5	OR8K3	11	56086707	Missense_Mutation	SNP	A	TCGA-SX-A7SO-01A-11D-A34Z-10	29343614	56086707	78919809	26	15452											
HTR3A	3359	hgsc.bcm.edu	37	chr11	113860244	113860244	+	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	ggacttcgagaagagcccgaGggacagatgtagccctcccc	10	5	13	13	2	0	3	0	0	0	3	2	7	1	5	4	2	2	1	4	2	2	2			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr11:113860244G>C	ENST00000504030.2	+	9	1641	c.1196G>C	c.(1195-1197)aGg>aCg	p.R399T	HTR3A_ENST00000535865.1_Missense_Mutation_p.R143T|HTR3A_ENST00000355556.2_Missense_Mutation_p.R437T|HTR3A_ENST00000299961.5_Missense_Mutation_p.R384T|HTR3A_ENST00000375498.2_Missense_Mutation_p.R405T|HTR3A_ENST00000506841.2_Missense_Mutation_p.R431T			P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A, ionotropic	399					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)	AAGAGCCCGAGGGACAGATGT	0.647																																					p.R437T		Atlas-SNP	.											.	HTR3A	93	.	0			c.G1310C						PASS	.						71	79	76					11																	113860244		2201	4296	6497	SO:0001583	missense	3359	exon8			GCCCGAGGGACAG	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.1196G>C	chr11.hg19:g.113860244G>C	ENSP00000424189:p.Arg399Thr	23.0	0.0	.		30.0	11.0	.	NM_213621	B4DSY6|G5E986|O60854|Q7KZM7|Q99918|Q9BSZ9	Missense_Mutation	SNP	ENST00000504030.2	hg19		.	.	.	.	.	.	.	.	.	.	G	6.392	0.440481	0.12104	.	.	ENSG00000166736	ENST00000504030;ENST00000355556;ENST00000375498;ENST00000506841;ENST00000535865;ENST00000299961	T;T;T;T;T;T	0.70399	1.9;-0.48;1.9;-0.48;1.9;1.9	5.4	2.34	0.29019	.	0.571132	0.21049	N	0.081029	T	0.55097	0.1899	L	0.29908	0.895	0.09310	N	1	B;B;B	0.26602	0.093;0.129;0.154	B;B;B	0.31101	0.124;0.108;0.124	T	0.43228	-0.9404	10	0.30078	T	0.28	-10.4059	7.7112	0.28679	0.1523:0.1371:0.7106:0.0	.	384;437;405	B4DSY6;G5E986;Q7KZM7	.;.;.	T	399;437;405;431;143;384	ENSP00000424189:R399T;ENSP00000347754:R437T;ENSP00000364648:R405T;ENSP00000424776:R431T;ENSP00000437776:R143T;ENSP00000299961:R384T	ENSP00000299961:R384T	R	+	2	0	HTR3A	113365454	0.000000	0.05858	0.008000	0.14137	0.002000	0.02628	0.094000	0.15107	1.423000	0.47198	0.650000	0.86243	AGG	.	.	.	none		0.647	HTR3A-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000360822.2	NM_000869		C	113860244	G	C	113860244	3	2	249	1	0	0	0	0	1	0	0	0	7451	1000	35	4	1366	4	HTR3A	11	113860244	Missense_Mutation	SNP	G	TCGA-SX-A7SO-01A-11D-A34Z-10	57773537	113860244	21146272	27	15453											
INHBE	83729	hgsc.bcm.edu	37	chr12	57850456	57850456	+	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	cagcccaggcattgctgcctCtttccattctgccgtcttca	5	13	7	16	1	4	0	1	0	3	0	5	0	5	0	4	1	4	2	4	1	0	4			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr12:57850456C>G	ENST00000266646.2	+	2	1094	c.878C>G	c.(877-879)tCt>tGt	p.S293C	INHBE_ENST00000551553.1_3'UTR	NM_031479.3	NP_113667.1	P58166	INHBE_HUMAN	inhibin, beta E	293					growth (GO:0040007)	extracellular region (GO:0005576)				breast(2)|central_nervous_system(1)|large_intestine(2)|lung(7)|prostate(1)|skin(2)	15						ATTGCTGCCTCTTTCCATTCT	0.612											OREG0021944	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S293C	GBM(191;1808 2166 15720 36624 50371)	Atlas-SNP	.											.	INHBE	38	.	0			c.C878G						PASS	.						105	80	88					12																	57850456		2203	4300	6503	SO:0001583	missense	83729	exon2			CTGCCTCTTTCCA		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.878C>G	chr12.hg19:g.57850456C>G	ENSP00000266646:p.Ser293Cys	39.0	0.0	.	1026	48.0	19.0	.	NM_031479		Missense_Mutation	SNP	ENST00000266646.2	hg19	CCDS8939.1	.	.	.	.	.	.	.	.	.	.	C	19.81	3.897332	0.72639	.	.	ENSG00000139269	ENST00000547970;ENST00000266646	T;T	0.64803	-0.12;-0.12	4.79	4.79	0.61399	Transforming growth factor-beta, C-terminal (3);	0.061993	0.64402	D	0.000003	D	0.83848	0.5343	M	0.92970	3.365	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	D	0.87710	0.2566	10	0.72032	D	0.01	-7.2053	17.1522	0.86781	0.0:1.0:0.0:0.0	.	293	P58166	INHBE_HUMAN	C	238;293	ENSP00000450212:S238C;ENSP00000266646:S293C	ENSP00000266646:S293C	S	+	2	0	INHBE	56136723	1.000000	0.71417	0.995000	0.50966	0.994000	0.84299	7.563000	0.82314	2.653000	0.90120	0.655000	0.94253	TCT	.	.	.	none		0.612	INHBE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406773.1	NM_031479		G	57850456	C	G	57850456	3	3	249	1	0	0	0	0	1	0	0	0	7751	913	32	4	884	4	INHBE	12	57850456	Missense_Mutation	SNP	C	TCGA-SX-A7SO-01A-11D-A34Z-10		57850456	76001439	28	15454											
PLBD2	196463	hgsc.bcm.edu	37	chr12	113823023	113823023	+	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	cttctcggtctcagcggcatGgtggtggtggctgacaagac	6	10	15	10	2	2	2	1	1	2	1	4	2	2	2	0	6	1	2	0	6	1	1			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr12:113823023G>A	ENST00000280800.3	+	9	1252	c.1221G>A	c.(1219-1221)atG>atA	p.M407I	PLBD2_ENST00000545182.2_Missense_Mutation_p.M375I	NM_173542.3	NP_775813.2	Q8NHP8	PLBL2_HUMAN	phospholipase B domain containing 2	407					lipid catabolic process (GO:0016042)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)			breast(1)|endometrium(1)|large_intestine(3)|lung(7)|prostate(1)	13						TCAGCGGCATGGTGGTGGTGG	0.627																																					p.M407I		Atlas-SNP	.											.	PLBD2	33	.	0			c.G1221A						PASS	.						169	122	138					12																	113823023		2203	4300	6503	SO:0001583	missense	196463	exon9			CGGCATGGTGGTG	BC030618	CCDS9168.1, CCDS53834.1	12q24.13	2013-10-11				ENSG00000151176			27283	protein-coding gene	gene with protein product	"PLB homolog 2 (Dictyostelium)", "mannose-6-phosphate protein associated protein p76"					17105447, 15193148, 19019078	Standard	NM_001159727		Approved	p76	uc001tve.2	Q8NHP8	OTTHUMG00000169567	ENST00000280800.3:c.1221G>A	chr12.hg19:g.113823023G>A	ENSP00000280800:p.Met407Ile	101.0	0.0	.		98.0	36.0	.	NM_173542	F5H5E2	Missense_Mutation	SNP	ENST00000280800.3	hg19	CCDS9168.1	.	.	.	.	.	.	.	.	.	.	G	9.882	1.201822	0.22121	.	.	ENSG00000151176	ENST00000545182;ENST00000280800	T;T	0.17370	2.28;2.28	4.52	4.52	0.55395	.	0.195034	0.51477	D	0.000092	T	0.17831	0.0428	L	0.45228	1.405	0.38915	D	0.957621	B;B	0.23128	0.08;0.007	B;B	0.23574	0.047;0.009	T	0.06006	-1.0851	10	0.29301	T	0.29	-29.7541	17.4488	0.87586	0.0:0.0:1.0:0.0	.	375;407	F5H5E2;Q8NHP8	.;PLBL2_HUMAN	I	375;407	ENSP00000443463:M375I;ENSP00000280800:M407I	ENSP00000280800:M407I	M	+	3	0	PLBD2	112307406	1.000000	0.71417	1.000000	0.80357	0.507000	0.33981	4.751000	0.62169	2.341000	0.79615	0.555000	0.69702	ATG	.	.	.	none		0.627	PLBD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404835.1	NM_173542		A	113823023	G	A	113823023	3	1	249	1	0	0	0	0	1	0	0	0	12033	1348	47	2	1255	2	PLBD2	12	113823023	Missense_Mutation	SNP	G	TCGA-SX-A7SO-01A-11D-A34Z-10	55972567	113823023	20028872	29	15455											
CUL4A	8451	hgsc.bcm.edu	37	chr13	113893814	113893814	+	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	atgtaccagctgttcagccgGgtgaggggcgggcagcaggc	7	6	18	10	2	1	1	1	1	0	0	1	1	1	1	2	5	4	5	2	5	1	2			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr13:113893814G>C	ENST00000375440.4	+	10	1068	c.984G>C	c.(982-984)cgG>cgC	p.R328R	CUL4A_ENST00000326335.4_Silent_p.R228R|CUL4A_ENST00000375441.3_Silent_p.R228R|CUL4A_ENST00000451881.1_Silent_p.R228R	NM_001008895.1	NP_001008895.1	Q13619	CUL4A_HUMAN	cullin 4A	328					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)			TGTTCAGCCGGGTGAGGGGCG	0.622																																					p.R328R		Atlas-SNP	.											.	CUL4A	50	.	0			c.G984C						PASS	.						68	64	65					13																	113893814		2203	4300	6503	SO:0001819	synonymous_variant	8451	exon10			CAGCCGGGTGAGG	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.984G>C	chr13.hg19:g.113893814G>C		93.0	0.0	.		97.0	41.0	.	NM_001008895	A2A2W2|O75834|Q589T6|Q5TC62|Q6UP08|Q9UP17	Silent	SNP	ENST00000375440.4	hg19	CCDS41908.1																																																																																			.	.	.	none		0.622	CUL4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045888.3	NM_003589		C	113893814	G	C	113893814	2	2	249	1	0	0	0	0	0	0	0	1	4059	1219	43	4		4	CUL4A	13	113893814	Silent	SNP	G	TCGA-SX-A7SO-01A-11D-A34Z-10		113893814	1276064	30	15456											
CASC5	57082	hgsc.bcm.edu	37	chr15	40916020	40916020	+	Frame_Shift_Del	DEL	C	C	-																															gagaaaatacttgaagaaaaCcctaaatttggaataggaaa																										TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr15:40916020delC	ENST00000346991.5	+	11	4026	c.3636delC	c.(3634-3636)aacfs	p.N1212fs	CASC5_ENST00000399668.2_Frame_Shift_Del_p.N1186fs			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	1212					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)		TTGAAGAAAACCCTAAATTTG	0.378																																					p.N1212fs		Atlas-Indel,Pindel	.											.	CASC5	269	.	0			c.3635delA						PASS	.						46	44	44					15																	40916020		1809	4077	5886	SO:0001589	frameshift_variant	57082	exon11			.	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.3636delC	chr15.hg19:g.40916020delC	ENSP00000335463:p.Asn1212fs	48.0	0.0	0		72.0	37.0	0.513889	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Frame_Shift_Del	DEL	ENST00000346991.5	hg19	CCDS42023.1																																																																																			.	.	.	none		0.378	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		-	40916020	C	-	40916020	7	5	249	1	0	1	0	1	0	0	0	0	2665	506	18	0	3674	0	CASC5	15	40916020	Frame_Shift_Del	DEL	C	TCGA-SX-A7SO-01A-11D-A34Z-10		40916020	61615372	31	15457											
ZNF280D	54816	hgsc.bcm.edu	37	chr15	56968913	56968913	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tatggtgttgcaattttaatAactttgaggcaaaacgggca	13	13	10	5	1	0	1	0	1	0	0	0	1	0	1	0	3	3	4	0	3	6	6			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr15:56968913A>G	ENST00000267807.7	-	13	1581	c.1365T>C	c.(1363-1365)gtT>gtC	p.V455V	ZNF280D_ENST00000559237.1_Silent_p.V442V|ZNF280D_ENST00000396245.1_Silent_p.V159V|ZNF280D_ENST00000559000.1_Silent_p.V442V	NM_017661.2	NP_060131.2	Q6N043	Z280D_HUMAN	zinc finger protein 280D	455					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(4)|large_intestine(7)|lung(12)|ovary(1)|skin(1)	30				all cancers(107;0.0399)|GBM - Glioblastoma multiforme(80;0.0787)		CAATTTTAATAACTTTGAGGC	0.303																																					p.V455V		Atlas-SNP	.											.	ZNF280D	82	.	0			c.T1365C						PASS	.						139	139	139					15																	56968913		2192	4291	6483	SO:0001819	synonymous_variant	54816	exon13			TTTAATAACTTTG	AB046804	CCDS32245.1, CCDS42041.1, CCDS58364.1	15q21.2	2008-05-02	2007-09-20	2007-09-20					25953	protein-coding gene	gene with protein product			"suppressor of hairy wing homolog 4 (Drosophila)"	SUHW4		10997877	Standard	XM_005254481		Approved	FLJ20086, ZNF634	uc002adu.3	Q6N043		ENST00000267807.7:c.1365T>C	chr15.hg19:g.56968913A>G		114.0	0.0	.		152.0	75.0	.	NM_017661	A1L495|B2RMT6|Q6MZM6|Q6N085|Q6P2R6|Q7Z6J5|Q9H0U5|Q9HCI8|Q9NXS0	Silent	SNP	ENST00000267807.7	hg19	CCDS32245.1	.	.	.	.	.	.	.	.	.	.	A	9.834	1.189114	0.21954	.	.	ENSG00000137871	ENST00000260435	.	.	.	5.53	4.4	0.53042	.	.	.	.	.	T	0.67524	0.2902	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69379	-0.5161	5	0.87932	D	0	-13.6503	10.5058	0.44832	0.9239:0.0:0.0761:0.0	.	.	.	.	S	291	.	ENSP00000260435:L291S	L	-	2	0	ZNF280D	54756205	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.894000	0.28350	0.935000	0.37341	0.528000	0.53228	TTA	.	.	.	none		0.303	ZNF280D-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418891.2	XM_370867		G	56968913	A	G	56968913	2	3	249	1	0	0	0	0	0	0	0	1	17829	349	13	3		3	ZNF280D	15	56968913	Silent	SNP	A	TCGA-SX-A7SO-01A-11D-A34Z-10	16052893	56968913	45562479	32	15458											
ZNF609	23060	hgsc.bcm.edu	37	chr15	64967353	64967353	+	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	cagggaatcttcaggagatgGgatgaaaatggaggggctcc	12	7	16	6	0	2	2	1	1	1	1	3	6	3	5	1	6	0	1	1	6	3	1			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr15:64967353G>C	ENST00000326648.3	+	4	2428	c.2300G>C	c.(2299-2301)gGg>gCg	p.G767A		NM_015042.1	NP_055857.1	O15014	ZN609_HUMAN	zinc finger protein 609	767						nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TCAGGAGATGGGATGAAAATG	0.512																																					p.G767A		Atlas-SNP	.											ZNF609,colon,carcinoma,0,1	ZNF609	106	.	0			c.G2300C						PASS	.						69	77	75					15																	64967353		2203	4298	6501	SO:0001583	missense	23060	exon4			GAGATGGGATGAA	BC014251	CCDS32270.1	15q22.1	2008-05-02				ENSG00000180357		"Zinc fingers, C2H2-type"	29003	protein-coding gene	gene with protein product						9205841	Standard	NM_015042		Approved	KIAA0295	uc002ann.3	O15014		ENST00000326648.3:c.2300G>C	chr15.hg19:g.64967353G>C	ENSP00000316527:p.Gly767Ala	45.0	0.0	.		65.0	30.0	.	NM_015042	Q0D2I2	Missense_Mutation	SNP	ENST00000326648.3	hg19	CCDS32270.1	.	.	.	.	.	.	.	.	.	.	G	4.931	0.172993	0.09391	.	.	ENSG00000180357	ENST00000326648	T	0.42131	0.98	5.88	4.97	0.65823	.	0.184234	0.47093	D	0.000243	T	0.36193	0.0958	L	0.34521	1.04	0.48632	D	0.99968	P	0.50156	0.932	P	0.47705	0.555	T	0.15065	-1.0450	10	0.05620	T	0.96	-11.1446	15.5658	0.76290	0.0:0.1368:0.8632:0.0	.	767	O15014	ZN609_HUMAN	A	767	ENSP00000316527:G767A	ENSP00000316527:G767A	G	+	2	0	ZNF609	62754406	1.000000	0.71417	0.990000	0.47175	0.905000	0.53344	4.377000	0.59562	1.483000	0.48342	0.655000	0.94253	GGG	.	.	.	none		0.512	ZNF609-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418130.1	XM_042833		C	64967353	G	C	64967353	3	2	249	1	0	0	0	0	1	0	0	0	18047	1232	43	4	2314	4	ZNF609	15	64967353	Missense_Mutation	SNP	G	TCGA-SX-A7SO-01A-11D-A34Z-10	7998440	64967353	37564039	33	15459											
ANPEP	290	hgsc.bcm.edu	37	chr15	90349600	90349600	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgttggggaggcggtaacgaTtccacgctttactttggtcc	6	13	13	9	3	0	0	0	0	0	0	2	2	2	1	2	5	2	3	2	5	2	6			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr15:90349600T>C	ENST00000300060.6	-	2	528	c.215A>G	c.(214-216)aAt>aGt	p.N72S		NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	72	Metalloprotease.				angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	GCGGTAACGATTCCACGCTTT	0.622																																					p.N72S	NSCLC(30;827 977 2459 19669 26125)	Atlas-SNP	.											.	ANPEP	124	.	0			c.A215G						PASS	.						135	120	125					15																	90349600		2200	4299	6499	SO:0001583	missense	290	exon2			TAACGATTCCACG	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"CD molecules"	500	protein-coding gene	gene with protein product	"aminopeptidase N", "aminopeptidase M", "microsomal aminopeptidase"	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.215A>G	chr15.hg19:g.90349600T>C	ENSP00000300060:p.Asn72Ser	129.0	0.0	.		158.0	65.0	.	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Missense_Mutation	SNP	ENST00000300060.6	hg19	CCDS10356.1	.	.	.	.	.	.	.	.	.	.	T	12.88	2.071000	0.36566	.	.	ENSG00000166825	ENST00000300060	T	0.03920	3.76	4.74	4.74	0.60224	.	0.203738	0.50627	D	0.000113	T	0.09818	0.0241	M	0.81239	2.535	0.36847	D	0.887699	B	0.30709	0.291	B	0.34038	0.174	T	0.07966	-1.0745	10	0.27785	T	0.31	.	12.1916	0.54275	0.0:0.0:0.0:1.0	.	72	P15144	AMPN_HUMAN	S	72	ENSP00000300060:N72S	ENSP00000300060:N72S	N	-	2	0	ANPEP	88150604	1.000000	0.71417	0.931000	0.37212	0.067000	0.16453	7.924000	0.87555	1.770000	0.52166	0.383000	0.25322	AAT	.	.	.	none		0.622	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1			C	90349600	T	C	90349600	3	2	249	1	0	0	0	0	1	0	0	0	710	1493	52	3	2768	3	ANPEP	15	90349600	Missense_Mutation	SNP	T	TCGA-SX-A7SO-01A-11D-A34Z-10	25382247	90349600	12181792	34	15460											
SEZ6L2	26470	hgsc.bcm.edu	37	chr16	29888690	29888690	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggcccagaggagagaaggCggcggcgcggctgaggtccc	7	2	20	12	5	0	3	0	1	0	2	1	5	1	4	2	7	0	1	2	7	1	0			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr16:29888690C>T	ENST00000308713.5	-	11	2338	c.1811G>A	c.(1810-1812)cGc>cAc	p.R604H	SEZ6L2_ENST00000537485.1_Missense_Mutation_p.R560H|SEZ6L2_ENST00000346932.5_Missense_Mutation_p.R490H|SEZ6L2_ENST00000350527.3_Missense_Mutation_p.R534H	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2	604	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GGAGAGAAGGCGGCGGCGCGG	0.662																																					p.R604H		Atlas-SNP	.											.	SEZ6L2	137	.	0			c.G1811A						PASS	.						17	20	19					16																	29888690		2191	4292	6483	SO:0001583	missense	26470	exon11			AGAAGGCGGCGGC	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.1811G>A	chr16.hg19:g.29888690C>T	ENSP00000312550:p.Arg604His	52.0	0.0	.		54.0	29.0	.	NM_001243332	B7Z1N0|F5H293|H7BXQ6|Q9BW82|Q9UJ45|Q9UJ46|Q9UJ47	Missense_Mutation	SNP	ENST00000308713.5	hg19	CCDS10659.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.860218	0.91433	.	.	ENSG00000174938	ENST00000350527;ENST00000308713;ENST00000346932;ENST00000537485	T;T;T;T	0.18502	2.21;2.21;2.21;2.21	5.57	5.57	0.84162	CUB (5);	0.000000	0.53938	D	0.000048	T	0.28134	0.0694	L	0.37630	1.12	0.42529	D	0.993034	D;D;P;D;D;D	0.71674	0.996;0.996;0.529;0.994;0.995;0.998	D;P;B;P;P;P	0.63192	0.912;0.852;0.067;0.706;0.806;0.834	T	0.00885	-1.1527	10	0.59425	D	0.04	.	11.7566	0.51878	0.0:0.9183:0.0:0.0817	.	560;604;490;534;604;534	F5H293;B7Z5L4;Q9BW82;Q6UXD5-2;Q6UXD5;Q6UXD5-3	.;.;.;.;SE6L2_HUMAN;.	H	534;604;490;560	ENSP00000310206:R534H;ENSP00000312550:R604H;ENSP00000319215:R490H;ENSP00000439412:R560H	ENSP00000312550:R604H	R	-	2	0	SEZ6L2	29796191	0.999000	0.42202	1.000000	0.80357	0.961000	0.63080	1.699000	0.37804	2.618000	0.88619	0.655000	0.94253	CGC	.	.	.	none		0.662	SEZ6L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255154.2	NM_012410		T	29888690	C	T	29888690	3	4	249	1	0	0	0	0	1	0	0	0	14157	768	27	1	992	1	SEZ6L2	16	29888690	Missense_Mutation	SNP	C	TCGA-SX-A7SO-01A-11D-A34Z-10		29888690	60466063	35	15461											
PIK3R5	23533	hgsc.bcm.edu	37	chr17	8784018	8784018	+	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	aagggagcagagatcaggtgCggcctgggccggcaggtcag	9	4	19	9	2	2	1	2	0	0	1	2	3	2	2	2	6	2	2	2	6	1	0			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr17:8784018C>T	ENST00000447110.1	-	19	2705	c.2581G>A	c.(2581-2583)Gca>Aca	p.A861T	PIK3R5_ENST00000584803.1_Missense_Mutation_p.A860T|PIK3R5_ENST00000581552.1_Missense_Mutation_p.A861T	NM_001142633.2|NM_001251851.1|NM_001251852.1|NM_001251853.1|NM_001251855.1	NP_001136105.1|NP_001238780.1|NP_001238781.1|NP_001238782.1|NP_001238784.1	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5	861					blood coagulation (GO:0007596)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|small molecule metabolic process (GO:0044281)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|G-protein beta/gamma-subunit complex binding (GO:0031683)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(14)|prostate(3)|skin(4)|urinary_tract(1)	34						AGATCAGGTGCGGCCTGGGCC	0.637																																					p.A861T	NSCLC(18;589 615 7696 20311 50332)	Atlas-SNP	.											.	PIK3R5	79	.	0			c.G2581A						PASS	.						75	69	71					17																	8784018		2203	4300	6503	SO:0001583	missense	23533	exon19			CAGGTGCGGCCTG	AF128881	CCDS11147.1, CCDS73986.1	17p13.1	2011-10-13	2008-02-04		ENSG00000141506	ENSG00000141506			30035	protein-coding gene	gene with protein product		611317				12507995	Standard	NM_014308		Approved	P101-PI3K, p101	uc002glt.3	Q8WYR1	OTTHUMG00000108197	ENST00000447110.1:c.2581G>A	chr17.hg19:g.8784018C>T	ENSP00000392812:p.Ala861Thr	52.0	0.0	.		66.0	26.0	.	NM_001142633	B0LPH4|D3DTS3|Q5G936|Q5G938|Q5G939|Q8IZ23|Q9Y2Y2	Missense_Mutation	SNP	ENST00000447110.1	hg19	CCDS11147.1	.	.	.	.	.	.	.	.	.	.	C	7.212	0.595670	0.13875	.	.	ENSG00000141506	ENST00000269300;ENST00000447110	T	0.77229	-1.08	5.17	-10.3	0.00346	.	1.078560	0.07024	N	0.827233	T	0.41282	0.1152	N	0.03608	-0.345	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.32851	-0.9891	10	0.11485	T	0.65	0.3415	1.3976	0.02264	0.232:0.1263:0.2009:0.4408	.	861	Q8WYR1	PI3R5_HUMAN	T	861	ENSP00000392812:A861T	ENSP00000269300:A861T	A	-	1	0	PIK3R5	8724743	0.000000	0.05858	0.000000	0.03702	0.134000	0.20937	-1.878000	0.01630	-3.029000	0.00267	-0.254000	0.11334	GCA	.	.	.	none		0.637	PIK3R5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000227003.2	NM_014308		T	8784018	C	T	8784018	3	4	249	1	0	0	0	0	1	0	0	0	11929	768	27	1	65	1	PIK3R5	17	8784018	Missense_Mutation	SNP	C	TCGA-SX-A7SO-01A-11D-A34Z-10		8784018	72411192	36	15462											
C17orf66	256957	hgsc.bcm.edu	37	chr17	34182703	34182703	+	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	ctggtggttttctgcatctaGtaagtccaggagcaagtgga	9	12	13	7	0	2	0	0	0	2	0	3	2	3	2	1	4	2	4	1	4	3	4			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr17:34182703G>T	ENST00000311880.2	-	14	1478	c.1330C>A	c.(1330-1332)Cta>Ata	p.L444I	C17orf66_ENST00000592980.1_Missense_Mutation_p.L404I	NM_152781.2	NP_689994.2	A2RTY3	HEAT9_HUMAN		444					hematopoietic progenitor cell differentiation (GO:0002244)					breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(6)|lung(11)|skin(2)|stomach(4)	38		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0184)		TCTGCATCTAGTAAGTCCAGG	0.542																																					p.L444I		Atlas-SNP	.											.	C17orf66	57	.	0			c.C1330A						PASS	.						122	112	116					17																	34182703		2203	4300	6503	SO:0001583	missense	256957	exon14			CATCTAGTAAGTC																												ENST00000311880.2:c.1330C>A	chr17.hg19:g.34182703G>T	ENSP00000309560:p.Leu444Ile	56.0	0.0	.		66.0	25.0	.	NM_152781	B4DX21|B4DXA4|B4DXF0|Q8N4R4|Q96M46	Missense_Mutation	SNP	ENST00000311880.2	hg19	CCDS11299.1	.	.	.	.	.	.	.	.	.	.	G	13.38	2.221343	0.39300	.	.	ENSG00000172653	ENST00000311880	T	0.30714	1.52	4.29	2.23	0.28157	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.34223	N	0.004141	T	0.37265	0.0997	L	0.32530	0.975	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.83275	0.992;0.996	T	0.09997	-1.0649	10	0.45353	T	0.12	.	6.4579	0.21940	0.2311:0.0:0.7689:0.0	.	404;444	A2RTY3-3;A2RTY3	.;CQ066_HUMAN	I	444	ENSP00000309560:L444I	ENSP00000309560:L444I	L	-	1	2	C17orf66	31206816	1.000000	0.71417	0.998000	0.56505	0.180000	0.23129	0.630000	0.24553	1.007000	0.39238	0.563000	0.77884	CTA	.	.	.	none		0.542	C17orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256487.1			T	34182703	G	T	34182703	3	4	249	1	0	0	0	0	1	0	0	0	1876	1020	36	4	390	4	C17orf66	17	34182703	Missense_Mutation	SNP	G	TCGA-SX-A7SO-01A-11D-A34Z-10	25398685	34182703	47012507	37	15463											
KRTAP4-3	85290	hgsc.bcm.edu	37	chr17	39323904	39323904	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tacagcaggtggtcgggcagCtgaaagggcagcggcagctg	9	5	18	9	2	0	1	0	1	0	0	1	1	0	1	0	5	5	6	0	5	2	1			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr17:39323904C>T	ENST00000391356.2	-	1	520	c.521G>A	c.(520-522)aGc>aAc	p.S174N		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	174	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)			GGTCGGGCAGCTGAAAGGGCA	0.607																																					p.S174N		Atlas-SNP	.											.	KRTAP4-3	40	.	0			c.G521A						PASS	.						24	27	26					17																	39323904		2107	4239	6346	SO:0001583	missense	85290	exon1			GGGCAGCTGAAAG	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.521G>A	chr17.hg19:g.39323904C>T	ENSP00000375151:p.Ser174Asn	157.0	0.0	.		148.0	64.0	.	NM_033187		Missense_Mutation	SNP	ENST00000391356.2	hg19	CCDS42331.1	.	.	.	.	.	.	.	.	.	.	.	14.96	2.692824	0.48202	.	.	ENSG00000196156	ENST00000391356	T	0.00622	6.16	5.15	4.16	0.48862	.	.	.	.	.	T	0.01222	0.0040	L	0.32530	0.975	0.09310	N	0.999997	P	0.42078	0.77	P	0.48368	0.575	T	0.54289	-0.8316	9	0.72032	D	0.01	.	13.6096	0.62068	0.0:0.8428:0.1572:0.0	.	174	Q9BYR4	KRA43_HUMAN	N	174	ENSP00000375151:S174N	ENSP00000375151:S174N	S	-	2	0	KRTAP4-3	36577430	0.259000	0.24043	0.006000	0.13384	0.005000	0.04900	1.066000	0.30604	1.240000	0.43803	0.655000	0.94253	AGC	.	.	.	none		0.607	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1			T	39323904	C	T	39323904	3	4	249	1	0	0	0	0	1	0	0	0	8559	797	28	2	70	2	KRTAP4-3	17	39323904	Missense_Mutation	SNP	C	TCGA-SX-A7SO-01A-11D-A34Z-10	5141201	39323904	41871306	38	15464											
RNF43	54894	hgsc.bcm.edu	37	chr17	56492851	56492851	+	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	caccgctgctgccagtaccaGtcctgtgcgtccaaagcctg	7	8	10	16	2	0	0	0	0	0	0	2	0	2	0	6	0	5	3	6	0	2	1			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr17:56492851G>C	ENST00000584437.1	-	1	2043	c.88C>G	c.(88-90)Ctg>Gtg	p.L30V	RNF43_ENST00000500597.2_Missense_Mutation_p.L30V|RNF43_ENST00000583753.1_Missense_Mutation_p.L30V|RNF43_ENST00000577716.1_Missense_Mutation_p.L30V|RNF43_ENST00000407977.2_Missense_Mutation_p.L30V|RNF43_ENST00000580014.1_5'Flank|RNF43_ENST00000581868.1_Intron|BZRAP1-AS1_ENST00000583841.1_RNA			Q68DV7	RNF43_HUMAN	ring finger protein 43	30					negative regulation of Wnt signaling pathway (GO:0030178)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|stem cell proliferation (GO:0072089)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GCCAGTACCAGTCCTGTGCGT	0.562																																					p.L30V		Atlas-SNP	.											.	RNF43	157	.	0			c.C88G						PASS	.						59	55	56					17																	56492851		2203	4300	6503	SO:0001583	missense	54894	exon2			GTACCAGTCCTGT		CCDS11607.1	17q23.2	2013-01-09						"RING-type (C3HC4) zinc fingers"	18505	protein-coding gene	gene with protein product		612482					Standard	NM_017763		Approved	FLJ20315, DKFZp781H0392, URCC	uc002iwh.4	Q68DV7		ENST00000584437.1:c.88C>G	chr17.hg19:g.56492851G>C	ENSP00000463069:p.Leu30Val	23.0	0.0	.		34.0	15.0	.	NM_017763	A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Missense_Mutation	SNP	ENST00000584437.1	hg19	CCDS11607.1	.	.	.	.	.	.	.	.	.	.	G	16.71	3.197704	0.58126	.	.	ENSG00000108375	ENST00000407977;ENST00000500597	T;T	0.12879	3.01;2.64	5.49	5.49	0.81192	.	0.455866	0.18523	N	0.138716	T	0.11965	0.0291	N	0.14661	0.345	0.38350	D	0.944324	P;P	0.43633	0.675;0.813	B;B	0.41813	0.367;0.202	T	0.18304	-1.0341	10	0.40728	T	0.16	-7.7124	18.7282	0.91722	0.0:0.0:1.0:0.0	.	30;30	Q68DV7-2;Q68DV7	.;RNF43_HUMAN	V	30	ENSP00000385328:L30V;ENSP00000441969:L30V	ENSP00000385328:L30V	L	-	1	2	RNF43	53847850	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.910000	0.75741	2.734000	0.93682	0.655000	0.94253	CTG	.	.	.	none		0.562	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	NM_017763		C	56492851	G	C	56492851	3	2	249	1	0	0	0	0	1	0	0	0	13508	1020	36	4	2299	4	RNF43	17	56492851	Missense_Mutation	SNP	G	TCGA-SX-A7SO-01A-11D-A34Z-10	17168947	56492851	24702359	39	15465											
TMC6	11322	hgsc.bcm.edu	37	chr17	76118811	76118811	+	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	gctgcccacccggtagctctCcccgaaagagtgagccatgc	8	6	11	16	2	1	2	0	1	1	1	2	3	1	2	5	1	4	3	5	1	2	1			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr17:76118811C>A	ENST00000590602.1	-	10	1261	c.1102G>T	c.(1102-1104)Gag>Tag	p.E368*	TMC6_ENST00000392467.3_Nonsense_Mutation_p.E368*|TMC6_ENST00000591436.1_Nonsense_Mutation_p.E7*|TMC6_ENST00000589553.1_Nonsense_Mutation_p.E141*|TMC6_ENST00000306591.7_Nonsense_Mutation_p.E368*|TMC6_ENST00000592076.1_5'UTR|TMC6_ENST00000322933.4_Nonsense_Mutation_p.E7*|TMC6_ENST00000322914.3_Nonsense_Mutation_p.E368*			Q7Z403	TMC6_HUMAN	transmembrane channel-like 6	368					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)			CGGTAGCTCTCCCCGAAAGAG	0.627																																					p.E368X		Atlas-SNP	.											.	TMC6	42	.	0			c.G1102T						PASS	.						48	44	45					17																	76118811		2200	4300	6500	SO:0001587	stop_gained	11322	exon10			AGCTCTCCCCGAA	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.1102G>T	chr17.hg19:g.76118811C>A	ENSP00000465261:p.Glu368*	24.0	0.0	.		25.0	11.0	.	NM_001127198	O43284|Q45VJ2|Q8IU98|Q8IUI7|Q8IWU8|Q8TEQ7|Q9HAG5	Nonsense_Mutation	SNP	ENST00000590602.1	hg19	CCDS32748.1	.	.	.	.	.	.	.	.	.	.	C	39	7.353198	0.98231	.	.	ENSG00000141524	ENST00000322914;ENST00000392467;ENST00000306591;ENST00000322933	.	.	.	4.0	2.93	0.34026	.	0.611200	0.17763	N	0.162833	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	-17.3755	7.2554	0.26173	0.0:0.8057:0.0:0.1943	.	.	.	.	X	368;368;368;7	.	ENSP00000306405:E368X	E	-	1	0	TMC6	73630406	0.975000	0.34042	1.000000	0.80357	0.937000	0.57800	2.464000	0.45067	2.032000	0.59987	0.462000	0.41574	GAG	.	.	.	none		0.627	TMC6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437146.1			A	76118811	C	A	76118811	4	1	249	1	0	0	0	0	0	1	0	0	16001	864	30	4	1359	4	TMC6	17	76118811	Nonsense_Mutation	SNP	C	TCGA-SX-A7SO-01A-11D-A34Z-10	19625960	76118811	5076399	40	15466											
ABCA7	10347	hgsc.bcm.edu	37	chr19	1043151	1043151	+	Missense_Mutation	SNP	A	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	tctgcagtgtcaggggacctAgcagcacagtgggcccctcc	7	7	13	14	0	2	0	1	0	1	0	3	1	3	1	4	3	3	3	4	3	1	1			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr19:1043151A>C	ENST00000263094.6	+	8	922	c.691A>C	c.(691-693)Agc>Cgc	p.S231R	ABCA7_ENST00000433129.1_Missense_Mutation_p.S231R|ABCA7_ENST00000435683.2_Missense_Mutation_p.S93R	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	231					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)		CAGGGGACCTAGCAGCACAGT	0.667																																					p.S231R		Atlas-SNP	.											.	ABCA7	174	.	0			c.A691C						PASS	.						45	48	47					19																	1043151		2203	4298	6501	SO:0001583	missense	10347	exon8			GGACCTAGCAGCA	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.691A>C	chr19.hg19:g.1043151A>C	ENSP00000263094:p.Ser231Arg	62.0	0.0	.		87.0	39.0	.	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	hg19	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	A	11.00	1.510090	0.27036	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.86432	-2.12;-2.12	3.57	-0.128	0.13506	.	.	.	.	.	T	0.78515	0.4295	L	0.44542	1.39	0.09310	N	1	B;B	0.11235	0.002;0.004	B;B	0.10450	0.005;0.004	T	0.62779	-0.6782	9	0.38643	T	0.18	.	3.1658	0.06535	0.506:0.2198:0.2742:0.0	.	93;231	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	R	231	ENSP00000263094:S231R;ENSP00000414062:S231R	ENSP00000263094:S231R	S	+	1	0	ABCA7	994151	0.000000	0.05858	0.001000	0.08648	0.055000	0.15305	0.299000	0.19138	-0.191000	0.10448	0.260000	0.18958	AGC	.	.	.	none		0.667	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		C	1043151	A	C	1043151	3	2	249	1	0	0	0	0	1	0	0	0	37	420	15	5	717	5	ABCA7	19	1043151	Missense_Mutation	SNP	A	TCGA-SX-A7SO-01A-11D-A34Z-10		1043151	58085832	41	15467											
SF4	57794	hgsc.bcm.edu	37	chr19	19408123	19408123	+	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	agcttctgtcggtagtacttGtacccttggctattgggctc	5	15	11	10	1	1	0	0	0	1	0	3	0	1	0	1	3	3	6	1	3	4	8			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr19:19408123G>T	ENST00000247001.5	-	8	1265	c.918C>A	c.(916-918)taC>taA	p.Y306*	SUGP1_ENST00000585763.1_5'UTR	NM_172231.3	NP_757386.2	Q8IWZ8	SUGP1_HUMAN	SURP and G patch domain containing 1	306					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						GGTAGTACTTGTACCCTTGGC	0.602																																					p.Y306X		Atlas-SNP	.											.	SUGP1	63	.	0			c.C918A						PASS	.						71	75	74					19																	19408123		2203	4300	6503	SO:0001587	stop_gained	57794	exon8			GTACTTGTACCCT	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.918C>A	chr19.hg19:g.19408123G>T	ENSP00000247001:p.Tyr306*	50.0	0.0	.		65.0	24.0	.	NM_172231	O60378|Q6P3X9|Q8TCQ4|Q8WWT4|Q8WWT5|Q9NTG3	Nonsense_Mutation	SNP	ENST00000247001.5	hg19	CCDS12399.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.494308	0.85069	.	.	ENSG00000105705	ENST00000247001	.	.	.	3.66	2.62	0.31277	.	0.202787	0.44097	D	0.000496	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.1097	0.25382	0.2133:0.0:0.7867:0.0	.	.	.	.	X	306	.	ENSP00000247001:Y306X	Y	-	3	2	SUGP1	19269123	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.335000	0.43929	2.069000	0.61940	0.491000	0.48974	TAC	.	.	.	none		0.602	SUGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460128.4	NM_021164		T	19408123	G	T	19408123	4	4	249	1	0	0	0	0	0	1	0	0	14168	1372	48	4	1047	4	SF4	19	19408123	Nonsense_Mutation	SNP	G	TCGA-SX-A7SO-01A-11D-A34Z-10	18364972	19408123	39720860	42	15468											
ZNF681	148213	hgsc.bcm.edu	37	chr19	23938352	23938352	+	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	catccctaaatttcaatggtTcctgaaaaacacacacacac	16	9	3	13	0	1	1	1	1	0	0	3	1	3	1	2	1	1	1	2	1	5	3			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr19:23938352T>A	ENST00000402377.3	-	2	146	c.5A>T	c.(4-6)gAa>gTa	p.E2V	ZNF681_ENST00000395385.3_Intron	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	2					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			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)				TTTCAATGGTTCCTGAAAAac	0.393																																					p.E2V		Atlas-SNP	.											.	ZNF681	76	.	0			c.A5T						PASS	.						42	45	44					19																	23938352		2199	4300	6499	SO:0001630	splice_region_variant	148213	exon2			AATGGTTCCTGAA	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.4-1A>T	chr19.hg19:g.23938352T>A		52.0	0.0	.		47.0	17.0	.	NM_138286	B3KVF7	Missense_Mutation	SNP	ENST00000402377.3	hg19	CCDS12414.2	.	.	.	.	.	.	.	.	.	.	.	8.628	0.893033	0.17613	.	.	ENSG00000196172	ENST00000402377	T	0.00856	5.61	1.05	-0.649	0.11461	Krueppel-associated box (1);	.	.	.	.	T	0.01661	0.0053	M	0.72479	2.2	0.09310	N	1	P	0.46859	0.885	P	0.45794	0.493	T	0.40646	-0.9552	9	0.72032	D	0.01	.	3.2374	0.06770	0.0:0.3224:0.0:0.6776	.	2	Q96N22	ZN681_HUMAN	V	2	ENSP00000384000:E2V	ENSP00000384000:E2V	E	-	2	0	ZNF681	23730192	0.035000	0.19736	0.035000	0.18076	0.035000	0.12851	-0.294000	0.08309	-0.466000	0.06943	-0.467000	0.05162	GAA	.	.	.	none		0.393	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286	Missense_Mutation	A	23938352	T	A	23938352	5	1	249	1	0	0	0	0	0	0	1	0	18100	1797	62	5	1944	5	ZNF681	19	23938352	Splice_Site	SNP	T	TCGA-SX-A7SO-01A-11D-A34Z-10	4530229	23938352	35190631	43	15469											
C19orf2	8725	hgsc.bcm.edu	37	chr19	30505796	30505796	+	Frame_Shift_Del	DEL	T	T	-																															ctgacttttgttttctaggcTttttctggaactgttataga																										TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr19:30505796delT	ENST00000542441.2	+	11	1725	c.1428delT	c.(1426-1428)gctfs	p.A476fs	URI1_ENST00000392271.1_Frame_Shift_Del_p.A400fs|URI1_ENST00000312051.6_Frame_Shift_Del_p.A436fs|URI1_ENST00000360605.4_Intron			O94763	RMP_HUMAN	URI1, prefoldin-like chaperone	476					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)										TTTTCTAGGCTTTTTCTGGAA	0.378																																					p.A476fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.1427delC						PASS	.						96	104	102					19																	30505796		2203	4299	6502	SO:0001589	frameshift_variant	8725	exon11			.	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.1428delT	chr19.hg19:g.30505796delT	ENSP00000442436:p.Ala476fs	49.0	0.0	0		78.0	40.0	0.512821	NM_003796	A8K805|H7BY42|Q8TC23|Q9UNU3	Frame_Shift_Del	DEL	ENST00000542441.2	hg19	CCDS12420.1																																																																																			.	.	.	none		0.378	URI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439756.1	NM_134447		-	30505796	T	-	30505796	7	5	249	1	0	1	0	1	0	0	0	0	1913	1596	56	0	1470	0	C19orf2	19	30505796	Frame_Shift_Del	DEL	T	TCGA-SX-A7SO-01A-11D-A34Z-10	6567444	30505796	28623187	44	15470											
TMC2	117532	hgsc.bcm.edu	37	chr20	2517943	2517943	+	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	ggagtgaaagggcgggtgaaGagcggctctccacacacagg	11	4	17	9	2	1	3	0	2	1	1	2	4	1	4	1	5	1	1	1	5	2	0			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr20:2517943G>A	ENST00000358864.1	+	2	78	c.63G>A	c.(61-63)aaG>aaA	p.K21K		NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	21	Arg/Asp/Glu/Lys-rich (highly charged).				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						GGCGGGTGAAGAGCGGCTCTC	0.632																																					p.K21K		Atlas-SNP	.											.	TMC2	121	.	0			c.G63A						PASS	.						57	49	51					20																	2517943		2201	4299	6500	SO:0001819	synonymous_variant	117532	exon2			GGTGAAGAGCGGC	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.63G>A	chr20.hg19:g.2517943G>A		26.0	0.0	.		38.0	12.0	.	NM_080751	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Silent	SNP	ENST00000358864.1	hg19	CCDS13029.2																																																																																			.	.	.	none		0.632	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2			A	2517943	G	A	2517943	2	1	249	1	0	0	0	0	0	0	0	1	15997	933	33	2		2	TMC2	20	2517943	Silent	SNP	G	TCGA-SX-A7SO-01A-11D-A34Z-10		2517943	60507577	45	15471											
RIPK4	54101	hgsc.bcm.edu	37	chr21	43176962	43176962	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcttcttggcttcttccaaaAgctccatgcgctccctgaaa	8	13	6	14	1	3	1	0	1	3	0	6	1	6	1	3	1	2	3	3	1	3	4			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr21:43176962A>G	ENST00000352483.2	-	2	261	c.197T>C	c.(196-198)cTt>cCt	p.L66P	RIPK4_ENST00000332512.3_Missense_Mutation_p.L66P|RIPK4_ENST00000542057.1_Missense_Mutation_p.L3P|RIPK4_ENST00000544709.1_Missense_Mutation_p.L3P			P57078	RIPK4_HUMAN	receptor-interacting serine-threonine kinase 4	66	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						TTCTTCCAAAAGCTCCATGCG	0.522																																					p.L66P		Atlas-SNP	.											.	RIPK4	151	.	0			c.T197C						PASS	.						62	60	60					21																	43176962		2203	4300	6503	SO:0001583	missense	54101	exon2			TCCAAAAGCTCCA	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.197T>C	chr21.hg19:g.43176962A>G	ENSP00000330161:p.Leu66Pro	43.0	0.0	.		34.0	22.0	.	NM_020639	Q96KH0	Missense_Mutation	SNP	ENST00000352483.2	hg19		.	.	.	.	.	.	.	.	.	.	A	21.1	4.094643	0.76870	.	.	ENSG00000183421	ENST00000332512;ENST00000352483;ENST00000544709;ENST00000542057	T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12	4.97	4.97	0.65823	.	0.000000	0.47852	D	0.000202	T	0.80099	0.4561	M	0.82716	2.605	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.83560	0.0106	10	0.87932	D	0	-18.798	14.1208	0.65186	1.0:0.0:0.0:0.0	.	66	P57078-2	.	P	66;66;3;3	ENSP00000332454:L66P;ENSP00000330161:L66P;ENSP00000441754:L3P;ENSP00000442901:L3P	ENSP00000332454:L66P	L	-	2	0	RIPK4	42050031	1.000000	0.71417	0.913000	0.36048	0.980000	0.70556	9.040000	0.93783	1.995000	0.58328	0.460000	0.39030	CTT	.	.	.	none		0.522	RIPK4-201	KNOWN	basic	protein_coding	protein_coding		NM_020639		G	43176962	A	G	43176962	3	3	249	1	0	0	0	0	1	0	0	0	13396	72	3	3	2185	3	RIPK4	21	43176962	Missense_Mutation	SNP	A	TCGA-SX-A7SO-01A-11D-A34Z-10		43176962	4952933	46	15472											
PLA2G6	8398	hgsc.bcm.edu	37	chr22	38565425	38565425	+	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	gtattgaccaggcggccaaaGaactgcatcttctgcggggc	9	8	13	11	2	2	2	0	1	2	1	2	2	2	2	2	4	3	2	2	4	3	3			TCGA-SX-A7SO-01A-11D-A34Z-10	TCGA-SX-A7SO-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	aa1c7a5a-c790-4454-a6b9-3e6510dd803a	f0bb345a-2e8b-4af6-8320-fc9be302a5ff	g.chr22:38565425G>T	ENST00000332509.3	-	2	192	c.9C>A	c.(7-9)ttC>ttA	p.F3L	PLA2G6_ENST00000402064.1_Missense_Mutation_p.F3L|PLA2G6_ENST00000335539.3_Missense_Mutation_p.F3L|PLA2G6_ENST00000435484.1_Missense_Mutation_p.F3L|PLA2G6_ENST00000436218.1_Missense_Mutation_p.F3L|PLA2G6_ENST00000447598.2_Missense_Mutation_p.F3L|PLA2G6_ENST00000417303.2_Missense_Mutation_p.F3L	NM_003560.2	NP_003551.2	O60733	PLPL9_HUMAN	phospholipase A2, group VI (cytosolic, calcium-independent)	3					cardiolipin acyl-chain remodeling (GO:0035965)|cardiolipin biosynthetic process (GO:0032049)|cell death (GO:0008219)|chemotaxis (GO:0006935)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phospholipid metabolic process (GO:0006644)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of exocytosis (GO:0045921)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of vasodilation (GO:0045909)|regulation of store-operated calcium channel activity (GO:1901339)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|urinary bladder smooth muscle contraction (GO:0014832)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipase A2 activity (GO:0004623)			breast(2)|endometrium(6)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	24	Melanoma(58;0.045)				Quinacrine(DB01103)	GGCGGCCAAAGAACTGCATCT	0.597																																					p.F3L		Atlas-SNP	.											.	PLA2G6	54	.	0			c.C9A						PASS	.						65	52	57					22																	38565425		2203	4300	6503	SO:0001583	missense	8398	exon2			GCCAAAGAACTGC	AF064594	CCDS13967.1, CCDS33645.1	22q13.1	2013-01-10			ENSG00000184381	ENSG00000184381	3.1.1.4	"Patatin-like phospholipase domain containing", "Parkinson disease", "Ankyrin repeat domain containing"	9039	protein-coding gene	gene with protein product	"neurodegeneration with brain iron accumulation 2"	603604				9417066, 16799181, 19029121	Standard	NM_001199562		Approved	iPLA2, PNPLA9, PARK14, iPLA2beta, NBIA2	uc003aux.1	O60733	OTTHUMG00000151246	ENST00000332509.3:c.9C>A	chr22.hg19:g.38565425G>T	ENSP00000333142:p.Phe3Leu	36.0	0.0	.		37.0	14.0	.	NM_003560	A8K597|B0QYE8|O75645|Q8N452|Q9UG29|Q9UIT0|Q9Y671	Missense_Mutation	SNP	ENST00000332509.3	hg19	CCDS13967.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.116009	0.77323	.	.	ENSG00000184381	ENST00000332509;ENST00000419848;ENST00000335539;ENST00000402064;ENST00000335538;ENST00000396860;ENST00000451461;ENST00000430886;ENST00000455341	T;T;T;T;T	0.76448	0.03;0.11;0.11;1.12;-1.02	4.63	3.61	0.41365	.	0.050453	0.85682	D	0.000000	T	0.76535	0.4001	N	0.19112	0.55	0.26351	N	0.977208	B;P;B	0.52577	0.048;0.954;0.09	B;D;B	0.66351	0.039;0.943;0.063	T	0.67256	-0.5716	10	0.45353	T	0.12	-21.5614	9.9606	0.41693	0.0976:0.0:0.9024:0.0	.	3;3;3	B7Z6K3;O60733-2;O60733	.;.;PA2G6_HUMAN	L	3	ENSP00000333142:F3L;ENSP00000335149:F3L;ENSP00000386100:F3L;ENSP00000395464:F3L;ENSP00000393761:F3L	ENSP00000333142:F3L	F	-	3	2	PLA2G6	36895371	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	1.538000	0.36094	0.953000	0.37825	0.555000	0.69702	TTC	.	.	.	none		0.597	PLA2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321860.1	NM_001004426		T	38565425	G	T	38565425	3	4	249	1	0	0	0	0	1	0	0	0	12015	933	33	4	2475	4	PLA2G6	22	38565425	Missense_Mutation	SNP	G	TCGA-SX-A7SO-01A-11D-A34Z-10		38565425	12739141	47	15473											
UBR4	23352	hgsc.bcm.edu	37	chr1	19526243	19526243	+	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	cactgactgaagttggttccGgggaactgagaaagtaataa	14	9	12	6	1	0	3	0	3	0	1	1	5	1	4	1	3	1	3	1	3	5	4			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr1:19526243G>C	ENST00000375254.3	-	3	307	c.280C>G	c.(280-282)Cgg>Ggg	p.R94G	UBR4_ENST00000375226.2_Missense_Mutation_p.R94G|UBR4_ENST00000375267.2_Missense_Mutation_p.R94G|UBR4_ENST00000375217.2_Missense_Mutation_p.R94G	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	94					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)		AGTTGGTTCCGGGGAACTGAG	0.438																																					p.R94G		Atlas-SNP	.											UBR4,NS,carcinoma,0,1	UBR4	415	.	0			c.C280G						PASS	.						58	62	61					1																	19526243		2203	4300	6503	SO:0001583	missense	23352	exon3			GGTTCCGGGGAAC	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.280C>G	chr1.hg19:g.19526243G>C	ENSP00000364403:p.Arg94Gly	32.0	0.0	.		30.0	10.0	.	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	hg19	CCDS189.1	.	.	.	.	.	.	.	.	.	.	G	17.85	3.490277	0.64074	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226	T;T;T;T	0.23147	1.92;1.92;1.92;1.92	5.45	4.53	0.55603	.	0.000000	0.85682	D	0.000000	T	0.33294	0.0858	N	0.22421	0.69	0.80722	D	1	D	0.60160	0.987	D	0.65010	0.931	T	0.10064	-1.0646	10	0.54805	T	0.06	.	12.1758	0.54184	0.0:0.0:0.5839:0.4161	.	94	Q5T4S7	UBR4_HUMAN	G	94	ENSP00000364403:R94G;ENSP00000364416:R94G;ENSP00000364365:R94G;ENSP00000364374:R94G	ENSP00000364365:R94G	R	-	1	2	UBR4	19398830	1.000000	0.71417	0.998000	0.56505	0.932000	0.56968	4.442000	0.59988	1.407000	0.46875	-0.188000	0.12872	CGG	.	.	.	none		0.438	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		C	19526243	G	C	19526243	3	2	250	1	0	0	0	0	1	0	0	0	16916	1115	39	4	15687	4	UBR4	1	19526243	Missense_Mutation	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10		19526243	229724378	1	15474											
MATN1	4146	hgsc.bcm.edu	37	chr1	31191691	31191691	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgatctgccgcagcgtggcCttgtccacgctgcccactcc	4	8	11	18	4	1	0	0	0	1	0	3	1	3	0	5	1	3	2	5	1	0	1			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr1:31191691C>T	ENST00000373765.4	-	3	590	c.555G>A	c.(553-555)aaG>aaA	p.K185K	MATN1-AS1_ENST00000414532.2_RNA|MATN1-AS1_ENST00000454613.1_RNA|MATN1_ENST00000477320.1_5'UTR|MATN1-AS1_ENST00000414763.1_RNA	NM_002379.3	NP_002370.1	P21941	MATN1_HUMAN	matrilin 1, cartilage matrix protein	185	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|growth plate cartilage chondrocyte morphogenesis (GO:0003429)|protein complex assembly (GO:0006461)|regulation of bone mineralization (GO:0030500)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.00792)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)|Ovarian(437;0.0563)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-05)|COAD - Colon adenocarcinoma(152;0.000726)|STAD - Stomach adenocarcinoma(196;0.0183)|READ - Rectum adenocarcinoma(331;0.0649)		GCAGCGTGGCCTTGTCCACGC	0.667																																					p.K185K		Atlas-SNP	.											.	MATN1	28	.	0			c.G555A						PASS	.						30	28	29					1																	31191691		2201	4300	6501	SO:0001819	synonymous_variant	4146	exon3			CGTGGCCTTGTCC	M55675	CCDS336.1	1p35	2008-02-05			ENSG00000162510	ENSG00000162510			6907	protein-coding gene	gene with protein product		115437		CRTM, CMP		2246248, 9083061	Standard	NM_002379		Approved		uc001brz.3	P21941	OTTHUMG00000003705	ENST00000373765.4:c.555G>A	chr1.hg19:g.31191691C>T		50.0	0.0	.		43.0	14.0	.	NM_002379	B2R7E3|Q5TBB9	Silent	SNP	ENST00000373765.4	hg19	CCDS336.1																																																																																			.	.	.	none		0.667	MATN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010458.1	NM_002379		T	31191691	C	T	31191691	2	4	250	1	0	0	0	0	0	0	0	1	9340	680	24	2		2	MATN1	1	31191691	Silent	SNP	C	TCGA-SX-A7SP-01A-11D-A34Z-10	11665448	31191691	218058930	2	15475											
AK3L1	205	hgsc.bcm.edu	37	chr1	65690462	65690463	+	In_Frame_Ins	INS	-	-	TAG																															tgacgtcactggtgaaccgtINStagtccagcaggaggatgat																										TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr1:65690462_65690463insTAG	ENST00000327299.7	+	4	671_672	c.466_467insTAG	c.(466-468)tta>tTAGta	p.157_158insV	AK4_ENST00000545314.1_In_Frame_Ins_p.157_158insV|AK4_ENST00000546702.1_In_Frame_Ins_p.105_106insV|AK4_ENST00000470888.2_3'UTR|AK4_ENST00000395334.2_In_Frame_Ins_p.157_158insV	NM_013410.3	NP_037542.1			adenylate kinase 4											breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)	9						TGGTGAACCGTTAGTCCAGCAG	0.421																																					p.L156delinsLV		Atlas-Indel,Pindel	.											.	AK4	22	.	0			c.466_467insTAG						PASS	.																																			SO:0001652	inframe_insertion	205	exon5			.	AK025926	CCDS629.1	1p31.3	2012-10-02	2010-06-15	2010-06-15	ENSG00000162433	ENSG00000162433	2.7.4.3	"Adenylate kinases"	363	protein-coding gene	gene with protein product		103030	"adenylate kinase 3", "adenylate kinase 3-like 1"	AK3, AK3L1		11485571	Standard	NM_203464		Approved		uc001dby.3	P27144	OTTHUMG00000009033	ENST00000327299.7:c.467_469dupTAG	chr1.hg19:g.65690463_65690465dupTAG	ENSP00000322175:p.Val157_Val157dup	98.0	0.0	0		153.0	40.0	0.261438	NM_203464		In_Frame_Ins	INS	ENST00000327299.7	hg19	CCDS629.1																																																																																			.	.	.	none		0.421	AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025040.2	NM_013410		TAG	65690463	-	TAG	65690462	7	5	250	1	0	1	1	0	0	0	0	0	442	1722	60	0	480	0	AK3L1	1	65690462	In_Frame_Ins	INS	-	TCGA-SX-A7SP-01A-11D-A34Z-10	34498771	65690462	183560159	3	15476											
ZNF326	284695	hgsc.bcm.edu	37	chr1	90493075	90493075	+	Frame_Shift_Del	DEL	G	G	-																															tagaggaagtggaagaagtaGaggaagtgagagaaggagga																										TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr1:90493075delG	ENST00000340281.4	+	12	1707	c.1564delG	c.(1564-1566)gagfs	p.E523fs	ZNF326_ENST00000370447.3_Frame_Shift_Del_p.E434fs|ZNF326_ENST00000455342.2_Frame_Shift_Del_p.E317fs	NM_182976.2	NP_892021.1	Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	523	Glu-rich.				mRNA processing (GO:0006397)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, elongation (GO:0032784)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	DBIRD complex (GO:0044609)|nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(7)|ovary(1)	25		all_lung(203;0.0116)|Lung NSC(277;0.0417)		all cancers(265;0.00728)|Epithelial(280;0.0265)		ggaagaagtagaggaagtgag	0.498																																					p.V521fs		Atlas-Indel,Pindel	.											.	ZNF326	60	.	0			c.1563delA						PASS	.						70	64	66					1																	90493075		2203	4300	6503	SO:0001589	frameshift_variant	284695	exon12			.	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.1564delG	chr1.hg19:g.90493075delG	ENSP00000340796:p.Glu523fs	73.0	0.0	0		101.0	27.0	0.267327	NM_182976	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	Frame_Shift_Del	DEL	ENST00000340281.4	hg19	CCDS727.1																																																																																			.	.	.	none		0.498	ZNF326-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029428.2	NM_181781		-	90493075	G	-	90493075	7	5	250	1	0	1	0	1	0	0	0	0	17858	943	33	0	1614	0	ZNF326	1	90493075	Frame_Shift_Del	DEL	G	TCGA-SX-A7SP-01A-11D-A34Z-10	24802613	90493075	158757546	4	15477											
DNTTIP2	30836	hgsc.bcm.edu	37	chr1	94341933	94341933	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcatcctcttcctcttcttTttcttcctcaatggcaacct	5	19	2	15	0	6	0	2	0	4	0	9	0	9	0	4	1	1	1	4	1	2	6			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr1:94341933T>C	ENST00000436063.2	-	2	1615	c.1558A>G	c.(1558-1560)Aaa>Gaa	p.K520E	DNTTIP2_ENST00000460191.1_5'UTR	NM_014597.4	NP_055412.2	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 2	520					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	38		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		tcctcttctttttcttcctcA	0.368																																					p.K520E		Atlas-SNP	.											.	DNTTIP2	59	.	0			c.A1558G						PASS	.						123	106	111					1																	94341933		1860	4081	5941	SO:0001583	missense	30836	exon2			CTTCTTTTTCTTC	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.1558A>G	chr1.hg19:g.94341933T>C	ENSP00000411010:p.Lys520Glu	201.0	0.0	.		259.0	74.0	.	NM_014597	Q12987|Q53H59|Q5TFJ4|Q6TLI0|Q76MJ8|Q86WX9	Missense_Mutation	SNP	ENST00000436063.2	hg19	CCDS44174.1	.	.	.	.	.	.	.	.	.	.	T	2.748	-0.260753	0.05791	.	.	ENSG00000067334	ENST00000436063	T	0.13538	2.58	4.78	-1.49	0.08718	.	0.927580	0.09139	N	0.843213	T	0.01189	0.0039	N	0.08118	0	0.18873	N	0.999989	B	0.06786	0.001	B	0.04013	0.001	T	0.47812	-0.9088	10	0.02654	T	1	.	6.8859	0.24199	0.0:0.2787:0.1252:0.5962	.	520	Q5QJE6	TDIF2_HUMAN	E	520	ENSP00000411010:K520E	ENSP00000352137:K520E	K	-	1	0	DNTTIP2	94114521	0.000000	0.05858	0.479000	0.27329	0.916000	0.54674	-0.269000	0.08596	-0.127000	0.11661	0.496000	0.49642	AAA	.	.	.	none		0.368	DNTTIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028317.2	NM_014597		C	94341933	T	C	94341933	3	2	250	1	0	0	0	0	1	0	0	0	4684	1850	64	3	736	3	DNTTIP2	1	94341933	Missense_Mutation	SNP	T	TCGA-SX-A7SP-01A-11D-A34Z-10	3848858	94341933	154908688	5	15478											
CEP170	9859	hgsc.bcm.edu	37	chr1	243319673	243319675	+	In_Frame_Del	DEL	TGT	TGT	-																															gagaagtacgtagacgggtaTgtttaggggaattacggttt																										TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr1:243319673_243319675delTGT	ENST00000366542.1	-	14	3810_3812	c.3759_3761delACA	c.(3757-3762)aaacat>aat	p.1253_1254KH>N	CEP170_ENST00000366543.1_Intron|CEP170_ENST00000490813.1_Intron|CEP170_ENST00000481987.1_5'UTR|CEP170_ENST00000366544.1_In_Frame_Del_p.1155_1156KH>N	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	1253	Targeting to centrosomes.|Targeting to microtubules.					centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)				NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			TAGACGGGTATGTTTAGGGGAAT	0.419																																					p.1254_1254del		Atlas-Indel,Pindel	.											.	CEP170	153	.	0			c.3760_3762del						PASS	.																																			SO:0001651	inframe_deletion	9859	exon14			.	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.3759_3761delACA	chr1.hg19:g.243319673_243319675delTGT	ENSP00000355500:p.Lys1253_His1254delinsAsn	105.0	0.0	0		119.0	37.0	0.310924	NM_014812	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	In_Frame_Del	DEL	ENST00000366542.1	hg19	CCDS44339.1																																																																																			.	.	.	none		0.419	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812		-	243319675	TGT	-	243319673	7	5	250	1	0	1	0	1	0	0	0	0	3252	1464	51	0	1051	0	CEP170	1	243319673	In_Frame_Del	DEL	TGT	TCGA-SX-A7SP-01A-11D-A34Z-10	148977740	243319673	5930948	6	15479											
PDCL3	79031	hgsc.bcm.edu	37	chr2	101183077	101183077	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaagaggagcagcgcatccTccagcagtcagtgggtgagt	11	6	15	9	1	1	3	1	1	0	2	3	4	3	4	2	2	3	3	2	2	1	0			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr2:101183077T>C	ENST00000264254.6	+	2	497	c.119T>C	c.(118-120)cTc>cCc	p.L40P		NM_024065.4	NP_076970.1	Q9H2J4	PDCL3_HUMAN	phosducin-like 3	40					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|protein folding (GO:0006457)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|viral process (GO:0016032)	cytoplasm (GO:0005737)	protein binding involved in protein folding (GO:0044183)			endometrium(3)|large_intestine(2)|liver(1)|lung(6)	12						CAGCGCATCCTCCAGCAGTCA	0.532																																					p.L40P		Atlas-SNP	.											.	PDCL3	27	.	0			c.T119C						PASS	.						64	63	63					2																	101183077		2203	4300	6503	SO:0001583	missense	79031	exon2			GCATCCTCCAGCA	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.119T>C	chr2.hg19:g.101183077T>C	ENSP00000264254:p.Leu40Pro	129.0	0.0	.		165.0	53.0	.	NM_024065	B2RA00|Q53S68	Missense_Mutation	SNP	ENST00000264254.6	hg19	CCDS33261.1	.	.	.	.	.	.	.	.	.	.	.	9.683	1.149916	0.21371	.	.	ENSG00000115539	ENST00000264254	T	0.41758	0.99	4.61	4.61	0.57282	Thioredoxin-like fold (1);Phosducin, thioredoxin-like domain (1);	0.302798	0.29066	N	0.013248	T	0.33789	0.0875	L	0.37750	1.13	0.58432	D	0.999999	B	0.06786	0.001	B	0.09377	0.004	T	0.09122	-1.0689	10	0.30854	T	0.27	-27.9473	14.0053	0.64459	0.0:0.0:0.0:1.0	.	40	Q9H2J4	PDCL3_HUMAN	P	40	ENSP00000264254:L40P	ENSP00000264254:L40P	L	+	2	0	PDCL3	100549509	0.214000	0.23563	0.845000	0.33349	0.207000	0.24258	1.019000	0.30014	1.728000	0.51552	0.363000	0.22086	CTC	.	.	.	none		0.532	PDCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329734.1	NM_024065		C	101183077	T	C	101183077	3	2	250	1	0	0	0	0	1	0	0	0	11635	1551	54	3	125	3	PDCL3	2	101183077	Missense_Mutation	SNP	T	TCGA-SX-A7SP-01A-11D-A34Z-10		101183077	142016296	7	15480											
DYTN	391475	hgsc.bcm.edu	37	chr2	207527877	207527877	+	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	tggctttgtgccctggtgctGtgcaaagtggtctctggtga	4	14	15	8	0	1	1	0	1	1	0	2	1	1	1	1	4	3	3	1	4	1	1			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr2:207527877G>C	ENST00000452335.2	-	11	1499	c.1383C>G	c.(1381-1383)caC>caG	p.H461Q		NM_001093730.1	NP_001087199.1	A2CJ06	DYTN_HUMAN	dystrotelin	461						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)		CCCTGGTGCTGTGCAAAGTGG	0.483																																					p.H461Q		Atlas-SNP	.											.	DYTN	168	.	0			c.C1383G						PASS	.						180	171	174					2																	207527877		2039	4193	6232	SO:0001583	missense	391475	exon11			GGTGCTGTGCAAA	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.1383C>G	chr2.hg19:g.207527877G>C	ENSP00000396593:p.His461Gln	312.0	0.0	.		353.0	108.0	.	NM_001093730		Missense_Mutation	SNP	ENST00000452335.2	hg19	CCDS46502.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.544248	0.00934	.	.	ENSG00000232125	ENST00000452335	T	0.08193	3.12	5.12	0.0828	0.14430	.	.	.	.	.	T	0.02380	0.0073	N	0.02916	-0.46	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45687	-0.9244	9	0.02654	T	1	-1.1026	4.4038	0.11399	0.0:0.2781:0.2036:0.5183	.	461	A2CJ06	DYTN_HUMAN	Q	461	ENSP00000396593:H461Q	ENSP00000396593:H461Q	H	-	3	2	DYTN	207236122	0.151000	0.22747	0.057000	0.19452	0.036000	0.12997	0.011000	0.13264	0.126000	0.18424	-0.284000	0.09977	CAC	.	.	.	none		0.483	DYTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336799.1			C	207527877	G	C	207527877	3	2	250	1	0	0	0	0	1	0	0	0	4863	1368	48	4	361	4	DYTN	2	207527877	Missense_Mutation	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10	106344800	207527877	35671496	8	15481											
RPL37A	6168	hgsc.bcm.edu	37	chr2	217364702	217364709	+	Frame_Shift_Del	DEL	TGGCACTG	TGGCACTG	-																															agagacgagctgtggggatcTggcactgtggttcctgcatg																										TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	TGGCACTG	TGGCACTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr2:217364702_217364709delTGGCACTG	ENST00000491306.1	+	3	849_856	c.163_170delTGGCACTG	c.(163-171)tggcactgtfs	p.WHC55fs	RPL37A_ENST00000427280.2_Frame_Shift_Del_p.WHC31fs|RPL37A_ENST00000600880.1_Frame_Shift_Del_p.WHC55fs|AC098820.3_ENST00000453157.1_RNA|RPL37A_ENST00000456586.1_Frame_Shift_Del_p.WHC31fs|AC098820.3_ENST00000438978.1_RNA|RPL37A_ENST00000441179.2_Frame_Shift_Del_p.WHC31fs|RPL37A_ENST00000446558.1_Frame_Shift_Del_p.WHC55fs|RPL37A_ENST00000598925.1_Frame_Shift_Del_p.WHC31fs	NM_000998.4	NP_000989.1	P61513	RL37A_HUMAN	ribosomal protein L37a	55					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.H56H(1)		NS(1)|ovary(1)	2		Renal(323;0.0458)		Epithelial(149;3.51e-06)|all cancers(144;0.000249)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGTGGGGATCTGGCACTGTGGTTCCTGC	0.452																																					p.54_57del		Atlas-Indel,Pindel	.											.	RPL37A	9	.	1	Substitution - coding silent(1)	ovary(1)	c.162_169del						PASS	.																																			SO:0001589	frameshift_variant	6168	exon3			.		CCDS2404.1	2q35	2011-04-06			ENSG00000197756	ENSG00000197756		"L ribosomal proteins"	10348	protein-coding gene	gene with protein product		613314				1437567	Standard	NM_000998		Approved	L37A	uc002vgf.3	P61513	OTTHUMG00000133052	ENST00000491306.1:c.163_170delTGGCACTG	chr2.hg19:g.217364702_217364709delTGGCACTG	ENSP00000418082:p.Trp55fs	101.0	0.0	0		104.0	21.0	0.201923	NM_000998	P12751|Q6FGF5	Frame_Shift_Del	DEL	ENST00000491306.1	hg19	CCDS2404.1																																																																																			.	.	.	none		0.452	RPL37A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256665.2	NM_000998		-	217364709	TGGCACTG	-	217364702	7	5	250	1	0	1	0	1	0	0	0	0	13603	1580	55	0	173	0	RPL37A	2	217364702	Frame_Shift_Del	DEL	TGGCACTG	TCGA-SX-A7SP-01A-11D-A34Z-10	9836825	217364702	25834671	9	15482											
TNS1	7145	hgsc.bcm.edu	37	chr2	218712647	218712647	+	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	ggaggagagtggagaagcccCtggccaggccccggggacac	9	2	18	12	1	0	2	0	0	0	2	0	6	0	4	5	7	1	0	5	7	1	0			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr2:218712647C>G	ENST00000171887.4	-	17	2670	c.2218G>C	c.(2218-2220)Ggg>Cgg	p.G740R	TNS1_ENST00000480665.1_5'Flank|TNS1_ENST00000430930.1_Missense_Mutation_p.G740R|TNS1_ENST00000419504.1_Missense_Mutation_p.G740R	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	740					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)		GGAGAAGCCCCTGGCCAGGCC	0.607																																					p.G740R		Atlas-SNP	.											.	TNS1	251	.	0			c.G2218C						PASS	.						18	22	21					2																	218712647		2203	4300	6503	SO:0001583	missense	7145	exon17			AAGCCCCTGGCCA	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.2218G>C	chr2.hg19:g.218712647C>G	ENSP00000171887:p.Gly740Arg	42.0	0.0	.		57.0	15.0	.	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	hg19	CCDS2407.1	.	.	.	.	.	.	.	.	.	.	C	14.54	2.567344	0.45694	.	.	ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930	D;D;D	0.91237	-2.79;-2.81;-2.8	4.45	4.45	0.53987	.	0.733784	0.13287	N	0.399289	D	0.84174	0.5414	N	0.19112	0.55	0.80722	D	1	B;D;P;P;P	0.56035	0.244;0.974;0.93;0.868;0.93	B;P;B;B;P	0.45913	0.07;0.497;0.36;0.383;0.462	T	0.80063	-0.1539	10	0.29301	T	0.29	.	9.3101	0.37898	0.0:0.7696:0.1478:0.0825	.	740;794;740;740;740	B2RU35;A1L0S7;Q9HBL0;E9PGF5;E9PF55	.;.;TENS1_HUMAN;.;.	R	740	ENSP00000171887:G740R;ENSP00000408724:G740R;ENSP00000406016:G740R	ENSP00000171887:G740R	G	-	1	0	TNS1	218420892	1.000000	0.71417	0.986000	0.45419	0.907000	0.53573	2.690000	0.47001	2.310000	0.77875	0.462000	0.41574	GGG	.	.	.	none		0.607	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		G	218712647	C	G	218712647	3	3	250	1	0	0	0	0	1	0	0	0	16355	681	24	4	3057	4	TNS1	2	218712647	Missense_Mutation	SNP	C	TCGA-SX-A7SP-01A-11D-A34Z-10	1347945	218712647	24486726	10	15483											
WNT7A	7476	hgsc.bcm.edu	37	chr3	13860881	13860881	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgcacgagcctgacacgcCgtggcacttacattccagct	8	8	11	14	3	0	1	0	1	0	0	1	2	1	1	3	2	4	3	3	2	1	2	rs387907231		TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr3:13860881C>T	ENST00000285018.4	-	4	914	c.610G>A	c.(610-612)Ggc>Agc	p.G204S		NM_004625.3	NP_004616.2	O00755	WNT7A_HUMAN	wingless-type MMTV integration site family, member 7A	204					asymmetric protein localization (GO:0008105)|canonical Wnt signaling pathway (GO:0060070)|cartilage condensation (GO:0001502)|cell fate commitment (GO:0045165)|cell proliferation in forebrain (GO:0021846)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system vasculogenesis (GO:0022009)|cerebellar granule cell differentiation (GO:0021707)|chondrocyte differentiation (GO:0002062)|dorsal/ventral pattern formation (GO:0009953)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment of cell polarity (GO:0030010)|lens fiber cell development (GO:0070307)|negative regulation of apoptotic process (GO:0043066)|negative regulation of neurogenesis (GO:0050768)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|non-canonical Wnt signaling pathway (GO:0035567)|oviduct development (GO:0060066)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|positive regulation of JNK cascade (GO:0046330)|positive regulation of synapse assembly (GO:0051965)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of axon diameter (GO:0031133)|response to estradiol (GO:0032355)|sex differentiation (GO:0007548)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration (GO:0014834)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|stem cell development (GO:0048864)|synapse organization (GO:0050808)|uterus morphogenesis (GO:0061038)|Wnt signaling pathway involved in wound healing, spreading of epidermal cells (GO:0035659)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|receptor binding (GO:0005102)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	24						CCTGACACGCCGTGGCACTTA	0.602																																					p.G204S		Atlas-SNP	.											.	WNT7A	70	.	0			c.G610A						PASS	.						109	100	103					3																	13860881		2203	4300	6503	SO:0001583	missense	7476	exon4			ACACGCCGTGGCA	D83175	CCDS2616.1	3p25	2008-07-18			ENSG00000154764	ENSG00000154764		"Wingless-type MMTV integration sites"	12786	protein-coding gene	gene with protein product	"proto-oncogene Wnt7a protein"	601570				8893824, 9161407	Standard	NM_004625		Approved		uc003bye.1	O00755	OTTHUMG00000129803	ENST00000285018.4:c.610G>A	chr3.hg19:g.13860881C>T	ENSP00000285018:p.Gly204Ser	56.0	0.0	.		66.0	31.0	.	NM_004625	Q96H90|Q9Y560	Missense_Mutation	SNP	ENST00000285018.4	hg19	CCDS2616.1	.	.	.	.	.	.	.	.	.	.	c	19.41	3.822077	0.71028	.	.	ENSG00000154764	ENST00000285018	D	0.83837	-1.77	4.29	4.29	0.51040	Secreted growth factor Wnt protein, conserved site (1);	0.101745	0.64402	D	0.000003	D	0.94732	0.8300	H	0.98542	4.26	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.97237	0.9888	10	0.87932	D	0	.	17.1402	0.86750	0.0:1.0:0.0:0.0	.	204	O00755	WNT7A_HUMAN	S	204	ENSP00000285018:G204S	ENSP00000285018:G204S	G	-	1	0	WNT7A	13835882	1.000000	0.71417	0.819000	0.32651	0.253000	0.25986	7.810000	0.86072	2.121000	0.65114	0.558000	0.71614	GGC	.	.	.	none		0.602	WNT7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252031.2	NM_004625		T	13860881	C	T	13860881	3	4	250	1	0	0	0	0	1	0	0	0	17406	652	23	1	443	1	WNT7A	3	13860881	Missense_Mutation	SNP	C	TCGA-SX-A7SP-01A-11D-A34Z-10		13860881	184161549	11	15484											
ARIH2	10425	hgsc.bcm.edu	37	chr3	49005966	49005966	+	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	caggttgtttttgttcaacaGgagtctcttgcatggctcag	7	15	11	8	0	3	0	2	0	1	0	4	1	3	1	0	3	2	5	0	3	1	5			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr3:49005966G>T	ENST00000356401.4	+	7	877		c.e7-1		ARIH2_ENST00000449376.1_Splice_Site|ARIH2_ENST00000490095.1_Splice_Site	NM_006321.2	NP_006312.1	O95376	ARI2_HUMAN	ariadne RBR E3 ubiquitin protein ligase 2						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)		TTGTTCAACAGGAGTCTCTTG	0.517																																					.		Atlas-SNP	.											.	ARIH2	32	.	0			c.539-1G>T						PASS	.						129	119	122					3																	49005966		2203	4300	6503	SO:0001630	splice_region_variant	10425	exon7			TCAACAGGAGTCT	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.539-1G>T	chr3.hg19:g.49005966G>T		66.0	0.0	.		88.0	43.0	.	NM_006321	Q9HBZ6|Q9UEM9	Splice_Site	SNP	ENST00000356401.4	hg19	CCDS2780.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.470290	0.84533	.	.	ENSG00000177479	ENST00000356401;ENST00000449376;ENST00000444790;ENST00000395481	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.1346	0.98019	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARIH2	48980970	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.444000	0.97578	2.765000	0.95021	0.655000	0.94253	.	.	.	.	none		0.517	ARIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257525.1	NM_006321	Intron	T	49005966	G	T	49005966	5	4	250	1	0	0	0	0	0	0	1	0	924	1014	35	4	556	4	ARIH2	3	49005966	Splice_Site	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10	35145085	49005966	149016464	12	15485											
TMF1	7110	hgsc.bcm.edu	37	chr3	69092928	69092928	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcagcatctctctctttgcaGgctagttgaactttcttttc	6	17	7	11	0	3	1	0	1	3	0	6	1	3	1	0	1	3	5	0	1	2	6			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr3:69092928G>A	ENST00000398559.2	-	4	1767	c.1551C>T	c.(1549-1551)gcC>gcT	p.A517A	CTD-2013N24.2_ENST00000597950.1_RNA|CTD-2013N24.2_ENST00000596274.1_RNA|CTD-2013N24.2_ENST00000482368.2_RNA|CTD-2013N24.2_ENST00000596523.1_RNA|CTD-2013N24.2_ENST00000598783.1_RNA|CTD-2013N24.2_ENST00000601735.1_RNA|CTD-2013N24.2_ENST00000596732.1_RNA|CTD-2013N24.2_ENST00000595925.1_RNA|TMF1_ENST00000543976.1_Silent_p.A520A			P82094	TMF1_HUMAN	TATA element modulatory factor 1	517					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)		TCTCTTTGCAGGCTAGTTGAA	0.323																																					p.A517A		Atlas-SNP	.											.	TMF1	77	.	0			c.C1551T						PASS	.						76	68	70					3																	69092928		1799	4082	5881	SO:0001819	synonymous_variant	7110	exon4			TTTGCAGGCTAGT		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.1551C>T	chr3.hg19:g.69092928G>A		359.0	0.0	.		572.0	28.0	.	NM_007114	B7ZLJ2|Q17R87|Q59GK0	Silent	SNP	ENST00000398559.2	hg19	CCDS43105.1																																																																																			.	.	.	none		0.323	TMF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352106.1	NM_007114		A	69092928	G	A	69092928	2	1	250	1	0	0	0	0	0	0	0	1	16240	987	35	2		2	TMF1	3	69092928	Silent	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10	20086962	69092928	128929502	13	15486											
MYH15	22989	hgsc.bcm.edu	37	chr3	108229380	108229399	+	Frame_Shift_Del	DEL	TTATTAAAGCAATCCACCAA	TTATTAAAGCAATCCACCAA	-																															aaggtctgacagatccatctTtattaaagcaatccaccaaa																										TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	TTATTAAAGCAATCCACCAA	TTATTAAAGCAATCCACCAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr3:108229380_108229399delTTATTAAAGCAATCCACCAA	ENST00000273353.3	-	2	95_114	c.39_58delTTGGTGGATTGCTTTAATAA	c.(37-60)ttttggtggattgctttaataaagfs	p.FWWIALIK13fs		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	13						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						AGATCCATCTTTATTAAAGCAATCCACCAAAAAAAGGCCC	0.427																																					p.14_20del		Atlas-INDEL	.											.	MYH15	223	.	0			c.40_59del						PASS	.																																			SO:0001589	frameshift_variant	22989	exon2			.	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.39_58delTTGGTGGATTGCTTTAATAA	chr3.hg19:g.108229380_108229399delTTATTAAAGCAATCCACCAA	ENSP00000273353:p.Phe13fs	137.0	0.0	0		196.0	15.0	0.0765306	NM_014981		Frame_Shift_Del	DEL	ENST00000273353.3	hg19	CCDS43127.1																																																																																			.	.	.	none		0.427	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		-	108229399	TTATTAAAGCAATCCACCAA	-	108229380	7	5	250	1	0	1	0	1	0	0	0	0	10041	1850	64	0	5946	0	MYH15	3	108229380	Frame_Shift_Del	DEL	TTATTAAAGCAATCCACCAA	TCGA-SX-A7SP-01A-11D-A34Z-10	39136452	108229380	89793050	14	15487											
PPP2R3A	5523	hgsc.bcm.edu	37	chr3	135797207	135797208	+	Splice_Site	DEL	AG	AG	-																															tttattttccttttggaaccAggttattcagagaatattct																										TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr3:135797207_135797208delAG	ENST00000264977.3	+	7	3161		c.e7-1		PPP2R3A_ENST00000334546.2_Splice_Site|PPP2R3A_ENST00000492624.2_Splice_Site|PPP2R3A_ENST00000490467.1_Splice_Site	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha						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						TTTTGGAACCAGGTTATTCAGA	0.322																																					.		Atlas-Indel,Pindel	.											.	PPP2R3A	114	.	0			.						PASS	.																																			SO:0001630	splice_region_variant	5523	.			.	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.2545-1AG>-	chr3.hg19:g.135797207_135797208delAG		534.0	0.0	0		712.0	277.0	0.389045	.	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Splice_Site	DEL	ENST00000264977.3	hg19	CCDS3087.1																																																																																			.	.	.	none		0.322	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718	Intron	-	135797208	AG	-	135797207	8	5	250	1	0	1	0	1	0	0	1	0	12398	202	7	0	2701	0	PPP2R3A	3	135797207	Splice_Site	DEL	AG	TCGA-SX-A7SP-01A-11D-A34Z-10	27567827	135797207	62225223	15	15488											
KLB	152831	hgsc.bcm.edu	37	chr4	39449950	39449950	+	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	ttgataaagtcagaatcaaaGgctattatgcattcaaactg	16	12	7	6	0	3	2	3	1	0	1	3	2	3	2	0	1	2	2	0	1	7	5			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr4:39449950G>C	ENST00000257408.4	+	5	2876	c.2779G>C	c.(2779-2781)Ggc>Cgc	p.G927R		NM_175737.3	NP_783864.1	Q86Z14	KLOTB_HUMAN	klotho beta	927	Glycosyl hydrolase-1 2.				carbohydrate metabolic process (GO:0005975)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor binding (GO:0017134)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|skin(6)	29						CAGAATCAAAGGCTATTATGC	0.299																																					p.G927R		Atlas-SNP	.											.	KLB	95	.	0			c.G2779C						PASS	.						34	37	36					4																	39449950		2199	4299	6498	SO:0001583	missense	152831	exon5			ATCAAAGGCTATT	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.2779G>C	chr4.hg19:g.39449950G>C	ENSP00000257408:p.Gly927Arg	225.0	0.0	.		291.0	90.0	.	NM_175737	Q2M3K8	Missense_Mutation	SNP	ENST00000257408.4	hg19	CCDS3451.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.785144	0.90282	.	.	ENSG00000134962	ENST00000257408	T	0.74737	-0.87	5.78	5.78	0.91487	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.90150	0.6922	M	0.92833	3.35	0.58432	D	0.999994	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.91708	0.5379	10	0.87932	D	0	-25.4111	20.0143	0.97474	0.0:0.0:1.0:0.0	.	918;927	B7ZL50;Q86Z14	.;KLOTB_HUMAN	R	927	ENSP00000257408:G927R	ENSP00000257408:G927R	G	+	1	0	KLB	39126345	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.061000	0.89467	2.740000	0.93945	0.313000	0.20887	GGC	.	.	.	none		0.299	KLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250429.1	NM_175737		C	39449950	G	C	39449950	3	2	250	1	0	0	0	0	1	0	0	0	8339	1000	35	4	2797	4	KLB	4	39449950	Missense_Mutation	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10		39449950	151704326	16	15489											
SLC10A4	201780	hgsc.bcm.edu	37	chr4	48487117	48487117	+	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	cctatcgggttgggcgtcttCattcgctacaaatacagccg	8	11	10	12	4	2	0	1	0	1	0	4	0	2	0	2	2	3	2	2	2	4	6			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr4:48487117C>A	ENST00000273861.4	+	2	978	c.759C>A	c.(757-759)ttC>ttA	p.F253L		NM_152679.3	NP_689892.1	Q96EP9	NTCP4_HUMAN	solute carrier family 10, member 4	253						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						TGGGCGTCTTCATTCGCTACA	0.547																																					p.F253L		Atlas-SNP	.											.	SLC10A4	23	.	0			c.C759A						PASS	.						129	123	125					4																	48487117		2203	4300	6503	SO:0001583	missense	201780	exon2			CGTCTTCATTCGC	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.759C>A	chr4.hg19:g.48487117C>A	ENSP00000273861:p.Phe253Leu	148.0	0.0	.		165.0	56.0	.	NM_152679	Q8WUZ2	Missense_Mutation	SNP	ENST00000273861.4	hg19	CCDS3482.1	.	.	.	.	.	.	.	.	.	.	C	15.84	2.951156	0.53186	.	.	ENSG00000145248	ENST00000273861	T	0.06528	3.29	5.03	5.03	0.67393	.	0.414564	0.29730	N	0.011353	T	0.03053	0.0090	N	0.01464	-0.85	0.45439	D	0.998413	B	0.06786	0.001	B	0.08055	0.003	T	0.54016	-0.8356	10	0.14252	T	0.57	-16.4047	18.9279	0.92552	0.0:1.0:0.0:0.0	.	253	Q96EP9	NTCP4_HUMAN	L	253	ENSP00000273861:F253L	ENSP00000273861:F253L	F	+	3	2	SLC10A4	48181874	1.000000	0.71417	1.000000	0.80357	0.708000	0.40852	2.030000	0.41108	2.771000	0.95319	0.563000	0.77884	TTC	.	.	.	none		0.547	SLC10A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219926.3	NM_152679		A	48487117	C	A	48487117	3	1	250	1	0	0	0	0	1	0	0	0	14389	825	29	4	765	4	SLC10A4	4	48487117	Missense_Mutation	SNP	C	TCGA-SX-A7SP-01A-11D-A34Z-10	9037167	48487117	142667159	17	15490											
YTHDC1	91746	hgsc.bcm.edu	37	chr4	69197866	69197866	+	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	tcatggttgttactctttatGaggaaaaatcttgcatcttg	10	17	8	6	0	4	1	1	1	3	0	4	2	4	2	0	2	2	3	0	2	4	6			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr4:69197866G>A	ENST00000344157.4	-	7	1412	c.1077C>T	c.(1075-1077)ctC>ctT	p.L359L	YTHDC1_ENST00000579690.1_Silent_p.L359L|YTHDC1_ENST00000355665.3_Silent_p.L341L	NM_001031732.2	NP_001026902.1	Q96MU7	YTDC1_HUMAN	YTH domain containing 1	359	YTH. {ECO:0000255|PROSITE- ProRule:PRU00225}.				mRNA splice site selection (GO:0006376)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	30						TACTCTTTATGAGGAAAAATC	0.333																																					p.L359L		Atlas-SNP	.											.	YTHDC1	81	.	0			c.C1077T						PASS	.						115	108	110					4																	69197866		2203	4300	6503	SO:0001819	synonymous_variant	91746	exon7			CTTTATGAGGAAA	AK098515	CCDS3522.2, CCDS33992.1	4q13.3	2009-01-14			ENSG00000083896	ENSG00000083896			30626	protein-coding gene	gene with protein product						12368078, 10564280	Standard	XM_005265706		Approved	YT521, KIAA1966, YT521-B	uc003hdx.3	Q96MU7	OTTHUMG00000129306	ENST00000344157.4:c.1077C>T	chr4.hg19:g.69197866G>A		125.0	0.0	.		125.0	27.0	.	NM_001031732	Q4W5Q3|Q7Z622|Q8TF35	Silent	SNP	ENST00000344157.4	hg19	CCDS33992.1																																																																																			.	.	.	none		0.333	YTHDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251437.1	NM_133370		A	69197866	G	A	69197866	2	1	250	1	0	0	0	0	0	0	0	1	17508	1277	45	2		2	YTHDC1	4	69197866	Silent	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10	20710749	69197866	121956410	18	15491											
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123160922	123160922	+	Missense_Mutation	SNP	T	T	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	accaaagcagaggagaagttTtggttcattcccatatacac	14	10	8	9	0	1	2	1	0	0	2	2	3	2	2	2	2	2	3	2	2	4	6			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr4:123160922T>G	ENST00000264501.4	+	29	4458	c.4085T>G	c.(4084-4086)tTt>tGt	p.F1362C	KIAA1109_ENST00000495260.1_3'UTR|KIAA1109_ENST00000388738.3_Missense_Mutation_p.F1362C|KIAA1109_ENST00000455637.1_Missense_Mutation_p.F1362C			Q2LD37	K1109_HUMAN	KIAA1109	1362					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						AGGAGAAGTTTTGGTTCATTC	0.423																																					p.F1362C		Atlas-SNP	.											.	KIAA1109	424	.	0			c.T4085G						PASS	.						112	105	107					4																	123160922		1937	4138	6075	SO:0001583	missense	84162	exon27			GAAGTTTTGGTTC	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.4085T>G	chr4.hg19:g.123160922T>G	ENSP00000264501:p.Phe1362Cys	120.0	0.0	.		157.0	58.0	.	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.08|19.08	3.757454|3.757454	0.69648|0.69648	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637|ENST00000424425	T;T;T|.	0.30182|.	2.14;2.14;1.54|.	5.98|5.98	5.98|5.98	0.97165|0.97165	.|.	0.152547|0.152547	0.28247|0.28247	U|U	0.016055|0.016055	T|T	0.49406|0.49406	0.1555|0.1555	N|N	0.14661|0.14661	0.345|0.345	0.41980|0.41980	D|D	0.990792|0.990792	D|.	0.63880|.	0.993|.	P|.	0.53185|.	0.72|.	T|T	0.47959|0.47959	-0.9076|-0.9076	10|6	0.62326|.	D|.	0.03|.	.|.	16.4731|16.4731	0.84124|0.84124	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1362|.	Q2LD37|.	K1109_HUMAN|.	C|L	1362|1193	ENSP00000264501:F1362C;ENSP00000373390:F1362C;ENSP00000389925:F1362C|.	ENSP00000264501:F1362C|.	F|F	+|+	2|3	0|2	KIAA1109|KIAA1109	123380372|123380372	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.907000|5.907000	0.69908|0.69908	2.293000|2.293000	0.77203|0.77203	0.528000|0.528000	0.53228|0.53228	TTT|TTT	.	.	.	none		0.423	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		G	123160922	T	G	123160922	3	3	250	1	0	0	0	0	1	0	0	0	8215	1841	64	5	4191	5	KIAA1109	4	123160922	Missense_Mutation	SNP	T	TCGA-SX-A7SP-01A-11D-A34Z-10	53963056	123160922	67993354	19	15492											
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123170744	123170744	+	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	ttgtggatgaaactgatcagCaagctgttccagatgtaact	12	12	10	7	0	1	3	1	2	0	1	2	4	2	4	1	1	4	4	1	1	3	3			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr4:123170744C>A	ENST00000264501.4	+	36	5990	c.5617C>A	c.(5617-5619)Caa>Aaa	p.Q1873K	KIAA1109_ENST00000388738.3_Missense_Mutation_p.Q1873K|KIAA1109_ENST00000455637.1_Missense_Mutation_p.Q1873K			Q2LD37	K1109_HUMAN	KIAA1109	1873					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						AACTGATCAGCAAGCTGTTCC	0.383																																					p.Q1873K		Atlas-SNP	.											.	KIAA1109	424	.	0			c.C5617A						PASS	.						126	118	120					4																	123170744		1834	4096	5930	SO:0001583	missense	84162	exon34			GATCAGCAAGCTG	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.5617C>A	chr4.hg19:g.123170744C>A	ENSP00000264501:p.Gln1873Lys	120.0	0.0	.		171.0	59.0	.	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.44|15.44	2.834437|2.834437	0.50951|0.50951	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637|ENST00000446180	T;T;T|.	0.23147|.	2.5;2.5;1.92|.	5.46|5.46	5.46|5.46	0.80206|0.80206	.|.	0.156761|.	0.27289|.	U|.	0.020053|.	T|T	0.54319|0.54319	0.1851|0.1851	N|N	0.19112|0.19112	0.55|0.55	0.44728|0.44728	D|D	0.997724|0.997724	B;B|.	0.18310|.	0.027;0.001|.	B;B|.	0.18561|.	0.022;0.004|.	T|T	0.49021|0.49021	-0.8982|-0.8982	10|5	0.40728|.	T|.	0.16|.	.|.	19.2917|19.2917	0.94102|0.94102	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1872;1873|.	Q2LD37-2;Q2LD37|.	.;K1109_HUMAN|.	K|R	1873|445	ENSP00000264501:Q1873K;ENSP00000373390:Q1873K;ENSP00000389925:Q1873K|.	ENSP00000264501:Q1873K|.	Q|S	+|+	1|3	0|2	KIAA1109|KIAA1109	123390194|123390194	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.931000|0.931000	0.56810|0.56810	4.621000|4.621000	0.61233|0.61233	2.557000|2.557000	0.86248|0.86248	0.455000|0.455000	0.32223|0.32223	CAA|AGC	.	.	.	none		0.383	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		A	123170744	C	A	123170744	3	1	250	1	0	0	0	0	1	0	0	0	8215	711	25	4	5751	4	KIAA1109	4	123170744	Missense_Mutation	SNP	C	TCGA-SX-A7SP-01A-11D-A34Z-10	9822	123170744	67983532	20	15493											
GPR98	84059	hgsc.bcm.edu	37	chr5	90041606	90041606	+	Missense_Mutation	SNP	T	T	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	gcctatggaattgttgcattTgctcaggtaatgatactgaa	11	14	10	6	0	1	2	1	2	0	0	1	3	1	3	1	2	3	4	1	2	5	6			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr5:90041606T>G	ENST00000405460.2	+	52	11064	c.10968T>G	c.(10966-10968)ttT>ttG	p.F3656L		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	3656	Calx-beta 24. {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)		TTGTTGCATTTGCTCAGGTAA	0.343																																					p.F3656L		Atlas-SNP	.											.	GPR98	605	.	0			c.T10968G						PASS	.						110	99	103					5																	90041606		1883	4110	5993	SO:0001583	missense	84059	exon52			TGCATTTGCTCAG	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.10968T>G	chr5.hg19:g.90041606T>G	ENSP00000384582:p.Phe3656Leu	44.0	0.0	.		43.0	13.0	.	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.9|24.9	4.586652|4.586652	0.86851|0.86851	.|.	.|.	ENSG00000164199|ENSG00000164199	ENST00000405460;ENST00000296619|ENST00000509621	T|.	0.28255|.	1.62|.	5.59|5.59	4.43|4.43	0.53597|0.53597	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.78227|0.78227	0.4250|0.4250	M|M	0.89534|0.89534	3.04|3.04	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.999;0.996|.	D;P|.	0.73380|.	0.98;0.836|.	T|T	0.79923|0.79923	-0.1598|-0.1598	10|5	0.72032|.	D|.	0.01|.	.|.	10.2968|10.2968	0.43629|0.43629	0.0:0.0815:0.0:0.9185|0.0:0.0815:0.0:0.9185	.|.	3656;3656|.	E7ETI5;Q8WXG9|.	.;GPR98_HUMAN|.	L|W	3656|1222	ENSP00000384582:F3656L|.	ENSP00000296619:F3656L|.	F|L	+|+	3|2	2|0	GPR98|GPR98	90077362|90077362	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.962000|0.962000	0.63368|0.63368	2.449000|2.449000	0.44935|0.44935	0.953000|0.953000	0.37825|0.37825	0.460000|0.460000	0.39030|0.39030	TTT|TTG	.	.	.	none		0.343	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		G	90041606	T	G	90041606	3	3	250	1	0	0	0	0	1	0	0	0	6728	1809	63	5	11174	5	GPR98	5	90041606	Missense_Mutation	SNP	T	TCGA-SX-A7SP-01A-11D-A34Z-10		90041606	90873654	21	15494											
GRM6	2916	hgsc.bcm.edu	37	chr5	178418914	178418914	+	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	gcctcaaccccactttcgccAtagttgccctcggaggccag	7	8	9	17	2	1	0	1	0	0	0	3	1	1	1	6	2	2	1	6	2	2	3			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr5:178418914A>T	ENST00000517717.1	-	3	713	c.675T>A	c.(673-675)taT>taA	p.Y225*	RP11-281O15.4_ENST00000519491.1_RNA|GRM6_ENST00000231188.5_Nonsense_Mutation_p.Y225*			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	225					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)		CACTTTCGCCATAGTTGCCCT	0.642																																					p.Y225X		Atlas-SNP	.											.	GRM6	149	.	0			c.T675A						PASS	.						76	64	68					5																	178418914		2203	4300	6503	SO:0001587	stop_gained	2916	exon2			TTCGCCATAGTTG	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.675T>A	chr5.hg19:g.178418914A>T	ENSP00000430767:p.Tyr225*	43.0	0.0	.		57.0	23.0	.	NM_000843		Nonsense_Mutation	SNP	ENST00000517717.1	hg19	CCDS4442.1	.	.	.	.	.	.	.	.	.	.	A	38	6.795385	0.97845	.	.	ENSG00000113262	ENST00000319065;ENST00000231188;ENST00000517717	.	.	.	5.48	-1.16	0.09678	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.4038	0.44246	0.5205:0.0:0.4795:0.0	.	.	.	.	X	173;225;225	.	ENSP00000231188:Y225X	Y	-	3	2	GRM6	178351520	0.859000	0.29813	0.992000	0.48379	0.846000	0.48090	0.051000	0.14141	-0.341000	0.08376	0.533000	0.62120	TAT	.	.	.	none		0.642	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2			T	178418914	A	T	178418914	4	4	250	1	0	0	0	0	0	1	0	0	6808	224	8	5	1994	5	GRM6	5	178418914	Nonsense_Mutation	SNP	A	TCGA-SX-A7SP-01A-11D-A34Z-10	88377308	178418914	2496346	22	15495											
SLC22A23	63027	hgsc.bcm.edu	37	chr6	3456326	3456326	+	Frame_Shift_Del	DEL	G	G	-																															gcagtggcgaagggggtggtGgggaggctggtccagttgcc																										TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr6:3456326delG	ENST00000406686.3	-	1	467	c.468delC	c.(466-468)cccfs	p.P156fs	SLC22A23_ENST00000436008.2_Frame_Shift_Del_p.P156fs|SLC22A23_ENST00000380298.2_Frame_Shift_Del_p.P156fs	NM_015482.1	NP_056297.1	A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23	156					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)				AGGGGGTGGTGGGGAGGCTGG	0.731																																					p.T157fs		Atlas-Indel,Pindel	.											.	SLC22A23	89	.	0			c.469delA						PASS	.						8	15	13					6																	3456326		690	1586	2276	SO:0001589	frameshift_variant	63027	exon1			.	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.468delC	chr6.hg19:g.3456326delG	ENSP00000385028:p.Pro156fs	67.0	0.0	0		76.0	21.0	0.276316	NM_015482	A1A5C8|Q5T8B8|Q6ZMH3|Q8IW73	Frame_Shift_Del	DEL	ENST00000406686.3	hg19	CCDS47363.1																																																																																			.	.	.	none		0.731	SLC22A23-006	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353059.1	NM_021945		-	3456326	G	-	3456326	7	5	250	1	0	1	0	1	0	0	0	0	14465	1335	47	0	1632	0	SLC22A23	6	3456326	Frame_Shift_Del	DEL	G	TCGA-SX-A7SP-01A-11D-A34Z-10		3456326	167658741	23	15496											
C6orf153	88745	hgsc.bcm.edu	37	chr6	42995142	42995142	+	Missense_Mutation	SNP	G	G	C																															gaacgaaagcaacagcaggaGctgcacctggccctgaagca																										TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr6:42995142G>C	ENST00000244496.5	+	6	580	c.570G>C	c.(568-570)gaG>gaC	p.E190D		NM_033112.2	NP_149103.1	Q96EU6	RRP36_HUMAN	ribosomal RNA processing 36 homolog (S. cerevisiae)	190					ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(5)|lung(1)|ovary(1)|prostate(1)	11						AACAGCAGGAGCTGCACCTGG	0.532																																					p.E190D		Atlas-SNP	.											.	RRP36	20	.	0			c.G570C						PASS	.						65	60	62					6																	42995142		2203	4300	6503	SO:0001583	missense	88745	exon6			GCAGGAGCTGCAC	BC011933	CCDS34453.1	6p21.1	2010-07-06	2010-07-06	2010-07-06	ENSG00000124541	ENSG00000124541			21374	protein-coding gene	gene with protein product		613475	"chromosome 6 open reading frame 153"	C6orf153		20038530	Standard	NM_033112		Approved	dJ20C7.4	uc003otp.1	Q96EU6	OTTHUMG00000014715	ENST00000244496.5:c.570G>C	chr6.hg19:g.42995142G>C	ENSP00000244496:p.Glu190Asp	84.0	0.0	.		85.0	33.0	.	NM_033112	Q9BRF6|Q9P0C8	Missense_Mutation	SNP	ENST00000244496.5	hg19	CCDS34453.1	.	.	.	.	.	.	.	.	.	.	G	10.83	1.462215	0.26248	.	.	ENSG00000124541	ENST00000244496	T	0.52295	0.67	5.55	-0.557	0.11800	.	0.254509	0.29653	N	0.011549	T	0.21267	0.0512	L	0.53617	1.68	0.32097	N	0.591077	B	0.30482	0.281	B	0.34931	0.192	T	0.04635	-1.0937	10	0.51188	T	0.08	.	5.2928	0.15737	0.4791:0.1479:0.373:0.0	.	190	Q96EU6	RRP36_HUMAN	D	190	ENSP00000244496:E190D	ENSP00000244496:E190D	E	+	3	2	RRP36	43103120	1.000000	0.71417	0.849000	0.33467	0.153000	0.21895	1.358000	0.34102	0.030000	0.15379	0.462000	0.41574	GAG	.	.	.	none		0.532	RRP36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040572.1	NM_033112		C	42995142	G	C	42995142	3	2	250	1	0	0	0	0	1	0	0	0	2340	962	34	4	592	4	C6orf153	6	42995142	Missense_Mutation	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10	39538816	42995142	128119925	24	15497	159	2									
C6orf153	88745	hgsc.bcm.edu	37	chr6	42995151	42995151	+	Silent	SNP	G	G	C																															caacagcaggagctgcacctGgccctgaagcaagaacgtcg																										TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr6:42995151G>C	ENST00000244496.5	+	6	589	c.579G>C	c.(577-579)ctG>ctC	p.L193L		NM_033112.2	NP_149103.1	Q96EU6	RRP36_HUMAN	ribosomal RNA processing 36 homolog (S. cerevisiae)	193					ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(5)|lung(1)|ovary(1)|prostate(1)	11						AGCTGCACCTGGCCCTGAAGC	0.552																																					p.L193L		Atlas-SNP	.											.	RRP36	20	.	0			c.G579C						PASS	.						64	60	62					6																	42995151		2203	4300	6503	SO:0001819	synonymous_variant	88745	exon6			GCACCTGGCCCTG	BC011933	CCDS34453.1	6p21.1	2010-07-06	2010-07-06	2010-07-06	ENSG00000124541	ENSG00000124541			21374	protein-coding gene	gene with protein product		613475	"chromosome 6 open reading frame 153"	C6orf153		20038530	Standard	NM_033112		Approved	dJ20C7.4	uc003otp.1	Q96EU6	OTTHUMG00000014715	ENST00000244496.5:c.579G>C	chr6.hg19:g.42995151G>C		88.0	0.0	.		84.0	31.0	.	NM_033112	Q9BRF6|Q9P0C8	Silent	SNP	ENST00000244496.5	hg19	CCDS34453.1																																																																																			.	.	.	none		0.552	RRP36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040572.1	NM_033112		C	42995151	G	C	42995151	2	2	250	1	0	0	0	0	0	0	0	1	2340	1335	47	4		4	C6orf153	6	42995151	Silent	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10	9	42995151	128119916	25	15498	159	2									
BMPER	168667	hgsc.bcm.edu	37	chr7	34125603	34125603	+	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	gtgcctgaactgtgtcaaggGacagtcaaggtaaagctccg	11	8	13	9	1	2	1	2	1	0	0	3	2	3	2	2	2	3	2	2	2	5	1			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr7:34125603G>A	ENST00000297161.2	+	14	2018	c.1644G>A	c.(1642-1644)ggG>ggA	p.G548G	BMPER_ENST00000426693.1_Silent_p.G548G	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	548	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|endothelial cell activation (GO:0042118)|inner ear development (GO:0048839)|negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of endothelial cell migration (GO:0010594)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|ureteric bud development (GO:0001657)	extracellular space (GO:0005615)				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						TGTGTCAAGGGACAGTCAAGG	0.507																																					p.G548G		Atlas-SNP	.											.	BMPER	131	.	0			c.G1644A						PASS	.						143	136	138					7																	34125603		2203	4300	6503	SO:0001819	synonymous_variant	168667	exon14			TCAAGGGACAGTC		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.1644G>A	chr7.hg19:g.34125603G>A		66.0	0.0	.		128.0	24.0	.	NM_133468	A8K1P8|Q8TF36	Silent	SNP	ENST00000297161.2	hg19	CCDS5442.1																																																																																			.	.	.	none		0.507	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468		A	34125603	G	A	34125603	2	1	250	1	0	0	0	0	0	0	0	1	1468	1161	41	2		2	BMPER	7	34125603	Silent	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10		34125603	125013060	26	15499											
MUC17	140453	hgsc.bcm.edu	37	chr7	100683299	100683299	+	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	tctcaactgctagtgaaggaAgtactctattaacaagtata	15	12	7	7	0	2	1	1	1	2	0	3	2	2	2	0	1	4	3	0	1	10	6			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr7:100683299A>T	ENST00000306151.4	+	3	8666	c.8602A>T	c.(8602-8604)Agt>Tgt	p.S2868C		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2868	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)					TAGTGAAGGAAGTACTCTATT	0.488																																					p.S2868C		Atlas-SNP	.											.	MUC17	804	.	0			c.A8602T						PASS	.						249	259	255					7																	100683299		2203	4300	6503	SO:0001583	missense	140453	exon3			GAAGGAAGTACTC	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.8602A>T	chr7.hg19:g.100683299A>T	ENSP00000302716:p.Ser2868Cys	51.0	0.0	.		82.0	38.0	.	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	6.149	0.395626	0.11638	.	.	ENSG00000169876	ENST00000306151	T	0.02682	4.2	0.911	-0.0914	0.13661	.	.	.	.	.	T	0.03651	0.0104	L	0.34521	1.04	0.09310	N	1	D	0.54964	0.969	P	0.49477	0.612	T	0.43653	-0.9378	9	0.62326	D	0.03	.	4.9824	0.14172	0.2504:0.0:0.7496:0.0	.	2868	Q685J3	MUC17_HUMAN	C	2868	ENSP00000302716:S2868C	ENSP00000302716:S2868C	S	+	1	0	MUC17	100470019	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.325000	0.07976	-0.037000	0.13646	0.113000	0.15668	AGT	.	.	.	none		0.488	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		T	100683299	A	T	100683299	3	4	250	1	0	0	0	0	1	0	0	0	9981	72	3	5	8612	5	MUC17	7	100683299	Missense_Mutation	SNP	A	TCGA-SX-A7SP-01A-11D-A34Z-10	66557696	100683299	58455364	27	15500											
ZNF862	643641	hgsc.bcm.edu	37	chr7	149545262	149545262	+	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	cagagacccacctggagatgTtctggccagcccggagccgc	8	5	13	15	2	1	2	0	0	1	2	1	5	1	3	5	3	2	1	5	3	0	1			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr7:149545262T>A	ENST00000223210.4	+	4	925	c.680T>A	c.(679-681)gTt>gAt	p.V227D		NM_001099220.1	NP_001092690.1	O60290	ZN862_HUMAN	zinc finger protein 862	227					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(1)	34						CCTGGAGATGTTCTGGCCAGC	0.607																																					p.V227D		Atlas-SNP	.											.	ZNF862	97	.	0			c.T680A						PASS	.						44	47	46					7																	149545262		1924	4142	6066	SO:0001583	missense	643641	exon4			GAGATGTTCTGGC	AB011115	CCDS47741.1	7q36.1	2013-01-11			ENSG00000106479	ENSG00000106479		"Zinc fingers, C2H2-type", "-"	34519	protein-coding gene	gene with protein product							Standard	NM_001099220		Approved		uc010lpn.3	O60290	OTTHUMG00000158093	ENST00000223210.4:c.680T>A	chr7.hg19:g.149545262T>A	ENSP00000223210:p.Val227Asp	51.0	0.0	.		81.0	37.0	.	NM_001099220	A0AUL8	Missense_Mutation	SNP	ENST00000223210.4	hg19	CCDS47741.1	.	.	.	.	.	.	.	.	.	.	T	8.241	0.806878	0.16467	.	.	ENSG00000106479	ENST00000223210	T	0.01159	5.25	4.92	1.13	0.20643	.	1.177670	0.06440	N	0.725840	T	0.01320	0.0043	L	0.40543	1.245	0.09310	N	1	P	0.40476	0.718	B	0.36030	0.216	T	0.48692	-0.9013	10	0.87932	D	0	-22.1868	4.9891	0.14205	0.0:0.0975:0.3728:0.5297	.	227	O60290	ZN862_HUMAN	D	227	ENSP00000223210:V227D	ENSP00000223210:V227D	V	+	2	0	ZNF862	149176195	0.000000	0.05858	0.000000	0.03702	0.190000	0.23558	0.176000	0.16782	0.194000	0.20326	-0.313000	0.08912	GTT	.	.	.	none		0.607	ZNF862-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350165.1	NM_001099220		A	149545262	T	A	149545262	3	1	250	1	0	0	0	0	1	0	0	0	18207	1725	60	5	694	5	ZNF862	7	149545262	Missense_Mutation	SNP	T	TCGA-SX-A7SP-01A-11D-A34Z-10	48861963	149545262	9593401	28	15501											
NFX1	4799	hgsc.bcm.edu	37	chr9	33295177	33295177	+	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	acgaccaggcagaaatccacCaaaacaggagggccaccgac	16	1	10	14	2	0	1	0	0	0	1	1	4	1	2	5	3	1	1	5	3	3	0			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr9:33295177C>T	ENST00000379540.3	+	2	847	c.785C>T	c.(784-786)cCa>cTa	p.P262L	NFX1_ENST00000318524.6_Missense_Mutation_p.P262L|NFX1_ENST00000379521.4_Missense_Mutation_p.P262L	NM_002504.4	NP_002495.2	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1	262					inflammatory response (GO:0006954)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)		AGAAATCCACCAAAACAGGAG	0.532																																					p.P262L		Atlas-SNP	.											.	NFX1	85	.	0			c.C785T						PASS	.						107	103	104					9																	33295177		2203	4300	6503	SO:0001583	missense	4799	exon2			ATCCACCAAAACA	U19759	CCDS6538.1, CCDS6539.1, CCDS6540.1	9p12	2013-12-13			ENSG00000086102	ENSG00000086102			7803	protein-coding gene	gene with protein product		603255				7964459, 2511169	Standard	NM_002504		Approved	NFX2, MGC20369, Tex42, TEG-42	uc003zsq.3	Q12986	OTTHUMG00000019772	ENST00000379540.3:c.785C>T	chr9.hg19:g.33295177C>T	ENSP00000368856:p.Pro262Leu	29.0	0.0	.		40.0	5.0	.	NM_147134	A8K6H8|Q5VXW6|Q96EL5|Q9BXI1	Missense_Mutation	SNP	ENST00000379540.3	hg19	CCDS6538.1	.	.	.	.	.	.	.	.	.	.	C	9.924	1.213089	0.22289	.	.	ENSG00000086102	ENST00000379540;ENST00000379521;ENST00000536210;ENST00000318524	T;T;T	0.42131	0.98;0.98;0.98	5.38	3.33	0.38152	.	0.490876	0.21846	N	0.068253	T	0.32285	0.0824	L	0.41236	1.265	0.36408	D	0.863562	P;P;P;P;P	0.50272	0.763;0.651;0.933;0.763;0.763	B;B;B;B;P	0.44897	0.361;0.153;0.386;0.293;0.463	T	0.28202	-1.0051	10	0.29301	T	0.29	.	5.9995	0.19513	0.1639:0.6577:0.0:0.1784	.	262;146;262;262;262	F5GXD0;A0JLR2;Q12986;Q12986-2;Q12986-3	.;.;NFX1_HUMAN;.;.	L	262	ENSP00000368856:P262L;ENSP00000368836:P262L;ENSP00000317695:P262L	ENSP00000317695:P262L	P	+	2	0	NFX1	33285177	0.613000	0.27009	0.998000	0.56505	0.550000	0.35303	1.142000	0.31540	1.265000	0.44215	0.551000	0.68910	CCA	.	.	.	none		0.532	NFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052069.1			T	33295177	C	T	33295177	3	4	250	1	0	0	0	0	1	0	0	0	10394	594	21	2	791	2	NFX1	9	33295177	Missense_Mutation	SNP	C	TCGA-SX-A7SP-01A-11D-A34Z-10		33295177	107918254	29	15502											
CDK5RAP2	55755	hgsc.bcm.edu	37	chr9	123313158	123313158	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagctttaggttaaagtttTctttcttcaattcagtgatt	9	19	8	5	0	4	1	2	1	2	0	4	2	4	2	0	2	1	3	0	2	4	9			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr9:123313158T>C	ENST00000349780.4	-	4	397	c.218A>G	c.(217-219)gAa>gGa	p.E73G	CDK5RAP2_ENST00000360190.4_Missense_Mutation_p.E73G|CDK5RAP2_ENST00000360822.3_Missense_Mutation_p.E73G|CDK5RAP2_ENST00000359309.3_Missense_Mutation_p.E73G	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	73					brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)			breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						GTTAAAGTTTTCTTTCTTCAA	0.393																																					p.E73G		Atlas-SNP	.											.	CDK5RAP2	157	.	0			c.A218G						PASS	.						97	100	99					9																	123313158		2203	4300	6503	SO:0001583	missense	55755	exon4			AAGTTTTCTTTCT	BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"centrosomin"	608201	"microcephaly, primary autosomal recessive 3"	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.218A>G	chr9.hg19:g.123313158T>C	ENSP00000343818:p.Glu73Gly	125.0	0.0	.		155.0	54.0	.	NM_018249	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Missense_Mutation	SNP	ENST00000349780.4	hg19	CCDS6823.1	.	.	.	.	.	.	.	.	.	.	T	29.1	4.976257	0.92982	.	.	ENSG00000136861	ENST00000360822;ENST00000359309;ENST00000349780;ENST00000360190;ENST00000345313	T;T;T;T	0.50813	0.73;0.73;0.73;0.73	6.08	6.08	0.98989	Spindle associated (1);	0.000000	0.64402	D	0.000011	T	0.74861	0.3772	M	0.89601	3.045	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	0.80484	-0.1362	10	0.87932	D	0	.	15.6338	0.76933	0.0:0.0:0.0:1.0	.	73;73;73	Q96SN8-2;Q96SN8-4;Q96SN8	.;.;CK5P2_HUMAN	G	73	ENSP00000354065:E73G;ENSP00000352258:E73G;ENSP00000343818:E73G;ENSP00000353317:E73G	ENSP00000341695:E73G	E	-	2	0	CDK5RAP2	122352979	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.545000	0.82128	2.333000	0.79357	0.482000	0.46254	GAA	.	.	.	none		0.393	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249		C	123313158	T	C	123313158	3	2	250	1	0	0	0	0	1	0	0	0	3148	1783	62	3	5603	3	CDK5RAP2	9	123313158	Missense_Mutation	SNP	T	TCGA-SX-A7SP-01A-11D-A34Z-10	90017981	123313158	17900273	30	15503											
BAT2L1	84726	hgsc.bcm.edu	37	chr9	134319670	134319670	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggctggcaaagaaaagggcGtcttagatctgtcgtatggg	11	9	15	6	2	2	2	0	0	2	2	3	2	2	2	0	4	0	3	0	4	5	2			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr9:134319670G>A	ENST00000357304.4	+	5	623	c.568G>A	c.(568-570)Gtc>Atc	p.V190I	PRRC2B_ENST00000458550.1_Missense_Mutation_p.V190I|PRRC2B_ENST00000405995.1_Missense_Mutation_p.V190I|PRRC2B_ENST00000372249.1_5'Flank	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	190							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						AGAAAAGGGCGTCTTAGATCT	0.552																																					p.V190I		Atlas-SNP	.											PRRC2B_ENST00000357304,NS,carcinoma,0,2	PRRC2B	266	.	0			c.G568A						PASS	.						49	51	50					9																	134319670		2038	4199	6237	SO:0001583	missense	84726	exon5			AAGGGCGTCTTAG	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.568G>A	chr9.hg19:g.134319670G>A	ENSP00000349856:p.Val190Ile	28.0	0.0	.		34.0	11.0	.	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	hg19	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.273583	0.80580	.	.	ENSG00000130723	ENST00000405995;ENST00000541684;ENST00000357304;ENST00000458550	T;T;T	0.21191	2.02;2.02;2.02	5.54	5.54	0.83059	BAT2, N-terminal (1);	0.410913	0.17223	U	0.182247	T	0.23846	0.0577	L	0.44542	1.39	0.80722	D	1	P	0.45428	0.858	B	0.40741	0.339	T	0.01977	-1.1236	10	0.49607	T	0.09	-25.7014	18.4643	0.90749	0.0:0.0:1.0:0.0	.	190	Q5JSZ5	PRC2B_HUMAN	I	190	ENSP00000384606:V190I;ENSP00000349856:V190I;ENSP00000398853:V190I	ENSP00000349856:V190I	V	+	1	0	PRRC2B	133309491	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.436000	0.66538	2.618000	0.88619	0.462000	0.41574	GTC	.	.	.	none		0.552	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	134319670	G	A	134319670	3	1	250	1	0	0	0	0	1	0	0	0	1320	1145	40	1	586	1	BAT2L1	9	134319670	Missense_Mutation	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10	11006512	134319670	6893761	31	15504											
ZNF37A	7587	hgsc.bcm.edu	37	chr10	38406703	38406703	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtaatgaatgtggagaaaaTatctttgaggaatccattct	14	13	10	4	0	2	3	0	2	2	1	3	5	3	4	1	3	0	1	1	3	6	4			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr10:38406703T>C	ENST00000361085.5	+	7	969	c.624T>C	c.(622-624)aaT>aaC	p.N208N	ZNF37A_ENST00000351773.3_Silent_p.N208N	NM_001178101.1|NM_003421.2	NP_001171572.1|NP_003412.1	P17032	ZN37A_HUMAN	zinc finger protein 37A	208					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|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						GTGGAGAAAATATCTTTGAGG	0.363																																					p.N208N		Atlas-SNP	.											.	ZNF37A	118	.	0			c.T624C						PASS	.						76	74	75					10																	38406703		2203	4300	6503	SO:0001819	synonymous_variant	7587	exon7			AGAAAATATCTTT	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.624T>C	chr10.hg19:g.38406703T>C		82.0	0.0	.		109.0	31.0	.	NM_003421	B3KRQ3|D3DRZ3|Q96B88	Silent	SNP	ENST00000361085.5	hg19	CCDS31183.1																																																																																			.	.	.	none		0.363	ZNF37A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047624.2	NM_003421		C	38406703	T	C	38406703	2	2	250	1	0	0	0	0	0	0	0	1	17884	1403	49	3		3	ZNF37A	10	38406703	Silent	SNP	T	TCGA-SX-A7SP-01A-11D-A34Z-10		38406703	97128044	32	15505											
SYT15	83849	hgsc.bcm.edu	37	chr10	46968622	46968622	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggcagcagctctgatgccGggcaggggtcccatggggca	7	5	18	11	1	1	1	0	1	1	0	2	2	2	1	2	6	3	5	2	6	0	0	rs577411839	byFrequency	TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr10:46968622G>A	ENST00000374321.4	-	3	380	c.314C>T	c.(313-315)cCg>cTg	p.P105L	SYT15_ENST00000503753.1_Missense_Mutation_p.P105L|SYT15_ENST00000374323.4_Missense_Mutation_p.P158L|RP11-38L15.3_ENST00000506914.1_RNA|SYT15_ENST00000374325.3_Missense_Mutation_p.P105L	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV	105						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						CTCTGATGCCGGGCAGGGGTC	0.677													G|||	2	0.000399361	0	0.0014	5008	,	,		34493	0		0	False		,,,				2504	0.001				p.P105L	Ovarian(57;1152 1428 19651 37745)	Atlas-SNP	.											.	SYT15	165	.	0			c.C314T						PASS	.						32	41	38					10																	46968622		2079	4209	6288	SO:0001583	missense	83849	exon3			GATGCCGGGCAGG	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.314C>T	chr10.hg19:g.46968622G>A	ENSP00000363441:p.Pro105Leu	16.0	0.0	.		24.0	6.0	.	NM_031912	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	Missense_Mutation	SNP	ENST00000374321.4	hg19	CCDS44376.1	.	.	.	.	.	.	.	.	.	.	.	0.006	-2.028849	0.00410	.	.	ENSG00000204176	ENST00000416127;ENST00000374325;ENST00000503753;ENST00000374323;ENST00000374321	T;T;T;T	0.14022	2.54;2.54;2.84;2.78	4.59	-3.51	0.04696	.	0.916532	0.09209	N	0.833581	T	0.05364	0.0142	N	0.16066	0.365	0.09310	N	0.999991	B;B	0.14012	0.002;0.009	B;B	0.11329	0.001;0.006	T	0.44436	-0.9328	10	0.08179	T	0.78	.	4.409	0.11423	0.3898:0.0:0.3705:0.2397	.	105;105	Q9BQS2;Q9BQS2-2	SYT15_HUMAN;.	L	105;105;105;158;105	ENSP00000363445:P105L;ENSP00000427607:P105L;ENSP00000363443:P158L;ENSP00000363441:P105L	ENSP00000363441:P105L	P	-	2	0	SYT15	46388628	0.001000	0.12720	0.001000	0.08648	0.005000	0.04900	-0.097000	0.11042	-0.539000	0.06273	-0.263000	0.10527	CCG	.	.	.	none		0.677	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367008.1	NM_031912		A	46968622	G	A	46968622	3	1	250	1	0	0	0	0	1	0	0	0	15483	1116	39	1	1029	1	SYT15	10	46968622	Missense_Mutation	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10	8561919	46968622	88566125	33	15506											
CNNM2	54805	hgsc.bcm.edu	37	chr10	104678459	104678459	+	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	gagaatgaggagacggtgatCatcgggctgcgactggagga	11	6	18	6	3	1	4	1	2	0	2	2	9	1	6	0	5	1	1	0	5	1	0			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr10:104678459C>A	ENST00000369878.4	+	1	410	c.222C>A	c.(220-222)atC>atA	p.I74I	CNNM2_ENST00000369875.3_Silent_p.I74I|CNNM2_ENST00000433628.2_Silent_p.I74I	NM_017649.4	NP_060119.3	Q9H8M5	CNNM2_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 2	74					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)		AGACGGTGATCATCGGGCTGC	0.706																																					p.I74I		Atlas-SNP	.											.	CNNM2	119	.	0			c.C222A						PASS	.						33	20	24					10																	104678459		2168	4270	6438	SO:0001819	synonymous_variant	54805	exon1			GGTGATCATCGGG	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.222C>A	chr10.hg19:g.104678459C>A		26.0	0.0	.		28.0	11.0	.	NM_199076	Q5T569|Q5T570|Q8WU59|Q9H952|Q9NRK5|Q9NXT4	Silent	SNP	ENST00000369878.4	hg19	CCDS44474.1																																																																																			.	.	.	none		0.706	CNNM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050113.3	NM_017649		A	104678459	C	A	104678459	2	1	250	1	0	0	0	0	0	0	0	1	3615	816	29	4		4	CNNM2	10	104678459	Silent	SNP	C	TCGA-SX-A7SP-01A-11D-A34Z-10	57709837	104678459	30856288	34	15507											
OR10A6	390093	hgsc.bcm.edu	37	chr11	7949415	7949415	+	Silent	SNP	G	G	C																															ttcttggtttccggtgagtaGccagatttgggttgtaaata																										TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr11:7949415G>C	ENST00000309838.2	-	1	794	c.795C>G	c.(793-795)ggC>ggG	p.G265G		NM_001004461.1	NP_001004461.1	Q8NH74	O10A6_HUMAN	olfactory receptor, family 10, subfamily A, member 6	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)|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)		CCGGTGAGTAGCCAGATTTGG	0.453																																					p.G265G		Atlas-SNP	.											.	OR10A6	49	.	0			c.C795G						PASS	.						148	137	141					11																	7949415		2201	4296	6497	SO:0001819	synonymous_variant	390093	exon1			TGAGTAGCCAGAT	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.795C>G	chr11.hg19:g.7949415G>C		134.0	0.0	.		140.0	53.0	.	NM_001004461	Q6IF59	Silent	SNP	ENST00000309838.2	hg19	CCDS31420.1																																																																																			.	.	.	none		0.453	OR10A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385703.1	NM_001004461		C	7949415	G	C	7949415	2	2	250	1	0	0	0	0	0	0	0	1	10901	958	34	4		4	OR10A6	11	7949415	Silent	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10		7949415	127057101	35	15508	160	2									
OR10A6	390093	hgsc.bcm.edu	37	chr11	7949417	7949417	+	Missense_Mutation	SNP	C	C	T																															cttggtttccggtgagtagcCagatttgggttgtaaataag																								rs374770684		TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr11:7949417C>T	ENST00000309838.2	-	1	792	c.793G>A	c.(793-795)Ggc>Agc	p.G265S		NM_001004461.1	NP_001004461.1	Q8NH74	O10A6_HUMAN	olfactory receptor, family 10, subfamily A, member 6	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)|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)		GGTGAGTAGCCAGATTTGGGT	0.453																																					p.G265S		Atlas-SNP	.											.	OR10A6	49	.	0			c.G793A						PASS	.	C	SER/GLY	1,4401	2.1+/-5.4	0,1,2200	148	137	140		793	0.8	1	11		140	0,8592		0,0,4296	no	missense	OR10A6	NM_001004461.1	56	0,1,6496	TT,TC,CC		0.0,0.0227,0.0077	benign	265/315	7949417	1,12993	2201	4296	6497	SO:0001583	missense	390093	exon1			AGTAGCCAGATTT	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.793G>A	chr11.hg19:g.7949417C>T	ENSP00000312470:p.Gly265Ser	130.0	0.0	.		138.0	50.0	.	NM_001004461	Q6IF59	Missense_Mutation	SNP	ENST00000309838.2	hg19	CCDS31420.1	.	.	.	.	.	.	.	.	.	.	C	1.923	-0.447830	0.04572	2.27E-4	0.0	ENSG00000175393	ENST00000309838	T	0.00058	8.79	4.43	0.818	0.18778	GPCR, rhodopsin-like superfamily (1);	0.926234	0.08901	N	0.877249	T	0.00039	0.0001	N	0.00873	-1.125	0.09310	N	1	B	0.18013	0.025	B	0.24541	0.054	T	0.09862	-1.0655	10	0.02654	T	1	.	6.8267	0.23887	0.0:0.3001:0.0:0.6999	.	265	Q8NH74	O10A6_HUMAN	S	265	ENSP00000312470:G265S	ENSP00000312470:G265S	G	-	1	0	OR10A6	7905993	0.000000	0.05858	0.973000	0.42090	0.985000	0.73830	-0.216000	0.09266	0.316000	0.23135	0.655000	0.94253	GGC	.	.	.	weak		0.453	OR10A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385703.1	NM_001004461		T	7949417	C	T	7949417	3	4	250	1	0	0	0	0	1	0	0	0	10901	594	21	2	154	2	OR10A6	11	7949417	Missense_Mutation	SNP	C	TCGA-SX-A7SP-01A-11D-A34Z-10	2	7949417	127057099	36	15509	160	2									
TMX2	51075	hgsc.bcm.edu	37	chr11	57506447	57506447	+	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	aataatatattcttttcagaTacaactgtacagggctaaat	16	14	5	6	0	2	1	1	0	1	1	2	1	2	1	0	1	3	2	0	1	9	9			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr11:57506447T>A	ENST00000278422.4	+	6	562	c.550T>A	c.(550-552)Tac>Aac	p.Y184N	C11orf31_ENST00000388857.4_5'Flank|C11orf31_ENST00000534355.1_5'Flank|TMX2_ENST00000378312.4_Splice_Site_p.Y146N|TMX2-CTNND1_ENST00000528395.1_Intron	NM_015959.3	NP_057043.1	Q9Y320	TMX2_HUMAN	thioredoxin-related transmembrane protein 2	184	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|urinary_tract(2)	12						TCTTTTCAGATACAACTGTAC	0.398																																					p.Y184N		Atlas-SNP	.											.	TMX2	29	.	0			c.T550A						PASS	.						77	77	77					11																	57506447		2201	4296	6497	SO:0001630	splice_region_variant	51075	exon6			TTCAGATACAACT	AF132965	CCDS7967.1, CCDS44601.1	11q12.1	2012-09-20	2009-02-23	2009-02-23	ENSG00000213593	ENSG00000213593		"Protein disulfide isomerases"	30739	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 12"		"thioredoxin domain containing 14"	TXNDC14		12670024	Standard	NM_015959		Approved	PDIA12	uc001nlc.2	Q9Y320	OTTHUMG00000167200	ENST00000278422.4:c.549-1T>A	chr11.hg19:g.57506447T>A		71.0	0.0	.		85.0	16.0	.	NM_015959	B7Z4R4|Q53G73|Q561W0|Q5J7Q7|Q8NBP9|Q9H3L1	Missense_Mutation	SNP	ENST00000278422.4	hg19	CCDS7967.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.375394	0.82682	.	.	ENSG00000213593	ENST00000378312;ENST00000278422	T;T	0.26810	1.71;1.71	5.95	5.95	0.96441	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.000000	0.85682	U	0.000000	T	0.52041	0.1710	M	0.74389	2.26	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.55451	-0.8139	10	0.87932	D	0	-5.8569	14.6535	0.68814	0.0:0.0:0.0:1.0	.	146;184	Q9Y320-2;Q9Y320	.;TMX2_HUMAN	N	146;184	ENSP00000367562:Y146N;ENSP00000278422:Y184N	ENSP00000278422:Y184N	Y	+	1	0	TMX2	57263023	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	7.033000	0.76504	2.279000	0.76181	0.533000	0.62120	TAC	.	.	.	none		0.398	TMX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393708.1	NM_015959	Missense_Mutation	A	57506447	T	A	57506447	5	1	250	1	0	0	0	0	0	0	1	0	16279	1420	49	5	572	5	TMX2	11	57506447	Splice_Site	SNP	T	TCGA-SX-A7SP-01A-11D-A34Z-10	49557030	57506447	77500069	37	15510											
CNTN5	53942	hgsc.bcm.edu	37	chr11	99690484	99690484	+	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	tttatcattcctcagatgccTtcaaacaagatggtaagtgt	12	14	7	8	0	3	2	3	0	0	2	4	2	4	2	2	1	2	1	2	1	4	5	rs199899455		TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr11:99690484T>A	ENST00000524871.1	+	4	555	c.265T>A	c.(265-267)Ttc>Atc	p.F89I	CNTN5_ENST00000528682.1_Missense_Mutation_p.F89I|CNTN5_ENST00000527185.1_Missense_Mutation_p.F89I|CNTN5_ENST00000279463.3_Missense_Mutation_p.F89I|CNTN5_ENST00000418526.2_Intron	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	89					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)		CTCAGATGCCTTCAAACAAGA	0.413																																					p.F89I		Atlas-SNP	.											.	CNTN5	324	.	0			c.T265A						PASS	.						27	26	26					11																	99690484		1829	4069	5898	SO:0001583	missense	53942	exon3			GATGCCTTCAAAC	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.265T>A	chr11.hg19:g.99690484T>A	ENSP00000435637:p.Phe89Ile	51.0	0.0	.		64.0	7.0	.	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	hg19	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	T	18.04	3.534345	0.64972	.	.	ENSG00000149972	ENST00000527185;ENST00000528682;ENST00000524871;ENST00000279463	T;T;T;T	0.55413	0.52;0.59;0.59;0.59	5.06	5.06	0.68205	.	0.238319	0.36234	N	0.002702	T	0.37376	0.1001	N	0.19112	0.55	0.44745	D	0.997741	B;B	0.27823	0.19;0.19	B;B	0.21151	0.02;0.033	T	0.20638	-1.0269	10	0.35671	T	0.21	.	14.699	0.69142	0.0:0.0:0.0:1.0	.	89;89	E9PKE8;O94779	.;CNTN5_HUMAN	I	89	ENSP00000433575:F89I;ENSP00000436185:F89I;ENSP00000435637:F89I;ENSP00000279463:F89I	ENSP00000279463:F89I	F	+	1	0	CNTN5	99195694	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	5.260000	0.65490	2.208000	0.71279	0.528000	0.53228	TTC	.	.	.	weak		0.413	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361		A	99690484	T	A	99690484	3	1	250	1	0	0	0	0	1	0	0	0	3646	1609	56	5	271	5	CNTN5	11	99690484	Missense_Mutation	SNP	T	TCGA-SX-A7SP-01A-11D-A34Z-10	42184037	99690484	35316032	38	15511											
DDX10	1662	hgsc.bcm.edu	37	chr11	108535923	108535923	+	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	cgggttcgggagcccgacccGacccggtgcggagcttcaat	6	6	15	14	6	1	0	1	0	0	0	2	4	1	2	3	4	3	2	3	4	1	2			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr11:108535923G>A	ENST00000322536.3	+	1	172	c.43G>A	c.(43-45)Gac>Aac	p.D15N	DDX10_ENST00000526794.1_Missense_Mutation_p.D15N	NM_004398.2	NP_004389.2	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	15					metabolic process (GO:0008152)		ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			breast(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|prostate(2)	27		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		AGCCCGACCCGACCCGGTGCG	0.582			T	NUP98	AML*																																p.D15N		Atlas-SNP	.		Dom	yes		11	11q22-q23	1662	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10		L	.	DDX10	70	.	0			c.G43A						PASS	.						26	31	29					11																	108535923		2198	4297	6495	SO:0001583	missense	1662	exon1			CGACCCGACCCGG	U28042	CCDS8342.1	11q22-q23	2005-10-11	2003-06-13		ENSG00000178105	ENSG00000178105		"DEAD-boxes"	2735	protein-coding gene	gene with protein product		601235	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 10 (RNA helicase)"			8660968	Standard	NM_004398		Approved	HRH-J8	uc001pkm.3	Q13206	OTTHUMG00000166540	ENST00000322536.3:c.43G>A	chr11.hg19:g.108535923G>A	ENSP00000314348:p.Asp15Asn	58.0	0.0	.		62.0	16.0	.	NM_004398	B2RCQ3|Q5BJD8	Missense_Mutation	SNP	ENST00000322536.3	hg19	CCDS8342.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.011847	0.93346	.	.	ENSG00000178105	ENST00000322536;ENST00000456020;ENST00000526794	T;T	0.44083	0.94;0.93	5.55	4.63	0.57726	.	0.240683	0.47852	D	0.000210	T	0.54935	0.1889	M	0.64997	1.995	0.34465	D	0.702219	D;D	0.89917	0.999;1.0	P;P	0.57911	0.734;0.829	T	0.66296	-0.5959	10	0.32370	T	0.25	-18.9435	14.3605	0.66768	0.0:0.1482:0.8518:0.0	.	15;15	Q13206;E9PIF2	DDX10_HUMAN;.	N	15	ENSP00000314348:D15N;ENSP00000432032:D15N	ENSP00000314348:D15N	D	+	1	0	DDX10	108041133	1.000000	0.71417	0.944000	0.38274	0.941000	0.58515	5.141000	0.64814	1.317000	0.45149	0.484000	0.47621	GAC	.	.	.	none		0.582	DDX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390343.1	NM_004398		A	108535923	G	A	108535923	3	1	250	1	0	0	0	0	1	0	0	0	4344	1058	37	1	45	1	DDX10	11	108535923	Missense_Mutation	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10	8845439	108535923	26470593	39	15512											
STRAP	11171	hgsc.bcm.edu	37	chr12	16043580	16043580	+	Frame_Shift_Del	DEL	A	A	-																															ggataaactgttacgcatatAtgacttgaacaaacctgaag																										TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr12:16043580delA	ENST00000419869.2	+	4	693	c.380delA	c.(379-381)tatfs	p.Y127fs	STRAP_ENST00000538352.1_Frame_Shift_Del_p.Y33fs|STRAP_ENST00000025399.6_Frame_Shift_Del_p.Y140fs	NM_007178.3	NP_009109.3	Q9Y3F4	STRAP_HUMAN	serine/threonine kinase receptor associated protein	127					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)				TTACGCATATATGACTTGAAC	0.279																																					p.Y127fs		Atlas-Indel,Pindel	.											.	STRAP	33	.	0			c.379delT						PASS	.						76	79	78					12																	16043580		2203	4300	6503	SO:0001589	frameshift_variant	11171	exon4			.	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.380delA	chr12.hg19:g.16043580delA	ENSP00000392270:p.Tyr127fs	187.0	0.0	0		171.0	57.0	0.333333	NM_007178	B2R5S5|B4DNJ6|Q5TZT4|Q9NTK0|Q9UQC8	Frame_Shift_Del	DEL	ENST00000419869.2	hg19	CCDS8676.1																																																																																			.	.	.	none		0.279	STRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401114.1	NM_007178		-	16043580	A	-	16043580	7	5	250	1	0	1	0	1	0	0	0	0	15338	449	16	0	394	0	STRAP	12	16043580	Frame_Shift_Del	DEL	A	TCGA-SX-A7SP-01A-11D-A34Z-10		16043580	117808315	40	15513											
PDE3A	5139	hgsc.bcm.edu	37	chr12	20774323	20774323	+	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	tctgcagctaaccatgtaaaGgctaaaaagcaaagtcgacc	16	7	8	10	1	1	0	0	0	1	0	2	1	1	0	2	1	4	5	2	1	7	3			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr12:20774323G>C	ENST00000359062.3	+	5	1558	c.1518G>C	c.(1516-1518)aaG>aaC	p.K506N	PDE3A_ENST00000544307.1_3'UTR	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	506					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)	ACCATGTAAAGGCTAAAAAGC	0.403																																					p.K506N		Atlas-SNP	.											.	PDE3A	184	.	0			c.G1518C						PASS	.						96	84	88					12																	20774323		2203	4300	6503	SO:0001583	missense	5139	exon5			TGTAAAGGCTAAA		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.1518G>C	chr12.hg19:g.20774323G>C	ENSP00000351957:p.Lys506Asn	62.0	0.0	.		85.0	17.0	.	NM_000921	O60865|Q13348|Q17RD1	Missense_Mutation	SNP	ENST00000359062.3	hg19	CCDS31754.1	.	.	.	.	.	.	.	.	.	.	G	10.44	1.351516	0.24512	.	.	ENSG00000172572	ENST00000359062	T	0.50813	0.73	5.57	1.34	0.21922	.	1.054050	0.07345	N	0.881400	T	0.26159	0.0638	N	0.14661	0.345	0.30219	N	0.796972	B	0.02656	0.0	B	0.01281	0.0	T	0.33523	-0.9865	10	0.21014	T	0.42	.	3.2508	0.06814	0.0937:0.3798:0.3107:0.2157	.	506	Q14432	PDE3A_HUMAN	N	506	ENSP00000351957:K506N	ENSP00000351957:K506N	K	+	3	2	PDE3A	20665590	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.210000	0.32370	0.685000	0.31468	0.591000	0.81541	AAG	.	.	.	none		0.403	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2			C	20774323	G	C	20774323	3	2	250	1	0	0	0	0	1	0	0	0	11644	991	35	4	1536	4	PDE3A	12	20774323	Missense_Mutation	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10	4730743	20774323	113077572	41	15514											
NCKAP5L	57701	hgsc.bcm.edu	37	chr12	50190029	50190029	+	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	gtggtggacaaggctgactgCgggggtctgagctgtgtgga	6	9	20	6	1	1	2	0	2	1	0	1	4	1	4	0	6	2	2	0	6	1	0			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr12:50190029C>T	ENST00000335999.6	-	8	1815	c.1614G>A	c.(1612-1614)ccG>ccA	p.P538P		NM_001037806.3	NP_001032895.2	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	534	Pro-rich.									central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(8)|prostate(2)	18						AGGCTGACTGCGGGGGTCTGA	0.637																																					p.P538P		Atlas-SNP	.											.	NCKAP5L	142	.	0			c.G1614A						PASS	.						19	22	21					12																	50190029		2135	4229	6364	SO:0001819	synonymous_variant	57701	exon8			TGACTGCGGGGGT	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.1614G>A	chr12.hg19:g.50190029C>T		44.0	0.0	.		56.0	21.0	.	NM_001037806	Q2TB26|Q71RH1|Q8N4W1|Q96HX2	Silent	SNP	ENST00000335999.6	hg19	CCDS41781.2	.	.	.	.	.	.	.	.	.	.	C	0.004	-2.248173	0.00271	.	.	ENSG00000167566	ENST00000433948	.	.	.	4.58	-8.12	0.01078	.	.	.	.	.	T	0.16041	0.0386	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.20773	-1.0265	4	.	.	.	-10.2704	2.9345	0.05810	0.1616:0.1869:0.4482:0.2033	.	.	.	.	T	253	.	.	A	-	1	0	NCKAP5L	48476296	0.269000	0.24143	0.000000	0.03702	0.000000	0.00434	-0.739000	0.04866	-1.604000	0.01595	-2.076000	0.00381	GCA	.	.	.	none		0.637	NCKAP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346884.2	XM_035497		T	50190029	C	T	50190029	2	4	250	1	0	0	0	0	0	0	0	1	10231	755	27	1		1	NCKAP5L	12	50190029	Silent	SNP	C	TCGA-SX-A7SP-01A-11D-A34Z-10	29415706	50190029	83661866	42	15515											
MDM1	56890	hgsc.bcm.edu	37	chr12	68719340	68719340	+	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	agtcaatccagctttcttacGcagaagtctatccaactgtt	11	13	6	11	1	3	1	1	0	2	1	5	1	5	1	2	0	3	3	2	0	5	4	rs372443907		TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr12:68719340G>T	ENST00000303145.7	-	4	600	c.514C>A	c.(514-516)Cgt>Agt	p.R172S	MDM1_ENST00000411698.2_Intron|MDM1_ENST00000540418.1_5'UTR|MDM1_ENST00000430606.2_3'UTR|MDM1_ENST00000545724.1_5'UTR|MDM1_ENST00000393543.3_3'UTR	NM_017440.4	NP_059136.2	Q8TC05	MDM1_HUMAN	Mdm1 nuclear protein homolog (mouse)	172					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)		GCTTTCTTACGCAGAAGTCTA	0.318																																					p.R172S		Atlas-SNP	.											.	MDM1	74	.	0			c.C514A						PASS	.						130	141	137					12																	68719340		2203	4300	6503	SO:0001583	missense	56890	exon4			TCTTACGCAGAAG	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.514C>A	chr12.hg19:g.68719340G>T	ENSP00000302537:p.Arg172Ser	110.0	0.0	.		126.0	47.0	.	NM_017440	B4DM65|E7EPQ3|O43406|Q8WTV9|Q9NR04	Missense_Mutation	SNP	ENST00000303145.7	hg19	CCDS8983.1	.	.	.	.	.	.	.	.	.	.	G	15.86	2.957474	0.53400	.	.	ENSG00000111554	ENST00000303145;ENST00000541686	T;T	0.20463	2.07;2.07	5.29	3.31	0.37934	.	0.501231	0.21482	N	0.073803	T	0.24661	0.0598	M	0.65975	2.015	0.21802	N	0.99953	P	0.39782	0.688	B	0.38985	0.287	T	0.10042	-1.0647	9	.	.	.	-0.4018	13.0634	0.59020	0.0:0.0:0.5863:0.4136	.	172	Q8TC05	MDM1_HUMAN	S	172;167	ENSP00000302537:R172S;ENSP00000446000:R167S	.	R	-	1	0	MDM1	67005607	0.827000	0.29292	0.019000	0.16419	0.967000	0.64934	4.952000	0.63618	1.357000	0.45904	0.561000	0.74099	CGT	.	.	.	alt		0.318	MDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402402.1	NM_020128		T	68719340	G	T	68719340	3	4	250	1	0	0	0	0	1	0	0	0	9419	1087	38	4	1674	4	MDM1	12	68719340	Missense_Mutation	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10	18529311	68719340	65132555	43	15516											
P2RX4	5025	hgsc.bcm.edu	37	chr12	121659899	121659899	+	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	cgctccttctttttccagatTccagatgcgaccactgtgtg	6	14	8	13	2	1	2	0	0	1	2	4	3	4	2	4	0	1	1	4	0	0	4			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr12:121659899T>A	ENST00000337233.4	+	4	665	c.357T>A	c.(355-357)atT>atA	p.I119I	P2RX4_ENST00000359949.7_Silent_p.I135I|P2RX4_ENST00000540930.1_3'UTR|P2RX4_ENST00000543171.1_Silent_p.I18I|P2RX4_ENST00000541532.1_Silent_p.I119I	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	119					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)					TTTTCCAGATTCCAGATGCGA	0.627																																					p.I135I		Atlas-SNP	.											.	P2RX4	27	.	0			c.T405A						PASS	.						97	113	107					12																	121659899		2203	4300	6503	SO:0001819	synonymous_variant	5025	exon5			CCAGATTCCAGAT	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.357T>A	chr12.hg19:g.121659899T>A		88.0	0.0	.		76.0	19.0	.	NM_001256796	E7EPF7|F6RU17|O00450|O14722|Q5U089|Q5U090|Q8N4N1|Q9UBG9	Silent	SNP	ENST00000337233.4	hg19	CCDS9214.1																																																																																			.	.	.	none		0.627	P2RX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402545.1	NM_175567		A	121659899	T	A	121659899	2	1	250	1	0	0	0	0	0	0	0	1	11349	1771	62	5		5	P2RX4	12	121659899	Silent	SNP	T	TCGA-SX-A7SP-01A-11D-A34Z-10	52940559	121659899	12191996	44	15517											
RNF34	80196	hgsc.bcm.edu	37	chr12	121858061	121858061	+	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	gtaggtacaaagtgaaatcaCttcagcaaacacagaagatg	18	7	9	7	0	2	3	2	1	0	2	2	3	2	3	0	1	3	3	0	1	6	3			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr12:121858061C>A	ENST00000392464.2	+	4	719	c.650C>A	c.(649-651)aCt>aAt	p.T217N	RNF34_ENST00000555076.1_Intron|RNF34_ENST00000361234.5_Missense_Mutation_p.T217N|RNF34_ENST00000392465.3_Missense_Mutation_p.T218N					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)		AGTGAAATCACTTCAGCAAAC	0.398																																					p.T218N		Atlas-SNP	.											.	RNF34	54	.	0			c.C653A						PASS	.						80	67	71					12																	121858061		2203	4300	6503	SO:0001583	missense	80196	exon5			AAATCACTTCAGC	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.650C>A	chr12.hg19:g.121858061C>A	ENSP00000376257:p.Thr217Asn	66.0	0.0	.		56.0	7.0	.	NM_194271		Missense_Mutation	SNP	ENST00000392464.2	hg19		.	.	.	.	.	.	.	.	.	.	C	15.81	2.944440	0.53079	.	.	ENSG00000170633	ENST00000361234;ENST00000392465;ENST00000392464;ENST00000354795	T;T;T	0.31769	2.11;2.11;1.48	5.33	5.33	0.75918	.	0.586691	0.18222	N	0.147843	T	0.15609	0.0376	N	0.03608	-0.345	0.80722	D	1	B;B	0.19583	0.022;0.037	B;B	0.23018	0.019;0.043	T	0.15122	-1.0448	10	0.17832	T	0.49	0.0034	14.8537	0.70319	0.0:1.0:0.0:0.0	.	217;218	Q969K3;Q969K3-2	RNF34_HUMAN;.	N	217;218;217;218	ENSP00000355137:T217N;ENSP00000376258:T218N;ENSP00000376257:T217N	ENSP00000346850:T218N	T	+	2	0	RNF34	120342444	0.993000	0.37304	0.947000	0.38551	0.881000	0.50899	4.069000	0.57541	2.651000	0.90000	0.561000	0.74099	ACT	.	.	.	none		0.398	RNF34-005	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000413892.1	NM_194271		A	121858061	C	A	121858061	3	1	250	1	0	0	0	0	1	0	0	0	13502	565	20	4	677	4	RNF34	12	121858061	Missense_Mutation	SNP	C	TCGA-SX-A7SP-01A-11D-A34Z-10	198162	121858061	11993834	45	15518											
PITPNM2	57605	hgsc.bcm.edu	37	chr12	123470897	123470897	+	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	cgcgtagccatccgtgatgaActgcggggtcagtgaggacg	8	7	16	10	5	1	3	1	3	0	0	2	4	2	4	2	3	3	1	2	3	2	1			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr12:123470897A>C	ENST00000542749.1	-	24	3790	c.3727T>G	c.(3727-3729)Ttc>Gtc	p.F1243V	PITPNM2_ENST00000280562.5_Splice_Site_p.F1237V|PITPNM2_ENST00000392428.1_Splice_Site_p.F964V|PITPNM2_ENST00000320201.4_Splice_Site_p.F1243V			Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein, membrane-associated 2	1243					metabolic process (GO:0008152)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)			NS(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	39	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		TCCGTGATGAACTGCGGGGTC	0.716																																					p.F1243V		Atlas-SNP	.											.	PITPNM2	105	.	0			c.T3727G						PASS	.						12	13	12					12																	123470897		2182	4271	6453	SO:0001630	splice_region_variant	57605	exon25			TGATGAACTGCGG	AF334585	CCDS9242.1, CCDS73543.1	12q24.31	2008-02-05				ENSG00000090975			21044	protein-coding gene	gene with protein product		608920				10022914	Standard	XM_005253582		Approved	RDGBA2, RDGB2, NIR3	uc001uej.1	Q9BZ72		ENST00000542749.1:c.3727-1T>G	chr12.hg19:g.123470897A>C		38.0	0.0	.		32.0	10.0	.	NM_020845	Q9P271	Missense_Mutation	SNP	ENST00000542749.1	hg19	CCDS9242.1	.	.	.	.	.	.	.	.	.	.	A	12.32	1.903220	0.33628	.	.	ENSG00000090975	ENST00000280562;ENST00000320201;ENST00000392428;ENST00000542749	T;T;T;T	0.43294	1.27;1.28;0.95;1.28	4.8	4.8	0.61643	.	0.065993	0.64402	D	0.000007	T	0.42314	0.1197	L	0.43152	1.355	0.80722	D	1	P;D	0.54047	0.712;0.964	P;P	0.53146	0.55;0.719	T	0.17653	-1.0362	10	0.10636	T	0.68	-37.789	10.908	0.47092	0.9234:0.0:0.0766:0.0	.	1237;1243	Q9BZ72-2;Q9BZ72	.;PITM2_HUMAN	V	1237;1243;964;1243	ENSP00000280562:F1237V;ENSP00000322218:F1243V;ENSP00000376223:F964V;ENSP00000437611:F1243V	ENSP00000280562:F1237V	F	-	1	0	PITPNM2	122036850	1.000000	0.71417	1.000000	0.80357	0.633000	0.38033	6.041000	0.70988	2.152000	0.67230	0.459000	0.35465	TTC	.	.	.	none		0.716	PITPNM2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401342.1	NM_020845	Missense_Mutation	C	123470897	A	C	123470897	5	2	250	1	0	0	0	0	0	0	1	0	11958	57	2	5	326	5	PITPNM2	12	123470897	Splice_Site	SNP	A	TCGA-SX-A7SP-01A-11D-A34Z-10	1612836	123470897	10380998	46	15519											
KCNRG	283518	hgsc.bcm.edu	37	chr13	50590073	50590073	+	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	gtgtttacagaacaaccttcAgcgccgacctggaatggtaa	12	9	10	10	2	1	1	1	0	0	1	1	3	1	2	3	2	4	2	3	2	5	4			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr13:50590073A>T	ENST00000312942.1	+	1	684	c.444A>T	c.(442-444)tcA>tcT	p.S148S	TRIM13_ENST00000478111.1_Intron|KCNRG_ENST00000360473.4_Silent_p.S148S|TRIM13_ENST00000378182.3_3'UTR	NM_173605.1	NP_775876.1	Q8N5I3	KCNRG_HUMAN	potassium channel regulator	148					protein homooligomerization (GO:0051260)	endoplasmic reticulum (GO:0005783)	identical protein binding (GO:0042802)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)	9		Acute lymphoblastic leukemia(7;3.41e-06)|Lung NSC(96;3.08e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.48e-10)|COAD - Colon adenocarcinoma(199;0.204)		AACAACCTTCAGCGCCGACCT	0.463																																					p.S148S		Atlas-SNP	.											.	KCNRG	29	.	0			c.A444T						PASS	.						145	128	134					13																	50590073		2203	4300	6503	SO:0001819	synonymous_variant	283518	exon1			ACCTTCAGCGCCG		CCDS9424.1, CCDS41889.1	13q14.11	2008-05-02			ENSG00000198553	ENSG00000198553			18893	protein-coding gene	gene with protein product							Standard	NM_173605		Approved		uc001vdu.3	Q8N5I3	OTTHUMG00000140140	ENST00000312942.1:c.444A>T	chr13.hg19:g.50590073A>T		137.0	0.0	.		167.0	58.0	.	NM_173605	A2A2X9|Q0P6D0|Q8IU75|Q8N3Q9	Silent	SNP	ENST00000312942.1	hg19	CCDS9424.1																																																																																			.	.	.	none		0.463	KCNRG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276308.1			T	50590073	A	T	50590073	2	4	250	1	0	0	0	0	0	0	0	1	8094	175	7	5		5	KCNRG	13	50590073	Silent	SNP	A	TCGA-SX-A7SP-01A-11D-A34Z-10		50590073	64579805	47	15520											
PCID2	55795	hgsc.bcm.edu	37	chr13	113832522	113832522	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtgtactttcaacacaccGtggacaggggaggaaatggg	11	7	14	9	2	1	0	1	0	0	0	1	3	1	3	2	5	2	1	2	5	3	2			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr13:113832522G>A	ENST00000337344.4	-	14	1266	c.1190C>T	c.(1189-1191)aCg>aTg	p.T397M	PCID2_ENST00000375459.1_Missense_Mutation_p.T395M|PCID2_ENST00000493650.1_5'UTR|PCID2_ENST00000246505.5_Missense_Mutation_p.T451M|PCID2_ENST00000375457.2_Missense_Mutation_p.T395M|PCID2_ENST00000375477.1_Missense_Mutation_p.T397M|PCID2_ENST00000375479.2_Missense_Mutation_p.T397M	NM_001127202.2	NP_001120674.1	Q5JVF3	PCID2_HUMAN	PCI domain containing 2	397					negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity (GO:2000117)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mRNA stability (GO:0043488)|spleen development (GO:0048536)					breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)	20	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_lung(25;0.216)|all_epithelial(44;0.234)	all cancers(43;0.104)			TCAACACACCGTGGACAGGGG	0.557																																					p.T451M		Atlas-SNP	.											.	PCID2	30	.	0			c.C1352T						PASS	.						213	160	178					13																	113832522		2203	4300	6503	SO:0001583	missense	55795	exon14			CACACCGTGGACA	AK002167	CCDS9532.2, CCDS58301.1, CCDS58302.1	13q34	2006-03-31			ENSG00000126226	ENSG00000126226			25653	protein-coding gene	gene with protein product		613713				12477932	Standard	NM_001127203		Approved	FLJ11305	uc031qnm.1	Q5JVF3	OTTHUMG00000017385	ENST00000337344.4:c.1190C>T	chr13.hg19:g.113832522G>A	ENSP00000337405:p.Thr397Met	61.0	0.0	.		55.0	17.0	.	NM_001258212	A6NK09|Q3ZCX1|Q5TC57|Q5TC58|Q9H7K1|Q9HBZ7|Q9NUK6|Q9NVY1|Q9NW44|Q9NWH3	Missense_Mutation	SNP	ENST00000337344.4	hg19	CCDS9532.2	.	.	.	.	.	.	.	.	.	.	G	10.74	1.435139	0.25813	.	.	ENSG00000126226	ENST00000337344;ENST00000375479;ENST00000375477;ENST00000246505;ENST00000375459;ENST00000375457;ENST00000375462;ENST00000246506;ENST00000351317	.	.	.	5.35	5.35	0.76521	.	0.362107	0.25833	N	0.028009	T	0.58750	0.2144	L	0.55990	1.75	0.09310	N	1	D;D	0.59357	0.96;0.985	P;B	0.54629	0.757;0.38	T	0.55685	-0.8102	9	0.59425	D	0.04	-27.4146	17.2683	0.87093	0.0:0.0:1.0:0.0	.	451;397	Q5JVF3-4;Q5JVF3	.;PCID2_HUMAN	M	397;397;397;451;395;395;374;397;374	.	ENSP00000246505:T451M	T	-	2	0	PCID2	112880523	1.000000	0.71417	0.733000	0.30861	0.169000	0.22640	6.309000	0.72825	2.507000	0.84556	0.655000	0.94253	ACG	.	.	.	none		0.557	PCID2-002	KNOWN	alternative_3_UTR|non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045897.1	NM_018386		A	113832522	G	A	113832522	3	1	250	1	0	0	0	0	1	0	0	0	11586	1145	40	1	13	1	PCID2	13	113832522	Missense_Mutation	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10	63242449	113832522	1337356	48	15521											
CPNE6	9362	hgsc.bcm.edu	37	chr14	24545746	24545746	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttgctatcaactttgaccCggaaaatcctgaatgtgaag	12	12	8	9	1	1	3	1	3	0	0	2	4	2	4	2	1	2	1	2	1	6	3			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr14:24545746C>T	ENST00000397016.2	+	14	1456	c.1145C>T	c.(1144-1146)cCg>cTg	p.P382L	CPNE6_ENST00000537691.1_Missense_Mutation_p.P437L|CPNE6_ENST00000216775.2_Missense_Mutation_p.P382L	NM_001280558.1	NP_001267487.1	O95741	CPNE6_HUMAN	copine VI (neuronal)	382	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				lipid metabolic process (GO:0006629)|nervous system development (GO:0007399)|synaptic transmission (GO:0007268)|vesicle-mediated transport (GO:0016192)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			endometrium(4)|large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(265;0.0184)		AACTTTGACCCGGAAAATCCT	0.582																																					p.P382L		Atlas-SNP	.											.	CPNE6	40	.	0			c.C1145T						PASS	.						101	104	103					14																	24545746		2203	4300	6503	SO:0001583	missense	9362	exon13			TTGACCCGGAAAA	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.1145C>T	chr14.hg19:g.24545746C>T	ENSP00000380211:p.Pro382Leu	31.0	0.0	.		31.0	11.0	.	NM_006032	B2RAG6|B7Z1M3|D3DS55|F5GXN1|Q53HA6|Q8WVG1	Missense_Mutation	SNP	ENST00000397016.2	hg19	CCDS9607.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.325572	0.81580	.	.	ENSG00000100884	ENST00000537691;ENST00000397016;ENST00000216775	T;T;T	0.22336	1.96;1.96;1.96	5.06	5.06	0.68205	von Willebrand factor, type A (2);Copine (1);	0.000000	0.64402	D	0.000020	T	0.43366	0.1244	M	0.82923	2.615	0.54753	D	0.999988	D;D	0.63880	0.993;0.981	P;P	0.56514	0.8;0.707	T	0.46442	-0.9191	10	0.72032	D	0.01	-34.9278	13.7833	0.63094	0.0:1.0:0.0:0.0	.	437;382	F5GXN1;O95741	.;CPNE6_HUMAN	L	437;382;382	ENSP00000440077:P437L;ENSP00000380211:P382L;ENSP00000216775:P382L	ENSP00000216775:P382L	P	+	2	0	CPNE6	23615586	0.031000	0.19500	0.969000	0.41365	0.889000	0.51656	1.889000	0.39718	2.617000	0.88574	0.563000	0.77884	CCG	.	.	.	none		0.582	CPNE6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071869.5			T	24545746	C	T	24545746	3	4	250	1	0	0	0	0	1	0	0	0	3818	652	23	1	1191	1	CPNE6	14	24545746	Missense_Mutation	SNP	C	TCGA-SX-A7SP-01A-11D-A34Z-10		24545746	82803794	49	15522											
PSMA6	5687	hgsc.bcm.edu	37	chr14	35783593	35783596	+	Frame_Shift_Del	DEL	TCTA	TCTA	-																															attacatgcctgtctactgtTctatcaattgatttcaaacc																										TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	TCTA	TCTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr14:35783593_35783596delTCTA	ENST00000261479.4	+	6	735_738	c.615_618delTCTA	c.(613-618)gttctafs	p.VL205fs	PSMA6_ENST00000555764.1_Frame_Shift_Del_p.VL126fs|PSMA6_ENST00000540871.1_Frame_Shift_Del_p.VL186fs|PSMA6_ENST00000553809.1_Frame_Shift_Del_p.VL211fs|PSMA6_ENST00000556506.1_Intron|KIAA0391_ENST00000557565.1_3'UTR	NM_002791.1	NP_002782.1	P60900	PSA6_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 6	205					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 NF-kappaB transcription factor activity (GO:0051092)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of inflammatory response (GO:0050727)|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)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|myofibril (GO:0030016)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysome (GO:0005844)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)|sarcomere (GO:0030017)	endopeptidase activity (GO:0004175)|NF-kappaB binding (GO:0051059)|purine ribonucleoside triphosphate binding (GO:0035639)|RNA binding (GO:0003723)|threonine-type endopeptidase activity (GO:0004298)			kidney(2)|large_intestine(1)|lung(5)|prostate(1)|urinary_tract(1)	10	Breast(36;0.0519)|Hepatocellular(127;0.158)		Lung(238;3.81e-05)|LUAD - Lung adenocarcinoma(48;5.59e-05)|Epithelial(34;0.00342)|all cancers(34;0.00973)	GBM - Glioblastoma multiforme(112;0.0234)		TGTCTACTGTTCTATCAATTGATT	0.328																																					p.205_206del		Atlas-Indel,Pindel	.											.	PSMA6	18	.	0			c.614_617del						PASS	.																																			SO:0001589	frameshift_variant	5687	exon6			.	X59417	CCDS9655.1, CCDS61437.1, CCDS61438.1	14q13	2003-03-12			ENSG00000100902	ENSG00000100902		"Proteasome (prosome, macropain) subunits"	9535	protein-coding gene	gene with protein product		602855				1888762, 8811196	Standard	NM_002791		Approved	IOTA, PROS27, p27K, MGC22756, MGC2333, MGC23846	uc001wtd.3	P60900	OTTHUMG00000140221	ENST00000261479.4:c.615_618delTCTA	chr14.hg19:g.35783593_35783596delTCTA	ENSP00000261479:p.Val205fs	316.0	0.0	0		377.0	102.0	0.270557	NM_002791	B2R7J9|B4DQR4|B4DXJ9|P34062|Q6IB60	Frame_Shift_Del	DEL	ENST00000261479.4	hg19	CCDS9655.1																																																																																			.	.	.	none		0.328	PSMA6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276684.1			-	35783596	TCTA	-	35783593	7	5	250	1	0	1	0	1	0	0	0	0	12681	1770	62	0	637	0	PSMA6	14	35783593	Frame_Shift_Del	DEL	TCTA	TCGA-SX-A7SP-01A-11D-A34Z-10	11237847	35783593	71565947	50	15523											
C14orf106	55320	hgsc.bcm.edu	37	chr14	45705110	45705110	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gttgtgctcaatccgctctaTaattacattactgtgccaat	10	15	6	10	1	2	0	1	0	1	0	3	0	3	0	2	0	4	3	2	0	6	5			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr14:45705110T>C	ENST00000310806.4	-	6	1713	c.1255A>G	c.(1255-1257)Ata>Gta	p.I419V		NM_018353.4	NP_060823.3	Q6P0N0	M18BP_HUMAN	MIS18 binding protein 1	419					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						ATCCGCTCTATAATTACATTA	0.308																																					p.I419V		Atlas-SNP	.											.	MIS18BP1	92	.	0			c.A1255G						PASS	.						103	96	98					14																	45705110		2201	4299	6500	SO:0001583	missense	55320	exon6			GCTCTATAATTAC	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.1255A>G	chr14.hg19:g.45705110T>C	ENSP00000309790:p.Ile419Val	312.0	0.0	.		349.0	116.0	.	NM_018353	D3DSA7|Q86V14|Q96PY4|Q9NUR5|Q9Y4X9	Missense_Mutation	SNP	ENST00000310806.4	hg19	CCDS9684.1	.	.	.	.	.	.	.	.	.	.	T	3.759	-0.049993	0.07407	.	.	ENSG00000129534	ENST00000310806	T	0.14266	2.52	5.76	-0.741	0.11112	SANT associated (1);	0.646080	0.15216	N	0.274189	T	0.06325	0.0163	N	0.14661	0.345	0.25662	N	0.985991	B	0.17465	0.022	B	0.19946	0.027	T	0.44345	-0.9334	10	0.08837	T	0.75	-3.5739	9.0435	0.36331	0.0:0.5491:0.0:0.4509	.	419	Q6P0N0	M18BP_HUMAN	V	419	ENSP00000309790:I419V	ENSP00000309790:I419V	I	-	1	0	MIS18BP1	44774860	0.995000	0.38212	0.982000	0.44146	0.904000	0.53231	0.212000	0.17497	-0.089000	0.12484	-0.256000	0.11100	ATA	.	.	.	none		0.308	MIS18BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276795.2			C	45705110	T	C	45705110	3	2	250	1	0	0	0	0	1	0	0	0	1740	1406	49	3	2191	3	C14orf106	14	45705110	Missense_Mutation	SNP	T	TCGA-SX-A7SP-01A-11D-A34Z-10	9921517	45705110	61644430	51	15524											
SIPA1L1	26037	hgsc.bcm.edu	37	chr14	72055984	72055984	+	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	ggagtggcagtacttgaagtGcccaaggagaacttggtgtt	10	10	15	6	0	0	2	0	1	0	1	0	4	0	3	1	4	3	3	1	4	4	4			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr14:72055984G>A	ENST00000555818.1	+	2	1743	c.1395G>A	c.(1393-1395)gtG>gtA	p.V465V	SIPA1L1_ENST00000358550.2_Silent_p.V465V|SIPA1L1_ENST00000381232.3_Silent_p.V465V	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	465					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)		TACTTGAAGTGCCCAAGGAGA	0.423																																					p.V465V		Atlas-SNP	.											.	SIPA1L1	219	.	0			c.G1395A						PASS	.						86	79	81					14																	72055984		2203	4300	6503	SO:0001819	synonymous_variant	26037	exon2			TGAAGTGCCCAAG	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.1395G>A	chr14.hg19:g.72055984G>A		96.0	0.0	.		109.0	36.0	.	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Silent	SNP	ENST00000555818.1	hg19	CCDS9807.1																																																																																			.	.	.	none		0.423	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		A	72055984	G	A	72055984	2	1	250	1	0	0	0	0	0	0	0	1	14342	1306	46	2		2	SIPA1L1	14	72055984	Silent	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10	26350874	72055984	35293556	52	15525											
BUB1B	701	hgsc.bcm.edu	37	chr15	40505677	40505677	+	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	gtctgattctcagaaacaggTtggtccttttcattcttata	9	17	7	8	0	4	2	2	1	3	1	6	2	5	2	1	2	1	1	1	2	3	7			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr15:40505677T>C	ENST00000287598.6	+	20	2873		c.e20+2		BUB1B_ENST00000412359.3_Splice_Site	NM_001211.5	NP_001202	O60566	BUB1B_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase B						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)		CAGAAACAGGTTGGTCCTTTT	0.388			"Mis, N, F, S"			rhabdomyosarcoma			Mosaic Variegated Aneuploidy Syndrome																												.		Atlas-SNP	.	yes	Rec		Mosaic variegated aneuploidy	15	15q15	701	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)		M	.	BUB1B	71	.	0			c.2678+2T>C						PASS	.						129	136	134					15																	40505677		2203	4300	6503	SO:0001630	splice_region_variant	701	exon20	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	AACAGGTTGGTCC	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.2678+2T>C	chr15.hg19:g.40505677T>C		68.0	0.0	.		74.0	28.0	.	NM_001211	B2R6U0|B4DL09|B4DLG3|O60501|O60627|O60758|O75389|Q59HH6|Q8WV50|Q96KM4	Splice_Site	SNP	ENST00000287598.6	hg19	CCDS10053.1	.	.	.	.	.	.	.	.	.	.	T	19.27	3.794831	0.70452	.	.	ENSG00000156970	ENST00000287598;ENST00000412359;ENST00000442874	.	.	.	5.0	5.0	0.66597	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7037	0.69174	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	BUB1B	38292969	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	3.805000	0.55575	1.872000	0.54250	0.402000	0.26972	.	.	.	.	none		0.388	BUB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252122.4		Intron	C	40505677	T	C	40505677	5	2	250	1	0	0	0	0	0	0	1	0	1573	1739	60	3	2758	3	BUB1B	15	40505677	Splice_Site	SNP	T	TCGA-SX-A7SP-01A-11D-A34Z-10		40505677	62025715	53	15526											
RNF111	54778	hgsc.bcm.edu	37	chr15	59358971	59358971	+	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	ttctgtttcaagatgactcaAggagaactacatctagtgct	12	13	8	8	0	4	3	2	1	2	2	4	4	4	3	0	1	3	2	0	1	5	4			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr15:59358971A>C	ENST00000557998.1	+	6	1662	c.1375A>C	c.(1375-1377)Agg>Cgg	p.R459R	RNF111_ENST00000434298.1_Silent_p.R459R|RNF111_ENST00000348370.4_Silent_p.R459R|RNF111_ENST00000559209.1_Silent_p.R459R|RNF111_ENST00000561186.1_Silent_p.R459R	NM_001270530.1	NP_001257459.1	Q6ZNA4	RN111_HUMAN	ring finger protein 111	459	Ser-rich.				gene expression (GO:0010467)|pattern specification process (GO:0007389)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein polyubiquitination (GO:0000209)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|SUMO polymer binding (GO:0032184)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35				all cancers(107;0.194)		AGATGACTCAAGGAGAACTAC	0.398																																					p.R459R	NSCLC(72;983 1365 10746 34387 47081)	Atlas-SNP	.											.	RNF111	179	.	0			c.A1375C						PASS	.						93	84	87					15																	59358971		2192	4291	6483	SO:0001819	synonymous_variant	54778	exon6			GACTCAAGGAGAA	AL157474	CCDS10169.1, CCDS58365.1, CCDS58366.1	15q21	2013-01-09			ENSG00000157450	ENSG00000157450		"RING-type (C3HC4) zinc fingers"	17384	protein-coding gene	gene with protein product		605840				11298452	Standard	NM_017610		Approved	ARK, Arkadia, FLJ38008, DKFZP761D081	uc002aft.4	Q6ZNA4	OTTHUMG00000132716	ENST00000557998.1:c.1375A>C	chr15.hg19:g.59358971A>C		54.0	0.0	.		73.0	20.0	.	NM_017610	C9JUS4|H0YN55|Q6P9A4|Q6ZMU2|Q7L428|Q7Z346|Q8N1P9|Q8WUA3|Q9NSR1	Silent	SNP	ENST00000557998.1	hg19	CCDS58366.1																																																																																			.	.	.	none		0.398	RNF111-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000416012.1	NM_017610		C	59358971	A	C	59358971	2	2	250	1	0	0	0	0	0	0	0	1	13438	63	3	5		5	RNF111	15	59358971	Silent	SNP	A	TCGA-SX-A7SP-01A-11D-A34Z-10	18853294	59358971	43172421	54	15527											
CORO2B	10391	hgsc.bcm.edu	37	chr15	69003120	69003120	+	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	gctgaagcggaacatgacggAggcgctcctggagctgcacg	9	5	16	11	4	0	2	0	2	0	0	1	5	1	5	1	4	4	4	1	4	2	0			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr15:69003120A>T	ENST00000566799.1	+	4	412	c.383A>T	c.(382-384)gAg>gTg	p.E128V	CORO2B_ENST00000261861.5_Missense_Mutation_p.E123V|CORO2B_ENST00000540068.1_Missense_Mutation_p.E123V|CORO2B_ENST00000543950.1_Missense_Mutation_p.E123V			Q9UQ03	COR2B_HUMAN	coronin, actin binding protein, 2B	128				E -> A (in Ref. 1; BAA36341). {ECO:0000305}.	actin cytoskeleton organization (GO:0030036)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|membrane (GO:0016020)	actin binding (GO:0003779)|actin filament binding (GO:0051015)			kidney(3)|large_intestine(13)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36						AACATGACGGAGGCGCTCCTG	0.657																																					p.E128V		Atlas-SNP	.											.	CORO2B	68	.	0			c.A383T						PASS	.						38	34	35					15																	69003120		2198	4297	6495	SO:0001583	missense	10391	exon4			TGACGGAGGCGCT	AB010098	CCDS53952.1, CCDS10229.2	15q22.31	2013-01-10	2001-11-28		ENSG00000103647	ENSG00000103647		"Coronins", "WD repeat domain containing"	2256	protein-coding gene	gene with protein product	"clipin C", "coronin, actin-binding, 2B"	605002	"coronin, actin-binding protein, 2B"			10224093, 10231032	Standard	NM_001190456		Approved	ClipinC, KIAA0925	uc021spj.1	Q9UQ03	OTTHUMG00000133288	ENST00000566799.1:c.383A>T	chr15.hg19:g.69003120A>T	ENSP00000454783:p.Glu128Val	33.0	0.0	.		30.0	10.0	.	NM_006091	A8K0W3|O94767|Q8TAN1	Missense_Mutation	SNP	ENST00000566799.1	hg19	CCDS10229.2	.	.	.	.	.	.	.	.	.	.	A	13.52	2.260878	0.39995	.	.	ENSG00000103647	ENST00000261861;ENST00000540068;ENST00000543950	T;T	0.05786	3.39;3.39	5.69	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	0.12135	0.0295	M	0.84082	2.675	0.58432	D	0.999995	B	0.09022	0.002	B	0.09377	0.004	T	0.01409	-1.1362	10	0.62326	D	0.03	-23.0641	11.3009	0.49304	0.8635:0.0:0.0:0.1365	.	128	Q9UQ03	COR2B_HUMAN	V	128;123;123	ENSP00000446250:E123V;ENSP00000443819:E123V	ENSP00000261861:E128V	E	+	2	0	CORO2B	66790174	1.000000	0.71417	0.981000	0.43875	0.374000	0.29953	7.075000	0.76798	0.942000	0.37525	0.533000	0.62120	GAG	.	.	.	none		0.657	CORO2B-203	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_006091		T	69003120	A	T	69003120	3	4	250	1	0	0	0	0	1	0	0	0	3759	304	11	5	397	5	CORO2B	15	69003120	Missense_Mutation	SNP	A	TCGA-SX-A7SP-01A-11D-A34Z-10	9644149	69003120	33528272	55	15528											
UBL7	84993	hgsc.bcm.edu	37	chr15	74742277	74742277	+	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	tacacttttcaggcgctcacCtggcatatcccggtatgagc	8	11	9	13	2	2	1	2	1	0	0	3	1	3	1	2	3	2	3	2	3	3	5			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr15:74742277C>G	ENST00000567435.1	-	7	1127	c.664G>C	c.(664-666)Ggt>Cgt	p.G222R	UBL7_ENST00000361351.4_Splice_Site_p.G222R|UBL7_ENST00000564488.1_Splice_Site_p.G222R|UBL7_ENST00000395081.2_Splice_Site_p.G222R|UBL7_ENST00000565335.1_Splice_Site_p.G222R			Q96S82	UBL7_HUMAN	ubiquitin-like 7	222										endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	9						AGGCGCTCACCTGGCATATCC	0.582																																					p.G222R		Atlas-SNP	.											.	UBL7	24	.	0			c.G664C						PASS	.						35	32	33					15																	74742277		2197	4296	6493	SO:0001630	splice_region_variant	84993	exon7			GCTCACCTGGCAT	BC007913	CCDS10263.1	15q23	2014-03-06	2014-03-06		ENSG00000138629	ENSG00000138629			28221	protein-coding gene	gene with protein product	"bone marrow stromal cell-derived ubiquitin-like", " ubiquitin-like protein SB132"	609748	"ubiquitin-like 7 (bone marrow stromal cell-derived)"			12644319	Standard	NM_201265		Approved	BMSC-UbP, MGC14421	uc002axy.1	Q96S82	OTTHUMG00000139001	ENST00000567435.1:c.664+1G>C	chr15.hg19:g.74742277C>G		68.0	0.0	.		57.0	26.0	.	NM_201265	D3DW57|Q96I03	Missense_Mutation	SNP	ENST00000567435.1	hg19	CCDS10263.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.737423	0.89482	.	.	ENSG00000138629	ENST00000361351;ENST00000395081	T;T	0.49139	0.79;0.79	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.66819	0.2828	M	0.64997	1.995	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.64533	-0.6385	9	.	.	.	-14.8599	17.469	0.87640	0.0:1.0:0.0:0.0	.	262;222	D3DW56;Q96S82	.;UBL7_HUMAN	R	222	ENSP00000354883:G222R;ENSP00000378518:G222R	.	G	-	1	0	UBL7	72529330	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	5.689000	0.68234	2.654000	0.90174	0.650000	0.86243	GGT	.	.	.	none		0.582	UBL7-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419627.1	NM_032907, NM_201265	Missense_Mutation	G	74742277	C	G	74742277	5	3	250	1	0	0	0	0	0	0	1	0	16902	695	24	4	498	4	UBL7	15	74742277	Splice_Site	SNP	C	TCGA-SX-A7SP-01A-11D-A34Z-10	5739157	74742277	27789115	56	15529											
MPI	4351	hgsc.bcm.edu	37	chr15	75183852	75183852	+	Frame_Shift_Del	DEL	A	A	-																															tcaaggacacctttaatggcAacctgcccttcctcttcaaa																										TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr15:75183852delA	ENST00000352410.4	+	3	344	c.277delA	c.(277-279)aacfs	p.N93fs	MPI_ENST00000564003.1_Frame_Shift_Del_p.N43fs|MPI_ENST00000566377.1_Frame_Shift_Del_p.N93fs|MPI_ENST00000535694.1_Frame_Shift_Del_p.N43fs|MPI_ENST00000323744.6_Frame_Shift_Del_p.N93fs|MPI_ENST00000562606.1_Frame_Shift_Del_p.N73fs|MPI_ENST00000563786.1_Frame_Shift_Del_p.N73fs|MPI_ENST00000565576.1_Frame_Shift_Del_p.N93fs|MPI_ENST00000563422.1_Frame_Shift_Del_p.N93fs			P34949	MPI_HUMAN	mannose phosphate isomerase	93					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)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	mannose-6-phosphate isomerase activity (GO:0004476)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	9						CTTTAATGGCAACCTGCCCTT	0.527																																					p.G92fs		Atlas-Indel,Pindel	.											.	MPI	32	.	0			c.276delC						PASS	.						209	173	185					15																	75183852		2197	4295	6492	SO:0001589	frameshift_variant	4351	exon3			.		CCDS10272.1, CCDS73756.1, CCDS73757.1, CCDS73758.1	15q24.1	2013-09-19			ENSG00000178802	ENSG00000178802	5.3.1.8		7216	protein-coding gene	gene with protein product	"mannose-6-phosphate isomerase"	154550					Standard	NM_002435		Approved		uc002azc.1	P34949	OTTHUMG00000142826	ENST00000352410.4:c.277delA	chr15.hg19:g.75183852delA	ENSP00000318318:p.Asn93fs	68.0	0.0	0		67.0	23.0	0.343284	NM_002435	A8K8K9|Q96AB0	Frame_Shift_Del	DEL	ENST00000352410.4	hg19	CCDS10272.1																																																																																			.	.	.	none		0.527	MPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286418.4			-	75183852	A	-	75183852	7	5	250	1	0	1	0	1	0	0	0	0	9736	130	5	0	287	0	MPI	15	75183852	Frame_Shift_Del	DEL	A	TCGA-SX-A7SP-01A-11D-A34Z-10	441575	75183852	27347540	57	15530											
RUNDC2A	92017	hgsc.bcm.edu	37	chr16	12145718	12145718	+	Missense_Mutation	SNP	A	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	tgccagatgccaaatgcaaaAaggagcggaagaagaaaaag	20	3	12	6	1	0	3	0	0	0	3	0	5	0	5	2	2	4	1	2	2	7	0			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr16:12145718A>C	ENST00000566228.1	+	8	832	c.763A>C	c.(763-765)Aag>Cag	p.K255Q	SNX29_ENST00000323433.4_5'Flank|SNX29_ENST00000306030.3_5'Flank|SNX29_ENST00000568359.1_3'UTR	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	255						extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						CAAATGCAAAAAGGAGCGGAA	0.403																																					p.K255Q		Atlas-SNP	.											.	SNX29	60	.	0			c.A763C						PASS	.						48	53	51					16																	12145718		2186	4295	6481	SO:0001583	missense	92017	exon8			TGCAAAAAGGAGC	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.763A>C	chr16.hg19:g.12145718A>C	ENSP00000456480:p.Lys255Gln	118.0	0.0	.		225.0	46.0	.	NM_032167	B5MDW2|Q8N2X2|Q9HA26	Missense_Mutation	SNP	ENST00000566228.1	hg19	CCDS10553.2	.	.	.	.	.	.	.	.	.	.	A	9.936	1.216256	0.22373	.	.	ENSG00000140660	ENST00000268271	.	.	.	5.78	5.78	0.91487	.	0.236638	0.41712	D	0.000837	T	0.69958	0.3169	M	0.62723	1.935	0.80722	D	1	.	.	.	.	.	.	T	0.66893	-0.5808	7	0.27785	T	0.31	-24.1715	14.9367	0.70960	1.0:0.0:0.0:0.0	.	.	.	.	Q	255	.	ENSP00000268271:K255Q	K	+	1	0	RUNDC2A	12053219	1.000000	0.71417	1.000000	0.80357	0.076000	0.17211	5.712000	0.68407	2.212000	0.71576	0.260000	0.18958	AAG	.	.	.	none		0.403	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422622.1			C	12145718	A	C	12145718	3	2	250	1	0	0	0	0	1	0	0	0	13756	15	1	5	793	5	RUNDC2A	16	12145718	Missense_Mutation	SNP	A	TCGA-SX-A7SP-01A-11D-A34Z-10		12145718	78209035	58	15531											
MKL2	57496	hgsc.bcm.edu	37	chr16	14340738	14340738	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccttcacagttcttgagtTcatctcctttgagaatgaca	9	14	7	11	1	4	3	2	3	2	1	5	4	4	3	2	0	0	2	2	0	1	5			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr16:14340738T>C	ENST00000341243.5	+	10	1588	c.1588T>C	c.(1588-1590)Tca>Cca	p.S530P	MKL2_ENST00000571589.1_Missense_Mutation_p.S541P|MKL2_ENST00000318282.5_Missense_Mutation_p.S541P|MKL2_ENST00000574045.1_Missense_Mutation_p.S541P			Q9ULH7	MKL2_HUMAN	MKL/myocardin-like 2	530					blood vessel morphogenesis (GO:0048514)|cardiac muscle tissue development (GO:0048738)|embryonic organ development (GO:0048568)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|muscle organ development (GO:0007517)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(6)|liver(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GTTCTTGAGTTCATCTCCTTT	0.473																																					p.S541P		Atlas-SNP	.											.	MKL2	103	.	0			c.T1621C						PASS	.						87	81	83					16																	14340738		2197	4300	6497	SO:0001583	missense	57496	exon12			TTGAGTTCATCTC	AB033069	CCDS32391.1	16p13.12	2012-11-29			ENSG00000186260	ENSG00000186260			29819	protein-coding gene	gene with protein product		609463				10574462	Standard	NM_014048		Approved	MRTF-B, FLJ31823	uc002dcg.3	Q9ULH7	OTTHUMG00000177379	ENST00000341243.5:c.1588T>C	chr16.hg19:g.14340738T>C	ENSP00000345841:p.Ser530Pro	65.0	0.0	.		88.0	36.0	.	NM_014048	A6ND53|B4DGT8|Q68CT1|Q6UB16|Q86WW2|Q8N226	Missense_Mutation	SNP	ENST00000341243.5	hg19		.	.	.	.	.	.	.	.	.	.	T	16.14	3.039094	0.55003	.	.	ENSG00000186260	ENST00000318282;ENST00000341243	.	.	.	5.83	5.83	0.93111	.	0.460090	0.23885	N	0.043606	T	0.33381	0.0861	N	0.21373	0.66	0.33071	D	0.535396	D;P	0.57899	0.981;0.937	P;P	0.52109	0.69;0.572	T	0.25641	-1.0126	9	0.05959	T	0.93	-18.8813	9.3958	0.38401	0.25:0.0:0.0:0.75	.	541;541	B4DGT8;Q9ULH7-4	.;.	P	541;530	.	ENSP00000339086:S541P	S	+	1	0	MKL2	14248239	0.235000	0.23794	0.156000	0.22583	0.822000	0.46500	1.036000	0.30228	2.225000	0.72522	0.533000	0.62120	TCA	.	.	.	none		0.473	MKL2-202	KNOWN	basic	protein_coding	protein_coding		NM_014048		C	14340738	T	C	14340738	3	2	250	1	0	0	0	0	1	0	0	0	9609	1783	62	3	1659	3	MKL2	16	14340738	Missense_Mutation	SNP	T	TCGA-SX-A7SP-01A-11D-A34Z-10	2195020	14340738	76014015	59	15532											
C16orf88	400506	hgsc.bcm.edu	37	chr16	19726133	19726133	+	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	acatgctcctcgcaaagggtGctgacacccttctttttctt	7	14	7	13	1	2	1	0	1	2	0	4	1	3	1	2	1	2	3	2	1	1	4			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr16:19726133G>T	ENST00000219837.7	-	2	303	c.225C>A	c.(223-225)agC>agA	p.S75R	KNOP1_ENST00000568230.1_5'Flank|IQCK_ENST00000320394.6_5'Flank|AC002550.5_ENST00000565916.1_RNA	NM_001012991.2	NP_001013009.2	Q1ED39	KNOP1_HUMAN	lysine-rich nucleolar protein 1	75	Lys-rich.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)										CGCAAAGGGTGCTGACACCct	0.532																																					p.S75R		Atlas-SNP	.											.	C16orf88	41	.	0			c.C225A						PASS	.						64	63	64					16																	19726133		2015	4190	6205	SO:0001583	missense	400506	exon2			AAGGGTGCTGACA	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.225C>A	chr16.hg19:g.19726133G>T	ENSP00000219837:p.Ser75Arg	68.0	0.0	.		74.0	16.0	.	NM_001012991	O43328|Q5FWF3	Missense_Mutation	SNP	ENST00000219837.7	hg19	CCDS42127.1	.	.	.	.	.	.	.	.	.	.	G	16.51	3.144187	0.57044	.	.	ENSG00000103550	ENST00000219837	T	0.29142	1.58	4.61	0.587	0.17439	.	2.395750	0.01104	N	0.005453	T	0.45357	0.1338	M	0.61703	1.905	0.09310	N	1	D	0.55385	0.971	P	0.58454	0.839	T	0.11717	-1.0576	9	.	.	.	-2.034	2.1892	0.03894	0.1029:0.1574:0.4003:0.3394	.	75	Q1ED39	CP088_HUMAN	R	75	ENSP00000219837:S75R	.	S	-	3	2	C16orf88	19633634	0.004000	0.15560	0.001000	0.08648	0.019000	0.09904	0.086000	0.14935	0.217000	0.20800	0.561000	0.74099	AGC	.	.	.	none		0.532	KNOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435993.2	NM_001012991		T	19726133	G	T	19726133	3	4	250	1	0	0	0	0	1	0	0	0	1843	1310	46	4	1167	4	C16orf88	16	19726133	Missense_Mutation	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10	5385395	19726133	70628620	60	15533											
GAS8	2622	hgsc.bcm.edu	37	chr16	90109648	90109648	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tatgaggcaaagctgctggcCttcgggatccctctggacaa	9	9	12	11	1	1	1	0	1	1	0	3	3	2	3	2	4	2	3	2	4	3	2			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr16:90109648C>T	ENST00000268699.4	+	11	1454	c.1332C>T	c.(1330-1332)gcC>gcT	p.A444A	URAHP_ENST00000517889.1_RNA|GAS8_ENST00000536122.1_Silent_p.A419A	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8	444					cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)				endometrium(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.029)		AGCTGCTGGCCTTCGGGATCC	0.647																																					p.A444A		Atlas-SNP	.											.	GAS8	29	.	0			c.C1332T						PASS	.						85	74	78					16																	90109648		2198	4300	6498	SO:0001819	synonymous_variant	2622	exon11			GCTGGCCTTCGGG	AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"growth arrest-specific 11"	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.1332C>T	chr16.hg19:g.90109648C>T		16.0	0.0	.		29.0	8.0	.	NM_001481	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Silent	SNP	ENST00000268699.4	hg19	CCDS10992.1																																																																																			.	.	.	none		0.647	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2			T	90109648	C	T	90109648	2	4	250	1	0	0	0	0	0	0	0	1	6258	668	24	2		2	GAS8	16	90109648	Silent	SNP	C	TCGA-SX-A7SP-01A-11D-A34Z-10	70383515	90109648	245105	61	15534											
RNMTL1	51031	hgsc.bcm.edu	37	chr17	686403	686403	+	5'Flank	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	ggaaggtcgcaggctcatttCagacgctctcaaggctggag	9	8	14	10	2	3	1	3	0	1	1	5	3	3	3	0	5	0	4	0	5	2	1			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr17:686403C>T	ENST00000301328.5	-	0	0				GLOD4_ENST00000536578.1_5'Flank|RNMTL1_ENST00000304478.4_Missense_Mutation_p.S132L|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)		AGGCTCATTTCAGACGCTCTC	0.453																																					p.S132L		Atlas-SNP	.											.	RNMTL1	25	.	0			c.C395T						PASS	.						93	84	87					17																	686403		2203	4300	6503	SO:0001631	upstream_gene_variant	55178	exon2			TCATTTCAGACGC	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			chr17.hg19:g.686403C>T	Exception_encountered	44.0	0.0	.		86.0	12.0	.	NM_018146	D3DTG9|D3DTH1|Q96B89|Q9H3J8|Q9HC37|Q9NVN1	Missense_Mutation	SNP	ENST00000301328.5	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.42|11.42	1.632684|1.632684	0.29068|0.29068	.|.	.|.	ENSG00000167699|ENSG00000171861	ENST00000397393|ENST00000304478	.|T	.|0.26957	.|1.7	5.41|5.41	3.42|3.42	0.39159|0.39159	.|RNA 2-O ribose methyltransferase, substrate binding (2);	.|0.595355	.|0.19011	.|N	.|0.125074	T|T	0.10508|0.10508	0.0257|0.0257	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B	.|0.02656	.|0.0	.|B	.|0.06405	.|0.002	T|T	0.15954|0.15954	-1.0419|-1.0419	6|10	0.87932|0.29301	D|T	0|0.29	-2.4585|-2.4585	3.4235|3.4235	0.07402|0.07402	0.1402:0.5684:0.136:0.1553|0.1402:0.5684:0.136:0.1553	.|.	.|132	.|Q9HC36	.|RMTL1_HUMAN	K|L	35|132	.|ENSP00000306080:S132L	ENSP00000380548:E35K|ENSP00000306080:S132L	E|S	-|+	1|2	0|0	GLOD4|RNMTL1	633153|633153	0.678000|0.678000	0.27586|0.27586	0.945000|0.945000	0.38365|0.38365	0.749000|0.749000	0.42624|0.42624	0.420000|0.420000	0.21263|0.21263	1.287000|1.287000	0.44583|0.44583	0.650000|0.650000	0.86243|0.86243	GAA|TCA	.	.	.	none		0.453	GLOD4-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000437190.1	NM_016080		T	686403	C	T	686403	1	4	250	0	1	0	0	0	0	0	0	0	13520	838	29	2		2	RNMTL1	17	686403	5'Flank	SNP	C	TCGA-SX-A7SP-01A-11D-A34Z-10		686403	80508807	62	15535											
SMCR8	140775	hgsc.bcm.edu	37	chr17	18219977	18219977	+	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	ctaaccctgatgagtctgccGacacagacctttacacctgc	10	9	7	15	1	1	3	0	2	1	1	1	4	1	3	4	0	4	0	4	0	2	3	rs577884923		TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr17:18219977G>A	ENST00000406438.3	+	1	1354	c.874G>A	c.(874-876)Gac>Aac	p.D292N	TOP3A_ENST00000582230.1_5'Flank|TOP3A_ENST00000321105.5_5'Flank|TOP3A_ENST00000542570.1_5'Flank	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	292						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						TGAGTCTGCCGACACAGACCT	0.507													G|||	1	0.000199681	0	0	5008	,	,		20724	0		0	False		,,,				2504	0.001				p.D292N		Atlas-SNP	.											.	SMCR8	62	.	0			c.G874A						PASS	.						83	77	79					17																	18219977		2203	4300	6503	SO:0001583	missense	140775	exon1			TCTGCCGACACAG	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.874G>A	chr17.hg19:g.18219977G>A	ENSP00000385025:p.Asp292Asn	70.0	0.0	.		100.0	26.0	.	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Missense_Mutation	SNP	ENST00000406438.3	hg19	CCDS11195.2	.	.	.	.	.	.	.	.	.	.	G	1.498	-0.552877	0.03996	.	.	ENSG00000176994	ENST00000406438	T	0.22945	1.93	6.03	1.61	0.23674	.	0.259532	0.43747	N	0.000538	T	0.10465	0.0256	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37056	-0.9722	10	0.07644	T	0.81	-52.6362	7.3193	0.26517	0.2138:0.1197:0.6665:0.0	.	292	Q8TEV9	SMCR8_HUMAN	N	292	ENSP00000385025:D292N	ENSP00000385025:D292N	D	+	1	0	SMCR8	18160702	0.013000	0.17824	0.000000	0.03702	0.088000	0.18126	0.765000	0.26546	0.077000	0.16863	-0.345000	0.07892	GAC	.	.	.	none		0.507	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775		A	18219977	G	A	18219977	3	1	250	1	0	0	0	0	1	0	0	0	14805	1058	37	1	876	1	SMCR8	17	18219977	Missense_Mutation	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10	17533574	18219977	62975233	63	15536											
CASC3	22794	hgsc.bcm.edu	37	chr17	38318253	38318254	+	Splice_Site	INS	-	-	G																															atccctttatctgtcctctaINSggagagcacagagcctgtgg																								rs200097668		TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr17:38318253_38318254insG	ENST00000264645.7	+	5	682		c.e5-1			NM_007359.4	NP_031385.2	O15234	CASC3_HUMAN	cancer susceptibility candidate 3						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						TCTGTCCTCTAGGAGAGCACAG	0.47																																					.		Atlas-Indel,Pindel	.											.	CASC3	39	.	0			c.457-2->G						PASS	.																																			SO:0001630	splice_region_variant	22794	exon5			.	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.457-1->G	chr17.hg19:g.38318255_38318255dupG		61.0	0.0	0		75.0	24.0	0.32	NM_007359	A8K8R0	Splice_Site	INS	ENST00000264645.7	hg19	CCDS11362.1																																																																																			.	.	.	none		0.47	CASC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257127.3	NM_007359	Intron	G	38318254	-	G	38318253	8	5	250	1	0	1	1	0	0	0	1	0	2663	434	15	0	473	0	CASC3	17	38318253	Splice_Site	INS	-	TCGA-SX-A7SP-01A-11D-A34Z-10	20098276	38318253	42876957	64	15537											
KRTAP4-7	100132476	hgsc.bcm.edu	37	chr17	39240805	39240805	+	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	ctgccgccccagctgctgccGcccctgctgctgcctgcgtc	1	8	11	21	3	0	0	0	0	0	0	1	0	0	0	7	0	8	4	7	0	0	0			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr17:39240805G>T	ENST00000391417.4	+	1	347	c.347G>T	c.(346-348)cGc>cTc	p.R116L		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	141	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)				NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						agctgctgccgcccctgctgc	0.672																																					p.R116L		Atlas-SNP	.											.	KRTAP4-7	49	.	0			c.G347T						PASS	.						18	18	18					17																	39240805		692	1587	2279	SO:0001583	missense	100132476	exon1			GCTGCCGCCCCTG	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.347G>T	chr17.hg19:g.39240805G>T	ENSP00000375236:p.Arg116Leu	11.0	0.0	.		20.0	6.0	.	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	hg19	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	6.805	0.517638	0.13005	.	.	ENSG00000240871	ENST00000391417	T	0.00606	6.26	3.15	2.13	0.27403	.	0.163808	0.19966	U	0.102091	T	0.00496	0.0016	.	.	.	0.09310	N	1	B	0.18461	0.028	B	0.15052	0.012	T	0.45804	-0.9236	9	0.28530	T	0.3	.	9.2621	0.37619	0.0:0.0:0.7821:0.2179	.	171	Q9BYR0	KRA47_HUMAN	L	116	ENSP00000375236:R116L	ENSP00000375236:R116L	R	+	2	0	KRTAP4-7	36494331	0.000000	0.05858	0.028000	0.17463	0.502000	0.33828	-0.081000	0.11321	0.603000	0.29913	0.289000	0.19496	CGC	.	.	.	none		0.672	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1			T	39240805	G	T	39240805	3	4	250	1	0	0	0	0	1	0	0	0	8562	1087	38	4	349	4	KRTAP4-7	17	39240805	Missense_Mutation	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10	922552	39240805	41954405	65	15538											
KIF2B	84643	hgsc.bcm.edu	37	chr17	51902187	51902187	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcagaaagagattgaagaggTtgaaacattacccactctgt	15	9	10	7	0	1	5	0	2	1	3	1	6	1	5	1	1	2	2	1	1	4	3			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr17:51902187T>C	ENST00000268919.4	+	1	1949	c.1793T>C	c.(1792-1794)gTt>gCt	p.V598A		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	598					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						ATTGAAGAGGTTGAAACATTA	0.418																																					p.V598A		Atlas-SNP	.											.	KIF2B	254	.	0			c.T1793C						PASS	.						149	142	144					17																	51902187		2203	4300	6503	SO:0001583	missense	84643	exon1			AAGAGGTTGAAAC	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.1793T>C	chr17.hg19:g.51902187T>C	ENSP00000268919:p.Val598Ala	38.0	0.0	.		73.0	16.0	.	NM_032559	Q96MA2|Q9BXG6	Missense_Mutation	SNP	ENST00000268919.4	hg19	CCDS32685.1	.	.	.	.	.	.	.	.	.	.	T	2.281	-0.364760	0.05103	.	.	ENSG00000141200	ENST00000268919;ENST00000416491	T	0.73469	-0.75	5.51	0.573	0.17363	.	2.001250	0.02726	N	0.114494	T	0.57799	0.2078	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.48811	-0.9002	10	0.49607	T	0.09	.	3.9988	0.09570	0.1503:0.2773:0.0:0.5724	.	598	Q8N4N8	KIF2B_HUMAN	A	598;486	ENSP00000268919:V598A	ENSP00000268919:V598A	V	+	2	0	KIF2B	49257186	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-1.122000	0.03267	0.447000	0.26695	0.533000	0.62120	GTT	.	.	.	none		0.418	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559		C	51902187	T	C	51902187	3	2	250	1	0	0	0	0	1	0	0	0	8305	1725	60	3	1795	3	KIF2B	17	51902187	Missense_Mutation	SNP	T	TCGA-SX-A7SP-01A-11D-A34Z-10	12661382	51902187	29293023	66	15539											
ZNF407	55628	hgsc.bcm.edu	37	chr18	72775890	72775890	+	Silent	SNP	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	gccatggcctctcaggagcgGgcacaggtggccttcaagaa	9	6	14	12	1	2	1	2	0	1	1	3	2	2	2	3	5	1	1	3	5	2	1			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr18:72775890G>A	ENST00000299687.5	+	8	6213	c.6213G>A	c.(6211-6213)cgG>cgA	p.R2071R		NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	2071					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)		CTCAGGAGCGGGCACAGGTGG	0.662																																					p.R2071R		Atlas-SNP	.											.	ZNF407	231	.	0			c.G6213A						PASS	.						38	46	44					18																	72775890		2113	4226	6339	SO:0001819	synonymous_variant	55628	exon8			GGAGCGGGCACAG	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.6213G>A	chr18.hg19:g.72775890G>A		44.0	0.0	.		62.0	24.0	.	NM_017757	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Silent	SNP	ENST00000299687.5	hg19	CCDS45885.1																																																																																			.	.	.	none		0.662	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		A	72775890	G	A	72775890	2	1	250	1	0	0	0	0	0	0	0	1	17899	1219	43	2		2	ZNF407	18	72775890	Silent	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10		72775890	5301358	67	15540											
KCNG2	26251	hgsc.bcm.edu	37	chr18	77659475	77659475	+	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	tgggcgcgcgccgcgacttcTccagcgtgcccgccagctat	4	7	13	17	7	1	0	0	0	1	0	2	1	1	0	4	1	3	1	4	1	1	2			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr18:77659475T>A	ENST00000316249.3	+	2	1060	c.1060T>A	c.(1060-1062)Tcc>Acc	p.S354T	KCNG2_ENST00000590307.1_3'UTR	NM_012283.1	NP_036415.1	Q9UJ96	KCNG2_HUMAN	potassium voltage-gated channel, subfamily G, member 2	354					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of heart contraction (GO:0008016)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(2)|endometrium(4)|lung(7)|skin(1)|upper_aerodigestive_tract(4)	18		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;6.92e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0244)		CCGCGACTTCTCCAGCGTGCC	0.711																																					p.S354T		Atlas-SNP	.											.	KCNG2	48	.	0			c.T1060A						PASS	.						21	22	21					18																	77659475		2200	4298	6498	SO:0001583	missense	26251	exon2			GACTTCTCCAGCG	AJ011021	CCDS12019.1	18q23	2011-07-05			ENSG00000178342	ENSG00000178342		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6249	protein-coding gene	gene with protein product		605696				10551266, 16382104	Standard	NM_012283		Approved	Kv6.2, KCNF2	uc010xfl.2	Q9UJ96	OTTHUMG00000044541	ENST00000316249.3:c.1060T>A	chr18.hg19:g.77659475T>A	ENSP00000315654:p.Ser354Thr	68.0	0.0	.		69.0	7.0	.	NM_012283		Missense_Mutation	SNP	ENST00000316249.3	hg19	CCDS12019.1	.	.	.	.	.	.	.	.	.	.	T	4.576	0.107034	0.08780	.	.	ENSG00000178342	ENST00000316249	D	0.97378	-4.36	3.35	-1.73	0.08081	Ion transport (1);	0.224075	0.36101	U	0.002787	D	0.86003	0.5829	N	0.04043	-0.29	0.29711	N	0.839401	B	0.12630	0.006	B	0.20955	0.032	T	0.79522	-0.1769	10	0.02654	T	1	.	4.7552	0.13080	0.6147:0.0:0.13:0.2553	.	354	Q9UJ96	KCNG2_HUMAN	T	354	ENSP00000315654:S354T	ENSP00000315654:S354T	S	+	1	0	KCNG2	75760463	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	4.723000	0.61965	-0.054000	0.13266	0.338000	0.21704	TCC	.	.	.	none		0.711	KCNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103906.1	NM_012283		A	77659475	T	A	77659475	3	1	250	1	0	0	0	0	1	0	0	0	8035	1551	54	5	1066	5	KCNG2	18	77659475	Missense_Mutation	SNP	T	TCGA-SX-A7SP-01A-11D-A34Z-10	4883585	77659475	417773	68	15541											
PRKCSH	5589	hgsc.bcm.edu	37	chr19	11560110	11560110	+	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	ctgtgcgggaaagagaccatGgtgaccagcaccacagagcc	12	4	13	12	1	0	3	0	1	0	2	0	5	0	4	4	2	3	1	4	2	1	0			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr19:11560110G>T	ENST00000589838.1	+	16	1470	c.1470G>T	c.(1468-1470)atG>atT	p.M490I	PRKCSH_ENST00000252455.2_Missense_Mutation_p.M490I|PRKCSH_ENST00000412601.1_Missense_Mutation_p.M487I|PRKCSH_ENST00000592741.1_Missense_Mutation_p.M497I|PRKCSH_ENST00000587327.1_Missense_Mutation_p.M487I|PRKCSH_ENST00000591462.1_Missense_Mutation_p.M487I			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	490					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|N-glycan processing (GO:0006491)|negative regulation of neuron projection development (GO:0010977)|nitrogen compound metabolic process (GO:0006807)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein N-linked glycosylation via asparagine (GO:0018279)|renal system development (GO:0072001)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|phosphoprotein binding (GO:0051219)|protein kinase C binding (GO:0005080)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(3)	19						AAGAGACCATGGTGACCAGCA	0.692																																					p.M490I		Atlas-SNP	.											.	PRKCSH	55	.	0			c.G1470T						PASS	.						60	55	57					19																	11560110		2203	4300	6503	SO:0001583	missense	5589	exon17			GACCATGGTGACC		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.1470G>T	chr19.hg19:g.11560110G>T	ENSP00000465461:p.Met490Ile	45.0	0.0	.		62.0	24.0	.	NM_002743	A8K318|Q96BU9|Q96D06|Q9P0W9	Missense_Mutation	SNP	ENST00000589838.1	hg19	CCDS32911.1	.	.	.	.	.	.	.	.	.	.	G	4.969	0.180061	0.09443	.	.	ENSG00000130175	ENST00000252455;ENST00000412601	D;D	0.82167	-1.58;-1.58	3.72	2.6	0.31112	Mannose-6-phosphate receptor, binding (1);	0.332477	0.28182	N	0.016285	T	0.66127	0.2758	N	0.12182	0.205	0.19945	N	0.999945	B;B;B;B	0.09022	0.002;0.002;0.0;0.001	B;B;B;B	0.08055	0.003;0.003;0.001;0.003	T	0.56456	-0.7976	10	0.35671	T	0.21	-13.6047	9.8819	0.41238	0.0:0.0:0.6528:0.3472	.	497;497;487;490	E7EQZ9;B4DJQ5;A8K318;P14314	.;.;.;GLU2B_HUMAN	I	490;487	ENSP00000252455:M490I;ENSP00000395616:M487I	ENSP00000252455:M490I	M	+	3	0	PRKCSH	11421110	0.719000	0.27986	0.851000	0.33527	0.320000	0.28249	0.689000	0.25437	1.895000	0.54865	0.563000	0.77884	ATG	.	.	.	none		0.692	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1			T	11560110	G	T	11560110	3	4	250	1	0	0	0	0	1	0	0	0	12526	1348	47	4	1553	4	PRKCSH	19	11560110	Missense_Mutation	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10		11560110	47568873	69	15542											
SLC1A6	6511	hgsc.bcm.edu	37	chr19	15061136	15061136	+	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	agctccagctcccgctgagaCaagtgctcgatgacggccgc	8	6	12	15	4	0	2	0	2	0	1	3	4	2	2	3	1	3	4	3	1	1	0			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr19:15061136C>A	ENST00000221742.3	-	9	1573	c.1566G>T	c.(1564-1566)ttG>ttT	p.L522F	SLC1A6_ENST00000430939.2_Missense_Mutation_p.L458F|SLC1A6_ENST00000600144.1_Missense_Mutation_p.L444F	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	522					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						CCCGCTGAGACAAGTGCTCGA	0.592																																					p.L522F		Atlas-SNP	.											.	SLC1A6	111	.	0			c.G1566T						PASS	.						61	57	58					19																	15061136		2203	4300	6503	SO:0001583	missense	6511	exon9			CTGAGACAAGTGC		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.1566G>T	chr19.hg19:g.15061136C>A	ENSP00000221742:p.Leu522Phe	74.0	0.0	.		58.0	16.0	.	NM_005071	Q8N753	Missense_Mutation	SNP	ENST00000221742.3	hg19	CCDS12321.1	.	.	.	.	.	.	.	.	.	.	c	18.63	3.664453	0.67700	.	.	ENSG00000105143	ENST00000430939;ENST00000221742	T;T	0.73363	-0.74;0.29	5.57	3.32	0.38043	.	0.000000	0.85682	D	0.000000	T	0.74230	0.3689	M	0.67953	2.075	0.80722	D	1	D;P	0.56035	0.974;0.87	P;P	0.48089	0.566;0.477	T	0.76366	-0.2985	10	0.66056	D	0.02	-14.2883	9.118	0.36769	0.0:0.7707:0.1471:0.0822	.	458;522	E7EV13;P48664	.;EAA4_HUMAN	F	458;522	ENSP00000409386:L458F;ENSP00000221742:L522F	ENSP00000221742:L522F	L	-	3	2	SLC1A6	14922136	1.000000	0.71417	0.945000	0.38365	0.916000	0.54674	0.886000	0.28241	1.356000	0.45884	0.544000	0.68410	TTG	.	.	.	none		0.592	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071		A	15061136	C	A	15061136	3	1	250	1	0	0	0	0	1	0	0	0	14449	477	17	4	132	4	SLC1A6	19	15061136	Missense_Mutation	SNP	C	TCGA-SX-A7SP-01A-11D-A34Z-10	3501026	15061136	44067847	70	15543											
ZNF616	90317	hgsc.bcm.edu	37	chr19	52618818	52618818	+	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	cgatgccttgcaaaagctgaAcggtcactgaagaccttgcc	11	8	10	12	2	1	3	1	2	0	1	1	4	1	3	3	1	5	2	3	1	4	2			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr19:52618818A>T	ENST00000600228.1	-	4	1860	c.1599T>A	c.(1597-1599)cgT>cgA	p.R533R	ZNF616_ENST00000330123.5_3'UTR	NM_178523.3	NP_848618.2	Q08AN1	ZN616_HUMAN	zinc finger protein 616	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)|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)		CAAAAGCTGAACGGTCACTGA	0.443																																					p.R533R		Atlas-SNP	.											.	ZNF616	109	.	0			c.T1599A						PASS	.						100	96	97					19																	52618818		2203	4300	6503	SO:0001819	synonymous_variant	90317	exon4			AGCTGAACGGTCA	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.1599T>A	chr19.hg19:g.52618818A>T		101.0	0.0	.		82.0	23.0	.	NM_178523	B3KRV1|Q0P658|Q658V7	Silent	SNP	ENST00000600228.1	hg19	CCDS33090.1																																																																																			.	.	.	none		0.443	ZNF616-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462451.1	XM_030892		T	52618818	A	T	52618818	2	4	250	1	0	0	0	0	0	0	0	1	18053	30	2	5		5	ZNF616	19	52618818	Silent	SNP	A	TCGA-SX-A7SP-01A-11D-A34Z-10	37557682	52618818	6510165	71	15544											
ISOC2	79763	hgsc.bcm.edu	37	chr19	55967191	55967191	+	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	ctgctccgtcagcatgactgGcacctcaagcagccgggcca	8	6	11	16	2	2	1	2	1	0	0	3	1	3	1	4	2	4	4	4	2	1	0			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr19:55967191G>T	ENST00000425675.2	-	3	220	c.160C>A	c.(160-162)Cca>Aca	p.P54T	ISOC2_ENST00000085068.3_Missense_Mutation_p.P54T|ISOC2_ENST00000438389.2_Intron			Q96AB3	ISOC2_HUMAN	isochorismatase domain containing 2	54					protein destabilization (GO:0031648)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			endometrium(1)|lung(4)|ovary(1)|stomach(1)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0535)		AGCATGACTGGCACCTCAAGC	0.667																																					p.P54T		Atlas-SNP	.											.	ISOC2	16	.	0			c.C160A						PASS	.						8	9	9					19																	55967191		2149	4217	6366	SO:0001583	missense	79763	exon3			TGACTGGCACCTC	AK027122	CCDS12925.1, CCDS46194.1, CCDS46195.1	19q13.42	2011-07-14			ENSG00000063241	ENSG00000063241			26278	protein-coding gene	gene with protein product		612928				17658461	Standard	NM_024710		Approved	FLJ23469	uc002qla.3	Q96AB3		ENST00000425675.2:c.160C>A	chr19.hg19:g.55967191G>T	ENSP00000401726:p.Pro54Thr	43.0	0.0	.		53.0	11.0	.	NM_001136201	Q6ZN91|Q9H5G0	Missense_Mutation	SNP	ENST00000425675.2	hg19	CCDS46195.1	.	.	.	.	.	.	.	.	.	.	G	16.39	3.109664	0.56398	.	.	ENSG00000063241	ENST00000085068;ENST00000425675	.	.	.	4.39	3.27	0.37495	Isochorismatase-like (3);	0.000000	0.85682	D	0.000000	T	0.80352	0.4607	M	0.91717	3.235	0.58432	D	0.999997	P;D	0.76494	0.956;0.999	P;D	0.66602	0.768;0.945	D	0.84554	0.0646	9	0.72032	D	0.01	-22.6752	12.0338	0.53412	0.0:0.0:0.8278:0.1722	.	54;54	Q96AB3;Q96AB3-2	ISOC2_HUMAN;.	T	54	.	ENSP00000085068:P54T	P	-	1	0	ISOC2	60659003	1.000000	0.71417	0.096000	0.21009	0.418000	0.31294	6.666000	0.74446	2.168000	0.68352	0.491000	0.48974	CCA	.	.	.	none		0.667	ISOC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453179.1	NM_024710		T	55967191	G	T	55967191	3	4	250	1	0	0	0	0	1	0	0	0	7870	1203	42	4	521	4	ISOC2	19	55967191	Missense_Mutation	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10	3348373	55967191	3161792	72	15545											
ZSCAN1	284312	hgsc.bcm.edu	37	chr19	58549300	58549300	+	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	cctgggccagcaagccccagGgacaccgaagcccagcgtct	9	3	12	17	2	1	0	0	0	1	0	1	2	1	1	6	2	4	1	6	2	2	0			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr19:58549300G>T	ENST00000282326.1	+	3	343	c.96G>T	c.(94-96)agG>agT	p.R32S	ZSCAN1_ENST00000391700.1_Missense_Mutation_p.R32S|ZSCAN1_ENST00000601162.1_Missense_Mutation_p.R32S	NM_182572.3	NP_872378.3	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	32					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)		CAAGCCCCAGGGACACCGAAG	0.701																																					p.R32S		Atlas-SNP	.											.	ZSCAN1	102	.	0			c.G96T						PASS	.						12	15	14					19																	58549300		2130	4230	6360	SO:0001583	missense	284312	exon3			CCCCAGGGACACC	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.96G>T	chr19.hg19:g.58549300G>T	ENSP00000282326:p.Arg32Ser	16.0	0.0	.		19.0	6.0	.	NM_182572	Q3B798|Q6WLH8|Q86WS8	Missense_Mutation	SNP	ENST00000282326.1	hg19	CCDS12969.1	.	.	.	.	.	.	.	.	.	.	G	3.301	-0.142840	0.06669	.	.	ENSG00000152467	ENST00000391700;ENST00000282326	T;T	0.05513	3.43;3.43	1.7	-0.919	0.10478	Retrovirus capsid, C-terminal (1);	.	.	.	.	T	0.04724	0.0128	L	0.34521	1.04	0.09310	N	1	B;B	0.26318	0.146;0.01	B;B	0.32533	0.147;0.002	T	0.47169	-0.9138	9	0.21540	T	0.41	.	2.8776	0.05636	0.2013:0.2973:0.5015:0.0	.	32;32	Q8NBB4;Q8NBB4-2	ZSCA1_HUMAN;.	S	32	ENSP00000375581:R32S;ENSP00000282326:R32S	ENSP00000282326:R32S	R	+	3	2	ZSCAN1	63241112	0.004000	0.15560	0.000000	0.03702	0.002000	0.02628	1.259000	0.32956	-0.144000	0.11314	-0.287000	0.09952	AGG	.	.	.	none		0.701	ZSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466427.1	NM_182572		T	58549300	G	T	58549300	3	4	250	1	0	0	0	0	1	0	0	0	18238	1223	43	4	98	4	ZSCAN1	19	58549300	Missense_Mutation	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10	2582109	58549300	579683	73	15546											
HNF4A	3172	hgsc.bcm.edu	37	chr20	43036091	43036091	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actgcaggctcaagaaatgcTtccgggctggcatgaagaag	12	7	13	9	1	1	3	1	1	0	2	2	3	2	3	1	3	2	5	1	3	4	1			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr20:43036091T>C	ENST00000316099.4	+	3	450	c.361T>C	c.(361-363)Ttc>Ctc	p.F121L	HNF4A_ENST00000316673.4_Missense_Mutation_p.F99L|HNF4A_ENST00000415691.2_Missense_Mutation_p.F121L|HNF4A_ENST00000457232.1_Missense_Mutation_p.F99L|MIR3646_ENST00000578301.1_RNA|HNF4A_ENST00000609795.1_Missense_Mutation_p.F99L|HNF4A_ENST00000443598.2_Missense_Mutation_p.F121L	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	121					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)			CAAGAAATGCTTCCGGGCTGG	0.602																																					p.F121L	Colon(79;2 1269 8820 14841 52347)	Atlas-SNP	.											.	HNF4A	150	.	0			c.T361C						PASS	.						76	65	68					20																	43036091		2203	4300	6503	SO:0001583	missense	3172	exon3			AAATGCTTCCGGG	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.361T>C	chr20.hg19:g.43036091T>C	ENSP00000312987:p.Phe121Leu	23.0	0.0	.		31.0	15.0	.	NM_178849	A5JW41|B2RPP8|O00659|O00723|Q14540|Q5QPB8|Q6B4V5|Q6B4V6|Q6B4V7|Q92653|Q92654|Q92655|Q99864|Q9NQH0	Missense_Mutation	SNP	ENST00000316099.4	hg19	CCDS13330.1	.	.	.	.	.	.	.	.	.	.	T	19.35	3.810261	0.70797	.	.	ENSG00000101076	ENST00000316673;ENST00000457232;ENST00000316099;ENST00000443598;ENST00000338692;ENST00000415691	D;D;D;D;D	0.96168	-3.93;-3.93;-3.93;-3.93;-3.93	5.69	5.69	0.88448	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (4);	0.088735	0.85682	D	0.000000	D	0.92714	0.7684	N	0.02736	-0.51	0.80722	D	1	D;P;P;D;D;D;B	0.89917	1.0;0.526;0.526;1.0;0.993;0.991;0.146	D;P;P;D;D;D;B	0.97110	1.0;0.557;0.557;1.0;0.951;0.919;0.174	D	0.90207	0.4261	10	0.08837	T	0.75	.	15.9429	0.79771	0.0:0.0:0.0:1.0	.	114;121;121;121;99;99;99	Q5QPB7;P41235;F1D8S2;P41235-3;F1D8T0;P41235-6;P41235-7	.;HNF4A_HUMAN;.;.;.;.;.	L	99;99;121;121;151;121	ENSP00000315180:F99L;ENSP00000396216:F99L;ENSP00000312987:F121L;ENSP00000410911:F121L;ENSP00000412111:F121L	ENSP00000312987:F121L	F	+	1	0	HNF4A	42469505	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.032000	0.88838	2.164000	0.68074	0.523000	0.50628	TTC	.	.	.	none		0.602	HNF4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079363.3			C	43036091	T	C	43036091	3	2	250	1	0	0	0	0	1	0	0	0	7260	1609	56	3	424	3	HNF4A	20	43036091	Missense_Mutation	SNP	T	TCGA-SX-A7SP-01A-11D-A34Z-10		43036091	19989429	74	15547											
PCK1	5105	hgsc.bcm.edu	37	chr20	56137207	56137207	+	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	cacccaagagcaaagagacaCagtgcccatccccaaaacag	17	2	7	15	0	0	2	0	0	0	2	1	3	1	2	4	0	3	1	4	0	4	0			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr20:56137207C>T	ENST00000319441.4	+	3	469	c.305C>T	c.(304-306)aCa>aTa	p.T102I	PCK1_ENST00000535860.1_Intron|PCK1_ENST00000543666.1_Intron	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	102					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			CAAAGAGACACAGTGCCCATC	0.542																																					p.T102I		Atlas-SNP	.											.	PCK1	95	.	0			c.C305T						PASS	.						103	91	95					20																	56137207		2203	4300	6503	SO:0001583	missense	5105	exon3			GAGACACAGTGCC		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.305C>T	chr20.hg19:g.56137207C>T	ENSP00000319814:p.Thr102Ile	52.0	0.0	.		55.0	10.0	.	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Missense_Mutation	SNP	ENST00000319441.4	hg19	CCDS13460.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.401418	0.83120	.	.	ENSG00000124253	ENST00000319441	T	0.11712	2.75	5.45	5.45	0.79879	Phosphoenolpyruvate carboxykinase, N-terminal (2);	0.091457	0.85682	D	0.000000	T	0.32645	0.0836	M	0.62088	1.915	0.80722	D	1	P	0.41748	0.761	P	0.60886	0.88	T	0.00690	-1.1608	10	0.87932	D	0	-7.538	19.2944	0.94117	0.0:1.0:0.0:0.0	.	102	P35558	PCKGC_HUMAN	I	102	ENSP00000319814:T102I	ENSP00000319814:T102I	T	+	2	0	PCK1	55570613	1.000000	0.71417	0.832000	0.32986	0.637000	0.38172	7.380000	0.79704	2.561000	0.86390	0.655000	0.94253	ACA	.	.	.	none		0.542	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2			T	56137207	C	T	56137207	3	4	250	1	0	0	0	0	1	0	0	0	11588	478	17	2	311	2	PCK1	20	56137207	Missense_Mutation	SNP	C	TCGA-SX-A7SP-01A-11D-A34Z-10	13101116	56137207	6888313	75	15548											
ASCC2	84164	hgsc.bcm.edu	37	chr22	30188510	30188510	+	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	ctttggttctcagcacctgaGggatggtgaatggcctgagg	7	11	15	8	0	1	3	1	3	1	0	2	4	1	4	2	5	1	2	2	5	1	2			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chr22:30188510G>C	ENST00000397771.2	-	19	2111	c.1934C>G	c.(1933-1935)cCt>cGt	p.P645R	ASCC2_ENST00000542393.1_Missense_Mutation_p.P569R|ASCC2_ENST00000307790.3_Missense_Mutation_p.P645R			Q9H1I8	ASCC2_HUMAN	activating signal cointegrator 1 complex subunit 2	645				P -> L (in Ref. 1; AAG45475). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					endometrium(3)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(5;0.000103)|Epithelial(10;0.0169)|all cancers(5;0.0259)			CAGCACCTGAGGGATGGTGAA	0.562																																					p.P645R		Atlas-SNP	.											.	ASCC2	53	.	0			c.C1934G						PASS	.						318	278	292					22																	30188510		2203	4300	6503	SO:0001583	missense	84164	exon18			ACCTGAGGGATGG	AY013289	CCDS13869.1, CCDS56226.1	22q12.1	2004-07-27			ENSG00000100325	ENSG00000100325			24103	protein-coding gene	gene with protein product	"ASC 1 complex subunit P100"	614216				12077347, 9847074	Standard	NM_032204		Approved	ASC1p100, FLJ21588, DKFZp586O0223	uc003agr.3	Q9H1I8	OTTHUMG00000067658	ENST00000397771.2:c.1934C>G	chr22.hg19:g.30188510G>C	ENSP00000380877:p.Pro645Arg	87.0	0.0	.		123.0	51.0	.	NM_032204	B7Z8E0|F5H6J9|Q4TT54|Q8TAZ0|Q9H711|Q9H9D6	Missense_Mutation	SNP	ENST00000397771.2	hg19	CCDS13869.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.519705	0.85495	.	.	ENSG00000100325	ENST00000307790;ENST00000397771;ENST00000542393	T;T;T	0.10288	2.89;2.89;2.89	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.30324	0.0761	L	0.60845	1.875	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.00311	-1.1827	10	0.34782	T	0.22	-8.3081	17.9377	0.89018	0.0:0.0:1.0:0.0	.	569;645	F5H6J9;Q9H1I8	.;ASCC2_HUMAN	R	645;645;569	ENSP00000305502:P645R;ENSP00000380877:P645R;ENSP00000437570:P569R	ENSP00000305502:P645R	P	-	2	0	ASCC2	28518510	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.301000	0.89951	2.651000	0.90000	0.563000	0.77884	CCT	.	.	.	none		0.562	ASCC2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322127.1	NM_032204		C	30188510	G	C	30188510	3	2	250	1	0	0	0	0	1	0	0	0	1032	1000	35	4	351	4	ASCC2	22	30188510	Missense_Mutation	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10		30188510	21116056	76	15549											
FAM48B1	100130302	hgsc.bcm.edu	37	chrX	24382435	24382435	+	IGR	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	ctgctgctgctgctcctgctCctgctctagctgctgctgct	1	14	10	16	0	1	0	0	0	1	0	3	0	3	0	2	0	10	10	2	0	1	1			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chrX:24382435C>G								AC004552.1 (15412 upstream) : PDK3 (100902 downstream)																							tgctcctgctcctgctctagc	0.627																																					p.P520A		Atlas-SNP	.											.	.	.	.	0			c.C1558G						PASS	.						2	2	2					X																	24382435		1085	2493	3578	SO:0001628	intergenic_variant	100130302	exon1			CCTGCTCCTGCTC																													chrX.hg19:g.24382435C>G		85.0	0.0	.		151.0	21.0	.	NM_001136234		Missense_Mutation	SNP		hg19																																																																																				.	.	.	none	0	0.627									G	24382435	C	G	24382435	1	3	250	0	1	0	0	0	0	0	0	0	5580	855	30	4		4	FAM48B1	23	24382435	IGR	SNP	C	TCGA-SX-A7SP-01A-11D-A34Z-10		24382435	130888125	77	15550											
DMD	1756	hgsc.bcm.edu	37	chrX	32486636	32486636	+	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	tgaatttttcggagtttattCatttgctcctctagcttttg	6	21	7	7	1	2	1	1	1	1	0	4	2	3	2	1	1	2	3	1	1	3	9			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chrX:32486636C>G	ENST00000357033.4	-	23	3347	c.3141G>C	c.(3139-3141)atG>atC	p.M1047I	DMD_ENST00000378677.2_Missense_Mutation_p.M1043I	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	1047					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)				GGAGTTTATTCATTTGCTCCT	0.368																																					p.M1047I		Atlas-SNP	.											.	DMD	2127	.	0			c.G3141C						PASS	.						56	47	50					X																	32486636		2202	4299	6501	SO:0001583	missense	1756	exon23			TTTATTCATTTGC	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.3141G>C	chrX.hg19:g.32486636C>G	ENSP00000354923:p.Met1047Ile	354.0	0.0	.		547.0	31.0	.	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	C	0.051	-1.249776	0.01469	.	.	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280	T;T	0.32988	1.43;1.43	5.12	4.26	0.50523	.	0.000000	0.40554	U	0.001066	T	0.18635	0.0447	L	0.31065	0.9	0.80722	D	1	B;B;B	0.11235	0.001;0.004;0.0	B;B;B	0.09377	0.004;0.003;0.002	T	0.06338	-1.0832	10	0.11485	T	0.65	.	8.0396	0.30513	0.0:0.746:0.0:0.254	.	1039;1047;1043	P11532-4;P11532;E9PDN5	.;DMD_HUMAN;.	I	1039;1043;1047;1047;924	ENSP00000367948:M1043I;ENSP00000354923:M1047I	ENSP00000354923:M1047I	M	-	3	0	DMD	32396557	1.000000	0.71417	0.847000	0.33407	0.461000	0.32589	1.510000	0.35790	1.042000	0.40150	0.538000	0.68166	ATG	.	.	.	none		0.368	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		G	32486636	C	G	32486636	3	3	250	1	0	0	0	0	1	0	0	0	4582	826	29	4	8387	4	DMD	23	32486636	Missense_Mutation	SNP	C	TCGA-SX-A7SP-01A-11D-A34Z-10	8104201	32486636	122783924	78	15551											
KDM6A	7403	hgsc.bcm.edu	37	chrX	44949073	44949073	+	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	ttccagtgtataggtttattCagcgacctggagatttggtc	8	15	11	7	1	1	1	1	0	0	1	3	3	2	1	2	3	1	2	2	3	3	7			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chrX:44949073C>T	ENST00000377967.4	+	25	3675	c.3634C>T	c.(3634-3636)Cag>Tag	p.Q1212*	KDM6A_ENST00000543216.1_Nonsense_Mutation_p.Q1133*|KDM6A_ENST00000536777.1_Nonsense_Mutation_p.Q1167*|KDM6A_ENST00000382899.4_Nonsense_Mutation_p.Q1219*	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	1212	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						TAGGTTTATTCAGCGACCTGG	0.398			"D, N, F, S"		"renal, oesophageal SCC, MM"																																p.Q1212X	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.C3634T						PASS	.						153	129	137					X																	44949073		2203	4300	6503	SO:0001587	stop_gained	7403	exon25			TTTATTCAGCGAC	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.3634C>T	chrX.hg19:g.44949073C>T	ENSP00000367203:p.Gln1212*	344.0	0.0	.		553.0	263.0	.	NM_021140	Q52LL9|Q5JVQ7	Nonsense_Mutation	SNP	ENST00000377967.4	hg19	CCDS14265.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	40|40	8.524194|8.524194	0.98848|0.98848	.|.	.|.	ENSG00000147050|ENSG00000147050	ENST00000334516;ENST00000377967;ENST00000536777;ENST00000382899;ENST00000543216|ENST00000414389;ENST00000433797	.|.	.|.	.|.	5.37|5.37	5.37|5.37	0.77165|0.77165	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.74619	.|0.3740	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.74009	.|-0.3802	.|3	0.87932|.	D|.	0|.	-7.8457|-7.8457	18.2517|18.2517	0.90006|0.90006	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|L	909;1212;1167;1219;1133|809;854	.|.	ENSP00000334340:Q909X|.	Q|S	+|+	1|2	0|0	KDM6A|KDM6A	44834017|44834017	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.396000|7.396000	0.79891|0.79891	2.249000|2.249000	0.74217|0.74217	0.468000|0.468000	0.43344|0.43344	CAG|TCA	.	.	.	none		0.398	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140		T	44949073	C	T	44949073	4	4	250	1	0	0	0	0	0	1	0	0	8144	827	29	2	3732	2	KDM6A	23	44949073	Nonsense_Mutation	SNP	C	TCGA-SX-A7SP-01A-11D-A34Z-10	12462437	44949073	110321487	79	15552											
RLIM	51132	hgsc.bcm.edu	37	chrX	73811367	73811367	+	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	taaccagcgatcgatgcagtGgacatggtactcatgggaac	12	8	12	9	2	1	0	1	0	0	0	2	4	1	2	1	3	5	2	1	3	3	2			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chrX:73811367G>T	ENST00000332687.6	-	4	2001	c.1783C>A	c.(1783-1785)Cac>Aac	p.H595N	RLIM_ENST00000349225.2_Missense_Mutation_p.H595N	NM_016120.3	NP_057204.2	Q9NVW2	RNF12_HUMAN	ring finger protein, LIM domain interacting	595					negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|random inactivation of X chromosome (GO:0060816)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TCGATGCAGTGGACATGGTAC	0.398																																					p.H595N	Esophageal Squamous(169;1899 1923 14997 18818 32118)	Atlas-SNP	.											.	RLIM	90	.	0			c.C1783A						PASS	.						138	110	119					X																	73811367		2203	4300	6503	SO:0001583	missense	51132	exon5			TGCAGTGGACATG	AF155109	CCDS14427.1	Xq13-q21	2013-01-09	2009-02-17	2009-02-17	ENSG00000131263	ENSG00000131263		"RING-type (C3HC4) zinc fingers"	13429	protein-coding gene	gene with protein product	"ring zinc finger protein NY-REN-43antigen", "LIM domain interacting ring finger protein"	300379	"ring finger protein 12"	RNF12		10508479	Standard	NM_016120		Approved	NY-REN-43, MGC15161	uc004ebw.3	Q9NVW2	OTTHUMG00000021859	ENST00000332687.6:c.1783C>A	chrX.hg19:g.73811367G>T	ENSP00000328059:p.His595Asn	205.0	0.0	.		364.0	167.0	.	NM_183353	B2RBQ1|D3DTE0|Q96D38|Q9Y598	Missense_Mutation	SNP	ENST00000332687.6	hg19	CCDS14427.1	.	.	.	.	.	.	.	.	.	.	G	15.48	2.846145	0.51164	.	.	ENSG00000131263	ENST00000332687;ENST00000349225	T;T	0.67345	-0.26;-0.26	5.41	4.53	0.55603	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, RING-H2-type (1);	0.047424	0.85682	D	0.000000	T	0.68403	0.2997	N	0.11927	0.2	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.74054	-0.3788	10	0.62326	D	0.03	-15.4496	15.294	0.73888	0.0:0.1368:0.8632:0.0	.	595	Q9NVW2	RNF12_HUMAN	N	595	ENSP00000328059:H595N;ENSP00000253571:H595N	ENSP00000328059:H595N	H	-	1	0	RLIM	73728092	1.000000	0.71417	0.985000	0.45067	0.989000	0.77384	9.416000	0.97383	1.038000	0.40049	0.600000	0.82982	CAC	.	.	.	none		0.398	RLIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057268.1	NM_016120		T	73811367	G	T	73811367	3	4	250	1	0	0	0	0	1	0	0	0	13403	1348	47	4	95	4	RLIM	23	73811367	Missense_Mutation	SNP	G	TCGA-SX-A7SP-01A-11D-A34Z-10	28862294	73811367	81459193	80	15553											
SMARCA1	6594	hgsc.bcm.edu	37	chrX	128614706	128614706	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctattgtcttccgataataaAgaatttccttttccaggagc	11	15	6	9	1	1	1	0	0	1	1	4	3	4	2	3	1	1	0	3	1	5	8			TCGA-SX-A7SP-01A-11D-A34Z-10	TCGA-SX-A7SP-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c6abb591-8bba-4022-b736-659828bb3947	68027171-3c57-48ce-b796-f96345b1c177	g.chrX:128614706A>G	ENST00000371122.4	-	19	2543	c.2414T>C	c.(2413-2415)cTt>cCt	p.L805P	SMARCA1_ENST00000371121.3_Missense_Mutation_p.L793P|SMARCA1_ENST00000371123.1_Missense_Mutation_p.L793P	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	805					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						CCGATAATAAAGAATTTCCTT	0.323																																					p.L805P		Atlas-SNP	.											.	SMARCA1	126	.	0			c.T2414C						PASS	.						57	56	57					X																	128614706		2203	4300	6503	SO:0001583	missense	6594	exon19			TAATAAAGAATTT	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.2414T>C	chrX.hg19:g.128614706A>G	ENSP00000360163:p.Leu805Pro	258.0	1.0	.		435.0	218.0	.	NM_003069	Q5JV41|Q5JV42	Missense_Mutation	SNP	ENST00000371122.4	hg19	CCDS14612.1	.	.	.	.	.	.	.	.	.	.	A	18.22	3.575258	0.65878	.	.	ENSG00000102038	ENST00000371121;ENST00000371123;ENST00000371122;ENST00000450039	D;D;D;D	0.91740	-2.9;-2.9;-2.9;-2.9	4.96	4.96	0.65561	ATPase, nucleosome remodelling ISWI, HAND domain (2);	0.000000	0.53938	D	0.000048	D	0.94886	0.8347	M	0.68952	2.095	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.71414	0.973;0.973;0.955;0.973	D	0.94695	0.7877	10	0.49607	T	0.09	-11.6576	13.7875	0.63119	1.0:0.0:0.0:0.0	.	784;805;793;805	E9PCY3;B7ZLQ5;P28370-2;P28370	.;.;.;SMCA1_HUMAN	P	793;793;805;784	ENSP00000360162:L793P;ENSP00000360164:L793P;ENSP00000360163:L805P;ENSP00000404275:L784P	ENSP00000360162:L793P	L	-	2	0	SMARCA1	128442387	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.278000	0.95766	1.630000	0.50440	0.430000	0.28490	CTT	.	.	.	none		0.323	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058206.1	NM_003069		G	128614706	A	G	128614706	3	3	250	1	0	0	0	0	1	0	0	0	14781	72	3	3	774	3	SMARCA1	23	128614706	Missense_Mutation	SNP	A	TCGA-SX-A7SP-01A-11D-A34Z-10	54803339	128614706	26655854	81	15554											
TMEM51	55092	hgsc.bcm.edu	37	chr1	15545967	15545967	+	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	ctctcccgtcctatgagtcaCtgacggggctcgacgagacc	7	8	11	15	4	2	3	1	2	1	1	5	5	3	3	3	2	0	1	3	2	1	1			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr1:15545967C>T	ENST00000428417.1	+	3	936	c.490C>T	c.(490-492)Ctg>Ttg	p.L164L	TMEM51_ENST00000434578.2_3'UTR|TMEM51_ENST00000376014.3_Silent_p.L164L|TMEM51_ENST00000400796.3_Silent_p.L164L|TMEM51_ENST00000376008.2_Silent_p.L164L	NM_001136217.1	NP_001129689.1	Q9NW97	TMM51_HUMAN	transmembrane protein 51	164						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(3)|large_intestine(2)|lung(5)|prostate(2)	14		Renal(390;0.00145)|Breast(348;0.00186)|Colorectal(325;0.00215)|all_lung(284;0.00459)|Lung NSC(340;0.0104)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;2.07e-06)|COAD - Colon adenocarcinoma(227;7.14e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000175)|KIRC - Kidney renal clear cell carcinoma(229;0.00141)|STAD - Stomach adenocarcinoma(313;0.00644)|READ - Rectum adenocarcinoma(331;0.0751)		CTATGAGTCACTGACGGGGCT	0.587																																					p.L164L		Atlas-SNP	.											.	TMEM51	28	.	0			c.C490T						PASS	.						79	78	79					1																	15545967		2203	4300	6503	SO:0001819	synonymous_variant	55092	exon3			GAGTCACTGACGG	AK098467	CCDS154.1	1p36.21	2008-02-05	2005-05-22	2005-05-22	ENSG00000171729	ENSG00000171729			25488	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 72"	C1orf72		12477932	Standard	NM_018022		Approved	FLJ10199	uc001avx.3	Q9NW97	OTTHUMG00000002046	ENST00000428417.1:c.490C>T	chr1.hg19:g.15545967C>T		319.0	0.0	.		286.0	116.0	.	NM_018022	A8K819	Silent	SNP	ENST00000428417.1	hg19	CCDS154.1																																																																																			.	.	.	none		0.587	TMEM51-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005699.3	NM_018022		T	15545967	C	T	15545967	2	4	251	1	0	0	0	0	0	0	0	1	16189	564	20	2		2	TMEM51	1	15545967	Silent	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10		15545967	233704654	1	15555											
PRPF38B	55119	hgsc.bcm.edu	37	chr1	109235289	109235289	+	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	ctgcagctgcggctcagcaaCagcagcagtgcggcggcggc	7	4	16	14	4	1	0	1	0	0	0	1	0	1	0	0	4	8	6	0	4	1	0			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr1:109235289C>A	ENST00000370025.4	+	1	345	c.76C>A	c.(76-78)Cag>Aag	p.Q26K	PRPF38B_ENST00000370021.1_5'UTR|PRPF38B_ENST00000370022.5_Missense_Mutation_p.Q26K|PRPF38B_ENST00000467302.1_3'UTR	NM_018061.2	NP_060531.2	Q5VTL8	PR38B_HUMAN	pre-mRNA processing factor 38B	26					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			NS(1)|kidney(3)|large_intestine(5)|lung(8)|prostate(1)|skin(1)	19		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0149)|Lung(183;0.0888)|COAD - Colon adenocarcinoma(174;0.113)|Epithelial(280;0.161)		ggctcagcaacagcagcagtg	0.672																																					p.Q26K		Atlas-SNP	.											.	PRPF38B	55	.	0			c.C76A						PASS	.						18	17	18					1																	109235289		2019	4001	6020	SO:0001583	missense	55119	exon1			CAGCAACAGCAGC	AL833950	CCDS788.1	1p13.3	2013-10-03	2013-10-03		ENSG00000134186	ENSG00000134186			25512	protein-coding gene	gene with protein product			"PRP38 pre-mRNA processing factor 38 (yeast) domain containing B"				Standard	NM_018061		Approved	FLJ10330, NET1	uc001dvv.4	Q5VTL8	OTTHUMG00000010991	ENST00000370025.4:c.76C>A	chr1.hg19:g.109235289C>A	ENSP00000359042:p.Gln26Lys	98.0	0.0	.		102.0	47.0	.	NM_018061	Q05DD6|Q32Q58|Q5VTL9|Q6PK39|Q7Z6E2|Q86WF3|Q8IWG9|Q9NW40	Missense_Mutation	SNP	ENST00000370025.4	hg19	CCDS788.1	.	.	.	.	.	.	.	.	.	.	C	15.50	2.853346	0.51270	.	.	ENSG00000134186	ENST00000370025;ENST00000370022	.	.	.	5.46	3.54	0.40534	.	0.326350	0.26241	N	0.025513	T	0.17746	0.0426	N	0.14661	0.345	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08889	-1.0700	9	0.11182	T	0.66	.	10.7726	0.46332	0.1297:0.8012:0.0:0.0691	.	26	Q5VTL8	PR38B_HUMAN	K	26	.	ENSP00000359039:Q26K	Q	+	1	0	PRPF38B	109036812	1.000000	0.71417	0.998000	0.56505	0.640000	0.38277	2.843000	0.48238	1.271000	0.44313	0.462000	0.41574	CAG	.	.	.	none		0.672	PRPF38B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030231.1	NM_018061		A	109235289	C	A	109235289	3	1	251	1	0	0	0	0	1	0	0	0	12578	479	17	4	78	4	PRPF38B	1	109235289	Missense_Mutation	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	93689322	109235289	140015332	2	15556											
TOMM40L	84134	hgsc.bcm.edu	37	chr1	161197092	161197092	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccctgggcttgccgggataTcacctccatgcggcctatgc	5	9	12	15	2	1	0	1	0	0	0	2	1	2	1	5	3	3	1	5	3	2	3			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr1:161197092T>C	ENST00000367988.3	+	4	497	c.228T>C	c.(226-228)taT>taC	p.Y76Y	TOMM40L_ENST00000545897.1_Silent_p.Y76Y|TOMM40L_ENST00000367987.1_Silent_p.Y76Y|NR1I3_ENST00000479324.1_5'Flank|MIR5187_ENST00000583479.1_RNA|TOMM40L_ENST00000474486.1_Intron	NM_032174.4	NP_115550.2	Q969M1	TM40L_HUMAN	translocase of outer mitochondrial membrane 40 homolog (yeast)-like	76					ion transport (GO:0006811)|protein transport (GO:0015031)	mitochondrial outer membrane (GO:0005741)|pore complex (GO:0046930)|protein complex (GO:0043234)	porin activity (GO:0015288)			large_intestine(2)|liver(4)|lung(4)	10	all_cancers(52;1.86e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			TGCCGGGATATCACCTCCATG	0.557											OREG0013943	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y76Y		Atlas-SNP	.											.	TOMM40L	19	.	0			c.T228C						PASS	.						86	80	82					1																	161197092		2203	4300	6503	SO:0001819	synonymous_variant	84134	exon4			GGGATATCACCTC		CCDS1227.1, CCDS65700.1	1q23.3	2008-02-05	2007-01-12		ENSG00000158882	ENSG00000158882			25756	protein-coding gene	gene with protein product			"translocase of outer mitochondrial membrane 40 homolog-like (yeast)"				Standard	NM_032174		Approved	FLJ12770, TOMM40B	uc001fzd.3	Q969M1	OTTHUMG00000034345	ENST00000367988.3:c.228T>C	chr1.hg19:g.161197092T>C		152.0	0.0	.	1814	160.0	79.0	.	NM_032174	B7Z4U0|D3DVG9	Silent	SNP	ENST00000367988.3	hg19	CCDS1227.1																																																																																			.	.	.	none		0.557	TOMM40L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083029.1	NM_032174		C	161197092	T	C	161197092	2	2	251	1	0	0	0	0	0	0	0	1	16371	1442	50	3		3	TOMM40L	1	161197092	Silent	SNP	T	TCGA-SX-A7SQ-01A-12D-A35Z-10	51961803	161197092	88053529	3	15557											
FCRLB	127943	hgsc.bcm.edu	37	chr1	161695843	161695843	+	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	atcccggtggagagcgcgccCatgttctccgctaaggtggc	6	8	14	13	4	1	1	0	0	1	1	3	2	2	1	3	4	1	2	3	4	1	2			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr1:161695843C>A	ENST00000367948.2	+	6	755	c.540C>A	c.(538-540)ccC>ccA	p.P180P	FCRLB_ENST00000336830.5_Silent_p.P180P|FCRLB_ENST00000495397.1_3'UTR|FCRLB_ENST00000367944.3_Silent_p.P173P|FCRLB_ENST00000367946.3_Silent_p.P180P|FCRLB_ENST00000392158.1_Silent_p.P180P|FCRLB_ENST00000367945.1_Silent_p.P173P			Q6BAA4	FCRLB_HUMAN	Fc receptor-like B	180	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)			AGAGCGCGCCCATGTTCTCCG	0.632											OREG0013944	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P180P		Atlas-SNP	.											.	FCRLB	35	.	0			c.C540A						PASS	.						35	37	36					1																	161695843		2203	4300	6503	SO:0001819	synonymous_variant	127943	exon4			CGCGCCCATGTTC	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.540C>A	chr1.hg19:g.161695843C>A		136.0	0.0	.	1818	145.0	70.0	.	NM_001002901	A2A3J5|A2A3J7|Q5VXA6|Q6BAA0|Q6BAA1|Q6BAA2|Q6BAA3|Q8IXZ7	Silent	SNP	ENST00000367948.2	hg19	CCDS30927.1																																																																																			.	.	.	none		0.632	FCRLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083585.1	NM_152378		A	161695843	C	A	161695843	2	1	251	1	0	0	0	0	0	0	0	1	5808	581	21	4		4	FCRLB	1	161695843	Silent	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	498751	161695843	87554778	4	15558											
LHX4	89884	hgsc.bcm.edu	37	chr1	180243426	180243426	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcttctccatggacgggacAggacaatcctatcaggactt	11	9	10	11	1	2	0	1	0	1	0	4	4	3	4	2	4	1	1	2	4	2	3			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr1:180243426A>G	ENST00000263726.2	+	6	1129	c.885A>G	c.(883-885)acA>acG	p.T295T	RP5-1180C10.2_ENST00000415414.1_RNA|RP5-1180C10.2_ENST00000440959.2_RNA	NM_033343.3	NP_203129.1	Q969G2	LHX4_HUMAN	LIM homeobox 4	295					medial motor column neuron differentiation (GO:0021526)|motor neuron axon guidance (GO:0008045)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|placenta development (GO:0001890)|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)			endometrium(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)	16						TGGACGGGACAGGACAATCCT	0.527																																					p.T295T		Atlas-SNP	.											.	LHX4	36	.	0			c.A885G						PASS	.						128	114	119					1																	180243426		2203	4300	6503	SO:0001819	synonymous_variant	89884	exon6			CGGGACAGGACAA	AB037683	CCDS1338.1	1q25.3	2011-06-20			ENSG00000121454	ENSG00000121454		"Homeoboxes / LIM class"	21734	protein-coding gene	gene with protein product		602146				11844481, 11567216	Standard	NM_033343		Approved	Gsh4	uc001goe.2	Q969G2	OTTHUMG00000035115	ENST00000263726.2:c.885A>G	chr1.hg19:g.180243426A>G		643.0	0.0	.		615.0	35.0	.	NM_033343	Q8NHE0|Q8NHM1|Q8TCJ1|Q8WWX2|Q969W2	Silent	SNP	ENST00000263726.2	hg19	CCDS1338.1																																																																																			.	.	.	none		0.527	LHX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084995.2	NM_033343		G	180243426	A	G	180243426	2	3	251	1	0	0	0	0	0	0	0	1	8780	175	7	3		3	LHX4	1	180243426	Silent	SNP	A	TCGA-SX-A7SQ-01A-12D-A35Z-10	18547583	180243426	69007195	5	15559											
ABCB10	23456	hgsc.bcm.edu	37	chr1	229685017	229685017	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagacacgaatggcattggCggcagcaccacacagaaaca	15	4	11	11	2	0	2	0	0	0	2	0	3	0	2	1	3	2	4	1	3	3	2			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr1:229685017C>T	ENST00000344517.4	-	2	724	c.682G>A	c.(682-684)Gcc>Acc	p.A228T	RNA5SP78_ENST00000364622.1_RNA	NM_012089.2	NP_036221.2	Q9NRK6	ABCBA_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 10	228	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)	31	Breast(184;0.143)|Ovarian(103;0.249)	Prostate(94;0.167)				ATGGCATTGGCGGCAGCACCA	0.522																																					p.A228T		Atlas-SNP	.											.	ABCB10	71	.	0			c.G682A						PASS	.						99	89	92					1																	229685017		2203	4300	6503	SO:0001583	missense	23456	exon2			CATTGGCGGCAGC	U18237	CCDS1580.1	1q32	2012-03-14			ENSG00000135776	ENSG00000135776		"ATP binding cassette transporters / subfamily B"	41	protein-coding gene	gene with protein product	"ATP-binding cassette sub-family B member 10, mitochondrial", "ATP-binding cassette transporter 10", "ABC transporter 10 protein", "mitochondrial ATP-binding cassette 2"	605454				7766993	Standard	NM_012089		Approved	EST20237, M-ABC2, MTABC2	uc001htp.4	Q9NRK6	OTTHUMG00000039471	ENST00000344517.4:c.682G>A	chr1.hg19:g.229685017C>T	ENSP00000355637:p.Ala228Thr	183.0	0.0	.		143.0	58.0	.	NM_012089	Q13040|Q6P1Q8|Q9H3V0	Missense_Mutation	SNP	ENST00000344517.4	hg19	CCDS1580.1	.	.	.	.	.	.	.	.	.	.	C	34	5.382531	0.95967	.	.	ENSG00000135776	ENST00000344517	D	0.89050	-2.46	5.62	5.62	0.85841	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	0.92299	0.7557	M	0.71871	2.18	0.80722	D	1	D	0.60575	0.988	P	0.52823	0.71	D	0.92507	0.6013	10	0.59425	D	0.04	-22.1817	19.6592	0.95857	0.0:1.0:0.0:0.0	.	228	Q9NRK6	ABCBA_HUMAN	T	228	ENSP00000355637:A228T	ENSP00000355637:A228T	A	-	1	0	ABCB10	227751640	1.000000	0.71417	0.817000	0.32601	0.547000	0.35210	5.749000	0.68704	2.653000	0.90120	0.655000	0.94253	GCC	.	.	.	none		0.522	ABCB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095240.1	NM_012089		T	229685017	C	T	229685017	3	4	251	1	0	0	0	0	1	0	0	0	41	768	27	1	1582	1	ABCB10	1	229685017	Missense_Mutation	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	49441591	229685017	19565604	6	15560											
RGS7	6000	hgsc.bcm.edu	37	chr1	240978050	240978050	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgacatttttaaccgatgtcTatctaactgtatttgccaat	11	17	5	8	1	2	1	0	1	2	0	2	2	2	1	2	0	3	1	2	0	5	7			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr1:240978050T>C	ENST00000407727.1	-	11	810	c.811A>G	c.(811-813)Aga>Gga	p.R271G	RGS7_ENST00000348120.2_Missense_Mutation_p.R218G|RGS7_ENST00000331110.7_Missense_Mutation_p.R245G|RGS7_ENST00000446183.2_Missense_Mutation_p.R187G|RGS7_ENST00000366565.1_Missense_Mutation_p.R271G|RGS7_ENST00000401882.1_Missense_Mutation_p.R218G|RGS7_ENST00000366562.4_Missense_Mutation_p.R271G|RGS7_ENST00000366563.1_Missense_Mutation_p.R271G|RGS7_ENST00000366564.1_Missense_Mutation_p.R271G			P49802	RGS7_HUMAN	regulator of G-protein signaling 7	271	G protein gamma.				G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite terminus (GO:0044292)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(51)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			AACCGATGTCTATCTAACTGT	0.289																																					p.R271G		Atlas-SNP	.											.	RGS7	308	.	0			c.A811G						PASS	.						107	112	110					1																	240978050		2202	4298	6500	SO:0001583	missense	6000	exon12			GATGTCTATCTAA	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.811A>G	chr1.hg19:g.240978050T>C	ENSP00000384428:p.Arg271Gly	68.0	0.0	.		47.0	19.0	.	NM_002924	Q5T3H4|Q8TD66|Q8TD67|Q8WW09|Q9UNU7|Q9Y6B9	Missense_Mutation	SNP	ENST00000407727.1	hg19		.	.	.	.	.	.	.	.	.	.	T	19.36	3.812134	0.70797	.	.	ENSG00000182901	ENST00000331110;ENST00000366565;ENST00000366564;ENST00000366563;ENST00000440928;ENST00000348120;ENST00000446183;ENST00000366562;ENST00000407727;ENST00000401882	T;T;T;T;T;T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55;1.55	6.06	4.87	0.63330	G-protein gamma domain (4);	0.000000	0.85682	D	0.000000	T	0.54967	0.1891	M	0.80616	2.505	0.54753	D	0.999984	D;D;D;D;D;P;D	0.71674	0.998;0.993;0.996;0.998;0.991;0.859;0.993	D;D;D;D;D;P;D	0.73708	0.981;0.964;0.966;0.967;0.939;0.681;0.964	T	0.59920	-0.7363	10	0.72032	D	0.01	-4.1718	11.3806	0.49754	0.0:0.0:0.272:0.728	.	187;245;218;271;271;271;271	B7Z223;B7Z257;P49802-4;P49802-2;P49802-5;P49802-3;P49802	.;.;.;.;.;.;RGS7_HUMAN	G	245;271;271;271;102;218;187;271;271;218	ENSP00000331485:R245G;ENSP00000355523:R271G;ENSP00000355522:R271G;ENSP00000355521:R271G;ENSP00000404399:R102G;ENSP00000341242:R218G;ENSP00000390138:R187G;ENSP00000355520:R271G;ENSP00000384428:R271G;ENSP00000385508:R218G	ENSP00000331485:R245G	R	-	1	2	RGS7	239044673	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.064000	0.41432	2.324000	0.78689	0.533000	0.62120	AGA	.	.	.	none		0.289	RGS7-204	KNOWN	basic	protein_coding	protein_coding		NM_002924		C	240978050	T	C	240978050	3	2	251	1	0	0	0	0	1	0	0	0	13323	1530	53	3	680	3	RGS7	1	240978050	Missense_Mutation	SNP	T	TCGA-SX-A7SQ-01A-12D-A35Z-10	11293033	240978050	8272571	7	15561											
OR2C3	81472	hgsc.bcm.edu	37	chr1	247695079	247695079	+	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	aacagagacaccacagccacGtgggaagaacaggtgttgaa	16	4	12	9	1	0	3	0	1	0	2	0	5	0	4	2	2	3	1	2	2	4	1			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr1:247695079G>T	ENST00000366487.3	-	2	1096	c.735C>A	c.(733-735)caC>caA	p.H245Q	GCSAML_ENST00000366491.2_Intron|GCSAML_ENST00000531662.1_Intron|GCSAML_ENST00000366489.1_Intron|GCSAML_ENST00000527541.1_Intron|GCSAML_ENST00000463359.1_Intron|GCSAML_ENST00000366490.3_Intron|GCSAML_ENST00000527084.1_Intron	NM_198074.4	NP_932340	Q8N628	OR2C3_HUMAN	olfactory receptor, family 2, subfamily C, member 3	245						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|large_intestine(2)|lung(31)|ovary(1)|prostate(1)|skin(2)	43	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0242)	OV - Ovarian serous cystadenocarcinoma(106;0.0241)			CCACAGCCACGTGGGAAGAAC	0.547																																					p.H245Q		Atlas-SNP	.											.	OR2C3	92	.	0			c.C735A						PASS	.						131	119	123					1																	247695079		2203	4300	6503	SO:0001583	missense	81472	exon2			AGCCACGTGGGAA	BC030717	CCDS1634.2	1q44	2014-02-19	2002-02-28		ENSG00000196242	ENSG00000196242		"GPCR / Class A : Olfactory receptors"	15005	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily C, member 4"	OR2C4, OR2C5P			Standard	NM_198074		Approved	OST742	uc009xgy.3	Q8N628	OTTHUMG00000040579	ENST00000366487.3:c.735C>A	chr1.hg19:g.247695079G>T	ENSP00000355443:p.His245Gln	194.0	0.0	.		192.0	97.0	.	NM_198074	Q5JQS4|Q6IEZ1|Q8NGW7	Missense_Mutation	SNP	ENST00000366487.3	hg19	CCDS1634.2	.	.	.	.	.	.	.	.	.	.	G	12.13	1.846827	0.32606	.	.	ENSG00000196242	ENST00000366487	T	0.00307	8.17	3.75	-2.12	0.07165	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37483	U	0.002072	T	0.00845	0.0028	H	0.97023	3.925	0.18873	N	0.999989	D	0.89917	1.0	D	0.81914	0.995	T	0.20739	-1.0266	10	0.87932	D	0	.	9.1023	0.36676	0.6294:0.0:0.3706:0.0	.	245	Q8N628	OR2C3_HUMAN	Q	245	ENSP00000355443:H245Q	ENSP00000355443:H245Q	H	-	3	2	OR2C3	245761702	0.280000	0.24249	0.237000	0.24090	0.318000	0.28184	0.023000	0.13533	-0.600000	0.05790	0.650000	0.86243	CAC	.	.	.	none		0.547	OR2C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097626.2	NM_198074		T	247695079	G	T	247695079	3	4	251	1	0	0	0	0	1	0	0	0	11000	1136	40	4	231	4	OR2C3	1	247695079	Missense_Mutation	SNP	G	TCGA-SX-A7SQ-01A-12D-A35Z-10	6717029	247695079	1555542	8	15562											
TMEM178	130733	hgsc.bcm.edu	37	chr2	39934204	39934204	+	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	attagatttaagaagaatcaCtgctggcttcctcggcatgg	11	12	10	8	1	1	3	1	0	0	3	3	3	2	3	1	3	1	3	1	3	4	4			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr2:39934204C>T	ENST00000281961.2	+	3	586	c.530C>T	c.(529-531)aCt>aTt	p.T177I	TMEM178A_ENST00000482239.1_3'UTR	NM_152390.2	NP_689603.2	Q8NBL3	T178A_HUMAN	transmembrane protein 178A	177						integral component of membrane (GO:0016021)											AGAAGAATCACTGCTGGCTTC	0.463																																					p.T177I		Atlas-SNP	.											.	.	.	.	0			c.C530T						PASS	.						81	74	77					2																	39934204		2203	4300	6503	SO:0001583	missense	130733	exon3			GAATCACTGCTGG	BC029530	CCDS1804.1	2p22.1	2012-06-29	2012-06-29	2012-06-29	ENSG00000152154	ENSG00000152154			28517	protein-coding gene	gene with protein product			"transmembrane protein 178"	TMEM178		12975309	Standard	NM_001167959		Approved	MGC33926	uc002rrt.3	Q8NBL3	OTTHUMG00000128591	ENST00000281961.2:c.530C>T	chr2.hg19:g.39934204C>T	ENSP00000281961:p.Thr177Ile	108.0	0.0	.		81.0	34.0	.	NM_152390	Q6UWI6|Q8N6N4	Missense_Mutation	SNP	ENST00000281961.2	hg19	CCDS1804.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.713634	0.89112	.	.	ENSG00000152154	ENST00000281961	T	0.69926	-0.44	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.80529	0.4640	M	0.69823	2.125	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.80621	-0.1301	9	.	.	.	-10.8653	16.2261	0.82293	0.0:1.0:0.0:0.0	.	177	Q8NBL3	TM178_HUMAN	I	177	ENSP00000281961:T177I	.	T	+	2	0	TMEM178	39787708	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	6.942000	0.75928	2.437000	0.82529	0.655000	0.94253	ACT	.	.	.	none		0.463	TMEM178A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250445.2	NM_152390		T	39934204	C	T	39934204	3	4	251	1	0	0	0	0	1	0	0	0	16107	565	20	2	540	2	TMEM178	2	39934204	Missense_Mutation	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10		39934204	203265169	9	15563											
MSH2	4436	hgsc.bcm.edu	37	chr2	47641475	47641475	+	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	atcagatgattccaactttgGacagtttgaactgactactt	12	14	7	8	0	1	4	1	3	0	1	2	5	2	5	1	1	3	1	1	1	3	5	rs587782567		TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr2:47641475G>C	ENST00000233146.2	+	5	1083	c.860G>C	c.(859-861)gGa>gCa	p.G287A	MSH2_ENST00000543555.1_Missense_Mutation_p.G221A|MSH2_ENST00000406134.1_Missense_Mutation_p.G287A	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	287			Missing (in HNPCC1). {ECO:0000269|PubMed:9718327}.		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)			TCCAACTTTGGACAGTTTGAA	0.323			"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.G287A		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.G860C						PASS	.						69	68	68					2																	47641475		2203	4298	6501	SO:0001583	missense	4436	exon5	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	ACTTTGGACAGTT	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.860G>C	chr2.hg19:g.47641475G>C	ENSP00000233146:p.Gly287Ala	216.0	0.0	.		196.0	69.0	.	NM_000251	B4E2Z2|O75488	Missense_Mutation	SNP	ENST00000233146.2	hg19	CCDS1834.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.085776	0.76642	.	.	ENSG00000095002	ENST00000233146;ENST00000543555;ENST00000406134;ENST00000419559;ENST00000432737;ENST00000453755;ENST00000448533;ENST00000394792	D;D;D	0.92858	-3.12;-3.12;-3.12	5.14	4.27	0.50696	DNA mismatch repair protein MutS, connector (1);	0.135085	0.52532	D	0.000064	D	0.96439	0.8838	M	0.92555	3.32	0.58432	D	0.999999	D;D;D	0.65815	0.977;0.987;0.995	P;P;D	0.64321	0.565;0.86;0.924	D	0.96993	0.9723	10	0.87932	D	0	-11.4068	13.6716	0.62430	0.075:0.0:0.925:0.0	.	287;287;287	E7EQQ1;E9PHA6;P43246	.;.;MSH2_HUMAN	A	287;221;287;287;287;287;287;287	ENSP00000233146:G287A;ENSP00000442697:G221A;ENSP00000384199:G287A	ENSP00000233146:G287A	G	+	2	0	MSH2	47494979	1.000000	0.71417	0.996000	0.52242	0.989000	0.77384	4.225000	0.58600	1.179000	0.42884	0.591000	0.81541	GGA	.	.	.	none		0.323	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3			C	47641475	G	C	47641475	3	2	251	1	0	0	0	0	1	0	0	0	9877	1174	41	4	878	4	MSH2	2	47641475	Missense_Mutation	SNP	G	TCGA-SX-A7SQ-01A-12D-A35Z-10	7707271	47641475	195557898	10	15564											
ZNF638	27332	hgsc.bcm.edu	37	chr2	71661907	71661907	+	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	caaagaaaggaaaaggagcaGaatgaggctgaagaaagaag	22	2	14	3	0	0	6	0	2	0	4	0	8	0	8	0	3	1	2	0	3	8	0			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr2:71661907G>A	ENST00000409544.1	+	28	6537	c.5907G>A	c.(5905-5907)caG>caA	p.Q1969Q	ZNF638_ENST00000355812.3_3'UTR|ZNF638_ENST00000264447.4_Silent_p.Q1969Q|ZNF638_ENST00000409407.1_Silent_p.Q909Q	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1969					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						AAAAGGAGCAGAATGAGGCTG	0.338																																					p.Q1969Q		Atlas-SNP	.											.	ZNF638	179	.	0			c.G5907A						PASS	.						72	85	80					2																	71661907		2203	4300	6503	SO:0001819	synonymous_variant	27332	exon28			GGAGCAGAATGAG	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.5907G>A	chr2.hg19:g.71661907G>A		507.0	0.0	.		436.0	192.0	.	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Silent	SNP	ENST00000409544.1	hg19	CCDS1917.1																																																																																			.	.	.	none		0.338	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		A	71661907	G	A	71661907	2	1	251	1	0	0	0	0	0	0	0	1	18067	933	33	2		2	ZNF638	2	71661907	Silent	SNP	G	TCGA-SX-A7SQ-01A-12D-A35Z-10	24020432	71661907	171537466	11	15565											
IWS1	55677	hgsc.bcm.edu	37	chr2	128262338	128262338	+	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	ctcctcctcaccctctttttCatcttcatcactgtccattt	5	18	1	17	0	6	0	4	0	2	0	9	0	9	0	4	0	0	0	4	0	0	4			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr2:128262338C>A	ENST00000295321.4	-	3	1400	c.1141G>T	c.(1141-1143)Gaa>Taa	p.E381*	IWS1_ENST00000455721.2_Nonsense_Mutation_p.E388*|AC010976.2_ENST00000599001.1_RNA|IWS1_ENST00000486662.1_5'Flank	NM_017969.2	NP_060439.2	Q96ST2	IWS1_HUMAN	IWS1 homolog (S. cerevisiae)	381	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)		CCCTCTTTTTCATCTTCATCA	0.418																																					p.E381X		Atlas-SNP	.											.	IWS1	61	.	0			c.G1141T						PASS	.						319	320	319					2																	128262338		2203	4300	6503	SO:0001587	stop_gained	55677	exon3			CTTTTTCATCTTC	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.1141G>T	chr2.hg19:g.128262338C>A	ENSP00000295321:p.Glu381*	116.0	0.0	.		92.0	8.0	.	NM_017969	Q2TB65|Q6P157|Q8N3E8|Q96MI7|Q9NV97|Q9NWH8	Nonsense_Mutation	SNP	ENST00000295321.4	hg19	CCDS2146.1	.	.	.	.	.	.	.	.	.	.	C	33	5.266173	0.95399	.	.	ENSG00000163166	ENST00000295321;ENST00000433551;ENST00000455721	.	.	.	5.58	5.58	0.84498	.	0.258394	0.39687	N	0.001284	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	-16.8485	14.4121	0.67121	0.1475:0.8525:0.0:0.0	.	.	.	.	X	381;334;388	.	ENSP00000295321:E381X	E	-	1	0	IWS1	127978808	0.953000	0.32496	0.997000	0.53966	0.091000	0.18340	2.826000	0.48104	2.617000	0.88574	0.563000	0.77884	GAA	.	.	.	none		0.418	IWS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254384.2	NM_017969		A	128262338	C	A	128262338	4	1	251	1	0	0	0	0	0	1	0	0	7938	835	29	4	1366	4	IWS1	2	128262338	Nonsense_Mutation	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	56600431	128262338	114937035	12	15566											
FAM128A	653784	hgsc.bcm.edu	37	chr2	132249824	132249824	+	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	ccgcccgccgcctgagccagCtcgtacagctccatctcctc	5	7	8	21	4	1	1	0	1	1	0	5	1	2	1	7	0	4	3	7	0	1	1			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr2:132249824C>T	ENST00000309451.6	-	1	171	c.126G>A	c.(124-126)gaG>gaA	p.E42E	MZT2A_ENST00000410036.2_Intron|MIR4784_ENST00000579560.1_RNA|AC093838.4_ENST00000438378.2_RNA	NM_001085365.1	NP_001078834.1	Q6P582	MZT2A_HUMAN	mitotic spindle organizing protein 2A	42				EEMELYELAQAAGGGIDPDVFK -> LQGGGRAGRRGLTGP ASVPAR (in Ref. 2; AAI04651). {ECO:0000305}.		centrosome (GO:0005813)|gamma-tubulin ring complex (GO:0008274)|spindle (GO:0005819)				breast(1)|lung(1)	2						CCTGAGCCAGCTCGTACAGCT	0.741																																					p.E42E		Atlas-SNP	.											.	MZT2A	6	.	0			c.G126A						PASS	.						8	13	11					2																	132249824		2150	4263	6413	SO:0001819	synonymous_variant	653784	exon1			AGCCAGCTCGTAC	BC018206	CCDS42758.1	2q21.1	2013-10-11	2010-07-22	2010-07-22	ENSG00000173272	ENSG00000173272			33187	protein-coding gene	gene with protein product	"mitotic-spindle organizing protein associated with a ring of gamma-tubulin 2A"	613449	"family with sequence similarity 128, member A"	FAM128A		20360068	Standard	NM_001085365		Approved	MOZART2A	uc002tsw.4	Q6P582	OTTHUMG00000153606	ENST00000309451.6:c.126G>A	chr2.hg19:g.132249824C>T		47.0	0.0	.		43.0	11.0	.	NM_001085365	Q3SWV8|Q8WVB2	Silent	SNP	ENST00000309451.6	hg19	CCDS42758.1																																																																																			.	.	.	none		0.741	MZT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331811.2			T	132249824	C	T	132249824	2	4	251	1	0	0	0	0	0	0	0	1	5438	796	28	2		2	FAM128A	2	132249824	Silent	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	3987486	132249824	110949549	13	15567											
FZD5	7855	hgsc.bcm.edu	37	chr2	208633223	208633223	+	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	gcataggaagaagcgcaggtCcggcgagcattggatctcca	11	6	14	10	3	1	1	0	0	1	1	3	4	2	3	2	4	2	3	2	4	3	2			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr2:208633223C>T	ENST00000295417.3	-	2	794	c.241G>A	c.(241-243)Gac>Aac	p.D81N		NM_003468.3	NP_003459.2	Q13467	FZD5_HUMAN	frizzled class receptor 5	81	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				angiogenesis (GO:0001525)|anterior/posterior axis specification, embryo (GO:0008595)|apoptotic process (GO:0006915)|apoptotic process involved in morphogenesis (GO:0060561)|axonogenesis (GO:0007409)|brain development (GO:0007420)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|canonical Wnt signaling pathway (GO:0060070)|cell maturation (GO:0048469)|cellular response to molecule of bacterial origin (GO:0071219)|chorionic trophoblast cell differentiation (GO:0060718)|embryonic axis specification (GO:0000578)|embryonic camera-type eye development (GO:0031076)|gonad development (GO:0008406)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|neuron differentiation (GO:0030182)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic camera-type eye development (GO:0031077)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of chorionic trophoblast cell proliferation (GO:1901382)|regulation of tight junction assembly (GO:2000810)|Spemann organizer formation (GO:0060061)|syncytiotrophoblast cell differentiation involved in labyrinthine layer development (GO:0060715)|T cell differentiation in thymus (GO:0033077)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	cell projection (GO:0042995)|cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			NS(1)|kidney(1)|lung(1)|ovary(2)|prostate(1)|skin(1)	7				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.13)|Lung(261;0.134)		AAGCGCAGGTCCGGCGAGCAT	0.652																																					p.D81N		Atlas-SNP	.											.	FZD5	22	.	0			c.G241A						PASS	.						81	69	73					2																	208633223		2203	4300	6503	SO:0001583	missense	7855	exon2			GCAGGTCCGGCGA	U43318	CCDS33366.1	2q33.3	2014-01-29	2014-01-29		ENSG00000163251	ENSG00000163251		"GPCR / Class F : Frizzled receptors"	4043	protein-coding gene	gene with protein product		601723	"frizzled (Drosophila) homolog 5", "chromosome 2 open reading frame 31", "frizzled homolog 5 (Drosophila)", "frizzled 5, seven transmembrane spanning receptor", "frizzled family receptor 5"	C2orf31		8626800, 11408929	Standard	NM_003468		Approved	HFZ5, DKFZP434E2135	uc002vcj.3	Q13467	OTTHUMG00000154790	ENST00000295417.3:c.241G>A	chr2.hg19:g.208633223C>T	ENSP00000354607:p.Asp81Asn	54.0	0.0	.		74.0	35.0	.	NM_003468	A8K2X1|B2RCZ1|Q53R22	Missense_Mutation	SNP	ENST00000295417.3	hg19	CCDS33366.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.612375	0.87258	.	.	ENSG00000163251	ENST00000295417	T	0.75938	-0.98	4.61	4.61	0.57282	Frizzled domain (5);	0.000000	0.85682	D	0.000000	D	0.86339	0.5909	M	0.82517	2.595	0.80722	D	1	D	0.61697	0.99	D	0.65323	0.934	D	0.89078	0.3474	10	0.87932	D	0	.	17.0784	0.86592	0.0:1.0:0.0:0.0	.	81	Q13467	FZD5_HUMAN	N	81	ENSP00000354607:D81N	ENSP00000354607:D81N	D	-	1	0	FZD5	208341468	0.999000	0.42202	1.000000	0.80357	0.993000	0.82548	4.046000	0.57376	2.126000	0.65437	0.561000	0.74099	GAC	.	.	.	none		0.652	FZD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337060.1	NM_003468		T	208633223	C	T	208633223	3	4	251	1	0	0	0	0	1	0	0	0	6140	855	30	2	1520	2	FZD5	2	208633223	Missense_Mutation	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	76383399	208633223	34566150	14	15568											
CLASP2	23122	hgsc.bcm.edu	37	chr3	33557518	33557518	+	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	ccggccaggtaacttacctcCttatgaggatctttatgtgc	8	13	9	11	1	1	1	0	1	1	0	2	2	2	2	4	3	3	1	4	3	4	5			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr3:33557518C>A	ENST00000468888.2	-	36	4177	c.4131G>T	c.(4129-4131)aaG>aaT	p.K1377N	CLASP2_ENST00000480013.1_Missense_Mutation_p.K1156N|CLASP2_ENST00000461133.3_Missense_Mutation_p.K1136N|CLASP2_ENST00000359576.5_Missense_Mutation_p.K1368N|CLASP2_ENST00000307312.7_Missense_Mutation_p.K858N|CLASP2_ENST00000539981.1_3'UTR|CLASP2_ENST00000399362.4_Missense_Mutation_p.K1376N			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	1157					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						AACTTACCTCCTTATGAGGAT	0.323																																					p.K1378N		Atlas-SNP	.											.	CLASP2	138	.	0			c.G4134T						PASS	.						104	98	100					3																	33557518		1834	4083	5917	SO:0001583	missense	23122	exon36			TACCTCCTTATGA	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.4131G>T	chr3.hg19:g.33557518C>A	ENSP00000419974:p.Lys1377Asn	76.0	0.0	.		115.0	50.0	.	NM_015097	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Missense_Mutation	SNP	ENST00000468888.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.28|17.28	3.350574|3.350574	0.61183|0.61183	.|.	.|.	ENSG00000163539|ENSG00000163539	ENST00000487553|ENST00000468888;ENST00000399362;ENST00000359576;ENST00000307312;ENST00000480013;ENST00000461133	.|T;T;T;T;T;T	.|0.65732	.|-0.17;-0.17;-0.17;-0.17;-0.17;-0.17	5.56|5.56	0.42|0.42	0.16444|0.16444	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.74496	.|0.3724	M|M	0.77616|0.77616	2.38|2.38	0.58432|0.58432	D|D	0.999991|0.999991	.|D;D	.|0.89917	.|1.0;0.976	.|D;D	.|0.83275	.|0.996;0.93	.|T	.|0.71593	.|-0.4546	.|10	.|0.37606	.|T	.|0.19	-10.8924|-10.8924	10.4753|10.4753	0.44661|0.44661	0.0:0.5725:0.0:0.4275|0.0:0.5725:0.0:0.4275	.|.	.|1368;1376	.|F5H604;E7ERI8	.|.;.	X|N	152|1377;1376;1368;858;1156;1136	.|ENSP00000419974:K1377N;ENSP00000382297:K1376N;ENSP00000352581:K1368N;ENSP00000304743:K858N;ENSP00000417518:K1156N;ENSP00000419305:K1136N	.|ENSP00000304743:K858N	G|K	-|-	1|3	0|2	CLASP2|CLASP2	33532522|33532522	0.999000|0.999000	0.42202|0.42202	1.000000|1.000000	0.80357|0.80357	0.965000|0.965000	0.64279|0.64279	0.692000|0.692000	0.25482|0.25482	0.130000|0.130000	0.18549|0.18549	-0.251000|-0.251000	0.11542|0.11542	GGA|AAG	.	.	.	none		0.323	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044		A	33557518	C	A	33557518	3	1	251	1	0	0	0	0	1	0	0	0	3457	680	24	4	429	4	CLASP2	3	33557518	Missense_Mutation	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10		33557518	164464912	15	15569											
GLYCTK	132158	hgsc.bcm.edu	37	chr3	52325107	52325107	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggactcacagctgatgaccTgctgctcgtgctgatctcag	7	10	12	12	1	2	3	2	3	1	0	4	4	2	4	1	1	4	4	1	1	0	0			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr3:52325107T>C	ENST00000436784.2	+	3	569	c.509T>C	c.(508-510)cTg>cCg	p.L170P	GLYCTK_ENST00000471180.1_Missense_Mutation_p.L43P|GLYCTK_ENST00000354773.4_Missense_Mutation_p.L170P|GLYCTK-AS1_ENST00000493616.1_RNA|GLYCTK_ENST00000461183.1_Missense_Mutation_p.L86P|GLYCTK_ENST00000477382.1_Missense_Mutation_p.L170P|GLYCTK_ENST00000473032.1_Missense_Mutation_p.L170P|GLYCTK_ENST00000305690.8_Missense_Mutation_p.L170P			Q8IVS8	GLCTK_HUMAN	glycerate kinase	170			L -> V (in dbSNP:rs35130772).		protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|glycerate kinase activity (GO:0008887)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|urinary_tract(1)	9				BRCA - Breast invasive adenocarcinoma(193;3.56e-05)|Kidney(197;0.00171)|KIRC - Kidney renal clear cell carcinoma(197;0.00194)|OV - Ovarian serous cystadenocarcinoma(275;0.235)		GCTGATGACCTGCTGCTCGTG	0.607																																					p.L170P		Atlas-SNP	.											.	GLYCTK	30	.	0			c.T509C						PASS	.						75	55	62					3																	52325107		2203	4300	6503	SO:0001583	missense	132158	exon3			ATGACCTGCTGCT		CCDS2852.1, CCDS46841.1	3p21.1	2008-01-22			ENSG00000168237	ENSG00000168237	2.7.1.31		24247	protein-coding gene	gene with protein product		610516				16753811	Standard	NM_145262		Approved	HBEBP4, HBEBP2	uc003ddo.3	Q8IVS8	OTTHUMG00000158380	ENST00000436784.2:c.509T>C	chr3.hg19:g.52325107T>C	ENSP00000389175:p.Leu170Pro	25.0	0.0	.		37.0	10.0	.	NM_001144951	Q0P630|Q2EZ43|Q6Y2K6|Q7Z6G5|Q86YR8|Q8TED2|Q8WTY2	Missense_Mutation	SNP	ENST00000436784.2	hg19	CCDS2852.1	.	.	.	.	.	.	.	.	.	.	T	18.53	3.643459	0.67244	.	.	ENSG00000168237	ENST00000461183;ENST00000473032;ENST00000305690;ENST00000354773;ENST00000471180;ENST00000436784;ENST00000477382	T;T;T;T;T;T;T	0.54071	0.59;0.59;0.59;0.59;0.59;0.59;0.59	5.29	4.1	0.47936	.	0.082341	0.52532	D	0.000075	T	0.70150	0.3191	M	0.74467	2.265	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.993	D;D;P	0.80764	0.994;0.991;0.906	T	0.71941	-0.4440	10	0.62326	D	0.03	-7.0727	12.2235	0.54447	0.0:0.0:0.1428:0.8572	.	170;170;170	Q8IVS8-2;Q8IVS8-4;Q8IVS8	.;.;GLCTK_HUMAN	P	86;170;170;170;43;170;170	ENSP00000417264:L86P;ENSP00000418951:L170P;ENSP00000301965:L170P;ENSP00000346825:L170P;ENSP00000417526:L43P;ENSP00000389175:L170P;ENSP00000419008:L170P	ENSP00000301965:L170P	L	+	2	0	GLYCTK	52300147	1.000000	0.71417	0.989000	0.46669	0.848000	0.48234	7.489000	0.81451	0.813000	0.34350	0.533000	0.62120	CTG	.	.	.	none		0.607	GLYCTK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350835.1	NM_145262		C	52325107	T	C	52325107	3	2	251	1	0	0	0	0	1	0	0	0	6489	1580	55	3	515	3	GLYCTK	3	52325107	Missense_Mutation	SNP	T	TCGA-SX-A7SQ-01A-12D-A35Z-10	18767589	52325107	145697323	16	15570											
RPN1	6184	hgsc.bcm.edu	37	chr3	128356918	128356918	+	Frame_Shift_Del	DEL	A	A	-																															ttggccccaggatcaagagcAactgggagcttgactgtgaa																										TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr3:128356918delA	ENST00000296255.3	-	3	405	c.357delT	c.(355-357)gttfs	p.V119fs	RPN1_ENST00000497289.1_5'UTR	NM_002950.3	NP_002941.1	P04843	RPN1_HUMAN	ribophorin I	119					cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|gene expression (GO:0010467)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)|rough endoplasmic reticulum (GO:0005791)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)|poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(2)|stomach(2)	13				GBM - Glioblastoma multiforme(114;0.189)		GATCAAGAGCAACTGGGAGCT	0.458			T	EVI1	AML																																p.A120fs		Pindel	.		Dom	yes		3	3q21.3-q25.2	6184	ribophorin I		L	.	RPN1	39	.	0			c.358delG						PASS	.						88	78	81					3																	128356918		2203	4300	6503	SO:0001589	frameshift_variant	6184	exon3			.		CCDS3051.1	3q21.3	2013-03-06			ENSG00000163902	ENSG00000163902			10381	protein-coding gene	gene with protein product	"oligosaccharyltransferase 1 homolog (S. cerevisiae)", "oligosaccharyltransferase complex subunit (non-catalytic)"	180470					Standard	NM_002950		Approved	OST1	uc003ekr.1	P04843	OTTHUMG00000159691	ENST00000296255.3:c.357delT	chr3.hg19:g.128356918delA	ENSP00000296255:p.Val119fs	122.0	0.0	.		167.0	31.0	0.186	NM_002950	B2R5Z0|D3DNB6|Q68DT1	Frame_Shift_Del	DEL	ENST00000296255.3	hg19	CCDS3051.1																																																																																			.	.	.	none		0.458	RPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356934.2	NM_002950		-	128356918	A	-	128356918	7	5	251	1	0	1	0	1	0	0	0	0	13620	117	5	0	1498	0	RPN1	3	128356918	Frame_Shift_Del	DEL	A	TCGA-SX-A7SQ-01A-12D-A35Z-10	76031811	128356918	69665512	17	15571											
ZIC1	7545	hgsc.bcm.edu	37	chr3	147128271	147128272	+	Missense_Mutation	DNP	GG	GG	TT																															cacagcctctttgctgcatcGgccgggggcttcgggggccc																										TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr3:147128271_147128272GG>TT	ENST00000282928.4	+	1	1101_1102	c.372_373GG>TT	c.(370-375)tcGGcc>tcTTcc	p.A125S		NM_003412.3	NP_003403.2	Q15915	ZIC1_HUMAN	Zic family member 1	125					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)	p.S124S(1)		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						TTGCTGCATCGGCCGGGGGCTT	0.713																																					p.S124S|p.A125S		Atlas-SNP	.											ZIC1,NS,carcinoma,0,1|.	ZIC1	141	.	1	Substitution - coding silent(1)	lung(1)	c.G372T|c.G373T						PASS	.																																			SO:0001583	missense	7545	exon1			TGCATCGGCCGGG|GCATCGGCCGGGG	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	Exception_encountered	chr3.hg19:g.147128271_147128272delinsTT	ENSP00000282928:p.Ala125Ser	112.0	0.0	.		148.0|151.0	92.0|95.0	.	NM_003412	Q2M3N1	Silent|Missense_Mutation	SNP	ENST00000282928.4	hg19	CCDS3136.1																																																																																			.	.	.	none		0.713	ZIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355497.1	NM_003412		TT	147128272	GG	TT	147128271	3	4	251	1	0	0	0	0	1	0	0	0	17690	1103	39	4	374	4	ZIC1	3	147128271	Missense_Mutation	DNP	GG	TCGA-SX-A7SQ-01A-12D-A35Z-10	18771353	147128271	50894159	18	15572											
ECT2	1894	hgsc.bcm.edu	37	chr3	172533501	172533501	+	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	ataaaaaagacttcaaaaaaGgtgagttttagtgaaagtat	20	11	8	2	0	1	3	1	2	0	1	1	3	1	3	0	1	0	2	0	1	9	5			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr3:172533501G>C	ENST00000392692.3	+	23	2684	c.2508G>C	c.(2506-2508)aaG>aaC	p.K836N	ECT2_ENST00000417960.1_Splice_Site_p.K804N|ECT2_ENST00000232458.5_Splice_Site_p.K805N|ECT2_ENST00000427830.1_Splice_Site_p.K805N|ECT2_ENST00000441497.2_Splice_Site_p.K805N|ECT2_ENST00000540509.1_Splice_Site_p.K836N	NM_001258315.1	NP_001245244.1	Q9H8V3	ECT2_HUMAN	epithelial cell transforming 2	836					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)			CTTCAAAAAAGGTGAGTTTTA	0.289																																					p.K836N		Atlas-SNP	.											.	ECT2	79	.	0			c.G2508C						PASS	.						58	64	62					3																	172533501		2199	4284	6483	SO:0001630	splice_region_variant	1894	exon23			AAAAAAGGTGAGT	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.2508+1G>C	chr3.hg19:g.172533501G>C		460.0	0.0	.		467.0	269.0	.	NM_001258315	Q0MT80|Q2M269|Q6U836|Q9NSV8|Q9NVW9	Missense_Mutation	SNP	ENST00000392692.3	hg19	CCDS58860.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.8|20.8	4.053607|4.053607	0.75960|0.75960	.|.	.|.	ENSG00000114346|ENSG00000114346	ENST00000437296|ENST00000232458;ENST00000392692;ENST00000427830;ENST00000417960;ENST00000441497;ENST00000540509	.|T;T;T;T;T;T	.|0.72615	.|-0.6;-0.66;-0.67;-0.6;-0.6;-0.66	5.54|5.54	4.66|4.66	0.58398|0.58398	.|.	.|0.174934	.|0.64402	.|D	.|0.000010	T|T	0.77471|0.77471	0.4135|0.4135	L|L	0.50333|0.50333	1.59|1.59	0.80722|0.80722	D|D	1|1	.|P;P;D;D;P	.|0.61697	.|0.929;0.875;0.99;0.99;0.923	.|P;P;D;D;P	.|0.66602	.|0.77;0.77;0.945;0.945;0.885	T|T	0.78809|0.78809	-0.2058|-0.2058	5|10	.|0.87932	.|D	.|0	-3.9212|-3.9212	10.3168|10.3168	0.43743|0.43743	0.1502:0.0:0.8498:0.0|0.1502:0.0:0.8498:0.0	.|.	.|836;281;836;805;804	.|Q9H8V3;Q96SJ9;Q9H8V3-3;G5E9L8;Q9H8V3-2	.|ECT2_HUMAN;.;.;.;.	R|N	176|805;836;805;804;805;836	.|ENSP00000232458:K805N;ENSP00000376457:K836N;ENSP00000401910:K805N;ENSP00000415876:K804N;ENSP00000412259:K805N;ENSP00000443160:K836N	.|ENSP00000232458:K805N	G|K	+|+	1|3	0|2	ECT2|ECT2	174016195|174016195	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.863000|0.863000	0.49368|0.49368	5.829000|5.829000	0.69316|0.69316	1.323000|1.323000	0.45263|0.45263	0.591000|0.591000	0.81541|0.81541	GGT|AAG	.	.	.	none		0.289	ECT2-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345994.2	NM_018098	Missense_Mutation	C	172533501	G	C	172533501	5	2	251	1	0	0	0	0	0	0	1	0	4903	1014	35	4	2497	4	ECT2	3	172533501	Splice_Site	SNP	G	TCGA-SX-A7SQ-01A-12D-A35Z-10	25405230	172533501	25488929	19	15573											
LRPAP1	4043	hgsc.bcm.edu	37	chr4	3519844	3519845	+	Frame_Shift_Ins	INS	-	-	C																															gcgcagcttctccttcagctINSccgtgtgcctgctgtgcagg																										TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr4:3519844_3519845insC	ENST00000500728.2	-	5	813_814	c.667_668insG	c.(667-669)gagfs	p.E223fs	LRPAP1_ENST00000296325.5_5'UTR	NM_002337.3	NP_002328.1	P30533	AMRP_HUMAN	low density lipoprotein receptor-related protein associated protein 1	223					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)		CTCCTTCAGCTCCGTGTGCCTG	0.634																																					p.E223fs		Atlas-Indel,Pindel	.											.	LRPAP1	29	.	0			c.668_669insG						PASS	.																																			SO:0001589	frameshift_variant	4043	exon5			.		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.668dupG	chr4.hg19:g.3519846_3519846dupC	ENSP00000421922:p.Glu223fs	50.0	0.0	0		50.0	30.0	0.6	NM_002337	D3DVR9|Q2M310|Q53HQ3|Q53HS6	Frame_Shift_Ins	INS	ENST00000500728.2	hg19	CCDS3371.1																																																																																			.	.	.	none		0.634	LRPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206659.4			C	3519845	-	C	3519844	7	5	251	1	0	1	1	0	0	0	0	0	8971	1551	54	0	421	0	LRPAP1	4	3519844	Frame_Shift_Ins	INS	-	TCGA-SX-A7SQ-01A-12D-A35Z-10		3519844	187634432	20	15574											
BOD1L	259282	hgsc.bcm.edu	37	chr4	13605423	13605423	+	Frame_Shift_Del	DEL	T	T	-																															ctgatttattttcgtccttcTtttttatgtctttactacta																										TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr4:13605423delT	ENST00000040738.5	-	10	3236	c.3101delA	c.(3100-3102)aagfs	p.K1035fs		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1035	Lys-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)										TTCGTCCTTCTTTTTTATGTC	0.368																																					p.K1034fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.3102delG						PASS	.						161	171	167					4																	13605423		2203	4300	6503	SO:0001589	frameshift_variant	259282	exon10			.	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"family with sequence similarity 44, member A", "biorientation of chromosomes in cell division 1-like"	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.3101delA	chr4.hg19:g.13605423delT	ENSP00000040738:p.Lys1035fs	95.0	0.0	0		92.0	37.0	0.402174	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Frame_Shift_Del	DEL	ENST00000040738.5	hg19	CCDS3411.2																																																																																			.	.	.	none		0.368	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		-	13605423	T	-	13605423	7	5	251	1	0	1	0	1	0	0	0	0	1483	1609	56	0	6122	0	BOD1L	4	13605423	Frame_Shift_Del	DEL	T	TCGA-SX-A7SQ-01A-12D-A35Z-10	10085579	13605423	177548853	21	15575											
SHISA3	152573	hgsc.bcm.edu	37	chr4	42400234	42400234	+	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	cttcgacacgctggacgctaCcatctgctgcggctcctgcg	5	9	11	16	5	1	0	0	0	1	0	3	2	2	1	2	2	4	4	2	2	1	2			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr4:42400234C>A	ENST00000319234.4	+	1	379	c.161C>A	c.(160-162)aCc>aAc	p.T54N		NM_001080505.1	NP_001073974.1	A0PJX4	SHSA3_HUMAN	shisa family member 3	54					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	12						CTGGACGCTACCATCTGCTGC	0.692																																					p.T54N		Atlas-SNP	.											.	SHISA3	27	.	0			c.C161A						PASS	.						21	20	21					4																	42400234		2199	4297	6496	SO:0001583	missense	152573	exon1			ACGCTACCATCTG	BC012029	CCDS33979.1	4p13	2013-07-31	2013-07-31		ENSG00000178343	ENSG00000178343		"Shisa homologs"	25159	protein-coding gene	gene with protein product			"shisa homolog 3 (Xenopus laevis)"				Standard	NM_001080505		Approved	hShisa3	uc003gwp.3	A0PJX4	OTTHUMG00000161043	ENST00000319234.4:c.161C>A	chr4.hg19:g.42400234C>A	ENSP00000326445:p.Thr54Asn	120.0	0.0	.		160.0	8.0	.	NM_001080505	A0PJX3|Q96EQ5	Missense_Mutation	SNP	ENST00000319234.4	hg19	CCDS33979.1	.	.	.	.	.	.	.	.	.	.	C	11.36	1.615227	0.28801	.	.	ENSG00000178343	ENST00000319234	T	0.42900	0.96	4.22	3.36	0.38483	.	0.156200	0.40144	N	0.001169	T	0.32941	0.0846	L	0.39898	1.24	0.47621	D	0.999473	B	0.17667	0.023	B	0.21708	0.036	T	0.07908	-1.0748	10	0.16896	T	0.51	-9.6593	12.9256	0.58258	0.164:0.8359:0.0:0.0	.	54	A0PJX4	SHSA3_HUMAN	N	54	ENSP00000326445:T54N	ENSP00000326445:T54N	T	+	2	0	SHISA3	42094991	0.998000	0.40836	1.000000	0.80357	0.290000	0.27261	3.071000	0.50041	0.943000	0.37553	0.467000	0.42956	ACC	.	.	.	none		0.692	SHISA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363539.1	NM_001080505		A	42400234	C	A	42400234	3	1	251	1	0	0	0	0	1	0	0	0	14294	507	18	4	163	4	SHISA3	4	42400234	Missense_Mutation	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	28794811	42400234	148754042	22	15576											
DDX60	55601	hgsc.bcm.edu	37	chr4	169204723	169204723	+	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	tggaaaacatgatacttttgCacagatctaagaacacgagg	16	9	9	7	1	1	3	0	1	1	2	1	5	1	4	0	2	4	1	0	2	5	4			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr4:169204723C>A	ENST00000393743.3	-	13	1887	c.1596G>T	c.(1594-1596)gtG>gtT	p.V532V		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	532					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)		GATACTTTTGCACAGATCTAA	0.308																																					p.V532V		Atlas-SNP	.											.	DDX60	304	.	0			c.G1596T						PASS	.						58	61	60					4																	169204723		2203	4300	6503	SO:0001819	synonymous_variant	55601	exon13			CTTTTGCACAGAT	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.1596G>T	chr4.hg19:g.169204723C>A		120.0	0.0	.		106.0	34.0	.	NM_017631	Q6PK35|Q9NVE3	Silent	SNP	ENST00000393743.3	hg19	CCDS34097.1																																																																																			.	.	.	none		0.308	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631		A	169204723	C	A	169204723	2	1	251	1	0	0	0	0	0	0	0	1	4380	697	25	4		4	DDX60	4	169204723	Silent	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	126804489	169204723	21949553	23	15577			1	34		2	2	17	C		4.496498e-05
DDX60	55601	hgsc.bcm.edu	37	chr4	169204739	169204739	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgcacagatctaagaacaCgagggtctctagatttttct	11	14	8	8	1	3	3	0	0	3	3	4	4	3	3	0	1	2	1	0	1	3	5			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr4:169204739C>T	ENST00000393743.3	-	13	1871	c.1580G>A	c.(1579-1581)cGt>cAt	p.R527H		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	527					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)		TCTAAGAACACGAGGGTCTCT	0.313																																					p.R527H		Atlas-SNP	.											.	DDX60	304	.	0			c.G1580A						PASS	.						52	54	53					4																	169204739		2203	4300	6503	SO:0001583	missense	55601	exon13			AGAACACGAGGGT	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.1580G>A	chr4.hg19:g.169204739C>T	ENSP00000377344:p.Arg527His	108.0	0.0	.		87.0	28.0	.	NM_017631	Q6PK35|Q9NVE3	Missense_Mutation	SNP	ENST00000393743.3	hg19	CCDS34097.1	.	.	.	.	.	.	.	.	.	.	C	4.070	0.010749	0.07912	.	.	ENSG00000137628	ENST00000393743	T	0.18174	2.23	3.89	-6.27	0.02026	.	1.776030	0.03004	N	0.148595	T	0.07818	0.0196	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.32745	-0.9895	10	0.11182	T	0.66	.	10.0525	0.42225	0.1034:0.2118:0.0:0.6847	.	527	Q8IY21	DDX60_HUMAN	H	527	ENSP00000377344:R527H	ENSP00000377344:R527H	R	-	2	0	DDX60	169441314	0.000000	0.05858	0.000000	0.03702	0.119000	0.20118	-2.385000	0.01062	-1.814000	0.01224	-0.261000	0.10672	CGT	.	.	.	none		0.313	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631		T	169204739	C	T	169204739	3	4	251	1	0	0	0	0	1	0	0	0	4380	536	19	1	3662	1	DDX60	4	169204739	Missense_Mutation	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	16	169204739	21949537	24	15578			1	34		2	2	17	C		4.496498e-05
SPCS3	60559	hgsc.bcm.edu	37	chr4	177249348	177249348	+	Splice_Site	DEL	G	G	-																															gtttattatatctttttataGgggaaacaggaatgtcactt																										TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr4:177249348delG	ENST00000503362.1	+	5	523		c.e5-1		SPCS3_ENST00000507001.1_Splice_Site	NM_021928.3	NP_068747.1	P61009	SPCS3_HUMAN	signal peptidase complex subunit 3 homolog (S. cerevisiae)						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|regulation of insulin secretion (GO:0050796)|signal peptide processing (GO:0006465)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|signal peptidase complex (GO:0005787)	peptidase activity (GO:0008233)			ovary(2)	2		Breast(14;0.0011)|Prostate(90;0.0129)|Melanoma(52;0.0133)|Renal(120;0.0376)|all_hematologic(60;0.124)		all cancers(43;2.43e-19)|Epithelial(43;1.84e-16)|OV - Ovarian serous cystadenocarcinoma(60;4.51e-09)|GBM - Glioblastoma multiforme(59;0.000142)|STAD - Stomach adenocarcinoma(60;0.00279)|LUSC - Lung squamous cell carcinoma(193;0.0319)		TCTTTTTATAGGGGAAACAGG	0.358																																					.		Atlas-INDEL	.											.	SPCS3	15	.	0			c.411-2G>-						PASS	.						122	107	112					4																	177249348		1838	4081	5919	SO:0001630	splice_region_variant	60559	exon5			.	AK092634	CCDS54823.1	4q34.2	2008-02-05				ENSG00000129128			26212	protein-coding gene	gene with protein product						12477932	Standard	NM_021928		Approved	FLJ22649, SPC22/23, SPC3, YLR066W, PRO3567	uc003iur.4	P61009		ENST00000503362.1:c.411-1G>-	chr4.hg19:g.177249348delG		87.0	0.0	0		54.0	16.0	0.296296	NM_021928	P12280|Q9H0S7	Splice_Site	DEL	ENST00000503362.1	hg19	CCDS54823.1																																																																																			.	.	.	none		0.358	SPCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362329.1	NM_021928	Intron	-	177249348	G	-	177249348	8	5	251	1	0	1	0	1	0	0	1	0	15037	1014	35	0	428	0	SPCS3	4	177249348	Splice_Site	DEL	G	TCGA-SX-A7SQ-01A-12D-A35Z-10	8044609	177249348	13904928	25	15579											
GPX8	493869	hgsc.bcm.edu	37	chr5	54456223	54456223	+	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	tctggaaaagtataaaggcaAagtaagttgcatcatctgat	16	11	9	5	0	3	1	1	1	2	0	3	2	3	2	0	2	1	5	0	2	7	4			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr5:54456223A>G	ENST00000503787.1	+	1	278	c.203A>G	c.(202-204)aAa>aGa	p.K68R	GPX8_ENST00000296734.6_Splice_Site_p.K68R|CDC20B_ENST00000296733.1_Intron|CDC20B_ENST00000334206.5_Intron|CDC20B_ENST00000322374.6_Intron|GPX8_ENST00000515370.1_Intron|GPX8_ENST00000506123.1_3'UTR|CDC20B_ENST00000381375.2_Intron|CDC20B_ENST00000331730.3_Intron	NM_001008397.2	NP_001008398.2	Q8TED1	GPX8_HUMAN	glutathione peroxidase 8 (putative)	68					response to oxidative stress (GO:0006979)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	glutathione peroxidase activity (GO:0004602)|peroxidase activity (GO:0004601)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|prostate(1)	11					Glutathione(DB00143)	TATAAAGGCAAAGTAAGTTGC	0.308																																					p.K68R		Atlas-SNP	.											.	GPX8	20	.	0			c.A203G						PASS	.						66	66	66					5																	54456223		2203	4300	6503	SO:0001630	splice_region_variant	493869	exon1			AAGGCAAAGTAAG	BC029424	CCDS34156.1	5q11.2	2008-09-29				ENSG00000164294			33100	protein-coding gene	gene with protein product							Standard	NM_001008397		Approved	UNQ847, EPLA847	uc003jpq.2	Q8TED1		ENST00000503787.1:c.204+1A>G	chr5.hg19:g.54456223A>G		142.0	0.0	.		158.0	93.0	.	NM_001008397		Missense_Mutation	SNP	ENST00000503787.1	hg19	CCDS34156.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.213873	0.79352	.	.	ENSG00000164294	ENST00000503787;ENST00000296734	T	0.06933	3.24	5.93	4.68	0.58851	Thioredoxin-like fold (2);	0.041745	0.85682	N	0.000000	T	0.14442	0.0349	M	0.80746	2.51	0.80722	D	1	B	0.16603	0.018	B	0.23716	0.048	T	0.01367	-1.1373	10	0.62326	D	0.03	.	10.1162	0.42591	0.9045:0.0:0.0955:0.0	.	68	Q8TED1	GPX8_HUMAN	R	68	ENSP00000423822:K68R	ENSP00000296734:K68R	K	+	2	0	GPX8	54491980	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.069000	0.57541	0.926000	0.37118	0.533000	0.62120	AAA	.	.	.	none		0.308	GPX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369717.1	NM_001008397	Missense_Mutation	G	54456223	A	G	54456223	5	3	251	1	0	0	0	0	0	0	1	0	6753	28	1	3	205	3	GPX8	5	54456223	Splice_Site	SNP	A	TCGA-SX-A7SQ-01A-12D-A35Z-10		54456223	126459037	26	15580											
THBS4	7060	hgsc.bcm.edu	37	chr5	79374755	79374755	+	Missense_Mutation	SNP	T	T	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	tctctgcagggcatggagatTgtacagaccatgaacagtga	12	9	12	8	0	1	4	0	2	1	2	2	5	1	4	1	2	3	3	1	2	2	2			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr5:79374755T>G	ENST00000350881.2	+	18	2467	c.2277T>G	c.(2275-2277)atT>atG	p.I759M	THBS4_ENST00000504720.1_3'UTR|THBS4_ENST00000511733.1_Missense_Mutation_p.I668M|CTD-2201I18.1_ENST00000503007.1_RNA|CTD-2201I18.1_ENST00000514042.1_RNA	NM_003248.4	NP_003239.2	P35443	TSP4_HUMAN	thrombospondin 4	759	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)		GCATGGAGATTGTACAGACCA	0.498																																					p.I759M		Atlas-SNP	.											.	THBS4	82	.	0			c.T2277G						PASS	.						115	103	107					5																	79374755		2203	4300	6503	SO:0001583	missense	7060	exon18			GGAGATTGTACAG		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.2277T>G	chr5.hg19:g.79374755T>G	ENSP00000339730:p.Ile759Met	95.0	0.0	.		83.0	21.0	.	NM_003248	B2R909|Q86TG2	Missense_Mutation	SNP	ENST00000350881.2	hg19	CCDS4049.1	.	.	.	.	.	.	.	.	.	.	T	18.52	3.641809	0.67244	.	.	ENSG00000113296	ENST00000350881;ENST00000511733	D;D	0.96522	-4.04;-4.04	5.06	-3.5	0.04710	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	0.97617	0.9219	M	0.88450	2.955	0.58432	D	0.999993	D	0.76494	0.999	D	0.91635	0.999	D	0.96356	0.9262	10	0.87932	D	0	-21.232	11.3397	0.49525	0.0:0.3915:0.0:0.6085	.	759	P35443	TSP4_HUMAN	M	759;668	ENSP00000339730:I759M;ENSP00000422298:I668M	ENSP00000339730:I759M	I	+	3	3	THBS4	79410511	0.687000	0.27671	0.973000	0.42090	0.993000	0.82548	-0.279000	0.08479	-0.685000	0.05177	-0.256000	0.11100	ATT	.	.	.	none		0.498	THBS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226977.1			G	79374755	T	G	79374755	3	3	251	1	0	0	0	0	1	0	0	0	15868	1800	63	5	2347	5	THBS4	5	79374755	Missense_Mutation	SNP	T	TCGA-SX-A7SQ-01A-12D-A35Z-10	24918532	79374755	101540505	27	15581											
PCDHGB2	56103	hgsc.bcm.edu	37	chr5	140742098	140742098	+	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	tcatggagccgctggggtccCttttgcctcagatactattt	6	14	10	11	1	2	1	2	0	0	1	3	2	3	2	3	3	3	1	3	3	2	5			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr5:140742098C>A	ENST00000522605.1	+	1	2396	c.2396C>A	c.(2395-2397)cCt>cAt	p.P799H	PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_5'Flank|PCDHGA2_ENST00000394576.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018923.2|NM_032096.1	NP_061746.1|NP_115267.1	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2	799					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)			GCTGGGGTCCCTTTTGCCTCA	0.413																																					p.P799H		Atlas-SNP	.											.	PCDHGB2	196	.	0			c.C2396A						PASS	.						61	61	61					5																	140742098		1820	4083	5903	SO:0001583	missense	56103	exon1			GGGTCCCTTTTGC	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.2396C>A	chr5.hg19:g.140742098C>A	ENSP00000429018:p.Pro799His	126.0	0.0	.		143.0	41.0	.	NM_018923	Q3MIJ3|Q9UN65	Missense_Mutation	SNP	ENST00000522605.1	hg19	CCDS54924.1	.	.	.	.	.	.	.	.	.	.	.	10.02	1.236268	0.22626	.	.	ENSG00000253910	ENST00000522605	T	0.50001	0.76	4.99	3.02	0.34903	.	.	.	.	.	T	0.35913	0.0948	N	0.14661	0.345	0.09310	N	1	D;P	0.54964	0.969;0.883	P;B	0.50970	0.655;0.346	T	0.08472	-1.0720	9	0.42905	T	0.14	.	5.6077	0.17389	0.1625:0.668:0.0:0.1694	.	799;799	Q9Y5G2-2;Q9Y5G2	.;PCDGE_HUMAN	H	799	ENSP00000429018:P799H	ENSP00000429018:P799H	P	+	2	0	PCDHGB2	140722282	0.000000	0.05858	0.008000	0.14137	0.084000	0.17831	0.900000	0.28431	2.301000	0.77427	0.467000	0.42956	CCT	.	.	.	none		0.413	PCDHGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374741.1	NM_018923		A	140742098	C	A	140742098	3	1	251	1	0	0	0	0	1	0	0	0	11570	681	24	4	2398	4	PCDHGB2	5	140742098	Missense_Mutation	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	61367343	140742098	40173162	28	15582											
EXOC2	55770	hgsc.bcm.edu	37	chr6	532588	532588	+	Missense_Mutation	SNP	T	T	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	caaagagtctttgatctagtTctttcaatgaggccatgcta	11	14	8	8	0	4	3	1	2	3	1	4	3	4	3	1	1	1	2	1	1	4	5			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr6:532588T>G	ENST00000230449.4	-	23	2396	c.2261A>C	c.(2260-2262)gAa>gCa	p.E754A	EXOC2_ENST00000448181.3_Missense_Mutation_p.E349A	NM_018303.5	NP_060773.3	Q96KP1	EXOC2_HUMAN	exocyst complex component 2	754					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)		TTGATCTAGTTCTTTCAATGA	0.348																																					p.E754A		Atlas-SNP	.											.	EXOC2	81	.	0			c.A2261C						PASS	.						107	105	105					6																	532588		2203	4300	6503	SO:0001583	missense	55770	exon23			TCTAGTTCTTTCA	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.2261A>C	chr6.hg19:g.532588T>G	ENSP00000230449:p.Glu754Ala	126.0	0.0	.		102.0	51.0	.	NM_018303	B2RBE6|Q5JPC8|Q96AN6|Q9NUZ8|Q9UJM7	Missense_Mutation	SNP	ENST00000230449.4	hg19	CCDS34327.1	.	.	.	.	.	.	.	.	.	.	T	14.96	2.690808	0.48097	.	.	ENSG00000112685	ENST00000230449;ENST00000448181	T;T	0.24151	1.87;1.87	5.77	5.77	0.91146	.	0.147993	0.64402	D	0.000014	T	0.09905	0.0243	L	0.29908	0.895	0.58432	D	0.999993	B	0.11235	0.004	B	0.12837	0.008	T	0.11203	-1.0597	10	0.17832	T	0.49	-5.4577	16.383	0.83481	0.0:0.0:0.0:1.0	.	754	Q96KP1	EXOC2_HUMAN	A	754;349	ENSP00000230449:E754A;ENSP00000398113:E349A	ENSP00000230449:E754A	E	-	2	0	EXOC2	477588	1.000000	0.71417	0.992000	0.48379	0.979000	0.70002	4.771000	0.62318	2.326000	0.78906	0.533000	0.62120	GAA	.	.	.	none		0.348	EXOC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039627.1	NM_018303		G	532588	T	G	532588	3	3	251	1	0	0	0	0	1	0	0	0	5304	1783	62	5	537	5	EXOC2	6	532588	Missense_Mutation	SNP	T	TCGA-SX-A7SQ-01A-12D-A35Z-10		532588	170582479	29	15583											
DSP	1832	hgsc.bcm.edu	37	chr6	7578720	7578720	+	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	gcagatgttcatgctcggtaCattgaactacttacaagatc	12	12	8	9	1	1	3	1	1	0	2	3	3	1	3	0	1	5	4	0	1	5	5			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr6:7578720C>T	ENST00000379802.3	+	22	3350	c.3009C>T	c.(3007-3009)taC>taT	p.Y1003Y	DSP_ENST00000418664.2_Silent_p.Y1003Y	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	1003	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)		ATGCTCGGTACATTGAACTAC	0.343																																					p.Y1003Y		Atlas-SNP	.											.	DSP	306	.	0			c.C3009T						PASS	.						140	143	142					6																	7578720		2203	4300	6503	SO:0001819	synonymous_variant	1832	exon22			TCGGTACATTGAA	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.3009C>T	chr6.hg19:g.7578720C>T		129.0	0.0	.		98.0	45.0	.	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	hg19	CCDS4501.1																																																																																			.	.	.	none		0.343	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		T	7578720	C	T	7578720	2	4	251	1	0	0	0	0	0	0	0	1	4783	489	17	2		2	DSP	6	7578720	Silent	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	7046132	7578720	163536347	30	15584											
PGC	5225	hgsc.bcm.edu	37	chr6	41712422	41712423	+	Missense_Mutation	DNP	TC	TC	AG																															gtaggccatgggctcgtaggTcacgctgaggtcaccaaagc																										TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr6:41712422_41712423TC>AG	ENST00000373025.3	-	2	245_246	c.183_184GA>CT	c.(181-186)gtGAcc>gtCTcc	p.T62S	PGC_ENST00000425343.2_Missense_Mutation_p.T62S	NM_002630.3	NP_002621.1	P20142	PEPC_HUMAN	progastricsin (pepsinogen C)	62					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)			GGCTCGTAGGTCACGCTGAGGT	0.579																																					p.T62S|p.V61V		Atlas-SNP	.											.	PGC	56	.	0			c.A184T|c.G183C						PASS	.																																			SO:0001583	missense	5225	exon2			CGTAGGTCACGCT|GTAGGTCACGCTG		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.183_184delinsAG	chr6.hg19:g.41712422_41712423delinsAG	ENSP00000362116:p.Thr62Ser	103.0|104.0	0.0	.		97.0|98.0	54.0	.	NM_002630	B4DVZ3|Q5T3D7|Q5T3D8	Missense_Mutation|Silent	SNP	ENST00000373025.3	hg19	CCDS4859.1																																																																																			.	.	.	none		0.579	PGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040521.2			AG	41712423	TC	AG	41712422	3	1	251	1	0	0	0	0	1	0	0	0	11792	1667	58	5	1323	5	PGC	6	41712422	Missense_Mutation	DNP	TC	TCGA-SX-A7SQ-01A-12D-A35Z-10	34133702	41712422	129402645	31	15585											
EFHC1	114327	hgsc.bcm.edu	37	chr6	52357086	52357086	+	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	agttaatcaggatgtgctctCatggagaaggcaaaattaac	15	10	10	6	0	2	1	2	0	1	1	3	3	2	2	0	3	2	3	0	3	5	2			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr6:52357086C>G	ENST00000371068.5	+	11	1973	c.1870C>G	c.(1870-1872)Cat>Gat	p.H624D	EFHC1_ENST00000433625.2_Intron|EFHC1_ENST00000538167.1_Missense_Mutation_p.H605D	NM_018100.3	NP_060570.2	Q5JVL4	EFHC1_HUMAN	EF-hand domain (C-terminal) containing 1	624						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)					GATGTGCTCTCATGGAGAAGG	0.423																																					p.H624D		Atlas-SNP	.											.	EFHC1	68	.	0			c.C1870G						PASS	.						120	102	108					6																	52357086		2203	4300	6503	SO:0001583	missense	114327	exon11			TGCTCTCATGGAG	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.1870C>G	chr6.hg19:g.52357086C>G	ENSP00000360107:p.His624Asp	98.0	0.0	.		87.0	38.0	.	NM_018100	B4DMU3|F5GZD8|Q5XKM4|Q6E1U7|Q6E1U8|Q8WUL2|Q9NVW6	Missense_Mutation	SNP	ENST00000371068.5	hg19	CCDS4942.1	.	.	.	.	.	.	.	.	.	.	C	9.168	1.020303	0.19433	.	.	ENSG00000096093	ENST00000371068;ENST00000538167	T;T	0.32023	1.47;1.47	4.72	3.84	0.44239	EF-hand-like domain (1);	0.490245	0.21349	N	0.075995	T	0.03608	0.0103	N	0.03000	-0.44	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.34030	-0.9845	10	0.07644	T	0.81	-10.9017	8.7093	0.34374	0.0:0.8961:0.0:0.1039	.	605;624	F5GZD8;Q5JVL4	.;EFHC1_HUMAN	D	624;605	ENSP00000360107:H624D;ENSP00000444521:H605D	ENSP00000360107:H624D	H	+	1	0	EFHC1	52465045	0.516000	0.26218	0.975000	0.42487	0.966000	0.64601	1.335000	0.33839	1.338000	0.45544	0.591000	0.81541	CAT	.	.	.	none		0.423	EFHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040905.2	NM_018100		G	52357086	C	G	52357086	3	3	251	1	0	0	0	0	1	0	0	0	4948	826	29	4	1922	4	EFHC1	6	52357086	Missense_Mutation	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	10644664	52357086	118757981	32	15586											
TINAG	27283	hgsc.bcm.edu	37	chr6	54216153	54216153	+	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	catatttttccatccaggaaActgagataatgaaagaaatc	17	11	6	7	0	0	3	0	2	0	2	3	5	2	4	2	1	1	0	2	1	5	4			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr6:54216153A>T	ENST00000259782.4	+	8	1180	c.1084A>T	c.(1084-1086)Act>Tct	p.T362S		NM_014464.3	NP_055279.3	Q9UJW2	TINAG_HUMAN	tubulointerstitial nephritis antigen	362					cell adhesion (GO:0007155)|immune response (GO:0006955)	basement membrane (GO:0005604)	cysteine-type endopeptidase activity (GO:0004197)|nucleotide binding (GO:0000166)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(1)	34	Lung NSC(77;0.0518)		LUSC - Lung squamous cell carcinoma(124;0.246)			CATCCAGGAAACTGAGATAAT	0.313																																					p.T362S		Atlas-SNP	.											.	TINAG	102	.	0			c.A1084T						PASS	.						93	92	92					6																	54216153		2201	4297	6498	SO:0001583	missense	27283	exon8			CAGGAAACTGAGA	AB022277	CCDS4955.1	6p12.1	2008-05-15			ENSG00000137251	ENSG00000137251			14599	protein-coding gene	gene with protein product		606749				10652240	Standard	NM_014464		Approved		uc003pcj.2	Q9UJW2	OTTHUMG00000014893	ENST00000259782.4:c.1084A>T	chr6.hg19:g.54216153A>T	ENSP00000259782:p.Thr362Ser	111.0	0.0	.		75.0	37.0	.	NM_014464	Q5T467|Q9UJW1|Q9ULZ4	Missense_Mutation	SNP	ENST00000259782.4	hg19	CCDS4955.1	.	.	.	.	.	.	.	.	.	.	A	14.71	2.617727	0.46736	.	.	ENSG00000137251	ENST00000339741;ENST00000259782;ENST00000370865	D	0.83673	-1.75	5.08	5.08	0.68730	Peptidase C1A, papain C-terminal (2);	0.000000	0.64402	D	0.000003	T	0.63570	0.2522	L	0.28400	0.85	0.80722	D	1	P	0.36683	0.565	B	0.37015	0.239	T	0.65751	-0.6092	10	0.22706	T	0.39	.	13.9813	0.64306	1.0:0.0:0.0:0.0	.	362	Q9UJW2	TINAG_HUMAN	S	221;362;41	ENSP00000259782:T362S	ENSP00000259782:T362S	T	+	1	0	TINAG	54324112	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	6.953000	0.75995	2.021000	0.59480	0.533000	0.62120	ACT	.	.	.	none		0.313	TINAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040984.1	NM_014464		T	54216153	A	T	54216153	3	4	251	1	0	0	0	0	1	0	0	0	15933	43	2	5	1114	5	TINAG	6	54216153	Missense_Mutation	SNP	A	TCGA-SX-A7SQ-01A-12D-A35Z-10	1859067	54216153	116898914	33	15587											
USP42	84132	hgsc.bcm.edu	37	chr7	6196544	6196544	+	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	gtcaccagcttggagactgtCgcccagttccggagagccca	8	7	12	14	2	1	2	1	0	0	2	3	4	2	2	4	2	2	2	4	2	0	2			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr7:6196544C>T	ENST00000306177.5	+	16	3959	c.3801C>T	c.(3799-3801)gtC>gtT	p.V1267V		NM_032172.2	NP_115548.1	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	1267					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)		TGGAGACTGTCGCCCAGTTCC	0.498																																					p.V1267V		Atlas-SNP	.											.	USP42	138	.	0			c.C3801T						PASS	.						40	43	42					7																	6196544		1896	4116	6012	SO:0001819	synonymous_variant	84132	exon16			GACTGTCGCCCAG	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.3801C>T	chr7.hg19:g.6196544C>T		100.0	0.0	.		158.0	42.0	.	NM_032172	A2RUE3|B5MDA5|Q0VIN8|Q3C166|Q6P9B4	Silent	SNP	ENST00000306177.5	hg19	CCDS47535.1																																																																																			.	.	.	none		0.498	USP42-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324262.3	XM_166526		T	6196544	C	T	6196544	2	4	251	1	0	0	0	0	0	0	0	1	17085	871	31	1		1	USP42	7	6196544	Silent	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10		6196544	152942119	34	15588											
THSD7A	221981	hgsc.bcm.edu	37	chr7	11446609	11446609	+	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	actgggcagggtttggactgGtccatcagggaagggcatgg	8	8	18	7	0	1	0	1	0	0	0	2	2	2	2	1	7	0	3	1	7	1	1			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr7:11446609G>C	ENST00000423059.4	-	21	4241	c.3990C>G	c.(3988-3990)gaC>gaG	p.D1330E	AC004160.4_ENST00000425837.1_RNA|AC004538.3_ENST00000445839.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	1330	TSP type-1 13. {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)		GTTTGGACTGGTCCATCAGGG	0.493										HNSCC(18;0.044)																											p.D1330E		Atlas-SNP	.											.	THSD7A	219	.	0			c.C3990G						PASS	.						98	99	98					7																	11446609		1978	4160	6138	SO:0001583	missense	221981	exon20			GGACTGGTCCATC		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.3990C>G	chr7.hg19:g.11446609G>C	ENSP00000406482:p.Asp1330Glu	151.0	0.0	.		185.0	43.0	.	NM_015204		Missense_Mutation	SNP	ENST00000423059.4	hg19	CCDS47543.1	.	.	.	.	.	.	.	.	.	.	G	14.30	2.493990	0.44352	.	.	ENSG00000005108	ENST00000262042;ENST00000423059	T	0.50277	0.75	6.14	0.196	0.15159	.	0.140343	0.64402	N	0.000005	T	0.10766	0.0263	N	0.00456	-1.48	0.24800	N	0.992709	B	0.02656	0.0	B	0.01281	0.0	T	0.39603	-0.9606	10	0.02654	T	1	.	7.2032	0.25893	0.0:0.3728:0.191:0.4362	.	1330	Q9UPZ6	THS7A_HUMAN	E	1330	ENSP00000406482:D1330E	ENSP00000262042:D1330E	D	-	3	2	THSD7A	11413134	0.994000	0.37717	0.998000	0.56505	0.998000	0.95712	0.353000	0.20130	0.019000	0.15079	0.650000	0.86243	GAC	.	.	.	none		0.493	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		C	11446609	G	C	11446609	3	2	251	1	0	0	0	0	1	0	0	0	15891	1252	44	4	1015	4	THSD7A	7	11446609	Missense_Mutation	SNP	G	TCGA-SX-A7SQ-01A-12D-A35Z-10	5250065	11446609	147692054	35	15589											
NFE2L3	9603	hgsc.bcm.edu	37	chr7	26224563	26224563	+	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	tctcagctttttgatgaaccAgattctgattctggcctttc	7	17	7	10	0	3	4	1	3	3	1	5	4	3	4	2	1	2	1	2	1	1	5			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr7:26224563A>T	ENST00000056233.3	+	4	1504	c.1245A>T	c.(1243-1245)ccA>ccT	p.P415P		NM_004289.6	NP_004280.5	Q9Y4A8	NF2L3_HUMAN	nuclear factor, erythroid 2-like 3	415					transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(5)|urinary_tract(7)	29						TTGATGAACCAGATTCTGATT	0.363																																					p.P415P		Atlas-SNP	.											.	NFE2L3	77	.	0			c.A1245T						PASS	.						95	101	99					7																	26224563		2203	4300	6503	SO:0001819	synonymous_variant	9603	exon4			TGAACCAGATTCT	AB010812	CCDS5396.1	7p15.2	2013-08-23	2013-08-23		ENSG00000050344	ENSG00000050344		"basic leucine zipper proteins"	7783	protein-coding gene	gene with protein product		604135	"nuclear factor (erythroid-derived 2)-like 3"			10037736	Standard	NM_004289		Approved	Nrf3	uc003sxq.3	Q9Y4A8	OTTHUMG00000023882	ENST00000056233.3:c.1245A>T	chr7.hg19:g.26224563A>T		71.0	0.0	.		102.0	28.0	.	NM_004289	Q6NUS0|Q7Z498|Q86UJ4|Q86VR5|Q9UQA4	Silent	SNP	ENST00000056233.3	hg19	CCDS5396.1																																																																																			.	.	.	none		0.363	NFE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214088.1			T	26224563	A	T	26224563	2	4	251	1	0	0	0	0	0	0	0	1	10376	175	7	5		5	NFE2L3	7	26224563	Silent	SNP	A	TCGA-SX-A7SQ-01A-12D-A35Z-10	14777954	26224563	132914100	36	15590											
CCDC146	57639	hgsc.bcm.edu	37	chr7	76922400	76922400	+	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	gagaaagaagacttcatcttCacttgcaattccaggataga	15	10	8	8	0	3	4	2	0	1	4	4	6	4	5	1	1	1	1	1	1	4	5			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr7:76922400C>T	ENST00000285871.4	+	18	2674	c.2547C>T	c.(2545-2547)ttC>ttT	p.F849F	CCDC146_ENST00000415740.2_3'UTR|CCDC146_ENST00000431197.1_Silent_p.F563F	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	849										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)				ACTTCATCTTCACTTGCAATT	0.428																																					p.F849F		Atlas-SNP	.											.	CCDC146	87	.	0			c.C2547T						PASS	.						112	109	110					7																	76922400		2203	4300	6503	SO:0001819	synonymous_variant	57639	exon18			CATCTTCACTTGC	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.2547C>T	chr7.hg19:g.76922400C>T		98.0	0.0	.		131.0	41.0	.	NM_020879	A8K8X6|Q9P223	Silent	SNP	ENST00000285871.4	hg19	CCDS34671.1																																																																																			.	.	.	none		0.428	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879		T	76922400	C	T	76922400	2	4	251	1	0	0	0	0	0	0	0	1	2782	825	29	2		2	CCDC146	7	76922400	Silent	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	50697837	76922400	82216263	37	15591											
MET	4233	hgsc.bcm.edu	37	chr7	116417463	116417463	+	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	ggcattttggttgtgtatatCatgggactttgttggacaat	8	17	12	4	0	1	0	1	0	0	0	1	2	1	2	0	4	0	4	0	4	3	7	rs121913244		TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr7:116417463C>T	ENST00000318493.6	+	16	3521	c.3334C>T	c.(3334-3336)Cat>Tat	p.H1112Y	MET_ENST00000397752.3_Missense_Mutation_p.H1094Y|MET_ENST00000539704.1_5'UTR			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.H1112Y(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)			TTGTGTATATCATGGGACTTT	0.343			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.H1112Y		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,colon,carcinoma,0,2	MET	412	.	1	Substitution - Missense(1)	kidney(1)	c.C3334T	GRCh37	CM993668	MET	M	rs121913244	PASS	.						188	175	179					7																	116417463		1832	4086	5918	SO:0001583	missense	4233	exon16	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	GTATATCATGGGA	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.3334C>T	chr7.hg19:g.116417463C>T	ENSP00000317272:p.His1112Tyr	97.0	0.0	.		109.0	64.0	.	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.615896	0.87359	.	.	ENSG00000105976	ENST00000397752;ENST00000318493	T;T	0.33654	1.4;1.4	5.29	5.29	0.74685	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	0.43919	0.1269	N	0.11364	0.135	0.80722	D	1	P;D	0.89917	0.937;1.0	P;D	0.91635	0.854;0.999	T	0.52711	-0.8539	10	0.51188	T	0.08	-16.8984	19.2953	0.94119	0.0:1.0:0.0:0.0	.	1112;1094	P08581-2;P08581	.;MET_HUMAN	Y	1094;1112	ENSP00000380860:H1094Y;ENSP00000317272:H1112Y	ENSP00000317272:H1112Y	H	+	1	0	MET	116204699	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.776000	0.85560	2.628000	0.89032	0.655000	0.94253	CAT	.	.	.	weak		0.343	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			T	116417463	C	T	116417463	3	4	251	1	0	0	0	0	1	0	0	0	9492	826	29	2	3392	2	MET	7	116417463	Missense_Mutation	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	39495063	116417463	42721200	38	15592											
TTC39B	158219	hgsc.bcm.edu	37	chr9	15225959	15225959	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtctgggcgcctgttgtgtAtcacatgatgcaaagtgaag	9	12	13	7	1	2	2	1	2	1	0	2	2	2	2	1	1	1	3	1	1	3	2			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr9:15225959A>G	ENST00000512701.2	-	3	363	c.327T>C	c.(325-327)gaT>gaC	p.D109D	TTC39B_ENST00000355694.2_Silent_p.D43D|TTC39B_ENST00000582994.1_5'UTR|TTC39B_ENST00000507285.1_5'UTR|TTC39B_ENST00000380850.4_Silent_p.D109D|TTC39B_ENST00000541445.1_Silent_p.D43D|TTC39B_ENST00000297615.5_Intron|TTC39B_ENST00000507993.1_Intron			Q5VTQ0	TT39B_HUMAN	tetratricopeptide repeat domain 39B	109										NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)	21						CCTGTTGTGTATCACATGATG	0.502																																					p.D109D		Atlas-SNP	.											.	TTC39B	83	.	0			c.T327C						PASS	.						125	114	118					9																	15225959		2203	4300	6503	SO:0001819	synonymous_variant	158219	exon3			TTGTGTATCACAT	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.327T>C	chr9.hg19:g.15225959A>G		64.0	0.0	.		60.0	25.0	.	NM_001168340	A5PLN1|B4DQ10|B4DQX4|B4DW93|Q8IVR7|Q8IXZ6|Q8N267	Silent	SNP	ENST00000512701.2	hg19	CCDS6477.2																																																																																			.	.	.	none		0.502	TTC39B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051758.3	NM_152574		G	15225959	A	G	15225959	2	3	251	1	0	0	0	0	0	0	0	1	16720	446	16	3		3	TTC39B	9	15225959	Silent	SNP	A	TCGA-SX-A7SQ-01A-12D-A35Z-10		15225959	125987472	39	15593											
SLC31A1	1317	hgsc.bcm.edu	37	chr9	116021053	116021053	+	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	atagcccgagagagcctgctGcgtaagtcacaagtcagcat	12	7	11	11	2	2	1	2	0	0	1	2	3	2	1	2	0	5	3	2	0	3	2			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr9:116021053G>A	ENST00000374212.4	+	4	434	c.282G>A	c.(280-282)ctG>ctA	p.L94L	CDC26_ENST00000490408.1_Intron|SLC31A1_ENST00000374210.6_Silent_p.L94L	NM_001859.3	NP_001850.1	O15431	COPT1_HUMAN	solute carrier family 31 (copper transporter), member 1	94					cellular copper ion homeostasis (GO:0006878)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	copper ion transmembrane transporter activity (GO:0005375)|copper uptake transmembrane transporter activity (GO:0015088)			breast(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	7					Bortezomib(DB00188)|Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	AGAGCCTGCTGCGTAAGTCAC	0.443																																					p.L94L	Ovarian(135;1049 1799 4519 17564 28677)	Atlas-SNP	.											.	SLC31A1	12	.	0			c.G282A						PASS	.						156	138	144					9																	116021053		2203	4300	6503	SO:0001819	synonymous_variant	1317	exon4			CCTGCTGCGTAAG	U83460	CCDS6789.1	9q32	2013-07-17	2013-07-17		ENSG00000136868	ENSG00000136868		"Solute carriers"	11016	protein-coding gene	gene with protein product	copper transport 1 homolog (S. cerevisiae)	603085		COPT1		9207117	Standard	NM_001859		Approved	hCTR1, CTR1	uc004bgu.3	O15431	OTTHUMG00000020519	ENST00000374212.4:c.282G>A	chr9.hg19:g.116021053G>A		87.0	0.0	.		89.0	34.0	.	NM_001859	A8K8Z6|Q53GR5|Q5T1M4	Silent	SNP	ENST00000374212.4	hg19	CCDS6789.1																																																																																			.	.	.	none		0.443	SLC31A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053715.1	NM_001859		A	116021053	G	A	116021053	2	1	251	1	0	0	0	0	0	0	0	1	14576	1306	46	2		2	SLC31A1	9	116021053	Silent	SNP	G	TCGA-SX-A7SQ-01A-12D-A35Z-10	100795094	116021053	25192378	40	15594											
SDCCAG3	10807	hgsc.bcm.edu	37	chr9	139304610	139304610	+	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	aggccggccgaatgccgaagAagggggagtccaggtccctg	9	4	17	11	3	0	1	0	0	0	1	2	4	2	2	5	5	1	0	5	5	3	0			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr9:139304610A>T	ENST00000357365.3	-	2	281	c.152T>A	c.(151-153)tTc>tAc	p.F51Y	SDCCAG3_ENST00000298537.7_Missense_Mutation_p.F51Y|PMPCA_ENST00000399219.3_5'Flank|PMPCA_ENST00000371720.1_5'Flank|SDCCAG3_ENST00000371725.3_Intron|PMPCA_ENST00000371717.3_5'Flank	NM_001039707.1	NP_001034796.1	Q96C92	SDCG3_HUMAN	serologically defined colon cancer antigen 3	51						cytoplasm (GO:0005737)				NS(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)	16		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.18e-06)|Epithelial(140;9.31e-06)		AATGCcgaagaagggggagtc	0.647																																					p.F51Y		Atlas-SNP	.											.	SDCCAG3	41	.	0			c.T152A						PASS	.						19	26	24					9																	139304610		1922	4116	6038	SO:0001583	missense	10807	exon2			CCGAAGAAGGGGG	AF039688	CCDS6999.2, CCDS43903.1, CCDS43904.1	9q34.3	2010-10-27			ENSG00000165689	ENSG00000165689			10667	protein-coding gene	gene with protein product						9610721	Standard	XM_005266050		Approved	NY-CO-3	uc004chi.3	Q96C92	OTTHUMG00000020928	ENST00000357365.3:c.152T>A	chr9.hg19:g.139304610A>T	ENSP00000349929:p.Phe51Tyr	161.0	0.0	.		117.0	57.0	.	NM_001039707	A6NCP1|O60525|Q5SXN1|Q5SXN2|Q5SXN3|Q5SXN4|Q5SXN8|Q6V704|Q9NVY5	Missense_Mutation	SNP	ENST00000357365.3	hg19	CCDS43904.1	.	.	.	.	.	.	.	.	.	.	A	15.27	2.784140	0.49997	.	.	ENSG00000165689	ENST00000357365;ENST00000298537	T;T	0.16196	2.45;2.36	3.11	1.93	0.25924	.	.	.	.	.	T	0.11537	0.0281	L	0.44542	1.39	0.80722	D	1	B;B	0.33238	0.403;0.378	B;B	0.32465	0.06;0.146	T	0.13522	-1.0506	9	0.15066	T	0.55	-12.2273	5.5118	0.16884	0.7535:0.0:0.0:0.2465	.	51;51	Q96C92-2;Q96C92	.;SDCG3_HUMAN	Y	51	ENSP00000349929:F51Y;ENSP00000298537:F51Y	ENSP00000298537:F51Y	F	-	2	0	SDCCAG3	138424431	0.955000	0.32602	0.989000	0.46669	0.963000	0.63663	1.092000	0.30927	0.543000	0.28864	0.533000	0.62120	TTC	.	.	.	none		0.647	SDCCAG3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055060.2	NM_006643		T	139304610	A	T	139304610	3	4	251	1	0	0	0	0	1	0	0	0	13971	246	9	5	1191	5	SDCCAG3	9	139304610	Missense_Mutation	SNP	A	TCGA-SX-A7SQ-01A-12D-A35Z-10	23283557	139304610	1908821	41	15595											
ABCA2	20	hgsc.bcm.edu	37	chr9	139905075	139905075	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acatgcccagagcccaccttGgtcaggttctcaatcttgac	9	10	8	14	0	3	2	2	1	2	1	4	2	3	2	3	2	2	1	3	2	1	3			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr9:139905075G>A	ENST00000371605.3	-	39	6315	c.6168C>T	c.(6166-6168)acC>acT	p.T2056T	ABCA2_ENST00000341511.6_Silent_p.T2057T|ABCA2_ENST00000265662.5_Silent_p.T2057T			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	2056	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)		AGCCCACCTTGGTCAGGTTCT	0.667																																					p.T2087T		Atlas-SNP	.											.	ABCA2	113	.	0			c.C6261T						PASS	.						99	102	101					9																	139905075		2039	4181	6220	SO:0001819	synonymous_variant	20	exon40			CACCTTGGTCAGG	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.6168C>T	chr9.hg19:g.139905075G>A		211.0	0.0	.		193.0	85.0	.	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Silent	SNP	ENST00000371605.3	hg19																																																																																				.	.	.	none		0.667	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606		A	139905075	G	A	139905075	2	1	251	1	0	0	0	0	0	0	0	1	32	1335	47	2		2	ABCA2	9	139905075	Silent	SNP	G	TCGA-SX-A7SQ-01A-12D-A35Z-10	600465	139905075	1308356	42	15596											
SUFU	51684	hgsc.bcm.edu	37	chr10	104356961	104356961	+	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	tggtgtcagtgccaagtgtgCctgggatgacctgagccggc	6	9	16	10	1	1	2	1	2	0	0	1	3	1	3	4	3	3	0	4	3	1	0			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr10:104356961C>A	ENST00000369902.3	+	7	987	c.821C>A	c.(820-822)gCc>gAc	p.A274D	SUFU_ENST00000423559.2_Missense_Mutation_p.A274D|SUFU_ENST00000369899.2_Missense_Mutation_p.A274D|SUFU_ENST00000471000.1_3'UTR	NM_016169.3	NP_057253.2	Q9UMX1	SUFU_HUMAN	suppressor of fused homolog (Drosophila)	274					cytoplasmic sequestering of transcription factor (GO:0042994)|heart looping (GO:0001947)|multicellular organismal development (GO:0007275)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of transcription factor import into nucleus (GO:0042992)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|skin development (GO:0043588)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|primary cilium (GO:0072372)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(7)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(2)	24		Colorectal(252;0.207)		Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242)		GCCAAGTGTGCCTGGGATGAC	0.582			"D, F, S"		medulloblastoma	medulloblastoma			Medulloblastoma, associated with Germline SUFU Mutation		OREG0020482	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A274D		Atlas-SNP	.	yes	Rec	yes	Medulloblastoma predisposition	10	10q24.32	51684	suppressor of fused homolog (Drosophila)		O	.	SUFU	44	.	0			c.C821A						PASS	.						115	105	108					10																	104356961		2203	4300	6503	SO:0001583	missense	51684	exon7	Familial Cancer Database		AGTGTGCCTGGGA	AF175770	CCDS7537.1, CCDS53571.1	10q24.32	2014-09-17			ENSG00000107882	ENSG00000107882			16466	protein-coding gene	gene with protein product		607035				15367681	Standard	NM_016169		Approved	SUFUH, SUFUXL, PRO1280	uc001kvy.2	Q9UMX1	OTTHUMG00000018966	ENST00000369902.3:c.821C>A	chr10.hg19:g.104356961C>A	ENSP00000358918:p.Ala274Asp	75.0	0.0	.	1381	95.0	42.0	.	NM_001178133	Q7LCP7|Q9NT90|Q9NZ07|Q9UHK2|Q9UHM8|Q9UMY0	Missense_Mutation	SNP	ENST00000369902.3	hg19	CCDS7537.1	.	.	.	.	.	.	.	.	.	.	C	18.90	3.721863	0.68959	.	.	ENSG00000107882	ENST00000369902;ENST00000369899;ENST00000423559	T;T;T	0.48836	0.8;0.8;0.8	6.03	6.03	0.97812	Suppressor of fused C-terminal (1);	0.048667	0.85682	D	0.000000	T	0.41581	0.1165	L	0.36672	1.1	0.58432	D	0.999997	B;B;B	0.34015	0.022;0.435;0.083	B;B;B	0.29353	0.009;0.101;0.017	T	0.16158	-1.0412	10	0.35671	T	0.21	-19.8645	20.5568	0.99304	0.0:1.0:0.0:0.0	.	274;274;274	Q9UMX1;Q9UMX1-2;Q9UMX1-3	SUFU_HUMAN;.;.	D	274	ENSP00000358918:A274D;ENSP00000358915:A274D;ENSP00000411597:A274D	ENSP00000358915:A274D	A	+	2	0	SUFU	104346951	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.617000	0.67716	2.861000	0.98227	0.655000	0.94253	GCC	.	.	.	none		0.582	SUFU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050089.1	NM_016169		A	104356961	C	A	104356961	3	1	251	1	0	0	0	0	1	0	0	0	15380	739	26	4	847	4	SUFU	10	104356961	Missense_Mutation	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10		104356961	31177786	43	15597											
TDRD1	56165	hgsc.bcm.edu	37	chr10	115947804	115947804	+	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	acaattttttgctttgtgagCaaaccaaacaatatttggct	13	15	6	7	0	0	1	0	1	0	0	0	1	0	1	1	1	4	3	1	1	5	6			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr10:115947804C>T	ENST00000369280.1	+	2	674	c.214C>T	c.(214-216)Caa>Taa	p.Q72*	TDRD1_ENST00000251864.2_Nonsense_Mutation_p.Q72*|TDRD1_ENST00000369282.1_Nonsense_Mutation_p.Q72*|TDRD1_ENST00000369281.2_Nonsense_Mutation_p.Q72*|TDRD1_ENST00000422662.1_5'UTR			Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	72					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ cell development (GO:0007281)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)	metal ion binding (GO:0046872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(5)	48		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		GCTTTGTGAGCAAACCAAACA	0.393																																					p.Q72X		Atlas-SNP	.											.	TDRD1	126	.	0			c.C214T						PASS	.						98	105	103					10																	115947804		2203	4300	6503	SO:0001587	stop_gained	56165	exon2			TGTGAGCAAACCA	AF285606	CCDS7588.1	10q26.11	2013-01-23			ENSG00000095627	ENSG00000095627		"Tudor domain containing"	11712	protein-coding gene	gene with protein product	"cancer/testis antigen 41.1"	605796				11279525	Standard	NM_198795		Approved	CT41.1	uc001lbg.1	Q9BXT4	OTTHUMG00000019083	ENST00000369280.1:c.214C>T	chr10.hg19:g.115947804C>T	ENSP00000358286:p.Gln72*	238.0	0.0	.		204.0	94.0	.	NM_198795	A6NEN3|A6NMN2|B3KVI4|B4E2L5|D3DRC2|Q4G0Y8|Q6P518|Q9H7B3	Nonsense_Mutation	SNP	ENST00000369280.1	hg19		.	.	.	.	.	.	.	.	.	.	C	36	5.622831	0.96660	.	.	ENSG00000095627	ENST00000369282;ENST00000251864;ENST00000369281;ENST00000369280	.	.	.	5.44	3.53	0.40419	.	0.113505	0.39909	N	0.001228	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-5.6592	10.9788	0.47482	0.3394:0.6606:0.0:0.0	.	.	.	.	X	72	.	ENSP00000251864:Q72X	Q	+	1	0	TDRD1	115937794	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	1.525000	0.35953	0.632000	0.30432	0.563000	0.77884	CAA	.	.	.	none		0.393	TDRD1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050457.2			T	115947804	C	T	115947804	4	4	251	1	0	0	0	0	0	1	0	0	15742	711	25	2	216	2	TDRD1	10	115947804	Nonsense_Mutation	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	11590843	115947804	19586943	44	15598											
FAM160A2	84067	hgsc.bcm.edu	37	chr11	6245688	6245688	+	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	tttggagattggccccttgaGgtatacggtgcccagggccc	6	10	14	11	1	0	2	0	1	0	1	0	3	0	2	4	5	2	1	4	5	2	5			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr11:6245688G>T	ENST00000449352.2	-	2	322	c.59C>A	c.(58-60)cCt>cAt	p.P20H	FAM160A2_ENST00000524416.1_Missense_Mutation_p.P20H|FAM160A2_ENST00000265978.4_Missense_Mutation_p.P20H			Q8N612	F16A2_HUMAN	family with sequence similarity 160, member A2	20					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						GGCCCCTTGAGGTATACGGTG	0.592																																					p.P20H		Atlas-SNP	.											.	FAM160A2	100	.	0			c.C59A						PASS	.						95	87	90					11																	6245688		2201	4296	6497	SO:0001583	missense	84067	exon2			CCTTGAGGTATAC		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.59C>A	chr11.hg19:g.6245688G>T	ENSP00000416918:p.Pro20His	125.0	0.0	.		123.0	45.0	.	NM_032127	Q9C0A4|Q9H0N3|Q9H624	Missense_Mutation	SNP	ENST00000449352.2	hg19	CCDS44530.1	.	.	.	.	.	.	.	.	.	.	G	16.94	3.261846	0.59431	.	.	ENSG00000051009	ENST00000449352;ENST00000265978;ENST00000524416	T;T;T	0.14766	3.1;3.1;2.48	5.74	5.74	0.90152	.	0.349704	0.25156	N	0.032716	T	0.18759	0.0450	L	0.29908	0.895	0.36059	D	0.841331	B;B;D	0.69078	0.146;0.065;0.997	B;B;P	0.57468	0.024;0.016;0.821	T	0.06844	-1.0804	10	0.11485	T	0.65	-12.051	14.5134	0.67804	0.0:0.1464:0.8536:0.0	.	20;20;20	E9PJK5;Q8N612;Q8N612-2	.;F16A2_HUMAN;.	H	20	ENSP00000416918:P20H;ENSP00000265978:P20H;ENSP00000431773:P20H	ENSP00000265978:P20H	P	-	2	0	FAM160A2	6202264	0.999000	0.42202	1.000000	0.80357	0.967000	0.64934	3.803000	0.55560	2.700000	0.92200	0.650000	0.86243	CCT	.	.	.	none		0.592	FAM160A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383759.1	NM_032127		T	6245688	G	T	6245688	3	4	251	1	0	0	0	0	1	0	0	0	5473	1000	35	4	2945	4	FAM160A2	11	6245688	Missense_Mutation	SNP	G	TCGA-SX-A7SQ-01A-12D-A35Z-10		6245688	128760828	45	15599											
PRKCDBP	112464	hgsc.bcm.edu	37	chr11	6341515	6341515	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggctgcgactcagagcgccCaggccgctctggatgcggcg	5	6	16	14	5	2	1	1	0	1	1	2	3	2	2	2	4	3	2	2	4	0	0			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr11:6341515C>T	ENST00000303927.3	-	1	362	c.192G>A	c.(190-192)ctG>ctA	p.L64L	PRKCDBP_ENST00000530979.1_Silent_p.L64L	NM_145040.2	NP_659477.2	Q969G5	PRDBP_HUMAN	protein kinase C, delta binding protein	64					cortical actin cytoskeleton organization (GO:0030866)|negative regulation of fermentation (GO:1901003)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	caveola (GO:0005901)|protein complex (GO:0043234)				large_intestine(3)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		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)		TCAGAGCGCCCAGGCCGCTCT	0.711																																					p.L64L		Atlas-SNP	.											.	PRKCDBP	19	.	0			c.G192A						PASS	.						6	6	6					11																	6341515		2108	4157	6265	SO:0001819	synonymous_variant	112464	exon1			AGCGCCCAGGCCG	AF339881	CCDS7762.1	11p15.4	2011-04-20			ENSG00000170955	ENSG00000170955			9400	protein-coding gene	gene with protein product	"sdr-related gene product that binds to c-kinase"					9054438	Standard	NM_145040		Approved	SRBC, HSRBC, MGC20400, cavin-3, CAVIN3	uc001mcu.1	Q969G5	OTTHUMG00000133378	ENST00000303927.3:c.192G>A	chr11.hg19:g.6341515C>T		50.0	0.0	.		40.0	17.0	.	NM_145040		Silent	SNP	ENST00000303927.3	hg19	CCDS7762.1																																																																																			.	.	.	none		0.711	PRKCDBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257228.2	NM_145040		T	6341515	C	T	6341515	2	4	251	1	0	0	0	0	0	0	0	1	12520	581	21	2		2	PRKCDBP	11	6341515	Silent	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	95827	6341515	128665001	46	15600											
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-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	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	chr11.hg19:g.6867588T>C		123.0	0.0	.		118.0	6.0	.	NM_178168	O95223|Q52M66|Q96R21|Q96R22	Silent	SNP	ENST00000299454.4	hg19	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	251	1	0	0	0	0	0	0	0	1	10900	1509	53	3		3	OR10A5	11	6867588	Silent	SNP	T	TCGA-SX-A7SQ-01A-12D-A35Z-10	526073	6867588	128138928	47	15601											
ARAP1	116985	hgsc.bcm.edu	37	chr11	72423565	72423565	+	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	ttcctctccctcgctcagcaGactggccacgcgcacggccc	5	7	9	20	4	2	1	1	0	1	1	5	1	3	1	4	2	1	3	4	2	0	1			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr11:72423565G>A	ENST00000393609.3	-	6	998	c.796C>T	c.(796-798)Ctg>Ttg	p.L266L	ARAP1_ENST00000334211.8_Silent_p.L21L|ARAP1_ENST00000426523.1_Silent_p.L21L|ARAP1_ENST00000393605.3_Silent_p.L26L|ARAP1_ENST00000429686.1_Silent_p.L21L|ARAP1_ENST00000359373.5_Silent_p.L266L|ARAP1_ENST00000455638.2_Silent_p.L266L	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	266					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						TCGCTCAGCAGACTGGCCACG	0.657																																					p.L266L	Ovarian(102;1198 1520 13195 17913 37529)	Atlas-SNP	.											.	ARAP1	168	.	0			c.C796T						PASS	.						170	133	145					11																	72423565		2200	4293	6493	SO:0001819	synonymous_variant	116985	exon6			TCAGCAGACTGGC	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.796C>T	chr11.hg19:g.72423565G>A		65.0	0.0	.		69.0	32.0	.	NM_001040118	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Silent	SNP	ENST00000393609.3	hg19	CCDS41687.1																																																																																			.	.	.	none		0.657	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118		A	72423565	G	A	72423565	2	1	251	1	0	0	0	0	0	0	0	1	838	933	33	2		2	ARAP1	11	72423565	Silent	SNP	G	TCGA-SX-A7SQ-01A-12D-A35Z-10	65555977	72423565	62582951	48	15602											
DLG2	1740	hgsc.bcm.edu	37	chr11	83770507	83770507	+	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	acacatcaacctcattcaccCgcaagatacaatcattgacc	15	8	3	15	1	4	2	4	1	0	1	4	2	4	2	3	0	2	1	3	0	4	3			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr11:83770507C>G	ENST00000532653.1	-	6	757	c.455G>C	c.(454-456)cGg>cCg	p.R152P	DLG2_ENST00000524982.1_Missense_Mutation_p.R152P|DLG2_ENST00000376106.3_5'UTR|DLG2_ENST00000418306.2_Missense_Mutation_p.R101P|DLG2_ENST00000537455.1_5'UTR|DLG2_ENST00000376104.2_Missense_Mutation_p.R257P|DLG2_ENST00000280241.8_Missense_Mutation_p.R191P|DLG2_ENST00000543673.1_Missense_Mutation_p.R257P|DLG2_ENST00000398301.2_Missense_Mutation_p.R191P|DLG2_ENST00000531015.1_Missense_Mutation_p.R119P|DLG2_ENST00000398309.2_Missense_Mutation_p.R152P|DLG2_ENST00000330014.6_Missense_Mutation_p.R91P			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)				CTCATTCACCCGCAAGATACA	0.443																																					p.R257P		Atlas-SNP	.											.	DLG2	448	.	0			c.G770C						PASS	.						67	60	63					11																	83770507		1894	4139	6033	SO:0001583	missense	1740	exon11			TTCACCCGCAAGA	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.455G>C	chr11.hg19:g.83770507C>G	ENSP00000435849:p.Arg152Pro	137.0	0.0	.		129.0	55.0	.	NM_001142699	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Missense_Mutation	SNP	ENST00000532653.1	hg19		.	.	.	.	.	.	.	.	.	.	C	28.2	4.899836	0.91962	.	.	ENSG00000150672	ENST00000398309;ENST00000376104;ENST00000418306;ENST00000543673;ENST00000280241;ENST00000330014;ENST00000524982;ENST00000532653;ENST00000546021;ENST00000531015;ENST00000398301;ENST00000398299	T;T;T;T;T;T;T;T;T;T;T	0.27890	1.64;1.64;1.64;1.64;1.64;1.64;1.64;1.64;1.64;1.64;1.64	5.17	5.17	0.71159	PDZ/DHR/GLGF (4);	0.095438	0.43416	D	0.000561	T	0.54431	0.1858	M	0.64170	1.965	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;0.999;0.998;1.0;1.0;1.0;0.999;1.0	D;D;D;D;D;D;D;D	0.97110	1.0;0.966;0.932;0.977;0.991;0.999;0.99;1.0	T	0.51568	-0.8689	9	.	.	.	.	18.6643	0.91483	0.0:1.0:0.0:0.0	.	119;152;152;91;191;257;152;101	E9PIW2;B7Z2T4;E9PN83;B7Z264;Q6ZSU2;Q15700-2;Q15700;Q15700-3	.;.;.;.;.;.;DLG2_HUMAN;.	P	152;257;101;257;191;91;152;152;257;119;191;69	ENSP00000381355:R152P;ENSP00000365272:R257P;ENSP00000402275:R101P;ENSP00000441994:R257P;ENSP00000280241:R191P;ENSP00000381353:R91P;ENSP00000432894:R152P;ENSP00000435849:R152P;ENSP00000433848:R119P;ENSP00000381346:R191P;ENSP00000381344:R69P	.	R	-	2	0	DLG2	83448155	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.762000	0.68809	2.420000	0.82092	0.460000	0.39030	CGG	.	.	.	none		0.443	DLG2-009	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000259253.2	NM_001364		G	83770507	C	G	83770507	3	3	251	1	0	0	0	0	1	0	0	0	4557	652	23	4	2279	4	DLG2	11	83770507	Missense_Mutation	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	11346942	83770507	51236009	49	15603											
TRIM49	57093	hgsc.bcm.edu	37	chr11	89531578	89531579	+	Frame_Shift_Del	DEL	AT	AT	-																															gattcttctctttccgatacAtattacagacaccaaaagcc																										TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr11:89531578_89531579delAT	ENST00000329758.1	-	8	1406_1407	c.1078_1079delAT	c.(1078-1080)atgfs	p.M360fs	TRIM49_ENST00000532501.2_Frame_Shift_Del_p.M283fs	NM_020358.2	NP_065091.1	P0CI25	TRI49_HUMAN	tripartite motif containing 49	360	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(14)|prostate(1)|skin(2)|stomach(1)	27		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				TTTCCGATACATATTACAGACA	0.436																																					p.360_360del		Atlas-Indel,Pindel	.											.	TRIM49	45	.	0			c.1079_1080del						PASS	.																																			SO:0001589	frameshift_variant	57093	exon8			.	AB037682	CCDS8287.1	11p11.12-q12	2012-05-21	2011-01-25	2004-11-17	ENSG00000168930	ENSG00000168930		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	13431	protein-coding gene	gene with protein product		606124	"ring finger protein 18", "tripartite motif-containing 49"	RNF18		11018261	Standard	NM_020358		Approved	TRIM49A	uc001pdb.3	P0CI25		ENST00000329758.1:c.1078_1079delAT	chr11.hg19:g.89531580_89531581delAT	ENSP00000327604:p.Met360fs	265.0	0.0	0		254.0	85.0	0.334646	NM_020358	A0AVR7|A0AVR9|Q6DJV1|Q9NS80	Frame_Shift_Del	DEL	ENST00000329758.1	hg19	CCDS8287.1																																																																																			.	.	.	none		0.436	TRIM49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395435.1	NM_020358		-	89531579	AT	-	89531578	7	5	251	1	0	1	0	1	0	0	0	0	16536	217	8	0	283	0	TRIM49	11	89531578	Frame_Shift_Del	DEL	AT	TCGA-SX-A7SQ-01A-12D-A35Z-10	5761071	89531578	45474938	50	15604											
KBTBD3	143879	hgsc.bcm.edu	37	chr11	105923709	105923709	+	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	ctgttgctgtggtagacctgCacttcatctgtgatttcatc	6	16	9	10	0	3	2	2	1	1	1	4	2	3	2	1	1	2	4	1	1	1	4			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr11:105923709C>A	ENST00000526793.1	-	3	1866	c.1707G>T	c.(1705-1707)gtG>gtT	p.V569V	KBTBD3_ENST00000531837.1_Silent_p.V569V|KBTBD3_ENST00000534815.1_Silent_p.V490V	NM_152433.3	NP_689646.2	Q8NAB2	KBTB3_HUMAN	kelch repeat and BTB (POZ) domain containing 3	565										NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|prostate(1)	25		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.43e-05)|Epithelial(105;0.00418)|all cancers(92;0.0299)		GGTAGACCTGCACTTCATCTG	0.383																																					p.V569V		Atlas-SNP	.											.	KBTBD3	59	.	0			c.G1707T						PASS	.						130	129	129					11																	105923709		2201	4298	6499	SO:0001819	synonymous_variant	143879	exon3			GACCTGCACTTCA	AK055247	CCDS8334.1	11q22.3	2013-01-08	2003-12-12	2003-12-17		ENSG00000182359		"BTB/POZ domain containing"	22934	protein-coding gene	gene with protein product			"BTB and kelch domain containing 3"	BKLHD3			Standard	NM_198439		Approved		uc001pjb.3	Q8NAB2		ENST00000526793.1:c.1707G>T	chr11.hg19:g.105923709C>A		141.0	0.0	.		131.0	54.0	.	NM_152433	Q6N066|Q86X38|Q96NK5	Silent	SNP	ENST00000526793.1	hg19	CCDS8334.1																																																																																			.	.	.	none		0.383	KBTBD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388705.2	NM_152433		A	105923709	C	A	105923709	2	1	251	1	0	0	0	0	0	0	0	1	8001	697	25	4		4	KBTBD3	11	105923709	Silent	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	16392131	105923709	29082807	51	15605											
TECTA	7007	hgsc.bcm.edu	37	chr11	120976623	120976623	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atggaagctcatctgagattAagttggccatcccagttttc	10	13	9	9	0	2	1	1	1	1	1	4	3	3	2	2	2	1	3	2	2	2	4			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr11:120976623A>G	ENST00000392793.1	+	3	419	c.148A>G	c.(148-150)Aag>Gag	p.K50E	TECTA_ENST00000264037.2_Missense_Mutation_p.K50E			O75443	TECTA_HUMAN	tectorin alpha	50					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)		ATCTGAGATTAAGTTGGCCAT	0.468																																					p.K50E		Atlas-SNP	.											.	TECTA	329	.	0			c.A148G						PASS	.						258	246	250					11																	120976623		2203	4299	6502	SO:0001583	missense	7007	exon2			GAGATTAAGTTGG	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.148A>G	chr11.hg19:g.120976623A>G	ENSP00000376543:p.Lys50Glu	76.0	0.0	.		45.0	16.0	.	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	hg19	CCDS8434.1	.	.	.	.	.	.	.	.	.	.	A	13.62	2.291183	0.40494	.	.	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.76186	-1.0;-1.0	5.78	4.59	0.56863	.	0.112533	0.64402	D	0.000009	T	0.60945	0.2308	N	0.25286	0.73	0.31391	N	0.677863	B	0.22003	0.063	B	0.19666	0.026	T	0.63959	-0.6519	10	0.42905	T	0.14	.	12.6491	0.56751	0.8622:0.1378:0.0:0.0	.	50	O75443	TECTA_HUMAN	E	50	ENSP00000376543:K50E;ENSP00000264037:K50E	ENSP00000264037:K50E	K	+	1	0	TECTA	120481833	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	2.732000	0.47352	2.204000	0.70986	0.528000	0.53228	AAG	.	.	.	none		0.468	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		G	120976623	A	G	120976623	3	3	251	1	0	0	0	0	1	0	0	0	15759	363	13	3	154	3	TECTA	11	120976623	Missense_Mutation	SNP	A	TCGA-SX-A7SQ-01A-12D-A35Z-10	15052914	120976623	14029893	52	15606											
AGAP2	116986	hgsc.bcm.edu	37	chr12	58131312	58131312	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctcccccggcggcggcggCggtggcggcggcagagaccg	3	2	19	17	8	0	1	0	0	0	1	1	2	1	1	4	8	0	1	4	8	0	0	rs561812307		TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr12:58131312C>T	ENST00000547588.1	-	1	717	c.718G>A	c.(718-720)Gcc>Acc	p.A240T	AGAP2_ENST00000257897.3_Intron	NM_001122772.2	NP_001116244.1	Q99490	AGAP2_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	240					axon guidance (GO:0007411)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|large_intestine(7)|lung(20)|prostate(3)|skin(1)|stomach(1)	48						gcggcggcggcggtggcggcg	0.706																																					p.A240T		Atlas-SNP	.											AGAP2_ENST00000547588,NS,carcinoma,0,1	AGAP2	167	.	0			c.G718A						PASS	.						4	6	5					12																	58131312		1428	3301	4729	SO:0001583	missense	116986	exon1			CGGCGGCGGTGGC	AF413077	CCDS8951.1, CCDS44932.1	12q13.2	2013-05-30	2008-09-22	2008-09-22	ENSG00000135439	ENSG00000135439		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16921	protein-coding gene	gene with protein product		605476	"centaurin, gamma 1"	CENTG1			Standard	NM_001122772		Approved		uc001spq.3	Q99490	OTTHUMG00000170285	ENST00000547588.1:c.718G>A	chr12.hg19:g.58131312C>T	ENSP00000449241:p.Ala240Thr	94.0	0.0	.		126.0	7.0	.	NM_001122772	A8K9F7|O00578|Q548E0|Q8IWU3	Missense_Mutation	SNP	ENST00000547588.1	hg19	CCDS44932.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.24|10.24	1.294811|1.294811	0.23564|0.23564	.|.	.|.	ENSG00000135439|ENSG00000135439	ENST00000547588|ENST00000328568	T|.	0.39997|.	1.05|.	3.81|3.81	-1.14|-1.14	0.09741|0.09741	.|.	1.354790|.	0.05448|.	N|.	0.548952|.	T|T	0.10508|0.10508	0.0257|0.0257	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B;B|.	0.14012|.	0.009;0.005|.	B;B|.	0.06405|.	0.002;0.001|.	T|T	0.24548|0.24548	-1.0157|-1.0157	10|5	0.56958|.	D|.	0.05|.	.|.	0.5619|0.5619	0.00680|0.00680	0.1874:0.3561:0.184:0.2724|0.1874:0.3561:0.184:0.2724	.|.	240;240|.	F8VVT9;Q99490|.	.;AGAP2_HUMAN|.	T|H	240|103	ENSP00000449241:A240T|.	ENSP00000449241:A240T|.	A|R	-|-	1|2	0|0	AGAP2|AGAP2	56417579|56417579	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.016000|0.016000	0.09150|0.09150	0.086000|0.086000	0.14935|0.14935	-0.555000|-0.555000	0.06142|0.06142	0.455000|0.455000	0.32223|0.32223	GCC|CGC	.	.	.	none		0.706	AGAP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408367.1	NM_014770		T	58131312	C	T	58131312	3	4	251	1	0	0	0	0	1	0	0	0	368	768	27	1	2936	1	AGAP2	12	58131312	Missense_Mutation	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10		58131312	75720583	53	15607											
PHLDA1	22822	hgsc.bcm.edu	37	chr12	76424940	76424940	+	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	tgctgctgctgctgctgttgCtgctgctgctgctggtgttg	0	16	15	10	0	0	0	0	0	0	0	0	0	0	0	0	1	10	12	0	1	0	2	rs549868413|rs57875368|rs111754051|rs71716769|rs80344196|rs398020175	byFrequency	TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr12:76424940C>T	ENST00000266671.5	-	1	2772	c.582G>A	c.(580-582)caG>caA	p.Q194Q	PHLDA1_ENST00000602540.1_Silent_p.Q53Q|RP11-290L1.3_ENST00000552367.1_RNA|RP11-290L1.2_ENST00000547721.1_RNA			Q8WV24	PHLA1_HUMAN	pleckstrin homology-like domain, family A, member 1	194	PH.|Poly-Gln.				apoptotic process (GO:0006915)|FasL biosynthetic process (GO:0045210)|forebrain neuron differentiation (GO:0021879)|positive regulation of apoptotic process (GO:0043065)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	14		Colorectal(145;0.09)				gctgctgttgctgctgctgct	0.652																																					p.Q194Q		Atlas-SNP	.											.	PHLDA1	39	.	0			c.G582A						PASS	.						4	4	4					12																	76424940		2019	3942	5961	SO:0001819	synonymous_variant	22822	exon1			CTGTTGCTGCTGC	Z50194	CCDS31861.1	12q15	2008-08-05				ENSG00000139289			8933	protein-coding gene	gene with protein product	"proline-histidine rich protein"	605335				12384558, 15037619	Standard	NM_007350		Approved	TDAG51, DT1P1B11, PHRIP	uc001sxu.3	Q8WV24		ENST00000266671.5:c.582G>A	chr12.hg19:g.76424940C>T		5.0	0.0	.		28.0	16.0	.	NM_007350	A1A4G9|Q15184|Q2TAN2|Q9NZ17	Silent	SNP	ENST00000266671.5	hg19	CCDS31861.1																																																																																			.	.	.	weak		0.652	PHLDA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405846.2	NM_007350		T	76424940	C	T	76424940	2	4	251	1	0	0	0	0	0	0	0	1	11855	796	28	2		2	PHLDA1	12	76424940	Silent	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	18293628	76424940	57426955	54	15608											
CLLU1OS	574016	hgsc.bcm.edu	37	chr12	92814817	92814817	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgtgcttccttcttcccaTcatcattgcccaagtgtgtc	5	15	6	15	0	3	0	2	0	1	0	6	0	5	0	4	0	2	1	4	0	1	4			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr12:92814817T>C	ENST00000378487.2	-	3	276	c.275A>G	c.(274-276)gAt>gGt	p.D92G	RP11-693J15.4_ENST00000508671.1_RNA|CLLU1_ENST00000378485.1_5'Flank|CLLU1OS_ENST00000538965.1_Missense_Mutation_p.D92G	NM_001025232.1	NP_001020403.1	Q5K130	CLU1O_HUMAN	chronic lymphocytic leukemia up-regulated 1 opposite strand	92										large_intestine(1)|lung(7)	8						CTTCTTCCCATCATCATTGCC	0.438																																					p.D92G		Atlas-SNP	.											.	CLLU1OS	14	.	0			c.A275G						PASS	.						504	468	480					12																	92814817		2203	4300	6503	SO:0001583	missense	574016	exon3			TTCCCATCATCAT	AJ845168	CCDS31871.1	12q22	2006-03-30	2006-03-30		ENSG00000205057	ENSG00000205057			24070	protein-coding gene	gene with protein product			"chronic lymphocytic leukemia up-regulated 1 overlapping strand"				Standard	NM_001025232		Approved		uc001tcb.1	Q5K130	OTTHUMG00000161990	ENST00000378487.2:c.275A>G	chr12.hg19:g.92814817T>C	ENSP00000367748:p.Asp92Gly	79.0	0.0	.		106.0	67.0	.	NM_001025232		Missense_Mutation	SNP	ENST00000378487.2	hg19	CCDS31871.1	.	.	.	.	.	.	.	.	.	.	T	3.155	-0.173406	0.06421	.	.	ENSG00000205057	ENST00000378487;ENST00000538965	.	.	.	3.22	-1.87	0.07737	.	.	.	.	.	T	0.16128	0.0388	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19976	-1.0289	8	0.87932	D	0	.	4.2494	0.10688	0.0:0.2396:0.4148:0.3456	.	92	Q5K130	CLU1O_HUMAN	G	92	.	ENSP00000367748:D92G	D	-	2	0	CLLU1OS	91338948	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.668000	0.05268	-0.372000	0.07992	-0.517000	0.04412	GAT	.	.	.	none		0.438	CLLU1OS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366646.1			C	92814817	T	C	92814817	3	2	251	1	0	0	0	0	1	0	0	0	3543	1435	50	3	34	3	CLLU1OS	12	92814817	Missense_Mutation	SNP	T	TCGA-SX-A7SQ-01A-12D-A35Z-10	16389877	92814817	41037078	55	15609											
STAB2	55576	hgsc.bcm.edu	37	chr12	104160113	104160113	+	Nonstop_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	tgaccccttgaggacactgtGagggcctggacgggagatgc	8	7	16	10	1	0	4	0	3	0	1	0	7	0	6	3	4	1	0	3	4	0	1			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr12:104160113G>T	ENST00000388887.2	+	69	7859	c.7655G>T	c.(7654-7656)tGa>tTa	p.*2552L	RP11-341G23.4_ENST00000551299.1_RNA|RP11-341G23.4_ENST00000550029.1_RNA	NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						AGGACACTGTGAGGGCCTGGA	0.537																																					p.X2552L		Atlas-SNP	.											.	STAB2	370	.	0			c.G7655T						PASS	.						101	84	90					12																	104160113		2203	4300	6503	SO:0001578	stop_lost	55576	exon69			CACTGTGAGGGCC	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.7655G>T	chr12.hg19:g.104160113G>T	ENSP00000373539:p.*2552Leuext*19	127.0	0.0	.		179.0	110.0	.	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	hg19	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	G	14.18	2.458045	0.43634	.	.	ENSG00000136011	ENST00000388887	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.9111	0.47110	0.0851:0.0:0.9149:0.0	.	.	.	.	L	2552	.	.	X	+	2	2	STAB2	102684243	0.985000	0.35326	0.802000	0.32245	0.013000	0.08279	1.448000	0.35112	2.710000	0.92621	0.542000	0.68232	TGA	.	.	.	none		0.537	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			T	104160113	G	T	104160113	4	4	251	1	0	0	0	0	0	0	0	0	15250	1285	45	4	7929	4	STAB2	12	104160113	Nonstop_Mutation	SNP	G	TCGA-SX-A7SQ-01A-12D-A35Z-10	11345296	104160113	29691782	56	15610											
ATP8A2	51761	hgsc.bcm.edu	37	chr13	26542768	26542768	+	Frame_Shift_Del	DEL	A	A	-																															aggtgcaggagctggaaaccAagtctcgagtcctgggaaaa																										TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr13:26542768delA	ENST00000381655.2	+	35	3470	c.3328delA	c.(3328-3330)aagfs	p.K1110fs	ATP8A2_ENST00000255283.8_Frame_Shift_Del_p.K1045fs	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	1070					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		GCTGGAAACCAAGTCTCGAGT	0.537																																					p.T1109fs		Atlas-Indel,Pindel	.											.	ATP8A2	181	.	0			c.3327delC						PASS	.						73	81	79					13																	26542768		1974	4165	6139	SO:0001589	frameshift_variant	51761	exon35			.	AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"ATPases / P-type"	13533	protein-coding gene	gene with protein product		605870	"ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2", "ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.3328delA	chr13.hg19:g.26542768delA	ENSP00000371070:p.Lys1110fs	176.0	0.0	0		243.0	79.0	0.325103	NM_016529	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Frame_Shift_Del	DEL	ENST00000381655.2	hg19	CCDS41873.1																																																																																			.	.	.	none		0.537	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529		-	26542768	A	-	26542768	7	5	251	1	0	1	0	1	0	0	0	0	1193	131	5	0	3466	0	ATP8A2	13	26542768	Frame_Shift_Del	DEL	A	TCGA-SX-A7SQ-01A-12D-A35Z-10		26542768	88627110	57	15611											
FREM2	341640	hgsc.bcm.edu	37	chr13	39450509	39450509	+	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	cacctttgaccttgacatccGattccaacaggtgtggctta	9	12	8	12	1	0	2	0	2	0	0	2	3	2	2	4	2	1	1	4	2	2	4			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr13:39450509G>T	ENST00000280481.7	+	20	8750	c.8534G>T	c.(8533-8535)cGa>cTa	p.R2845L		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2845					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)		CTTGACATCCGATTCCAACAG	0.433																																					p.R2845L		Atlas-SNP	.											.	FREM2	385	.	0			c.G8534T						PASS	.						110	92	98					13																	39450509		2203	4300	6503	SO:0001583	missense	341640	exon20			ACATCCGATTCCA	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.8534G>T	chr13.hg19:g.39450509G>T	ENSP00000280481:p.Arg2845Leu	72.0	0.0	.		84.0	56.0	.	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	hg19	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	G	32	5.136846	0.94517	.	.	ENSG00000150893	ENST00000280481	T	0.63913	-0.07	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.82351	0.5018	M	0.86028	2.79	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.83912	0.0296	10	0.62326	D	0.03	.	19.8108	0.96545	0.0:0.0:1.0:0.0	.	2845	Q5SZK8	FREM2_HUMAN	L	2845	ENSP00000280481:R2845L	ENSP00000280481:R2845L	R	+	2	0	FREM2	38348509	1.000000	0.71417	0.998000	0.56505	0.915000	0.54546	9.776000	0.99001	2.698000	0.92095	0.563000	0.77884	CGA	.	.	.	none		0.433	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39450509	G	T	39450509	3	4	251	1	0	0	0	0	1	0	0	0	6052	1058	37	4	8612	4	FREM2	13	39450509	Missense_Mutation	SNP	G	TCGA-SX-A7SQ-01A-12D-A35Z-10	12907741	39450509	75719369	58	15612											
ARHGEF7	8874	hgsc.bcm.edu	37	chr13	111926181	111926181	+	Missense_Mutation	SNP	T	T	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	tgaggagttgggggagttcaTggagaccaaaggtgccagca	11	7	17	6	0	1	2	1	1	0	1	1	5	1	4	2	5	2	3	2	5	1	2			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr13:111926181T>G	ENST00000375741.2	+	11	1407	c.1157T>G	c.(1156-1158)aTg>aGg	p.M386R	ARHGEF7_ENST00000317133.5_Missense_Mutation_p.M365R|ARHGEF7_ENST00000370623.3_Missense_Mutation_p.M293R|ARHGEF7_ENST00000544132.1_Intron|ARHGEF7_ENST00000375736.4_Missense_Mutation_p.M208R|ARHGEF7_ENST00000478679.1_Missense_Mutation_p.M130R|ARHGEF7_ENST00000375737.5_Missense_Mutation_p.M283R|ARHGEF7_ENST00000375723.1_Missense_Mutation_p.M208R|ARHGEF7_ENST00000218789.5_Missense_Mutation_p.M208R|ARHGEF7_ENST00000375739.2_Missense_Mutation_p.M336R|ARHGEF7_ENST00000426073.2_Missense_Mutation_p.M208R|ARHGEF7_ENST00000483189.1_3'UTR	NM_001113511.1|NM_145735.2	NP_001106983.1|NP_663788.1	Q14155	ARHG7_HUMAN	Rho guanine nucleotide exchange factor (GEF) 7	386	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|hematopoietic progenitor cell differentiation (GO:0002244)|lamellipodium assembly (GO:0030032)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of GTPase activity (GO:0043547)|positive regulation of lamellipodium morphogenesis (GO:2000394)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase binding (GO:0019901)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	41	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			GGGGAGTTCATGGAGACCAAA	0.552																																					p.M386R		Atlas-SNP	.											.	ARHGEF7	157	.	0			c.T1157G						PASS	.						109	100	103					13																	111926181		2203	4300	6503	SO:0001583	missense	8874	exon11			AGTTCATGGAGAC	D63476	CCDS9521.1, CCDS32009.1, CCDS45068.1, CCDS45069.1	13q33.3	2013-01-10			ENSG00000102606	ENSG00000102606		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	15607	protein-coding gene	gene with protein product	"SH3 domain-containing proline-rich protein", "PAK-interacting exchange factor beta", "rho", "guanine nucleotide exchange factor 7"	605477				9207241, 9726964	Standard	NM_003899		Approved	KIAA0142, PIXB, DKFZp761K1021, Nbla10314, DKFZp686C12170, BETA-PIX, COOL1, P85SPR, P85, P85COOL1, P50BP, PAK3, P50	uc001vrs.2	Q14155	OTTHUMG00000017357	ENST00000375741.2:c.1157T>G	chr13.hg19:g.111926181T>G	ENSP00000364893:p.Met386Arg	94.0	0.0	.		128.0	61.0	.	NM_001113511	B1ALK6|B1ALK8|Q3LIA4|Q5W9H0|Q6P9G3|Q6PII2|Q86W63|Q8N3M1	Missense_Mutation	SNP	ENST00000375741.2	hg19	CCDS45068.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.468353	0.84533	.	.	ENSG00000102606	ENST00000317133;ENST00000375741;ENST00000375739;ENST00000370623;ENST00000545635;ENST00000466143;ENST00000218789;ENST00000375736;ENST00000426073;ENST00000375737;ENST00000375723;ENST00000478679	T;T;T;T;T;T;T;T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05	4.87	4.87	0.63330	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	T	0.81307	0.4795	M	0.87827	2.91	0.80722	D	1	D;D;D;D;D;D	0.89917	0.993;1.0;0.993;0.998;1.0;1.0	D;D;D;D;D;D	0.97110	0.993;1.0;0.993;0.997;1.0;0.999	D	0.85178	0.1002	10	0.87932	D	0	.	14.498	0.67702	0.0:0.0:0.0:1.0	.	130;283;130;336;386;365	E9PDQ5;B7Z6G2;B7Z344;Q14155-2;Q14155;Q14155-3	.;.;.;.;ARHG7_HUMAN;.	R	365;386;336;293;363;208;208;208;208;283;208;130	ENSP00000325994:M365R;ENSP00000364893:M386R;ENSP00000364891:M336R;ENSP00000359657:M293R;ENSP00000418067:M208R;ENSP00000218789:M208R;ENSP00000364888:M208R;ENSP00000397068:M208R;ENSP00000364889:M283R;ENSP00000364875:M208R;ENSP00000417596:M130R	ENSP00000218789:M208R	M	+	2	0	ARHGEF7	110724182	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	7.549000	0.82163	1.823000	0.53134	0.477000	0.44152	ATG	.	.	.	none		0.552	ARHGEF7-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113511		G	111926181	T	G	111926181	3	3	251	1	0	0	0	0	1	0	0	0	911	1464	51	5	1199	5	ARHGEF7	13	111926181	Missense_Mutation	SNP	T	TCGA-SX-A7SQ-01A-12D-A35Z-10	72475672	111926181	3243697	59	15613											
TGM1	7051	hgsc.bcm.edu	37	chr14	24718615	24718615	+	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	ccatccccaggggctggggcCacatccacctggatgacacc	8	5	11	17	0	0	1	0	1	0	0	2	2	2	2	7	5	0	1	7	5	0	0			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr14:24718615C>G	ENST00000206765.6	-	15	2481	c.2358G>C	c.(2356-2358)gtG>gtC	p.V786V	TGM1_ENST00000544573.1_Silent_p.V344V	NM_000359.2	NP_000350.1	P22735	TGM1_HUMAN	transglutaminase 1	786					cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|organ morphogenesis (GO:0009887)|peptide cross-linking (GO:0018149)	cell-cell adherens junction (GO:0005913)|cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|intrinsic component of membrane (GO:0031224)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)	24				GBM - Glioblastoma multiforme(265;0.0186)	L-Glutamine(DB00130)	GGGCTGGGGCCACATCCACCT	0.632																																					p.V786V		Atlas-SNP	.											.	TGM1	73	.	0			c.G2358C						PASS	.						68	63	65					14																	24718615		2203	4300	6503	SO:0001819	synonymous_variant	7051	exon15			TGGGGCCACATCC	D90287	CCDS9622.1	14q11.2	2013-05-02	2013-05-02		ENSG00000092295	ENSG00000092295	2.3.2.13	"Transglutaminases"	11777	protein-coding gene	gene with protein product	"K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase"	190195	"transglutaminase 1 (K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase)"	ICR2		11390390	Standard	NM_000359		Approved	TGASE, TGK, LI, LI1	uc001wod.3	P22735	OTTHUMG00000029329	ENST00000206765.6:c.2358G>C	chr14.hg19:g.24718615C>G		55.0	0.0	.		60.0	19.0	.	NM_000359	B4DWR7|Q197M4	Silent	SNP	ENST00000206765.6	hg19	CCDS9622.1																																																																																			.	.	.	none		0.632	TGM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073160.6	NM_000359		G	24718615	C	G	24718615	2	3	251	1	0	0	0	0	0	0	0	1	15841	581	21	4		4	TGM1	14	24718615	Silent	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10		24718615	82630925	60	15614											
EFTUD1	79631	hgsc.bcm.edu	37	chr15	82545087	82545087	+	Frame_Shift_Del	DEL	T	T	-																															atagtgatccctcggatctgTtcatcttctctgctgtccat																										TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr15:82545087delT	ENST00000268206.7	-	4	357	c.189delA	c.(187-189)gaafs	p.E63fs	EFTUD1_ENST00000359445.3_Intron	NM_024580.5	NP_078856.4	Q7Z2Z2	ETUD1_HUMAN	elongation factor Tu GTP binding domain containing 1	63	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				GTP catabolic process (GO:0006184)|mature ribosome assembly (GO:0042256)		GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ribosome binding (GO:0043022)|translation elongation factor activity (GO:0003746)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32						CTCGGATCTGTTCATCTTCTC	0.358																																					p.Q64fs		Atlas-Indel,Pindel	.											.	EFTUD1	74	.	0			c.190delC						PASS	.						121	105	110					15																	82545087		1851	4085	5936	SO:0001589	frameshift_variant	79631	exon4			.	AK056656	CCDS42070.1, CCDS42071.1	15q25.2	2012-07-04			ENSG00000140598	ENSG00000140598			25789	protein-coding gene	gene with protein product	"ribosome assembly 1 homolog (yeast)"					14702039	Standard	NM_024580		Approved	FLJ13119, FAM42A, HsT19294, RIA1	uc002bgt.1	Q7Z2Z2	OTTHUMG00000172573	ENST00000268206.7:c.189delA	chr15.hg19:g.82545087delT	ENSP00000268206:p.Glu63fs	229.0	0.0	0		199.0	88.0	0.442211	NM_024580	A6NKY5|B7Z6I0|Q9H8Z6	Frame_Shift_Del	DEL	ENST00000268206.7	hg19	CCDS42071.1																																																																																			.	.	.	none		0.358	EFTUD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419252.1	NM_024580		-	82545087	T	-	82545087	7	5	251	1	0	1	0	1	0	0	0	0	4962	1722	60	0	3241	0	EFTUD1	15	82545087	Frame_Shift_Del	DEL	T	TCGA-SX-A7SQ-01A-12D-A35Z-10		82545087	19986305	61	15615											
ANPEP	290	hgsc.bcm.edu	37	chr15	90349503	90349503	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaacggacggtgctggagccCttaaaaacgtacaggcccct	12	6	11	12	3	0	0	0	0	0	0	0	2	0	2	3	4	5	2	3	4	5	2			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr15:90349503C>T	ENST00000300060.6	-	2	625	c.312G>A	c.(310-312)aaG>aaA	p.K104K		NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	104	Metalloprotease.				angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	TGCTGGAGCCCTTAAAAACGT	0.587																																					p.K104K	NSCLC(30;827 977 2459 19669 26125)	Atlas-SNP	.											.	ANPEP	124	.	0			c.G312A						PASS	.						96	76	83					15																	90349503		2200	4299	6499	SO:0001819	synonymous_variant	290	exon2			GGAGCCCTTAAAA	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"CD molecules"	500	protein-coding gene	gene with protein product	"aminopeptidase N", "aminopeptidase M", "microsomal aminopeptidase"	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.312G>A	chr15.hg19:g.90349503C>T		91.0	0.0	.		87.0	46.0	.	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Silent	SNP	ENST00000300060.6	hg19	CCDS10356.1																																																																																			.	.	.	none		0.587	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1			T	90349503	C	T	90349503	2	4	251	1	0	0	0	0	0	0	0	1	710	680	24	2		2	ANPEP	15	90349503	Silent	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	7804416	90349503	12181889	62	15616											
MAN2A2	4122	hgsc.bcm.edu	37	chr15	91453418	91453418	+	Silent	SNP	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	gggtttcctgtgctgagcggGgatttcttctcctatgcgga	4	14	14	9	2	2	1	0	1	2	0	4	3	3	3	2	4	3	2	2	4	1	4			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr15:91453418G>A	ENST00000559717.1	+	10	1932	c.1473G>A	c.(1471-1473)ggG>ggA	p.G491G	MAN2A2_ENST00000431652.2_Intron|MAN2A2_ENST00000430376.2_5'Flank|MAN2A2_ENST00000360468.3_Silent_p.G491G			P49641	MA2A2_HUMAN	mannosidase, alpha, class 2A, member 2	491					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)			TGCTGAGCGGGGATTTCTTCT	0.572																																					p.G491G		Atlas-SNP	.											.	MAN2A2	99	.	0			c.G1473A						PASS	.						86	89	88					15																	91453418		2198	4298	6496	SO:0001819	synonymous_variant	4122	exon9			GAGCGGGGATTTC	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.1473G>A	chr15.hg19:g.91453418G>A		85.0	0.0	.		91.0	31.0	.	NM_006122	A6NH12|A8K1E8|Q13754	Silent	SNP	ENST00000559717.1	hg19	CCDS32332.1																																																																																			.	.	.	none		0.572	MAN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418246.5	NM_006122		A	91453418	G	A	91453418	2	1	251	1	0	0	0	0	0	0	0	1	9222	1219	43	2		2	MAN2A2	15	91453418	Silent	SNP	G	TCGA-SX-A7SQ-01A-12D-A35Z-10	1103915	91453418	11077974	63	15617											
SOLH	6650	hgsc.bcm.edu	37	chr16	603351	603352	+	Missense_Mutation	DNP	GA	GA	AT																															tcccccaggcaggtcctggtGatcttgtcccagctagaggg																										TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr16:603351_603352GA>AT	ENST00000219611.2	+	14	3459_3460	c.3096_3097GA>AT	c.(3094-3099)gtGAtc>gtATtc	p.I1033F	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	1033					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)										AGGTCCTGGTGATCTTGTCCCA	0.663																																					p.V1032V|p.I1033F		Atlas-SNP	.											.	SOLH	47	.	0			c.G3096A|c.A3097T						PASS	.																																			SO:0001583	missense	6650	exon14			CCTGGTGATCTTG|CTGGTGATCTTGT	U85647	CCDS10410.1	16p13.3	2013-06-27	2013-06-27	2013-06-27	ENSG00000103326	ENSG00000103326			11182	protein-coding gene	gene with protein product		603267	"small optic lobes (Drosophila) homolog", "small optic lobes homolog (Drosophila)"	SOLH		9722942	Standard	NM_005632		Approved		uc002chi.3	O75808	OTTHUMG00000119059	Exception_encountered	chr16.hg19:g.603351_603352delinsAT	ENSP00000219611:p.Ile1033Phe	228.0|226.0	0.0	.		262.0|268.0	61.0|64.0	.	NM_005632	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Silent|Missense_Mutation	SNP	ENST00000219611.2	hg19	CCDS10410.1																																																																																			.	.	.	none		0.663	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1	NM_005632		AT	603352	GA	AT	603351	3	1	251	1	0	0	0	0	1	0	0	0	14938	1277	45	2	3138	2	SOLH	16	603351	Missense_Mutation	DNP	GA	TCGA-SX-A7SQ-01A-12D-A35Z-10		603351	89751402	64	15618											
UNKL	64718	hgsc.bcm.edu	37	chr16	1464001	1464001	+	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	ggtgaacggccggtgctgcgCgcacttgtgctgtgaaaaca	8	8	15	10	4	0	2	0	2	0	0	0	2	0	2	1	3	5	3	1	3	3	1			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr16:1464001C>G	ENST00000389221.4	-	2	132	c.133G>C	c.(133-135)Gcg>Ccg	p.A45P	UNKL_ENST00000301712.5_Missense_Mutation_p.A45P|UNKL_ENST00000503648.1_5'UTR|UNKL_ENST00000397462.1_Missense_Mutation_p.A45P|LA16c-312E8.2_ENST00000568554.1_RNA|UNKL_ENST00000508903.2_Missense_Mutation_p.A45P	NM_001193388.1	NP_001180317	Q9H9P5	UNKL_HUMAN	unkempt family zinc finger-like	45					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)				CGGTGCTGCGCGCACTTGTGC	0.657											OREG0023546	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A45P		Atlas-SNP	.											.	UNKL	46	.	0			c.G133C						PASS	.						23	20	21					16																	1464001		2088	4094	6182	SO:0001583	missense	64718	exon2			GCTGCGCGCACTT	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.133G>C	chr16.hg19:g.1464001C>G	ENSP00000373873:p.Ala45Pro	187.0	0.0	.	596	327.0	102.0	.	NM_001193388	B0QYN6|B1GXI8|Q96EV1|Q96RZ1|Q9BWL5|Q9H5K0|Q9UJJ8	Missense_Mutation	SNP	ENST00000389221.4	hg19	CCDS53981.1	.	.	.	.	.	.	.	.	.	.	C	16.34	3.096929	0.56075	.	.	ENSG00000059145	ENST00000389221;ENST00000508903;ENST00000397462;ENST00000301712	T	0.64085	-0.08	3.98	-3.9	0.04181	.	0.482216	0.19853	N	0.104584	T	0.47563	0.1452	N	0.24115	0.695	0.80722	D	1	P	0.45634	0.863	P	0.47470	0.548	T	0.45585	-0.9251	10	0.30078	T	0.28	.	11.3882	0.49798	0.0:0.2219:0.0:0.7781	.	45	Q9H9P5-5	.	P	45	ENSP00000373873:A45P	ENSP00000301712:A45P	A	-	1	0	UNKL	1404002	1.000000	0.71417	0.469000	0.27204	0.948000	0.59901	1.162000	0.31786	-0.653000	0.05401	-0.253000	0.11424	GCG	.	.	.	none		0.657	UNKL-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001037125		G	1464001	C	G	1464001	3	3	251	1	0	0	0	0	1	0	0	0	17013	768	27	4	1435	4	UNKL	16	1464001	Missense_Mutation	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	860650	1464001	88890752	65	15619											
SCNN1B	6338	hgsc.bcm.edu	37	chr16	23387172	23387172	+	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	aacaaccgggacttcccagaCtggggtgagcgggggcacgg	9	4	17	11	3	0	2	0	1	0	1	1	3	1	3	2	6	3	1	2	6	2	1			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr16:23387172C>A	ENST00000343070.2	+	8	1442	c.1266C>A	c.(1264-1266)gaC>gaA	p.D422E	SCNN1B_ENST00000307331.5_Missense_Mutation_p.D467E|SCNN1B_ENST00000568085.1_Missense_Mutation_p.D386E|SCNN1B_ENST00000568923.1_Missense_Mutation_p.D395E	NM_000336.2	NP_000327.2	P51168	SCNNB_HUMAN	sodium channel, non-voltage-gated 1, beta subunit	422					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)	ACTTCCCAGACTGGGGTGAGC	0.617																																					p.D422E		Atlas-SNP	.											SCNN1B,right_lower_lobe,carcinoma,0,1	SCNN1B	81	.	0			c.C1266A						PASS	.						78	72	74					16																	23387172		2197	4300	6497	SO:0001583	missense	6338	exon8			CCCAGACTGGGGT	X87159	CCDS10609.1	16p12.2-p12.1	2012-02-28	2012-02-28		ENSG00000168447	ENSG00000168447		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10600	protein-coding gene	gene with protein product	"Liddle syndrome"	600760	"sodium channel, nonvoltage-gated 1, beta", "sodium channel, non-voltage-gated 1, beta"				Standard	NM_000336		Approved	ENaCbeta	uc002dln.3	P51168	OTTHUMG00000131608	ENST00000343070.2:c.1266C>A	chr16.hg19:g.23387172C>A	ENSP00000345751:p.Asp422Glu	105.0	1.0	.		144.0	59.0	.	NM_000336	C5HTZ2|O60891|Q96KG2|Q9UJ32|Q9UMU5	Missense_Mutation	SNP	ENST00000343070.2	hg19	CCDS10609.1	.	.	.	.	.	.	.	.	.	.	C	19.82	3.899251	0.72754	.	.	ENSG00000168447	ENST00000343070;ENST00000307331	T;T	0.69175	-0.36;-0.38	4.65	4.65	0.58169	.	0.078108	0.52532	D	0.000074	T	0.64271	0.2583	L	0.41236	1.265	0.46044	D	0.998833	B	0.25048	0.117	B	0.35655	0.207	T	0.63466	-0.6631	10	0.42905	T	0.14	-18.6204	16.8451	0.85978	0.0:1.0:0.0:0.0	.	422	P51168	SCNNB_HUMAN	E	422;467	ENSP00000345751:D422E;ENSP00000302874:D467E	ENSP00000302874:D467E	D	+	3	2	SCNN1B	23294673	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	2.267000	0.43329	2.277000	0.76020	0.651000	0.88453	GAC	.	.	.	none		0.617	SCNN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254495.2			A	23387172	C	A	23387172	3	1	251	1	0	0	0	0	1	0	0	0	13941	564	20	4	1292	4	SCNN1B	16	23387172	Missense_Mutation	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	21923171	23387172	66967581	66	15620											
NUP93	9688	hgsc.bcm.edu	37	chr16	56864565	56864565	+	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	ctgggagagtttaaaacctgGttccaggagtacatgaacag	13	9	12	7	0	0	2	0	1	0	1	1	4	1	3	2	3	3	3	2	3	4	4			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr16:56864565G>T	ENST00000308159.5	+	10	1174	c.1053G>T	c.(1051-1053)tgG>tgT	p.W351C	NUP93_ENST00000569842.1_Missense_Mutation_p.W351C|NUP93_ENST00000564887.1_Missense_Mutation_p.W228C|NUP93_ENST00000542526.1_Missense_Mutation_p.W228C	NM_014669.4	NP_055484.3	Q8N1F7	NUP93_HUMAN	nucleoporin 93kDa	351					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(2)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						TTAAAACCTGGTTCCAGGAGT	0.532																																					p.W351C	Colon(33;610 796 1305 1705 38917)	Atlas-SNP	.											.	NUP93	75	.	0			c.G1053T						PASS	.						96	92	93					16																	56864565		2198	4300	6498	SO:0001583	missense	9688	exon10			AACCTGGTTCCAG	D42085	CCDS10769.1, CCDS55996.1	16q13	2008-02-05			ENSG00000102900	ENSG00000102900			28958	protein-coding gene	gene with protein product		614351				9348540, 9531546	Standard	NM_014669		Approved	KIAA0095	uc002eka.3	Q8N1F7	OTTHUMG00000133278	ENST00000308159.5:c.1053G>T	chr16.hg19:g.56864565G>T	ENSP00000310668:p.Trp351Cys	72.0	0.0	.		80.0	25.0	.	NM_014669	B3KPQ8|Q14705	Missense_Mutation	SNP	ENST00000308159.5	hg19	CCDS10769.1	.	.	.	.	.	.	.	.	.	.	G	13.34	2.208959	0.39003	.	.	ENSG00000102900	ENST00000308159;ENST00000542526	T;T	0.41065	1.01;1.01	5.11	5.11	0.69529	.	0.052513	0.85682	D	0.000000	T	0.26195	0.0639	N	0.11560	0.145	0.80722	D	1	B	0.06786	0.001	B	0.11329	0.006	T	0.05550	-1.0878	10	0.41790	T	0.15	-9.7303	13.8537	0.63513	0.0:0.0:0.8473:0.1527	.	351	Q8N1F7	NUP93_HUMAN	C	351;228	ENSP00000310668:W351C;ENSP00000440235:W228C	ENSP00000310668:W351C	W	+	3	0	NUP93	55422066	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.583000	0.74053	2.525000	0.85131	0.650000	0.86243	TGG	.	.	.	none		0.532	NUP93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257058.4	NM_014669		T	56864565	G	T	56864565	3	4	251	1	0	0	0	0	1	0	0	0	10779	1270	44	4	1087	4	NUP93	16	56864565	Missense_Mutation	SNP	G	TCGA-SX-A7SQ-01A-12D-A35Z-10	33477393	56864565	33490188	67	15621											
C17orf100	388327	hgsc.bcm.edu	37	chr17	6555545	6555545	+	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	tgcgcggagagcccgaccccGcggccaagccggccgcccgc	5	1	15	20	8	0	1	0	0	0	1	0	3	0	1	7	3	3	0	7	3	1	0	rs74923988		TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr17:6555545G>C	ENST00000391428.2	+	1	575	c.312G>C	c.(310-312)ccG>ccC	p.P104P	MED31_ENST00000574128.1_5'Flank|MED31_ENST00000225728.3_5'Flank|MED31_ENST00000575197.1_5'Flank|CTC-281F24.1_ENST00000576138.1_RNA	NM_001105520.1	NP_001098990.1	A8MU93	CQ100_HUMAN	chromosome 17 open reading frame 100	104																	GCCCGACCCCGCGGCCAAGCC	0.672																																					p.P104P		Atlas-SNP	.											.	C17orf100	4	.	0			c.G312C						PASS	.						12	15	14					17																	6555545		1832	3972	5804	SO:0001819	synonymous_variant	388327	exon1			GACCCCGCGGCCA	BC028174, BC038956, BC052606	CCDS73952.1	17p13.2	2014-04-10			ENSG00000212734	ENSG00000256806			34494	protein-coding gene	gene with protein product							Standard	NM_001105520		Approved	LOC388327	uc010clp.1	A8MU93	OTTHUMG00000188340	ENST00000391428.2:c.312G>C	chr17.hg19:g.6555545G>C		76.0	0.0	.		126.0	6.0	.	NM_001105520		Silent	SNP	ENST00000391428.2	hg19																																																																																				.	G|0.500;C|0.500	0.500	weak		0.672	C17orf100-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255575.2	NM_001105520		C	6555545	G	C	6555545	2	2	251	1	0	0	0	0	0	0	0	1	1849	1074	38	4		4	C17orf100	17	6555545	Silent	SNP	G	TCGA-SX-A7SQ-01A-12D-A35Z-10		6555545	74639665	68	15622											
PRPSAP2	5636	hgsc.bcm.edu	37	chr17	18770619	18770619	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctaggggtggagatgggcaaAgtgcaggtttaccaggaacc	11	7	16	7	0	0	1	0	0	0	1	0	3	0	2	2	6	3	3	2	6	4	3			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr17:18770619A>G	ENST00000268835.2	+	4	427	c.144A>G	c.(142-144)aaA>aaG	p.K48K	PRPSAP2_ENST00000542013.1_Silent_p.K48K|PRPSAP2_ENST00000419071.2_Intron|PRPSAP2_ENST00000536323.1_Intron	NM_002767.3	NP_002758.1	O60256	KPRB_HUMAN	phosphoribosyl pyrophosphate synthetase-associated protein 2	48					bone development (GO:0060348)|negative regulation of catalytic activity (GO:0043086)|nucleobase-containing compound metabolic process (GO:0006139)|nucleotide biosynthetic process (GO:0009165)	ribose phosphate diphosphokinase complex (GO:0002189)	enzyme inhibitor activity (GO:0004857)|magnesium ion binding (GO:0000287)|ribose phosphate diphosphokinase activity (GO:0004749)			endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	11						AGATGGGCAAAGTGCAGGTTT	0.453																																					p.K48K		Atlas-SNP	.											.	PRPSAP2	23	.	0			c.A144G						PASS	.						156	153	154					17																	18770619		2203	4300	6503	SO:0001819	synonymous_variant	5636	exon3			GGGCAAAGTGCAG	AB007851	CCDS11200.1, CCDS58525.1, CCDS58526.1, CCDS58527.1	17p12-p11.2	2008-05-14			ENSG00000141127	ENSG00000141127			9467	protein-coding gene	gene with protein product		603762				9806849	Standard	NM_002767		Approved	PAP41	uc002gup.2	O60256	OTTHUMG00000059406	ENST00000268835.2:c.144A>G	chr17.hg19:g.18770619A>G		83.0	0.0	.		83.0	46.0	.	NM_001243940	B4E1M8|B4E329|B7ZKZ1|E7EMY2|Q6IAS2	Silent	SNP	ENST00000268835.2	hg19	CCDS11200.1																																																																																			.	.	.	none		0.453	PRPSAP2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132112.3	NM_002767		G	18770619	A	G	18770619	2	3	251	1	0	0	0	0	0	0	0	1	12592	69	3	3		3	PRPSAP2	17	18770619	Silent	SNP	A	TCGA-SX-A7SQ-01A-12D-A35Z-10	12215074	18770619	62424591	69	15623											
SRCIN1	80725	hgsc.bcm.edu	37	chr17	36714573	36714573	+	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	tgccgccgcgccgcctccgaCacgcgcatgctcagctctgc	4	6	11	20	7	2	0	1	0	1	0	3	1	3	0	5	0	4	3	5	0	0	0			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr17:36714573C>A	ENST00000264659.7	-	11	2315	c.2091G>T	c.(2089-2091)gtG>gtT	p.V697V	SRCIN1_ENST00000578925.1_Silent_p.V731V|SRCIN1_ENST00000398579.4_5'UTR	NM_025248.2	NP_079524.2	Q9C0H9	SRCN1_HUMAN	SRC kinase signaling inhibitor 1	569					exocytosis (GO:0006887)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell migration (GO:0030334)|regulation of dendritic spine morphogenesis (GO:0061001)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	protein kinase binding (GO:0019901)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	19						CCGCCTCCGACACGCGCATGC	0.692											OREG0024362	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V697V		Atlas-SNP	.											.	SRCIN1	66	.	0			c.G2091T						PASS	.						24	27	26					17																	36714573		2099	4219	6318	SO:0001819	synonymous_variant	80725	exon11			CTCCGACACGCGC		CCDS45660.1	17q12	2009-12-14			ENSG00000017373	ENSG00000277363			29506	protein-coding gene	gene with protein product	"p130Cas-associated protein", "SNAP-25-interacting protein"	610786				11214970	Standard	NM_025248		Approved	SNIP, p140Cap, KIAA1684	uc002hqd.3	Q9C0H9		ENST00000264659.7:c.2091G>T	chr17.hg19:g.36714573C>A		95.0	0.0	.	865	124.0	78.0	.	NM_025248	Q75T46|Q8N4W8	Silent	SNP	ENST00000264659.7	hg19	CCDS45660.1																																																																																			.	.	.	none		0.692	SRCIN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441878.4	NM_025248		A	36714573	C	A	36714573	2	1	251	1	0	0	0	0	0	0	0	1	15148	465	17	4		4	SRCIN1	17	36714573	Silent	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	17943954	36714573	44480637	70	15624											
HAP1	9001	hgsc.bcm.edu	37	chr17	39887810	39887810	+	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	caagagtgtcgagttgagagGcctggagggagacaaagagg	13	5	18	5	1	0	4	0	1	0	4	1	8	0	5	1	4	0	1	1	4	2	1			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr17:39887810G>A	ENST00000310778.5	-	6	1013	c.1004C>T	c.(1003-1005)gCc>gTc	p.A335V	HAP1_ENST00000341193.5_Splice_Site_p.A343V|RN7SL399P_ENST00000471648.2_RNA|HAP1_ENST00000347901.4_Splice_Site_p.A335V|HAP1_ENST00000393939.2_Splice_Site_p.A335V|JUP_ENST00000540235.1_Intron			P54257	HAP1_HUMAN	huntingtin-associated protein 1	335	Glu-rich.|HAP1 N-terminal.				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)			GAGTTGAGAGGCCTGGAGGGA	0.547																																					p.A343V		Atlas-SNP	.											.	HAP1	48	.	0			c.C1028T						PASS	.						137	112	120					17																	39887810		2203	4300	6503	SO:0001630	splice_region_variant	9001	exon6			TGAGAGGCCTGGA	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.1003-1C>T	chr17.hg19:g.39887810G>A		210.0	0.0	.		224.0	75.0	.	NM_001079870	A8MQB5|O75358|Q59GK4|Q9H4G3|Q9HA98|Q9NY90	Missense_Mutation	SNP	ENST00000310778.5	hg19		.	.	.	.	.	.	.	.	.	.	G	14.47	2.546491	0.45383	.	.	ENSG00000173805	ENST00000393939;ENST00000310778;ENST00000347901;ENST00000341193	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	4.14	3.09	0.35607	.	0.219300	0.23282	N	0.049895	T	0.43122	0.1233	L	0.46947	1.48	0.42390	D	0.992525	D;D;P;P	0.71674	0.998;0.998;0.709;0.601	D;D;P;P	0.80764	0.994;0.994;0.528;0.659	T	0.29640	-1.0005	10	0.62326	D	0.03	-10.2963	7.3085	0.26461	0.1301:0.0:0.8699:0.0	.	335;343;335;335	P54257-3;P54257-4;P54257-2;P54257	.;.;.;HAP1_HUMAN	V	335;335;335;343	ENSP00000377513:A335V;ENSP00000309392:A335V;ENSP00000334002:A335V;ENSP00000343170:A343V	ENSP00000309392:A335V	A	-	2	0	HAP1	37141336	1.000000	0.71417	0.973000	0.42090	0.889000	0.51656	3.914000	0.56401	0.844000	0.35094	0.655000	0.94253	GCC	.	.	.	none		0.547	HAP1-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000389619.1	NM_003949	Missense_Mutation	A	39887810	G	A	39887810	5	1	251	1	0	0	0	0	0	0	1	0	6960	1217	42	2	879	2	HAP1	17	39887810	Splice_Site	SNP	G	TCGA-SX-A7SQ-01A-12D-A35Z-10	3173237	39887810	41307400	71	15625											
EZH1	2145	hgsc.bcm.edu	37	chr17	40864332	40864332	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgcacgtcttggtccccagaAgcctggctattgaacagaag	10	9	11	11	1	1	3	0	1	1	2	2	3	2	3	3	2	3	2	3	2	4	3			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr17:40864332A>G	ENST00000428826.2	-	12	1497	c.1376T>C	c.(1375-1377)cTt>cCt	p.L459P	EZH1_ENST00000585893.1_Missense_Mutation_p.L419P|EZH1_ENST00000590078.1_Missense_Mutation_p.L389P|EZH1_ENST00000415827.2_Missense_Mutation_p.L450P|EZH1_ENST00000590783.1_5'Flank|EZH1_ENST00000592743.1_Missense_Mutation_p.L459P|EZH1_ENST00000435174.1_Missense_Mutation_p.L320P			Q92800	EZH1_HUMAN	enhancer of zeste 1 polycomb repressive complex 2 subunit	459					anatomical structure morphogenesis (GO:0009653)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)			breast(1)|endometrium(4)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	27		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0784)		GGTCCCCAGAAGCCTGGCTAT	0.527																																					p.L459P		Atlas-SNP	.											.	EZH1	62	.	0			c.T1376C						PASS	.						128	115	119					17																	40864332		2203	4300	6503	SO:0001583	missense	2145	exon12			CCCAGAAGCCTGG		CCDS32659.1	17q21.1-q21.3	2014-05-28	2014-05-28			ENSG00000108799		"Chromatin-modifying enzymes / K-methyltransferases"	3526	protein-coding gene	gene with protein product		601674	"enhancer of zeste (Drosophila) homolog 1", "enhancer of zeste homolog 1 (Drosophila)"			8921387	Standard	NM_001991		Approved	KIAA0388, KMT6B	uc002iaz.3	Q92800		ENST00000428826.2:c.1376T>C	chr17.hg19:g.40864332A>G	ENSP00000404658:p.Leu459Pro	104.0	0.0	.		118.0	67.0	.	NM_001991	A6NCH6|B4DIJ1|B4DIZ7|B4DSS2|B4E3R7|O43287|Q14459|Q53XP3	Missense_Mutation	SNP	ENST00000428826.2	hg19	CCDS32659.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.529451	0.85706	.	.	ENSG00000108799	ENST00000264646;ENST00000428826;ENST00000415827;ENST00000435174	T;T	0.80909	-1.43;-1.43	5.42	5.42	0.78866	SANT domain, DNA binding (1);	0.000000	0.85682	D	0.000000	D	0.88815	0.6539	M	0.78637	2.42	0.80722	D	1	D;P;P;P;P	0.62365	0.991;0.841;0.841;0.507;0.868	D;P;P;P;P	0.67382	0.951;0.776;0.776;0.599;0.602	D	0.88699	0.3214	10	0.42905	T	0.14	.	15.6252	0.76851	1.0:0.0:0.0:0.0	.	320;419;465;389;459	Q92800-5;Q92800-3;Q92800-2;Q92800-4;Q92800	.;.;.;.;EZH1_HUMAN	P	462;459;419;320	ENSP00000404658:L459P;ENSP00000404071:L320P	ENSP00000264646:L462P	L	-	2	0	EZH1	38117858	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.103000	0.94232	2.275000	0.75901	0.528000	0.53228	CTT	.	.	.	none		0.527	EZH1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452347.1	NM_001991		G	40864332	A	G	40864332	3	3	251	1	0	0	0	0	1	0	0	0	5335	72	3	3	907	3	EZH1	17	40864332	Missense_Mutation	SNP	A	TCGA-SX-A7SQ-01A-12D-A35Z-10	976522	40864332	40330878	72	15626											
MPP2	4355	hgsc.bcm.edu	37	chr17	41975630	41975630	+	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	acctccctggagcactgtacCttggccagggatcttactat	8	11	9	13	0	1	0	0	0	1	0	2	2	2	2	4	3	3	2	4	3	3	4			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr17:41975630C>T	ENST00000461854.1	-	3	235	c.150G>A	c.(148-150)aaG>aaA	p.K50K	MPP2_ENST00000473246.1_5'UTR|MPP2_ENST00000518766.1_Splice_Site_p.K95K|MPP2_ENST00000269095.4_Splice_Site_p.K50K|MPP2_ENST00000520305.1_Intron|MPP2_ENST00000377184.3_Splice_Site_p.K67K|MPP2_ENST00000536246.1_Splice_Site_p.K39K|MPP2_ENST00000523501.1_Splice_Site_p.K39K			Q14168	MPP2_HUMAN	membrane protein, palmitoylated 2 (MAGUK p55 subfamily member 2)	50	L27 1. {ECO:0000255|PROSITE- ProRule:PRU00365}.				nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			breast(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)		AGCACTGTACCTTGGCCAGGG	0.572																																					p.K50K		Atlas-SNP	.											.	MPP2	67	.	0			c.G150A						PASS	.						122	108	113					17																	41975630		2203	4300	6503	SO:0001630	splice_region_variant	4355	exon3			CTGTACCTTGGCC		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.150+1G>A	chr17.hg19:g.41975630C>T		76.0	0.0	.		110.0	38.0	.	NM_005374	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Silent	SNP	ENST00000461854.1	hg19																																																																																				.	.	.	none		0.572	MPP2-003	KNOWN	non_canonical_polymorphism|basic	protein_coding	protein_coding	OTTHUMT00000258388.2	NM_005374	Silent	T	41975630	C	T	41975630	5	4	251	1	0	0	0	0	0	0	1	0	9741	695	24	2	1552	2	MPP2	17	41975630	Splice_Site	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	1111298	41975630	39219580	73	15627											
TANC2	26115	hgsc.bcm.edu	37	chr17	61497660	61497660	+	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	cccagccaggggctcccggtCatccagagcccaccctcctc	6	5	9	21	1	1	1	1	0	0	1	5	1	4	1	7	3	2	1	7	3	0	0			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr17:61497660C>T	ENST00000424789.2	+	25	4321	c.4317C>T	c.(4315-4317)gtC>gtT	p.V1439V	RP11-269G24.3_ENST00000583552.1_RNA|TANC2_ENST00000389520.4_Silent_p.V1449V	NM_025185.3	NP_079461.2	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	1439					in utero embryonic development (GO:0001701)					breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|upper_aerodigestive_tract(3)	44						GGCTCCCGGTCATCCAGAGCC	0.567																																					p.V1439V		Atlas-SNP	.											.	TANC2	266	.	0			c.C4317T						PASS	.						54	55	55					17																	61497660		1934	4150	6084	SO:0001819	synonymous_variant	26115	exon25			CCCGGTCATCCAG	AB032974	CCDS45754.1	17q23.3	2013-01-11				ENSG00000170921		"Ankyrin repeat domain containing", "Tetratricopeptide (TTC) repeat domain containing"	30212	protein-coding gene	gene with protein product	"rolling pebbles homolog B (Drosophila)"	615047					Standard	NM_025185		Approved	DKFZP564D166, FLJ10215, FLJ11824, KIAA1148, KIAA1636, rols, ROLSA	uc002jal.4	Q9HCD6		ENST00000424789.2:c.4317C>T	chr17.hg19:g.61497660C>T		86.0	0.0	.		103.0	33.0	.	NM_025185	Q9HAC3|Q9NW88|Q9NXY9|Q9ULS2	Silent	SNP	ENST00000424789.2	hg19	CCDS45754.1																																																																																			.	.	.	none		0.567	TANC2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444765.1			T	61497660	C	T	61497660	2	4	251	1	0	0	0	0	0	0	0	1	15557	813	29	2		2	TANC2	17	61497660	Silent	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	19522030	61497660	19697550	74	15628											
DDX5	1655	hgsc.bcm.edu	37	chr17	62496291	62496291	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgcagcactgtaaacaccaTtctgagtttttgccccaaaa	12	12	6	11	0	1	1	0	1	1	0	1	1	1	1	3	0	4	4	3	0	4	5			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr17:62496291T>C	ENST00000225792.5	-	13	1996	c.1595A>G	c.(1594-1596)aAt>aGt	p.N532S	DDX5_ENST00000450599.2_Missense_Mutation_p.N453S|MIR5047_ENST00000579212.1_RNA|DDX5_ENST00000578804.1_Missense_Mutation_p.N532S|MIR3064_ENST00000581130.1_RNA|DDX5_ENST00000580026.1_5'UTR	NM_004396.3	NP_004387.1	P17844	DDX5_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 5	532	Transactivation domain.				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)			GTAAACACCATTCTGAGTTTT	0.423			T	ETV4	prostate																																p.N532S	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.A1595G						PASS	.						138	142	141					17																	62496291		2203	4300	6503	SO:0001583	missense	1655	exon13			ACACCATTCTGAG	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.1595A>G	chr17.hg19:g.62496291T>C	ENSP00000225792:p.Asn532Ser	139.0	0.0	.		151.0	42.0	.	NM_004396	B4DLW8|B5BU21|D3DU32|E7ETL9|O75681|Q53Y61	Missense_Mutation	SNP	ENST00000225792.5	hg19	CCDS11659.1	.	.	.	.	.	.	.	.	.	.	T	7.653	0.683306	0.14907	.	.	ENSG00000108654	ENST00000540698;ENST00000450599;ENST00000225792	.	.	.	5.56	4.46	0.54185	.	0.443060	0.27478	N	0.019189	T	0.37732	0.1014	N	0.12182	0.205	0.80722	D	1	B;B;B	0.17465	0.016;0.022;0.022	B;B;B	0.21151	0.011;0.033;0.033	T	0.11518	-1.0584	9	0.14656	T	0.56	-18.6472	13.0086	0.58720	0.0:0.0:0.1349:0.8651	.	453;532;532	B4DLW8;B5BUE6;P17844	.;.;DDX5_HUMAN	S	532;462;521	.	ENSP00000225792:N521S	N	-	2	0	DDX5	59926753	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.816000	0.69222	1.030000	0.39839	0.477000	0.44152	AAT	.	.	.	none		0.423	DDX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444030.1	NM_004396		C	62496291	T	C	62496291	3	2	251	1	0	0	0	0	1	0	0	0	4369	1493	52	3	253	3	DDX5	17	62496291	Missense_Mutation	SNP	T	TCGA-SX-A7SQ-01A-12D-A35Z-10	998631	62496291	18698919	75	15629											
ABCA5	23461	hgsc.bcm.edu	37	chr17	67286078	67286078	+	Frame_Shift_Del	DEL	A	A	-																															ttttcttctactgtcaaaacAtcaaagtgtatatctaactg																										TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr17:67286078delA	ENST00000392676.3	-	13	1771	c.1707delT	c.(1705-1707)gatfs	p.D569fs	ABCA5_ENST00000392677.2_Frame_Shift_Del_p.D569fs|ABCA5_ENST00000588877.1_Frame_Shift_Del_p.D569fs			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	569	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	CTGTCAAAACATCAAAGTGTA	0.313																																					p.V570fs		Atlas-Indel,Pindel	.											.	ABCA5	162	.	0			c.1708delG						PASS	.						104	100	101					17																	67286078		2202	4291	6493	SO:0001589	frameshift_variant	23461	exon13			.	U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"ATP binding cassette transporters / subfamily A"	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.1707delT	chr17.hg19:g.67286078delA	ENSP00000376443:p.Asp569fs	69.0	0.0	0		71.0	44.0	0.619718	NM_172232	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Frame_Shift_Del	DEL	ENST00000392676.3	hg19	CCDS11685.1																																																																																			.	.	.	none		0.313	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672		-	67286078	A	-	67286078	7	5	251	1	0	1	0	1	0	0	0	0	35	214	8	0	3329	0	ABCA5	17	67286078	Frame_Shift_Del	DEL	A	TCGA-SX-A7SQ-01A-12D-A35Z-10	4789787	67286078	13909132	76	15630											
RNF213	57674	hgsc.bcm.edu	37	chr17	78332113	78332113	+	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	ccctctggaagcgggtccaaGgtgctgtcacccctctgctg	5	9	12	15	1	3	0	1	0	2	0	4	1	4	1	4	3	3	2	4	3	2	0			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr17:78332113G>A	ENST00000582970.1	+	37	11031	c.10888G>A	c.(10888-10890)Ggt>Agt	p.G3630S	CTD-2047H16.4_ENST00000572151.1_RNA|CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000508628.2_Missense_Mutation_p.G3679S|RNF213_ENST00000336301.6_Missense_Mutation_p.G1703S	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3630					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)			GCGGGTCCAAGGTGCTGTCAC	0.572																																					p.G3630S		Atlas-SNP	.											.	RNF213	766	.	0			c.G10888A						PASS	.						72	63	66					17																	78332113		2203	4300	6503	SO:0001583	missense	57674	exon37			GTCCAAGGTGCTG	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.10888G>A	chr17.hg19:g.78332113G>A	ENSP00000464087:p.Gly3630Ser	100.0	0.0	.		133.0	71.0	.	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	hg19	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	G	6.321	0.427276	0.11987	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.19532	2.14	5.58	0.672	0.17935	.	0.974902	0.08475	N	0.940385	T	0.09468	0.0233	N	0.19112	0.55	0.09310	N	1	B;B	0.24823	0.112;0.006	B;B	0.17722	0.019;0.005	T	0.34104	-0.9842	10	0.02654	T	1	.	4.1346	0.10164	0.5287:0.1834:0.2879:0.0	.	3679;1703	C9JCP4;Q63HN8	.;RN213_HUMAN	S	3630;3679;1703	ENSP00000338218:G1703S	ENSP00000338218:G1703S	G	+	1	0	RNF213	75946708	0.964000	0.33143	0.001000	0.08648	0.041000	0.13682	1.847000	0.39299	0.010000	0.14839	-0.185000	0.12909	GGT	.	.	.	none		0.572	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		A	78332113	G	A	78332113	3	1	251	1	0	0	0	0	1	0	0	0	13490	1000	35	2	11349	2	RNF213	17	78332113	Missense_Mutation	SNP	G	TCGA-SX-A7SQ-01A-12D-A35Z-10	11046035	78332113	2863097	77	15631											
KIAA0802	23255	hgsc.bcm.edu	37	chr18	8819148	8819148	+	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	caagctgaaggagtcggacaGgtgctcggccagtgagaatc	11	6	15	9	2	0	2	0	2	0	1	3	5	0	4	1	4	2	2	1	4	3	0			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr18:8819148G>T	ENST00000306329.11	+	11	4004	c.4004G>T	c.(4003-4005)aGg>aTg	p.R1335M	SOGA2_ENST00000306285.7_Missense_Mutation_p.R341M|SOGA2_ENST00000518815.1_Missense_Mutation_p.R341M|SOGA2_ENST00000400050.3_Missense_Mutation_p.R975M|SOGA2_ENST00000517570.1_Missense_Mutation_p.R975M|SOGA2_ENST00000359865.3_Missense_Mutation_p.R1016M																							GAGTCGGACAGGTGCTCGGCC	0.622																																					p.R1016M		Atlas-SNP	.											.	.	.	.	0			c.G3047T						PASS	.						52	49	50					18																	8819148		2203	4300	6503	SO:0001583	missense	23255	exon13			CGGACAGGTGCTC																												ENST00000306329.11:c.4004G>T	chr18.hg19:g.8819148G>T	ENSP00000305027:p.Arg1335Met	109.0	0.0	.		93.0	38.0	.	NM_015210		Missense_Mutation	SNP	ENST00000306329.11	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.5|25.5	4.642986|4.642986	0.87859|0.87859	.|.	.|.	ENSG00000168502|ENSG00000168502	ENST00000519823|ENST00000306329;ENST00000517570;ENST00000359865;ENST00000400050;ENST00000306285	.|T;T;T;T	.|0.50813	.|0.73;0.73;0.73;0.73	5.77|5.77	5.77|5.77	0.91146|0.91146	.|.	.|0.000000	.|0.53938	.|D	.|0.000058	T|T	0.65668|0.65668	0.2713|0.2713	L|L	0.49640|0.49640	1.575|1.575	0.40122|0.40122	D|D	0.976615|0.976615	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.996;0.999	T|T	0.60747|0.60747	-0.7202|-0.7202	5|10	.|0.39692	.|T	.|0.17	-41.8804|-41.8804	20.3473|20.3473	0.98799|0.98799	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1326;1016	.|Q9Y4B5;Q9Y4B5-3	.|CC165_HUMAN;.	H|M	121|1037;975;1016;975;341	.|ENSP00000429556:R975M;ENSP00000352927:R1016M;ENSP00000382924:R975M;ENSP00000303670:R341M	.|ENSP00000303670:R341M	Q|R	+|+	3|2	2|0	CCDC165|CCDC165	8809148|8809148	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	6.417000|6.417000	0.73337|0.73337	2.884000|2.884000	0.98904|0.98904	0.655000|0.655000	0.94253|0.94253	CAG|AGG	.	.	.	none		0.622	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1			T	8819148	G	T	8819148	3	4	251	1	0	0	0	0	1	0	0	0	8201	1000	35	4	3089	4	KIAA0802	18	8819148	Missense_Mutation	SNP	G	TCGA-SX-A7SQ-01A-12D-A35Z-10		8819148	69258100	78	15632											
C19orf44	84167	hgsc.bcm.edu	37	chr19	16617533	16617539	+	Frame_Shift_Del	DEL	CGCTTGA	CGCTTGA	-																															gtttagaataaatattttatCgcttgacggtctggctccag																								rs201618251|rs537357343		TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	CGCTTGA	CGCTTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr19:16617533_16617539delCGCTTGA	ENST00000221671.3	+	4	1253_1259	c.1097_1103delCGCTTGA	c.(1096-1104)tcgcttgacfs	p.SLD366fs	C19orf44_ENST00000594035.1_Frame_Shift_Del_p.SLD366fs|CTD-3222D19.2_ENST00000409035.1_Intron	NM_032207.2	NP_115583.1	Q9H6X5	CS044_HUMAN	chromosome 19 open reading frame 44	366										endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	16						AATATTTTATCGCTTGACGGTCTGGCT	0.324																																					p.366_368del		Atlas-Indel,Pindel	.											.	C19orf44	47	.	0			c.1096_1102del						PASS	.																																			SO:0001589	frameshift_variant	84167	exon4			.	AK025395	CCDS12345.1, CCDS74306.1	19p13.11	2011-11-24			ENSG00000105072	ENSG00000105072			26141	protein-coding gene	gene with protein product						12477932	Standard	NM_032207		Approved	FLJ21742	uc002neh.1	Q9H6X5		ENST00000221671.3:c.1097_1103delCGCTTGA	chr19.hg19:g.16617533_16617539delCGCTTGA	ENSP00000221671:p.Ser366fs	257.0	0.0	0		222.0	69.0	0.310811	NM_032207	Q8N6Y7	Frame_Shift_Del	DEL	ENST00000221671.3	hg19	CCDS12345.1																																																																																			.	.	.	none		0.324	C19orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461218.1	NM_032207		-	16617539	CGCTTGA	-	16617533	7	5	251	1	0	1	0	1	0	0	0	0	1929	893	31	0	1107	0	C19orf44	19	16617533	Frame_Shift_Del	DEL	CGCTTGA	TCGA-SX-A7SQ-01A-12D-A35Z-10		16617533	42511450	79	15633											
ZNF14	7561	hgsc.bcm.edu	37	chr19	19823847	19823847	+	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	ggcatctggctagtggtttcTccacatttgctacctcttct	5	16	8	12	0	4	0	0	0	4	0	5	0	4	0	2	3	2	4	2	3	2	5			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr19:19823847T>A	ENST00000344099.3	-	4	381	c.243A>T	c.(241-243)ggA>ggT	p.G81G		NM_021030.2	NP_066358.2	P17017	ZNF14_HUMAN	zinc finger protein 14	81					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(2)|endometrium(1)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32		Renal(1328;0.0474)				TAGTGGTTTCTCCACATTTGC	0.353																																					p.G81G		Atlas-SNP	.											.	ZNF14	89	.	0			c.A243T						PASS	.						118	111	113					19																	19823847		2203	4300	6503	SO:0001819	synonymous_variant	7561	exon4			GGTTTCTCCACAT	AA286756	CCDS12409.1	19p13.11	2013-01-08	2006-05-10					"Zinc fingers, C2H2-type", "-"	12924	protein-coding gene	gene with protein product		194556	"zinc finger protein 14 (KOX 6)"				Standard	NM_021030		Approved	KOX6, GIOT-4	uc002nnk.1	P17017		ENST00000344099.3:c.243A>T	chr19.hg19:g.19823847T>A		93.0	0.0	.		107.0	47.0	.	NM_021030	B9EGA4|Q9ULZ5	Silent	SNP	ENST00000344099.3	hg19	CCDS12409.1																																																																																			.	.	.	none		0.353	ZNF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460775.1	NM_021030		A	19823847	T	A	19823847	2	1	251	1	0	0	0	0	0	0	0	1	17740	1538	54	5		5	ZNF14	19	19823847	Silent	SNP	T	TCGA-SX-A7SQ-01A-12D-A35Z-10	3206314	19823847	39305136	80	15634											
C19orf46	163183	hgsc.bcm.edu	37	chr19	36497828	36497828	+	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	cacacgctcagctgcccctcGtaggtccacctggagggcct	6	7	11	17	2	1	0	1	0	0	0	3	1	2	1	5	3	2	3	5	3	1	1			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr19:36497828G>T	ENST00000324444.3	-	4	553	c.442C>A	c.(442-444)Cga>Aga	p.R148R	SYNE4_ENST00000340477.5_Intron|ALKBH6_ENST00000495116.2_5'Flank|AC002116.8_ENST00000473572.2_RNA	NM_001039876.1	NP_001034965.1	Q8N205	SYNE4_HUMAN	spectrin repeat containing, nuclear envelope family member 4	148					establishment of epithelial cell apical/basal polarity (GO:0045198)	integral component of nuclear outer membrane (GO:0031309)											GCTGCCCCTCGTAGGTCCACC	0.647																																					p.R148R		Atlas-SNP	.											.	.	.	.	0			c.C442A						PASS	.						13	20	18					19																	36497828		2001	4045	6046	SO:0001819	synonymous_variant	163183	exon4			CCCCTCGTAGGTC	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.442C>A	chr19.hg19:g.36497828G>T		60.0	0.0	.		70.0	30.0	.	NM_001039876	A8MRS0|A8MYE3|Q7Z7L3	Silent	SNP	ENST00000324444.3	hg19	CCDS42553.1																																																																																			.	.	.	none		0.647	SYNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109525.3	NM_001039876		T	36497828	G	T	36497828	2	4	251	1	0	0	0	0	0	0	0	1	1931	1153	40	4		4	C19orf46	19	36497828	Silent	SNP	G	TCGA-SX-A7SQ-01A-12D-A35Z-10	16673981	36497828	22631155	81	15635											
GPCPD1	56261	hgsc.bcm.edu	37	chr20	5574056	5574056	+	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	aatggttgctttccatagcaTgctgtgaagaaagaaaatta	15	12	9	5	0	0	3	0	1	0	2	1	3	1	3	1	1	3	4	1	1	7	4			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr20:5574056T>C	ENST00000379019.4	-	4	360	c.148A>G	c.(148-150)Atg>Gtg	p.M50V		NM_019593.3	NP_062539.1	Q9NPB8	GPCP1_HUMAN	glycerophosphocholine phosphodiesterase GDE1 homolog (S. cerevisiae)	50	CBM20. {ECO:0000255|PROSITE- ProRule:PRU00594}.				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						TTCCATAGCATGCTGTGAAGA	0.348																																					p.M50V		Atlas-SNP	.											.	GPCPD1	52	.	0			c.A148G						PASS	.						106	106	106					20																	5574056		2203	4300	6503	SO:0001630	splice_region_variant	56261	exon4			ATAGCATGCTGTG		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.147-1A>G	chr20.hg19:g.5574056T>C		65.0	0.0	.		87.0	25.0	.	NM_019593	D3DW06|Q9BQL8|Q9NUX0	Missense_Mutation	SNP	ENST00000379019.4	hg19	CCDS13090.1	.	.	.	.	.	.	.	.	.	.	T	5.033	0.191778	0.09547	.	.	ENSG00000125772	ENST00000379019	D	0.93076	-3.16	5.35	1.93	0.25924	Carbohydrate-binding-like fold (1);Glycoside hydrolase, carbohydrate-binding (2);Immunoglobulin-like fold (1);	0.886744	0.10053	N	0.721935	T	0.81842	0.4908	N	0.04508	-0.205	0.19945	N	0.999944	B	0.02656	0.0	B	0.01281	0.0	T	0.70483	-0.4859	10	0.28530	T	0.3	-3.2258	5.3794	0.16183	0.0:0.2796:0.2234:0.497	.	50	Q9NPB8	GPCP1_HUMAN	V	50	ENSP00000368305:M50V	ENSP00000368305:M50V	M	-	1	0	GPCPD1	5522056	0.000000	0.05858	0.991000	0.47740	0.901000	0.52897	-0.520000	0.06252	0.879000	0.35944	0.454000	0.30748	ATG	.	.	.	none		0.348	GPCPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077869.1	NM_019593	Missense_Mutation	C	5574056	T	C	5574056	5	2	251	1	0	0	0	0	0	0	1	0	6610	1478	51	3	1938	3	GPCPD1	20	5574056	Splice_Site	SNP	T	TCGA-SX-A7SQ-01A-12D-A35Z-10		5574056	57451464	82	15636											
RBM39	9584	hgsc.bcm.edu	37	chr20	34313043	34313043	+	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	acagaagactgtccttgcatCtctttcctcaggagttaaat	11	13	7	10	0	2	2	1	0	1	2	5	3	4	3	2	1	1	2	2	1	3	3			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr20:34313043C>G	ENST00000253363.6	-	7	474	c.451G>C	c.(451-453)Gat>Cat	p.D151H	RBM39_ENST00000407261.4_5'UTR|RBM39_ENST00000528062.3_Missense_Mutation_p.D129H|RBM39_ENST00000361162.6_Missense_Mutation_p.D151H			Q14498	RBM39_HUMAN	RNA binding motif protein 39	151					mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	all_epithelial(2;0.00295)|Lung NSC(9;0.00453)|Breast(12;0.00544)|all_lung(11;0.00676)					GTCCTTGCATCTCTTTCCTCA	0.318																																					p.D151H		Atlas-SNP	.											.	RBM39	68	.	0			c.G451C						PASS	.						95	94	94					20																	34313043		2202	4300	6502	SO:0001583	missense	9584	exon7			TTGCATCTCTTTC	L10910	CCDS13265.1, CCDS13266.1, CCDS56186.1	20q11.22	2014-07-03	2006-07-11	2006-07-11	ENSG00000131051	ENSG00000131051		"RNA binding motif (RRM) containing"	15923	protein-coding gene	gene with protein product	"coactivator of activating protein-1 and estrogen receptors", "functional spliceosome-associated protein 59"	604739	"RNA-binding region (RNP1, RRM) containing 2"	RNPC2		8227358, 15694343, 21551269	Standard	NM_184234		Approved	CC1.3, HCC1, CAPER, fSAP59, CAPERalpha	uc002xeb.3	Q14498	OTTHUMG00000032358	ENST00000253363.6:c.451G>C	chr20.hg19:g.34313043C>G	ENSP00000253363:p.Asp151His	245.0	0.0	.		286.0	175.0	.	NM_184234	A2RRD3|A5D8W2|B0BLV3|E1P5S0|E1P5S1|Q14499	Missense_Mutation	SNP	ENST00000253363.6	hg19	CCDS13266.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.6|28.6	4.937994|4.937994	0.92526|0.92526	.|.	.|.	ENSG00000131051|ENSG00000131051	ENST00000253363;ENST00000361162;ENST00000528062;ENST00000374038;ENST00000427743;ENST00000434927|ENST00000448303	T;T;T;T;T;T|T	0.52057|0.06142	0.68;0.68;0.68;0.9;0.9;0.68|3.34	5.0|5.0	5.0|5.0	0.66597|0.66597	Nucleotide-binding, alpha-beta plait (1);|.	0.046134|.	0.85682|.	D|.	0.000000|.	T|T	0.30324|0.30324	0.0761|0.0761	M|M	0.86651|0.86651	2.83|2.83	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D|.	0.97110|.	1.0;1.0;0.999;0.999;0.997|.	T|T	0.13415|0.13415	-1.0510|-1.0510	10|7	0.51188|0.87932	T|D	0.08|0	.|.	18.4905|18.4905	0.90844|0.90844	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	129;129;151;151;127|.	B4DRA0;A2RRD3;Q14498-2;Q14498;B3KWX7|.	.;.;.;RBM39_HUMAN;.|.	H|T	151;151;129;150;129;151|23	ENSP00000253363:D151H;ENSP00000354437:D151H;ENSP00000436747:D129H;ENSP00000363150:D150H;ENSP00000406801:D129H;ENSP00000393493:D151H|ENSP00000394824:R23T	ENSP00000253363:D151H|ENSP00000394824:R23T	D|R	-|-	1|2	0|0	RBM39|RBM39	33776457|33776457	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.567000|7.567000	0.82357|0.82357	2.599000|2.599000	0.87857|0.87857	0.655000|0.655000	0.94253|0.94253	GAT|AGA	.	.	.	none		0.318	RBM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078931.2	NM_184237		G	34313043	C	G	34313043	3	3	251	1	0	0	0	0	1	0	0	0	13146	913	32	4	1185	4	RBM39	20	34313043	Missense_Mutation	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	28738987	34313043	28712477	83	15637											
SFRS6	6431	hgsc.bcm.edu	37	chr20	42089554	42089554	+	Missense_Mutation	SNP	A	A	G																															taaagtcaaaatccagatcaAggagccagtcccgttccaat																										TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr20:42089554A>G	ENST00000244020.3	+	6	992	c.886A>G	c.(886-888)Agg>Ggg	p.R296G		NM_006275.5	NP_006266.2	Q13247	SRSF6_HUMAN	serine/arginine-rich splicing factor 6	296	Arg/Ser-rich (RS domain).				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell death (GO:0060548)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of keratinocyte proliferation (GO:0010837)|regulation of wound healing (GO:0061041)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|upper_aerodigestive_tract(2)	5						ATCCAGATCAAGGAGCCAGTC	0.488																																					p.R296G		Atlas-SNP	.											.	SRSF6	37	.	0			c.A886G						PASS	.						77	77	77					20																	42089554		2203	4300	6503	SO:0001583	missense	6431	exon6			AGATCAAGGAGCC	U30883	CCDS13318.1	20q12-q13.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000124193	ENSG00000124193		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10788	protein-coding gene	gene with protein product	"pre-mRNA splicing factor SRP55", "SR splicing factor 6"	601944	"splicing factor, arginine/serine-rich 6"	SFRS6		7556075, 20516191	Standard	NM_006275		Approved	SRP55, B52	uc010zwg.2	Q13247	OTTHUMG00000032502	ENST00000244020.3:c.886A>G	chr20.hg19:g.42089554A>G	ENSP00000244020:p.Arg296Gly	219.0	0.0	.		226.0	130.0	.	NM_006275	B7Z6J3|E1P5W6|Q13244|Q13245|Q96J06|Q9UJB8|Q9Y3N7	Missense_Mutation	SNP	ENST00000244020.3	hg19	CCDS13318.1	.	.	.	.	.	.	.	.	.	.	A	13.55	2.270378	0.40194	.	.	ENSG00000124193	ENST00000244020	T	0.16196	2.36	5.93	4.82	0.62117	.	0.195808	0.53938	D	0.000057	T	0.29093	0.0723	L	0.45051	1.395	0.32963	D	0.521249	D	0.54601	0.967	P	0.60789	0.879	T	0.39461	-0.9613	10	0.66056	D	0.02	.	10.9196	0.47156	0.8363:0.1637:0.0:0.0	.	296	Q13247	SRSF6_HUMAN	G	296	ENSP00000244020:R296G	ENSP00000244020:R296G	R	+	1	2	SRSF6	41522968	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.355000	0.52262	1.043000	0.40175	0.477000	0.44152	AGG	.	.	.	none		0.488	SRSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079292.1	NM_006275		G	42089554	A	G	42089554	3	3	251	1	0	0	0	0	1	0	0	0	14194	63	3	3	908	3	SFRS6	20	42089554	Missense_Mutation	SNP	A	TCGA-SX-A7SQ-01A-12D-A35Z-10	7776511	42089554	20935966	84	15638	161	2									
SFRS6	6431	hgsc.bcm.edu	37	chr20	42089559	42089559	+	Silent	SNP	C	C	T																															tcaaaatccagatcaaggagCcagtcccgttccaattcgcc																										TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr20:42089559C>T	ENST00000244020.3	+	6	997	c.891C>T	c.(889-891)agC>agT	p.S297S		NM_006275.5	NP_006266.2	Q13247	SRSF6_HUMAN	serine/arginine-rich splicing factor 6	297	Arg/Ser-rich (RS domain).				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell death (GO:0060548)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of keratinocyte proliferation (GO:0010837)|regulation of wound healing (GO:0061041)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|upper_aerodigestive_tract(2)	5						GATCAAGGAGCCAGTCCCGTT	0.488																																					p.S297S		Atlas-SNP	.											.	SRSF6	37	.	0			c.C891T						PASS	.						80	79	80					20																	42089559		2203	4300	6503	SO:0001819	synonymous_variant	6431	exon6			AAGGAGCCAGTCC	U30883	CCDS13318.1	20q12-q13.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000124193	ENSG00000124193		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10788	protein-coding gene	gene with protein product	"pre-mRNA splicing factor SRP55", "SR splicing factor 6"	601944	"splicing factor, arginine/serine-rich 6"	SFRS6		7556075, 20516191	Standard	NM_006275		Approved	SRP55, B52	uc010zwg.2	Q13247	OTTHUMG00000032502	ENST00000244020.3:c.891C>T	chr20.hg19:g.42089559C>T		207.0	0.0	.		230.0	132.0	.	NM_006275	B7Z6J3|E1P5W6|Q13244|Q13245|Q96J06|Q9UJB8|Q9Y3N7	Silent	SNP	ENST00000244020.3	hg19	CCDS13318.1																																																																																			.	.	.	none		0.488	SRSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079292.1	NM_006275		T	42089559	C	T	42089559	2	4	251	1	0	0	0	0	0	0	0	1	14194	738	26	2		2	SFRS6	20	42089559	Silent	SNP	C	TCGA-SX-A7SQ-01A-12D-A35Z-10	5	42089559	20935961	85	15639	161	2									
CBS	875	hgsc.bcm.edu	37	chr21	44479371	44479371	+	Frame_Shift_Del	DEL	A	A	-																															gtgaggtcctcctccttcagAaagcccttctgcagcatcca																										TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr21:44479371delA	ENST00000398165.3	-	13	1447	c.1188delT	c.(1186-1188)tttfs	p.F396fs	CBS_ENST00000398158.1_Frame_Shift_Del_p.F396fs|CBS_ENST00000359624.3_Frame_Shift_Del_p.F396fs|CBS_ENST00000352178.5_Frame_Shift_Del_p.F396fs|CBS_ENST00000398168.1_Frame_Shift_Del_p.F396fs|CBS_ENST00000544202.1_Frame_Shift_Del_p.F308fs	NM_000071.2	NP_000062.1	P35520	CBS_HUMAN	cystathionine-beta-synthase	396					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)	CCTCCTTCAGAAAGCCCTTCT	0.682																																					p.L397X		Atlas-Indel,Pindel	.											.	CBS	85	.	0			c.1189delC						PASS	.						74	73	73					21																	44479371		2203	4300	6503	SO:0001589	frameshift_variant	875	exon13			.	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.1188delT	chr21.hg19:g.44479371delA	ENSP00000381231:p.Phe396fs	59.0	0.0	0		32.0	15.0	0.46875	NM_000071	B2R993|D3DSK4|Q99425|Q9BWC5	Frame_Shift_Del	DEL	ENST00000398165.3	hg19	CCDS13693.1																																																																																			.	.	.	none		0.682	CBS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195525.1	NM_000071		-	44479371	A	-	44479371	7	5	251	1	0	1	0	1	0	0	0	0	2713	243	9	0	487	0	CBS	21	44479371	Frame_Shift_Del	DEL	A	TCGA-SX-A7SQ-01A-12D-A35Z-10		44479371	3650524	86	15640											
HIRA	7290	hgsc.bcm.edu	37	chr22	19344494	19344495	+	Frame_Shift_Ins	INS	-	-	C																															agagatcggggatggcaggaINSggatgggagagaggagacgg																										TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr22:19344494_19344495insC	ENST00000263208.5	-	19	2570_2571	c.2314_2315insG	c.(2314-2316)ctcfs	p.L772fs	HIRA_ENST00000546308.1_Frame_Shift_Ins_p.L728fs|HIRA_ENST00000541063.1_Frame_Shift_Ins_p.L728fs|HIRA_ENST00000340170.4_Intron	NM_003325.3	NP_003316.3	P54198	HIRA_HUMAN	histone cell cycle regulator	772	Interaction with PAX3. {ECO:0000250}.|Interaction with histone H2B.|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)					GGATGGCAGGAGGATGGGAGAG	0.594																																					p.L772fs		Atlas-INDEL	.											.	HIRA	100	.	0			c.2315_2316insG						PASS	.																																			SO:0001589	frameshift_variant	7290	exon19			.	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.2314_2315insG	chr22.hg19:g.19344494_19344495insC	ENSP00000263208:p.Leu772fs	96.0	0.0	0		125.0	34.0	0.272	NM_003325	Q05BU9|Q8IXN2	Frame_Shift_Ins	INS	ENST00000263208.5	hg19	CCDS13759.1																																																																																			.	.	.	none		0.594	HIRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316488.2	NM_003325		C	19344495	-	C	19344494	7	5	251	1	0	1	1	0	0	0	0	0	7127	304	11	0	766	0	HIRA	22	19344494	Frame_Shift_Ins	INS	-	TCGA-SX-A7SQ-01A-12D-A35Z-10		19344494	31960072	87	15641	162	2									
HIRA	7290	hgsc.bcm.edu	37	chr22	19344495	19344496	+	Frame_Shift_Ins	INS	-	-	AT																															gagatcggggatggcaggagINSgatgggagagaggagacggc																								rs374953578		TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr22:19344495_19344496insAT	ENST00000263208.5	-	19	2569_2570	c.2313_2314insAT	c.(2311-2316)atcctcfs	p.L772fs	HIRA_ENST00000546308.1_Frame_Shift_Ins_p.L728fs|HIRA_ENST00000541063.1_Frame_Shift_Ins_p.L728fs|HIRA_ENST00000340170.4_Intron	NM_003325.3	NP_003316.3	P54198	HIRA_HUMAN	histone cell cycle regulator	772	Interaction with PAX3. {ECO:0000250}.|Interaction with histone H2B.|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)					GATGGCAGGAGGATGGGAGAGA	0.589																																					p.L772fs		Atlas-Indel,Pindel	.											.	HIRA	100	.	0			c.2314_2315insAT						PASS	.																																			SO:0001589	frameshift_variant	7290	exon19			.	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.2313_2314insAT	chr22.hg19:g.19344495_19344496insAT	ENSP00000263208:p.Leu772fs	98.0	0.0	0		126.0	33.0	0.261905	NM_003325	Q05BU9|Q8IXN2	Frame_Shift_Ins	INS	ENST00000263208.5	hg19	CCDS13759.1																																																																																			.	.	.	none		0.589	HIRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316488.2	NM_003325		AT	19344496	-	AT	19344495	7	5	251	1	0	1	1	0	0	0	0	0	7127	1000	35	0	767	0	HIRA	22	19344495	Frame_Shift_Ins	INS	-	TCGA-SX-A7SQ-01A-12D-A35Z-10	1	19344495	31960071	88	15642	162	2									
MYO18B	84700	hgsc.bcm.edu	37	chr22	26286842	26286842	+	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	cgggaggtccaggagctcaaGgtgagtggtcaggggtggcc	7	6	20	8	1	2	1	2	1	0	0	3	3	3	3	2	8	1	1	2	8	1	0			TCGA-SX-A7SQ-01A-12D-A35Z-10	TCGA-SX-A7SQ-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2aa8e8d1-bc6d-4efa-82ef-120034ca6bcc	8ccf0feb-ec04-4877-b269-2a824a396344	g.chr22:26286842G>A	ENST00000407587.2	+	26	4606	c.4437G>A	c.(4435-4437)aaG>aaA	p.K1479K	CTA-125H2.2_ENST00000597548.1_RNA|CTA-125H2.2_ENST00000597614.2_RNA|CTA-125H2.2_ENST00000609820.1_RNA|CTA-125H2.2_ENST00000608921.1_RNA|CTA-125H2.2_ENST00000609275.1_RNA|CTA-125H2.2_ENST00000594542.1_RNA|CTA-125H2.2_ENST00000607895.1_RNA|CTA-125H2.2_ENST00000609889.1_RNA|CTA-125H2.2_ENST00000453457.3_RNA|CTA-125H2.2_ENST00000596813.1_RNA|CTA-125H2.2_ENST00000609823.1_RNA|MYO18B_ENST00000335473.7_Splice_Site_p.K1478K|CTA-125H2.2_ENST00000600211.1_RNA|MYO18B_ENST00000536101.1_Splice_Site_p.K1478K|CTA-125H2.2_ENST00000609809.1_RNA|CTA-125H2.2_ENST00000609157.1_RNA|CTA-125H2.2_ENST00000609570.1_RNA|CTA-125H2.2_ENST00000597284.1_RNA|CTA-125H2.2_ENST00000599080.1_RNA|CTA-125H2.2_ENST00000593715.1_RNA|CTA-125H2.2_ENST00000608115.1_RNA|CTA-125H2.2_ENST00000595102.1_RNA|CTA-125H2.2_ENST00000608257.1_RNA|CTA-125H2.2_ENST00000594585.1_RNA|CTA-125H2.2_ENST00000608507.1_RNA			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1478	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						AGGAGCTCAAGGTGAGTGGTC	0.597																																					p.K1478K		Atlas-SNP	.											.	MYO18B	322	.	0			c.G4434A						PASS	.						39	47	44					22																	26286842		2046	4193	6239	SO:0001630	splice_region_variant	84700	exon26			GCTCAAGGTGAGT	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.4437+1G>A	chr22.hg19:g.26286842G>A		74.0	0.0	.		66.0	34.0	.	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	hg19																																																																																				.	.	.	none		0.597	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	Silent	A	26286842	G	A	26286842	5	1	251	1	0	0	0	0	0	0	1	0	10073	1014	35	2	4532	2	MYO18B	22	26286842	Splice_Site	SNP	G	TCGA-SX-A7SQ-01A-12D-A35Z-10	6942347	26286842	25017724	89	15643											
MMEL1	79258	hgsc.bcm.edu	37	chr1	2560862	2560862	+	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	ccccctccaggaaccccgggCgcttctgccctgcacggccg	4	5	11	21	4	1	0	0	0	1	0	2	1	2	1	7	3	3	2	7	3	1	1			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr1:2560862C>A	ENST00000378412.3	-	2	223	c.62G>T	c.(61-63)cGc>cTc	p.R21L	MMEL1_ENST00000502556.1_Missense_Mutation_p.R21L|MMEL1_ENST00000511099.1_5'Flank|MMEL1_ENST00000288709.6_Missense_Mutation_p.R12L			Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	21						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)		GAACCCCGGGCGCTTCTGCCC	0.701																																					p.R21L		Atlas-SNP	.											.	MMEL1	64	.	0			c.G62T						PASS	.						11	12	12					1																	2560862		1892	3662	5554	SO:0001583	missense	79258	exon2			CCCGGGCGCTTCT	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.62G>T	chr1.hg19:g.2560862C>A	ENSP00000367668:p.Arg21Leu	260.0	0.0	.		156.0	62.0	.	NM_033467	B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9	Missense_Mutation	SNP	ENST00000378412.3	hg19	CCDS30569.2	.	.	.	.	.	.	.	.	.	.	c	6.219	0.408527	0.11812	.	.	ENSG00000142606	ENST00000378411;ENST00000288709;ENST00000378412;ENST00000502556	D;D;D	0.85629	-1.58;-1.56;-2.01	3.25	-2.69	0.06022	.	1.614800	0.02734	N	0.115427	T	0.79522	0.4460	L	0.52011	1.625	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.61287	-0.7093	10	0.56958	D	0.05	-4.1883	4.0829	0.09934	0.0:0.363:0.3467:0.2902	.	21	Q495T6	MMEL1_HUMAN	L	21;12;21;21	ENSP00000288709:R12L;ENSP00000367668:R21L;ENSP00000422492:R21L	ENSP00000288709:R12L	R	-	2	0	MMEL1	2550722	0.024000	0.19004	0.001000	0.08648	0.220000	0.24768	-0.695000	0.05109	-0.301000	0.08882	0.455000	0.32223	CGC	.	.	.	none		0.701	MMEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002395.2	NM_033467		A	2560862	C	A	2560862	3	1	252	1	0	0	0	0	1	0	0	0	9653	768	27	4	2369	4	MMEL1	1	2560862	Missense_Mutation	SNP	C	TCGA-SX-A7SR-01A-12D-A35Z-10		2560862	246689759	1	15644											
CLSTN1	22883	hgsc.bcm.edu	37	chr1	9815300	9815300	+	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	cgaatgactccctcaccagtGgatttatccactaccactgc	10	10	6	15	1	1	1	1	1	0	0	3	3	3	2	4	1	2	0	4	1	3	3			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr1:9815300G>T	ENST00000377298.4	-	4	1104	c.312C>A	c.(310-312)tcC>tcA	p.S104S	CLSTN1_ENST00000377288.3_Silent_p.S104S|CLSTN1_ENST00000361311.4_Silent_p.S94S	NM_001009566.1	NP_001009566.1	O94985	CSTN1_HUMAN	calsyntenin 1	104	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)|calcium ion binding (GO:0005509)|kinesin binding (GO:0019894)|X11-like protein binding (GO:0042988)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(9)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	36	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)		CCTCACCAGTGGATTTATCCA	0.468																																					p.S104S		Atlas-SNP	.											.	CLSTN1	88	.	0			c.C312A						PASS	.						208	195	199					1																	9815300		2203	4300	6503	SO:0001819	synonymous_variant	22883	exon4			ACCAGTGGATTTA	AB020718	CCDS105.1, CCDS30580.1	1p36.22	2011-07-01			ENSG00000171603	ENSG00000171603		"Cadherins / Cadherin-related"	17447	protein-coding gene	gene with protein product	"cadherin-related family member 12"	611321				10048485	Standard	XM_005263432		Approved	CSTN1, KIAA0911, CDHR12	uc001aqh.3	O94985	OTTHUMG00000001451	ENST00000377298.4:c.312C>A	chr1.hg19:g.9815300G>T		127.0	0.0	.		121.0	44.0	.	NM_001009566	A8K183|Q5SR52|Q5UE58|Q71MN0|Q8N4K9	Silent	SNP	ENST00000377298.4	hg19	CCDS30580.1																																																																																			.	.	.	none		0.468	CLSTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004239.1			T	9815300	G	T	9815300	2	4	252	1	0	0	0	0	0	0	0	1	3563	1335	47	4		4	CLSTN1	1	9815300	Silent	SNP	G	TCGA-SX-A7SR-01A-12D-A35Z-10	7254438	9815300	239435321	2	15645											
PRDM2	7799	hgsc.bcm.edu	37	chr1	14075886	14075886	+	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	cgggcgaggagctcctggtcTggtacaatggggaagacaac	10	6	16	9	2	1	1	0	0	1	1	2	4	2	3	1	6	3	2	1	6	4	1			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr1:14075886T>A	ENST00000235372.7	+	6	1271	c.415T>A	c.(415-417)Tgg>Agg	p.W139R	PRDM2_ENST00000503842.1_5'Flank|PRDM2_ENST00000343137.4_5'Flank|PRDM2_ENST00000413440.1_5'Flank|PRDM2_ENST00000311066.5_Missense_Mutation_p.W139R|PRDM2_ENST00000505823.1_5'Flank|PRDM2_ENST00000502727.1_3'UTR|PRDM2_ENST00000376048.5_Missense_Mutation_p.W139R	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	139	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		GCTCCTGGTCTGGTACAATGG	0.667																																					p.W139R		Atlas-SNP	.											.	PRDM2	147	.	0			c.T415A						PASS	.						16	18	17					1																	14075886		2195	4290	6485	SO:0001583	missense	7799	exon6			CTGGTCTGGTACA	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.415T>A	chr1.hg19:g.14075886T>A	ENSP00000235372:p.Trp139Arg	184.0	0.0	.		168.0	62.0	.	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Missense_Mutation	SNP	ENST00000235372.7	hg19	CCDS150.1	.	.	.	.	.	.	.	.	.	.	t	28.6	4.933126	0.92458	.	.	ENSG00000116731	ENST00000484063;ENST00000376048;ENST00000235372;ENST00000311066;ENST00000400800	D;D;D;D	0.88818	-2.43;-2.43;-2.43;-2.43	3.69	3.69	0.42338	SET domain (3);	0.000000	0.85682	D	0.000000	D	0.94178	0.8132	M	0.88512	2.96	0.52501	D	0.999955	D;D;D	0.64830	0.983;0.979;0.994	D;P;D	0.71184	0.91;0.854;0.972	D	0.94188	0.7438	10	0.56958	D	0.05	.	10.6381	0.45577	0.0:0.0:0.0:1.0	.	139;139;139	Q13029;Q13029-2;B1AJZ4	PRDM2_HUMAN;.;.	R	130;139;139;139;139	ENSP00000423010:W130R;ENSP00000365216:W139R;ENSP00000235372:W139R;ENSP00000312352:W139R	ENSP00000235372:W139R	W	+	1	0	PRDM2	13948473	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.486000	0.60286	1.661000	0.50771	0.524000	0.50904	TGG	.	.	.	none		0.667	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231		A	14075886	T	A	14075886	3	1	252	1	0	0	0	0	1	0	0	0	12468	1580	55	5	433	5	PRDM2	1	14075886	Missense_Mutation	SNP	T	TCGA-SX-A7SR-01A-12D-A35Z-10	4260586	14075886	235174735	3	15646											
MACF1	23499	hgsc.bcm.edu	37	chr1	39760763	39760763	+	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	aacaggatgtgtttcgttctCtacaagatacagcagaacta	14	11	8	8	1	1	2	0	0	1	2	3	3	1	3	0	1	5	3	0	1	6	5			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr1:39760763C>G	ENST00000372915.3	+	18	2302	c.2215C>G	c.(2215-2217)Cta>Gta	p.L739V	MACF1_ENST00000539005.1_Missense_Mutation_p.L739V|MACF1_ENST00000361689.2_Missense_Mutation_p.L739V|MACF1_ENST00000545844.1_Missense_Mutation_p.L739V|MACF1_ENST00000567887.1_Missense_Mutation_p.L771V|MACF1_ENST00000564288.1_Missense_Mutation_p.L734V|MACF1_ENST00000317713.7_Missense_Mutation_p.L739V			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	739					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)			GTTTCGTTCTCTACAAGATAC	0.458																																					p.L739V		Atlas-SNP	.											.	MACF1	909	.	0			c.C2215G						PASS	.						99	96	97					1																	39760763		2203	4300	6503	SO:0001583	missense	23499	exon20			CGTTCTCTACAAG	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.2215C>G	chr1.hg19:g.39760763C>G	ENSP00000362006:p.Leu739Val	107.0	0.0	.		89.0	31.0	.	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.	.	.	.	.	.	.	.	.	.	C	12.77	2.038986	0.35989	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000524432;ENST00000530262;ENST00000372900	D;D;D;D;D;D;D	0.96136	-3.92;-3.92;-3.92;-3.92;-3.92;-3.92;-3.92	5.72	5.72	0.89469	.	.	.	.	.	D	0.94424	0.8206	N	0.13098	0.295	0.80722	D	1	D;B	0.69078	0.997;0.122	D;B	0.81914	0.995;0.113	D	0.89130	0.3509	9	0.02654	T	1	.	20.2441	0.98394	0.0:1.0:0.0:0.0	.	739;704	F8W8Q1;Q9UPN3-3	.;.	V	739;739;739;739;739;697;888;899	ENSP00000439537:L739V;ENSP00000362006:L739V;ENSP00000354573:L739V;ENSP00000313438:L739V;ENSP00000444364:L739V;ENSP00000435070:L697V;ENSP00000437059:L888V	ENSP00000313438:L739V	L	+	1	2	MACF1	39533350	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.906000	0.48735	2.865000	0.98341	0.655000	0.94253	CTA	.	.	.	none		0.458	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		G	39760763	C	G	39760763	3	3	252	1	0	0	0	0	1	0	0	0	9151	912	32	4	2285	4	MACF1	1	39760763	Missense_Mutation	SNP	C	TCGA-SX-A7SR-01A-12D-A35Z-10	25684877	39760763	209489858	4	15647											
ST6GALNAC5	81849	hgsc.bcm.edu	37	chr1	77528710	77528710	+	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	ttattatgaaccttttggacCtgatgaatgtacaatgtacc	12	15	7	7	0	0	3	0	3	0	0	0	4	0	4	3	1	3	2	3	1	7	6			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr1:77528710C>T	ENST00000477717.1	+	5	1065	c.830C>T	c.(829-831)cCt>cTt	p.P277L		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	277					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						CCTTTTGGACCTGATGAATGT	0.418																																					p.P277L		Atlas-SNP	.											.	ST6GALNAC5	59	.	0			c.C830T						PASS	.						129	126	127					1																	77528710		2203	4300	6503	SO:0001583	missense	81849	exon5			TTGGACCTGATGA		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.830C>T	chr1.hg19:g.77528710C>T	ENSP00000417583:p.Pro277Leu	133.0	0.0	.		102.0	34.0	.	NM_030965	B1AK82	Missense_Mutation	SNP	ENST00000477717.1	hg19	CCDS673.1	.	.	.	.	.	.	.	.	.	.	C	15.53	2.862062	0.51482	.	.	ENSG00000117069	ENST00000477717;ENST00000438953	T	0.29917	1.55	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.38957	0.1060	L	0.54323	1.7	0.80722	D	1	D	0.69078	0.997	D	0.72075	0.976	T	0.04767	-1.0928	10	0.08837	T	0.75	-18.842	20.3422	0.98769	0.0:1.0:0.0:0.0	.	277	Q9BVH7	SIA7E_HUMAN	L	277;187	ENSP00000417583:P277L	ENSP00000406658:P187L	P	+	2	0	ST6GALNAC5	77301298	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.440000	0.80464	2.810000	0.96702	0.655000	0.94253	CCT	.	.	.	none		0.418	ST6GALNAC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026692.2	NM_030965		T	77528710	C	T	77528710	3	4	252	1	0	0	0	0	1	0	0	0	15239	681	24	2	848	2	ST6GALNAC5	1	77528710	Missense_Mutation	SNP	C	TCGA-SX-A7SR-01A-12D-A35Z-10	37767947	77528710	171721911	5	15648											
C1orf51	148523	hgsc.bcm.edu	37	chr1	150259058	150259058	+	Missense_Mutation	SNP	T	T	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	tctcctttagccatggtcctTtaggcactggaaccggcatt	7	13	9	12	1	1	0	0	0	1	0	3	1	2	1	4	4	2	2	4	4	3	5			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr1:150259058T>G	ENST00000290363.5	+	5	1299	c.850T>G	c.(850-852)Tta>Gta	p.L284V	C1orf51_ENST00000369095.1_Missense_Mutation_p.L284V|C1orf51_ENST00000369094.1_Missense_Mutation_p.L196V	NM_144697.2	NP_653298.1	Q8N365	CIART_HUMAN		284					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)			CCATGGTCCTTTAGGCACTGG	0.557																																					p.L284V		Atlas-SNP	.											.	C1orf51	35	.	0			c.T850G						PASS	.						220	184	196					1																	150259058		2203	4300	6503	SO:0001583	missense	148523	exon5			GGTCCTTTAGGCA																												ENST00000290363.5:c.850T>G	chr1.hg19:g.150259058T>G	ENSP00000290363:p.Leu284Val	100.0	0.0	.		89.0	32.0	.	NM_144697	B2RD43|D3DV01|Q8N795|Q96MG6	Missense_Mutation	SNP	ENST00000290363.5	hg19	CCDS949.1	.	.	.	.	.	.	.	.	.	.	T	15.20	2.762504	0.49574	.	.	ENSG00000159208	ENST00000447007;ENST00000369095;ENST00000369094;ENST00000417398;ENST00000290363	.	.	.	5.65	0.569	0.17340	.	0.809409	0.10750	N	0.638487	T	0.14614	0.0353	L	0.54323	1.7	0.23168	N	0.998187	B	0.27351	0.176	B	0.27608	0.081	T	0.29640	-1.0005	9	0.42905	T	0.14	-1.9282	2.739	0.05248	0.1411:0.0757:0.2763:0.5069	.	284	Q8N365	CA051_HUMAN	V	196;284;196;196;284	.	ENSP00000290363:L284V	L	+	1	2	C1orf51	148525682	0.594000	0.26849	0.909000	0.35828	0.945000	0.59286	-0.213000	0.09305	-0.059000	0.13154	0.533000	0.62120	TTA	.	.	.	none		0.557	C1orf51-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035058.1			G	150259058	T	G	150259058	3	3	252	1	0	0	0	0	1	0	0	0	2045	1838	64	5	868	5	C1orf51	1	150259058	Missense_Mutation	SNP	T	TCGA-SX-A7SR-01A-12D-A35Z-10	72730348	150259058	98991563	6	15649											
GOLPH3L	55204	hgsc.bcm.edu	37	chr1	150621097	150621097	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtattggtcactggatgagtAgtcatgtcaaatagcaggaa	13	11	12	5	0	3	1	3	1	0	0	3	3	3	3	0	3	1	3	0	3	5	4			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr1:150621097A>G	ENST00000271732.3	-	5	602	c.558T>C	c.(556-558)acT>acC	p.T186T	GOLPH3L_ENST00000540514.1_Silent_p.T142T	NM_018178.5	NP_060648.2	Q9H4A5	GLP3L_HUMAN	golgi phosphoprotein 3-like	186	Beta-hairpin required for oligomerization. {ECO:0000250}.				Golgi organization (GO:0007030)|positive regulation of protein secretion (GO:0050714)	Golgi membrane (GO:0000139)|trans-Golgi network membrane (GO:0032588)	phosphatidylinositol-4-phosphate binding (GO:0070273)			breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)	8	all_cancers(9;3.09e-52)|all_epithelial(9;4.47e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-31)|Breast(34;0.000615)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;1.2e-23)|all cancers(9;4.81e-23)|OV - Ovarian serous cystadenocarcinoma(6;1.93e-15)|BRCA - Breast invasive adenocarcinoma(12;0.000479)|LUSC - Lung squamous cell carcinoma(543;0.171)			CTGGATGAGTAGTCATGTCAA	0.433																																					p.T186T		Atlas-SNP	.											.	GOLPH3L	20	.	0			c.T558C						PASS	.						90	83	85					1																	150621097		2203	4300	6503	SO:0001819	synonymous_variant	55204	exon5			ATGAGTAGTCATG	AJ296153	CCDS966.1	1q21	2008-02-05			ENSG00000143457	ENSG00000143457			24882	protein-coding gene	gene with protein product		612208					Standard	NM_018178		Approved	GPP34R	uc001evj.2	Q9H4A5	OTTHUMG00000035009	ENST00000271732.3:c.558T>C	chr1.hg19:g.150621097A>G		180.0	0.0	.		171.0	57.0	.	NM_018178	B1AN09|B7Z6N3|Q9NVK0	Silent	SNP	ENST00000271732.3	hg19	CCDS966.1																																																																																			.	.	.	none		0.433	GOLPH3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084734.1	NM_018178		G	150621097	A	G	150621097	2	3	252	1	0	0	0	0	0	0	0	1	6576	407	15	3		3	GOLPH3L	1	150621097	Silent	SNP	A	TCGA-SX-A7SR-01A-12D-A35Z-10	362039	150621097	98629524	7	15650											
ARHGEF11	9826	hgsc.bcm.edu	37	chr1	156906702	156906702	+	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	agggagccatctgtccatctAgctgcttctgtgtggaaact	8	12	11	10	0	3	0	0	0	3	0	4	2	4	2	2	2	4	2	2	2	2	2			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr1:156906702A>C	ENST00000361409.2	-	39	5158	c.4416T>G	c.(4414-4416)gcT>gcG	p.A1472A	ARHGEF11_ENST00000487682.1_5'UTR|ARHGEF11_ENST00000368194.3_Silent_p.A1512A|ARHGEF11_ENST00000315174.8_Silent_p.A888A|MIR765_ENST00000390226.1_RNA	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	1472					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)					CTGTCCATCTAGCTGCTTCTG	0.597																																					p.A1512A		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.T4536G						PASS	.						125	125	125					1																	156906702		2203	4300	6503	SO:0001819	synonymous_variant	9826	exon40			CCATCTAGCTGCT	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.4416T>G	chr1.hg19:g.156906702A>C		119.0	0.0	.		95.0	33.0	.	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Silent	SNP	ENST00000361409.2	hg19	CCDS1162.1																																																																																			.	.	.	none		0.597	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236		C	156906702	A	C	156906702	2	2	252	1	0	0	0	0	0	0	0	1	896	407	15	5		5	ARHGEF11	1	156906702	Silent	SNP	A	TCGA-SX-A7SR-01A-12D-A35Z-10	6285605	156906702	92343919	8	15651											
ATP1A4	480	hgsc.bcm.edu	37	chr1	160144537	160144537	+	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	tcgtcacgggggtggaggagGgtgaggaggcagggtgccca	7	5	22	7	2	1	1	1	1	0	0	2	4	1	4	1	8	1	1	1	8	0	0			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr1:160144537G>C	ENST00000368081.4	+	15	2782	c.2311G>C	c.(2311-2313)Ggc>Cgc	p.G771R	ATP1A4_ENST00000418334.1_3'UTR|ATP1A4_ENST00000470705.1_5'Flank	NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	771					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)			GGTGGAGGAGGGTGAGGAGGC	0.577																																					p.G771R		Atlas-SNP	.											.	ATP1A4	167	.	0			c.G2311C						PASS	.						78	62	67					1																	160144537		2203	4300	6503	SO:0001630	splice_region_variant	480	exon15			GAGGAGGGTGAGG	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.2311+1G>C	chr1.hg19:g.160144537G>C		97.0	0.0	.		94.0	39.0	.	NM_144699	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Missense_Mutation	SNP	ENST00000368081.4	hg19	CCDS1197.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.407652	0.83340	.	.	ENSG00000132681	ENST00000368081	D	0.98044	-4.68	4.27	4.27	0.50696	HAD-like domain (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.99447	0.9804	H	0.99937	4.99	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97675	1.0169	10	0.87932	D	0	.	14.5908	0.68362	0.0:0.0:1.0:0.0	.	771	Q13733	AT1A4_HUMAN	R	771	ENSP00000357060:G771R	ENSP00000357060:G771R	G	+	1	0	ATP1A4	158411161	1.000000	0.71417	1.000000	0.80357	0.771000	0.43674	9.381000	0.97205	2.371000	0.80710	0.655000	0.94253	GGC	.	.	.	none		0.577	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699	Missense_Mutation	C	160144537	G	C	160144537	5	2	252	1	0	0	0	0	0	0	1	0	1131	1246	43	4	2369	4	ATP1A4	1	160144537	Splice_Site	SNP	G	TCGA-SX-A7SR-01A-12D-A35Z-10	3237835	160144537	89106084	9	15652											
CNST	163882	hgsc.bcm.edu	37	chr1	246829056	246829056	+	Frame_Shift_Del	DEL	T	T	-																															cttgctgtgcatagcaacggTtttcctcagtgttggaggaa																										TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr1:246829056delT	ENST00000366513.4	+	11	2296	c.2027delT	c.(2026-2028)gttfs	p.V676fs		NM_152609.2	NP_689822.2	Q6PJW8	CNST_HUMAN	consortin, connexin sorting protein	676					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						ATAGCAACGGTTTTCCTCAGT	0.443																																					p.V676fs		Atlas-Indel,Pindel	.											.	CNST	73	.	0			c.2026delG						PASS	.						205	178	187					1																	246829056		2203	4300	6503	SO:0001589	frameshift_variant	163882	exon11			.	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.2027delT	chr1.hg19:g.246829056delT	ENSP00000355470:p.Val676fs	117.0	0.0	0		88.0	29.0	0.329545	NM_152609	Q5VSY9|Q5VTM7|Q8IYA9|Q8N3L5|Q8NB09|Q8TEI2|Q96MR5	Frame_Shift_Del	DEL	ENST00000366513.4	hg19	CCDS1628.1																																																																																			.	.	.	none		0.443	CNST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096780.1	NM_152609		-	246829056	T	-	246829056	7	5	252	1	0	1	0	1	0	0	0	0	3636	1725	60	0	2080	0	CNST	1	246829056	Frame_Shift_Del	DEL	T	TCGA-SX-A7SR-01A-12D-A35Z-10	86684519	246829056	2421565	10	15653											
GREB1	9687	hgsc.bcm.edu	37	chr2	11706689	11706689	+	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	ctgcgggctttctcctcgtgGgggtcaagtcccccagcctg	3	10	13	15	2	2	0	1	0	1	0	5	0	3	0	4	3	2	1	4	3	1	1			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr2:11706689G>C	ENST00000381486.2	+	4	661	c.361G>C	c.(361-363)Ggg>Cgg	p.G121R	GREB1_ENST00000381483.2_Missense_Mutation_p.G121R|GREB1_ENST00000263834.5_Missense_Mutation_p.G121R|GREB1_ENST00000234142.5_Missense_Mutation_p.G121R|GREB1_ENST00000389825.3_Missense_Mutation_p.G11R	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	121						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)		TCTCCTCGTGGGGGTCAAGTC	0.592																																					p.G121R	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.G361C						PASS	.						100	92	95					2																	11706689		2203	4300	6503	SO:0001583	missense	9687	exon4			CTCGTGGGGGTCA		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.361G>C	chr2.hg19:g.11706689G>C	ENSP00000370896:p.Gly121Arg	82.0	0.0	.		69.0	30.0	.	NM_148903	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	hg19	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	G	35	5.440620	0.96168	.	.	ENSG00000196208	ENST00000381486;ENST00000263834;ENST00000389825;ENST00000381483;ENST00000234142	T;T;T;T;T	0.77750	2.5;1.47;-1.12;1.54;2.5	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.88492	0.6451	M	0.73962	2.25	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;1.0;0.999	D	0.89301	0.3626	10	0.87932	D	0	-44.3346	19.4103	0.94670	0.0:0.0:1.0:0.0	.	121;11;121;121	Q4ZG55-2;F8W6E5;Q4ZG55-3;Q4ZG55	.;.;.;GREB1_HUMAN	R	121;121;11;121;121	ENSP00000370896:G121R;ENSP00000263834:G121R;ENSP00000374475:G11R;ENSP00000370892:G121R;ENSP00000234142:G121R	ENSP00000234142:G121R	G	+	1	0	GREB1	11624140	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.671000	0.98627	2.583000	0.87209	0.655000	0.94253	GGG	.	.	.	none		0.592	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		C	11706689	G	C	11706689	3	2	252	1	0	0	0	0	1	0	0	0	6767	1232	43	4	371	4	GREB1	2	11706689	Missense_Mutation	SNP	G	TCGA-SX-A7SR-01A-12D-A35Z-10		11706689	231492684	11	15654											
SMC6	79677	hgsc.bcm.edu	37	chr2	17902443	17902443	+	Frame_Shift_Del	DEL	A	A	-																															tttcatgtttcaaggactctAaattagtcttcattgtactt																										TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr2:17902443delA	ENST00000448223.2	-	10	1081	c.812delT	c.(811-813)ttafs	p.L271fs	SMC6_ENST00000381272.4_Frame_Shift_Del_p.L297fs|SMC6_ENST00000402989.1_Frame_Shift_Del_p.L271fs|SMC6_ENST00000351948.4_Frame_Shift_Del_p.L271fs	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	271					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					CAAGGACTCTAAATTAGTCTT	0.343																																					p.L271fs		Atlas-Indel,Pindel	.											.	SMC6	102	.	0			c.813delA						PASS	.						133	135	134					2																	17902443		2202	4300	6502	SO:0001589	frameshift_variant	79677	exon10			.	AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"Structural maintenance of chromosomes proteins"	20466	protein-coding gene	gene with protein product		609387	"SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.812delT	chr2.hg19:g.17902443delA	ENSP00000404092:p.Leu271fs	341.0	0.0	0		366.0	114.0	0.311475	NM_001142286	A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Frame_Shift_Del	DEL	ENST00000448223.2	hg19	CCDS1690.1																																																																																			.	.	.	none		0.343	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207359.1	NM_024624		-	17902443	A	-	17902443	7	5	252	1	0	1	0	1	0	0	0	0	14800	372	13	0	2539	0	SMC6	2	17902443	Frame_Shift_Del	DEL	A	TCGA-SX-A7SR-01A-12D-A35Z-10	6195754	17902443	225296930	12	15655											
CCDC121	79635	hgsc.bcm.edu	37	chr2	27850108	27850108	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acaggagtattcaaaaataaAccgctttgctgccaacttca	15	10	6	10	1	2	0	2	0	0	0	2	1	2	1	2	1	4	3	2	1	6	5			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr2:27850108A>G	ENST00000324364.3	-	2	739	c.559T>C	c.(559-561)Ttt>Ctt	p.F187L	CCDC121_ENST00000394775.3_Missense_Mutation_p.F349L|GPN1_ENST00000424214.1_5'Flank|GPN1_ENST00000264718.3_5'Flank|GPN1_ENST00000458167.2_5'Flank|GPN1_ENST00000503738.1_5'Flank|GPN1_ENST00000610189.1_5'Flank|GPN1_ENST00000407583.3_5'Flank|ZNF512_ENST00000556601.1_Intron|RP11-158I13.2_ENST00000505973.1_RNA|GPN1_ENST00000515877.1_5'Flank	NM_024584.4	NP_078860.2	Q6ZUS5	CC121_HUMAN	coiled-coil domain containing 121	187										breast(1)|endometrium(3)|large_intestine(2)|lung(6)|prostate(2)	14	Acute lymphoblastic leukemia(172;0.155)					TCAAAAATAAACCGCTTTGCT	0.463																																					p.F349L		Atlas-SNP	.											.	CCDC121	43	.	0			c.T1045C						PASS	.						63	67	65					2																	27850108		2203	4300	6503	SO:0001583	missense	79635	exon2			AAATAAACCGCTT	AK125354	CCDS1759.1, CCDS46247.1	2p23.2	2008-02-05			ENSG00000176714	ENSG00000176714			25833	protein-coding gene	gene with protein product							Standard	NM_024584		Approved	FLJ43364, FLJ13646	uc002rld.3	Q6ZUS5	OTTHUMG00000128427	ENST00000324364.3:c.559T>C	chr2.hg19:g.27850108A>G	ENSP00000339087:p.Phe187Leu	96.0	0.0	.		78.0	27.0	.	NM_001142683	B3KW66|J3KQZ8|Q9H8G6	Missense_Mutation	SNP	ENST00000324364.3	hg19	CCDS1759.1	.	.	.	.	.	.	.	.	.	.	A	8.696	0.908553	0.17833	.	.	ENSG00000176714	ENST00000324364;ENST00000394775	T;T	0.27890	1.64;1.64	5.36	-6.38	0.01957	.	3.036110	0.00839	N	0.001729	T	0.11836	0.0288	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.18871	0.023	T	0.14811	-1.0459	10	0.11794	T	0.64	-29.1841	2.0948	0.03665	0.2432:0.3863:0.2444:0.1261	.	187	Q6ZUS5	CC121_HUMAN	L	187;349	ENSP00000339087:F187L;ENSP00000412150:F349L	ENSP00000339087:F187L	F	-	1	0	CCDC121	27703612	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.256000	0.08757	-1.009000	0.03400	0.482000	0.46254	TTT	.	.	.	none		0.463	CCDC121-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250215.1	NM_024584		G	27850108	A	G	27850108	3	3	252	1	0	0	0	0	1	0	0	0	2759	43	2	3	281	3	CCDC121	2	27850108	Missense_Mutation	SNP	A	TCGA-SX-A7SR-01A-12D-A35Z-10	9947665	27850108	215349265	13	15656											
XDH	7498	hgsc.bcm.edu	37	chr2	31600100	31600100	+	Frame_Shift_Del	DEL	C	C	-																															cttgaatgctgagaaatactCcccctaaaagagatcaggaa																										TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr2:31600100delC	ENST00000379416.3	-	14	1294	c.1246delG	c.(1246-1248)gagfs	p.E416fs		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	416					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)	GAGAAATACTCCCCCTAAAAG	0.517																																					p.E416fs	Colon(66;682 1445 30109 40147)	Atlas-Indel,Pindel	.											.	XDH	191	.	0			c.1247delA						PASS	.						96	93	94					2																	31600100		2203	4300	6503	SO:0001589	frameshift_variant	7498	exon14			.	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.1246delG	chr2.hg19:g.31600100delC	ENSP00000368727:p.Glu416fs	77.0	0.0	0		72.0	31.0	0.430556	NM_000379	Q16681|Q16712|Q4PJ16	Frame_Shift_Del	DEL	ENST00000379416.3	hg19	CCDS1775.1																																																																																			.	.	.	none		0.517	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379		-	31600100	C	-	31600100	7	5	252	1	0	1	0	1	0	0	0	0	17438	864	30	0	2847	0	XDH	2	31600100	Frame_Shift_Del	DEL	C	TCGA-SX-A7SR-01A-12D-A35Z-10	3749992	31600100	211599273	14	15657											
SLC38A11	151258	hgsc.bcm.edu	37	chr2	165809229	165809229	+	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	tattttacctgtaacatatgAaacccagaataaaagcaata	19	11	4	7	0	0	2	0	1	0	1	0	2	0	2	2	0	4	2	2	0	10	7			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr2:165809229A>T	ENST00000409149.3	-	2	340	c.49T>A	c.(49-51)Tca>Aca	p.S17T	SLC38A11_ENST00000303735.4_Missense_Mutation_p.S17T|SLC38A11_ENST00000409058.1_Intron|SLC38A11_ENST00000409662.1_Missense_Mutation_p.S17T	NM_001199148.1	NP_001186077.1	Q08AI6	S38AB_HUMAN	solute carrier family 38, member 11	17					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(4)|lung(8)|ovary(1)	15						GTAACATATGAAACCCAGAAT	0.358																																					p.S17T		Atlas-SNP	.											.	SLC38A11	41	.	0			c.T49A						PASS	.						57	61	60					2																	165809229		2203	4300	6503	SO:0001583	missense	151258	exon2			CATATGAAACCCA		CCDS2224.1, CCDS56142.1	2q24.3	2013-05-22			ENSG00000169507	ENSG00000169507		"Solute carriers"	26836	protein-coding gene	gene with protein product							Standard	NM_173512		Approved	FLJ39822, AVT2	uc002ucw.2	Q08AI6	OTTHUMG00000132144	ENST00000409149.3:c.49T>A	chr2.hg19:g.165809229A>T	ENSP00000386272:p.Ser17Thr	163.0	0.0	.		157.0	40.0	.	NM_173512	B4DF99|Q8N887	Missense_Mutation	SNP	ENST00000409149.3	hg19	CCDS56142.1	.	.	.	.	.	.	.	.	.	.	A	15.35	2.806168	0.50421	.	.	ENSG00000169507	ENST00000303735;ENST00000409149;ENST00000409662	T;T;T	0.02525	4.26;4.26;4.26	5.56	4.36	0.52297	.	0.161948	0.53938	D	0.000055	T	0.02304	0.0071	N	0.04705	-0.18	0.30984	N	0.722188	B;B	0.26809	0.16;0.132	B;B	0.36766	0.232;0.149	T	0.35574	-0.9783	10	0.31617	T	0.26	.	11.3997	0.49862	0.6358:0.3642:0.0:0.0	.	17;17	Q08AI6;Q08AI6-2	S38AB_HUMAN;.	T	17	ENSP00000306178:S17T;ENSP00000386272:S17T;ENSP00000386774:S17T	ENSP00000306178:S17T	S	-	1	0	SLC38A11	165517475	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.776000	0.55356	2.116000	0.64780	0.528000	0.53228	TCA	.	.	.	none		0.358	SLC38A11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333390.1	NM_173512		T	165809229	A	T	165809229	3	4	252	1	0	0	0	0	1	0	0	0	14616	246	9	5	1141	5	SLC38A11	2	165809229	Missense_Mutation	SNP	A	TCGA-SX-A7SR-01A-12D-A35Z-10	134209129	165809229	77390144	15	15658											
MAGI1	9223	hgsc.bcm.edu	37	chr3	65350346	65350346	+	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	gacatggtgctcacctgtgtTgcttggggtgctttgaactc	5	14	13	9	0	1	1	1	1	0	0	2	2	1	1	1	3	4	4	1	3	1	3			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr3:65350346T>A	ENST00000497477.2	-	19	3143	c.3144A>T	c.(3142-3144)gcA>gcT	p.A1048A	MAGI1_ENST00000483466.1_Silent_p.A1144A|MAGI1_ENST00000402939.2_Silent_p.A1115A|MAGI1_ENST00000330909.8_Silent_p.A1143A			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	1134	Interaction with FCHSD2.|PDZ 5. {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)		TCACCTGTGTTGCTTGGGGTG	0.383																																					p.A1144A		Atlas-SNP	.											.	MAGI1	481	.	0			c.A3432T						PASS	.						166	169	168					3																	65350346		2203	4300	6503	SO:0001819	synonymous_variant	9223	exon21			CTGTGTTGCTTGG	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.3144A>T	chr3.hg19:g.65350346T>A		212.0	0.0	.		166.0	69.0	.	NM_004742	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Silent	SNP	ENST00000497477.2	hg19		.	.	.	.	.	.	.	.	.	.	T	9.995	1.231942	0.22626	.	.	ENSG00000151276	ENST00000460329	.	.	.	6.17	-1.61	0.08399	.	.	.	.	.	T	0.51805	0.1696	.	.	.	0.58432	D	0.999993	.	.	.	.	.	.	T	0.45977	-0.9224	4	.	.	.	-4.4862	7.3714	0.26804	0.2789:0.0:0.328:0.3931	.	.	.	.	L	1024	.	.	Q	-	2	0	MAGI1	65325386	.	.	0.988000	0.46212	0.933000	0.57130	.	.	-0.057000	0.13199	0.533000	0.62120	CAA	.	.	.	none		0.383	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742		A	65350346	T	A	65350346	2	1	252	1	0	0	0	0	0	0	0	1	9197	1799	63	5		5	MAGI1	3	65350346	Silent	SNP	T	TCGA-SX-A7SR-01A-12D-A35Z-10		65350346	132672084	16	15659											
SLC41A3	54946	hgsc.bcm.edu	37	chr3	125725271	125725271	+	Frame_Shift_Del	DEL	C	C	-																															taaatagaggtttttgctaaCaaacaaaaaggaaaataaaa																								rs111477552|rs377657493	byFrequency	TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr3:125725271delC	ENST00000315891.6	-	12	1741	c.1503delG	c.(1501-1503)ttgfs	p.L502fs	SLC41A3_ENST00000383598.2_3'UTR|SLC41A3_ENST00000360370.4_3'UTR|SLC41A3_ENST00000346785.5_Frame_Shift_Del_p.L466fs	NM_001008485.1|NM_017836.3	NP_001008485|NP_060306.3	Q96GZ6	S41A3_HUMAN	solute carrier family 41, member 3	502						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)		TTTTTGCTAACAAACAAAAAG	0.353																																					p.L502X		Atlas-Indel,Pindel	.											.	SLC41A3	80	.	0			c.1504delT						PASS	.						30	29	29					3																	125725271		2200	4271	6471	SO:0001589	frameshift_variant	54946	exon12			.		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.1503delG	chr3.hg19:g.125725271delC	ENSP00000326070:p.Leu502fs	322.0	0.0	0		219.0	72.0	0.328767	NM_001008485	A6ND60|B3KSD9|B7Z4Y2|C9JE96|E7ENY4|Q8N342|Q8NB27|Q9H9I6|Q9HAB1|Q9NX30	Frame_Shift_Del	DEL	ENST00000315891.6	hg19	CCDS33843.1																																																																																			.	.	.	alt		0.353	SLC41A3-024	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370886.1	NM_017836		-	125725271	C	-	125725271	7	5	252	1	0	1	0	1	0	0	0	0	14644	477	17	0	24	0	SLC41A3	3	125725271	Frame_Shift_Del	DEL	C	TCGA-SX-A7SR-01A-12D-A35Z-10	60374925	125725271	72297159	17	15660											
TF	7018	hgsc.bcm.edu	37	chr3	133497449	133497449	+	Frame_Shift_Del	DEL	T	T	-																															gcactcctggaagcctgcacTttccgtagaccttaaaatct																										TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr3:133497449delT	ENST00000402696.3	+	17	2567	c.2082delT	c.(2080-2082)actfs	p.T694fs	TF_ENST00000264998.3_Frame_Shift_Del_p.T567fs	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	694					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)	AAGCCTGCACTTTCCGTAGAC	0.468																																					p.T694fs		Atlas-Indel,Pindel	.											.	TF	116	.	0			c.2081delC						PASS	.						70	65	66					3																	133497449		2203	4300	6503	SO:0001589	frameshift_variant	7018	exon17			.		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.2082delT	chr3.hg19:g.133497449delT	ENSP00000385834:p.Thr694fs	100.0	0.0	0		90.0	26.0	0.288889	NM_001063	O43890|Q1HBA5|Q9NQB8|Q9UHV0	Frame_Shift_Del	DEL	ENST00000402696.3	hg19	CCDS3080.1																																																																																			.	.	.	none		0.468	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063		-	133497449	T	-	133497449	7	5	252	1	0	1	0	1	0	0	0	0	15797	1596	56	0	2148	0	TF	3	133497449	Frame_Shift_Del	DEL	T	TCGA-SX-A7SR-01A-12D-A35Z-10	7772178	133497449	64524981	18	15661											
LAMP3	27074	hgsc.bcm.edu	37	chr3	182871611	182871611	+	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	ccaggaaccgtggaggcaggTgcagctgtgcgggtggtatt	7	8	18	8	2	0	0	0	0	0	0	0	2	0	2	2	6	4	4	2	6	2	2	rs201353315		TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr3:182871611T>A	ENST00000265598.3	-	2	873	c.618A>T	c.(616-618)gcA>gcT	p.A206A	LAMP3_ENST00000466939.1_Silent_p.A182A	NM_014398.3	NP_055213.2	Q9UQV4	LAMP3_HUMAN	lysosomal-associated membrane protein 3	206	Thr-rich.				cell proliferation (GO:0008283)|immune system process (GO:0002376)	alveolar lamellar body membrane (GO:0097233)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(9)|ovary(2)|prostate(2)	28	all_cancers(143;9.14e-14)|Ovarian(172;0.0355)		all cancers(12;2.91e-44)|Epithelial(37;5.52e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;4.16e-21)			TGGAGGCAGGTGCAGCTGTGC	0.552																																					p.A206A		Atlas-SNP	.											.	LAMP3	48	.	0			c.A618T						PASS	.						112	110	111					3																	182871611		2203	4300	6503	SO:0001819	synonymous_variant	27074	exon2			GGCAGGTGCAGCT	AB013924	CCDS3242.1	3q26.3-q27	2011-11-24			ENSG00000078081	ENSG00000078081		"CD molecules"	14582	protein-coding gene	gene with protein product		605883				9721848	Standard	NM_014398		Approved	LAMP, TSC403, DC-LAMP, DCLAMP, CD208	uc003flh.4	Q9UQV4	OTTHUMG00000158387	ENST00000265598.3:c.618A>T	chr3.hg19:g.182871611T>A		159.0	0.0	.		145.0	50.0	.	NM_014398	D3DNS4|O94781|Q8NEC8	Silent	SNP	ENST00000265598.3	hg19	CCDS3242.1																																																																																			.	G|0.001;T|0.999	.	weak		0.552	LAMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350863.1			A	182871611	T	A	182871611	2	1	252	1	0	0	0	0	0	0	0	1	8626	1683	59	5		5	LAMP3	3	182871611	Silent	SNP	T	TCGA-SX-A7SR-01A-12D-A35Z-10	49374162	182871611	15150819	19	15662											
AFP	174	hgsc.bcm.edu	37	chr4	74316462	74316462	+	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	acaaactattggcctgtggcGagggagcggtgagtgtctgc	8	9	16	8	2	1	1	0	1	1	0	1	3	1	2	1	4	3	0	1	4	2	2			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr4:74316462G>A	ENST00000395792.2	+	11	1520	c.1420G>A	c.(1420-1422)Gag>Aag	p.E474K	AFP_ENST00000226359.2_Missense_Mutation_p.E474K	NM_001134.1	NP_001125.1	P02771	FETA_HUMAN	alpha-fetoprotein	474	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)			GGCCTGTGGCGAGGGAGCGGT	0.522									Alpha-Fetoprotein, Hereditary Persistence of																												p.E474K		Atlas-SNP	.											.	AFP	60	.	0			c.G1420A						PASS	.						160	138	145					4																	74316462		2203	4300	6503	SO:0001583	missense	174	exon11	Familial Cancer Database	HPAFP	TGTGGCGAGGGAG	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.1420G>A	chr4.hg19:g.74316462G>A	ENSP00000379138:p.Glu474Lys	125.0	0.0	.		147.0	28.0	.	NM_001134	B2RBU3	Missense_Mutation	SNP	ENST00000395792.2	hg19	CCDS3556.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.015123	0.75161	.	.	ENSG00000081051	ENST00000395792;ENST00000226359	T;T	0.58358	0.34;0.34	4.93	4.93	0.64822	Serum albumin-like (1);Serum albumin, N-terminal (3);	0.060634	0.64402	D	0.000004	T	0.75034	0.3795	M	0.86864	2.845	0.30067	N	0.810355	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	T	0.75528	-0.3286	10	0.87932	D	0	.	13.8287	0.63366	0.0:0.0:1.0:0.0	.	316;474	B4DMX4;P02771	.;FETA_HUMAN	K	474	ENSP00000379138:E474K;ENSP00000226359:E474K	ENSP00000226359:E474K	E	+	1	0	AFP	74535326	1.000000	0.71417	0.205000	0.23548	0.890000	0.51754	5.131000	0.64751	2.715000	0.92844	0.561000	0.74099	GAG	.	.	.	none		0.522	AFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252284.3			A	74316462	G	A	74316462	3	1	252	1	0	0	0	0	1	0	0	0	363	1059	37	1	1462	1	AFP	4	74316462	Missense_Mutation	SNP	G	TCGA-SX-A7SR-01A-12D-A35Z-10		74316462	116837814	20	15663											
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123175369	123175369	+	Missense_Mutation	SNP	A	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	ggatgaaggagtcgaatctgAtgatttgaaaaaagatctac	16	10	11	4	1	2	5	0	4	2	1	3	8	2	7	0	2	1	0	0	2	6	2			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr4:123175369A>C	ENST00000264501.4	+	38	6315	c.5942A>C	c.(5941-5943)gAt>gCt	p.D1981A	KIAA1109_ENST00000388738.3_Missense_Mutation_p.D1981A|KIAA1109_ENST00000455637.1_Missense_Mutation_p.D1981A			Q2LD37	K1109_HUMAN	KIAA1109	1981					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						GTCGAATCTGATGATTTGAAA	0.373																																					p.D1981A		Atlas-SNP	.											.	KIAA1109	424	.	0			c.A5942C						PASS	.						119	107	111					4																	123175369		1849	4086	5935	SO:0001583	missense	84162	exon36			AATCTGATGATTT	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.5942A>C	chr4.hg19:g.123175369A>C	ENSP00000264501:p.Asp1981Ala	79.0	0.0	.		141.0	64.0	.	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.8|22.8	4.334620|4.334620	0.81801|0.81801	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637|ENST00000446180	T;T;T|.	0.23754|.	2.49;2.49;1.89|.	5.36|5.36	5.36|5.36	0.76844|0.76844	.|.	0.000000|.	0.51477|.	U|.	0.000082|.	T|T	0.55529|0.55529	0.1926|0.1926	L|L	0.31664|0.31664	0.95|0.95	0.54753|0.54753	D|D	0.999989|0.999989	D;D|.	0.76494|.	0.999;0.998|.	D;D|.	0.83275|.	0.996;0.991|.	T|T	0.52660|0.52660	-0.8546|-0.8546	10|5	0.29301|.	T|.	0.29|.	.|.	15.3548|15.3548	0.74418|0.74418	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1980;1981|.	Q2LD37-2;Q2LD37|.	.;K1109_HUMAN|.	A|L	1981|554	ENSP00000264501:D1981A;ENSP00000373390:D1981A;ENSP00000389925:D1981A|.	ENSP00000264501:D1981A|.	D|M	+|+	2|1	0|0	KIAA1109|KIAA1109	123394819|123394819	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	9.262000|9.262000	0.95591|0.95591	2.034000|2.034000	0.60081|0.60081	0.482000|0.482000	0.46254|0.46254	GAT|ATG	.	.	.	none		0.373	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		C	123175369	A	C	123175369	3	2	252	1	0	0	0	0	1	0	0	0	8215	333	12	5	6084	5	KIAA1109	4	123175369	Missense_Mutation	SNP	A	TCGA-SX-A7SR-01A-12D-A35Z-10	48858907	123175369	67978907	21	15664											
HMGCS1	3157	hgsc.bcm.edu	37	chr5	43294814	43294814	+	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	gtgctagaacagatgcaaggGaaccatatactgaagatgtg	15	8	12	6	0	0	4	0	1	0	3	0	5	0	5	1	1	5	2	1	1	7	3			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr5:43294814G>C	ENST00000325110.6	-	7	1261	c.1055C>G	c.(1054-1056)tCc>tGc	p.S352C	HMGCS1_ENST00000433297.2_Missense_Mutation_p.S352C	NM_001098272.2	NP_001091742.1	Q01581	HMCS1_HUMAN	3-hydroxy-3-methylglutaryl-CoA synthase 1 (soluble)	352					brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|lipid metabolic process (GO:0006629)|liver development (GO:0001889)|male gonad development (GO:0008584)|response to acid chemical (GO:0001101)|response to drug (GO:0042493)|response to lipoprotein particle (GO:0055094)|response to low light intensity stimulus (GO:0009645)|response to purine-containing compound (GO:0014074)|response to tellurium ion (GO:0046690)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hydroxymethylglutaryl-CoA synthase activity (GO:0004421)|isomerase activity (GO:0016853)|organic acid binding (GO:0043177)			NS(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|stomach(1)|urinary_tract(1)	15						AGATGCAAGGGAACCATATAC	0.353																																					p.S352C		Atlas-SNP	.											.	HMGCS1	33	.	0			c.C1055G						PASS	.						159	159	159					5																	43294814		2203	4300	6503	SO:0001583	missense	3157	exon7			GCAAGGGAACCAT		CCDS34154.1	5p14-p13	2012-10-02	2010-04-30			ENSG00000112972	2.3.3.10		5007	protein-coding gene	gene with protein product	"3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) synthase"	142940	"3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble)"	HMGCS			Standard	NM_001098272		Approved		uc003jnq.5	Q01581		ENST00000325110.6:c.1055C>G	chr5.hg19:g.43294814G>C	ENSP00000322706:p.Ser352Cys	89.0	0.0	.		54.0	17.0	.	NM_001098272	B2RDL8	Missense_Mutation	SNP	ENST00000325110.6	hg19	CCDS34154.1	.	.	.	.	.	.	.	.	.	.	G	10.30	1.312009	0.23821	.	.	ENSG00000112972	ENST00000325110;ENST00000433297;ENST00000545275	T;T	0.78707	-1.2;-1.2	5.65	3.79	0.43588	Hydroxymethylglutaryl-coenzyme A synthase C-terminal (1);Thiolase-like (1);	0.043346	0.85682	D	0.000000	T	0.56702	0.2003	N	0.02334	-0.595	0.43512	D	0.995771	B	0.13594	0.008	B	0.23852	0.049	T	0.51236	-0.8731	10	0.24483	T	0.36	-9.5747	16.8813	0.86064	0.0:0.4758:0.5242:0.0	.	352	Q01581	HMCS1_HUMAN	C	352;352;341	ENSP00000322706:S352C;ENSP00000399402:S352C	ENSP00000322706:S352C	S	-	2	0	HMGCS1	43330571	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.702000	0.54800	1.370000	0.46153	0.460000	0.39030	TCC	.	.	.	none		0.353	HMGCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368022.1			C	43294814	G	C	43294814	3	2	252	1	0	0	0	0	1	0	0	0	7239	1174	41	4	527	4	HMGCS1	5	43294814	Missense_Mutation	SNP	G	TCGA-SX-A7SR-01A-12D-A35Z-10		43294814	137620446	22	15665											
EDIL3	10085	hgsc.bcm.edu	37	chr5	83362406	83362406	+	Missense_Mutation	SNP	A	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	taatcacaccagtaactctcAttttcctttgcaaatttatc	12	16	2	11	0	2	0	2	0	1	0	5	0	3	0	2	0	2	2	2	0	4	7			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr5:83362406A>C	ENST00000296591.5	-	7	1089	c.671T>G	c.(670-672)aTg>aGg	p.M224R	EDIL3_ENST00000380138.3_Missense_Mutation_p.M214R|EDIL3_ENST00000510271.1_5'UTR	NM_005711.3	NP_005702.3	O43854	EDIL3_HUMAN	EGF-like repeats and discoidin I-like domains 3	224	F5/8 type C 1. {ECO:0000255|PROSITE- ProRule:PRU00081}.				cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|prostate(5)|skin(3)	31		Lung NSC(167;0.000121)|all_lung(232;0.000154)|Ovarian(174;0.0425)		OV - Ovarian serous cystadenocarcinoma(54;4.3e-40)|Epithelial(54;4.79e-32)|all cancers(79;1.54e-26)		AGTAACTCTCATTTTCCTTTG	0.348																																					p.M224R		Atlas-SNP	.											.	EDIL3	94	.	0			c.T671G						PASS	.						101	108	106					5																	83362406		2203	4300	6503	SO:0001583	missense	10085	exon7			ACTCTCATTTTCC	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.671T>G	chr5.hg19:g.83362406A>C	ENSP00000296591:p.Met224Arg	101.0	0.0	.		119.0	45.0	.	NM_005711	B2R763|O43855|Q5D094|Q8N610	Missense_Mutation	SNP	ENST00000296591.5	hg19	CCDS4062.1	.	.	.	.	.	.	.	.	.	.	A	17.86	3.491718	0.64074	.	.	ENSG00000164176	ENST00000296591;ENST00000380138	D;D	0.98060	-4.69;-4.69	5.93	5.93	0.95920	Coagulation factor 5/8 C-terminal type domain (4);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.97845	0.9292	L	0.45051	1.395	0.80722	D	1	D;D;D	0.65815	0.995;0.965;0.967	D;P;P	0.66351	0.943;0.884;0.897	D	0.99174	1.0865	10	0.87932	D	0	-29.0243	16.3756	0.83387	1.0:0.0:0.0:0.0	.	1;214;224	B7Z865;O43854-2;O43854	.;.;EDIL3_HUMAN	R	224;214	ENSP00000296591:M224R;ENSP00000369483:M214R	ENSP00000296591:M224R	M	-	2	0	EDIL3	83398162	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.962000	0.93254	2.270000	0.75569	0.460000	0.39030	ATG	.	.	.	none		0.348	EDIL3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239258.1	NM_005711		C	83362406	A	C	83362406	3	2	252	1	0	0	0	0	1	0	0	0	4917	217	8	5	791	5	EDIL3	5	83362406	Missense_Mutation	SNP	A	TCGA-SX-A7SR-01A-12D-A35Z-10	40067592	83362406	97552854	23	15666											
SLC35A4	113829	hgsc.bcm.edu	37	chr5	139947338	139947338	+	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	cctgctgctcctcattctgtActgcctcatctcaggcttgt	4	15	7	15	0	4	0	3	0	2	0	6	0	5	0	3	1	4	4	3	1	1	3			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr5:139947338A>T	ENST00000514199.1	+	2	2270	c.584A>T	c.(583-585)tAc>tTc	p.Y195F	SLC35A4_ENST00000323146.3_Missense_Mutation_p.Y195F|APBB3_ENST00000507279.1_Intron			Q96G79	S35A4_HUMAN	solute carrier family 35, member A4	195	Leu-rich.					Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sugar:proton symporter activity (GO:0005351)			endometrium(4)|kidney(2)|large_intestine(3)|lung(4)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCATTCTGTACTGCCTCATC	0.587																																					p.Y195F		Atlas-SNP	.											.	SLC35A4	25	.	0			c.A584T						PASS	.						103	98	100					5																	139947338		2203	4300	6503	SO:0001583	missense	113829	exon3			TTCTGTACTGCCT	AJ420598	CCDS4231.1	5q31.3	2013-05-22			ENSG00000176087	ENSG00000176087		"Solute carriers"	20753	protein-coding gene	gene with protein product							Standard	NM_080670		Approved		uc003lgg.1	Q96G79	OTTHUMG00000129495	ENST00000514199.1:c.584A>T	chr5.hg19:g.139947338A>T	ENSP00000424566:p.Tyr195Phe	69.0	0.0	.		57.0	20.0	.	NM_080670	A8K013	Missense_Mutation	SNP	ENST00000514199.1	hg19	CCDS4231.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.279959	0.80692	.	.	ENSG00000176087	ENST00000323146;ENST00000514199	T;T	0.41400	1.0;1.0	4.68	4.68	0.58851	.	0.000000	0.64402	D	0.000001	T	0.52869	0.1761	L	0.39085	1.19	0.58432	D	0.999991	D	0.76494	0.999	D	0.85130	0.997	T	0.49551	-0.8928	9	.	.	.	-10.1141	13.9451	0.64080	1.0:0.0:0.0:0.0	.	195	Q96G79	S35A4_HUMAN	F	195	ENSP00000327133:Y195F;ENSP00000424566:Y195F	.	Y	+	2	0	SLC35A4	139927522	1.000000	0.71417	1.000000	0.80357	0.784000	0.44337	8.714000	0.91412	1.961000	0.56991	0.379000	0.24179	TAC	.	.	.	none		0.587	SLC35A4-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372815.1	NM_080670		T	139947338	A	T	139947338	3	4	252	1	0	0	0	0	1	0	0	0	14586	391	14	5	586	5	SLC35A4	5	139947338	Missense_Mutation	SNP	A	TCGA-SX-A7SR-01A-12D-A35Z-10	56584932	139947338	40967922	24	15667											
DCTN4	51164	hgsc.bcm.edu	37	chr5	150111032	150111032	+	Missense_Mutation	SNP	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	ctcgtggtcgctgaagcctgGttccaagaccatatttgtcc	7	12	10	12	2	0	2	0	1	0	1	4	2	2	2	4	2	1	2	4	2	3	3			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr5:150111032G>A	ENST00000447998.2	-	6	672	c.557C>T	c.(556-558)aCc>aTc	p.T186I	DCTN4_ENST00000521093.1_5'Flank|DCTN4_ENST00000424236.1_Missense_Mutation_p.T129I|DCTN4_ENST00000446090.2_Missense_Mutation_p.T193I	NM_016221.3	NP_057305.1	Q9UJW0	DCTN4_HUMAN	dynactin 4 (p62)	186					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|nucleus (GO:0005634)	protein N-terminus binding (GO:0047485)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	10		Medulloblastoma(196;0.167)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTGAAGCCTGGTTCCAAGACC	0.408																																					p.T193I		Atlas-SNP	.											.	DCTN4	35	.	0			c.C578T						PASS	.						62	60	61					5																	150111032		2203	4300	6503	SO:0001583	missense	51164	exon7			AGCCTGGTTCCAA	AF195120	CCDS4310.1, CCDS47310.1, CCDS47311.1	5q31-q32	2008-05-23			ENSG00000132912	ENSG00000132912			15518	protein-coding gene	gene with protein product		614758				10843801, 16554302	Standard	NM_016221		Approved		uc010jhi.3	Q9UJW0	OTTHUMG00000130079	ENST00000447998.2:c.557C>T	chr5.hg19:g.150111032G>A	ENSP00000416968:p.Thr186Ile	73.0	0.0	.		60.0	17.0	.	NM_001135643	B3KWW0|D3DQH0|E5RGT5|Q8TAN8	Missense_Mutation	SNP	ENST00000447998.2	hg19	CCDS4310.1	.	.	.	.	.	.	.	.	.	.	G	16.28	3.079487	0.55753	.	.	ENSG00000132912	ENST00000447998;ENST00000424236;ENST00000446090;ENST00000521728;ENST00000518015	T;T;T;T;T	0.23147	1.92;1.92;1.92;1.92;1.92	5.53	4.64	0.57946	.	0.049705	0.85682	D	0.000000	T	0.24084	0.0583	L	0.44542	1.39	0.80722	D	1	B;P	0.35411	0.444;0.5	B;B	0.33042	0.097;0.157	T	0.02398	-1.1165	10	0.44086	T	0.13	-38.4966	15.5558	0.76192	0.0:0.0:0.8608:0.1391	.	193;186	Q9UJW0-3;Q9UJW0	.;DCTN4_HUMAN	I	186;129;193;43;129	ENSP00000416968:T186I;ENSP00000411251:T129I;ENSP00000414906:T193I;ENSP00000428987:T43I;ENSP00000430993:T129I	ENSP00000411251:T129I	T	-	2	0	DCTN4	150091225	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.062000	0.93920	1.287000	0.44583	0.563000	0.77884	ACC	.	.	.	none		0.408	DCTN4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252372.1			A	150111032	G	A	150111032	3	1	252	1	0	0	0	0	1	0	0	0	4311	1261	44	2	857	2	DCTN4	5	150111032	Missense_Mutation	SNP	G	TCGA-SX-A7SR-01A-12D-A35Z-10	10163694	150111032	30804228	25	15668											
CDHR2	54825	hgsc.bcm.edu	37	chr5	176019773	176019773	+	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	atgtggacaagaacagtcagGaaatcaaggcaagatggggg	16	5	15	5	0	2	2	2	0	0	2	2	4	2	4	0	5	1	1	0	5	5	0			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr5:176019773G>A	ENST00000510636.1	+	31	4058	c.3784G>A	c.(3784-3786)Gaa>Aaa	p.E1262K	CDHR2_ENST00000261944.5_Missense_Mutation_p.E1262K|CDHR2_ENST00000506348.1_Missense_Mutation_p.E1262K	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	1262					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						GAACAGTCAGGAAATCAAGGC	0.542																																					p.E1262K		Atlas-SNP	.											CDHR2,NS,malignant_melanoma,0,1	CDHR2	152	.	0			c.G3784A						PASS	.						150	125	133					5																	176019773		2203	4300	6503	SO:0001583	missense	54825	exon31			AGTCAGGAAATCA	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.3784G>A	chr5.hg19:g.176019773G>A	ENSP00000424565:p.Glu1262Lys	143.0	0.0	.		84.0	29.0	.	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	hg19	CCDS34297.1	.	.	.	.	.	.	.	.	.	.	g	0.051	-1.250934	0.01469	.	.	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.55052	0.54;0.54;0.54	3.63	0.234	0.15390	.	.	.	.	.	T	0.29524	0.0736	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24941	-1.0146	9	0.06891	T	0.86	-0.0319	5.9006	0.18964	0.5753:0.0:0.4247:0.0	.	1262	Q9BYE9	CDHR2_HUMAN	K	1262	ENSP00000424565:E1262K;ENSP00000261944:E1262K;ENSP00000421078:E1262K	ENSP00000261944:E1262K	E	+	1	0	CDHR2	175952379	0.000000	0.05858	0.488000	0.27440	0.363000	0.29612	-0.278000	0.08490	0.191000	0.20236	0.459000	0.35465	GAA	.	.	.	none		0.542	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675		A	176019773	G	A	176019773	3	1	252	1	0	0	0	0	1	0	0	0	3121	1175	41	2	3902	2	CDHR2	5	176019773	Missense_Mutation	SNP	G	TCGA-SX-A7SR-01A-12D-A35Z-10	25908741	176019773	4895487	26	15669											
PPARD	5467	hgsc.bcm.edu	37	chr6	35387920	35387920	+	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	gcagacctctcccggagctcCtcgccaccctcactgctgga	6	7	9	19	2	2	1	1	0	1	1	5	3	3	3	5	2	2	3	5	2	0	0			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr6:35387920C>A	ENST00000311565.4	+	5	496	c.147C>A	c.(145-147)tcC>tcA	p.S49S	PPARD_ENST00000444397.1_Silent_p.S49S|PPARD_ENST00000418635.2_Intron|PPARD_ENST00000360694.3_Silent_p.S49S|PPARD_ENST00000337400.2_Silent_p.S49S|PPARD_ENST00000448077.2_Silent_p.S10S|PPARD_ENST00000540939.1_Intron	NM_001171818.1	NP_001165289.1	Q03181	PPARD_HUMAN	peroxisome proliferator-activated receptor delta	49					adipose tissue development (GO:0060612)|anagen (GO:0042640)|apoptotic signaling pathway (GO:0097190)|axon ensheathment (GO:0008366)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cell-substrate adhesion (GO:0031589)|cellular response to hypoxia (GO:0071456)|cholesterol metabolic process (GO:0008203)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|fatty acid beta-oxidation (GO:0006635)|fatty acid catabolic process (GO:0009062)|fatty acid transport (GO:0015908)|gene expression (GO:0010467)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|heart development (GO:0007507)|intracellular receptor signaling pathway (GO:0030522)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)|lipid metabolic process (GO:0006629)|mRNA transcription (GO:0009299)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of inflammatory response (GO:0050728)|negative regulation of smooth muscle cell migration (GO:0014912)|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)|phospholipid biosynthetic process (GO:0008654)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epidermis development (GO:0045684)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of insulin secretion (GO:0032024)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasodilation (GO:0045909)|proteoglycan metabolic process (GO:0006029)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to activity (GO:0014823)|response to glucose (GO:0009749)|response to vitamin A (GO:0033189)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vitamin A metabolic process (GO:0006776)|wound healing (GO:0042060)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|linoleic acid binding (GO:0070539)|lipid binding (GO:0008289)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(4)|liver(2)|lung(9)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23					Bezafibrate(DB01393)|Icosapent(DB00159)|Sulindac(DB00605)|Treprostinil(DB00374)	CCCGGAGCTCCTCGCCACCCT	0.677																																					p.S49S		Atlas-SNP	.											.	PPARD	46	.	0			c.C147A						PASS	.						53	51	52					6																	35387920		2203	4300	6503	SO:0001819	synonymous_variant	5467	exon5			GAGCTCCTCGCCA	L07592	CCDS4803.1, CCDS4804.1, CCDS54994.1, CCDS54995.1	6p21.2	2013-01-16	2006-10-17		ENSG00000112033	ENSG00000112033		"Nuclear hormone receptors"	9235	protein-coding gene	gene with protein product		600409	"peroxisome proliferative activated receptor, delta"			1333051	Standard	NM_177435		Approved	NUC1, NUCII, FAAR, NR1C2	uc003okm.3	Q03181	OTTHUMG00000014567	ENST00000311565.4:c.147C>A	chr6.hg19:g.35387920C>A		52.0	0.0	.		40.0	16.0	.	NM_001171818	A8K6J6|B4E3V3|B6ZGS1|B7Z3W1|E9PE18|Q5D1P0|Q7Z5K0|Q9BUD4	Silent	SNP	ENST00000311565.4	hg19	CCDS4803.1																																																																																			.	.	.	none		0.677	PPARD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040288.1	NM_006238		A	35387920	C	A	35387920	2	1	252	1	0	0	0	0	0	0	0	1	12305	668	24	4		4	PPARD	6	35387920	Silent	SNP	C	TCGA-SX-A7SR-01A-12D-A35Z-10		35387920	135727147	27	15670											
RUNX2	860	hgsc.bcm.edu	37	chr6	45390463	45390463	+	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	caacagcagcagcagcagcaGcaacagcagcagcagcagca	16	0	11	14	0	0	0	0	0	0	0	0	0	0	0	0	0	13	11	0	0	2	0			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr6:45390463G>A	ENST00000371438.1	+	2	550	c.192G>A	c.(190-192)caG>caA	p.Q64Q	RUNX2_ENST00000465038.2_Silent_p.Q64Q|RUNX2_ENST00000371432.3_Silent_p.Q50Q|RUNX2_ENST00000371436.6_Silent_p.Q64Q|RUNX2_ENST00000576263.1_Silent_p.Q64Q|RUNX2_ENST00000541979.1_Silent_p.Q132Q|RUNX2_ENST00000352853.5_Silent_p.Q132Q|RP1-244F24.1_ENST00000606796.1_RNA|RUNX2_ENST00000359524.5_Silent_p.Q50Q	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	64	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						agcagcagcagcaacagcagc	0.736																																					p.Q64Q		Atlas-SNP	.											RUNX2_ENST00000352853,NS,carcinoma,0,2	RUNX2	128	.	0			c.G192A						PASS	.						11	16	14					6																	45390463		1448	3096	4544	SO:0001819	synonymous_variant	860	exon3			GCAGCAGCAACAG	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.192G>A	chr6.hg19:g.45390463G>A		63.0	0.0	.		45.0	4.0	.	NM_001024630	O14614|O14615|O95181	Silent	SNP	ENST00000371438.1	hg19	CCDS43467.2																																																																																			.	.	.	none		0.736	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		A	45390463	G	A	45390463	2	1	252	1	0	0	0	0	0	0	0	1	13761	962	34	2		2	RUNX2	6	45390463	Silent	SNP	G	TCGA-SX-A7SR-01A-12D-A35Z-10	10002543	45390463	125724604	28	15671											
LAMB1	3912	hgsc.bcm.edu	37	chr7	107572669	107572669	+	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	ggcactcaggacatcttggtCcaagtccatggctttctgcc	7	11	10	13	0	3	0	1	0	2	0	5	1	5	1	3	4	1	2	3	4	1	2			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr7:107572669C>T	ENST00000222399.6	-	28	4572	c.4342G>A	c.(4342-4344)Gac>Aac	p.D1448N	LAMB1_ENST00000474380.1_5'UTR|LAMB1_ENST00000393561.1_Missense_Mutation_p.D1472N	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	1448	Domain I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						ACATCTTGGTCCAAGTCCATG	0.517																																					p.D1448N		Atlas-SNP	.											.	LAMB1	185	.	0			c.G4342A						PASS	.						173	159	163					7																	107572669		2203	4300	6503	SO:0001583	missense	3912	exon28			CTTGGTCCAAGTC	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.4342G>A	chr7.hg19:g.107572669C>T	ENSP00000222399:p.Asp1448Asn	152.0	0.0	.		145.0	63.0	.	NM_002291	Q14D91	Missense_Mutation	SNP	ENST00000222399.6	hg19	CCDS5750.1	.	.	.	.	.	.	.	.	.	.	C	34	5.389844	0.95988	.	.	ENSG00000091136	ENST00000393561;ENST00000222399	T;T	0.32515	1.45;1.45	5.21	5.21	0.72293	.	.	.	.	.	T	0.54095	0.1837	M	0.62723	1.935	0.80722	D	1	P;D	0.76494	0.885;0.999	P;D	0.70487	0.468;0.969	T	0.52185	-0.8609	9	0.52906	T	0.07	.	18.9339	0.92577	0.0:1.0:0.0:0.0	.	1448;1472	P07942;G3XAI2	LAMB1_HUMAN;.	N	1472;1448	ENSP00000377191:D1472N;ENSP00000222399:D1448N	ENSP00000222399:D1448N	D	-	1	0	LAMB1	107359905	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.320000	0.79064	2.708000	0.92522	0.655000	0.94253	GAC	.	.	.	none		0.517	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291		T	107572669	C	T	107572669	3	4	252	1	0	0	0	0	1	0	0	0	8617	855	30	2	1046	2	LAMB1	7	107572669	Missense_Mutation	SNP	C	TCGA-SX-A7SR-01A-12D-A35Z-10		107572669	51565994	29	15672											
ABCB8	11194	hgsc.bcm.edu	37	chr7	150725694	150725694	+	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	cttccagacattctcagctgTcaggtaaaaacggaaaaacc	15	8	7	11	1	2	1	2	0	1	1	4	2	3	2	2	2	3	2	2	2	5	3			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr7:150725694T>A	ENST00000297504.6	+	1	158	c.92T>A	c.(91-93)gTc>gAc	p.V31D	RP11-148K1.10_ENST00000479085.1_RNA|ABCB8_ENST00000498578.1_Missense_Mutation_p.V31D|ABCB8_ENST00000358849.4_Missense_Mutation_p.V31D|ABCB8_ENST00000477092.1_Missense_Mutation_p.V31D|ABCB8_ENST00000477719.1_Missense_Mutation_p.V31D|ABCB8_ENST00000542328.1_Nonsense_Mutation_p.C47*|ABCB8_ENST00000356058.4_Missense_Mutation_p.V31D			Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 8	31					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)	TTCTCAGCTGTCAGGTAAAAA	0.632											OREG0018445	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V31D		Atlas-SNP	.											.	ABCB8	65	.	0			c.T92A						PASS	.						41	39	40					7																	150725694		2203	4300	6503	SO:0001583	missense	11194	exon1			CAGCTGTCAGGTA	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.92T>A	chr7.hg19:g.150725694T>A	ENSP00000297504:p.Val31Asp	81.0	0.0	.	1734	69.0	11.0	.	NM_007188	A5D8W3|B2RBL8|B3KND2|B4DG02|G3XAP3|O95787|Q53GM0	Missense_Mutation	SNP	ENST00000297504.6	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	26.8|26.8	4.772126|4.772126	0.90108|0.90108	.|.	.|.	ENSG00000197150|ENSG00000197150	ENST00000542328|ENST00000461373;ENST00000358849;ENST00000360651;ENST00000297504;ENST00000498578;ENST00000356058;ENST00000477719;ENST00000477092	.|D;D;D;D;D;D	.|0.91686	.|-2.75;-2.75;-2.89;-2.53;-2.23;-2.26	4.99|4.99	-0.764|-0.764	0.11027|0.11027	.|.	.|0.847859	.|0.10224	.|N	.|0.700511	.|D	.|0.86087	.|0.5849	L|L	0.27053|0.27053	0.805|0.805	0.43364|0.43364	D|D	0.995446|0.995446	.|B;P;P;P;P	.|0.51351	.|0.232;0.664;0.573;0.664;0.944	.|B;B;P;B;P	.|0.47346	.|0.193;0.261;0.448;0.368;0.544	.|T	.|0.78011	.|-0.2371	.|10	0.15066|0.46703	T|T	0.55|0.11	-0.4325|-0.4325	4.4338|4.4338	0.11540|0.11540	0.0:0.3635:0.1804:0.4561|0.0:0.3635:0.1804:0.4561	.|.	.|31;31;31;31;31	.|A5D8W3;Q9NUT2;Q9NUT2-2;C9JTY4;E7ENE8	.|.;ABCB8_HUMAN;.;.;.	X|D	47|31	.|ENSP00000351717:V31D;ENSP00000297504:V31D;ENSP00000418271:V31D;ENSP00000348353:V31D;ENSP00000419891:V31D;ENSP00000419558:V31D	ENSP00000438776:C47X|ENSP00000297504:V31D	C|V	+|+	3|2	2|0	ABCB8|ABCB8	150356627|150356627	1.000000|1.000000	0.71417|0.71417	0.902000|0.902000	0.35471|0.35471	0.779000|0.779000	0.44077|0.44077	0.244000|0.244000	0.18124|0.18124	-0.269000|-0.269000	0.09298|0.09298	-0.256000|-0.256000	0.11100|0.11100	TGT|GTC	.	.	.	none		0.632	ABCB8-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351733.2	NM_007188		A	150725694	T	A	150725694	3	1	252	1	0	0	0	0	1	0	0	0	47	1667	58	5	94	5	ABCB8	7	150725694	Missense_Mutation	SNP	T	TCGA-SX-A7SR-01A-12D-A35Z-10	43153025	150725694	8412969	30	15673											
C8orf80	389643	hgsc.bcm.edu	37	chr8	27918040	27918040	+	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	ggctttgatgctctcattcaGaaggtcttcgtgggcttgcc	5	14	12	10	1	3	2	2	1	2	1	5	2	3	2	1	3	2	3	1	3	1	4			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr8:27918040G>T	ENST00000413272.2	-	8	1142	c.1000C>A	c.(1000-1002)Ctg>Atg	p.L334M	NUGGC_ENST00000341513.6_Missense_Mutation_p.L334M	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	334					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)										CTCTCATTCAGAAGGTCTTCG	0.537											OREG0018675	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L334M		Atlas-SNP	.											.	.	.	.	0			c.C1000A						PASS	.						57	58	57					8																	27918040		1960	4147	6107	SO:0001583	missense	389643	exon8			CATTCAGAAGGTC	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.1000C>A	chr8.hg19:g.27918040G>T	ENSP00000408697:p.Leu334Met	100.0	0.0	.	99	91.0	29.0	.	NM_001010906	Q6ZP73	Missense_Mutation	SNP	ENST00000413272.2	hg19	CCDS47833.1	.	.	.	.	.	.	.	.	.	.	G	16.42	3.117376	0.56505	.	.	ENSG00000189233	ENST00000413272;ENST00000341513	D;D	0.96334	-3.98;-3.98	5.67	3.84	0.44239	.	0.099090	0.41712	D	0.000832	D	0.96491	0.8855	M	0.71036	2.16	0.30739	N	0.746356	D	0.53151	0.958	P	0.56751	0.805	D	0.93916	0.7201	10	0.46703	T	0.11	-4.7393	7.9242	0.29865	0.0861:0.1608:0.7531:0.0	.	334	Q68CJ6	SLIP_HUMAN	M	334	ENSP00000408697:L334M;ENSP00000345031:L334M	ENSP00000345031:L334M	L	-	1	2	C8orf80	27973959	1.000000	0.71417	0.996000	0.52242	0.825000	0.46686	2.049000	0.41288	0.720000	0.32209	0.585000	0.79938	CTG	.	.	.	none		0.537	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906		T	27918040	G	T	27918040	3	4	252	1	0	0	0	0	1	0	0	0	2441	933	33	4	1438	4	C8orf80	8	27918040	Missense_Mutation	SNP	G	TCGA-SX-A7SR-01A-12D-A35Z-10		27918040	118445982	31	15674											
KIAA0146	23514	hgsc.bcm.edu	37	chr8	48625228	48625240	+	Frame_Shift_Del	DEL	AGAGTCTGCTGCT	AGAGTCTGCTGCT	-																															tgtcttcaaattgtagctgaAgagtctgctgcttctggagc																								rs547240956		TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	AGAGTCTGCTGCT	AGAGTCTGCTGCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr8:48625228_48625240delAGAGTCTGCTGCT	ENST00000297423.4	+	15	2366_2378	c.1982_1994delAGAGTCTGCTGCT	c.(1981-1995)aagagtctgctgcttfs	p.KSLLL661fs	SPIDR_ENST00000518074.1_Frame_Shift_Del_p.KSLLL601fs|SPIDR_ENST00000517693.1_Frame_Shift_Del_p.KSLLL136fs|SPIDR_ENST00000521214.1_3'UTR|SPIDR_ENST00000541342.1_Frame_Shift_Del_p.KSLLL591fs	NM_001080394.2|NM_001282916.1	NP_001073863.1|NP_001269845.1	Q14159	SPIDR_HUMAN	scaffolding protein involved in DNA repair	661					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)											TTGTAGCTGAAGAGTCTGCTGCTTCTGGAGCAA	0.399																																					p.661_665del		Atlas-Indel,Pindel	.											.	KIAA0146	64	.	0			c.1981_1993del						PASS	.																																			SO:0001589	frameshift_variant	23514	exon15			.	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.1982_1994delAGAGTCTGCTGCT	chr8.hg19:g.48625228_48625240delAGAGTCTGCTGCT	ENSP00000297423:p.Lys661fs	85.0	0.0	0		78.0	15.0	0.192308	NM_001080394	B4DFV2|B4E0Y6|Q96BI5	Frame_Shift_Del	DEL	ENST00000297423.4	hg19	CCDS43737.1																																																																																			.	.	.	none		0.399	SPIDR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377611.1	NM_001080394		-	48625240	AGAGTCTGCTGCT	-	48625228	7	5	252	1	0	1	0	1	0	0	0	0	8164	72	3	0	2040	0	KIAA0146	8	48625228	Frame_Shift_Del	DEL	AGAGTCTGCTGCT	TCGA-SX-A7SR-01A-12D-A35Z-10	20707188	48625228	97738794	32	15675											
ANKS6	203286	hgsc.bcm.edu	37	chr9	101540705	101540705	+	Splice_Site	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	tggacattcggttccaccagGactgccaaaggaacgcagag	12	6	12	11	2	0	1	0	0	0	1	2	4	1	4	3	4	2	2	3	4	2	2			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr9:101540705G>A	ENST00000353234.4	-	7	1417	c.1370C>T	c.(1369-1371)tCc>tTc	p.S457F	ANKS6_ENST00000375019.2_Splice_Site_p.S156F|ANKS6_ENST00000540940.1_Splice_Site_p.S262F|ANKS6_ENST00000375018.1_Splice_Site_p.S457F			Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain containing 6	457						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)				GTTCCACCAGGACTGCCAAAG	0.572																																					p.S457F		Atlas-SNP	.											.	ANKS6	59	.	0			c.C1370T						PASS	.						29	34	32					9																	101540705		2117	4219	6336	SO:0001630	splice_region_variant	203286	exon7			CACCAGGACTGCC	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.1369-1C>T	chr9.hg19:g.101540705G>A		169.0	0.0	.		125.0	48.0	.	NM_173551	A0SE62|Q5VSL0|Q5VSL2|Q5VSL3|Q5VSL4|Q68DB8|Q6P2R2|Q8N9L6|Q96D62	Missense_Mutation	SNP	ENST00000353234.4	hg19	CCDS43856.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.460139	0.84317	.	.	ENSG00000165138	ENST00000375019;ENST00000375018;ENST00000353234;ENST00000540940	T;T;T;T	0.72167	1.69;-0.62;-0.63;1.94	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	D	0.82949	0.5148	M	0.65498	2.005	0.58432	D	0.999994	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.996	D	0.84479	0.0604	10	0.72032	D	0.01	-24.47	16.6649	0.85250	0.0:0.0:1.0:0.0	.	457;457	Q68DC2-4;Q68DC2	.;ANKS6_HUMAN	F	156;457;457;262	ENSP00000364159:S156F;ENSP00000364158:S457F;ENSP00000297837:S457F;ENSP00000442189:S262F	ENSP00000297837:S457F	S	-	2	0	ANKS6	100580526	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	8.949000	0.93012	2.525000	0.85131	0.655000	0.94253	TCC	.	.	.	none		0.572	ANKS6-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277053.1	NM_173551	Missense_Mutation	A	101540705	G	A	101540705	5	1	252	1	0	0	0	0	0	0	1	0	692	1188	41	2	1281	2	ANKS6	9	101540705	Splice_Site	SNP	G	TCGA-SX-A7SR-01A-12D-A35Z-10		101540705	39672726	33	15676											
PPP6C	5537	hgsc.bcm.edu	37	chr9	127916020	127916020	+	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	acaaaatctgctcatctattAactagcaaaaaaggataaca	20	9	4	8	0	3	0	1	0	2	0	3	1	3	1	0	1	4	2	0	1	9	4			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr9:127916020A>T	ENST00000373547.4	-	6	560	c.461T>A	c.(460-462)tTa>tAa	p.L154*	PPP6C_ENST00000373546.3_Splice_Site_p.L7*|PPP6C_ENST00000451402.1_Splice_Site_p.L191*|PPP6C_ENST00000415905.1_Splice_Site_p.L132*	NM_002721.4	NP_002712.1	O00743	PPP6_HUMAN	protein phosphatase 6, catalytic subunit	154					G1/S transition of mitotic cell cycle (GO:0000082)|protein dephosphorylation (GO:0006470)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			NS(2)|endometrium(1)|large_intestine(4)|liver(1)|lung(2)|ovary(1)|skin(3)	14						CTCATCTATTAACTAGCAAAA	0.343																																					p.L191X		Atlas-SNP	.											.	PPP6C	108	.	0			c.T572A						PASS	.						48	47	48					9																	127916020		2203	4300	6503	SO:0001630	splice_region_variant	5537	exon7			TCTATTAACTAGC	AF035158	CCDS6861.1, CCDS48018.1, CCDS48019.1	9q33.3	2010-03-17			ENSG00000119414	ENSG00000119414		"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9323	protein-coding gene	gene with protein product		612725				9143513	Standard	NM_002721		Approved	PP6	uc004bpg.4	O00743	OTTHUMG00000020671	ENST00000373547.4:c.460-1T>A	chr9.hg19:g.127916020A>T		57.0	0.0	.		50.0	20.0	.	NM_001123355	B2R5V6|B7Z2W9|B7Z5K9|Q5U0A2|Q9UIC9	Nonsense_Mutation	SNP	ENST00000373547.4	hg19	CCDS6861.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.576849	0.86645	.	.	ENSG00000119414	ENST00000373547;ENST00000451402;ENST00000415905;ENST00000373546	.	.	.	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-29.0263	14.9689	0.71217	1.0:0.0:0.0:0.0	.	.	.	.	X	154;191;132;7	.	ENSP00000362647:L7X	L	-	2	0	PPP6C	126955841	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.910000	0.92685	2.132000	0.65825	0.377000	0.23210	TTA	.	.	.	none		0.343	PPP6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054060.1	NM_016294	Nonsense_Mutation	T	127916020	A	T	127916020	5	4	252	1	0	0	0	0	0	0	1	0	12417	376	13	5	464	5	PPP6C	9	127916020	Splice_Site	SNP	A	TCGA-SX-A7SR-01A-12D-A35Z-10	26375315	127916020	13297411	34	15677											
SH2D3C	10044	hgsc.bcm.edu	37	chr9	130502080	130502080	+	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	ccgtgctgccccagggctcaGggccctctggtggggccgag	3	6	17	15	2	2	0	1	0	1	0	2	1	2	0	5	5	2	2	5	5	0	0			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr9:130502080G>A	ENST00000314830.8	-	11	2401	c.2288C>T	c.(2287-2289)cCt>cTt	p.P763L	SH2D3C_ENST00000373274.3_Missense_Mutation_p.P603L|SH2D3C_ENST00000373276.3_Missense_Mutation_p.P695L|SH2D3C_ENST00000420366.1_Missense_Mutation_p.P605L|SH2D3C_ENST00000429553.1_Missense_Mutation_p.P409L|SH2D3C_ENST00000373277.4_Missense_Mutation_p.P606L	NM_170600.2	NP_733745.1	Q8N5H7	SH2D3_HUMAN	SH2 domain containing 3C	763	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						CCAGGGCTCAGGGCCCTCTGG	0.662																																					p.P763L		Atlas-SNP	.											.	SH2D3C	102	.	0			c.C2288T						PASS	.						19	17	17					9																	130502080		2199	4295	6494	SO:0001583	missense	10044	exon11			GGCTCAGGGCCCT	AF124251	CCDS6877.1, CCDS6878.1, CCDS48026.1, CCDS48028.1, CCDS59145.1	9q33.1-q33.3	2013-02-14	2002-01-14		ENSG00000095370	ENSG00000095370		"SH2 domain containing"	16884	protein-coding gene	gene with protein product		604722	"SH2 domain-containing 3C"			10187783	Standard	NM_170600		Approved	NSP3	uc004bsc.3	Q8N5H7	OTTHUMG00000020717	ENST00000314830.8:c.2288C>T	chr9.hg19:g.130502080G>A	ENSP00000317817:p.Pro763Leu	173.0	0.0	.		149.0	47.0	.	NM_170600	A8K5S8|E9PG48|Q5HYE5|Q5JU31|Q6UY42|Q8N6X3|Q9Y2X5	Missense_Mutation	SNP	ENST00000314830.8	hg19	CCDS6877.1	.	.	.	.	.	.	.	.	.	.	G	12.34	1.908323	0.33721	.	.	ENSG00000095370	ENST00000373277;ENST00000420366;ENST00000373276;ENST00000373274;ENST00000429553;ENST00000314830	T;T;T;T;T;T	0.21031	2.86;2.86;2.61;2.86;2.03;2.84	5.24	5.24	0.73138	Guanine-nucleotide dissociation stimulator CDC25 (2);	0.349077	0.35040	N	0.003483	T	0.08268	0.0206	N	0.02213	-0.635	0.58432	D	0.999997	B;B;B;B;B	0.16396	0.0;0.017;0.0;0.0;0.001	B;B;B;B;B	0.15052	0.001;0.012;0.002;0.003;0.003	T	0.24764	-1.0151	10	0.08381	T	0.77	-12.6255	13.6889	0.62533	0.0:0.1545:0.8455:0.0	.	603;763;695;606;605	E9PG48;Q8N5H7;E7EUN5;Q8N5H7-2;Q8N5H7-5	.;SH2D3_HUMAN;.;.;.	L	606;605;695;603;409;763	ENSP00000362374:P606L;ENSP00000388536:P605L;ENSP00000362373:P695L;ENSP00000362371:P603L;ENSP00000394632:P409L;ENSP00000317817:P763L	ENSP00000317817:P763L	P	-	2	0	SH2D3C	129541901	0.730000	0.28100	0.976000	0.42696	0.919000	0.55068	1.793000	0.38764	2.732000	0.93576	0.561000	0.74099	CCT	.	.	.	none		0.662	SH2D3C-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054264.1	NM_005489		A	130502080	G	A	130502080	3	1	252	1	0	0	0	0	1	0	0	0	14247	1000	35	2	302	2	SH2D3C	9	130502080	Missense_Mutation	SNP	G	TCGA-SX-A7SR-01A-12D-A35Z-10	2586060	130502080	10711351	35	15678											
GBGT1	26301	hgsc.bcm.edu	37	chr9	136030630	136030630	+	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	tggtagatgtgctgcagaagCtctgggttgaaggttccctc	7	12	14	8	0	1	3	0	1	1	2	3	3	2	3	1	3	3	6	1	3	3	3			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr9:136030630C>G	ENST00000372040.3	-	6	605	c.294G>C	c.(292-294)gaG>gaC	p.E98D	GBGT1_ENST00000372043.3_Missense_Mutation_p.E98D|GBGT1_ENST00000540636.1_Missense_Mutation_p.E81D|RALGDS_ENST00000542690.1_Missense_Mutation_p.A111P|GBGT1_ENST00000472281.1_5'UTR|GBGT1_ENST00000372038.3_Missense_Mutation_p.A111P	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	98					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)		GCTGCAGAAGCTCTGGGTTGA	0.632																																					p.E98D		Atlas-SNP	.											.	GBGT1	25	.	0			c.G294C						PASS	.						114	104	107					9																	136030630		2203	4300	6503	SO:0001583	missense	26301	exon6			CAGAAGCTCTGGG	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.294G>C	chr9.hg19:g.136030630C>G	ENSP00000361110:p.Glu98Asp	142.0	0.0	.		89.0	27.0	.	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Missense_Mutation	SNP	ENST00000372040.3	hg19	CCDS6960.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	4.731|4.731	0.135935|0.135935	0.09032|0.09032	.|.	.|.	ENSG00000160271;ENSG00000148288|ENSG00000148288	ENST00000542690;ENST00000372038|ENST00000372043;ENST00000372040;ENST00000540636	T;T|T;T;T	0.38560|0.01234	1.7;1.13|5.13;5.13;5.13	4.98|4.98	2.08|2.08	0.27032|0.27032	.|.	.|0.438261	.|0.23016	.|N	.|0.052913	T|T	0.00875|0.00875	0.0029|0.0029	N|N	0.25144|0.25144	0.715|0.715	0.09310|0.09310	N|N	0.999999|0.999999	B|B;B	0.06786|0.06786	0.001|0.001;0.001	B|B;B	0.09377|0.12156	0.004|0.004;0.007	T|T	0.49437|0.49437	-0.8940|-0.8940	9|10	0.87932|0.02654	D|T	0|1	-8.294|-8.294	2.9566|2.9566	0.05878|0.05878	0.1451:0.5578:0.1406:0.1565|0.1451:0.5578:0.1406:0.1565	.|.	111|81;98	F5H6M6|B7Z8S5;Q8N5D6	.|.;GBGT1_HUMAN	P|D	111|98;98;81	ENSP00000437518:A111P;ENSP00000361108:A111P|ENSP00000361113:E98D;ENSP00000361110:E98D;ENSP00000437663:E81D	ENSP00000361108:A111P|ENSP00000361110:E98D	A|E	-|-	1|3	0|2	GBGT1;RALGDS|GBGT1	135020451|135020451	0.001000|0.001000	0.12720|0.12720	0.017000|0.017000	0.16124|0.16124	0.019000|0.019000	0.09904|0.09904	-0.033000|-0.033000	0.12246|0.12246	0.135000|0.135000	0.18707|0.18707	-0.305000|-0.305000	0.09177|0.09177	GCT|GAG	.	.	.	none		0.632	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996		G	136030630	C	G	136030630	3	3	252	1	0	0	0	0	1	0	0	0	6279	796	28	4	757	4	GBGT1	9	136030630	Missense_Mutation	SNP	C	TCGA-SX-A7SR-01A-12D-A35Z-10	5528550	136030630	5182801	36	15679											
DPP7	29952	hgsc.bcm.edu	37	chr9	140008368	140008368	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggccccgaggtcgcgtcgtAgcgcgcggagcagctctgcg	4	5	18	14	8	1	0	0	0	1	0	3	2	1	1	2	3	4	3	2	3	1	1			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr9:140008368A>G	ENST00000371579.2	-	4	438	c.434T>C	c.(433-435)cTa>cCa	p.L145P		NM_013379.2	NP_037511.2	Q9UHL4	DPP2_HUMAN	dipeptidyl-peptidase 7	145						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)		GTCGCGTCGTAGCGCGCGGAG	0.746																																					p.L145P		Atlas-SNP	.											.	DPP7	22	.	0			c.T434C						PASS	.						8	8	8					9																	140008368		2136	4172	6308	SO:0001583	missense	29952	exon4			CGTCGTAGCGCGC	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.434T>C	chr9.hg19:g.140008368A>G	ENSP00000360635:p.Leu145Pro	57.0	0.0	.		47.0	13.0	.	NM_013379	A8K7U7|Q5VSF1|Q969X4	Missense_Mutation	SNP	ENST00000371579.2	hg19	CCDS7030.1	.	.	.	.	.	.	.	.	.	.	A	14.49	2.551014	0.45383	.	.	ENSG00000176978	ENST00000371579	D	0.93366	-3.21	4.5	4.5	0.54988	.	0.000000	0.64402	D	0.000007	D	0.97315	0.9122	H	0.95151	3.63	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97574	1.0106	10	0.72032	D	0.01	-33.7912	10.0965	0.42478	1.0:0.0:0.0:0.0	.	145	Q9UHL4	DPP2_HUMAN	P	145	ENSP00000360635:L145P	ENSP00000360635:L145P	L	-	2	0	DPP7	139128189	0.937000	0.31787	0.066000	0.19879	0.003000	0.03518	3.290000	0.51755	1.888000	0.54679	0.454000	0.30748	CTA	.	.	.	none		0.746	DPP7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055279.1	NM_013379		G	140008368	A	G	140008368	3	3	252	1	0	0	0	0	1	0	0	0	4733	420	15	3	1084	3	DPP7	9	140008368	Missense_Mutation	SNP	A	TCGA-SX-A7SR-01A-12D-A35Z-10	3977738	140008368	1205063	37	15680											
NET1	10276	hgsc.bcm.edu	37	chr10	5494436	5494436	+	Frame_Shift_Del	DEL	T	T	-																															tgcactgtggtcagagatgcTggacatcaccatgaaggagt																										TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr10:5494436delT	ENST00000355029.4	+	5	621	c.479delT	c.(478-480)ctgfs	p.L160fs	NET1_ENST00000380359.3_Frame_Shift_Del_p.L106fs|NET1_ENST00000542715.1_5'UTR	NM_001047160.2	NP_001040625.1	Q7Z628	ARHG8_HUMAN	neuroepithelial cell transforming 1	160					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						TCAGAGATGCTGGACATCACC	0.532																																					p.L160fs		Atlas-Indel,Pindel	.											.	NET1	82	.	0			c.478delC						PASS	.						97	85	89					10																	5494436		2203	4300	6503	SO:0001589	frameshift_variant	10276	exon5			.	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.479delT	chr10.hg19:g.5494436delT	ENSP00000347134:p.Leu160fs	76.0	0.0	0		106.0	35.0	0.330189	NM_001047160	Q12773|Q96D82|Q99903|Q9UEN6	Frame_Shift_Del	DEL	ENST00000355029.4	hg19	CCDS41483.1																																																																																			.	.	.	none		0.532	NET1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046553.3	NM_005863		-	5494436	T	-	5494436	7	5	252	1	0	1	0	1	0	0	0	0	10345	1580	55	0	594	0	NET1	10	5494436	Frame_Shift_Del	DEL	T	TCGA-SX-A7SR-01A-12D-A35Z-10		5494436	130040311	38	15681											
CUBN	8029	hgsc.bcm.edu	37	chr10	17164807	17164807	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagttacctgtaacttcccaTtgtattaacacatgtgcctc	11	14	5	11	0	0	0	0	0	0	0	2	0	1	0	3	0	4	3	3	0	5	6			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr10:17164807T>C	ENST00000377833.4	-	6	645	c.580A>G	c.(580-582)Atg>Gtg	p.M194V		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	194	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TAACTTCCCATTGTATTAACA	0.368																																					p.M194V		Atlas-SNP	.											.	CUBN	515	.	0			c.A580G						PASS	.						64	57	59					10																	17164807		2203	4300	6503	SO:0001583	missense	8029	exon6			TTCCCATTGTATT	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.580A>G	chr10.hg19:g.17164807T>C	ENSP00000367064:p.Met194Val	145.0	0.0	.		132.0	53.0	.	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	T	1.180	-0.638441	0.03557	.	.	ENSG00000107611	ENST00000377833;ENST00000433666	D;D	0.91407	-2.84;-2.84	5.22	-5.63	0.02474	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	2.038200	0.02936	N	0.139880	T	0.67702	0.2921	N	0.00894	-1.105	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.65772	-0.6087	10	0.14656	T	0.56	.	2.2608	0.04067	0.1568:0.2399:0.373:0.2303	.	194	O60494	CUBN_HUMAN	V	194;81	ENSP00000367064:M194V;ENSP00000415970:M81V	ENSP00000367064:M194V	M	-	1	0	CUBN	17204813	0.108000	0.22018	0.001000	0.08648	0.501000	0.33797	-0.357000	0.07651	-1.082000	0.03101	-1.292000	0.01352	ATG	.	.	.	none		0.368	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		C	17164807	T	C	17164807	3	2	252	1	0	0	0	0	1	0	0	0	4053	1493	52	3	10539	3	CUBN	10	17164807	Missense_Mutation	SNP	T	TCGA-SX-A7SR-01A-12D-A35Z-10	11670371	17164807	118369940	39	15682											
TUBGCP2	10844	hgsc.bcm.edu	37	chr10	135095734	135095735	+	Missense_Mutation	DNP	GC	GC	AT																															ggaggccacgcaccttcctgGcgagctccttccgggcccgc																										TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr10:135095734_135095735GC>AT	ENST00000252936.3	-	15	2440_2441	c.2401_2402GC>AT	c.(2401-2403)GCc>ATc	p.A801I	TUBGCP2_ENST00000417178.2_Missense_Mutation_p.A671I|TUBGCP2_ENST00000543663.1_Missense_Mutation_p.A829I|TUBGCP2_ENST00000368563.2_Missense_Mutation_p.A801I|TUBGCP2_ENST00000368562.1_Missense_Mutation_p.A394I			Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2	801					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)		CACCTTCCTGGCGAGCTCCTTC	0.688																																					p.A829V|p.A829T		Atlas-SNP	.											.	TUBGCP2	79	.	0			c.C2486T|c.G2485A						PASS	.																																			SO:0001583	missense	10844	exon17			TTCCTGGCGAGCT|TCCTGGCGAGCTC	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.2401_2402delinsAT	chr10.hg19:g.135095734_135095735delinsAT	ENSP00000252936:p.Ala801Ile	75.0|73.0	0.0	.		54.0|53.0	17.0	.	NM_001256617	B4DM18|B7ZKL8|F5H4E0|F5H4L0|O43632|Q5VWX7	Missense_Mutation	SNP	ENST00000252936.3	hg19	CCDS7676.1																																																																																			.	.	.	none		0.688	TUBGCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051148.1			AT	135095735	GC	AT	135095734	3	1	252	1	0	0	0	0	1	0	0	0	16778	1203	42	2	318	2	TUBGCP2	10	135095734	Missense_Mutation	DNP	GC	TCGA-SX-A7SR-01A-12D-A35Z-10	117930927	135095734	439013	40	15683											
PIK3C2A	5286	hgsc.bcm.edu	37	chr11	17156501	17156501	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctaccagaatttgcatggAgtctgagaagatcataaatt	14	12	8	7	0	2	3	1	1	1	3	3	5	3	4	2	1	2	1	2	1	5	4			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr11:17156501A>G	ENST00000265970.7	-	10	1972	c.1973T>C	c.(1972-1974)cTc>cCc	p.L658P	PIK3C2A_ENST00000531428.1_Intron|PIK3C2A_ENST00000540361.1_Missense_Mutation_p.L278P	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	658					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						ATTTGCATGGAGTCTGAGAAG	0.378																																					p.L658P		Atlas-SNP	.											.	PIK3C2A	148	.	0			c.T1973C						PASS	.						140	138	139					11																	17156501		2200	4293	6493	SO:0001583	missense	5286	exon10			GCATGGAGTCTGA	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.1973T>C	chr11.hg19:g.17156501A>G	ENSP00000265970:p.Leu658Pro	95.0	0.0	.		89.0	32.0	.	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	hg19	CCDS7824.1	.	.	.	.	.	.	.	.	.	.	A	19.20	3.781930	0.70222	.	.	ENSG00000011405	ENST00000265970;ENST00000540361	T;T	0.68331	-0.32;0.14	5.59	4.48	0.54585	.	0.190360	0.47852	N	0.000211	T	0.79311	0.4424	M	0.72894	2.215	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.80246	-0.1462	10	0.72032	D	0.01	-2.1001	11.3443	0.49552	0.9293:0.0:0.0707:0.0	.	658	O00443	P3C2A_HUMAN	P	658;278	ENSP00000265970:L658P;ENSP00000438687:L278P	ENSP00000265970:L658P	L	-	2	0	PIK3C2A	17113077	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.637000	0.83313	0.987000	0.38709	0.477000	0.44152	CTC	.	.	.	none		0.378	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		G	17156501	A	G	17156501	3	3	252	1	0	0	0	0	1	0	0	0	11916	304	11	3	3179	3	PIK3C2A	11	17156501	Missense_Mutation	SNP	A	TCGA-SX-A7SR-01A-12D-A35Z-10		17156501	117850015	41	15684											
FJX1	24147	hgsc.bcm.edu	37	chr11	35641396	35641396	+	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	cgcttccccgagctggccgcCcttgcagacccccacgctca	5	6	9	21	4	1	1	1	0	0	1	2	2	2	1	6	1	2	4	6	1	0	2			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr11:35641396C>G	ENST00000317811.4	+	1	1662	c.1212C>G	c.(1210-1212)gcC>gcG	p.A404A	FJX1_ENST00000532914.1_3'UTR	NM_014344.3	NP_055159.2	Q86VR8	FJX1_HUMAN	four jointed box 1 (Drosophila)	404					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)				AGCTGGCCGCCCTTGCAGACC	0.711																																					p.A404A	Melanoma(161;10 2587 27165 47356)	Atlas-SNP	.											.	FJX1	32	.	0			c.C1212G						PASS	.						4	5	5					11																	35641396		1828	3908	5736	SO:0001819	synonymous_variant	24147	exon1			GGCCGCCCTTGCA	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.1212C>G	chr11.hg19:g.35641396C>G		142.0	0.0	.		112.0	28.0	.	NM_014344	B2RCA9|Q9UGK6	Silent	SNP	ENST00000317811.4	hg19	CCDS44570.1																																																																																			.	.	.	none		0.711	FJX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389078.1	NM_014344		G	35641396	C	G	35641396	2	3	252	1	0	0	0	0	0	0	0	1	5908	610	22	4		4	FJX1	11	35641396	Silent	SNP	C	TCGA-SX-A7SR-01A-12D-A35Z-10	18484895	35641396	99365120	42	15685											
CNTF	1270	hgsc.bcm.edu	37	chr11	58391563	58391569	+	Frame_Shift_Del	DEL	AGTGGCA	AGTGGCA	-																															gactctgcggatgggatgccAgtggcaagcactgatcagtg																										TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	AGTGGCA	AGTGGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr11:58391563_58391569delAGTGGCA	ENST00000361987.4	+	2	251_257	c.171_177delAGTGGCA	c.(169-177)ccagtggcafs	p.PVA57fs	ZFP91-CNTF_ENST00000389919.4_3'UTR	NM_000614.3	NP_000605.1	P26441	CNTF_HUMAN	ciliary neurotrophic factor	57					ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|growth (GO:0040007)|muscle organ morphogenesis (GO:0048644)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of photoreceptor cell differentiation (GO:0046533)|neuron development (GO:0048666)|positive regulation of cell proliferation (GO:0008284)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of retinal cell programmed cell death (GO:0046668)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor activity (GO:0008083)|interleukin-6 receptor binding (GO:0005138)			NS(1)|breast(1)|kidney(2)|large_intestine(4)|lung(1)|ovary(1)	10		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				ATGGGATGCCAGTGGCAAGCACTGATC	0.527																																					p.57_59del		Atlas-Indel,Pindel	.											.	CNTF	22	.	0			c.170_176del						PASS	.																																			SO:0001589	frameshift_variant	1270	exon2			.	BC068030	CCDS31554.1	11q12	2011-07-21			ENSG00000242689	ENSG00000242689			2169	protein-coding gene	gene with protein product		118945				1840538, 1714745	Standard	NM_000614		Approved	HCNTF	uc001nna.4	P26441	OTTHUMG00000137476	ENST00000361987.4:c.171_177delAGTGGCA	chr11.hg19:g.58391563_58391569delAGTGGCA	ENSP00000355370:p.Pro57fs	91.0	0.0	0		108.0	33.0	0.305556	NM_000614	B2RAB2	Frame_Shift_Del	DEL	ENST00000361987.4	hg19	CCDS31554.1																																																																																			.	.	.	none		0.527	CNTF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268673.1	NM_000614		-	58391569	AGTGGCA	-	58391563	7	5	252	1	0	1	0	1	0	0	0	0	3639	175	7	0	177	0	CNTF	11	58391563	Frame_Shift_Del	DEL	AGTGGCA	TCGA-SX-A7SR-01A-12D-A35Z-10	22750167	58391563	76614953	43	15686											
UCP3	7352	hgsc.bcm.edu	37	chr11	73715620	73715620	+	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	atagcattcctcatgatgttGggcaaagttcctgttaggaa	11	13	10	7	0	1	1	1	1	0	0	3	2	3	2	2	2	1	5	2	2	4	5			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr11:73715620G>T	ENST00000314032.4	-	5	1104	c.552C>A	c.(550-552)ccC>ccA	p.P184P	UCP3_ENST00000426995.2_Silent_p.P184P|UCP3_ENST00000545271.1_5'Flank|UCP3_ENST00000348534.4_Intron	NM_003356.3	NP_003347.1	P55916	UCP3_HUMAN	uncoupling protein 3 (mitochondrial, proton carrier)	184					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)					TCATGATGTTGGGCAAAGTTC	0.562																																					p.P184P		Atlas-SNP	.											.	UCP3	31	.	0			c.C552A						PASS	.						182	134	151					11																	73715620		2200	4293	6493	SO:0001819	synonymous_variant	7352	exon5			GATGTTGGGCAAA	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.552C>A	chr11.hg19:g.73715620G>T		103.0	0.0	.		63.0	14.0	.	NM_003356	O60475|Q96HL3	Silent	SNP	ENST00000314032.4	hg19	CCDS8229.1																																																																																			.	.	.	none		0.562	UCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398200.1	NM_003356		T	73715620	G	T	73715620	2	4	252	1	0	0	0	0	0	0	0	1	16944	1335	47	4		4	UCP3	11	73715620	Silent	SNP	G	TCGA-SX-A7SR-01A-12D-A35Z-10	15324057	73715620	61290896	44	15687											
PDE3A	5139	hgsc.bcm.edu	37	chr12	20803382	20803382	+	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	ctttatctctcaaataggtaAatgatgatgttggaatagat	14	15	8	4	0	2	3	1	2	1	1	3	4	2	4	0	2	0	2	0	2	7	6			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr12:20803382A>T	ENST00000359062.3	+	14	2813	c.2773A>T	c.(2773-2775)Aat>Tat	p.N925Y	PDE3A_ENST00000544307.1_3'UTR	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	925	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP-mediated signaling (GO:0019934)|diterpenoid metabolic process (GO:0016101)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)|negative regulation of vascular permeability (GO:0043116)|oocyte maturation (GO:0001556)|positive regulation of oocyte development (GO:0060282)|positive regulation of vascular permeability (GO:0043117)|regulation of meiosis (GO:0040020)|response to cAMP (GO:0051591)|response to drug (GO:0042493)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(7)|lung(29)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	58	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811)	CAAATAGGTAAATGATGATGT	0.284																																					p.N925Y		Atlas-SNP	.											.	PDE3A	184	.	0			c.A2773T						PASS	.						120	120	120					12																	20803382		2203	4300	6503	SO:0001583	missense	5139	exon14			TAGGTAAATGATG		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.2773A>T	chr12.hg19:g.20803382A>T	ENSP00000351957:p.Asn925Tyr	131.0	0.0	.		161.0	33.0	.	NM_000921	O60865|Q13348|Q17RD1	Missense_Mutation	SNP	ENST00000359062.3	hg19	CCDS31754.1	.	.	.	.	.	.	.	.	.	.	A	19.56	3.850442	0.71719	.	.	ENSG00000172572	ENST00000359062	T	0.77877	-1.13	5.96	5.96	0.96718	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.205141	0.52532	D	0.000063	D	0.88020	0.6325	M	0.77712	2.385	0.47183	D	0.999345	D	0.76494	0.999	D	0.71184	0.972	D	0.89336	0.3650	10	0.87932	D	0	.	16.4484	0.83959	1.0:0.0:0.0:0.0	.	925	Q14432	PDE3A_HUMAN	Y	925	ENSP00000351957:N925Y	ENSP00000351957:N925Y	N	+	1	0	PDE3A	20694649	1.000000	0.71417	0.985000	0.45067	0.899000	0.52679	6.909000	0.75735	2.285000	0.76669	0.533000	0.62120	AAT	.	.	.	none		0.284	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2			T	20803382	A	T	20803382	3	4	252	1	0	0	0	0	1	0	0	0	11644	14	1	5	2827	5	PDE3A	12	20803382	Missense_Mutation	SNP	A	TCGA-SX-A7SR-01A-12D-A35Z-10		20803382	113048513	45	15688											
KRT5	3852	hgsc.bcm.edu	37	chr12	52913749	52913749	+	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	cgagcccaaagccaccaccaGctccaccgccgaaaccaaat	14	2	6	19	3	0	0	0	0	0	0	1	2	1	0	8	0	4	1	8	0	3	0			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr12:52913749G>T	ENST00000252242.4	-	1	722	c.332C>A	c.(331-333)gCt>gAt	p.A111D		NM_000424.3	NP_000415.2	P13647	K2C5_HUMAN	keratin 5	111	Gly-rich.|Head.				cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|hemidesmosome assembly (GO:0031581)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)			endometrium(5)|kidney(1)|large_intestine(8)|lung(15)|prostate(4)|skin(2)	35				BRCA - Breast invasive adenocarcinoma(357;0.189)		gccaccaccagctccaccgcc	0.617																																					p.A111D		Atlas-SNP	.											.	KRT5	88	.	0			c.C332A						PASS	.						114	123	120					12																	52913749		2203	4300	6503	SO:0001583	missense	3852	exon1			CCACCAGCTCCAC		CCDS8830.1	12q13.13	2013-01-16	2008-08-01		ENSG00000186081	ENSG00000186081		"-", "Intermediate filaments type II, keratins (basic)"	6442	protein-coding gene	gene with protein product		148040	"epidermolysis bullosa simplex 2 Dowling-Meara/Kobner/Weber-Cockayne types", "keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types)"	EBS2		1713141, 16831889	Standard	NM_000424		Approved	KRT5A	uc001san.3	P13647	OTTHUMG00000169657	ENST00000252242.4:c.332C>A	chr12.hg19:g.52913749G>T	ENSP00000252242:p.Ala111Asp	95.0	0.0	.		120.0	30.0	.	NM_000424	Q6PI71|Q6UBJ0|Q8TA91	Missense_Mutation	SNP	ENST00000252242.4	hg19	CCDS8830.1	.	.	.	.	.	.	.	.	.	.	G	12.45	1.940206	0.34283	.	.	ENSG00000186081	ENST00000252242;ENST00000456000;ENST00000551275;ENST00000546577	D;T;T	0.95885	-3.84;-1.02;1.19	5.73	2.87	0.33458	.	0.273876	0.26153	N	0.026035	D	0.89945	0.6862	L	0.31476	0.935	0.28550	N	0.911671	B	0.27559	0.181	B	0.22880	0.042	T	0.82764	-0.0296	10	0.49607	T	0.09	.	8.3726	0.32423	0.1332:0.3506:0.5161:0.0	.	111	P13647	K2C5_HUMAN	D	111;76;76;111	ENSP00000252242:A111D;ENSP00000448041:A76D;ENSP00000449651:A111D	ENSP00000252242:A111D	A	-	2	0	KRT5	51200016	0.000000	0.05858	0.782000	0.31804	0.980000	0.70556	-0.269000	0.08596	0.323000	0.23307	0.655000	0.94253	GCT	.	.	.	none		0.617	KRT5-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405312.1			T	52913749	G	T	52913749	3	4	252	1	0	0	0	0	1	0	0	0	8486	971	34	4	1476	4	KRT5	12	52913749	Missense_Mutation	SNP	G	TCGA-SX-A7SR-01A-12D-A35Z-10	32110367	52913749	80938146	46	15689											
RBMS2	5939	hgsc.bcm.edu	37	chr12	56975006	56975007	+	Frame_Shift_Ins	INS	-	-	T																															tgtgaagccatcatcacccaINSctttaatggaaaatatatta																										TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr12:56975006_56975007insT	ENST00000262031.5	+	6	676_677	c.581_582insT	c.(580-585)cactttfs	p.F195fs	RBMS2_ENST00000542360.1_Frame_Shift_Ins_p.F50fs|RBMS2_ENST00000552247.2_Frame_Shift_Ins_p.F195fs|RBMS2_ENST00000550726.1_Frame_Shift_Ins_p.F70fs	NM_002898.3	NP_002889.1	Q15434	RBMS2_HUMAN	RNA binding motif, single stranded interacting protein 2	195	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				RNA processing (GO:0006396)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|large_intestine(2)|lung(8)|prostate(3)|skin(2)|urinary_tract(1)	18						ATCATCACCCACTTTAATGGAA	0.495																																					p.H194fs		Atlas-Indel,Pindel	.											.	RBMS2	29	.	0			c.581_582insT						PASS	.																																			SO:0001589	frameshift_variant	5939	exon6			.	D28483	CCDS8923.1	12q13.13	2013-02-12			ENSG00000076067	ENSG00000076067		"RNA binding motif (RRM) containing"	9909	protein-coding gene	gene with protein product		602387				8041632	Standard	NM_002898		Approved	SCR3	uc001sln.2	Q15434	OTTHUMG00000170488	Exception_encountered	chr12.hg19:g.56975006_56975007insT	ENSP00000262031:p.Phe195fs	101.0	0.0	0		110.0	59.0	0.536364	NM_002898		Frame_Shift_Ins	INS	ENST00000262031.5	hg19	CCDS8923.1																																																																																			.	.	.	none		0.495	RBMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409366.2	NM_002898		T	56975007	-	T	56975006	7	5	252	1	0	1	1	0	0	0	0	0	13162	159	6	0	603	0	RBMS2	12	56975006	Frame_Shift_Ins	INS	-	TCGA-SX-A7SR-01A-12D-A35Z-10	4061257	56975006	76876889	47	15690											
SDR9C7	121214	hgsc.bcm.edu	37	chr12	57324030	57324030	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttatgctgtcagagaaggcCtcaacgccaaacttggagac	12	8	10	11	1	2	2	2	0	0	2	2	4	2	2	2	2	3	1	2	2	4	2			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr12:57324030C>T	ENST00000293502.1	-	2	683	c.540G>A	c.(538-540)gaG>gaA	p.E180E		NM_148897.2	NP_683695.1	Q8NEX9	DR9C7_HUMAN	short chain dehydrogenase/reductase family 9C, member 7	180					oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	retinol dehydrogenase activity (GO:0004745)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|pancreas(1)	7						CAGAGAAGGCCTCAACGCCAA	0.547																																					p.E180E		Atlas-SNP	.											.	SDR9C7	31	.	0			c.G540A						PASS	.						128	126	126					12																	57324030		2203	4300	6503	SO:0001819	synonymous_variant	121214	exon2			GAAGGCCTCAACG	AY044434	CCDS8926.1	12q13.3	2014-09-04			ENSG00000170426	ENSG00000170426	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	29958	protein-coding gene	gene with protein product		609769				12234675, 19027726	Standard	NM_148897		Approved	SDR-O, RDHS	uc010sqw.2	Q8NEX9	OTTHUMG00000171004	ENST00000293502.1:c.540G>A	chr12.hg19:g.57324030C>T		92.0	0.0	.		111.0	44.0	.	NM_148897	B3KVB4	Silent	SNP	ENST00000293502.1	hg19	CCDS8926.1																																																																																			.	.	.	none		0.547	SDR9C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411211.1	NM_148897		T	57324030	C	T	57324030	2	4	252	1	0	0	0	0	0	0	0	1	13987	680	24	2		2	SDR9C7	12	57324030	Silent	SNP	C	TCGA-SX-A7SR-01A-12D-A35Z-10	349024	57324030	76527865	48	15691											
PAWR	5074	hgsc.bcm.edu	37	chr12	80083574	80083574	+	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	ccgcagcttcctcttctcgaTctgccccttgcctttcctgg	2	14	7	18	2	3	0	0	0	3	0	6	1	5	0	6	1	3	2	6	1	0	4			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr12:80083574T>A	ENST00000328827.4	-	2	823	c.451A>T	c.(451-453)Atc>Ttc	p.I151F	PAWR_ENST00000547571.1_5'UTR|RP11-530C5.1_ENST00000551995.1_lincRNA	NM_002583.2	NP_002574.2	Q96IZ0	PAWR_HUMAN	PRKC, apoptosis, WT1, regulator	151	Selective for apoptosis induction in cancer cells (SAC).				actin filament bundle assembly (GO:0051017)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|interleukin-2 biosynthetic process (GO:0042094)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of amyloid precursor protein biosynthetic process (GO:0042986)|positive regulation of apoptotic process (GO:0043065)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|enzyme binding (GO:0019899)|leucine zipper domain binding (GO:0043522)|transcription corepressor activity (GO:0003714)			NS(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						CTCTTCTCGATCTGCCCCTTG	0.726																																					p.I151F		Atlas-SNP	.											.	PAWR	14	.	0			c.A451T						PASS	.						12	12	12					12																	80083574		2199	4297	6496	SO:0001583	missense	5074	exon2			TCTCGATCTGCCC	U63809	CCDS31863.1	12q21.2	2013-03-07			ENSG00000177425	ENSG00000177425			8614	protein-coding gene	gene with protein product	"prostate apoptosis response-4"	601936				8943350, 9790775	Standard	NM_002583		Approved	par-4, PAR4	uc001syx.3	Q96IZ0	OTTHUMG00000170080	ENST00000328827.4:c.451A>T	chr12.hg19:g.80083574T>A	ENSP00000328088:p.Ile151Phe	86.0	0.0	.		83.0	20.0	.	NM_002583	O75796|Q6FHY9|Q8N700	Missense_Mutation	SNP	ENST00000328827.4	hg19	CCDS31863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	31|31	5.100151|5.100151	0.94197|0.94197	.|.	.|.	ENSG00000177425|ENSG00000177425	ENST00000551712|ENST00000328827	.|T	.|0.09630	.|2.96	3.6|3.6	3.6|3.6	0.41247|0.41247	.|.	.|0.059454	.|0.64402	.|D	.|0.000003	T|T	0.21962|0.21962	0.0529|0.0529	L|L	0.48642|0.48642	1.525|1.525	0.80722|0.80722	D|D	1|1	.|D	.|0.67145	.|0.996	.|D	.|0.64410	.|0.925	T|T	0.00926|0.00926	-1.1512|-1.1512	5|9	.|.	.|.	.|.	-3.2716|-3.2716	12.3682|12.3682	0.55240|0.55240	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|151	.|Q96IZ0	.|PAWR_HUMAN	V|F	96|151	.|ENSP00000328088:I151F	.|.	D|I	-|-	2|1	0|0	PAWR|PAWR	78607705|78607705	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	6.617000|6.617000	0.74210|0.74210	1.482000|1.482000	0.48325|0.48325	0.460000|0.460000	0.39030|0.39030	GAT|ATC	.	.	.	none		0.726	PAWR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407175.1	NM_002583		A	80083574	T	A	80083574	3	1	252	1	0	0	0	0	1	0	0	0	11484	1435	50	5	595	5	PAWR	12	80083574	Missense_Mutation	SNP	T	TCGA-SX-A7SR-01A-12D-A35Z-10	22759544	80083574	53768321	49	15692											
NUDT4	11163	hgsc.bcm.edu	37	chr12	93793130	93793130	+	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	tgtaaccgctgcacagacctCtgggttgccatctagtgtaa	9	11	10	11	1	2	1	0	0	2	1	2	1	2	1	3	1	3	5	3	1	3	4	rs142846389		TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr12:93793130C>A	ENST00000415493.2	+	5	945	c.518C>A	c.(517-519)tCt>tAt	p.S173Y	NUDT4_ENST00000549992.1_Missense_Mutation_p.S121Y|NUDT4_ENST00000548662.1_Missense_Mutation_p.S121Y|NUDT4_ENST00000337179.5_Missense_Mutation_p.S174Y|NUDT4_ENST00000547014.1_Missense_Mutation_p.S122Y	NM_019094.4	NP_061967.3	Q9NZJ9	NUDT4_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 4	173					calcium-mediated signaling (GO:0019722)|cyclic nucleotide metabolic process (GO:0009187)|cyclic-nucleotide-mediated signaling (GO:0019935)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|regulation of RNA export from nucleus (GO:0046831)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular (GO:0005622)	diphosphoinositol-polyphosphate diphosphatase activity (GO:0008486)|inositol diphosphate tetrakisphosphate diphosphatase activity (GO:0052840)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity (GO:0052846)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052847)|inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity (GO:0052843)|inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052848)|inositol-3-diphosphate-1,2,4,5,6-pentakisphosphate diphosphatase activity (GO:0052844)|inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity (GO:0052845)|metal ion binding (GO:0046872)|snoRNA binding (GO:0030515)			endometrium(2)|kidney(1)|lung(2)	5						GCACAGACCTCTGGGTTGCCA	0.498																																					p.S174Y		Atlas-SNP	.											.	NUDT4	6	.	0			c.C521A						PASS	.						111	119	117					12																	93793130		2203	4300	6503	SO:0001583	missense	11163	exon5			AGACCTCTGGGTT	AF067803	CCDS9044.1, CCDS44952.1, CCDS73504.1	12q21	2008-09-04			ENSG00000173598	ENSG00000173598		"Nudix motif containing"	8051	protein-coding gene	gene with protein product	"diphosphoinositol polyphosphate phosphohydrolase type 2"	609229				10777568, 11376937	Standard	XM_005268595		Approved	DIPP2, HDCMB47P, KIAA0487, DIPP2alpha, DIPP2beta	uc001tcm.3	Q9NZJ9	OTTHUMG00000170155	ENST00000415493.2:c.518C>A	chr12.hg19:g.93793130C>A	ENSP00000406612:p.Ser173Tyr	139.0	0.0	.		145.0	19.0	.	NM_199040	B7Z916|Q4AEJ6|Q53EZ2|Q68DD7|Q9NPC5|Q9NS30|Q9NZK0|Q9NZK1	Missense_Mutation	SNP	ENST00000415493.2	hg19	CCDS44952.1	.	.	.	.	.	.	.	.	.	.	C	14.36	2.511311	0.44660	.	.	ENSG00000173598	ENST00000337179;ENST00000415493;ENST00000549992;ENST00000548662;ENST00000547014	T;T	0.34859	1.34;1.34	5.53	5.53	0.82687	.	0.259165	0.46442	D	0.000298	T	0.29158	0.0725	L	0.27053	0.805	0.49582	D	0.999805	P;P	0.37276	0.589;0.454	B;B	0.31245	0.126;0.059	T	0.14671	-1.0464	10	0.87932	D	0	-30.8911	19.8241	0.96610	0.0:1.0:0.0:0.0	.	174;173	Q9NZJ9-2;Q9NZJ9	.;NUDT4_HUMAN	Y	174;173;121;121;122	ENSP00000338352:S174Y;ENSP00000406612:S173Y	ENSP00000338352:S174Y	S	+	2	0	NUDT4	92317261	1.000000	0.71417	0.996000	0.52242	0.160000	0.22226	6.247000	0.72411	2.758000	0.94735	0.655000	0.94253	TCT	.	C|1.000;T|0.000	.	alt		0.498	NUDT4-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000407702.1	NM_019094		A	93793130	C	A	93793130	3	1	252	1	0	0	0	0	1	0	0	0	10748	913	32	4	539	4	NUDT4	12	93793130	Missense_Mutation	SNP	C	TCGA-SX-A7SR-01A-12D-A35Z-10	13709556	93793130	40058765	50	15693											
METAP2	84101	hgsc.bcm.edu	37	chr12	95907668	95907668	+	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	0	0	0	0	0	0	0	0	aaagaagttgtcagcagaggAgatgactattaaacttagtc	16	10	10	5	0	1	4	1	1	0	3	2	5	1	4	0	1	2	2	0	1	6	4			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr12:95907668A>T	ENST00000258499.3	-	0	4022				METAP2_ENST00000261220.9_Silent_p.G452G|METAP2_ENST00000323666.5_Silent_p.G475G|METAP2_ENST00000551840.1_Silent_p.G474G|METAP2_ENST00000546753.1_Silent_p.G452G|METAP2_ENST00000550777.1_Silent_p.G439G	NM_001278393.1|NM_032147.2	NP_001265322.1|NP_115523.2	Q9H0E7	UBP44_HUMAN	ubiquitin specific peptidase 44						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						TCAGCAGAGGAGATGACTATT	0.378																																					p.G475G		Atlas-SNP	.											.	METAP2	28	.	0			c.A1425T						PASS	.						121	105	110					12																	95907668		2203	4300	6503	SO:0001628	intergenic_variant	10988	exon11			CAGAGGAGATGAC	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			chr12.hg19:g.95907668A>T		107.0	0.0	.		127.0	36.0	.	NM_006838	B2RDW3	Silent	SNP	ENST00000258499.3	hg19	CCDS9053.1																																																																																			.	.	.	none		0.378	USP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408312.1	NM_032147		T	95907668	A	T	95907668	1	4	252	0	1	0	0	0	0	0	0	0	9494	291	11	5		5	METAP2	12	95907668	IGR	SNP	A	TCGA-SX-A7SR-01A-12D-A35Z-10	2114538	95907668	37944227	51	15694											
ATXN2	6311	hgsc.bcm.edu	37	chr12	112036794	112036794	+	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	tgctgctgttgctgctgctgCtgctgctgctgctgctgctg	0	15	14	12	0	0	0	0	0	0	0	0	0	0	0	0	0	12	13	0	0	0	1			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr12:112036794C>T	ENST00000377617.3	-	1	686	c.525G>A	c.(523-525)caG>caA	p.Q175Q	ATXN2_ENST00000542287.2_Intron|ATXN2_ENST00000550104.1_Silent_p.Q175Q|ATXN2_ENST00000389153.4_5'Flank|ATXN2_ENST00000608853.1_Silent_p.Q15Q|RP11-686G8.2_ENST00000547021.1_RNA|ATXN2_ENST00000549455.1_5'UTR|ATXN2_ENST00000535949.1_Intron	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	175	Poly-Gln.				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						gctgctgctgctgctgctgct	0.731																																					p.Q175Q		Atlas-SNP	.											.	ATXN2	99	.	0			c.G525A						PASS	.						1	1	1					12																	112036794		704	1738	2442	SO:0001819	synonymous_variant	6311	exon1			CTGCTGCTGCTGC	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.525G>A	chr12.hg19:g.112036794C>T		15.0	0.0	.		20.0	7.0	.	NM_002973	A6NLD4|Q6ZQZ7|Q99493	Silent	SNP	ENST00000377617.3	hg19	CCDS31902.1																																																																																			.	.	.	none		0.731	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973		T	112036794	C	T	112036794	2	4	252	1	0	0	0	0	0	0	0	1	1211	796	28	2		2	ATXN2	12	112036794	Silent	SNP	C	TCGA-SX-A7SR-01A-12D-A35Z-10	16129126	112036794	21815101	52	15695											
ANAPC5	51433	hgsc.bcm.edu	37	chr12	121747554	121747554	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgctgaagccacctggcacTtggccactaagaacatggca	11	7	10	13	0	0	2	0	1	0	1	0	2	0	2	3	3	3	3	3	3	3	2			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr12:121747554T>C	ENST00000261819.3	-	16	2127	c.2006A>G	c.(2005-2007)aAg>aGg	p.K669R	ANAPC5_ENST00000344395.4_Missense_Mutation_p.K557R|ANAPC5_ENST00000441917.2_Missense_Mutation_p.K557R|ANAPC5_ENST00000541887.1_Missense_Mutation_p.K656R|ANAPC5_ENST00000535482.1_Missense_Mutation_p.K335R|ANAPC5_ENST00000544314.1_5'UTR	NM_016237.4	NP_057321.2	Q9UJX4	APC5_HUMAN	anaphase promoting complex subunit 5	669					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)			breast(6)|endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(3)	31	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CACCTGGCACTTGGCCACTAA	0.522																																					p.K669R		Atlas-SNP	.											.	ANAPC5	60	.	0			c.A2006G						PASS	.						86	78	81					12																	121747554		2203	4300	6503	SO:0001583	missense	51433	exon16			TGGCACTTGGCCA	AF191339	CCDS9220.1, CCDS45000.1	12q24.31	2014-08-12			ENSG00000089053	ENSG00000089053		"Anaphase promoting complex subunits"	15713	protein-coding gene	gene with protein product		606948				9469815	Standard	NM_016237		Approved	APC5	uc001uag.3	Q9UJX4	OTTHUMG00000169157	ENST00000261819.3:c.2006A>G	chr12.hg19:g.121747554T>C	ENSP00000261819:p.Lys669Arg	100.0	0.0	.		115.0	49.0	.	NM_016237	E9PFB2|Q8N4H7|Q9BQD4	Missense_Mutation	SNP	ENST00000261819.3	hg19	CCDS9220.1	.	.	.	.	.	.	.	.	.	.	T	14.89	2.669258	0.47677	.	.	ENSG00000089053	ENST00000441917;ENST00000541887;ENST00000261819;ENST00000535482;ENST00000544314;ENST00000344395	T;T;T;T;T	0.75589	-0.95;-0.95;-0.95;-0.95;-0.95	5.75	5.75	0.90469	Tetratricopeptide-like helical (1);	0.050321	0.85682	D	0.000000	T	0.65943	0.2740	L	0.32530	0.975	0.80722	D	1	B;B;B	0.20368	0.044;0.002;0.005	B;B;B	0.22753	0.041;0.002;0.003	T	0.61043	-0.7142	10	0.32370	T	0.25	.	15.2318	0.73395	0.0:0.0:0.0:1.0	.	335;557;669	F5H0N1;E9PFB2;Q9UJX4	.;.;APC5_HUMAN	R	557;656;669;335;271;557	ENSP00000415061:K557R;ENSP00000439875:K656R;ENSP00000261819:K669R;ENSP00000438754:K335R;ENSP00000343787:K557R	ENSP00000261819:K669R	K	-	2	0	ANAPC5	120231937	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.267000	0.65530	2.189000	0.69895	0.454000	0.30748	AAG	.	.	.	none		0.522	ANAPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402582.1			C	121747554	T	C	121747554	3	2	252	1	0	0	0	0	1	0	0	0	605	1609	56	3	269	3	ANAPC5	12	121747554	Missense_Mutation	SNP	T	TCGA-SX-A7SR-01A-12D-A35Z-10	9710760	121747554	12104341	53	15696											
NEK3	4752	hgsc.bcm.edu	37	chr13	52730287	52730287	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaaagagctctgccgaaggAgccctccccaatcattctca	12	7	7	15	1	3	1	2	0	2	1	5	3	4	2	4	1	3	1	4	1	4	1			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr13:52730287A>G	ENST00000400357.2	-	1	1333	c.40T>C	c.(40-42)Tcc>Ccc	p.S14P	NEK3_ENST00000339406.3_Missense_Mutation_p.S14P|NEK3_ENST00000452082.2_Missense_Mutation_p.S35P|NEK3_ENST00000378101.2_Missense_Mutation_p.S14P			P51956	NEK3_HUMAN	NIMA-related kinase 3	14	Interaction with VAV2.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.			S -> F (in Ref. 1; BAC15599). {ECO:0000305}.	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)		CTGCCGAAGGAGCCCTCCCCA	0.502																																					p.S14P		Atlas-SNP	.											.	NEK3	41	.	0			c.T40C						PASS	.						68	64	65					13																	52730287		1924	4148	6072	SO:0001583	missense	4752	exon2			CGAAGGAGCCCTC	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.40T>C	chr13.hg19:g.52730287A>G	ENSP00000383210:p.Ser14Pro	76.0	0.0	.		83.0	28.0	.	NM_002498	A8K2J4|Q5TAP2|Q8J023|Q8WUN5	Missense_Mutation	SNP	ENST00000400357.2	hg19	CCDS53871.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.636807	0.87760	.	.	ENSG00000136098	ENST00000339406;ENST00000378101;ENST00000400357;ENST00000452082;ENST00000547422;ENST00000550841	T;T;T;T;T;T	0.54071	1.65;1.65;1.65;1.65;0.59;1.9	5.91	4.7	0.59300	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.100564	0.64402	D	0.000001	T	0.72471	0.3464	.	.	.	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.97110	0.995;1.0;0.999	T	0.75695	-0.3228	9	0.87932	D	0	.	12.2965	0.54849	0.8729:0.0:0.0:0.127	.	14;35;14	P51956;Q6ZN64;F8VS47	NEK3_HUMAN;.;.	P	14;14;14;35;14;14	ENSP00000339429:S14P;ENSP00000367341:S14P;ENSP00000383210:S14P;ENSP00000404197:S35P;ENSP00000448716:S14P;ENSP00000449679:S14P	ENSP00000448782:S14P	S	-	1	0	NEK3	51628288	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.283000	0.72646	1.018000	0.39521	0.533000	0.62120	TCC	.	.	.	none		0.502	NEK3-002	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045047.3			G	52730287	A	G	52730287	3	3	252	1	0	0	0	0	1	0	0	0	10332	304	11	3	1540	3	NEK3	13	52730287	Missense_Mutation	SNP	A	TCGA-SX-A7SR-01A-12D-A35Z-10		52730287	62439591	54	15697											
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77853046	77853046	+	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	acaaaggccaacctcaataaTctatttaaaaggaaaaaata	22	8	4	7	0	2	0	1	0	1	0	2	1	2	1	2	2	1	0	2	2	11	5			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr13:77853046T>G	ENST00000544440.2	-	4	498	c.481A>C	c.(481-483)Att>Ctt	p.I161L	MYCBP2_ENST00000360084.5_5'UTR|MYCBP2_ENST00000407578.2_Splice_Site_p.I199L|MYCBP2_ENST00000357337.6_Splice_Site_p.I161L					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)		ACCTCAATAATCTATTTAAAA	0.358																																					p.I199L		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.A595C						PASS	.						29	32	31					13																	77853046		2203	4299	6502	SO:0001630	splice_region_variant	23077	exon4			CAATAATCTATTT	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.481-1A>C	chr13.hg19:g.77853046T>G		119.0	0.0	.		120.0	42.0	.	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	hg19		.	.	.	.	.	.	.	.	.	.	T	18.82	3.704169	0.68615	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	T;T;T	0.33654	1.41;1.4;1.41	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.49864	0.1582	L	0.58810	1.83	0.80722	D	1	P	0.35745	0.518	P	0.47827	0.558	T	0.51325	-0.8720	10	0.72032	D	0.01	.	16.0351	0.80621	0.0:0.0:0.0:1.0	.	161	O75592	MYCB2_HUMAN	L	161;199;161	ENSP00000349892:I161L;ENSP00000384288:I199L;ENSP00000444596:I161L	ENSP00000349892:I161L	I	-	1	0	MYCBP2	76751047	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	8.040000	0.89188	2.186000	0.69663	0.533000	0.62120	ATT	.	.	.	none		0.358	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057	Missense_Mutation	G	77853046	T	G	77853046	5	3	252	1	0	0	0	0	0	0	1	0	10025	1449	50	5	13761	5	MYCBP2	13	77853046	Splice_Site	SNP	T	TCGA-SX-A7SR-01A-12D-A35Z-10	25122759	77853046	37316832	55	15698											
TEP1	7011	hgsc.bcm.edu	37	chr14	20839416	20839416	+	Frame_Shift_Del	DEL	A	A	-																															ggatccttgggctgcaggacAaatatgccatactccttgtg																										TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr14:20839416delA	ENST00000262715.5	-	51	7318	c.7278delT	c.(7276-7278)tttfs	p.F2426fs	TEP1_ENST00000556935.1_Frame_Shift_Del_p.F2318fs	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	2426					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)		GCTGCAGGACAAATATGCCAT	0.423																																					p.V2427fs		Atlas-Indel,Pindel	.											.	TEP1	224	.	0			c.7279delG						PASS	.						187	174	178					14																	20839416		2203	4300	6503	SO:0001589	frameshift_variant	7011	exon51			.		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.7278delT	chr14.hg19:g.20839416delA	ENSP00000262715:p.Phe2426fs	174.0	0.0	0		113.0	32.0	0.283186	NM_007110	A0AUV9	Frame_Shift_Del	DEL	ENST00000262715.5	hg19	CCDS9548.1																																																																																			.	.	.	none		0.423	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		-	20839416	A	-	20839416	7	5	252	1	0	1	0	1	0	0	0	0	15771	127	5	0	625	0	TEP1	14	20839416	Frame_Shift_Del	DEL	A	TCGA-SX-A7SR-01A-12D-A35Z-10		20839416	86510124	56	15699											
ATL1	51062	hgsc.bcm.edu	37	chr14	51081222	51081222	+	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	aatccaaactttgatggaaaAttgaaaggtttgtgtctttt	13	16	8	4	0	1	2	0	2	1	0	2	3	2	3	1	2	1	1	1	2	5	5			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr14:51081222A>T	ENST00000358385.6	+	8	1096	c.855A>T	c.(853-855)aaA>aaT	p.K285N	ATL1_ENST00000354525.4_Missense_Mutation_p.K285N|ATL1_ENST00000441560.2_Missense_Mutation_p.K285N|ATL1_ENST00000357032.3_Missense_Mutation_p.K285N	NM_015915.4	NP_056999.2	Q8WXF7	ATLA1_HUMAN	atlastin GTPase 1	285	GB1/RHD3-type G.				axonogenesis (GO:0007409)|cell death (GO:0008219)|endoplasmic reticulum organization (GO:0007029)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi cis cisterna (GO:0000137)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(2)|large_intestine(4)|liver(1)|lung(6)|ovary(1)|skin(3)	18						TTGATGGAAAATTGAAAGGTT	0.338																																					p.K285N		Atlas-SNP	.											.	ATL1	46	.	0			c.A855T						PASS	.						94	85	88					14																	51081222		2203	4300	6503	SO:0001583	missense	51062	exon8			TGGAAAATTGAAA	AF131801	CCDS9700.1, CCDS32077.1	14q21.3	2014-09-17	2008-09-17	2008-09-17	ENSG00000198513	ENSG00000198513			11231	protein-coding gene	gene with protein product	"atlastin"	606439	"spastic paraplegia 3A (autosomal dominant)"	SPG3, SPG3A		8252041, 7825576	Standard	NM_015915		Approved	FSP1, AD-FSP	uc001wyd.4	Q8WXF7	OTTHUMG00000140297	ENST00000358385.6:c.855A>T	chr14.hg19:g.51081222A>T	ENSP00000351155:p.Lys285Asn	136.0	0.0	.		131.0	43.0	.	NM_015915	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Missense_Mutation	SNP	ENST00000358385.6	hg19	CCDS9700.1	.	.	.	.	.	.	.	.	.	.	A	6.428	0.447080	0.12223	.	.	ENSG00000198513	ENST00000441560;ENST00000358385;ENST00000357032;ENST00000354525	D;D;D;D	0.88896	-2.44;-2.44;-2.44;-2.44	5.63	3.28	0.37604	Guanylate-binding protein, N-terminal (1);	0.041939	0.85682	D	0.000000	T	0.81039	0.4740	L	0.29908	0.895	0.43364	D	0.995448	B;B	0.23806	0.068;0.091	B;B	0.20767	0.031;0.018	T	0.73161	-0.4070	10	0.44086	T	0.13	-19.0005	9.245	0.37520	0.7855:0.0:0.2145:0.0	.	285;285	Q8WXF7;G5E9T1	ATLA1_HUMAN;.	N	285	ENSP00000413675:K285N;ENSP00000351155:K285N;ENSP00000349534:K285N;ENSP00000346522:K285N	ENSP00000346522:K285N	K	+	3	2	ATL1	50150972	1.000000	0.71417	0.761000	0.31378	0.056000	0.15407	1.929000	0.40114	0.502000	0.28037	0.460000	0.39030	AAA	.	.	.	none		0.338	ATL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276884.2			T	51081222	A	T	51081222	3	4	252	1	0	0	0	0	1	0	0	0	1106	98	4	5	885	5	ATL1	14	51081222	Missense_Mutation	SNP	A	TCGA-SX-A7SR-01A-12D-A35Z-10	30241806	51081222	56268318	57	15700											
GNPNAT1	64841	hgsc.bcm.edu	37	chr14	53248584	53248584	+	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	ctagagtcacatcttctacaActgtaacataataatcccca	15	11	3	12	0	3	1	1	0	2	1	4	1	4	1	2	0	3	1	2	0	6	6			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr14:53248584A>T	ENST00000216410.3	-	4	450	c.263T>A	c.(262-264)gTt>gAt	p.V88D	GNPNAT1_ENST00000554230.1_Missense_Mutation_p.V17D	NM_198066.3	NP_932332.1	Q96EK6	GNA1_HUMAN	glucosamine-phosphate N-acetyltransferase 1	88	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|glucosamine metabolic process (GO:0006041)|liver development (GO:0001889)|N-acetylglucosamine metabolic process (GO:0006044)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|membrane (GO:0016020)	glucosamine 6-phosphate N-acetyltransferase activity (GO:0004343)|monosaccharide binding (GO:0048029)	p.K80fs*17(1)		liver(1)|lung(1)|prostate(1)|skin(1)	4	Breast(41;0.176)					ATCTTCTACAACTGTAACATA	0.353																																					p.V88D		Atlas-SNP	.											.	GNPNAT1	14	.	1	Deletion - Frameshift(1)	liver(1)	c.T263A						PASS	.						98	99	99					14																	53248584		2203	4300	6503	SO:0001583	missense	64841	exon4			TCTACAACTGTAA	AK001469	CCDS9712.1	14q22.1	2011-11-16			ENSG00000100522	ENSG00000100522	2.3.1.4		19980	protein-coding gene	gene with protein product							Standard	NM_198066		Approved	Gpnat1, FLJ10607	uc001xab.3	Q96EK6	OTTHUMG00000152334	ENST00000216410.3:c.263T>A	chr14.hg19:g.53248584A>T	ENSP00000216410:p.Val88Asp	74.0	0.0	.		87.0	29.0	.	NM_198066		Missense_Mutation	SNP	ENST00000216410.3	hg19	CCDS9712.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.651373	0.88056	.	.	ENSG00000100522	ENST00000216410;ENST00000554230;ENST00000557604	.	.	.	5.52	5.52	0.82312	GCN5-related N-acetyltransferase (GNAT) domain (1);Acyl-CoA N-acyltransferase (2);	0.000000	0.85682	D	0.000000	D	0.87192	0.6116	H	0.95611	3.695	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.91052	0.4879	9	0.87932	D	0	-13.8082	15.9507	0.79835	1.0:0.0:0.0:0.0	.	88	Q96EK6	GNA1_HUMAN	D	88;17;88	.	ENSP00000216410:V88D	V	-	2	0	GNPNAT1	52318334	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.877000	0.92386	2.232000	0.73038	0.528000	0.53228	GTT	.	.	.	none		0.353	GNPNAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276898.1			T	53248584	A	T	53248584	3	4	252	1	0	0	0	0	1	0	0	0	6551	43	2	5	303	5	GNPNAT1	14	53248584	Missense_Mutation	SNP	A	TCGA-SX-A7SR-01A-12D-A35Z-10	2167362	53248584	54100956	58	15701											
PTPN21	11099	hgsc.bcm.edu	37	chr14	88945296	88945296	+	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	gagcccttccacgatgttctTcttcccagagagaaggtccg	8	10	10	13	2	2	2	0	0	2	2	5	5	5	2	4	1	1	1	4	1	1	4			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr14:88945296T>A	ENST00000556564.1	-	13	2763	c.2479A>T	c.(2479-2481)Aag>Tag	p.K827*	PTPN21_ENST00000328736.3_Nonsense_Mutation_p.K827*	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	827					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						ACGATGTTCTTCTTCCCAGAG	0.652																																					p.K827X		Atlas-SNP	.											.	PTPN21	113	.	0			c.A2479T						PASS	.						44	51	48					14																	88945296		2203	4300	6503	SO:0001587	stop_gained	11099	exon13			TGTTCTTCTTCCC	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.2479A>T	chr14.hg19:g.88945296T>A	ENSP00000452414:p.Lys827*	87.0	0.0	.		67.0	16.0	.	NM_007039		Nonsense_Mutation	SNP	ENST00000556564.1	hg19	CCDS9884.1	.	.	.	.	.	.	.	.	.	.	T	40	8.015674	0.98610	.	.	ENSG00000070778	ENST00000328736;ENST00000556564	.	.	.	5.42	5.42	0.78866	.	0.292618	0.36591	N	0.002511	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.4652	0.75394	0.0:0.0:0.0:1.0	.	.	.	.	X	827	.	ENSP00000330276:K827X	K	-	1	0	PTPN21	88015049	1.000000	0.71417	0.861000	0.33841	0.222000	0.24845	4.961000	0.63681	2.057000	0.61298	0.460000	0.39030	AAG	.	.	.	none		0.652	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1			A	88945296	T	A	88945296	4	1	252	1	0	0	0	0	0	1	0	0	12799	1792	62	5	1073	5	PTPN21	14	88945296	Nonsense_Mutation	SNP	T	TCGA-SX-A7SR-01A-12D-A35Z-10	35696712	88945296	18404244	59	15702											
MTA1	9112	hgsc.bcm.edu	37	chr14	105930891	105930891	+	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	tggagagaggccaggaccaaAccgcagtaacatggtaaggg	14	4	15	8	1	0	1	0	0	0	1	0	4	0	3	3	5	2	3	3	5	3	2			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr14:105930891A>T	ENST00000331320.7	+	14	1545	c.1331A>T	c.(1330-1332)aAc>aTc	p.N444I	MTA1_ENST00000435036.2_5'UTR|MTA1_ENST00000406191.1_Missense_Mutation_p.N444I|MTA1_ENST00000405646.1_Missense_Mutation_p.N427I	NM_001203258.1|NM_004689.3	NP_001190187.1|NP_004680.2	Q13330	MTA1_HUMAN	metastasis associated 1	444					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)		CCAGGACCAAACCGCAGTAAC	0.597																																					p.N444I		Atlas-SNP	.											.	MTA1	61	.	0			c.A1331T						PASS	.						52	53	53					14																	105930891		2202	4300	6502	SO:0001583	missense	9112	exon14			GACCAAACCGCAG	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.1331A>T	chr14.hg19:g.105930891A>T	ENSP00000333633:p.Asn444Ile	117.0	0.0	.		76.0	27.0	.	NM_004689	A5PLK4|Q86SW2|Q8NFI8|Q96GI8	Missense_Mutation	SNP	ENST00000331320.7	hg19	CCDS32169.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.561353	0.86335	.	.	ENSG00000182979	ENST00000414153;ENST00000331320;ENST00000406191;ENST00000405646;ENST00000434050;ENST00000550551	T;T;T;T	0.32515	1.46;1.46;1.45;1.45	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.50718	0.1632	.	.	.	0.80722	D	1	D;P	0.76494	0.999;0.527	D;B	0.67103	0.949;0.157	T	0.47156	-0.9139	9	0.34782	T	0.22	-41.8187	13.862	0.63566	1.0:0.0:0.0:0.0	.	236;444	Q59FW1;Q13330	.;MTA1_HUMAN	I	353;444;444;427;236;33	ENSP00000333633:N444I;ENSP00000385702:N444I;ENSP00000384180:N427I;ENSP00000394106:N236I	ENSP00000333633:N444I	N	+	2	0	MTA1	105001936	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.331000	0.59273	1.978000	0.57642	0.379000	0.24179	AAC	.	.	.	none		0.597	MTA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317849.15			T	105930891	A	T	105930891	3	4	252	1	0	0	0	0	1	0	0	0	9915	43	2	5	1385	5	MTA1	14	105930891	Missense_Mutation	SNP	A	TCGA-SX-A7SR-01A-12D-A35Z-10	16985595	105930891	1418649	60	15703											
TEX9	374618	hgsc.bcm.edu	37	chr15	56686971	56686972	+	Frame_Shift_Del	DEL	TT	TT	-																															agtagaaaaatacaaaactcTtttcgaagaagcaaacaaaa																										TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr15:56686971_56686972delTT	ENST00000352903.2	+	9	791_792	c.767_768delTT	c.(766-768)cttfs	p.L256fs	TEX9_ENST00000558083.2_Frame_Shift_Del_p.L181fs|TEX9_ENST00000560582.1_Frame_Shift_Del_p.L12fs|RP11-48G14.2_ENST00000564401.1_lincRNA|TEX9_ENST00000561221.2_Frame_Shift_Del_p.L256fs|TEX9_ENST00000537232.1_Frame_Shift_Del_p.L181fs	NM_198524.1	NP_940926.1	Q8N6V9	TEX9_HUMAN	testis expressed 9	256										cervix(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	14				all cancers(107;0.0394)|GBM - Glioblastoma multiforme(80;0.056)		TACAAAACTCTTTTCGAAGAAG	0.307																																					p.256_256del		Atlas-Indel,Pindel	.											.	TEX9	29	.	0			c.766_767del						PASS	.																																			SO:0001589	frameshift_variant	374618	exon9			.	BC028119	CCDS10157.1, CCDS66776.1	15q21.3	2007-03-13	2007-03-13		ENSG00000151575	ENSG00000151575			29585	protein-coding gene	gene with protein product			"testis expressed sequence 9"				Standard	XM_005254361		Approved		uc002adp.3	Q8N6V9	OTTHUMG00000132035	ENST00000352903.2:c.767_768delTT	chr15.hg19:g.56686973_56686974delTT	ENSP00000342169:p.Leu256fs	535.0	0.0	0		447.0	161.0	0.360179	NM_198524	B4DH73	Frame_Shift_Del	DEL	ENST00000352903.2	hg19	CCDS10157.1																																																																																			.	.	.	none		0.307	TEX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255048.2	NM_198524		-	56686972	TT	-	56686971	7	5	252	1	0	1	0	1	0	0	0	0	15796	1609	56	0	801	0	TEX9	15	56686971	Frame_Shift_Del	DEL	TT	TCGA-SX-A7SR-01A-12D-A35Z-10		56686971	45844421	61	15704											
RASGRF1	5923	hgsc.bcm.edu	37	chr15	79339110	79339110	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcaggaagatgctgctgaCgtcgtcgtgtgtgatgggag	7	11	17	6	3	1	3	1	2	0	1	3	5	1	5	0	2	2	3	0	2	1	1			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr15:79339110C>T	ENST00000419573.3	-	5	1130	c.856G>A	c.(856-858)Gtc>Atc	p.V286I	RASGRF1_ENST00000560334.1_5'UTR|RASGRF1_ENST00000558480.2_Missense_Mutation_p.V286I	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	286	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						ATGCTGCTGACGTCGTCGTGT	0.577																																					p.V286I		Atlas-SNP	.											.	RASGRF1	168	.	0			c.G856A						PASS	.						193	152	166					15																	79339110		2196	4293	6489	SO:0001583	missense	5923	exon5			TGCTGACGTCGTC	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.856G>A	chr15.hg19:g.79339110C>T	ENSP00000405963:p.Val286Ile	107.0	0.0	.		66.0	20.0	.	NM_001145648	F8VPA5|H0YKF2|J3KQP9|Q16027	Missense_Mutation	SNP	ENST00000419573.3	hg19	CCDS10309.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.092158	0.76756	.	.	ENSG00000058335	ENST00000419573;ENST00000394741	T	0.60797	0.16	4.03	4.03	0.46877	Dbl homology (DH) domain (5);	0.083759	0.48767	D	0.000176	T	0.45196	0.1330	N	0.20328	0.56	0.80722	D	1	P;P;P;P	0.44776	0.843;0.843;0.743;0.698	B;B;B;B	0.44108	0.408;0.441;0.441;0.314	T	0.39143	-0.9628	10	0.30078	T	0.28	.	13.7003	0.62604	0.0:1.0:0.0:0.0	.	286;286;286;286	A8K270;Q8IUU5;Q13972;F8VPA5	.;.;RGRF1_HUMAN;.	I	286	ENSP00000405963:V286I	ENSP00000378224:V286I	V	-	1	0	RASGRF1	77126165	1.000000	0.71417	0.964000	0.40570	0.736000	0.42039	7.434000	0.80377	2.072000	0.62099	0.655000	0.94253	GTC	.	.	.	none		0.577	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891		T	79339110	C	T	79339110	3	4	252	1	0	0	0	0	1	0	0	0	13085	536	19	1	3061	1	RASGRF1	15	79339110	Missense_Mutation	SNP	C	TCGA-SX-A7SR-01A-12D-A35Z-10	22652139	79339110	23192282	62	15705											
SPATA8	145946	hgsc.bcm.edu	37	chr15	97328262	97328262	+	Frame_Shift_Del	DEL	A	A	-																															cggaaggatccaaagggttcAaaggcgaagggtgccatctg																										TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr15:97328262delA	ENST00000328504.3	+	3	500	c.233delA	c.(232-234)caafs	p.Q78fs	SPATA8_ENST00000558553.1_Frame_Shift_Del_p.S37fs|SPATA8-AS1_ENST00000558722.1_RNA	NM_173499.3	NP_775770.1	Q6RVD6	SPAT8_HUMAN	spermatogenesis associated 8	78										large_intestine(4)|lung(8)|ovary(1)|skin(3)	16	Melanoma(26;0.0142)|Lung NSC(78;0.041)|all_lung(78;0.0468)		OV - Ovarian serous cystadenocarcinoma(32;0.0718)			CAAAGGGTTCAAAGGCGAAGG	0.443																																					p.Q78fs		Atlas-Indel,Pindel	.											.	SPATA8	42	.	0			c.232delC						PASS	.						159	147	151					15																	97328262		2197	4298	6495	SO:0001589	frameshift_variant	145946	exon3			.	AY489187	CCDS10376.1	15q26	2008-02-05			ENSG00000185594	ENSG00000185594			28676	protein-coding gene	gene with protein product		613948					Standard	NM_173499		Approved	MGC44294	uc002bue.3	Q6RVD6	OTTHUMG00000149847	ENST00000328504.3:c.233delA	chr15.hg19:g.97328262delA	ENSP00000328149:p.Gln78fs	66.0	0.0	0		43.0	15.0	0.348837	NM_173499	Q2KJ07	Frame_Shift_Del	DEL	ENST00000328504.3	hg19	CCDS10376.1																																																																																			.	.	.	none		0.443	SPATA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313533.1	NM_173499		-	97328262	A	-	97328262	7	5	252	1	0	1	0	1	0	0	0	0	15027	130	5	0	243	0	SPATA8	15	97328262	Frame_Shift_Del	DEL	A	TCGA-SX-A7SR-01A-12D-A35Z-10	17989152	97328262	5203130	63	15706											
LASS3	204219	hgsc.bcm.edu	37	chr15	100943017	100943018	+	Frame_Shift_Ins	INS	-	-	T																															tggtagcctcttcttcttccINStcttcctcttcctcttcata																								rs541833197	byFrequency	TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr15:100943017_100943018insT	ENST00000394113.1	-	14	1742_1743	c.1052_1053insA	c.(1051-1053)gagfs	p.E351fs	RP11-168G16.2_ENST00000560718.1_RNA|RP11-168G16.2_ENST00000560643.1_RNA|CERS3_ENST00000284382.4_Frame_Shift_Ins_p.E351fs|CERS3_ENST00000560944.1_5'UTR|CERS3_ENST00000538112.2_Frame_Shift_Ins_p.E351fs			Q8IU89	CERS3_HUMAN	ceramide synthase 3	351	Poly-Glu.				ceramide biosynthetic process (GO:0046513)|keratinocyte differentiation (GO:0030216)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)	p.E351E(1)									cttcttcttcctcttcctcttc	0.485																																					p.E351fs		Atlas-INDEL	.											LASS3,colon,carcinoma,0,1	.	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.1053_1054insA						PASS	.																																			SO:0001589	frameshift_variant	204219	exon13			.		CCDS10384.1	15q26.3	2012-11-19	2011-07-08	2011-07-08	ENSG00000154227	ENSG00000154227		"Homeoboxes / CERS class"	23752	protein-coding gene	gene with protein product		615276	"LAG1 longevity assurance homolog 3 (S. cerevisiae)", "LAG1 homolog, ceramide synthase 3"	LASS3			Standard	NM_178842		Approved	MGC27091	uc002bwb.3	Q8IU89	OTTHUMG00000172568	ENST00000394113.1:c.1053dupA	chr15.hg19:g.100943018_100943018dupT	ENSP00000377672:p.Glu351fs	58.0	0.0	0		67.0	25.0	0.373134	NM_178842	Q8NE64|Q8NEN6	Frame_Shift_Ins	INS	ENST00000394113.1	hg19	CCDS10384.1																																																																																			.	.	.	none		0.485	CERS3-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313594.4	NM_178842		T	100943018	-	T	100943017	7	5	252	1	0	1	1	0	0	0	0	0	8647	680	24	0	102	0	LASS3	15	100943017	Frame_Shift_Ins	INS	-	TCGA-SX-A7SR-01A-12D-A35Z-10	3614755	100943017	1588375	64	15707											
LRRK1	79705	hgsc.bcm.edu	37	chr15	101550745	101550745	+	Frame_Shift_Del	DEL	A	A	-																															cttcaaaaactgacagcttcAaaaaattgtttagaaaaatt																										TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr15:101550745delA	ENST00000388948.3	+	8	1439	c.1080delA	c.(1078-1080)tcafs	p.S360fs	LRRK1_ENST00000284395.5_Frame_Shift_Del_p.S357fs	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)			TGACAGCTTCAAAAAATTGTT	0.368																																					p.S360X		Atlas-Indel,Pindel	.											.	LRRK1	310	.	0			c.1079delC						PASS	.						64	62	62					15																	101550745		1808	4077	5885	SO:0001589	frameshift_variant	79705	exon8			.	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.1080delA	chr15.hg19:g.101550745delA	ENSP00000373600:p.Ser360fs	285.0	0.0	0		216.0	67.0	0.310185	NM_024652		Frame_Shift_Del	DEL	ENST00000388948.3	hg19	CCDS42086.1																																																																																			.	.	.	none		0.368	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		-	101550745	A	-	101550745	7	5	252	1	0	1	0	1	0	0	0	0	9039	117	5	0	1106	0	LRRK1	15	101550745	Frame_Shift_Del	DEL	A	TCGA-SX-A7SR-01A-12D-A35Z-10	607728	101550745	980647	65	15708											
CHD9	80205	hgsc.bcm.edu	37	chr16	53301317	53301317	+	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	aaagtgaaggagatgaaaagCccaaactccggagaccctgt	16	5	11	9	1	0	4	0	2	0	2	1	6	1	4	3	2	2	0	3	2	5	0			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr16:53301317C>G	ENST00000398510.3	+	20	4519	c.4432C>G	c.(4432-4434)Ccc>Gcc	p.P1478A	CHD9_ENST00000564845.1_Missense_Mutation_p.P1478A|CHD9_ENST00000566029.1_Missense_Mutation_p.P1478A|CHD9_ENST00000447540.1_Missense_Mutation_p.P1478A			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	1478					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)				AGATGAAAAGCCCAAACTCCG	0.398																																					p.P1478A		Atlas-SNP	.											.	CHD9	203	.	0			c.C4432G						PASS	.						129	124	126					16																	53301317		1860	4104	5964	SO:0001583	missense	80205	exon21			GAAAAGCCCAAAC	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.4432C>G	chr16.hg19:g.53301317C>G	ENSP00000381522:p.Pro1478Ala	113.0	0.0	.		146.0	75.0	.	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Missense_Mutation	SNP	ENST00000398510.3	hg19		.	.	.	.	.	.	.	.	.	.	C	23.5	4.426732	0.83667	.	.	ENSG00000177200	ENST00000447540;ENST00000398510;ENST00000219084	D;D	0.85556	-2.0;-2.0	5.1	4.15	0.48705	.	0.222920	0.31461	N	0.007614	D	0.90892	0.7138	M	0.78223	2.4	0.58432	D	0.999999	P;D;D;D	0.64830	0.63;0.984;0.99;0.994	P;D;P;P	0.63703	0.459;0.917;0.76;0.879	D	0.91002	0.4843	10	0.48119	T	0.1	-1.7269	13.907	0.63843	0.0:0.926:0.0:0.074	.	1004;1478;1478;1478	B4DR07;Q3L8U1-3;Q3L8U1;Q3L8U1-2	.;.;CHD9_HUMAN;.	A	1478;1478;1004	ENSP00000396345:P1478A;ENSP00000381522:P1478A	ENSP00000219084:P1004A	P	+	1	0	CHD9	51858818	1.000000	0.71417	0.997000	0.53966	0.975000	0.68041	6.005000	0.70716	1.285000	0.44548	0.650000	0.86243	CCC	.	.	.	none		0.398	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		G	53301317	C	G	53301317	3	3	252	1	0	0	0	0	1	0	0	0	3334	739	26	4	4510	4	CHD9	16	53301317	Missense_Mutation	SNP	C	TCGA-SX-A7SR-01A-12D-A35Z-10		53301317	37053436	66	15709											
CCDC135	84229	hgsc.bcm.edu	37	chr16	57735929	57735929	+	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	tcagtacgctgctctgctccAtgcttatcggctctggctat	5	14	9	13	2	3	0	1	0	2	0	5	0	4	0	1	2	4	7	1	2	3	3			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr16:57735929A>T	ENST00000360716.3	+	6	807	c.586A>T	c.(586-588)Atg>Ttg	p.M196L	CCDC135_ENST00000394337.4_Missense_Mutation_p.M196L|CCDC135_ENST00000336825.8_Intron|RP11-405F3.4_ENST00000563062.1_RNA			Q8IY82	CC135_HUMAN		196					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						GCTCTGCTCCATGCTTATCGG	0.587																																					p.M196L		Atlas-SNP	.											.	CCDC135	97	.	0			c.A586T						PASS	.						181	137	152					16																	57735929		2198	4300	6498	SO:0001583	missense	84229	exon5			TGCTCCATGCTTA																												ENST00000360716.3:c.586A>T	chr16.hg19:g.57735929A>T	ENSP00000353942:p.Met196Leu	92.0	0.0	.		72.0	31.0	.	NM_032269	A8K943|Q8NAA0|Q9H080	Missense_Mutation	SNP	ENST00000360716.3	hg19	CCDS10787.1	.	.	.	.	.	.	.	.	.	.	A	1.504	-0.551352	0.03996	.	.	ENSG00000159625	ENST00000394337;ENST00000360716	T;T	0.14893	2.47;2.47	5.09	0.938	0.19500	.	0.352176	0.30252	N	0.010045	T	0.05731	0.0150	N	0.05177	-0.1	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37126	-0.9719	10	0.02654	T	1	-29.2494	8.5455	0.33419	0.4764:0.4138:0.0:0.1098	.	196	Q8IY82	CC135_HUMAN	L	196	ENSP00000377869:M196L;ENSP00000353942:M196L	ENSP00000353942:M196L	M	+	1	0	CCDC135	56293430	0.683000	0.27633	1.000000	0.80357	0.483000	0.33249	-0.062000	0.11674	0.743000	0.32719	0.366000	0.22137	ATG	.	.	.	none		0.587	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2			T	57735929	A	T	57735929	3	4	252	1	0	0	0	0	1	0	0	0	2771	217	8	5	600	5	CCDC135	16	57735929	Missense_Mutation	SNP	A	TCGA-SX-A7SR-01A-12D-A35Z-10	4434612	57735929	32618824	67	15710											
SGSM2	9905	hgsc.bcm.edu	37	chr17	2274584	2274584	+	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	gacatgatcgagatgcagggCtttgggcccagcctgccagc	8	7	14	12	1	0	2	0	1	0	1	1	4	0	2	3	2	4	2	3	2	0	1			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr17:2274584C>A	ENST00000426855.2	+	12	1492	c.1317C>A	c.(1315-1317)ggC>ggA	p.G439G	SGSM2_ENST00000268989.3_Silent_p.G484G|SGSM2_ENST00000574563.1_Silent_p.G439G	NM_001098509.1	NP_001091979.1	O43147	SGSM2_HUMAN	small G protein signaling modulator 2	439					late endosome to Golgi transport (GO:0034499)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)		AGATGCAGGGCTTTGGGCCCA	0.662																																					p.G484G		Atlas-SNP	.											.	SGSM2	60	.	0			c.C1452A						PASS	.						31	29	30					17																	2274584		2201	4298	6499	SO:0001819	synonymous_variant	9905	exon13			GCAGGGCTTTGGG	BC039204	CCDS32526.1, CCDS45570.1	17p13.3	2013-07-10	2007-08-14	2007-08-14		ENSG00000141258		"Small G protein signaling modulators"	29026	protein-coding gene	gene with protein product		611418	"RUN and TBC1 domain containing 1"	RUTBC1		9455477, 17509819, 21808068	Standard	NM_014853		Approved	KIAA0397	uc002fum.4	O43147		ENST00000426855.2:c.1317C>A	chr17.hg19:g.2274584C>A		72.0	0.0	.		84.0	18.0	.	NM_014853	A5LGW2|B4DH69|Q49AC2|Q6ZUY2|Q8IXU4	Silent	SNP	ENST00000426855.2	hg19	CCDS45570.1																																																																																			.	.	.	none		0.662	SGSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438186.1	NM_014853		A	2274584	C	A	2274584	2	1	252	1	0	0	0	0	0	0	0	1	14236	784	28	4		4	SGSM2	17	2274584	Silent	SNP	C	TCGA-SX-A7SR-01A-12D-A35Z-10		2274584	78920626	68	15711											
CYB5D2	124936	hgsc.bcm.edu	37	chr17	4060165	4060165	+	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	tccgtctatccttagtggagGtgtgagcagagactggattg	8	12	14	7	1	1	2	0	1	1	1	3	5	3	4	2	3	1	1	2	3	2	3			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr17:4060165G>T	ENST00000301391.3	+	4	1084	c.584G>T	c.(583-585)gGt>gTt	p.G195V	CYB5D2_ENST00000573984.1_Intron|CYB5D2_ENST00000575251.1_Missense_Mutation_p.G83V|CYB5D2_ENST00000575411.2_3'UTR	NM_144611.3	NP_653212.1	Q8WUJ1	NEUFC_HUMAN	cytochrome b5 domain containing 2	195					nervous system development (GO:0007399)	extracellular region (GO:0005576)	heme binding (GO:0020037)			breast(1)|large_intestine(3)|liver(2)|ovary(1)	7						CTTAGTGGAGGTGTGAGCAGA	0.557											OREG0024097	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G195V		Atlas-SNP	.											.	CYB5D2	22	.	0			c.G584T						PASS	.						48	44	46					17																	4060165		2203	4300	6503	SO:0001583	missense	124936	exon4			GTGGAGGTGTGAG	AK172844	CCDS11044.1, CCDS58501.1	17p13.2	2006-03-10							28471	protein-coding gene	gene with protein product							Standard	NM_144611		Approved	MGC32124	uc002fxm.4	Q8WUJ1		ENST00000301391.3:c.584G>T	chr17.hg19:g.4060165G>T	ENSP00000301391:p.Gly195Val	129.0	0.0	.	615	110.0	49.0	.	NM_144611	B2R7R6|D3DTJ9|I3L1K2	Missense_Mutation	SNP	ENST00000301391.3	hg19	CCDS11044.1	.	.	.	.	.	.	.	.	.	.	G	16.34	3.094421	0.56075	.	.	ENSG00000167740	ENST00000301391	T	0.80824	-1.42	4.95	4.95	0.65309	.	0.110364	0.64402	D	0.000009	D	0.91462	0.7305	M	0.90483	3.12	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.93098	0.6506	10	0.87932	D	0	-17.1409	16.9081	0.86133	0.0:0.0:1.0:0.0	.	195	Q8WUJ1	NEUFC_HUMAN	V	195	ENSP00000301391:G195V	ENSP00000301391:G195V	G	+	2	0	CYB5D2	4006914	1.000000	0.71417	1.000000	0.80357	0.155000	0.21991	7.025000	0.76449	2.563000	0.86464	0.561000	0.74099	GGT	.	.	.	none		0.557	CYB5D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438698.1	NM_144611		T	4060165	G	T	4060165	3	4	252	1	0	0	0	0	1	0	0	0	4127	1261	44	4	598	4	CYB5D2	17	4060165	Missense_Mutation	SNP	G	TCGA-SX-A7SR-01A-12D-A35Z-10	1785581	4060165	77135045	69	15712			1	35		2	2	26	N	G_C	7.187193e-05
CYB5D2	124936	hgsc.bcm.edu	37	chr17	4060190	4060190	+	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	agcagagactggattggcgtCcccaggaagctgtataagcc	11	7	13	10	1	0	1	0	0	0	1	1	4	1	3	3	3	3	3	3	3	3	3			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr17:4060190C>T	ENST00000301391.3	+	4	1109	c.609C>T	c.(607-609)gtC>gtT	p.V203V	CYB5D2_ENST00000573984.1_Intron|CYB5D2_ENST00000575251.1_Silent_p.V91V|CYB5D2_ENST00000575411.2_3'UTR	NM_144611.3	NP_653212.1	Q8WUJ1	NEUFC_HUMAN	cytochrome b5 domain containing 2	203					nervous system development (GO:0007399)	extracellular region (GO:0005576)	heme binding (GO:0020037)			breast(1)|large_intestine(3)|liver(2)|ovary(1)	7						GGATTGGCGTCCCCAGGAAGC	0.567											OREG0024097	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V203V		Atlas-SNP	.											.	CYB5D2	22	.	0			c.C609T						PASS	.						56	51	53					17																	4060190		2203	4300	6503	SO:0001819	synonymous_variant	124936	exon4			TGGCGTCCCCAGG	AK172844	CCDS11044.1, CCDS58501.1	17p13.2	2006-03-10							28471	protein-coding gene	gene with protein product							Standard	NM_144611		Approved	MGC32124	uc002fxm.4	Q8WUJ1		ENST00000301391.3:c.609C>T	chr17.hg19:g.4060190C>T		128.0	0.0	.	615	104.0	46.0	.	NM_144611	B2R7R6|D3DTJ9|I3L1K2	Silent	SNP	ENST00000301391.3	hg19	CCDS11044.1																																																																																			.	.	.	none		0.567	CYB5D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438698.1	NM_144611		T	4060190	C	T	4060190	2	4	252	1	0	0	0	0	0	0	0	1	4127	842	30	2		2	CYB5D2	17	4060190	Silent	SNP	C	TCGA-SX-A7SR-01A-12D-A35Z-10	25	4060190	77135020	70	15713			1	35		2	2	26	N	G_C	7.187193e-05
ULK2	9706	hgsc.bcm.edu	37	chr17	19720216	19720216	+	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	aagttttcttcctgaatatgCtgcatatctggaagggacta	11	14	9	7	0	2	1	0	1	2	0	3	3	3	3	1	2	2	3	1	2	6	6			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr17:19720216C>T	ENST00000395544.4	-	13	1441	c.942G>A	c.(940-942)caG>caA	p.Q314Q	ULK2_ENST00000361658.2_Silent_p.Q314Q|ULK2_ENST00000580130.1_Intron	NM_014683.3	NP_055498.3	Q8IYT8	ULK2_HUMAN	unc-51 like autophagy activating kinase 2	314					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)					CCTGAATATGCTGCATATCTG	0.348																																					p.Q314Q		Atlas-SNP	.											.	ULK2	142	.	0			c.G942A						PASS	.						78	78	78					17																	19720216		2203	4300	6503	SO:0001819	synonymous_variant	9706	exon13			AATATGCTGCATA	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.942G>A	chr17.hg19:g.19720216C>T		157.0	0.0	.		165.0	74.0	.	NM_001142610	A8MY69|O75119	Silent	SNP	ENST00000395544.4	hg19	CCDS11213.1																																																																																			.	.	.	none		0.348	ULK2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132375.2	NM_014683		T	19720216	C	T	19720216	2	4	252	1	0	0	0	0	0	0	0	1	16988	796	28	2		2	ULK2	17	19720216	Silent	SNP	C	TCGA-SX-A7SR-01A-12D-A35Z-10	15660026	19720216	61474994	71	15714											
EFCAB5	374786	hgsc.bcm.edu	37	chr17	28418892	28418892	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcattttgttattccagagaTtgaaaatgtcagggaagtcc	12	14	9	6	0	2	2	2	1	0	1	4	4	4	3	2	1	0	1	2	1	4	5			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr17:28418892T>C	ENST00000394835.3	+	21	4133	c.3941T>C	c.(3940-3942)aTt>aCt	p.I1314T	EFCAB5_ENST00000320856.5_Missense_Mutation_p.I1190T|RP11-1148O4.2_ENST00000582938.1_RNA|EFCAB5_ENST00000394832.2_Intron	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	1314							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						ATTCCAGAGATTGAAAATGTC	0.383																																					p.I1314T		Atlas-SNP	.											.	EFCAB5	122	.	0			c.T3941C						PASS	.						97	91	93					17																	28418892		1896	4115	6011	SO:0001583	missense	374786	exon21			CAGAGATTGAAAA	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.3941T>C	chr17.hg19:g.28418892T>C	ENSP00000378312:p.Ile1314Thr	115.0	0.0	.		126.0	39.0	.	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Missense_Mutation	SNP	ENST00000394835.3	hg19	CCDS11254.2	.	.	.	.	.	.	.	.	.	.	T	12.19	1.863578	0.32884	.	.	ENSG00000176927	ENST00000394835;ENST00000320856;ENST00000419434	T;T;T	0.11821	2.74;2.75;2.76	5.54	5.54	0.83059	.	0.392046	0.25214	N	0.032292	T	0.20536	0.0494	L	0.60455	1.87	0.80722	D	1	D;P	0.56521	0.976;0.944	P;P	0.51701	0.677;0.546	T	0.01524	-1.1333	10	0.45353	T	0.12	-5.0614	6.6082	0.22737	0.0:0.1706:0.0:0.8294	.	1190;1314	E7EVS9;A4FU69	.;EFCB5_HUMAN	T	1314;1190;996	ENSP00000378312:I1314T;ENSP00000322003:I1190T;ENSP00000417009:I996T	ENSP00000322003:I1190T	I	+	2	0	EFCAB5	25443018	1.000000	0.71417	1.000000	0.80357	0.512000	0.34134	3.543000	0.53633	2.107000	0.64212	0.533000	0.62120	ATT	.	.	.	none		0.383	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529		C	28418892	T	C	28418892	3	2	252	1	0	0	0	0	1	0	0	0	4940	1493	52	3	4190	3	EFCAB5	17	28418892	Missense_Mutation	SNP	T	TCGA-SX-A7SR-01A-12D-A35Z-10	8698676	28418892	52776318	72	15715											
CRLF3	51379	hgsc.bcm.edu	37	chr17	29120581	29120581	+	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	aatcaacgttggggtctatgTgcaatactatgaattcagtt	12	14	9	6	1	3	1	2	1	1	0	3	1	3	1	0	2	3	3	0	2	7	6			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr17:29120581T>A	ENST00000324238.6	-	5	837	c.713A>T	c.(712-714)cAc>cTc	p.H238L	CTD-2349P21.9_ENST00000580085.1_lincRNA|CRLF3_ENST00000544695.1_Missense_Mutation_p.H122L|CRLF3_ENST00000577725.1_Intron	NM_015986.3	NP_057070.3	Q8IUI8	CRLF3_HUMAN	cytokine receptor-like factor 3	238	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of cell growth (GO:0030308)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	17		all_hematologic(16;0.014)|Acute lymphoblastic leukemia(14;0.0236)|Myeloproliferative disorder(56;0.0255)				GGGGTCTATGTGCAATACTAT	0.458																																					p.H238L	Pancreas(30;346 881 29244 33464 41299)	Atlas-SNP	.											.	CRLF3	36	.	0			c.A713T						PASS	.						104	100	101					17																	29120581		2203	4300	6503	SO:0001583	missense	51379	exon5			TCTATGTGCAATA	AF120151	CCDS32607.1	17q11.2	2008-05-02				ENSG00000176390			17177	protein-coding gene	gene with protein product		614853					Standard	NM_015986		Approved	CREME9, CYTOR4	uc002hfr.4	Q8IUI8		ENST00000324238.6:c.713A>T	chr17.hg19:g.29120581T>A	ENSP00000318804:p.His238Leu	127.0	0.0	.		129.0	74.0	.	NM_015986	A6NJF3|B2R8C3|Q2MLY7|Q9UNI3|Q9Y6M8	Missense_Mutation	SNP	ENST00000324238.6	hg19	CCDS32607.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.821473	0.90873	.	.	ENSG00000176390	ENST00000324238;ENST00000544695	T;T	0.24151	1.87;1.87	5.64	5.64	0.86602	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.085303	0.85682	D	0.000000	T	0.29783	0.0744	L	0.48642	1.525	0.80722	D	1	P	0.41848	0.763	B	0.42422	0.387	T	0.03945	-1.0990	10	0.62326	D	0.03	-11.32	15.8343	0.78787	0.0:0.0:0.0:1.0	.	238	Q8IUI8	CRLF3_HUMAN	L	238;122	ENSP00000318804:H238L;ENSP00000444188:H122L	ENSP00000318804:H238L	H	-	2	0	CRLF3	26144707	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.631000	0.83237	2.150000	0.67090	0.482000	0.46254	CAC	.	.	.	none		0.458	CRLF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444354.1			A	29120581	T	A	29120581	3	1	252	1	0	0	0	0	1	0	0	0	3890	1696	59	5	631	5	CRLF3	17	29120581	Missense_Mutation	SNP	T	TCGA-SX-A7SR-01A-12D-A35Z-10	701689	29120581	52074629	73	15716											
SCRN2	90507	hgsc.bcm.edu	37	chr17	45916327	45916327	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctccgggtgttgggccgagAtgtccgtgccaatgctcagc	5	9	15	12	3	1	1	1	0	0	1	3	2	3	1	4	2	3	3	4	2	1	1			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr17:45916327A>G	ENST00000290216.9	-	5	727	c.602T>C	c.(601-603)aTc>aCc	p.I201T	SCRN2_ENST00000584123.1_Missense_Mutation_p.I209T|SCRN2_ENST00000407215.3_Missense_Mutation_p.I201T	NM_001145023.1|NM_138355.3	NP_001138495.1|NP_612364.2	Q96FV2	SCRN2_HUMAN	secernin 2	201						extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)			cervix(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	14						TTGGGCCGAGATGTCCGTGCC	0.587																																					p.I201T		Atlas-SNP	.											.	SCRN2	35	.	0			c.T602C						PASS	.						84	88	87					17																	45916327		2203	4300	6503	SO:0001583	missense	90507	exon5			GCCGAGATGTCCG	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.602T>C	chr17.hg19:g.45916327A>G	ENSP00000290216:p.Ile201Thr	67.0	0.0	.		52.0	10.0	.	NM_138355	A8K3N1|B7Z8S7|E9PBV5|Q96AC3|Q9BU04	Missense_Mutation	SNP	ENST00000290216.9	hg19	CCDS11519.1	.	.	.	.	.	.	.	.	.	.	A	15.65	2.895935	0.52121	.	.	ENSG00000141295	ENST00000290216;ENST00000407215	T;T	0.22743	1.94;1.94	5.52	5.52	0.82312	.	0.204208	0.50627	D	0.000110	T	0.37972	0.1023	M	0.90759	3.145	0.51012	D	0.999909	P;P;P	0.36354	0.549;0.549;0.549	B;B;B	0.43413	0.419;0.419;0.419	T	0.36890	-0.9729	10	0.49607	T	0.09	-16.3059	9.1893	0.37189	0.9175:0.0:0.0825:0.0	.	201;201;201	E9PBV5;Q96FV2;B7Z8S7	.;SCRN2_HUMAN;.	T	201	ENSP00000290216:I201T;ENSP00000383935:I201T	ENSP00000290216:I201T	I	-	2	0	SCRN2	43271326	1.000000	0.71417	1.000000	0.80357	0.148000	0.21650	7.472000	0.80996	2.091000	0.63221	0.533000	0.62120	ATC	.	.	.	none		0.587	SCRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441383.1	NM_138355		G	45916327	A	G	45916327	3	3	252	1	0	0	0	0	1	0	0	0	13952	333	12	3	709	3	SCRN2	17	45916327	Missense_Mutation	SNP	A	TCGA-SX-A7SR-01A-12D-A35Z-10	16795746	45916327	35278883	74	15717											
CACNA1G	8913	hgsc.bcm.edu	37	chr17	48674235	48674235	+	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	ccctgcgtcgcgccgcaccaGcagcagcgggtcggcagagc	6	3	15	17	6	0	1	0	0	0	1	2	1	0	1	3	2	5	4	3	2	0	0			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr17:48674235G>T	ENST00000359106.5	+	16	3209	c.3209G>T	c.(3208-3210)aGc>aTc	p.S1070I	CACNA1G_ENST00000502264.1_Missense_Mutation_p.S1047I|CACNA1G_ENST00000503485.1_Missense_Mutation_p.S1070I|CACNA1G_ENST00000360761.4_Missense_Mutation_p.S1047I|CACNA1G_ENST00000515165.1_Missense_Mutation_p.S1070I|CACNA1G_ENST00000352832.5_Missense_Mutation_p.S1047I|CACNA1G_ENST00000510115.1_Missense_Mutation_p.S1047I|CACNA1G_ENST00000515765.1_Missense_Mutation_p.S1070I|CACNA1G_ENST00000505165.1_Missense_Mutation_p.S1070I|CACNA1G_ENST00000507896.1_Missense_Mutation_p.S1070I|CACNA1G_ENST00000358244.5_Missense_Mutation_p.S1047I|CACNA1G_ENST00000416767.4_Missense_Mutation_p.S1070I|CACNA1G_ENST00000510366.1_Missense_Mutation_p.S1070I|CACNA1G_ENST00000515411.1_Missense_Mutation_p.S1070I|CACNA1G_ENST00000514717.1_Missense_Mutation_p.S1047I|CACNA1G_ENST00000514181.1_Missense_Mutation_p.S1070I|CACNA1G_ENST00000514079.1_Missense_Mutation_p.S1070I|CACNA1G_ENST00000512389.1_Missense_Mutation_p.S1070I|CACNA1G_ENST00000513964.1_Missense_Mutation_p.S1070I|CACNA1G_ENST00000507609.1_Missense_Mutation_p.S1070I|CACNA1G_ENST00000442258.2_Missense_Mutation_p.S1047I|CACNA1G_ENST00000513689.2_Missense_Mutation_p.S1070I|CACNA1G_ENST00000429973.2_Missense_Mutation_p.S1070I|CACNA1G_ENST00000507336.1_Missense_Mutation_p.S1070I|CACNA1G_ENST00000354983.4_Missense_Mutation_p.S1047I|CACNA1G_ENST00000507510.2_Missense_Mutation_p.S1070I	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	1070					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)	CGCCGCACCAGCAGCAGCGGG	0.687																																					p.S1070I		Atlas-SNP	.											.	CACNA1G	659	.	0			c.G3209T						PASS	.						6	7	7					17																	48674235		1921	4043	5964	SO:0001583	missense	8913	exon16			GCACCAGCAGCAG	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.3209G>T	chr17.hg19:g.48674235G>T	ENSP00000352011:p.Ser1070Ile	110.0	0.0	.		118.0	5.0	.	NM_001256360	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Missense_Mutation	SNP	ENST00000359106.5	hg19	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	g	18.51	3.639706	0.67244	.	.	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	0.97209	-4.13;-4.12;-4.29;-4.07;-4.1;-4.11;-4.15;-4.22;-4.19;-4.2;-4.22;-4.09;-4.11;-4.16;-4.11;-4.05;-4.15;-4.1;-4.09;-4.15;-4.11;-4.11;-4.14;-4.08;-4.15;-4.14	4.87	4.87	0.63330	.	0.478379	0.24303	N	0.039707	D	0.97284	0.9112	L	0.45137	1.4	0.38458	D	0.947139	P;B;P;B;B;P;P;B;P;P;P;B;B;D;P;B;B;P;B;P;B;B;B;B;D;P	0.61697	0.498;0.084;0.722;0.399;0.356;0.822;0.549;0.228;0.549;0.871;0.579;0.313;0.356;0.975;0.722;0.019;0.356;0.933;0.356;0.825;0.437;0.07;0.351;0.28;0.99;0.488	B;B;B;B;B;B;B;B;B;P;B;B;B;P;B;B;B;P;B;P;B;B;B;B;D;B	0.66497	0.131;0.042;0.282;0.342;0.197;0.227;0.282;0.09;0.19;0.695;0.096;0.272;0.14;0.793;0.227;0.028;0.089;0.668;0.09;0.466;0.098;0.058;0.043;0.065;0.944;0.182	D	0.98346	1.0541	10	0.48119	T	0.1	.	16.2113	0.82164	0.0:0.0:1.0:0.0	.	1047;1070;1070;1070;1070;1070;1070;1070;1070;1070;1070;1047;1070;1070;1070;1070;1070;1047;1070;1047;1047;1047;1047;1070;1047;1070	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;.;.	I	1047;1047;1070;1047;1047;1047;1070;1070;1047;1070;1070;1070;1070;1070;1070;1047;1070;1070;1070;1070;1047;1070;1070;1070;1070;1070	ENSP00000353990:S1047I;ENSP00000339302:S1047I;ENSP00000392390:S1070I;ENSP00000347078:S1047I;ENSP00000409759:S1047I;ENSP00000425522:S1047I;ENSP00000426261:S1070I;ENSP00000425451:S1070I;ENSP00000422407:S1047I;ENSP00000426814:S1070I;ENSP00000427238:S1070I;ENSP00000423112:S1070I;ENSP00000420918:S1070I;ENSP00000426172:S1070I;ENSP00000423045:S1070I;ENSP00000427173:S1047I;ENSP00000426098:S1070I;ENSP00000425698:S1070I;ENSP00000426232:S1070I;ENSP00000423317:S1070I;ENSP00000350979:S1047I;ENSP00000352011:S1070I;ENSP00000414388:S1070I;ENSP00000423155:S1070I;ENSP00000422268:S1070I;ENSP00000421518:S1070I	ENSP00000339302:S1047I	S	+	2	0	CACNA1G	46029234	1.000000	0.71417	1.000000	0.80357	0.354000	0.29330	8.006000	0.88564	2.258000	0.74832	0.561000	0.74099	AGC	.	.	.	none		0.687	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		T	48674235	G	T	48674235	3	4	252	1	0	0	0	0	1	0	0	0	2546	971	34	4	3271	4	CACNA1G	17	48674235	Missense_Mutation	SNP	G	TCGA-SX-A7SR-01A-12D-A35Z-10	2757908	48674235	32520975	75	15718											
NT5C	30833	hgsc.bcm.edu	37	chr17	73127154	73127154	+	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	ccacaccttctcacccacacAgtggtggtacttcagcaggg	9	8	9	15	0	2	0	2	0	1	0	3	0	2	0	3	3	2	2	3	3	1	3			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr17:73127154A>T	ENST00000245552.2	-	3	409	c.322T>A	c.(322-324)Tgt>Agt	p.C108S	NT5C_ENST00000582160.1_Missense_Mutation_p.C22S|NT5C_ENST00000579082.1_5'UTR|NT5C_ENST00000582170.1_Missense_Mutation_p.C108S|NT5C_ENST00000578337.1_Missense_Mutation_p.C22S	NM_014595.2	NP_055410.1	Q8TCD5	NT5C_HUMAN	5', 3'-nucleotidase, cytosolic	108					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)	TCACCCACACAGTGGTGGTAC	0.617																																					p.C108S		Atlas-SNP	.											.	NT5C	3	.	0			c.T322A						PASS	.						18	22	21					17																	73127154		2194	4295	6489	SO:0001583	missense	30833	exon3			CCACACAGTGGTG	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.322T>A	chr17.hg19:g.73127154A>T	ENSP00000245552:p.Cys108Ser	225.0	0.0	.		223.0	52.0	.	NM_001252377	Q96HS6|Q9NP82	Missense_Mutation	SNP	ENST00000245552.2	hg19	CCDS11715.1	.	.	.	.	.	.	.	.	.	.	A	15.68	2.904872	0.52333	.	.	ENSG00000125458	ENST00000245552	T	0.41065	1.01	5.09	3.99	0.46301	HAD-like domain (2);	0.114961	0.64402	N	0.000010	T	0.53400	0.1794	L	0.47078	1.49	0.41943	D	0.990625	D	0.63880	0.993	D	0.74023	0.982	T	0.53236	-0.8467	10	0.66056	D	0.02	-3.5863	9.0684	0.36478	0.8359:0.0:0.0:0.1641	.	108	Q8TCD5	NT5C_HUMAN	S	108	ENSP00000245552:C108S	ENSP00000245552:C108S	C	-	1	0	NT5C	70638749	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.811000	0.55620	0.769000	0.33313	0.459000	0.35465	TGT	.	.	.	none		0.617	NT5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445853.1			T	73127154	A	T	73127154	3	4	252	1	0	0	0	0	1	0	0	0	10691	188	7	5	295	5	NT5C	17	73127154	Missense_Mutation	SNP	A	TCGA-SX-A7SR-01A-12D-A35Z-10	24452919	73127154	8068056	76	15719											
LPPR3	79948	hgsc.bcm.edu	37	chr19	814451	814451	+	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	caccaggtaggcagcgatgcCcgccccgatgaggaagccgg	9	3	15	14	4	0	1	0	1	0	0	0	4	0	2	5	4	3	2	5	4	2	1			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr19:814451C>T	ENST00000520876.3	-	7	892	c.814G>A	c.(814-816)Ggc>Agc	p.G272S	MIR3187_ENST00000583431.1_RNA|LPPR3_ENST00000359894.2_Missense_Mutation_p.G300S	NM_001270366.1	NP_001257295.1	Q6T4P5	LPPR3_HUMAN		272						integral component of membrane (GO:0016021)	phosphatidate phosphatase activity (GO:0008195)										GCAGCGATGCCCGCCCCGATG	0.662																																					p.G300S		Atlas-SNP	.											.	.	.	.	0			c.G898A						PASS	.						26	27	27					19																	814451		2191	4294	6485	SO:0001583	missense	0	exon6			CGATGCCCGCCCC																												ENST00000520876.3:c.814G>A	chr19.hg19:g.814451C>T	ENSP00000430297:p.Gly272Ser	60.0	0.0	.		29.0	15.0	.	NM_024888	Q86XQ4|Q96EH1|Q9BQF9|Q9HAJ4	Missense_Mutation	SNP	ENST00000520876.3	hg19	CCDS58636.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.68|13.68	2.307986|2.307986	0.40895|0.40895	.|.	.|.	ENSG00000129951|ENSG00000129951	ENST00000517665|ENST00000300947;ENST00000359894;ENST00000520876	.|T;T	.|0.74315	.|-0.83;-0.83	4.66|4.66	4.66|4.66	0.58398|0.58398	.|Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.114726|0.114726	0.64402|0.64402	D|D	0.000019|0.000019	T|T	0.72755|0.72755	0.3500|0.3500	L|L	0.35414|0.35414	1.06|1.06	0.40705|0.40705	D|D	0.982513|0.982513	.|B;B;P	.|0.46952	.|0.317;0.368;0.887	.|B;P;P	.|0.49597	.|0.335;0.466;0.616	T|T	0.75056|0.75056	-0.3452|-0.3452	6|10	.|0.42905	.|T	.|0.14	-7.2365|-7.2365	16.5199|16.5199	0.84311|0.84311	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|273;272;300	.|Q6T4P5-2;Q6T4P5;Q6T4P5-3	.|.;LPPR3_HUMAN;.	E|S	60|273;300;272	.|ENSP00000352962:G300S;ENSP00000430297:G272S	.|ENSP00000300947:G273S	G|G	-|-	2|1	0|0	AC006273.1|AC006273.1	765451|765451	0.996000|0.996000	0.38824|0.38824	0.916000|0.916000	0.36221|0.36221	0.143000|0.143000	0.21401|0.21401	3.475000|3.475000	0.53136|0.53136	2.137000|2.137000	0.66172|0.66172	0.555000|0.555000	0.69702|0.69702	GGG|GGC	.	.	.	none		0.662	LPPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379096.3			T	814451	C	T	814451	3	4	252	1	0	0	0	0	1	0	0	0	8933	623	22	2	1350	2	LPPR3	19	814451	Missense_Mutation	SNP	C	TCGA-SX-A7SR-01A-12D-A35Z-10		814451	58314532	77	15720											
MKNK2	2872	hgsc.bcm.edu	37	chr19	2041888	2041888	+	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	cccagccgcagtcgctgccaCagcggcccacgaagggcggg	7	2	15	17	5	0	0	0	0	0	0	1	1	0	0	4	3	3	2	4	3	1	0			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr19:2041888C>T	ENST00000591601.1	-	10	931	c.896G>A	c.(895-897)tGt>tAt	p.C299Y	MKNK2_ENST00000250896.3_Missense_Mutation_p.C299Y|MKNK2_ENST00000309340.7_Missense_Mutation_p.C299Y|MKNK2_ENST00000591142.1_Missense_Mutation_p.C43Y|MKNK2_ENST00000541165.1_Missense_Mutation_p.C168Y|MKNK2_ENST00000591588.1_Missense_Mutation_p.C43Y|MKNK2_ENST00000588014.1_Missense_Mutation_p.C43Y			Q9HBH9	MKNK2_HUMAN	MAP kinase interacting serine/threonine kinase 2	299	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)		GTCGCTGCCACAGCGGCCCAC	0.711																																					p.C299Y		Atlas-SNP	.											.	MKNK2	56	.	0			c.G896A						PASS	.						17	15	15					19																	2041888		2031	3979	6010	SO:0001583	missense	2872	exon11			CTGCCACAGCGGC	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.896G>A	chr19.hg19:g.2041888C>T	ENSP00000467811:p.Cys299Tyr	98.0	0.0	.		57.0	24.0	.	NM_017572	Q6GPI3|Q9HBH8|Q9UHR0|Q9Y2N6	Missense_Mutation	SNP	ENST00000591601.1	hg19	CCDS12080.1	.	.	.	.	.	.	.	.	.	.	C	19.11	3.763123	0.69763	.	.	ENSG00000099875	ENST00000309340;ENST00000250896;ENST00000541165;ENST00000545627	T;T;T	0.38887	1.11;1.11;1.11	4.12	4.12	0.48240	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.46776	0.1410	N	0.12182	0.205	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	0.57774	-0.7753	10	0.87932	D	0	-4.0557	15.5219	0.75871	0.0:1.0:0.0:0.0	.	104;299;299;201	Q59GN5;Q9HBH9;Q9HBH9-2;Q9NT28	.;MKNK2_HUMAN;.;.	Y	299;299;168;239	ENSP00000309485:C299Y;ENSP00000250896:C299Y;ENSP00000438904:C168Y	ENSP00000250896:C299Y	C	-	2	0	MKNK2	1992888	1.000000	0.71417	0.998000	0.56505	0.263000	0.26337	7.366000	0.79548	2.137000	0.66172	0.555000	0.69702	TGT	.	.	.	none		0.711	MKNK2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449312.1	NM_199054		T	2041888	C	T	2041888	3	4	252	1	0	0	0	0	1	0	0	0	9612	478	17	2	612	2	MKNK2	19	2041888	Missense_Mutation	SNP	C	TCGA-SX-A7SR-01A-12D-A35Z-10	1227437	2041888	57087095	78	15721											
KLK7	5650	hgsc.bcm.edu	37	chr19	51485606	51485606	+	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	cttctcctgcagtttccaagGctaaggatagcagtaagatc	11	11	9	10	0	1	1	0	0	1	1	4	2	2	2	2	2	2	5	2	2	4	5			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr19:51485606G>T	ENST00000391807.1	-	2	151	c.50C>A	c.(49-51)gCc>gAc	p.A17D	KLK7_ENST00000595638.1_5'UTR|KLK7_ENST00000597707.1_Intron|CTB-147C22.9_ENST00000594512.1_RNA|KLK7_ENST00000336317.4_5'UTR|KLK7_ENST00000595820.1_Missense_Mutation_p.A17D	NM_139277.2	NP_644806.1	P49862	KLK7_HUMAN	kallikrein-related peptidase 7	17					epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(2)	19		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00382)|GBM - Glioblastoma multiforme(134;0.00895)		AGTTTCCAAGGCTAAGGATAG	0.597																																					p.S59R		Atlas-SNP	.											.	KLK7	40	.	0			c.C177A						PASS	.						63	47	53					19																	51485606		2203	4299	6502	SO:0001583	missense	5650	exon2			TCCAAGGCTAAGG	L33404	CCDS12812.1, CCDS59414.1	19q13.33	2011-09-07	2006-10-27			ENSG00000169035		"Kallikreins", "Serine peptidases / Serine peptidases"	6368	protein-coding gene	gene with protein product		604438	"kallikrein 7 (chymotryptic, stratum corneum)"	PRSS6		8034709, 16800724, 16800723	Standard	NM_005046		Approved	SCCE	uc021uyj.1	P49862		ENST00000391807.1:c.50C>A	chr19.hg19:g.51485606G>T	ENSP00000375683:p.Ala17Asp	70.0	0.0	.		50.0	9.0	.	NM_001243126	A8K0U5|Q8N5N9|Q8NFV7	Missense_Mutation	SNP	ENST00000391807.1	hg19	CCDS12812.1	.	.	.	.	.	.	.	.	.	.	g	10.70	1.424474	0.25639	.	.	ENSG00000169035	ENST00000304045;ENST00000391807	D	0.94000	-3.33	3.65	2.61	0.31194	.	.	.	.	.	D	0.92805	0.7712	L	0.49571	1.57	0.30110	N	0.806664	D	0.61080	0.989	P	0.55112	0.769	D	0.88031	0.2775	9	0.62326	D	0.03	.	7.0792	0.25221	0.1278:0.0:0.8722:0.0	.	17	P49862	KLK7_HUMAN	D	17	ENSP00000375683:A17D	ENSP00000304791:A17D	A	-	2	0	KLK7	56177418	0.072000	0.21174	0.114000	0.21550	0.005000	0.04900	0.592000	0.23984	0.893000	0.36288	0.645000	0.84053	GCC	.	.	.	none		0.597	KLK7-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464344.1	NM_005046		T	51485606	G	T	51485606	3	4	252	1	0	0	0	0	1	0	0	0	8416	1203	42	4	731	4	KLK7	19	51485606	Missense_Mutation	SNP	G	TCGA-SX-A7SR-01A-12D-A35Z-10	49443718	51485606	7643377	79	15722											
EPS8L1	54869	hgsc.bcm.edu	37	chr19	55591174	55591174	+	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	tgggcacaggagatgctgctGcgagtgtctcccgaccatgt	7	9	14	11	2	1	1	0	0	1	1	2	4	1	1	2	2	3	3	2	2	0	0			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr19:55591174G>A	ENST00000201647.6	+	5	290	c.234G>A	c.(232-234)ctG>ctA	p.L78L	EPS8L1_ENST00000245618.5_5'Flank|EPS8L1_ENST00000592824.1_3'UTR|EPS8L1_ENST00000588359.1_5'Flank|EPS8L1_ENST00000586329.1_Silent_p.L60L|EPS8L1_ENST00000540810.1_Silent_p.L14L	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1	78					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)		AGATGCTGCTGCGAGTGTCTC	0.667																																					p.L78L	Ovarian(149;255 1863 3636 27051 29647)	Atlas-SNP	.											.	EPS8L1	122	.	0			c.G234A						PASS	.						89	67	74					19																	55591174		2203	4300	6503	SO:0001819	synonymous_variant	54869	exon5			GCTGCTGCGAGTG	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.234G>A	chr19.hg19:g.55591174G>A		91.0	0.0	.		67.0	21.0	.	NM_133180	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	Silent	SNP	ENST00000201647.6	hg19	CCDS12914.1																																																																																			.	.	.	none		0.667	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451713.1	NM_017729		A	55591174	G	A	55591174	2	1	252	1	0	0	0	0	0	0	0	1	5197	1306	46	2		2	EPS8L1	19	55591174	Silent	SNP	G	TCGA-SX-A7SR-01A-12D-A35Z-10	4105568	55591174	3537809	80	15723											
NNAT	4826	hgsc.bcm.edu	37	chr20	36151076	36151076	+	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	tttctcgtcgcaggtgttcaGgtactccctgcagaagctgg	6	12	12	11	2	2	1	1	0	1	1	5	1	3	1	1	3	3	5	1	3	2	3			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr20:36151076G>T	ENST00000062104.2	+	3	278	c.161G>T	c.(160-162)aGg>aTg	p.R54M	BLCAP_ENST00000373537.2_Intron|BLCAP_ENST00000414542.2_Intron|BLCAP_ENST00000397131.1_Intron|BLCAP_ENST00000397137.1_Intron|BLCAP_ENST00000397134.1_5'Flank|NNAT_ENST00000346199.2_Missense_Mutation_p.R27M|BLCAP_ENST00000397135.1_Intron	NM_005386.2	NP_005377.1	Q16517	NNAT_HUMAN	neuronatin	54					brain development (GO:0007420)|neuron differentiation (GO:0030182)|positive regulation of insulin secretion (GO:0032024)|protein lipoylation (GO:0009249)|regulation of protein localization (GO:0032880)|response to glucose (GO:0009749)|transport (GO:0006810)	cytoplasm (GO:0005737)				endometrium(1)|kidney(1)|lung(1)	3		Myeloproliferative disorder(115;0.00878)				CAGGTGTTCAGGTACTCCCTG	0.687																																					p.R54M		Atlas-SNP	.											NNAT,NS,carcinoma,0,1	NNAT	8	.	0			c.G161T						PASS	.						59	43	48					20																	36151076		2203	4300	6503	SO:0001583	missense	4826	exon3			TGTTCAGGTACTC		CCDS13296.1, CCDS13297.1	20q11.2-q12	2007-12-07			ENSG00000053438	ENSG00000053438			7860	protein-coding gene	gene with protein product		603106				8660979	Standard	NM_005386		Approved	Peg5	uc002xhd.3	Q16517	OTTHUMG00000032420	ENST00000062104.2:c.161G>T	chr20.hg19:g.36151076G>T	ENSP00000062104:p.Arg54Met	96.0	0.0	.		71.0	30.0	.	NM_005386	B2R558|E1P5V6|Q16596|Q5U0N3	Missense_Mutation	SNP	ENST00000062104.2	hg19	CCDS13296.1	.	.	.	.	.	.	.	.	.	.	G	17.27	3.346799	0.61073	.	.	ENSG00000053438	ENST00000062104;ENST00000346199	.	.	.	5.0	4.05	0.47172	.	0.000000	0.53938	D	0.000058	T	0.47544	0.1451	.	.	.	0.30345	N	0.785383	D;P	0.58268	0.982;0.927	P;P	0.52793	0.709;0.702	T	0.52704	-0.8540	8	0.87932	D	0	-12.1953	8.6775	0.34187	0.1003:0.0:0.8997:0.0	.	27;54	Q16517-2;Q16517	.;NNAT_HUMAN	M	54;27	.	ENSP00000062104:R54M	R	+	2	0	NNAT	35584490	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.344000	0.44010	2.780000	0.95670	0.644000	0.83932	AGG	.	.	.	none		0.687	NNAT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079116.2	NM_005386		T	36151076	G	T	36151076	3	4	252	1	0	0	0	0	1	0	0	0	10515	1000	35	4	171	4	NNAT	20	36151076	Missense_Mutation	SNP	G	TCGA-SX-A7SR-01A-12D-A35Z-10		36151076	26874444	81	15724											
GTSF1L	149699	hgsc.bcm.edu	37	chr20	42355169	42355169	+	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	aacagcctcatgttcctccaGatttttgatggggaccacgt	9	12	9	11	1	1	2	1	1	0	1	3	3	3	3	4	2	2	1	4	2	1	3	rs17826038	byFrequency	TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr20:42355169G>A	ENST00000373003.1	-	1	469	c.166C>T	c.(166-168)Ctg>Ttg	p.L56L	GTSF1L_ENST00000373005.2_Silent_p.L56L	NM_001008901.1|NM_176791.3	NP_001008901.1|NP_789761.1	Q9H1H1	GTSFL_HUMAN	gametocyte specific factor 1-like	56			L -> V (in dbSNP:rs17826038).				metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	5		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			TGTTCCTCCAGATTTTTGATG	0.522																																					p.L56L		Atlas-SNP	.											.	GTSF1L	14	.	0			c.C166T						PASS	.						125	111	116					20																	42355169		2203	4300	6503	SO:0001819	synonymous_variant	149699	exon1			CCTCCAGATTTTT	AK058060	CCDS13323.1, CCDS33471.1	20q13.12	2007-11-27	2007-11-27	2007-11-27	ENSG00000124196	ENSG00000124196			16198	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 65", "family with sequence similarity 112, member A"	C20orf65, FAM112A			Standard	NM_176791		Approved	dJ1028D15.4	uc002xld.3	Q9H1H1	OTTHUMG00000032510	ENST00000373003.1:c.166C>T	chr20.hg19:g.42355169G>A		173.0	0.0	.		132.0	48.0	.	NM_001008901	Q5JWH5	Silent	SNP	ENST00000373003.1	hg19	CCDS13323.1																																																																																			.	G|0.981;C|0.019	.	alt		0.522	GTSF1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079313.1	NM_176791		A	42355169	G	A	42355169	2	1	252	1	0	0	0	0	0	0	0	1	6894	933	33	2		2	GTSF1L	20	42355169	Silent	SNP	G	TCGA-SX-A7SR-01A-12D-A35Z-10	6204093	42355169	20670351	82	15725											
PRIC285	85441	hgsc.bcm.edu	37	chr20	62198210	62198210	+	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	ggctcacctgggcaccgtggGaaacgacacagatgcacctc	10	5	12	14	2	1	1	1	0	0	1	2	3	1	2	3	3	2	3	3	3	1	0			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr20:62198210G>C	ENST00000467148.1	-	6	2570	c.2501C>G	c.(2500-2502)tCc>tGc	p.S834C	HELZ2_ENST00000427522.2_Missense_Mutation_p.S265C	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	834	Interaction with THRAP3.				cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										GGCACCGTGGGAAACGACACA	0.711																																					p.S834C		Atlas-SNP	.											.	.	.	.	0			c.C2501G						PASS	.						31	36	34					20																	62198210		2199	4298	6497	SO:0001583	missense	85441	exon7			CCGTGGGAAACGA	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.2501C>G	chr20.hg19:g.62198210G>C	ENSP00000417401:p.Ser834Cys	48.0	0.0	.		36.0	12.0	.	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	hg19	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.989411	0.53934	.	.	ENSG00000130589	ENST00000427522;ENST00000467148	D;D	0.93659	-3.26;-3.26	5.13	5.13	0.70059	.	0.247072	0.42420	D	0.000715	D	0.96454	0.8843	M	0.75777	2.31	0.45541	D	0.998499	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.991	D	0.96215	0.9156	10	0.48119	T	0.1	-45.9206	18.5866	0.91192	0.0:0.0:1.0:0.0	.	834;265	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	C	265;834	ENSP00000393257:S265C;ENSP00000417401:S834C	ENSP00000393257:S265C	S	-	2	0	RP4-697K14.7	61668654	1.000000	0.71417	0.900000	0.35374	0.009000	0.06853	6.746000	0.74866	2.399000	0.81585	0.561000	0.74099	TCC	.	.	.	none		0.711	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		C	62198210	G	C	62198210	3	2	252	1	0	0	0	0	1	0	0	0	12495	1174	41	4	5504	4	PRIC285	20	62198210	Missense_Mutation	SNP	G	TCGA-SX-A7SR-01A-12D-A35Z-10	19843041	62198210	827310	83	15726											
MX2	4600	hgsc.bcm.edu	37	chr21	42770936	42770936	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaggccgacaagatgttctTtctaattgaggtgaggattt	10	13	13	5	1	2	3	0	2	2	1	2	6	2	5	1	4	0	1	1	4	2	5			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr21:42770936T>C	ENST00000330714.3	+	9	1446	c.1262T>C	c.(1261-1263)tTt>tCt	p.F421S	MX2_ENST00000496774.1_3'UTR	NM_002463.1	NP_002454.1	P20592	MX2_HUMAN	MX dynamin-like GTPase 2	421					cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|defense response to virus (GO:0051607)|GTP catabolic process (GO:0006184)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of nucleocytoplasmic transport (GO:0046822)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	34		Prostate(19;1.57e-07)|all_epithelial(19;0.0222)				AAGATGTTCTTTCTAATTGAG	0.577																																					p.F421S		Atlas-SNP	.											.	MX2	84	.	0			c.T1262C						PASS	.						74	77	76					21																	42770936		2203	4300	6503	SO:0001583	missense	4600	exon9			TGTTCTTTCTAAT		CCDS13672.1	21q22.3	2014-07-15	2014-07-15		ENSG00000183486	ENSG00000183486			7533	protein-coding gene	gene with protein product	"interferon-regulated resistance GTP-binding protein MXB", "second interferon-induced protein p78"	147890	"myxovirus (influenza) resistance 2, homolog of murine", "myxovirus (influenza virus) resistance 2 (mouse)"			2481229, 8798556	Standard	NM_002463		Approved	MXB	uc002yzf.1	P20592	OTTHUMG00000086753	ENST00000330714.3:c.1262T>C	chr21.hg19:g.42770936T>C	ENSP00000333657:p.Phe421Ser	111.0	0.0	.		79.0	28.0	.	NM_002463	B7Z5D3|D3DSI7	Missense_Mutation	SNP	ENST00000330714.3	hg19	CCDS13672.1	.	.	.	.	.	.	.	.	.	.	T	19.56	3.849740	0.71603	.	.	ENSG00000183486	ENST00000330714	T	0.74315	-0.83	3.96	3.96	0.45880	Dynamin central domain (1);	0.000000	0.85682	D	0.000000	D	0.83862	0.5346	M	0.83774	2.66	0.80722	D	1	D	0.56746	0.977	P	0.61722	0.893	D	0.85784	0.1363	10	0.66056	D	0.02	-11.5518	10.8722	0.46889	0.0:0.0:0.0:1.0	.	421	P20592	MX2_HUMAN	S	421	ENSP00000333657:F421S	ENSP00000333657:F421S	F	+	2	0	MX2	41692806	1.000000	0.71417	0.970000	0.41538	0.785000	0.44390	3.190000	0.50973	1.737000	0.51674	0.402000	0.26972	TTT	.	.	.	none		0.577	MX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195147.1	NM_002463		C	42770936	T	C	42770936	3	2	252	1	0	0	0	0	1	0	0	0	10005	1841	64	3	1292	3	MX2	21	42770936	Missense_Mutation	SNP	T	TCGA-SX-A7SR-01A-12D-A35Z-10		42770936	5358959	84	15727											
TBC1D10A	83874	hgsc.bcm.edu	37	chr22	30690962	30690962	+	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	atgcatgagcaagacagcggCaatgggcgcctgggcctggc	9	5	16	11	2	0	2	0	1	0	1	0	2	0	2	2	4	3	3	2	4	2	0			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr22:30690962C>A	ENST00000215790.7	-	5	771	c.607G>T	c.(607-609)Gcc>Tcc	p.A203S	TBC1D10A_ENST00000403362.1_Missense_Mutation_p.A115S|TBC1D10A_ENST00000403477.3_Missense_Mutation_p.A210S|RP1-130H16.18_ENST00000447976.1_Missense_Mutation_p.A77S	NM_031937.2	NP_114143.1	Q9BXI6	TB10A_HUMAN	TBC1 domain family, member 10A	203	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				activation of cysteine-type endopeptidase activity (GO:0097202)|positive regulation of proteolysis (GO:0045862)|retrograde transport, endosome to Golgi (GO:0042147)	extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rab GTPase activator activity (GO:0005097)			cervix(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	23						AAGACAGCGGCAATGGGCGCC	0.667																																					p.A210S		Atlas-SNP	.											.	TBC1D10A	49	.	0			c.G628T						PASS	.						69	71	70					22																	30690962		2203	4300	6503	SO:0001583	missense	83874	exon5			CAGCGGCAATGGG	AF331038	CCDS13874.1, CCDS56227.1	22q12.2	2013-07-09	2005-03-10	2005-03-10	ENSG00000099992	ENSG00000099992			23609	protein-coding gene	gene with protein product	"EBP50-PDZ interactor of 64 kD"	610020	"TBC1 domain family, member 10"	TBC1D10		11285285, 20404108	Standard	NM_001204240		Approved	EPI64, AC004997.C22.2	uc010gvu.3	Q9BXI6	OTTHUMG00000150924	ENST00000215790.7:c.607G>T	chr22.hg19:g.30690962C>A	ENSP00000215790:p.Ala203Ser	101.0	0.0	.		68.0	20.0	.	NM_001204240	B3KXT8|O76053|Q20WK7|Q543A2	Missense_Mutation	SNP	ENST00000215790.7	hg19	CCDS13874.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.450603	0.84101	.	.	ENSG00000248751;ENSG00000099992;ENSG00000099992;ENSG00000099992;ENSG00000099992	ENST00000434291;ENST00000215790;ENST00000403477;ENST00000403362;ENST00000393906	T;T;T;T;T	0.06449	3.3;3.3;3.3;3.3;3.3	4.33	3.29	0.37713	Rab-GAP/TBC domain (4);	0.051488	0.85682	N	0.000000	T	0.29524	0.0736	M	0.91561	3.22	0.80722	D	1	D;D;D;D	0.71674	0.998;0.975;0.998;0.998	D;D;D;D	0.70016	0.951;0.919;0.951;0.967	T	0.31308	-0.9948	10	0.87932	D	0	.	12.5231	0.56072	0.1684:0.8316:0.0:0.0	.	203;210;203;203	Q20WK7;B3KXT8;Q9BXI6;A7E244	.;.;TB10A_HUMAN;.	S	77;203;210;115;115	ENSP00000401535:A77S;ENSP00000215790:A203S;ENSP00000384996:A210S;ENSP00000385050:A115S;ENSP00000377484:A115S	ENSP00000331267:A64S	A	-	1	0	TBC1D10A;RP1-130H16.18	29020962	1.000000	0.71417	0.806000	0.32338	0.901000	0.52897	7.592000	0.82676	1.150000	0.42419	0.561000	0.74099	GCC	.	.	.	none		0.667	TBC1D10A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320550.1	NM_031937		A	30690962	C	A	30690962	3	1	252	1	0	0	0	0	1	0	0	0	15610	710	25	4	939	4	TBC1D10A	22	30690962	Missense_Mutation	SNP	C	TCGA-SX-A7SR-01A-12D-A35Z-10		30690962	20613604	85	15728											
MORC2	22880	hgsc.bcm.edu	37	chr22	31331096	31331096	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctgctgggggcgttcctgAtcacagcaggtaaagggggc	7	8	17	9	1	2	1	1	1	1	0	3	1	3	1	1	5	2	4	1	5	2	2			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chr22:31331096A>G	ENST00000397641.3	-	19	2273	c.1865T>C	c.(1864-1866)aTc>aCc	p.I622T	MORC2_ENST00000469915.1_5'Flank|MORC2-AS1_ENST00000441558.1_RNA|MORC2_ENST00000215862.4_Missense_Mutation_p.I560T			Q9Y6X9	MORC2_HUMAN	MORC family CW-type zinc finger 2	622						cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	21						GGCGTTCCTGATCACAGCAGG	0.577																																					p.I560T		Atlas-SNP	.											.	MORC2	78	.	0			c.T1679C						PASS	.						25	28	27					22																	31331096		2203	4300	6503	SO:0001583	missense	22880	exon20			TTCCTGATCACAG	AB020659	CCDS33636.1	22q12.2	2005-06-15	2005-06-15	2005-06-15	ENSG00000133422	ENSG00000133422			23573	protein-coding gene	gene with protein product			"zinc finger, CW-type with coiled-coil domain 1", "zinc finger, CW type with coiled-coil domain 1"	ZCWCC1		14607086	Standard	XM_005261391		Approved	ZCW3, KIAA0852, AC004542.C22.1	uc003aje.1	Q9Y6X9	OTTHUMG00000151193	ENST00000397641.3:c.1865T>C	chr22.hg19:g.31331096A>G	ENSP00000380763:p.Ile622Thr	117.0	0.0	.		78.0	31.0	.	NM_014941	B2RNB1|Q9UF28|Q9Y6V2	Missense_Mutation	SNP	ENST00000397641.3	hg19		.	.	.	.	.	.	.	.	.	.	A	14.91	2.675729	0.47781	.	.	ENSG00000133422	ENST00000397641;ENST00000215862	T;T	0.11495	2.77;2.77	5.76	5.76	0.90799	.	0.113886	0.64402	D	0.000005	T	0.12987	0.0315	L	0.51422	1.61	0.80722	D	1	P	0.44734	0.842	B	0.42692	0.395	T	0.13495	-1.0507	10	0.13853	T	0.58	.	14.6387	0.68708	1.0:0.0:0.0:0.0	.	622	Q9Y6X9	MORC2_HUMAN	T	622;560	ENSP00000380763:I622T;ENSP00000215862:I560T	ENSP00000215862:I560T	I	-	2	0	MORC2	29661096	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.554000	0.82212	2.201000	0.70794	0.533000	0.62120	ATC	.	.	.	none		0.577	MORC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321710.2	NM_014941		G	31331096	A	G	31331096	3	3	252	1	0	0	0	0	1	0	0	0	9709	333	12	3	1265	3	MORC2	22	31331096	Missense_Mutation	SNP	A	TCGA-SX-A7SR-01A-12D-A35Z-10	640134	31331096	19973470	86	15729											
ARHGAP6	395	hgsc.bcm.edu	37	chrX	11160422	11160422	+	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	tccccagatatcgaaaggctCctctgacagatctagggaaa	13	8	9	11	1	2	3	0	1	2	2	5	5	4	4	3	2	0	1	3	2	4	2			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chrX:11160422C>T	ENST00000337414.4	-	12	3060	c.2188G>A	c.(2188-2190)Gag>Aag	p.E730K	ARHGAP6_ENST00000303025.6_Missense_Mutation_p.E527K|ARHGAP6_ENST00000380736.1_Missense_Mutation_p.E527K|ARHGAP6_ENST00000534860.1_Missense_Mutation_p.E555K	NM_013427.2	NP_038286.2	O43182	RHG06_HUMAN	Rho GTPase activating protein 6	730					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						TCGAAAGGCTCCTCTGACAGA	0.328																																					p.E730K		Atlas-SNP	.											.	ARHGAP6	130	.	0			c.G2188A						PASS	.						87	85	86					X																	11160422		2203	4300	6503	SO:0001583	missense	395	exon12			AAGGCTCCTCTGA	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.2188G>A	chrX.hg19:g.11160422C>T	ENSP00000338967:p.Glu730Lys	200.0	0.0	.		151.0	95.0	.	NM_013427	B2RWQ0|O43437|Q9P1B3|Q9UK81|Q9UK82	Missense_Mutation	SNP	ENST00000337414.4	hg19	CCDS14140.1	.	.	.	.	.	.	.	.	.	.	C	19.15	3.771539	0.69992	.	.	ENSG00000047648	ENST00000534860;ENST00000380736;ENST00000303025;ENST00000337414	T;T;T;T	0.28454	1.73;1.65;1.65;1.61	5.24	5.24	0.73138	.	0.111709	0.39083	N	0.001463	T	0.37892	0.1020	M	0.65975	2.015	0.80722	D	1	P;P	0.46064	0.872;0.872	B;B	0.42738	0.396;0.396	T	0.21930	-1.0231	10	0.32370	T	0.25	.	18.0066	0.89211	0.0:1.0:0.0:0.0	.	730;730	O43182;A8KAL3	RHG06_HUMAN;.	K	555;527;527;730	ENSP00000438135:E555K;ENSP00000370112:E527K;ENSP00000302312:E527K;ENSP00000338967:E730K	ENSP00000302312:E527K	E	-	1	0	ARHGAP6	11070343	1.000000	0.71417	0.998000	0.56505	0.931000	0.56810	6.483000	0.73617	2.186000	0.69663	0.594000	0.82650	GAG	.	.	.	none		0.328	ARHGAP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055760.2	NM_013427		T	11160422	C	T	11160422	3	4	252	1	0	0	0	0	1	0	0	0	887	864	30	2	744	2	ARHGAP6	23	11160422	Missense_Mutation	SNP	C	TCGA-SX-A7SR-01A-12D-A35Z-10		11160422	144110138	87	15730											
GPRASP1	9737	hgsc.bcm.edu	37	chrX	101909675	101909675	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtctgggcccagggaagaTcccaatagcaggtccaggtt	9	8	14	10	0	1	1	0	0	1	1	3	2	3	2	3	5	1	2	3	5	3	2	rs369864268		TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chrX:101909675T>C	ENST00000361600.5	+	5	1635	c.834T>C	c.(832-834)gaT>gaC	p.D278D	GPRASP1_ENST00000415986.1_Silent_p.D278D|GPRASP1_ENST00000444152.1_Silent_p.D278D|GPRASP1_ENST00000537097.1_Silent_p.D278D|RP4-769N13.7_ENST00000602441.1_RNA	NM_014710.4	NP_055525.3	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting protein 1	278					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						CCAGGGAAGATCCCAATAGCA	0.468																																					p.D278D		Atlas-SNP	.											.	GPRASP1	140	.	0			c.T834C						PASS	.						107	108	107					X																	101909675		2203	4300	6503	SO:0001819	synonymous_variant	9737	exon3			GGAAGATCCCAAT	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.834T>C	chrX.hg19:g.101909675T>C		91.0	0.0	.		61.0	43.0	.	NM_001099411	O43168|Q96LA1	Silent	SNP	ENST00000361600.5	hg19	CCDS35352.1																																																																																			.	.	.	alt		0.468	GPRASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057634.2	NM_014710		C	101909675	T	C	101909675	2	2	252	1	0	0	0	0	0	0	0	1	6729	1432	50	3		3	GPRASP1	23	101909675	Silent	SNP	T	TCGA-SX-A7SR-01A-12D-A35Z-10	90749253	101909675	53360885	88	15731											
RGAG1	57529	hgsc.bcm.edu	37	chrX	109697329	109697329	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaagcagcccggggctcaTgctctgtggaggaagagatg	10	6	17	8	1	2	1	1	0	1	1	2	5	2	4	1	5	3	3	1	5	2	0			TCGA-SX-A7SR-01A-12D-A35Z-10	TCGA-SX-A7SR-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4ac24403-4088-4192-a6ee-57913809b464	3c89ac32-79c6-4277-ace0-1bc1779f3be8	g.chrX:109697329T>C	ENST00000465301.2	+	3	3730	c.3484T>C	c.(3484-3486)Tgc>Cgc	p.C1162R	RGAG1_ENST00000540313.1_Missense_Mutation_p.C1162R	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	1162										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						CCGGGGCTCATGCTCTGTGGA	0.502																																					p.C1162R		Atlas-SNP	.											.	RGAG1	168	.	0			c.T3484C						PASS	.						97	90	92					X																	109697329		2203	4300	6503	SO:0001583	missense	57529	exon3			GGCTCATGCTCTG	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.3484T>C	chrX.hg19:g.109697329T>C	ENSP00000419786:p.Cys1162Arg	178.0	0.0	.		160.0	121.0	.	NM_020769	Q9P2M8	Missense_Mutation	SNP	ENST00000465301.2	hg19	CCDS14552.1	.	.	.	.	.	.	.	.	.	.	T	8.415	0.845068	0.16963	.	.	ENSG00000243978	ENST00000465301;ENST00000540313;ENST00000540483	T;T	0.45276	0.9;0.9	4.02	2.82	0.32997	.	0.628162	0.13294	N	0.398806	T	0.36936	0.0985	L	0.27053	0.805	0.18873	N	0.999985	P	0.48016	0.904	P	0.51355	0.667	T	0.09975	-1.0650	9	.	.	.	-0.0425	6.6276	0.22839	0.0:0.0:0.2422:0.7578	.	1162	Q8NET4	RGAG1_HUMAN	R	1162;1162;723	ENSP00000419786:C1162R;ENSP00000441452:C1162R	.	C	+	1	0	RGAG1	109583985	0.000000	0.05858	0.006000	0.13384	0.954000	0.61252	-0.659000	0.05323	0.672000	0.31204	0.486000	0.48141	TGC	.	.	.	none		0.502	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		C	109697329	T	C	109697329	3	2	252	1	0	0	0	0	1	0	0	0	13287	1464	51	3	3486	3	RGAG1	23	109697329	Missense_Mutation	SNP	T	TCGA-SX-A7SR-01A-12D-A35Z-10	7787654	109697329	45573231	89	15732											
CPSF3L	54973	hgsc.bcm.edu	37	chr1	1248221	1248221	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catcttcttggcctcgccatGcaccagcagcacgctctccg	6	9	8	18	3	3	0	0	0	3	0	5	0	3	0	4	1	3	4	4	1	0	2			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr1:1248221G>A	ENST00000435064.1	-	12	1322	c.1240C>T	c.(1240-1242)Cat>Tat	p.H414Y	CPSF3L_ENST00000450926.2_Missense_Mutation_p.H392Y|CPSF3L_ENST00000462432.1_5'UTR|CPSF3L_ENST00000540437.1_Missense_Mutation_p.H420Y|CPSF3L_ENST00000419704.1_Missense_Mutation_p.H313Y|CPSF3L_ENST00000421495.2_Missense_Mutation_p.H156Y|CPSF3L_ENST00000411962.1_Missense_Mutation_p.H316Y|CPSF3L_ENST00000545578.1_Missense_Mutation_p.H385Y	NM_001256460.1|NM_017871.5	NP_001243389.1|NP_060341.2	Q5TA45	INT11_HUMAN	cleavage and polyadenylation specific factor 3-like	414					snRNA processing (GO:0016180)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|integrator complex (GO:0032039)	hydrolase activity (GO:0016787)			endometrium(4)|kidney(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(3)	13	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(86;4.35e-21)|Colorectal(212;0.000166)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.00235)|BRCA - Breast invasive adenocarcinoma(365;0.00255)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0349)|Lung(427;0.201)		GCCTCGCCATGCACCAGCAGC	0.652																																					p.H420Y		Atlas-SNP	.											.	CPSF3L	33	.	0			c.C1258T						PASS	.						45	43	44					1																	1248221		2202	4295	6497	SO:0001583	missense	54973	exon14			CGCCATGCACCAG	AL136813	CCDS21.1, CCDS57959.1, CCDS57960.1, CCDS57961.1, CCDS72678.1	1p36.33	2008-02-05			ENSG00000127054	ENSG00000127054			26052	protein-coding gene	gene with protein product	"integrator complex subunit 11"	611354				15684398, 16239144	Standard	NM_001256456		Approved	FLJ20542, RC-68, CPSF73L, INT11, INTS11	uc001aee.2	Q5TA45	OTTHUMG00000003330	ENST00000435064.1:c.1240C>T	chr1.hg19:g.1248221G>A	ENSP00000413493:p.His414Tyr	74.0	0.0	.		40.0	17.0	.	NM_001256456	A8K5S2|B3KPR3|B4DM87|G3V1S5|Q5TA46|Q5TA48|Q5TA52|Q5TA53|Q5TA54|Q7L3D7|Q96HY1|Q9BW36|Q9H0F9|Q9H8R5|Q9HAA6|Q9NWX9	Missense_Mutation	SNP	ENST00000435064.1	hg19	CCDS21.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.659224	0.88154	.	.	ENSG00000127054	ENST00000435064;ENST00000411962;ENST00000419704;ENST00000540437;ENST00000450926;ENST00000545578	T;T;T;T;T	0.77098	-0.53;-0.53;-0.53;-0.53;-1.07	5.56	5.56	0.83823	RNA-metabolising metallo-beta-lactamase (1);	0.000000	0.85682	D	0.000000	D	0.93605	0.7958	H	0.98996	4.395	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.95947	0.8951	10	0.87932	D	0	-33.6557	19.5079	0.95127	0.0:0.0:1.0:0.0	.	392;385;316;313;420;414	Q5TA45-3;B4DM87;C9IYS7;Q5TA45-2;G3V1S5;Q5TA45	.;.;.;.;.;INT11_HUMAN	Y	414;316;313;420;392;385	ENSP00000413493:H414Y;ENSP00000404886:H313Y;ENSP00000445001:H420Y;ENSP00000392848:H392Y;ENSP00000444672:H385Y	ENSP00000400548:H316Y	H	-	1	0	CPSF3L	1238084	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.758000	0.91663	2.611000	0.88343	0.563000	0.77884	CAT	.	.	.	none		0.652	CPSF3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009360.2	NM_017871		A	1248221	G	A	1248221	3	1	253	1	0	0	0	0	1	0	0	0	3829	1319	46	2	586	2	CPSF3L	1	1248221	Missense_Mutation	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10		1248221	248002400	1	15733											
CROCC	9696	hgsc.bcm.edu	37	chr1	17287328	17287328	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcgacgcctgctgggctccCtggaggaggcgcgtggcact	5	6	17	13	4	0	0	0	0	0	0	1	3	1	2	2	5	2	3	2	5	0	0			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr1:17287328C>T	ENST00000375541.5	+	27	4177	c.4108C>T	c.(4108-4110)Ctg>Ttg	p.L1370L		NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		GCTGGGCTCCCTGGAGGAGGC	0.697											OREG0013143	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L1370L		Atlas-SNP	.											.	CROCC	185	.	0			c.C4108T						PASS	.						4	5	5					1																	17287328		2042	4015	6057	SO:0001819	synonymous_variant	9696	exon27			GGCTCCCTGGAGG	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"rootletin, ciliary rootlet protein"	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.4108C>T	chr1.hg19:g.17287328C>T		14.0	0.0	.	716	7.0	5.0	.	NM_014675		Silent	SNP	ENST00000375541.5	hg19	CCDS30616.1																																																																																			.	.	.	none		0.697	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675		T	17287328	C	T	17287328	2	4	253	1	0	0	0	0	0	0	0	1	3895	680	24	2		2	CROCC	1	17287328	Silent	SNP	C	TCGA-SX-A7SS-01A-11D-A35Z-10	16039107	17287328	231963293	2	15734											
ZBTB40	9923	hgsc.bcm.edu	37	chr1	22816649	22816649	+	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	catctgtggtgagccccgagGagtttgcgctcttgttggaa	6	12	14	9	2	2	1	0	1	2	0	2	4	2	3	2	3	2	3	2	3	1	3			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr1:22816649G>A	ENST00000375647.4	+	2	415	c.208G>A	c.(208-210)Gag>Aag	p.E70K	ZBTB40_ENST00000404138.1_Missense_Mutation_p.E70K|ZBTB40_ENST00000374651.4_Missense_Mutation_p.E70K	NM_014870.3	NP_055685.3	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40	70	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)		GAGCCCCGAGGAGTTTGCGCT	0.507																																					p.E70K		Atlas-SNP	.											.	ZBTB40	87	.	0			c.G208A						PASS	.						82	74	77					1																	22816649		2203	4300	6503	SO:0001583	missense	9923	exon3			CCCGAGGAGTTTG	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.208G>A	chr1.hg19:g.22816649G>A	ENSP00000364798:p.Glu70Lys	92.0	0.0	.		88.0	33.0	.	NM_001083621	O75066|Q5TFU5|Q8N1R1	Missense_Mutation	SNP	ENST00000375647.4	hg19	CCDS224.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.781627	0.90282	.	.	ENSG00000184677	ENST00000404138;ENST00000374649;ENST00000375647;ENST00000400239;ENST00000374651	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	4.61	4.61	0.57282	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.53938	D	0.000053	T	0.80210	0.4581	M	0.73217	2.22	0.34524	D	0.708489	D;D	0.76494	0.999;0.999	D;D	0.79784	0.987;0.993	D	0.85064	0.0936	10	0.40728	T	0.16	-21.3726	16.3638	0.83307	0.0:0.0:1.0:0.0	.	70;70	F8WAI8;Q9NUA8	.;ZBT40_HUMAN	K	70	ENSP00000384527:E70K;ENSP00000364798:E70K;ENSP00000383098:E70K;ENSP00000363782:E70K	ENSP00000363780:E70K	E	+	1	0	ZBTB40	22689236	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.780000	0.99024	2.248000	0.74166	0.591000	0.81541	GAG	.	.	.	none		0.507	ZBTB40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008094.1	NM_014870		A	22816649	G	A	22816649	3	1	253	1	0	0	0	0	1	0	0	0	17554	1175	41	2	210	2	ZBTB40	1	22816649	Missense_Mutation	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10	5529321	22816649	226433972	3	15735											
RUNX3	864	hgsc.bcm.edu	37	chr1	25229150	25229150	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcggagaatgggttcagttcCgaggtgcctggaggacagca	9	8	16	8	2	1	1	1	0	0	1	3	5	2	3	2	5	2	3	2	5	1	2	rs567207182		TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr1:25229150C>T	ENST00000308873.6	-	5	719	c.711G>A	c.(709-711)tcG>tcA	p.S237S	RUNX3_ENST00000540420.1_Silent_p.S144S|RUNX3_ENST00000338888.3_Silent_p.S251S|RUNX3_ENST00000399916.1_Silent_p.S251S|RUNX3_ENST00000496967.1_5'UTR	NM_004350.2	NP_004341.1	Q13761	RUNX3_HUMAN	runt-related transcription factor 3	237	Pro/Ser/Thr-rich.				axon guidance (GO:0007411)|cell maturation (GO:0048469)|chondrocyte differentiation (GO:0002062)|hair follicle morphogenesis (GO:0031069)|interferon-gamma production (GO:0032609)|negative regulation of cell cycle (GO:0045786)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peripheral nervous system neuron development (GO:0048935)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(3)	18		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00131)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;2.85e-26)|Colorectal(126;4.35e-08)|COAD - Colon adenocarcinoma(152;1.92e-06)|GBM - Glioblastoma multiforme(114;0.000102)|STAD - Stomach adenocarcinoma(196;0.000766)|KIRC - Kidney renal clear cell carcinoma(1967;0.00148)|BRCA - Breast invasive adenocarcinoma(304;0.00173)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.136)		GGTTCAGTTCCGAGGTGCCTG	0.617													C|||	1	0.000199681	0	0	5008	,	,		14814	0		0	False		,,,				2504	0.001				p.S251S		Atlas-SNP	.											.	RUNX3	72	.	0			c.G753A						PASS	.						60	54	56					1																	25229150		2170	4261	6431	SO:0001819	synonymous_variant	864	exon6			CAGTTCCGAGGTG	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.711G>A	chr1.hg19:g.25229150C>T		129.0	0.0	.		117.0	12.0	.	NM_001031680	B1AJV5|Q12969|Q13760	Silent	SNP	ENST00000308873.6	hg19	CCDS257.1																																																																																			.	.	.	none		0.617	RUNX3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009284.1	NM_004350		T	25229150	C	T	25229150	2	4	253	1	0	0	0	0	0	0	0	1	13762	639	23	1		1	RUNX3	1	25229150	Silent	SNP	C	TCGA-SX-A7SS-01A-11D-A35Z-10	2412501	25229150	224021471	4	15736											
ZMYM6	9204	hgsc.bcm.edu	37	chr1	35453543	35453543	+	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	acaaaattgttaacatacgtGaatttaatgcattgctcttt	14	16	5	6	1	1	1	0	1	1	0	1	1	1	1	0	0	4	3	0	0	6	7			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr1:35453543G>A	ENST00000357182.4	-	16	3367	c.3140C>T	c.(3139-3141)tCa>tTa	p.S1047L	ZMYM6_ENST00000373340.2_Intron|ZMYM6_ENST00000487874.1_Intron|RP11-244H3.1_ENST00000417456.1_RNA|ZMYM6_ENST00000493328.1_5'UTR|ZMYM6NB_ENST00000373337.3_5'Flank	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6	1047					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)				taacatacgtgaatttaatgc	0.353																																					p.S1047L		Atlas-SNP	.											.	ZMYM6	110	.	0			c.C3140T						PASS	.						45	40	42					1																	35453543		1243	2620	3863	SO:0001583	missense	9204	exon16			ATACGTGAATTTA	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.3140C>T	chr1.hg19:g.35453543G>A	ENSP00000349708:p.Ser1047Leu	172.0	0.0	.		123.0	48.0	.	NM_007167	B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	Missense_Mutation	SNP	ENST00000357182.4	hg19	CCDS387.2	.	.	.	.	.	.	.	.	.	.	G	15.62	2.888269	0.52014	.	.	ENSG00000163867	ENST00000357182	T	0.20463	2.07	4.2	4.2	0.49525	Ribonuclease H-like (1);	0.074167	0.56097	D	0.000037	T	0.40247	0.1109	M	0.76838	2.35	0.80722	D	1	D	0.69078	0.997	D	0.63488	0.915	T	0.13953	-1.0490	10	0.16420	T	0.52	-12.7494	12.3464	0.55124	0.0:0.0:1.0:0.0	.	1047	O95789	ZMYM6_HUMAN	L	1047	ENSP00000349708:S1047L	ENSP00000349708:S1047L	S	-	2	0	ZMYM6	35226130	1.000000	0.71417	0.993000	0.49108	0.992000	0.81027	1.528000	0.35985	2.634000	0.89283	0.650000	0.86243	TCA	.	.	.	none		0.353	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011999.1	NM_007167		A	35453543	G	A	35453543	3	1	253	1	0	0	0	0	1	0	0	0	17716	1294	45	2	841	2	ZMYM6	1	35453543	Missense_Mutation	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10	10224393	35453543	213797078	5	15737											
PPOX	5498	hgsc.bcm.edu	37	chr1	161140540	161140541	+	Frame_Shift_Ins	INS	-	-	CTTGGTCCATCTA																															aaggagatgccgagccactgINScttggtccatctacacaagg																										TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr1:161140540_161140541insCTTGGTCCATCTA	ENST00000367999.4	+	11	1495_1496	c.1229_1230insCTTGGTCCATCTA	c.(1228-1233)tgcttgfs	p.-411fs	PPOX_ENST00000495483.1_3'UTR|PPOX_ENST00000352210.5_Frame_Shift_Ins_p.-411fs|PPOX_ENST00000432542.2_Frame_Shift_Ins_p.-156fs|PPOX_ENST00000535223.1_Frame_Shift_Ins_p.-74fs|B4GALT3_ENST00000470882.1_5'Flank|PPOX_ENST00000544598.1_Frame_Shift_Ins_p.-119fs	NM_001122764.1	NP_001116236.1	P50336	PPOX_HUMAN	protoporphyrinogen oxidase						heme biosynthetic process (GO:0006783)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound biosynthetic process (GO:0006779)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	integral component of mitochondrial inner membrane (GO:0031305)|intrinsic component of mitochondrial inner membrane (GO:0031304)|mitochondrial intermembrane space (GO:0005758)|mitochondrial membrane (GO:0031966)	flavin adenine dinucleotide binding (GO:0050660)|oxygen-dependent protoporphyrinogen oxidase activity (GO:0004729)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(3)	15	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			CCGAGCCACTGCTTGGTCCATC	0.515																																					p.C410fs		Atlas-Indel,Pindel	.											.	PPOX	34	.	0			c.1229_1230insCTTGGTCCATCTA						PASS	.																																			SO:0001589	frameshift_variant	5498	exon11			.	BC002357	CCDS1221.1	1q22	2008-02-05			ENSG00000143224	ENSG00000143224	1.3.3.4		9280	protein-coding gene	gene with protein product		600923	"variegate porphyria"	VP		8575762, 10457135	Standard	NM_000309		Approved	PPO	uc001fyg.2	P50336	OTTHUMG00000034342	ENST00000367999.4:c.1230_1242dupCTTGGTCCATCTA	chr1.hg19:g.161140540_161140541insCTTGGTCCATCTA	ENSP00000356978:p.Leu411fs	78.0	0.0	0		60.0	10.0	0.166667	NM_001122764	D3DVG0|Q5VTW8	Frame_Shift_Ins	INS	ENST00000367999.4	hg19	CCDS1221.1																																																																																			.	.	.	none		0.515	PPOX-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082993.1	NM_000309		CTTGGTCCATCTA	161140541	-	CTTGGTCCATCTA	161140540	7	5	253	1	0	1	1	0	0	0	0	0	12358	1319	46	0	1267	0	PPOX	1	161140540	Frame_Shift_Ins	INS	-	TCGA-SX-A7SS-01A-11D-A35Z-10	125686997	161140540	88110081	6	15738											
RASAL2	9462	hgsc.bcm.edu	37	chr1	178063786	178063786	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcatgttggatcggatcctTctggagtccgtgtgccagca	6	11	14	10	2	1	0	0	0	1	0	4	3	3	3	3	4	2	3	3	4	0	2			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr1:178063786T>C	ENST00000367649.3	+	1	511	c.159T>C	c.(157-159)ctT>ctC	p.L53L	RASAL2_ENST00000448150.3_Silent_p.L35L|RASAL2-AS1_ENST00000421505.1_lincRNA			Q9UJF2	NGAP_HUMAN	RAS protein activator like 2	0	PH.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Ras GTPase activator activity (GO:0005099)			biliary_tract(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(2)|lung(25)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54						ATCGGATCCTTCTGGAGTCCG	0.627																																					p.L53L		Atlas-SNP	.											.	RASAL2	334	.	0			c.T159C						PASS	.						47	38	41					1																	178063786		2203	4300	6503	SO:0001819	synonymous_variant	9462	exon1			GATCCTTCTGGAG	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	ENST00000367649.3:c.159T>C	chr1.hg19:g.178063786T>C		221.0	0.0	.		193.0	79.0	.	NM_170692	F8W755|O95174|Q2TB22|Q5TFU9	Silent	SNP	ENST00000367649.3	hg19	CCDS1321.2																																																																																			.	.	.	none		0.627	RASAL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352415.1	NM_170692		C	178063786	T	C	178063786	2	2	253	1	0	0	0	0	0	0	0	1	13077	1770	62	3		3	RASAL2	1	178063786	Silent	SNP	T	TCGA-SX-A7SS-01A-11D-A35Z-10	16923246	178063786	71186835	7	15739											
CDC73	79577	hgsc.bcm.edu	37	chr1	193119495	193119495	+	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	taacagatacgatcaggaaaGattcaaaggaaaagaaggca	21	5	10	5	1	2	3	2	0	0	3	2	6	2	5	0	3	2	1	0	3	7	3			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr1:193119495G>C	ENST00000367435.3	+	9	1074	c.890G>C	c.(889-891)aGa>aCa	p.R297T		NM_024529.4	NP_078805.3	Q6P1J9	CDC73_HUMAN	cell division cycle 73	297	Interaction with POLR2A and PAF1.				cell cycle (GO:0007049)|cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|protein destabilization (GO:0031648)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleus (GO:0005634)	RNA polymerase II core binding (GO:0000993)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(14)|ovary(1)|pancreas(1)|parathyroid(51)|skin(1)|upper_aerodigestive_tract(1)	87						GATCAGGAAAGATTCAAAGGA	0.393																																					p.R297T		Atlas-SNP	.											.	CDC73	163	.	0			c.G890C						PASS	.						120	119	119					1																	193119495		2203	4300	6503	SO:0001583	missense	79577	exon9			AGGAAAGATTCAA	AF312865	CCDS1382.1	1q25	2014-09-17	2013-01-17	2005-07-20	ENSG00000134371	ENSG00000134371			16783	protein-coding gene	gene with protein product	"Paf1/RNA polymerase II complex component"	607393	"chromosome 1 open reading frame 28", "hyperparathyroidism 2 (with jaw tumor)", "cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)", "hyperparathyroidism 1"	C1orf28, HRPT2, HRPT1		11318611, 15632063, 18755853	Standard	NM_024529		Approved	parafibromin, FIHP	uc001gtb.3	Q6P1J9	OTTHUMG00000035676	ENST00000367435.3:c.890G>C	chr1.hg19:g.193119495G>C	ENSP00000356405:p.Arg297Thr	93.0	0.0	.		90.0	32.0	.	NM_024529	A6NLZ8|B2RBR2|Q6PK51|Q96A07|Q9H245|Q9H5L7	Missense_Mutation	SNP	ENST00000367435.3	hg19	CCDS1382.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.571388	0.86542	.	.	ENSG00000134371	ENST00000367435;ENST00000445394	T	0.64260	-0.09	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.79052	0.4381	M	0.85945	2.785	0.80722	D	1	D	0.54207	0.965	P	0.58780	0.845	T	0.81564	-0.0875	10	0.56958	D	0.05	-21.1674	16.9636	0.86279	0.0:0.0:1.0:0.0	.	297	Q6P1J9	CDC73_HUMAN	T	297	ENSP00000356405:R297T	ENSP00000356405:R297T	R	+	2	0	CDC73	191386118	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.330000	0.79181	2.613000	0.88420	0.655000	0.94253	AGA;AGG	.	.	.	none		0.393	CDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086696.2	NM_024529		C	193119495	G	C	193119495	3	2	253	1	0	0	0	0	1	0	0	0	3087	942	33	4	924	4	CDC73	1	193119495	Missense_Mutation	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10	15055709	193119495	56131126	8	15740											
DISP1	84976	hgsc.bcm.edu	37	chr1	223176848	223176848	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccatttcagaagcatctcgAatttttttcgaaaaagtatt	13	15	6	7	2	2	1	1	0	1	1	4	3	2	1	1	0	1	2	1	0	5	6			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr1:223176848A>G	ENST00000284476.6	+	8	2273	c.2109A>G	c.(2107-2109)cgA>cgG	p.R703R		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	703					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)		AAGCATCTCGAATTTTTTTCG	0.418																																					p.R703R		Atlas-SNP	.											.	DISP1	145	.	0			c.A2109G						PASS	.						129	130	130					1																	223176848		2203	4300	6503	SO:0001819	synonymous_variant	84976	exon10			ATCTCGAATTTTT	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.2109A>G	chr1.hg19:g.223176848A>G		104.0	0.0	.		106.0	58.0	.	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Silent	SNP	ENST00000284476.6	hg19	CCDS1536.1																																																																																			.	.	.	none		0.418	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890		G	223176848	A	G	223176848	2	3	253	1	0	0	0	0	0	0	0	1	4541	233	9	3		3	DISP1	1	223176848	Silent	SNP	A	TCGA-SX-A7SS-01A-11D-A35Z-10	30057353	223176848	26073773	9	15741											
DISC1	27185	hgsc.bcm.edu	37	chr1	232094574	232094574	+	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	atttcctttttttcccccagAaacaagtgtgaaggaaaata	14	13	6	8	0	0	2	0	1	0	1	2	3	2	3	3	1	1	0	3	1	6	5			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr1:232094574A>G	ENST00000439617.2	+	10	2035	c.1982A>G	c.(1981-1983)gAa>gGa	p.E661G	DISC1_ENST00000366637.3_5'UTR|DISC1_ENST00000535983.1_Intron|DISC1_ENST00000537876.1_Splice_Site_p.R545R|DISC1_ENST00000427560.1_3'UTR	NM_001164537.1|NM_001164540.1|NM_018662.2	NP_001158009.1|NP_001158012.1|NP_061132.2	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	661	Interaction with ATF4 and ATF5.|Interaction with TRAF3IP1.|Necessary and sufficient for interaction with PCNT and localization at the centrosome.				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)				TTTCCCCCAGAAACAAGTGTG	0.358																																					p.E693G		Atlas-SNP	.											.	DISC1	207	.	0			c.A2078G						PASS	.						134	119	123					1																	232094574		1844	4087	5931	SO:0001630	splice_region_variant	27185	exon11			CCCCAGAAACAAG	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	ENST00000439617.2:c.1982-1A>G	chr1.hg19:g.232094574A>G		118.0	0.0	.		141.0	77.0	.	NM_001164537	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Missense_Mutation	SNP	ENST00000439617.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.22|11.22	1.575582|1.575582	0.28092|0.28092	.|.	.|.	ENSG00000162946|ENSG00000162946	ENST00000439617;ENST00000366637;ENST00000366638;ENST00000532576|ENST00000422590	T|.	0.10960|.	2.82|.	5.25|5.25	2.93|2.93	0.34026|0.34026	.|.	0.882695|.	0.09800|.	N|.	0.754132|.	T|T	0.36082|0.36082	0.0954|0.0954	N|N	0.20685|0.20685	0.6|0.6	0.80722|0.80722	D|D	1|1	P;B;P;D;B;B;B;B|.	0.60575|.	0.617;0.202;0.617;0.988;0.202;0.202;0.202;0.202|.	B;B;B;P;B;B;B;B|.	0.56343|.	0.306;0.097;0.242;0.796;0.158;0.097;0.097;0.097|.	T|T	0.06267|0.06267	-1.0836|-1.0836	9|5	.|.	.|.	.|.	.|.	5.0735|5.0735	0.14618|0.14618	0.6221:0.0:0.0788:0.2991|0.6221:0.0:0.0788:0.2991	.|.	693;539;693;661;539;661;661;661|.	C4P096;C4P094;E2QRA4;C4P098;F5H1F1;C4P0A4;Q9NRI5-2;Q9NRI5|.	.;.;.;.;.;.;.;DISC1_HUMAN|.	G|E	661;661;693;539|64	ENSP00000403888:E661G|.	.|.	E|K	+|+	2|1	0|0	DISC1|DISC1	230161197|230161197	0.900000|0.900000	0.30661|0.30661	0.670000|0.670000	0.29842|0.29842	0.008000|0.008000	0.06430|0.06430	0.726000|0.726000	0.25984|0.25984	0.439000|0.439000	0.26476|0.26476	-0.336000|-0.336000	0.08194|0.08194	GAA|AAA	.	.	.	none		0.358	DISC1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000092351.2	NM_018662	Missense_Mutation	G	232094574	A	G	232094574	5	3	253	1	0	0	0	0	0	0	1	0	4540	260	9	3	2752	3	DISC1	1	232094574	Splice_Site	SNP	A	TCGA-SX-A7SS-01A-11D-A35Z-10	8917726	232094574	17156047	10	15742											
C2orf70	339778	hgsc.bcm.edu	37	chr2	26798881	26798881	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccatggagaagagccacacTcccttcagccaaggcggcca	11	4	11	15	1	1	2	1	0	0	2	2	3	2	2	5	3	2	0	5	3	2	1			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr2:26798881T>C	ENST00000329615.3	+	2	217	c.186T>C	c.(184-186)acT>acC	p.T62T	C2orf70_ENST00000409392.1_Missense_Mutation_p.S50P	NM_001105519.1	NP_001098989.1	A6NJV1	CB070_HUMAN	chromosome 2 open reading frame 70	62						nucleus (GO:0005634)				breast(3)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(2)	13						AGAGCCACACTCCCTTCAGCC	0.632																																					p.T62T		Atlas-SNP	.											.	C2orf70	26	.	0			c.T186C						PASS	.						113	123	120					2																	26798881		2100	4228	6328	SO:0001819	synonymous_variant	339778	exon2			CCACACTCCCTTC		CCDS42661.1	2p23.3	2011-05-09			ENSG00000173557	ENSG00000173557			27938	protein-coding gene	gene with protein product	"hypothetical protein LOC339778"						Standard	NM_001105519		Approved	LOC339778	uc010eyn.3	A6NJV1	OTTHUMG00000151994	ENST00000329615.3:c.186T>C	chr2.hg19:g.26798881T>C		106.0	0.0	.		86.0	44.0	.	NM_001105519		Silent	SNP	ENST00000329615.3	hg19	CCDS42661.1	.	.	.	.	.	.	.	.	.	.	T	3.981	-0.006358	0.07773	.	.	ENSG00000173557	ENST00000409392	.	.	.	4.68	-0.428	0.12306	.	.	.	.	.	T	0.37945	0.1022	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.39563	-0.9608	5	0.87932	D	0	-0.6075	5.2587	0.15561	0.0:0.3001:0.4213:0.2786	.	.	.	.	P	50	.	ENSP00000386615:S50P	S	+	1	0	C2orf70	26652385	0.000000	0.05858	0.000000	0.03702	0.176000	0.22953	-0.100000	0.10990	-0.085000	0.12573	0.260000	0.18958	TCC	.	.	.	none		0.632	C2orf70-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353258.1	NM_001105519		C	26798881	T	C	26798881	2	2	253	1	0	0	0	0	0	0	0	1	2192	1538	54	3		3	C2orf70	2	26798881	Silent	SNP	T	TCGA-SX-A7SS-01A-11D-A35Z-10		26798881	216400492	11	15743											
MTA3	57504	hgsc.bcm.edu	37	chr2	42931435	42931435	+	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	gcctcagaatcctctcttagGgagagcctgtgagagctgct	8	10	12	11	0	2	3	1	1	1	3	4	5	3	3	3	1	3	2	3	1	2	1			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr2:42931435G>A	ENST00000405094.1	+	12	1127	c.1127G>A	c.(1126-1128)gGg>gAg	p.G376E	MTA3_ENST00000407270.3_Missense_Mutation_p.G376E|MTA3_ENST00000405592.1_Missense_Mutation_p.G319E|MTA3_ENST00000472767.1_3'UTR|MTA3_ENST00000406652.1_Missense_Mutation_p.G319E|MTA3_ENST00000406911.1_Missense_Mutation_p.G375E			Q9BTC8	MTA3_HUMAN	metastasis associated 1 family, member 3	376						intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(9)|ovary(2)|stomach(1)	15						CCTCTCTTAGGGAGAGCCTGT	0.517																																					p.G376E		Atlas-SNP	.											.	MTA3	39	.	0			c.G1127A						PASS	.						105	104	104					2																	42931435		1939	4130	6069	SO:0001583	missense	57504	exon12			TCTTAGGGAGAGC	AB033092	CCDS46267.1, CCDS62900.1	2p22.1	2013-01-25	2004-12-15		ENSG00000057935	ENSG00000057935		"GATA zinc finger domain containing"	23784	protein-coding gene	gene with protein product		609050	"metastasis associated gene family, member 3"			12705869, 14613024	Standard	NM_001282755		Approved	KIAA1266	uc002rsq.3	Q9BTC8	OTTHUMG00000150452	ENST00000405094.1:c.1127G>A	chr2.hg19:g.42931435G>A	ENSP00000385823:p.Gly376Glu	140.0	0.0	.		118.0	48.0	.	NM_020744	Q9NSP2|Q9ULF4	Missense_Mutation	SNP	ENST00000405094.1	hg19		.	.	.	.	.	.	.	.	.	.	G	24.9	4.580971	0.86748	.	.	ENSG00000057935	ENST00000405592;ENST00000406652;ENST00000407270;ENST00000282366;ENST00000406911;ENST00000405094	D;D;D;D;D	0.99683	-6.39;-6.39;-6.39;-6.39;-6.39	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	D	0.99677	0.9879	M	0.78637	2.42	0.80722	D	1	D;D;D	0.76494	0.998;0.995;0.999	D;D;D	0.72982	0.963;0.972;0.979	D	0.98212	1.0473	10	0.72032	D	0.01	-19.9737	20.1931	0.98233	0.0:0.0:1.0:0.0	.	375;376;319	E7EQY4;Q9BTC8-2;D6W5A2	.;.;.	E	319;319;376;376;375;376	ENSP00000383973:G319E;ENSP00000384249:G319E;ENSP00000385045:G376E;ENSP00000385241:G375E;ENSP00000385823:G376E	ENSP00000282366:G376E	G	+	2	0	MTA3	42784939	1.000000	0.71417	0.161000	0.22692	0.689000	0.40095	7.568000	0.82369	2.771000	0.95319	0.563000	0.77884	GGG	.	.	.	none		0.517	MTA3-017	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000318159.1	NM_020744		A	42931435	G	A	42931435	3	1	253	1	0	0	0	0	1	0	0	0	9917	1232	43	2	1173	2	MTA3	2	42931435	Missense_Mutation	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10	16132554	42931435	200267938	12	15744											
ABCG8	64241	hgsc.bcm.edu	37	chr2	44100948	44100948	+	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	gtcagatttccaacgacttcCgagacctgcccaccctcctc	8	9	6	18	2	1	2	1	0	0	2	5	4	4	2	6	0	2	0	6	0	1	2	rs137852991		TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr2:44100948C>T	ENST00000272286.2	+	9	1324	c.1234C>T	c.(1234-1236)Cga>Tga	p.R412*		NM_022437.2	NP_071882.1	Q9H221	ABCG8_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 8	412	ABC transmembrane type-2.				ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|phospholipid transport (GO:0015914)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|protein heterodimerization activity (GO:0046982)|sterol transporter activity (GO:0015248)	p.R412*(1)		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)	CAACGACTTCCGAGACCTGCC	0.537																																					p.R412X		Atlas-SNP	.											ABCG8,NS,carcinoma,0,1	ABCG8	98	.	1	Substitution - Nonsense(1)	endometrium(1)	c.C1234T	GRCh37	CM003583	ABCG8	M	rs137852991	PASS	.						185	184	184					2																	44100948		2203	4300	6503	SO:0001587	stop_gained	64241	exon9			GACTTCCGAGACC	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.1234C>T	chr2.hg19:g.44100948C>T	ENSP00000272286:p.Arg412*	60.0	0.0	.		58.0	3.0	.	NM_022437	Q53QN8	Nonsense_Mutation	SNP	ENST00000272286.2	hg19	CCDS1815.1	.	.	.	.	.	.	.	.	.	.	C	37	6.316278	0.97467	.	.	ENSG00000143921	ENST00000272286	.	.	.	5.16	4.19	0.49359	.	0.110224	0.64402	D	0.000017	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.54	0.84383	0.1692:0.8308:0.0:0.0	.	.	.	.	X	412	.	ENSP00000272286:R412X	R	+	1	2	ABCG8	43954452	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.074000	0.41529	2.420000	0.82092	0.561000	0.74099	CGA	.	.	.	weak		0.537	ABCG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250671.1	NM_022437		T	44100948	C	T	44100948	4	4	253	1	0	0	0	0	0	1	0	0	72	644	23	1	1268	1	ABCG8	2	44100948	Nonsense_Mutation	SNP	C	TCGA-SX-A7SS-01A-11D-A35Z-10	1169513	44100948	199098425	13	15745											
WDR33	55339	hgsc.bcm.edu	37	chr2	128482691	128482691	+	Missense_Mutation	SNP	A	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	gctcttcttttaggtttctgAtatcaaaaagtttacagaga	12	16	7	6	0	4	2	1	1	3	1	4	3	4	2	0	1	1	3	0	1	5	7			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr2:128482691A>C	ENST00000322313.4	-	9	1108	c.950T>G	c.(949-951)aTc>aGc	p.I317S		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	317					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)		TAGGTTTCTGATATCAAAAAG	0.403																																					p.I317S		Atlas-SNP	.											.	WDR33	136	.	0			c.T950G						PASS	.						99	98	98					2																	128482691		2203	4300	6503	SO:0001583	missense	55339	exon9			TTTCTGATATCAA		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.950T>G	chr2.hg19:g.128482691A>C	ENSP00000325377:p.Ile317Ser	142.0	0.0	.		116.0	48.0	.	NM_018383	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Missense_Mutation	SNP	ENST00000322313.4	hg19	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	A	19.38	3.816481	0.70912	.	.	ENSG00000136709	ENST00000322313	T	0.01438	4.89	5.43	5.43	0.79202	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	0.07279	0.0184	M	0.64170	1.965	0.80722	D	1	D	0.65815	0.995	D	0.72982	0.979	T	0.03784	-1.1004	10	0.87932	D	0	-6.5886	15.4804	0.75521	1.0:0.0:0.0:0.0	.	317	Q9C0J8	WDR33_HUMAN	S	317	ENSP00000325377:I317S	ENSP00000325377:I317S	I	-	2	0	WDR33	128199161	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.109000	0.94291	2.058000	0.61347	0.460000	0.39030	ATC	.	.	.	none		0.403	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383		C	128482691	A	C	128482691	3	2	253	1	0	0	0	0	1	0	0	0	17299	333	12	5	3116	5	WDR33	2	128482691	Missense_Mutation	SNP	A	TCGA-SX-A7SS-01A-11D-A35Z-10	84381743	128482691	114716682	14	15746											
MBD5	55777	hgsc.bcm.edu	37	chr2	149243320	149243320	+	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	tcaaactgtaggtgatatgtCatcaataaacaatactttga	16	13	6	6	0	3	2	3	2	0	0	3	2	3	2	0	1	3	1	0	1	8	5			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr2:149243320C>T	ENST00000407073.1	+	11	3852	c.2855C>T	c.(2854-2856)tCa>tTa	p.S952L	MBD5_ENST00000404807.1_Missense_Mutation_p.S1185L	NM_018328.4	NP_060798.2	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	952					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)		GGTGATATGTCATCAATAAAC	0.358																																					p.S952L		Atlas-SNP	.											.	MBD5	164	.	0			c.C2855T						PASS	.						41	37	39					2																	149243320		2203	4300	6503	SO:0001583	missense	55777	exon11			ATATGTCATCAAT	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.2855C>T	chr2.hg19:g.149243320C>T	ENSP00000386049:p.Ser952Leu	159.0	0.0	.		133.0	47.0	.	NM_018328	A5HMQ4|A7E2B1|Q53SR1|Q9NUV6	Missense_Mutation	SNP	ENST00000407073.1	hg19	CCDS33302.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.5|27.5	4.833069|4.833069	0.91036|0.91036	.|.	.|.	ENSG00000204406|ENSG00000204406	ENST00000416015|ENST00000407073;ENST00000404807	.|T;T	.|0.26660	.|1.72;1.72	5.47|5.47	5.47|5.47	0.80525|0.80525	.|.	.|0.122895	.|0.37483	.|N	.|0.002076	T|T	0.16257|0.16257	0.0391|0.0391	N|N	0.14661|0.14661	0.345|0.345	0.35544|0.35544	D|D	0.803325|0.803325	.|P;P	.|0.42518	.|0.782;0.782	.|B;B	.|0.31614	.|0.098;0.133	T|T	0.19582|0.19582	-1.0301|-1.0301	5|10	.|0.72032	.|D	.|0.01	-1.3737|-1.3737	19.3258|19.3258	0.94261|0.94261	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1185;952	.|E9PHH0;Q9P267	.|.;MBD5_HUMAN	Y|L	925|952;1185	.|ENSP00000386049:S952L;ENSP00000384672:S1185L	.|ENSP00000384672:S1185L	H|S	+|+	1|2	0|0	MBD5|MBD5	148959790|148959790	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.677000|5.677000	0.68142|0.68142	2.579000|2.579000	0.87056|0.87056	0.591000|0.591000	0.81541|0.81541	CAT|TCA	.	.	.	none		0.358	MBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318111.2			T	149243320	C	T	149243320	3	4	253	1	0	0	0	0	1	0	0	0	9354	838	29	2	2877	2	MBD5	2	149243320	Missense_Mutation	SNP	C	TCGA-SX-A7SS-01A-11D-A35Z-10	20760629	149243320	93956053	15	15747											
TTN	7273	hgsc.bcm.edu	37	chr2	179606399	179606399	+	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	ttaatagcactccattaaagAaccactgaattttaggtttg	14	14	6	7	0	0	2	0	1	0	1	1	2	1	2	2	1	2	2	2	1	7	6			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr2:179606399A>T	ENST00000591111.1	-	46	10834	c.10610T>A	c.(10609-10611)tTc>tAc	p.F3537Y	TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.F3683Y|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.F3616Y|TTN_ENST00000589042.1_Missense_Mutation_p.F3854Y|TTN_ENST00000460472.2_Missense_Mutation_p.F3491Y|TTN-AS1_ENST00000582847.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13872	Ig-like 21.				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)			TCCATTAAAGAACCACTGAAT	0.403																																					p.F3854Y		Atlas-SNP	.											.	TTN	18412	.	0			c.T11561A						PASS	.						118	114	115					2																	179606399		1916	4118	6034	SO:0001583	missense	7273	exon48			TTAAAGAACCACT	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.10610T>A	chr2.hg19:g.179606399A>T	ENSP00000465570:p.Phe3537Tyr	168.0	0.0	.		124.0	41.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	14.22	2.470726	0.43942	.	.	ENSG00000155657	ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T	0.40756	1.02;1.02;1.02	6.07	6.07	0.98685	.	.	.	.	.	T	0.39436	0.1078	N	0.05280	-0.08	0.24253	N	0.995318	P;P;P	0.51537	0.946;0.946;0.946	P;P;P	0.54060	0.741;0.741;0.741	T	0.46978	-0.9152	9	0.87932	D	0	.	16.635	0.85050	1.0:0.0:0.0:0.0	.	3491;3616;3683	D3DPF9;E7EQE6;E7ET18	.;.;.	Y	3491;3683;3616;3491	ENSP00000434586:F3491Y;ENSP00000340554:F3683Y;ENSP00000352154:F3616Y	ENSP00000340554:F3683Y	F	-	2	0	TTN	179314644	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	6.141000	0.71744	2.330000	0.79161	0.477000	0.44152	TTC	.	.	.	none		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179606399	A	T	179606399	3	4	253	1	0	0	0	0	1	0	0	0	16747	246	9	5	93228	5	TTN	2	179606399	Missense_Mutation	SNP	A	TCGA-SX-A7SS-01A-11D-A35Z-10	30363079	179606399	63592974	16	15748											
MYO1B	4430	hgsc.bcm.edu	37	chr2	192206229	192206230	+	Frame_Shift_Ins	INS	-	-	A																															tatgtggcagctgtttgtggINSaaaaggagcagaagttaatc																										TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr2:192206229_192206230insA	ENST00000392318.3	+	5	636_637	c.389_390insA	c.(388-393)ggaaaafs	p.GK130fs	MYO1B_ENST00000339514.4_Frame_Shift_Ins_p.GK130fs|MYO1B_ENST00000392316.1_Frame_Shift_Ins_p.GK130fs|MYO1B_ENST00000304164.4_Frame_Shift_Ins_p.GK130fs	NM_001130158.1	NP_001123630.1	O43795	MYO1B_HUMAN	myosin IB	130	Myosin motor.				actin filament bundle assembly (GO:0051017)|actin filament organization (GO:0007015)|actin filament-based movement (GO:0030048)|metabolic process (GO:0008152)|post-Golgi vesicle-mediated transport (GO:0006892)	actin filament (GO:0005884)|brush border (GO:0005903)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			NS(1)|central_nervous_system(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(19)|ovary(1)	55			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			GCTGTTTGTGGAAAAGGAGCAG	0.381																																					p.G130fs		Atlas-Indel,Pindel	.											.	MYO1B	160	.	0			c.389_390insA						PASS	.																																			SO:0001589	frameshift_variant	4430	exon5			.	L29138	CCDS2311.1, CCDS46477.1	2q12-q34	2011-09-27			ENSG00000128641	ENSG00000128641		"Myosins / Myosin superfamily : Class I"	7596	protein-coding gene	gene with protein product		606537				8022818, 8449985	Standard	NM_012223		Approved	myr1	uc010fsg.2	O43795	OTTHUMG00000132718	ENST00000392318.3:c.393dupA	chr2.hg19:g.192206233_192206233dupA	ENSP00000376132:p.Gly130fs	154.0	0.0	0		86.0	32.0	0.372093	NM_012223	O43794|Q7Z6L5	Frame_Shift_Ins	INS	ENST00000392318.3	hg19	CCDS46477.1																																																																																			.	.	.	none		0.381	MYO1B-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334774.1	NM_012223		A	192206230	-	A	192206229	7	5	253	1	0	1	1	0	0	0	0	0	10076	1174	41	0	403	0	MYO1B	2	192206229	Frame_Shift_Ins	INS	-	TCGA-SX-A7SS-01A-11D-A35Z-10	12599830	192206229	50993144	17	15749											
COL4A3	1285	hgsc.bcm.edu	37	chr2	228176530	228176530	+	Frame_Shift_Del	DEL	G	G	-																															ttccatcaactgtgaaagctGgggaattagaaaaaataata																										TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr2:228176530delG	ENST00000396578.3	+	52	5119	c.4957delG	c.(4957-4959)gggfs	p.G1653fs	AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000433324.1_RNA|AC097662.2_ENST00000396588.2_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	1653	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)		TGTGAAAGCTGGGGAATTAGA	0.318																																					p.A1652fs		Pindel	.											.	COL4A3	293	.	0			c.4956delT						PASS	.						62	62	62					2																	228176530		1802	4070	5872	SO:0001589	frameshift_variant	1285	exon52			.		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.4957delG	chr2.hg19:g.228176530delG	ENSP00000379823:p.Gly1653fs	642.0	0.0	.		502.0	112.0	0.223	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Frame_Shift_Del	DEL	ENST00000396578.3	hg19	CCDS42829.1																																																																																			.	.	.	none		0.318	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091		-	228176530	G	-	228176530	7	5	253	1	0	1	0	1	0	0	0	0	3693	1357	47	0	5163	0	COL4A3	2	228176530	Frame_Shift_Del	DEL	G	TCGA-SX-A7SS-01A-11D-A35Z-10	35970301	228176530	15022843	18	15750											
UGT1A9	54600	hgsc.bcm.edu	37	chr2	234581095	234581095	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgtggtcttcgccaggggaaTactttgccactatcttgaag	8	12	11	10	2	2	1	0	1	2	0	3	2	2	2	2	3	2	0	2	3	4	5			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr2:234581095T>C	ENST00000354728.4	+	1	597	c.515T>C	c.(514-516)aTa>aCa	p.I172T	UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000609637.1_Missense_Mutation_p.I172T			O60656	UD19_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A9	172					cellular glucuronidation (GO:0052695)|cellular lipid metabolic process (GO:0044255)|drug metabolic process (GO:0017144)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|metabolic process (GO:0008152)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|small molecule metabolic process (GO:0044281)|xenobiotic glucuronidation (GO:0052697)|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)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)			breast(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	37		Breast(86;0.000766)|all_lung(227;0.00269)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0331)|Lung NSC(271;0.0459)|Lung SC(224;0.128)		Epithelial(121;1.26e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000436)|Lung(119;0.00347)|LUSC - Lung squamous cell carcinoma(224;0.00757)	Acetaminophen(DB00316)|Buprenorphine(DB00921)|Canagliflozin(DB08907)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Entacapone(DB00494)|Etodolac(DB00749)|Ezogabine(DB04953)|Flurbiprofen(DB00712)|Haloperidol(DB00502)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ketobemidone(DB06738)|Lumiracoxib(DB01283)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Nateglinide(DB00731)|Niflumic Acid(DB04552)|Oxazepam(DB00842)|Propofol(DB00818)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sulfamethoxazole(DB01015)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zileuton(DB00744)	GCCAGGGGAATACTTTGCCAC	0.468																																					p.I172T		Atlas-SNP	.											.	UGT1A9	79	.	0			c.T515C						PASS	.						170	172	171					2																	234581095		2203	4300	6503	SO:0001583	missense	54600	exon1			GGGGAATACTTTG	AF056188	CCDS2505.1	2q37	2010-03-05	2005-07-20		ENSG00000241119	ENSG00000241119		"UDP glucuronosyltransferases"	12541	other	complex locus constituent		606434	"UDP glycosyltransferase 1 family, polypeptide A9"			9295054, 1910331	Standard	NM_021027		Approved	HLUGP4, LUGP4, UGT1AI		O60656	OTTHUMG00000059124	ENST00000354728.4:c.515T>C	chr2.hg19:g.234581095T>C	ENSP00000346768:p.Ile172Thr	117.0	0.0	.		86.0	38.0	.	NM_021027	B8K285|P36509|Q9HAX0	Missense_Mutation	SNP	ENST00000354728.4	hg19	CCDS2505.1	.	.	.	.	.	.	.	.	.	.	T	0.009	-1.809371	0.00606	.	.	ENSG00000241119	ENST00000354728	T	0.60171	0.21	3.41	0.854	0.19007	.	.	.	.	.	T	0.40094	0.1103	L	0.28694	0.88	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.003	T	0.22452	-1.0216	9	0.21014	T	0.42	.	7.6603	0.28400	0.0:0.1854:0.0:0.8146	.	172;172	Q5DSZ5;O60656	.;UD19_HUMAN	T	172	ENSP00000346768:I172T	ENSP00000346768:I172T	I	+	2	0	UGT1A9	234245834	0.009000	0.17119	0.005000	0.12908	0.099000	0.18886	1.826000	0.39092	0.066000	0.16515	0.362000	0.22060	ATA	.	.	.	none		0.468	UGT1A9-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130995.1	NM_021027		C	234581095	T	C	234581095	3	2	253	1	0	0	0	0	1	0	0	0	16964	1406	49	3	517	3	UGT1A9	2	234581095	Missense_Mutation	SNP	T	TCGA-SX-A7SS-01A-11D-A35Z-10	6404565	234581095	8618278	19	15751											
ZNF660	285349	hgsc.bcm.edu	37	chr3	44636593	44636593	+	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	cactaaggagaaaccctataAatgtagtgagtgtgggaaag	16	8	12	5	0	0	2	0	1	0	1	0	4	0	3	1	2	1	1	1	2	7	4			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr3:44636593A>T	ENST00000322734.2	+	3	1241	c.908A>T	c.(907-909)aAa>aTa	p.K303I	RP11-944L7.4_ENST00000457331.1_RNA	NM_173658.2	NP_775929.2	Q6AZW8	ZN660_HUMAN	zinc finger protein 660	303					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(2)|lung(4)	6				KIRC - Kidney renal clear cell carcinoma(197;0.0468)|Kidney(197;0.0585)		AAACCCTATAAATGTAGTGAG	0.378																																					p.K303I		Atlas-SNP	.											.	ZNF660	28	.	0			c.A908T						PASS	.						62	63	63					3																	44636593		2203	4300	6503	SO:0001583	missense	285349	exon3			CCTATAAATGTAG	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.908A>T	chr3.hg19:g.44636593A>T	ENSP00000324605:p.Lys303Ile	228.0	0.0	.		243.0	151.0	.	NM_173658	Q7Z331|Q8N9M8	Missense_Mutation	SNP	ENST00000322734.2	hg19	CCDS2716.1	.	.	.	.	.	.	.	.	.	.	A	16.02	3.003841	0.54254	.	.	ENSG00000144792	ENST00000322734	T	0.20881	2.04	4.21	4.21	0.49690	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.30039	0.0752	M	0.64170	1.965	0.80722	D	1	P	0.37122	0.583	P	0.45343	0.477	T	0.04041	-1.0982	8	.	.	.	.	12.6704	0.56864	1.0:0.0:0.0:0.0	.	303	Q6AZW8	ZN660_HUMAN	I	303	ENSP00000324605:K303I	.	K	+	2	0	ZNF660	44611597	0.000000	0.05858	1.000000	0.80357	0.992000	0.81027	0.027000	0.13621	1.887000	0.54652	0.528000	0.53228	AAA	.	.	.	none		0.378	ZNF660-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256756.4	NM_173658		T	44636593	A	T	44636593	3	4	253	1	0	0	0	0	1	0	0	0	18082	14	1	5	910	5	ZNF660	3	44636593	Missense_Mutation	SNP	A	TCGA-SX-A7SS-01A-11D-A35Z-10		44636593	153385837	20	15752											
RNF123	63891	hgsc.bcm.edu	37	chr3	49740161	49740162	+	Frame_Shift_Ins	INS	-	-	A																															gggatgaatacaaggcttccINSaatcctcatgcttccttcag																										TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr3:49740161_49740162insA	ENST00000327697.6	+	20	1869_1870	c.1725_1726insA	c.(1726-1728)aatfs	p.N576fs	RNF123_ENST00000432042.1_Frame_Shift_Ins_p.N430fs	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	576					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)		ACAAGGCTTCCAATCCTCATGC	0.569																																					p.S575fs		Atlas-Indel,Pindel	.											.	RNF123	100	.	0			c.1725_1726insA						PASS	.																																			SO:0001589	frameshift_variant	63891	exon20			.	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.1727dupA	chr3.hg19:g.49740163_49740163dupA	ENSP00000328287:p.Asn576fs	65.0	0.0	0		68.0	14.0	0.205882	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Frame_Shift_Ins	INS	ENST00000327697.6	hg19	CCDS33758.1																																																																																			.	.	.	none		0.569	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064		A	49740162	-	A	49740161	7	5	253	1	0	1	1	0	0	0	0	0	13446	581	21	0	1799	0	RNF123	3	49740161	Frame_Shift_Ins	INS	-	TCGA-SX-A7SS-01A-11D-A35Z-10	5103568	49740161	148282269	21	15753											
ITIH1	3697	hgsc.bcm.edu	37	chr3	52822035	52822035	+	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	agccttgcagccttctcctaCtcattccagctccaataccc	8	11	4	18	0	2	0	1	0	1	0	5	0	4	0	6	0	6	2	6	0	3	5			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr3:52822035C>A	ENST00000273283.2	+	17	1982	c.1958C>A	c.(1957-1959)aCt>aAt	p.T653N	ITIH1_ENST00000405128.3_Missense_Mutation_p.T19N|ITIH1_ENST00000537050.1_Missense_Mutation_p.T365N|ITIH1_ENST00000542827.1_Intron|ITIH1_ENST00000540715.1_Missense_Mutation_p.T511N	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	653	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)		CCTTCTCCTACTCATTCCAGC	0.617																																					p.T653N		Atlas-SNP	.											.	ITIH1	108	.	0			c.C1958A						PASS	.						136	125	129					3																	52822035		2203	4300	6503	SO:0001583	missense	3697	exon17			CTCCTACTCATTC		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.1958C>A	chr3.hg19:g.52822035C>A	ENSP00000273283:p.Thr653Asn	194.0	0.0	.		173.0	41.0	.	NM_002215	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Missense_Mutation	SNP	ENST00000273283.2	hg19	CCDS2864.1	.	.	.	.	.	.	.	.	.	.	C	13.90	2.374837	0.42105	.	.	ENSG00000055957	ENST00000273283;ENST00000540715;ENST00000537050;ENST00000428133;ENST00000405128	T;T;T;T;T	0.11604	4.82;4.69;4.51;3.98;2.76	4.0	4.0	0.46444	.	0.496604	0.21728	N	0.070006	T	0.10723	0.0262	N	0.14661	0.345	0.25779	N	0.984742	B;P;D;P	0.67145	0.13;0.704;0.996;0.842	B;B;P;B	0.53649	0.039;0.138;0.731;0.397	T	0.20874	-1.0262	10	0.24483	T	0.36	-19.4772	11.9255	0.52817	0.0:1.0:0.0:0.0	.	511;19;254;653	F5H165;B5MCP1;Q9P1C5;P19827	.;.;.;ITIH1_HUMAN	N	653;511;365;206;19	ENSP00000273283:T653N;ENSP00000443973:T511N;ENSP00000443847:T365N;ENSP00000395836:T206N;ENSP00000384589:T19N	ENSP00000273283:T653N	T	+	2	0	ITIH1	52797075	0.039000	0.19947	0.357000	0.25798	0.136000	0.21042	1.311000	0.33562	2.525000	0.85131	0.655000	0.94253	ACT	.	.	.	none		0.617	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215		A	52822035	C	A	52822035	3	1	253	1	0	0	0	0	1	0	0	0	7910	565	20	4	2024	4	ITIH1	3	52822035	Missense_Mutation	SNP	C	TCGA-SX-A7SS-01A-11D-A35Z-10	3081874	52822035	145200395	22	15754											
DNAH12	201625	hgsc.bcm.edu	37	chr3	57419454	57419454	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagttctataaatgacctttTcttcctctccatagccatgt	9	16	4	12	0	3	1	0	1	3	0	5	1	4	1	4	0	1	1	4	0	4	7			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr3:57419454T>C	ENST00000351747.2	-	31	4868	c.4688A>G	c.(4687-4689)gAa>gGa	p.E1563G		NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	1563	AAA 2. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						AATGACCTTTTCTTCCTCTCC	0.388																																					p.E1563G		Atlas-SNP	.											.	DNAH12	182	.	0			c.A4688G						PASS	.						240	209	218					3																	57419454		692	1591	2283	SO:0001583	missense	201625	exon31			ACCTTTTCTTCCT	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.4688A>G	chr3.hg19:g.57419454T>C	ENSP00000295937:p.Glu1563Gly	82.0	0.0	.		92.0	9.0	.	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000351747.2	hg19		.	.	.	.	.	.	.	.	.	.	T	17.35	3.368116	0.61513	.	.	ENSG00000174844	ENST00000351747;ENST00000495027	T;T	0.52754	0.65;0.65	5.73	5.73	0.89815	ATPase, dynein-related, AAA domain (1);	.	.	.	.	T	0.47985	0.1475	N	0.20610	0.595	0.80722	D	1	D	0.58268	0.982	P	0.56278	0.795	T	0.40627	-0.9553	9	0.27082	T	0.32	.	16.0246	0.80532	0.0:0.0:0.0:1.0	.	1563	Q6ZR08	DYH12_HUMAN	G	1563;1586	ENSP00000295937:E1563G;ENSP00000418137:E1586G	ENSP00000295937:E1563G	E	-	2	0	DNAH12	57394494	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.896000	0.87350	2.175000	0.68902	0.533000	0.62120	GAA	.	.	.	none		0.388	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504		C	57419454	T	C	57419454	3	2	253	1	0	0	0	0	1	0	0	0	4602	1783	62	3	4706	3	DNAH12	3	57419454	Missense_Mutation	SNP	T	TCGA-SX-A7SS-01A-11D-A35Z-10	4597419	57419454	140602976	23	15755											
EPHA6	285220	hgsc.bcm.edu	37	chr3	97311466	97311466	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcttaaaaggatccttcccGgccattggggtggaggcgtt	7	11	13	10	2	1	0	0	0	1	0	3	2	3	2	3	6	0	1	3	6	2	4			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr3:97311466G>A	ENST00000514100.1	+	9	815	c.573G>A	c.(571-573)ccG>ccA	p.P191P	EPHA6_ENST00000389672.5_Silent_p.P799P|EPHA6_ENST00000442602.2_Silent_p.P165P|EPHA6_ENST00000502694.1_Silent_p.P191P	NM_001278300.1	NP_001265229.1	Q9UF33	EPHA6_HUMAN	EPH receptor A6	705	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						GATCCTTCCCGGCCATTGGGG	0.448																																					p.P799P		Atlas-SNP	.											.	EPHA6	439	.	0			c.G2397A						PASS	.						60	61	61					3																	97311466		1820	4086	5906	SO:0001819	synonymous_variant	285220	exon12			CTTCCCGGCCATT	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.573G>A	chr3.hg19:g.97311466G>A		117.0	0.0	.		119.0	33.0	.	NM_001080448	D6RAL5	Silent	SNP	ENST00000514100.1	hg19																																																																																				.	.	.	none		0.448	EPHA6-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000359997.1	NM_001080448		A	97311466	G	A	97311466	2	1	253	1	0	0	0	0	0	0	0	1	5173	1103	39	1		1	EPHA6	3	97311466	Silent	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10	39892012	97311466	100710964	24	15756											
MBNL1	4154	hgsc.bcm.edu	37	chr3	152132779	152132779	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttcatccacccccacattTaaaaacgcagttggagataa	14	10	5	12	1	2	1	1	0	1	1	3	2	3	1	3	1	1	2	3	1	4	5			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr3:152132779T>C	ENST00000463374.1	+	2	735	c.224T>C	c.(223-225)tTa>tCa	p.L75S	MBNL1_ENST00000324210.5_Missense_Mutation_p.L75S|MBNL1_ENST00000545754.1_Missense_Mutation_p.L75S|MBNL1_ENST00000498502.1_Missense_Mutation_p.L75S|MBNL1_ENST00000492948.1_Missense_Mutation_p.L75S|MBNL1_ENST00000485910.1_Missense_Mutation_p.L75S|MBNL1_ENST00000485509.1_Missense_Mutation_p.L75S|MBNL1_ENST00000493459.1_Missense_Mutation_p.L18S|MBNL1_ENST00000282488.7_Missense_Mutation_p.L75S|MBNL1_ENST00000355460.2_Missense_Mutation_p.L75S|MBNL1_ENST00000282486.6_Missense_Mutation_p.L75S|MBNL1_ENST00000324196.5_Missense_Mutation_p.L75S|MBNL1_ENST00000357472.3_Missense_Mutation_p.L75S	NM_207293.1	NP_997176.1	Q9NR56	MBNL1_HUMAN	muscleblind-like splicing regulator 1	75					alternative mRNA splicing, via spliceosome (GO:0000380)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|mRNA splice site selection (GO:0006376)|myoblast differentiation (GO:0045445)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|skeletal muscle tissue development (GO:0007519)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			CCCCCACATTTAAAAACGCAG	0.433																																					p.L75S		Atlas-SNP	.											.	MBNL1	100	.	0			c.T224C						PASS	.						119	112	115					3																	152132779		2203	4300	6503	SO:0001583	missense	4154	exon3			CACATTTAAAAAC	Y13829	CCDS3163.1, CCDS3164.1, CCDS3165.1, CCDS3166.1, CCDS3167.1, CCDS3168.1, CCDS54656.1	3q25	2013-01-18	2012-02-23	2003-03-14	ENSG00000152601	ENSG00000152601		"Zinc fingers, CCCH-type domain containing"	6923	protein-coding gene	gene with protein product		606516	"muscleblind (Drosophila)-like", "muscleblind-like (Drosophila)"	MBNL			Standard	NM_021038		Approved	KIAA0428, EXP42, EXP40, EXP35, EXP	uc003ezm.3	Q9NR56	OTTHUMG00000159163	ENST00000463374.1:c.224T>C	chr3.hg19:g.152132779T>C	ENSP00000418108:p.Leu75Ser	135.0	0.0	.		191.0	115.0	.	NM_207292	E9PBW7|O43311|O43797|Q86UV8|Q86UV9|Q96P92|Q96RE3	Missense_Mutation	SNP	ENST00000463374.1	hg19	CCDS3165.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	29.3|29.3	4.997318|4.997318	0.93167|0.93167	.|.	.|.	ENSG00000152601|ENSG00000152601	ENST00000282486;ENST00000282488;ENST00000355460;ENST00000493459;ENST00000324210;ENST00000459747;ENST00000498502;ENST00000324196;ENST00000545754;ENST00000357472;ENST00000485910;ENST00000463374;ENST00000465907;ENST00000492948;ENST00000485509|ENST00000464596	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T|.	0.46451|.	0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87|.	5.8|5.8	5.8|5.8	0.92144|0.92144	.|.	0.000000|.	0.64402|.	D|.	0.000001|.	D|.	0.83968|.	0.5369|.	M|M	0.89904|0.89904	3.07|3.07	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D;D;D|.	0.97110|.	0.996;0.999;0.994;0.998;0.999;0.992;0.998;1.0|.	D|.	0.87138|.	0.2201|.	10|.	0.87932|.	D|.	0|.	-6.3313|-6.3313	16.1606|16.1606	0.81704|0.81704	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	75;75;75;75;75;18;75;75|.	E9PBW7;Q9NR56-3;Q96RE3;Q9NR56;Q86UV8;Q86VM6;Q9NR56-2;Q96P92|.	.;.;.;MBNL1_HUMAN;.;.;.;.|.	S|Q	75;75;75;18;75;19;75;75;75;75;75;75;75;75;75|74	ENSP00000282486:L75S;ENSP00000282488:L75S;ENSP00000347637:L75S;ENSP00000419347:L18S;ENSP00000319429:L75S;ENSP00000417169:L19S;ENSP00000420327:L75S;ENSP00000319374:L75S;ENSP00000437491:L75S;ENSP00000350064:L75S;ENSP00000418427:L75S;ENSP00000418108:L75S;ENSP00000417630:L75S;ENSP00000420103:L75S;ENSP00000418876:L75S|.	ENSP00000282486:L75S|.	L|X	+|+	2|1	0|0	MBNL1|MBNL1	153615469|153615469	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	7.930000|7.930000	0.87610|0.87610	2.227000|2.227000	0.72691|0.72691	0.460000|0.460000	0.39030|0.39030	TTA|TAA	.	.	.	none		0.433	MBNL1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353604.1	NM_021038		C	152132779	T	C	152132779	3	2	253	1	0	0	0	0	1	0	0	0	9360	1764	61	3	230	3	MBNL1	3	152132779	Missense_Mutation	SNP	T	TCGA-SX-A7SS-01A-11D-A35Z-10	54821313	152132779	45889651	25	15757											
TNFSF10	8743	hgsc.bcm.edu	37	chr3	172224318	172224318	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccccaaaaaaactggcttcAtggtccatgtctatcaagtg	12	10	8	11	0	3	0	2	0	1	0	4	0	4	0	3	2	1	1	3	2	5	2			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr3:172224318A>G	ENST00000241261.2	-	5	932	c.810T>C	c.(808-810)caT>caC	p.H270H	TNFSF10_ENST00000420541.2_3'UTR	NM_003810.3	NP_003801.1	P50591	TNF10_HUMAN	tumor necrosis factor (ligand) superfamily, member 10	270					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|immune response (GO:0006955)|male gonad development (GO:0008584)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to insulin (GO:0032868)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)			breast(2)|cervix(1)|large_intestine(1)|lung(6)|ovary(1)|skin(4)	15	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.67e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)			AACTGGCTTCATGGTCCATGT	0.368																																					p.H270H		Atlas-SNP	.											.	TNFSF10	30	.	0			c.T810C						PASS	.						70	67	68					3																	172224318		2203	4300	6503	SO:0001819	synonymous_variant	8743	exon5			GGCTTCATGGTCC	U37518	CCDS3219.1, CCDS54680.1	3q26	2006-09-20			ENSG00000121858	ENSG00000121858		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11925	protein-coding gene	gene with protein product		603598				8777713, 8663110	Standard	NM_003810		Approved	TRAIL, Apo-2L, TL2, CD253	uc003fid.3	P50591	OTTHUMG00000156917	ENST00000241261.2:c.810T>C	chr3.hg19:g.172224318A>G		262.0	0.0	.		275.0	175.0	.	NM_003810	A1Y9B3	Silent	SNP	ENST00000241261.2	hg19	CCDS3219.1																																																																																			.	.	.	none		0.368	TNFSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346601.1			G	172224318	A	G	172224318	2	3	253	1	0	0	0	0	0	0	0	1	16313	214	8	3		3	TNFSF10	3	172224318	Silent	SNP	A	TCGA-SX-A7SS-01A-11D-A35Z-10	20091539	172224318	25798112	26	15758											
EHHADH	1962	hgsc.bcm.edu	37	chr3	184947277	184947277	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagtctggggagaagctgggTtcctcttgcaccagggagaa	9	8	16	8	0	2	2	0	0	2	2	3	5	3	2	2	4	2	3	2	4	2	2			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr3:184947277T>C	ENST00000231887.3	-	4	481	c.406A>G	c.(406-408)Acc>Gcc	p.T136A	EHHADH_ENST00000475987.1_5'UTR|EHHADH_ENST00000456310.1_Missense_Mutation_p.T40A	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	136	Enoyl-CoA hydratase / isomerase.				fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			AGAAGCTGGGTTCCTCTTGCA	0.468																																					p.T136A		Atlas-SNP	.											.	EHHADH	73	.	0			c.A406G						PASS	.						97	85	89					3																	184947277		2203	4300	6503	SO:0001583	missense	1962	exon4			GCTGGGTTCCTCT	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.406A>G	chr3.hg19:g.184947277T>C	ENSP00000231887:p.Thr136Ala	60.0	0.0	.		90.0	36.0	.	NM_001966	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	hg19	CCDS33901.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.239203	0.79800	.	.	ENSG00000113790	ENST00000537544;ENST00000231887;ENST00000456310	T;T	0.73897	-0.79;-0.79	6.07	4.9	0.64082	Crotonase, core (1);	0.135951	0.64402	D	0.000003	T	0.80939	0.4720	M	0.88031	2.925	0.80722	D	1	P	0.49559	0.925	P	0.46510	0.519	D	0.83620	0.0139	10	0.87932	D	0	-17.9369	11.8215	0.52240	0.1316:0.0:0.0:0.8684	.	136	Q08426	ECHP_HUMAN	A	136;136;40	ENSP00000231887:T136A;ENSP00000387746:T40A	ENSP00000231887:T136A	T	-	1	0	EHHADH	186429971	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.466000	0.60148	1.086000	0.41228	0.528000	0.53228	ACC	.	.	.	none		0.468	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1			C	184947277	T	C	184947277	3	2	253	1	0	0	0	0	1	0	0	0	4984	1725	60	3	1781	3	EHHADH	3	184947277	Missense_Mutation	SNP	T	TCGA-SX-A7SS-01A-11D-A35Z-10	12722959	184947277	13075153	27	15759											
TMEM156	80008	hgsc.bcm.edu	37	chr4	38990469	38990469	+	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	gcactacagggattatacttActctgccacttttgcactct	9	14	6	12	0	2	0	0	0	2	0	2	1	2	1	1	1	5	2	1	1	4	6			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr4:38990469A>C	ENST00000381938.3	-	4	847		c.e4+1			NM_024943.1	NP_079219.1	Q8N614	TM156_HUMAN	transmembrane protein 156							integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|stomach(1)	10						GATTATACTTACTCTGCCACT	0.358																																					.		Atlas-SNP	.											.	TMEM156	31	.	0			c.739+2T>G						PASS	.						156	157	157					4																	38990469		2203	4300	6503	SO:0001630	splice_region_variant	80008	exon5			ATACTTACTCTGC	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.739+1T>G	chr4.hg19:g.38990469A>C		72.0	0.0	.		61.0	30.0	.	NM_024943	Q9H5N9	Splice_Site	SNP	ENST00000381938.3	hg19	CCDS3448.1	.	.	.	.	.	.	.	.	.	.	A	11.88	1.771644	0.31320	.	.	ENSG00000121895	ENST00000381938	.	.	.	5.51	5.51	0.81932	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.9433	0.52913	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TMEM156	38666864	1.000000	0.71417	1.000000	0.80357	0.171000	0.22731	4.188000	0.58351	2.317000	0.78254	0.459000	0.35465	.	.	.	.	none		0.358	TMEM156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250435.3	NM_024943	Intron	C	38990469	A	C	38990469	5	2	253	1	0	0	0	0	0	0	1	0	16085	405	14	5	161	5	TMEM156	4	38990469	Splice_Site	SNP	A	TCGA-SX-A7SS-01A-11D-A35Z-10		38990469	152163807	28	15760											
RASGEF1B	153020	hgsc.bcm.edu	37	chr4	82369435	82369435	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggacattctttctgtatgTctgctagggaataagcgaag	10	13	11	7	1	3	0	0	0	3	0	3	3	3	2	0	2	2	2	0	2	5	5			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr4:82369435T>C	ENST00000264400.2	-	5	593	c.442A>G	c.(442-444)Aca>Gca	p.T148A	RASGEF1B_ENST00000509081.1_Splice_Site_p.T147A|RASGEF1B_ENST00000335927.7_Splice_Site_p.T106A	NM_152545.1	NP_689758.1	Q0VAM2	RGF1B_HUMAN	RasGEF domain family, member 1B	148	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				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						TTTCTGTATGTCTGCTAGGGA	0.473																																					p.T148A		Atlas-SNP	.											.	RASGEF1B	44	.	0			c.A442G						PASS	.						117	106	110					4																	82369435		2203	4300	6503	SO:0001583	missense	153020	exon5			TGTATGTCTGCTA	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.442A>G	chr4.hg19:g.82369435T>C	ENSP00000264400:p.Thr148Ala	96.0	0.0	.		79.0	23.0	.	NM_152545	Q0VAM1|Q4W5L7|Q4W5M3|Q96MY8	Missense_Mutation	SNP	ENST00000264400.2	hg19	CCDS34022.1	.	.	.	.	.	.	.	.	.	.	T	5.620	0.299156	0.10622	.	.	ENSG00000138670	ENST00000509081;ENST00000264400;ENST00000335927	T;T;T	0.28069	1.63;1.63;1.63	5.31	2.9	0.33743	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (2);	0.421187	0.27735	N	0.018077	T	0.13970	0.0338	N	0.11560	0.145	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.09552	-1.0669	10	0.12430	T	0.62	.	9.1866	0.37174	0.0:0.1481:0.0:0.8519	.	106;147;148	Q0VAM2-2;Q0VAM2-3;Q0VAM2	.;.;RGF1B_HUMAN	A	147;148;106	ENSP00000425393:T147A;ENSP00000264400:T148A;ENSP00000338437:T106A	ENSP00000264400:T148A	T	-	1	0	RASGEF1B	82588459	0.997000	0.39634	0.997000	0.53966	0.918000	0.54935	0.682000	0.25335	0.489000	0.27749	0.482000	0.46254	ACA	.	.	.	none		0.473	RASGEF1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362830.1	NM_152545		C	82369435	T	C	82369435	3	2	253	1	0	0	0	0	1	0	0	0	13083	1667	58	3	1019	3	RASGEF1B	4	82369435	Missense_Mutation	SNP	T	TCGA-SX-A7SS-01A-11D-A35Z-10	43378966	82369435	108784841	29	15761											
WDFY3	23001	hgsc.bcm.edu	37	chr4	85731169	85731169	+	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	tttgaaatggctgtgtatttGaggggaagacattcatggcg	10	13	14	4	1	1	3	1	2	0	1	1	4	1	4	0	4	0	2	0	4	3	4	rs79515377		TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr4:85731169G>T	ENST00000295888.4	-	14	2623	c.2216C>A	c.(2215-2217)tCa>tAa	p.S739*	WDFY3-AS1_ENST00000510449.1_RNA|WDFY3_ENST00000322366.6_Nonsense_Mutation_p.S739*	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	739					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)		CTGTGTATTTGAGGGGAAGAC	0.388																																					p.S739X		Atlas-SNP	.											.	WDFY3	314	.	0			c.C2216A						PASS	.						155	149	151					4																	85731169		2203	4300	6503	SO:0001587	stop_gained	23001	exon14			GTATTTGAGGGGA	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.2216C>A	chr4.hg19:g.85731169G>T	ENSP00000295888:p.Ser739*	154.0	0.0	.		155.0	61.0	.	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Nonsense_Mutation	SNP	ENST00000295888.4	hg19	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	G	43	10.432204	0.99404	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.6593	0.99626	0.0:0.0:1.0:0.0	.	.	.	.	X	739	.	ENSP00000295888:S739X	S	-	2	0	WDFY3	85950193	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	9.338000	0.96553	2.885000	0.99019	0.655000	0.94253	TCA	.	.	.	weak		0.388	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		T	85731169	G	T	85731169	4	4	253	1	0	0	0	0	0	1	0	0	17282	1294	45	4	8627	4	WDFY3	4	85731169	Nonsense_Mutation	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10	3361734	85731169	105423107	30	15762											
ANK2	287	hgsc.bcm.edu	37	chr4	114153415	114153415	+	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	aatcagagcactgctacagaGgtaagactgtcagccctaaa	15	7	9	10	0	2	3	2	0	0	3	2	3	2	3	1	1	4	3	1	1	5	3			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr4:114153415G>A	ENST00000357077.4	+	5	536	c.483G>A	c.(481-483)gaG>gaA	p.E161E	ANK2_ENST00000264366.6_Splice_Site_p.E161E|ANK2_ENST00000506722.1_Splice_Site_p.E140E|ANK2_ENST00000394537.3_Splice_Site_p.E161E	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	161					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)		CTGCTACAGAGGTAAGACTGT	0.373																																					p.E161E		Atlas-SNP	.											.	ANK2	576	.	0			c.G483A						PASS	.						108	99	102					4																	114153415		2203	4300	6503	SO:0001630	splice_region_variant	287	exon5			TACAGAGGTAAGA	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.483+1G>A	chr4.hg19:g.114153415G>A		74.0	0.0	.		55.0	23.0	.	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Silent	SNP	ENST00000357077.4	hg19	CCDS3702.1																																																																																			.	.	.	none		0.373	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148	Silent	A	114153415	G	A	114153415	5	1	253	1	0	0	0	0	0	0	1	0	621	1014	35	2	526	2	ANK2	4	114153415	Splice_Site	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10	28422246	114153415	77000861	31	15763											
CCNA2	890	hgsc.bcm.edu	37	chr4	122740067	122740067	+	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	tcaaacttaattctcccaaaAactggaataaaaaatacttt	19	12	2	8	0	2	0	1	0	1	0	3	1	2	1	1	1	3	0	1	1	9	5			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr4:122740067A>C	ENST00000274026.5	-	6	1307	c.1004T>G	c.(1003-1005)tTt>tGt	p.F335C		NM_001237.3	NP_001228	P20248	CCNA2_HUMAN	cyclin A2	335					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic G2 DNA damage checkpoint (GO:0007095)|mitotic nuclear division (GO:0007067)|organ regeneration (GO:0031100)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|response to estradiol (GO:0032355)|response to glucagon (GO:0033762)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	12						TTCTCCCAAAAACTGGAATAA	0.383																																					p.F335C		Atlas-SNP	.											.	CCNA2	30	.	0			c.T1004G						PASS	.						65	66	66					4																	122740067		2203	4300	6503	SO:0001630	splice_region_variant	890	exon6			CCCAAAAACTGGA		CCDS3723.1	4q27	2012-07-12			ENSG00000145386	ENSG00000145386			1578	protein-coding gene	gene with protein product		123835		CCNA, CCN1		1675006	Standard	NM_001237		Approved		uc003iec.4	P20248	OTTHUMG00000133072	ENST00000274026.5:c.1003-1T>G	chr4.hg19:g.122740067A>C		158.0	0.0	.		151.0	65.0	.	NM_001237	A8K7B6|Q2M3U6|Q4W5P4|Q6LER8	Missense_Mutation	SNP	ENST00000274026.5	hg19	CCDS3723.1	.	.	.	.	.	.	.	.	.	.	A	18.32	3.598714	0.66332	.	.	ENSG00000145386	ENST00000274026	T	0.26067	1.76	6.02	6.02	0.97574	Cyclin, C-terminal (1);Cyclin-like (3);	0.226591	0.47455	D	0.000226	T	0.58104	0.2099	M	0.91768	3.24	0.54753	D	0.999987	D	0.89917	1.0	D	0.85130	0.997	T	0.67019	-0.5776	10	0.87932	D	0	.	11.3618	0.49648	0.8331:0.0:0.0:0.1669	.	335	P20248	CCNA2_HUMAN	C	335	ENSP00000274026:F335C	ENSP00000274026:F335C	F	-	2	0	CCNA2	122959517	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	3.008000	0.49544	2.311000	0.77944	0.533000	0.62120	TTT	.	.	.	none		0.383	CCNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256712.2	NM_001237	Missense_Mutation	C	122740067	A	C	122740067	5	2	253	1	0	0	0	0	0	0	1	0	2912	28	1	5	306	5	CCNA2	4	122740067	Splice_Site	SNP	A	TCGA-SX-A7SS-01A-11D-A35Z-10	8586652	122740067	68414209	32	15764											
ZNF827	152485	hgsc.bcm.edu	37	chr4	146686704	146686704	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacctcctccttacctttcTctggcttttcctcactgttc	3	17	3	18	0	2	0	1	0	1	0	7	0	5	0	6	1	1	2	6	1	1	5			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr4:146686704T>C	ENST00000508784.1	-	12	3274	c.3047A>G	c.(3046-3048)gAg>gGg	p.E1016G	ZNF827_ENST00000513320.1_Missense_Mutation_p.E666G|ZNF827_ENST00000379448.4_Missense_Mutation_p.E1016G			Q17R98	ZN827_HUMAN	zinc finger protein 827	1016					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	all_hematologic(180;0.151)					CTTACCTTTCTCTGGCTTTTC	0.537																																					p.E1016G		Atlas-SNP	.											.	ZNF827	102	.	0			c.A3047G						PASS	.						72	65	67					4																	146686704		2203	4300	6503	SO:0001583	missense	152485	exon12			CCTTTCTCTGGCT	AK091130	CCDS34072.1	4q31.22	2013-01-08			ENSG00000151612	ENSG00000151612		"Zinc fingers, C2H2-type"	27193	protein-coding gene	gene with protein product						12477932	Standard	NM_178835		Approved		uc003ikm.3	Q17R98	OTTHUMG00000161362	ENST00000508784.1:c.3047A>G	chr4.hg19:g.146686704T>C	ENSP00000421863:p.Glu1016Gly	58.0	0.0	.		57.0	29.0	.	NM_178835	B7ZL52|Q7Z4S7|Q8N279	Missense_Mutation	SNP	ENST00000508784.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.48|19.48	3.834667|3.834667	0.71373|0.71373	.|.	.|.	ENSG00000151612|ENSG00000151612	ENST00000508784;ENST00000513320;ENST00000379448;ENST00000281318;ENST00000440280|ENST00000511659	T;T;T|.	0.64260|.	-0.09;-0.09;-0.09|.	5.81|5.81	5.81|5.81	0.92471|0.92471	.|.	0.143012|.	0.64402|.	D|.	0.000006|.	T|T	0.53318|0.53318	0.1789|0.1789	N|N	0.24115|0.24115	0.695|0.695	0.58432|0.58432	D|D	0.999996|0.999996	B;P;P;P|.	0.38711|.	0.361;0.455;0.59;0.643|.	B;B;B;B|.	0.38921|.	0.187;0.091;0.187;0.285|.	T|T	0.50074|0.50074	-0.8870|-0.8870	10|5	0.54805|.	T|.	0.06|.	-20.6979|-20.6979	16.1519|16.1519	0.81629|0.81629	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	666;1016;1016;666|.	G5E9Z1;Q17R98;Q17R98-2;E7ESI8|.	.;ZN827_HUMAN;.;.|.	G|G	1016;666;1016;1015;666|117	ENSP00000421863:E1016G;ENSP00000423130:E666G;ENSP00000368761:E1016G|.	ENSP00000281318:E1015G|.	E|R	-|-	2|1	0|2	ZNF827|ZNF827	146906154|146906154	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	7.168000|7.168000	0.77570|0.77570	2.216000|2.216000	0.71823|0.71823	0.533000|0.533000	0.62120|0.62120	GAG|AGA	.	.	.	none		0.537	ZNF827-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000364654.2	NM_178835		C	146686704	T	C	146686704	3	2	253	1	0	0	0	0	1	0	0	0	18192	1551	54	3	194	3	ZNF827	4	146686704	Missense_Mutation	SNP	T	TCGA-SX-A7SS-01A-11D-A35Z-10	23946637	146686704	44467572	33	15765											
SLC45A2	51151	hgsc.bcm.edu	37	chr5	33954590	33954590	+	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	gtgctctcagcagtgactttAatgtcattgccctgcgagtc	7	13	10	11	1	2	1	2	1	1	0	4	2	2	1	1	0	4	2	1	0	1	3			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr5:33954590A>T	ENST00000296589.4	-	4	1054	c.908T>A	c.(907-909)tTa>tAa	p.L303*	SLC45A2_ENST00000509381.1_Silent_p.I194I|SLC45A2_ENST00000382102.3_Nonsense_Mutation_p.L303*|SLC45A2_ENST00000345083.5_Nonsense_Mutation_p.L195*|SLC45A2_ENST00000342059.3_Nonsense_Mutation_p.L244*	NM_016180.3	NP_057264	Q9UMX9	S45A2_HUMAN	solute carrier family 45, member 2	303					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						CAGTGACTTTAATGTCATTGC	0.493																																					p.L303X	Ovarian(31;380 859 8490 22203 49048)	Atlas-SNP	.											.	SLC45A2	100	.	0			c.T908A						PASS	.						183	138	154					5																	33954590		2203	4300	6503	SO:0001587	stop_gained	51151	exon4			GACTTTAATGTCA	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.908T>A	chr5.hg19:g.33954590A>T	ENSP00000296589:p.Leu303*	114.0	0.0	.		86.0	39.0	.	NM_016180	Q6P2P0|Q9BTM3	Nonsense_Mutation	SNP	ENST00000296589.4	hg19	CCDS3901.1	.	.	.	.	.	.	.	.	.	.	A	33	5.261044	0.95368	.	.	ENSG00000164175	ENST00000296589;ENST00000342059;ENST00000382102;ENST00000510600;ENST00000345083	.	.	.	5.85	5.85	0.93711	.	0.356296	0.35320	N	0.003295	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	-14.0922	16.2291	0.82321	1.0:0.0:0.0:0.0	.	.	.	.	X	303;244;303;128;195	.	ENSP00000296589:L303X	L	-	2	0	SLC45A2	33990347	1.000000	0.71417	1.000000	0.80357	0.375000	0.29983	8.710000	0.91388	2.238000	0.73509	0.528000	0.53228	TTA	.	.	.	none		0.493	SLC45A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207443.2	NM_016180		T	33954590	A	T	33954590	4	4	253	1	0	0	0	0	0	1	0	0	14654	372	13	5	715	5	SLC45A2	5	33954590	Nonsense_Mutation	SNP	A	TCGA-SX-A7SS-01A-11D-A35Z-10		33954590	146960670	34	15766											
DAB2	1601	hgsc.bcm.edu	37	chr5	39383191	39383191	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcacggaaaggatcaggattAggggtgggaaagaagttgag	14	7	17	3	1	2	2	2	1	0	1	2	6	2	6	0	6	0	1	0	6	4	2			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr5:39383191A>G	ENST00000320816.6	-	10	1337	c.870T>C	c.(868-870)ccT>ccC	p.P290P	DAB2_ENST00000339788.6_Intron|DAB2_ENST00000509337.1_Silent_p.P269P|DAB2_ENST00000512525.1_5'Flank|DAB2_ENST00000545653.1_Silent_p.P269P	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	290	Required for localization to clathrin- coated pits. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cell morphogenesis involved in differentiation (GO:0000904)|cell proliferation (GO:0008283)|cellular response to transforming growth factor beta stimulus (GO:0071560)|clathrin coat assembly (GO:0048268)|endoderm development (GO:0007492)|excretion (GO:0007588)|in utero embryonic development (GO:0001701)|leading edge cell differentiation (GO:0035026)|membrane organization (GO:0061024)|myeloid cell differentiation (GO:0030099)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein binding (GO:0032091)|negative regulation of protein localization to plasma membrane (GO:1903077)|negative regulation of transcription, DNA-templated (GO:0045892)|pinocytosis (GO:0006907)|positive regulation of cell migration (GO:0030335)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of endocytosis (GO:0045807)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor recycling (GO:0001921)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|clathrin coat of coated pit (GO:0030132)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	cargo receptor activity (GO:0038024)|clathrin adaptor activity (GO:0035615)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein C-terminus binding (GO:0008022)|SMAD binding (GO:0046332)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47	all_lung(31;0.000197)		Epithelial(62;0.137)			GATCAGGATTAGGGGTGGGAA	0.473																																					p.P290P		Atlas-SNP	.											.	DAB2	124	.	0			c.T870C						PASS	.						142	148	146					5																	39383191		2203	4300	6503	SO:0001819	synonymous_variant	1601	exon10			AGGATTAGGGGTG	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.870T>C	chr5.hg19:g.39383191A>G		162.0	0.0	.		135.0	51.0	.	NM_001343	A6NES5|Q13598|Q9BTY0|Q9UK04	Silent	SNP	ENST00000320816.6	hg19	CCDS34149.1																																																																																			.	.	.	none		0.473	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343		G	39383191	A	G	39383191	2	3	253	1	0	0	0	0	0	0	0	1	4220	407	15	3		3	DAB2	5	39383191	Silent	SNP	A	TCGA-SX-A7SS-01A-11D-A35Z-10	5428601	39383191	141532069	35	15767											
ELL2	22936	hgsc.bcm.edu	37	chr5	95234239	95234240	+	Frame_Shift_Ins	INS	-	-	AGGTCTTG																															gactaaaactgtcaacaggtINSaggtcttgagtcccccggcc																										TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr5:95234239_95234240insAGGTCTTG	ENST00000237853.4	-	8	1578_1579	c.1229_1230insCAAGACCT	c.(1228-1230)ctafs	p.-410fs	ELL2_ENST00000431061.2_Frame_Shift_Ins_p.-160fs	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2						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)		TGTCAACAGGTAGGTCTTGAGT	0.485																																					p.L410fs		Atlas-Indel,Pindel	.											.	ELL2	63	.	0			c.1230_1231insCAAGACCT						PASS	.																																			SO:0001589	frameshift_variant	22936	exon8			.	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.1222_1229dupCAAGACCT	chr5.hg19:g.95234240_95234247dupAGGTCTTG	ENSP00000237853:p.Leu410fs	170.0	0.0	0		137.0	32.0	0.233577	NM_012081	B4DNK7	Frame_Shift_Ins	INS	ENST00000237853.4	hg19	CCDS4080.1																																																																																			.	.	.	none		0.485	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081		AGGTCTTG	95234240	-	AGGTCTTG	95234239	7	5	253	1	0	1	1	0	0	0	0	0	5065	1625	57	0	712	0	ELL2	5	95234239	Frame_Shift_Ins	INS	-	TCGA-SX-A7SS-01A-11D-A35Z-10	55851048	95234239	85681021	36	15768											
FTMT	94033	hgsc.bcm.edu	37	chr5	121187742	121187742	+	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	gtgcgctgctgcttcgcgctCccgctgcgttgggccccggg	0	9	16	16	6	0	0	0	0	0	0	2	0	1	0	3	2	4	6	3	2	0	2			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr5:121187742C>A	ENST00000321339.1	+	1	93	c.84C>A	c.(82-84)ctC>ctA	p.L28L		NM_177478.1	NP_803431.1	Q8N4E7	FTMT_HUMAN	ferritin mitochondrial	28					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)		GCTTCGCGCTCCCGCTGCGTT	0.751																																					p.L28L		Atlas-SNP	.											.	FTMT	71	.	0			c.C84A						PASS	.						11	13	13					5																	121187742		2194	4277	6471	SO:0001819	synonymous_variant	94033	exon1			CGCGCTCCCGCTG	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.84C>A	chr5.hg19:g.121187742C>A		33.0	0.0	.		26.0	12.0	.	NM_177478		Silent	SNP	ENST00000321339.1	hg19	CCDS4128.1																																																																																			.	.	.	none		0.751	FTMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250884.1	NM_177478		A	121187742	C	A	121187742	2	1	253	1	0	0	0	0	0	0	0	1	6092	842	30	4		4	FTMT	5	121187742	Silent	SNP	C	TCGA-SX-A7SS-01A-11D-A35Z-10	25953503	121187742	59727518	37	15769											
SLC23A1	9963	hgsc.bcm.edu	37	chr5	138716053	138716054	+	Frame_Shift_Ins	INS	-	-	T																															aatcaccacctccaccacgcINStggacaccatgattgcaccc																										TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr5:138716053_138716054insT	ENST00000348729.3	-	6	536_537	c.490_491insA	c.(490-492)agcfs	p.S164fs	SLC23A1_ENST00000503919.1_5'Flank|SLC23A1_ENST00000353963.3_Frame_Shift_Ins_p.S168fs	NM_005847.4	NP_005838	Q9UHI7	S23A1_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 1	164					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)	CTCCACCACGCTGGACACCATG	0.584																																					p.S168fs		Atlas-Indel,Pindel	.											.	SLC23A1	51	.	0			c.503_504insA						PASS	.																																			SO:0001589	frameshift_variant	9963	exon6			.	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.491dupA	chr5.hg19:g.138716054_138716054dupT	ENSP00000302701:p.Ser164fs	110.0	0.0	0		94.0	33.0	0.351064	NM_152685	O95191|Q8WWB6|Q9UGH4|Q9UI39	Frame_Shift_Ins	INS	ENST00000348729.3	hg19	CCDS4212.1																																																																																			.	.	.	none		0.584	SLC23A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374185.1	NM_152685		T	138716054	-	T	138716053	7	5	253	1	0	1	1	0	0	0	0	0	14475	797	28	0	1341	0	SLC23A1	5	138716053	Frame_Shift_Ins	INS	-	TCGA-SX-A7SS-01A-11D-A35Z-10	17528311	138716053	42199207	38	15770											
PCDHGB3	56102	hgsc.bcm.edu	37	chr5	140751854	140751854	+	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	gaggtgcgcacggcgcgtacCttgggcgacagggaggccgc	6	4	19	12	6	0	0	0	0	0	0	0	3	0	1	2	5	2	2	2	5	1	2			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr5:140751854C>A	ENST00000576222.1	+	1	2024	c.1893C>A	c.(1891-1893)acC>acA	p.T631T	PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA6_ENST00000517434.1_5'Flank|PCDHGB1_ENST00000523390.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3	631	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)			CGGCGCGTACCTTGGGCGACA	0.667																																					p.T631T		Atlas-SNP	.											.	PCDHGB3	168	.	0			c.C1893A						PASS	.						37	42	41					5																	140751854		2147	4254	6401	SO:0001819	synonymous_variant	56102	exon1			GCGTACCTTGGGC	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.1893C>A	chr5.hg19:g.140751854C>A		66.0	0.0	.		58.0	25.0	.	NM_018924	A7E229|Q9Y5C7	Silent	SNP	ENST00000576222.1	hg19	CCDS58980.1																																																																																			.	.	.	none		0.667	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		A	140751854	C	A	140751854	2	1	253	1	0	0	0	0	0	0	0	1	11571	668	24	4		4	PCDHGB3	5	140751854	Silent	SNP	C	TCGA-SX-A7SS-01A-11D-A35Z-10	2035801	140751854	40163406	39	15771											
WWC1	23286	hgsc.bcm.edu	37	chr5	167812372	167812372	+	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	gcttgcacagcaggagtaccAgcaactgcatgccgtctggg	9	7	13	12	1	1	0	0	0	1	0	1	1	1	1	2	2	7	6	2	2	2	2			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr5:167812372A>T	ENST00000265293.4	+	3	888	c.386A>T	c.(385-387)cAg>cTg	p.Q129L	WWC1_ENST00000521089.1_Missense_Mutation_p.Q129L	NM_001161661.1|NM_001161662.1|NM_015238.2	NP_001155133.1|NP_001155134.1|NP_056053.1	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	129					cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|hippo signaling (GO:0035329)|negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of MAPK cascade (GO:0043410)|regulation of hippo signaling (GO:0035330)|regulation of intracellular transport (GO:0032386)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(1)|skin(4)	43	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		CAGGAGTACCAGCAACTGCAT	0.592																																					p.Q129L		Atlas-SNP	.											.	WWC1	98	.	0			c.A386T						PASS	.						84	86	85					5																	167812372		2203	4300	6503	SO:0001583	missense	23286	exon3			AGTACCAGCAACT	AF506799	CCDS4366.1, CCDS54945.1	5q34	2014-06-13	2006-11-09		ENSG00000113645	ENSG00000113645		"WW, C2 and coiled-coil domain containing"	29435	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 168"	610533	"WW, C2 and coiled-coil domain containing 1"			10048485, 12559952	Standard	NM_001161661		Approved	KIBRA, KIAA0869, PPP1R168	uc011den.2	Q8IX03	OTTHUMG00000130408	ENST00000265293.4:c.386A>T	chr5.hg19:g.167812372A>T	ENSP00000265293:p.Gln129Leu	92.0	0.0	.		68.0	34.0	.	NM_015238	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Missense_Mutation	SNP	ENST00000265293.4	hg19	CCDS4366.1	.	.	.	.	.	.	.	.	.	.	A	13.16	2.154225	0.38021	.	.	ENSG00000113645	ENST00000265293;ENST00000521089	T;T	0.05580	3.42;3.42	5.62	3.3	0.37823	.	0.091306	0.43579	D	0.000560	T	0.03783	0.0107	N	0.24115	0.695	0.34096	D	0.661339	B;B;B	0.26147	0.143;0.007;0.005	B;B;B	0.29077	0.098;0.013;0.01	T	0.31280	-0.9949	10	0.08599	T	0.76	.	5.7876	0.18343	0.6246:0.0:0.3754:0.0	.	129;35;129	Q8IX03-2;B3KX05;Q8IX03	.;.;KIBRA_HUMAN	L	129	ENSP00000265293:Q129L;ENSP00000427772:Q129L	ENSP00000265293:Q129L	Q	+	2	0	WWC1	167744950	0.998000	0.40836	0.999000	0.59377	0.903000	0.53119	1.318000	0.33643	0.985000	0.38656	0.459000	0.35465	CAG	.	.	.	none		0.592	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238		T	167812372	A	T	167812372	3	4	253	1	0	0	0	0	1	0	0	0	17423	188	7	5	396	5	WWC1	5	167812372	Missense_Mutation	SNP	A	TCGA-SX-A7SS-01A-11D-A35Z-10	27060518	167812372	13102888	40	15772											
MCM3	4172	hgsc.bcm.edu	37	chr6	52141273	52141273	+	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	cctgcttccagacggcgctcTcctgggaagtgagaaggtaa	9	8	13	11	2	1	2	0	1	1	2	3	4	2	3	3	3	1	3	3	3	3	2			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr6:52141273T>A	ENST00000229854.7	-	9	1243	c.1167A>T	c.(1165-1167)ggA>ggT	p.G389G	MCM3_ENST00000596288.1_Splice_Site_p.G434G|MCM3_ENST00000476448.1_5'UTR|MCM3_ENST00000419835.2_Splice_Site_p.G343G			P25205	MCM3_HUMAN	minichromosome maintenance complex component 3	389	MCM.				DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	alpha DNA polymerase:primase complex (GO:0005658)|centrosome (GO:0005813)|intracellular membrane-bounded organelle (GO:0043231)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Lung NSC(77;0.0931)					GACGGCGCTCTCCTGGGAAGT	0.507																																					p.G434G		Atlas-SNP	.											.	MCM3	63	.	0			c.A1302T						PASS	.						43	40	41					6																	52141273		2203	4300	6503	SO:0001630	splice_region_variant	4172	exon9			GCGCTCTCCTGGG	X62153	CCDS4940.1, CCDS4940.2, CCDS75468.1	6p12	2008-02-05	2007-04-04		ENSG00000112118	ENSG00000112118			6945	protein-coding gene	gene with protein product		602693	"minichromosome maintenance deficient (S. cerevisiae) 3", "MCM3 minichromosome maintenance deficient 3 (S. cerevisiae)"			1549468	Standard	NM_002388		Approved		uc011dwu.2	P25205	OTTHUMG00000014844	ENST00000229854.7:c.1166-1A>T	chr6.hg19:g.52141273T>A		88.0	0.0	.		68.0	56.0	.	NM_002388	B4DWW4|Q92660|Q9BTR3|Q9NUE7	Silent	SNP	ENST00000229854.7	hg19																																																																																				.	.	.	none		0.507	MCM3-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470784.1		Silent	A	52141273	T	A	52141273	5	1	253	1	0	0	0	0	0	0	1	0	9394	1565	54	5	1295	5	MCM3	6	52141273	Splice_Site	SNP	T	TCGA-SX-A7SS-01A-11D-A35Z-10		52141273	118973794	41	15773											
KIAA1586	57691	hgsc.bcm.edu	37	chr6	56917572	56917572	+	Missense_Mutation	SNP	A	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	aacagacacagaaaataatgAagtgagcaaaaatcactgca	22	5	7	7	0	1	4	1	2	0	2	1	4	1	4	0	0	3	2	0	0	7	1			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr6:56917572A>C	ENST00000370733.4	+	4	482	c.275A>C	c.(274-276)gAa>gCa	p.E92A	KIAA1586_ENST00000488682.1_3'UTR|KIAA1586_ENST00000545356.1_Missense_Mutation_p.E65A	NM_020931.2	NP_065982.1	Q9HCI6	K1586_HUMAN	KIAA1586	92							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)			GAAAATAATGAAGTGAGCAAA	0.333																																					p.E92A		Atlas-SNP	.											.	KIAA1586	59	.	0			c.A275C						PASS	.						69	69	69					6																	56917572		2203	4300	6503	SO:0001583	missense	57691	exon4			ATAATGAAGTGAG	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.275A>C	chr6.hg19:g.56917572A>C	ENSP00000359768:p.Glu92Ala	233.0	0.0	.		176.0	144.0	.	NM_020931	A8K4M3|Q8IW25	Missense_Mutation	SNP	ENST00000370733.4	hg19	CCDS34480.1	.	.	.	.	.	.	.	.	.	.	a	10.12	1.262690	0.23051	.	.	ENSG00000168116	ENST00000370733;ENST00000545356	T;T	0.32988	1.44;1.43	3.87	1.41	0.22369	.	.	.	.	.	T	0.05135	0.0137	N	0.08118	0	0.09310	N	1	B;B	0.12630	0.006;0.006	B;B	0.14023	0.01;0.01	T	0.38478	-0.9659	9	0.62326	D	0.03	.	5.6065	0.17383	0.7671:0.0:0.2329:0.0	.	65;92	F5H2N6;Q9HCI6	.;K1586_HUMAN	A	92;65	ENSP00000359768:E92A;ENSP00000445507:E65A	ENSP00000359768:E92A	E	+	2	0	KIAA1586	57025531	0.182000	0.23173	0.000000	0.03702	0.064000	0.16182	1.360000	0.34125	0.183000	0.20059	0.383000	0.25322	GAA	.	.	.	none		0.333	KIAA1586-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041033.1	NM_020931		C	56917572	A	C	56917572	3	2	253	1	0	0	0	0	1	0	0	0	8252	246	9	5	289	5	KIAA1586	6	56917572	Missense_Mutation	SNP	A	TCGA-SX-A7SS-01A-11D-A35Z-10	4776299	56917572	114197495	42	15774											
HBS1L	10767	hgsc.bcm.edu	37	chr6	135358037	135358037	+	Intron	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	cttccctagctttgaacttaGaactttagttcgtgatgatg	9	16	8	8	1	0	4	0	3	0	1	2	4	1	4	1	0	3	2	1	0	5	7			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr6:135358037G>C	ENST00000367837.5	-	4	637				HBS1L_ENST00000367820.2_Intron|HBS1L_ENST00000314674.3_Intron|HBS1L_ENST00000415177.2_Intron|HBS1L_ENST00000367822.5_Missense_Mutation_p.L520V|HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000367826.2_Intron|HBS1L_ENST00000367824.4_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)	p.L520L(1)		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)		TTTGAACTTAGAACTTTAGTT	0.368																																					p.L520V		Atlas-SNP	.											HBS1L_ENST00000367822,NS,carcinoma,0,1	HBS1L	75	.	1	Substitution - coding silent(1)	endometrium(1)	c.C1558G						PASS	.						45	41	42					6																	135358037		692	1591	2283	SO:0001627	intron_variant	10767	exon5			AACTTAGAACTTT	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+2673C>G	chr6.hg19:g.135358037G>C		97.0	0.0	.		120.0	97.0	.	NM_001145207	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Missense_Mutation	SNP	ENST00000367837.5	hg19	CCDS5173.1	.	.	.	.	.	.	.	.	.	.	G	2.970	-0.212719	0.06140	.	.	ENSG00000112339	ENST00000367822	.	.	.	5.32	-2.6	0.06190	.	.	.	.	.	T	0.20047	0.0482	.	.	.	0.43885	D	0.996509	B	0.12630	0.006	B	0.16289	0.015	T	0.19647	-1.0299	7	0.59425	D	0.04	.	0.8108	0.01093	0.2713:0.3313:0.174:0.2234	.	520	Q9Y450-2	.	V	520	.	ENSP00000356796:L520V	L	-	1	2	HBS1L	135399730	0.010000	0.17322	0.359000	0.25824	0.108000	0.19459	-0.189000	0.09629	-0.497000	0.06641	0.655000	0.94253	CTA	.	.	.	none		0.368	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2			C	135358037	G	C	135358037	1	2	253	0	1	0	0	0	0	0	0	0	6994	933	33	4		4	HBS1L	6	135358037	Intron	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10	78440465	135358037	35757030	43	15775											
PCLO	27445	hgsc.bcm.edu	37	chr7	82578940	82578940	+	Missense_Mutation	SNP	T	T	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	ccatatctggatgcagtactTtctgtggacttatatcatca	10	15	7	9	0	4	0	2	0	2	0	4	2	4	2	1	2	2	2	1	2	4	5			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr7:82578940T>G	ENST00000333891.9	-	6	11301	c.10964A>C	c.(10963-10965)aAa>aCa	p.K3655T	PCLO_ENST00000423517.2_Missense_Mutation_p.K3655T|PCLO_ENST00000437081.1_Missense_Mutation_p.K375T	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						ATGCAGTACTTTCTGTGGACT	0.473																																					p.K3655T		Atlas-SNP	.											.	PCLO	1506	.	0			c.A10964C						PASS	.						188	183	185					7																	82578940		1919	4123	6042	SO:0001583	missense	27445	exon6			AGTACTTTCTGTG	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.10964A>C	chr7.hg19:g.82578940T>G	ENSP00000334319:p.Lys3655Thr	111.0	0.0	.		150.0	75.0	.	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	11.43	1.635879	0.29068	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517;ENST00000437081	T;T	0.26810	1.71;1.72	5.7	5.7	0.88788	.	.	.	.	.	T	0.50205	0.1602	M	0.72118	2.19	0.39015	D	0.959633	P;D;D	0.76494	0.608;0.999;0.999	B;D;D	0.67382	0.244;0.951;0.951	T	0.56798	-0.7919	9	0.87932	D	0	.	15.9619	0.79936	0.0:0.0:0.0:1.0	.	3586;3655;3655	Q9Y6V0;Q9Y6V0-5;Q9Y6V0-6	PCLO_HUMAN;.;.	T	3586;3655;3655;375	ENSP00000334319:K3655T;ENSP00000388393:K3655T	ENSP00000334319:K3655T	K	-	2	0	PCLO	82416876	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.689000	0.61723	2.167000	0.68274	0.528000	0.53228	AAA	.	.	.	none		0.473	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		G	82578940	T	G	82578940	3	3	253	1	0	0	0	0	1	0	0	0	11590	1841	64	5	4561	5	PCLO	7	82578940	Missense_Mutation	SNP	T	TCGA-SX-A7SS-01A-11D-A35Z-10		82578940	76559723	44	15776											
FAM71F2	346653	hgsc.bcm.edu	37	chr7	128315818	128315818	+	Frame_Shift_Del	DEL	C	C	-																															tcggtgccctccctgccactCcccaatgtcctcctgatggc																										TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr7:128315818delC	ENST00000480462.1	+	2	376	c.270delC	c.(268-270)ctcfs	p.L90fs	FAM71F2_ENST00000378704.3_Frame_Shift_Del_p.L81fs|FAM71F2_ENST00000460349.1_3'UTR|FAM71F2_ENST00000477515.1_Frame_Shift_Del_p.L90fs			Q6NXP2	F71F2_HUMAN	family with sequence similarity 71, member F2	90										NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(2)	7						CCCTGCCACTCCCCAATGTCC	0.592																																					p.L90fs		Pindel	.											.	FAM71F2	19	.	0			c.269delT						PASS	.						46	46	46					7																	128315818		1942	4148	6090	SO:0001589	frameshift_variant	346653	exon2			.	BC047310	CCDS47701.1, CCDS47702.1	7q32.1	2009-04-17	2007-11-20	2007-11-20	ENSG00000205085	ENSG00000205085			27998	protein-coding gene	gene with protein product			"family with sequence similarity 137, member B"	FAM137B		12477932	Standard	XM_006715964		Approved		uc003vnk.4	Q6NXP2	OTTHUMG00000158275	ENST00000480462.1:c.270delC	chr7.hg19:g.128315818delC	ENSP00000420140:p.Leu90fs	52.0	0.0	.		65.0	10.0	0.154	NM_001012454	Q0VGF6|Q0VGF7|Q86X39	Frame_Shift_Del	DEL	ENST00000480462.1	hg19	CCDS47701.1																																																																																			.	.	.	none		0.592	FAM71F2-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350537.1			-	128315818	C	-	128315818	7	5	253	1	0	1	0	1	0	0	0	0	5620	842	30	0	276	0	FAM71F2	7	128315818	Frame_Shift_Del	DEL	C	TCGA-SX-A7SS-01A-11D-A35Z-10	45736878	128315818	30822845	45	15777	163	2									
FAM71F2	346653	hgsc.bcm.edu	37	chr7	128315824	128315824	+	Frame_Shift_Del	DEL	T	T	-																															ccctccctgccactccccaaTgtcctcctgatggccaatgt																										TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr7:128315824delT	ENST00000480462.1	+	2	382	c.276delT	c.(274-276)aatfs	p.N92fs	FAM71F2_ENST00000378704.3_Frame_Shift_Del_p.N83fs|FAM71F2_ENST00000460349.1_3'UTR|FAM71F2_ENST00000477515.1_Frame_Shift_Del_p.N92fs			Q6NXP2	F71F2_HUMAN	family with sequence similarity 71, member F2	92										NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(2)	7						CACTCCCCAATGTCCTCCTGA	0.602																																					p.N92fs		Atlas-INDEL	.											.	FAM71F2	19	.	0			c.275delA						PASS	.						48	47	47					7																	128315824		1941	4152	6093	SO:0001589	frameshift_variant	346653	exon2			.	BC047310	CCDS47701.1, CCDS47702.1	7q32.1	2009-04-17	2007-11-20	2007-11-20	ENSG00000205085	ENSG00000205085			27998	protein-coding gene	gene with protein product			"family with sequence similarity 137, member B"	FAM137B		12477932	Standard	XM_006715964		Approved		uc003vnk.4	Q6NXP2	OTTHUMG00000158275	ENST00000480462.1:c.276delT	chr7.hg19:g.128315824delT	ENSP00000420140:p.Asn92fs	50.0	0.0	0		69.0	34.0	0.492754	NM_001012454	Q0VGF6|Q0VGF7|Q86X39	Frame_Shift_Del	DEL	ENST00000480462.1	hg19	CCDS47701.1																																																																																			.	.	.	none		0.602	FAM71F2-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350537.1			-	128315824	T	-	128315824	7	5	253	1	0	1	0	1	0	0	0	0	5620	1461	51	0	282	0	FAM71F2	7	128315824	Frame_Shift_Del	DEL	T	TCGA-SX-A7SS-01A-11D-A35Z-10	6	128315824	30822839	46	15778	163	2									
JHDM1D	80853	hgsc.bcm.edu	37	chr7	139818990	139818990	+	Frame_Shift_Del	DEL	G	G	-																															ggaatttgaaaagatctggtGtttttagccttttctccatc																										TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr7:139818990delG	ENST00000397560.2	-	9	1266	c.1169delC	c.(1168-1170)acafs	p.T390fs	JHDM1D_ENST00000006967.5_Frame_Shift_Del_p.T390fs	NM_030647.1	NP_085150.1	Q6ZMT4	KDM7A_HUMAN		390					histone H3-K27 demethylation (GO:0071557)|histone H3-K36 demethylation (GO:0070544)|histone H3-K9 demethylation (GO:0033169)|histone H4-K20 demethylation (GO:0035574)|midbrain development (GO:0030901)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K27 specific) (GO:0071558)|histone demethylase activity (H3-K36 specific) (GO:0051864)|histone demethylase activity (H3-K9 specific) (GO:0032454)|histone demethylase activity (H4-K20 specific) (GO:0035575)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)	22	Melanoma(164;0.0142)					AAGATCTGGTGTTTTTAGCCT	0.308																																					p.T390fs		Atlas-Indel,Pindel	.											.	JHDM1D	54	.	0			c.1170delA						PASS	.						132	129	130					7																	139818990		1792	4064	5856	SO:0001589	frameshift_variant	80853	exon9			.																												ENST00000397560.2:c.1169delC	chr7.hg19:g.139818990delG	ENSP00000380692:p.Thr390fs	128.0	0.0	0		221.0	95.0	0.429864	NM_030647	A4D1S9|C9JJH9|C9JQU2|Q6MZL8|Q9C0E5	Frame_Shift_Del	DEL	ENST00000397560.2	hg19	CCDS43658.1																																																																																			.	.	.	none		0.308	JHDM1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348460.1			-	139818990	G	-	139818990	7	5	253	1	0	1	0	1	0	0	0	0	7955	1377	48	0	1704	0	JHDM1D	7	139818990	Frame_Shift_Del	DEL	G	TCGA-SX-A7SS-01A-11D-A35Z-10	11503166	139818990	19319673	47	15779											
SLC4A2	6522	hgsc.bcm.edu	37	chr7	150773188	150773188	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgtccacagctgcctcccTggccttccccttcatcctca	5	11	5	20	0	2	0	2	0	0	0	6	0	6	0	7	1	2	1	7	1	0	2			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr7:150773188T>C	ENST00000485713.1	+	22	4600	c.3560T>C	c.(3559-3561)cTg>cCg	p.L1187P	SLC4A2_ENST00000461735.1_Missense_Mutation_p.L1173P|FASTK_ENST00000489884.1_5'Flank|SLC4A2_ENST00000392826.2_Missense_Mutation_p.L1178P|RP11-148K1.12_ENST00000485974.1_RNA|SLC4A2_ENST00000413384.2_Missense_Mutation_p.L1187P|SLC4A2_ENST00000310317.5_Missense_Mutation_p.L1105P	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	1187	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)		GCTGCCTCCCTGGCCTTCCCC	0.642																																					p.L1187P		Atlas-SNP	.											.	SLC4A2	98	.	0			c.T3560C						PASS	.						106	100	102					7																	150773188		2203	4300	6503	SO:0001583	missense	6522	exon22			CCTCCCTGGCCTT		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.3560T>C	chr7.hg19:g.150773188T>C	ENSP00000419412:p.Leu1187Pro	44.0	0.0	.		84.0	41.0	.	NM_003040	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Missense_Mutation	SNP	ENST00000485713.1	hg19	CCDS5917.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.466972	0.84425	.	.	ENSG00000164889	ENST00000485713;ENST00000413384;ENST00000310317;ENST00000392826;ENST00000461735	T;T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14;-0.14	5.56	5.56	0.83823	.	0.000000	0.64402	D	0.000009	T	0.80497	0.4634	M	0.82823	2.61	0.80722	D	1	D;D;D	0.89917	0.969;1.0;1.0	P;D;D	0.91635	0.828;0.999;0.997	D	0.83661	0.0161	10	0.87932	D	0	.	14.5667	0.68182	0.0:0.0:0.0:1.0	.	1178;1173;1187	F8W682;P04920-2;P04920	.;.;B3A2_HUMAN	P	1187;1187;1105;1178;1173	ENSP00000419412:L1187P;ENSP00000405600:L1187P;ENSP00000311402:L1105P;ENSP00000376571:L1178P;ENSP00000419164:L1173P	ENSP00000311402:L1105P	L	+	2	0	SLC4A2	150404121	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.125000	0.65367	0.533000	0.62120	CTG	.	.	.	none		0.642	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040		C	150773188	T	C	150773188	3	2	253	1	0	0	0	0	1	0	0	0	14667	1580	55	3	3642	3	SLC4A2	7	150773188	Missense_Mutation	SNP	T	TCGA-SX-A7SS-01A-11D-A35Z-10	10954198	150773188	8365475	48	15780											
AP3M2	10947	hgsc.bcm.edu	37	chr8	42015584	42015584	+	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	tcgaacattcttaaagaactCataaagcctcctaccatcct	14	11	3	13	1	2	1	1	0	1	1	5	2	4	1	4	0	4	0	4	0	7	4			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr8:42015584C>T	ENST00000518421.1	+	4	690	c.399C>T	c.(397-399)ctC>ctT	p.L133L	AP3M2_ENST00000520685.1_Intron|AP3M2_ENST00000174653.3_Silent_p.L133L|AP3M2_ENST00000517922.1_Silent_p.L133L|AP3M2_ENST00000396926.3_Silent_p.L133L	NM_001134296.1	NP_001127768.1	P53677	AP3M2_HUMAN	adaptor-related protein complex 3, mu 2 subunit	133					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)				endometrium(3)|kidney(1)|large_intestine(1)|lung(10)|prostate(1)|stomach(1)	17	all_cancers(6;8.14e-25)|all_epithelial(6;2.41e-27)|all_lung(13;5.09e-13)|Lung NSC(13;8.38e-12)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|Colorectal(10;0.00165)|OV - Ovarian serous cystadenocarcinoma(14;0.00346)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024)			TTAAAGAACTCATAAAGCCTC	0.458																																					p.L133L		Atlas-SNP	.											.	AP3M2	41	.	0			c.C399T						PASS	.						150	137	142					8																	42015584		2203	4300	6503	SO:0001819	synonymous_variant	10947	exon4			AGAACTCATAAAG	D38293	CCDS6125.1	8p11.2	2008-07-07			ENSG00000070718	ENSG00000070718			570	protein-coding gene	gene with protein product		610469				7601449	Standard	NM_006803		Approved	CLA20, AP47B	uc003xoo.3	P53677	OTTHUMG00000164060	ENST00000518421.1:c.399C>T	chr8.hg19:g.42015584C>T		101.0	0.0	.		90.0	35.0	.	NM_001134296	B2RCR0|D3DSY2|Q7Z472	Silent	SNP	ENST00000518421.1	hg19	CCDS6125.1																																																																																			.	.	.	none		0.458	AP3M2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376996.1			T	42015584	C	T	42015584	2	4	253	1	0	0	0	0	0	0	0	1	748	813	29	2		2	AP3M2	8	42015584	Silent	SNP	C	TCGA-SX-A7SS-01A-11D-A35Z-10		42015584	104348438	49	15781											
ARMC1	55156	hgsc.bcm.edu	37	chr8	66517664	66517664	+	Missense_Mutation	SNP	T	T	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	ttaaaatacttacctcagctTtcaaatctgaacggattcgc	13	13	5	10	2	3	1	2	1	1	0	4	2	3	2	1	1	4	1	1	1	6	5	rs561352733		TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr8:66517664T>G	ENST00000276569.3	-	5	819	c.575A>C	c.(574-576)aAa>aCa	p.K192T	ARMC1_ENST00000458464.2_Missense_Mutation_p.K90T	NM_018120.4	NP_060590.1	Q9NVT9	ARMC1_HUMAN	armadillo repeat containing 1	192					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)			TACCTCAGCTTTCAAATCTGA	0.333																																					p.K192T		Atlas-SNP	.											.	ARMC1	22	.	0			c.A575C						PASS	.						73	74	73					8																	66517664		2203	4300	6503	SO:0001583	missense	55156	exon5			TCAGCTTTCAAAT	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.575A>C	chr8.hg19:g.66517664T>G	ENSP00000276569:p.Lys192Thr	209.0	0.0	.		201.0	86.0	.	NM_018120	B4E2W7|Q9H018|Q9H820	Missense_Mutation	SNP	ENST00000276569.3	hg19	CCDS6181.1	.	.	.	.	.	.	.	.	.	.	T	14.85	2.659799	0.47572	.	.	ENSG00000104442	ENST00000276569;ENST00000458464	T;T	0.45668	0.89;0.89	5.36	5.36	0.76844	Heavy metal-associated domain, HMA (1);	0.043521	0.85682	D	0.000000	T	0.38161	0.1030	L	0.52573	1.65	0.58432	D	0.999999	B;B	0.31318	0.319;0.087	B;B	0.26416	0.069;0.018	T	0.20240	-1.0281	10	0.39692	T	0.17	.	15.366	0.74523	0.0:0.0:0.0:1.0	.	90;192	B4E2W7;Q9NVT9	.;ARMC1_HUMAN	T	192;90	ENSP00000276569:K192T;ENSP00000388572:K90T	ENSP00000276569:K192T	K	-	2	0	ARMC1	66680218	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	5.835000	0.69368	2.028000	0.59812	0.454000	0.30748	AAA	.	.	.	none		0.333	ARMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378480.1	NM_018120		G	66517664	T	G	66517664	3	3	253	1	0	0	0	0	1	0	0	0	949	1841	64	5	285	5	ARMC1	8	66517664	Missense_Mutation	SNP	T	TCGA-SX-A7SS-01A-11D-A35Z-10	24502080	66517664	79846358	50	15782											
TLN1	7094	hgsc.bcm.edu	37	chr9	35697810	35697810	+	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	agtgctcatctcgaagctctGaaggcagaaacttgtactgc	11	10	10	10	1	3	2	1	1	2	1	4	3	3	2	0	1	5	4	0	1	4	2			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr9:35697810G>T	ENST00000314888.9	-	57	7957	c.7604C>A	c.(7603-7605)tCa>tAa	p.S2535*	TLN1_ENST00000540444.1_Nonsense_Mutation_p.S2423*	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	2535					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)			TCGAAGCTCTGAAGGCAGAAA	0.552											OREG0019174	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S2535X		Atlas-SNP	.											.	TLN1	185	.	0			c.C7604A						PASS	.						90	88	89					9																	35697810		2203	4300	6503	SO:0001587	stop_gained	7094	exon57			AGCTCTGAAGGCA	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.7604C>A	chr9.hg19:g.35697810G>T	ENSP00000316029:p.Ser2535*	97.0	0.0	.	857	84.0	45.0	.	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Nonsense_Mutation	SNP	ENST00000314888.9	hg19	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	G	50	16.117539	0.99854	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	.	.	.	5.23	5.23	0.72850	.	0.380728	0.27826	N	0.017689	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.3191	18.9866	0.92773	0.0:0.0:1.0:0.0	.	.	.	.	X	2535;2423	.	ENSP00000316029:S2535X	S	-	2	0	TLN1	35687810	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	7.629000	0.83207	2.721000	0.93114	0.563000	0.77884	TCA	.	.	.	none		0.552	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		T	35697810	G	T	35697810	4	4	253	1	0	0	0	0	0	1	0	0	15959	1294	45	4	25	4	TLN1	9	35697810	Nonsense_Mutation	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10		35697810	105515621	51	15783											
CREB3	57704	hgsc.bcm.edu	37	chr9	35736483	35736484	+	IGR	INS	-	-	A																															tgccgaaagacagcacacacINScagtggttggacggctcaga																										TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr9:35736483_35736484insA	ENST00000378103.3	-	0	3611				GBA2_ENST00000467252.1_5'Flank|CREB3_ENST00000486056.1_3'UTR|CREB3_ENST00000353704.2_Frame_Shift_Ins_p.Q293fs	NM_020944.2	NP_065995.1	Q9HCG7	GBA2_HUMAN	glucosidase, beta (bile acid) 2						bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|central nervous system neuron development (GO:0021954)|glucosylceramide catabolic process (GO:0006680)|glycoside catabolic process (GO:0016139)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)	beta-glucosidase activity (GO:0008422)|glucosylceramidase activity (GO:0004348)			NS(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(4)|skin(3)	21	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			ACAGCACACACCAGTGGTTGGA	0.619											OREG0019176	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H292fs		Atlas-Indel,Pindel	.											.	CREB3	24	.	0			c.876_877insA						PASS	.																																			SO:0001628	intergenic_variant	10488	exon9			.	AJ309567	CCDS6589.1	9p13.2	2013-09-11			ENSG00000070610	ENSG00000070610			18986	protein-coding gene	gene with protein product	"bile acid beta-glucosidase", "non-lysosomal glucosylceramidase"	609471	"spastic paraplegia 46 (autosomal recessive)"	SPG46		11489889, 23332916, 23332917	Standard	NM_020944		Approved	KIAA1605, AD035, DKFZp762K054	uc003zxw.3	Q9HCG7	OTTHUMG00000021024		chr9.hg19:g.35736483_35736484insA		77.0	0.0	0	857	44.0	19.0	0.431818	NM_006368	D3DRP2|Q5TCV6|Q96A51|Q96LY1|Q96SJ2|Q9H2L8	Frame_Shift_Ins	INS	ENST00000378103.3	hg19	CCDS6589.1																																																																																			.	.	.	none		0.619	GBA2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055456.1	NM_020944		A	35736484	-	A	35736483	6	5	253	0	1	1	1	0	0	0	0	0	3857	506	18	0		0	CREB3	9	35736483	IGR	INS	-	TCGA-SX-A7SS-01A-11D-A35Z-10	38673	35736483	105476948	52	15784											
SPTLC1	10558	hgsc.bcm.edu	37	chr9	94821586	94821604	+	Splice_Site	DEL	TATCTCTGCAAGGAAAAGA	TATCTCTGCAAGGAAAAGA	-																															aatagcaaagcaggcagctcTatctctgcaaggaaaagaga																								rs575148158|rs376271947		TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	TATCTCTGCAAGGAAAAGA	TATCTCTGCAAGGAAAAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr9:94821586_94821604delTATCTCTGCAAGGAAAAGA	ENST00000262554.2	-	7	566_570	c.561_565delTCTTTTCCTTGCAGAGATA	c.(559-567)gttcttttc>gttc	p.LF188fs	SPTLC1_ENST00000482632.1_5'UTR	NM_006415.2	NP_006406.1	O15269	SPTC1_HUMAN	serine palmitoyltransferase, long chain base subunit 1	188					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphinganine biosynthetic process (GO:0046511)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|serine C-palmitoyltransferase complex (GO:0017059)|SPOTS complex (GO:0035339)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)	p.?(1)		breast(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	14					L-Serine(DB00133)	CAGGCAGCTCTATCTCTGCAAGGAAAAGAGATCCACCAA	0.402																																					p.187_189del		Pindel	.											.	SPTLC1	42	.	1	Unknown(1)	ovary(1)	c.561_566del						PASS	.																																			SO:0001630	splice_region_variant	10558	exon7			.	Y08685	CCDS6692.1, CCDS6693.1	9q22.31	2014-09-17	2003-12-02		ENSG00000090054	ENSG00000090054	2.3.1.50		11277	protein-coding gene	gene with protein product		605712	"hereditary sensory neuropathy, type 1"	HSN1		9363775	Standard	NM_006415		Approved	LCB1, SPTI, HSAN1, hLCB1	uc004arl.1	O15269	OTTHUMG00000021047	ENST00000262554.2:c.561-1TCTTTTCCTTGCAGAGATA>-	chr9.hg19:g.94821586_94821604delTATCTCTGCAAGGAAAAGA		82.0	0.0	.		52.0	10.0	0.192	NM_006415	A8K681|Q5VWB4|Q96IX6	In_Frame_Del	DEL	ENST00000262554.2	hg19	CCDS6692.1																																																																																			.	.	.	none		0.402	SPTLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055553.1	NM_006415	Frame_Shift_Del	-	94821604	TATCTCTGCAAGGAAAAGA	-	94821586	8	5	253	1	0	1	0	1	0	0	1	0	15135	1530	53	0	892	0	SPTLC1	9	94821586	Splice_Site	DEL	TATCTCTGCAAGGAAAAGA	TCGA-SX-A7SS-01A-11D-A35Z-10	59085103	94821586	46391845	53	15785											
C9orf3	84909	hgsc.bcm.edu	37	chr9	97522664	97522664	+	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	tttgcctgcaaatcgttggaGggagcagttagactattacg	10	12	12	7	2	0	1	0	0	0	1	1	3	0	3	1	2	4	4	1	2	4	5			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr9:97522664G>C	ENST00000375315.2	+	1	599	c.599G>C	c.(598-600)aGg>aCg	p.R200T	C9orf3_ENST00000277198.2_Missense_Mutation_p.R200T|C9orf3_ENST00000297979.5_Missense_Mutation_p.R200T	NM_001193329.1	NP_001180258.1	Q8N6M6	AMPO_HUMAN	chromosome 9 open reading frame 3	200					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)		AATCGTTGGAGGGAGCAGTTA	0.498																																					p.R200T		Atlas-SNP	.											.	C9orf3	100	.	0			c.G599C						PASS	.						84	74	77					9																	97522664		2203	4300	6503	SO:0001583	missense	84909	exon2			GTTGGAGGGAGCA	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.599G>C	chr9.hg19:g.97522664G>C	ENSP00000364464:p.Arg200Thr	73.0	0.0	.		52.0	19.0	.	NM_001193331	Q5T9B1|Q5T9B3|Q5T9B4|Q8WUL6|Q96M23|Q96SS1	Missense_Mutation	SNP	ENST00000375315.2	hg19	CCDS55328.1	.	.	.	.	.	.	.	.	.	.	G	13.25	2.180287	0.38511	.	.	ENSG00000148120	ENST00000277198;ENST00000297979;ENST00000375315;ENST00000427193;ENST00000424143	T;T;T;T;T	0.25912	2.56;2.54;2.75;1.77;2.58	4.69	3.79	0.43588	.	0.205241	0.40818	N	0.001006	T	0.33265	0.0857	L	0.60455	1.87	0.80722	D	1	P;D;P;P	0.62365	0.745;0.991;0.763;0.9	B;P;P;P	0.56434	0.276;0.798;0.463;0.65	T	0.06881	-1.0802	10	0.49607	T	0.09	-17.7167	4.3309	0.11062	0.3002:0.0:0.6998:0.0	.	200;200;200;200	Q8N6M6;Q8N6M6-4;Q8N6M6-2;Q8N6M6-3	AMPO_HUMAN;.;.;.	T	200;200;200;74;23	ENSP00000277198:R200T;ENSP00000297979:R200T;ENSP00000364464:R200T;ENSP00000387736:R74T;ENSP00000402171:R23T	ENSP00000277198:R200T	R	+	2	0	C9orf3	96562485	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	1.756000	0.38390	2.591000	0.87537	0.467000	0.42956	AGG	.	.	.	none		0.498	C9orf3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032823		C	97522664	G	C	97522664	3	2	253	1	0	0	0	0	1	0	0	0	2479	1000	35	4	601	4	C9orf3	9	97522664	Missense_Mutation	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10	2701078	97522664	43690767	54	15786											
TTLL11	158135	hgsc.bcm.edu	37	chr9	124751966	124751966	+	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	ctggggtctttaatgaggtaGattccatcaccctgacaacc	10	11	9	11	0	2	3	1	2	1	1	3	3	3	3	3	3	1	1	3	3	3	4			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr9:124751966G>C	ENST00000373776.3	-	4	1234	c.1047C>G	c.(1045-1047)atC>atG	p.I349M	TTLL11_ENST00000321582.5_Missense_Mutation_p.I349M|TTLL11_ENST00000474723.1_5'UTR	NM_194252.2	NP_919228.2	Q8NHH1	TTL11_HUMAN	tubulin tyrosine ligase-like family, member 11	349	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				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						TAATGAGGTAGATTCCATCAC	0.532																																					p.I349M		Atlas-SNP	.											.	TTLL11	67	.	0			c.C1047G						PASS	.						113	121	118					9																	124751966		2203	4300	6503	SO:0001583	missense	158135	exon4			GAGGTAGATTCCA	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.1047C>G	chr9.hg19:g.124751966G>C	ENSP00000362881:p.Ile349Met	109.0	0.0	.		78.0	27.0	.	NM_001139442		Missense_Mutation	SNP	ENST00000373776.3	hg19	CCDS6834.2	.	.	.	.	.	.	.	.	.	.	G	21.3	4.133337	0.77662	.	.	ENSG00000175764	ENST00000321582;ENST00000373776	T;T	0.14144	2.53;2.53	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	T	0.48484	0.1502	M	0.92784	3.345	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.62982	-0.6738	10	0.87932	D	0	.	17.1382	0.86745	0.0:0.0:1.0:0.0	.	349;349	F8W6M1;Q8NHH1	.;TTL11_HUMAN	M	349	ENSP00000321346:I349M;ENSP00000362881:I349M	ENSP00000321346:I349M	I	-	3	3	TTLL11	123791787	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.472000	0.97709	2.283000	0.76528	0.549000	0.68633	ATC	.	.	.	none		0.532	TTLL11-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053907.1	XM_088486		C	124751966	G	C	124751966	3	2	253	1	0	0	0	0	1	0	0	0	16736	932	33	4	1457	4	TTLL11	9	124751966	Missense_Mutation	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10	27229302	124751966	16461465	55	15787											
DNA2	1763	hgsc.bcm.edu	37	chr10	70182647	70182647	+	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	acatgttgttgcaactataaGctaaaaacaaggaaaacaga	20	8	7	6	0	0	1	0	0	0	1	0	2	0	2	0	1	5	4	0	1	9	5			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr10:70182647G>T	ENST00000358410.3	-	15	2259	c.2209C>A	c.(2209-2211)Ctt>Att	p.L737I	DNA2_ENST00000399179.2_Intron|DNA2_ENST00000399180.2_Splice_Site_p.L823I	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2	737	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						GCAACTATAAGCTAAAAACAA	0.294																																					p.L737I		Atlas-SNP	.											.	DNA2	76	.	0			c.C2209A						PASS	.						33	33	33					10																	70182647		1795	4064	5859	SO:0001630	splice_region_variant	1763	exon15			CTATAAGCTAAAA	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.2209-1C>A	chr10.hg19:g.70182647G>T		138.0	0.0	.		170.0	108.0	.	NM_001080449	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Missense_Mutation	SNP	ENST00000358410.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.90|14.90	2.673086|2.673086	0.47781|0.47781	.|.	.|.	ENSG00000138346|ENSG00000138346	ENST00000399180;ENST00000358410|ENST00000440722	D;D|.	0.81996|.	-1.56;-1.56|.	5.8|5.8	5.8|5.8	0.92144|0.92144	.|.	0.805718|.	0.11759|.	N|.	0.532301|.	T|T	0.71239|0.71239	0.3316|0.3316	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	D|D	1|1	B|.	0.20459|.	0.045|.	B|.	0.23716|.	0.048|.	T|T	0.66905|0.66905	-0.5805|-0.5805	10|5	0.27785|.	T|.	0.31|.	.|.	18.2358|18.2358	0.89949|0.89949	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	737|.	P51530|.	DNA2L_HUMAN|.	I|N	823;737|58	ENSP00000382133:L823I;ENSP00000351185:L737I|.	ENSP00000351185:L737I|.	L|T	-|-	1|2	0|0	DNA2|DNA2	69852653|69852653	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	6.533000|6.533000	0.73829|0.73829	2.754000|2.754000	0.94517|0.94517	0.585000|0.585000	0.79938|0.79938	CTT|ACT	.	.	.	none		0.294	DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2		Missense_Mutation	T	70182647	G	T	70182647	5	4	253	1	0	0	0	0	0	0	1	0	4598	985	34	4	1001	4	DNA2	10	70182647	Splice_Site	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10		70182647	65352100	56	15788											
TET1	80312	hgsc.bcm.edu	37	chr10	70432683	70432683	+	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	catgtcaaggaattgatccaGagacttgtggagcttcattc	11	12	10	8	0	2	2	2	1	0	1	4	5	3	4	1	2	1	1	1	2	2	4			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr10:70432683G>C	ENST00000373644.4	+	8	4914	c.4705G>C	c.(4705-4707)Gag>Cag	p.E1569Q		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1569					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						AATTGATCCAGAGACTTGTGG	0.393																																					p.E1569Q		Atlas-SNP	.											.	TET1	255	.	0			c.G4705C						PASS	.						231	213	219					10																	70432683		2203	4300	6503	SO:0001583	missense	80312	exon8			GATCCAGAGACTT	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.4705G>C	chr10.hg19:g.70432683G>C	ENSP00000362748:p.Glu1569Gln	89.0	0.0	.		96.0	54.0	.	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	hg19	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	G	15.57	2.873167	0.51695	.	.	ENSG00000138336	ENST00000373644;ENST00000545846	T	0.09163	3.01	5.35	3.02	0.34903	TET cysteine-rich domain (1);	0.315805	0.34133	N	0.004223	T	0.09379	0.0231	L	0.43923	1.385	0.34559	D	0.71219	B	0.20671	0.047	B	0.21917	0.037	T	0.09552	-1.0669	10	0.52906	T	0.07	.	6.1008	0.20045	0.1921:0.1458:0.6621:0.0	.	1569	Q8NFU7	TET1_HUMAN	Q	1569;41	ENSP00000362748:E1569Q	ENSP00000362748:E1569Q	E	+	1	0	TET1	70102689	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	6.613000	0.74192	0.471000	0.27319	0.585000	0.79938	GAG	.	.	.	none		0.393	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		C	70432683	G	C	70432683	3	2	253	1	0	0	0	0	1	0	0	0	15781	943	33	4	4731	4	TET1	10	70432683	Missense_Mutation	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10	250036	70432683	65102064	57	15789											
NEUROG3	50674	hgsc.bcm.edu	37	chr10	71332496	71332496	+	Missense_Mutation	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	accgcgcagggcgtccagtgCcgagttgaggttgtgcattc	6	9	15	11	4	0	1	0	1	0	0	2	2	1	1	3	2	2	4	3	2	0	3			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr10:71332496C>T	ENST00000242462.4	-	2	333	c.304G>A	c.(304-306)Gca>Aca	p.A102T		NM_020999.3	NP_066279.2	Q9Y4Z2	NGN3_HUMAN	neurogenin 3	102	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				central nervous system development (GO:0007417)|endocrine pancreas development (GO:0031018)|epithelial cell differentiation (GO:0030855)|forebrain development (GO:0030900)|hindbrain development (GO:0030902)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|peripheral nervous system development (GO:0007422)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of dendrite morphogenesis (GO:0048814)|spinal cord development (GO:0021510)|transdifferentiation (GO:0060290)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription coactivator activity (GO:0003713)			endometrium(4)|large_intestine(2)|lung(6)|prostate(1)	13						GCGTCCAGTGCCGAGTTGAGG	0.632																																					p.A102T		Atlas-SNP	.											.	NEUROG3	33	.	0			c.G304A						PASS	.						100	65	77					10																	71332496		2203	4300	6503	SO:0001583	missense	50674	exon2			CCAGTGCCGAGTT	AJ133776	CCDS31212.1	10q21.3	2013-05-21			ENSG00000122859	ENSG00000122859		"Basic helix-loop-helix proteins"	13806	protein-coding gene	gene with protein product		604882				9000438, 10677506	Standard	NM_020999		Approved	Atoh5, Math4B, ngn3, bHLHa7	uc001jpp.3	Q9Y4Z2	OTTHUMG00000018391	ENST00000242462.4:c.304G>A	chr10.hg19:g.71332496C>T	ENSP00000242462:p.Ala102Thr	124.0	0.0	.		103.0	53.0	.	NM_020999	Q5VVI0|Q6DJX6|Q9BY24	Missense_Mutation	SNP	ENST00000242462.4	hg19	CCDS31212.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.671709	0.88348	.	.	ENSG00000122859	ENST00000242462	D	0.98329	-4.87	4.53	4.53	0.55603	Helix-loop-helix DNA-binding (5);	0.000000	0.40728	N	0.001030	D	0.98982	0.9653	M	0.92649	3.33	0.80722	D	1	D	0.69078	0.997	D	0.73380	0.98	D	0.99267	1.0892	10	0.87932	D	0	-15.9262	10.508	0.44845	0.0:0.9052:0.0:0.0948	.	102	Q9Y4Z2	NGN3_HUMAN	T	102	ENSP00000242462:A102T	ENSP00000242462:A102T	A	-	1	0	NEUROG3	71002502	1.000000	0.71417	0.932000	0.37286	0.710000	0.40934	5.808000	0.69165	2.307000	0.77673	0.591000	0.81541	GCA	.	.	.	none		0.632	NEUROG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048464.1	NM_020999		T	71332496	C	T	71332496	3	4	253	1	0	0	0	0	1	0	0	0	10361	739	26	2	344	2	NEUROG3	10	71332496	Missense_Mutation	SNP	C	TCGA-SX-A7SS-01A-11D-A35Z-10	899813	71332496	64202251	58	15790											
DUPD1	338599	hgsc.bcm.edu	37	chr10	76818209	76818209	+	Missense_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	cccttcctcctccatcttcgGcgacagcctcttggcagatg	5	11	8	17	2	2	1	0	0	2	1	6	2	5	1	5	2	1	1	5	2	0	3			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr10:76818209G>A	ENST00000338487.5	-	1	63	c.64C>T	c.(64-66)Ccg>Tcg	p.P22S		NM_001003892.1	NP_001003892.1	Q68J44	DUPD1_HUMAN	dual specificity phosphatase and pro isomerase domain containing 1	22					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)					TCCATCTTCGGCGACAGCCTC	0.552																																					p.P22S		Atlas-SNP	.											.	DUPD1	30	.	0			c.C64T						PASS	.						86	79	82					10																	76818209		2203	4300	6503	SO:0001583	missense	338599	exon1			TCTTCGGCGACAG		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.64C>T	chr10.hg19:g.76818209G>A	ENSP00000340609:p.Pro22Ser	56.0	0.0	.		79.0	45.0	.	NM_001003892	B2RP93	Missense_Mutation	SNP	ENST00000338487.5	hg19	CCDS31223.1	.	.	.	.	.	.	.	.	.	.	G	2.665	-0.278797	0.05642	.	.	ENSG00000188716	ENST00000338487	T	0.04758	3.56	3.74	0.838	0.18902	.	4.428410	0.00520	N	0.000188	T	0.04318	0.0119	N	0.22421	0.69	0.09310	N	1	B	0.26635	0.155	B	0.25405	0.06	T	0.37291	-0.9712	10	0.32370	T	0.25	-4.5968	4.2727	0.10794	0.2154:0.1879:0.5966:0.0	.	22	Q68J44	DUPD1_HUMAN	S	22	ENSP00000340609:P22S	ENSP00000340609:P22S	P	-	1	0	DUPD1	76488215	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.474000	0.22148	0.191000	0.20236	-0.244000	0.11960	CCG	.	.	.	none		0.552	DUPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048777.2	XM_291741		A	76818209	G	A	76818209	3	1	253	1	0	0	0	0	1	0	0	0	4806	1203	42	2	610	2	DUPD1	10	76818209	Missense_Mutation	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10	5485713	76818209	58716538	59	15791											
PYROXD2	84795	hgsc.bcm.edu	37	chr10	100152221	100152222	+	Frame_Shift_Ins	INS	-	-	T																															ttcaggaaggtgatctgcggINStgatgtgttggacagcacca																										TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr10:100152221_100152222insT	ENST00000370575.4	-	10	1077_1078	c.1029_1030insA	c.(1027-1032)tcaccgfs	p.P344fs	PYROXD2_ENST00000483923.1_5'UTR|MIR1287_ENST00000408492.1_RNA	NM_032709.2	NP_116098.2	Q8N2H3	PYRD2_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 2	344							oxidoreductase activity (GO:0016491)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	12						GTGATCTGCGGTGATGTGTTGG	0.54																																					p.P344fs		Atlas-Indel,Pindel	.											.	PYROXD2	43	.	0			c.1030_1031insA						PASS	.																																			SO:0001589	frameshift_variant	84795	exon10			.	AK074429	CCDS7474.1	10q24.2	2009-04-22	2009-04-22	2009-04-22	ENSG00000119943	ENSG00000119943			23517	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 33"	C10orf33			Standard	NM_032709		Approved	FLJ23849	uc001kpc.3	Q8N2H3	OTTHUMG00000018877	ENST00000370575.4:c.1030dupA	chr10.hg19:g.100152222_100152222dupT	ENSP00000359607:p.Pro344fs	60.0	0.0	0		67.0	45.0	0.671642	NM_032709	D3DR61|Q5TAA9|Q9BRQ1	Frame_Shift_Ins	INS	ENST00000370575.4	hg19	CCDS7474.1																																																																																			.	.	.	none		0.54	PYROXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049782.2	NM_032709		T	100152222	-	T	100152221	7	5	253	1	0	1	1	0	0	0	0	0	12880	1261	44	0	743	0	PYROXD2	10	100152221	Frame_Shift_Ins	INS	-	TCGA-SX-A7SS-01A-11D-A35Z-10	23334012	100152221	35382526	60	15792											
BTRC	8945	hgsc.bcm.edu	37	chr10	103294516	103294516	+	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	taatggcatgatggtgacctGctccaaagatcgttccattg	10	12	10	9	1	0	3	0	2	0	1	3	3	2	3	3	2	1	3	3	2	2	3			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr10:103294516G>C	ENST00000370187.3	+	10	1314	c.1196G>C	c.(1195-1197)tGc>tCc	p.C399S	BTRC_ENST00000393441.4_Missense_Mutation_p.C358S|BTRC_ENST00000408038.2_Missense_Mutation_p.C363S	NM_033637.3	NP_378663.1	Q9Y297	FBW1A_HUMAN	beta-transducin repeat containing E3 ubiquitin protein ligase	399					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cellular response to organic cyclic compound (GO:0071407)|G2/M transition of mitotic cell cycle (GO:0000086)|mammary gland epithelial cell proliferation (GO:0033598)|mitotic cell cycle (GO:0000278)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein dephosphorylation (GO:0006470)|protein destabilization (GO:0031648)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(4)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	27		Colorectal(252;0.234)		Epithelial(162;1.05e-08)|all cancers(201;6.59e-07)		ATGGTGACCTGCTCCAAAGAT	0.483																																					p.C399S		Atlas-SNP	.											.	BTRC	64	.	0			c.G1196C						PASS	.						288	229	249					10																	103294516		2203	4300	6503	SO:0001583	missense	8945	exon10			TGACCTGCTCCAA	Y14153	CCDS7511.1, CCDS7512.1, CCDS73183.1	10q24.32	2013-01-10	2012-02-23		ENSG00000166167	ENSG00000166167		"F-boxes / WD-40 domains", "WD repeat domain containing"	1144	protein-coding gene	gene with protein product		603482	"beta-transducin repeat containing"			9660940, 10331953, 18354483	Standard	NM_033637		Approved	bTrCP, betaTrCP, FBXW1A, Fwd1, beta-TrCP1, bTrCP1	uc001kta.4	Q9Y297	OTTHUMG00000018932	ENST00000370187.3:c.1196G>C	chr10.hg19:g.103294516G>C	ENSP00000359206:p.Cys399Ser	128.0	0.0	.		133.0	35.0	.	NM_033637	B5MD49|Q5W141|Q5W142|Q9Y213	Missense_Mutation	SNP	ENST00000370187.3	hg19	CCDS7512.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.760650	0.89932	.	.	ENSG00000166167	ENST00000370187;ENST00000393441;ENST00000408038	T;T;T	0.58797	0.31;0.31;0.31	5.51	5.51	0.81932	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.196293	0.46758	D	0.000272	T	0.71685	0.3369	L	0.45744	1.44	0.80722	D	1	D;D;D	0.89917	0.997;1.0;1.0	D;D;D	0.91635	0.969;0.991;0.999	T	0.69431	-0.5147	10	0.41790	T	0.15	-9.4875	19.4137	0.94687	0.0:0.0:1.0:0.0	.	373;363;399	B7Z3H4;Q9Y297-2;Q9Y297	.;.;FBW1A_HUMAN	S	399;358;363	ENSP00000359206:C399S;ENSP00000377088:C358S;ENSP00000385339:C363S	ENSP00000359206:C399S	C	+	2	0	BTRC	103284506	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.597000	0.87782	0.655000	0.94253	TGC	.	.	.	none		0.483	BTRC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049936.1	NM_033637		C	103294516	G	C	103294516	3	2	253	1	0	0	0	0	1	0	0	0	1571	1319	46	4	1234	4	BTRC	10	103294516	Missense_Mutation	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10	3142295	103294516	32240231	61	15793											
IGSF22	283284	hgsc.bcm.edu	37	chr11	18738437	18738444	+	Frame_Shift_Del	DEL	ACTTCCAC	ACTTCCAC	-																															cttcagctccttcccattgaActtccacacaaagttgggct																										TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	ACTTCCAC	ACTTCCAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr11:18738437_18738444delACTTCCAC	ENST00000513874.1	-	10	1216_1223	c.1077_1084delGTGGAAGT	c.(1075-1086)gtgtggaagttcfs	p.WKF360fs	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	360										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						TTCCCATTGAACTTCCACACAAAGTTGG	0.505																																					p.360_362del		Atlas-Indel,Pindel	.											.	IGSF22	211	.	0			c.1078_1085del						PASS	.																																			SO:0001589	frameshift_variant	283284	exon10			.	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.1077_1084delGTGGAAGT	chr11.hg19:g.18738437_18738444delACTTCCAC	ENSP00000421191:p.Trp360fs	159.0	0.0	0		101.0	23.0	0.227723	NM_173588	A6NNA0|D6RGV7	Frame_Shift_Del	DEL	ENST00000513874.1	hg19	CCDS41625.2																																																																																			.	.	.	none		0.505	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588		-	18738444	ACTTCCAC	-	18738437	7	5	253	1	0	1	0	1	0	0	0	0	7607	43	2	0	2952	0	IGSF22	11	18738437	Frame_Shift_Del	DEL	ACTTCCAC	TCGA-SX-A7SS-01A-11D-A35Z-10		18738437	116268079	62	15794											
FTH1	2495	hgsc.bcm.edu	37	chr11	61732247	61732247	+	Missense_Mutation	SNP	T	T	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	gtgtgcttgtcaaagagataTtccgccaagccagattcggg	10	10	12	9	2	1	2	1	0	0	2	3	3	2	2	3	1	2	1	3	1	3	4			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr11:61732247T>G	ENST00000273550.7	-	4	738	c.504A>C	c.(502-504)gaA>gaC	p.E168D	BEST1_ENST00000449131.2_3'UTR|FTH1_ENST00000532601.1_Missense_Mutation_p.E98D|FTH1_ENST00000529191.1_Intron|FTH1_ENST00000529631.1_Intron|FTH1_ENST00000526640.1_Missense_Mutation_p.E138D	NM_002032.2	NP_002023.2	P02794	FRIH_HUMAN	ferritin, heavy polypeptide 1	168					cellular iron ion homeostasis (GO:0006879)|immune response (GO:0006955)|intracellular sequestering of iron ion (GO:0006880)|iron ion transport (GO:0006826)|membrane organization (GO:0061024)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fibroblast proliferation (GO:0048147)|post-Golgi vesicle-mediated transport (GO:0006892)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular ferritin complex (GO:0008043)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ferric iron binding (GO:0008199)|ferroxidase activity (GO:0004322)|iron ion binding (GO:0005506)			NS(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8					Iron Dextran(DB00893)	CAAAGAGATATTCCGCCAAGC	0.522																																					p.E168D		Atlas-SNP	.											.	FTH1	18	.	0			c.A504C						PASS	.						57	55	55					11																	61732247		1872	4092	5964	SO:0001583	missense	2495	exon4			GAGATATTCCGCC		CCDS41655.1	11q13	2012-10-02			ENSG00000167996	ENSG00000167996			3976	protein-coding gene	gene with protein product	"apoferritin", "placenta immunoregulatory factor", "proliferation-inducing protein 15"	134770		FTHL6		3020541	Standard	NM_002032		Approved	FTH, PLIF, PIG15, FHC	uc001nsu.3	P02794		ENST00000273550.7:c.504A>C	chr11.hg19:g.61732247T>G	ENSP00000273550:p.Glu168Asp	343.0	0.0	.		289.0	114.0	.	NM_002032	B3KNR5|Q3KRA8|Q3SWW1	Missense_Mutation	SNP	ENST00000273550.7	hg19	CCDS41655.1	.	.	.	.	.	.	.	.	.	.	.	14.79	2.640495	0.47153	.	.	ENSG00000167996	ENST00000273550;ENST00000406545;ENST00000526640;ENST00000532601	T;T;T	0.71103	-0.54;-0.54;-0.54	5.13	0.569	0.17340	Ferritin/ribonucleotide reductase-like (1);Ferritin-related (1);	0.000000	0.85682	D	0.000000	T	0.75072	0.3800	M	0.92649	3.33	0.54753	D	0.999983	B	0.10296	0.003	B	0.21546	0.035	T	0.72469	-0.4284	10	0.66056	D	0.02	.	10.9125	0.47116	0.0:0.697:0.0:0.303	.	168	P02794	FRIH_HUMAN	D	168;217;138;98	ENSP00000273550:E168D;ENSP00000433321:E138D;ENSP00000435111:E98D	ENSP00000273550:E168D	E	-	3	2	FTH1	61488823	1.000000	0.71417	0.992000	0.48379	0.907000	0.53573	0.791000	0.26915	0.064000	0.16427	-1.670000	0.00746	GAA	.	.	.	none		0.522	FTH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388444.1	NM_002032		G	61732247	T	G	61732247	3	3	253	1	0	0	0	0	1	0	0	0	6089	1490	52	5	51	5	FTH1	11	61732247	Missense_Mutation	SNP	T	TCGA-SX-A7SS-01A-11D-A35Z-10	42993810	61732247	73274269	63	15795											
MRPL49	740	hgsc.bcm.edu	37	chr11	64892052	64892052	+	Missense_Mutation	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	agtttgtggagcgcctgttaCcggctaccaggatcccagat	8	10	12	11	2	0	1	0	0	0	1	1	3	1	3	4	3	3	3	4	3	2	3			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr11:64892052C>T	ENST00000279242.2	+	2	176	c.157C>T	c.(157-159)Ccg>Tcg	p.P53S	FAU_ENST00000529639.1_5'Flank|FAU_ENST00000525297.1_5'Flank|FAU_ENST00000279259.3_5'Flank|FAU_ENST00000527548.1_5'Flank|MRPL49_ENST00000524482.1_3'UTR|FAU_ENST00000529259.1_5'Flank|MRPL49_ENST00000531705.1_Missense_Mutation_p.P53S|MRPL49_ENST00000534078.1_Intron|FAU_ENST00000531743.1_5'Flank|MRPL49_ENST00000526171.1_Missense_Mutation_p.P53S|FAU_ENST00000434372.2_5'Flank	NM_004927.3	NP_004918.1	Q13405	RM49_HUMAN	mitochondrial ribosomal protein L49	53					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	structural constituent of ribosome (GO:0003735)			endometrium(1)|ovary(1)	2						GCGCCTGTTACCGGCTACCAG	0.532																																					p.P53S		Atlas-SNP	.											.	MRPL49	5	.	0			c.C157T						PASS	.						95	95	95					11																	64892052		2201	4297	6498	SO:0001583	missense	740	exon2			CTGTTACCGGCTA		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	ENST00000279242.2:c.157C>T	chr11.hg19:g.64892052C>T	ENSP00000279242:p.Pro53Ser	169.0	0.0	.		129.0	61.0	.	NM_004927	B2R4G6	Missense_Mutation	SNP	ENST00000279242.2	hg19	CCDS8096.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.428742	0.83667	.	.	ENSG00000149792	ENST00000526171;ENST00000279242;ENST00000531705	T;T;T	0.61274	0.63;0.66;0.12	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.77605	0.4155	M	0.81341	2.54	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.78650	-0.2121	10	0.51188	T	0.08	-14.1545	17.02	0.86431	0.0:1.0:0.0:0.0	.	53	Q13405	RM49_HUMAN	S	53	ENSP00000437177:P53S;ENSP00000279242:P53S;ENSP00000436740:P53S	ENSP00000279242:P53S	P	+	1	0	MRPL49	64648628	1.000000	0.71417	0.999000	0.59377	0.546000	0.35178	6.539000	0.73856	2.632000	0.89209	0.655000	0.94253	CCG	.	.	.	none		0.532	MRPL49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385293.1	NM_004927		T	64892052	C	T	64892052	3	4	253	1	0	0	0	0	1	0	0	0	9820	507	18	2	163	2	MRPL49	11	64892052	Missense_Mutation	SNP	C	TCGA-SX-A7SS-01A-11D-A35Z-10	3159805	64892052	70114464	64	15796											
C11orf54	28970	hgsc.bcm.edu	37	chr11	93494797	93494797	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttggatacttcttacctgcAgagtttctctatcgcattga	8	16	7	10	1	2	2	0	1	2	1	4	3	2	3	1	1	3	3	1	1	3	7			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr11:93494797A>G	ENST00000331239.4	+	9	1070	c.891A>G	c.(889-891)gcA>gcG	p.A297A	C11orf54_ENST00000528288.1_Silent_p.A247A|C11orf54_ENST00000528099.1_Silent_p.A297A|C11orf54_ENST00000354421.3_Silent_p.A297A|C11orf54_ENST00000540113.1_Silent_p.A278A			Q9H0W9	CK054_HUMAN	chromosome 11 open reading frame 54	297					metabolic process (GO:0008152)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|large_intestine(1)|lung(5)	8		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TCTTACCTGCAGAGTTTCTCT	0.363																																					p.A247A		Atlas-SNP	.											.	C11orf54	23	.	0			c.A741G						PASS	.						132	120	124					11																	93494797		2201	4298	6499	SO:0001819	synonymous_variant	28970	exon8			ACCTGCAGAGTTT	AF092133	CCDS8294.1, CCDS66204.1, CCDS73365.1, CCDS73366.1	11q21	2012-08-09			ENSG00000182919	ENSG00000182919			30204	protein-coding gene	gene with protein product		615810				16522806	Standard	NM_014039		Approved	PTD012	uc001pef.3	Q9H0W9	OTTHUMG00000167452	ENST00000331239.4:c.891A>G	chr11.hg19:g.93494797A>G		123.0	0.0	.		104.0	45.0	.	NM_014039	A8K850|Q6FI88|Q6XYB0|Q96EI3|Q96IX1|Q9Y6B4	Silent	SNP	ENST00000331239.4	hg19																																																																																				.	.	.	none		0.363	C11orf54-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394671.1	NM_014039		G	93494797	A	G	93494797	2	3	253	1	0	0	0	0	0	0	0	1	1651	175	7	3		3	C11orf54	11	93494797	Silent	SNP	A	TCGA-SX-A7SS-01A-11D-A35Z-10	28602745	93494797	41511719	65	15797											
GPR19	2842	hgsc.bcm.edu	37	chr12	12814283	12814283	+	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	tgccaacgtagttttttttgGccatccttgaacttgttgtg	6	18	9	8	1	0	1	0	1	0	0	1	1	1	1	3	1	3	3	3	1	3	8			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr12:12814283G>C	ENST00000540510.1	-	2	1292	c.1100C>G	c.(1099-1101)gCc>gGc	p.A367G	GPR19_ENST00000332427.2_Missense_Mutation_p.A367G			P46093	GPR4_HUMAN	G protein-coupled receptor 19	329					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	17		Prostate(47;0.0802)		BRCA - Breast invasive adenocarcinoma(232;0.048)		GTTTTTTTTGGCCATCCTTGA	0.393																																					p.A367G		Atlas-SNP	.											.	GPR19	47	.	0			c.C1100G						PASS	.						197	183	188					12																	12814283		2203	4300	6503	SO:0001583	missense	2842	exon4			TTTTTGGCCATCC		CCDS8652.1	12p12.3	2014-01-30				ENSG00000183150		"GPCR / Class A : Orphans"	4473	protein-coding gene	gene with protein product		602927					Standard	NM_006143		Approved		uc001raq.2	Q15760		ENST00000540510.1:c.1100C>G	chr12.hg19:g.12814283G>C	ENSP00000441832:p.Ala367Gly	120.0	0.0	.		125.0	41.0	.	NM_006143	A8K3T3|B0M0K1|Q6NWM4	Missense_Mutation	SNP	ENST00000540510.1	hg19	CCDS8652.1	.	.	.	.	.	.	.	.	.	.	G	16.19	3.053890	0.55218	.	.	ENSG00000183150	ENST00000540510;ENST00000332427	T;T	0.69306	-0.39;-0.39	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.69922	0.3165	N	0.14661	0.345	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.69101	-0.5234	10	0.29301	T	0.29	-24.4311	19.3003	0.94141	0.0:0.0:1.0:0.0	.	367	Q15760	GPR19_HUMAN	G	367	ENSP00000441832:A367G;ENSP00000333744:A367G	ENSP00000333744:A367G	A	-	2	0	GPR19	12705550	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.858000	0.99539	2.658000	0.90341	0.650000	0.86243	GCC	.	.	.	none		0.393	GPR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400662.1	NM_006143		C	12814283	G	C	12814283	3	2	253	1	0	0	0	0	1	0	0	0	6686	1203	42	4	151	4	GPR19	12	12814283	Missense_Mutation	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10		12814283	121037612	66	15798											
IPO8	10526	hgsc.bcm.edu	37	chr12	30792466	30792466	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tacccaagaaaacaatctgtAtcattcatccattgatttat	15	14	3	9	0	3	2	2	1	1	1	4	2	4	2	2	0	2	1	2	0	7	6			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr12:30792466A>G	ENST00000256079.4	-	21	2810	c.2472T>C	c.(2470-2472)gaT>gaC	p.D824D	IPO8_ENST00000544829.1_Silent_p.D619D	NM_006390.3	NP_006381.2	O15397	IPO8_HUMAN	importin 8	824					intracellular protein transport (GO:0006886)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	Ran GTPase binding (GO:0008536)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(16)|liver(1)|lung(22)|prostate(2)|skin(2)|urinary_tract(2)	52	all_lung(12;6.66e-10)|Lung NSC(12;4.84e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					AACAATCTGTATCATTCATCC	0.343																																					p.D824D		Atlas-SNP	.											.	IPO8	105	.	0			c.T2472C						PASS	.						122	113	116					12																	30792466		2203	4300	6503	SO:0001819	synonymous_variant	10526	exon21			ATCTGTATCATTC	U77494	CCDS8719.1, CCDS53773.1	12p11.21	2011-05-23	2003-03-11	2003-03-14	ENSG00000133704	ENSG00000133704		"Importins"	9853	protein-coding gene	gene with protein product		605600	"RAN binding protein 8"	RANBP8		9214382	Standard	NM_006390		Approved	IMP8	uc001rjd.3	O15397	OTTHUMG00000169172	ENST00000256079.4:c.2472T>C	chr12.hg19:g.30792466A>G		166.0	0.0	.		184.0	62.0	.	NM_006390	B7Z7M3	Silent	SNP	ENST00000256079.4	hg19	CCDS8719.1																																																																																			.	.	.	none		0.343	IPO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402700.2	NM_006390		G	30792466	A	G	30792466	2	3	253	1	0	0	0	0	0	0	0	1	7805	446	16	3		3	IPO8	12	30792466	Silent	SNP	A	TCGA-SX-A7SS-01A-11D-A35Z-10	17978183	30792466	103059429	67	15799											
ZFC3H1	196441	hgsc.bcm.edu	37	chr12	72017305	72017306	+	Frame_Shift_Ins	INS	-	-	CCATG																															ataagatgtatgtaggccaaINSccatgccaaacatcgatcac																										TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr12:72017305_72017306insCCATG	ENST00000378743.3	-	24	4936_4937	c.4578_4579insCATGG	c.(4576-4581)tggttgfs	p.L1527fs		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	1527					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						ATGTAGGCCAACCATGCCAAAC	0.307																																					p.L1527fs		Atlas-Indel,Pindel	.											.	ZFC3H1	172	.	0			c.4579_4580insCATGG						PASS	.																																			SO:0001589	frameshift_variant	196441	exon24			.	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.4574_4578dupCATGG	chr12.hg19:g.72017306_72017310dupCCATG	ENSP00000368017:p.Leu1527fs	106.0	0.0	0		204.0	77.0	0.377451	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Frame_Shift_Ins	INS	ENST00000378743.3	hg19	CCDS41813.1																																																																																			.	.	.	none		0.307	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		CCATG	72017306	-	CCATG	72017305	7	5	253	1	0	1	1	0	0	0	0	0	17645	40	2	0	1438	0	ZFC3H1	12	72017305	Frame_Shift_Ins	INS	-	TCGA-SX-A7SS-01A-11D-A35Z-10	41224839	72017305	61834590	68	15800											
GTF3A	219402	hgsc.bcm.edu	37	chr13	28006937	28006937	+	IGR	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	aaacgacatgccaaggcccaCgagggtgtgtacggatagcc	12	5	13	11	3	0	0	0	0	0	0	0	3	0	1	3	3	4	1	3	3	4	2			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr13:28006937C>G	ENST00000381116.1	-	0	1104				GTF3A_ENST00000381140.4_Missense_Mutation_p.H186Q|MTIF3_ENST00000461838.1_5'Flank|GTF3A_ENST00000470606.1_3'UTR			Q9H2K0	IF3M_HUMAN	mitochondrial translational initiation factor 3						formation of translation initiation complex (GO:0001732)|regulation of translational initiation (GO:0006446)|ribosome disassembly (GO:0032790)	mitochondrion (GO:0005739)	ribosomal small subunit binding (GO:0043024)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	7		Lung SC(185;0.0161)	Colorectal(13;0.00042)|READ - Rectum adenocarcinoma(15;0.105)	all cancers(112;0.108)|OV - Ovarian serous cystadenocarcinoma(117;0.157)		CCAAGGCCCACGAGGGTGTGT	0.537																																					p.H186Q		Atlas-SNP	.											GTF3A,NS,carcinoma,0,1	GTF3A	11	.	0			c.C558G						PASS	.						51	46	47					13																	28006937		1568	3582	5150	SO:0001628	intergenic_variant	2971	exon5			GGCCCACGAGGGT	BC046166	CCDS9322.1	13q12.2	2007-05-03			ENSG00000122033	ENSG00000122033			29788	protein-coding gene	gene with protein product						12095986	Standard	NM_152912		Approved	IF-3mt, IF3(mt)	uc001uri.3	Q9H2K0	OTTHUMG00000016633		chr13.hg19:g.28006937C>G		155.0	0.0	.		140.0	54.0	.	NM_002097	Q05BL8|Q5W0V0|Q86X68	Missense_Mutation	SNP	ENST00000381116.1	hg19	CCDS9322.1	.	.	.	.	.	.	.	.	.	.	C	13.18	2.160143	0.38119	.	.	ENSG00000122034	ENST00000381140;ENST00000439403	D;D	0.81908	-1.55;-1.55	5.83	-4.3	0.03710	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	0.91157	0.7215	M	0.91406	3.205	0.42190	D	0.991722	D	0.89917	1.0	D	0.97110	1.0	D	0.92191	0.5759	9	0.87932	D	0	-33.4783	15.88	0.79197	0.0:0.3529:0.0:0.6471	.	186	Q92664	TF3A_HUMAN	Q	186;56	ENSP00000370532:H186Q;ENSP00000393050:H56Q	ENSP00000370532:H186Q	H	+	3	2	GTF3A	26904937	0.910000	0.30920	0.717000	0.30585	0.048000	0.14542	-0.039000	0.12124	-0.765000	0.04645	-1.223000	0.01593	CAC	.	.	.	none		0.537	MTIF3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044300.1	NM_152912		G	28006937	C	G	28006937	1	3	253	0	1	0	0	0	0	0	0	0	6878	535	19	4		4	GTF3A	13	28006937	IGR	SNP	C	TCGA-SX-A7SS-01A-11D-A35Z-10		28006937	87162941	69	15801											
DHRS4	10901	hgsc.bcm.edu	37	chr14	24424419	24424419	+	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	accgggagcggctggtggccAcggtgagctgcagggaaatg	8	5	19	9	3	0	1	0	1	0	0	0	3	0	3	2	6	3	3	2	6	1	0			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr14:24424419A>T	ENST00000313250.5	+	2	507	c.304A>T	c.(304-306)Acg>Tcg	p.T102S	DHRS4_ENST00000543741.2_Missense_Mutation_p.T102S|DHRS4_ENST00000382761.3_Missense_Mutation_p.T84S|DHRS4_ENST00000397073.2_Missense_Mutation_p.T84S|DHRS4_ENST00000397074.3_Missense_Mutation_p.T102S|DHRS4_ENST00000559632.1_Missense_Mutation_p.T102S|DHRS4_ENST00000558263.1_Missense_Mutation_p.T102S|DHRS4_ENST00000308178.8_Missense_Mutation_p.T84S|DHRS4_ENST00000397075.3_Missense_Mutation_p.T102S|DHRS4_ENST00000558581.1_Missense_Mutation_p.T102S|DHRS4-AS1_ENST00000556379.1_RNA|DHRS4_ENST00000421831.1_Missense_Mutation_p.T84S	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	102				T -> M (in Ref. 1; AAD02292). {ECO:0000305}.	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)	GCTGGTGGCCACGGTGAGCTG	0.652																																					p.T102S		Atlas-SNP	.											.	DHRS4	22	.	0			c.A304T						PASS	.						19	23	21					14																	24424419		2201	4298	6499	SO:0001583	missense	10901	exon2			GTGGCCACGGTGA	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.304A>T	chr14.hg19:g.24424419A>T	ENSP00000326219:p.Thr102Ser	202.0	0.0	.		170.0	76.0	.	NM_021004	B2RB10|B7WNS9|D3YTB8|E2QRL8|O95162|Q20CR0|Q2LC19|Q2LE81|Q58IU4|Q6E0Y1|Q6UWU3|Q71UQ6|Q8TD03|Q9H3N5|Q9NV08	Missense_Mutation	SNP	ENST00000313250.5	hg19	CCDS9605.1	.	.	.	.	.	.	.	.	.	.	.	12.04	1.818425	0.32145	.	.	ENSG00000157326	ENST00000313250;ENST00000421831;ENST00000397073;ENST00000308178;ENST00000382761;ENST00000397075;ENST00000397074;ENST00000543741	T;T;D;D;D;D;D;D	0.87571	1.03;1.02;-2.27;-2.27;-2.27;-2.27;-2.27;-2.27	3.78	3.78	0.43462	NAD(P)-binding domain (1);	0.264094	0.42294	D	0.000732	T	0.81059	0.4744	N	0.20483	0.58	0.33769	D	0.622794	P;B;B;B;B;B	0.48911	0.917;0.0;0.0;0.002;0.409;0.003	P;B;B;B;B;B	0.49799	0.622;0.002;0.001;0.006;0.273;0.01	T	0.82275	-0.0538	10	0.22706	T	0.39	.	10.5463	0.45062	1.0:0.0:0.0:0.0	.	102;102;102;102;102;102	Q9BTZ2-5;F5GWZ1;Q9BTZ2-2;Q9BTZ2-7;Q9BTZ2-4;Q9BTZ2	.;.;.;.;.;DHRS4_HUMAN	S	102;84;84;84;84;102;102;102	ENSP00000326219:T102S;ENSP00000404147:T84S;ENSP00000380263:T84S;ENSP00000311993:T84S;ENSP00000372209:T84S;ENSP00000380265:T102S;ENSP00000380264:T102S;ENSP00000440508:T102S	ENSP00000311993:T84S	T	+	1	0	DHRS4	23494259	0.466000	0.25823	0.992000	0.48379	0.573000	0.36030	2.775000	0.47702	1.597000	0.50072	0.392000	0.25879	ACG	.	.	.	none		0.652	DHRS4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071857.3			T	24424419	A	T	24424419	3	4	253	1	0	0	0	0	1	0	0	0	4494	159	6	5	310	5	DHRS4	14	24424419	Missense_Mutation	SNP	A	TCGA-SX-A7SS-01A-11D-A35Z-10		24424419	82925121	70	15802											
ZBTB25	7597	hgsc.bcm.edu	37	chr14	64957106	64957106	+	Frame_Shift_Del	DEL	A	A	-																															ggtgaataaatatcatcttgAaatagttagaaaaagcagca																										TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr14:64957106delA	ENST00000608382.1	-	2	337	c.146delT	c.(145-147)ttcfs	p.F49fs	ZBTB25_ENST00000555424.1_Frame_Shift_Del_p.F49fs|ZBTB25_ENST00000394715.1_Frame_Shift_Del_p.F49fs|ZBTB25_ENST00000555220.1_Frame_Shift_Del_p.F49fs	NM_006977.2	NP_008908.2	P24278	ZBT25_HUMAN	zinc finger and BTB domain containing 25	49	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				gene expression (GO:0010467)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(2)|skin(2)	10				all cancers(60;0.00865)|OV - Ovarian serous cystadenocarcinoma(108;0.0102)|BRCA - Breast invasive adenocarcinoma(234;0.0469)		TATCATCTTGAAATAGTTAGA	0.313																																					p.F49fs		Atlas-Indel,Pindel	.											.	ZBTB25	27	.	0			c.147delC						PASS	.						58	60	59					14																	64957106		2203	4300	6503	SO:0001589	frameshift_variant	7597	exon2			.	X16576	CCDS9765.1	14q23-q24	2013-01-08	2005-05-22	2005-05-22	ENSG00000089775	ENSG00000089775		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	13112	protein-coding gene	gene with protein product		194541	"zinc finger protein 46 (KUP)", "chromosome 14 open reading frame 51"	ZNF46, C14orf51			Standard	NM_006977		Approved	KUP	uc001xhf.3	P24278	OTTHUMG00000141310	ENST00000608382.1:c.146delT	chr14.hg19:g.64957106delA	ENSP00000476746:p.Phe49fs	364.0	0.0	0		285.0	113.0	0.396491	NM_006977	B3KUX6|Q8IYH9	Frame_Shift_Del	DEL	ENST00000608382.1	hg19	CCDS9765.1																																																																																			.	.	.	none		0.313	ZBTB25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280649.2	NM_006977		-	64957106	A	-	64957106	7	5	253	1	0	1	0	1	0	0	0	0	17544	246	9	0	1169	0	ZBTB25	14	64957106	Frame_Shift_Del	DEL	A	TCGA-SX-A7SS-01A-11D-A35Z-10	40532687	64957106	42392434	71	15803											
TTC7B	145567	hgsc.bcm.edu	37	chr14	91142993	91142993	+	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	ggtatcctgctcagcacagcGtcccggttggcctgaaaaaa	10	8	11	12	2	1	1	1	1	0	0	3	1	3	1	3	3	3	4	3	3	4	2	rs149388931		TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr14:91142993G>A	ENST00000328459.6	-	9	1147	c.1026C>T	c.(1024-1026)gaC>gaT	p.D342D	RP11-661G16.1_ENST00000554967.1_RNA|TTC7B_ENST00000357056.2_Silent_p.D342D	NM_001010854.1	NP_001010854.1	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B	342								p.D342D(1)		NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	36		Melanoma(154;0.222)				TCAGCACAGCGTCCCGGTTGG	0.532													G|||	1	0.000199681	0	0	5008	,	,		19900	0.001		0	False		,,,				2504	0				p.D342D		Atlas-SNP	.											TTC7B,NS,carcinoma,0,1	TTC7B	93	.	1	Substitution - coding silent(1)	endometrium(1)	c.C1026T						PASS	.	G		0,4406		0,0,2203	125	102	110		1026	-10.1	0.2	14	dbSNP_134	110	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TTC7B	NM_001010854.1		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		342/844	91142993	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	145567	exon9			CACAGCGTCCCGG	BC035865	CCDS32140.1	14q32.12	2013-01-11	2004-06-02	2004-06-04		ENSG00000165914		"Tetratricopeptide (TTC) repeat domain containing"	19858	protein-coding gene	gene with protein product			"tetratricopeptide repeat domain 7 like 1"	TTC7L1			Standard	XM_005267367		Approved		uc001xyp.3	Q86TV6		ENST00000328459.6:c.1026C>T	chr14.hg19:g.91142993G>A		47.0	0.0	.		48.0	15.0	.	NM_001010854	Q86U24|Q86VT3	Silent	SNP	ENST00000328459.6	hg19	CCDS32140.1	.	.	.	.	.	.	.	.	.	.	G	0.952	-0.706004	0.03255	0.0	1.16E-4	ENSG00000165914	ENST00000554462	.	.	.	5.15	-10.1	0.00402	.	.	.	.	.	T	0.55657	0.1934	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.66188	-0.5986	4	.	.	.	-13.7471	12.5361	0.56142	0.732:0.0:0.1834:0.0847	.	.	.	.	C	12	.	.	R	-	1	0	TTC7B	90212746	0.524000	0.26282	0.175000	0.22980	0.153000	0.21895	-0.170000	0.09897	-2.269000	0.00684	-2.956000	0.00083	CGC	.	G|1.000;A|0.000	0.000	weak		0.532	TTC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411364.2			A	91142993	G	A	91142993	2	1	253	1	0	0	0	0	0	0	0	1	16725	1136	40	1		1	TTC7B	14	91142993	Silent	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10	26185887	91142993	16206547	72	15804											
APBA2	321	hgsc.bcm.edu	37	chr15	29346965	29346966	+	Frame_Shift_Ins	INS	-	-	CT																															cttcccgaggccaagcacccINScggagacccccagagaggct																										TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr15:29346965_29346966insCT	ENST00000558402.1	+	5	1477_1478	c.878_879insCT	c.(877-882)cccggafs	p.G294fs	APBA2_ENST00000558330.1_Frame_Shift_Ins_p.G294fs|APBA2_ENST00000561069.1_Frame_Shift_Ins_p.G294fs|APBA2_ENST00000411764.1_Frame_Shift_Ins_p.G294fs|APBA2_ENST00000558259.1_Frame_Shift_Ins_p.G294fs			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	294					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)		GCCAAGCACCCCGGAGACCCCC	0.663																																					p.P293fs		Atlas-INDEL	.											.	APBA2	132	.	0			c.878_879insCT						PASS	.																																			SO:0001589	frameshift_variant	321	exon3			.	AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"X11-like", "amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	Exception_encountered	chr15.hg19:g.29346965_29346966insCT	ENSP00000453293:p.Gly294fs	32.0	0.0	0		26.0	10.0	0.384615	NM_005503	E9PGI4|O60571|Q5XKC0	Frame_Shift_Ins	INS	ENST00000558402.1	hg19	CCDS10022.1																																																																																			.	.	.	none		0.663	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503		CT	29346966	-	CT	29346965	7	5	253	1	0	1	1	0	0	0	0	0	757	623	22	0	880	0	APBA2	15	29346965	Frame_Shift_Ins	INS	-	TCGA-SX-A7SS-01A-11D-A35Z-10		29346965	73184427	73	15805											
MAPKBP1	23005	hgsc.bcm.edu	37	chr15	42109123	42109123	+	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	cccaggtctgaaactgctagCatcggcgagccgggaccggc	8	5	14	14	4	1	1	0	1	1	0	2	3	1	2	3	4	4	2	3	4	2	1			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr15:42109123C>A	ENST00000456763.2	+	15	1815	c.1619C>A	c.(1618-1620)gCa>gAa	p.A540E	MAPKBP1_ENST00000457542.2_Missense_Mutation_p.A534E|MAPKBP1_ENST00000221214.6_Missense_Mutation_p.A417E|MAPKBP1_ENST00000260357.7_Missense_Mutation_p.A373E|MAPKBP1_ENST00000514566.1_Missense_Mutation_p.A534E	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	540										breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		AAACTGCTAGCATCGGCGAGC	0.592																																					p.A540E		Atlas-SNP	.											.	MAPKBP1	120	.	0			c.C1619A						PASS	.						93	95	95					15																	42109123		2203	4300	6503	SO:0001583	missense	23005	exon15			TGCTAGCATCGGC	AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"WD repeat domain containing"	29536	protein-coding gene	gene with protein product			"mitogen activated protein kinase binding protein 1"			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.1619C>A	chr15.hg19:g.42109123C>A	ENSP00000393099:p.Ala540Glu	70.0	0.0	.		42.0	16.0	.	NM_001128608	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Missense_Mutation	SNP	ENST00000456763.2	hg19	CCDS45239.1	.	.	.	.	.	.	.	.	.	.	c	21.5	4.160189	0.78226	.	.	ENSG00000137802	ENST00000457542;ENST00000221214;ENST00000260357;ENST00000456763;ENST00000514566	T;T;T;T;T	0.71579	1.2;1.2;0.73;-0.58;0.73	5.63	5.63	0.86233	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	0.89924	0.6856	H	0.96430	3.82	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.999;0.999;1.0;0.999	D	0.92621	0.6108	10	0.87932	D	0	-12.8407	19.7096	0.96089	0.0:1.0:0.0:0.0	.	373;417;534;540;534	F8WC21;O60336-3;O60336-2;O60336;O60336-6	.;.;.;MABP1_HUMAN;.	E	534;417;373;540;534	ENSP00000397570:A534E;ENSP00000221214:A417E;ENSP00000260357:A373E;ENSP00000393099:A540E;ENSP00000426154:A534E	ENSP00000221214:A417E	A	+	2	0	MAPKBP1	39896415	1.000000	0.71417	0.802000	0.32245	0.055000	0.15305	7.815000	0.86186	2.652000	0.90054	0.655000	0.94253	GCA	.	.	.	none		0.592	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359745.1	NM_014994		A	42109123	C	A	42109123	3	1	253	1	0	0	0	0	1	0	0	0	9299	710	25	4	1673	4	MAPKBP1	15	42109123	Missense_Mutation	SNP	C	TCGA-SX-A7SS-01A-11D-A35Z-10	12762158	42109123	60422269	74	15806											
RCN2	5955	hgsc.bcm.edu	37	chr15	77227974	77227974	+	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	gtgatgatactgtgacttggGatgaatataacattcagatg	13	13	11	4	0	1	5	1	4	0	1	1	6	1	6	0	1	2	0	0	1	4	5			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr15:77227974G>C	ENST00000394885.3	+	3	581	c.358G>C	c.(358-360)Gat>Cat	p.D120H	RCN2_ENST00000394883.3_Intron|RCN2_ENST00000320963.5_Missense_Mutation_p.D120H	NM_002902.2	NP_002893.1	Q14257	RCN2_HUMAN	reticulocalbin 2, EF-hand calcium binding domain	120	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.					endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(2)|large_intestine(2)|lung(1)	7						TGTGACTTGGGATGAATATAA	0.373																																					p.D120H		Atlas-SNP	.											.	RCN2	16	.	0			c.G358C						PASS	.						225	196	206					15																	77227974		2196	4294	6490	SO:0001583	missense	5955	exon3			ACTTGGGATGAAT	X78669	CCDS10291.1, CCDS61719.1	15q22.33-q24.1	2013-01-10			ENSG00000117906	ENSG00000117906		"EF-hand domain containing"	9935	protein-coding gene	gene with protein product	"Reticulocalbin 2, EF-hand calcium binding domain (endoplasmic reticulum calcium-binding protein, 55kD)"	602584				9533013, 7624774	Standard	NM_002902		Approved	ERC-55, E6BP, ERC55, TCBP49	uc002bcd.3	Q14257	OTTHUMG00000143730	ENST00000394885.3:c.358G>C	chr15.hg19:g.77227974G>C	ENSP00000378349:p.Asp120His	145.0	0.0	.		103.0	43.0	.	NM_002902	A8MTG6|F8WCY5|Q53XN8	Missense_Mutation	SNP	ENST00000394885.3	hg19	CCDS10291.1	.	.	.	.	.	.	.	.	.	.	G	16.18	3.051489	0.55218	.	.	ENSG00000117906	ENST00000394885;ENST00000320963	T;T	0.74209	-0.82;-0.82	5.74	5.74	0.90152	EF-hand-like domain (1);	0.189000	0.56097	D	0.000037	T	0.82135	0.4971	M	0.72576	2.205	0.80722	D	1	D;D	0.61080	0.989;0.966	P;P	0.60345	0.847;0.873	D	0.83656	0.0158	10	0.87932	D	0	-30.4362	10.9266	0.47195	0.1131:0.0:0.8869:0.0	.	120;120	F8WCY5;Q14257	.;RCN2_HUMAN	H	120	ENSP00000378349:D120H;ENSP00000319739:D120H	ENSP00000319739:D120H	D	+	1	0	RCN2	75015029	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	4.439000	0.59968	2.709000	0.92574	0.591000	0.81541	GAT	.	.	.	none		0.373	RCN2-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289795.1	NM_002902		C	77227974	G	C	77227974	3	2	253	1	0	0	0	0	1	0	0	0	13193	1174	41	4	368	4	RCN2	15	77227974	Missense_Mutation	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10	35118851	77227974	25303418	75	15807											
AMDHD2	51005	hgsc.bcm.edu	37	chr16	2577574	2577574	+	Missense_Mutation	SNP	A	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	ccccccaggttgttcctcagAtccctgtgaagagtggtggt	6	11	12	12	0	1	3	1	1	0	2	3	3	3	3	5	3	0	2	5	3	1	2			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr16:2577574A>C	ENST00000293971.6	+	4	467	c.373A>C	c.(373-375)Atc>Ctc	p.I125L	AMDHD2_ENST00000565570.1_Intron|ATP6C_ENST00000569317.1_Missense_Mutation_p.I78L|AMDHD2_ENST00000302956.4_Missense_Mutation_p.I125L|AMDHD2_ENST00000413459.3_Missense_Mutation_p.I125L|CEMP1_ENST00000382350.1_Intron	NM_015944.3	NP_057028.2	Q9Y303	NAGA_HUMAN	amidohydrolase domain containing 2	125					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						TGTTCCTCAGATCCCTGTGAA	0.647																																					p.I125L		Atlas-SNP	.											.	AMDHD2	33	.	0			c.A373C						PASS	.						82	64	70					16																	2577574		2197	4300	6497	SO:0001583	missense	51005	exon4			CCTCAGATCCCTG	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.373A>C	chr16.hg19:g.2577574A>C	ENSP00000293971:p.Ile125Leu	82.0	0.0	.		56.0	14.0	.	NM_001145815	B4DL77|Q8WV54	Missense_Mutation	SNP	ENST00000293971.6	hg19		.	.	.	.	.	.	.	.	.	.	A	7.181	0.589511	0.13812	.	.	ENSG00000162066	ENST00000413459;ENST00000302956;ENST00000293971	T;T;T	0.08193	3.12;3.12;3.12	5.09	5.09	0.68999	Amidohydrolase 1 (1);Metal-dependent hydrolase, composite domain (1);	0.164761	0.53938	D	0.000047	T	0.06234	0.0161	N	0.12527	0.23	0.80722	D	1	B;B;B	0.23249	0.082;0.011;0.004	B;B;B	0.28553	0.091;0.044;0.026	T	0.44467	-0.9326	10	0.30078	T	0.28	-19.5213	13.8369	0.63415	1.0:0.0:0.0:0.0	.	125;125;125	Q9Y303-3;Q9Y303;Q9Y303-2	.;NAGA_HUMAN;.	L	125	ENSP00000391596:I125L;ENSP00000307481:I125L;ENSP00000293971:I125L	ENSP00000293971:I125L	I	+	1	0	AMDHD2	2517575	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.941000	0.49011	2.142000	0.66516	0.459000	0.35465	ATC	.	.	.	none		0.647	AMDHD2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000435652.1	NM_015944		C	2577574	A	C	2577574	3	2	253	1	0	0	0	0	1	0	0	0	568	333	12	5	387	5	AMDHD2	16	2577574	Missense_Mutation	SNP	A	TCGA-SX-A7SS-01A-11D-A35Z-10		2577574	87777179	76	15808											
ABCC6	368	hgsc.bcm.edu	37	chr16	16267179	16267179	+	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	gtcctttcctgctggccatcCtgccctgtcagggtcatcca	4	12	9	16	0	2	0	2	0	0	0	6	0	6	0	6	2	2	1	6	2	0	1			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr16:16267179C>A	ENST00000205557.7	-	21	2778	c.2749G>T	c.(2749-2751)Gga>Tga	p.G917*		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	917					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)	GCTGGCCATCCTGCCCTGTCA	0.577																																					p.G917X		Atlas-SNP	.											.	ABCC6	110	.	0			c.G2749T						PASS	.						118	98	105					16																	16267179		2197	4300	6497	SO:0001587	stop_gained	368	exon21			GCCATCCTGCCCT	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.2749G>T	chr16.hg19:g.16267179C>A	ENSP00000205557:p.Gly917*	117.0	0.0	.		101.0	35.0	.	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Nonsense_Mutation	SNP	ENST00000205557.7	hg19	CCDS10568.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	36|36	5.808638|5.808638	0.96967|0.96967	.|.	.|.	ENSG00000091262|ENSG00000091262	ENST00000205557|ENST00000456970	.|D	.|0.90385	.|-2.66	4.54|4.54	2.57|2.57	0.30868|0.30868	.|.	0.145914|.	0.30940|.	U|.	0.008566|.	.|D	.|0.89160	.|0.6636	.|.	.|.	.|.	0.09310|0.09310	N|N	0.999995|0.999995	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.80984	.|-0.1138	.|6	0.42905|0.66056	T|D	0.14|0.02	.|.	7.0018|7.0018	0.24813|0.24813	0.0:0.786:0.0:0.214|0.0:0.786:0.0:0.214	.|.	.|.	.|.	.|.	X|H	917|858	.|ENSP00000405002:Q858H	ENSP00000205557:G917X|ENSP00000405002:Q858H	G|Q	-|-	1|3	0|2	ABCC6|ABCC6	16174680|16174680	0.497000|0.497000	0.26067|0.26067	0.002000|0.002000	0.10522|0.10522	0.014000|0.014000	0.08584|0.08584	0.950000|0.950000	0.29122|0.29122	0.366000|0.366000	0.24427|0.24427	0.542000|0.542000	0.68232|0.68232	GGA|CAG	.	.	.	none		0.577	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2			A	16267179	C	A	16267179	4	1	253	1	0	0	0	0	0	1	0	0	57	690	24	4	1806	4	ABCC6	16	16267179	Nonsense_Mutation	SNP	C	TCGA-SX-A7SS-01A-11D-A35Z-10	13689605	16267179	74087574	77	15809											
PALB2	79728	hgsc.bcm.edu	37	chr16	23641617	23641624	+	Frame_Shift_Del	DEL	CAAAGTCT	CAAAGTCT	-																															tttttcaagcttaagaggtcCaaagtcttcatcaggtaact																										TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	CAAAGTCT	CAAAGTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr16:23641617_23641624delCAAAGTCT	ENST00000261584.4	-	5	2003_2010	c.1851_1858delAGACTTTG	c.(1849-1860)gaagactttggafs	p.DFG618fs		NM_024675.3	NP_078951.2	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2	618					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)		TTAAGAGGTCCAAAGTCTTCATCAGGTA	0.413			"F, N, Mis"			"Wilms tumor, medulloblastoma, AML ,breast"		Involved in tolerance or repair of DNA crosslinks																													p.618_620del		Atlas-Indel,Pindel	.	yes	Rec		"Fanconi anaemia N, breast cancer susceptibility "	16	16p12.1	79728	partner and localizer of BRCA2		"L, O, E"	.	PALB2	108	.	0			c.1852_1859del						PASS	.																																			SO:0001589	frameshift_variant	79728	exon5			.		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.1851_1858delAGACTTTG	chr16.hg19:g.23641617_23641624delCAAAGTCT	ENSP00000261584:p.Asp618fs	207.0	0.0	0		201.0	102.0	0.507463	NM_024675	A6NIE1|Q8N7Y6|Q8ND31|Q9H6W1	Frame_Shift_Del	DEL	ENST00000261584.4	hg19	CCDS32406.1																																																																																			.	.	.	none		0.413	PALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435287.2	NM_024675		-	23641624	CAAAGTCT	-	23641617	7	5	253	1	0	1	0	1	0	0	0	0	11413	603	21	0	1738	0	PALB2	16	23641617	Frame_Shift_Del	DEL	CAAAGTCT	TCGA-SX-A7SS-01A-11D-A35Z-10	7374438	23641617	66713136	78	15810											
TAOK2	9344	hgsc.bcm.edu	37	chr16	29998173	29998173	+	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	cttgtaccccaggagaggagCattgttggccaggaggaggc	9	7	16	9	0	0	1	0	0	0	1	0	5	0	4	3	6	2	3	3	6	1	4			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr16:29998173C>A	ENST00000308893.4	+	16	3623	c.2580C>A	c.(2578-2580)agC>agA	p.S860R	TAOK2_ENST00000543033.1_Missense_Mutation_p.S747R|TAOK2_ENST00000416441.2_Missense_Mutation_p.S687R|TAOK2_ENST00000279394.3_Intron	NM_001252043.1|NM_016151.3	NP_001238972.1|NP_057235.2	Q9UL54	TAOK2_HUMAN	TAO kinase 2	860	Glu-rich.				actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|focal adhesion assembly (GO:0048041)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein targeting to membrane (GO:0006612)|regulation of cell growth (GO:0001558)|regulation of cell shape (GO:0008360)|response to stress (GO:0006950)|stress-activated MAPK cascade (GO:0051403)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleolus (GO:0005730)|nucleus (GO:0005634)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase binding (GO:0031434)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(3)|skin(1)	22						AGGAGAGGAGCATTGTTGGCC	0.577																																					p.S860R		Atlas-SNP	.											.	TAOK2	142	.	0			c.C2580A						PASS	.						98	98	98					16																	29998173		2197	4300	6497	SO:0001583	missense	9344	exon16			GAGGAGCATTGTT	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.2580C>A	chr16.hg19:g.29998173C>A	ENSP00000310094:p.Ser860Arg	140.0	0.0	.		166.0	111.0	.	NM_016151	A5PKY1|A7MCZ2|B2RN35|B7ZM88|O94957|Q6UW73|Q7LC09|Q9NSW2	Missense_Mutation	SNP	ENST00000308893.4	hg19	CCDS10663.1	.	.	.	.	.	.	.	.	.	.	C	6.082	0.383409	0.11524	.	.	ENSG00000149930	ENST00000308893;ENST00000543033	T;T	0.69926	-0.44;-0.44	5.32	3.28	0.37604	.	0.497301	0.18706	N	0.133460	T	0.37625	0.1010	N	0.03608	-0.345	0.18873	N	0.999988	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.09377	0.001;0.004;0.001	T	0.17806	-1.0357	9	.	.	.	.	8.0473	0.30557	0.0:0.6917:0.2053:0.103	.	1051;687;860	Q86V37;Q9UL54-3;Q9UL54	.;.;TAOK2_HUMAN	R	860;747	ENSP00000310094:S860R;ENSP00000440336:S747R	.	S	+	3	2	TAOK2	29905674	0.995000	0.38212	0.991000	0.47740	0.900000	0.52787	1.367000	0.34204	1.225000	0.43566	0.563000	0.77884	AGC	.	.	.	none		0.577	TAOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255152.2	NM_016151		A	29998173	C	A	29998173	3	1	253	1	0	0	0	0	1	0	0	0	15560	709	25	4	2638	4	TAOK2	16	29998173	Missense_Mutation	SNP	C	TCGA-SX-A7SS-01A-11D-A35Z-10	6356556	29998173	60356580	79	15811											
HYDIN	54768	hgsc.bcm.edu	37	chr16	71101222	71101222	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attaagagcgccagcacctcTtctccgatgccctccacgtc	8	9	7	17	3	2	1	0	0	2	1	5	2	3	1	5	0	3	1	5	0	1	2			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr16:71101222T>C	ENST00000393567.2	-	15	2196	c.2046A>G	c.(2044-2046)gaA>gaG	p.E682E	HYDIN_ENST00000543639.1_5'Flank|HYDIN_ENST00000393550.2_Silent_p.E697E|HYDIN_ENST00000448089.2_Silent_p.E682E|HYDIN_ENST00000541601.1_Silent_p.E699E|HYDIN_ENST00000448691.1_Silent_p.E682E|HYDIN_ENST00000538248.1_Silent_p.E709E|HYDIN_ENST00000288168.10_Silent_p.E699E|HYDIN_ENST00000321489.5_Silent_p.E682E	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	682					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)				CCAGCACCTCTTCTCCGATGC	0.547																																					p.E709E		Atlas-SNP	.											.	HYDIN	788	.	0			c.A2127G						PASS	.						69	61	64					16																	71101222		2198	4300	6498	SO:0001819	synonymous_variant	54768	exon15			CACCTCTTCTCCG	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.2046A>G	chr16.hg19:g.71101222T>C		44.0	0.0	.		58.0	16.0	.	NM_001198542	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	hg19	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	T	9.980	1.227788	0.22542	.	.	ENSG00000157423	ENST00000542890	.	.	.	4.99	-0.229	0.13094	.	.	.	.	.	T	0.50497	0.1619	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37009	-0.9724	4	.	.	.	.	5.1347	0.14928	0.1409:0.3851:0.0:0.4739	.	.	.	.	R	84	.	.	K	-	2	0	HYDIN	69658723	0.998000	0.40836	0.999000	0.59377	0.982000	0.71751	0.373000	0.20484	-0.024000	0.13941	0.491000	0.48974	AAG	.	.	.	none		0.547	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			C	71101222	T	C	71101222	2	2	253	1	0	0	0	0	0	0	0	1	7474	1606	56	3		3	HYDIN	16	71101222	Silent	SNP	T	TCGA-SX-A7SS-01A-11D-A35Z-10	41103049	71101222	19253531	80	15812											
LRRC50	123872	hgsc.bcm.edu	37	chr16	84189316	84189316	+	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	cgcacaacaagctgagtgacCcggagatcctgagcattctg	11	7	11	12	2	1	4	0	3	1	1	2	5	2	4	2	1	3	3	2	1	2	1			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr16:84189316C>T	ENST00000378553.5	+	5	827	c.703C>T	c.(703-705)Ccg>Tcg	p.P235S	DNAAF1_ENST00000334315.5_Missense_Mutation_p.P235S	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	235					axonemal dynein complex assembly (GO:0070286)|cilium morphogenesis (GO:0060271)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|left/right pattern formation (GO:0060972)|lung development (GO:0030324)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|regulation of cilium beat frequency (GO:0003356)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dynein binding (GO:0045502)			NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						GCTGAGTGACCCGGAGATCCT	0.453																																					p.P235S		Atlas-SNP	.											.	DNAAF1	81	.	0			c.C703T						PASS	.						127	103	111					16																	84189316		2200	4300	6500	SO:0001583	missense	123872	exon5			AGTGACCCGGAGA	BC024009	CCDS10943.2	16q24.1	2012-05-03	2011-06-09	2011-06-09	ENSG00000154099	ENSG00000154099			30539	protein-coding gene	gene with protein product	"outer row dynein assembly 7 homolog (Chlamydomonas)"	613190	"leucine rich repeat containing 50"	LRRC50		19944405	Standard	NM_178452		Approved	FLJ25330, ODA7, CILD13	uc002fhl.4	Q8NEP3	OTTHUMG00000128517	ENST00000378553.5:c.703C>T	chr16.hg19:g.84189316C>T	ENSP00000367815:p.Pro235Ser	95.0	0.0	.		130.0	28.0	.	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Missense_Mutation	SNP	ENST00000378553.5	hg19	CCDS10943.2	.	.	.	.	.	.	.	.	.	.	C	14.51	2.555524	0.45487	.	.	ENSG00000154099	ENST00000334315;ENST00000378553	T;T	0.21031	2.03;2.03	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.26521	0.0648	L	0.55481	1.735	0.58432	D	0.999997	P	0.35542	0.508	B	0.39531	0.302	T	0.02925	-1.1093	10	0.22706	T	0.39	-13.7883	18.3021	0.90167	0.0:1.0:0.0:0.0	.	235	Q8NEP3	DAAF1_HUMAN	S	235	ENSP00000334593:P235S;ENSP00000367815:P235S	ENSP00000334593:P235S	P	+	1	0	DNAAF1	82746817	1.000000	0.71417	0.121000	0.21740	0.027000	0.11550	7.358000	0.79466	2.318000	0.78349	0.655000	0.94253	CCG	.	.	.	none		0.453	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452		T	84189316	C	T	84189316	3	4	253	1	0	0	0	0	1	0	0	0	9016	623	22	2	721	2	LRRC50	16	84189316	Missense_Mutation	SNP	C	TCGA-SX-A7SS-01A-11D-A35Z-10	13088094	84189316	6165437	81	15813											
USP10	9100	hgsc.bcm.edu	37	chr16	84778731	84778731	+	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	ttgtaacagcccccagaactCcacagactctgtcagtgaca	12	8	7	14	0	2	3	1	1	1	2	3	3	3	3	3	0	3	1	3	0	2	2			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr16:84778731C>T	ENST00000219473.7	+	4	757	c.644C>T	c.(643-645)tCc>tTc	p.S215F	USP10_ENST00000570191.1_Missense_Mutation_p.S219F|USP10_ENST00000562743.1_3'UTR	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	215					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						CCCCAGAACTCCACAGACTCT	0.592																																					p.S219F		Atlas-SNP	.											.	USP10	51	.	0			c.C656T						PASS	.						25	25	25					16																	84778731		1967	4145	6112	SO:0001583	missense	9100	exon5			AGAACTCCACAGA	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.644C>T	chr16.hg19:g.84778731C>T	ENSP00000219473:p.Ser215Phe	157.0	0.0	.		137.0	35.0	.	NM_001272075	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Missense_Mutation	SNP	ENST00000219473.7	hg19	CCDS45537.1	.	.	.	.	.	.	.	.	.	.	C	12.30	1.896996	0.33535	.	.	ENSG00000103194	ENST00000219473	T	0.07800	3.16	5.17	5.17	0.71159	.	1.000500	0.08066	N	0.999021	T	0.09379	0.0231	L	0.35414	1.06	0.32033	N	0.59923	B;B	0.14012	0.009;0.001	B;B	0.13407	0.009;0.002	T	0.03773	-1.1005	10	0.51188	T	0.08	-3.5155	11.1822	0.48636	0.0:0.916:0.0:0.084	.	219;215	Q14694-3;Q14694	.;UBP10_HUMAN	F	215	ENSP00000219473:S215F	ENSP00000219473:S215F	S	+	2	0	USP10	83336232	1.000000	0.71417	0.054000	0.19295	0.728000	0.41692	4.964000	0.63701	2.403000	0.81681	0.491000	0.48974	TCC	.	.	.	none		0.592	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1			T	84778731	C	T	84778731	3	4	253	1	0	0	0	0	1	0	0	0	17053	855	30	2	658	2	USP10	16	84778731	Missense_Mutation	SNP	C	TCGA-SX-A7SS-01A-11D-A35Z-10	589415	84778731	5576022	82	15814											
MYH4	4622	hgsc.bcm.edu	37	chr17	10366192	10366192	+	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	tattacttacatctgtggccAtcagctcttcctggtcatca	8	15	6	12	0	5	0	3	0	2	0	6	0	6	0	2	2	3	1	2	2	3	4			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr17:10366192A>T	ENST00000255381.2	-	11	1108	c.998T>A	c.(997-999)aTg>aAg	p.M333K	RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	333	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						ATCTGTGGCCATCAGCTCTTC	0.428																																					p.M333K		Atlas-SNP	.											.	MYH4	349	.	0			c.T998A						PASS	.						118	112	114					17																	10366192		2203	4300	6503	SO:0001583	missense	4622	exon11			GTGGCCATCAGCT		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.998T>A	chr17.hg19:g.10366192A>T	ENSP00000255381:p.Met333Lys	65.0	0.0	.		94.0	36.0	.	NM_017533		Missense_Mutation	SNP	ENST00000255381.2	hg19	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	A	14.32	2.499918	0.44455	.	.	ENSG00000141048	ENST00000255381	D	0.85629	-2.01	5.37	5.37	0.77165	Myosin head, motor domain (2);	0.320982	0.21520	U	0.073229	T	0.70439	0.3224	N	0.10809	0.05	0.49299	D	0.999774	B	0.02656	0.0	B	0.06405	0.002	T	0.65957	-0.6042	10	0.06365	T	0.9	.	15.6589	0.77165	1.0:0.0:0.0:0.0	.	333	Q9Y623	MYH4_HUMAN	K	333	ENSP00000255381:M333K	ENSP00000255381:M333K	M	-	2	0	MYH4	10306917	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.108000	0.71522	2.153000	0.67306	0.528000	0.53228	ATG	.	.	.	none		0.428	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		T	10366192	A	T	10366192	3	4	253	1	0	0	0	0	1	0	0	0	10044	217	8	5	4941	5	MYH4	17	10366192	Missense_Mutation	SNP	A	TCGA-SX-A7SS-01A-11D-A35Z-10		10366192	70829018	83	15815											
SRCIN1	80725	hgsc.bcm.edu	37	chr17	36708714	36708714	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccagcgtgtccgtgacccCgcggcagcgcttgaggagcc	5	5	16	15	5	0	2	0	2	0	0	1	3	1	3	5	3	3	2	5	3	0	1	rs370322301		TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr17:36708714C>T	ENST00000264659.7	-	13	2673	c.2449G>A	c.(2449-2451)Ggg>Agg	p.G817R	SRCIN1_ENST00000578925.1_Missense_Mutation_p.G851R|SRCIN1_ENST00000398579.4_5'UTR	NM_025248.2	NP_079524.2	Q9C0H9	SRCN1_HUMAN	SRC kinase signaling inhibitor 1	689					exocytosis (GO:0006887)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell migration (GO:0030334)|regulation of dendritic spine morphogenesis (GO:0061001)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	protein kinase binding (GO:0019901)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	19						TCCGTGACCCCGCGGCAGCGC	0.637																																					p.G817R		Atlas-SNP	.											SRCIN1,NS,carcinoma,0,1	SRCIN1	66	.	0			c.G2449A						PASS	.	C	ARG/GLY	0,4048		0,0,2024	15	18	17		2449	4.1	0.9	17		17	1,8363		0,1,4181	no	missense	SRCIN1	NM_025248.2	125	0,1,6205	TT,TC,CC		0.012,0.0,0.0081	benign	817/1184	36708714	1,12411	2024	4182	6206	SO:0001583	missense	80725	exon13			TGACCCCGCGGCA		CCDS45660.1	17q12	2009-12-14			ENSG00000017373	ENSG00000277363			29506	protein-coding gene	gene with protein product	"p130Cas-associated protein", "SNAP-25-interacting protein"	610786				11214970	Standard	NM_025248		Approved	SNIP, p140Cap, KIAA1684	uc002hqd.3	Q9C0H9		ENST00000264659.7:c.2449G>A	chr17.hg19:g.36708714C>T	ENSP00000264659:p.Gly817Arg	114.0	0.0	.		113.0	33.0	.	NM_025248	Q75T46|Q8N4W8	Missense_Mutation	SNP	ENST00000264659.7	hg19	CCDS45660.1	.	.	.	.	.	.	.	.	.	.	C	16.25	3.071632	0.55646	0.0	1.2E-4	ENSG00000017373	ENST00000264659;ENST00000542707;ENST00000398579	T;T	0.45276	0.9;0.93	5.05	4.09	0.47781	.	0.339539	0.30302	N	0.009923	T	0.31327	0.0793	L	0.40543	1.245	0.31267	N	0.692233	P;P;P;P	0.48503	0.911;0.709;0.813;0.489	B;B;B;B	0.41412	0.356;0.141;0.213;0.141	T	0.30446	-0.9978	10	0.27082	T	0.32	-17.7161	8.7631	0.34687	0.0:0.8266:0.0:0.1734	.	123;689;689;817	Q9C0H9-4;Q9C0H9-2;Q9C0H9;Q9C0H9-5	.;.;SRCN1_HUMAN;.	R	817;598;671	ENSP00000264659:G817R;ENSP00000445368:G598R	ENSP00000264659:G817R	G	-	1	0	SRCIN1	33962240	0.973000	0.33851	0.921000	0.36526	0.977000	0.68977	2.487000	0.45268	1.362000	0.46000	0.561000	0.74099	GGG	.	.	.	weak		0.637	SRCIN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441878.4	NM_025248		T	36708714	C	T	36708714	3	4	253	1	0	0	0	0	1	0	0	0	15148	652	23	1	1130	1	SRCIN1	17	36708714	Missense_Mutation	SNP	C	TCGA-SX-A7SS-01A-11D-A35Z-10	26342522	36708714	44486496	84	15816											
KRT19	3880	hgsc.bcm.edu	37	chr17	39684113	39684113	+	Frame_Shift_Del	DEL	G	G	-																															tcctggatggtcgtgtagtaGtggctgtagtcgcgggaggg																										TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr17:39684113delG	ENST00000361566.3	-	1	447	c.387delC	c.(385-387)cacfs	p.H129fs		NM_002276.4	NP_002267.2	P08727	K1C19_HUMAN	keratin 19	129	Linker 1.|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)				TCGTGTAGTAGTGGCTGTAGT	0.706																																					p.Y130fs		Atlas-Indel,Pindel	.											.	KRT19	41	.	0			c.388delT						PASS	.						28	35	33					17																	39684113		2199	4298	6497	SO:0001589	frameshift_variant	3880	exon1			.		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.387delC	chr17.hg19:g.39684113delG	ENSP00000355124:p.His129fs	93.0	0.0	0		76.0	28.0	0.368421	NM_002276	B2R874|Q5XG83|Q6NW33|Q7L5M9|Q96A53|Q96FV1|Q9BYF9|Q9P1Y4	Frame_Shift_Del	DEL	ENST00000361566.3	hg19	CCDS11399.1																																																																																			.	.	.	none		0.706	KRT19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257285.1	NM_002276		-	39684113	G	-	39684113	7	5	253	1	0	1	0	1	0	0	0	0	8463	1020	36	0	839	0	KRT19	17	39684113	Frame_Shift_Del	DEL	G	TCGA-SX-A7SS-01A-11D-A35Z-10	2975399	39684113	41511097	85	15817											
NBR1	4077	hgsc.bcm.edu	37	chr17	41343586	41343586	+	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	acctgagagcttgctccagtCtaataccctgatgtaagccc	10	10	8	13	0	1	2	0	2	1	1	2	3	2	2	4	0	4	3	4	0	3	4			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr17:41343586C>G	ENST00000422280.1	+	10	1520	c.1061C>G	c.(1060-1062)tCt>tGt	p.S354C	NBR1_ENST00000389312.4_Missense_Mutation_p.S354C|NBR1_ENST00000590996.1_Missense_Mutation_p.S354C|NBR1_ENST00000589872.1_Missense_Mutation_p.S354C|NBR1_ENST00000542611.1_Missense_Mutation_p.S333C|NBR1_ENST00000341165.6_Missense_Mutation_p.S354C	NM_031858.2	NP_114064.1	Q14596	NBR1_HUMAN	neighbor of BRCA1 gene 1	354					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)		TTGCTCCAGTCTAATACCCTG	0.478																																					p.S354C		Atlas-SNP	.											.	NBR1	55	.	0			c.C1061G						PASS	.						27	26	27					17																	41343586		1840	4090	5930	SO:0001583	missense	4077	exon10			TCCAGTCTAATAC	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.1061C>G	chr17.hg19:g.41343586C>G	ENSP00000411250:p.Ser354Cys	213.0	0.0	.		281.0	76.0	.	NM_031862	Q13173|Q15026|Q5J7Q8|Q96GB6|Q9NRF7	Missense_Mutation	SNP	ENST00000422280.1	hg19	CCDS45694.1	.	.	.	.	.	.	.	.	.	.	C	15.12	2.739376	0.49045	.	.	ENSG00000188554	ENST00000422280;ENST00000542611;ENST00000341165;ENST00000389312;ENST00000389311	T;T;T;T	0.49432	1.36;0.78;1.36;1.36	5.37	5.37	0.77165	.	0.426202	0.26824	N	0.022311	T	0.51312	0.1667	N	0.25647	0.755	0.09310	N	1	D;D;D;D	0.65815	0.995;0.995;0.995;0.995	P;P;P;P	0.58820	0.784;0.784;0.846;0.784	T	0.48502	-0.9030	10	0.66056	D	0.02	-6.7866	13.8872	0.63714	0.1516:0.8484:0.0:0.0	.	354;333;354;354	A8K1U0;B7Z5R6;Q14596-2;Q14596	.;.;.;NBR1_HUMAN	C	354;333;354;354;354	ENSP00000411250:S354C;ENSP00000437545:S333C;ENSP00000343479:S354C;ENSP00000373963:S354C	ENSP00000343479:S354C	S	+	2	0	NBR1	38597112	0.968000	0.33430	0.920000	0.36463	0.709000	0.40893	2.358000	0.44134	2.528000	0.85240	0.655000	0.94253	TCT	.	.	.	none		0.478	NBR1-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453461.1	NM_005899		G	41343586	C	G	41343586	3	3	253	1	0	0	0	0	1	0	0	0	10207	913	32	4	1095	4	NBR1	17	41343586	Missense_Mutation	SNP	C	TCGA-SX-A7SS-01A-11D-A35Z-10	1659473	41343586	39851624	86	15818											
MAP3K3	4215	hgsc.bcm.edu	37	chr17	61767096	61767096	+	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	gaggaatgtgccaaccaagtGtgaggagctgtccctggcta	10	8	14	9	0	0	1	0	1	0	0	1	4	1	3	3	3	3	2	3	3	4	1			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr17:61767096G>A	ENST00000361733.3	+	11	1383		c.e11+1		MAP3K3_ENST00000361357.3_Splice_Site|MAP3K3_ENST00000577395.1_Splice_Site|MAP3K3_ENST00000584573.1_Splice_Site|MAP3K3_ENST00000579585.1_Splice_Site	NM_002401.3	NP_002392.2	Q99759	M3K3_HUMAN	mitogen-activated protein kinase kinase kinase 3						activation of MAPKK activity (GO:0000186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein autophosphorylation (GO:0046777)	cytosol (GO:0005829)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)			breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	28						CCAACCAAGTGTGAGGAGCTG	0.632																																					.		Atlas-SNP	.											.	MAP3K3	56	.	0			c.1156+1G>A						PASS	.						34	31	32					17																	61767096		2203	4300	6503	SO:0001630	splice_region_variant	4215	exon12			CCAAGTGTGAGGA	U78876	CCDS32701.1, CCDS32702.1	17q	2011-06-09				ENSG00000198909		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6855	protein-coding gene	gene with protein product	"MAP/ERK kinase kinase 3", "MAPK/ERK kinase kinase 3"	602539		MEKK3		9006902	Standard	NM_002401		Approved	MAPKKK3	uc002jbf.3	Q99759		ENST00000361733.3:c.1063+1G>A	chr17.hg19:g.61767096G>A		108.0	0.0	.		99.0	20.0	.	NM_203351	B2RCW2|D3DU15|Q5BKZ6|Q8N3I9	Splice_Site	SNP	ENST00000361733.3	hg19	CCDS32702.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.591205	0.86851	.	.	ENSG00000198909	ENST00000361357;ENST00000361733	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4437	0.94838	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MAP3K3	59120828	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.685000	0.84117	2.600000	0.87896	0.561000	0.74099	.	.	.	.	none		0.632	MAP3K3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000443867.1	NM_002401	Intron	A	61767096	G	A	61767096	5	1	253	1	0	0	0	0	0	0	1	0	9258	1391	48	2	1203	2	MAP3K3	17	61767096	Splice_Site	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10	20423510	61767096	19428114	87	15819											
QRICH2	84074	hgsc.bcm.edu	37	chr17	74288747	74288747	+	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	ccaggttggaccaagccaggCtgatatgcaccaggctgcac	10	6	12	13	0	0	1	0	1	0	0	0	2	0	2	4	4	3	5	4	4	2	2			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr17:74288747C>T	ENST00000262765.5	-	4	1742	c.1563G>A	c.(1561-1563)caG>caA	p.Q521Q		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	521	Gln-rich.									breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						CCAAGCCAGGCTGATATGCAC	0.537																																					p.Q521Q		Atlas-SNP	.											.	QRICH2	143	.	0			c.G1563A						PASS	.						151	124	133					17																	74288747		2203	4300	6503	SO:0001819	synonymous_variant	84074	exon4			GCCAGGCTGATAT	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.1563G>A	chr17.hg19:g.74288747C>T		87.0	0.0	.		90.0	5.0	.	NM_032134	A2RRE1|Q96LM3	Silent	SNP	ENST00000262765.5	hg19	CCDS32741.1																																																																																			.	.	.	none		0.537	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134		T	74288747	C	T	74288747	2	4	253	1	0	0	0	0	0	0	0	1	12893	796	28	2		2	QRICH2	17	74288747	Silent	SNP	C	TCGA-SX-A7SS-01A-11D-A35Z-10	12521651	74288747	6906463	88	15820											
FSCN2	25794	hgsc.bcm.edu	37	chr17	79503808	79503808	+	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	ttcagcgacggcgcctaccgGatccgaggtgcgtggcgggg	5	6	18	12	7	1	0	1	0	0	0	2	3	2	1	3	6	3	0	3	6	1	2			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr17:79503808G>A	ENST00000417245.2	+	4	1402	c.1266G>A	c.(1264-1266)cgG>cgA	p.R422R	FSCN2_ENST00000334850.7_Silent_p.R446R	NM_001077182.2|NM_012418.3	NP_001070650.1|NP_036550.1	O14926	FSCN2_HUMAN	fascin actin-bundling protein 2, retinal	422					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)			GCGCCTACCGGATCCGAGGTG	0.741																																					p.R446R		Atlas-SNP	.											.	FSCN2	35	.	0			c.G1338A						PASS	.						8	10	10					17																	79503808		1928	4087	6015	SO:0001819	synonymous_variant	25794	exon4			CTACCGGATCCGA	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.1266G>A	chr17.hg19:g.79503808G>A		368.0	0.0	.		441.0	128.0	.	NM_001077182	A0AVC4|A8MRA6	Silent	SNP	ENST00000417245.2	hg19	CCDS45811.1																																																																																			.	.	.	none		0.741	FSCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394746.1	NM_012418		A	79503808	G	A	79503808	2	1	253	1	0	0	0	0	0	0	0	1	6075	1161	41	2		2	FSCN2	17	79503808	Silent	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10	5215061	79503808	1691402	89	15821											
ROCK1	6093	hgsc.bcm.edu	37	chr18	18624118	18624118	+	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	acttcaaatgtccagatttaTccagcagcatgttatcaggc	12	12	7	10	0	2	1	2	0	0	1	4	1	4	1	2	1	2	3	2	1	3	4			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr18:18624118T>A	ENST00000399799.2	-	6	1560	c.620A>T	c.(619-621)gAt>gTt	p.D207V		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	207	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					TCCAGATTTATCCAGCAGCAT	0.323																																					p.D207V		Atlas-SNP	.											.	ROCK1	162	.	0			c.A620T						PASS	.						106	113	110					18																	18624118		2203	4300	6503	SO:0001583	missense	6093	exon6			GATTTATCCAGCA		CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"Pleckstrin homology (PH) domain containing"	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.620A>T	chr18.hg19:g.18624118T>A	ENSP00000382697:p.Asp207Val	81.0	0.0	.		108.0	29.0	.	NM_005406	B0YJ91|Q2KHM4|Q59GZ4	Missense_Mutation	SNP	ENST00000399799.2	hg19	CCDS11870.2	.	.	.	.	.	.	.	.	.	.	T	25.7	4.660341	0.88154	.	.	ENSG00000067900	ENST00000399799	T	0.32753	1.44	4.91	4.91	0.64330	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	0.54838	0.1883	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.59941	-0.7359	10	0.87932	D	0	.	14.6987	0.69142	0.0:0.0:0.0:1.0	.	207	Q13464	ROCK1_HUMAN	V	207	ENSP00000382697:D207V	ENSP00000382697:D207V	D	-	2	0	ROCK1	16878116	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.834000	0.86773	2.035000	0.60131	0.528000	0.53228	GAT	.	.	.	none		0.323	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2	NM_005406		A	18624118	T	A	18624118	3	1	253	1	0	0	0	0	1	0	0	0	13530	1435	50	5	3556	5	ROCK1	18	18624118	Missense_Mutation	SNP	T	TCGA-SX-A7SS-01A-11D-A35Z-10		18624118	59453130	90	15822											
DCC	1630	hgsc.bcm.edu	37	chr18	50589777	50589777	+	Missense_Mutation	SNP	A	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	aaagcctgtgcccactgtgaAttggatgaagaatggagatg	13	9	13	6	0	0	4	0	2	0	2	0	6	0	5	2	2	2	0	2	2	4	1			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr18:50589777A>C	ENST00000442544.2	+	6	1704	c.1088A>C	c.(1087-1089)aAt>aCt	p.N363T	DCC_ENST00000581580.1_Missense_Mutation_p.N18T|DCC_ENST00000412726.1_Missense_Mutation_p.N211T|DCC_ENST00000580146.1_3'UTR	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	363	Ig-like C2-type 4.				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)		CCCACTGTGAATTGGATGAAG	0.363																																					p.N363T		Atlas-SNP	.											.	DCC	360	.	0			c.A1088C						PASS	.						258	236	244					18																	50589777		2203	4300	6503	SO:0001583	missense	1630	exon6			CTGTGAATTGGAT	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.1088A>C	chr18.hg19:g.50589777A>C	ENSP00000389140:p.Asn363Thr	113.0	0.0	.		143.0	76.0	.	NM_005215		Missense_Mutation	SNP	ENST00000442544.2	hg19	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	A	13.52	2.262590	0.39995	.	.	ENSG00000187323	ENST00000442544;ENST00000304775;ENST00000412726	T;T	0.64991	-0.13;-0.13	5.95	5.95	0.96441	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.127696	0.53938	D	0.000048	T	0.24699	0.0599	N	0.00077	-2.24	0.35591	D	0.807111	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.16289	0.006;0.006;0.015	T	0.40079	-0.9582	10	0.25751	T	0.34	.	15.3941	0.74778	1.0:0.0:0.0:0.0	.	211;211;363	E7EQM8;B4DYX2;P43146	.;.;DCC_HUMAN	T	363;296;211	ENSP00000389140:N363T;ENSP00000397322:N211T	ENSP00000304146:N296T	N	+	2	0	DCC	48843775	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.881000	0.56152	2.276000	0.75962	0.528000	0.53228	AAT	.	.	.	none		0.363	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		C	50589777	A	C	50589777	3	2	253	1	0	0	0	0	1	0	0	0	4284	101	4	5	1110	5	DCC	18	50589777	Missense_Mutation	SNP	A	TCGA-SX-A7SS-01A-11D-A35Z-10	31965659	50589777	27487471	91	15823											
RAX	30062	hgsc.bcm.edu	37	chr18	56936510	56936510	+	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	agcccggcaggctctgcagcGccgtggcgcccccgcccggc	3	3	15	20	6	1	0	0	0	1	0	1	0	1	0	5	4	3	3	5	4	0	0	rs568443004	byFrequency	TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr18:56936510G>C	ENST00000334889.3	-	3	953	c.767C>G	c.(766-768)gCg>gGg	p.A256G	RAX_ENST00000256852.7_3'UTR	NM_013435.2	NP_038463.2	Q9Y2V3	RX_HUMAN	retina and anterior neural fold homeobox	256					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)		GCTCTGCAGCGCCGTggcgcc	0.821																																					p.A256G	GBM(150;770 1898 17679 24325 37807)	Atlas-SNP	.											.	RAX	19	.	0			c.C767G						PASS	.						1	2	2					18																	56936510		490	1309	1799	SO:0001583	missense	30062	exon3			TGCAGCGCCGTGG	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.767C>G	chr18.hg19:g.56936510G>C	ENSP00000334813:p.Ala256Gly	59.0	0.0	.		77.0	50.0	.	NM_013435	Q86V11	Missense_Mutation	SNP	ENST00000334889.3	hg19	CCDS11972.1	.	.	.	.	.	.	.	.	.	.	G	16.47	3.133512	0.56828	.	.	ENSG00000134438	ENST00000334889	D	0.89746	-2.56	4.16	4.16	0.48862	.	0.386572	0.29218	N	0.012795	D	0.86460	0.5938	L	0.55481	1.735	0.43846	D	0.996431	B	0.27166	0.17	B	0.26693	0.072	D	0.85448	0.1159	10	0.49607	T	0.09	.	15.204	0.73162	0.0:0.0:1.0:0.0	.	256	Q9Y2V3	RX_HUMAN	G	256	ENSP00000334813:A256G	ENSP00000334813:A256G	A	-	2	0	RAX	55087490	0.943000	0.32029	0.727000	0.30756	0.605000	0.37080	5.576000	0.67437	1.854000	0.53819	0.561000	0.74099	GCG	.	.	.	none		0.821	RAX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256128.2			C	56936510	G	C	56936510	3	2	253	1	0	0	0	0	1	0	0	0	13109	1087	38	4	277	4	RAX	18	56936510	Missense_Mutation	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10	6346733	56936510	21140738	92	15824											
FSD1	79187	hgsc.bcm.edu	37	chr19	4306010	4306010	+	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	aattcagagctttatctactCcctgaaacagatgctgctga	12	12	7	10	0	2	4	1	2	1	2	3	4	3	4	1	0	5	3	1	0	4	4			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr19:4306010C>A	ENST00000221856.6	+	2	230	c.83C>A	c.(82-84)tCc>tAc	p.S28Y	FSD1_ENST00000597590.1_Missense_Mutation_p.S28Y	NM_024333.2	NP_077309.1	Q9BTV5	FSD1_HUMAN	fibronectin type III and SPRY domain containing 1	28					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.034)|STAD - Stomach adenocarcinoma(1328;0.18)		TTTATCTACTCCCTGAAACAG	0.547																																					p.S28Y		Atlas-SNP	.											.	FSD1	51	.	0			c.C83A						PASS	.						135	134	134					19																	4306010		2203	4300	6503	SO:0001583	missense	79187	exon2			TCTACTCCCTGAA	AF316829	CCDS12127.1	19p13.3	2013-02-11	2005-03-01			ENSG00000105255		"Fibronectin type III domain containing"	13745	protein-coding gene	gene with protein product		609828	"fibronectin type 3 and SPRY domain containing 1"			11267680	Standard	NM_024333		Approved	MGC3213, MIR1	uc002lzy.2	Q9BTV5		ENST00000221856.6:c.83C>A	chr19.hg19:g.4306010C>A	ENSP00000221856:p.Ser28Tyr	118.0	0.0	.		82.0	34.0	.	NM_024333	B2RDT0|Q9BXN0|Q9HAG4	Missense_Mutation	SNP	ENST00000221856.6	hg19	CCDS12127.1	.	.	.	.	.	.	.	.	.	.	C	15.06	2.720049	0.48728	.	.	ENSG00000105255	ENST00000221856	T	0.47528	0.84	4.22	4.22	0.49857	B-box, C-terminal (1);	0.397945	0.25189	N	0.032470	T	0.49167	0.1541	L	0.46157	1.445	0.37051	D	0.897617	P;P	0.50528	0.936;0.823	P;P	0.50708	0.648;0.492	T	0.59584	-0.7427	10	0.72032	D	0.01	.	10.2079	0.43124	0.0:0.7967:0.2032:0.0	.	15;28	B4DIC5;Q9BTV5	.;FSD1_HUMAN	Y	28	ENSP00000221856:S28Y	ENSP00000221856:S28Y	S	+	2	0	FSD1	4257010	0.966000	0.33281	1.000000	0.80357	0.598000	0.36846	1.937000	0.40193	1.912000	0.55364	0.491000	0.48974	TCC	.	.	.	none		0.547	FSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458091.1	NM_024333		A	4306010	C	A	4306010	3	1	253	1	0	0	0	0	1	0	0	0	6077	855	30	4	89	4	FSD1	19	4306010	Missense_Mutation	SNP	C	TCGA-SX-A7SS-01A-11D-A35Z-10		4306010	54822973	93	15825											
TMEM146	257062	hgsc.bcm.edu	37	chr19	5739405	5739405	+	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	cagacttatatatattattcAaatactgggggattcagttt	13	16	7	5	0	2	1	2	0	0	1	2	2	2	2	0	2	1	1	0	2	7	9			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr19:5739405A>T	ENST00000381624.3	+	7	589	c.528A>T	c.(526-528)tcA>tcT	p.S176S	CATSPERD_ENST00000381614.2_5'UTR	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	176					multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)											TATATTATTCAAATACTGGGG	0.294																																					p.S176S		Atlas-SNP	.											.	.	.	.	0			c.A528T						PASS	.						85	84	85					19																	5739405		1795	4076	5871	SO:0001819	synonymous_variant	257062	exon7			TTATTCAAATACT	BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898			28598	protein-coding gene	gene with protein product			"transmembrane protein 146"	TMEM146		21224844	Standard	NM_152784		Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036	ENST00000381624.3:c.528A>T	chr19.hg19:g.5739405A>T		81.0	0.0	.		67.0	20.0	.	NM_152784	Q6ZRP1	Silent	SNP	ENST00000381624.3	hg19	CCDS12149.2																																																																																			.	.	.	none		0.294	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784		T	5739405	A	T	5739405	2	4	253	1	0	0	0	0	0	0	0	1	16072	117	5	5		5	TMEM146	19	5739405	Silent	SNP	A	TCGA-SX-A7SS-01A-11D-A35Z-10	1433395	5739405	53389578	94	15826											
MUC16	94025	hgsc.bcm.edu	37	chr19	9068211	9068211	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtgggcttttcagtgcctTggatggatgttctgctagag	5	16	14	6	0	2	1	1	0	1	1	2	3	2	3	1	3	2	3	1	3	1	6			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr19:9068211T>C	ENST00000397910.4	-	3	19438	c.19235A>G	c.(19234-19236)cAa>cGa	p.Q6412R		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6414	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						TTCAGTGCCTTGGATGGATGT	0.483																																					p.Q6412R		Atlas-SNP	.											.	MUC16	4315	.	0			c.A19235G						PASS	.						178	178	178					19																	9068211		2041	4183	6224	SO:0001583	missense	94025	exon3			GTGCCTTGGATGG	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.19235A>G	chr19.hg19:g.9068211T>C	ENSP00000381008:p.Gln6412Arg	165.0	0.0	.		146.0	6.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	2.917	-0.224039	0.06061	.	.	ENSG00000181143	ENST00000397910	T	0.02323	4.34	2.15	-3.61	0.04556	.	.	.	.	.	T	0.01489	0.0048	N	0.08118	0	.	.	.	B	0.18310	0.027	B	0.13407	0.009	T	0.45745	-0.9240	8	0.87932	D	0	.	3.206	0.06666	0.2279:0.0:0.3944:0.3778	.	6412	B5ME49	.	R	6412	ENSP00000381008:Q6412R	ENSP00000381008:Q6412R	Q	-	2	0	MUC16	8929211	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.511000	0.06321	-1.244000	0.02516	-1.830000	0.00593	CAA	.	.	.	none		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9068211	T	C	9068211	3	2	253	1	0	0	0	0	1	0	0	0	9980	1812	63	3	24616	3	MUC16	19	9068211	Missense_Mutation	SNP	T	TCGA-SX-A7SS-01A-11D-A35Z-10	3328806	9068211	50060772	95	15827											
ZNF490	57474	hgsc.bcm.edu	37	chr19	12693708	12693709	+	Frame_Shift_Ins	INS	-	-	T																															gttcatcttcaatatcctggINStctttccatttttcccctaa																										TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr19:12693708_12693709insT	ENST00000311437.6	-	4	427_428	c.305_306insA	c.(304-306)gacfs	p.D102fs	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	102	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	18						CAATATCCTGGTCTTTCCATTT	0.317																																					p.D102fs		Atlas-Indel,Pindel	.											.	ZNF490	42	.	0			c.306_307insA						PASS	.																																			SO:0001589	frameshift_variant	57474	exon4			.	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.306dupA	chr19.hg19:g.12693709_12693709dupT	ENSP00000311521:p.Asp102fs	108.0	0.0	0		79.0	32.0	0.405063	NM_020714		Frame_Shift_Ins	INS	ENST00000311437.6	hg19	CCDS12272.1																																																																																			.	.	.	none		0.317	ZNF490-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344073.1	NM_020714		T	12693709	-	T	12693708	7	5	253	1	0	1	1	0	0	0	0	0	17953	1252	44	0	1291	0	ZNF490	19	12693708	Frame_Shift_Ins	INS	-	TCGA-SX-A7SS-01A-11D-A35Z-10	3625497	12693708	46435275	96	15828											
IL12RB1	3594	hgsc.bcm.edu	37	chr19	18180414	18180414	+	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	ctgcaggtggcaaggcccccGtcctggcccacaggctgcca	6	5	13	17	1	0	0	0	0	0	0	1	0	1	0	5	5	2	3	5	5	1	0	rs371543581		TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr19:18180414G>A	ENST00000600835.2	-	11	1429	c.1131C>T	c.(1129-1131)gaC>gaT	p.D377D	IL12RB1_ENST00000593993.2_Silent_p.D377D			P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1	377	Fibronectin type-III 4. {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						CAAGGCCCCCGTCCTGGCCCA	0.627																																					p.D377D		Atlas-SNP	.											.	IL12RB1	92	.	0			c.C1131T						PASS	.	G		0,4042		0,0,2021	57	63	61		1131	-8.4	0	19		61	2,8348		0,2,4173	no	coding-synonymous	IL12RB1	NM_005535.1		0,2,6194	AA,AG,GG		0.024,0.0,0.0161		377/663	18180414	2,12390	2021	4175	6196	SO:0001819	synonymous_variant	3594	exon10			GCCCCCGTCCTGG	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.1131C>T	chr19.hg19:g.18180414G>A		39.0	0.0	.		20.0	10.0	.	NM_005535	A8K308|B2RPF1|B7ZKK3|Q8N6Q7	Silent	SNP	ENST00000600835.2	hg19	CCDS54232.1																																																																																			.	.	.	weak		0.627	IL12RB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466525.3			A	18180414	G	A	18180414	2	1	253	1	0	0	0	0	0	0	0	1	7633	1136	40	1		1	IL12RB1	19	18180414	Silent	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10	5486706	18180414	40948569	97	15829											
NCAN	1463	hgsc.bcm.edu	37	chr19	19338444	19338444	+	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	cacggctccaccctcccctgCtgcagagaccaaggtgtatt	8	8	9	16	1	0	1	0	0	0	1	2	2	2	1	5	2	2	4	5	2	2	2			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr19:19338444C>A	ENST00000252575.6	+	8	2114	c.2015C>A	c.(2014-2016)gCt>gAt	p.A672D	NCAN_ENST00000538881.1_Missense_Mutation_p.A123D	NM_004386.2	NP_004377.2	O14594	NCAN_HUMAN	neurocan	672					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)	CCCTCCCCTGCTGCAGAGACC	0.617																																					p.A672D		Atlas-SNP	.											.	NCAN	277	.	0			c.C2015A						PASS	.						93	97	96					19																	19338444		2203	4300	6503	SO:0001583	missense	1463	exon8			CCCCTGCTGCAGA	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.2015C>A	chr19.hg19:g.19338444C>A	ENSP00000252575:p.Ala672Asp	71.0	0.0	.		46.0	19.0	.	NM_004386	Q9UPK6	Missense_Mutation	SNP	ENST00000252575.6	hg19	CCDS12397.1	.	.	.	.	.	.	.	.	.	.	C	11.48	1.651240	0.29336	.	.	ENSG00000130287	ENST00000539499;ENST00000252575;ENST00000538881	D;D	0.85339	-1.85;-1.97	4.31	-1.71	0.08133	.	0.647616	0.12787	N	0.439143	T	0.68329	0.2989	L	0.27053	0.805	0.09310	N	1	B;B	0.18863	0.031;0.011	B;B	0.18263	0.021;0.006	T	0.51276	-0.8726	10	0.13853	T	0.58	.	3.5545	0.07860	0.1714:0.4363:0.0:0.3924	.	686;672	Q4LE67;O14594	.;NCAN_HUMAN	D	686;672;123	ENSP00000252575:A672D;ENSP00000442202:A123D	ENSP00000252575:A672D	A	+	2	0	NCAN	19199444	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.175000	0.09825	-0.268000	0.09312	-0.339000	0.08088	GCT	.	.	.	none		0.617	NCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460111.2	NM_004386		A	19338444	C	A	19338444	3	1	253	1	0	0	0	0	1	0	0	0	10211	797	28	4	2041	4	NCAN	19	19338444	Missense_Mutation	SNP	C	TCGA-SX-A7SS-01A-11D-A35Z-10	1158030	19338444	39790539	98	15830											
ZNF737	100129842	hgsc.bcm.edu	37	chr19	20728068	20728068	+	Missense_Mutation	SNP	T	T	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	ctttgccacattcttcacatTtgtagggtttctctccgcta	6	17	6	12	1	3	0	1	0	2	0	5	0	4	0	2	1	1	3	2	1	2	7	rs146757334	byFrequency	TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr19:20728068T>G	ENST00000427401.4	-	4	1035	c.941A>C	c.(940-942)aAa>aCa	p.K314T		NM_001159293.1	NP_001152765.1	O75373	ZN737_HUMAN	zinc finger protein 737	314					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|lung(7)|ovary(1)|stomach(1)|urinary_tract(1)	13						TTCTTCACATTTGTAGGGTTT	0.428																																					p.K314T		Atlas-SNP	.											.	ZNF737	50	.	0			c.A941C						PASS	.						35	34	34					19																	20728068		692	1591	2283	SO:0001583	missense	100129842	exon4			TCACATTTGTAGG	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.941A>C	chr19.hg19:g.20728068T>G	ENSP00000395733:p.Lys314Thr	91.0	0.0	.		67.0	29.0	.	NM_001159293	C9JHM3	Missense_Mutation	SNP	ENST00000427401.4	hg19	CCDS54238.1	.	.	.	.	.	.	.	.	.	.	-	9.442	1.088262	0.20390	.	.	ENSG00000237440	ENST00000427401	T	0.08458	3.09	0.801	0.801	0.18679	.	.	.	.	.	T	0.13670	0.0331	L	0.58925	1.835	0.09310	N	1	P	0.47409	0.895	P	0.52343	0.696	T	0.15549	-1.0433	9	0.66056	D	0.02	.	3.5302	0.07774	0.0:0.0:0.417:0.583	.	314	C9JHM3	.	T	314	ENSP00000395733:K314T	ENSP00000395733:K314T	K	-	2	0	ZNF737	20519908	0.000000	0.05858	0.183000	0.23137	0.184000	0.23303	-1.481000	0.02323	0.147000	0.19030	0.145000	0.16022	AAA	.	T|0.998;C|0.002	.	alt		0.428	ZNF737-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447844.2	NM_145289		G	20728068	T	G	20728068	3	3	253	1	0	0	0	0	1	0	0	0	18138	1841	64	5	673	5	ZNF737	19	20728068	Missense_Mutation	SNP	T	TCGA-SX-A7SS-01A-11D-A35Z-10	1389624	20728068	38400915	99	15831											
RYR1	6261	hgsc.bcm.edu	37	chr19	38949843	38949843	+	Missense_Mutation	SNP	T	T	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	cctcctggcccctgaagacgTgatcagctgctgcctggacc	6	8	11	16	1	1	3	1	2	0	1	2	4	2	4	6	2	3	2	6	2	1	0			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr19:38949843T>G	ENST00000359596.3	+	19	2225	c.2225T>G	c.(2224-2226)gTg>gGg	p.V742G	RYR1_ENST00000360985.3_Missense_Mutation_p.V742G|RYR1_ENST00000355481.4_Missense_Mutation_p.V742G			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	742	B30.2/SPRY 1. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CCTGAAGACGTGATCAGCTGC	0.632																																					p.V742G		Atlas-SNP	.											.	RYR1	708	.	0			c.T2225G						PASS	.						109	88	95					19																	38949843		2203	4300	6503	SO:0001583	missense	6261	exon19			AAGACGTGATCAG	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.2225T>G	chr19.hg19:g.38949843T>G	ENSP00000352608:p.Val742Gly	62.0	0.0	.		51.0	17.0	.	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	t	14.51	2.557863	0.45590	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.73152	-0.72;-0.72;-0.72	4.36	4.36	0.52297	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.64402	U	0.000015	D	0.86834	0.6028	M	0.92691	3.335	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.89980	0.4100	10	0.87932	D	0	.	13.3946	0.60843	0.0:0.0:0.0:1.0	.	742;742	P21817-2;P21817	.;RYR1_HUMAN	G	742	ENSP00000352608:V742G;ENSP00000347667:V742G;ENSP00000354254:V742G	ENSP00000347667:V742G	V	+	2	0	RYR1	43641683	1.000000	0.71417	0.999000	0.59377	0.567000	0.35839	7.868000	0.87116	1.827000	0.53221	0.375000	0.23000	GTG	.	.	.	none		0.632	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			G	38949843	T	G	38949843	3	3	253	1	0	0	0	0	1	0	0	0	13781	1696	59	5	2299	5	RYR1	19	38949843	Missense_Mutation	SNP	T	TCGA-SX-A7SS-01A-11D-A35Z-10	18221775	38949843	20179140	100	15832											
SUPT5H	6829	hgsc.bcm.edu	37	chr19	39964953	39964953	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccagccccagcccccagagcTaccaccaggtggcgccaagc	9	2	10	20	1	0	1	0	0	0	1	0	1	0	1	8	2	5	1	8	2	2	1			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr19:39964953T>C	ENST00000599117.1	+	28	3098	c.2731T>C	c.(2731-2733)Tac>Cac	p.Y911H	SUPT5H_ENST00000359191.6_Missense_Mutation_p.Y907H|SUPT5H_ENST00000402194.2_Missense_Mutation_p.Y907H|SUPT5H_ENST00000432763.2_Missense_Mutation_p.Y911H|SUPT5H_ENST00000598725.1_Missense_Mutation_p.Y911H			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	911	10 X 8 AA approximate tandem repeats of P-[TS]-P-S-P-[QA]-[SG]-Y, motif CTR2.|Pro-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)			CCCCCAGAGCTACCACCAGGT	0.617											OREG0025462	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y911H		Atlas-SNP	.											.	SUPT5H	119	.	0			c.T2731C						PASS	.						76	73	74					19																	39964953		2203	4300	6503	SO:0001583	missense	6829	exon26			CAGAGCTACCACC	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.2731T>C	chr19.hg19:g.39964953T>C	ENSP00000470252:p.Tyr911His	282.0	0.0	.	889	168.0	59.0	.	NM_003169	O43279|Q59G52|Q99639	Missense_Mutation	SNP	ENST00000599117.1	hg19	CCDS12536.1	.	.	.	.	.	.	.	.	.	.	T	17.21	3.330351	0.60743	.	.	ENSG00000196235	ENST00000432763;ENST00000402194;ENST00000378524;ENST00000359191	.	.	.	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.64746	0.2626	L	0.54323	1.7	0.80722	D	1	P;D;B	0.56035	0.776;0.974;0.258	B;P;B	0.55391	0.258;0.775;0.054	T	0.64588	-0.6372	8	.	.	.	-16.7403	13.5134	0.61526	0.0:0.0:0.0:1.0	.	703;907;911	B4DJK4;O00267-2;O00267	.;.;SPT5H_HUMAN	H	911;907;889;911	.	.	Y	+	1	0	SUPT5H	44656793	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	5.927000	0.70080	2.034000	0.60081	0.379000	0.24179	TAC	.	.	.	none		0.617	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1	NM_003169		C	39964953	T	C	39964953	3	2	253	1	0	0	0	0	1	0	0	0	15411	1522	53	3	2833	3	SUPT5H	19	39964953	Missense_Mutation	SNP	T	TCGA-SX-A7SS-01A-11D-A35Z-10	1015110	39964953	19164030	101	15833											
ZNF324B	388569	hgsc.bcm.edu	37	chr19	58966867	58966867	+	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	tcacagagtaccgggtgcctGggaggcagcccaggacgcct	8	5	15	13	2	1	1	1	0	0	1	1	3	1	3	4	4	3	2	4	4	1	1			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr19:58966867G>T	ENST00000336614.4	+	4	663	c.556G>T	c.(556-558)Ggg>Tgg	p.G186W	ZNF324B_ENST00000391696.1_Missense_Mutation_p.G176W|ZNF324B_ENST00000545523.1_Missense_Mutation_p.G186W	NM_207395.2	NP_997278.2	Q6AW86	Z324B_HUMAN	zinc finger protein 324B	186					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		CCGGGTGCCTGGGAGGCAGCC	0.667																																					p.G186W		Atlas-SNP	.											.	ZNF324B	58	.	0			c.G556T						PASS	.						34	41	39					19																	58966867		2203	4300	6503	SO:0001583	missense	388569	exon4			GTGCCTGGGAGGC	AK127750	CCDS33138.1	19q13.43	2013-01-08				ENSG00000249471		"Zinc fingers, C2H2-type", "-"	33107	protein-coding gene	gene with protein product							Standard	NM_207395		Approved	FLJ45850	uc002qsv.1	Q6AW86		ENST00000336614.4:c.556G>T	chr19.hg19:g.58966867G>T	ENSP00000337473:p.Gly186Trp	89.0	0.0	.		51.0	24.0	.	NM_207395	B2RTZ6|Q6ZMX8|Q6ZS42	Missense_Mutation	SNP	ENST00000336614.4	hg19	CCDS33138.1	.	.	.	.	.	.	.	.	.	.	G	10.82	1.459539	0.26248	.	.	ENSG00000249471	ENST00000336614;ENST00000545523;ENST00000391696	T;T;T	0.08458	3.3;3.3;3.09	2.48	-2.19	0.07015	.	0.628796	0.13278	N	0.399985	T	0.12433	0.0302	L	0.32530	0.975	0.09310	N	1	D;D	0.69078	0.997;0.989	P;P	0.62813	0.907;0.775	T	0.13629	-1.0502	10	0.52906	T	0.07	.	7.2895	0.26358	0.4723:0.0:0.5277:0.0	.	186;176	Q6AW86;C9JTQ8	Z324B_HUMAN;.	W	186;186;176	ENSP00000337473:G186W;ENSP00000438930:G186W;ENSP00000375578:G176W	ENSP00000337473:G186W	G	+	1	0	ZNF324B	63658679	0.013000	0.17824	0.000000	0.03702	0.001000	0.01503	0.815000	0.27253	-0.429000	0.07329	-0.658000	0.03865	GGG	.	.	.	none		0.667	ZNF324B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467038.1	NM_207395		T	58966867	G	T	58966867	3	4	253	1	0	0	0	0	1	0	0	0	17857	1348	47	4	566	4	ZNF324B	19	58966867	Missense_Mutation	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10	19001914	58966867	162116	102	15834											
ZNFX1	57169	hgsc.bcm.edu	37	chr20	47865692	47865692	+	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	ccaggcggaactcgcagggcAggctgcagcctccttcgggt	6	6	15	14	3	0	0	0	0	0	0	3	1	1	1	3	5	3	4	3	5	1	1			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr20:47865692A>T	ENST00000396105.1	-	14	4115	c.3869T>A	c.(3868-3870)cTg>cAg	p.L1290Q	ZNFX1_ENST00000371752.1_Missense_Mutation_p.L1290Q|ZNFX1_ENST00000371754.4_Intron	NM_021035.2	NP_066363.1	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	1290							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(8)|kidney(7)|large_intestine(15)|liver(1)|lung(17)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	60			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			CTCGCAGGGCAGGCTGCAGCC	0.582																																					p.L1290Q		Atlas-SNP	.											.	ZNFX1	194	.	0			c.T3869A						PASS	.						81	82	82					20																	47865692		2203	4300	6503	SO:0001583	missense	57169	exon14			CAGGGCAGGCTGC	AK022641	CCDS13417.1	20q13.13	2014-02-12			ENSG00000124201	ENSG00000124201			29271	protein-coding gene	gene with protein product						10718198	Standard	NM_021035		Approved	KIAA1404, FLJ11277	uc002xui.3	Q9P2E3	OTTHUMG00000032696	ENST00000396105.1:c.3869T>A	chr20.hg19:g.47865692A>T	ENSP00000379412:p.Leu1290Gln	125.0	0.0	.		145.0	86.0	.	NM_021035	Q9BQM7|Q9BQM8|Q9H8C1|Q9H9S2|Q9NUM1|Q9NWW1	Missense_Mutation	SNP	ENST00000396105.1	hg19	CCDS13417.1	.	.	.	.	.	.	.	.	.	.	A	6.376	0.437429	0.12104	.	.	ENSG00000124201	ENST00000371752;ENST00000396105	D;D	0.86562	-2.14;-2.14	6.07	4.96	0.65561	.	0.307250	0.31370	N	0.007768	T	0.76828	0.4042	L	0.31926	0.97	0.26692	N	0.971326	B	0.12013	0.005	B	0.09377	0.004	T	0.59653	-0.7414	10	0.13853	T	0.58	-5.7428	6.7253	0.23353	0.6309:0.134:0.0:0.2351	.	1290	Q9P2E3	ZNFX1_HUMAN	Q	1290	ENSP00000360817:L1290Q;ENSP00000379412:L1290Q	ENSP00000360817:L1290Q	L	-	2	0	ZNFX1	47299099	0.988000	0.35896	1.000000	0.80357	0.983000	0.72400	1.024000	0.30077	1.080000	0.41073	0.533000	0.62120	CTG	.	.	.	none		0.582	ZNFX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079647.2	NM_021035		T	47865692	A	T	47865692	3	4	253	1	0	0	0	0	1	0	0	0	18217	188	7	5	1891	5	ZNFX1	20	47865692	Missense_Mutation	SNP	A	TCGA-SX-A7SS-01A-11D-A35Z-10		47865692	15159828	103	15835											
SLC9A8	23315	hgsc.bcm.edu	37	chr20	48429466	48429466	+	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	ggaagctccgcaggatggggGagaagatggcggaagaggag	12	3	21	5	2	0	3	0	0	0	3	1	8	1	7	1	7	1	2	1	7	3	0			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr20:48429466G>C	ENST00000361573.2	+	1	49	c.7G>C	c.(7-9)Gag>Cag	p.E3Q	SLC9A8_ENST00000541138.1_5'UTR|SLC9A8_ENST00000417961.1_Missense_Mutation_p.E3Q|SLC9A8_ENST00000539601.1_5'UTR			Q9Y2E8	SL9A8_HUMAN	solute carrier family 9, subfamily A (NHE8, cation proton antiporter 8), member 8	3					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)			CAGGATGGGGGAGAAGATGGC	0.731																																					p.E3Q		Atlas-SNP	.											.	SLC9A8	63	.	0			c.G7C						PASS	.						22	27	25					20																	48429466		1595	2909	4504	SO:0001583	missense	23315	exon1			ATGGGGGAGAAGA	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.7G>C	chr20.hg19:g.48429466G>C	ENSP00000354966:p.Glu3Gln	29.0	0.0	.		29.0	19.0	.	NM_001260491	B4DTQ8|Q2M1U9|Q68CZ8|Q9BX15|Q9Y507	Missense_Mutation	SNP	ENST00000361573.2	hg19	CCDS13421.1	.	.	.	.	.	.	.	.	.	.	G	15.72	2.916117	0.52546	.	.	ENSG00000197818	ENST00000417961;ENST00000361573	T;T	0.64618	-0.11;-0.11	5.78	3.74	0.42951	.	0.638943	0.14719	N	0.302454	T	0.38295	0.1035	N	0.08118	0	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.15037	-1.0451	10	0.18710	T	0.47	.	9.5823	0.39495	0.0:0.1538:0.6865:0.1597	.	3;3	Q9Y2E8-2;Q9Y2E8	.;SL9A8_HUMAN	Q	3	ENSP00000416418:E3Q;ENSP00000354966:E3Q	ENSP00000354966:E3Q	E	+	1	0	SLC9A8	47862873	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.561000	0.36342	1.437000	0.47472	0.549000	0.68633	GAG	.	.	.	none		0.731	SLC9A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106483.3	XM_030524		C	48429466	G	C	48429466	3	2	253	1	0	0	0	0	1	0	0	0	14733	1175	41	4	9	4	SLC9A8	20	48429466	Missense_Mutation	SNP	G	TCGA-SX-A7SS-01A-11D-A35Z-10	563774	48429466	14596054	104	15836											
CTCFL	140690	hgsc.bcm.edu	37	chr20	56099187	56099187	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttcctcctccttcaggccTttttccggcatcaactcgag	5	15	6	15	2	2	0	2	0	0	0	7	1	6	0	5	2	1	1	5	2	1	5			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr20:56099187T>C	ENST00000608263.1	-	1	736	c.75A>G	c.(73-75)aaA>aaG	p.K25K	CTCFL_ENST00000432255.2_Silent_p.K25K|CTCFL_ENST00000608440.1_Silent_p.K25K|CTCFL_ENST00000481655.2_Silent_p.K25K|CTCFL_ENST00000422869.2_Silent_p.K25K|CTCFL_ENST00000371196.2_Silent_p.K25K|CTCFL_ENST00000502686.2_Intron|CTCFL_ENST00000429804.3_Silent_p.K25K|CTCFL_ENST00000608858.1_Intron|CTCFL_ENST00000608903.1_Intron|CTCFL_ENST00000243914.3_Silent_p.K25K|CTCFL_ENST00000608158.1_Silent_p.K25K|CTCFL_ENST00000423479.3_Silent_p.K25K|CTCFL_ENST00000539382.1_Intron|CTCFL_ENST00000608425.1_Silent_p.K25K|CTCFL_ENST00000433949.3_Intron|CTCFL_ENST00000609232.1_Silent_p.K25K	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	25					cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			CCTTCAGGCCTTTTTCCGGCA	0.502																																					p.K25K		Atlas-SNP	.											.,1	CTCFL	97	.	0			c.A75G						PASS	.						231	258	249					20																	56099187		2203	4300	6503	SO:0001819	synonymous_variant	140690	exon1			CAGGCCTTTTTCC		CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"Zinc fingers, C2H2-type"	16234	protein-coding gene	gene with protein product	"cancer/testis antigen 27"	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.75A>G	chr20.hg19:g.56099187T>C		49.0	0.0	.		54.0	3.0	.	NM_001269044	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Silent	SNP	ENST00000608263.1	hg19	CCDS13459.1																																																																																			.	.	.	none		0.502	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618		C	56099187	T	C	56099187	2	2	253	1	0	0	0	0	0	0	0	1	4003	1606	56	3		3	CTCFL	20	56099187	Silent	SNP	T	TCGA-SX-A7SS-01A-11D-A35Z-10	7669721	56099187	6926333	105	15837											
DONSON	29980	hgsc.bcm.edu	37	chr21	34951869	34951869	+	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	ttcacattcacactccgtgcCttcatgaaaatgtaaagaaa	15	11	5	10	1	3	2	3	1	0	1	4	2	4	2	2	0	1	1	2	0	5	4			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr21:34951869C>A	ENST00000303071.5	-	9	1417		c.e9-1		DONSON_ENST00000453626.1_Intron|DONSON_ENST00000303113.6_Splice_Site|DONSON_ENST00000432378.1_Intron	NM_017613.3	NP_060083.1	Q9NYP3	DONS_HUMAN	downstream neighbor of SON						multicellular organismal development (GO:0007275)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(1)|ovary(1)	11						CACTCCGTGCCTTCATGAAAA	0.378																																					.		Atlas-SNP	.											.	DONSON	34	.	0			c.1351-1G>T						PASS	.						99	92	94					21																	34951869		2203	4300	6503	SO:0001630	splice_region_variant	29980	exon10			CCGTGCCTTCATG	AF000002	CCDS13632.1	21q22.1	2008-07-31			ENSG00000159147	ENSG00000159147			2993	protein-coding gene	gene with protein product		611428		C21orf60		10773462, 10950926	Standard	NM_017613		Approved	B17, C2TA, DKFZP434M035	uc002ysk.4	Q9NYP3	OTTHUMG00000065904	ENST00000303071.5:c.1351-1G>T	chr21.hg19:g.34951869C>A		116.0	0.0	.		66.0	26.0	.	NM_017613	Q8NC53|Q9NSR9|Q9NVZ5|Q9NYP1|Q9NYP2	Splice_Site	SNP	ENST00000303071.5	hg19	CCDS13632.1	.	.	.	.	.	.	.	.	.	.	C	14.09	2.432562	0.43224	.	.	ENSG00000159147	ENST00000303113;ENST00000303071;ENST00000437395;ENST00000440810	.	.	.	5.76	5.76	0.90799	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6299	0.95698	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DONSON	33873739	1.000000	0.71417	1.000000	0.80357	0.348000	0.29142	5.242000	0.65389	2.740000	0.93945	0.447000	0.29281	.	.	.	.	none		0.378	DONSON-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141184.1	NM_017613	Intron	A	34951869	C	A	34951869	5	1	253	1	0	0	0	0	0	0	1	0	4708	695	24	4	358	4	DONSON	21	34951869	Splice_Site	SNP	C	TCGA-SX-A7SS-01A-11D-A35Z-10		34951869	13178026	106	15838											
HIC2	23119	hgsc.bcm.edu	37	chr22	21799452	21799458	+	Frame_Shift_Del	DEL	TCCACAG	TCCACAG	-																															tggacacagacatggtcagcTccacagtgttccagcagatc																										TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	TCCACAG	TCCACAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr22:21799452_21799458delTCCACAG	ENST00000443632.2	+	2	640_646	c.268_274delTCCACAG	c.(268-276)tccacagtgfs	p.STV90fs	HIC2_ENST00000407598.2_Frame_Shift_Del_p.STV90fs|HIC2_ENST00000407464.2_Frame_Shift_Del_p.STV90fs			Q96JB3	HIC2_HUMAN	hypermethylated in cancer 2	90	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			NS(1)|endometrium(4)|large_intestine(1)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16	Melanoma(16;0.000465)|Ovarian(15;0.00438)|Colorectal(54;0.0968)	Lung SC(17;0.0262)|all_lung(157;0.205)				CATGGTCAGCTCCACAGTGTTCCAGCA	0.585																																					p.89_91del	NSCLC(23;437 858 2282 27947 40366)	Atlas-INDEL	.											.	HIC2	42	.	0			c.267_273del						PASS	.																																			SO:0001589	frameshift_variant	23119	exon3			.	AB028943	CCDS13789.1	22q11.21	2013-01-09			ENSG00000169635	ENSG00000169635		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	18595	protein-coding gene	gene with protein product		607712				11554746	Standard	NM_015094		Approved	KIAA1020, HRG22, ZBTB30, ZNF907	uc002zur.4	Q96JB3	OTTHUMG00000150781	ENST00000443632.2:c.268_274delTCCACAG	chr22.hg19:g.21799452_21799458delTCCACAG	ENSP00000387757:p.Ser90fs	72.0	0.0	0		40.0	11.0	0.275	NM_015094	Q504T6|Q96KR3|Q9NSM9|Q9UPX9	Frame_Shift_Del	DEL	ENST00000443632.2	hg19	CCDS13789.1																																																																																			.	.	.	none		0.585	HIC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320061.2			-	21799458	TCCACAG	-	21799452	7	5	253	1	0	1	0	1	0	0	0	0	7109	1551	54	0	274	0	HIC2	22	21799452	Frame_Shift_Del	DEL	TCCACAG	TCGA-SX-A7SS-01A-11D-A35Z-10		21799452	29505114	107	15839											
NIPSNAP1	8508	hgsc.bcm.edu	37	chr22	29957632	29957632	+	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	ctcccttcggaactccaggtActcctgtgggcatggtggta	6	11	12	12	1	0	0	0	0	0	0	4	1	3	1	3	5	2	3	3	5	3	3			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr22:29957632A>T	ENST00000216121.7	-	6	696	c.442T>A	c.(442-444)Tac>Aac	p.Y148N		NM_001202502.1|NM_003634.3	NP_001189431.1|NP_003625.2	Q9BPW8	NIPS1_HUMAN	nipsnap homolog 1 (C. elegans)	148					sensory perception of pain (GO:0019233)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|synaptic membrane (GO:0097060)	neurotransmitter binding (GO:0042165)	p.?(1)		large_intestine(2)|lung(2)|skin(1)	5						AACTCCAGGTACTCCTGTGGG	0.587																																					p.Y148N		Atlas-SNP	.											.	NIPSNAP1	17	.	1	Unknown(1)	lung(1)	c.T442A						PASS	.						99	92	94					22																	29957632		2203	4300	6503	SO:0001583	missense	8508	exon6			CCAGGTACTCCTG	AJ001258	CCDS13860.1	22q12	2013-09-12	2001-11-28		ENSG00000184117	ENSG00000184117			7827	protein-coding gene	gene with protein product	"4-nitrophenylphosphatase domain and non-neuronal SNAP25-like 1"	603249	"NIPSNAP, C. elegans, homolog 1"			9661659	Standard	NM_003634		Approved		uc003afx.4	Q9BPW8	OTTHUMG00000151294	ENST00000216121.7:c.442T>A	chr22.hg19:g.29957632A>T	ENSP00000216121:p.Tyr148Asn	49.0	0.0	.		30.0	19.0	.	NM_003634	B2RAY3|O43800	Missense_Mutation	SNP	ENST00000216121.7	hg19	CCDS13860.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	26.8|26.8	4.773116|4.773116	0.90108|0.90108	.|.	.|.	ENSG00000184117|ENSG00000184117	ENST00000415100|ENST00000216121;ENST00000437094	.|T;T	.|0.70631	.|0.91;-0.5	4.61|4.61	4.61|4.61	0.57282|0.57282	.|Dimeric alpha-beta barrel (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.76278|0.76278	0.3965|0.3965	L|L	0.59436|0.59436	1.845|1.845	0.80722|0.80722	D|D	1|1	.|P;P	.|0.52692	.|0.955;0.955	.|P;P	.|0.53450	.|0.726;0.635	T|T	0.79928|0.79928	-0.1596|-0.1596	5|10	.|0.87932	.|D	.|0	.|.	14.4366|14.4366	0.67284|0.67284	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|128;148	.|B4DQI7;Q9BPW8	.|.;NIPS1_HUMAN	E|N	164|148;13	.|ENSP00000216121:Y148N;ENSP00000403448:Y13N	.|ENSP00000216121:Y148N	V|Y	-|-	2|1	0|0	NIPSNAP1|NIPSNAP1	28287632|28287632	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.920000|0.920000	0.55202|0.55202	8.822000|8.822000	0.92013|0.92013	2.070000|2.070000	0.61991|0.61991	0.379000|0.379000	0.24179|0.24179	GTA|TAC	.	.	.	none		0.587	NIPSNAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322117.1			T	29957632	A	T	29957632	3	4	253	1	0	0	0	0	1	0	0	0	10436	391	14	5	432	5	NIPSNAP1	22	29957632	Missense_Mutation	SNP	A	TCGA-SX-A7SS-01A-11D-A35Z-10	8158180	29957632	21346934	108	15840											
SMTN	6525	hgsc.bcm.edu	37	chr22	31486118	31486118	+	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	tgtctggccccaaagagaccCctgctgcccagagccccacc	8	5	9	19	0	1	2	0	0	1	2	1	3	1	2	8	1	3	1	8	1	1	0			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr22:31486118C>A	ENST00000347557.2	+	8	1035	c.817C>A	c.(817-819)Cct>Act	p.P273T	SMTN_ENST00000333137.7_Missense_Mutation_p.P273T|SMTN_ENST00000358743.1_Missense_Mutation_p.P273T	NM_001207017.1|NM_006932.4	NP_001193946.1|NP_008863.3	P53814	SMTN_HUMAN	smoothelin	273	Pro-rich.				muscle organ development (GO:0007517)|smooth muscle contraction (GO:0006939)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)			breast(2)|endometrium(2)|large_intestine(5)|lung(9)|ovary(3)|pancreas(1)|prostate(3)	25						CAAAGAGACCCCTGCTGCCCA	0.637																																					p.P329T		Atlas-SNP	.											.	SMTN	219	.	0			c.C985A						PASS	.						55	55	55					22																	31486118		2203	4300	6503	SO:0001583	missense	6525	exon7			GAGACCCCTGCTG	AY061972	CCDS13886.1, CCDS13887.1, CCDS13888.1, CCDS74845.1, CCDS74846.1	22q12	2006-01-27			ENSG00000183963	ENSG00000183963			11126	protein-coding gene	gene with protein product		602127				9244445, 8707825	Standard	NM_006932		Approved		uc011ale.2	P53814	OTTHUMG00000151203	ENST00000347557.2:c.817C>A	chr22.hg19:g.31486118C>A	ENSP00000328635:p.Pro273Thr	152.0	0.0	.		101.0	37.0	.	NM_001207018	O00569|O95769|O95937|Q8N4H8|Q8WWW1|Q8WWW2|Q9P1S8|Q9UIT1|Q9UIT2	Missense_Mutation	SNP	ENST00000347557.2	hg19	CCDS13886.1	.	.	.	.	.	.	.	.	.	.	C	4.350	0.064425	0.08388	.	.	ENSG00000183963	ENST00000358743;ENST00000347557;ENST00000333137;ENST00000329852;ENST00000404496	T;T;T	0.67698	0.14;-0.28;-0.28	4.14	0.863	0.19062	.	0.210963	0.24276	N	0.039954	T	0.42921	0.1224	N	0.17082	0.46	0.58432	D	0.999999	B;B;B;B;B;B	0.14438	0.01;0.003;0.006;0.007;0.003;0.01	B;B;B;B;B;B	0.15484	0.013;0.004;0.005;0.008;0.009;0.007	T	0.08576	-1.0715	10	0.26408	T	0.33	-1.1918	6.0239	0.19644	0.0:0.6593:0.0:0.3407	.	329;327;265;273;273;273	E7ETT8;B4E229;B5MC56;E7EWD0;P53814;P53814-5	.;.;.;.;SMTN_HUMAN;.	T	273;273;273;273;265	ENSP00000351593:P273T;ENSP00000328635:P273T;ENSP00000329532:P273T	ENSP00000329393:P273T	P	+	1	0	SMTN	29816118	0.130000	0.22417	0.941000	0.38009	0.108000	0.19459	0.092000	0.15066	0.289000	0.22422	-0.251000	0.11542	CCT	.	.	.	none		0.637	SMTN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321766.1	NM_134270		A	31486118	C	A	31486118	3	1	253	1	0	0	0	0	1	0	0	0	14827	623	22	4	843	4	SMTN	22	31486118	Missense_Mutation	SNP	C	TCGA-SX-A7SS-01A-11D-A35Z-10	1528486	31486118	19818448	109	15841											
PKDREJ	10343	hgsc.bcm.edu	37	chr22	46656408	46656408	+	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	ctctagcacactaccgttatCtgcaactcctgtcattctga	9	13	5	14	1	4	1	1	1	3	0	5	1	5	1	2	0	4	3	2	0	4	4			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr22:46656408C>A	ENST00000253255.5	-	1	2811	c.2812G>T	c.(2812-2814)Gat>Tat	p.D938Y		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	938					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)		CTACCGTTATCTGCAACTCCT	0.428																																					p.D938Y		Atlas-SNP	.											.	PKDREJ	195	.	0			c.G2812T						PASS	.						173	181	179					22																	46656408		2203	4300	6503	SO:0001583	missense	10343	exon1			CGTTATCTGCAAC	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.2812G>T	chr22.hg19:g.46656408C>A	ENSP00000253255:p.Asp938Tyr	128.0	0.0	.		89.0	4.0	.	NM_006071	B1AJY3|O95850	Missense_Mutation	SNP	ENST00000253255.5	hg19	CCDS14073.1	.	.	.	.	.	.	.	.	.	.	C	11.98	1.800967	0.31869	.	.	ENSG00000130943	ENST00000253255	T	0.39056	1.1	5.33	-0.92	0.10475	.	0.787491	0.11134	N	0.595970	T	0.28333	0.0700	L	0.43152	1.355	0.09310	N	1	P	0.42337	0.776	B	0.32289	0.143	T	0.11372	-1.0590	10	0.66056	D	0.02	-2.6123	8.9992	0.36072	0.0:0.3715:0.4915:0.137	.	938	Q9NTG1	PKDRE_HUMAN	Y	938	ENSP00000253255:D938Y	ENSP00000253255:D938Y	D	-	1	0	PKDREJ	45035072	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	0.056000	0.14256	-0.198000	0.10333	-0.176000	0.13171	GAT	.	.	.	none		0.428	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		A	46656408	C	A	46656408	3	1	253	1	0	0	0	0	1	0	0	0	11977	913	32	4	3953	4	PKDREJ	22	46656408	Missense_Mutation	SNP	C	TCGA-SX-A7SS-01A-11D-A35Z-10	15170290	46656408	4648158	110	15842											
TBC1D22A	25771	hgsc.bcm.edu	37	chr22	47290719	47290719	+	Missense_Mutation	SNP	A	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	gcatgagccctgaagcgttgAtcctgcagcccaaggtgacg	9	7	13	12	2	0	4	0	4	0	0	1	4	1	4	3	1	4	3	3	1	2	1			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chr22:47290719A>C	ENST00000337137.4	+	7	1043	c.877A>C	c.(877-879)Atc>Ctc	p.I293L	TBC1D22A_ENST00000407381.3_Missense_Mutation_p.I234L|TBC1D22A_ENST00000380995.1_Missense_Mutation_p.I246L|TBC1D22A_ENST00000406733.1_Missense_Mutation_p.I246L|TBC1D22A_ENST00000355704.3_Missense_Mutation_p.I215L	NM_001284304.1|NM_001284305.1|NM_014346.2	NP_001271233.1|NP_001271234.1|NP_055161.1	Q8WUA7	TB22A_HUMAN	TBC1 domain family, member 22A	293	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						protein homodimerization activity (GO:0042803)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(3)|large_intestine(10)|lung(5)|ovary(2)|prostate(1)	22		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)		TGAAGCGTTGATCCTGCAGCC	0.542																																					p.I293L		Atlas-SNP	.											.	TBC1D22A	54	.	0			c.A877C						PASS	.						206	154	172					22																	47290719		2203	4300	6503	SO:0001583	missense	25771	exon7			GCGTTGATCCTGC	AK125705	CCDS14078.1, CCDS63511.1, CCDS63512.1, CCDS74877.1	22q13	2008-01-22	2005-01-05	2005-01-05	ENSG00000054611	ENSG00000054611			1309	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 4"	C22orf4			Standard	XM_005261496		Approved		uc003bib.3	Q8WUA7	OTTHUMG00000150332	ENST00000337137.4:c.877A>C	chr22.hg19:g.47290719A>C	ENSP00000336724:p.Ile293Leu	105.0	0.0	.		76.0	26.0	.	NM_014346	B0QYI2|B0QYI3|B9A6M3|Q5TE47|Q6ZUH2|Q92680|Q9BVD6|Q9UGG0|Q9UGT2|Q9UGU6|Q9UH25|Q9Y4W5	Missense_Mutation	SNP	ENST00000337137.4	hg19	CCDS14078.1	.	.	.	.	.	.	.	.	.	.	A	0.013	-1.608035	0.00842	.	.	ENSG00000054611	ENST00000337137;ENST00000380995;ENST00000407381;ENST00000355704;ENST00000406733	T;T;T;T;T	0.03801	3.8;3.8;3.8;3.8;3.8	5.06	1.7	0.24286	Rab-GAP/TBC domain (4);	0.340608	0.32719	N	0.005728	T	0.01905	0.0060	N	0.05306	-0.075	0.09310	N	0.999998	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.19666	0.001;0.026;0.006;0.001	T	0.48822	-0.9001	10	0.02654	T	1	.	6.5479	0.22416	0.6247:0.2948:0.0805:0.0	.	293;215;234;293	B9A6M3;Q8WUA7-2;B0QYI1;Q8WUA7	.;.;.;TB22A_HUMAN	L	293;246;234;215;246	ENSP00000336724:I293L;ENSP00000370383:I246L;ENSP00000384036:I234L;ENSP00000347932:I215L;ENSP00000385634:I246L	ENSP00000336724:I293L	I	+	1	0	TBC1D22A	45669383	0.985000	0.35326	0.000000	0.03702	0.074000	0.17049	2.196000	0.42686	-0.027000	0.13873	-0.291000	0.09656	ATC	.	.	.	none		0.542	TBC1D22A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317600.3	NM_014346		C	47290719	A	C	47290719	3	2	253	1	0	0	0	0	1	0	0	0	15623	333	12	5	903	5	TBC1D22A	22	47290719	Missense_Mutation	SNP	A	TCGA-SX-A7SS-01A-11D-A35Z-10	634311	47290719	4013847	111	15843											
KDM6A	7403	hgsc.bcm.edu	37	chrX	44937747	44937747	+	Missense_Mutation	SNP	T	T	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	gccttgctggagctcttaagTtaggtaagccttaaattaaa	12	13	9	7	0	1	0	0	0	1	0	1	1	1	1	2	2	3	4	2	2	7	6			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chrX:44937747T>G	ENST00000377967.4	+	19	2976	c.2935T>G	c.(2935-2937)Tta>Gta	p.L979V	KDM6A_ENST00000543216.1_Missense_Mutation_p.L900V|KDM6A_ENST00000382899.4_Missense_Mutation_p.L986V|KDM6A_ENST00000536777.1_Missense_Mutation_p.L934V	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	979	Interaction with SUPT6H. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0?(6)		NS(1)|breast(7)|central_nervous_system(27)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(24)|kidney(24)|large_intestine(9)|liver(1)|lung(21)|oesophagus(11)|pancreas(2)|prostate(5)|skin(1)|soft_tissue(1)|urinary_tract(29)	170						AGCTCTTAAGTTAGGTAAGCC	0.343			"D, N, F, S"		"renal, oesophageal SCC, MM"																																p.L979V	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.T2935G						PASS	.						85	74	78					X																	44937747		2203	4300	6503	SO:0001583	missense	7403	exon19			CTTAAGTTAGGTA	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.2935T>G	chrX.hg19:g.44937747T>G	ENSP00000367203:p.Leu979Val	437.0	0.0	.		340.0	283.0	.	NM_021140	Q52LL9|Q5JVQ7	Missense_Mutation	SNP	ENST00000377967.4	hg19	CCDS14265.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.6|20.6	4.017728|4.017728	0.75161|0.75161	.|.	.|.	ENSG00000147050|ENSG00000147050	ENST00000334516;ENST00000377967;ENST00000536777;ENST00000382899;ENST00000543216|ENST00000414389;ENST00000433797	T;T;T;T|.	0.71103|.	-0.54;-0.54;-0.54;-0.54|.	5.36|5.36	5.36|5.36	0.76844|0.76844	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.78521|0.78521	0.4296|0.4296	M|M	0.86268|0.86268	2.805|2.805	0.80722|0.80722	D|D	1|1	D;D;P;P;P;P|.	0.63880|.	0.993;0.974;0.797;0.864;0.921;0.944|.	D;D;P;B;D;P|.	0.70487|.	0.952;0.969;0.779;0.234;0.957;0.529|.	T|T	0.81357|0.81357	-0.0969|-0.0969	10|5	0.87932|.	D|.	0|.	-7.2923|-7.2923	14.4858|14.4858	0.67616|0.67616	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	618;986;934;1031;945;979|.	B4E0L8;F8W8R6;F5H6S1;B7ZKN5;B4E253;O15550|.	.;.;.;.;.;KDM6A_HUMAN|.	V|G	676;979;934;986;900|576;621	ENSP00000367203:L979V;ENSP00000437405:L934V;ENSP00000372355:L986V;ENSP00000443078:L900V|.	ENSP00000334340:L676V|.	L|V	+|+	1|2	2|0	KDM6A|KDM6A	44822691|44822691	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	5.449000|5.449000	0.66619|0.66619	1.800000|1.800000	0.52685|0.52685	0.437000|0.437000	0.28790|0.28790	TTA|GTT	.	.	.	none		0.343	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140		G	44937747	T	G	44937747	3	3	253	1	0	0	0	0	1	0	0	0	8144	1722	60	5	3009	5	KDM6A	23	44937747	Missense_Mutation	SNP	T	TCGA-SX-A7SS-01A-11D-A35Z-10		44937747	110332813	112	15844											
HDAC6	10013	hgsc.bcm.edu	37	chrX	48661330	48661330	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctatccccaatctagcggAggtaaagaagaaaggcaaaa	17	6	9	9	1	2	2	0	0	2	2	3	3	3	3	2	3	1	2	2	3	9	3			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chrX:48661330A>G	ENST00000334136.5	+	3	324	c.146A>G	c.(145-147)gAg>gGg	p.E49G	HDAC6_ENST00000469223.1_3'UTR|HDAC6_ENST00000376619.2_Missense_Mutation_p.E49G|HDAC6_ENST00000413163.2_5'UTR|HDAC6_ENST00000444343.2_Missense_Mutation_p.E63G			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	49					aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	AATCTAGCGGAGGTAAAGAAG	0.507																																					p.E49G	Pancreas(112;205 1675 2305 8976 15959)	Atlas-SNP	.											.	HDAC6	111	.	0			c.A146G						PASS	.						65	52	56					X																	48661330		2200	4300	6500	SO:0001583	missense	10013	exon3			TAGCGGAGGTAAA	AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 90"	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.146A>G	chrX.hg19:g.48661330A>G	ENSP00000334061:p.Glu49Gly	202.0	0.0	.		149.0	120.0	.	NM_006044	O94975|Q6NT75|Q7L3E5|Q96CY0	Missense_Mutation	SNP	ENST00000334136.5	hg19	CCDS14306.1	.	.	.	.	.	.	.	.	.	.	A	18.70	3.679096	0.68042	.	.	ENSG00000094631	ENST00000423941;ENST00000438518;ENST00000376643;ENST00000444343;ENST00000376610;ENST00000334136;ENST00000376619;ENST00000436813;ENST00000441703;ENST00000426196;ENST00000443563;ENST00000440653	T;T;T	0.64085	-0.08;-0.07;-0.07	4.42	4.42	0.53409	.	0.513308	0.18131	N	0.150754	T	0.63674	0.2531	L	0.34521	1.04	0.80722	D	1	D;P;P	0.65815	0.995;0.919;0.827	P;P;P	0.57425	0.82;0.45;0.526	T	0.64449	-0.6405	10	0.54805	T	0.06	-19.7689	10.7808	0.46377	1.0:0.0:0.0:0.0	.	39;49;49	B4DZN1;Q9UBN7;Q9BRX7	.;HDAC6_HUMAN;.	G	49;49;49;63;49;49;49;49;49;49;49;49	ENSP00000398566:E63G;ENSP00000334061:E49G;ENSP00000365804:E49G	ENSP00000334061:E49G	E	+	2	0	HDAC6	48546274	1.000000	0.71417	0.468000	0.27192	0.916000	0.54674	4.544000	0.60691	1.744000	0.51775	0.486000	0.48141	GAG	.	.	.	none		0.507	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044		G	48661330	A	G	48661330	3	3	253	1	0	0	0	0	1	0	0	0	7018	304	11	3	152	3	HDAC6	23	48661330	Missense_Mutation	SNP	A	TCGA-SX-A7SS-01A-11D-A35Z-10	3723583	48661330	106609230	113	15845											
FAM123B	139285	hgsc.bcm.edu	37	chrX	63412149	63412149	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaggccatgctgtctgtcaTactgtccatgtcctgttctg	6	14	10	11	0	3	1	1	0	2	1	5	1	5	1	3	1	2	2	3	1	1	2			TCGA-SX-A7SS-01A-11D-A35Z-10	TCGA-SX-A7SS-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a5b9c2f-52f8-4f4c-864e-288f4a31f85f	b78095c0-dd7d-406b-9d5c-0e0a56f03118	g.chrX:63412149T>C	ENST00000330258.3	-	2	1290	c.1018A>G	c.(1018-1020)Atg>Gtg	p.M340V	AMER1_ENST00000403336.1_Missense_Mutation_p.M340V|AMER1_ENST00000374869.3_Missense_Mutation_p.M340V	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	340					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)									CTGTCTGTCATACTGTCCATG	0.537																																					p.M340V		Atlas-SNP	.											.	.	.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.A1018G						PASS	.						171	148	155					X																	63412149		2203	4300	6503	SO:0001583	missense	139285	exon2			CTGTCATACTGTC	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.1018A>G	chrX.hg19:g.63412149T>C	ENSP00000329117:p.Met340Val	53.0	0.0	.		27.0	27.0	.	NM_152424	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	hg19	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	T	4.090	0.014768	0.07959	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	T;T;T	0.15139	2.45;2.45;2.45	5.18	5.18	0.71444	.	0.097775	0.64402	D	0.000001	T	0.06050	0.0157	N	0.04508	-0.205	0.33997	D	0.64987	B	0.31383	0.321	B	0.29176	0.099	T	0.21042	-1.0257	10	0.05833	T	0.94	-11.8023	7.9073	0.29769	0.0:0.0931:0.0:0.9069	.	340	Q5JTC6	F123B_HUMAN	V	340	ENSP00000364003:M340V;ENSP00000329117:M340V;ENSP00000384722:M340V	ENSP00000329117:M340V	M	-	1	0	FAM123B	63328874	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.105000	0.41825	2.047000	0.60756	0.430000	0.28490	ATG	.	.	.	none		0.537	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		C	63412149	T	C	63412149	3	2	253	1	0	0	0	0	1	0	0	0	5427	1406	49	3	2393	3	FAM123B	23	63412149	Missense_Mutation	SNP	T	TCGA-SX-A7SS-01A-11D-A35Z-10	14750819	63412149	91858411	114	15846											
DMAP1	55929	hgsc.bcm.edu	37	chr1	44680529	44680529	+	Missense_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	tcttccactggcgacgtgcaGcggaggagggcaaggactac	9	6	15	11	3	1	0	0	0	1	0	2	4	2	3	1	5	3	2	1	5	2	2			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr1:44680529G>A	ENST00000372289.2	+	3	615	c.352G>A	c.(352-354)Gcg>Acg	p.A118T	DMAP1_ENST00000361745.6_Missense_Mutation_p.A118T|DMAP1_ENST00000488433.1_3'UTR|DMAP1_ENST00000315913.5_Missense_Mutation_p.A118T	NM_019100.4	NP_061973.1	Q9NPF5	DMAP1_HUMAN	DNA methyltransferase 1 associated protein 1	118					chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA methylation (GO:0006306)|DNA repair (GO:0006281)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription factor import into nucleus (GO:0042993)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|RNA polymerase II repressing transcription factor binding (GO:0001103)|transcription corepressor activity (GO:0003714)			breast(1)|cervix(1)|endometrium(6)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(166;0.155)					GCGACGTGCAGCGGAGGAGGG	0.572																																					p.A118T		Atlas-SNP	.											.	DMAP1	35	.	0			c.G352A						PASS	.						79	70	73					1																	44680529		2203	4300	6503	SO:0001583	missense	55929	exon4			CGTGCAGCGGAGG	AB037846	CCDS509.1	1p34	2009-07-13			ENSG00000178028	ENSG00000178028			18291	protein-coding gene	gene with protein product		605077				10888872, 10718198	Standard	XM_005271039		Approved	DNMAP1, FLJ11543, KIAA1425, DNMTAP1, EAF2, MEAF2, SWC4	uc001clq.1	Q9NPF5	OTTHUMG00000007577	ENST00000372289.2:c.352G>A	chr1.hg19:g.44680529G>A	ENSP00000361363:p.Ala118Thr	106.0	0.0	.		150.0	60.0	.	NM_001034023	A8K001|D3DPY8|Q0JSM4|Q5TG41|Q7Z3H7|Q9H0S8|Q9P2C2	Missense_Mutation	SNP	ENST00000372289.2	hg19	CCDS509.1	.	.	.	.	.	.	.	.	.	.	G	17.21	3.332860	0.60853	.	.	ENSG00000178028	ENST00000361745;ENST00000446292;ENST00000372283;ENST00000440641;ENST00000436069;ENST00000437511;ENST00000315913;ENST00000372289;ENST00000372290	T;T;T;T;T;T;T;T	0.24908	1.83;1.83;1.83;1.83;1.83;1.83;1.83;1.83	5.27	5.27	0.74061	.	0.048507	0.85682	D	0.000000	T	0.28067	0.0692	N	0.20610	0.595	0.80722	D	1	B;B;B;B;D;B	0.62365	0.126;0.383;0.056;0.335;0.991;0.126	B;B;B;B;P;B	0.58820	0.031;0.343;0.029;0.19;0.846;0.031	T	0.02037	-1.1225	10	0.12103	T	0.63	-11.2103	14.1424	0.65327	0.0:0.0:0.85:0.15	.	118;118;118;118;144;118	B4DQG8;B4DEF2;B4DTH3;B4DTU6;B4DU03;Q9NPF5	.;.;.;.;.;DMAP1_HUMAN	T	118;118;144;118;144;144;118;118;89	ENSP00000354697:A118T;ENSP00000409200:A118T;ENSP00000401099:A118T;ENSP00000400269:A144T;ENSP00000402494:A144T;ENSP00000312697:A118T;ENSP00000361363:A118T;ENSP00000361364:A89T	ENSP00000312697:A118T	A	+	1	0	DMAP1	44453116	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	7.447000	0.80620	2.614000	0.88457	0.655000	0.94253	GCG	.	.	.	none		0.572	DMAP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020027.3	NM_019100		A	44680529	G	A	44680529	3	1	254	1	0	0	0	0	1	0	0	0	4578	971	34	2	362	2	DMAP1	1	44680529	Missense_Mutation	SNP	G	TCGA-SX-A7SU-01A-11D-A35Z-10		44680529	204570092	1	15847											
OTUD7B	56957	hgsc.bcm.edu	37	chr1	149916007	149916007	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtggtaacaaggcaccccTgtgaagtccatccttagagt	10	9	12	10	0	0	2	0	1	0	1	2	2	2	2	4	3	1	2	4	3	4	2			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr1:149916007T>C	ENST00000369135.4	-	12	2575	c.2281A>G	c.(2281-2283)Agg>Ggg	p.R761G		NM_020205.2	NP_064590.2	Q6GQQ9	OTU7B_HUMAN	OTU deubiquitinase 7B	761					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)			AAGGCACCCCTGTGAAGTCCA	0.622																																					p.R761G		Atlas-SNP	.											.	OTUD7B	76	.	0			c.A2281G						PASS	.						35	37	37					1																	149916007		1944	4142	6086	SO:0001583	missense	56957	exon12			CACCCCTGTGAAG	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.2281A>G	chr1.hg19:g.149916007T>C	ENSP00000358131:p.Arg761Gly	37.0	0.0	.		60.0	27.0	.	NM_020205	B7Z643|D3DUZ8|Q5SZ60|Q8WWA7|Q9NQ53|Q9UFF4	Missense_Mutation	SNP	ENST00000369135.4	hg19	CCDS41389.1	.	.	.	.	.	.	.	.	.	.	T	3.697	-0.062382	0.07273	.	.	ENSG00000163113	ENST00000369135;ENST00000543330	T	0.29655	1.56	4.8	-0.468	0.12146	.	0.596176	0.17810	N	0.161235	T	0.03305	0.0096	N	0.08118	0	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.42865	-0.9426	9	.	.	.	-8.4456	3.9978	0.09566	0.0:0.2797:0.3849:0.3354	.	761	Q6GQQ9	OTU7B_HUMAN	G	761	ENSP00000358131:R761G	.	R	-	1	2	OTUD7B	148182631	0.922000	0.31269	0.189000	0.23252	0.672000	0.39443	0.923000	0.28757	0.006000	0.14734	0.374000	0.22700	AGG	.	.	.	none		0.622	OTUD7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034146.3	NM_020205		C	149916007	T	C	149916007	3	2	254	1	0	0	0	0	1	0	0	0	11326	1579	55	3	254	3	OTUD7B	1	149916007	Missense_Mutation	SNP	T	TCGA-SX-A7SU-01A-11D-A35Z-10	105235478	149916007	99334614	2	15848											
HNRPLL	92906	hgsc.bcm.edu	37	chr2	38812820	38812820	+	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	aaagcggattctgaattgagAgcagaagaactttgttgcct	13	11	11	6	1	1	4	0	2	1	3	1	6	1	5	1	1	4	2	1	1	4	4			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr2:38812820A>T	ENST00000449105.3	-	3	851	c.512T>A	c.(511-513)cTc>cAc	p.L171H	HNRNPLL_ENST00000409636.1_Missense_Mutation_p.L166H|HNRNPLL_ENST00000410076.1_Missense_Mutation_p.L166H|HNRNPLL_ENST00000378915.3_Missense_Mutation_p.L171H|HNRNPLL_ENST00000608859.1_Missense_Mutation_p.L171H|HNRNPLL_ENST00000358367.4_Missense_Mutation_p.L171H|HNRNPLL_ENST00000409328.1_Missense_Mutation_p.L171H			Q8WVV9	HNRLL_HUMAN	heterogeneous nuclear ribonucleoprotein L-like	171	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|positive regulation of RNA splicing (GO:0033120)	membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)										CTGAATTGAGAGCAGAAGAAC	0.383																																					p.L171H		Atlas-SNP	.											.	HNRPLL	19	.	0			c.T512A						PASS	.						121	118	119					2																	38812820		2203	4300	6503	SO:0001583	missense	92906	exon3			ATTGAGAGCAGAA	BC008217	CCDS46261.1, CCDS1796.2	2p22	2014-02-10		2013-06-12	ENSG00000143889	ENSG00000143889		"RNA binding motif (RRM) containing"	25127	protein-coding gene	gene with protein product		611208		HNRPLL		18669861	Standard	NM_138394		Approved		uc021vgc.1	Q8WVV9	OTTHUMG00000102075	ENST00000449105.3:c.512T>A	chr2.hg19:g.38812820A>T	ENSP00000390625:p.Leu171His	75.0	0.0	.		145.0	67.0	.	NM_138394	Q53T80|Q5JB51|Q5JB52|Q659B9|Q8IVH5|Q8IVH6|Q96HR5	Missense_Mutation	SNP	ENST00000449105.3	hg19		.	.	.	.	.	.	.	.	.	.	A	21.0	4.086464	0.76642	.	.	ENSG00000143889	ENST00000449105;ENST00000409636;ENST00000378915;ENST00000409328;ENST00000358367;ENST00000410076;ENST00000425682	D	0.83335	-1.71	5.63	5.63	0.86233	.	0.000000	0.64402	D	0.000008	D	0.90635	0.7063	M	0.83118	2.625	0.50313	D	0.999869	D;D	0.69078	0.997;0.997	P;P	0.61722	0.893;0.893	D	0.92089	0.5679	10	0.87932	D	0	.	15.8534	0.78952	1.0:0.0:0.0:0.0	.	166;171	C9J9G0;D6W592	.;.	H	171;166;171;171;171;166;110	ENSP00000396669:L110H	ENSP00000351136:L171H	L	-	2	0	HNRPLL	38666324	0.987000	0.35691	0.997000	0.53966	0.735000	0.41995	9.210000	0.95106	2.154000	0.67381	0.533000	0.62120	CTC	.	.	.	none		0.383	HNRNPLL-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000219887.2	NM_138394		T	38812820	A	T	38812820	3	4	254	1	0	0	0	0	1	0	0	0	7284	304	11	5	1160	5	HNRPLL	2	38812820	Missense_Mutation	SNP	A	TCGA-SX-A7SU-01A-11D-A35Z-10		38812820	204386553	3	15849											
TTLL4	9654	hgsc.bcm.edu	37	chr2	219619110	219619110	+	Nonstop_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	ccctcctggctgtgagcccaTaactggcctctctccaaaag	8	9	8	16	0	1	1	0	1	1	0	4	1	3	1	5	2	2	1	5	2	3	1			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr2:219619110T>A	ENST00000392102.1	+	20	3938	c.3598T>A	c.(3598-3600)Taa>Aaa	p.*1200K	TTLL4_ENST00000457313.1_3'UTR|TTLL4_ENST00000442769.1_Nonstop_Mutation_p.*1136K|TTLL4_ENST00000258398.4_Nonstop_Mutation_p.*1200K	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	0					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)		TGTGAGCCCATAACTGGCCTC	0.557																																					p.X1200K	GBM(172;1818 2053 15407 20943 49753)	Atlas-SNP	.											.	TTLL4	96	.	0			c.T3598A						PASS	.						70	70	70					2																	219619110		2203	4300	6503	SO:0001578	stop_lost	9654	exon20			AGCCCATAACTGG		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.3598T>A	chr2.hg19:g.219619110T>A	ENSP00000375951:p.*1200Lysext*28	81.0	0.0	.		93.0	36.0	.	NM_014640	A8K6V5|Q8WW29	Missense_Mutation	SNP	ENST00000392102.1	hg19	CCDS2422.1	.	.	.	.	.	.	.	.	.	.	T	10.53	1.376609	0.24857	.	.	ENSG00000135912	ENST00000392102;ENST00000442769;ENST00000258398	.	.	.	4.92	3.73	0.42828	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.4435	0.27198	0.0:0.0977:0.0:0.9023	.	.	.	.	K	1200;1136;1200	.	.	X	+	1	0	TTLL4	219327354	0.759000	0.28416	0.391000	0.26233	0.148000	0.21650	1.529000	0.35996	0.877000	0.35895	0.528000	0.53228	TAA	.	.	.	none		0.557	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640		A	219619110	T	A	219619110	4	1	254	1	0	0	0	0	0	0	0	0	16741	1419	49	5	3668	5	TTLL4	2	219619110	Nonstop_Mutation	SNP	T	TCGA-SX-A7SU-01A-11D-A35Z-10	180806290	219619110	23580263	4	15850											
IMPG2	50939	hgsc.bcm.edu	37	chr3	100964931	100964931	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcatctgctgagggccatgCagcttgaaaggtattatcct	9	13	10	9	0	2	2	1	2	1	0	3	2	3	2	2	2	3	4	2	2	3	4			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr3:100964931C>T	ENST00000193391.7	-	12	1445	c.1258G>A	c.(1258-1260)Gca>Aca	p.A420T		NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	420					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	GAGGGCCATGCAGCTTGAAAG	0.423																																					p.A420T		Atlas-SNP	.											.	IMPG2	164	.	0			c.G1258A						PASS	.						76	86	83					3																	100964931		2203	4300	6503	SO:0001583	missense	50939	exon12			GCCATGCAGCTTG	AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148			18362	protein-coding gene	gene with protein product		607056				10542133	Standard	NM_016247		Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.1258G>A	chr3.hg19:g.100964931C>T	ENSP00000193391:p.Ala420Thr	63.0	0.0	.		146.0	6.0	.	NM_016247	A8MWT5|Q9UKD4|Q9UKK5	Missense_Mutation	SNP	ENST00000193391.7	hg19	CCDS2940.1	.	.	.	.	.	.	.	.	.	.	C	18.42	3.620949	0.66787	.	.	ENSG00000081148	ENST00000193391	T	0.22539	1.95	5.91	5.91	0.95273	.	0.319686	0.30695	N	0.009080	T	0.12774	0.0310	N	0.08118	0	0.31449	N	0.67096	P;B	0.34462	0.454;0.309	B;B	0.26770	0.073;0.073	T	0.04216	-1.0968	10	0.37606	T	0.19	-4.6946	20.2983	0.98569	0.0:1.0:0.0:0.0	.	420;420	F1T0J3;Q9BZV3	.;IMPG2_HUMAN	T	420	ENSP00000193391:A420T	ENSP00000193391:A420T	A	-	1	0	IMPG2	102447621	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	4.941000	0.63540	2.802000	0.96397	0.655000	0.94253	GCA	.	.	.	none		0.423	IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353256.3			T	100964931	C	T	100964931	3	4	254	1	0	0	0	0	1	0	0	0	7736	710	25	2	2499	2	IMPG2	3	100964931	Missense_Mutation	SNP	C	TCGA-SX-A7SU-01A-11D-A35Z-10		100964931	97057499	5	15851											
SPATA16	83893	hgsc.bcm.edu	37	chr3	172835337	172835337	+	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	tgccctttgtcatttttgttCtttcaagtgtgatttctacc	5	21	6	9	0	4	1	2	1	2	0	4	1	4	1	2	0	2	1	2	0	2	7			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr3:172835337C>A	ENST00000351008.3	-	2	368	c.185G>T	c.(184-186)aGa>aTa	p.R62I		NM_031955.5	NP_114161.3	Q9BXB7	SPT16_HUMAN	spermatogenesis associated 16	62					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)			CATTTTTGTTCTTTCAAGTGT	0.388																																					p.R62I		Atlas-SNP	.											.	SPATA16	111	.	0			c.G185T						PASS	.						323	310	314					3																	172835337		2203	4300	6503	SO:0001583	missense	83893	exon2			TTTGTTCTTTCAA	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.185G>T	chr3.hg19:g.172835337C>A	ENSP00000341765:p.Arg62Ile	102.0	0.0	.		132.0	46.0	.	NM_031955	Q0R0N4|Q0R0S0|Q0R0W2|Q0R129|Q0R131|Q0R140|Q0R1B8|Q0R1G5|Q0R1I2|Q0R1J6|Q0R1S4|Q0R202|Q0R280|Q0R2F8|Q0R2N6|Q0R2N7|Q0R2R0|Q0R2R1|Q0R2S3|Q0R2S4|Q0R2S5|Q0R2T4|Q0R2T7|Q0R2U2|Q0R2U8|Q0R2U9|Q0R2V5|Q0R2V7|Q8NE67	Missense_Mutation	SNP	ENST00000351008.3	hg19	CCDS3221.1	.	.	.	.	.	.	.	.	.	.	C	14.17	2.456127	0.43634	.	.	ENSG00000144962	ENST00000351008	T	0.25749	1.78	5.27	5.27	0.74061	.	0.000000	0.64402	D	0.000015	T	0.33702	0.0872	L	0.29908	0.895	0.44508	D	0.997459	D	0.63880	0.993	P	0.60682	0.878	T	0.06698	-1.0812	10	0.87932	D	0	-19.4976	11.2051	0.48765	0.0:0.915:0.0:0.085	.	62	Q9BXB7	SPT16_HUMAN	I	62	ENSP00000341765:R62I	ENSP00000341765:R62I	R	-	2	0	SPATA16	174318031	0.960000	0.32886	0.985000	0.45067	0.578000	0.36192	1.129000	0.31381	2.450000	0.82876	0.650000	0.86243	AGA	.	.	.	none		0.388	SPATA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346322.1	NM_031955		A	172835337	C	A	172835337	3	1	254	1	0	0	0	0	1	0	0	0	15013	913	32	4	1564	4	SPATA16	3	172835337	Missense_Mutation	SNP	C	TCGA-SX-A7SU-01A-11D-A35Z-10	71870406	172835337	25187093	6	15852											
PPP1R2	5504	hgsc.bcm.edu	37	chr3	195250521	195250521	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgagaggtcactatcctcCtctccactgctttcttgttc	5	15	8	13	0	3	1	1	1	2	1	7	2	5	1	3	2	1	2	3	2	1	4			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr3:195250521C>T	ENST00000328432.3	-	4	732	c.372G>A	c.(370-372)gaG>gaA	p.E124E	RNU6ATAC24P_ENST00000516811.1_RNA	NM_006241.4	NP_006232.1	P41236	IPP2_HUMAN	protein phosphatase 1, regulatory (inhibitor) subunit 2	124					generation of precursor metabolites and energy (GO:0006091)|glycogen metabolic process (GO:0005977)|negative regulation of catalytic activity (GO:0043086)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of signal transduction (GO:0009966)		protein serine/threonine phosphatase inhibitor activity (GO:0004865)			endometrium(2)|kidney(1)|large_intestine(1)|urinary_tract(2)	6	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)		Epithelial(36;2.64e-22)|all cancers(36;2.69e-20)|OV - Ovarian serous cystadenocarcinoma(49;3.52e-19)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;9.55e-05)		CACTATCCTCCTCTCCACTGC	0.393																																					p.E124E		Atlas-SNP	.											.	PPP1R2	11	.	0			c.G372A						PASS	.						88	72	77					3																	195250521		2203	4300	6503	SO:0001819	synonymous_variant	5504	exon4			ATCCTCCTCTCCA	U68111	CCDS3309.1	3q29	2012-04-17			ENSG00000184203	ENSG00000184203	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	9288	protein-coding gene	gene with protein product		601792				9126490, 8119416	Standard	XM_006713682		Approved	IPP2	uc003fup.3	P41236	OTTHUMG00000155887	ENST00000328432.3:c.372G>A	chr3.hg19:g.195250521C>T		71.0	0.0	.		105.0	42.0	.	NM_006241		Silent	SNP	ENST00000328432.3	hg19	CCDS3309.1																																																																																			.	.	.	none		0.393	PPP1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342133.1	NM_006241		T	195250521	C	T	195250521	2	4	254	1	0	0	0	0	0	0	0	1	12380	680	24	2		2	PPP1R2	3	195250521	Silent	SNP	C	TCGA-SX-A7SU-01A-11D-A35Z-10	22415184	195250521	2771909	7	15853											
FRYL	285527	hgsc.bcm.edu	37	chr4	48552657	48552657	+	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	gctgctactgtatcgggattCtagtctgtgatgttgccgat	6	15	12	8	2	2	1	0	1	2	0	3	3	2	2	1	1	3	4	1	1	3	5			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr4:48552657C>G	ENST00000503238.1	-	35	4584	c.4585G>C	c.(4585-4587)Gaa>Caa	p.E1529Q	FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000537810.1_Missense_Mutation_p.E1529Q|FRYL_ENST00000358350.4_Missense_Mutation_p.E1529Q|FRYL_ENST00000507711.1_Missense_Mutation_p.E1529Q|FRYL_ENST00000507873.2_5'UTR			O94915	FRYL_HUMAN	FRY-like	1529					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						TATCGGGATTCTAGTCTGTGA	0.373																																					p.E1529Q		Atlas-SNP	.											.	FRYL	242	.	0			c.G4585C						PASS	.						186	169	174					4																	48552657		1890	4106	5996	SO:0001583	missense	285527	exon38			GGGATTCTAGTCT	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.4585G>C	chr4.hg19:g.48552657C>G	ENSP00000426064:p.Glu1529Gln	28.0	0.0	.		51.0	19.0	.	NM_015030	O95640|Q8WTZ5|Q9NT40	Missense_Mutation	SNP	ENST00000503238.1	hg19	CCDS43227.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.83|19.83	3.900152|3.900152	0.72754|0.72754	.|.	.|.	ENSG00000075539|ENSG00000075539	ENST00000503238;ENST00000358350;ENST00000537810;ENST00000507711|ENST00000514617	T;T;T;T|.	0.55588|.	1.82;1.82;1.82;0.51|.	5.53|5.53	5.53|5.53	0.82687|0.82687	Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.75236|0.75236	0.3822|0.3822	M|M	0.68593|0.68593	2.085|2.085	0.80722|0.80722	D|D	1|1	D;D;P;P|.	0.63880|.	0.981;0.993;0.941;0.938|.	D;D;P;P|.	0.72982|.	0.932;0.979;0.71;0.849|.	T|T	0.73398|0.73398	-0.3995|-0.3995	10|5	0.33141|.	T|.	0.24|.	.|.	19.4662|19.4662	0.94943|0.94943	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1529;360;1529;1529|.	F2Z2S2;Q6ZR29;O94915;F5GX82|.	.;.;FRYL_HUMAN;.|.	Q|T	1529|399	ENSP00000426064:E1529Q;ENSP00000351113:E1529Q;ENSP00000441114:E1529Q;ENSP00000421584:E1529Q|.	ENSP00000351113:E1529Q|.	E|R	-|-	1|2	0|0	FRYL|FRYL	48247414|48247414	1.000000|1.000000	0.71417|0.71417	0.950000|0.950000	0.38849|0.38849	0.080000|0.080000	0.17528|0.17528	7.484000|7.484000	0.81180|0.81180	2.582000|2.582000	0.87167|0.87167	0.655000|0.655000	0.94253|0.94253	GAA|AGA	.	.	.	none		0.373	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			G	48552657	C	G	48552657	3	3	254	1	0	0	0	0	1	0	0	0	6071	922	32	4	4564	4	FRYL	4	48552657	Missense_Mutation	SNP	C	TCGA-SX-A7SU-01A-11D-A35Z-10		48552657	142601619	8	15854											
FAM190A	401145	hgsc.bcm.edu	37	chr4	91321220	91321221	+	Missense_Mutation	DNP	GA	GA	AC																															atttgggatcttgtgaactgGatgaagatgatctaatgctt																										TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr4:91321220_91321221GA>AC	ENST00000509176.1	+	4	1831_1832	c.1543_1544GA>AC	c.(1543-1545)GAt>ACt	p.D515T	CCSER1_ENST00000333691.8_Missense_Mutation_p.D515T|CCSER1_ENST00000432775.2_Missense_Mutation_p.D515T	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	515																	TTGTGAACTGGATGAAGATGAT	0.332																																					p.D515N|p.D515A		Atlas-SNP	.											FAM190A_ENST00000509176,colon,carcinoma,0,3|FAM190A_ENST00000509176,colon,carcinoma,+1,12	.	.	.	0			c.G1543A|c.A1544C						PASS	.																																			SO:0001583	missense	401145	exon4			GAACTGGATGAAG|AACTGGATGAAGA		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	Exception_encountered	chr4.hg19:g.91321220_91321221delinsAC	ENSP00000425040:p.Asp515Thr	79.0	0.0	.		119.0|118.0	48.0|47.0	.	NM_001145065	Q4W5M0|Q86V57	Missense_Mutation	SNP	ENST00000509176.1	hg19	CCDS47099.1																																																																																			.	.	.	none		0.332	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065		AC	91321221	GA	AC	91321220	3	1	254	1	0	0	0	0	1	0	0	0	5525	1174	41	2	1553	2	FAM190A	4	91321220	Missense_Mutation	DNP	GA	TCGA-SX-A7SU-01A-11D-A35Z-10	42768563	91321220	99833056	9	15855											
FRG1	2483	hgsc.bcm.edu	37	chr4	190884267	190884267	+	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	ggagagccaaattgaaagccGacagatactgcaagtgactg	15	6	12	8	1	0	4	0	2	0	2	0	6	0	4	2	1	4	1	2	1	4	2	rs373037319		TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr4:190884267G>A	ENST00000226798.4	+	9	982	c.760G>A	c.(760-762)Gac>Aac	p.D254N		NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	254					mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		ATTGAAAGCCGACAGATACTG	0.299																																					p.D254N		Atlas-SNP	.											FRG1,middle_lobe,carcinoma,0,1	FRG1	76	.	0			c.G760A						PASS	.						99	111	107					4																	190884267		2203	4300	6503	SO:0001583	missense	2483	exon9			AAAGCCGACAGAT	L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536			3954	protein-coding gene	gene with protein product		601278				8733123	Standard	XM_005262880		Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.760G>A	chr4.hg19:g.190884267G>A	ENSP00000226798:p.Asp254Asn	32.0	0.0	.		54.0	5.0	.	NM_004477	A8K775	Missense_Mutation	SNP	ENST00000226798.4	hg19	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	.	21.9	4.222509	0.79464	.	.	ENSG00000109536	ENST00000226798	T	0.65916	-0.18	4.0	4.0	0.46444	.	0.000000	0.85682	D	0.000000	T	0.80994	0.4731	M	0.89715	3.055	0.80722	D	1	D	0.76494	0.999	D	0.66716	0.946	D	0.85581	0.1240	10	0.72032	D	0.01	-19.8783	14.0213	0.64558	0.0:0.0:1.0:0.0	.	254	Q14331	FRG1_HUMAN	N	254	ENSP00000226798:D254N	ENSP00000226798:D254N	D	+	1	0	FRG1	191121261	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	9.201000	0.95017	1.976000	0.57569	0.479000	0.44913	GAC	.	.	.	weak		0.299	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477		A	190884267	G	A	190884267	3	1	254	1	0	0	0	0	1	0	0	0	6053	1058	37	1	794	1	FRG1	4	190884267	Missense_Mutation	SNP	G	TCGA-SX-A7SU-01A-11D-A35Z-10	99563047	190884267	270009	10	15856											
C5orf55	116349	hgsc.bcm.edu	37	chr5	442810	442810	+	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	gtatgacagacgtttgattcCcaaccttctccgctttggtt	7	15	8	11	2	1	3	0	2	1	1	3	3	2	3	3	1	1	4	3	1	2	6			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr5:442810C>T	ENST00000408966.2	-	1	448	c.128G>A	c.(127-129)gGg>gAg	p.G43E	EXOC3_ENST00000512944.1_5'Flank	NM_138464.2	NP_612473.1	Q8N2X6	CE055_HUMAN	chromosome 5 open reading frame 55	43						extracellular region (GO:0005576)				large_intestine(1)|lung(2)	3						CGTTTGATTCCCAACCTTCTC	0.597																																					p.G43E		Atlas-SNP	.											.	C5orf55	11	.	0			c.G128A						PASS	.						149	166	161					5																	442810		1980	4155	6135	SO:0001583	missense	116349	exon1			TGATTCCCAACCT	BC014011	CCDS43298.1	5p15.33	2012-02-24			ENSG00000221990	ENSG00000221990			25175	protein-coding gene	gene with protein product						12477932	Standard	NM_138464		Approved		uc010ita.3	Q8N2X6	OTTHUMG00000162235	ENST00000408966.2:c.128G>A	chr5.hg19:g.442810C>T	ENSP00000386139:p.Gly43Glu	56.0	0.0	.		103.0	41.0	.	NM_138464	Q96CR9	Missense_Mutation	SNP	ENST00000408966.2	hg19	CCDS43298.1	.	.	.	.	.	.	.	.	.	.	C	5.021	0.189573	0.09547	.	.	ENSG00000221990	ENST00000408966	T	0.46451	0.87	0.677	-1.35	0.09114	.	.	.	.	.	T	0.21307	0.0513	N	0.08118	0	0.09310	N	1	P	0.50710	0.938	B	0.43754	0.43	T	0.14254	-1.0479	8	0.87932	D	0	.	.	.	.	.	43	Q8N2X6	CE055_HUMAN	E	43	ENSP00000386139:G43E	ENSP00000386139:G43E	G	-	2	0	C5orf55	495810	0.002000	0.14202	0.001000	0.08648	0.023000	0.10783	0.811000	0.27198	-0.457000	0.07033	0.205000	0.17691	GGG	.	.	.	none		0.597	C5orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368033.1	NM_138464		T	442810	C	T	442810	3	4	254	1	0	0	0	0	1	0	0	0	2313	623	22	2	235	2	C5orf55	5	442810	Missense_Mutation	SNP	C	TCGA-SX-A7SU-01A-11D-A35Z-10		442810	180472450	11	15857											
COL4A3BP	10087	hgsc.bcm.edu	37	chr5	74677819	74677819	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaattacaaactatccaagtTtcagggtcattttcagtcaa	15	13	5	8	0	4	0	4	0	0	0	5	0	5	0	1	1	2	1	1	1	6	5			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr5:74677819T>C	ENST00000405807.4	-	15	1993	c.1572A>G	c.(1570-1572)gaA>gaG	p.E524E	COL4A3BP_ENST00000261415.7_Silent_p.E498E|COL4A3BP_ENST00000508692.1_5'UTR|COL4A3BP_ENST00000380494.5_Silent_p.E652E	NM_005713.2	NP_005704.1	Q9Y5P4	C43BP_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen) binding protein	524	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|ceramide metabolic process (GO:0006672)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi ceramide transport (GO:0035621)|heart morphogenesis (GO:0003007)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lipid homeostasis (GO:0055088)|mitochondrion morphogenesis (GO:0070584)|muscle contraction (GO:0006936)|protein phosphorylation (GO:0006468)|response to endoplasmic reticulum stress (GO:0034976)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ceramide binding (GO:0097001)|ceramide transporter activity (GO:0035620)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein kinase activity (GO:0004672)			breast(1)|kidney(1)|large_intestine(5)|lung(4)|skin(3)|stomach(1)|urinary_tract(1)	16		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;1e-53)		CTATCCAAGTTTCAGGGTCAT	0.358																																					p.E652E		Atlas-SNP	.											.	COL4A3BP	72	.	0			c.A1956G						PASS	.						72	72	72					5																	74677819		2203	4300	6503	SO:0001819	synonymous_variant	10087	exon16			CCAAGTTTCAGGG	AF136450	CCDS4028.1, CCDS4029.1, CCDS47235.1	5q13.3	2013-01-10	2007-06-08	2007-06-08	ENSG00000113163	ENSG00000113163		"StAR-related lipid transfer (START) domain containing", "Pleckstrin homology (PH) domain containing"	2205	protein-coding gene	gene with protein product	"ceramide transporter", "StAR-related lipid transfer (START) domain containing 11"	604677				10212244	Standard	NM_001130105		Approved	GPBP, STARD11, CERT	uc003kdt.3	Q9Y5P4	OTTHUMG00000102068	ENST00000405807.4:c.1572A>G	chr5.hg19:g.74677819T>C		161.0	0.0	.		339.0	146.0	.	NM_001130105	A8K7S2|B3KUB7|Q53YV1|Q53YV2|Q96Q85|Q96Q88|Q9H2S7|Q9H2S8	Silent	SNP	ENST00000405807.4	hg19	CCDS4028.1	.	.	.	.	.	.	.	.	.	.	T	10.21	1.287259	0.23478	.	.	ENSG00000113163	ENST00000508809	.	.	.	6.04	2.29	0.28610	.	.	.	.	.	T	0.53997	0.1831	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41466	-0.9507	4	.	.	.	-14.7757	6.1178	0.20136	0.0:0.1942:0.1241:0.6817	.	.	.	.	D	26	.	.	N	-	1	0	COL4A3BP	74713575	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.125000	0.31332	0.161000	0.19458	0.529000	0.55759	AAC	.	.	.	none		0.358	COL4A3BP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219875.2	NM_005713		C	74677819	T	C	74677819	2	2	254	1	0	0	0	0	0	0	0	1	3694	1838	64	3		3	COL4A3BP	5	74677819	Silent	SNP	T	TCGA-SX-A7SU-01A-11D-A35Z-10	74235009	74677819	106237441	12	15858											
PHAX	51808	hgsc.bcm.edu	37	chr5	125939501	125939501	+	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	ccacctgttgctggaggaaaGaagattaacaacatatgggg	14	8	12	7	0	0	2	0	0	0	2	0	4	0	4	2	4	3	2	2	4	5	3			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr5:125939501G>C	ENST00000297540.4	+	2	1031	c.336G>C	c.(334-336)aaG>aaC	p.K112N	PHAX_ENST00000514725.1_3'UTR	NM_032177.3	NP_115553.2	Q9H814	PHAX_HUMAN	phosphorylated adaptor for RNA export	112	Necessary for interaction with CBP80. {ECO:0000250}.				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						CTGGAGGAAAGAAGATTAACA	0.468																																					p.K112N		Atlas-SNP	.											.	PHAX	20	.	0			c.G336C						PASS	.						76	73	74					5																	125939501		2203	4300	6503	SO:0001583	missense	51808	exon2			AGGAAAGAAGATT	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.336G>C	chr5.hg19:g.125939501G>C	ENSP00000297540:p.Lys112Asn	211.0	0.0	.		274.0	119.0	.	NM_032177	Q9H8W1	Missense_Mutation	SNP	ENST00000297540.4	hg19	CCDS4138.1	.	.	.	.	.	.	.	.	.	.	G	15.01	2.706865	0.48412	.	.	ENSG00000164902	ENST00000297540;ENST00000456348	T	0.23552	1.9	5.74	3.96	0.45880	.	0.155351	0.56097	D	0.000029	T	0.28134	0.0694	L	0.59436	1.845	0.39908	D	0.973988	P	0.48089	0.905	P	0.45119	0.47	T	0.06570	-1.0819	10	0.62326	D	0.03	-21.8128	8.3183	0.32113	0.2939:0.0:0.7061:0.0	.	112	Q9H814	PHAX_HUMAN	N	112	ENSP00000297540:K112N	ENSP00000297540:K112N	K	+	3	2	PHAX	125967400	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	1.025000	0.30090	0.781000	0.33589	0.655000	0.94253	AAG	.	.	.	none		0.468	PHAX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250924.1	NM_032177		C	125939501	G	C	125939501	3	2	254	1	0	0	0	0	1	0	0	0	11820	933	33	4	342	4	PHAX	5	125939501	Missense_Mutation	SNP	G	TCGA-SX-A7SU-01A-11D-A35Z-10	51261682	125939501	54975759	13	15859											
CTNNA1	1495	hgsc.bcm.edu	37	chr5	138266330	138266330	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatgattatgatggagatgAcagactttacccggtgagca	12	10	12	7	1	0	6	0	4	0	2	0	7	0	6	1	2	2	2	1	2	2	3			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr5:138266330A>G	ENST00000302763.7	+	15	2269	c.2179A>G	c.(2179-2181)Aca>Gca	p.T727A	CTNNA1_ENST00000355078.5_Missense_Mutation_p.T624A|CTNNA1_ENST00000518825.1_Missense_Mutation_p.T727A|CTNNA1_ENST00000540387.1_Missense_Mutation_p.T357A	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	727					adherens junction organization (GO:0034332)|aging (GO:0007568)|apical junction assembly (GO:0043297)|axon regeneration (GO:0031103)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular protein localization (GO:0034613)|cellular response to indole-3-methanol (GO:0071681)|epithelial cell-cell adhesion (GO:0090136)|establishment or maintenance of cell polarity (GO:0007163)|gap junction assembly (GO:0016264)|male gonad development (GO:0008584)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell motility (GO:2000146)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|negative regulation of neuroblast proliferation (GO:0007406)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of smoothened signaling pathway (GO:0045880)|protein heterooligomerization (GO:0051291)|response to estrogen (GO:0043627)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|catenin complex (GO:0016342)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|gamma-catenin binding (GO:0045295)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|vinculin binding (GO:0017166)			NS(1)|breast(7)|cervix(2)|endometrium(4)|kidney(6)|large_intestine(16)|lung(9)|oesophagus(2)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	52			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GATGGAGATGACAGACTTTAC	0.567																																					p.T727A		Atlas-SNP	.											.	CTNNA1	114	.	0			c.A2179G						PASS	.						162	153	156					5																	138266330		2203	4300	6503	SO:0001583	missense	1495	exon15			GAGATGACAGACT	D13866	CCDS34243.1, CCDS75315.1	5q31.2	2008-02-05	2002-08-29			ENSG00000044115			2509	protein-coding gene	gene with protein product		116805	"catenin (cadherin-associated protein), alpha 1 (102kD)"			1924379	Standard	XM_005271898		Approved	CAP102	uc003ldh.3	P35221		ENST00000302763.7:c.2179A>G	chr5.hg19:g.138266330A>G	ENSP00000304669:p.Thr727Ala	97.0	0.0	.		170.0	76.0	.	NM_001903	Q12795|Q8N1C0	Missense_Mutation	SNP	ENST00000302763.7	hg19	CCDS34243.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.634797	0.87760	.	.	ENSG00000044115	ENST00000355078;ENST00000302763;ENST00000537034;ENST00000541863;ENST00000518825;ENST00000540387;ENST00000520520	T;T;T;T;T	0.39997	1.05;1.05;1.05;1.05;1.05	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.61850	0.2380	M	0.64404	1.975	0.80722	D	1	D;D;D	0.89917	1.0;0.995;0.998	D;D;D	0.85130	0.997;0.986;0.983	T	0.58962	-0.7543	10	0.35671	T	0.21	-19.3613	16.0443	0.80707	1.0:0.0:0.0:0.0	.	727;604;727	G3XAM7;B4DKT9;P35221	.;.;CTNA1_HUMAN	A	624;727;727;712;727;357;2	ENSP00000347190:T624A;ENSP00000304669:T727A;ENSP00000427821:T727A;ENSP00000438476:T357A;ENSP00000430076:T2A	ENSP00000304669:T727A	T	+	1	0	CTNNA1	138294229	1.000000	0.71417	0.998000	0.56505	0.802000	0.45316	9.057000	0.93889	2.326000	0.78906	0.533000	0.62120	ACA	.	.	.	none		0.567	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903		G	138266330	A	G	138266330	3	3	254	1	0	0	0	0	1	0	0	0	4014	275	10	3	2233	3	CTNNA1	5	138266330	Missense_Mutation	SNP	A	TCGA-SX-A7SU-01A-11D-A35Z-10	12326829	138266330	42648930	14	15860											
F12	2161	hgsc.bcm.edu	37	chr5	176830954	176830954	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccagtacagcgcggcgatgtAggggtgcgccccgcgtagcg	6	5	17	13	7	0	0	0	0	0	0	0	1	0	0	3	3	4	3	3	3	3	3			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr5:176830954A>G	ENST00000253496.3	-	10	1204	c.1156T>C	c.(1156-1158)Tac>Cac	p.Y386H	F12_ENST00000514943.1_5'Flank	NM_000505.3	NP_000496.2	P00748	FA12_HUMAN	coagulation factor XII (Hageman factor)	386	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|plasma kallikrein-kinin cascade (GO:0002353)|positive regulation of blood coagulation (GO:0030194)|positive regulation of fibrinolysis (GO:0051919)|positive regulation of plasminogen activation (GO:0010756)|protein autoprocessing (GO:0016540)|protein processing (GO:0016485)|response to misfolded protein (GO:0051788)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	misfolded protein binding (GO:0051787)|serine-type aminopeptidase activity (GO:0070009)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	12	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Ethanolamine Oleate(DB06689)	GCGGCGATGTAGGGGTGCGCC	0.706									Hereditary Angioedema		OREG0017088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y386H		Atlas-SNP	.											.	F12	35	.	0			c.T1156C						PASS	.						12	15	14					5																	176830954		2188	4284	6472	SO:0001583	missense	2161	exon10	Familial Cancer Database	HAE, type I-III, Hereditary Angioneurotic Edema, HANE,	CGATGTAGGGGTG	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.1156T>C	chr5.hg19:g.176830954A>G	ENSP00000253496:p.Tyr386His	75.0	0.0	.	1934	135.0	54.0	.	NM_000505	P78339	Missense_Mutation	SNP	ENST00000253496.3	hg19	CCDS34302.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.648256	0.87958	.	.	ENSG00000131187	ENST00000253496	T	0.62498	0.02	5.61	5.61	0.85477	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.42682	D	0.000678	T	0.67183	0.2866	N	0.20845	0.615	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.72394	-0.4307	10	0.87932	D	0	.	14.7703	0.69671	1.0:0.0:0.0:0.0	.	386	P00748	FA12_HUMAN	H	386	ENSP00000253496:Y386H	ENSP00000253496:Y386H	Y	-	1	0	F12	176763560	1.000000	0.71417	1.000000	0.80357	0.424000	0.31475	4.136000	0.58004	2.137000	0.66172	0.459000	0.35465	TAC	.	.	.	none		0.706	F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373217.1			G	176830954	A	G	176830954	3	3	254	1	0	0	0	0	1	0	0	0	5341	420	15	3	711	3	F12	5	176830954	Missense_Mutation	SNP	A	TCGA-SX-A7SU-01A-11D-A35Z-10	38564624	176830954	4084306	15	15861											
SYCP2L	221711	hgsc.bcm.edu	37	chr6	10935326	10935326	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatcagagaaagaaataccCgagcaaaataacaccacatc	20	4	5	12	1	1	2	1	0	0	2	2	4	1	2	3	0	3	1	3	0	6	2			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr6:10935326C>T	ENST00000283141.6	+	21	2015	c.1719C>T	c.(1717-1719)ccC>ccT	p.P573P		NM_001040274.2	NP_001035364.2	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like	573						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)			AAGAAATACCCGAGCAAAATA	0.313																																					p.P573P		Atlas-SNP	.											.	SYCP2L	101	.	0			c.C1719T						PASS	.						77	71	73					6																	10935326		1794	4077	5871	SO:0001819	synonymous_variant	221711	exon21			AATACCCGAGCAA	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.1719C>T	chr6.hg19:g.10935326C>T		233.0	0.0	.		390.0	153.0	.	NM_001040274	A6NDS5|Q08GK5|Q6ZRM2|Q96EJ2	Silent	SNP	ENST00000283141.6	hg19	CCDS43423.1																																																																																			.	.	.	none		0.313	SYCP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039845.3	NM_194299		T	10935326	C	T	10935326	2	4	254	1	0	0	0	0	0	0	0	1	15445	639	23	1		1	SYCP2L	6	10935326	Silent	SNP	C	TCGA-SX-A7SU-01A-11D-A35Z-10		10935326	160179741	16	15862											
C6orf58	352999	hgsc.bcm.edu	37	chr6	127911437	127911437	+	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	agaatgtagtcctggttcttCtaaatatgcttgacaatgtg	11	15	9	6	0	2	2	0	1	2	1	3	2	3	2	1	1	1	3	1	1	6	6			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr6:127911437C>G	ENST00000329722.7	+	5	892	c.880C>G	c.(880-882)Cta>Gta	p.L294V		NM_001010905.1	NP_001010905.1	Q6P5S2	CF058_HUMAN	chromosome 6 open reading frame 58	294						extracellular vesicular exosome (GO:0070062)				kidney(3)|large_intestine(3)|liver(1)|lung(7)|pancreas(1)	15				GBM - Glioblastoma multiforme(226;0.0405)|all cancers(137;0.156)		CCTGGTTCTTCTAAATATGCT	0.338																																					p.L294V		Atlas-SNP	.											.	C6orf58	35	.	0			c.C880G						PASS	.						135	139	138					6																	127911437		2203	4300	6503	SO:0001583	missense	352999	exon5			GTTCTTCTAAATA	BC062712	CCDS34533.1	6q22.33	2011-12-13			ENSG00000184530	ENSG00000184530			20960	protein-coding gene	gene with protein product							Standard	NM_001010905		Approved		uc003qbh.4	Q6P5S2	OTTHUMG00000015530	ENST00000329722.7:c.880C>G	chr6.hg19:g.127911437C>G	ENSP00000328069:p.Leu294Val	34.0	0.0	.		36.0	13.0	.	NM_001010905	B4E1I0|Q5VUP2	Missense_Mutation	SNP	ENST00000329722.7	hg19	CCDS34533.1	.	.	.	.	.	.	.	.	.	.	C	13.49	2.251728	0.39797	.	.	ENSG00000184530	ENST00000329722	T	0.53423	0.62	5.11	-6.07	0.02158	.	0.135773	0.50627	N	0.000106	T	0.17152	0.0412	M	0.74546	2.27	0.09310	N	1	B	0.32862	0.387	B	0.34873	0.191	T	0.18053	-1.0349	10	0.59425	D	0.04	-3.1435	0.0452	0.00010	0.3222:0.1806:0.2115:0.2856	.	294	Q6P5S2	CF058_HUMAN	V	294	ENSP00000328069:L294V	ENSP00000328069:L294V	L	+	1	2	C6orf58	127953130	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	-0.091000	0.11146	-1.770000	0.01295	-0.136000	0.14681	CTA	.	.	.	none		0.338	C6orf58-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042152.1	NM_001010905		G	127911437	C	G	127911437	3	3	254	1	0	0	0	0	1	0	0	0	2369	912	32	4	898	4	C6orf58	6	127911437	Missense_Mutation	SNP	C	TCGA-SX-A7SU-01A-11D-A35Z-10	116976111	127911437	43203630	17	15863											
CITED2	10370	hgsc.bcm.edu	37	chr6	139694378	139694378	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttgatgcggtccaaacccAtttctatcaccaaggacata	12	10	6	13	1	2	1	1	1	1	0	3	2	3	2	4	2	2	0	4	2	4	4			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr6:139694378A>G	ENST00000367651.2	-	2	919	c.704T>C	c.(703-705)aTg>aCg	p.M235T	CITED2_ENST00000537332.1_Missense_Mutation_p.M235T|CITED2_ENST00000536159.1_Missense_Mutation_p.M235T	NM_006079.4	NP_006070.2	Q99967	CITE2_HUMAN	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	235	Asp/Glu-rich (acidic).				adrenal cortex formation (GO:0035802)|bone morphogenesis (GO:0060349)|cardiac neural crest cell development involved in heart development (GO:0061308)|cell aging (GO:0007569)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|cranial nerve morphogenesis (GO:0021602)|decidualization (GO:0046697)|determination of left/right symmetry (GO:0007368)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|endocardial cushion development (GO:0003197)|erythrocyte development (GO:0048821)|granulocyte differentiation (GO:0030851)|heart development (GO:0007507)|heart looping (GO:0001947)|hematopoietic progenitor cell differentiation (GO:0002244)|left/right axis specification (GO:0070986)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell migration (GO:0030336)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900164)|outflow tract morphogenesis (GO:0003151)|peripheral nervous system development (GO:0007422)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of gene expression (GO:0010628)|positive regulation of male gonad development (GO:2000020)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|pulmonary artery morphogenesis (GO:0061156)|regulation of organ formation (GO:0003156)|regulation of RNA biosynthetic process (GO:2001141)|response to estrogen (GO:0043627)|response to fluid shear stress (GO:0034405)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|sex determination (GO:0007530)|skeletal muscle cell differentiation (GO:0035914)|spleen development (GO:0048536)|thymus development (GO:0048538)|transforming growth factor beta receptor signaling pathway (GO:0007179)|trophectodermal cell differentiation (GO:0001829)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|LBD domain binding (GO:0050693)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			large_intestine(1)|lung(4)	5	Breast(32;0.226)			GBM - Glioblastoma multiforme(68;0.000171)|OV - Ovarian serous cystadenocarcinoma(155;0.00134)		GTCCAAACCCATTTCTATCAC	0.547																																					p.M240T	NSCLC(98;1219 1550 33720 43229 49330)	Atlas-SNP	.											.	CITED2	16	.	0			c.T719C						PASS	.						79	80	80					6																	139694378		2203	4300	6503	SO:0001583	missense	10370	exon2			AAACCCATTTCTA	U65093	CCDS5195.1, CCDS75530.1	6q23.3	2008-08-29			ENSG00000164442	ENSG00000164442			1987	protein-coding gene	gene with protein product		602937				8901575, 10552932	Standard	NM_006079		Approved	MRG1	uc021zfz.2	Q99967	OTTHUMG00000015691	ENST00000367651.2:c.704T>C	chr6.hg19:g.139694378A>G	ENSP00000356623:p.Met235Thr	87.0	0.0	.		108.0	50.0	.	NM_001168389	O95426|Q5VTF4	Missense_Mutation	SNP	ENST00000367651.2	hg19	CCDS5195.1	.	.	.	.	.	.	.	.	.	.	A	16.62	3.175054	0.57692	.	.	ENSG00000164442	ENST00000367651;ENST00000536159;ENST00000537332;ENST00000392312	T;T;T	0.66099	-0.19;-0.19;-0.19	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.34513	0.0900	N	0.24115	0.695	0.58432	D	0.999997	B	0.23128	0.08	B	0.28709	0.093	T	0.26121	-1.0112	9	.	.	.	-3.6977	15.9141	0.79496	1.0:0.0:0.0:0.0	.	235	Q99967	CITE2_HUMAN	T	235;235;235;179	ENSP00000356623:M235T;ENSP00000442831:M235T;ENSP00000444198:M235T	.	M	-	2	0	CITED2	139736071	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.875000	0.92372	2.156000	0.67533	0.533000	0.62120	ATG	.	.	.	none		0.547	CITED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042463.1			G	139694378	A	G	139694378	3	3	254	1	0	0	0	0	1	0	0	0	3442	217	8	3	112	3	CITED2	6	139694378	Missense_Mutation	SNP	A	TCGA-SX-A7SU-01A-11D-A35Z-10	11782941	139694378	31420689	18	15864											
PACRG	135138	hgsc.bcm.edu	37	chr6	163483263	163483263	+	Frame_Shift_Del	DEL	T	T	-																															aaatgacatttccctatgagTtttttgctcggcaaggaatc																										TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr6:163483263delT	ENST00000337019.3	+	4	597	c.373delT	c.(373-375)tttfs	p.F126fs	PACRG_ENST00000366888.2_Frame_Shift_Del_p.F126fs|PACRG_ENST00000366889.2_Frame_Shift_Del_p.F126fs	NM_152410.2	NP_689623.2	Q96M98	PACRG_HUMAN	PARK2 co-regulated	126					spermatid development (GO:0007286)	cell body (GO:0044297)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm midpiece (GO:0097225)				endometrium(2)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)		TCCCTATGAGTTTTTTGCTCG	0.418																																					p.E124fs		Atlas-Indel,Pindel	.											.	PACRG	48	.	0			c.372delG						PASS	.						98	96	97					6																	163483263		2203	4300	6503	SO:0001589	frameshift_variant	135138	exon3			.	AK057286	CCDS5284.1, CCDS43524.1	6q26	2004-07-01			ENSG00000112530	ENSG00000112530			19152	protein-coding gene	gene with protein product		608427				12547187	Standard	NM_001080378		Approved	PARK2CRG, FLJ32724, Glup, HAK005771	uc003qua.3	Q96M98	OTTHUMG00000016116	ENST00000337019.3:c.373delT	chr6.hg19:g.163483263delT	ENSP00000337946:p.Phe126fs	89.0	0.0	0		173.0	69.0	0.398844	NM_001080379	E1P5B5|Q6IMB8|Q8IZM1|Q8NHP5|Q9H1V9	Frame_Shift_Del	DEL	ENST00000337019.3	hg19	CCDS5284.1																																																																																			.	.	.	none		0.418	PACRG-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400424.1	NM_152410		-	163483263	T	-	163483263	7	5	254	1	0	1	0	1	0	0	0	0	11377	1725	60	0	383	0	PACRG	6	163483263	Frame_Shift_Del	DEL	T	TCGA-SX-A7SU-01A-11D-A35Z-10	23788885	163483263	7631804	19	15865											
SGK223	157285	hgsc.bcm.edu	37	chr8	8235005	8235005	+	Frame_Shift_Del	DEL	G	G	-																															agcactccttggggaagctcGggccccgcttctcctgctct																								rs538380081		TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr8:8235005delG	ENST00000520004.1	-	3	1178	c.914delC	c.(913-915)ccgfs	p.P305fs	SGK223_ENST00000330777.4_Frame_Shift_Del_p.P305fs			Q86YV5	SG223_HUMAN		305							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GGGGAAGCTCGGGCCCCGCTT	0.672																																					p.P305fs	GBM(34;731 755 10259 33573 33867)	Atlas-Indel,Pindel	.											.	.	.	.	0			c.915delG						PASS	.						12	17	15					8																	8235005		1892	4045	5937	SO:0001589	frameshift_variant	0	exon2			.																												ENST00000520004.1:c.914delC	chr8.hg19:g.8235005delG	ENSP00000428054:p.Pro305fs	111.0	0.0	0		174.0	65.0	0.373563	NM_001080826	Q8N3N5	Frame_Shift_Del	DEL	ENST00000520004.1	hg19	CCDS43706.1																																																																																			.	.	.	none		0.672	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1			-	8235005	G	-	8235005	7	5	254	1	0	1	0	1	0	0	0	0	14223	1116	39	0	3310	0	SGK223	8	8235005	Frame_Shift_Del	DEL	G	TCGA-SX-A7SU-01A-11D-A35Z-10		8235005	138129017	20	15866											
SMARCA2	6595	hgsc.bcm.edu	37	chr9	2039785	2039785	+	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	cagcagcagcaacagcagcaGcagcagcagcagcagcagca	15	0	12	14	0	0	0	0	0	0	0	0	0	0	0	0	0	13	12	0	0	1	0			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr9:2039785G>A	ENST00000382203.1	+	4	884	c.675G>A	c.(673-675)caG>caA	p.Q225Q	SMARCA2_ENST00000382194.1_Silent_p.Q225Q|SMARCA2_ENST00000349721.2_Silent_p.Q225Q|SMARCA2_ENST00000357248.2_Silent_p.Q225Q|SMARCA2_ENST00000491574.1_3'UTR|RP11-264I13.2_ENST00000426860.1_RNA			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	225	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)		aacagcagcagcagcagcagc	0.637																																					p.Q225Q		Atlas-SNP	.											.	SMARCA2	313	.	0			c.G675A						PASS	.						9	12	11					9																	2039785		2093	4139	6232	SO:0001819	synonymous_variant	6595	exon4			GCAGCAGCAGCAG	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.675G>A	chr9.hg19:g.2039785G>A		57.0	0.0	.		106.0	11.0	.	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Silent	SNP	ENST00000382203.1	hg19	CCDS34977.1																																																																																			.	.	.	none		0.637	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070		A	2039785	G	A	2039785	2	1	254	1	0	0	0	0	0	0	0	1	14782	962	34	2		2	SMARCA2	9	2039785	Silent	SNP	G	TCGA-SX-A7SU-01A-11D-A35Z-10		2039785	139173646	21	15867			1	36		2	2	25	G		3.178577e-05
SMARCA2	6595	hgsc.bcm.edu	37	chr9	2039809	2039809	+	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	cagcagcagcagcagcagcaGcagcagcaacagcagccgca	14	0	12	15	1	0	0	0	0	0	0	0	0	0	0	1	0	12	11	1	0	1	0			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr9:2039809G>A	ENST00000382203.1	+	4	908	c.699G>A	c.(697-699)caG>caA	p.Q233Q	SMARCA2_ENST00000382194.1_Silent_p.Q233Q|SMARCA2_ENST00000349721.2_Silent_p.Q233Q|SMARCA2_ENST00000357248.2_Silent_p.Q233Q|SMARCA2_ENST00000491574.1_3'UTR|RP11-264I13.2_ENST00000426860.1_RNA			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	233	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)		agcagcagcagcagcagcaac	0.587																																					p.Q233Q		Atlas-SNP	.											.	SMARCA2	313	.	0			c.G699A						PASS	.						9	12	11					9																	2039809		2085	4079	6164	SO:0001819	synonymous_variant	6595	exon4			GCAGCAGCAGCAG	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.699G>A	chr9.hg19:g.2039809G>A		72.0	0.0	.		110.0	15.0	.	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Silent	SNP	ENST00000382203.1	hg19	CCDS34977.1																																																																																			.	.	.	none		0.587	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070		A	2039809	G	A	2039809	2	1	254	1	0	0	0	0	0	0	0	1	14782	962	34	2		2	SMARCA2	9	2039809	Silent	SNP	G	TCGA-SX-A7SU-01A-11D-A35Z-10	24	2039809	139173622	22	15868			1	36		2	2	25	G		3.178577e-05
UBAP2	55833	hgsc.bcm.edu	37	chr9	33944463	33944463	+	Missense_Mutation	SNP	T	T	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	caatggtcgtgctgggaagcTgcaaaagcttgttcacagtg	10	10	13	8	1	1	0	1	0	0	0	2	1	1	1	0	2	4	5	0	2	4	2			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr9:33944463T>G	ENST00000379238.1	-	14	1562	c.1445A>C	c.(1444-1446)cAg>cCg	p.Q482P	UBAP2_ENST00000418786.2_Missense_Mutation_p.Q429P|UBAP2_ENST00000449054.1_Missense_Mutation_p.Q482P|UBAP2_ENST00000379225.1_Missense_Mutation_p.Q115P|UBAP2_ENST00000360802.1_Missense_Mutation_p.Q482P|UBAP2_ENST00000539807.1_Missense_Mutation_p.Q237P|UBAP2_ENST00000379239.4_Missense_Mutation_p.Q215P					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)		GCTGGGAAGCTGCAAAAGCTT	0.512																																					p.Q482P		Atlas-SNP	.											.	UBAP2	82	.	0			c.A1445C						PASS	.						126	114	118					9																	33944463		2203	4300	6503	SO:0001583	missense	55833	exon14			GGAAGCTGCAAAA	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.1445A>C	chr9.hg19:g.33944463T>G	ENSP00000368540:p.Gln482Pro	109.0	0.0	.		154.0	77.0	.	NM_018449		Missense_Mutation	SNP	ENST00000379238.1	hg19	CCDS6547.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.962763	0.53507	.	.	ENSG00000137073	ENST00000379238;ENST00000449054;ENST00000360802;ENST00000431417;ENST00000379239;ENST00000539807;ENST00000418786;ENST00000379225	T;T;T;T;T;T;T	0.26810	2.58;2.58;2.58;2.35;2.36;2.01;1.71	5.53	5.53	0.82687	.	0.327428	0.32503	N	0.006019	T	0.45256	0.1333	L	0.53249	1.67	0.52501	D	0.999952	D;D;D;D;D;B;D;D	0.76494	0.986;0.999;0.974;0.986;0.986;0.031;0.998;0.997	P;D;P;P;P;B;D;P	0.69824	0.744;0.966;0.663;0.663;0.744;0.013;0.925;0.854	T	0.21211	-1.0252	10	0.33141	T	0.24	-6.8583	15.6764	0.77326	0.0:0.0:0.0:1.0	.	429;407;237;215;391;115;407;482	E7EWG4;F5H4D5;F5H2U4;A6NCA8;F5H2C8;A2A306;B4DH66;Q5T6F2	.;.;.;.;.;.;.;UBAP2_HUMAN	P	482;482;482;391;215;237;429;115	ENSP00000368540:Q482P;ENSP00000416932:Q482P;ENSP00000354039:Q482P;ENSP00000368541:Q215P;ENSP00000439329:Q237P;ENSP00000404436:Q429P;ENSP00000368527:Q115P	ENSP00000354039:Q482P	Q	-	2	0	UBAP2	33934463	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	2.623000	0.46435	2.111000	0.64477	0.528000	0.53228	CAG	.	.	.	none		0.512	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449		G	33944463	T	G	33944463	3	3	254	1	0	0	0	0	1	0	0	0	16849	1580	55	5	1978	5	UBAP2	9	33944463	Missense_Mutation	SNP	T	TCGA-SX-A7SU-01A-11D-A35Z-10	31904654	33944463	107268968	23	15869											
HNRNPH3	3189	hgsc.bcm.edu	37	chr10	70098346	70098346	+	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	gctgggacagcgaccgggacCatatgatagaccaataggag	13	5	14	9	2	0	2	0	1	0	1	0	6	0	5	3	3	1	1	3	3	4	3			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr10:70098346C>A	ENST00000265866.7	+	4	503	c.338C>A	c.(337-339)cCa>cAa	p.P113Q	HNRNPH3_ENST00000469172.1_3'UTR|HNRNPH3_ENST00000354695.5_Missense_Mutation_p.P113Q|HNRNPH3_ENST00000441000.2_Intron	NM_012207.2|NM_021644.3	NP_036339.1|NP_067676.2	P31942	HNRH3_HUMAN	heterogeneous nuclear ribonucleoprotein H3 (2H9)	113	Gly-rich.				epithelial cell differentiation (GO:0030855)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)|ovary(2)|prostate(2)	11						CGACCGGGACCATATGATAGA	0.438																																					p.P113Q		Atlas-SNP	.											.	HNRNPH3	33	.	0			c.C338A						PASS	.						192	188	190					10																	70098346		2203	4300	6503	SO:0001583	missense	3189	exon4			CGGGACCATATGA		CCDS7278.1, CCDS7279.1	10q22	2013-02-12		2008-04-18	ENSG00000096746	ENSG00000096746		"RNA binding motif (RRM) containing"	5043	protein-coding gene	gene with protein product		602324		HNRPH3		8999868	Standard	NM_021644		Approved	2H9	uc001jnw.4	P31942	OTTHUMG00000018349	ENST00000265866.7:c.338C>A	chr10.hg19:g.70098346C>A	ENSP00000265866:p.Pro113Gln	120.0	0.0	.		156.0	65.0	.	NM_012207	A8K682|B3KRE1|Q9BSX1|Q9NP53|Q9NP96|Q9NPA7|Q9NPI4|Q9UFU4|Q9Y4J5	Missense_Mutation	SNP	ENST00000265866.7	hg19	CCDS7278.1	.	.	.	.	.	.	.	.	.	.	C	16.40	3.113676	0.56398	.	.	ENSG00000096746	ENST00000265866;ENST00000354695	T;T	0.15834	2.59;2.39	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.47691	0.1459	M	0.77103	2.36	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.994	T	0.36407	-0.9749	10	0.66056	D	0.02	.	20.6397	0.99537	0.0:1.0:0.0:0.0	.	113;113	P31942-2;P31942	.;HNRH3_HUMAN	Q	113	ENSP00000265866:P113Q;ENSP00000346726:P113Q	ENSP00000265866:P113Q	P	+	2	0	HNRNPH3	69768352	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.880000	0.98712	0.650000	0.86243	CCA	.	.	.	none		0.438	HNRNPH3-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090165.1			A	70098346	C	A	70098346	3	1	254	1	0	0	0	0	1	0	0	0	7275	594	21	4	348	4	HNRNPH3	10	70098346	Missense_Mutation	SNP	C	TCGA-SX-A7SU-01A-11D-A35Z-10		70098346	65436401	24	15870											
PANK1	53354	hgsc.bcm.edu	37	chr10	91359120	91359120	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggttatcaaggcagtacggcTttttttgacacaattcagga	11	13	10	7	1	2	1	2	1	0	0	2	2	2	2	0	4	1	4	0	4	4	6	rs371501466		TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr10:91359120T>C	ENST00000307534.4	-	3	1354	c.1199A>G	c.(1198-1200)aAg>aGg	p.K400R	PANK1_ENST00000371774.2_Missense_Mutation_p.K202R|PANK1_ENST00000342512.3_Missense_Mutation_p.K175R|PANK1_ENST00000322191.6_Missense_Mutation_p.K175R	NM_148977.2	NP_683878.1	Q8TE04	PANK1_HUMAN	pantothenate kinase 1	400					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						GCAGTACGGCTTTTTTTGACA	0.438																																					p.K400R		Atlas-SNP	.											.,3	PANK1	35	.	0			c.A1199G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS	0,4406		0,0,2203	231	209	217		524,1199,524	3.5	1	10		217	1,8599		0,1,4299	no	missense,missense,missense	PANK1	NM_138316.3,NM_148977.2,NM_148978.2	26,26,26	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	benign,benign,benign	175/315,400/599,175/374	91359120	1,13005	2203	4300	6503	SO:0001583	missense	53354	exon3			TACGGCTTTTTTT	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.1199A>G	chr10.hg19:g.91359120T>C	ENSP00000302108:p.Lys400Arg	170.0	0.0	.		257.0	97.0	.	NM_148977	A6NIP0|Q7RTX6|Q7Z495|Q8TBQ8	Missense_Mutation	SNP	ENST00000307534.4	hg19	CCDS31244.1	.	.	.	.	.	.	.	.	.	.	T	10.35	1.325206	0.24080	0.0	1.16E-4	ENSG00000152782	ENST00000342512;ENST00000322191;ENST00000371774;ENST00000307534;ENST00000371775	D;D;D;D	0.99519	-6.07;-6.07;-6.07;-6.07	5.89	3.48	0.39840	.	0.111375	0.64402	D	0.000008	D	0.96043	0.8711	N	0.11064	0.09	0.42341	D	0.992337	B;B;B;B	0.22800	0.0;0.075;0.0;0.0	B;B;B;B	0.18263	0.002;0.021;0.005;0.001	D	0.92579	0.6073	10	0.14656	T	0.56	.	8.0173	0.30389	0.1215:0.066:0.0:0.8125	.	202;400;175;175	Q8TE04-4;Q8TE04;Q8TE04-3;Q8TE04-2	.;PANK1_HUMAN;.;.	R	175;175;202;400;263	ENSP00000345118:K175R;ENSP00000318526:K175R;ENSP00000360839:K202R;ENSP00000302108:K400R	ENSP00000302108:K400R	K	-	2	0	PANK1	91349100	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.257000	0.32932	0.439000	0.26476	0.455000	0.32223	AAG	.	.	.	none		0.438	PANK1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				C	91359120	T	C	91359120	3	2	254	1	0	0	0	0	1	0	0	0	11423	1609	56	3	617	3	PANK1	10	91359120	Missense_Mutation	SNP	T	TCGA-SX-A7SU-01A-11D-A35Z-10	21260774	91359120	44175627	25	15871											
OR8H3	390152	hgsc.bcm.edu	37	chr11	55889939	55889939	+	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	tccagatggctctgtttatgCtatttctcctcatataccta	8	17	5	11	0	3	1	1	0	2	1	5	1	4	1	3	1	2	3	3	1	5	7			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr11:55889939C>T	ENST00000313472.3	+	1	91	c.91C>T	c.(91-93)Cta>Tta	p.L31L		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	31						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)					TCTGTTTATGCTATTTCTCCT	0.458																																					p.L31L		Atlas-SNP	.											.	OR8H3	92	.	0			c.C91T						PASS	.						226	218	220					11																	55889939		2201	4296	6497	SO:0001819	synonymous_variant	390152	exon1			TTTATGCTATTTC	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.91C>T	chr11.hg19:g.55889939C>T		67.0	0.0	.		126.0	67.0	.	NM_001005201	Q6IFB7	Silent	SNP	ENST00000313472.3	hg19	CCDS31519.1																																																																																			.	.	.	none		0.458	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201		T	55889939	C	T	55889939	2	4	254	1	0	0	0	0	0	0	0	1	11246	796	28	2		2	OR8H3	11	55889939	Silent	SNP	C	TCGA-SX-A7SU-01A-11D-A35Z-10		55889939	79116577	26	15872											
TMEM109	79073	hgsc.bcm.edu	37	chr11	60689497	60689497	+	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	ccttgctgatcctctacgccCtgctgagccggctcactggc	4	10	10	17	2	2	2	1	2	1	0	3	2	3	2	4	2	4	3	4	2	1	2			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr11:60689497C>G	ENST00000227525.3	+	4	995	c.592C>G	c.(592-594)Ctg>Gtg	p.L198V	TMEM109_ENST00000536171.1_Missense_Mutation_p.L198V|TMEM132A_ENST00000453848.2_5'Flank|TMEM132A_ENST00000005286.4_5'Flank|RP11-881M11.4_ENST00000543907.1_RNA	NM_024092.2	NP_076997.1	Q9BVC6	TM109_HUMAN	transmembrane protein 109	198					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						CCTCTACGCCCTGCTGAGCCG	0.682																																					p.L198V		Atlas-SNP	.											.	TMEM109	24	.	0			c.C592G						PASS	.						40	43	42					11																	60689497		2203	4298	6501	SO:0001583	missense	79073	exon4			TACGCCCTGCTGA		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.592C>G	chr11.hg19:g.60689497C>G	ENSP00000227525:p.Leu198Val	47.0	0.0	.		62.0	36.0	.	NM_024092		Missense_Mutation	SNP	ENST00000227525.3	hg19	CCDS7996.1	.	.	.	.	.	.	.	.	.	.	C	18.47	3.630859	0.67015	.	.	ENSG00000110108	ENST00000227525;ENST00000540407;ENST00000536171	.	.	.	4.9	-5.32	0.02722	.	0.384411	0.20666	N	0.087928	T	0.35711	0.0941	L	0.54323	1.7	0.28670	N	0.905657	B	0.13594	0.008	B	0.20767	0.031	T	0.39502	-0.9611	9	0.62326	D	0.03	-10.2472	9.1152	0.36753	0.0:0.5283:0.1885:0.2832	.	198	Q9BVC6	TM109_HUMAN	V	198;120;198	.	ENSP00000227525:L198V	L	+	1	2	TMEM109	60446073	0.007000	0.16637	0.996000	0.52242	0.962000	0.63368	-1.096000	0.03353	-0.317000	0.08677	-0.302000	0.09304	CTG	.	.	.	none		0.682	TMEM109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396343.1	NM_024092		G	60689497	C	G	60689497	3	3	254	1	0	0	0	0	1	0	0	0	16037	680	24	4	602	4	TMEM109	11	60689497	Missense_Mutation	SNP	C	TCGA-SX-A7SU-01A-11D-A35Z-10	4799558	60689497	74317019	27	15873											
MOGAT2	80168	hgsc.bcm.edu	37	chr11	75428970	75428970	+	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	ccttgtttatgccgtgggagCgcaggctgcagacacttgct	6	11	13	11	2	0	1	0	0	0	1	0	2	0	2	2	2	4	5	2	2	1	4			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr11:75428970C>T	ENST00000198801.5	+	1	107	c.37C>T	c.(37-39)Cgc>Tgc	p.R13C	MOGAT2_ENST00000526712.1_5'Flank	NM_025098.2	NP_079374.2	Q3SYC2	MOGT2_HUMAN	monoacylglycerol O-acyltransferase 2	13					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)					GCCGTGGGAGCGCAGGCTGCA	0.597																																					p.R13C		Atlas-SNP	.											.	MOGAT2	49	.	0			c.C37T						PASS	.						131	88	103					11																	75428970		2200	4293	6493	SO:0001583	missense	80168	exon1			TGGGAGCGCAGGC	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.37C>T	chr11.hg19:g.75428970C>T	ENSP00000198801:p.Arg13Cys	71.0	0.0	.		106.0	45.0	.	NM_025098	A8K7I3|Q3SYC1|Q6ZQZ2|Q86UH6|Q9H630	Missense_Mutation	SNP	ENST00000198801.5	hg19	CCDS8240.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.847489	0.51164	.	.	ENSG00000166391	ENST00000198801	T	0.48522	0.81	4.87	4.87	0.63330	.	0.120026	0.53938	N	0.000043	T	0.54870	0.1885	M	0.91768	3.24	0.80722	D	1	P;D	0.53745	0.579;0.962	B;B	0.40602	0.22;0.334	T	0.68375	-0.5425	10	0.72032	D	0.01	2.0293	11.0357	0.47799	0.1859:0.8141:0.0:0.0	.	13;13	Q3SYC2;Q3SYC2-3	MOGT2_HUMAN;.	C	13	ENSP00000198801:R13C	ENSP00000198801:R13C	R	+	1	0	MOGAT2	75106618	0.994000	0.37717	1.000000	0.80357	0.907000	0.53573	1.299000	0.33424	2.390000	0.81377	0.557000	0.71058	CGC	.	.	.	none		0.597	MOGAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383520.1	NM_025098		T	75428970	C	T	75428970	3	4	254	1	0	0	0	0	1	0	0	0	9702	768	27	1	39	1	MOGAT2	11	75428970	Missense_Mutation	SNP	C	TCGA-SX-A7SU-01A-11D-A35Z-10	14739473	75428970	59577546	28	15874											
KATNAL1	84056	hgsc.bcm.edu	37	chr13	30814596	30814596	+	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	accaatttaataaattctcaCcttccatggccttctaatcc	12	14	2	13	0	2	0	1	0	2	0	5	0	4	0	5	1	0	0	5	1	5	7			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr13:30814596C>A	ENST00000380615.3	-	6	894		c.e6+1		KATNAL1_ENST00000380617.3_Splice_Site	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)		TAAATTCTCACCTTCCATGGC	0.378																																					.		Atlas-SNP	.											.	KATNAL1	53	.	0			c.726+1G>T						PASS	.						96	91	93					13																	30814596		2203	4300	6503	SO:0001630	splice_region_variant	84056	exon7			TTCTCACCTTCCA	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.726+1G>T	chr13.hg19:g.30814596C>A		53.0	0.0	.		81.0	27.0	.	NM_001014380		Splice_Site	SNP	ENST00000380615.3	hg19	CCDS31956.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.046053	0.75846	.	.	ENSG00000102781	ENST00000380615;ENST00000380617	.	.	.	4.69	4.69	0.59074	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.1853	0.89791	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KATNAL1	29712596	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	7.818000	0.86416	2.597000	0.87782	0.655000	0.94253	.	.	.	.	none		0.378	KATNAL1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044346.2	NM_032116	Intron	A	30814596	C	A	30814596	5	1	254	1	0	0	0	0	0	0	1	0	7992	521	18	4	769	4	KATNAL1	13	30814596	Splice_Site	SNP	C	TCGA-SX-A7SU-01A-11D-A35Z-10		30814596	84355282	29	15875											
ANPEP	290	hgsc.bcm.edu	37	chr15	90340880	90340880	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgctcagggcggcctcccAgggcatgtactgtctctctt	4	11	12	14	1	3	0	1	0	2	0	5	0	4	0	2	3	2	4	2	3	1	2			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr15:90340880A>G	ENST00000300060.6	-	15	2396	c.2083T>C	c.(2083-2085)Tgg>Cgg	p.W695R	ANPEP_ENST00000558177.1_5'UTR	NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	695	Metalloprotease.				angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	GCGGCCTCCCAGGGCATGTAC	0.557																																					p.W695R	NSCLC(30;827 977 2459 19669 26125)	Atlas-SNP	.											.	ANPEP	124	.	0			c.T2083C						PASS	.						135	127	130					15																	90340880		2200	4299	6499	SO:0001583	missense	290	exon15			CCTCCCAGGGCAT	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"CD molecules"	500	protein-coding gene	gene with protein product	"aminopeptidase N", "aminopeptidase M", "microsomal aminopeptidase"	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.2083T>C	chr15.hg19:g.90340880A>G	ENSP00000300060:p.Trp695Arg	101.0	0.0	.		128.0	58.0	.	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Missense_Mutation	SNP	ENST00000300060.6	hg19	CCDS10356.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.656308	0.88056	.	.	ENSG00000166825	ENST00000300060	T	0.07800	3.16	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.44052	0.1275	H	0.97806	4.08	0.80722	D	1	D	0.69078	0.997	D	0.66716	0.946	T	0.65018	-0.6270	10	0.87932	D	0	.	14.6536	0.68817	1.0:0.0:0.0:0.0	.	695	P15144	AMPN_HUMAN	R	695	ENSP00000300060:W695R	ENSP00000300060:W695R	W	-	1	0	ANPEP	88141884	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.142000	0.94618	2.202000	0.70862	0.533000	0.62120	TGG	.	.	.	none		0.557	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1			G	90340880	A	G	90340880	3	3	254	1	0	0	0	0	1	0	0	0	710	188	7	3	848	3	ANPEP	15	90340880	Missense_Mutation	SNP	A	TCGA-SX-A7SU-01A-11D-A35Z-10		90340880	12190512	30	15876											
ANPEP	290	hgsc.bcm.edu	37	chr15	90349683	90349683	+	Silent	SNP	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	ggggtggtggaggccacgggGgagctgttggcgttcttgtt	3	11	21	6	2	1	0	0	0	1	0	1	2	1	2	1	8	1	4	1	8	0	4			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr15:90349683G>A	ENST00000300060.6	-	2	445	c.132C>T	c.(130-132)tcC>tcT	p.S44S		NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	44	Cytosolic Ser/Thr-rich junction.				angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	AGGCCACGGGGGAGCTGTTGG	0.632																																					p.S44S	NSCLC(30;827 977 2459 19669 26125)	Atlas-SNP	.											.	ANPEP	124	.	0			c.C132T						PASS	.						116	122	120					15																	90349683		2200	4299	6499	SO:0001819	synonymous_variant	290	exon2			CACGGGGGAGCTG	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"CD molecules"	500	protein-coding gene	gene with protein product	"aminopeptidase N", "aminopeptidase M", "microsomal aminopeptidase"	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.132C>T	chr15.hg19:g.90349683G>A		79.0	0.0	.		107.0	42.0	.	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Silent	SNP	ENST00000300060.6	hg19	CCDS10356.1																																																																																			.	.	.	none		0.632	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1			A	90349683	G	A	90349683	2	1	254	1	0	0	0	0	0	0	0	1	710	1219	43	2		2	ANPEP	15	90349683	Silent	SNP	G	TCGA-SX-A7SU-01A-11D-A35Z-10	8803	90349683	12181709	31	15877											
NFAT5	10725	hgsc.bcm.edu	37	chr16	69687291	69687291	+	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	gactgagggcagccgtggctCagtgaaagatagaacacagc	13	5	14	9	1	1	4	1	2	0	2	1	5	1	4	1	2	3	2	1	2	3	1			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr16:69687291C>G	ENST00000354436.2	+	4	1229	c.911C>G	c.(910-912)tCa>tGa	p.S304*	NFAT5_ENST00000432919.1_Nonsense_Mutation_p.S322*|NFAT5_ENST00000567239.1_Nonsense_Mutation_p.S322*|NFAT5_ENST00000393742.2_Nonsense_Mutation_p.S228*|NFAT5_ENST00000349945.1_Nonsense_Mutation_p.S228*|NFAT5_ENST00000566899.1_Nonsense_Mutation_p.S228*	NM_006599.3	NP_006590.1	O94916	NFAT5_HUMAN	nuclear factor of activated T-cells 5, tonicity-responsive	304	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				cytokine production (GO:0001816)|excretion (GO:0007588)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of calcineurin-NFAT signaling cascade (GO:0070884)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						AGCCGTGGCTCAGTGAAAGAT	0.408																																					p.S322X		Atlas-SNP	.											.	NFAT5	184	.	0			c.C965G						PASS	.						88	85	86					16																	69687291		2198	4300	6498	SO:0001587	stop_gained	10725	exon5			GTGGCTCAGTGAA	AF134870	CCDS10881.1, CCDS10882.1, CCDS45519.1	16q22.1	2009-11-24			ENSG00000102908	ENSG00000102908		"Nuclear factor of activated T-cells"	7774	protein-coding gene	gene with protein product		604708				10377394	Standard	NM_173214		Approved	TONEBP, KIAA0827, NFATL1, OREBP, NFATZ, NF-AT5	uc002exl.2	O94916	OTTHUMG00000137572	ENST00000354436.2:c.911C>G	chr16.hg19:g.69687291C>G	ENSP00000346420:p.Ser304*	105.0	0.0	.		199.0	72.0	.	NM_001113178	A2RRB4|A6H8V5|E9PHR7|O95693|Q7LA65|Q969Q8|Q96QH3|Q9UN18	Nonsense_Mutation	SNP	ENST00000354436.2	hg19	CCDS10881.1	.	.	.	.	.	.	.	.	.	.	C	40	8.432947	0.98808	.	.	ENSG00000102908	ENST00000432919;ENST00000426654;ENST00000349945;ENST00000354436;ENST00000393742	.	.	.	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-2.4058	18.6222	0.91324	0.0:1.0:0.0:0.0	.	.	.	.	X	322;322;228;304;228	.	ENSP00000338806:S228X	S	+	2	0	NFAT5	68244792	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.712000	0.84684	2.473000	0.83533	0.460000	0.39030	TCA	.	.	.	none		0.408	NFAT5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268952.2	NM_138714		G	69687291	C	G	69687291	4	3	254	1	0	0	0	0	0	1	0	0	10367	838	29	4	983	4	NFAT5	16	69687291	Nonsense_Mutation	SNP	C	TCGA-SX-A7SU-01A-11D-A35Z-10		69687291	20667462	32	15878											
SYNRG	11276	hgsc.bcm.edu	37	chr17	35944776	35944776	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctggtttcttggggtgcgatGctggagtagggtgcattttt	4	16	16	5	1	1	0	0	0	1	0	1	2	1	1	0	5	3	4	0	5	1	5			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr17:35944776G>A	ENST00000339208.6	-	6	709	c.569C>T	c.(568-570)gCa>gTa	p.A190V	SYNRG_ENST00000502449.2_Missense_Mutation_p.A190V|SYNRG_ENST00000346661.4_Missense_Mutation_p.A190V|SYNRG_ENST00000394378.2_Missense_Mutation_p.A190V|SYNRG_ENST00000345615.4_Missense_Mutation_p.A190V|SYNRG_ENST00000591288.1_Missense_Mutation_p.A190V|SYNRG_ENST00000585472.1_Missense_Mutation_p.A189V	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma	190					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						GGGGTGCGATGCTGGAGTAGG	0.403																																					p.A190V		Atlas-SNP	.											.	SYNRG	101	.	0			c.C569T						PASS	.						153	153	153					17																	35944776		2203	4300	6503	SO:0001583	missense	11276	exon6			TGCGATGCTGGAG	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.569C>T	chr17.hg19:g.35944776G>A	ENSP00000343610:p.Ala190Val	104.0	0.0	.		198.0	106.0	.	NM_001163544	A8MWU4|B7ZKZ2|B7ZKZ3|Q17RI2|Q5BKU5|Q6ZT17	Missense_Mutation	SNP	ENST00000339208.6	hg19	CCDS11321.1	.	.	.	.	.	.	.	.	.	.	G	19.17	3.775527	0.70107	.	.	ENSG00000006114	ENST00000346661;ENST00000339208;ENST00000345615;ENST00000502449;ENST00000394378;ENST00000394379	T;T;T;T;T	0.48201	1.34;1.34;0.83;0.83;0.82	5.43	4.45	0.53987	.	0.244651	0.42172	D	0.000746	T	0.39462	0.1079	L	0.45581	1.43	0.38111	D	0.937568	P;B;B;B;B;P;P	0.43578	0.811;0.018;0.018;0.018;0.018;0.763;0.763	B;B;B;B;B;B;B	0.40534	0.332;0.016;0.016;0.016;0.016;0.229;0.311	T	0.32561	-0.9902	10	0.29301	T	0.29	-12.9037	10.8313	0.46663	0.146:0.0:0.854:0.0	.	190;190;190;190;190;190;190	A8MYE0;B7ZKZ2;Q9UMZ2-3;A8MWU4;Q9UMZ2-4;Q9UMZ2-5;Q9UMZ2	.;.;.;.;.;.;SYNRG_HUMAN	V	190	ENSP00000005279:A190V;ENSP00000343610:A190V;ENSP00000315722:A190V;ENSP00000424893:A190V;ENSP00000377903:A190V	ENSP00000343610:A190V	A	-	2	0	SYNRG	33018889	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	3.080000	0.50112	2.548000	0.85928	0.555000	0.69702	GCA	.	.	.	none		0.403	SYNRG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256811.2	NM_007247		A	35944776	G	A	35944776	3	1	254	1	0	0	0	0	1	0	0	0	15472	1319	46	2	3516	2	SYNRG	17	35944776	Missense_Mutation	SNP	G	TCGA-SX-A7SU-01A-11D-A35Z-10		35944776	45250434	33	15879											
KRTAP9-3	83900	hgsc.bcm.edu	37	chr17	39388890	39388890	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttccagctgctgccagccttGctgccacccaacttgctgtc	5	11	8	17	0	0	0	0	0	0	0	2	0	1	0	5	0	8	4	5	0	1	3			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr17:39388890G>A	ENST00000411528.2	+	1	176	c.137G>A	c.(136-138)tGc>tAc	p.C46Y		NM_031962.2	NP_114168.1	Q9BYQ3	KRA93_HUMAN	keratin associated protein 9-3	46	16 X 5 AA repeats of C-C-[RQVSHE]-[SPTN]- [TASPI].					keratin filament (GO:0045095)				breast(1)|endometrium(3)|lung(2)|ovary(1)|prostate(1)	8		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			TGCCAGCCTTGCTGCCACCCA	0.622																																					p.C46Y		Atlas-SNP	.											.	KRTAP9-3	11	.	0			c.G137A						PASS	.						61	63	62					17																	39388890		2099	4296	6395	SO:0001583	missense	83900	exon1			AGCCTTGCTGCCA	AJ406947	CCDS11385.1	17q21.2	2013-06-25			ENSG00000204873	ENSG00000204873		"Keratin associated proteins"	16927	protein-coding gene	gene with protein product						11279113	Standard	NM_031962		Approved	KAP9.3	uc021txg.1	Q9BYQ3	OTTHUMG00000133427	ENST00000411528.2:c.137G>A	chr17.hg19:g.39388890G>A	ENSP00000392189:p.Cys46Tyr	53.0	0.0	.		130.0	81.0	.	NM_031962		Missense_Mutation	SNP	ENST00000411528.2	hg19	CCDS11385.1	.	.	.	.	.	.	.	.	.	.	.	13.26	2.183006	0.38511	.	.	ENSG00000204873	ENST00000411528	T	0.01647	4.71	2.45	2.45	0.29901	.	.	.	.	.	T	0.07188	0.0182	M	0.87682	2.9	0.37889	D	0.930631	.	.	.	.	.	.	T	0.01930	-1.1245	7	0.87932	D	0	.	5.2525	0.15529	0.1612:0.0:0.8388:0.0	.	.	.	.	Y	46	ENSP00000392189:C46Y	ENSP00000392189:C46Y	C	+	2	0	KRTAP9-3	36642416	0.005000	0.15991	0.997000	0.53966	0.496000	0.33645	-0.284000	0.08422	1.700000	0.51204	0.400000	0.26472	TGC	.	.	.	none		0.622	KRTAP9-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257290.1			A	39388890	G	A	39388890	3	1	254	1	0	0	0	0	1	0	0	0	8581	1319	46	2	139	2	KRTAP9-3	17	39388890	Missense_Mutation	SNP	G	TCGA-SX-A7SU-01A-11D-A35Z-10	3444114	39388890	41806320	34	15880											
KATNAL2	83473	hgsc.bcm.edu	37	chr18	44625645	44625646	+	In_Frame_Ins	INS	-	-	AGA																															tgccatgttacgccgcctggINSagaagaggattctggtcgat																										TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr18:44625645_44625646insAGA	ENST00000245121.5	+	13	1221_1222	c.1027_1028insAGA	c.(1027-1029)gag>gAGAag	p.344_345insK	KATNAL2_ENST00000356157.7_In_Frame_Ins_p.416_417insK	NM_031303.2	NP_112593.2			katanin p60 subunit A-like 2											central_nervous_system(2)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	27						ACGCCGCCTGGAGAAGAGGATT	0.569																																					p.E343delinsEK		Atlas-Indel,Pindel	.											KATNAL2,colon,carcinoma,0,1	KATNAL2	64	.	0			c.1027_1028insAGA						PASS	.																																			SO:0001652	inframe_insertion	83473	exon13			.	BC034999	CCDS32828.1	18q21.1	2010-04-21			ENSG00000167216	ENSG00000167216		"ATPases / AAA-type"	25387	protein-coding gene	gene with protein product		614697				12477932	Standard	NM_031303		Approved	MGC33211, DKFZP667C165	uc002lco.3	Q8IYT4		ENST00000245121.5:c.1031_1033dupAGA	chr18.hg19:g.44625649_44625651dupAGA	ENSP00000245121:p.Lys344_Lys344dup	77.0	0.0	0		79.0	35.0	0.443038	NM_031303		In_Frame_Ins	INS	ENST00000245121.5	hg19	CCDS32828.1																																																																																			.	.	.	none		0.569	KATNAL2-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446138.2	NM_031303		AGA	44625646	-	AGA	44625645	7	5	254	1	0	1	1	0	0	0	0	0	7993	1175	41	0	1073	0	KATNAL2	18	44625645	In_Frame_Ins	INS	-	TCGA-SX-A7SU-01A-11D-A35Z-10		44625645	33451603	35	15881											
ABCA7	10347	hgsc.bcm.edu	37	chr19	1056069	1056069	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgcatggccccacagatacGgaggcttctcgctggggggc	6	7	15	13	2	1	1	0	0	1	1	2	2	1	2	2	6	2	3	2	6	1	2	rs374185879		TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr19:1056069G>A	ENST00000263094.6	+	32	4474	c.4243G>A	c.(4243-4245)Gga>Aga	p.G1415R	ABCA7_ENST00000433129.1_Missense_Mutation_p.G1415R|ABCA7_ENST00000435683.2_Missense_Mutation_p.G1277R	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1415					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)		CCACAGATACGGAGGCTTCTC	0.716																																					p.G1415R		Atlas-SNP	.											.	ABCA7	174	.	0			c.G4243A						PASS	.	G	ARG/GLY	1,4403	2.1+/-5.4	0,1,2201	25	30	29		4243	2.8	1	19		29	0,8594		0,0,4297	no	missense	ABCA7	NM_019112.3	125	0,1,6498	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	1415/2147	1056069	1,12997	2202	4297	6499	SO:0001583	missense	10347	exon32			AGATACGGAGGCT	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.4243G>A	chr19.hg19:g.1056069G>A	ENSP00000263094:p.Gly1415Arg	47.0	0.0	.		55.0	22.0	.	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	hg19	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	G	14.23	2.474727	0.43942	2.27E-4	0.0	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.97688	-4.49;-4.49	2.75	2.75	0.32379	.	.	.	.	.	D	0.98381	0.9462	M	0.83312	2.635	0.39760	D	0.972017	D	0.89917	1.0	D	0.73708	0.981	D	0.98917	1.0782	9	0.87932	D	0	.	11.1665	0.48545	0.0:0.0:1.0:0.0	.	1415	Q8IZY2	ABCA7_HUMAN	R	1415	ENSP00000263094:G1415R;ENSP00000414062:G1415R	ENSP00000263094:G1415R	G	+	1	0	ABCA7	1007069	0.980000	0.34600	0.957000	0.39632	0.040000	0.13550	1.241000	0.32743	1.859000	0.53934	0.561000	0.74099	GGA	.	.	.	weak		0.716	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		A	1056069	G	A	1056069	3	1	254	1	0	0	0	0	1	0	0	0	37	1117	39	1	4365	1	ABCA7	19	1056069	Missense_Mutation	SNP	G	TCGA-SX-A7SU-01A-11D-A35Z-10		1056069	58072914	36	15882											
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-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	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_ENST00000412601.1_Silent_p.E322E|PRKCSH_ENST00000592741.1_Silent_p.E322E|PRKCSH_ENST00000591462.1_Silent_p.E322E|PRKCSH_ENST00000252455.2_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	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	chr19.hg19:g.11558370G>A		90.0	2.0	.		132.0	6.0	.	NM_001001329	A8K318|Q96BU9|Q96D06|Q9P0W9	Silent	SNP	ENST00000589838.1	hg19	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	254	1	0	0	0	0	0	0	0	1	12526	991	35	2		2	PRKCSH	19	11558370	Silent	SNP	G	TCGA-SX-A7SU-01A-11D-A35Z-10	10502301	11558370	47570613	37	15883											
PEPD	5184	hgsc.bcm.edu	37	chr19	33902620	33902621	+	In_Frame_Ins	INS	-	-	CGTGTC																															tcggtcgttgggagctccggINScgtgtccgtagtgtagcacg																								rs370370158		TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr19:33902620_33902621insCGTGTC	ENST00000244137.7	-	11	808_809	c.775_776insGACACG	c.(775-777)gcc>gGACACGcc	p.258_259insGH	PEPD_ENST00000436370.3_In_Frame_Ins_p.194_195insGH|PEPD_ENST00000397032.4_In_Frame_Ins_p.217_218insGH	NM_000285.3	NP_000276.2	P12955	PEPD_HUMAN	peptidase D	258					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)					GGGAGCTCCGGCGTGTCCGTAG	0.599																																					p.A259delinsGHA		Pindel	.											.	PEPD	48	.	0			c.776_777insGACACG						PASS	.																																			SO:0001652	inframe_insertion	5184	exon11			.	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.770_775dupGACACG	chr19.hg19:g.33902621_33902626dupCGTGTC	ENSP00000244137:p.Gly257_His258dup	48.0	0.0	.		41.0	13.0	0.317	NM_000285	A8K3Z1|A8K416|A8K696|A8MX47|B4DDB7|B4DGJ1|E9PCE8|Q8TBN9|Q9BT75	In_Frame_Ins	INS	ENST00000244137.7	hg19	CCDS42544.1																																																																																			.	.	.	none		0.599	PEPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451432.3	NM_000285		CGTGTC	33902621	-	CGTGTC	33902620	7	5	254	1	0	1	1	0	0	0	0	0	11735	1203	42	0	725	0	PEPD	19	33902620	In_Frame_Ins	INS	-	TCGA-SX-A7SU-01A-11D-A35Z-10	22344250	33902620	25226363	38	15884											
NCCRP1	342897	hgsc.bcm.edu	37	chr19	39687821	39687821	+	Missense_Mutation	SNP	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	agccggcgcagccgtccgagGctcacgcccggcagctgctg	5	4	15	17	6	1	0	1	0	0	0	2	1	2	0	4	3	4	5	4	3	0	0			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr19:39687821G>A	ENST00000339852.4	+	1	221	c.199G>A	c.(199-201)Gct>Act	p.A67T		NM_001001414.1	NP_001001414.1	Q6ZVX7	FBX50_HUMAN	non-specific cytotoxic cell receptor protein 1 homolog (zebrafish)	67					positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				kidney(1)|large_intestine(2)|liver(1)|lung(4)|ovary(1)|urinary_tract(1)	10						GCCGTCCGAGGCTCACGCCCG	0.786																																					p.A67T	Melanoma(107;1207 1556 14956 29427 52130)	Atlas-SNP	.											.	NCCRP1	25	.	0			c.G199A						PASS	.						1	1	1					19																	39687821		934	2129	3063	SO:0001583	missense	342897	exon1			TCCGAGGCTCACG	AK123941, BC067874	CCDS12529.1	19q13.2	2013-07-31	2008-11-19		ENSG00000188505	ENSG00000188505			33739	protein-coding gene	gene with protein product		615901					Standard	NM_001001414		Approved	LOC342897, NCCRP-1, FBXO50	uc002okq.1	Q6ZVX7		ENST00000339852.4:c.199G>A	chr19.hg19:g.39687821G>A	ENSP00000342137:p.Ala67Thr	16.0	0.0	.		19.0	5.0	.	NM_001001414	Q6NVV5	Missense_Mutation	SNP	ENST00000339852.4	hg19	CCDS12529.1	.	.	.	.	.	.	.	.	.	.	G	18.14	3.558257	0.65538	.	.	ENSG00000188505	ENST00000339852	T	0.33865	1.39	3.41	0.908	0.19326	.	0.556062	0.14784	U	0.298637	T	0.18841	0.0452	N	0.19112	0.55	0.09310	N	1	B	0.23058	0.079	B	0.17098	0.017	T	0.14755	-1.0461	10	0.30854	T	0.27	.	5.1669	0.15090	0.0:0.2537:0.5253:0.221	.	67	Q6ZVX7	NCRP1_HUMAN	T	67	ENSP00000342137:A67T	ENSP00000342137:A67T	A	+	1	0	NCCRP1	44379661	0.862000	0.29867	0.118000	0.21660	0.202000	0.24057	0.983000	0.29552	0.606000	0.29965	0.313000	0.20887	GCT	.	.	.	none		0.786	NCCRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463829.1	NM_001001414		A	39687821	G	A	39687821	3	1	254	1	0	0	0	0	1	0	0	0	10220	1203	42	2	201	2	NCCRP1	19	39687821	Missense_Mutation	SNP	G	TCGA-SX-A7SU-01A-11D-A35Z-10	5785201	39687821	19441162	39	15885											
KCNB1	3745	hgsc.bcm.edu	37	chr20	48098450	48098450	+	Splice_Site	DEL	C	C	-																															gcccccagatcccagactcaCcttggcagccacagaggaat																										TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr20:48098450delC	ENST00000371741.4	-	1	734		c.e1+1			NM_004975.2	NP_004966.1	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 1						energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|dendrite membrane (GO:0032590)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(22)|pancreas(2)|prostate(7)|skin(4)|stomach(1)|urinary_tract(1)	53			BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Dalfampridine(DB06637)	CCCAGACTCACCTTGGCAGCC	0.567																																					.		Atlas-Indel,Pindel	.											.	KCNB1	142	.	0			c.567+2G>-						PASS	.						118	108	111					20																	48098450		2203	4300	6503	SO:0001630	splice_region_variant	3745	exon2			.	AF026005	CCDS13418.1	20q13.2	2012-07-05			ENSG00000158445	ENSG00000158445		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	6231	protein-coding gene	gene with protein product		600397				7774931, 16382104	Standard	NM_004975		Approved	Kv2.1	uc002xur.1	Q14721	OTTHUMG00000033051	ENST00000371741.4:c.567+1G>-	chr20.hg19:g.48098450delC		80.0	0.0	0		109.0	50.0	0.458716	NM_004975	Q14193	Splice_Site	DEL	ENST00000371741.4	hg19	CCDS13418.1																																																																																			.	.	.	none		0.567	KCNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080374.3	NM_004975	Intron	-	48098450	C	-	48098450	8	5	254	1	0	1	0	1	0	0	1	0	8019	521	18	0	2016	0	KCNB1	20	48098450	Splice_Site	DEL	C	TCGA-SX-A7SU-01A-11D-A35Z-10		48098450	14927070	40	15886											
MTMR3	8897	hgsc.bcm.edu	37	chr22	30416092	30416092	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttcttccaatcccagtagAtgcaaaagttggctatggta	12	12	9	8	0	1	1	0	0	1	1	3	1	3	1	2	2	1	6	2	2	6	6			TCGA-SX-A7SU-01A-11D-A35Z-10	TCGA-SX-A7SU-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06de0d9e-db97-4250-a774-fa0f4eabbe74	7d1da0d0-0c30-4440-b607-036215cc6509	g.chr22:30416092A>G	ENST00000401950.2	+	17	2786	c.2444A>G	c.(2443-2445)gAt>gGt	p.D815G	CTA-85E5.10_ENST00000453743.2_RNA|MTMR3_ENST00000351488.3_Missense_Mutation_p.D815G|MTMR3_ENST00000406629.1_Missense_Mutation_p.D815G|MTMR3_ENST00000323630.5_Missense_Mutation_p.D679G|CTA-85E5.10_ENST00000429350.1_RNA|MTMR3_ENST00000333027.3_Missense_Mutation_p.D815G	NM_021090.3	NP_066576.1	Q13615	MTMR3_HUMAN	myotubularin related protein 3	815					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)			ATCCCAGTAGATGCAAAAGTT	0.517																																					p.D815G		Atlas-SNP	.											.	MTMR3	106	.	0			c.A2444G						PASS	.						124	113	117					22																	30416092		2203	4300	6503	SO:0001583	missense	8897	exon17			CAGTAGATGCAAA	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.2444A>G	chr22.hg19:g.30416092A>G	ENSP00000384651:p.Asp815Gly	129.0	0.0	.		167.0	37.0	.	NM_153050	A5PL26|A7MD32|Q9NYN5|Q9NYN6|Q9UDX6|Q9UEG3	Missense_Mutation	SNP	ENST00000401950.2	hg19	CCDS13870.1	.	.	.	.	.	.	.	.	.	.	A	3.772	-0.047509	0.07407	.	.	ENSG00000100330	ENST00000401950;ENST00000333027;ENST00000323630;ENST00000351488;ENST00000406629	D;D;D;D;D	0.93426	-3.03;-3.0;-3.22;-3.05;-3.0	4.88	3.84	0.44239	.	1.378970	0.04300	N	0.347180	D	0.87022	0.6074	N	0.19112	0.55	0.09310	N	1	P;P;P	0.41848	0.763;0.651;0.763	B;B;B	0.35770	0.21;0.104;0.21	T	0.77811	-0.2449	10	0.23302	T	0.38	.	8.6349	0.33941	0.9129:0.0:0.0871:0.0	.	815;815;815	Q13615-3;Q13615;Q13615-2	.;MTMR3_HUMAN;.	G	815;815;679;815;815	ENSP00000384651:D815G;ENSP00000331649:D815G;ENSP00000318070:D679G;ENSP00000307271:D815G;ENSP00000384077:D815G	ENSP00000318070:D679G	D	+	2	0	MTMR3	28746092	0.032000	0.19561	0.168000	0.22838	0.187000	0.23431	1.914000	0.39966	0.987000	0.38709	0.533000	0.62120	GAT	.	.	.	none		0.517	MTMR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322066.1	NM_021090		G	30416092	A	G	30416092	3	3	254	1	0	0	0	0	1	0	0	0	9952	333	12	3	2502	3	MTMR3	22	30416092	Missense_Mutation	SNP	A	TCGA-SX-A7SU-01A-11D-A35Z-10		30416092	20888474	41	15887											
CDC14A	8556	hgsc.bcm.edu	37	chr1	100856289	100856289	+	Splice_Site	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	ttttatctcctctttctagtCatacagtttgtcaagaaaga	11	17	5	8	0	5	2	2	0	3	2	6	2	5	2	1	0	1	1	1	0	5	6			TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chr1:100856289C>T	ENST00000336454.3	+	4	573	c.218C>T	c.(217-219)tCa>tTa	p.S73L	CDC14A_ENST00000544534.1_Splice_Site_p.S73L|CDC14A_ENST00000370125.2_Splice_Site_p.S73L|CDC14A_ENST00000542213.1_Splice_Site_p.S15L|CDC14A_ENST00000370124.3_Splice_Site_p.S73L|CDC14A_ENST00000361544.6_Splice_Site_p.S73L	NM_003672.3	NP_003663.2	Q9UNH5	CC14A_HUMAN	cell division cycle 14A	73	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)		TCTTTCTAGTCATACAGTTTG	0.368																																					p.S73L		Atlas-SNP	.											.	CDC14A	65	.	0			c.C218T						PASS	.						102	97	99					1																	100856289		2203	4300	6503	SO:0001630	splice_region_variant	8556	exon4			TCTAGTCATACAG	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.217-1C>T	chr1.hg19:g.100856289C>T		57.0	0.0	.		62.0	47.0	.	NM_033313	A6MA65|B1AQ14|B1AQ15|O43171|O60727|O60728|Q52LH9|Q8IXX0	Missense_Mutation	SNP	ENST00000336454.3	hg19	CCDS769.1	.	.	.	.	.	.	.	.	.	.	C	18.55	3.648522	0.67358	.	.	ENSG00000079335	ENST00000542213;ENST00000455467;ENST00000370125;ENST00000361544;ENST00000370124;ENST00000336454;ENST00000544534	T;T;T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88;0.88;0.88	5.62	5.62	0.85841	.	0.061993	0.64402	D	0.000002	T	0.32793	0.0841	M	0.67700	2.07	0.80722	D	1	P;P;B;P;P;B	0.42483	0.781;0.674;0.01;0.479;0.781;0.006	B;B;B;B;B;B	0.35655	0.207;0.102;0.022;0.061;0.207;0.01	T	0.42582	-0.9443	10	0.72032	D	0.01	-12.363	18.4311	0.90625	0.0:1.0:0.0:0.0	.	15;73;73;73;73;73	F5H7B3;A6MA65;Q9UNH5-3;Q9UNH5;Q9UNH5-2;Q52LH9	.;.;.;CC14A_HUMAN;.;.	L	15;74;73;73;73;73;73	ENSP00000442640:S15L;ENSP00000388501:S74L;ENSP00000359143:S73L;ENSP00000354916:S73L;ENSP00000359142:S73L;ENSP00000336739:S73L;ENSP00000442543:S73L	ENSP00000336739:S73L	S	+	2	0	CDC14A	100628877	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	4.880000	0.63107	2.648000	0.89879	0.561000	0.74099	TCA	.	.	.	none		0.368	CDC14A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000030220.1	NM_033312	Missense_Mutation	T	100856289	C	T	100856289	5	4	255	1	0	0	0	0	0	0	1	0	3058	840	29	2	232	2	CDC14A	1	100856289	Splice_Site	SNP	C	TCGA-UN-AAZ9-01A-11D-A382-10		100856289	148394332	1	15888											
CENPF	1063	hgsc.bcm.edu	37	chr1	214819565	214819565	+	Frame_Shift_Del	DEL	C	C	-																															aaaaagaaaatctgacaaaaCaaatacaagaaaaacaaggt																										TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chr1:214819565delC	ENST00000366955.3	+	13	6820	c.6652delC	c.(6652-6654)caafs	p.Q2218fs		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2314	2 X 177 AA tandem repeats.|Interaction with NDE1 and NDEL1.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		TCTGACAAAACAAATACAAGA	0.348																																					p.K2217fs	Colon(80;575 1284 11000 14801 43496)	Atlas-Indel,Pindel	.											.	CENPF	321	.	0			c.6651delA						PASS	.						45	51	49					1																	214819565		2198	4300	6498	SO:0001589	frameshift_variant	1063	exon13			.	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"mitosin"	600236	"centromere protein F, 350/400kDa (mitosin)"			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.6652delC	chr1.hg19:g.214819565delC	ENSP00000355922:p.Gln2218fs	299.0	0.0	0		286.0	240.0	0.839161	NM_016343	Q13171|Q13246|Q5VVM7	Frame_Shift_Del	DEL	ENST00000366955.3	hg19	CCDS31023.1																																																																																			.	.	.	none		0.348	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343		-	214819565	C	-	214819565	7	5	255	1	0	1	0	1	0	0	0	0	3233	479	17	0	6698	0	CENPF	1	214819565	Frame_Shift_Del	DEL	C	TCGA-UN-AAZ9-01A-11D-A382-10	113963276	214819565	34431056	2	15889											
TTN	7273	hgsc.bcm.edu	37	chr2	179505994	179505999	+	In_Frame_Del	DEL	TTTTTA	TTTTTA	-																															gttttttaactttttctagtTttttaggttctactttaggt																										TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	TTTTTA	TTTTTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chr2:179505994_179505999delTTTTTA	ENST00000591111.1	-	170	35903_35908	c.35679_35684delTAAAAA	c.(35677-35685)cctaaaaaa>cca	p.KK11894del	TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342992.6_In_Frame_Del_p.KK10967del|TTN-AS1_ENST00000418062.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342175.6_In_Frame_Del_p.KK4662del|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000589042.1_In_Frame_Del_p.KK13535del|TTN_ENST00000359218.5_In_Frame_Del_p.KK4595del|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_In_Frame_Del_p.KK4470del|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	11894	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)			TTTTTCTAGTTTTTTAGGTTCTACTT	0.282																																					p.13535_13536del		Atlas-Indel,Pindel	.											.	TTN	18412	.	0			c.40603_40608del						PASS	.																																			SO:0001651	inframe_deletion	7273	exon220			.	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.35679_35684delTAAAAA	chr2.hg19:g.179505994_179505999delTTTTTA	ENSP00000465570:p.Lys11894_Lys11895del	125.0	0.0	0		128.0	48.0	0.375	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	In_Frame_Del	DEL	ENST00000591111.1	hg19																																																																																				.	.	.	none		0.282	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		-	179505999	TTTTTA	-	179505994	7	5	255	1	0	1	0	1	0	0	0	0	16747	1841	64	0	67658	0	TTN	2	179505994	In_Frame_Del	DEL	TTTTTA	TCGA-UN-AAZ9-01A-11D-A382-10		179505994	63693379	3	15890											
TRH	7200	hgsc.bcm.edu	37	chr3	129695840	129695840	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caaaggagctgggaagaagaGgaggaggaggaagagagaga	18	1	20	2	0	0	4	0	0	0	4	0	12	0	10	0	6	1	1	0	6	4	0			TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chr3:129695840G>A	ENST00000302649.3	+	3	1037	c.510G>A	c.(508-510)gaG>gaA	p.E170E	TRH_ENST00000507066.1_Silent_p.E166E	NM_007117.3	NP_009048.1	P20396	TRH_HUMAN	thyrotropin-releasing hormone	170					adult walking behavior (GO:0007628)|cell-cell signaling (GO:0007267)|eating behavior (GO:0042755)|histamine metabolic process (GO:0001692)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of feeding behavior (GO:2000252)|negative regulation of glutamate secretion (GO:0014050)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|positive regulation of insulin secretion (GO:0032024)|response to cold (GO:0009409)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	thyrotropin-releasing hormone activity (GO:0008437)	p.E170E(1)		NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)	14						Gggaagaagaggaggaggagg	0.642																																					p.E170E	Esophageal Squamous(60;321 1330 17401 41911)	Atlas-SNP	.											TRH,right_upper_lobe,carcinoma,0,2	TRH	30	.	1	Substitution - coding silent(1)	prostate(1)	c.G510A						PASS	.						33	35	34					3																	129695840		2202	4300	6502	SO:0001819	synonymous_variant	7200	exon3			AGAAGAGGAGGAG		CCDS3066.1	3q13.3-q21	2013-02-28				ENSG00000170893		"Endogenous ligands"	12298	protein-coding gene	gene with protein product	"prothyroliberin"	613879				2126343, 1900134	Standard	NM_007117		Approved		uc003enc.4	P20396		ENST00000302649.3:c.510G>A	chr3.hg19:g.129695840G>A		52.0	0.0	.		80.0	4.0	.	NM_007117	B2R8R1|Q2TB83	Silent	SNP	ENST00000302649.3	hg19	CCDS3066.1																																																																																			.	.	.	none		0.642	TRH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356592.1	NM_007117		A	129695840	G	A	129695840	2	1	255	1	0	0	0	0	0	0	0	1	16490	991	35	2		2	TRH	3	129695840	Silent	SNP	G	TCGA-UN-AAZ9-01A-11D-A382-10		129695840	68326590	4	15891											
SLC7A14	57709	hgsc.bcm.edu	37	chr3	170244698	170244698	+	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	tccccactgcacccgccgggGgtccagcgaggtgaagaagc	8	4	14	15	3	0	2	0	1	0	1	2	3	2	2	5	3	3	1	5	3	2	0			TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chr3:170244698G>T	ENST00000231706.5	-	2	343	c.28C>A	c.(28-30)Ccc>Acc	p.P10T	CLDN11_ENST00000451576.1_Intron|CLDN11_ENST00000486975.1_Intron	NM_020949.2	NP_066000.2	Q8TBB6	S7A14_HUMAN	solute carrier family 7, member 14	10					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)			ACCCGCCGGGGGTCCAGCGAG	0.582																																					p.P10T		Atlas-SNP	.											.	SLC7A14	110	.	0			c.C28A						PASS	.						41	39	39					3																	170244698		2203	4300	6503	SO:0001583	missense	57709	exon2			GCCGGGGGTCCAG	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.28C>A	chr3.hg19:g.170244698G>T	ENSP00000231706:p.Pro10Thr	63.0	0.0	.		93.0	28.0	.	NM_020949	B3KV33|Q9HCF9	Missense_Mutation	SNP	ENST00000231706.5	hg19	CCDS33892.1	.	.	.	.	.	.	.	.	.	.	G	18.79	3.698447	0.68386	.	.	ENSG00000013293	ENST00000231706	D	0.90324	-2.65	5.26	5.26	0.73747	.	0.118551	0.64402	D	0.000019	D	0.92424	0.7595	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.93470	0.6818	10	0.72032	D	0.01	.	19.2442	0.93895	0.0:0.0:1.0:0.0	.	10	Q8TBB6	S7A14_HUMAN	T	10	ENSP00000231706:P10T	ENSP00000231706:P10T	P	-	1	0	SLC7A14	171727392	1.000000	0.71417	1.000000	0.80357	0.273000	0.26683	9.401000	0.97294	2.614000	0.88457	0.561000	0.74099	CCC	.	.	.	none		0.582	SLC7A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352598.2	NM_020949		T	170244698	G	T	170244698	3	4	255	1	0	0	0	0	1	0	0	0	14709	1232	43	4	2315	4	SLC7A14	3	170244698	Missense_Mutation	SNP	G	TCGA-UN-AAZ9-01A-11D-A382-10	40548858	170244698	27777732	5	15892											
MSH3	4437	hgsc.bcm.edu	37	chr5	79950745	79950745	+	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	ccgcagcgcccccagcgcccCcagctcccgccttcccgccc	3	3	8	27	5	0	0	0	0	0	0	2	0	2	0	9	0	3	2	9	0	0	1	rs144629981|rs3045983|rs557874766	byFrequency	TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chr5:79950745C>G	ENST00000265081.6	+	1	279	c.199C>G	c.(199-201)Cca>Gca	p.P67A	DHFR_ENST00000505337.1_5'Flank|DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000513048.1_5'Flank|DHFR_ENST00000439211.2_5'UTR|DHFR_ENST00000504396.1_5'Flank	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	67					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)		CCCAGCGCCCCCAGCTCCCGC	0.731								Mismatch excision repair (MMR)					C|||	1091	0.217851	0.2678	0.1916	5008	,	,		6483	0.0476		0.2356	False		,,,				2504	0.3262				p.P67A	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											MSH3,NS,carcinoma,0,1	MSH3	129	.	0			c.C199G						PASS	.						3	4	3					5																	79950745		1702	3410	5112	SO:0001583	missense	4437	exon1			GCGCCCCCAGCTC	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.199C>G	chr5.hg19:g.79950745C>G	ENSP00000265081:p.Pro67Ala	27.0	0.0	.		70.0	23.0	.	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	hg19	CCDS34195.1	.	.	.	.	.	.	.	.	.	.	C	6.333	0.429466	0.11987	.	.	ENSG00000113318	ENST00000265081;ENST00000535995	D	0.85484	-1.99	.	.	.	.	.	.	.	.	T	0.70150	0.3191	N	0.19112	0.55	0.19945	N	0.999946	B	0.18741	0.03	B	0.17098	0.017	T	0.53507	-0.8429	6	.	.	.	0.6693	.	.	.	.	67	P20585	MSH3_HUMAN	A	67;58	ENSP00000265081:P67A	.	P	+	1	0	MSH3	79986501	0.560000	0.26570	0.857000	0.33713	0.119000	0.20118	0.055000	0.14229	0.064000	0.16427	0.064000	0.15345	CCA	.	.	.	none		0.731	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		G	79950745	C	G	79950745	3	3	255	1	0	0	0	0	1	0	0	0	9878	623	22	4	201	4	MSH3	5	79950745	Missense_Mutation	SNP	C	TCGA-UN-AAZ9-01A-11D-A382-10		79950745	100964515	6	15893											
EPB41L4A	64097	hgsc.bcm.edu	37	chr5	111602024	111602024	+	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	ttcacctgcaagaaaaactgAtatctaaaagagaaacaaaa	22	7	5	7	0	2	3	1	1	1	2	2	4	2	3	1	0	3	1	1	0	9	3			TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chr5:111602024A>T	ENST00000261486.5	-	5	615	c.339T>A	c.(337-339)taT>taA	p.Y113*		NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	113	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(2)|skin(1)	34		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		AGAAAAACTGATATCTAAAAG	0.463																																					p.Y113X		Atlas-SNP	.											.	EPB41L4A	130	.	0			c.T339A						PASS	.						32	33	32					5																	111602024		1878	4109	5987	SO:0001587	stop_gained	64097	exon5			AAACTGATATCTA	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.339T>A	chr5.hg19:g.111602024A>T	ENSP00000261486:p.Tyr113*	454.0	0.0	.		684.0	190.0	.	NM_022140	A4FUI6	Nonsense_Mutation	SNP	ENST00000261486.5	hg19	CCDS43350.1	.	.	.	.	.	.	.	.	.	.	A	36	5.879440	0.97062	.	.	ENSG00000129595	ENST00000261486	.	.	.	5.91	-4.25	0.03766	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.0521	0.58960	0.5598:0.0:0.4402:0.0	.	.	.	.	X	113	.	ENSP00000261486:Y113X	Y	-	3	2	EPB41L4A	111629923	0.989000	0.36119	0.970000	0.41538	0.897000	0.52465	0.329000	0.19698	-0.675000	0.05246	-0.256000	0.11100	TAT	.	.	.	none		0.463	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1			T	111602024	A	T	111602024	4	4	255	1	0	0	0	0	0	1	0	0	5157	340	12	5	1797	5	EPB41L4A	5	111602024	Nonsense_Mutation	SNP	A	TCGA-UN-AAZ9-01A-11D-A382-10	31651279	111602024	69313236	7	15894											
TRIM36	55521	hgsc.bcm.edu	37	chr5	114462477	114462477	+	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	aaaatttctgcatgcctataGtaactaaggtaaatggttgt	14	14	8	5	0	1	0	0	0	1	0	1	0	1	0	1	2	3	4	1	2	8	7			TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chr5:114462477G>C	ENST00000282369.3	-	10	2031	c.1910C>G	c.(1909-1911)aCt>aGt	p.T637S	TRIM36_ENST00000514154.1_Missense_Mutation_p.T482S|TRIM36_ENST00000513154.1_Missense_Mutation_p.T625S	NM_018700.3	NP_061170.2	Q9NQ86	TRI36_HUMAN	tripartite motif containing 36	637	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				acrosome reaction (GO:0007340)|regulation of cell cycle (GO:0051726)	acrosomal vesicle (GO:0001669)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	37		all_cancers(142;0.00133)|all_epithelial(76;2.41e-05)|Prostate(80;0.00955)|Ovarian(225;0.0443)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;3.62e-08)|Epithelial(69;7.69e-08)|all cancers(49;9.33e-06)		CATGCCTATAGTAACTAAGGT	0.378																																					p.T637S		Atlas-SNP	.											.	TRIM36	126	.	0			c.C1910G						PASS	.						94	95	94					5																	114462477		2202	4300	6502	SO:0001583	missense	55521	exon10			CCTATAGTAACTA	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.1910C>G	chr5.hg19:g.114462477G>C	ENSP00000282369:p.Thr637Ser	100.0	0.0	.		193.0	70.0	.	NM_018700	A1L3Z1|A6NDD0|B7Z3V4|B7ZAV7|E9PFI8|Q0P5Z9	Missense_Mutation	SNP	ENST00000282369.3	hg19	CCDS4115.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.511711	0.85389	.	.	ENSG00000152503	ENST00000282369;ENST00000513154;ENST00000514154	T;T;T	0.66995	-0.24;-0.24;-0.24	5.37	5.37	0.77165	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.103031	0.64402	D	0.000004	T	0.78470	0.4288	L	0.53249	1.67	0.80722	D	1	P;P	0.39696	0.477;0.683	B;P	0.58391	0.26;0.838	T	0.73927	-0.3828	10	0.34782	T	0.22	.	19.4818	0.95013	0.0:0.0:1.0:0.0	.	625;637	E9PFI8;Q9NQ86	.;TRI36_HUMAN	S	637;625;482	ENSP00000282369:T637S;ENSP00000423934:T625S;ENSP00000424259:T482S	ENSP00000282369:T637S	T	-	2	0	TRIM36	114490376	1.000000	0.71417	0.658000	0.29665	0.759000	0.43091	9.203000	0.95033	2.658000	0.90341	0.591000	0.81541	ACT	.	.	.	none		0.378	TRIM36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250854.2	NM_018700		C	114462477	G	C	114462477	3	2	255	1	0	0	0	0	1	0	0	0	16522	1029	36	4	280	4	TRIM36	5	114462477	Missense_Mutation	SNP	G	TCGA-UN-AAZ9-01A-11D-A382-10	2860453	114462477	66452783	8	15895											
FOXC1	2296	hgsc.bcm.edu	37	chr6	1611915	1611916	+	Frame_Shift_Ins	INS	-	-	G																															ggcgagcgcgggggccacttINSgcagggcgcgcccgggggcg																										TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chr6:1611915_1611916insG	ENST00000380874.2	+	1	1235_1236	c.1235_1236insG	c.(1234-1239)ttgcagfs	p.Q413fs		NM_001453.2	NP_001444.2	Q12948	FOXC1_HUMAN	forkhead box C1	413					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)		GGGGGCCACTTGCAgggcgcgc	0.782																																					p.L412fs	Pancreas(133;719 1821 3197 26645 35015)	Atlas-Indel,Pindel	.											.	FOXC1	19	.	0			c.1235_1236insG						PASS	.																																			SO:0001589	frameshift_variant	2296	exon1			.	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.1236dupG	chr6.hg19:g.1611916_1611916dupG	ENSP00000370256:p.Gln413fs	43.0	0.0	0		61.0	50.0	0.819672	NM_001453	Q86UP7|Q9BYM1|Q9NUE5|Q9UDD0|Q9UP06	Frame_Shift_Ins	INS	ENST00000380874.2	hg19	CCDS4473.1																																																																																			.	.	.	none		0.782	FOXC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043450.1			G	1611916	-	G	1611915	7	5	255	1	0	1	1	0	0	0	0	0	6001	1821	63	0	1237	0	FOXC1	6	1611915	Frame_Shift_Ins	INS	-	TCGA-UN-AAZ9-01A-11D-A382-10		1611915	169503152	9	15896											
RFX6	222546	hgsc.bcm.edu	37	chr6	117237249	117237249	+	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	ttaatggaaactttgaagagGtaagaatgacaaagaatgct	18	10	10	3	0	0	5	0	2	0	3	0	6	0	6	0	2	2	2	0	2	7	3			TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chr6:117237249G>A	ENST00000332958.2	+	8	874		c.e8+1		RFX6_ENST00000471966.1_Splice_Site	NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6						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						CTTTGAAGAGGTAAGAATGAC	0.308																																					.		Atlas-SNP	.											.	RFX6	141	.	0			c.858+1G>A						PASS	.						111	109	110					6																	117237249		2203	4300	6503	SO:0001630	splice_region_variant	222546	exon8			GAAGAGGTAAGAA	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.858+1G>A	chr6.hg19:g.117237249G>A		84.0	0.0	.		57.0	44.0	.	NM_173560	Q5T6B3	Splice_Site	SNP	ENST00000332958.2	hg19	CCDS5113.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.498525	0.85069	.	.	ENSG00000185002	ENST00000332958	.	.	.	5.75	5.75	0.90469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.9384	0.97150	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RFX6	117343942	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	9.476000	0.97823	2.717000	0.92951	0.585000	0.79938	.	.	.	.	none		0.308	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560	Intron	A	117237249	G	A	117237249	5	1	255	1	0	0	0	0	0	0	1	0	13280	1275	44	2	889	2	RFX6	6	117237249	Splice_Site	SNP	G	TCGA-UN-AAZ9-01A-11D-A382-10	115625334	117237249	53877818	10	15897											
GPR158	57512	hgsc.bcm.edu	37	chr10	25464395	25464395	+	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	tcctctgcctcctgcttgctCagctgggattgggagctgtt	3	14	12	12	0	2	0	1	0	1	0	4	2	4	2	3	2	5	5	3	2	0	3			TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chr10:25464395C>T	ENST00000376351.3	+	1	405	c.46C>T	c.(46-48)Cag>Tag	p.Q16*	GPR158-AS1_ENST00000449643.1_RNA	NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	16					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						CCTGCTTGCTCAGCTGGGATT	0.637																																					p.Q16X		Atlas-SNP	.											.	GPR158	255	.	0			c.C46T						PASS	.						35	41	39					10																	25464395		2203	4293	6496	SO:0001587	stop_gained	57512	exon1			CTTGCTCAGCTGG	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.46C>T	chr10.hg19:g.25464395C>T	ENSP00000365529:p.Gln16*	55.0	0.0	.		105.0	42.0	.	NM_020752	Q6QR81|Q9ULT3	Nonsense_Mutation	SNP	ENST00000376351.3	hg19	CCDS31166.1	.	.	.	.	.	.	.	.	.	.	C	39	7.530076	0.98342	.	.	ENSG00000151025	ENST00000376351	.	.	.	4.72	4.72	0.59763	.	1.302630	0.05575	N	0.571782	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	.	11.0535	0.47905	0.0:0.9137:0.0:0.0863	.	.	.	.	X	16	.	ENSP00000365529:Q16X	Q	+	1	0	GPR158	25504401	0.641000	0.27251	0.139000	0.22197	0.942000	0.58702	3.736000	0.55052	2.462000	0.83206	0.467000	0.42956	CAG	.	.	.	none		0.637	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110		T	25464395	C	T	25464395	4	4	255	1	0	0	0	0	0	1	0	0	6670	827	29	2	48	2	GPR158	10	25464395	Nonsense_Mutation	SNP	C	TCGA-UN-AAZ9-01A-11D-A382-10		25464395	110070352	11	15898											
HRASLS5	117245	hgsc.bcm.edu	37	chr11	63258431	63258432	+	Frame_Shift_Ins	INS	-	-	G																															gtactggcggttcgcgaggcINSgggtttggggaggggtgggg																								rs148328959		TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chr11:63258431_63258432insG	ENST00000301790.4	-	1	234_235	c.75_76insC	c.(73-78)cccgccfs	p.A26fs	HRASLS5_ENST00000539221.1_Frame_Shift_Ins_p.A26fs|HRASLS5_ENST00000540857.1_Frame_Shift_Ins_p.A26fs			Q96KN8	HRSL5_HUMAN	HRAS-like suppressor family, member 5	26							transferase activity, transferring acyl groups (GO:0016746)			endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	14						GTTCGCGAGGCGGGTTTGGGGA	0.723																																					p.A26fs		Atlas-INDEL	.											.	HRASLS5	28	.	0			c.76_77insC						PASS	.																																			SO:0001589	frameshift_variant	117245	exon1			.	AJ416558	CCDS8044.1, CCDS53646.1, CCDS53647.1	11q13.2	2006-08-16			ENSG00000168004	ENSG00000168004			24978	protein-coding gene	gene with protein product		611474					Standard	NM_001146729		Approved	HRLP5	uc001nwy.2	Q96KN8	OTTHUMG00000167806	ENST00000301790.4:c.76dupC	chr11.hg19:g.63258434_63258434dupG	ENSP00000301790:p.Ala26fs	109.0	0.0	0		189.0	13.0	0.0687831	NM_001146728	B7X6T1|F5GZ87|F5H4Y9	Frame_Shift_Ins	INS	ENST00000301790.4	hg19	CCDS8044.1																																																																																			.	.	.	none		0.723	HRASLS5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396375.1	NM_054108		G	63258432	-	G	63258431	7	5	255	1	0	1	1	0	0	0	0	0	7358	768	27	0	787	0	HRASLS5	11	63258431	Frame_Shift_Ins	INS	-	TCGA-UN-AAZ9-01A-11D-A382-10		63258431	71748085	12	15899											
GEFT	115557	hgsc.bcm.edu	37	chr12	58006909	58006909	+	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	gaaactgaggcagacagtggTcaggcaggaccatatgaggt	13	6	15	7	0	1	3	1	2	0	1	1	5	1	4	1	5	1	2	1	5	2	1			TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chr12:58006909T>A	ENST00000286494.4	+	2	754	c.294T>A	c.(292-294)ggT>ggA	p.G98G	AC025165.8_ENST00000356672.3_RNA|AC025165.8_ENST00000444467.1_RNA|ARHGEF25_ENST00000333972.7_Silent_p.G137G|AC025165.8_ENST00000610219.1_RNA|AC025165.8_ENST00000593846.1_RNA	NM_182947.3	NP_891992	Q86VW2	ARHGP_HUMAN	Rho guanine nucleotide exchange factor (GEF) 25	98						cytosol (GO:0005829)|myofibril (GO:0030016)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	28						CAGACAGTGGTCAGGCAGGAC	0.587																																					p.G137G		Atlas-SNP	.											.	ARHGEF25	111	.	0			c.T411A						PASS	.						34	29	30					12																	58006909		2203	4300	6503	SO:0001819	synonymous_variant	115557	exon3			CAGTGGTCAGGCA		CCDS8947.1, CCDS44931.1	12q13.3	2011-11-16			ENSG00000240771	ENSG00000240771		"Rho guanine nucleotide exchange factors"	30275	protein-coding gene	gene with protein product	"RAC/CDC42 exchange factor"	610215				12547822	Standard	NM_182947		Approved	GEFT, p63RhoGEF	uc009zpy.4	Q86VW2	OTTHUMG00000152516	ENST00000286494.4:c.294T>A	chr12.hg19:g.58006909T>A		54.0	0.0	.		94.0	42.0	.	NM_001111270	A6NJH5|A9CQZ6|F8W7Z4|Q8WV84|Q96E63	Silent	SNP	ENST00000286494.4	hg19	CCDS8947.1																																																																																			.	.	.	none		0.587	ARHGEF25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000326561.1	NM_133483		A	58006909	T	A	58006909	2	1	255	1	0	0	0	0	0	0	0	1	6335	1654	58	5		5	GEFT	12	58006909	Silent	SNP	T	TCGA-UN-AAZ9-01A-11D-A382-10		58006909	75844986	13	15900											
CHFR	55743	hgsc.bcm.edu	37	chr12	133428243	133428243	+	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	cgggtcctgctcgcgctccgCtctccggtcgggcatgggct	1	9	15	16	6	1	0	0	0	1	0	6	0	3	0	3	4	1	5	3	4	0	0			TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chr12:133428243C>G	ENST00000432561.2	-	12	1562	c.1489G>C	c.(1489-1491)Gcg>Ccg	p.A497P	CHFR_ENST00000541837.2_5'UTR|CHFR_ENST00000537522.1_Missense_Mutation_p.A119P|CHFR_ENST00000266880.7_Missense_Mutation_p.A496P|CHFR_ENST00000315585.7_Missense_Mutation_p.A456P|CHFR_ENST00000450056.2_Missense_Mutation_p.A485P|CHFR_ENST00000443047.2_Missense_Mutation_p.A405P			Q96EP1	CHFR_HUMAN	checkpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase	497			A -> V (common polymorphism; dbSNP:rs2306541). {ECO:0000269|PubMed:11948416, ECO:0000269|PubMed:15489334}.		mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|modification-dependent protein catabolic process (GO:0019941)|protein polyubiquitination (GO:0000209)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)|PML body (GO:0016605)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.00552)|all_epithelial(31;0.226)		OV - Ovarian serous cystadenocarcinoma(86;2.59e-08)|Epithelial(86;6.38e-07)|all cancers(50;1.56e-05)		TCGCGCTCCGCTCTCCGGTCG	0.652																																					p.A497P		Atlas-SNP	.											.	CHFR	83	.	0			c.G1489C						PASS	.						74	77	76					12																	133428243		2203	4300	6503	SO:0001583	missense	55743	exon12			GCTCCGCTCTCCG	AK001658	CCDS31937.1, CCDS53847.1, CCDS53848.1, CCDS53849.1	12q24.33	2012-02-23	2012-02-23			ENSG00000072609		"RING-type (C3HC4) zinc fingers"	20455	protein-coding gene	gene with protein product		605209	"checkpoint with forkhead and ring finger domains"			10935642, 11807090	Standard	NM_001161344		Approved	FLJ10796, RNF196	uc001ulf.2	Q96EP1		ENST00000432561.2:c.1489G>C	chr12.hg19:g.133428243C>G	ENSP00000392395:p.Ala497Pro	60.0	0.0	.		114.0	43.0	.	NM_001161344	A6NEN5|B4DZ77|B4E2L6|Q96SL3|Q9NRT4|Q9NT32|Q9NVD5	Missense_Mutation	SNP	ENST00000432561.2	hg19	CCDS53849.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.116277	0.77323	.	.	ENSG00000072609	ENST00000315585;ENST00000443047;ENST00000450056;ENST00000266880;ENST00000537522;ENST00000541228;ENST00000432561	T;T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56;1.56	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.52517	0.1739	L	0.55481	1.735	0.80722	D	1	B;D;D;D;D	0.67145	0.036;0.995;0.991;0.995;0.996	B;D;D;D;D	0.69479	0.059;0.964;0.921;0.964;0.956	T	0.22452	-1.0216	10	0.33940	T	0.23	-16.074	20.6634	0.99662	0.0:1.0:0.0:0.0	.	405;496;497;485;456	Q96EP1-5;Q96EP1-4;Q96EP1;Q96EP1-2;Q96EP1-3	.;.;CHFR_HUMAN;.;.	P	456;405;485;496;119;297;497	ENSP00000320557:A456P;ENSP00000416431:A405P;ENSP00000398735:A485P;ENSP00000266880:A496P;ENSP00000442327:A119P;ENSP00000392395:A497P	ENSP00000266880:A496P	A	-	1	0	CHFR	131938316	1.000000	0.71417	0.994000	0.49952	0.268000	0.26511	3.975000	0.56859	2.894000	0.99253	0.655000	0.94253	GCG	.	.	.	none		0.652	CHFR-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397130.2			G	133428243	C	G	133428243	3	3	255	1	0	0	0	0	1	0	0	0	3339	797	28	4	533	4	CHFR	12	133428243	Missense_Mutation	SNP	C	TCGA-UN-AAZ9-01A-11D-A382-10	75421334	133428243	423652	14	15901											
KIAA0247	9766	hgsc.bcm.edu	37	chr14	70171432	70171432	+	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	gctgtttgtgctgctgcagcCaaagctgaagtctttccatc	7	13	10	11	0	1	1	0	1	1	0	3	1	2	1	2	0	5	6	2	0	2	2			TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chr14:70171432C>G	ENST00000342745.4	+	4	744	c.431C>G	c.(430-432)cCa>cGa	p.P144R		NM_014734.3	NP_055549.1	Q92537	K0247_HUMAN	KIAA0247	144						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|lung(4)|ovary(3)|upper_aerodigestive_tract(1)	10				all cancers(60;0.00155)|BRCA - Breast invasive adenocarcinoma(234;0.0164)|OV - Ovarian serous cystadenocarcinoma(108;0.0196)		CTGCTGCAGCCAAAGCTGAAG	0.562																																					p.P144R		Atlas-SNP	.											.	KIAA0247	30	.	0			c.C431G						PASS	.						83	68	73					14																	70171432		2203	4300	6503	SO:0001583	missense	9766	exon4			TGCAGCCAAAGCT	D87434	CCDS9796.1	14q24.1	2012-11-29			ENSG00000100647	ENSG00000100647			19956	protein-coding gene	gene with protein product						9039502	Standard	NM_014734		Approved		uc001xlk.3	Q92537	OTTHUMG00000171234	ENST00000342745.4:c.431C>G	chr14.hg19:g.70171432C>G	ENSP00000344424:p.Pro144Arg	62.0	0.0	.		52.0	45.0	.	NM_014734		Missense_Mutation	SNP	ENST00000342745.4	hg19	CCDS9796.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.861030	0.91433	.	.	ENSG00000100647	ENST00000342745	T	0.66099	-0.19	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.78400	0.4277	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.79808	-0.1647	10	0.72032	D	0.01	-13.2989	19.2191	0.93789	0.0:1.0:0.0:0.0	.	144	Q92537	K0247_HUMAN	R	144	ENSP00000344424:P144R	ENSP00000344424:P144R	P	+	2	0	KIAA0247	69241185	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.426000	0.80270	2.541000	0.85698	0.561000	0.74099	CCA	.	.	.	none		0.562	KIAA0247-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412453.1	NM_014734		G	70171432	C	G	70171432	3	3	255	1	0	0	0	0	1	0	0	0	8172	594	21	4	441	4	KIAA0247	14	70171432	Missense_Mutation	SNP	C	TCGA-UN-AAZ9-01A-11D-A382-10		70171432	37178108	15	15902											
SNRPA1	6627	hgsc.bcm.edu	37	chr15	101827180	101827180	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tataaatcacatacaatctgTaatgcttcttattggttacc	13	16	4	8	0	3	0	1	0	2	0	3	0	3	0	1	1	3	3	1	1	8	8			TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chr15:101827180T>C	ENST00000254193.6	-	5	464	c.392A>G	c.(391-393)tAc>tGc	p.Y131C	SNRPA1_ENST00000560856.1_5'UTR	NM_003090.2	NP_003081.2	P09661	RU2A_HUMAN	small nuclear ribonucleoprotein polypeptide A'	131	LRRCT.				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)			ATACAATCTGTAATGCTTCTT	0.373																																					p.Y131C		Atlas-SNP	.											.	SNRPA1	11	.	0			c.A392G						PASS	.						116	119	118					15																	101827180		2203	4299	6502	SO:0001583	missense	6627	exon5			AATCTGTAATGCT	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.392A>G	chr15.hg19:g.101827180T>C	ENSP00000254193:p.Tyr131Cys	51.0	0.0	.		52.0	16.0	.	NM_003090	B2R5I6|Q8TBD2	Missense_Mutation	SNP	ENST00000254193.6	hg19	CCDS10391.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.439257	0.83885	.	.	ENSG00000131876	ENST00000254193	T	0.62941	-0.01	5.62	5.62	0.85841	U2A&apos (1);/phosphoprotein 32 family A, C-terminal (1);	0.060291	0.64402	D	0.000002	D	0.85513	0.5714	H	0.96239	3.79	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90103	0.4186	10	0.87932	D	0	-11.2598	14.9907	0.71387	0.0:0.0:0.0:1.0	.	131	P09661	RU2A_HUMAN	C	131	ENSP00000254193:Y131C	ENSP00000254193:Y131C	Y	-	2	0	SNRPA1	99644703	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.564000	0.82326	2.127000	0.65507	0.533000	0.62120	TAC	.	.	.	none		0.373	SNRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313621.2	NM_003090		C	101827180	T	C	101827180	3	2	255	1	0	0	0	0	1	0	0	0	14873	1638	57	3	395	3	SNRPA1	15	101827180	Missense_Mutation	SNP	T	TCGA-UN-AAZ9-01A-11D-A382-10		101827180	704212	16	15903											
CCDC64B	146439	hgsc.bcm.edu	37	chr16	3079566	3079566	+	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	cggggtgtctccgggtgcgtCggcgccctggccctggtcgc	0	8	18	15	6	1	0	0	0	1	0	4	0	1	0	3	6	1	0	3	6	0	0			TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chr16:3079566C>T	ENST00000572449.1	-	6	999	c.937G>A	c.(937-939)Gac>Aac	p.D313N	CCDC64B_ENST00000573514.1_Missense_Mutation_p.D106N|CCDC64B_ENST00000389347.4_Missense_Mutation_p.D313N|RP11-473M20.5_ENST00000382225.3_RNA			A1A5D9	BICR2_HUMAN	coiled-coil domain containing 64B	313										breast(1)|endometrium(2)|large_intestine(1)	4						CCGGGTGCGTCGGCGCCCTGG	0.682																																					p.D313N		Atlas-SNP	.											.	CCDC64B	19	.	0			c.G937A						PASS	.						7	8	8					16																	3079566		1861	4038	5899	SO:0001583	missense	146439	exon5			GTGCGTCGGCGCC	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.937G>A	chr16.hg19:g.3079566C>T	ENSP00000459043:p.Asp313Asn	45.0	0.0	.		89.0	41.0	.	NM_001103175	Q658L9	Missense_Mutation	SNP	ENST00000572449.1	hg19	CCDS45393.1	.	.	.	.	.	.	.	.	.	.	C	14.22	2.469255	0.43839	.	.	ENSG00000162069	ENST00000389347	T	0.30182	1.54	4.61	-0.595	0.11660	.	2.409390	0.01588	N	0.021386	T	0.18882	0.0453	N	0.21448	0.665	0.09310	N	1	B	0.12013	0.005	B	0.06405	0.002	T	0.10917	-1.0609	10	0.16420	T	0.52	-0.5399	4.1455	0.10214	0.0:0.4688:0.1861:0.345	.	313	A1A5D9	BICR2_HUMAN	N	313	ENSP00000373998:D313N	ENSP00000373998:D313N	D	-	1	0	CCDC64B	3019567	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	1.142000	0.31540	0.317000	0.23160	0.491000	0.48974	GAC	.	.	.	none		0.682	CCDC64B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436991.1			T	3079566	C	T	3079566	3	4	255	1	0	0	0	0	1	0	0	0	2838	884	31	1	609	1	CCDC64B	16	3079566	Missense_Mutation	SNP	C	TCGA-UN-AAZ9-01A-11D-A382-10		3079566	87275187	17	15904											
FBXL19	54620	hgsc.bcm.edu	37	chr16	30953551	30953551	+	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	cgtgccctggacctcagctgGacaggtgtctccaagaagca	9	7	12	13	1	2	1	1	0	1	1	3	3	2	3	3	3	3	2	3	3	2	0			TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chr16:30953551G>T	ENST00000380310.2	+	8	1634	c.1476G>T	c.(1474-1476)tgG>tgT	p.W492C	FBXL19_ENST00000562319.1_Missense_Mutation_p.W472C|FBXL19_ENST00000565690.1_Missense_Mutation_p.W356C|FBXL19_ENST00000338343.4_Missense_Mutation_p.W472C|FBXL19_ENST00000471231.2_Missense_Mutation_p.W180C	NM_001099784.2	NP_001093254.2	Q6PCT2	FXL19_HUMAN	F-box and leucine-rich repeat protein 19	492					proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)	SCF ubiquitin ligase complex (GO:0019005)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|lung(5)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16						ACCTCAGCTGGACAGGTGTCT	0.632											OREG0023741	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.W492C		Atlas-SNP	.											.	FBXL19	74	.	0			c.G1476T						PASS	.						37	40	39					16																	30953551		2037	4186	6223	SO:0001583	missense	54620	exon8			CAGCTGGACAGGT	AK127701	CCDS45465.1, CCDS73873.1	16p11.2	2014-02-20			ENSG00000099364	ENSG00000099364		"F-boxes / Leucine-rich repeats"	25300	protein-coding gene	gene with protein product	"jumonji C domain-containing histone demethylase 1C"	609085					Standard	NM_001099784		Approved	DKFZp434K0410, Fbl19, JHDM1C, CXXC11	uc002eab.2	Q6PCT2	OTTHUMG00000132403	ENST00000380310.2:c.1476G>T	chr16.hg19:g.30953551G>T	ENSP00000369666:p.Trp492Cys	55.0	0.0	.	821	63.0	32.0	.	NM_001099784	A8MT10|Q8N789|Q9NT14	Missense_Mutation	SNP	ENST00000380310.2	hg19	CCDS45465.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.51|18.51	3.639759|3.639759	0.67244|0.67244	.|.	.|.	ENSG00000099364|ENSG00000099364	ENST00000427128|ENST00000338343;ENST00000380310	.|T;T	.|0.51817	.|0.69;0.69	4.73|4.73	4.73|4.73	0.59995|0.59995	.|.	.|0.835286	.|0.10889	.|N	.|0.622978	T|T	0.66177|0.66177	0.2763|0.2763	L|L	0.61036|0.61036	1.89|1.89	0.58432|0.58432	D|D	0.999998|0.999998	.|D;D	.|0.71674	.|0.979;0.998	.|P;P	.|0.62649	.|0.905;0.85	T|T	0.64198|0.64198	-0.6464|-0.6464	5|10	.|0.56958	.|D	.|0.05	-11.5857|-11.5857	16.9952|16.9952	0.86365|0.86365	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|492;449	.|Q6PCT2;Q6PCT2-2	.|FXL19_HUMAN;.	Y|C	384|472;492	.|ENSP00000339712:W472C;ENSP00000369666:W492C	.|ENSP00000339712:W472C	D|W	+|+	1|3	0|0	FBXL19|FBXL19	30861052|30861052	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	4.088000|4.088000	0.57678|0.57678	2.631000|2.631000	0.89168|0.89168	0.655000|0.655000	0.94253|0.94253	GAC|TGG	.	.	.	none		0.632	FBXL19-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_019085		T	30953551	G	T	30953551	3	4	255	1	0	0	0	0	1	0	0	0	5722	1183	41	4	1506	4	FBXL19	16	30953551	Missense_Mutation	SNP	G	TCGA-UN-AAZ9-01A-11D-A382-10	27873985	30953551	59401202	18	15905											
SERPINF1	5176	hgsc.bcm.edu	37	chr17	1675238	1675238	+	Missense_Mutation	SNP	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	caggcccagagtcctgacggGcaaccctcgcttggacctgc	7	6	12	16	2	0	2	0	1	0	1	2	3	1	3	4	3	2	2	4	3	1	1			TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chr17:1675238G>A	ENST00000254722.4	+	5	675	c.512G>A	c.(511-513)gGc>gAc	p.G171D		NM_002615.5	NP_002606.3	P36955	PEDF_HUMAN	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1	171					aging (GO:0007568)|cell proliferation (GO:0008283)|kidney development (GO:0001822)|multicellular organismal development (GO:0007275)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of inflammatory response (GO:0050728)|positive regulation of neurogenesis (GO:0050769)|regulation of proteolysis (GO:0030162)|response to glucocorticoid (GO:0051384)|response to retinoic acid (GO:0032526)|short-term memory (GO:0007614)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	16						GTCCTGACGGGCAACCCTCGC	0.557																																					p.G171D		Atlas-SNP	.											.	SERPINF1	31	.	0			c.G512A						PASS	.						70	66	67					17																	1675238		2203	4300	6503	SO:0001583	missense	5176	exon5			TGACGGGCAACCC	M76979	CCDS11012.1	17p13.3	2014-02-18	2005-08-18		ENSG00000132386	ENSG00000132386		"Serine (or cysteine) peptidase inhibitors"	8824	protein-coding gene	gene with protein product	"pigment epithelium-derived factor", "proliferation-inducing protein 35"	172860	"serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1"	PEDF		8434014, 24172014	Standard	NM_002615		Approved	EPC-1, PIG35	uc002ftl.3	P36955	OTTHUMG00000090571	ENST00000254722.4:c.512G>A	chr17.hg19:g.1675238G>A	ENSP00000254722:p.Gly171Asp	77.0	0.0	.		114.0	53.0	.	NM_002615	F1T092|Q13236|Q2TU83|Q96CT1|Q96R01|Q9BWA4	Missense_Mutation	SNP	ENST00000254722.4	hg19	CCDS11012.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.236450	0.79800	.	.	ENSG00000132386	ENST00000254722	T	0.35605	1.3	5.79	5.79	0.91817	Serpin domain (3);	0.000000	0.85682	D	0.000000	T	0.62109	0.2401	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.55134	-0.8188	10	0.27785	T	0.31	.	20.0212	0.97504	0.0:0.0:1.0:0.0	.	171	P36955	PEDF_HUMAN	D	171	ENSP00000254722:G171D	ENSP00000254722:G171D	G	+	2	0	SERPINF1	1621988	1.000000	0.71417	0.999000	0.59377	0.277000	0.26821	7.935000	0.87658	2.735000	0.93741	0.561000	0.74099	GGC	.	.	.	none		0.557	SERPINF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207109.4	NM_002615		A	1675238	G	A	1675238	3	1	255	1	0	0	0	0	1	0	0	0	14127	1203	42	2	526	2	SERPINF1	17	1675238	Missense_Mutation	SNP	G	TCGA-UN-AAZ9-01A-11D-A382-10		1675238	79519972	19	15906											
OR1A1	8383	hgsc.bcm.edu	37	chr17	3119721	3119721	+	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	accaattatagcctaaaagaCgcagtgatcactgtaatgta	16	10	7	8	1	1	2	1	1	0	1	1	2	1	2	2	0	1	3	2	0	7	5			TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chr17:3119721C>T	ENST00000304094.1	+	1	807	c.807C>T	c.(805-807)gaC>gaT	p.D269D		NM_014565.2	NP_055380.2	Q9P1Q5	OR1A1_HUMAN	olfactory receptor, family 1, subfamily A, member 1	269						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	23						GCCTAAAAGACGCAGTGATCA	0.478																																					p.D269D		Atlas-SNP	.											OR1A1,NS,carcinoma,0,1	OR1A1	54	.	0			c.C807T						PASS	.						153	135	141					17																	3119721		2203	4300	6503	SO:0001819	synonymous_variant	8383	exon1			AAAAGACGCAGTG	AF087918	CCDS11022.1	17p13.3	2012-08-09			ENSG00000172146	ENSG00000172146		"GPCR / Class A : Olfactory receptors"	8179	protein-coding gene	gene with protein product						10673334	Standard	NM_014565		Approved	OR17-7	uc010vrc.2	Q9P1Q5	OTTHUMG00000090637	ENST00000304094.1:c.807C>T	chr17.hg19:g.3119721C>T		123.0	0.0	.		164.0	7.0	.	NM_014565	A5D914|Q6IFM1|Q6NTA9|Q96R87	Silent	SNP	ENST00000304094.1	hg19	CCDS11022.1																																																																																			.	.	.	none		0.478	OR1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207292.1	NM_014565		T	3119721	C	T	3119721	2	4	255	1	0	0	0	0	0	0	0	1	10956	535	19	1		1	OR1A1	17	3119721	Silent	SNP	C	TCGA-UN-AAZ9-01A-11D-A382-10	1444483	3119721	78075489	20	15907											
PER1	5187	hgsc.bcm.edu	37	chr17	8045218	8045218	+	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	ctcagaaaaccgaggctgctGcttctgcatggctcggagcc	8	8	12	13	2	2	1	1	0	1	1	3	3	2	2	2	3	5	5	2	3	2	1			TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chr17:8045218G>A	ENST00000317276.4	-	22	3742	c.3505C>T	c.(3505-3507)Cag>Tag	p.Q1169*	PER1_ENST00000578089.1_5'Flank|PER1_ENST00000581082.1_Nonsense_Mutation_p.Q1146*	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	1169	CRY binding domain. {ECO:0000250}.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						CGAGGCTGCTGCTTCTGCATG	0.627			T	ETV6	"AML, CMML"			Other conserved DNA damage response genes																													p.Q1169X		Atlas-SNP	.		Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	.	PER1	104	.	0			c.C3505T						PASS	.						53	61	58					17																	8045218		2203	4300	6503	SO:0001587	stop_gained	5187	exon22			GCTGCTGCTTCTG	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.3505C>T	chr17.hg19:g.8045218G>A	ENSP00000314420:p.Gln1169*	63.0	0.0	.		87.0	38.0	.	NM_002616	B2RPA8|B4DI49|D3DTR3	Nonsense_Mutation	SNP	ENST00000317276.4	hg19	CCDS11131.1	.	.	.	.	.	.	.	.	.	.	G	44	10.821248	0.99473	.	.	ENSG00000179094	ENST00000317276	.	.	.	5.67	5.67	0.87782	.	0.058964	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	-16.6624	12.2416	0.54546	0.0:0.0:0.8302:0.1698	.	.	.	.	X	1169	.	ENSP00000314420:Q1169X	Q	-	1	0	PER1	7985943	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	5.071000	0.64382	2.697000	0.92050	0.655000	0.94253	CAG	.	.	.	none		0.627	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2			A	8045218	G	A	8045218	4	1	255	1	0	0	0	0	0	1	0	0	11736	1328	46	2	375	2	PER1	17	8045218	Nonsense_Mutation	SNP	G	TCGA-UN-AAZ9-01A-11D-A382-10	4925497	8045218	73149992	21	15908											
MYO18A	399687	hgsc.bcm.edu	37	chr17	27447674	27447674	+	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	cctggccagcttggtcaaagTccagggagaggatctgggag	9	7	16	9	0	2	1	1	0	1	1	3	4	3	3	3	5	1	1	3	5	1	1			TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chr17:27447674T>A	ENST00000527372.1	-	7	1868	c.1688A>T	c.(1687-1689)gAc>gTc	p.D563V	MYO18A_ENST00000533112.1_Missense_Mutation_p.D563V|MYO18A_ENST00000531253.1_Missense_Mutation_p.D563V|MYO18A_ENST00000354329.4_Missense_Mutation_p.D563V	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	563	Myosin motor.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			TTGGTCAAAGTCCAGGGAGAG	0.572																																					p.D563V	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.A1688T						PASS	.						48	56	53					17																	27447674		2014	4174	6188	SO:0001583	missense	399687	exon7			TCAAAGTCCAGGG	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.1688A>T	chr17.hg19:g.27447674T>A	ENSP00000437073:p.Asp563Val	140.0	0.0	.		226.0	88.0	.	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	hg19	CCDS45642.1	.	.	.	.	.	.	.	.	.	.	T	27.9	4.877086	0.91664	.	.	ENSG00000196535	ENST00000354329;ENST00000359450;ENST00000533112;ENST00000531253;ENST00000527372;ENST00000458428	D;D;D;D	0.87334	-2.24;-2.24;-2.24;-2.24	5.73	5.73	0.89815	Myosin head, motor domain (3);DNA recombination/repair protein RecA, monomer-monomer interface (1);	0.042693	0.85682	D	0.000000	D	0.93025	0.7780	M	0.76574	2.34	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.996;0.977;0.977;0.995	D;P;P;P;D	0.76575	0.988;0.9;0.847;0.847;0.959	D	0.93772	0.7076	10	0.87932	D	0	.	15.7063	0.77583	0.0:0.0:0.0:1.0	.	232;175;563;563;563	Q92614-2;F8W6Y3;Q92614-3;Q92614-4;Q92614	.;.;.;.;MY18A_HUMAN	V	563;563;563;563;563;175	ENSP00000346291:D563V;ENSP00000435932:D563V;ENSP00000434228:D563V;ENSP00000437073:D563V	ENSP00000346291:D563V	D	-	2	0	MYO18A	24471800	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.662000	0.83803	2.197000	0.70478	0.533000	0.62120	GAC	.	.	.	none		0.572	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		A	27447674	T	A	27447674	3	1	255	1	0	0	0	0	1	0	0	0	10072	1667	58	5	4620	5	MYO18A	17	27447674	Missense_Mutation	SNP	T	TCGA-UN-AAZ9-01A-11D-A382-10	19402456	27447674	53747536	22	15909											
FTCD	10841	hgsc.bcm.edu	37	chr21	47565766	47565766	+	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	ccgccgccaccgagccgcccCcgggggccgcagagcgggca	5	0	16	20	7	0	1	0	0	0	1	0	2	0	1	8	3	2	2	8	3	0	0			TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chr21:47565766C>G	ENST00000291670.5	-	9	1107	c.1064G>C	c.(1063-1065)gGg>gCg	p.G355A	FTCD_ENST00000355384.2_Missense_Mutation_p.G355A|FTCD_ENST00000397743.1_Missense_Mutation_p.G355A|FTCD_ENST00000359679.2_Missense_Mutation_p.G355A|FTCD_ENST00000397746.3_Missense_Mutation_p.G355A|FTCD_ENST00000498355.2_5'UTR|FTCD_ENST00000397748.1_Missense_Mutation_p.G355A	NM_006657.2	NP_006648.1	O95954	FTCD_HUMAN	formimidoyltransferase cyclodeaminase	355	Cyclodeaminase/cyclohydrolase. {ECO:0000250}.				cellular nitrogen compound metabolic process (GO:0034641)|cytoskeleton organization (GO:0007010)|folic acid-containing compound metabolic process (GO:0006760)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	folic acid binding (GO:0005542)|formimidoyltetrahydrofolate cyclodeaminase activity (GO:0030412)|glutamate formimidoyltransferase activity (GO:0030409)			endometrium(1)|large_intestine(2)|lung(9)|pancreas(1)|prostate(3)|skin(3)	19	Breast(49;0.214)			Colorectal(79;0.235)	Tetrahydrofolic acid(DB00116)	cgagccgcccccgGGGGCCGC	0.781																																					p.G355A		Atlas-SNP	.											.	FTCD	59	.	0			c.G1064C						PASS	.						1	2	2					21																	47565766		825	1870	2695	SO:0001583	missense	10841	exon9			CCGCCCCCGGGGG	U91541	CCDS13731.1	21q22.3	2013-06-10	2013-06-10		ENSG00000160282	ENSG00000160282	2.1.2.5, 4.3.1.4		3974	protein-coding gene	gene with protein product		606806	"formiminotransferase cyclodeaminase"			10029623, 10773664	Standard	NM_006657		Approved		uc002zif.3	O95954	OTTHUMG00000090488	ENST00000291670.5:c.1064G>C	chr21.hg19:g.47565766C>G	ENSP00000291670:p.Gly355Ala	261.0	0.0	.		563.0	256.0	.	NM_206965	B9EGD0|Q86V03|Q9HCT4|Q9HCT5|Q9HCT6|Q9UHJ2	Missense_Mutation	SNP	ENST00000291670.5	hg19	CCDS13731.1	.	.	.	.	.	.	.	.	.	.	C	16.37	3.104888	0.56291	.	.	ENSG00000160282	ENST00000291670;ENST00000397748;ENST00000359679;ENST00000355384;ENST00000397746;ENST00000397743	T;T;T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05;-1.05;-1.05	4.91	4.91	0.64330	Cyclodeaminase/cyclohydrolase (2);	0.000000	0.85682	D	0.000000	D	0.90621	0.7059	H	0.95151	3.63	0.58432	D	0.999996	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.92495	0.6003	10	0.87932	D	0	.	11.2899	0.49244	0.0:0.91:0.0:0.09	.	355;355;355	B7WPK3;O95954-2;O95954	.;.;FTCD_HUMAN	A	355	ENSP00000291670:G355A;ENSP00000380856:G355A;ENSP00000352707:G355A;ENSP00000347545:G355A;ENSP00000380854:G355A;ENSP00000380851:G355A	ENSP00000291670:G355A	G	-	2	0	FTCD	46390194	0.968000	0.33430	0.963000	0.40424	0.157000	0.22087	3.958000	0.56737	2.279000	0.76181	0.453000	0.30009	GGG	.	.	.	none		0.781	FTCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206962.1	NM_006657		G	47565766	C	G	47565766	3	3	255	1	0	0	0	0	1	0	0	0	6088	623	22	4	585	4	FTCD	21	47565766	Missense_Mutation	SNP	C	TCGA-UN-AAZ9-01A-11D-A382-10		47565766	564129	23	15910											
FAM48B1	100130302	hgsc.bcm.edu	37	chrX	24382384	24382384	+	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	ctgctgctattgctgctgctGctgctgctgctgctgctgct	1	15	12	13	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	0	0	1	2			TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chrX:24382384G>A								AC004552.1 (15361 upstream) : PDK3 (100953 downstream)																							tgctgctgctgctgctgctgc	0.582																																					p.A503T		Atlas-SNP	.											.	.	.	.	0			c.G1507A						PASS	.						4	4	4					X																	24382384		1400	3165	4565	SO:0001628	intergenic_variant	100130302	exon1			GCTGCTGCTGCTG																													chrX.hg19:g.24382384G>A		218.0	0.0	.		216.0	22.0	.	NM_001136234		Missense_Mutation	SNP		hg19																																																																																				.	.	.	none	0	0.582									A	24382384	G	A	24382384	1	1	255	0	1	0	0	0	0	0	0	0	5580	1319	46	2		2	FAM48B1	23	24382384	IGR	SNP	G	TCGA-UN-AAZ9-01A-11D-A382-10		24382384	130888176	24	15911											
DOCK11	139818	hgsc.bcm.edu	37	chrX	117817167	117817167	+	Missense_Mutation	SNP	T	T	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	ggtaaaagaattatctgacaTtatccatgagcaggcaagta	16	10	9	6	0	1	3	0	2	1	1	2	3	2	3	1	2	1	4	1	2	7	4			TCGA-UN-AAZ9-01A-11D-A382-10	TCGA-UN-AAZ9-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c956b4f3-cd21-4ff0-8b37-32cd8da4ea6a	5295faa5-5eb5-4e32-abfe-7c9e1d725be6	g.chrX:117817167T>G	ENST00000276202.7	+	52	6152	c.6089T>G	c.(6088-6090)aTt>aGt	p.I2030S	DOCK11_ENST00000276204.6_Missense_Mutation_p.I2030S	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	2030	DHR-2.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						TTATCTGACATTATCCATGAG	0.368																																					p.I2030S		Atlas-SNP	.											.	DOCK11	185	.	0			c.T6089G						PASS	.						90	84	86					X																	117817167		2203	4300	6503	SO:0001583	missense	139818	exon52			CTGACATTATCCA	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.6089T>G	chrX.hg19:g.117817167T>G	ENSP00000276202:p.Ile2030Ser	466.0	0.0	.		450.0	345.0	.	NM_144658	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Missense_Mutation	SNP	ENST00000276202.7	hg19	CCDS35373.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.412721	0.83340	.	.	ENSG00000147251	ENST00000276204;ENST00000276202	T;T	0.19105	2.17;2.18	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.45696	0.1355	M	0.66939	2.045	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.44019	-0.9355	10	0.87932	D	0	-14.345	14.4074	0.67090	0.0:0.0:0.0:1.0	.	2030;2030	A6NIW2;Q5JSL3	.;DOC11_HUMAN	S	2030	ENSP00000276204:I2030S;ENSP00000276202:I2030S	ENSP00000276202:I2030S	I	+	2	0	DOCK11	117701195	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.621000	0.83083	2.001000	0.58596	0.486000	0.48141	ATT	.	.	.	none		0.368	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658		G	117817167	T	G	117817167	3	3	255	1	0	0	0	0	1	0	0	0	4688	1493	52	5	6295	5	DOCK11	23	117817167	Missense_Mutation	SNP	T	TCGA-UN-AAZ9-01A-11D-A382-10	93434783	117817167	37453393	25	15912											
CLIC4	25932	hgsc.bcm.edu	37	chr1	25140695	25140695	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaggaatttcttgaagaagTcttatgccctcccaagtgag	11	12	10	8	0	2	4	0	3	2	1	3	5	3	5	2	1	1	0	2	1	5	3			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr1:25140695T>C	ENST00000374379.4	+	3	490	c.293T>C	c.(292-294)gTc>gCc	p.V98A	CLIC4_ENST00000497755.1_3'UTR	NM_013943.2	NP_039234.1	Q9Y696	CLIC4_HUMAN	chloride intracellular channel 4	98	Required for insertion into the membrane. {ECO:0000305}.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cell differentiation (GO:0030154)|cellular response to calcium ion (GO:0071277)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|endothelial cell morphogenesis (GO:0001886)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|fertilization (GO:0009566)|keratinocyte differentiation (GO:0030216)|multicellular organism growth (GO:0035264)|negative regulation of cell migration (GO:0030336)|regulation of cytoskeleton organization (GO:0051493)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|vacuolar acidification (GO:0007035)	actin cytoskeleton (GO:0015629)|apical part of cell (GO:0045177)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|microvillus (GO:0005902)|midbody (GO:0030496)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			large_intestine(3)|lung(2)|skin(1)	6		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000778)|all_lung(284;0.00106)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0479)|OV - Ovarian serous cystadenocarcinoma(117;1.06e-24)|Colorectal(126;1.03e-07)|COAD - Colon adenocarcinoma(152;4.93e-06)|STAD - Stomach adenocarcinoma(196;0.000418)|GBM - Glioblastoma multiforme(114;0.000451)|BRCA - Breast invasive adenocarcinoma(304;0.00215)|KIRC - Kidney renal clear cell carcinoma(1967;0.00216)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.18)		CTTGAAGAAGTCTTATGCCCT	0.403																																					p.V98A		Atlas-SNP	.											.	CLIC4	20	.	0			c.T293C						PASS	.						81	86	84					1																	25140695		2203	4300	6503	SO:0001583	missense	25932	exon3			AAGAAGTCTTATG	AF097330	CCDS256.1	1p	2012-09-26			ENSG00000169504	ENSG00000169504		"Ion channels / Chloride channels : Intracellular"	13518	protein-coding gene	gene with protein product		606536				9139710, 10070163	Standard	NM_013943		Approved	DKFZP566G223, CLIC4L, P64H1, H1, huH1, p64H1	uc001bjo.2	Q9Y696	OTTHUMG00000003327	ENST00000374379.4:c.293T>C	chr1.hg19:g.25140695T>C	ENSP00000363500:p.Val98Ala	180.0	0.0	.		163.0	75.0	.	NM_013943	Q9UFW9|Q9UQJ6	Missense_Mutation	SNP	ENST00000374379.4	hg19	CCDS256.1	.	.	.	.	.	.	.	.	.	.	T	16.56	3.156029	0.57259	.	.	ENSG00000169504	ENST00000374379;ENST00000444041	T	0.41065	1.01	5.85	5.85	0.93711	Glutathione S-transferase/chloride channel, C-terminal (1);Thioredoxin-like fold (2);	0.054502	0.64402	D	0.000001	T	0.34542	0.0901	N	0.25992	0.78	0.29632	N	0.845361	B;B	0.31459	0.092;0.324	B;B	0.38921	0.138;0.285	T	0.24764	-1.0151	10	0.10902	T	0.67	-14.6151	15.2247	0.73342	0.0:0.0:0.0:1.0	.	78;98	B3KTR3;Q9Y696	.;CLIC4_HUMAN	A	98	ENSP00000363500:V98A	ENSP00000363500:V98A	V	+	2	0	CLIC4	25013282	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.902000	0.69869	2.234000	0.73211	0.533000	0.62120	GTC	.	.	.	none		0.403	CLIC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009332.1	NM_013943		C	25140695	T	C	25140695	3	2	256	1	0	0	0	0	1	0	0	0	3530	1667	58	3	303	3	CLIC4	1	25140695	Missense_Mutation	SNP	T	TCGA-UZ-A9PJ-01A-11D-A382-10		25140695	224109926	1	15913											
ACADM	34	hgsc.bcm.edu	37	chr1	76211529	76211529	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttctgatccagatcctaaagCtcctgctaataaagccttta	12	13	5	11	0	1	2	0	1	1	1	4	2	4	2	4	0	3	2	4	0	6	6			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr1:76211529C>T	ENST00000370841.4	+	8	1075	c.638C>T	c.(637-639)gCt>gTt	p.A213V	ACADM_ENST00000541113.1_Missense_Mutation_p.A177V|ACADM_ENST00000420607.2_Missense_Mutation_p.A217V|ACADM_ENST00000370834.5_Missense_Mutation_p.A246V|ACADM_ENST00000543667.1_Missense_Mutation_p.A24V	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	213					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)	GATCCTAAAGCTCCTGCTAAT	0.393																																					p.A217V		Atlas-SNP	.											ACADM,NS,carcinoma,0,1	ACADM	50	.	0			c.C650T						PASS	.						100	99	100					1																	76211529		2203	4300	6503	SO:0001583	missense	34	exon8			CTAAAGCTCCTGC	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.638C>T	chr1.hg19:g.76211529C>T	ENSP00000359878:p.Ala213Val	49.0	0.0	.		65.0	30.0	.	NM_001127328	Q5T4U4|Q9NYF1	Missense_Mutation	SNP	ENST00000370841.4	hg19	CCDS668.1	.	.	.	.	.	.	.	.	.	.	C	11.95	1.792473	0.31685	.	.	ENSG00000117054	ENST00000370841;ENST00000370834;ENST00000541113;ENST00000543667;ENST00000420607	D;D;D;D;D	0.97924	-4.61;-4.54;-4.58;-4.15;-4.61	5.83	3.94	0.45596	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA oxidase/dehydrogenase, central domain (1);	0.516485	0.23727	N	0.045173	D	0.93080	0.7797	M	0.67397	2.05	0.22684	N	0.99886	B;B;B;B;B	0.14012	0.009;0.002;0.003;0.008;0.002	B;B;B;B;B	0.11329	0.005;0.001;0.005;0.006;0.002	D	0.89120	0.3502	10	0.49607	T	0.09	.	8.7825	0.34800	0.0:0.7664:0.0:0.2336	.	177;127;246;217;213	B7Z9I1;B4DVE0;Q5T4U5;P11310-2;P11310	.;.;.;.;ACADM_HUMAN	V	213;246;177;24;217	ENSP00000359878:A213V;ENSP00000359871:A246V;ENSP00000442324:A177V;ENSP00000446176:A24V;ENSP00000409612:A217V	ENSP00000359871:A246V	A	+	2	0	ACADM	75984117	0.584000	0.26766	0.857000	0.33713	0.361000	0.29550	0.724000	0.25954	0.780000	0.33566	0.585000	0.79938	GCT	.	.	.	none		0.393	ACADM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026967.1			T	76211529	C	T	76211529	3	4	256	1	0	0	0	0	1	0	0	0	113	797	28	2	680	2	ACADM	1	76211529	Missense_Mutation	SNP	C	TCGA-UZ-A9PJ-01A-11D-A382-10	51070834	76211529	173039092	2	15914											
BCAR3	8412	hgsc.bcm.edu	37	chr1	94054942	94054942	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagagagtcacgaactaggAagtcaccatctcgctgcaca	14	6	9	12	2	3	1	2	0	1	1	4	4	3	2	1	1	2	2	1	1	3	1			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr1:94054942A>G	ENST00000370244.1	-	7	809	c.521T>C	c.(520-522)tTc>tCc	p.F174S	BCAR3_ENST00000260502.6_Missense_Mutation_p.F174S|RP5-1033H22.2_ENST00000431770.1_RNA|BCAR3_ENST00000370247.3_Missense_Mutation_p.F83S|BCAR3_ENST00000370243.1_Missense_Mutation_p.F174S|RP5-1033H22.2_ENST00000417401.1_RNA|RP5-1033H22.2_ENST00000427243.1_RNA	NM_001261408.1	NP_001248337.1	O75815	BCAR3_HUMAN	breast cancer anti-estrogen resistance 3	174	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				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)		ACGAACTAGGAAGTCACCATC	0.483																																					p.F174S		Atlas-SNP	.											.	BCAR3	62	.	0			c.T521C						PASS	.						53	53	53					1																	94054942		2203	4300	6503	SO:0001583	missense	8412	exon5			ACTAGGAAGTCAC	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.521T>C	chr1.hg19:g.94054942A>G	ENSP00000359264:p.Phe174Ser	31.0	0.0	.		36.0	14.0	.	NM_001261409	D3DT43|Q5TEW3|Q6UW40|Q9BR50	Missense_Mutation	SNP	ENST00000370244.1	hg19	CCDS745.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.632314	0.87660	.	.	ENSG00000137936	ENST00000370247;ENST00000260502;ENST00000370244;ENST00000370243	D;D;D;D	0.83506	-1.73;-1.73;-1.73;-1.73	5.1	5.1	0.69264	SH2 motif (4);	0.000000	0.85682	D	0.000000	D	0.94568	0.8250	H	0.99090	4.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96857	0.9629	10	0.87932	D	0	-3.8704	15.167	0.72837	1.0:0.0:0.0:0.0	.	174;83	O75815;Q5TEW3	BCAR3_HUMAN;.	S	83;174;174;174	ENSP00000359267:F83S;ENSP00000260502:F174S;ENSP00000359264:F174S;ENSP00000359263:F174S	ENSP00000260502:F174S	F	-	2	0	BCAR3	93827530	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	8.848000	0.92172	2.052000	0.61016	0.533000	0.62120	TTC	.	.	.	none		0.483	BCAR3-003	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028420.1			G	94054942	A	G	94054942	3	3	256	1	0	0	0	0	1	0	0	0	1349	246	9	3	1988	3	BCAR3	1	94054942	Missense_Mutation	SNP	A	TCGA-UZ-A9PJ-01A-11D-A382-10	17843413	94054942	155195679	3	15915											
CELSR2	1952	hgsc.bcm.edu	37	chr1	109794683	109794683	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcttctccatcaccagccAaagtggtggtgggctggtat	7	10	12	12	1	2	0	1	0	1	0	3	0	2	0	4	4	1	3	4	4	2	2			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr1:109794683A>G	ENST00000271332.3	+	1	2043	c.1982A>G	c.(1981-1983)cAa>cGa	p.Q661R		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	661	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		ATCACCAGCCAAAGTGGTGGT	0.567																																					p.Q661R	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.A1982G						PASS	.						138	130	133					1																	109794683		2203	4300	6503	SO:0001583	missense	1952	exon1			CCAGCCAAAGTGG	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.1982A>G	chr1.hg19:g.109794683A>G	ENSP00000271332:p.Gln661Arg	72.0	0.0	.		70.0	32.0	.	NM_001408	Q5T2Y7|Q92566	Missense_Mutation	SNP	ENST00000271332.3	hg19	CCDS796.1	.	.	.	.	.	.	.	.	.	.	N	16.85	3.236767	0.58886	.	.	ENSG00000143126	ENST00000271332	T	0.51071	0.72	4.95	4.95	0.65309	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.43919	0.1269	N	0.24115	0.695	0.54753	D	0.999985	D	0.76494	0.999	D	0.79108	0.992	T	0.43343	-0.9397	9	0.37606	T	0.19	.	14.8253	0.70107	1.0:0.0:0.0:0.0	.	661	Q9HCU4	CELR2_HUMAN	R	661	ENSP00000271332:Q661R	ENSP00000271332:Q661R	Q	+	2	0	CELSR2	109596206	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.709000	0.91379	2.102000	0.63906	0.529000	0.55759	CAA	.	.	.	none		0.567	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		G	109794683	A	G	109794683	3	3	256	1	0	0	0	0	1	0	0	0	3224	130	5	3	1984	3	CELSR2	1	109794683	Missense_Mutation	SNP	A	TCGA-UZ-A9PJ-01A-11D-A382-10	15739741	109794683	139455938	4	15916											
CTTNBP2NL	55917	hgsc.bcm.edu	37	chr1	112999757	112999757	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaagaggtgacacaagccAttcacctactccagggaaag	14	6	9	12	0	1	2	1	1	0	1	3	3	3	3	4	2	2	0	4	2	4	2			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr1:112999757A>G	ENST00000271277.6	+	6	1868	c.1643A>G	c.(1642-1644)cAt>cGt	p.H548R	CTTNBP2NL_ENST00000607039.1_3'UTR	NM_018704.2	NP_061174.1	Q9P2B4	CT2NL_HUMAN	CTTNBP2 N-terminal like	548					negative regulation of transmembrane transport (GO:0034763)|negative regulation of transporter activity (GO:0032410)|protein dephosphorylation (GO:0006470)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	protein phosphatase 2A binding (GO:0051721)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	29		all_cancers(81;0.00064)|all_epithelial(167;0.000415)|all_lung(203;0.00045)|Lung NSC(69;0.000705)		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)		GACACAAGCCATTCACCTACT	0.552																																					p.H548R		Atlas-SNP	.											.	CTTNBP2NL	65	.	0			c.A1643G						PASS	.						158	146	150					1																	112999757		2203	4300	6503	SO:0001583	missense	55917	exon6			CAAGCCATTCACC	AB037854	CCDS845.1	1p13.2	2008-02-05			ENSG00000143079	ENSG00000143079			25330	protein-coding gene	gene with protein product		615100				10718198	Standard	NM_018704		Approved	DKFZp547A023	uc001ebx.3	Q9P2B4	OTTHUMG00000011154	ENST00000271277.6:c.1643A>G	chr1.hg19:g.112999757A>G	ENSP00000271277:p.His548Arg	135.0	0.0	.		119.0	57.0	.	NM_018704	B3KMS5|Q96B40	Missense_Mutation	SNP	ENST00000271277.6	hg19	CCDS845.1	.	.	.	.	.	.	.	.	.	.	A	13.00	2.105932	0.37145	.	.	ENSG00000143079	ENST00000271277	T	0.21543	2.0	5.55	5.55	0.83447	.	0.118926	0.56097	D	0.000024	T	0.27278	0.0669	L	0.51422	1.61	0.53688	D	0.999971	D	0.57899	0.981	D	0.69824	0.966	T	0.02093	-1.1215	10	0.25106	T	0.35	-15.3785	14.5055	0.67750	1.0:0.0:0.0:0.0	.	548	Q9P2B4	CT2NL_HUMAN	R	548	ENSP00000271277:H548R	ENSP00000271277:H548R	H	+	2	0	CTTNBP2NL	112801280	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.619000	0.61218	2.108000	0.64289	0.379000	0.24179	CAT	.	.	.	none		0.552	CTTNBP2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030686.1	NM_018704		G	112999757	A	G	112999757	3	3	256	1	0	0	0	0	1	0	0	0	4048	217	8	3	1657	3	CTTNBP2NL	1	112999757	Missense_Mutation	SNP	A	TCGA-UZ-A9PJ-01A-11D-A382-10	3205074	112999757	136250864	5	15917											
DHX9	1660	hgsc.bcm.edu	37	chr1	182822459	182822459	+	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	agaaaataattctgaggtagGggcctctggctatggtgttc	10	12	13	6	0	2	2	0	1	2	1	3	2	2	2	1	5	0	3	1	5	5	5			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr1:182822459G>A	ENST00000367549.3	+	5	493	c.383G>A	c.(382-384)gGg>gAg	p.G128E		NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	128	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						TCTGAGGTAGGGGCCTCTGGC	0.388																																					p.G128E	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.G383A						PASS	.						57	59	58					1																	182822459		1820	4076	5896	SO:0001583	missense	1660	exon5			AGGTAGGGGCCTC	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.383G>A	chr1.hg19:g.182822459G>A	ENSP00000356520:p.Gly128Glu	224.0	0.0	.		223.0	121.0	.	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Missense_Mutation	SNP	ENST00000367549.3	hg19	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	G	0.033	-1.321463	0.01320	.	.	ENSG00000135829	ENST00000399175;ENST00000367549	T	0.03580	3.88	5.85	3.59	0.41128	.	0.192677	0.43919	N	0.000511	T	0.02571	0.0078	L	0.31065	0.9	0.28768	N	0.90053	B	0.02656	0.0	B	0.04013	0.001	T	0.45205	-0.9277	10	0.02654	T	1	.	8.8523	0.35208	0.2076:0.0:0.7924:0.0	.	128	Q08211	DHX9_HUMAN	E	128	ENSP00000356520:G128E	ENSP00000356520:G128E	G	+	2	0	DHX9	181089082	0.998000	0.40836	0.324000	0.25361	0.236000	0.25371	2.876000	0.48498	0.558000	0.29135	0.650000	0.86243	GGG	.	.	.	none		0.388	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		A	182822459	G	A	182822459	3	1	256	1	0	0	0	0	1	0	0	0	4518	1232	43	2	397	2	DHX9	1	182822459	Missense_Mutation	SNP	G	TCGA-UZ-A9PJ-01A-11D-A382-10	69822702	182822459	66428162	6	15918											
ESRRG	2104	hgsc.bcm.edu	37	chr1	216850790	216850798	+	In_Frame_Del	DEL	TGGAATCAA	TGGAATCAA	-																															cttgatgaaggacgaacagcTggaatcaatgtgtcgatctt																										TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	TGGAATCAA	TGGAATCAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr1:216850790_216850798delTGGAATCAA	ENST00000408911.3	-	2	245_253	c.92_100delTTGATTCCA	c.(91-102)attgattccagc>agc	p.IDS31del	ESRRG_ENST00000391890.3_In_Frame_Del_p.IDS8del|ESRRG_ENST00000361395.2_In_Frame_Del_p.IDS8del|ESRRG_ENST00000493748.1_In_Frame_Del_p.IDS8del|ESRRG_ENST00000360012.3_In_Frame_Del_p.IDS8del|ESRRG_ENST00000366938.2_In_Frame_Del_p.IDS8del|ESRRG_ENST00000487276.1_In_Frame_Del_p.IDS8del|ESRRG_ENST00000366937.1_In_Frame_Del_p.IDS36del|ESRRG_ENST00000359162.2_In_Frame_Del_p.IDS8del|ESRRG_ENST00000361525.3_In_Frame_Del_p.IDS8del|ESRRG_ENST00000366940.2_In_Frame_Del_p.IDS8del|ESRRG_ENST00000493603.1_In_Frame_Del_p.IDS8del|ESRRG_ENST00000463665.1_In_Frame_Del_p.IDS8del	NM_001438.3	NP_001429.2	P62508	ERR3_HUMAN	estrogen-related receptor gamma	31					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)	GACGAACAGCTGGAATCAATGTGTCGATC	0.522																																					p.36_39del		Atlas-Indel,Pindel	.											.	ESRRG	111	.	0			c.108_116del						PASS	.																																			SO:0001651	inframe_deletion	2104	exon3			.	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.92_100delTTGATTCCA	chr1.hg19:g.216850790_216850798delTGGAATCAA	ENSP00000386171:p.Ile31_Ser33del	44.0	0.0	0		53.0	17.0	0.320755	NM_001243518	A8K4I0|A8K6I2|B3KY84|E9PGB7|F8W8J3|O75454|O96021|Q68DA0|Q6P274|Q6PK28|Q6TS38|Q9R1F3|Q9UNJ4	In_Frame_Del	DEL	ENST00000408911.3	hg19	CCDS41468.1																																																																																			.	.	.	none		0.522	ESRRG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089882.2	NM_206595		-	216850798	TGGAATCAA	-	216850790	7	5	256	1	0	1	0	1	0	0	0	0	5264	1580	55	0	1300	0	ESRRG	1	216850790	In_Frame_Del	DEL	TGGAATCAA	TCGA-UZ-A9PJ-01A-11D-A382-10	34028331	216850790	32399831	7	15919											
DNMT3A	1788	hgsc.bcm.edu	37	chr2	25461998	25461998	+	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	ggcccaggagctttcaccaaCctgttcataccgggaaggtt	9	9	11	12	1	2	0	2	0	0	0	2	2	2	2	4	4	3	3	4	4	3	4			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr2:25461998C>A	ENST00000264709.3	-	20	2746		c.e20+1		DNMT3A_ENST00000321117.5_Splice_Site|DNMT3A_ENST00000402667.1_Splice_Site|DNMT3A_ENST00000380746.4_Splice_Site|DNMT3A_ENST00000474887.1_Splice_Site	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha						C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTTCACCAACCTGTTCATAC	0.607			"Mis, F, N, S"		AML																																.		Atlas-SNP	.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	.	DNMT3A	1807	.	0			c.1841+1G>T						PASS	.						52	48	49					2																	25461998		2203	4300	6503	SO:0001630	splice_region_variant	1788	exon17			CACCAACCTGTTC		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.2408+1G>T	chr2.hg19:g.25461998C>A		75.0	0.0	.		73.0	36.0	.	NM_153759	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Splice_Site	SNP	ENST00000264709.3	hg19	CCDS33157.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.205133	0.79127	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	.	.	.	5.64	4.75	0.60458	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5916	0.61964	0.1566:0.8434:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DNMT3A	25315502	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.783000	0.85696	1.367000	0.46095	0.561000	0.74099	.	.	.	.	none		0.607	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552	Intron	A	25461998	C	A	25461998	5	1	256	1	0	0	0	0	0	0	1	0	4678	521	18	4	345	4	DNMT3A	2	25461998	Splice_Site	SNP	C	TCGA-UZ-A9PJ-01A-11D-A382-10		25461998	217737375	8	15920											
TANK	10010	hgsc.bcm.edu	37	chr2	162087645	162087645	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagacacctcttttgaatcActttctaaattcaatgtcaa	14	14	4	9	0	5	2	3	1	2	1	5	3	5	2	1	0	0	0	1	0	6	5			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr2:162087645A>G	ENST00000392749.2	+	7	923	c.684A>G	c.(682-684)tcA>tcG	p.S228S	TANK_ENST00000402568.1_Intron|TANK_ENST00000405852.1_Silent_p.S228S|TANK_ENST00000406287.1_Intron|AC009299.2_ENST00000445372.1_RNA|TANK_ENST00000259075.2_Silent_p.S228S|AC009299.2_ENST00000421122.2_RNA	NM_001199135.1	NP_001186064.1	Q92844	TANK_HUMAN	TRAF family member-associated NFKB activator	228					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						CTTTTGAATCACTTTCTAAAT	0.448																																					p.S228S		Atlas-SNP	.											.	TANK	35	.	0			c.A684G						PASS	.						126	122	123					2																	162087645		2203	4300	6503	SO:0001819	synonymous_variant	10010	exon7			TGAATCACTTTCT	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.684A>G	chr2.hg19:g.162087645A>G		185.0	0.0	.		194.0	99.0	.	NM_004180	D3DPB5|Q7Z4J6|Q92885	Silent	SNP	ENST00000392749.2	hg19	CCDS2215.1																																																																																			.	.	.	none		0.448	TANK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324232.1	NM_133484		G	162087645	A	G	162087645	2	3	256	1	0	0	0	0	0	0	0	1	15558	146	6	3		3	TANK	2	162087645	Silent	SNP	A	TCGA-UZ-A9PJ-01A-11D-A382-10	136625647	162087645	81111728	9	15921											
CDCA7	83879	hgsc.bcm.edu	37	chr2	174230206	174230206	+	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	gacctgcccagaagccgtcgCtccagatcatccgtgaccct	8	7	9	17	3	1	3	1	1	0	2	4	4	3	3	6	0	2	1	6	0	1	0			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr2:174230206C>G	ENST00000347703.3	+	6	828	c.684C>G	c.(682-684)cgC>cgG	p.R228R	CDCA7_ENST00000306721.3_Silent_p.R307R|CDCA7_ENST00000392567.2_Silent_p.R228R|CDCA7_ENST00000410019.3_Silent_p.R186R|CDCA7_ENST00000410101.3_Silent_p.R263R	NM_145810.2	NP_665809.1	Q9BWT1	CDCA7_HUMAN	cell division cycle associated 7	228					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)			GAAGCCGTCGCTCCAGATCAT	0.433																																					p.R307R		Atlas-SNP	.											.	CDCA7	48	.	0			c.C921G						PASS	.						76	77	77					2																	174230206		2203	4300	6503	SO:0001819	synonymous_variant	83879	exon7			CCGTCGCTCCAGA	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.684C>G	chr2.hg19:g.174230206C>G		78.0	0.0	.		83.0	39.0	.	NM_031942	B4DLP8|B4DV66|Q53EW5|Q580W9|Q658K4|Q658N4|Q8NBY9|Q96BV8|Q96SP5	Silent	SNP	ENST00000347703.3	hg19	CCDS2253.1																																																																																			.	.	.	none		0.433	CDCA7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255400.1	NM_031942		G	174230206	C	G	174230206	2	3	256	1	0	0	0	0	0	0	0	1	3092	784	28	4		4	CDCA7	2	174230206	Silent	SNP	C	TCGA-UZ-A9PJ-01A-11D-A382-10	12142561	174230206	68969167	10	15922											
TTN	7273	hgsc.bcm.edu	37	chr2	179469796	179469796	+	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	taagtgcctttgtcctcccgGaccgctttgggaatgctaag	7	12	11	11	2	0	0	0	0	0	0	2	2	2	2	4	2	2	2	4	2	3	4			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr2:179469796G>A	ENST00000591111.1	-	230	49409	c.49185C>T	c.(49183-49185)gtC>gtT	p.V16395V	TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Silent_p.V9096V|TTN_ENST00000460472.2_Silent_p.V8971V|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Silent_p.V18036V|TTN_ENST00000342992.6_Silent_p.V15468V|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342175.6_Silent_p.V9163V|TTN-AS1_ENST00000589234.1_RNA			Q8WZ42	TITIN_HUMAN	titin	16395	Ig-like 100.				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)			TGTCCTCCCGGACCGCTTTGG	0.448																																					p.V18036V		Atlas-SNP	.											.	TTN	18412	.	0			c.C54108T						PASS	.						243	226	232					2																	179469796		1919	4124	6043	SO:0001819	synonymous_variant	7273	exon280			CTCCCGGACCGCT	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.49185C>T	chr2.hg19:g.179469796G>A		72.0	0.0	.		57.0	27.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.	.	none		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179469796	G	A	179469796	2	1	256	1	0	0	0	0	0	0	0	1	16747	1161	41	2		2	TTN	2	179469796	Silent	SNP	G	TCGA-UZ-A9PJ-01A-11D-A382-10	5239590	179469796	63729577	11	15923											
MARCH4	57574	hgsc.bcm.edu	37	chr2	217124358	217124358	+	Missense_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	ctggttgacagcctgccaccGtttaaagatgcggtacaccg	9	9	11	12	3	0	2	0	1	0	1	0	2	0	2	4	2	4	3	4	2	3	4			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr2:217124358G>A	ENST00000273067.4	-	4	2676	c.910C>T	c.(910-912)Cgg>Tgg	p.R304W	AC012513.6_ENST00000417481.1_RNA	NM_020814.2	NP_065865.1	Q9P2E8	MARH4_HUMAN	membrane-associated ring finger (C3HC4) 4, E3 ubiquitin protein ligase	304						Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(1)	20		Renal(323;0.0854)		Epithelial(149;2.19e-05)|all cancers(144;0.00121)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0125)		GCCTGCCACCGTTTAAAGATG	0.552																																					p.R304W		Atlas-SNP	.											.	MARCH4	50	.	0			c.C910T						PASS	.						72	62	65					2																	217124358		2203	4300	6503	SO:0001583	missense	57574	exon4			GCCACCGTTTAAA	AB037820	CCDS33376.1	2q35	2013-01-09	2012-02-23		ENSG00000144583	ENSG00000144583		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	29269	protein-coding gene	gene with protein product		608208	"membrane-associated ring finger (C3HC4) 4"			10718198, 14722266	Standard	NM_020814		Approved	KIAA1399, MARCH-IV, RNF174	uc002vgb.3	Q9P2E8	OTTHUMG00000154824	ENST00000273067.4:c.910C>T	chr2.hg19:g.217124358G>A	ENSP00000273067:p.Arg304Trp	60.0	0.0	.		68.0	37.0	.	NM_020814	Q4KMN7|Q86WR8	Missense_Mutation	SNP	ENST00000273067.4	hg19	CCDS33376.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.630141	0.87660	.	.	ENSG00000144583	ENST00000273067	T	0.60797	0.16	5.51	3.62	0.41486	.	0.000000	0.85682	D	0.000000	T	0.74336	0.3703	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.78486	-0.2185	10	0.87932	D	0	-3.9764	13.8298	0.63373	0.0:0.0:0.7219:0.2781	.	304	Q9P2E8	MARH4_HUMAN	W	304	ENSP00000273067:R304W	ENSP00000273067:R304W	R	-	1	2	MARCH4	216832603	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.743000	0.62110	1.302000	0.44855	0.561000	0.74099	CGG	.	.	.	none		0.552	MARCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337272.2	NM_020814		A	217124358	G	A	217124358	3	1	256	1	0	0	0	0	1	0	0	0	9310	1144	40	1	326	1	MARCH4	2	217124358	Missense_Mutation	SNP	G	TCGA-UZ-A9PJ-01A-11D-A382-10	37654562	217124358	26075015	12	15924											
CELSR3	1951	hgsc.bcm.edu	37	chr3	48698992	48699004	+	Frame_Shift_Del	DEL	CGCCCGGCCTCGC	CGCCCGGCCTCGC	-																															ccgccagcgagtagactaggCgcccggcctcgccggcgtcc																										TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	CGCCCGGCCTCGC	CGCCCGGCCTCGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr3:48698992_48699004delCGCCCGGCCTCGC	ENST00000164024.4	-	1	1344_1356	c.1064_1076delGCGAGGCCGGGCG	c.(1063-1077)ggcgaggccgggcgcfs	p.GEAGR355fs	RP11-148G20.1_ENST00000421275.1_RNA|CELSR3_ENST00000544264.1_Frame_Shift_Del_p.GEAGR355fs	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	355	Cadherin 1. {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)		GTAGACTAGGCGCCCGGCCTCGCCGGCGTCCGG	0.667																																					p.355_359del		Atlas-INDEL	.											.	CELSR3	237	.	0			c.1065_1077del						PASS	.																																			SO:0001589	frameshift_variant	1951	exon1			.	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.1064_1076delGCGAGGCCGGGCG	chr3.hg19:g.48698992_48699004delCGCCCGGCCTCGC	ENSP00000164024:p.Gly355fs	65.0	0.0	0		45.0	19.0	0.422222	NM_001407	O75092	Frame_Shift_Del	DEL	ENST00000164024.4	hg19	CCDS2775.1																																																																																			.	.	.	none		0.667	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		-	48699004	CGCCCGGCCTCGC	-	48698992	7	5	256	1	0	1	0	1	0	0	0	0	3225	768	27	0	9002	0	CELSR3	3	48698992	Frame_Shift_Del	DEL	CGCCCGGCCTCGC	TCGA-UZ-A9PJ-01A-11D-A382-10		48698992	149323438	13	15925											
RBM15B	29890	hgsc.bcm.edu	37	chr3	51431303	51431303	+	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	ggcggcttctcaggaacctgGtctcctacttgaaacagaag	10	9	11	11	1	2	2	1	1	2	1	4	3	2	3	2	4	3	1	2	4	4	3			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr3:51431303G>T	ENST00000323686.4	+	1	2573	c.2473G>T	c.(2473-2475)Gtc>Ttc	p.V825F		NM_013286.4	NP_037418.3	Q8NDT2	RB15B_HUMAN	RNA binding motif protein 15B	825	Interaction with Epstein-Barr virus BMLF1.|SPOC. {ECO:0000255|PROSITE- ProRule:PRU00249}.				mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|large_intestine(5)|lung(3)	12				BRCA - Breast invasive adenocarcinoma(193;0.000224)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CAGGAACCTGGTCTCCTACTT	0.637																																					p.V825F		Atlas-SNP	.											.	RBM15B	47	.	0			c.G2473T						PASS	.						27	31	30					3																	51431303		2203	4300	6503	SO:0001583	missense	29890	exon1			AACCTGGTCTCCT	AL831838	CCDS33764.1	3p21.1	2013-02-12			ENSG00000179837	ENSG00000259956		"RNA binding motif (RRM) containing"	24303	protein-coding gene	gene with protein product		612602				16129689	Standard	NM_013286		Approved	HUMAGCGB, OTT3	uc003dbd.3	Q8NDT2	OTTHUMG00000156896	ENST00000323686.4:c.2473G>T	chr3.hg19:g.51431303G>T	ENSP00000313890:p.Val825Phe	75.0	0.0	.		85.0	40.0	.	NM_013286	A4QPG7|Q6QE19|Q9BV96	Missense_Mutation	SNP	ENST00000323686.4	hg19	CCDS33764.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.484143	0.84854	.	.	ENSG00000179837	ENST00000323686;ENST00000540284;ENST00000541145;ENST00000536338	T	0.27890	1.64	5.95	5.95	0.96441	Spen Paralogue and Orthologue SPOC, C-terminal-like (2);Spen paralogue/orthologue C-terminal, metazoa (1);Spen paralogue and orthologue SPOC, C-terminal (1);	.	.	.	.	T	0.63721	0.2535	M	0.85542	2.76	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.66913	-0.5803	9	0.87932	D	0	-21.6876	20.3931	0.98965	0.0:0.0:1.0:0.0	.	825	Q8NDT2	RB15B_HUMAN	F	825;146;498;244	ENSP00000313890:V825F	ENSP00000313890:V825F	V	+	1	0	RBM15B	51406343	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.835000	0.99442	2.824000	0.97209	0.655000	0.94253	GTC	.	.	.	none		0.637	RBM15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346489.1	NM_013286		T	51431303	G	T	51431303	3	4	256	1	0	0	0	0	1	0	0	0	13130	1261	44	4	2475	4	RBM15B	3	51431303	Missense_Mutation	SNP	G	TCGA-UZ-A9PJ-01A-11D-A382-10	2732311	51431303	146591127	14	15926											
PBRM1	55193	hgsc.bcm.edu	37	chr3	52661338	52661338	+	Frame_Shift_Del	DEL	T	T	-																															ggtggctgaagagatcatgcTgtctccgtcctcgatatcgt																										TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr3:52661338delT	ENST00000296302.7	-	13	1493	c.1492delA	c.(1492-1494)agcfs	p.S498fs	PBRM1_ENST00000409767.1_Frame_Shift_Del_p.S498fs|PBRM1_ENST00000410007.1_Frame_Shift_Del_p.S498fs|PBRM1_ENST00000337303.4_Frame_Shift_Del_p.S498fs|PBRM1_ENST00000356770.4_Frame_Shift_Del_p.S466fs|PBRM1_ENST00000409057.1_Frame_Shift_Del_p.S498fs|PBRM1_ENST00000409114.3_Frame_Shift_Del_p.S498fs|PBRM1_ENST00000394830.3_Frame_Shift_Del_p.S498fs			Q86U86	PB1_HUMAN	polybromo 1	498					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)		GAGATCATGCTGTCTCCGTCC	0.448			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.S498fs		Atlas-Indel,Pindel	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.1493delG						PASS	.						150	133	139					3																	52661338		2203	4300	6503	SO:0001589	frameshift_variant	55193	exon14			.	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.1492delA	chr3.hg19:g.52661338delT	ENSP00000296302:p.Ser498fs	39.0	0.0	0		32.0	16.0	0.5	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Frame_Shift_Del	DEL	ENST00000296302.7	hg19																																																																																				.	.	.	none		0.448	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		-	52661338	T	-	52661338	7	5	256	1	0	1	0	1	0	0	0	0	11498	1580	55	0	3480	0	PBRM1	3	52661338	Frame_Shift_Del	DEL	T	TCGA-UZ-A9PJ-01A-11D-A382-10	1230035	52661338	145361092	15	15927											
ERC2	26059	hgsc.bcm.edu	37	chr3	55768837	55768837	+	Missense_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	tactagtcggtctttttcccGcttgagggccatgacttctt	5	16	9	11	2	2	2	0	2	2	0	4	2	3	2	2	2	1	1	2	2	2	7	rs367719934		TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr3:55768837G>A	ENST00000288221.6	-	15	2929	c.2674C>T	c.(2674-2676)Cgg>Tgg	p.R892W		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	892						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)		TCTTTTTCCCGCTTGAGGGCC	0.488																																					p.R890W		Atlas-SNP	.											.	ERC2	221	.	0			c.C2668T						PASS	.						105	99	101					3																	55768837		1867	4112	5979	SO:0001583	missense	26059	exon14			TTTCCCGCTTGAG	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.2674C>T	chr3.hg19:g.55768837G>A	ENSP00000288221:p.Arg892Trp	95.0	0.0	.		98.0	39.0	.	NM_015576	Q2T9F6|Q86TK4	Missense_Mutation	SNP	ENST00000288221.6	hg19	CCDS46851.1	.	.	.	.	.	.	.	.	.	.	G	19.05	3.752617	0.69533	.	.	ENSG00000187672	ENST00000288221	T	0.52526	0.66	5.67	2.82	0.32997	.	0.000000	0.85682	D	0.000000	T	0.67126	0.2860	M	0.71581	2.175	0.47737	D	0.999501	D	0.89917	1.0	D	0.79784	0.993	T	0.70831	-0.4765	10	0.87932	D	0	-10.8864	15.9917	0.80211	0.0:0.0:0.4556:0.5444	.	892	O15083	ERC2_HUMAN	W	892	ENSP00000288221:R892W	ENSP00000288221:R892W	R	-	1	2	ERC2	55743877	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.909000	0.39917	0.286000	0.22352	0.655000	0.94253	CGG	.	.	.	alt		0.488	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576		A	55768837	G	A	55768837	3	1	256	1	0	0	0	0	1	0	0	0	5213	1086	38	1	211	1	ERC2	3	55768837	Missense_Mutation	SNP	G	TCGA-UZ-A9PJ-01A-11D-A382-10	3107499	55768837	142253593	16	15928											
POLN	353497	hgsc.bcm.edu	37	chr4	2087397	2087397	+	Missense_Mutation	SNP	T	T	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	gtccttgattttcttgtactTctgcaaaaaactctccaaaa	12	15	4	10	0	3	1	0	1	3	0	5	1	4	1	2	0	3	2	2	0	6	6			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr4:2087397T>G	ENST00000511885.2	-	21	2493	c.2140A>C	c.(2140-2142)Aag>Cag	p.K714Q	POLN_ENST00000382865.1_Missense_Mutation_p.K714Q			Q7Z5Q5	DPOLN_HUMAN	polymerase (DNA directed) nu	714					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)			TTCTTGTACTTCTGCAAAAAA	0.537								DNA polymerases (catalytic subunits)																													p.K714Q		Atlas-SNP	.											.	POLN	82	.	0			c.A2140C						PASS	.						93	96	95					4																	2087397		2203	4300	6503	SO:0001583	missense	353497	exon19			TGTACTTCTGCAA	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.2140A>C	chr4.hg19:g.2087397T>G	ENSP00000435506:p.Lys714Gln	65.0	0.0	.		60.0	25.0	.	NM_181808	A2A336|B4E158|Q4TTW4|Q6ZNF4	Missense_Mutation	SNP	ENST00000511885.2	hg19	CCDS3360.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.75|15.75	2.925348|2.925348	0.52759|0.52759	.|.	.|.	ENSG00000130997|ENSG00000130997	ENST00000511885;ENST00000382865;ENST00000253313;ENST00000382857|ENST00000511098	D;D|.	0.96619|.	-4.07;-4.07|.	4.4|4.4	4.4|4.4	0.53042|0.53042	DNA-directed DNA polymerase, family A, palm domain (2);|.	0.135939|.	0.51477|.	D|.	0.000098|.	T|T	0.51176|0.51176	0.1659|0.1659	L|L	0.42487|0.42487	1.325|1.325	0.34686|0.34686	D|D	0.725274|0.725274	D;D;B|.	0.89917|.	1.0;0.998;0.382|.	D;D;B|.	0.77004|.	0.989;0.969;0.374|.	T|T	0.60767|0.60767	-0.7198|-0.7198	10|5	0.72032|.	D|.	0.01|.	-23.9851|-23.9851	10.2175|10.2175	0.43177|0.43177	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	245;405;714|.	C9JDP8;E9PE06;Q7Z5Q5|.	.;.;DPOLN_HUMAN|.	Q|S	714;714;405;245|346	ENSP00000435506:K714Q;ENSP00000372316:K714Q|.	ENSP00000253313:K405Q|.	K|R	-|-	1|3	0|2	POLN|POLN	2057195|2057195	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	4.234000|4.234000	0.58658|0.58658	1.962000|1.962000	0.57031|0.57031	0.528000|0.528000	0.53228|0.53228	AAG|AGA	.	.	.	none		0.537	POLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205684.2	NM_181808		G	2087397	T	G	2087397	3	3	256	1	0	0	0	0	1	0	0	0	12214	1792	62	5	586	5	POLN	4	2087397	Missense_Mutation	SNP	T	TCGA-UZ-A9PJ-01A-11D-A382-10		2087397	189066879	17	15929											
C4orf23	152992	hgsc.bcm.edu	37	chr4	8469719	8469719	+	Missense_Mutation	SNP	A	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	aaaagaggactcagtacattAagagcaggcggggctgccct	13	6	13	9	1	1	2	1	0	0	2	1	3	1	3	1	4	3	3	1	4	4	2			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr4:8469719A>C	ENST00000389737.4	+	9	1573	c.1573A>C	c.(1573-1575)Aag>Cag	p.K525Q	TRMT44_ENST00000513449.2_Missense_Mutation_p.K284Q	NM_152544.2	NP_689757.2	Q8IYL2	TRM44_HUMAN	tRNA methyltransferase 44 homolog (S. cerevisiae)	525					tRNA processing (GO:0008033)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)										TCAGTACATTAAGAGCAGGCG	0.552																																					p.K525Q		Atlas-SNP	.											.	TRMT44	7	.	0			c.A1573C						PASS	.						49	55	53					4																	8469719		2203	4300	6503	SO:0001583	missense	152992	exon9			TACATTAAGAGCA	AK093044	CCDS3402.1, CCDS3402.2	4p16.1	2012-06-12	2012-06-12	2012-06-12	ENSG00000155275	ENSG00000155275			26653	protein-coding gene	gene with protein product	"tRNA methyltransferase 44 homolog (S. cerevisiae)"	614309	"chromosome 4 open reading frame 23", "methyltransferase like 19"	C4orf23, METTL19		21658913	Standard	NM_152544		Approved	FLJ35725, TRM44	uc003glg.2	Q8IYL2	OTTHUMG00000160935	ENST00000389737.4:c.1573A>C	chr4.hg19:g.8469719A>C	ENSP00000374387:p.Lys525Gln	191.0	0.0	.		137.0	67.0	.	NM_152544	Q8NA95	Missense_Mutation	SNP	ENST00000389737.4	hg19	CCDS3402.2	.	.	.	.	.	.	.	.	.	.	A	9.766	1.171459	0.21621	.	.	ENSG00000155275	ENST00000513449;ENST00000389737;ENST00000285635	T;T	0.18016	2.24;2.24	5.18	0.253	0.15551	.	1.019340	0.07792	N	0.955045	T	0.11495	0.0280	N	0.19112	0.55	0.09310	N	1	B;B	0.12630	0.001;0.006	B;B	0.13407	0.009;0.007	T	0.38672	-0.9650	10	0.21014	T	0.42	-2.6415	11.5332	0.50622	0.2948:0.6278:0.0774:0.0	.	525;284	Q8IYL2;Q8IYL2-2	TRM44_HUMAN;.	Q	284;525;133	ENSP00000424643:K284Q;ENSP00000374387:K525Q	ENSP00000285635:K133Q	K	+	1	0	METTL19	8520619	0.001000	0.12720	0.000000	0.03702	0.217000	0.24651	0.531000	0.23052	0.163000	0.19507	0.533000	0.62120	AAG	.	.	.	none		0.552	TRMT44-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359197.2	NM_152544		C	8469719	A	C	8469719	3	2	256	1	0	0	0	0	1	0	0	0	2258	363	13	5	1607	5	C4orf23	4	8469719	Missense_Mutation	SNP	A	TCGA-UZ-A9PJ-01A-11D-A382-10	6382322	8469719	182684557	18	15930											
FASTKD3	79072	hgsc.bcm.edu	37	chr5	7867537	7867537	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaatcagactttccccaagAatacaaagattgcgaacttc	15	10	6	10	1	1	3	1	0	0	3	3	4	2	3	2	0	3	1	2	0	6	5			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr5:7867537A>G	ENST00000264669.5	-	2	796	c.660T>C	c.(658-660)atT>atC	p.I220I	MTRR_ENST00000264668.2_5'Flank|MTRR_ENST00000440940.2_5'Flank|MTRR_ENST00000502509.1_Intron|FASTKD3_ENST00000513658.1_Intron|MTRR_ENST00000341013.6_5'Flank	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	220					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						TTTCCCCAAGAATACAAAGAT	0.428																																					p.I220I		Atlas-SNP	.											.	FASTKD3	88	.	0			c.T660C						PASS	.						108	108	108					5																	7867537		2203	4300	6503	SO:0001819	synonymous_variant	79072	exon2			CCCAAGAATACAA	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.660T>C	chr5.hg19:g.7867537A>G		83.0	0.0	.		89.0	45.0	.	NM_024091	Q9BVD3	Silent	SNP	ENST00000264669.5	hg19	CCDS3873.1																																																																																			.	.	.	none		0.428	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091		G	7867537	A	G	7867537	2	3	256	1	0	0	0	0	0	0	0	1	5694	242	9	3		3	FASTKD3	5	7867537	Silent	SNP	A	TCGA-UZ-A9PJ-01A-11D-A382-10		7867537	173047723	19	15931											
C5orf43	643155	hgsc.bcm.edu	37	chr5	60455870	60455870	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcctcaatcatcttggccaaTttccaagacagtacagcact	12	10	6	13	0	3	1	2	0	1	1	4	1	4	1	3	1	2	2	3	1	4	3	rs140323722		TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr5:60455870T>C	ENST00000339020.3	-	3	554	c.129A>G	c.(127-129)aaA>aaG	p.K43K	CTC-436P18.1_ENST00000506902.1_RNA|SMIM15_ENST00000507416.1_Silent_p.K43K	NM_001048249.3	NP_001041714.1	Q7Z3B0	SIM15_HUMAN	small integral membrane protein 15	43						integral component of membrane (GO:0016021)											TCTTGGCCAATTTCCAAGACA	0.443																																					p.K43K		Atlas-SNP	.											.	.	.	.	0			c.A129G						PASS	.	T		0,4406		0,0,2203	158	144	149		129	-1.3	0.9	5	dbSNP_134	149	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	C5orf43	NM_001048249.3		0,2,6501	CC,CT,TT		0.0233,0.0,0.0154		43/75	60455870	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	643155	exon3			GGCCAATTTCCAA		CCDS34165.1	5q12	2013-06-21	2012-12-03	2012-12-03	ENSG00000188725	ENSG00000188725			33861	protein-coding gene	gene with protein product			"chromosome 5 open reading frame 43"	C5orf43			Standard	NM_001048249		Approved	DKFZP686E2158	uc010iwm.1	Q7Z3B0	OTTHUMG00000162241	ENST00000339020.3:c.129A>G	chr5.hg19:g.60455870T>C		80.0	0.0	.		74.0	33.0	.	NM_001048249	B9EJC4	Silent	SNP	ENST00000339020.3	hg19	CCDS34165.1																																																																																			.	T|1.000;C|0.000	0.000	weak		0.443	SMIM15-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368078.1	NM_001048249		C	60455870	T	C	60455870	2	2	256	1	0	0	0	0	0	0	0	1	2304	1490	52	3		3	C5orf43	5	60455870	Silent	SNP	T	TCGA-UZ-A9PJ-01A-11D-A382-10	52588333	60455870	120459390	20	15932											
CCDC99	54908	hgsc.bcm.edu	37	chr5	169026069	169026069	+	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	ctagatattgagcgaaaactTtttgcaaatgaaagatgcct	15	12	8	6	1	0	4	0	2	0	2	0	5	0	4	1	0	4	1	1	0	6	5			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr5:169026069T>G	ENST00000265295.4	+	10	1509	c.1230T>G	c.(1228-1230)ctT>ctG	p.L410L		NM_017785.4	NP_060255.3			spindle apparatus coiled-coil protein 1																		AGCGAAAACTTTTTGCAAATG	0.353																																					p.L410L		Atlas-SNP	.											.	.	.	.	0			c.T1230G						PASS	.						49	51	51					5																	169026069		2203	4300	6503	SO:0001819	synonymous_variant	54908	exon10			AAAACTTTTTGCA	BC012568	CCDS4370.1	5q35.1	2012-09-27	2012-09-27	2012-09-27	ENSG00000040275	ENSG00000040275			26010	protein-coding gene	gene with protein product	"spindly homolog (Drosophila)"		"coiled-coil domain containing 99"	CCDC99		20427577	Standard	NM_017785		Approved	FLJ20364, hSpindly	uc003mae.4	Q96EA4	OTTHUMG00000130438	ENST00000265295.4:c.1230T>G	chr5.hg19:g.169026069T>G		243.0	0.0	.		255.0	124.0	.	NM_017785		Silent	SNP	ENST00000265295.4	hg19	CCDS4370.1																																																																																			.	.	.	none		0.353	SPDL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252829.2	NM_017785		G	169026069	T	G	169026069	2	3	256	1	0	0	0	0	0	0	0	1	2878	1828	64	5		5	CCDC99	5	169026069	Silent	SNP	T	TCGA-UZ-A9PJ-01A-11D-A382-10	108570199	169026069	11889191	21	15933											
CANX	821	hgsc.bcm.edu	37	chr5	179132798	179132798	+	Missense_Mutation	SNP	T	T	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	ggatgaccttgacgatgtcaTtgaagaggtagaagactcaa	14	9	12	6	1	2	6	2	3	0	3	2	8	2	7	1	2	0	1	1	2	4	3			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr5:179132798T>G	ENST00000247461.4	+	2	316	c.116T>G	c.(115-117)aTt>aGt	p.I39S	CANX_ENST00000452673.2_Missense_Mutation_p.I39S|CANX_ENST00000512607.2_De_novo_Start_OutOfFrame|CANX_ENST00000504734.1_Missense_Mutation_p.I39S|CANX_ENST00000415618.2_Missense_Mutation_p.I74S	NM_001746.3	NP_001737.1	P27824	CALX_HUMAN	calnexin	39					aging (GO:0007568)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein folding (GO:0061077)|clathrin-mediated endocytosis (GO:0072583)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|protein secretion (GO:0009306)|synaptic vesicle endocytosis (GO:0048488)	axon (GO:0030424)|dendrite cytoplasm (GO:0032839)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|ER-mitochondrion membrane contact site (GO:0044233)|extracellular vesicular exosome (GO:0070062)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ribosome (GO:0005840)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|kidney(4)|large_intestine(2)|lung(7)|prostate(2)|urinary_tract(3)	22	all_cancers(89;0.000129)|all_epithelial(37;5.59e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0413)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Antihemophilic Factor(DB00025)|Tenecteplase(DB00031)	gacgatgtcattgaagaggta	0.413																																					p.I39S		Atlas-SNP	.											.	CANX	47	.	0			c.T116G						PASS	.						416	340	366					5																	179132798		2203	4300	6503	SO:0001583	missense	821	exon2			ATGTCATTGAAGA	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.116T>G	chr5.hg19:g.179132798T>G	ENSP00000247461:p.Ile39Ser	71.0	0.0	.		66.0	26.0	.	NM_001746	B2R5V8|B4DGP8|B4E2T8|D3DWQ3|D6R9K3	Missense_Mutation	SNP	ENST00000247461.4	hg19	CCDS4447.1	.	.	.	.	.	.	.	.	.	.	T	15.48	2.847345	0.51164	.	.	ENSG00000127022	ENST00000514383;ENST00000502296;ENST00000504734;ENST00000415618;ENST00000452673;ENST00000247461;ENST00000502498;ENST00000507307;ENST00000502673;ENST00000513246;ENST00000354394;ENST00000376953	T;T;T;T;D;T	0.82433	0.81;0.79;0.81;0.81;-1.61;0.14	4.57	4.57	0.56435	.	0.541869	0.20879	N	0.084024	T	0.65616	0.2708	N	0.04959	-0.14	0.80722	D	1	B;B;B	0.30236	0.001;0.274;0.001	B;B;B	0.32762	0.001;0.152;0.001	T	0.63051	-0.6723	10	0.21540	T	0.41	-9.4725	10.4884	0.44735	0.0:0.0:0.0:1.0	.	74;39;39	B4DGP8;Q6ZP56;P27824	.;.;CALX_HUMAN	S	39;39;39;74;39;39;39;39;39;39;31;39	ENSP00000424063:I39S;ENSP00000394817:I74S;ENSP00000391646:I39S;ENSP00000247461:I39S;ENSP00000425246:I39S;ENSP00000421107:I39S	ENSP00000247461:I39S	I	+	2	0	CANX	179065404	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.122000	0.50446	2.035000	0.60131	0.459000	0.35465	ATT	.	.	.	none		0.413	CANX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253500.2	NM_001024649		G	179132798	T	G	179132798	3	3	256	1	0	0	0	0	1	0	0	0	2620	1493	52	5	118	5	CANX	5	179132798	Missense_Mutation	SNP	T	TCGA-UZ-A9PJ-01A-11D-A382-10	10106729	179132798	1782462	22	15934											
GFPT2	9945	hgsc.bcm.edu	37	chr5	179758509	179758509	+	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	tcttaccagaaatttcctcaGatctttgtaatttgtgatga	11	17	6	7	0	3	4	1	2	2	2	4	4	4	4	2	0	1	1	2	0	3	5			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr5:179758509G>A	ENST00000253778.8	-	5	554	c.385C>T	c.(385-387)Ctg>Ttg	p.L129L		NM_005110.2	NP_005101.1	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2	129	Glutamine amidotransferase type-2. {ECO:0000255|PROSITE-ProRule:PRU00609}.				carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|energy reserve metabolic process (GO:0006112)|fructose 6-phosphate metabolic process (GO:0006002)|glutamine metabolic process (GO:0006541)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)	carbohydrate binding (GO:0030246)|glutamine-fructose-6-phosphate transaminase (isomerizing) activity (GO:0004360)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)	AATTTCCTCAGATCTTTGTAA	0.428																																					p.L129L		Atlas-SNP	.											.	GFPT2	74	.	0			c.C385T						PASS	.						80	79	79					5																	179758509		1837	4094	5931	SO:0001819	synonymous_variant	9945	exon5			TCCTCAGATCTTT	AB016789	CCDS43411.1	5q	2008-07-18			ENSG00000131459	ENSG00000131459			4242	protein-coding gene	gene with protein product	"glutamine: fructose-6-phosphate aminotransferase 2"	603865				10198162	Standard	NM_005110		Approved	GFAT2	uc003mlw.1	O94808	OTTHUMG00000163442	ENST00000253778.8:c.385C>T	chr5.hg19:g.179758509G>A		81.0	0.0	.		94.0	45.0	.	NM_005110	Q53XM2|Q9BWS4	Silent	SNP	ENST00000253778.8	hg19	CCDS43411.1																																																																																			.	.	.	none		0.428	GFPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373444.4	NM_005110		A	179758509	G	A	179758509	2	1	256	1	0	0	0	0	0	0	0	1	6353	933	33	2		2	GFPT2	5	179758509	Silent	SNP	G	TCGA-UZ-A9PJ-01A-11D-A382-10	625711	179758509	1156751	23	15935											
BPHL	670	hgsc.bcm.edu	37	chr6	3119054	3119059	+	In_Frame_Del	DEL	CACGGG	CACGGG	-																															gaagcccgggatccacgtccCacgggccggacccgcggccg																										TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	CACGGG	CACGGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr6:3119054_3119059delCACGGG	ENST00000380379.5	+	1	129_134	c.80_85delCACGGG	c.(79-87)ccacgggcc>ccc	p.RA28del	BPHL_ENST00000380368.2_5'UTR|BPHL_ENST00000380375.3_5'UTR|BPHL_ENST00000434640.1_Intron	NM_004332.2	NP_004323.2	Q86WA6	BPHL_HUMAN	biphenyl hydrolase-like (serine hydrolase)	28					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)				ATCCACGTCCCACGGGCCGGACCCGC	0.752																																					p.27_28del		Atlas-Indel,Pindel	.											.	BPHL	32	.	0			c.79_84del						PASS	.																																			SO:0001651	inframe_deletion	670	exon1			.	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.80_85delCACGGG	chr6.hg19:g.3119054_3119059delCACGGG	ENSP00000369739:p.Arg28_Ala29del	59.0	0.0	0		46.0	15.0	0.326087	NM_004332	Q00306|Q13855|Q3KP51	In_Frame_Del	DEL	ENST00000380379.5	hg19	CCDS4483.2																																																																																			.	.	.	none		0.752	BPHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039670.5			-	3119059	CACGGG	-	3119054	7	5	256	1	0	1	0	1	0	0	0	0	1491	594	21	0	82	0	BPHL	6	3119054	In_Frame_Del	DEL	CACGGG	TCGA-UZ-A9PJ-01A-11D-A382-10		3119054	167996013	24	15936											
HLA-G	3135	hgsc.bcm.edu	37	chr6	29797430	29797430	+	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	cagagatacacgtgccatgtGcagcatgaggggctgccgga	10	6	15	10	2	0	2	0	1	0	1	0	4	0	3	2	3	5	3	2	3	1	1			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr6:29797430G>T	ENST00000360323.6	+	4	879	c.855G>T	c.(853-855)gtG>gtT	p.V285V	HLA-G_ENST00000376815.3_Intron|HLA-G_ENST00000376818.3_Silent_p.V193V|HLA-G_ENST00000376828.2_Silent_p.V290V|HLA-G_ENST00000428701.1_Silent_p.V285V			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	285	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						CGTGCCATGTGCAGCATGAGG	0.592																																					p.V285V		Atlas-SNP	.											.	HLA-G	90	.	0			c.G855T						PASS	.						58	58	58					6																	29797430		2203	4300	6503	SO:0001819	synonymous_variant	3135	exon5			CCATGTGCAGCAT		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.855G>T	chr6.hg19:g.29797430G>T		66.0	0.0	.		94.0	6.0	.	NM_002127		Silent	SNP	ENST00000360323.6	hg19	CCDS4668.1																																																																																			.	.	.	none		0.592	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127		T	29797430	G	T	29797430	2	4	256	1	0	0	0	0	0	0	0	1	7219	1306	46	4		4	HLA-G	6	29797430	Silent	SNP	G	TCGA-UZ-A9PJ-01A-11D-A382-10	26678376	29797430	141317637	25	15937											
CRIP3	401262	hgsc.bcm.edu	37	chr6	43275411	43275411	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaagctgctggggctgagAggagtggtgcagccagggct	7	7	19	8	0	0	2	0	2	0	1	0	4	0	3	1	5	4	5	1	5	1	0			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr6:43275411A>G	ENST00000274990.4	-	4	271	c.267T>C	c.(265-267)ccT>ccC	p.P89P	CRIP3_ENST00000372569.3_Silent_p.P89P|ZNF318_ENST00000607252.1_5'UTR			Q6Q6R5	CRIP3_HUMAN	cysteine-rich protein 3	89					T cell proliferation (GO:0042098)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)			TGGGGCTGAGAGGAGTGGTGC	0.612																																					p.P89P		Atlas-SNP	.											.	CRIP3	30	.	0			c.T267C						PASS	.						48	52	51					6																	43275411		2203	4300	6503	SO:0001819	synonymous_variant	401262	exon4			GCTGAGAGGAGTG	AY555741	CCDS4894.2	6p21	2008-02-05			ENSG00000146215	ENSG00000146215			17751	protein-coding gene	gene with protein product						15380775	Standard	NM_206922		Approved	TLP-A, bA480N24.2, TLP	uc003ouu.1	Q6Q6R5	OTTHUMG00000014727	ENST00000274990.4:c.267T>C	chr6.hg19:g.43275411A>G		89.0	0.0	.		86.0	40.0	.	NM_206922	A2A436|Q5T043|Q6Q6R4|Q6Q6R6|Q6Q6R7	Silent	SNP	ENST00000274990.4	hg19		.	.	.	.	.	.	.	.	.	.	A	7.649	0.682533	0.14907	.	.	ENSG00000146215	ENST00000416431	.	.	.	5.28	2.51	0.30379	.	.	.	.	.	T	0.37732	0.1014	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.22977	-1.0201	4	.	.	.	-37.293	5.0692	0.14598	0.2608:0.1501:0.5891:0.0	.	.	.	.	P	37	.	.	S	-	1	0	CRIP3	43383389	0.993000	0.37304	0.924000	0.36721	0.731000	0.41821	1.442000	0.35046	0.304000	0.22809	-0.242000	0.12053	TCT	.	.	.	none		0.612	CRIP3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000313968.1			G	43275411	A	G	43275411	2	3	256	1	0	0	0	0	0	0	0	1	3878	291	11	3		3	CRIP3	6	43275411	Silent	SNP	A	TCGA-UZ-A9PJ-01A-11D-A382-10	13477981	43275411	127839656	26	15938											
IGF2R	3482	hgsc.bcm.edu	37	chr6	160467612	160467612	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtatgacttttatataaaTgtgtgtggcccggtgtctgt	9	16	11	5	1	1	1	0	1	1	0	1	1	1	1	1	2	0	1	1	2	6	5			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr6:160467612T>C	ENST00000356956.1	+	15	2134	c.1986T>C	c.(1984-1986)aaT>aaC	p.N662N		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	662					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)	TTTATATAAATGTGTGTGGCC	0.423																																					p.N662N		Atlas-SNP	.											.	IGF2R	251	.	0			c.T1986C						PASS	.						71	80	77					6																	160467612		2203	4300	6503	SO:0001819	synonymous_variant	3482	exon15			TATAAATGTGTGT	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.1986T>C	chr6.hg19:g.160467612T>C		65.0	0.0	.		65.0	25.0	.	NM_000876	Q7Z7G9|Q96PT5	Silent	SNP	ENST00000356956.1	hg19	CCDS5273.1																																																																																			.	.	.	none		0.423	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		C	160467612	T	C	160467612	2	2	256	1	0	0	0	0	0	0	0	1	7583	1461	51	3		3	IGF2R	6	160467612	Silent	SNP	T	TCGA-UZ-A9PJ-01A-11D-A382-10	117192201	160467612	10647455	27	15939											
PHF10	55274	hgsc.bcm.edu	37	chr6	170112545	170112545	+	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	tcgccatcatctgaatcaccAtcactgtctagagcagggag	11	9	9	12	1	5	2	3	1	2	1	6	3	5	3	2	1	1	1	2	1	2	1			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr6:170112545A>T	ENST00000339209.4	-	8	1017	c.894T>A	c.(892-894)gaT>gaA	p.D298E	PHF10_ENST00000366780.4_Missense_Mutation_p.D296E	NM_018288.3|NM_133325.2	NP_060758.2|NP_579866.2	Q8WUB8	PHF10_HUMAN	PHD finger protein 10	298	Essential to induce neural progenitor proliferation. {ECO:0000250}.				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)		CTGAATCACCATCACTGTCTA	0.478																																					p.D298E		Atlas-SNP	.											.	PHF10	76	.	0			c.T894A						PASS	.						161	158	159					6																	170112545		2203	4300	6503	SO:0001583	missense	55274	exon8			ATCACCATCACTG	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.894T>A	chr6.hg19:g.170112545A>T	ENSP00000341805:p.Asp298Glu	161.0	0.0	.		151.0	74.0	.	NM_018288	Q2YDA3|Q53HG8|Q9BXD2|Q9NV26	Missense_Mutation	SNP	ENST00000339209.4	hg19	CCDS5308.2	.	.	.	.	.	.	.	.	.	.	a	13.28	2.190749	0.38707	.	.	ENSG00000130024	ENST00000366780;ENST00000339209	D;D	0.87650	-2.28;-2.27	5.35	-7.28	0.01456	.	0.095024	0.64402	N	0.000001	T	0.60117	0.2244	L	0.35723	1.085	0.44754	D	0.997758	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.09377	0.004;0.002;0.001	T	0.15983	-1.0418	10	0.25751	T	0.34	-18.3504	9.5202	0.39131	0.4785:0.1052:0.4163:0.0	.	210;296;298	Q5T069;Q8WUB8-2;Q8WUB8	.;.;PHF10_HUMAN	E	296;298	ENSP00000355743:D296E;ENSP00000341805:D298E	ENSP00000341805:D298E	D	-	3	2	PHF10	169854470	0.012000	0.17670	0.491000	0.27477	0.856000	0.48823	-0.917000	0.04025	-1.277000	0.02411	-1.413000	0.01118	GAT	.	.	.	none		0.478	PHF10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346732.1	NM_018288		T	170112545	A	T	170112545	3	4	256	1	0	0	0	0	1	0	0	0	11828	214	8	5	622	5	PHF10	6	170112545	Missense_Mutation	SNP	A	TCGA-UZ-A9PJ-01A-11D-A382-10	9644933	170112545	1002522	28	15940											
MET	4233	hgsc.bcm.edu	37	chr7	116417457	116417457	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcacagggcattttggttgtGtatatcatgggactttgttg	7	16	13	5	0	1	0	1	0	0	0	1	1	1	1	0	3	0	5	0	3	2	7			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr7:116417457G>A	ENST00000318493.6	+	16	3515	c.3328G>A	c.(3328-3330)Gta>Ata	p.V1110I	MET_ENST00000539704.1_5'UTR|MET_ENST00000397752.3_Missense_Mutation_p.V1092I			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)			TTTTGGTTGTGTATATCATGG	0.338			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.V1110I		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.G3328A	GRCh37	CM990852	MET	M		PASS	.						191	176	180					7																	116417457		1827	4084	5911	SO:0001583	missense	4233	exon16	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	GGTTGTGTATATC	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.3328G>A	chr7.hg19:g.116417457G>A	ENSP00000317272:p.Val1110Ile	82.0	0.0	.		151.0	55.0	.	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.834124	0.91036	.	.	ENSG00000105976	ENST00000397752;ENST00000318493	T;T	0.64991	-0.13;-0.13	5.16	5.16	0.70880	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.81178	0.4768	M	0.80422	2.495	0.80722	D	1	D;D	0.76494	0.999;0.99	D;D	0.85130	0.997;0.99	D	0.83726	0.0195	10	0.87932	D	0	.	19.0107	0.92871	0.0:0.0:1.0:0.0	.	1110;1092	P08581-2;P08581	.;MET_HUMAN	I	1092;1110	ENSP00000380860:V1092I;ENSP00000317272:V1110I	ENSP00000317272:V1110I	V	+	1	0	MET	116204693	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	9.813000	0.99286	2.560000	0.86352	0.563000	0.77884	GTA	.	.	.	none		0.338	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			A	116417457	G	A	116417457	3	1	256	1	0	0	0	0	1	0	0	0	9492	1377	48	2	3386	2	MET	7	116417457	Missense_Mutation	SNP	G	TCGA-UZ-A9PJ-01A-11D-A382-10		116417457	42721206	29	15941											
NUP205	23165	hgsc.bcm.edu	37	chr7	135255937	135255937	+	Missense_Mutation	SNP	T	T	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	acaacctgaagctgttcaccTtcttgataagattttgaaga	13	13	7	8	0	2	5	1	3	1	2	2	5	2	5	2	0	2	2	2	0	4	6			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr7:135255937T>G	ENST00000285968.6	+	2	139	c.113T>G	c.(112-114)cTt>cGt	p.L38R	NUP205_ENST00000440390.2_5'UTR|NUP205_ENST00000489493.1_3'UTR	NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	38					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						GCTGTTCACCTTCTTGATAAG	0.333																																					p.L38R		Atlas-SNP	.											.	NUP205	198	.	0			c.T113G						PASS	.						84	85	85					7																	135255937		2203	4300	6503	SO:0001583	missense	23165	exon2			TTCACCTTCTTGA	D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"chromosome 7 open reading frame 14"	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.113T>G	chr7.hg19:g.135255937T>G	ENSP00000285968:p.Leu38Arg	362.0	0.0	.		522.0	160.0	.	NM_015135	A6H8X3|Q86YC1	Missense_Mutation	SNP	ENST00000285968.6	hg19	CCDS34759.1	.	.	.	.	.	.	.	.	.	.	T	9.099	1.003717	0.19121	.	.	ENSG00000155561	ENST00000285968	T	0.28069	1.63	5.44	5.44	0.79542	.	0.294988	0.35291	N	0.003315	T	0.15565	0.0375	N	0.16478	0.41	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.13683	-1.0500	10	0.10636	T	0.68	-16.5036	7.0046	0.24830	0.0:0.0783:0.1626:0.7591	.	38	Q92621	NU205_HUMAN	R	38	ENSP00000285968:L38R	ENSP00000285968:L38R	L	+	2	0	NUP205	134906477	1.000000	0.71417	0.998000	0.56505	0.870000	0.49936	2.571000	0.45990	2.069000	0.61940	0.477000	0.44152	CTT	.	.	.	none		0.333	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1			G	135255937	T	G	135255937	3	3	256	1	0	0	0	0	1	0	0	0	10766	1609	56	5	119	5	NUP205	7	135255937	Missense_Mutation	SNP	T	TCGA-UZ-A9PJ-01A-11D-A382-10	18838480	135255937	23882726	30	15942											
POLB	5423	hgsc.bcm.edu	37	chr8	42218840	42218840	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtccagtggtgacatggatgTtctcctgacccatcccagct	7	11	10	13	0	1	2	0	2	1	0	4	3	3	3	4	2	1	2	4	2	0	1			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr8:42218840T>C	ENST00000265421.4	+	10	748	c.578T>C	c.(577-579)gTt>gCt	p.V193A	POLB_ENST00000538005.1_Missense_Mutation_p.V39A	NM_002690.2	NP_002681.1	P06746	DPOLB_HUMAN	polymerase (DNA directed), beta	193					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neuron apoptotic process (GO:0051402)|pyrimidine dimer repair (GO:0006290)|response to ethanol (GO:0045471)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|enzyme binding (GO:0019899)|lyase activity (GO:0016829)|metal ion binding (GO:0046872)|microtubule binding (GO:0008017)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(1)	16	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;3.18e-11)|Lung(22;0.00467)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|LUSC - Lung squamous cell carcinoma(45;0.024)		Cytarabine(DB00987)	GACATGGATGTTCTCCTGACC	0.428								DNA polymerases (catalytic subunits)																													p.V193A		Atlas-SNP	.											.	POLB	60	.	0			c.T578C						PASS	.						172	144	153					8																	42218840		2203	4300	6503	SO:0001583	missense	5423	exon10			TGGATGTTCTCCT		CCDS6129.1	8p12-p11	2012-10-02			ENSG00000070501	ENSG00000070501	2.7.7.7	"DNA polymerases"	9174	protein-coding gene	gene with protein product		174760					Standard	NM_002690		Approved		uc003xoz.2	P06746	OTTHUMG00000164093	ENST00000265421.4:c.578T>C	chr8.hg19:g.42218840T>C	ENSP00000265421:p.Val193Ala	89.0	0.0	.		61.0	24.0	.	NM_002690	B2RC78|Q3KP48|Q6FI34	Missense_Mutation	SNP	ENST00000265421.4	hg19	CCDS6129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.75|15.75	2.926490|2.926490	0.52759|0.52759	.|.	.|.	ENSG00000070501|ENSG00000070501	ENST00000518579;ENST00000517393|ENST00000265421;ENST00000520008;ENST00000518925;ENST00000538005	.|T;T;T;T	.|0.36340	.|1.26;1.26;1.26;1.26	5.58|5.58	5.58|5.58	0.84498|0.84498	.|DNA-directed DNA polymerase X (1);	.|0.168551	.|0.51477	.|D	.|0.000087	T|T	0.34716|0.34716	0.0907|0.0907	L|L	0.50993|0.50993	1.605|1.605	0.52099|0.52099	D|D	0.999946|0.999946	.|B;B	.|0.10296	.|0.002;0.003	.|B;B	.|0.16289	.|0.012;0.015	T|T	0.09143|0.09143	-1.0688|-1.0688	5|10	.|0.42905	.|T	.|0.14	-10.0579|-10.0579	13.6995|13.6995	0.62599|0.62599	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|193;193	.|Q53EV2;P06746	.|.;DPOLB_HUMAN	L|A	51;9|193;39;228;39	.|ENSP00000265421:V193A;ENSP00000430610:V39A;ENSP00000430784:V228A;ENSP00000440497:V39A	.|ENSP00000265421:V193A	F|V	+|+	1|2	0|0	POLB|POLB	42337997|42337997	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.018000|0.018000	0.09664|0.09664	7.846000|7.846000	0.86887|0.86887	2.124000|2.124000	0.65301|0.65301	0.460000|0.460000	0.39030|0.39030	TTC|GTT	.	.	.	none		0.428	POLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377242.1	NM_002690		C	42218840	T	C	42218840	3	2	256	1	0	0	0	0	1	0	0	0	12196	1725	60	3	616	3	POLB	8	42218840	Missense_Mutation	SNP	T	TCGA-UZ-A9PJ-01A-11D-A382-10		42218840	104145182	31	15943											
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77775575	77775575	+	Missense_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	tcaaagaggaggaattagagGccaccaaacccgaaaaacac	19	3	9	10	1	1	2	1	0	0	2	1	5	1	4	3	3	2	0	3	3	6	1			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr8:77775575G>A	ENST00000521891.2	+	11	10073	c.9625G>A	c.(9625-9627)Gcc>Acc	p.A3209T	ZFHX4_ENST00000455469.2_Missense_Mutation_p.A3164T|ZFHX4_ENST00000518282.1_Missense_Mutation_p.A3183T|ZFHX4_ENST00000050961.6_Missense_Mutation_p.A3160T	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	3160					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)			GGAATTAGAGGCCACCAAACC	0.418										HNSCC(33;0.089)																											p.A3209T		Atlas-SNP	.											.	ZFHX4	878	.	0			c.G9625A						PASS	.						109	107	107					8																	77775575		1873	4111	5984	SO:0001583	missense	79776	exon11			TTAGAGGCCACCA		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.9625G>A	chr8.hg19:g.77775575G>A	ENSP00000430497:p.Ala3209Thr	164.0	0.0	.		124.0	44.0	.	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	hg19	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	G	7.146	0.582749	0.13749	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.50813	0.73;0.78;0.77;0.74	4.71	2.61	0.31194	.	0.176572	0.26931	U	0.021774	T	0.27419	0.0673	N	0.12182	0.205	0.36396	D	0.862813	B	0.06786	0.001	B	0.06405	0.002	T	0.17561	-1.0365	10	0.39692	T	0.17	.	10.0281	0.42083	0.2015:0.0:0.7985:0.0	.	3164	Q86UP3-4	.	T	3209;3193;3164;3160;3183	ENSP00000430497:A3209T;ENSP00000399605:A3164T;ENSP00000050961:A3160T;ENSP00000430848:A3183T	ENSP00000050961:A3160T	A	+	1	0	ZFHX4	77938130	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	2.398000	0.44486	1.084000	0.41184	0.561000	0.74099	GCC	.	.	.	none		0.418	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		A	77775575	G	A	77775575	3	1	256	1	0	0	0	0	1	0	0	0	17647	1203	42	2	9663	2	ZFHX4	8	77775575	Missense_Mutation	SNP	G	TCGA-UZ-A9PJ-01A-11D-A382-10	35556735	77775575	68588447	32	15944											
HRSP12	10247	hgsc.bcm.edu	37	chr8	99118223	99118223	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatgtcagccagaagaacagTtgttttcaccactagaagat	14	11	8	8	0	2	4	2	0	0	4	2	4	2	4	2	0	2	2	2	0	5	5			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr8:99118223T>C	ENST00000254878.3	-	4	382	c.238A>G	c.(238-240)Act>Gct	p.T80A		NM_005836.2	NP_005827.1	P52758	UK114_HUMAN	heat-responsive protein 12	80					regulation of translational termination (GO:0006449)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	deaminase activity (GO:0019239)|endonuclease activity (GO:0004519)|poly(A) RNA binding (GO:0044822)			large_intestine(3)|lung(1)|ovary(1)|urinary_tract(1)	6	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.214)			AGAAGAACAGTTGTTTTCACC	0.308																																					p.T80A		Atlas-SNP	.											.	HRSP12	13	.	0			c.A238G						PASS	.						156	154	154					8																	99118223		2202	4300	6502	SO:0001583	missense	10247	exon4			GAACAGTTGTTTT	BC008418	CCDS6276.1	8q22	2014-05-09			ENSG00000132541	ENSG00000132541			16897	protein-coding gene	gene with protein product	"translational inhibitor p14.5"	602487				8973653, 9405234, 20817725	Standard	NM_005836		Approved	UK114, P14.5, PSP	uc003yii.1	P52758	OTTHUMG00000164670	ENST00000254878.3:c.238A>G	chr8.hg19:g.99118223T>C	ENSP00000254878:p.Thr80Ala	89.0	0.0	.		69.0	41.0	.	NM_005836	Q6FHU9|Q6IBG0	Missense_Mutation	SNP	ENST00000254878.3	hg19	CCDS6276.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.3|21.3	4.135850|4.135850	0.77662|0.77662	.|.	.|.	ENSG00000132541|ENSG00000132541	ENST00000520507|ENST00000254878	.|.	.|.	.|.	5.53|5.53	5.53|5.53	0.82687|0.82687	.|Endoribonuclease L-PSP/chorismate mutase-like (2);	.|0.050056	.|0.85682	.|D	.|0.000000	T|T	0.80138|0.80138	0.4568|0.4568	H|H	0.98487|0.98487	4.245|4.245	0.80722|0.80722	D|D	1|1	.|P	.|0.34826	.|0.471	.|B	.|0.35510	.|0.204	D|D	0.84843|0.84843	0.0809|0.0809	5|9	.|0.72032	.|D	.|0.01	.|.	13.1896|13.1896	0.59702|0.59702	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|80	.|P52758	.|UK114_HUMAN	S|A	90|80	.|.	.|ENSP00000254878:T80A	N|T	-|-	2|1	0|0	HRSP12|HRSP12	99187399|99187399	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.954000|0.954000	0.61252|0.61252	6.663000|6.663000	0.74431|0.74431	2.110000|2.110000	0.64415|0.64415	0.379000|0.379000	0.24179|0.24179	AAC|ACT	.	.	.	none		0.308	HRSP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379687.1	NM_005836		C	99118223	T	C	99118223	3	2	256	1	0	0	0	0	1	0	0	0	7367	1725	60	3	187	3	HRSP12	8	99118223	Missense_Mutation	SNP	T	TCGA-UZ-A9PJ-01A-11D-A382-10	21342648	99118223	47245799	33	15945											
RNF19A	25897	hgsc.bcm.edu	37	chr8	101299802	101299803	+	Frame_Shift_Ins	INS	-	-	T																															ctaagcataaattcttcgtaINStttttccatcaagacatcat																										TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr8:101299802_101299803insT	ENST00000519449.1	-	3	916_917	c.600_601insA	c.(598-603)aaatacfs	p.Y201fs	RNF19A_ENST00000341084.2_Frame_Shift_Ins_p.Y201fs	NM_001280539.1|NM_015435.3	NP_001267468.1|NP_056250.3	Q9NV58	RN19A_HUMAN	ring finger protein 19A, RBR E3 ubiquitin protein ligase	201					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)			AATTCTTCGTATTTTTCCATCA	0.386																																					p.Y201fs		Atlas-Indel,Pindel	.											.	RNF19A	67	.	0			c.601_602insA						PASS	.																																			SO:0001589	frameshift_variant	25897	exon2			.	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.601dupA	chr8.hg19:g.101299807_101299807dupT	ENSP00000428968:p.Tyr201fs	77.0	0.0	0		95.0	39.0	0.410526	NM_183419	A3KCU9|Q52LG1|Q9H5H9|Q9H8M8|Q9UFG0|Q9UFX6|Q9Y4Y1	Frame_Shift_Ins	INS	ENST00000519449.1	hg19	CCDS6286.1																																																																																			.	.	.	none		0.386	RNF19A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380004.1	NM_015435		T	101299803	-	T	101299802	7	5	256	1	0	1	1	0	0	0	0	0	13483	449	16	0	1951	0	RNF19A	8	101299802	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PJ-01A-11D-A382-10	2181579	101299802	45064220	34	15946											
RIMS2	9699	hgsc.bcm.edu	37	chr8	104924308	104924308	+	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	taacctggcaaccatctaaaGatggagatcgtttaattggt	13	12	9	7	1	1	2	0	0	1	2	2	3	1	2	2	3	2	2	2	3	5	5			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr8:104924308G>A	ENST00000436393.2	+	4	1295	c.1054G>A	c.(1054-1056)Gat>Aat	p.D352N	RIMS2_ENST00000406091.3_Missense_Mutation_p.D574N|RIMS2_ENST00000262231.10_Missense_Mutation_p.D429N|RIMS2_ENST00000507740.1_Missense_Mutation_p.D382N			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	652					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)			ACCATCTAAAGATGGAGATCG	0.328										HNSCC(12;0.0054)																											p.D574N		Atlas-SNP	.											.	RIMS2	1357	.	0			c.G1720A						PASS	.						109	105	107					8																	104924308		1824	4085	5909	SO:0001583	missense	9699	exon6			TCTAAAGATGGAG	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.1054G>A	chr8.hg19:g.104924308G>A	ENSP00000390665:p.Asp352Asn	100.0	0.0	.		80.0	37.0	.	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	ENST00000436393.2	hg19		.	.	.	.	.	.	.	.	.	.	G	34	5.311317	0.95655	.	.	ENSG00000176406	ENST00000504942;ENST00000329869;ENST00000406091;ENST00000402998;ENST00000515551;ENST00000262231;ENST00000507740;ENST00000408894;ENST00000436393	T;T;T;T;T;T;T	0.22945	1.93;2.4;2.08;2.11;2.11;2.04;2.36	5.92	5.92	0.95590	PDZ/DHR/GLGF (1);	.	.	.	.	T	0.46946	0.1419	L	0.43923	1.385	0.80722	D	1	P;D;P;D;D	0.71674	0.623;0.976;0.887;0.998;0.998	P;D;D;D;D	0.85130	0.559;0.99;0.937;0.997;0.997	T	0.16867	-1.0388	9	0.49607	T	0.09	.	20.3343	0.98733	0.0:0.0:1.0:0.0	.	652;352;429;382;574	Q9UQ26;D6RA03;Q9UQ26-1;Q9UQ26-3;F8WD47	RIMS2_HUMAN;.;.;.;.	N	574;605;574;652;382;429;382;382;352	ENSP00000427018:D574N;ENSP00000384892:D574N;ENSP00000425205:D382N;ENSP00000262231:D429N;ENSP00000423559:D382N;ENSP00000386228:D382N;ENSP00000390665:D352N	ENSP00000262231:D429N	D	+	1	0	RIMS2	104993484	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.822000	0.97130	0.650000	0.86243	GAT	.	.	.	none		0.328	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117		A	104924308	G	A	104924308	3	1	256	1	0	0	0	0	1	0	0	0	13381	942	33	2	1868	2	RIMS2	8	104924308	Missense_Mutation	SNP	G	TCGA-UZ-A9PJ-01A-11D-A382-10	3624506	104924308	41439714	35	15947											
STX17	55014	hgsc.bcm.edu	37	chr9	102691077	102691077	+	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	tagtatcaaaggtgcagaatCtgggacaagttgcatgaaga	15	9	12	5	0	2	3	1	1	1	2	2	4	2	4	0	2	2	4	0	2	6	3			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr9:102691077C>A	ENST00000259400.6	+	3	277	c.141C>A	c.(139-141)atC>atA	p.I47I	STX17_ENST00000534052.1_Silent_p.I47I|STX17_ENST00000525640.1_Silent_p.I47I|RP11-60I3.4_ENST00000524512.1_RNA	NM_017919.2	NP_060389.2	P56962	STX17_HUMAN	syntaxin 17	47					autophagic vacuole fusion (GO:0000046)|endoplasmic reticulum-Golgi intermediate compartment organization (GO:0097111)|ER to Golgi vesicle-mediated transport (GO:0006888)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|protein localization to pre-autophagosomal structure (GO:0034497)	autophagic vacuole membrane (GO:0000421)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|ER to Golgi transport vesicle (GO:0030134)|ER-mitochondrion membrane contact site (GO:0044233)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|smooth endoplasmic reticulum membrane (GO:0030868)|SNARE complex (GO:0031201)	protein phosphatase binding (GO:0019903)|SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			endometrium(2)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189)				GGTGCAGAATCTGGGACAAGT	0.358																																					p.I47I		Atlas-SNP	.											.	STX17	17	.	0			c.C141A						PASS	.						84	87	86					9																	102691077		2203	4300	6503	SO:0001819	synonymous_variant	55014	exon3			CAGAATCTGGGAC	AL834371	CCDS6745.1	9q31.1	2008-02-05			ENSG00000136874	ENSG00000136874			11432	protein-coding gene	gene with protein product		604204				9852078	Standard	NM_017919		Approved	FLJ20651	uc004bal.4	P56962	OTTHUMG00000020359	ENST00000259400.6:c.141C>A	chr9.hg19:g.102691077C>A		93.0	0.0	.		65.0	35.0	.	NM_017919	Q4VXC2	Silent	SNP	ENST00000259400.6	hg19	CCDS6745.1																																																																																			.	.	.	none		0.358	STX17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053398.3	NM_017919		A	102691077	C	A	102691077	2	1	256	1	0	0	0	0	0	0	0	1	15352	903	32	4		4	STX17	9	102691077	Silent	SNP	C	TCGA-UZ-A9PJ-01A-11D-A382-10		102691077	38522354	36	15948											
C9orf86	55684	hgsc.bcm.edu	37	chr9	139730244	139730244	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaccagctggacatggacgcCacgctggaggagctgtcggt	9	6	15	11	3	0	0	0	0	0	0	1	4	0	4	2	5	3	3	2	5	1	0			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr9:139730244C>T	ENST00000311502.7	+	8	992	c.756C>T	c.(754-756)gcC>gcT	p.A252A	RABL6_ENST00000357466.2_Silent_p.A252A|RABL6_ENST00000371675.3_Silent_p.A137A|RABL6_ENST00000466096.1_3'UTR|RABL6_ENST00000371663.4_Silent_p.A253A|RABL6_ENST00000432842.2_Silent_p.A214A			Q3YEC7	RABL6_HUMAN	RAB, member RAS oncogene family-like 6	252	Small GTPase-like.				small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)										ACATGGACGCCACGCTGGAGG	0.682																																					p.A253A		Atlas-SNP	.											.	.	.	.	0			c.C759T						PASS	.						18	26	24					9																	139730244		2067	4062	6129	SO:0001819	synonymous_variant	55684	exon8			GGACGCCACGCTG	AK094382	CCDS48058.1, CCDS55352.1, CCDS55353.1	9q34.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000196642	ENSG00000196642			24703	protein-coding gene	gene with protein product	"Rab-like protein 1", "partner of ARF"	610615	"chromosome 9 open reading frame 86"	C9orf86		14702039, 16582619, 17962191, 19433581	Standard	NM_024718		Approved	FLJ10101, FLJ13045, pp8875, bA216L13.9, Parf, RBEL1	uc004cjj.1	Q3YEC7	OTTHUMG00000020947	ENST00000311502.7:c.756C>T	chr9.hg19:g.139730244C>T		173.0	0.0	.		157.0	73.0	.	NM_001173988	A8QVZ7|A8QVZ8|C6K8I4|C6K8I5|Q4F968|Q5T5R7|Q8IWK1|Q8TCL4|Q8WU94|Q96SR8|Q9BU21|Q9H935	Silent	SNP	ENST00000311502.7	hg19	CCDS48058.1																																																																																			.	.	.	none		0.682	RABL6-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055141.4	NM_024718		T	139730244	C	T	139730244	2	4	256	1	0	0	0	0	0	0	0	1	2504	581	21	2		2	C9orf86	9	139730244	Silent	SNP	C	TCGA-UZ-A9PJ-01A-11D-A382-10	37039167	139730244	1483187	37	15949											
IPO7	10527	hgsc.bcm.edu	37	chr11	9430091	9430091	+	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	cctgatcgagaaacagcaccAggggatatatccccttatac	13	8	8	12	1	0	2	0	1	0	1	2	4	1	3	4	2	3	1	4	2	5	4			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr11:9430091A>C	ENST00000379719.3	+	3	367	c.225A>C	c.(223-225)ccA>ccC	p.P75P		NM_006391.2	NP_006382.1	O95373	IPO7_HUMAN	importin 7	75	Importin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00115}.				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)		AAACAGCACCAGGGGATATAT	0.368																																					p.P75P		Atlas-SNP	.											.	IPO7	72	.	0			c.A225C						PASS	.						67	69	68					11																	9430091		2201	4296	6497	SO:0001819	synonymous_variant	10527	exon3			AGCACCAGGGGAT	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.225A>C	chr11.hg19:g.9430091A>C		81.0	0.0	.		86.0	39.0	.	NM_006391	A6NNM5|B2R786|Q1RMF7|Q9H177|Q9NTE3	Silent	SNP	ENST00000379719.3	hg19	CCDS31425.1																																																																																			.	.	.	none		0.368	IPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386022.1	NM_006391		C	9430091	A	C	9430091	2	2	256	1	0	0	0	0	0	0	0	1	7804	175	7	5		5	IPO7	11	9430091	Silent	SNP	A	TCGA-UZ-A9PJ-01A-11D-A382-10		9430091	125576425	38	15950											
RBP5	9746	hgsc.bcm.edu	37	chr12	7280907	7280907	+	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	cacatcaaactgcacagtgtAgtttcggaaggtgctgagcg	11	9	12	9	2	1	1	1	1	0	0	2	2	1	2	0	2	4	4	0	2	3	2			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr12:7280907A>G	ENST00000266546.6	+	0	0				RP11-273B20.1_ENST00000538062.1_RNA|RBP5_ENST00000266560.3_Missense_Mutation_p.Y61H|RBP5_ENST00000542370.1_Missense_Mutation_p.Y61H|RP11-273B20.1_ENST00000544657.1_RNA	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3						homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						TGCACAGTGTAGTTTCGGAAG	0.592																																					p.Y61H		Atlas-SNP	.											.	RBP5	20	.	0			c.T181C						PASS	.						165	134	144					12																	7280907		2203	4300	6503	SO:0001631	upstream_gene_variant	83758	exon2			CAGTGTAGTTTCG	AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182		"Cadherins / Cadherin-related"	18371	protein-coding gene	gene with protein product	"cadherin-related family member 14"	611324				12498782	Standard	NM_014718		Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167		chr12.hg19:g.7280907A>G	Exception_encountered	119.0	0.0	.		116.0	59.0	.	NM_031491	D3DUT6|O94831|Q2T9J5|Q5UE57	Missense_Mutation	SNP	ENST00000266546.6	hg19	CCDS8575.1	.	.	.	.	.	.	.	.	.	.	A	8.724	0.914971	0.17907	.	.	ENSG00000139194	ENST00000266560;ENST00000542370	T;T	0.07800	3.16;3.16	3.55	3.55	0.40652	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.062472	0.64402	D	0.000003	T	0.16171	0.0389	L	0.49126	1.545	0.58432	D	0.999996	P	0.48294	0.908	P	0.56278	0.795	T	0.06552	-1.0820	10	0.20046	T	0.44	.	13.1516	0.59492	1.0:0.0:0.0:0.0	.	61	P82980	RET5_HUMAN	H	61	ENSP00000266560:Y61H;ENSP00000438083:Y61H	ENSP00000266560:Y61H	Y	-	1	0	RBP5	7172174	1.000000	0.71417	0.848000	0.33437	0.075000	0.17131	5.670000	0.68088	1.841000	0.53522	0.402000	0.26972	TAC	.	.	.	none		0.592	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398560.2	NM_014718		G	7280907	A	G	7280907	1	3	256	0	1	0	0	0	0	0	0	0	13172	420	15	3		3	RBP5	12	7280907	5'Flank	SNP	A	TCGA-UZ-A9PJ-01A-11D-A382-10		7280907	126570988	39	15951											
C12orf74	338809	hgsc.bcm.edu	37	chr12	93100476	93100476	+	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	ggagcctctcctcggccctcGctgaggagcctgccaaagaa	8	6	12	15	2	1	2	0	1	1	1	4	4	1	4	5	3	3	1	5	3	2	0			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr12:93100476G>A	ENST00000397833.3	+	2	520	c.69G>A	c.(67-69)tcG>tcA	p.S23S	C12orf74_ENST00000544406.2_Silent_p.S23S	NM_001037671.3|NM_001178097.2	NP_001032760.1|NP_001171568.1	Q32Q52	CL074_HUMAN	chromosome 12 open reading frame 74	23										kidney(1)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(2)	10						CTCGGCCCTCGCTGAGGAGCC	0.567																																					p.S23S		Atlas-SNP	.											.	C12orf74	17	.	0			c.G69A						PASS	.						31	34	33					12																	93100476		1909	4119	6028	SO:0001819	synonymous_variant	338809	exon2			GCCCTCGCTGAGG	BC043363	CCDS41819.1, CCDS53818.1	12q22	2012-08-16			ENSG00000214215	ENSG00000214215			27887	protein-coding gene	gene with protein product						12477932	Standard	NM_001037671		Approved		uc001tch.2	Q32Q52	OTTHUMG00000170105	ENST00000397833.3:c.69G>A	chr12.hg19:g.93100476G>A		46.0	0.0	.		62.0	31.0	.	NM_001037671	F5H4P0	Silent	SNP	ENST00000397833.3	hg19	CCDS41819.1																																																																																			.	.	.	none		0.567	C12orf74-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407285.1	NM_001037671		A	93100476	G	A	93100476	2	1	256	1	0	0	0	0	0	0	0	1	1716	1074	38	1		1	C12orf74	12	93100476	Silent	SNP	G	TCGA-UZ-A9PJ-01A-11D-A382-10	85819569	93100476	40751419	40	15952											
GJA3	2700	hgsc.bcm.edu	37	chr13	20716205	20716205	+	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	ctgggtctccgaggggcaagGgcggctggtgcatctgggcc	4	7	19	11	2	2	0	0	0	2	0	3	1	2	0	2	7	1	3	2	7	1	0			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr13:20716205G>A	ENST00000241125.3	-	2	1399	c.1223C>T	c.(1222-1224)cCc>cTc	p.P408L		NM_021954.3	NP_068773.2	Q9Y6H8	CXA3_HUMAN	gap junction protein, alpha 3, 46kDa	408					cell-cell signaling (GO:0007267)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)	gap junction channel activity (GO:0005243)			NS(1)|endometrium(1)|kidney(1)|lung(1)|pancreas(1)|prostate(1)|skin(1)	7		all_cancers(29;1.4e-21)|all_epithelial(30;8.75e-19)|all_lung(29;1.28e-17)|Lung SC(185;0.0257)|Ovarian(182;0.0822)		all cancers(112;0.000554)|Epithelial(112;0.000872)|OV - Ovarian serous cystadenocarcinoma(117;0.0105)|Lung(94;0.0251)|LUSC - Lung squamous cell carcinoma(192;0.0784)		GAGGGGCAAGGGCGGCTGGTG	0.736																																					p.P408L		Atlas-SNP	.											.	GJA3	32	.	0			c.C1223T						PASS	.						5	5	5					13																	20716205		1907	3719	5626	SO:0001583	missense	2700	exon2			GGCAAGGGCGGCT	AF075290	CCDS9289.1	13q12.11	2008-02-05	2007-01-16		ENSG00000121743	ENSG00000121743		"Ion channels / Gap junction proteins (connexins)"	4277	protein-coding gene	gene with protein product	"connexin 46"	121015	"gap junction protein, alpha 3, 46kD (connexin 46)", "gap junction protein, alpha 3, 46kDa (connexin 46)"	CZP3		10205266, 7342922	Standard	NM_021954		Approved	CX46	uc001umx.1	Q9Y6H8	OTTHUMG00000016510	ENST00000241125.3:c.1223C>T	chr13.hg19:g.20716205G>A	ENSP00000241125:p.Pro408Leu	105.0	0.0	.		102.0	50.0	.	NM_021954	Q0VAB7|Q9H537	Missense_Mutation	SNP	ENST00000241125.3	hg19	CCDS9289.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.652921	0.88056	.	.	ENSG00000121743	ENST00000241125	D	0.88586	-2.4	4.35	4.35	0.52113	.	.	.	.	.	D	0.91868	0.7426	L	0.39245	1.2	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92995	0.6418	9	0.66056	D	0.02	.	16.8836	0.86070	0.0:0.0:1.0:0.0	.	408	Q9Y6H8	CXA3_HUMAN	L	408	ENSP00000241125:P408L	ENSP00000241125:P408L	P	-	2	0	GJA3	19614205	1.000000	0.71417	0.022000	0.16811	0.060000	0.15804	9.035000	0.93752	1.968000	0.57251	0.313000	0.20887	CCC	.	.	.	none		0.736	GJA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044059.3	NM_021954		A	20716205	G	A	20716205	3	1	256	1	0	0	0	0	1	0	0	0	6409	1232	43	2	88	2	GJA3	13	20716205	Missense_Mutation	SNP	G	TCGA-UZ-A9PJ-01A-11D-A382-10		20716205	94453673	41	15953											
INTS6	26512	hgsc.bcm.edu	37	chr13	51961636	51961636	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtttgtgacagctatgccaAggctgagatccaaaaggcct	12	9	11	9	0	0	2	0	2	0	1	1	3	1	2	3	2	2	3	3	2	4	2			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr13:51961636A>G	ENST00000311234.4	-	7	1252	c.780T>C	c.(778-780)ccT>ccC	p.P260P	INTS6_ENST00000425000.1_5'UTR|INTS6_ENST00000497989.1_Silent_p.P82P|INTS6_ENST00000490542.1_5'Flank|INTS6_ENST00000420668.2_3'UTR|INTS6_ENST00000398119.2_Silent_p.P247P|INTS6_ENST00000463928.1_Silent_p.P260P	NM_012141.2	NP_036273.1	Q9UL03	INT6_HUMAN	integrator complex subunit 6	260					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)		AGCTATGCCAAGGCTGAGATC	0.403																																					p.P260P		Atlas-SNP	.											.	INTS6	72	.	0			c.T780C						PASS	.						73	68	70					13																	51961636		2203	4300	6503	SO:0001819	synonymous_variant	26512	exon7			ATGCCAAGGCTGA	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.780T>C	chr13.hg19:g.51961636A>G		37.0	0.0	.		34.0	12.0	.	NM_012141	Q0P664|Q6PJP4|Q9UFK0|Q9Y5M9	Silent	SNP	ENST00000311234.4	hg19	CCDS9428.1																																																																																			.	.	.	none		0.403	INTS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045023.1	NM_012141		G	51961636	A	G	51961636	2	3	256	1	0	0	0	0	0	0	0	1	7789	59	3	3		3	INTS6	13	51961636	Silent	SNP	A	TCGA-UZ-A9PJ-01A-11D-A382-10	31245431	51961636	63208242	42	15954											
ACOT2	10965	hgsc.bcm.edu	37	chr14	74036423	74036423	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggctggtgaagcgcgacgTgcgaacgcccttggccgtgg	5	6	18	12	7	0	1	0	1	0	0	0	3	0	1	2	4	3	1	2	4	2	1			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr14:74036423T>C	ENST00000238651.5	+	1	661	c.479T>C	c.(478-480)gTg>gCg	p.V160A	ACOT2_ENST00000538782.1_Intron	NM_006821.5	NP_006812.3	P49753	ACOT2_HUMAN	acyl-CoA thioesterase 2	160					acyl-CoA metabolic process (GO:0006637)|long-chain fatty acid metabolic process (GO:0001676)|very long-chain fatty acid metabolic process (GO:0000038)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)			breast(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	13				BRCA - Breast invasive adenocarcinoma(234;0.0033)|OV - Ovarian serous cystadenocarcinoma(108;0.0639)		AAGCGCGACGTGCGAACGCCC	0.721																																					p.V160A		Atlas-SNP	.											.	ACOT2	24	.	0			c.T479C						PASS	.						11	10	10					14																	74036423		1955	3921	5876	SO:0001583	missense	10965	exon1			GCGACGTGCGAAC	AY005822, AK001939	CCDS9816.1	14q24.3	2013-09-20			ENSG00000119673	ENSG00000119673		"Acyl CoA thioesterases"	18431	protein-coding gene	gene with protein product	"mitochondrial acyl-CoA thioesterase 1"	609972				16103133, 16940157	Standard	NM_006821		Approved	Mte1, ZAP128	uc001xon.5	P49753	OTTHUMG00000171608	ENST00000238651.5:c.479T>C	chr14.hg19:g.74036423T>C	ENSP00000238651:p.Val160Ala	161.0	0.0	.		137.0	49.0	.	NM_006821	Q3I5F8|Q53EK4|Q9NUX4	Missense_Mutation	SNP	ENST00000238651.5	hg19	CCDS9816.1	.	.	.	.	.	.	.	.	.	.	T	13.68	2.310408	0.40895	.	.	ENSG00000119673	ENST00000238651	T	0.72505	-0.66	3.58	2.39	0.29439	Acyl-CoA thioester hydrolase/bile acid-CoA amino acid N-acetyltransferase (1);	0.069512	0.56097	D	0.000026	D	0.83238	0.5211	M	0.87180	2.865	0.44771	D	0.997779	D	0.89917	1.0	D	0.81914	0.995	T	0.82739	-0.0308	10	0.87932	D	0	-17.2886	9.1588	0.37009	0.1635:0.0:0.0:0.8365	.	160	P49753	ACOT2_HUMAN	A	160	ENSP00000238651:V160A	ENSP00000238651:V160A	V	+	2	0	ACOT2	73106176	1.000000	0.71417	0.998000	0.56505	0.031000	0.12232	2.461000	0.45040	0.365000	0.24400	0.260000	0.18958	GTG	.	.	.	none		0.721	ACOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414435.1	NM_006821		C	74036423	T	C	74036423	3	2	256	1	0	0	0	0	1	0	0	0	152	1696	59	3	481	3	ACOT2	14	74036423	Missense_Mutation	SNP	T	TCGA-UZ-A9PJ-01A-11D-A382-10		74036423	33313117	43	15955											
MYST1	84148	hgsc.bcm.edu	37	chr16	31131564	31131564	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggagggccgagaggaattctAtgtacactacgtgggctgtg	9	9	16	7	2	1	1	0	0	1	1	1	4	1	3	1	4	2	2	1	4	4	4			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr16:31131564A>G	ENST00000543774.2	+	3	604	c.269A>G	c.(268-270)tAt>tGt	p.Y90C	RP11-196G11.4_ENST00000576336.1_RNA|KAT8_ENST00000448516.2_Missense_Mutation_p.Y90C|KAT8_ENST00000219797.4_Missense_Mutation_p.Y90C			Q9H7Z6	KAT8_HUMAN	K(lysine) acetyltransferase 8	90	Chromo.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|myeloid cell differentiation (GO:0030099)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	histone acetyltransferase complex (GO:0000123)|kinetochore (GO:0000776)|MLL1 complex (GO:0071339)|MSL complex (GO:0072487)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|histone acetyltransferase activity (GO:0004402)|metal ion binding (GO:0046872)|methylated histone binding (GO:0035064)|transcription factor binding (GO:0008134)	p.Y90C(1)									GAGGAATTCTATGTACACTAC	0.542																																					p.Y90C		Atlas-SNP	.											MYST1,rectum,NS,+1,1	.	.	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A269G						PASS	.						153	138	143					16																	31131564		2197	4300	6497	SO:0001583	missense	84148	exon2			AATTCTATGTACA	AF217501	CCDS10706.1, CCDS45468.1	16p11.1	2013-01-10	2011-07-21	2011-07-21	ENSG00000103510	ENSG00000103510	2.3.1.48	"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing"	17933	protein-coding gene	gene with protein product		609912	"MYST histone acetyltransferase 1"	MYST1		10786633	Standard	NM_032188		Approved	MOF, FLJ14040, hMOF, ZC2HC8	uc002eax.3	Q9H7Z6	OTTHUMG00000132410	ENST00000543774.2:c.269A>G	chr16.hg19:g.31131564A>G	ENSP00000456933:p.Tyr90Cys	145.0	0.0	.		118.0	51.0	.	NM_182958	A8K4Z1|G5E9P2|Q659G0|Q7LC17|Q8IY59|Q8WYB4|Q8WZ14|Q9HAC5|Q9NR35	Missense_Mutation	SNP	ENST00000543774.2	hg19	CCDS10706.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.321720	0.81580	.	.	ENSG00000103510	ENST00000219797;ENST00000448516	T;T	0.56103	0.48;0.48	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.79690	0.4489	M	0.93420	3.415	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.85166	0.0995	10	0.87932	D	0	-14.9295	15.1835	0.72978	1.0:0.0:0.0:0.0	.	90;90	Q9H7Z6;G5E9P2	KAT8_HUMAN;.	C	90	ENSP00000219797:Y90C;ENSP00000406037:Y90C	ENSP00000219797:Y90C	Y	+	2	0	KAT8	31039065	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.286000	0.89916	2.235000	0.73313	0.533000	0.62120	TAT	.	.	.	none		0.542	KAT8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000255546.3	NM_032188		G	31131564	A	G	31131564	3	3	256	1	0	0	0	0	1	0	0	0	10109	449	16	3	275	3	MYST1	16	31131564	Missense_Mutation	SNP	A	TCGA-UZ-A9PJ-01A-11D-A382-10		31131564	59223189	44	15956											
LRRC36	55282	hgsc.bcm.edu	37	chr16	67384190	67384190	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgttgacagcaggattgaaAtgggtaagttttctccctgt	10	14	11	6	0	1	2	0	2	1	0	2	3	1	3	1	2	1	4	1	2	2	5			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr16:67384190A>G	ENST00000329956.6	+	5	593	c.574A>G	c.(574-576)Atg>Gtg	p.M192V	LRRC36_ENST00000290940.7_5'UTR|LRRC36_ENST00000541146.1_5'UTR|LRRC36_ENST00000563189.1_Missense_Mutation_p.M71V|LRRC36_ENST00000435835.3_Missense_Mutation_p.M71V|LRRC36_ENST00000563303.1_3'UTR	NM_018296.5	NP_060766.5	Q1X8D7	LRC36_HUMAN	leucine rich repeat containing 36	192										endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	24		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0669)|Epithelial(162;0.161)		CAGGATTGAAATGGGTAAGTT	0.383																																					p.M192V		Atlas-SNP	.											.	LRRC36	68	.	0			c.A574G						PASS	.						133	139	137					16																	67384190		2198	4300	6498	SO:0001583	missense	55282	exon5			ATTGAAATGGGTA	BC026156	CCDS32467.1, CCDS58474.1	16q22.1	2008-02-05				ENSG00000159708			25615	protein-coding gene	gene with protein product						12477932	Standard	NM_001161575		Approved	FLJ11004	uc002esv.3	Q1X8D7		ENST00000329956.6:c.574A>G	chr16.hg19:g.67384190A>G	ENSP00000329943:p.Met192Val	84.0	0.0	.		89.0	43.0	.	NM_018296	A4FTV6|A6NDE9|A8K8E6|Q7Z5K5	Missense_Mutation	SNP	ENST00000329956.6	hg19	CCDS32467.1	.	.	.	.	.	.	.	.	.	.	A	11.64	1.697963	0.30142	.	.	ENSG00000159708	ENST00000329956;ENST00000435835	T;T	0.28069	3.35;1.63	5.51	1.97	0.26223	.	0.820676	0.11062	N	0.603836	T	0.13200	0.0320	N	0.08118	0	0.80722	D	1	B;B;B	0.09022	0.0;0.002;0.002	B;B;B	0.09377	0.002;0.004;0.004	T	0.15235	-1.0444	10	0.22706	T	0.39	2.7672	3.6735	0.08283	0.6641:0.0:0.1759:0.16	.	71;71;192	B7Z7B3;Q1X8D7-2;Q1X8D7	.;.;LRC36_HUMAN	V	192;71	ENSP00000329943:M192V;ENSP00000411122:M71V	ENSP00000329943:M192V	M	+	1	0	LRRC36	65941691	0.991000	0.36638	0.670000	0.29842	0.711000	0.40976	0.260000	0.18424	0.053000	0.16036	-0.379000	0.06801	ATG	.	.	.	none		0.383	LRRC36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421770.1	NM_018296		G	67384190	A	G	67384190	3	3	256	1	0	0	0	0	1	0	0	0	8997	101	4	3	620	3	LRRC36	16	67384190	Missense_Mutation	SNP	A	TCGA-UZ-A9PJ-01A-11D-A382-10	36252626	67384190	22970563	45	15957											
SPIRE2	84501	hgsc.bcm.edu	37	chr16	89920723	89920723	+	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	aagcttcgggaggacgagccGcatctggagacgcctcgggc	8	5	16	12	5	1	1	0	0	1	1	3	5	1	3	2	4	2	2	2	4	1	1	rs148030912		TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr16:89920723G>T	ENST00000378247.3	+	4	718	c.675G>T	c.(673-675)ccG>ccT	p.P225P	SPIRE2_ENST00000393062.2_Silent_p.P225P	NM_032451.1	NP_115827.1	Q8WWL2	SPIR2_HUMAN	spire-type actin nucleation factor 2	225					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)		AGGACGAGCCGCATCTGGAGA	0.657																																					p.P225P		Atlas-SNP	.											SPIRE2,caecum,carcinoma,0,1	SPIRE2	63	.	0			c.G675T						PASS	.						39	35	36					16																	89920723		2193	4286	6479	SO:0001819	synonymous_variant	84501	exon4			CGAGCCGCATCTG	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.675G>T	chr16.hg19:g.89920723G>T		109.0	0.0	.		94.0	46.0	.	NM_032451	A4QPB1|Q2TA98|Q6P433|Q8ND47|Q96JJ5	Silent	SNP	ENST00000378247.3	hg19	CCDS32516.1																																																																																			.	G|1.000;A|0.000	.	alt		0.657	SPIRE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421843.1	XM_047462		T	89920723	G	T	89920723	2	4	256	1	0	0	0	0	0	0	0	1	15084	1074	38	4		4	SPIRE2	16	89920723	Silent	SNP	G	TCGA-UZ-A9PJ-01A-11D-A382-10	22536533	89920723	434030	46	15958											
KIAA0664	23277	hgsc.bcm.edu	37	chr17	2594073	2594073	+	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	attctccaggtctttttggcTgaggataagggtggggatgg	7	13	16	5	0	2	1	0	1	2	0	3	3	2	3	1	7	0	1	1	7	1	4			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr17:2594073T>C	ENST00000570628.2	-	26	3852		c.e26-2		CLUH_ENST00000435359.1_Splice_Site|RP11-74E22.6_ENST00000608984.1_lincRNA|CLUH_ENST00000538975.1_Splice_Site			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog						intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)											TCTTTTTGGCTGAGGATAAGG	0.622																																					.		Atlas-SNP	.											.	.	.	.	0			c.3747-2A>G						PASS	.						25	28	27					17																	2594073		1868	4098	5966	SO:0001630	splice_region_variant	23277	exon27			TTTGGCTGAGGAT	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.3747-2A>G	chr17.hg19:g.2594073T>C		36.0	0.0	.		40.0	21.0	.	NM_015229	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Splice_Site	SNP	ENST00000570628.2	hg19	CCDS45572.1	.	.	.	.	.	.	.	.	.	.	T	13.58	2.278446	0.40294	.	.	ENSG00000132361	ENST00000435359;ENST00000322335;ENST00000538975	.	.	.	4.54	4.54	0.55810	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.0378	0.58881	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	KIAA0664	2540823	1.000000	0.71417	0.990000	0.47175	0.448000	0.32197	7.383000	0.79741	1.808000	0.52836	0.482000	0.46254	.	.	.	.	none		0.622	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229	Intron	C	2594073	T	C	2594073	5	2	256	1	0	0	0	0	0	0	1	0	8196	1594	55	3	188	3	KIAA0664	17	2594073	Splice_Site	SNP	T	TCGA-UZ-A9PJ-01A-11D-A382-10		2594073	78601137	47	15959											
SYNRG	11276	hgsc.bcm.edu	37	chr17	35969394	35969394	+	Missense_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	accagaaccagctcctggccGcagcgccatcttgctcccga	8	6	9	18	3	1	1	0	0	1	1	3	2	3	1	6	1	4	3	6	1	1	1			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr17:35969394G>A	ENST00000339208.6	-	1	150	c.10C>T	c.(10-12)Cgg>Tgg	p.R4W	SYNRG_ENST00000394378.2_Missense_Mutation_p.R4W|SYNRG_ENST00000346661.4_Missense_Mutation_p.R4W|SYNRG_ENST00000585472.1_Missense_Mutation_p.R4W|SYNRG_ENST00000502449.2_Missense_Mutation_p.R4W|SYNRG_ENST00000591288.1_Missense_Mutation_p.R4W|SYNRG_ENST00000345615.4_Missense_Mutation_p.R4W|RP11-697E22.1_ENST00000591689.1_RNA	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma	4					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						GCTCCTGGCCGCAGCGCCATC	0.726																																					p.R4W		Atlas-SNP	.											.	SYNRG	101	.	0			c.C10T						PASS	.						3	3	3					17																	35969394		1737	3608	5345	SO:0001583	missense	11276	exon1			CTGGCCGCAGCGC	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.10C>T	chr17.hg19:g.35969394G>A	ENSP00000343610:p.Arg4Trp	27.0	0.0	.		42.0	26.0	.	NM_001163544	A8MWU4|B7ZKZ2|B7ZKZ3|Q17RI2|Q5BKU5|Q6ZT17	Missense_Mutation	SNP	ENST00000339208.6	hg19	CCDS11321.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.052424	0.75960	.	.	ENSG00000006114	ENST00000346661;ENST00000339208;ENST00000345615;ENST00000502449;ENST00000394378;ENST00000394379	T;T;T;T;T	0.59224	0.9;0.91;0.28;0.28;0.29	4.6	4.6	0.57074	.	.	.	.	.	T	0.69904	0.3163	L	0.50333	1.59	0.54753	D	0.999987	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	0.80764	0.994;0.994;0.994;0.994;0.994;0.994;0.994	T	0.73011	-0.4117	9	0.87932	D	0	.	14.2726	0.66159	0.0:0.0:1.0:0.0	.	4;4;4;4;4;4;4	A8MYE0;B7ZKZ2;Q9UMZ2-3;A8MWU4;Q9UMZ2-4;Q9UMZ2-5;Q9UMZ2	.;.;.;.;.;.;SYNRG_HUMAN	W	4	ENSP00000005279:R4W;ENSP00000343610:R4W;ENSP00000315722:R4W;ENSP00000424893:R4W;ENSP00000377903:R4W	ENSP00000343610:R4W	R	-	1	2	SYNRG	33043507	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	4.018000	0.57174	2.383000	0.81215	0.591000	0.81541	CGG	.	.	.	none		0.726	SYNRG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256811.2	NM_007247		A	35969394	G	A	35969394	3	1	256	1	0	0	0	0	1	0	0	0	15472	1086	38	1	4095	1	SYNRG	17	35969394	Missense_Mutation	SNP	G	TCGA-UZ-A9PJ-01A-11D-A382-10	33375321	35969394	45225816	48	15960											
SPATA20	64847	hgsc.bcm.edu	37	chr17	48626272	48626272	+	Missense_Mutation	SNP	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	aggactttgtgagtgtgaagGtagaccgtgaggagcggcct	9	9	17	6	2	0	4	0	3	0	1	0	6	0	6	2	4	1	1	2	4	2	2	rs540627294		TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr17:48626272G>A	ENST00000356488.4	+	4	498	c.415G>A	c.(415-417)Gta>Ata	p.V139I	SPATA20_ENST00000006658.6_Missense_Mutation_p.V155I|SPATA20_ENST00000393244.3_Missense_Mutation_p.V95I|SPATA20_ENST00000511937.1_3'UTR	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	139					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)			GAGTGTGAAGGTAGACCGTGA	0.587													G|||	1	0.000199681	0	0	5008	,	,		20328	0		0	False		,,,				2504	0.001				p.V155I		Atlas-SNP	.											.	SPATA20	59	.	0			c.G463A						PASS	.						178	132	148					17																	48626272		2203	4300	6503	SO:0001583	missense	64847	exon5			GTGAAGGTAGACC		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.415G>A	chr17.hg19:g.48626272G>A	ENSP00000348878:p.Val139Ile	91.0	0.0	.		100.0	67.0	.	NM_022827	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Missense_Mutation	SNP	ENST00000356488.4	hg19	CCDS58563.1	.	.	.	.	.	.	.	.	.	.	G	18.82	3.705844	0.68615	.	.	ENSG00000006282	ENST00000006658;ENST00000356488;ENST00000393244	T;T;T	0.54479	0.57;0.57;0.57	4.72	3.75	0.43078	Thioredoxin-like fold (2);Domain of unknown function DUF255 (1);	0.222830	0.37136	N	0.002224	T	0.70911	0.3278	M	0.85373	2.75	0.44388	D	0.997296	D;P;P	0.56521	0.976;0.954;0.888	P;P;P	0.61070	0.883;0.878;0.806	T	0.75863	-0.3167	10	0.72032	D	0.01	-1.6906	12.653	0.56772	0.0809:0.0:0.9191:0.0	.	139;139;155	B4DZC5;Q8TB22;Q8TB22-2	.;SPT20_HUMAN;.	I	155;139;95	ENSP00000006658:V155I;ENSP00000348878:V139I;ENSP00000376935:V95I	ENSP00000006658:V155I	V	+	1	0	SPATA20	45981271	1.000000	0.71417	1.000000	0.80357	0.569000	0.35902	5.966000	0.70395	0.981000	0.38548	0.436000	0.28706	GTA	.	.	.	none		0.587	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827		A	48626272	G	A	48626272	3	1	256	1	0	0	0	0	1	0	0	0	15018	1261	44	2	481	2	SPATA20	17	48626272	Missense_Mutation	SNP	G	TCGA-UZ-A9PJ-01A-11D-A382-10	12656878	48626272	32568938	49	15961											
ADAMTS10	81794	hgsc.bcm.edu	37	chr19	8654145	8654145	+	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	ccggccccaggtgaggctggGctgaagacgccctcgatggt	6	6	16	13	3	0	3	0	2	0	1	1	4	0	3	4	5	0	2	4	5	1	0			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr19:8654145G>C	ENST00000597188.1	-	18	2409	c.2139C>G	c.(2137-2139)agC>agG	p.S713R	ADAMTS10_ENST00000270328.4_Missense_Mutation_p.S713R|ADAMTS10_ENST00000595838.1_Missense_Mutation_p.S200R	NM_030957.2	NP_112219.3	Q9H324	ATS10_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 10	713	Spacer.					extracellular matrix (GO:0031012)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(16)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(3)|skin(10)|urinary_tract(1)	53						GTGAGGCTGGGCTGAAGACGC	0.662																																					p.S713R		Atlas-SNP	.											.	ADAMTS10	132	.	0			c.C2139G						PASS	.						54	46	48					19																	8654145		2203	4300	6503	SO:0001583	missense	81794	exon18			GGCTGGGCTGAAG	AF163762	CCDS12206.1, CCDS62529.1	19p13.2	2014-08-12	2005-08-19		ENSG00000142303	ENSG00000142303		"ADAM metallopeptidases with thrombospondin type 1 motif"	13201	protein-coding gene	gene with protein product		608990	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 10"				Standard	XM_005272499		Approved	ADAM-TS10	uc002mkj.1	Q9H324	OTTHUMG00000182216	ENST00000597188.1:c.2139C>G	chr19.hg19:g.8654145G>C	ENSP00000471851:p.Ser713Arg	95.0	0.0	.		51.0	21.0	.	NM_030957	M0QZE4	Missense_Mutation	SNP	ENST00000597188.1	hg19	CCDS12206.1	.	.	.	.	.	.	.	.	.	.	G	7.625	0.677679	0.14841	.	.	ENSG00000142303	ENST00000270328;ENST00000393912	T	0.51325	0.71	5.21	1.29	0.21616	ADAM-TS Spacer 1 (1);	0.242826	0.39083	N	0.001480	T	0.37652	0.1011	N	0.16743	0.435	0.29576	N	0.84954	B;B;P	0.41188	0.328;0.254;0.741	B;B;P	0.48141	0.063;0.219;0.568	T	0.36016	-0.9765	10	0.49607	T	0.09	.	10.3729	0.44064	0.274:0.0:0.726:0.0	.	467;713;200	Q59FE5;Q9H324;E9PCI6	.;ATS10_HUMAN;.	R	713;467	ENSP00000270328:S713R	ENSP00000270328:S713R	S	-	3	2	ADAMTS10	8560145	1.000000	0.71417	0.343000	0.25615	0.023000	0.10783	1.797000	0.38804	0.513000	0.28278	-0.345000	0.07892	AGC	.	.	.	none		0.662	ADAMTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460085.3	NM_030957		C	8654145	G	C	8654145	3	2	256	1	0	0	0	0	1	0	0	0	256	1194	42	4	1208	4	ADAMTS10	19	8654145	Missense_Mutation	SNP	G	TCGA-UZ-A9PJ-01A-11D-A382-10		8654145	50474838	50	15962											
UPF1	5976	hgsc.bcm.edu	37	chr19	18964067	18964067	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttttttacctcaagacatgcGgctcatgcagggggatgaga	10	11	12	8	1	2	2	2	1	0	2	2	4	2	3	1	3	3	2	1	3	2	3			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr19:18964067G>A	ENST00000599848.1	+	8	1306	c.1097G>A	c.(1096-1098)cGg>cAg	p.R366Q	UPF1_ENST00000262803.5_Missense_Mutation_p.R355Q			Q92900	RENT1_HUMAN	UPF1 regulator of nonsense transcripts homolog (yeast)	366	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						CAAGACATGCGGCTCATGCAG	0.537																																					p.R355Q		Atlas-SNP	.											.	UPF1	88	.	0			c.G1064A						PASS	.						57	53	54					19																	18964067		2203	4300	6503	SO:0001583	missense	5976	exon8			ACATGCGGCTCAT	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.1097G>A	chr19.hg19:g.18964067G>A	ENSP00000470142:p.Arg366Gln	96.0	0.0	.		93.0	48.0	.	NM_002911	O00239|O43343|Q86Z25|Q92842	Missense_Mutation	SNP	ENST00000599848.1	hg19		.	.	.	.	.	.	.	.	.	.	G	21.8	4.199893	0.79015	.	.	ENSG00000005007	ENST00000262803	D	0.90563	-2.69	4.69	3.65	0.41850	.	0.000000	0.85682	D	0.000000	D	0.88584	0.6476	M	0.75615	2.305	0.80722	D	1	P;P	0.51791	0.913;0.948	B;B	0.38880	0.148;0.284	D	0.88849	0.3318	10	0.87932	D	0	-29.4704	12.3484	0.55134	0.0834:0.0:0.9166:0.0	.	366;355	Q92900;Q92900-2	RENT1_HUMAN;.	Q	355	ENSP00000262803:R355Q	ENSP00000262803:R355Q	R	+	2	0	UPF1	18825067	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.374000	0.97172	1.113000	0.41760	0.609000	0.83330	CGG	.	.	.	none		0.537	UPF1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464684.1	NM_002911		A	18964067	G	A	18964067	3	1	256	1	0	0	0	0	1	0	0	0	17015	1116	39	1	1094	1	UPF1	19	18964067	Missense_Mutation	SNP	G	TCGA-UZ-A9PJ-01A-11D-A382-10	10309922	18964067	40164916	51	15963											
EXOSC5	56915	hgsc.bcm.edu	37	chr19	41898792	41898792	+	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	caggcagcccaatcttcggcCtcaggatcacttcgagtgtg	8	9	11	13	2	3	0	2	0	1	0	5	2	3	1	2	3	1	1	2	3	1	2	rs370634546		TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr19:41898792C>A	ENST00000221233.4	-	2	392	c.242G>T	c.(241-243)aGg>aTg	p.R81M	CTC-435M10.3_ENST00000604424.1_Intron|CTC-435M10.3_ENST00000540732.1_Intron|EXOSC5_ENST00000596905.1_Intron|BCKDHA_ENST00000595085.1_Intron	NM_020158.3	NP_064543.3	Q9NQT4	EXOS5_HUMAN	exosome component 5	81					defense response to virus (GO:0051607)|DNA deamination (GO:0045006)|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)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|transcriptionally active chromatin (GO:0035327)	3'-5'-exoribonuclease activity (GO:0000175)|RNA binding (GO:0003723)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|urinary_tract(1)	7						AATCTTCGGCCTCAGGATCAC	0.592																																					p.R81M		Atlas-SNP	.											.	EXOSC5	18	.	0			c.G242T						PASS	.						92	67	75					19																	41898792		2203	4300	6503	SO:0001583	missense	56915	exon2			TTCGGCCTCAGGA	AF285785	CCDS12580.1	19q13.1	2008-02-05				ENSG00000077348			24662	protein-coding gene	gene with protein product	"exosome component Rrp46"	606492				11110791, 11812149	Standard	NM_020158		Approved	hRrp46p, Rrp46p, RRP46, RRP41B, MGC12901, p12B	uc002oqo.3	Q9NQT4		ENST00000221233.4:c.242G>T	chr19.hg19:g.41898792C>A	ENSP00000221233:p.Arg81Met	83.0	0.0	.		65.0	5.0	.	NM_020158	Q32Q81|Q8NG16|Q96I89	Missense_Mutation	SNP	ENST00000221233.4	hg19	CCDS12580.1	.	.	.	.	.	.	.	.	.	.	C	18.67	3.674170	0.67928	.	.	ENSG00000077348	ENST00000221233	T	0.64438	-0.1	4.95	3.87	0.44632	Ribosomal protein S5 domain 2-type fold (1);Exoribonuclease, phosphorolytic domain 1 (1);	0.115804	0.64402	D	0.000009	T	0.77980	0.4212	M	0.86953	2.85	0.54753	D	0.999988	D	0.65815	0.995	P	0.61722	0.893	T	0.81949	-0.0699	10	0.87932	D	0	-37.0339	12.3853	0.55328	0.0:0.9039:0.0:0.0961	.	81	Q9NQT4	EXOS5_HUMAN	M	81	ENSP00000221233:R81M	ENSP00000221233:R81M	R	-	2	0	EXOSC5	46590632	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.008000	0.40893	2.568000	0.86640	0.555000	0.69702	AGG	.	.	.	alt		0.592	EXOSC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463492.1	NM_020158		A	41898792	C	A	41898792	3	1	256	1	0	0	0	0	1	0	0	0	5320	681	24	4	485	4	EXOSC5	19	41898792	Missense_Mutation	SNP	C	TCGA-UZ-A9PJ-01A-11D-A382-10	22934725	41898792	17230191	52	15964											
NLRP13	126204	hgsc.bcm.edu	37	chr19	56423298	56423298	+	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	aatgtgaaattggagagaggCactttcagccttacctaact	13	11	9	8	0	1	2	1	1	0	1	1	4	1	3	2	2	3	1	2	2	4	4			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr19:56423298C>T	ENST00000342929.3	-	5	1884	c.1885G>A	c.(1885-1887)Gcc>Acc	p.A629T	NLRP13_ENST00000588751.1_Missense_Mutation_p.A629T	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	629							ATP binding (GO:0005524)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		TGGAGAGAGGCACTTTCAGCC	0.418																																					p.A629T		Atlas-SNP	.											.	NLRP13	220	.	0			c.G1885A						PASS	.						101	94	96					19																	56423298		2203	4300	6503	SO:0001583	missense	126204	exon5			GAGAGGCACTTTC	AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"Nucleotide-binding domain and leucine rich repeat containing"	22937	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"	609660	"NACHT, leucine rich repeat and PYD containing 13"	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.1885G>A	chr19.hg19:g.56423298C>T	ENSP00000343891:p.Ala629Thr	143.0	0.0	.		182.0	100.0	.	NM_176810	Q7RTR5	Missense_Mutation	SNP	ENST00000342929.3	hg19	CCDS33119.1	.	.	.	.	.	.	.	.	.	.	C	8.248	0.808302	0.16467	.	.	ENSG00000173572	ENST00000342929	D	0.88046	-2.33	2.37	2.37	0.29283	.	.	.	.	.	T	0.72179	0.3428	N	0.14661	0.345	0.09310	N	1	B	0.33739	0.422	B	0.30251	0.113	T	0.58853	-0.7563	9	0.14656	T	0.56	.	8.7605	0.34672	0.0:1.0:0.0:0.0	.	629	Q86W25	NAL13_HUMAN	T	629	ENSP00000343891:A629T	ENSP00000343891:A629T	A	-	1	0	NLRP13	61115110	0.000000	0.05858	0.001000	0.08648	0.085000	0.17905	-1.407000	0.02488	1.285000	0.44548	0.543000	0.68304	GCC	.	.	.	none		0.418	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810		T	56423298	C	T	56423298	3	4	256	1	0	0	0	0	1	0	0	0	10482	710	25	2	1272	2	NLRP13	19	56423298	Missense_Mutation	SNP	C	TCGA-UZ-A9PJ-01A-11D-A382-10	14524506	56423298	2705685	53	15965											
RIN2	54453	hgsc.bcm.edu	37	chr20	19956369	19956369	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catgacccaggtcaagaactAtttgtctcagagctcggagc	11	9	10	11	1	2	3	2	1	1	2	4	4	2	4	1	2	3	1	1	2	3	2			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr20:19956369A>G	ENST00000255006.6	+	8	1996	c.1847A>G	c.(1846-1848)tAt>tGt	p.Y616C	RIN2_ENST00000440354.2_Intron|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	567					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						GTCAAGAACTATTTGTCTCAG	0.498																																					p.Y616C		Atlas-SNP	.											.	RIN2	126	.	0			c.A1847G						PASS	.						23	25	24					20																	19956369		2068	4208	6276	SO:0001583	missense	54453	exon8			AGAACTATTTGTC	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.1847A>G	chr20.hg19:g.19956369A>G	ENSP00000255006:p.Tyr616Cys	197.0	0.0	.		172.0	79.0	.	NM_001242581	Q00425|Q5TFT8|Q9BQL3|Q9H071	Missense_Mutation	SNP	ENST00000255006.6	hg19	CCDS56182.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.970260	0.74246	.	.	ENSG00000132669	ENST00000255006	T	0.30714	1.52	5.95	5.95	0.96441	.	0.057617	0.64402	N	0.000001	T	0.54679	0.1873	M	0.69463	2.115	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.53005	-0.8499	9	.	.	.	-9.6229	16.066	0.80870	1.0:0.0:0.0:0.0	.	567	Q8WYP3	RIN2_HUMAN	C	616	ENSP00000255006:Y616C	.	Y	+	2	0	RIN2	19904369	1.000000	0.71417	0.944000	0.38274	0.882000	0.50991	9.307000	0.96226	2.277000	0.76020	0.533000	0.62120	TAT	.	.	.	none		0.498	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1			G	19956369	A	G	19956369	3	3	256	1	0	0	0	0	1	0	0	0	13385	449	16	3	1726	3	RIN2	20	19956369	Missense_Mutation	SNP	A	TCGA-UZ-A9PJ-01A-11D-A382-10		19956369	43069151	54	15966											
PCK1	5105	hgsc.bcm.edu	37	chr20	56138684	56138684	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggccgcatttcccagcgccTgcgggaagaccaacctggcc	7	5	12	17	4	0	1	0	0	0	1	1	2	1	2	6	3	3	1	6	3	2	1			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr20:56138684T>C	ENST00000319441.4	+	6	1026	c.862T>C	c.(862-864)Tgc>Cgc	p.C288R	PCK1_ENST00000535860.1_Missense_Mutation_p.C156R|PCK1_ENST00000543666.1_Intron	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	288					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			TCCCAGCGCCTGCGGGAAGAC	0.542																																					p.C288R		Atlas-SNP	.											.	PCK1	95	.	0			c.T862C						PASS	.						79	79	79					20																	56138684		2203	4300	6503	SO:0001583	missense	5105	exon6			AGCGCCTGCGGGA		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.862T>C	chr20.hg19:g.56138684T>C	ENSP00000319814:p.Cys288Arg	89.0	0.0	.		86.0	28.0	.	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Missense_Mutation	SNP	ENST00000319441.4	hg19	CCDS13460.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.450060	0.84101	.	.	ENSG00000124253	ENST00000319441;ENST00000535860	T;T	0.08546	3.08;3.08	5.27	5.27	0.74061	Phosphoenolpyruvate carboxykinase, C-terminal (1);Phosphoenolpyruvate carboxykinase, GTP-utilising, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.46795	0.1411	H	0.98542	4.26	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68853	-0.5299	10	0.87932	D	0	-25.1308	15.1956	0.73084	0.0:0.0:0.0:1.0	.	288	P35558	PCKGC_HUMAN	R	288;156	ENSP00000319814:C288R;ENSP00000444342:C156R	ENSP00000319814:C288R	C	+	1	0	PCK1	55572090	1.000000	0.71417	0.999000	0.59377	0.878000	0.50629	7.587000	0.82613	2.006000	0.58801	0.459000	0.35465	TGC	.	.	.	none		0.542	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2			C	56138684	T	C	56138684	3	2	256	1	0	0	0	0	1	0	0	0	11588	1580	55	3	880	3	PCK1	20	56138684	Missense_Mutation	SNP	T	TCGA-UZ-A9PJ-01A-11D-A382-10	36182315	56138684	6886836	55	15967											
SON	6651	hgsc.bcm.edu	37	chr21	34927348	34927348	+	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	agtcatactccaagtcgtcgAcgaaggtctagatctgtggg	10	10	12	9	3	3	1	1	0	2	1	6	3	4	1	1	2	1	0	1	2	4	2			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr21:34927348A>T	ENST00000356577.4	+	3	6286	c.5811A>T	c.(5809-5811)cgA>cgT	p.R1937R	SON_ENST00000381692.2_Intron|SON_ENST00000300278.4_Silent_p.R1937R|SON_ENST00000290239.6_Silent_p.R1937R|SON_ENST00000381679.4_Silent_p.R1937R	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	1937	2 X 19 AA repeats of P-S-R-R-R-R-S-R-S-V- V-R-R-R-S-F-S-I-S.|7 X 7 AA repeats of P-S-R-R-S-R-[TS].				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						CAAGTCGTCGACGAAGGTCTA	0.577																																					p.R1937R		Atlas-SNP	.											.	SON	343	.	0			c.A5811T						PASS	.						30	30	30					21																	34927348		2184	4275	6459	SO:0001819	synonymous_variant	6651	exon3			TCGTCGACGAAGG	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.5811A>T	chr21.hg19:g.34927348A>T		44.0	0.0	.		55.0	27.0	.	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Silent	SNP	ENST00000356577.4	hg19	CCDS13629.1	.	.	.	.	.	.	.	.	.	.	A	4.663	0.123277	0.08931	.	.	ENSG00000159140	ENST00000436227	.	.	.	5.53	-3.72	0.04411	.	.	.	.	.	T	0.42877	0.1222	.	.	.	0.25553	N	0.987064	.	.	.	.	.	.	T	0.43940	-0.9360	4	.	.	.	.	14.7121	0.69241	0.4215:0.0:0.5785:0.0	.	.	.	.	V	932	.	.	D	+	2	0	SON	33849218	0.000000	0.05858	0.201000	0.23476	0.946000	0.59487	-0.249000	0.08842	-0.726000	0.04895	-0.256000	0.11100	GAC	.	.	.	none		0.577	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		T	34927348	A	T	34927348	2	4	256	1	0	0	0	0	0	0	0	1	14939	262	10	5		5	SON	21	34927348	Silent	SNP	A	TCGA-UZ-A9PJ-01A-11D-A382-10		34927348	13202547	56	15968											
MORC3	23515	hgsc.bcm.edu	37	chr21	37747537	37747537	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtgaattacgatgttgatgtAgttgatgagattttaggaca	12	15	12	2	1	0	4	0	4	0	1	0	7	0	5	0	1	1	3	0	1	4	6			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr21:37747537A>G	ENST00000400485.1	+	17	2839	c.2763A>G	c.(2761-2763)gtA>gtG	p.V921V	MORC3_ENST00000487909.1_3'UTR	NM_015358.2	NP_056173.1	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	921					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						ATGTTGATGTAGTTGATGAGA	0.363																																					p.V921V		Atlas-SNP	.											.	MORC3	78	.	0			c.A2763G						PASS	.						163	151	155					21																	37747537		1916	4124	6040	SO:0001819	synonymous_variant	23515	exon17			TGATGTAGTTGAT	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.2763A>G	chr21.hg19:g.37747537A>G		52.0	0.0	.		73.0	35.0	.	NM_015358	A8KA92|Q9UEZ2	Silent	SNP	ENST00000400485.1	hg19	CCDS42924.1																																																																																			.	.	.	none		0.363	MORC3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000194640.1	NM_015358		G	37747537	A	G	37747537	2	3	256	1	0	0	0	0	0	0	0	1	9710	407	15	3		3	MORC3	21	37747537	Silent	SNP	A	TCGA-UZ-A9PJ-01A-11D-A382-10	2820189	37747537	10382358	57	15969											
C21orf2	755	hgsc.bcm.edu	37	chr21	45751780	45751780	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtctcagcagcggagctgAgggagctcagtgtgcagcat	9	7	15	10	1	2	1	2	1	1	0	3	3	2	3	0	2	6	5	0	2	0	0			TCGA-UZ-A9PJ-01A-11D-A382-10	TCGA-UZ-A9PJ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	beb8581d-8471-4411-9521-4bf057f7d14a	b67bfe0e-ad19-4c1c-a9f3-cee65c1fee86	g.chr21:45751780A>G	ENST00000339818.4	-	5	698	c.491T>C	c.(490-492)cTc>cCc	p.L164P	C21orf2_ENST00000397956.3_Missense_Mutation_p.L164P|C21orf2_ENST00000496321.1_5'UTR|AP001062.7_ENST00000448927.1_RNA|C21orf2_ENST00000325223.7_Missense_Mutation_p.L164P|AP001062.8_ENST00000422357.1_RNA	NM_001271440.1|NM_004928.2	NP_001258369.1|NP_004919.1	O43822	CU002_HUMAN	chromosome 21 open reading frame 2	164					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)		AGCGGAGCTGAGGGAGCTCAG	0.687																																					p.L164P		Atlas-SNP	.											.	C21orf2	10	.	0			c.T491C						PASS	.						50	42	45					21																	45751780		2202	4300	6502	SO:0001583	missense	755	exon5			GAGCTGAGGGAGC	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.491T>C	chr21.hg19:g.45751780A>G	ENSP00000344566:p.Leu164Pro	57.0	0.0	.		55.0	22.0	.	NM_004928	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Missense_Mutation	SNP	ENST00000339818.4	hg19	CCDS13709.1	.	.	.	.	.	.	.	.	.	.	A	12.36	1.915165	0.33815	.	.	ENSG00000160226	ENST00000339818;ENST00000380160;ENST00000397956;ENST00000325223	T;T;T	0.36520	1.64;1.25;1.59	4.72	-0.634	0.11516	.	1.444430	0.03680	N	0.245363	T	0.25938	0.0632	N	0.22421	0.69	0.09310	N	1	P;D;P;P	0.56035	0.744;0.974;0.627;0.744	B;P;B;B	0.46208	0.341;0.507;0.184;0.341	T	0.11717	-1.0576	10	0.27082	T	0.32	-4.2235	2.5485	0.04742	0.4003:0.0:0.2579:0.3418	.	164;164;164;123	G5E952;Q8N5X6;O43822;O43822-2	.;.;CU002_HUMAN;.	P	164;200;164;164	ENSP00000344566:L164P;ENSP00000381047:L164P;ENSP00000317302:L164P	ENSP00000317302:L164P	L	-	2	0	C21orf2	44576208	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	0.486000	0.22340	-0.044000	0.13491	0.533000	0.62120	CTC	.	.	.	none		0.687	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928		G	45751780	A	G	45751780	3	3	256	1	0	0	0	0	1	0	0	0	2125	304	11	3	291	3	C21orf2	21	45751780	Missense_Mutation	SNP	A	TCGA-UZ-A9PJ-01A-11D-A382-10	8004243	45751780	2378115	58	15970											
TNNI3K	100526835	hgsc.bcm.edu	37	chr1	74905231	74905231	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcactcggtacaccatcaaaGcagatgtcttcagctatgct	11	10	8	12	1	3	1	2	0	1	1	4	1	3	1	1	1	4	5	1	1	3	3			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr1:74905231G>A	ENST00000370899.3	+	22	2276	c.2239G>A	c.(2239-2241)Gca>Aca	p.A747T	TNNI3K_ENST00000326637.3_Missense_Mutation_p.A646T|TNNI3K_ENST00000370891.2_Missense_Mutation_p.A747T|FPGT-TNNI3K_ENST00000557284.2_Missense_Mutation_p.A760T	NM_001199327.1	NP_001186256			FPGT-TNNI3K readthrough																		CACCATCAAAGCAGATGTCTT	0.473																																					p.A747T		Atlas-SNP	.											.	.	.	.	0			c.G2239A						PASS	.						161	134	143					1																	74905231		2203	4300	6503	SO:0001583	missense	100526835	exon22			ATCAAAGCAGATG			1p31.3	2014-03-14			ENSG00000259030	ENSG00000259030			42952	other	readthrough							Standard	NM_001112808		Approved		uc001dge.2		OTTHUMG00000166281	ENST00000370899.3:c.2239G>A	chr1.hg19:g.74905231G>A	ENSP00000359936:p.Ala747Thr	92.0	0.0	.		95.0	36.0	.	NM_001199327		Missense_Mutation	SNP	ENST00000370899.3	hg19		.	.	.	.	.	.	.	.	.	.	G	29.3	4.992671	0.93167	.	.	ENSG00000259030;ENSG00000259030;ENSG00000116783;ENSG00000116783	ENST00000370899;ENST00000557284;ENST00000370891;ENST00000326637	D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66	5.96	5.96	0.96718	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.87565	0.6209	L	0.46157	1.445	0.80722	D	1	D;D;D	0.71674	0.998;0.997;0.997	D;D;D	0.69824	0.966;0.942;0.942	D	0.87440	0.2394	10	0.72032	D	0.01	.	20.4144	0.99026	0.0:0.0:1.0:0.0	.	646;747;747	Q59H18;Q59H18-1;Q59H18-4	TNI3K_HUMAN;.;.	T	747;747;747;646	ENSP00000359936:A747T;ENSP00000450895:A747T;ENSP00000359928:A747T;ENSP00000322251:A646T	ENSP00000322251:A646T	A	+	1	0	RP11-653A5.2;AC093158.1	74677819	1.000000	0.71417	0.996000	0.52242	0.484000	0.33280	7.443000	0.80521	2.833000	0.97629	0.555000	0.69702	GCA	.	.	.	none		0.473	FPGT-TNNI3K-003	NOVEL	basic|appris_candidate|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000026438.3			A	74905231	G	A	74905231	3	1	257	1	0	0	0	0	1	0	0	0	16341	971	34	2	2369	2	TNNI3K	1	74905231	Missense_Mutation	SNP	G	TCGA-UZ-A9PK-01A-11D-A382-10		74905231	174345390	1	15971											
DR1	1810	hgsc.bcm.edu	37	chr1	93812241	93812241	+	Frame_Shift_Del	DEL	C	C	-																															aacgatgatgatctcactatCcccagagctgctatcaataa																										TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr1:93812241delC	ENST00000370272.4	+	1	797	c.39delC	c.(37-39)atcfs	p.I13fs	RP4-717I23.3_ENST00000413606.1_RNA|DR1_ENST00000370267.1_Frame_Shift_Del_p.I13fs|RP4-717I23.3_ENST00000451302.2_RNA	NM_001938.2	NP_001929.1	Q01658	NC2B_HUMAN	down-regulator of transcription 1, TBP-binding (negative cofactor 2)	13					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)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			endometrium(3)|large_intestine(1)	4		all_lung(203;0.00252)|Lung NSC(277;0.011)|Melanoma(281;0.155)		all cancers(265;0.0032)|GBM - Glioblastoma multiforme(16;0.0165)|Epithelial(280;0.0977)		ATCTCACTATCCCCAGAGCTG	0.507																																					p.I13fs		Pindel	.											.	DR1	10	.	0			c.38delT						PASS	.						87	89	88					1																	93812241		2203	4300	6503	SO:0001589	frameshift_variant	1810	exon1			.	M97388	CCDS744.1	1p22.1	2008-02-05			ENSG00000117505	ENSG00000117505			3017	protein-coding gene	gene with protein product		601482				1339312, 9040789	Standard	NM_001938		Approved	NC2, NC2-BETA	uc001dpu.3	Q01658	OTTHUMG00000010862	ENST00000370272.4:c.39delC	chr1.hg19:g.93812241delC	ENSP00000359295:p.Ile13fs	137.0	0.0	.		110.0	30.0	0.273	NM_001938		Frame_Shift_Del	DEL	ENST00000370272.4	hg19	CCDS744.1																																																																																			.	.	.	none		0.507	DR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029976.2	NM_001938		-	93812241	C	-	93812241	7	5	257	1	0	1	0	1	0	0	0	0	4754	845	30	0	41	0	DR1	1	93812241	Frame_Shift_Del	DEL	C	TCGA-UZ-A9PK-01A-11D-A382-10	18907010	93812241	155438380	2	15972											
HIST2H2BE	8349	hgsc.bcm.edu	37	chr1	149858172	149858172	+	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	ctttttaggggccggagcggAttttgccggttcaggcatgg	5	12	16	8	3	1	0	1	0	0	0	1	2	1	2	2	7	2	2	2	7	1	6			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr1:149858172A>T	ENST00000369155.2	-	1	60	c.19T>A	c.(19-21)Tcc>Acc	p.S7T	BOLA1_ENST00000369153.2_5'Flank|HIST2H2AC_ENST00000331380.2_5'Flank	NM_003528.2	NP_003519.1	Q16778	H2B2E_HUMAN	histone cluster 2, H2be	7					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)			GCCGGAGCGGATTTTGCCGGT	0.512																																					p.S7T		Atlas-SNP	.											.	HIST2H2BE	33	.	0			c.T19A						PASS	.						62	63	63					1																	149858172		2203	4300	6503	SO:0001583	missense	8349	exon1			GAGCGGATTTTGC	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.19T>A	chr1.hg19:g.149858172A>T	ENSP00000358151:p.Ser7Thr	159.0	0.0	.		154.0	58.0	.	NM_003528	A3KMC7|A8K110|Q4KMY1|Q5QNX0|Q9UE88	Missense_Mutation	SNP	ENST00000369155.2	hg19	CCDS936.1	.	.	.	.	.	.	.	.	.	.	A	15.64	2.893516	0.52121	.	.	ENSG00000184678	ENST00000369155	T	0.17691	2.26	5.99	5.99	0.97316	Histone-fold (2);	0.000000	0.85682	D	0.000000	T	0.11793	0.0287	M	0.69823	2.125	0.26659	N	0.971944	B	0.02656	0.0	B	0.01281	0.0	T	0.04115	-1.0976	10	0.56958	D	0.05	.	15.377	0.74615	1.0:0.0:0.0:0.0	.	7	Q16778	H2B2E_HUMAN	T	7	ENSP00000358151:S7T	ENSP00000358151:S7T	S	-	1	0	HIST2H2BE	148124796	0.951000	0.32395	0.984000	0.44739	0.961000	0.63080	3.076000	0.50081	2.305000	0.77605	0.529000	0.55759	TCC	.	.	.	none		0.512	HIST2H2BE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033455.1	NM_003528		T	149858172	A	T	149858172	3	4	257	1	0	0	0	0	1	0	0	0	7186	333	12	5	365	5	HIST2H2BE	1	149858172	Missense_Mutation	SNP	A	TCGA-UZ-A9PK-01A-11D-A382-10	56045931	149858172	99392449	3	15973											
ECM1	1893	hgsc.bcm.edu	37	chr1	150482014	150482014	+	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	ttcttccctccaggcttcacGgctacaggacagaggcagct	8	9	10	14	1	2	1	1	0	1	1	4	2	4	2	2	4	2	4	2	4	1	4	rs200429908		TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr1:150482014G>T	ENST00000369047.4	+	2	203	c.78G>T	c.(76-78)acG>acT	p.T26T	ECM1_ENST00000369049.4_Silent_p.T26T|ECM1_ENST00000346569.6_Silent_p.T26T|ECM1_ENST00000470432.1_3'UTR	NM_004425.3	NP_004416.2	Q16610	ECM1_HUMAN	extracellular matrix protein 1	26					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)			CAGGCTTCACGGCTACAGGAC	0.597																																					p.T26T	Melanoma(156;1696 2560 11093 19685)	Atlas-SNP	.											.	ECM1	96	.	0			c.G78T						PASS	.						73	70	71					1																	150482014		2203	4300	6503	SO:0001819	synonymous_variant	1893	exon2			CTTCACGGCTACA	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.78G>T	chr1.hg19:g.150482014G>T		83.0	0.0	.		97.0	36.0	.	NM_022664	A8K8S0|B4DW49|B4DY60|O43266|Q5T5G4|Q5T5G5|Q5T5G6|Q8IZ60	Silent	SNP	ENST00000369047.4	hg19	CCDS953.1																																																																																			.	G|0.999;A|0.001	.	alt		0.597	ECM1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035832.2	NM_004425		T	150482014	G	T	150482014	2	4	257	1	0	0	0	0	0	0	0	1	4899	1103	39	4		4	ECM1	1	150482014	Silent	SNP	G	TCGA-UZ-A9PK-01A-11D-A382-10	623842	150482014	98768607	4	15974											
EFNA1	1942	hgsc.bcm.edu	37	chr1	155104053	155104053	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtctgagaagttccagcgcTtcacacctttcaccctgggc	7	11	9	14	1	3	1	2	1	1	1	4	2	4	1	3	1	1	2	3	1	1	3			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr1:155104053T>C	ENST00000368407.3	+	2	849	c.331T>C	c.(331-333)Ttc>Ctc	p.F111L	EFNA1_ENST00000469878.1_3'UTR|EFNA1_ENST00000368406.2_Missense_Mutation_p.F111L	NM_004428.2	NP_004419.2	P20827	EFNA1_HUMAN	ephrin-A1	111	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|aortic valve morphogenesis (GO:0003180)|axon guidance (GO:0007411)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|endocardial cushion to mesenchymal transition involved in heart valve formation (GO:0003199)|ephrin receptor signaling pathway (GO:0048013)|mitral valve morphogenesis (GO:0003183)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|notochord formation (GO:0014028)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of angiogenesis (GO:0045765)|regulation of axonogenesis (GO:0050770)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|substrate adhesion-dependent cell spreading (GO:0034446)	anchored component of plasma membrane (GO:0046658)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ephrin receptor binding (GO:0046875)|receptor binding (GO:0005102)			breast(1)|endometrium(1)|kidney(1)|lung(1)|skin(1)	5	all_epithelial(22;4.71e-30)|all_lung(78;3.15e-27)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;2.28e-10)|all cancers(21;6.16e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000395)|LUSC - Lung squamous cell carcinoma(543;0.193)			GTTCCAGCGCTTCACACCTTT	0.567																																					p.F111L		Atlas-SNP	.											.	EFNA1	10	.	0			c.T331C						PASS	.						53	47	49					1																	155104053		2203	4300	6503	SO:0001583	missense	1942	exon2			CAGCGCTTCACAC		CCDS1091.1, CCDS1092.1	1q21-q22	2011-03-09			ENSG00000169242	ENSG00000169242		"Ephrins"	3221	protein-coding gene	gene with protein product		191164		TNFAIP4, EPLG1		2233719, 8660976	Standard	NM_182685		Approved	LERK1, ECKLG	uc001fhh.3	P20827	OTTHUMG00000035312	ENST00000368407.3:c.331T>C	chr1.hg19:g.155104053T>C	ENSP00000357392:p.Phe111Leu	253.0	0.0	.		249.0	84.0	.	NM_182685	D3DV86|Q5SR60|Q5SR61|Q6I9T9|Q8N578	Missense_Mutation	SNP	ENST00000368407.3	hg19	CCDS1091.1	.	.	.	.	.	.	.	.	.	.	T	33	5.231564	0.95207	.	.	ENSG00000169242	ENST00000368407;ENST00000368406	D;D	0.94280	-3.39;-3.39	5.22	5.22	0.72569	Ephrin, conserved site (1);Cupredoxin (2);	0.000000	0.85682	D	0.000000	D	0.96009	0.8700	M	0.83012	2.62	0.58432	D	0.999993	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.96161	0.9115	10	0.54805	T	0.06	-1.3233	13.3345	0.60509	0.0:0.0:0.0:1.0	.	111;111	P20827-2;P20827	.;EFNA1_HUMAN	L	111	ENSP00000357392:F111L;ENSP00000357391:F111L	ENSP00000357391:F111L	F	+	1	0	EFNA1	153370677	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.616000	0.83018	2.097000	0.63578	0.533000	0.62120	TTC	.	.	.	none		0.567	EFNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085428.1	NM_004428		C	155104053	T	C	155104053	3	2	257	1	0	0	0	0	1	0	0	0	4952	1609	56	3	337	3	EFNA1	1	155104053	Missense_Mutation	SNP	T	TCGA-UZ-A9PK-01A-11D-A382-10	4622039	155104053	94146568	5	15975											
GMCL1	64395	hgsc.bcm.edu	37	chr2	70074701	70074701	+	Missense_Mutation	SNP	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	tgtcatgaaacagctcattgGttcatctaacttatttgtga	11	16	7	7	0	4	2	3	2	1	0	4	2	4	2	0	1	3	2	0	1	3	5			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr2:70074701G>A	ENST00000282570.3	+	7	1036	c.785G>A	c.(784-786)gGt>gAt	p.G262D		NM_178439.3	NP_848526.1	Q96IK5	GMCL1_HUMAN	germ cell-less, spermatogenesis associated 1	262					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)	nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)				endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	15						CAGCTCATTGGTTCATCTAAC	0.358																																					p.G262D		Atlas-SNP	.											.	GMCL1	50	.	0			c.G785A						PASS	.						172	183	179					2																	70074701		2203	4299	6502	SO:0001583	missense	64395	exon7			TCATTGGTTCATC	AK023119	CCDS1895.1	2p13.3	2013-01-09	2012-08-20		ENSG00000087338	ENSG00000087338		"BTB/POZ domain containing"	23843	protein-coding gene	gene with protein product	"spermatogenesis associated 29"		"germ cell-less homolog 1 (Drosophila)"				Standard	NM_178439		Approved	FLJ13057, BTBD13, GCL1, SPATA29	uc002sfu.3	Q96IK5	OTTHUMG00000129643	ENST00000282570.3:c.785G>A	chr2.hg19:g.70074701G>A	ENSP00000282570:p.Gly262Asp	88.0	0.0	.		98.0	50.0	.	NM_178439	Q9H826|Q9H8V7|Q9H927	Missense_Mutation	SNP	ENST00000282570.3	hg19	CCDS1895.1	.	.	.	.	.	.	.	.	.	.	G	8.869	0.948779	0.18356	.	.	ENSG00000087338	ENST00000282570	T	0.68331	-0.32	4.84	4.84	0.62591	BTB/Kelch-associated (2);	0.416817	0.27936	N	0.017242	T	0.47563	0.1452	N	0.14661	0.345	0.31480	N	0.667243	B	0.06786	0.001	B	0.12837	0.008	T	0.49234	-0.8961	10	0.29301	T	0.29	-2.464	11.2063	0.48771	0.0:0.1853:0.8147:0.0	.	262	Q96IK5	GMCL1_HUMAN	D	262	ENSP00000282570:G262D	ENSP00000282570:G262D	G	+	2	0	GMCL1	69928205	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.322000	0.59215	2.509000	0.84616	0.650000	0.86243	GGT	.	.	.	none		0.358	GMCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251841.2	NM_178439		A	70074701	G	A	70074701	3	1	257	1	0	0	0	0	1	0	0	0	6492	1261	44	2	811	2	GMCL1	2	70074701	Missense_Mutation	SNP	G	TCGA-UZ-A9PK-01A-11D-A382-10		70074701	173124672	6	15976											
PTCD3	55037	hgsc.bcm.edu	37	chr2	86352186	86352186	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaacattcctattgcacaaTgatccgaggaatggtgaagg	13	10	11	7	1	0	3	0	3	0	0	2	5	2	4	2	3	2	1	2	3	5	3			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr2:86352186T>C	ENST00000254630.7	+	10	851	c.785T>C	c.(784-786)aTg>aCg	p.M262T	PTCD3_ENST00000409277.3_3'UTR	NM_017952.5	NP_060422.4	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3	262					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						TATTGCACAATGATCCGAGGA	0.388																																					p.M262T		Atlas-SNP	.											.	PTCD3	51	.	0			c.T785C						PASS	.						94	89	91					2																	86352186		2203	4300	6503	SO:0001583	missense	55037	exon10			GCACAATGATCCG		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.785T>C	chr2.hg19:g.86352186T>C	ENSP00000254630:p.Met262Thr	88.0	0.0	.		109.0	36.0	.	NM_017952	A6NHD2|D6W5M1|Q597H0|Q658Y9|Q9BUZ8|Q9NWL0	Missense_Mutation	SNP	ENST00000254630.7	hg19	CCDS33235.1	.	.	.	.	.	.	.	.	.	.	T	19.09	3.758936	0.69763	.	.	ENSG00000132300	ENST00000254630	T	0.27104	1.69	5.63	5.63	0.86233	.	0.189515	0.56097	D	0.000027	T	0.53449	0.1797	M	0.92459	3.31	0.80722	D	1	P	0.45634	0.863	P	0.52514	0.701	T	0.65269	-0.6209	10	0.87932	D	0	-13.1111	14.8254	0.70107	0.0:0.0:0.0:1.0	.	262	Q96EY7	PTCD3_HUMAN	T	262	ENSP00000254630:M262T	ENSP00000254630:M262T	M	+	2	0	PTCD3	86205697	1.000000	0.71417	0.962000	0.40283	0.976000	0.68499	6.686000	0.74548	2.145000	0.66743	0.533000	0.62120	ATG	.	.	.	none		0.388	PTCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329854.1	NM_017952		C	86352186	T	C	86352186	3	2	257	1	0	0	0	0	1	0	0	0	12739	1464	51	3	823	3	PTCD3	2	86352186	Missense_Mutation	SNP	T	TCGA-UZ-A9PK-01A-11D-A382-10	16277485	86352186	156847187	7	15977											
MPP4	58538	hgsc.bcm.edu	37	chr2	202514863	202514863	+	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	tactcacgcccattcatttcGtaactctttttagtacgagt	9	16	5	11	3	3	0	2	0	1	0	4	1	3	0	1	0	3	2	1	0	4	8	rs376163949		TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr2:202514863G>T	ENST00000409474.3	-	19	1614	c.1407C>A	c.(1405-1407)taC>taA	p.Y469*	MPP4_ENST00000428900.2_Nonsense_Mutation_p.Y445*|MPP4_ENST00000315506.7_Nonsense_Mutation_p.Y425*|MPP4_ENST00000447335.2_Nonsense_Mutation_p.Y462*|MPP4_ENST00000396886.3_Nonsense_Mutation_p.Y394*|MPP4_ENST00000409143.1_Nonsense_Mutation_p.Y411*|MPP4_ENST00000359962.5_Nonsense_Mutation_p.Y469*	NM_033066.2	NP_149055	Q96JB8	MPP4_HUMAN	membrane protein, palmitoylated 4 (MAGUK p55 subfamily member 4)	469	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				protein localization to synapse (GO:0035418)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|presynaptic membrane (GO:0042734)		p.Y469Y(1)		kidney(1)|lung(11)	12						CATTCATTTCGTAACTCTTTT	0.353																																					p.Y469X		Atlas-SNP	.											MPP4_ENST00000409474,NS,carcinoma,0,1	MPP4	93	.	1	Substitution - coding silent(1)	breast(1)	c.C1407A						PASS	.						104	90	95					2																	202514863		1844	4088	5932	SO:0001587	stop_gained	58538	exon19			CATTTCGTAACTC	AF316032	CCDS46491.1	2q33.2	2008-05-15			ENSG00000082126	ENSG00000082126			13680	protein-coding gene	gene with protein product		606575		DLG6		11414766	Standard	NM_033066		Approved		uc002uyk.4	Q96JB8	OTTHUMG00000154525	ENST00000409474.3:c.1407C>A	chr2.hg19:g.202514863G>T	ENSP00000387278:p.Tyr469*	94.0	0.0	.		104.0	6.0	.	NM_033066	C9IZK4|Q53TT3|Q6ZNH6|Q96Q43|Q96Q44	Nonsense_Mutation	SNP	ENST00000409474.3	hg19	CCDS46491.1	.	.	.	.	.	.	.	.	.	.	A	38	6.664329	0.97747	.	.	ENSG00000082126	ENST00000409474;ENST00000315506;ENST00000396886;ENST00000359962;ENST00000315549;ENST00000374605;ENST00000428900;ENST00000409143;ENST00000447335	.	.	.	5.51	5.51	0.81932	.	0.371594	0.28859	N	0.013908	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.6368	0.51209	0.9312:0.0:0.0688:0.0	.	.	.	.	X	469;425;394;469;434;398;445;411;462	.	ENSP00000319363:Y425X	Y	-	3	2	MPP4	202223108	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	1.191000	0.32138	1.113000	0.41760	-0.361000	0.07541	TAC	.	.	.	alt		0.353	MPP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335748.2			T	202514863	G	T	202514863	4	4	257	1	0	0	0	0	0	1	0	0	9743	1140	40	4	522	4	MPP4	2	202514863	Nonsense_Mutation	SNP	G	TCGA-UZ-A9PK-01A-11D-A382-10	116162677	202514863	40684510	8	15978											
LRRFIP2	9209	hgsc.bcm.edu	37	chr3	37107344	37107344	+	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	tccaagacctgagcagcttcCtgagacacaacagtgatggc	12	7	10	12	0	0	4	0	3	0	2	2	5	2	4	3	1	3	2	3	1	2	1			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr3:37107344C>A	ENST00000336686.4	-	23	1736	c.1656G>T	c.(1654-1656)caG>caT	p.Q552H	MLH1_ENST00000536378.1_3'UTR|LRRFIP2_ENST00000440230.1_Missense_Mutation_p.Q255H|LRRFIP2_ENST00000421276.2_Missense_Mutation_p.Q255H|LRRFIP2_ENST00000396428.2_Missense_Mutation_p.Q334H|LRRFIP2_ENST00000354379.4_Missense_Mutation_p.Q231H|LRRFIP2_ENST00000421307.1_Missense_Mutation_p.Q552H			Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting protein 2	552					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						GAGCAGCTTCCTGAGACACAA	0.493																																					p.Q552H		Atlas-SNP	.											.	LRRFIP2	71	.	1	Whole gene deletion(1)	ovary(1)	c.G1656T						PASS	.						99	98	99					3																	37107344		2203	4300	6503	SO:0001583	missense	9209	exon24			AGCTTCCTGAGAC	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.1656G>T	chr3.hg19:g.37107344C>A	ENSP00000338727:p.Gln552His	134.0	0.0	.		164.0	75.0	.	NM_006309	A8K649|A8MXR0|B4DY63|Q68CV3|Q9NXH5	Missense_Mutation	SNP	ENST00000336686.4	hg19	CCDS2664.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.92|19.92	3.915615|3.915615	0.73098|0.73098	.|.	.|.	ENSG00000093167|ENSG00000093167	ENST00000440742|ENST00000421307;ENST00000354379;ENST00000336686;ENST00000421276;ENST00000396428;ENST00000440230	.|T;T;T;T;T;T	.|0.44881	.|0.91;0.91;0.91;0.91;0.91;0.91	6.17|6.17	5.3|5.3	0.74995|0.74995	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.62732	.|0.2452	M|M	0.76328|0.76328	2.33|2.33	0.58432|0.58432	D|D	0.999997|0.999997	.|D;D;D;D	.|0.71674	.|0.995;0.996;0.994;0.998	.|D;D;D;D	.|0.85130	.|0.978;0.93;0.964;0.997	.|T	.|0.66256	.|-0.5969	.|10	.|0.66056	.|D	.|0.02	-6.844|-6.844	11.0179|11.0179	0.47701|0.47701	0.0:0.8037:0.13:0.0663|0.0:0.8037:0.13:0.0663	.|.	.|334;231;255;552	.|A8MXR0;Q9Y608-2;Q9Y608-4;Q9Y608	.|.;.;.;LRRF2_HUMAN	X|H	134|552;231;552;255;334;255	.|ENSP00000392217:Q552H;ENSP00000346349:Q231H;ENSP00000338727:Q552H;ENSP00000416364:Q255H;ENSP00000379705:Q334H;ENSP00000405480:Q255H	.|ENSP00000338727:Q552H	G|Q	-|-	1|3	0|2	LRRFIP2|LRRFIP2	37082348|37082348	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	1.849000|1.849000	0.39318|0.39318	1.616000|1.616000	0.50265|0.50265	0.655000|0.655000	0.94253|0.94253	GGA|CAG	.	.	.	none		0.493	LRRFIP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253335.3	NM_006309		A	37107344	C	A	37107344	3	1	257	1	0	0	0	0	1	0	0	0	9035	680	24	4	533	4	LRRFIP2	3	37107344	Missense_Mutation	SNP	C	TCGA-UZ-A9PK-01A-11D-A382-10		37107344	160915086	9	15979											
DLEC1	30	hgsc.bcm.edu	37	chr3	38163861	38163861	+	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	accctgcggctccggggccaAggctcctatgatgagagata	9	7	13	12	2	0	3	0	2	0	1	2	4	2	3	4	4	1	2	4	4	3	2			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr3:38163861A>G	ENST00000333167.8	-	0	1785				DLEC1_ENST00000346219.3_Missense_Mutation_p.K1701R|DLEC1_ENST00000452631.2_Silent_p.Q1745Q|ACAA1_ENST00000480865.1_5'Flank|DLEC1_ENST00000308059.6_Silent_p.Q1742Q|Y_RNA_ENST00000365095.1_RNA	NM_001607.3	NP_001598.1	P09110	THIK_HUMAN	acetyl-CoA acyltransferase 1						alpha-linolenic acid metabolic process (GO:0036109)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acetyl-CoA C-acyltransferase activity (GO:0003988)|palmitoyl-CoA oxidase activity (GO:0016401)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	9				KIRC - Kidney renal clear cell carcinoma(284;0.0523)|Kidney(284;0.0657)		TCCGGGGCCAAGGCTCCTATG	0.622																																					p.K1701R		Atlas-SNP	.											.	DLEC1	278	.	0			c.A5102G						PASS	.						59	64	62					3																	38163861		2019	4189	6208	SO:0001628	intergenic_variant	9940	exon36			GGGCCAAGGCTCC	X14813	CCDS2673.1, CCDS46794.1	3p22.2	2012-05-16	2010-04-30		ENSG00000060971	ENSG00000060971	2.3.1.16		82	protein-coding gene	gene with protein product	"peroxisomal 3-oxoacyl-Coenzyme A thiolase"	604054	"acetyl-Coenzyme A acyltransferase 1"				Standard	NM_001607		Approved		uc003cht.3	P09110	OTTHUMG00000131087		chr3.hg19:g.38163861A>G		127.0	0.0	.		176.0	87.0	.	NM_007337	G5E935|Q96CA6	Missense_Mutation	SNP	ENST00000333167.8	hg19	CCDS2673.1	.	.	.	.	.	.	.	.	.	.	A	19.59	3.856224	0.71834	.	.	ENSG00000008226	ENST00000346219	T	0.05786	3.39	4.86	-2.38	0.06622	.	1.890310	0.02332	N	0.074018	T	0.06188	0.0160	.	.	.	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.24764	-1.0151	9	0.87932	D	0	0.102	5.6407	0.17562	0.3921:0.2598:0.3481:0.0	.	1701	Q9Y238-3	.	R	1701	ENSP00000315914:K1701R	ENSP00000315914:K1701R	K	+	2	0	DLEC1	38138865	0.000000	0.05858	0.612000	0.29024	0.919000	0.55068	-0.264000	0.08658	-0.349000	0.08274	0.459000	0.35465	AAG	.	.	.	none		0.622	ACAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342980.1	NM_001607		G	38163861	A	G	38163861	1	3	257	0	1	0	0	0	0	0	0	0	4554	72	3	3		3	DLEC1	3	38163861	IGR	SNP	A	TCGA-UZ-A9PK-01A-11D-A382-10	1056517	38163861	159858569	10	15980											
XIRP1	165904	hgsc.bcm.edu	37	chr3	39229398	39229398	+	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	ggctgtgtctcaaacatccaCctgtagccctgcacatcacc	9	9	7	16	0	2	0	2	0	1	0	4	0	3	0	4	1	3	3	4	1	2	1			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr3:39229398C>A	ENST00000340369.3	-	2	1767	c.1539G>T	c.(1537-1539)agG>agT	p.R513S	XIRP1_ENST00000396251.1_Missense_Mutation_p.R513S|XIRP1_ENST00000421646.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	513					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)		CAAACATCCACCTGTAGCCCT	0.627																																					p.R513S		Atlas-SNP	.											.	XIRP1	173	.	0			c.G1539T						PASS	.						94	87	90					3																	39229398		2203	4300	6503	SO:0001583	missense	165904	exon2			CATCCACCTGTAG	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.1539G>T	chr3.hg19:g.39229398C>A	ENSP00000343140:p.Arg513Ser	59.0	0.0	.		107.0	29.0	.	NM_001198621	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	hg19	CCDS2683.1	.	.	.	.	.	.	.	.	.	.	C	13.62	2.290208	0.40494	.	.	ENSG00000168334	ENST00000396251;ENST00000340369	T;T	0.38401	1.14;1.14	5.17	2.37	0.29283	.	0.299854	0.34291	N	0.004084	T	0.43299	0.1241	M	0.64170	1.965	0.80722	D	1	D;P	0.58268	0.982;0.828	P;B	0.55055	0.767;0.234	T	0.31052	-0.9957	10	0.87932	D	0	.	4.8529	0.13545	0.0:0.5878:0.1562:0.2559	.	513;513	Q702N8;Q702N8-2	XIRP1_HUMAN;.	S	513	ENSP00000379550:R513S;ENSP00000343140:R513S	ENSP00000343140:R513S	R	-	3	2	XIRP1	39204402	1.000000	0.71417	0.983000	0.44433	0.949000	0.60115	1.046000	0.30354	0.283000	0.22279	0.655000	0.94253	AGG	.	.	.	none		0.627	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522		A	39229398	C	A	39229398	3	1	257	1	0	0	0	0	1	0	0	0	17441	506	18	4	3996	4	XIRP1	3	39229398	Missense_Mutation	SNP	C	TCGA-UZ-A9PK-01A-11D-A382-10	1065537	39229398	158793032	11	15981											
BAP1	8314	hgsc.bcm.edu	37	chr3	52439133	52439133	+	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	gctcccagcttacctgcatgGgggacttggcataattgtga	8	11	12	10	0	0	1	0	1	0	0	1	2	1	2	2	3	3	4	2	3	2	4			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr3:52439133G>T	ENST00000460680.1	-	11	1580	c.1109C>A	c.(1108-1110)cCc>cAc	p.P370H	BAP1_ENST00000296288.5_Missense_Mutation_p.P352H	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		TACCTGCATGGGGGACTTGGC	0.542			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.P370H	GBM(101;493 1458 7992 21037 25532)	Atlas-SNP	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	0			c.C1109A						PASS	.						85	95	92					3																	52439133		2203	4300	6503	SO:0001583	missense	8314	exon11			TGCATGGGGGACT	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1109C>A	chr3.hg19:g.52439133G>T	ENSP00000417132:p.Pro370His	119.0	0.0	.		152.0	39.0	.	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Missense_Mutation	SNP	ENST00000460680.1	hg19	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.042149	0.93685	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	T;T	0.75260	-0.81;-0.92	5.72	5.72	0.89469	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (1);	0.000000	0.85682	D	0.000000	D	0.85168	0.5635	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.85506	0.1194	10	0.72032	D	0.01	-9.2799	19.885	0.96909	0.0:0.0:1.0:0.0	.	370	Q92560	BAP1_HUMAN	H	370;352	ENSP00000417132:P370H;ENSP00000296288:P352H	ENSP00000296288:P352H	P	-	2	0	BAP1	52414173	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.768000	0.98965	2.705000	0.92388	0.655000	0.94253	CCC	.	.	.	none		0.542	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			T	52439133	G	T	52439133	3	4	257	1	0	0	0	0	1	0	0	0	1311	1232	43	4	1108	4	BAP1	3	52439133	Missense_Mutation	SNP	G	TCGA-UZ-A9PK-01A-11D-A382-10	13209735	52439133	145583297	12	15982											
LRRIQ4	344657	hgsc.bcm.edu	37	chr3	169539716	169539716	+	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	ttttcttcacaataatgtcaAaagacataaaatcagtagaa	19	12	4	6	0	4	2	3	0	1	2	4	2	4	2	0	0	0	1	0	0	8	6			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr3:169539716A>T	ENST00000340806.6	+	1	7	c.7A>T	c.(7-9)Aaa>Taa	p.K3*		NM_001080460.1	NP_001073929.1	A6NIV6	LRIQ4_HUMAN	leucine-rich repeats and IQ motif containing 4	3										breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	30						AATAATGTCAAAAGACATAAA	0.318																																					p.K3X		Atlas-SNP	.											.	LRRIQ4	68	.	0			c.A7T						PASS	.						43	40	41					3																	169539716		1833	4086	5919	SO:0001587	stop_gained	344657	exon1			ATGTCAAAAGACA		CCDS46951.1	3q26.2	2008-08-08	2008-06-12	2008-06-12	ENSG00000188306	ENSG00000188306			34298	protein-coding gene	gene with protein product	"leucine rich repeat containing 64"						Standard	NM_001080460		Approved	LRRC64	uc003fgb.3	A6NIV6	OTTHUMG00000164420	ENST00000340806.6:c.7A>T	chr3.hg19:g.169539716A>T	ENSP00000342188:p.Lys3*	354.0	1.0	.		433.0	237.0	.	NM_001080460		Nonsense_Mutation	SNP	ENST00000340806.6	hg19	CCDS46951.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.138694	0.77775	.	.	ENSG00000188306	ENST00000340806	.	.	.	5.39	1.69	0.24217	.	2.757410	0.00853	N	0.001846	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.3243	0.26547	0.7289:0.0:0.2711:0.0	.	.	.	.	X	3	.	ENSP00000342188:K3X	K	+	1	0	LRRIQ4	171022410	0.056000	0.20664	0.001000	0.08648	0.060000	0.15804	1.033000	0.30191	0.442000	0.26555	0.459000	0.35465	AAA	.	.	.	none		0.318	LRRIQ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378698.1	NM_001080460		T	169539716	A	T	169539716	4	4	257	1	0	0	0	0	0	1	0	0	9038	15	1	5	9	5	LRRIQ4	3	169539716	Nonsense_Mutation	SNP	A	TCGA-UZ-A9PK-01A-11D-A382-10	117100583	169539716	28482714	13	15983											
NAALADL2	254827	hgsc.bcm.edu	37	chr3	175184939	175184939	+	Frame_Shift_Del	DEL	T	T	-																															tgttcttggggaggaacagcTtttggcaatattggctcata																										TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr3:175184939delT	ENST00000454872.1	+	8	1628	c.1500delT	c.(1498-1500)gctfs	p.A500fs	NAALADL2_ENST00000473253.1_3'UTR	NM_207015.2	NP_996898.2	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 2	500						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)		GAGGAACAGCTTTTGGCAATA	0.383																																					p.A500fs		Pindel	.											.	NAALADL2	86	.	0			c.1499delC						PASS	.						71	68	69					3																	175184939		1876	4108	5984	SO:0001589	frameshift_variant	254827	exon8			.		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.1500delT	chr3.hg19:g.175184939delT	ENSP00000404705:p.Ala500fs	162.0	0.0	.		190.0	71.0	0.374	NM_207015	Q658X9|Q6H9J8|Q6H9J9|Q6PG38	Frame_Shift_Del	DEL	ENST00000454872.1	hg19	CCDS46960.1																																																																																			.	.	.	none		0.383	NAALADL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347390.2	NM_207015		-	175184939	T	-	175184939	7	5	257	1	0	1	0	1	0	0	0	0	10137	1596	56	0	1530	0	NAALADL2	3	175184939	Frame_Shift_Del	DEL	T	TCGA-UZ-A9PK-01A-11D-A382-10	5645223	175184939	22837491	14	15984											
DGKQ	1609	hgsc.bcm.edu	37	chr4	959714	959715	+	Splice_Site	INS	-	-	C																															ggccagccacagtggtcacaINScctttggtagccccggcctc																										TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr4:959714_959715insC	ENST00000273814.3	-	13	1653		c.e13+1		DGKQ_ENST00000502309.1_Intron	NM_001347.3	NP_001338.2	P52824	DGKQ_HUMAN	diacylglycerol kinase, theta 110kDa						blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|protein kinase C signaling (GO:0070528)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to ATP (GO:0033198)|thrombin receptor signaling pathway (GO:0070493)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|phospholipase binding (GO:0043274)			breast(1)|endometrium(2)|kidney(2)|lung(2)|prostate(2)	9			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			CAGTGGTCACACCTTTGGTAGC	0.688																																					.	Esophageal Squamous(17;537 645 4447 26373)	Atlas-Indel,Pindel	.											.	DGKQ	29	.	0			c.1579+2->G						PASS	.																																			SO:0001630	splice_region_variant	1609	exon14			.	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.1579+1->G	chr4.hg19:g.959716_959716dupC		150.0	0.0	0		123.0	45.0	0.365854	NM_001347	Q6P3W4	Splice_Site	INS	ENST00000273814.3	hg19	CCDS3342.1																																																																																			.	.	.	none		0.688	DGKQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000200888.1		Intron	C	959715	-	C	959714	8	5	257	1	0	1	1	0	0	0	1	0	4475	173	6	0	1291	0	DGKQ	4	959714	Splice_Site	INS	-	TCGA-UZ-A9PK-01A-11D-A382-10		959714	190194562	15	15985											
LEF1	51176	hgsc.bcm.edu	37	chr4	108999439	108999439	+	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	gtacactcagcaacgacattCgctctcatttctttcatgta	10	14	5	12	2	4	0	3	0	2	0	6	1	4	0	0	0	3	4	0	0	3	5	rs375238109		TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr4:108999439C>T	ENST00000265165.1	-	8	1599	c.945G>A	c.(943-945)gcG>gcA	p.A315A	LEF1_ENST00000510624.1_Silent_p.A219A|LEF1_ENST00000438313.2_Silent_p.A287A|LEF1_ENST00000503879.1_5'UTR|LEF1_ENST00000379951.2_Silent_p.A287A	NM_016269.4	NP_057353.1	Q9UJU2	LEF1_HUMAN	lymphoid enhancer-binding factor 1	315					alpha-beta T cell differentiation (GO:0046632)|anatomical structure regression (GO:0060033)|apoptotic process involved in morphogenesis (GO:0060561)|apoptotic process involved in patterning of blood vessels (GO:1902262)|B cell proliferation (GO:0042100)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cell chemotaxis (GO:0060326)|cellular response to cytokine stimulus (GO:0071345)|cellular response to interleukin-4 (GO:0071353)|chorio-allantoic fusion (GO:0060710)|dentate gyrus development (GO:0021542)|embryonic limb morphogenesis (GO:0030326)|epithelial to mesenchymal transition (GO:0001837)|eye pigmentation (GO:0048069)|face morphogenesis (GO:0060325)|forebrain neuroblast division (GO:0021873)|forebrain neuron differentiation (GO:0021879)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|mammary gland development (GO:0030879)|muscle fiber development (GO:0048747)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic process in bone marrow (GO:0071866)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA binding (GO:0043392)|negative regulation of estrogen receptor binding (GO:0071899)|negative regulation of interleukin-13 production (GO:0032696)|negative regulation of interleukin-4 production (GO:0032713)|negative regulation of interleukin-5 production (GO:0032714)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|neutrophil differentiation (GO:0030223)|odontoblast differentiation (GO:0071895)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|paraxial mesoderm formation (GO:0048341)|patterning of blood vessels (GO:0001569)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of cell cycle process (GO:0090068)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation in bone marrow (GO:0071864)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of gene expression (GO:0010628)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell-cell adhesion (GO:0022407)|regulation of striated muscle tissue development (GO:0016202)|sensory perception of taste (GO:0050909)|somitogenesis (GO:0001756)|sprouting angiogenesis (GO:0002040)|steroid hormone mediated signaling pathway (GO:0043401)|T cell receptor V(D)J recombination (GO:0033153)|T-helper 1 cell differentiation (GO:0045063)|tongue development (GO:0043586)|trachea gland development (GO:0061153)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|C2H2 zinc finger domain binding (GO:0070742)|chromatin binding (GO:0003682)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|enhancer binding (GO:0035326)|estrogen receptor activity (GO:0030284)|estrogen receptor binding (GO:0030331)|gamma-catenin binding (GO:0045295)|histone binding (GO:0042393)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(14)|prostate(1)|urinary_tract(1)	25				OV - Ovarian serous cystadenocarcinoma(123;0.000224)		CAACGACATTCGCTCTCATTT	0.428																																					p.A315A		Atlas-SNP	.											.	LEF1	93	.	0			c.G945A						PASS	.	T	,,,	1,4405	2.1+/-5.4	0,1,2202	270	266	268		861,861,657,945	-6.5	0.8	4		268	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LEF1	NM_001130713.2,NM_001130714.2,NM_001166119.1,NM_016269.4	,,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,,	287/372,287/387,219/304,315/400	108999439	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	51176	exon8			GACATTCGCTCTC		CCDS3679.1, CCDS47122.1, CCDS47123.1, CCDS54791.1	4q23-q25	2011-07-08			ENSG00000138795	ENSG00000138795			6551	protein-coding gene	gene with protein product		153245				1783375	Standard	NM_016269		Approved	TCF1ALPHA, TCF10, TCF7L3	uc003hyt.2	Q9UJU2	OTTHUMG00000131809	ENST00000265165.1:c.945G>A	chr4.hg19:g.108999439C>T		122.0	0.0	.		122.0	52.0	.	NM_016269	B4DG38|B7Z8E2|E9PDK3|Q3ZCU4|Q9HAZ0	Silent	SNP	ENST00000265165.1	hg19	CCDS3679.1																																																																																			.	.	.	weak		0.428	LEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254749.2			T	108999439	C	T	108999439	2	4	257	1	0	0	0	0	0	0	0	1	8721	871	31	1		1	LEF1	4	108999439	Silent	SNP	C	TCGA-UZ-A9PK-01A-11D-A382-10	108039725	108999439	82154837	16	15986											
NDST4	64579	hgsc.bcm.edu	37	chr4	115997318	115997318	+	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	acaatgtcagcctcttccctGacaagaaggagatggcatct	12	9	9	11	0	3	3	1	1	2	2	4	4	4	3	2	2	1	1	2	2	3	1			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr4:115997318G>A	ENST00000264363.2	-	2	1553	c.875C>T	c.(874-876)tCa>tTa	p.S292L		NM_022569.1	NP_072091.1	Q9H3R1	NDST4_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 4	292	Heparan sulfate N-deacetylase 4.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(43)|ovary(1)|prostate(7)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	81		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)		CCTCTTCCCTGACAAGAAGGA	0.433																																					p.S292L		Atlas-SNP	.											.	NDST4	193	.	0			c.C875T						PASS	.						172	154	160					4																	115997318		2203	4300	6503	SO:0001583	missense	64579	exon2			TTCCCTGACAAGA	AB036429	CCDS3706.1	4q26	2008-02-05			ENSG00000138653	ENSG00000138653		"Sulfotransferases, membrane-bound"	20779	protein-coding gene	gene with protein product		615039				11087757	Standard	NM_022569		Approved		uc003ibu.3	Q9H3R1	OTTHUMG00000132916	ENST00000264363.2:c.875C>T	chr4.hg19:g.115997318G>A	ENSP00000264363:p.Ser292Leu	104.0	0.0	.		100.0	36.0	.	NM_022569	Q2KHM8	Missense_Mutation	SNP	ENST00000264363.2	hg19	CCDS3706.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.641655	0.87859	.	.	ENSG00000138653	ENST00000264363	T	0.37915	1.17	5.79	5.79	0.91817	.	0.058271	0.64402	D	0.000001	T	0.60051	0.2239	M	0.72894	2.215	0.80722	D	1	P	0.40266	0.71	P	0.56216	0.794	T	0.59118	-0.7514	10	0.87932	D	0	.	20.0367	0.97561	0.0:0.0:1.0:0.0	.	292	Q9H3R1	NDST4_HUMAN	L	292	ENSP00000264363:S292L	ENSP00000264363:S292L	S	-	2	0	NDST4	116216767	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.807000	0.99171	2.727000	0.93392	0.591000	0.81541	TCA	.	.	.	none		0.433	NDST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256427.1	NM_022569		A	115997318	G	A	115997318	3	1	257	1	0	0	0	0	1	0	0	0	10265	1294	45	2	1795	2	NDST4	4	115997318	Missense_Mutation	SNP	G	TCGA-UZ-A9PK-01A-11D-A382-10	6997879	115997318	75156958	17	15987											
TIGD6	81789	hgsc.bcm.edu	37	chr5	149375126	149375127	+	Frame_Shift_Ins	INS	-	-	T																															ccacttgcatcagccactcaINSttaaacagatcccttgtcat																										TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr5:149375126_149375127insT	ENST00000296736.3	-	2	1559_1560	c.785_786insA	c.(784-786)aatfs	p.N262fs	TIGD6_ENST00000515406.2_Frame_Shift_Ins_p.N262fs	NM_030953.3	NP_112215.1	Q17RP2	TIGD6_HUMAN	tigger transposable element derived 6	262	DDE.					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)			TCAGCCACTCATTAAACAGATC	0.525																																					p.N262fs		Atlas-Indel,Pindel	.											.	TIGD6	29	.	0			c.786_787insA						PASS	.																																			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.786dupA	chr5.hg19:g.149375128_149375128dupT	ENSP00000296736:p.Asn262fs	164.0	0.0	0		166.0	59.0	0.355422	NM_001243253	B3KTZ8|Q96MQ4|Q9H0X7	Frame_Shift_Ins	INS	ENST00000296736.3	hg19	CCDS4301.1																																																																																			.	.	.	none		0.525	TIGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252324.1	NM_030953		T	149375127	-	T	149375126	7	5	257	1	0	1	1	0	0	0	0	0	15912	214	8	0	783	0	TIGD6	5	149375126	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PK-01A-11D-A382-10		149375126	31540134	18	15988											
FAM71B	153745	hgsc.bcm.edu	37	chr5	156592638	156592638	+	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	gtgttggggtactgcagtaaCtctctactggtggcctcagg	6	12	14	9	0	2	0	1	0	1	0	3	0	2	0	1	5	4	4	1	5	3	4			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr5:156592638C>G	ENST00000302938.4	-	1	637	c.542G>C	c.(541-543)aGt>aCt	p.S181T		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	181						nucleus (GO:0005634)				NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ACTGCAGTAACTCTCTACTGG	0.493																																					p.S181T		Atlas-SNP	.											.	FAM71B	145	.	0			c.G542C						PASS	.						174	175	175					5																	156592638		2203	4300	6503	SO:0001583	missense	153745	exon1			CAGTAACTCTCTA		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.542G>C	chr5.hg19:g.156592638C>G	ENSP00000305596:p.Ser181Thr	139.0	0.0	.		161.0	55.0	.	NM_130899	Q1EDD9|Q8TC64|Q96LY8	Missense_Mutation	SNP	ENST00000302938.4	hg19	CCDS4335.1	.	.	.	.	.	.	.	.	.	.	C	13.54	2.269023	0.40095	.	.	ENSG00000170613	ENST00000302938	T	0.16196	2.36	4.56	1.49	0.22878	.	0.531595	0.18243	N	0.147193	T	0.24661	0.0598	L	0.43923	1.385	0.09310	N	1	D	0.76494	0.999	D	0.74023	0.982	T	0.06752	-1.0809	10	0.30078	T	0.28	-10.0605	4.4562	0.11643	0.0:0.6087:0.1849:0.2064	.	181	Q8TC56	FA71B_HUMAN	T	181	ENSP00000305596:S181T	ENSP00000305596:S181T	S	-	2	0	FAM71B	156525216	0.010000	0.17322	0.007000	0.13788	0.003000	0.03518	0.949000	0.29109	0.599000	0.29845	-0.136000	0.14681	AGT	.	.	.	none		0.493	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899		G	156592638	C	G	156592638	3	3	257	1	0	0	0	0	1	0	0	0	5615	565	20	4	1283	4	FAM71B	5	156592638	Missense_Mutation	SNP	C	TCGA-UZ-A9PK-01A-11D-A382-10	7217512	156592638	24322622	19	15989											
CYFIP2	26999	hgsc.bcm.edu	37	chr5	156738675	156738675	+	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	cataattttctacccaggtgGacgtgcacccagagcagcat	11	9	9	12	1	1	1	0	0	1	1	1	2	1	2	2	2	4	3	2	2	2	4			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr5:156738675G>T	ENST00000521420.1	+	10	1009	c.918G>T	c.(916-918)tgG>tgT	p.W306C	CYFIP2_ENST00000522463.1_Missense_Mutation_p.W136C|CYFIP2_ENST00000435847.2_Missense_Mutation_p.W6C|CYFIP2_ENST00000377576.3_Missense_Mutation_p.W332C|CYFIP2_ENST00000347377.6_Missense_Mutation_p.W332C|CYFIP2_ENST00000318218.6_Missense_Mutation_p.W332C|CYFIP2_ENST00000442283.2_5'UTR|CYFIP2_ENST00000541131.1_Missense_Mutation_p.W257C					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)			TACCCAGGTGGACGTGCACCC	0.602																																					p.W332C		Atlas-SNP	.											.	CYFIP2	354	.	0			c.G996T						PASS	.						32	34	33					5																	156738675		2134	4251	6385	SO:0001583	missense	26999	exon11			CAGGTGGACGTGC	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.918G>T	chr5.hg19:g.156738675G>T	ENSP00000430904:p.Trp306Cys	207.0	0.0	.		188.0	57.0	.	NM_001037332		Missense_Mutation	SNP	ENST00000521420.1	hg19		.	.	.	.	.	.	.	.	.	.	G	22.8	4.331186	0.81690	.	.	ENSG00000055163	ENST00000318218;ENST00000522463;ENST00000521420;ENST00000347377;ENST00000377576;ENST00000541131;ENST00000435847	T;T;T;T;T;T;T	0.45276	2.07;2.07;2.09;2.09;2.09;2.09;0.9	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.66703	0.2816	M	0.77486	2.375	0.80722	D	1	D;D;P;D;D;P	0.89917	1.0;1.0;0.719;1.0;1.0;0.943	D;D;B;D;D;D	0.97110	1.0;1.0;0.222;0.998;0.999;0.941	T	0.65047	-0.6263	10	0.34782	T	0.22	-13.0951	19.0225	0.92920	0.0:0.0:1.0:0.0	.	196;136;306;332;332;332	A8MUM2;E7EW33;E7EVJ5;E7EVF4;Q96F07-2;Q96F07	.;.;.;.;.;CYFP2_HUMAN	C	332;136;306;332;332;257;6	ENSP00000325817:W332C;ENSP00000428009:W136C;ENSP00000430904:W306C;ENSP00000313567:W332C;ENSP00000366799:W332C;ENSP00000444645:W257C;ENSP00000403793:W6C	ENSP00000325817:W332C	W	+	3	0	CYFIP2	156671253	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	9.792000	0.99085	2.496000	0.84212	0.655000	0.94253	TGG	.	.	.	none		0.602	CYFIP2-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000373710.1	NM_001037332		T	156738675	G	T	156738675	3	4	257	1	0	0	0	0	1	0	0	0	4140	1183	41	4	1034	4	CYFIP2	5	156738675	Missense_Mutation	SNP	G	TCGA-UZ-A9PK-01A-11D-A382-10	146037	156738675	24176585	20	15990											
LRFN2	57497	hgsc.bcm.edu	37	chr6	40399746	40399746	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atggagacctccaccatggcCgtggcctctccggcagcatt	7	8	11	15	2	1	1	0	0	1	1	3	2	2	1	6	4	1	2	6	4	0	1			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr6:40399746C>T	ENST00000338305.6	-	2	1649	c.1107G>A	c.(1105-1107)acG>acA	p.T369T		NM_020737.1	NP_065788.1	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III domain containing 2	369	Ig-like.					cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	58	Ovarian(28;0.0418)|Colorectal(47;0.196)					CCACCATGGCCGTGGCCTCTC	0.607																																					p.T369T		Atlas-SNP	.											.	LRFN2	133	.	0			c.G1107A						PASS	.						62	45	51					6																	40399746		2203	4300	6503	SO:0001819	synonymous_variant	57497	exon2			CATGGCCGTGGCC	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.1107G>A	chr6.hg19:g.40399746C>T		50.0	0.0	.		57.0	20.0	.	NM_020737	A5PKU3|Q5SYP9	Silent	SNP	ENST00000338305.6	hg19	CCDS34443.1																																																																																			.	.	.	none		0.607	LRFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040488.1	XM_166372		T	40399746	C	T	40399746	2	4	257	1	0	0	0	0	0	0	0	1	8945	639	23	1		1	LRFN2	6	40399746	Silent	SNP	C	TCGA-UZ-A9PK-01A-11D-A382-10		40399746	130715321	21	15991											
LCA5	167691	hgsc.bcm.edu	37	chr6	80223369	80223369	+	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	aacaagatcagtatctttccGaagtggctctctattgaggc	11	12	9	9	1	3	2	1	1	2	1	5	3	4	2	1	2	1	2	1	2	5	4			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr6:80223369G>A	ENST00000392959.1	-	4	891	c.280C>T	c.(280-282)Cgg>Tgg	p.R94W	LCA5_ENST00000467898.3_Missense_Mutation_p.R94W|LCA5_ENST00000369846.4_Missense_Mutation_p.R94W	NM_181714.3	NP_859065.2	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	94					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)		GTATCTTTCCGAAGTGGCTCT	0.453																																					p.R94W		Atlas-SNP	.											.	LCA5	71	.	0			c.C280T						PASS	.						153	163	160					6																	80223369		2203	4299	6502	SO:0001583	missense	167691	exon3			CTTTCCGAAGTGG		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.280C>T	chr6.hg19:g.80223369G>A	ENSP00000376686:p.Arg94Trp	90.0	0.0	.		70.0	22.0	.	NM_001122769	E1P542|Q9BWX7	Missense_Mutation	SNP	ENST00000392959.1	hg19	CCDS4990.1	.	.	.	.	.	.	.	.	.	.	G	9.229	1.035405	0.19590	.	.	ENSG00000135338	ENST00000369846;ENST00000392959	T;T	0.33216	1.42;1.42	6.07	3.32	0.38043	.	0.549102	0.20451	N	0.092094	T	0.06690	0.0171	N	0.22421	0.69	0.29390	N	0.862704	B;B	0.17465	0.022;0.004	B;B	0.09377	0.004;0.002	T	0.23904	-1.0175	10	0.54805	T	0.06	-0.1203	4.3299	0.11059	0.141:0.1334:0.6021:0.1235	.	94;94	B4DRL2;Q86VQ0	.;LCA5_HUMAN	W	94	ENSP00000358861:R94W;ENSP00000376686:R94W	ENSP00000358861:R94W	R	-	1	2	LCA5	80280088	0.999000	0.42202	0.997000	0.53966	0.177000	0.22998	1.043000	0.30316	0.439000	0.26476	0.655000	0.94253	CGG	.	.	.	none		0.453	LCA5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259269.1	NM_181714		A	80223369	G	A	80223369	3	1	257	1	0	0	0	0	1	0	0	0	8663	1057	37	1	1837	1	LCA5	6	80223369	Missense_Mutation	SNP	G	TCGA-UZ-A9PK-01A-11D-A382-10	39823623	80223369	90891698	22	15992											
GFRA2	2675	hgsc.bcm.edu	37	chr8	21560336	21560336	+	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	cctggacagacgtgcaggtgGtgatgacactggtccccaag	9	7	14	11	1	0	3	0	2	0	1	1	4	1	4	3	4	1	1	3	4	1	0	rs76990589		TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr8:21560336G>C	ENST00000524240.1	-	7	1849	c.1199C>G	c.(1198-1200)aCc>aGc	p.T400S	GFRA2_ENST00000400782.4_Missense_Mutation_p.T295S|GFRA2_ENST00000518077.1_Missense_Mutation_p.T267S|GFRA2_ENST00000517328.1_Missense_Mutation_p.T400S	NM_001495.4	NP_001486.4	O00451	GFRA2_HUMAN	GDNF family receptor alpha 2	400					negative regulation of protein autophosphorylation (GO:0031953)|nervous system development (GO:0007399)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	anchored component of membrane (GO:0031225)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|prostate(1)|skin(1)	7				Colorectal(74;0.0189)|COAD - Colon adenocarcinoma(73;0.0727)		CGTGCAGGTGGTGATGACACT	0.632																																					p.T400S		Atlas-SNP	.											.	GFRA2	23	.	0			c.C1199G						PASS	.						79	86	83					8																	21560336		2102	4221	6323	SO:0001583	missense	2675	exon7			CAGGTGGTGATGA	AF002700	CCDS47816.1, CCDS55207.1	8p21.3	2008-05-02			ENSG00000168546	ENSG00000168546			4244	protein-coding gene	gene with protein product		601956				9177201	Standard	NM_001165038		Approved	RETL2, GDNFRB, NTNRA, TRNR2	uc003wzu.1	O00451	OTTHUMG00000163897	ENST00000524240.1:c.1199C>G	chr8.hg19:g.21560336G>C	ENSP00000428518:p.Thr400Ser	107.0	0.0	.		83.0	30.0	.	NM_001495	E9PD47|O15316|O15328|Q58J92|Q6GTR9|Q7Z5C2	Missense_Mutation	SNP	ENST00000524240.1	hg19	CCDS47816.1	.	.	.	.	.	.	.	.	.	.	G	6.929	0.541169	0.13250	.	.	ENSG00000168546	ENST00000524240;ENST00000400782;ENST00000517328;ENST00000518077;ENST00000517892	T;T;T;T;T	0.28069	2.05;1.64;2.05;1.63;1.64	4.88	3.99	0.46301	.	0.292251	0.33346	N	0.005012	T	0.19485	0.0468	N	0.25144	0.715	0.38692	D	0.952799	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.08055	0.002;0.003;0.0	T	0.07385	-1.0775	10	0.14252	T	0.57	-31.8924	12.7087	0.57078	0.0:0.1663:0.8337:0.0	.	267;295;400	O00451-2;E9PD47;O00451	.;.;GFRA2_HUMAN	S	400;295;400;267;295	ENSP00000428518:T400S;ENSP00000383592:T295S;ENSP00000429445:T400S;ENSP00000429206:T267S;ENSP00000429979:T295S	ENSP00000383592:T295S	T	-	2	0	GFRA2	21604616	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	2.820000	0.48057	1.163000	0.42636	0.561000	0.74099	ACC	.	.	.	alt		0.632	GFRA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376254.3	NM_001495		C	21560336	G	C	21560336	3	2	257	1	0	0	0	0	1	0	0	0	6355	1261	44	4	207	4	GFRA2	8	21560336	Missense_Mutation	SNP	G	TCGA-UZ-A9PK-01A-11D-A382-10		21560336	124803686	23	15993											
ENTPD4	9583	hgsc.bcm.edu	37	chr8	23306313	23306313	+	Frame_Shift_Del	DEL	A	A	-																															atttcggattatgacaacagAaaaatataaaagtgaaacag																										TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr8:23306313delA	ENST00000358689.4	-	3	383	c.148delT	c.(148-150)tctfs	p.S50fs	ENTPD4_ENST00000356206.6_Frame_Shift_Del_p.S50fs|ENTPD4_ENST00000417069.2_Frame_Shift_Del_p.S50fs	NM_001128930.2|NM_004901.4	NP_001122402.1|NP_004892.1	Q9Y227	ENTP4_HUMAN	ectonucleoside triphosphate diphosphohydrolase 4	50					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)		ATGACAACAGAAAAATATAAA	0.378																																					p.S50fs		Atlas-Indel,Pindel	.											.	ENTPD4	56	.	0			c.149delC						PASS	.						108	114	112					8																	23306313		2203	4300	6503	SO:0001589	frameshift_variant	9583	exon3			.	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.148delT	chr8.hg19:g.23306313delA	ENSP00000351520:p.Ser50fs	119.0	0.0	0		116.0	41.0	0.353448	NM_004901	D3DSS3|O15092	Frame_Shift_Del	DEL	ENST00000358689.4	hg19	CCDS6041.1																																																																																			.	.	.	none		0.378	ENTPD4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215142.1	NM_004901		-	23306313	A	-	23306313	7	5	257	1	0	1	0	1	0	0	0	0	5143	246	9	0	1746	0	ENTPD4	8	23306313	Frame_Shift_Del	DEL	A	TCGA-UZ-A9PK-01A-11D-A382-10	1745977	23306313	123057709	24	15994											
ANK1	286	hgsc.bcm.edu	37	chr8	41551435	41551438	+	Frame_Shift_Del	DEL	GCGC	GCGC	-																															ccaatgacgctgcaaagcagGcgcaggctggtggtgtctcc																										TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	GCGC	GCGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr8:41551435_41551438delGCGC	ENST00000347528.4	-	29	3593_3596	c.3510_3513delGCGC	c.(3508-3513)ctgcgcfs	p.LR1170fs	ANK1_ENST00000396945.1_Frame_Shift_Del_p.LR1170fs|ANK1_ENST00000265709.8_Frame_Shift_Del_p.LR1211fs|ANK1_ENST00000289734.7_Frame_Shift_Del_p.LR1170fs|ANK1_ENST00000379758.2_Frame_Shift_Del_p.LR1170fs|ANK1_ENST00000352337.4_Frame_Shift_Del_p.LR1170fs|ANK1_ENST00000396942.1_Frame_Shift_Del_p.LR1170fs	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	1170	ZU5 2. {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)	p.R1171H(1)		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)			TGCAAAGCAGGCGCAGGCTGGTGG	0.652																																					p.1212_1213del		Atlas-Indel,Pindel	.											.	ANK1	497	.	1	Substitution - Missense(1)	large_intestine(1)	c.3634_3637del						PASS	.																																			SO:0001589	frameshift_variant	286	exon30			.	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.3510_3513delGCGC	chr8.hg19:g.41551435_41551438delGCGC	ENSP00000339620:p.Leu1170fs	216.0	0.0	0		251.0	81.0	0.322709	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Frame_Shift_Del	DEL	ENST00000347528.4	hg19	CCDS6119.1																																																																																			.	.	.	none		0.652	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		-	41551438	GCGC	-	41551435	7	5	257	1	0	1	0	1	0	0	0	0	620	1190	42	0	2514	0	ANK1	8	41551435	Frame_Shift_Del	DEL	GCGC	TCGA-UZ-A9PK-01A-11D-A382-10	18245122	41551435	104812587	25	15995											
NBN	4683	hgsc.bcm.edu	37	chr8	90965471	90965471	+	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	ctcatttaaaatgttacttaCagatattttgctactttctg	11	19	4	7	0	2	1	1	0	1	1	2	1	2	1	0	0	4	2	0	0	6	9			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr8:90965471C>T	ENST00000265433.3	-	11	2000		c.e11+1		NBN_ENST00000409330.1_Splice_Site	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin						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)			ATGTTACTTACAGATATTTTG	0.343								Homologous recombination																													.		Atlas-SNP	.											.	NBN	86	.	0			c.1845+1G>A						PASS	.						203	198	199					8																	90965471		2203	4299	6502	SO:0001630	splice_region_variant	4683	exon12			TACTTACAGATAT	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.1845+1G>A	chr8.hg19:g.90965471C>T		56.0	0.0	.		62.0	17.0	.	NM_002485	B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Splice_Site	SNP	ENST00000265433.3	hg19	CCDS6249.1	.	.	.	.	.	.	.	.	.	.	C	12.53	1.964595	0.34659	.	.	ENSG00000104320	ENST00000265433;ENST00000409330	.	.	.	5.29	5.29	0.74685	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.4314	0.67254	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NBN	91034647	0.998000	0.40836	0.998000	0.56505	0.234000	0.25298	3.894000	0.56250	2.469000	0.83416	0.650000	0.86243	.	.	.	.	none		0.343	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	NM_001024688	Intron	T	90965471	C	T	90965471	5	4	257	1	0	0	0	0	0	0	1	0	10198	492	17	2	442	2	NBN	8	90965471	Splice_Site	SNP	C	TCGA-UZ-A9PK-01A-11D-A382-10	49414036	90965471	55398551	26	15996											
VPS13B	157680	hgsc.bcm.edu	37	chr8	100865879	100865879	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttgaactttactgtgtggAgatctgctgtggggacctgc	6	14	14	7	0	1	2	0	1	1	1	1	4	1	3	1	3	4	2	1	3	2	3			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr8:100865879A>G	ENST00000358544.2	+	56	10448	c.10337A>G	c.(10336-10338)gAg>gGg	p.E3446G	VPS13B_ENST00000357162.2_Missense_Mutation_p.E3421G|VPS13B_ENST00000395996.1_3'UTR	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	3446					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)			TACTGTGTGGAGATCTGCTGT	0.512																																					p.E3446G	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.A10337G						PASS	.						70	67	68					8																	100865879		2203	4300	6503	SO:0001583	missense	157680	exon56			GTGTGGAGATCTG	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.10337A>G	chr8.hg19:g.100865879A>G	ENSP00000351346:p.Glu3446Gly	158.0	0.0	.		168.0	50.0	.	NM_017890	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	hg19	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	A	18.63	3.666129	0.67700	.	.	ENSG00000132549	ENST00000357162;ENST00000358544	T;T	0.70399	-0.48;-0.48	5.43	5.43	0.79202	.	0.127455	0.52532	D	0.000080	T	0.68604	0.3019	L	0.50333	1.59	0.80722	D	1	B;D	0.53619	0.095;0.961	B;B	0.44224	0.042;0.444	T	0.72827	-0.4175	10	0.56958	D	0.05	.	15.4706	0.75437	1.0:0.0:0.0:0.0	.	3421;3446	Q7Z7G8-2;Q7Z7G8	.;VP13B_HUMAN	G	3421;3446	ENSP00000349685:E3421G;ENSP00000351346:E3446G	ENSP00000349685:E3421G	E	+	2	0	VPS13B	100935055	1.000000	0.71417	0.661000	0.29709	0.306000	0.27790	4.545000	0.60698	2.036000	0.60181	0.528000	0.53228	GAG	.	.	.	none		0.512	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		G	100865879	A	G	100865879	3	3	257	1	0	0	0	0	1	0	0	0	17202	304	11	3	10749	3	VPS13B	8	100865879	Missense_Mutation	SNP	A	TCGA-UZ-A9PK-01A-11D-A382-10	9900408	100865879	45498143	27	15997											
C9orf66	157983	hgsc.bcm.edu	37	chr9	214701	214701	+	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	agagcgcgccgtctgccccaGtatcgggaggccagttccgc	6	6	14	15	5	1	1	0	0	1	1	3	2	2	2	5	2	2	2	5	2	1	2			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr9:214701G>T	ENST00000382387.2	-	1	1192	c.696C>A	c.(694-696)taC>taA	p.Y232*	DOCK8_ENST00000453981.1_5'Flank|DOCK8_ENST00000432829.2_5'Flank	NM_152569.2	NP_689782.2	Q5T8R8	CI066_HUMAN	chromosome 9 open reading frame 66	232	Arg-rich.									central_nervous_system(1)|cervix(1)|kidney(1)|skin(1)	4	all_lung(41;0.218)	all_cancers(5;2.09e-12)|all_epithelial(5;6.16e-09)|all_lung(10;1.15e-08)|Lung NSC(10;1.91e-08)|Acute lymphoblastic leukemia(5;0.00457)|all_hematologic(5;0.0332)|Breast(48;0.0646)|Prostate(43;0.137)	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)		GTCTGCCCCAGTATCGGGAGG	0.786																																					p.Y232X		Atlas-SNP	.											.	C9orf66	16	.	0			c.C696A						PASS	.						4	4	4					9																	214701		1792	3538	5330	SO:0001587	stop_gained	157983	exon1			GCCCCAGTATCGG	AK055720	CCDS6439.1	9p24.3	2008-02-05			ENSG00000183784	ENSG00000183784			26436	protein-coding gene	gene with protein product							Standard	NM_152569		Approved	FLJ31158	uc003zge.4	Q5T8R8	OTTHUMG00000021017	ENST00000382387.2:c.696C>A	chr9.hg19:g.214701G>T	ENSP00000371824:p.Tyr232*	96.0	0.0	.		100.0	41.0	.	NM_152569	Q96NB0	Nonsense_Mutation	SNP	ENST00000382387.2	hg19	CCDS6439.1	.	.	.	.	.	.	.	.	.	.	.	37	6.298205	0.97453	.	.	ENSG00000183784	ENST00000382387	.	.	.	3.91	1.81	0.25067	.	.	.	.	.	.	.	.	.	.	.	0.35445	D	0.795188	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	4.6513	0.12596	0.1264:0.227:0.6465:0.0	.	.	.	.	X	232	.	ENSP00000371824:Y232X	Y	-	3	2	C9orf66	204701	0.079000	0.21365	0.068000	0.19968	0.006000	0.05464	1.997000	0.40786	0.937000	0.37394	0.484000	0.47621	TAC	.	.	.	none		0.786	C9orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055436.1	NM_152569		T	214701	G	T	214701	4	4	257	1	0	0	0	0	0	1	0	0	2492	1024	36	4	195	4	C9orf66	9	214701	Nonsense_Mutation	SNP	G	TCGA-UZ-A9PK-01A-11D-A382-10		214701	140998730	28	15998											
DMRT3	58524	hgsc.bcm.edu	37	chr9	990923	990923	+	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	tgatgggtgtccatttgtgtCaaagcagtccatttacaccg	9	13	10	9	1	1	1	1	1	0	0	3	1	3	1	3	1	2	1	3	1	2	3			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr9:990923C>G	ENST00000190165.2	+	2	1375	c.1337C>G	c.(1336-1338)tCa>tGa	p.S446*		NM_021240.2	NP_067063.1	Q9NQL9	DMRT3_HUMAN	doublesex and mab-3 related transcription factor 3	446					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)		CCATTTGTGTCAAAGCAGTCC	0.527																																					p.S446X		Atlas-SNP	.											.	DMRT3	83	.	0			c.C1337G						PASS	.						91	89	90					9																	990923		2203	4300	6503	SO:0001587	stop_gained	58524	exon2			TTGTGTCAAAGCA	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.1337C>G	chr9.hg19:g.990923C>G	ENSP00000190165:p.Ser446*	108.0	0.0	.		99.0	35.0	.	NM_021240	Q7LA03|Q7LCH8|Q96SC7|Q9NRQ9	Nonsense_Mutation	SNP	ENST00000190165.2	hg19	CCDS6443.1	.	.	.	.	.	.	.	.	.	.	C	35	5.504853	0.96371	.	.	ENSG00000064218	ENST00000190165	.	.	.	5.22	5.22	0.72569	.	0.558234	0.17930	N	0.157210	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	-2.7083	12.1775	0.54194	0.0:0.922:0.0:0.078	.	.	.	.	X	446	.	ENSP00000190165:S446X	S	+	2	0	DMRT3	980923	0.995000	0.38212	0.061000	0.19648	0.891000	0.51852	4.428000	0.59894	2.424000	0.82194	0.655000	0.94253	TCA	.	.	.	none		0.527	DMRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051490.1	NM_021240		G	990923	C	G	990923	4	3	257	1	0	0	0	0	0	1	0	0	4589	838	29	4	1343	4	DMRT3	9	990923	Nonsense_Mutation	SNP	C	TCGA-UZ-A9PK-01A-11D-A382-10	776222	990923	140222508	29	15999											
KCNV2	169522	hgsc.bcm.edu	37	chr9	2718860	2718860	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcgtgggtaaggtgggtcAggtgttgcgcgtcatgcgcc	5	9	18	9	4	2	0	2	0	0	0	2	0	2	0	1	4	3	2	1	4	1	2			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr9:2718860A>G	ENST00000382082.3	+	1	1359	c.1121A>G	c.(1120-1122)cAg>cGg	p.Q374R		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	374					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)		AAGGTGGGTCAGGTGTTGCGC	0.672																																					p.Q374R		Atlas-SNP	.											.	KCNV2	72	.	0			c.A1121G						PASS	.						98	79	85					9																	2718860		2203	4300	6503	SO:0001583	missense	169522	exon1			TGGGTCAGGTGTT	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.1121A>G	chr9.hg19:g.2718860A>G	ENSP00000371514:p.Gln374Arg	55.0	0.0	.		61.0	23.0	.	NM_133497	Q5T6X0	Missense_Mutation	SNP	ENST00000382082.3	hg19	CCDS6447.1	.	.	.	.	.	.	.	.	.	.	A	14.50	2.553862	0.45487	.	.	ENSG00000168263	ENST00000382082	D	0.98164	-4.76	5.07	5.07	0.68467	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.95840	0.8646	N	0.10916	0.065	0.58432	D	0.999999	P	0.51791	0.948	P	0.56278	0.795	D	0.94056	0.7322	10	0.06625	T	0.88	.	14.8658	0.70416	1.0:0.0:0.0:0.0	.	374	Q8TDN2	KCNV2_HUMAN	R	374	ENSP00000371514:Q374R	ENSP00000371514:Q374R	Q	+	2	0	KCNV2	2708860	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	9.339000	0.96797	1.908000	0.55244	0.460000	0.39030	CAG	.	.	.	none		0.672	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497		G	2718860	A	G	2718860	3	3	257	1	0	0	0	0	1	0	0	0	8102	188	7	3	1123	3	KCNV2	9	2718860	Missense_Mutation	SNP	A	TCGA-UZ-A9PK-01A-11D-A382-10	1727937	2718860	138494571	30	16000											
IFNK	56832	hgsc.bcm.edu	37	chr9	27524419	27524419	+	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	ttgctggcaccctatccctgGactgtaacttactgaacgtt	8	13	8	12	1	0	1	0	1	0	0	1	2	1	2	2	2	4	4	2	2	4	5			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr9:27524419G>T	ENST00000276943.2	+	1	108	c.85G>T	c.(85-87)Gac>Tac	p.D29Y	MOB3B_ENST00000262244.5_Intron	NM_020124.2	NP_064509.2	Q9P0W0	IFNK_HUMAN	interferon, kappa	29					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|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 (GO:0030101)|natural killer cell activation involved in immune response (GO:0002323)|negative regulation of cell proliferation (GO:0008285)|positive regulation of innate immune response (GO:0045089)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of transcription, DNA-templated (GO:0006355)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|T cell activation involved in immune response (GO:0002286)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			large_intestine(1)	1		all_neural(11;7.9e-11)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.000158)		CCTATCCCTGGACTGTAACTT	0.408																																					p.D29Y		Atlas-SNP	.											.	IFNK	14	.	0			c.G85T						PASS	.						108	103	105					9																	27524419		2203	4300	6503	SO:0001583	missense	56832	exon1			TCCCTGGACTGTA	AF384048	CCDS6521.1	9p21.2	2008-02-05			ENSG00000147896	ENSG00000147896		"Interferons"	21714	protein-coding gene	gene with protein product		615326				12391192, 11514542	Standard	NM_020124		Approved		uc003zqp.3	Q9P0W0	OTTHUMG00000019715	ENST00000276943.2:c.85G>T	chr9.hg19:g.27524419G>T	ENSP00000276943:p.Asp29Tyr	133.0	0.0	.		153.0	60.0	.	NM_020124	Q5T166	Missense_Mutation	SNP	ENST00000276943.2	hg19	CCDS6521.1	.	.	.	.	.	.	.	.	.	.	G	12.68	2.010976	0.35511	.	.	ENSG00000147896	ENST00000276943	T	0.16897	2.31	5.67	-5.19	0.02832	Four-helical cytokine-like, core (1);	1.187680	0.05921	N	0.633525	T	0.30541	0.0768	M	0.76002	2.32	0.09310	N	1	D	0.62365	0.991	P	0.57324	0.818	T	0.45411	-0.9263	10	0.87932	D	0	-7.6703	6.5888	0.22636	0.43:0.3306:0.2394:0.0	.	29	Q9P0W0	IFNK_HUMAN	Y	29	ENSP00000276943:D29Y	ENSP00000276943:D29Y	D	+	1	0	IFNK	27514419	0.000000	0.05858	0.012000	0.15200	0.272000	0.26649	-1.028000	0.03589	-0.809000	0.04381	-0.300000	0.09419	GAC	.	.	.	none		0.408	IFNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051968.1	NM_020124		T	27524419	G	T	27524419	3	4	257	1	0	0	0	0	1	0	0	0	7558	1174	41	4	87	4	IFNK	9	27524419	Missense_Mutation	SNP	G	TCGA-UZ-A9PK-01A-11D-A382-10	24805559	27524419	113689012	31	16001											
NUDT2	318	hgsc.bcm.edu	37	chr9	34343386	34343386	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttggctcagttcaaggagaTgaaggcagcgctccaagaag	12	7	14	8	1	2	3	2	1	0	2	3	4	3	3	1	3	1	5	1	3	4	2	rs368502630		TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr9:34343386T>C	ENST00000379158.2	+	5	750	c.392T>C	c.(391-393)aTg>aCg	p.M131T	NUDT2_ENST00000379155.5_Missense_Mutation_p.M131T|NUDT2_ENST00000346365.4_Missense_Mutation_p.M131T	NM_001161.4	NP_001152.1	P50583	AP4A_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 2	131	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				apoptotic process (GO:0006915)|nucleobase-containing compound metabolic process (GO:0006139)	mitochondrion (GO:0005739)	bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity (GO:0004081)|bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity (GO:0008803)|GTP binding (GO:0005525)			lung(3)	3			LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.126)		TTCAAGGAGATGAAGGCAGCG	0.572																																					p.M131T	Melanoma(95;1683 1957 4276 39813)	Atlas-SNP	.											.	NUDT2	7	.	0			c.T392C						PASS	.	T	THR/MET,THR/MET,THR/MET	0,4406		0,0,2203	42	42	42		392,392,392	5.9	1	9		42	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	NUDT2	NM_001161.4,NM_147172.2,NM_147173.2	81,81,81	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	131/148,131/148,131/148	34343386	1,13005	2203	4300	6503	SO:0001583	missense	318	exon4			AGGAGATGAAGGC	U30313	CCDS6552.1	9p13	2008-07-21			ENSG00000164978	ENSG00000164978		"Nudix motif containing"	8049	protein-coding gene	gene with protein product	"Ap4A hydrolase 1", "Ap4Aase", "bis(5'-nucleosyl)-tetraphosphatase (asymmetrical)", "diadenosine tetraphosphatase", "diadenosine 5',5''-P1,P4-tetraphosphate pyrophosphohydrolase"	602852		APAH1		7487923, 9479504	Standard	NM_001161		Approved		uc022bga.1	P50583	OTTHUMG00000019817	ENST00000379158.2:c.392T>C	chr9.hg19:g.34343386T>C	ENSP00000368455:p.Met131Thr	98.0	0.0	.		106.0	25.0	.	NM_147173	D3DRM0|Q5T589	Missense_Mutation	SNP	ENST00000379158.2	hg19	CCDS6552.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.243920	0.79912	0.0	1.16E-4	ENSG00000164978	ENST00000337747;ENST00000379154;ENST00000379155;ENST00000346365;ENST00000379158	T;T;T	0.07114	3.22;3.22;3.22	5.88	5.88	0.94601	NUDIX hydrolase domain (3);NUDIX hydrolase domain-like (1);	0.162705	0.64402	D	0.000003	T	0.18130	0.0435	L	0.33189	0.99	0.80722	D	1	D	0.57571	0.98	D	0.81914	0.995	T	0.13202	-1.0518	10	0.14252	T	0.57	-14.7876	16.2987	0.82793	0.0:0.0:0.0:1.0	.	131	P50583	AP4A_HUMAN	T	131	ENSP00000368452:M131T;ENSP00000344187:M131T;ENSP00000368455:M131T	ENSP00000338397:M131T	M	+	2	0	NUDT2	34333386	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	7.797000	0.85911	2.257000	0.74773	0.459000	0.35465	ATG	.	.	.	weak		0.572	NUDT2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052160.2	NM_001161		C	34343386	T	C	34343386	3	2	257	1	0	0	0	0	1	0	0	0	10744	1464	51	3	398	3	NUDT2	9	34343386	Missense_Mutation	SNP	T	TCGA-UZ-A9PK-01A-11D-A382-10	6818967	34343386	106870045	32	16002											
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84607291	84607291	+	Missense_Mutation	SNP	T	T	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	tgcagaaagtgcaggaaagtTtgtggggcttaccctctgtg	9	11	14	7	0	1	1	0	0	1	1	1	2	1	2	1	3	3	4	1	3	3	2	rs201182137	byFrequency	TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr9:84607291T>G	ENST00000344803.2	+	4	1953	c.1906T>G	c.(1906-1908)Ttg>Gtg	p.L636V		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	636					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GCAGGAAAGTTTGTGGGGCTT	0.478													G|||	3	0.000599042	8e-04	0	5008	,	,		19868	0		0.001	False		,,,				2504	0.001				p.L636V		Atlas-SNP	.											FAM75D4,NS,carcinoma,0,2	.	.	.	0			c.T1906G						PASS	.	G	VAL/LEU	0,3730		0,0,1865	101	98	99		1906	-3.7	0	9		99	1,8223		0,1,4111	no	missense	FAM75D1	NM_001001670.2	32	0,1,5976	GG,GT,TT		0.0122,0.0,0.0084	benign	636/1577	84607291	1,11953	1865	4112	5977	SO:0001583	missense	389763	exon4			GAAAGTTTGTGGG		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.1906T>G	chr9.hg19:g.84607291T>G	ENSP00000341988:p.Leu636Val	128.0	1.0	.		118.0	6.0	.	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	hg19	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	G	4.363	0.066840	0.08388	0.0	1.22E-4	ENSG00000214929	ENST00000344803	T	0.05786	3.39	3.83	-3.67	0.04476	.	1.454400	0.04584	N	0.395509	T	0.02970	0.0088	N	0.11023	0.085	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.43261	-0.9402	10	0.16420	T	0.52	0.4754	3.7406	0.08528	0.108:0.096:0.4463:0.3497	.	636	Q6ZQQ2	F75D1_HUMAN	V	636	ENSP00000341988:L636V	ENSP00000341988:L636V	L	+	1	2	FAM75D1	83797111	0.011000	0.17503	0.002000	0.10522	0.000000	0.00434	-0.756000	0.04777	-1.293000	0.02362	-0.729000	0.03580	TTG	.	.	.	weak		0.478	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		G	84607291	T	G	84607291	3	3	257	1	0	0	0	0	1	0	0	0	5939	1838	64	5	1920	5	FLJ46321	9	84607291	Missense_Mutation	SNP	T	TCGA-UZ-A9PK-01A-11D-A382-10	50263905	84607291	56606140	33	16003											
HABP4	22927	hgsc.bcm.edu	37	chr9	99246828	99246828	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatcttcaagaacagaccagAccaaagcctgagtttaacat	17	8	6	10	0	2	4	1	1	1	3	2	4	2	4	3	0	3	1	3	0	5	3			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr9:99246828A>G	ENST00000375249.4	+	6	987	c.912A>G	c.(910-912)agA>agG	p.R304R	HABP4_ENST00000375251.3_Silent_p.R199R|HABP4_ENST00000466976.1_3'UTR	NM_014282.2	NP_055097.2			hyaluronan binding protein 4											NS(1)|cervix(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	13		Acute lymphoblastic leukemia(62;0.0169)|all_hematologic(171;0.214)				AACAGACCAGACCAAAGCCTG	0.398																																					p.R304R		Atlas-SNP	.											.	HABP4	25	.	0			c.A912G						PASS	.						120	113	115					9																	99246828		2203	4300	6503	SO:0001819	synonymous_variant	22927	exon6			GACCAGACCAAAG	AF241831	CCDS6719.1	9q22.3-q31	2008-02-05			ENSG00000130956	ENSG00000130956			17062	protein-coding gene	gene with protein product						9523163, 10887182	Standard	XM_005251812		Approved	IHABP4, SERBP1L	uc010msg.3	Q5JVS0	OTTHUMG00000020298	ENST00000375249.4:c.912A>G	chr9.hg19:g.99246828A>G		316.0	0.0	.		327.0	109.0	.	NM_014282		Silent	SNP	ENST00000375249.4	hg19	CCDS6719.1																																																																																			.	.	.	none		0.398	HABP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053269.1	NM_014282		G	99246828	A	G	99246828	2	3	257	1	0	0	0	0	0	0	0	1	6946	272	10	3		3	HABP4	9	99246828	Silent	SNP	A	TCGA-UZ-A9PK-01A-11D-A382-10	14639537	99246828	41966603	34	16004											
TNC	3371	hgsc.bcm.edu	37	chr9	117803252	117803252	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accctgagacaggttcacttTcctcaaagcccttcatggcg	9	10	8	14	1	3	1	3	1	0	1	4	2	4	1	3	2	1	1	3	2	1	3			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr9:117803252T>C	ENST00000350763.4	-	19	5771	c.5360A>G	c.(5359-5361)gAa>gGa	p.E1787G	TNC_ENST00000423613.2_Missense_Mutation_p.E1514G|TNC_ENST00000341037.4_Missense_Mutation_p.E1605G|TNC_ENST00000535648.1_Missense_Mutation_p.E1332G|TNC_ENST00000340094.3_Missense_Mutation_p.E1423G|TNC_ENST00000345230.3_Missense_Mutation_p.E1150G|TNC_ENST00000542877.1_Missense_Mutation_p.E1424G|TNC_ENST00000346706.3_Missense_Mutation_p.E1241G|TNC_ENST00000537320.1_Missense_Mutation_p.E1150G	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1787	Fibronectin type-III 13. {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						AGGTTCACTTTCCTCAAAGCC	0.498																																					p.E1787G		Atlas-SNP	.											.	TNC	282	.	0			c.A5360G						PASS	.						179	157	165					9																	117803252		2203	4300	6503	SO:0001583	missense	3371	exon19			TCACTTTCCTCAA		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.5360A>G	chr9.hg19:g.117803252T>C	ENSP00000265131:p.Glu1787Gly	114.0	0.0	.		140.0	42.0	.	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	hg19	CCDS6811.1	.	.	.	.	.	.	.	.	.	.	T	19.10	3.761583	0.69763	.	.	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	T;T;T;T;T;T;T;T;T	0.58060	0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36	5.93	5.93	0.95920	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.79975	0.4539	M	0.93720	3.45	0.26344	N	0.977311	D;D	0.89917	1.0;1.0	D;D	0.87578	0.995;0.998	T	0.77542	-0.2549	10	0.59425	D	0.04	.	16.3789	0.83431	0.0:0.0:0.0:1.0	.	1514;1787	E9PC84;P24821	.;TENA_HUMAN	G	1423;1332;1241;1150;1787;1605;1514;1150;1424	ENSP00000344400:E1423G;ENSP00000438152:E1332G;ENSP00000344555:E1241G;ENSP00000345861:E1150G;ENSP00000265131:E1787G;ENSP00000339553:E1605G;ENSP00000411406:E1514G;ENSP00000443478:E1150G;ENSP00000442242:E1424G	ENSP00000344400:E1423G	E	-	2	0	TNC	116843073	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.679000	0.84048	2.267000	0.75376	0.533000	0.62120	GAA	.	.	.	none		0.498	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160		C	117803252	T	C	117803252	3	2	257	1	0	0	0	0	1	0	0	0	16282	1783	62	3	1285	3	TNC	9	117803252	Missense_Mutation	SNP	T	TCGA-UZ-A9PK-01A-11D-A382-10	18556424	117803252	23410179	35	16005											
CUBN	8029	hgsc.bcm.edu	37	chr10	17107509	17107509	+	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	gcaatgctgttttgttacctGttgctgcactgattgcttca	6	17	9	9	0	1	1	1	1	0	0	1	1	1	1	1	0	5	8	1	0	2	6			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr10:17107509G>C	ENST00000377833.4	-	22	3202	c.3137C>G	c.(3136-3138)aCa>aGa	p.T1046R		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	1046					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)	TTTGTTACCTGTTGCTGCACT	0.413																																					p.T1046R		Atlas-SNP	.											.	CUBN	515	.	0			c.C3137G						PASS	.						208	182	191					10																	17107509		2203	4300	6503	SO:0001583	missense	8029	exon22			TTACCTGTTGCTG	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.3137C>G	chr10.hg19:g.17107509G>C	ENSP00000367064:p.Thr1046Arg	117.0	0.0	.		104.0	38.0	.	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	G	9.635	1.137432	0.21123	.	.	ENSG00000107611	ENST00000377833	T	0.76578	-1.03	5.92	-3.02	0.05446	CUB (1);	1.836900	0.02981	N	0.145596	T	0.72518	0.3470	L	0.45228	1.405	0.47511	D	0.999447	B	0.20459	0.045	B	0.21151	0.033	T	0.53606	-0.8415	10	0.29301	T	0.29	.	14.9627	0.71169	0.0:0.0695:0.4674:0.4631	.	1046	O60494	CUBN_HUMAN	R	1046	ENSP00000367064:T1046R	ENSP00000367064:T1046R	T	-	2	0	CUBN	17147515	0.983000	0.35010	0.031000	0.17742	0.732000	0.41865	1.542000	0.36137	-0.299000	0.08909	0.650000	0.86243	ACA	.	.	.	none		0.413	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		C	17107509	G	C	17107509	3	2	257	1	0	0	0	0	1	0	0	0	4053	1377	48	4	7918	4	CUBN	10	17107509	Missense_Mutation	SNP	G	TCGA-UZ-A9PK-01A-11D-A382-10		17107509	118427238	36	16006											
ABCC2	1244	hgsc.bcm.edu	37	chr10	101605502	101605502	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatattgcttccattgggcTccacgacctccgagagaagc	10	9	10	12	2	0	2	0	0	0	2	3	5	3	2	4	1	2	2	4	1	2	4			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr10:101605502T>C	ENST00000370449.4	+	29	4222	c.4109T>C	c.(4108-4110)cTc>cCc	p.L1370P		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	1370	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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)	TCCATTGGGCTCCACGACCTC	0.507											OREG0020434	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L1370P		Atlas-SNP	.											.	ABCC2	160	.	0			c.T4109C						PASS	.						93	80	85					10																	101605502		2203	4300	6503	SO:0001583	missense	1244	exon29			TTGGGCTCCACGA	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.4109T>C	chr10.hg19:g.101605502T>C	ENSP00000359478:p.Leu1370Pro	107.0	0.0	.	1360	127.0	36.0	.	NM_000392	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Missense_Mutation	SNP	ENST00000370449.4	hg19	CCDS7484.1	.	.	.	.	.	.	.	.	.	.	T	23.7	4.449048	0.84101	.	.	ENSG00000023839	ENST00000370449	D	0.94457	-3.43	5.61	5.61	0.85477	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.96352	0.8810	L	0.53617	1.68	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96920	0.9673	10	0.87932	D	0	0.7125	16.1025	0.81194	0.0:0.0:0.0:1.0	.	1370	Q92887	MRP2_HUMAN	P	1370	ENSP00000359478:L1370P	ENSP00000359478:L1370P	L	+	2	0	ABCC2	101595492	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	7.994000	0.88315	2.254000	0.74563	0.533000	0.62120	CTC	.	.	.	none		0.507	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392		C	101605502	T	C	101605502	3	2	257	1	0	0	0	0	1	0	0	0	53	1551	54	3	4223	3	ABCC2	10	101605502	Missense_Mutation	SNP	T	TCGA-UZ-A9PK-01A-11D-A382-10	84497993	101605502	33929245	37	16007											
DPCD	25911	hgsc.bcm.edu	37	chr10	103360511	103360512	+	Frame_Shift_Ins	INS	-	-	A																															cagtgagaaagtggcgtgtgINSaaaagtgccctgggagccat																										TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr10:103360511_103360512insA	ENST00000370151.4	+	3	211_212	c.162_163insA	c.(163-165)aaafs	p.K55fs	DPCD_ENST00000370147.1_Frame_Shift_Ins_p.K55fs|DPCD_ENST00000370148.2_Frame_Shift_Ins_p.K55fs|MIR3158-1_ENST00000583596.1_RNA	NM_015448.1	NP_056263.1	Q9BVM2	DPCD_HUMAN	deleted in primary ciliary dyskinesia homolog (mouse)	55					determination of left/right symmetry (GO:0007368)|epithelial cilium movement (GO:0003351)|lateral ventricle development (GO:0021670)|left/right pattern formation (GO:0060972)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)	nucleus (GO:0005634)				endometrium(1)|large_intestine(1)|lung(2)|skin(1)	5						AGTGGCGTGTGAAAAGTGCCCT	0.554																																					p.V54fs		Atlas-Indel,Pindel	.											.	DPCD	15	.	0			c.162_163insA						PASS	.																																			SO:0001589	frameshift_variant	25911	exon3			.		CCDS7514.1	10q24.32	2012-05-03			ENSG00000166171	ENSG00000166171			24542	protein-coding gene	gene with protein product						14630615	Standard	NM_015448		Approved	DKFZP566F084, RP11-529I10.4	uc001ktn.3	Q9BVM2	OTTHUMG00000018934	ENST00000370151.4:c.166dupA	chr10.hg19:g.103360515_103360515dupA	ENSP00000359170:p.Lys55fs	99.0	0.0	0		103.0	30.0	0.291262	NM_015448	A8K289|Q6QNL3|Q8N5R1|Q9UFY6	Frame_Shift_Ins	INS	ENST00000370151.4	hg19	CCDS7514.1																																																																																			.	.	.	none		0.554	DPCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049958.2			A	103360512	-	A	103360511	7	5	257	1	0	1	1	0	0	0	0	0	4713	1277	45	0	172	0	DPCD	10	103360511	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PK-01A-11D-A382-10	1755009	103360511	32174236	38	16008											
NHLRC2	374354	hgsc.bcm.edu	37	chr10	115636691	115636691	+	Frame_Shift_Del	DEL	T	T	-																															agacactggacatcatagaaTtttggtcgtttggaagaatg																										TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr10:115636691delT	ENST00000369301.3	+	3	955	c.743delT	c.(742-744)attfs	p.I248fs		NM_198514.3	NP_940916.2	Q8NBF2	NHLC2_HUMAN	NHL repeat containing 2	248										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)		CATCATAGAATTTTGGTCGTT	0.353																																					p.I248fs		Atlas-Indel,Pindel	.											NHLRC2,NS,carcinoma,0,1	NHLRC2	56	.	0			c.742delA						PASS	.						55	57	57					10																	115636691		2157	4275	6432	SO:0001589	frameshift_variant	374354	exon3			.	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.743delT	chr10.hg19:g.115636691delT	ENSP00000358307:p.Ile248fs	63.0	0.0	0		62.0	16.0	0.258065	NM_198514	Q8N1H1|Q8N5A6	Frame_Shift_Del	DEL	ENST00000369301.3	hg19	CCDS7585.1																																																																																			.	.	.	none		0.353	NHLRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050446.1	NM_198514		-	115636691	T	-	115636691	7	5	257	1	0	1	0	1	0	0	0	0	10413	1493	52	0	753	0	NHLRC2	10	115636691	Frame_Shift_Del	DEL	T	TCGA-UZ-A9PK-01A-11D-A382-10	12276180	115636691	19898056	39	16009											
CPXM2	119587	hgsc.bcm.edu	37	chr10	125521473	125521473	+	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	tggcacaccctcctccgggcGtctgtcatgaggcggtgtgt	4	10	14	13	3	2	1	1	1	1	0	4	1	4	1	3	4	0	1	3	4	0	0	rs547897756		TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr10:125521473G>A	ENST00000241305.3	-	11	1846	c.1692C>T	c.(1690-1692)gaC>gaT	p.D564D	CPXM2_ENST00000368854.3_5'UTR	NM_198148.2	NP_937791.2	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2	564					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)		TCCTCCGGGCGTCTGTCATGA	0.652													G|||	1	0.000199681	0	0	5008	,	,		16148	0.001		0	False		,,,				2504	0				p.D564D		Atlas-SNP	.											CPXM2,colon,carcinoma,-2,1	CPXM2	120	.	0			c.C1692T						PASS	.						42	42	42					10																	125521473		2203	4300	6503	SO:0001819	synonymous_variant	119587	exon11			CCGGGCGTCTGTC	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.1692C>T	chr10.hg19:g.125521473G>A		72.0	0.0	.		65.0	22.0	.	NM_198148	B4E3Q2	Silent	SNP	ENST00000241305.3	hg19	CCDS7637.1																																																																																			.	.	.	none		0.652	CPXM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050853.1	NM_198148		A	125521473	G	A	125521473	2	1	257	1	0	0	0	0	0	0	0	1	3840	1136	40	1		1	CPXM2	10	125521473	Silent	SNP	G	TCGA-UZ-A9PK-01A-11D-A382-10	9884782	125521473	10013274	40	16010											
RNF17	56163	hgsc.bcm.edu	37	chr13	25378553	25378553	+	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	atataaatagtcctggagatTtctatcttcagttggtaagt	12	16	8	5	0	3	1	1	0	2	1	4	2	4	1	1	2	0	2	1	2	6	8			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr13:25378553T>A	ENST00000255324.5	+	15	2129	c.2077T>A	c.(2077-2079)Ttc>Atc	p.F693I	RNF17_ENST00000381921.1_Missense_Mutation_p.F693I|RNF17_ENST00000255325.6_Intron	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	693					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)		TCCTGGAGATTTCTATCTTCA	0.279																																					p.F693I		Atlas-SNP	.											.	RNF17	259	.	0			c.T2077A						PASS	.						65	64	64					13																	25378553		2198	4299	6497	SO:0001583	missense	56163	exon15			GGAGATTTCTATC	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.2077T>A	chr13.hg19:g.25378553T>A	ENSP00000255324:p.Phe693Ile	99.0	0.0	.		92.0	34.0	.	NM_001184993	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Missense_Mutation	SNP	ENST00000255324.5	hg19	CCDS9308.2	.	.	.	.	.	.	.	.	.	.	T	19.45	3.830362	0.71258	.	.	ENSG00000132972	ENST00000255324;ENST00000381921;ENST00000429047;ENST00000418120	T;T;T	0.14640	2.49;2.49;2.49	5.25	5.25	0.73442	Maternal tudor protein (1);	0.062472	0.64402	D	0.000006	T	0.36413	0.0966	M	0.74258	2.255	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.09487	-1.0672	10	0.49607	T	0.09	.	12.6676	0.56851	0.0:0.0:0.0:1.0	.	693;693	B7Z7S1;Q9BXT8	.;RNF17_HUMAN	I	693;693;552;17	ENSP00000255324:F693I;ENSP00000371346:F693I;ENSP00000388892:F17I	ENSP00000255324:F693I	F	+	1	0	RNF17	24276553	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	5.412000	0.66392	1.985000	0.57927	0.482000	0.46254	TTC	.	.	.	none		0.279	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994		A	25378553	T	A	25378553	3	1	257	1	0	0	0	0	1	0	0	0	13474	1841	64	5	2135	5	RNF17	13	25378553	Missense_Mutation	SNP	T	TCGA-UZ-A9PK-01A-11D-A382-10		25378553	89791325	41	16011											
LMO7	4008	hgsc.bcm.edu	37	chr13	76427487	76427487	+	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	ccaccccgagaagccattccCcttcagcttcacagtcaggc	9	7	7	18	1	3	1	3	0	0	1	4	2	4	1	6	1	2	1	6	1	1	3			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr13:76427487C>T	ENST00000321797.8	+	26	4646	c.3925C>T	c.(3925-3927)Cct>Tct	p.P1309S	LMO7_ENST00000357063.3_Missense_Mutation_p.P1594S|LMO7_ENST00000377534.3_Missense_Mutation_p.P1594S|LMO7_ENST00000341547.4_Missense_Mutation_p.P1260S|LMO7_ENST00000465261.2_Missense_Mutation_p.P1309S|LMO7_ENST00000526202.1_Missense_Mutation_p.P1186S			Q8WWI1	LMO7_HUMAN	LIM domain 7	1594					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)		AAGCCATTCCCCTTCAGCTTC	0.552																																					p.P1309S		Atlas-SNP	.											.	LMO7	334	.	0			c.C3925T						PASS	.						50	43	45					13																	76427487		2203	4300	6503	SO:0001583	missense	4008	exon25			CATTCCCCTTCAG	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.3925C>T	chr13.hg19:g.76427487C>T	ENSP00000317802:p.Pro1309Ser	98.0	0.0	.		77.0	26.0	.	NM_015842	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	hg19		.	.	.	.	.	.	.	.	.	.	C	12.47	1.948732	0.34377	.	.	ENSG00000136153	ENST00000341547;ENST00000357063;ENST00000377534;ENST00000321797;ENST00000526202;ENST00000465261	T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91	5.54	1.78	0.24846	.	0.550372	0.18949	N	0.126737	T	0.35970	0.0950	M	0.72118	2.19	0.09310	N	1	B;B;B	0.23377	0.011;0.084;0.028	B;B;B	0.16289	0.005;0.015;0.014	T	0.35151	-0.9800	10	0.54805	T	0.06	-3.1545	3.9455	0.09346	0.2622:0.4635:0.0:0.2743	.	1186;1260;1309	E9PMS6;Q8WWI1-3;E9PLH4	.;.;.	S	1260;1594;1594;1309;1186;1309	ENSP00000342112:P1260S;ENSP00000349571:P1594S;ENSP00000366757:P1594S;ENSP00000317802:P1309S;ENSP00000431129:P1186S;ENSP00000433352:P1309S	ENSP00000317802:P1309S	P	+	1	0	LMO7	75325488	0.003000	0.15002	0.023000	0.16930	0.185000	0.23345	-0.032000	0.12266	0.011000	0.14865	0.555000	0.69702	CCT	.	.	.	none		0.552	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358		T	76427487	C	T	76427487	3	4	257	1	0	0	0	0	1	0	0	0	8862	623	22	2	4894	2	LMO7	13	76427487	Missense_Mutation	SNP	C	TCGA-UZ-A9PK-01A-11D-A382-10	51048934	76427487	38742391	42	16012											
SIPA1L1	26037	hgsc.bcm.edu	37	chr14	72196928	72196928	+	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	tggaccaagccctgcccaacGacgtcctcttcagtagcacg	9	7	9	16	3	2	0	1	0	1	0	3	2	3	1	4	1	4	2	4	1	3	2			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr14:72196928G>T	ENST00000555818.1	+	18	5182	c.4834G>T	c.(4834-4836)Gac>Tac	p.D1612Y	SIPA1L1_ENST00000537413.1_Missense_Mutation_p.D1066Y|SIPA1L1_ENST00000381232.3_Missense_Mutation_p.D1591Y|SIPA1L1_ENST00000554874.1_3'UTR|SIPA1L1_ENST00000358550.2_Missense_Mutation_p.D1591Y	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	1612					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)		CCTGCCCAACGACGTCCTCTT	0.547																																					p.D1612Y		Atlas-SNP	.											.	SIPA1L1	219	.	0			c.G4834T						PASS	.						113	96	102					14																	72196928		2203	4300	6503	SO:0001583	missense	26037	exon18			CCCAACGACGTCC	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.4834G>T	chr14.hg19:g.72196928G>T	ENSP00000450832:p.Asp1612Tyr	132.0	0.0	.		121.0	43.0	.	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	hg19	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.587630	0.86851	.	.	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550;ENST00000537413	T;T;T;T	0.62788	0.0;0.0;0.0;0.0	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.80193	0.4578	M	0.74467	2.265	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.994;1.0	D;D;D;P;D	0.97110	1.0;0.986;0.999;0.886;1.0	T	0.82345	-0.0503	10	0.87932	D	0	-21.812	19.0376	0.92985	0.0:0.0:1.0:0.0	.	1066;1612;1066;1591;1612	F5GYF8;A6H8W6;B4DYX7;O43166-2;O43166	.;.;.;.;SI1L1_HUMAN	Y	1591;1612;1591;1066	ENSP00000370630:D1591Y;ENSP00000450832:D1612Y;ENSP00000351352:D1591Y;ENSP00000440682:D1066Y	ENSP00000351352:D1612Y	D	+	1	0	SIPA1L1	71266681	1.000000	0.71417	0.748000	0.31131	0.966000	0.64601	9.300000	0.96151	2.491000	0.84063	0.462000	0.41574	GAC	.	.	.	none		0.547	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		T	72196928	G	T	72196928	3	4	257	1	0	0	0	0	1	0	0	0	14342	1058	37	4	4900	4	SIPA1L1	14	72196928	Missense_Mutation	SNP	G	TCGA-UZ-A9PK-01A-11D-A382-10		72196928	35152612	43	16013											
C14orf102	55051	hgsc.bcm.edu	37	chr14	90769166	90769166	+	Frame_Shift_Del	DEL	T	T	-																															ttttccataaagactgtgaaTttttgatatcgaaaaggtac																										TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr14:90769166delT	ENST00000354366.3	-	6	1541	c.1309delA	c.(1309-1311)attfs	p.I437fs	NRDE2_ENST00000357904.3_Frame_Shift_Del_p.I206fs	NM_017970.3	NP_060440.2	Q9H7Z3	NRDE2_HUMAN	NRDE-2, necessary for RNA interference, domain containing	437																	AGACTGTGAATTTTTGATATC	0.428																																					p.I437fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.1310delT						PASS	.						68	69	69					14																	90769166		2203	4300	6503	SO:0001589	frameshift_variant	55051	exon6			.	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.1309delA	chr14.hg19:g.90769166delT	ENSP00000346335:p.Ile437fs	88.0	0.0	0		99.0	32.0	0.323232	NM_017970	B4DH71|Q4G0A7|Q9NWH6	Frame_Shift_Del	DEL	ENST00000354366.3	hg19	CCDS9890.1																																																																																			.	.	.	none		0.428	NRDE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411264.1	NM_017970		-	90769166	T	-	90769166	7	5	257	1	0	1	0	1	0	0	0	0	1737	1493	52	0	2221	0	C14orf102	14	90769166	Frame_Shift_Del	DEL	T	TCGA-UZ-A9PK-01A-11D-A382-10	18572238	90769166	16580374	44	16014											
ABCC1	4363	hgsc.bcm.edu	37	chr16	16215909	16215909	+	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	ccggtctattcccatttcaaCgagaccttgctgggggtcag	7	11	11	12	2	3	1	2	0	1	1	4	2	4	1	3	3	2	1	3	3	2	4			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr16:16215909C>T	ENST00000399410.3	+	24	3643	c.3468C>T	c.(3466-3468)aaC>aaT	p.N1156N	ABCC1_ENST00000351154.5_Silent_p.N1097N|ABCC1_ENST00000346370.5_Silent_p.N1100N|ABCC1_ENST00000345148.5_Silent_p.N1156N|ABCC1_ENST00000399408.2_Silent_p.N1166N|ABCC1_ENST00000349029.5_Silent_p.N1041N	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	1156	ABC transmembrane type-1 2. {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)	CCCATTTCAACGAGACCTTGC	0.602																																					p.N1156N		Atlas-SNP	.											.	ABCC1	156	.	0			c.C3468T						PASS	.						47	51	50					16																	16215909		2177	4291	6468	SO:0001819	synonymous_variant	4363	exon24			TTTCAACGAGACC	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.3468C>T	chr16.hg19:g.16215909C>T		148.0	0.0	.		189.0	102.0	.	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Silent	SNP	ENST00000399410.3	hg19	CCDS42122.1																																																																																			.	.	.	none		0.602	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996		T	16215909	C	T	16215909	2	4	257	1	0	0	0	0	0	0	0	1	49	535	19	1		1	ABCC1	16	16215909	Silent	SNP	C	TCGA-UZ-A9PK-01A-11D-A382-10		16215909	74138844	45	16015											
SIAH1	6477	hgsc.bcm.edu	37	chr16	48395959	48395959	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaagcaccagggcacggacaGgaataaggcctaaactcaca	16	3	11	11	1	1	0	1	0	0	0	1	3	1	2	2	4	2	2	2	4	5	2			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr16:48395959G>A	ENST00000380006.2	-	1	1834	c.381C>T	c.(379-381)tcC>tcT	p.S127S	SIAH1_ENST00000573005.1_5'Flank|SIAH1_ENST00000356721.3_Silent_p.S158S|SIAH1_ENST00000394725.2_Silent_p.S127S			Q8IUQ4	SIAH1_HUMAN	siah E3 ubiquitin protein ligase 1	127	SBD.				anatomical structure morphogenesis (GO:0009653)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell cycle (GO:0007049)|nervous system development (GO:0007399)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein catabolic process (GO:0030163)|protein destabilization (GO:0031648)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|proteolysis (GO:0006508)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	beta-catenin destruction complex (GO:0030877)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ligase activity (GO:0016874)|protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(1)|ovary(1)|stomach(1)	7		all_cancers(37;0.157)|all_lung(18;0.11)|Breast(268;0.238)				GGCACGGACAGGAATAAGGCC	0.473																																					p.S158S		Atlas-SNP	.											.	SIAH1	33	.	0			c.C474T						PASS	.						82	61	69					16																	48395959		2200	4300	6500	SO:0001819	synonymous_variant	6477	exon2			CGGACAGGAATAA	U76247	CCDS10735.1, CCDS32444.1	16q12.1	2013-06-03	2012-02-23		ENSG00000196470	ENSG00000196470			10857	protein-coding gene	gene with protein product		602212	"seven in absentia homolog 1 (Drosophila)"			9403064, 9334332	Standard	NM_001006610		Approved	hSIAH1	uc002efo.1	Q8IUQ4	OTTHUMG00000175417	ENST00000380006.2:c.381C>T	chr16.hg19:g.48395959G>A		125.0	0.0	.		140.0	34.0	.	NM_001006610	A0FKF3|O43269|Q49A58|Q92880	Silent	SNP	ENST00000380006.2	hg19	CCDS10735.1																																																																																			.	.	.	none		0.473	SIAH1-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256842.12			A	48395959	G	A	48395959	2	1	257	1	0	0	0	0	0	0	0	1	14312	987	35	2		2	SIAH1	16	48395959	Silent	SNP	G	TCGA-UZ-A9PK-01A-11D-A382-10	32180050	48395959	41958794	46	16016											
C16orf86	388284	hgsc.bcm.edu	37	chr16	67702481	67702482	+	Frame_Shift_Ins	INS	-	-	T																															actgctccacttgtccccccINSgctctctcctcagtacaagt																								rs376801265		TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr16:67702481_67702482insT	ENST00000403458.4	+	4	1087_1088	c.932_933insT	c.(931-936)ccgctcfs	p.L312fs	ENKD1_ENST00000602644.1_5'Flank|ENKD1_ENST00000243878.4_5'Flank|ENKD1_ENST00000602409.1_5'Flank	NM_001012984.2	NP_001013002.2	Q6ZW13	CP086_HUMAN	chromosome 16 open reading frame 86	312										endometrium(2)|lung(4)	6		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.047)|all cancers(182;0.228)		CTTGTCCCCCCGCTCTCTCCTC	0.609											OREG0023886	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P311fs		Atlas-Indel,Pindel	.											.	C16orf86	20	.	0			c.932_933insT						PASS	.																																			SO:0001589	frameshift_variant	388284	exon4			.		CCDS32468.2	16q22.1	2008-10-30			ENSG00000159761	ENSG00000159761			33755	protein-coding gene	gene with protein product							Standard	NM_001012984		Approved	FLJ41802	uc002ety.3	Q6ZW13	OTTHUMG00000150527	Exception_encountered	chr16.hg19:g.67702481_67702482insT	ENSP00000384117:p.Leu312fs	80.0	0.0	0	1101	114.0	57.0	0.5	NM_001012984	B5MCW6	Frame_Shift_Ins	INS	ENST00000403458.4	hg19	CCDS32468.2																																																																																			.	.	.	none		0.609	C16orf86-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318767.2	NM_001012984		T	67702482	-	T	67702481	7	5	257	1	0	1	1	0	0	0	0	0	1841	652	23	0	946	0	C16orf86	16	67702481	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PK-01A-11D-A382-10	19306522	67702481	22652272	47	16017											
SLC16A13	201232	hgsc.bcm.edu	37	chr17	6941759	6941759	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcccaactcacctctctccTccatcatggccccttcctcc	5	10	4	22	0	3	0	2	0	1	0	8	0	7	0	8	2	1	0	8	2	1	1			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr17:6941759T>C	ENST00000308027.6	+	3	940	c.632T>C	c.(631-633)cTc>cCc	p.L211P		NM_201566.2	NP_963860.1	Q7RTY0	MOT13_HUMAN	solute carrier family 16, member 13	211						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						ACCTCTCTCCTCCATCATGGC	0.627																																					p.L211P		Atlas-SNP	.											.	SLC16A13	28	.	0			c.T632C						PASS	.						128	114	119					17																	6941759		2203	4300	6503	SO:0001583	missense	201232	exon3			CTCTCCTCCATCA	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.632T>C	chr17.hg19:g.6941759T>C	ENSP00000309751:p.Leu211Pro	79.0	0.0	.		111.0	63.0	.	NM_201566	A3KMG3|A5PKU5|Q2VP92	Missense_Mutation	SNP	ENST00000308027.6	hg19	CCDS11085.1	.	.	.	.	.	.	.	.	.	.	T	19.89	3.911210	0.72983	.	.	ENSG00000174327	ENST00000308027	T	0.65364	-0.15	5.46	5.46	0.80206	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.77968	0.4210	M	0.83483	2.645	0.80722	D	1	D	0.59767	0.986	D	0.63597	0.916	T	0.81335	-0.0979	10	0.72032	D	0.01	.	11.9187	0.52779	0.0:0.0:0.0:1.0	.	211	Q7RTY0	MOT13_HUMAN	P	211	ENSP00000309751:L211P	ENSP00000309751:L211P	L	+	2	0	SLC16A13	6882483	0.987000	0.35691	0.255000	0.24374	0.994000	0.84299	4.424000	0.59868	2.057000	0.61298	0.460000	0.39030	CTC	.	.	.	none		0.627	SLC16A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219923.2			C	6941759	T	C	6941759	3	2	257	1	0	0	0	0	1	0	0	0	14419	1551	54	3	642	3	SLC16A13	17	6941759	Missense_Mutation	SNP	T	TCGA-UZ-A9PK-01A-11D-A382-10		6941759	74253451	48	16018											
MYH13	8735	hgsc.bcm.edu	37	chr17	10222337	10222337	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggaactcagcctccctctTcttgttcatctcaatctggg	6	14	7	14	0	6	0	3	0	4	0	8	1	7	1	2	2	2	1	2	2	2	3			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr17:10222337T>C	ENST00000418404.3	-	26	3671	c.3508A>G	c.(3508-3510)Aag>Gag	p.K1170E	RP11-401O9.4_ENST00000609088.1_RNA|MYH13_ENST00000252172.4_Missense_Mutation_p.K1170E|RP11-401O9.3_ENST00000577743.1_RNA			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	1170					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						GCCTCCCTCTTCTTGTTCATC	0.582																																					p.K1170E		Atlas-SNP	.											.	MYH13	533	.	0			c.A3508G						PASS	.						140	147	144					17																	10222337		2203	4300	6503	SO:0001583	missense	8735	exon27			CCCTCTTCTTGTT	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.3508A>G	chr17.hg19:g.10222337T>C	ENSP00000404570:p.Lys1170Glu	118.0	0.0	.		211.0	115.0	.	NM_003802	O95252|Q9P0U8	Missense_Mutation	SNP	ENST00000418404.3	hg19	CCDS45613.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.641331	0.87859	.	.	ENSG00000006788	ENST00000252172	D	0.84873	-1.91	4.05	4.05	0.47172	Myosin tail (1);	.	.	.	.	D	0.94532	0.8239	H	0.97540	4.025	0.43517	D	0.995783	P	0.45011	0.848	P	0.62435	0.902	D	0.95834	0.8860	9	0.66056	D	0.02	.	13.4569	0.61204	0.0:0.0:0.0:1.0	.	1170	Q9UKX3	MYH13_HUMAN	E	1170	ENSP00000252172:K1170E	ENSP00000252172:K1170E	K	-	1	0	MYH13	10163062	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.971000	0.70440	1.815000	0.52974	0.482000	0.46254	AAG	.	.	.	none		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		C	10222337	T	C	10222337	3	2	257	1	0	0	0	0	1	0	0	0	10039	1792	62	3	2368	3	MYH13	17	10222337	Missense_Mutation	SNP	T	TCGA-UZ-A9PK-01A-11D-A382-10	3280578	10222337	70972873	49	16019											
DNAH9	1770	hgsc.bcm.edu	37	chr17	11845791	11845791	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctcactgagggagctggagCtcggcttaaaggtgagcgcg	8	7	17	9	3	1	2	1	2	0	0	2	4	1	4	0	4	3	4	0	4	2	1			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr17:11845791C>T	ENST00000262442.4	+	67	12900	c.12832C>T	c.(12832-12834)Ctc>Ttc	p.L4278F	DNAH9_ENST00000454412.2_Missense_Mutation_p.L4202F|DNAH9_ENST00000608377.1_Missense_Mutation_p.L590F|DNAH9_ENST00000396001.2_3'UTR	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	4278					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)		GGAGCTGGAGCTCGGCTTAAA	0.567																																					p.L4278F		Atlas-SNP	.											.	DNAH9	695	.	0			c.C12832T						PASS	.						66	60	62					17																	11845791		2203	4300	6503	SO:0001583	missense	1770	exon67			CTGGAGCTCGGCT	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.12832C>T	chr17.hg19:g.11845791C>T	ENSP00000262442:p.Leu4278Phe	99.0	0.0	.		109.0	36.0	.	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	hg19	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	C	18.22	3.574755	0.65878	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703;ENST00000396001	T;T;T	0.09630	2.96;2.96;2.96	4.86	3.89	0.44902	Dynein heavy chain (1);	0.142496	0.47852	D	0.000204	T	0.47395	0.1443	H	0.97587	4.035	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.66756	-0.5843	10	0.87932	D	0	.	13.5144	0.61533	0.0:0.9244:0.0:0.0756	.	4278	Q9NYC9	DYH9_HUMAN	F	4278;4202;2784;590	ENSP00000262442:L4278F;ENSP00000414874:L4202F;ENSP00000379323:L590F	ENSP00000262442:L4278F	L	+	1	0	DNAH9	11786516	0.986000	0.35501	0.977000	0.42913	0.806000	0.45545	2.527000	0.45615	1.266000	0.44231	0.462000	0.41574	CTC	.	.	.	none		0.567	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11845791	C	T	11845791	3	4	257	1	0	0	0	0	1	0	0	0	4610	797	28	2	13098	2	DNAH9	17	11845791	Missense_Mutation	SNP	C	TCGA-UZ-A9PK-01A-11D-A382-10	1623454	11845791	69349419	50	16020											
C17orf71	55181	hgsc.bcm.edu	37	chr17	57289014	57289014	+	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	cttgcccaggctcttcgagtGtacagtcaacatgctagagg	9	10	11	11	1	2	1	1	0	1	1	3	2	2	1	1	2	4	3	1	2	3	4			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr17:57289014G>A	ENST00000543872.2	+	2	1866	c.1602G>A	c.(1600-1602)gtG>gtA	p.V534V	SMG8_ENST00000580498.1_Intron|CTD-2510F5.6_ENST00000577660.1_Intron|SMG8_ENST00000578922.1_Silent_p.V534V|SMG8_ENST00000300917.5_Silent_p.V534V			Q8ND04	SMG8_HUMAN	SMG8 nonsense mediated mRNA decay factor	534					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						CTCTTCGAGTGTACAGTCAAC	0.458																																					p.V534V		Atlas-SNP	.											.	SMG8	79	.	0			c.G1602A						PASS	.						91	82	85					17																	57289014		2203	4300	6503	SO:0001819	synonymous_variant	55181	exon1			TCGAGTGTACAGT	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.1602G>A	chr17.hg19:g.57289014G>A		152.0	0.0	.		228.0	117.0	.	NM_018149	Q8N5U5|Q8TDN0|Q9H5P5|Q9NVQ1	Silent	SNP	ENST00000543872.2	hg19	CCDS11615.1																																																																																			.	.	.	none		0.458	SMG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445960.2	NM_018149		A	57289014	G	A	57289014	2	1	257	1	0	0	0	0	0	0	0	1	1880	1364	48	2		2	C17orf71	17	57289014	Silent	SNP	G	TCGA-UZ-A9PK-01A-11D-A382-10	45443223	57289014	23906196	51	16021											
NAT9	26151	hgsc.bcm.edu	37	chr17	72767943	72767946	+	Frame_Shift_Del	DEL	ACTC	ACTC	-																															cagaagccactgatgctcggActcactcactgtcagtctga																										TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	ACTC	ACTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr17:72767943_72767946delACTC	ENST00000357814.3	-	7	614_617	c.541_544delGAGT	c.(541-546)gagtccfs	p.ES181fs	NAT9_ENST00000583476.1_3'UTR|NAT9_ENST00000578822.1_Frame_Shift_Del_p.ES186fs|NAT9_ENST00000582870.1_Frame_Shift_Del_p.ES185fs|NAT9_ENST00000580216.1_5'Flank|NAT9_ENST00000582524.1_Stop_Codon_Del|NAT9_ENST00000581136.1_Frame_Shift_Del_p.ES176fs|NAT9_ENST00000583757.1_Stop_Codon_Del|NAT9_ENST00000580301.1_Frame_Shift_Del_p.ES180fs|NAT9_ENST00000580632.1_Frame_Shift_Del_p.ES181fs	NM_015654.3	NP_056469.2	Q9BTE0	NAT9_HUMAN	N-acetyltransferase 9 (GCN5-related, putative)	181						protein complex (GO:0043234)	N-acetyltransferase activity (GO:0008080)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)	8						TGATGCTCGGACTCACTCACTGTC	0.559																																					p.181_182del		Atlas-Indel,Pindel	.											.	NAT9	16	.	0			c.542_545del						PASS	.																																			SO:0001589	frameshift_variant	26151	exon7			.	AK123115	CCDS11706.1	17q25.2	2011-11-25	2008-09-24		ENSG00000109065	ENSG00000109065			23133	protein-coding gene	gene with protein product			"N-acetyltransferase 9"			14608357	Standard	NM_015654		Approved	DKFZP564C103	uc002jlq.3	Q9BTE0		ENST00000357814.3:c.541_544delGAGT	chr17.hg19:g.72767947_72767950delACTC	ENSP00000350467:p.Glu181fs	78.0	0.0	0		115.0	56.0	0.486957	NM_015654	B2R7F0|Q9BTD0|Q9Y3T3	Frame_Shift_Del	DEL	ENST00000357814.3	hg19	CCDS11706.1																																																																																			.	.	.	none		0.559	NAT9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000443700.1	NM_015654		-	72767946	ACTC	-	72767943	7	5	257	1	0	1	0	1	0	0	0	0	10189	275	10	0	83	0	NAT9	17	72767943	Frame_Shift_Del	DEL	ACTC	TCGA-UZ-A9PK-01A-11D-A382-10	15478929	72767943	8427267	52	16022											
ALPK2	115701	hgsc.bcm.edu	37	chr18	56246259	56246259	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctgctgctgtggtgtgagaAgtctctcttttatcactctg	5	16	11	9	0	4	1	1	1	3	1	5	2	4	1	0	1	2	3	0	1	2	2			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr18:56246259A>G	ENST00000361673.3	-	4	1962	c.1749T>C	c.(1747-1749)acT>acC	p.T583T	ALPK2_ENST00000587399.1_5'UTR	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	583						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						TGGTGTGAGAAGTCTCTCTTT	0.488											OREG0025011	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T583T		Atlas-SNP	.											.	ALPK2	487	.	0			c.T1749C						PASS	.						112	98	103					18																	56246259		2203	4300	6503	SO:0001819	synonymous_variant	115701	exon4			GTGAGAAGTCTCT	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.1749T>C	chr18.hg19:g.56246259A>G		135.0	0.0	.	1014	139.0	47.0	.	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	hg19	CCDS11966.2																																																																																			.	.	.	none		0.488	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		G	56246259	A	G	56246259	2	3	257	1	0	0	0	0	0	0	0	1	545	59	3	3		3	ALPK2	18	56246259	Silent	SNP	A	TCGA-UZ-A9PK-01A-11D-A382-10		56246259	21830989	53	16023											
ALPK2	115701	hgsc.bcm.edu	37	chr18	56246453	56246453	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taagtcctttccccccactcTcttgtcagctgccgtctccc	4	13	5	19	1	3	0	1	0	2	0	7	0	5	0	6	0	2	1	6	0	1	3			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr18:56246453T>C	ENST00000361673.3	-	4	1768	c.1555A>G	c.(1555-1557)Aga>Gga	p.R519G	ALPK2_ENST00000587399.1_5'Flank	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	519						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						CCCCCCACTCTCTTGTCAGCT	0.517											OREG0025011	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R519G		Atlas-SNP	.											.	ALPK2	487	.	0			c.A1555G						PASS	.						215	216	215					18																	56246453		2203	4300	6503	SO:0001583	missense	115701	exon4			CCACTCTCTTGTC	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.1555A>G	chr18.hg19:g.56246453T>C	ENSP00000354991:p.Arg519Gly	97.0	0.0	.	1014	82.0	22.0	.	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	hg19	CCDS11966.2	.	.	.	.	.	.	.	.	.	.	T	15.35	2.806447	0.50421	.	.	ENSG00000198796	ENST00000361673	T	0.55052	0.54	5.14	1.07	0.20283	.	1.544590	0.04399	N	0.363947	T	0.44871	0.1314	L	0.31752	0.955	0.09310	N	1	B	0.24963	0.115	B	0.25614	0.062	T	0.40887	-0.9539	10	0.39692	T	0.17	-1.5845	12.1854	0.54236	0.0:0.0:0.4301:0.5699	.	519	Q86TB3	ALPK2_HUMAN	G	519	ENSP00000354991:R519G	ENSP00000354991:R519G	R	-	1	2	ALPK2	54397433	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.462000	0.21956	0.270000	0.21984	0.533000	0.62120	AGA	.	.	.	none		0.517	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		C	56246453	T	C	56246453	3	2	257	1	0	0	0	0	1	0	0	0	545	1559	54	3	4997	3	ALPK2	18	56246453	Missense_Mutation	SNP	T	TCGA-UZ-A9PK-01A-11D-A382-10	194	56246453	21830795	54	16024											
ODF3L2	284451	hgsc.bcm.edu	37	chr19	464231	464231	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggggcatggtgtaggcattAggggcaggggctgaggtgtc	6	8	22	5	0	0	1	0	1	0	0	1	1	0	1	0	9	0	5	0	9	2	2			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr19:464231A>G	ENST00000315489.4	-	4	718	c.483T>C	c.(481-483)ccT>ccC	p.P161P	ODF3L2_ENST00000382696.3_Silent_p.P125P	NM_182577.2	NP_872383.1	Q3SX64	OD3L2_HUMAN	outer dense fiber of sperm tails 3-like 2	161	Pro-rich.					cytoplasmic microtubule (GO:0005881)				large_intestine(1)|lung(2)	3						TGTAGGCATTAGGGGCAGGGG	0.711																																					p.P161P		Atlas-SNP	.											.	ODF3L2	18	.	0			c.T483C						PASS	.						6	7	7					19																	464231		1948	3822	5770	SO:0001819	synonymous_variant	284451	exon4			GGCATTAGGGGCA	AK097378	CCDS12027.1	19p13.3	2010-04-23	2008-07-04	2008-07-04		ENSG00000181781			26841	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 19"	C19orf19		14702039	Standard	NM_182577		Approved	FLJ40059	uc002lor.3	Q3SX64		ENST00000315489.4:c.483T>C	chr19.hg19:g.464231A>G		87.0	0.0	.		84.0	18.0	.	NM_182577	Q3SX65|Q8N1L2	Silent	SNP	ENST00000315489.4	hg19	CCDS12027.1																																																																																			.	.	.	none		0.711	ODF3L2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451849.2	NM_182577		G	464231	A	G	464231	2	3	257	1	0	0	0	0	0	0	0	1	10839	407	15	3		3	ODF3L2	19	464231	Silent	SNP	A	TCGA-UZ-A9PK-01A-11D-A382-10		464231	58664752	55	16025											
UBXN6	80700	hgsc.bcm.edu	37	chr19	4446696	4446696	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaggtggtctcgctcagcaCgtagaactcctcggggtcct	7	9	12	13	3	2	1	1	0	1	1	6	1	4	1	2	4	2	3	2	4	3	1	rs563472721		TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr19:4446696C>T	ENST00000301281.6	-	8	845	c.721G>A	c.(721-723)Gtg>Atg	p.V241M	CTB-50L17.7_ENST00000588798.1_RNA|MIR4746_ENST00000579802.1_RNA|UBXN6_ENST00000394765.3_Missense_Mutation_p.V188M	NM_025241.2	NP_079517.1	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	241	PUB.					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						TCGCTCAGCACGTAGAACTCC	0.677																																					p.V241M		Atlas-SNP	.											.	UBXN6	27	.	0			c.G721A						PASS	.						41	39	39					19																	4446696		2203	4299	6502	SO:0001583	missense	80700	exon8			TCAGCACGTAGAA	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.721G>A	chr19.hg19:g.4446696C>T	ENSP00000301281:p.Val241Met	108.0	0.0	.		114.0	46.0	.	NM_025241	D6W626|Q96AH1|Q96IK9|Q9BZV0	Missense_Mutation	SNP	ENST00000301281.6	hg19	CCDS12129.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.123000	0.77436	.	.	ENSG00000167671	ENST00000301281;ENST00000394765	T;T	0.39056	1.54;1.1	4.82	4.82	0.62117	PUG domain (1);PUB domain (1);	0.000000	0.85682	D	0.000000	T	0.67221	0.2870	M	0.81802	2.56	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.996;1.0	T	0.72994	-0.4122	10	0.72032	D	0.01	-49.8103	16.8633	0.86023	0.0:1.0:0.0:0.0	.	188;241	Q9BZV1-2;Q9BZV1	.;UBXN6_HUMAN	M	241;188	ENSP00000301281:V241M;ENSP00000378246:V188M	ENSP00000301281:V241M	V	-	1	0	UBXN6	4397696	1.000000	0.71417	0.994000	0.49952	0.566000	0.35808	5.377000	0.66184	2.227000	0.72691	0.491000	0.48974	GTG	.	.	.	none		0.677	UBXN6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458447.3	NM_025241		T	4446696	C	T	4446696	3	4	257	1	0	0	0	0	1	0	0	0	16929	536	19	1	620	1	UBXN6	19	4446696	Missense_Mutation	SNP	C	TCGA-UZ-A9PK-01A-11D-A382-10	3982465	4446696	54682287	56	16026											
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11113759	11113759	+	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	cggtgaaggtgatccacgtgGagagtgggaagatcctcaca	11	7	15	8	2	1	4	1	2	0	2	3	6	3	5	2	4	0	0	2	4	2	0			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr19:11113759G>T	ENST00000429416.3	+	13	2148	c.1867G>T	c.(1867-1869)Gag>Tag	p.E623*	SMARCA4_ENST00000590574.1_Nonsense_Mutation_p.E623*|SMARCA4_ENST00000413806.3_Nonsense_Mutation_p.E623*|SMARCA4_ENST00000589677.1_Nonsense_Mutation_p.E623*|SMARCA4_ENST00000541122.2_Nonsense_Mutation_p.E623*|SMARCA4_ENST00000344626.4_Nonsense_Mutation_p.E623*|SMARCA4_ENST00000444061.3_Nonsense_Mutation_p.E623*|SMARCA4_ENST00000358026.2_Nonsense_Mutation_p.E623*|SMARCA4_ENST00000450717.3_Nonsense_Mutation_p.E623*	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	623					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)				GATCCACGTGGAGAGTGGGAA	0.602			"F, N, Mis"		NSCLC																																p.E623X		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.G1867T						PASS	.						85	84	84					19																	11113759		2203	4300	6503	SO:0001587	stop_gained	6597	exon12			CACGTGGAGAGTG	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.1867G>T	chr19.hg19:g.11113759G>T	ENSP00000395654:p.Glu623*	111.0	0.0	.		90.0	38.0	.	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Nonsense_Mutation	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	G	39	7.430867	0.98279	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	.	.	.	4.57	4.57	0.56435	.	0.059842	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	-47.5138	16.6596	0.85238	0.0:0.0:1.0:0.0	.	.	.	.	X	623;623;687;623;623;623;623;623	.	ENSP00000343896:E623X	E	+	1	0	SMARCA4	10974759	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	9.601000	0.98297	2.526000	0.85167	0.563000	0.77884	GAG	.	.	.	none		0.602	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		T	11113759	G	T	11113759	4	4	257	1	0	0	0	0	0	1	0	0	14783	1175	41	4	1909	4	SMARCA4	19	11113759	Nonsense_Mutation	SNP	G	TCGA-UZ-A9PK-01A-11D-A382-10	6667063	11113759	48015224	57	16027											
LDLR	3949	hgsc.bcm.edu	37	chr19	11217362	11217363	+	Splice_Site	DEL	TG	TG	-																															gatgaagttggctgcgttaaTggtgagcgctggccatctgg																										TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr19:11217362_11217363delTG	ENST00000558518.1	+	5	1003_1004	c.816_817delTG	c.(814-819)aatgtg>aatg	p.V273fs	LDLR_ENST00000558013.1_Splice_Site_p.V273fs|LDLR_ENST00000455727.2_Intron|LDLR_ENST00000545707.1_Splice_Site_p.V146fs|LDLR_ENST00000535915.1_Splice_Site_p.V232fs|LDLR_ENST00000557933.1_Splice_Site_p.V273fs	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor	273					cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|intestinal cholesterol absorption (GO:0030299)|lipid metabolic process (GO:0006629)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|phototransduction, visible light (GO:0007603)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol homeostasis (GO:2000188)|regulation of phosphatidylcholine catabolic process (GO:0010899)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.?(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Porfimer(DB00707)	GCTGCGTTAATGGTGAGCGCTG	0.54																																					p.272_272del	GBM(18;201 575 7820 21545)	Atlas-Indel,Pindel	.											.	LDLR	72	.	1	Unknown(1)	lung(1)	c.815_816del						PASS	.																																			SO:0001630	splice_region_variant	3949	exon5			.	AY114155	CCDS12254.1, CCDS56083.1, CCDS56084.1, CCDS56085.1, CCDS58651.1	19p13.2	2014-09-17	2008-08-01		ENSG00000130164	ENSG00000130164		"Low density lipoprotein receptors"	6547	protein-coding gene	gene with protein product	"familial hypercholesterolemia"	606945					Standard	NM_000527		Approved	LDLCQ2	uc002mqk.4	P01130		ENST00000558518.1:c.817+1TG>-	chr19.hg19:g.11217362_11217363delTG		148.0	0.0	0		120.0	48.0	0.4	NM_001195798	B4DII3|B4DJZ8|B4DR00|B4DTQ3|C0JYY8|H0YLU8|H0YNT7|Q53ZD9|Q59FQ1|Q9UDH7	Frame_Shift_Del	DEL	ENST00000558518.1	hg19	CCDS12254.1																																																																																			.	.	.	none		0.54	LDLR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415973.2		Frame_Shift_Del	-	11217363	TG	-	11217362	8	5	257	1	0	1	0	1	0	0	1	0	8711	1478	51	0	834	0	LDLR	19	11217362	Splice_Site	DEL	TG	TCGA-UZ-A9PK-01A-11D-A382-10	103603	11217362	47911621	58	16028											
ELAVL3	1995	hgsc.bcm.edu	37	chr19	11577519	11577519	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtcatgttctggggcaggtAgttgacgatgaggttggtct	6	13	17	5	1	3	2	1	2	2	0	3	3	3	2	0	6	0	5	0	6	1	4			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr19:11577519A>G	ENST00000359227.3	-	2	557	c.133T>C	c.(133-135)Tac>Cac	p.Y45H	CTC-398G3.6_ENST00000585656.1_3'UTR|ELAVL3_ENST00000438662.2_Missense_Mutation_p.Y45H|RN7SL669P_ENST00000581926.1_RNA	NM_001420.3|NM_032281.2	NP_001411.2|NP_115657.2	Q14576	ELAV3_HUMAN	ELAV like neuron-specific RNA binding protein 3	45	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)		AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)			breast(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15						TGGGGCAGGTAGTTGACGATG	0.602																																					p.Y45H		Atlas-SNP	.											.	ELAVL3	58	.	0			c.T133C						PASS	.						149	127	134					19																	11577519		2203	4300	6503	SO:0001583	missense	1995	exon2			GCAGGTAGTTGAC		CCDS32912.1, CCDS45978.1	19p13.2	2013-10-03	2013-10-03			ENSG00000196361		"RNA binding motif (RRM) containing"	3314	protein-coding gene	gene with protein product	"Hu antigen C", "paraneoplastic limbic encephalitis antigen 21", "paraneoplastic cerebellar degeneration-associated antigen", "ELAV-like protein 3"	603458	"ELAV (embryonic lethal, abnormal vision, Drosophila)-like 3 (Hu antigen C)"			9799595	Standard	NM_001420		Approved	HUC, PLE21, DKFZp547J036, HUCL, MGC20653	uc002mry.1	Q14576		ENST00000359227.3:c.133T>C	chr19.hg19:g.11577519A>G	ENSP00000352162:p.Tyr45His	129.0	0.0	.		102.0	32.0	.	NM_032281	Q16135|Q96CL8|Q96QS9	Missense_Mutation	SNP	ENST00000359227.3	hg19	CCDS32912.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.214625	0.79352	.	.	ENSG00000196361	ENST00000359227;ENST00000438662	T;T	0.73897	-0.79;3.4	4.83	3.82	0.43975	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.72969	0.3527	N	0.13352	0.335	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.76071	0.987;0.986	T	0.75033	-0.3460	10	0.87932	D	0	.	9.5216	0.39138	0.9149:0.0:0.085:0.0	.	45;45	Q14576;Q14576-2	ELAV3_HUMAN;.	H	45	ENSP00000352162:Y45H;ENSP00000390878:Y45H	ENSP00000352162:Y45H	Y	-	1	0	ELAVL3	11438519	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.943000	0.92975	0.887000	0.36136	0.523000	0.50628	TAC	.	.	.	none		0.602	ELAVL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458827.2	NM_001420		G	11577519	A	G	11577519	3	3	257	1	0	0	0	0	1	0	0	0	5053	420	15	3	994	3	ELAVL3	19	11577519	Missense_Mutation	SNP	A	TCGA-UZ-A9PK-01A-11D-A382-10	360157	11577519	47551464	59	16029											
ZBTB32	27033	hgsc.bcm.edu	37	chr19	36205913	36205913	+	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	caggcctgaagaaacatcagGaggagccagagaaaccctca	16	3	11	11	0	2	3	2	1	0	2	2	6	2	5	3	3	3	0	3	3	3	0			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr19:36205913G>A	ENST00000392197.2	+	3	703	c.385G>A	c.(385-387)Gag>Aag	p.E129K	ZBTB32_ENST00000262630.3_Missense_Mutation_p.E129K			Q9Y2Y4	ZBT32_HUMAN	zinc finger and BTB domain containing 32	129					DNA repair (GO:0006281)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cytokine production (GO:0001817)|T cell proliferation (GO:0042098)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(1)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	14	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GAAACATCAGGAGGAGCCAGA	0.572																																					p.E129K		Atlas-SNP	.											.	ZBTB32	33	.	0			c.G385A						PASS	.						45	48	47					19																	36205913		2203	4300	6503	SO:0001583	missense	27033	exon2			CATCAGGAGGAGC	AF130255	CCDS12471.1	19q13.1	2013-01-08			ENSG00000011590	ENSG00000011590		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	16763	protein-coding gene	gene with protein product	"repressor of GATA"	605859				10572087	Standard	XM_005258739		Approved	TZFP, FAZF, FAXF, Rog, ZNF538	uc002oay.3	Q9Y2Y4	OTTHUMG00000048118	ENST00000392197.2:c.385G>A	chr19.hg19:g.36205913G>A	ENSP00000376035:p.Glu129Lys	147.0	0.0	.		173.0	17.0	.	NM_014383	Q8WVP2	Missense_Mutation	SNP	ENST00000392197.2	hg19	CCDS12471.1	.	.	.	.	.	.	.	.	.	.	G	10.90	1.482481	0.26598	.	.	ENSG00000011590	ENST00000262630;ENST00000392197	T;T	0.09073	3.02;3.02	4.6	3.56	0.40772	.	0.471504	0.18012	N	0.154527	T	0.05593	0.0147	L	0.27053	0.805	0.28847	N	0.896287	B	0.27997	0.197	B	0.19148	0.024	T	0.28650	-1.0037	10	0.27785	T	0.31	-7.7093	8.4166	0.32674	0.1093:0.0:0.8907:0.0	.	129	Q9Y2Y4	ZBT32_HUMAN	K	129	ENSP00000262630:E129K;ENSP00000376035:E129K	ENSP00000262630:E129K	E	+	1	0	ZBTB32	40897753	0.482000	0.25948	0.266000	0.24541	0.184000	0.23303	0.556000	0.23438	0.916000	0.36871	0.655000	0.94253	GAG	.	.	.	none		0.572	ZBTB32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109491.3	NM_014383		A	36205913	G	A	36205913	3	1	257	1	0	0	0	0	1	0	0	0	17547	1175	41	2	387	2	ZBTB32	19	36205913	Missense_Mutation	SNP	G	TCGA-UZ-A9PK-01A-11D-A382-10	24628394	36205913	22923070	60	16030											
PPP1R15A	23645	hgsc.bcm.edu	37	chr19	49376934	49376934	+	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	ctgtctcccagccttctgatAaggacactgcaaggttctga	9	11	9	12	0	3	2	0	2	3	0	4	3	3	3	2	2	2	2	2	2	2	3			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr19:49376934A>T	ENST00000200453.5	+	2	713	c.444A>T	c.(442-444)atA>atT	p.I148I		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	148					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)		GCCTTCTGATAAGGACACTGC	0.532																																					p.I148I		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.A444T						PASS	.						146	135	139					19																	49376934		2203	4300	6503	SO:0001819	synonymous_variant	23645	exon2			TCTGATAAGGACA	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.444A>T	chr19.hg19:g.49376934A>T		112.0	0.0	.		136.0	48.0	.	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Silent	SNP	ENST00000200453.5	hg19	CCDS12738.1																																																																																			.	.	.	none		0.532	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330		T	49376934	A	T	49376934	2	4	257	1	0	0	0	0	0	0	0	1	12373	352	13	5		5	PPP1R15A	19	49376934	Silent	SNP	A	TCGA-UZ-A9PK-01A-11D-A382-10	13171021	49376934	9752049	61	16031											
POFUT1	23509	hgsc.bcm.edu	37	chr20	30803187	30803187	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacccactggccccctgagaAgcgggtggcatactgctttg	7	8	12	14	1	0	1	0	1	0	1	0	2	0	1	3	3	3	2	3	3	2	2			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr20:30803187A>G	ENST00000375749.3	+	3	424	c.362A>G	c.(361-363)aAg>aGg	p.K121R	POFUT1_ENST00000375730.3_Missense_Mutation_p.K121R|POFUT1_ENST00000486717.1_3'UTR|POFUT1_ENST00000539210.1_Intron	NM_015352.1	NP_056167.1	Q9H488	OFUT1_HUMAN	protein O-fucosyltransferase 1	121					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)			CCCCCTGAGAAGCGGGTGGCA	0.597																																					p.K121R		Atlas-SNP	.											.	POFUT1	52	.	0			c.A362G						PASS	.						78	84	82					20																	30803187		2203	4300	6503	SO:0001583	missense	23509	exon3			CTGAGAAGCGGGT	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.362A>G	chr20.hg19:g.30803187A>G	ENSP00000364902:p.Lys121Arg	135.0	0.0	.		141.0	57.0	.	NM_172236	A8K4R8|E1P5M4|Q14685|Q5W185|Q9BW76	Missense_Mutation	SNP	ENST00000375749.3	hg19	CCDS13198.1	.	.	.	.	.	.	.	.	.	.	A	13.72	2.322856	0.41096	.	.	ENSG00000101346	ENST00000375749;ENST00000375730	T;T	0.30448	1.53;1.53	5.64	-2.63	0.06133	.	0.492888	0.25987	N	0.027029	T	0.20414	0.0491	L	0.37697	1.125	0.80722	D	1	B;B	0.11235	0.001;0.004	B;B	0.13407	0.009;0.004	T	0.15752	-1.0426	10	0.17832	T	0.49	-15.5232	13.9147	0.63890	0.4791:0.0:0.5209:0.0	.	121;121	Q9H488;Q9H488-2	OFUT1_HUMAN;.	R	121	ENSP00000364902:K121R;ENSP00000364882:K121R	ENSP00000364882:K121R	K	+	2	0	POFUT1	30266848	0.995000	0.38212	0.916000	0.36221	0.996000	0.88848	0.605000	0.24179	-0.744000	0.04778	0.533000	0.62120	AAG	.	.	.	none		0.597	POFUT1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078613.1	NM_015352		G	30803187	A	G	30803187	3	3	257	1	0	0	0	0	1	0	0	0	12190	72	3	3	372	3	POFUT1	20	30803187	Missense_Mutation	SNP	A	TCGA-UZ-A9PK-01A-11D-A382-10		30803187	32222333	62	16032											
NEFH	4744	hgsc.bcm.edu	37	chr22	29885848	29885848	+	Missense_Mutation	SNP	T	T	A																															cgagaaggccaagtccccagTgaaggaagaagctaagtccc																								rs464517		TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr22:29885848T>A	ENST00000310624.6	+	4	2252	c.2219T>A	c.(2218-2220)gTg>gAg	p.V740E		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	746	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AAGTCCCCAGTGAAGGAAGAA	0.547																																					p.V740E		Atlas-SNP	.											.	NEFH	178	.	0			c.T2219A						PASS	.						101	102	102					22																	29885848		2203	4300	6503	SO:0001583	missense	4744	exon4			CCCCAGTGAAGGA		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.2219T>A	chr22.hg19:g.29885848T>A	ENSP00000311997:p.Val740Glu	193.0	0.0	.		279.0	46.0	.	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	hg19	CCDS13858.1	.	.	.	.	.	.	.	.	.	.	T	0.201	-1.044796	0.01997	.	.	ENSG00000100285	ENST00000328842;ENST00000310624	D	0.82344	-1.6	4.0	2.89	0.33648	.	0.451396	0.18731	N	0.132724	T	0.72220	0.3433	L	0.51422	1.61	0.26362	N	0.977028	B	0.17667	0.023	B	0.12156	0.007	T	0.53683	-0.8404	10	0.13470	T	0.59	.	4.1768	0.10356	0.496:0.0989:0.0:0.4051	rs464517;rs464517	746	P12036	NFH_HUMAN	E	740	ENSP00000311997:V740E	ENSP00000311997:V740E	V	+	2	0	NEFH	28215848	0.000000	0.05858	0.465000	0.27155	0.670000	0.39368	-2.059000	0.01393	0.375000	0.24679	0.418000	0.28097	GTG	.	T|1.000;|0.000	.	weak		0.547	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		A	29885848	T	A	29885848	3	1	257	1	0	0	0	0	1	0	0	0	10321	1696	59	5	2233	5	NEFH	22	29885848	Missense_Mutation	SNP	T	TCGA-UZ-A9PK-01A-11D-A382-10		29885848	21418718	63	16033	164	2									
NEFH	4744	hgsc.bcm.edu	37	chr22	29885853	29885858	+	In_Frame_Del	DEL	GAAGAA	GAAGAA	-																															aggccaagtccccagtgaagGaagaagctaagtccccagag																								rs59890097|rs570663492|rs377642315|rs532587474	byFrequency	TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	GAAGAA	GAAGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr22:29885853_29885858delGAAGAA	ENST00000310624.6	+	4	2257_2262	c.2224_2229delGAAGAA	c.(2224-2229)gaagaadel	p.EE742del		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	748	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						CCCAGTGAAGGAAGAAGCTAAGTCCC	0.553																																					p.741_743del		Atlas-INDEL	.											.	NEFH	178	.	0			c.2223_2228del						PASS	.																																			SO:0001651	inframe_deletion	4744	exon4			.		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"Intermediate filaments type IV"	7737	protein-coding gene	gene with protein product		162230	"neurofilament, heavy polypeptide 200kDa"				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.2224_2229delGAAGAA	chr22.hg19:g.29885853_29885858delGAAGAA	ENSP00000311997:p.Glu742_Glu743del	326.0	0.0	0		290.0	20.0	0.0689655	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Del	DEL	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.	.	weak		0.553	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		-	29885858	GAAGAA	-	29885853	7	5	257	1	0	1	0	1	0	0	0	0	10321	1175	41	0	2238	0	NEFH	22	29885853	In_Frame_Del	DEL	GAAGAA	TCGA-UZ-A9PK-01A-11D-A382-10	5	29885853	21418713	64	16034	164	2									
EP300	2033	hgsc.bcm.edu	37	chr22	41542756	41542756	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actctagatggccctctaccTgacccaagtatgatccgtgg	9	10	9	13	1	2	3	0	2	2	1	3	3	3	3	4	2	1	1	4	2	4	3			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chr22:41542756T>C	ENST00000263253.7	+	11	3286	c.2067T>C	c.(2065-2067)ccT>ccC	p.P689P		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	689					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						GCCCTCTACCTGACCCAAGTA	0.373			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.P689P		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300	367	.	0			c.T2067C						PASS	.						93	91	92					22																	41542756		2203	4300	6503	SO:0001819	synonymous_variant	2033	exon11	Familial Cancer Database	Broad Thumb-Hallux syndrome	TCTACCTGACCCA	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.2067T>C	chr22.hg19:g.41542756T>C		64.0	0.0	.		81.0	27.0	.	NM_001429	B1AKC2	Silent	SNP	ENST00000263253.7	hg19	CCDS14010.1																																																																																			.	.	.	none		0.373	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		C	41542756	T	C	41542756	2	2	257	1	0	0	0	0	0	0	0	1	5150	1567	55	3		3	EP300	22	41542756	Silent	SNP	T	TCGA-UZ-A9PK-01A-11D-A382-10	11656903	41542756	9761810	65	16035											
USP11	8237	hgsc.bcm.edu	37	chrX	47103934	47103934	+	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	ccaactcagatgatgaggacGatggggatgagaaaggtgag	14	6	16	5	1	1	5	1	4	0	2	1	9	1	7	1	4	1	0	1	4	2	0			TCGA-UZ-A9PK-01A-11D-A382-10	TCGA-UZ-A9PK-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	9cb79cdb-d48d-4fd8-bdce-1f969be4a55f	36e67294-52d8-43b6-a9c0-0ed08f740cb3	g.chrX:47103934G>A	ENST00000218348.3	+	14	1957	c.1957G>A	c.(1957-1959)Gat>Aat	p.D653N	USP11_ENST00000377107.2_Missense_Mutation_p.D610N	NM_004651.3	NP_004642.2	P51784	UBP11_HUMAN	ubiquitin specific peptidase 11	653	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						TGATGAGGACGATGGGGATGA	0.572																																					p.D653N		Atlas-SNP	.											.	USP11	93	.	0			c.G1957A						PASS	.						77	61	67					X																	47103934		2203	4300	6503	SO:0001583	missense	8237	exon14			GAGGACGATGGGG	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.1957G>A	chrX.hg19:g.47103934G>A	ENSP00000218348:p.Asp653Asn	109.0	0.0	.		103.0	71.0	.	NM_004651	B2RTX1|Q8IUG6|Q9BWE1	Missense_Mutation	SNP	ENST00000218348.3	hg19	CCDS14277.1	.	.	.	.	.	.	.	.	.	.	G	13.82	2.350316	0.41599	.	.	ENSG00000102226	ENST00000377107;ENST00000218348	T;T	0.20738	2.06;2.05	5.29	5.29	0.74685	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.135164	0.33631	N	0.004707	T	0.15132	0.0365	N	0.16066	0.365	0.37750	D	0.925941	B;P	0.52463	0.041;0.953	B;P	0.46237	0.026;0.508	T	0.13791	-1.0496	10	0.16420	T	0.52	-7.848	13.3561	0.60629	0.0:0.0:1.0:0.0	.	380;653	B3KP28;P51784	.;UBP11_HUMAN	N	610;653	ENSP00000366311:D610N;ENSP00000218348:D653N	ENSP00000218348:D653N	D	+	1	0	USP11	46988878	0.983000	0.35010	0.533000	0.28001	0.881000	0.50899	3.296000	0.51802	2.217000	0.71921	0.600000	0.82982	GAT	.	.	.	none		0.572	USP11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_004651		A	47103934	G	A	47103934	3	1	257	1	0	0	0	0	1	0	0	0	17054	1058	37	1	2011	1	USP11	23	47103934	Missense_Mutation	SNP	G	TCGA-UZ-A9PK-01A-11D-A382-10		47103934	108166626	66	16036											
SPOCD1	90853	hgsc.bcm.edu	37	chr1	32265460	32265460	+	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	cctcttcagcctccattgggCcactctgtaggggaggcgtg	5	10	13	13	1	3	0	1	0	2	0	4	1	4	1	4	4	1	1	4	4	1	3			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr1:32265460C>T	ENST00000360482.2	-	6	1862	c.1733G>A	c.(1732-1734)gGc>gAc	p.G578D	SPOCD1_ENST00000373648.2_Missense_Mutation_p.G519D|SPOCD1_ENST00000257100.3_Missense_Mutation_p.G71D|SPOCD1_ENST00000533231.1_Missense_Mutation_p.G578D	NM_144569.4	NP_653170.3	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1	578					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)		CTCCATTGGGCCACTCTGTAG	0.622																																					p.G578D		Atlas-SNP	.											.	SPOCD1	109	.	0			c.G1733A						PASS	.						56	56	56					1																	32265460		2203	4300	6503	SO:0001583	missense	90853	exon6			ATTGGGCCACTCT	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.1733G>A	chr1.hg19:g.32265460C>T	ENSP00000353670:p.Gly578Asp	108.0	0.0	.		101.0	44.0	.	NM_144569	Q24JU3|Q6PI90|Q8N869|Q8N8U0|Q8NBC6|Q96LN6	Missense_Mutation	SNP	ENST00000360482.2	hg19	CCDS347.1	.	.	.	.	.	.	.	.	.	.	C	16.15	3.041247	0.55003	.	.	ENSG00000134668	ENST00000257100;ENST00000360482;ENST00000373648;ENST00000533231;ENST00000528791	T;T;T;T	0.51071	0.99;1.99;0.72;1.97	3.95	0.984	0.19773	.	.	.	.	.	T	0.24509	0.0594	N	0.14661	0.345	0.09310	N	1	B;B	0.23891	0.093;0.056	B;B	0.24541	0.054;0.024	T	0.19679	-1.0298	9	0.22706	T	0.39	-0.0365	2.9274	0.05788	0.218:0.5427:0.0:0.2393	.	578;578	Q6ZMY3-2;Q6ZMY3	.;SPOC1_HUMAN	D	71;578;519;578;71	ENSP00000257100:G71D;ENSP00000353670:G578D;ENSP00000362752:G519D;ENSP00000435851:G578D	ENSP00000257100:G71D	G	-	2	0	SPOCD1	32038047	0.000000	0.05858	0.000000	0.03702	0.335000	0.28730	0.008000	0.13197	0.218000	0.20820	0.551000	0.68910	GGC	.	.	.	none		0.622	SPOCD1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000381912.1	NM_144569		T	32265460	C	T	32265460	3	4	258	1	0	0	0	0	1	0	0	0	15090	739	26	2	1961	2	SPOCD1	1	32265460	Missense_Mutation	SNP	C	TCGA-UZ-A9PL-01A-11D-A382-10		32265460	216985161	1	16037											
SFPQ	6421	hgsc.bcm.edu	37	chr1	35656516	35656516	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggcagcagcatgtgtggcAaagcgaactcgaagctgtct	11	7	14	9	2	1	0	0	0	1	0	2	2	1	0	0	2	5	5	0	2	3	0			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr1:35656516A>G	ENST00000357214.5	-	3	1196	c.1098T>C	c.(1096-1098)ttT>ttC	p.F366F		NM_005066.2	NP_005057.1	P23246	SFPQ_HUMAN	splicing factor proline/glutamine-rich	366	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				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)				CATGTGTGGCAAAGCGAACTC	0.453			T	TFE3	papillary renal cell																																p.F366F		Atlas-SNP	.		Dom	yes		1	1p34.3	6421	splicing factor proline/glutamine rich(polypyrimidine tract binding protein associated)		E	.	SFPQ	51	.	0			c.T1098C						PASS	.						76	74	75					1																	35656516		2203	4300	6503	SO:0001819	synonymous_variant	6421	exon3			TGTGGCAAAGCGA	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.1098T>C	chr1.hg19:g.35656516A>G		183.0	0.0	.		192.0	93.0	.	NM_005066	P30808|Q5SZ71	Silent	SNP	ENST00000357214.5	hg19	CCDS388.1																																																																																			.	.	.	none		0.453	SFPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011984.4	NM_005066		G	35656516	A	G	35656516	2	3	258	1	0	0	0	0	0	0	0	1	14173	127	5	3		3	SFPQ	1	35656516	Silent	SNP	A	TCGA-UZ-A9PL-01A-11D-A382-10	3391056	35656516	213594105	2	16038											
LRRC8D	55144	hgsc.bcm.edu	37	chr1	90400895	90400895	+	Missense_Mutation	SNP	T	T	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	ttgcttcagaacctgcagcaTttgcatatcactgggaacaa	12	11	8	10	0	2	1	2	0	0	1	2	2	2	2	1	1	6	4	1	1	4	4			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr1:90400895T>G	ENST00000337338.5	+	3	2675	c.2268T>G	c.(2266-2268)caT>caG	p.H756Q	LRRC8D_ENST00000394593.3_Missense_Mutation_p.H756Q	NM_001134479.1	NP_001127951.1	Q7L1W4	LRC8D_HUMAN	leucine rich repeat containing 8 family, member D	756					ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(2)|skin(1)	29		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)		ACCTGCAGCATTTGCATATCA	0.383																																					p.H756Q		Atlas-SNP	.											.	LRRC8D	78	.	0			c.T2268G						PASS	.						97	97	97					1																	90400895		2203	4300	6503	SO:0001583	missense	55144	exon3			GCAGCATTTGCAT	AK001332	CCDS726.1	1p22.2	2008-02-05	2005-06-29	2005-06-29	ENSG00000171492	ENSG00000171492			16992	protein-coding gene	gene with protein product		612890	"leucine rich repeat containing 5"	LRRC5			Standard	NM_018103		Approved	FLJ10470	uc001dnn.3	Q7L1W4	OTTHUMG00000010583	ENST00000337338.5:c.2268T>G	chr1.hg19:g.90400895T>G	ENSP00000338887:p.His756Gln	184.0	0.0	.		212.0	94.0	.	NM_018103	D3DT29|Q6UWB2|Q9NVW3	Missense_Mutation	SNP	ENST00000337338.5	hg19	CCDS726.1	.	.	.	.	.	.	.	.	.	.	T	9.831	1.188401	0.21954	.	.	ENSG00000171492	ENST00000337338;ENST00000394593	T;T	0.57273	0.41;0.41	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.24812	0.0602	L	0.31371	0.925	0.52501	D	0.999957	B	0.20164	0.042	B	0.27262	0.078	T	0.13575	-1.0504	9	.	.	.	.	10.8883	0.46981	0.0:0.0695:0.0:0.9305	.	756	Q7L1W4	LRC8D_HUMAN	Q	756	ENSP00000338887:H756Q;ENSP00000378093:H756Q	.	H	+	3	2	LRRC8D	90173483	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.826000	0.39092	2.326000	0.78906	0.533000	0.62120	CAT	.	.	.	none		0.383	LRRC8D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029203.2	NM_018103		G	90400895	T	G	90400895	3	3	258	1	0	0	0	0	1	0	0	0	9031	1490	52	5	2270	5	LRRC8D	1	90400895	Missense_Mutation	SNP	T	TCGA-UZ-A9PL-01A-11D-A382-10	54744379	90400895	158849726	3	16039											
INSRR	3645	hgsc.bcm.edu	37	chr1	156811515	156811515	+	Missense_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	ggactcgggggccatccagcGcacgggcagcagccccttcc	6	4	14	17	3	0	0	0	0	0	0	3	1	2	1	5	4	3	3	5	4	0	1	rs201172210		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr1:156811515G>A	ENST00000368195.3	-	20	3865	c.3469C>T	c.(3469-3471)Cgc>Tgc	p.R1157C	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	1157	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)					GCCATCCAGCGCACGGGCAGC	0.627																																					p.R1157C		Atlas-SNP	.											INSRR_ENST00000368195,NS,carcinoma,+2,2	INSRR	309	.	0			c.C3469T						PASS	.	G	,CYS/ARG	0,4406		0,0,2203	79	75	77		,3469	5.1	1	1		77	3,8597	3.0+/-9.4	0,3,4297	yes	intron,missense	INSRR,NTRK1	NM_001007792.1,NM_014215.2	,180	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	,probably-damaging	,1157/1298	156811515	3,13003	2203	4300	6503	SO:0001583	missense	3645	exon20			TCCAGCGCACGGG	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.3469C>T	chr1.hg19:g.156811515G>A	ENSP00000357178:p.Arg1157Cys	182.0	0.0	.		174.0	43.0	.	NM_014215	O60724|Q5VZS3	Missense_Mutation	SNP	ENST00000368195.3	hg19	CCDS1160.1	.	.	.	.	.	.	.	.	.	.	G	19.75	3.885533	0.72410	0.0	3.49E-4	ENSG00000027644	ENST00000368195	D	0.83755	-1.76	5.07	5.07	0.68467	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.47093	D	0.000245	D	0.88746	0.6520	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89679	0.3889	9	0.87932	D	0	.	12.2864	0.54795	0.0:0.0:0.8305:0.1695	.	1157	P14616	INSRR_HUMAN	C	1157	ENSP00000357178:R1157C	ENSP00000357178:R1157C	R	-	1	0	INSRR	155078139	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.247000	0.58750	2.639000	0.89480	0.561000	0.74099	CGC	.	.	.	weak		0.627	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		A	156811515	G	A	156811515	3	1	258	1	0	0	0	0	1	0	0	0	7781	1087	38	1	435	1	INSRR	1	156811515	Missense_Mutation	SNP	G	TCGA-UZ-A9PL-01A-11D-A382-10	66410620	156811515	92439106	4	16040											
CFHR4	3080	hgsc.bcm.edu	37	chr1	196887456	196887456	+	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	ttgaatttatgtgtaaattgGgatataatgcgaatacatca	15	15	8	3	1	1	1	1	1	0	0	1	3	1	2	0	1	2	1	0	1	8	8			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr1:196887456G>A	ENST00000367421.3	+	2	135				CFHR4_ENST00000251424.4_Missense_Mutation_p.G306R|CFHR4_ENST00000608469.1_Missense_Mutation_p.G176R|CFHR4_ENST00000367416.2_Missense_Mutation_p.G552R|CFHR4_ENST00000367418.2_Missense_Mutation_p.G306R			P36980	FHR2_HUMAN	complement factor H-related 2							extracellular region (GO:0005576)				large_intestine(2)|ovary(1)|skin(3)	6						GTGTAAATTGGGATATAATGC	0.333																																					p.G553R		Atlas-SNP	.											.	CFHR4	141	.	0			c.G1657A						PASS	.						172	180	177					1																	196887456		2202	4300	6502	SO:0001627	intron_variant	10877	exon10			AAATTGGGATATA	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.59-31129G>A	chr1.hg19:g.196887456G>A		456.0	1.0	.		450.0	189.0	.	NM_001201550	Q14310|Q5T9T1	Missense_Mutation	SNP	ENST00000367421.3	hg19		.	.	.	.	.	.	.	.	.	.	G	7.601	0.672808	0.14776	.	.	ENSG00000134365	ENST00000367416;ENST00000367418;ENST00000251424;ENST00000538553	D;D;D	0.84223	-1.82;-1.82;-1.82	3.24	2.28	0.28536	Complement control module (1);	.	.	.	.	T	0.75715	0.3887	L	0.46157	1.445	0.09310	N	1	P;P;P	0.46706	0.825;0.883;0.685	B;B;B	0.34093	0.175;0.105;0.04	T	0.63932	-0.6525	9	0.48119	T	0.1	.	8.3994	0.32576	0.0:0.2442:0.7558:0.0	.	552;553;306	C9J7J7;Q5DVJ7;Q92496	.;.;FHR4_HUMAN	R	552;306;306;306	ENSP00000356386:G552R;ENSP00000356388:G306R;ENSP00000251424:G306R	ENSP00000251424:G306R	G	+	1	0	CFHR4	195154079	0.004000	0.15560	0.006000	0.13384	0.053000	0.15095	1.009000	0.29886	0.433000	0.26313	0.436000	0.28706	GGA	.	.	.	none		0.333	CFHR2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005666		A	196887456	G	A	196887456	1	1	258	0	1	0	0	0	0	0	0	0	3289	1233	43	2		2	CFHR4	1	196887456	Intron	SNP	G	TCGA-UZ-A9PL-01A-11D-A382-10	40075941	196887456	52363165	5	16041											
ALMS1	7840	hgsc.bcm.edu	37	chr2	73613036	73613036	+	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	catggccgggcgagctggagGaggaggaggaggaggaggag	10	2	24	5	2	0	0	0	0	0	0	0	9	0	8	1	10	1	1	1	10	0	0	rs61156725|rs72319667|rs3074417	byFrequency	TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr2:73613036G>C	ENST00000264448.6	+	1	151	c.40G>C	c.(40-42)Gag>Cag	p.E14Q	ALMS1_ENST00000409009.1_Missense_Mutation_p.E14Q|ALMS1_ENST00000377715.1_Missense_Mutation_p.E14Q	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	14	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CGAGCTggaggaggaggagga	0.692																																					p.E14Q		Atlas-SNP	.											.	ALMS1	384	.	1	Deletion - In frame(1)	ovary(1)	c.G40C						PASS	.						3	4	4					2																	73613036		1509	3234	4743	SO:0001583	missense	7840	exon1			CTGGAGGAGGAGG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.40G>C	chr2.hg19:g.73613036G>C	ENSP00000264448:p.Glu14Gln	149.0	0.0	.		241.0	19.0	.	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.731519	0.48939	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.26373	2.4;2.61;1.74	3.19	3.19	0.36642	.	0.259523	0.20097	U	0.099311	T	0.32436	0.0829	N	0.19112	0.55	0.22317	N	0.999202	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.03493	-1.1031	10	0.87932	D	0	.	10.1262	0.42652	0.0:0.0:1.0:0.0	.	14;14	B8ZZJ3;Q8TCU4	.;ALMS1_HUMAN	Q	14	ENSP00000386627:E14Q;ENSP00000264448:E14Q;ENSP00000366944:E14Q	ENSP00000264448:E14Q	E	+	1	0	ALMS1	73466544	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	2.034000	0.41145	2.070000	0.61991	0.484000	0.47621	GAG	.	.	.	none		0.692	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		C	73613036	G	C	73613036	3	2	258	1	0	0	0	0	1	0	0	0	535	1175	41	4	42	4	ALMS1	2	73613036	Missense_Mutation	SNP	G	TCGA-UZ-A9PL-01A-11D-A382-10		73613036	169586337	6	16042											
SEMA4C	54910	hgsc.bcm.edu	37	chr2	97532110	97532110	+	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	ccagtgggctccgtcagcgtCagtgtcaggaagtcctggat	7	9	14	11	2	3	0	3	0	0	0	5	2	5	2	3	3	1	1	3	3	1	0			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr2:97532110C>T	ENST00000305476.5	-	3	300	c.168G>A	c.(166-168)ctG>ctA	p.L56L		NM_017789.4	NP_060259.4	Q9C0C4	SEM4C_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C	56	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						CCGTCAGCGTCAGTGTCAGGA	0.652																																					p.L56L		Atlas-SNP	.											.	SEMA4C	56	.	0			c.G168A						PASS	.						85	85	85					2																	97532110		2203	4300	6503	SO:0001819	synonymous_variant	54910	exon3			CAGCGTCAGTGTC	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.168G>A	chr2.hg19:g.97532110C>T		230.0	0.0	.		170.0	71.0	.	NM_017789	Q32MJ3|Q7Z5X0	Silent	SNP	ENST00000305476.5	hg19	CCDS2029.1																																																																																			.	.	.	none		0.652	SEMA4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252957.1	NM_017789		T	97532110	C	T	97532110	2	4	258	1	0	0	0	0	0	0	0	1	14046	813	29	2		2	SEMA4C	2	97532110	Silent	SNP	C	TCGA-UZ-A9PL-01A-11D-A382-10	23919074	97532110	145667263	7	16043											
TTN	7273	hgsc.bcm.edu	37	chr2	179474203	179474203	+	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	tcatcctttatccatgtaatAgttgggtaaggtgatccaga	11	14	9	7	0	1	2	1	1	0	1	4	2	4	2	3	2	0	3	3	2	4	6			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr2:179474203A>T	ENST00000591111.1	-	223	47135	c.46911T>A	c.(46909-46911)acT>acA	p.T15637T	TTN_ENST00000342992.6_Silent_p.T14710T|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000342175.6_Silent_p.T8405T|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000359218.5_Silent_p.T8338T|TTN_ENST00000460472.2_Silent_p.T8213T|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Silent_p.T17278T			Q8WZ42	TITIN_HUMAN	titin	15637	Ig-like 98.				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)			TCCATGTAATAGTTGGGTAAG	0.413																																					p.T17278T		Atlas-SNP	.											.	TTN	18412	.	0			c.T51834A						PASS	.						100	94	96					2																	179474203		1890	4114	6004	SO:0001819	synonymous_variant	7273	exon273			TGTAATAGTTGGG	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.46911T>A	chr2.hg19:g.179474203A>T		62.0	0.0	.		79.0	40.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.	.	none		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179474203	A	T	179474203	2	4	258	1	0	0	0	0	0	0	0	1	16747	407	15	5		5	TTN	2	179474203	Silent	SNP	A	TCGA-UZ-A9PL-01A-11D-A382-10	81942093	179474203	63725170	8	16044											
TTN	7273	hgsc.bcm.edu	37	chr2	179611761	179611761	+	Intron	SNP	T	T	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	gtaccagtggggtttggtccTccagtaggaatagaatatct	10	12	12	7	0	1	1	0	0	1	1	3	2	3	2	3	4	1	3	3	4	6	5			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr2:179611761T>A	ENST00000591111.1	-	46	10585				TTN_ENST00000342992.6_Intron|TTN_ENST00000360870.5_Silent_p.G5122G|TTN_ENST00000342175.6_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590773.1_RNA|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)			GGTTTGGTCCTCCAGTAGGAA	0.473																																					p.G5122G		Atlas-SNP	.											.	TTN	18412	.	0			c.A15366T						PASS	.						89	92	91					2																	179611761		2203	4300	6503	SO:0001627	intron_variant	7273	exon46			TGGTCCTCCAGTA	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.10361-5113A>T	chr2.hg19:g.179611761T>A		139.0	0.0	.		122.0	48.0	.	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.	.	none		0.473	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179611761	T	A	179611761	1	1	258	0	1	0	0	0	0	0	0	0	16747	1538	54	5		5	TTN	2	179611761	Intron	SNP	T	TCGA-UZ-A9PL-01A-11D-A382-10	137558	179611761	63587612	9	16045											
CREB1	1385	hgsc.bcm.edu	37	chr2	208420472	208420472	+	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	acagattgccacattagcccAggtataaaatacatggagag	16	8	9	8	0	0	2	0	0	0	2	0	3	0	2	2	2	3	1	2	2	5	5			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr2:208420472A>G	ENST00000432329.2	+	2	364	c.113A>G	c.(112-114)cAg>cGg	p.Q38R	CREB1_ENST00000374397.4_Splice_Site_p.Q38R|CREB1_ENST00000430624.1_Splice_Site_p.Q38R|CREB1_ENST00000353267.3_Splice_Site_p.Q38R|CREB1_ENST00000536726.1_Splice_Site_p.Q38R	NM_134442.3	NP_604391.1	P16220	CREB1_HUMAN	cAMP responsive element binding protein 1	38					activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|cellular response to zinc ion (GO:0071294)|circadian rhythm (GO:0007623)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|lactation (GO:0007595)|lung saccule development (GO:0060430)|memory (GO:0007613)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription by competitive promoter binding (GO:0010944)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|pituitary gland development (GO:0021983)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of hormone secretion (GO:0046887)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of cell size (GO:0008361)|response to drug (GO:0042493)|response to glucagon (GO:0033762)|response to organic substance (GO:0010033)|secretory granule organization (GO:0033363)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|Type I pneumocyte differentiation (GO:0060509)|viral process (GO:0016032)	nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	cAMP response element binding (GO:0035497)|enzyme binding (GO:0019899)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)		EWSR1/CREB1(44)	NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|upper_aerodigestive_tract(1)	5				LUSC - Lung squamous cell carcinoma(261;0.0768)|Epithelial(149;0.127)|Lung(261;0.145)	Adenosine monophosphate(DB00131)|Naloxone(DB01183)	ACATTAGCCCAGGTATAAAAT	0.418			T	EWSR1	"clear cell sarcoma, angiomatoid fibrous histiocytoma"																																p.Q38R		Atlas-SNP	.		Dom	yes		2	2q34	1385	cAMP responsive element binding protein 1		M	.	CREB1	21	.	0			c.A113G						PASS	.						56	51	53					2																	208420472		2203	4300	6503	SO:0001630	splice_region_variant	1385	exon2			TAGCCCAGGTATA	M27691	CCDS2374.1, CCDS2375.1	2q34	2013-01-10			ENSG00000118260	ENSG00000118260		"basic leucine zipper proteins"	2345	protein-coding gene	gene with protein product		123810					Standard	NM_134442		Approved		uc002vcc.3	P16220	OTTHUMG00000132936	ENST00000432329.2:c.114+1A>G	chr2.hg19:g.208420472A>G		126.0	0.0	.		125.0	15.0	.	NM_004379	P21934|Q6V963|Q9UMA7	Missense_Mutation	SNP	ENST00000432329.2	hg19	CCDS2375.1	.	.	.	.	.	.	.	.	.	.	A	18.37	3.609554	0.66558	.	.	ENSG00000118260	ENST00000430624;ENST00000432329;ENST00000353267;ENST00000445803;ENST00000536726;ENST00000374397;ENST00000452474;ENST00000414681	T;T;T;T;T;T;D	0.81499	0.36;0.18;0.36;-1.37;-1.3;-0.51;-1.5	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.85128	0.5626	M	0.64404	1.975	0.80722	D	1	D;P;P	0.52996	0.957;0.799;0.835	P;B;B	0.53954	0.738;0.214;0.275	D	0.85493	0.1186	10	0.48119	T	0.1	-7.8185	16.3197	0.82945	1.0:0.0:0.0:0.0	.	38;38;38	F5H0V3;Q53X93;P16220	.;.;CREB1_HUMAN	R	38	ENSP00000405539:Q38R;ENSP00000387699:Q38R;ENSP00000236995:Q38R;ENSP00000407227:Q38R;ENSP00000445892:Q38R;ENSP00000363518:Q38R;ENSP00000392428:Q38R	ENSP00000236995:Q38R	Q	+	2	0	CREB1	208128717	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.135000	0.89608	2.302000	0.77476	0.533000	0.62120	CAG	.	.	.	none		0.418	CREB1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256467.3	NM_134442	Missense_Mutation	G	208420472	A	G	208420472	5	3	258	1	0	0	0	0	0	0	1	0	3856	202	7	3	115	3	CREB1	2	208420472	Splice_Site	SNP	A	TCGA-UZ-A9PL-01A-11D-A382-10	28808711	208420472	34778901	10	16046											
ANKZF1	55139	hgsc.bcm.edu	37	chr2	220099756	220099756	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggagccttccacacagtcAtcccaggcagttgctgcccc	8	7	10	16	0	1	0	1	0	0	0	3	2	3	1	5	2	3	3	5	2	0	2			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr2:220099756A>G	ENST00000323348.5	+	10	1587	c.1413A>G	c.(1411-1413)tcA>tcG	p.S471S	ANKZF1_ENST00000409849.1_Silent_p.S261S|ANKZF1_ENST00000410034.3_Silent_p.S471S|GLB1L_ENST00000497855.1_5'Flank	NM_018089.2	NP_060559.2	Q9H8Y5	ANKZ1_HUMAN	ankyrin repeat and zinc finger domain containing 1	471						membrane (GO:0016020)	metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	23		Renal(207;0.0474)		Epithelial(149;1.2e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCACACAGTCATCCCAGGCAG	0.572																																					p.S471S		Atlas-SNP	.											.	ANKZF1	45	.	0			c.A1413G						PASS	.						47	52	50					2																	220099756		1968	4157	6125	SO:0001819	synonymous_variant	55139	exon10			ACAGTCATCCCAG	AF364318	CCDS42821.1, CCDS63129.1	2q35	2013-01-10			ENSG00000163516	ENSG00000163516		"Zinc fingers, C2H2-type", "Ankyrin repeat domain containing"	25527	protein-coding gene	gene with protein product						12477932	Standard	NM_018089		Approved	FLJ10415, ZNF744	uc002vkg.3	Q9H8Y5	OTTHUMG00000154533	ENST00000323348.5:c.1413A>G	chr2.hg19:g.220099756A>G		100.0	0.0	.		96.0	51.0	.	NM_001042410	Q9NVZ4	Silent	SNP	ENST00000323348.5	hg19	CCDS42821.1																																																																																			.	.	.	none		0.572	ANKZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335790.1	NM_018089		G	220099756	A	G	220099756	2	3	258	1	0	0	0	0	0	0	0	1	693	204	8	3		3	ANKZF1	2	220099756	Silent	SNP	A	TCGA-UZ-A9PL-01A-11D-A382-10	11679284	220099756	23099617	11	16047											
SPEG	10290	hgsc.bcm.edu	37	chr2	220336993	220336993	+	Missense_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	gcgccccgcaggtggtggctGtgacggggaggatggtcaca	6	6	19	10	3	1	1	1	1	0	0	1	3	1	3	2	7	0	2	2	7	0	0			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr2:220336993G>A	ENST00000312358.7	+	15	4012	c.3880G>A	c.(3880-3882)Gtg>Atg	p.V1294M	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1294	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		GGTGGTGGCTGTGACGGGGAG	0.652																																					p.V1294M		Atlas-SNP	.											.	SPEG	272	.	0			c.G3880A						PASS	.						50	56	54					2																	220336993		1987	4153	6140	SO:0001583	missense	10290	exon15			GTGGCTGTGACGG	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.3880G>A	chr2.hg19:g.220336993G>A	ENSP00000311684:p.Val1294Met	89.0	0.0	.		116.0	53.0	.	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	hg19	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	G	14.58	2.576553	0.45902	.	.	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.57595	0.39	4.61	4.61	0.57282	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.35040	N	0.003484	T	0.69788	0.3150	M	0.72894	2.215	0.80722	D	1	D	0.71674	0.998	D	0.64687	0.928	T	0.74203	-0.3741	10	0.62326	D	0.03	.	16.221	0.82258	0.0:0.0:1.0:0.0	.	1294	Q15772	SPEG_HUMAN	M	1294	ENSP00000311684:V1294M	ENSP00000265327:V1294M	V	+	1	0	SPEG	220045237	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	5.635000	0.67841	2.117000	0.64856	0.555000	0.69702	GTG	.	.	.	none		0.652	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		A	220336993	G	A	220336993	3	1	258	1	0	0	0	0	1	0	0	0	15048	1377	48	2	3950	2	SPEG	2	220336993	Missense_Mutation	SNP	G	TCGA-UZ-A9PL-01A-11D-A382-10	237237	220336993	22862380	12	16048											
SLC4A3	6508	hgsc.bcm.edu	37	chr2	220493130	220493131	+	Frame_Shift_Ins	INS	-	-	G																															ccgtctgggcctgcaggtccINSgggtgcccttggaggagccc																										TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr2:220493130_220493131insG	ENST00000358055.3	+	3	567_568	c.55_56insG	c.(55-57)cggfs	p.R19fs	SLC4A3_ENST00000317151.3_Frame_Shift_Ins_p.R19fs|SLC4A3_ENST00000373762.3_Frame_Shift_Ins_p.R19fs|SLC4A3_ENST00000273063.6_Frame_Shift_Ins_p.R19fs|SLC4A3_ENST00000373760.2_Frame_Shift_Ins_p.R19fs|AC009955.8_ENST00000455896.1_RNA			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	19					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCTGCAGGTCCGGGTGCCCTTG	0.639																																					p.R19fs		Pindel	.											.	SLC4A3	144	.	0			c.55_56insG						PASS	.																																			SO:0001589	frameshift_variant	6508	exon3			.		CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"Solute carriers"	11029	protein-coding gene	gene with protein product	"Anion exchanger 3, neuronal"	106195	"solute carrier family 4, anion exchanger, member 3"			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.58dupG	chr2.hg19:g.220493133_220493133dupG	ENSP00000350756:p.Arg19fs	154.0	0.0	.		152.0	49.0	0.322	NM_005070	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Frame_Shift_Ins	INS	ENST00000358055.3	hg19	CCDS2445.1																																																																																			.	.	.	none		0.639	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070		G	220493131	-	G	220493130	7	5	258	1	0	1	1	0	0	0	0	0	14668	643	23	0	61	0	SLC4A3	2	220493130	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PL-01A-11D-A382-10	156137	220493130	22706243	13	16049											
SCG2	7857	hgsc.bcm.edu	37	chr2	224463553	224463553	+	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	ccactgctgtgtctcataatCatcactcatgtccattggaa	10	13	6	12	0	4	0	4	0	1	0	6	1	5	1	2	1	1	1	2	1	2	2			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr2:224463553C>T	ENST00000305409.2	-	2	680	c.448G>A	c.(448-450)Gat>Aat	p.D150N		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)		GTCTCATAATCATCACTCATG	0.418																																					p.D150N		Atlas-SNP	.											.	SCG2	99	.	0			c.G448A						PASS	.						174	171	172					2																	224463553		2203	4300	6503	SO:0001583	missense	7857	exon2			CATAATCATCACT	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.448G>A	chr2.hg19:g.224463553C>T	ENSP00000304133:p.Asp150Asn	58.0	0.0	.		75.0	26.0	.	NM_003469	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000305409.2	hg19	CCDS2457.1	.	.	.	.	.	.	.	.	.	.	C	19.36	3.812797	0.70912	.	.	ENSG00000171951	ENST00000305409	T	0.02050	4.48	5.5	5.5	0.81552	.	0.226336	0.43919	D	0.000519	T	0.07548	0.0190	L	0.46157	1.445	0.49687	D	0.999817	D	0.53462	0.96	P	0.54460	0.753	T	0.04203	-1.0969	10	0.72032	D	0.01	.	19.775	0.96388	0.0:1.0:0.0:0.0	.	150	P13521	SCG2_HUMAN	N	150	ENSP00000304133:D150N	ENSP00000304133:D150N	D	-	1	0	SCG2	224171797	1.000000	0.71417	0.992000	0.48379	0.957000	0.61999	6.115000	0.71566	2.741000	0.93983	0.585000	0.79938	GAT	.	.	.	none		0.418	SCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256870.2	NM_003469		T	224463553	C	T	224463553	3	4	258	1	0	0	0	0	1	0	0	0	13904	826	29	2	1409	2	SCG2	2	224463553	Missense_Mutation	SNP	C	TCGA-UZ-A9PL-01A-11D-A382-10	3970423	224463553	18735820	14	16050											
C3orf20	84077	hgsc.bcm.edu	37	chr3	14803122	14803123	+	Splice_Site	DNP	GG	GG	AC																															gccggatgactacaaattcaGgtaaaacaggaaacacgcag																										TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr3:14803122_14803123GG>AC	ENST00000253697.3	+	15	2947	c.2495_2495GG>AC	c.(2494-2496)aGGg>aACgg	p.R832N	C3orf20_ENST00000412910.1_Splice_Site_p.R710N|C3orf20_ENST00000435614.1_Splice_Site_p.R710N	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	832						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						TACAAATTCAGGTAAAACAGGA	0.53																																					p.S832N|.		Atlas-SNP	.											.	C3orf20	109	.	0			c.G2495A|c.2495+1G>C						PASS	.																																			SO:0001630	splice_region_variant	84077	exon15			AATTCAGGTAAAA|ATTCAGGTAAAAC	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	Exception_encountered	chr3.hg19:g.14803122_14803123delinsAC		83.0	0.0	.		60.0|58.0	25.0	.	NM_032137	Q7L0U6|Q8NCP2|Q9H0I7	Missense_Mutation|Splice_Site	SNP	ENST00000253697.3	hg19	CCDS33706.1																																																																																			.	.	.	none		0.53	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137	Missense_Mutation	AC	14803123	GG	AC	14803122	5	1	258	1	0	0	0	0	0	0	1	0	2215	1014	35	2	2545	2	C3orf20	3	14803122	Splice_Site	DNP	GG	TCGA-UZ-A9PL-01A-11D-A382-10		14803122	183219308	15	16051											
UQCRC1	7384	hgsc.bcm.edu	37	chr3	48637112	48637118	+	Frame_Shift_Del	DEL	CAGATCT	CAGATCT	-																															ggtcatagatgtacttggagCagatctcacgtaccacactg																								rs3172495		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	CAGATCT	CAGATCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr3:48637112_48637118delCAGATCT	ENST00000203407.5	-	12	1744_1750	c.1328_1334delAGATCTG	c.(1327-1335)gagatctgcfs	p.EIC443fs		NM_003365.2	NP_003356.2	P31930	QCR1_HUMAN	ubiquinol-cytochrome c reductase core protein I	443					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)|respiratory electron transport chain (GO:0022904)|response to activity (GO:0014823)|response to alkaloid (GO:0043279)|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)	metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	16				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		GTACTTGGAGCAGATCTCACGTACCAC	0.565																																					p.443_445del	NSCLC(81;1112 1427 27031 32409 45529)	Atlas-Indel,Pindel	.											.	UQCRC1	42	.	0			c.1329_1335del						PASS	.																																			SO:0001589	frameshift_variant	7384	exon12			.	BC009586	CCDS2774.1	3p21	2011-07-04			ENSG00000010256	ENSG00000010256	1.10.2.2	"Mitochondrial respiratory chain complex / Complex III"	12585	protein-coding gene	gene with protein product		191328				8407948	Standard	NM_003365		Approved	D3S3191, QCR1, UQCR1	uc003cub.1	P31930	OTTHUMG00000133539	ENST00000203407.5:c.1328_1334delAGATCTG	chr3.hg19:g.48637112_48637118delCAGATCT	ENSP00000203407:p.Glu443fs	43.0	0.0	0		38.0	12.0	0.315789	NM_003365	B2R7R8|Q96DD2	Frame_Shift_Del	DEL	ENST00000203407.5	hg19	CCDS2774.1																																																																																			.	.	.	none		0.565	UQCRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257517.1	NM_003365		-	48637118	CAGATCT	-	48637112	7	5	258	1	0	1	0	1	0	0	0	0	17031	710	25	0	116	0	UQCRC1	3	48637112	Frame_Shift_Del	DEL	CAGATCT	TCGA-UZ-A9PL-01A-11D-A382-10	33833990	48637112	149385318	16	16052											
KBTBD8	84541	hgsc.bcm.edu	37	chr3	67053891	67053891	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcattatggtcatcaggaacTcggagatcgatcaaaagaat	15	10	9	7	2	4	2	4	0	0	2	6	5	4	3	0	3	1	0	0	3	5	1			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr3:67053891T>C	ENST00000417314.2	+	3	549	c.500T>C	c.(499-501)cTc>cCc	p.L167P	KBTBD8_ENST00000460576.1_Intron|KBTBD8_ENST00000469661.1_Intron|KBTBD8_ENST00000295568.4_Missense_Mutation_p.L141P			Q8NFY9	KBTB8_HUMAN	kelch repeat and BTB (POZ) domain containing 8	167	BACK.					cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)				breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)	20		Lung NSC(201;0.0765)		BRCA - Breast invasive adenocarcinoma(55;6.02e-06)|KIRC - Kidney renal clear cell carcinoma(39;0.105)|Kidney(39;0.125)		CATCAGGAACTCGGAGATCGA	0.378																																					p.L167P		Atlas-SNP	.											.	KBTBD8	101	.	0			c.T500C						PASS	.						63	63	63					3																	67053891		2203	4300	6503	SO:0001583	missense	84541	exon3			AGGAACTCGGAGA	AF385438	CCDS2906.1, CCDS2906.2	3p14	2013-01-08			ENSG00000163376	ENSG00000163376		"BTB/POZ domain containing"	30691	protein-coding gene	gene with protein product	"T-cell activation kelch repeat protein"					11347906	Standard	NM_032505		Approved	TA-KRP, KIAA1842	uc003dmy.3	Q8NFY9	OTTHUMG00000158779	ENST00000417314.2:c.500T>C	chr3.hg19:g.67053891T>C	ENSP00000401878:p.Leu167Pro	162.0	0.0	.		133.0	64.0	.	NM_032505	B4DTW6|Q96JI5	Missense_Mutation	SNP	ENST00000417314.2	hg19	CCDS2906.2	.	.	.	.	.	.	.	.	.	.	T	18.91	3.723529	0.68959	.	.	ENSG00000163376	ENST00000295568;ENST00000484414;ENST00000417314;ENST00000460784	D;D;D;D	0.84370	-1.53;-1.53;-1.53;-1.84	5.01	5.01	0.66863	BTB/Kelch-associated (2);	0.066397	0.64402	D	0.000016	D	0.94545	0.8243	H	0.95224	3.64	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	D	0.96098	0.9067	10	0.87932	D	0	.	15.0085	0.71530	0.0:0.0:0.0:1.0	.	167	Q8NFY9	KBTB8_HUMAN	P	141;90;167;141	ENSP00000295568:L141P;ENSP00000417341:L90P;ENSP00000401878:L167P;ENSP00000418075:L141P	ENSP00000295568:L141P	L	+	2	0	KBTBD8	67136581	1.000000	0.71417	0.993000	0.49108	0.985000	0.73830	7.976000	0.88070	1.999000	0.58509	0.405000	0.27470	CTC	.	.	.	none		0.378	KBTBD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352189.1	NM_032505		C	67053891	T	C	67053891	3	2	258	1	0	0	0	0	1	0	0	0	8006	1551	54	3	510	3	KBTBD8	3	67053891	Missense_Mutation	SNP	T	TCGA-UZ-A9PL-01A-11D-A382-10	18416779	67053891	130968539	17	16053											
UMPS	7372	hgsc.bcm.edu	37	chr3	124458913	124458913	+	Frame_Shift_Del	DEL	C	C	-																															ctgggcagatctagtaaatgCtcacgtggtgccaggctcag																										TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr3:124458913delC	ENST00000232607.2	+	4	1131	c.1025delC	c.(1024-1026)gctfs	p.A342fs	UMPS_ENST00000413078.2_Intron|UMPS_ENST00000536109.1_Frame_Shift_Del_p.A250fs|UMPS_ENST00000538242.1_Frame_Shift_Del_p.A164fs	NM_000373.3	NP_000364.1	P11172	UMPS_HUMAN	uridine monophosphate synthetase	342	OMPdecase.				'de novo' pyrimidine nucleobase biosynthetic process (GO:0006207)|'de novo' UMP biosynthetic process (GO:0044205)|cellular response to drug (GO:0035690)|female pregnancy (GO:0007565)|lactation (GO:0007595)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|small molecule metabolic process (GO:0044281)|UMP biosynthetic process (GO:0006222)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	orotate phosphoribosyltransferase activity (GO:0004588)|orotidine-5'-phosphate decarboxylase activity (GO:0004590)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	16				GBM - Glioblastoma multiforme(114;0.146)	Fluorouracil(DB00544)	CTAGTAAATGCTCACGTGGTG	0.483																																					p.A342fs		Atlas-INDEL	.											.	UMPS	43	.	0			c.1024delG						PASS	.						98	100	99					3																	124458913		2203	4300	6503	SO:0001589	frameshift_variant	7372	exon4			.		CCDS3029.1	3q13	2008-02-04	2008-02-04		ENSG00000114491	ENSG00000114491	2.4.2.10, 4.1.1.23		12563	protein-coding gene	gene with protein product	"orotate phosphoribosyl transferase and orotidine-5'-decarboxylase"	613891				2767686	Standard	NM_000373		Approved		uc003ehl.4	P11172	OTTHUMG00000159431	ENST00000232607.2:c.1025delC	chr3.hg19:g.124458913delC	ENSP00000232607:p.Ala342fs	198.0	0.0	0		133.0	45.0	0.338346	NM_000373	B5LY68|B5LY72|O00758|O00759|O00760|Q16862|Q9H3Q2|Q9UG49	Frame_Shift_Del	DEL	ENST00000232607.2	hg19	CCDS3029.1																																																																																			.	.	.	none		0.483	UMPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355271.1	NM_000373		-	124458913	C	-	124458913	7	5	258	1	0	1	0	1	0	0	0	0	16993	797	28	0	1039	0	UMPS	3	124458913	Frame_Shift_Del	DEL	C	TCGA-UZ-A9PL-01A-11D-A382-10	57405022	124458913	73563517	18	16054	165	2									
UMPS	7372	hgsc.bcm.edu	37	chr3	124458915	124458920	+	In_Frame_Del	DEL	CACGTG	CACGTG	-																															gggcagatctagtaaatgctCacgtggtgccaggctcagga																								rs374066947		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	CACGTG	CACGTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr3:124458915_124458920delCACGTG	ENST00000232607.2	+	4	1133_1138	c.1027_1032delCACGTG	c.(1027-1032)cacgtgdel	p.HV343del	UMPS_ENST00000413078.2_Intron|UMPS_ENST00000536109.1_In_Frame_Del_p.HV251del|UMPS_ENST00000538242.1_In_Frame_Del_p.HV165del	NM_000373.3	NP_000364.1	P11172	UMPS_HUMAN	uridine monophosphate synthetase	343	OMPdecase.				'de novo' pyrimidine nucleobase biosynthetic process (GO:0006207)|'de novo' UMP biosynthetic process (GO:0044205)|cellular response to drug (GO:0035690)|female pregnancy (GO:0007565)|lactation (GO:0007595)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|small molecule metabolic process (GO:0044281)|UMP biosynthetic process (GO:0006222)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	orotate phosphoribosyltransferase activity (GO:0004588)|orotidine-5'-phosphate decarboxylase activity (GO:0004590)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	16				GBM - Glioblastoma multiforme(114;0.146)	Fluorouracil(DB00544)	AGTAAATGCTCACGTGGTGCCAGGCT	0.49																																					p.342_344del		Atlas-INDEL	.											.	UMPS	43	.	0			c.1026_1031del						PASS	.																																			SO:0001651	inframe_deletion	7372	exon4			.		CCDS3029.1	3q13	2008-02-04	2008-02-04		ENSG00000114491	ENSG00000114491	2.4.2.10, 4.1.1.23		12563	protein-coding gene	gene with protein product	"orotate phosphoribosyl transferase and orotidine-5'-decarboxylase"	613891				2767686	Standard	NM_000373		Approved		uc003ehl.4	P11172	OTTHUMG00000159431	ENST00000232607.2:c.1027_1032delCACGTG	chr3.hg19:g.124458915_124458920delCACGTG	ENSP00000232607:p.His343_Val344del	202.0	0.0	0		135.0	45.0	0.333333	NM_000373	B5LY68|B5LY72|O00758|O00759|O00760|Q16862|Q9H3Q2|Q9UG49	In_Frame_Del	DEL	ENST00000232607.2	hg19	CCDS3029.1																																																																																			.	.	.	none		0.49	UMPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355271.1	NM_000373		-	124458920	CACGTG	-	124458915	7	5	258	1	0	1	0	1	0	0	0	0	16993	826	29	0	1041	0	UMPS	3	124458915	In_Frame_Del	DEL	CACGTG	TCGA-UZ-A9PL-01A-11D-A382-10	2	124458915	73563515	19	16055	165	2									
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178943786	178943786	+	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	gctaacacttcaaattattcGtattatggaaaatatctggc	14	14	6	7	1	2	0	1	0	1	0	3	1	2	1	0	2	1	2	0	2	8	7	rs371049193		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr3:178943786G>T	ENST00000263967.3	+	17	2610	c.2453G>T	c.(2452-2454)cGt>cTt	p.R818L		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	818	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	CAAATTATTCGTATTATGGAA	0.348		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.R818L	Colon(199;1504 1750 3362 26421 31210 32040)	Atlas-SNP	.		Dom	yes		3	3q26.3	5290	"phosphoinositide-3-kinase, catalytic, alpha polypeptide"		"E, O"	.	PIK3CA	8460	.	0			c.G2453T						PASS	.						98	91	93					3																	178943786		1839	4090	5929	SO:0001583	missense	5290	exon17			TTATTCGTATTAT		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.2453G>T	chr3.hg19:g.178943786G>T	ENSP00000263967:p.Arg818Leu	77.0	0.0	.		80.0	4.0	.	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	hg19	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.155593	0.78114	.	.	ENSG00000121879	ENST00000263967	T	0.79247	-1.25	5.46	5.46	0.80206	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.123751	0.52532	D	0.000078	T	0.82010	0.4944	M	0.74467	2.265	0.80722	D	1	B	0.33318	0.408	B	0.39339	0.297	T	0.82653	-0.0351	10	0.62326	D	0.03	-7.3047	19.3097	0.94182	0.0:0.0:1.0:0.0	.	818	P42336	PK3CA_HUMAN	L	818	ENSP00000263967:R818L	ENSP00000263967:R818L	R	+	2	0	PIK3CA	180426480	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.373000	0.59537	2.569000	0.86673	0.557000	0.71058	CGT	.	.	.	alt		0.348	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			T	178943786	G	T	178943786	3	4	258	1	0	0	0	0	1	0	0	0	11920	1145	40	4	2515	4	PIK3CA	3	178943786	Missense_Mutation	SNP	G	TCGA-UZ-A9PL-01A-11D-A382-10	54484871	178943786	19078644	20	16056											
ATP10D	57205	hgsc.bcm.edu	37	chr4	47593159	47593159	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagaggactaaagctctcAagaagtggagaggggctgga	14	5	17	5	0	1	3	1	0	1	3	2	7	1	5	0	6	1	2	0	6	4	1			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr4:47593159A>G	ENST00000273859.3	+	23	4311	c.4042A>G	c.(4042-4044)Aag>Gag	p.K1348E		NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	1348					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						TAAAGCTCTCAAGAAGTGGAG	0.473																																					p.K1348E		Atlas-SNP	.											.	ATP10D	168	.	0			c.A4042G						PASS	.						95	97	97					4																	47593159		2203	4299	6502	SO:0001583	missense	57205	exon23			GCTCTCAAGAAGT	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.4042A>G	chr4.hg19:g.47593159A>G	ENSP00000273859:p.Lys1348Glu	136.0	0.0	.		143.0	81.0	.	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	hg19	CCDS3476.1	.	.	.	.	.	.	.	.	.	.	A	17.60	3.429275	0.62844	.	.	ENSG00000145246	ENST00000273859	T	0.38722	1.12	4.62	4.62	0.57501	.	0.059193	0.64402	D	0.000002	T	0.42040	0.1185	M	0.69823	2.125	0.80722	D	1	B	0.21147	0.052	B	0.26864	0.074	T	0.30707	-0.9969	10	0.13108	T	0.6	-15.5389	13.3654	0.60680	1.0:0.0:0.0:0.0	.	1348	Q9P241	AT10D_HUMAN	E	1348	ENSP00000273859:K1348E	ENSP00000273859:K1348E	K	+	1	0	ATP10D	47287916	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	4.713000	0.61895	1.917000	0.55516	0.377000	0.23210	AAG	.	.	.	none		0.473	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453		G	47593159	A	G	47593159	3	3	258	1	0	0	0	0	1	0	0	0	1118	131	5	3	4128	3	ATP10D	4	47593159	Missense_Mutation	SNP	A	TCGA-UZ-A9PL-01A-11D-A382-10		47593159	143561117	21	16057											
LPHN3	23284	hgsc.bcm.edu	37	chr4	62936619	62936619	+	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	accggctcatttggtcactaGtctatagaagatgacacaga	13	10	9	9	1	3	4	2	1	1	3	3	4	3	4	1	2	0	1	1	2	4	4			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr4:62936619G>T	ENST00000514591.1	+	25	4732	c.4403G>T	c.(4402-4404)aGt>aTt	p.S1468I	LPHN3_ENST00000512091.2_3'UTR|LPHN3_ENST00000507164.1_3'UTR|LPHN3_ENST00000507625.1_Missense_Mutation_p.S1527I|LPHN3_ENST00000506720.1_Missense_Mutation_p.S1579I|LPHN3_ENST00000514996.1_Missense_Mutation_p.S1502I|LPHN3_ENST00000514157.1_3'UTR|RP11-84A1.3_ENST00000504135.1_RNA|LPHN3_ENST00000545650.1_Missense_Mutation_p.S1468I|LPHN3_ENST00000506700.1_3'UTR|LPHN3_ENST00000506746.1_Missense_Mutation_p.S1570I|LPHN3_ENST00000508946.1_Missense_Mutation_p.S1511I|RP11-84A1.3_ENST00000509461.1_RNA|LPHN3_ENST00000504896.1_3'UTR|LPHN3_ENST00000511324.1_3'UTR|RP11-84A1.3_ENST00000506704.1_RNA|LPHN3_ENST00000508693.1_3'UTR|LPHN3_ENST00000509896.1_3'UTR			Q9HAR2	LPHN3_HUMAN	latrophilin 3	1446					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						TTGGTCACTAGTCTATAGAAG	0.448																																					p.S1468I		Atlas-SNP	.											.	LPHN3	800	.	0			c.G4403T						PASS	.						45	46	46					4																	62936619		692	1591	2283	SO:0001583	missense	23284	exon23			TCACTAGTCTATA	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.4403G>T	chr4.hg19:g.62936619G>T	ENSP00000422533:p.Ser1468Ile	64.0	0.0	.		77.0	34.0	.	NM_015236	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	hg19	CCDS54768.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.44|18.44	3.624809|3.624809	0.66901|0.66901	.|.	.|.	ENSG00000150471|ENSG00000150471	ENST00000514591;ENST00000545650;ENST00000295349;ENST00000507625;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996|ENST00000502815	D;D;D;T;T;T;T|.	0.84800|.	-1.83;-1.83;-1.9;-1.37;-1.41;-1.43;-1.39|.	5.5|5.5	5.5|5.5	0.81552|0.81552	GPCR, family 2, latrophilin, C-terminal (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.77384|.	0.4122|.	M|M	0.75777|0.75777	2.31|2.31	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.999;0.999|.	D;D|.	0.87578|.	0.998;0.998|.	T|.	0.76575|.	-0.2909|.	10|.	0.87932|.	D|.	0|.	.|.	19.4053|19.4053	0.94646|0.94646	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1468;1446|.	E9PE04;Q9HAR2|.	.;LPHN3_HUMAN|.	I|Y	1468;1468;1446;1527;1511;1579;1570;1502|916	ENSP00000422533:S1468I;ENSP00000439831:S1468I;ENSP00000421372:S1527I;ENSP00000421627:S1511I;ENSP00000420931:S1579I;ENSP00000425884:S1570I;ENSP00000424258:S1502I|.	ENSP00000295349:S1446I|.	S|X	+|+	2|3	0|2	LPHN3|LPHN3	62619214|62619214	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.965000|0.965000	0.64279|0.64279	9.370000|9.370000	0.97159|0.97159	2.607000|2.607000	0.88179|0.88179	0.591000|0.591000	0.81541|0.81541	AGT|TAG	.	.	.	none		0.448	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			T	62936619	G	T	62936619	3	4	258	1	0	0	0	0	1	0	0	0	8924	1029	36	4	4493	4	LPHN3	4	62936619	Missense_Mutation	SNP	G	TCGA-UZ-A9PL-01A-11D-A382-10	15343460	62936619	128217657	22	16058											
SH3RF1	57630	hgsc.bcm.edu	37	chr4	170037559	170037559	+	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	gagaagcactggtgatgcttGgggaagtcagtggagcagct	10	8	17	6	0	1	2	1	1	0	1	1	5	1	4	0	4	4	4	0	4	2	1			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr4:170037559G>T	ENST00000284637.9	-	10	2341	c.2000C>A	c.(1999-2001)cCa>cAa	p.P667Q	SH3RF1_ENST00000508685.1_5'UTR	NM_020870.3	NP_065921.2	Q7Z6J0	SH3R1_HUMAN	SH3 domain containing ring finger 1	667					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)		GGTGATGCTTGGGGAAGTCAG	0.607																																					p.P667Q		Atlas-SNP	.											.	SH3RF1	60	.	0			c.C2000A						PASS	.						64	55	58					4																	170037559		2203	4300	6503	SO:0001583	missense	57630	exon10			ATGCTTGGGGAAG	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.2000C>A	chr4.hg19:g.170037559G>T	ENSP00000284637:p.Pro667Gln	83.0	0.0	.		93.0	4.0	.	NM_020870	Q05BT2|Q8IW46|Q9HAM2|Q9P234	Missense_Mutation	SNP	ENST00000284637.9	hg19	CCDS34099.1	.	.	.	.	.	.	.	.	.	.	G	11.12	1.544876	0.27652	.	.	ENSG00000154447	ENST00000284637	T	0.17691	2.26	5.49	3.75	0.43078	.	0.326104	0.37857	N	0.001901	T	0.29882	0.0747	L	0.60455	1.87	0.36906	D	0.890651	D	0.54047	0.964	P	0.52267	0.694	T	0.12041	-1.0563	10	0.37606	T	0.19	-2.4822	17.3497	0.87320	0.0:0.0:0.7757:0.2243	.	667	Q7Z6J0	SH3R1_HUMAN	Q	667	ENSP00000284637:P667Q	ENSP00000284637:P667Q	P	-	2	0	SH3RF1	170274134	1.000000	0.71417	0.003000	0.11579	0.000000	0.00434	5.877000	0.69675	0.279000	0.22186	-3.073000	0.00066	CCA	.	.	.	none		0.607	SH3RF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363382.3	NM_020870		T	170037559	G	T	170037559	3	4	258	1	0	0	0	0	1	0	0	0	14271	1348	47	4	678	4	SH3RF1	4	170037559	Missense_Mutation	SNP	G	TCGA-UZ-A9PL-01A-11D-A382-10	107100940	170037559	21116717	23	16059											
C6	729	hgsc.bcm.edu	37	chr5	41201803	41201803	+	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	gttttcctggtagtacttatCtactactatttgtctgtaac	8	19	6	8	0	2	0	0	0	2	0	3	0	3	0	1	1	4	4	1	1	7	10			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr5:41201803C>A	ENST00000263413.3	-	3	421	c.157G>T	c.(157-159)Gat>Tat	p.D53Y	C6_ENST00000337836.5_Missense_Mutation_p.D53Y	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	53	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)		p.D53Y(1)		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)				TAGTACTTATCTACTACTATT	0.393																																					p.D53Y		Atlas-SNP	.											C6,NS,carcinoma,0,1	C6	197	.	1	Substitution - Missense(1)	lung(1)	c.G157T						PASS	.						91	92	91					5																	41201803		2203	4300	6503	SO:0001583	missense	729	exon3			ACTTATCTACTAC	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.157G>T	chr5.hg19:g.41201803C>A	ENSP00000263413:p.Asp53Tyr	78.0	0.0	.		79.0	37.0	.	NM_001115131		Missense_Mutation	SNP	ENST00000263413.3	hg19	CCDS3936.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.204041	0.79127	.	.	ENSG00000039537	ENST00000337836;ENST00000263413;ENST00000417809	T;T;T	0.53423	0.62;0.62;0.62	5.92	-1.99	0.07457	.	0.226533	0.51477	D	0.000094	T	0.65144	0.2663	M	0.82323	2.585	0.09310	N	0.999999	D	0.76494	0.999	D	0.72338	0.977	T	0.62067	-0.6932	10	0.87932	D	0	-4.1584	11.7594	0.51894	0.0:0.5428:0.0:0.4572	.	53	P13671	CO6_HUMAN	Y	53	ENSP00000338861:D53Y;ENSP00000263413:D53Y;ENSP00000396565:D53Y	ENSP00000263413:D53Y	D	-	1	0	C6	41237560	0.002000	0.14202	0.000000	0.03702	0.862000	0.49288	-0.031000	0.12287	-0.800000	0.04433	0.655000	0.94253	GAT	.	.	.	none		0.393	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1			A	41201803	C	A	41201803	3	1	258	1	0	0	0	0	1	0	0	0	2317	913	32	4	2711	4	C6	5	41201803	Missense_Mutation	SNP	C	TCGA-UZ-A9PL-01A-11D-A382-10		41201803	139713457	24	16060											
HCN1	348980	hgsc.bcm.edu	37	chr5	45462104	45462104	+	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	gcgagatcatatgtcatgtgGaatatctgttgaccaaaata	14	12	9	6	1	3	2	2	1	1	1	3	4	3	3	1	1	0	1	1	1	6	4			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr5:45462104G>T	ENST00000303230.4	-	3	912	c.855C>A	c.(853-855)ttC>ttA	p.F285L		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	285					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						ATGTCATGTGGAATATCTGTT	0.373																																					p.F285L		Atlas-SNP	.											.	HCN1	298	.	0			c.C855A						PASS	.						52	52	52					5																	45462104		2203	4300	6503	SO:0001583	missense	348980	exon3			CATGTGGAATATC	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.855C>A	chr5.hg19:g.45462104G>T	ENSP00000307342:p.Phe285Leu	231.0	0.0	.		208.0	97.0	.	NM_021072		Missense_Mutation	SNP	ENST00000303230.4	hg19	CCDS3952.1	.	.	.	.	.	.	.	.	.	.	G	19.23	3.788182	0.70337	.	.	ENSG00000164588	ENST00000303230	D	0.98362	-4.89	5.53	4.66	0.58398	Ion transport (1);	0.000000	0.64402	D	0.000002	D	0.96661	0.8910	N	0.21324	0.655	0.58432	D	0.999996	P	0.38048	0.616	P	0.48334	0.574	D	0.96289	0.9212	10	0.45353	T	0.12	.	14.1403	0.65316	0.072:0.0:0.928:0.0	.	285	O60741	HCN1_HUMAN	L	285	ENSP00000307342:F285L	ENSP00000307342:F285L	F	-	3	2	HCN1	45497861	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.589000	0.53972	1.351000	0.45789	0.650000	0.86243	TTC	.	.	.	none		0.373	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072		T	45462104	G	T	45462104	3	4	258	1	0	0	0	0	1	0	0	0	7003	1165	41	4	1841	4	HCN1	5	45462104	Missense_Mutation	SNP	G	TCGA-UZ-A9PL-01A-11D-A382-10	4260301	45462104	135453156	25	16061											
BDP1	55814	hgsc.bcm.edu	37	chr5	70793235	70793235	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagagcaagaattcacattcAaaaacttcagttgaaaaggt	18	9	8	6	0	3	3	3	1	0	2	3	4	3	3	0	1	2	2	0	1	6	4			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr5:70793235A>G	ENST00000358731.4	+	13	2201	c.1938A>G	c.(1936-1938)tcA>tcG	p.S646S	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	646					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)		ATTCACATTCAAAAACTTCAG	0.348																																					p.S646S		Atlas-SNP	.											.	BDP1	204	.	0			c.A1938G						PASS	.						75	69	71					5																	70793235		1806	4078	5884	SO:0001819	synonymous_variant	55814	exon13			ACATTCAAAAACT	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.1938A>G	chr5.hg19:g.70793235A>G		339.0	1.0	.		356.0	166.0	.	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Silent	SNP	ENST00000358731.4	hg19	CCDS43328.1																																																																																			.	.	.	none		0.348	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429		G	70793235	A	G	70793235	2	3	258	1	0	0	0	0	0	0	0	1	1395	117	5	3		3	BDP1	5	70793235	Silent	SNP	A	TCGA-UZ-A9PL-01A-11D-A382-10	25331131	70793235	110122025	26	16062											
AP3B1	8546	hgsc.bcm.edu	37	chr5	77511925	77511925	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgagcatatcgagttagcAtgtggattatgacaacctgc	11	11	10	9	2	0	1	0	1	0	0	2	4	1	2	2	1	4	3	2	1	4	3			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr5:77511925A>G	ENST00000255194.6	-	7	915	c.740T>C	c.(739-741)aTg>aCg	p.M247T	AP3B1_ENST00000519295.1_Missense_Mutation_p.M198T	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	247					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)		TCGAGTTAGCATGTGGATTAT	0.423									Hermansky-Pudlak syndrome																												p.M247T		Atlas-SNP	.											.	AP3B1	94	.	0			c.T740C						PASS	.						143	135	138					5																	77511925		2203	4300	6503	SO:0001583	missense	8546	exon7	Familial Cancer Database	HPS, HPS1-8	GTTAGCATGTGGA	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.740T>C	chr5.hg19:g.77511925A>G	ENSP00000255194:p.Met247Thr	78.0	0.0	.		80.0	29.0	.	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Missense_Mutation	SNP	ENST00000255194.6	hg19	CCDS4041.1	.	.	.	.	.	.	.	.	.	.	A	18.26	3.585230	0.66105	.	.	ENSG00000132842	ENST00000255194;ENST00000519295;ENST00000535760;ENST00000535667	T;T	0.25250	1.81;1.81	5.54	5.54	0.83059	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.37376	0.1001	L	0.50847	1.595	0.80722	D	1	B	0.32968	0.392	P	0.45276	0.475	T	0.25117	-1.0141	10	0.87932	D	0	-11.4846	15.6919	0.77461	1.0:0.0:0.0:0.0	.	247	O00203	AP3B1_HUMAN	T	247;198;247;151	ENSP00000255194:M247T;ENSP00000430597:M198T	ENSP00000255194:M247T	M	-	2	0	AP3B1	77547681	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.284000	0.95882	2.112000	0.64535	0.533000	0.62120	ATG	.	.	.	none		0.423	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2			G	77511925	A	G	77511925	3	3	258	1	0	0	0	0	1	0	0	0	744	217	8	3	2628	3	AP3B1	5	77511925	Missense_Mutation	SNP	A	TCGA-UZ-A9PL-01A-11D-A382-10	6718690	77511925	103403335	27	16063											
GPR98	84059	hgsc.bcm.edu	37	chr5	90016841	90016841	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatttggctgtgagtgtgcAgtgggagacagtatctgaaa	10	12	15	4	0	1	4	0	3	1	1	1	5	1	4	0	2	1	3	0	2	2	2			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr5:90016841A>G	ENST00000405460.2	+	45	9809	c.9713A>G	c.(9712-9714)cAg>cGg	p.Q3238R		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	3238					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)		GTGAGTGTGCAGTGGGAGACA	0.368																																					p.Q3238R		Atlas-SNP	.											.	GPR98	605	.	0			c.A9713G						PASS	.						166	164	164					5																	90016841		1932	4157	6089	SO:0001583	missense	84059	exon45			GTGTGCAGTGGGA	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.9713A>G	chr5.hg19:g.90016841A>G	ENSP00000384582:p.Gln3238Arg	88.0	0.0	.		88.0	45.0	.	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.95|18.95	3.732376|3.732376	0.69189|0.69189	.|.	.|.	ENSG00000164199|ENSG00000164199	ENST00000405460;ENST00000296619|ENST00000509621	T|.	0.26373|.	1.74|.	5.66|5.66	5.66|5.66	0.87406|0.87406	.|.	0.142471|.	0.64402|.	D|.	0.000008|.	T|T	0.54711|0.54711	0.1875|0.1875	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	B;B|.	0.26195|.	0.144;0.057|.	B;B|.	0.18263|.	0.021;0.01|.	T|T	0.51521|0.51521	-0.8695|-0.8695	10|5	0.59425|.	D|.	0.04|.	.|.	15.9011|15.9011	0.79377|0.79377	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	3238;3238|.	E7ETI5;Q8WXG9|.	.;GPR98_HUMAN|.	R|G	3238|804	ENSP00000384582:Q3238R|.	ENSP00000296619:Q3238R|.	Q|S	+|+	2|1	0|0	GPR98|GPR98	90052597|90052597	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	6.532000|6.532000	0.73825|0.73825	2.158000|2.158000	0.67659|0.67659	0.528000|0.528000	0.53228|0.53228	CAG|AGT	.	.	.	none		0.368	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		G	90016841	A	G	90016841	3	3	258	1	0	0	0	0	1	0	0	0	6728	188	7	3	9891	3	GPR98	5	90016841	Missense_Mutation	SNP	A	TCGA-UZ-A9PL-01A-11D-A382-10	12504916	90016841	90898419	28	16064											
FAM13B	51306	hgsc.bcm.edu	37	chr5	137295872	137295873	+	Frame_Shift_Ins	INS	-	-	T																															accagaatcaagtgtgacaaINStttatcactgtcaaataaca																								rs149593352	byFrequency	TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr5:137295872_137295873insT	ENST00000033079.3	-	12	1726_1727	c.1275_1276insA	c.(1273-1278)aaattgfs	p.L426fs	FAM13B_ENST00000420893.2_Frame_Shift_Ins_p.L426fs|FAM13B_ENST00000425075.2_Frame_Shift_Ins_p.L308fs	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	426					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						AAGTGTGACAATTTATCACTGT	0.277																																					p.L426fs		Pindel	.											.	FAM13B	46	.	0			c.1276_1277insA						PASS	.																																			SO:0001589	frameshift_variant	51306	exon12			.	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.1276dupA	chr5.hg19:g.137295875_137295875dupT	ENSP00000033079:p.Leu426fs	340.0	0.0	.		355.0	90.0	0.254	NM_001101800	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Frame_Shift_Ins	INS	ENST00000033079.3	hg19	CCDS4195.1																																																																																			.	.	.	none		0.277	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1			T	137295873	-	T	137295872	7	5	258	1	0	1	1	0	0	0	0	0	5457	98	4	0	1589	0	FAM13B	5	137295872	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PL-01A-11D-A382-10	47279031	137295872	43619388	29	16065											
DIAPH1	1729	hgsc.bcm.edu	37	chr5	140909206	140909206	+	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	gtcagaacagcctcattcacCtccaggatgacattcttaat	12	11	6	12	0	4	2	3	1	1	1	5	3	5	3	3	1	2	0	3	1	2	3			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr5:140909206C>G	ENST00000398557.4	-	20	2780	c.2640G>C	c.(2638-2640)gaG>gaC	p.E880D	DIAPH1_ENST00000494967.1_5'UTR|DIAPH1_ENST00000389054.3_Missense_Mutation_p.E877D|DIAPH1_ENST00000398562.2_Missense_Mutation_p.E856D|DIAPH1_ENST00000520569.1_Missense_Mutation_p.E823D|DIAPH1_ENST00000253811.6_Missense_Mutation_p.E881D|DIAPH1_ENST00000398566.3_Missense_Mutation_p.E872D|DIAPH1_ENST00000518047.1_Missense_Mutation_p.E868D|DIAPH1_ENST00000389057.5_Missense_Mutation_p.E871D	NM_005219.4	NP_005210.3	O60610	DIAP1_HUMAN	diaphanous-related formin 1	880	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament polymerization (GO:0030041)|cellular response to histamine (GO:0071420)|cytoskeleton organization (GO:0007010)|positive regulation of cell migration (GO:0030335)|protein localization to microtubule (GO:0035372)|regulation of cell shape (GO:0008360)|regulation of microtubule-based process (GO:0032886)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|ruffle membrane (GO:0032587)	ion channel binding (GO:0044325)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|pancreas(1)|skin(2)|stomach(2)	23			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTCATTCACCTCCAGGATGA	0.483																																					p.E880D		Atlas-SNP	.											.	DIAPH1	64	.	0			c.G2640C						PASS	.						122	115	118					5																	140909206		1995	4191	6186	SO:0001583	missense	1729	exon20			ATTCACCTCCAGG	BC007411		5q31	2013-05-24	2013-05-24		ENSG00000131504	ENSG00000131504			2876	protein-coding gene	gene with protein product		602121	"diaphanous (Drosophila, homolog) 1", "diaphanous homolog 1 (Drosophila)"	DFNA1		9360932, 1350680	Standard	NM_005219		Approved	hDIA1, LFHL1	uc003llb.4	O60610	OTTHUMG00000149893	ENST00000398557.4:c.2640G>C	chr5.hg19:g.140909206C>G	ENSP00000381565:p.Glu880Asp	90.0	0.0	.		84.0	35.0	.	NM_005219	A6NF18|B7ZKW2|E9PEZ2|Q17RN4|Q59FH8|Q9UC76	Missense_Mutation	SNP	ENST00000398557.4	hg19	CCDS43374.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.252794	0.59212	.	.	ENSG00000131504	ENST00000389054;ENST00000520569;ENST00000398562;ENST00000389057;ENST00000398566;ENST00000398557;ENST00000253811;ENST00000518047	T;T;T;T;T;T;T;T	0.19105	2.17;2.17;2.17;2.17;2.17;2.17;2.17;2.17	5.06	2.88	0.33553	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.135356	0.47455	D	0.000228	T	0.27765	0.0683	M	0.73598	2.24	0.49915	D	0.999837	B;P;P	0.38167	0.345;0.621;0.621	B;B;B	0.41510	0.11;0.359;0.359	T	0.12811	-1.0533	10	0.87932	D	0	.	9.7631	0.40543	0.0:0.7815:0.0:0.2185	.	823;871;880	E7ERW8;E9PEZ2;O60610	.;.;DIAP1_HUMAN	D	877;823;856;871;872;880;881;868	ENSP00000373706:E877D;ENSP00000429282:E823D;ENSP00000381570:E856D;ENSP00000373709:E871D;ENSP00000381572:E872D;ENSP00000381565:E880D;ENSP00000253811:E881D;ENSP00000428268:E868D	ENSP00000253811:E881D	E	-	3	2	DIAPH1	140889390	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.497000	0.35649	1.267000	0.44247	0.650000	0.86243	GAG	.	.	.	none		0.483	DIAPH1-203	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_005219		G	140909206	C	G	140909206	3	3	258	1	0	0	0	0	1	0	0	0	4520	680	24	4	1214	4	DIAPH1	5	140909206	Missense_Mutation	SNP	C	TCGA-UZ-A9PL-01A-11D-A382-10	3613334	140909206	40006054	30	16066											
SOX4	6659	hgsc.bcm.edu	37	chr6	21594835	21594835	+	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	gcgagagctcggactcgggcGccggcctcgagctgggaatc	6	5	17	13	6	0	1	0	0	0	1	4	5	0	3	2	4	2	2	2	4	1	0			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr6:21594835G>T	ENST00000244745.1	+	1	864	c.70G>T	c.(70-72)Gcc>Tcc	p.A24S	SOX4_ENST00000543472.1_Missense_Mutation_p.A24S	NM_003107.2	NP_003098.1	Q06945	SOX4_HUMAN	SRY (sex determining region Y)-box 4	24					ascending aorta morphogenesis (GO:0035910)|atrial septum primum morphogenesis (GO:0003289)|canonical Wnt signaling pathway (GO:0060070)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac ventricle formation (GO:0003211)|cellular response to glucose stimulus (GO:0071333)|DNA damage response, detection of DNA damage (GO:0042769)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endocrine pancreas development (GO:0031018)|glial cell development (GO:0021782)|glial cell proliferation (GO:0014009)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|kidney morphogenesis (GO:0060993)|limb bud formation (GO:0060174)|mitral valve morphogenesis (GO:0003183)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of protein ubiquitination (GO:0031397)|neural tube formation (GO:0001841)|neuroepithelial cell differentiation (GO:0060563)|noradrenergic neuron differentiation (GO:0003357)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin secretion (GO:0032024)|positive regulation of N-terminal peptidyl-lysine acetylation (GO:2000761)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|positive regulation of Wnt signaling pathway (GO:0030177)|pro-B cell differentiation (GO:0002328)|protein stabilization (GO:0050821)|regulation of protein stability (GO:0031647)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|spinal cord development (GO:0021510)|spinal cord motor neuron differentiation (GO:0021522)|sympathetic nervous system development (GO:0048485)|T cell differentiation (GO:0030217)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			kidney(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	6	Ovarian(93;0.163)		all cancers(50;0.0751)|Epithelial(50;0.155)			GGACTCGGGCGCCGGCCTCGA	0.731																																					p.A24S		Atlas-SNP	.											.	SOX4	11	.	0			c.G70T						PASS	.						8	10	10					6																	21594835		2161	4225	6386	SO:0001583	missense	6659	exon1			TCGGGCGCCGGCC	AF070669	CCDS4547.1	6p22.3	2008-02-05			ENSG00000124766	ENSG00000124766		"SRY (sex determining region Y)-boxes"	11200	protein-coding gene	gene with protein product		184430				8268656, 9730625	Standard	NM_003107		Approved		uc003ndi.3	Q06945	OTTHUMG00000016101	ENST00000244745.1:c.70G>T	chr6.hg19:g.21594835G>T	ENSP00000244745:p.Ala24Ser	92.0	0.0	.		91.0	4.0	.	NM_003107		Missense_Mutation	SNP	ENST00000244745.1	hg19	CCDS4547.1	.	.	.	.	.	.	.	.	.	.	G	14.49	2.549614	0.45383	.	.	ENSG00000124766	ENST00000244745;ENST00000543472	D;D	0.97906	-4.6;-4.6	5.12	3.32	0.38043	.	0.083581	0.47093	U	0.000254	D	0.90621	0.7059	L	0.55481	1.735	0.37428	D	0.913929	P	0.36974	0.576	B	0.33620	0.167	D	0.86855	0.2026	10	0.12430	T	0.62	.	7.3985	0.26950	0.0808:0.0:0.6231:0.2961	.	24	Q06945	SOX4_HUMAN	S	24	ENSP00000244745:A24S;ENSP00000438412:A24S	ENSP00000244745:A24S	A	+	1	0	SOX4	21702814	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.213000	0.42844	0.536000	0.28733	0.555000	0.69702	GCC	.	.	.	none		0.731	SOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043301.1	NM_003107		T	21594835	G	T	21594835	3	4	258	1	0	0	0	0	1	0	0	0	14966	1087	38	4	72	4	SOX4	6	21594835	Missense_Mutation	SNP	G	TCGA-UZ-A9PL-01A-11D-A382-10		21594835	149520232	31	16067											
TEAD3	7005	hgsc.bcm.edu	37	chr6	35443200	35443200	+	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	tggatgaagttgatcatgtaCtcgcacatgggcgagcggtg	9	10	15	7	3	1	2	1	2	0	0	2	4	1	3	0	3	2	3	0	3	2	2			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr6:35443200C>T	ENST00000402886.3	-	10	1080	c.927G>A	c.(925-927)gaG>gaA	p.E309E	TEAD3_ENST00000338863.7_Silent_p.E369E			Q99594	TEAD3_HUMAN	TEA domain family member 3	369	Transcriptional activation. {ECO:0000255}.				female pregnancy (GO:0007565)|gene expression (GO:0010467)|hippo signaling (GO:0035329)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	10						TGATCATGTACTCGCACATGG	0.557																																					p.E369E		Atlas-SNP	.											.	TEAD3	52	.	0			c.G1107A						PASS	.						102	99	100					6																	35443200		2203	4300	6503	SO:0001819	synonymous_variant	7005	exon12			CATGTACTCGCAC	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.927G>A	chr6.hg19:g.35443200C>T		47.0	0.0	.		61.0	41.0	.	NM_003214	O95910|Q5BJG7|Q8N6Y4	Silent	SNP	ENST00000402886.3	hg19																																																																																				.	.	.	none		0.557	TEAD3-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316961.2			T	35443200	C	T	35443200	2	4	258	1	0	0	0	0	0	0	0	1	15752	564	20	2		2	TEAD3	6	35443200	Silent	SNP	C	TCGA-UZ-A9PL-01A-11D-A382-10	13848365	35443200	135671867	32	16068											
TBCC	6903	hgsc.bcm.edu	37	chr6	42713428	42713428	+	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	ttcttgggctgcagcccccgGcgccgctcggccaaggccgc	3	6	14	18	5	1	0	0	0	1	0	2	0	1	0	5	4	2	3	5	4	1	2			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr6:42713428G>T	ENST00000372876.1	-	1	406	c.384C>A	c.(382-384)cgC>cgA	p.R128R	TBCC_ENST00000244625.2_Silent_p.R128R	NM_003192.2	NP_003183	Q15814	TBCC_HUMAN	tubulin folding cofactor C	128					'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)			GCAGCCCCCGGCGCCGCTCGG	0.627																																					p.R128R		Atlas-SNP	.											.	TBCC	31	.	0			c.C384A						PASS	.						16	20	19					6																	42713428		2183	4276	6459	SO:0001819	synonymous_variant	6903	exon1			CCCCCGGCGCCGC	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.384C>A	chr6.hg19:g.42713428G>T		103.0	0.0	.		103.0	48.0	.	NM_003192	Q53Y43|Q5T787	Silent	SNP	ENST00000372876.1	hg19	CCDS4872.1																																																																																			.	.	.	none		0.627	TBCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040559.1	NM_003192		T	42713428	G	T	42713428	2	4	258	1	0	0	0	0	0	0	0	1	15643	1190	42	4		4	TBCC	6	42713428	Silent	SNP	G	TCGA-UZ-A9PL-01A-11D-A382-10	7270228	42713428	128401639	33	16069											
MAP3K7	6885	hgsc.bcm.edu	37	chr6	91296573	91296573	+	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	tcaccggccgaagacgaggaGgaggaggaggcggcagaggc	11	1	20	9	4	1	2	1	0	0	2	1	8	1	6	2	8	0	1	2	8	1	0			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr6:91296573G>C	ENST00000369329.3	-	1	191	c.30C>G	c.(28-30)tcC>tcG	p.S10S	MAP3K7_ENST00000369327.3_Silent_p.S10S|MAP3K7_ENST00000369332.3_Silent_p.S10S|MAP3K7_ENST00000369325.3_Silent_p.S10S	NM_145331.2	NP_663304.1	O43318	M3K7_HUMAN	mitogen-activated protein kinase kinase kinase 7	10	Interaction with MAPK8IP1. {ECO:0000250}.|Poly-Ser.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|Fc-epsilon receptor signaling pathway (GO:0038095)|histone H3 acetylation (GO:0043966)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of ripoptosome assembly involved in necroptotic process (GO:1902443)|neural tube formation (GO:0001841)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|regulation of reactive oxygen species metabolic process (GO:2000377)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase activity (GO:0004708)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)			endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	28		all_cancers(76;6.4e-08)|Acute lymphoblastic leukemia(125;1.43e-09)|Prostate(29;9.32e-09)|all_hematologic(105;3.69e-06)|all_epithelial(107;0.000187)|Ovarian(999;0.0164)		OV - Ovarian serous cystadenocarcinoma(136;2.05e-11)|all cancers(137;3.25e-11)|GBM - Glioblastoma multiforme(226;0.0416)|BRCA - Breast invasive adenocarcinoma(108;0.0429)		AAGACGAGGAGGAGGAGGAGG	0.647																																					p.S10S		Atlas-SNP	.											.	MAP3K7	100	.	0			c.C30G						PASS	.						39	39	39					6																	91296573		2203	4300	6503	SO:0001819	synonymous_variant	6885	exon1			CGAGGAGGAGGAG	AB009356	CCDS5027.1, CCDS5028.1, CCDS5029.1, CCDS5030.1	6q15	2011-06-09			ENSG00000135341	ENSG00000135341		"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6859	protein-coding gene	gene with protein product		602614		TAK1		9466656	Standard	NM_003188		Approved	MEKK7	uc003pnz.2	O43318	OTTHUMG00000015217	ENST00000369329.3:c.30C>G	chr6.hg19:g.91296573G>C		60.0	0.0	.		48.0	23.0	.	NM_145333	B2RE27|E1P523|O43317|O43319|Q5TDN2|Q5TDN3|Q5TDT7|Q9NTR3|Q9NZ70	Silent	SNP	ENST00000369329.3	hg19	CCDS5028.1																																																																																			.	.	.	none		0.647	MAP3K7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041530.1	NM_145331		C	91296573	G	C	91296573	2	2	258	1	0	0	0	0	0	0	0	1	9262	987	35	4		4	MAP3K7	6	91296573	Silent	SNP	G	TCGA-UZ-A9PL-01A-11D-A382-10	48583145	91296573	79818494	34	16070											
AHI1	54806	hgsc.bcm.edu	37	chr6	135784363	135784363	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcttatttcatcatcttgAtgagaatctgaagaaactga	14	13	8	6	0	4	5	2	4	2	2	4	7	4	5	0	0	2	1	0	0	4	3			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr6:135784363A>G	ENST00000367800.4	-	6	1047	c.831T>C	c.(829-831)caT>caC	p.H277H	AHI1_ENST00000457866.2_Silent_p.H277H|AHI1_ENST00000327035.6_Silent_p.H277H	NM_001134830.1	NP_001128302.1	Q8N157	AHI1_HUMAN	Abelson helper integration site 1	277	Interaction with HAP1.				cellular protein localization (GO:0034613)|central nervous system development (GO:0007417)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|cloaca development (GO:0035844)|heart looping (GO:0001947)|hindbrain development (GO:0030902)|Kupffer's vesicle development (GO:0070121)|left/right axis specification (GO:0070986)|morphogenesis of a polarized epithelium (GO:0001738)|negative regulation of apoptotic process (GO:0043066)|otic vesicle development (GO:0071599)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of polarized epithelial cell differentiation (GO:0030862)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pronephric duct morphogenesis (GO:0039023)|pronephric nephron tubule morphogenesis (GO:0039008)|protein localization to organelle (GO:0033365)|regulation of behavior (GO:0050795)|retina layer formation (GO:0010842)|specification of axis polarity (GO:0065001)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vesicle targeting (GO:0006903)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|nonmotile primary cilium (GO:0031513)|photoreceptor outer segment (GO:0001750)|primary cilium (GO:0072372)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)	37	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		CATCATCTTGATGAGAATCTG	0.343																																					p.H277H		Atlas-SNP	.											.	AHI1	81	.	0			c.T831C						PASS	.						150	139	143					6																	135784363		1873	4106	5979	SO:0001819	synonymous_variant	54806	exon7			ATCTTGATGAGAA	AJ459824	CCDS47483.1, CCDS47484.1	6q23.2	2013-01-10	2005-11-29		ENSG00000135541	ENSG00000135541		"WD repeat domain containing"	21575	protein-coding gene	gene with protein product	"Jouberin"	608894	"Abelson helper integration site"			15060101, 16240161	Standard	NM_017651		Approved	FLJ20069, ORF1, JBTS3	uc003qgj.3	Q8N157	OTTHUMG00000015631	ENST00000367800.4:c.831T>C	chr6.hg19:g.135784363A>G		47.0	0.0	.		43.0	20.0	.	NM_001134832	E1P584|Q4FD35|Q504T3|Q5TCP9|Q6P098|Q6PIT6|Q8NDX0|Q9H0H2	Silent	SNP	ENST00000367800.4	hg19	CCDS47483.1																																																																																			.	.	.	none		0.343	AHI1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391948.1	NM_017651		G	135784363	A	G	135784363	2	3	258	1	0	0	0	0	0	0	0	1	413	330	12	3		3	AHI1	6	135784363	Silent	SNP	A	TCGA-UZ-A9PL-01A-11D-A382-10	44487790	135784363	35330704	35	16071											
RNF139	83940	hgsc.bcm.edu	37	chr8	125499771	125499771	+	IGR	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	gctgctgctgaatctgacagGgaattgaacgaagatgacag	13	8	13	7	1	1	5	0	4	1	1	1	7	1	6	0	1	3	3	0	1	4	1			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr8:125499771G>C	ENST00000276692.6	-	0	1018				RNF139_ENST00000303545.3_Missense_Mutation_p.R627S|RP11-158K1.3_ENST00000518639.1_RNA	NM_032026.3	NP_114415.1	Q6P1N9	TATD1_HUMAN	TatD DNase domain containing 1						DNA catabolic process (GO:0006308)	intracellular organelle (GO:0043229)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	15	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			AATCTGACAGGGAATTGAACG	0.393																																					p.R627S		Atlas-SNP	.											.	RNF139	57	.	0			c.G1881C						PASS	.						93	92	93					8																	125499771		2203	4300	6503	SO:0001628	intergenic_variant	11236	exon2			TGACAGGGAATTG	AF212250	CCDS6351.1, CCDS55273.1	8q24.13	2004-06-07			ENSG00000147687	ENSG00000147687			24220	protein-coding gene	gene with protein product						12477932	Standard	NM_032026		Approved	CDA11	uc003yrd.2	Q6P1N9	OTTHUMG00000165068		chr8.hg19:g.125499771G>C		136.0	0.0	.		88.0	42.0	.	NM_007218	B2R5J0|Q8TD02|Q9BY40	Missense_Mutation	SNP	ENST00000276692.6	hg19	CCDS6351.1	.	.	.	.	.	.	.	.	.	.	G	3.586	-0.084525	0.07097	.	.	ENSG00000170881	ENST00000303545	T	0.22945	1.93	5.64	2.65	0.31530	.	0.522447	0.21142	N	0.079461	T	0.08537	0.0212	N	0.03608	-0.345	0.29212	N	0.874533	B	0.06786	0.001	B	0.04013	0.001	T	0.33523	-0.9865	10	0.09084	T	0.74	-8.8311	5.7273	0.18020	0.1441:0.0965:0.6257:0.1336	.	627	Q8WU17	RN139_HUMAN	S	627	ENSP00000304051:R627S	ENSP00000304051:R627S	R	+	3	2	RNF139	125568952	1.000000	0.71417	1.000000	0.80357	0.783000	0.44284	1.109000	0.31135	0.408000	0.25621	-1.134000	0.01955	AGG	.	.	.	none		0.393	TATDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381655.1	NM_032026		C	125499771	G	C	125499771	1	2	258	0	1	0	0	0	0	0	0	0	13455	1223	43	4		4	RNF139	8	125499771	IGR	SNP	G	TCGA-UZ-A9PL-01A-11D-A382-10		125499771	20864251	36	16072											
C9orf43	257169	hgsc.bcm.edu	37	chr9	116185621	116185621	+	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	tccagaaaagcaagtcatttCtgggtctctctggaaatcag	12	11	9	9	0	5	1	2	0	3	1	7	2	6	2	1	2	1	1	1	2	4	1			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr9:116185621C>T	ENST00000288462.4	+	7	945	c.499C>T	c.(499-501)Ctg>Ttg	p.L167L	C9orf43_ENST00000374165.1_Silent_p.L167L	NM_152786.1	NP_689999.1	Q8TAL5	CI043_HUMAN	chromosome 9 open reading frame 43	167										breast(2)|large_intestine(6)|lung(2)|ovary(1)|pancreas(1)|prostate(3)	15						CAAGTCATTTCTGGGTCTCTC	0.453																																					p.L167L		Atlas-SNP	.											C9orf43,NS,carcinoma,0,1	C9orf43	49	.	0			c.C499T						PASS	.						80	76	77					9																	116185621		2203	4300	6503	SO:0001819	synonymous_variant	257169	exon7			TCATTTCTGGGTC	BC026884	CCDS6796.1	9q33.1	2012-03-15			ENSG00000157653	ENSG00000157653			23570	protein-coding gene	gene with protein product						12477932	Standard	NM_152786		Approved	MGC17358	uc004bhp.3	Q8TAL5	OTTHUMG00000020526	ENST00000288462.4:c.499C>T	chr9.hg19:g.116185621C>T		82.0	0.0	.		68.0	28.0	.	NM_152786		Silent	SNP	ENST00000288462.4	hg19	CCDS6796.1																																																																																			.	.	.	none		0.453	C9orf43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053739.1	NM_152786		T	116185621	C	T	116185621	2	4	258	1	0	0	0	0	0	0	0	1	2485	912	32	2		2	C9orf43	9	116185621	Silent	SNP	C	TCGA-UZ-A9PL-01A-11D-A382-10		116185621	25027810	37	16073											
TNFSF8	944	hgsc.bcm.edu	37	chr9	117666251	117666257	+	Frame_Shift_Del	DEL	TCAAGAG	TCAAGAG	-																															agaagatggacaacacattcTcaagaggaaaggtgcttgta																										TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	TCAAGAG	TCAAGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr9:117666251_117666257delTCAAGAG	ENST00000223795.2	-	4	772_778	c.659_665delCTCTTGA	c.(658-666)cctcttgagfs	p.PLE220fs	TNFSF8_ENST00000474301.1_Intron	NM_001244.3	NP_001235.1	P32971	TNFL8_HUMAN	tumor necrosis factor (ligand) superfamily, member 8	220					apoptotic process (GO:0006915)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor binding (GO:0005102)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(3)|urinary_tract(1)	12						CAACACATTCTCAAGAGGAAAGGTGCT	0.42																																					p.220_222del		Atlas-Indel,Pindel	.											.	TNFSF8	34	.	0			c.660_666del						PASS	.																																			SO:0001589	frameshift_variant	944	exon4			.	L09753	CCDS6810.1, CCDS75884.1	9q33	2008-02-05			ENSG00000106952	ENSG00000106952		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11938	protein-coding gene	gene with protein product		603875		CD30LG		8391931, 9349718	Standard	NM_001244		Approved	CD153	uc004bji.2	P32971	OTTHUMG00000021025	ENST00000223795.2:c.659_665delCTCTTGA	chr9.hg19:g.117666251_117666257delTCAAGAG	ENSP00000223795:p.Pro220fs	73.0	0.0	0		64.0	27.0	0.421875	NM_001244	O43404	Frame_Shift_Del	DEL	ENST00000223795.2	hg19	CCDS6810.1																																																																																			.	.	.	none		0.42	TNFSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055464.1			-	117666257	TCAAGAG	-	117666251	7	5	258	1	0	1	0	1	0	0	0	0	16323	1551	54	0	43	0	TNFSF8	9	117666251	Frame_Shift_Del	DEL	TCAAGAG	TCGA-UZ-A9PL-01A-11D-A382-10	1480630	117666251	23547180	38	16074											
SEC16A	9919	hgsc.bcm.edu	37	chr9	139368591	139368591	+	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	tacaaaggccggtagtagtaGtaggcggccaggtcctgagg	10	7	16	8	2	0	1	0	1	0	0	1	1	1	1	3	6	1	4	3	6	6	5			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr9:139368591G>T	ENST00000371706.3	-	1	2976	c.2943C>A	c.(2941-2943)taC>taA	p.Y981*	SEC16A_ENST00000431893.2_Nonsense_Mutation_p.Y981*|SEC16A_ENST00000290037.6_Nonsense_Mutation_p.Y981*|SEC16A_ENST00000313050.7_Nonsense_Mutation_p.Y1159*			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	981	Poly-Tyr.|Pro-rich.|Required for endoplasmic reticulum localization.				COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		GGTAGTAGTAGTAGGCGGCCA	0.652																																					p.Y1159X		Atlas-SNP	.											.	SEC16A	249	.	0			c.C3477A						PASS	.						50	57	55					9																	139368591		2034	4181	6215	SO:0001587	stop_gained	9919	exon3			GTAGTAGTAGGCG	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.2943C>A	chr9.hg19:g.139368591G>T	ENSP00000360771:p.Tyr981*	158.0	0.0	.		155.0	85.0	.	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Nonsense_Mutation	SNP	ENST00000371706.3	hg19		.	.	.	.	.	.	.	.	.	.	G	37	6.605004	0.97701	.	.	ENSG00000148396	ENST00000313050;ENST00000371706;ENST00000290037;ENST00000431893;ENST00000404925;ENST00000398348	.	.	.	5.38	0.014	0.14098	.	0.376195	0.26507	N	0.023987	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05351	T	0.99	-7.7001	9.9781	0.41797	0.4482:0.0:0.5518:0.0	.	.	.	.	X	1159;981;981;981;549;83	.	ENSP00000290037:Y981X	Y	-	3	2	SEC16A	138488412	1.000000	0.71417	0.941000	0.38009	0.285000	0.27093	1.404000	0.34623	0.026000	0.15269	0.462000	0.41574	TAC	.	.	.	none		0.652	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459		T	139368591	G	T	139368591	4	4	258	1	0	0	0	0	0	1	0	0	13999	1024	36	4	3716	4	SEC16A	9	139368591	Nonsense_Mutation	SNP	G	TCGA-UZ-A9PL-01A-11D-A382-10	21702340	139368591	1844840	39	16075											
PGBD3	267004	hgsc.bcm.edu	37	chr10	50723698	50723698	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaccagttcgaaacagaacAaaagagggcttgaataccat	18	6	9	8	1	0	4	0	1	0	3	1	5	0	4	2	1	3	2	2	1	6	3			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr10:50723698A>G	ENST00000374127.3	-	2	1664	c.1463T>C	c.(1462-1464)tTg>tCg	p.L488S	ERCC6-PGBD3_ENST00000515869.1_Missense_Mutation_p.L956S|ERCC6_ENST00000355832.5_Intron|ERCC6-PGBD3_ENST00000447839.2_Missense_Mutation_p.L956S|PGBD3_ENST00000603152.1_Missense_Mutation_p.L956S|PGBD3_ENST00000508005.2_Missense_Mutation_p.L488S	NM_170753.2	NP_736609.2	Q8N328	PGBD3_HUMAN	piggyBac transposable element derived 3	488										breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|lung(16)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	33						GAAACAGAACAAAAGAGGGCT	0.418																																					p.S488S		Atlas-SNP	.											.	PGBD3	58	.	0			c.C1463C						PASS	.						134	127	130					10																	50723698		2203	4300	6503	SO:0001583	missense	267004	exon2			CAGAACAAAAGAG	AK074682	CCDS7230.1	10q11	2011-03-24			ENSG00000243251	ENSG00000243251			19400	protein-coding gene	gene with protein product							Standard	NM_170753		Approved	FLJ90201		Q8N328	OTTHUMG00000018193	ENST00000374127.3:c.1463T>C	chr10.hg19:g.50723698A>G	ENSP00000363242:p.Leu488Ser	43.0	0.0	.		39.0	20.0	.	NM_170753	B3KQC4|Q5W0M0|Q6PIH0	Silent	SNP	ENST00000374127.3	hg19	CCDS7230.1	.	.	.	.	.	.	.	.	.	.	A	9.207	1.029955	0.19512	.	.	ENSG00000243251;ENSG00000243251;ENSG00000258838;ENSG00000258838	ENST00000374127;ENST00000508005;ENST00000515869;ENST00000447839	T;T;T;T	0.17528	2.27;2.27;2.27;2.27	0.706	-1.01	0.10169	.	.	.	.	.	T	0.06188	0.0160	N	0.00621	-1.32	0.19300	N	0.999975	D;P	0.63880	0.993;0.874	P;P	0.51355	0.667;0.663	T	0.17745	-1.0359	8	0.23302	T	0.38	-17.488	.	.	.	.	956;488	E7EV46;Q8N328	.;PGBD3_HUMAN	S	488;488;956;956	ENSP00000363242:L488S;ENSP00000426963:L488S;ENSP00000423550:L956S;ENSP00000387966:L956S	ENSP00000387966:L956S	L	-	2	0	PGBD3;RP11-123B3.6	50393704	0.469000	0.25846	0.276000	0.24689	0.965000	0.64279	-0.098000	0.11024	-0.361000	0.08125	0.402000	0.26972	TTG	.	.	.	none		0.418	PGBD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047988.1			G	50723698	A	G	50723698	3	3	258	1	0	0	0	0	1	0	0	0	11789	131	5	3	322	3	PGBD3	10	50723698	Missense_Mutation	SNP	A	TCGA-UZ-A9PL-01A-11D-A382-10		50723698	84811049	40	16076											
IFIT2	3433	hgsc.bcm.edu	37	chr10	91065753	91065753	+	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	attccttggagagcagcctaCggcaactaaaatgccatttc	12	10	8	11	1	0	1	0	0	0	1	2	2	1	1	3	2	5	2	3	2	4	5			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr10:91065753C>T	ENST00000371826.3	+	2	209	c.40C>T	c.(40-42)Cgg>Tgg	p.R14W	LIPA_ENST00000371837.1_Intron|LIPA_ENST00000487618.1_Intron	NM_001547.4	NP_001538.4	P09913	IFIT2_HUMAN	interferon-induced protein with tetratricopeptide repeats 2	14					apoptotic mitochondrial changes (GO:0008637)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|negative regulation of protein binding (GO:0032091)|positive regulation of apoptotic process (GO:0043065)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|skin(1)	12		Colorectal(252;0.0161)				GAGCAGCCTACGGCAACTAAA	0.408																																					p.R14W		Atlas-SNP	.											.	IFIT2	39	.	0			c.C40T						PASS	.						87	86	86					10																	91065753		1861	4104	5965	SO:0001583	missense	3433	exon2			AGCCTACGGCAAC	M14660	CCDS41548.1	10q23.31	2013-01-11			ENSG00000119922	ENSG00000119922		"Tetratricopeptide (TTC) repeat domain containing"	5409	protein-coding gene	gene with protein product		147040		IFI54, G10P2		3175763, 3360121	Standard	NM_001547		Approved	IFI-54, ISG-54K, cig42, GARG-39	uc009xts.3	P09913	OTTHUMG00000018707	ENST00000371826.3:c.40C>T	chr10.hg19:g.91065753C>T	ENSP00000360891:p.Arg14Trp	98.0	0.0	.		107.0	42.0	.	NM_001547	Q5T767	Missense_Mutation	SNP	ENST00000371826.3	hg19	CCDS41548.1	.	.	.	.	.	.	.	.	.	.	C	13.80	2.345071	0.41498	.	.	ENSG00000119922	ENST00000371826	T	0.50001	0.76	4.58	0.669	0.17918	.	0.949995	0.08725	N	0.902872	T	0.28797	0.0714	N	0.21448	0.665	0.09310	N	1	B	0.26445	0.149	B	0.15052	0.012	T	0.23691	-1.0181	10	0.62326	D	0.03	-0.004	3.4206	0.07392	0.1212:0.5514:0.1178:0.2096	.	14	P09913	IFIT2_HUMAN	W	14	ENSP00000360891:R14W	ENSP00000360891:R14W	R	+	1	2	IFIT2	91055733	0.000000	0.05858	0.000000	0.03702	0.945000	0.59286	-0.229000	0.09098	0.133000	0.18654	-0.126000	0.14955	CGG	.	.	.	none		0.408	IFIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049293.1	NM_001547		T	91065753	C	T	91065753	3	4	258	1	0	0	0	0	1	0	0	0	7530	527	19	1	46	1	IFIT2	10	91065753	Missense_Mutation	SNP	C	TCGA-UZ-A9PL-01A-11D-A382-10	40342055	91065753	44468994	41	16077											
BTRC	8945	hgsc.bcm.edu	37	chr10	103190124	103190124	+	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	ctctatgcccaggtctctgtGgctgggctgctccagcctgg	3	11	13	14	0	2	0	0	0	2	0	4	0	3	0	3	4	3	3	3	4	1	1			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr10:103190124G>A	ENST00000370187.3	+	2	189	c.71G>A	c.(70-72)tGg>tAg	p.W24*	BTRC_ENST00000393441.4_Nonsense_Mutation_p.W9*|BTRC_ENST00000408038.2_Intron	NM_033637.3	NP_378663.1	Q9Y297	FBW1A_HUMAN	beta-transducin repeat containing E3 ubiquitin protein ligase	24					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cellular response to organic cyclic compound (GO:0071407)|G2/M transition of mitotic cell cycle (GO:0000086)|mammary gland epithelial cell proliferation (GO:0033598)|mitotic cell cycle (GO:0000278)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein dephosphorylation (GO:0006470)|protein destabilization (GO:0031648)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(4)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	27		Colorectal(252;0.234)		Epithelial(162;1.05e-08)|all cancers(201;6.59e-07)		AGGTCTCTGTGGCTGGGCTGC	0.542																																					p.W24X		Atlas-SNP	.											.	BTRC	64	.	0			c.G71A						PASS	.						79	75	76					10																	103190124		2203	4300	6503	SO:0001587	stop_gained	8945	exon2			CTCTGTGGCTGGG	Y14153	CCDS7511.1, CCDS7512.1, CCDS73183.1	10q24.32	2013-01-10	2012-02-23		ENSG00000166167	ENSG00000166167		"F-boxes / WD-40 domains", "WD repeat domain containing"	1144	protein-coding gene	gene with protein product		603482	"beta-transducin repeat containing"			9660940, 10331953, 18354483	Standard	NM_033637		Approved	bTrCP, betaTrCP, FBXW1A, Fwd1, beta-TrCP1, bTrCP1	uc001kta.4	Q9Y297	OTTHUMG00000018932	ENST00000370187.3:c.71G>A	chr10.hg19:g.103190124G>A	ENSP00000359206:p.Trp24*	66.0	0.0	.		62.0	25.0	.	NM_001256856	B5MD49|Q5W141|Q5W142|Q9Y213	Nonsense_Mutation	SNP	ENST00000370187.3	hg19	CCDS7512.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.974959	0.92919	.	.	ENSG00000166167	ENST00000370187;ENST00000393441;ENST00000370183	.	.	.	5.72	5.72	0.89469	.	0.082898	0.52532	D	0.000065	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.1493	20.2406	0.98372	0.0:0.0:1.0:0.0	.	.	.	.	X	24;9;6	.	ENSP00000359202:W6X	W	+	2	0	BTRC	103180114	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.098000	0.76974	2.857000	0.98124	0.650000	0.86243	TGG	.	.	.	none		0.542	BTRC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049936.1	NM_033637		A	103190124	G	A	103190124	4	1	258	1	0	0	0	0	0	1	0	0	1571	1357	47	2	77	2	BTRC	10	103190124	Nonsense_Mutation	SNP	G	TCGA-UZ-A9PL-01A-11D-A382-10	12124371	103190124	32344623	42	16078											
MADD	8567	hgsc.bcm.edu	37	chr11	47305994	47305994	+	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	agattgacgagctgcagaatCagaaggaagcagaagagcct	16	5	13	7	1	1	6	1	1	0	5	1	8	1	7	1	1	4	3	1	1	4	1			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr11:47305994C>A	ENST00000311027.5	+	12	2200	c.2035C>A	c.(2035-2037)Cag>Aag	p.Q679K	MADD_ENST00000402799.1_Missense_Mutation_p.Q679K|MADD_ENST00000406482.1_Missense_Mutation_p.Q679K|MADD_ENST00000342922.4_Missense_Mutation_p.Q679K|MADD_ENST00000402192.2_Missense_Mutation_p.Q679K|MADD_ENST00000407859.3_Missense_Mutation_p.Q679K|MADD_ENST00000349238.3_Missense_Mutation_p.Q679K|MADD_ENST00000395336.3_Missense_Mutation_p.Q679K|MADD_ENST00000395344.3_Missense_Mutation_p.Q679K	NM_003682.3	NP_003673.3			MAP-kinase activating death domain											breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		GCTGCAGAATCAGAAGGAAGC	0.592																																					p.Q679K		Atlas-SNP	.											.	MADD	172	.	0			c.C2035A						PASS	.						78	83	81					11																	47305994		2201	4298	6499	SO:0001583	missense	8567	exon12			CAGAATCAGAAGG	AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"DENN/MADD domain containing"	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.2035C>A	chr11.hg19:g.47305994C>A	ENSP00000310933:p.Gln679Lys	91.0	0.0	.		96.0	54.0	.	NM_130474		Missense_Mutation	SNP	ENST00000311027.5	hg19	CCDS7930.1	.	.	.	.	.	.	.	.	.	.	C	12.62	1.993769	0.35131	.	.	ENSG00000110514	ENST00000342922;ENST00000395342;ENST00000402799;ENST00000406482;ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395344;ENST00000395336;ENST00000402192	T;T;T;T;T;T;T;T;T	0.05649	3.56;3.45;3.45;3.56;3.56;3.41;3.45;3.56;3.56	5.96	5.96	0.96718	.	0.918311	0.09568	N	0.784571	T	0.03695	0.0105	N	0.08118	0	0.80722	D	1	B;B;B;B;B;B;B;B;B;B	0.15141	0.005;0.0;0.002;0.0;0.0;0.0;0.001;0.012;0.001;0.001	B;B;B;B;B;B;B;B;B;B	0.17979	0.006;0.0;0.014;0.001;0.001;0.0;0.007;0.02;0.006;0.007	T	0.47018	-0.9149	10	0.12103	T	0.63	-4.7229	7.8312	0.29344	0.0:0.8128:0.0:0.1872	.	679;679;679;679;679;679;679;679;679;679	B5MEE5;A8K8S7;Q8WXG6-7;F8W9P9;Q8WXG6-6;Q8WXG6-5;Q8WXG6-2;Q8WXG6-4;Q8WXG6;Q8WXG6-3	.;.;.;.;.;.;.;.;MADD_HUMAN;.	K	679	ENSP00000343902:Q679K;ENSP00000385585:Q679K;ENSP00000384435:Q679K;ENSP00000304505:Q679K;ENSP00000310933:Q679K;ENSP00000384204:Q679K;ENSP00000378753:Q679K;ENSP00000378745:Q679K;ENSP00000384287:Q679K	ENSP00000310933:Q679K	Q	+	1	0	MADD	47262570	1.000000	0.71417	0.966000	0.40874	0.968000	0.65278	4.541000	0.60670	2.832000	0.97577	0.655000	0.94253	CAG	.	.	.	none		0.592	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1			A	47305994	C	A	47305994	3	1	258	1	0	0	0	0	1	0	0	0	9159	827	29	4	2077	4	MADD	11	47305994	Missense_Mutation	SNP	C	TCGA-UZ-A9PL-01A-11D-A382-10		47305994	87700522	43	16079											
CCDC83	220047	hgsc.bcm.edu	37	chr11	85630396	85630397	+	Frame_Shift_Ins	INS	-	-	TG																															gcctgttcaccataggattaINStgtaaacttgggccccctgg																										TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr11:85630396_85630397insTG	ENST00000342404.3	+	11	1301_1302	c.1085_1086insTG	c.(1084-1089)tatgtafs	p.YV362fs	CCDC83_ENST00000376067.1_Frame_Shift_Ins_p.YV262fs|CCDC83_ENST00000280245.4_Frame_Shift_Ins_p.YV393fs|RP11-90K17.2_ENST00000531414.1_RNA			Q8IWF9	CCD83_HUMAN	coiled-coil domain containing 83	362										breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|skin(3)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				CCATAGGATTATGTAAACTTGG	0.396																																					p.Y393fs		Pindel	.											.	CCDC83	48	.	0			c.1178_1179insTG						PASS	.																																			SO:0001589	frameshift_variant	220047	exon12			.	AK124113	CCDS8271.1, CCDS66196.1	11q14.1-q14.2	2014-01-21			ENSG00000150676	ENSG00000150676			28535	protein-coding gene	gene with protein product						12477932	Standard	XM_005273842		Approved	MGC34732, FLJ42119, CT148	uc001pbg.1	Q8IWF9	OTTHUMG00000166978	ENST00000342404.3:c.1086_1087dupTG	chr11.hg19:g.85630397_85630398dupTG	ENSP00000344512:p.Tyr362fs	194.0	0.0	.		187.0	53.0	0.283	NM_173556	B2RA49|Q6X7T2|Q6ZVT5|Q8N9Y1	Frame_Shift_Ins	INS	ENST00000342404.3	hg19																																																																																				.	.	.	none		0.396	CCDC83-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392215.1	NM_173556		TG	85630397	-	TG	85630396	7	5	258	1	0	1	1	0	0	0	0	0	2859	449	16	0	1220	0	CCDC83	11	85630396	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PL-01A-11D-A382-10	38324402	85630396	49376120	44	16080											
CACNA2D4	93589	hgsc.bcm.edu	37	chr12	2027591	2027592	+	Frame_Shift_Ins	INS	-	-	G																															ttgggagttgcaggcatggtINSgggcctggggttggggaggg																										TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr12:2027591_2027592insG	ENST00000382722.5	-	1	410_411	c.48_49insC	c.(46-51)cccaccfs	p.T17fs	CACNA2D4_ENST00000586184.1_Frame_Shift_Ins_p.T17fs|CACNA2D4_ENST00000585732.1_Frame_Shift_Ins_p.T17fs|RP5-1096D14.3_ENST00000544163.1_RNA|CACNA2D4_ENST00000587995.1_Frame_Shift_Ins_p.T17fs	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	17					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)		GCAGGCATGGTGGGCCTGGGGT	0.644																																					p.T17fs	Colon(2;101 179 21030 23310 28141)	Atlas-INDEL	.											.	CACNA2D4	220	.	0			c.49_50insC						PASS	.																																			SO:0001589	frameshift_variant	93589	exon1			.	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.49dupC	chr12.hg19:g.2027594_2027594dupG	ENSP00000372169:p.Thr17fs	82.0	0.0	0		136.0	10.0	0.0735294	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Frame_Shift_Ins	INS	ENST00000382722.5	hg19	CCDS44785.1																																																																																			.	.	.	none		0.644	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2			G	2027592	-	G	2027591	7	5	258	1	0	1	1	0	0	0	0	0	2553	1696	59	0	3516	0	CACNA2D4	12	2027591	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PL-01A-11D-A382-10		2027591	131824304	45	16081											
SLCO1C1	53919	hgsc.bcm.edu	37	chr12	20854365	20854365	+	Frame_Shift_Del	DEL	G	G	-																															gatatcccttcttcactggtGggagttattgatggtagttt																										TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr12:20854365delG	ENST00000266509.2	+	3	611	c.243delG	c.(241-243)gtgfs	p.V81fs	SLCO1C1_ENST00000545102.1_Intron|SLCO1C1_ENST00000540354.1_Frame_Shift_Del_p.V81fs|SLCO1C1_ENST00000381552.1_Frame_Shift_Del_p.V81fs|SLCO1C1_ENST00000545604.1_Frame_Shift_Del_p.V81fs	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	81					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)	CTTCACTGGTGGGAGTTATTG	0.408																																					p.V81fs		Atlas-Indel,Pindel	.											.	SLCO1C1	216	.	0			c.242delT						PASS	.						160	139	146					12																	20854365		2203	4299	6502	SO:0001589	frameshift_variant	53919	exon3			.	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.243delG	chr12.hg19:g.20854365delG	ENSP00000266509:p.Val81fs	114.0	0.0	0		132.0	73.0	0.55303	NM_017435	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Frame_Shift_Del	DEL	ENST00000266509.2	hg19	CCDS8683.1																																																																																			.	.	.	none		0.408	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435		-	20854365	G	-	20854365	7	5	258	1	0	1	0	1	0	0	0	0	14738	1335	47	0	249	0	SLCO1C1	12	20854365	Frame_Shift_Del	DEL	G	TCGA-UZ-A9PL-01A-11D-A382-10	18826774	20854365	112997530	46	16082											
MAP3K12	7786	hgsc.bcm.edu	37	chr12	53877202	53877202	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttctccattgtgtttccaTgcaggaggccccgggaaggg	6	10	14	11	1	1	0	0	0	1	0	3	2	2	2	4	4	1	3	4	4	1	3			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr12:53877202T>C	ENST00000267079.2	-	11	1670	c.1445A>G	c.(1444-1446)cAt>cGt	p.H482R	MAP3K12_ENST00000547035.1_Missense_Mutation_p.H515R|MAP3K12_ENST00000547488.1_Missense_Mutation_p.H515R	NM_001193511.1|NM_006301.3	NP_001180440.1|NP_006292.3	Q12852	M3K12_HUMAN	mitogen-activated protein kinase kinase kinase 12	482					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						TGTGTTTCCATGCAGGAGGCC	0.542																																					p.H515R		Atlas-SNP	.											.	MAP3K12	160	.	0			c.A1544G						PASS	.						130	128	129					12																	53877202		2203	4300	6503	SO:0001583	missense	7786	exon10			TTTCCATGCAGGA	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.1445A>G	chr12.hg19:g.53877202T>C	ENSP00000267079:p.His482Arg	92.0	0.0	.		150.0	44.0	.	NM_001193511	B3KSS9|G3V1Y2|Q86VQ5|Q8WY25	Missense_Mutation	SNP	ENST00000267079.2	hg19	CCDS8860.1	.	.	.	.	.	.	.	.	.	.	T	14.81	2.646194	0.47258	.	.	ENSG00000139625	ENST00000267079;ENST00000547488;ENST00000547035	T;T;T	0.16897	2.31;2.31;2.31	5.42	5.42	0.78866	.	0.000000	0.47093	D	0.000250	T	0.10252	0.0251	N	0.12746	0.255	0.44946	D	0.997963	B;B	0.19331	0.035;0.02	B;B	0.20577	0.03;0.021	T	0.24154	-1.0168	10	0.18710	T	0.47	.	13.2975	0.60305	0.0:0.0:0.0:1.0	.	515;482	G3V1Y2;Q12852	.;M3K12_HUMAN	R	482;515;515	ENSP00000267079:H482R;ENSP00000449038:H515R;ENSP00000448689:H515R	ENSP00000267079:H482R	H	-	2	0	MAP3K12	52163469	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.040000	0.64191	2.196000	0.70406	0.533000	0.62120	CAT	.	.	.	none		0.542	MAP3K12-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406267.1	NM_006301		C	53877202	T	C	53877202	3	2	258	1	0	0	0	0	1	0	0	0	9253	1464	51	3	1154	3	MAP3K12	12	53877202	Missense_Mutation	SNP	T	TCGA-UZ-A9PL-01A-11D-A382-10	33022837	53877202	79974693	47	16083											
LRIG3	121227	hgsc.bcm.edu	37	chr12	59282143	59282149	+	Frame_Shift_Del	DEL	ATCAGGG	ATCAGGG	-																															ttctggcagaactcccaggcAtcagggctgatcctgttgat																								rs369199158		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	ATCAGGG	ATCAGGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr12:59282143_59282149delATCAGGG	ENST00000320743.3	-	7	1195_1201	c.909_915delCCCTGAT	c.(907-915)agccctgatfs	p.SPD303fs	LRIG3_ENST00000379141.4_Frame_Shift_Del_p.SPD243fs	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	303					otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)			LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			ACTCCCAGGCATCAGGGCTGATCCTGT	0.488			T	ROS1	NSCLC																																p.304_306del		Atlas-Indel,Pindel	.		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	.	LRIG3	120	.	0			c.910_916del						PASS	.																																			SO:0001589	frameshift_variant	121227	exon7			.	AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"Immunoglobulin superfamily / I-set domain containing"	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.909_915delCCCTGAT	chr12.hg19:g.59282143_59282149delATCAGGG	ENSP00000326759:p.Ser303fs	65.0	0.0	0		90.0	22.0	0.244444	NM_153377	Q6UXL7|Q8NC72	Frame_Shift_Del	DEL	ENST00000320743.3	hg19	CCDS8960.1																																																																																			.	.	.	none		0.488	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377		-	59282149	ATCAGGG	-	59282143	7	5	258	1	0	1	0	1	0	0	0	0	8953	214	8	0	2496	0	LRIG3	12	59282143	Frame_Shift_Del	DEL	ATCAGGG	TCGA-UZ-A9PL-01A-11D-A382-10	5404941	59282143	74569752	48	16084											
C12orf64	283310	hgsc.bcm.edu	37	chr12	80648329	80648329	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgttggtggagtttggaacTgcactgagcaagactgtcca	9	11	14	7	0	0	2	0	1	0	1	1	4	1	4	1	3	3	4	1	3	2	2			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr12:80648329T>C	ENST00000547103.1	+	14	1399	c.1393T>C	c.(1393-1395)Tgc>Cgc	p.C465R	OTOGL_ENST00000458043.2_Missense_Mutation_p.C465R			Q3ZCN5	OTOGL_HUMAN	otogelin-like	465					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						AGTTTGGAACTGCACTGAGCA	0.303																																					p.C465R		Atlas-SNP	.											.	OTOGL	235	.	0			c.T1393C						PASS	.						114	106	109					12																	80648329		1793	4064	5857	SO:0001583	missense	283310	exon14			TGGAACTGCACTG	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.1393T>C	chr12.hg19:g.80648329T>C	ENSP00000447211:p.Cys465Arg	65.0	0.0	.		88.0	47.0	.	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	hg19		.	.	.	.	.	.	.	.	.	.	T	21.9	4.211483	0.79240	.	.	ENSG00000165899	ENST00000547103;ENST00000458043	T;T	0.67345	-0.26;-0.26	5.68	5.68	0.88126	.	.	.	.	.	D	0.88028	0.6327	H	0.97131	3.945	0.80722	D	1	.	.	.	.	.	.	D	0.92025	0.5629	7	0.87932	D	0	.	15.9323	0.79672	0.0:0.0:0.0:1.0	.	.	.	.	R	465	ENSP00000447211:C465R;ENSP00000400895:C465R	ENSP00000400895:C465R	C	+	1	0	OTOGL	79172460	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.552000	0.82192	2.175000	0.68902	0.533000	0.62120	TGC	.	.	.	none		0.303	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591		C	80648329	T	C	80648329	3	2	258	1	0	0	0	0	1	0	0	0	1709	1580	55	3	1447	3	C12orf64	12	80648329	Missense_Mutation	SNP	T	TCGA-UZ-A9PL-01A-11D-A382-10	21366186	80648329	53203566	49	16085											
KIAA1704	55425	hgsc.bcm.edu	37	chr13	45594477	45594477	+	Frame_Shift_Del	DEL	G	G	-																															ttcctcaggaaacacaagaaGcaaggaagtcatccagtaag																										TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr13:45594477delG	ENST00000379151.4	+	7	821	c.718delG	c.(718-720)gcafs	p.A240fs	RP11-321C24.1_ENST00000437748.2_lincRNA|GPALPP1_ENST00000357537.3_Frame_Shift_Del_p.A70fs|GPALPP1_ENST00000361121.2_Frame_Shift_Del_p.A240fs	NM_018559.2	NP_061029.2	Q8IXQ4	GPAM1_HUMAN	GPALPP motifs containing 1	240																	AACACAAGAAGCAAGGAAGTC	0.294																																					p.E239fs		Atlas-Indel,Pindel	.											.	KIAA1704	36	.	0			c.717delA						PASS	.						92	93	92					13																	45594477		2203	4300	6503	SO:0001589	frameshift_variant	55425	exon7			.	AB051491	CCDS9394.1	13q14.12	2013-08-13	2013-08-12	2013-08-12	ENSG00000133114	ENSG00000133114			20298	protein-coding gene	gene with protein product			"KIAA1704"	KIAA1704		11214970	Standard	NM_018559		Approved	bA245H20.2, AD029, LSR7	uc001uzq.3	Q8IXQ4	OTTHUMG00000016841	ENST00000379151.4:c.718delG	chr13.hg19:g.45594477delG	ENSP00000368447:p.Ala240fs	325.0	0.0	0		377.0	156.0	0.413793	NM_018559	A8K8X8|Q05BX8|Q05D87|Q5T3Z3|Q5T3Z5|Q9C0F9|Q9H2R0|Q9P0W6	Frame_Shift_Del	DEL	ENST00000379151.4	hg19	CCDS9394.1																																																																																			.	.	.	none		0.294	GPALPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044749.2	NM_018559		-	45594477	G	-	45594477	7	5	258	1	0	1	0	1	0	0	0	0	8259	971	34	0	744	0	KIAA1704	13	45594477	Frame_Shift_Del	DEL	G	TCGA-UZ-A9PL-01A-11D-A382-10		45594477	69575401	50	16086											
DZIP1	22873	hgsc.bcm.edu	37	chr13	96242581	96242581	+	Frame_Shift_Del	DEL	C	C	-																															tttacagctgacttgatgttCaaggaattctcgaatttgat																										TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr13:96242581delC	ENST00000376829.2	-	17	2646	c.1795delG	c.(1795-1797)gaafs	p.E599fs	DZIP1_ENST00000361156.3_Frame_Shift_Del_p.E580fs|DZIP1_ENST00000347108.3_Frame_Shift_Del_p.E599fs|DZIP1_ENST00000361396.2_Frame_Shift_Del_p.E580fs	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	599					cilium assembly (GO:0042384)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(20)|lung(11)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	38	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			ACTTGATGTTCAAGGAATTCT	0.353																																					p.E599fs		Atlas-Indel,Pindel	.											.	DZIP1	195	.	0			c.1796delA						PASS	.						196	176	183					13																	96242581		2203	4300	6503	SO:0001589	frameshift_variant	22873	exon17			.	AB023213	CCDS9477.1, CCDS9478.1	13q32.1	2013-05-22	2013-05-22		ENSG00000134874	ENSG00000134874		"Zinc fingers, C2H2-type"	20908	protein-coding gene	gene with protein product		608671	"DAZ interacting protein 1"				Standard	NM_014934		Approved	KIAA0996, DZIP	uc001vmk.4	Q86YF9	OTTHUMG00000017224	ENST00000376829.2:c.1795delG	chr13.hg19:g.96242581delC	ENSP00000366025:p.Glu599fs	106.0	0.0	0		80.0	40.0	0.5	NM_198968	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Frame_Shift_Del	DEL	ENST00000376829.2	hg19	CCDS9478.1																																																																																			.	.	.	none		0.353	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934		-	96242581	C	-	96242581	7	5	258	1	0	1	0	1	0	0	0	0	4865	835	29	0	836	0	DZIP1	13	96242581	Frame_Shift_Del	DEL	C	TCGA-UZ-A9PL-01A-11D-A382-10	50648104	96242581	18927297	51	16087											
SYNE2	23224	hgsc.bcm.edu	37	chr14	64634024	64634024	+	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	agtgagcctcaagctcccacTtagtgacgtagctgtgaaga	11	9	11	10	1	1	4	1	3	0	1	2	4	2	4	2	0	3	3	2	0	4	2			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr14:64634024T>A	ENST00000344113.4	+	91	16891	c.16679T>A	c.(16678-16680)cTt>cAt	p.L5560H	SYNE2_ENST00000357395.3_Missense_Mutation_p.L1945H|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000358025.3_Missense_Mutation_p.L5560H|SYNE2_ENST00000554584.1_Missense_Mutation_p.L5435H|SYNE2_ENST00000394768.2_Missense_Mutation_p.L1945H|SYNE2_ENST00000555002.1_Missense_Mutation_p.L2194H	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5560					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)		AAGCTCCCACTTAGTGACGTA	0.463																																					p.L5560H		Atlas-SNP	.											.	SYNE2	577	.	0			c.T16679A						PASS	.						63	60	61					14																	64634024		2203	4300	6503	SO:0001583	missense	23224	exon91			TCCCACTTAGTGA	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.16679T>A	chr14.hg19:g.64634024T>A	ENSP00000341781:p.Leu5560His	160.0	0.0	.		168.0	74.0	.	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	T	15.96	2.986805	0.53934	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	T;T;T;T;T;T	0.70282	0.28;3.56;0.27;-0.47;3.59;3.56	5.78	5.78	0.91487	.	0.000000	0.49916	D	0.000137	T	0.80670	0.4667	L	0.51914	1.62	0.80722	D	1	P;D;B;P	0.89917	0.698;1.0;0.405;0.671	P;D;B;B	0.91635	0.599;0.999;0.172;0.264	T	0.79852	-0.1628	10	0.42905	T	0.14	.	16.3971	0.83610	0.0:0.0:0.0:1.0	.	1945;5435;5560;5560	Q8WXH0-7;G3V5X4;Q8WXH0;Q8WXH0-2	.;.;SYNE2_HUMAN;.	H	5560;1945;5560;5435;5441;2194;1945	ENSP00000350719:L5560H;ENSP00000349969:L1945H;ENSP00000341781:L5560H;ENSP00000452570:L5435H;ENSP00000450831:L2194H;ENSP00000378249:L1945H	ENSP00000261678:L5441H	L	+	2	0	SYNE2	63703777	0.958000	0.32768	0.953000	0.39169	0.505000	0.33919	4.070000	0.57548	2.330000	0.79161	0.533000	0.62120	CTT	.	.	.	none		0.463	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		A	64634024	T	A	64634024	3	1	258	1	0	0	0	0	1	0	0	0	15458	1609	56	5	17037	5	SYNE2	14	64634024	Missense_Mutation	SNP	T	TCGA-UZ-A9PL-01A-11D-A382-10		64634024	42715516	52	16088											
SPTLC2	9517	hgsc.bcm.edu	37	chr14	78028818	78028818	+	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	gcatgattcagttcatcactCagaatcaggcaaccctgcaa	13	9	7	12	0	5	2	5	1	0	1	5	2	5	2	1	1	2	4	1	1	3	2			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr14:78028818C>G	ENST00000216484.2	-	6	964	c.771G>C	c.(769-771)ctG>ctC	p.L257L		NM_004863.3	NP_004854.1	O15270	SPTC2_HUMAN	serine palmitoyltransferase, long chain base subunit 2	257					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphinganine biosynthetic process (GO:0046511)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|serine C-palmitoyltransferase complex (GO:0017059)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(5)	19			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0346)	L-Serine(DB00133)	GTTCATCACTCAGAATCAGGC	0.433																																					p.L257L		Atlas-SNP	.											.	SPTLC2	55	.	0			c.G771C						PASS	.						100	84	89					14																	78028818		2203	4300	6503	SO:0001819	synonymous_variant	9517	exon6			ATCACTCAGAATC	AB011098	CCDS9865.1	14q24.3	2014-09-17			ENSG00000100596	ENSG00000100596	2.3.1.50		11278	protein-coding gene	gene with protein product		605713				8921873, 9363775	Standard	NM_004863		Approved	KIAA0526, LCB2, LCB2A, hLCB2a	uc001xub.3	O15270		ENST00000216484.2:c.771G>C	chr14.hg19:g.78028818C>G		79.0	0.0	.		80.0	41.0	.	NM_004863	Q16685	Silent	SNP	ENST00000216484.2	hg19	CCDS9865.1	.	.	.	.	.	.	.	.	.	.	C	5.462	0.270283	0.10349	.	.	ENSG00000100596	ENST00000554901	.	.	.	5.73	2.89	0.33648	.	.	.	.	.	T	0.57095	0.2030	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49437	-0.8940	4	.	.	.	-12.241	7.7474	0.28877	0.0:0.6152:0.2506:0.1341	.	.	.	.	Q	194	.	.	E	-	1	0	SPTLC2	77098571	0.997000	0.39634	1.000000	0.80357	0.702000	0.40608	0.578000	0.23773	0.430000	0.26230	-0.259000	0.10710	GAG	.	.	.	none		0.433	SPTLC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414030.1	NM_004863		G	78028818	C	G	78028818	2	3	258	1	0	0	0	0	0	0	0	1	15136	813	29	4		4	SPTLC2	14	78028818	Silent	SNP	C	TCGA-UZ-A9PL-01A-11D-A382-10	13394794	78028818	29320722	53	16089											
FLRT2	23768	hgsc.bcm.edu	37	chr14	86089469	86089469	+	Frame_Shift_Del	DEL	G	G	-																															cagacgacgtcccacagcatGggctccccctttctgctggc																										TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr14:86089469delG	ENST00000330753.4	+	2	2378	c.1611delG	c.(1609-1611)atgfs	p.M537fs	FLRT2_ENST00000554746.1_Frame_Shift_Del_p.M537fs	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	537					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)		CCCACAGCATGGGCTCCCCCT	0.572																																					p.M537fs		Atlas-Indel,Pindel	.											.	FLRT2	168	.	0			c.1610delT						PASS	.						94	96	96					14																	86089469		2203	4300	6503	SO:0001589	frameshift_variant	23768	exon2			.	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.1611delG	chr14.hg19:g.86089469delG	ENSP00000332879:p.Met537fs	98.0	0.0	0		106.0	41.0	0.386792	NM_013231	A0AV84|B7ZLP3	Frame_Shift_Del	DEL	ENST00000330753.4	hg19	CCDS9877.1																																																																																			.	.	.	none		0.572	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			-	86089469	G	-	86089469	7	5	258	1	0	1	0	1	0	0	0	0	5946	1348	47	0	1613	0	FLRT2	14	86089469	Frame_Shift_Del	DEL	G	TCGA-UZ-A9PL-01A-11D-A382-10	8060651	86089469	21260071	54	16090											
FMN1	342184	hgsc.bcm.edu	37	chr15	33261121	33261122	+	Frame_Shift_Ins	INS	-	-	G																															gggagttaggaagtgggggtINSgggggtgggggtggtggagg																										TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr15:33261121_33261122insG	ENST00000559047.1	-	5	2779_2780	c.2780_2781insC	c.(2779-2781)ccafs	p.P927fs	FMN1_ENST00000561249.1_Frame_Shift_Ins_p.P829fs|FMN1_ENST00000334528.9_Frame_Shift_Ins_p.P704fs|SNORD77_ENST00000391113.1_RNA			Q68DA7	FMN1_HUMAN	formin 1	927	FH1.|Pro-rich.				actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		GAAgtgggggtgggggtggggg	0.673																																					p.P704fs		Atlas-INDEL	.											FMN1_ENST00000334528,NS,carcinoma,0,2	FMN1	174	.	0			c.2112_2113insC						PASS	.																																			SO:0001589	frameshift_variant	342184	exon4			.	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.2781dupC	chr15.hg19:g.33261126_33261126dupG	ENSP00000454047:p.Pro927fs	19.0	0.0	0		30.0	10.0	0.333333	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Frame_Shift_Ins	INS	ENST00000559047.1	hg19																																																																																				.	.	.	none		0.673	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184		G	33261122	-	G	33261121	7	5	258	1	0	1	1	0	0	0	0	0	5956	1683	59	0	1534	0	FMN1	15	33261121	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PL-01A-11D-A382-10		33261121	69270271	55	16091											
MAPKBP1	23005	hgsc.bcm.edu	37	chr15	42107832	42107839	+	Frame_Shift_Del	DEL	AAATCATC	AAATCATC	-																															gttccactaggacctcattaAaatcatctatgtggatggga																										TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	AAATCATC	AAATCATC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr15:42107832_42107839delAAATCATC	ENST00000456763.2	+	13	1542_1549	c.1346_1353delAAATCATC	c.(1345-1353)aaaatcatcfs	p.KII449fs	MAPKBP1_ENST00000260357.7_Frame_Shift_Del_p.KII282fs|MAPKBP1_ENST00000514566.1_Frame_Shift_Del_p.KII443fs|MAPKBP1_ENST00000221214.6_Frame_Shift_Del_p.KII326fs|MAPKBP1_ENST00000457542.2_Frame_Shift_Del_p.KII443fs	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	449										breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		GACCTCATTAAAATCATCTATGTGGATG	0.548																																					p.449_451del		Atlas-Indel,Pindel	.											.	MAPKBP1	120	.	0			c.1345_1352del						PASS	.																																			SO:0001589	frameshift_variant	23005	exon13			.	AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"WD repeat domain containing"	29536	protein-coding gene	gene with protein product			"mitogen activated protein kinase binding protein 1"			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.1346_1353delAAATCATC	chr15.hg19:g.42107832_42107839delAAATCATC	ENSP00000393099:p.Lys449fs	67.0	0.0	0		60.0	26.0	0.433333	NM_001128608	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Frame_Shift_Del	DEL	ENST00000456763.2	hg19	CCDS45239.1																																																																																			.	.	.	none		0.548	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359745.1	NM_014994		-	42107839	AAATCATC	-	42107832	7	5	258	1	0	1	0	1	0	0	0	0	9299	14	1	0	1392	0	MAPKBP1	15	42107832	Frame_Shift_Del	DEL	AAATCATC	TCGA-UZ-A9PL-01A-11D-A382-10	8846711	42107832	60423560	56	16092											
SPG11	80208	hgsc.bcm.edu	37	chr15	44955757	44955757	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcggcggggactggcaccAacagcatcggtagaacccgc	9	4	13	15	4	0	1	0	0	0	1	2	2	0	2	3	5	3	3	3	5	3	1			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr15:44955757A>G	ENST00000261866.7	-	1	105	c.89T>C	c.(88-90)tTg>tCg	p.L30S	SPG11_ENST00000427534.2_Missense_Mutation_p.L30S|SPG11_ENST00000558319.1_Missense_Mutation_p.L30S|SPG11_ENST00000559193.1_Missense_Mutation_p.L30S|SPG11_ENST00000535302.2_Missense_Mutation_p.L30S	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	30					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)		GACTGGCACCAACAGCATCGG	0.736																																					p.L30S		Atlas-SNP	.											.	SPG11	207	.	0			c.T89C						PASS	.						6	8	7					15																	44955757		2085	4129	6214	SO:0001583	missense	80208	exon1			GGCACCAACAGCA		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.89T>C	chr15.hg19:g.44955757A>G	ENSP00000261866:p.Leu30Ser	60.0	0.0	.		56.0	29.0	.	NM_025137	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Missense_Mutation	SNP	ENST00000261866.7	hg19	CCDS10112.1	.	.	.	.	.	.	.	.	.	.	A	17.62	3.434670	0.62955	.	.	ENSG00000104133	ENST00000261866;ENST00000535302;ENST00000427534	D;T;T	0.83419	-1.72;-1.49;-1.48	5.53	5.53	0.82687	.	0.473484	0.17960	N	0.156202	D	0.89234	0.6657	M	0.64997	1.995	0.39216	D	0.963406	D;D;D;D	0.89917	1.0;0.986;0.986;1.0	D;P;P;D	0.91635	0.989;0.791;0.791;0.999	D	0.90279	0.4313	10	0.87932	D	0	.	12.0478	0.53489	1.0:0.0:0.0:0.0	.	30;30;30;30	C4B7M2;F5H3N6;B9EK60;Q96JI7	.;.;.;SPTCS_HUMAN	S	30	ENSP00000261866:L30S;ENSP00000445278:L30S;ENSP00000396110:L30S	ENSP00000261866:L30S	L	-	2	0	SPG11	42743049	1.000000	0.71417	0.993000	0.49108	0.068000	0.16541	4.217000	0.58547	2.103000	0.63969	0.533000	0.62120	TTG	.	.	.	none		0.736	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1			G	44955757	A	G	44955757	3	3	258	1	0	0	0	0	1	0	0	0	15053	131	5	3	7402	3	SPG11	15	44955757	Missense_Mutation	SNP	A	TCGA-UZ-A9PL-01A-11D-A382-10	2847925	44955757	57575635	57	16093											
ST8SIA2	8128	hgsc.bcm.edu	37	chr15	92987941	92987941	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctggtaaccatgaacccctcGgtcatccagcgggcctttga	8	9	10	14	2	1	2	1	2	0	0	3	2	2	2	5	3	3	1	5	3	2	2	rs533826176	byFrequency	TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr15:92987941G>A	ENST00000268164.3	+	5	861	c.624G>A	c.(622-624)tcG>tcA	p.S208S	ST8SIA2_ENST00000539113.1_Silent_p.S187S	NM_006011.3	NP_006002.1	Q92186	SIA8B_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	208					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|ganglioside biosynthetic process (GO:0001574)|N-glycan processing (GO:0006491)|nervous system development (GO:0007399)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	early endosome (GO:0005769)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|recycling endosome (GO:0055037)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			endometrium(2)|large_intestine(6)|lung(9)|skin(2)|urinary_tract(1)	20	Lung NSC(78;0.0893)|all_lung(78;0.125)		BRCA - Breast invasive adenocarcinoma(143;0.0355)|OV - Ovarian serous cystadenocarcinoma(32;0.203)			TGAACCCCTCGGTCATCCAGC	0.592													G|||	4	0.000798722	0	0	5008	,	,		18491	0		0	False		,,,				2504	0.0041				p.S208S		Atlas-SNP	.											.	ST8SIA2	41	.	0			c.G624A						PASS	.						67	67	67					15																	92987941		2198	4298	6496	SO:0001819	synonymous_variant	8128	exon5			CCCCTCGGTCATC	U33551	CCDS10372.1	15q26	2013-03-01	2003-01-14	2005-02-07	ENSG00000140557	ENSG00000140557		"Sialyltransferases"	10870	protein-coding gene	gene with protein product		602546	"sialyltransferase 8 (alpha-2, 8-sialytransferase) B"	SIAT8B		7559389	Standard	NM_006011		Approved	STX, ST8SIA-II, HsT19690	uc002bra.3	Q92186	OTTHUMG00000149843	ENST00000268164.3:c.624G>A	chr15.hg19:g.92987941G>A		115.0	0.0	.		129.0	62.0	.	NM_006011	Q4VAZ0|Q92470|Q92746	Silent	SNP	ENST00000268164.3	hg19	CCDS10372.1																																																																																			.	.	.	none		0.592	ST8SIA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313526.1	NM_006011		A	92987941	G	A	92987941	2	1	258	1	0	0	0	0	0	0	0	1	15244	1103	39	1		1	ST8SIA2	15	92987941	Silent	SNP	G	TCGA-UZ-A9PL-01A-11D-A382-10	48032184	92987941	9543451	58	16094											
ACSM2A	123876	hgsc.bcm.edu	37	chr16	20476871	20476871	+	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	ctcccaagcccagccctgtgGtgggtgaatgggaaggggaa	9	6	16	10	0	0	1	0	1	0	0	1	3	1	3	3	5	2	0	3	5	4	0	rs199594429		TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr16:20476871G>T	ENST00000573854.1	+	3	324	c.210G>T	c.(208-210)tgG>tgT	p.W70C	ACSM2A_ENST00000575558.1_3'UTR|ACSM2A_ENST00000396104.2_Missense_Mutation_p.W70C|ACSM2A_ENST00000575690.1_Missense_Mutation_p.W70C|ACSM2A_ENST00000417235.2_5'UTR|ACSM2A_ENST00000536134.1_5'UTR|ACSM2A_ENST00000219054.6_Missense_Mutation_p.W70C|ACSM2A_ENST00000424070.1_Missense_Mutation_p.W70C	NM_001010845.2	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member 2A	70					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						CAGCCCTGTGGTGGGTGAATG	0.547																																					p.W70C		Atlas-SNP	.											.	ACSM2A	120	.	0			c.G210T						PASS	.						36	37	36					16																	20476871		2203	4298	6501	SO:0001583	missense	123876	exon4			CCTGTGGTGGGTG	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.210G>T	chr16.hg19:g.20476871G>T	ENSP00000459451:p.Trp70Cys	242.0	0.0	.		241.0	98.0	.	NM_001010845	B3KTT9|O75202	Missense_Mutation	SNP	ENST00000573854.1	hg19	CCDS32401.1	.	.	.	.	.	.	.	.	.	.	G	13.09	2.134248	0.37630	.	.	ENSG00000183747	ENST00000219054;ENST00000424070;ENST00000396104	T;T;T	0.40225	1.04;1.04;1.04	3.76	3.76	0.43208	.	0.000000	0.41605	D	0.000844	T	0.59390	0.2190	L	0.60067	1.865	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.63120	-0.6708	10	0.54805	T	0.06	-9.9549	14.7458	0.69490	0.0:0.0:1.0:0.0	.	70	Q08AH3	ACS2A_HUMAN	C	70	ENSP00000219054:W70C;ENSP00000394904:W70C;ENSP00000379411:W70C	ENSP00000219054:W70C	W	+	3	0	ACSM2A	20384372	1.000000	0.71417	1.000000	0.80357	0.103000	0.19146	7.394000	0.79862	1.809000	0.52856	0.298000	0.19748	TGG	.	G|1.000;A|0.000	.	alt		0.547	ACSM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436764.1	NM_001010845		T	20476871	G	T	20476871	3	4	258	1	0	0	0	0	1	0	0	0	183	1270	44	4	216	4	ACSM2A	16	20476871	Missense_Mutation	SNP	G	TCGA-UZ-A9PL-01A-11D-A382-10		20476871	69877882	59	16095											
SMPD3	55512	hgsc.bcm.edu	37	chr16	68405808	68405808	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccgtgaatagatgtagggccGgcgggccgactgcagtgggg	7	6	19	9	4	0	2	0	1	0	1	0	3	0	2	3	5	1	2	3	5	3	2			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr16:68405808G>A	ENST00000219334.5	-	3	880	c.277C>T	c.(277-279)Cgg>Tgg	p.R93W	SMPD3_ENST00000566009.1_5'Flank|SMPD3_ENST00000563226.1_Missense_Mutation_p.R93W|SMPD3_ENST00000568373.1_Missense_Mutation_p.R93W	NM_018667.3	NP_061137.1	Q9NY59	NSMA2_HUMAN	sphingomyelin phosphodiesterase 3, neutral membrane (neutral sphingomyelinase II)	93					cell cycle (GO:0007049)|glycosphingolipid metabolic process (GO:0006687)|hematopoietic progenitor cell differentiation (GO:0002244)|peptide hormone secretion (GO:0030072)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	Golgi cis cisterna (GO:0000137)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0184)|Epithelial(162;0.0785)	Phosphatidylserine(DB00144)	ATGTAGGGCCGGCGGGCCGAC	0.637																																					p.R93W		Atlas-SNP	.											.	SMPD3	52	.	0			c.C277T						PASS	.						12	15	14					16																	68405808		2173	4269	6442	SO:0001583	missense	55512	exon3			AGGGCCGGCGGGC	AJ250460	CCDS10867.1	16q22.1	2008-02-05			ENSG00000103056	ENSG00000103056			14240	protein-coding gene	gene with protein product		605777				10823942	Standard	NM_018667		Approved	NSMASE2	uc002ewa.3	Q9NY59	OTTHUMG00000137559	ENST00000219334.5:c.277C>T	chr16.hg19:g.68405808G>A	ENSP00000219334:p.Arg93Trp	171.0	0.0	.		129.0	54.0	.	NM_018667	B7ZL82|Q2M1S8	Missense_Mutation	SNP	ENST00000219334.5	hg19	CCDS10867.1	.	.	.	.	.	.	.	.	.	.	G	18.75	3.690967	0.68271	.	.	ENSG00000103056	ENST00000219334	T	0.58797	0.31	5.3	-0.865	0.10662	.	0.152827	0.56097	D	0.000027	T	0.47395	0.1443	L	0.57536	1.79	0.37982	D	0.933636	B;B;B	0.22541	0.071;0.071;0.071	B;B;B	0.14578	0.011;0.011;0.011	T	0.46162	-0.9211	10	0.87932	D	0	-24.3484	8.4591	0.32917	0.0792:0.0:0.2842:0.6365	.	93;93;93	B7ZL82;B7ZL84;Q9NY59	.;.;NSMA2_HUMAN	W	93	ENSP00000219334:R93W	ENSP00000219334:R93W	R	-	1	2	SMPD3	66963309	0.998000	0.40836	0.987000	0.45799	0.938000	0.57974	0.321000	0.19558	0.011000	0.14865	0.655000	0.94253	CGG	.	.	.	none		0.637	SMPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268895.3	NM_018667		A	68405808	G	A	68405808	3	1	258	1	0	0	0	0	1	0	0	0	14819	1115	39	1	1718	1	SMPD3	16	68405808	Missense_Mutation	SNP	G	TCGA-UZ-A9PL-01A-11D-A382-10	47928937	68405808	21948945	60	16096											
GLG1	2734	hgsc.bcm.edu	37	chr16	74505131	74505131	+	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	atgtccttctggtgtttgttCtgtatcagacactccatcag	7	16	8	10	0	4	1	2	0	2	1	6	1	6	1	2	1	0	3	2	1	1	4			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr16:74505131C>T	ENST00000422840.2	-	15	2168	c.2169G>A	c.(2167-2169)caG>caA	p.Q723Q	GLG1_ENST00000447066.2_Silent_p.Q712Q|GLG1_ENST00000205061.5_Silent_p.Q723Q	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	723					blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						GGTGTTTGTTCTGTATCAGAC	0.483																																					p.Q723Q		Atlas-SNP	.											.	GLG1	106	.	0			c.G2169A						PASS	.						363	306	325					16																	74505131		2198	4300	6498	SO:0001819	synonymous_variant	2734	exon15			TTTGTTCTGTATC		CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"golgi apparatus protein 1"			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.2169G>A	chr16.hg19:g.74505131C>T		87.0	0.0	.		79.0	37.0	.	NM_001145667	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Silent	SNP	ENST00000422840.2	hg19	CCDS45527.1																																																																																			.	.	.	none		0.483	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201		T	74505131	C	T	74505131	2	4	258	1	0	0	0	0	0	0	0	1	6443	912	32	2		2	GLG1	16	74505131	Silent	SNP	C	TCGA-UZ-A9PL-01A-11D-A382-10	6099323	74505131	15849622	61	16097											
KRT10	3858	hgsc.bcm.edu	37	chr17	38975316	38975316	+	Missense_Mutation	SNP	G	G	A																															gccgccggaactgccgccgtGgccgccgccgtggccgccgc																										TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr17:38975316G>A	ENST00000269576.5	-	7	1480	c.1471C>T	c.(1471-1473)Cac>Tac	p.H491Y	TMEM99_ENST00000301665.3_5'Flank	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	491	Gly-rich.|Ser-rich.|Tail.			Missing (in Ref. 1; AAA60544). {ECO:0000305}.	cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)			NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				ctgccgccgtggccgccgccg	0.801																																					p.H491Y		Atlas-SNP	.											.	KRT10	56	.	0			c.C1471T						PASS	.						1	1	1					17																	38975316		219	517	736	SO:0001583	missense	3858	exon7			CGCCGTGGCCGCC	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"-", "Intermediate filaments type I, keratins (acidic)"	6413	protein-coding gene	gene with protein product	"cytokeratin 10", "epidermolytic hyperkeratosis"	148080	"keratosis palmaris et plantaris"	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.1471C>T	chr17.hg19:g.38975316G>A	ENSP00000269576:p.His491Tyr	26.0	0.0	.		98.0	13.0	.	NM_000421	Q14664|Q8N175	Missense_Mutation	SNP	ENST00000269576.5	hg19	CCDS11377.1	.	.	.	.	.	.	.	.	.	.	g	15.09	2.731363	0.48939	.	.	ENSG00000186395	ENST00000269576	D	0.83591	-1.74	5.21	-9.23	0.00672	.	2.489830	0.01848	N	0.035767	T	0.64724	0.2624	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.59397	-0.7462	10	0.45353	T	0.12	.	9.3977	0.38412	0.3538:0.2897:0.3564:0.0	.	491	P13645	K1C10_HUMAN	Y	491	ENSP00000269576:H491Y	ENSP00000269576:H491Y	H	-	1	0	KRT10	36228842	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-4.792000	0.00185	-2.762000	0.00369	-2.316000	0.00254	CAC	.	.	.	none		0.801	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421		A	38975316	G	A	38975316	3	1	258	1	0	0	0	0	1	0	0	0	8455	1348	47	2	291	2	KRT10	17	38975316	Missense_Mutation	SNP	G	TCGA-UZ-A9PL-01A-11D-A382-10		38975316	42219894	62	16098	166	2									
KRT10	3858	hgsc.bcm.edu	37	chr17	38975319	38975319	+	Missense_Mutation	SNP	C	C	T																															gccggaactgccgccgtggcCgccgccgtggccgccgccgg																										TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr17:38975319C>T	ENST00000269576.5	-	7	1477	c.1468G>A	c.(1468-1470)Ggc>Agc	p.G490S	TMEM99_ENST00000301665.3_5'Flank	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	490	Gly-rich.|Ser-rich.|Tail.			Missing (in Ref. 8; AAA59199). {ECO:0000305}.	cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)			NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				ccgccgtggccgccgccgtgg	0.791																																					p.G490S		Atlas-SNP	.											.	KRT10	56	.	0			c.G1468A						PASS	.																																			SO:0001583	missense	3858	exon7			CGTGGCCGCCGCC	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"-", "Intermediate filaments type I, keratins (acidic)"	6413	protein-coding gene	gene with protein product	"cytokeratin 10", "epidermolytic hyperkeratosis"	148080	"keratosis palmaris et plantaris"	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.1468G>A	chr17.hg19:g.38975319C>T	ENSP00000269576:p.Gly490Ser	20.0	0.0	.		104.0	19.0	.	NM_000421	Q14664|Q8N175	Missense_Mutation	SNP	ENST00000269576.5	hg19	CCDS11377.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.546565	0.86022	.	.	ENSG00000186395	ENST00000269576	D	0.96587	-4.06	4.38	4.38	0.52667	.	0.845686	0.09879	N	0.743932	D	0.94778	0.8314	N	0.08118	0	0.27860	N	0.940431	D	0.89917	1.0	D	0.76071	0.987	D	0.87790	0.2618	10	0.18710	T	0.47	.	12.7512	0.57310	0.0:1.0:0.0:0.0	.	490	P13645	K1C10_HUMAN	S	490	ENSP00000269576:G490S	ENSP00000269576:G490S	G	-	1	0	KRT10	36228845	0.019000	0.18553	0.876000	0.34364	0.184000	0.23303	0.448000	0.21726	2.739000	0.93911	0.603000	0.83216	GGC	.	.	.	none		0.791	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421		T	38975319	C	T	38975319	3	4	258	1	0	0	0	0	1	0	0	0	8455	652	23	1	294	1	KRT10	17	38975319	Missense_Mutation	SNP	C	TCGA-UZ-A9PL-01A-11D-A382-10	3	38975319	42219891	63	16099	166	2									
ACSF2	80221	hgsc.bcm.edu	37	chr17	48538115	48538115	+	Missense_Mutation	SNP	T	T	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	ggggtgcaccaaaaagcatcTtaacagcaagactgtgggcc	13	6	12	10	0	1	1	0	0	1	1	1	1	1	1	2	3	4	3	2	3	4	1			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr17:48538115T>G	ENST00000300441.4	+	2	310	c.206T>G	c.(205-207)cTt>cGt	p.L69R	ACSF2_ENST00000427954.2_Missense_Mutation_p.L94R|ACSF2_ENST00000502667.1_Missense_Mutation_p.L69R|ACSF2_ENST00000504392.1_Missense_Mutation_p.L69R|ACSF2_ENST00000541920.1_Intron	NM_025149.4	NP_079425.3	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2	69					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ligase activity (GO:0016874)			endometrium(7)|kidney(3)|large_intestine(1)|lung(1)|stomach(1)	13	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			AAAAAGCATCTTAACAGCAAG	0.572																																					p.L69R		Atlas-SNP	.											.	ACSF2	46	.	0			c.T206G						PASS	.						112	89	97					17																	48538115		2203	4300	6503	SO:0001583	missense	80221	exon2			AGCATCTTAACAG	AK024573, BC012053	CCDS11567.1, CCDS74103.1, CCDS74104.1, CCDS74105.1	17q21.33	2007-10-17			ENSG00000167107	ENSG00000167107		"Acyl-CoA synthetase family"	26101	protein-coding gene	gene with protein product		610465				17762044	Standard	NM_001288968		Approved	FLJ20920, ACSMW	uc002iqu.2	Q96CM8	OTTHUMG00000162128	ENST00000300441.4:c.206T>G	chr17.hg19:g.48538115T>G	ENSP00000300441:p.Leu69Arg	92.0	0.0	.		161.0	106.0	.	NM_025149	B4DFQ6|B4DHT5|B4DUF5|Q9H7G2	Missense_Mutation	SNP	ENST00000300441.4	hg19	CCDS11567.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.437471	0.83885	.	.	ENSG00000167107	ENST00000300441;ENST00000506582;ENST00000504392;ENST00000427954;ENST00000502667	T;T;T;T;T	0.50813	0.73;2.72;0.73;1.01;0.73	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.74711	0.3752	M	0.89534	3.04	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;0.994;0.998	T	0.80578	-0.1320	10	0.72032	D	0.01	-11.7183	15.7252	0.77751	0.0:0.0:0.0:1.0	.	69;94;69;69	B4DHT5;B4DFQ6;E9PF16;Q96CM8	.;.;.;ACSF2_HUMAN	R	69;69;69;94;69	ENSP00000300441:L69R;ENSP00000424842:L69R;ENSP00000425964:L69R;ENSP00000401831:L94R;ENSP00000421884:L69R	ENSP00000300441:L69R	L	+	2	0	ACSF2	45893114	1.000000	0.71417	0.089000	0.20774	0.006000	0.05464	6.840000	0.75369	2.191000	0.70037	0.533000	0.62120	CTT	.	.	.	none		0.572	ACSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367423.3	NM_025149		G	48538115	T	G	48538115	3	3	258	1	0	0	0	0	1	0	0	0	175	1609	56	5	212	5	ACSF2	17	48538115	Missense_Mutation	SNP	T	TCGA-UZ-A9PL-01A-11D-A382-10	9562796	48538115	32657095	64	16100											
CNDP2	55748	hgsc.bcm.edu	37	chr18	72180835	72180835	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaacatcctgatccccggcAttaacgaggccgtggccgcc	8	6	12	15	4	0	1	0	1	0	0	2	3	2	2	6	4	2	1	6	4	2	1			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr18:72180835A>G	ENST00000324262.4	+	8	1100	c.784A>G	c.(784-786)Att>Gtt	p.I262V	CNDP2_ENST00000324301.8_Missense_Mutation_p.I178V|CNDP2_ENST00000579847.1_Missense_Mutation_p.I262V	NM_018235.2	NP_060705.2	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2 (metallopeptidase M20 family)	262					cellular nitrogen compound metabolic process (GO:0034641)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)			breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(5)|ovary(2)|skin(2)|stomach(3)	24		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)		GATCCCCGGCATTAACGAGGC	0.602																																					p.I262V		Atlas-SNP	.											.	CNDP2	55	.	0			c.A784G						PASS	.						65	55	59					18																	72180835		2203	4300	6503	SO:0001583	missense	55748	exon8			CCCGGCATTAACG	AK001692	CCDS12006.1, CCDS54190.1	18q22.3	2014-07-14	2004-07-12		ENSG00000133313	ENSG00000133313	3.4.13.18		24437	protein-coding gene	gene with protein product	"cytosolic nonspecific dipeptidase"	169800	"peptidase A"	PEPA		12473676	Standard	NM_018235		Approved	FLJ10830, CN2, HsT2298, CPGL	uc002llm.2	Q96KP4	OTTHUMG00000132853	ENST00000324262.4:c.784A>G	chr18.hg19:g.72180835A>G	ENSP00000325548:p.Ile262Val	43.0	0.0	.		33.0	12.0	.	NM_018235	B3KUG4|Q8WY59|Q9BQ94|Q9NVB4	Missense_Mutation	SNP	ENST00000324262.4	hg19	CCDS12006.1	.	.	.	.	.	.	.	.	.	.	A	14.11	2.439001	0.43326	.	.	ENSG00000133313	ENST00000324262;ENST00000324301	T	0.18016	2.24	5.74	4.56	0.56223	Peptidase M20, dimerisation (1);	0.087910	0.85682	N	0.000000	T	0.12944	0.0314	L	0.31526	0.94	0.58432	D	0.999998	B;B	0.15930	0.001;0.015	B;B	0.26517	0.017;0.07	T	0.10776	-1.0615	10	0.26408	T	0.33	-0.029	8.8536	0.35214	0.8049:0.1279:0.0671:0.0	.	178;262	Q96KP4-2;Q96KP4	.;CNDP2_HUMAN	V	262;178	ENSP00000325548:I262V	ENSP00000325548:I262V	I	+	1	0	CNDP2	70331815	1.000000	0.71417	0.973000	0.42090	0.801000	0.45260	5.174000	0.65015	0.970000	0.38263	0.533000	0.62120	ATT	.	.	.	none		0.602	CNDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256327.1	NM_018235		G	72180835	A	G	72180835	3	3	258	1	0	0	0	0	1	0	0	0	3596	217	8	3	810	3	CNDP2	18	72180835	Missense_Mutation	SNP	A	TCGA-UZ-A9PL-01A-11D-A382-10		72180835	5896413	65	16101											
ZNF556	80032	hgsc.bcm.edu	37	chr19	2877876	2877876	+	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	atcctttcaacgacacgtgaGaattcacaacggggagaaac	15	7	9	10	3	2	2	2	1	0	2	3	5	3	2	1	2	3	0	1	2	4	2			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr19:2877876G>C	ENST00000307635.2	+	4	1007	c.920G>C	c.(919-921)aGa>aCa	p.R307T	ZNF556_ENST00000586426.1_Missense_Mutation_p.R306T	NM_024967.1	NP_079243.1	Q9HAH1	ZN556_HUMAN	zinc finger protein 556	307					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(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)		CGACACGTGAGAATTCACAAC	0.502																																					p.R307T		Atlas-SNP	.											.	ZNF556	73	.	0			c.G920C						PASS	.						56	54	55					19																	2877876		2203	4300	6503	SO:0001583	missense	80032	exon4			ACGTGAGAATTCA	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.920G>C	chr19.hg19:g.2877876G>C	ENSP00000302603:p.Arg307Thr	128.0	0.0	.		148.0	63.0	.	NM_024967	Q96GM3	Missense_Mutation	SNP	ENST00000307635.2	hg19	CCDS12097.1	.	.	.	.	.	.	.	.	.	.	G	11.03	1.519533	0.27211	.	.	ENSG00000172000	ENST00000307635	T	0.25414	1.8	2.3	1.18	0.20946	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.25606	0.0623	M	0.62723	1.935	0.22096	N	0.999363	P	0.41624	0.757	B	0.40565	0.333	T	0.13124	-1.0521	9	0.66056	D	0.02	.	6.4298	0.21790	0.0:0.3097:0.6903:0.0	.	307	Q9HAH1	ZN556_HUMAN	T	307	ENSP00000302603:R307T	ENSP00000302603:R307T	R	+	2	0	ZNF556	2828876	0.000000	0.05858	0.002000	0.10522	0.155000	0.21991	0.438000	0.21559	0.137000	0.18759	0.407000	0.27541	AGA	.	.	.	none		0.502	ZNF556-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451638.2	NM_024967		C	2877876	G	C	2877876	3	2	258	1	0	0	0	0	1	0	0	0	17999	942	33	4	934	4	ZNF556	19	2877876	Missense_Mutation	SNP	G	TCGA-UZ-A9PL-01A-11D-A382-10		2877876	56251107	66	16102											
TMEM145	284339	hgsc.bcm.edu	37	chr19	42817621	42817621	+	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	ccccgcgcccgggccaagtaCgtgcggggcaacctcagttc	6	5	13	17	5	1	0	1	0	0	0	2	0	1	0	5	3	3	3	5	3	3	2			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr19:42817621C>T	ENST00000301204.3	+	1	134	c.93C>T	c.(91-93)taC>taT	p.Y31Y	TMEM145_ENST00000598766.1_Silent_p.Y31Y	NM_173633.2	NP_775904.2	Q8NBT3	TM145_HUMAN	transmembrane protein 145	31					G-protein coupled receptor signaling pathway (GO:0007186)|response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|prostate(4)|skin(1)|urinary_tract(1)	27		Prostate(69;0.00682)				GGGCCAAGTACGTGCGGGGCA	0.766																																					p.Y31Y		Atlas-SNP	.											.	TMEM145	55	.	0			c.C93T						PASS	.						3	4	4					19																	42817621		1445	2532	3977	SO:0001819	synonymous_variant	284339	exon1			CAAGTACGTGCGG	AK075286	CCDS12603.1	19q13.2	2008-02-05				ENSG00000167619			26912	protein-coding gene	gene with protein product							Standard	NM_173633		Approved	FLJ90805	uc002otk.1	Q8NBT3		ENST00000301204.3:c.93C>T	chr19.hg19:g.42817621C>T		79.0	0.0	.		82.0	31.0	.	NM_173633		Silent	SNP	ENST00000301204.3	hg19	CCDS12603.1																																																																																			.	.	.	none		0.766	TMEM145-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463737.1	NM_173633		T	42817621	C	T	42817621	2	4	258	1	0	0	0	0	0	0	0	1	16071	547	19	1		1	TMEM145	19	42817621	Silent	SNP	C	TCGA-UZ-A9PL-01A-11D-A382-10	39939745	42817621	16311362	67	16103											
PPP1R13L	10848	hgsc.bcm.edu	37	chr19	45889399	45889399	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggcgcgcgcggcgggcctTgcgcggggagcccgccttcc	2	4	19	16	8	0	0	0	0	0	0	1	2	1	1	4	5	2	0	4	5	0	2			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr19:45889399T>C	ENST00000418234.2	-	9	1933	c.1855A>G	c.(1855-1857)Aag>Gag	p.K619E	PPP1R13L_ENST00000360957.5_Missense_Mutation_p.K619E	NM_001142502.1	NP_001135974.1	Q8WUF5	IASPP_HUMAN	protein phosphatase 1, regulatory subunit 13 like	619					apoptotic process (GO:0006915)|cardiac muscle contraction (GO:0060048)|cardiac right ventricle morphogenesis (GO:0003215)|embryonic camera-type eye development (GO:0031076)|hair cycle (GO:0042633)|multicellular organism growth (GO:0035264)|multicellular organismal homeostasis (GO:0048871)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|ventricular cardiac muscle tissue development (GO:0003229)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0182)		CGGCGGGCCTTGCGCGGGGAG	0.677																																					p.K619E	Pancreas(61;1447 1663 31419 50578)	Atlas-SNP	.											.	PPP1R13L	66	.	0			c.A1855G						PASS	.						6	8	7					19																	45889399		2156	4212	6368	SO:0001583	missense	10848	exon9			GGGCCTTGCGCGG	AF078036	CCDS33050.1	19q13.32	2013-01-10	2011-10-04		ENSG00000104881	ENSG00000104881		"Ankyrin repeat domain containing"	18838	protein-coding gene	gene with protein product		607463	"protein phosphatase 1, regulatory (inhibitor) subunit 13 like"			10336463	Standard	NM_006663		Approved	RAI, IASPP	uc002pbo.3	Q8WUF5		ENST00000418234.2:c.1855A>G	chr19.hg19:g.45889399T>C	ENSP00000403902:p.Lys619Glu	41.0	0.0	.		30.0	16.0	.	NM_001142502	Q2PNZ9|Q5DU71|Q5I1X4|Q6P1R7|Q6PKF8|Q9Y290	Missense_Mutation	SNP	ENST00000418234.2	hg19	CCDS33050.1	.	.	.	.	.	.	.	.	.	.	T	16.38	3.106921	0.56291	.	.	ENSG00000104881	ENST00000418234;ENST00000360957;ENST00000221478	T;T	0.57752	0.38;0.38	4.99	4.99	0.66335	Src homology-3 domain (1);	0.103779	0.64402	D	0.000004	T	0.34250	0.0891	N	0.24115	0.695	0.38248	D	0.941515	P;P	0.48407	0.91;0.769	B;B	0.37015	0.239;0.094	T	0.29458	-1.0011	10	0.25106	T	0.35	.	12.6956	0.57001	0.0:0.0:0.0:1.0	.	619;198	Q8WUF5;A7YME7	IASPP_HUMAN;.	E	619;619;193	ENSP00000403902:K619E;ENSP00000354218:K619E	ENSP00000221478:K193E	K	-	1	0	PPP1R13L	50581239	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.812000	0.38952	2.102000	0.63906	0.459000	0.35465	AAG	.	.	.	none		0.677	PPP1R13L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457586.1	NM_006663		C	45889399	T	C	45889399	3	2	258	1	0	0	0	0	1	0	0	0	12368	1821	63	3	651	3	PPP1R13L	19	45889399	Missense_Mutation	SNP	T	TCGA-UZ-A9PL-01A-11D-A382-10	3071778	45889399	13239584	68	16104											
CHD6	84181	hgsc.bcm.edu	37	chr20	40086018	40086018	+	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	gaatttcgagtgatgaggcgAtacaccttcacagctttgct	10	12	10	9	2	1	2	1	2	0	0	2	5	1	2	1	1	3	2	1	1	2	4			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr20:40086018A>T	ENST00000373233.3	-	18	2892	c.2715T>A	c.(2713-2715)taT>taA	p.Y905*	CHD6_ENST00000309279.7_Intron	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	905	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				TGATGAGGCGATACACCTTCA	0.527																																					p.Y905X		Atlas-SNP	.											.	CHD6	312	.	0			c.T2715A						PASS	.						144	110	121					20																	40086018		2203	4300	6503	SO:0001587	stop_gained	84181	exon18			GAGGCGATACACC	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.2715T>A	chr20.hg19:g.40086018A>T	ENSP00000362330:p.Tyr905*	94.0	0.0	.		126.0	39.0	.	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Nonsense_Mutation	SNP	ENST00000373233.3	hg19	CCDS13317.1	.	.	.	.	.	.	.	.	.	.	A	42	9.300881	0.99130	.	.	ENSG00000124177	ENST00000373233	.	.	.	5.42	3.18	0.36537	.	0.000000	0.51477	D	0.000085	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.8164	9.2947	0.37808	0.8543:0.0:0.1457:0.0	.	.	.	.	X	905	.	ENSP00000362330:Y905X	Y	-	3	2	CHD6	39519432	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.745000	0.38278	1.011000	0.39340	0.482000	0.46254	TAT	.	.	.	none		0.527	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			T	40086018	A	T	40086018	4	4	258	1	0	0	0	0	0	1	0	0	3331	340	12	5	5512	5	CHD6	20	40086018	Nonsense_Mutation	SNP	A	TCGA-UZ-A9PL-01A-11D-A382-10		40086018	22939502	69	16105											
PTK6	5753	hgsc.bcm.edu	37	chr20	62168498	62168499	+	Frame_Shift_Ins	INS	-	-	C																															gggcacatagccctgggccaINScggccccacccgcctcgtcc																										TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr20:62168498_62168499insC	ENST00000217185.2	-	1	196_197	c.169_170insG	c.(169-171)gtgfs	p.V57fs	PTK6_ENST00000542869.1_5'UTR	NM_005975.3	NP_005966.1	Q13882	PTK6_HUMAN	protein tyrosine kinase 6	57	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|intestinal epithelial cell differentiation (GO:0060575)|negative regulation of growth (GO:0045926)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of neuron projection development (GO:0010976)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|ruffle (GO:0001726)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			endometrium(3)|kidney(1)|lung(5)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	15	all_cancers(38;2.51e-11)		Epithelial(9;1.5e-08)|all cancers(9;8.67e-08)|BRCA - Breast invasive adenocarcinoma(10;6.43e-06)		Vandetanib(DB05294)	GCCCTGGGCCACGGCCCCACCC	0.688																																					p.V57fs		Atlas-INDEL	.											.	PTK6	33	.	0			c.170_171insG						PASS	.																																			SO:0001589	frameshift_variant	5753	exon1			.	U61412	CCDS13524.1, CCDS74750.1	20q13.3	2013-02-18	2013-02-18		ENSG00000101213	ENSG00000101213	2.7.10.1	"SH2 domain containing"	9617	protein-coding gene	gene with protein product		602004	"PTK6 protein tyrosine kinase 6"			8247543, 9284935	Standard	NM_005975		Approved	BRK	uc002yfg.4	Q13882	OTTHUMG00000033039	ENST00000217185.2:c.170dupG	chr20.hg19:g.62168499_62168499dupC	ENSP00000217185:p.Val57fs	67.0	0.0	0		98.0	10.0	0.102041	NM_001256358	B2RCR3|B4DW46|Q58F01	Frame_Shift_Ins	INS	ENST00000217185.2	hg19	CCDS13524.1																																																																																			.	.	.	none		0.688	PTK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080313.1			C	62168499	-	C	62168498	7	5	258	1	0	1	1	0	0	0	0	0	12775	159	6	0	1217	0	PTK6	20	62168498	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PL-01A-11D-A382-10	22082480	62168498	857022	70	16106											
ADAMTS1	9510	hgsc.bcm.edu	37	chr21	28217050	28217050	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaaggcgtgcaggcggaggCgcgtggtcccgtgtcccggg	5	5	19	12	6	0	0	0	0	0	0	2	1	2	1	2	6	1	1	2	6	1	0			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr21:28217050C>T	ENST00000284984.3	-	1	678	c.224G>A	c.(223-225)cGc>cAc	p.R75H		NM_006988.3	NP_008919.3	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 1	75					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)		CAGGCGGAGGCGCGTGGTCCC	0.706											OREG0026151	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R75H		Atlas-SNP	.											.	ADAMTS1	131	.	0			c.G224A						PASS	.						7	9	9					21																	28217050		2179	4262	6441	SO:0001583	missense	9510	exon1			CGGAGGCGCGTGG	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.224G>A	chr21.hg19:g.28217050C>T	ENSP00000284984:p.Arg75His	69.0	0.0	.	800	68.0	27.0	.	NM_006988	D3DSD5|Q9NSJ8|Q9P2K0|Q9UH83|Q9UP80	Missense_Mutation	SNP	ENST00000284984.3	hg19	CCDS33524.1	.	.	.	.	.	.	.	.	.	.	C	11.39	1.625463	0.28889	.	.	ENSG00000154734	ENST00000284984	T	0.05786	3.39	4.06	-1.13	0.09775	Peptidase M12B, propeptide (1);	.	.	.	.	T	0.02193	0.0068	N	0.03324	-0.35	0.39418	D	0.966863	B	0.11235	0.004	B	0.09377	0.004	T	0.48896	-0.8994	9	0.09338	T	0.73	.	7.6505	0.28346	0.4991:0.4049:0.0:0.096	.	75	Q9UHI8	ATS1_HUMAN	H	75	ENSP00000284984:R75H	ENSP00000284984:R75H	R	-	2	0	ADAMTS1	27138921	0.366000	0.25014	0.967000	0.41034	0.769000	0.43574	0.373000	0.20484	-0.033000	0.13736	-0.410000	0.06199	CGC	.	.	.	none		0.706	ADAMTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171650.2			T	28217050	C	T	28217050	3	4	258	1	0	0	0	0	1	0	0	0	255	768	27	1	2715	1	ADAMTS1	21	28217050	Missense_Mutation	SNP	C	TCGA-UZ-A9PL-01A-11D-A382-10		28217050	19912845	71	16107											
CECR6	27439	hgsc.bcm.edu	37	chr22	17600499	17600499	+	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	ctccaggccccggcagccgaGgaagaagaggttcttgagca	10	5	14	12	2	1	3	0	1	1	2	2	5	2	4	4	4	2	3	4	4	2	2			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chr22:17600499G>T	ENST00000331437.3	-	1	1644	c.1519C>A	c.(1519-1521)Ctc>Atc	p.L507I	AC006946.15_ENST00000441544.1_5'Flank|CECR6_ENST00000399875.1_Missense_Mutation_p.L152I	NM_031890.3	NP_114096.1	Q9BXQ6	CECR6_HUMAN	cat eye syndrome chromosome region, candidate 6	507										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)		CGGCAGCCGAGGAAGAAGAGG	0.706																																					p.L507I		Atlas-SNP	.											.	CECR6	11	.	0			c.C1519A						PASS	.						4	5	5					22																	17600499		2090	4119	6209	SO:0001583	missense	27439	exon1			AGCCGAGGAAGAA	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.1519C>A	chr22.hg19:g.17600499G>T	ENSP00000329318:p.Leu507Ile	32.0	0.0	.		26.0	11.0	.	NM_031890	A8MYY1	Missense_Mutation	SNP	ENST00000331437.3	hg19	CCDS13740.1	.	.	.	.	.	.	.	.	.	.	G	13.62	2.291089	0.40494	.	.	ENSG00000183307	ENST00000399875;ENST00000331437	.	.	.	4.63	4.63	0.57726	.	0.559654	0.15368	U	0.266033	T	0.41396	0.1157	L	0.29908	0.895	0.31742	N	0.635717	D	0.59767	0.986	P	0.53593	0.73	T	0.30851	-0.9964	9	0.22109	T	0.4	.	12.0274	0.53380	0.0:0.0:0.8275:0.1725	.	507	Q9BXQ6	CECR6_HUMAN	I	152;507	.	ENSP00000329318:L507I	L	-	1	0	CECR6	15980499	1.000000	0.71417	0.997000	0.53966	0.704000	0.40688	3.107000	0.50329	2.290000	0.77057	0.561000	0.74099	CTC	.	.	.	none		0.706	CECR6-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000075359.4	NM_031890		T	17600499	G	T	17600499	3	4	258	1	0	0	0	0	1	0	0	0	3210	1000	35	4	221	4	CECR6	22	17600499	Missense_Mutation	SNP	G	TCGA-UZ-A9PL-01A-11D-A382-10		17600499	33704067	72	16108											
AR	367	hgsc.bcm.edu	37	chrX	66765229	66765229	+	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	agcagcagcagcagcagcaaGagactagccccaggcagcag	14	1	13	13	0	0	1	0	0	0	1	0	2	0	1	2	1	8	8	2	1	2	1			TCGA-UZ-A9PL-01A-11D-A382-10	TCGA-UZ-A9PL-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fd5fd508-d8c8-4630-9580-0c780b3202e1	6b5fdcae-db39-4f26-a632-d6da690b51ab	g.chrX:66765229G>C	ENST00000374690.3	+	1	765	c.241G>C	c.(241-243)Gag>Cag	p.E81Q	AR_ENST00000396044.3_Missense_Mutation_p.E81Q|AR_ENST00000504326.1_Missense_Mutation_p.E81Q|AR_ENST00000513847.1_3'UTR	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	79	Gln-rich.|Modulating.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	gcagcagcaagagactagccc	0.642									Androgen Insensitivity Syndrome																												p.E81Q		Atlas-SNP	.											.	AR	249	.	0			c.G241C						PASS	.						11	10	10					X																	66765229		2156	4212	6368	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	CAGCAAGAGACTA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.241G>C	chrX.hg19:g.66765229G>C	ENSP00000363822:p.Glu81Gln	125.0	0.0	.		119.0	9.0	.	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	N	0.251	-1.006630	0.02112	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.71934	-0.61;-0.61;-0.61	5.2	-5.32	0.02722	.	.	.	.	.	T	0.50120	0.1597	N	0.05280	-0.08	0.09310	N	1	B;B;B	0.34329	0.078;0.025;0.449	B;B;B	0.38921	0.026;0.016;0.285	T	0.36841	-0.9731	9	0.20046	T	0.44	.	17.1942	0.86888	0.0:0.7494:0.1481:0.1025	.	81;81;79	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	Q	81;81;81;73	ENSP00000363822:E81Q;ENSP00000421155:E81Q;ENSP00000379359:E81Q	ENSP00000363822:E81Q	E	+	1	0	AR	66681954	0.000000	0.05858	0.001000	0.08648	0.047000	0.14425	-2.343000	0.01099	-1.154000	0.02825	-0.206000	0.12725	GAG	.	.	.	none		0.642	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		C	66765229	G	C	66765229	3	2	258	1	0	0	0	0	1	0	0	0	836	943	33	4	243	4	AR	23	66765229	Missense_Mutation	SNP	G	TCGA-UZ-A9PL-01A-11D-A382-10		66765229	88505331	73	16109											
AGTRAP	57085	hgsc.bcm.edu	37	chr1	11810188	11810188	+	Missense_Mutation	SNP	A	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	ccagacgattgactcagcagAggcgcccgcagatccctttg	9	7	11	14	3	1	4	1	1	0	3	2	5	2	4	3	1	1	2	3	1	0	2			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr1:11810188A>C	ENST00000314340.5	+	5	473	c.419A>C	c.(418-420)gAg>gCg	p.E140A	AGTRAP_ENST00000376627.2_3'UTR|AGTRAP_ENST00000491346.1_3'UTR|AGTRAP_ENST00000376629.4_Missense_Mutation_p.E133A|AGTRAP_ENST00000452018.2_3'UTR|AGTRAP_ENST00000510878.1_Silent_p.R105R|AGTRAP_ENST00000376637.3_3'UTR|AGTRAP_ENST00000400895.2_3'UTR	NM_020350.4	NP_065083.3	Q6RW13	ATRAP_HUMAN	angiotensin II receptor-associated protein	140					regulation of blood pressure (GO:0008217)|response to hypoxia (GO:0001666)	cell cortex (GO:0005938)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	angiotensin type II receptor activity (GO:0004945)		AGTRAP/BRAF(2)	endometrium(1)|lung(3)|prostate(1)	5	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;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.46e-06)|COAD - Colon adenocarcinoma(227;0.000256)|BRCA - Breast invasive adenocarcinoma(304;0.0003)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		GACTCAGCAGAGGCGCCCGCA	0.607																																					p.E140A		Atlas-SNP	.											.	AGTRAP	9	.	0			c.A419C						PASS	.						67	63	65					1																	11810188		2203	4300	6503	SO:0001583	missense	57085	exon5			CAGCAGAGGCGCC	AF165187	CCDS136.1, CCDS30585.1, CCDS30586.1, CCDS41248.1, CCDS44056.1	1p36.22	2008-02-05			ENSG00000177674	ENSG00000177674			13539	protein-coding gene	gene with protein product		608729				11733189	Standard	NM_001040194		Approved	ATRAP	uc001asv.3	Q6RW13	OTTHUMG00000002230	ENST00000314340.5:c.419A>C	chr1.hg19:g.11810188A>C	ENSP00000319713:p.Glu140Ala	75.0	0.0	.		60.0	11.0	.	NM_020350	A8MVQ5|Q5SNV4|Q5SNV5|Q96AC0|Q96PL4|Q9NRW9	Missense_Mutation	SNP	ENST00000314340.5	hg19	CCDS136.1	.	.	.	.	.	.	.	.	.	.	A	13.02	2.113706	0.37339	.	.	ENSG00000177674	ENST00000376629;ENST00000314340	T;T	0.50001	0.76;0.76	5.0	2.56	0.30785	.	0.549006	0.14015	U	0.347205	T	0.38772	0.1053	L	0.48362	1.52	0.09310	N	0.999995	B;B	0.15141	0.01;0.012	B;B	0.14578	0.004;0.011	T	0.25606	-1.0127	10	0.33940	T	0.23	.	8.9656	0.35874	0.632:0.368:0.0:0.0	.	133;140	Q6RW13-2;Q6RW13	.;ATRAP_HUMAN	A	133;140	ENSP00000365816:E133A;ENSP00000319713:E140A	ENSP00000319713:E140A	E	+	2	0	AGTRAP	11732775	0.796000	0.28864	0.007000	0.13788	0.104000	0.19210	2.023000	0.41040	0.330000	0.23485	0.459000	0.35465	GAG	.	.	.	none		0.607	AGTRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006335.1	NM_020350		C	11810188	A	C	11810188	3	2	259	1	0	0	0	0	1	0	0	0	403	304	11	5	538	5	AGTRAP	1	11810188	Missense_Mutation	SNP	A	TCGA-UZ-A9PM-01A-21D-A382-10		11810188	237440433	1	16110											
KIAA2013	90231	hgsc.bcm.edu	37	chr1	11985315	11985315	+	Missense_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	ggtcttgaagcagctccgccGctggcatgtccaagagctcc	7	8	12	14	2	1	2	0	1	1	1	4	2	4	2	4	2	3	5	4	2	2	1			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr1:11985315G>A	ENST00000376572.3	-	1	1165	c.980C>T	c.(979-981)gCg>gTg	p.A327V	KIAA2013_ENST00000376576.3_Missense_Mutation_p.A327V	NM_138346.2	NP_612355.1	Q8IYS2	K2013_HUMAN	KIAA2013	327						integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	7	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00149)|all_lung(284;0.00189)|Breast(348;0.00586)|Colorectal(325;0.0062)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0556)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CAGCTCCGCCGCTGGCATGTC	0.597																																					p.A327V		Atlas-SNP	.											.	KIAA2013	25	.	0			c.C980T						PASS	.						38	39	38					1																	11985315		2203	4300	6503	SO:0001583	missense	90231	exon1			TCCGCCGCTGGCA	AB095933	CCDS141.1	1p36.22	2011-02-09			ENSG00000116685	ENSG00000116685			28513	protein-coding gene	gene with protein product						12477932	Standard	NM_138346		Approved	MGC33867, RP5-1077B9.1	uc001atk.3	Q8IYS2	OTTHUMG00000002391	ENST00000376572.3:c.980C>T	chr1.hg19:g.11985315G>A	ENSP00000365756:p.Ala327Val	135.0	0.0	.		150.0	25.0	.	NM_138346	Q5JXC1|Q8IVF8|Q8NDI7|Q9BSY1	Missense_Mutation	SNP	ENST00000376572.3	hg19	CCDS141.1	.	.	.	.	.	.	.	.	.	.	G	2.727	-0.265373	0.05754	.	.	ENSG00000116685	ENST00000376572;ENST00000376576	.	.	.	3.9	0.917	0.19380	.	0.346810	0.27522	N	0.018998	T	0.07234	0.0183	N	0.00707	-1.245	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.08055	0.003;0.003	T	0.31280	-0.9949	9	0.24483	T	0.36	-22.5578	4.5612	0.12161	0.2713:0.185:0.5437:0.0	.	327;327	Q8IYS2-2;Q8IYS2	.;K2013_HUMAN	V	327	.	ENSP00000365756:A327V	A	-	2	0	KIAA2013	11907902	0.897000	0.30589	0.001000	0.08648	0.003000	0.03518	3.278000	0.51662	0.413000	0.25759	-0.346000	0.07831	GCG	.	.	.	none		0.597	KIAA2013-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006858.1	NM_138346		A	11985315	G	A	11985315	3	1	259	1	0	0	0	0	1	0	0	0	8274	1087	38	1	936	1	KIAA2013	1	11985315	Missense_Mutation	SNP	G	TCGA-UZ-A9PM-01A-21D-A382-10	175127	11985315	237265306	2	16111											
KHDRBS1	10657	hgsc.bcm.edu	37	chr1	32479924	32479929	+	In_Frame_Del	DEL	GAGAAG	GAGAAG	-																															acctgcccgaactcatggccGagaaggactcgctcgacccg																										TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	GAGAAG	GAGAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr1:32479924_32479929delGAGAAG	ENST00000327300.7	+	1	495_500	c.328_333delGAGAAG	c.(328-333)gagaagdel	p.EK110del	KHDRBS1_ENST00000492989.1_In_Frame_Del_p.EK110del|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)				ACTCATGGCCGAGAAGGACTCGCTCG	0.684																																					p.109_111del	Ovarian(173;401 1982 12359 31110 42403)	Atlas-Indel,Pindel	.											.	KHDRBS1	34	.	0			c.327_332del						PASS	.																																			SO:0001651	inframe_deletion	10657	exon1			.	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.328_333delGAGAAG	chr1.hg19:g.32479924_32479929delGAGAAG	ENSP00000313829:p.Glu110_Lys111del	98.0	0.0	0		131.0	12.0	0.0916031	NM_006559		In_Frame_Del	DEL	ENST00000327300.7	hg19	CCDS350.1																																																																																			.	.	.	none		0.684	KHDRBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011199.4	NM_006559		-	32479929	GAGAAG	-	32479924	7	5	259	1	0	1	0	1	0	0	0	0	8153	1059	37	0	330	0	KHDRBS1	1	32479924	In_Frame_Del	DEL	GAGAAG	TCGA-UZ-A9PM-01A-21D-A382-10	20494609	32479924	216770697	3	16112											
MACF1	23499	hgsc.bcm.edu	37	chr1	39901268	39901268	+	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	gctgaacacaaacctcatatTgacaaactactaaagatagg	18	8	6	9	0	1	3	1	2	0	1	1	3	1	3	1	1	4	1	1	1	8	5			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr1:39901268T>A	ENST00000372915.3	+	68	17598	c.17511T>A	c.(17509-17511)atT>atA	p.I5837I	MACF1_ENST00000539005.1_Silent_p.I3749I|MACF1_ENST00000567887.1_Silent_p.I5978I|MACF1_ENST00000317713.7_Silent_p.I3879I|MACF1_ENST00000289893.4_Silent_p.I4381I|MACF1_ENST00000564288.1_Silent_p.I5941I|MACF1_ENST00000361689.2_Silent_p.I3879I|MACF1_ENST00000545844.1_Silent_p.I3879I			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	5837					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)			AACCTCATATTGACAAACTAC	0.343																																					p.I3879I		Atlas-SNP	.											.	MACF1	909	.	0			c.T11637A						PASS	.						90	90	90					1																	39901268		2203	4300	6503	SO:0001819	synonymous_variant	23499	exon66			TCATATTGACAAA	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.17511T>A	chr1.hg19:g.39901268T>A		187.0	0.0	.		229.0	45.0	.	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Silent	SNP	ENST00000372915.3	hg19		.	.	.	.	.	.	.	.	.	.	T	9.384	1.073667	0.20147	.	.	ENSG00000127603	ENST00000372925	.	.	.	5.9	2.37	0.29283	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.2174	0.37355	0.0:0.2811:0.0:0.7189	.	.	.	.	R	2883	.	.	X	+	1	0	MACF1	39673855	0.985000	0.35326	1.000000	0.80357	0.840000	0.47671	0.184000	0.16939	0.488000	0.27723	-0.263000	0.10527	TGA	.	.	.	none		0.343	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		A	39901268	T	A	39901268	2	1	259	1	0	0	0	0	0	0	0	1	9151	1800	63	5		5	MACF1	1	39901268	Silent	SNP	T	TCGA-UZ-A9PM-01A-21D-A382-10	7421344	39901268	209349353	4	16113											
SMAP2	64744	hgsc.bcm.edu	37	chr1	40880943	40880943	+	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	aacttcgatctctctttctaGatgctcctgtggcctgctcc	5	15	7	14	1	3	1	0	0	3	1	7	2	5	1	3	1	3	2	3	1	2	3			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr1:40880943G>T	ENST00000487871.1	+	2	264		c.e2-1		SMAP2_ENST00000539317.1_Splice_Site			Q8WU79	SMAP2_HUMAN	small ArfGAP2						regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			central_nervous_system(3)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(2)|upper_aerodigestive_tract(1)	24	Lung NSC(20;1.56e-05)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;1.04e-17)			TCTCTTTCTAGATGCTCCTGT	0.463																																					.		Atlas-SNP	.											.	SMAP2	48	.	0			c.572-1G>T						PASS	.						219	211	214					1																	40880943		2203	4300	6503	SO:0001630	splice_region_variant	64744	exon7			TTTCTAGATGCTC	AL137764	CCDS451.1, CCDS55592.1, CCDS55593.1, CCDS72763.1	1p35.3-p34.1	2008-09-22	2008-09-05	2008-01-09	ENSG00000084070	ENSG00000084070		"ADP-ribosylation factor GTPase activating proteins"	25082	protein-coding gene	gene with protein product			"stromal membrane-associated protein 1-like", "stromal membrane-associated GTPase-activating protein 2"	SMAP1L		16571680	Standard	NM_001198978		Approved		uc001cfj.3	Q8WU79	OTTHUMG00000007301	ENST00000487871.1:c.265-1G>T	chr1.hg19:g.40880943G>T		106.0	0.0	.		105.0	9.0	.	NM_022733	B2R7T1|B7Z5B5|B7Z8V2|D3DPV2|Q5QPL2|Q96C93|Q9NST2|Q9UJL8	Splice_Site	SNP	ENST00000487871.1	hg19		.	.	.	.	.	.	.	.	.	.	G	21.3	4.131745	0.77662	.	.	ENSG00000084070	ENST00000435168;ENST00000372718;ENST00000372708;ENST00000539317	.	.	.	6.08	6.08	0.98989	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.1573	0.89696	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SMAP2	40653530	1.000000	0.71417	0.999000	0.59377	0.984000	0.73092	6.291000	0.72719	2.894000	0.99253	0.655000	0.94253	.	.	.	.	none		0.463	SMAP2-004	KNOWN	mRNA_end_NF|basic	processed_transcript	protein_coding	OTTHUMT00000019077.1	NM_022733	Intron	T	40880943	G	T	40880943	5	4	259	1	0	0	0	0	0	0	1	0	14780	956	33	4	597	4	SMAP2	1	40880943	Splice_Site	SNP	G	TCGA-UZ-A9PM-01A-21D-A382-10	979675	40880943	208369678	5	16114											
S100A7L2	645922	hgsc.bcm.edu	37	chr1	153410759	153410759	+	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	ctccactgtattggcgaaacAtcgcgactatgtccaacatg	11	10	8	12	3	0	0	0	0	0	0	3	2	2	0	2	1	2	1	2	1	4	3			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr1:153410759A>T	ENST00000368725.2	-	2	79	c.80T>A	c.(79-81)aTg>aAg	p.M27K		NM_001045479.1	NP_001038944.2	Q5SY68	S1A7B_HUMAN	S100 calcium binding protein A7-like 2	16	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)			NS(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	8	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)			TTGGCGAAACATCGCGACTAT	0.433																																					p.M27K		Atlas-SNP	.											.	S100A7L2	36	.	0			c.T80A						PASS	.						197	161	173					1																	153410759		2203	4300	6503	SO:0001583	missense	645922	exon2			CGAAACATCGCGA			1q21.3	2013-01-10			ENSG00000197364	ENSG00000197364		"EF-hand domain containing"	21655	protein-coding gene	gene with protein product							Standard	NM_001045479		Approved	s100a7b	uc010pdx.2	Q5SY68	OTTHUMG00000013129	ENST00000368725.2:c.80T>A	chr1.hg19:g.153410759A>T	ENSP00000357714:p.Met27Lys	91.0	0.0	.		88.0	18.0	.	NM_001045479		Missense_Mutation	SNP	ENST00000368725.2	hg19		.	.	.	.	.	.	.	.	.	.	.	7.736	0.700320	0.15106	.	.	ENSG00000197364	ENST00000368725;ENST00000368724;ENST00000453814	T;T;T	0.06528	3.29;3.29;3.29	2.01	-0.664	0.11406	EF-hand-like domain (1);	.	.	.	.	T	0.01730	0.0055	L	0.44542	1.39	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.44922	-0.9296	9	0.72032	D	0.01	.	4.5322	0.12011	0.6351:0.0:0.3649:0.0	.	16	Q5SY68	S1A7B_HUMAN	K	16;16;27	ENSP00000357714:M16K;ENSP00000357713:M16K;ENSP00000405610:M27K	ENSP00000357713:M16K	M	-	2	0	S100A7L2	151677383	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	1.141000	0.31528	-0.166000	0.10890	0.416000	0.27883	ATG	.	.	.	none		0.433	S100A7L2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000036797.2	NM_001045479		T	153410759	A	T	153410759	3	4	259	1	0	0	0	0	1	0	0	0	13798	217	8	5	266	5	S100A7L2	1	153410759	Missense_Mutation	SNP	A	TCGA-UZ-A9PM-01A-21D-A382-10	112529816	153410759	95839862	6	16115											
CD1D	912	hgsc.bcm.edu	37	chr1	158152692	158152692	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccaaggcctggctgtcccGtggccccagtcctggccctg	3	7	13	18	1	0	0	0	0	0	0	2	0	2	0	7	4	0	1	7	4	1	0			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr1:158152692G>A	ENST00000368171.3	+	5	1131	c.632G>A	c.(631-633)cGt>cAt	p.R211H		NM_001766.3	NP_001757.1	P15813	CD1D_HUMAN	CD1d molecule	211	Ig-like.				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)					TGGCTGTCCCGTGGCCCCAGT	0.572																																					p.R211H		Atlas-SNP	.											.	CD1D	60	.	0			c.G632A						PASS	.						77	80	79					1																	158152692		2203	4300	6503	SO:0001583	missense	912	exon5			TGTCCCGTGGCCC	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.632G>A	chr1.hg19:g.158152692G>A	ENSP00000357153:p.Arg211His	123.0	0.0	.		140.0	22.0	.	NM_001766	D3DVD5|Q5W0J3|Q9UMM3|Q9Y5M4	Missense_Mutation	SNP	ENST00000368171.3	hg19	CCDS1173.1	.	.	.	.	.	.	.	.	.	.	G	13.89	2.370682	0.42003	.	.	ENSG00000158473	ENST00000368171	T	0.14022	2.54	4.66	1.73	0.24493	Immunoglobulin-like (1);MHC class I-like antigen recognition (1);	1.035360	0.07603	N	0.923929	T	0.02610	0.0079	L	0.33189	0.99	0.09310	N	0.999999	D	0.55172	0.97	B	0.38458	0.274	T	0.34254	-0.9836	10	0.22706	T	0.39	0.2225	4.2364	0.10627	0.2121:0.2105:0.5773:0.0	.	211	P15813	CD1D_HUMAN	H	211	ENSP00000357153:R211H	ENSP00000357153:R211H	R	+	2	0	CD1D	156419316	0.003000	0.15002	0.721000	0.30653	0.981000	0.71138	0.290000	0.18975	0.664000	0.31047	0.655000	0.94253	CGT	.	.	.	none		0.572	CD1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058340.1	NM_001766		A	158152692	G	A	158152692	3	1	259	1	0	0	0	0	1	0	0	0	2979	1145	40	1	646	1	CD1D	1	158152692	Missense_Mutation	SNP	G	TCGA-UZ-A9PM-01A-21D-A382-10	4741933	158152692	91097929	7	16116											
CCT4	10575	hgsc.bcm.edu	37	chr2	62099619	62099619	+	Missense_Mutation	SNP	A	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	ttcactaaacaacgaataacAcatagggcatcatgaatgga	18	8	7	8	1	2	1	2	1	0	0	2	3	2	2	0	2	3	1	0	2	7	4			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr2:62099619A>C	ENST00000394440.3	-	11	1526	c.1230T>G	c.(1228-1230)tgT>tgG	p.C410W	CCT4_ENST00000538252.1_Missense_Mutation_p.C354W|AC107081.5_ENST00000425779.1_RNA|CCT4_ENST00000544185.1_Missense_Mutation_p.C260W|CCT4_ENST00000461540.2_Intron|CCT4_ENST00000544079.1_Missense_Mutation_p.C380W	NM_006430.3	NP_006421.2	P50991	TCPD_HUMAN	chaperonin containing TCP1, subunit 4 (delta)	410					'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)			AACGAATAACACATAGGGCAT	0.343																																					p.C410W		Atlas-SNP	.											.	CCT4	38	.	0			c.T1230G						PASS	.						74	69	71					2																	62099619		2203	4300	6503	SO:0001583	missense	10575	exon11			AATAACACATAGG		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.1230T>G	chr2.hg19:g.62099619A>C	ENSP00000377958:p.Cys410Trp	177.0	0.0	.		188.0	27.0	.	NM_006430	B2R6I3|B7Z8B1|F5H5W3|O14870|Q53QP9|Q96C51	Missense_Mutation	SNP	ENST00000394440.3	hg19	CCDS33206.1	.	.	.	.	.	.	.	.	.	.	A	16.28	3.079180	0.55753	.	.	ENSG00000115484	ENST00000394440;ENST00000544079;ENST00000544185;ENST00000538252	T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24	5.77	3.4	0.38934	.	0.000000	0.85682	D	0.000000	D	0.90964	0.7159	H	0.97516	4.02	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.90431	0.4424	10	0.66056	D	0.02	-9.4227	9.3135	0.37919	0.79:0.0:0.21:0.0	.	380;410	F5H5W3;P50991	.;TCPD_HUMAN	W	410;380;260;354	ENSP00000377958:C410W;ENSP00000443061:C380W;ENSP00000443451:C260W;ENSP00000442174:C354W	ENSP00000377958:C410W	C	-	3	2	CCT4	61953123	1.000000	0.71417	0.999000	0.59377	0.974000	0.67602	3.544000	0.53640	0.539000	0.28788	-0.250000	0.11733	TGT	.	.	.	none		0.343	CCT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325548.2			C	62099619	A	C	62099619	3	2	259	1	0	0	0	0	1	0	0	0	2957	157	6	5	405	5	CCT4	2	62099619	Missense_Mutation	SNP	A	TCGA-UZ-A9PM-01A-21D-A382-10		62099619	181099754	8	16117											
VWA3B	200403	hgsc.bcm.edu	37	chr2	98736067	98736067	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcgaatggactggctcaccaGcaagagccggcagatttttg	10	8	13	10	2	1	2	1	0	0	2	1	4	1	3	2	3	2	3	2	3	2	2			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr2:98736067G>A	ENST00000477737.1	+	4	587	c.383G>A	c.(382-384)aGc>aAc	p.S128N	VWA3B_ENST00000435344.1_Missense_Mutation_p.S128N|VWA3B_ENST00000451075.2_Intron	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	128										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						TGGCTCACCAGCAAGAGCCGG	0.483																																					p.S128N		Atlas-SNP	.											.	VWA3B	138	.	0			c.G383A						PASS	.						152	148	149					2																	98736067		1966	4147	6113	SO:0001583	missense	200403	exon4			TCACCAGCAAGAG	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.383G>A	chr2.hg19:g.98736067G>A	ENSP00000417955:p.Ser128Asn	119.0	0.0	.		137.0	6.0	.	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	hg19	CCDS42718.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.408008	0.83340	.	.	ENSG00000168658	ENST00000435344;ENST00000477737	T;T	0.38401	1.14;1.14	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.53786	0.1818	M	0.70842	2.15	0.80722	D	1	D;D	0.58970	0.966;0.984	B;P	0.55824	0.376;0.785	T	0.52749	-0.8534	10	0.54805	T	0.06	.	15.466	0.75400	0.0:0.1391:0.8609:0.0	.	128;128	Q502W6;Q502W6-8	VWA3B_HUMAN;.	N	128	ENSP00000401959:S128N;ENSP00000417955:S128N	ENSP00000411168:S128N	S	+	2	0	VWA3B	98102499	1.000000	0.71417	0.983000	0.44433	0.975000	0.68041	5.358000	0.66064	2.865000	0.98341	0.655000	0.94253	AGC	.	.	.	none		0.483	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992		A	98736067	G	A	98736067	3	1	259	1	0	0	0	0	1	0	0	0	17253	971	34	2	393	2	VWA3B	2	98736067	Missense_Mutation	SNP	G	TCGA-UZ-A9PM-01A-21D-A382-10	36636448	98736067	144463306	9	16118											
DNAH7	56171	hgsc.bcm.edu	37	chr2	196825319	196825319	+	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	gcagacatggcctcccagtgCctggggcgcaaaccaggatt	9	6	13	13	1	0	1	0	0	0	1	1	2	1	2	4	4	2	2	4	4	1	1			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr2:196825319C>T	ENST00000312428.6	-	18	2656	c.2556G>A	c.(2554-2556)agG>agA	p.R852R		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	852	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						CCTCCCAGTGCCTGGGGCGCA	0.443																																					p.R852R		Atlas-SNP	.											.	DNAH7	512	.	0			c.G2556A						PASS	.						118	120	119					2																	196825319		1932	4123	6055	SO:0001819	synonymous_variant	56171	exon18			CCAGTGCCTGGGG	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.2556G>A	chr2.hg19:g.196825319C>T		88.0	0.0	.		73.0	12.0	.	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	hg19	CCDS42794.1																																																																																			.	.	.	none		0.443	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		T	196825319	C	T	196825319	2	4	259	1	0	0	0	0	0	0	0	1	4608	738	26	2		2	DNAH7	2	196825319	Silent	SNP	C	TCGA-UZ-A9PM-01A-21D-A382-10	98089252	196825319	46374054	10	16119											
ZFYVE20	64145	hgsc.bcm.edu	37	chr3	15132018	15132018	+	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	tctcgtttcaacaacctgtcCtttgcttttttagccttctg	5	19	5	12	1	3	0	1	0	2	0	5	0	4	0	3	0	4	2	3	0	3	6			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr3:15132018C>G	ENST00000253699.3	-	5	790	c.177G>C	c.(175-177)aaG>aaC	p.K59N	ZFYVE20_ENST00000435849.3_Missense_Mutation_p.K59N|ZFYVE20_ENST00000476527.2_Missense_Mutation_p.K59N|ZFYVE20_ENST00000449964.2_5'UTR	NM_022340.2	NP_071735.2	Q9H1K0	RBNS5_HUMAN	zinc finger, FYVE domain containing 20	59					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						ACAACCTGTCCTTTGCTTTTT	0.423																																					p.K59N		Atlas-SNP	.											.	ZFYVE20	61	.	0			c.G177C						PASS	.						193	166	175					3																	15132018		2203	4300	6503	SO:0001583	missense	64145	exon5			CCTGTCCTTTGCT	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.177G>C	chr3.hg19:g.15132018C>G	ENSP00000253699:p.Lys59Asn	94.0	0.0	.		109.0	15.0	.	NM_022340	B4DWY8|C9J4P5|Q3KP30|Q59EY8|Q8NAQ1	Missense_Mutation	SNP	ENST00000253699.3	hg19	CCDS2623.1	.	.	.	.	.	.	.	.	.	.	C	19.89	3.911580	0.72983	.	.	ENSG00000131381	ENST00000253699;ENST00000476527;ENST00000435849	T;T;T	0.73469	0.44;0.44;-0.75	5.7	3.93	0.45458	.	0.048887	0.85682	D	0.000000	T	0.81064	0.4745	L	0.56769	1.78	0.46609	D	0.999126	P;D	0.76494	0.718;0.999	B;D	0.68765	0.109;0.96	T	0.79907	-0.1605	10	0.54805	T	0.06	-39.4085	9.7229	0.40313	0.0:0.7889:0.0:0.2111	.	59;59	B4DWY8;Q9H1K0	.;RBNS5_HUMAN	N	59	ENSP00000253699:K59N;ENSP00000422551:K59N;ENSP00000391039:K59N	ENSP00000253699:K59N	K	-	3	2	ZFYVE20	15107022	1.000000	0.71417	1.000000	0.80357	0.810000	0.45777	2.534000	0.45676	0.774000	0.33427	-0.237000	0.12165	AAG	.	.	.	none		0.423	ZFYVE20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252102.2	NM_022340		G	15132018	C	G	15132018	3	3	259	1	0	0	0	0	1	0	0	0	17678	680	24	4	2217	4	ZFYVE20	3	15132018	Missense_Mutation	SNP	C	TCGA-UZ-A9PM-01A-21D-A382-10		15132018	182890412	11	16120											
PARP14	54625	hgsc.bcm.edu	37	chr3	122437700	122437701	+	Missense_Mutation	DNP	GA	GA	AT																															gagaaaagaaaaaaacagttGatgtcaaaattaatcatcgg																										TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr3:122437700_122437701GA>AT	ENST00000474629.2	+	14	4968_4969	c.4702_4703GA>AT	c.(4702-4704)GAt>ATt	p.D1568I	PARP14_ENST00000475640.1_3'UTR	NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1568	WWE. {ECO:0000255|PROSITE- ProRule:PRU00248}.				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)		AAAAACAGTTGATGTCAAAATT	0.376																																					p.D1568N|p.D1568V		Atlas-SNP	.											.	PARP14	242	.	0			c.G4702A|c.A4703T						PASS	.																																			SO:0001583	missense	54625	exon14			ACAGTTGATGTCA|CAGTTGATGTCAA	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	Exception_encountered	chr3.hg19:g.122437700_122437701delinsAT	ENSP00000418194:p.Asp1568Ile	113.0|111.0	0.0	.		163.0|161.0	25.0	.	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	hg19	CCDS46894.1																																																																																			.	.	.	none		0.376	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		AT	122437701	GA	AT	122437700	3	1	259	1	0	0	0	0	1	0	0	0	11465	1290	45	2	4756	2	PARP14	3	122437700	Missense_Mutation	DNP	GA	TCGA-UZ-A9PM-01A-21D-A382-10	107305682	122437700	75584730	12	16121											
PLXND1	23129	hgsc.bcm.edu	37	chr3	129285459	129285459	+	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	gggcagcacgtaacgctcttCataaagggaggaacactgca	13	6	12	10	2	2	0	1	0	1	0	2	2	2	2	0	3	4	5	0	3	4	3			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr3:129285459C>T	ENST00000324093.4	-	23	4280	c.4102G>A	c.(4102-4104)Gaa>Aaa	p.E1368K	PLXND1_ENST00000393239.1_Missense_Mutation_p.E1368K	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1368					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						TAACGCTCTTCATAAAGGGAG	0.617																																					p.E1368K	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.G4102A						PASS	.						69	62	64					3																	129285459		2203	4300	6503	SO:0001583	missense	23129	exon23			GCTCTTCATAAAG	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.4102G>A	chr3.hg19:g.129285459C>T	ENSP00000317128:p.Glu1368Lys	44.0	0.0	.		53.0	18.0	.	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	hg19	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.755199	0.89843	.	.	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.35048	1.38;1.33	4.97	4.09	0.47781	Plexin, cytoplasmic RasGAP domain (1);	35.924200	0.00757	U	0.001109	T	0.51261	0.1664	L	0.40543	1.245	0.58432	D	0.999992	D	0.53619	0.961	P	0.54629	0.757	T	0.07539	-1.0767	10	0.87932	D	0	.	13.5873	0.61940	0.0:0.924:0.0:0.076	.	1368	Q9Y4D7	PLXD1_HUMAN	K	1368	ENSP00000317128:E1368K;ENSP00000376931:E1368K	ENSP00000317128:E1368K	E	-	1	0	PLXND1	130768149	1.000000	0.71417	0.994000	0.49952	0.919000	0.55068	4.423000	0.59861	1.061000	0.40601	0.563000	0.77884	GAA	.	.	.	none		0.617	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103		T	129285459	C	T	129285459	3	4	259	1	0	0	0	0	1	0	0	0	12134	835	29	2	1731	2	PLXND1	3	129285459	Missense_Mutation	SNP	C	TCGA-UZ-A9PM-01A-21D-A382-10	6847759	129285459	68736971	13	16122											
PLOD2	5352	hgsc.bcm.edu	37	chr3	145841934	145841934	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atataccataccttcacagtAtaattgaaatatttggctga	15	14	5	7	0	1	2	1	2	0	0	1	2	1	2	2	1	2	2	2	1	7	9			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr3:145841934A>G	ENST00000360060.3	-	2	369	c.192T>C	c.(190-192)taT>taC	p.Y64Y	PLOD2_ENST00000494950.1_Silent_p.Y9Y|PLOD2_ENST00000282903.5_Silent_p.Y64Y	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	64					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)	CCTTCACAGTATAATTGAAAT	0.328																																					p.Y64Y		Atlas-SNP	.											.	PLOD2	81	.	0			c.T192C						PASS	.						143	139	140					3																	145841934		2202	4300	6502	SO:0001819	synonymous_variant	5352	exon2			CACAGTATAATTG	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.192T>C	chr3.hg19:g.145841934A>G		57.0	0.0	.		72.0	11.0	.	NM_182943	B3KWS3|Q59ED2|Q8N170	Silent	SNP	ENST00000360060.3	hg19	CCDS3131.1																																																																																			.	.	.	none		0.328	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935		G	145841934	A	G	145841934	2	3	259	1	0	0	0	0	0	0	0	1	12109	456	16	3		3	PLOD2	3	145841934	Silent	SNP	A	TCGA-UZ-A9PM-01A-21D-A382-10	16556475	145841934	52180496	14	16123											
OTUD4	54726	hgsc.bcm.edu	37	chr4	146071985	146071985	+	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	ttttgtccagaagtggaaggTtttttcatcttcttccctga	7	18	8	8	0	3	2	1	1	2	1	5	3	5	3	2	2	0	1	2	2	2	7			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr4:146071985T>A	ENST00000447906.2	-	12	1228	c.1041A>T	c.(1039-1041)aaA>aaT	p.K347N	OTUD4_ENST00000455611.2_5'UTR|Y_RNA_ENST00000459374.1_RNA|OTUD4_ENST00000454497.2_Missense_Mutation_p.K282N			Q01804	OTUD4_HUMAN	OTU deubiquitinase 4	347					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)					AAGTGGAAGGTTTTTTCATCT	0.433																																					p.K282N		Atlas-SNP	.											.	OTUD4	120	.	0			c.A846T						PASS	.						80	75	77					4																	146071985		2203	4300	6503	SO:0001583	missense	54726	exon12			GGAAGGTTTTTTC		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.1041A>T	chr4.hg19:g.146071985T>A	ENSP00000395487:p.Lys347Asn	95.0	0.0	.		86.0	18.0	.	NM_001102653	B4DYS4|Q147U2|Q1ZYK1|Q6PG39|Q96MQ5|Q9NT94|Q9UPV6	Missense_Mutation	SNP	ENST00000447906.2	hg19		.	.	.	.	.	.	.	.	.	.	T	20.7	4.030197	0.75504	.	.	ENSG00000164164	ENST00000454497;ENST00000447906;ENST00000514973	T;T;T	0.34667	1.35;1.35;1.4	5.84	0.973	0.19710	.	0.000000	0.85682	D	0.000000	T	0.47154	0.1430	L	0.55481	1.735	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.77557	0.99;0.978	T	0.30563	-0.9974	10	0.27785	T	0.31	-23.5677	8.8141	0.34985	0.0:0.4241:0.0:0.5759	.	347;346	G3V0I6;Q01804	.;OTUD4_HUMAN	N	282;347;281	ENSP00000409279:K282N;ENSP00000395487:K347N;ENSP00000425972:K281N	ENSP00000395487:K347N	K	-	3	2	OTUD4	146291435	0.864000	0.29904	0.992000	0.48379	0.995000	0.86356	-0.169000	0.09911	0.491000	0.27793	0.533000	0.62120	AAA	.	.	.	none		0.433	OTUD4-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000365117.2	NM_017493		A	146071985	T	A	146071985	3	1	259	1	0	0	0	0	1	0	0	0	11321	1722	60	5	2343	5	OTUD4	4	146071985	Missense_Mutation	SNP	T	TCGA-UZ-A9PM-01A-21D-A382-10		146071985	45082291	15	16124											
RXFP1	59350	hgsc.bcm.edu	37	chr4	159568062	159568062	+	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	gtactcattgtcagcttgtaGgatctttggccattctgtcc	6	16	9	10	0	4	0	2	0	2	0	5	1	5	1	2	2	2	3	2	2	2	6			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr4:159568062G>C	ENST00000307765.5	+	16	1716	c.1465G>C	c.(1465-1467)Gga>Cga	p.G489R	RXFP1_ENST00000460056.2_Missense_Mutation_p.G408R|RXFP1_ENST00000343542.5_Missense_Mutation_p.G441R|RXFP1_ENST00000470033.1_Missense_Mutation_p.G456R|RXFP1_ENST00000448688.2_Missense_Mutation_p.G384R	NM_001253727.1|NM_001253728.1|NM_001253730.1|NM_001253732.1|NM_001253733.1|NM_021634.3	NP_001240656.1|NP_001240657.1|NP_001240659.1|NP_001240661.1|NP_001240662.1|NP_067647.2	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1	489					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|lung connective tissue development (GO:0060427)|nipple morphogenesis (GO:0060658)|parturition (GO:0007567)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)	p.G489R(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|liver(2)|lung(22)|prostate(1)|skin(10)	49	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)		TCAGCTTGTAGGATCTTTGGC	0.388																																					p.G516R		Atlas-SNP	.											RXFP1,NS,carcinoma,-1,1	RXFP1	98	.	1	Substitution - Missense(1)	lung(1)	c.G1546C						PASS	.						138	128	131					4																	159568062		1915	4142	6057	SO:0001583	missense	59350	exon16			CTTGTAGGATCTT	AF190500	CCDS43276.1, CCDS58929.1, CCDS58930.1, CCDS75204.1, CCDS75205.1, CCDS75206.1	4q31.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000171509	ENSG00000171509		"GPCR / Class A : Relaxin family peptide receptors"	19718	protein-coding gene	gene with protein product		606654	"leucine-rich repeat-containing G protein-coupled receptor 7"	LGR7		15956688, 16507880	Standard	NM_021634		Approved	RXFPR1	uc003ipz.3	Q9HBX9	OTTHUMG00000149973	ENST00000307765.5:c.1465G>C	chr4.hg19:g.159568062G>C	ENSP00000303248:p.Gly489Arg	127.0	1.0	.		108.0	16.0	.	NM_001253727	B4DHD1|B4DTV2|Q2M215|Q3KU24|Q3KU25|Q3KU26	Missense_Mutation	SNP	ENST00000307765.5	hg19	CCDS43276.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.646174	0.87958	.	.	ENSG00000171509	ENST00000460056;ENST00000307765;ENST00000448688;ENST00000343542;ENST00000470033;ENST00000440678	T;T;T;T;T	0.39406	1.08;1.08;1.08;1.08;1.08	5.74	5.74	0.90152	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.73202	0.3557	M	0.90814	3.15	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	0.998;1.0;1.0;0.997;0.996;0.996;0.998;1.0	T	0.78316	-0.2251	10	0.87932	D	0	.	19.9294	0.97114	0.0:0.0:1.0:0.0	.	500;516;384;441;456;408;359;489	B3KV27;B4DGP2;B4DHD1;Q9HBX9-4;Q9HBX9-2;E9PCA3;Q59H16;Q9HBX9	.;.;.;.;.;.;.;RXFP1_HUMAN	R	408;489;384;441;456;359	ENSP00000423306:G408R;ENSP00000303248:G489R;ENSP00000414885:G384R;ENSP00000345889:G441R;ENSP00000420712:G456R	ENSP00000303248:G489R	G	+	1	0	RXFP1	159787512	1.000000	0.71417	0.624000	0.29186	0.684000	0.39900	9.777000	0.99008	2.701000	0.92244	0.650000	0.86243	GGA	.	.	.	none		0.388	RXFP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314865.1	NM_021634		C	159568062	G	C	159568062	3	2	259	1	0	0	0	0	1	0	0	0	13772	1001	35	4	1527	4	RXFP1	4	159568062	Missense_Mutation	SNP	G	TCGA-UZ-A9PM-01A-21D-A382-10	13496077	159568062	31586214	16	16125											
FNIP2	57600	hgsc.bcm.edu	37	chr4	159690401	159690401	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccagaagctcttcaacaaaAggggcagcagcggcagctcc	12	5	11	13	1	2	1	1	0	1	1	4	1	4	1	2	3	5	5	2	3	4	1			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr4:159690401A>G	ENST00000264433.6	+	1	112	c.37A>G	c.(37-39)Agg>Ggg	p.R13G		NM_020840.1	NP_065891.1	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	13					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)		CTTCAACAAAAGGGGCAGCAG	0.741																																					p.R13G		Atlas-SNP	.											.	FNIP2	90	.	0			c.A37G						PASS	.						3	4	4					4																	159690401		1502	3576	5078	SO:0001583	missense	57600	exon1			AACAAAAGGGGCA	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.37A>G	chr4.hg19:g.159690401A>G	ENSP00000264433:p.Arg13Gly	63.0	0.0	.		86.0	4.0	.	NM_020840	Q05DC3|Q96I31|Q9H994	Missense_Mutation	SNP	ENST00000264433.6	hg19	CCDS47155.1	.	.	.	.	.	.	.	.	.	.	A	15.71	2.912811	0.52439	.	.	ENSG00000052795	ENST00000264433	T	0.27402	1.67	2.95	2.95	0.34219	.	.	.	.	.	T	0.26231	0.0640	L	0.29908	0.895	0.80722	D	1	P	0.46142	0.873	P	0.46659	0.523	T	0.02766	-1.1113	9	0.52906	T	0.07	.	8.6275	0.33899	1.0:0.0:0.0:0.0	.	13	Q9P278	FNIP2_HUMAN	G	13	ENSP00000264433:R13G	ENSP00000264433:R13G	R	+	1	2	FNIP2	159909851	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	3.809000	0.55606	1.210000	0.43336	0.459000	0.35465	AGG	.	.	.	none		0.741	FNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366602.1	NM_020840		G	159690401	A	G	159690401	3	3	259	1	0	0	0	0	1	0	0	0	5983	63	3	3	39	3	FNIP2	4	159690401	Missense_Mutation	SNP	A	TCGA-UZ-A9PM-01A-21D-A382-10	122339	159690401	31463875	17	16126											
KCTD16	57528	hgsc.bcm.edu	37	chr5	143586905	143586905	+	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	aagtctttggagaaactttgAatgaaagcagagaccctgat	15	10	10	6	0	1	5	0	3	1	2	1	7	1	5	1	1	2	1	1	1	4	2			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr5:143586905A>T	ENST00000507359.3	+	2	1719	c.628A>T	c.(628-630)Aat>Tat	p.N210Y	KCTD16_ENST00000512467.1_Missense_Mutation_p.N210Y	NM_020768.3	NP_065819.1	Q68DU8	KCD16_HUMAN	potassium channel tetramerization domain containing 16	210					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)				large_intestine(5)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	21		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			AGAAACTTTGAATGAAAGCAG	0.463																																					p.N210Y		Atlas-SNP	.											.	KCTD16	70	.	0			c.A628T						PASS	.						60	65	63					5																	143586905		2203	4300	6503	SO:0001583	missense	57528	exon3			ACTTTGAATGAAA	AB037738	CCDS34260.1	5q32	2013-06-20	2013-06-20		ENSG00000183775	ENSG00000183775			29244	protein-coding gene	gene with protein product		613423	"potassium channel tetramerisation domain containing 16"			10718198	Standard	NM_020768		Approved	KIAA1317	uc003lnm.1	Q68DU8	OTTHUMG00000163172	ENST00000507359.3:c.628A>T	chr5.hg19:g.143586905A>T	ENSP00000426548:p.Asn210Tyr	149.0	0.0	.		167.0	31.0	.	NM_020768	Q9P2M9	Missense_Mutation	SNP	ENST00000507359.3	hg19	CCDS34260.1	.	.	.	.	.	.	.	.	.	.	A	17.29	3.352573	0.61293	.	.	ENSG00000183775	ENST00000512467;ENST00000507359	T;T	0.61859	0.07;0.07	5.69	4.51	0.55191	.	0.043674	0.85682	D	0.000000	T	0.77445	0.4131	M	0.85945	2.785	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.80589	-0.1315	10	0.87932	D	0	.	12.9381	0.58327	0.8645:0.1355:0.0:0.0	.	210	Q68DU8	KCD16_HUMAN	Y	210	ENSP00000424151:N210Y;ENSP00000426548:N210Y	ENSP00000426548:N210Y	N	+	1	0	KCTD16	143567098	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.281000	0.95811	0.968000	0.38212	0.459000	0.35465	AAT	.	.	.	none		0.463	KCTD16-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371898.3	XM_098368		T	143586905	A	T	143586905	3	4	259	1	0	0	0	0	1	0	0	0	8110	246	9	5	630	5	KCTD16	5	143586905	Missense_Mutation	SNP	A	TCGA-UZ-A9PM-01A-21D-A382-10		143586905	37328355	18	16127											
SFXN1	94081	hgsc.bcm.edu	37	chr5	174937182	174937182	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtcgtcaattacaccaacAgaagtggagacgcacccctc	12	6	8	15	3	1	2	1	0	0	2	3	3	1	2	4	1	2	1	4	1	4	1			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr5:174937182A>G	ENST00000321442.5	+	4	660	c.406A>G	c.(406-408)Aga>Gga	p.R136G	SFXN1_ENST00000502393.1_Missense_Mutation_p.R136G	NM_022754.5	NP_073591.2	Q9H9B4	SFXN1_HUMAN	sideroflexin 1	136					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)			TTACACCAACAGAAGTGGAGA	0.488																																					p.R136G		Atlas-SNP	.											.	SFXN1	23	.	0			c.A406G						PASS	.						145	111	122					5																	174937182		2203	4300	6503	SO:0001583	missense	94081	exon4			ACCAACAGAAGTG	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.406A>G	chr5.hg19:g.174937182A>G	ENSP00000316905:p.Arg136Gly	79.0	0.0	.		105.0	18.0	.	NM_022754	B3KPW3|D3DQN2|Q9HA53	Missense_Mutation	SNP	ENST00000321442.5	hg19	CCDS4394.1	.	.	.	.	.	.	.	.	.	.	A	17.22	3.333836	0.60853	.	.	ENSG00000164466	ENST00000507017;ENST00000321442;ENST00000506963	T;T;T	0.38560	1.13;1.13;1.13	5.48	-0.0886	0.13672	.	0.000000	0.85682	D	0.000000	T	0.68568	0.3015	M	0.92691	3.335	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.992;1.0	T	0.72484	-0.4279	10	0.42905	T	0.14	-25.9016	14.118	0.65167	0.4683:0.5317:0.0:0.0	.	136;136	D6RFI0;Q9H9B4	.;SFXN1_HUMAN	G	136	ENSP00000420961:R136G;ENSP00000316905:R136G;ENSP00000421467:R136G	ENSP00000316905:R136G	R	+	1	2	SFXN1	174869788	0.997000	0.39634	0.478000	0.27316	0.523000	0.34469	0.631000	0.24568	-0.233000	0.09797	0.533000	0.62120	AGA	.	.	.	none		0.488	SFXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252980.2	NM_022754		G	174937182	A	G	174937182	3	3	259	1	0	0	0	0	1	0	0	0	14207	180	7	3	416	3	SFXN1	5	174937182	Missense_Mutation	SNP	A	TCGA-UZ-A9PM-01A-21D-A382-10	31350277	174937182	5978078	19	16128											
ZNF318	24149	hgsc.bcm.edu	37	chr6	43316086	43316086	+	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	ttggaggaggagtttgagaaCgatgacactttttctgggct	9	13	14	5	1	1	2	0	2	1	1	1	7	1	5	0	4	1	2	0	4	1	4			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr6:43316086C>T	ENST00000361428.2	-	6	3125	c.3048G>A	c.(3046-3048)tcG>tcA	p.S1016S	ZNF318_ENST00000318149.3_Silent_p.S1016S	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	1016					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)	p.S1016S(1)		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)			AGTTTGAGAACGATGACACTT	0.378																																					p.S1016S		Atlas-SNP	.											ZNF318,NS,carcinoma,-1,1	ZNF318	175	.	1	Substitution - coding silent(1)	lung(1)	c.G3048A						PASS	.						214	219	217					6																	43316086		2203	4300	6503	SO:0001819	synonymous_variant	24149	exon6			TGAGAACGATGAC	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.3048G>A	chr6.hg19:g.43316086C>T		109.0	0.0	.		126.0	18.0	.	NM_014345	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Silent	SNP	ENST00000361428.2	hg19	CCDS4895.2																																																																																			.	.	.	none		0.378	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345		T	43316086	C	T	43316086	2	4	259	1	0	0	0	0	0	0	0	1	17848	523	19	1		1	ZNF318	6	43316086	Silent	SNP	C	TCGA-UZ-A9PM-01A-21D-A382-10		43316086	127798981	20	16129											
AP4M1	9179	hgsc.bcm.edu	37	chr7	99702504	99702504	+	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	ccctgcctctcagggatcccTgctgaaggtggatgtgcagg	6	9	14	12	0	1	1	1	1	1	0	3	3	2	3	3	4	3	2	3	4	1	0			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr7:99702504T>A	ENST00000359593.4	+	8	772	c.614T>A	c.(613-615)cTg>cAg	p.L205Q	MCM7_ENST00000303887.5_5'Flank|MCM7_ENST00000343023.6_5'Flank|AP4M1_ENST00000429084.1_Missense_Mutation_p.L212Q|AP4M1_ENST00000421755.1_Missense_Mutation_p.L205Q|AP4M1_ENST00000422582.1_Missense_Mutation_p.L77Q	NM_004722.3	NP_004713.2	O00189	AP4M1_HUMAN	adaptor-related protein complex 4, mu 1 subunit	205	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)					CAGGGATCCCTGCTGAAGGTG	0.567																																					p.L205Q	Pancreas(174;1182 2812 29595 49511)	Atlas-SNP	.											AP4M1,NS,carcinoma,0,1	AP4M1	39	.	0			c.T614A						PASS	.						114	112	113					7																	99702504		2203	4300	6503	SO:0001583	missense	9179	exon8			GATCCCTGCTGAA	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.614T>A	chr7.hg19:g.99702504T>A	ENSP00000352603:p.Leu205Gln	102.0	1.0	.		115.0	29.0	.	NM_004722	D6W5U1|Q8WV65|Q9UHK9	Missense_Mutation	SNP	ENST00000359593.4	hg19	CCDS5685.1	.	.	.	.	.	.	.	.	.	.	T	14.92	2.679179	0.47886	.	.	ENSG00000221838	ENST00000438383;ENST00000429084;ENST00000359593;ENST00000439416;ENST00000421755;ENST00000422582	T;T;T;T;T;T	0.24350	1.86;1.86;1.86;1.86;1.86;1.86	4.53	2.09	0.27110	Clathrin adaptor, mu subunit, C-terminal (3);	0.158542	0.42548	D	0.000695	T	0.30510	0.0767	L	0.49350	1.555	0.41749	D	0.989653	D;P;P;P	0.62365	0.991;0.792;0.76;0.466	P;B;P;P	0.54544	0.755;0.42;0.51;0.51	T	0.05869	-1.0859	10	0.87932	D	0	-40.5241	4.6856	0.12755	0.1682:0.0948:0.0:0.737	.	161;157;212;205	C9JMG3;B4DKN7;C9JC87;O00189	.;.;.;AP4M1_HUMAN	Q	137;212;205;161;205;77	ENSP00000401613:L137Q;ENSP00000403663:L212Q;ENSP00000352603:L205Q;ENSP00000414286:L161Q;ENSP00000412185:L205Q;ENSP00000406676:L77Q	ENSP00000352603:L205Q	L	+	2	0	AP4M1	99540440	1.000000	0.71417	0.278000	0.24718	0.652000	0.38707	3.109000	0.50345	0.245000	0.21373	0.459000	0.35465	CTG	.	.	.	none		0.567	AP4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336772.4	NM_004722		A	99702504	T	A	99702504	3	1	259	1	0	0	0	0	1	0	0	0	753	1580	55	5	644	5	AP4M1	7	99702504	Missense_Mutation	SNP	T	TCGA-UZ-A9PM-01A-21D-A382-10		99702504	59436159	21	16130											
ACHE	43	hgsc.bcm.edu	37	chr7	100488697	100488697	+	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	1	0	0	0	0	0	0	0	0	tgaagcctgggcaggtgctgGgagcctccgaggctaggggg	6	6	20	9	1	0	1	0	1	0	0	1	3	1	2	3	6	3	3	3	6	2	1			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr7:100488697G>T	ENST00000412389.1	-	3	1879				ACHE_ENST00000428317.1_Intron|ACHE_ENST00000419336.2_Intron|ACHE_ENST00000241069.5_Intron|ACHE_ENST00000411582.1_Missense_Mutation_p.P579H|UFSP1_ENST00000388761.2_5'Flank|ACHE_ENST00000302913.4_Missense_Mutation_p.P579H			P22303	ACES_HUMAN	acetylcholinesterase (Yt blood group)						acetylcholine catabolic process (GO:0006581)|acetylcholine catabolic process in synaptic cleft (GO:0001507)|amyloid precursor protein metabolic process (GO:0042982)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|choline metabolic process (GO:0019695)|DNA replication (GO:0006260)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|negative regulation of synaptic transmission, cholinergic (GO:0032223)|nervous system development (GO:0007399)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter receptor biosynthetic process (GO:0045212)|osteoblast development (GO:0002076)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of protein secretion (GO:0050714)|protein tetramerization (GO:0051262)|receptor internalization (GO:0031623)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of receptor recycling (GO:0001919)|response to wounding (GO:0009611)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	acetylcholine binding (GO:0042166)|acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|cholinesterase activity (GO:0004104)|collagen binding (GO:0005518)|hydrolase activity (GO:0016787)|laminin binding (GO:0043236)|protein homodimerization activity (GO:0042803)|serine hydrolase activity (GO:0017171)			large_intestine(3)|lung(7)|skin(3)|urinary_tract(3)	16	Lung NSC(181;0.041)|all_lung(186;0.0581)				Ambenonium(DB01122)|Choline(DB00122)|Decamethonium(DB01245)|Demecarium(DB00944)|Dipivefrin(DB00449)|Donepezil(DB00843)|Edrophonium(DB01010)|Ephedrine(DB01364)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Minaprine(DB00805)|Neostigmine(DB01400)|Physostigmine(DB00981)|Pralidoxime(DB00733)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Tubocurarine(DB01199)	GCAGGTGCTGGGAGCCTCCGA	0.711																																					p.P579H		Atlas-SNP	.											.	ACHE	80	.	0			c.C1736A						PASS	.						6	6	6					7																	100488697		2052	4096	6148	SO:0001627	intron_variant	43	exon5			GTGCTGGGAGCCT		CCDS5709.1, CCDS5710.1, CCDS64736.1	7q22	2014-07-19	2014-01-02		ENSG00000087085	ENSG00000087085	3.1.1.7	"Blood group antigens"	108	protein-coding gene	gene with protein product	"Yt blood group"	100740	"acetylcholinesterase (YT blood group)", "acetylcholinesterase (Yt blood group)", "acetylcholinesterase"	YT		1380483	Standard	XM_005250357		Approved		uc003uxe.3	P22303	OTTHUMG00000157033	ENST00000412389.1:c.1723+92C>A	chr7.hg19:g.100488697G>T		203.0	0.0	.		253.0	23.0	.	NM_015831	A4D2E2|B7ZKZ0|D6W5X7|Q16169|Q29S23|Q2M324|Q504V3|Q53F46|Q86TM9|Q86YX9|Q9BXP7	Missense_Mutation	SNP	ENST00000412389.1	hg19	CCDS5709.1	.	.	.	.	.	.	.	.	.	.	G	18.03	3.531760	0.64972	.	.	ENSG00000087085	ENST00000302913;ENST00000411582	T;T	0.66638	-0.22;-0.22	4.33	4.33	0.51752	.	.	.	.	.	T	0.55909	0.1950	N	0.08118	0	0.23238	N	0.998064	D	0.58268	0.982	P	0.50490	0.642	T	0.52426	-0.8577	9	0.62326	D	0.03	.	12.6808	0.56920	0.0:0.0:1.0:0.0	.	579	P22303-2	.	H	579	ENSP00000303211:P579H;ENSP00000404865:P579H	ENSP00000303211:P579H	P	-	2	0	ACHE	100326633	1.000000	0.71417	0.993000	0.49108	0.842000	0.47809	2.750000	0.47500	2.117000	0.64856	0.448000	0.29417	CCC	.	.	.	none		0.711	ACHE-013	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347201.1	NM_015831		T	100488697	G	T	100488697	1	4	259	0	1	0	0	0	0	0	0	0	141	1232	43	4		4	ACHE	7	100488697	Intron	SNP	G	TCGA-UZ-A9PM-01A-21D-A382-10	786193	100488697	58649966	22	16131											
CUX1	1523	hgsc.bcm.edu	37	chr7	101882669	101882669	+	Missense_Mutation	SNP	A	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	accgccctctgtcggcaccgAgtacagccagggcgccagcc	7	4	12	18	4	1	0	0	0	1	0	2	1	1	0	6	2	3	2	6	2	1	1			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr7:101882669A>C	ENST00000292535.7	+	23	3730	c.3692A>C	c.(3691-3693)gAg>gCg	p.E1231A	CUX1_ENST00000360264.3_Missense_Mutation_p.E1242A|CUX1_ENST00000556210.1_Missense_Mutation_p.E1073A|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000292538.4_Intron|AC005088.1_ENST00000580604.1_RNA|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000550008.2_Missense_Mutation_p.E1175A|CUX1_ENST00000546411.2_Missense_Mutation_p.E1129A|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000549414.2_Missense_Mutation_p.E1209A|CUX1_ENST00000560541.1_Intron	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	1231					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						GTCGGCACCGAGTACAGCCAG	0.647																																					p.E1242A		Atlas-SNP	.											.	CUX1	253	.	0			c.A3725C						PASS	.						26	29	28					7																	101882669		2203	4300	6503	SO:0001583	missense	1523	exon23			GCACCGAGTACAG	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.3692A>C	chr7.hg19:g.101882669A>C	ENSP00000292535:p.Glu1231Ala	81.0	0.0	.		96.0	24.0	.	NM_001202543	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000292535.7	hg19	CCDS5721.1	.	.	.	.	.	.	.	.	.	.	A	16.06	3.015092	0.54468	.	.	ENSG00000257923	ENST00000360264;ENST00000292535;ENST00000549414;ENST00000550008;ENST00000546411;ENST00000556210	T;T;T;T;T;T	0.62639	0.01;0.02;0.01;0.01;0.01;0.02	5.04	5.04	0.67666	.	0.168540	0.50627	D	0.000107	T	0.48714	0.1515	N	0.19112	0.55	0.80722	D	1	B;B	0.22211	0.039;0.066	B;B	0.20767	0.008;0.031	T	0.47249	-0.9132	10	0.51188	T	0.08	-14.4248	14.7647	0.69629	1.0:0.0:0.0:0.0	.	1231;1242	P39880;P39880-3	CUX1_HUMAN;.	A	1242;1231;1209;1175;1129;1073	ENSP00000353401:E1242A;ENSP00000292535:E1231A;ENSP00000446630:E1209A;ENSP00000447373:E1175A;ENSP00000450125:E1129A;ENSP00000451558:E1073A	ENSP00000292535:E1231A	E	+	2	0	CUX1	101669389	1.000000	0.71417	0.988000	0.46212	0.885000	0.51271	7.431000	0.80335	1.902000	0.55061	0.459000	0.35465	GAG	.	.	.	none		0.647	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913		C	101882669	A	C	101882669	3	2	259	1	0	0	0	0	1	0	0	0	4066	304	11	5	3849	5	CUX1	7	101882669	Missense_Mutation	SNP	A	TCGA-UZ-A9PM-01A-21D-A382-10	1393972	101882669	57255994	23	16132											
EFCAB1	79645	hgsc.bcm.edu	37	chr8	49644024	49644024	+	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	tactcctcccaccaagtcatAaaaaagctttataagacagt	16	10	4	11	0	1	1	1	0	0	1	3	1	3	1	3	0	2	1	3	0	7	5	rs201126478		TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr8:49644024A>T	ENST00000262103.3	-	2	177	c.97T>A	c.(97-99)Tat>Aat	p.Y33N	EFCAB1_ENST00000521002.1_Intron|EFCAB1_ENST00000433756.1_Intron|EFCAB1_ENST00000523092.1_Intron	NM_024593.3	NP_078869.1	Q9HAE3	EFCB1_HUMAN	EF-hand calcium binding domain 1	33							calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|urinary_tract(2)	14		all_epithelial(80;0.0134)|Lung NSC(129;0.0207)|all_lung(136;0.0464)				ACCAAGTCATAAAAAAGCTTT	0.328																																					p.Y33N		Atlas-SNP	.											.	EFCAB1	27	.	0			c.T97A						PASS	.						77	73	75					8																	49644024		2203	4300	6503	SO:0001583	missense	79645	exon2			AGTCATAAAAAAG		CCDS6145.1, CCDS47853.1	8q11.21	2013-01-10			ENSG00000034239	ENSG00000034239		"EF-hand domain containing"	25678	protein-coding gene	gene with protein product						12477932	Standard	NM_024593		Approved	FLJ11767	uc003xqo.2	Q9HAE3	OTTHUMG00000164203	ENST00000262103.3:c.97T>A	chr8.hg19:g.49644024A>T	ENSP00000262103:p.Tyr33Asn	118.0	0.0	.		93.0	15.0	.	NM_024593	B4DSB4|E7EVN7	Missense_Mutation	SNP	ENST00000262103.3	hg19	CCDS6145.1	.	.	.	.	.	.	.	.	.	.	A	1.323	-0.598936	0.03744	.	.	ENSG00000034239	ENST00000262103;ENST00000450553	T	0.66638	-0.22	4.77	3.61	0.41365	EF-hand-like domain (1);	0.212638	0.48767	D	0.000174	T	0.44371	0.1290	N	0.17082	0.46	0.36437	D	0.865288	B	0.06786	0.001	B	0.04013	0.001	T	0.36792	-0.9733	10	0.24483	T	0.36	.	6.1507	0.20310	0.8034:0.0:0.1966:0.0	.	33	Q9HAE3	EFCB1_HUMAN	N	33	ENSP00000262103:Y33N	ENSP00000262103:Y33N	Y	-	1	0	EFCAB1	49806577	1.000000	0.71417	0.810000	0.32431	0.051000	0.14879	2.404000	0.44539	0.957000	0.37930	0.528000	0.53228	TAT	.	A|0.999;G|0.001	.	alt		0.328	EFCAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377778.1	NM_024593		T	49644024	A	T	49644024	3	4	259	1	0	0	0	0	1	0	0	0	4935	362	13	5	558	5	EFCAB1	8	49644024	Missense_Mutation	SNP	A	TCGA-UZ-A9PM-01A-21D-A382-10		49644024	96719998	24	16133											
TMEM65	157378	hgsc.bcm.edu	37	chr8	125335567	125335567	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actactgttaaatacctgccAtagttgaaattcccaaaata	16	12	4	9	0	0	1	0	1	0	0	1	1	1	1	3	0	3	2	3	0	9	7			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr8:125335567A>G	ENST00000297632.6	-	4	1001	c.467T>C	c.(466-468)aTg>aCg	p.M156T		NM_194291.2	NP_919267.2	Q6PI78	TMM65_HUMAN	transmembrane protein 65	156						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				cervix(1)|endometrium(1)|large_intestine(2)|lung(1)|prostate(1)	6	Lung NSC(37;1.18e-11)|Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			AATACCTGCCATAGTTGAAAT	0.259																																					p.M156T		Atlas-SNP	.											.	TMEM65	14	.	0			c.T467C						PASS	.						29	33	31					8																	125335567		2168	4228	6396	SO:0001583	missense	157378	exon4			CCTGCCATAGTTG	BC032396	CCDS6348.1	8q24.13	2006-11-24			ENSG00000164983	ENSG00000164983			25203	protein-coding gene	gene with protein product						12477932	Standard	NM_194291		Approved		uc010mdl.3	Q6PI78	OTTHUMG00000165021	ENST00000297632.6:c.467T>C	chr8.hg19:g.125335567A>G	ENSP00000297632:p.Met156Thr	339.0	0.0	.		368.0	90.0	.	NM_194291	Q8N5G8|Q8WVK5	Missense_Mutation	SNP	ENST00000297632.6	hg19	CCDS6348.1	.	.	.	.	.	.	.	.	.	.	A	14.30	2.493605	0.44352	.	.	ENSG00000164983	ENST00000297632	T	0.56444	0.46	5.9	4.74	0.60224	.	0.000000	0.85682	D	0.000000	T	0.60932	0.2307	M	0.88450	2.955	0.54753	D	0.999989	B	0.18310	0.027	B	0.24701	0.055	T	0.62473	-0.6847	10	0.87932	D	0	.	11.9759	0.53091	0.9322:0.0:0.0678:0.0	.	156	Q6PI78	TMM65_HUMAN	T	156	ENSP00000297632:M156T	ENSP00000297632:M156T	M	-	2	0	TMEM65	125404748	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.854000	0.86942	1.054000	0.40438	0.472000	0.43445	ATG	.	.	.	none		0.259	TMEM65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381464.1	NM_194291		G	125335567	A	G	125335567	3	3	259	1	0	0	0	0	1	0	0	0	16206	217	8	3	271	3	TMEM65	8	125335567	Missense_Mutation	SNP	A	TCGA-UZ-A9PM-01A-21D-A382-10	75691543	125335567	21028455	25	16134											
COL27A1	85301	hgsc.bcm.edu	37	chr9	116931634	116931634	+	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	cccggcgcaattcctgtcctCcagcccccggcccacgagca	6	5	9	21	4	0	0	0	0	0	0	3	1	3	0	7	2	2	2	7	2	1	1			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr9:116931634C>T	ENST00000356083.3	+	3	2190	c.1799C>T	c.(1798-1800)tCc>tTc	p.S600F		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	600	Pro-rich.				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						TTCCTGTCCTCCAGCCCCCGG	0.652																																					p.S600F		Atlas-SNP	.											.	COL27A1	200	.	0			c.C1799T						PASS	.						54	64	60					9																	116931634		2203	4300	6503	SO:0001583	missense	85301	exon3			TGTCCTCCAGCCC	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.1799C>T	chr9.hg19:g.116931634C>T	ENSP00000348385:p.Ser600Phe	36.0	0.0	.		38.0	8.0	.	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	hg19	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	C	14.62	2.589711	0.46214	.	.	ENSG00000196739	ENST00000356083;ENST00000357257;ENST00000374106;ENST00000451716	D;D	0.91843	-2.63;-2.92	5.41	5.41	0.78517	.	.	.	.	.	D	0.93135	0.7814	L	0.32530	0.975	0.46678	D	0.999156	D;D	0.89917	0.997;1.0	D;D	0.80764	0.98;0.994	D	0.92621	0.6108	9	0.41790	T	0.15	.	14.6955	0.69118	0.0:1.0:0.0:0.0	.	600;547	Q8IZC6;Q5T1U7	CORA1_HUMAN;.	F	600;600;547;547	ENSP00000348385:S600F;ENSP00000391328:S547F	ENSP00000348385:S600F	S	+	2	0	COL27A1	115971455	1.000000	0.71417	0.999000	0.59377	0.929000	0.56500	3.639000	0.54339	2.537000	0.85549	0.563000	0.77884	TCC	.	.	.	none		0.652	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888		T	116931634	C	T	116931634	3	4	259	1	0	0	0	0	1	0	0	0	3687	855	30	2	1809	2	COL27A1	9	116931634	Missense_Mutation	SNP	C	TCGA-UZ-A9PM-01A-21D-A382-10		116931634	24281797	26	16135											
C5	727	hgsc.bcm.edu	37	chr9	123738998	123738998	+	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	ctgggttgaataaaagccacCtccatacctctgctcttctg	9	12	7	13	0	3	1	0	1	3	0	4	1	4	1	4	1	3	2	4	1	4	4			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr9:123738998C>T	ENST00000223642.1	-	29	3873	c.3844G>A	c.(3844-3846)Ggt>Agt	p.G1282S		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	1282					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)	TAAAAGCCACCTCCATACCTC	0.413																																					p.G1282S		Atlas-SNP	.											.	C5	124	.	0			c.G3844A						PASS	.						143	142	143					9																	123738998		2203	4300	6503	SO:0001583	missense	727	exon29			AGCCACCTCCATA	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.3844G>A	chr9.hg19:g.123738998C>T	ENSP00000223642:p.Gly1282Ser	152.0	0.0	.		157.0	38.0	.	NM_001735	Q14CJ0|Q27I61	Missense_Mutation	SNP	ENST00000223642.1	hg19	CCDS6826.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.789232	0.90367	.	.	ENSG00000106804	ENST00000223642	T	0.66995	-0.24	5.38	5.38	0.77491	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);	0.155990	0.56097	D	0.000025	D	0.87099	0.6093	H	0.94306	3.52	0.58432	D	0.999997	D	0.76494	0.999	D	0.79108	0.992	D	0.90526	0.4492	10	0.72032	D	0.01	.	18.1225	0.89576	0.0:1.0:0.0:0.0	.	1282	P01031	CO5_HUMAN	S	1282	ENSP00000223642:G1282S	ENSP00000223642:G1282S	G	-	1	0	C5	122778819	1.000000	0.71417	0.999000	0.59377	0.967000	0.64934	5.446000	0.66600	2.501000	0.84356	0.563000	0.77884	GGT	.	.	.	none		0.413	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735		T	123738998	C	T	123738998	3	4	259	1	0	0	0	0	1	0	0	0	2282	681	24	2	1238	2	C5	9	123738998	Missense_Mutation	SNP	C	TCGA-UZ-A9PM-01A-21D-A382-10	6807364	123738998	17474433	27	16136											
ANK3	288	hgsc.bcm.edu	37	chr10	61956291	61956291	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtgacctcttaccttcccAgcagcatctggagatgcact	8	11	9	13	0	2	2	0	1	2	1	3	3	3	2	3	2	4	3	3	2	1	2			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr10:61956291A>G	ENST00000280772.2	-	15	1973	c.1782T>C	c.(1780-1782)gcT>gcC	p.A594A	ANK3_ENST00000503366.1_Silent_p.A577A|ANK3_ENST00000373827.2_Silent_p.A588A	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	594					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						TTACCTTCCCAGCAGCATCTG	0.433																																					p.A594A		Atlas-SNP	.											.	ANK3	703	.	0			c.T1782C						PASS	.						73	66	69					10																	61956291		2203	4300	6503	SO:0001819	synonymous_variant	288	exon15			CTTCCCAGCAGCA	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.1782T>C	chr10.hg19:g.61956291A>G		56.0	0.0	.		58.0	13.0	.	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	hg19	CCDS7258.1																																																																																			.	.	.	none		0.433	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		G	61956291	A	G	61956291	2	3	259	1	0	0	0	0	0	0	0	1	622	175	7	3		3	ANK3	10	61956291	Silent	SNP	A	TCGA-UZ-A9PM-01A-21D-A382-10		61956291	73578456	28	16137											
COX15	1355	hgsc.bcm.edu	37	chr10	101480822	101480822	+	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	taggagttggtgggtttcagGcaactaaatatgaaaaaaaa	17	10	11	3	0	1	1	1	1	0	0	1	2	1	2	0	4	1	3	0	4	9	5			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr10:101480822G>C	ENST00000016171.5	-	6	804	c.754C>G	c.(754-756)Cct>Gct	p.P252A	CUTC_ENST00000493385.1_Intron|COX15_ENST00000370483.5_Missense_Mutation_p.P252A			Q7KZN9	COX15_HUMAN	cytochrome c oxidase assembly homolog 15 (yeast)	252					cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)|oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)			endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	13		Colorectal(252;0.234)		Epithelial(162;3.08e-10)|all cancers(201;2.43e-08)		TGGGTTTCAGGCAACTAAATA	0.433																																					p.P252A		Atlas-SNP	.											.	COX15	25	.	0			c.C754G						PASS	.						95	82	86					10																	101480822		2203	4300	6503	SO:0001583	missense	1355	exon6			TTTCAGGCAACTA	AF044323	CCDS7481.1, CCDS7482.1	10q24	2014-09-17	2012-10-15		ENSG00000014919	ENSG00000014919		"Mitochondrial respiratory chain complex assembly factors"	2263	protein-coding gene	gene with protein product		603646	"COX15 (yeast) homolog, cytochrome c oxidase assembly protein", "COX15 homolog, cytochrome c oxidase assembly protein (yeast)"			9878253	Standard	NM_078470		Approved		uc001kqb.4	Q7KZN9	OTTHUMG00000018893	ENST00000016171.5:c.754C>G	chr10.hg19:g.101480822G>C	ENSP00000016171:p.Pro252Ala	116.0	0.0	.		121.0	14.0	.	NM_078470	A8K6I9|O60556|O75878|Q5TD00|Q5TD01|Q7Z3Q3|Q9NTN0	Missense_Mutation	SNP	ENST00000016171.5	hg19	CCDS7482.1	.	.	.	.	.	.	.	.	.	.	G	4.012	-0.000496	0.07819	.	.	ENSG00000014919	ENST00000370483;ENST00000016171	D;D	0.81996	-1.56;-1.56	4.93	4.93	0.64822	.	0.232381	0.43747	D	0.000531	T	0.73410	0.3583	L	0.33189	0.99	0.50632	D	0.999881	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.002	T	0.68416	-0.5414	10	0.02654	T	1	-13.3644	18.1574	0.89696	0.0:0.0:1.0:0.0	.	252;252	Q7KZN9-2;Q7KZN9	.;COX15_HUMAN	A	252	ENSP00000359514:P252A;ENSP00000016171:P252A	ENSP00000016171:P252A	P	-	1	0	COX15	101470812	1.000000	0.71417	1.000000	0.80357	0.279000	0.26890	3.666000	0.54540	2.274000	0.75844	0.555000	0.69702	CCT	.	.	.	none		0.433	COX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049818.1	NP_510870		C	101480822	G	C	101480822	3	2	259	1	0	0	0	0	1	0	0	0	3766	1203	42	4	564	4	COX15	10	101480822	Missense_Mutation	SNP	G	TCGA-UZ-A9PM-01A-21D-A382-10	39524531	101480822	34053925	29	16138											
GDPD5	81544	hgsc.bcm.edu	37	chr11	75160942	75160942	+	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	tcactcacctgcagggagatCagcagcacctcccactcgtc	9	7	8	17	1	3	1	3	0	0	1	6	2	4	1	3	1	3	3	3	1	0	0			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr11:75160942C>A	ENST00000336898.3	-	7	1299	c.462G>T	c.(460-462)ctG>ctT	p.L154L	GDPD5_ENST00000376282.3_Intron|GDPD5_ENST00000443276.2_3'UTR|GDPD5_ENST00000529721.1_Silent_p.L154L|GDPD5_ENST00000526177.1_Silent_p.L16L|GDPD5_ENST00000533805.1_5'UTR|GDPD5_ENST00000533784.1_Intron	NM_030792.6	NP_110419.5	Q8WTR4	GDPD5_HUMAN	glycerophosphodiester phosphodiesterase domain containing 5	154					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						GCAGGGAGATCAGCAGCACCT	0.627																																					p.L154L		Atlas-SNP	.											.	GDPD5	49	.	0			c.G462T						PASS	.						50	47	48					11																	75160942		2200	4293	6493	SO:0001819	synonymous_variant	81544	exon7			GGAGATCAGCAGC	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.462G>T	chr11.hg19:g.75160942C>A		103.0	0.0	.		106.0	22.0	.	NM_030792	Q49AQ5|Q6UX76|Q7Z4S0|Q8N781|Q8NCB7|Q8TB77	Silent	SNP	ENST00000336898.3	hg19	CCDS8238.1																																																																																			.	.	.	none		0.627	GDPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384409.1	NM_030792		A	75160942	C	A	75160942	2	1	259	1	0	0	0	0	0	0	0	1	6334	813	29	4		4	GDPD5	11	75160942	Silent	SNP	C	TCGA-UZ-A9PM-01A-21D-A382-10		75160942	59845574	30	16139											
LRP6	4040	hgsc.bcm.edu	37	chr12	12279762	12279762	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acaacatcctctggcagataAagtatacagttccagacaca	16	8	6	11	0	1	2	0	0	1	2	3	2	3	2	2	1	2	3	2	1	5	4	rs373215297		TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr12:12279762A>G	ENST00000261349.4	-	20	4251	c.4175T>C	c.(4174-4176)tTt>tCt	p.F1392S	LRP6_ENST00000543091.1_Missense_Mutation_p.F1347S|BCL2L14_ENST00000396369.1_Intron|LRP6_ENST00000540415.1_Intron	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1392					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)				CTGGCAGATAAAGTATACAGT	0.438																																					p.F1392S		Atlas-SNP	.											.	LRP6	170	.	0			c.T4175C						PASS	.	A	SER/PHE	0,4406		0,0,2203	153	133	140		4175	5.7	1	12		140	1,8599	1.2+/-3.3	0,1,4299	no	missense	LRP6	NM_002336.2	155	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	probably-damaging	1392/1614	12279762	1,13005	2203	4300	6503	SO:0001583	missense	4040	exon20			CAGATAAAGTATA	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.4175T>C	chr12.hg19:g.12279762A>G	ENSP00000261349:p.Phe1392Ser	135.0	0.0	.		104.0	8.0	.	NM_002336	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	hg19	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.721771	0.89298	0.0	1.16E-4	ENSG00000070018	ENST00000261349;ENST00000543091	T;T	0.39787	1.06;1.06	5.73	5.73	0.89815	.	0.000000	0.64402	D	0.000005	T	0.61173	0.2326	M	0.62723	1.935	0.80722	D	1	P;D	0.76494	0.95;0.999	P;D	0.87578	0.648;0.998	T	0.57081	-0.7872	10	0.26408	T	0.33	.	16.0143	0.80425	1.0:0.0:0.0:0.0	.	1347;1392	F5H7J9;O75581	.;LRP6_HUMAN	S	1392;1347	ENSP00000261349:F1392S;ENSP00000442472:F1347S	ENSP00000261349:F1392S	F	-	2	0	LRP6	12171029	1.000000	0.71417	0.996000	0.52242	0.963000	0.63663	8.870000	0.92336	2.174000	0.68829	0.460000	0.39030	TTT	.	.	.	weak		0.438	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			G	12279762	A	G	12279762	3	3	259	1	0	0	0	0	1	0	0	0	8969	14	1	3	682	3	LRP6	12	12279762	Missense_Mutation	SNP	A	TCGA-UZ-A9PM-01A-21D-A382-10		12279762	121572133	31	16140											
RBMS2	5939	hgsc.bcm.edu	37	chr12	56975290	56975290	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttggccaaggaatgcagacAtggtaagaggacctctgagg	12	7	14	8	0	1	3	0	1	1	2	1	5	1	5	2	5	1	2	2	5	3	2			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr12:56975290A>G	ENST00000262031.5	+	7	825	c.730A>G	c.(730-732)Atg>Gtg	p.M244V	RBMS2_ENST00000550726.1_Missense_Mutation_p.M119V|RBMS2_ENST00000552247.2_Missense_Mutation_p.M244V|RBMS2_ENST00000542360.1_Missense_Mutation_p.M99V	NM_002898.3	NP_002889.1	Q15434	RBMS2_HUMAN	RNA binding motif, single stranded interacting protein 2	244					RNA processing (GO:0006396)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|large_intestine(2)|lung(8)|prostate(3)|skin(2)|urinary_tract(1)	18						GAATGCAGACATGGTAAGAGG	0.468																																					p.M244V		Atlas-SNP	.											.	RBMS2	29	.	0			c.A730G						PASS	.						51	45	47					12																	56975290		2203	4300	6503	SO:0001583	missense	5939	exon7			GCAGACATGGTAA	D28483	CCDS8923.1	12q13.13	2013-02-12			ENSG00000076067	ENSG00000076067		"RNA binding motif (RRM) containing"	9909	protein-coding gene	gene with protein product		602387				8041632	Standard	NM_002898		Approved	SCR3	uc001sln.2	Q15434	OTTHUMG00000170488	ENST00000262031.5:c.730A>G	chr12.hg19:g.56975290A>G	ENSP00000262031:p.Met244Val	80.0	0.0	.		78.0	15.0	.	NM_002898		Missense_Mutation	SNP	ENST00000262031.5	hg19	CCDS8923.1	.	.	.	.	.	.	.	.	.	.	A	9.246	1.039458	0.19669	.	.	ENSG00000076067	ENST00000262031;ENST00000552247;ENST00000550726;ENST00000542360	T;T;T	0.19938	2.84;2.75;2.11	5.21	1.4	0.22301	.	0.291510	0.31577	N	0.007408	T	0.10637	0.0260	L	0.27053	0.805	0.26901	N	0.967112	B;B;B	0.24675	0.035;0.0;0.109	B;B;B	0.20767	0.013;0.004;0.031	T	0.30563	-0.9974	10	0.14252	T	0.57	.	5.7609	0.18199	0.7203:0.0:0.1514:0.1282	.	99;119;244	F5H5C8;F8VV01;Q15434	.;.;RBMS2_HUMAN	V	244;244;119;99	ENSP00000262031:M244V;ENSP00000447426:M244V;ENSP00000449678:M119V	ENSP00000262031:M244V	M	+	1	0	RBMS2	55261557	0.853000	0.29707	1.000000	0.80357	0.993000	0.82548	1.763000	0.38461	0.363000	0.24346	0.533000	0.62120	ATG	.	.	.	none		0.468	RBMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409366.2	NM_002898		G	56975290	A	G	56975290	3	3	259	1	0	0	0	0	1	0	0	0	13162	217	8	3	756	3	RBMS2	12	56975290	Missense_Mutation	SNP	A	TCGA-UZ-A9PM-01A-21D-A382-10	44695528	56975290	76876605	32	16141											
BEST3	144453	hgsc.bcm.edu	37	chr12	70072597	70072597	+	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	gttgcaagatttccaaaccaGatgaatggaacccaatattt	15	11	7	8	0	0	3	0	1	0	2	1	4	1	4	3	1	3	2	3	1	6	4			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr12:70072597G>A	ENST00000330891.5	-	5	784	c.558C>T	c.(556-558)atC>atT	p.I186I	BEST3_ENST00000476098.1_Silent_p.I24I|BEST3_ENST00000553096.1_Silent_p.I80I|BEST3_ENST00000488961.1_Silent_p.I24I|BEST3_ENST00000331471.4_Silent_p.I186I	NM_001282613.1|NM_032735.2	NP_001269542.1|NP_116124.2	Q8N1M1	BEST3_HUMAN	bestrophin 3	186					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)			TTCCAAACCAGATGAATGGAA	0.343																																					p.I186I		Atlas-SNP	.											.	BEST3	129	.	0			c.C558T						PASS	.						112	105	107					12																	70072597		1870	4104	5974	SO:0001819	synonymous_variant	144453	exon5			AAACCAGATGAAT	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.558C>T	chr12.hg19:g.70072597G>A		96.0	0.0	.		74.0	6.0	.	NM_032735	B5MDI8|F8VVZ2|Q53YQ7|Q8N356|Q8NFT9|Q9BR80	Silent	SNP	ENST00000330891.5	hg19	CCDS8992.2																																																																																			.	.	.	none		0.343	BEST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313908.2	NM_152439		A	70072597	G	A	70072597	2	1	259	1	0	0	0	0	0	0	0	1	1406	932	33	2		2	BEST3	12	70072597	Silent	SNP	G	TCGA-UZ-A9PM-01A-21D-A382-10	13097307	70072597	63779298	33	16142											
GIT2	9815	hgsc.bcm.edu	37	chr12	110403363	110403363	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttcttagcagcttttgccaAttcagacaaatccaggctgc	10	12	7	12	0	2	1	1	0	1	1	3	1	3	1	2	1	4	3	2	1	3	5	rs570446364		TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr12:110403363A>G	ENST00000355312.3	-	9	783	c.784T>C	c.(784-786)Ttg>Ctg	p.L262L	GIT2_ENST00000547815.1_Silent_p.L262L|GIT2_ENST00000356259.4_Silent_p.L262L|GIT2_ENST00000320063.9_Silent_p.L262L|GIT2_ENST00000553118.1_Silent_p.L262L|TCHP_ENST00000550780.1_Intron|GIT2_ENST00000343646.5_Silent_p.L262L|GIT2_ENST00000338373.5_Silent_p.L262L|GIT2_ENST00000354574.4_Silent_p.L264L|GIT2_ENST00000551209.1_Silent_p.L261L|GIT2_ENST00000361006.5_Silent_p.L262L|GIT2_ENST00000360185.4_Silent_p.L262L|GIT2_ENST00000457474.2_Silent_p.L264L	NM_057169.3	NP_476510.1	Q14161	GIT2_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 2	262					behavioral response to pain (GO:0048266)|regulation of ARF GTPase activity (GO:0032312)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(8)|skin(4)	27						GCTTTTGCCAATTCAGACAAA	0.378													A|||	1	0.000199681	0	0	5008	,	,		19792	0		0	False		,,,				2504	0.001				p.L264L		Atlas-SNP	.											.	GIT2	81	.	0			c.T790C						PASS	.						56	54	55					12																	110403363		2202	4299	6501	SO:0001819	synonymous_variant	9815	exon10			TTGCCAATTCAGA	AF124491	CCDS9138.1, CCDS9139.1, CCDS44968.1, CCDS44969.1, CCDS55884.1	12q24.1	2013-01-10	2008-09-05			ENSG00000139436		"ADP-ribosylation factor GTPase activating proteins", "Ankyrin repeat domain containing"	4273	protein-coding gene	gene with protein product		608564	"G protein-coupled receptor kinase interactor 2"			9826657, 10896954	Standard	NM_139201		Approved	KIAA0148	uc001tps.2	Q14161	OTTHUMG00000169313	ENST00000355312.3:c.784T>C	chr12.hg19:g.110403363A>G		183.0	0.0	.		187.0	8.0	.	NM_001135213	Q86U59|Q96CI2|Q9BV91|Q9Y5V2	Silent	SNP	ENST00000355312.3	hg19	CCDS9138.1																																																																																			.	.	.	none		0.378	GIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403407.1	NM_057169		G	110403363	A	G	110403363	2	3	259	1	0	0	0	0	0	0	0	1	6404	98	4	3		3	GIT2	12	110403363	Silent	SNP	A	TCGA-UZ-A9PM-01A-21D-A382-10	40330766	110403363	23448532	34	16143											
ZIC2	7546	hgsc.bcm.edu	37	chr13	100637680	100637680	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcccccagcgccgagccccAgagcagctccaacctgtccc	7	4	9	21	2	0	1	0	0	0	1	3	2	3	1	8	0	5	2	8	0	1	0			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr13:100637680A>G	ENST00000376335.3	+	3	1636	c.1343A>G	c.(1342-1344)cAg>cGg	p.Q448R	ZIC2_ENST00000477213.1_3'UTR	NM_007129.3	NP_009060.2	O95409	ZIC2_HUMAN	Zic family member 2	448					brain development (GO:0007420)|developmental pigmentation (GO:0048066)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|retinal ganglion cell axon guidance (GO:0031290)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(2)|liver(2)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					GCCGAGCCCCAGAGCAGCTCC	0.786																																					p.Q448R	Pancreas(97;119 1522 31925 44771 48764)	Atlas-SNP	.											.	ZIC2	25	.	0			c.A1343G						PASS	.						7	9	9					13																	100637680		1854	4010	5864	SO:0001583	missense	7546	exon3			AGCCCCAGAGCAG	AF104902	CCDS9495.1	13q32	2013-01-08	2011-05-19		ENSG00000043355	ENSG00000043355		"Zinc fingers, C2H2-type"	12873	protein-coding gene	gene with protein product	"Zinc finger protein of the cerebellum 2"	603073	"Zic family member 2 (odd-paired Drosophila homolog)", "Zic family member 2 (odd-paired homolog, Drosophila)"			9771712	Standard	NM_007129		Approved	HPE5	uc001von.3	O95409	OTTHUMG00000017279	ENST00000376335.3:c.1343A>G	chr13.hg19:g.100637680A>G	ENSP00000365514:p.Gln448Arg	274.0	0.0	.		249.0	35.0	.	NM_007129	Q5VYA9|Q9H309	Missense_Mutation	SNP	ENST00000376335.3	hg19	CCDS9495.1	.	.	.	.	.	.	.	.	.	.	A	1.938	-0.444304	0.04604	.	.	ENSG00000043355	ENST00000376335	T	0.66638	-0.22	3.33	2.14	0.27477	.	0.199334	0.43919	N	0.000508	T	0.52224	0.1721	L	0.46157	1.445	0.49687	D	0.999818	B	0.02656	0.0	B	0.01281	0.0	T	0.34254	-0.9836	10	0.17832	T	0.49	.	7.3557	0.26717	0.8867:0.0:0.1133:0.0	.	448	O95409	ZIC2_HUMAN	R	448	ENSP00000365514:Q448R	ENSP00000365514:Q448R	Q	+	2	0	ZIC2	99435681	1.000000	0.71417	0.998000	0.56505	0.311000	0.27955	3.628000	0.54259	0.466000	0.27193	0.260000	0.18958	CAG	.	.	.	none		0.786	ZIC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045618.2	NM_007129		G	100637680	A	G	100637680	3	3	259	1	0	0	0	0	1	0	0	0	17691	188	7	3	1353	3	ZIC2	13	100637680	Missense_Mutation	SNP	A	TCGA-UZ-A9PM-01A-21D-A382-10		100637680	14532198	35	16144											
NEO1	4756	hgsc.bcm.edu	37	chr15	73562439	73562439	+	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	atgccaccagtgggagttcaGgcttccattctgagtcatga	9	11	11	10	0	3	2	2	2	1	0	4	3	4	3	3	2	1	2	3	2	0	3			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr15:73562439G>C	ENST00000339362.5	+	18	3030	c.2583G>C	c.(2581-2583)caG>caC	p.Q861H	NEO1_ENST00000560262.1_Missense_Mutation_p.Q861H|NEO1_ENST00000261908.6_Missense_Mutation_p.Q861H|NEO1_ENST00000558964.1_Missense_Mutation_p.Q861H			Q92859	NEO1_HUMAN	neogenin 1	861	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|iron ion homeostasis (GO:0055072)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						TGGGAGTTCAGGCTTCCATTC	0.483																																					p.Q861H		Atlas-SNP	.											.	NEO1	102	.	0			c.G2583C						PASS	.						169	177	174					15																	73562439		2198	4297	6495	SO:0001583	missense	4756	exon17			AGTTCAGGCTTCC	U61262	CCDS10247.1, CCDS53957.1, CCDS58378.1	15q22.3-q23	2014-06-20	2010-06-24		ENSG00000067141	ENSG00000067141		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7754	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 2"	601907	"neogenin (chicken) homolog 1"			9121761	Standard	NM_002499		Approved	NGN, HsT17534, IGDCC2, NTN1R2	uc002avm.4	Q92859	OTTHUMG00000133509	ENST00000339362.5:c.2583G>C	chr15.hg19:g.73562439G>C	ENSP00000341198:p.Gln861His	124.0	0.0	.		101.0	17.0	.	NM_001172623	B7ZKM9|B7ZKN0|O00340|Q17RX1	Missense_Mutation	SNP	ENST00000339362.5	hg19	CCDS10247.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.152137	0.78001	.	.	ENSG00000067141	ENST00000339362;ENST00000379842;ENST00000261908	T;T	0.57107	0.42;0.42	5.41	5.41	0.78517	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.68174	0.2972	M	0.65320	2	0.80722	D	1	D;D;D;D	0.89917	0.999;0.992;0.996;1.0	D;D;D;D	0.85130	0.997;0.96;0.98;0.984	T	0.67503	-0.5654	10	0.48119	T	0.1	-10.4247	12.8567	0.57890	0.0749:0.0:0.9251:0.0	.	861;861;583;861	B7ZKM9;B7ZKN0;E7EUX3;Q92859	.;.;.;NEO1_HUMAN	H	861;583;861	ENSP00000341198:Q861H;ENSP00000261908:Q861H	ENSP00000261908:Q861H	Q	+	3	2	NEO1	71349492	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.773000	0.75006	2.697000	0.92050	0.563000	0.77884	CAG	.	.	.	none		0.483	NEO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257472.2	NM_002499		C	73562439	G	C	73562439	3	2	259	1	0	0	0	0	1	0	0	0	10343	991	35	4	2649	4	NEO1	15	73562439	Missense_Mutation	SNP	G	TCGA-UZ-A9PM-01A-21D-A382-10		73562439	28968953	36	16145											
TBC1D2B	23102	hgsc.bcm.edu	37	chr15	78316564	78316564	+	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	gaaggggagctgggcgccacGgtgggaggaggcccgttgcc	6	4	21	10	3	0	0	0	0	0	0	0	4	0	3	3	7	2	2	3	7	1	1	rs527349478		TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr15:78316564G>T	ENST00000300584.3	-	6	1403	c.1404C>A	c.(1402-1404)acC>acA	p.T468T	TBC1D2B_ENST00000409931.3_Silent_p.T468T	NM_015079.5|NM_144572.1	NP_055894.6|NP_653173.1	Q9UPU7	TBD2B_HUMAN	TBC1 domain family, member 2B	468							Rab GTPase activator activity (GO:0005097)			breast(3)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26						TGGGCGCCACGGTGGGAGGAG	0.617																																					p.T468T		Atlas-SNP	.											.	TBC1D2B	104	.	0			c.C1404A						PASS	.						63	51	55					15																	78316564		2196	4293	6489	SO:0001819	synonymous_variant	23102	exon6			CGCCACGGTGGGA	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.1404C>A	chr15.hg19:g.78316564G>T		55.0	0.0	.		56.0	4.0	.	NM_144572	A7MD42|Q8N1F9|Q9NXM0	Silent	SNP	ENST00000300584.3	hg19	CCDS45314.1	.	.	.	.	.	.	.	.	.	.	G	3.403	-0.121820	0.06838	.	.	ENSG00000167202	ENST00000418039	.	.	.	4.28	-8.56	0.00904	.	.	.	.	.	T	0.14141	0.0342	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.18398	-1.0338	4	.	.	.	.	0.2637	0.00222	0.3539:0.1785:0.2125:0.2551	.	.	.	.	Q	350	.	.	P	-	2	0	TBC1D2B	76103619	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.300000	0.02751	-2.233000	0.00716	-2.916000	0.00090	CCG	.	.	.	none		0.617	TBC1D2B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328369.3	NM_015079		T	78316564	G	T	78316564	2	4	259	1	0	0	0	0	0	0	0	1	15631	1103	39	4		4	TBC1D2B	15	78316564	Silent	SNP	G	TCGA-UZ-A9PM-01A-21D-A382-10	4754125	78316564	24214828	37	16146											
C16orf62	57020	hgsc.bcm.edu	37	chr16	19576253	19576253	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attggagtttggggactatcAccctctgaaacccataactg	11	11	9	10	0	2	1	1	1	1	0	2	3	2	3	2	3	2	1	2	3	3	4			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr16:19576253A>G	ENST00000251143.5	+	2	110	c.98A>G	c.(97-99)cAc>cGc	p.H33R	C16orf62_ENST00000538853.1_Missense_Mutation_p.H122R|C16orf62_ENST00000417362.2_Missense_Mutation_p.H33R|C16orf62_ENST00000542263.1_Missense_Mutation_p.H122R|C16orf62_ENST00000438132.3_Missense_Mutation_p.H122R			Q7Z3J2	CP062_HUMAN	chromosome 16 open reading frame 62	33						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						GGGGACTATCACCCTCTGAAA	0.418																																					p.H122R		Atlas-SNP	.											.	C16orf62	164	.	0			c.A365G						PASS	.						120	104	109					16																	19576253		2197	4300	6497	SO:0001583	missense	57020	exon2			ACTATCACCCTCT		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.98A>G	chr16.hg19:g.19576253A>G	ENSP00000251143:p.His33Arg	166.0	0.0	.		142.0	25.0	.	NM_020314	A8K2M1|O43329|Q69YI1|Q6PDA0|Q7L371|Q86W66|Q8WXA5|Q9H0L7|Q9H7C8	Missense_Mutation	SNP	ENST00000251143.5	hg19		.	.	.	.	.	.	.	.	.	.	A	20.4	3.979057	0.74360	.	.	ENSG00000103544	ENST00000438132;ENST00000538853;ENST00000542263;ENST00000251143;ENST00000417362	T;T;T;T;T	0.59364	0.27;0.27;0.27;0.27;0.27	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.76126	0.3944	M	0.79011	2.435	0.80722	D	1	D;D;D	0.89917	0.96;0.996;1.0	D;D;D	0.83275	0.923;0.99;0.996	T	0.79155	-0.1920	10	0.62326	D	0.03	-29.32	14.632	0.68663	1.0:0.0:0.0:0.0	.	122;33;122	F5H7K1;Q7Z3J2;E7EWW0	.;CP062_HUMAN;.	R	122;122;122;33;33	ENSP00000400815:H122R;ENSP00000444363:H122R;ENSP00000442468:H122R;ENSP00000251143:H33R;ENSP00000395973:H33R	ENSP00000251143:H33R	H	+	2	0	C16orf62	19483754	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.725000	0.84808	2.056000	0.61249	0.374000	0.22700	CAC	.	.	.	none		0.418	C16orf62-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_020314		G	19576253	A	G	19576253	3	3	259	1	0	0	0	0	1	0	0	0	1827	159	6	3	104	3	C16orf62	16	19576253	Missense_Mutation	SNP	A	TCGA-UZ-A9PM-01A-21D-A382-10		19576253	70778500	38	16147											
ITGAD	3681	hgsc.bcm.edu	37	chr16	31424561	31424561	+	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	tccagaaaagctcactggacCagctaggtgtgtttccccca	10	9	9	13	0	1	1	1	0	0	1	3	2	3	2	4	2	2	3	4	2	3	2			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr16:31424561C>A	ENST00000389202.2	+	16	2039	c.1990C>A	c.(1990-1992)Cag>Aag	p.Q664K		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	664					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						CTCACTGGACCAGCTAGGTGT	0.597																																					p.Q664K		Atlas-SNP	.											.	ITGAD	154	.	0			c.C1990A						PASS	.						79	74	76					16																	31424561		2197	4300	6497	SO:0001583	missense	3681	exon16			CTGGACCAGCTAG	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.1990C>A	chr16.hg19:g.31424561C>A	ENSP00000373854:p.Gln664Lys	78.0	0.0	.		83.0	10.0	.	NM_005353	Q15575|Q15576	Missense_Mutation	SNP	ENST00000389202.2	hg19	CCDS32438.1	.	.	.	.	.	.	.	.	.	.	C	4.269	0.048941	0.08243	.	.	ENSG00000156886	ENST00000444228;ENST00000389202	T	0.45276	0.9	5.24	4.29	0.51040	Integrin alpha-2 (1);	.	.	.	.	T	0.32224	0.0822	L	0.46157	1.445	0.09310	N	1	B;B	0.16166	0.016;0.016	B;B	0.21360	0.034;0.034	T	0.33007	-0.9885	9	0.06494	T	0.89	.	9.7171	0.40281	0.0:0.904:0.0:0.096	.	680;664	Q59H14;Q13349	.;ITAD_HUMAN	K	680;664	ENSP00000373854:Q664K	ENSP00000373854:Q664K	Q	+	1	0	ITGAD	31332062	0.026000	0.19158	0.003000	0.11579	0.005000	0.04900	0.687000	0.25407	1.223000	0.43536	0.604000	0.83254	CAG	.	.	.	none		0.597	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353		A	31424561	C	A	31424561	3	1	259	1	0	0	0	0	1	0	0	0	7891	595	21	4	2052	4	ITGAD	16	31424561	Missense_Mutation	SNP	C	TCGA-UZ-A9PM-01A-21D-A382-10	11848308	31424561	58930192	39	16148											
ZNF423	23090	hgsc.bcm.edu	37	chr16	49764694	49764694	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcattacctccaggacagcGgtgggcccggtggtccgtca	6	8	14	13	3	1	0	1	0	0	0	3	1	3	1	4	5	3	1	4	5	1	1	rs146233664		TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr16:49764694G>A	ENST00000561648.1	-	3	318	c.265C>T	c.(265-267)Cgc>Tgc	p.R89C	ZNF423_ENST00000562520.1_Missense_Mutation_p.R29C|ZNF423_ENST00000262383.2_Missense_Mutation_p.R89C|ZNF423_ENST00000563137.2_Missense_Mutation_p.R29C|ZNF423_ENST00000562871.1_Missense_Mutation_p.R29C	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	89					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)				CCAGGACAGCGGTGGGCCCGG	0.517																																					p.R89C		Atlas-SNP	.											.	ZNF423	463	.	0			c.C265T						PASS	.	G	CYS/ARG	0,4396		0,0,2198	158	136	143		265	5.2	1	16	dbSNP_134	143	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZNF423	NM_015069.2	180	0,1,6497	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	89/1285	49764694	1,12995	2198	4300	6498	SO:0001583	missense	23090	exon3			GACAGCGGTGGGC	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.265C>T	chr16.hg19:g.49764694G>A	ENSP00000455426:p.Arg89Cys	99.0	0.0	.		98.0	27.0	.	NM_015069	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	hg19	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	G	15.53	2.860384	0.51482	0.0	1.16E-4	ENSG00000102935	ENST00000262383	T	0.29917	1.55	5.15	5.15	0.70609	.	0.199102	0.43416	D	0.000570	T	0.23330	0.0564	N	0.08118	0	0.40060	D	0.975881	P	0.49253	0.921	P	0.49301	0.606	T	0.06391	-1.0829	9	.	.	.	.	14.4984	0.67704	0.0:0.0:0.7833:0.2167	.	89	Q2M1K9	ZN423_HUMAN	C	89	ENSP00000262383:R89C	.	R	-	1	0	ZNF423	48322195	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.272000	0.58908	2.558000	0.86282	0.313000	0.20887	CGC	.	G|1.000;A|0.000	0.000	weak		0.517	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		A	49764694	G	A	49764694	3	1	259	1	0	0	0	0	1	0	0	0	17910	1116	39	1	3613	1	ZNF423	16	49764694	Missense_Mutation	SNP	G	TCGA-UZ-A9PM-01A-21D-A382-10	18340133	49764694	40590059	40	16149											
POLR2C	5432	hgsc.bcm.edu	37	chr16	57499934	57499934	+	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	attcattgctcacaggcttgGtgagtactccttttactagg	8	15	9	9	0	2	1	2	1	0	0	3	1	3	1	1	3	3	3	1	3	3	7			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr16:57499934G>C	ENST00000219252.5	+	3	543		c.e3+1		POLR2C_ENST00000564651.1_Splice_Site	NM_032940.2	NP_116558.1	P19387	RPB3_HUMAN	polymerase (RNA) II (DNA directed) polypeptide C, 33kDa						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)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, core complex (GO:0005665)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(2)|upper_aerodigestive_tract(1)	10						CACAGGCTTGGTGAGTACTCC	0.478																																					.		Atlas-SNP	.											.	POLR2C	24	.	0			c.205+1G>C						PASS	.						151	144	147					16																	57499934		2198	4300	6498	SO:0001630	splice_region_variant	5432	exon3			GGCTTGGTGAGTA		CCDS10782.1	16q13-q21	2013-01-21	2002-08-29		ENSG00000102978	ENSG00000102978		"RNA polymerase subunits"	9189	protein-coding gene	gene with protein product	"RNA polymerase II subunit 3"	180663	"polymerase (RNA) II (DNA directed) polypeptide C (33kD)"			8034326	Standard	NM_032940		Approved	RPB3	uc002elt.1	P19387	OTTHUMG00000133464	ENST00000219252.5:c.205+1G>C	chr16.hg19:g.57499934G>C		125.0	0.0	.		133.0	15.0	.	NM_032940	O15161	Splice_Site	SNP	ENST00000219252.5	hg19	CCDS10782.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.053137	0.75960	.	.	ENSG00000102978	ENST00000219252	.	.	.	5.48	5.48	0.80851	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.3397	0.90300	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	POLR2C	56057435	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	9.869000	0.99810	2.593000	0.87608	0.561000	0.74099	.	.	.	.	none		0.478	POLR2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257340.3	NM_032940	Intron	C	57499934	G	C	57499934	5	2	259	1	0	0	0	0	0	0	1	0	12223	1275	44	4	216	4	POLR2C	16	57499934	Splice_Site	SNP	G	TCGA-UZ-A9PM-01A-21D-A382-10	7735240	57499934	32854819	41	16150											
C17orf104	284071	hgsc.bcm.edu	37	chr17	42744973	42744973	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtcaatcacatagaaggacTaacaaagcctggagaagaaa	19	6	9	7	0	2	3	2	0	0	3	2	5	2	4	1	2	2	0	1	2	7	2			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr17:42744973T>C	ENST00000409122.2	+	5	1836	c.1694T>C	c.(1693-1695)cTa>cCa	p.L565P	C17orf104_ENST00000409464.1_Missense_Mutation_p.L399P|C17orf104_ENST00000359945.3_Missense_Mutation_p.L565P	NM_001145080.2	NP_001138552.2	A2RUB1	CQ104_HUMAN	chromosome 17 open reading frame 104	565										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						ATAGAAGGACTAACAAAGCCT	0.348																																					p.L565P		Atlas-SNP	.											.	C17orf104	75	.	0			c.T1694C						PASS	.						29	31	30					17																	42744973		2200	4297	6497	SO:0001583	missense	284071	exon5			AAGGACTAACAAA		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.1694T>C	chr17.hg19:g.42744973T>C	ENSP00000386452:p.Leu565Pro	96.0	0.0	.		118.0	50.0	.	NM_001145080	B4DXJ2|B5MD93|B9EGQ6|C4AM97|Q4G0Y1|Q8IVZ7|Q8NA45	Missense_Mutation	SNP	ENST00000409122.2	hg19	CCDS45703.2	.	.	.	.	.	.	.	.	.	.	T	11.86	1.763636	0.31228	.	.	ENSG00000180336	ENST00000359945;ENST00000409122;ENST00000409464	T;T;T	0.37411	1.2;1.2;1.22	5.66	4.51	0.55191	.	0.136458	0.33753	N	0.004589	T	0.44414	0.1292	L	0.34521	1.04	0.58432	D	0.999999	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.71656	0.974;0.974;0.974	T	0.29701	-1.0003	10	0.44086	T	0.13	-19.4828	9.8411	0.40999	0.2645:0.0:0.0:0.7355	.	565;565;399	A2RUB1-5;A2RUB1;A2RUB1-1	.;CQ104_HUMAN;.	P	565;565;399	ENSP00000353028:L565P;ENSP00000386452:L565P;ENSP00000386586:L399P	ENSP00000353028:L565P	L	+	2	0	C17orf104	40100499	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	1.526000	0.35964	2.151000	0.67156	0.533000	0.62120	CTA	.	.	.	none		0.348	C17orf104-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329171.2	NM_001145080		C	42744973	T	C	42744973	3	2	259	1	0	0	0	0	1	0	0	0	1853	1522	53	3	1712	3	C17orf104	17	42744973	Missense_Mutation	SNP	T	TCGA-UZ-A9PM-01A-21D-A382-10		42744973	38450237	42	16151											
SETBP1	26040	hgsc.bcm.edu	37	chr18	42643077	42643077	+	Frame_Shift_Del	DEL	G	G	-																															gaagaagaggttcaagcggcGggagatcgaagccatccagt																								rs371946489		TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr18:42643077delG	ENST00000282030.5	+	6	4501	c.4205delG	c.(4204-4206)cggfs	p.R1402fs		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	1402						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)		TTCAAGCGGCGGGAGATCGAA	0.537									Schinzel-Giedion syndrome																												p.R1402fs		Atlas-Indel,Pindel	.											.	SETBP1	577	.	0			c.4204delC						PASS	.						49	48	48					18																	42643077		2203	4300	6503	SO:0001589	frameshift_variant	26040	exon6	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	.	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.4205delG	chr18.hg19:g.42643077delG	ENSP00000282030:p.Arg1402fs	139.0	0.0	0		140.0	22.0	0.157143	NM_015559	A6H8W5|Q6P6C3|Q9UEF3	Frame_Shift_Del	DEL	ENST00000282030.5	hg19	CCDS11923.2																																																																																			.	.	.	none		0.537	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110		-	42643077	G	-	42643077	7	5	259	1	0	1	0	1	0	0	0	0	14142	1116	39	0	4416	0	SETBP1	18	42643077	Frame_Shift_Del	DEL	G	TCGA-UZ-A9PM-01A-21D-A382-10		42643077	35434171	43	16152											
MUC16	94025	hgsc.bcm.edu	37	chr19	9075997	9075997	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgcagaagtggtggtgggaaGctgagtggaagtctgctctg	8	10	18	5	0	2	2	0	1	2	1	2	4	2	4	0	4	3	3	0	4	3	0			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr19:9075997G>A	ENST00000397910.4	-	3	11652	c.11449C>T	c.(11449-11451)Ctt>Ttt	p.L3817F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3818	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						GTGGTGGGAAGCTGAGTGGAA	0.507																																					p.L3817F		Atlas-SNP	.											.	MUC16	4315	.	0			c.C11449T						PASS	.						230	219	223					19																	9075997		2074	4222	6296	SO:0001583	missense	94025	exon3			TGGGAAGCTGAGT	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.11449C>T	chr19.hg19:g.9075997G>A	ENSP00000381008:p.Leu3817Phe	117.0	0.0	.		127.0	22.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	4.495	0.091754	0.08632	.	.	ENSG00000181143	ENST00000397910	T	0.03124	4.04	1.74	-0.625	0.11548	.	.	.	.	.	T	0.02083	0.0065	N	0.08118	0	.	.	.	B	0.31383	0.321	B	0.34301	0.179	T	0.43669	-0.9377	8	0.87932	D	0	.	2.8375	0.05519	0.2006:0.3036:0.4958:0.0	.	3817	B5ME49	.	F	3817	ENSP00000381008:L3817F	ENSP00000381008:L3817F	L	-	1	0	MUC16	8936997	0.000000	0.05858	0.001000	0.08648	0.231000	0.25187	-1.717000	0.01876	-0.091000	0.12440	0.313000	0.20887	CTT	.	.	.	none		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9075997	G	A	9075997	3	1	259	1	0	0	0	0	1	0	0	0	9980	971	34	2	32402	2	MUC16	19	9075997	Missense_Mutation	SNP	G	TCGA-UZ-A9PM-01A-21D-A382-10		9075997	50052986	44	16153											
ZNF493	284443	hgsc.bcm.edu	37	chr19	21607521	21607521	+	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	tgaagagaaaccctacaaatGtgaaaaatgtggcaaaactt	19	8	8	6	0	0	3	0	2	0	1	0	4	0	3	1	1	3	1	1	1	8	2			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr19:21607521G>T	ENST00000355504.4	+	2	1942	c.1676G>T	c.(1675-1677)tGt>tTt	p.C559F	ZNF493_ENST00000392288.2_Missense_Mutation_p.C687F|CTD-2561J22.3_ENST00000600810.1_Intron	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	559					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|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						CCCTACAAATGTGAAAAATGT	0.343																																					p.C687F		Atlas-SNP	.											.	ZNF493	178	.	0			c.G2060T						PASS	.						33	37	35					19																	21607521		2202	4296	6498	SO:0001583	missense	284443	exon4			ACAAATGTGAAAA	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.1676G>T	chr19.hg19:g.21607521G>T	ENSP00000347691:p.Cys559Phe	216.0	0.0	.		247.0	36.0	.	NM_001076678	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	hg19	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	13.82	2.349952	0.41599	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	D;D	0.85088	-1.94;-1.94	1.06	1.06	0.20224	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.93271	0.7856	H	0.95437	3.67	0.80722	D	1	D;D	0.89917	1.0;0.997	D;P	0.85130	0.997;0.789	D	0.92138	0.5718	9	0.87932	D	0	.	8.9275	0.35650	0.0:0.0:1.0:0.0	.	559;687	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	F	687;559	ENSP00000376110:C687F;ENSP00000347691:C559F	ENSP00000347691:C559F	C	+	2	0	ZNF493	21399361	1.000000	0.71417	0.047000	0.18901	0.046000	0.14306	4.613000	0.61176	0.458000	0.26988	0.467000	0.42956	TGT	.	.	.	none		0.343	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		T	21607521	G	T	21607521	3	4	259	1	0	0	0	0	1	0	0	0	17956	1377	48	4	2137	4	ZNF493	19	21607521	Missense_Mutation	SNP	G	TCGA-UZ-A9PM-01A-21D-A382-10	12531524	21607521	37521462	45	16154											
ERCC2	2068	hgsc.bcm.edu	37	chr19	45867362	45867362	+	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	tcgtcccgcaggcgctgctcGtctgtctctttgatcctgcg	2	13	11	15	5	2	1	0	1	2	0	7	1	4	1	2	1	2	3	2	1	0	1	rs547544775		TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr19:45867362G>A	ENST00000391945.4	-	10	908	c.831C>T	c.(829-831)gaC>gaT	p.D277D	ERCC2_ENST00000221481.6_3'UTR|ERCC2_ENST00000391940.4_Silent_p.D253D|ERCC2_ENST00000485403.2_Silent_p.D253D|ERCC2_ENST00000391944.3_Silent_p.D199D	NM_000400.3	NP_000391.1	P18074	ERCC2_HUMAN	excision repair cross-complementation group 2	277	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				7-methylguanosine mRNA capping (GO:0006370)|aging (GO:0007568)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|central nervous system myelin formation (GO:0032289)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|embryonic cleavage (GO:0040016)|erythrocyte maturation (GO:0043249)|extracellular matrix organization (GO:0030198)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|hair follicle maturation (GO:0048820)|hematopoietic stem cell differentiation (GO:0060218)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|MMXD complex (GO:0071817)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		GGCGCTGCTCGTCTGTCTCTT	0.721			"Mis, N, F, S"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				G|||	1	0.000199681	0	0	5008	,	,		11449	0		0	False		,,,				2504	0.001				p.D277D		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.C831T						PASS	.						8	11	10					19																	45867362		2115	4221	6336	SO:0001819	synonymous_variant	2068	exon10	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	CTGCTCGTCTGTC		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.831C>T	chr19.hg19:g.45867362G>A		81.0	0.0	.		91.0	17.0	.	NM_000400	Q2TB78|Q2YDY2|Q7KZU6|Q8N721	Silent	SNP	ENST00000391945.4	hg19	CCDS33049.1																																																																																			.	.	.	none		0.721	ERCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109626.2	NM_000400		A	45867362	G	A	45867362	2	1	259	1	0	0	0	0	0	0	0	1	5215	1136	40	1		1	ERCC2	19	45867362	Silent	SNP	G	TCGA-UZ-A9PM-01A-21D-A382-10	24259841	45867362	13261621	46	16155											
NXT1	29107	hgsc.bcm.edu	37	chr20	23334728	23334728	+	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	ggatcaggcctgcagagctgCtgaggagtttgtcaatgtct	8	11	14	8	0	3	2	2	1	1	1	3	4	3	4	1	3	3	4	1	3	1	1			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr20:23334728C>A	ENST00000254998.2	+	2	437	c.50C>A	c.(49-51)gCt>gAt	p.A17D	RP3-322G13.5_ENST00000444981.1_RNA|RP3-322G13.7_ENST00000442884.1_RNA|AL096677.1_ENST00000596205.1_5'Flank|RP3-322G13.5_ENST00000452395.1_RNA|RP3-322G13.5_ENST00000442440.1_RNA	NM_013248.2	NP_037380.1	Q9UKK6	NXT1_HUMAN	nuclear transport factor 2-like export factor 1	17	NTF2. {ECO:0000255|PROSITE- ProRule:PRU00137}.				protein export from nucleus (GO:0006611)|RNA export from nucleus (GO:0006405)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)				NS(1)|endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	6	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)					TGCAGAGCTGCTGAGGAGTTT	0.547																																					p.A17D		Atlas-SNP	.											.	NXT1	12	.	0			c.C50A						PASS	.						96	92	93					20																	23334728		2203	4300	6503	SO:0001583	missense	29107	exon2			GAGCTGCTGAGGA	AF156957	CCDS13150.1	20p12-p11.2	2014-05-12	2014-05-12		ENSG00000132661	ENSG00000132661			15913	protein-coding gene	gene with protein product		605811	"NTX2-like export factor1", "NTF2-like export factor 1"			10567585, 11259602	Standard	NM_013248		Approved	P15, MTR2	uc002wsx.1	Q9UKK6	OTTHUMG00000032059	ENST00000254998.2:c.50C>A	chr20.hg19:g.23334728C>A	ENSP00000254998:p.Ala17Asp	113.0	0.0	.		108.0	17.0	.	NM_013248		Missense_Mutation	SNP	ENST00000254998.2	hg19	CCDS13150.1	.	.	.	.	.	.	.	.	.	.	C	19.82	3.897600	0.72639	.	.	ENSG00000132661	ENST00000254998	.	.	.	5.32	4.37	0.52481	Nuclear transport factor 2, Eukaryote (1);Nuclear transport factor 2 (1);	0.060915	0.64402	D	0.000002	T	0.80949	0.4722	M	0.90019	3.08	0.43152	D	0.994922	D	0.69078	0.997	D	0.70935	0.971	D	0.85059	0.0933	9	0.87932	D	0	.	12.1184	0.53878	0.0:0.8279:0.1721:0.0	.	17	Q9UKK6	NXT1_HUMAN	D	17	.	ENSP00000254998:A17D	A	+	2	0	NXT1	23282728	1.000000	0.71417	0.018000	0.16275	0.958000	0.62258	6.916000	0.75776	1.604000	0.50143	0.655000	0.94253	GCT	.	.	.	none		0.547	NXT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078313.2	NM_013248		A	23334728	C	A	23334728	3	1	259	1	0	0	0	0	1	0	0	0	10801	797	28	4	52	4	NXT1	20	23334728	Missense_Mutation	SNP	C	TCGA-UZ-A9PM-01A-21D-A382-10		23334728	39690792	47	16156											
CLIC6	54102	hgsc.bcm.edu	37	chr21	36042470	36042470	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccggcgggggacggcgtagaAgcgggggtcccggcggggga	5	2	24	10	7	0	1	0	0	0	1	1	3	1	3	2	9	1	1	2	9	2	1	rs557556798|rs62213790	byFrequency	TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr21:36042470A>G	ENST00000360731.3	+	1	783	c.783A>G	c.(781-783)gaA>gaG	p.E261E	CLIC6_ENST00000349499.2_Silent_p.E261E			Q96NY7	CLIC6_HUMAN	chloride intracellular channel 6	261	13 X 10 AA tandem repeat of G-D-[SNG]- [VIM]-[DEQ]-A-[EAG]-[GDVE]-[PRG]-[LAVP].					chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	voltage-gated chloride channel activity (GO:0005247)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19						ACGGCGTAGAAGCGGGGGTCC	0.761																																					p.E261E		Atlas-SNP	.											CLIC6,NS,carcinoma,0,1	CLIC6	49	.	0			c.A783G						PASS	.						1	2	2					21																	36042470		755	1897	2652	SO:0001819	synonymous_variant	54102	exon1			CGTAGAAGCGGGG	AF426169	CCDS13638.1	21q22.12	2012-09-26			ENSG00000159212	ENSG00000159212		"Ion channels / Chloride channels : Intracellular"	2065	protein-coding gene	gene with protein product		615321		CLIC1L		10830953	Standard	NM_053277		Approved	CLIC5	uc002yuf.1	Q96NY7	OTTHUMG00000086237	ENST00000360731.3:c.783A>G	chr21.hg19:g.36042470A>G		14.0	2.0	.		29.0	3.0	.	NM_053277	A8K0U8|Q8IX31	Silent	SNP	ENST00000360731.3	hg19																																																																																				.	.	.	weak		0.761	CLIC6-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000194156.1			G	36042470	A	G	36042470	2	3	259	1	0	0	0	0	0	0	0	1	3532	69	3	3		3	CLIC6	21	36042470	Silent	SNP	A	TCGA-UZ-A9PM-01A-21D-A382-10		36042470	12087425	48	16157											
SEC14L3	266629	hgsc.bcm.edu	37	chr22	30860885	30860885	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagcccacagggaacagttTggtagctggagagatagaag	13	7	15	6	0	0	2	0	0	0	2	0	5	0	4	1	3	3	4	1	3	5	4			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr22:30860885T>C	ENST00000215812.4	-	8	676	c.586A>G	c.(586-588)Aaa>Gaa	p.K196E	SEC14L3_ENST00000539629.1_Missense_Mutation_p.K137E|SEC14L3_ENST00000401751.1_Missense_Mutation_p.K137E|SEC14L3_ENST00000403066.1_Missense_Mutation_p.K137E|SEC14L3_ENST00000402286.1_Missense_Mutation_p.K119E|SEC14L3_ENST00000540910.1_Missense_Mutation_p.K119E|SEC14L3_ENST00000415957.2_Missense_Mutation_p.K137E	NM_174975.4	NP_777635.1	Q9UDX4	S14L3_HUMAN	SEC14-like 3 (S. cerevisiae)	196	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)	GGGAACAGTTTGGTAGCTGGA	0.438																																					p.K196E	Esophageal Squamous(108;290 1516 3584 23771 37333)	Atlas-SNP	.											.	SEC14L3	46	.	0			c.A586G						PASS	.						129	117	121					22																	30860885		2203	4300	6503	SO:0001583	missense	266629	exon8			ACAGTTTGGTAGC	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.586A>G	chr22.hg19:g.30860885T>C	ENSP00000215812:p.Lys196Glu	79.0	0.0	.		66.0	10.0	.	NM_174975	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000215812.4	hg19	CCDS13877.1	.	.	.	.	.	.	.	.	.	.	T	15.27	2.784925	0.49997	.	.	ENSG00000100012	ENST00000403066;ENST00000415957;ENST00000215812;ENST00000402286;ENST00000401751;ENST00000539629;ENST00000540910	T;T;T;T;T;T;T	0.77229	-1.08;-1.08;-1.08;-1.08;-1.08;-1.08;-1.08	5.4	4.35	0.52113	Cellular retinaldehyde-binding/triple function, C-terminal (5);	0.092809	0.64402	D	0.000001	D	0.87924	0.6300	M	0.91196	3.185	0.80722	D	1	D;B	0.58970	0.984;0.068	P;B	0.59221	0.854;0.155	D	0.89075	0.3472	10	0.87932	D	0	-13.0241	11.3853	0.49782	0.1359:0.0:0.0:0.8641	.	119;196	E9PE57;Q9UDX4	.;S14L3_HUMAN	E	137;137;196;119;137;137;119	ENSP00000385941:K137E;ENSP00000401864:K137E;ENSP00000215812:K196E;ENSP00000385004:K119E;ENSP00000383896:K137E;ENSP00000444691:K137E;ENSP00000439752:K119E	ENSP00000215812:K196E	K	-	1	0	SEC14L3	29190885	1.000000	0.71417	0.989000	0.46669	0.024000	0.10985	7.561000	0.82288	0.866000	0.35629	-0.336000	0.08194	AAA	.	.	.	none		0.438	SEC14L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321950.4	NM_174975		C	30860885	T	C	30860885	3	2	259	1	0	0	0	0	1	0	0	0	13996	1821	63	3	636	3	SEC14L3	22	30860885	Missense_Mutation	SNP	T	TCGA-UZ-A9PM-01A-21D-A382-10		30860885	20443681	49	16158											
APOBEC3G	60489	hgsc.bcm.edu	37	chr22	39479829	39479829	+	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	tacctgtgttatgaggtggaGcgcatgcacaatgacacctg	10	10	12	9	1	0	2	0	2	0	0	0	3	0	3	2	2	3	3	2	2	3	2			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr22:39479829G>A	ENST00000407997.3	+	5	1032	c.675G>A	c.(673-675)gaG>gaA	p.E225E	APOBEC3G_ENST00000461827.1_3'UTR|APOBEC3G_ENST00000452957.2_Silent_p.E225E	NM_021822.3	NP_068594.1	Q9HC16	ABC3G_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3G	225	Necessary for homooligomerization.				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)					ATGAGGTGGAGCGCATGCACA	0.552																																					p.E225E		Atlas-SNP	.											.	APOBEC3G	69	.	0			c.G675A						PASS	.						121	99	106					22																	39479829		2203	4300	6503	SO:0001819	synonymous_variant	60489	exon5			GGTGGAGCGCATG	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.675G>A	chr22.hg19:g.39479829G>A		88.0	0.0	.		89.0	16.0	.	NM_021822	B2RDR9|Q45F02|Q5TF77|Q7Z2N1|Q7Z2N4|Q9H9H8	Silent	SNP	ENST00000407997.3	hg19	CCDS13984.1																																																																																			.	.	.	none		0.552	APOBEC3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321219.1	NM_021822		A	39479829	G	A	39479829	2	1	259	1	0	0	0	0	0	0	0	1	794	962	34	2		2	APOBEC3G	22	39479829	Silent	SNP	G	TCGA-UZ-A9PM-01A-21D-A382-10	8618944	39479829	11824737	50	16159											
SAPS2	9701	hgsc.bcm.edu	37	chr22	50876323	50876323	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcaacatcgacgctgacgaGgacagtgtgagcaagccggg	11	6	14	10	4	1	2	1	2	0	0	2	5	1	3	1	2	3	2	1	2	2	1			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chr22:50876323G>A	ENST00000216061.5	+	18	2203	c.1833G>A	c.(1831-1833)gaG>gaA	p.E611E	PPP6R2_ENST00000395741.3_Silent_p.E585E|PPP6R2_ENST00000359139.3_Silent_p.E584E|PPP6R2_ENST00000395744.3_Silent_p.E584E			O75170	PP6R2_HUMAN	protein phosphatase 6, regulatory subunit 2	611						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						ACGCTGACGAGGACAGTGTGA	0.627																																					p.E611E		Atlas-SNP	.											.	PPP6R2	71	.	0			c.G1833A						PASS	.						43	30	35					22																	50876323		2180	4247	6427	SO:0001819	synonymous_variant	9701	exon17			TGACGAGGACAGT	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.1833G>A	chr22.hg19:g.50876323G>A		34.0	0.0	.		38.0	6.0	.	NM_001242898	A6PVG3|B7Z7T3|Q5U5P3|Q7Z2L2|Q7Z5G5|Q7Z731|Q9UGB9	Silent	SNP	ENST00000216061.5	hg19																																																																																				.	.	.	none		0.627	PPP6R2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316809.1	NM_014678		A	50876323	G	A	50876323	2	1	259	1	0	0	0	0	0	0	0	1	13850	991	35	2		2	SAPS2	22	50876323	Silent	SNP	G	TCGA-UZ-A9PM-01A-21D-A382-10	11396494	50876323	428243	51	16160											
HUWE1	10075	hgsc.bcm.edu	37	chrX	53641606	53641606	+	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	cttctgcggcatgattagacCttgggggaggagcagtggca	8	9	16	8	1	1	2	0	1	1	1	1	4	1	4	1	5	2	3	1	5	1	3			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chrX:53641606C>G	ENST00000342160.3	-	22	2607	c.2150G>C	c.(2149-2151)aGg>aCg	p.R717T	HUWE1_ENST00000218328.8_Missense_Mutation_p.R717T|HUWE1_ENST00000262854.6_Missense_Mutation_p.R717T			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	717					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						ATGATTAGACCTTGGGGGAGG	0.478																																					p.R717T		Atlas-SNP	.											.	HUWE1	724	.	0			c.G2150C						PASS	.						151	130	137					X																	53641606		2203	4300	6503	SO:0001583	missense	10075	exon23			TTAGACCTTGGGG	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.2150G>C	chrX.hg19:g.53641606C>G	ENSP00000340648:p.Arg717Thr	68.0	0.0	.		51.0	11.0	.	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	hg19	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	C	17.49	3.403533	0.62288	.	.	ENSG00000086758	ENST00000342160;ENST00000262854;ENST00000218328	T;T;T	0.44482	0.92;0.92;0.92	5.46	5.46	0.80206	E3 ubiquitin ligase, domain of unknown function DUF913 (1);	0.506668	0.20511	N	0.090900	T	0.45256	0.1333	L	0.46157	1.445	0.58432	D	0.999999	P	0.48503	0.911	P	0.47827	0.558	T	0.20806	-1.0264	10	0.21014	T	0.42	.	16.9953	0.86366	0.0:1.0:0.0:0.0	.	717	Q7Z6Z7	HUWE1_HUMAN	T	717	ENSP00000340648:R717T;ENSP00000262854:R717T;ENSP00000218328:R717T	ENSP00000218328:R717T	R	-	2	0	HUWE1	53658331	1.000000	0.71417	0.997000	0.53966	0.830000	0.47004	7.090000	0.76916	2.275000	0.75901	0.600000	0.82982	AGG	.	.	.	none		0.478	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		G	53641606	C	G	53641606	3	3	259	1	0	0	0	0	1	0	0	0	7468	681	24	4	11222	4	HUWE1	23	53641606	Missense_Mutation	SNP	C	TCGA-UZ-A9PM-01A-21D-A382-10		53641606	101628954	52	16161											
ARR3	407	hgsc.bcm.edu	37	chrX	69500417	69500417	+	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	ttctacccacagcatcctagGagacctgacagccaggtgag	11	7	10	13	0	1	3	0	2	1	1	2	4	2	3	4	2	3	1	4	2	2	3			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chrX:69500417G>C	ENST00000307959.8	+	14	1049	c.998G>C	c.(997-999)gGa>gCa	p.G333A	ARR3_ENST00000374495.3_Missense_Mutation_p.G333A|RAB41_ENST00000276066.4_5'Flank|RAB41_ENST00000374473.2_5'Flank	NM_004312.2	NP_004303.2	P36575	ARRC_HUMAN	arrestin 3, retinal (X-arrestin)	333					endocytosis (GO:0006897)|regulation of protein phosphorylation (GO:0001932)|signal transduction (GO:0007165)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202)				endometrium(3)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)	16						AGCATCCTAGGAGACCTGACA	0.498																																					p.G333A		Atlas-SNP	.											.	ARR3	41	.	0			c.G998C						PASS	.						64	61	62					X																	69500417		2203	4300	6503	SO:0001583	missense	407	exon14			TCCTAGGAGACCT		CCDS14399.1	Xq13.1	2013-10-11			ENSG00000120500	ENSG00000120500			710	protein-coding gene	gene with protein product	"arrestin 4"	301770				8224247	Standard	NM_004312		Approved	ARRX	uc004dyb.2	P36575	OTTHUMG00000021768	ENST00000307959.8:c.998G>C	chrX.hg19:g.69500417G>C	ENSP00000311538:p.Gly333Ala	25.0	0.0	.		25.0	12.0	.	NM_004312	B5B0B9|Q5JT23|Q5JT24|Q6IBF5|Q96EN2	Missense_Mutation	SNP	ENST00000307959.8	hg19	CCDS14399.1	.	.	.	.	.	.	.	.	.	.	G	17.94	3.511400	0.64522	.	.	ENSG00000120500	ENST00000374495;ENST00000374480;ENST00000307959	T;T	0.18338	2.22;2.22	5.21	4.34	0.51931	Immunoglobulin E-set (1);Arrestin, C-terminal (1);Arrestin-like, C-terminal (1);	0.227351	0.45361	D	0.000374	T	0.38746	0.1052	M	0.89840	3.065	0.33699	D	0.614329	P;D	0.55172	0.882;0.97	B;P	0.53593	0.281;0.73	T	0.62238	-0.6896	10	0.87932	D	0	-7.5091	10.158	0.42833	0.0946:0.0:0.9054:0.0	.	333;333	P36575;P36575-2	ARRC_HUMAN;.	A	333	ENSP00000363619:G333A;ENSP00000311538:G333A	ENSP00000311538:G333A	G	+	2	0	ARR3	69417142	1.000000	0.71417	0.791000	0.31998	0.990000	0.78478	4.957000	0.63652	0.965000	0.38133	0.600000	0.82982	GGA	.	.	.	none		0.498	ARR3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057055.2	NM_004312		C	69500417	G	C	69500417	3	2	259	1	0	0	0	0	1	0	0	0	979	1174	41	4	1048	4	ARR3	23	69500417	Missense_Mutation	SNP	G	TCGA-UZ-A9PM-01A-21D-A382-10	15858811	69500417	85770143	53	16162											
NHSL2	340527	hgsc.bcm.edu	37	chrX	71354534	71354534	+	5'UTR	SNP	T	T	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	ttgctccacgcagtctgacaTtgtgcccatcaacatctctg	8	12	7	14	1	3	1	1	1	2	0	5	1	4	1	2	0	3	2	2	0	1	2			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chrX:71354534T>A	ENST00000373677.1	+	0	1036				NHSL2_ENST00000540800.1_Missense_Mutation_p.I247N|NHSL2_ENST00000535692.1_5'UTR|RGAG4_ENST00000609883.1_5'Flank|RGAG4_ENST00000545866.1_5'Flank|NHSL2_ENST00000510661.1_Missense_Mutation_p.I60N			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)					CAGTCTGACATTGTGCCCATC	0.527																																					p.I247N		Atlas-SNP	.											.	NHSL2	148	.	0			c.T740A						PASS	.						97	75	81					X																	71354534		692	1591	2283	SO:0001623	5_prime_UTR_variant	340527	exon4			CTGACATTGTGCC			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.-227T>A	chrX.hg19:g.71354534T>A		44.0	0.0	.		44.0	13.0	.	NM_001013627	B2RN94	Missense_Mutation	SNP	ENST00000373677.1	hg19		.	.	.	.	.	.	.	.	.	.	t	17.20	3.329482	0.60743	.	.	ENSG00000204131	ENST00000540800;ENST00000510661	T;T	0.56776	0.71;0.44	5.27	5.27	0.74061	.	.	.	.	.	T	0.53045	0.1772	L	0.34521	1.04	0.80722	D	1	P;P	0.52692	0.955;0.955	P;P	0.54312	0.643;0.748	T	0.50423	-0.8830	8	.	.	.	.	12.1115	0.53842	0.0:0.0:0.0:1.0	.	247;60	F5H593;D6RBM4	.;.	N	247;60	ENSP00000444617:I247N;ENSP00000424079:I60N	.	I	+	2	0	NHSL2	71271259	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.634000	0.83273	1.763000	0.52060	0.378000	0.23410	ATT	.	.	.	none		0.527	NHSL2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057170.1	NM_001013627		A	71354534	T	A	71354534	1	1	259	0	1	0	0	0	0	0	0	0	10419	1493	52	5		5	NHSL2	23	71354534	5'UTR	SNP	T	TCGA-UZ-A9PM-01A-21D-A382-10	1854117	71354534	83916026	54	16163											
POU3F4	5456	hgsc.bcm.edu	37	chrX	82763464	82763464	+	Frame_Shift_Del	DEL	G	G	-																															ctccaaagtgattacttgcaGggagttcccagcaatgggca																										TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chrX:82763464delG	ENST00000373200.2	+	1	196	c.132delG	c.(130-132)cagfs	p.Q44fs	RP3-326L13.3_ENST00000607789.1_lincRNA|RP3-326L13.2_ENST00000607095.1_RNA	NM_000307.3	NP_000298	P49335	PO3F4_HUMAN	POU class 3 homeobox 4	44					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						ATTACTTGCAGGGAGTTCCCA	0.612																																					p.Q44fs		Atlas-Indel,Pindel	.											.	POU3F4	136	.	0			c.131delA						PASS	.						38	30	33					X																	82763464		2203	4300	6503	SO:0001589	frameshift_variant	5456	exon1			.	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.132delG	chrX.hg19:g.82763464delG	ENSP00000362296:p.Gln44fs	93.0	0.0	0		87.0	33.0	0.37931	NM_000307	B2RC71|Q5H9G9|Q99410	Frame_Shift_Del	DEL	ENST00000373200.2	hg19	CCDS14450.1																																																																																			.	.	.	none		0.612	POU3F4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057368.2	NM_000307		-	82763464	G	-	82763464	7	5	259	1	0	1	0	1	0	0	0	0	12284	991	35	0	134	0	POU3F4	23	82763464	Frame_Shift_Del	DEL	G	TCGA-UZ-A9PM-01A-21D-A382-10	11408930	82763464	72507096	55	16164											
VAMP7	6845	hgsc.bcm.edu	37	chrX	155171620	155171620	+	3'UTR	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	ctgtgtgaagaaataggaaaGaagaagttaccattaaccaa	19	8	9	5	0	0	4	0	1	0	3	0	5	0	5	2	1	2	1	2	1	9	3			TCGA-UZ-A9PM-01A-21D-A382-10	TCGA-UZ-A9PM-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dfef537-01d1-4b16-a21d-4e9503040705	0ec588cf-97a6-49af-a772-c55a2af2cf9b	g.chrX:155171620G>T	ENST00000286448.6	+	0	833				VAMP7_ENST00000460621.1_3'UTR|VAMP7_ENST00000262640.6_Missense_Mutation_p.K200N	NM_001145149.2|NM_005638.5	NP_001138621.1|NP_005629.1	P51809	VAMP7_HUMAN	vesicle-associated membrane protein 7						calcium ion-dependent exocytosis (GO:0017156)|endosome to lysosome transport (GO:0008333)|eosinophil degranulation (GO:0043308)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi to plasma membrane protein transport (GO:0043001)|membrane organization (GO:0061024)|neutrophil degranulation (GO:0043312)|phagocytosis, engulfment (GO:0006911)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of protein targeting to vacuolar membrane (GO:1900483)|SNARE complex assembly (GO:0035493)|triglyceride transport (GO:0034197)|vesicle fusion (GO:0006906)|vesicle fusion with Golgi apparatus (GO:0048280)|vesicle-mediated transport (GO:0016192)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|SNARE complex (GO:0031201)|synapse (GO:0045202)				large_intestine(1)|lung(8)	9	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)					AAATAGGAAAGAAGAAGTTAC	0.413																																					p.K200N		Atlas-SNP	.											.	VAMP7	39	.	0			c.G600T						PASS	.						220	211	214					X																	155171620		2203	4296	6499	SO:0001624	3_prime_UTR_variant	6845	exon7			AGGAAAGAAGAAG	AJ295938	CCDS14770.4, CCDS48199.1, CCDS55548.1	Xq28 and Yq12	2013-02-13	2007-12-05	2007-12-05	ENSG00000124333	ENSG00000124333		"Pseudoautosomal regions / PAR2", "Vesicle-associated membrane proteins"	11486	protein-coding gene	gene with protein product		300053	"synaptobrevin-like 1"	SYBL1		8640232, 11440841	Standard	NM_001145149		Approved	VAMP-7, TI-VAMP	uc004fns.3	P51809	OTTHUMG00000022679	ENST00000286448.6:c.*5G>T	chrX.hg19:g.155171620G>T		476.0	0.0	.		339.0	83.0	.	NM_001185183	Q53GY7|Q7Z409|Q9H4A7	Missense_Mutation	SNP	ENST00000286448.6	hg19	CCDS14770.4	.	.	.	.	.	.	.	.	.	.	G	6.602	0.479414	0.12581	.	.	ENSG00000124333	ENST00000262640	T	0.24350	1.86	2.6	-0.913	0.10500	.	44.072800	0.00166	N	0.000001	T	0.17916	0.0430	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.26189	-1.0110	9	0.59425	D	0.04	.	2.8345	0.05510	0.1657:0.0:0.3548:0.4795	.	200	P51809-2	.	N	200	ENSP00000262640:K200N	ENSP00000262640:K200N	K	+	3	2	VAMP7	154824814	0.926000	0.31397	0.025000	0.17156	0.147000	0.21601	0.598000	0.24074	-0.055000	0.13244	0.279000	0.19357	AAG	.	.	.	none		0.413	VAMP7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058843.1	NM_005638		T	155171620	G	T	155171620	1	4	259	0	1	0	0	0	0	0	0	0	17129	933	33	4		4	VAMP7	23	155171620	3'UTR	SNP	G	TCGA-UZ-A9PM-01A-21D-A382-10	72408156	155171620	98940	56	16165											
B4GALT2	8704	hgsc.bcm.edu	37	chr1	44450687	44450687	+	Frame_Shift_Del	DEL	C	C	-																															tataccgctgcggcgaccaaCcccgccactttgccattgcc																										TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr1:44450687delC	ENST00000356836.6	+	4	1490	c.700delC	c.(700-702)cccfs	p.P234fs	B4GALT2_ENST00000481924.1_3'UTR|B4GALT2_ENST00000372324.1_Frame_Shift_Del_p.P234fs|B4GALT2_ENST00000309519.7_Frame_Shift_Del_p.P263fs|B4GALT2_ENST00000434555.2_Frame_Shift_Del_p.P168fs	NM_001005417.2|NM_030587.2	NP_001005417.1|NP_085076.2	O60909	B4GT2_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 2	234					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|galactosyltransferase activity (GO:0008378)|lactose synthase activity (GO:0004461)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)			endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			N-Acetyl-D-glucosamine(DB00141)	CGGCGACCAACCCCGCCACTT	0.617																																					p.Q262fs		Atlas-INDEL	.											B4GALT2_ENST00000309519,NS,carcinoma,0,2	B4GALT2	35	.	0			c.786delA						PASS	.						55	53	54					1																	44450687		2203	4300	6503	SO:0001589	frameshift_variant	8704	exon4			.	AF038660	CCDS506.1, CCDS55596.1	1p34-p33	2013-02-19			ENSG00000117411	ENSG00000117411		"Beta 4-glycosyltransferases"	925	protein-coding gene	gene with protein product		604013				9405390, 9597550	Standard	NM_003780		Approved	beta4Gal-T2	uc010okl.2	O60909	OTTHUMG00000008296	ENST00000356836.6:c.700delC	chr1.hg19:g.44450687delC	ENSP00000349293:p.Pro234fs	65.0	0.0	0		46.0	11.0	0.23913	NM_030587	B3KTP0|B4DE14|D3DPY6|D3DPY7|O60511|Q4V9L9|Q5T4X5|Q5T4Y5|Q9BUP6|Q9NSY7	Frame_Shift_Del	DEL	ENST00000356836.6	hg19	CCDS506.1																																																																																			.	.	.	none		0.617	B4GALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022840.1	NM_003780		-	44450687	C	-	44450687	7	5	260	1	0	1	0	1	0	0	0	0	1271	507	18	0	710	0	B4GALT2	1	44450687	Frame_Shift_Del	DEL	C	TCGA-UZ-A9PN-01A-11D-A382-10		44450687	204799934	1	16166											
COL11A1	1301	hgsc.bcm.edu	37	chr1	103470193	103470193	+	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	atcatcaccaggaggacctgGaggaccttgaggacctcgtt	10	8	12	11	1	2	1	2	1	0	0	3	6	2	6	4	5	0	1	4	5	0	2			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr1:103470193G>C	ENST00000370096.3	-	19	2182	c.1870C>G	c.(1870-1872)Cca>Gca	p.P624A	COL11A1_ENST00000461720.1_5'UTR|COL11A1_ENST00000512756.1_Missense_Mutation_p.P508A|COL11A1_ENST00000353414.4_Missense_Mutation_p.P585A|COL11A1_ENST00000358392.2_Missense_Mutation_p.P636A	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	624	Collagen-like 3.|Collagen-like 4.|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)		GGAGGACCTGGAGGACCTTGA	0.328																																					p.P636A		Atlas-SNP	.											.	COL11A1	972	.	0			c.C1906G						PASS	.						40	36	38					1																	103470193		2203	4300	6503	SO:0001583	missense	1301	exon19			GACCTGGAGGACC	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.1870C>G	chr1.hg19:g.103470193G>C	ENSP00000359114:p.Pro624Ala	501.0	0.0	.		504.0	112.0	.	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	hg19	CCDS778.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.615873	0.87359	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000512756	D;D;D;D	0.93953	-3.32;-3.32;-3.32;-3.32	5.83	5.83	0.93111	.	0.115539	0.64402	D	0.000013	D	0.96380	0.8819	M	0.76328	2.33	0.80722	D	1	D;D;D;D	0.89917	0.997;0.996;1.0;1.0	D;D;D;D	0.87578	0.992;0.987;0.997;0.998	D	0.95297	0.8400	10	0.48119	T	0.1	.	20.1162	0.97934	0.0:0.0:1.0:0.0	.	508;585;636;624	E9PCU0;P12107-3;P12107-2;P12107	.;.;.;COBA1_HUMAN	A	624;636;585;508	ENSP00000359114:P624A;ENSP00000351163:P636A;ENSP00000302551:P585A;ENSP00000426533:P508A	ENSP00000302551:P585A	P	-	1	0	COL11A1	103242781	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	5.562000	0.67346	2.756000	0.94617	0.655000	0.94253	CCA	.	.	.	none		0.328	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		C	103470193	G	C	103470193	3	2	260	1	0	0	0	0	1	0	0	0	3669	1174	41	4	3746	4	COL11A1	1	103470193	Missense_Mutation	SNP	G	TCGA-UZ-A9PN-01A-11D-A382-10	59019506	103470193	145780428	2	16167											
NPR1	4881	hgsc.bcm.edu	37	chr1	153651789	153651789	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctggcccaggtgaaggcgCgccccgacttgctgccgggc	4	5	15	17	4	0	1	0	1	0	0	0	2	0	1	5	4	2	1	5	4	1	1			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr1:153651789C>T	ENST00000368680.3	+	1	677	c.205C>T	c.(205-207)Cgc>Tgc	p.R69C		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	69					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)	GGTGAAGGCGCGCCCCGACTT	0.736																																					p.R69C	Pancreas(141;1349 1870 15144 15830 40702)	Atlas-SNP	.											.	NPR1	104	.	0			c.C205T						PASS	.						3	4	4					1																	153651789		1837	3626	5463	SO:0001583	missense	4881	exon1			AAGGCGCGCCCCG	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.205C>T	chr1.hg19:g.153651789C>T	ENSP00000357669:p.Arg69Cys	60.0	0.0	.		48.0	12.0	.	NM_000906	B0ZBF0|Q5SR08|Q6P4Q3	Missense_Mutation	SNP	ENST00000368680.3	hg19	CCDS1051.1	.	.	.	.	.	.	.	.	.	.	C	11.85	1.762841	0.31228	.	.	ENSG00000169418	ENST00000368680	D	0.83335	-1.71	3.73	2.8	0.32819	Extracellular ligand-binding receptor (1);	0.471967	0.20468	N	0.091747	T	0.58906	0.2155	N	0.22421	0.69	0.19300	N	0.99997	P	0.44816	0.844	P	0.44359	0.447	T	0.54655	-0.8261	10	0.72032	D	0.01	.	6.4211	0.21744	0.2105:0.5851:0.2044:0.0	.	69	P16066	ANPRA_HUMAN	C	69	ENSP00000357669:R69C	ENSP00000357669:R69C	R	+	1	0	NPR1	151918413	0.024000	0.19004	0.905000	0.35620	0.811000	0.45836	0.786000	0.26844	0.738000	0.32606	0.462000	0.41574	CGC	.	.	.	none		0.736	NPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090034.1	NM_000906		T	153651789	C	T	153651789	3	4	260	1	0	0	0	0	1	0	0	0	10601	768	27	1	207	1	NPR1	1	153651789	Missense_Mutation	SNP	C	TCGA-UZ-A9PN-01A-11D-A382-10	50181596	153651789	95598832	3	16168											
IQGAP3	128239	hgsc.bcm.edu	37	chr1	156524143	156524143	+	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	ttaatcaggaccacagctgaGagcatctccacagccacgaa	14	6	8	13	1	2	1	1	1	1	1	3	4	2	2	3	1	3	2	3	1	2	1	rs370248624		TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr1:156524143G>T	ENST00000361170.2	-	13	1342	c.1332C>A	c.(1330-1332)ctC>ctA	p.L444L		NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	444					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)					CCACAGCTGAGAGCATCTCCA	0.612																																					p.L444L		Atlas-SNP	.											.	IQGAP3	146	.	0			c.C1332A						PASS	.						43	43	43					1																	156524143		2203	4300	6503	SO:0001819	synonymous_variant	128239	exon13			AGCTGAGAGCATC	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.1332C>A	chr1.hg19:g.156524143G>T		177.0	0.0	.		160.0	24.0	.	NM_178229	Q5T3H8	Silent	SNP	ENST00000361170.2	hg19	CCDS1144.1																																																																																			.	.	.	none		0.612	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229		T	156524143	G	T	156524143	2	4	260	1	0	0	0	0	0	0	0	1	7823	929	33	4		4	IQGAP3	1	156524143	Silent	SNP	G	TCGA-UZ-A9PN-01A-11D-A382-10	2872354	156524143	92726478	4	16169											
TOMM40L	84134	hgsc.bcm.edu	37	chr1	161198533	161198536	+	Frame_Shift_Del	DEL	ACAC	ACAC	-																															tggagtggagtttgaggcaaAcacaaggctacaagacacaa																										TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	ACAC	ACAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr1:161198533_161198536delACAC	ENST00000367988.3	+	9	982_985	c.713_716delACAC	c.(712-717)aacacafs	p.NT238fs	TOMM40L_ENST00000545897.1_Frame_Shift_Del_p.NT204fs|TOMM40L_ENST00000367987.1_Frame_Shift_Del_p.NT238fs|TOMM40L_ENST00000474486.1_3'UTR|MIR5187_ENST00000583479.1_RNA|NR1I3_ENST00000479324.1_5'Flank	NM_032174.4	NP_115550.2	Q969M1	TM40L_HUMAN	translocase of outer mitochondrial membrane 40 homolog (yeast)-like	238					ion transport (GO:0006811)|protein transport (GO:0015031)	mitochondrial outer membrane (GO:0005741)|pore complex (GO:0046930)|protein complex (GO:0043234)	porin activity (GO:0015288)			large_intestine(2)|liver(4)|lung(4)	10	all_cancers(52;1.86e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			TTTGAGGCAAACACAAGGCTACAA	0.485																																					p.238_239del		Atlas-Indel,Pindel	.											.	TOMM40L	19	.	0			c.712_715del						PASS	.																																			SO:0001589	frameshift_variant	84134	exon9			.		CCDS1227.1, CCDS65700.1	1q23.3	2008-02-05	2007-01-12		ENSG00000158882	ENSG00000158882			25756	protein-coding gene	gene with protein product			"translocase of outer mitochondrial membrane 40 homolog-like (yeast)"				Standard	NM_032174		Approved	FLJ12770, TOMM40B	uc001fzd.3	Q969M1	OTTHUMG00000034345	ENST00000367988.3:c.713_716delACAC	chr1.hg19:g.161198533_161198536delACAC	ENSP00000356967:p.Asn238fs	144.0	0.0	0		109.0	26.0	0.238532	NM_032174	B7Z4U0|D3DVG9	Frame_Shift_Del	DEL	ENST00000367988.3	hg19	CCDS1227.1																																																																																			.	.	.	none		0.485	TOMM40L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083029.1	NM_032174		-	161198536	ACAC	-	161198533	7	5	260	1	0	1	0	1	0	0	0	0	16371	43	2	0	743	0	TOMM40L	1	161198533	Frame_Shift_Del	DEL	ACAC	TCGA-UZ-A9PN-01A-11D-A382-10	4674390	161198533	88052088	5	16170											
CACNA1S	779	hgsc.bcm.edu	37	chr1	201030418	201030418	+	Missense_Mutation	SNP	T	T	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	gttcttgtccagctcacagtTcttgtactcagtctctccct	5	16	6	14	0	5	0	2	0	3	0	8	0	7	0	2	0	2	4	2	0	1	5			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr1:201030418T>G	ENST00000362061.3	-	25	3458	c.3232A>C	c.(3232-3234)Aac>Cac	p.N1078H	CACNA1S_ENST00000367338.3_Missense_Mutation_p.N1078H	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1078					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)	AGCTCACAGTTCTTGTACTCA	0.552																																					p.N1078H		Atlas-SNP	.											.	CACNA1S	249	.	0			c.A3232C						PASS	.						131	105	114					1																	201030418		2203	4300	6503	SO:0001583	missense	779	exon25			CACAGTTCTTGTA	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.3232A>C	chr1.hg19:g.201030418T>G	ENSP00000355192:p.Asn1078His	102.0	0.0	.		76.0	14.0	.	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	hg19	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	T	17.96	3.516695	0.64634	.	.	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.96365	-3.99;-3.91	5.21	4.07	0.47477	.	0.129861	0.64402	D	0.000001	D	0.97870	0.9300	M	0.90922	3.16	0.43740	D	0.996231	P	0.44521	0.837	P	0.58577	0.841	D	0.97740	1.0208	10	0.87932	D	0	.	9.0753	0.36517	0.0:0.1511:0.0:0.8489	.	1078	Q13698	CAC1S_HUMAN	H	1078	ENSP00000355192:N1078H;ENSP00000356307:N1078H	ENSP00000355192:N1078H	N	-	1	0	CACNA1S	199297041	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.036000	0.41165	0.914000	0.36822	0.459000	0.35465	AAC	.	.	.	none		0.552	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		G	201030418	T	G	201030418	3	3	260	1	0	0	0	0	1	0	0	0	2549	1783	62	5	2469	5	CACNA1S	1	201030418	Missense_Mutation	SNP	T	TCGA-UZ-A9PN-01A-11D-A382-10	39831885	201030418	48220203	6	16171											
NVL	4931	hgsc.bcm.edu	37	chr1	224424263	224424263	+	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	ttccaaatttacatctgcatCcagtggtggtttggtaccat	9	15	8	9	0	1	0	0	0	1	0	3	0	3	0	3	3	3	3	3	3	3	5			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr1:224424263C>A	ENST00000281701.6	-	20	2570	c.2311G>T	c.(2311-2313)Gat>Tat	p.D771Y	NVL_ENST00000391875.2_Missense_Mutation_p.D665Y|NVL_ENST00000482491.1_Missense_Mutation_p.D495Y|NVL_ENST00000340871.4_Missense_Mutation_p.D582Y|NVL_ENST00000361463.3_3'UTR|NVL_ENST00000469075.1_Missense_Mutation_p.D680Y	NM_002533.3	NP_002524.2	O15381	NVL_HUMAN	nuclear VCP-like	771						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|prostate(1)|skin(4)|soft_tissue(1)|urinary_tract(1)	42				GBM - Glioblastoma multiforme(131;0.00501)		ACATCTGCATCCAGTGGTGGT	0.408																																					p.D771Y		Atlas-SNP	.											.	NVL	74	.	0			c.G2311T						PASS	.						145	137	140					1																	224424263		2203	4300	6503	SO:0001583	missense	4931	exon20			CTGCATCCAGTGG	U78772	CCDS1541.1, CCDS1542.1, CCDS58062.1, CCDS58063.1	1q41-q42.2	2010-04-21			ENSG00000143748	ENSG00000143748		"ATPases / AAA-type"	8070	protein-coding gene	gene with protein product	"Nuclear valosin-containing protein-like", "nuclear VCP-like protein"	602426				9286697	Standard	NM_002533		Approved		uc001hok.3	O15381	OTTHUMG00000037536	ENST00000281701.6:c.2311G>T	chr1.hg19:g.224424263C>A	ENSP00000281701:p.Asp771Tyr	191.0	0.0	.		169.0	51.0	.	NM_002533	B4DMC4|B4DP98|Q96EM7	Missense_Mutation	SNP	ENST00000281701.6	hg19	CCDS1541.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.50|16.50	3.141513|3.141513	0.57044|0.57044	.|.	.|.	ENSG00000143748|ENSG00000143748	ENST00000281701;ENST00000391875;ENST00000469075;ENST00000482491;ENST00000340871|ENST00000469968	D;D;D;D;D|.	0.95001|.	-3.58;-3.58;-3.58;-3.58;-3.58|.	5.67|5.67	5.67|5.67	0.87782|0.87782	.|.	0.199823|.	0.52532|.	D|.	0.000077|.	T|T	0.78419|0.78419	0.4280|0.4280	M|M	0.84082|0.84082	2.675|2.675	0.80722|0.80722	D|D	1|1	P;P;P|.	0.45283|.	0.855;0.699;0.855|.	B;B;B|.	0.43052|.	0.242;0.162;0.406|.	T|T	0.79329|0.79329	-0.1848|-0.1848	10|5	0.52906|.	T|.	0.07|.	-8.2467|-8.2467	15.5999|15.5999	0.76616|0.76616	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	582;680;771|.	B4DMC4;B4DP98;O15381|.	.;.;NVL_HUMAN|.	Y|V	771;665;680;495;582|653	ENSP00000281701:D771Y;ENSP00000375747:D665Y;ENSP00000417826:D680Y;ENSP00000417213:D495Y;ENSP00000341362:D582Y|.	ENSP00000281701:D771Y|.	D|G	-|-	1|2	0|0	NVL|NVL	222490886|222490886	0.998000|0.998000	0.40836|0.40836	0.994000|0.994000	0.49952|0.49952	0.908000|0.908000	0.53690|0.53690	4.387000|4.387000	0.59626|0.59626	2.831000|2.831000	0.97527|0.97527	0.655000|0.655000	0.94253|0.94253	GAT|GGA	.	.	.	none		0.408	NVL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091453.2	NM_002533		A	224424263	C	A	224424263	3	1	260	1	0	0	0	0	1	0	0	0	10787	855	30	4	275	4	NVL	1	224424263	Missense_Mutation	SNP	C	TCGA-UZ-A9PN-01A-11D-A382-10	23393845	224424263	24826358	7	16172											
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125405388	125405388	+	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	atacagagctgacccgagtgCggggcgctaaccctgagaag	11	5	14	11	3	0	3	0	2	0	2	0	5	0	3	2	2	4	2	2	2	3	2	rs200795882		TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr2:125405388C>T	ENST00000431078.1	+	13	2291	c.1927C>T	c.(1927-1929)Cgg>Tgg	p.R643W		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	643	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		GACCCGAGTGCGGGGCGCTAA	0.562													C|||	1	0.000199681	8e-04	0	5008	,	,		19738	0		0	False		,,,				2504	0				p.R643W		Atlas-SNP	.											CNTNAP5,caecum,carcinoma,0,2	CNTNAP5	405	.	0			c.C1927T						PASS	.	C	TRP/ARG	3,4167		0,3,2082	39	41	41		1927	2.2	0	2		41	3,8413		0,3,4205	yes	missense	CNTNAP5	NM_130773.2	101	0,6,6287	TT,TC,CC		0.0356,0.0719,0.0477	probably-damaging	643/1307	125405388	6,12580	2085	4208	6293	SO:0001583	missense	129684	exon13			CGAGTGCGGGGCG	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.1927C>T	chr2.hg19:g.125405388C>T	ENSP00000399013:p.Arg643Trp	297.0	0.0	.		273.0	72.0	.	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	hg19	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	C	13.90	2.376451	0.42105	7.19E-4	3.56E-4	ENSG00000155052	ENST00000431078	T	0.11385	2.78	5.2	2.17	0.27698	.	0.624103	0.14114	N	0.340507	T	0.15176	0.0366	M	0.61703	1.905	0.09310	N	1	D	0.58620	0.983	B	0.43018	0.405	T	0.11641	-1.0579	10	0.72032	D	0.01	.	13.8889	0.63726	0.3906:0.6093:0.0:0.0	.	643	Q8WYK1	CNTP5_HUMAN	W	643	ENSP00000399013:R643W	ENSP00000399013:R643W	R	+	1	2	CNTNAP5	125121858	0.380000	0.25131	0.012000	0.15200	0.339000	0.28857	1.823000	0.39062	0.661000	0.30985	0.561000	0.74099	CGG	.	.	.	weak		0.562	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			T	125405388	C	T	125405388	3	4	260	1	0	0	0	0	1	0	0	0	3652	759	27	1	1977	1	CNTNAP5	2	125405388	Missense_Mutation	SNP	C	TCGA-UZ-A9PN-01A-11D-A382-10		125405388	117793985	8	16173											
LRP1B	53353	hgsc.bcm.edu	37	chr2	141598582	141598582	+	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	agccttgccacattaatttgCgtttcatcaaattctgagct	10	15	6	10	1	3	1	2	1	1	0	3	1	3	1	2	0	4	2	2	0	2	5	rs373983727		TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr2:141598582C>T	ENST00000389484.3	-	30	5990	c.5019G>A	c.(5017-5019)acG>acA	p.T1673T		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1673					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)		CATTAATTTGCGTTTCATCAA	0.418										TSP Lung(27;0.18)																											p.T1673T	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.G5019A						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	135	121	126		5019	-10.9	1	2		126	0,8600		0,0,4300	no	coding-synonymous	LRP1B	NM_018557.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		1673/4600	141598582	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	53353	exon30			AATTTGCGTTTCA	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.5019G>A	chr2.hg19:g.141598582C>T		109.0	0.0	.		86.0	13.0	.	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	hg19	CCDS2182.1																																																																																			.	.	.	weak		0.418	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141598582	C	T	141598582	2	4	260	1	0	0	0	0	0	0	0	1	8962	755	27	1		1	LRP1B	2	141598582	Silent	SNP	C	TCGA-UZ-A9PN-01A-11D-A382-10	16193194	141598582	101600791	9	16174											
ANKRD44	91526	hgsc.bcm.edu	37	chr2	197870520	197870520	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctcgctcagccacgtggCgtggccacgagcagctgcat	7	6	13	15	4	1	0	1	0	0	0	2	1	1	0	2	2	5	5	2	2	0	0	rs150303870		TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr2:197870520C>T	ENST00000328737.2	-	21	2246	c.2170G>A	c.(2170-2172)Gcc>Acc	p.A724T	ANKRD44_ENST00000337207.5_Missense_Mutation_p.A724T|ANKRD44_ENST00000450567.1_Missense_Mutation_p.A724T|ANKRD44_ENST00000282272.8_Missense_Mutation_p.A741T			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	749										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)			AGCCACGTGGCGTGGCCACGA	0.527																																					p.A749T		Atlas-SNP	.											.	ANKRD44	281	.	0			c.G2245A						PASS	.	C	THR/ALA	0,4406		0,0,2203	154	150	151		2245	5.3	1	2	dbSNP_134	151	1,8599	1.2+/-3.3	0,1,4299	no	missense	ANKRD44	NM_001195144.1	58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	749/994	197870520	1,13005	2203	4300	6503	SO:0001583	missense	91526	exon21			ACGTGGCGTGGCC	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.2170G>A	chr2.hg19:g.197870520C>T	ENSP00000331516:p.Ala724Thr	183.0	0.0	.		160.0	40.0	.	NM_001195144	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Missense_Mutation	SNP	ENST00000328737.2	hg19		.	.	.	.	.	.	.	.	.	.	C	13.35	2.210902	0.39102	0.0	1.16E-4	ENSG00000065413	ENST00000424317;ENST00000282272;ENST00000328737;ENST00000450567;ENST00000337207	T;T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14;-0.14	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.62804	0.2458	N	0.16130	0.375	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.61691	-0.7011	10	0.34782	T	0.22	.	12.4427	0.55634	0.0:0.9242:0.0:0.0758	.	767	Q8N8A2-2	.	T	564;741;724;724;724	ENSP00000403415:A564T;ENSP00000282272:A741T;ENSP00000331516:A724T;ENSP00000402420:A724T;ENSP00000338794:A724T	ENSP00000282272:A741T	A	-	1	0	ANKRD44	197578765	0.960000	0.32886	0.994000	0.49952	0.986000	0.74619	2.068000	0.41471	2.767000	0.95098	0.655000	0.94253	GCC	.	C|1.000;T|0.000	0.000	weak		0.527	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697		T	197870520	C	T	197870520	3	4	260	1	0	0	0	0	1	0	0	0	672	768	27	1	613	1	ANKRD44	2	197870520	Missense_Mutation	SNP	C	TCGA-UZ-A9PN-01A-11D-A382-10	56271938	197870520	45328853	10	16175											
GIGYF2	26058	hgsc.bcm.edu	37	chr2	233651983	233651983	+	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	tggagaagatgaagatggagGttggcgactagctggatcaa	13	8	16	4	1	1	4	1	1	0	3	1	8	1	6	0	5	1	2	0	5	4	2			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr2:233651983G>T	ENST00000409547.1	+	11	967	c.656G>T	c.(655-657)gGt>gTt	p.G219V	GIGYF2_ENST00000373566.3_Missense_Mutation_p.G241V|GIGYF2_ENST00000452341.2_Missense_Mutation_p.G50V|GIGYF2_ENST00000373563.4_Missense_Mutation_p.G219V|GIGYF2_ENST00000409480.1_Missense_Mutation_p.G241V|GIGYF2_ENST00000409451.3_Missense_Mutation_p.G241V|GIGYF2_ENST00000409196.3_Missense_Mutation_p.G219V	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	219	Arg-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)		GAAGATGGAGGTTGGCGACTA	0.463																																					p.G241V		Atlas-SNP	.											.	GIGYF2	288	.	0			c.G722T						PASS	.						124	126	125					2																	233651983		2203	4300	6503	SO:0001583	missense	26058	exon11			ATGGAGGTTGGCG	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.656G>T	chr2.hg19:g.233651983G>T	ENSP00000386537:p.Gly219Val	136.0	0.0	.		123.0	37.0	.	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	hg19	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.117800	0.77323	.	.	ENSG00000204120	ENST00000373566;ENST00000414511;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000535418;ENST00000423659;ENST00000409196;ENST00000409451;ENST00000440945;ENST00000445650;ENST00000452341;ENST00000421778	T;T;T;T;T;T;T;T;T;T	0.79247	-0.96;-0.91;-0.96;-0.91;-0.99;-0.91;-0.96;-1.07;-1.25;-0.73	5.93	5.05	0.67936	.	0.054310	0.85682	D	0.000000	D	0.85301	0.5665	L	0.52573	1.65	0.80722	D	1	D;P;P;P	0.76494	0.999;0.757;0.912;0.573	D;B;B;B	0.78314	0.991;0.341;0.255;0.168	D	0.86420	0.1754	10	0.59425	D	0.04	-13.7649	17.2528	0.87047	0.0:0.1256:0.8744:0.0	.	50;241;219;219	E9PC50;A6H8W4;Q6Y7W6;E9PBB0	.;.;PERQ2_HUMAN;.	V	241;168;219;241;219;219;168;219;241;219;50;50;46	ENSP00000362667:G241V;ENSP00000362664:G219V;ENSP00000386765:G241V;ENSP00000386537:G219V;ENSP00000404195:G168V;ENSP00000387070:G219V;ENSP00000387170:G241V;ENSP00000410297:G219V;ENSP00000392218:G50V;ENSP00000411505:G50V	ENSP00000362664:G219V	G	+	2	0	GIGYF2	233360227	1.000000	0.71417	0.982000	0.44146	0.915000	0.54546	9.230000	0.95299	1.493000	0.48517	-0.165000	0.13383	GGT	.	.	.	none		0.463	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		T	233651983	G	T	233651983	3	4	260	1	0	0	0	0	1	0	0	0	6385	1261	44	4	752	4	GIGYF2	2	233651983	Missense_Mutation	SNP	G	TCGA-UZ-A9PN-01A-11D-A382-10	35781463	233651983	9547390	11	16176											
UGT1A10	54575	hgsc.bcm.edu	37	chr2	234545301	234545301	+	Missense_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	ggttcaccatgcagtcggtgGtggagaaacttatcctcagg	9	10	13	9	1	2	1	2	0	0	1	4	2	3	1	2	5	2	2	2	5	2	2	rs371430642		TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr2:234545301G>A	ENST00000344644.5	+	1	202	c.133G>A	c.(133-135)Gtg>Atg	p.V45M	UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000373445.1_Missense_Mutation_p.V45M	NM_019075.2	NP_061948.1	Q9HAW8	UD110_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A10	45					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)	GCAGTCGGTGGTGGAGAAACT	0.522																																					p.V45M		Atlas-SNP	.											.	UGT1A10	71	.	0			c.G133A						PASS	.						97	81	86					2																	234545301		2203	4297	6500	SO:0001583	missense	54575	exon1			TCGGTGGTGGAGA	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.133G>A	chr2.hg19:g.234545301G>A	ENSP00000343838:p.Val45Met	115.0	0.0	.		77.0	22.0	.	NM_019075	O00474|Q6NT91|Q7Z6H8	Missense_Mutation	SNP	ENST00000344644.5	hg19	CCDS33403.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.757072	0.49468	.	.	ENSG00000242515	ENST00000344644;ENST00000373445	T;T	0.62364	0.03;0.03	3.67	2.77	0.32553	.	.	.	.	.	T	0.74898	0.3777	M	0.75150	2.29	0.32795	N	0.500625	D;D	0.89917	1.0;0.999	D;D	0.81914	0.995;0.992	T	0.78277	-0.2266	9	0.72032	D	0.01	.	8.077	0.30722	0.0918:0.1602:0.748:0.0	.	45;45	Q9HAW8;Q7Z6H8	UD110_HUMAN;.	M	45	ENSP00000343838:V45M;ENSP00000362544:V45M	ENSP00000343838:V45M	V	+	1	0	UGT1A10	234210040	0.000000	0.05858	0.722000	0.30670	0.806000	0.45545	-0.506000	0.06359	0.885000	0.36088	0.405000	0.27470	GTG	.	.	.	alt		0.522	UGT1A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130986.1	NM_019075		A	234545301	G	A	234545301	3	1	260	1	0	0	0	0	1	0	0	0	16957	1261	44	2	135	2	UGT1A10	2	234545301	Missense_Mutation	SNP	G	TCGA-UZ-A9PN-01A-11D-A382-10	893318	234545301	8654072	12	16177											
CAMK2N2	94032	hgsc.bcm.edu	37	chr3	183979036	183979036	+	Frame_Shift_Del	DEL	C	C	-																															cggggtctgcgccgaagcggCccatcttgtcttcgctgtag																										TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr3:183979036delC	ENST00000296238.3	-	1	215	c.38delG	c.(37-39)ggcfs	p.G13fs	EIF2B5_ENST00000444495.1_Intron|ECE2_ENST00000402825.3_Intron	NM_033259.2	NP_150284.1	Q96S95	CK2N2_HUMAN	calcium/calmodulin-dependent protein kinase II inhibitor 2	13						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)			GCCGAAGCGGCCCATCTTGTC	0.736																																					p.G13fs		Atlas-Indel,Pindel	.											.	CAMK2N2	2	.	0			c.39delC						PASS	.						22	24	23					3																	183979036		2202	4300	6502	SO:0001589	frameshift_variant	94032	exon1			.	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.38delG	chr3.hg19:g.183979036delC	ENSP00000296238:p.Gly13fs	115.0	0.0	0		105.0	40.0	0.380952	NM_033259		Frame_Shift_Del	DEL	ENST00000296238.3	hg19	CCDS3257.1																																																																																			.	.	.	none		0.736	CAMK2N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346010.1	NM_033259		-	183979036	C	-	183979036	7	5	260	1	0	1	0	1	0	0	0	0	2606	739	26	0	209	0	CAMK2N2	3	183979036	Frame_Shift_Del	DEL	C	TCGA-UZ-A9PN-01A-11D-A382-10		183979036	14043394	13	16178											
C4orf3	401152	hgsc.bcm.edu	37	chr4	120221731	120221731	+	5'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	0	0	0	0	0	0	0	acaaccctagaaaccgaaaaTgcttaagttcccggactttg	14	9	7	11	2	0	1	0	0	0	1	1	3	1	2	3	1	3	2	3	1	6	4			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr4:120221731T>C	ENST00000504110.1	-	0	345				C4orf3_ENST00000399075.4_Missense_Mutation_p.H120R	NM_001001701.3	NP_001001701.2	Q8WVX3	CD003_HUMAN	chromosome 4 open reading frame 3							integral component of membrane (GO:0016021)				breast(1)|large_intestine(1)|lung(4)	6						AAACCGAAAATGCTTAAGTTC	0.622																																					p.H120R		Atlas-SNP	.											.	C4orf3	16	.	0			c.A359G						PASS	.						67	71	70					4																	120221731		1938	4123	6061	SO:0001623	5_prime_UTR_variant	401152	exon2			CGAAAATGCTTAA		CCDS43266.1, CCDS54798.1	4q26	2012-02-24			ENSG00000164096	ENSG00000164096			19225	protein-coding gene	gene with protein product	"HCV F-transactivated protein 1"						Standard	NM_001001701		Approved		uc021xrf.1	Q8WVX3	OTTHUMG00000161333	ENST00000504110.1:c.-41A>G	chr4.hg19:g.120221731T>C		69.0	0.0	.		53.0	8.0	.	NM_001170330	Q6J203	Missense_Mutation	SNP	ENST00000504110.1	hg19	CCDS43266.1	.	.	.	.	.	.	.	.	.	.	T	13.59	2.283765	0.40394	.	.	ENSG00000164096	ENST00000399075	T	0.35236	1.32	4.69	-9.37	0.00626	.	.	.	.	.	T	0.22513	0.0543	.	.	.	0.09310	N	1.0	.	.	.	.	.	.	T	0.40534	-0.9558	5	0.72032	D	0.01	3.2825	1.6478	0.02765	0.1686:0.1153:0.2784:0.4377	.	.	.	.	R	120	ENSP00000382026:H120R	ENSP00000382026:H120R	H	-	2	0	C4orf3	120441179	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.183000	0.01255	-1.509000	0.01798	-1.100000	0.02121	CAT	.	.	.	none		0.622	C4orf3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364576.3	NM_001001701		C	120221731	T	C	120221731	1	2	260	0	1	0	0	0	0	0	0	0	2262	1464	51	3		3	C4orf3	4	120221731	5'UTR	SNP	T	TCGA-UZ-A9PN-01A-11D-A382-10		120221731	70932545	14	16179											
NNT	23530	hgsc.bcm.edu	37	chr5	43624161	43624161	+	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	tagttggtggtggtgttgctGggcttgcttctgcaggcgca	3	14	17	7	1	1	0	0	0	1	0	1	0	1	0	0	5	3	7	0	5	1	5			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr5:43624161G>A	ENST00000264663.5	+	6	936	c.715G>A	c.(715-717)Ggg>Agg	p.G239R	NNT_ENST00000512996.2_Missense_Mutation_p.G108R|NNT_ENST00000344920.4_Missense_Mutation_p.G239R	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	239					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					TGGTGTTGCTGGGCTTGCTTC	0.408																																					p.G239R		Atlas-SNP	.											.	NNT	92	.	0			c.G715A						PASS	.						358	327	338					5																	43624161		2203	4300	6503	SO:0001583	missense	23530	exon6			GTTGCTGGGCTTG	U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.715G>A	chr5.hg19:g.43624161G>A	ENSP00000264663:p.Gly239Arg	123.0	0.0	.		95.0	22.0	.	NM_182977	Q16796|Q2TB60|Q8N3V4	Missense_Mutation	SNP	ENST00000264663.5	hg19	CCDS3949.1	.	.	.	.	.	.	.	.	.	.	G	35	5.538687	0.96474	.	.	ENSG00000112992	ENST00000264663;ENST00000344920;ENST00000512996	D;D;D	0.97665	-4.48;-4.48;-4.48	6.04	6.04	0.98038	Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 (1);Alanine dehydrogenase/PNT, C-terminal (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99492	0.9819	H	0.99985	5.235	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97472	1.0041	10	0.87932	D	0	-10.7542	20.5792	0.99380	0.0:0.0:1.0:0.0	.	239	Q13423	NNTM_HUMAN	R	239;239;108	ENSP00000264663:G239R;ENSP00000343873:G239R;ENSP00000426343:G108R	ENSP00000264663:G239R	G	+	1	0	NNT	43659918	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.334000	0.96470	2.873000	0.98535	0.561000	0.74099	GGG	.	.	.	none		0.408	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977		A	43624161	G	A	43624161	3	1	260	1	0	0	0	0	1	0	0	0	10517	1348	47	2	733	2	NNT	5	43624161	Missense_Mutation	SNP	G	TCGA-UZ-A9PN-01A-11D-A382-10		43624161	137291099	15	16180											
HNRNPA0	10949	hgsc.bcm.edu	37	chr5	137088931	137088931	+	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	ccccagctactgcctccaccGccgccgccgccgccgctctt	3	6	8	24	6	1	0	0	0	1	0	2	0	2	0	10	0	3	2	10	0	1	2			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr5:137088931G>A	ENST00000314940.4	-	1	1108	c.825C>T	c.(823-825)ggC>ggT	p.G275G		NM_006805.3	NP_006796.1	Q13151	ROA0_HUMAN	heterogeneous nuclear ribonucleoprotein A0	275	Gly-rich.				3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|inflammatory response (GO:0006954)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|response to lipopolysaccharide (GO:0032496)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)	p.G275G(1)		large_intestine(1)|lung(2)|skin(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			Tgcctccaccgccgccgccgc	0.632																																					p.G275G		Atlas-SNP	.											HNRNPA0,colon,carcinoma,0,1	HNRNPA0	17	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C825T						PASS	.						9	13	11					5																	137088931		1925	3891	5816	SO:0001819	synonymous_variant	10949	exon1			TCCACCGCCGCCG	U23803	CCDS4193.1	5q31	2013-02-12		2007-08-16	ENSG00000177733	ENSG00000177733		"RNA binding motif (RRM) containing"	5030	protein-coding gene	gene with protein product		609409		HNRPA0		7585247	Standard	NM_006805		Approved	hnRNPA0	uc003lbt.3	Q13151	OTTHUMG00000129156	ENST00000314940.4:c.825C>T	chr5.hg19:g.137088931G>A		97.0	0.0	.		80.0	4.0	.	NM_006805	Q6IB18	Silent	SNP	ENST00000314940.4	hg19	CCDS4193.1																																																																																			.	.	.	none		0.632	HNRNPA0-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251221.1	NM_006805		A	137088931	G	A	137088931	2	1	260	1	0	0	0	0	0	0	0	1	7263	1074	38	1		1	HNRNPA0	5	137088931	Silent	SNP	G	TCGA-UZ-A9PN-01A-11D-A382-10	93464770	137088931	43826329	16	16181											
PCDHB15	56121	hgsc.bcm.edu	37	chr5	140626523	140626523	+	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	caaacctcctacaccctgttCgtccgcgagaacaacagccc	11	6	6	18	3	0	1	0	0	0	1	3	2	2	1	5	0	5	1	5	0	4	2			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr5:140626523C>T	ENST00000231173.3	+	1	1377	c.1377C>T	c.(1375-1377)ttC>ttT	p.F459F		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	459	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(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)			ACACCCTGTTCGTCCGCGAGA	0.627																																					p.F459F		Atlas-SNP	.											.	PCDHB15	138	.	0			c.C1377T						PASS	.						83	87	86					5																	140626523		2203	4297	6500	SO:0001819	synonymous_variant	56121	exon1			CCTGTTCGTCCGC	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.1377C>T	chr5.hg19:g.140626523C>T		121.0	0.0	.		91.0	19.0	.	NM_018935	Q8IUX5	Silent	SNP	ENST00000231173.3	hg19	CCDS4257.1																																																																																			.	.	.	none		0.627	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935		T	140626523	C	T	140626523	2	4	260	1	0	0	0	0	0	0	0	1	11547	883	31	1		1	PCDHB15	5	140626523	Silent	SNP	C	TCGA-UZ-A9PN-01A-11D-A382-10	3537592	140626523	40288737	17	16182											
C5orf45	51149	hgsc.bcm.edu	37	chr5	179267940	179267940	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acggctgcacggaggctggaCggtgctcctgctccacttcc	5	8	13	15	3	0	0	0	0	0	0	3	2	3	2	3	5	3	5	3	5	0	1	rs112467347		TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr5:179267940C>T	ENST00000292586.6	-	6	559	c.469G>A	c.(469-471)Gtc>Atc	p.V157I	C5orf45_ENST00000523084.1_Missense_Mutation_p.V23I|C5orf45_ENST00000518219.1_Missense_Mutation_p.V157I|C5orf45_ENST00000403396.2_Missense_Mutation_p.V199I|C5orf45_ENST00000376931.2_Missense_Mutation_p.V102I|C5orf45_ENST00000520698.1_Missense_Mutation_p.V102I|C5orf45_ENST00000523267.1_Intron|C5orf45_ENST00000521333.1_Intron|C5orf45_ENST00000518235.1_Missense_Mutation_p.V157I	NM_016175.3	NP_057259.2	Q6NTE8	CE045_HUMAN	chromosome 5 open reading frame 45	157										breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12						GGAGGCTGGACGGTGCTCCTG	0.632																																					p.V157I		Atlas-SNP	.											C5orf45,NS,carcinoma,0,1	C5orf45	23	.	0			c.G469A						PASS	.	C	ILE/VAL,ILE/VAL	0,4406		0,0,2203	51	42	45		304,469	1.7	0	5	dbSNP_132	45	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	C5orf45	NM_001017987.2,NM_016175.3	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	102/289,157/344	179267940	1,13005	2203	4300	6503	SO:0001583	missense	51149	exon6			GCTGGACGGTGCT		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.469G>A	chr5.hg19:g.179267940C>T	ENSP00000292586:p.Val157Ile	84.0	0.0	.		76.0	20.0	.	NM_016175	B5MD09|E9PAK6|Q7Z3D8|Q9BUC1|Q9UN54	Missense_Mutation	SNP	ENST00000292586.6	hg19	CCDS34319.1	.	.	.	.	.	.	.	.	.	.	C	2.766	-0.256704	0.05829	0.0	1.16E-4	ENSG00000161010	ENST00000403396;ENST00000518235;ENST00000520698;ENST00000376931;ENST00000518219;ENST00000523084;ENST00000292586	T;T;T;T;T;T;T	0.35789	1.78;1.84;1.69;2.06;1.86;1.29;3.02	2.61	1.74	0.24563	.	1.280390	0.05906	N	0.630909	T	0.19565	0.0470	N	0.17674	0.51	0.09310	N	1	B;B;B;B;B	0.20780	0.005;0.005;0.003;0.003;0.048	B;B;B;B;B	0.08055	0.002;0.003;0.002;0.003;0.003	T	0.20773	-1.0265	10	0.06365	T	0.9	0.2268	5.6775	0.17757	0.0:0.8445:0.0:0.1555	.	102;157;102;157;199	E7EMV9;B7Z1T6;E9PAK6;Q6NTE8;Q6NTE8-2	.;.;.;CE045_HUMAN;.	I	199;157;102;102;157;23;157	ENSP00000384599:V199I;ENSP00000430298:V157I;ENSP00000427849:V102I;ENSP00000366130:V102I;ENSP00000428460:V157I;ENSP00000429107:V23I;ENSP00000292586:V157I	ENSP00000292586:V157I	V	-	1	0	C5orf45	179200546	0.000000	0.05858	0.002000	0.10522	0.015000	0.08874	-0.217000	0.09253	0.685000	0.31468	-0.263000	0.10527	GTC	.	C|0.500;T|0.500	0.500	weak		0.632	C5orf45-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373760.2	NM_016175		T	179267940	C	T	179267940	3	4	260	1	0	0	0	0	1	0	0	0	2306	536	19	1	570	1	C5orf45	5	179267940	Missense_Mutation	SNP	C	TCGA-UZ-A9PN-01A-11D-A382-10	38641417	179267940	1647320	18	16183											
HIVEP1	3096	hgsc.bcm.edu	37	chr6	12163682	12163682	+	Missense_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	tccccacactcatttgtttaGccaccttcctttgcattccc	6	15	3	17	0	1	0	1	0	0	0	4	0	4	0	6	0	2	2	6	0	1	6			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr6:12163682G>A	ENST00000379388.2	+	9	7477	c.7145G>A	c.(7144-7146)aGc>aAc	p.S2382N	HIVEP1_ENST00000541134.1_Missense_Mutation_p.S247N	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	2382					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)				CATTTGTTTAGCCACCTTCCT	0.522																																					p.S2382N		Atlas-SNP	.											.	HIVEP1	242	.	0			c.G7145A						PASS	.						96	103	101					6																	12163682		2081	4225	6306	SO:0001583	missense	3096	exon9			TGTTTAGCCACCT	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.7145G>A	chr6.hg19:g.12163682G>A	ENSP00000368698:p.Ser2382Asn	93.0	0.0	.		77.0	10.0	.	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	hg19	CCDS43426.1	.	.	.	.	.	.	.	.	.	.	G	33	5.249744	0.95305	.	.	ENSG00000095951	ENST00000379388;ENST00000541134;ENST00000542327	T;T	0.62105	1.47;0.05	6.03	6.03	0.97812	.	0.000000	0.40640	N	0.001057	T	0.78020	0.4218	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.78102	-0.2335	10	0.72032	D	0.01	-21.0673	20.5666	0.99351	0.0:0.0:1.0:0.0	.	2382	P15822	ZEP1_HUMAN	N	2382;247;364	ENSP00000368698:S2382N;ENSP00000445617:S247N	ENSP00000368698:S2382N	S	+	2	0	HIVEP1	12271668	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	9.041000	0.93788	2.854000	0.98071	0.655000	0.94253	AGC	.	.	.	none		0.522	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114		A	12163682	G	A	12163682	3	1	260	1	0	0	0	0	1	0	0	0	7193	971	34	2	7175	2	HIVEP1	6	12163682	Missense_Mutation	SNP	G	TCGA-UZ-A9PN-01A-11D-A382-10		12163682	158951385	19	16184											
DAXX	1616	hgsc.bcm.edu	37	chr6	33289303	33289303	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttatagaggaatgggaccacCtcagggtggtctgctgtctg	8	11	14	8	0	3	1	1	0	2	1	3	3	3	3	2	4	1	1	2	4	3	2			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr6:33289303C>T	ENST00000374542.5	-	3	453	c.249G>A	c.(247-249)gaG>gaA	p.E83E	DAXX_ENST00000414083.2_Silent_p.E8E|DAXX_ENST00000266000.6_Silent_p.E83E|DAXX_ENST00000477162.1_Intron	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	83	Necessary for interaction with USP7 and ATRX.				activation of JUN kinase activity (GO:0007257)|androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|chromatin remodeling (GO:0006338)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mitotic cytokinesis (GO:0000281)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of neuron death (GO:1901216)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|PML body (GO:0016605)|SWI/SNF superfamily-type complex (GO:0070603)	androgen receptor binding (GO:0050681)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|histone binding (GO:0042393)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|receptor signaling protein activity (GO:0005057)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(2)|lung(7)|ovary(3)|pancreas(18)|prostate(3)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	55						ATGGGACCACCTCAGGGTGGT	0.547			"Mis, F, N"		Pancreatic neuroendocrine tumors. Paediatric GBM																																p.E95E		Atlas-SNP	.		Rec	yes		6	6p21.3	1616	death-domain associated protein		E	.	DAXX	111	.	0			c.G285A						PASS	.						57	62	60					6																	33289303		2203	4300	6503	SO:0001819	synonymous_variant	1616	exon3			GACCACCTCAGGG	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.249G>A	chr6.hg19:g.33289303C>T		109.0	0.0	.		112.0	24.0	.	NM_001141970	B4E1I3|F5H082|O14747|O15141|O15208|Q5STK9|Q9BWI3	Silent	SNP	ENST00000374542.5	hg19	CCDS4776.1																																																																																			.	.	.	none		0.547	DAXX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076403.1			T	33289303	C	T	33289303	2	4	260	1	0	0	0	0	0	0	0	1	4245	680	24	2		2	DAXX	6	33289303	Silent	SNP	C	TCGA-UZ-A9PN-01A-11D-A382-10	21125621	33289303	137825764	20	16185											
ASCC3	10973	hgsc.bcm.edu	37	chr6	101109798	101109798	+	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	cgttgttataattattccttCcccaaatttgtcaaattgtg	10	18	5	8	1	1	0	1	0	0	0	3	0	3	0	3	0	0	2	3	0	5	8			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr6:101109798C>T	ENST00000369162.2	-	16	2931	c.2587G>A	c.(2587-2589)Gaa>Aaa	p.E863K		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	863	Helicase C-terminal 1. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		ATTATTCCTTCCCCAAATTTG	0.403																																					p.E863K		Atlas-SNP	.											.	ASCC3	205	.	0			c.G2587A						PASS	.						170	164	166					6																	101109798		2203	4300	6503	SO:0001583	missense	10973	exon16			TTCCTTCCCCAAA	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.2587G>A	chr6.hg19:g.101109798C>T	ENSP00000358159:p.Glu863Lys	106.0	0.0	.		102.0	21.0	.	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	hg19	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.215570	0.79352	.	.	ENSG00000112249	ENST00000369162	D	0.91464	-2.85	5.76	5.76	0.90799	Helicase, C-terminal (1);	0.105493	0.64402	N	0.000005	D	0.91178	0.7221	L	0.55990	1.75	0.80722	D	1	P	0.52316	0.952	P	0.52598	0.703	D	0.90088	0.4175	10	0.48119	T	0.1	.	20.3431	0.98773	0.0:1.0:0.0:0.0	.	863	Q8N3C0	HELC1_HUMAN	K	863	ENSP00000358159:E863K	ENSP00000358159:E863K	E	-	1	0	ASCC3	101216519	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.626000	0.61269	2.880000	0.98712	0.650000	0.86243	GAA	.	.	.	none		0.403	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		T	101109798	C	T	101109798	3	4	260	1	0	0	0	0	1	0	0	0	1033	864	30	2	4129	2	ASCC3	6	101109798	Missense_Mutation	SNP	C	TCGA-UZ-A9PN-01A-11D-A382-10	67820495	101109798	70005269	21	16186											
COL1A2	1278	hgsc.bcm.edu	37	chr7	94041426	94041426	+	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	cggccccgctggaaaagaagGtcctgtcgtaagtattgctc	9	9	12	11	3	0	1	0	0	0	1	3	2	1	2	3	3	1	4	3	3	5	3			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr7:94041426G>T	ENST00000297268.6	+	24	1868	c.1397G>T	c.(1396-1398)gGt>gTt	p.G466V		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	466			Missing (in OI2). {ECO:0000269|PubMed:18996919}.		blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	GGAAAAGAAGGTCCTGTCGTA	0.368										HNSCC(75;0.22)																											p.G466V		Atlas-SNP	.											.	COL1A2	240	.	0			c.G1397T						PASS	.						93	88	90					7																	94041426		2203	4300	6503	SO:0001583	missense	1278	exon24			AAGAAGGTCCTGT	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.1397G>T	chr7.hg19:g.94041426G>T	ENSP00000297268:p.Gly466Val	135.0	0.0	.		165.0	32.0	.	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	hg19	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	G	15.19	2.760033	0.49468	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.99186	-5.53	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	D	0.99548	0.9838	H	0.94698	3.57	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98372	1.0554	10	0.87932	D	0	.	20.5471	0.99284	0.0:0.0:1.0:0.0	.	466	P08123	CO1A2_HUMAN	V	466;467	ENSP00000297268:G466V	ENSP00000297268:G466V	G	+	2	0	COL1A2	93879362	1.000000	0.71417	0.977000	0.42913	0.382000	0.30200	9.825000	0.99386	2.941000	0.99782	0.655000	0.94253	GGT	.	.	.	none		0.368	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		T	94041426	G	T	94041426	3	4	260	1	0	0	0	0	1	0	0	0	3680	1261	44	4	1491	4	COL1A2	7	94041426	Missense_Mutation	SNP	G	TCGA-UZ-A9PN-01A-11D-A382-10		94041426	65097237	22	16187											
AGK	55750	hgsc.bcm.edu	37	chr7	141352709	141352709	+	Frame_Shift_Del	DEL	A	A	-																															aagagagaacagatgctcacAagccccacccagtgagcagc																										TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr7:141352709delA	ENST00000355413.4	+	16	1514	c.1254delA	c.(1252-1254)acafs	p.T418fs	RP5-894A10.2_ENST00000467537.1_RNA|AGK_ENST00000473247.1_Frame_Shift_Del_p.T390fs	NM_018238.3	NP_060708.1	Q53H12	AGK_HUMAN	acylglycerol kinase	418					ceramide biosynthetic process (GO:0046513)|glycerolipid metabolic process (GO:0046486)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acylglycerol kinase activity (GO:0047620)|ATP binding (GO:0005524)|ceramide kinase activity (GO:0001729)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(1)|endometrium(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(3)	17	Melanoma(164;0.0171)					AGATGCTCACAAGCCCCACCC	0.542																																					p.T418fs		Atlas-Indel,Pindel	.											AGK,NS,carcinoma,0,1	AGK	43	.	0			c.1253delC						PASS	.						82	79	80					7																	141352709		2203	4300	6503	SO:0001589	frameshift_variant	55750	exon16			.	BC022777	CCDS5865.1	7q34	2010-05-04	2007-01-11	2007-01-11	ENSG00000006530	ENSG00000006530	2.7.1.94		21869	protein-coding gene	gene with protein product		610345	"multiple substrate lipid kinase"	MULK		15252046, 15939762, 17135245	Standard	NM_018238		Approved	FLJ10842	uc003vwi.2	Q53H12	OTTHUMG00000157499	ENST00000355413.4:c.1254delA	chr7.hg19:g.141352709delA	ENSP00000347581:p.Thr418fs	74.0	0.0	0		67.0	14.0	0.208955	NM_018238	Q75KN1|Q96GC3|Q9NP48	Frame_Shift_Del	DEL	ENST00000355413.4	hg19	CCDS5865.1																																																																																			.	.	.	none		0.542	AGK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348969.1	NM_018238		-	141352709	A	-	141352709	7	5	260	1	0	1	0	1	0	0	0	0	383	117	5	0	1312	0	AGK	7	141352709	Frame_Shift_Del	DEL	A	TCGA-UZ-A9PN-01A-11D-A382-10	47311283	141352709	17785954	23	16188											
ST18	9705	hgsc.bcm.edu	37	chr8	53025847	53025847	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccgttccagattgctgtacaTatctgtgagtgtatttacat	9	16	8	8	1	1	2	0	1	1	1	2	2	2	2	2	0	3	4	2	0	4	7			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr8:53025847T>C	ENST00000276480.7	-	26	3738	c.3055A>G	c.(3055-3057)Atg>Gtg	p.M1019V		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	1019					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				TTGCTGTACATATCTGTGAGT	0.448																																					p.M1019V		Atlas-SNP	.											.	ST18	212	.	0			c.A3055G						PASS	.						159	138	145					8																	53025847		2203	4300	6503	SO:0001583	missense	9705	exon26			TGTACATATCTGT	AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"Zinc fingers, C2HC-type containing"	18695	protein-coding gene	gene with protein product	"neural zinc finger transcription factor 3"		"zinc finger protein 387", "suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.3055A>G	chr8.hg19:g.53025847T>C	ENSP00000276480:p.Met1019Val	130.0	0.0	.		80.0	16.0	.	NM_014682	Q17RY1	Missense_Mutation	SNP	ENST00000276480.7	hg19	CCDS6149.1	.	.	.	.	.	.	.	.	.	.	T	19.92	3.916209	0.73098	.	.	ENSG00000147488	ENST00000276480	T	0.56103	0.48	5.97	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.69024	0.3065	M	0.67397	2.05	0.58432	D	0.999994	D	0.59767	0.986	D	0.69654	0.965	T	0.71951	-0.4437	10	0.87932	D	0	-17.6121	13.4666	0.61258	0.0:0.0:0.1306:0.8694	.	1019	O60284	ST18_HUMAN	V	1019	ENSP00000276480:M1019V	ENSP00000276480:M1019V	M	-	1	0	ST18	53188400	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.040000	0.89188	1.063000	0.40649	0.477000	0.44152	ATG	.	.	.	none		0.448	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1			C	53025847	T	C	53025847	3	2	260	1	0	0	0	0	1	0	0	0	15224	1406	49	3	92	3	ST18	8	53025847	Missense_Mutation	SNP	T	TCGA-UZ-A9PN-01A-11D-A382-10		53025847	93338175	24	16189											
TOPORS	10210	hgsc.bcm.edu	37	chr9	32542179	32542179	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctcacccggtcagtcccggTagatgcagtccttgatctgt	6	12	10	13	2	3	2	2	1	2	1	6	2	5	2	3	2	1	2	3	2	1	2			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr9:32542179T>C	ENST00000360538.2	-	3	2460	c.2344A>G	c.(2344-2346)Acc>Gcc	p.T782A	TOPORS_ENST00000379858.1_Missense_Mutation_p.T717A	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	782	Arg-rich.|Interaction with TOP1.				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)		TCAGTCCCGGTAGATGCAGTC	0.443																																					p.T782A		Atlas-SNP	.											.	TOPORS	127	.	0			c.A2344G						PASS	.						105	104	104					9																	32542179		2203	4300	6503	SO:0001583	missense	10210	exon3			TCCCGGTAGATGC	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.2344A>G	chr9.hg19:g.32542179T>C	ENSP00000353735:p.Thr782Ala	166.0	0.0	.		134.0	24.0	.	NM_005802	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	hg19	CCDS6527.1	.	.	.	.	.	.	.	.	.	.	T	3.362	-0.130299	0.06753	.	.	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.14266	2.52;2.52	6.01	3.7	0.42460	.	0.125216	0.36972	N	0.002314	T	0.04003	0.0112	N	0.03608	-0.345	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.41233	-0.9520	10	0.07175	T	0.84	-7.1549	3.2108	0.06682	0.0:0.2476:0.2157:0.5367	.	782	Q9NS56	TOPRS_HUMAN	A	782;717	ENSP00000353735:T782A;ENSP00000369187:T717A	ENSP00000353735:T782A	T	-	1	0	TOPORS	32532179	0.000000	0.05858	0.986000	0.45419	0.940000	0.58332	-0.893000	0.04127	1.115000	0.41800	0.528000	0.53228	ACC	.	.	.	none		0.443	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		C	32542179	T	C	32542179	3	2	260	1	0	0	0	0	1	0	0	0	16382	1638	57	3	797	3	TOPORS	9	32542179	Missense_Mutation	SNP	T	TCGA-UZ-A9PN-01A-11D-A382-10		32542179	108671252	25	16190											
CERCAM	51148	hgsc.bcm.edu	37	chr9	131183331	131183331	+	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	ctctggagcggctggactacCcccgggccaggatggccctc	5	6	14	16	2	1	0	0	0	1	0	2	3	1	3	4	6	2	1	4	6	1	1			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr9:131183331C>T	ENST00000372838.4	+	1	573	c.175C>T	c.(175-177)Ccc>Tcc	p.P59S	CERCAM_ENST00000372842.1_5'UTR|CERCAM_ENST00000493788.1_3'UTR	NM_016174.4	NP_057258.3	Q5T4B2	GT253_HUMAN	cerebral endothelial cell adhesion molecule	59					cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|leukocyte cell-cell adhesion (GO:0007159)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(2)|lung(9)|ovary(1)|pancreas(2)	20						GCTGGACTACCCCCGGGCCAG	0.721																																					p.P59S		Atlas-SNP	.											.	CERCAM	104	.	0			c.C175T						PASS	.						4	8	7					9																	131183331		654	1516	2170	SO:0001583	missense	51148	exon1			GACTACCCCCGGG	AB040935	CCDS6901.2, CCDS69675.1	9q34.13	2008-02-05	2007-10-17	2007-10-17	ENSG00000167123	ENSG00000167123			23723	protein-coding gene	gene with protein product	"glycosyltransferase 25 domain containing 3"		"cerebral cell adhesion molecule"	CEECAM1		10608765	Standard	NM_016174		Approved	GLT25D3, CerCAM	uc004buz.4	Q5T4B2	OTTHUMG00000020747	ENST00000372838.4:c.175C>T	chr9.hg19:g.131183331C>T	ENSP00000361929:p.Pro59Ser	83.0	0.0	.		34.0	9.0	.	NM_016174	A7MD00|C4AMA2|Q0VDF3|Q2VPJ4|Q4KMP2|Q5T4B1|Q8N107|Q96EZ5|Q9P226|Q9UMW5	Missense_Mutation	SNP	ENST00000372838.4	hg19	CCDS6901.2	.	.	.	.	.	.	.	.	.	.	C	34	5.403639	0.96051	.	.	ENSG00000167123	ENST00000372838;ENST00000413863	D	0.85484	-1.99	4.54	4.54	0.55810	.	0.000000	0.85682	D	0.000000	D	0.92786	0.7706	M	0.86502	2.82	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.93976	0.7254	10	0.87932	D	0	1.6041	14.813	0.70010	0.0:1.0:0.0:0.0	.	59	Q5T4B2	GT253_HUMAN	S	59	ENSP00000361929:P59S	ENSP00000361929:P59S	P	+	1	0	CERCAM	130223152	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.807000	0.75201	2.351000	0.79841	0.491000	0.48974	CCC	.	.	.	none		0.721	CERCAM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054435.2	NM_016174		T	131183331	C	T	131183331	3	4	260	1	0	0	0	0	1	0	0	0	3268	623	22	2	177	2	CERCAM	9	131183331	Missense_Mutation	SNP	C	TCGA-UZ-A9PN-01A-11D-A382-10	98641152	131183331	10030100	26	16191											
PDHX	8050	hgsc.bcm.edu	37	chr11	35006233	35006233	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttactccaatcataaaagaTgctgctgctaaaggtatcca	14	11	6	10	0	1	1	1	0	0	1	3	1	3	1	2	1	4	4	2	1	7	4			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr11:35006233T>C	ENST00000227868.4	+	9	1224	c.1140T>C	c.(1138-1140)gaT>gaC	p.D380D	PDHX_ENST00000477173.3_3'UTR|PDHX_ENST00000448838.3_Silent_p.D365D|PDHX_ENST00000430469.2_Silent_p.D153D			O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	380					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)			TCATAAAAGATGCTGCTGCTA	0.393																																					p.D380D		Atlas-SNP	.											.	PDHX	40	.	0			c.T1140C						PASS	.						129	126	127					11																	35006233		2202	4298	6500	SO:0001819	synonymous_variant	8050	exon9			AAAAGATGCTGCT	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.1140T>C	chr11.hg19:g.35006233T>C		145.0	0.0	.		88.0	18.0	.	NM_003477	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Silent	SNP	ENST00000227868.4	hg19	CCDS7896.1	.	.	.	.	.	.	.	.	.	.	T	2.267	-0.367827	0.05069	.	.	ENSG00000110435	ENST00000526309	.	.	.	5.64	3.35	0.38373	.	.	.	.	.	T	0.54062	0.1835	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45205	-0.9277	4	.	.	.	-13.8697	5.4179	0.16384	0.0:0.1506:0.1472:0.7022	.	.	.	.	T	68	.	.	M	+	2	0	PDHX	34962809	1.000000	0.71417	0.996000	0.52242	0.240000	0.25518	0.591000	0.23969	0.434000	0.26340	0.533000	0.62120	ATG	.	.	.	none		0.393	PDHX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390017.1	NM_003477		C	35006233	T	C	35006233	2	2	260	1	0	0	0	0	0	0	0	1	11674	1461	51	3		3	PDHX	11	35006233	Silent	SNP	T	TCGA-UZ-A9PN-01A-11D-A382-10		35006233	100000283	27	16192											
GLYAT	10249	hgsc.bcm.edu	37	chr11	58477502	58477502	+	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	aggggtcccctcaggccccaGgagacagcaggtgggaaagg	10	3	17	11	0	1	1	1	0	0	1	2	3	2	2	4	7	1	1	4	7	1	0			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr11:58477502G>T	ENST00000344743.3	-	6	769	c.628C>A	c.(628-630)Ctg>Atg	p.L210M	GLYAT_ENST00000529732.1_Missense_Mutation_p.L210M	NM_201648.2	NP_964011.2	Q6IB77	GLYAT_HUMAN	glycine-N-acyltransferase	210					acyl-CoA metabolic process (GO:0006637)|glycine metabolic process (GO:0006544)|monocarboxylic acid metabolic process (GO:0032787)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)|glycine N-benzoyltransferase activity (GO:0047962)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|autonomic_ganglia(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16		Breast(21;0.0044)|all_epithelial(135;0.0157)			Glycine(DB00145)	TCAGGCCCCAGGAGACAGCAG	0.542																																					p.L210M		Atlas-SNP	.											.	GLYAT	53	.	0			c.C628A						PASS	.						73	77	76					11																	58477502		2201	4295	6496	SO:0001583	missense	10249	exon6			GCCCCAGGAGACA	AF023466	CCDS7970.1, CCDS7971.1	11q12.1	2008-03-11					2.3.1.13		13734	protein-coding gene	gene with protein product		607424					Standard	NM_201648		Approved	GAT, ACGNAT	uc001nnb.3	Q6IB77		ENST00000344743.3:c.628C>A	chr11.hg19:g.58477502G>T	ENSP00000340200:p.Leu210Met	115.0	0.0	.		118.0	21.0	.	NM_201648	O14833|Q96QK7	Missense_Mutation	SNP	ENST00000344743.3	hg19	CCDS7970.1	.	.	.	.	.	.	.	.	.	.	G	10.51	1.369214	0.24771	.	.	ENSG00000149124	ENST00000344743;ENST00000529732	T;T	0.18657	2.2;2.2	6.06	3.17	0.36434	Acyl-CoA N-acyltransferase (2);Glycine N-acyltransferase, C-terminal (1);	0.397208	0.22261	N	0.062407	T	0.44664	0.1304	M	0.83384	2.64	0.09310	N	1	D	0.71674	0.998	D	0.64237	0.923	T	0.37174	-0.9717	10	0.49607	T	0.09	-24.7357	11.5202	0.50546	0.2089:0.0:0.7911:0.0	.	210	Q6IB77	GLYAT_HUMAN	M	210	ENSP00000340200:L210M;ENSP00000431688:L210M	ENSP00000340200:L210M	L	-	1	2	GLYAT	58234078	0.549000	0.26481	0.197000	0.23402	0.004000	0.04260	1.080000	0.30779	0.151000	0.19162	-0.813000	0.03139	CTG	.	.	.	none		0.542	GLYAT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394593.1			T	58477502	G	T	58477502	3	4	260	1	0	0	0	0	1	0	0	0	6486	991	35	4	266	4	GLYAT	11	58477502	Missense_Mutation	SNP	G	TCGA-UZ-A9PN-01A-11D-A382-10	23471269	58477502	76529014	28	16193											
GPR137	56834	hgsc.bcm.edu	37	chr11	64056714	64056714	+	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	ccaggccccagtccccctcaCcctaggcccctgtgccaagt	6	6	8	21	0	1	0	1	0	0	0	2	0	2	0	9	2	1	0	9	2	2	1			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr11:64056714C>A	ENST00000313074.3	+	7	1236	c.1131C>A	c.(1129-1131)caC>caA	p.H377Q	KCNK4_ENST00000394525.2_5'Flank|GPR137_ENST00000539851.1_3'UTR|GPR137_ENST00000438980.2_3'UTR|KCNK4_ENST00000538767.1_5'Flank|GPR137_ENST00000411458.1_Missense_Mutation_p.H435Q|KCNK4_ENST00000422670.2_5'Flank|GPR137_ENST00000377702.4_3'UTR|RP11-783K16.10_ENST00000539086.1_RNA	NM_020155.3	NP_064540.3	Q96N19	G137A_HUMAN	G protein-coupled receptor 137	377						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(1)|lung(4)|skin(1)	10						GTCCCCCTCACCCTAGGCCCC	0.657																																					p.H435Q		Atlas-SNP	.											.	GPR137	52	.	0			c.C1305A						PASS	.						82	84	83					11																	64056714		2201	4297	6498	SO:0001583	missense	56834	exon9			CCCTCACCCTAGG	AJ250392	CCDS8066.1, CCDS53655.1, CCDS53656.1, CCDS53657.1, CCDS53658.1	11q13.1	2014-02-12	2006-01-26		ENSG00000173264	ENSG00000173264		"GPCR / Unclassified : 7TM orphan receptors"	24300	protein-coding gene	gene with protein product						10873569, 12732197	Standard	NM_001170726		Approved	C11orf4, GPR137A, TM7SF1L1	uc010rni.2	Q96N19	OTTHUMG00000167817	ENST00000313074.3:c.1131C>A	chr11.hg19:g.64056714C>A	ENSP00000321698:p.His377Gln	123.0	0.0	.		157.0	13.0	.	NM_001170726	B4DTG7|B7Z7M1|Q4G0Y9|Q8N4K6	Missense_Mutation	SNP	ENST00000313074.3	hg19	CCDS8066.1	.	.	.	.	.	.	.	.	.	.	c	3.770	-0.047901	0.07407	.	.	ENSG00000173264	ENST00000411458;ENST00000313074	T;T	0.44482	0.92;0.97	5.27	-10.5	0.00291	.	4.032870	0.00357	N	0.000023	T	0.16599	0.0399	N	0.08118	0	0.09310	N	0.999993	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.17961	-1.0352	10	0.66056	D	0.02	-0.3046	0.0787	0.00029	0.2624:0.2081:0.2079:0.3215	.	435;377	B4DTG7;Q96N19	.;G137A_HUMAN	Q	435;377	ENSP00000411827:H435Q;ENSP00000321698:H377Q	ENSP00000321698:H377Q	H	+	3	2	GPR137	63813290	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-2.168000	0.01270	-2.053000	0.00901	-0.215000	0.12644	CAC	.	.	.	none		0.657	GPR137-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396412.1	NM_020155		A	64056714	C	A	64056714	3	1	260	1	0	0	0	0	1	0	0	0	6652	506	18	4	1445	4	GPR137	11	64056714	Missense_Mutation	SNP	C	TCGA-UZ-A9PN-01A-11D-A382-10	5579212	64056714	70949802	29	16194											
RELA	5970	hgsc.bcm.edu	37	chr11	65422254	65422277	+	In_Frame_Del	DEL	AGGGCCTGGGGCTAGGACTGGGAC	AGGGCCTGGGGCTAGGACTGGGAC	-																															ggtggggccacagcctgaggAgggcctggggctaggactgg																										TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	AGGGCCTGGGGCTAGGACTGGGAC	AGGGCCTGGGGCTAGGACTGGGAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr11:65422254_65422277delAGGGCCTGGGGCTAGGACTGGGAC	ENST00000406246.3	-	11	1489_1512	c.1228_1251delGTCCCAGTCCTAGCCCCAGGCCCT	c.(1228-1251)gtcccagtcctagccccaggccctdel	p.VPVLAPGP410del	RELA_ENST00000308639.9_In_Frame_Del_p.VPVLAPGP407del|RELA_ENST00000525693.1_3'UTR	NM_001243984.1|NM_001243985.1|NM_021975.3	NP_001230913.1|NP_001230914.1|NP_068810.3	Q04206	TF65_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog A	410					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						CAGCCTGAGGAgggcctggggctaggactgggacaggggctggg	0.696																																					p.410_418del		Atlas-Indel,Pindel	.											.	RELA	44	.	0			c.1229_1252del						PASS	.																																			SO:0001651	inframe_deletion	5970	exon11			.	Z22951	CCDS31609.1, CCDS44651.1, CCDS73322.1	11q13	2013-07-09	2013-07-09		ENSG00000173039	ENSG00000173039			9955	protein-coding gene	gene with protein product		164014	"nuclear factor of kappa light polypeptide gene enhancer in B-cells 3"	NFKB3		2001591	Standard	NM_021975		Approved	p65	uc001ofg.3	Q04206	OTTHUMG00000166566	ENST00000406246.3:c.1228_1251delGTCCCAGTCCTAGCCCCAGGCCCT	chr11.hg19:g.65422254_65422277delAGGGCCTGGGGCTAGGACTGGGAC	ENSP00000384273:p.Val410_Pro417del	146.0	0.0	0		110.0	17.0	0.154545	NM_021975	Q6GTV1|Q6SLK1	In_Frame_Del	DEL	ENST00000406246.3	hg19	CCDS31609.1																																																																																			.	.	.	none		0.696	RELA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390457.2	NM_021975		-	65422277	AGGGCCTGGGGCTAGGACTGGGAC	-	65422254	7	5	260	1	0	1	0	1	0	0	0	0	13229	291	11	0	408	0	RELA	11	65422254	In_Frame_Del	DEL	AGGGCCTGGGGCTAGGACTGGGAC	TCGA-UZ-A9PN-01A-11D-A382-10	1365540	65422254	69584262	30	16195											
TWF1	5756	hgsc.bcm.edu	37	chr12	44198327	44198327	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tagatattttcagaagtctgTactttccatttctggctctg	8	18	7	8	0	4	2	1	0	3	2	5	2	5	2	1	1	1	2	1	1	4	7			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr12:44198327T>C	ENST00000395510.2	-	2	203	c.74A>G	c.(73-75)tAc>tGc	p.Y25C	TWF1_ENST00000547564.1_5'UTR|TWF1_ENST00000552521.1_5'UTR|TWF1_ENST00000325127.4_Missense_Mutation_p.Y59C|TWF1_ENST00000548315.1_Missense_Mutation_p.Y25C	NM_001242397.1|NM_002822.4	NP_001229326.1|NP_002813.3	Q12792	TWF1_HUMAN	twinfilin actin-binding protein 1	25	ADF-H 1. {ECO:0000255|PROSITE- ProRule:PRU00599}.				barbed-end actin filament capping (GO:0051016)|negative regulation of actin filament polymerization (GO:0030837)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of actin phosphorylation (GO:0043538)|sequestering of actin monomers (GO:0042989)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|myofibril (GO:0030016)|perinuclear region of cytoplasm (GO:0048471)|ruffle membrane (GO:0032587)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|stomach(1)	14	all_cancers(12;0.00125)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.0474)		CAGAAGTCTGTACTTTCCATT	0.284																																					p.Y25C		Atlas-SNP	.											TWF1,NS,carcinoma,0,1	TWF1	37	.	0			c.A74G						PASS	.						42	46	45					12																	44198327		2197	4266	6463	SO:0001583	missense	5756	exon2			AGTCTGTACTTTC	U02680	CCDS31780.1, CCDS31780.2, CCDS55818.1	12q12	2013-04-25	2013-04-25	2006-11-13					9620	protein-coding gene	gene with protein product		610932	"protein tyrosine kinase 9", "PTK9 protein tyrosine kinase 9", "twinfilin, actin-binding protein, homolog 1 (Drosophila)"	PTK9		7507208	Standard	NM_002822		Approved	A6	uc001rob.3	Q12792		ENST00000395510.2:c.74A>G	chr12.hg19:g.44198327T>C	ENSP00000378886:p.Tyr25Cys	501.0	0.0	.		461.0	106.0	.	NM_002822	A8K5A8|B3KXS6|B4DLX9|Q59G07|Q5U0B1|Q6FHJ1|Q6FHL6|Q6NUK9|Q86XL6|Q8TCD3	Missense_Mutation	SNP	ENST00000395510.2	hg19	CCDS31780.2	.	.	.	.	.	.	.	.	.	.	T	15.99	2.996118	0.54147	.	.	ENSG00000151239	ENST00000395510;ENST00000325127;ENST00000548315;ENST00000546662	T;T;T;T	0.38240	1.39;1.39;1.39;1.15	5.6	4.46	0.54185	Actin-binding, cofilin/tropomyosin type (3);	0.406531	0.30483	N	0.009534	T	0.57051	0.2027	M	0.79475	2.455	0.80722	D	1	D;D	0.63880	0.969;0.993	D;D	0.67725	0.927;0.953	T	0.58233	-0.7672	10	0.51188	T	0.08	-7.5652	10.7348	0.46117	0.0:0.0743:0.0:0.9257	.	25;25	Q12792-3;Q12792	.;TWF1_HUMAN	C	25;59;25;63	ENSP00000378886:Y25C;ENSP00000321058:Y59C;ENSP00000449428:Y25C;ENSP00000448221:Y63C	ENSP00000321058:Y59C	Y	-	2	0	TWF1	42484594	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.146000	0.58072	0.957000	0.37930	0.482000	0.46254	TAC	.	.	.	none		0.284	TWF1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403956.1	NM_002822		C	44198327	T	C	44198327	3	2	260	1	0	0	0	0	1	0	0	0	16793	1638	57	3	1010	3	TWF1	12	44198327	Missense_Mutation	SNP	T	TCGA-UZ-A9PN-01A-11D-A382-10		44198327	89653568	31	16196											
HOXC6	3223	hgsc.bcm.edu	37	chr12	54422350	54422350	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttatcctgccacctcgcCgggggccaggacgtcctccc	4	8	10	19	3	0	0	0	0	0	0	5	1	4	1	8	3	1	0	8	3	1	1			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr12:54422350C>T	ENST00000243108.4	+	1	209	c.45C>T	c.(43-45)gcC>gcT	p.A15A	RP11-834C11.14_ENST00000512206.1_RNA|HOXC4_ENST00000303406.4_Intron|RP11-834C11.12_ENST00000513209.1_Intron|HOXC6_ENST00000394331.3_Intron	NM_004503.3	NP_004494.1	P09630	HXC6_HUMAN	homeobox C6	15					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						GCCACCTCGCCGGGGGCCAGG	0.527																																					p.A15A		Atlas-SNP	.											.	HOXC6	30	.	0			c.C45T						PASS	.						75	71	73					12																	54422350		2203	4300	6503	SO:0001819	synonymous_variant	3223	exon1			CCTCGCCGGGGGC		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.45C>T	chr12.hg19:g.54422350C>T		164.0	0.0	.		168.0	43.0	.	NM_004503	B2RBV2|Q6DK09	Silent	SNP	ENST00000243108.4	hg19	CCDS8871.1																																																																																			.	.	.	none		0.527	HOXC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358943.2			T	54422350	C	T	54422350	2	4	260	1	0	0	0	0	0	0	0	1	7322	639	23	1		1	HOXC6	12	54422350	Silent	SNP	C	TCGA-UZ-A9PN-01A-11D-A382-10	10224023	54422350	79429545	32	16197											
ERBB3	2065	hgsc.bcm.edu	37	chr12	56495550	56495550	+	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	ttgcccactccaccctgtacCcatcatgcccactgcaggca	8	8	6	19	0	1	0	1	0	0	0	2	0	2	0	5	1	4	3	5	1	1	2			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr12:56495550C>T	ENST00000267101.3	+	28	4180	c.3740C>T	c.(3739-3741)cCc>cTc	p.P1247L	RP11-603J24.9_ENST00000548861.1_Intron|PA2G4_ENST00000303305.6_5'Flank|ERBB3_ENST00000450146.2_Missense_Mutation_p.P604L|ERBB3_ENST00000549832.1_Missense_Mutation_p.P367L|RP11-603J24.17_ENST00000548595.1_RNA|ERBB3_ENST00000415288.2_Missense_Mutation_p.P1188L|PA2G4_ENST00000552766.1_5'Flank|ERBB3_ENST00000553131.1_Missense_Mutation_p.P488L	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	1247					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			CACCCTGTACCCATCATGCCC	0.547																																					p.P1247L		Atlas-SNP	.											.	ERBB3	350	.	0			c.C3740T						PASS	.						87	73	78					12																	56495550		2203	4300	6503	SO:0001583	missense	2065	exon28			CTGTACCCATCAT	M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"lethal congenital contracture syndrome 2"	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.3740C>T	chr12.hg19:g.56495550C>T	ENSP00000267101:p.Pro1247Leu	100.0	0.0	.		99.0	21.0	.	NM_001982	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Missense_Mutation	SNP	ENST00000267101.3	hg19	CCDS31833.1	.	.	.	.	.	.	.	.	.	.	C	16.46	3.130261	0.56721	.	.	ENSG00000065361	ENST00000267101;ENST00000450146;ENST00000415288;ENST00000550070;ENST00000553131;ENST00000549832	T;T;T;T;T	0.80824	-1.21;-1.21;-1.2;-1.42;-1.2	5.82	5.82	0.92795	.	0.301833	0.28853	N	0.013924	T	0.73830	0.3637	N	0.19112	0.55	0.46874	D	0.999236	P;P;B	0.45827	0.867;0.79;0.084	B;B;B	0.44085	0.44;0.255;0.051	T	0.76318	-0.3003	10	0.49607	T	0.09	.	17.5929	0.88003	0.0:1.0:0.0:0.0	.	1188;367;1247	P21860-4;B3KWG5;P21860	.;.;ERBB3_HUMAN	L	1247;604;1188;370;488;367	ENSP00000267101:P1247L;ENSP00000399178:P604L;ENSP00000408340:P1188L;ENSP00000449129:P488L;ENSP00000448729:P367L	ENSP00000267101:P1247L	P	+	2	0	ERBB3	54781817	0.990000	0.36364	0.957000	0.39632	0.920000	0.55202	3.899000	0.56288	2.752000	0.94435	0.655000	0.94253	CCC	.	.	.	none		0.547	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3			T	56495550	C	T	56495550	3	4	260	1	0	0	0	0	1	0	0	0	5210	623	22	2	3981	2	ERBB3	12	56495550	Missense_Mutation	SNP	C	TCGA-UZ-A9PN-01A-11D-A382-10	2073200	56495550	77356345	33	16198											
STAB2	55576	hgsc.bcm.edu	37	chr12	104056744	104056744	+	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	ttgtcccgattctgccccatCgatgtgatgaaacaaagaga	12	10	9	10	2	1	3	0	2	1	1	3	6	2	3	3	0	2	0	3	0	2	2			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr12:104056744C>T	ENST00000388887.2	+	18	2194	c.1990C>T	c.(1990-1992)Cga>Tga	p.R664*		NM_017564.9	NP_060034.9			stabilin 2									p.R664*(1)		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						TCTGCCCCATCGATGTGATGA	0.468																																					p.R664X		Atlas-SNP	.											STAB2,NS,carcinoma,0,1	STAB2	370	.	1	Substitution - Nonsense(1)	kidney(1)	c.C1990T						PASS	.						131	128	129					12																	104056744		2203	4300	6503	SO:0001587	stop_gained	55576	exon18			CCCCATCGATGTG	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.1990C>T	chr12.hg19:g.104056744C>T	ENSP00000373539:p.Arg664*	149.0	1.0	.		153.0	51.0	.	NM_017564		Nonsense_Mutation	SNP	ENST00000388887.2	hg19	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	C	40	8.530526	0.98850	.	.	ENSG00000136011	ENST00000388887	.	.	.	5.31	4.36	0.52297	.	0.063415	0.64402	D	0.000017	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.4226	0.21752	0.3716:0.542:0.0:0.0864	.	.	.	.	X	664	.	ENSP00000373539:R664X	R	+	1	2	STAB2	102580874	0.890000	0.30428	0.998000	0.56505	0.699000	0.40488	1.183000	0.32041	2.478000	0.83669	0.655000	0.94253	CGA	.	.	.	none		0.468	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			T	104056744	C	T	104056744	4	4	260	1	0	0	0	0	0	1	0	0	15250	876	31	1	2060	1	STAB2	12	104056744	Nonsense_Mutation	SNP	C	TCGA-UZ-A9PN-01A-11D-A382-10	47561194	104056744	29795151	34	16199											
ZNF770	54989	hgsc.bcm.edu	37	chr15	35275396	35275396	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgacaaatactacatttaaaAggcagactatgagttagttg	16	12	8	5	0	0	3	0	2	0	1	0	3	0	3	0	1	2	3	0	1	7	7			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr15:35275396A>G	ENST00000356321.4	-	3	584	c.240T>C	c.(238-240)ccT>ccC	p.P80P		NM_014106.3	NP_054825.2	Q6IQ21	ZN770_HUMAN	zinc finger protein 770	80					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)		TACATTTAAAAGGCAGACTAT	0.353																																					p.P80P		Atlas-SNP	.											.	ZNF770	64	.	0			c.T240C						PASS	.						85	85	85					15																	35275396		2201	4298	6499	SO:0001819	synonymous_variant	54989	exon3			TTTAAAAGGCAGA	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.240T>C	chr15.hg19:g.35275396A>G		65.0	0.0	.		77.0	21.0	.	NM_014106	Q6ZMZ6|Q9NWV2	Silent	SNP	ENST00000356321.4	hg19	CCDS10042.1																																																																																			.	.	.	none		0.353	ZNF770-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251896.2	NM_014106		G	35275396	A	G	35275396	2	3	260	1	0	0	0	0	0	0	0	1	18155	59	3	3		3	ZNF770	15	35275396	Silent	SNP	A	TCGA-UZ-A9PN-01A-11D-A382-10		35275396	67255996	35	16200											
SPTBN5	51332	hgsc.bcm.edu	37	chr15	42148681	42148682	+	Frame_Shift_Ins	INS	-	-	G																															catggccttctccagctgctINSgcacccgggcggccacctcg																										TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr15:42148681_42148682insG	ENST00000320955.6	-	53	9150_9151	c.8923_8924insC	c.(8923-8925)cagfs	p.Q2975fs		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	2975					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)		CTCCAGCTGCTGCACCCGGGCG	0.693																																					p.Q2940fs		Atlas-Indel,Pindel	.											.	SPTBN5	171	.	0			c.8819_8820insC						PASS	.																																			SO:0001589	frameshift_variant	51332	exon53			.	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.8924dupC	chr15.hg19:g.42148682_42148682dupG	ENSP00000317790:p.Gln2975fs	80.0	0.0	0		73.0	16.0	0.219178	NM_016642		Frame_Shift_Ins	INS	ENST00000320955.6	hg19																																																																																				.	.	.	none		0.693	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		G	42148682	-	G	42148681	7	5	260	1	0	1	1	0	0	0	0	0	15134	1580	55	0	2164	0	SPTBN5	15	42148681	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PN-01A-11D-A382-10	6873285	42148681	60382711	36	16201											
SH3GL3	6457	hgsc.bcm.edu	37	chr15	84228033	84228033	+	Missense_Mutation	SNP	A	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	tgaaaaaataagtggtgctgAaggaactaaactagacgatg	18	8	11	4	1	0	3	0	2	0	1	0	5	0	4	0	2	3	1	0	2	9	3			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr15:84228033A>C	ENST00000427482.2	+	2	380	c.74A>C	c.(73-75)gAa>gCa	p.E25A	SH3GL3_ENST00000324537.5_Missense_Mutation_p.E33A|SH3GL3_ENST00000535412.1_Missense_Mutation_p.E25A|SH3GL3_ENST00000434347.1_Missense_Mutation_p.E33A	NM_003027.3	NP_003018.3	Q99963	SH3G3_HUMAN	SH3-domain GRB2-like 3	25	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				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						AGTGGTGCTGAAGGAACTAAA	0.279											OREG0023396	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E25A		Atlas-SNP	.											.	SH3GL3	91	.	0			c.A74C						PASS	.						79	79	79					15																	84228033		2203	4299	6502	SO:0001583	missense	6457	exon2			GTGCTGAAGGAAC	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.74A>C	chr15.hg19:g.84228033A>C	ENSP00000391372:p.Glu25Ala	307.0	0.0	.	1227	325.0	65.0	.	NM_003027	O43553|O43554	Missense_Mutation	SNP	ENST00000427482.2	hg19	CCDS10325.2	.	.	.	.	.	.	.	.	.	.	A	18.62	3.662604	0.67700	.	.	ENSG00000140600	ENST00000427482;ENST00000535412;ENST00000324537;ENST00000434347	T;T;T;T	0.40756	1.02;1.02;1.02;1.02	4.63	3.51	0.40186	BAR (3);	0.053790	0.64402	D	0.000001	T	0.60340	0.2261	M	0.78049	2.395	0.80722	D	1	D;D;D;D	0.89917	0.982;0.978;0.997;1.0	P;P;D;D	0.78314	0.739;0.621;0.976;0.991	T	0.59679	-0.7409	10	0.51188	T	0.08	-14.5796	8.1715	0.31258	0.9036:0.0:0.0964:0.0	.	25;25;25;33	Q8IVP1;Q99963-4;Q99963;Q99963-3	.;.;SH3G3_HUMAN;.	A	25;25;33;33	ENSP00000391372:E25A;ENSP00000439239:E25A;ENSP00000320092:E33A;ENSP00000397871:E33A	ENSP00000320092:E33A	E	+	2	0	SH3GL3	82019037	1.000000	0.71417	0.928000	0.36995	0.996000	0.88848	7.870000	0.87175	0.805000	0.34159	0.460000	0.39030	GAA	.	.	.	none		0.279	SH3GL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347797.1	NM_003027		C	84228033	A	C	84228033	3	2	260	1	0	0	0	0	1	0	0	0	14265	246	9	5	80	5	SH3GL3	15	84228033	Missense_Mutation	SNP	A	TCGA-UZ-A9PN-01A-11D-A382-10	42079352	84228033	18303359	37	16202											
AGBL1	123624	hgsc.bcm.edu	37	chr15	87089231	87089231	+	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	ctcctttgttgggctattgtAggttttctgtgacttccatg	4	19	10	8	0	1	1	0	1	1	0	3	1	3	1	2	2	0	4	2	2	2	8			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr15:87089231A>G	ENST00000441037.2	+	19	2642		c.e19-1		AGBL1_ENST00000389298.3_Splice_Site|AGBL1_ENST00000421325.2_Splice_Site	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1						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						GGGCTATTGTAGGTTTTCTGT	0.428																																					.		Atlas-SNP	.											.	AGBL1	151	.	0			c.2548-2A>G						PASS	.						133	121	125					15																	87089231		1886	4119	6005	SO:0001630	splice_region_variant	123624	exon19			TATTGTAGGTTTT	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.2548-1A>G	chr15.hg19:g.87089231A>G		99.0	0.0	.		97.0	21.0	.	NM_152336	A1A4X5|A6NJH6|C9JHL5	Splice_Site	SNP	ENST00000441037.2	hg19	CCDS58398.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.092020	0.76756	.	.	ENSG00000166748	ENST00000441037;ENST00000421325;ENST00000389298	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.981	0.71311	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	AGBL1	84890235	1.000000	0.71417	0.938000	0.37757	0.821000	0.46438	8.589000	0.90817	2.320000	0.78422	0.528000	0.53228	.	.	.	.	none		0.428	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	Intron	G	87089231	A	G	87089231	5	3	260	1	0	0	0	0	0	0	1	0	375	434	15	3	2616	3	AGBL1	15	87089231	Splice_Site	SNP	A	TCGA-UZ-A9PN-01A-11D-A382-10	2861198	87089231	15442161	38	16203											
RHBDL1	9028	hgsc.bcm.edu	37	chr16	727363	727363	+	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	ggcctgctccgcatcagcctGctctacctggcaggcgtgct	4	9	12	16	2	2	0	1	0	1	0	3	0	3	0	4	3	5	5	4	3	1	1			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr16:727363G>A	ENST00000219551.2	+	4	885	c.858G>A	c.(856-858)ctG>ctA	p.L286L	LA16c-313D11.9_ENST00000567091.1_RNA|RHBDL1_ENST00000352681.3_Silent_p.L221L|STUB1_ENST00000565677.1_5'Flank|LA16c-313D11.9_ENST00000571933.1_RNA|STUB1_ENST00000219548.4_5'Flank			O75783	RHBL1_HUMAN	rhomboid, veinlet-like 1 (Drosophila)	286					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)				GCATCAGCCTGCTCTACCTGG	0.711																																					p.L286L		Atlas-SNP	.											.	RHBDL1	14	.	0			c.G858A						PASS	.						17	14	15					16																	727363		2180	4267	6447	SO:0001819	synonymous_variant	9028	exon4			CAGCCTGCTCTAC	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.858G>A	chr16.hg19:g.727363G>A		54.0	0.0	.		73.0	19.0	.	NM_003961	A2IDC0|A2IDC1|Q0VAX4|Q9NQ85	Silent	SNP	ENST00000219551.2	hg19	CCDS10418.1																																																																																			.	.	.	none		0.711	RHBDL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000241619.1	NM_003961		A	727363	G	A	727363	2	1	260	1	0	0	0	0	0	0	0	1	13334	1306	46	2		2	RHBDL1	16	727363	Silent	SNP	G	TCGA-UZ-A9PN-01A-11D-A382-10		727363	89627390	39	16204											
DCTPP1	79077	hgsc.bcm.edu	37	chr16	30435726	30435726	+	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	tggagagcactgctagcggcAgatccacacggcagcgggct	9	5	15	12	3	0	2	0	0	0	2	1	3	1	2	1	4	4	5	1	4	1	1			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr16:30435726A>T	ENST00000319285.4	-	3	435	c.341T>A	c.(340-342)cTg>cAg	p.L114Q	ZNF771_ENST00000566625.1_Intron|DCTPP1_ENST00000568434.1_5'UTR|DCTPP1_ENST00000568973.1_5'UTR|DCTPP1_ENST00000565758.1_5'UTR|DCTPP1_ENST00000567983.1_Missense_Mutation_p.L15Q	NM_024096.1	NP_077001.1	Q9H773	DCTP1_HUMAN	dCTP pyrophosphatase 1	114					nucleoside triphosphate catabolic process (GO:0009143)|protein homotetramerization (GO:0051289)	cytosol (GO:0005829)	dCTP diphosphatase activity (GO:0047840)|magnesium ion binding (GO:0000287)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|pyrimidine deoxyribonucleotide binding (GO:0032556)			kidney(1)|large_intestine(3)|upper_aerodigestive_tract(1)	5						TGCTAGCGGCAGATCCACACG	0.612																																					p.L114Q		Atlas-SNP	.											.	DCTPP1	12	.	0			c.T341A						PASS	.						62	58	59					16																	30435726		2197	4300	6497	SO:0001583	missense	79077	exon3			AGCGGCAGATCCA	BC001344	CCDS10680.1	16p11.2	2009-02-11			ENSG00000179958	ENSG00000179958	3.6.1.12		28777	protein-coding gene	gene with protein product	"XTP3-transactivated protein A"	615840				15740738	Standard	NM_024096		Approved	MGC5627, RS21C6, CDA03, XTP3TPA	uc002dyf.3	Q9H773	OTTHUMG00000132416	ENST00000319285.4:c.341T>A	chr16.hg19:g.30435726A>T	ENSP00000322524:p.Leu114Gln	73.0	0.0	.		66.0	19.0	.	NM_024096		Missense_Mutation	SNP	ENST00000319285.4	hg19	CCDS10680.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.277925	0.80692	.	.	ENSG00000179958	ENST00000319285	.	.	.	5.48	5.48	0.80851	NTP pyrophosphohydrolase MazG, putative catalytic core (1);	0.068721	0.56097	D	0.000021	D	0.87649	0.6230	H	0.97023	3.925	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91634	0.5321	9	0.87932	D	0	-6.6874	14.5404	0.67990	1.0:0.0:0.0:0.0	.	114	Q9H773	DCTP1_HUMAN	Q	114	.	ENSP00000322524:L114Q	L	-	2	0	DCTPP1	30343227	1.000000	0.71417	0.258000	0.24420	0.853000	0.48598	7.565000	0.82337	2.086000	0.62901	0.477000	0.44152	CTG	.	.	.	none		0.612	DCTPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255553.2	NM_024096		T	30435726	A	T	30435726	3	4	260	1	0	0	0	0	1	0	0	0	4314	188	7	5	175	5	DCTPP1	16	30435726	Missense_Mutation	SNP	A	TCGA-UZ-A9PN-01A-11D-A382-10	29708363	30435726	59919027	40	16205											
NFATC3	4775	hgsc.bcm.edu	37	chr16	68248266	68248266	+	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	gacttggaacaccagccatcAggttcagcagagaaatggcc	13	6	11	11	0	2	1	2	0	0	1	2	4	2	2	3	3	3	2	3	3	2	2			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr16:68248266A>G	ENST00000346183.3	+	10	3130				NFATC3_ENST00000575270.1_Intron|NFATC3_ENST00000329524.4_Silent_p.S1047S|NFATC3_ENST00000349223.5_Intron|RP11-96D1.5_ENST00000569088.1_RNA|NFATC3_ENST00000535127.2_3'UTR	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3						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)		ACCAGCCATCAGGTTCAGCAG	0.423																																					p.S1047S		Atlas-SNP	.											.	NFATC3	190	.	0			c.A3141G						PASS	.						208	169	182					16																	68248266		2198	4300	6498	SO:0001627	intron_variant	4775	exon10			GCCATCAGGTTCA	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.3107-11987A>G	chr16.hg19:g.68248266A>G		117.0	0.0	.		89.0	22.0	.	NM_004555	O75211|Q14516|Q99840|Q99841|Q99842	Silent	SNP	ENST00000346183.3	hg19	CCDS10860.1																																																																																			.	.	.	none		0.423	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555		G	68248266	A	G	68248266	1	3	260	0	1	0	0	0	0	0	0	0	10371	175	7	3		3	NFATC3	16	68248266	Intron	SNP	A	TCGA-UZ-A9PN-01A-11D-A382-10	37812540	68248266	22106487	41	16206											
SLC25A11	8402	hgsc.bcm.edu	37	chr17	4842400	4842400	+	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	ctgccttcaggatactggtgAgggcatggaagctggttttg	7	12	15	7	0	1	1	1	1	0	0	1	3	1	3	1	5	3	3	1	5	2	4			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr17:4842400A>T	ENST00000225665.7	-	2	543	c.203T>A	c.(202-204)cTc>cAc	p.L68H	RNF167_ENST00000575111.1_5'Flank|RNF167_ENST00000572430.1_5'Flank|RNF167_ENST00000576229.1_5'Flank|RNF167_ENST00000262482.6_5'Flank|SLC25A11_ENST00000544061.2_Intron|RNF167_ENST00000571816.1_5'Flank	NM_001165417.1|NM_003562.4	NP_001158889.1|NP_003553.2	Q02978	M2OM_HUMAN	solute carrier family 25 (mitochondrial carrier; oxoglutarate carrier), member 11	68					alpha-ketoglutarate transport (GO:0015742)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxoglutarate:malate antiporter activity (GO:0015367)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)	10						GATACTGGTGAGGGCATGGAA	0.567																																					p.L68H	Esophageal Squamous(144;1178 2388 18010 48797)	Atlas-SNP	.											.	SLC25A11	22	.	0			c.T203A						PASS	.						135	123	127					17																	4842400		2203	4300	6503	SO:0001583	missense	8402	exon2			CTGGTGAGGGCAT	X66114	CCDS11059.1, CCDS54069.1	17p13.3	2013-05-22			ENSG00000108528	ENSG00000108528		"Solute carriers"	10981	protein-coding gene	gene with protein product		604165		SLC20A4		10072597, 1457818	Standard	NM_003562		Approved	OGC	uc002fzo.2	Q02978	OTTHUMG00000099395	ENST00000225665.7:c.203T>A	chr17.hg19:g.4842400A>T	ENSP00000225665:p.Leu68His	111.0	0.0	.		92.0	17.0	.	NM_003562	F5GY65|O75537|Q969P7	Missense_Mutation	SNP	ENST00000225665.7	hg19	CCDS11059.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.074333	0.76415	.	.	ENSG00000108528	ENST00000225665	D	0.81499	-1.5	5.97	4.9	0.64082	Mitochondrial carrier domain (2);	0.230475	0.36815	N	0.002398	D	0.88388	0.6423	M	0.87381	2.88	0.80722	D	1	D;D	0.59767	0.986;0.986	P;P	0.61275	0.886;0.886	D	0.89563	0.3808	10	0.72032	D	0.01	-6.7086	9.5961	0.39576	0.9188:0.0:0.0812:0.0	.	68;68	Q6IBH0;Q02978	.;M2OM_HUMAN	H	68	ENSP00000225665:L68H	ENSP00000225665:L68H	L	-	2	0	SLC25A11	4783145	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.148000	0.71788	2.288000	0.76882	0.533000	0.62120	CTC	.	.	.	none		0.567	SLC25A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216852.4	NM_003562		T	4842400	A	T	4842400	3	4	260	1	0	0	0	0	1	0	0	0	14486	304	11	5	769	5	SLC25A11	17	4842400	Missense_Mutation	SNP	A	TCGA-UZ-A9PN-01A-11D-A382-10		4842400	76352810	42	16207											
SLC46A1	113235	hgsc.bcm.edu	37	chr17	26729265	26729266	+	Frame_Shift_Del	DEL	TC	TC	-																															ctgacactcaccctgctctgTctctctcaccagcttggaga																										TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr17:26729265_26729266delTC	ENST00000440501.1	-	3	1250_1251	c.1155_1156delGA	c.(1153-1158)gagacafs	p.ET385fs	SLC46A1_ENST00000321666.5_Intron|CTD-2350C19.1_ENST00000583956.1_RNA|SLC46A1_ENST00000584729.1_5'UTR|CTD-2350C19.2_ENST00000580714.1_RNA	NM_080669.4	NP_542400.2	Q96NT5	PCFT_HUMAN	solute carrier family 46 (folate transporter), member 1	385					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)	CCCTGCTCTGTCTCTCTCACCA	0.54																																					p.386_386del		Atlas-Indel,Pindel	.											.	SLC46A1	17	.	0			c.1156_1157del						PASS	.																																			SO:0001589	frameshift_variant	113235	exon3			.	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.1155_1156delGA	chr17.hg19:g.26729271_26729272delTC	ENSP00000395653:p.Glu385fs	102.0	0.0	0		87.0	15.0	0.172414	NM_080669	Q1HE20|Q86T92|Q8TEG3|Q96FL0	Frame_Shift_Del	DEL	ENST00000440501.1	hg19																																																																																				.	.	.	none		0.54	SLC46A1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_080669		-	26729266	TC	-	26729265	7	5	260	1	0	1	0	1	0	0	0	0	14657	1667	58	0	236	0	SLC46A1	17	26729265	Frame_Shift_Del	DEL	TC	TCGA-UZ-A9PN-01A-11D-A382-10	21886865	26729265	54465945	43	16208											
TMUB2	79089	hgsc.bcm.edu	37	chr17	42267972	42267972	+	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	ctctgaacattaccgacaacTgtgtgattcactgccaccgc	10	10	7	14	2	2	2	1	2	1	0	2	3	2	2	3	0	4	0	3	0	3	2			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr17:42267972T>A	ENST00000587989.1	+	4	859	c.706T>A	c.(706-708)Tgt>Agt	p.C236S	TMUB2_ENST00000538716.2_Missense_Mutation_p.C236S|TMUB2_ENST00000319511.6_Missense_Mutation_p.C216S|TMUB2_ENST00000589184.1_Missense_Mutation_p.L50Q|TMUB2_ENST00000592825.1_3'UTR|TMUB2_ENST00000590235.1_3'UTR|TMUB2_ENST00000589785.1_Missense_Mutation_p.C216S|TMUB2_ENST00000357984.3_Missense_Mutation_p.C216S|TMUB2_ENST00000446571.3_Missense_Mutation_p.C179S|TMUB2_ENST00000587172.1_3'UTR			Q71RG4	TMUB2_HUMAN	transmembrane and ubiquitin-like domain containing 2	236	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.					integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(1)|lung(3)	8		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.113)		TACCGACAACTGTGTGATTCA	0.592																																					p.C236S		Atlas-SNP	.											.	TMUB2	29	.	0			c.T706A						PASS	.						82	74	77					17																	42267972		2203	4300	6503	SO:0001583	missense	79089	exon4			GACAACTGTGTGA		CCDS11479.1, CCDS54134.1	17q21	2006-06-27				ENSG00000168591			28459	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_177441		Approved	MGC3123	uc002ifo.3	Q71RG4		ENST00000587989.1:c.706T>A	chr17.hg19:g.42267972T>A	ENSP00000466971:p.Cys236Ser	89.0	0.0	.		100.0	25.0	.	NM_001076674	B3KU81|Q8NDI2|Q9BPZ5|Q9HAG3	Missense_Mutation	SNP	ENST00000587989.1	hg19	CCDS54134.1	.	.	.	.	.	.	.	.	.	.	T	13.67	2.305926	0.40795	.	.	ENSG00000168591	ENST00000446571;ENST00000357984;ENST00000538716;ENST00000319511	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.77	4.67	0.58626	Ubiquitin supergroup (1);Ubiquitin (2);	0.131169	0.64402	D	0.000001	T	0.18800	0.0451	N	0.01529	-0.815	0.44635	D	0.997618	B;B;B	0.34329	0.449;0.006;0.449	B;B;B	0.38921	0.191;0.008;0.285	T	0.11567	-1.0582	10	0.12430	T	0.62	-9.458	12.0139	0.53303	0.0:0.0:0.1449:0.8551	.	179;216;236	E7ESS3;Q71RG4-2;Q71RG4	.;.;TMUB2_HUMAN	S	179;216;236;216	ENSP00000413127:C179S;ENSP00000350672:C216S;ENSP00000444565:C236S;ENSP00000313214:C216S	ENSP00000313214:C216S	C	+	1	0	TMUB2	39623498	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.592000	0.46171	0.989000	0.38761	0.459000	0.35465	TGT	.	.	.	none		0.592	TMUB2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457711.1	NM_177441		A	42267972	T	A	42267972	3	1	260	1	0	0	0	0	1	0	0	0	16277	1580	55	5	716	5	TMUB2	17	42267972	Missense_Mutation	SNP	T	TCGA-UZ-A9PN-01A-11D-A382-10	15538707	42267972	38927238	44	16209											
TNRC6C	57690	hgsc.bcm.edu	37	chr17	76089791	76089791	+	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	tggcagtgtccccactgggcCtaccatcaacaccaccatcc	9	7	7	18	0	1	0	1	0	0	0	3	0	3	0	7	2	2	1	7	2	2	1			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr17:76089791C>G	ENST00000588061.1	+	18	4980	c.4253C>G	c.(4252-4254)cCt>cGt	p.P1418R	TNRC6C_ENST00000335749.4_Missense_Mutation_p.P1415R|TNRC6C_ENST00000541771.1_Missense_Mutation_p.P1418R|TNRC6C_ENST00000544502.1_Missense_Mutation_p.P1415R|TNRC6C_ENST00000301624.4_Missense_Mutation_p.P1418R|TNRC6C_ENST00000588847.1_Missense_Mutation_p.P1415R			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	1418	Silencing domain; interaction with CNOT1 and PAN3.|Sufficient for translational repression when tethered to a target mRNA.				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)			CCCACTGGGCCTACCATCAAC	0.542																																					p.P1418R		Atlas-SNP	.											.	TNRC6C	173	.	0			c.C4253G						PASS	.						91	96	95					17																	76089791		2166	4277	6443	SO:0001583	missense	57690	exon17			CTGGGCCTACCAT	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.4253C>G	chr17.hg19:g.76089791C>G	ENSP00000468647:p.Pro1418Arg	89.0	0.0	.		103.0	31.0	.	NM_018996	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Missense_Mutation	SNP	ENST00000588061.1	hg19	CCDS45798.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.135974	0.77662	.	.	ENSG00000078687	ENST00000455761;ENST00000395801;ENST00000335749;ENST00000301624;ENST00000541771;ENST00000544502	T;T;T;T	0.18016	2.24;2.26;2.26;2.24	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.41766	0.1173	M	0.76574	2.34	0.80722	D	1	D;P	0.57257	0.979;0.695	P;B	0.58454	0.839;0.232	T	0.04915	-1.0918	10	0.51188	T	0.08	-15.04	20.6647	0.99678	0.0:1.0:0.0:0.0	.	1415;1418	G3XAB8;Q9HCJ0	.;TNR6C_HUMAN	R	1418;1415;1415;1418;1418;1415	ENSP00000336783:P1415R;ENSP00000301624:P1418R;ENSP00000440310:P1418R;ENSP00000442421:P1415R	ENSP00000301624:P1418R	P	+	2	0	TNRC6C	73601386	1.000000	0.71417	0.991000	0.47740	0.989000	0.77384	5.773000	0.68898	2.890000	0.99128	0.655000	0.94253	CCT	.	.	.	none		0.542	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996		G	76089791	C	G	76089791	3	3	260	1	0	0	0	0	1	0	0	0	16354	681	24	4	4307	4	TNRC6C	17	76089791	Missense_Mutation	SNP	C	TCGA-UZ-A9PN-01A-11D-A382-10	33821819	76089791	5105419	45	16210											
SETBP1	26040	hgsc.bcm.edu	37	chr18	42529882	42529882	+	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	agaaacattcaactctccatTatgacacgggcctcccacag	13	8	6	14	1	2	2	1	1	1	1	4	2	3	2	3	1	2	0	3	1	3	2			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr18:42529882T>A	ENST00000282030.5	+	4	873	c.577T>A	c.(577-579)Tat>Aat	p.Y193N		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	193						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)		AACTCTCCATTATGACACGGG	0.517									Schinzel-Giedion syndrome																												p.Y193N		Atlas-SNP	.											.	SETBP1	577	.	0			c.T577A						PASS	.						66	60	62					18																	42529882		2203	4300	6503	SO:0001583	missense	26040	exon4	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	CTCCATTATGACA	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.577T>A	chr18.hg19:g.42529882T>A	ENSP00000282030:p.Tyr193Asn	77.0	0.0	.		75.0	19.0	.	NM_015559	A6H8W5|Q6P6C3|Q9UEF3	Missense_Mutation	SNP	ENST00000282030.5	hg19	CCDS11923.2	.	.	.	.	.	.	.	.	.	.	T	18.73	3.686317	0.68157	.	.	ENSG00000152217	ENST00000282030	T	0.70749	-0.51	5.79	5.79	0.91817	.	0.080224	0.53938	D	0.000049	T	0.73329	0.3573	L	0.36672	1.1	0.39128	D	0.961792	D	0.53745	0.962	P	0.54924	0.764	T	0.75777	-0.3198	10	0.46703	T	0.11	.	16.1341	0.81471	0.0:0.0:0.0:1.0	.	193	Q9Y6X0	SETBP_HUMAN	N	193	ENSP00000282030:Y193N	ENSP00000282030:Y193N	Y	+	1	0	SETBP1	40783880	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.244000	0.58728	2.220000	0.72140	0.528000	0.53228	TAT	.	.	.	none		0.517	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110		A	42529882	T	A	42529882	3	1	260	1	0	0	0	0	1	0	0	0	14142	1754	61	5	780	5	SETBP1	18	42529882	Missense_Mutation	SNP	T	TCGA-UZ-A9PN-01A-11D-A382-10		42529882	35547366	46	16211											
TMX3	54495	hgsc.bcm.edu	37	chr18	66365251	66365251	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaacatttgttgacttggaAgtggccgaattagagccctg	11	11	11	8	1	0	2	0	1	0	1	0	4	0	3	2	2	2	1	2	2	4	4			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr18:66365251A>G	ENST00000299608.2	-	7	726	c.410T>C	c.(409-411)cTt>cCt	p.L137P	TMX3_ENST00000562706.1_Missense_Mutation_p.L137P|TMX3_ENST00000443099.2_Missense_Mutation_p.L110P	NM_019022.3	NP_061895.3	Q96JJ7	TMX3_HUMAN	thioredoxin-related transmembrane protein 3	137					cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	17						TTGACTTGGAAGTGGCCGAAT	0.308																																					p.L137P		Atlas-SNP	.											.	TMX3	44	.	0			c.T410C						PASS	.						86	78	81					18																	66365251		2203	4300	6503	SO:0001583	missense	54495	exon7			CTTGGAAGTGGCC	BX647846	CCDS32840.1	18q22	2011-10-19	2009-02-23	2009-02-23		ENSG00000166479		"Protein disulfide isomerases"	24718	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 13"		"thioredoxin domain containing 10"	TXNDC10		15623505	Standard	NM_019022		Approved	FLJ20793, KIAA1830, PDIA13	uc002lkf.3	Q96JJ7		ENST00000299608.2:c.410T>C	chr18.hg19:g.66365251A>G	ENSP00000299608:p.Leu137Pro	55.0	0.0	.		57.0	14.0	.	NM_019022	B3KV75|Q52LT7|Q8N5J0|Q9NWJ9	Missense_Mutation	SNP	ENST00000299608.2	hg19	CCDS32840.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.083448	0.76642	.	.	ENSG00000166479	ENST00000299608;ENST00000544714;ENST00000443099	T;T	0.14144	2.53;2.56	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.35451	0.0932	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.998	T	0.08229	-1.0732	10	0.87932	D	0	.	13.5227	0.61576	1.0:0.0:0.0:0.0	.	110;137;137	B4DIE3;Q96JJ7-2;Q96JJ7	.;.;TMX3_HUMAN	P	137;137;110	ENSP00000299608:L137P;ENSP00000402605:L110P	ENSP00000299608:L137P	L	-	2	0	TMX3	64516231	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.992000	0.88273	2.141000	0.66446	0.533000	0.62120	CTT	.	.	.	none		0.308	TMX3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420155.1	NM_019022		G	66365251	A	G	66365251	3	3	260	1	0	0	0	0	1	0	0	0	16280	72	3	3	994	3	TMX3	18	66365251	Missense_Mutation	SNP	A	TCGA-UZ-A9PN-01A-11D-A382-10	23835369	66365251	11711997	47	16212											
C19orf28	126321	hgsc.bcm.edu	37	chr19	3544832	3544832	+	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	cgcaggcgggtcggccacagCaggaggctacagagacacag	11	2	16	12	3	0	1	0	0	0	1	1	3	0	2	1	5	2	3	1	5	1	1			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr19:3544832C>T	ENST00000355415.2	-	9	1564	c.1395G>A	c.(1393-1395)ctG>ctA	p.L465L	MFSD12_ENST00000398558.4_Silent_p.L465L|MFSD12_ENST00000389395.3_Silent_p.L465L|AC005786.7_ENST00000589360.1_RNA	NM_174983.3	NP_778148.2	Q6NUT3	MFS12_HUMAN	major facilitator superfamily domain containing 12	465					transport (GO:0006810)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				cervix(1)|endometrium(2)|lung(4)|urinary_tract(2)	9						TCGGCCACAGCAGGAGGCTAC	0.662											OREG0025153	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L465L		Atlas-SNP	.											.	MFSD12	22	.	0			c.G1395A						PASS	.						32	43	40					19																	3544832		2179	4266	6445	SO:0001819	synonymous_variant	126321	exon9			CCACAGCAGGAGG	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.1395G>A	chr19.hg19:g.3544832C>T		66.0	0.0	.	612	34.0	19.0	.	NM_001042680	A8MXP7|D6W615|E9PAJ8|Q8N459	Silent	SNP	ENST00000355415.2	hg19	CCDS42465.1																																																																																			.	.	.	none		0.662	MFSD12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452949.2	NM_174983		T	3544832	C	T	3544832	2	4	260	1	0	0	0	0	0	0	0	1	1919	697	25	2		2	C19orf28	19	3544832	Silent	SNP	C	TCGA-UZ-A9PN-01A-11D-A382-10		3544832	55584151	48	16213											
BRD4	23476	hgsc.bcm.edu	37	chr19	15350822	15350822	+	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	cataagcggggagggggcttCgcggaggtgacctaggagaa	10	5	19	7	3	0	2	0	1	0	1	1	5	0	4	1	7	1	1	1	7	3	3	rs200902225		TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr19:15350822C>T	ENST00000263377.2	-	15	3402	c.3181G>A	c.(3181-3183)Gaa>Aaa	p.E1061K		NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	1061	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)			GAGGGGGCTTCGCGGAGGTGA	0.557			T	C15orf55	lethal midline carcinoma of young people																																p.E1061K		Atlas-SNP	.		Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	.	BRD4	172	.	0			c.G3181A						PASS	.						34	37	36					19																	15350822		2203	4300	6503	SO:0001583	missense	23476	exon15			GGGCTTCGCGGAG	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.3181G>A	chr19.hg19:g.15350822C>T	ENSP00000263377:p.Glu1061Lys	63.0	0.0	.		45.0	17.0	.	NM_058243	O60433|Q4G0X8|Q86YS8|Q96PD3	Missense_Mutation	SNP	ENST00000263377.2	hg19	CCDS12328.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.938039	0.52972	.	.	ENSG00000141867	ENST00000263377	T	0.34275	1.37	4.41	4.41	0.53225	.	0.000000	0.50627	D	0.000109	T	0.22820	0.0551	L	0.29908	0.895	0.80722	D	1	P	0.49253	0.921	B	0.31390	0.129	T	0.08391	-1.0724	10	0.38643	T	0.18	-8.7097	15.7874	0.78319	0.0:1.0:0.0:0.0	.	1061	O60885	BRD4_HUMAN	K	1061	ENSP00000263377:E1061K	ENSP00000263377:E1061K	E	-	1	0	BRD4	15211822	1.000000	0.71417	0.997000	0.53966	0.936000	0.57629	7.175000	0.77632	1.979000	0.57680	0.561000	0.74099	GAA	.	.	.	weak		0.557	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243		T	15350822	C	T	15350822	3	4	260	1	0	0	0	0	1	0	0	0	1506	893	31	1	931	1	BRD4	19	15350822	Missense_Mutation	SNP	C	TCGA-UZ-A9PN-01A-11D-A382-10	11805990	15350822	43778161	49	16214											
AKT2	208	hgsc.bcm.edu	37	chr19	40743897	40743897	+	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	ttgatgtcgcggtataccacGtcccgcgagtgcaagtactc	8	10	11	12	5	0	1	0	1	0	0	3	2	1	1	2	1	3	3	2	1	4	4	rs150206349		TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr19:40743897G>T	ENST00000392038.2	-	9	1108	c.810C>A	c.(808-810)gaC>gaA	p.D270E	AKT2_ENST00000311278.6_Missense_Mutation_p.D270E|AKT2_ENST00000579047.1_Missense_Mutation_p.D208E|AKT2_ENST00000424901.1_Missense_Mutation_p.D270E	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	270	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)			GGTATACCACGTCCCGCGAGT	0.592			A		"ovarian, pancreatic "																																p.D270E		Atlas-SNP	.		Dom	yes		19	19q13.1-q13.2	208	v-akt murine thymoma viral oncogene homolog 2		E	.	AKT2	53	.	0			c.C810A						PASS	.						121	84	96					19																	40743897		2203	4300	6503	SO:0001583	missense	208	exon9			TACCACGTCCCGC	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.810C>A	chr19.hg19:g.40743897G>T	ENSP00000375892:p.Asp270Glu	75.0	0.0	.		48.0	13.0	.	NM_001626	B2RBD8|Q05BV0|Q0VAN0|Q0VAN1|Q68GC0	Missense_Mutation	SNP	ENST00000392038.2	hg19	CCDS12552.1	.	.	.	.	.	.	.	.	.	.	G	14.47	2.545765	0.45280	.	.	ENSG00000105221	ENST00000392038;ENST00000391844;ENST00000424901;ENST00000311278;ENST00000391845	T;T;T	0.24908	1.83;1.83;1.83	5.04	-1.24	0.09435	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.158114	0.56097	D	0.000023	T	0.17238	0.0414	L	0.37507	1.11	0.46113	D	0.99887	B;B;B	0.13145	0.001;0.007;0.0	B;B;B	0.13407	0.002;0.009;0.003	T	0.06826	-1.0805	10	0.44086	T	0.13	.	9.7769	0.40626	0.7366:0.0:0.2634:0.0	.	208;270;270	B4DG79;Q0VAN0;P31751	.;.;AKT2_HUMAN	E	270;171;270;270;90	ENSP00000375892:D270E;ENSP00000399532:D270E;ENSP00000309428:D270E	ENSP00000309428:D270E	D	-	3	2	AKT2	45435737	0.149000	0.22717	0.992000	0.48379	0.920000	0.55202	-0.327000	0.07955	-0.005000	0.14395	-0.355000	0.07637	GAC	.	G|1.000;A|0.000	.	alt		0.592	AKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268029.1	NM_001626		T	40743897	G	T	40743897	3	4	260	1	0	0	0	0	1	0	0	0	480	1136	40	4	659	4	AKT2	19	40743897	Missense_Mutation	SNP	G	TCGA-UZ-A9PN-01A-11D-A382-10	25393075	40743897	18385086	50	16215											
PRR12	57479	hgsc.bcm.edu	37	chr19	50104787	50104787	+	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	gaaacccccacccactccacCtcctgccccgactcctcagc	8	5	4	24	1	1	0	1	0	0	0	4	2	4	0	9	0	3	0	9	0	1	0			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr19:50104787C>G	ENST00000418929.2	+	6	4397	c.4385C>G	c.(4384-4386)cCt>cGt	p.P1462R		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	0							DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		cccactccacctcctgccccg	0.682																																					p.P1462R		Atlas-SNP	.											.	PRR12	157	.	0			c.C4385G						PASS	.						3	6	5					19																	50104787		1546	3424	4970	SO:0001583	missense	57479	exon6			CTCCACCTCCTGC	AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"KIAA1205"	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.4385C>G	chr19.hg19:g.50104787C>G	ENSP00000394510:p.Pro1462Arg	126.0	0.0	.		76.0	17.0	.	NM_020719	E9PB06|Q8N4J6	Missense_Mutation	SNP	ENST00000418929.2	hg19	CCDS46143.1	.	.	.	.	.	.	.	.	.	.	C	6.153	0.396514	0.11638	.	.	ENSG00000126464	ENST00000418929;ENST00000246798;ENST00000314734	.	.	.	2.41	1.34	0.21922	.	.	.	.	.	T	0.36193	0.0958	.	.	.	0.36279	D	0.855686	P	0.48016	0.904	B	0.42625	0.393	T	0.36915	-0.9728	7	0.38643	T	0.18	-0.189	6.3508	0.21375	0.2937:0.7063:0.0:0.0	.	1462	Q9ULL5-3	.	R	1462;642;642	.	ENSP00000246798:P642R	P	+	2	0	PRR12	54796599	0.002000	0.14202	0.718000	0.30602	0.862000	0.49288	1.602000	0.36783	0.546000	0.28920	0.313000	0.20887	CCT	.	.	.	none		0.682	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719		G	50104787	C	G	50104787	3	3	260	1	0	0	0	0	1	0	0	0	12594	681	24	4	4407	4	PRR12	19	50104787	Missense_Mutation	SNP	C	TCGA-UZ-A9PN-01A-11D-A382-10	9360890	50104787	9024196	51	16216											
TNNT1	7138	hgsc.bcm.edu	37	chr19	55656921	55656921	+	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	taggatctcaccttggtttgGggcgttcctcttctgttggt	3	17	12	9	1	3	0	1	0	3	0	5	1	4	1	2	5	0	3	2	5	1	6			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr19:55656921G>T	ENST00000588981.1	-	6	323	c.119C>A	c.(118-120)cCc>cAc	p.P40H	TNNT1_ENST00000587465.2_5'UTR|TNNT1_ENST00000592920.1_5'UTR|TNNT1_ENST00000587758.1_Missense_Mutation_p.P29H|TNNT1_ENST00000536926.1_Intron|TNNT1_ENST00000291901.8_Missense_Mutation_p.P40H|TNNT1_ENST00000356783.5_Missense_Mutation_p.P29H|TNNT1_ENST00000585321.2_5'UTR|TNNT1_ENST00000588426.1_Intron	NM_003283.4	NP_003274.3	P13805	TNNT1_HUMAN	troponin T type 1 (skeletal, slow)	40					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)		CCTTGGTTTGGGGCGTTCCTC	0.542																																					p.P40H		Atlas-SNP	.											TNNT1,NS,carcinoma,0,2	TNNT1	28	.	0			c.C119A						PASS	.						166	173	171					19																	55656921		2203	4300	6503	SO:0001583	missense	7138	exon6			GGTTTGGGGCGTT		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.119C>A	chr19.hg19:g.55656921G>T	ENSP00000467176:p.Pro40His	106.0	0.0	.		70.0	3.0	.	NM_001126132	O95472|Q16061|Q5U0E1	Missense_Mutation	SNP	ENST00000588981.1	hg19	CCDS12917.1	.	.	.	.	.	.	.	.	.	.	G	15.07	2.722866	0.48728	.	.	ENSG00000105048	ENST00000291901;ENST00000356783;ENST00000429737	D;D	0.99880	-7.45;-7.45	3.72	3.72	0.42706	.	0.072594	0.56097	D	0.000035	D	0.99822	0.9921	M	0.66439	2.03	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;1.0;0.999	D;D;D;D	0.83275	0.99;0.996;0.996;0.99	D	0.96025	0.9012	10	0.72032	D	0.01	-17.4076	13.8205	0.63318	0.0:0.0:1.0:0.0	.	40;29;40;40	Q56R94;P13805-2;P13805-3;P13805	.;.;.;TNNT1_HUMAN	H	40;29;55	ENSP00000291901:P40H;ENSP00000349233:P29H	ENSP00000291901:P40H	P	-	2	0	TNNT1	60348733	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	6.019000	0.70818	2.006000	0.58801	0.590000	0.80494	CCC	.	.	.	none		0.542	TNNT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451825.2	NM_003283		T	55656921	G	T	55656921	3	4	260	1	0	0	0	0	1	0	0	0	16342	1232	43	4	753	4	TNNT1	19	55656921	Missense_Mutation	SNP	G	TCGA-UZ-A9PN-01A-11D-A382-10	5552134	55656921	3472062	52	16217											
RPL28	6158	hgsc.bcm.edu	37	chr19	55897936	55897936	+	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	ccttgtgccgcctccttcccAggagcccaataacttgaagg	8	9	9	15	1	0	1	0	1	0	0	2	2	2	2	6	2	3	0	6	2	3	4			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr19:55897936A>G	ENST00000344063.2	+	3	710		c.e3-1		RPL28_ENST00000558815.1_Splice_Site|RPL28_ENST00000559463.1_Splice_Site|RPL28_ENST00000560055.1_Splice_Site|RPL28_ENST00000558752.1_Splice_Site|RPL28_ENST00000558131.1_Splice_Site|RPL28_ENST00000458349.2_Splice_Site|TMEM238_ENST00000444469.3_5'Flank|RPL28_ENST00000428193.2_Splice_Site|RPL28_ENST00000431533.2_Splice_Site|RPL28_ENST00000560583.1_Splice_Site			P46779	RL28_HUMAN	ribosomal protein L28						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(2)|large_intestine(2)|lung(1)	6	Breast(117;0.191)	Renal(1328;0.245)	LUSC - Lung squamous cell carcinoma(43;0.13)|BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0443)		CCTCCTTCCCAGGAGCCCAAT	0.612																																					.		Atlas-SNP	.											.	RPL28	31	.	0			c.82-2A>G						PASS	.						63	65	64					19																	55897936		2203	4300	6503	SO:0001630	splice_region_variant	6158	exon3			CTTCCCAGGAGCC	U14969	CCDS12924.1, CCDS46189.1, CCDS46190.1, CCDS46191.1, CCDS46192.1	19q13.4	2011-04-06				ENSG00000108107		"L ribosomal proteins"	10330	protein-coding gene	gene with protein product	"60S ribosomal protein L28"	603638				7772601, 9582194	Standard	NM_001136134		Approved	FLJ43307, L28	uc010yga.2	P46779		ENST00000344063.2:c.82-1A>G	chr19.hg19:g.55897936A>G		137.0	0.0	.		85.0	23.0	.	NM_001136137	B2R4A6|B4DEP9|C9JB50|E9PB24|G5E9L2|Q6IAY0|Q96FX1|Q9BWQ0	Splice_Site	SNP	ENST00000344063.2	hg19	CCDS12924.1	.	.	.	.	.	.	.	.	.	.	A	18.04	3.535153	0.64972	.	.	ENSG00000108107	ENST00000344063;ENST00000426763;ENST00000428193;ENST00000431533;ENST00000458349	.	.	.	3.37	3.37	0.38596	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.4015	0.44233	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RPL28	60589748	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	5.754000	0.68743	1.791000	0.52520	0.533000	0.62120	.	.	.	.	none		0.612	RPL28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416277.2	NM_000991	Intron	G	55897936	A	G	55897936	5	3	260	1	0	0	0	0	0	0	1	0	13590	202	7	3	86	3	RPL28	19	55897936	Splice_Site	SNP	A	TCGA-UZ-A9PN-01A-11D-A382-10	241015	55897936	3231047	53	16218											
OGFR	11054	hgsc.bcm.edu	37	chr20	61443936	61443936	+	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	ggggaccccgaccacgaggcCagcacccagggtcggacctg	8	2	15	16	3	0	0	0	0	0	0	1	4	0	2	6	5	1	1	6	5	0	0			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr20:61443936C>A	ENST00000290291.6	+	7	994	c.969C>A	c.(967-969)gcC>gcA	p.A323A	OGFR_ENST00000370461.1_Silent_p.A271A	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	323					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)					ACCACGAGGCCAGCACCCAGG	0.701																																					p.A323A		Atlas-SNP	.											.	OGFR	63	.	0			c.C969A						PASS	.						5	6	6					20																	61443936		2122	4164	6286	SO:0001819	synonymous_variant	11054	exon7			CGAGGCCAGCACC	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.969C>A	chr20.hg19:g.61443936C>A		215.0	0.0	.		177.0	35.0	.	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Silent	SNP	ENST00000290291.6	hg19	CCDS13504.1																																																																																			.	.	.	none		0.701	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1			A	61443936	C	A	61443936	2	1	260	1	0	0	0	0	0	0	0	1	10850	581	21	4		4	OGFR	20	61443936	Silent	SNP	C	TCGA-UZ-A9PN-01A-11D-A382-10		61443936	1581584	54	16219											
KRTAP10-8	386681	hgsc.bcm.edu	37	chr21	46032797	46032797	+	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	tgctcccgcctggcctgctgAggcctctgctcaggccagga	4	8	13	16	1	2	1	1	1	1	0	3	2	3	2	5	4	3	3	5	4	0	0			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chr21:46032797A>T	ENST00000334662.2	+	1	802	c.780A>T	c.(778-780)tgA>tgT	p.*260C	TSPEAR_ENST00000323084.4_Intron	NM_198695.2	NP_941968.2	P60410	KR108_HUMAN	keratin associated protein 10-8	0						keratin filament (GO:0045095)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	17						tggcctgcTGAGGCCTCTGCT	0.711																																					p.X260C		Atlas-SNP	.											.	KRTAP10-8	34	.	0			c.A780T						PASS	.						29	33	32					21																	46032797		2195	4284	6479	SO:0001578	stop_lost	386681	exon1			CTGCTGAGGCCTC	AB076355	CCDS13713.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000187766	ENSG00000187766		"Keratin associated proteins"	20525	protein-coding gene	gene with protein product			"keratin associated protein 18-8"	KRTAP18-8			Standard	NM_198695		Approved	KRTAP18.8, KAP10.8	uc002zfo.1	P60410	OTTHUMG00000057632	ENST00000334662.2:c.780A>T	chr21.hg19:g.46032797A>T	ENSP00000335565:p.*260Cysext*11	48.0	0.0	.		24.0	11.0	.	NM_198695	A0JNW4	Missense_Mutation	SNP	ENST00000334662.2	hg19	CCDS13713.1	.	.	.	.	.	.	.	.	.	.	a	0.016	-1.512184	0.00984	.	.	ENSG00000187766	ENST00000334662	.	.	.	3.5	-1.98	0.07480	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.4751	0.11731	0.1872:0.5795:0.0:0.2333	.	.	.	.	C	260	.	.	X	+	3	0	KRTAP10-8	44857225	0.454000	0.25728	0.018000	0.16275	0.002000	0.02628	-0.652000	0.05366	-0.465000	0.06953	-0.644000	0.03951	TGA	.	.	.	none		0.711	KRTAP10-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128035.1	NM_198695		T	46032797	A	T	46032797	4	4	260	1	0	0	0	0	0	0	0	0	8522	317	11	5	782	5	KRTAP10-8	21	46032797	Nonstop_Mutation	SNP	A	TCGA-UZ-A9PN-01A-11D-A382-10		46032797	2097098	55	16220											
NLGN4X	57502	hgsc.bcm.edu	37	chrX	5811459	5811459	+	Missense_Mutation	SNP	T	T	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	catagggaaatgatgtcatgTctggtggaggaacctttgtg	10	12	14	5	0	2	1	1	1	1	0	2	4	2	4	1	4	1	0	1	4	3	2			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chrX:5811459T>G	ENST00000381095.3	-	6	2477	c.1850A>C	c.(1849-1851)gAc>gCc	p.D617A	NLGN4X_ENST00000275857.6_Missense_Mutation_p.D617A|NLGN4X_ENST00000538097.1_Missense_Mutation_p.D617A|NLGN4X_ENST00000381093.2_Missense_Mutation_p.D637A|NLGN4X_ENST00000381092.1_Missense_Mutation_p.D617A	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	617					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						TGATGTCATGTCTGGTGGAGG	0.493																																					p.D617A		Atlas-SNP	.											.	NLGN4X	191	.	0			c.A1850C						PASS	.						125	106	112					X																	5811459		2203	4297	6500	SO:0001583	missense	57502	exon6			GTCATGTCTGGTG	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.1850A>C	chrX.hg19:g.5811459T>G	ENSP00000370485:p.Asp617Ala	251.0	1.0	.		216.0	95.0	.	NM_181332	Q6UX10|Q9ULG0	Missense_Mutation	SNP	ENST00000381095.3	hg19	CCDS14126.1	.	.	.	.	.	.	.	.	.	.	T	5.476	0.272923	0.10349	.	.	ENSG00000146938	ENST00000381095;ENST00000381093;ENST00000275857;ENST00000381092;ENST00000538097	T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16	4.0	4.0	0.46444	.	0.444374	0.16752	N	0.200994	T	0.54415	0.1857	L	0.46157	1.445	0.58432	D	0.999996	B;B;B	0.16396	0.017;0.017;0.013	B;B;B	0.15484	0.009;0.013;0.012	T	0.51911	-0.8645	10	0.42905	T	0.14	.	11.5189	0.50539	0.0:0.0:0.0:1.0	.	674;617;637	A6NMU8;Q8N0W4;Q8N0W4-2	.;NLGNX_HUMAN;.	A	617;637;617;617;617	ENSP00000370485:D617A;ENSP00000370483:D637A;ENSP00000275857:D617A;ENSP00000370482:D617A;ENSP00000439203:D617A	ENSP00000275857:D617A	D	-	2	0	NLGN4X	5821459	1.000000	0.71417	0.757000	0.31301	0.019000	0.09904	6.912000	0.75753	1.290000	0.44636	0.417000	0.27973	GAC	.	.	.	none		0.493	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742		G	5811459	T	G	5811459	3	3	260	1	0	0	0	0	1	0	0	0	10471	1667	58	5	604	5	NLGN4X	23	5811459	Missense_Mutation	SNP	T	TCGA-UZ-A9PN-01A-11D-A382-10		5811459	149459101	56	16221											
PPP1R3F	89801	hgsc.bcm.edu	37	chrX	49143255	49143255	+	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	tctcccgtccttctgcagggGcaaaatcccaccctcctcag	7	9	7	18	1	3	0	1	0	2	0	7	0	6	0	5	2	1	2	5	2	2	1			TCGA-UZ-A9PN-01A-11D-A382-10	TCGA-UZ-A9PN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	206e9cb3-201a-42f0-9d9e-4477dfe96585	9d87e73d-61d7-487c-9e1b-4dbc1285612b	g.chrX:49143255G>A	ENST00000055335.6	+	4	2119	c.2103G>A	c.(2101-2103)ggG>ggA	p.G701G	PPP1R3F_ENST00000438316.1_Silent_p.G372G|PPP1R3F_ENST00000466508.1_Silent_p.G355G|PPP1R3F_ENST00000376188.1_Silent_p.G355G|PPP1R3F_ENST00000495799.1_Silent_p.G355G	NM_033215.4	NP_149992.3	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory subunit 3F	701					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)					TTCTGCAGGGGCAAAATCCCA	0.597																																					p.G701G		Atlas-SNP	.											.	PPP1R3F	56	.	0			c.G2103A						PASS	.						48	30	36					X																	49143255		2202	4300	6502	SO:0001819	synonymous_variant	89801	exon4			GCAGGGGCAAAAT		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.2103G>A	chrX.hg19:g.49143255G>A		102.0	0.0	.		98.0	52.0	.	NM_033215	A2VDJ8|B3KPW2|E9PCM3	Silent	SNP	ENST00000055335.6	hg19	CCDS35254.1																																																																																			.	.	.	none		0.597	PPP1R3F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060819.2	NM_033215		A	49143255	G	A	49143255	2	1	260	1	0	0	0	0	0	0	0	1	12385	1190	42	2		2	PPP1R3F	23	49143255	Silent	SNP	G	TCGA-UZ-A9PN-01A-11D-A382-10	43331796	49143255	106127305	57	16222											
COL16A1	1307	hgsc.bcm.edu	37	chr1	32149737	32149737	+	Frame_Shift_Del	DEL	G	G	-																															ccaggtcggcccacgccttcGgggccctgctctcctttggg																								rs373053106		TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr1:32149737delG	ENST00000373672.3	-	32	2772	c.2256delC	c.(2254-2256)cccfs	p.P752fs	COL16A1_ENST00000373668.3_Frame_Shift_Del_p.P752fs|COL16A1_ENST00000271069.6_Frame_Shift_Del_p.P751fs	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	752	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)		CCACGCCTTCGGGGCCCTGCT	0.682																																					p.E753fs	Colon(143;498 1786 21362 25193 36625)	Atlas-Indel,Pindel	.											.	COL16A1	137	.	0			c.2257delG						PASS	.						16	21	20					1																	32149737		1978	4128	6106	SO:0001589	frameshift_variant	1307	exon32			.	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.2256delC	chr1.hg19:g.32149737delG	ENSP00000362776:p.Pro752fs	184.0	0.0	0		205.0	72.0	0.35122	NM_001856	Q16593|Q59F89|Q71RG9	Frame_Shift_Del	DEL	ENST00000373672.3	hg19	CCDS41297.1																																																																																			.	.	.	none		0.682	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856		-	32149737	G	-	32149737	7	5	261	1	0	1	0	1	0	0	0	0	3675	1103	39	0	2718	0	COL16A1	1	32149737	Frame_Shift_Del	DEL	G	TCGA-UZ-A9PO-01A-11D-A382-10		32149737	217100884	1	16223											
PABPC4	8761	hgsc.bcm.edu	37	chr1	40031014	40031014	+	Missense_Mutation	SNP	A	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	aggagatgagaagcagacgaAgccaaaccctttgcttcttc	13	8	10	10	1	1	3	0	1	1	3	2	6	1	3	2	1	4	2	2	1	3	3			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr1:40031014A>C	ENST00000372857.3	-	8	1801	c.1009T>G	c.(1009-1011)Ttc>Gtc	p.F337V	RP11-69E11.8_ENST00000415255.1_RNA|PABPC4_ENST00000372862.3_Missense_Mutation_p.F337V|PABPC4_ENST00000372858.3_Missense_Mutation_p.F337V|PABPC4_ENST00000372856.3_Missense_Mutation_p.F337V|SNORA55_ENST00000364587.1_RNA	NM_003819.3	NP_003810.1	Q13310	PABP4_HUMAN	poly(A) binding protein, cytoplasmic 4 (inducible form)	337	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				blood coagulation (GO:0007596)|RNA catabolic process (GO:0006401)|RNA processing (GO:0006396)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|prostate(1)|skin(3)	21	Lung NSC(20;1.55e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.89e-18)|Epithelial(16;6.17e-17)|all cancers(16;1.18e-15)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			AAGCAGACGAAGCCAAACCCT	0.502																																					p.F337V		Atlas-SNP	.											.	PABPC4	56	.	0			c.T1009G						PASS	.						74	71	72					1																	40031014		2203	4300	6503	SO:0001583	missense	8761	exon8			AGACGAAGCCAAA	U33818	CCDS438.1, CCDS44114.1, CCDS44115.1	1p34.2	2013-02-12	2001-11-28		ENSG00000090621	ENSG00000090621		"RNA binding motif (RRM) containing"	8557	protein-coding gene	gene with protein product		603407	"poly(A)-binding protein, cytoplasmic 4 (inducible form)"			10543404	Standard	NM_001135653		Approved	iPABP, APP-1	uc001cdl.2	Q13310	OTTHUMG00000009097	ENST00000372857.3:c.1009T>G	chr1.hg19:g.40031014A>C	ENSP00000361948:p.Phe337Val	55.0	0.0	.		59.0	19.0	.	NM_001135653	B1ANQ8|Q4VC03|Q6P0N3	Missense_Mutation	SNP	ENST00000372857.3	hg19	CCDS438.1	.	.	.	.	.	.	.	.	.	.	A	33	5.223893	0.95139	.	.	ENSG00000090621	ENST00000372862;ENST00000372858;ENST00000372857;ENST00000372856	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	6.16	6.16	0.99307	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.68915	0.3053	H	0.95114	3.625	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.996;0.984;0.999	T	0.79024	-0.1972	10	0.87932	D	0	.	16.8061	0.85666	1.0:0.0:0.0:0.0	.	337;337;337	Q13310;Q13310-2;Q4VC03	PABP4_HUMAN;.;.	V	337	ENSP00000361953:F337V;ENSP00000361949:F337V;ENSP00000361948:F337V;ENSP00000361947:F337V	ENSP00000361947:F337V	F	-	1	0	PABPC4	39803601	1.000000	0.71417	0.994000	0.49952	0.990000	0.78478	9.307000	0.96226	2.367000	0.80283	0.528000	0.53228	TTC	.	.	.	none		0.502	PABPC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025220.1	NM_001135653		C	40031014	A	C	40031014	3	2	261	1	0	0	0	0	1	0	0	0	11373	72	3	5	1005	5	PABPC4	1	40031014	Missense_Mutation	SNP	A	TCGA-UZ-A9PO-01A-11D-A382-10	7881277	40031014	209219607	2	16224											
SLC6A9	6536	hgsc.bcm.edu	37	chr1	44475672	44475672	+	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	tgatcctccagacccccaggCacccctggcttgcaaactgg	8	7	9	17	0	0	2	0	1	0	1	2	2	2	2	6	3	2	3	6	3	1	1			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr1:44475672C>T	ENST00000360584.2	-	4	694	c.503G>A	c.(502-504)tGc>tAc	p.C168Y	SLC6A9_ENST00000475075.2_Intron|SLC6A9_ENST00000492434.2_5'UTR|SLC6A9_ENST00000372306.3_Missense_Mutation_p.C95Y|SLC6A9_ENST00000537678.1_Missense_Mutation_p.C30Y|SLC6A9_ENST00000372310.3_Missense_Mutation_p.C95Y|SLC6A9_ENST00000357730.2_Missense_Mutation_p.C114Y|SLC6A9_ENST00000372307.3_Missense_Mutation_p.C30Y	NM_201649.3	NP_964012.2	P48067	SC6A9_HUMAN	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	168					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)			endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(2)	22	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			Glycine(DB00145)	GACCCCCAGGCACCCCTGGCT	0.602																																					p.C168Y		Atlas-SNP	.											.	SLC6A9	109	.	0			c.G503A						PASS	.						67	72	70					1																	44475672		2203	4300	6503	SO:0001583	missense	6536	exon4			CCCAGGCACCCCT	S70609	CCDS30695.1, CCDS41316.1, CCDS41317.1	1p33	2013-05-22			ENSG00000196517	ENSG00000196517		"Solute carriers"	11056	protein-coding gene	gene with protein product		601019				8183239, 7587377	Standard	NM_006934		Approved	GLYT1	uc001cll.4	P48067	OTTHUMG00000008294	ENST00000360584.2:c.503G>A	chr1.hg19:g.44475672C>T	ENSP00000353791:p.Cys168Tyr	193.0	0.0	.		212.0	54.0	.	NM_201649	A6NDH1|A6NII2|A6NNZ8|Q5TAB8|Q5TAB9|Q5TAC0	Missense_Mutation	SNP	ENST00000360584.2	hg19	CCDS41317.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.446464	0.84101	.	.	ENSG00000196517	ENST00000372307;ENST00000372306;ENST00000372310;ENST00000360584;ENST00000357730;ENST00000537678;ENST00000528803	T;T;T;T;T;T;T	0.74632	-0.86;-0.86;-0.86;-0.86;-0.86;-0.86;-0.86	5.4	5.4	0.78164	.	0.046641	0.85682	D	0.000000	D	0.88455	0.6441	M	0.87097	2.86	0.80722	D	1	D;D;D;D;D;D	0.89917	0.998;0.997;0.995;0.996;0.996;1.0	D;D;D;D;D;D	0.91635	0.994;0.95;0.95;0.946;0.946;0.999	D	0.89341	0.3654	10	0.62326	D	0.03	.	18.9633	0.92685	0.0:1.0:0.0:0.0	.	99;95;30;95;114;168	B7Z3W8;B7Z8W5;B7Z3A9;P48067-2;P48067-3;P48067	.;.;.;.;.;SC6A9_HUMAN	Y	30;95;95;168;114;30;114	ENSP00000361381:C30Y;ENSP00000361380:C95Y;ENSP00000361384:C95Y;ENSP00000353791:C168Y;ENSP00000350362:C114Y;ENSP00000442523:C30Y;ENSP00000435652:C114Y	ENSP00000350362:C114Y	C	-	2	0	SLC6A9	44248259	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.018000	0.40991	2.813000	0.96785	0.561000	0.74099	TGC	.	.	.	none		0.602	SLC6A9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000022825.2	NM_201649		T	44475672	C	T	44475672	3	4	261	1	0	0	0	0	1	0	0	0	14704	710	25	2	1661	2	SLC6A9	1	44475672	Missense_Mutation	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	4444658	44475672	204774949	3	16225											
CYP4A11	1579	hgsc.bcm.edu	37	chr1	47403742	47403742	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttgcctccccatagccaaTgaggacaggcacttgggaat	10	9	10	12	0	0	1	0	1	0	0	1	3	1	3	4	3	2	1	4	3	3	3			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr1:47403742T>C	ENST00000310638.4	-	2	294	c.263A>G	c.(262-264)cAt>cGt	p.H88R	CYP4A11_ENST00000371905.1_Missense_Mutation_p.H88R|CYP4A11_ENST00000457840.2_5'UTR|CYP4A11_ENST00000462347.1_Missense_Mutation_p.H88R|CYP4A11_ENST00000371904.4_Missense_Mutation_p.H88R	NM_000778.3	NP_000769.2	Q02928	CP4AB_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 11	88					arachidonic acid metabolic process (GO:0019369)|cellular lipid metabolic process (GO:0044255)|epoxygenase P450 pathway (GO:0019373)|fatty acid metabolic process (GO:0006631)|leukotriene B4 catabolic process (GO:0036101)|leukotriene metabolic process (GO:0006691)|long-chain fatty acid metabolic process (GO:0001676)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of icosanoid secretion (GO:0032305)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)			endometrium(2)|kidney(5)|large_intestine(6)|lung(6)|ovary(5)|prostate(3)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	36					Cisplatin(DB00515)|Clofibrate(DB00636)|Dexamethasone(DB01234)|Estrone(DB00655)|Ethanol(DB00898)|Lansoprazole(DB00448)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Rifampicin(DB01045)|Tretinoin(DB00755)	CCATAGCCAATGAGGACAGGC	0.507																																					p.H88R		Atlas-SNP	.											.	CYP4A11	77	.	0			c.A263G						PASS	.						226	178	195					1																	47403742		2203	4300	6503	SO:0001583	missense	1579	exon2			AGCCAATGAGGAC	L04751	CCDS543.1	1p33	2008-02-05	2003-01-14		ENSG00000187048	ENSG00000187048		"Cytochrome P450s"	2642	protein-coding gene	gene with protein product		601310	"cytochrome P450, subfamily IVA, polypeptide 11"	CYP4A2		7679927	Standard	NM_000778		Approved	CYP4AII	uc001cqp.4	Q02928	OTTHUMG00000008020	ENST00000310638.4:c.263A>G	chr1.hg19:g.47403742T>C	ENSP00000311095:p.His88Arg	132.0	0.0	.		122.0	40.0	.	NM_000778	Q06766|Q16865|Q16866|Q5VSP8|Q86SU6|Q8IWY5	Missense_Mutation	SNP	ENST00000310638.4	hg19	CCDS543.1	.	.	.	.	.	.	.	.	.	.	-	4.775	0.144108	0.09134	.	.	ENSG00000187048	ENST00000310638;ENST00000371904;ENST00000371905	T;T;T	0.67865	-0.29;-0.29;-0.29	5.51	-6.14	0.02111	.	0.665630	0.13942	N	0.352126	T	0.23649	0.0572	N	0.00648	-1.295	0.09310	N	0.999998	B	0.02656	0.0	B	0.04013	0.001	T	0.38735	-0.9647	10	0.17369	T	0.5	.	6.3399	0.21316	0.5397:0.1961:0.0:0.2642	.	88	Q02928	CP4AB_HUMAN	R	88	ENSP00000311095:H88R;ENSP00000360971:H88R;ENSP00000360972:H88R	ENSP00000311095:H88R	H	-	2	0	CYP4A11	47176329	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-1.790000	0.01759	-1.037000	0.03283	-0.451000	0.05528	CAT	.	.	.	none		0.507	CYP4A11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022022.1	NM_000778		C	47403742	T	C	47403742	3	2	261	1	0	0	0	0	1	0	0	0	4185	1464	51	3	1340	3	CYP4A11	1	47403742	Missense_Mutation	SNP	T	TCGA-UZ-A9PO-01A-11D-A382-10	2928070	47403742	201846879	4	16226											
MYSM1	114803	hgsc.bcm.edu	37	chr1	59127169	59127169	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taacatctgctgtacttcaaAtttgtaaggtaagcctagaa	14	13	7	7	0	2	1	1	0	1	1	2	1	2	1	1	1	4	4	1	1	7	7			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr1:59127169A>G	ENST00000472487.1	-	18	2218	c.2179T>C	c.(2179-2181)Ttt>Ctt	p.F727L	MYSM1_ENST00000493821.1_5'UTR	NM_001085487.2	NP_001078956.1	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1	727					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)					TGTACTTCAAATTTGTAAGGT	0.343																																					p.F727L		Atlas-SNP	.											.	MYSM1	50	.	0			c.T2179C						PASS	.						134	120	124					1																	59127169		1832	4080	5912	SO:0001583	missense	114803	exon18			CTTCAAATTTGTA	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.2179T>C	chr1.hg19:g.59127169A>G	ENSP00000418734:p.Phe727Leu	67.0	0.0	.		58.0	15.0	.	NM_001085487	A8KA54|B3KX65|Q68DD3|Q6AI53|Q7Z3G8|Q96PX3	Missense_Mutation	SNP	ENST00000472487.1	hg19	CCDS41343.1	.	.	.	.	.	.	.	.	.	.	A	18.42	3.619113	0.66787	.	.	ENSG00000162601	ENST00000472487	T	0.24350	1.86	5.13	5.13	0.70059	.	0.104089	0.64402	D	0.000002	T	0.43700	0.1259	M	0.63843	1.955	0.44694	D	0.997685	D	0.69078	0.997	D	0.75020	0.985	T	0.23655	-1.0182	10	0.15952	T	0.53	-16.8799	12.8107	0.57637	1.0:0.0:0.0:0.0	.	727	Q5VVJ2	MYSM1_HUMAN	L	727	ENSP00000418734:F727L	ENSP00000418734:F727L	F	-	1	0	MYSM1	58899757	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.045000	0.64220	2.158000	0.67659	0.377000	0.23210	TTT	.	.	.	none		0.343	MYSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026343.2	XM_055481		G	59127169	A	G	59127169	3	3	261	1	0	0	0	0	1	0	0	0	10108	101	4	3	319	3	MYSM1	1	59127169	Missense_Mutation	SNP	A	TCGA-UZ-A9PO-01A-11D-A382-10	11723427	59127169	190123452	5	16227											
CCDC18	343099	hgsc.bcm.edu	37	chr1	93671122	93671122	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aactaactgtgaaaaagaaaAtaaaaggctacaagaaaggt	23	6	8	4	0	0	3	0	1	0	2	0	3	0	3	0	2	3	1	0	2	11	3			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr1:93671122A>G	ENST00000343253.7	+	8	1353	c.851A>G	c.(850-852)aAt>aGt	p.N284S	CCDC18_ENST00000401026.3_Missense_Mutation_p.N284S|CCDC18_ENST00000338949.4_Missense_Mutation_p.N83S|CCDC18_ENST00000334652.5_5'UTR|CCDC18_ENST00000557479.1_Missense_Mutation_p.N402S			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	284										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)		GAAAAAGAAAATAAAAGGCTA	0.289																																					p.N284S		Atlas-SNP	.											.	CCDC18	93	.	0			c.A851G						PASS	.						61	61	61					1																	93671122		1800	4053	5853	SO:0001583	missense	343099	exon8			AAGAAAATAAAAG			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.851A>G	chr1.hg19:g.93671122A>G	ENSP00000343377:p.Asn284Ser	351.0	0.0	.		334.0	95.0	.	NM_206886	Q6ZU17	Missense_Mutation	SNP	ENST00000343253.7	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.67|15.67	2.902271|2.902271	0.52227|0.52227	.|.	.|.	ENSG00000122483|ENSG00000122483	ENST00000370276|ENST00000343253;ENST00000401026;ENST00000557479;ENST00000338949;ENST00000455267	.|.	.|.	.|.	5.84|5.84	5.84|5.84	0.93424|0.93424	.|.	.|0.169095	.|0.50627	.|D	.|0.000110	T|T	0.30293|0.30293	0.0760|0.0760	L|L	0.51422|0.51422	1.61|1.61	0.80722|0.80722	D|D	1|1	.|P	.|0.47910	.|0.902	.|B	.|0.43301	.|0.415	T|T	0.19484|0.19484	-1.0304|-1.0304	5|9	.|0.09084	.|T	.|0.74	.|.	12.0845|12.0845	0.53690|0.53690	0.9314:0.0:0.0686:0.0|0.9314:0.0:0.0686:0.0	.|.	.|402	.|G3V388	.|.	V|S	338|284;284;402;83;4	.|.	.|ENSP00000344380:N83S	I|N	+|+	1|2	0|0	CCDC18|CCDC18	93443710|93443710	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.918000|0.918000	0.54935|0.54935	2.192000|2.192000	0.42649|0.42649	2.234000|2.234000	0.73211|0.73211	0.528000|0.528000	0.53228|0.53228	ATA|AAT	.	.	.	none		0.289	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886		G	93671122	A	G	93671122	3	3	261	1	0	0	0	0	1	0	0	0	2796	101	4	3	1235	3	CCDC18	1	93671122	Missense_Mutation	SNP	A	TCGA-UZ-A9PO-01A-11D-A382-10	34543953	93671122	155579499	6	16228											
OLFML2B	25903	hgsc.bcm.edu	37	chr1	161989728	161989728	+	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	ccttcaagtcctggctgtctGcctcccgcagcttctggagc	4	11	10	16	1	3	0	1	0	2	0	5	1	5	1	4	2	3	3	4	2	1	2			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr1:161989728G>T	ENST00000294794.3	-	2	842	c.419C>A	c.(418-420)gCa>gAa	p.A140E	OLFML2B_ENST00000367940.2_Missense_Mutation_p.A140E	NM_015441.1	NP_056256.1	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B	140					extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)			CTGGCTGTCTGCCTCCCGCAG	0.577																																					p.A140E		Atlas-SNP	.											.	OLFML2B	114	.	0			c.C419A						PASS	.						52	51	51					1																	161989728		2203	4300	6503	SO:0001583	missense	25903	exon2			CTGTCTGCCTCCC	BX648975	CCDS1236.1, CCDS72966.1	1q23.1	2008-02-05			ENSG00000162745	ENSG00000162745			24558	protein-coding gene	gene with protein product							Standard	XM_005245075		Approved	DKFZP586L151	uc001gbu.3	Q68BL8	OTTHUMG00000024047	ENST00000294794.3:c.419C>A	chr1.hg19:g.161989728G>T	ENSP00000294794:p.Ala140Glu	68.0	0.0	.		64.0	13.0	.	NM_015441	B7ZA39|Q5VU96|Q6NX46|Q86X11|Q9Y3X6	Missense_Mutation	SNP	ENST00000294794.3	hg19	CCDS1236.1	.	.	.	.	.	.	.	.	.	.	G	12.71	2.018710	0.35606	.	.	ENSG00000162745	ENST00000294794;ENST00000367940	T;T	0.49139	0.79;0.79	4.64	3.72	0.42706	.	.	.	.	.	T	0.39009	0.1062	L	0.43923	1.385	0.32334	N	0.560703	D;D	0.59767	0.961;0.986	P;P	0.53062	0.454;0.717	T	0.39702	-0.9601	8	0.56958	D	0.05	.	13.9466	0.64089	0.084:0.0:0.916:0.0	.	140;140	F2Z3N3;Q68BL8	.;OLM2B_HUMAN	E	140	ENSP00000294794:A140E;ENSP00000356917:A140E	ENSP00000294794:A140E	A	-	2	0	OLFML2B	160256352	1.000000	0.71417	0.739000	0.30968	0.577000	0.36160	7.202000	0.77856	0.694000	0.31654	-1.134000	0.01955	GCA	.	.	.	none		0.577	OLFML2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060552.2	NM_015441		T	161989728	G	T	161989728	3	4	261	1	0	0	0	0	1	0	0	0	10865	1319	46	4	1861	4	OLFML2B	1	161989728	Missense_Mutation	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	68318606	161989728	87260893	7	16229											
DYRK3	8444	hgsc.bcm.edu	37	chr1	206821237	206821237	+	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	gggtctatgatcacaaacttCgacagtacgtggccctaaaa	13	9	9	10	2	2	1	1	1	1	0	3	2	2	1	1	2	2	1	1	2	5	4			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr1:206821237C>A	ENST00000367109.2	+	3	862	c.694C>A	c.(694-696)Cga>Aga	p.R232R	DYRK3_ENST00000367106.1_Silent_p.R212R|DYRK3_ENST00000367108.3_Silent_p.R212R|DYRK3_ENST00000489878.1_Intron	NM_003582.2	NP_003573.2	O43781	DYRK3_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	232	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				erythrocyte differentiation (GO:0030218)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(9)|lung(8)|skin(1)|stomach(2)	25	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			TCACAAACTTCGACAGTACGT	0.468																																					p.R232R	Melanoma(164;427 2622 26826 51707)	Atlas-SNP	.											DYRK3_ENST00000367109,NS,carcinoma,0,3	DYRK3	146	.	0			c.C694A						PASS	.						72	68	69					1																	206821237		2203	4300	6503	SO:0001819	synonymous_variant	8444	exon3			AAACTTCGACAGT	Y12735	CCDS30999.1, CCDS31000.1	1q32	2008-07-18			ENSG00000143479	ENSG00000143479	2.7.12.1		3094	protein-coding gene	gene with protein product	"regulatory erythroid kinase", "dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 5", "protein kinase Dyrk3"	603497				9748265	Standard	NM_003582		Approved	RED, REDK, hYAK3-2	uc001hej.3	O43781	OTTHUMG00000036339	ENST00000367109.2:c.694C>A	chr1.hg19:g.206821237C>A		138.0	0.0	.		152.0	42.0	.	NM_003582	D3DT79|Q7Z752|Q9HBY6|Q9HBY7	Silent	SNP	ENST00000367109.2	hg19	CCDS30999.1																																																																																			.	.	.	none		0.468	DYRK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088458.1	NM_003582		A	206821237	C	A	206821237	2	1	261	1	0	0	0	0	0	0	0	1	4859	876	31	4		4	DYRK3	1	206821237	Silent	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	44831509	206821237	42429384	8	16230											
SMEK2	57223	hgsc.bcm.edu	37	chr2	55795473	55795473	+	Frame_Shift_Del	DEL	T	T	-																															aaattcatctttaagtccaaTtatccgcctcataaagcgaa																										TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr2:55795473delT	ENST00000345102.5	-	13	2093	c.1792delA	c.(1792-1794)attfs	p.I598fs	SMEK2_ENST00000407823.3_Frame_Shift_Del_p.I566fs|SNORA12_ENST00000390873.1_RNA|SMEK2_ENST00000272313.5_Frame_Shift_Del_p.I513fs	NM_001122964.1	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	598					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)			TTAAGTCCAATTATCCGCCTC	0.318																																					p.I598fs		Atlas-Indel,Pindel	.											.	SMEK2	86	.	0			c.1793delT						PASS	.						58	62	61					2																	55795473		2203	4297	6500	SO:0001589	frameshift_variant	57223	exon13			.	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.1792delA	chr2.hg19:g.55795473delT	ENSP00000339769:p.Ile598fs	160.0	0.0	0		144.0	34.0	0.236111	NM_001122964	Q6P9B0|Q86XB8|Q9BQJ0|Q9BRK2|Q9H913|Q9P2G0	Frame_Shift_Del	DEL	ENST00000345102.5	hg19	CCDS46289.1																																																																																			.	.	.	none		0.318	SMEK2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251483.1	NM_020463		-	55795473	T	-	55795473	7	5	261	1	0	1	0	1	0	0	0	0	14807	1493	52	0	777	0	SMEK2	2	55795473	Frame_Shift_Del	DEL	T	TCGA-UZ-A9PO-01A-11D-A382-10		55795473	187403900	9	16231											
FASTKD1	79675	hgsc.bcm.edu	37	chr2	170403017	170403017	+	Frame_Shift_Del	DEL	T	T	-																															tcagttgtttcgcagtcataTtatccaaatacatgtgatca																										TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr2:170403017delT	ENST00000453153.2	-	8	1758	c.1412delA	c.(1411-1413)aatfs	p.N471fs	FASTKD1_ENST00000453929.2_Frame_Shift_Del_p.N471fs	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	471					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						CGCAGTCATATTATCCAAATA	0.383																																					p.N471fs		Atlas-Indel,Pindel	.											.	FASTKD1	86	.	0			c.1413delT						PASS	.						120	105	110					2																	170403017		2203	4300	6503	SO:0001589	frameshift_variant	79675	exon8			.	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.1412delA	chr2.hg19:g.170403017delT	ENSP00000400513:p.Asn471fs	265.0	0.0	0		248.0	66.0	0.266129	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Frame_Shift_Del	DEL	ENST00000453153.2	hg19	CCDS33318.1																																																																																			.	.	.	none		0.383	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622		-	170403017	T	-	170403017	7	5	261	1	0	1	0	1	0	0	0	0	5692	1493	52	0	1163	0	FASTKD1	2	170403017	Frame_Shift_Del	DEL	T	TCGA-UZ-A9PO-01A-11D-A382-10	114607544	170403017	72796356	10	16232											
IHH	3549	hgsc.bcm.edu	37	chr2	219920563	219920563	+	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	ctccggcagggaagcagccgCccgtcttggctgcggccgag	5	5	16	15	5	1	0	0	0	1	0	2	2	2	1	4	4	3	3	4	4	1	1			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr2:219920563C>A	ENST00000295731.6	-	3	601	c.602G>T	c.(601-603)gGc>gTc	p.G201V	MIR3131_ENST00000583592.1_RNA	NM_002181.3	NP_002172.2	Q14623	IHH_HUMAN	indian hedgehog	201					bone resorption (GO:0045453)|camera-type eye photoreceptor cell fate commitment (GO:0060220)|cartilage development (GO:0051216)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-cell signaling (GO:0007267)|chondrocyte proliferation (GO:0035988)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic pattern specification (GO:0009880)|embryonic skeletal joint development (GO:0072498)|epithelial cell morphogenesis (GO:0003382)|epithelial cell-cell adhesion (GO:0090136)|head morphogenesis (GO:0060323)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|intein-mediated protein splicing (GO:0016539)|maternal process involved in female pregnancy (GO:0060135)|multicellular organism growth (GO:0035264)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of eye pigmentation (GO:0048074)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|negative regulation of signal transduction (GO:0009968)|negative regulation of T cell differentiation in thymus (GO:0033085)|neuron development (GO:0048666)|osteoblast differentiation (GO:0001649)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteoglycan metabolic process (GO:0006029)|regulation of growth (GO:0040008)|response to estradiol (GO:0032355)|retinal pigment epithelium development (GO:0003406)|skeletal system development (GO:0001501)|smooth muscle tissue development (GO:0048745)|smoothened signaling pathway (GO:0007224)|somite development (GO:0061053)|vitelline membrane formation (GO:0030704)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|patched binding (GO:0005113)|peptidase activity (GO:0008233)			breast(1)|endometrium(2)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	14		Renal(207;0.0915)		Epithelial(149;1.13e-06)|all cancers(144;0.000188)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GAAGCAGCCGCCCGTCTTGGC	0.667																																					p.G201V		Atlas-SNP	.											.	IHH	33	.	0			c.G602T						PASS	.						17	18	18					2																	219920563		2198	4295	6493	SO:0001583	missense	3549	exon3			CAGCCGCCCGTCT	L38517	CCDS33380.1	2q33-q35	2013-02-15	2013-02-15		ENSG00000163501	ENSG00000163501			5956	protein-coding gene	gene with protein product		600726	"Indian hedgehog (Drosophila) homolog", "Indian hedgehog homolog (Drosophila)"			7590746, 14770182	Standard	NM_002181		Approved	HHG2, BDA1	uc002vjo.2	Q14623	OTTHUMG00000154631	ENST00000295731.6:c.602G>T	chr2.hg19:g.219920563C>A	ENSP00000295731:p.Gly201Val	44.0	0.0	.		37.0	13.0	.	NM_002181	B9EGM5|O43322|Q8N4B9	Missense_Mutation	SNP	ENST00000295731.6	hg19	CCDS33380.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.783324	0.90282	.	.	ENSG00000163501	ENST00000295731	D	0.99483	-5.99	5.29	5.29	0.74685	Hedgehog/intein hint, N-terminal (1);Peptidase C46, hedgehog protein, hint region (1);	0.155258	0.56097	D	0.000023	D	0.99569	0.9845	M	0.87456	2.885	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	D	0.98302	1.0519	10	0.66056	D	0.02	-7.1352	18.5642	0.91112	0.0:1.0:0.0:0.0	.	201	Q14623	IHH_HUMAN	V	201	ENSP00000295731:G201V	ENSP00000295731:G201V	G	-	2	0	IHH	219628807	1.000000	0.71417	0.998000	0.56505	0.980000	0.70556	7.729000	0.84864	2.469000	0.83416	0.561000	0.74099	GGC	.	.	.	none		0.667	IHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336408.2	NM_002181		A	219920563	C	A	219920563	3	1	261	1	0	0	0	0	1	0	0	0	7614	739	26	4	637	4	IHH	2	219920563	Missense_Mutation	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	49517546	219920563	23278810	11	16233											
ATG4B	23192	hgsc.bcm.edu	37	chr2	242611647	242611647	+	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	tggaaagattcttcgactcaGaagatgaagactttgaaatc	15	11	9	6	1	2	6	1	2	1	4	4	8	2	7	0	1	0	0	0	1	4	3			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr2:242611647G>T	ENST00000404914.3	+	13	1253	c.1150G>T	c.(1150-1152)Gaa>Taa	p.E384*	ATG4B_ENST00000396411.3_Nonsense_Mutation_p.E310*|ATG4B_ENST00000402096.1_Nonsense_Mutation_p.E322*|ATG4B_ENST00000405546.3_3'UTR|ATG4B_ENST00000474739.2_Nonsense_Mutation_p.E370*	NM_013325.4|NM_178326.2	NP_037457.3|NP_847896.1	Q9Y4P1	ATG4B_HUMAN	autophagy related 4B, cysteine peptidase	384					autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|positive regulation of autophagy (GO:0010508)|positive regulation of protein catabolic process (GO:0045732)|protein transport (GO:0015031)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	cysteine-type peptidase activity (GO:0008234)|endopeptidase activity (GO:0004175)			breast(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		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;2.44e-33)|all cancers(36;5.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.75e-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;0.0848)		CTTCGACTCAGAAGATGAAGA	0.537																																					p.E384X	Melanoma(78;458 1323 6342 12171 39523)	Atlas-SNP	.											.	ATG4B	35	.	0			c.G1150T						PASS	.						94	92	93					2																	242611647		1916	4102	6018	SO:0001587	stop_gained	23192	exon13			GACTCAGAAGATG	AB023160	CCDS46564.1, CCDS46565.1	2q37.3	2014-02-12	2012-06-06	2005-09-11	ENSG00000168397	ENSG00000168397			20790	protein-coding gene	gene with protein product		611338	"APG4 autophagy 4 homolog B (S. cerevisiae)", "ATG4 autophagy related 4 homolog B (S. cerevisiae)"	APG4B		12446702	Standard	NM_013325		Approved	Apg4B, KIAA0943, DKFZp586D1822, AUTL1	uc002wbv.3	Q9Y4P1	OTTHUMG00000151514	ENST00000404914.3:c.1150G>T	chr2.hg19:g.242611647G>T	ENSP00000384259:p.Glu384*	73.0	0.0	.		89.0	20.0	.	NM_013325	B7WNK2|Q53NU4|Q6ZUV8|Q8WYM9|Q96K07|Q96K96|Q96SZ1|Q9Y2F2	Nonsense_Mutation	SNP	ENST00000404914.3	hg19	CCDS46564.1	.	.	.	.	.	.	.	.	.	.	G	38	7.119008	0.98077	.	.	ENSG00000168397	ENST00000337606;ENST00000402096;ENST00000404914;ENST00000474739;ENST00000396411	.	.	.	5.55	4.66	0.58398	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	-3.9894	15.725	0.77747	0.0:0.0:0.8623:0.1377	.	.	.	.	X	501;322;384;370;310	.	ENSP00000336547:E501X	E	+	1	0	ATG4B	242260320	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.660000	0.91121	1.326000	0.45319	0.655000	0.94253	GAA	.	.	.	none		0.537	ATG4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322967.3	NM_013325		T	242611647	G	T	242611647	4	4	261	1	0	0	0	0	0	1	0	0	1097	943	33	4	1220	4	ATG4B	2	242611647	Nonsense_Mutation	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	22691084	242611647	587726	12	16234											
FBLN2	2199	hgsc.bcm.edu	37	chr3	13672240	13672240	+	Missense_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	agcgctgcagccaggagtgtGccaacatctatggctcctac	9	8	11	13	1	1	0	0	0	1	0	2	1	2	1	3	2	6	3	3	2	3	2			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr3:13672240G>A	ENST00000295760.7	+	14	2938	c.2869G>A	c.(2869-2871)Gcc>Acc	p.A957T	FBLN2_ENST00000535798.1_Missense_Mutation_p.A983T|FBLN2_ENST00000404922.3_Missense_Mutation_p.A1004T|FBLN2_ENST00000492059.1_Missense_Mutation_p.A1004T	NM_001998.2	NP_001989.2	P98095	FBLN2_HUMAN	fibulin 2	957	EGF-like 8; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(3)|prostate(3)|urinary_tract(1)	24			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)			CCAGGAGTGTGCCAACATCTA	0.632																																					p.A1004T		Atlas-SNP	.											.	FBLN2	137	.	0			c.G3010A						PASS	.						34	40	38					3																	13672240		2196	4299	6495	SO:0001583	missense	2199	exon15			GAGTGTGCCAACA	X82494	CCDS46761.1, CCDS46762.1	3p25-p24	2010-06-15			ENSG00000163520	ENSG00000163520		"Fibulins"	3601	protein-coding gene	gene with protein product		135821				7806230	Standard	NM_001165035		Approved		uc011ava.2	P98095	OTTHUMG00000155437	ENST00000295760.7:c.2869G>A	chr3.hg19:g.13672240G>A	ENSP00000295760:p.Ala957Thr	111.0	0.0	.		109.0	25.0	.	NM_001004019	B7Z9C5|Q8IUI0|Q8IUI1	Missense_Mutation	SNP	ENST00000295760.7	hg19	CCDS46762.1	.	.	.	.	.	.	.	.	.	.	G	16.61	3.171629	0.57584	.	.	ENSG00000163520	ENST00000535798;ENST00000404922;ENST00000295760;ENST00000492059	D;D;D;D	0.86956	-2.19;-2.17;-2.13;-2.17	5.26	3.42	0.39159	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.115243	0.64402	N	0.000016	T	0.63546	0.2520	N	0.00677	-1.265	0.53688	D	0.999973	B;B;B	0.18166	0.016;0.013;0.026	B;B;B	0.22601	0.04;0.034;0.025	T	0.55398	-0.8147	10	0.34782	T	0.22	.	8.5938	0.33703	0.2416:0.0:0.7584:0.0	.	957;1004;983	P98095;P98095-2;F5H1F3	FBLN2_HUMAN;.;.	T	983;1004;957;1004	ENSP00000445705:A983T;ENSP00000384169:A1004T;ENSP00000295760:A957T;ENSP00000420042:A1004T	ENSP00000295760:A957T	A	+	1	0	FBLN2	13647241	1.000000	0.71417	0.928000	0.36995	0.989000	0.77384	4.954000	0.63631	0.573000	0.29400	0.561000	0.74099	GCC	.	.	.	none		0.632	FBLN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340083.3	NM_001004019		A	13672240	G	A	13672240	3	1	261	1	0	0	0	0	1	0	0	0	5706	1319	46	2	1754	2	FBLN2	3	13672240	Missense_Mutation	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10		13672240	184350190	13	16235											
CMC1	152100	hgsc.bcm.edu	37	chr3	28361046	28361046	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgcaaaatggaatacctgAaggaaagggaagaattcaga	20	6	11	4	0	1	3	1	1	0	2	1	6	1	6	1	3	2	1	1	3	9	2			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr3:28361046A>G	ENST00000466830.1	+	4	446	c.247A>G	c.(247-249)Aag>Gag	p.K83E	AZI2_ENST00000295748.3_5'Flank|CMC1_ENST00000469102.1_3'UTR|CMC1_ENST00000423894.1_Missense_Mutation_p.K53E	NM_182523.1	NP_872329.1	Q7Z7K0	COXM1_HUMAN	C-x(9)-C motif containing 1	83						mitochondrion (GO:0005739)	metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(3)	5						GGAATACCTGAAGGAAAGGGA	0.343																																					p.K83E		Atlas-SNP	.											.	CMC1	9	.	0			c.A247G						PASS	.						77	79	78					3																	28361046		2203	4298	6501	SO:0001583	missense	152100	exon4			TACCTGAAGGAAA	BC052644	CCDS33722.1	3p24.1	2013-10-18	2013-10-18	2008-06-20	ENSG00000187118	ENSG00000187118			28783	protein-coding gene	gene with protein product		615166	"chromosome 3 open reading frame 68", "COX assembly mitochondrial protein 1 homolog (S. cerevisiae)"	C3orf68		18443040	Standard	NM_182523		Approved	MGC61571	uc003cea.3	Q7Z7K0	OTTHUMG00000155660	ENST00000466830.1:c.247A>G	chr3.hg19:g.28361046A>G	ENSP00000418348:p.Lys83Glu	405.0	0.0	.		356.0	106.0	.	NM_182523	Q68DJ7	Missense_Mutation	SNP	ENST00000466830.1	hg19	CCDS33722.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.64|13.64	2.296267|2.296267	0.40594|0.40594	.|.	.|.	ENSG00000187118|ENSG00000187118	ENST00000418849|ENST00000466830;ENST00000423894	.|T;T	.|0.42513	.|0.97;0.97	5.72|5.72	4.54|4.54	0.55810|0.55810	.|.	.|0.257041	.|0.44483	.|D	.|0.000450	T|T	0.36468|0.36468	0.0968|0.0968	L|L	0.41356|0.41356	1.27|1.27	0.80722|0.80722	D|D	1|1	.|B	.|0.21905	.|0.062	.|B	.|0.27715	.|0.082	T|T	0.09796|0.09796	-1.0658|-1.0658	5|10	.|0.37606	.|T	.|0.19	-11.3586|-11.3586	12.8107|12.8107	0.57637|0.57637	0.8632:0.1368:0.0:0.0|0.8632:0.1368:0.0:0.0	.|.	.|83	.|Q7Z7K0	.|COXAM_HUMAN	G|E	89|83;53	.|ENSP00000418348:K83E;ENSP00000404581:K53E	.|ENSP00000404581:K53E	E|K	+|+	2|1	0|0	CMC1|CMC1	28336050|28336050	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	5.951000|5.951000	0.70273|0.70273	0.960000|0.960000	0.38005|0.38005	0.460000|0.460000	0.39030|0.39030	GAA|AAG	.	.	.	none		0.343	CMC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341087.1	NM_182523		G	28361046	A	G	28361046	3	3	261	1	0	0	0	0	1	0	0	0	3579	247	9	3	261	3	CMC1	3	28361046	Missense_Mutation	SNP	A	TCGA-UZ-A9PO-01A-11D-A382-10	14688806	28361046	169661384	14	16236											
GOLGA4	2803	hgsc.bcm.edu	37	chr3	37368460	37368460	+	Frame_Shift_Del	DEL	C	C	-																															ttcacatcttggaagaaaaaCttaagtcagtggaaagttca																										TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr3:37368460delC	ENST00000361924.2	+	14	5457	c.5083delC	c.(5083-5085)cttfs	p.L1695fs	GOLGA4_ENST00000356847.4_Frame_Shift_Del_p.L1717fs|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1695	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						GGAAGAAAAACTTAAGTCAGT	0.368																																					p.K1716fs		Atlas-Indel,Pindel	.											.	GOLGA4	173	.	0			c.5148delA						PASS	.						106	116	113					3																	37368460		2201	4296	6497	SO:0001589	frameshift_variant	2803	exon15			.	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.5083delC	chr3.hg19:g.37368460delC	ENSP00000354486:p.Leu1695fs	278.0	0.0	0		271.0	85.0	0.313653	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Frame_Shift_Del	DEL	ENST00000361924.2	hg19	CCDS2666.1																																																																																			.	.	.	none		0.368	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		-	37368460	C	-	37368460	7	5	261	1	0	1	0	1	0	0	0	0	6562	565	20	0	5207	0	GOLGA4	3	37368460	Frame_Shift_Del	DEL	C	TCGA-UZ-A9PO-01A-11D-A382-10	9007414	37368460	160653970	15	16237											
C3orf67	200844	hgsc.bcm.edu	37	chr3	58817468	58817468	+	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	actgctggtacttatgctgaCattacagttgtccacctggg	8	13	10	10	0	0	1	0	1	0	0	1	1	1	1	2	2	4	4	2	2	3	4			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr3:58817468C>T	ENST00000482387.1	-	10	1840	c.1744G>A	c.(1744-1746)Gtc>Atc	p.V582I	RP11-147N17.1_ENST00000463703.1_RNA|RP11-147N17.1_ENST00000482372.1_RNA|RP11-147N17.1_ENST00000493123.1_RNA|RP11-147N17.1_ENST00000492031.1_RNA|C3orf67_ENST00000295966.7_Missense_Mutation_p.V456I			Q6ZVT6	CC067_HUMAN	chromosome 3 open reading frame 67	582										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)		CTTATGCTGACATTACAGTTG	0.537																																					p.V456I		Atlas-SNP	.											.	C3orf67	45	.	0			c.G1366A						PASS	.						189	148	161					3																	58817468		2203	4300	6503	SO:0001583	missense	200844	exon13			TGCTGACATTACA	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.1744G>A	chr3.hg19:g.58817468C>T	ENSP00000417122:p.Val582Ile	151.0	0.0	.		147.0	43.0	.	NM_198463	B9EKV6|Q6ZV69	Missense_Mutation	SNP	ENST00000482387.1	hg19		.	.	.	.	.	.	.	.	.	.	C	17.87	3.494293	0.64186	.	.	ENSG00000163689	ENST00000295966;ENST00000482387	T;T	0.20881	2.1;2.04	5.92	5.04	0.67666	.	0.071801	0.56097	D	0.000033	T	0.23532	0.0569	L	0.52759	1.655	0.80722	D	1	P;P	0.51537	0.724;0.946	B;P	0.45610	0.292;0.487	T	0.00402	-1.1762	9	.	.	.	-11.6553	11.7693	0.51949	0.0:0.8666:0.0:0.1334	.	456;582	Q6ZVT6-2;Q6ZVT6	.;CC067_HUMAN	I	456;582	ENSP00000295966:V456I;ENSP00000417122:V582I	.	V	-	1	0	C3orf67	58792508	0.985000	0.35326	0.993000	0.49108	0.996000	0.88848	2.410000	0.44592	2.809000	0.96659	0.467000	0.42956	GTC	.	.	.	none		0.537	C3orf67-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000353803.1	NM_198463		T	58817468	C	T	58817468	3	4	261	1	0	0	0	0	1	0	0	0	2243	478	17	2	341	2	C3orf67	3	58817468	Missense_Mutation	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	21449008	58817468	139204962	16	16238											
CASR	846	hgsc.bcm.edu	37	chr3	121976017	121976017	+	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	agcccttcttcccaacttgaCgctgggatacaggatatttg	9	12	9	11	1	1	1	0	1	1	0	2	3	2	3	2	2	3	1	2	2	3	6			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr3:121976017C>A	ENST00000490131.1	+	3	647	c.275C>A	c.(274-276)aCg>aAg	p.T92K	CASR_ENST00000296154.5_Missense_Mutation_p.T92K|CASR_ENST00000498619.1_Missense_Mutation_p.T92K	NM_000388.3	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor	92					anatomical structure morphogenesis (GO:0009653)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|chemosensory behavior (GO:0007635)|detection of calcium ion (GO:0005513)|G-protein coupled receptor signaling pathway (GO:0007186)|metabolic process (GO:0008152)|ossification (GO:0001503)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)	p.T92M(1)		NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(45)|ovary(4)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	84				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	CCCAACTTGACGCTGGGATAC	0.443																																					p.T92K		Atlas-SNP	.											CASR,colon,carcinoma,0,2	CASR	190	.	1	Substitution - Missense(1)	lung(1)	c.C275A						PASS	.						118	119	118					3																	121976017		2203	4300	6503	SO:0001583	missense	846	exon3			ACTTGACGCTGGG	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.275C>A	chr3.hg19:g.121976017C>A	ENSP00000418685:p.Thr92Lys	146.0	0.0	.		134.0	48.0	.	NM_001178065	Q13912|Q16108|Q16109|Q16110|Q16379|Q2M1T0|Q4PJ19	Missense_Mutation	SNP	ENST00000490131.1	hg19	CCDS3010.1	.	.	.	.	.	.	.	.	.	.	C	17.93	3.509339	0.64522	.	.	ENSG00000036828	ENST00000490131;ENST00000498619;ENST00000296154	D;D;D	0.83335	-1.71;-1.71;-1.71	5.84	5.84	0.93424	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.89128	0.6627	L	0.58969	1.84	0.80722	D	1	D;D	0.62365	0.991;0.984	P;P	0.62435	0.902;0.779	D	0.89049	0.3454	10	0.62326	D	0.03	.	19.1433	0.93455	0.0:1.0:0.0:0.0	.	92;92	E7ENE0;P41180	.;CASR_HUMAN	K	92	ENSP00000418685:T92K;ENSP00000420194:T92K;ENSP00000296154:T92K	ENSP00000296154:T92K	T	+	2	0	CASR	123458707	1.000000	0.71417	0.992000	0.48379	0.163000	0.22366	5.999000	0.70665	2.760000	0.94817	0.655000	0.94253	ACG	.	.	.	none		0.443	CASR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355761.1	NM_000388		A	121976017	C	A	121976017	3	1	261	1	0	0	0	0	1	0	0	0	2684	536	19	4	281	4	CASR	3	121976017	Missense_Mutation	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	63158549	121976017	76046413	17	16239											
MAGEF1	64110	hgsc.bcm.edu	37	chr3	184428718	184428718	+	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	gatgccggccctagcactggCcctggccctcatactggctt	5	9	11	16	1	1	0	1	0	0	0	1	1	1	0	4	4	3	2	4	4	2	3			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr3:184428718C>A	ENST00000317897.3	-	1	1118	c.892G>T	c.(892-894)Gcc>Tcc	p.A298S		NM_022149.4	NP_071432.2	Q9HAY2	MAGF1_HUMAN	melanoma antigen family F, 1	298						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)			ctagcactggccctggccctc	0.607																																					p.A298S		Atlas-SNP	.											.	MAGEF1	27	.	0			c.G892T						PASS	.						43	42	43					3																	184428718		2203	4300	6503	SO:0001583	missense	64110	exon1			CACTGGCCCTGGC	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.892G>T	chr3.hg19:g.184428718C>A	ENSP00000315064:p.Ala298Ser	65.0	0.0	.		72.0	23.0	.	NM_022149	Q9H215	Missense_Mutation	SNP	ENST00000317897.3	hg19	CCDS3269.1	.	.	.	.	.	.	.	.	.	.	C	9.883	1.202224	0.22121	.	.	ENSG00000177383	ENST00000317897	T	0.04406	3.63	3.3	2.42	0.29668	.	1.672500	0.04158	N	0.322526	T	0.06280	0.0162	L	0.48218	1.51	0.09310	N	1	P	0.40970	0.734	B	0.37015	0.239	T	0.36311	-0.9753	10	0.46703	T	0.11	.	6.1885	0.20510	0.0:0.861:0.0:0.139	.	298	Q9HAY2	MAGF1_HUMAN	S	298	ENSP00000315064:A298S	ENSP00000315064:A298S	A	-	1	0	MAGEF1	185911412	0.002000	0.14202	0.005000	0.12908	0.038000	0.13279	1.110000	0.31147	0.968000	0.38212	0.561000	0.74099	GCC	.	.	.	none		0.607	MAGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345417.1	NM_022149		A	184428718	C	A	184428718	3	1	261	1	0	0	0	0	1	0	0	0	9194	739	26	4	35	4	MAGEF1	3	184428718	Missense_Mutation	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	62452701	184428718	13593712	18	16240											
DGKQ	1609	hgsc.bcm.edu	37	chr4	960305	960305	+	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	ggctgttcgtccatcagcatCgtccgctggactgcagaggt	6	10	13	12	3	1	1	1	0	0	1	5	2	3	2	2	3	2	5	2	3	0	1	rs373354724		TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr4:960305C>T	ENST00000273814.3	-	12	1450	c.1377G>A	c.(1375-1377)acG>acA	p.T459T	DGKQ_ENST00000502309.1_5'UTR	NM_001347.3	NP_001338.2	P52824	DGKQ_HUMAN	diacylglycerol kinase, theta 110kDa	459	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				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)			CCATCAGCATCGTCCGCTGGA	0.701																																					p.T459T	Esophageal Squamous(17;537 645 4447 26373)	Atlas-SNP	.											.	DGKQ	29	.	0			c.G1377A						PASS	.	C		1,4403	2.1+/-5.4	0,1,2201	45	46	45		1377	-4.7	0.1	4		45	0,8596		0,0,4298	no	coding-synonymous	DGKQ	NM_001347.2		0,1,6499	TT,TC,CC		0.0,0.0227,0.0077		459/943	960305	1,12999	2202	4298	6500	SO:0001819	synonymous_variant	1609	exon12			CAGCATCGTCCGC	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.1377G>A	chr4.hg19:g.960305C>T		95.0	0.0	.		103.0	23.0	.	NM_001347	Q6P3W4	Silent	SNP	ENST00000273814.3	hg19	CCDS3342.1	.	.	.	.	.	.	.	.	.	.	C	0.112	-1.137407	0.01742	2.27E-4	0.0	ENSG00000145214	ENST00000509465	.	.	.	3.92	-4.66	0.03329	.	.	.	.	.	T	0.29458	0.0734	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.27971	-1.0058	4	.	.	.	.	8.4341	0.32775	0.0:0.6571:0.1026:0.2404	.	.	.	.	Q	406	.	.	R	-	2	0	DGKQ	950305	0.000000	0.05858	0.050000	0.19076	0.016000	0.09150	-3.570000	0.00427	-1.914000	0.01078	-1.851000	0.00568	CGA	.	.	.	weak		0.701	DGKQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000200888.1			T	960305	C	T	960305	2	4	261	1	0	0	0	0	0	0	0	1	4475	871	31	1		1	DGKQ	4	960305	Silent	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10		960305	190193971	19	16241											
HGFAC	3083	hgsc.bcm.edu	37	chr4	3443797	3443797	+	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	ggccccttcctcctcctcctCctgctgctgctgctgctgcc	0	12	8	21	0	0	0	0	0	0	0	5	0	5	0	8	1	6	5	8	1	0	1	rs538844201	byFrequency	TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr4:3443797C>G	ENST00000382774.3	+	1	184	c.69C>G	c.(67-69)ctC>ctG	p.L23L	HGFAC_ENST00000511533.1_Silent_p.L23L	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	23					proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		TCCTCCTCCTCCTGCTGCTGC	0.716													C|||	2	0.000399361	8e-04	0	5008	,	,		13350	0		0	False		,,,				2504	0.001				p.L23L		Atlas-SNP	.											HGFAC,NS,carcinoma,0,2	HGFAC	69	.	0			c.C69G						PASS	.						13	16	15					4																	3443797		1723	3604	5327	SO:0001819	synonymous_variant	3083	exon1			CCTCCTCCTGCTG	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.69C>G	chr4.hg19:g.3443797C>G		57.0	0.0	.		52.0	6.0	.	NM_001528	Q14726|Q2M1W7|Q53X47	Silent	SNP	ENST00000382774.3	hg19	CCDS3369.1																																																																																			.	.	.	none		0.716	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3			G	3443797	C	G	3443797	2	3	261	1	0	0	0	0	0	0	0	1	7093	842	30	4		4	HGFAC	4	3443797	Silent	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	2483492	3443797	187710479	20	16242											
SORCS2	57537	hgsc.bcm.edu	37	chr4	7691237	7691237	+	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	actgccacctgcacctgcacCtgcgctgggcagacaacccc	8	5	9	19	1	0	1	0	0	0	1	0	1	0	1	6	1	5	4	6	1	1	0			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr4:7691237C>G	ENST00000507866.2	+	11	1622	c.1513C>G	c.(1513-1515)Ctg>Gtg	p.L505V	SORCS2_ENST00000329016.9_Missense_Mutation_p.L333V	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	505					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						GCACCTGCACCTGCGCTGGGC	0.562																																					p.L505V		Atlas-SNP	.											.	SORCS2	98	.	0			c.C1513G						PASS	.						33	37	35					4																	7691237		2130	4246	6376	SO:0001583	missense	57537	exon11			CTGCACCTGCGCT	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.1513C>G	chr4.hg19:g.7691237C>G	ENSP00000422185:p.Leu505Val	33.0	0.0	.		26.0	11.0	.	NM_020777	Q9P2L7	Missense_Mutation	SNP	ENST00000507866.2	hg19	CCDS47008.1	.	.	.	.	.	.	.	.	.	.	C	17.16	3.319262	0.60524	.	.	ENSG00000184985	ENST00000507866;ENST00000329016	T;T	0.39406	1.08;1.08	3.24	2.36	0.29203	VPS10 (1);	0.000000	0.64402	D	0.000019	T	0.43233	0.1238	M	0.83223	2.63	0.48087	D	0.999589	P;P	0.48694	0.748;0.914	B;B	0.38842	0.247;0.283	T	0.53401	-0.8444	10	0.66056	D	0.02	.	10.9698	0.47432	0.0:0.9033:0.0:0.0967	.	333;505	B5MED8;Q96PQ0	.;SORC2_HUMAN	V	505;333	ENSP00000422185:L505V;ENSP00000329124:L333V	ENSP00000329124:L333V	L	+	1	2	SORCS2	7742137	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.097000	0.50251	0.655000	0.30866	0.557000	0.71058	CTG	.	.	.	none		0.562	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777		G	7691237	C	G	7691237	3	3	261	1	0	0	0	0	1	0	0	0	14944	680	24	4	1555	4	SORCS2	4	7691237	Missense_Mutation	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	4247440	7691237	183463039	21	16243											
BOD1L	259282	hgsc.bcm.edu	37	chr4	13603230	13603230	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgttcctggtggtgcatcaTtatctcccaggacaacacct	8	13	8	12	0	2	0	1	0	1	0	4	1	3	1	3	3	2	2	3	3	2	3			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr4:13603230T>C	ENST00000040738.5	-	10	5429	c.5294A>G	c.(5293-5295)aAt>aGt	p.N1765S		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1765						nucleus (GO:0005634)	DNA binding (GO:0003677)										TGGTGCATCATTATCTCCCAG	0.522																																					p.N1765S		Atlas-SNP	.											.	.	.	.	0			c.A5294G						PASS	.						270	259	263					4																	13603230		2203	4300	6503	SO:0001583	missense	259282	exon10			GCATCATTATCTC	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.5294A>G	chr4.hg19:g.13603230T>C	ENSP00000040738:p.Asn1765Ser	77.0	0.0	.		61.0	17.0	.	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	hg19	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	T	6.387	0.439432	0.12104	.	.	ENSG00000038219	ENST00000040738	T	0.09538	2.97	4.81	-3.17	0.05202	.	1.190080	0.05960	N	0.640395	T	0.07369	0.0186	L	0.27053	0.805	0.09310	N	1	B	0.25667	0.131	B	0.25140	0.058	T	0.40961	-0.9535	10	0.38643	T	0.18	-0.5436	5.7719	0.18257	0.0:0.2174:0.396:0.3865	.	1765	Q8NFC6	BOD1L_HUMAN	S	1765	ENSP00000040738:N1765S	ENSP00000040738:N1765S	N	-	2	0	BOD1L	13212328	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	0.224000	0.17738	-0.717000	0.04955	0.459000	0.35465	AAT	.	.	.	none		0.522	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		C	13603230	T	C	13603230	3	2	261	1	0	0	0	0	1	0	0	0	1483	1493	52	3	3929	3	BOD1L	4	13603230	Missense_Mutation	SNP	T	TCGA-UZ-A9PO-01A-11D-A382-10	5911993	13603230	177551046	22	16244											
STAP1	26228	hgsc.bcm.edu	37	chr4	68442967	68442967	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atggagaggcttcattcttaCagtaacagaggtaggaagct	13	10	12	6	0	2	2	1	0	1	2	2	4	2	3	0	4	3	4	0	4	4	5			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr4:68442967C>T	ENST00000265404.2	+	4	435	c.353C>T	c.(352-354)aCa>aTa	p.T118I	STAP1_ENST00000396225.1_Missense_Mutation_p.T118I	NM_012108.2	NP_036240.1	Q9ULZ2	STAP1_HUMAN	signal transducing adaptor family member 1	118	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)				NS(1)|large_intestine(1)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	12						TTCATTCTTACAGTAACAGAG	0.378																																					p.T118I		Atlas-SNP	.											.	STAP1	46	.	0			c.C353T						PASS	.						81	74	76					4																	68442967		2203	4300	6503	SO:0001583	missense	26228	exon4			TTCTTACAGTAAC	AB023483	CCDS3515.1	4q13.2	2013-02-14	2007-08-09		ENSG00000035720	ENSG00000035720		"SH2 domain containing"	24133	protein-coding gene	gene with protein product	"BCR downstream signaling 1"	604298				10518561, 10679268	Standard	NM_012108		Approved	STAP-1, BRDG1	uc003hde.4	Q9ULZ2	OTTHUMG00000129304	ENST00000265404.2:c.353C>T	chr4.hg19:g.68442967C>T	ENSP00000265404:p.Thr118Ile	261.0	0.0	.		355.0	74.0	.	NM_012108	B2R980	Missense_Mutation	SNP	ENST00000265404.2	hg19	CCDS3515.1	.	.	.	.	.	.	.	.	.	.	C	17.92	3.507469	0.64410	.	.	ENSG00000035720	ENST00000265404;ENST00000396225	T;T	0.30714	1.52;1.52	5.01	5.01	0.66863	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	T	0.56262	0.1973	M	0.77103	2.36	0.48762	D	0.999709	D	0.89917	1.0	D	0.87578	0.998	T	0.59547	-0.7434	10	0.87932	D	0	-18.0375	14.0103	0.64493	0.0:1.0:0.0:0.0	.	118	Q9ULZ2	STAP1_HUMAN	I	118	ENSP00000265404:T118I;ENSP00000379527:T118I	ENSP00000265404:T118I	T	+	2	0	STAP1	68125562	1.000000	0.71417	0.998000	0.56505	0.793000	0.44817	3.789000	0.55454	2.764000	0.94973	0.655000	0.94253	ACA	.	.	.	none		0.378	STAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251434.1	NM_012108		T	68442967	C	T	68442967	3	4	261	1	0	0	0	0	1	0	0	0	15264	478	17	2	367	2	STAP1	4	68442967	Missense_Mutation	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	54839737	68442967	122711309	23	16245											
YTHDC1	91746	hgsc.bcm.edu	37	chr4	69203170	69203170	+	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	ccacttcaagcccaattctcTgatgtttaaagaaaaaggga	15	10	7	9	0	2	2	1	1	1	1	3	3	2	3	2	1	1	1	2	1	6	4			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr4:69203170T>C	ENST00000344157.4	-	4	795		c.e4-2		YTHDC1_ENST00000355665.3_Splice_Site|YTHDC1_ENST00000579690.1_Splice_Site	NM_001031732.2	NP_001026902.1	Q96MU7	YTDC1_HUMAN	YTH domain containing 1						mRNA splice site selection (GO:0006376)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	30						CCCAATTCTCTGATGTTTAAA	0.403																																					.		Atlas-SNP	.											.	YTHDC1	81	.	0			c.460-2A>G						PASS	.						73	69	70					4																	69203170		2203	4300	6503	SO:0001630	splice_region_variant	91746	exon5			ATTCTCTGATGTT	AK098515	CCDS3522.2, CCDS33992.1	4q13.3	2009-01-14			ENSG00000083896	ENSG00000083896			30626	protein-coding gene	gene with protein product						12368078, 10564280	Standard	XM_005265706		Approved	YT521, KIAA1966, YT521-B	uc003hdx.3	Q96MU7	OTTHUMG00000129306	ENST00000344157.4:c.460-2A>G	chr4.hg19:g.69203170T>C		66.0	0.0	.		96.0	24.0	.	NM_133370	Q4W5Q3|Q7Z622|Q8TF35	Splice_Site	SNP	ENST00000344157.4	hg19	CCDS33992.1	.	.	.	.	.	.	.	.	.	.	T	17.67	3.446512	0.63178	.	.	ENSG00000083896	ENST00000344157;ENST00000355665	.	.	.	5.55	5.55	0.83447	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8641	0.70401	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	YTHDC1	68885765	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.367000	0.73099	2.097000	0.63578	0.377000	0.23210	.	.	.	.	none		0.403	YTHDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251437.1	NM_133370	Intron	C	69203170	T	C	69203170	5	2	261	1	0	0	0	0	0	0	1	0	17508	1594	55	3	1781	3	YTHDC1	4	69203170	Splice_Site	SNP	T	TCGA-UZ-A9PO-01A-11D-A382-10	760203	69203170	121951106	24	16246											
FSTL5	56884	hgsc.bcm.edu	37	chr4	162307261	162307261	+	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	gtaaatatcaaaagcctcctGtatttctcctctgatggtaa	12	14	6	9	0	3	1	1	1	2	0	5	1	4	1	3	1	1	3	3	1	7	5			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr4:162307261G>T	ENST00000306100.5	-	16	2618	c.2182C>A	c.(2182-2184)Cag>Aag	p.Q728K	FSTL5_ENST00000536695.1_Missense_Mutation_p.Q727K|FSTL5_ENST00000427802.2_Missense_Mutation_p.Q718K|RP11-234O6.2_ENST00000508189.1_RNA|FSTL5_ENST00000379164.4_Missense_Mutation_p.Q727K	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	728						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)		AAAGCCTCCTGTATTTCTCCT	0.418																																					p.Q728K		Atlas-SNP	.											.	FSTL5	207	.	0			c.C2182A						PASS	.						87	83	84					4																	162307261		2203	4300	6503	SO:0001583	missense	56884	exon16			CCTCCTGTATTTC	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.2182C>A	chr4.hg19:g.162307261G>T	ENSP00000305334:p.Gln728Lys	92.0	0.0	.		109.0	49.0	.	NM_020116	E9PCP6|Q9NSW7|Q9ULF7	Missense_Mutation	SNP	ENST00000306100.5	hg19	CCDS3802.1	.	.	.	.	.	.	.	.	.	.	G	13.58	2.278192	0.40294	.	.	ENSG00000168843	ENST00000306100;ENST00000379164;ENST00000427802;ENST00000536695	T;T;T;T	0.28255	1.62;1.62;1.62;1.62	5.76	5.76	0.90799	WD40/YVTN repeat-like-containing domain (1);	0.637840	0.17348	N	0.177509	T	0.18923	0.0454	N	0.16656	0.425	0.22457	N	0.999086	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.13072	-1.0523	10	0.09843	T	0.71	.	13.876	0.63653	0.0:0.0:0.8477:0.1523	.	718;727;728	E9PCP6;F8VZ90;Q8N475	.;.;FSTL5_HUMAN	K	728;727;718;727	ENSP00000305334:Q728K;ENSP00000368462:Q727K;ENSP00000389270:Q718K;ENSP00000440409:Q727K	ENSP00000305334:Q728K	Q	-	1	0	FSTL5	162526711	1.000000	0.71417	0.501000	0.27601	0.994000	0.84299	4.802000	0.62539	2.702000	0.92279	0.655000	0.94253	CAG	.	.	.	none		0.418	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116		T	162307261	G	T	162307261	3	4	261	1	0	0	0	0	1	0	0	0	6087	1386	48	4	365	4	FSTL5	4	162307261	Missense_Mutation	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	93104091	162307261	28847015	25	16247											
MAP3K1	4214	hgsc.bcm.edu	37	chr5	56161247	56161247	+	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	tttcaactagaaccttcagaCccaatgttatggagaaaaac	16	10	6	9	0	2	3	2	0	0	3	2	4	2	3	2	1	3	1	2	1	7	4			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr5:56161247C>G	ENST00000399503.3	+	5	1116	c.1116C>G	c.(1114-1116)gaC>gaG	p.D372E		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	372					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)		AACCTTCAGACCCAATGTTAT	0.318																																					p.D372E		Atlas-SNP	.											.	MAP3K1	355	.	0			c.C1116G						PASS	.						81	73	75					5																	56161247		1806	4073	5879	SO:0001583	missense	4214	exon5			TTCAGACCCAATG	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.1116C>G	chr5.hg19:g.56161247C>G	ENSP00000382423:p.Asp372Glu	145.0	0.0	.		132.0	29.0	.	NM_005921		Missense_Mutation	SNP	ENST00000399503.3	hg19	CCDS43318.1	.	.	.	.	.	.	.	.	.	.	C	15.18	2.758012	0.49468	.	.	ENSG00000095015	ENST00000399503	T	0.68479	-0.33	5.42	0.882	0.19172	.	0.056041	0.64402	D	0.000002	T	0.72961	0.3526	L	0.52573	1.65	0.44531	D	0.997488	D	0.64830	0.994	D	0.72625	0.978	T	0.72178	-0.4369	10	0.87932	D	0	.	9.7787	0.40634	0.0:0.5535:0.0:0.4465	.	372	Q13233	M3K1_HUMAN	E	372	ENSP00000382423:D372E	ENSP00000382423:D372E	D	+	3	2	MAP3K1	56197004	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	0.513000	0.22770	0.305000	0.22832	0.650000	0.86243	GAC	.	.	.	none		0.318	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066		G	56161247	C	G	56161247	3	3	261	1	0	0	0	0	1	0	0	0	9250	506	18	4	1134	4	MAP3K1	5	56161247	Missense_Mutation	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10		56161247	124754013	26	16248			1	37		2	2	20	N	C_A	6.444273e-05
MAP3K1	4214	hgsc.bcm.edu	37	chr5	56161266	56161266	+	Missense_Mutation	SNP	A	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	acccaatgttatggagaaaaActttaaagaattttgaggta	17	12	8	4	0	0	3	0	1	0	2	0	4	0	3	1	2	1	2	1	2	8	6			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr5:56161266A>C	ENST00000399503.3	+	5	1135	c.1135A>C	c.(1135-1137)Act>Cct	p.T379P		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	379					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)		ATGGAGAAAAACTTTAAAGAA	0.328																																					p.T379P		Atlas-SNP	.											.	MAP3K1	355	.	0			c.A1135C						PASS	.						63	57	59					5																	56161266		1794	4064	5858	SO:0001583	missense	4214	exon5			AGAAAAACTTTAA	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.1135A>C	chr5.hg19:g.56161266A>C	ENSP00000382423:p.Thr379Pro	140.0	0.0	.		117.0	28.0	.	NM_005921		Missense_Mutation	SNP	ENST00000399503.3	hg19	CCDS43318.1	.	.	.	.	.	.	.	.	.	.	A	14.83	2.651480	0.47362	.	.	ENSG00000095015	ENST00000399503	T	0.69175	-0.38	5.42	5.42	0.78866	.	0.189699	0.44688	N	0.000429	T	0.57902	0.2085	L	0.43152	1.355	0.47819	D	0.999526	D	0.54397	0.966	B	0.41860	0.368	T	0.64339	-0.6431	10	0.87932	D	0	.	10.1654	0.42877	0.9252:0.0:0.0748:0.0	.	379	Q13233	M3K1_HUMAN	P	379	ENSP00000382423:T379P	ENSP00000382423:T379P	T	+	1	0	MAP3K1	56197023	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.286000	0.72665	2.176000	0.68965	0.528000	0.53228	ACT	.	.	.	none		0.328	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066		C	56161266	A	C	56161266	3	2	261	1	0	0	0	0	1	0	0	0	9250	43	2	5	1153	5	MAP3K1	5	56161266	Missense_Mutation	SNP	A	TCGA-UZ-A9PO-01A-11D-A382-10	19	56161266	124753994	27	16249			1	37		2	2	20	N	C_A	6.444273e-05
COL4A3BP	10087	hgsc.bcm.edu	37	chr5	74676981	74676981	+	Frame_Shift_Del	DEL	A	A	-																															tgggcttaccaaggtttgacAaatcatagcaacatttattt																										TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr5:74676981delA	ENST00000405807.4	-	16	2084	c.1663delT	c.(1663-1665)tgtfs	p.C555fs	COL4A3BP_ENST00000508692.1_5'UTR|COL4A3BP_ENST00000380494.5_Frame_Shift_Del_p.C683fs|COL4A3BP_ENST00000261415.7_Frame_Shift_Del_p.C529fs	NM_005713.2	NP_005704.1	Q9Y5P4	C43BP_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen) binding protein	555	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|ceramide metabolic process (GO:0006672)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi ceramide transport (GO:0035621)|heart morphogenesis (GO:0003007)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lipid homeostasis (GO:0055088)|mitochondrion morphogenesis (GO:0070584)|muscle contraction (GO:0006936)|protein phosphorylation (GO:0006468)|response to endoplasmic reticulum stress (GO:0034976)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ceramide binding (GO:0097001)|ceramide transporter activity (GO:0035620)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein kinase activity (GO:0004672)			breast(1)|kidney(1)|large_intestine(5)|lung(4)|skin(3)|stomach(1)|urinary_tract(1)	16		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;1e-53)		AAGGTTTGACAAATCATAGCA	0.378																																					p.C683fs		Atlas-Indel,Pindel	.											.	COL4A3BP	72	.	0			c.2048delG						PASS	.						204	184	191					5																	74676981		2203	4300	6503	SO:0001589	frameshift_variant	10087	exon17			.	AF136450	CCDS4028.1, CCDS4029.1, CCDS47235.1	5q13.3	2013-01-10	2007-06-08	2007-06-08	ENSG00000113163	ENSG00000113163		"StAR-related lipid transfer (START) domain containing", "Pleckstrin homology (PH) domain containing"	2205	protein-coding gene	gene with protein product	"ceramide transporter", "StAR-related lipid transfer (START) domain containing 11"	604677				10212244	Standard	NM_001130105		Approved	GPBP, STARD11, CERT	uc003kdt.3	Q9Y5P4	OTTHUMG00000102068	ENST00000405807.4:c.1663delT	chr5.hg19:g.74676981delA	ENSP00000383996:p.Cys555fs	83.0	0.0	0		73.0	22.0	0.30137	NM_001130105	A8K7S2|B3KUB7|Q53YV1|Q53YV2|Q96Q85|Q96Q88|Q9H2S7|Q9H2S8	Frame_Shift_Del	DEL	ENST00000405807.4	hg19	CCDS4028.1																																																																																			.	.	.	none		0.378	COL4A3BP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219875.2	NM_005713		-	74676981	A	-	74676981	7	5	261	1	0	1	0	1	0	0	0	0	3694	130	5	0	219	0	COL4A3BP	5	74676981	Frame_Shift_Del	DEL	A	TCGA-UZ-A9PO-01A-11D-A382-10	18515715	74676981	106238279	28	16250											
ERAP1	51752	hgsc.bcm.edu	37	chr5	96130824	96130824	+	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	accgcagcatccagtgcataAtctgcttgatttatcttgtc	9	14	7	11	1	2	1	0	1	2	0	4	1	3	1	2	0	3	4	2	0	2	5			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr5:96130824A>T	ENST00000443439.2	-	5	906	c.840T>A	c.(838-840)gaT>gaA	p.D280E	ERAP1_ENST00000296754.3_Missense_Mutation_p.D280E	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	280					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)		CCAGTGCATAATCTGCTTGAT	0.398																																					p.D280E		Atlas-SNP	.											.	ERAP1	59	.	0			c.T840A						PASS	.						74	68	70					5																	96130824		2203	4300	6503	SO:0001583	missense	51752	exon5			TGCATAATCTGCT	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.840T>A	chr5.hg19:g.96130824A>T	ENSP00000406304:p.Asp280Glu	91.0	0.0	.		64.0	18.0	.	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Missense_Mutation	SNP	ENST00000443439.2	hg19	CCDS47250.1	.	.	.	.	.	.	.	.	.	.	A	5.737	0.320456	0.10845	.	.	ENSG00000164307	ENST00000296754;ENST00000443439;ENST00000414384	T;T	0.02421	4.3;4.3	5.91	2.3	0.28687	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.495676	0.24708	N	0.036252	T	0.01592	0.0051	N	0.16098	0.37	0.29821	N	0.830791	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.09377	0.004;0.004;0.004	T	0.43637	-0.9379	10	0.11182	T	0.66	.	5.5807	0.17248	0.5888:0.1402:0.2711:0.0	.	280;280;280	A8K6H1;Q9NZ08;Q9NZ08-2	.;ERAP1_HUMAN;.	E	280	ENSP00000296754:D280E;ENSP00000406304:D280E	ENSP00000296754:D280E	D	-	3	2	ERAP1	96156580	0.005000	0.15991	0.960000	0.40013	0.987000	0.75469	0.017000	0.13399	0.501000	0.28013	0.528000	0.53228	GAT	.	.	.	none		0.398	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442		T	96130824	A	T	96130824	3	4	261	1	0	0	0	0	1	0	0	0	5205	98	4	5	2078	5	ERAP1	5	96130824	Missense_Mutation	SNP	A	TCGA-UZ-A9PO-01A-11D-A382-10	21453843	96130824	84784436	29	16251											
PCDHB8	56128	hgsc.bcm.edu	37	chr5	140559171	140559171	+	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	ccacctgttcgccctcaggtCgctggactacgaggccctgc	5	8	11	17	3	1	0	1	0	0	0	3	2	1	1	4	3	2	2	4	3	1	2			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr5:140559171C>G	ENST00000239444.2	+	1	1801	c.1556C>G	c.(1555-1557)tCg>tGg	p.S519W	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	519	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)			GCCCTCAGGTCGCTGGACTAC	0.687																																					p.S519W		Atlas-SNP	.											.	PCDHB8	199	.	0			c.C1556G						PASS	.						85	138	120					5																	140559171		2202	4298	6500	SO:0001583	missense	56128	exon1			TCAGGTCGCTGGA	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.1556C>G	chr5.hg19:g.140559171C>G	ENSP00000239444:p.Ser519Trp	311.0	0.0	.		381.0	50.0	.	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	hg19	CCDS4250.1	.	.	.	.	.	.	.	.	.	.	C	12.77	2.037758	0.35989	.	.	ENSG00000120322	ENST00000239444	T	0.01918	4.56	4.22	4.22	0.49857	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.21307	0.0513	H	0.96805	3.885	0.42207	D	0.991799	D	0.76494	0.999	D	0.71414	0.973	T	0.45977	-0.9224	9	0.87932	D	0	.	16.2834	0.82708	0.0:1.0:0.0:0.0	.	519	Q9UN66	PCDB8_HUMAN	W	519	ENSP00000239444:S519W	ENSP00000239444:S519W	S	+	2	0	PCDHB8	140539355	0.544000	0.26441	0.160000	0.22671	0.174000	0.22865	5.765000	0.68834	1.915000	0.55452	0.298000	0.19748	TCG	.	.	.	none		0.687	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120		G	140559171	C	G	140559171	3	3	261	1	0	0	0	0	1	0	0	0	11555	893	31	4	1558	4	PCDHB8	5	140559171	Missense_Mutation	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	44428347	140559171	40356089	30	16252											
PCDHGA3	56112	hgsc.bcm.edu	37	chr5	140725344	140725344	+	Missense_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	tggagctggcgcctcgctccGcagagcccggctacctggtg	4	7	15	15	4	0	1	0	0	0	1	2	2	1	2	4	4	3	4	4	4	1	1			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr5:140725344G>A	ENST00000253812.6	+	1	1744	c.1744G>A	c.(1744-1746)Gca>Aca	p.A582T	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	582	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)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCTCGCTCCGCAGAGCCCGG	0.682																																					p.A582T		Atlas-SNP	.											.	PCDHGA3	246	.	0			c.G1744A						PASS	.						77	86	83					5																	140725344		2203	4299	6502	SO:0001583	missense	56112	exon1			CGCTCCGCAGAGC	AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"Cadherins / Protocadherins : Clustered"	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.1744G>A	chr5.hg19:g.140725344G>A	ENSP00000253812:p.Ala582Thr	121.0	0.0	.		112.0	29.0	.	NM_032011	Q9Y5D4	Missense_Mutation	SNP	ENST00000253812.6	hg19	CCDS47290.1	.	.	.	.	.	.	.	.	.	.	.	19.07	3.754999	0.69648	.	.	ENSG00000254245	ENST00000253812	T	0.55413	0.52	5.27	5.27	0.74061	Cadherin (3);Cadherin-like (1);	0.000000	0.33005	U	0.005383	T	0.62612	0.2442	M	0.71036	2.16	0.31719	N	0.638499	P;D	0.60160	0.955;0.987	P;P	0.53224	0.538;0.721	T	0.71955	-0.4436	10	0.66056	D	0.02	.	12.3063	0.54904	0.0:0.0:0.7209:0.2791	.	582;582	Q9Y5H0-2;Q9Y5H0	.;PCDG3_HUMAN	T	582	ENSP00000253812:A582T	ENSP00000253812:A582T	A	+	1	0	PCDHGA3	140705528	0.934000	0.31675	0.999000	0.59377	0.968000	0.65278	1.731000	0.38135	2.636000	0.89361	0.558000	0.71614	GCA	.	.	.	none		0.682	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916		A	140725344	G	A	140725344	3	1	261	1	0	0	0	0	1	0	0	0	11562	1087	38	1	1746	1	PCDHGA3	5	140725344	Missense_Mutation	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	166173	140725344	40189916	31	16253											
PCDHGB5	56102	hgsc.bcm.edu	37	chr5	140777735	140777740	+	Intron	DEL	TGCCAG	TGCCAG	-																															gctgggccgggctgagaggcTgccagtgctctttctcttcc																										TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	TGCCAG	TGCCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr5:140777735_140777740delTGCCAG	ENST00000576222.1	+	1	2546				PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3						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)			GCTGAGAGGCTGCCAGTGCTCTTTCT	0.612											OREG0016860	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.14_15del		Pindel	.											.	.	.	.	0			c.40_45del						PASS	.																																			SO:0001627	intron_variant	56101	exon1			.	AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"Cadherins / Protocadherins : Clustered"	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.2415+25359TGCCAG>-	chr5.hg19:g.140777735_140777740delTGCCAG		323.0	0.0	.	1659	305.0	38.0	0.125	NM_032099	A7E229|Q9Y5C7	In_Frame_Del	DEL	ENST00000576222.1	hg19	CCDS58980.1																																																																																			.	.	.	none		0.612	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		-	140777740	TGCCAG	-	140777735	6	5	261	0	1	1	0	1	0	0	0	0	11573	1580	55	0		0	PCDHGB5	5	140777735	Intron	DEL	TGCCAG	TCGA-UZ-A9PO-01A-11D-A382-10	52391	140777735	40137525	32	16254											
MXD3	83463	hgsc.bcm.edu	37	chr5	176734952	176734952	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgtcgggcccgctgctccTgatcctccagcttctgcgga	3	10	12	16	3	1	1	0	1	1	0	5	2	4	2	4	2	3	4	4	2	0	1			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr5:176734952T>C	ENST00000439742.2	-	5	813	c.335A>G	c.(334-336)cAg>cGg	p.Q112R	MXD3_ENST00000427908.2_Missense_Mutation_p.Q112R|MXD3_ENST00000513063.1_Missense_Mutation_p.Q112R|MXD3_ENST00000423571.2_Missense_Mutation_p.Q112R	NM_031300.3	NP_112590.1	Q9BW11	MAD3_HUMAN	MAX dimerization protein 3	112					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)			CCGCTGCTCCTGATCCTCCAG	0.711																																					p.Q112R		Atlas-SNP	.											.	MXD3	13	.	0			c.A335G						PASS	.						5	5	5					5																	176734952		2039	4057	6096	SO:0001583	missense	83463	exon5			TGCTCCTGATCCT	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.335A>G	chr5.hg19:g.176734952T>C	ENSP00000401867:p.Gln112Arg	77.0	0.0	.		78.0	26.0	.	NM_001142935	B4E0J1|Q53HK1|Q7Z4Y0|Q8NDJ7|Q96ME3	Missense_Mutation	SNP	ENST00000439742.2	hg19	CCDS4416.1	.	.	.	.	.	.	.	.	.	.	T	19.07	3.756279	0.69648	.	.	ENSG00000213347	ENST00000427908;ENST00000423571;ENST00000439742;ENST00000303165;ENST00000513063;ENST00000513169;ENST00000502529	D;D;D;D;T;T	0.88431	-2.38;-2.38;-2.38;-2.38;0.86;0.86	5.0	5.0	0.66597	Helix-loop-helix DNA-binding (3);	0.000000	0.85682	D	0.000000	D	0.92990	0.7769	M	0.68593	2.085	0.58432	D	0.999999	D;D;D;D	0.71674	0.992;0.998;0.997;0.979	D;D;D;P	0.80764	0.979;0.994;0.986;0.867	D	0.91821	0.5467	10	0.30078	T	0.28	-0.4458	15.0117	0.71555	0.0:0.0:0.0:1.0	.	112;103;112;112	Q9BW11-3;F8W9D2;Q9BW11;B4E0J1	.;.;MAD3_HUMAN;.	R	112;112;112;103;112;29;102	ENSP00000416921:Q112R;ENSP00000389716:Q112R;ENSP00000401867:Q112R;ENSP00000421463:Q112R;ENSP00000427104:Q29R;ENSP00000425029:Q102R	ENSP00000307720:Q103R	Q	-	2	0	MXD3	176667558	1.000000	0.71417	1.000000	0.80357	0.755000	0.42902	4.827000	0.62723	2.007000	0.58848	0.459000	0.35465	CAG	.	.	.	none		0.711	MXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253427.1			C	176734952	T	C	176734952	3	2	261	1	0	0	0	0	1	0	0	0	10007	1580	55	3	374	3	MXD3	5	176734952	Missense_Mutation	SNP	T	TCGA-UZ-A9PO-01A-11D-A382-10	35957217	176734952	4180308	33	16255											
BRD2	6046	hgsc.bcm.edu	37	chr6	32942389	32942389	+	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	ttgcaacttacccctgccaaCccaccacccccggaggtgtc	8	7	7	19	1	0	0	0	0	0	0	1	1	0	1	7	2	5	1	7	2	3	2	rs562023725		TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr6:32942389C>A	ENST00000374825.4	+	3	1881	c.180C>A	c.(178-180)aaC>aaA	p.N60K	BRD2_ENST00000374831.4_Missense_Mutation_p.N60K|BRD2_ENST00000449085.2_Missense_Mutation_p.N13K|BRD2_ENST00000395289.2_Missense_Mutation_p.N60K|BRD2_ENST00000443797.2_5'UTR|BRD2_ENST00000395287.1_Missense_Mutation_p.N60K|XXbac-BPG181M17.6_ENST00000580587.1_RNA	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	60					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						CCCCTGCCAACCCACCACCCC	0.537																																					p.N60K		Atlas-SNP	.											.	BRD2	70	.	0			c.C180A						PASS	.						79	76	77					6																	32942389		2203	4300	6503	SO:0001583	missense	6046	exon3			TGCCAACCCACCA	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.180C>A	chr6.hg19:g.32942389C>A	ENSP00000363958:p.Asn60Lys	112.0	0.0	.		132.0	38.0	.	NM_005104	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Missense_Mutation	SNP	ENST00000374825.4	hg19	CCDS4762.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.33|15.33	2.800419|2.800419	0.50315|0.50315	.|.	.|.	ENSG00000204256|ENSG00000204256	ENST00000374825;ENST00000374831;ENST00000395289;ENST00000395287;ENST00000449085|ENST00000456339;ENST00000449025	T;T;T;T;T|.	0.18174|.	2.23;2.23;2.23;2.23;2.23|.	5.36|5.36	0.465|0.465	0.16711|0.16711	Bromodomain (1);|.	0.000000|.	0.51477|.	D|.	0.000084|.	T|T	0.58821|0.58821	0.2149|0.2149	M|M	0.78344|0.78344	2.41|2.41	0.80722|0.80722	D|D	1|1	P;D|.	0.53885|.	0.828;0.963|.	B;B|.	0.44224|.	0.3;0.444|.	T|T	0.60495|0.60495	-0.7252|-0.7252	10|5	0.19590|.	T|.	0.45|.	-24.1895|-24.1895	9.5375|9.5375	0.39231|0.39231	0.0:0.6248:0.0:0.3752|0.0:0.6248:0.0:0.3752	.|.	60;60|.	A2AAU0;P25440|.	.;BRD2_HUMAN|.	K|N	60;60;60;60;13|62;66	ENSP00000363958:N60K;ENSP00000363964:N60K;ENSP00000378704:N60K;ENSP00000378702:N60K;ENSP00000409145:N13K|.	ENSP00000363958:N60K|.	N|T	+|+	3|2	2|0	BRD2|BRD2	33050367|33050367	0.920000|0.920000	0.31207|0.31207	0.999000|0.999000	0.59377|0.59377	0.933000|0.933000	0.57130|0.57130	0.060000|0.060000	0.14342|0.14342	0.108000|0.108000	0.17862|0.17862	0.643000|0.643000	0.83706|0.83706	AAC|ACC	.	.	.	alt		0.537	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2			A	32942389	C	A	32942389	3	1	261	1	0	0	0	0	1	0	0	0	1504	506	18	4	186	4	BRD2	6	32942389	Missense_Mutation	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10		32942389	138172678	34	16256											
AARS2	57505	hgsc.bcm.edu	37	chr6	44279883	44279883	+	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	atgggaaaggtctcgacccaCatcttccaggtcgttatggt	9	11	11	10	2	2	0	0	0	2	0	5	2	3	1	2	4	0	1	2	4	2	2			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr6:44279883C>T	ENST00000244571.4	-	2	363	c.361G>A	c.(361-363)Gtg>Atg	p.V121M	RP11-444E17.6_ENST00000505802.1_Intron	NM_020745.3	NP_065796			alanyl-tRNA synthetase 2, mitochondrial									p.V121M(1)		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)			TCTCGACCCACATCTTCCAGG	0.527																																					p.V121M		Atlas-SNP	.											AARS2,NS,carcinoma,0,1	AARS2	77	.	1	Substitution - Missense(1)	prostate(1)	c.G361A						PASS	.						190	150	163					6																	44279883		2203	4300	6503	SO:0001583	missense	57505	exon2			GACCCACATCTTC	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.361G>A	chr6.hg19:g.44279883C>T	ENSP00000244571:p.Val121Met	102.0	0.0	.		108.0	33.0	.	NM_020745		Missense_Mutation	SNP	ENST00000244571.4	hg19	CCDS34464.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.815634	0.90790	.	.	ENSG00000124608	ENST00000244571	D	0.84944	-1.92	4.9	4.9	0.64082	Alanyl-tRNA synthetase, class IIc, core domain (1);Alanyl-tRNA synthetase, class IIc, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.95554	0.8555	H	0.98407	4.225	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97295	0.9927	10	0.87932	D	0	-19.9207	18.2752	0.90080	0.0:1.0:0.0:0.0	.	121	Q5JTZ9	SYAM_HUMAN	M	121	ENSP00000244571:V121M	ENSP00000244571:V121M	V	-	1	0	AARS2	44387861	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.651000	0.83577	2.540000	0.85666	0.436000	0.28706	GTG	.	.	.	none		0.527	AARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040741.2	NM_020745		T	44279883	C	T	44279883	3	4	261	1	0	0	0	0	1	0	0	0	20	478	17	2	2680	2	AARS2	6	44279883	Missense_Mutation	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	11337494	44279883	126835184	35	16257											
CDK19	23097	hgsc.bcm.edu	37	chr6	110943359	110943359	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggtatggaatctggcagcCggcaaatacactaaaaatca	15	7	11	8	1	2	0	1	0	1	0	2	1	2	1	1	5	2	3	1	5	7	3			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr6:110943359C>T	ENST00000368911.3	-	11	1221	c.1042G>A	c.(1042-1044)Ggc>Agc	p.G348S	CDK19_ENST00000413605.2_Missense_Mutation_p.G224S|CDK19_ENST00000323817.3_Missense_Mutation_p.G288S	NM_015076.3	NP_055891.1	Q9BWU1	CDK19_HUMAN	cyclin-dependent kinase 19	348							ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)	p.G348C(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(2)|prostate(2)|skin(1)	22						ATCTGGCAGCCGGCAAATACA	0.313																																					p.G348S		Atlas-SNP	.											CDK19,NS,carcinoma,0,1	CDK19	51	.	1	Substitution - Missense(1)	lung(1)	c.G1042A						PASS	.						138	144	142					6																	110943359		2203	4300	6503	SO:0001583	missense	23097	exon11			GGCAGCCGGCAAA	AL122055	CCDS5085.1, CCDS75503.1	6q21	2011-10-25	2009-12-16	2009-12-16	ENSG00000155111	ENSG00000155111		"Cyclin-dependent kinases"	19338	protein-coding gene	gene with protein product		614720	"cyclin-dependent kinase (CDC2-like) 11", "cell division cycle 2-like 6 (CDK8-like)"	CDK11, CDC2L6		10470851, 19884882	Standard	XM_005266871		Approved	KIAA1028, bA346C16.3	uc003puh.1	Q9BWU1	OTTHUMG00000015365	ENST00000368911.3:c.1042G>A	chr6.hg19:g.110943359C>T	ENSP00000357907:p.Gly348Ser	93.0	0.0	.		76.0	22.0	.	NM_015076	Q5JQZ7|Q5JR00|Q8TC78|Q9UPX2	Missense_Mutation	SNP	ENST00000368911.3	hg19	CCDS5085.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.068014	0.76301	.	.	ENSG00000155111	ENST00000368911;ENST00000323817;ENST00000392576;ENST00000413605	T;T;T	0.62639	0.11;0.01;0.41	5.56	5.56	0.83823	Protein kinase-like domain (1);	0.090722	0.85682	D	0.000000	T	0.53433	0.1796	M	0.75615	2.305	0.80722	D	1	B;B	0.33073	0.396;0.343	B;B	0.25614	0.042;0.062	T	0.59899	-0.7367	10	0.51188	T	0.08	-18.5719	19.8942	0.96945	0.0:1.0:0.0:0.0	.	224;348	B4DUB1;Q9BWU1	.;CDK19_HUMAN	S	348;288;287;224	ENSP00000357907:G348S;ENSP00000317665:G288S;ENSP00000410604:G224S	ENSP00000317665:G288S	G	-	1	0	CDK19	111050052	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.367000	0.79558	2.778000	0.95560	0.557000	0.71058	GGC	.	.	.	none		0.313	CDK19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041804.1	NM_015076		T	110943359	C	T	110943359	3	4	261	1	0	0	0	0	1	0	0	0	3137	652	23	1	478	1	CDK19	6	110943359	Missense_Mutation	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	66663476	110943359	60171708	36	16258											
UPP1	7378	hgsc.bcm.edu	37	chr7	48146603	48146603	+	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	0	0	0	0	0	0	0	0	0	aagaagctggtgcaggagctGttgctgtgttctgcagagct	8	11	15	7	0	1	2	0	0	1	2	1	3	1	3	0	2	6	8	0	2	2	2	rs567267997		TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr7:48146603G>C	ENST00000331803.4	+	8	1193	c.570G>C	c.(568-570)ctG>ctC	p.L190L	UPP1_ENST00000482015.1_3'UTR|UPP1_ENST00000395564.4_Silent_p.L190L|UPP1_ENST00000429491.2_Silent_p.L53L|UPP1_ENST00000341253.4_Silent_p.L190L			Q16831	UPP1_HUMAN	uridine phosphorylase 1	190					cellular response to glucose starvation (GO:0042149)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide catabolic process (GO:0009166)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)|uridine metabolic process (GO:0046108)	cytosol (GO:0005829)	uridine phosphorylase activity (GO:0004850)			breast(1)|endometrium(2)|large_intestine(1)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	18					Fluorouracil(DB00544)	TGCAGGAGCTGTTGCTGTGTT	0.552													G|||	1	0.000199681	8e-04	0	5008	,	,		21337	0		0	False		,,,				2504	0				p.L190L		Atlas-SNP	.											.	UPP1	35	.	0			c.G570C						PASS	.						128	117	121					7																	48146603		2203	4300	6503	SO:0001819	synonymous_variant	7378	exon7			GGAGCTGTTGCTG	AK096167	CCDS5507.1	7p12.3	2012-10-02	2003-08-28	2003-08-29	ENSG00000183696	ENSG00000183696	2.4.2.3		12576	protein-coding gene	gene with protein product		191730	"uridine phosphorylase"	UP		752472, 11807789	Standard	NM_003364		Approved	UPASE, UPP, UDRPASE	uc003toj.3	Q16831	OTTHUMG00000129253	ENST00000331803.4:c.570G>C	chr7.hg19:g.48146603G>C		50.0	0.0	.		87.0	23.0	.	NM_003364	D3DVM4|Q15362	Silent	SNP	ENST00000331803.4	hg19	CCDS5507.1																																																																																			.	.	.	none		0.552	UPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251360.1	NM_003364		C	48146603	G	C	48146603	2	2	261	1	0	0	0	0	0	0	0	1	17024	1364	48	4		4	UPP1	7	48146603	Silent	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10		48146603	110992060	37	16259											
UPK3B	80761	hgsc.bcm.edu	37	chr7	76140096	76140096	+	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	acgcgtccagccagacccaaGgggctgggggccctgctgga	7	4	16	14	2	0	1	0	0	0	1	1	2	1	2	4	5	2	2	4	5	1	0			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr7:76140096G>T	ENST00000257632.5	+	1	255	c.127G>T	c.(127-129)Ggg>Tgg	p.G43W	UPK3B_ENST00000419923.2_Missense_Mutation_p.G43W|UPK3B_ENST00000334348.3_Intron|UPK3B_ENST00000394849.1_Intron|UPK3B_ENST00000443097.2_Intron|UPK3B_ENST00000448265.3_Missense_Mutation_p.G43W			Q9BT76	UPK3B_HUMAN	uroplakin 3B	43					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)				CCAGACCCAAGGGGCTGGGGG	0.706																																					p.G43W		Atlas-SNP	.											.	UPK3B	15	.	0			c.G127T						PASS	.						13	16	15					7																	76140096		2196	4298	6494	SO:0001583	missense	80761	exon1			ACCCAAGGGGCTG	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.127G>T	chr7.hg19:g.76140096G>T	ENSP00000257632:p.Gly43Trp	152.0	0.0	.		174.0	51.0	.	NM_030570	A6NHH5|A8K231|A8MZA8|B3KPU5|Q75MM5|Q86W06	Missense_Mutation	SNP	ENST00000257632.5	hg19	CCDS5588.1	.	.	.	.	.	.	.	.	.	.	.	19.45	3.829710	0.71258	.	.	ENSG00000243566	ENST00000419923;ENST00000448265;ENST00000257632	T;T;T	0.44482	0.92;0.92;0.92	4.3	0.385	0.16249	.	.	.	.	.	T	0.38931	0.1059	N	0.08118	0	0.09310	N	0.999999	D	0.89917	1.0	D	0.78314	0.991	T	0.27400	-1.0075	9	0.87932	D	0	-1.0315	7.1484	0.25595	0.4081:0.0:0.5919:0.0	.	43	Q9BT76	UPK3B_HUMAN	W	43	ENSP00000441602:G43W;ENSP00000441284:G43W;ENSP00000257632:G43W	ENSP00000257632:G43W	G	+	1	0	UPK3B	75978032	0.005000	0.15991	0.002000	0.10522	0.697000	0.40408	-0.267000	0.08619	0.167000	0.19631	0.407000	0.27541	GGG	.	.	.	none		0.706	UPK3B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313978.2	NM_030570		T	76140096	G	T	76140096	3	4	261	1	0	0	0	0	1	0	0	0	17023	1000	35	4	129	4	UPK3B	7	76140096	Missense_Mutation	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	27993493	76140096	82998567	38	16260											
CSMD1	64478	hgsc.bcm.edu	37	chr8	3046428	3046428	+	Missense_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	cctgaattcccgagccctccGtaactatgatcttccatata	10	12	5	14	2	1	2	0	2	1	0	4	3	4	2	5	0	2	1	5	0	5	6	rs374772217		TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr8:3046428G>A	ENST00000520002.1	-	36	6062	c.5507C>T	c.(5506-5508)aCg>aTg	p.T1836M	CSMD1_ENST00000539096.1_Missense_Mutation_p.T1835M|CSMD1_ENST00000542608.1_Missense_Mutation_p.T1835M|CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000537824.1_Missense_Mutation_p.T1835M|CSMD1_ENST00000602723.1_Missense_Mutation_p.T1836M|CSMD1_ENST00000602557.1_Missense_Mutation_p.T1836M|CSMD1_ENST00000400186.3_Missense_Mutation_p.T1836M			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1836	CUB 11. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CGAGCCCTCCGTAACTATGAT	0.483																																					p.T1835M		Atlas-SNP	.											CSMD1_ENST00000537824,NS,carcinoma,0,2	CSMD1	1469	.	0			c.C5504T						PASS	.						59	56	57					8																	3046428		1884	4103	5987	SO:0001583	missense	64478	exon35			CCCTCCGTAACTA			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.5507C>T	chr8.hg19:g.3046428G>A	ENSP00000430733:p.Thr1836Met	129.0	1.0	.		134.0	9.0	.	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.	.	.	.	.	.	.	.	.	.	G	11.59	1.683295	0.29872	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.60548	0.18;0.18;0.18;0.18;0.18	5.53	5.53	0.82687	CUB (5);	0.136796	0.49305	D	0.000155	T	0.69708	0.3141	L	0.46614	1.455	0.09310	N	0.999999	D;B;D	0.61697	0.99;0.133;0.976	P;B;P	0.61397	0.888;0.425;0.888	T	0.64428	-0.6410	10	0.66056	D	0.02	.	19.4679	0.94950	0.0:0.0:1.0:0.0	.	1836;1836;1836	E5RIG2;Q96PZ7;Q96PZ7-4	.;CSMD1_HUMAN;.	M	1836;1836;1698;1835;1835;1835	ENSP00000383047:T1836M;ENSP00000430733:T1836M;ENSP00000441462:T1835M;ENSP00000446243:T1835M;ENSP00000441675:T1835M	ENSP00000320445:T1698M	T	-	2	0	CSMD1	3033835	1.000000	0.71417	0.006000	0.13384	0.054000	0.15201	5.984000	0.70548	2.582000	0.87167	0.637000	0.83480	ACG	.	.	.	alt		0.483	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	3046428	G	A	3046428	3	1	261	1	0	0	0	0	1	0	0	0	3946	1145	40	1	5334	1	CSMD1	8	3046428	Missense_Mutation	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10		3046428	143317594	39	16261											
BHLHE22	27319	hgsc.bcm.edu	37	chr8	65494023	65494023	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggtagcggcagcggcggcAgcagcagcagcagcagcagc	9	1	18	13	4	0	0	0	0	0	0	0	0	0	0	0	4	9	9	0	4	1	1	rs62519837		TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr8:65494023A>G	ENST00000321870.1	+	1	1210	c.676A>G	c.(676-678)Agc>Ggc	p.S226G	RP11-21C4.1_ENST00000517909.1_RNA	NM_152414.4	NP_689627.1	Q8NFJ8	BHE22_HUMAN	basic helix-loop-helix family, member e22	226	Ser-rich.				anterior commissure morphogenesis (GO:0021960)|cerebral cortex regionalization (GO:0021796)|corpus callosum morphogenesis (GO:0021540)|corticospinal tract morphogenesis (GO:0021957)|negative regulation of transcription, DNA-templated (GO:0045892)|retinal bipolar neuron differentiation (GO:0060040)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.S234delS(1)|p.S226G(1)		NS(1)|central_nervous_system(1)|lung(1)|prostate(1)|skin(1)	5						cagcggcggcagcagcagcag	0.706																																					p.S226G	Colon(113;104 1586 2865 9855 18065)	Atlas-SNP	.											BHLHE22,extremity,malignant_melanoma,0,1	BHLHE22	21	.	2	Substitution - Missense(1)|Deletion - In frame(1)	central_nervous_system(1)|skin(1)	c.A676G						PASS	.						3	4	4					8																	65494023		1652	3428	5080	SO:0001583	missense	27319	exon1			GGCGGCAGCAGCA	U80755	CCDS6179.1	8q12.1	2009-01-12	2009-01-12	2009-01-12		ENSG00000180828		"Basic helix-loop-helix proteins"	11963	protein-coding gene	gene with protein product		613483	"trinucleotide repeat containing 20", "basic helix-loop-helix domain containing, class B, 5"	TNRC20, BHLHB5		9225980, 12213201, 18557763	Standard	NM_152414		Approved	CAGL85, Beta3, bHLHe22	uc003xvi.3	Q8NFJ8		ENST00000321870.1:c.676A>G	chr8.hg19:g.65494023A>G	ENSP00000318799:p.Ser226Gly	24.0	1.0	.		26.0	5.0	.	NM_152414		Missense_Mutation	SNP	ENST00000321870.1	hg19	CCDS6179.1	.	.	.	.	.	.	.	.	.	.	A	0.001	-3.714868	0.00005	.	.	ENSG00000180828	ENST00000321870	T	0.80033	-1.33	0.79	-1.26	0.09376	.	.	.	.	.	T	0.48642	0.1511	N	0.00926	-1.1	0.09310	N	1	B	0.26041	0.14	B	0.32805	0.153	T	0.47368	-0.9123	9	0.15499	T	0.54	.	3.5404	0.07809	0.3747:0.0:0.6253:0.0	rs62519837	226	Q8NFJ8	BHE22_HUMAN	G	226	ENSP00000318799:S226G	ENSP00000318799:S226G	S	+	1	0	BHLHE22	65656577	0.273000	0.24181	0.215000	0.23724	0.107000	0.19398	-0.535000	0.06142	-0.333000	0.08476	0.136000	0.15936	AGC	.	G|1.000;|0.000	1.000	weak		0.706	BHLHE22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378549.1	NM_152414		G	65494023	A	G	65494023	3	3	261	1	0	0	0	0	1	0	0	0	1421	188	7	3	678	3	BHLHE22	8	65494023	Missense_Mutation	SNP	A	TCGA-UZ-A9PO-01A-11D-A382-10	62447595	65494023	80869999	40	16262											
RECK	8434	hgsc.bcm.edu	37	chr9	36058855	36058855	+	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	aaaaagtgaatcccgactaaAacatctgttgcagcgagccc	15	7	8	11	2	1	1	0	1	1	0	2	3	2	1	2	0	4	2	2	0	5	2			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr9:36058855A>T	ENST00000377966.3	+	3	757	c.191A>T	c.(190-192)aAa>aTa	p.K64I	RECK_ENST00000479053.1_3'UTR	NM_021111.2	NP_066934.1	O95980	RECK_HUMAN	reversion-inducing-cysteine-rich protein with kazal motifs	64	5 X Knot repeats.				blood vessel maturation (GO:0001955)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)			TCCCGACTAAAACATCTGTTG	0.328																																					p.K64I		Atlas-SNP	.											.	RECK	73	.	0			c.A191T						PASS	.						73	76	75					9																	36058855		2203	4300	6503	SO:0001583	missense	8434	exon3			GACTAAAACATCT	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.191A>T	chr9.hg19:g.36058855A>T	ENSP00000367202:p.Lys64Ile	69.0	0.0	.		51.0	15.0	.	NM_021111	B2RNS1|Q5W0K6|Q8WX37	Missense_Mutation	SNP	ENST00000377966.3	hg19	CCDS6597.1	.	.	.	.	.	.	.	.	.	.	A	15.70	2.911043	0.52439	.	.	ENSG00000122707	ENST00000377966	T	0.47528	0.84	5.75	4.41	0.53225	.	0.053124	0.64402	D	0.000001	T	0.40040	0.1101	N	0.14661	0.345	0.38896	D	0.957211	P;P;P	0.52316	0.952;0.61;0.911	P;B;P	0.52267	0.694;0.265;0.653	T	0.45041	-0.9288	10	0.66056	D	0.02	-20.6618	10.0337	0.42116	0.9083:0.0:0.0917:0.0	.	64;64;64	B2RCE6;O95980;Q6P9E2	.;RECK_HUMAN;.	I	64	ENSP00000367202:K64I	ENSP00000367202:K64I	K	+	2	0	RECK	36048855	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.883000	0.56168	2.196000	0.70406	0.402000	0.26972	AAA	.	.	.	none		0.328	RECK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052409.1			T	36058855	A	T	36058855	3	4	261	1	0	0	0	0	1	0	0	0	13213	14	1	5	201	5	RECK	9	36058855	Missense_Mutation	SNP	A	TCGA-UZ-A9PO-01A-11D-A382-10		36058855	105154576	41	16263											
DOLK	22845	hgsc.bcm.edu	37	chr9	131709023	131709023	+	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	cctcaccaggggtgaagcagCggggcagcaggtacagcagg	10	3	17	11	1	1	1	1	1	0	0	1	1	1	1	2	6	5	5	2	6	2	1	rs377658203		TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr9:131709023C>T	ENST00000372586.3	-	1	875	c.560G>A	c.(559-561)cGc>cAc	p.R187H	RP11-101E3.5_ENST00000482796.1_Intron|NUP188_ENST00000372577.2_5'Flank	NM_014908.3	NP_055723.1	Q9UPQ8	DOLK_HUMAN	dolichol kinase	187					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)	p.R187H(1)		breast(1)|large_intestine(5)|lung(3)|ovary(1)|urinary_tract(1)	11						GGTGAAGCAGCGGGGCAGCAG	0.542																																					p.R187H		Atlas-SNP	.											DOLK,caecum,carcinoma,0,1	DOLK	39	.	1	Substitution - Missense(1)	large_intestine(1)	c.G560A						PASS	.						83	81	82					9																	131709023		2203	4300	6503	SO:0001583	missense	22845	exon1			AAGCAGCGGGGCA	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.560G>A	chr9.hg19:g.131709023C>T	ENSP00000361667:p.Arg187His	51.0	0.0	.		40.0	9.0	.	NM_014908	Q5SRE6	Missense_Mutation	SNP	ENST00000372586.3	hg19	CCDS6915.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.375916	0.82682	.	.	ENSG00000175283	ENST00000372586;ENST00000515348	D	0.90620	-2.7	5.07	5.07	0.68467	.	0.000000	0.64402	D	0.000005	D	0.94430	0.8208	M	0.66939	2.045	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	D	0.93720	0.7032	10	0.38643	T	0.18	-0.0738	17.4448	0.87575	0.0:1.0:0.0:0.0	.	187	Q9UPQ8	DOLK_HUMAN	H	187	ENSP00000361667:R187H	ENSP00000361667:R187H	R	-	2	0	DOLK	130748844	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.487000	0.81328	2.327000	0.79052	0.462000	0.41574	CGC	.	.	.	alt		0.542	DOLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054515.1	NM_014908		T	131709023	C	T	131709023	3	4	261	1	0	0	0	0	1	0	0	0	4705	768	27	1	1060	1	DOLK	9	131709023	Missense_Mutation	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	95650168	131709023	9504408	42	16264											
GTF3C4	9329	hgsc.bcm.edu	37	chr9	135546223	135546223	+	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	ccgaggaccaccgcgtgtctGtgtccacggcccgcagcatc	6	6	12	17	5	1	0	0	0	1	0	3	2	2	1	5	2	1	2	5	2	0	0			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr9:135546223G>C	ENST00000372146.4	+	1	802	c.238G>C	c.(238-240)Gtg>Ctg	p.V80L	DDX31_ENST00000372153.1_5'Flank|DDX31_ENST00000544003.1_5'Flank|DDX31_ENST00000480876.1_5'Flank|DDX31_ENST00000372159.3_5'Flank|DDX31_ENST00000310532.2_5'Flank|GTF3C4_ENST00000483873.2_Missense_Mutation_p.V80L	NM_012204.2	NP_036336.2	Q9UKN8	TF3C4_HUMAN	general transcription factor IIIC, polypeptide 4, 90kDa	80					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)		CCGCGTGTCTGTGTCCACGGC	0.677																																					p.V80L	Pancreas(142;417 1875 11086 31973 47667)	Atlas-SNP	.											.	GTF3C4	53	.	0			c.G238C						PASS	.						23	26	25					9																	135546223		2200	4297	6497	SO:0001583	missense	9329	exon1			GTGTCTGTGTCCA	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.238G>C	chr9.hg19:g.135546223G>C	ENSP00000361219:p.Val80Leu	62.0	0.0	.		74.0	18.0	.	NM_012204	Q5VZJ7	Missense_Mutation	SNP	ENST00000372146.4	hg19	CCDS6953.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.963035	0.74016	.	.	ENSG00000125484	ENST00000372146	T	0.59906	0.23	3.64	3.64	0.41730	Transcription factor IIIC, 90kDa subunit, N-terminal (1);	0.081587	0.48286	D	0.000197	T	0.49098	0.1537	N	0.14661	0.345	0.39940	D	0.974402	P	0.47034	0.889	P	0.48704	0.587	T	0.60944	-0.7162	10	0.72032	D	0.01	-8.035	14.8255	0.70107	0.0:0.0:1.0:0.0	.	80	Q9UKN8	TF3C4_HUMAN	L	80	ENSP00000361219:V80L	ENSP00000361219:V80L	V	+	1	0	GTF3C4	134536044	1.000000	0.71417	0.931000	0.37212	0.159000	0.22180	7.975000	0.88055	2.011000	0.59026	0.455000	0.32223	GTG	.	.	.	none		0.677	GTF3C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054792.1			C	135546223	G	C	135546223	3	2	261	1	0	0	0	0	1	0	0	0	6882	1377	48	4	240	4	GTF3C4	9	135546223	Missense_Mutation	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	3837200	135546223	5667208	43	16265											
ANXA7	310	hgsc.bcm.edu	37	chr10	75147485	75147485	+	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	aaatgctgctttaattttttGcctctgatcattggaacggt	9	17	8	7	1	2	1	1	1	1	0	2	2	2	2	1	2	4	2	1	2	3	6			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr10:75147485G>T	ENST00000372921.5	-	7	651	c.595C>A	c.(595-597)Caa>Aaa	p.Q199K	ANXA7_ENST00000492380.1_5'UTR|ANXA7_ENST00000535178.1_Missense_Mutation_p.Q69K	NM_001156.3	NP_001147.1	P20073	ANXA7_HUMAN	annexin A7	221					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)					TTAATTTTTTGCCTCTGATCA	0.448																																					p.Q221K		Atlas-SNP	.											.	ANXA7	50	.	0			c.C661A						PASS	.						230	217	221					10																	75147485		2203	4300	6503	SO:0001583	missense	310	exon8			TTTTTTGCCTCTG	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.595C>A	chr10.hg19:g.75147485G>T	ENSP00000362012:p.Gln199Lys	87.0	0.0	.		89.0	26.0	.	NM_004034	Q5F2H3|Q5T0M6|Q5T0M7	Missense_Mutation	SNP	ENST00000372921.5	hg19	CCDS7325.1	.	.	.	.	.	.	.	.	.	.	G	32	5.149064	0.94645	.	.	ENSG00000138279	ENST00000372921;ENST00000372919;ENST00000535178	T;T;T	0.03580	3.88;3.88;3.88	5.96	5.96	0.96718	Annexin repeat, conserved site (1);	0.000000	0.64402	D	0.000001	T	0.11750	0.0286	L	0.44542	1.39	0.58432	D	0.999999	D;D;D;D;D	0.64830	0.966;0.994;0.977;0.977;0.981	P;P;P;P;P	0.59357	0.66;0.856;0.696;0.529;0.76	T	0.00142	-1.1997	10	0.66056	D	0.02	.	17.913	0.88940	0.0:0.0:1.0:0.0	.	199;199;126;199;221	Q53HM8;B2R7L2;B4DWU2;P20073-2;P20073	.;.;.;.;ANXA7_HUMAN	K	199;221;69	ENSP00000362012:Q199K;ENSP00000362010:Q221K;ENSP00000442864:Q69K	ENSP00000362010:Q221K	Q	-	1	0	ANXA7	74817491	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.569000	0.82380	2.831000	0.97527	0.650000	0.86243	CAA	.	.	.	none		0.448	ANXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048646.2	NM_001156		T	75147485	G	T	75147485	3	4	261	1	0	0	0	0	1	0	0	0	723	1328	46	4	833	4	ANXA7	10	75147485	Missense_Mutation	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10		75147485	60387262	44	16266											
HSPA12A	259217	hgsc.bcm.edu	37	chr10	118434763	118434763	+	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	gcggggtccaggccaaagagGacggcacccttgaggatggt	9	5	17	10	2	0	2	0	1	0	1	1	4	1	4	3	7	0	1	3	7	1	1			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr10:118434763G>A	ENST00000369209.3	-	12	1661	c.1557C>T	c.(1555-1557)gtC>gtT	p.V519V	RP11-498B4.5_ENST00000433600.1_RNA	NM_025015.2	NP_079291.2	O43301	HS12A_HUMAN	heat shock 70kDa protein 12A	519						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)		GGCCAAAGAGGACGGCACCCT	0.682																																					p.V519V		Atlas-SNP	.											.	HSPA12A	81	.	0			c.C1557T						PASS	.						38	44	42					10																	118434763		2045	4187	6232	SO:0001819	synonymous_variant	259217	exon12			AAAGAGGACGGCA	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.1557C>T	chr10.hg19:g.118434763G>A		131.0	0.0	.		155.0	48.0	.	NM_025015		Silent	SNP	ENST00000369209.3	hg19	CCDS41569.1																																																																																			.	.	.	none		0.682	HSPA12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050530.1	NM_025015		A	118434763	G	A	118434763	2	1	261	1	0	0	0	0	0	0	0	1	7411	1161	41	2		2	HSPA12A	10	118434763	Silent	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	43287278	118434763	17099984	45	16267											
TRPM5	10078	hgsc.bcm.edu	37	chr11	2427988	2427988	+	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	ctggactgtctcccaggtgaCgaccttctggtccagggggt	5	10	14	12	1	2	1	0	1	2	0	4	3	3	2	3	5	0	0	3	5	0	1			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr11:2427988C>T	ENST00000333256.6	+	0	1686				TRPM5_ENST00000452833.1_Missense_Mutation_p.V1054I|TRPM5_ENST00000528453.1_Missense_Mutation_p.V1052I|AC124057.5_ENST00000433035.1_RNA|TRPM5_ENST00000155858.6_Missense_Mutation_p.V1052I|TRPM5_ENST00000533060.1_Missense_Mutation_p.V1052I			Q9Y5U2	TSSC4_HUMAN	tumor suppressing subtransferable candidate 4											endometrium(3)|large_intestine(1)|lung(4)	8		all_epithelial(84;0.000161)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.0137)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.00145)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCCCAGGTGACGACCTTCTGG	0.622																																					p.V1052I		Atlas-SNP	.											.	TRPM5	86	.	0			c.G3154A						PASS	.						79	77	77					11																	2427988		2202	4299	6501	SO:0001628	intergenic_variant	29850	exon21			AGGTGACGACCTT	AF125568	CCDS7735.1, CCDS73241.1	11p15.5	2008-02-05			ENSG00000184281	ENSG00000184281			12386	protein-coding gene	gene with protein product		603852				10072438	Standard	XM_005252722		Approved		uc001lwl.3	Q9Y5U2	OTTHUMG00000009895		chr11.hg19:g.2427988C>T		67.0	0.0	.		80.0	9.0	.	NM_014555	C9JS66|Q86VL2|Q9BRS6	Missense_Mutation	SNP	ENST00000333256.6	hg19	CCDS7735.1	.	.	.	.	.	.	.	.	.	.	c	0.390	-0.923796	0.02377	.	.	ENSG00000070985	ENST00000533881;ENST00000155858;ENST00000452833;ENST00000533060;ENST00000528453	T;T;T;T;T	0.60797	0.33;0.27;0.27;0.16;0.27	3.96	0.932	0.19466	.	0.266195	0.35124	N	0.003423	T	0.30070	0.0753	N	0.12182	0.205	0.09310	N	0.999991	B;B;B	0.12013	0.005;0.005;0.005	B;B;B	0.12837	0.006;0.006;0.008	T	0.07731	-1.0757	10	0.25106	T	0.35	-23.707	3.527	0.07762	0.0:0.4529:0.196:0.3511	.	1052;1054;1052	E9PRW0;Q9NZQ8-2;Q9NZQ8	.;.;TRPM5_HUMAN	I	1046;1052;1054;1052;1052	ENSP00000434383:V1046I;ENSP00000155858:V1052I;ENSP00000387965:V1054I;ENSP00000434121:V1052I;ENSP00000436809:V1052I	ENSP00000155858:V1052I	V	-	1	0	TRPM5	2384564	0.134000	0.22483	0.788000	0.31933	0.012000	0.07955	0.380000	0.20602	0.271000	0.22005	-0.215000	0.12644	GTC	.	.	.	none		0.622	TSSC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027369.3	NM_005706		T	2427988	C	T	2427988	1	4	261	0	1	0	0	0	0	0	0	0	16601	536	19	1		1	TRPM5	11	2427988	IGR	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10		2427988	132578528	46	16268											
SMPD1	6609	hgsc.bcm.edu	37	chr11	6411941	6411941	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggatgggcctggtgctggCgctggcgctggcgctggcgc	1	9	20	11	4	0	0	0	0	0	0	0	1	0	1	1	7	1	4	1	7	0	1	rs550365194|rs550067660|rs71467507|rs78250081|rs558809956|rs3838786	byFrequency	TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr11:6411941C>T	ENST00000342245.4	+	1	281	c.113C>T	c.(112-114)gCg>gTg	p.A38V	SMPD1_ENST00000527275.1_Missense_Mutation_p.A38V|SMPD1_ENST00000533196.1_3'UTR|SMPD1_ENST00000299397.3_Missense_Mutation_p.A38V|SMPD1_ENST00000356761.2_Missense_Mutation_p.A38V	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	38					cell death (GO:0008219)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of MAP kinase activity (GO:0043407)|nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein dephosphorylation (GO:0035307)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)|sphingomyelin metabolic process (GO:0006684)|termination of signal transduction (GO:0023021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lamellar body (GO:0042599)|lysosomal lumen (GO:0043202)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(3)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Amlodipine(DB00381)|Chlorpromazine(DB00477)|Desipramine(DB01151)	ctggtgctggcgctggcgctg	0.711																																					p.A38V		Atlas-SNP	.											.	SMPD1	108	.	0			c.C113T						PASS	.						11	14	13					11																	6411941		2185	4258	6443	SO:0001583	missense	6609	exon1			TGCTGGCGCTGGC	AB209775	CCDS31409.1, CCDS44531.1, CCDS31409.2	11p15.4-p15.1	2010-04-28	2008-02-04		ENSG00000166311	ENSG00000166311	3.1.4.12		11120	protein-coding gene	gene with protein product	"acid sphingomyelinase"	607608				1711683	Standard	NM_000543		Approved	ASM	uc001mcw.3	P17405	OTTHUMG00000165453	ENST00000342245.4:c.113C>T	chr11.hg19:g.6411941C>T	ENSP00000340409:p.Ala38Val	69.0	0.0	.		101.0	9.0	.	NM_000543	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Missense_Mutation	SNP	ENST00000342245.4	hg19	CCDS44531.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.234305	0.39498	.	.	ENSG00000166311	ENST00000299397;ENST00000356761;ENST00000342245;ENST00000527275	T;T;T;T	0.09723	2.95;2.95;2.95;2.95	4.54	-1.08	0.09936	.	.	.	.	.	T	0.04363	0.0120	N	0.08118	0	0.09310	N	1	B;B	0.15473	0.002;0.013	B;B	0.10450	0.002;0.005	T	0.47275	-0.9130	9	0.12103	T	0.63	.	6.8659	0.24093	0.0:0.5614:0.262:0.1766	.	38;38	E9PKS3;G3XAB5	.;.	V	38	ENSP00000299397:A38V;ENSP00000349203:A38V;ENSP00000340409:A38V;ENSP00000435350:A38V	ENSP00000299397:A38V	A	+	2	0	SMPD1	6368517	0.000000	0.05858	0.130000	0.21974	0.033000	0.12548	-2.110000	0.01334	-0.479000	0.06813	-1.305000	0.01319	GCG	.	.	.	weak		0.711	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543		T	6411941	C	T	6411941	3	4	261	1	0	0	0	0	1	0	0	0	14817	768	27	1	115	1	SMPD1	11	6411941	Missense_Mutation	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	3983953	6411941	128594575	47	16269											
KIAA1826	84437	hgsc.bcm.edu	37	chr11	105880566	105880567	+	Frame_Shift_Ins	INS	-	-	TG																															ctgaagccgctcatgttccaINStgtctaaatgccgcagcctc																										TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr11:105880566_105880567insTG	ENST00000301919.4	-	3	2148_2149	c.733_734insCA	c.(733-735)atgfs	p.M245fs	MSANTD4_ENST00000529805.1_5'Flank	NM_032424.1	NP_115800.1	Q8NCY6	MSD4_HUMAN	Myb/SANT-like DNA-binding domain containing 4 with coiled-coils	245						nucleus (GO:0005634)											CTCATGTTCCATGTCTAAATGC	0.465																																					p.M245fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.734_735insCA						PASS	.																																			SO:0001589	frameshift_variant	84437	exon3			.	AB058729	CCDS31663.1	11q22	2012-03-13	2012-03-13	2012-03-13	ENSG00000170903	ENSG00000170903			29383	protein-coding gene	gene with protein product			"KIAA1826"	KIAA1826			Standard	XM_005271697		Approved		uc001piz.3	Q8NCY6	OTTHUMG00000166240	ENST00000301919.4:c.732_733dupCA	chr11.hg19:g.105880567_105880568dupTG	ENSP00000304713:p.Met245fs	84.0	0.0	0		87.0	25.0	0.287356	NM_032424	Q96JK1|Q96JZ3|Q9H2N4	Frame_Shift_Ins	INS	ENST00000301919.4	hg19	CCDS31663.1																																																																																			.	.	.	none		0.465	MSANTD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388619.1	NM_032424		TG	105880567	-	TG	105880566	7	5	261	1	0	1	1	0	0	0	0	0	8267	217	8	0	307	0	KIAA1826	11	105880566	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PO-01A-11D-A382-10	99468625	105880566	29125950	48	16270											
KIF5A	3798	hgsc.bcm.edu	37	chr12	57968953	57968953	+	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	aaatcagaagtcaagtctgtGgtcaagcggtgccggcagct	11	8	13	9	2	4	1	3	0	1	1	4	1	4	1	1	3	3	2	1	3	4	0			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr12:57968953G>T	ENST00000455537.2	+	16	2077	c.1803G>T	c.(1801-1803)gtG>gtT	p.V601V	KIF5A_ENST00000286452.5_Silent_p.V512V	NM_004984.2	NP_004975.2	Q12840	KIF5A_HUMAN	kinesin family member 5A	601					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein localization (GO:0008104)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(32)|ovary(2)|prostate(2)|skin(2)	62						TCAAGTCTGTGGTCAAGCGGT	0.557																																					p.V601V		Atlas-SNP	.											.	KIF5A	143	.	0			c.G1803T						PASS	.						62	52	55					12																	57968953		2203	4300	6503	SO:0001819	synonymous_variant	3798	exon16			GTCTGTGGTCAAG	U06698	CCDS8945.1	12q13.13	2011-07-15	2004-02-13			ENSG00000155980		"Kinesins"	6323	protein-coding gene	gene with protein product		602821	"spastic paraplegia 10 (autosomal dominant)"	SPG10		9858832, 10441583, 16489470	Standard	NM_004984		Approved	D12S1889, NKHC, MY050	uc001sor.1	Q12840	OTTHUMG00000170143	ENST00000455537.2:c.1803G>T	chr12.hg19:g.57968953G>T		101.0	0.0	.		153.0	36.0	.	NM_004984	A6H8M5|Q4LE26	Silent	SNP	ENST00000455537.2	hg19	CCDS8945.1																																																																																			.	.	.	none		0.557	KIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407634.1	NM_004984		T	57968953	G	T	57968953	2	4	261	1	0	0	0	0	0	0	0	1	8312	1335	47	4		4	KIF5A	12	57968953	Silent	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10		57968953	75882942	49	16271											
DDX54	79039	hgsc.bcm.edu	37	chr12	113602055	113602055	+	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	gcgcgcatcacctggctgcaCaggtctcggctggaggcgtt	5	8	15	13	4	2	0	1	0	1	0	3	1	2	1	1	5	1	5	1	5	0	1			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr12:113602055C>G	ENST00000306014.5	-	15	1782	c.1755G>C	c.(1753-1755)ctG>ctC	p.L585L	DDX54_ENST00000549271.1_5'Flank|DDX54_ENST00000314045.7_Silent_p.L585L	NM_024072.3	NP_076977.3	Q8TDD1	DDX54_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	585					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						CCTGGCTGCACAGGTCTCGGC	0.642																																					p.L585L		Atlas-SNP	.											.	DDX54	73	.	0			c.G1755C						PASS	.						39	35	37					12																	113602055		2203	4299	6502	SO:0001819	synonymous_variant	79039	exon15			GCTGCACAGGTCT	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.1755G>C	chr12.hg19:g.113602055C>G		47.0	0.0	.		54.0	21.0	.	NM_024072	Q86YT8|Q9BRZ1	Silent	SNP	ENST00000306014.5	hg19	CCDS31907.1																																																																																			.	.	.	none		0.642	DDX54-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405435.1	NM_024072		G	113602055	C	G	113602055	2	3	261	1	0	0	0	0	0	0	0	1	4374	465	17	4		4	DDX54	12	113602055	Silent	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	55633102	113602055	20249840	50	16272											
CCDC64	92558	hgsc.bcm.edu	37	chr12	120530940	120530940	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcgctgaaggcaaacgacTcttctcattcttcaggaaaa	13	10	7	11	2	4	1	2	1	3	0	6	3	4	2	0	2	1	2	0	2	4	3			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr12:120530940T>C	ENST00000397558.2	+	9	1697	c.1697T>C	c.(1696-1698)cTc>cCc	p.L566P	CCDC64_ENST00000257583.4_Missense_Mutation_p.L263P|CCDC64_ENST00000546857.1_3'UTR|CCDC64_ENST00000446727.2_Missense_Mutation_p.L237P	NM_207311.2	NP_997194.2	Q6ZP65	BICR1_HUMAN	coiled-coil domain containing 64	566					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)					GGCAAACGACTCTTCTCATTC	0.612																																					p.L566P		Atlas-SNP	.											.	CCDC64	40	.	0			c.T1697C						PASS	.						27	32	30					12																	120530940		2008	4157	6165	SO:0001583	missense	92558	exon9			AACGACTCTTCTC	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.1697T>C	chr12.hg19:g.120530940T>C	ENSP00000380690:p.Leu566Pro	94.0	0.0	.		106.0	19.0	.	NM_207311	A8MUC8|B4DWL0|B5MDJ0|O95000	Missense_Mutation	SNP	ENST00000397558.2	hg19	CCDS41845.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.199926	0.79015	.	.	ENSG00000135127	ENST00000397558;ENST00000446727;ENST00000548673;ENST00000257583	T;T	0.62364	0.61;0.03	4.9	4.9	0.64082	.	1.075700	0.07390	U	0.888905	T	0.76371	0.3978	L	0.50333	1.59	0.80722	D	1	D;D;D	0.71674	0.993;0.998;0.998	P;D;D	0.69142	0.858;0.962;0.914	T	0.67887	-0.5554	10	0.72032	D	0.01	-0.4316	14.6842	0.69037	0.0:0.0:0.0:1.0	.	263;237;566	B4DWL0;B4DNE7;Q6ZP65	.;.;BICR1_HUMAN	P	566;237;284;263	ENSP00000380690:L566P;ENSP00000399658:L237P	ENSP00000257583:L263P	L	+	2	0	CCDC64	119015323	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.852000	0.69488	2.054000	0.61138	0.459000	0.35465	CTC	.	.	.	none		0.612	CCDC64-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403390.2	NM_207311		C	120530940	T	C	120530940	3	2	261	1	0	0	0	0	1	0	0	0	2837	1551	54	3	1731	3	CCDC64	12	120530940	Missense_Mutation	SNP	T	TCGA-UZ-A9PO-01A-11D-A382-10	6928885	120530940	13320955	51	16273											
EP400	57634	hgsc.bcm.edu	37	chr12	132547068	132547068	+	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	tgcacatttccagcttctcaGgcagcagcagcagcagcagc	10	7	10	14	0	1	0	1	0	1	0	3	0	2	0	1	1	8	8	1	1	0	2	rs68030464|rs367737531|rs60930033		TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr12:132547068G>A	ENST00000333577.4	+	48	8373	c.8264G>A	c.(8263-8265)aGg>aAg	p.R2755K	EP400_ENST00000389562.2_Missense_Mutation_p.R2718K|EP400_ENST00000332482.4_Missense_Mutation_p.R2682K|EP400_ENST00000330386.6_Missense_Mutation_p.R2638K|EP400_ENST00000389561.2_Missense_Mutation_p.R2719K			Q96L91	EP400_HUMAN	E1A binding protein p400	2755	Interaction with ZNF42. {ECO:0000250}.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.R2718K(2)		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)		CAGCTTCTCAGgcagcagcag	0.567																																					p.R2719K		Atlas-SNP	.											EP400,NS,carcinoma,0,2	EP400	370	.	2	Substitution - Missense(2)	lung(2)	c.G8156A						PASS	.						48	48	48					12																	132547068		2203	4300	6503	SO:0001583	missense	57634	exon47			TTCTCAGGCAGCA	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.8264G>A	chr12.hg19:g.132547068G>A	ENSP00000333602:p.Arg2755Lys	77.0	0.0	.		100.0	4.0	.	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	hg19		.	.	.	.	.	.	.	.	.	.	G	15.46	2.840128	0.51057	.	.	ENSG00000183495	ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000541296	D;D;D;D;D	0.90133	-2.62;-2.62;-2.62;-2.62;-2.62	4.89	4.89	0.63831	.	0.266539	0.31542	N	0.007465	D	0.91264	0.7246	L	0.27053	0.805	0.26223	N	0.97913	D;D;D	0.53312	0.959;0.959;0.959	D;D;D	0.65684	0.937;0.937;0.937	D	0.84986	0.0891	10	0.29301	T	0.29	.	17.0403	0.86487	0.0:0.0:1.0:0.0	.	2719;2638;2718	Q96L91-2;Q96L91-4;Q96L91-5	.;.;.	K	2755;2719;2718;2682;2638;2719	ENSP00000333602:R2755K;ENSP00000374212:R2719K;ENSP00000374213:R2718K;ENSP00000331737:R2682K;ENSP00000330620:R2638K	ENSP00000330620:R2638K	R	+	2	0	EP400	131113021	1.000000	0.71417	0.878000	0.34440	0.286000	0.27126	5.957000	0.70323	2.236000	0.73375	0.561000	0.74099	AGG	.	.	.	none		0.567	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		A	132547068	G	A	132547068	3	1	261	1	0	0	0	0	1	0	0	0	5151	1000	35	2	8335	2	EP400	12	132547068	Missense_Mutation	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	12016128	132547068	1304827	52	16274											
FRY	10129	hgsc.bcm.edu	37	chr13	32813948	32813948	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggactgtgccacgtgggtcaAtgtggtctgtcgataccttc	6	12	13	10	2	2	0	1	0	1	0	4	2	2	1	2	3	2	0	2	3	2	2			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr13:32813948A>G	ENST00000380250.3	+	46	7113	c.6617A>G	c.(6616-6618)aAt>aGt	p.N2206S		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	2206						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)		ACGTGGGTCAATGTGGTCTGT	0.408																																					p.N2206S		Atlas-SNP	.											.	FRY	312	.	0			c.A6617G						PASS	.						93	93	93					13																	32813948		1959	4159	6118	SO:0001583	missense	10129	exon46			GGGTCAATGTGGT	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.6617A>G	chr13.hg19:g.32813948A>G	ENSP00000369600:p.Asn2206Ser	128.0	0.0	.		96.0	24.0	.	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	hg19	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	A	12.39	1.922762	0.33908	.	.	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.20738	2.05	6.07	0.907	0.19321	.	0.127673	0.64402	N	0.000001	T	0.12347	0.0300	L	0.28556	0.865	0.80722	D	1	B	0.23128	0.08	B	0.26864	0.074	T	0.18840	-1.0324	10	0.07482	T	0.82	.	9.8227	0.40891	0.7452:0.0:0.2548:0.0	.	2206	Q5TBA9	FRY_HUMAN	S	2206;1043	ENSP00000369600:N2206S	ENSP00000369600:N2206S	N	+	2	0	FRY	31711948	0.945000	0.32115	0.180000	0.23079	0.989000	0.77384	1.981000	0.40628	-0.046000	0.13446	0.533000	0.62120	AAT	.	.	.	none		0.408	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		G	32813948	A	G	32813948	3	3	261	1	0	0	0	0	1	0	0	0	6070	101	4	3	6799	3	FRY	13	32813948	Missense_Mutation	SNP	A	TCGA-UZ-A9PO-01A-11D-A382-10		32813948	82355930	53	16275											
UGGT2	55757	hgsc.bcm.edu	37	chr13	96508522	96508522	+	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	tctttcagtctgttgacgaaGccaacggggccacctatatt	9	12	9	11	2	3	1	1	1	2	0	3	2	3	1	3	2	2	1	3	2	4	5			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr13:96508522G>T	ENST00000376747.3	-	34	3968	c.3898C>A	c.(3898-3900)Ctt>Att	p.L1300I		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	1300	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						TGTTGACGAAGCCAACGGGGC	0.378																																					p.L1300I		Atlas-SNP	.											.	UGGT2	127	.	0			c.C3898A						PASS	.						137	143	141					13																	96508522		2203	4300	6503	SO:0001583	missense	55757	exon34			GACGAAGCCAACG	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.3898C>A	chr13.hg19:g.96508522G>T	ENSP00000365938:p.Leu1300Ile	208.0	0.0	.		195.0	61.0	.	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	hg19	CCDS9480.1	.	.	.	.	.	.	.	.	.	.	G	18.60	3.659435	0.67586	.	.	ENSG00000102595	ENST00000376747	T	0.48201	0.82	5.18	4.33	0.51752	.	0.000000	0.85682	D	0.000000	T	0.74658	0.3745	M	0.92555	3.32	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81180	-0.1050	10	0.87932	D	0	-5.3529	13.4302	0.61051	0.076:0.0:0.924:0.0	.	1300	Q9NYU1	UGGG2_HUMAN	I	1300	ENSP00000365938:L1300I	ENSP00000365938:L1300I	L	-	1	0	UGGT2	95306523	1.000000	0.71417	1.000000	0.80357	0.492000	0.33523	7.654000	0.83653	1.159000	0.42565	0.655000	0.94253	CTT	.	.	.	none		0.378	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121		T	96508522	G	T	96508522	3	4	261	1	0	0	0	0	1	0	0	0	16954	971	34	4	676	4	UGGT2	13	96508522	Missense_Mutation	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	63694574	96508522	18661356	54	16276											
CHD8	57680	hgsc.bcm.edu	37	chr14	21875030	21875030	+	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	ctcaccaggtccatgtgcttGagactatcaagcagcttgca	10	10	9	12	0	2	1	2	1	0	1	3	2	3	1	2	1	4	4	2	1	2	3			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr14:21875030G>C	ENST00000557364.1	-	14	3155	c.2892C>G	c.(2890-2892)ctC>ctG	p.L964L	CHD8_ENST00000555962.1_Intron|CHD8_ENST00000430710.3_Silent_p.L685L|CHD8_ENST00000399982.2_Silent_p.L964L			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	964	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				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)		CCATGTGCTTGAGACTATCAA	0.428																																					p.L964L		Atlas-SNP	.											.	CHD8	339	.	0			c.C2892G						PASS	.						82	76	78					14																	21875030		1955	4150	6105	SO:0001819	synonymous_variant	57680	exon13			GTGCTTGAGACTA	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.2892C>G	chr14.hg19:g.21875030G>C		82.0	0.0	.		86.0	29.0	.	NM_001170629	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Silent	SNP	ENST00000557364.1	hg19	CCDS53885.1	.	.	.	.	.	.	.	.	.	.	G	7.953	0.745301	0.15710	.	.	ENSG00000100888	ENST00000555935	.	.	.	5.21	-0.0436	0.13859	.	.	.	.	.	T	0.50309	0.1608	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34725	-0.9817	4	.	.	.	-14.3711	4.8051	0.13316	0.0697:0.3534:0.3354:0.2416	.	.	.	.	E	190	.	.	Q	-	1	0	CHD8	20944870	0.870000	0.30015	0.995000	0.50966	0.981000	0.71138	-0.125000	0.10579	-0.171000	0.10797	-0.254000	0.11334	CAA	.	.	.	none		0.428	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920		C	21875030	G	C	21875030	2	2	261	1	0	0	0	0	0	0	0	1	3333	1277	45	4		4	CHD8	14	21875030	Silent	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10		21875030	85474510	55	16277											
SLC8A3	6547	hgsc.bcm.edu	37	chr14	70634950	70634950	+	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	aagggaagggttctccgggtAccagattggcaggatgacac	11	7	15	8	1	1	2	0	1	1	1	2	4	1	4	2	5	1	3	2	5	3	3			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr14:70634950A>T	ENST00000381269.2	-	2	943	c.190T>A	c.(190-192)Tac>Aac	p.Y64N	SLC8A3_ENST00000528359.1_Missense_Mutation_p.Y64N|SLC8A3_ENST00000356921.2_Missense_Mutation_p.Y64N|SLC8A3_ENST00000357887.3_Missense_Mutation_p.Y64N|SLC8A3_ENST00000534137.1_Missense_Mutation_p.Y64N	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	64					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)		TTCTCCGGGTACCAGATTGGC	0.552																																					p.Y64N		Atlas-SNP	.											.	SLC8A3	234	.	0			c.T190A						PASS	.						72	61	65					14																	70634950		2203	4300	6503	SO:0001583	missense	6547	exon2			CCGGGTACCAGAT	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.190T>A	chr14.hg19:g.70634950A>T	ENSP00000370669:p.Tyr64Asn	123.0	0.0	.		143.0	39.0	.	NM_183002	Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	Missense_Mutation	SNP	ENST00000381269.2	hg19	CCDS35498.1	.	.	.	.	.	.	.	.	.	.	A	11.21	1.571033	0.28003	.	.	ENSG00000100678	ENST00000356921;ENST00000381269;ENST00000357887;ENST00000534137;ENST00000528359	T;T;T;T;T	0.32988	1.5;1.43;1.57;1.5;1.57	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.39600	0.1084	N	0.26042	0.785	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.995;0.998	D;D;D;D	0.85130	0.997;0.997;0.979;0.986	T	0.10359	-1.0633	10	0.15952	T	0.53	.	14.5806	0.68288	1.0:0.0:0.0:0.0	.	64;64;64;64	P57103-2;P57103;Q96QG2;Q96QG1	.;NAC3_HUMAN;.;.	N	64	ENSP00000349392:Y64N;ENSP00000370669:Y64N;ENSP00000350560:Y64N;ENSP00000436688:Y64N;ENSP00000433531:Y64N	ENSP00000349392:Y64N	Y	-	1	0	SLC8A3	69704703	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.989000	0.63870	2.030000	0.59900	0.460000	0.39030	TAC	.	.	.	none		0.552	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390736.1			T	70634950	A	T	70634950	3	4	261	1	0	0	0	0	1	0	0	0	14721	391	14	5	2732	5	SLC8A3	14	70634950	Missense_Mutation	SNP	A	TCGA-UZ-A9PO-01A-11D-A382-10	48759920	70634950	36714590	56	16278											
TECPR2	9895	hgsc.bcm.edu	37	chr14	102880977	102880977	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agactttctctgccaggggcTctgtaactcccagctggtgt	6	12	11	12	0	2	1	0	0	2	1	4	1	3	1	2	3	3	3	2	3	1	2			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr14:102880977T>C	ENST00000359520.7	+	5	711	c.485T>C	c.(484-486)cTc>cCc	p.L162P	TECPR2_ENST00000558678.1_Missense_Mutation_p.L162P|TECPR2_ENST00000561228.1_3'UTR	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	162					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						TGCCAGGGGCTCTGTAACTCC	0.527																																					p.L162P		Atlas-SNP	.											.	TECPR2	114	.	0			c.T485C						PASS	.						141	129	133					14																	102880977		2203	4300	6503	SO:0001583	missense	9895	exon5			AGGGGCTCTGTAA	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.485T>C	chr14.hg19:g.102880977T>C	ENSP00000352510:p.Leu162Pro	82.0	0.0	.		84.0	17.0	.	NM_001172631	A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	Missense_Mutation	SNP	ENST00000359520.7	hg19	CCDS32162.1	.	.	.	.	.	.	.	.	.	.	T	11.18	1.563760	0.27915	.	.	ENSG00000196663	ENST00000359520;ENST00000380088	T	0.22336	1.96	4.89	3.74	0.42951	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.718657	0.12822	N	0.436353	T	0.18841	0.0452	L	0.48642	1.525	0.54753	D	0.99998	B;P;P	0.48998	0.087;0.918;0.836	B;B;B	0.38106	0.091;0.265;0.203	T	0.02093	-1.1215	10	0.66056	D	0.02	.	10.3322	0.43829	0.0:0.0779:0.0:0.9221	.	162;162;162	B4DK51;A5PKY3;O15040	.;.;TCPR2_HUMAN	P	162	ENSP00000352510:L162P	ENSP00000352510:L162P	L	+	2	0	TECPR2	101950730	0.978000	0.34361	0.519000	0.27824	0.122000	0.20287	2.546000	0.45778	0.707000	0.31934	0.459000	0.35465	CTC	.	.	.	none		0.527	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415056.2	NM_014844		C	102880977	T	C	102880977	3	2	261	1	0	0	0	0	1	0	0	0	15756	1551	54	3	499	3	TECPR2	14	102880977	Missense_Mutation	SNP	T	TCGA-UZ-A9PO-01A-11D-A382-10	32246027	102880977	4468563	57	16279											
GABRG3	2567	hgsc.bcm.edu	37	chr15	27773100	27773105	+	In_Frame_Del	DEL	AGATGG	AGATGG	-																															tactacatccagattcctcaAgatggattcctgagcgaata																								rs200568627		TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	AGATGG	AGATGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr15:27773100_27773105delAGATGG	ENST00000333743.6	+	9	1338_1343	c.1084_1089delAGATGG	c.(1084-1089)agatggdel	p.RW362del	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	362					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)	p.R362T(1)		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)	AGATTCCTCAAGATGGATTCCTGAGC	0.374																																					p.361_363del	NSCLC(114;800 1656 7410 37729 45293)	Atlas-Indel,Pindel	.											.	GABRG3	115	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.1083_1088del						PASS	.																																			SO:0001651	inframe_deletion	2567	exon9			.		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.1084_1089delAGATGG	chr15.hg19:g.27773100_27773105delAGATGG	ENSP00000331912:p.Arg362_Trp363del	64.0	0.0	0		53.0	12.0	0.226415	NM_033223	G3V594|Q9HD46|Q9NYT2	In_Frame_Del	DEL	ENST00000333743.6	hg19	CCDS45195.1																																																																																			.	.	.	none		0.374	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2			-	27773105	AGATGG	-	27773100	7	5	261	1	0	1	0	1	0	0	0	0	6180	64	3	0	1118	0	GABRG3	15	27773100	In_Frame_Del	DEL	AGATGG	TCGA-UZ-A9PO-01A-11D-A382-10		27773100	74758292	58	16280											
SCAMP2	10066	hgsc.bcm.edu	37	chr15	75140977	75141001	+	Frame_Shift_Del	DEL	ATGTAGATCCCTATTTGACAAAAAA	ATGTAGATCCCTATTTGACAAAAAA	-																															ggatgccaaccaactggatgAtgtagatccctatttgacaa																										TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	ATGTAGATCCCTATTTGACAAAAAA	ATGTAGATCCCTATTTGACAAAAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr15:75140977_75141001delATGTAGATCCCTATTTGACAAAAAA	ENST00000268099.9	-	7	783_807	c.674_698delTTTTTTGTCAAATAGGGATCTACAT	c.(673-699)tttttttgtcaaatagggatctacatcfs	p.FFCQIGIYI225fs		NM_005697.3	NP_005688.2	O15127	SCAM2_HUMAN	secretory carrier membrane protein 2	225					post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|recycling endosome membrane (GO:0055038)|trans-Golgi network membrane (GO:0032588)|transport vesicle (GO:0030133)		p.C227fs*3(1)		kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	9						CAACTGGATGATGTAGATCCCTATTTGACAAAAAAATACAAAGAA	0.498																																					p.225_233del		Atlas-Indel,Pindel	.											.	SCAMP2	18	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.675_699del						PASS	.																																			SO:0001589	frameshift_variant	10066	exon7			.	AF005038	CCDS10271.1	15q23-q25	2013-02-21			ENSG00000140497	ENSG00000140497		"Secretory carrier membrane proteins"	10564	protein-coding gene	gene with protein product		606912				9378760	Standard	NM_005697		Approved		uc002azb.1	O15127	OTTHUMG00000142817	ENST00000268099.9:c.674_698delTTTTTTGTCAAATAGGGATCTACAT	chr15.hg19:g.75140977_75141001delATGTAGATCCCTATTTGACAAAAAA	ENSP00000268099:p.Phe225fs	79.0	0.0	0		86.0	13.0	0.151163	NM_005697	B2RDF0|Q9BQE8	Frame_Shift_Del	DEL	ENST00000268099.9	hg19	CCDS10271.1																																																																																			.	.	.	none		0.498	SCAMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286403.3	NM_005697		-	75141001	ATGTAGATCCCTATTTGACAAAAAA	-	75140977	7	5	261	1	0	1	0	1	0	0	0	0	13884	333	12	0	303	0	SCAMP2	15	75140977	Frame_Shift_Del	DEL	ATGTAGATCCCTATTTGACAAAAAA	TCGA-UZ-A9PO-01A-11D-A382-10	47367877	75140977	27390415	59	16281											
C15orf39	56905	hgsc.bcm.edu	37	chr15	75498964	75498964	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctggatggcaccttcttgcGgggggtgccagctgaggggt	4	10	18	9	1	2	1	0	1	2	0	2	2	2	2	2	7	3	2	2	7	0	2			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr15:75498964G>A	ENST00000360639.2	+	2	895	c.575G>A	c.(574-576)cGg>cAg	p.R192Q	C15orf39_ENST00000567617.1_Missense_Mutation_p.R192Q|C15orf39_ENST00000394987.4_Missense_Mutation_p.R192Q			Q6ZRI6	CO039_HUMAN	chromosome 15 open reading frame 39	192						cytoplasm (GO:0005737)		p.V194fs*132(1)		autonomic_ganglia(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16						ACCTTCTTGCGGGGGGTGCCA	0.627																																					p.R192Q		Atlas-SNP	.											.,1	C15orf39	64	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.G575A						PASS	.						37	41	40					15																	75498964		2197	4291	6488	SO:0001583	missense	56905	exon2			TCTTGCGGGGGGT	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.575G>A	chr15.hg19:g.75498964G>A	ENSP00000353854:p.Arg192Gln	58.0	1.0	.		41.0	7.0	.	NM_015492	B3KWI3|C9J888|Q71JB1|Q7L3S0|Q8N3F2|Q96FB6|Q9NTU5	Missense_Mutation	SNP	ENST00000360639.2	hg19	CCDS10276.1	.	.	.	.	.	.	.	.	.	.	G	11.04	1.523013	0.27211	.	.	ENSG00000167173	ENST00000360639;ENST00000394987	T;T	0.65178	-0.14;-0.14	5.13	1.38	0.22167	.	0.643074	0.13616	N	0.374763	T	0.49558	0.1564	L	0.57536	1.79	0.09310	N	1	P	0.41673	0.759	B	0.35859	0.212	T	0.34925	-0.9809	10	0.33940	T	0.23	-2.3691	5.3924	0.16251	0.2698:0.2193:0.5109:0.0	.	192	Q6ZRI6	CO039_HUMAN	Q	192	ENSP00000353854:R192Q;ENSP00000378438:R192Q	ENSP00000353854:R192Q	R	+	2	0	C15orf39	73286017	0.002000	0.14202	0.569000	0.28460	0.861000	0.49209	0.198000	0.17217	0.410000	0.25675	0.561000	0.74099	CGG	.	.	.	none		0.627	C15orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286410.1	NM_015492		A	75498964	G	A	75498964	3	1	261	1	0	0	0	0	1	0	0	0	1795	1116	39	1	577	1	C15orf39	15	75498964	Missense_Mutation	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	357987	75498964	27032428	60	16282											
UNKL	64718	hgsc.bcm.edu	37	chr16	1417847	1417848	+	Frame_Shift_Del	DEL	AC	AC	-																															agtcccagatgctcccggggAcaccgttcaaacctgagtgt																										TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr16:1417847_1417848delAC	ENST00000389221.4	-	13	1587_1588	c.1588_1589delGT	c.(1588-1590)gtcfs	p.V530fs	UNKL_ENST00000403703.1_Frame_Shift_Del_p.V32fs|UNKL_ENST00000508903.2_Frame_Shift_Del_p.V533fs|UNKL_ENST00000391893.2_Frame_Shift_Del_p.V29fs|UNKL_ENST00000248104.7_Frame_Shift_Del_p.V29fs|UNKL_ENST00000402641.2_Frame_Shift_Del_p.V32fs|UNKL_ENST00000397464.1_Frame_Shift_Del_p.V32fs	NM_001193388.1	NP_001180317	Q9H9P5	UNKL_HUMAN	unkempt family zinc finger-like	530	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)				GCTCCCGGGGACACCGTTCAAA	0.649																																					p.533_533del		Atlas-Indel,Pindel	.											.	UNKL	46	.	0			c.1598_1599del						PASS	.																																			SO:0001589	frameshift_variant	64718	exon13			.	BC011924	CCDS32359.1, CCDS53980.1, CCDS61787.1	16p13.3	2014-03-10	2013-10-17		ENSG00000059145	ENSG00000059145		"Zinc fingers, CCCH-type domain containing"	14184	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 28", "unkempt homolog (Drosophila)-like"	C16orf28		20148946	Standard	NM_001193389		Approved	ZC3HDC5L, ZC3H5L, FLJ23360	uc031qup.1	Q9H9P5	OTTHUMG00000128553	ENST00000389221.4:c.1588_1589delGT	chr16.hg19:g.1417849_1417850delAC	ENSP00000373873:p.Val530fs	151.0	0.0	0		193.0	65.0	0.336788	NM_001193388	B0QYN6|B1GXI8|Q96EV1|Q96RZ1|Q9BWL5|Q9H5K0|Q9UJJ8	Frame_Shift_Del	DEL	ENST00000389221.4	hg19	CCDS53981.1																																																																																			.	.	.	none		0.649	UNKL-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001037125		-	1417848	AC	-	1417847	7	5	261	1	0	1	0	1	0	0	0	0	17013	275	10	0	615	0	UNKL	16	1417847	Frame_Shift_Del	DEL	AC	TCGA-UZ-A9PO-01A-11D-A382-10		1417847	88936906	61	16283											
CASKIN1	57524	hgsc.bcm.edu	37	chr16	2228947	2228947	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggatcttctcctccaccgcCtgcagcgccgcggccaggca	5	6	11	19	5	2	0	0	0	2	0	4	1	3	1	6	3	2	2	6	3	0	1			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr16:2228947C>T	ENST00000343516.6	-	19	4247	c.4155G>A	c.(4153-4155)caG>caA	p.Q1385Q	CASKIN1_ENST00000564289.1_5'Flank	NM_020764.3	NP_065815.1	Q8WXD9	CSKI1_HUMAN	CASK interacting protein 1	1385					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						CCTCCACCGCCTGCAGCGCCG	0.796																																					p.Q1385Q		Atlas-SNP	.											.	CASKIN1	130	.	0			c.G4155A						PASS	.						4	4	4					16																	2228947		1175	2788	3963	SO:0001819	synonymous_variant	57524	exon19			CACCGCCTGCAGC	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.4155G>A	chr16.hg19:g.2228947C>T		1.0	0.0	.		5.0	4.0	.	NM_020764	Q9P2P0	Silent	SNP	ENST00000343516.6	hg19	CCDS42103.1																																																																																			.	.	.	none		0.796	CASKIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435055.1	NM_020764		T	2228947	C	T	2228947	2	4	261	1	0	0	0	0	0	0	0	1	2668	680	24	2		2	CASKIN1	16	2228947	Silent	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	811100	2228947	88125806	62	16284											
SRRM2	23524	hgsc.bcm.edu	37	chr16	2815043	2815043	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctccatcatccccagagcTcaacaacaagtgtcttaccc	11	10	4	16	0	4	1	2	0	2	1	6	1	5	1	4	0	4	1	4	0	4	2	rs541886234	byFrequency	TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr16:2815043T>C	ENST00000301740.8	+	11	5063	c.4514T>C	c.(4513-4515)cTc>cCc	p.L1505P		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	1505	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						TCCCCAGAGCTCAACAACAAG	0.532																																					p.L1505P		Atlas-SNP	.											SRRM2,colon,carcinoma,0,1	SRRM2	263	.	0			c.T4514C						PASS	.						134	137	136					16																	2815043		2198	4300	6498	SO:0001583	missense	23524	exon11			CAGAGCTCAACAA	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.4514T>C	chr16.hg19:g.2815043T>C	ENSP00000301740:p.Leu1505Pro	72.0	0.0	.		84.0	26.0	.	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	hg19	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	T	11.18	1.562907	0.27915	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	T	0.26957	1.7	5.9	4.8	0.61643	.	0.229124	0.31113	N	0.008221	T	0.22360	0.0539	L	0.36672	1.1	0.45930	D	0.998763	P	0.42039	0.769	B	0.42343	0.384	T	0.01753	-1.1281	10	0.39692	T	0.17	-1.9891	9.9236	0.41478	0.0:0.0:0.1788:0.8212	.	1505	Q9UQ35	SRRM2_HUMAN	P	1505;1505;757	ENSP00000301740:L1505P	ENSP00000301740:L1505P	L	+	2	0	SRRM2	2755044	0.987000	0.35691	1.000000	0.80357	0.990000	0.78478	0.820000	0.27323	1.045000	0.40225	0.533000	0.62120	CTC	.	.	.	none		0.532	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			C	2815043	T	C	2815043	3	2	261	1	0	0	0	0	1	0	0	0	15181	1551	54	3	4552	3	SRRM2	16	2815043	Missense_Mutation	SNP	T	TCGA-UZ-A9PO-01A-11D-A382-10	586096	2815043	87539710	63	16285											
CLDN6	9074	hgsc.bcm.edu	37	chr16	3065429	3065429	+	Silent	SNP	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	ggggcagatgttgagtagcgGgccatgtaatggctggggcc	7	8	19	7	1	0	2	0	1	0	1	0	2	0	2	2	6	1	5	2	6	2	3			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr16:3065429G>A	ENST00000396925.1	-	3	1022	c.594C>T	c.(592-594)gcC>gcT	p.A198A	CLDN6_ENST00000328796.4_Silent_p.A198A|CLDN6_ENST00000572154.1_Intron			P56747	CLD6_HUMAN	claudin 6	198					calcium-independent cell-cell adhesion (GO:0016338)|cell-cell junction organization (GO:0045216)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	10						TTGAGTAGCGGGCCATGTAAT	0.652																																					p.A198A		Atlas-SNP	.											.	CLDN6	31	.	0			c.C594T						PASS	.						43	49	47					16																	3065429		2198	4300	6498	SO:0001819	synonymous_variant	9074	exon2			GTAGCGGGCCATG	AJ249735	CCDS10488.1	16p13.3	2008-08-01			ENSG00000184697	ENSG00000184697		"Claudins"	2048	protein-coding gene	gene with protein product		615798				9892664, 18234789	Standard	NM_021195		Approved		uc002csu.4	P56747	OTTHUMG00000128999	ENST00000396925.1:c.594C>T	chr16.hg19:g.3065429G>A		93.0	0.0	.		117.0	28.0	.	NM_021195	B3KQP9|D3DUA5	Silent	SNP	ENST00000396925.1	hg19	CCDS10488.1																																																																																			.	.	.	none		0.652	CLDN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250988.1	NM_021195		A	3065429	G	A	3065429	2	1	261	1	0	0	0	0	0	0	0	1	3491	1219	43	2		2	CLDN6	16	3065429	Silent	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	250386	3065429	87289324	64	16286											
UQCRC2	7385	hgsc.bcm.edu	37	chr16	21974187	21974187	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagattgacaaagctgtggcCtttcagaatccgcagactcg	12	9	10	10	2	1	4	1	1	0	3	3	4	2	4	2	1	1	2	2	1	3	2			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr16:21974187C>T	ENST00000268379.4	+	6	1259	c.495C>T	c.(493-495)gcC>gcT	p.A165A	UQCRC2_ENST00000561553.1_Silent_p.A165A	NM_003366.2	NP_003357.2	P22695	QCR2_HUMAN	ubiquinol-cytochrome c reductase core protein II	165					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(4)|prostate(1)|skin(1)	15				GBM - Glioblastoma multiforme(48;0.0264)		AAGCTGTGGCCTTTCAGAATC	0.398																																					p.A165A	Colon(123;450 1645 12841 25393 45623)	Atlas-SNP	.											.	UQCRC2	46	.	0			c.C495T						PASS	.						85	76	79					16																	21974187		2198	4300	6498	SO:0001819	synonymous_variant	7385	exon6			TGTGGCCTTTCAG	J04973	CCDS10601.1	16p12	2011-07-04			ENSG00000140740	ENSG00000140740	1.10.2.2	"Mitochondrial respiratory chain complex / Complex III"	12586	protein-coding gene	gene with protein product		191329				8288258, 2547763	Standard	NM_003366		Approved	QCR2, UQCR2	uc002djx.3	P22695	OTTHUMG00000131585	ENST00000268379.4:c.495C>T	chr16.hg19:g.21974187C>T		80.0	0.0	.		97.0	48.0	.	NM_003366	B3KSN4|Q9BQ05	Silent	SNP	ENST00000268379.4	hg19	CCDS10601.1																																																																																			.	.	.	none		0.398	UQCRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254466.1	NM_003366		T	21974187	C	T	21974187	2	4	261	1	0	0	0	0	0	0	0	1	17032	668	24	2		2	UQCRC2	16	21974187	Silent	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	18908758	21974187	68380566	65	16287											
ERN2	10595	hgsc.bcm.edu	37	chr16	23711991	23711991	+	Missense_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	agtctgcaggtgccagggggGtctcctgctgcttctccacc	4	10	13	14	0	3	0	0	0	3	0	5	0	3	0	4	4	4	3	4	4	0	1			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr16:23711991G>A	ENST00000457008.2	-	12	1276	c.1238C>T	c.(1237-1239)aCc>aTc	p.T413I	ERN2_ENST00000256797.4_Missense_Mutation_p.T513I					endoplasmic reticulum to nucleus signaling 2											large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)		TGCCAGGGGGGTCTCCTGCTG	0.627																																					p.T513I		Atlas-SNP	.											.	ERN2	131	.	0			c.C1538T						PASS	.						58	59	59					16																	23711991		2197	4300	6497	SO:0001583	missense	10595	exon13			AGGGGGGTCTCCT	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.1238C>T	chr16.hg19:g.23711991G>A	ENSP00000413812:p.Thr413Ile	79.0	0.0	.		96.0	43.0	.	NM_033266		Missense_Mutation	SNP	ENST00000457008.2	hg19		.	.	.	.	.	.	.	.	.	.	G	7.968	0.748362	0.15710	.	.	ENSG00000134398	ENST00000256797;ENST00000457008	T;T	0.60424	0.19;0.23	4.27	-2.79	0.05841	.	1.458410	0.04022	N	0.299985	T	0.33933	0.0880	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.08617	-1.0713	10	0.37606	T	0.19	.	0.7973	0.01068	0.1835:0.2906:0.247:0.2789	.	413;465	E7ETG2;A5YM65	.;.	I	513;413	ENSP00000256797:T513I;ENSP00000413812:T413I	ENSP00000256797:T513I	T	-	2	0	ERN2	23619492	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.286000	0.08399	-0.459000	0.07013	-0.258000	0.10820	ACC	.	.	.	none		0.627	ERN2-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000434886.1			A	23711991	G	A	23711991	3	1	261	1	0	0	0	0	1	0	0	0	5240	1261	44	2	1426	2	ERN2	16	23711991	Missense_Mutation	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	1737804	23711991	66642762	66	16288											
MBTPS1	8720	hgsc.bcm.edu	37	chr16	84132688	84132688	+	Missense_Mutation	SNP	T	T	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	cttgagggaacgaaagacttTtcgttggggcgtgacccgtt	8	11	14	8	4	0	3	0	2	0	1	1	5	0	4	1	3	1	2	1	3	2	5			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr16:84132688T>G	ENST00000343411.3	-	3	886	c.391A>C	c.(391-393)Aaa>Caa	p.K131Q		NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	131					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						CGAAAGACTTTTCGTTGGGGC	0.413																																					p.K131Q		Atlas-SNP	.											.	MBTPS1	85	.	0			c.A391C						PASS	.						172	162	166					16																	84132688		2200	4300	6500	SO:0001583	missense	8720	exon3			AGACTTTTCGTTG	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.391A>C	chr16.hg19:g.84132688T>G	ENSP00000344223:p.Lys131Gln	160.0	0.0	.		172.0	29.0	.	NM_003791	A8K6V8|Q24JQ2|Q9UF67	Missense_Mutation	SNP	ENST00000343411.3	hg19	CCDS10941.1	.	.	.	.	.	.	.	.	.	.	T	11.86	1.763541	0.31228	.	.	ENSG00000140943	ENST00000343411	T	0.42900	0.96	5.61	5.61	0.85477	.	0.259036	0.44902	D	0.000407	T	0.26882	0.0658	N	0.20685	0.6	0.32674	N	0.516437	B	0.10296	0.003	B	0.06405	0.002	T	0.30031	-0.9992	10	0.17369	T	0.5	-13.823	11.7501	0.51843	0.0:0.0:0.1471:0.8529	.	131	Q14703	MBTP1_HUMAN	Q	131	ENSP00000344223:K131Q	ENSP00000344223:K131Q	K	-	1	0	MBTPS1	82690189	1.000000	0.71417	0.994000	0.49952	0.833000	0.47200	5.752000	0.68728	2.139000	0.66308	0.528000	0.53228	AAA	.	.	.	none		0.413	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269080.2	NM_003791		G	84132688	T	G	84132688	3	3	261	1	0	0	0	0	1	0	0	0	9368	1850	64	5	2851	5	MBTPS1	16	84132688	Missense_Mutation	SNP	T	TCGA-UZ-A9PO-01A-11D-A382-10	60420697	84132688	6222065	67	16289											
WIPF2	147179	hgsc.bcm.edu	37	chr17	38430244	38430244	+	Frame_Shift_Del	DEL	T	T	-																															tctatcaccactgtccggtcTttcttgggtgagtagctagc																										TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr17:38430244delT	ENST00000323571.4	+	6	1413	c.1173delT	c.(1171-1173)tctfs	p.S391fs	WIPF2_ENST00000585043.1_Frame_Shift_Del_p.S391fs|WIPF2_ENST00000583130.1_Frame_Shift_Del_p.S391fs|WIPF2_ENST00000494757.1_3'UTR|WIPF2_ENST00000394103.3_Frame_Shift_Del_p.S133fs|WIPF2_ENST00000536600.1_Frame_Shift_Del_p.S133fs	NM_133264.4	NP_573571.1	Q8TF74	WIPF2_HUMAN	WAS/WASL interacting protein family, member 2	391					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	30						CTGTCCGGTCTTTCTTGGGTG	0.592										HNSCC(43;0.11)																											p.S391fs		Atlas-Indel,Pindel	.											.	WIPF2	55	.	0			c.1172delC						PASS	.						135	110	119					17																	38430244		2203	4300	6503	SO:0001589	frameshift_variant	147179	exon6			.	BC025965	CCDS11364.1	17q21.2	2006-10-12			ENSG00000171475	ENSG00000171475			30923	protein-coding gene	gene with protein product		609692				12213210, 11829459	Standard	XM_005257083		Approved	WICH, WIRE	uc002hug.1	Q8TF74	OTTHUMG00000133331	ENST00000323571.4:c.1173delT	chr17.hg19:g.38430244delT	ENSP00000320924:p.Ser391fs	113.0	0.0	0		130.0	57.0	0.438462	NM_133264	A8K0L3|Q658J8|Q71RE1|Q8TE44	Frame_Shift_Del	DEL	ENST00000323571.4	hg19	CCDS11364.1																																																																																			.	.	.	none		0.592	WIPF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257157.2	NM_133264		-	38430244	T	-	38430244	7	5	261	1	0	1	0	1	0	0	0	0	17380	1596	56	0	1191	0	WIPF2	17	38430244	Frame_Shift_Del	DEL	T	TCGA-UZ-A9PO-01A-11D-A382-10		38430244	42764966	68	16290											
PPM1E	22843	hgsc.bcm.edu	37	chr17	56833454	56833454	+	Silent	SNP	G	G	A																															tgcggcggcggcgagccggaGccggaacccgaacccgaacc																								rs77856248		TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	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	.	0			c.G96A						PASS	.						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	chr17.hg19:g.56833454G>A		206.0	0.0	.		298.0	34.0	.	NM_014906	Q8N8J9|Q96DB8	Silent	SNP	ENST00000308249.2	hg19	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	261	1	0	0	0	0	0	0	0	1	12348	962	34	2		2	PPM1E	17	56833454	Silent	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	18403210	56833454	24361756	69	16291	167	2									
PPM1E	22843	hgsc.bcm.edu	37	chr17	56833457	56833457	+	Silent	SNP	G	G	C																															ggcggcggcgagccggagccGgaacccgaacccgaacccga																								rs3834568|rs201186780|rs74256772	byFrequency	TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	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	.	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	chr17.hg19:g.56833457G>C		202.0	2.0	.		294.0	41.0	.	NM_014906	Q8N8J9|Q96DB8	Silent	SNP	ENST00000308249.2	hg19	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	261	1	0	0	0	0	0	0	0	1	12348	1103	39	4		4	PPM1E	17	56833457	Silent	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	3	56833457	24361753	70	16292	167	2									
PPM1E	22843	hgsc.bcm.edu	37	chr17	56833490	56833490	+	Silent	SNP	G	G	A																															gaacccgaacccgaacccgaGtccgagcccgagcccgaacc																								rs59676153		TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	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	.	0			c.G132A						PASS	.																																			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	chr17.hg19:g.56833490G>A		206.0	0.0	.		307.0	35.0	.	NM_014906	Q8N8J9|Q96DB8	Silent	SNP	ENST00000308249.2	hg19	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	261	1	0	0	0	0	0	0	0	1	12348	1020	36	2		2	PPM1E	17	56833490	Silent	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	33	56833490	24361720	71	16293	168	2									
PPM1E	22843	hgsc.bcm.edu	37	chr17	56833497	56833497	+	Missense_Mutation	SNP	C	C	T																															aacccgaacccgagtccgagCccgagcccgaacctgaactg																								rs61052860		TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	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	.	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	chr17.hg19:g.56833497C>T	ENSP00000312411:p.Pro47Ser	204.0	0.0	.		317.0	16.0	.	NM_014906	Q8N8J9|Q96DB8	Missense_Mutation	SNP	ENST00000308249.2	hg19	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	261	1	0	0	0	0	1	0	0	0	12348	739	26	2	141	2	PPM1E	17	56833497	Missense_Mutation	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	7	56833497	24361713	72	16294	168	2									
MGAT5B	146664	hgsc.bcm.edu	37	chr17	74943970	74943970	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccacgccccgcagagcccctTtgtcctggcccccaatgcca	6	6	8	21	2	0	1	0	0	0	1	1	1	1	1	9	1	2	1	9	1	1	1			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr17:74943970T>C	ENST00000569840.2	+	17	2556	c.1982T>C	c.(1981-1983)tTt>tCt	p.F661S	MGAT5B_ENST00000428789.2_Missense_Mutation_p.F670S|RP11-87G24.3_ENST00000564292.1_RNA|MGAT5B_ENST00000301618.4_Missense_Mutation_p.F659S	NM_001199172.1	NP_001186101.1	Q3V5L5	MGT5B_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B	661					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						CAGAGCCCCTTTGTCCTGGCC	0.706																																					p.F670S		Atlas-SNP	.											.	MGAT5B	98	.	0			c.T2009C						PASS	.						34	33	34					17																	74943970		2202	4300	6502	SO:0001583	missense	146664	exon15			GCCCCTTTGTCCT	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.1982T>C	chr17.hg19:g.74943970T>C	ENSP00000456037:p.Phe661Ser	112.0	0.0	.		141.0	25.0	.	NM_198955	Q6P3S8|Q6P6B3|Q766X5|Q76D04|Q96LS2	Missense_Mutation	SNP	ENST00000569840.2	hg19	CCDS59299.1	.	.	.	.	.	.	.	.	.	.	T	6.753	0.507770	0.12883	.	.	ENSG00000167889	ENST00000301618;ENST00000428789	T;T	0.42900	0.97;0.96	4.66	3.34	0.38264	.	0.269957	0.36167	N	0.002753	T	0.28466	0.0704	L	0.34521	1.04	0.09310	N	0.999997	B;B;B	0.16802	0.019;0.004;0.001	B;B;B	0.17722	0.019;0.002;0.001	T	0.10753	-1.0616	10	0.32370	T	0.25	-9.8741	7.6968	0.28600	0.0:0.1868:0.0:0.8132	.	66;670;659	Q3V5L5-4;Q3V5L5-2;Q3V5L5-5	.;.;.	S	659;670	ENSP00000301618:F659S;ENSP00000391227:F670S	ENSP00000301618:F659S	F	+	2	0	MGAT5B	72455565	0.108000	0.22018	0.935000	0.37517	0.286000	0.27126	2.066000	0.41452	1.731000	0.51592	0.455000	0.32223	TTT	.	.	.	none		0.706	MGAT5B-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460624.2	NM_144677		C	74943970	T	C	74943970	3	2	261	1	0	0	0	0	1	0	0	0	9556	1841	64	3	2139	3	MGAT5B	17	74943970	Missense_Mutation	SNP	T	TCGA-UZ-A9PO-01A-11D-A382-10	18110473	74943970	6251240	73	16295											
NPTX1	4884	hgsc.bcm.edu	37	chr17	78450218	78450227	+	Frame_Shift_Del	DEL	CAGGTGCGCG	CAGGTGCGCG	-																															ggcagagggcgagcagcgcaCaggtgcgcgcggcgcggccg																										TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	CAGGTGCGCG	CAGGTGCGCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr17:78450218_78450227delCAGGTGCGCG	ENST00000306773.4	-	1	177_186	c.20_29delCGCGCACCTG	c.(19-30)gcgcgcacctgtfs	p.ARTC7fs	NPTX1_ENST00000575212.1_Intron	NM_002522.3	NP_002513.2	Q15818	NPTX1_HUMAN	neuronal pentraxin I	7				Missing (in Ref. 1; AAC50727). {ECO:0000305}.	axonogenesis involved in innervation (GO:0060385)|cellular response to glucose stimulus (GO:0071333)|cellular response to potassium ion (GO:0035865)|central nervous system development (GO:0007417)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial transport (GO:0006839)|synaptic transmission (GO:0007268)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			kidney(1)|large_intestine(2)|liver(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(1)	11	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487)			GAGCAGCGCACAGGTgcgcgcggcgcggcc	0.79																																					p.7_10del		Atlas-INDEL	.											.	NPTX1	28	.	0			c.21_30del						PASS	.																																			SO:0001589	frameshift_variant	4884	exon1			.	U61849	CCDS32762.1	17q25.3	2008-05-14				ENSG00000171246			7952	protein-coding gene	gene with protein product		602367				8884281	Standard	NM_002522		Approved		uc002jyp.1	Q15818		ENST00000306773.4:c.20_29delCGCGCACCTG	chr17.hg19:g.78450218_78450227delCAGGTGCGCG	ENSP00000307549:p.Ala7fs	24.0	0.0	0		38.0	15.0	0.394737	NM_002522	B3KXH3|Q5FWE6	Frame_Shift_Del	DEL	ENST00000306773.4	hg19	CCDS32762.1																																																																																			.	.	.	none		0.79	NPTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438051.1			-	78450227	CAGGTGCGCG	-	78450218	7	5	261	1	0	1	0	1	0	0	0	0	10609	478	17	0	1289	0	NPTX1	17	78450218	Frame_Shift_Del	DEL	CAGGTGCGCG	TCGA-UZ-A9PO-01A-11D-A382-10	3506248	78450218	2744992	74	16296											
LPIN2	9663	hgsc.bcm.edu	37	chr18	2931299	2931299	+	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	gaggcccccgcaaagggagaGggtaacgtcaggcaagtcca	12	3	15	11	2	1	1	1	0	0	1	2	3	2	1	3	4	1	3	3	4	3	1			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr18:2931299G>C	ENST00000261596.4	-	9	1649	c.1411C>G	c.(1411-1413)Ctc>Gtc	p.L471V		NM_014646.2	NP_055461.1	Q92539	LPIN2_HUMAN	lipin 2	471					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)		CAAAGGGAGAGGGTAACGTCA	0.542																																					p.L471V		Atlas-SNP	.											.	LPIN2	75	.	0			c.C1411G						PASS	.						68	61	63					18																	2931299		2203	4300	6503	SO:0001583	missense	9663	exon9			GGGAGAGGGTAAC	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.1411C>G	chr18.hg19:g.2931299G>C	ENSP00000261596:p.Leu471Val	49.0	0.0	.		41.0	15.0	.	NM_014646	A7MD25|D3DUH3	Missense_Mutation	SNP	ENST00000261596.4	hg19	CCDS11829.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.465248	0.84425	.	.	ENSG00000101577	ENST00000261596	D	0.84730	-1.89	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	D	0.92993	0.7770	M	0.87269	2.87	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	D	0.93312	0.6685	10	0.62326	D	0.03	-22.4301	14.5421	0.68002	0.0695:0.0:0.9305:0.0	.	471	Q92539	LPIN2_HUMAN	V	471	ENSP00000261596:L471V	ENSP00000261596:L471V	L	-	1	0	LPIN2	2921299	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.252000	0.72447	2.815000	0.96918	0.650000	0.86243	CTC	.	.	.	none		0.542	LPIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254363.2	NM_014646		C	2931299	G	C	2931299	3	2	261	1	0	0	0	0	1	0	0	0	8926	1000	35	4	1327	4	LPIN2	18	2931299	Missense_Mutation	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10		2931299	75145949	75	16297											
EPB41L3	23136	hgsc.bcm.edu	37	chr18	5395104	5395104	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgcatcccccgtgatgactaTtcgcttctcaattcttgtct	6	16	6	13	2	3	2	1	2	3	0	6	2	4	2	2	0	1	2	2	0	2	5			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr18:5395104T>C	ENST00000341928.2	-	21	3455	c.3115A>G	c.(3115-3117)Ata>Gta	p.I1039V	EPB41L3_ENST00000542146.1_Missense_Mutation_p.I344V|EPB41L3_ENST00000540638.2_Missense_Mutation_p.I817V|EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000427684.2_Missense_Mutation_p.I336V|EPB41L3_ENST00000400111.3_Missense_Mutation_p.I817V|EPB41L3_ENST00000342933.3_Missense_Mutation_p.I1039V|EPB41L3_ENST00000544123.1_Missense_Mutation_p.I870V	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	1039	C-terminal (CTD).				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						GTGATGACTATTCGCTTCTCA	0.453																																					p.I1039V		Atlas-SNP	.											.	EPB41L3	222	.	0			c.A3115G						PASS	.						148	126	134					18																	5395104		2203	4300	6503	SO:0001583	missense	23136	exon21			TGACTATTCGCTT	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.3115A>G	chr18.hg19:g.5395104T>C	ENSP00000343158:p.Ile1039Val	80.0	0.0	.		79.0	24.0	.	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	hg19	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	T	28.5	4.926796	0.92319	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000427684;ENST00000542146;ENST00000342933;ENST00000400111	D;D;D;D;D;D	0.82081	-1.57;-1.57;-1.57;-1.57;-1.57;-1.57	5.93	5.93	0.95920	Band 4.1, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.90590	0.7050	M	0.72479	2.2	0.80722	D	1	P;P;D;D;D;P;D;D	0.71674	0.858;0.943;0.995;0.962;0.993;0.923;0.998;0.998	P;D;D;P;D;P;D;D	0.87578	0.856;0.946;0.992;0.883;0.987;0.54;0.998;0.991	D	0.91479	0.5203	10	0.87932	D	0	.	16.3943	0.83563	0.0:0.0:0.0:1.0	.	870;336;344;431;708;817;1039;274	F5GX05;E7EUF8;F5H7W5;B7Z8M8;A8K968;Q9Y2J2-2;Q9Y2J2;B3KT50	.;.;.;.;.;.;E41L3_HUMAN;.	V	1039;708;870;708;336;344;1039;817	ENSP00000343158:I1039V;ENSP00000441174:I870V;ENSP00000392195:I336V;ENSP00000442233:I344V;ENSP00000341138:I1039V;ENSP00000382981:I817V	ENSP00000343158:I1039V	I	-	1	0	EPB41L3	5385104	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	7.991000	0.88244	2.281000	0.76405	0.533000	0.62120	ATA	.	.	.	none		0.453	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		C	5395104	T	C	5395104	3	2	261	1	0	0	0	0	1	0	0	0	5156	1493	52	3	156	3	EPB41L3	18	5395104	Missense_Mutation	SNP	T	TCGA-UZ-A9PO-01A-11D-A382-10	2463805	5395104	72682144	76	16298											
PTPRM	5797	hgsc.bcm.edu	37	chr18	8244180	8244180	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgacgaggctttctcattcAtggacacgcacaatctgaat	11	10	9	11	3	3	1	2	1	2	0	4	4	3	2	0	2	0	2	0	2	2	2			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr18:8244180A>G	ENST00000332175.8	+	15	3462	c.2425A>G	c.(2425-2427)Atg>Gtg	p.M809V	PTPRM_ENST00000580170.1_Missense_Mutation_p.M809V|PTPRM_ENST00000400053.4_Missense_Mutation_p.M747V|PTPRM_ENST00000444013.1_Missense_Mutation_p.M596V|PTPRM_ENST00000400060.4_Missense_Mutation_p.M809V	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	809					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)				TTTCTCATTCATGGACACGCA	0.483																																					p.M809V		Atlas-SNP	.											.	PTPRM	185	.	0			c.A2425G						PASS	.						153	134	141					18																	8244180		2203	4300	6503	SO:0001583	missense	5797	exon15			TCATTCATGGACA	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.2425A>G	chr18.hg19:g.8244180A>G	ENSP00000331418:p.Met809Val	125.0	0.0	.		135.0	42.0	.	NM_001105244	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	hg19	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	A	13.14	2.147098	0.37923	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	T;T;T;T	0.44881	1.3;1.23;1.05;0.91	5.71	4.56	0.56223	.	0.080339	0.85682	D	0.000000	T	0.40272	0.1110	M	0.62723	1.935	0.52501	D	0.999953	B;B;B	0.18461	0.028;0.0;0.0	B;B;B	0.17722	0.019;0.0;0.001	T	0.19031	-1.0318	10	0.35671	T	0.21	.	11.5687	0.50822	0.9303:0.0:0.0697:0.0	.	596;809;809	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	V	809;809;747;596	ENSP00000331418:M809V;ENSP00000382933:M809V;ENSP00000382927:M747V;ENSP00000387608:M596V	ENSP00000331418:M809V	M	+	1	0	PTPRM	8234180	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.121000	0.71602	1.003000	0.39130	0.455000	0.32223	ATG	.	.	.	none		0.483	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			G	8244180	A	G	8244180	3	3	261	1	0	0	0	0	1	0	0	0	12819	217	8	3	2483	3	PTPRM	18	8244180	Missense_Mutation	SNP	A	TCGA-UZ-A9PO-01A-11D-A382-10	2849076	8244180	69833068	77	16299											
PTPRM	5797	hgsc.bcm.edu	37	chr18	8380303	8380303	+	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	tgtgtttgcagagctataaaCagccttcagcttttatagtc	10	15	8	8	0	1	1	1	0	0	1	2	1	1	1	1	0	5	4	1	0	5	7			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr18:8380303C>T	ENST00000332175.8	+	27	4794	c.3757C>T	c.(3757-3759)Cag>Tag	p.Q1253*	PTPRM_ENST00000580170.1_Nonsense_Mutation_p.Q1266*|PTPRM_ENST00000400053.4_Nonsense_Mutation_p.Q1191*|PTPRM_ENST00000444013.1_Nonsense_Mutation_p.Q1040*|PTPRM_ENST00000400060.4_Nonsense_Mutation_p.Q1267*	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	1253	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				GAGCTATAAACAGCCTTCAGC	0.423																																					p.Q1266X		Atlas-SNP	.											.	PTPRM	185	.	0			c.C3796T						PASS	.						85	78	80					18																	8380303		2203	4300	6503	SO:0001587	stop_gained	5797	exon29			TATAAACAGCCTT	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.3757C>T	chr18.hg19:g.8380303C>T	ENSP00000331418:p.Gln1253*	75.0	0.0	.		58.0	22.0	.	NM_001105244	A7MBN1|D3DUH8|J3QL11	Nonsense_Mutation	SNP	ENST00000332175.8	hg19	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	C	51	17.626486	0.99890	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	.	.	.	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	.	20.1184	0.97949	0.0:1.0:0.0:0.0	.	.	.	.	X	1253;1267;1191;1040	.	ENSP00000331418:Q1253X	Q	+	1	0	PTPRM	8370303	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.769000	0.95229	0.655000	0.94253	CAG	.	.	.	none		0.423	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			T	8380303	C	T	8380303	4	4	261	1	0	0	0	0	0	1	0	0	12819	479	17	2	3910	2	PTPRM	18	8380303	Nonsense_Mutation	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	136123	8380303	69696945	78	16300											
KDSR	2531	hgsc.bcm.edu	37	chr18	61018276	61018276	+	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	ggtgatcacggcccggctggGgtacacgctgcccaggtaat	7	7	15	12	3	1	1	1	1	0	0	1	1	1	1	2	6	2	4	2	6	2	2			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr18:61018276G>T	ENST00000406396.3	-	6	845	c.454C>A	c.(454-456)Ccc>Acc	p.P152T	KDSR_ENST00000326575.5_Intron	NM_002035.2	NP_002026.1	Q06136	KDSR_HUMAN	3-ketodihydrosphingosine reductase	152					3-keto-sphinganine metabolic process (GO:0006666)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3-dehydrosphinganine reductase activity (GO:0047560)			endometrium(2)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	9						GCCCGGCTGGGGTACACGCTG	0.552																																					p.P152T		Atlas-SNP	.											.	KDSR	17	.	0			c.C454A						PASS	.						75	74	75					18																	61018276		2203	4300	6503	SO:0001583	missense	2531	exon6			GGCTGGGGTACAC		CCDS11982.1	18q21	2011-09-20	2008-02-20	2008-02-20	ENSG00000119537	ENSG00000119537	1.1.1.102	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	4021	protein-coding gene	gene with protein product	"3-dehydrosphinganine reductase", "short chain dehydrogenase/reductase family 35C, member 1"	136440	"follicular lymphoma variant translocation 1"	FVT1		8417785, 15328338, 17420465, 19027726	Standard	NM_002035		Approved	DHSR, SDR35C1	uc010dpw.3	Q06136	OTTHUMG00000132792	ENST00000406396.3:c.454C>A	chr18.hg19:g.61018276G>T	ENSP00000385083:p.Pro152Thr	100.0	0.0	.		102.0	32.0	.	NM_002035	B2R5Y1|B4DMX0	Missense_Mutation	SNP	ENST00000406396.3	hg19	CCDS11982.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.987666	0.74589	.	.	ENSG00000119537	ENST00000406396	D	0.86769	-2.17	5.95	5.95	0.96441	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.76026	0.3930	N	0.00560	-1.38	0.80722	D	1	D	0.58970	0.984	P	0.54815	0.761	T	0.78558	-0.2158	10	0.10377	T	0.69	.	20.3931	0.98965	0.0:0.0:1.0:0.0	.	152	Q06136	KDSR_HUMAN	T	152	ENSP00000385083:P152T	ENSP00000385083:P152T	P	-	1	0	KDSR	59169256	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.617000	0.67716	2.824000	0.97209	0.655000	0.94253	CCC	.	.	.	none		0.552	KDSR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256200.2			T	61018276	G	T	61018276	3	4	261	1	0	0	0	0	1	0	0	0	8147	1232	43	4	564	4	KDSR	18	61018276	Missense_Mutation	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	52637973	61018276	17058972	79	16301											
JSRP1	126306	hgsc.bcm.edu	37	chr19	2254452	2254452	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagctactcacgtggggcaCgctgccggagtcggccagcc	6	5	14	16	4	1	0	1	0	0	0	2	1	1	1	4	4	4	3	4	4	1	1	rs566252055		TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr19:2254452C>T	ENST00000300961.6	-	3	203	c.139G>A	c.(139-141)Gtg>Atg	p.V47M	JSRP1_ENST00000586471.2_Missense_Mutation_p.V47M	NM_144616.3	NP_653217.1	Q96MG2	JSPR1_HUMAN	junctional sarcoplasmic reticulum protein 1	47	Mediates interaction with CACNA1S. {ECO:0000250}.				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)		ACGTGGGGCACGCTGCCGGAG	0.667													C|||	1	0.000199681	0	0	5008	,	,		15668	0		0	False		,,,				2504	0.001				p.V47M		Atlas-SNP	.											.	JSRP1	18	.	0			c.G139A						PASS	.						42	39	40					19																	2254452		2201	4300	6501	SO:0001583	missense	126306	exon3			GGGGCACGCTGCC	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.139G>A	chr19.hg19:g.2254452C>T	ENSP00000300961:p.Val47Met	103.0	0.0	.		110.0	36.0	.	NM_144616		Missense_Mutation	SNP	ENST00000300961.6	hg19	CCDS12086.1	.	.	.	.	.	.	.	.	.	.	c	6.447	0.450553	0.12223	.	.	ENSG00000167476	ENST00000300961	T	0.18338	2.22	3.23	-4.87	0.03123	.	3.543170	0.00710	N	0.000821	T	0.06962	0.0177	N	0.08118	0	0.09310	N	1	P	0.36712	0.566	B	0.27887	0.084	T	0.16808	-1.0390	10	0.30854	T	0.27	0.0	6.6524	0.22969	0.2046:0.311:0.4844:0.0	.	47	Q96MG2	JSPR1_HUMAN	M	47	ENSP00000300961:V47M	ENSP00000300961:V47M	V	-	1	0	JSRP1	2205452	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.189000	0.09629	-1.280000	0.02402	-2.474000	0.00201	GTG	.	.	.	none		0.667	JSRP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451266.2	NM_144616		T	2254452	C	T	2254452	3	4	261	1	0	0	0	0	1	0	0	0	7973	536	19	1	876	1	JSRP1	19	2254452	Missense_Mutation	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10		2254452	56874531	80	16302											
PRAM1	84106	hgsc.bcm.edu	37	chr19	8563902	8563902	+	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	gggaaaggcgctggagtcgcGcttcggctcgctggactgag	6	7	18	10	5	0	1	0	1	0	0	3	4	0	4	0	5	0	4	0	5	1	1	rs564707710		TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr19:8563902G>T	ENST00000423345.4	-	2	1310	c.790C>A	c.(790-792)Cgc>Agc	p.R264S	PRAM1_ENST00000255612.3_Missense_Mutation_p.R264S			Q96QH2	PRAM_HUMAN	PML-RARA regulated adaptor molecule 1	312	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						CTGGAGTCGCGCTTCGGCTCG	0.647																																					p.R264S		Atlas-SNP	.											.	PRAM1	53	.	0			c.C790A						PASS	.						35	40	38					19																	8563902		2177	4280	6457	SO:0001583	missense	84106	exon2			AGTCGCGCTTCGG	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.790C>A	chr19.hg19:g.8563902G>T	ENSP00000408342:p.Arg264Ser	89.0	0.0	.		71.0	4.0	.	NM_032152	Q8N6W7	Missense_Mutation	SNP	ENST00000423345.4	hg19	CCDS45954.2	.	.	.	.	.	.	.	.	.	.	G	2.680	-0.275657	0.05679	.	.	ENSG00000133246	ENST00000255612;ENST00000423345	T;T	0.13089	2.62;2.62	3.91	1.63	0.23807	.	.	.	.	.	T	0.06554	0.0168	N	0.08118	0	0.09310	N	1	B;B	0.25563	0.012;0.129	B;B	0.28385	0.089;0.049	T	0.42716	-0.9435	9	0.09590	T	0.72	.	9.9374	0.41559	0.0:0.4064:0.5936:0.0	.	264;312	Q96QH2-2;Q96QH2	.;PRAM_HUMAN	S	264	ENSP00000255612:R264S;ENSP00000408342:R264S	ENSP00000255612:R264S	R	-	1	0	PRAM1	8469902	0.001000	0.12720	0.009000	0.14445	0.002000	0.02628	0.646000	0.24797	0.558000	0.29135	0.591000	0.81541	CGC	.	.	.	none		0.647	PRAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397040.3	NM_032152		T	8563902	G	T	8563902	3	4	261	1	0	0	0	0	1	0	0	0	12433	1087	38	4	1255	4	PRAM1	19	8563902	Missense_Mutation	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	6309450	8563902	50565081	81	16303											
ATG4D	84971	hgsc.bcm.edu	37	chr19	10662945	10662945	+	Missense_Mutation	SNP	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	ggacccaagctgtaccgtggGcttctatgctggagacagga	9	8	14	10	1	1	1	0	0	1	1	1	4	1	3	2	4	3	4	2	4	3	3			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr19:10662945G>A	ENST00000309469.4	+	9	1360	c.1187G>A	c.(1186-1188)gGc>gAc	p.G396D	MIR1238_ENST00000408483.1_RNA|ATG4D_ENST00000540862.1_Missense_Mutation_p.G63D|RNU7-140P_ENST00000459546.1_RNA	NM_032885.4	NP_116274.3	Q86TL0	ATG4D_HUMAN	autophagy related 4D, cysteine peptidase	396					apoptotic process (GO:0006915)|autophagy (GO:0006914)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activity (GO:0004197)			NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	19			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)			TGTACCGTGGGCTTCTATGCT	0.612																																					p.G396D		Atlas-SNP	.											.	ATG4D	47	.	0			c.G1187A						PASS	.						72	64	66					19																	10662945		2203	4300	6503	SO:0001583	missense	84971	exon9			CCGTGGGCTTCTA	AJ312332	CCDS12241.1	19p13.2	2014-02-12	2012-06-06	2005-09-11	ENSG00000130734	ENSG00000130734			20789	protein-coding gene	gene with protein product		611340	"AUT-like 4, cysteine endopeptidase (S. cerevisiae)", "APG4 autophagy 4 homolog D (S. cerevisiae)", "ATG4 autophagy related 4 homolog D (S. cerevisiae)"	AUTL4, APG4D		12446702	Standard	NM_032885		Approved	APG4-D	uc002mov.3	Q86TL0	OTTHUMG00000180582	ENST00000309469.4:c.1187G>A	chr19.hg19:g.10662945G>A	ENSP00000311318:p.Gly396Asp	48.0	0.0	.		49.0	18.0	.	NM_032885	Q969K0	Missense_Mutation	SNP	ENST00000309469.4	hg19	CCDS12241.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.820094	0.90873	.	.	ENSG00000130734	ENST00000309469;ENST00000540862	T	0.56776	0.44	5.28	5.28	0.74379	.	0.049049	0.85682	D	0.000000	T	0.77438	0.4130	M	0.91768	3.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.82238	-0.0556	10	0.87932	D	0	-24.6618	13.7396	0.62840	0.0:0.1548:0.8452:0.0	.	333;396	B4DGM8;Q86TL0	.;ATG4D_HUMAN	D	396;63	ENSP00000311318:G396D	ENSP00000311318:G396D	G	+	2	0	ATG4D	10523945	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.438000	0.80431	2.635000	0.89317	0.561000	0.74099	GGC	.	.	.	none		0.612	ATG4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452022.1	NM_032885		A	10662945	G	A	10662945	3	1	261	1	0	0	0	0	1	0	0	0	1099	1203	42	2	1221	2	ATG4D	19	10662945	Missense_Mutation	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	2099043	10662945	48466038	82	16304											
DOCK6	57572	hgsc.bcm.edu	37	chr19	11358812	11358812	+	Missense_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	tggctctgggcggctacagcGttccacggcttcatcctgcc	4	10	12	15	3	2	0	1	0	1	0	4	0	4	0	3	4	3	4	3	4	1	3	rs546562962		TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr19:11358812G>A	ENST00000294618.7	-	7	747	c.736C>T	c.(736-738)Cgc>Tgc	p.R246C		NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	246					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						CGGCTACAGCGTTCCACGGCT	0.592													G|||	1	0.000199681	0	0	5008	,	,		16037	0.001		0	False		,,,				2504	0				p.R246C		Atlas-SNP	.											.	DOCK6	104	.	0			c.C736T						PASS	.						29	33	31					19																	11358812		1940	4127	6067	SO:0001583	missense	57572	exon7			TACAGCGTTCCAC		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.736C>T	chr19.hg19:g.11358812G>A	ENSP00000294618:p.Arg246Cys	44.0	0.0	.		51.0	17.0	.	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Missense_Mutation	SNP	ENST00000294618.7	hg19	CCDS45975.1	.	.	.	.	.	.	.	.	.	.	G	15.87	2.960106	0.53400	.	.	ENSG00000130158	ENST00000294618	T	0.18502	2.21	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.43033	0.1229	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.66351	0.943	T	0.46247	-0.9205	10	0.66056	D	0.02	-27.3549	15.4991	0.75680	0.0:0.0:1.0:0.0	.	246	Q96HP0	DOCK6_HUMAN	C	246	ENSP00000294618:R246C	ENSP00000294618:R246C	R	-	1	0	DOCK6	11219812	1.000000	0.71417	0.998000	0.56505	0.431000	0.31685	2.251000	0.43187	2.240000	0.73641	0.462000	0.41574	CGC	.	.	.	none		0.592	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812		A	11358812	G	A	11358812	3	1	261	1	0	0	0	0	1	0	0	0	4693	1145	40	1	5575	1	DOCK6	19	11358812	Missense_Mutation	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	695867	11358812	47770171	83	16305											
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-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	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	chr19.hg19:g.12502155T>G	ENSP00000411084:p.Lys353Gln	98.0	0.0	.		77.0	6.0	.	NM_001080821		Missense_Mutation	SNP	ENST00000430385.3	hg19	CCDS45989.1	.	.	.	.	.	.	.	.	.	.	G	0.033	-1.323810	0.01309	.	.	ENSG00000196466	ENST00000419318;ENST00000430385	T;T	0.04406	3.63;3.63	1.31	-1.61	0.08399	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02418	0.0074	N	0.12527	0.23	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.49041	-0.8980	9	0.14252	T	0.57	.	6.8386	0.23951	0.0:0.0:0.2963:0.7037	.	353	Q96GE5	ZN799_HUMAN	Q	321;353	ENSP00000415278:K321Q;ENSP00000411084:K353Q	ENSP00000415278:K321Q	K	-	1	0	ZNF799	12363155	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.687000	0.05156	-0.936000	0.03723	-1.919000	0.00516	AAA	.	.	.	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	261	1	0	0	0	0	1	0	0	0	18178	1792	62	5	878	5	ZNF799	19	12502155	Missense_Mutation	SNP	T	TCGA-UZ-A9PO-01A-11D-A382-10	1143343	12502155	46626828	84	16306											
GLT25D1	79709	hgsc.bcm.edu	37	chr19	17670124	17670124	+	Missense_Mutation	SNP	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	tcccctctccctgcagggtgGctacggaccacaacatggat	8	8	10	15	1	1	0	0	0	1	0	3	2	2	2	4	4	3	2	4	4	2	1			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr19:17670124G>A	ENST00000252599.4	+	2	385	c.265G>A	c.(265-267)Gct>Act	p.A89T		NM_024656.2	NP_078932.2	Q8NBJ5	GT251_HUMAN	collagen beta(1-O)galactosyltransferase 1	89					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)|membrane (GO:0016020)	procollagen galactosyltransferase activity (GO:0050211)										CTGCAGGGTGGCTACGGACCA	0.612																																					p.A89T		Atlas-SNP	.											.	.	.	.	0			c.G265A						PASS	.						133	97	109					19																	17670124		2129	4145	6274	SO:0001583	missense	79709	exon2			AGGGTGGCTACGG	AK075541	CCDS12363.1	19p13.11	2013-02-27	2013-02-27	2013-02-27	ENSG00000130309	ENSG00000130309			26182	protein-coding gene	gene with protein product			"glycosyltransferase 25 domain containing 1"	GLT25D1		19075007	Standard	NM_024656		Approved	FLJ22329	uc002nhc.1	Q8NBJ5		ENST00000252599.4:c.265G>A	chr19.hg19:g.17670124G>A	ENSP00000252599:p.Ala89Thr	81.0	0.0	.		88.0	25.0	.	NM_024656	Q8NC64	Missense_Mutation	SNP	ENST00000252599.4	hg19	CCDS12363.1	.	.	.	.	.	.	.	.	.	.	G	19.36	3.811846	0.70797	.	.	ENSG00000130309	ENST00000252599	D	0.85171	-1.95	3.65	3.65	0.41850	.	0.116516	0.56097	D	0.000023	D	0.90140	0.6919	M	0.74546	2.27	0.58432	D	0.999999	D	0.56287	0.975	D	0.65573	0.936	D	0.88542	0.3110	10	0.27082	T	0.32	-16.0455	13.2343	0.59961	0.0:0.0:1.0:0.0	.	89	Q8NBJ5	GT251_HUMAN	T	89	ENSP00000252599:A89T	ENSP00000252599:A89T	A	+	1	0	GLT25D1	17531124	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	9.636000	0.98440	1.773000	0.52216	0.423000	0.28283	GCT	.	.	.	none		0.612	COLGALT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464216.1	NM_024656		A	17670124	G	A	17670124	3	1	261	1	0	0	0	0	1	0	0	0	6473	1203	42	2	271	2	GLT25D1	19	17670124	Missense_Mutation	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	5167969	17670124	41458859	85	16307											
ZNF536	9745	hgsc.bcm.edu	37	chr19	31039335	31039335	+	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	tgaagaaggagaaggacatgAaggacaaagccctggctgac	16	4	14	7	0	0	5	0	3	0	2	0	8	0	7	1	4	1	1	1	4	5	0			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr19:31039335A>T	ENST00000355537.3	+	4	2956	c.2809A>T	c.(2809-2811)Aag>Tag	p.K937*		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	937					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)					GAAGGACATGAAGGACAAAGC	0.507																																					p.K937X		Atlas-SNP	.											.	ZNF536	424	.	0			c.A2809T						PASS	.						154	162	159					19																	31039335		2203	4300	6503	SO:0001587	stop_gained	9745	exon4			GACATGAAGGACA		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.2809A>T	chr19.hg19:g.31039335A>T	ENSP00000347730:p.Lys937*	48.0	0.0	.		70.0	16.0	.	NM_014717	A2RU18	Nonsense_Mutation	SNP	ENST00000355537.3	hg19	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	A	36	5.608908	0.96637	.	.	ENSG00000198597	ENST00000355537	.	.	.	5.42	4.41	0.53225	.	0.210674	0.50627	D	0.000108	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-32.4704	11.24	0.48964	0.9279:0.0:0.0721:0.0	.	.	.	.	X	937	.	ENSP00000347730:K937X	K	+	1	0	ZNF536	35731175	1.000000	0.71417	0.897000	0.35233	0.918000	0.54935	4.613000	0.61176	0.890000	0.36211	0.402000	0.26972	AAG	.	.	.	none		0.507	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		T	31039335	A	T	31039335	4	4	261	1	0	0	0	0	0	1	0	0	17986	247	9	5	2819	5	ZNF536	19	31039335	Nonsense_Mutation	SNP	A	TCGA-UZ-A9PO-01A-11D-A382-10	13369211	31039335	28089648	86	16308											
GPATCH1	55094	hgsc.bcm.edu	37	chr19	33597758	33597758	+	Missense_Mutation	SNP	T	T	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	gacacacagtaagcaccaacTgaatgcctccaaacgggctg	14	5	9	13	1	0	1	0	1	0	0	1	2	1	1	3	1	4	3	3	1	4	1			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr19:33597758T>G	ENST00000170564.2	+	10	1552	c.1238T>G	c.(1237-1239)cTg>cGg	p.L413R		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	413					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)					AAGCACCAACTGAATGCCTCC	0.493																																					p.L413R	Pancreas(67;88 1713 4567 18227)	Atlas-SNP	.											.	GPATCH1	79	.	0			c.T1238G						PASS	.						102	78	86					19																	33597758		2203	4300	6503	SO:0001583	missense	55094	exon10			ACCAACTGAATGC	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.1238T>G	chr19.hg19:g.33597758T>G	ENSP00000170564:p.Leu413Arg	113.0	0.0	.		137.0	51.0	.	NM_018025	Q8IZV6|Q8N3B7|Q9NW94	Missense_Mutation	SNP	ENST00000170564.2	hg19	CCDS12428.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.411269	0.83340	.	.	ENSG00000076650	ENST00000170564	T	0.37915	1.17	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.65322	0.2680	M	0.87381	2.88	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.72117	-0.4387	10	0.72032	D	0.01	-9.9437	14.873	0.70474	0.0:0.0:0.0:1.0	.	413	Q9BRR8	GPTC1_HUMAN	R	413	ENSP00000170564:L413R	ENSP00000170564:L413R	L	+	2	0	GPATCH1	38289598	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	6.656000	0.74396	2.175000	0.68902	0.533000	0.62120	CTG	.	.	.	none		0.493	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025		G	33597758	T	G	33597758	3	3	261	1	0	0	0	0	1	0	0	0	6597	1580	55	5	1276	5	GPATCH1	19	33597758	Missense_Mutation	SNP	T	TCGA-UZ-A9PO-01A-11D-A382-10	2558423	33597758	25531225	87	16309											
ZNF790	388536	hgsc.bcm.edu	37	chr19	37314679	37314679	+	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	agaaatctacagccacatccCtgaacatcatcaactgttgg	14	9	6	12	0	3	2	2	1	1	1	4	2	4	2	2	1	4	1	2	1	4	2			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr19:37314679C>T	ENST00000356725.4	-	3	143	c.23G>A	c.(22-24)aGg>aAg	p.R8K	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	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)|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)			AGCCACATCCCTGAACATCAT	0.388																																					p.R8K		Atlas-SNP	.											.	ZNF790	89	.	0			c.G23A						PASS	.						76	75	75					19																	37314679		2203	4300	6503	SO:0001583	missense	388536	exon3			ACATCCCTGAACA	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.23G>A	chr19.hg19:g.37314679C>T	ENSP00000349161:p.Arg8Lys	113.0	0.0	.		78.0	12.0	.	NM_206894		Missense_Mutation	SNP	ENST00000356725.4	hg19	CCDS12496.1	.	.	.	.	.	.	.	.	.	.	C	15.12	2.739068	0.49045	.	.	ENSG00000197863	ENST00000356725;ENST00000528994;ENST00000525288;ENST00000527645	T;T;T;T	0.01369	4.97;4.97;4.97;4.97	3.53	-0.991	0.10235	Krueppel-associated box (4);	.	.	.	.	T	0.01029	0.0034	N	0.25286	0.73	0.22127	N	0.999348	B	0.14012	0.009	B	0.18561	0.022	T	0.48422	-0.9037	9	0.10902	T	0.67	.	5.9232	0.19094	0.0:0.4735:0.0:0.5265	.	8	Q6PG37	ZN790_HUMAN	K	8	ENSP00000349161:R8K;ENSP00000435944:R8K;ENSP00000433389:R8K;ENSP00000434537:R8K	ENSP00000349161:R8K	R	-	2	0	ZNF790	42006519	0.025000	0.19082	0.467000	0.27180	0.667000	0.39255	-0.407000	0.07178	0.006000	0.14734	0.585000	0.79938	AGG	.	.	.	none		0.388	ZNF790-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385341.2	NM_206894		T	37314679	C	T	37314679	3	4	261	1	0	0	0	0	1	0	0	0	18174	681	24	2	1899	2	ZNF790	19	37314679	Missense_Mutation	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	3716921	37314679	21814304	88	16310											
PLD3	23646	hgsc.bcm.edu	37	chr19	40883752	40883752	+	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	atcccatatgcccgtgtcaaCcacaacaagtacatggtgac	13	8	7	13	1	1	1	1	1	0	0	2	1	2	1	3	1	4	1	3	1	5	2			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr19:40883752C>G	ENST00000409587.1	+	12	1642	c.1245C>G	c.(1243-1245)aaC>aaG	p.N415K	PLD3_ENST00000409419.1_Missense_Mutation_p.N415K|PLD3_ENST00000409281.1_Missense_Mutation_p.N415K|PLD3_ENST00000356508.5_Missense_Mutation_p.N415K|PLD3_ENST00000409735.4_Missense_Mutation_p.N415K			Q8IV08	PLD3_HUMAN	phospholipase D family, member 3	415	PLD phosphodiesterase 2. {ECO:0000255|PROSITE-ProRule:PRU00153}.				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)			CCCGTGTCAACCACAACAAGT	0.602																																					p.N415K		Atlas-SNP	.											.	PLD3	71	.	0			c.C1245G						PASS	.						85	68	74					19																	40883752		2203	4300	6503	SO:0001583	missense	23646	exon12			TGTCAACCACAAC	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.1245C>G	chr19.hg19:g.40883752C>G	ENSP00000387050:p.Asn415Lys	125.0	0.0	.		117.0	39.0	.	NM_012268	Q92853|Q9BW87	Missense_Mutation	SNP	ENST00000409587.1	hg19	CCDS33027.1	.	.	.	.	.	.	.	.	.	.	C	19.81	3.896740	0.72639	.	.	ENSG00000105223	ENST00000409419;ENST00000409587;ENST00000356508;ENST00000409735;ENST00000409281	T;T;T;T;T	0.54071	0.59;0.59;0.59;0.59;0.59	4.96	1.68	0.24146	Phospholipase D/Transphosphatidylase (2);	0.047083	0.85682	D	0.000000	T	0.68229	0.2978	M	0.92833	3.35	0.58432	D	0.999999	P	0.50819	0.939	P	0.55087	0.768	T	0.69480	-0.5134	10	0.72032	D	0.01	-12.6506	6.2698	0.20949	0.0:0.6146:0.0:0.3854	.	415	Q8IV08	PLD3_HUMAN	K	415	ENSP00000386293:N415K;ENSP00000387050:N415K;ENSP00000348901:N415K;ENSP00000386938:N415K;ENSP00000387022:N415K	ENSP00000348901:N415K	N	+	3	2	PLD3	45575592	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	1.648000	0.37271	0.609000	0.30018	-0.136000	0.14681	AAC	.	.	.	none		0.602	PLD3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327721.1	NM_012268		G	40883752	C	G	40883752	3	3	261	1	0	0	0	0	1	0	0	0	12054	506	18	4	1283	4	PLD3	19	40883752	Missense_Mutation	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	3569073	40883752	18245231	89	16311											
PAFAH1B3	5050	hgsc.bcm.edu	37	chr19	42804227	42804227	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtccgtggttgttggtgccCacccagaccaccacaatctg	7	10	10	14	1	1	1	0	0	1	1	2	1	2	1	5	2	1	2	5	2	1	2			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr19:42804227C>T	ENST00000262890.3	-	4	564	c.303G>A	c.(301-303)gtG>gtA	p.V101V	PRR19_ENST00000341747.3_5'Flank|PRR19_ENST00000598490.1_5'Flank|PAFAH1B3_ENST00000538771.1_Silent_p.V101V	NM_002573.3	NP_002564.1	Q15102	PA1B3_HUMAN	platelet-activating factor acetylhydrolase 1b, catalytic subunit 3 (29kDa)	101					brain development (GO:0007420)|lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|nervous system development (GO:0007399)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)			breast(1)|large_intestine(2)|ovary(1)	4		Prostate(69;0.0704)				TGTTGGTGCCCACCCAGACCA	0.587																																					p.V101V		Atlas-SNP	.											.	PAFAH1B3	12	.	0			c.G303A						PASS	.						112	103	106					19																	42804227		2203	4300	6503	SO:0001819	synonymous_variant	5050	exon5			GGTGCCCACCCAG	D63391	CCDS12602.1	19q13.1	2011-10-24	2010-02-10			ENSG00000079462			8576	protein-coding gene	gene with protein product	"PAF-AH1b alpha 1 subunit"	603074	"platelet-activating factor acetylhydrolase, isoform Ib, gamma subunit (29kD)", "platelet-activating factor acetylhydrolase, isoform Ib, gamma subunit 29kDa", "platelet-activating factor acetylhydrolase, isoform Ib, subunit 3 (29kDa)"			7669037	Standard	NM_002573		Approved		uc010xwj.1	Q15102		ENST00000262890.3:c.303G>A	chr19.hg19:g.42804227C>T		61.0	0.0	.		91.0	20.0	.	NM_001145940	Q53X88	Silent	SNP	ENST00000262890.3	hg19	CCDS12602.1																																																																																			.	.	.	none		0.587	PAFAH1B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463726.1	NM_002573		T	42804227	C	T	42804227	2	4	261	1	0	0	0	0	0	0	0	1	11393	581	21	2		2	PAFAH1B3	19	42804227	Silent	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	1920475	42804227	16324756	90	16312											
MEGF8	1954	hgsc.bcm.edu	37	chr19	42873075	42873075	+	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	agtgtgcaaacgggcaccacGactgcaacgagacgcagaat	14	4	12	11	4	0	2	0	0	0	2	0	4	0	2	1	1	4	4	1	1	3	0	rs374088709		TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr19:42873075G>A	ENST00000251268.6	+	37	6562	c.6562G>A	c.(6562-6564)Gac>Aac	p.D2188N	MEGF8_ENST00000334370.4_Missense_Mutation_p.D2121N|MEGF8_ENST00000378073.4_5'Flank	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	2188	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)				CGGGCACCACGACTGCAACGA	0.647																																					p.D2188N		Atlas-SNP	.											.	MEGF8	358	.	0			c.G6562A						PASS	.	G	ASN/ASP	0,4406		0,0,2203	85	88	87		6361	4.8	1	19		87	1,8599	1.2+/-3.3	0,1,4299	no	missense	MEGF8	NM_001410.2	23	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	2121/2779	42873075	1,13005	2203	4300	6503	SO:0001583	missense	1954	exon37			CACCACGACTGCA	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.6562G>A	chr19.hg19:g.42873075G>A	ENSP00000251268:p.Asp2188Asn	74.0	0.0	.		76.0	26.0	.	NM_001271938	A8KAY0|O75097	Missense_Mutation	SNP	ENST00000251268.6	hg19		.	.	.	.	.	.	.	.	.	.	G	8.552	0.875736	0.17395	0.0	1.16E-4	ENSG00000105429	ENST00000334370;ENST00000251268	T;T	0.40756	1.02;1.02	4.76	4.76	0.60689	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.168758	0.39475	N	0.001349	T	0.17874	0.0429	N	0.01817	-0.705	0.80722	D	1	P;P	0.46327	0.499;0.876	B;B	0.39738	0.048;0.308	T	0.16958	-1.0385	10	0.08837	T	0.75	-29.0533	16.9259	0.86176	0.0:0.0:1.0:0.0	.	2188;2121	Q7Z7M0;Q7Z7M0-2	MEGF8_HUMAN;.	N	2121;2188	ENSP00000334219:D2121N;ENSP00000251268:D2188N	ENSP00000251268:D2188N	D	+	1	0	MEGF8	47564915	1.000000	0.71417	0.989000	0.46669	0.248000	0.25809	4.142000	0.58044	2.375000	0.81037	0.561000	0.74099	GAC	.	.	.	weak		0.647	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		A	42873075	G	A	42873075	3	1	261	1	0	0	0	0	1	0	0	0	9470	1058	37	1	6503	1	MEGF8	19	42873075	Missense_Mutation	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	68848	42873075	16255908	91	16313											
PTH2	113091	hgsc.bcm.edu	37	chr19	49926468	49926468	+	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	agttctgggactggcacctaCctgaggaccccgaccggggg	7	6	15	13	2	1	1	0	1	1	0	1	4	1	3	5	5	1	2	5	5	1	2			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr19:49926468C>A	ENST00000270631.1	-	1	230		c.e1+1		CTD-3148I10.1_ENST00000576655.1_5'Flank	NM_178449.3	NP_848544.1	Q96A98	TIP39_HUMAN	parathyroid hormone 2						neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(262;0.0015)|GBM - Glioblastoma multiforme(486;0.044)|Lung(386;0.0785)|LUSC - Lung squamous cell carcinoma(496;0.0836)		CTGGCACCTACCTGAGGACCC	0.647																																					.		Atlas-SNP	.											.	PTH2	20	.	0			c.128+1G>T						PASS	.						25	32	30					19																	49926468		2203	4298	6501	SO:0001630	splice_region_variant	113091	exon2			CACCTACCTGAGG	AY037555	CCDS12763.1	19q13.33	2013-02-28				ENSG00000142538		"Endogenous ligands"	30828	protein-coding gene	gene with protein product	"tuberoinfundibular 39 residues"	608386				11861531	Standard	NM_178449		Approved	TIP39	uc002pnn.1	Q96A98		ENST00000270631.1:c.128+1G>T	chr19.hg19:g.49926468C>A		158.0	0.0	.		182.0	21.0	.	NM_178449	Q96DJ4	Splice_Site	SNP	ENST00000270631.1	hg19	CCDS12763.1	.	.	.	.	.	.	.	.	.	.	C	13.36	2.213488	0.39102	.	.	ENSG00000142538	ENST00000270631	.	.	.	4.17	3.04	0.35103	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.6353	0.45560	0.1924:0.8076:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PTH2	54618280	1.000000	0.71417	0.901000	0.35422	0.274000	0.26718	1.941000	0.40233	2.047000	0.60756	0.306000	0.20318	.	.	.	.	none		0.647	PTH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465366.1	NM_178449	Intron	A	49926468	C	A	49926468	5	1	261	1	0	0	0	0	0	0	1	0	12770	521	18	4	181	4	PTH2	19	49926468	Splice_Site	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	7053393	49926468	9202515	92	16314											
SCAF1	58506	hgsc.bcm.edu	37	chr19	50161046	50161046	+	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	gaagctgcacacgcaggagcGggcggtggaggaggtgaagc	10	3	20	8	3	0	1	0	1	0	0	0	5	0	4	0	6	4	3	0	6	2	0			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr19:50161046G>T	ENST00000360565.3	+	10	3771	c.3647G>T	c.(3646-3648)cGg>cTg	p.R1216L	IRF3_ENST00000599680.1_5'Flank	NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	1216	Necessary for interaction with the CTD domain of POLR2A.				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)		ACGCAGGAGCGGGCGGTGGAG	0.587																																					p.R1216L		Atlas-SNP	.											.	SCAF1	78	.	0			c.G3647T						PASS	.						68	49	56					19																	50161046		2203	4300	6503	SO:0001583	missense	58506	exon10			AGGAGCGGGCGGT	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.3647G>T	chr19.hg19:g.50161046G>T	ENSP00000353769:p.Arg1216Leu	137.0	0.0	.		138.0	34.0	.	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Missense_Mutation	SNP	ENST00000360565.3	hg19	CCDS33074.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.159295	0.78226	.	.	ENSG00000126461	ENST00000360565	T	0.56103	0.48	5.2	4.16	0.48862	.	0.105611	0.36591	N	0.002502	T	0.65302	0.2678	M	0.62088	1.915	0.52501	D	0.999958	D	0.61080	0.989	P	0.60789	0.879	T	0.69487	-0.5132	10	0.87932	D	0	-18.7043	12.7901	0.57528	0.0803:0.0:0.9197:0.0	.	1216	Q9H7N4	SFR19_HUMAN	L	1216	ENSP00000353769:R1216L	ENSP00000353769:R1216L	R	+	2	0	SCAF1	54852858	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.326000	0.72905	1.426000	0.47256	0.637000	0.83480	CGG	.	.	.	none		0.587	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228		T	50161046	G	T	50161046	3	4	261	1	0	0	0	0	1	0	0	0	13881	1116	39	4	3681	4	SCAF1	19	50161046	Missense_Mutation	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	234578	50161046	8967937	93	16315											
PTOV1	53635	hgsc.bcm.edu	37	chr19	50357983	50357983	+	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	caagcctacgtgaaccaaggCgagaacctgtgagtgccggg	11	5	14	11	3	0	3	0	2	0	1	0	4	0	3	4	2	5	0	4	2	5	1	rs149977568		TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr19:50357983C>T	ENST00000601675.1	+	3	488	c.384C>T	c.(382-384)ggC>ggT	p.G128G	PTOV1_ENST00000391842.1_Silent_p.G128G|PTOV1_ENST00000599732.1_Silent_p.G128G|PTOV1_ENST00000221557.9_Silent_p.G96G|AC018766.6_ENST00000601211.1_RNA|PTOV1_ENST00000601638.1_Silent_p.G96G|MIR4749_ENST00000578197.1_RNA|PTOV1_ENST00000598325.1_3'UTR|PTOV1_ENST00000600603.1_Silent_p.G96G|AC018766.5_ENST00000593654.1_RNA			Q86YD1	PTOV1_HUMAN	prostate tumor overexpressed 1	128					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)		TGAACCAAGGCGAGAACCTGT	0.667																																					p.G128G		Atlas-SNP	.											PTOV1,colon,carcinoma,0,1	PTOV1	41	.	0			c.C384T						PASS	.	C		0,4406		0,0,2203	41	41	41		384	0.8	1	19	dbSNP_134	41	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PTOV1	NM_017432.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		128/417	50357983	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	53635	exon3			CCAAGGCGAGAAC	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.384C>T	chr19.hg19:g.50357983C>T		83.0	0.0	.		81.0	27.0	.	NM_017432	Q6UXX7|Q96BU3|Q9HBN4|Q9NYL1	Silent	SNP	ENST00000601675.1	hg19	CCDS12782.1																																																																																			.	C|1.000;T|0.000	0.000	weak		0.667	PTOV1-007	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465347.1	NM_017432		T	50357983	C	T	50357983	2	4	261	1	0	0	0	0	0	0	0	1	12780	755	27	1		1	PTOV1	19	50357983	Silent	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	196937	50357983	8771000	94	16316											
ZNF468	90333	hgsc.bcm.edu	37	chr19	53344638	53344638	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgactgaaaactttgtcacaTtcttcacattcataaggttt	12	15	5	9	1	4	1	3	1	1	0	4	2	4	1	0	1	1	1	0	1	3	6			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr19:53344638T>C	ENST00000595646.1	-	4	1029	c.909A>G	c.(907-909)gaA>gaG	p.E303E	ZNF468_ENST00000243639.4_3'UTR|ZNF468_ENST00000390651.4_Silent_p.E250E|ZNF468_ENST00000396409.4_Silent_p.E250E|ZNF28_ENST00000594602.1_Intron			Q5VIY5	ZN468_HUMAN	zinc finger protein 468	303					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(3)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(134;0.0358)		CTTTGTCACATTCTTCACATT	0.393																																					p.E303E		Atlas-SNP	.											.	ZNF468	46	.	0			c.A909G						PASS	.						124	124	124					19																	53344638		2203	4300	6503	SO:0001819	synonymous_variant	90333	exon4			GTCACATTCTTCA	AK023558	CCDS33094.1, CCDS62781.1	19q13.41	2013-01-08				ENSG00000204604		"Zinc fingers, C2H2-type", "-"	33105	protein-coding gene	gene with protein product						16144304	Standard	NM_001277120		Approved		uc002qaf.3	Q5VIY5		ENST00000595646.1:c.909A>G	chr19.hg19:g.53344638T>C		64.0	0.0	.		57.0	17.0	.	NM_001008801	A8MV20|Q5CZB8|Q5VIY4|Q68DI7	Silent	SNP	ENST00000595646.1	hg19	CCDS33094.1																																																																																			.	.	.	none		0.393	ZNF468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463098.1	NM_001008801		C	53344638	T	C	53344638	2	2	261	1	0	0	0	0	0	0	0	1	17940	1490	52	3		3	ZNF468	19	53344638	Silent	SNP	T	TCGA-UZ-A9PO-01A-11D-A382-10	2986655	53344638	5784345	95	16317											
C20orf96	140680	hgsc.bcm.edu	37	chr20	270903	270903	+	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	agtcccccaagactcaccggAacctggaactcctggactat	11	7	8	15	1	1	1	1	0	0	1	3	4	3	4	5	3	2	0	5	3	4	1			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr20:270903A>T	ENST00000360321.2	-	2	204	c.66T>A	c.(64-66)gtT>gtA	p.V22V	C20orf96_ENST00000400269.3_Intron|C20orf96_ENST00000382369.5_Missense_Mutation_p.S27T	NM_080571.1|NM_153269.2	NP_542138.1|NP_695001.2	Q9NUD7	CT096_HUMAN	chromosome 20 open reading frame 96	22										endometrium(3)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	12		all_cancers(10;0.00959)|Lung NSC(37;0.227)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			GACTCACCGGAACCTGGAACT	0.602																																					p.V22V		Atlas-SNP	.											.	C20orf96	28	.	0			c.T66A						PASS	.						43	35	38					20																	270903		2203	4299	6502	SO:0001819	synonymous_variant	140680	exon2			CACCGGAACCTGG	AL034548	CCDS12994.1, CCDS74685.1	20p13	2012-10-30			ENSG00000196476	ENSG00000196476			16227	protein-coding gene	gene with protein product							Standard	NM_153269		Approved	dJ1103G7.2	uc002wde.2	Q9NUD7	OTTHUMG00000031626	ENST00000360321.2:c.66T>A	chr20.hg19:g.270903A>T		93.0	0.0	.		133.0	47.0	.	NM_153269	A3KPE0|B2RPH9|Q8N840|Q8NAX5	Silent	SNP	ENST00000360321.2	hg19	CCDS12994.1	.	.	.	.	.	.	.	.	.	.	A	9.570	1.120835	0.20877	.	.	ENSG00000196476	ENST00000382369	T	0.48201	0.82	3.72	1.3	0.21679	.	.	.	.	.	T	0.31199	0.0789	.	.	.	0.09310	N	0.999993	B;B	0.18461	0.028;0.028	B;B	0.19148	0.024;0.013	T	0.22556	-1.0213	8	0.45353	T	0.12	-8.7257	4.0059	0.09600	0.5699:0.2091:0.0:0.221	.	27;27	B7Z971;Q5JYC3	.;.	T	27	ENSP00000371806:S27T	ENSP00000371806:S27T	S	-	1	0	C20orf96	218903	0.042000	0.20092	0.001000	0.08648	0.004000	0.04260	0.982000	0.29539	0.240000	0.21263	0.454000	0.30748	TCC	.	.	.	none		0.602	C20orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077439.2	NM_153269		T	270903	A	T	270903	2	4	261	1	0	0	0	0	0	0	0	1	2124	233	9	5		5	C20orf96	20	270903	Silent	SNP	A	TCGA-UZ-A9PO-01A-11D-A382-10		270903	62754617	96	16318											
PI3	5266	hgsc.bcm.edu	37	chr20	43804687	43804687	+	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	ggtgcgccatgttgaatcccCctaaccgctgcttgaaagat	9	10	10	12	2	0	3	0	2	0	1	1	3	1	3	4	1	3	3	4	1	3	3			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr20:43804687C>A	ENST00000243924.3	+	2	312	c.265C>A	c.(265-267)Cct>Act	p.P89T		NM_002638.3	NP_002629.1	P19957	ELAF_HUMAN	peptidase inhibitor 3, skin-derived	89	WAP. {ECO:0000255|PROSITE- ProRule:PRU00722}.				copulation (GO:0007620)|negative regulation of endopeptidase activity (GO:0010951)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			large_intestine(1)|lung(5)|skin(1)	7		Myeloproliferative disorder(115;0.0122)				GTTGAATCCCCCTAACCGCTG	0.527																																					p.P89T		Atlas-SNP	.											.	PI3	21	.	0			c.C265A						PASS	.						125	111	115					20																	43804687		2203	4300	6503	SO:0001583	missense	5266	exon2			AATCCCCCTAACC	D13156	CCDS13344.1	20q13.12	2013-01-21	2008-10-03		ENSG00000124102	ENSG00000124102		"WAP four-disulfide core domain containing"	8947	protein-coding gene	gene with protein product	"skin-derived antileukoproteinase", "trappin-2"	182257	"protease inhibitor 3, skin-derived (SKALP)"			8287685, 12206714	Standard	NM_002638		Approved	ESI, SKALP, ELAFIN, WAP3, WFDC14, cementoin	uc002xng.3	P19957	OTTHUMG00000032567	ENST00000243924.3:c.265C>A	chr20.hg19:g.43804687C>A	ENSP00000243924:p.Pro89Thr	120.0	0.0	.		152.0	64.0	.	NM_002638	E1P618|Q6FG74	Missense_Mutation	SNP	ENST00000243924.3	hg19	CCDS13344.1	.	.	.	.	.	.	.	.	.	.	C	13.89	2.371223	0.42003	.	.	ENSG00000124102	ENST00000243924	T	0.21543	2.0	4.49	0.108	0.14548	Whey acidic protein, 4-disulphide core (5);	0.000000	0.42682	D	0.000668	T	0.28699	0.0711	M	0.77103	2.36	0.09310	N	1	D	0.52996	0.957	P	0.52646	0.705	T	0.11792	-1.0573	10	0.51188	T	0.08	.	3.0572	0.06188	0.3109:0.4474:0.1512:0.0906	.	89	P19957	ELAF_HUMAN	T	89	ENSP00000243924:P89T	ENSP00000243924:P89T	P	+	1	0	PI3	43238101	0.000000	0.05858	0.000000	0.03702	0.049000	0.14656	0.424000	0.21330	-0.037000	0.13646	0.650000	0.86243	CCT	.	.	.	none		0.527	PI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079418.3	NM_002638		A	43804687	C	A	43804687	3	1	261	1	0	0	0	0	1	0	0	0	11877	623	22	4	271	4	PI3	20	43804687	Missense_Mutation	SNP	C	TCGA-UZ-A9PO-01A-11D-A382-10	43533784	43804687	19220833	97	16319											
CASS4	57091	hgsc.bcm.edu	37	chr20	55028020	55028020	+	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	cggaactgtgaaaaggaagaGactgtgcagttgaccccaaa	15	6	12	8	1	0	3	0	2	0	1	0	6	0	5	2	2	2	2	2	2	5	1			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr20:55028020G>C	ENST00000360314.3	+	6	2013	c.1788G>C	c.(1786-1788)gaG>gaC	p.E596D	CASS4_ENST00000371336.3_Missense_Mutation_p.E596D|CASS4_ENST00000434344.1_Intron	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	596					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						AAAAGGAAGAGACTGTGCAGT	0.453																																					p.E596D		Atlas-SNP	.											.	CASS4	121	.	0			c.G1788C						PASS	.						83	85	84					20																	55028020		2203	4300	6503	SO:0001583	missense	57091	exon5			GGAAGAGACTGTG	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.1788G>C	chr20.hg19:g.55028020G>C	ENSP00000353462:p.Glu596Asp	105.0	0.0	.		129.0	29.0	.	NM_020356	E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Missense_Mutation	SNP	ENST00000360314.3	hg19	CCDS33492.1	.	.	.	.	.	.	.	.	.	.	G	8.770	0.925662	0.18056	.	.	ENSG00000087589	ENST00000360314;ENST00000371336	T;T	0.14640	2.49;2.49	6.08	0.544	0.17185	.	0.532223	0.21203	N	0.078421	T	0.08980	0.0222	L	0.29908	0.895	0.19775	N	0.999955	B;B;B	0.25048	0.011;0.096;0.117	B;B;B	0.31812	0.022;0.083;0.136	T	0.35871	-0.9771	10	0.23891	T	0.37	-13.133	5.4087	0.16336	0.0614:0.1971:0.2921:0.4494	.	542;596;596	B4DII4;Q9NQ75-2;Q9NQ75	.;.;CASS4_HUMAN	D	596	ENSP00000353462:E596D;ENSP00000360387:E596D	ENSP00000353462:E596D	E	+	3	2	CASS4	54461427	0.006000	0.16342	0.003000	0.11579	0.431000	0.31685	-0.032000	0.12266	-0.097000	0.12307	0.591000	0.81541	GAG	.	.	.	none		0.453	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079789.2	NM_020356		C	55028020	G	C	55028020	3	2	261	1	0	0	0	0	1	0	0	0	2685	933	33	4	1806	4	CASS4	20	55028020	Missense_Mutation	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	11223333	55028020	7997500	98	16320											
CTCFL	140690	hgsc.bcm.edu	37	chr20	56098318	56098318	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagccaataactggttcttcTcctgctcttcctcgagctaa	8	13	6	14	1	3	0	0	0	3	0	6	1	4	0	3	1	4	3	3	1	3	5			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr20:56098318T>C	ENST00000608263.1	-	2	1221	c.560A>G	c.(559-561)gAg>gGg	p.E187G	CTCFL_ENST00000502686.2_Intron|CTCFL_ENST00000608425.1_Missense_Mutation_p.E187G|CTCFL_ENST00000608158.1_Missense_Mutation_p.E187G|CTCFL_ENST00000608858.1_Intron|CTCFL_ENST00000432255.2_Missense_Mutation_p.E187G|CTCFL_ENST00000422869.2_Missense_Mutation_p.E187G|CTCFL_ENST00000609232.1_Missense_Mutation_p.E187G|CTCFL_ENST00000608903.1_Intron|CTCFL_ENST00000539382.1_5'UTR|CTCFL_ENST00000608440.1_Missense_Mutation_p.E187G|CTCFL_ENST00000371196.2_Missense_Mutation_p.E187G|CTCFL_ENST00000429804.3_Missense_Mutation_p.E187G|CTCFL_ENST00000243914.3_Missense_Mutation_p.E187G|CTCFL_ENST00000423479.3_Missense_Mutation_p.E187G|CTCFL_ENST00000481655.2_Missense_Mutation_p.E187G|CTCFL_ENST00000433949.3_5'UTR	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	187					cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			CTGGTTCTTCTCCTGCTCTTC	0.353																																					p.E187G		Atlas-SNP	.											.	CTCFL	97	.	0			c.A560G						PASS	.						109	107	108					20																	56098318		2202	4300	6502	SO:0001583	missense	140690	exon2			TTCTTCTCCTGCT		CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"Zinc fingers, C2H2-type"	16234	protein-coding gene	gene with protein product	"cancer/testis antigen 27"	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.560A>G	chr20.hg19:g.56098318T>C	ENSP00000476783:p.Glu187Gly	99.0	0.0	.		104.0	46.0	.	NM_001269044	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Missense_Mutation	SNP	ENST00000608263.1	hg19	CCDS13459.1	.	.	.	.	.	.	.	.	.	.	T	15.18	2.758101	0.49468	.	.	ENSG00000124092	ENST00000423479;ENST00000243914;ENST00000371196;ENST00000429804;ENST00000433949;ENST00000422109;ENST00000426658;ENST00000432255;ENST00000422869	T;T;T;T;T;T;T;T;T	0.12569	2.67;2.69;2.69;2.85;2.73;3.0;2.71;3.3;2.74	4.43	-1.1	0.09872	.	0.000000	0.36665	N	0.002471	T	0.18299	0.0439	M	0.64997	1.995	0.09310	N	1	B;D;D;D;B;D;B;B	0.64830	0.005;0.994;0.986;0.988;0.006;0.986;0.006;0.006	B;P;P;P;B;P;B;B	0.57204	0.004;0.755;0.617;0.815;0.002;0.722;0.008;0.005	T	0.10086	-1.0645	10	0.30078	T	0.28	-5.3288	3.0409	0.06138	0.3026:0.1863:0.0:0.5111	.	187;187;187;187;187;187;187;187	A6XGM3;A6XGM0;A6XGM9;A6XGM8;A6XGM2;E7EUE3;A6XGL8;Q8NI51	.;.;.;.;.;.;.;CTCFL_HUMAN	G	187	ENSP00000415579:E187G;ENSP00000243914:E187G;ENSP00000360239:E187G;ENSP00000415329:E187G;ENSP00000392034:E187G;ENSP00000413713:E187G;ENSP00000403369:E187G;ENSP00000409344:E187G;ENSP00000399061:E187G	ENSP00000243914:E187G	E	-	2	0	CTCFL	55531724	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	0.332000	0.19751	0.112000	0.17975	-0.353000	0.07706	GAG	.	.	.	none		0.353	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618		C	56098318	T	C	56098318	3	2	261	1	0	0	0	0	1	0	0	0	4003	1551	54	3	1467	3	CTCFL	20	56098318	Missense_Mutation	SNP	T	TCGA-UZ-A9PO-01A-11D-A382-10	1070298	56098318	6927202	99	16321											
USP25	29761	hgsc.bcm.edu	37	chr21	17250242	17250242	+	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	actggtggatgaaatggaagAaaaggatatactagctgtag	16	9	13	3	0	0	2	0	1	0	1	0	5	0	5	0	4	2	2	0	4	8	4			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr21:17250242A>T	ENST00000285679.6	+	23	3296	c.2927A>T	c.(2926-2928)gAa>gTa	p.E976V	USP25_ENST00000351097.5_Missense_Mutation_p.E371V|USP25_ENST00000400183.2_Missense_Mutation_p.E1046V|USP25_ENST00000285681.2_Missense_Mutation_p.E1008V	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	976					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)		GAAATGGAAGAAAAGGATATA	0.373																																					p.E976V		Atlas-SNP	.											.	USP25	156	.	0			c.A2927T						PASS	.						109	111	110					21																	17250242		2203	4300	6503	SO:0001583	missense	29761	exon23			TGGAAGAAAAGGA	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.2927A>T	chr21.hg19:g.17250242A>T	ENSP00000285679:p.Glu976Val	189.0	0.0	.		175.0	43.0	.	NM_013396	C0LSZ0|Q6DHZ9|Q9H9W1	Missense_Mutation	SNP	ENST00000285679.6	hg19	CCDS33515.1	.	.	.	.	.	.	.	.	.	.	A	16.80	3.222083	0.58560	.	.	ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000351097;ENST00000400183	T;T;T;T	0.34472	1.77;1.78;1.36;1.77	5.67	4.52	0.55395	.	0.138081	0.64402	D	0.000004	T	0.49029	0.1533	L	0.51422	1.61	0.49483	D	0.999797	P;D;P;P	0.61697	0.868;0.99;0.696;0.938	B;P;B;B	0.61477	0.408;0.889;0.283;0.446	T	0.47302	-0.9128	10	0.62326	D	0.03	-14.8111	11.4049	0.49892	0.9285:0.0:0.0715:0.0	.	1046;371;1008;976	Q9UHP3-3;Q96B65;Q9UHP3-1;Q9UHP3	.;.;.;UBP25_HUMAN	V	1008;976;371;1046	ENSP00000285681:E1008V;ENSP00000285679:E976V;ENSP00000299574:E371V;ENSP00000383044:E1046V	ENSP00000285679:E976V	E	+	2	0	USP25	16172113	1.000000	0.71417	1.000000	0.80357	0.195000	0.23768	5.898000	0.69838	0.982000	0.38575	-0.297000	0.09499	GAA	.	.	.	none		0.373	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			T	17250242	A	T	17250242	3	4	261	1	0	0	0	0	1	0	0	0	17068	246	9	5	3017	5	USP25	21	17250242	Missense_Mutation	SNP	A	TCGA-UZ-A9PO-01A-11D-A382-10		17250242	30879653	100	16322											
TRPM2	7226	hgsc.bcm.edu	37	chr21	45789155	45789155	+	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	tgagcagcagctacaaggaaGgcgagctcatcaccatcgga	13	5	12	11	2	2	1	2	1	0	0	3	4	2	3	1	3	5	4	1	3	3	1			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr21:45789155G>C	ENST00000397928.1	+	5	1145	c.700G>C	c.(700-702)Ggc>Cgc	p.G234R	TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000397932.2_Missense_Mutation_p.G234R|TRPM2_ENST00000300481.9_Missense_Mutation_p.G234R|TRPM2_ENST00000300482.5_Missense_Mutation_p.G234R	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	234					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						CTACAAGGAAGGCGAGCTCAT	0.682																																					p.G234R		Atlas-SNP	.											.	TRPM2	196	.	0			c.G700C						PASS	.						55	47	50					21																	45789155		2203	4300	6503	SO:0001583	missense	7226	exon5			AAGGAAGGCGAGC	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.700G>C	chr21.hg19:g.45789155G>C	ENSP00000381023:p.Gly234Arg	223.0	0.0	.		229.0	78.0	.	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	hg19	CCDS13710.1	.	.	.	.	.	.	.	.	.	.	G	16.42	3.116916	0.56505	.	.	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932	T;T;T;T	0.04317	3.65;3.65;3.65;3.65	3.51	2.62	0.31277	.	0.137153	0.48286	U	0.000189	T	0.10637	0.0260	L	0.41236	1.265	0.36762	D	0.883366	D;D	0.76494	0.999;0.998	D;P	0.65684	0.937;0.901	T	0.09975	-1.0650	10	0.72032	D	0.01	-14.17	7.6316	0.28243	0.1987:0.0:0.8013:0.0	.	234;234	E9PGK7;O94759	.;TRPM2_HUMAN	R	234	ENSP00000300482:G234R;ENSP00000381023:G234R;ENSP00000300481:G234R;ENSP00000381026:G234R	ENSP00000300481:G234R	G	+	1	0	TRPM2	44613583	0.104000	0.21937	0.028000	0.17463	0.829000	0.46940	0.627000	0.24506	0.803000	0.34113	0.467000	0.42956	GGC	.	.	.	none		0.682	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307		C	45789155	G	C	45789155	3	2	261	1	0	0	0	0	1	0	0	0	16598	1000	35	4	718	4	TRPM2	21	45789155	Missense_Mutation	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	28538913	45789155	2340740	101	16323											
PIWIL3	440822	hgsc.bcm.edu	37	chr22	25158388	25158388	+	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	agctgatccaggtgctctggGtcccccaggtgcctcttgtt	4	12	12	13	0	2	1	0	1	2	0	4	1	4	1	4	3	3	3	4	3	0	2			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr22:25158388G>T	ENST00000332271.5	-	2	495	c.79C>A	c.(79-81)Ccc>Acc	p.P27T	PIWIL3_ENST00000527701.1_5'UTR|PIWIL3_ENST00000532537.2_5'UTR|PIWIL3_ENST00000533313.1_5'UTR	NM_001008496.3|NM_001255975.1	NP_001008496.2|NP_001242904.1	Q7Z3Z3	PIWL3_HUMAN	piwi-like RNA-mediated gene silencing 3	27					cell differentiation (GO:0030154)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	RNA binding (GO:0003723)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(15)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						GGTGCTCTGGGTCCCCCAGGT	0.557																																					p.P27T		Atlas-SNP	.											.	PIWIL3	115	.	0			c.C79A						PASS	.						101	89	93					22																	25158388		2203	4300	6503	SO:0001583	missense	440822	exon2			CTCTGGGTCCCCC	AB079368	CCDS33623.1	22q11.23	2013-02-15	2013-02-15		ENSG00000184571	ENSG00000184571		"Argonaute/PIWI family"	18443	protein-coding gene	gene with protein product		610314	"piwi-like 3 (Drosophila)"			12906857	Standard	NM_001008496		Approved	HIWI3	uc003abd.2	Q7Z3Z3	OTTHUMG00000150788	ENST00000332271.5:c.79C>A	chr22.hg19:g.25158388G>T	ENSP00000330031:p.Pro27Thr	50.0	0.0	.		79.0	27.0	.	NM_001008496		Missense_Mutation	SNP	ENST00000332271.5	hg19	CCDS33623.1	.	.	.	.	.	.	.	.	.	.	G	7.407	0.633980	0.14322	.	.	ENSG00000184571	ENST00000332271	T	0.04406	3.63	1.01	-0.0703	0.13748	.	2.009740	0.03872	N	0.275757	T	0.02380	0.0073	N	0.16478	0.41	0.09310	N	0.999996	P;B	0.45531	0.86;0.347	B;B	0.28991	0.097;0.032	T	0.40270	-0.9572	10	0.25751	T	0.34	-1.0153	3.3689	0.07213	0.2945:0.0:0.7055:0.0	.	27;27	B4DYF7;Q7Z3Z3	.;PIWL3_HUMAN	T	27	ENSP00000330031:P27T	ENSP00000330031:P27T	P	-	1	0	PIWIL3	23488388	0.004000	0.15560	0.007000	0.13788	0.042000	0.13812	0.226000	0.17776	0.001000	0.14605	0.563000	0.77884	CCC	.	.	.	none		0.557	PIWIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320084.2	NM_001008496		T	25158388	G	T	25158388	3	4	261	1	0	0	0	0	1	0	0	0	11966	1261	44	4	2649	4	PIWIL3	22	25158388	Missense_Mutation	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10		25158388	26146178	102	16324											
KCTD17	79734	hgsc.bcm.edu	37	chr22	37458580	37458581	+	Missense_Mutation	DNP	GG	GG	CT																															tctagctgttacaagccagaGgcacccggatgtgaggcccc																								rs377601872		TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr22:37458580_37458581GG>CT	ENST00000403888.3	+	9	913_914	c.912_913GG>CT	c.(910-915)gaGGca>gaCTca	p.304_305EA>DS	KCTD17_ENST00000402077.3_Missense_Mutation_p.280_281EA>DS	NM_001282684.1	NP_001269613.1	Q8N5Z5	KCD17_HUMAN	potassium channel tetramerization domain containing 17	304	Pro-rich.				protein homooligomerization (GO:0051260)		identical protein binding (GO:0042802)			NS(1)|breast(1)|endometrium(1)|lung(1)|prostate(1)	5						ACAAGCCAGAGGCACCCGGATG	0.604																																					p.E280D|p.A281S		Atlas-SNP	.											.	KCTD17	17	.	0			c.G840C|c.G841T						PASS	.																																			SO:0001583	missense	79734	exon8			GCCAGAGGCACCC|CCAGAGGCACCCG	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	Exception_encountered	chr22.hg19:g.37458580_37458581delinsCT	ENSP00000385096:p.E304_A305delinsDS	36.0	0.0	.		54.0	12.0|11.0	.	NM_024681	B0QYA9|B0QYB0|O95517	Missense_Mutation	SNP	ENST00000403888.3	hg19																																																																																				.	.	.	none|alt		0.604	KCTD17-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000318781.1	NM_024681		CT	37458581	GG	CT	37458580	3	2	261	1	0	0	0	0	1	0	0	0	8111	991	35	4	870	4	KCTD17	22	37458580	Missense_Mutation	DNP	GG	TCGA-UZ-A9PO-01A-11D-A382-10	12300192	37458580	13845986	103	16325											
SLC16A8	23539	hgsc.bcm.edu	37	chr22	38476908	38476913	+	In_Frame_Del	DEL	ACTGGG	ACTGGG	-																															agcaacaccaggcccagcgcActggggaagcggggcgcgcc																										TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	ACTGGG	ACTGGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chr22:38476908_38476913delACTGGG	ENST00000320521.5	-	4	1240_1245	c.1132_1137delCCCAGT	c.(1132-1137)cccagtdel	p.PS378del	SLC16A8_ENST00000469516.1_Intron	NM_013356.2	NP_037488.2	O95907	MOT3_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 8	378					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)	GGCCCAGCGCACTGGGGAAGCGGGGC	0.723																																					p.378_380del		Atlas-Indel,Pindel	.											.	SLC16A8	13	.	0			c.1133_1138del						PASS	.																																			SO:0001651	inframe_deletion	23539	exon4			.	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.1132_1137delCCCAGT	chr22.hg19:g.38476908_38476913delACTGGG	ENSP00000321735:p.Pro378_Ser379del	87.0	0.0	0		68.0	10.0	0.147059	NM_013356	Q9UBE2	In_Frame_Del	DEL	ENST00000320521.5	hg19	CCDS13966.1																																																																																			.	.	.	none		0.723	SLC16A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321724.1	NM_013356		-	38476913	ACTGGG	-	38476908	7	5	261	1	0	1	0	1	0	0	0	0	14427	156	6	0	385	0	SLC16A8	22	38476908	In_Frame_Del	DEL	ACTGGG	TCGA-UZ-A9PO-01A-11D-A382-10	1018328	38476908	12827658	104	16326											
TLR7	51284	hgsc.bcm.edu	37	chrX	12905654	12905654	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttttgatggtatgcctccaaAtctaaagaatctctctttgg	10	16	7	8	0	3	2	0	1	3	1	5	2	4	2	2	2	1	1	2	2	5	5			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chrX:12905654A>G	ENST00000380659.3	+	3	2166	c.2027A>G	c.(2026-2028)aAt>aGt	p.N676S		NM_016562.3	NP_057646.1	Q9NYK1	TLR7_HUMAN	toll-like receptor 7	676					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|single-stranded RNA binding (GO:0003727)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(4)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	44					Hydroxychloroquine(DB01611)|Imiquimod(DB00724)	ATGCCTCCAAATCTAAAGAAT	0.373																																					p.N676S		Atlas-SNP	.											.	TLR7	125	.	0			c.A2027G						PASS	.						78	86	83					X																	12905654		2203	4300	6503	SO:0001583	missense	51284	exon3			CTCCAAATCTAAA	AF240467	CCDS14151.1	Xp22.3	2008-02-05			ENSG00000196664	ENSG00000196664			15631	protein-coding gene	gene with protein product		300365				11022119	Standard	NM_016562		Approved		uc004cvc.3	Q9NYK1	OTTHUMG00000021137	ENST00000380659.3:c.2027A>G	chrX.hg19:g.12905654A>G	ENSP00000370034:p.Asn676Ser	81.0	0.0	.		95.0	52.0	.	NM_016562	D1CS69|Q9NR98	Missense_Mutation	SNP	ENST00000380659.3	hg19	CCDS14151.1	.	.	.	.	.	.	.	.	.	.	A	0.013	-1.631507	0.00813	.	.	ENSG00000196664	ENST00000380659	T	0.58210	0.35	5.46	3.07	0.35406	.	0.358388	0.28203	N	0.016219	T	0.20700	0.0498	N	0.03253	-0.375	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.31081	-0.9956	10	0.02654	T	1	.	5.7284	0.18026	0.6453:0.1306:0.2241:0.0	.	676	Q9NYK1	TLR7_HUMAN	S	676	ENSP00000370034:N676S	ENSP00000370034:N676S	N	+	2	0	TLR7	12815575	0.000000	0.05858	0.049000	0.19019	0.968000	0.65278	0.793000	0.26944	0.250000	0.21479	0.430000	0.28490	AAT	.	.	.	none		0.373	TLR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055769.1	NM_016562		G	12905654	A	G	12905654	3	3	261	1	0	0	0	0	1	0	0	0	15968	101	4	3	2033	3	TLR7	23	12905654	Missense_Mutation	SNP	A	TCGA-UZ-A9PO-01A-11D-A382-10		12905654	142364906	105	16327											
MAGED2	10916	hgsc.bcm.edu	37	chrX	54841870	54841870	+	Missense_Mutation	SNP	T	T	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	acgaagctgatatcggacccTgggccaaagcccggatccag	11	5	12	13	3	0	1	0	1	0	0	2	4	1	3	4	3	2	1	4	3	3	1			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chrX:54841870T>G	ENST00000375068.1	+	12	1809	c.1576T>G	c.(1576-1578)Tgg>Ggg	p.W526G	MAGED2_ENST00000375058.1_Missense_Mutation_p.W526G|MAGED2_ENST00000375062.4_Missense_Mutation_p.W441G|MAGED2_ENST00000347546.4_Missense_Mutation_p.W508G|MAGED2_ENST00000375053.2_Missense_Mutation_p.W526G|MAGED2_ENST00000396224.1_Missense_Mutation_p.W526G|MAGED2_ENST00000218439.4_Missense_Mutation_p.W526G|MAGED2_ENST00000375060.1_Missense_Mutation_p.W441G|SNORA11_ENST00000408789.1_RNA			Q9UNF1	MAGD2_HUMAN	melanoma antigen family D, 2	526						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						TATCGGACCCTGGGCCAAAGC	0.602																																					p.W526G		Atlas-SNP	.											.	MAGED2	74	.	0			c.T1576G						PASS	.						24	23	24					X																	54841870		2202	4300	6502	SO:0001583	missense	10916	exon12			GGACCCTGGGCCA	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.1576T>G	chrX.hg19:g.54841870T>G	ENSP00000364209:p.Trp526Gly	192.0	0.0	.		165.0	104.0	.	NM_201222	A6NMX0|O76058|Q5BJF3|Q8NAL6|Q9H218|Q9P0U9|Q9UM52	Missense_Mutation	SNP	ENST00000375068.1	hg19	CCDS14362.1	.	.	.	.	.	.	.	.	.	.	T	12.57	1.977243	0.34848	.	.	ENSG00000102316	ENST00000375068;ENST00000375053;ENST00000347546;ENST00000343474;ENST00000375062;ENST00000218439;ENST00000375058;ENST00000375060;ENST00000396224	T;T;T;T;T;T;T;T;T	0.42131	3.95;3.95;3.99;3.95;0.98;3.95;3.95;0.98;3.95	4.73	4.73	0.59995	.	0.000000	0.42682	D	0.000669	T	0.41073	0.1143	N	0.22421	0.69	0.33869	D	0.634786	D;D	0.65815	0.995;0.99	P;P	0.59115	0.795;0.852	T	0.49551	-0.8928	10	0.22109	T	0.4	.	9.941	0.41580	0.0:0.0:0.0:1.0	.	441;526	Q5H907;Q9UNF1	.;MAGD2_HUMAN	G	526;526;470;508;441;526;526;441;526	ENSP00000364209:W526G;ENSP00000364193:W526G;ENSP00000336962:W470G;ENSP00000340290:W508G;ENSP00000364202:W441G;ENSP00000218439:W526G;ENSP00000364198:W526G;ENSP00000364200:W441G;ENSP00000379526:W526G	ENSP00000218439:W526G	W	+	1	0	MAGED2	54858595	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.231000	0.43009	1.682000	0.51000	0.417000	0.27973	TGG	.	.	.	none		0.602	MAGED2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056821.2	NM_014599		G	54841870	T	G	54841870	3	3	261	1	0	0	0	0	1	0	0	0	9191	1580	55	5	1618	5	MAGED2	23	54841870	Missense_Mutation	SNP	T	TCGA-UZ-A9PO-01A-11D-A382-10	41936216	54841870	100428690	106	16328											
ABCD1	215	hgsc.bcm.edu	37	chrX	153005611	153005611	+	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	ggcaagagctccctgttccgGatcctgggtgggctctggcc	4	9	15	13	1	1	1	0	0	1	1	4	2	4	2	4	5	1	4	4	5	1	1			TCGA-UZ-A9PO-01A-11D-A382-10	TCGA-UZ-A9PO-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	72b12c65-5631-49f5-843b-4bc9f58ce902	41481a6b-9b6c-44cb-8db2-6b911dab119d	g.chrX:153005611G>T	ENST00000218104.3	+	6	1953	c.1554G>T	c.(1552-1554)cgG>cgT	p.R518R	U52111.14_ENST00000434284.1_RNA	NM_000033.3	NP_000024.2	P33897	ABCD1_HUMAN	ATP-binding cassette, sub-family D (ALD), member 1	518	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.		R -> Q (in ALD; CALD-type). {ECO:0000269|PubMed:11438993, ECO:0000269|PubMed:21700483}.|R -> W (in ALD; CALD-type). {ECO:0000269|PubMed:8040304}.		alpha-linolenic acid metabolic process (GO:0036109)|ATP catabolic process (GO:0006200)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|linoleic acid metabolic process (GO:0043651)|long-chain fatty acid catabolic process (GO:0042758)|peroxisomal long-chain fatty acid import (GO:0015910)|peroxisomal membrane transport (GO:0015919)|peroxisome organization (GO:0007031)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid catabolic process (GO:0042760)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|peroxisomal fatty-acyl-CoA transporter activity (GO:0005325)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|urinary_tract(2)	18	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CCCTGTTCCGGATCCTGGGTG	0.647																																					p.R518R		Atlas-SNP	.											.	ABCD1	59	.	0			c.G1554T						PASS	.						96	87	90					X																	153005611		2203	4300	6503	SO:0001819	synonymous_variant	215	exon6			GTTCCGGATCCTG	Z21876	CCDS14728.1	Xq28	2012-03-14			ENSG00000101986	ENSG00000101986		"ATP binding cassette transporters / subfamily D"	61	protein-coding gene	gene with protein product		300371		ALD		8441467, 6795626	Standard	NM_000033		Approved	AMN, ALDP, adrenoleukodystrophy	uc004fif.2	P33897	OTTHUMG00000024215	ENST00000218104.3:c.1554G>T	chrX.hg19:g.153005611G>T		39.0	0.0	.		42.0	26.0	.	NM_000033	Q6GTZ2	Silent	SNP	ENST00000218104.3	hg19	CCDS14728.1	.	.	.	.	.	.	.	.	.	.	G	4.664	0.123534	0.08931	.	.	ENSG00000101986	ENST00000443684	.	.	.	4.93	-0.346	0.12620	.	.	.	.	.	T	0.50017	0.1591	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.32877	-0.9890	4	.	.	.	-23.4028	4.8323	0.13447	0.0853:0.4009:0.3745:0.1392	.	.	.	.	V	186	.	.	G	+	2	0	ABCD1	152658805	0.998000	0.40836	0.989000	0.46669	0.475000	0.33008	0.355000	0.20163	-0.429000	0.07329	-0.563000	0.04171	GGA	.	.	.	none		0.647	ABCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061041.1	NM_000033		T	153005611	G	T	153005611	2	4	261	1	0	0	0	0	0	0	0	1	60	1161	41	4		4	ABCD1	23	153005611	Silent	SNP	G	TCGA-UZ-A9PO-01A-11D-A382-10	98163741	153005611	2264949	107	16329											
SLC35E2	9906	hgsc.bcm.edu	37	chr1	1670432	1670432	+	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	agccgggccttgtgctgataTaaacagcaaggaacgagggt	12	7	14	8	2	0	1	0	1	0	0	0	3	0	2	2	3	5	2	2	3	5	3			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr1:1670432T>A	ENST00000246421.4	-	3	802	c.387A>T	c.(385-387)ttA>ttT	p.L129F	SLC35E2_ENST00000355439.2_Missense_Mutation_p.L129F|SLC35E2_ENST00000400924.1_Missense_Mutation_p.L129F|RP1-283E3.8_ENST00000598846.1_RNA	NM_182838.2	NP_878258.1	P0CK97	S35E2_HUMAN	solute carrier family 35, member E2	129						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)		TGTGCTGATATAAACAGCAAG	0.537																																					p.L129F		Atlas-SNP	.											SLC35E2,NS,carcinoma,0,1	SLC35E2	13	.	0			c.A387T						PASS	.						108	140	129					1																	1670432		2203	4298	6501	SO:0001583	missense	9906	exon3			CTGATATAAACAG	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.387A>T	chr1.hg19:g.1670432T>A	ENSP00000246421:p.Leu129Phe	1349.0	0.0	.		790.0	101.0	.	NM_182838	B3KWR0|O75035|Q2TAY8|Q569F8|Q5CZA4|Q5QPR8|Q9Y3J8	Missense_Mutation	SNP	ENST00000246421.4	hg19	CCDS33.1	.	.	.	.	.	.	.	.	.	.	t	18.64	3.666694	0.67814	.	.	ENSG00000215790	ENST00000355439;ENST00000400924;ENST00000246421	D;D;D	0.95447	-3.71;-3.71;-3.71	2.89	-3.2	0.05156	Drug/metabolite transporter (1);	0.000000	0.56097	U	0.000040	D	0.94932	0.8361	M	0.67953	2.075	0.22954	N	0.998514	D;D	0.57899	0.957;0.981	P;P	0.54889	0.727;0.763	D	0.91334	0.5092	10	0.49607	T	0.09	-21.6831	11.2951	0.49274	0.0:0.8127:0.0:0.1873	.	129;129	P0CK97;P0CK97-2	S35E2_HUMAN;.	F	129	ENSP00000347614:L129F;ENSP00000383714:L129F;ENSP00000246421:L129F	ENSP00000246421:L129F	L	-	3	2	SLC35E2	1660292	0.925000	0.31364	0.949000	0.38748	0.955000	0.61496	0.050000	0.14120	-0.786000	0.04516	0.433000	0.28618	TTA	.	T|1.000;|0.000	.	alt		0.537	SLC35E2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000002210.3	XM_049733		A	1670432	T	A	1670432	3	1	262	1	0	0	0	0	1	0	0	0	14598	1403	49	5	1679	5	SLC35E2	1	1670432	Missense_Mutation	SNP	T	TCGA-UZ-A9PP-01A-11D-A42J-10		1670432	247580189	1	16330											
ICMT	23463	hgsc.bcm.edu	37	chr1	6285207	6285207	+	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	ccctcttcttatactccaggTactcctctccaaaaaagtga	11	12	4	14	0	3	1	0	1	3	0	6	1	5	1	4	1	2	1	4	1	6	4			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr1:6285207T>A	ENST00000343813.5	-	5	816	c.788A>T	c.(787-789)tAc>tTc	p.Y263F	ICMT_ENST00000495791.1_5'Flank	NM_012405.3	NP_036537.1	O60725	ICMT_HUMAN	isoprenylcysteine carboxyl methyltransferase	263					C-terminal protein methylation (GO:0006481)|cellular protein modification process (GO:0006464)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|multicellular organism growth (GO:0035264)|positive regulation of cell proliferation (GO:0008284)|protein targeting to membrane (GO:0006612)|regulation of Ras protein signal transduction (GO:0046578)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cAMP response element binding protein binding (GO:0008140)|protein C-terminal carboxyl O-methyltransferase activity (GO:0003880)|protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferase activity (GO:0004671)			NS(1)|endometrium(2)	3	Ovarian(185;0.0634)	all_cancers(23;5.85e-39)|all_epithelial(116;2.4e-22)|all_lung(118;2.65e-08)|Lung NSC(185;6.45e-07)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000688)|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;5.52e-38)|GBM - Glioblastoma multiforme(13;6.51e-32)|OV - Ovarian serous cystadenocarcinoma(86;3.03e-19)|Colorectal(212;7.08e-08)|COAD - Colon adenocarcinoma(227;8.35e-06)|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;0.182)		ATACTCCAGGTACTCCTCTCC	0.562																																					p.Y263F		Atlas-SNP	.											.	ICMT	13	.	0			c.A788T						PASS	.						99	106	104					1																	6285207		2203	4300	6503	SO:0001583	missense	23463	exon5			TCCAGGTACTCCT	AF064084	CCDS61.1	1p36	2010-04-29			ENSG00000116237	ENSG00000116237	2.1.1.100		5350	protein-coding gene	gene with protein product	"protein-S-isoprenylcysteine O-methyltransferase"	605851				9614111, 10441503	Standard	XM_005263437		Approved	PCCMT, HSTE14, PPMT	uc001amk.3	O60725	OTTHUMG00000001254	ENST00000343813.5:c.788A>T	chr1.hg19:g.6285207T>A	ENSP00000343552:p.Tyr263Phe	61.0	0.0	.		41.0	17.0	.	NM_012405	Q6FHT0	Missense_Mutation	SNP	ENST00000343813.5	hg19	CCDS61.1	.	.	.	.	.	.	.	.	.	.	T	33	5.239596	0.95240	.	.	ENSG00000116237	ENST00000343813;ENST00000535068	.	.	.	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	D	0.84056	0.5388	M	0.86805	2.84	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86757	0.1964	9	0.72032	D	0.01	.	15.482	0.75534	0.0:0.0:0.0:1.0	.	263	O60725	ICMT_HUMAN	F	263;167	.	ENSP00000343552:Y263F	Y	-	2	0	ICMT	6207794	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.438000	0.80431	2.246000	0.74042	0.533000	0.62120	TAC	.	.	.	none		0.562	ICMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003681.1	NM_012405		A	6285207	T	A	6285207	3	1	262	1	0	0	0	0	1	0	0	0	7492	1638	57	5	70	5	ICMT	1	6285207	Missense_Mutation	SNP	T	TCGA-UZ-A9PP-01A-11D-A42J-10	4614775	6285207	242965414	2	16331											
KLHDC7A	127707	hgsc.bcm.edu	37	chr1	18808387	18808387	+	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	tctcaggccatcttccagggCaggctggctcccaggacagc	7	7	12	15	0	2	0	1	0	2	0	5	1	4	1	3	5	1	3	3	5	0	1			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr1:18808387C>A	ENST00000400664.1	+	1	964	c.912C>A	c.(910-912)ggC>ggA	p.G304G		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	304						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)		TCTTCCAGGGCAGGCTGGCTC	0.632																																					p.G304G		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.C912A						PASS	.						48	46	47					1																	18808387		2203	4300	6503	SO:0001819	synonymous_variant	127707	exon1			CCAGGGCAGGCTG	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.912C>A	chr1.hg19:g.18808387C>A		121.0	0.0	.		61.0	28.0	.	NM_152375	Q8N8W6	Silent	SNP	ENST00000400664.1	hg19	CCDS185.2																																																																																			.	.	.	none		0.632	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375		A	18808387	C	A	18808387	2	1	262	1	0	0	0	0	0	0	0	1	8367	697	25	4		4	KLHDC7A	1	18808387	Silent	SNP	C	TCGA-UZ-A9PP-01A-11D-A42J-10	12523180	18808387	230442234	3	16332											
LEPRE1	64175	hgsc.bcm.edu	37	chr1	43224941	43224941	+	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	atcgtagtcatagggcccttCgcagagggcacggcactcct	8	8	12	13	3	1	1	1	0	0	1	4	1	2	1	2	3	0	4	2	3	2	3			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr1:43224941C>T	ENST00000296388.5	-	3	790	c.739G>A	c.(739-741)Gaa>Aaa	p.E247K	LEPRE1_ENST00000236040.4_Missense_Mutation_p.E247K|LEPRE1_ENST00000397054.3_Missense_Mutation_p.E247K			Q32P28	P3H1_HUMAN	leucine proline-enriched proteoglycan (leprecan) 1	247					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)	TAGGGCCCTTCGCAGAGGGCA	0.577																																					p.E247K		Atlas-SNP	.											.	LEPRE1	130	.	0			c.G739A						PASS	.						112	102	106					1																	43224941		2203	4300	6503	SO:0001583	missense	64175	exon3			GCCCTTCGCAGAG	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.739G>A	chr1.hg19:g.43224941C>T	ENSP00000296388:p.Glu247Lys	199.0	0.0	.		121.0	7.0	.	NM_001146289	Q7KZR4|Q96BR8|Q96SK8|Q96SL5|Q96SN3|Q9H6K3|Q9HC86|Q9HC87	Missense_Mutation	SNP	ENST00000296388.5	hg19	CCDS472.2	.	.	.	.	.	.	.	.	.	.	C	36	5.747510	0.96882	.	.	ENSG00000117385	ENST00000397054;ENST00000236040;ENST00000296388;ENST00000540027;ENST00000372526	T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	D	0.85410	0.5690	M	0.89715	3.055	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.996;0.996	D	0.87957	0.2727	10	0.87932	D	0	-23.3075	17.3244	0.87243	0.0:1.0:0.0:0.0	.	247;112;247	Q32P28-3;B4DNM8;Q32P28	.;.;P3H1_HUMAN	K	247;247;247;112;204	ENSP00000380245:E247K;ENSP00000236040:E247K;ENSP00000296388:E247K;ENSP00000361604:E204K	ENSP00000236040:E247K	E	-	1	0	LEPRE1	42997528	1.000000	0.71417	0.995000	0.50966	0.867000	0.49689	7.298000	0.78815	2.682000	0.91365	0.563000	0.77884	GAA	.	.	.	none		0.577	LEPRE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019790.2	NM_022356		T	43224941	C	T	43224941	3	4	262	1	0	0	0	0	1	0	0	0	8736	893	31	1	1542	1	LEPRE1	1	43224941	Missense_Mutation	SNP	C	TCGA-UZ-A9PP-01A-11D-A42J-10	24416554	43224941	206025680	4	16333											
BCAR3	8412	hgsc.bcm.edu	37	chr1	94048486	94048486	+	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	aggggcttgtgtccacacccGaggactgaggtggcagcttg	7	8	16	10	1	0	1	0	1	0	0	1	3	1	2	2	5	1	3	2	5	0	2			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr1:94048486G>C	ENST00000370244.1	-	9	1346	c.1058C>G	c.(1057-1059)tCg>tGg	p.S353W	BCAR3_ENST00000466632.1_5'UTR|BCAR3_ENST00000370247.3_Missense_Mutation_p.S262W|BCAR3_ENST00000260502.6_Missense_Mutation_p.S353W|BCAR3_ENST00000539242.1_Missense_Mutation_p.S29W|BCAR3_ENST00000370243.1_Missense_Mutation_p.S353W	NM_001261408.1	NP_001248337.1	O75815	BCAR3_HUMAN	breast cancer anti-estrogen resistance 3	353					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)		GTCCACACCCGAGGACTGAGG	0.567																																					p.S353W		Atlas-SNP	.											.	BCAR3	62	.	0			c.C1058G						PASS	.						35	37	36					1																	94048486		2199	4296	6495	SO:0001583	missense	8412	exon7			ACACCCGAGGACT	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.1058C>G	chr1.hg19:g.94048486G>C	ENSP00000359264:p.Ser353Trp	22.0	0.0	.		11.0	5.0	.	NM_001261409	D3DT43|Q5TEW3|Q6UW40|Q9BR50	Missense_Mutation	SNP	ENST00000370244.1	hg19	CCDS745.1	.	.	.	.	.	.	.	.	.	.	G	7.432	0.638822	0.14386	.	.	ENSG00000137936	ENST00000370247;ENST00000260502;ENST00000370244;ENST00000370243;ENST00000539242	T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85	5.16	2.18	0.27775	.	0.617466	0.17140	N	0.185513	T	0.19565	0.0470	N	0.19112	0.55	0.09310	N	1	P;P;D	0.54772	0.923;0.95;0.968	B;P;B	0.49085	0.346;0.6;0.346	T	0.03514	-1.1029	10	0.72032	D	0.01	-11.4446	5.4129	0.16358	0.1485:0.0:0.5671:0.2844	.	133;353;262	B3KNL6;O75815;Q5TEW3	.;BCAR3_HUMAN;.	W	262;353;353;353;29	ENSP00000359267:S262W;ENSP00000260502:S353W;ENSP00000359264:S353W;ENSP00000359263:S353W;ENSP00000441343:S29W	ENSP00000260502:S353W	S	-	2	0	BCAR3	93821074	0.175000	0.23083	0.004000	0.12327	0.179000	0.23085	1.152000	0.31663	0.657000	0.30906	0.655000	0.94253	TCG	.	.	.	none		0.567	BCAR3-003	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028420.1			C	94048486	G	C	94048486	3	2	262	1	0	0	0	0	1	0	0	0	1349	1059	37	4	1443	4	BCAR3	1	94048486	Missense_Mutation	SNP	G	TCGA-UZ-A9PP-01A-11D-A42J-10	50823545	94048486	155202135	5	16334											
ZBTB7B	51043	hgsc.bcm.edu	37	chr1	154987953	154987953	+	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	gtccccagagctacgaacccTatgagggtgaggaagaagaa	14	5	13	9	1	0	5	0	2	0	3	1	7	1	6	3	2	3	1	3	2	6	2			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr1:154987953T>A	ENST00000368426.3	+	3	954	c.817T>A	c.(817-819)Tat>Aat	p.Y273N	ZBTB7B_ENST00000292176.2_Missense_Mutation_p.Y273N|ZBTB7B_ENST00000417934.2_Missense_Mutation_p.Y307N|ZBTB7B_ENST00000535420.1_Missense_Mutation_p.Y273N	NM_001256455.1	NP_001243384.1	O15156	ZBT7B_HUMAN	zinc finger and BTB domain containing 7B	273					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)			CTACGAACCCTATGAGGGTGA	0.672																																					p.Y307N		Atlas-SNP	.											.	ZBTB7B	69	.	0			c.T919A						PASS	.						35	36	35					1																	154987953		2201	4300	6501	SO:0001583	missense	51043	exon4			GAACCCTATGAGG	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.817T>A	chr1.hg19:g.154987953T>A	ENSP00000357411:p.Tyr273Asn	154.0	0.0	.		102.0	47.0	.	NM_001252406	B4E3K5|D3DV83|J3KQQ3|Q68DR2|Q96EP2	Missense_Mutation	SNP	ENST00000368426.3	hg19	CCDS1081.1	.	.	.	.	.	.	.	.	.	.	T	10.95	1.494967	0.26774	.	.	ENSG00000160685	ENST00000535420;ENST00000368426;ENST00000417934;ENST00000292176	T;T;T;T	0.09350	3.02;3.02;2.99;3.02	4.3	4.3	0.51218	.	0.830066	0.10696	N	0.644657	T	0.02848	0.0085	N	0.24115	0.695	0.18873	N	0.999987	B;B;B	0.22604	0.021;0.072;0.021	B;B;B	0.19666	0.026;0.018;0.026	T	0.40232	-0.9574	10	0.30078	T	0.28	.	11.4451	0.50118	0.0:0.0:0.0:1.0	.	273;273;307	A8K6F4;O15156;B4E3K5	.;ZBT7B_HUMAN;.	N	273;273;307;273	ENSP00000438647:Y273N;ENSP00000357411:Y273N;ENSP00000406286:Y307N;ENSP00000292176:Y273N	ENSP00000292176:Y273N	Y	+	1	0	ZBTB7B	153254577	0.000000	0.05858	0.824000	0.32777	0.815000	0.46073	-0.170000	0.09897	1.808000	0.52836	0.379000	0.24179	TAT	.	.	.	none		0.672	ZBTB7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091083.1	NM_015872		A	154987953	T	A	154987953	3	1	262	1	0	0	0	0	1	0	0	0	17566	1522	53	5	819	5	ZBTB7B	1	154987953	Missense_Mutation	SNP	T	TCGA-UZ-A9PP-01A-11D-A42J-10	60939467	154987953	94262668	6	16335											
RC3H1	149041	hgsc.bcm.edu	37	chr1	173921219	173921219	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtcacatgaccagggagagtAttggctataatcatttcctt	11	13	9	8	0	2	2	2	1	0	1	3	3	3	2	2	2	0	2	2	2	3	6			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr1:173921219A>G	ENST00000367696.2	-	14	2779	c.2428T>C	c.(2428-2430)Tac>Cac	p.Y810H	RC3H1_ENST00000258349.4_Missense_Mutation_p.Y810H|RC3H1_ENST00000367694.2_Missense_Mutation_p.Y810H			Q5TC82	RC3H1_HUMAN	ring finger and CCCH-type domains 1	810					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						CAGGGAGAGTATTGGCTATAA	0.393																																					p.Y810H		Atlas-SNP	.											.	RC3H1	110	.	0			c.T2428C						PASS	.						141	126	131					1																	173921219		2203	4300	6503	SO:0001583	missense	149041	exon13			GAGAGTATTGGCT	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.2428T>C	chr1.hg19:g.173921219A>G	ENSP00000356669:p.Tyr810His	70.0	0.0	.		45.0	19.0	.	NM_172071	B3KVK1|Q5W180|Q5W181|Q8IVE6|Q8N9V1	Missense_Mutation	SNP	ENST00000367696.2	hg19	CCDS30940.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.209630	0.79240	.	.	ENSG00000135870	ENST00000367696;ENST00000258349;ENST00000367694	T;T;T	0.61158	0.14;0.14;0.13	5.92	4.77	0.60923	.	0.162470	0.56097	D	0.000025	T	0.62134	0.2403	L	0.55481	1.735	0.53005	D	0.999963	D;D;D;D	0.89917	0.999;0.999;1.0;0.999	D;D;D;D	0.85130	0.994;0.994;0.997;0.994	T	0.67252	-0.5717	10	0.66056	D	0.02	-8.6265	12.306	0.54902	0.873:0.0:0.0:0.127	.	810;810;810;810	B9EGU6;B7ZMB3;Q5TC82-2;Q5TC82	.;.;.;RC3H1_HUMAN	H	810	ENSP00000356669:Y810H;ENSP00000258349:Y810H;ENSP00000356667:Y810H	ENSP00000258349:Y810H	Y	-	1	0	RC3H1	172187842	1.000000	0.71417	0.728000	0.30774	0.978000	0.69477	8.962000	0.93254	1.011000	0.39340	0.477000	0.44152	TAC	.	.	.	none		0.393	RC3H1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090733.2	NM_172071		G	173921219	A	G	173921219	3	3	262	1	0	0	0	0	1	0	0	0	13179	449	16	3	1001	3	RC3H1	1	173921219	Missense_Mutation	SNP	A	TCGA-UZ-A9PP-01A-11D-A42J-10	18933266	173921219	75329402	7	16336											
LRRN2	10446	hgsc.bcm.edu	37	chr1	204587083	204587083	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggggagcagacacaacccGgacagaaggggcactccagc	13	1	15	12	1	0	2	0	0	0	2	1	5	1	4	2	5	3	2	2	5	2	0	rs535832685		TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr1:204587083G>A	ENST00000367175.1	-	1	4250	c.2038C>T	c.(2038-2040)Cgg>Tgg	p.R680W	RP11-430C7.4_ENST00000453895.1_RNA|LRRN2_ENST00000367176.3_Missense_Mutation_p.R680W|LRRN2_ENST00000367177.3_Missense_Mutation_p.R680W|LRRN2_ENST00000496057.1_5'Flank			O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2	680					cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|liver(1)|lung(22)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			GACACAACCCGGACAGAAGGG	0.632													G|||	1	0.000199681	0	0.0014	5008	,	,		14704	0		0	False		,,,				2504	0				p.R680W		Atlas-SNP	.											.	LRRN2	81	.	0			c.C2038T						PASS	.						70	77	75					1																	204587083		2203	4300	6503	SO:0001583	missense	10446	exon3			CAACCCGGACAGA	AF030435	CCDS1448.1	1q32.1	2013-01-11	2007-01-31	2007-01-31	ENSG00000170382	ENSG00000170382		"Immunoglobulin superfamily / I-set domain containing"	16914	protein-coding gene	gene with protein product	"leucine rich and ankyrin repeats 1", "fibronectin type III, immunoglobulin and leucine rich repeat domain 7"	605492	"leucine rich repeat neuronal 5"	LRRN5		9662332	Standard	NM_006338		Approved	GAC1, LRANK1, FIGLER7	uc001hbf.1	O75325	OTTHUMG00000035989	ENST00000367175.1:c.2038C>T	chr1.hg19:g.204587083G>A	ENSP00000356143:p.Arg680Trp	203.0	0.0	.		116.0	44.0	.	NM_006338	B2R624|Q5T0Y0|Q6UXM0|Q8N182	Missense_Mutation	SNP	ENST00000367175.1	hg19	CCDS1448.1	.	.	.	.	.	.	.	.	.	.	G	17.44	3.390987	0.62066	.	.	ENSG00000170382	ENST00000367176;ENST00000367177;ENST00000367175	T;T;T	0.62364	0.03;0.03;0.03	4.94	4.03	0.46877	.	0.240456	0.21555	N	0.072663	T	0.41119	0.1145	N	0.08118	0	0.43390	D	0.9955	B	0.19073	0.033	B	0.15484	0.013	T	0.35822	-0.9773	10	0.72032	D	0.01	.	10.4288	0.44395	0.0917:0.0:0.9083:0.0	.	680	O75325	LRRN2_HUMAN	W	680	ENSP00000356144:R680W;ENSP00000356145:R680W;ENSP00000356143:R680W	ENSP00000356143:R680W	R	-	1	2	LRRN2	202853706	0.731000	0.28111	0.820000	0.32676	0.525000	0.34531	4.080000	0.57620	1.316000	0.45131	0.561000	0.74099	CGG	.	.	.	none		0.632	LRRN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089894.1	NM_006338		A	204587083	G	A	204587083	3	1	262	1	0	0	0	0	1	0	0	0	9042	1115	39	1	107	1	LRRN2	1	204587083	Missense_Mutation	SNP	G	TCGA-UZ-A9PP-01A-11D-A42J-10	30665864	204587083	44663538	8	16337											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228509045	228509045	+	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	gtcaggctctgtgcccacagGttggggccccagcagccccc	5	6	13	17	0	2	0	1	0	1	0	2	0	2	0	5	4	3	3	5	4	0	1			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr1:228509045G>A	ENST00000422127.1	+	55	14547	c.14503G>A	c.(14503-14505)Gtt>Att	p.V4835I	OBSCN_ENST00000570156.2_Splice_Site_p.V5792I|OBSCN_ENST00000366709.4_Splice_Site_p.V1954I|OBSCN_ENST00000366707.4_Splice_Site_p.V2469I|OBSCN_ENST00000284548.11_Splice_Site_p.V4835I	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4835					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)				GTGCCCACAGGTTGGGGCCCC	0.632																																					p.V5792I		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G17374A						PASS	.						17	18	18					1																	228509045		1977	4147	6124	SO:0001630	splice_region_variant	84033	exon66			CCACAGGTTGGGG	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.14503-1G>A	chr1.hg19:g.228509045G>A		83.0	0.0	.		36.0	10.0	.	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	14.54	2.565516	0.45694	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.62364	0.42;0.03;0.06;0.56	4.68	1.25	0.21368	.	1.586350	0.03728	N	0.252908	T	0.47002	0.1422	N	0.19112	0.55	0.19300	N	0.999973	B;B	0.06786	0.001;0.001	B;B	0.10450	0.002;0.005	T	0.23154	-1.0196	9	.	.	.	.	7.4965	0.27492	0.0967:0.4639:0.4394:0.0	.	4835;4835	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	I	4835;4835;2469;1954	ENSP00000284548:V4835I;ENSP00000409493:V4835I;ENSP00000355668:V2469I;ENSP00000355670:V1954I	.	V	+	1	0	OBSCN	226575668	0.647000	0.27304	0.073000	0.20177	0.062000	0.15995	0.764000	0.26532	0.057000	0.16193	0.563000	0.77884	GTT	.	.	.	none		0.632	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	Missense_Mutation	A	228509045	G	A	228509045	5	1	262	1	0	0	0	0	0	0	1	0	10819	1275	44	2	14717	2	OBSCN	1	228509045	Splice_Site	SNP	G	TCGA-UZ-A9PP-01A-11D-A42J-10	23921962	228509045	20741576	9	16338											
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54873419	54873419	+	Missense_Mutation	SNP	T	T	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	cgtcactgacagcagcagccTcagcgctgaggccatcagac	10	5	11	15	2	3	3	3	2	0	1	3	3	3	3	2	1	4	3	2	1	0	0			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr2:54873419T>G	ENST00000356805.4	+	23	4954	c.4673T>G	c.(4672-4674)cTc>cGc	p.L1558R	SPTBN1_ENST00000333896.5_Missense_Mutation_p.L1545R	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1558					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)			AGCAGCAGCCTCAGCGCTGAG	0.597																																					p.L1558R		Atlas-SNP	.											.	SPTBN1	378	.	0			c.T4673G						PASS	.						59	64	62					2																	54873419		2203	4300	6503	SO:0001583	missense	6711	exon23			GCAGCCTCAGCGC		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.4673T>G	chr2.hg19:g.54873419T>G	ENSP00000349259:p.Leu1558Arg	188.0	0.0	.		105.0	6.0	.	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	hg19	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	T	8.805	0.933832	0.18206	.	.	ENSG00000115306	ENST00000356805;ENST00000333896	T;T	0.49432	0.78;0.78	5.8	0.634	0.17718	.	0.327233	0.33496	N	0.004851	T	0.35128	0.0921	L	0.42245	1.32	0.26816	N	0.968888	B;B	0.17465	0.0;0.022	B;B	0.24006	0.0;0.05	T	0.28235	-1.0050	10	0.15952	T	0.53	.	10.3045	0.43672	0.0:0.379:0.0:0.621	.	1545;1558	Q01082-3;Q01082	.;SPTB2_HUMAN	R	1558;1545	ENSP00000349259:L1558R;ENSP00000334156:L1545R	ENSP00000334156:L1545R	L	+	2	0	SPTBN1	54726923	0.578000	0.26717	0.502000	0.27614	0.792000	0.44763	1.002000	0.29796	-0.101000	0.12219	-0.366000	0.07423	CTC	.	.	.	none		0.597	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			G	54873419	T	G	54873419	3	3	262	1	0	0	0	0	1	0	0	0	15131	1551	54	5	4872	5	SPTBN1	2	54873419	Missense_Mutation	SNP	T	TCGA-UZ-A9PP-01A-11D-A42J-10		54873419	188325954	10	16339											
POLR1A	25885	hgsc.bcm.edu	37	chr2	86297161	86297161	+	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	cttgggaacaaggtactgctGatcagtgcaggccaggacgt	10	8	14	9	1	1	1	1	1	0	0	1	3	1	3	1	4	4	3	1	4	3	2			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr2:86297161G>A	ENST00000263857.6	-	13	2224	c.1846C>T	c.(1846-1848)Cag>Tag	p.Q616*	POLR1A_ENST00000409681.1_Nonsense_Mutation_p.Q616*			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	616					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						AGGTACTGCTGATCAGTGCAG	0.577																																					p.Q616X		Atlas-SNP	.											.	POLR1A	137	.	0			c.C1846T						PASS	.						36	39	38					2																	86297161		2051	4179	6230	SO:0001587	stop_gained	25885	exon13			ACTGCTGATCAGT	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.1846C>T	chr2.hg19:g.86297161G>A	ENSP00000263857:p.Gln616*	27.0	0.0	.		21.0	9.0	.	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Nonsense_Mutation	SNP	ENST00000263857.6	hg19	CCDS42706.1	.	.	.	.	.	.	.	.	.	.	G	42	9.370452	0.99151	.	.	ENSG00000068654	ENST00000263857;ENST00000409681	.	.	.	5.3	4.4	0.53042	.	0.172789	0.51477	D	0.000098	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	-22.8516	8.3408	0.32243	0.0:0.3834:0.4874:0.1292	.	.	.	.	X	616	.	ENSP00000263857:Q616X	Q	-	1	0	POLR1A	86150672	1.000000	0.71417	0.997000	0.53966	0.979000	0.70002	4.626000	0.61269	2.479000	0.83701	0.655000	0.94253	CAG	.	.	.	none		0.577	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425		A	86297161	G	A	86297161	4	1	262	1	0	0	0	0	0	1	0	0	12216	1299	45	2	3404	2	POLR1A	2	86297161	Nonsense_Mutation	SNP	G	TCGA-UZ-A9PP-01A-11D-A42J-10	31423742	86297161	156902212	11	16340											
VPS24	51652	hgsc.bcm.edu	37	chr2	86769412	86769412	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acaactctcatttcctttctTatcttcaatgaccactcatt	10	17	1	13	0	5	1	3	1	3	0	7	1	6	1	2	0	1	0	2	0	3	5	rs540948421		TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr2:86769412T>C	ENST00000263856.4	-	2	197	c.69A>G	c.(67-69)atA>atG	p.I23M	CHMP3_ENST00000439940.2_Missense_Mutation_p.I52M|CHMP3_ENST00000409225.2_Intron|CHMP3_ENST00000409727.1_Missense_Mutation_p.I23M|RNF103-CHMP3_ENST00000604011.1_Missense_Mutation_p.I52M	NM_001193517.1|NM_016079.3	NP_001180446.1|NP_057163.1	Q9Y3E7	CHMP3_HUMAN	charged multivesicular body protein 3	23	Intramolecular interaction with C- terminus.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|endosomal transport (GO:0016197)|membrane organization (GO:0061024)|positive regulation of viral release from host cell (GO:1902188)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)											TTTCCTTTCTTATCTTCAATG	0.323																																					p.I52M		Atlas-SNP	.											.	.	.	.	0			c.A156G						PASS	.						119	113	115					2																	86769412		2203	4298	6501	SO:0001583	missense	100526767	exon4			CTTTCTTATCTTC	AF219226	CCDS33236.1, CCDS42707.1, CCDS54375.1	2p11.2	2011-09-21	2011-09-21	2011-09-21	ENSG00000115561	ENSG00000115561		"Charged multivesicular body proteins"	29865	protein-coding gene	gene with protein product		610052	"vacuolar protein sorting 24 (yeast)", "vacuolar protein sorting 24 homolog (S. cerevisiae)"	VPS24		11549700, 12878588	Standard	NM_016079		Approved	NEDF, CGI-149		Q9Y3E7	OTTHUMG00000153189	ENST00000263856.4:c.69A>G	chr2.hg19:g.86769412T>C	ENSP00000263856:p.Ile23Met	227.0	0.0	.		142.0	64.0	.	NM_001198954	A8K3W0|B4DG34|B8ZZM0|B8ZZX5|Q3ZTS9|Q53S71|Q53SU5|Q9NZ51	Missense_Mutation	SNP	ENST00000263856.4	hg19	CCDS33236.1	.	.	.	.	.	.	.	.	.	.	T	13.98	2.397581	0.42512	.	.	ENSG00000115561;ENSG00000115561;ENSG00000115561;ENSG00000249884	ENST00000263856;ENST00000409727;ENST00000439940;ENST00000440757	T;D;T;T	0.89196	-0.73;-2.48;-0.73;-0.73	5.39	-0.595	0.11660	.	0.045218	0.85682	D	0.000000	D	0.87180	0.6113	L	0.56280	1.765	0.51767	D	0.999938	B;P;B	0.43701	0.159;0.815;0.064	B;P;B	0.46389	0.091;0.515;0.065	D	0.84790	0.0778	10	0.51188	T	0.08	-27.6725	12.7264	0.57173	0.0:0.0:0.5733:0.4267	.	52;23;23	Q9Y3E7-3;Q9Y3E7-4;Q9Y3E7	.;.;CHMP3_HUMAN	M	23;23;52;130	ENSP00000263856:I23M;ENSP00000387045:I23M;ENSP00000405575:I52M;ENSP00000392995:I130M	ENSP00000392995:I130M	I	-	3	3	VPS24;RNF103-VPS24	86622923	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	0.593000	0.23999	0.049000	0.15920	0.533000	0.62120	ATA	.	.	.	none		0.323	CHMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330015.2	NM_016079		C	86769412	T	C	86769412	3	2	262	1	0	0	0	0	1	0	0	0	17207	1744	61	3	619	3	VPS24	2	86769412	Missense_Mutation	SNP	T	TCGA-UZ-A9PP-01A-11D-A42J-10	472251	86769412	156429961	12	16341											
MERTK	10461	hgsc.bcm.edu	37	chr2	112686995	112686995	+	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	aattgctcaatcagtgtaccTaatatataccaggacaccac	15	10	5	11	0	2	0	2	0	0	0	2	1	2	1	3	1	3	2	3	1	7	6			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr2:112686995T>G	ENST00000295408.4	+	2	617	c.360T>G	c.(358-360)ccT>ccG	p.P120P	RN7SL297P_ENST00000483161.2_RNA|MERTK_ENST00000421804.2_Silent_p.P120P|MERTK_ENST00000409780.1_Intron			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	120	Ig-like C2-type 1.				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						TCAGTGTACCTAATATATACC	0.393																																					p.P120P		Atlas-SNP	.											.	MERTK	112	.	0			c.T360G						PASS	.						116	107	110					2																	112686995		2203	4300	6503	SO:0001819	synonymous_variant	10461	exon2			TGTACCTAATATA	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.360T>G	chr2.hg19:g.112686995T>G		188.0	0.0	.		116.0	41.0	.	NM_006343	Q9HBB4	Silent	SNP	ENST00000295408.4	hg19	CCDS2094.1																																																																																			.	.	.	none		0.393	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2			G	112686995	T	G	112686995	2	3	262	1	0	0	0	0	0	0	0	1	9486	1509	53	5		5	MERTK	2	112686995	Silent	SNP	T	TCGA-UZ-A9PP-01A-11D-A42J-10	25917583	112686995	130512378	13	16342											
FAM123C	205147	hgsc.bcm.edu	37	chr2	131519874	131519874	+	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	cgcagctggaccccaaagggGgacccgcagccctctgtgga	8	4	14	15	2	1	0	0	0	1	0	1	3	1	3	4	4	2	3	4	4	1	0			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr2:131519874G>A	ENST00000423981.1	+	2	339	c.229G>A	c.(229-231)Gga>Aga	p.G77R	AMER3_ENST00000321420.4_Missense_Mutation_p.G77R	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2	Q8N944	AMER3_HUMAN	APC membrane recruitment protein 3	77					Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	lipid binding (GO:0008289)	p.G77R(1)									CCCCAAAGGGGGACCCGCAGC	0.647																																					p.G77R		Atlas-SNP	.											FAM123C,NS,carcinoma,0,1	.	.	.	1	Substitution - Missense(1)	lung(1)	c.G229A						PASS	.						18	27	24					2																	131519874		2197	4299	6496	SO:0001583	missense	205147	exon2			AAAGGGGGACCCG	AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171		"-"	26771	protein-coding gene	gene with protein product			"family with sequence similarity 123C"	FAM123C		20843316	Standard	NM_001105195		Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.229G>A	chr2.hg19:g.131519874G>A	ENSP00000392700:p.Gly77Arg	140.0	0.0	.		80.0	4.0	.	NM_152698	B7ZLH6	Missense_Mutation	SNP	ENST00000423981.1	hg19	CCDS2164.1	.	.	.	.	.	.	.	.	.	.	G	14.95	2.689763	0.48097	.	.	ENSG00000178171	ENST00000321420;ENST00000431758;ENST00000458606;ENST00000423981	T;T	0.47528	0.84;0.84	4.89	1.02	0.19986	.	0.000000	0.47455	D	0.000240	T	0.38374	0.1038	L	0.29908	0.895	0.09310	N	1	P	0.48162	0.906	P	0.49752	0.621	T	0.17961	-1.0352	10	0.40728	T	0.16	.	6.6426	0.22917	0.3965:0.0:0.6035:0.0	.	77	Q8N944	F123C_HUMAN	R	77	ENSP00000314914:G77R;ENSP00000392700:G77R	ENSP00000314914:G77R	G	+	1	0	FAM123C	131236344	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.726000	0.25984	0.213000	0.20722	-0.291000	0.09656	GGA	.	.	.	none		0.647	AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3	NM_152698		A	131519874	G	A	131519874	3	1	262	1	0	0	0	0	1	0	0	0	5428	1233	43	2	231	2	FAM123C	2	131519874	Missense_Mutation	SNP	G	TCGA-UZ-A9PP-01A-11D-A42J-10	18832879	131519874	111679499	14	16343											
SCN9A	6335	hgsc.bcm.edu	37	chr2	167094694	167094694	+	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	tttagaagcatttccagaatGaagatgtaagtgaagatctt	15	13	9	4	0	1	6	0	2	1	4	2	6	2	6	1	0	1	2	1	0	6	5			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr2:167094694G>T	ENST00000409435.1	-	19	3710	c.3711C>A	c.(3709-3711)ttC>ttA	p.F1237L	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Missense_Mutation_p.F1238L|SCN9A_ENST00000409672.1_Missense_Mutation_p.F1226L|SCN9A_ENST00000375387.4_Missense_Mutation_p.F1238L			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	1237					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)	TTTCCAGAATGAAGATGTAAG	0.333																																					p.F1226L		Atlas-SNP	.											.	SCN9A	296	.	0			c.C3678A						PASS	.						49	50	50					2																	167094694		2158	4288	6446	SO:0001583	missense	6335	exon20			CAGAATGAAGATG	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.3711C>A	chr2.hg19:g.167094694G>T	ENSP00000386330:p.Phe1237Leu	301.0	0.0	.		136.0	51.0	.	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Missense_Mutation	SNP	ENST00000409435.1	hg19	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.084556	0.76642	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435	D;D;D;D	0.98987	-5.3;-5.3;-5.3;-5.3	5.25	3.44	0.39384	.	0.000000	0.64402	D	0.000007	D	0.99423	0.9796	H	0.97732	4.065	0.50467	D	0.999872	D	0.69078	0.997	D	0.71870	0.975	D	0.98781	1.0732	10	0.87932	D	0	.	8.1778	0.31292	0.3304:0.0:0.6696:0.0	.	1226	E7EUN6	.	L	1226;1238;1238;1237	ENSP00000386306:F1226L;ENSP00000364536:F1238L;ENSP00000304748:F1238L;ENSP00000386330:F1237L	ENSP00000304748:F1238L	F	-	3	2	SCN9A	166802940	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	1.781000	0.38644	0.599000	0.29845	0.655000	0.94253	TTC	.	.	.	none		0.333	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		T	167094694	G	T	167094694	3	4	262	1	0	0	0	0	1	0	0	0	13938	1281	45	4	2287	4	SCN9A	2	167094694	Missense_Mutation	SNP	G	TCGA-UZ-A9PP-01A-11D-A42J-10	35574820	167094694	76104679	15	16344											
ATP5G3	518	hgsc.bcm.edu	37	chr2	176043935	176043935	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctgaaactccctttggattAgctgagacacaccattctgg	10	12	8	11	0	2	2	0	2	2	1	3	4	3	3	2	2	2	1	2	2	2	3			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr2:176043935A>G	ENST00000284727.4	-	4	3188	c.164T>C	c.(163-165)cTa>cCa	p.L55P	ATP5G3_ENST00000392541.3_Missense_Mutation_p.L55P|ATP5G3_ENST00000409194.1_Missense_Mutation_p.L55P|Y_RNA_ENST00000363251.1_RNA	NM_001002258.4|NM_001689.4	NP_001002258.1|NP_001680.1	P48201	AT5G3_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C3 (subunit 9)	55					ATP hydrolysis coupled proton transport (GO:0015991)|ATP synthesis coupled proton transport (GO:0015986)	integral component of membrane (GO:0016021)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045263)	hydrogen ion transmembrane transporter activity (GO:0015078)|lipid binding (GO:0008289)|transporter activity (GO:0005215)			large_intestine(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.147)			CCTTTGGATTAGCTGAGACAC	0.448																																					p.L55P	GBM(30;387 605 18606 28805 47989)	Atlas-SNP	.											.	ATP5G3	11	.	0			c.T164C						PASS	.						90	83	85					2																	176043935		2203	4300	6503	SO:0001583	missense	518	exon4			TGGATTAGCTGAG	BC106881	CCDS2263.1	2q31.1	2012-10-12	2010-06-11		ENSG00000154518	ENSG00000154518		"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	843	protein-coding gene	gene with protein product		602736	"ATP synthase, H+ transporting, mitochondrial F0 complex, subunit c (subunit 9) isoform 3", "ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C3 (subunit 9)"			7698763	Standard	NM_001002258		Approved		uc002ujz.4	P48201	OTTHUMG00000132425	ENST00000284727.4:c.164T>C	chr2.hg19:g.176043935A>G	ENSP00000284727:p.Leu55Pro	69.0	0.0	.		52.0	21.0	.	NM_001190329	B2R4Z0|D3DPF0|Q4ZFX7	Missense_Mutation	SNP	ENST00000284727.4	hg19	CCDS2263.1	.	.	.	.	.	.	.	.	.	.	A	15.62	2.886484	0.51908	.	.	ENSG00000154518	ENST00000284727;ENST00000409194;ENST00000392541	T;T;T	0.25250	1.81;1.81;1.81	5.79	4.63	0.57726	.	0.131340	0.51477	D	0.000083	T	0.20333	0.0489	L	0.29908	0.895	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.02042	-1.1224	10	0.45353	T	0.12	-13.4739	13.1837	0.59670	0.8669:0.1331:0.0:0.0	.	55	P48201	AT5G3_HUMAN	P	55	ENSP00000284727:L55P;ENSP00000387317:L55P;ENSP00000376324:L55P	ENSP00000284727:L55P	L	-	2	0	ATP5G3	175752181	0.999000	0.42202	0.999000	0.59377	0.993000	0.82548	2.870000	0.48451	1.010000	0.39314	0.455000	0.32223	CTA	.	.	.	none		0.448	ATP5G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255563.1	NM_001689		G	176043935	A	G	176043935	3	3	262	1	0	0	0	0	1	0	0	0	1155	420	15	3	276	3	ATP5G3	2	176043935	Missense_Mutation	SNP	A	TCGA-UZ-A9PP-01A-11D-A42J-10	8949241	176043935	67155438	16	16345											
TTN	7273	hgsc.bcm.edu	37	chr2	179644087	179644087	+	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	agaaatgtcaactgccatctTttcttctccatcttcttcaa	10	16	3	12	0	7	1	2	0	5	1	8	1	7	1	2	0	2	0	2	0	3	5			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr2:179644087T>A	ENST00000591111.1	-	23	4056	c.3832A>T	c.(3832-3834)Aag>Tag	p.K1278*	RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000342992.6_Nonsense_Mutation_p.K1278*|TTN_ENST00000359218.5_Nonsense_Mutation_p.K1232*|TTN_ENST00000460472.2_Nonsense_Mutation_p.K1232*|TTN_ENST00000360870.5_Nonsense_Mutation_p.K1278*|TTN_ENST00000589042.1_Nonsense_Mutation_p.K1278*|TTN_ENST00000342175.6_Nonsense_Mutation_p.K1232*			Q8WZ42	TITIN_HUMAN	titin	33471					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)			ACTGCCATCTTTTCTTCTCCA	0.318																																					p.K1278X		Atlas-SNP	.											.	TTN	18412	.	0			c.A3832T						PASS	.						41	40	41					2																	179644087		2203	4297	6500	SO:0001587	stop_gained	7273	exon23			CCATCTTTTCTTC	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.3832A>T	chr2.hg19:g.179644087T>A	ENSP00000465570:p.Lys1278*	135.0	0.0	.		105.0	47.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Nonsense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	44	10.638742	0.99442	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	.	.	.	5.87	5.87	0.94306	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.2813	0.82687	0.0:0.0:0.0:1.0	.	.	.	.	X	1278;1232;1232;1232;1232;1278	.	ENSP00000340554:K1232X	K	-	1	0	TTN	179352332	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	5.478000	0.66806	2.244000	0.73946	0.533000	0.62120	AAG	.	.	.	none		0.318	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179644087	T	A	179644087	4	1	262	1	0	0	0	0	0	1	0	0	16747	1850	64	5	107516	5	TTN	2	179644087	Nonsense_Mutation	SNP	T	TCGA-UZ-A9PP-01A-11D-A42J-10	3600152	179644087	63555286	17	16346											
ZNF589	51385	hgsc.bcm.edu	37	chr3	48309513	48309513	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatcctattccaggtttccAtgcaggaaatcaactccacc	11	11	5	14	0	2	0	2	0	0	0	6	1	6	1	5	2	2	2	5	2	3	3			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr3:48309513A>G	ENST00000354698.3	+	4	404	c.332A>G	c.(331-333)cAt>cGt	p.H111R	ZNF589_ENST00000412564.1_Intron|ZNF589_ENST00000440261.2_Missense_Mutation_p.H110R|ZNF589_ENST00000427617.2_Intron	NM_016089.2	NP_057173.2	Q86UQ0	ZN589_HUMAN	zinc finger protein 589	111					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)|lung(1)|ovary(1)|skin(1)	4				BRCA - Breast invasive adenocarcinoma(193;0.000649)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CCAGGTTTCCATGCAGGAAAT	0.507																																					p.H111R	Colon(9;319 328 25374 27611 50948)	Atlas-SNP	.											.	ZNF589	20	.	0			c.A332G						PASS	.						70	71	71					3																	48309513		1983	4185	6168	SO:0001583	missense	51385	exon4			GTTTCCATGCAGG	AF114816	CCDS43085.1	3p21	2013-01-08			ENSG00000164048	ENSG00000164048		"Zinc fingers, C2H2-type", "-"	16747	protein-coding gene	gene with protein product						10029171	Standard	NM_016089		Approved	SZF1	uc003csl.4	Q86UQ0	OTTHUMG00000156833	ENST00000354698.3:c.332A>G	chr3.hg19:g.48309513A>G	ENSP00000346729:p.His111Arg	64.0	0.0	.		31.0	26.0	.	NM_016089	Q86UC9|Q9BRI6|Q9BRY3|Q9Y611|Q9Y612	Missense_Mutation	SNP	ENST00000354698.3	hg19	CCDS43085.1	.	.	.	.	.	.	.	.	.	.	A	5.998	0.368098	0.11352	.	.	ENSG00000164048	ENST00000354698;ENST00000440261;ENST00000296437	T;T	0.05996	3.36;4.89	1.17	-0.0169	0.13970	.	.	.	.	.	T	0.02571	0.0078	N	0.08118	0	0.09310	N	1	P;P;B	0.36712	0.566;0.523;0.389	B;B;B	0.34180	0.177;0.023;0.01	T	0.42716	-0.9435	9	0.25106	T	0.35	.	2.8669	0.05604	0.543:0.0:0.457:0.0	.	110;108;111	B4DQF9;Q86UQ0-2;Q86UQ0	.;.;ZN589_HUMAN	R	111;110;108	ENSP00000346729:H111R;ENSP00000408719:H110R	ENSP00000296437:H108R	H	+	2	0	ZNF589	48284517	0.000000	0.05858	0.001000	0.08648	0.532000	0.34746	0.801000	0.27055	-0.015000	0.14150	0.383000	0.25322	CAT	.	.	.	none		0.507	ZNF589-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346124.1	NM_016089		G	48309513	A	G	48309513	3	3	262	1	0	0	0	0	1	0	0	0	18033	217	8	3	346	3	ZNF589	3	48309513	Missense_Mutation	SNP	A	TCGA-UZ-A9PP-01A-11D-A42J-10		48309513	149712917	18	16347											
RBM27	54439	hgsc.bcm.edu	37	chr5	145583374	145583374	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcaagtcctggctggccaagTtactggagccgatgtgagtg	8	10	14	9	1	1	1	1	1	0	0	2	3	2	2	3	3	2	2	3	3	3	1			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr5:145583374T>C	ENST00000265271.5	+	1	212	c.46T>C	c.(46-48)Tta>Cta	p.L16L	RBM27_ENST00000506502.1_Silent_p.L16L	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	16					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)			GCTGGCCAAGTTACTGGAGCC	0.711																																					p.L16L		Atlas-SNP	.											.	RBM27	119	.	0			c.T46C						PASS	.						11	13	12					5																	145583374		1260	2948	4208	SO:0001819	synonymous_variant	54439	exon1			GCCAAGTTACTGG	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.46T>C	chr5.hg19:g.145583374T>C		202.0	0.0	.		106.0	35.0	.	NM_018989	Q8IYW9	Silent	SNP	ENST00000265271.5	hg19	CCDS43378.1																																																																																			.	.	.	none		0.711	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128		C	145583374	T	C	145583374	2	2	262	1	0	0	0	0	0	0	0	1	13140	1722	60	3		3	RBM27	5	145583374	Silent	SNP	T	TCGA-UZ-A9PP-01A-11D-A42J-10		145583374	35331886	19	16348											
HIVEP1	3096	hgsc.bcm.edu	37	chr6	12123780	12123781	+	Frame_Shift_Ins	INS	-	-	C																															cgagacctggaagctcaatgINSccatgatcaagaaaagtcag																										TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr6:12123780_12123781insC	ENST00000379388.2	+	4	4084_4085	c.3752_3753insC	c.(3751-3756)tgccatfs	p.H1252fs	HIVEP1_ENST00000541134.1_5'Flank	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	1252					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)				GAAGCTCAATGCCATGATCAAG	0.475																																					p.C1251fs		Atlas-Indel,Pindel	.											.	HIVEP1	242	.	0			c.3752_3753insC						PASS	.																																			SO:0001589	frameshift_variant	3096	exon4			.	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"Zinc fingers, C2H2-type"	4920	protein-coding gene	gene with protein product		194540	"human immunodeficiency virus type I enhancer-binding protein 1", "zinc finger protein 40"	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.3754dupC	chr6.hg19:g.12123782_12123782dupC	ENSP00000368698:p.His1252fs	60.0	0.0	0		43.0	23.0	0.534884	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Frame_Shift_Ins	INS	ENST00000379388.2	hg19	CCDS43426.1																																																																																			.	.	.	none		0.475	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114		C	12123781	-	C	12123780	7	5	262	1	0	1	1	0	0	0	0	0	7193	1319	46	0	3762	0	HIVEP1	6	12123780	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PP-01A-11D-A42J-10		12123780	158991287	20	16349											
OR10C1	442194	hgsc.bcm.edu	37	chr6	29408295	29408295	+	Missense_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	catcttctctttgcccttctGcggccccaataccatcccgc	5	12	5	19	2	3	0	0	0	3	0	5	0	4	0	5	1	3	0	5	1	2	4			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr6:29408295G>A	ENST00000444197.2	+	1	1213	c.503G>A	c.(502-504)tGc>tAc	p.C168Y	OR11A1_ENST00000377149.1_Intron	NM_013941.3	NP_039229.3	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C, member 1 (gene/pseudogene)	168						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|kidney(1)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						TTGCCCTTCTGCGGCCCCAAT	0.592																																					p.C168Y		Atlas-SNP	.											.	OR10C1	58	.	0			c.G503A						PASS	.						121	135	130					6																	29408295		1509	2709	4218	SO:0001583	missense	442194	exon1			CCTTCTGCGGCCC		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.503G>A	chr6.hg19:g.29408295G>A	ENSP00000419119:p.Cys168Tyr	36.0	0.0	.		34.0	13.0	.	NM_013941	Q5SUN7|Q96R18	Missense_Mutation	SNP	ENST00000444197.2	hg19	CCDS34364.1	.	.	.	.	.	.	.	.	.	.	G	13.81	2.346866	0.41599	.	.	ENSG00000206474	ENST00000444197	T	0.00245	8.45	3.53	3.53	0.40419	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42548	D	0.000681	T	0.00440	0.0014	H	0.94462	3.54	0.41362	D	0.987435	D	0.89917	1.0	D	0.97110	1.0	T	0.54728	-0.8250	10	0.72032	D	0.01	.	12.0891	0.53715	0.0:0.1749:0.8251:0.0	.	168	Q96KK4	O10C1_HUMAN	Y	168	ENSP00000419119:C168Y	ENSP00000419119:C168Y	C	+	2	0	OR10C1	29516274	1.000000	0.71417	1.000000	0.80357	0.309000	0.27889	5.166000	0.64965	1.805000	0.52779	0.508000	0.49915	TGC	.	.	.	none		0.592	OR10C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076415.2			A	29408295	G	A	29408295	3	1	262	1	0	0	0	0	1	0	0	0	10905	1319	46	2	505	2	OR10C1	6	29408295	Missense_Mutation	SNP	G	TCGA-UZ-A9PP-01A-11D-A42J-10	17284515	29408295	141706772	21	16350											
MICA	100507436	hgsc.bcm.edu	37	chr6	31379810	31379810	+	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	cttccagcttctatccccggAatatcatactgacctggcgt	8	12	7	14	2	2	1	1	1	1	0	4	2	4	2	4	2	2	1	4	2	4	5			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr6:31379810A>T	ENST00000449934.2	+	4	754	c.700A>T	c.(700-702)Aat>Tat	p.N234Y	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)				CTATCCCCGGAATATCATACT	0.582																																					p.N234Y		Atlas-SNP	.											.	MICA	21	.	0			c.A700T						PASS	.						16	19	18					6																	31379810		692	1589	2281	SO:0001583	missense	100507436	exon4			CCCCGGAATATCA	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.700A>T	chr6.hg19:g.31379810A>T	ENSP00000413079:p.Asn234Tyr	88.0	0.0	.		63.0	25.0	.	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	hg19	CCDS56412.1	.	.	.	.	.	.	.	.	.	.	N	13.54	2.268509	0.40095	.	.	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.14640	2.49;2.49	2.52	-1.33	0.09172	.	0.698014	0.11634	U	0.544522	T	0.17662	0.0424	M	0.83774	2.66	0.09310	N	1	D;D	0.76494	0.999;0.999	D;D	0.72982	0.979;0.949	T	0.04065	-1.0980	10	0.87932	D	0	.	3.5133	0.07716	0.33:0.2458:0.4242:0.0	.	96;234	Q5SS58;Q96QC4	.;.	Y	96;234;191;234;125	ENSP00000413079:N234Y;ENSP00000402410:N125Y	ENSP00000365394:N234Y	N	+	1	0	MICA	31487789	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	0.220000	0.17660	-0.118000	0.11851	0.365000	0.22127	AAT	.	.	.	none		0.582	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519		T	31379810	A	T	31379810	3	4	262	1	0	0	0	0	1	0	0	0	9575	246	9	5	714	5	MICA	6	31379810	Missense_Mutation	SNP	A	TCGA-UZ-A9PP-01A-11D-A42J-10	1971515	31379810	139735257	22	16351											
BAI3	577	hgsc.bcm.edu	37	chr6	69772840	69772840	+	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	ttgcagaaattatactgtcaTtaattccaaaatcatcgtgg	14	14	6	7	1	2	1	2	0	0	1	4	1	3	1	1	1	2	1	1	1	6	5			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr6:69772840T>A	ENST00000370598.1	+	16	3169	c.2348T>A	c.(2347-2349)aTt>aAt	p.I783N		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	783					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)				TATACTGTCATTAATTCCAAA	0.353																																					p.I783N		Atlas-SNP	.											.	BAI3	451	.	0			c.T2348A						PASS	.						102	95	97					6																	69772840		2203	4300	6503	SO:0001583	missense	577	exon16			CTGTCATTAATTC	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.2348T>A	chr6.hg19:g.69772840T>A	ENSP00000359630:p.Ile783Asn	79.0	0.0	.		63.0	30.0	.	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	hg19	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	T	17.55	3.416826	0.62511	.	.	ENSG00000135298	ENST00000370598	T	0.09817	2.94	5.54	5.54	0.83059	Domain of unknown function DUF3497 (1);	0.132236	0.50627	D	0.000118	T	0.08891	0.0220	L	0.34521	1.04	0.80722	D	1	P	0.41188	0.741	P	0.47528	0.549	T	0.03875	-1.0996	10	0.87932	D	0	.	15.6727	0.77292	0.0:0.0:0.0:1.0	.	783	O60242	BAI3_HUMAN	N	783	ENSP00000359630:I783N	ENSP00000359630:I783N	I	+	2	0	BAI3	69829561	1.000000	0.71417	0.965000	0.40720	0.934000	0.57294	6.725000	0.74752	2.094000	0.63399	0.397000	0.26171	ATT	.	.	.	none		0.353	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			A	69772840	T	A	69772840	3	1	262	1	0	0	0	0	1	0	0	0	1300	1493	52	5	2402	5	BAI3	6	69772840	Missense_Mutation	SNP	T	TCGA-UZ-A9PP-01A-11D-A42J-10	38393030	69772840	101342227	23	16352											
ITGB8	3696	hgsc.bcm.edu	37	chr7	20449400	20449400	+	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	cagagtgtcagcctcaaaaaAggtcagtgaattctaaaaaa	18	8	8	7	0	4	2	3	1	1	1	4	2	4	2	1	1	1	0	1	1	7	2			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr7:20449400A>G	ENST00000222573.4	+	13	2870	c.2186A>G	c.(2185-2187)aAg>aGg	p.K729R	ITGB8_ENST00000537992.1_Splice_Site_p.K594R	NM_002214.2	NP_002205.1	P26012	ITB8_HUMAN	integrin, beta 8	729					cartilage development (GO:0051216)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|ganglioside metabolic process (GO:0001573)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of gene expression (GO:0010629)|placenta blood vessel development (GO:0060674)|positive regulation of gene expression (GO:0010628)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	extracellular matrix protein binding (GO:1990430)|receptor activity (GO:0004872)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(4)|stomach(2)|urinary_tract(1)	37						GCCTCAAAAAAGGTCAGTGAA	0.318																																					p.K729R		Atlas-SNP	.											.	ITGB8	159	.	0			c.A2186G						PASS	.						73	79	77					7																	20449400		2203	4299	6502	SO:0001630	splice_region_variant	3696	exon13			CAAAAAAGGTCAG		CCDS5370.1	7p15.3	2010-03-23			ENSG00000105855	ENSG00000105855		"Integrins"	6163	protein-coding gene	gene with protein product		604160					Standard	XM_005249751		Approved		uc003suu.3	P26012	OTTHUMG00000023594	ENST00000222573.4:c.2187+1A>G	chr7.hg19:g.20449400A>G		113.0	0.0	.		64.0	25.0	.	NM_002214	A4D133|B4DHD4	Missense_Mutation	SNP	ENST00000222573.4	hg19	CCDS5370.1	.	.	.	.	.	.	.	.	.	.	A	19.04	3.749231	0.69533	.	.	ENSG00000105855	ENST00000537992;ENST00000222573	T;T	0.51071	0.72;0.72	6.06	6.06	0.98353	.	0.000000	0.64402	D	0.000002	T	0.36744	0.0978	L	0.47716	1.5	0.53005	D	0.999961	P	0.42409	0.779	B	0.32149	0.141	T	0.37197	-0.9716	10	0.56958	D	0.05	.	10.8727	0.46894	0.9303:0.0:0.0697:0.0	.	729	P26012	ITB8_HUMAN	R	594;729	ENSP00000441561:K594R;ENSP00000222573:K729R	ENSP00000222573:K729R	K	+	2	0	ITGB8	20415925	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.810000	0.62598	2.324000	0.78689	0.533000	0.62120	AAG	.	.	.	none		0.318	ITGB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059915.3	NM_002214	Missense_Mutation	G	20449400	A	G	20449400	5	3	262	1	0	0	0	0	0	0	1	0	7908	86	3	3	2236	3	ITGB8	7	20449400	Splice_Site	SNP	A	TCGA-UZ-A9PP-01A-11D-A42J-10		20449400	138689263	24	16353											
URGCP	55665	hgsc.bcm.edu	37	chr7	43917041	43917041	+	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	ccttcaggagccctgtgaccCagcggacgggcatgctcagc	7	6	13	15	2	2	1	2	1	0	0	2	3	2	3	3	3	4	2	3	3	0	1			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr7:43917041C>A	ENST00000453200.1	-	6	2514	c.2021G>T	c.(2020-2022)tGg>tTg	p.W674L	URGCP_ENST00000336086.6_Missense_Mutation_p.W631L|URGCP_ENST00000223341.7_Missense_Mutation_p.W631L|URGCP_ENST00000402306.3_Missense_Mutation_p.W665L|URGCP-MRPS24_ENST00000603700.1_Intron|URGCP_ENST00000497914.1_5'UTR|URGCP_ENST00000443736.1_Missense_Mutation_p.W631L|URGCP_ENST00000447717.3_Missense_Mutation_p.W631L			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	674					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						CCCTGTGACCCAGCGGACGGG	0.642																																					p.W674L		Atlas-SNP	.											.	URGCP	170	.	0			c.G2021T						PASS	.						29	33	32					7																	43917041		2118	4226	6344	SO:0001583	missense	55665	exon6			GTGACCCAGCGGA		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.2021G>T	chr7.hg19:g.43917041C>A	ENSP00000396918:p.Trp674Leu	42.0	0.0	.		24.0	12.0	.	NM_001077663	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Missense_Mutation	SNP	ENST00000453200.1	hg19	CCDS47578.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.068660	0.76301	.	.	ENSG00000106608	ENST00000223341;ENST00000336086;ENST00000402306;ENST00000443736;ENST00000453200;ENST00000447717	T;T;T;T;T;T	0.22134	2.01;2.01;1.98;2.01;1.97;2.01	5.97	5.97	0.96955	.	0.056596	0.85682	D	0.000000	T	0.52403	0.1732	M	0.84082	2.675	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.54583	-0.8272	10	0.87932	D	0	-31.708	17.9218	0.88969	0.0:1.0:0.0:0.0	.	665;674	Q8TCY9-2;Q8TCY9	.;URGCP_HUMAN	L	631;631;665;631;674;631	ENSP00000223341:W631L;ENSP00000336872:W631L;ENSP00000384955:W665L;ENSP00000392136:W631L;ENSP00000396918:W674L;ENSP00000402803:W631L	ENSP00000223341:W631L	W	-	2	0	URGCP	43883566	1.000000	0.71417	1.000000	0.80357	0.605000	0.37080	7.262000	0.78410	2.837000	0.97791	0.655000	0.94253	TGG	.	.	.	none		0.642	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664		A	43917041	C	A	43917041	3	1	262	1	0	0	0	0	1	0	0	0	17038	595	21	4	778	4	URGCP	7	43917041	Missense_Mutation	SNP	C	TCGA-UZ-A9PP-01A-11D-A42J-10	23467641	43917041	115221622	25	16354											
MDH2	4191	hgsc.bcm.edu	37	chr7	75693752	75693752	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggtcaaggctaaagccggAgcaggtagagtctcaggcag	11	6	16	8	1	2	1	2	0	1	1	3	2	2	2	1	5	2	4	1	5	4	2			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr7:75693752A>G	ENST00000315758.5	+	7	823	c.729A>G	c.(727-729)ggA>ggG	p.G243G	MDH2_ENST00000432020.2_Silent_p.G201G|MDH2_ENST00000443006.1_Silent_p.G136G	NM_005918.2	NP_005909.2	P40926	MDHM_HUMAN	malate dehydrogenase 2, NAD (mitochondrial)	243					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						CTAAAGCCGGAGCAGGTAGAG	0.647																																					p.G243G		Atlas-SNP	.											.	MDH2	35	.	0			c.A729G						PASS	.						25	25	25					7																	75693752		2198	4299	6497	SO:0001819	synonymous_variant	4191	exon7			AGCCGGAGCAGGT		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.729A>G	chr7.hg19:g.75693752A>G		121.0	0.0	.		79.0	37.0	.	NM_005918	A8K414|B2RE78|B4DE44|E9PDB2|O43682	Silent	SNP	ENST00000315758.5	hg19	CCDS5581.1																																																																																			.	.	.	none		0.647	MDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252851.1			G	75693752	A	G	75693752	2	3	262	1	0	0	0	0	0	0	0	1	9417	291	11	3		3	MDH2	7	75693752	Silent	SNP	A	TCGA-UZ-A9PP-01A-11D-A42J-10	31776711	75693752	83444911	26	16355											
MLL5	55904	hgsc.bcm.edu	37	chr7	104742604	104742604	+	Missense_Mutation	SNP	T	T	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	tgaaactgaagttccagcacTtaataaatgtcctaccaagt	15	11	6	9	0	0	2	0	2	0	0	2	2	2	2	3	0	3	2	3	0	7	4			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr7:104742604T>G	ENST00000311117.3	+	17	2704	c.2159T>G	c.(2158-2160)cTt>cGt	p.L720R	KMT2E_ENST00000334914.7_5'UTR|CTB-152G17.6_ENST00000607968.1_RNA|KMT2E_ENST00000334877.4_Missense_Mutation_p.L720R|KMT2E_ENST00000257745.4_Missense_Mutation_p.L720R	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	720					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										GTTCCAGCACTTAATAAATGT	0.299																																					p.L720R		Atlas-SNP	.											.	MLL5	173	.	0			c.T2159G						PASS	.						67	72	70					7																	104742604		2202	4298	6500	SO:0001583	missense	55904	exon16			CAGCACTTAATAA	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	18541	protein-coding gene	gene with protein product		608444	"myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.2159T>G	chr7.hg19:g.104742604T>G	ENSP00000312379:p.Leu720Arg	141.0	0.0	.		81.0	23.0	.	NM_018682	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	hg19	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	T	11.60	1.687786	0.29962	.	.	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745	D;D;D	0.92048	-2.96;-2.59;-2.96	5.75	5.75	0.90469	.	0.461581	0.23362	N	0.049019	D	0.84741	0.5539	L	0.29908	0.895	0.80722	D	1	P	0.36199	0.543	B	0.34452	0.183	T	0.81824	-0.0755	10	0.10636	T	0.68	.	11.188	0.48669	0.137:0.0:0.0:0.863	.	720	Q8IZD2	MLL5_HUMAN	R	720;720;720;640;720	ENSP00000312379:L720R;ENSP00000335599:L720R;ENSP00000257745:L720R	ENSP00000257745:L720R	L	+	2	0	MLL5	104529840	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.598000	0.54038	2.201000	0.70794	0.533000	0.62120	CTT	.	.	.	none		0.299	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			G	104742604	T	G	104742604	3	3	262	1	0	0	0	0	1	0	0	0	9631	1609	56	5	2217	5	MLL5	7	104742604	Missense_Mutation	SNP	T	TCGA-UZ-A9PP-01A-11D-A42J-10	29048852	104742604	54396059	27	16356											
WASL	8976	hgsc.bcm.edu	37	chr7	123332492	123332492	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgttctgctccactttttttAgctgagcaccctctctaatt	6	18	5	12	0	2	1	0	1	2	0	4	1	3	1	2	0	3	4	2	0	2	7			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr7:123332492A>G	ENST00000223023.4	-	9	1588	c.1256T>C	c.(1255-1257)cTa>cCa	p.L419P		NM_003941.2	NP_003932.3	O00401	WASL_HUMAN	Wiskott-Aldrich syndrome-like	419	WH2 1. {ECO:0000255|PROSITE- ProRule:PRU00406}.				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						CACTTTTTTTAGCTGAGCACC	0.502																																					p.L419P		Atlas-SNP	.											.	WASL	70	.	0			c.T1256C						PASS	.						77	74	75					7																	123332492		2203	4300	6503	SO:0001583	missense	8976	exon9			TTTTTTAGCTGAG	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.1256T>C	chr7.hg19:g.123332492A>G	ENSP00000223023:p.Leu419Pro	73.0	0.0	.		44.0	14.0	.	NM_003941	A1JUI9|Q7Z746	Missense_Mutation	SNP	ENST00000223023.4	hg19	CCDS34743.1	.	.	.	.	.	.	.	.	.	.	A	16.69	3.192537	0.58017	.	.	ENSG00000106299	ENST00000223023	D	0.99849	-7.15	5.79	5.79	0.91817	Wiscott-Aldrich syndrome, C-terminal (1);Actin-binding WH2 (3);	0.000000	0.64402	D	0.000002	D	0.99832	0.9924	M	0.86502	2.82	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96750	0.9553	10	0.72032	D	0.01	-17.53	16.1172	0.81314	1.0:0.0:0.0:0.0	.	419	O00401	WASL_HUMAN	P	419	ENSP00000223023:L419P	ENSP00000223023:L419P	L	-	2	0	WASL	123119728	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.884000	0.92432	2.201000	0.70794	0.528000	0.53228	CTA	.	.	.	none		0.502	WASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348522.1	NM_003941		G	123332492	A	G	123332492	3	3	262	1	0	0	0	0	1	0	0	0	17268	420	15	3	273	3	WASL	7	123332492	Missense_Mutation	SNP	A	TCGA-UZ-A9PP-01A-11D-A42J-10	18589888	123332492	35806171	28	16357											
BRAF	673	hgsc.bcm.edu	37	chr7	140453136	140453136	+	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	acccactccatcgagatttcActgtagctagaccaaaatca	14	9	5	13	1	2	2	2	0	0	2	4	3	3	2	3	0	1	2	3	0	4	3	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		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.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(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)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	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.V600E	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,adenoma,0,1	BRAF	36346	.	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	c.T1799A						PASS	.						112	104	107					7																	140453136		2203	4300	6503	SO:0001583	missense	673	exon15	Familial Cancer Database	CFC, CFCS	GATTTCACTGTAG	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.1799T>A	chr7.hg19:g.140453136A>T	ENSP00000288602:p.Val600Glu	55.0	0.0	.		50.0	19.0	.	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	hg19	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	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|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA	.	.	.	weak		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		T	140453136	A	T	140453136	3	4	262	1	0	0	0	0	1	0	0	0	1498	159	6	5	517	5	BRAF	7	140453136	Missense_Mutation	SNP	A	TCGA-UZ-A9PP-01A-11D-A42J-10	17120644	140453136	18685527	29	16358											
INTS9	55756	hgsc.bcm.edu	37	chr8	28671112	28671113	+	Missense_Mutation	DNP	AG	AG	GA																															agacttccactgcatccttgAgaggagaaggtaacagcctg																										TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr8:28671112_28671113AG>GA	ENST00000521022.1	-	7	586_587	c.505_506CT>TC	c.(505-507)CTc>TCc	p.L169S	INTS9_ENST00000521777.1_Missense_Mutation_p.L145S|INTS9_ENST00000397363.4_Missense_Mutation_p.L63S|INTS9_ENST00000416984.2_Missense_Mutation_p.L148S	NM_018250.3	NP_060720.2	Q9NV88	INT9_HUMAN	integrator complex subunit 9	169					snRNA processing (GO:0016180)	cytoplasm (GO:0005737)|integrator complex (GO:0032039)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|pancreas(2)|prostate(1)|urinary_tract(2)	19		Ovarian(32;0.0439)		KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.152)		TGCATCCTTGAGAGGAGAAGGT	0.421																																					p.L169P|p.L169F		Atlas-SNP	.											.	INTS9	43	.	0			c.T506C|c.C505T						PASS	.																																			SO:0001583	missense	55756	exon7			TCCTTGAGAGGAG|CCTTGAGAGGAGA	BC025267	CCDS34873.1, CCDS55215.1, CCDS55216.1	8p21.1	2008-02-05			ENSG00000104299	ENSG00000104299			25592	protein-coding gene	gene with protein product		611352				16239144	Standard	NM_001172562		Approved	FLJ10871, CPSF2L, RC-74	uc011lav.2	Q9NV88	OTTHUMG00000164030	ENST00000521022.1:c.505_506delinsGA	chr8.hg19:g.28671112_28671113delinsGA	ENSP00000429065:p.Leu169Ser	145.0|142.0	0.0	.		71.0|72.0	61.0|62.0	.	NM_018250	B7Z560|B7Z6M5|O00224|Q8TB16	Missense_Mutation	SNP	ENST00000521022.1	hg19	CCDS34873.1																																																																																			.	.	.	none		0.421	INTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376846.1	NM_018250		GA	28671113	AG	GA	28671112	3	3	262	1	0	0	0	0	1	0	0	0	7792	304	11	3	1514	3	INTS9	8	28671112	Missense_Mutation	DNP	AG	TCGA-UZ-A9PP-01A-11D-A42J-10		28671112	117692910	30	16359											
KCNB2	9312	hgsc.bcm.edu	37	chr8	73480085	73480085	+	Missense_Mutation	SNP	T	T	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	atgctccaggagagttaagaTcaatgtggggggcctcaacc	11	8	13	9	0	2	2	2	0	0	2	3	3	3	2	3	4	2	2	3	4	3	1			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr8:73480085T>G	ENST00000523207.1	+	2	704	c.116T>G	c.(115-117)aTc>aGc	p.I39S		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	39					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)	AGAGTTAAGATCAATGTGGGG	0.572																																					p.I39S		Atlas-SNP	.											.	KCNB2	228	.	0			c.T116G						PASS	.						80	81	80					8																	73480085		2203	4300	6503	SO:0001583	missense	9312	exon2			TTAAGATCAATGT	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.116T>G	chr8.hg19:g.73480085T>G	ENSP00000430846:p.Ile39Ser	106.0	0.0	.		55.0	42.0	.	NM_004770	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	hg19	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.552042	0.86127	.	.	ENSG00000182674	ENST00000523207	T	0.80393	-1.37	5.71	5.71	0.89125	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.329901	0.17562	U	0.169793	D	0.91402	0.7287	M	0.91354	3.2	0.51012	D	0.999906	D	0.59767	0.986	D	0.64687	0.928	D	0.92898	0.6337	10	0.87932	D	0	.	15.9958	0.80243	0.0:0.0:0.0:1.0	.	39	Q92953	KCNB2_HUMAN	S	39	ENSP00000430846:I39S	ENSP00000430846:I39S	I	+	2	0	KCNB2	73642639	1.000000	0.71417	0.994000	0.49952	0.989000	0.77384	7.841000	0.86834	2.188000	0.69820	0.533000	0.62120	ATC	.	.	.	none		0.572	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		G	73480085	T	G	73480085	3	3	262	1	0	0	0	0	1	0	0	0	8020	1435	50	5	118	5	KCNB2	8	73480085	Missense_Mutation	SNP	T	TCGA-UZ-A9PP-01A-11D-A42J-10	44808973	73480085	72883937	31	16360											
ZCCHC7	84186	hgsc.bcm.edu	37	chr9	37349376	37349376	+	Missense_Mutation	SNP	A	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	caaacctggaccacccaaaaAgccgaagaccccttcaagac	16	3	6	16	1	1	2	1	0	0	2	1	4	1	3	6	1	2	0	6	1	5	1			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr9:37349376A>C	ENST00000336755.5	+	7	1116	c.1010A>C	c.(1009-1011)aAg>aCg	p.K337T	ZCCHC7_ENST00000461038.1_3'UTR|ZCCHC7_ENST00000534928.1_Missense_Mutation_p.K47T	NM_032226.2	NP_115602.2	Q8N3Z6	ZCHC7_HUMAN	zinc finger, CCHC domain containing 7	337						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)		CCACCCAAAAAGCCGAAGACC	0.413																																					p.K337T		Atlas-SNP	.											.	ZCCHC7	56	.	0			c.A1010C						PASS	.						148	130	136					9																	37349376		2203	4300	6503	SO:0001583	missense	84186	exon7			CCAAAAAGCCGAA	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.1010A>C	chr9.hg19:g.37349376A>C	ENSP00000337839:p.Lys337Thr	110.0	0.0	.		52.0	21.0	.	NM_032226	B2RCI4|D3DRQ0|Q5T0Q8|Q5T0Q9|Q5T0R0|Q8N2M1|Q8N4J2|Q8TBK8|Q9H648|Q9P0F0	Missense_Mutation	SNP	ENST00000336755.5	hg19	CCDS6608.2	.	.	.	.	.	.	.	.	.	.	A	20.8	4.047988	0.75846	.	.	ENSG00000147905	ENST00000336755;ENST00000534928	T;T	0.75821	-0.97;-0.97	5.7	4.36	0.52297	Zinc finger, CCHC retroviral-type (1);	0.284260	0.37053	N	0.002279	T	0.75443	0.3850	L	0.54323	1.7	0.38274	D	0.942228	D	0.63880	0.993	P	0.56343	0.796	T	0.76075	-0.3092	10	0.37606	T	0.19	-21.0409	6.5841	0.22610	0.7103:0.1622:0.1274:0.0	.	337	Q8N3Z6	ZCHC7_HUMAN	T	337;47	ENSP00000337839:K337T;ENSP00000443113:K47T	ENSP00000337839:K337T	K	+	2	0	ZCCHC7	37339376	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	0.957000	0.29215	2.176000	0.68965	0.445000	0.29226	AAG	.	.	.	none		0.413	ZCCHC7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052453.2	NM_032226		C	37349376	A	C	37349376	3	2	262	1	0	0	0	0	1	0	0	0	17605	72	3	5	1032	5	ZCCHC7	9	37349376	Missense_Mutation	SNP	A	TCGA-UZ-A9PP-01A-11D-A42J-10		37349376	103864055	32	16361											
C9orf3	84909	hgsc.bcm.edu	37	chr9	97767897	97767897	+	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	gaaggaagaggtgtttgaaaAggtaggggttcccgagacgg	12	7	18	4	2	0	3	0	1	0	2	1	6	1	4	1	6	0	3	1	6	5	3			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr9:97767897A>G	ENST00000375315.2	+	12	2114	c.2114A>G	c.(2113-2115)aAg>aGg	p.K705R	C9orf3_ENST00000297979.5_Splice_Site_p.K606R|C9orf3_ENST00000425634.2_Splice_Site_p.K67R|C9orf3_ENST00000433691.2_Splice_Site_p.K46R	NM_001193329.1	NP_001180258.1	Q8N6M6	AMPO_HUMAN	chromosome 9 open reading frame 3	705					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)		GTGTTTGAAAAGGTAGGGGTT	0.493																																					p.K705R		Atlas-SNP	.											.	C9orf3	100	.	0			c.A2114G						PASS	.						99	104	102					9																	97767897		2203	4300	6503	SO:0001630	splice_region_variant	84909	exon12			TTGAAAAGGTAGG	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.2115+1A>G	chr9.hg19:g.97767897A>G		200.0	0.0	.		115.0	40.0	.	NM_001193329	Q5T9B1|Q5T9B3|Q5T9B4|Q8WUL6|Q96M23|Q96SS1	Missense_Mutation	SNP	ENST00000375315.2	hg19	CCDS55328.1	.	.	.	.	.	.	.	.	.	.	A	19.52	3.842859	0.71488	.	.	ENSG00000148120	ENST00000297979;ENST00000375315;ENST00000424143;ENST00000428313;ENST00000375316;ENST00000425634;ENST00000433691;ENST00000375314	T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93	4.11	4.11	0.48088	Peptidase M1, leukotriene A4 hydrolase, aminopeptidase C-terminal (1);Armadillo-type fold (1);	0.062989	0.64402	D	0.000008	T	0.57344	0.2047	M	0.65975	2.015	0.80722	D	1	P;D;D;P;P;D	0.76494	0.945;0.999;0.982;0.885;0.827;0.974	P;D;P;P;B;P	0.83275	0.703;0.996;0.832;0.666;0.359;0.806	T	0.54111	-0.8342	10	0.19147	T	0.46	-15.1115	11.2577	0.49063	1.0:0.0:0.0:0.0	.	46;67;124;705;606;606	B4DU39;B4DQU3;E9PF71;Q8N6M6;Q8N6M6-4;Q8N6M6-2	.;.;.;AMPO_HUMAN;.;.	R	606;705;429;487;124;67;46;69	ENSP00000297979:K606R;ENSP00000364464:K705R;ENSP00000402171:K429R;ENSP00000401854:K487R;ENSP00000411815:K67R;ENSP00000399365:K46R	ENSP00000297979:K606R	K	+	2	0	C9orf3	96807718	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	5.849000	0.69465	1.854000	0.53819	0.459000	0.35465	AAG	.	.	.	none		0.493	C9orf3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032823	Missense_Mutation	G	97767897	A	G	97767897	5	3	262	1	0	0	0	0	0	0	1	0	2479	86	3	3	1855	3	C9orf3	9	97767897	Splice_Site	SNP	A	TCGA-UZ-A9PP-01A-11D-A42J-10	60418521	97767897	43445534	33	16362											
OAT	4942	hgsc.bcm.edu	37	chr10	126097337	126097337	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cataggaagaactttgtggtAgttgaaaagtttagtaatat	15	14	10	2	0	0	2	0	1	0	1	0	3	0	3	0	2	1	4	0	2	9	8			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr10:126097337A>G	ENST00000368845.5	-	3	489	c.397T>C	c.(397-399)Tac>Cac	p.Y133H	OAT_ENST00000467675.1_5'UTR|OAT_ENST00000539214.1_5'UTR	NM_000274.3	NP_000265.1	P04181	OAT_HUMAN	ornithine aminotransferase	133					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-proline biosynthetic process (GO:0055129)|protein hexamerization (GO:0034214)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ornithine-oxo-acid transaminase activity (GO:0004587)|pyridoxal phosphate binding (GO:0030170)			endometrium(2)|large_intestine(1)|lung(2)	5		all_lung(145;0.0271)|Lung NSC(174;0.0436)|Colorectal(57;0.102)|all_neural(114;0.116)			L-Ornithine(DB00129)	ACTTTGTGGTAGTTGAAAAGT	0.284																																					p.Y133H		Atlas-SNP	.											.	OAT	25	.	0			c.T397C						PASS	.						68	71	70					10																	126097337		2203	4300	6503	SO:0001583	missense	4942	exon3			TGTGGTAGTTGAA	BC016928	CCDS7639.1, CCDS53586.1	10q26	2014-09-17	2010-01-20		ENSG00000065154	ENSG00000065154	2.6.1.13		8091	protein-coding gene	gene with protein product	"Ornithine aminotransferase", "ornithine aminotransferase precursor", "gyrate atrophy"	613349				1682785	Standard	NM_000274		Approved	HOGA	uc001lhp.3	P04181	OTTHUMG00000019213	ENST00000368845.5:c.397T>C	chr10.hg19:g.126097337A>G	ENSP00000357838:p.Tyr133His	293.0	0.0	.		175.0	47.0	.	NM_000274	D3DRF0|Q16068|Q16069|Q68CS0|Q6IAV9|Q9UD03	Missense_Mutation	SNP	ENST00000368845.5	hg19	CCDS7639.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.413753	0.83449	.	.	ENSG00000065154	ENST00000368845	D	0.86164	-2.08	5.0	5.0	0.66597	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.91882	0.7430	L	0.59967	1.855	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92611	0.6099	10	0.66056	D	0.02	0.1642	15.4281	0.75069	1.0:0.0:0.0:0.0	.	133	P04181	OAT_HUMAN	H	133	ENSP00000357838:Y133H	ENSP00000357838:Y133H	Y	-	1	0	OAT	126087327	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.959000	0.93110	2.195000	0.70347	0.455000	0.32223	TAC	.	.	.	none		0.284	OAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050863.1	NM_000274		G	126097337	A	G	126097337	3	3	262	1	0	0	0	0	1	0	0	0	10810	420	15	3	954	3	OAT	10	126097337	Missense_Mutation	SNP	A	TCGA-UZ-A9PP-01A-11D-A42J-10		126097337	9437410	34	16363											
MUC2	4583	hgsc.bcm.edu	37	chr11	1092801	1092802	+	In_Frame_Ins	INS	-	-	CCTCCAACA																															caccaaccaccactcccatcINSaccaccaccaccacggtgac																								rs528672869|rs534872608	byFrequency	TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr11:1092801_1092802insCCTCCAACA	ENST00000441003.2	+	30	4647_4648	c.4620_4621insCCTCCAACA	c.(4621-4623)acc>CCTCCAACAacc	p.1540_1541insPPT	MUC2_ENST00000359061.5_In_Frame_Ins_p.1541_1542insPPT|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)	ccactcccatcaccaccaccac	0.629																																					p.I1540delinsIPPT		Atlas-INDEL	.											.	MUC2	614	.	0			c.4620_4621insCCTCCAACA						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	Exception_encountered	chr11.hg19:g.1092801_1092802insCCTCCAACA	ENSP00000415183:p.Ile1540_Thr1541insProProThr	49.0	0.0	0		31.0	13.0	0.419355	NM_002457	Q14878	In_Frame_Ins	INS	ENST00000441003.2	hg19																																																																																				.	.	.	none		0.629	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		CCTCCAACA	1092802	-	CCTCCAACA	1092801	7	5	262	1	0	1	1	0	0	0	0	0	9982	816	29	0	4738	0	MUC2	11	1092801	In_Frame_Ins	INS	-	TCGA-UZ-A9PP-01A-11D-A42J-10		1092801	133913715	35	16364											
CALCA	796	hgsc.bcm.edu	37	chr11	14992664	14992664	+	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	ctgtcttacctgaatggtgcTgcatggaggctgcctgcctg	5	12	13	11	0	1	1	0	1	1	0	1	2	1	2	3	3	5	3	3	3	2	1			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr11:14992664T>A	ENST00000486207.1	-	1	83	c.75A>T	c.(73-75)gcA>gcT	p.A25A	CALCA_ENST00000361010.3_Silent_p.A25A|CALCA_ENST00000331587.4_Silent_p.A25A|CALCA_ENST00000396372.2_Silent_p.A25A|CALCB_ENST00000523376.1_Intron|CALCA_ENST00000359642.3_Silent_p.A25A			P06881	CALCA_HUMAN	calcitonin-related polypeptide alpha	25					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						TGAATGGTGCTGCATGGAGGC	0.512																																					p.A25A		Atlas-SNP	.											.	CALCA	30	.	0			c.A75T						PASS	.						101	91	94					11																	14992664		2200	4294	6494	SO:0001819	synonymous_variant	796	exon2			TGGTGCTGCATGG	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.75A>T	chr11.hg19:g.14992664T>A		53.0	0.0	.		32.0	10.0	.	NM_001033953	Q93048|Q9UCP0	Silent	SNP	ENST00000486207.1	hg19	CCDS31432.1																																																																																			.	.	.	none		0.512	CALCA-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357068.1	NM_001741		A	14992664	T	A	14992664	2	1	262	1	0	0	0	0	0	0	0	1	2577	1567	55	5		5	CALCA	11	14992664	Silent	SNP	T	TCGA-UZ-A9PP-01A-11D-A42J-10	13899863	14992664	120013852	36	16365											
LTBP3	4054	hgsc.bcm.edu	37	chr11	65320922	65320922	+	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	gctggggacacttgtggcacTtgctctggccccaggcagtg	5	9	15	12	0	1	0	0	0	1	0	1	1	1	1	2	5	1	4	2	5	0	2			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr11:65320922T>A	ENST00000301873.5	-	4	1212	c.944A>T	c.(943-945)aAg>aTg	p.K315M	LTBP3_ENST00000322147.4_Missense_Mutation_p.K315M|LTBP3_ENST00000536982.1_Intron	NM_001130144.2	NP_001123616.1	Q9NS15	LTBP3_HUMAN	latent transforming growth factor beta binding protein 3	315	TB 1.				bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|extracellular matrix organization (GO:0030198)|lung saccule development (GO:0060430)|negative regulation of bone mineralization (GO:0030502)|negative regulation of chondrocyte differentiation (GO:0032331)|positive regulation of bone resorption (GO:0045780)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of mesenchymal stem cell proliferation (GO:1902462)|transforming growth factor beta activation (GO:0036363)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(3)	23						CTTGTGGCACTTGCTCTGGCC	0.667																																					p.K315M		Atlas-SNP	.											.	LTBP3	55	.	0			c.A944T						PASS	.						29	30	30					11																	65320922		2193	4291	6484	SO:0001583	missense	4054	exon4			TGGCACTTGCTCT	AF135960	CCDS8103.1, CCDS44647.1	11q12	2011-10-20			ENSG00000168056	ENSG00000168056		"Latent transforming growth factor, beta binding proteins"	6716	protein-coding gene	gene with protein product		602090		LTBP2		7719025	Standard	NM_001164266		Approved		uc001oej.3	Q9NS15	OTTHUMG00000166575	ENST00000301873.5:c.944A>T	chr11.hg19:g.65320922T>A	ENSP00000301873:p.Lys315Met	70.0	0.0	.		46.0	17.0	.	NM_001130144	O15107|Q96HB9|Q9H7K2|Q9UFN4	Missense_Mutation	SNP	ENST00000301873.5	hg19	CCDS44647.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.396831	0.83120	.	.	ENSG00000168056	ENST00000322147;ENST00000301873;ENST00000530866;ENST00000530426	D;D;D;T	0.87887	-1.61;-1.68;-2.31;1.95	4.8	4.8	0.61643	Matrix fibril-associated (3);TGF-beta binding (1);	0.000000	0.85682	D	0.000000	D	0.91019	0.7175	L	0.55481	1.735	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.999;0.999	D	0.91440	0.5173	10	0.62326	D	0.03	.	12.3307	0.55038	0.0:0.0:0.0:1.0	.	226;198;315;315	E9PKW1;B9EG76;Q9NS15;Q9NS15-2	.;.;LTBP3_HUMAN;.	M	315;315;226;36	ENSP00000326647:K315M;ENSP00000301873:K315M;ENSP00000435276:K226M;ENSP00000432476:K36M	ENSP00000301873:K315M	K	-	2	0	LTBP3	65077498	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.758000	0.55220	2.022000	0.59522	0.413000	0.27773	AAG	.	.	.	none		0.667	LTBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390538.1	NM_021070		A	65320922	T	A	65320922	3	1	262	1	0	0	0	0	1	0	0	0	9082	1609	56	5	3067	5	LTBP3	11	65320922	Missense_Mutation	SNP	T	TCGA-UZ-A9PP-01A-11D-A42J-10	50328258	65320922	69685594	37	16366											
ABCG4	64137	hgsc.bcm.edu	37	chr11	119020846	119020846	+	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	tcccacctacccaagcgctcAgccgtggacatcgagttcgt	8	8	9	16	4	1	0	1	0	0	0	4	2	2	1	4	1	3	2	4	1	2	2			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr11:119020846A>T	ENST00000449422.2	+	2	359	c.171A>T	c.(169-171)tcA>tcT	p.S57S	ABCG4_ENST00000307417.3_Silent_p.S57S|ABCG4_ENST00000531739.1_Silent_p.S57S	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	57					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)		CCAAGCGCTCAGCCGTGGACA	0.642																																					p.S57S		Atlas-SNP	.											.	ABCG4	77	.	0			c.A171T						PASS	.						80	86	84					11																	119020846		2200	4295	6495	SO:0001819	synonymous_variant	64137	exon2			GCGCTCAGCCGTG	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.171A>T	chr11.hg19:g.119020846A>T		92.0	0.0	.		58.0	31.0	.	NM_022169	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Silent	SNP	ENST00000449422.2	hg19	CCDS8415.1																																																																																			.	.	.	none		0.642	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169		T	119020846	A	T	119020846	2	4	262	1	0	0	0	0	0	0	0	1	70	175	7	5		5	ABCG4	11	119020846	Silent	SNP	A	TCGA-UZ-A9PP-01A-11D-A42J-10	53699924	119020846	15985670	38	16367											
CMAS	55907	hgsc.bcm.edu	37	chr12	22208120	22208120	+	Missense_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	accatgatgaaattgagaatGtggccaaacaatttggtgca	15	10	10	6	0	0	3	0	3	0	1	0	4	0	3	2	2	2	1	2	2	4	2			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr12:22208120G>A	ENST00000229329.2	+	2	428	c.298G>A	c.(298-300)Gtg>Atg	p.V100M		NM_018686.4	NP_061156.1	Q8NFW8	NEUA_HUMAN	cytidine monophosphate N-acetylneuraminic acid synthetase	100					lipopolysaccharide biosynthetic process (GO:0009103)|N-acetylneuraminate metabolic process (GO:0006054)	membrane (GO:0016020)|nucleus (GO:0005634)	N-acylneuraminate cytidylyltransferase activity (GO:0008781)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	24						AATTGAGAATGTGGCCAAACA	0.343																																					p.V100M		Atlas-SNP	.											.	CMAS	45	.	0			c.G298A						PASS	.						86	82	84					12																	22208120		2203	4300	6503	SO:0001583	missense	55907	exon2			GAGAATGTGGCCA	AF271388	CCDS8696.1	12p12.1	2008-08-04			ENSG00000111726	ENSG00000111726			18290	protein-coding gene	gene with protein product	"CMP-Neu5Ac synthetase"	603316				8889549, 7566098	Standard	NM_018686		Approved		uc001rfm.4	Q8NFW8	OTTHUMG00000169097	ENST00000229329.2:c.298G>A	chr12.hg19:g.22208120G>A	ENSP00000229329:p.Val100Met	181.0	0.0	.		157.0	42.0	.	NM_018686	Q96AX5|Q9NQZ0	Missense_Mutation	SNP	ENST00000229329.2	hg19	CCDS8696.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.604159	0.87157	.	.	ENSG00000111726	ENST00000229329	.	.	.	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	D	0.85771	0.5774	M	0.91972	3.26	0.58432	D	0.999997	D	0.76494	0.999	D	0.79784	0.993	D	0.88715	0.3225	9	0.87932	D	0	-18.9373	17.6578	0.88182	0.0:0.0:1.0:0.0	.	100	Q8NFW8	NEUA_HUMAN	M	100	.	ENSP00000229329:V100M	V	+	1	0	CMAS	22099387	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.109000	0.94291	2.597000	0.87782	0.591000	0.81541	GTG	.	.	.	none		0.343	CMAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402235.1	NM_018686		A	22208120	G	A	22208120	3	1	262	1	0	0	0	0	1	0	0	0	3577	1377	48	2	304	2	CMAS	12	22208120	Missense_Mutation	SNP	G	TCGA-UZ-A9PP-01A-11D-A42J-10		22208120	111643775	39	16368											
TPCN1	53373	hgsc.bcm.edu	37	chr12	113733831	113733831	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagcagcagtgcagcccccGccgcccagcagcccccaggc	7	2	11	21	2	1	0	1	0	0	0	1	0	1	0	6	1	6	4	6	1	0	0			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr12:113733831G>A	ENST00000335509.6	+	28	2715	c.2401G>A	c.(2401-2403)Gcc>Acc	p.A801T	TPCN1_ENST00000541517.1_Missense_Mutation_p.A873T|TPCN1_ENST00000550785.1_Missense_Mutation_p.A873T|TPCN1_ENST00000392569.4_Missense_Mutation_p.A733T	NM_017901.4	NP_060371.2	Q9ULQ1	TPC1_HUMAN	two pore segment channel 1	801					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						TGCAGCCCCCGCCGCCCAGCA	0.612																																					p.A873T		Atlas-SNP	.											TPCN1,colon,carcinoma,0,1	TPCN1	109	.	0			c.G2617A						PASS	.						26	32	30					12																	113733831		2202	4300	6502	SO:0001583	missense	53373	exon29			GCCCCCGCCGCCC	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.2401G>A	chr12.hg19:g.113733831G>A	ENSP00000335300:p.Ala801Thr	181.0	0.0	.		147.0	54.0	.	NM_001143819	A7E258|Q86XS9|Q8NC20	Missense_Mutation	SNP	ENST00000335509.6	hg19	CCDS31908.1	.	.	.	.	.	.	.	.	.	.	G	0.084	-1.178598	0.01633	.	.	ENSG00000186815	ENST00000335509;ENST00000550785;ENST00000541517;ENST00000392569	T;T;T;T	0.39787	1.06;1.06;1.06;1.06	5.33	-10.7	0.00240	.	2.170010	0.01720	N	0.028217	T	0.11965	0.0291	N	0.02011	-0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.21348	-1.0248	10	0.02654	T	1	-1.6346	7.2145	0.25951	0.6415:0.1268:0.0874:0.1443	.	873;801	Q9ULQ1-3;Q9ULQ1	.;TPC1_HUMAN	T	801;873;873;733	ENSP00000335300:A801T;ENSP00000448083:A873T;ENSP00000438125:A873T;ENSP00000376350:A733T	ENSP00000335300:A801T	A	+	1	0	TPCN1	112218214	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.447000	0.01010	-1.860000	0.01154	-1.108000	0.02087	GCC	.	.	.	none		0.612	TPCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405156.3	NM_017901		A	113733831	G	A	113733831	3	1	262	1	0	0	0	0	1	0	0	0	16407	1087	38	1	2727	1	TPCN1	12	113733831	Missense_Mutation	SNP	G	TCGA-UZ-A9PP-01A-11D-A42J-10	91525711	113733831	20118064	40	16369											
KNTC1	9735	hgsc.bcm.edu	37	chr12	123065184	123065184	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaggacgaatgtgaagaaatGttgaaactatttaaagaggt	18	10	11	2	1	0	4	0	2	0	2	0	6	0	5	0	2	1	1	0	2	8	4			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr12:123065184G>A	ENST00000333479.7	+	33	3126	c.2949G>A	c.(2947-2949)atG>atA	p.M983I	KNTC1_ENST00000450485.2_Intron	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	983					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)		GTGAAGAAATGTTGAAACTAT	0.303																																					p.M983I		Atlas-SNP	.											.	KNTC1	182	.	0			c.G2949A						PASS	.						83	77	79					12																	123065184		1851	4091	5942	SO:0001583	missense	9735	exon33			AGAAATGTTGAAA		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.2949G>A	chr12.hg19:g.123065184G>A	ENSP00000328236:p.Met983Ile	254.0	0.0	.		194.0	104.0	.	NM_014708	A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	hg19	CCDS45002.1	.	.	.	.	.	.	.	.	.	.	G	4.710	0.132087	0.08981	.	.	ENSG00000184445	ENST00000333479	T	0.13657	2.57	5.9	1.99	0.26369	.	1.288510	0.05264	N	0.516315	T	0.07503	0.0189	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35475	-0.9787	10	0.21014	T	0.42	4.0371	7.1155	0.25414	0.0:0.5751:0.255:0.1699	.	983	P50748	KNTC1_HUMAN	I	983	ENSP00000328236:M983I	ENSP00000328236:M983I	M	+	3	0	KNTC1	121631137	0.008000	0.16893	0.044000	0.18714	0.704000	0.40688	0.201000	0.17276	0.814000	0.34374	-0.519000	0.04390	ATG	.	.	.	none		0.303	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2			A	123065184	G	A	123065184	3	1	262	1	0	0	0	0	1	0	0	0	8435	1377	48	2	3075	2	KNTC1	12	123065184	Missense_Mutation	SNP	G	TCGA-UZ-A9PP-01A-11D-A42J-10	9331353	123065184	10786711	41	16370											
COL4A1	1282	hgsc.bcm.edu	37	chr13	110844571	110844572	+	Missense_Mutation	DNP	GC	GC	AG																															gtttacttactggcactcctGcaacaccatctctgccaggc																										TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr13:110844571_110844572GC>AG	ENST00000375820.4	-	24	1646_1647	c.1525_1526GC>CT	c.(1525-1527)GCa>CTa	p.A509L	COL4A1_ENST00000543140.1_Missense_Mutation_p.A509L	NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	509	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)			TGGCACTCCTGCAACACCATCT	0.515																																					p.A509V|p.A509P		Atlas-SNP	.											.	COL4A1	372	.	0			c.C1526T|c.G1525C						PASS	.																																			SO:0001583	missense	1282	exon24			ACTCCTGCAACAC|CTCCTGCAACACC	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.1525_1526delinsAG	chr13.hg19:g.110844571_110844572delinsAG	ENSP00000364979:p.Ala509Leu	64.0|65.0	0.0	.		33.0|34.0	9.0	.	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Missense_Mutation	SNP	ENST00000375820.4	hg19	CCDS9511.1																																																																																			.	.	.	none		0.515	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3			AG	110844572	GC	AG	110844571	3	1	262	1	0	0	0	0	1	0	0	0	3691	1319	46	2	3599	2	COL4A1	13	110844571	Missense_Mutation	DNP	GC	TCGA-UZ-A9PP-01A-11D-A42J-10		110844571	4325307	42	16371											
CTAGE5	4253	hgsc.bcm.edu	37	chr14	39777771	39777775	+	Frame_Shift_Del	DEL	AAATG	AAATG	-																															atgactgaattatatcaagaAaatgaaatgaaactccacag																										TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	AAATG	AAATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr14:39777771_39777775delAAATG	ENST00000280083.3	+	13	1487_1491	c.1173_1177delAAATG	c.(1171-1179)gaaaatgaafs	p.ENE391fs	CTAGE5_ENST00000341502.5_Frame_Shift_Del_p.ENE391fs|CTAGE5_ENST00000396158.2_Frame_Shift_Del_p.ENE396fs|CTAGE5_ENST00000341749.3_Frame_Shift_Del_p.ENE379fs|RP11-407N17.3_ENST00000603904.1_Frame_Shift_Del_p.ENE362fs|CTAGE5_ENST00000553352.1_Frame_Shift_Del_p.ENE362fs|CTAGE5_ENST00000396165.4_Frame_Shift_Del_p.ENE362fs|CTAGE5_ENST00000557038.1_Frame_Shift_Del_p.ENE311fs|CTAGE5_ENST00000556148.1_Frame_Shift_Del_p.ENE316fs|CTAGE5_ENST00000348007.3_Frame_Shift_Del_p.ENE391fs|RP11-407N17.3_ENST00000553728.1_Frame_Shift_Del_p.ENE926fs			O15320	CTGE5_HUMAN	CTAGE family, member 5	391					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)		TATATCAAGAAAATGAAATGAAACT	0.293																																					p.396_397del		Atlas-Indel,Pindel	.											.	CTAGE5	75	.	0			c.1187_1191del						PASS	.																																			SO:0001589	frameshift_variant	4253	exon13			.	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.1173_1177delAAATG	chr14.hg19:g.39777776_39777780delAAATG	ENSP00000280083:p.Glu391fs	312.0	0.0	0		211.0	46.0	0.218009	NM_001247989	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Frame_Shift_Del	DEL	ENST00000280083.3	hg19	CCDS9674.1																																																																																			.	.	.	none		0.293	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930		-	39777775	AAATG	-	39777771	7	5	262	1	0	1	0	1	0	0	0	0	3996	11	1	0	1254	0	CTAGE5	14	39777771	Frame_Shift_Del	DEL	AAATG	TCGA-UZ-A9PP-01A-11D-A42J-10		39777771	67571769	43	16372											
DDHD1	80821	hgsc.bcm.edu	37	chr14	53522531	53522531	+	Missense_Mutation	SNP	T	T	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	gttgagaaagcttggcttcaTatgttcataaggtaaaggat	13	13	11	4	0	2	1	2	1	0	1	2	3	2	2	0	3	1	5	0	3	5	7			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr14:53522531T>G	ENST00000323669.5	-	10	2091	c.2092A>C	c.(2092-2094)Atg>Ctg	p.M698L	DDHD1_ENST00000357758.3_Missense_Mutation_p.M698L|DDHD1_ENST00000395606.1_Missense_Mutation_p.M705L|DDHD1_ENST00000555621.1_5'Flank	NM_001160148.1	NP_001153620.1	Q8NEL9	DDHD1_HUMAN	DDHD domain containing 1	698	DDHD. {ECO:0000255|PROSITE- ProRule:PRU00378}.				cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)	25	Breast(41;0.037)					CTTGGCTTCATATGTTCATAA	0.408																																					p.M705L		Atlas-SNP	.											.	DDHD1	202	.	0			c.A2113C						PASS	.						207	201	203					14																	53522531		2203	4300	6503	SO:0001583	missense	80821	exon11			GCTTCATATGTTC	AB051492	CCDS9714.1, CCDS53895.1, CCDS53896.1	14q21	2012-11-23			ENSG00000100523	ENSG00000100523			19714	protein-coding gene	gene with protein product	"phosphatidic acid-preferring phospholipase A1"	614603	"spastic paraplegia 28 (autosomal recessive)"	SPG28		11214970, 20359546	Standard	NM_030637		Approved	KIAA1705, PA-PLA1	uc001xai.3	Q8NEL9	OTTHUMG00000140305	ENST00000323669.5:c.2092A>C	chr14.hg19:g.53522531T>G	ENSP00000327104:p.Met698Leu	79.0	0.0	.		52.0	23.0	.	NM_001160147	G5E9D1|Q8WVH3|Q96LL2|Q9C0F8	Missense_Mutation	SNP	ENST00000323669.5	hg19	CCDS53895.1	.	.	.	.	.	.	.	.	.	.	T	14.82	2.649974	0.47362	.	.	ENSG00000100523	ENST00000323669;ENST00000395606;ENST00000357758;ENST00000395610	.	.	.	5.75	5.75	0.90469	DDHD (2);	0.043024	0.85682	D	0.000000	T	0.38134	0.1029	N	0.14661	0.345	0.46167	D	0.998908	B;B;B;B	0.11235	0.004;0.002;0.003;0.003	B;B;B;B	0.15052	0.007;0.007;0.012;0.004	T	0.32666	-0.9898	9	0.05351	T	0.99	-19.4471	16.0487	0.80740	0.0:0.0:0.0:1.0	.	94;705;698;698	Q2VYF2;G5E9D1;Q8NEL9;Q8NEL9-2	.;.;DDHD1_HUMAN;.	L	698;705;698;569	.	ENSP00000327104:M698L	M	-	1	0	DDHD1	52592281	1.000000	0.71417	0.995000	0.50966	0.984000	0.73092	3.384000	0.52478	2.189000	0.69895	0.533000	0.62120	ATG	.	.	.	none		0.408	DDHD1-003	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276901.1			G	53522531	T	G	53522531	3	3	262	1	0	0	0	0	1	0	0	0	4328	1406	49	5	626	5	DDHD1	14	53522531	Missense_Mutation	SNP	T	TCGA-UZ-A9PP-01A-11D-A42J-10	13744760	53522531	53827009	44	16373											
ULK3	25989	hgsc.bcm.edu	37	chr15	75135403	75135403	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcccaggcgctcggtgaggAtgaagccgtccaggcgcggg	6	5	18	12	5	0	2	0	2	0	0	2	3	1	3	3	5	2	1	3	5	1	0			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr15:75135403A>G	ENST00000440863.2	-	1	135	c.44T>C	c.(43-45)aTc>aCc	p.I15T	ULK3_ENST00000568667.1_5'Flank|ULK3_ENST00000569437.1_Missense_Mutation_p.I15T	NM_001099436.1	NP_001092906	Q6PHR2	ULK3_HUMAN	unc-51 like kinase 3	15	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						CTCGGTGAGGATGAAGCCGTC	0.776																																					p.I15T		Atlas-SNP	.											.	ULK3	30	.	0			c.T44C						PASS	.						3	5	4					15																	75135403		1571	3479	5050	SO:0001583	missense	25989	exon1			GTGAGGATGAAGC	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.44T>C	chr15.hg19:g.75135403A>G	ENSP00000400312:p.Ile15Thr	153.0	0.0	.		98.0	29.0	.	NM_001099436	B2RXK3|B4DRQ7|D3DW68|Q9NPN5|Q9UFS4	Missense_Mutation	SNP	ENST00000440863.2	hg19	CCDS45305.1	.	.	.	.	.	.	.	.	.	.	A	14.25	2.480633	0.44044	.	.	ENSG00000140474	ENST00000440863	T	0.23552	1.9	4.54	4.54	0.55810	Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.117629	0.53938	D	0.000046	T	0.15262	0.0368	N	0.13272	0.32	0.80722	D	1	B;B	0.17038	0.002;0.02	B;B	0.24006	0.01;0.05	T	0.08534	-1.0717	10	0.14252	T	0.57	.	12.8187	0.57679	1.0:0.0:0.0:0.0	.	15;15	Q6PHR2;Q6PHR2-3	ULK3_HUMAN;.	T	15	ENSP00000400312:I15T	ENSP00000400312:I15T	I	-	2	0	ULK3	72922456	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	7.408000	0.80041	1.903000	0.55091	0.459000	0.35465	ATC	.	.	.	none		0.776	ULK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421734.4	NM_015518		G	75135403	A	G	75135403	3	3	262	1	0	0	0	0	1	0	0	0	16989	333	12	3	1438	3	ULK3	15	75135403	Missense_Mutation	SNP	A	TCGA-UZ-A9PP-01A-11D-A42J-10		75135403	27395989	45	16374											
SLC28A1	9154	hgsc.bcm.edu	37	chr15	85476403	85476403	+	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	ccacctcgttgattgcagccTctgtgatggctgccccttgt	4	13	10	14	1	1	2	0	2	1	0	2	2	1	2	5	1	3	3	5	1	0	3			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr15:85476403T>A	ENST00000286749.3	+	12	1201	c.1111T>A	c.(1111-1113)Tct>Act	p.S371T	SLC28A1_ENST00000538177.1_Intron|SLC28A1_ENST00000537216.1_Missense_Mutation_p.S371T|SLC28A1_ENST00000537624.1_Missense_Mutation_p.S371T|SLC28A1_ENST00000394573.1_Missense_Mutation_p.S371T			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	371					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)	GATTGCAGCCTCTGTGATGGC	0.572																																					p.S371T		Atlas-SNP	.											.	SLC28A1	118	.	0			c.T1111A						PASS	.						194	163	174					15																	85476403		2203	4299	6502	SO:0001583	missense	9154	exon13			GCAGCCTCTGTGA	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.1111T>A	chr15.hg19:g.85476403T>A	ENSP00000286749:p.Ser371Thr	55.0	0.0	.		34.0	14.0	.	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Missense_Mutation	SNP	ENST00000286749.3	hg19	CCDS10334.1	.	.	.	.	.	.	.	.	.	.	T	17.46	3.395020	0.62066	.	.	ENSG00000156222	ENST00000537216;ENST00000537624;ENST00000286749;ENST00000394573	T;T;T;T	0.08634	3.07;3.07;3.07;3.07	4.4	3.27	0.37495	Na dependent nucleoside transporter, C-terminal (1);	0.112318	0.64402	D	0.000006	T	0.15869	0.0382	M	0.82823	2.61	0.80722	D	1	B;B;B	0.34264	0.432;0.446;0.432	B;B;B	0.40940	0.344;0.329;0.344	T	0.00837	-1.1546	10	0.49607	T	0.09	-10.8731	8.0882	0.30784	0.0:0.0977:0.0:0.9023	.	371;371;371	B7Z533;F5H560;O00337	.;.;S28A1_HUMAN	T	371	ENSP00000440546:S371T;ENSP00000444700:S371T;ENSP00000286749:S371T;ENSP00000378074:S371T	ENSP00000286749:S371T	S	+	1	0	SLC28A1	83277407	1.000000	0.71417	0.141000	0.22245	0.782000	0.44232	7.597000	0.82733	0.718000	0.32166	0.460000	0.39030	TCT	.	.	.	none		0.572	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2			A	85476403	T	A	85476403	3	1	262	1	0	0	0	0	1	0	0	0	14544	1551	54	5	1224	5	SLC28A1	15	85476403	Missense_Mutation	SNP	T	TCGA-UZ-A9PP-01A-11D-A42J-10	10341000	85476403	17054989	46	16375											
PRR14	78994	hgsc.bcm.edu	37	chr16	30666905	30666905	+	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	tacaccaatgggactgcctcGaccaatcaggtgaggggctc	10	7	12	12	1	1	1	1	1	0	0	3	3	1	2	3	4	2	1	3	4	3	1			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr16:30666905G>A	ENST00000542965.2	+	9	1853	c.1397G>A	c.(1396-1398)cGa>cAa	p.R466Q	PRR14_ENST00000571654.1_3'UTR|FBRS_ENST00000356166.6_5'Flank|PRR14_ENST00000300835.4_Missense_Mutation_p.R466Q			Q9BWN1	PRR14_HUMAN	proline rich 14	466										breast(3)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	18			Colorectal(24;0.103)			GGACTGCCTCGACCAATCAGG	0.527																																					p.R466Q		Atlas-SNP	.											.	PRR14	45	.	0			c.G1397A						PASS	.						59	50	53					16																	30666905		2197	4300	6497	SO:0001583	missense	78994	exon10			TGCCTCGACCAAT	AK074783	CCDS10687.1	16p11.2	2008-02-05			ENSG00000156858	ENSG00000156858			28458	protein-coding gene	gene with protein product						12477932	Standard	NM_024031		Approved	MGC3121	uc002dyy.3	Q9BWN1	OTTHUMG00000132414	ENST00000542965.2:c.1397G>A	chr16.hg19:g.30666905G>A	ENSP00000441641:p.Arg466Gln	70.0	0.0	.		81.0	47.0	.	NM_024031	Q8WTX2	Missense_Mutation	SNP	ENST00000542965.2	hg19	CCDS10687.1	.	.	.	.	.	.	.	.	.	.	G	19.67	3.870580	0.72065	.	.	ENSG00000156858	ENST00000287463;ENST00000300835;ENST00000542965	T;T	0.58060	0.36;0.36	4.9	4.9	0.64082	.	0.234286	0.32218	N	0.006402	T	0.69251	0.3090	M	0.61703	1.905	0.40056	D	0.975836	D	0.89917	1.0	D	0.81914	0.995	T	0.73528	-0.3954	10	0.72032	D	0.01	-5.1769	14.9896	0.71377	0.0:0.0:1.0:0.0	.	466	Q9BWN1	PRR14_HUMAN	Q	439;466;466	ENSP00000300835:R466Q;ENSP00000441641:R466Q	ENSP00000287463:R439Q	R	+	2	0	PRR14	30574406	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	3.651000	0.54431	2.289000	0.77006	0.467000	0.42956	CGA	.	.	.	none		0.527	PRR14-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434433.1	NM_024031		A	30666905	G	A	30666905	3	1	262	1	0	0	0	0	1	0	0	0	12596	1058	37	1	1431	1	PRR14	16	30666905	Missense_Mutation	SNP	G	TCGA-UZ-A9PP-01A-11D-A42J-10		30666905	59687848	47	16376											
VMO1	284013	hgsc.bcm.edu	37	chr17	4688689	4688689	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagaataagcgcgcgtcgtTcagcgcagtgtcatcgccga	9	7	13	12	7	2	1	2	0	0	1	4	2	2	1	1	0	2	3	1	0	2	2			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr17:4688689T>C	ENST00000328739.5	-	3	656	c.577A>G	c.(577-579)Aac>Gac	p.N193D	VMO1_ENST00000416307.2_3'UTR|VMO1_ENST00000441199.2_3'UTR|VMO1_ENST00000354194.4_3'UTR	NM_182566.2	NP_872372.1	Q7Z5L0	VMO1_HUMAN	vitelline membrane outer layer 1 homolog (chicken)	193						extracellular vesicular exosome (GO:0070062)				kidney(2)|large_intestine(3)|liver(1)|lung(3)|ovary(1)|pancreas(1)	11						CGCGCGTCGTTCAGCGCAGTG	0.637																																					p.N193D		Atlas-SNP	.											.	VMO1	19	.	0			c.A577G						PASS	.						39	38	38					17																	4688689		2203	4300	6503	SO:0001583	missense	284013	exon3			CGTCGTTCAGCGC	AF521892	CCDS11055.1, CCDS45585.1, CCDS45586.1, CCDS45587.1	17p13.2	2013-03-07	2005-11-14						30387	protein-coding gene	gene with protein product						22025569	Standard	NM_182566		Approved		uc002fyx.3	Q7Z5L0		ENST00000328739.5:c.577A>G	chr17.hg19:g.4688689T>C	ENSP00000328397:p.Asn193Asp	41.0	0.0	.		29.0	5.0	.	NM_182566	C9JQ15|E9PAU9|E9PGP4|Q3SXP1|Q8IUY1	Missense_Mutation	SNP	ENST00000328739.5	hg19	CCDS11055.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.614127	0.87359	.	.	ENSG00000182853	ENST00000328739	T	0.52983	0.64	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.67804	0.2932	M	0.76838	2.35	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.72414	-0.4301	10	0.87932	D	0	-28.9276	12.295	0.54840	0.0:0.0:0.0:1.0	.	193	Q7Z5L0	VMO1_HUMAN	D	193	ENSP00000328397:N193D	ENSP00000328397:N193D	N	-	1	0	VMO1	4635429	1.000000	0.71417	0.768000	0.31515	0.847000	0.48162	6.415000	0.73328	2.016000	0.59253	0.459000	0.35465	AAC	.	.	.	none		0.637	VMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439587.1	NM_182566		C	4688689	T	C	4688689	3	2	262	1	0	0	0	0	1	0	0	0	17189	1783	62	3	35	3	VMO1	17	4688689	Missense_Mutation	SNP	T	TCGA-UZ-A9PP-01A-11D-A42J-10		4688689	76506521	48	16377											
OMG	4974	hgsc.bcm.edu	37	chr17	29622689	29622689	+	Missense_Mutation	SNP	T	T	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	ccacctgttattgtaaagggTtatctcttgcaactgaaaga	12	13	8	8	0	1	2	0	1	1	1	2	2	1	2	2	1	2	4	2	1	6	5			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr17:29622689T>G	ENST00000247271.4	-	2	922	c.661A>C	c.(661-663)Acc>Ccc	p.T221P	NF1_ENST00000358273.4_Intron|NF1_ENST00000356175.3_Intron	NM_002544.4	NP_002535.3	P23515	OMGP_HUMAN	oligodendrocyte myelin glycoprotein	221					cell adhesion (GO:0007155)|negative regulation of axonogenesis (GO:0050771)|neuron projection regeneration (GO:0031102)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of axonogenesis (GO:0050770)|regulation of collateral sprouting of intact axon in response to injury (GO:0048683)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.0?(8)|p.?(3)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)|stomach(1)	13		all_cancers(10;6.97e-11)|all_epithelial(10;0.0051)|all_hematologic(16;0.0149)|Breast(31;0.0155)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|all_lung(9;0.0468)|Lung NSC(157;0.094)		UCEC - Uterine corpus endometrioid carcinoma (4;6.64e-05)|all cancers(4;1.81e-13)|Epithelial(4;4.04e-12)|OV - Ovarian serous cystadenocarcinoma(4;9.49e-12)|GBM - Glioblastoma multiforme(4;0.121)		TTGTAAAGGGTTATCTCTTGC	0.383																																					p.T221P		Atlas-SNP	.											.	OMG	30	.	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	c.A661C						PASS	.						168	160	163					17																	29622689		2203	4300	6503	SO:0001583	missense	4974	exon2			AAAGGGTTATCTC		CCDS11265.1	17q11-q12	2008-07-18			ENSG00000126861	ENSG00000126861			8135	protein-coding gene	gene with protein product		164345				1899288, 2277079	Standard	NM_002544		Approved	OMGP	uc002hgj.3	P23515	OTTHUMG00000132870	ENST00000247271.4:c.661A>C	chr17.hg19:g.29622689T>G	ENSP00000247271:p.Thr221Pro	100.0	0.0	.		79.0	23.0	.	NM_002544	E1P659	Missense_Mutation	SNP	ENST00000247271.4	hg19	CCDS11265.1	.	.	.	.	.	.	.	.	.	.	T	15.04	2.715414	0.48622	.	.	ENSG00000126861	ENST00000247271	T	0.58060	0.36	5.72	4.61	0.57282	.	0.092549	0.47093	D	0.000251	T	0.61413	0.2345	L	0.46157	1.445	0.80722	D	1	P	0.46142	0.873	P	0.59487	0.858	T	0.58228	-0.7673	10	0.37606	T	0.19	-3.0707	12.2612	0.54651	0.1274:0.0:0.0:0.8726	.	221	P23515	OMGP_HUMAN	P	221	ENSP00000247271:T221P	ENSP00000247271:T221P	T	-	1	0	OMG	26646815	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.403000	0.59729	1.055000	0.40461	0.528000	0.53228	ACC	.	.	.	none		0.383	OMG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256350.2	NM_002544		G	29622689	T	G	29622689	3	3	262	1	0	0	0	0	1	0	0	0	10873	1725	60	5	665	5	OMG	17	29622689	Missense_Mutation	SNP	T	TCGA-UZ-A9PP-01A-11D-A42J-10	24934000	29622689	51572521	49	16378											
BPTF	2186	hgsc.bcm.edu	37	chr17	65944312	65944312	+	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	tggagcagaaacgtagcaagCagaatgccactaagctgtca	15	6	11	9	1	1	2	1	0	0	2	1	3	1	3	1	1	6	5	1	1	5	2			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr17:65944312C>T	ENST00000321892.4	+	25	8255	c.8194C>T	c.(8194-8196)Cag>Tag	p.Q2732*	BPTF_ENST00000306378.6_Nonsense_Mutation_p.Q2606*|BPTF_ENST00000335221.5_Nonsense_Mutation_p.Q2589*|RP11-855A2.3_ENST00000577385.1_RNA|BPTF_ENST00000424123.3_Nonsense_Mutation_p.Q2450*			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2732					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)			ACGTAGCAAGCAGAATGCCAC	0.453																																					p.Q2606X		Atlas-SNP	.											.	BPTF	415	.	0			c.C7816T						PASS	.						122	122	122					17																	65944312		2203	4300	6503	SO:0001587	stop_gained	2186	exon23			AGCAAGCAGAATG	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.8194C>T	chr17.hg19:g.65944312C>T	ENSP00000315454:p.Gln2732*	113.0	0.0	.		96.0	21.0	.	NM_182641	Q6NX67|Q7Z7D6|Q9UIG2	Nonsense_Mutation	SNP	ENST00000321892.4	hg19		.	.	.	.	.	.	.	.	.	.	C	50	16.265582	0.99859	.	.	ENSG00000171634	ENST00000306378;ENST00000335221;ENST00000321892;ENST00000424123	.	.	.	5.75	5.75	0.90469	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-7.5331	19.9341	0.97130	0.0:1.0:0.0:0.0	.	.	.	.	X	2606;2589;2732;260	.	ENSP00000307208:Q2606X	Q	+	1	0	BPTF	63374774	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.480000	0.45206	2.711000	0.92665	0.563000	0.77884	CAG	.	.	.	none		0.453	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		T	65944312	C	T	65944312	4	4	262	1	0	0	0	0	0	1	0	0	1497	711	25	2	8292	2	BPTF	17	65944312	Nonsense_Mutation	SNP	C	TCGA-UZ-A9PP-01A-11D-A42J-10	36321623	65944312	15250898	50	16379											
NPC1	4864	hgsc.bcm.edu	37	chr18	21112245	21112245	+	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	ttttggctttatttactgatGgccctatgagagagagagac	10	14	11	6	0	0	4	0	2	0	3	0	7	0	4	1	2	1	1	1	2	3	7			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr18:21112245G>T	ENST00000269228.5	-	25	4312	c.3758C>A	c.(3757-3759)cCa>cAa	p.P1253Q	NPC1_ENST00000412552.2_Missense_Mutation_p.P935Q	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	1253					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)					ATTTACTGATGGCCCTATGAG	0.483																																					p.P1253Q		Atlas-SNP	.											.	NPC1	114	.	0			c.C3758A						PASS	.						166	153	158					18																	21112245		2203	4300	6503	SO:0001583	missense	4864	exon25			ACTGATGGCCCTA	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.3758C>A	chr18.hg19:g.21112245G>T	ENSP00000269228:p.Pro1253Gln	66.0	0.0	.		67.0	22.0	.	NM_000271	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	hg19	CCDS11878.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.051325	0.75960	.	.	ENSG00000141458	ENST00000269228;ENST00000412552	D;D	0.94723	-3.5;-3.42	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.97362	0.9137	M	0.77616	2.38	0.80722	D	1	D;D	0.76494	0.992;0.999	D;D	0.72338	0.964;0.977	D	0.97027	0.9747	10	0.72032	D	0.01	-14.4897	20.8794	0.99867	0.0:0.0:1.0:0.0	.	1264;1253	Q59GR1;O15118	.;NPC1_HUMAN	Q	1253;935	ENSP00000269228:P1253Q;ENSP00000408606:P935Q	ENSP00000269228:P1253Q	P	-	2	0	NPC1	19366243	1.000000	0.71417	0.585000	0.28666	0.304000	0.27724	8.841000	0.92131	2.941000	0.99782	0.655000	0.94253	CCA	.	.	.	none		0.483	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271		T	21112245	G	T	21112245	3	4	262	1	0	0	0	0	1	0	0	0	10577	1348	47	4	82	4	NPC1	18	21112245	Missense_Mutation	SNP	G	TCGA-UZ-A9PP-01A-11D-A42J-10		21112245	56965003	51	16380											
KATNAL2	83473	hgsc.bcm.edu	37	chr18	44595931	44595931	+	Missense_Mutation	SNP	T	T	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	taacatttctgcatccaccaTtgtcagcaaatggagagggg	12	10	10	9	0	2	1	1	0	1	1	3	2	3	1	2	3	3	2	2	3	2	3			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr18:44595931T>G	ENST00000245121.5	+	10	946	c.752T>G	c.(751-753)aTt>aGt	p.I251S	KATNAL2_ENST00000356157.7_Missense_Mutation_p.I323S|KATNAL2_ENST00000592005.1_Intron	NM_031303.2	NP_112593.2			katanin p60 subunit A-like 2											central_nervous_system(2)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	27						GCATCCACCATTGTCAGCAAA	0.358																																					p.I251S		Atlas-SNP	.											.	KATNAL2	64	.	0			c.T752G						PASS	.						92	88	89					18																	44595931		2203	4300	6503	SO:0001583	missense	83473	exon10			CCACCATTGTCAG	BC034999	CCDS32828.1	18q21.1	2010-04-21			ENSG00000167216	ENSG00000167216		"ATPases / AAA-type"	25387	protein-coding gene	gene with protein product		614697				12477932	Standard	NM_031303		Approved	MGC33211, DKFZP667C165	uc002lco.3	Q8IYT4		ENST00000245121.5:c.752T>G	chr18.hg19:g.44595931T>G	ENSP00000245121:p.Ile251Ser	109.0	0.0	.		62.0	35.0	.	NM_031303		Missense_Mutation	SNP	ENST00000245121.5	hg19	CCDS32828.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.653075	0.88056	.	.	ENSG00000167216	ENST00000356157;ENST00000245121;ENST00000454462	D;D	0.95103	-3.61;-3.61	5.78	5.78	0.91487	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.96506	0.8860	L	0.60012	1.86	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97051	0.9764	10	0.87932	D	0	-7.6939	16.1021	0.81178	0.0:0.0:0.0:1.0	.	323	Q8IYT4	KATL2_HUMAN	S	323;251;91	ENSP00000348478:I323S;ENSP00000245121:I251S	ENSP00000245121:I251S	I	+	2	0	KATNAL2	42849929	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	6.267000	0.72546	2.210000	0.71456	0.533000	0.62120	ATT	.	.	.	none		0.358	KATNAL2-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446138.2	NM_031303		G	44595931	T	G	44595931	3	3	262	1	0	0	0	0	1	0	0	0	7993	1493	52	5	786	5	KATNAL2	18	44595931	Missense_Mutation	SNP	T	TCGA-UZ-A9PP-01A-11D-A42J-10	23483686	44595931	33481317	52	16381											
ALPK2	115701	hgsc.bcm.edu	37	chr18	56149190	56149190	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agggatttcagtcccagcatTttgcaatacttgttacactg	10	14	8	9	0	1	0	1	0	0	0	2	1	2	1	1	1	4	3	1	1	3	6			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr18:56149190T>C	ENST00000361673.3	-	13	6591	c.6378A>G	c.(6376-6378)aaA>aaG	p.K2126K		NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	2126	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						GTCCCAGCATTTTGCAATACT	0.408																																					p.K2126K		Atlas-SNP	.											.	ALPK2	487	.	0			c.A6378G						PASS	.						178	163	168					18																	56149190		2203	4300	6503	SO:0001819	synonymous_variant	115701	exon13			CAGCATTTTGCAA	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.6378A>G	chr18.hg19:g.56149190T>C		113.0	0.0	.		56.0	23.0	.	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	hg19	CCDS11966.2																																																																																			.	.	.	none		0.408	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		C	56149190	T	C	56149190	2	2	262	1	0	0	0	0	0	0	0	1	545	1838	64	3		3	ALPK2	18	56149190	Silent	SNP	T	TCGA-UZ-A9PP-01A-11D-A42J-10	11553259	56149190	21928058	53	16382											
DAZAP1	26528	hgsc.bcm.edu	37	chr19	1418337	1418342	+	In_Frame_Del	DEL	GCCAGC	GCCAGC	-																															actgtgtggggacggtgctgGccagcagaccgcacacgcta																										TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	GCCAGC	GCCAGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr19:1418337_1418342delGCCAGC	ENST00000233078.4	+	3	366_371	c.205_210delGCCAGC	c.(205-210)gccagcdel	p.AS69del	DAZAP1_ENST00000336761.6_In_Frame_Del_p.AS69del|DAZAP1_ENST00000586579.1_3'UTR	NM_018959.2	NP_061832.2	Q96EP5	DAZP1_HUMAN	DAZ associated protein 1	69	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				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)		GACGGTGCTGGCCAGCAGACCGCACA	0.515																																					p.68_70del		Atlas-Indel,Pindel	.											.	DAZAP1	52	.	0			c.204_209del						PASS	.																																			SO:0001651	inframe_deletion	26528	exon3			.		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.205_210delGCCAGC	chr19.hg19:g.1418337_1418342delGCCAGC	ENSP00000233078:p.Ala69_Ser70del	56.0	0.0	0		40.0	14.0	0.35	NM_018959	Q96MJ3|Q9NRR9	In_Frame_Del	DEL	ENST00000233078.4	hg19	CCDS12065.1																																																																																			.	.	.	none		0.515	DAZAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449522.3	NM_170711		-	1418342	GCCAGC	-	1418337	7	5	262	1	0	1	0	1	0	0	0	0	4246	1203	42	0	215	0	DAZAP1	19	1418337	In_Frame_Del	DEL	GCCAGC	TCGA-UZ-A9PP-01A-11D-A42J-10		1418337	57710646	54	16383											
SAFB	6294	hgsc.bcm.edu	37	chr19	5664085	5664085	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggccgccctggatgagcgcTaccattctgactttaaccgc	7	9	11	14	3	1	2	0	2	1	0	1	3	1	3	4	2	3	1	4	2	2	4			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr19:5664085T>C	ENST00000292123.5	+	16	2313	c.2206T>C	c.(2206-2208)Tac>Cac	p.Y736H	SAFB_ENST00000454510.1_Missense_Mutation_p.Y667H|SAFB_ENST00000433404.1_Missense_Mutation_p.Y566H|SAFB_ENST00000592224.1_Missense_Mutation_p.Y735H|SAFB_ENST00000588852.1_Missense_Mutation_p.Y736H|SAFB_ENST00000538656.1_Missense_Mutation_p.Y578H	NM_001201338.1|NM_001201339.1|NM_002967.3	NP_001188267.1|NP_001188268.1|NP_002958.2	Q15424	SAFB1_HUMAN	scaffold attachment factor B	736	Arg-rich.|Interaction with POLR2A.|Interaction with SAFB2.				chromatin organization (GO:0006325)|growth (GO:0040007)|hormone metabolic process (GO:0042445)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(6)|ovary(2)|skin(1)	23				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)		GGATGAGCGCTACCATTCTGA	0.622																																					p.Y736H	Colon(88;338 1345 6184 8214 20897)	Atlas-SNP	.											.	SAFB	74	.	0			c.T2206C						PASS	.						48	47	47					19																	5664085		2203	4300	6503	SO:0001583	missense	6294	exon16			GAGCGCTACCATT	L43631	CCDS12142.1, CCDS56077.1, CCDS59339.1, CCDS59340.1	19p13.3-p13.2	2013-02-12				ENSG00000160633		"RNA binding motif (RRM) containing"	10520	protein-coding gene	gene with protein product	"Hsp27 ERE-TATA binding protein"	602895				9605873, 8600450	Standard	NM_002967		Approved	HET, SAFB1	uc002mcg.3	Q15424		ENST00000292123.5:c.2206T>C	chr19.hg19:g.5664085T>C	ENSP00000292123:p.Tyr736His	47.0	0.0	.		38.0	19.0	.	NM_002967	A0AV56|B7Z5B6|B7ZLP6|F5H0H3|O60406|Q59HH8	Missense_Mutation	SNP	ENST00000292123.5	hg19	CCDS12142.1	.	.	.	.	.	.	.	.	.	.	T	14.31	2.496184	0.44352	.	.	ENSG00000160633	ENST00000454510;ENST00000540206;ENST00000433404;ENST00000292123;ENST00000538656	T;T;T;T	0.12039	2.75;2.9;2.72;2.73	4.99	4.99	0.66335	.	0.000000	0.45606	D	0.000353	T	0.15176	0.0366	M	0.76574	2.34	0.42698	D	0.993605	P;P;P;P;P;P;P	0.39759	0.56;0.56;0.687;0.56;0.56;0.56;0.56	B;B;B;B;B;B;B	0.37833	0.132;0.132;0.259;0.132;0.132;0.132;0.132	T	0.05131	-1.0904	10	0.12766	T	0.61	-20.0369	8.9747	0.35928	0.0:0.0842:0.0:0.9158	.	535;578;667;735;736;736;735	B7Z1C7;B7Z2F6;F5H0H3;B7ZLP5;A0AV56;Q15424;B7ZLP6	.;.;.;.;.;SAFB1_HUMAN;.	H	667;631;566;736;578	ENSP00000415895:Y667H;ENSP00000404545:Y566H;ENSP00000292123:Y736H;ENSP00000438880:Y578H	ENSP00000292123:Y736H	Y	+	1	0	SAFB	5615085	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.510000	0.67018	2.008000	0.58898	0.460000	0.39030	TAC	.	.	.	none		0.622	SAFB-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000451641.2			C	5664085	T	C	5664085	3	2	262	1	0	0	0	0	1	0	0	0	13819	1522	53	3	2268	3	SAFB	19	5664085	Missense_Mutation	SNP	T	TCGA-UZ-A9PP-01A-11D-A42J-10	4245748	5664085	53464898	55	16384											
MLLT1	4298	hgsc.bcm.edu	37	chr19	6270658	6270658	+	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	ccacgaagtgctggatgtcaCattgctcggggccgcggaca	8	7	14	12	4	1	0	1	0	0	0	2	3	1	2	2	4	2	2	2	4	1	1			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr19:6270658C>T	ENST00000252674.7	-	2	288	c.125G>A	c.(124-126)tGt>tAt	p.C42Y		NM_005934.3	NP_005925.2	Q03111	ENL_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1	42	YEATS. {ECO:0000255|PROSITE- ProRule:PRU00376}.				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						CTGGATGTCACATTGCTCGGG	0.627			T	MLL	AL						OREG0025198	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C42Y		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.G125A						PASS	.						119	92	101					19																	6270658		2203	4300	6503	SO:0001583	missense	4298	exon2			ATGTCACATTGCT		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.125G>A	chr19.hg19:g.6270658C>T	ENSP00000252674:p.Cys42Tyr	52.0	0.0	.	632	36.0	19.0	.	NM_005934	Q14768	Missense_Mutation	SNP	ENST00000252674.7	hg19	CCDS12160.1	.	.	.	.	.	.	.	.	.	.	C	15.14	2.745359	0.49151	.	.	ENSG00000130382	ENST00000252674	.	.	.	5.41	5.41	0.78517	.	0.154638	0.64402	D	0.000013	T	0.29458	0.0734	N	0.08118	0	0.46317	D	0.998986	B	0.19200	0.034	B	0.17979	0.02	T	0.17471	-1.0368	9	0.15952	T	0.53	-10.324	10.1806	0.42965	0.0:0.9095:0.0:0.0905	.	42	Q03111	ENL_HUMAN	Y	42	.	ENSP00000252674:C42Y	C	-	2	0	MLLT1	6221658	0.991000	0.36638	0.969000	0.41365	0.970000	0.65996	6.004000	0.70709	2.537000	0.85549	0.561000	0.74099	TGT	.	.	.	none		0.627	MLLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452909.1	NM_005934		T	6270658	C	T	6270658	3	4	262	1	0	0	0	0	1	0	0	0	9632	478	17	2	1598	2	MLLT1	19	6270658	Missense_Mutation	SNP	C	TCGA-UZ-A9PP-01A-11D-A42J-10	606573	6270658	52858325	56	16385											
MUC16	94025	hgsc.bcm.edu	37	chr19	9064158	9064158	+	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	tggaaggatgcacggcttctGtatgtgcagtgtctttgtaa	8	14	13	6	1	2	0	0	0	2	0	2	2	2	2	0	3	2	5	0	3	3	4	rs567112342		TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr19:9064158G>C	ENST00000397910.4	-	3	23491	c.23288C>G	c.(23287-23289)aCa>aGa	p.T7763R		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7765	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						CACGGCTTCTGTATGTGCAGT	0.488													g|||	1	0.000199681	0	0	5008	,	,		22175	0		0	False		,,,				2504	0.001				p.T7763R		Atlas-SNP	.											.	MUC16	4315	.	0			c.C23288G						PASS	.						370	348	355					19																	9064158		2079	4201	6280	SO:0001583	missense	94025	exon3			GCTTCTGTATGTG	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.23288C>G	chr19.hg19:g.9064158G>C	ENSP00000381008:p.Thr7763Arg	133.0	0.0	.		96.0	39.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	3.147	-0.175028	0.06421	.	.	ENSG00000181143	ENST00000397910	T	0.28666	1.6	1.52	1.52	0.23074	.	.	.	.	.	T	0.35335	0.0928	L	0.34521	1.04	.	.	.	D	0.71674	0.998	P	0.61328	0.887	T	0.45234	-0.9275	8	0.87932	D	0	.	6.441	0.21849	0.0:0.0:1.0:0.0	.	7763	B5ME49	.	R	7763	ENSP00000381008:T7763R	ENSP00000381008:T7763R	T	-	2	0	MUC16	8925158	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	-0.908000	0.04063	1.138000	0.42230	0.195000	0.17529	ACA	.	.	.	none		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9064158	G	C	9064158	3	2	262	1	0	0	0	0	1	0	0	0	9980	1377	48	4	20563	4	MUC16	19	9064158	Missense_Mutation	SNP	G	TCGA-UZ-A9PP-01A-11D-A42J-10	2793500	9064158	50064825	57	16386											
PRKCSH	5589	hgsc.bcm.edu	37	chr19	11558367	11558367	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggaggaggaggaggaggaGgaggaagaagaggctgaaga	16	1	23	1	0	0	4	0	1	0	3	0	13	0	12	0	9	0	1	0	9	3	0			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr19:11558367G>A	ENST00000589838.1	+	10	963	c.963G>A	c.(961-963)gaG>gaA	p.E321E	PRKCSH_ENST00000592741.1_Silent_p.E321E|PRKCSH_ENST00000587327.1_Silent_p.E321E|PRKCSH_ENST00000412601.1_Silent_p.E321E|PRKCSH_ENST00000252455.2_Silent_p.E321E|PRKCSH_ENST00000591462.1_Silent_p.E321E			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	321	Glu-rich (acidic).				cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|N-glycan processing (GO:0006491)|negative regulation of neuron projection development (GO:0010977)|nitrogen compound metabolic process (GO:0006807)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein N-linked glycosylation via asparagine (GO:0018279)|renal system development (GO:0072001)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|phosphoprotein binding (GO:0051219)|protein kinase C binding (GO:0005080)|RNA binding (GO:0003723)	p.E321_E322delEE(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(3)	19						aggaggaggaggaggaagaag	0.632																																					p.E321E		Atlas-SNP	.											.	PRKCSH	55	.	1	Deletion - In frame(1)	central_nervous_system(1)	c.G963A						PASS	.						28	28	28					19																	11558367		2200	4298	6498	SO:0001819	synonymous_variant	5589	exon11			GGAGGAGGAGGAA		CCDS32911.1, CCDS45977.1, CCDS74286.1	19p13.2	2014-01-30			ENSG00000130175	ENSG00000130175	2.7.11.1	"EF-hand domain containing"	9411	protein-coding gene	gene with protein product		177060	"polycystic liver disease"	G19P1, PCLD, PLD1		12529853	Standard	NM_002743		Approved		uc002mrt.3	P14314	OTTHUMG00000182029	ENST00000589838.1:c.963G>A	chr19.hg19:g.11558367G>A		108.0	0.0	.		74.0	9.0	.	NM_001001329	A8K318|Q96BU9|Q96D06|Q9P0W9	Silent	SNP	ENST00000589838.1	hg19	CCDS32911.1																																																																																			.	.	.	none		0.632	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1			A	11558367	G	A	11558367	2	1	262	1	0	0	0	0	0	0	0	1	12526	991	35	2		2	PRKCSH	19	11558367	Silent	SNP	G	TCGA-UZ-A9PP-01A-11D-A42J-10	2494209	11558367	47570616	58	16387											
AKAP8	10270	hgsc.bcm.edu	37	chr19	15483755	15483755	+	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	ccctgcatgcccatcacgccGtagtcgggagccatggactg	7	7	12	15	3	1	0	1	0	0	0	2	2	1	2	4	2	3	2	4	2	1	1			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr19:15483755G>A	ENST00000269701.2	-	5	828	c.768C>T	c.(766-768)taC>taT	p.Y256Y		NM_005858.3	NP_005849.1	O43823	AKAP8_HUMAN	A kinase (PRKA) anchor protein 8	256					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						CCATCACGCCGTAGTCGGGAG	0.692																																					p.Y256Y	GBM(190;1671 2163 3274 27186 30476)	Atlas-SNP	.											.	AKAP8	68	.	0			c.C768T						PASS	.						16	17	17					19																	15483755		2202	4296	6498	SO:0001819	synonymous_variant	10270	exon5			CACGCCGTAGTCG	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.768C>T	chr19.hg19:g.15483755G>A		110.0	0.0	.		67.0	25.0	.	NM_005858		Silent	SNP	ENST00000269701.2	hg19	CCDS12329.1																																																																																			.	.	.	none		0.692	AKAP8-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461293.3	NM_005858		A	15483755	G	A	15483755	2	1	262	1	0	0	0	0	0	0	0	1	457	1140	40	1		1	AKAP8	19	15483755	Silent	SNP	G	TCGA-UZ-A9PP-01A-11D-A42J-10	3925388	15483755	43645228	59	16388											
ATP1A3	478	hgsc.bcm.edu	37	chr19	42482815	42482815	+	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	ggcattctggaaggcctcctTcatttcctcgtccagaggct	6	12	10	13	1	2	1	1	0	1	1	6	2	5	2	4	4	0	2	4	4	1	3			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr19:42482815T>A	ENST00000302102.5	-	12	1723	c.1573A>T	c.(1573-1575)Aag>Tag	p.K525*	ATP1A3_ENST00000545399.1_Nonsense_Mutation_p.K538*|ATP1A3_ENST00000602133.1_Nonsense_Mutation_p.K495*|ATP1A3_ENST00000543770.1_Nonsense_Mutation_p.K536*	NM_152296.4	NP_689509.1	P13637	AT1A3_HUMAN	ATPase, Na+/K+ transporting, alpha 3 polypeptide	525					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						AAGGCCTCCTTCATTTCCTCG	0.662																																					p.K538X		Atlas-SNP	.											.	ATP1A3	117	.	0			c.A1612T						PASS	.						79	73	75					19																	42482815		2203	4300	6503	SO:0001587	stop_gained	478	exon12			CCTCCTTCATTTC		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.1573A>T	chr19.hg19:g.42482815T>A	ENSP00000302397:p.Lys525*	48.0	0.0	.		36.0	18.0	.	NM_001256214	B7Z2T0|B7Z401|F5H6J6|Q16732|Q16735|Q969K5	Nonsense_Mutation	SNP	ENST00000302102.5	hg19	CCDS12594.1	.	.	.	.	.	.	.	.	.	.	T	40	8.091975	0.98648	.	.	ENSG00000105409	ENST00000302102;ENST00000441343;ENST00000545399;ENST00000368080;ENST00000535899;ENST00000543770	.	.	.	4.02	4.02	0.46733	.	0.174631	0.48286	D	0.000184	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.2493	0.49015	0.0:0.0:0.0:1.0	.	.	.	.	X	525;525;538;495;269;536	.	ENSP00000302397:K525X	K	-	1	0	ATP1A3	47174655	1.000000	0.71417	1.000000	0.80357	0.788000	0.44548	2.706000	0.47135	1.833000	0.53350	0.459000	0.35465	AAG	.	.	.	none		0.662	ATP1A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268107.1	NM_152296		A	42482815	T	A	42482815	4	1	262	1	0	0	0	0	0	1	0	0	1130	1792	62	5	1516	5	ATP1A3	19	42482815	Nonsense_Mutation	SNP	T	TCGA-UZ-A9PP-01A-11D-A42J-10	26999060	42482815	16646168	60	16389											
APOC4	346	hgsc.bcm.edu	37	chr19	45448498	45448498	+	Missense_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	gttcctcgaatccaaagacaGcctcttgaagaagacccaca	14	7	7	13	1	1	4	0	1	1	3	4	5	3	4	4	0	1	1	4	0	4	2			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr19:45448498G>A	ENST00000592954.1	+	3	360	c.320G>A	c.(319-321)aGc>aAc	p.S107N	APOC4-APOC2_ENST00000589057.1_Intron|APOC2_ENST00000591597.1_5'Flank|APOC4_ENST00000419266.2_Missense_Mutation_p.S107N|APOC2_ENST00000590360.1_5'Flank|APOC2_ENST00000252490.4_5'Flank|APOC2_ENST00000592257.1_5'Flank	NM_001646.2	NP_001637.1	P55056	APOC4_HUMAN	apolipoprotein C-IV	107					lipid metabolic process (GO:0006629)|positive regulation of sequestering of triglyceride (GO:0010890)|triglyceride homeostasis (GO:0070328)	high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	lipid transporter activity (GO:0005319)			breast(1)|endometrium(1)|lung(2)	4	Lung NSC(12;0.00858)|all_lung(12;0.0197)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00334)|Epithelial(262;0.178)		TCCAAAGACAGCCTCTTGAAG	0.577																																					p.S107N		Atlas-SNP	.											.	APOC4	6	.	0			c.G320A						PASS	.						180	178	179					19																	45448498		2203	4300	6503	SO:0001583	missense	346	exon3			AAGACAGCCTCTT	U32576	CCDS12649.1	19q13.2	2013-09-30			ENSG00000267467	ENSG00000267467		"Apolipoproteins"	611	protein-coding gene	gene with protein product		600745				8530039	Standard	NM_001646		Approved			P55056	OTTHUMG00000180845	ENST00000592954.1:c.320G>A	chr19.hg19:g.45448498G>A	ENSP00000468236:p.Ser107Asn	88.0	0.0	.		39.0	15.0	.	NM_001646	B3KWY6|Q53YY8	Missense_Mutation	SNP	ENST00000592954.1	hg19	CCDS12649.1	.	.	.	.	.	.	.	.	.	.	G	7.462	0.644959	0.14451	.	.	ENSG00000224916	ENST00000419266;ENST00000436871	T;T	0.23348	1.91;1.91	4.26	-2.32	0.06745	.	1.088790	0.07066	N	0.834612	T	0.16041	0.0386	L	0.38838	1.175	0.09310	N	1	B	0.14805	0.011	B	0.12837	0.008	T	0.34875	-0.9811	10	0.16420	T	0.52	-3.9741	4.8774	0.13664	0.4377:0.1779:0.3844:0.0	.	107	P55056	APOC4_HUMAN	N	107	ENSP00000406381:S107N;ENSP00000412935:S107N	ENSP00000406381:S107N	S	+	2	0	APOC4	50140338	0.001000	0.12720	0.422000	0.26621	0.142000	0.21351	0.285000	0.18883	-0.339000	0.08401	0.298000	0.19748	AGC	.	.	.	none		0.577	APOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453255.1	NM_001646		A	45448498	G	A	45448498	3	1	262	1	0	0	0	0	1	0	0	0	800	971	34	2	330	2	APOC4	19	45448498	Missense_Mutation	SNP	G	TCGA-UZ-A9PP-01A-11D-A42J-10	2965683	45448498	13680485	61	16390											
MYH14	79784	hgsc.bcm.edu	37	chr19	50714027	50714028	+	Splice_Site	DNP	CG	CG	TC																															tactactccggcctcatctaCgtgagtgggctcctgctggg																										TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	C|G	C|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr19:50714027_50714028CG>TC	ENST00000596571.1	+	1	405	c.405_405CG>TC	c.(403-405)taCG>taTCg	p.Y135Y	MYH14_ENST00000601313.1_Splice_Site_p.Y135Y|MYH14_ENST00000440075.2_Splice_Site_p.Y135Y|MYH14_ENST00000376970.2_Splice_Site_p.Y135Y|MYH14_ENST00000425460.1_Splice_Site_p.Y135Y|MYH14_ENST00000598205.1_Splice_Site_p.Y135Y|MYH14_ENST00000262269.8_Splice_Site_p.Y135Y			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	135	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)		GCCTCATCTACGTGAGTGGGCT	0.644																																					p.Y135Y|.		Atlas-SNP	.											.	MYH14	261	.	0			c.C405T|c.405+1G>C						PASS	.																																			SO:0001630	splice_region_variant	79784	exon2			CATCTACGTGAGT|ATCTACGTGAGTG	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		Exception_encountered	chr19.hg19:g.50714027_50714028delinsTC		109.0|110.0	0.0	.		63.0|65.0	29.0|30.0	.	NM_001077186	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent|Splice_Site	SNP	ENST00000596571.1	hg19	CCDS59411.1																																																																																			.	.	.	none		0.644	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	Silent	TC	50714028	CG	TC	50714027	5	4	262	1	0	0	0	0	0	0	1	0	10040	550	19	1	407	1	MYH14	19	50714027	Splice_Site	DNP	CG	TCGA-UZ-A9PP-01A-11D-A42J-10	5265529	50714027	8414956	62	16391											
ESF1	51575	hgsc.bcm.edu	37	chr20	13763764	13763765	+	Frame_Shift_Ins	INS	-	-	T																															tctaaaccgctggtcactcaINSttatttcttgtttggatgac																										TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr20:13763764_13763765insT	ENST00000202816.1	-	2	129_130	c.22_23insA	c.(22-24)atgfs	p.M8fs	NDUFAF5_ENST00000463598.1_5'Flank|NDUFAF5_ENST00000378106.5_5'Flank	NM_001276380.1|NM_016649.3	NP_001263309.1|NP_057733.2	Q9H501	ESF1_HUMAN	ESF1, nucleolar pre-rRNA processing protein, homolog (S. cerevisiae)	8					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|skin(1)|stomach(1)	31						CTGGTCACTCATTATTTCTTGT	0.347																																					p.M8fs		Atlas-Indel,Pindel	.											.	ESF1	77	.	0			c.23_24insA						PASS	.																																			SO:0001589	frameshift_variant	51575	exon2			.		CCDS13117.1	20p12.1	2007-02-12	2006-11-13	2006-11-13	ENSG00000089048	ENSG00000089048			15898	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 6"	C20orf6			Standard	NM_016649		Approved	bA526K24.1	uc002wok.2	Q9H501	OTTHUMG00000031906	ENST00000202816.1:c.23dupA	chr20.hg19:g.13763766_13763766dupT	ENSP00000202816:p.Met8fs	57.0	0.0	0		60.0	17.0	0.283333	NM_001276380	Q86X92|Q9H9Q5|Q9HA35|Q9NX93|Q9P1S6	Frame_Shift_Ins	INS	ENST00000202816.1	hg19	CCDS13117.1																																																																																			.	.	.	none		0.347	ESF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078049.1	NM_016649		T	13763765	-	T	13763764	7	5	262	1	0	1	1	0	0	0	0	0	5253	217	8	0	2584	0	ESF1	20	13763764	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PP-01A-11D-A42J-10		13763764	49261756	63	16392											
PHF20	51230	hgsc.bcm.edu	37	chr20	34459634	34459634	+	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	cactgacttgccactcctttGgggatggatccggggctgca	6	10	13	12	1	0	1	0	1	0	0	2	3	2	3	3	5	2	2	3	5	0	2			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr20:34459634G>C	ENST00000374012.3	+	9	1294	c.1165G>C	c.(1165-1167)Ggg>Cgg	p.G389R	PHF20_ENST00000481202.1_3'UTR|PHF20_ENST00000439301.1_3'UTR			Q9BVI0	PHF20_HUMAN	PHD finger protein 20	389					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)					CCACTCCTTTGGGGATGGATC	0.478																																					p.G389R		Atlas-SNP	.											.	PHF20	94	.	0			c.G1165C						PASS	.						120	122	121					20																	34459634		2203	4300	6503	SO:0001583	missense	51230	exon9			TCCTTTGGGGATG	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.1165G>C	chr20.hg19:g.34459634G>C	ENSP00000363124:p.Gly389Arg	104.0	0.0	.		88.0	46.0	.	NM_016436	A7E235|B2RB56|E1P5S3|Q566Q2|Q5JWY9|Q66K49|Q9BWV4|Q9BXA3|Q9BZW3|Q9H421|Q9H4J6|Q9NZ22	Missense_Mutation	SNP	ENST00000374012.3	hg19	CCDS13268.1	.	.	.	.	.	.	.	.	.	.	G	17.38	3.374080	0.61735	.	.	ENSG00000025293	ENST00000374012;ENST00000339089;ENST00000374000	T;T;T	0.45668	1.51;0.89;0.89	5.62	5.62	0.85841	.	0.181111	0.47455	D	0.000222	T	0.42653	0.1212	L	0.43152	1.355	0.80722	D	1	P;P	0.51933	0.845;0.949	P;P	0.49752	0.467;0.621	T	0.11227	-1.0596	10	0.11485	T	0.65	.	15.156	0.72743	0.0:0.0:1.0:0.0	.	389;389	Q9BVI0;Q66K49	PHF20_HUMAN;.	R	389	ENSP00000363124:G389R;ENSP00000341900:G389R;ENSP00000363112:G389R	ENSP00000341900:G389R	G	+	1	0	PHF20	33923048	1.000000	0.71417	0.987000	0.45799	0.629000	0.37895	4.775000	0.62346	2.652000	0.90054	0.591000	0.81541	GGG	.	.	.	none		0.478	PHF20-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078949.2	NM_016436		C	34459634	G	C	34459634	3	2	262	1	0	0	0	0	1	0	0	0	11838	1348	47	4	1195	4	PHF20	20	34459634	Missense_Mutation	SNP	G	TCGA-UZ-A9PP-01A-11D-A42J-10	20695870	34459634	28565886	64	16393											
SEMG2	6407	hgsc.bcm.edu	37	chr20	43850357	43850357	+	Frame_Shift_Del	DEL	A	A	-																															tatcaattaccaggtggatcAaaaggccaattgccaagcgg																								rs372121807		TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr20:43850357delA	ENST00000372769.3	+	2	174	c.84delA	c.(82-84)tcafs	p.S28fs		NM_003008.2	NP_002999.1	Q02383	SEMG2_HUMAN	semenogelin II	28					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)				CAGGTGGATCAAAAGGCCAAT	0.398																																					p.S28X		Atlas-Indel,Pindel	.											.	SEMG2	92	.	0			c.83delC						PASS	.						81	80	80					20																	43850357		2203	4300	6503	SO:0001589	frameshift_variant	6407	exon2			.		CCDS13346.1	20q12-q13.1	2008-07-02			ENSG00000124157	ENSG00000124157			10743	protein-coding gene	gene with protein product	"Semenogelin 2"	182141				1517240, 9523691	Standard	NM_003008		Approved	SGII	uc002xnk.3	Q02383	OTTHUMG00000032566	ENST00000372769.3:c.84delA	chr20.hg19:g.43850357delA	ENSP00000361855:p.Ser28fs	190.0	0.0	0		156.0	87.0	0.557692	NM_003008	Q53ZU2|Q6X2M5|Q6X2M6	Frame_Shift_Del	DEL	ENST00000372769.3	hg19	CCDS13346.1																																																																																			.	.	.	none		0.398	SEMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079417.1	NM_003008		-	43850357	A	-	43850357	7	5	262	1	0	1	0	1	0	0	0	0	14058	117	5	0	90	0	SEMG2	20	43850357	Frame_Shift_Del	DEL	A	TCGA-UZ-A9PP-01A-11D-A42J-10	9390723	43850357	19175163	65	16394											
PRIC285	85441	hgsc.bcm.edu	37	chr20	62193551	62193551	+	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	ccgctccaggaacctgctggGgatcactgagagggggcagc	8	5	16	12	1	1	1	1	1	0	1	2	4	2	3	3	5	3	3	3	5	1	0			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr20:62193551G>C	ENST00000467148.1	-	10	6472	c.6403C>G	c.(6403-6405)Ccc>Gcc	p.P2135A	HELZ2_ENST00000427522.2_Missense_Mutation_p.P1566A	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2135	Interaction with THRAP3.				cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										AACCTGCTGGGGATCACTGAG	0.672																																					p.P2135A		Atlas-SNP	.											.	.	.	.	0			c.C6403G						PASS	.						11	13	13					20																	62193551		2168	4244	6412	SO:0001583	missense	85441	exon11			TGCTGGGGATCAC	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.6403C>G	chr20.hg19:g.62193551G>C	ENSP00000417401:p.Pro2135Ala	69.0	0.0	.		73.0	19.0	.	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	hg19	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	G	9.651	1.141671	0.21205	.	.	ENSG00000130589	ENST00000427522;ENST00000467148	T;T	0.80033	-1.33;-1.22	2.52	-1.22	0.09494	.	1.595590	0.03742	N	0.255101	T	0.72162	0.3426	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	0.54629	-0.8265	10	0.66056	D	0.02	-10.8255	2.2456	0.04031	0.1157:0.1269:0.3287:0.4288	.	2135;1566	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	A	1566;2135	ENSP00000393257:P1566A;ENSP00000417401:P2135A	ENSP00000393257:P1566A	P	-	1	0	RP4-697K14.7	61663995	0.000000	0.05858	0.005000	0.12908	0.703000	0.40648	-0.571000	0.05889	-0.220000	0.09988	0.313000	0.20887	CCC	.	.	.	none		0.672	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		C	62193551	G	C	62193551	3	2	262	1	0	0	0	0	1	0	0	0	12495	1232	43	4	1586	4	PRIC285	20	62193551	Missense_Mutation	SNP	G	TCGA-UZ-A9PP-01A-11D-A42J-10	18343194	62193551	831969	66	16395											
IL10RB	3588	hgsc.bcm.edu	37	chr21	34648956	34648956	+	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	ccttgacggaatgtgatttcTcaagtctttccaagtatggt	9	15	9	8	1	2	2	1	2	2	0	4	3	3	3	2	2	0	1	2	2	4	4			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr21:34648956T>A	ENST00000290200.2	+	3	337	c.229T>A	c.(229-231)Tca>Aca	p.S77T	AP000295.9_ENST00000433395.2_Silent_p.S204S	NM_000628.4	NP_000619.3	Q08334	I10R2_HUMAN	interleukin 10 receptor, beta	77	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|inflammatory response (GO:0006954)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|interleukin-28 receptor complex (GO:0032002)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	14						ATGTGATTTCTCAAGTCTTTC	0.413																																					p.S77T	Melanoma(67;315 1275 21667 21943 44564)	Atlas-SNP	.											.	IL10RB	37	.	0			c.T229A						PASS	.						226	201	209					21																	34648956		2203	4300	6503	SO:0001583	missense	3588	exon3			GATTTCTCAAGTC	U08988	CCDS13623.1	21q22.11	2014-09-17			ENSG00000243646	ENSG00000243646		"Interleukins and interleukin receptors", "CD molecules"	5965	protein-coding gene	gene with protein product		123889		CRFB4, D21S58, D21S66		8314576, 9312047	Standard	NM_000628		Approved	CRF2-4, CDW210B, IL-10R2		Q08334	OTTHUMG00000065128	ENST00000290200.2:c.229T>A	chr21.hg19:g.34648956T>A	ENSP00000290200:p.Ser77Thr	91.0	0.0	.		52.0	20.0	.	NM_000628	Q9BUU4	Missense_Mutation	SNP	ENST00000290200.2	hg19	CCDS13623.1	.	.	.	.	.	.	.	.	.	.	T	15.79	2.937266	0.52972	.	.	ENSG00000243646	ENST00000290200;ENST00000539894	T	0.69435	-0.4	5.73	4.55	0.56014	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.148799	0.44902	D	0.000416	T	0.71239	0.3316	L	0.55017	1.72	0.28360	N	0.920525	D;D;D;P	0.89917	1.0;1.0;1.0;0.947	D;D;D;P	0.75484	0.986;0.986;0.986;0.668	T	0.62647	-0.6810	10	0.02654	T	1	-5.4307	10.0206	0.42041	0.0:0.0:0.1697:0.8303	.	79;77;77;77	Q6ZVU9;Q08334;B4DSX5;F5H766	.;I10R2_HUMAN;.;.	T	77	ENSP00000290200:S77T	ENSP00000290200:S77T	S	+	1	0	IL10RB	33570826	1.000000	0.71417	0.957000	0.39632	0.271000	0.26615	4.110000	0.57831	1.066000	0.40716	0.533000	0.62120	TCA	.	.	.	none		0.413	IL10RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139831.3			A	34648956	T	A	34648956	3	1	262	1	0	0	0	0	1	0	0	0	7628	1551	54	5	239	5	IL10RB	21	34648956	Missense_Mutation	SNP	T	TCGA-UZ-A9PP-01A-11D-A42J-10		34648956	13480939	67	16396											
COL18A1	80781	hgsc.bcm.edu	37	chr21	46896343	46896343	+	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	ctggaggcagcagcacggaaGattccagaagtgaagaagtc	14	5	14	8	1	0	4	0	1	0	3	2	6	1	6	1	3	2	3	1	3	4	1			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr21:46896343G>A	ENST00000359759.4	+	5	2143	c.2122G>A	c.(2122-2124)Gat>Aat	p.D708N	COL18A1_ENST00000400337.2_Missense_Mutation_p.D293N|COL18A1_ENST00000355480.5_Missense_Mutation_p.D473N			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	708	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)		CAGCACGGAAGATTCCAGAAG	0.627																																					p.D473N		Atlas-SNP	.											.	COL18A1	129	.	0			c.G1417A						PASS	.						73	78	76					21																	46896343		2092	4213	6305	SO:0001583	missense	80781	exon5			ACGGAAGATTCCA		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.2122G>A	chr21.hg19:g.46896343G>A	ENSP00000352798:p.Asp708Asn	90.0	0.0	.		64.0	32.0	.	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	hg19		.	.	.	.	.	.	.	.	.	.	G	14.41	2.526689	0.44969	.	.	ENSG00000182871	ENST00000400337;ENST00000400347;ENST00000355480;ENST00000359759;ENST00000539645	D;D;D	0.90788	-2.73;-2.69;-2.6	3.85	2.95	0.34219	.	0.864751	0.10135	U	0.711574	D	0.86439	0.5933	L	0.39245	1.2	0.09310	N	0.999996	P;P;P	0.49961	0.884;0.93;0.827	B;P;B	0.44647	0.341;0.456;0.342	T	0.74811	-0.3538	10	0.30854	T	0.27	.	7.9022	0.29742	0.1233:0.0:0.8766:0.0	.	708;473;293	P39060;P39060-1;P39060-2	COIA1_HUMAN;.;.	N	293;293;473;708;708	ENSP00000383191:D293N;ENSP00000347665:D473N;ENSP00000352798:D708N	ENSP00000347665:D473N	D	+	1	0	COL18A1	45720771	0.542000	0.26426	0.214000	0.23707	0.174000	0.22865	3.652000	0.54439	0.918000	0.36919	0.391000	0.25812	GAT	.	.	.	none		0.627	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			A	46896343	G	A	46896343	3	1	262	1	0	0	0	0	1	0	0	0	3677	942	33	2	2254	2	COL18A1	21	46896343	Missense_Mutation	SNP	G	TCGA-UZ-A9PP-01A-11D-A42J-10	12247387	46896343	1233552	68	16397											
TRMT2A	27037	hgsc.bcm.edu	37	chr22	20104104	20104104	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctcagggcactgctgctcTcctggccacagctctccatg	6	9	10	16	0	3	0	1	0	2	0	5	0	3	0	3	2	4	5	3	2	0	0			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chr22:20104104T>C	ENST00000252136.7	-	2	444	c.56A>G	c.(55-57)gAg>gGg	p.E19G	RANBP1_ENST00000331821.3_5'Flank|TRMT2A_ENST00000403707.3_Missense_Mutation_p.E19G|TRMT2A_ENST00000492988.1_5'Flank|TRMT2A_ENST00000439169.2_Missense_Mutation_p.E19G|RANBP1_ENST00000402752.1_5'Flank|TRMT2A_ENST00000404751.3_Missense_Mutation_p.E19G|RANBP1_ENST00000430524.1_Intron	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)	19					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						ACTGCTGCTCTCCTGGCCACA	0.697																																					p.E19G		Atlas-SNP	.											.	TRMT2A	34	.	0			c.A56G						PASS	.						17	22	20					22																	20104104		2106	4119	6225	SO:0001583	missense	27037	exon2			CTGCTCTCCTGGC	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.56A>G	chr22.hg19:g.20104104T>C	ENSP00000252136:p.Glu19Gly	43.0	0.0	.		25.0	7.0	.	NM_001257994	D3DX25|Q32P57|Q96ME6|Q9H732	Missense_Mutation	SNP	ENST00000252136.7	hg19	CCDS13774.1	.	.	.	.	.	.	.	.	.	.	T	16.64	3.180784	0.57800	.	.	ENSG00000099899	ENST00000252136;ENST00000403707;ENST00000404751;ENST00000439169;ENST00000445045	T;T;T	0.44083	0.93;0.93;0.93	5.01	5.01	0.66863	.	0.442996	0.22937	N	0.053835	T	0.31009	0.0783	L	0.29908	0.895	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.07947	-1.0746	10	0.36615	T	0.2	-5.047	11.3948	0.49836	0.0:0.0:0.0:1.0	.	19;19;19	B4E213;F2Z2W7;Q8IZ69	.;.;TRM2A_HUMAN	G	19;19;19;19;7	ENSP00000252136:E19G;ENSP00000385807:E19G;ENSP00000395738:E19G	ENSP00000252136:E19G	E	-	2	0	TRMT2A	18484104	0.543000	0.26434	0.144000	0.22314	0.089000	0.18198	0.964000	0.29306	2.023000	0.59567	0.402000	0.26972	GAG	.	.	.	none		0.697	TRMT2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318168.3	NM_022727		C	20104104	T	C	20104104	3	2	262	1	0	0	0	0	1	0	0	0	16577	1551	54	3	1865	3	TRMT2A	22	20104104	Missense_Mutation	SNP	T	TCGA-UZ-A9PP-01A-11D-A42J-10		20104104	31200462	69	16398											
PNPLA4	8228	hgsc.bcm.edu	37	chrX	7868821	7868821	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcctcttgcttgggggaaaaAgggcttggttgagtctcacc	7	12	13	9	0	2	1	1	1	2	0	4	2	3	2	2	4	1	3	2	4	2	4			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chrX:7868821A>G	ENST00000381042.4	-	7	838	c.668T>C	c.(667-669)cTt>cCt	p.L223P	PNPLA4_ENST00000444736.1_Missense_Mutation_p.L223P|PNPLA4_ENST00000537427.1_Missense_Mutation_p.L136P	NM_004650.2	NP_004641.1	P41247	PLPL4_HUMAN	patatin-like phospholipase domain containing 4	223					lipid catabolic process (GO:0016042)		triglyceride lipase activity (GO:0004806)			kidney(1)|large_intestine(3)|lung(2)|prostate(1)	7		Colorectal(8;0.0329)|Medulloblastoma(8;0.232)				TGGGGGAAAAAGGGCTTGGTT	0.353																																					p.L223P		Atlas-SNP	.											.	PNPLA4	24	.	0			c.T668C						PASS	.						57	52	54					X																	7868821		2203	4299	6502	SO:0001583	missense	8228	exon7			GGAAAAAGGGCTT	U03886	CCDS14129.1, CCDS55368.1	Xp22.3	2014-03-14			ENSG00000006757	ENSG00000006757	3.1.1.3	"Patatin-like phospholipase domain containing"	24887	protein-coding gene	gene with protein product		300102				7806223, 16799181, 19029121	Standard	NM_004650		Approved	DXS1283E, GS2, iPLA2eta	uc011mhr.1	P41247	OTTHUMG00000021103	ENST00000381042.4:c.668T>C	chrX.hg19:g.7868821A>G	ENSP00000370430:p.Leu223Pro	240.0	0.0	.		148.0	6.0	.	NM_004650	A8K1H3|B4E362|Q8WW83	Missense_Mutation	SNP	ENST00000381042.4	hg19	CCDS14129.1	.	.	.	.	.	.	.	.	.	.	A	13.79	2.341460	0.41498	.	.	ENSG00000006757	ENST00000381042;ENST00000444736;ENST00000537427	T;T;T	0.81078	-1.45;-1.45;-1.45	4.38	4.38	0.52667	Acyl transferase/acyl hydrolase/lysophospholipase (1);	0.193685	0.33127	N	0.005243	D	0.89866	0.6839	M	0.89715	3.055	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	D	0.90635	0.4570	10	0.87932	D	0	-22.634	9.3053	0.37872	1.0:0.0:0.0:0.0	.	223	P41247	PLPL4_HUMAN	P	223;223;136	ENSP00000370430:L223P;ENSP00000415245:L223P;ENSP00000443157:L136P	ENSP00000370430:L223P	L	-	2	0	PNPLA4	7828821	1.000000	0.71417	0.139000	0.22197	0.388000	0.30384	5.486000	0.66856	1.452000	0.47756	0.481000	0.45027	CTT	.	.	.	none		0.353	PNPLA4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055687.1	NM_004650		G	7868821	A	G	7868821	3	3	262	1	0	0	0	0	1	0	0	0	12174	72	3	3	97	3	PNPLA4	23	7868821	Missense_Mutation	SNP	A	TCGA-UZ-A9PP-01A-11D-A42J-10		7868821	147401739	70	16399											
BCOR	54880	hgsc.bcm.edu	37	chrX	39930898	39930898	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgaagaactgacctcacagtAagcagcgggtagacataaaa	17	6	10	8	1	1	4	1	2	0	2	1	4	1	4	1	1	3	3	1	1	6	3			TCGA-UZ-A9PP-01A-11D-A42J-10	TCGA-UZ-A9PP-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b34905a0-79be-4958-821c-f27af735d65e	09c514d0-26ff-4e99-b400-1019a9243565	g.chrX:39930898A>G	ENST00000378444.4	-	5	3271	c.3043T>C	c.(3043-3045)Tac>Cac	p.Y1015H	BCOR_ENST00000397354.3_Missense_Mutation_p.Y1015H|BCOR_ENST00000342274.4_Missense_Mutation_p.Y1015H|BCOR_ENST00000378455.4_Intron	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	1015					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						ACCTCACAGTAAGCAGCGGGT	0.328			"F, N, S, T"	RARA	"retinoblastoma, AML, APL(translocation)"		oculo-facio-cardio-dental genetic																														p.Y1015H		Atlas-SNP	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	0			c.T3043C						PASS	.						82	77	79					X																	39930898		2202	4296	6498	SO:0001583	missense	54880	exon5			CACAGTAAGCAGC	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.3043T>C	chrX.hg19:g.39930898A>G	ENSP00000367705:p.Tyr1015His	234.0	0.0	.		148.0	126.0	.	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Missense_Mutation	SNP	ENST00000378444.4	hg19	CCDS48093.1	.	.	.	.	.	.	.	.	.	.	A	16.01	3.002638	0.54254	.	.	ENSG00000183337	ENST00000397354;ENST00000378444;ENST00000342274;ENST00000406200	T;T;T;T	0.12879	2.64;2.64;2.64;2.64	5.87	5.87	0.94306	.	.	.	.	.	T	0.19087	0.0458	L	0.29908	0.895	0.34462	D	0.701845	D;P	0.57257	0.979;0.955	P;P	0.51487	0.671;0.542	T	0.14671	-1.0464	9	0.87932	D	0	-15.5403	15.4001	0.74834	1.0:0.0:0.0:0.0	.	1015;1015	Q6W2J9;Q6W2J9-2	BCOR_HUMAN;.	H	1015	ENSP00000380512:Y1015H;ENSP00000367705:Y1015H;ENSP00000345923:Y1015H;ENSP00000384485:Y1015H	ENSP00000345923:Y1015H	Y	-	1	0	BCOR	39815842	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.170000	0.64990	2.088000	0.63022	0.486000	0.48141	TAC	.	.	.	none		0.328	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		G	39930898	A	G	39930898	3	3	262	1	0	0	0	0	1	0	0	0	1386	362	13	3	2268	3	BCOR	23	39930898	Missense_Mutation	SNP	A	TCGA-UZ-A9PP-01A-11D-A42J-10	32062077	39930898	115339662	71	16400											
ATAD3B	83858	hgsc.bcm.edu	37	chr1	1426049	1426049	+	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	ctcagctggccgtgtcctggCaggtgagtcaggctccggca	5	8	15	13	2	2	1	2	1	0	0	4	1	4	1	3	5	1	4	3	5	0	0			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr1:1426049C>T	ENST00000308647.7	+	15	1728	c.1612C>T	c.(1612-1614)Cag>Tag	p.Q538*		NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	538						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)		CGTGTCCTGGCAGGTGAGTCA	0.667																																					p.Q538X		Atlas-SNP	.											.	ATAD3B	68	.	0			c.C1612T						PASS	.						16	18	17					1																	1426049		2161	4212	6373	SO:0001587	stop_gained	83858	exon15			TCCTGGCAGGTGA	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.1612C>T	chr1.hg19:g.1426049C>T	ENSP00000311766:p.Gln538*	183.0	0.0	.		131.0	43.0	.	NM_031921	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Nonsense_Mutation	SNP	ENST00000308647.7	hg19	CCDS30.1	.	.	.	.	.	.	.	.	.	.	c	24.8	4.566605	0.86439	.	.	ENSG00000160072	ENST00000378737;ENST00000308647	.	.	.	2.55	2.55	0.30701	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	12.43	0.55569	0.0:1.0:0.0:0.0	.	.	.	.	X	372;538	.	ENSP00000311766:Q538X	Q	+	1	0	ATAD3B	1415912	1.000000	0.71417	0.998000	0.56505	0.070000	0.16714	7.377000	0.79668	1.416000	0.47057	0.205000	0.17691	CAG	.	.	.	none		0.667	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921		T	1426049	C	T	1426049	4	4	263	1	0	0	0	0	0	1	0	0	1074	711	25	2	1670	2	ATAD3B	1	1426049	Nonsense_Mutation	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10		1426049	247824572	1	16401											
MYSM1	114803	hgsc.bcm.edu	37	chr1	59165666	59165666	+	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	ctaagcctcaccctggctgtGcccccgccgccgctaccacg	5	6	9	21	4	1	0	1	0	0	0	1	0	1	0	7	1	3	2	7	1	2	2			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr1:59165666G>T	ENST00000472487.1	-	1	98	c.59C>A	c.(58-60)gCa>gAa	p.A20E		NM_001085487.2	NP_001078956.1	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1	20					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)					CCCTGGCTGTGCCCCCGCCGC	0.662																																					p.A20E		Atlas-SNP	.											.	MYSM1	50	.	0			c.C59A						PASS	.						32	42	39					1																	59165666		1908	4114	6022	SO:0001583	missense	114803	exon1			GGCTGTGCCCCCG	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.59C>A	chr1.hg19:g.59165666G>T	ENSP00000418734:p.Ala20Glu	57.0	0.0	.		43.0	14.0	.	NM_001085487	A8KA54|B3KX65|Q68DD3|Q6AI53|Q7Z3G8|Q96PX3	Missense_Mutation	SNP	ENST00000472487.1	hg19	CCDS41343.1	.	.	.	.	.	.	.	.	.	.	G	4.008	-0.001209	0.07819	.	.	ENSG00000162601	ENST00000472487	T	0.22134	1.97	4.53	1.54	0.23209	.	1.367050	0.04456	N	0.373450	T	0.13457	0.0326	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.26608	-1.0098	10	0.30854	T	0.27	-0.2712	4.2456	0.10670	0.2083:0.1914:0.6003:0.0	.	20	Q5VVJ2	MYSM1_HUMAN	E	20	ENSP00000418734:A20E	ENSP00000418734:A20E	A	-	2	0	MYSM1	58938254	0.995000	0.38212	0.098000	0.21074	0.449000	0.32228	2.129000	0.42055	0.597000	0.29811	0.561000	0.74099	GCA	.	.	.	none		0.662	MYSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026343.2	XM_055481		T	59165666	G	T	59165666	3	4	263	1	0	0	0	0	1	0	0	0	10108	1319	46	4	2507	4	MYSM1	1	59165666	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	57739617	59165666	190084955	2	16402											
FUBP1	8880	hgsc.bcm.edu	37	chr1	78426050	78426050	+	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	gaggagccgggcctggtggtCcaggattataaggtgcaggg	8	7	19	7	1	0	0	0	0	0	0	1	3	1	2	3	7	2	1	3	7	2	2			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr1:78426050C>G	ENST00000370768.2	-	15	1556	c.1475G>C	c.(1474-1476)gGa>gCa	p.G492A	FUBP1_ENST00000436586.2_Missense_Mutation_p.G513A|FUBP1_ENST00000370767.1_Missense_Mutation_p.G492A	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1	492	Pro-rich.				positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						GCCTGGTGGTCCAGGATTATA	0.532			"F, N"		oligodendroglioma																																p.G492A		Atlas-SNP	.		Rec	yes		1	1p13.1	8880	far upstream element (FUSE) binding protein 1		O	.	FUBP1	112	.	0			c.G1475C						PASS	.						38	43	41					1																	78426050		2203	4300	6503	SO:0001583	missense	8880	exon15			GGTGGTCCAGGAT	U05040	CCDS683.1	1p31.1	2008-02-05			ENSG00000162613	ENSG00000162613			4004	protein-coding gene	gene with protein product		603444		FUBP		8125259	Standard	XM_005271309		Approved	FBP	uc001dii.3	Q96AE4	OTTHUMG00000040799	ENST00000370768.2:c.1475G>C	chr1.hg19:g.78426050C>G	ENSP00000359804:p.Gly492Ala	311.0	0.0	.		242.0	102.0	.	NM_003902	Q12828	Missense_Mutation	SNP	ENST00000370768.2	hg19	CCDS683.1	.	.	.	.	.	.	.	.	.	.	C	16.79	3.220035	0.58560	.	.	ENSG00000162613	ENST00000370773;ENST00000370767;ENST00000370768;ENST00000394922;ENST00000436586	T;T;T	0.34472	1.36;1.42;1.38	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.42381	0.1200	L	0.46741	1.465	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.73708	0.981;0.981	T	0.05920	-1.0856	10	0.12103	T	0.63	-15.6155	19.9795	0.97321	0.0:1.0:0.0:0.0	.	513;492	B4DT31;Q96AE4	.;FUBP1_HUMAN	A	491;492;492;477;513	ENSP00000359803:G492A;ENSP00000359804:G492A;ENSP00000389536:G513A	ENSP00000294623:G491A	G	-	2	0	FUBP1	78198638	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.818000	0.86416	2.720000	0.93068	0.650000	0.86243	GGA	.	.	.	none		0.532	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902		G	78426050	C	G	78426050	3	3	263	1	0	0	0	0	1	0	0	0	6099	855	30	4	483	4	FUBP1	1	78426050	Missense_Mutation	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10	19260384	78426050	170824571	3	16403											
CCT3	7203	hgsc.bcm.edu	37	chr1	156303343	156303343	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttattctcctcttaccaagaAtaattactgatgtggtccca	11	15	5	10	0	2	2	0	1	2	1	4	2	3	2	3	1	2	0	3	1	6	5			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr1:156303343A>G	ENST00000295688.3	-	5	579	c.299T>C	c.(298-300)aTt>aCt	p.I100T	CCT3_ENST00000368256.3_5'UTR|CCT3_ENST00000368261.3_Missense_Mutation_p.I55T|CCT3_ENST00000368259.2_Missense_Mutation_p.I62T|CCT3_ENST00000472765.2_Missense_Mutation_p.I55T	NM_005998.4	NP_005989.3	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 (gamma)	100					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|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)					CTTACCAAGAATAATTACTGA	0.398																																					p.I100T		Atlas-SNP	.											.	CCT3	61	.	0			c.T299C						PASS	.						117	120	119					1																	156303343		2203	4300	6503	SO:0001583	missense	7203	exon5			CCAAGAATAATTA	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.299T>C	chr1.hg19:g.156303343A>G	ENSP00000295688:p.Ile100Thr	65.0	0.0	.		47.0	23.0	.	NM_005998	A6NE14|Q5SZY1|Q9BR64	Missense_Mutation	SNP	ENST00000295688.3	hg19	CCDS1140.2	.	.	.	.	.	.	.	.	.	.	A	24.9	4.583526	0.86748	.	.	ENSG00000163468	ENST00000295688;ENST00000368259;ENST00000368261;ENST00000472765;ENST00000413555;ENST00000496684;ENST00000533194;ENST00000446905;ENST00000478640;ENST00000415548	D;D;D;D;D;D;D;D;D;D	0.91577	-1.56;-1.56;-1.56;-1.56;-1.56;-1.56;-1.56;-1.56;-1.56;-2.87	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	D	0.96658	0.8909	H	0.98005	4.125	0.80722	D	1	D;P;D	0.67145	0.996;0.916;0.99	D;P;D	0.71184	0.972;0.836;0.953	D	0.97801	1.0244	10	0.87932	D	0	-13.7794	12.6112	0.56552	1.0:0.0:0.0:0.0	.	62;100;100	P49368-2;E9PAQ6;P49368	.;.;TCPG_HUMAN	T	100;62;55;55;124;100;21;86;79;100	ENSP00000295688:I100T;ENSP00000357242:I62T;ENSP00000357244:I55T;ENSP00000431543:I55T;ENSP00000413308:I124T;ENSP00000434232:I100T;ENSP00000434481:I21T;ENSP00000388799:I86T;ENSP00000435026:I79T;ENSP00000413431:I100T	ENSP00000295688:I100T	I	-	2	0	CCT3	154569967	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.593000	0.90832	2.234000	0.73211	0.528000	0.53228	ATT	.	.	.	none		0.398	CCT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060602.3	NM_005998		G	156303343	A	G	156303343	3	3	263	1	0	0	0	0	1	0	0	0	2956	101	4	3	1378	3	CCT3	1	156303343	Missense_Mutation	SNP	A	TCGA-UZ-A9PR-01A-11D-A42J-10	77877293	156303343	92947278	4	16404											
SLAMF6	114836	hgsc.bcm.edu	37	chr1	160460386	160460386	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcttcttttcctcaaaacaaGtaacagcagtatgatgaaac	15	12	5	9	0	3	2	1	2	2	0	4	2	4	2	1	0	4	3	1	0	6	5	rs148686177		TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr1:160460386G>A	ENST00000368057.3	-	4	796	c.736C>T	c.(736-738)Ctt>Ttt	p.L246F	SLAMF6_ENST00000368059.3_Missense_Mutation_p.L246F|SLAMF6_ENST00000368055.1_Missense_Mutation_p.L135F			Q96DU3	SLAF6_HUMAN	SLAM family member 6	246						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)			CTCAAAACAAGTAACAGCAGT	0.388																																					p.L246F		Atlas-SNP	.											.	SLAMF6	46	.	0			c.C736T						PASS	.	G	PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU	1,4405	2.1+/-5.4	0,1,2202	88	87	87		736,589,403,736	-6.6	0	1	dbSNP_134	87	0,8600		0,0,4300	no	missense,missense,missense,missense	SLAMF6	NM_001184714.1,NM_001184715.1,NM_001184716.1,NM_052931.4	22,22,22,22	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	246/333,197/283,135/222,246/332	160460386	1,13005	2203	4300	6503	SO:0001583	missense	114836	exon4			AAACAAGTAACAG	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.736C>T	chr1.hg19:g.160460386G>A	ENSP00000357036:p.Leu246Phe	300.0	0.0	.		271.0	117.0	.	NM_052931	A6NMW2|B2R8X8|Q14CF0|Q5TAS4|Q5TAS6|Q5TAT3|Q96DV0	Missense_Mutation	SNP	ENST00000368057.3	hg19	CCDS53394.1	.	.	.	.	.	.	.	.	.	.	G	1.642	-0.516181	0.04200	2.27E-4	0.0	ENSG00000162739	ENST00000368059;ENST00000368057;ENST00000368055	T;T;T	0.39592	1.07;1.07;1.07	3.27	-6.55	0.01854	.	7.407340	0.00166	N	0.000000	T	0.05227	0.0139	N	0.12182	0.205	0.09310	N	1	B;B;B;B;B	0.24963	0.001;0.01;0.002;0.115;0.115	B;B;B;B;B	0.19666	0.001;0.007;0.001;0.026;0.026	T	0.08046	-1.0741	10	0.15066	T	0.55	8.6317	2.1038	0.03686	0.3812:0.1275:0.3644:0.1269	.	135;135;197;246;246	B7Z6A7;Q5TAS6;B4E1U5;Q96DU3;B2R8X8	.;.;.;SLAF6_HUMAN;.	F	246;246;135	ENSP00000357038:L246F;ENSP00000357036:L246F;ENSP00000357034:L135F	ENSP00000357034:L135F	L	-	1	0	SLAMF6	158727010	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.995000	0.00317	-1.752000	0.01325	-0.302000	0.09304	CTT	.	G|1.000;A|0.000	0.000	weak		0.388	SLAMF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059010.1	NM_052931		A	160460386	G	A	160460386	3	1	263	1	0	0	0	0	1	0	0	0	14381	1029	36	2	282	2	SLAMF6	1	160460386	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	4157043	160460386	88790235	5	16405											
RABGAP1L	9910	hgsc.bcm.edu	37	chr1	174247864	174247864	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accctgcaaatgagcgatttTggtatttcagcagaaagact	13	11	9	8	1	1	3	1	1	0	2	1	4	1	3	1	1	3	3	1	1	3	4			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr1:174247864T>C	ENST00000251507.4	+	10	1444	c.1270T>C	c.(1270-1272)Tgg>Cgg	p.W424R	RABGAP1L_ENST00000357444.6_Missense_Mutation_p.W387R|RABGAP1L_ENST00000367689.3_Missense_Mutation_p.W71R	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						TGAGCGATTTTGGTATTTCAG	0.423																																					p.W424R		Atlas-SNP	.											.	RABGAP1L	103	.	0			c.T1270C						PASS	.						151	154	153					1																	174247864		2203	4300	6503	SO:0001583	missense	9910	exon10			CGATTTTGGTATT	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.1270T>C	chr1.hg19:g.174247864T>C	ENSP00000251507:p.Trp424Arg	100.0	0.0	.		103.0	44.0	.	NM_014857	B7ZAA4	Missense_Mutation	SNP	ENST00000251507.4	hg19	CCDS1314.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.070853	0.76301	.	.	ENSG00000152061	ENST00000357444;ENST00000367689;ENST00000251507;ENST00000457696;ENST00000367692	T;T;T	0.53206	0.63;3.24;0.64	5.2	4.08	0.47627	.	0.000000	0.85682	D	0.000000	T	0.67785	0.2930	M	0.80982	2.52	0.80722	D	1	D;D;D;D;D	0.89917	0.999;0.976;1.0;1.0;1.0	D;P;D;D;D	0.91635	0.998;0.694;0.999;0.999;0.999	T	0.70303	-0.4909	10	0.87932	D	0	.	10.7636	0.46279	0.0:0.0752:0.0:0.9248	.	436;71;424;424;387	B7WPG6;Q5JZA9;F1LJ00;Q5R372;Q5R372-2	.;.;.;RBG1L_HUMAN;.	R	387;71;424;436;436	ENSP00000350027:W387R;ENSP00000251507:W424R;ENSP00000403136:W436R	ENSP00000251507:W424R	W	+	1	0	RABGAP1L	172514487	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.660000	0.83776	0.834000	0.34852	0.254000	0.18369	TGG	.	.	.	none		0.423	RABGAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084497.1	NM_001243765		C	174247864	T	C	174247864	3	2	263	1	0	0	0	0	1	0	0	0	12978	1812	63	3	1304	3	RABGAP1L	1	174247864	Missense_Mutation	SNP	T	TCGA-UZ-A9PR-01A-11D-A42J-10	13787478	174247864	75002757	6	16406											
TNN	63923	hgsc.bcm.edu	37	chr1	175087824	175087824	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acgtctgccaacggagagacCagggaggttccagtggggaa	11	5	16	9	2	1	1	0	0	1	1	2	5	2	4	3	5	2	1	3	5	2	1			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr1:175087824C>T	ENST00000239462.4	+	11	2627	c.2514C>T	c.(2512-2514)acC>acT	p.T838T		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	838	Fibronectin type-III 7. {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)		ACGGAGAGACCAGGGAGGTTC	0.622																																					p.T838T		Atlas-SNP	.											.	TNN	297	.	0			c.C2514T						PASS	.						93	82	86					1																	175087824		2203	4300	6503	SO:0001819	synonymous_variant	63923	exon11			AGAGACCAGGGAG	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.2514C>T	chr1.hg19:g.175087824C>T		387.0	0.0	.		312.0	135.0	.	NM_022093	B9EGP3|Q5R360	Silent	SNP	ENST00000239462.4	hg19	CCDS30943.1																																																																																			.	.	.	none		0.622	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527		T	175087824	C	T	175087824	2	4	263	1	0	0	0	0	0	0	0	1	16335	581	21	2		2	TNN	1	175087824	Silent	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10	839960	175087824	74162797	7	16407											
TNN	63923	hgsc.bcm.edu	37	chr1	175105980	175105980	+	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	ttgacaagctacacaacctcAccaccggcactccagcgcgg	11	5	8	17	3	1	1	1	1	0	0	2	1	2	1	4	2	4	2	4	2	3	2			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr1:175105980A>T	ENST00000239462.4	+	17	3564	c.3451A>T	c.(3451-3453)Acc>Tcc	p.T1151S		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	1151	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		ACACAACCTCACCACCGGCAC	0.453																																					p.T1151S		Atlas-SNP	.											.	TNN	297	.	0			c.A3451T						PASS	.						79	73	75					1																	175105980		2203	4300	6503	SO:0001583	missense	63923	exon17			AACCTCACCACCG	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.3451A>T	chr1.hg19:g.175105980A>T	ENSP00000239462:p.Thr1151Ser	121.0	0.0	.		82.0	34.0	.	NM_022093	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	hg19	CCDS30943.1	.	.	.	.	.	.	.	.	.	.	A	17.97	3.517376	0.64634	.	.	ENSG00000120332	ENST00000239462;ENST00000539081	D	0.85088	-1.94	5.13	5.13	0.70059	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.105272	0.64402	D	0.000004	D	0.89787	0.6816	L	0.60067	1.865	0.41191	D	0.986309	D	0.60575	0.988	D	0.63488	0.915	D	0.90621	0.4559	10	0.56958	D	0.05	.	14.9007	0.70678	1.0:0.0:0.0:0.0	.	1151	Q9UQP3	TENN_HUMAN	S	1151;974	ENSP00000239462:T1151S	ENSP00000239462:T1151S	T	+	1	0	TNN	173372603	1.000000	0.71417	1.000000	0.80357	0.202000	0.24057	8.631000	0.90991	2.057000	0.61298	0.533000	0.62120	ACC	.	.	.	none		0.453	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527		T	175105980	A	T	175105980	3	4	263	1	0	0	0	0	1	0	0	0	16335	159	6	5	3513	5	TNN	1	175105980	Missense_Mutation	SNP	A	TCGA-UZ-A9PR-01A-11D-A42J-10	18156	175105980	74144641	8	16408											
PPP1R15B	84919	hgsc.bcm.edu	37	chr1	204380034	204380034	+	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	agagaaaagcctgtgctgcaGggtccaaagcacttcccttg	11	8	11	11	0	0	1	0	0	0	1	2	2	2	1	3	1	4	3	3	1	3	2			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr1:204380034G>T	ENST00000367188.4	-	1	885	c.506C>A	c.(505-507)cCt>cAt	p.P169H	RP11-739N20.2_ENST00000443515.1_RNA	NM_032833.3	NP_116222.3	Q5SWA1	PR15B_HUMAN	protein phosphatase 1, regulatory subunit 15B	169					ER overload response (GO:0006983)|regulation of translation (GO:0006417)|response to hydrogen peroxide (GO:0042542)	protein phosphatase type 1 complex (GO:0000164)	protein serine/threonine phosphatase activity (GO:0004722)			breast(3)|cervix(1)|kidney(4)|large_intestine(3)|lung(16)|ovary(1)|pancreas(2)|skin(1)|urinary_tract(3)	34	all_cancers(21;0.0032)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.179)|all_epithelial(62;0.193)|Prostate(682;0.227)		all cancers(3;1.14e-29)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.139)			CTGTGCTGCAGGGTCCAAAGC	0.552																																					p.P169H		Atlas-SNP	.											.	PPP1R15B	67	.	0			c.C506A						PASS	.						88	90	89					1																	204380034		2203	4300	6503	SO:0001583	missense	84919	exon1			GCTGCAGGGTCCA	AK027650	CCDS1445.1	1q32.1	2012-04-17	2011-10-04		ENSG00000158615	ENSG00000158615		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14951	protein-coding gene	gene with protein product		613257	"protein phosphatase 1, regulatory (inhibitor) subunit 15B"			11948623	Standard	XM_005245551		Approved	FLJ14744	uc001hav.4	Q5SWA1	OTTHUMG00000036105	ENST00000367188.4:c.506C>A	chr1.hg19:g.204380034G>T	ENSP00000356156:p.Pro169His	185.0	0.0	.		163.0	58.0	.	NM_032833	Q53GQ4|Q658M2|Q6P156|Q96SN1	Missense_Mutation	SNP	ENST00000367188.4	hg19	CCDS1445.1	.	.	.	.	.	.	.	.	.	.	G	11.77	1.737847	0.30774	.	.	ENSG00000158615	ENST00000367188;ENST00000543650	T	0.19250	2.16	4.81	2.9	0.33743	Protein phosphatase 1, regulatory subunit 15B, N-terminal (1);	0.675157	0.12952	N	0.425762	T	0.34658	0.0905	L	0.40543	1.245	0.22034	N	0.999405	D	0.71674	0.998	D	0.67382	0.951	T	0.12811	-1.0533	10	0.72032	D	0.01	-0.192	11.3319	0.49482	0.0:0.3548:0.6452:0.0	.	169	Q5SWA1	PR15B_HUMAN	H	169;79	ENSP00000356156:P169H	ENSP00000356156:P169H	P	-	2	0	PPP1R15B	202646657	0.974000	0.33945	0.047000	0.18901	0.010000	0.07245	2.242000	0.43106	0.593000	0.29745	-0.176000	0.13171	CCT	.	.	.	none		0.552	PPP1R15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087974.1	NM_032833		T	204380034	G	T	204380034	3	4	263	1	0	0	0	0	1	0	0	0	12374	1000	35	4	1643	4	PPP1R15B	1	204380034	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	29274054	204380034	44870587	9	16409											
EMILIN1	11117	hgsc.bcm.edu	37	chr2	27305967	27305967	+	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	gggtgctggacagtgaggggCagctgcggctggtgggctcc	4	7	21	9	1	0	1	0	1	0	0	1	2	1	2	1	7	3	5	1	7	0	0			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr2:27305967C>T	ENST00000380320.4	+	4	2027	c.1528C>T	c.(1528-1530)Cag>Tag	p.Q510*		NM_007046.3	NP_008977	Q9Y6C2	EMIL1_HUMAN	elastin microfibril interfacer 1	510					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)			breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(1)|lung(14)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	26	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAGTGAGGGGCAGCTGCGGCT	0.692																																					p.Q510X		Atlas-SNP	.											.	EMILIN1	75	.	0			c.C1528T						PASS	.						18	21	20					2																	27305967		2202	4300	6502	SO:0001587	stop_gained	11117	exon4			GAGGGGCAGCTGC	AF088916	CCDS1733.1	2p23.3-p23.2	2008-02-05			ENSG00000138080	ENSG00000138080		"EMI domain containing"	19880	protein-coding gene	gene with protein product		130660					Standard	NM_007046		Approved	DKFZp586M121, gp115	uc002rii.4	Q9Y6C2	OTTHUMG00000097069	ENST00000380320.4:c.1528C>T	chr2.hg19:g.27305967C>T	ENSP00000369677:p.Gln510*	94.0	0.0	.		58.0	6.0	.	NM_007046	A5PL03|H0Y7A0|Q53SY9|Q96G58|Q96IH6|Q9UG76	Nonsense_Mutation	SNP	ENST00000380320.4	hg19	CCDS1733.1	.	.	.	.	.	.	.	.	.	.	C	41	8.853643	0.98978	.	.	ENSG00000138080	ENST00000380320	.	.	.	5.28	5.28	0.74379	.	0.451866	0.23141	N	0.051461	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	-11.7746	14.3929	0.66991	0.0:1.0:0.0:0.0	.	.	.	.	X	510	.	ENSP00000369677:Q510X	Q	+	1	0	EMILIN1	27159471	0.154000	0.22792	0.998000	0.56505	0.954000	0.61252	1.807000	0.38902	2.493000	0.84123	0.561000	0.74099	CAG	.	.	.	none		0.692	EMILIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214185.1	NM_007046		T	27305967	C	T	27305967	4	4	263	1	0	0	0	0	0	1	0	0	5095	711	25	2	1542	2	EMILIN1	2	27305967	Nonsense_Mutation	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10		27305967	215893406	10	16410											
ERLEC1	27248	hgsc.bcm.edu	37	chr2	54040085	54040085	+	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	caaatttttttcccatattaGgacaaggatagtgggaaaac	15	12	8	6	0	0	0	0	0	0	0	1	3	1	3	1	3	1	0	1	3	7	6			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr2:54040085G>C	ENST00000185150.4	+	11	1232		c.e11-1		GPR75-ASB3_ENST00000352846.3_Intron|ERLEC1_ENST00000378239.5_Splice_Site|ASB3_ENST00000498475.2_Intron|ERLEC1_ENST00000405123.3_Splice_Site|ASB3_ENST00000406625.2_Intron	NM_015701.4	NP_056516.2	Q96DZ1	ERLEC_HUMAN	endoplasmic reticulum lectin 1						ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum lumen (GO:0005788)	glycoprotein binding (GO:0001948)			endometrium(2)|large_intestine(4)|lung(8)|ovary(2)|stomach(1)|urinary_tract(1)	18						TCCCATATTAGGACAAGGATA	0.393																																					.		Atlas-SNP	.											.	ERLEC1	32	.	0			c.940-1G>C						PASS	.						88	83	85					2																	54040085		2203	4300	6503	SO:0001630	splice_region_variant	27248	exon10			ATATTAGGACAAG	AF131849	CCDS1848.1, CCDS46283.1, CCDS46284.1	2p16	2010-03-19	2009-08-26	2009-08-26	ENSG00000068912	ENSG00000068912			25222	protein-coding gene	gene with protein product	"erlectin 1"	611229	"chromosome 2 open reading frame 30"	C2orf30		9110174, 8619474, 16531414, 18264092	Standard	NM_015701		Approved	CL25084, XTP3TPB, XTP3-B, ERLECTIN	uc002rxl.3	Q96DZ1	OTTHUMG00000129281	ENST00000185150.4:c.1102-1G>C	chr2.hg19:g.54040085G>C		161.0	0.0	.		133.0	53.0	.	NM_001127398	B2RDB4|B5MC72|O95901|Q6UWN7|Q9NUY7|Q9UQL4	Splice_Site	SNP	ENST00000185150.4	hg19	CCDS1848.1	.	.	.	.	.	.	.	.	.	.	G	18.00	3.524487	0.64747	.	.	ENSG00000068912	ENST00000405123;ENST00000185150;ENST00000378239	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.3626	0.98863	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ERLEC1	53893589	1.000000	0.71417	1.000000	0.80357	0.569000	0.35902	8.932000	0.92897	2.885000	0.99019	0.655000	0.94253	.	.	.	.	none		0.393	ERLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251404.1	NM_015701	Intron	C	54040085	G	C	54040085	5	2	263	1	0	0	0	0	0	0	1	0	5233	1014	35	4	1143	4	ERLEC1	2	54040085	Splice_Site	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	26734118	54040085	189159288	11	16411											
AUP1	165545	hgsc.bcm.edu	37	chr2	74755400	74755400	+	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	ttgatacaccgtgaaagggaCgaaaagtgaccacagcagtt	15	7	11	8	2	0	3	0	3	0	0	0	5	0	4	2	1	2	2	2	1	4	3	rs377142567		TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr2:74755400C>T	ENST00000404568.3	-	0	0				DQX1_ENST00000393951.2_5'Flank|AUP1_ENST00000377526.3_Missense_Mutation_p.V216I|HTRA2_ENST00000352222.3_5'Flank|HTRA2_ENST00000258080.3_5'Flank	NM_133637.2	NP_598376.2	Q8TE96	DQX1_HUMAN	DEAQ box RNA-dependent ATPase 1							nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	18						GTGAAAGGGACGAAAAGTGAC	0.537																																					p.V216I		Atlas-SNP	.											.	AUP1	29	.	0			c.G646A						PASS	.	C	ILE/VAL	0,4080		0,0,2040	74	80	78		646	5.1	1	2		78	1,8385		0,1,4192	no	missense	AUP1	NM_181575.3	29	0,1,6232	TT,TC,CC		0.0119,0.0,0.0080	benign	216/411	74755400	1,12465	2040	4193	6233	SO:0001631	upstream_gene_variant	550	exon6			AAGGGACGAAAAG	AK074337	CCDS1949.2	2p12	2010-04-20	2009-01-15		ENSG00000144045	ENSG00000144045			20410	protein-coding gene	gene with protein product			"DEAQ box polypeptide 1 (RNA-dependent ATPase)"				Standard	NM_133637		Approved	FLJ23757	uc010yrw.2	Q8TE96	OTTHUMG00000129965		chr2.hg19:g.74755400C>T	Exception_encountered	86.0	0.0	.		70.0	39.0	.	NM_181575	Q6B017|Q8NAM8	Missense_Mutation	SNP	ENST00000404568.3	hg19	CCDS1949.2	.	.	.	.	.	.	.	.	.	.	C	14.05	2.420097	0.42918	0.0	1.19E-4	ENSG00000115307	ENST00000377526;ENST00000258081;ENST00000412627	D	0.92805	-3.11	5.1	5.1	0.69264	.	0.065407	0.64402	D	0.000010	D	0.83557	0.5280	N	0.25426	0.745	0.44485	D	0.997421	P;P;P	0.44429	0.835;0.835;0.75	B;B;B	0.35114	0.06;0.097;0.196	T	0.83241	-0.0058	10	0.41790	T	0.15	-14.846	9.4342	0.38628	0.0:0.9061:0.0:0.0939	.	273;282;216	E7EU18;Q9Y679;Q9Y679-2	.;AUP1_HUMAN;.	I	216;280;218	ENSP00000366748:V216I	ENSP00000258081:V280I	V	-	1	0	AUP1	74608908	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.606000	0.46291	2.655000	0.90218	0.462000	0.41574	GTC	.	.	.	weak		0.537	DQX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252230.3	NM_133637		T	74755400	C	T	74755400	1	4	263	0	1	0	0	0	0	0	0	0	1220	536	19	1		1	AUP1	2	74755400	5'Flank	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10	20715315	74755400	168443973	12	16412											
POLR1A	25885	hgsc.bcm.edu	37	chr2	86327239	86327239	+	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	cgtacaggccgtttgccgatGggttccccaggctgtccagg	5	9	14	13	3	0	0	0	0	0	0	2	1	2	0	5	4	2	4	5	4	1	3			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr2:86327239G>A	ENST00000263857.6	-	2	512	c.134C>T	c.(133-135)cCa>cTa	p.P45L	POLR1A_ENST00000409681.1_Missense_Mutation_p.P45L			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	45					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						GTTTGCCGATGGGTTCCCCAG	0.498																																					p.P45L		Atlas-SNP	.											.	POLR1A	137	.	0			c.C134T						PASS	.						92	95	94					2																	86327239		1924	4149	6073	SO:0001583	missense	25885	exon2			GCCGATGGGTTCC	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.134C>T	chr2.hg19:g.86327239G>A	ENSP00000263857:p.Pro45Leu	138.0	0.0	.		90.0	38.0	.	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	hg19	CCDS42706.1	.	.	.	.	.	.	.	.	.	.	G	19.03	3.748536	0.69533	.	.	ENSG00000068654	ENST00000263857;ENST00000409681	T;T	0.39997	1.05;1.05	5.93	5.93	0.95920	RNA polymerase Rpb1, domain 1 (1);	0.109298	0.64402	D	0.000007	T	0.73024	0.3534	M	0.90483	3.12	0.80722	D	1	D;D	0.69078	0.997;0.991	D;D	0.72075	0.976;0.92	T	0.77517	-0.2558	10	0.87932	D	0	-13.9436	20.3363	0.98740	0.0:0.0:1.0:0.0	.	45;45	B9ZVN9;O95602	.;RPA1_HUMAN	L	45	ENSP00000263857:P45L;ENSP00000386300:P45L	ENSP00000263857:P45L	P	-	2	0	POLR1A	86180750	1.000000	0.71417	0.984000	0.44739	0.759000	0.43091	7.215000	0.77966	2.814000	0.96858	0.563000	0.77884	CCA	.	.	.	none		0.498	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425		A	86327239	G	A	86327239	3	1	263	1	0	0	0	0	1	0	0	0	12216	1348	47	2	5160	2	POLR1A	2	86327239	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	11571839	86327239	156872134	13	16413											
ITPR1	3708	hgsc.bcm.edu	37	chr3	4824382	4824382	+	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	cggtgaggatggggcggcgtCccccaggaacgtggggcaca	7	4	19	11	4	0	1	0	1	0	0	1	3	1	3	2	8	1	1	2	8	1	0			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr3:4824382C>T	ENST00000443694.2	+	47	6422	c.6422C>T	c.(6421-6423)tCc>tTc	p.S2141F	ITPR1_ENST00000354582.6_Missense_Mutation_p.S2141F|ITPR1_ENST00000423119.2_Missense_Mutation_p.S2108F|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000302640.8_Missense_Mutation_p.S2141F|ITPR1_ENST00000357086.4_Missense_Mutation_p.S2108F|ITPR1_ENST00000456211.2_Missense_Mutation_p.S2093F			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	2156					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)	GGGGCGGCGTCCCCCAGGAAC	0.527																																					p.S2141F		Atlas-SNP	.											.	ITPR1	659	.	0			c.C6422T						PASS	.						101	111	107					3																	4824382		2077	4182	6259	SO:0001583	missense	3708	exon49			CGGCGTCCCCCAG	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.6422C>T	chr3.hg19:g.4824382C>T	ENSP00000401671:p.Ser2141Phe	209.0	0.0	.		176.0	81.0	.	NM_001168272	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	hg19	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808639	0.90707	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000426160;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.92595	-3.06;-3.07;-3.07;-3.07;-3.05;-3.06	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	D	0.96809	0.8958	M	0.89534	3.04	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.72625	0.959;0.978	D	0.97432	1.0016	10	0.66056	D	0.02	.	18.6589	0.91465	0.0:1.0:0.0:0.0	.	2156;2108	Q14643;G5E9P1	ITPR1_HUMAN;.	F	2156;2141;2141;2108;602;2108;2093;2141	ENSP00000306253:S2141F;ENSP00000346595:S2141F;ENSP00000405934:S2108F;ENSP00000349597:S2108F;ENSP00000397885:S2093F;ENSP00000401671:S2141F	ENSP00000306253:S2141F	S	+	2	0	ITPR1	4799382	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	7.752000	0.85141	2.402000	0.81655	0.650000	0.86243	TCC	.	.	.	none		0.527	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		T	4824382	C	T	4824382	3	4	263	1	0	0	0	0	1	0	0	0	7927	855	30	2	6657	2	ITPR1	3	4824382	Missense_Mutation	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10		4824382	193198048	14	16414											
SNRK	54861	hgsc.bcm.edu	37	chr3	43389082	43389082	+	Frame_Shift_Del	DEL	G	G	-																															tgggcggaagtgtctgttcaGggtggaagaagatgaagagg																										TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr3:43389082delG	ENST00000296088.7	+	7	1635	c.1331delG	c.(1330-1332)aggfs	p.R444fs	SNRK-AS1_ENST00000422681.1_RNA|RP11-188P20.3_ENST00000607513.1_RNA|SNRK_ENST00000429705.2_Frame_Shift_Del_p.R444fs|SNRK_ENST00000437827.1_Frame_Shift_Del_p.R238fs|SNRK_ENST00000454177.1_Frame_Shift_Del_p.R444fs	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)		TGTCTGTTCAGGGTGGAAGAA	0.542																																					p.R444fs		Atlas-Indel,Pindel	.											.	SNRK	118	.	0			c.1330delA						PASS	.						103	111	108					3																	43389082		2019	4191	6210	SO:0001589	frameshift_variant	54861	exon6			.	D43636	CCDS43075.1	3p22.1	2005-08-09			ENSG00000163788	ENSG00000163788			30598	protein-coding gene	gene with protein product		612760				8654423, 7788527	Standard	NM_017719		Approved	FLJ20224, HSNFRK, KIAA0096	uc003cmt.4	Q9NRH2	OTTHUMG00000156491	ENST00000296088.7:c.1331delG	chr3.hg19:g.43389082delG	ENSP00000296088:p.Arg444fs	85.0	0.0	0		83.0	44.0	0.53012	NM_001100594		Frame_Shift_Del	DEL	ENST00000296088.7	hg19	CCDS43075.1																																																																																			.	.	.	none		0.542	SNRK-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344325.1	NM_017719		-	43389082	G	-	43389082	7	5	263	1	0	1	0	1	0	0	0	0	14864	1000	35	0	1349	0	SNRK	3	43389082	Frame_Shift_Del	DEL	G	TCGA-UZ-A9PR-01A-11D-A42J-10	38564700	43389082	154633348	15	16415											
QRICH1	54870	hgsc.bcm.edu	37	chr3	49114436	49114436	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcaaaggagatggtgttctcTagggaattattcatattgca	12	14	10	5	0	3	1	2	0	1	1	4	3	3	2	0	3	1	2	0	3	5	6			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr3:49114436T>C	ENST00000395443.2	-	2	487	c.15A>G	c.(13-15)ctA>ctG	p.L5L	QRICH1_ENST00000357496.2_Silent_p.L5L|QRICH1_ENST00000424300.1_Silent_p.L5L	NM_198880.1	NP_942581.1	Q2TAL8	QRIC1_HUMAN	glutamine-rich 1	5	CARD.					nucleus (GO:0005634)				breast(2)|endometrium(5)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(193;8.88e-05)|Kidney(197;0.00239)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		TGGTGTTCTCTAGGGAATTAT	0.433																																					p.L5L		Atlas-SNP	.											.	QRICH1	48	.	0			c.A15G						PASS	.						100	100	100					3																	49114436		2203	4300	6503	SO:0001819	synonymous_variant	54870	exon2			GTTCTCTAGGGAA		CCDS2787.1	3p21.31	2011-06-03			ENSG00000198218	ENSG00000198218			24713	protein-coding gene	gene with protein product						12477932	Standard	NM_017730		Approved	FLJ20259	uc003cvv.3	Q2TAL8	OTTHUMG00000156772	ENST00000395443.2:c.15A>G	chr3.hg19:g.49114436T>C		93.0	0.0	.		83.0	36.0	.	NM_198880	Q4G0F7|Q7L621|Q8TEA5	Silent	SNP	ENST00000395443.2	hg19	CCDS2787.1																																																																																			.	.	.	none		0.433	QRICH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345669.1	NM_017730		C	49114436	T	C	49114436	2	2	263	1	0	0	0	0	0	0	0	1	12892	1509	53	3		3	QRICH1	3	49114436	Silent	SNP	T	TCGA-UZ-A9PR-01A-11D-A42J-10	5725354	49114436	148907994	16	16416											
PTPRG	5793	hgsc.bcm.edu	37	chr3	62278935	62278935	+	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	acaaaaatggtgctgttcttAttgcagatgaatcagaccct	13	12	8	8	0	2	3	1	1	1	2	2	3	2	3	1	1	2	3	1	1	4	3			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr3:62278935A>T	ENST00000474889.1	+	30	4668	c.4291A>T	c.(4291-4293)Att>Ttt	p.I1431F	PTPRG-AS1_ENST00000474795.1_RNA|PTPRG-AS1_ENST00000479018.1_RNA|PTPRG-AS1_ENST00000498655.1_RNA|PTPRG-AS1_ENST00000475371.1_RNA|PTPRG_ENST00000295874.10_Missense_Mutation_p.I1402F|PTPRG-AS1_ENST00000495542.1_RNA|PTPRG-AS1_ENST00000462497.1_RNA|PTPRG-AS1_ENST00000490916.1_RNA|PTPRG-AS1_ENST00000466893.1_RNA	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	1431					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)		TGCTGTTCTTATTGCAGATGA	0.413																																					p.I1431F		Atlas-SNP	.											.	PTPRG	153	.	0			c.A4291T						PASS	.						135	128	130					3																	62278935		2203	4299	6502	SO:0001583	missense	5793	exon30			GTTCTTATTGCAG	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.4291A>T	chr3.hg19:g.62278935A>T	ENSP00000418112:p.Ile1431Phe	259.0	0.0	.		232.0	107.0	.	NM_002841	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Missense_Mutation	SNP	ENST00000474889.1	hg19	CCDS2895.1	.	.	.	.	.	.	.	.	.	.	A	11.94	1.787350	0.31593	.	.	ENSG00000144724	ENST00000474889;ENST00000295874	T;T	0.52983	0.64;0.71	5.45	5.45	0.79879	.	0.330007	0.36972	N	0.002320	T	0.33206	0.0855	N	0.22421	0.69	0.09310	N	0.999999	B;B;B	0.27264	0.037;0.173;0.024	B;B;B	0.28709	0.006;0.093;0.038	T	0.29458	-1.0011	10	0.62326	D	0.03	.	8.2166	0.31516	0.8808:0.0:0.1192:0.0	.	677;1402;1431	B7Z3T1;P23470-2;P23470	.;.;PTPRG_HUMAN	F	1431;1402	ENSP00000418112:I1431F;ENSP00000295874:I1402F	ENSP00000295874:I1402F	I	+	1	0	PTPRG	62253975	0.044000	0.20184	0.193000	0.23327	0.955000	0.61496	1.731000	0.38135	2.086000	0.62901	0.528000	0.53228	ATT	.	.	.	none		0.413	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841		T	62278935	A	T	62278935	3	4	263	1	0	0	0	0	1	0	0	0	12815	449	16	5	4409	5	PTPRG	3	62278935	Missense_Mutation	SNP	A	TCGA-UZ-A9PR-01A-11D-A42J-10	13164499	62278935	135743495	17	16417											
CADPS	8618	hgsc.bcm.edu	37	chr3	62739258	62739258	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgctgcttccgcgggtccTcttctccacggtagatggca	4	11	11	15	3	2	1	0	0	2	1	5	1	4	1	4	3	2	4	4	3	1	3			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr3:62739258T>C	ENST00000383710.4	-	3	1095	c.746A>G	c.(745-747)gAg>gGg	p.E249G	CADPS_ENST00000357948.3_Missense_Mutation_p.E249G|CADPS_ENST00000283269.9_Missense_Mutation_p.E249G|CADPS_ENST00000490353.2_Missense_Mutation_p.E249G	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	249					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)		CCGCGGGTCCTCTTCTCCACG	0.572																																					p.E249G		Atlas-SNP	.											.	CADPS	387	.	0			c.A746G						PASS	.						62	63	63					3																	62739258		2203	4300	6503	SO:0001583	missense	8618	exon3			GGGTCCTCTTCTC	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.746A>G	chr3.hg19:g.62739258T>C	ENSP00000373215:p.Glu249Gly	149.0	0.0	.		149.0	51.0	.	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Missense_Mutation	SNP	ENST00000383710.4	hg19	CCDS46858.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.849507	0.91277	.	.	ENSG00000163618	ENST00000383709;ENST00000383710;ENST00000357948;ENST00000283269;ENST00000490353	D;D;D;D	0.89617	-2.54;-2.54;-2.54;-2.54	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	D	0.93710	0.7990	M	0.77103	2.36	0.80722	D	1	D;P;P	0.59767	0.986;0.873;0.799	P;P;B	0.61201	0.885;0.461;0.214	D	0.94364	0.7590	10	0.87932	D	0	.	16.2824	0.82697	0.0:0.0:0.0:1.0	.	249;249;249	Q9ULU8-2;Q9ULU8-3;Q9ULU8	.;.;CAPS1_HUMAN	G	249	ENSP00000373215:E249G;ENSP00000350632:E249G;ENSP00000283269:E249G;ENSP00000418736:E249G	ENSP00000283269:E249G	E	-	2	0	CADPS	62714298	1.000000	0.71417	0.998000	0.56505	0.882000	0.50991	8.040000	0.89188	2.250000	0.74265	0.533000	0.62120	GAG	.	.	.	none		0.572	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394		C	62739258	T	C	62739258	3	2	263	1	0	0	0	0	1	0	0	0	2572	1551	54	3	3500	3	CADPS	3	62739258	Missense_Mutation	SNP	T	TCGA-UZ-A9PR-01A-11D-A42J-10	460323	62739258	135283172	18	16418											
CP	1356	hgsc.bcm.edu	37	chr3	148930300	148930300	+	Frame_Shift_Del	DEL	T	T	-																															tgtagggcctagaggcaaggTtttttaagtgtacataaact																										TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr3:148930300delT	ENST00000264613.6	-	2	594	c.332delA	c.(331-333)aacfs	p.N111fs		NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	111	F5/8 type A 1.|Plastocyanin-like 1.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	AGAGGCAAGGTTTTTTAAGTG	0.388																																					p.N111fs		Atlas-Indel,Pindel	.											.	CP	112	.	0			c.333delC						PASS	.						118	120	119					3																	148930300		2203	4300	6503	SO:0001589	frameshift_variant	1356	exon2			.	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.332delA	chr3.hg19:g.148930300delT	ENSP00000264613:p.Asn111fs	104.0	0.0	0		91.0	39.0	0.428571	NM_000096	Q14063|Q2PP18|Q9UKS4	Frame_Shift_Del	DEL	ENST00000264613.6	hg19	CCDS3141.1																																																																																			.	.	.	none		0.388	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096		-	148930300	T	-	148930300	7	5	263	1	0	1	0	1	0	0	0	0	3789	1725	60	0	2937	0	CP	3	148930300	Frame_Shift_Del	DEL	T	TCGA-UZ-A9PR-01A-11D-A42J-10	86191042	148930300	49092130	19	16419											
ATP13A4	84239	hgsc.bcm.edu	37	chr3	193175211	193175211	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	taactaccatggcatgtgccGgcactcccttgatgtggaaa	10	10	10	11	1	0	1	0	1	0	0	1	2	1	2	3	3	3	2	3	3	3	3			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr3:193175211G>A	ENST00000342695.4	-	15	2040	c.1718C>T	c.(1717-1719)cCg>cTg	p.P573L	ATP13A4_ENST00000392443.3_Missense_Mutation_p.P554L	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	573						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)		GGCATGTGCCGGCACTCCCTT	0.458																																					p.P573L		Atlas-SNP	.											ATP13A4,NS,adenocarcinoma,0,1	ATP13A4	154	.	0			c.C1718T						PASS	.						173	171	172					3																	193175211		2203	4300	6503	SO:0001583	missense	84239	exon15			TGTGCCGGCACTC	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.1718C>T	chr3.hg19:g.193175211G>A	ENSP00000339182:p.Pro573Leu	150.0	0.0	.		128.0	55.0	.	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Missense_Mutation	SNP	ENST00000342695.4	hg19	CCDS3304.2	.	.	.	.	.	.	.	.	.	.	G	11.28	1.591176	0.28357	.	.	ENSG00000127249	ENST00000392443;ENST00000342695	D;D	0.86627	-1.88;-2.15	5.03	4.15	0.48705	ATPase, cation-transporting, domain N (1);ATPase, P-type, cytoplasmic domain N (1);	0.295841	0.29587	N	0.011729	T	0.66655	0.2811	N	0.01800	-0.715	0.80722	D	1	B;B;B	0.19073	0.008;0.003;0.033	B;B;B	0.15484	0.009;0.005;0.013	T	0.59878	-0.7371	10	0.21540	T	0.41	-22.0958	8.9035	0.35510	0.1058:0.0:0.8942:0.0	.	554;573;573	B7WPN9;Q4VNC1-2;Q4VNC1	.;.;AT134_HUMAN	L	554;573	ENSP00000376238:P554L;ENSP00000339182:P573L	ENSP00000339182:P573L	P	-	2	0	ATP13A4	194657905	0.774000	0.28592	0.794000	0.32065	0.608000	0.37181	2.473000	0.45145	1.223000	0.43536	0.655000	0.94253	CCG	.	.	.	none		0.458	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279		A	193175211	G	A	193175211	3	1	263	1	0	0	0	0	1	0	0	0	1126	1116	39	1	1936	1	ATP13A4	3	193175211	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	44244911	193175211	4847219	20	16420											
CCDC149	91050	hgsc.bcm.edu	37	chr4	24878300	24878300	+	Frame_Shift_Del	DEL	T	T	-																															cttccttcttactctccagcTtcctcttacacaccaggtac																										TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr4:24878300delT	ENST00000389609.4	-	3	226	c.83delA	c.(82-84)aagfs	p.K28fs	CCDC149_ENST00000428116.2_5'UTR|CCDC149_ENST00000504487.1_Frame_Shift_Del_p.K28fs|CCDC149_ENST00000502801.1_Frame_Shift_Del_p.K28fs	NM_173463.4	NP_775734.2	Q6ZUS6	CC149_HUMAN	coiled-coil domain containing 149	108										cervix(1)|endometrium(1)|large_intestine(2)|lung(3)	7		Breast(46;0.173)				ACTCTCCAGCTTCCTCTTACA	0.507																																					p.K28fs		Atlas-Indel,Pindel	.											.	CCDC149	41	.	0			c.84delG						PASS	.						107	88	94					4																	24878300		692	1591	2283	SO:0001589	frameshift_variant	91050	exon3			.		CCDS33967.1, CCDS47036.1, CCDS33967.2	4p15.2	2008-03-03				ENSG00000181982			25405	protein-coding gene	gene with protein product						17457313	Standard	NM_173463		Approved	DKFZp761B107	uc003grc.3	Q6ZUS6		ENST00000389609.4:c.83delA	chr4.hg19:g.24878300delT	ENSP00000374260:p.Lys28fs	82.0	0.0	0		55.0	18.0	0.327273	NM_173463	A6NJE7|B4DK90|B4DZG3|G5EA04|Q6NW41|Q8N3K8	Frame_Shift_Del	DEL	ENST00000389609.4	hg19	CCDS33967.2																																																																																			.	.	.	none		0.507	CCDC149-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000360157.1	NM_173463		-	24878300	T	-	24878300	7	5	263	1	0	1	0	1	0	0	0	0	2785	1609	56	0	1554	0	CCDC149	4	24878300	Frame_Shift_Del	DEL	T	TCGA-UZ-A9PR-01A-11D-A42J-10		24878300	166275976	21	16421											
N4BP2	55728	hgsc.bcm.edu	37	chr4	40122134	40122134	+	Frame_Shift_Del	DEL	A	A	-																															aagactattggtcagaggacAaaaaggaacagaaaaactga																										TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr4:40122134delA	ENST00000261435.6	+	9	2819	c.2403delA	c.(2401-2403)acafs	p.T801fs		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	801					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						GTCAGAGGACAAAAAGGAACA	0.358																																					p.T801fs		Atlas-Indel,Pindel	.											.	N4BP2	166	.	0			c.2402delC						PASS	.						55	55	55					4																	40122134		2203	4300	6503	SO:0001589	frameshift_variant	55728	exon9			.	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"BCL-3 binding protein"					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.2403delA	chr4.hg19:g.40122134delA	ENSP00000261435:p.Thr801fs	229.0	0.0	0		184.0	71.0	0.38587	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Frame_Shift_Del	DEL	ENST00000261435.6	hg19	CCDS3457.1																																																																																			.	.	.	none		0.358	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177		-	40122134	A	-	40122134	7	5	263	1	0	1	0	1	0	0	0	0	10117	117	5	0	2429	0	N4BP2	4	40122134	Frame_Shift_Del	DEL	A	TCGA-UZ-A9PR-01A-11D-A42J-10	15243834	40122134	151032142	22	16422											
LIMCH1	22998	hgsc.bcm.edu	37	chr4	41621302	41621303	+	Frame_Shift_Del	DEL	GA	GA	-																															cggacttcccatggtgagccGaaatcagcagtgccttttaa																										TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr4:41621302_41621303delGA	ENST00000313860.7	+	8	834_835	c.780_781delGA	c.(778-783)ccgaaafs	p.K261fs	LIMCH1_ENST00000509277.1_Frame_Shift_Del_p.K107fs|LIMCH1_ENST00000513024.1_Frame_Shift_Del_p.K102fs|LIMCH1_ENST00000396595.3_Frame_Shift_Del_p.K107fs|LIMCH1_ENST00000512820.1_Frame_Shift_Del_p.K261fs|LIMCH1_ENST00000511496.1_Frame_Shift_Del_p.K102fs|LIMCH1_ENST00000503057.1_Frame_Shift_Del_p.K102fs|LIMCH1_ENST00000514096.1_Frame_Shift_Del_p.K114fs|LIMCH1_ENST00000381753.4_Frame_Shift_Del_p.K107fs|LIMCH1_ENST00000512632.1_Frame_Shift_Del_p.K261fs|LIMCH1_ENST00000509454.1_Frame_Shift_Del_p.K109fs|LIMCH1_ENST00000508501.1_Frame_Shift_Del_p.K261fs|LIMCH1_ENST00000512946.1_Frame_Shift_Del_p.K261fs|LIMCH1_ENST00000509638.1_Frame_Shift_Del_p.K102fs	NM_014988.2	NP_055803.2	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1	261					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						ATGGTGAGCCGAAATCAGCAGT	0.53																																					p.260_260del		Atlas-Indel,Pindel	.											LIMCH1_ENST00000503057,NS,carcinoma,-1,2	LIMCH1	233	.	0			c.779_780del						PASS	.																																			SO:0001589	frameshift_variant	22998	exon8			.	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.780_781delGA	chr4.hg19:g.41621302_41621303delGA	ENSP00000316891:p.Lys261fs	119.0	0.0	0		112.0	52.0	0.464286	NM_014988	A8MXC3|E9PHM7|Q503B5|Q5CZB1|Q5CZB6|Q5H9S8|Q68E07|Q6PJ44|Q7Z3G5|Q8N3S9|Q8N6M2	Frame_Shift_Del	DEL	ENST00000313860.7	hg19	CCDS33977.1																																																																																			.	.	.	none		0.53	LIMCH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361249.2	NM_014988		-	41621303	GA	-	41621302	7	5	263	1	0	1	0	1	0	0	0	0	8804	1045	37	0	838	0	LIMCH1	4	41621302	Frame_Shift_Del	DEL	GA	TCGA-UZ-A9PR-01A-11D-A42J-10	1499168	41621302	149532974	23	16423											
LPHN3	23284	hgsc.bcm.edu	37	chr4	62598714	62598715	+	Frame_Shift_Del	DEL	GT	GT	-																															tggatggcacaggatttgtaGtgtatgatggagctttgttc																										TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr4:62598714_62598715delGT	ENST00000514591.1	+	7	966_967	c.637_638delGT	c.(637-639)gtgfs	p.V213fs	LPHN3_ENST00000512091.2_Frame_Shift_Del_p.V213fs|LPHN3_ENST00000509896.1_Frame_Shift_Del_p.V281fs|LPHN3_ENST00000506720.1_Frame_Shift_Del_p.V281fs|LPHN3_ENST00000504896.1_Frame_Shift_Del_p.V213fs|LPHN3_ENST00000514996.1_Frame_Shift_Del_p.V213fs|LPHN3_ENST00000545650.1_Frame_Shift_Del_p.V213fs|LPHN3_ENST00000506746.1_Frame_Shift_Del_p.V281fs|LPHN3_ENST00000508946.1_Frame_Shift_Del_p.V213fs|LPHN3_ENST00000514157.1_Frame_Shift_Del_p.V213fs|LPHN3_ENST00000507164.1_Frame_Shift_Del_p.V281fs|LPHN3_ENST00000507625.1_Frame_Shift_Del_p.V281fs|LPHN3_ENST00000511324.1_Frame_Shift_Del_p.V281fs|LPHN3_ENST00000508693.1_Frame_Shift_Del_p.V281fs|LPHN3_ENST00000506700.1_Frame_Shift_Del_p.V213fs			Q9HAR2	LPHN3_HUMAN	latrophilin 3	213	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						AGGATTTGTAGTGTATGATGGA	0.441																																					p.212_213del		Atlas-Indel,Pindel	.											.	LPHN3	800	.	0			c.636_637del						PASS	.																																			SO:0001589	frameshift_variant	23284	exon5			.	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.637_638delGT	chr4.hg19:g.62598716_62598717delGT	ENSP00000422533:p.Val213fs	107.0	0.0	0		98.0	45.0	0.459184	NM_015236	E9PE04|O94867|Q9NWK5	Frame_Shift_Del	DEL	ENST00000514591.1	hg19	CCDS54768.1																																																																																			.	.	.	none		0.441	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			-	62598715	GT	-	62598714	7	5	263	1	0	1	0	1	0	0	0	0	8924	1029	36	0	655	0	LPHN3	4	62598714	Frame_Shift_Del	DEL	GT	TCGA-UZ-A9PR-01A-11D-A42J-10	20977412	62598714	128555562	24	16424											
SLC4A4	8671	hgsc.bcm.edu	37	chr4	72423545	72423545	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actttcctgcaggtgttgtgTctggccctgctttggatcct	3	16	11	11	0	1	0	0	0	1	0	3	1	3	1	3	3	2	3	3	3	0	3			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr4:72423545T>C	ENST00000264485.5	+	22	2997	c.2880T>C	c.(2878-2880)tgT>tgC	p.C960C	SLC4A4_ENST00000351898.6_Silent_p.C876C|SLC4A4_ENST00000340595.3_Silent_p.C916C|SLC4A4_ENST00000425175.1_Silent_p.C960C	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	960					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)	AGGTGTTGTGTCTGGCCCTGC	0.483																																					p.C960C		Atlas-SNP	.											.	SLC4A4	269	.	0			c.T2880C						PASS	.						152	119	130					4																	72423545		2203	4300	6503	SO:0001819	synonymous_variant	8671	exon22			GTTGTGTCTGGCC	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.2880T>C	chr4.hg19:g.72423545T>C		109.0	0.0	.		91.0	36.0	.	NM_001098484	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Silent	SNP	ENST00000264485.5	hg19	CCDS43236.1																																																																																			.	.	.	none		0.483	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		C	72423545	T	C	72423545	2	2	263	1	0	0	0	0	0	0	0	1	14669	1673	58	3		3	SLC4A4	4	72423545	Silent	SNP	T	TCGA-UZ-A9PR-01A-11D-A42J-10	9824831	72423545	118730731	25	16425											
LPCAT1	79888	hgsc.bcm.edu	37	chr5	1501608	1501608	+	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	gccgggggctgctcgggttcCttctccgcagagcccaggga	4	7	16	14	3	1	1	0	0	1	1	4	2	2	2	4	4	2	4	4	4	0	2			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr5:1501608C>A	ENST00000283415.3	-	2	378	c.246G>T	c.(244-246)aaG>aaT	p.K82N		NM_024830.3	NP_079106.3	Q8NF37	PCAT1_HUMAN	lysophosphatidylcholine acyltransferase 1	82					cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|negative regulation of phosphatidylcholine biosynthetic process (GO:2001246)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein catabolic process (GO:0045732)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|surfactant homeostasis (GO:0043129)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkenylglycerophosphocholine O-acyltransferase activity (GO:0047159)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|1-alkylglycerophosphocholine O-acyltransferase activity (GO:0047191)|calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)		GCTCGGGTTCCTTCTCCGCAG	0.667																																					p.K82N		Atlas-SNP	.											.	LPCAT1	70	.	0			c.G246T						PASS	.						34	37	36					5																	1501608		2199	4299	6498	SO:0001583	missense	79888	exon2			GGGTTCCTTCTCC	BC020166	CCDS3864.1	5p15.33	2013-01-10	2007-12-17	2007-12-17	ENSG00000153395	ENSG00000153395		"EF-hand domain containing"	25718	protein-coding gene	gene with protein product		610472	"acyltransferase like 2"	AYTL2		8619474, 16704971	Standard	NM_024830		Approved	FLJ12443	uc003jcm.3	Q8NF37	OTTHUMG00000131017	ENST00000283415.3:c.246G>T	chr5.hg19:g.1501608C>A	ENSP00000283415:p.Lys82Asn	200.0	0.0	.		161.0	76.0	.	NM_024830	Q1HAQ1|Q7Z4G6|Q8N3U7|Q8WUL8|Q9GZW6	Missense_Mutation	SNP	ENST00000283415.3	hg19	CCDS3864.1	.	.	.	.	.	.	.	.	.	.	C	6.293	0.422250	0.11928	.	.	ENSG00000153395	ENST00000283415	T	0.71698	-0.59	4.35	2.07	0.26955	.	0.437567	0.24851	N	0.035086	T	0.60157	0.2247	L	0.54323	1.7	0.30348	N	0.785034	B	0.10296	0.003	B	0.21708	0.036	T	0.53229	-0.8468	10	0.27785	T	0.31	-13.6788	6.1162	0.20127	0.0:0.5524:0.0:0.4476	.	82	Q8NF37	PCAT1_HUMAN	N	82	ENSP00000283415:K82N	ENSP00000283415:K82N	K	-	3	2	LPCAT1	1554608	0.329000	0.24696	0.207000	0.23584	0.024000	0.10985	0.425000	0.21346	0.793000	0.33875	0.491000	0.48974	AAG	.	.	.	none		0.667	LPCAT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304032.1	NM_024830		A	1501608	C	A	1501608	3	1	263	1	0	0	0	0	1	0	0	0	8917	680	24	4	1410	4	LPCAT1	5	1501608	Missense_Mutation	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10		1501608	179413652	26	16426											
NR2F1	7025	hgsc.bcm.edu	37	chr5	92923881	92923881	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcaacatccccttcttccCggatctgcagatcaccgacc	8	8	6	19	3	3	1	1	0	2	1	5	3	5	2	6	1	2	2	6	1	1	2			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr5:92923881C>T	ENST00000327111.3	+	2	2409	c.722C>T	c.(721-723)cCg>cTg	p.P241L	NR2F1-AS1_ENST00000513055.1_RNA	NM_005654.4	NP_005645.1	P10589	COT1_HUMAN	nuclear receptor subfamily 2, group F, member 1	241					cerebral cortex regionalization (GO:0021796)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|retinoic acid-responsive element binding (GO:0044323)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(4)|large_intestine(6)|lung(2)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	21		all_cancers(142;1.62e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0416)|all cancers(79;9.57e-18)		CCCTTCTTCCCGGATCTGCAG	0.637																																					p.P241L		Atlas-SNP	.											.	NR2F1	56	.	0			c.C722T						PASS	.						84	80	81					5																	92923881		2203	4300	6503	SO:0001583	missense	7025	exon2			TCTTCCCGGATCT	BC004154	CCDS4068.1	5q14	2013-01-16			ENSG00000175745	ENSG00000175745		"Nuclear hormone receptors"	7975	protein-coding gene	gene with protein product		132890		ERBAL3, TFCOUP1		8530078	Standard	NM_005654		Approved	EAR-3, COUP-TFI, TCFCOUP1, SVP44	uc003kkj.3	P10589	OTTHUMG00000119079	ENST00000327111.3:c.722C>T	chr5.hg19:g.92923881C>T	ENSP00000325819:p.Pro241Leu	121.0	0.0	.		113.0	11.0	.	NM_005654		Missense_Mutation	SNP	ENST00000327111.3	hg19	CCDS4068.1	.	.	.	.	.	.	.	.	.	.	C	33	5.201256	0.94997	.	.	ENSG00000175745	ENST00000327111	D	0.96334	-3.98	4.54	4.54	0.55810	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.96558	0.8877	L	0.28649	0.875	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97507	1.0064	10	0.66056	D	0.02	.	17.0631	0.86552	0.0:1.0:0.0:0.0	.	241	P10589	COT1_HUMAN	L	241	ENSP00000325819:P241L	ENSP00000325819:P241L	P	+	2	0	NR2F1	92949637	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.606000	0.82863	2.327000	0.79052	0.462000	0.41574	CCG	.	.	.	none		0.637	NR2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239293.2	NM_005654		T	92923881	C	T	92923881	3	4	263	1	0	0	0	0	1	0	0	0	10634	652	23	1	728	1	NR2F1	5	92923881	Missense_Mutation	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10	91422273	92923881	87991379	27	16427											
PCDHB16	57717	hgsc.bcm.edu	37	chr5	140563836	140563836	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgctgtacccgctgcagaacGgctccgcgccctgcactgag	6	7	12	16	4	0	2	0	1	0	1	1	2	1	2	3	1	5	6	3	1	2	1	rs535302272	byFrequency	TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr5:140563836G>A	ENST00000361016.2	+	1	2857	c.1702G>A	c.(1702-1704)Ggc>Agc	p.G568S		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	568	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCTGCAGAACGGCTCCGCGCC	0.711													G|||	2	0.000399361	8e-04	0	5008	,	,		13663	0		0	False		,,,				2504	0.001				p.G568S		Atlas-SNP	.											PCDHB16,NS,carcinoma,0,1	PCDHB16	159	.	0			c.G1702A						PASS	.						14	17	16					5																	140563836		1969	3923	5892	SO:0001583	missense	57717	exon1			CAGAACGGCTCCG	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.1702G>A	chr5.hg19:g.140563836G>A	ENSP00000354293:p.Gly568Ser	49.0	0.0	.		41.0	2.0	.	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	hg19	CCDS4251.1	.	.	.	.	.	.	.	.	.	.	g	12.66	2.005258	0.35415	.	.	ENSG00000196963	ENST00000361016	T	0.60797	0.16	4.12	2.28	0.28536	Cadherin (1);Cadherin-like (1);	1.832600	0.03875	N	0.276324	T	0.41719	0.1171	N	0.20807	0.61	0.09310	N	1	B	0.22003	0.063	B	0.17979	0.02	T	0.27123	-1.0083	10	0.45353	T	0.12	.	3.1416	0.06457	0.2646:0.0:0.4112:0.3242	.	568	Q9NRJ7	PCDBG_HUMAN	S	568	ENSP00000354293:G568S	ENSP00000354293:G568S	G	+	1	0	PCDHB16	140544020	0.000000	0.05858	0.984000	0.44739	0.978000	0.69477	0.941000	0.29005	0.212000	0.20703	0.479000	0.44913	GGC	.	.	.	none		0.711	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		A	140563836	G	A	140563836	3	1	263	1	0	0	0	0	1	0	0	0	11548	1116	39	1	1704	1	PCDHB16	5	140563836	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	47639955	140563836	40351424	28	16428											
SH3TC2	79628	hgsc.bcm.edu	37	chr5	148421039	148421039	+	Missense_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	gtaccaggccccgctgacctGtcaccaaagacacgccttcc	9	6	8	18	2	1	2	1	1	0	1	2	2	2	2	7	1	1	2	7	1	2	2			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr5:148421039G>A	ENST00000515425.1	-	6	772	c.671C>T	c.(670-672)aCa>aTa	p.T224I	SH3TC2_ENST00000538184.1_5'UTR|SH3TC2_ENST00000512049.1_Missense_Mutation_p.T217I|SH3TC2_ENST00000394358.2_Missense_Mutation_p.T109I	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	224					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)			CCGCTGACCTGTCACCAAAGA	0.562																																					p.T224I		Atlas-SNP	.											.	SH3TC2	178	.	0			c.C671T						PASS	.						86	70	76					5																	148421039		2203	4300	6503	SO:0001583	missense	79628	exon6			TGACCTGTCACCA	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.671C>T	chr5.hg19:g.148421039G>A	ENSP00000423660:p.Thr224Ile	176.0	0.0	.		142.0	66.0	.	NM_024577	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Missense_Mutation	SNP	ENST00000515425.1	hg19	CCDS4293.1	.	.	.	.	.	.	.	.	.	.	G	19.50	3.839329	0.71488	.	.	ENSG00000169247	ENST00000515425;ENST00000512049;ENST00000394358	T;T;T	0.32988	1.43;1.43;1.43	5.59	3.74	0.42951	.	0.545786	0.17852	N	0.159814	T	0.40956	0.1138	L	0.29908	0.895	0.38988	D	0.959097	D;D;D	0.63880	0.993;0.992;0.992	P;P;P	0.60949	0.881;0.851;0.851	T	0.39761	-0.9598	10	0.72032	D	0.01	-1.1698	15.1929	0.73060	0.0:0.4049:0.5951:0.0	.	109;217;224	C9JLC3;Q14CC0;Q8TF17	.;.;S3TC2_HUMAN	I	224;217;109	ENSP00000423660:T224I;ENSP00000421860:T217I;ENSP00000377886:T109I	ENSP00000313025:T224I	T	-	2	0	SH3TC2	148401232	1.000000	0.71417	0.627000	0.29227	0.978000	0.69477	3.194000	0.51005	0.662000	0.31006	0.650000	0.86243	ACA	.	.	.	none		0.562	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577		A	148421039	G	A	148421039	3	1	263	1	0	0	0	0	1	0	0	0	14275	1377	48	2	3243	2	SH3TC2	5	148421039	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	7857203	148421039	32494221	29	16429											
TIGD6	81789	hgsc.bcm.edu	37	chr5	149375763	149375765	+	In_Frame_Del	DEL	TCC	TCC	-																															tttcttcaaatttggtgcgaTcctttaagaatgtagataaa																										TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr5:149375763_149375765delTCC	ENST00000296736.3	-	2	921_923	c.147_149delGGA	c.(145-150)aaggat>aat	p.49_50KD>N	TIGD6_ENST00000515406.2_In_Frame_Del_p.49_50KD>N	NM_030953.3	NP_112215.1	Q17RP2	TIGD6_HUMAN	tigger transposable element derived 6	49	HTH psq-type. {ECO:0000255|PROSITE- ProRule:PRU00320}.					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)			TTTGGTGCGATCCTTTAAGAATG	0.443																																					p.50_50del		Atlas-Indel,Pindel	.											.	TIGD6	29	.	0			c.148_150del						PASS	.																																			SO:0001651	inframe_deletion	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.147_149delGGA	chr5.hg19:g.149375763_149375765delTCC	ENSP00000296736:p.Lys49_Asp50delinsAsn	110.0	0.0	0		95.0	33.0	0.347368	NM_001243253	B3KTZ8|Q96MQ4|Q9H0X7	In_Frame_Del	DEL	ENST00000296736.3	hg19	CCDS4301.1																																																																																			.	.	.	none		0.443	TIGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252324.1	NM_030953		-	149375765	TCC	-	149375763	7	5	263	1	0	1	0	1	0	0	0	0	15912	1435	50	0	1420	0	TIGD6	5	149375763	In_Frame_Del	DEL	TCC	TCGA-UZ-A9PR-01A-11D-A42J-10	954724	149375763	31539497	30	16430											
SCAND3	114821	hgsc.bcm.edu	37	chr6	28539881	28539881	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcaattttaaagcaatcTcagcaagctcaggatagtca	15	9	8	9	0	3	0	3	0	1	0	4	1	3	1	0	1	4	5	0	1	6	3			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr6:28539881T>C	ENST00000452236.2	-	4	4402	c.3785A>G	c.(3784-3786)gAg>gGg	p.E1262G		NM_052923.1	NP_443155.1														NS(3)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(14)|liver(1)|lung(29)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)	71						taaagcaatctcagcaagctc	0.358																																					p.E1262G		Atlas-SNP	.											.	SCAND3	156	.	0			c.A3785G						PASS	.						69	72	71					6																	28539881		2203	4300	6503	SO:0001583	missense	114821	exon4			GCAATCTCAGCAA																												ENST00000452236.2:c.3785A>G	chr6.hg19:g.28539881T>C	ENSP00000395259:p.Glu1262Gly	308.0	1.0	.		231.0	79.0	.	NM_052923		Missense_Mutation	SNP	ENST00000452236.2	hg19	CCDS34355.1	.	.	.	.	.	.	.	.	.	.	T	15.46	2.839296	0.51057	.	.	ENSG00000232040	ENST00000452236	T	0.23348	1.91	2.53	2.53	0.30540	HAT dimerisation (1);Ribonuclease H-like (1);	1.392160	0.05202	U	0.505216	T	0.28134	0.0694	L	0.53249	1.67	0.26555	N	0.973832	D	0.69078	0.997	D	0.79108	0.992	T	0.09250	-1.0683	10	0.35671	T	0.21	.	6.9733	0.24660	0.0:0.0:0.0:1.0	.	1262	Q6R2W3	SCND3_HUMAN	G	1262	ENSP00000395259:E1262G	ENSP00000395259:E1262G	E	-	2	0	SCAND3	28647860	0.994000	0.37717	0.999000	0.59377	0.952000	0.60782	1.895000	0.39778	1.405000	0.46838	0.533000	0.62120	GAG	.	.	.	none		0.358	SCAND3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000043551.3			C	28539881	T	C	28539881	3	2	263	1	0	0	0	0	1	0	0	0	13889	1551	54	3	196	3	SCAND3	6	28539881	Missense_Mutation	SNP	T	TCGA-UZ-A9PR-01A-11D-A42J-10		28539881	142575186	31	16431											
C6orf222	389384	hgsc.bcm.edu	37	chr6	36298147	36298148	+	Frame_Shift_Ins	INS	-	-	A																															cctcagggcccgtcctcacgINSaagaagttcagcatggtctt																										TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr6:36298147_36298148insA	ENST00000437635.2	-	2	497_498	c.320_321insT	c.(319-321)ttcfs	p.F107fs		NM_001010903.4	NP_001010903.3	P0C671	CF222_HUMAN	chromosome 6 open reading frame 222	107										breast(4)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|skin(4)|urinary_tract(4)	26						CCGTCCTCACGAAGAAGTTCAG	0.634																																					p.F107fs		Atlas-INDEL	.											C6orf222,NS,carcinoma,0,1	C6orf222	72	.	0			c.321_322insT						PASS	.																																			SO:0001589	frameshift_variant	389384	exon2			.		CCDS34439.1	6p21.31	2012-02-22			ENSG00000189325	ENSG00000189325			33769	protein-coding gene	gene with protein product							Standard	NM_001010903		Approved	DKFZp779B1540	uc003oly.3	P0C671	OTTHUMG00000014591	ENST00000437635.2:c.321dupT	chr6.hg19:g.36298149_36298149dupA	ENSP00000418983:p.Phe107fs	48.0	0.0	0		39.0	15.0	0.384615	NM_001010903	B2RTY8	Frame_Shift_Ins	INS	ENST00000437635.2	hg19	CCDS34439.1																																																																																			.	.	.	none		0.634	C6orf222-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040338.2	NM_001010903		A	36298148	-	A	36298147	7	5	263	1	0	1	1	0	0	0	0	0	2358	1049	37	0	1681	0	C6orf222	6	36298147	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PR-01A-11D-A42J-10	7758266	36298147	134816920	32	16432	169	2									
C6orf222	389384	hgsc.bcm.edu	37	chr6	36298150	36298150	+	Silent	SNP	G	G	A																															tcagggcccgtcctcacgaaGaagttcagcatggtcttcag																										TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr6:36298150G>A	ENST00000437635.2	-	2	495	c.318C>T	c.(316-318)ttC>ttT	p.F106F		NM_001010903.4	NP_001010903.3	P0C671	CF222_HUMAN	chromosome 6 open reading frame 222	106										breast(4)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|skin(4)|urinary_tract(4)	26						TCCTCACGAAGAAGTTCAGCA	0.627																																					p.F106F		Atlas-SNP	.											.	C6orf222	72	.	0			c.C318T						PASS	.						73	70	71					6																	36298150		2203	4300	6503	SO:0001819	synonymous_variant	389384	exon2			CACGAAGAAGTTC		CCDS34439.1	6p21.31	2012-02-22			ENSG00000189325	ENSG00000189325			33769	protein-coding gene	gene with protein product							Standard	NM_001010903		Approved	DKFZp779B1540	uc003oly.3	P0C671	OTTHUMG00000014591	ENST00000437635.2:c.318C>T	chr6.hg19:g.36298150G>A		48.0	0.0	.		42.0	16.0	.	NM_001010903	B2RTY8	Silent	SNP	ENST00000437635.2	hg19	CCDS34439.1																																																																																			.	.	.	none		0.627	C6orf222-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040338.2	NM_001010903		A	36298150	G	A	36298150	2	1	263	1	0	0	0	0	0	0	0	1	2358	933	33	2		2	C6orf222	6	36298150	Silent	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	3	36298150	134816917	33	16433	169	2									
IBTK	25998	hgsc.bcm.edu	37	chr6	82950058	82950058	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcattcctgccaaaaacaTccttgatagttgcagcattg	11	11	9	10	0	0	1	0	1	0	0	2	1	2	1	3	1	4	4	3	1	3	5			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr6:82950058T>C	ENST00000306270.7	-	2	695	c.146A>G	c.(145-147)gAt>gGt	p.D49G	IBTK_ENST00000503631.1_Missense_Mutation_p.D49G|IBTK_ENST00000510291.1_Missense_Mutation_p.D49G	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	49					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)			central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		GCCAAAAACATCCTTGATAGT	0.443																																					p.D49G		Atlas-SNP	.											.	IBTK	128	.	0			c.A146G						PASS	.						148	139	142					6																	82950058		2203	4300	6503	SO:0001583	missense	25998	exon2			AAAACATCCTTGA	AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"BTB/POZ domain containing", "Ankyrin repeat domain containing"	17853	protein-coding gene	gene with protein product		606457	"Bruton agammaglobulinemia tyrosine kinase inhibitor"	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.146A>G	chr6.hg19:g.82950058T>C	ENSP00000305721:p.Asp49Gly	153.0	0.0	.		105.0	44.0	.	NM_015525	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Missense_Mutation	SNP	ENST00000306270.7	hg19	CCDS34490.1	.	.	.	.	.	.	.	.	.	.	T	19.33	3.806574	0.70682	.	.	ENSG00000005700	ENST00000306270;ENST00000503631;ENST00000510291	T;T;T	0.59638	0.25;0.25;0.25	5.78	5.78	0.91487	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.73009	0.3532	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	0.91635	0.999;0.999;0.999;0.999	T	0.77752	-0.2470	10	0.72032	D	0.01	-23.4179	16.0962	0.81127	0.0:0.0:0.0:1.0	.	49;49;49;49	E9PDR5;E7EPI0;Q9P2D0-2;Q9P2D0	.;.;.;IBTK_HUMAN	G	49	ENSP00000305721:D49G;ENSP00000422762:D49G;ENSP00000426405:D49G	ENSP00000305721:D49G	D	-	2	0	IBTK	83006777	1.000000	0.71417	1.000000	0.80357	0.501000	0.33797	7.671000	0.83941	2.207000	0.71202	0.459000	0.35465	GAT	.	.	.	none		0.443	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525		C	82950058	T	C	82950058	3	2	263	1	0	0	0	0	1	0	0	0	7483	1435	50	3	4027	3	IBTK	6	82950058	Missense_Mutation	SNP	T	TCGA-UZ-A9PR-01A-11D-A42J-10	46651908	82950058	88165009	34	16434											
SMPDL3A	10924	hgsc.bcm.edu	37	chr6	123124850	123124850	+	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	ttacaactaatccaaaccttAggatcatcagtctaaacaca	17	10	3	11	0	3	0	2	0	1	0	4	1	4	1	2	1	4	0	2	1	7	4			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr6:123124850A>C	ENST00000368440.4	+	5	787	c.610A>C	c.(610-612)Agg>Cgg	p.R204R	SMPDL3A_ENST00000539041.1_Silent_p.R73R	NM_006714.3	NP_006705.1	Q92484	ASM3A_HUMAN	sphingomyelin phosphodiesterase, acid-like 3A	204					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)		TCCAAACCTTAGGATCATCAG	0.343																																					p.R204R		Atlas-SNP	.											.	SMPDL3A	31	.	0			c.A610C						PASS	.						127	122	124					6																	123124850		2203	4300	6503	SO:0001819	synonymous_variant	10924	exon5			AACCTTAGGATCA	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.610A>C	chr6.hg19:g.123124850A>C		174.0	0.0	.		143.0	50.0	.	NM_006714	B7Z729|Q8WV13	Silent	SNP	ENST00000368440.4	hg19	CCDS5128.1																																																																																			.	.	.	none		0.343	SMPDL3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042039.1	NM_006714		C	123124850	A	C	123124850	2	2	263	1	0	0	0	0	0	0	0	1	14821	411	15	5		5	SMPDL3A	6	123124850	Silent	SNP	A	TCGA-UZ-A9PR-01A-11D-A42J-10	40174792	123124850	47990217	35	16435											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152510469	152510469	+	Missense_Mutation	SNP	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	tatcatcagcactgatatagGcagagagggtgtccttcagc	11	10	11	9	0	3	2	3	1	0	1	4	3	4	2	1	2	2	2	1	2	3	4			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr6:152510469G>A	ENST00000367255.5	-	128	23820	c.23219C>T	c.(23218-23220)gCc>gTc	p.A7740V	SYNE1_ENST00000448038.1_Missense_Mutation_p.A7669V|SYNE1_ENST00000423061.1_Missense_Mutation_p.A7669V|SYNE1_ENST00000356820.4_Missense_Mutation_p.A2264V|SYNE1_ENST00000341594.5_Missense_Mutation_p.A7352V|SYNE1_ENST00000265368.4_Missense_Mutation_p.A7740V	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	7740					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)		ACTGATATAGGCAGAGAGGGT	0.423										HNSCC(10;0.0054)																											p.A7740V		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C23219T						PASS	.						154	150	152					6																	152510469		2203	4300	6503	SO:0001583	missense	23345	exon128			ATATAGGCAGAGA	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.23219C>T	chr6.hg19:g.152510469G>A	ENSP00000356224:p.Ala7740Val	74.0	0.0	.		88.0	44.0	.	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	9.442	1.088347	0.20390	.	.	ENSG00000131018	ENST00000367255;ENST00000367257;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000367251	T;T;T;T;T;T;T;T	0.36520	1.25;1.25;1.25;1.25;1.25;1.25;1.25;1.25	5.99	5.11	0.69529	.	0.270973	0.28042	N	0.016838	T	0.06234	0.0161	N	0.04043	-0.29	0.09310	N	1	B;B;B;B	0.09022	0.001;0.001;0.002;0.001	B;B;B;B	0.11329	0.003;0.003;0.006;0.003	T	0.21348	-1.0248	10	0.30078	T	0.28	.	8.3176	0.32111	0.1333:0.0:0.7401:0.1266	.	7740;7740;7669;7669	Q8NF91;E7EQI5;Q8NF91-4;E9PEL9	SYNE1_HUMAN;.;.;.	V	7740;386;7669;7740;7669;7352;2264;662	ENSP00000356224:A7740V;ENSP00000356226:A386V;ENSP00000396024:A7669V;ENSP00000265368:A7740V;ENSP00000390975:A7669V;ENSP00000341887:A7352V;ENSP00000349276:A2264V;ENSP00000356220:A662V	ENSP00000265368:A7740V	A	-	2	0	SYNE1	152552162	0.254000	0.23992	0.845000	0.33349	0.831000	0.47069	1.811000	0.38942	1.509000	0.48786	0.655000	0.94253	GCC	.	.	.	none		0.423	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152510469	G	A	152510469	3	1	263	1	0	0	0	0	1	0	0	0	15457	1203	42	2	3323	2	SYNE1	6	152510469	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	29385619	152510469	18604598	36	16436											
UPP1	7378	hgsc.bcm.edu	37	chr7	48139322	48139322	+	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	caaaaatgaaagaagatattCtctatcatttcaatctcacc	17	12	3	9	0	4	3	3	1	2	2	6	3	4	3	1	0	0	0	1	0	7	4			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr7:48139322C>A	ENST00000331803.4	+	5	723	c.100C>A	c.(100-102)Ctc>Atc	p.L34I	UPP1_ENST00000482015.1_Intron|UPP1_ENST00000429491.2_Intron|UPP1_ENST00000395564.4_Missense_Mutation_p.L34I|UPP1_ENST00000341253.4_Missense_Mutation_p.L34I			Q16831	UPP1_HUMAN	uridine phosphorylase 1	34					cellular response to glucose starvation (GO:0042149)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide catabolic process (GO:0009166)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)|uridine metabolic process (GO:0046108)	cytosol (GO:0005829)	uridine phosphorylase activity (GO:0004850)			breast(1)|endometrium(2)|large_intestine(1)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	18					Fluorouracil(DB00544)	AGAAGATATTCTCTATCATTT	0.398																																					p.L34I		Atlas-SNP	.											.	UPP1	35	.	0			c.C100A						PASS	.						137	135	136					7																	48139322		2203	4300	6503	SO:0001583	missense	7378	exon4			GATATTCTCTATC	AK096167	CCDS5507.1	7p12.3	2012-10-02	2003-08-28	2003-08-29	ENSG00000183696	ENSG00000183696	2.4.2.3		12576	protein-coding gene	gene with protein product		191730	"uridine phosphorylase"	UP		752472, 11807789	Standard	NM_003364		Approved	UPASE, UPP, UDRPASE	uc003toj.3	Q16831	OTTHUMG00000129253	ENST00000331803.4:c.100C>A	chr7.hg19:g.48139322C>A	ENSP00000330032:p.Leu34Ile	59.0	0.0	.		94.0	24.0	.	NM_003364	D3DVM4|Q15362	Missense_Mutation	SNP	ENST00000331803.4	hg19	CCDS5507.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.182020	0.78677	.	.	ENSG00000183696	ENST00000416681;ENST00000331803;ENST00000341253;ENST00000395564;ENST00000436673	T;T;T;T;T	0.60797	0.46;0.16;0.16;0.16;0.47	5.43	4.52	0.55395	.	0.132798	0.48767	D	0.000165	T	0.74442	0.3717	M	0.83774	2.66	0.80722	D	1	D;D	0.71674	0.998;0.991	D;D	0.83275	0.996;0.949	T	0.76315	-0.3004	10	0.87932	D	0	-13.8768	8.0456	0.30547	0.0:0.806:0.0:0.194	.	34;34	B4DND0;Q16831	.;UPP1_HUMAN	I	34	ENSP00000405209:L34I;ENSP00000330032:L34I;ENSP00000342878:L34I;ENSP00000378931:L34I;ENSP00000390118:L34I	ENSP00000330032:L34I	L	+	1	0	UPP1	48105847	0.984000	0.35163	0.755000	0.31263	0.864000	0.49448	2.384000	0.44362	1.188000	0.43014	0.563000	0.77884	CTC	.	.	.	none		0.398	UPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251360.1	NM_003364		A	48139322	C	A	48139322	3	1	263	1	0	0	0	0	1	0	0	0	17024	913	32	4	106	4	UPP1	7	48139322	Missense_Mutation	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10		48139322	110999341	37	16437											
NPTX2	4885	hgsc.bcm.edu	37	chr7	98257796	98257796	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catatgggaccgcgtccttcGcgcacaagaaattgtcaaca	12	8	9	12	4	1	1	1	0	0	1	3	2	2	2	2	1	1	1	2	1	4	3			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr7:98257796G>A	ENST00000265634.3	+	5	1316	c.1151G>A	c.(1150-1152)cGc>cAc	p.R384H		NM_002523.2	NP_002514.1	P47972	NPTX2_HUMAN	neuronal pentraxin II	384	Pentaxin.				synaptic transmission (GO:0007268)	extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18	all_cancers(62;2.28e-09)|all_epithelial(64;4.86e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0128)|all_lung(186;0.0142)		STAD - Stomach adenocarcinoma(171;0.215)			CGCGTCCTTCGCGCACAAGAA	0.567																																					p.R384H		Atlas-SNP	.											.	NPTX2	45	.	0			c.G1151A						PASS	.						98	77	84					7																	98257796		2203	4300	6503	SO:0001583	missense	4885	exon5			TCCTTCGCGCACA		CCDS5657.1	7q21.3-q22.1	2008-04-30			ENSG00000106236	ENSG00000106236			7953	protein-coding gene	gene with protein product	"apexin"	600750				8530029	Standard	NM_002523		Approved		uc003upl.2	P47972	OTTHUMG00000154369	ENST00000265634.3:c.1151G>A	chr7.hg19:g.98257796G>A	ENSP00000265634:p.Arg384His	159.0	0.0	.		242.0	49.0	.	NM_002523	A4D267|Q86XV7|Q96G70	Missense_Mutation	SNP	ENST00000265634.3	hg19	CCDS5657.1	.	.	.	.	.	.	.	.	.	.	G	18.83	3.707444	0.68615	.	.	ENSG00000106236	ENST00000265634	T	0.58797	0.31	5.94	4.88	0.63580	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.142653	0.64402	D	0.000014	T	0.56381	0.1981	L	0.36672	1.1	0.09310	N	0.999998	D	0.57571	0.98	P	0.52758	0.708	T	0.53158	-0.8478	10	0.62326	D	0.03	-27.9605	10.4311	0.44409	0.1933:0.0:0.8067:0.0	.	384	P47972	NPTX2_HUMAN	H	384	ENSP00000265634:R384H	ENSP00000265634:R384H	R	+	2	0	NPTX2	98095732	0.088000	0.21588	0.292000	0.24919	0.792000	0.44763	1.644000	0.37228	2.826000	0.97356	0.561000	0.74099	CGC	.	.	.	none		0.567	NPTX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334982.1	NM_002523		A	98257796	G	A	98257796	3	1	263	1	0	0	0	0	1	0	0	0	10610	1087	38	1	1169	1	NPTX2	7	98257796	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	50118474	98257796	60880867	38	16438											
TNPO3	23534	hgsc.bcm.edu	37	chr7	128626881	128626881	+	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	agtgctgagccatgtgatctCggcagacagagcaaatgtta	12	9	12	8	1	1	4	0	2	1	2	2	4	1	4	1	1	3	4	1	1	2	1			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr7:128626881C>A	ENST00000265388.5	-	12	1735	c.1592G>T	c.(1591-1593)cGa>cTa	p.R531L	TNPO3_ENST00000482320.1_Missense_Mutation_p.R465L|TNPO3_ENST00000471166.1_Missense_Mutation_p.R565L|TNPO3_ENST00000471234.1_Intron|TNPO3_ENST00000393245.1_Missense_Mutation_p.R565L			Q9Y5L0	TNPO3_HUMAN	transportin 3	531					splicing factor protein import into nucleus (GO:0035048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(3)	22						CATGTGATCTCGGCAGACAGA	0.507																																					p.R531L	Pancreas(147;583 2585 39696 52331)	Atlas-SNP	.											.	TNPO3	148	.	0			c.G1592T						PASS	.						116	113	114					7																	128626881		2203	4300	6503	SO:0001583	missense	23534	exon12			TGATCTCGGCAGA	AF145029	CCDS5809.1, CCDS55162.1	7q32.2	2014-02-03			ENSG00000064419	ENSG00000064419		"Importins"	17103	protein-coding gene	gene with protein product	"importin 12"	610032	"limb girdle muscular dystrophy 1F (autosomal dominant)"	LGMD1F		10366588, 10713112, 23543484, 23667635	Standard	NM_012470		Approved	TRN-SR, MTR10A, TRN-SR2, IPO12	uc003vol.2	Q9Y5L0	OTTHUMG00000158409	ENST00000265388.5:c.1592G>T	chr7.hg19:g.128626881C>A	ENSP00000265388:p.Arg531Leu	253.0	0.0	.		408.0	95.0	.	NM_012470	A4D1K9|C9IZM0|Q6NUM1|Q96G71|Q96GU9|Q9Y3R2	Missense_Mutation	SNP	ENST00000265388.5	hg19	CCDS5809.1	.	.	.	.	.	.	.	.	.	.	C	33	5.209311	0.95069	.	.	ENSG00000064419	ENST00000393245;ENST00000265388;ENST00000482320;ENST00000471166	T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25	6.17	6.17	0.99709	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.75064	0.3799	L	0.58101	1.795	0.80722	D	1	D;B	0.59767	0.986;0.426	P;B	0.54759	0.76;0.175	T	0.72327	-0.4327	10	0.40728	T	0.16	.	18.3732	0.90420	0.0:1.0:0.0:0.0	.	565;531	C9J7E5;Q9Y5L0	.;TNPO3_HUMAN	L	565;531;465;565	ENSP00000376936:R565L;ENSP00000265388:R531L;ENSP00000420089:R465L;ENSP00000418267:R565L	ENSP00000265388:R531L	R	-	2	0	TNPO3	128414117	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.685000	0.84117	2.941000	0.99782	0.655000	0.94253	CGA	.	.	.	none		0.507	TNPO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350929.1	NM_012470		A	128626881	C	A	128626881	3	1	263	1	0	0	0	0	1	0	0	0	16349	884	31	4	1223	4	TNPO3	7	128626881	Missense_Mutation	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10	30369085	128626881	30511782	39	16439											
PRSS55	203074	hgsc.bcm.edu	37	chr8	10396206	10396206	+	Missense_Mutation	SNP	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	tgtcaaacagaaacctatggGctccccagtctcgggagtcc	10	8	10	13	1	2	1	1	0	1	1	5	2	4	2	4	2	2	1	4	2	3	1	rs200907557	byFrequency	TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr8:10396206G>A	ENST00000328655.3	+	5	1002	c.962G>A	c.(961-963)gGc>gAc	p.G321D	PRSS55_ENST00000522210.1_Intron|PRSS51_ENST00000523024.1_RNA	NM_198464.3	NP_940866.2	Q6UWB4	PRS55_HUMAN	protease, serine, 55	321						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)	31						AAACCTATGGGCTCCCCAGTC	0.532																																					p.G321D		Atlas-SNP	.											.	PRSS55	67	.	0			c.G962A						PASS	.						98	111	107					8																	10396206		2203	4300	6503	SO:0001583	missense	203074	exon5			CTATGGGCTCCCC	AY358867	CCDS5976.1, CCDS56523.1	8p23.1	2014-01-21			ENSG00000184647	ENSG00000184647		"Serine peptidases / Serine peptidases"	30824	protein-coding gene	gene with protein product		615144				12975309, 18844450	Standard	NM_198464		Approved	T-SP1, UNQ9391, CT153	uc003wta.3	Q6UWB4	OTTHUMG00000129345	ENST00000328655.3:c.962G>A	chr8.hg19:g.10396206G>A	ENSP00000333003:p.Gly321Asp	145.0	0.0	.		94.0	44.0	.	NM_198464	E5RJX5	Missense_Mutation	SNP	ENST00000328655.3	hg19	CCDS5976.1	.	.	.	.	.	.	.	.	.	.	G	0.578	-0.838381	0.02692	.	.	ENSG00000184647	ENST00000328655	D	0.88277	-2.36	3.64	-1.68	0.08212	.	1.695820	0.03580	N	0.229930	T	0.75598	0.3871	N	0.14661	0.345	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.61496	-0.7051	10	0.13470	T	0.59	.	2.6794	0.05089	0.3215:0.0:0.3306:0.3479	.	321	Q6UWB4	PRS55_HUMAN	D	321	ENSP00000333003:G321D	ENSP00000333003:G321D	G	+	2	0	PRSS55	10433616	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.489000	0.06490	-0.380000	0.07894	0.655000	0.94253	GGC	.	G|0.999;C|0.001	.	alt		0.532	PRSS55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251493.3	NM_198464		A	10396206	G	A	10396206	3	1	263	1	0	0	0	0	1	0	0	0	12644	1203	42	2	980	2	PRSS55	8	10396206	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10		10396206	135967816	40	16440											
RP1L1	94137	hgsc.bcm.edu	37	chr8	10468692	10468692	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctcgtccgccaactcataTgtcatgagtatgggctcttc	7	13	9	12	2	4	1	2	1	2	0	7	1	5	1	2	1	1	2	2	1	3	3			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr8:10468692T>C	ENST00000382483.3	-	4	3139	c.2916A>G	c.(2914-2916)acA>acG	p.T972T		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	972					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)		CCAACTCATATGTCATGAGTA	0.627																																					p.T972T		Atlas-SNP	.											.	RP1L1	453	.	0			c.A2916G						PASS	.						53	58	56					8																	10468692		1955	4146	6101	SO:0001819	synonymous_variant	94137	exon4			CTCATATGTCATG	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.2916A>G	chr8.hg19:g.10468692T>C		121.0	0.0	.		86.0	41.0	.	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	hg19	CCDS43708.1																																																																																			.	.	.	none		0.627	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			C	10468692	T	C	10468692	2	2	263	1	0	0	0	0	0	0	0	1	13546	1451	51	3		3	RP1L1	8	10468692	Silent	SNP	T	TCGA-UZ-A9PR-01A-11D-A42J-10	72486	10468692	135895330	41	16441											
DOCK5	80005	hgsc.bcm.edu	37	chr8	25177162	25177162	+	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	tcagtagtctattaccaagtCaagcagccctgttggtatga	11	12	9	9	0	3	1	2	1	1	0	3	1	3	1	2	1	3	4	2	1	6	5			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr8:25177162C>T	ENST00000276440.7	+	15	1556	c.1512C>T	c.(1510-1512)gtC>gtT	p.V504V		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	504	DHR-1.				positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		ATTACCAAGTCAAGCAGCCCT	0.398																																					p.V504V	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											.	DOCK5	167	.	0			c.C1512T						PASS	.						99	91	94					8																	25177162		2197	4285	6482	SO:0001819	synonymous_variant	80005	exon15			CCAAGTCAAGCAG		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.1512C>T	chr8.hg19:g.25177162C>T		63.0	0.0	.		57.0	25.0	.	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Silent	SNP	ENST00000276440.7	hg19	CCDS6047.1	.	.	.	.	.	.	.	.	.	.	C	10.13	1.266657	0.23136	.	.	ENSG00000147459	ENST00000444569	.	.	.	5.78	4.89	0.63831	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2778	0.73756	0.0:0.7126:0.2873:0.0	.	.	.	.	X	276	.	.	Q	+	1	0	DOCK5	25233079	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.182000	0.42556	1.554000	0.49487	0.655000	0.94253	CAA	.	.	.	none		0.398	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940		T	25177162	C	T	25177162	2	4	263	1	0	0	0	0	0	0	0	1	4692	813	29	2		2	DOCK5	8	25177162	Silent	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10	14708470	25177162	121186860	42	16442											
ADAM2	2515	hgsc.bcm.edu	37	chr8	39691500	39691500	+	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	agtatatggtttcccttcaaTtacaattttgtaggatgcct	10	17	7	7	0	1	0	1	0	0	0	2	1	2	1	2	2	2	3	2	2	6	8	rs150036296		TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr8:39691500T>A	ENST00000265708.4	-	3	254	c.151A>T	c.(151-153)Att>Ttt	p.I51F	ADAM2_ENST00000379853.2_Missense_Mutation_p.I51F|ADAM2_ENST00000523181.1_5'UTR|ADAM2_ENST00000521880.1_Missense_Mutation_p.I51F|ADAM2_ENST00000347580.4_Missense_Mutation_p.I51F	NM_001464.3	NP_001455.3	Q99965	ADAM2_HUMAN	ADAM metallopeptidase domain 2	51					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)		TTCCCTTCAATTACAATTTTG	0.279																																					p.I51F		Atlas-SNP	.											.	ADAM2	124	.	0			c.A151T						PASS	.						66	68	67					8																	39691500		2203	4288	6491	SO:0001583	missense	2515	exon3			CTTCAATTACAAT	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.151A>T	chr8.hg19:g.39691500T>A	ENSP00000265708:p.Ile51Phe	52.0	0.0	.		84.0	29.0	.	NM_001464	P78326|Q9UQQ8	Missense_Mutation	SNP	ENST00000265708.4	hg19	CCDS34884.1	.	.	.	.	.	.	.	.	.	.	T	14.35	2.509966	0.44660	.	.	ENSG00000104755	ENST00000347580;ENST00000379853;ENST00000265708;ENST00000521880	T;T;T;T	0.06608	3.28;3.28;3.28;3.28	4.72	4.72	0.59763	Peptidase M12B, propeptide (1);	.	.	.	.	T	0.16514	0.0397	L	0.48935	1.535	0.39409	D	0.96672	D;D;D;D	0.89917	0.999;1.0;1.0;0.999	D;D;D;D	0.91635	0.997;0.999;0.997;0.998	T	0.01413	-1.1361	8	.	.	.	.	10.7702	0.46319	0.0:0.0:0.0:1.0	.	51;51;51;51	B4DWY7;Q6P2G0;Q99965-2;Q99965	.;.;.;ADAM2_HUMAN	F	51	ENSP00000343854:I51F;ENSP00000369182:I51F;ENSP00000265708:I51F;ENSP00000429352:I51F	.	I	-	1	0	ADAM2	39810657	0.958000	0.32768	0.882000	0.34594	0.043000	0.13939	2.930000	0.48924	2.104000	0.64026	0.528000	0.53228	ATT	.	T|0.999;G|0.001	.	alt		0.279	ADAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376926.1	NM_001464		A	39691500	T	A	39691500	3	1	263	1	0	0	0	0	1	0	0	0	241	1493	52	5	2128	5	ADAM2	8	39691500	Missense_Mutation	SNP	T	TCGA-UZ-A9PR-01A-11D-A42J-10	14514338	39691500	106672522	43	16443											
SLC20A2	6575	hgsc.bcm.edu	37	chr8	42275393	42275393	+	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	aacagcccagccacagggacGgtcacgaaccaggccacgaa	14	1	11	15	3	1	0	1	0	0	0	1	3	1	1	4	3	4	0	4	3	3	0			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr8:42275393G>T	ENST00000342228.3	-	11	2256	c.1887C>A	c.(1885-1887)acC>acA	p.T629T	SLC20A2_ENST00000520262.1_Silent_p.T629T|SLC20A2_ENST00000520179.1_Silent_p.T629T	NM_006749.4	NP_006740.1	Q08357	S20A2_HUMAN	solute carrier family 20 (phosphate transporter), member 2	629					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)			CCACAGGGACGGTCACGAACC	0.587																																					p.T629T		Atlas-SNP	.											.	SLC20A2	64	.	0			c.C1887A						PASS	.						79	72	74					8																	42275393		2203	4300	6503	SO:0001819	synonymous_variant	6575	exon11			AGGGACGGTCACG		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.1887C>A	chr8.hg19:g.42275393G>T		180.0	0.0	.		164.0	76.0	.	NM_001257181		Silent	SNP	ENST00000342228.3	hg19	CCDS6132.1																																																																																			.	.	.	none		0.587	SLC20A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377578.1			T	42275393	G	T	42275393	2	4	263	1	0	0	0	0	0	0	0	1	14452	1103	39	4		4	SLC20A2	8	42275393	Silent	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	2583893	42275393	104088629	44	16444											
CHD7	55636	hgsc.bcm.edu	37	chr8	61778469	61778469	+	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	ttgatgggggggatgaaataGaaaacaatgaaaatgatgaa	19	8	13	1	0	0	6	0	5	0	1	0	7	0	7	0	3	1	0	0	3	8	2			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr8:61778469G>A	ENST00000423902.2	+	38	9450	c.8971G>A	c.(8971-8973)Gaa>Aaa	p.E2991K	CHD7_ENST00000524602.1_Missense_Mutation_p.E942K	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2991					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			GGATGAAATAGAAAACAATGA	0.423																																					p.E2991K		Atlas-SNP	.											.	CHD7	534	.	0			c.G8971A						PASS	.						17	18	18					8																	61778469		1897	4123	6020	SO:0001583	missense	55636	exon38			GAAATAGAAAACA	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.8971G>A	chr8.hg19:g.61778469G>A	ENSP00000392028:p.Glu2991Lys	132.0	0.0	.		104.0	43.0	.	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	hg19	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	G	14.02	2.411068	0.42817	.	.	ENSG00000171316	ENST00000307121;ENST00000423902;ENST00000524602	D;T	0.83755	-1.76;1.77	4.47	4.47	0.54385	.	0.000000	0.47852	D	0.000205	T	0.73393	0.3581	N	0.22421	0.69	0.45403	D	0.998385	B	0.30914	0.3	B	0.23275	0.045	T	0.75693	-0.3229	10	0.72032	D	0.01	-17.0826	17.4855	0.87687	0.0:0.0:1.0:0.0	.	2991	Q9P2D1	CHD7_HUMAN	K	2991;2991;942	ENSP00000392028:E2991K;ENSP00000437061:E942K	ENSP00000307304:E2991K	E	+	1	0	CHD7	61941023	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.536000	0.67180	2.169000	0.68431	0.655000	0.94253	GAA	.	.	.	none		0.423	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		A	61778469	G	A	61778469	3	1	263	1	0	0	0	0	1	0	0	0	3332	943	33	2	9117	2	CHD7	8	61778469	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	19503076	61778469	84585553	45	16445											
C8orf37	157657	hgsc.bcm.edu	37	chr8	96259954	96259954	+	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	atgcccgtgttcctttcttcTttatcaactttgcttttaat	6	21	4	10	1	3	0	1	0	2	0	4	0	4	0	2	0	3	2	2	0	3	8			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr8:96259954T>A	ENST00000286688.5	-	6	526	c.515A>T	c.(514-516)aAg>aTg	p.K172M		NM_177965.3	NP_808880.1	Q96NL8	CH037_HUMAN	chromosome 8 open reading frame 37	172						cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)		p.K172M(1)		kidney(1)|large_intestine(1)|lung(5)	7	Breast(36;3.41e-05)					TCCTTTCTTCTTTATCAACTT	0.398																																					p.K172M		Atlas-SNP	.											C8orf37,colon,carcinoma,0,1	C8orf37	15	.	1	Substitution - Missense(1)	large_intestine(1)	c.A515T						PASS	.						174	157	163					8																	96259954		2203	4300	6503	SO:0001583	missense	157657	exon6			TTCTTCTTTATCA	AK055162	CCDS6268.1	8q22.1	2014-01-28			ENSG00000156172	ENSG00000156172			27232	protein-coding gene	gene with protein product		614477				22177090	Standard	NM_177965		Approved	FLJ30600, CORD16, RP64	uc003yho.2	Q96NL8	OTTHUMG00000164663	ENST00000286688.5:c.515A>T	chr8.hg19:g.96259954T>A	ENSP00000286688:p.Lys172Met	99.0	0.0	.		91.0	47.0	.	NM_177965		Missense_Mutation	SNP	ENST00000286688.5	hg19	CCDS6268.1	.	.	.	.	.	.	.	.	.	.	T	15.83	2.949731	0.53186	.	.	ENSG00000156172	ENST00000286688	D	0.83419	-1.72	5.42	2.98	0.34508	.	0.169978	0.50627	D	0.000105	D	0.85906	0.5806	M	0.69823	2.125	0.31460	N	0.669699	D	0.69078	0.997	P	0.58873	0.847	D	0.84150	0.0422	10	0.87932	D	0	-11.6379	5.4681	0.16654	0.0:0.1483:0.1478:0.7039	.	172	Q96NL8	CH037_HUMAN	M	172	ENSP00000286688:K172M	ENSP00000286688:K172M	K	-	2	0	C8orf37	96329130	1.000000	0.71417	0.489000	0.27452	0.730000	0.41778	2.446000	0.44908	0.352000	0.24053	0.459000	0.35465	AAG	.	.	.	none		0.398	C8orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379672.1	NM_177965		A	96259954	T	A	96259954	3	1	263	1	0	0	0	0	1	0	0	0	2425	1609	56	5	112	5	C8orf37	8	96259954	Missense_Mutation	SNP	T	TCGA-UZ-A9PR-01A-11D-A42J-10	34481485	96259954	50104068	46	16446											
POP1	10940	hgsc.bcm.edu	37	chr8	99168546	99168546	+	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	cagaggaggtaatggatgcaGggtgtcaagaatcggcaggg	12	6	18	5	1	1	2	1	0	0	2	2	4	1	4	0	6	1	3	0	6	3	1			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr8:99168546G>T	ENST00000401707.2	+	15	2407	c.2326G>T	c.(2326-2328)Ggg>Tgg	p.G776W	POP1_ENST00000349693.3_Missense_Mutation_p.G776W	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)	776					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)			AATGGATGCAGGGTGTCAAGA	0.547																																					p.G776W		Atlas-SNP	.											.	POP1	85	.	0			c.G2326T						PASS	.						126	124	125					8																	99168546		2203	4300	6503	SO:0001583	missense	10940	exon15			GATGCAGGGTGTC	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.2326G>T	chr8.hg19:g.99168546G>T	ENSP00000385787:p.Gly776Trp	128.0	0.0	.		97.0	41.0	.	NM_001145860	A8K5W9|Q15037	Missense_Mutation	SNP	ENST00000401707.2	hg19	CCDS6277.1	.	.	.	.	.	.	.	.	.	.	G	11.27	1.590008	0.28357	.	.	ENSG00000104356	ENST00000401707;ENST00000349693	T;T	0.36520	1.25;1.25	5.19	4.31	0.51392	.	1.118330	0.06500	N	0.736162	T	0.26159	0.0638	N	0.22421	0.69	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.22034	-1.0228	10	0.66056	D	0.02	-6.2211	4.6366	0.12527	0.1876:0.0:0.6369:0.1755	.	776	Q99575	POP1_HUMAN	W	776	ENSP00000385787:G776W;ENSP00000339529:G776W	ENSP00000339529:G776W	G	+	1	0	POP1	99237722	0.724000	0.28038	0.719000	0.30619	0.043000	0.13939	1.668000	0.37481	1.170000	0.42753	0.591000	0.81541	GGG	.	.	.	none		0.547	POP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379470.1	NM_015029		T	99168546	G	T	99168546	3	4	263	1	0	0	0	0	1	0	0	0	12258	1000	35	4	2380	4	POP1	8	99168546	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	2908592	99168546	47195476	47	16447											
BAI1	575	hgsc.bcm.edu	37	chr8	143558843	143558843	+	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	cgcacctgcaggcccccccaGtttgggggcaacccctgtga	6	6	12	17	1	0	1	0	1	0	0	0	1	0	1	6	3	2	4	6	3	1	1			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr8:143558843G>A	ENST00000517894.1	+	6	2214	c.1320G>A	c.(1318-1320)caG>caA	p.Q440Q	BAI1_ENST00000323289.5_Silent_p.Q440Q			O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	440	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(28)|ovary(4)|pancreas(1)|prostate(7)	57	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					GGCCCCCCCAGTTTGGGGGCA	0.657																																					p.Q440Q		Atlas-SNP	.											.	BAI1	146	.	0			c.G1320A						PASS	.						44	51	49					8																	143558843		1978	4152	6130	SO:0001819	synonymous_variant	575	exon5			CCCCCAGTTTGGG	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.1320G>A	chr8.hg19:g.143558843G>A		80.0	0.0	.		65.0	25.0	.	NM_001702		Silent	SNP	ENST00000517894.1	hg19																																																																																				.	.	.	none		0.657	BAI1-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379963.3	NM_001702		A	143558843	G	A	143558843	2	1	263	1	0	0	0	0	0	0	0	1	1298	1020	36	2		2	BAI1	8	143558843	Silent	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	44390297	143558843	2805179	48	16448											
VCP	7415	hgsc.bcm.edu	37	chr9	35066717	35066717	+	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	caggaagtacggcttaaggtAtacctcgaagagattaccag	14	8	11	8	2	0	1	0	0	0	1	1	4	0	2	2	3	3	3	2	3	7	5			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr9:35066717A>T	ENST00000358901.6	-	4	1295	c.400T>A	c.(400-402)Tac>Aac	p.Y134N		NM_007126.3	NP_009057.1	P55072	TERA_HUMAN	valosin containing protein	134					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|aggresome assembly (GO:0070842)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|establishment of protein localization (GO:0045184)|positive regulation of Lys63-specific deubiquitinase activity (GO:1903007)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein K63-linked deubiquitination (GO:1903006)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|retrograde protein transport, ER to cytosol (GO:0030970)|translesion synthesis (GO:0019985)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Hrd1p ubiquitin ligase complex (GO:0000836)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|site of double-strand break (GO:0035861)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|deubiquitinase activator activity (GO:0035800)|lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|protein domain specific binding (GO:0019904)|protein phosphatase binding (GO:0019903)|ubiquitin-specific protease binding (GO:1990381)			breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			GGCTTAAGGTATACCTCGAAG	0.473																																					p.Y134N		Atlas-SNP	.											.	VCP	64	.	0			c.T400A						PASS	.						134	111	119					9																	35066717		2203	4300	6503	SO:0001583	missense	7415	exon4			TAAGGTATACCTC	AC004472	CCDS6573.1	9p13.3	2014-09-17	2011-01-25		ENSG00000165280	ENSG00000165280		"ATPases / AAA-type"	12666	protein-coding gene	gene with protein product		601023	"valosin-containing protein"			8595912, 7553851	Standard	NM_007126		Approved	IBMPFD, p97	uc003zvy.2	P55072	OTTHUMG00000019855	ENST00000358901.6:c.400T>A	chr9.hg19:g.35066717A>T	ENSP00000351777:p.Tyr134Asn	107.0	0.0	.		92.0	37.0	.	NM_007126	B2R5T8|Q0V924|Q2TAI5|Q969G7|Q9UCD5	Missense_Mutation	SNP	ENST00000358901.6	hg19	CCDS6573.1	.	.	.	.	.	.	.	.	.	.	A	28.8	4.952555	0.92660	.	.	ENSG00000165280	ENST00000358901;ENST00000448530;ENST00000417448	D;D;D	0.96745	-4.11;-4.11;-4.11	5.79	5.79	0.91817	Cell division protein 48, Cdc48, domain 2 (1);	0.000000	0.85682	D	0.000000	D	0.98764	0.9584	H	0.96208	3.785	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99609	1.0980	10	0.62326	D	0.03	-0.0218	16.1376	0.81497	1.0:0.0:0.0:0.0	.	134	P55072	TERA_HUMAN	N	134;89;89	ENSP00000351777:Y134N;ENSP00000392088:Y89N;ENSP00000399456:Y89N	ENSP00000351777:Y134N	Y	-	1	0	VCP	35056717	1.000000	0.71417	0.997000	0.53966	0.980000	0.70556	9.066000	0.93949	2.212000	0.71576	0.533000	0.62120	TAC	.	.	.	none		0.473	VCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052290.1	NM_007126		T	35066717	A	T	35066717	3	4	263	1	0	0	0	0	1	0	0	0	17152	449	16	5	2076	5	VCP	9	35066717	Missense_Mutation	SNP	A	TCGA-UZ-A9PR-01A-11D-A42J-10		35066717	106146714	49	16449											
NPR2	4882	hgsc.bcm.edu	37	chr9	35805967	35805967	+	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	ctttctacttggagggcctgGacctcagccccaaaggtaag	9	9	11	12	0	2	0	1	0	1	0	2	2	2	2	4	4	2	1	4	4	3	4			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr9:35805967G>C	ENST00000342694.2	+	14	2443	c.2188G>C	c.(2188-2190)Gac>Cac	p.D730H		NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2	730	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	GGAGGGCCTGGACCTCAGCCC	0.522																																					p.D730H		Atlas-SNP	.											.	NPR2	162	.	0			c.G2188C						PASS	.						65	68	67					9																	35805967		2203	4300	6503	SO:0001583	missense	4882	exon14			GGCCTGGACCTCA	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.2188G>C	chr9.hg19:g.35805967G>C	ENSP00000341083:p.Asp730His	79.0	0.0	.		75.0	25.0	.	NM_003995	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Missense_Mutation	SNP	ENST00000342694.2	hg19	CCDS6590.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.40|11.40	1.626506|1.626506	0.28978|0.28978	.|.	.|.	ENSG00000159899|ENSG00000159899	ENST00000342694|ENST00000421267	T|.	0.63744|.	-0.06|.	5.82|5.82	5.82|5.82	0.92795|0.92795	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.46145|.	D|.	0.000309|.	T|T	0.57140|0.57140	0.2033|0.2033	N|N	0.26092|0.26092	0.79|0.79	0.58432|0.58432	D|D	0.999998|0.999998	B;P|.	0.37158|.	0.291;0.585|.	B;B|.	0.35353|.	0.1;0.201|.	T|T	0.49960|0.49960	-0.8883|-0.8883	10|5	0.49607|.	T|.	0.09|.	.|.	18.6867|18.6867	0.91567|0.91567	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	730;730|.	P20594-2;P20594|.	.;ANPRB_HUMAN|.	H|C	730|76	ENSP00000341083:D730H|.	ENSP00000341083:D730H|.	D|W	+|+	1|3	0|0	NPR2|NPR2	35795967|35795967	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	5.608000|5.608000	0.67654|0.67654	2.756000|2.756000	0.94617|0.94617	0.563000|0.563000	0.77884|0.77884	GAC|TGG	.	.	.	none		0.522	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1			C	35805967	G	C	35805967	3	2	263	1	0	0	0	0	1	0	0	0	10602	1174	41	4	2242	4	NPR2	9	35805967	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	739250	35805967	105407464	50	16450											
PAX5	5079	hgsc.bcm.edu	37	chr9	36966620	36966620	+	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	ctcaaacacgcggtccagcaCctccagctgctgctgtgtga	8	8	10	15	2	1	1	1	1	0	0	3	1	3	1	3	1	5	4	3	1	1	0			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr9:36966620C>T	ENST00000358127.4	-	6	780	c.706G>A	c.(706-708)Gtg>Atg	p.V236M	PAX5_ENST00000523145.1_Missense_Mutation_p.V128M|PAX5_ENST00000522003.1_Missense_Mutation_p.V128M|PAX5_ENST00000520154.1_Missense_Mutation_p.V236M|PAX5_ENST00000523241.1_Missense_Mutation_p.V236M|PAX5_ENST00000414447.1_Missense_Mutation_p.V193M|PAX5_ENST00000377847.2_Missense_Mutation_p.V236M|PAX5_ENST00000377852.2_Missense_Mutation_p.V236M|PAX5_ENST00000520281.1_Missense_Mutation_p.V193M|PAX5_ENST00000446742.1_Missense_Mutation_p.V170M|PAX5_ENST00000377853.2_Missense_Mutation_p.V236M	NM_001280554.1|NM_001280556.1|NM_016734.1	NP_001267483.1|NP_001267485.1|NP_057953.1	Q02548	PAX5_HUMAN	paired box 5	236					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.?(41)	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)		CGGTCCAGCACCTCCAGCTGC	0.607			"T, Mis, D, F, S"	"IGH@, ETV6, PML, FOXP1, ZNF521, ELN"	"NHL, ALL, B-ALL"																																p.V236M		Atlas-SNP	.		Dom	yes		9	9p13	5079	paired box gene 5 (B-cell lineage specific activator protein)		L	.	PAX5	250	.	41	Unknown(41)	haematopoietic_and_lymphoid_tissue(41)	c.G706A						PASS	.						121	97	105					9																	36966620		2203	4300	6503	SO:0001583	missense	5079	exon6			CCAGCACCTCCAG		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.706G>A	chr9.hg19:g.36966620C>T	ENSP00000350844:p.Val236Met	119.0	0.0	.		85.0	40.0	.	NM_016734	A3QVP6|A3QVP7|A3QVP8|C0KTF6|C0KTF7|C0KTF8|C0KTF9|C0KTG0|O75933|Q5SFM2|Q6S728|Q6S729|Q6S730|Q6S731|Q6S732	Missense_Mutation	SNP	ENST00000358127.4	hg19	CCDS6607.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.015018	0.93404	.	.	ENSG00000196092	ENST00000358127;ENST00000377849;ENST00000377853;ENST00000377852;ENST00000523241;ENST00000520154;ENST00000520281;ENST00000446742;ENST00000522003;ENST00000523145;ENST00000414447;ENST00000377847;ENST00000524340	D;D;D;D;D;D;D;D;D;D;D;T	0.97811	-4.06;-4.05;-4.05;-4.55;-4.55;-4.51;-3.73;-1.79;-2.38;-4.52;-4.54;1.42	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.98153	0.9390	L	0.46885	1.475	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.71674	0.971;0.996;0.998;0.99;0.998;0.975;0.988;0.971;0.99;0.99	P;P;D;P;D;P;P;P;P;P	0.79784	0.543;0.823;0.949;0.675;0.993;0.805;0.862;0.543;0.675;0.675	D	0.99640	1.0988	10	0.72032	D	0.01	.	19.4277	0.94751	0.0:1.0:0.0:0.0	.	193;193;170;236;44;236;236;236;236;236	C0KTF8;C0KTF7;C0KTF9;C0KTF6;C0KTE2;E7ERW5;E7EQT0;Q6S730;Q6S731;Q02548	.;.;.;.;.;.;.;.;.;PAX5_HUMAN	M	236;128;236;236;236;236;193;170;128;128;193;236;44	ENSP00000350844:V236M;ENSP00000367084:V236M;ENSP00000367083:V236M;ENSP00000429637:V236M;ENSP00000429291:V236M;ENSP00000430773:V193M;ENSP00000404687:V170M;ENSP00000429359:V128M;ENSP00000429197:V128M;ENSP00000412188:V193M;ENSP00000367078:V236M;ENSP00000429404:V44M	ENSP00000350844:V236M	V	-	1	0	PAX5	36956620	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.398000	0.79919	2.568000	0.86640	0.655000	0.94253	GTG	.	.	.	none		0.607	PAX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052433.1			T	36966620	C	T	36966620	3	4	263	1	0	0	0	0	1	0	0	0	11489	507	18	2	489	2	PAX5	9	36966620	Missense_Mutation	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10	1160653	36966620	104246811	51	16451											
USP20	10868	hgsc.bcm.edu	37	chr9	132630512	132630512	+	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	gtggcgggggcagctcgcagGccgagacggagctgctgatc	6	5	19	11	4	0	2	0	1	0	1	2	4	0	3	1	5	3	5	1	5	0	0			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr9:132630512G>C	ENST00000315480.4	+	11	1077	c.919G>C	c.(919-921)Gcc>Ccc	p.A307P	USP20_ENST00000372429.3_Missense_Mutation_p.A307P|USP20_ENST00000358355.1_Missense_Mutation_p.A307P			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	307	USP.				endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				CAGCTCGCAGGCCGAGACGGA	0.647																																					p.A307P		Atlas-SNP	.											.	USP20	186	.	0			c.G919C						PASS	.						42	53	49					9																	132630512		2074	4201	6275	SO:0001583	missense	10868	exon11			TCGCAGGCCGAGA	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"Ubiquitin-specific peptidases"	12619	protein-coding gene	gene with protein product		615143	"ubiquitin specific protease 20"			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.919G>C	chr9.hg19:g.132630512G>C	ENSP00000313811:p.Ala307Pro	150.0	0.0	.		95.0	37.0	.	NM_001008563	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Missense_Mutation	SNP	ENST00000315480.4	hg19	CCDS43892.1	.	.	.	.	.	.	.	.	.	.	G	11.66	1.705110	0.30232	.	.	ENSG00000136878	ENST00000372429;ENST00000315480;ENST00000358355	T;T;T	0.18657	2.2;2.2;2.2	4.95	4.95	0.65309	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	2.873660	0.01084	N	0.005051	T	0.22322	0.0538	L	0.29908	0.895	0.52501	D	0.999959	B	0.20459	0.045	B	0.18871	0.023	T	0.05533	-1.0879	10	0.40728	T	0.16	.	12.3196	0.54977	0.0:0.0:0.8311:0.1689	.	307	Q9Y2K6	UBP20_HUMAN	P	307	ENSP00000361506:A307P;ENSP00000313811:A307P;ENSP00000351122:A307P	ENSP00000313811:A307P	A	+	1	0	USP20	131670333	1.000000	0.71417	0.999000	0.59377	0.342000	0.28953	2.433000	0.44793	2.291000	0.77112	0.561000	0.74099	GCC	.	.	.	none		0.647	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2			C	132630512	G	C	132630512	3	2	263	1	0	0	0	0	1	0	0	0	17064	1203	42	4	953	4	USP20	9	132630512	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	95663892	132630512	8582919	52	16452											
SEC24C	9632	hgsc.bcm.edu	37	chr10	75526876	75526876	+	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	gcccattgcagaggccccagGgaaactgaagaacagagatg	14	4	13	10	0	0	4	0	1	0	3	0	6	0	5	3	2	3	1	3	2	3	1			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr10:75526876G>A	ENST00000339365.2	+	15	2120	c.1958G>A	c.(1957-1959)gGg>gAg	p.G653E	SEC24C_ENST00000411652.2_Missense_Mutation_p.G534E|SEC24C_ENST00000535742.1_Intron|SEC24C_ENST00000345254.4_Missense_Mutation_p.G653E|SEC24C_ENST00000540668.1_Intron	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	653					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)					GAGGCCCCAGGGAAACTGAAG	0.468																																					p.G653E		Atlas-SNP	.											.	SEC24C	86	.	0			c.G1958A						PASS	.						89	88	88					10																	75526876		2203	4300	6503	SO:0001583	missense	9632	exon14			CCCCAGGGAAACT	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.1958G>A	chr10.hg19:g.75526876G>A	ENSP00000343405:p.Gly653Glu	123.0	0.0	.		103.0	44.0	.	NM_198597	B4DZT4|Q8WV25	Missense_Mutation	SNP	ENST00000339365.2	hg19	CCDS7332.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.550641	0.86127	.	.	ENSG00000176986	ENST00000345254;ENST00000339365;ENST00000411652	D;D;D	0.82344	-1.6;-1.6;-1.6	5.57	5.57	0.84162	Sec23/Sec24, trunk domain (1);	0.000000	0.85682	D	0.000000	D	0.94251	0.8154	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	0.999;1.0;1.0	D	0.95471	0.8551	10	0.87932	D	0	-9.8933	19.6032	0.95572	0.0:0.0:1.0:0.0	.	534;653;653	E7EP00;G5EA31;P53992	.;.;SC24C_HUMAN	E	653;653;534	ENSP00000321845:G653E;ENSP00000343405:G653E;ENSP00000402913:G534E	ENSP00000343405:G653E	G	+	2	0	SEC24C	75196882	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.643000	0.89663	0.555000	0.69702	GGG	.	.	.	none		0.468	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1			A	75526876	G	A	75526876	3	1	263	1	0	0	0	0	1	0	0	0	14009	1232	43	2	2008	2	SEC24C	10	75526876	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10		75526876	60007871	53	16453											
FGFBP3	143282	hgsc.bcm.edu	37	chr10	93667973	93667973	+	Missense_Mutation	SNP	A	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	gccgttccagaaattgacaaAgaagttgcagagggagtgcc	13	7	13	8	1	0	4	0	1	0	3	1	5	1	5	3	1	2	3	3	1	3	3			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr10:93667973A>C	ENST00000311575.5	-	2	917	c.754T>G	c.(754-756)Ttt>Gtt	p.F252V	RP11-402D21.2_ENST00000610263.1_RNA	NM_152429.4	NP_689642.3	Q8TAT2	FGFP3_HUMAN	fibroblast growth factor binding protein 3	252					positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of vascular permeability (GO:0043117)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	fibroblast growth factor binding (GO:0017134)|heparin binding (GO:0008201)			large_intestine(1)|prostate(1)	2		Colorectal(252;0.162)				AAATTGACAAAGAAGTTGCAG	0.647																																					p.F252V		Atlas-SNP	.											.	FGFBP3	6	.	0			c.T754G						PASS	.						48	51	50					10																	93667973		2203	4299	6502	SO:0001583	missense	143282	exon2			TGACAAAGAAGTT	AK075410	CCDS7418.1	10q23.33	2006-12-14	2006-12-14	2006-12-14	ENSG00000174721	ENSG00000174721			23428	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 13"	C10orf13			Standard	NM_152429		Approved	MGC39320	uc001khq.4	Q8TAT2	OTTHUMG00000018751	ENST00000311575.5:c.754T>G	chr10.hg19:g.93667973A>C	ENSP00000339067:p.Phe252Val	47.0	0.0	.		40.0	16.0	.	NM_152429	B2RD68|Q8NBN0	Missense_Mutation	SNP	ENST00000311575.5	hg19	CCDS7418.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.631498	0.87660	.	.	ENSG00000174721	ENST00000311575	T	0.20200	2.09	4.45	4.45	0.53987	.	0.000000	0.64402	D	0.000001	T	0.44829	0.1312	M	0.74258	2.255	0.48236	D	0.999614	D	0.89917	1.0	D	0.91635	0.999	T	0.45906	-0.9229	10	0.87932	D	0	-3.1889	11.6122	0.51066	1.0:0.0:0.0:0.0	.	252	Q8TAT2	FGFP3_HUMAN	V	252	ENSP00000339067:F252V	ENSP00000339067:F252V	F	-	1	0	FGFBP3	93657953	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.802000	0.55553	1.988000	0.58038	0.533000	0.62120	TTT	.	.	.	none		0.647	FGFBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049379.1	NM_152429		C	93667973	A	C	93667973	3	2	263	1	0	0	0	0	1	0	0	0	5869	72	3	5	26	5	FGFBP3	10	93667973	Missense_Mutation	SNP	A	TCGA-UZ-A9PR-01A-11D-A42J-10	18141097	93667973	41866774	54	16454											
C11orf40	143501	hgsc.bcm.edu	37	chr11	4599028	4599028	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggctctctttctctgggcAccagcgcctgcactagagcc	5	11	10	15	1	2	1	0	0	2	1	4	1	2	1	3	2	3	3	3	2	1	3			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr11:4599028A>G	ENST00000307616.1	-	1	22	c.23T>C	c.(22-24)gTg>gCg	p.V8A		NM_144663.1	NP_653264.1	Q8WZ69	CK040_HUMAN	chromosome 11 open reading frame 40	8										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)		ttctctgggcaccagcgcctg	0.498																																					p.V8A		Atlas-SNP	.											.	C11orf40	37	.	0			c.T23C						PASS	.						36	31	32					11																	4599028		2191	4276	6467	SO:0001583	missense	143501	exon1			CTGGGCACCAGCG		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.23T>C	chr11.hg19:g.4599028A>G	ENSP00000302918:p.Val8Ala	64.0	0.0	.		40.0	10.0	.	NM_144663		Missense_Mutation	SNP	ENST00000307616.1	hg19	CCDS31354.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.754303	0.00663	.	.	ENSG00000171987	ENST00000307616	T	0.54866	0.55	0.235	-0.47	0.12131	.	.	.	.	.	T	0.25754	0.0627	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.15752	-1.0426	8	0.87932	D	0	.	.	.	.	.	8	Q8WZ69	CK040_HUMAN	A	8	ENSP00000302918:V8A	ENSP00000302918:V8A	V	-	2	0	C11orf40	4555604	0.003000	0.15002	0.001000	0.08648	0.001000	0.01503	-0.597000	0.05713	-2.313000	0.00648	-2.381000	0.00232	GTG	.	.	.	none		0.498	C11orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383529.1	NM_144663		G	4599028	A	G	4599028	3	3	263	1	0	0	0	0	1	0	0	0	1641	159	6	3	645	3	C11orf40	11	4599028	Missense_Mutation	SNP	A	TCGA-UZ-A9PR-01A-11D-A42J-10		4599028	130407488	55	16455											
PRRG4	79056	hgsc.bcm.edu	37	chr11	32858352	32858352	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaagccagagagatttttgtGgatgaagataaaacggtaat	16	10	12	3	1	0	4	0	1	0	3	0	7	0	5	1	2	2	1	1	2	5	4			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr11:32858352G>A	ENST00000257836.3	+	3	505	c.252G>A	c.(250-252)gtG>gtA	p.V84V		NM_024081.5	NP_076986.1	Q9BZD6	TMG4_HUMAN	proline rich Gla (G-carboxyglutamic acid) 4 (transmembrane)	84	Gla. {ECO:0000255|PROSITE- ProRule:PRU00463}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			large_intestine(2)|lung(2)|prostate(2)|urinary_tract(1)	7	Breast(20;0.206)					AGATTTTTGTGGATGAAGATA	0.358																																					p.V84V		Atlas-SNP	.											.	PRRG4	15	.	0			c.G252A						PASS	.						72	73	73					11																	32858352		2202	4299	6501	SO:0001819	synonymous_variant	79056	exon3			TTTTGTGGATGAA	AF326351	CCDS7881.1	11p13	2008-02-05			ENSG00000135378	ENSG00000135378			30799	protein-coding gene	gene with protein product		611690				11171957	Standard	NM_024081		Approved	TMG4	uc001mtx.3	Q9BZD6	OTTHUMG00000166219	ENST00000257836.3:c.252G>A	chr11.hg19:g.32858352G>A		150.0	0.0	.		96.0	35.0	.	NM_024081		Silent	SNP	ENST00000257836.3	hg19	CCDS7881.1																																																																																			.	.	.	none		0.358	PRRG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388446.1	NM_024081		A	32858352	G	A	32858352	2	1	263	1	0	0	0	0	0	0	0	1	12618	1335	47	2		2	PRRG4	11	32858352	Silent	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	28259324	32858352	102148164	56	16456											
ADAMTS8	11095	hgsc.bcm.edu	37	chr11	130281414	130281414	+	Missense_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	ggggtccttgcactcacggtGtgaaaactgtactcctcctc	7	11	10	13	1	1	1	1	1	0	0	5	1	4	1	3	3	3	2	3	3	3	2			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr11:130281414G>A	ENST00000257359.6	-	6	2354	c.1648C>T	c.(1648-1650)Cac>Tac	p.H550Y		NM_007037.4	NP_008968.4	Q9UP79	ATS8_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 8	550	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				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)		CACTCACGGTGTGAAAACTGT	0.597																																					p.H550Y		Atlas-SNP	.											.	ADAMTS8	172	.	0			c.C1648T						PASS	.						76	81	79					11																	130281414		2017	4162	6179	SO:0001583	missense	11095	exon6			CACGGTGTGAAAA	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.1648C>T	chr11.hg19:g.130281414G>A	ENSP00000257359:p.His550Tyr	105.0	0.0	.		98.0	46.0	.	NM_007037	Q9NZS0	Missense_Mutation	SNP	ENST00000257359.6	hg19	CCDS41732.1	.	.	.	.	.	.	.	.	.	.	G	2.888	-0.230363	0.05983	.	.	ENSG00000134917	ENST00000257359;ENST00000414575	T	0.52754	0.65	5.58	-2.86	0.05717	.	0.619078	0.19024	N	0.124760	T	0.16599	0.0399	N	0.10664	0.02	0.22562	N	0.998988	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.001	T	0.29971	-0.9994	10	0.05351	T	0.99	.	5.4963	0.16805	0.4596:0.0:0.324:0.2164	.	550;31	Q9UP79;B3KVX9	ATS8_HUMAN;.	Y	550;579	ENSP00000257359:H550Y	ENSP00000257359:H550Y	H	-	1	0	ADAMTS8	129786624	0.000000	0.05858	0.560000	0.28344	0.982000	0.71751	-0.457000	0.06745	-0.431000	0.07307	0.591000	0.81541	CAC	.	.	.	none		0.597	ADAMTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385636.1	NM_007037		A	130281414	G	A	130281414	3	1	263	1	0	0	0	0	1	0	0	0	272	1377	48	2	1037	2	ADAMTS8	11	130281414	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	97423062	130281414	4725102	57	16457											
KDM5A	5927	hgsc.bcm.edu	37	chr12	427414	427417	+	Frame_Shift_Del	DEL	AAGT	AAGT	-																															cagcttcttcatgacatccaAagtgacttgttgcggatctg																								rs542998005		TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	AAGT	AAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr12:427414_427417delAAGT	ENST00000399788.2	-	19	3114_3117	c.2752_2755delACTT	c.(2752-2757)actttgfs	p.TL918fs	KDM5A_ENST00000382815.4_Frame_Shift_Del_p.TL918fs	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	918					chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|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 coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						ATGACATCCAAAGTGACTTGTTGC	0.5			T	NUP98	AML																																p.918_919del		Atlas-Indel,Pindel	.		Dom	yes		12	12p11	5927	"lysine (K)-specific demethylase 5A, JARID1A"		L	.	KDM5A	307	.	0			c.2753_2756del						PASS	.																																			SO:0001589	frameshift_variant	5927	exon19			.		CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614		"Chromatin-modifying enzymes / K-demethylases", "Zinc fingers, PHD-type"	9886	protein-coding gene	gene with protein product		180202	"retinoblastoma-binding protein 2", "Jumonji, AT rich interactive domain 1A (RBBP2-like)", "jumonji, AT rich interactive domain 1A"	RBBP2, JARID1A		1857421	Standard	NM_001042603		Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.2752_2755delACTT	chr12.hg19:g.427414_427417delAAGT	ENSP00000382688:p.Thr918fs	107.0	0.0	0		85.0	27.0	0.317647	NM_001042603	A8MV76|Q4LE72|Q86XZ1	Frame_Shift_Del	DEL	ENST00000399788.2	hg19	CCDS41736.1																																																																																			.	.	.	none		0.5	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397812.1	NM_005056		-	427417	AAGT	-	427414	7	5	263	1	0	1	0	1	0	0	0	0	8140	11	1	0	2357	0	KDM5A	12	427414	Frame_Shift_Del	DEL	AAGT	TCGA-UZ-A9PR-01A-11D-A42J-10		427414	133424481	58	16458											
CACNA2D4	93589	hgsc.bcm.edu	37	chr12	1995492	1995492	+	Missense_Mutation	SNP	T	T	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	ccttcatactgccgctcacgTccaccaaaatcactatgtcc	10	10	4	17	2	3	0	3	0	0	0	5	0	5	0	5	0	2	1	5	0	4	3			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr12:1995492T>G	ENST00000382722.5	-	8	1252	c.890A>C	c.(889-891)gAc>gCc	p.D297A	CACNA2D4_ENST00000585708.1_Missense_Mutation_p.D233A|CACNA2D4_ENST00000586184.1_Missense_Mutation_p.D297A|CACNA2D4_ENST00000588077.1_Missense_Mutation_p.D233A|CACNA2D4_ENST00000587995.1_Missense_Mutation_p.D297A|CACNA2D4_ENST00000585732.1_Intron	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	297	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)		GCCGCTCACGTCCACCAAAAT	0.483																																					p.D297A	Colon(2;101 179 21030 23310 28141)	Atlas-SNP	.											.	CACNA2D4	220	.	0			c.A890C						PASS	.						117	114	115					12																	1995492		2088	4212	6300	SO:0001583	missense	93589	exon8			CTCACGTCCACCA	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.890A>C	chr12.hg19:g.1995492T>G	ENSP00000372169:p.Asp297Ala	163.0	0.0	.		144.0	22.0	.	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Missense_Mutation	SNP	ENST00000382722.5	hg19	CCDS44785.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.434780	0.83885	.	.	ENSG00000151062	ENST00000456077;ENST00000280663;ENST00000382722	T	0.62788	0.0	5.17	5.17	0.71159	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	T	0.80737	0.4680	M	0.90759	3.145	0.80722	D	1	D	0.55605	0.972	P	0.60012	0.867	D	0.85404	0.1133	10	0.87932	D	0	.	15.0248	0.71659	0.0:0.0:0.0:1.0	.	297	Q7Z3S7	CA2D4_HUMAN	A	233;297;297	ENSP00000372169:D297A	ENSP00000280663:D297A	D	-	2	0	CACNA2D4	1865753	1.000000	0.71417	0.287000	0.24848	0.983000	0.72400	7.867000	0.87062	1.959000	0.56917	0.533000	0.62120	GAC	.	.	.	none		0.483	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2			G	1995492	T	G	1995492	3	3	263	1	0	0	0	0	1	0	0	0	2553	1667	58	5	2647	5	CACNA2D4	12	1995492	Missense_Mutation	SNP	T	TCGA-UZ-A9PR-01A-11D-A42J-10	1568078	1995492	131856403	59	16459											
A2M	2	hgsc.bcm.edu	37	chr12	9221412	9221412	+	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	acatcttgcagaaccgtgaaGaacaagctcagtgtctgatt	13	10	9	9	1	3	4	1	2	2	2	3	4	3	4	1	0	4	2	1	0	4	2			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr12:9221412G>C	ENST00000318602.7	-	34	4597	c.4290C>G	c.(4288-4290)ttC>ttG	p.F1430L	A2M-AS1_ENST00000499762.1_RNA	NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	1430					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)	GAACCGTGAAGAACAAGCTCA	0.403																																					p.F1430L		Atlas-SNP	.											.	A2M	180	.	0			c.C4290G						PASS	.						72	69	70					12																	9221412		1889	4108	5997	SO:0001583	missense	2	exon34			CGTGAAGAACAAG	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.4290C>G	chr12.hg19:g.9221412G>C	ENSP00000323929:p.Phe1430Leu	87.0	0.0	.		68.0	25.0	.	NM_000014	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Missense_Mutation	SNP	ENST00000318602.7	hg19	CCDS44827.1	.	.	.	.	.	.	.	.	.	.	G	12.85	2.062257	0.36373	.	.	ENSG00000175899	ENST00000318602;ENST00000540099	T	0.21031	2.03	4.39	2.55	0.30701	Alpha-macroglobulin, receptor-binding (3);	0.976288	0.08422	N	0.948210	T	0.11922	0.0290	N	0.12746	0.255	0.30277	N	0.791725	B	0.14012	0.009	B	0.19148	0.024	T	0.25779	-1.0122	10	0.87932	D	0	.	3.9445	0.09343	0.2917:0.1798:0.5285:0.0	.	1430	P01023	A2MG_HUMAN	L	1430;1445	ENSP00000323929:F1430L	ENSP00000323929:F1430L	F	-	3	2	A2M	9112679	0.993000	0.37304	0.882000	0.34594	0.755000	0.42902	0.316000	0.19469	0.587000	0.29643	0.655000	0.94253	TTC	.	.	.	none		0.403	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014		C	9221412	G	C	9221412	3	2	263	1	0	0	0	0	1	0	0	0	4	933	33	4	146	4	A2M	12	9221412	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	7225920	9221412	124630483	60	16460											
PRICKLE1	144165	hgsc.bcm.edu	37	chr12	42860028	42860028	+	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	cacaggtttcacagtactccGcatagagagactcaaaacag	15	7	8	11	1	2	2	2	0	0	2	3	3	3	2	1	1	2	3	1	1	4	3			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr12:42860028G>T	ENST00000455697.1	-	6	1028	c.743C>A	c.(742-744)gCg>gAg	p.A248E	RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000345127.3_Missense_Mutation_p.A248E|PRICKLE1_ENST00000548696.1_Missense_Mutation_p.A248E|PRICKLE1_ENST00000445766.2_Missense_Mutation_p.A248E|PRICKLE1_ENST00000552240.1_Missense_Mutation_p.A248E	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	248	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)	p.A248V(1)		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)		ACAGTACTCCGCATAGAGAGA	0.522																																					p.A248E		Atlas-SNP	.											PRICKLE1,rectum,carcinoma,0,1	PRICKLE1	105	.	1	Substitution - Missense(1)	large_intestine(1)	c.C743A						PASS	.						76	73	74					12																	42860028		2203	4300	6503	SO:0001583	missense	144165	exon6			TACTCCGCATAGA	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.743C>A	chr12.hg19:g.42860028G>T	ENSP00000401060:p.Ala248Glu	141.0	0.0	.		118.0	5.0	.	NM_001144882	Q14C83|Q71QF8|Q96N00	Missense_Mutation	SNP	ENST00000455697.1	hg19	CCDS8742.1	.	.	.	.	.	.	.	.	.	.	G	35	5.519420	0.96416	.	.	ENSG00000139174	ENST00000455697;ENST00000445766;ENST00000548696;ENST00000345127;ENST00000552240	D;D;D;D;D	0.88431	-2.38;-2.38;-2.38;-2.38;-2.38	5.18	5.18	0.71444	Zinc finger, LIM-type (2);	0.094019	0.64402	D	0.000001	D	0.95589	0.8566	M	0.93462	3.42	0.80722	D	1	P	0.51240	0.943	P	0.59546	0.859	D	0.96420	0.9311	10	0.72032	D	0.01	-4.697	19.0641	0.93103	0.0:0.0:1.0:0.0	.	248	Q96MT3	PRIC1_HUMAN	E	248	ENSP00000401060:A248E;ENSP00000398947:A248E;ENSP00000448359:A248E;ENSP00000345064:A248E;ENSP00000449819:A248E	ENSP00000345064:A248E	A	-	2	0	PRICKLE1	41146295	1.000000	0.71417	0.663000	0.29738	0.994000	0.84299	9.813000	0.99286	2.590000	0.87494	0.561000	0.74099	GCG	.	.	.	none		0.522	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1			T	42860028	G	T	42860028	3	4	263	1	0	0	0	0	1	0	0	0	12496	1087	38	4	1764	4	PRICKLE1	12	42860028	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	33638616	42860028	90991867	61	16461											
MLL2	8085	hgsc.bcm.edu	37	chr12	49427988	49427988	+	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	gccttccgggacttgcggtgTacaccaatctgctcctctag	6	11	10	14	2	2	0	0	0	2	0	4	1	4	1	4	2	3	2	4	2	3	4			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr12:49427988T>G	ENST00000301067.7	-	38	10601	c.10602A>C	c.(10600-10602)gtA>gtC	p.V3534V	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3534	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)										ACTTGCGGTGTACACCAATCT	0.557																																					p.V3534V		Atlas-SNP	.											.	MLL2	1173	.	0			c.A10602C						PASS	.						107	107	107					12																	49427988		2036	4195	6231	SO:0001819	synonymous_variant	8085	exon38			GCGGTGTACACCA	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.10602A>C	chr12.hg19:g.49427988T>G		50.0	0.0	.		47.0	19.0	.	NM_003482	O14687	Silent	SNP	ENST00000301067.7	hg19	CCDS44873.1																																																																																			.	.	.	none		0.557	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			G	49427988	T	G	49427988	2	3	263	1	0	0	0	0	0	0	0	1	9628	1625	57	5		5	MLL2	12	49427988	Silent	SNP	T	TCGA-UZ-A9PR-01A-11D-A42J-10	6567960	49427988	84423907	62	16462											
GEFT	115557	hgsc.bcm.edu	37	chr12	58009476	58009476	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggaacacagcctggatatgTatacaagaacagcattaagg	16	8	10	7	0	0	1	0	0	0	1	0	3	0	3	1	3	5	2	1	3	7	4			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr12:58009476T>C	ENST00000286494.4	+	12	1680	c.1220T>C	c.(1219-1221)gTa>gCa	p.V407A	AC025165.8_ENST00000444467.1_RNA|ARHGEF25_ENST00000333972.7_Missense_Mutation_p.V446A|AC025165.8_ENST00000593846.1_RNA|AC025165.8_ENST00000610219.1_RNA|AC025165.8_ENST00000356672.3_RNA	NM_182947.3	NP_891992	Q86VW2	ARHGP_HUMAN	Rho guanine nucleotide exchange factor (GEF) 25	407	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cytosol (GO:0005829)|myofibril (GO:0030016)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	28						CCTGGATATGTATACAAGAAC	0.557																																					p.V446A		Atlas-SNP	.											.	ARHGEF25	111	.	0			c.T1337C						PASS	.						86	82	84					12																	58009476		2203	4300	6503	SO:0001583	missense	115557	exon13			GATATGTATACAA		CCDS8947.1, CCDS44931.1	12q13.3	2011-11-16			ENSG00000240771	ENSG00000240771		"Rho guanine nucleotide exchange factors"	30275	protein-coding gene	gene with protein product	"RAC/CDC42 exchange factor"	610215				12547822	Standard	NM_182947		Approved	GEFT, p63RhoGEF	uc009zpy.4	Q86VW2	OTTHUMG00000152516	ENST00000286494.4:c.1220T>C	chr12.hg19:g.58009476T>C	ENSP00000286494:p.Val407Ala	141.0	0.0	.		111.0	48.0	.	NM_001111270	A6NJH5|A9CQZ6|F8W7Z4|Q8WV84|Q96E63	Missense_Mutation	SNP	ENST00000286494.4	hg19	CCDS8947.1	.	.	.	.	.	.	.	.	.	.	t	18.73	3.686721	0.68157	.	.	ENSG00000240771	ENST00000333972;ENST00000300189;ENST00000286494	T;T	0.12255	2.7;2.7	4.91	4.91	0.64330	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.34460	N	0.003949	T	0.21509	0.0518	L	0.34521	1.04	0.41536	D	0.988484	P;P;P	0.49961	0.93;0.786;0.606	P;P;B	0.56865	0.808;0.574;0.165	T	0.00844	-1.1543	10	0.59425	D	0.04	.	12.823	0.57704	0.0:0.0:0.0:1.0	.	446;407;255	F8W7Z4;Q86VW2;Q96M35	.;ARHGP_HUMAN;.	A	446;255;407	ENSP00000335560:V446A;ENSP00000286494:V407A	ENSP00000286494:V407A	V	+	2	0	ARHGEF25	56295743	0.992000	0.36948	0.998000	0.56505	0.967000	0.64934	2.333000	0.43912	2.200000	0.70718	0.459000	0.35465	GTA	.	.	.	none		0.557	ARHGEF25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000326561.1	NM_133483		C	58009476	T	C	58009476	3	2	263	1	0	0	0	0	1	0	0	0	6335	1638	57	3	1488	3	GEFT	12	58009476	Missense_Mutation	SNP	T	TCGA-UZ-A9PR-01A-11D-A42J-10	8581488	58009476	75842419	63	16463											
AMDHD1	144193	hgsc.bcm.edu	37	chr12	96354188	96354188	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttccccagaggaaaaactgcTactgaagctgctgatgacat	13	9	9	10	0	0	4	0	3	0	1	1	5	1	5	2	1	5	3	2	1	4	2			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr12:96354188T>C	ENST00000266736.2	+	5	706	c.600T>C	c.(598-600)gcT>gcC	p.A200A		NM_152435.2	NP_689648.2	Q96NU7	HUTI_HUMAN	amidohydrolase domain containing 1	200					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	imidazolonepropionase activity (GO:0050480)|metal ion binding (GO:0046872)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|skin(1)	22						GAAAAACTGCTACTGAAGCTG	0.413																																					p.A200A		Atlas-SNP	.											.	AMDHD1	56	.	0			c.T600C						PASS	.						72	68	69					12																	96354188		2203	4300	6503	SO:0001819	synonymous_variant	144193	exon5			AACTGCTACTGAA	AB075878	CCDS9057.1	12q23.1	2006-02-02				ENSG00000139344			28577	protein-coding gene	gene with protein product							Standard	NM_152435		Approved	MGC35366	uc001tel.2	Q96NU7	OTTHUMG00000170353	ENST00000266736.2:c.600T>C	chr12.hg19:g.96354188T>C		144.0	0.0	.		121.0	56.0	.	NM_152435	A8K463|Q68CI8	Silent	SNP	ENST00000266736.2	hg19	CCDS9057.1																																																																																			.	.	.	none		0.413	AMDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408640.1	NM_152435		C	96354188	T	C	96354188	2	2	263	1	0	0	0	0	0	0	0	1	567	1509	53	3		3	AMDHD1	12	96354188	Silent	SNP	T	TCGA-UZ-A9PR-01A-11D-A42J-10	38344712	96354188	37497707	64	16464											
UHRF1BP1L	23074	hgsc.bcm.edu	37	chr12	100452754	100452754	+	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	ctataatactccttcaagagCttcttccgcttcaatcggcc	9	13	5	14	2	3	1	2	0	1	1	6	1	5	1	3	1	2	2	3	1	5	7			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr12:100452754C>G	ENST00000279907.7	-	14	2513	c.2301G>C	c.(2299-2301)aaG>aaC	p.K767N	UHRF1BP1L_ENST00000545232.2_Missense_Mutation_p.K417N	NM_015054.1	NP_055869.1	A0JNW5	UH1BL_HUMAN	UHRF1 binding protein 1-like	767										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(21)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	50						CCTTCAAGAGCTTCTTCCGCT	0.423																																					p.K767N		Atlas-SNP	.											.	UHRF1BP1L	144	.	0			c.G2301C						PASS	.						90	95	93					12																	100452754		2203	4300	6503	SO:0001583	missense	23074	exon14			CAAGAGCTTCTTC		CCDS31882.1, CCDS31883.1	12q23.1	2011-04-15	2008-08-15		ENSG00000111647	ENSG00000111647			29102	protein-coding gene	gene with protein product							Standard	XM_005268737		Approved	KIAA0701	uc001tgq.3	A0JNW5	OTTHUMG00000170195	ENST00000279907.7:c.2301G>C	chr12.hg19:g.100452754C>G	ENSP00000279907:p.Lys767Asn	133.0	0.0	.		93.0	36.0	.	NM_015054	A0PJE5|O75183|Q8NDL1|Q96C30|Q9BTS5|Q9H0F1	Missense_Mutation	SNP	ENST00000279907.7	hg19	CCDS31882.1	.	.	.	.	.	.	.	.	.	.	C	13.01	2.109066	0.37242	.	.	ENSG00000111647	ENST00000279907;ENST00000545232	T;T	0.11712	2.78;2.75	6.02	1.02	0.19986	.	0.050512	0.85682	D	0.000000	T	0.27933	0.0688	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.01218	-1.1415	10	0.72032	D	0.01	-14.4859	11.2229	0.48866	0.0:0.5744:0.0:0.4256	.	767	A0JNW5	UH1BL_HUMAN	N	767;417	ENSP00000279907:K767N;ENSP00000444824:K417N	ENSP00000279907:K767N	K	-	3	2	UHRF1BP1L	98976885	0.914000	0.31030	0.999000	0.59377	0.772000	0.43724	0.021000	0.13489	0.138000	0.18790	-0.813000	0.03139	AAG	.	.	.	none		0.423	UHRF1BP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407875.1	NM_001006947		G	100452754	C	G	100452754	3	3	263	1	0	0	0	0	1	0	0	0	16981	796	28	4	2125	4	UHRF1BP1L	12	100452754	Missense_Mutation	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10	4098566	100452754	33399141	65	16465											
ACACB	32	hgsc.bcm.edu	37	chr12	109687792	109687792	+	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	tgtgcttgcttttgaagataCatgatcacggatatcatcgg	10	14	10	7	2	2	3	2	2	0	1	3	4	2	4	0	2	3	2	0	2	3	5			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr12:109687792C>A	ENST00000338432.7	+	41	5792	c.5673C>A	c.(5671-5673)taC>taA	p.Y1891*	ACACB_ENST00000543201.1_Nonsense_Mutation_p.Y557*|ACACB_ENST00000377854.5_Nonsense_Mutation_p.Y1821*|ACACB_ENST00000377848.3_Nonsense_Mutation_p.Y1891*			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	1891	Carboxyltransferase.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	TTTGAAGATACATGATCACGG	0.517																																					p.Y1891X		Atlas-SNP	.											.	ACACB	330	.	0			c.C5673A						PASS	.						138	132	134					12																	109687792		2203	4300	6503	SO:0001587	stop_gained	32	exon40			AAGATACATGATC	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.5673C>A	chr12.hg19:g.109687792C>A	ENSP00000341044:p.Tyr1891*	53.0	0.0	.		40.0	20.0	.	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Nonsense_Mutation	SNP	ENST00000338432.7	hg19	CCDS31898.1	.	.	.	.	.	.	.	.	.	.	C	41	8.656271	0.98903	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027;ENST00000543201	.	.	.	5.57	-5.5	0.02576	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.864	0.86025	0.0:0.3736:0.0:0.6264	.	.	.	.	X	1891;1891;1821;1122;557	.	ENSP00000341044:Y1891X	Y	+	3	2	ACACB	108172175	0.029000	0.19370	0.082000	0.20525	0.002000	0.02628	-0.588000	0.05774	-1.142000	0.02869	-0.808000	0.03180	TAC	.	.	.	none		0.517	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		A	109687792	C	A	109687792	4	1	263	1	0	0	0	0	0	1	0	0	107	489	17	4	5831	4	ACACB	12	109687792	Nonsense_Mutation	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10	9235038	109687792	24164103	66	16466											
HTR2A	3356	hgsc.bcm.edu	37	chr13	47408978	47408978	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcaactagcctatcacacAcagctcaccttttcattcac	11	10	4	16	1	4	0	4	0	0	0	4	0	4	0	2	1	3	2	2	1	3	5			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr13:47408978A>G	ENST00000378688.4	-	3	1541	c.1410T>C	c.(1408-1410)tgT>tgC	p.C470C	HTR2A_ENST00000543956.1_Silent_p.C386C|HTR2A_ENST00000542664.1_Silent_p.C470C			P28223	5HT2A_HUMAN	5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled	470					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)	CCTATCACACACAGCTCACCT	0.413																																					p.C470C		Atlas-SNP	.											.	HTR2A	98	.	0			c.T1410C						PASS	.						102	99	100					13																	47408978		2203	4300	6503	SO:0001819	synonymous_variant	3356	exon4			TCACACACAGCTC	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.1410T>C	chr13.hg19:g.47408978A>G		68.0	0.0	.		66.0	25.0	.	NM_000621	B2RAC5|B4DZ79|F5GWE8|Q5T8C0	Silent	SNP	ENST00000378688.4	hg19	CCDS9405.1																																																																																			.	.	.	none		0.413	HTR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044835.3	NM_000621		G	47408978	A	G	47408978	2	3	263	1	0	0	0	0	0	0	0	1	7448	157	6	3		3	HTR2A	13	47408978	Silent	SNP	A	TCGA-UZ-A9PR-01A-11D-A42J-10		47408978	67760900	67	16467											
OR4K2	390431	hgsc.bcm.edu	37	chr14	20345243	20345243	+	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	tcacagacaagattctgtctGtgttttataccatctttact	10	17	5	9	0	4	2	1	0	3	2	4	2	4	2	1	0	2	1	1	0	4	6			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr14:20345243G>C	ENST00000298642.2	+	1	853	c.817G>C	c.(817-819)Gtg>Ctg	p.V273L		NM_001005501.1	NP_001005501.1	Q8NGD2	OR4K2_HUMAN	olfactory receptor, family 4, subfamily K, member 2	273						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(16)|ovary(2)|skin(9)|upper_aerodigestive_tract(2)	43	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		GATTCTGTCTGTGTTTTATAC	0.383																																					p.V273L		Atlas-SNP	.											.	OR4K2	97	.	0			c.G817C						PASS	.						142	143	143					14																	20345243		2203	4300	6503	SO:0001583	missense	390431	exon1			CTGTCTGTGTTTT		CCDS32023.1	14q11.2	2013-09-23			ENSG00000165762	ENSG00000165762		"GPCR / Class A : Olfactory receptors"	14728	protein-coding gene	gene with protein product							Standard	NM_001005501		Approved		uc001vwh.1	Q8NGD2	OTTHUMG00000170624	ENST00000298642.2:c.817G>C	chr14.hg19:g.20345243G>C	ENSP00000298642:p.Val273Leu	12.0	0.0	.		15.0	8.0	.	NM_001005501	B2RNK8|Q6IFA5	Missense_Mutation	SNP	ENST00000298642.2	hg19	CCDS32023.1	.	.	.	.	.	.	.	.	.	.	.	16.88	3.243649	0.58995	.	.	ENSG00000165762	ENST00000298642	T	0.00245	8.45	5.16	4.27	0.50696	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44688	D	0.000435	T	0.00241	0.0007	L	0.28344	0.845	0.30016	N	0.81477	P	0.51147	0.942	P	0.55508	0.777	T	0.63047	-0.6724	10	0.49607	T	0.09	.	11.2916	0.49254	0.0883:0.0:0.9117:0.0	.	273	Q8NGD2	OR4K2_HUMAN	L	273	ENSP00000298642:V273L	ENSP00000298642:V273L	V	+	1	0	OR4K2	19415083	0.002000	0.14202	1.000000	0.80357	0.956000	0.61745	0.041000	0.13927	1.407000	0.46875	0.591000	0.81541	GTG	.	.	.	none		0.383	OR4K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409864.1			C	20345243	G	C	20345243	3	2	263	1	0	0	0	0	1	0	0	0	11079	1377	48	4	819	4	OR4K2	14	20345243	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10		20345243	87004297	68	16468											
LTB4R2	56413	hgsc.bcm.edu	37	chr14	24780907	24780907	+	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	ccgcggcaatggagacccggGgggtgggatggagaaggacg	9	3	21	8	4	0	2	0	0	0	2	0	6	0	4	2	8	0	1	2	8	2	0			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr14:24780907G>A	ENST00000528054.1	+	1	2747	c.1130G>A	c.(1129-1131)gGg>gAg	p.G377E	LTB4R_ENST00000396789.4_5'Flank|LTB4R2_ENST00000533293.1_Missense_Mutation_p.G346E|LTB4R2_ENST00000543919.1_Missense_Mutation_p.G346E|CIDEB_ENST00000258807.5_5'Flank|LTB4R_ENST00000345363.3_5'UTR|LTB4R_ENST00000396782.2_5'Flank|CIDEB_ENST00000555817.1_5'Flank|CIDEB_ENST00000336557.5_5'Flank			Q9NPC1	LT4R2_HUMAN	leukotriene B4 receptor 2	377					chemotaxis (GO:0006935)|keratinocyte migration (GO:0051546)|negative regulation of adenylate cyclase activity (GO:0007194)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	leukotriene B4 receptor activity (GO:0001632)|leukotriene receptor activity (GO:0004974)			endometrium(1)|lung(1)|ovary(1)	3				GBM - Glioblastoma multiforme(265;0.018)		GGAGACCCGGGGGGTGGGATG	0.667																																					p.G346E		Atlas-SNP	.											.	LTB4R2	18	.	0			c.G1037A						PASS	.						33	40	38					14																	24780907		2192	4259	6451	SO:0001583	missense	56413	exon2			ACCCGGGGGGTGG	AB008193	CCDS9625.1, CCDS9625.2	14q12	2014-04-11			ENSG00000213906	ENSG00000213906		"GPCR / Class A : Leukotriene receptors"	19260	protein-coding gene	gene with protein product		605773				11006272, 10934229	Standard	NM_001164692		Approved	BLTR2, BLT2, JULF2, NOP9	uc001wor.3	Q9NPC1	OTTHUMG00000186500	ENST00000528054.1:c.1130G>A	chr14.hg19:g.24780907G>A	ENSP00000432146:p.Gly377Glu	68.0	0.0	.		44.0	21.0	.	NM_019839	Q5KU28|Q9NPE5	Missense_Mutation	SNP	ENST00000528054.1	hg19		.	.	.	.	.	.	.	.	.	.	G	31	5.073887	0.94000	.	.	ENSG00000213906	ENST00000528054;ENST00000533293;ENST00000543919	T;T;T	0.71103	-0.54;-0.48;-0.48	4.19	4.19	0.49359	.	0.730840	0.11363	U	0.571663	T	0.59252	0.2180	N	0.19112	0.55	0.80722	D	1	B	0.18461	0.028	B	0.12156	0.007	T	0.56950	-0.7894	10	0.87932	D	0	.	14.4001	0.67037	0.0:0.0:1.0:0.0	.	377	Q9NPC1	LT4R2_HUMAN	E	377;346;346	ENSP00000432146:G377E;ENSP00000433290:G346E;ENSP00000445772:G346E	ENSP00000337731:G377E	G	+	2	0	LTB4R2	23850747	0.087000	0.21565	0.925000	0.36789	0.935000	0.57460	1.180000	0.32005	2.059000	0.61396	0.467000	0.42956	GGG	.	.	.	none		0.667	LTB4R2-001	KNOWN	basic|appris_principal|readthrough_transcript	protein_coding	protein_coding	OTTHUMT00000073194.4			A	24780907	G	A	24780907	3	1	263	1	0	0	0	0	1	0	0	0	9079	1232	43	2	1039	2	LTB4R2	14	24780907	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	4435664	24780907	82568633	69	16469											
FANCM	57697	hgsc.bcm.edu	37	chr14	45654450	45654450	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggaagtttttagatgatgaaGcagaactttctgaagaagat	15	12	11	3	0	1	7	0	3	1	4	1	8	1	8	0	1	2	2	0	1	6	4			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr14:45654450G>A	ENST00000267430.5	+	18	4631	c.4546G>A	c.(4546-4548)Gca>Aca	p.A1516T	FANCM_ENST00000555013.1_3'UTR|FANCM_ENST00000542564.2_Missense_Mutation_p.A1490T	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1516					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						AGATGATGAAGCAGAACTTTC	0.294								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.A1516T		Atlas-SNP	.											.	FANCM	225	.	0			c.G4546A						PASS	.						62	66	65					14																	45654450		2203	4293	6496	SO:0001583	missense	57697	exon18	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GATGAAGCAGAAC	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.4546G>A	chr14.hg19:g.45654450G>A	ENSP00000267430:p.Ala1516Thr	350.0	0.0	.		294.0	121.0	.	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	hg19	CCDS32070.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.4|27.4	4.823629|4.823629	0.90873|0.90873	.|.	.|.	ENSG00000187790|ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250|ENST00000554809	T;T;T|.	0.75704|.	-0.96;-0.96;-0.96|.	5.77|5.77	5.77|5.77	0.91146|0.91146	.|.	0.540042|.	0.20546|.	N|.	0.090204|.	D|D	0.82318|0.82318	0.5011|0.5011	M|M	0.83953|0.83953	2.67|2.67	0.45621|0.45621	D|D	0.998559|0.998559	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.83275|.	0.996;0.996|.	T|T	0.83003|0.83003	-0.0176|-0.0176	10|5	0.87932|.	D|.	0|.	.|.	18.5433|18.5433	0.91037|0.91037	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1490;1516|.	B2RTQ9;Q8IYD8|.	.;FANCM_HUMAN|.	T|N	1516;1490;1032|448	ENSP00000267430:A1516T;ENSP00000442493:A1490T;ENSP00000452033:A1032T|.	ENSP00000267430:A1516T|.	A|S	+|+	1|2	0|0	FANCM|FANCM	44724200|44724200	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.926000|0.926000	0.56050|0.56050	6.146000|6.146000	0.71777|0.71777	2.720000|2.720000	0.93068|0.93068	0.650000|0.650000	0.86243|0.86243	GCA|AGC	.	.	.	none		0.294	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		A	45654450	G	A	45654450	3	1	263	1	0	0	0	0	1	0	0	0	5678	971	34	2	4616	2	FANCM	14	45654450	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	20873543	45654450	61695090	70	16470											
RDH12	145226	hgsc.bcm.edu	37	chr14	68191956	68191956	+	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	aatctatccgagcctttgctGagggctttctggcaggtgag	7	12	13	9	1	2	2	0	2	2	0	3	3	3	2	2	3	2	3	2	3	2	3			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr14:68191956G>A	ENST00000551171.1	+	5	652	c.328G>A	c.(328-330)Gag>Aag	p.E110K	RDH12_ENST00000267502.3_Missense_Mutation_p.E110K|RDH12_ENST00000539142.1_Missense_Mutation_p.E110K	NM_152443.2	NP_689656.2	Q96NR8	RDH12_HUMAN	retinol dehydrogenase 12 (all-trans/9-cis/11-cis)	110					photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	intracellular (GO:0005622)|photoreceptor inner segment membrane (GO:0060342)	retinol dehydrogenase activity (GO:0004745)			large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(4)	12				all cancers(60;0.000704)|OV - Ovarian serous cystadenocarcinoma(108;0.00161)|BRCA - Breast invasive adenocarcinoma(234;0.00953)	Vitamin A(DB00162)	AGCCTTTGCTGAGGGCTTTCT	0.527																																					p.E110K		Atlas-SNP	.											.	RDH12	43	.	0			c.G328A						PASS	.						81	77	78					14																	68191956		2203	4300	6503	SO:0001583	missense	145226	exon5			TTTGCTGAGGGCT	AK054835	CCDS9787.1	14q24.1	2013-02-14	2006-05-09		ENSG00000139988	ENSG00000139988	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	19977	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 7C, member 2"	608830	"retinol dehydrogenase 12 (all-trans and 9-cis)"			12226107, 19027726	Standard	NM_152443		Approved	FLJ30273, SDR7C2, LCA13, RP53	uc001xjz.4	Q96NR8		ENST00000551171.1:c.328G>A	chr14.hg19:g.68191956G>A	ENSP00000449079:p.Glu110Lys	154.0	0.0	.		102.0	39.0	.	NM_152443	B2RDA2|Q8TAW6	Missense_Mutation	SNP	ENST00000551171.1	hg19	CCDS9787.1	.	.	.	.	.	.	.	.	.	.	G	11.76	1.736183	0.30774	.	.	ENSG00000139988	ENST00000551171;ENST00000267502;ENST00000539142	D;D;D	0.89875	-2.58;-2.58;-2.58	5.52	5.52	0.82312	NAD(P)-binding domain (1);	0.230531	0.45867	D	0.000327	T	0.81187	0.4770	N	0.21448	0.665	0.35066	D	0.762009	B	0.14805	0.011	B	0.26864	0.074	T	0.76735	-0.2850	10	0.11794	T	0.64	.	13.1381	0.59421	0.0755:0.0:0.9245:0.0	.	110	Q96NR8	RDH12_HUMAN	K	110	ENSP00000449079:E110K;ENSP00000267502:E110K;ENSP00000438715:E110K	ENSP00000267502:E110K	E	+	1	0	RDH12	67261709	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	2.700000	0.47085	2.873000	0.98535	0.563000	0.77884	GAG	.	.	.	none		0.527	RDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406918.1			A	68191956	G	A	68191956	3	1	263	1	0	0	0	0	1	0	0	0	13204	1291	45	2	338	2	RDH12	14	68191956	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	22537506	68191956	39157584	71	16471											
PCNX	22990	hgsc.bcm.edu	37	chr14	71568714	71568714	+	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	tttttgtatttaggatcattTtacttctccagatgaatatg	10	20	6	5	0	2	2	1	1	1	1	3	3	2	3	1	1	1	1	1	1	5	9			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr14:71568714T>A	ENST00000304743.2	+	31	6043	c.5597T>A	c.(5596-5598)tTt>tAt	p.F1866Y	PCNX_ENST00000556272.1_3'UTR|PCNX_ENST00000439984.3_Missense_Mutation_p.F1755Y|PCNX_ENST00000238570.5_Missense_Mutation_p.F1794Y	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1866						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)		TAGGATCATTTTACTTCTCCA	0.333																																					p.F1866Y		Atlas-SNP	.											.	PCNX	198	.	0			c.T5597A						PASS	.						48	48	48					14																	71568714		2203	4300	6503	SO:0001583	missense	22990	exon31			ATCATTTTACTTC	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.5597T>A	chr14.hg19:g.71568714T>A	ENSP00000304192:p.Phe1866Tyr	77.0	0.0	.		92.0	48.0	.	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	hg19	CCDS9806.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	27.7|27.7	4.852501|4.852501	0.91355|0.91355	.|.	.|.	ENSG00000100731|ENSG00000100731	ENST00000304743;ENST00000238570;ENST00000439984|ENST00000554691	T;T;T|.	0.50813|.	0.73;0.73;0.73|.	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	0.043971|.	0.85682|.	D|.	0.000000|.	T|T	0.81716|0.81716	0.4881|0.4881	M|M	0.91196|0.91196	3.185|3.185	0.34571|0.34571	D|D	0.713417|0.713417	D;D;D|.	0.76494|.	0.989;0.999;0.999|.	D;D;D|.	0.91635|.	0.969;0.999;0.994|.	D|D	0.90107|0.90107	0.4189|0.4189	10|5	0.66056|.	D|.	0.02|.	.|.	15.598|15.598	0.76602|0.76602	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1794;1755;1866|.	Q96RV3-3;B2RTR6;Q96RV3|.	.;.;PCX1_HUMAN|.	Y|I	1866;1794;1755|853	ENSP00000304192:F1866Y;ENSP00000238570:F1794Y;ENSP00000396617:F1755Y|.	ENSP00000238570:F1794Y|.	F|L	+|+	2|1	0|2	PCNX|PCNX	70638467|70638467	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.967000|0.967000	0.64934|0.64934	7.655000|7.655000	0.83696|0.83696	2.094000|2.094000	0.63399|0.63399	0.533000|0.533000	0.62120|0.62120	TTT|TTA	.	.	.	none		0.333	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		A	71568714	T	A	71568714	3	1	263	1	0	0	0	0	1	0	0	0	11598	1841	64	5	5719	5	PCNX	14	71568714	Missense_Mutation	SNP	T	TCGA-UZ-A9PR-01A-11D-A42J-10	3376758	71568714	35780826	72	16472											
DDX24	57062	hgsc.bcm.edu	37	chr14	94528900	94528900	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttacttggaggaggggcagcAttcctcttctgccactgcaa	8	11	11	11	0	2	0	0	0	2	0	3	2	3	2	2	4	4	3	2	4	2	4			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr14:94528900A>G	ENST00000330836.5	-	3	917	c.786T>C	c.(784-786)aaT>aaC	p.N262N	DDX24_ENST00000555054.1_Silent_p.N219N|DDX24_ENST00000544005.1_Silent_p.N12N	NM_020414.3	NP_065147.1	Q9GZR7	DDX24_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 24	262	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)		GAGGGGCAGCATTCCTCTTCT	0.488																																					p.N262N		Atlas-SNP	.											.	DDX24	82	.	0			c.T786C						PASS	.						100	91	94					14																	94528900		2203	4300	6503	SO:0001819	synonymous_variant	57062	exon3			GGCAGCATTCCTC	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.786T>C	chr14.hg19:g.94528900A>G		77.0	0.0	.		68.0	32.0	.	NM_020414	E7EMJ4|Q4V9L5	Silent	SNP	ENST00000330836.5	hg19	CCDS9918.1																																																																																			.	.	.	none		0.488	DDX24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412861.1	NM_020414		G	94528900	A	G	94528900	2	3	263	1	0	0	0	0	0	0	0	1	4353	214	8	3		3	DDX24	14	94528900	Silent	SNP	A	TCGA-UZ-A9PR-01A-11D-A42J-10	22960186	94528900	12820640	73	16473											
SLC24A5	283652	hgsc.bcm.edu	37	chr15	48429007	48429007	+	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	cctgtcttgccaaagctatgGagagaagtgaacaacagcca	14	7	10	10	0	1	2	0	1	1	1	1	4	1	3	3	1	5	1	3	1	5	2			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr15:48429007G>A	ENST00000341459.3	+	6	791	c.718G>A	c.(718-720)Gag>Aag	p.E240K	SLC24A5_ENST00000449382.2_Missense_Mutation_p.E180K	NM_205850.2	NP_995322.1	Q71RS6	NCKX5_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 5	240					ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|negative regulation of melanin biosynthetic process (GO:0048022)|response to stimulus (GO:0050896)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|skin(1)|upper_aerodigestive_tract(1)	27		all_lung(180;0.00217)		all cancers(107;3.29e-10)|GBM - Glioblastoma multiforme(94;7.32e-07)		CAAAGCTATGGAGAGAAGTGA	0.388																																					p.E240K		Atlas-SNP	.											.	SLC24A5	64	.	0			c.G718A						PASS	.						76	74	75					15																	48429007		2198	4297	6495	SO:0001583	missense	283652	exon6			GCTATGGAGAGAA	AF348468	CCDS10128.1	15q21.1	2014-01-28	2013-07-18		ENSG00000188467	ENSG00000188467		"Solute carriers"	20611	protein-coding gene	gene with protein product	"oculocutaneous albinism 6 (autosomal recessive)"	609802	"solute carrier family 24, member 5"			23364476	Standard	XM_005254308		Approved	JSX, OCA6	uc001zwe.3	Q71RS6	OTTHUMG00000131494	ENST00000341459.3:c.718G>A	chr15.hg19:g.48429007G>A	ENSP00000341550:p.Glu240Lys	197.0	0.0	.		115.0	48.0	.	NM_205850	A5X8Z8|A5X8Z9|Q14CT4|Q6DKH3	Missense_Mutation	SNP	ENST00000341459.3	hg19	CCDS10128.1	.	.	.	.	.	.	.	.	.	.	G	15.99	2.994782	0.54041	.	.	ENSG00000188467	ENST00000341459;ENST00000449382	T;T	0.75260	-0.92;-0.92	5.42	5.42	0.78866	.	0.417747	0.28021	N	0.016905	T	0.68677	0.3027	L	0.50333	1.59	0.32783	N	0.502204	P;B	0.35077	0.483;0.22	B;B	0.24974	0.057;0.039	T	0.75004	-0.3470	10	0.39692	T	0.17	.	19.5924	0.95520	0.0:0.0:1.0:0.0	.	180;240	A5X8Z9;Q71RS6	.;NCKX5_HUMAN	K	240;180	ENSP00000341550:E240K;ENSP00000389966:E180K	ENSP00000341550:E240K	E	+	1	0	SLC24A5	46216299	1.000000	0.71417	0.972000	0.41901	0.640000	0.38277	4.436000	0.59948	2.689000	0.91719	0.655000	0.94253	GAG	.	.	.	none		0.388	SLC24A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254340.2	NM_205850		A	48429007	G	A	48429007	3	1	263	1	0	0	0	0	1	0	0	0	14482	1175	41	2	740	2	SLC24A5	15	48429007	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10		48429007	54102385	74	16474											
ZNF609	23060	hgsc.bcm.edu	37	chr15	64972427	64972427	+	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	tctttttccccatatggcagCaaggtctcaggtggtgaaga	9	12	11	9	0	2	2	1	1	2	1	4	2	3	2	2	4	1	2	2	4	3	3			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr15:64972427C>T	ENST00000326648.3	+	6	3941	c.3813C>T	c.(3811-3813)agC>agT	p.S1271S		NM_015042.1	NP_055857.1	O15014	ZN609_HUMAN	zinc finger protein 609	1271						nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CATATGGCAGCAAGGTCTCAG	0.517																																					p.S1271S		Atlas-SNP	.											.	ZNF609	106	.	0			c.C3813T						PASS	.						102	94	97					15																	64972427		2202	4299	6501	SO:0001819	synonymous_variant	23060	exon6			TGGCAGCAAGGTC	BC014251	CCDS32270.1	15q22.1	2008-05-02				ENSG00000180357		"Zinc fingers, C2H2-type"	29003	protein-coding gene	gene with protein product						9205841	Standard	NM_015042		Approved	KIAA0295	uc002ann.3	O15014		ENST00000326648.3:c.3813C>T	chr15.hg19:g.64972427C>T		131.0	0.0	.		80.0	38.0	.	NM_015042	Q0D2I2	Silent	SNP	ENST00000326648.3	hg19	CCDS32270.1																																																																																			.	.	.	none		0.517	ZNF609-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418130.1	XM_042833		T	64972427	C	T	64972427	2	4	263	1	0	0	0	0	0	0	0	1	18047	709	25	2		2	ZNF609	15	64972427	Silent	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10	16543420	64972427	37558965	75	16475											
MYO9A	4649	hgsc.bcm.edu	37	chr15	72175994	72175994	+	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	caaagagtggcgaaacctctGactgggtagtaggtttcact	11	10	12	8	1	2	2	1	1	1	1	2	3	2	2	1	3	1	3	1	3	4	3			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr15:72175994G>A	ENST00000356056.5	-	28	5811	c.5339C>T	c.(5338-5340)tCa>tTa	p.S1780L	MYO9A_ENST00000444904.1_Missense_Mutation_p.S1761L|MYO9A_ENST00000564571.1_Missense_Mutation_p.S1780L|MYO9A_ENST00000424560.1_Missense_Mutation_p.S1851L	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1780	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						CGAAACCTCTGACTGGGTAGT	0.438																																					p.S1780L		Atlas-SNP	.											.	MYO9A	203	.	0			c.C5339T						PASS	.						224	220	221					15																	72175994		2199	4297	6496	SO:0001583	missense	4649	exon28			ACCTCTGACTGGG	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.5339C>T	chr15.hg19:g.72175994G>A	ENSP00000348349:p.Ser1780Leu	166.0	0.0	.		132.0	69.0	.	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	hg19	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	G	11.87	1.766171	0.31228	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	D;D;D	0.85339	-1.95;-1.97;-1.94	5.08	3.1	0.35709	.	.	.	.	.	D	0.89674	0.6783	M	0.64997	1.995	0.09310	N	0.999998	D;D	0.76494	0.999;0.999	D;D	0.72075	0.962;0.976	T	0.79888	-0.1613	9	0.41790	T	0.15	.	10.7053	0.45952	0.0728:0.1322:0.7949:0.0	.	1851;1780	B2RTY4-4;B2RTY4	.;MYO9A_HUMAN	L	1780;1851;1761	ENSP00000348349:S1780L;ENSP00000399162:S1851L;ENSP00000398250:S1761L	ENSP00000348349:S1780L	S	-	2	0	MYO9A	69963048	0.440000	0.25618	0.001000	0.08648	0.044000	0.14063	3.725000	0.54970	0.572000	0.29383	0.557000	0.71058	TCA	.	.	.	none		0.438	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		A	72175994	G	A	72175994	3	1	263	1	0	0	0	0	1	0	0	0	10091	1294	45	2	2367	2	MYO9A	15	72175994	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	7203567	72175994	30355398	76	16476											
IQGAP1	8826	hgsc.bcm.edu	37	chr15	91017793	91017793	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caaagtgaccaggattttcaGgaggagcttgaccttatgaa	13	10	11	7	0	1	3	1	3	0	0	1	6	1	6	2	3	1	1	2	3	3	4			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr15:91017793G>A	ENST00000268182.5	+	23	2776	c.2652G>A	c.(2650-2652)caG>caA	p.Q884Q	IQGAP1_ENST00000560020.1_3'UTR|IQGAP1_ENST00000560738.1_Silent_p.Q312Q	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	884					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)			AGGATTTTCAGGAGGAGCTTG	0.453																																					p.Q884Q		Atlas-SNP	.											.	IQGAP1	140	.	0			c.G2652A						PASS	.						102	91	94					15																	91017793		2198	4298	6496	SO:0001819	synonymous_variant	8826	exon23			TTTTCAGGAGGAG	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.2652G>A	chr15.hg19:g.91017793G>A		128.0	0.0	.		109.0	54.0	.	NM_003870	A7MBM3	Silent	SNP	ENST00000268182.5	hg19	CCDS10362.1																																																																																			.	.	.	none		0.453	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870		A	91017793	G	A	91017793	2	1	263	1	0	0	0	0	0	0	0	1	7821	991	35	2		2	IQGAP1	15	91017793	Silent	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	18841799	91017793	11513599	77	16477											
ZKSCAN2	342357	hgsc.bcm.edu	37	chr16	25255502	25255502	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctacagccccatacaattTgctcttccgatgacaggctt	10	11	7	13	1	1	1	0	1	1	0	2	2	2	1	3	1	5	3	3	1	3	5			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr16:25255502T>C	ENST00000328086.7	-	6	2388	c.1585A>G	c.(1585-1587)Aaa>Gaa	p.K529E		NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	529					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)		CCATACAATTTGCTCTTCCGA	0.512																																					p.K529E		Atlas-SNP	.											.	ZKSCAN2	90	.	0			c.A1585G						PASS	.						68	68	68					16																	25255502		2197	4300	6497	SO:0001583	missense	342357	exon6			ACAATTTGCTCTT	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.1585A>G	chr16.hg19:g.25255502T>C	ENSP00000331626:p.Lys529Glu	121.0	0.0	.		96.0	39.0	.	NM_001012981	A1L3B4|Q6ZN77	Missense_Mutation	SNP	ENST00000328086.7	hg19	CCDS32410.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.168672	0.78339	.	.	ENSG00000155592	ENST00000328086;ENST00000536768	T	0.41065	1.01	5.48	4.31	0.51392	SANT domain, DNA binding (1);	0.088025	0.49305	D	0.000148	T	0.28034	0.0691	N	0.17474	0.49	0.31663	N	0.645383	P;P	0.45348	0.856;0.856	B;B	0.42462	0.388;0.388	T	0.36720	-0.9736	10	0.87932	D	0	-31.0046	9.086	0.36581	0.0:0.0:0.1848:0.8152	.	325;529	B4DYF0;Q63HK3	.;ZKSC2_HUMAN	E	529	ENSP00000331626:K529E	ENSP00000331626:K529E	K	-	1	0	ZKSCAN2	25163003	0.998000	0.40836	0.995000	0.50966	0.996000	0.88848	1.341000	0.33907	2.205000	0.71048	0.533000	0.62120	AAA	.	.	.	none		0.512	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981		C	25255502	T	C	25255502	3	2	263	1	0	0	0	0	1	0	0	0	17699	1821	63	3	1326	3	ZKSCAN2	16	25255502	Missense_Mutation	SNP	T	TCGA-UZ-A9PR-01A-11D-A42J-10		25255502	65099251	78	16478											
XPO6	23214	hgsc.bcm.edu	37	chr16	28164063	28164063	+	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	ctcgattcttcttaggtgaaCactcacaaagagccgaagaa	14	9	8	10	2	3	3	1	1	2	2	4	5	3	3	1	1	2	0	1	1	5	3			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr16:28164063C>A	ENST00000304658.5	-	8	1641	c.1141G>T	c.(1141-1143)Gtt>Ttt	p.V381F	XPO6_ENST00000565698.1_Missense_Mutation_p.V367F|XPO6_ENST00000561488.1_5'Flank	NM_015171.3	NP_055986.1	Q96QU8	XPO6_HUMAN	exportin 6	381					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						CTTAGGTGAACACTCACAAAG	0.408																																					p.V381F		Atlas-SNP	.											.	XPO6	177	.	0			c.G1141T						PASS	.						79	71	73					16																	28164063		1860	4092	5952	SO:0001583	missense	23214	exon8			GGTGAACACTCAC	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.1141G>T	chr16.hg19:g.28164063C>A	ENSP00000302790:p.Val381Phe	170.0	0.0	.		125.0	56.0	.	NM_015171	A1L3W4|D3DWF9|Q2YDX3|Q53G88|Q68G50|Q76N88|Q96CP8|Q9BT21	Missense_Mutation	SNP	ENST00000304658.5	hg19	CCDS42135.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.515668	0.85389	.	.	ENSG00000169180	ENST00000304658	T	0.47177	0.85	5.91	5.91	0.95273	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.61602	0.2360	L	0.60455	1.87	0.80722	D	1	D;D	0.64830	0.978;0.994	P;P	0.56916	0.573;0.809	T	0.60727	-0.7206	10	0.54805	T	0.06	-12.4721	17.7923	0.88558	0.0:1.0:0.0:0.0	.	381;381	B7ZM10;Q96QU8	.;XPO6_HUMAN	F	381	ENSP00000302790:V381F	ENSP00000302790:V381F	V	-	1	0	XPO6	28071564	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.629000	0.83207	2.793000	0.96121	0.655000	0.94253	GTT	.	.	.	none		0.408	XPO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433732.1	XM_055195		A	28164063	C	A	28164063	3	1	263	1	0	0	0	0	1	0	0	0	17460	478	17	4	2304	4	XPO6	16	28164063	Missense_Mutation	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10	2908561	28164063	62190690	79	16479											
WDR81	124997	hgsc.bcm.edu	37	chr17	1628392	1628392	+	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	tcgatcccaggcagctggctCcggccccggggggcacccac	5	4	14	18	3	0	0	0	0	0	0	3	1	2	0	5	6	1	4	5	6	0	0			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr17:1628392C>T	ENST00000409644.1	+	1	139	c.139C>T	c.(139-141)Ccg>Tcg	p.P47S	RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000437219.2_Intron|WDR81_ENST00000446363.1_Intron|WDR81_ENST00000309182.5_Intron|WDR81_ENST00000419248.1_Intron	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	47					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)		GCAGCTGGCTCCGGCCCCGGG	0.741																																					p.P47S		Atlas-SNP	.											.	WDR81	180	.	0			c.C139T						PASS	.						3	5	5					17																	1628392		625	1502	2127	SO:0001583	missense	124997	exon1			CTGGCTCCGGCCC	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.139C>T	chr17.hg19:g.1628392C>T	ENSP00000386609:p.Pro47Ser	59.0	0.0	.		63.0	17.0	.	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Missense_Mutation	SNP	ENST00000409644.1	hg19	CCDS54062.1	.	.	.	.	.	.	.	.	.	.	C	12.29	1.894622	0.33442	.	.	ENSG00000167716	ENST00000409644	T	0.48522	0.81	5.73	1.3	0.21679	.	.	.	.	.	T	0.43787	0.1263	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	T	0.36065	-0.9763	6	0.49607	T	0.09	.	8.0818	0.30750	0.1074:0.3321:0.4923:0.0682	.	.	.	.	S	47	ENSP00000386609:P47S	ENSP00000386609:P47S	P	+	1	0	WDR81	1575142	0.000000	0.05858	0.041000	0.18516	0.942000	0.58702	0.243000	0.18106	0.304000	0.22809	0.650000	0.86243	CCG	.	.	.	none		0.741	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348		T	1628392	C	T	1628392	3	4	263	1	0	0	0	0	1	0	0	0	17342	855	30	2	203	2	WDR81	17	1628392	Missense_Mutation	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10		1628392	79566818	80	16480											
KIAA0664	23277	hgsc.bcm.edu	37	chr17	2598316	2598316	+	Missense_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	gctcgtcggcgggcaggtggGccacggggtttgggtaggag	4	7	22	8	4	0	0	0	0	0	0	2	1	0	1	1	8	0	4	1	8	1	2			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr17:2598316G>A	ENST00000570628.2	-	16	2675	c.2570C>T	c.(2569-2571)gCc>gTc	p.A857V	CLUH_ENST00000538975.1_Missense_Mutation_p.A857V|CLUH_ENST00000435359.1_Missense_Mutation_p.A857V			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	857					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)											GGGCAGGTGGGCCACGGGGTT	0.637																																					p.A857V		Atlas-SNP	.											.	.	.	.	0			c.C2570T						PASS	.						36	44	41					17																	2598316		1974	4160	6134	SO:0001583	missense	23277	exon16			AGGTGGGCCACGG	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.2570C>T	chr17.hg19:g.2598316G>A	ENSP00000458986:p.Ala857Val	76.0	0.0	.		103.0	31.0	.	NM_015229	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Missense_Mutation	SNP	ENST00000570628.2	hg19	CCDS45572.1	.	.	.	.	.	.	.	.	.	.	g	20.9	4.065557	0.76187	.	.	ENSG00000132361	ENST00000435359;ENST00000322335;ENST00000538975	D;D	0.81499	-1.5;-1.5	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.75598	0.3871	L	0.38838	1.175	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.12837	0.008;0.008	T	0.69472	-0.5136	10	0.46703	T	0.11	.	18.6994	0.91615	0.0:0.0:1.0:0.0	.	857;858	O75153;C9J6D7	K0664_HUMAN;.	V	857;858;857	ENSP00000388872:A857V;ENSP00000439628:A857V	ENSP00000320468:A858V	A	-	2	0	KIAA0664	2545066	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	9.472000	0.97709	2.663000	0.90544	0.556000	0.70494	GCC	.	.	.	none		0.637	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229		A	2598316	G	A	2598316	3	1	263	1	0	0	0	0	1	0	0	0	8196	1203	42	2	1403	2	KIAA0664	17	2598316	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	969924	2598316	78596894	81	16481											
NOS2	4843	hgsc.bcm.edu	37	chr17	26096089	26096089	+	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	catcggggtgagctgagaggCccccaggtgggacagcttct	7	7	16	11	1	1	2	0	2	1	1	2	4	1	3	2	5	2	2	2	5	0	1			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr17:26096089C>G	ENST00000313735.6	-	17	2181	c.1948G>C	c.(1948-1950)Gcc>Ccc	p.A650P		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	650	Flavodoxin-like. {ECO:0000255|PROSITE- ProRule:PRU00088}.				arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	AGCTGAGAGGCCCCCAGGTGG	0.622																																					p.A650P		Atlas-SNP	.											NOS2,NS,adenocarcinoma,0,1	NOS2	113	.	0			c.G1948C						PASS	.						38	37	37					17																	26096089		2203	4299	6502	SO:0001583	missense	4843	exon17			GAGAGGCCCCCAG	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.1948G>C	chr17.hg19:g.26096089C>G	ENSP00000327251:p.Ala650Pro	51.0	1.0	.		52.0	30.0	.	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Missense_Mutation	SNP	ENST00000313735.6	hg19	CCDS11223.1	.	.	.	.	.	.	.	.	.	.	C	32	5.113167	0.94339	.	.	ENSG00000007171	ENST00000313735;ENST00000379105;ENST00000302153	T	0.68624	-0.34	5.16	5.16	0.70880	Flavodoxin/nitric oxide synthase (2);	0.000000	0.85682	D	0.000000	D	0.89262	0.6665	H	0.98370	4.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.93452	0.6803	10	0.72032	D	0.01	.	17.6452	0.88146	0.0:1.0:0.0:0.0	.	615;650	F8WEM3;P35228	.;NOS2_HUMAN	P	650;611;615	ENSP00000327251:A650P	ENSP00000305638:A615P	A	-	1	0	NOS2	23120216	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.818000	0.86416	2.397000	0.81536	0.462000	0.41574	GCC	.	.	.	none		0.622	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625		G	26096089	C	G	26096089	3	3	263	1	0	0	0	0	1	0	0	0	10550	739	26	4	1557	4	NOS2	17	26096089	Missense_Mutation	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10	23497773	26096089	55099121	82	16482											
PEX12	5193	hgsc.bcm.edu	37	chr17	33903054	33903054	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggagtaggcagggcagtcAatgacttgatggtttcttga	9	12	15	5	0	2	3	1	3	1	0	2	4	2	4	0	4	0	4	0	4	2	4			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr17:33903054A>G	ENST00000225873.4	-	3	1434	c.827T>C	c.(826-828)tTg>tCg	p.L276S	SNORD7_ENST00000384567.1_RNA|RP11-1094M14.11_ENST00000592381.1_lincRNA	NM_000286.2	NP_000277.1	O00623	PEX12_HUMAN	peroxisomal biogenesis factor 12	276					peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	integral component of peroxisomal membrane (GO:0005779)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(8)	18				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CAGGGCAGTCAATGACTTGAT	0.468																																					p.L276S		Atlas-SNP	.											.	PEX12	36	.	0			c.T827C						PASS	.						200	161	174					17																	33903054		2203	4300	6503	SO:0001583	missense	5193	exon3			GCAGTCAATGACT	U91521	CCDS11296.1	17q21.1	2011-02-10			ENSG00000108733	ENSG00000108733			8854	protein-coding gene	gene with protein product		601758				9090384	Standard	NM_000286		Approved		uc002hjp.3	O00623	OTTHUMG00000132951	ENST00000225873.4:c.827T>C	chr17.hg19:g.33903054A>G	ENSP00000225873:p.Leu276Ser	172.0	0.0	.		238.0	63.0	.	NM_000286	B2R6M2	Missense_Mutation	SNP	ENST00000225873.4	hg19	CCDS11296.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.008782	0.75046	.	.	ENSG00000108733	ENST00000424525;ENST00000225873	D	0.84800	-1.9	5.04	5.04	0.67666	.	0.071674	0.56097	D	0.000026	D	0.84906	0.5576	M	0.67953	2.075	0.47094	D	0.99931	D	0.54601	0.967	P	0.47573	0.55	T	0.82641	-0.0357	10	0.15066	T	0.55	-9.1479	14.1306	0.65250	1.0:0.0:0.0:0.0	.	276	O00623	PEX12_HUMAN	S	276	ENSP00000225873:L276S	ENSP00000225873:L276S	L	-	2	0	PEX12	30927167	1.000000	0.71417	0.010000	0.14722	0.982000	0.71751	8.533000	0.90617	2.114000	0.64651	0.533000	0.62120	TTG	.	.	.	none		0.468	PEX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256489.2	NM_000286		G	33903054	A	G	33903054	3	3	263	1	0	0	0	0	1	0	0	0	11747	131	5	3	256	3	PEX12	17	33903054	Missense_Mutation	SNP	A	TCGA-UZ-A9PR-01A-11D-A42J-10	7806965	33903054	47292156	83	16483											
KRT13	3860	hgsc.bcm.edu	37	chr17	39659323	39659323	+	Frame_Shift_Del	DEL	C	C	-																															ctccacgttgacctggccgaCcacctggttgctaaattcct																										TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr17:39659323delC	ENST00000246635.3	-	4	809	c.763delG	c.(763-765)gtcfs	p.V255fs	KRT13_ENST00000587544.1_Frame_Shift_Del_p.V255fs|AC019349.5_ENST00000411759.1_RNA|KRT13_ENST00000336861.3_Frame_Shift_Del_p.V255fs|KRT13_ENST00000587118.1_5'Flank	NM_153490.2	NP_705694	P13646	K1C13_HUMAN	keratin 13	255	Linker 12.|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)				ACCTGGCCGACCACCTGGTTG	0.577																																					p.V255fs		Atlas-Indel,Pindel	.											.	KRT13	72	.	0			c.764delT						PASS	.						205	199	201					17																	39659323		2203	4300	6503	SO:0001589	frameshift_variant	3860	exon4			.		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.763delG	chr17.hg19:g.39659323delC	ENSP00000246635:p.Val255fs	77.0	0.0	0		93.0	23.0	0.247312	NM_002274	Q53G54|Q6AZK5|Q8N240	Frame_Shift_Del	DEL	ENST00000246635.3	hg19	CCDS11396.1																																																																																			.	.	.	none		0.577	KRT13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257297.1	NM_153490		-	39659323	C	-	39659323	7	5	263	1	0	1	0	1	0	0	0	0	8457	507	18	0	633	0	KRT13	17	39659323	Frame_Shift_Del	DEL	C	TCGA-UZ-A9PR-01A-11D-A42J-10	5756269	39659323	41535887	84	16484											
MED13	9969	hgsc.bcm.edu	37	chr17	60043908	60043908	+	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	gctgcctgagaaaaccattcTgctaccaacttttctgatag	11	12	7	11	0	2	2	0	2	2	1	2	3	2	2	3	0	5	2	3	0	5	5			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr17:60043908T>A	ENST00000397786.2	-	19	4372	c.4296A>T	c.(4294-4296)gcA>gcT	p.A1432A		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1432					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						AAAACCATTCTGCTACCAACT	0.393																																					p.A1432A		Atlas-SNP	.											.	MED13	181	.	0			c.A4296T						PASS	.						153	137	142					17																	60043908		1872	4114	5986	SO:0001819	synonymous_variant	9969	exon19			CCATTCTGCTACC	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.4296A>T	chr17.hg19:g.60043908T>A		135.0	0.0	.		135.0	36.0	.	NM_005121	B2RU05|O60334	Silent	SNP	ENST00000397786.2	hg19	CCDS42366.1																																																																																			.	.	.	none		0.393	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		A	60043908	T	A	60043908	2	1	263	1	0	0	0	0	0	0	0	1	9437	1567	55	5		5	MED13	17	60043908	Silent	SNP	T	TCGA-UZ-A9PR-01A-11D-A42J-10	20384585	60043908	21151302	85	16485											
LAMA3	3909	hgsc.bcm.edu	37	chr18	21523876	21523876	+	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	tggtctttgcactggggacaGatgggaaaaaattgaggatc	12	10	14	5	0	1	2	0	1	1	1	2	5	1	5	0	5	1	1	0	5	3	2			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr18:21523876G>A	ENST00000313654.9	+	69	9392	c.9151G>A	c.(9151-9153)Gat>Aat	p.D3051N	LAMA3_ENST00000399516.3_Missense_Mutation_p.D2995N|LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000269217.6_Missense_Mutation_p.D1442N|LAMA3_ENST00000587184.1_Missense_Mutation_p.D1386N	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	3051	Laminin G-like 4. {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)					ACTGGGGACAGATGGGAAAAA	0.473																																					p.D3051N		Atlas-SNP	.											.	LAMA3	397	.	0			c.G9151A						PASS	.						104	94	98					18																	21523876		2203	4300	6503	SO:0001583	missense	3909	exon69			GGGACAGATGGGA	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.9151G>A	chr18.hg19:g.21523876G>A	ENSP00000324532:p.Asp3051Asn	108.0	0.0	.		85.0	43.0	.	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	hg19	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	G	7.994	0.753846	0.15778	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000269217	T;T;T	0.63096	-0.02;-0.02;-0.02	5.23	3.46	0.39613	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	T	0.58466	0.2124	L	0.53249	1.67	0.09310	N	1	B;P;P;P	0.36392	0.285;0.551;0.525;0.525	B;B;B;B	0.40285	0.131;0.325;0.245;0.245	T	0.47420	-0.9119	9	0.34782	T	0.22	.	9.2006	0.37256	0.2181:0.0:0.7819:0.0	.	1386;1442;2995;3051	Q6VU69;B0YJ33;Q6VU67;Q16787	.;.;.;LAMA3_HUMAN	N	3051;2995;1442	ENSP00000324532:D3051N;ENSP00000382432:D2995N;ENSP00000269217:D1442N	ENSP00000269217:D1442N	D	+	1	0	LAMA3	19777874	0.944000	0.32072	0.003000	0.11579	0.061000	0.15899	3.534000	0.53568	0.793000	0.33875	-0.793000	0.03317	GAT	.	.	.	none		0.473	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		A	21523876	G	A	21523876	3	1	263	1	0	0	0	0	1	0	0	0	8614	942	33	2	9600	2	LAMA3	18	21523876	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10		21523876	56553372	86	16486											
HDHD2	84064	hgsc.bcm.edu	37	chr18	44635149	44635149	+	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	ttttcttcatctgatgctcgAtatttccctgaaatgaaagt	10	17	6	8	1	3	3	1	3	2	0	5	4	4	3	1	0	1	1	1	0	3	5			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr18:44635149A>C	ENST00000300605.6	-	7	836	c.684T>G	c.(682-684)taT>taG	p.Y228*	RP11-49K24.8_ENST00000591183.1_RNA|HDHD2_ENST00000587841.1_5'UTR	NM_032124.4	NP_115500.1	Q9H0R4	HDHD2_HUMAN	haloacid dehalogenase-like hydrolase domain containing 2	228						extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)			kidney(2)|large_intestine(2)|lung(1)|skin(1)	6						CTGATGCTCGATATTTCCCTG	0.443																																					p.Y228X		Atlas-SNP	.											.	HDHD2	12	.	0			c.T684G						PASS	.						151	129	136					18																	44635149		2203	4300	6503	SO:0001587	stop_gained	84064	exon7			TGCTCGATATTTC	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.684T>G	chr18.hg19:g.44635149A>C	ENSP00000300605:p.Tyr228*	89.0	0.0	.		86.0	43.0	.	NM_032124	A8K7T3|Q96NV4	Nonsense_Mutation	SNP	ENST00000300605.6	hg19	CCDS32829.1	.	.	.	.	.	.	.	.	.	.	A	7.137	0.581046	0.13686	.	.	ENSG00000167220	ENST00000300605	.	.	.	5.93	-8.84	0.00803	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	-21.4898	20.0742	0.97736	0.7148:0.0:0.2852:0.0	.	.	.	.	X	228	.	ENSP00000300605:Y228X	Y	-	3	2	HDHD2	42889147	0.067000	0.21026	0.202000	0.23494	0.198000	0.23893	-0.733000	0.04898	-1.956000	0.01022	-1.934000	0.00508	TAT	.	.	.	none		0.443	HDHD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450668.2	NM_032124		C	44635149	A	C	44635149	4	2	263	1	0	0	0	0	0	1	0	0	7030	340	12	5	99	5	HDHD2	18	44635149	Nonsense_Mutation	SNP	A	TCGA-UZ-A9PR-01A-11D-A42J-10	23111273	44635149	33442099	87	16487											
TMEM147	10430	hgsc.bcm.edu	37	chr19	36037600	36037600	+	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	atgaaggccagcgtggatgtGgcagacctgataggtctaaa	12	8	14	7	1	1	3	0	2	1	1	1	4	1	4	2	4	1	1	2	4	4	2			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr19:36037600G>T	ENST00000222284.5	+	4	379	c.234G>T	c.(232-234)gtG>gtT	p.V78V	AD000090.2_ENST00000590717.1_RNA|TMEM147_ENST00000392205.1_Silent_p.V78V|AD000090.2_ENST00000589137.1_RNA|TMEM147_ENST00000392204.2_Silent_p.V29V|AD000090.2_ENST00000444728.1_RNA|AD000090.2_ENST00000588286.1_RNA	NM_032635.3	NP_116024.1	Q9BVK8	TM147_HUMAN	transmembrane protein 147	78						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(2)|prostate(1)	6	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			GCGTGGATGTGGCAGACCTGA	0.572																																					p.V78V		Atlas-SNP	.											.	TMEM147	13	.	0			c.G234T						PASS	.						119	106	111					19																	36037600		2203	4300	6503	SO:0001819	synonymous_variant	10430	exon4			GGATGTGGCAGAC	BC001118	CCDS12466.1, CCDS56091.1	19q13.12	2010-08-13			ENSG00000105677	ENSG00000105677			30414	protein-coding gene	gene with protein product		613585				20538592	Standard	NM_032635		Approved	NIFIE14, MGC1936	uc002oaj.2	Q9BVK8	OTTHUMG00000048105	ENST00000222284.5:c.234G>T	chr19.hg19:g.36037600G>T		88.0	0.0	.		80.0	31.0	.	NM_032635	A8MWW0|O75790	Silent	SNP	ENST00000222284.5	hg19	CCDS12466.1																																																																																			.	.	.	none		0.572	TMEM147-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109469.2	NM_032635		T	36037600	G	T	36037600	2	4	263	1	0	0	0	0	0	0	0	1	16073	1335	47	4		4	TMEM147	19	36037600	Silent	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10		36037600	23091383	88	16488			1	38		2	2	12	N	TA_G	3.695413e-05
TMEM147	10430	hgsc.bcm.edu	37	chr19	36037611	36037612	+	Missense_Mutation	DNP	TA	TA	AT																															cgtggatgtggcagacctgaTaggtctaaaccttgtcatgt																										TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	T|A	T|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr19:36037611_36037612TA>AT	ENST00000222284.5	+	4	390_391	c.245_246TA>AT	c.(244-246)aTA>aAT	p.I82N	AD000090.2_ENST00000590717.1_RNA|TMEM147_ENST00000392205.1_Missense_Mutation_p.I82N|AD000090.2_ENST00000589137.1_RNA|TMEM147_ENST00000392204.2_Missense_Mutation_p.I33N|AD000090.2_ENST00000444728.1_RNA|AD000090.2_ENST00000588286.1_RNA	NM_032635.3	NP_116024.1	Q9BVK8	TM147_HUMAN	transmembrane protein 147	82						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(2)|prostate(1)	6	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			GCAGACCTGATAGGTCTAAACC	0.569																																					p.I82K|p.I82I		Atlas-SNP	.											.	TMEM147	13	.	0			c.T245A|c.A246T						PASS	.																																			SO:0001583	missense	10430	exon4			ACCTGATAGGTCT|CCTGATAGGTCTA	BC001118	CCDS12466.1, CCDS56091.1	19q13.12	2010-08-13			ENSG00000105677	ENSG00000105677			30414	protein-coding gene	gene with protein product		613585				20538592	Standard	NM_032635		Approved	NIFIE14, MGC1936	uc002oaj.2	Q9BVK8	OTTHUMG00000048105	Exception_encountered	chr19.hg19:g.36037611_36037612delinsAT	ENSP00000222284:p.Ile82Asn	82.0|84.0	0.0	.		81.0	30.0	.	NM_032635	A8MWW0|O75790	Missense_Mutation|Silent	SNP	ENST00000222284.5	hg19	CCDS12466.1																																																																																			.	.	.	none		0.569	TMEM147-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109469.2	NM_032635		AT	36037612	TA	AT	36037611	3	1	263	1	0	0	0	0	1	0	0	0	16073	1406	49	5	259	5	TMEM147	19	36037611	Missense_Mutation	DNP	TA	TCGA-UZ-A9PR-01A-11D-A42J-10	11	36037611	23091372	89	16489			1	38		2	2	12	N	TA_G	3.695413e-05
TSKS	60385	hgsc.bcm.edu	37	chr19	50243159	50243159	+	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	tggagggagcacatcttcaaGtgtagatggtccagagtggc	10	9	15	7	0	2	2	1	0	1	2	3	4	3	4	1	4	1	2	1	4	2	2			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr19:50243159G>T	ENST00000246801.3	-	11	1735	c.1653C>A	c.(1651-1653)caC>caA	p.H551Q	TSKS_ENST00000358830.3_Missense_Mutation_p.H351Q	NM_021733.1	NP_068379.1	Q9UJT2	TSKS_HUMAN	testis-specific serine kinase substrate	551					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)		ACATCTTCAAGTGTAGATGGT	0.592																																					p.H551Q		Atlas-SNP	.											.	TSKS	97	.	0			c.C1653A						PASS	.						102	93	96					19																	50243159		2203	4300	6503	SO:0001583	missense	60385	exon11			CTTCAAGTGTAGA	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.1653C>A	chr19.hg19:g.50243159G>T	ENSP00000246801:p.His551Gln	82.0	0.0	.		56.0	26.0	.	NM_021733	Q8WXJ0	Missense_Mutation	SNP	ENST00000246801.3	hg19	CCDS12780.1	.	.	.	.	.	.	.	.	.	.	G	8.131	0.783184	0.16189	.	.	ENSG00000126467	ENST00000246801;ENST00000358830	T;T	0.29397	1.57;1.57	5.44	0.262	0.15597	.	0.000000	0.49916	D	0.000129	T	0.34687	0.0906	N	0.24115	0.695	0.24288	N	0.995176	D	0.69078	0.997	D	0.78314	0.991	T	0.16335	-1.0406	10	0.66056	D	0.02	-21.087	8.6712	0.34152	0.4246:0.0:0.5754:0.0	.	551	Q9UJT2	TSKS_HUMAN	Q	551;351	ENSP00000246801:H551Q;ENSP00000351691:H351Q	ENSP00000246801:H551Q	H	-	3	2	TSKS	54934971	0.983000	0.35010	0.349000	0.25694	0.037000	0.13140	0.292000	0.19011	-0.097000	0.12307	-0.921000	0.02739	CAC	.	.	.	none		0.592	TSKS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465795.1	NM_021733		T	50243159	G	T	50243159	3	4	263	1	0	0	0	0	1	0	0	0	16638	1020	36	4	129	4	TSKS	19	50243159	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	14205548	50243159	8885824	90	16490											
SIGLEC11	114132	hgsc.bcm.edu	37	chr19	50461600	50461600	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gacgttccaggccttacagcGgagcctgaggccggagctga	8	6	15	12	3	0	2	0	2	0	0	1	5	1	4	4	4	4	2	4	4	1	2			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr19:50461600G>A	ENST00000447370.2	-	8	1681	c.1591C>T	c.(1591-1593)Cgc>Tgc	p.R531C	SIGLEC11_ENST00000426971.2_Intron|CTC-326K19.6_ENST00000451973.1_Missense_Mutation_p.R17C	NM_052884.2	NP_443116.2	Q96RL6	SIG11_HUMAN	sialic acid binding Ig-like lectin 11	531					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(6)|pancreas(1)|prostate(1)|skin(1)	32		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00107)|OV - Ovarian serous cystadenocarcinoma(262;0.00517)		GCCTTACAGCGGAGCCTGAGG	0.667																																					p.R531C		Atlas-SNP	.											.	SIGLEC11	70	.	0			c.C1591T						PASS	.						34	40	38					19																	50461600		2203	4300	6503	SO:0001583	missense	114132	exon8			TACAGCGGAGCCT	AF337818	CCDS12790.2, CCDS46150.1	19q13.3	2013-01-29			ENSG00000161640	ENSG00000161640		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	15622	protein-coding gene	gene with protein product		607157				11986327	Standard	NM_052884		Approved		uc010ybi.2	Q96RL6	OTTHUMG00000157077	ENST00000447370.2:c.1591C>T	chr19.hg19:g.50461600G>A	ENSP00000412361:p.Arg531Cys	164.0	0.0	.		118.0	13.0	.	NM_052884		Missense_Mutation	SNP	ENST00000447370.2	hg19	CCDS12790.2	.	.	.	.	.	.	.	.	.	.	T	19.39	3.819248	0.71028	.	.	ENSG00000161640	ENST00000447370	D	0.86769	-2.17	3.0	0.352	0.16051	.	0.523323	0.19200	N	0.120203	D	0.85788	0.5778	L	0.42245	1.32	0.23966	N	0.996325	D	0.62365	0.991	P	0.54706	0.759	T	0.77835	-0.2440	10	0.66056	D	0.02	.	8.643	0.33989	0.0:0.0:0.6364:0.3636	.	531	Q96RL6	SIG11_HUMAN	C	531	ENSP00000412361:R531C	ENSP00000412361:R531C	R	-	1	0	SIGLEC11	55153412	0.000000	0.05858	0.287000	0.24848	0.128000	0.20619	-1.909000	0.01586	-0.055000	0.13244	-0.371000	0.07208	CGC	.	.	.	none		0.667	SIGLEC11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347382.1	NM_052884		A	50461600	G	A	50461600	3	1	263	1	0	0	0	0	1	0	0	0	14320	1116	39	1	521	1	SIGLEC11	19	50461600	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	218441	50461600	8667383	91	16491											
PLCB1	23236	hgsc.bcm.edu	37	chr20	8626784	8626784	+	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	gttttcagtttggcaacaaaCctgctggcccaaaacatgtc	11	11	8	11	0	1	0	1	0	0	0	2	0	1	0	2	2	4	4	2	2	4	3			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr20:8626784C>T	ENST00000338037.6	+	5	447	c.420C>T	c.(418-420)aaC>aaT	p.N140N	PLCB1_ENST00000378637.2_Silent_p.N140N|PLCB1_ENST00000378641.3_Silent_p.N140N	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	140					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						TGGCAACAAACCTGCTGGCCC	0.388																																					p.Q140H		Atlas-SNP	.											.	PLCB1	394	.	0			c.A420T						PASS	.						130	124	126					20																	8626784		2203	4300	6503	SO:0001819	synonymous_variant	23236	exon5			AACAAACCTGCTG	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.420C>T	chr20.hg19:g.8626784C>T		86.0	0.0	.		66.0	37.0	.	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Missense_Mutation	SNP	ENST00000338037.6	hg19	CCDS13102.1																																																																																			.	.	.	none		0.388	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3			T	8626784	C	T	8626784	2	4	263	1	0	0	0	0	0	0	0	1	12034	506	18	2		2	PLCB1	20	8626784	Silent	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10		8626784	54398736	92	16492											
C20orf3	57136	hgsc.bcm.edu	37	chr20	24964632	24964632	+	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	ccagcatcaagaaggtcactCggaaaactctgccgctaaag	14	6	9	12	2	3	1	2	0	1	1	4	2	3	2	2	2	3	2	2	2	6	1			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr20:24964632C>T	ENST00000217456.2	-	2	409	c.119G>A	c.(118-120)cGa>cAa	p.R40Q	APMAP_ENST00000447138.1_Missense_Mutation_p.R40Q	NM_020531.2	NP_065392.1	Q9HDC9	APMAP_HUMAN	adipocyte plasma membrane associated protein	40					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)										GAAGGTCACTCGGAAAACTCT	0.517																																					p.R40Q		Atlas-SNP	.											.	APMAP	3	.	0			c.G119A						PASS	.						76	77	77					20																	24964632		2203	4300	6503	SO:0001583	missense	57136	exon2			GTCACTCGGAAAA	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.119G>A	chr20.hg19:g.24964632C>T	ENSP00000217456:p.Arg40Gln	87.0	0.0	.		55.0	23.0	.	NM_020531	A8K514|B4DXG1|Q6UVZ8|Q9GZS8|Q9NUB2	Missense_Mutation	SNP	ENST00000217456.2	hg19	CCDS13166.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.80|14.80	2.642456|2.642456	0.47153|0.47153	.|.	.|.	ENSG00000101474|ENSG00000101474	ENST00000451442|ENST00000217456;ENST00000447138	.|T;T	.|0.29397	.|2.0;1.57	6.08|6.08	3.82|3.82	0.43975|0.43975	.|.	.|0.284309	.|0.34652	.|N	.|0.003795	T|T	0.19846|0.19846	0.0477|0.0477	L|L	0.28740|0.28740	0.885|0.885	0.42535|0.42535	D|D	0.993057|0.993057	.|B;B;B	.|0.15473	.|0.013;0.007;0.004	.|B;B;B	.|0.10450	.|0.005;0.002;0.001	T|T	0.06356|0.06356	-1.0831|-1.0831	5|10	.|0.27785	.|T	.|0.31	-3.365|-3.365	7.9026|7.9026	0.29744|0.29744	0.1637:0.7461:0.0:0.0902|0.1637:0.7461:0.0:0.0902	.|.	.|40;24;40	.|Q9HDC9-2;A2A2F9;Q9HDC9	.|.;.;APMAP_HUMAN	K|Q	25|40	.|ENSP00000217456:R40Q;ENSP00000415373:R40Q	.|ENSP00000217456:R40Q	E|R	-|-	1|2	0|0	C20orf3|C20orf3	24912632|24912632	0.956000|0.956000	0.32656|0.32656	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	1.986000|1.986000	0.40677|0.40677	1.568000|1.568000	0.49683|0.49683	0.655000|0.655000	0.94253|0.94253	GAG|CGA	.	.	.	none		0.517	APMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078380.2	NM_020531		T	24964632	C	T	24964632	3	4	263	1	0	0	0	0	1	0	0	0	2111	884	31	1	1163	1	C20orf3	20	24964632	Missense_Mutation	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10	16337848	24964632	38060888	93	16493											
WFDC6	140870	hgsc.bcm.edu	37	chr20	44163124	44163139	+	Frame_Shift_Del	DEL	ATGGTATAAAGTAAGG	ATGGTATAAAGTAAGG	-																															ggttattcaagctcctccttAtggtataaagtaaggctgac																								rs181120845		TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	ATGGTATAAAGTAAGG	ATGGTATAAAGTAAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr20:44163124_44163139delATGGTATAAAGTAAGG	ENST00000372670.3	-	3	315_330	c.228_243delCCTTACTTTATACCAT	c.(226-243)agccttactttataccatfs	p.SLTLYH76fs	WFDC6_ENST00000600168.1_Frame_Shift_Del_p.ALLYTI134fs	NM_080827.1	NP_543017.1	Q9BQY6	WFDC6_HUMAN	WAP four-disulfide core domain 6	76	BPTI/Kunitz inhibitor. {ECO:0000255|PROSITE-ProRule:PRU00031}.					extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|kidney(1)|large_intestine(2)|lung(2)	6		Myeloproliferative disorder(115;0.0122)				GCTCCTCCTTATGGTATAAAGTAAGGCTGACCTGTG	0.477																																					p.77_82del	Ovarian(123;591 1661 9833 14622 45877)	Atlas-Indel,Pindel	.											.	WFDC6	13	.	0			c.229_244del						PASS	.																																			SO:0001589	frameshift_variant	140870	exon3			.	AL031663	CCDS13358.1	20q13.11	2013-01-21	2003-02-21	2003-02-21	ENSG00000243543	ENSG00000243543		"WAP four-disulfide core domain containing"	16164	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 171"	C20orf171		12206714	Standard	NM_080827		Approved	dJ461P17.11, WAP6		Q9BQY6	OTTHUMG00000046354	ENST00000372670.3:c.228_243delCCTTACTTTATACCAT	chr20.hg19:g.44163124_44163139delATGGTATAAAGTAAGG	ENSP00000361755:p.Ser76fs	102.0	0.0	0		75.0	27.0	0.36	NM_080827	Q3MJ23|Q5JYQ4|Q8NFV6	Frame_Shift_Del	DEL	ENST00000372670.3	hg19	CCDS13358.1																																																																																			.	.	.	none		0.477	WFDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000107008.2			-	44163139	ATGGTATAAAGTAAGG	-	44163124	7	5	263	1	0	1	0	1	0	0	0	0	17367	446	16	0	21	0	WFDC6	20	44163124	Frame_Shift_Del	DEL	ATGGTATAAAGTAAGG	TCGA-UZ-A9PR-01A-11D-A42J-10	19198492	44163124	18862396	94	16494											
TMPRSS15	5651	hgsc.bcm.edu	37	chr21	19701538	19701538	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttatttcaactacatcgttAatattttctaagtcaaattc	13	18	2	8	1	3	0	2	0	1	0	5	0	3	0	0	0	2	1	0	0	7	9			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr21:19701538A>G	ENST00000284885.3	-	15	1761	c.1728T>C	c.(1726-1728)atT>atC	p.I576I		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	576	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						CTACATCGTTAATATTTTCTA	0.294																																					p.I576I		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.T1728C						PASS	.						86	84	84					21																	19701538		2203	4297	6500	SO:0001819	synonymous_variant	5651	exon15			ATCGTTAATATTT		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.1728T>C	chr21.hg19:g.19701538A>G		312.0	1.0	.		229.0	117.0	.	NM_002772	Q2NKL7	Silent	SNP	ENST00000284885.3	hg19	CCDS13571.1																																																																																			.	.	.	none		0.294	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		G	19701538	A	G	19701538	2	3	263	1	0	0	0	0	0	0	0	1	16258	358	13	3		3	TMPRSS15	21	19701538	Silent	SNP	A	TCGA-UZ-A9PR-01A-11D-A42J-10		19701538	28428357	95	16495											
TMPRSS15	5651	hgsc.bcm.edu	37	chr21	19701570	19701570	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcaaattcttgaaaatgaaGttgtatattctttccttttt	11	20	5	5	0	3	2	1	2	2	0	4	2	4	2	1	0	0	2	1	0	6	9			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr21:19701570G>A	ENST00000284885.3	-	15	1729	c.1696C>T	c.(1696-1698)Ctt>Ttt	p.L566F		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	566	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						TGAAAATGAAGTTGTATATTC	0.308																																					p.L566F		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.C1696T						PASS	.						70	68	69					21																	19701570		2202	4297	6499	SO:0001583	missense	5651	exon15			AATGAAGTTGTAT		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.1696C>T	chr21.hg19:g.19701570G>A	ENSP00000284885:p.Leu566Phe	325.0	1.0	.		226.0	95.0	.	NM_002772	Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	hg19	CCDS13571.1	.	.	.	.	.	.	.	.	.	.	G	18.07	3.541595	0.65085	.	.	ENSG00000154646	ENST00000284885	T	0.33865	1.39	5.4	4.49	0.54785	CUB (5);	0.000000	0.64402	D	0.000002	T	0.65270	0.2675	M	0.88031	2.925	0.45227	D	0.998237	D	0.89917	1.0	D	0.97110	1.0	T	0.72411	-0.4302	9	.	.	.	.	14.0641	0.64817	0.0:0.1523:0.8477:0.0	.	566	P98073	ENTK_HUMAN	F	566	ENSP00000284885:L566F	.	L	-	1	0	TMPRSS15	18623441	1.000000	0.71417	0.996000	0.52242	0.989000	0.77384	4.205000	0.58466	1.371000	0.46172	0.561000	0.74099	CTT	.	.	.	none		0.308	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		A	19701570	G	A	19701570	3	1	263	1	0	0	0	0	1	0	0	0	16258	1029	36	2	1407	2	TMPRSS15	21	19701570	Missense_Mutation	SNP	G	TCGA-UZ-A9PR-01A-11D-A42J-10	32	19701570	28428325	96	16496											
GART	2618	hgsc.bcm.edu	37	chr21	34901233	34901234	+	Missense_Mutation	DNP	TC	TC	AT																															ctttaatttttagtaatagaTcattagaaacctggagaacg																								rs376223183		TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr21:34901233_34901234TC>AT	ENST00000381831.3	-	8	996_997	c.733_734GA>AT	c.(733-735)GAt>ATt	p.D245I	GART_ENST00000381815.4_Missense_Mutation_p.D245I|GART_ENST00000361093.5_Missense_Mutation_p.D245I|GART_ENST00000381839.3_Missense_Mutation_p.D245I|GART_ENST00000497313.1_5'Flank	NM_001136005.1	NP_001129477.1	P22102	PUR2_HUMAN	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	245	ATP-grasp.				'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|glycine metabolic process (GO:0006544)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|phosphoribosylamine-glycine ligase activity (GO:0004637)|phosphoribosylformylglycinamidine cyclo-ligase activity (GO:0004641)|phosphoribosylglycinamide formyltransferase activity (GO:0004644)			NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(13)|ovary(3)|prostate(5)|urinary_tract(1)	31					Pemetrexed(DB00642)	TAGTAATAGATCATTAGAAACC	0.396																																					p.D245V|p.D245N		Atlas-SNP	.											.	GART	81	.	0			c.A734T|c.G733A						PASS	.																																			SO:0001583	missense	2618	exon8			AATAGATCATTAG|ATAGATCATTAGA	M32082	CCDS13627.1, CCDS13628.1	21q22.11	2012-10-02			ENSG00000159131	ENSG00000159131	2.1.2.2, 6.3.3.1, 6.3.4.13		4163	protein-coding gene	gene with protein product		138440		PRGS, PGFT		2050105	Standard	NM_001136005		Approved		uc002yrx.3	P22102	OTTHUMG00000065628	ENST00000381831.3:c.733_734delinsAT	chr21.hg19:g.34901233_34901234delinsAT	ENSP00000371253:p.Asp245Ile	62.0|60.0	0.0	.		41.0	12.0	.	NM_001136005	A8K945|A8KA32|D3DSF3|D3DSF4|O14659|Q52M77	Missense_Mutation	SNP	ENST00000381831.3	hg19	CCDS13627.1																																																																																			.	.	.	alt|none		0.396	GART-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140626.3	NM_000819		AT	34901234	TC	AT	34901233	3	1	263	1	0	0	0	0	1	0	0	0	6250	1435	50	5	2362	5	GART	21	34901233	Missense_Mutation	DNP	TC	TCGA-UZ-A9PR-01A-11D-A42J-10	15199663	34901233	13228662	97	16497											
COL6A2	1292	hgsc.bcm.edu	37	chr21	47538955	47538955	+	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	cttcttcaggggtatcaaggCaacagtggagccccaggaag	11	7	13	10	0	3	0	2	0	1	0	3	2	3	2	2	5	2	2	2	5	4	3			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr21:47538955C>T	ENST00000300527.4	+	14	1295	c.1191C>T	c.(1189-1191)ggC>ggT	p.G397G	COL6A2_ENST00000397763.1_Silent_p.G397G|COL6A2_ENST00000357838.4_Silent_p.G397G|COL6A2_ENST00000310645.5_Silent_p.G397G|COL6A2_ENST00000409416.1_Silent_p.G397G	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	397	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)		GGTATCAAGGCAACAGTGGAG	0.662																																					p.G397G		Atlas-SNP	.											.	COL6A2	351	.	0			c.C1191T						PASS	.						47	42	44					21																	47538955		2201	4298	6499	SO:0001819	synonymous_variant	1292	exon14			TCAAGGCAACAGT	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.1191C>T	chr21.hg19:g.47538955C>T		356.0	1.0	.		273.0	88.0	.	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Silent	SNP	ENST00000300527.4	hg19	CCDS13728.1																																																																																			.	.	.	none		0.662	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1			T	47538955	C	T	47538955	2	4	263	1	0	0	0	0	0	0	0	1	3702	697	25	2		2	COL6A2	21	47538955	Silent	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10	12637722	47538955	590940	98	16498											
DIP2A	23181	hgsc.bcm.edu	37	chr21	47917012	47917012	+	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	ttcgtctgtggaaacctacaCccctccaggtattgataaac	11	11	7	12	1	1	1	0	1	1	0	3	2	2	2	4	2	3	1	4	2	5	5			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr21:47917012C>T	ENST00000417564.2	+	4	416	c.395C>T	c.(394-396)aCc>aTc	p.T132I	DIP2A_ENST00000427143.2_Missense_Mutation_p.T68I|DIP2A_ENST00000466639.1_Missense_Mutation_p.T132I|DIP2A_ENST00000435722.3_Missense_Mutation_p.T132I|DIP2A_ENST00000457905.3_Missense_Mutation_p.T132I|DIP2A_ENST00000318711.7_Missense_Mutation_p.T132I|DIP2A_ENST00000400274.1_Missense_Mutation_p.T132I			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	132					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)		GAAACCTACACCCCTCCAGGT	0.448																																					p.T132I		Atlas-SNP	.											.	DIP2A	332	.	0			c.C395T						PASS	.						121	113	115					21																	47917012		1965	4139	6104	SO:0001583	missense	23181	exon4			CCTACACCCCTCC	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.395C>T	chr21.hg19:g.47917012C>T	ENSP00000392066:p.Thr132Ile	129.0	0.0	.		109.0	41.0	.	NM_206891	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Missense_Mutation	SNP	ENST00000417564.2	hg19	CCDS46655.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.383169	0.82792	.	.	ENSG00000160305	ENST00000400274;ENST00000427143;ENST00000318711;ENST00000358985;ENST00000457905;ENST00000466639;ENST00000435722;ENST00000417564	T;T;T;T;T;T;T	0.31247	1.77;1.77;1.8;1.74;1.5;1.74;1.8	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.59224	0.2178	M	0.80746	2.51	0.80722	D	1	P;P;D;P;D;D	0.89917	0.929;0.753;1.0;0.825;0.995;0.992	P;P;D;P;D;P	0.87578	0.821;0.456;0.998;0.739;0.959;0.908	T	0.57382	-0.7821	10	0.35671	T	0.21	-25.05	18.4623	0.90743	0.0:1.0:0.0:0.0	.	132;68;132;132;132;132	E9PER1;E7EMA5;Q14689-3;Q14689;Q14689-4;Q14689-2	.;.;.;DIP2A_HUMAN;.;.	I	132;68;132;132;132;132;132;132	ENSP00000383133:T132I;ENSP00000400528:T68I;ENSP00000323633:T132I;ENSP00000393434:T132I;ENSP00000430249:T132I;ENSP00000415089:T132I;ENSP00000392066:T132I	ENSP00000323633:T132I	T	+	2	0	DIP2A	46741440	1.000000	0.71417	0.847000	0.33407	0.992000	0.81027	7.680000	0.84062	2.595000	0.87683	0.655000	0.94253	ACC	.	.	.	none		0.448	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151		T	47917012	C	T	47917012	3	4	263	1	0	0	0	0	1	0	0	0	4529	507	18	2	409	2	DIP2A	21	47917012	Missense_Mutation	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10	378057	47917012	212883	99	16499											
PI4KA	5297	hgsc.bcm.edu	37	chr22	21153483	21153483	+	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	aggatctgcagaatgggctcCatgaccttcggggtgtccct	7	10	13	11	1	1	2	0	1	1	1	4	3	3	3	3	4	1	2	3	4	1	1			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr22:21153483C>A	ENST00000572273.1	-	16	1958	c.1728G>T	c.(1726-1728)atG>atT	p.M576I	PI4KA_ENST00000255882.6_Missense_Mutation_p.M634I			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	576					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)			GAATGGGCTCCATGACCTTCG	0.562																																					p.M634I	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											.	PI4KA	313	.	0			c.G1902T						PASS	.						90	78	82					22																	21153483		2203	4300	6503	SO:0001583	missense	5297	exon16			GGGCTCCATGACC	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.1728G>T	chr22.hg19:g.21153483C>A	ENSP00000458238:p.Met576Ile	69.0	0.0	.		57.0	23.0	.	NM_058004	Q7Z625|Q9UPG2	Missense_Mutation	SNP	ENST00000572273.1	hg19		.	.	.	.	.	.	.	.	.	.	C	17.03	3.285111	0.59867	.	.	ENSG00000241973	ENST00000255882	.	.	.	4.55	4.55	0.56014	.	0.000000	0.85682	D	0.000000	T	0.58104	0.2099	L	0.54323	1.7	0.80722	D	1	B;B	0.24768	0.111;0.067	B;B	0.22601	0.025;0.04	T	0.55749	-0.8092	9	0.25751	T	0.34	-35.0254	17.4787	0.87667	0.0:1.0:0.0:0.0	.	634;576	D3DX33;P42356	.;PI4KA_HUMAN	I	576	.	ENSP00000255882:M576I	M	-	3	0	PI4KA	19483483	1.000000	0.71417	1.000000	0.80357	0.813000	0.45954	7.651000	0.83577	2.348000	0.79779	0.491000	0.48974	ATG	.	.	.	none		0.562	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004		A	21153483	C	A	21153483	3	1	263	1	0	0	0	0	1	0	0	0	11880	594	21	4	4566	4	PI4KA	22	21153483	Missense_Mutation	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10		21153483	30151083	100	16500											
C22orf43	51233	hgsc.bcm.edu	37	chr22	23964292	23964292	+	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	tcttacctgggcatcatcatCatcatcatcatcacagtcat	11	13	4	13	0	9	0	8	0	1	0	9	0	9	0	1	1	1	1	1	1	1	1			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr22:23964292C>A	ENST00000317749.5	-	4	667	c.370G>T	c.(370-372)Gat>Tat	p.D124Y		NM_016449.3	NP_057533.2	Q6PGQ1	DRIC1_HUMAN		124	Asp-rich.									endometrium(1)|large_intestine(3)|lung(5)|pancreas(1)|skin(1)	11						Gcatcatcatcatcatcatca	0.428																																					p.D124Y		Atlas-SNP	.											.	C22orf43	18	.	0			c.G370T						PASS	.						91	77	82					22																	23964292		1980	4156	6136	SO:0001583	missense	51233	exon4			CATCATCATCATC																												ENST00000317749.5:c.370G>T	chr22.hg19:g.23964292C>A	ENSP00000316137:p.Asp124Tyr	64.0	0.0	.		56.0	15.0	.	NM_016449	Q6ICJ8|Q6P4I3|Q9NU31	Missense_Mutation	SNP	ENST00000317749.5	hg19	CCDS42985.1	.	.	.	.	.	.	.	.	.	.	c	4.413	0.076434	0.08485	.	.	ENSG00000189269	ENST00000317749	T	0.40756	1.02	0.333	-0.666	0.11399	.	.	.	.	.	T	0.36690	0.0976	N	0.08118	0	0.09310	N	1	D	0.76494	0.999	D	0.72982	0.979	T	0.25710	-1.0124	8	0.87932	D	0	.	.	.	.	.	124	Q6PGQ1	CV043_HUMAN	Y	124	ENSP00000316137:D124Y	ENSP00000316137:D124Y	D	-	1	0	C22orf43	22294292	0.004000	0.15560	0.001000	0.08648	0.001000	0.01503	-0.994000	0.03716	-0.537000	0.06290	-0.524000	0.04348	GAT	.	.	.	none		0.428	C22orf43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319708.2			A	23964292	C	A	23964292	3	1	263	1	0	0	0	0	1	0	0	0	2152	826	29	4	355	4	C22orf43	22	23964292	Missense_Mutation	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10	2810809	23964292	27340274	101	16501											
DRG1	4733	hgsc.bcm.edu	37	chr22	31816283	31816283	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttgattgttctggatgtcCtgaaacctttgggacataag	9	15	10	7	0	2	2	0	2	2	0	3	4	3	4	2	2	1	1	2	2	2	5			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr22:31816283C>T	ENST00000331457.4	+	5	615	c.454C>T	c.(454-456)Ctg>Ttg	p.L152L	DRG1_ENST00000433341.1_3'UTR	NM_004147.3	NP_004138.1	Q9Y295	DRG1_HUMAN	developmentally regulated GTP binding protein 1	152	OBG-type G. {ECO:0000255|PROSITE- ProRule:PRU01047}.				multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|polysome (GO:0005844)	GTP binding (GO:0005525)|identical protein binding (GO:0042802)|transcription factor binding (GO:0008134)	p.L152M(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|urinary_tract(1)	11						TCTGGATGTCCTGAAACCTTT	0.403																																					p.L152L		Atlas-SNP	.											DRG1,bladder,carcinoma,-2,1	DRG1	28	.	1	Substitution - Missense(1)	endometrium(1)	c.C454T						PASS	.						87	82	84					22																	31816283		2203	4300	6503	SO:0001819	synonymous_variant	4733	exon5			GATGTCCTGAAAC	AJ005940	CCDS13897.1	22q12.2	2010-02-26	2001-11-28		ENSG00000185721	ENSG00000185721			3029	protein-coding gene	gene with protein product		603952	"developmentally regulated GTP-binding protein 1"	NEDD3		7929244, 1449490	Standard	NM_004147		Approved		uc003aku.3	Q9Y295	OTTHUMG00000030792	ENST00000331457.4:c.454C>T	chr22.hg19:g.31816283C>T		129.0	0.0	.		102.0	53.0	.	NM_004147	B2RDS8|Q6FGP8|Q8WW69|Q9UGF2	Silent	SNP	ENST00000331457.4	hg19	CCDS13897.1																																																																																			.	.	.	none		0.403	DRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075680.5	NM_004147		T	31816283	C	T	31816283	2	4	263	1	0	0	0	0	0	0	0	1	4763	680	24	2		2	DRG1	22	31816283	Silent	SNP	C	TCGA-UZ-A9PR-01A-11D-A42J-10	7851991	31816283	19488283	102	16502											
TBC1D22A	25771	hgsc.bcm.edu	37	chr22	47287237	47287248	+	In_Frame_Del	DEL	GAGCACTATTAC	GAGCACTATTAC	-																															aagaatattttgcatttattGagcactattacgattctagg																								rs117270140	byFrequency	TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	GAGCACTATTAC	GAGCACTATTAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chr22:47287237_47287248delGAGCACTATTAC	ENST00000337137.4	+	6	950_961	c.784_795delGAGCACTATTAC	c.(784-795)gagcactattacdel	p.EHYY262del	TBC1D22A_ENST00000406733.1_In_Frame_Del_p.EHYY215del|TBC1D22A_ENST00000355704.3_In_Frame_Del_p.EHYY184del|TBC1D22A_ENST00000407381.3_In_Frame_Del_p.EHYY203del|TBC1D22A_ENST00000380995.1_In_Frame_Del_p.EHYY215del	NM_001284304.1|NM_001284305.1|NM_014346.2	NP_001271233.1|NP_001271234.1|NP_055161.1	Q8WUA7	TB22A_HUMAN	TBC1 domain family, member 22A	262	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						protein homodimerization activity (GO:0042803)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(3)|large_intestine(10)|lung(5)|ovary(2)|prostate(1)	22		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)		TGCATTTATTGAGCACTATTACGATTCTAGGA	0.41																																					p.261_265del		Atlas-Indel,Pindel	.											.	TBC1D22A	54	.	0			c.783_794del						PASS	.																																			SO:0001651	inframe_deletion	25771	exon6			.	AK125705	CCDS14078.1, CCDS63511.1, CCDS63512.1, CCDS74877.1	22q13	2008-01-22	2005-01-05	2005-01-05	ENSG00000054611	ENSG00000054611			1309	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 4"	C22orf4			Standard	XM_005261496		Approved		uc003bib.3	Q8WUA7	OTTHUMG00000150332	ENST00000337137.4:c.784_795delGAGCACTATTAC	chr22.hg19:g.47287237_47287248delGAGCACTATTAC	ENSP00000336724:p.Glu262_Tyr265del	278.0	0.0	0		176.0	31.0	0.176136	NM_014346	B0QYI2|B0QYI3|B9A6M3|Q5TE47|Q6ZUH2|Q92680|Q9BVD6|Q9UGG0|Q9UGT2|Q9UGU6|Q9UH25|Q9Y4W5	In_Frame_Del	DEL	ENST00000337137.4	hg19	CCDS14078.1																																																																																			.	.	.	none		0.41	TBC1D22A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317600.3	NM_014346		-	47287248	GAGCACTATTAC	-	47287237	7	5	263	1	0	1	0	1	0	0	0	0	15623	1291	45	0	806	0	TBC1D22A	22	47287237	In_Frame_Del	DEL	GAGCACTATTAC	TCGA-UZ-A9PR-01A-11D-A42J-10	15470954	47287237	4017329	103	16503											
EFHC2	80258	hgsc.bcm.edu	37	chrX	44008117	44008117	+	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	tcgcaggaataggtgatggcAtaccaagccaaacatcttca	14	8	9	10	1	2	1	1	1	1	0	3	2	2	2	2	3	3	2	2	3	5	3			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chrX:44008117A>T	ENST00000420999.1	-	15	2257	c.2174T>A	c.(2173-2175)aTg>aAg	p.M725K	EFHC2_ENST00000343571.3_5'UTR	NM_025184.3	NP_079460.2	Q5JST6	EFHC2_HUMAN	EF-hand domain (C-terminal) containing 2	725							calcium ion binding (GO:0005509)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	29						AGGTGATGGCATACCAAGCCA	0.378																																					p.M725K		Atlas-SNP	.											.	EFHC2	81	.	0			c.T2174A						PASS	.						81	68	72					X																	44008117		1873	4089	5962	SO:0001583	missense	80258	exon15			GATGGCATACCAA	AK026254	CCDS55405.1	Xp11	2014-01-31			ENSG00000183690	ENSG00000183690		"EF-hand domain containing"	26233	protein-coding gene	gene with protein product		300817	"mental retardation, X-linked 74"	MRX74		17221867	Standard	NM_025184		Approved	FLJ22843	uc004dgb.4	Q5JST6	OTTHUMG00000021393	ENST00000420999.1:c.2174T>A	chrX.hg19:g.44008117A>T	ENSP00000404232:p.Met725Lys	263.0	1.0	.		157.0	143.0	.	NM_025184	Q5JST8|Q68DK4|Q8NEI0|Q9H653	Missense_Mutation	SNP	ENST00000420999.1	hg19	CCDS55405.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	4.147|4.147	0.025585|0.025585	0.08054|0.08054	.|.	.|.	ENSG00000183690|ENSG00000183690	ENST00000343571;ENST00000333807;ENST00000420999|ENST00000441230	T;T|.	0.65916|.	-0.17;-0.18|.	5.52|5.52	-0.196|-0.196	0.13232|0.13232	.|.	0.626150|.	0.16544|.	N|.	0.209813|.	T|.	0.36717|.	0.0977|.	L|L	0.57536|0.57536	1.79|1.79	0.09310|0.09310	N|N	1|1	B|.	0.10296|.	0.003|.	B|.	0.06405|.	0.002|.	T|.	0.34900|.	-0.9810|.	10|.	0.07175|.	T|.	0.84|.	-5.6211|-5.6211	1.4427|1.4427	0.02357|0.02357	0.3921:0.1429:0.0876:0.3774|0.3921:0.1429:0.0876:0.3774	.|.	725|.	Q5JST6|.	EFHC2_HUMAN|.	K|X	138;725;753|705	ENSP00000333823:M725K;ENSP00000404232:M753K|.	ENSP00000333823:M725K|.	M|Y	-|-	2|3	0|2	EFHC2|EFHC2	43893061|43893061	0.585000|0.585000	0.26774|0.26774	0.358000|0.358000	0.25811|0.25811	0.080000|0.080000	0.17528|0.17528	0.391000|0.391000	0.20784|0.20784	-0.049000|-0.049000	0.13379|0.13379	0.412000|0.412000	0.27726|0.27726	ATG|TAT	.	.	.	none		0.378	EFHC2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056312.2	NM_025184		T	44008117	A	T	44008117	3	4	263	1	0	0	0	0	1	0	0	0	4949	217	8	5	79	5	EFHC2	23	44008117	Missense_Mutation	SNP	A	TCGA-UZ-A9PR-01A-11D-A42J-10		44008117	111262443	104	16504											
SUV39H1	6839	hgsc.bcm.edu	37	chrX	48558807	48558807	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcgggccttcgtgtacatcaAtgagtaccgtgttggtgagg	7	11	15	8	3	1	2	1	2	0	0	2	2	1	2	2	3	2	3	2	3	3	4			TCGA-UZ-A9PR-01A-11D-A42J-10	TCGA-UZ-A9PR-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	22f04597-4f4f-47c4-9d69-6b3b3f20701d	f568a26d-8461-430f-82d6-b31750f9addc	g.chrX:48558807A>G	ENST00000376687.3	+	3	681	c.491A>G	c.(490-492)aAt>aGt	p.N164S	SUV39H1_ENST00000453214.2_Intron|SUV39H1_ENST00000337852.6_Missense_Mutation_p.N175S|AF196970.3_ENST00000416061.1_RNA	NM_003173.2	NP_003164.1	O43463	SUV91_HUMAN	suppressor of variegation 3-9 homolog 1 (Drosophila)	164					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						GTGTACATCAATGAGTACCGT	0.632																																					p.N164S		Atlas-SNP	.											.	SUV39H1	36	.	0			c.A491G						PASS	.						62	47	52					X																	48558807		2203	4300	6503	SO:0001583	missense	6839	exon3			ACATCAATGAGTA	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.491A>G	chrX.hg19:g.48558807A>G	ENSP00000365877:p.Asn164Ser	93.0	0.0	.		81.0	76.0	.	NM_003173	B2R6E8|B4DST0|Q53G60|Q6FHK6	Missense_Mutation	SNP	ENST00000376687.3	hg19	CCDS14304.1	.	.	.	.	.	.	.	.	.	.	A	20.5	3.994484	0.74703	.	.	ENSG00000101945	ENST00000337852;ENST00000376687;ENST00000448548;ENST00000422496	D;D	0.89196	-2.48;-2.48	4.61	4.61	0.57282	Pre-SET zinc-binding sub-group (1);Pre-SET domain (1);	0.000000	0.85682	D	0.000000	D	0.88009	0.6322	L	0.46614	1.455	0.80722	D	1	P;P	0.42123	0.771;0.771	P;P	0.48488	0.475;0.579	D	0.86401	0.1742	10	0.38643	T	0.18	.	11.0625	0.47955	1.0:0.0:0.0:0.0	.	175;164	B4DST0;O43463	.;SUV91_HUMAN	S	175;164;162;22	ENSP00000337976:N175S;ENSP00000365877:N164S	ENSP00000337976:N175S	N	+	2	0	SUV39H1	48443751	1.000000	0.71417	0.993000	0.49108	0.987000	0.75469	9.297000	0.96120	1.505000	0.48720	0.409000	0.27619	AAT	.	.	.	none		0.632	SUV39H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058909.1	NM_003173		G	48558807	A	G	48558807	3	3	263	1	0	0	0	0	1	0	0	0	15424	101	4	3	501	3	SUV39H1	23	48558807	Missense_Mutation	SNP	A	TCGA-UZ-A9PR-01A-11D-A42J-10	4550690	48558807	106711753	105	16505											
C1orf86	199990	hgsc.bcm.edu	37	chr1	2125123	2125123	+	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	tggggcagctgcgcagggccGcggcaccctccacagacggc	6	3	16	16	4	0	1	0	0	0	1	1	1	1	1	3	5	2	4	3	5	0	0	rs200185087	byFrequency	TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr1:2125123G>T	ENST00000378546.4	-	3	449	c.425C>A	c.(424-426)gCg>gAg	p.A142E	C1orf86_ENST00000400919.3_5'UTR|C1orf86_ENST00000487186.1_5'UTR|C1orf86_ENST00000378545.3_Missense_Mutation_p.A245E	NM_182533.2	NP_872339	Q6NZ36	FAP20_HUMAN	chromosome 1 open reading frame 86	142					cellular response to DNA damage stimulus (GO:0006974)|interstrand cross-link repair (GO:0036297)|translesion synthesis (GO:0019985)	cell junction (GO:0030054)|chromosome (GO:0005694)|Fanconi anaemia nuclear complex (GO:0043240)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|metal ion binding (GO:0046872)|polyubiquitin binding (GO:0031593)|ubiquitin binding (GO:0043130)			central_nervous_system(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4	all_cancers(77;0.000134)|all_epithelial(69;4.45e-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;1.09e-37)|OV - Ovarian serous cystadenocarcinoma(86;1.5e-23)|GBM - Glioblastoma multiforme(42;1.61e-08)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00437)|STAD - Stomach adenocarcinoma(132;0.0134)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)		GCGCAGGGCCGCGGCACCCTC	0.711																																					p.A142E		Atlas-SNP	.											.	C1orf86	20	.	0			c.C425A						PASS	.						17	23	21					1																	2125123		2043	4103	6146	SO:0001583	missense	199990	exon3			AGGGCCGCGGCAC	AK126870	CCDS38.2, CCDS57965.1, CCDS72686.1, CCDS72687.1	1p36.33	2013-05-22			ENSG00000162585	ENSG00000162585			26428	protein-coding gene	gene with protein product		615183				14702039	Standard	NM_182533		Approved	FLJ31031, FAAP20	uc031pkt.1	Q6NZ36	OTTHUMG00000001404	ENST00000378546.4:c.425C>A	chr1.hg19:g.2125123G>T	ENSP00000367808:p.Ala142Glu	88.0	0.0	.		102.0	42.0	.	NM_001256946	A6PW39|A6PW40|A6PW41|A8MQT6|F2Z2L4|Q6ZT64|Q71M24|Q96ND7	Missense_Mutation	SNP	ENST00000378546.4	hg19	CCDS38.2	.	.	.	.	.	.	.	.	.	.	G	12.57	1.978697	0.34942	.	.	ENSG00000162585	ENST00000400918;ENST00000378546;ENST00000378545	T;T;T	0.44881	0.92;0.95;0.91	4.05	-5.63	0.02474	.	1.543580	0.04329	N	0.352089	T	0.22205	0.0535	.	.	.	0.09310	N	1	B	0.11235	0.004	B	0.12837	0.008	T	0.11446	-1.0587	9	0.33141	T	0.24	6.0E-4	2.3251	0.04221	0.5065:0.2024:0.172:0.1192	.	142	Q6NZ36	CA086_HUMAN	E	142;142;245	ENSP00000383709:A142E;ENSP00000367808:A142E;ENSP00000367807:A245E	ENSP00000367807:A245E	A	-	2	0	C1orf86	2114983	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.396000	0.07278	-0.914000	0.03827	-0.367000	0.07326	GCG	.	.	.	alt		0.711	C1orf86-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316541.1	NM_182533		T	2125123	G	T	2125123	3	4	264	1	0	0	0	0	1	0	0	0	2065	1087	38	4	365	4	C1orf86	1	2125123	Missense_Mutation	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10		2125123	247125498	1	16506											
C1orf127	148345	hgsc.bcm.edu	37	chr1	11008797	11008797	+	Frame_Shift_Del	DEL	A	A	-																															atccctgcttcccctgggggAggctggggacctcgctgagc																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr1:11008797delA	ENST00000377008.4	-	11	1340	c.894delT	c.(892-894)cctfs	p.P300fs	C1orf127_ENST00000377004.4_Frame_Shift_Del_p.P467fs			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	300	Pro-rich.									NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		CCCCTGGGGGAGGCTGGGGAC	0.652																																					p.P466fs		Atlas-Indel,Pindel	.											.	C1orf127	134	.	0			c.1396delC						PASS	.						53	62	59					1																	11008797		2203	4300	6503	SO:0001589	frameshift_variant	148345	exon12			.	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.894delT	chr1.hg19:g.11008797delA	ENSP00000366207:p.Pro300fs	69.0	0.0	0		69.0	25.0	0.362319	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Frame_Shift_Del	DEL	ENST00000377008.4	hg19																																																																																				.	.	.	none		0.652	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507		-	11008797	A	-	11008797	7	5	264	1	0	1	0	1	0	0	0	0	1996	291	11	0	1080	0	C1orf127	1	11008797	Frame_Shift_Del	DEL	A	TCGA-UZ-A9PS-01A-11D-A42J-10	8883674	11008797	238241824	2	16507											
C1orf127	148345	hgsc.bcm.edu	37	chr1	11009850	11009850	+	Missense_Mutation	SNP	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	tcctcagtgcagcagttgagGcaggcgactctgttcctgaa	8	10	12	11	1	2	2	1	2	1	0	4	3	4	2	2	2	2	5	2	2	1	2			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr1:11009850G>A	ENST00000377008.4	-	10	1066	c.620C>T	c.(619-621)gCc>gTc	p.A207V	C1orf127_ENST00000377004.4_Missense_Mutation_p.A374V			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	207										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)		AGCAGTTGAGGCAGGCGACTC	0.602																																					p.A374V		Atlas-SNP	.											.	C1orf127	134	.	0			c.C1121T						PASS	.						50	48	49					1																	11009850		2197	4291	6488	SO:0001583	missense	148345	exon11			GTTGAGGCAGGCG	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.620C>T	chr1.hg19:g.11009850G>A	ENSP00000366207:p.Ala207Val	96.0	0.0	.		102.0	40.0	.	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.97|18.97	3.735300|3.735300	0.69189|0.69189	.|.	.|.	ENSG00000175262|ENSG00000175262	ENST00000377004;ENST00000377008|ENST00000418570;ENST00000520253	T;T|.	0.25579|.	1.79;1.79|.	4.33|4.33	-0.909|-0.909	0.10514|0.10514	.|.	1.285140|.	0.05693|.	N|.	0.592657|.	T|T	0.21590|0.21590	0.0520|0.0520	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	P;P;P|.	0.35745|.	0.518;0.518;0.518|.	B;B;B|.	0.36464|.	0.225;0.225;0.225|.	T|T	0.30794|0.30794	-0.9966|-0.9966	10|5	0.16896|.	T|.	0.51|.	-0.5709|-0.5709	7.1323|7.1323	0.25508|0.25508	0.5857:0.0:0.4143:0.0|0.5857:0.0:0.4143:0.0	.|.	225;225;207|.	B7ZLG7;Q8N9H9-2;Q8N9H9|.	.;.;CA127_HUMAN|.	V|S	374;207|209;352	ENSP00000366203:A374V;ENSP00000366207:A207V|.	ENSP00000366203:A374V|.	A|P	-|-	2|1	0|0	C1orf127|C1orf127	10932437|10932437	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.790000|0.790000	0.44656|0.44656	0.275000|0.275000	0.18698|0.18698	-0.069000|-0.069000	0.12931|0.12931	0.467000|0.467000	0.42956|0.42956	GCC|CCT	.	.	.	none		0.602	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507		A	11009850	G	A	11009850	3	1	264	1	0	0	0	0	1	0	0	0	1996	1203	42	2	1358	2	C1orf127	1	11009850	Missense_Mutation	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10	1053	11009850	238240771	3	16508											
PRDM2	7799	hgsc.bcm.edu	37	chr1	14105779	14105779	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggtttttggaactcatactAatatgagacggcatcagcgt	12	12	10	7	2	2	1	2	1	0	1	2	3	2	2	0	3	3	2	0	3	4	5			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr1:14105779A>G	ENST00000235372.7	+	8	2345	c.1489A>G	c.(1489-1491)Aat>Gat	p.N497D	PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000343137.4_Missense_Mutation_p.N296D|PRDM2_ENST00000311066.5_Missense_Mutation_p.N497D|PRDM2_ENST00000413440.1_Missense_Mutation_p.N296D|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000503842.1_Intron	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	497					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)		AACTCATACTAATATGAGACG	0.438																																					p.N497D		Atlas-SNP	.											.	PRDM2	147	.	0			c.A1489G						PASS	.						40	38	39					1																	14105779		2203	4300	6503	SO:0001583	missense	7799	exon8			CATACTAATATGA	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.1489A>G	chr1.hg19:g.14105779A>G	ENSP00000235372:p.Asn497Asp	273.0	0.0	.		299.0	12.0	.	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Missense_Mutation	SNP	ENST00000235372.7	hg19	CCDS150.1	.	.	.	.	.	.	.	.	.	.	A	15.30	2.791949	0.50102	.	.	ENSG00000116731	ENST00000235372;ENST00000311066;ENST00000400800;ENST00000413440;ENST00000343137	T;T;T;T	0.75367	-0.93;-0.93;-0.93;-0.93	5.62	5.62	0.85841	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);	0.000000	0.85682	D	0.000000	T	0.80099	0.4561	L	0.32530	0.975	0.53688	D	0.999976	D;D;D;D	0.89917	0.999;1.0;0.989;0.999	D;D;D;D	0.91635	0.998;0.999;0.969;0.997	T	0.81904	-0.0719	10	0.62326	D	0.03	.	14.651	0.68797	1.0:0.0:0.0:0.0	.	497;355;497;497	A8MW16;Q5THJ0;Q13029;Q13029-2	.;.;PRDM2_HUMAN;.	D	497;497;497;296;296	ENSP00000235372:N497D;ENSP00000312352:N497D;ENSP00000411103:N296D;ENSP00000341621:N296D	ENSP00000235372:N497D	N	+	1	0	PRDM2	13978366	1.000000	0.71417	0.065000	0.19835	0.710000	0.40934	8.962000	0.93254	2.129000	0.65627	0.533000	0.62120	AAT	.	.	.	none		0.438	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231		G	14105779	A	G	14105779	3	3	264	1	0	0	0	0	1	0	0	0	12468	362	13	3	1515	3	PRDM2	1	14105779	Missense_Mutation	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	3095929	14105779	235144842	4	16509											
OTUD3	23252	hgsc.bcm.edu	37	chr1	20220906	20220906	+	Missense_Mutation	SNP	T	T	C																															ttttgctggcaatgatgcaaTtgtagcctttgcaagaaatc																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr1:20220906T>C	ENST00000375120.3	+	3	417	c.416T>C	c.(415-417)aTt>aCt	p.I139T	OTUD3_ENST00000466697.1_3'UTR	NM_015207.1	NP_056022.1	Q5T2D3	OTUD3_HUMAN	OTU deubiquitinase 3	139	OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.				protein K11-linked deubiquitination (GO:0035871)|protein K6-linked deubiquitination (GO:0044313)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|kidney(2)|large_intestine(4)|lung(1)|skin(1)	9		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000276)|Lung NSC(340;0.000338)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.12e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000142)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.000408)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		AATGATGCAATTGTAGCCTTT	0.383																																					p.I139T		Atlas-SNP	.											.	OTUD3	25	.	0			c.T416C						PASS	.						158	148	151					1																	20220906		1883	4117	6000	SO:0001583	missense	23252	exon3			ATGCAATTGTAGC	AB007928	CCDS41279.1	1p36.13	2014-02-24	2014-02-24		ENSG00000169914	ENSG00000169914		"OTU domain containing"	29038	protein-coding gene	gene with protein product		611758	"OTU domain containing 3"			9455484, 23827681	Standard	NM_015207		Approved	KIAA0459, DUBA4	uc001bcs.4	Q5T2D3	OTTHUMG00000002696	ENST00000375120.3:c.416T>C	chr1.hg19:g.20220906T>C	ENSP00000364261:p.Ile139Thr	69.0	0.0	.		73.0	35.0	.	NM_015207	O75047	Missense_Mutation	SNP	ENST00000375120.3	hg19	CCDS41279.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.652050	0.88056	.	.	ENSG00000169914	ENST00000375120	T	0.55588	0.51	5.92	5.92	0.95590	Ovarian tumour, otubain (2);	0.000000	0.85682	D	0.000000	T	0.78923	0.4360	M	0.92604	3.325	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.84259	0.0482	10	0.87932	D	0	.	15.1888	0.73025	0.0:0.0:0.0:1.0	.	139	Q5T2D3	OTUD3_HUMAN	T	139	ENSP00000364261:I139T	ENSP00000364261:I139T	I	+	2	0	OTUD3	20093493	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.019000	0.76412	2.263000	0.75096	0.533000	0.62120	ATT	.	.	.	none		0.383	OTUD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007655.1			C	20220906	T	C	20220906	3	2	264	1	0	0	0	0	1	0	0	0	11320	1493	52	3	426	3	OTUD3	1	20220906	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	6115127	20220906	229029715	5	16510	170	2									
OTUD3	23252	hgsc.bcm.edu	37	chr1	20220910	20220910	+	Silent	SNP	A	A	G																															gctggcaatgatgcaattgtAgcctttgcaagaaatcatca																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr1:20220910A>G	ENST00000375120.3	+	3	421	c.420A>G	c.(418-420)gtA>gtG	p.V140V	OTUD3_ENST00000466697.1_3'UTR	NM_015207.1	NP_056022.1	Q5T2D3	OTUD3_HUMAN	OTU deubiquitinase 3	140	OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.				protein K11-linked deubiquitination (GO:0035871)|protein K6-linked deubiquitination (GO:0044313)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|kidney(2)|large_intestine(4)|lung(1)|skin(1)	9		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000276)|Lung NSC(340;0.000338)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.12e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000142)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.000408)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		ATGCAATTGTAGCCTTTGCAA	0.378																																					p.V140V		Atlas-SNP	.											.	OTUD3	25	.	0			c.A420G						PASS	.						156	148	150					1																	20220910		1879	4117	5996	SO:0001819	synonymous_variant	23252	exon3			AATTGTAGCCTTT	AB007928	CCDS41279.1	1p36.13	2014-02-24	2014-02-24		ENSG00000169914	ENSG00000169914		"OTU domain containing"	29038	protein-coding gene	gene with protein product		611758	"OTU domain containing 3"			9455484, 23827681	Standard	NM_015207		Approved	KIAA0459, DUBA4	uc001bcs.4	Q5T2D3	OTTHUMG00000002696	ENST00000375120.3:c.420A>G	chr1.hg19:g.20220910A>G		72.0	0.0	.		75.0	37.0	.	NM_015207	O75047	Silent	SNP	ENST00000375120.3	hg19	CCDS41279.1																																																																																			.	.	.	none		0.378	OTUD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007655.1			G	20220910	A	G	20220910	2	3	264	1	0	0	0	0	0	0	0	1	11320	407	15	3		3	OTUD3	1	20220910	Silent	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	4	20220910	229029711	6	16511	170	2									
USP48	84196	hgsc.bcm.edu	37	chr1	22041910	22041910	+	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	cacagaatatcttcattaaaAtttaattcctcctcttcttt	12	18	1	10	0	4	1	1	0	3	1	6	1	6	1	2	0	0	0	2	0	5	8			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr1:22041910A>T	ENST00000308271.9	-	15	2583	c.1935T>A	c.(1933-1935)aaT>aaA	p.N645K	USP48_ENST00000529637.1_Missense_Mutation_p.N644K|USP48_ENST00000374732.3_Missense_Mutation_p.N183K|USP48_ENST00000400301.1_Missense_Mutation_p.N645K	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	645	DUSP 2. {ECO:0000255|PROSITE- ProRule:PRU00613}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		CTTCATTAAAATTTAATTCCT	0.303																																					p.N645K		Atlas-SNP	.											.	USP48	91	.	0			c.T1935A						PASS	.						71	74	73					1																	22041910		2202	4298	6500	SO:0001583	missense	84196	exon15			ATTAAAATTTAAT	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.1935T>A	chr1.hg19:g.22041910A>T	ENSP00000309262:p.Asn645Lys	502.0	1.0	.		512.0	200.0	.	NM_032236	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000308271.9	hg19	CCDS30623.1	.	.	.	.	.	.	.	.	.	.	A	13.67	2.307579	0.40795	.	.	ENSG00000090686	ENST00000400301;ENST00000308271;ENST00000374732;ENST00000529637	T;T;T;T	0.40756	1.02;1.02;1.02;1.17	5.17	4.04	0.47022	Peptidase C19, ubiquitin-specific peptidase, DUSP domain (1);	0.360545	0.33161	N	0.005218	T	0.29783	0.0744	L	0.53249	1.67	0.42183	D	0.991695	B;B;B;B;B	0.23249	0.059;0.006;0.01;0.006;0.082	B;B;B;B;B	0.21708	0.02;0.01;0.022;0.01;0.036	T	0.13202	-1.0518	10	0.02654	T	1	.	6.0987	0.20035	0.7524:0.1629:0.0847:0.0	.	644;645;645;645;183	B7ZKS7;B7ZKS3;Q86UV5-2;Q86UV5;Q86UV5-5	.;.;.;UBP48_HUMAN;.	K	645;645;183;644	ENSP00000383157:N645K;ENSP00000309262:N645K;ENSP00000363864:N183K;ENSP00000431949:N644K	ENSP00000309262:N645K	N	-	3	2	USP48	21914497	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.387000	0.34430	0.820000	0.34516	0.533000	0.62120	AAT	.	.	.	none		0.303	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236		T	22041910	A	T	22041910	3	4	264	1	0	0	0	0	1	0	0	0	17091	98	4	5	1224	5	USP48	1	22041910	Missense_Mutation	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	1821000	22041910	227208711	7	16512											
KIAA0467	23334	hgsc.bcm.edu	37	chr1	43906920	43906920	+	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	ggggatttgggttcccccaaAacaactgatgacattgtcct	10	11	10	10	0	0	2	0	2	0	0	2	3	2	3	3	3	2	1	3	3	3	3			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr1:43906920A>T	ENST00000562955.1	+	52	7209	c.7209A>T	c.(7207-7209)aaA>aaT	p.K2403N	SZT2_ENST00000372442.1_Missense_Mutation_p.K1561N	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	2460					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						GTTCCCCCAAAACAACTGATG	0.572																																					p.K2403N		Atlas-SNP	.											.	SZT2	383	.	0			c.A7209T						PASS	.						119	129	125					1																	43906920		2203	4300	6503	SO:0001583	missense	23334	exon52			CCCCAAAACAACT	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.7209A>T	chr1.hg19:g.43906920A>T	ENSP00000457168:p.Lys2403Asn	114.0	0.0	.		112.0	54.0	.	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Missense_Mutation	SNP	ENST00000562955.1	hg19	CCDS30694.2	.	.	.	.	.	.	.	.	.	.	A	18.79	3.698115	0.68386	.	.	ENSG00000198198	ENST00000372442	.	.	.	5.41	4.28	0.50868	.	0.106321	0.64402	D	0.000004	T	0.52058	0.1711	L	0.46157	1.445	0.27018	N	0.964522	D	0.89917	1.0	D	0.91635	0.999	T	0.42430	-0.9452	9	0.62326	D	0.03	.	6.8705	0.24119	0.8287:0.0:0.1713:0.0	.	2403	Q5T011-5	.	N	1561	.	ENSP00000361519:K1561N	K	+	3	2	SZT2	43679507	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.179000	0.42528	2.186000	0.69663	0.482000	0.46254	AAA	.	.	.	none		0.572	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		T	43906920	A	T	43906920	3	4	264	1	0	0	0	0	1	0	0	0	8185	11	1	5	4825	5	KIAA0467	1	43906920	Missense_Mutation	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	21865010	43906920	205343701	8	16513											
RPRD2	23248	hgsc.bcm.edu	37	chr1	150337371	150337371	+	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	accacagtactatcgtctatCattggatgaagtggctccgg	10	11	10	10	2	2	1	1	1	1	0	4	2	3	2	2	3	1	2	2	3	4	4			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr1:150337371C>A	ENST00000369068.4	+	1	185	c.181C>A	c.(181-183)Cat>Aat	p.H61N	RPRD2_ENST00000539519.1_Missense_Mutation_p.H61N|RPRD2_ENST00000492220.1_Intron|RPRD2_ENST00000369067.3_Missense_Mutation_p.H61N|RPRD2_ENST00000401000.4_Missense_Mutation_p.H61N	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	61	CID. {ECO:0000255|PROSITE- ProRule:PRU00724}.					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						TATCGTCTATCATTGGATGAA	0.483																																					p.H61N		Atlas-SNP	.											.	RPRD2	189	.	0			c.C181A						PASS	.						111	108	109					1																	150337371		1960	4155	6115	SO:0001583	missense	23248	exon1			GTCTATCATTGGA	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.181C>A	chr1.hg19:g.150337371C>A	ENSP00000358064:p.His61Asn	129.0	0.0	.		136.0	46.0	.	NM_015203	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Missense_Mutation	SNP	ENST00000369068.4	hg19	CCDS44216.1	.	.	.	.	.	.	.	.	.	.	C	17.41	3.383325	0.61845	.	.	ENSG00000163125	ENST00000401000;ENST00000539519;ENST00000369067;ENST00000369068	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	4.42	4.42	0.53409	ENTH/VHS (2);RNA polymerase II, large subunit, CTD (2);	0.175243	0.50627	D	0.000104	T	0.37461	0.1004	L	0.44542	1.39	0.43095	D	0.994776	D;D;D	0.56968	0.967;0.967;0.978	P;P;P	0.53649	0.637;0.537;0.731	T	0.04900	-1.0919	10	0.28530	T	0.3	-9.375	17.1984	0.86900	0.0:1.0:0.0:0.0	.	61;61;61	B4E2Q6;Q5VT52;Q5VT52-3	.;RPRD2_HUMAN;.	N	61	ENSP00000383785:H61N;ENSP00000445482:H61N;ENSP00000358063:H61N;ENSP00000358064:H61N	ENSP00000358063:H61N	H	+	1	0	RPRD2	148603995	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	2.209000	0.42806	2.449000	0.82847	0.655000	0.94253	CAT	.	.	.	none		0.483	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203		A	150337371	C	A	150337371	3	1	264	1	0	0	0	0	1	0	0	0	13630	826	29	4	183	4	RPRD2	1	150337371	Missense_Mutation	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	106430451	150337371	98913250	9	16514											
CACNA1E	777	hgsc.bcm.edu	37	chr1	181765855	181765855	+	Missense_Mutation	SNP	A	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	cagggagcggggacgatcaaAagagcgaaagcatcttctct	13	6	13	9	3	3	1	1	0	2	1	4	5	3	3	0	3	3	1	0	3	3	1			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr1:181765855A>C	ENST00000367573.2	+	47	6260	c.6260A>C	c.(6259-6261)aAa>aCa	p.K2087T	CACNA1E_ENST00000367567.4_Missense_Mutation_p.K1651T|CACNA1E_ENST00000357570.5_Missense_Mutation_p.K2038T|CACNA1E_ENST00000526775.1_Missense_Mutation_p.K2025T|CACNA1E_ENST00000367570.1_Missense_Mutation_p.K2044T|CACNA1E_ENST00000360108.3_Missense_Mutation_p.K2068T|CACNA1E_ENST00000358338.5_Missense_Mutation_p.K1976T	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	2087					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						GGACGATCAAAAGAGCGAAAG	0.572																																					p.K2087T		Atlas-SNP	.											.	CACNA1E	778	.	0			c.A6260C						PASS	.						48	51	50					1																	181765855		1979	4168	6147	SO:0001583	missense	777	exon47			GATCAAAAGAGCG	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.6260A>C	chr1.hg19:g.181765855A>C	ENSP00000356545:p.Lys2087Thr	115.0	0.0	.		128.0	47.0	.	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	hg19	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.447471	0.84101	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.97328	-4.25;-4.25;-4.17;-4.24;-4.34;-4.17;-4.17	5.91	5.91	0.95273	.	0.676128	0.14977	N	0.287490	D	0.97666	0.9235	L	0.42245	1.32	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.937;0.996	D	0.97817	1.0254	10	0.72032	D	0.01	.	16.0098	0.80391	1.0:0.0:0.0:0.0	.	2025;2044	Q15878-2;Q15878-3	.;.	T	2044;2025;2038;1976;1651;2068;2087	ENSP00000356542:K2044T;ENSP00000434814:K2025T;ENSP00000350183:K2038T;ENSP00000351101:K1976T;ENSP00000356539:K1651T;ENSP00000353222:K2068T;ENSP00000356545:K2087T	ENSP00000350183:K2038T	K	+	2	0	CACNA1E	180032478	1.000000	0.71417	0.994000	0.49952	0.984000	0.73092	6.736000	0.74811	2.254000	0.74563	0.533000	0.62120	AAA	.	.	.	none		0.572	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		C	181765855	A	C	181765855	3	2	264	1	0	0	0	0	1	0	0	0	2544	14	1	5	6313	5	CACNA1E	1	181765855	Missense_Mutation	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	31428484	181765855	67484766	10	16515											
USH2A	7399	hgsc.bcm.edu	37	chr1	215853630	215853630	+	Missense_Mutation	SNP	A	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	tcagagtccaagggcttaaaAtttctcctgcatggtttgca	10	13	9	9	0	2	1	1	0	1	1	4	1	3	1	2	2	2	4	2	2	3	3			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr1:215853630A>C	ENST00000307340.3	-	62	12541	c.12155T>G	c.(12154-12156)aTt>aGt	p.I4052S	USH2A_ENST00000366943.2_Missense_Mutation_p.I4052S	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	4052	Fibronectin type-III 25. {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)		AGGGCTTAAAATTTCTCCTGC	0.438										HNSCC(13;0.011)																											p.I4052S		Atlas-SNP	.											.	USH2A	1168	.	0			c.T12155G						PASS	.						123	126	125					1																	215853630		2203	4300	6503	SO:0001583	missense	7399	exon62			CTTAAAATTTCTC	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.12155T>G	chr1.hg19:g.215853630A>C	ENSP00000305941:p.Ile4052Ser	129.0	0.0	.		98.0	46.0	.	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	A	15.16	2.751331	0.49257	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.44083	0.93;0.93	5.25	5.25	0.73442	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.360514	0.19602	N	0.110361	T	0.16214	0.0390	N	0.02345	-0.59	0.25312	N	0.989196	B	0.27625	0.183	B	0.25614	0.062	T	0.18713	-1.0328	10	0.07990	T	0.79	.	9.6563	0.39928	0.9223:0.0:0.0777:0.0	.	4052	O75445	USH2A_HUMAN	S	4052	ENSP00000305941:I4052S;ENSP00000355910:I4052S	ENSP00000305941:I4052S	I	-	2	0	USH2A	213920253	1.000000	0.71417	0.994000	0.49952	0.983000	0.72400	4.018000	0.57174	1.987000	0.57996	0.528000	0.53228	ATT	.	.	.	none		0.438	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		C	215853630	A	C	215853630	3	2	264	1	0	0	0	0	1	0	0	0	17048	101	4	5	3497	5	USH2A	1	215853630	Missense_Mutation	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	34087775	215853630	33396991	11	16516											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228525744	228525744	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agtatgtggaggtcctggatGcagcccacccactgcgctgg	7	8	14	12	1	0	0	0	0	0	0	1	2	1	2	3	4	3	3	3	4	1	1			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr1:228525744G>A	ENST00000422127.1	+	67	16944	c.16900G>A	c.(16900-16902)Gca>Aca	p.A5634T	OBSCN_ENST00000570156.2_Missense_Mutation_p.A6591T|OBSCN_ENST00000366709.4_Missense_Mutation_p.A2753T|OBSCN_ENST00000366707.4_Missense_Mutation_p.A3268T|OBSCN_ENST00000284548.11_Missense_Mutation_p.A5634T	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5634	SH3.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GGTCCTGGATGCAGCCCACCC	0.632																																					p.A6591T		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G19771A						PASS	.						35	36	36					1																	228525744		2182	4279	6461	SO:0001583	missense	84033	exon78			CTGGATGCAGCCC	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.16900G>A	chr1.hg19:g.228525744G>A	ENSP00000409493:p.Ala5634Thr	53.0	0.0	.		58.0	16.0	.	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.56|15.56	2.869835|2.869835	0.51588|0.51588	.|.	.|.	ENSG00000154358|ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709|ENST00000441106	T;T;T;T|.	0.30981|.	1.51;1.51;1.51;1.51|.	4.35|4.35	1.93|1.93	0.25924|0.25924	Src homology-3 domain (2);|.	0.094130|.	0.45126|.	D|.	0.000387|.	T|T	0.27697|0.27697	0.0681|0.0681	N|N	0.14661|0.14661	0.345|0.345	0.29310|0.29310	N|N	0.868084|0.868084	B;B|.	0.29988|.	0.172;0.264|.	B;B|.	0.28011|.	0.039;0.085|.	T|T	0.25047|0.25047	-1.0143|-1.0143	10|5	0.54805|.	T|.	0.06|.	.|.	11.1252|11.1252	0.48315|0.48315	0.0:0.0:0.3104:0.6896|0.0:0.0:0.3104:0.6896	.|.	5634;5634|.	Q5VST9;Q5VST9-3|.	OBSCN_HUMAN;.|.	T|Y	5634;5634;3268;2753|249	ENSP00000284548:A5634T;ENSP00000409493:A5634T;ENSP00000355668:A3268T;ENSP00000355670:A2753T|.	ENSP00000284548:A5634T|.	A|C	+|+	1|2	0|0	OBSCN|OBSCN	226592367|226592367	1.000000|1.000000	0.71417|0.71417	0.267000|0.267000	0.24556|0.24556	0.522000|0.522000	0.34438|0.34438	4.088000|4.088000	0.57678|0.57678	0.292000|0.292000	0.22492|0.22492	-0.500000|-0.500000	0.04577|0.04577	GCA|TGC	.	.	.	none		0.632	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228525744	G	A	228525744	3	1	264	1	0	0	0	0	1	0	0	0	10819	1319	46	2	17162	2	OBSCN	1	228525744	Missense_Mutation	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10	12672114	228525744	20724877	12	16517											
NUP133	55746	hgsc.bcm.edu	37	chr1	229606482	229606482	+	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	cagcttttcggcatgctcacAgagcaacagtcgagtggcca	10	8	11	12	2	1	1	1	0	0	1	3	2	1	1	1	2	4	4	1	2	1	2			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr1:229606482A>T	ENST00000261396.3	-	15	2012	c.1921T>A	c.(1921-1923)Tgt>Agt	p.C641S	NUP133_ENST00000537506.1_Missense_Mutation_p.C625S	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	641					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)				GCATGCTCACAGAGCAACAGT	0.478																																					p.C641S		Atlas-SNP	.											.	NUP133	111	.	0			c.T1921A						PASS	.						104	94	97					1																	229606482		2203	4300	6503	SO:0001583	missense	55746	exon15			GCTCACAGAGCAA		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.1921T>A	chr1.hg19:g.229606482A>T	ENSP00000261396:p.Cys641Ser	171.0	0.0	.		138.0	65.0	.	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Missense_Mutation	SNP	ENST00000261396.3	hg19	CCDS1579.1	.	.	.	.	.	.	.	.	.	.	A	14.30	2.495539	0.44352	.	.	ENSG00000069248	ENST00000366681;ENST00000261396;ENST00000366679;ENST00000537506	T;T;T	0.23754	1.89;1.89;1.9	5.56	5.56	0.83823	Nucleoporin, Nup133/Nup155-like, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.29850	0.0746	M	0.73598	2.24	0.80722	D	1	B	0.14438	0.01	B	0.17433	0.018	T	0.06826	-1.0805	10	0.27785	T	0.31	-21.0231	11.7266	0.51712	0.8679:0.0:0.0:0.132	.	641	Q8WUM0	NU133_HUMAN	S	641;641;641;625	ENSP00000261396:C641S;ENSP00000355640:C641S;ENSP00000443496:C625S	ENSP00000261396:C641S	C	-	1	0	NUP133	227673105	1.000000	0.71417	0.999000	0.59377	0.922000	0.55478	5.911000	0.69939	2.240000	0.73641	0.533000	0.62120	TGT	.	.	.	none		0.478	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230		T	229606482	A	T	229606482	3	4	264	1	0	0	0	0	1	0	0	0	10761	188	7	5	1597	5	NUP133	1	229606482	Missense_Mutation	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	1080738	229606482	19644139	13	16518											
OR2T2	401992	hgsc.bcm.edu	37	chr1	248616710	248616734	+	Frame_Shift_Del	DEL	CGTGCTGATGCTGCTTATCCCTCTA	CGTGCTGATGCTGCTTATCCCTCTA	-																															accctgatgtatgcctgctgCgtgctgatgctgcttatccc																								rs199823862|rs201716034|rs376194718		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	CGTGCTGATGCTGCTTATCCCTCTA	CGTGCTGATGCTGCTTATCCCTCTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr1:248616710_248616734delCGTGCTGATGCTGCTTATCCCTCTA	ENST00000342927.3	+	1	634_658	c.612_636delCGTGCTGATGCTGCTTATCCCTCTA	c.(610-636)tgcgtgctgatgctgcttatccctctafs	p.CVLMLLIPL204fs		NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T, member 2	204						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)			ATGCCTGCTGCGTGCTGATGCTGCTTATCCCTCTATCTGTCATCT	0.529																																					p.204_212del		Pindel	.											.	OR2T2	73	.	0			c.611_635del						PASS	.																																			SO:0001589	frameshift_variant	401992	exon1			.	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.612_636delCGTGCTGATGCTGCTTATCCCTCTA	chr1.hg19:g.248616710_248616734delCGTGCTGATGCTGCTTATCCCTCTA	ENSP00000343062:p.Cys204fs	261.0	0.0	.		218.0	21.0	0.096	NM_001004136	B2RNM1|B9EH01	Frame_Shift_Del	DEL	ENST00000342927.3	hg19	CCDS31116.1																																																																																			.	.	.	alt		0.529	OR2T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097421.1	NM_001004136		-	248616734	CGTGCTGATGCTGCTTATCCCTCTA	-	248616710	7	5	264	1	0	1	0	1	0	0	0	0	11027	776	27	0	614	0	OR2T2	1	248616710	Frame_Shift_Del	DEL	CGTGCTGATGCTGCTTATCCCTCTA	TCGA-UZ-A9PS-01A-11D-A42J-10	19010228	248616710	633911	14	16519											
SH3YL1	26751	hgsc.bcm.edu	37	chr2	253096	253096	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttgcttctgatttcaaattGgaaggtatagggttattcac	10	17	9	5	0	3	1	2	1	1	0	3	2	3	2	0	3	1	3	0	3	5	8			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr2:253096G>A	ENST00000405430.1	-	4	397	c.21C>T	c.(19-21)tcC>tcT	p.S7S	SH3YL1_ENST00000468321.1_5'UTR|SH3YL1_ENST00000356150.5_Silent_p.S7S|SH3YL1_ENST00000402632.1_Silent_p.S7S|SH3YL1_ENST00000403657.1_5'UTR|SH3YL1_ENST00000403712.2_Silent_p.S7S|SH3YL1_ENST00000403658.1_5'UTR			Q96HL8	SH3Y1_HUMAN	SH3 and SYLF domain containing 1	7					phosphatidylinositol biosynthetic process (GO:0006661)|regulation of ruffle assembly (GO:1900027)	ruffle membrane (GO:0032587)	phosphatase binding (GO:0019902)|phosphatidylinositol binding (GO:0035091)	p.S7S(1)		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)		ATTTCAAATTGGAAGGTATAG	0.289																																					p.S7S		Atlas-SNP	.											SH3YL1_ENST00000405430,NS,carcinoma,0,2	SH3YL1	49	.	1	Substitution - coding silent(1)	endometrium(1)	c.C21T						PASS	.						187	150	161					2																	253096		692	1591	2283	SO:0001819	synonymous_variant	26751	exon2			CAAATTGGAAGGT		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.21C>T	chr2.hg19:g.253096G>A		51.0	0.0	.		64.0	24.0	.	NM_001159597	A8K8E7|B7WNJ4|B7WPL6|Q8NEL2|Q9H5X4|Q9Y3V5	Silent	SNP	ENST00000405430.1	hg19																																																																																				.	.	.	none		0.289	SH3YL1-003	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322352.1	NM_015677		A	253096	G	A	253096	2	1	264	1	0	0	0	0	0	0	0	1	14276	1335	47	2		2	SH3YL1	2	253096	Silent	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10		253096	242946277	15	16520											
GPR113	165082	hgsc.bcm.edu	37	chr2	26537464	26537464	+	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	acaggttccacttgaagcccTgggcctcgaagcagctcatg	9	8	11	13	1	1	1	1	1	0	0	3	2	2	1	3	2	3	3	3	2	2	2	rs148640513		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr2:26537464T>A	ENST00000311519.1	-	7	949	c.950A>T	c.(949-951)cAg>cTg	p.Q317L	GPR113_ENST00000541401.1_Intron|GPR113_ENST00000333478.6_Missense_Mutation_p.Q118L|GPR113_ENST00000421160.2_Missense_Mutation_p.Q248L|GPR113_ENST00000459892.1_Intron	NM_001145168.1	NP_001138640.1	Q8IZF5	GP113_HUMAN	G protein-coupled receptor 113	317					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)					CTTGAAGCCCTGGGCCTCGAA	0.592																																					p.Q317L		Atlas-SNP	.											.	GPR113	134	.	0			c.A950T						PASS	.						117	92	101					2																	26537464		2203	4300	6503	SO:0001583	missense	165082	exon7			AAGCCCTGGGCCT	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.950A>T	chr2.hg19:g.26537464T>A	ENSP00000307831:p.Gln317Leu	160.0	0.0	.		167.0	70.0	.	NM_001145168	B4DF15|E9PEV1|Q53TA5|Q6UXT7|Q6UXX3|Q86SL7|Q8IXD8|Q8TDT3	Missense_Mutation	SNP	ENST00000311519.1	hg19	CCDS46239.1	.	.	.	.	.	.	.	.	.	.	T	15.86	2.957123	0.53293	.	.	ENSG00000173567	ENST00000333478;ENST00000421160;ENST00000311519	T;T;T	0.28895	1.59;3.13;3.13	5.43	1.65	0.23941	.	.	.	.	.	T	0.26448	0.0646	L	0.58101	1.795	0.80722	D	1	B;P;B	0.42248	0.138;0.774;0.038	B;B;B	0.39299	0.131;0.296;0.024	T	0.02909	-1.1095	8	.	.	.	-17.5326	7.2931	0.26376	0.0:0.3383:0.0:0.6617	.	248;118;317	E9PEV1;Q8IZF5-2;Q8IZF5	.;.;GP113_HUMAN	L	118;248;317	ENSP00000327396:Q118L;ENSP00000388537:Q248L;ENSP00000307831:Q317L	.	Q	-	2	0	GPR113	26390968	0.995000	0.38212	1.000000	0.80357	0.816000	0.46133	-0.005000	0.12855	0.359000	0.24239	0.459000	0.35465	CAG	.	T|1.000;C|0.000	.	alt		0.592	GPR113-004	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316892.1	NM_153835		A	26537464	T	A	26537464	3	1	264	1	0	0	0	0	1	0	0	0	6637	1580	55	5	2406	5	GPR113	2	26537464	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	26284368	26537464	216661909	16	16521											
C2orf71	388939	hgsc.bcm.edu	37	chr2	29296881	29296881	+	Missense_Mutation	SNP	A	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	catatctttccttttgcctgAagcaggatctcccatgagct	8	14	7	12	0	2	2	0	2	2	0	4	3	3	3	3	1	3	2	3	1	2	4			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr2:29296881A>C	ENST00000331664.5	-	1	246	c.247T>G	c.(247-249)Tca>Gca	p.S83A		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	83					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						CTTTTGCCTGAAGCAGGATCT	0.512																																					p.S83A		Atlas-SNP	.											.	C2orf71	146	.	0			c.T247G						PASS	.						192	177	182					2																	29296881		1924	4149	6073	SO:0001583	missense	388939	exon1			TGCCTGAAGCAGG		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.247T>G	chr2.hg19:g.29296881A>C	ENSP00000332809:p.Ser83Ala	137.0	0.0	.		158.0	56.0	.	NM_001029883		Missense_Mutation	SNP	ENST00000331664.5	hg19	CCDS42669.1	.	.	.	.	.	.	.	.	.	.	A	3.559	-0.090111	0.07053	.	.	ENSG00000179270	ENST00000331664	T	0.19669	2.13	3.98	-3.53	0.04667	.	0.256680	0.27509	N	0.019056	T	0.07234	0.0183	N	0.05383	-0.06	0.09310	N	1	B	0.11235	0.004	B	0.16289	0.015	T	0.15780	-1.0425	10	0.33141	T	0.24	-2.444	4.4009	0.11386	0.4215:0.399:0.0761:0.1033	.	83	A6NGG8	CB071_HUMAN	A	83	ENSP00000332809:S83A	ENSP00000332809:S83A	S	-	1	0	C2orf71	29150385	0.006000	0.16342	0.039000	0.18376	0.862000	0.49288	-0.319000	0.08039	-0.669000	0.05289	0.459000	0.35465	TCA	.	.	.	none		0.512	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		C	29296881	A	C	29296881	3	2	264	1	0	0	0	0	1	0	0	0	2193	246	9	5	3627	5	C2orf71	2	29296881	Missense_Mutation	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	2759417	29296881	213902492	17	16522											
PCBP1	5093	hgsc.bcm.edu	37	chr2	70315518	70315518	+	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	cccatgccacccatgacctgGagggaccacctctagatgcc	9	6	9	17	0	1	2	0	1	1	1	1	4	1	4	7	2	2	0	7	2	1	1			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr2:70315518G>T	ENST00000303577.5	+	1	934	c.643G>T	c.(643-645)Gag>Tag	p.E215*	PCBP1-AS1_ENST00000411429.1_RNA|PCBP1-AS1_ENST00000415742.1_RNA|PCBP1-AS1_ENST00000457770.1_RNA|PCBP1-AS1_ENST00000439670.2_RNA|PCBP1-AS1_ENST00000415060.2_RNA|PCBP1-AS1_ENST00000601396.1_RNA|PCBP1-AS1_ENST00000415222.1_RNA|PCBP1-AS1_ENST00000439892.1_RNA|PCBP1-AS1_ENST00000418308.1_RNA|AC016700.2_ENST00000455541.1_lincRNA|PCBP1-AS1_ENST00000419963.1_RNA|PCBP1-AS1_ENST00000456161.1_RNA|PCBP1-AS1_ENST00000423402.1_RNA|PCBP1-AS1_ENST00000434781.1_RNA|PCBP1-AS1_ENST00000425601.1_RNA|PCBP1-AS1_ENST00000609075.1_RNA|PCBP1-AS1_ENST00000444410.1_RNA|PCBP1-AS1_ENST00000596573.1_RNA|PCBP1-AS1_ENST00000418564.1_RNA|PCBP1-AS1_ENST00000421843.1_RNA|PCBP1-AS1_ENST00000452431.1_RNA|PCBP1-AS1_ENST00000458698.2_RNA|PCBP1-AS1_ENST00000429599.2_RNA|PCBP1-AS1_ENST00000432604.1_RNA|PCBP1-AS1_ENST00000416395.1_RNA|PCBP1-AS1_ENST00000413436.1_RNA|PCBP1-AS1_ENST00000413069.1_RNA|PCBP1-AS1_ENST00000596665.1_RNA|PCBP1-AS1_ENST00000610168.1_RNA|PCBP1-AS1_ENST00000420309.1_RNA|PCBP1-AS1_ENST00000413791.1_RNA|PCBP1-AS1_ENST00000599673.1_RNA|PCBP1-AS1_ENST00000437456.1_RNA|PCBP1-AS1_ENST00000435880.2_RNA|PCBP1-AS1_ENST00000596028.1_RNA|PCBP1-AS1_ENST00000595459.1_RNA|PCBP1-AS1_ENST00000425333.1_RNA|PCBP1-AS1_ENST00000457076.1_RNA|PCBP1-AS1_ENST00000458686.1_RNA|PCBP1-AS1_ENST00000366234.3_RNA|PCBP1-AS1_ENST00000444320.1_RNA|PCBP1-AS1_ENST00000442040.1_RNA|PCBP1-AS1_ENST00000449178.1_RNA|PCBP1-AS1_ENST00000422515.1_RNA|PCBP1-AS1_ENST00000421255.1_RNA|PCBP1-AS1_ENST00000594548.1_RNA|PCBP1-AS1_ENST00000416068.1_RNA|PCBP1-AS1_ENST00000437019.1_RNA	NM_006196.3	NP_006187.2	Q15365	PCBP1_HUMAN	poly(rC) binding protein 1	215					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.E215Q(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|skin(1)	12						CCATGACCTGGAGGGACCACC	0.612																																					p.E215X	Colon(85;1146 1307 3484 18706 25380)	Atlas-SNP	.											PCBP1,NS,carcinoma,0,1	PCBP1	28	.	1	Substitution - Missense(1)	endometrium(1)	c.G643T						PASS	.						36	37	36					2																	70315518		2203	4300	6503	SO:0001587	stop_gained	5093	exon1			GACCTGGAGGGAC		CCDS1898.1	2p13-p12	2013-07-16	2001-11-28		ENSG00000169564	ENSG00000169564			8647	protein-coding gene	gene with protein product	"heterogeneous nuclear ribonucleoprotein E1"	601209	"poly(rC)-binding protein 1"			8833161	Standard	NM_006196		Approved	HNRPE1, hnRNP-E1, HNRPX, hnRNP-X	uc002sgf.3	Q15365	OTTHUMG00000129645	ENST00000303577.5:c.643G>T	chr2.hg19:g.70315518G>T	ENSP00000305556:p.Glu215*	101.0	0.0	.		120.0	57.0	.	NM_006196	Q13157|Q14975	Nonsense_Mutation	SNP	ENST00000303577.5	hg19	CCDS1898.1	.	.	.	.	.	.	.	.	.	.	G	38	6.876858	0.97904	.	.	ENSG00000169564	ENST00000303577	.	.	.	4.82	4.82	0.62117	.	0.453218	0.16777	N	0.199971	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	.	13.6585	0.62352	0.0:0.0:1.0:0.0	.	.	.	.	X	215	.	ENSP00000305556:E215X	E	+	1	0	PCBP1	70169022	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.492000	0.53259	2.696000	0.92011	0.650000	0.86243	GAG	.	.	.	none		0.612	PCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251844.1	NM_006196		T	70315518	G	T	70315518	4	4	264	1	0	0	0	0	0	1	0	0	11507	1175	41	4	645	4	PCBP1	2	70315518	Nonsense_Mutation	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10	41018637	70315518	172883855	18	16523											
R3HDM1	23518	hgsc.bcm.edu	37	chr2	136396355	136396355	+	Frame_Shift_Del	DEL	T	T	-																															cccagcagaggcgccagataTttaggtattggaagcatgtt																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr2:136396355delT	ENST00000264160.4	+	13	1358	c.988delT	c.(988-990)tttfs	p.F330fs	R3HDM1_ENST00000409606.1_Frame_Shift_Del_p.F330fs|R3HDM1_ENST00000409478.1_Frame_Shift_Del_p.F286fs|R3HDM1_ENST00000443537.2_3'UTR|R3HDM1_ENST00000329971.3_Frame_Shift_Del_p.F286fs|R3HDM1_ENST00000410054.1_Frame_Shift_Del_p.F274fs	NM_001282798.1|NM_015361.2	NP_001269727.1|NP_056176.2	Q15032	R3HD1_HUMAN	R3H domain containing 1	330							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)		GCGCCAGATATTTAGGTATTG	0.343																																					p.I329fs		Atlas-Indel,Pindel	.											.	R3HDM1	84	.	0			c.987delA						PASS	.						72	77	76					2																	136396355		2203	4299	6502	SO:0001589	frameshift_variant	23518	exon13			.	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.988delT	chr2.hg19:g.136396355delT	ENSP00000264160:p.Phe330fs	89.0	0.0	0		133.0	52.0	0.390977	NM_015361	A8K1V0|B3KXQ9|E9PBB4|E9PG42|G5E9G8|Q8IW32	Frame_Shift_Del	DEL	ENST00000264160.4	hg19	CCDS2177.1																																																																																			.	.	.	none		0.343	R3HDM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254659.1	NM_015361		-	136396355	T	-	136396355	7	5	264	1	0	1	0	1	0	0	0	0	12900	1493	52	0	1030	0	R3HDM1	2	136396355	Frame_Shift_Del	DEL	T	TCGA-UZ-A9PS-01A-11D-A42J-10	66080837	136396355	106803018	19	16524											
SESTD1	91404	hgsc.bcm.edu	37	chr2	179997038	179997038	+	Missense_Mutation	SNP	T	T	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	aaaagcctctcacactgtgcTggctctcaatctcttcgtgt	8	13	7	13	1	3	0	2	0	3	0	7	0	3	0	1	1	2	2	1	1	3	1			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr2:179997038T>G	ENST00000428443.3	-	10	1281	c.965A>C	c.(964-966)cAg>cCg	p.Q322P		NM_178123.4	NP_835224.3	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	322							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)			CACACTGTGCTGGCTCTCAAT	0.478																																					p.Q322P		Atlas-SNP	.											.	SESTD1	66	.	0			c.A965C						PASS	.						276	296	289					2																	179997038		2203	4300	6503	SO:0001583	missense	91404	exon10			CTGTGCTGGCTCT	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.965A>C	chr2.hg19:g.179997038T>G	ENSP00000415332:p.Gln322Pro	65.0	0.0	.		61.0	23.0	.	NM_178123	Q53R38|Q53SP3|Q5GM69|Q8N6M1|Q96LQ2	Missense_Mutation	SNP	ENST00000428443.3	hg19	CCDS33338.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.399544	0.83120	.	.	ENSG00000187231	ENST00000428443	T	0.35048	1.33	6.0	6.0	0.97389	.	0.000000	0.85682	D	0.000000	T	0.37128	0.0992	N	0.14661	0.345	0.80722	D	1	D	0.53885	0.963	P	0.55785	0.784	T	0.15925	-1.0420	9	.	.	.	-13.1246	16.5156	0.84299	0.0:0.0:0.0:1.0	.	322	Q86VW0	SESD1_HUMAN	P	322	ENSP00000415332:Q322P	.	Q	-	2	0	SESTD1	179705283	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.102000	0.71486	2.291000	0.77112	0.519000	0.50382	CAG	.	.	.	none		0.478	SESTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335916.2	NM_178123		G	179997038	T	G	179997038	3	3	264	1	0	0	0	0	1	0	0	0	14140	1580	55	5	1161	5	SESTD1	2	179997038	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	43600683	179997038	63202335	20	16525											
CERKL	375298	hgsc.bcm.edu	37	chr2	182468798	182468798	+	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	tttacatagcaagtcatactTagaatcacctgaaaaaaaaa	20	10	4	7	0	2	2	2	1	0	1	2	2	2	2	1	0	3	1	1	0	10	5			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr2:182468798T>A	ENST00000339098.5	-	2	246	c.247A>T	c.(247-249)Aag>Tag	p.K83*	CERKL_ENST00000410087.3_Nonsense_Mutation_p.K83*|CERKL_ENST00000374970.2_Nonsense_Mutation_p.K83*|CERKL_ENST00000374969.2_Nonsense_Mutation_p.K83*|CERKL_ENST00000479558.1_5'UTR|CERKL_ENST00000409440.3_Nonsense_Mutation_p.K83*			Q49MI3	CERKL_HUMAN	ceramide kinase-like	83					negative regulation of apoptotic process (GO:0043066)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(13)|ovary(3)|skin(3)	32			OV - Ovarian serous cystadenocarcinoma(117;0.088)			AAGTCATACTTAGAATCACCT	0.363																																					p.K83X		Atlas-SNP	.											.	CERKL	138	.	0			c.A247T						PASS	.						37	37	37					2																	182468798		2201	4294	6495	SO:0001587	stop_gained	375298	exon2			CATACTTAGAATC	BC020465	CCDS33340.1, CCDS33341.1, CCDS42789.1, CCDS46466.1, CCDS54425.1	2q31.3	2005-01-04			ENSG00000188452	ENSG00000188452			21699	protein-coding gene	gene with protein product			"retinitis pigmentosa 26 (autosomal recessive)"	RP26		14681825	Standard	NR_027689		Approved		uc002uny.3	Q49MI3	OTTHUMG00000154315	ENST00000339098.5:c.247A>T	chr2.hg19:g.182468798T>A	ENSP00000341159:p.Lys83*	81.0	0.0	.		109.0	48.0	.	NM_001160277	B2RPL2|B4DEY1|Q49MH9|Q49MI0|Q49MI1|Q49MI2|Q5DVJ2|Q5DVJ4|Q5DVJ5|Q6UZF6|Q6ZP59	Nonsense_Mutation	SNP	ENST00000339098.5	hg19	CCDS42789.1	.	.	.	.	.	.	.	.	.	.	T	15.06	2.720717	0.48728	.	.	ENSG00000188452	ENST00000410087;ENST00000409440;ENST00000374969;ENST00000339098;ENST00000374970	.	.	.	5.4	2.99	0.34606	.	0.821591	0.10973	N	0.613588	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.9745	0.64262	0.0:0.0:0.236:0.764	.	.	.	.	X	83	.	ENSP00000341159:K83X	K	-	1	0	CERKL	182177043	0.982000	0.34865	0.014000	0.15608	0.524000	0.34500	1.038000	0.30254	0.033000	0.15463	-1.333000	0.01266	AAG	.	.	.	none		0.363	CERKL-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334811.1			A	182468798	T	A	182468798	4	1	264	1	0	0	0	0	0	1	0	0	3270	1763	61	5	1481	5	CERKL	2	182468798	Nonsense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	2471760	182468798	60730575	21	16526											
ZSWIM2	151112	hgsc.bcm.edu	37	chr2	187703706	187703706	+	Frame_Shift_Del	DEL	C	C	-																															ctgcaaaaggtgacaggaagCtttttctctaaaagtagctc																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr2:187703706delC	ENST00000295131.2	-	4	513	c.474delG	c.(472-474)aagfs	p.K158fs		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	158					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			TGACAGGAAGCTTTTTCTCTA	0.308																																					p.L159fs		Atlas-Indel,Pindel	.											.	ZSWIM2	119	.	0			c.475delC						PASS	.						150	154	153					2																	187703706		2203	4299	6502	SO:0001589	frameshift_variant	151112	exon4			.	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"Zinc fingers, SWIM-type", "Zinc fingers, ZZ-type"	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.474delG	chr2.hg19:g.187703706delC	ENSP00000295131:p.Lys158fs	52.0	0.0	0		50.0	26.0	0.52	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Frame_Shift_Del	DEL	ENST00000295131.2	hg19	CCDS33348.1																																																																																			.	.	.	none		0.308	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521		-	187703706	C	-	187703706	7	5	264	1	0	1	0	1	0	0	0	0	18253	796	28	0	1451	0	ZSWIM2	2	187703706	Frame_Shift_Del	DEL	C	TCGA-UZ-A9PS-01A-11D-A42J-10	5234908	187703706	55495667	22	16527											
EPHA4	2043	hgsc.bcm.edu	37	chr2	222321422	222321422	+	Frame_Shift_Del	DEL	G	G	-																															ggaaaacataggaagtgagaGggttcaggcctttgatatct																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr2:222321422delG	ENST00000281821.2	-	7	1555	c.1514delC	c.(1513-1515)cctfs	p.P505fs	EPHA4_ENST00000409854.1_Frame_Shift_Del_p.P505fs|EPHA4_ENST00000392071.4_Frame_Shift_Del_p.P454fs|EPHA4_ENST00000409938.1_Frame_Shift_Del_p.P505fs	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	505	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		GGAAGTGAGAGGGTTCAGGCC	0.493																																					p.P505fs		Atlas-Indel,Pindel	.											.	EPHA4	263	.	0			c.1515delT						PASS	.						151	132	139					2																	222321422		2203	4300	6503	SO:0001589	frameshift_variant	2043	exon7			.	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.1514delC	chr2.hg19:g.222321422delG	ENSP00000281821:p.Pro505fs	98.0	0.0	0		96.0	44.0	0.458333	NM_004438	A8K2P1|B2R601|B7Z6Q8|Q2M380	Frame_Shift_Del	DEL	ENST00000281821.2	hg19	CCDS2447.1																																																																																			.	.	.	none		0.493	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			-	222321422	G	-	222321422	7	5	264	1	0	1	0	1	0	0	0	0	5171	1000	35	0	1490	0	EPHA4	2	222321422	Frame_Shift_Del	DEL	G	TCGA-UZ-A9PS-01A-11D-A42J-10	34617716	222321422	20877951	23	16528											
TRIP12	9320	hgsc.bcm.edu	37	chr2	230633435	230633435	+	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	aacaaaaacttcacagcccgActataacagaaataaatata	22	7	3	9	1	1	1	1	0	0	1	1	2	1	1	1	0	4	0	1	0	10	6			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr2:230633435A>G	ENST00000283943.5	-	40	5857	c.5679T>C	c.(5677-5679)agT>agC	p.S1893S	TRIP12_ENST00000389044.4_Splice_Site_p.S1941S|TRIP12_ENST00000389045.3_Splice_Site_p.S1623S	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1893	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		TCACAGCCCGACTATAACAGA	0.348																																					p.S1893S		Atlas-SNP	.											.	TRIP12	207	.	0			c.T5679C						PASS	.						57	55	55					2																	230633435		2203	4300	6503	SO:0001630	splice_region_variant	9320	exon40			AGCCCGACTATAA	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.5679-1T>C	chr2.hg19:g.230633435A>G		64.0	0.0	.		84.0	35.0	.	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Silent	SNP	ENST00000283943.5	hg19	CCDS33391.1																																																																																			.	.	.	none		0.348	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238	Silent	G	230633435	A	G	230633435	5	3	264	1	0	0	0	0	0	0	1	0	16568	289	10	3	307	3	TRIP12	2	230633435	Splice_Site	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	8312013	230633435	12565938	24	16529											
TRIP12	9320	hgsc.bcm.edu	37	chr2	230663701	230663701	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgtacttaaccttccccaTgtttttggattcaagcttgc	7	17	7	10	0	1	0	1	0	0	0	2	1	2	1	3	1	4	3	3	1	3	7			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr2:230663701T>C	ENST00000283943.5	-	22	3325	c.3147A>G	c.(3145-3147)acA>acG	p.T1049T	TRIP12_ENST00000389044.4_Silent_p.T1097T|TRIP12_ENST00000389045.3_Silent_p.T779T|TRIP12_ENST00000543084.1_3'UTR	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1049					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		ACCTTCCCCATGTTTTTGGAT	0.458																																					p.T1049T		Atlas-SNP	.											.	TRIP12	207	.	0			c.A3147G						PASS	.						160	153	155					2																	230663701		2203	4300	6503	SO:0001819	synonymous_variant	9320	exon22			TCCCCATGTTTTT	L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.3147A>G	chr2.hg19:g.230663701T>C		94.0	0.0	.		95.0	44.0	.	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Silent	SNP	ENST00000283943.5	hg19	CCDS33391.1																																																																																			.	.	.	none		0.458	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238		C	230663701	T	C	230663701	2	2	264	1	0	0	0	0	0	0	0	1	16568	1451	51	3		3	TRIP12	2	230663701	Silent	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	30266	230663701	12535672	25	16530											
PER2	8864	hgsc.bcm.edu	37	chr2	239167228	239167228	+	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	cggggaagctgacccccaggCtgtccttttccatggcaggg	6	8	14	13	1	0	1	0	1	0	0	2	2	2	2	4	5	1	3	4	5	1	2	rs202103918		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr2:239167228C>G	ENST00000254657.3	-	15	1964	c.1685G>C	c.(1684-1686)aGc>aCc	p.S562T	AC096574.4_ENST00000456601.1_RNA|PER2_ENST00000254658.3_3'UTR	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	562	CSNK1E binding domain. {ECO:0000250}.				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)		GACCCCCAGGCTGTCCTTTTC	0.527																																					p.S562T		Atlas-SNP	.											.	PER2	85	.	0			c.G1685C						PASS	.						62	58	59					2																	239167228		2203	4300	6503	SO:0001583	missense	8864	exon15			CCCAGGCTGTCCT	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.1685G>C	chr2.hg19:g.239167228C>G	ENSP00000254657:p.Ser562Thr	81.0	0.0	.		84.0	39.0	.	NM_022817	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Missense_Mutation	SNP	ENST00000254657.3	hg19	CCDS2528.1	.	.	.	.	.	.	.	.	.	.	C	11.82	1.752339	0.31046	.	.	ENSG00000132326	ENST00000254657	T	0.11712	2.75	4.79	4.79	0.61399	.	.	.	.	.	T	0.27697	0.0681	L	0.58428	1.81	0.80722	D	1	P;B	0.52842	0.956;0.168	D;B	0.65010	0.931;0.018	T	0.00440	-1.1738	9	0.42905	T	0.14	-18.6957	15.7283	0.77780	0.0:1.0:0.0:0.0	.	562;562	B4DH14;O15055	.;PER2_HUMAN	T	562	ENSP00000254657:S562T	ENSP00000254657:S562T	S	-	2	0	PER2	238831967	0.009000	0.17119	0.973000	0.42090	0.026000	0.11368	1.058000	0.30504	2.391000	0.81399	0.555000	0.69702	AGC	.	C|1.000;T|0.000	.	alt		0.527	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817		G	239167228	C	G	239167228	3	3	264	1	0	0	0	0	1	0	0	0	11737	797	28	4	2118	4	PER2	2	239167228	Missense_Mutation	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	8503527	239167228	4032145	26	16531											
THAP4	51078	hgsc.bcm.edu	37	chr2	242541346	242541347	+	Silent	DNP	TG	TG	GC																															ctccttggcgaaggagatccTggcgatggagtgggatgcga																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr2:242541346_242541347TG>GC	ENST00000407315.1	-	5	2009_2010	c.1578_1579CA>GC	c.(1576-1581)gcCAgg>gcGCgg	p.526_527AR>AR	THAP4_ENST00000402136.1_Silent_p.114_115AR>AR|THAP4_ENST00000402545.1_Silent_p.114_115AR>AR|THAP4_ENST00000497486.1_5'UTR	NM_015963.5	NP_057047.4	Q8WY91	THAP4_HUMAN	THAP domain containing 4	526							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)		AAGGAGATCCTGGCGATGGAGT	0.639																																					p.R527R|p.A526A		Atlas-SNP	.											.	THAP4	27	.	0			c.A1579C|c.C1578G						PASS	.																																			SO:0001819	synonymous_variant	51078	exon5			AGATCCTGGCGAT|GATCCTGGCGATG	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.1578_1579delinsGC	chr2.hg19:g.242541346_242541347delinsGC		50.0	0.0	.		42.0|41.0	17.0|16.0	.	NM_015963	Q53NU7|Q6GRN0|Q6IPJ3|Q9NW26|Q9Y325	Silent	SNP	ENST00000407315.1	hg19	CCDS2551.1																																																																																			.	.	.	none		0.639	THAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257267.3	NM_015963		GC	242541347	TG	GC	242541346	2	3	264	1	0	0	0	0	0	0	0	1	15858	1579	55	5		5	THAP4	2	242541346	Silent	DNP	TG	TCGA-UZ-A9PS-01A-11D-A42J-10	3374118	242541346	658027	27	16532											
CNTN6	27255	hgsc.bcm.edu	37	chr3	1424987	1424987	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggatggtagaacctcaactGgccccaaggggaacttctct	10	9	11	11	0	2	1	1	0	1	1	3	3	2	3	3	5	3	1	3	5	5	2			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr3:1424987G>A	ENST00000446702.2	+	19	3039	c.2412G>A	c.(2410-2412)ctG>ctA	p.L804L	CNTN6_ENST00000539053.1_Silent_p.L732L|CNTN6_ENST00000350110.2_Silent_p.L804L			Q9UQ52	CNTN6_HUMAN	contactin 6	804					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		AACCTCAACTGGCCCCAAGGG	0.438																																					p.L804L		Atlas-SNP	.											.	CNTN6	245	.	0			c.G2412A						PASS	.						186	193	191					3																	1424987		2203	4300	6503	SO:0001819	synonymous_variant	27255	exon19			TCAACTGGCCCCA	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"Immunoglobulin superfamily / I-set domain containing", "Fibronectin type III domain containing"	2176	protein-coding gene	gene with protein product	"neural adhesion molecule"	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.2412G>A	chr3.hg19:g.1424987G>A		135.0	0.0	.		203.0	45.0	.	NM_014461	Q2KHM2	Silent	SNP	ENST00000446702.2	hg19	CCDS2557.1																																																																																			.	.	.	none		0.438	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461		A	1424987	G	A	1424987	2	1	264	1	0	0	0	0	0	0	0	1	3647	1335	47	2		2	CNTN6	3	1424987	Silent	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10		1424987	196597443	28	16533											
ZNF385D	79750	hgsc.bcm.edu	37	chr3	21478596	21478596	+	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	tgccagtggctgtcgttgggCttttttccactttagaggtg	4	16	13	8	1	0	1	0	0	0	1	2	1	1	1	2	3	1	3	2	3	1	6	rs368223028		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr3:21478596C>T	ENST00000281523.2	-	5	1057	c.539G>A	c.(538-540)aGc>aAc	p.S180N	ZNF385D_ENST00000494118.1_5'UTR	NM_024697.2	NP_078973.1	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	180	Thr-rich.					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						TGTCGTTGGGCTTTTTTCCAC	0.478																																					p.S180N		Atlas-SNP	.											.	ZNF385D	93	.	0			c.G539A						PASS	.						174	155	162					3																	21478596		2203	4300	6503	SO:0001583	missense	79750	exon5			GTTGGGCTTTTTT	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.539G>A	chr3.hg19:g.21478596C>T	ENSP00000281523:p.Ser180Asn	96.0	0.0	.		136.0	35.0	.	NM_024697		Missense_Mutation	SNP	ENST00000281523.2	hg19	CCDS2636.1	.	.	.	.	.	.	.	.	.	.	C	13.12	2.143723	0.37825	.	.	ENSG00000151789	ENST00000281523	T	0.45276	0.9	6.09	4.22	0.49857	.	0.295113	0.41194	D	0.000939	T	0.22859	0.0552	L	0.27053	0.805	0.24203	N	0.995504	B	0.22276	0.067	B	0.19391	0.025	T	0.06303	-1.0834	10	0.21014	T	0.42	-5.7655	2.7247	0.05210	0.1956:0.534:0.1249:0.1455	.	180	Q9H6B1	Z385D_HUMAN	N	180	ENSP00000281523:S180N	ENSP00000281523:S180N	S	-	2	0	ZNF385D	21453600	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	2.076000	0.41548	2.891000	0.99171	0.655000	0.94253	AGC	.	.	.	alt		0.478	ZNF385D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252884.1	NM_024697		T	21478596	C	T	21478596	3	4	264	1	0	0	0	0	1	0	0	0	17890	797	28	2	664	2	ZNF385D	3	21478596	Missense_Mutation	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	20053609	21478596	176543834	29	16534											
USP4	7375	hgsc.bcm.edu	37	chr3	49315762	49315762	+	Frame_Shift_Del	DEL	A	A	-																															ctgcaagcctcatcatccccAaagccctgctgagagctgct																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr3:49315762delA	ENST00000265560.4	-	22	2902	c.2856delT	c.(2854-2856)tttfs	p.F952fs	USP4_ENST00000351842.4_Frame_Shift_Del_p.F905fs|C3orf62_ENST00000343010.3_5'Flank	NM_003363.3	NP_003354.2	Q13107	UBP4_HUMAN	ubiquitin specific peptidase 4 (proto-oncogene)	952					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)		CATCATCCCCAAAGCCCTGCT	0.507																																					p.G953fs		Pindel	.											.	USP4	72	.	0			c.2857delG						PASS	.						120	118	119					3																	49315762		2203	4300	6503	SO:0001589	frameshift_variant	7375	exon22			.	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.2856delT	chr3.hg19:g.49315762delA	ENSP00000265560:p.Phe952fs	68.0	0.0	.		112.0	43.0	0.384	NM_003363	A8K6Y0|C9IY91|O43452|O43453|Q08AK8	Frame_Shift_Del	DEL	ENST00000265560.4	hg19	CCDS2793.1																																																																																			.	.	.	none		0.507	USP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346069.1	NM_199443		-	49315762	A	-	49315762	7	5	264	1	0	1	0	1	0	0	0	0	17083	127	5	0	39	0	USP4	3	49315762	Frame_Shift_Del	DEL	A	TCGA-UZ-A9PS-01A-11D-A42J-10	27837166	49315762	148706668	30	16535											
AMT	275	hgsc.bcm.edu	37	chr3	49456530	49456530	+	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	ccctgccagcttcacctctgGgtttttcagaatagctgttg	6	14	9	12	0	3	1	2	0	1	1	3	1	3	1	3	1	3	4	3	1	2	5			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr3:49456530G>C	ENST00000273588.3	-	7	1053	c.751C>G	c.(751-753)Cca>Gca	p.P251A	AMT_ENST00000546031.1_Missense_Mutation_p.P154A|AMT_ENST00000395338.2_Missense_Mutation_p.P251A|AMT_ENST00000538581.1_Missense_Mutation_p.P195A|AMT_ENST00000458307.2_Missense_Mutation_p.P207A|AMT_ENST00000476226.1_5'UTR	NM_000481.3	NP_000472.2	P48728	GCST_HUMAN	aminomethyltransferase	251					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)	TTCACCTCTGGGTTTTTCAGA	0.572																																					p.P251A		Atlas-SNP	.											.	AMT	22	.	0			c.C751G						PASS	.						44	46	45					3																	49456530		2203	4300	6503	SO:0001583	missense	275	exon7			CCTCTGGGTTTTT	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.751C>G	chr3.hg19:g.49456530G>C	ENSP00000273588:p.Pro251Ala	121.0	0.0	.		167.0	98.0	.	NM_001164712	A8K3I5|B4DE61|B4DJQ0|E9PBG1|Q96IG6	Missense_Mutation	SNP	ENST00000273588.3	hg19	CCDS2797.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.07|11.07	1.531135|1.531135	0.27387|0.27387	.|.	.|.	ENSG00000145020|ENSG00000145020	ENST00000395338;ENST00000458307;ENST00000273588;ENST00000538581;ENST00000546031;ENST00000430521|ENST00000427987	T;T;T;T;T;T|.	0.74315|.	-0.83;-0.83;-0.83;-0.83;-0.83;-0.83|.	5.28|5.28	1.06|1.06	0.20224|0.20224	Glycine cleavage T-protein, N-terminal (1);|.	0.317346|0.317346	0.36134|0.36134	N|N	0.002773|0.002773	T|T	0.22126|0.22126	0.0533|0.0533	N|N	0.13352|0.13352	0.335|0.335	0.32666|0.32666	N|N	0.517387|0.517387	B;B;B;B|.	0.16166|.	0.001;0.016;0.001;0.001|.	B;B;B;B|.	0.21360|.	0.003;0.034;0.003;0.003|.	T|T	0.17806|0.17806	-1.0357|-1.0357	10|6	0.24483|.	T|.	0.36|.	-15.0969|-15.0969	4.9721|4.9721	0.14121|0.14121	0.1775:0.0:0.5332:0.2893|0.1775:0.0:0.5332:0.2893	.|.	195;207;251;251|.	B4DE61;B4DJQ0;E9PBG1;P48728|.	.;.;.;GCST_HUMAN|.	A|R	251;207;251;195;154;195|248	ENSP00000378747:P251A;ENSP00000415619:P207A;ENSP00000273588:P251A;ENSP00000443200:P195A;ENSP00000440672:P154A;ENSP00000388068:P195A|.	ENSP00000273588:P251A|.	P|P	-|-	1|2	0|0	AMT|AMT	49431534|49431534	1.000000|1.000000	0.71417|0.71417	0.958000|0.958000	0.39756|0.39756	0.720000|0.720000	0.41350|0.41350	1.685000|1.685000	0.37659|0.37659	0.618000|0.618000	0.30179|0.30179	-0.136000|-0.136000	0.14681|0.14681	CCA|CCC	.	.	.	none		0.572	AMT-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346216.2	NM_000481		C	49456530	G	C	49456530	3	2	264	1	0	0	0	0	1	0	0	0	589	1232	43	4	500	4	AMT	3	49456530	Missense_Mutation	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10	140768	49456530	148565900	31	16536											
GNAI2	2771	hgsc.bcm.edu	37	chr3	50294444	50294444	+	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	tcacagacacgtccatcatcCtcttcctcaacaagaaggac	13	8	5	15	1	4	2	3	0	1	2	7	3	7	3	3	1	1	0	3	1	3	1			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr3:50294444C>A	ENST00000313601.6	+	7	1183	c.799C>A	c.(799-801)Ctc>Atc	p.L267I	GNAI2_ENST00000451956.1_Missense_Mutation_p.L230I|GNAI2_ENST00000536647.1_Missense_Mutation_p.L186I|GNAI2_ENST00000440628.1_Missense_Mutation_p.L215I|GNAI2_ENST00000491100.1_3'UTR|GNAI2_ENST00000422163.1_Missense_Mutation_p.L251I|GNAI2_ENST00000266027.5_Missense_Mutation_p.L251I	NM_002070.2	NP_002061.1	P04899	GNAI2_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 2	267					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)		GTCCATCATCCTCTTCCTCAA	0.507											OREG0015582	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L267I		Atlas-SNP	.											.	GNAI2	42	.	0			c.C799A						PASS	.						186	157	166					3																	50294444		2203	4300	6503	SO:0001583	missense	2771	exon7			ATCATCCTCTTCC	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.799C>A	chr3.hg19:g.50294444C>A	ENSP00000312999:p.Leu267Ile	105.0	0.0	.	968	106.0	78.0	.	NM_002070	B3KTZ0|B4DYA0|B4E2X5|Q6B6N3|Q8IZ71	Missense_Mutation	SNP	ENST00000313601.6	hg19	CCDS2813.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.933965	0.92458	.	.	ENSG00000114353	ENST00000422163;ENST00000313601;ENST00000536647;ENST00000540560;ENST00000440628;ENST00000451956;ENST00000266027	D;D;D;D;D;D	0.95788	-3.81;-3.81;-3.81;-3.81;-3.81;-3.81	4.48	4.48	0.54585	.	0.000000	0.85682	D	0.000000	D	0.98235	0.9416	H	0.94964	3.605	0.80722	D	1	P;P;D;D	0.56968	0.939;0.949;0.978;0.973	D;D;D;D	0.73380	0.954;0.98;0.954;0.923	D	0.99032	1.0821	10	0.87932	D	0	.	15.0562	0.71915	0.0:1.0:0.0:0.0	.	230;267;251;251	B4DYA0;P04899;B3KTZ0;P04899-2	.;GNAI2_HUMAN;.;.	I	251;267;186;267;215;230;251	ENSP00000406871:L251I;ENSP00000312999:L267I;ENSP00000444360:L186I;ENSP00000395736:L215I;ENSP00000406369:L230I;ENSP00000266027:L251I	ENSP00000266027:L251I	L	+	1	0	GNAI2	50269448	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.604000	0.82830	2.517000	0.84864	0.650000	0.86243	CTC	.	.	.	none		0.507	GNAI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346688.1	NM_002070		A	50294444	C	A	50294444	3	1	264	1	0	0	0	0	1	0	0	0	6512	681	24	4	836	4	GNAI2	3	50294444	Missense_Mutation	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	837914	50294444	147727986	32	16537											
STAB1	23166	hgsc.bcm.edu	37	chr3	52551367	52551367	+	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	tgtctcatccaccacgggggCtgccacattcacgccgagtg	7	8	11	15	3	2	0	2	0	1	0	4	1	3	0	4	2	1	1	4	2	0	1			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr3:52551367C>T	ENST00000321725.6	+	43	4597	c.4521C>T	c.(4519-4521)ggC>ggT	p.G1507G		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	1507	EGF-like 12. {ECO:0000255|PROSITE- ProRule:PRU00076, ECO:0000305}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		ACCACGGGGGCTGCCACATTC	0.617																																					p.G1507G		Atlas-SNP	.											.	STAB1	178	.	0			c.C4521T						PASS	.						42	44	43					3																	52551367		2203	4299	6502	SO:0001819	synonymous_variant	23166	exon43			CGGGGGCTGCCAC	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.4521C>T	chr3.hg19:g.52551367C>T		162.0	0.0	.		213.0	61.0	.	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Silent	SNP	ENST00000321725.6	hg19	CCDS33768.1																																																																																			.	.	.	none		0.617	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		T	52551367	C	T	52551367	2	4	264	1	0	0	0	0	0	0	0	1	15249	784	28	2		2	STAB1	3	52551367	Silent	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	2256923	52551367	145471063	33	16538											
ZBTB11	27107	hgsc.bcm.edu	37	chr3	101371385	101371385	+	Missense_Mutation	SNP	A	A	C																															atactctcttagctgagtgaAttttcttccacatttttcac																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr3:101371385A>C	ENST00000312938.4	-	10	3179	c.2599T>G	c.(2599-2601)Ttc>Gtc	p.F867V		NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	867					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						AGCTGAGTGAATTTTCTTCCA	0.373																																					p.F867V		Atlas-SNP	.											.	ZBTB11	77	.	0			c.T2599G						PASS	.						160	164	162					3																	101371385		2202	4300	6502	SO:0001583	missense	27107	exon10			GAGTGAATTTTCT	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.2599T>G	chr3.hg19:g.101371385A>C	ENSP00000326200:p.Phe867Val	107.0	0.0	.		157.0	74.0	.	NM_014415	Q2NKP9	Missense_Mutation	SNP	ENST00000312938.4	hg19	CCDS2943.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.202625	0.79127	.	.	ENSG00000066422	ENST00000312938	T	0.73469	-0.75	5.29	4.14	0.48551	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	0.61776	0.2374	N	0.19112	0.55	0.80722	D	1	P	0.41393	0.748	B	0.41374	0.355	T	0.65096	-0.6251	10	0.87932	D	0	-10.2042	11.1725	0.48579	0.9276:0.0:0.0724:0.0	.	867	O95625	ZBT11_HUMAN	V	867	ENSP00000326200:F867V	ENSP00000326200:F867V	F	-	1	0	ZBTB11	102854075	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	7.100000	0.76989	0.958000	0.37956	0.528000	0.53228	TTC	.	.	.	none		0.373	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415		C	101371385	A	C	101371385	3	2	264	1	0	0	0	0	1	0	0	0	17536	101	4	5	570	5	ZBTB11	3	101371385	Missense_Mutation	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	48820018	101371385	96651045	34	16539	171	2									
ZBTB11	27107	hgsc.bcm.edu	37	chr3	101371390	101371390	+	Missense_Mutation	SNP	C	C	T																															ctcttagctgagtgaattttCttccacatttttcacacacc																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr3:101371390C>T	ENST00000312938.4	-	10	3174	c.2594G>A	c.(2593-2595)aGa>aAa	p.R865K		NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	865					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						AGTGAATTTTCTTCCACATTT	0.368																																					p.R865K		Atlas-SNP	.											.	ZBTB11	77	.	0			c.G2594A						PASS	.						159	163	161					3																	101371390		2202	4300	6502	SO:0001583	missense	27107	exon10			AATTTTCTTCCAC	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.2594G>A	chr3.hg19:g.101371390C>T	ENSP00000326200:p.Arg865Lys	106.0	0.0	.		159.0	75.0	.	NM_014415	Q2NKP9	Missense_Mutation	SNP	ENST00000312938.4	hg19	CCDS2943.1	.	.	.	.	.	.	.	.	.	.	C	10.25	1.297368	0.23650	.	.	ENSG00000066422	ENST00000312938	T	0.38722	1.12	5.29	3.5	0.40072	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.048362	0.85682	N	0.000000	T	0.18173	0.0436	N	0.08118	0	0.80722	D	1	B	0.09022	0.002	B	0.10450	0.005	T	0.13791	-1.0496	10	0.02654	T	1	-12.5319	9.1783	0.37125	0.0:0.7777:0.0:0.2223	.	865	O95625	ZBT11_HUMAN	K	865	ENSP00000326200:R865K	ENSP00000326200:R865K	R	-	2	0	ZBTB11	102854080	1.000000	0.71417	0.992000	0.48379	0.981000	0.71138	3.794000	0.55492	0.721000	0.32231	0.650000	0.86243	AGA	.	.	.	none		0.368	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415		T	101371390	C	T	101371390	3	4	264	1	0	0	0	0	1	0	0	0	17536	913	32	2	575	2	ZBTB11	3	101371390	Missense_Mutation	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	5	101371390	96651040	35	16540	171	2									
ACAP2	23527	hgsc.bcm.edu	37	chr3	195000100	195000100	+	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	ggaaacgatttagtttctctGgattattggatgccatttgg	9	16	11	5	1	1	0	0	0	1	0	2	4	1	3	1	4	2	1	1	4	3	6			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr3:195000100G>T	ENST00000326793.6	-	23	2524	c.2294C>A	c.(2293-2295)cCa>cAa	p.P765Q	ACAP2_ENST00000472860.1_5'UTR|ACAP2-IT1_ENST00000419899.1_RNA	NM_012287.5	NP_036419.3	Q15057	ACAP2_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	765					cellular response to nerve growth factor stimulus (GO:1990090)|protein localization to endosome (GO:0036010)|regulation of ARF GTPase activity (GO:0032312)	endosome membrane (GO:0010008)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	27						TAGTTTCTCTGGATTATTGGA	0.318																																					p.P765Q		Atlas-SNP	.											.	ACAP2	72	.	0			c.C2294A						PASS	.						64	68	67					3																	195000100		2203	4291	6494	SO:0001583	missense	23527	exon23			TTCTCTGGATTAT		CCDS33924.1	3q29	2013-01-10	2008-09-22	2008-09-22	ENSG00000114331	ENSG00000114331		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	16469	protein-coding gene	gene with protein product		607766	"centaurin, beta 2"	CENTB2		11050434, 11062263	Standard	NM_012287		Approved	KIAA0041, CNT-B2	uc003fun.4	Q15057	OTTHUMG00000155885	ENST00000326793.6:c.2294C>A	chr3.hg19:g.195000100G>T	ENSP00000324287:p.Pro765Gln	186.0	0.0	.		284.0	79.0	.	NM_012287	A8K2V4|Q8N5Z8|Q9UQR3	Missense_Mutation	SNP	ENST00000326793.6	hg19	CCDS33924.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.871995	0.91587	.	.	ENSG00000114331	ENST00000326793	T	0.47528	0.84	6.02	6.02	0.97574	.	0.113510	0.64402	D	0.000009	T	0.74253	0.3692	M	0.85373	2.75	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.76767	-0.2838	10	0.87932	D	0	.	19.5352	0.95251	0.0:0.0:1.0:0.0	.	765	Q15057	ACAP2_HUMAN	Q	765	ENSP00000324287:P765Q	ENSP00000324287:P765Q	P	-	2	0	ACAP2	196481389	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.133000	0.94460	2.850000	0.98022	0.650000	0.86243	CCA	.	.	.	none		0.318	ACAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342126.2	NM_012287		T	195000100	G	T	195000100	3	4	264	1	0	0	0	0	1	0	0	0	119	1348	47	4	46	4	ACAP2	3	195000100	Missense_Mutation	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10	93628710	195000100	3022330	36	16541											
LRRC66	339977	hgsc.bcm.edu	37	chr4	52861134	52861134	+	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	gagtggatttctgcactggtTccttgttagcaggagtgaca	8	13	13	7	0	1	1	0	1	1	0	2	4	2	3	1	3	2	4	1	3	1	4			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr4:52861134T>A	ENST00000343457.3	-	4	2060	c.2054A>T	c.(2053-2055)gAa>gTa	p.E685V		NM_001024611.1	NP_001019782.1	Q68CR7	LRC66_HUMAN	leucine rich repeat containing 66	685						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						CTGCACTGGTTCCTTGTTAGC	0.517																																					p.E685V		Atlas-SNP	.											.	LRRC66	128	.	0			c.A2054T						PASS	.						87	84	85					4																	52861134		2004	4173	6177	SO:0001583	missense	339977	exon4			ACTGGTTCCTTGT	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.2054A>T	chr4.hg19:g.52861134T>A	ENSP00000341944:p.Glu685Val	38.0	0.0	.		48.0	21.0	.	NM_001024611		Missense_Mutation	SNP	ENST00000343457.3	hg19	CCDS43229.1	.	.	.	.	.	.	.	.	.	.	T	14.83	2.651422	0.47362	.	.	ENSG00000188993	ENST00000343457	T	0.36340	1.26	4.37	-0.899	0.10547	.	0.798338	0.10965	N	0.614504	T	0.23886	0.0578	L	0.36672	1.1	0.09310	N	1	P	0.50943	0.94	B	0.40982	0.345	T	0.15636	-1.0430	10	0.87932	D	0	-3.7352	4.4438	0.11588	0.0:0.2796:0.1775:0.5428	.	685	Q68CR7	LRC66_HUMAN	V	685	ENSP00000341944:E685V	ENSP00000341944:E685V	E	-	2	0	LRRC66	52555891	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.196000	0.17176	-0.214000	0.10078	-0.250000	0.11733	GAA	.	.	.	none		0.517	LRRC66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361473.1	NM_001024611		A	52861134	T	A	52861134	3	1	264	1	0	0	0	0	1	0	0	0	9025	1783	62	5	592	5	LRRC66	4	52861134	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10		52861134	138293142	37	16542											
MOBKL1A	92597	hgsc.bcm.edu	37	chr4	71844887	71844887	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catgtctgtggcaaaaactaTactcaaacgcctctttaggg	12	11	8	10	1	3	0	1	0	2	0	3	0	3	0	1	2	3	1	1	2	6	4			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr4:71844887T>C	ENST00000309395.2	+	5	653	c.452T>C	c.(451-453)aTa>aCa	p.I151T	MOB1B_ENST00000396051.2_Missense_Mutation_p.I156T|MOB1B_ENST00000511449.1_Intron	NM_001244766.1|NM_173468.3	NP_001231695.1|NP_775739.1	Q7L9L4	MOB1B_HUMAN	MOB kinase activator 1B	151					hippo signaling (GO:0035329)|positive regulation of phosphorylation (GO:0042327)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	kinase activator activity (GO:0019209)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)										GCAAAAACTATACTCAAACGC	0.398																																					p.I156T		Atlas-SNP	.											.	.	.	.	0			c.T467C						PASS	.						158	157	157					4																	71844887		2203	4300	6503	SO:0001583	missense	92597	exon6			AAACTATACTCAA	BC038112	CCDS34002.1, CCDS58903.1	4q13.3	2011-09-28	2011-09-28	2011-09-27	ENSG00000173542	ENSG00000173542		"MOB kinase activators"	29801	protein-coding gene	gene with protein product	"Mob4A protein"	609282	"MOB1, Mps One Binder kinase activator-like 1A (yeast)", "MOB1 Mps One Binder homolog B (yeast)"	MOBKL1A		15067004	Standard	NM_173468		Approved	MOB4A	uc003hfw.3	Q7L9L4	OTTHUMG00000160844	ENST00000309395.2:c.452T>C	chr4.hg19:g.71844887T>C	ENSP00000310189:p.Ile151Thr	83.0	0.0	.		96.0	36.0	.	NM_001244766	B2R8U6|B4DRY3|Q8IY23	Missense_Mutation	SNP	ENST00000309395.2	hg19	CCDS34002.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.520487	0.85495	.	.	ENSG00000173542	ENST00000309395;ENST00000396051	.	.	.	5.26	5.26	0.73747	.	0.044863	0.85682	D	0.000000	D	0.86952	0.6057	H	0.95745	3.715	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.996	D	0.90963	0.4814	9	0.87932	D	0	-46.1108	15.1665	0.72833	0.0:0.0:0.0:1.0	.	156;151	B4DRY3;Q7L9L4	.;MOB1B_HUMAN	T	151;156	.	ENSP00000310189:I151T	I	+	2	0	MOBKL1A	72063751	1.000000	0.71417	0.997000	0.53966	0.978000	0.69477	8.040000	0.89188	1.984000	0.57885	0.459000	0.35465	ATA	.	.	.	none		0.398	MOB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362634.1	NM_173468		C	71844887	T	C	71844887	3	2	264	1	0	0	0	0	1	0	0	0	9689	1406	49	3	470	3	MOBKL1A	4	71844887	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	18983753	71844887	119309389	38	16543											
SHROOM3	57619	hgsc.bcm.edu	37	chr4	77680809	77680809	+	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	aaagagatgccagcagaagtGaatgaggaagaggaacaggc	18	3	15	5	0	0	5	0	2	0	3	0	8	0	7	1	3	3	1	1	3	5	0			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr4:77680809G>T	ENST00000296043.6	+	9	6263	c.5310G>T	c.(5308-5310)gtG>gtT	p.V1770V	RP11-359D14.2_ENST00000452412.1_RNA|RP11-359D14.3_ENST00000449007.1_RNA	NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	1770	ASD2. {ECO:0000255|PROSITE- ProRule:PRU00638}.				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)			CAGCAGAAGTGAATGAGGAAG	0.448																																					p.V1770V		Atlas-SNP	.											.	SHROOM3	134	.	0			c.G5310T						PASS	.						111	93	99					4																	77680809		2203	4300	6503	SO:0001819	synonymous_variant	57619	exon9			AGAAGTGAATGAG	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.5310G>T	chr4.hg19:g.77680809G>T		167.0	0.0	.		171.0	82.0	.	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Silent	SNP	ENST00000296043.6	hg19	CCDS3579.2																																																																																			.	.	.	none		0.448	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859		T	77680809	G	T	77680809	2	4	264	1	0	0	0	0	0	0	0	1	14308	1277	45	4		4	SHROOM3	4	77680809	Silent	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10	5835922	77680809	113473467	39	16544											
FRAS1	80144	hgsc.bcm.edu	37	chr4	79188585	79188585	+	Splice_Site	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	tgccaaagtggagtgtgcccGggtaagaagcaggggcattt	10	8	16	7	1	0	1	0	0	0	1	0	2	0	2	2	4	3	3	2	4	3	2			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr4:79188585G>T	ENST00000325942.6	+	9	1420	c.980G>T	c.(979-981)cGg>cTg	p.R327L	FRAS1_ENST00000264895.6_Splice_Site_p.R327L|FRAS1_ENST00000264899.6_Splice_Site_p.R327L	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	327	VWFC 5. {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						GAGTGTGCCCGGGTAAGAAGC	0.547																																					p.R327L		Atlas-SNP	.											.	FRAS1	779	.	0			c.G980T						PASS	.						55	59	58					4																	79188585		2046	4189	6235	SO:0001630	splice_region_variant	80144	exon9			GTGCCCGGGTAAG	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.981+1G>T	chr4.hg19:g.79188585G>T		123.0	0.0	.		122.0	48.0	.	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	hg19	CCDS54772.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	6.298|6.298	0.423096|0.423096	0.11928|0.11928	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000502446|ENST00000325942;ENST00000264895;ENST00000264899;ENST00000534913	.|T;T;T	.|0.71698	.|-0.59;-0.59;-0.59	5.19|5.19	-10.3|-10.3	0.00346|0.00346	.|von Willebrand factor, type C (4);	.|0.722452	.|0.13283	.|N	.|0.399620	T|T	0.39517|0.39517	0.1081|0.1081	N|N	0.12961|0.12961	0.28|0.28	0.22066|0.22066	N|N	0.999381|0.999381	.|B;B;B;B	.|0.09022	.|0.0;0.0;0.001;0.002	.|B;B;B;B	.|0.13407	.|0.007;0.007;0.005;0.009	T|T	0.11036|0.11036	-1.0604|-1.0604	5|10	.|0.33940	.|T	.|0.23	.|.	4.1729|4.1729	0.10337|0.10337	0.3378:0.0883:0.4013:0.1726|0.3378:0.0883:0.4013:0.1726	.|.	.|327;327;327;327	.|E9PHH6;Q86XX4;E7EWM9;A2RRR8	.|.;FRAS1_HUMAN;.;.	W|L	256|327;327;327;67	.|ENSP00000326330:R327L;ENSP00000264895:R327L;ENSP00000264899:R327L	.|ENSP00000264895:R327L	G|R	+|+	1|2	0|0	FRAS1|FRAS1	79407609|79407609	0.003000|0.003000	0.15002|0.15002	0.337000|0.337000	0.25536|0.25536	0.014000|0.014000	0.08584|0.08584	-0.399000|-0.399000	0.07250|0.07250	-2.237000|-2.237000	0.00712|0.00712	-3.042000|-3.042000	0.00070|0.00070	GGG|CGG	.	.	.	none		0.547	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		Missense_Mutation	T	79188585	G	T	79188585	5	4	264	1	0	0	0	0	0	0	1	0	6049	1130	39	4	1014	4	FRAS1	4	79188585	Splice_Site	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10	1507776	79188585	111965691	40	16545											
ANK2	287	hgsc.bcm.edu	37	chr4	114279656	114279656	+	Frame_Shift_Del	DEL	T	T	-																															cctactgcacccatggagaaTgtgccttttactgaaagcaa																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr4:114279656delT	ENST00000357077.4	+	38	9935	c.9882delT	c.(9880-9882)aatfs	p.N3294fs	ANK2_ENST00000264366.6_Frame_Shift_Del_p.N3261fs|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000510275.2_Intron|ANK2_ENST00000509550.1_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	3294					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)		CCATGGAGAATGTGCCTTTTA	0.453																																					p.N3294fs		Atlas-Indel,Pindel	.											.	ANK2	576	.	0			c.9881delA						PASS	.						105	100	102					4																	114279656		2203	4300	6503	SO:0001589	frameshift_variant	287	exon38			.	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"Ankyrin repeat domain containing"	493	protein-coding gene	gene with protein product		106410	"long (electrocardiographic) QT syndrome 4"	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.9882delT	chr4.hg19:g.114279656delT	ENSP00000349588:p.Asn3294fs	91.0	0.0	0		101.0	50.0	0.49505	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Frame_Shift_Del	DEL	ENST00000357077.4	hg19	CCDS3702.1																																																																																			.	.	.	none		0.453	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		-	114279656	T	-	114279656	7	5	264	1	0	1	0	1	0	0	0	0	621	1461	51	0	10097	0	ANK2	4	114279656	Frame_Shift_Del	DEL	T	TCGA-UZ-A9PS-01A-11D-A42J-10	35091071	114279656	76874620	41	16546											
NDST4	64579	hgsc.bcm.edu	37	chr4	115749045	115749046	+	Frame_Shift_Ins	INS	-	-	G																															tctgtgtagcagtttggataINSgttccacattatgatctcgg																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr4:115749045_115749046insG	ENST00000264363.2	-	14	3223_3224	c.2545_2546insC	c.(2545-2547)ctafs	p.L849fs		NM_022569.1	NP_072091.1	Q9H3R1	NDST4_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 4	849	Heparan sulfate N-sulfotransferase 4.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(43)|ovary(1)|prostate(7)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	81		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)		CAGTTTGGATAGTTCCACATTA	0.431																																					p.L849fs		Atlas-Indel,Pindel	.											.	NDST4	193	.	0			c.2546_2547insC						PASS	.																																			SO:0001589	frameshift_variant	64579	exon14			.	AB036429	CCDS3706.1	4q26	2008-02-05			ENSG00000138653	ENSG00000138653		"Sulfotransferases, membrane-bound"	20779	protein-coding gene	gene with protein product		615039				11087757	Standard	NM_022569		Approved		uc003ibu.3	Q9H3R1	OTTHUMG00000132916	ENST00000264363.2:c.2546dupC	chr4.hg19:g.115749046_115749046dupG	ENSP00000264363:p.Leu849fs	65.0	0.0	0		55.0	30.0	0.545455	NM_022569	Q2KHM8	Frame_Shift_Ins	INS	ENST00000264363.2	hg19	CCDS3706.1																																																																																			.	.	.	none		0.431	NDST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256427.1	NM_022569		G	115749046	-	G	115749045	7	5	264	1	0	1	1	0	0	0	0	0	10265	420	15	0	76	0	NDST4	4	115749045	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PS-01A-11D-A42J-10	1469389	115749045	75405231	42	16547											
USP53	54532	hgsc.bcm.edu	37	chr4	120189437	120189437	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tttaaggatgtgaaaagcctGtaattcataagtcagataat	16	13	8	4	0	2	2	2	1	0	1	2	3	2	3	1	1	1	1	1	1	6	6			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr4:120189437G>A	ENST00000274030.6	+	14	2329	c.1150G>A	c.(1150-1152)Gta>Ata	p.V384I	USP53_ENST00000450251.1_Missense_Mutation_p.V384I	NM_019050.2	NP_061923.2			ubiquitin specific peptidase 53											breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	27						TGAAAAGCCTGTAATTCATAA	0.289																																					p.V384I		Atlas-SNP	.											.	USP53	69	.	0			c.G1150A						PASS	.						49	48	49					4																	120189437		1807	4076	5883	SO:0001583	missense	54532	exon13			AAGCCTGTAATTC	BC017382	CCDS43265.1	4q26	2010-05-12	2005-08-08		ENSG00000145390	ENSG00000145390		"Ubiquitin-specific peptidases"	29255	protein-coding gene	gene with protein product			"ubiquitin specific protease 53"			10718198, 14715245	Standard	NM_019050		Approved	KIAA1350	uc003ics.4	Q70EK8	OTTHUMG00000161331	ENST00000274030.6:c.1150G>A	chr4.hg19:g.120189437G>A	ENSP00000274030:p.Val384Ile	373.0	1.0	.		350.0	132.0	.	NM_019050		Missense_Mutation	SNP	ENST00000274030.6	hg19	CCDS43265.1	.	.	.	.	.	.	.	.	.	.	G	5.203	0.223010	0.09863	.	.	ENSG00000145390	ENST00000274030;ENST00000450251	T;T	0.42513	0.97;0.97	5.36	-0.763	0.11030	.	0.499782	0.19980	N	0.101785	T	0.13798	0.0334	N	0.01705	-0.755	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.17592	-1.0364	10	0.34782	T	0.22	0.1555	5.6415	0.17567	0.4731:0.0:0.2531:0.2738	.	384	Q70EK8	UBP53_HUMAN	I	384	ENSP00000274030:V384I;ENSP00000409906:V384I	ENSP00000274030:V384I	V	+	1	0	USP53	120408885	0.000000	0.05858	0.020000	0.16555	0.706000	0.40770	0.322000	0.19576	-0.017000	0.14103	-0.253000	0.11424	GTA	.	.	.	none		0.289	USP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364564.2	XM_052597		A	120189437	G	A	120189437	3	1	264	1	0	0	0	0	1	0	0	0	17096	1377	48	2	1188	2	USP53	4	120189437	Missense_Mutation	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10	4440392	120189437	70964839	43	16548											
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123159421	123159421	+	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	gcctttgttggctggtgaaaAggaaagtccttcatctgttg	8	14	12	7	0	2	1	1	1	1	0	3	2	3	2	2	3	0	3	2	3	3	4			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr4:123159421A>T	ENST00000264501.4	+	28	4122	c.3749A>T	c.(3748-3750)aAg>aTg	p.K1250M	KIAA1109_ENST00000495260.1_3'UTR|KIAA1109_ENST00000388738.3_Missense_Mutation_p.K1250M|KIAA1109_ENST00000455637.1_Missense_Mutation_p.K1250M			Q2LD37	K1109_HUMAN	KIAA1109	1250					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						GCTGGTGAAAAGGAAAGTCCT	0.428																																					p.K1250M		Atlas-SNP	.											.	KIAA1109	424	.	0			c.A3749T						PASS	.						140	130	133					4																	123159421		1892	4124	6016	SO:0001583	missense	84162	exon26			GTGAAAAGGAAAG	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.3749A>T	chr4.hg19:g.123159421A>T	ENSP00000264501:p.Lys1250Met	99.0	0.0	.		115.0	48.0	.	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.21|16.21	3.059532|3.059532	0.55325|0.55325	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637|ENST00000424425	T;T;T|.	0.27557|.	2.25;2.25;1.66|.	5.68|5.68	4.49|4.49	0.54785|0.54785	.|.	0.121477|0.121477	0.31784|0.31784	U|U	0.007068|0.007068	T|T	0.29783|0.29783	0.0744|0.0744	N|N	0.19112|0.19112	0.55|0.55	0.30998|0.30998	N|N	0.720613|0.720613	P|.	0.43094|.	0.799|.	P|.	0.45946|.	0.498|.	T|T	0.28364|0.28364	-1.0046|-1.0046	10|6	0.72032|.	D|.	0.01|.	.|.	9.5739|9.5739	0.39445|0.39445	0.8588:0.0:0.1412:0.0|0.8588:0.0:0.1412:0.0	.|.	1250|.	Q2LD37|.	K1109_HUMAN|.	M|N	1250|1081	ENSP00000264501:K1250M;ENSP00000373390:K1250M;ENSP00000389925:K1250M|.	ENSP00000264501:K1250M|.	K|K	+|+	2|3	0|2	KIAA1109|KIAA1109	123378871|123378871	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.941000|0.941000	0.58515|0.58515	4.307000|4.307000	0.59123|0.59123	0.990000|0.990000	0.38787|0.38787	0.477000|0.477000	0.44152|0.44152	AAG|AAA	.	.	.	none		0.428	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		T	123159421	A	T	123159421	3	4	264	1	0	0	0	0	1	0	0	0	8215	72	3	5	3851	5	KIAA1109	4	123159421	Missense_Mutation	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	2969984	123159421	67994855	44	16549											
CDH10	1008	hgsc.bcm.edu	37	chr5	24535913	24535913	+	Frame_Shift_Del	DEL	A	A	-																															catcggcatctgtagctgtgActtgcaccacagaagtacct																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr5:24535913delA	ENST00000264463.4	-	4	1052	c.545delT	c.(544-546)gtcfs	p.V182fs		NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 (T2-cadherin)	182	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(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)		TGTAGCTGTGACTTGCACCAC	0.463										HNSCC(23;0.051)																											p.V182fs		Atlas-Indel,Pindel	.											.	CDH10	391	.	0			c.546delC						PASS	.						107	98	101					5																	24535913		2203	4300	6503	SO:0001589	frameshift_variant	1008	exon4			.	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.545delT	chr5.hg19:g.24535913delA	ENSP00000264463:p.Val182fs	67.0	0.0	0		45.0	28.0	0.622222	NM_006727	Q9ULB3	Frame_Shift_Del	DEL	ENST00000264463.4	hg19	CCDS3892.1																																																																																			.	.	.	none		0.463	CDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207345.2	NM_006727		-	24535913	A	-	24535913	7	5	264	1	0	1	0	1	0	0	0	0	3098	275	10	0	1857	0	CDH10	5	24535913	Frame_Shift_Del	DEL	A	TCGA-UZ-A9PS-01A-11D-A42J-10		24535913	156379347	45	16550											
GZMK	3003	hgsc.bcm.edu	37	chr5	54327207	54327207	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtcagcttcaaacagccgcaAaactcaataaacatgtcaag	17	7	6	11	1	4	0	4	0	0	0	4	0	4	0	1	0	5	2	1	0	7	2			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr5:54327207A>G	ENST00000231009.2	+	4	449	c.379A>G	c.(379-381)Aaa>Gaa	p.K127E	CTD-2313F11.1_ENST00000609699.1_RNA|CTD-2313F11.1_ENST00000609792.1_RNA|CTD-2313F11.1_ENST00000595218.1_RNA|CTD-2313F11.1_ENST00000596137.1_RNA	NM_002104.2	NP_002095.1	P49863	GRAK_HUMAN	granzyme K (granzyme 3; tryptase II)	127	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)	15		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)				AACAGCCGCAAAACTCAATAA	0.443																																					p.K127E		Atlas-SNP	.											.	GZMK	39	.	0			c.A379G						PASS	.						74	79	77					5																	54327207		2203	4300	6503	SO:0001583	missense	3003	exon4			GCCGCAAAACTCA	BC035802	CCDS3964.1	5q11.2	2008-05-15	2005-08-17		ENSG00000113088	ENSG00000113088			4711	protein-coding gene	gene with protein product		600784	"granzyme K (serine protease, granzyme 3; tryptase II)"			7758581	Standard	NM_002104		Approved	TRYP2, PRSS	uc003jpl.1	P49863	OTTHUMG00000097009	ENST00000231009.2:c.379A>G	chr5.hg19:g.54327207A>G	ENSP00000231009:p.Lys127Glu	160.0	0.0	.		177.0	77.0	.	NM_002104	B2R563	Missense_Mutation	SNP	ENST00000231009.2	hg19	CCDS3964.1	.	.	.	.	.	.	.	.	.	.	A	6.131	0.392489	0.11638	.	.	ENSG00000113088	ENST00000231009	D	0.88664	-2.41	4.78	0.361	0.16107	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.503112	0.19871	N	0.104186	T	0.76492	0.3995	L	0.33668	1.02	0.09310	N	0.999996	B	0.02656	0.0	B	0.08055	0.003	T	0.56649	-0.7944	10	0.08837	T	0.75	.	4.6689	0.12680	0.62:0.158:0.222:0.0	.	127	P49863	GRAK_HUMAN	E	127	ENSP00000231009:K127E	ENSP00000231009:K127E	K	+	1	0	GZMK	54362964	0.033000	0.19621	0.012000	0.15200	0.341000	0.28922	1.879000	0.39618	-0.075000	0.12798	-0.316000	0.08728	AAA	.	.	.	none		0.443	GZMK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214098.1	NM_002104		G	54327207	A	G	54327207	3	3	264	1	0	0	0	0	1	0	0	0	6925	15	1	3	393	3	GZMK	5	54327207	Missense_Mutation	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	29791294	54327207	126588053	46	16551											
MAST4	375449	hgsc.bcm.edu	37	chr5	66448607	66448607	+	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	cagccgattgtgatccacagTtcggggaagaactacggctt	10	9	12	10	3	0	2	0	1	0	1	2	4	1	3	2	3	3	2	2	3	3	4			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr5:66448607T>A	ENST00000403625.2	+	25	3733	c.3438T>A	c.(3436-3438)agT>agA	p.S1146R	MAST4_ENST00000261569.7_Missense_Mutation_p.S952R|MAST4_ENST00000403666.1_Missense_Mutation_p.S957R|MAST4_ENST00000405643.1_Missense_Mutation_p.S967R|MAST4_ENST00000404260.3_Missense_Mutation_p.S1149R	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	1149	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.					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)		TGATCCACAGTTCGGGGAAGA	0.532																																					p.S1146R		Atlas-SNP	.											.	MAST4	218	.	0			c.T3438A						PASS	.						89	90	90					5																	66448607		1970	4163	6133	SO:0001583	missense	375449	exon25			CCACAGTTCGGGG	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.3438T>A	chr5.hg19:g.66448607T>A	ENSP00000385727:p.Ser1146Arg	126.0	0.0	.		121.0	48.0	.	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	hg19	CCDS54861.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.09|14.09	2.431177|2.431177	0.43122|0.43122	.|.	.|.	ENSG00000069020|ENSG00000069020	ENST00000443808|ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569;ENST00000432399	.|T;T;T;T;T	.|0.40756	.|1.02;1.02;1.02;1.02;1.02	6.17|6.17	-3.57|-3.57	0.04612|0.04612	.|PDZ/DHR/GLGF (2);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.28200|0.28200	0.0696|0.0696	N|N	0.02286|0.02286	-0.61|-0.61	0.33633|0.33633	D|D	0.606291|0.606291	.|D;P	.|0.71674	.|0.998;0.712	.|D;B	.|0.79108	.|0.992;0.327	T|T	0.38693|0.38693	-0.9649|-0.9649	5|10	.|0.05620	.|T	.|0.96	-18.4408|-18.4408	14.5549|14.5549	0.68094|0.68094	0.0:0.5151:0.0:0.4849|0.0:0.5151:0.0:0.4849	.|.	.|1149;957	.|O15021;O15021-3	.|MAST4_HUMAN;.	I|R	203|1149;1146;957;967;967;952;885	.|ENSP00000385048:S1149R;ENSP00000385727:S1146R;ENSP00000384313:S957R;ENSP00000384099:S967R;ENSP00000261569:S952R	.|ENSP00000261569:S952R	F|S	+|+	1|3	0|2	MAST4|MAST4	66484363|66484363	0.699000|0.699000	0.27786|0.27786	0.769000|0.769000	0.31535|0.31535	0.947000|0.947000	0.59692|0.59692	-0.116000|-0.116000	0.10724|0.10724	-0.539000|-0.539000	0.06273|0.06273	0.533000|0.533000	0.62120|0.62120	TTC|AGT	.	.	.	none		0.532	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			A	66448607	T	A	66448607	3	1	264	1	0	0	0	0	1	0	0	0	9334	1722	60	5	3666	5	MAST4	5	66448607	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	12121400	66448607	114466653	47	16552											
AGGF1	55109	hgsc.bcm.edu	37	chr5	76326724	76326724	+	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	gctgcaagcggcaggtgcggGagatcgagaagctgctgcat	9	6	17	9	3	0	2	0	0	0	2	1	4	0	2	0	3	6	6	0	3	2	0			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr5:76326724G>A	ENST00000312916.7	+	1	515	c.133G>A	c.(133-135)Gag>Aag	p.E45K	AGGF1_ENST00000503538.1_Intron|AGGF1_ENST00000506806.1_Missense_Mutation_p.E45K	NM_018046.4	NP_060516.2	Q8N302	AGGF1_HUMAN	angiogenic factor with G patch and FHA domains 1	45					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)		GCAGGTGCGGGAGATCGAGAA	0.657																																					p.E45K		Atlas-SNP	.											.	AGGF1	71	.	0			c.G133A						PASS	.						62	60	61					5																	76326724		2203	4300	6503	SO:0001583	missense	55109	exon1			GTGCGGGAGATCG	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.133G>A	chr5.hg19:g.76326724G>A	ENSP00000316109:p.Glu45Lys	979.0	1.0	.		916.0	356.0	.	NM_018046	O00581|Q53YS3|Q9BU84|Q9NW66	Missense_Mutation	SNP	ENST00000312916.7	hg19	CCDS4035.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.026317	0.75390	.	.	ENSG00000164252	ENST00000312916;ENST00000506806	T;T	0.79033	1.36;-1.23	4.04	4.04	0.47022	.	0.131176	0.51477	D	0.000092	T	0.63402	0.2508	N	0.24115	0.695	0.33944	D	0.643624	B;B	0.28998	0.048;0.23	B;B	0.28849	0.029;0.095	T	0.68685	-0.5343	10	0.26408	T	0.33	-20.5081	11.9022	0.52690	0.0:0.0:1.0:0.0	.	45;45	Q8N302;Q8N302-3	AGGF1_HUMAN;.	K	45	ENSP00000316109:E45K;ENSP00000424733:E45K	ENSP00000316109:E45K	E	+	1	0	AGGF1	76362480	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.934000	0.56553	2.258000	0.74832	0.555000	0.69702	GAG	.	.	.	none		0.657	AGGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219971.2	NM_018046		A	76326724	G	A	76326724	3	1	264	1	0	0	0	0	1	0	0	0	382	1175	41	2	135	2	AGGF1	5	76326724	Missense_Mutation	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10	9878117	76326724	104588536	48	16553											
APC	324	hgsc.bcm.edu	37	chr5	112177639	112177639	+	Missense_Mutation	SNP	T	T	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	tccatagtaagtagtttacaTcaagctgctgctgctgcatg	10	13	9	9	0	1	0	1	0	0	0	2	0	2	0	1	0	6	8	1	0	5	5			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr5:112177639T>G	ENST00000457016.1	+	16	6728	c.6348T>G	c.(6346-6348)caT>caG	p.H2116Q	APC_ENST00000257430.4_Missense_Mutation_p.H2116Q|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Missense_Mutation_p.H2116Q			P25054	APC_HUMAN	adenomatous polyposis coli	2116	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)		GTAGTTTACATCAAGCTGCTG	0.408		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.H2116Q	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.T6348G						PASS	.						105	109	108					5																	112177639		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,	TTTACATCAAGCT	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.6348T>G	chr5.hg19:g.112177639T>G	ENSP00000413133:p.His2116Gln	84.0	0.0	.		111.0	50.0	.	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	hg19	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	T	12.77	2.038546	0.35989	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.91011	-2.77;-2.77;-2.77	5.9	1.66	0.24008	.	0.042186	0.85682	D	0.000000	D	0.89283	0.6671	L	0.39245	1.2	0.51233	D	0.999917	D;D	0.67145	0.996;0.996	P;P	0.56788	0.806;0.737	D	0.85416	0.1140	9	.	.	.	-17.2926	9.2445	0.37518	0.0:0.2467:0.0:0.7533	.	2118;2116	Q4LE70;P25054	.;APC_HUMAN	Q	2116	ENSP00000413133:H2116Q;ENSP00000257430:H2116Q;ENSP00000427089:H2116Q	.	H	+	3	2	APC	112205538	0.990000	0.36364	1.000000	0.80357	0.990000	0.78478	0.132000	0.15891	0.335000	0.23614	-0.263000	0.10527	CAT	.	.	.	none		0.408	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112177639	T	G	112177639	3	3	264	1	0	0	0	0	1	0	0	0	763	1432	50	5	6406	5	APC	5	112177639	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	35850915	112177639	68737621	49	16554											
FBXO38	81545	hgsc.bcm.edu	37	chr5	147806844	147806844	+	Frame_Shift_Del	DEL	T	T	-																															agatgggccagtcgaagcagTttcccctcgaggaaagcagc																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr5:147806844delT	ENST00000340253.5	+	15	2155	c.1987delT	c.(1987-1989)tttfs	p.F663fs	CTD-2283N19.1_ENST00000520980.2_RNA|FBXO38_ENST00000296701.6_Intron|FBXO38_ENST00000394370.3_Frame_Shift_Del_p.F663fs|FBXO38_ENST00000513826.1_Intron			Q6PIJ6	FBX38_HUMAN	F-box protein 38	663					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)			GTCGAAGCAGTTTCCCCTCGA	0.478																																					p.Q662fs		Atlas-Indel,Pindel	.											.	FBXO38	115	.	0			c.1986delG						PASS	.						62	57	59					5																	147806844		2203	4300	6503	SO:0001589	frameshift_variant	81545	exon15			.	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.1987delT	chr5.hg19:g.147806844delT	ENSP00000342023:p.Phe663fs	248.0	0.0	0		259.0	124.0	0.478764	NM_030793	Q6PK72|Q7Z2U0|Q86VN3|Q9BXY6|Q9H837|Q9HC40	Frame_Shift_Del	DEL	ENST00000340253.5	hg19																																																																																				.	.	.	none		0.478	FBXO38-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000252185.2	NM_030793		-	147806844	T	-	147806844	7	5	264	1	0	1	0	1	0	0	0	0	5753	1725	60	0	2041	0	FBXO38	5	147806844	Frame_Shift_Del	DEL	T	TCGA-UZ-A9PS-01A-11D-A42J-10	35629205	147806844	33108416	50	16555											
ARHGEF37	389337	hgsc.bcm.edu	37	chr5	149006771	149006772	+	In_Frame_Ins	INS	-	-	TGGCCA																															tctgcctcggggccaaatcgINStggccatccttcaaaacaag																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr5:149006771_149006772insTGGCCA	ENST00000333677.6	+	11	1760_1761	c.1597_1598insTGGCCA	c.(1597-1599)gtg>gTGGCCAtg	p.533_534insAM		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	533	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						GGGCCAAATCGTGGCCATCCTT	0.609																																					p.V533delinsVAM		Atlas-Indel,Pindel	.											.	ARHGEF37	45	.	0			c.1597_1598insTGGCCA						PASS	.																																			SO:0001652	inframe_insertion	389337	exon11			.	BC041325	CCDS43385.1	5q33.1	2012-07-24			ENSG00000183111	ENSG00000183111		"Rho guanine nucleotide exchange factors"	34430	protein-coding gene	gene with protein product							Standard	XM_005268448		Approved	FLJ41603	uc003lra.1	A1IGU5	OTTHUMG00000163491	ENST00000333677.6:c.1598_1603dupTGGCCA	chr5.hg19:g.149006772_149006777dupTGGCCA	ENSP00000328083:p.Val533_Ala534insAlaMet	97.0	0.0	0		94.0	22.0	0.234043	NM_001001669	Q6ZW51	In_Frame_Ins	INS	ENST00000333677.6	hg19	CCDS43385.1																																																																																			.	.	.	none		0.609	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1	NM_001001669		TGGCCA	149006772	-	TGGCCA	149006771	7	5	264	1	0	1	1	0	0	0	0	0	906	1145	40	0	1635	0	ARHGEF37	5	149006771	In_Frame_Ins	INS	-	TCGA-UZ-A9PS-01A-11D-A42J-10	1199927	149006771	31908489	51	16556											
ODZ2	57451	hgsc.bcm.edu	37	chr5	167622284	167622285	+	Frame_Shift_Ins	INS	-	-	CCCGCCAGGATGGCACGTGAGT																															aaaatacggctacaccatcaINScccgccaggatggcacgtga																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr5:167622284_167622285insCCCGCCAGGATGGCACGTGAGT	ENST00000518659.1	+	15	2923_2924	c.2884_2885insCCCGCCAGGATGGCACGTGAGT	c.(2884-2886)accfs	p.-962fs	TENM2_ENST00000545108.1_Frame_Shift_Ins_p.-962fs|TENM2_ENST00000519204.1_Frame_Shift_Ins_p.-841fs|TENM2_ENST00000403607.2_Frame_Shift_Ins_p.-786fs|TENM2_ENST00000520394.1_Frame_Shift_Ins_p.-730fs	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2						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)										CTACACCATCACCCGCCAGGAT	0.545																																					p.T953_R954delinsTRQDGTX		Pindel	.											.	.	.	.	0			c.2857_2858insCCCGCCAGGATGGCACGTGAGT						PASS	.																																			SO:0001589	frameshift_variant	57451	exon15			.	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	Exception_encountered	chr5.hg19:g.167622284_167622285insCCCGCCAGGATGGCACGTGAGT	ENSP00000429430:p.Thr962fs	84.0	0.0	.		88.0	21.0	0.239	NM_001122679	Q9ULU2	Frame_Shift_Ins	INS	ENST00000518659.1	hg19																																																																																				.	.	.	none		0.545	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		CCCGCCAGGATGGCACGTGAGT	167622285	-	CCCGCCAGGATGGCACGTGAGT	167622284	7	5	264	1	0	1	1	0	0	0	0	0	10842	159	6	0	2915	0	ODZ2	5	167622284	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PS-01A-11D-A42J-10	18615513	167622284	13292976	52	16557											
NPM1	4869	hgsc.bcm.edu	37	chr5	170818328	170818329	+	Frame_Shift_Ins	INS	-	-	A																															gtcagtttaggggctggtgcINSaaaggatgagttgcacattg																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr5:170818328_170818329insA	ENST00000296930.5	+	3	459_460	c.158_159insA	c.(157-162)gcaaagfs	p.AK53fs	NPM1_ENST00000351986.6_Frame_Shift_Ins_p.AK53fs|NPM1_ENST00000517671.1_Frame_Shift_Ins_p.AK53fs|NPM1_ENST00000393820.2_Frame_Shift_Ins_p.AK53fs	NM_002520.6	NP_002511.1	P06748	NPM_HUMAN	nucleophosmin (nucleolar phosphoprotein B23, numatrin)	53	Necessary for interaction with APEX1.|Required for interaction with SENP3.				cell aging (GO:0007569)|CENP-A containing nucleosome assembly (GO:0034080)|centrosome cycle (GO:0007098)|DNA repair (GO:0006281)|intracellular protein transport (GO:0006886)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of centrosome duplication (GO:0010826)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|nucleocytoplasmic transport (GO:0006913)|nucleosome assembly (GO:0006334)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of translation (GO:0045727)|protein localization (GO:0008104)|protein oligomerization (GO:0051259)|regulation of centriole replication (GO:0046599)|regulation of eIF2 alpha phosphorylation by dsRNA (GO:0060735)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of endoribonuclease activity (GO:0060699)|response to stress (GO:0006950)|ribosome assembly (GO:0042255)|signal transduction (GO:0007165)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle pole centrosome (GO:0031616)	histone binding (GO:0042393)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|unfolded protein binding (GO:0051082)		NPM1/ALK(632)	central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4261)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	4269	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			GGGGCTGGTGCAAAGGATGAGT	0.411			"T, F "	"ALK, RARA, MLF1"	"NHL, APL, AML"																																p.A53fs		Atlas-INDEL	.		Dom	yes		5	5q35	4869	"nucleophosmin (nucleolar phosphoprotein B23, numatrin)"		L	.	NPM1	5003	.	0			c.158_159insA						PASS	.																																			SO:0001589	frameshift_variant	4869	exon3			.	M26697	CCDS4376.1, CCDS4377.1, CCDS43399.1	5q35.1	2014-09-17			ENSG00000181163	ENSG00000181163			7910	protein-coding gene	gene with protein product	"nucleolar phosphoprotein B23", "numatrin", "nucleophosmin/nucleoplasmin family, member 1"	164040				8471164, 8122112	Standard	NM_002520		Approved	B23, NPM	uc003mbi.3	P06748	OTTHUMG00000130465	ENST00000296930.5:c.161dupA	chr5.hg19:g.170818331_170818331dupA	ENSP00000296930:p.Ala53fs	29.0	0.0	0		26.0	12.0	0.461538	NM_199185	A8K3N7|B5BU00|D3DQL6|P08693|Q12826|Q13440|Q13441|Q14115|Q5EU94|Q5EU95|Q5EU96|Q5EU97|Q5EU98|Q5EU99|Q6V962|Q8WTW5|Q96AT6|Q96DC4|Q96EA5|Q9BYG9|Q9UDJ7	Frame_Shift_Ins	INS	ENST00000296930.5	hg19	CCDS4376.1																																																																																			.	.	.	none		0.411	NPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252858.2	NM_002520		A	170818329	-	A	170818328	7	5	264	1	0	1	1	0	0	0	0	0	10594	710	25	0	168	0	NPM1	5	170818328	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PS-01A-11D-A42J-10	3196044	170818328	10096932	53	16558											
C6orf146	222826	hgsc.bcm.edu	37	chr6	4073537	4073537	+	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	tatggtacttccttcattaaGaggacaattccataattgaa	14	14	6	7	0	1	2	1	1	0	1	3	3	3	3	2	2	1	1	2	2	6	8			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr6:4073537G>C	ENST00000274673.3	-	6	677	c.274C>G	c.(274-276)Ctt>Gtt	p.L92V	FAM217A_ENST00000380188.2_5'UTR	NM_173563.2	NP_775834.2	Q8IXS0	F217A_HUMAN	family with sequence similarity 217, member A	92																	CCTTCATTAAGAGGACAATTC	0.284																																					p.L92V		Atlas-SNP	.											.	.	.	.	0			c.C274G						PASS	.						88	91	90					6																	4073537		2200	4298	6498	SO:0001583	missense	222826	exon6			CATTAAGAGGACA	BC039349	CCDS4489.1	6p25.1	2012-02-07	2012-02-07	2012-02-07	ENSG00000145975	ENSG00000145975			21362	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 146"	C6orf146			Standard	NM_173563		Approved	MGC43581	uc003mvx.3	Q8IXS0	OTTHUMG00000014159	ENST00000274673.3:c.274C>G	chr6.hg19:g.4073537G>C	ENSP00000274673:p.Leu92Val	141.0	0.0	.		167.0	72.0	.	NM_173563	Q5JYK1	Missense_Mutation	SNP	ENST00000274673.3	hg19	CCDS4489.1	.	.	.	.	.	.	.	.	.	.	G	3.603	-0.081079	0.07141	.	.	ENSG00000145975	ENST00000274673;ENST00000470599;ENST00000498677;ENST00000492651	T	0.13657	2.57	4.94	2.43	0.29744	.	0.789154	0.10830	N	0.629459	T	0.01523	0.0049	N	0.12746	0.255	0.19300	N	0.999974	B	0.17038	0.02	B	0.15484	0.013	T	0.48658	-0.9016	10	0.08381	T	0.77	-3.6355	4.8234	0.13403	0.1733:0.1967:0.63:0.0	.	92	Q8IXS0	CF146_HUMAN	V	92;220;29;29	ENSP00000274673:L92V	ENSP00000274673:L92V	L	-	1	0	C6orf146	4018536	0.351000	0.24887	0.297000	0.24988	0.263000	0.26337	0.157000	0.16402	0.340000	0.23745	0.467000	0.42956	CTT	.	.	.	none		0.284	FAM217A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352577.2	NM_173563		C	4073537	G	C	4073537	3	2	264	1	0	0	0	0	1	0	0	0	2337	942	33	4	1260	4	C6orf146	6	4073537	Missense_Mutation	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10		4073537	167041530	54	16559											
HIST1H4E	8367	hgsc.bcm.edu	37	chr6	26204932	26204932	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaggcgctaagcgtcaccgTaaggtcctgcgagataacat	11	7	13	10	4	1	1	1	0	0	1	2	3	2	2	2	3	3	2	2	3	3	3	rs147263244		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr6:26204932T>C	ENST00000360441.4	+	1	75	c.60T>C	c.(58-60)cgT>cgC	p.R20R		NM_003545.3	NP_003536.1	P62805	H4_HUMAN	histone cluster 1, H4e	20					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(2)	18		all_hematologic(11;0.196)				AGCGTCACCGTAAGGTCCTGC	0.552																																					p.R20R		Atlas-SNP	.											.	HIST1H4E	22	.	0			c.T60C						PASS	.						86	85	85					6																	26204932		2203	4300	6503	SO:0001819	synonymous_variant	8367	exon1			TCACCGTAAGGTC	Z80787	CCDS4593.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000198518	ENSG00000276966		"Histones / Replication-dependent"	4790	protein-coding gene	gene with protein product		602830	"H4 histone family, member J", "histone 1, H4e"	H4FJ		9119399, 12408966	Standard	NM_003545		Approved	H4/j	uc003ngy.3	P62805	OTTHUMG00000014441	ENST00000360441.4:c.60T>C	chr6.hg19:g.26204932T>C		92.0	0.0	.		104.0	46.0	.	NM_003545	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000360441.4	hg19	CCDS4593.1																																																																																			.	T|1.000;A|0.000	.	alt		0.552	HIST1H4E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040104.1	NM_003545		C	26204932	T	C	26204932	2	2	264	1	0	0	0	0	0	0	0	1	7176	1625	57	3		3	HIST1H4E	6	26204932	Silent	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	22131395	26204932	144910135	55	16560											
GTF2H4	2968	hgsc.bcm.edu	37	chr6	30877807	30877807	+	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	cctcatcctcaaccccatttTccgccagaacctccgcattg	8	10	4	19	2	2	1	2	0	0	1	5	1	5	1	8	0	2	1	8	0	2	3			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr6:30877807T>A	ENST00000259895.4	+	4	564	c.341T>A	c.(340-342)tTc>tAc	p.F114Y	GTF2H4_ENST00000539324.1_Missense_Mutation_p.F58Y|GTF2H4_ENST00000376316.2_Missense_Mutation_p.F114Y|RN7SL175P_ENST00000580375.1_RNA	NM_001517.4	NP_001508.1	Q92759	TF2H4_HUMAN	general transcription factor IIH, polypeptide 4, 52kDa	114					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						AACCCCATTTTCCGCCAGAAC	0.567								Nucleotide excision repair (NER)																													p.F114Y		Atlas-SNP	.											.	GTF2H4	38	.	0			c.T341A						PASS	.						115	132	126					6																	30877807		1510	2708	4218	SO:0001583	missense	2968	exon4			CCATTTTCCGCCA	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.341T>A	chr6.hg19:g.30877807T>A	ENSP00000259895:p.Phe114Tyr	75.0	0.0	.		77.0	22.0	.	NM_001517	B4DTJ5|Q76KU4	Missense_Mutation	SNP	ENST00000259895.4	hg19	CCDS34386.1	.	.	.	.	.	.	.	.	.	.	T	29.6	5.016695	0.93404	.	.	ENSG00000213780	ENST00000259895;ENST00000539324;ENST00000376316;ENST00000453897	T;T;T;T	0.60299	0.2;0.2;0.2;0.2	5.6	5.6	0.85130	.	0.000000	0.64402	U	0.000001	T	0.68641	0.3023	M	0.83012	2.62	0.80722	D	1	D;D;P;P	0.63046	0.992;0.959;0.825;0.825	P;P;P;P	0.61397	0.888;0.71;0.467;0.467	T	0.73392	-0.3997	10	0.51188	T	0.08	-11.768	13.7555	0.62935	0.0:0.0:0.0:1.0	.	120;58;114;114	B4DNU0;B4DTJ5;Q53HH3;Q92759	.;.;.;TF2H4_HUMAN	Y	114;58;114;114	ENSP00000259895:F114Y;ENSP00000442700:F58Y;ENSP00000365493:F114Y;ENSP00000410160:F114Y	ENSP00000259895:F114Y	F	+	2	0	GTF2H4	30985786	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.991000	0.76232	2.130000	0.65690	0.482000	0.46254	TTC	.	.	.	none		0.567	GTF2H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076044.3	NM_001517		A	30877807	T	A	30877807	3	1	264	1	0	0	0	0	1	0	0	0	6872	1783	62	5	351	5	GTF2H4	6	30877807	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	4672875	30877807	140237260	56	16561											
SPDEF	25803	hgsc.bcm.edu	37	chr6	34508841	34508841	+	Missense_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	ggaactgctcctccgacatgGcgcacagctccttgcccgcc	6	7	10	18	3	0	0	0	0	0	0	3	2	3	1	5	2	4	3	5	2	1	1			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr6:34508841G>A	ENST00000374037.3	-	3	968	c.554C>T	c.(553-555)gCc>gTc	p.A185V	SPDEF_ENST00000544425.1_Missense_Mutation_p.A185V	NM_012391.2	NP_036523.1	O95238	SPDEF_HUMAN	SAM pointed domain containing ETS transcription factor	185	PNT. {ECO:0000255|PROSITE- ProRule:PRU00762}.				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						CTCCGACATGGCGCACAGCTC	0.652																																					p.A185V		Atlas-SNP	.											.	SPDEF	34	.	0			c.C554T						PASS	.						33	32	32					6																	34508841		2202	4299	6501	SO:0001583	missense	25803	exon3			GACATGGCGCACA	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.554C>T	chr6.hg19:g.34508841G>A	ENSP00000363149:p.Ala185Val	68.0	0.0	.		57.0	23.0	.	NM_001252294	B4DWH8|F5H778	Missense_Mutation	SNP	ENST00000374037.3	hg19	CCDS4794.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.319042	0.81469	.	.	ENSG00000124664	ENST00000374037;ENST00000544425	T;T	0.32023	1.47;1.47	5.65	4.77	0.60923	Sterile alpha motif/pointed domain (2);Pointed domain (3);	0.358823	0.31636	N	0.007318	T	0.26376	0.0644	M	0.73962	2.25	0.52099	D	0.999947	P;P	0.44521	0.837;0.521	B;B	0.42593	0.392;0.272	T	0.09185	-1.0686	10	0.46703	T	0.11	.	15.4502	0.75268	0.0:0.0:0.8599:0.1401	.	185;185	F5H778;O95238	.;SPDEF_HUMAN	V	185	ENSP00000363149:A185V;ENSP00000442715:A185V	ENSP00000363149:A185V	A	-	2	0	SPDEF	34616819	1.000000	0.71417	0.989000	0.46669	0.971000	0.66376	6.742000	0.74843	1.342000	0.45619	0.561000	0.74099	GCC	.	.	.	none		0.652	SPDEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040246.1	NM_012391		A	34508841	G	A	34508841	3	1	264	1	0	0	0	0	1	0	0	0	15038	1203	42	2	469	2	SPDEF	6	34508841	Missense_Mutation	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10	3631034	34508841	136606226	57	16562											
GPR110	266977	hgsc.bcm.edu	37	chr6	46973599	46973599	+	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	aaggcagacaacttgttgaaCagaagttgtcgcagctataa	15	9	10	7	1	0	3	0	1	0	2	1	3	0	3	0	1	3	5	0	1	6	5			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr6:46973599C>A	ENST00000371253.2	-	13	2762	c.2547G>T	c.(2545-2547)ctG>ctT	p.L849L	GPR110_ENST00000449332.2_5'UTR|GPR110_ENST00000283297.5_Silent_p.L652L	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	849					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						ACTTGTTGAACAGAAGTTGTC	0.373																																					p.L849L		Atlas-SNP	.											.	GPR110	102	.	0			c.G2547T						PASS	.						72	59	64					6																	46973599		2203	4300	6503	SO:0001819	synonymous_variant	266977	exon13			GTTGAACAGAAGT	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.2547G>T	chr6.hg19:g.46973599C>A		69.0	0.0	.		75.0	29.0	.	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Silent	SNP	ENST00000371253.2	hg19	CCDS34471.1																																																																																			.	.	.	none		0.373	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840		A	46973599	C	A	46973599	2	1	264	1	0	0	0	0	0	0	0	1	6634	465	17	4		4	GPR110	6	46973599	Silent	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	12464758	46973599	124141468	58	16563											
ARHGAP18	93663	hgsc.bcm.edu	37	chr6	129963090	129963090	+	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	agaatcctgggaaattgatcGatcaaatggaggcttctcca	13	10	10	8	1	2	2	1	1	1	1	5	5	3	4	2	3	0	1	2	3	3	2			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr6:129963090G>T	ENST00000368149.2	-	2	275	c.187C>A	c.(187-189)Cga>Aga	p.R63R		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)		GAAATTGATCGATCAAATGGA	0.388																																					p.R63R		Atlas-SNP	.											.	ARHGAP18	52	.	0			c.C187A						PASS	.						141	138	139					6																	129963090		2203	4300	6503	SO:0001819	synonymous_variant	93663	exon2			TTGATCGATCAAA	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.187C>A	chr6.hg19:g.129963090G>T		90.0	0.0	.		98.0	6.0	.	NM_033515		Silent	SNP	ENST00000368149.2	hg19	CCDS34535.1																																																																																			.	.	.	none		0.388	ARHGAP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042185.2	NM_033515		T	129963090	G	T	129963090	2	4	264	1	0	0	0	0	0	0	0	1	868	1066	37	4		4	ARHGAP18	6	129963090	Silent	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10	82989491	129963090	41151977	59	16564											
UTRN	7402	hgsc.bcm.edu	37	chr6	144744729	144744729	+	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	gtacatgccttaaataacgtCaacagagtgctgcaggtttt	12	12	9	8	1	1	1	1	0	0	1	1	1	1	1	1	1	6	4	1	1	5	5			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr6:144744729C>A	ENST00000367545.3	+	4	279	c.279C>A	c.(277-279)gtC>gtA	p.V93V		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	93	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				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)		TAAATAACGTCAACAGAGTGC	0.413																																					p.V93V		Atlas-SNP	.											.	UTRN	327	.	0			c.C279A						PASS	.						204	179	187					6																	144744729		2203	4300	6503	SO:0001819	synonymous_variant	7402	exon4			TAACGTCAACAGA	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.279C>A	chr6.hg19:g.144744729C>A		80.0	0.0	.		73.0	27.0	.	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Silent	SNP	ENST00000367545.3	hg19	CCDS34547.1																																																																																			.	.	.	none		0.413	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			A	144744729	C	A	144744729	2	1	264	1	0	0	0	0	0	0	0	1	17115	813	29	4		4	UTRN	6	144744729	Silent	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	14781639	144744729	26370338	60	16565											
RBM16	22828	hgsc.bcm.edu	37	chr6	155153549	155153549	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccctttaatacagcctggaAttccaccccaacggggaatc	11	9	7	14	1	0	0	0	0	0	0	3	2	2	2	5	3	3	0	5	3	5	4			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr6:155153549A>G	ENST00000367178.3	+	20	3412	c.2836A>G	c.(2836-2838)Att>Gtt	p.I946V	SCAF8_ENST00000417268.1_Missense_Mutation_p.I946V|TIAM2_ENST00000461783.3_5'Flank|SCAF8_ENST00000367186.4_Missense_Mutation_p.I1012V	NM_014892.3	NP_055707.3	Q9UPN6	SCAF8_HUMAN	SR-related CTD-associated factor 8	946	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						ACAGCCTGGAATTCCACCCCA	0.502																																					p.I946V		Atlas-SNP	.											.	SCAF8	122	.	0			c.A2836G						PASS	.						148	160	156					6																	155153549		2203	4300	6503	SO:0001583	missense	22828	exon20			CCTGGAATTCCAC	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.2836A>G	chr6.hg19:g.155153549A>G	ENSP00000356146:p.Ile946Val	115.0	0.0	.		83.0	31.0	.	NM_014892	B7Z888|Q5TBU6|Q6NSK3|Q9BQN8|Q9BX43	Missense_Mutation	SNP	ENST00000367178.3	hg19	CCDS5247.1	.	.	.	.	.	.	.	.	.	.	A	1.796	-0.478336	0.04414	.	.	ENSG00000213079	ENST00000367178;ENST00000417268;ENST00000367186	T;T;T	0.42513	0.99;0.99;0.97	5.58	-2.13	0.07144	.	0.310943	0.25708	U	0.028827	T	0.07098	0.0180	N	0.19112	0.55	0.21105	N	0.999786	P;P;P	0.35272	0.493;0.493;0.493	B;B;B	0.32928	0.155;0.155;0.155	T	0.40924	-0.9537	10	0.15952	T	0.53	.	6.918	0.24371	0.4362:0.4171:0.0598:0.087	.	991;1012;946	B7Z876;B7Z888;Q9UPN6	.;.;SCAF8_HUMAN	V	946;946;1012	ENSP00000356146:I946V;ENSP00000413098:I946V;ENSP00000356154:I1012V	ENSP00000356146:I946V	I	+	1	0	SCAF8	155195241	1.000000	0.71417	0.828000	0.32881	0.019000	0.09904	0.787000	0.26858	-0.163000	0.10946	-1.089000	0.02181	ATT	.	.	.	none		0.502	SCAF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042798.1	NM_014892		G	155153549	A	G	155153549	3	3	264	1	0	0	0	0	1	0	0	0	13131	101	4	3	2914	3	RBM16	6	155153549	Missense_Mutation	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	10408820	155153549	15961518	61	16566											
MAGI2	9863	hgsc.bcm.edu	37	chr7	77885345	77885345	+	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	tctgtatggctcaggttctgTacattctgctggttgatctc	5	17	10	9	0	5	1	1	1	4	0	6	1	5	1	0	3	2	6	0	3	2	5			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr7:77885345T>A	ENST00000354212.4	-	10	2215	c.1962A>T	c.(1960-1962)gtA>gtT	p.V654V	MAGI2_ENST00000419488.1_Silent_p.V654V|MAGI2_ENST00000535697.1_Silent_p.V491V|MAGI2_ENST00000522391.1_Silent_p.V654V|MAGI2_ENST00000536571.1_Silent_p.V486V	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	654	PDZ 3. {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)				TCAGGTTCTGTACATTCTGCT	0.458																																					p.V654V		Atlas-SNP	.											.	MAGI2	246	.	0			c.A1962T						PASS	.						72	60	64					7																	77885345		2203	4300	6503	SO:0001819	synonymous_variant	9863	exon10			GTTCTGTACATTC	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.1962A>T	chr7.hg19:g.77885345T>A		73.0	0.0	.		71.0	34.0	.	NM_012301	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Silent	SNP	ENST00000354212.4	hg19	CCDS5594.1																																																																																			.	.	.	none		0.458	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		A	77885345	T	A	77885345	2	1	264	1	0	0	0	0	0	0	0	1	9198	1625	57	5		5	MAGI2	7	77885345	Silent	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10		77885345	81253318	62	16567											
SEMA3E	9723	hgsc.bcm.edu	37	chr7	83023614	83023614	+	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	acacacacacagaacttaccCgctttgaagaaatctccata	16	8	4	13	1	1	3	0	1	1	2	2	3	1	3	2	0	2	1	2	0	5	3			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr7:83023614C>A	ENST00000307792.3	-	13	1966	c.1499G>T	c.(1498-1500)cGg>cTg	p.R500L	SEMA3E_ENST00000427262.1_Splice_Site_p.R440L	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	500	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)				aGAACTTACCCGCTTTGAAGA	0.313																																					p.R500L		Atlas-SNP	.											.	SEMA3E	125	.	0			c.G1499T						PASS	.						46	46	46					7																	83023614		2203	4297	6500	SO:0001630	splice_region_variant	9723	exon13			CTTACCCGCTTTG	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.1500+1G>T	chr7.hg19:g.83023614C>A		48.0	0.0	.		74.0	25.0	.	NM_012431	B4E1P1|Q75M94|Q75M97	Missense_Mutation	SNP	ENST00000307792.3	hg19	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	C	32	5.174122	0.94807	.	.	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514	T;T	0.11712	2.75;2.75	5.97	5.97	0.96955	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.35422	0.0931	M	0.72479	2.2	0.80722	D	1	D	0.69078	0.997	D	0.71656	0.974	T	0.00920	-1.1514	10	0.62326	D	0.03	.	20.4324	0.99085	0.0:1.0:0.0:0.0	.	500	O15041	SEM3E_HUMAN	L	500;440;500	ENSP00000303212:R500L;ENSP00000405052:R440L	ENSP00000303212:R500L	R	-	2	0	SEMA3E	82861550	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	5.122000	0.64697	2.833000	0.97629	0.585000	0.79938	CGG	.	.	.	none		0.313	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431	Missense_Mutation	A	83023614	C	A	83023614	5	1	264	1	0	0	0	0	0	0	1	0	14041	666	23	4	848	4	SEMA3E	7	83023614	Splice_Site	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	5138269	83023614	76115049	63	16568											
GATAD1	57798	hgsc.bcm.edu	37	chr7	92085728	92085728	+	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	gaagatggaatacttggaatTtgtttgtcatgcaccttctg	10	15	10	6	0	2	1	1	0	1	1	2	4	2	3	1	2	2	2	1	2	4	5			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr7:92085728T>A	ENST00000287957.3	+	5	939	c.662T>A	c.(661-663)tTt>tAt	p.F221Y	AC007566.10_ENST00000427458.1_RNA	NM_021167.4	NP_066990.3	Q8WUU5	GATD1_HUMAN	GATA zinc finger domain containing 1	221						nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|lung(3)	6	all_cancers(62;1.63e-10)|all_epithelial(64;8.33e-10)|Breast(17;0.00311)|all_lung(186;0.0498)|Lung NSC(181;0.0676)		STAD - Stomach adenocarcinoma(171;4.51e-05)|GBM - Glioblastoma multiforme(5;8.83e-05)|all cancers(6;0.000136)|Lung(22;0.123)|Epithelial(20;0.179)|LUSC - Lung squamous cell carcinoma(200;0.225)			TACTTGGAATTTGTTTGTCAT	0.433																																					p.F221Y		Atlas-SNP	.											.	GATAD1	10	.	0			c.T662A						PASS	.						163	148	153					7																	92085728		2203	4300	6503	SO:0001583	missense	57798	exon5			TGGAATTTGTTTG		CCDS5625.1	7q21-q22	2014-09-17			ENSG00000157259	ENSG00000157259		"GATA zinc finger domain containing"	29941	protein-coding gene	gene with protein product	"ocular development associated gene"	614518				12062807	Standard	NM_021167		Approved	ODAG, RG083M05.2, FLJ22489	uc003ulx.2	Q8WUU5	OTTHUMG00000131201	ENST00000287957.3:c.662T>A	chr7.hg19:g.92085728T>A	ENSP00000287957:p.Phe221Tyr	73.0	0.0	.		70.0	33.0	.	NM_021167	B2RE37|D6W5Q5|Q8N5Y5|Q99995|Q9H689	Missense_Mutation	SNP	ENST00000287957.3	hg19	CCDS5625.1	.	.	.	.	.	.	.	.	.	.	T	35	5.436365	0.96168	.	.	ENSG00000157259	ENST00000287957	T	0.68624	-0.34	5.77	5.77	0.91146	.	0.046872	0.85682	D	0.000000	T	0.72598	0.3480	M	0.82193	2.58	0.80722	D	1	P	0.40250	0.709	B	0.40410	0.328	T	0.78016	-0.2369	10	0.87932	D	0	-14.2119	16.1448	0.81559	0.0:0.0:0.0:1.0	.	221	Q8WUU5	GATD1_HUMAN	Y	221	ENSP00000287957:F221Y	ENSP00000287957:F221Y	F	+	2	0	GATAD1	91923664	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.010000	0.88615	2.210000	0.71456	0.472000	0.43445	TTT	.	.	.	none		0.433	GATAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253929.2	NM_021167		A	92085728	T	A	92085728	3	1	264	1	0	0	0	0	1	0	0	0	6266	1841	64	5	680	5	GATAD1	7	92085728	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	9062114	92085728	67052935	64	16569											
CUX1	1523	hgsc.bcm.edu	37	chr7	101891877	101891877	+	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	caccgaggagcccaagtctcAgggagaggccgagcgggagg	10	2	18	11	3	1	1	1	0	1	1	2	6	1	3	3	5	2	0	3	5	1	0			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr7:101891877A>T	ENST00000292535.7	+	24	4111	c.4073A>T	c.(4072-4074)cAg>cTg	p.Q1358L	CUX1_ENST00000393824.3_Intron|CUX1_ENST00000546411.2_Missense_Mutation_p.Q1256L|CUX1_ENST00000360264.3_Missense_Mutation_p.Q1369L|CUX1_ENST00000556210.1_Missense_Mutation_p.Q1200L|CUX1_ENST00000550008.2_Missense_Mutation_p.Q1302L|CUX1_ENST00000292538.4_Intron|CUX1_ENST00000549414.2_Missense_Mutation_p.Q1336L|CUX1_ENST00000560541.1_Intron|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000547394.2_Intron	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	1358					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						CCCAAGTCTCAGGGAGAGGCC	0.791																																					p.Q1369L		Atlas-SNP	.											.	CUX1	253	.	0			c.A4106T						PASS	.						3	3	3					7																	101891877		1346	2553	3899	SO:0001583	missense	1523	exon24			AGTCTCAGGGAGA	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.4073A>T	chr7.hg19:g.101891877A>T	ENSP00000292535:p.Gln1358Leu	50.0	0.0	.		38.0	14.0	.	NM_001202543	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000292535.7	hg19	CCDS5721.1	.	.	.	.	.	.	.	.	.	.	A	13.22	2.172495	0.38315	.	.	ENSG00000257923	ENST00000360264;ENST00000292535;ENST00000549414;ENST00000550008;ENST00000546411;ENST00000556210	T;T;T;T;T;T	0.61158	0.17;0.18;0.16;0.13;0.14;0.15	3.09	3.09	0.35607	.	7.025930	0.01253	U	0.008923	T	0.71048	0.3294	L	0.44542	1.39	0.80722	D	1	P;P	0.42039	0.659;0.769	P;P	0.61397	0.775;0.888	T	0.54957	-0.8215	10	0.31617	T	0.26	.	11.7319	0.51741	1.0:0.0:0.0:0.0	.	1358;1369	P39880;P39880-3	CUX1_HUMAN;.	L	1369;1358;1336;1302;1256;1200	ENSP00000353401:Q1369L;ENSP00000292535:Q1358L;ENSP00000446630:Q1336L;ENSP00000447373:Q1302L;ENSP00000450125:Q1256L;ENSP00000451558:Q1200L	ENSP00000292535:Q1358L	Q	+	2	0	CUX1	101678597	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	2.124000	0.42006	1.398000	0.46701	0.402000	0.26972	CAG	.	.	.	none		0.791	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913		T	101891877	A	T	101891877	3	4	264	1	0	0	0	0	1	0	0	0	4066	188	7	5	4234	5	CUX1	7	101891877	Missense_Mutation	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	9806149	101891877	57246786	65	16570											
HIPK2	28996	hgsc.bcm.edu	37	chr7	139305300	139305300	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctccatgttctggaaacaTgatttgacgctgttcatgca	10	14	8	9	1	3	2	1	2	2	0	4	3	3	3	1	1	2	4	1	1	1	3			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr7:139305300T>C	ENST00000406875.3	-	7	1723	c.1629A>G	c.(1627-1629)tcA>tcG	p.S543S	HIPK2_ENST00000342645.6_Silent_p.S543S|HIPK2_ENST00000428878.2_Silent_p.S543S	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	543	Interaction with SKI and SMAD1.				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)			breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					TCTGGAAACATGATTTGACGC	0.502											OREG0018361	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S543S		Atlas-SNP	.											.	HIPK2	192	.	0			c.A1629G						PASS	.						279	262	267					7																	139305300		2041	4230	6271	SO:0001819	synonymous_variant	28996	exon7			GAAACATGATTTG	AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"homeodomain-interacting protein kinase 2"			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.1629A>G	chr7.hg19:g.139305300T>C		73.0	0.0	.	1647	98.0	43.0	.	NM_022740	Q75MR7|Q8WWI4|Q9H2Y1	Silent	SNP	ENST00000406875.3	hg19																																																																																				.	.	.	none		0.502	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740		C	139305300	T	C	139305300	2	2	264	1	0	0	0	0	0	0	0	1	7124	1451	51	3		3	HIPK2	7	139305300	Silent	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	37413423	139305300	19833363	66	16571											
MLL3	58508	hgsc.bcm.edu	37	chr7	151874432	151874433	+	Frame_Shift_Del	DEL	TT	TT	-																															acttcaaccccctcaaggtcTttaacatccagttccttcac																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr7:151874432_151874433delTT	ENST00000262189.6	-	38	8323_8324	c.8105_8106delAA	c.(8104-8106)aaafs	p.K2702fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.K2702fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2702	Asp-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)										CCTCAAGGTCTTTAACATCCAG	0.386																																					p.2702_2703del		Atlas-Indel,Pindel	.											.	MLL3	1564	.	0			c.8106_8107del						PASS	.																																			SO:0001589	frameshift_variant	58508	exon38			.	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"Chromatin-modifying enzymes / K-methyltransferases", "Zinc fingers, PHD-type"	13726	protein-coding gene	gene with protein product		606833	"myeloid/lymphoid or mixed-lineage leukemia 3"	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.8105_8106delAA	chr7.hg19:g.151874432_151874433delTT	ENSP00000262189:p.Lys2702fs	86.0	0.0	0		88.0	33.0	0.375	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	hg19	CCDS5931.1																																																																																			.	.	.	none		0.386	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			-	151874433	TT	-	151874432	7	5	264	1	0	1	0	1	0	0	0	0	9629	1606	56	0	6717	0	MLL3	7	151874432	Frame_Shift_Del	DEL	TT	TCGA-UZ-A9PS-01A-11D-A42J-10	12569132	151874432	7264231	67	16572											
DPP6	1804	hgsc.bcm.edu	37	chr7	154684050	154684050	+	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	tgccttccttgcagatttacCcggacgaaagccattacttt	9	13	7	12	2	0	1	0	0	0	1	1	3	1	2	4	1	5	1	4	1	3	6	rs186233086		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr7:154684050C>A	ENST00000377770.3	+	26	2599	c.2458C>A	c.(2458-2460)Ccg>Acg	p.P820T	DPP6_ENST00000404039.1_Missense_Mutation_p.P756T|DPP6_ENST00000427557.1_Missense_Mutation_p.P713T|DPP6_ENST00000332007.3_Missense_Mutation_p.P758T			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	820					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			GCAGATTTACCCGGACGAAAG	0.517																																					p.P820T	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-SNP	.											.	DPP6	383	.	0			c.C2458A						PASS	.						87	92	91					7																	154684050		2008	4163	6171	SO:0001583	missense	1804	exon26			ATTTACCCGGACG	M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"dipeptidylpeptidase VI", "dipeptidylpeptidase 6"			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.2458C>A	chr7.hg19:g.154684050C>A	ENSP00000367001:p.Pro820Thr	99.0	0.0	.		115.0	49.0	.	NM_130797		Missense_Mutation	SNP	ENST00000377770.3	hg19		.	.	.	.	.	.	.	.	.	.	C	15.88	2.962931	0.53507	.	.	ENSG00000130226	ENST00000404039;ENST00000377770;ENST00000332007;ENST00000427557	T;T;T;T	0.54675	0.56;0.56;0.56;0.56	4.66	4.66	0.58398	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.66819	0.2828	L	0.53561	1.675	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.97110	0.986;0.999;1.0;0.999	T	0.62077	-0.6930	10	0.18710	T	0.47	-16.57	17.5681	0.87926	0.0:1.0:0.0:0.0	.	713;758;820;756	E9PDL2;P42658-2;P42658;E9PF59	.;.;DPP6_HUMAN;.	T	756;820;758;713	ENSP00000385578:P756T;ENSP00000367001:P820T;ENSP00000328226:P758T;ENSP00000397303:P713T	ENSP00000328226:P758T	P	+	1	0	DPP6	154314983	1.000000	0.71417	0.984000	0.44739	0.083000	0.17756	6.962000	0.76048	2.147000	0.66899	0.655000	0.94253	CCG	.	C|1.000;T|0.000	.	alt		0.517	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797		A	154684050	C	A	154684050	3	1	264	1	0	0	0	0	1	0	0	0	4732	623	22	4	2676	4	DPP6	7	154684050	Missense_Mutation	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	2809618	154684050	4454613	68	16573											
DLC1	10395	hgsc.bcm.edu	37	chr8	12957624	12957624	+	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	ccgactggctgctgctgctgCtggtctgcgtggagttggaa	4	11	16	10	2	1	0	0	0	1	0	1	3	1	2	1	4	5	6	1	4	1	1			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr8:12957624C>G	ENST00000276297.4	-	9	2631	c.2222G>C	c.(2221-2223)aGc>aCc	p.S741T	DLC1_ENST00000358919.2_Missense_Mutation_p.S304T|DLC1_ENST00000512044.2_Missense_Mutation_p.S338T|DLC1_ENST00000520226.1_Missense_Mutation_p.S230T	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	741	Focal adhesion-targeting (FAT).|Poly-Ser.				actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						GCTGCTGCTGCTGGTCTGCGT	0.627																																					p.S741T		Atlas-SNP	.											DLC1,bladder,carcinoma,0,3	DLC1	411	.	0			c.G2222C						PASS	.						56	47	50					8																	12957624		2203	4300	6503	SO:0001583	missense	10395	exon9			CTGCTGCTGGTCT	AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"Rho GTPase activating proteins", "StAR-related lipid transfer (START) domain containing"	2897	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 12"	604258	"deleted in liver cancer 1"			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.2222G>C	chr8.hg19:g.12957624C>G	ENSP00000276297:p.Ser741Thr	51.0	0.0	.		63.0	6.0	.	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Missense_Mutation	SNP	ENST00000276297.4	hg19	CCDS5989.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.320479	0.81469	.	.	ENSG00000164741	ENST00000276297;ENST00000358919;ENST00000512044;ENST00000520226	T;T;T;T	0.07688	3.42;3.19;3.19;3.17	4.57	4.57	0.56435	.	0.000000	0.85682	D	0.000000	T	0.31979	0.0814	M	0.80422	2.495	0.80722	D	1	D;B;D	0.65815	0.995;0.103;0.99	P;B;D	0.72982	0.795;0.132;0.979	T	0.09975	-1.0650	10	0.66056	D	0.02	.	17.9274	0.88987	0.0:1.0:0.0:0.0	.	741;338;304	Q96QB1;E9PDZ8;Q96QB1-1	RHG07_HUMAN;.;.	T	741;304;338;230	ENSP00000276297:S741T;ENSP00000351797:S304T;ENSP00000422595:S338T;ENSP00000428028:S230T	ENSP00000276297:S741T	S	-	2	0	DLC1	13001995	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.462000	0.80851	2.527000	0.85204	0.561000	0.74099	AGC	.	.	.	none		0.627	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		G	12957624	C	G	12957624	3	3	264	1	0	0	0	0	1	0	0	0	4552	797	28	4	2404	4	DLC1	8	12957624	Missense_Mutation	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10		12957624	133406398	69	16574											
DUSP4	1846	hgsc.bcm.edu	37	chr8	29195962	29195962	+	Silent	SNP	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	gcgtccagcatgtctctccgGgcagcatggtaggcactgcc	6	8	13	14	2	1	0	0	0	1	0	4	0	3	0	3	3	3	5	3	3	1	1			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr8:29195962G>A	ENST00000240100.2	-	3	1025	c.636C>T	c.(634-636)gcC>gcT	p.A212A	DUSP4_ENST00000240101.2_Silent_p.A121A	NM_001394.6	NP_001385.1	Q13115	DUS4_HUMAN	dual specificity phosphatase 4	212	Tyrosine-protein phosphatase.				endoderm formation (GO:0001706)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein dephosphorylation (GO:0006470)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|protein tyrosine/threonine phosphatase activity (GO:0008330)			endometrium(1)|large_intestine(1)|lung(4)	6				KIRC - Kidney renal clear cell carcinoma(542;0.094)|Kidney(114;0.113)		TGTCTCTCCGGGCAGCATGGT	0.562																																					p.A212A		Atlas-SNP	.											.	DUSP4	58	.	0			c.C636T						PASS	.						89	69	76					8																	29195962		2203	4300	6503	SO:0001819	synonymous_variant	1846	exon3			TCTCCGGGCAGCA	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.636C>T	chr8.hg19:g.29195962G>A		77.0	0.0	.		74.0	27.0	.	NM_001394	B2RBU5|D3DSU4|G5E930|Q13524	Silent	SNP	ENST00000240100.2	hg19	CCDS6072.1																																																																																			.	.	.	none		0.562	DUSP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257249.1	NM_001394		A	29195962	G	A	29195962	2	1	264	1	0	0	0	0	0	0	0	1	4829	1219	43	2		2	DUSP4	8	29195962	Silent	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10	16238338	29195962	117168060	70	16575											
COL14A1	7373	hgsc.bcm.edu	37	chr8	121170481	121170481	+	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	aaacttcttgtgactccaacTtcaggtaaaaacaattgact	15	12	5	9	0	2	2	1	2	1	0	3	2	3	2	1	1	3	1	1	1	6	5			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr8:121170481T>A	ENST00000297848.3	+	3	471	c.201T>A	c.(199-201)acT>acA	p.T67T	COL14A1_ENST00000537875.1_Silent_p.T67T|COL14A1_ENST00000309791.4_Silent_p.T67T|COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000247781.3_Silent_p.T67T	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)			TGACTCCAACTTCAGGTAAAA	0.348																																					p.T67T		Atlas-SNP	.											.	COL14A1	292	.	0			c.T201A						PASS	.						61	62	61					8																	121170481		2203	4299	6502	SO:0001819	synonymous_variant	7373	exon3			TCCAACTTCAGGT		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.201T>A	chr8.hg19:g.121170481T>A		109.0	0.0	.		100.0	48.0	.	NM_021110		Silent	SNP	ENST00000297848.3	hg19	CCDS34938.1																																																																																			.	.	.	none		0.348	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		A	121170481	T	A	121170481	2	1	264	1	0	0	0	0	0	0	0	1	3673	1596	56	5		5	COL14A1	8	121170481	Silent	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	91974519	121170481	25193541	71	16576											
TTC39B	158219	hgsc.bcm.edu	37	chr9	15211355	15211355	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacagcctgcaacaccacaaTggtactgtagcccaaggcat	13	6	9	13	0	0	0	0	0	0	0	0	1	0	0	3	2	5	4	3	2	5	2			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr9:15211355T>C	ENST00000512701.2	-	5	559	c.523A>G	c.(523-525)Att>Gtt	p.I175V	TTC39B_ENST00000380850.4_Missense_Mutation_p.I175V|TTC39B_ENST00000355694.2_Missense_Mutation_p.I109V|TTC39B_ENST00000541445.1_Missense_Mutation_p.I109V|TTC39B_ENST00000582994.1_5'Flank|TTC39B_ENST00000297615.5_Missense_Mutation_p.I106V|TTC39B_ENST00000507285.1_Missense_Mutation_p.I10V|TTC39B_ENST00000507993.1_Missense_Mutation_p.I10V			Q5VTQ0	TT39B_HUMAN	tetratricopeptide repeat domain 39B	175										NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)	21						AACACCACAATGGTACTGTAG	0.453																																					p.I175V		Atlas-SNP	.											.	TTC39B	83	.	0			c.A523G						PASS	.						149	127	135					9																	15211355		2203	4300	6503	SO:0001583	missense	158219	exon5			CCACAATGGTACT	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.523A>G	chr9.hg19:g.15211355T>C	ENSP00000422496:p.Ile175Val	129.0	0.0	.		123.0	47.0	.	NM_001168340	A5PLN1|B4DQ10|B4DQX4|B4DW93|Q8IVR7|Q8IXZ6|Q8N267	Missense_Mutation	SNP	ENST00000512701.2	hg19	CCDS6477.2	.	.	.	.	.	.	.	.	.	.	T	22.3	4.269430	0.80469	.	.	ENSG00000155158	ENST00000380850;ENST00000297615;ENST00000355694;ENST00000512701;ENST00000507285;ENST00000507993;ENST00000541445	T;T;T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0;1.0;1.0	5.79	5.79	0.91817	.	0.058027	0.64402	N	0.000002	T	0.60599	0.2281	M	0.63428	1.95	0.80722	D	1	P;P;D;P;P	0.65815	0.51;0.565;0.995;0.597;0.597	B;P;D;P;P	0.78314	0.327;0.456;0.991;0.53;0.53	T	0.55805	-0.8083	10	0.23302	T	0.38	-18.5916	15.7917	0.78369	0.0:0.0:0.0:1.0	.	106;175;175;109;109	F5H705;E9PAQ9;E9PE60;A5PLN1;Q5VTQ0	.;.;.;.;TT39B_HUMAN	V	175;106;109;175;10;10;109	ENSP00000370231:I175V;ENSP00000297615:I106V;ENSP00000347920:I109V;ENSP00000422496:I175V;ENSP00000426539:I10V;ENSP00000423392:I10V;ENSP00000442880:I109V	ENSP00000297615:I106V	I	-	1	0	TTC39B	15201355	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	7.701000	0.84566	2.218000	0.71995	0.533000	0.62120	ATT	.	.	.	none		0.453	TTC39B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051758.3	NM_152574		C	15211355	T	C	15211355	3	2	264	1	0	0	0	0	1	0	0	0	16720	1464	51	3	1610	3	TTC39B	9	15211355	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10		15211355	126002076	72	16577											
KIAA1797	54914	hgsc.bcm.edu	37	chr9	20740261	20740261	+	Missense_Mutation	SNP	T	T	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	acatggcttgataaaagccaTtatgcacttactacaaatgc	15	11	6	9	0	0	1	0	1	0	0	0	1	0	1	1	1	5	2	1	1	6	5			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr9:20740261T>G	ENST00000380249.1	+	7	678	c.314T>G	c.(313-315)aTt>aGt	p.I105S	FOCAD_ENST00000338382.6_Missense_Mutation_p.I105S	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	105						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											ATAAAAGCCATTATGCACTTA	0.313																																					p.I105S		Atlas-SNP	.											.	.	.	.	0			c.T314G						PASS	.						76	78	77					9																	20740261		2203	4297	6500	SO:0001583	missense	54914	exon7			AAGCCATTATGCA	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.314T>G	chr9.hg19:g.20740261T>G	ENSP00000369599:p.Ile105Ser	357.0	0.0	.		449.0	185.0	.	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	hg19	CCDS34993.1	.	.	.	.	.	.	.	.	.	.	T	19.26	3.793357	0.70452	.	.	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.24538	1.85;1.85	5.54	5.54	0.83059	Domain of unknown function DUF3730 (1);	0.320980	0.32819	N	0.005603	T	0.25419	0.0618	N	0.19112	0.55	0.43191	D	0.995023	P	0.46512	0.879	P	0.48598	0.583	T	0.04017	-1.0984	10	0.87932	D	0	-3.8635	13.8993	0.63792	0.0:0.0:0.0:1.0	.	105	Q5VW36	K1797_HUMAN	S	105	ENSP00000369599:I105S;ENSP00000344307:I105S	ENSP00000344307:I105S	I	+	2	0	KIAA1797	20730261	1.000000	0.71417	0.949000	0.38748	0.844000	0.47949	3.640000	0.54350	2.103000	0.63969	0.454000	0.30748	ATT	.	.	.	none		0.313	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		G	20740261	T	G	20740261	3	3	264	1	0	0	0	0	1	0	0	0	8265	1493	52	5	328	5	KIAA1797	9	20740261	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	5528906	20740261	120473170	73	16578											
ZFP37	7539	hgsc.bcm.edu	37	chr9	115805449	115805449	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttataaggtttctccttagtAtgagttctttgatgtataat	10	20	7	4	0	2	2	0	2	2	0	3	2	2	2	1	1	0	4	1	1	6	9			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr9:115805449A>G	ENST00000374227.3	-	4	1476	c.1449T>C	c.(1447-1449)caT>caC	p.H483H	ZFP37_ENST00000555206.1_Silent_p.H484H|ZFP37_ENST00000553380.1_Silent_p.H498H	NM_001282515.1|NM_001282518.1	NP_001269444.1|NP_001269447.1	Q9Y6Q3	ZFP37_HUMAN	ZFP37 zinc finger protein	483					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						TCTCCTTAGTATGAGTTCTTT	0.373																																					p.H483H		Atlas-SNP	.											.	ZFP37	93	.	0			c.T1449C						PASS	.						75	73	74					9																	115805449		2203	4300	6503	SO:0001819	synonymous_variant	7539	exon4			CTTAGTATGAGTT	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.1449T>C	chr9.hg19:g.115805449A>G		60.0	0.0	.		71.0	18.0	.	NM_003408	A0AVJ9|B4DVX4|G3V3L7|Q5T7Q4	Silent	SNP	ENST00000374227.3	hg19	CCDS6787.1																																																																																			.	.	.	none		0.373	ZFP37-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055439.1	NM_003408		G	115805449	A	G	115805449	2	3	264	1	0	0	0	0	0	0	0	1	17660	446	16	3		3	ZFP37	9	115805449	Silent	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	95065188	115805449	25407982	74	16579											
PHYHD1	254295	hgsc.bcm.edu	37	chr9	131689459	131689459	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attctccacccaggaagaggAgcagcttcgagcccaggtag	11	6	12	12	1	1	1	0	0	1	1	3	4	1	3	3	3	3	3	3	3	2	3			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr9:131689459A>G	ENST00000372592.3	+	4	1109	c.176A>G	c.(175-177)gAg>gGg	p.E59G	PHYHD1_ENST00000353176.5_Missense_Mutation_p.E59G|PHYHD1_ENST00000421063.2_Missense_Mutation_p.E59G|PHYHD1_ENST00000308941.5_Missense_Mutation_p.E59G	NM_001100876.1	NP_001094346.1	Q5SRE7	PHYD1_HUMAN	phytanoyl-CoA dioxygenase domain containing 1	59							dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|skin(1)|stomach(3)	10						CAGGAAGAGGAGCAGCTTCGA	0.582											OREG0019526	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E59G		Atlas-SNP	.											.	PHYHD1	29	.	0			c.A176G						PASS	.						137	118	124					9																	131689459		2203	4300	6503	SO:0001583	missense	254295	exon2			AAGAGGAGCAGCT	BC051300	CCDS6914.1, CCDS43885.1, CCDS43886.1	9q34.13	2010-08-13			ENSG00000175287	ENSG00000175287			23396	protein-coding gene	gene with protein product						12477932	Standard	NM_174933		Approved	MGC16638	uc004bwp.2	Q5SRE7	OTTHUMG00000020764	ENST00000372592.3:c.176A>G	chr9.hg19:g.131689459A>G	ENSP00000361673:p.Glu59Gly	67.0	0.0	.	1589	71.0	37.0	.	NM_001100877	A6PWN9|A6PWP0|B3KT57|B4E3X8|Q5SRE9|Q5SRF0|Q7Z623|Q7Z7P9|Q96GM4	Missense_Mutation	SNP	ENST00000372592.3	hg19	CCDS43885.1	.	.	.	.	.	.	.	.	.	.	A	15.58	2.876179	0.51801	.	.	ENSG00000175287	ENST00000372592;ENST00000428610;ENST00000308941;ENST00000419552;ENST00000353176;ENST00000426694;ENST00000421063	D;D;D	0.89810	-2.54;-2.57;-2.57	5.32	5.32	0.75619	.	0.100735	0.64402	D	0.000003	D	0.90868	0.7131	M	0.73598	2.24	0.58432	D	0.999999	P;P;D	0.54397	0.734;0.605;0.966	B;B;P	0.49887	0.373;0.412;0.625	D	0.91285	0.5054	10	0.51188	T	0.08	-23.6398	14.0941	0.65008	1.0:0.0:0.0:0.0	.	59;59;59	Q5SRE7-2;Q5SRE7;Q5SRE7-3	.;PHYD1_HUMAN;.	G	59	ENSP00000361673:E59G;ENSP00000340945:E59G;ENSP00000409928:E59G	ENSP00000309515:E59G	E	+	2	0	PHYHD1	130729280	1.000000	0.71417	0.998000	0.56505	0.324000	0.28378	3.925000	0.56484	2.002000	0.58637	0.533000	0.62120	GAG	.	.	.	none		0.582	PHYHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054506.2	NM_174933		G	131689459	A	G	131689459	3	3	264	1	0	0	0	0	1	0	0	0	11872	304	11	3	182	3	PHYHD1	9	131689459	Missense_Mutation	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	15884010	131689459	9523972	75	16580											
DOLK	22845	hgsc.bcm.edu	37	chr9	131708203	131708203	+	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	ggccagcggatctcccccatGgtgctaccgaagatggaggc	8	6	14	13	2	1	1	0	0	1	1	2	4	1	3	4	5	3	1	4	5	2	1			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr9:131708203G>T	ENST00000372586.3	-	1	1695	c.1380C>A	c.(1378-1380)acC>acA	p.T460T	RP11-101E3.5_ENST00000482796.1_Intron|NUP188_ENST00000372577.2_5'Flank	NM_014908.3	NP_055723.1	Q9UPQ8	DOLK_HUMAN	dolichol kinase	460	CTP-binding.				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						TCTCCCCCATGGTGCTACCGA	0.547																																					p.T460T		Atlas-SNP	.											.	DOLK	39	.	0			c.C1380A						PASS	.						85	86	86					9																	131708203		2203	4300	6503	SO:0001819	synonymous_variant	22845	exon1			CCCCATGGTGCTA	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.1380C>A	chr9.hg19:g.131708203G>T		115.0	0.0	.		111.0	39.0	.	NM_014908	Q5SRE6	Silent	SNP	ENST00000372586.3	hg19	CCDS6915.1																																																																																			.	.	.	none		0.547	DOLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054515.1	NM_014908		T	131708203	G	T	131708203	2	4	264	1	0	0	0	0	0	0	0	1	4705	1335	47	4		4	DOLK	9	131708203	Silent	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10	18744	131708203	9505228	76	16581											
AGPAT2	10555	hgsc.bcm.edu	37	chr9	139568332	139568332	+	Frame_Shift_Del	DEL	T	T	-																															cgcagggacgtccgccgcagTgaggccgctggtggggatgg																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr9:139568332delT	ENST00000371696.2	-	6	774	c.709delA	c.(709-711)actfs	p.T237fs	AGPAT2_ENST00000538402.1_Frame_Shift_Del_p.T237fs|AGPAT2_ENST00000371694.3_Frame_Shift_Del_p.T205fs	NM_006412.3	NP_006403.2	O15120	PLCB_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 2	237					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)		TCCGCCGCAGTGAGGCCGCTG	0.672																																					p.T237fs		Atlas-Indel,Pindel	.											.	AGPAT2	17	.	0			c.710delC						PASS	.						38	37	37					9																	139568332		2196	4296	6492	SO:0001589	frameshift_variant	10555	exon6			.	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.709delA	chr9.hg19:g.139568332delT	ENSP00000360761:p.Thr237fs	97.0	0.0	0		96.0	34.0	0.354167	NM_006412	O00516|O15106|Q5VUD3|Q5VUD4|Q9BSV7|Q9BWR7	Frame_Shift_Del	DEL	ENST00000371696.2	hg19	CCDS7003.1																																																																																			.	.	.	none		0.672	AGPAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055090.1	NM_006412		-	139568332	T	-	139568332	7	5	264	1	0	1	0	1	0	0	0	0	387	1696	59	0	131	0	AGPAT2	9	139568332	Frame_Shift_Del	DEL	T	TCGA-UZ-A9PS-01A-11D-A42J-10	7860129	139568332	1645099	77	16582											
TUBB2C	10383	hgsc.bcm.edu	37	chr9	140137032	140137033	+	Frame_Shift_Ins	INS	-	-	A																															tcggtgctggatgttgtgagINSaaaggaggctgagagctgtg																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr9:140137032_140137033insA	ENST00000340384.4	+	4	510_511	c.362_363insA	c.(361-366)agaaagfs	p.RK121fs		NM_006088.5	NP_006079.1	P68371	TBB4B_HUMAN	tubulin, beta 4B class IVb	121					'de novo' posttranslational protein folding (GO:0051084)|cellular component movement (GO:0006928)|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)|natural killer cell mediated cytotoxicity (GO:0042267)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|vesicle (GO:0031982)	double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|MHC class I protein binding (GO:0042288)|structural constituent of cytoskeleton (GO:0005200)|unfolded protein binding (GO:0051082)									Albendazole(DB00518)|Mebendazole(DB00643)	GATGTTGTGAGAAAGGAGGCTG	0.604																																					p.R121fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.362_363insA						PASS	.																																			SO:0001589	frameshift_variant	10383	exon4			.	BC019359	CCDS7039.1	9q34.3	2011-10-10	2011-10-10	2011-10-10	ENSG00000188229	ENSG00000188229		"Tubulins"	20771	protein-coding gene	gene with protein product	"class IVb beta-tubulin"	602660	"tubulin, beta 2C"	TUBB2C		3999141	Standard	NM_006088		Approved	Beta2	uc004cmh.1	P68371	OTTHUMG00000131783	ENST00000340384.4:c.365dupA	chr9.hg19:g.140137035_140137035dupA	ENSP00000341289:p.Arg121fs	78.0	0.0	0		61.0	18.0	0.295082	NM_006088	A2BFA2|P05217	Frame_Shift_Ins	INS	ENST00000340384.4	hg19	CCDS7039.1																																																																																			.	.	.	none		0.604	TUBB4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254715.1	NM_006088		A	140137033	-	A	140137032	7	5	264	1	0	1	1	0	0	0	0	0	16768	942	33	0	376	0	TUBB2C	9	140137032	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PS-01A-11D-A42J-10	568700	140137032	1076399	78	16583											
UPF2	26019	hgsc.bcm.edu	37	chr10	11998440	11998440	+	Missense_Mutation	SNP	T	T	A																															gaatactattatatttcacaTtccagatgtttatcatacaa																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr10:11998440T>A	ENST00000356352.2	-	12	2926	c.2453A>T	c.(2452-2454)aAt>aTt	p.N818I	UPF2_ENST00000357604.5_Missense_Mutation_p.N818I|UPF2_ENST00000397053.2_Missense_Mutation_p.N818I			Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog (yeast)	818	MIF4G 3.|Sufficient for interaction with EIF4A1 and EIF1.|Sufficient for interaction with UPF3A and UPF3B.				gene expression (GO:0010467)|liver development (GO:0001889)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|organ regeneration (GO:0031100)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(14)|lung(17)|ovary(2)|skin(3)|urinary_tract(2)	56		Renal(717;0.228)				ATATTTCACATTCCAGATGTT	0.393																																					p.N818I		Atlas-SNP	.											.	UPF2	111	.	0			c.A2453T						PASS	.						151	152	152					10																	11998440		2203	4300	6503	SO:0001583	missense	26019	exon13			TTCACATTCCAGA	AB037829	CCDS7086.1	10p14-p13	2011-06-21			ENSG00000151461	ENSG00000151461			17854	protein-coding gene	gene with protein product	"smg-3 homolog, nonsense mediated mRNA decay factor (C. elegans)"	605529				11073994, 11113196	Standard	NM_080599		Approved	RENT2, DKFZP434D222, KIAA1408, smg-3	uc001ilb.3	Q9HAU5	OTTHUMG00000017678	ENST00000356352.2:c.2453A>T	chr10.hg19:g.11998440T>A	ENSP00000348708:p.Asn818Ile	84.0	0.0	.		90.0	39.0	.	NM_080599	A6NLJ5|D3DRS0|Q14BM1|Q5W0J4|Q8N8U1|Q9H1J2|Q9NWL1|Q9P2D9|Q9Y4M9	Missense_Mutation	SNP	ENST00000356352.2	hg19	CCDS7086.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.433991	0.83776	.	.	ENSG00000151461	ENST00000356352;ENST00000357604;ENST00000397053	T;T;T	0.20463	2.07;2.07;2.07	5.53	5.53	0.82687	MIF4G-like, type 3 (2);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.000000	0.85682	D	0.000000	T	0.37517	0.1006	L	0.60957	1.885	0.80722	D	1	P	0.49862	0.929	P	0.57204	0.815	T	0.03728	-1.1009	10	0.33141	T	0.24	.	15.6297	0.76893	0.0:0.0:0.0:1.0	.	818	Q9HAU5	RENT2_HUMAN	I	818	ENSP00000348708:N818I;ENSP00000350221:N818I;ENSP00000380244:N818I	ENSP00000348708:N818I	N	-	2	0	UPF2	12038446	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.482000	0.81143	2.097000	0.63578	0.397000	0.26171	AAT	.	.	.	none		0.393	UPF2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046783.1			A	11998440	T	A	11998440	3	1	264	1	0	0	0	0	1	0	0	0	17016	1493	52	5	1405	5	UPF2	10	11998440	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10		11998440	123536307	79	16584	172	2									
UPF2	26019	hgsc.bcm.edu	37	chr10	11998442	11998442	+	Missense_Mutation	SNP	C	C	A																															atactattatatttcacattCcagatgtttatcatacaaca																								rs367800253		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr10:11998442C>A	ENST00000356352.2	-	12	2924	c.2451G>T	c.(2449-2451)tgG>tgT	p.W817C	UPF2_ENST00000357604.5_Missense_Mutation_p.W817C|UPF2_ENST00000397053.2_Missense_Mutation_p.W817C			Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog (yeast)	817	MIF4G 3.|Sufficient for interaction with EIF4A1 and EIF1.|Sufficient for interaction with UPF3A and UPF3B.				gene expression (GO:0010467)|liver development (GO:0001889)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|organ regeneration (GO:0031100)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(14)|lung(17)|ovary(2)|skin(3)|urinary_tract(2)	56		Renal(717;0.228)				ATTTCACATTCCAGATGTTTA	0.398																																					p.W817C		Atlas-SNP	.											.	UPF2	111	.	0			c.G2451T						PASS	.						150	152	152					10																	11998442		2203	4300	6503	SO:0001583	missense	26019	exon13			CACATTCCAGATG	AB037829	CCDS7086.1	10p14-p13	2011-06-21			ENSG00000151461	ENSG00000151461			17854	protein-coding gene	gene with protein product	"smg-3 homolog, nonsense mediated mRNA decay factor (C. elegans)"	605529				11073994, 11113196	Standard	NM_080599		Approved	RENT2, DKFZP434D222, KIAA1408, smg-3	uc001ilb.3	Q9HAU5	OTTHUMG00000017678	ENST00000356352.2:c.2451G>T	chr10.hg19:g.11998442C>A	ENSP00000348708:p.Trp817Cys	84.0	0.0	.		87.0	39.0	.	NM_080599	A6NLJ5|D3DRS0|Q14BM1|Q5W0J4|Q8N8U1|Q9H1J2|Q9NWL1|Q9P2D9|Q9Y4M9	Missense_Mutation	SNP	ENST00000356352.2	hg19	CCDS7086.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.224664	0.79576	.	.	ENSG00000151461	ENST00000356352;ENST00000357604;ENST00000397053	T;T;T	0.22336	1.96;1.96;1.96	5.53	5.53	0.82687	MIF4G-like, type 3 (2);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.000000	0.85682	D	0.000000	T	0.46756	0.1409	M	0.67953	2.075	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.19128	-1.0315	10	0.36615	T	0.2	.	19.4313	0.94768	0.0:1.0:0.0:0.0	.	817	Q9HAU5	RENT2_HUMAN	C	817	ENSP00000348708:W817C;ENSP00000350221:W817C;ENSP00000380244:W817C	ENSP00000348708:W817C	W	-	3	0	UPF2	12038448	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.277000	0.78572	2.596000	0.87737	0.484000	0.47621	TGG	.	.	.	none		0.398	UPF2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046783.1			A	11998442	C	A	11998442	3	1	264	1	0	0	0	0	1	0	0	0	17016	856	30	4	1407	4	UPF2	10	11998442	Missense_Mutation	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	2	11998442	123536305	80	16585	172	2									
ERCC6	2074	hgsc.bcm.edu	37	chr10	50679145	50679146	+	Frame_Shift_Ins	INS	-	-	A																															cttttagcactctatttgtcINSaaaaactgcttgaagatttg																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr10:50679145_50679146insA	ENST00000355832.5	-	17	3023_3024	c.2945_2946insT	c.(2944-2946)ttgfs	p.L982fs	ERCC6_ENST00000542458.1_Frame_Shift_Ins_p.L352fs|ERCC6_ENST00000465653.1_5'Flank|RP11-123B3.2_ENST00000423283.1_RNA	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	982	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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						CTCTATTTGTCAAAAACTGCTT	0.332								Direct reversal of damage;Nucleotide excision repair (NER)																													p.T982fs		Atlas-Indel,Pindel	.											.	ERCC6	162	.	0			c.2946_2947insT						PASS	.																																			SO:0001589	frameshift_variant	2074	exon17			.	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.2946dupT	chr10.hg19:g.50679150_50679150dupA	ENSP00000348089:p.Leu982fs	72.0	0.0	0		70.0	34.0	0.485714	NM_000124	D3DX94|Q5W0L9	Frame_Shift_Ins	INS	ENST00000355832.5	hg19	CCDS7229.1																																																																																			.	.	.	none		0.332	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124		A	50679146	-	A	50679145	7	5	264	1	0	1	1	0	0	0	0	0	5219	825	29	0	1555	0	ERCC6	10	50679145	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PS-01A-11D-A42J-10	38680703	50679145	84855602	81	16586											
MYPN	84665	hgsc.bcm.edu	37	chr10	69918255	69918255	+	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	cattatagatgctacaaaatTtgtcagcttctgagggtcag	12	13	9	7	0	3	2	2	1	1	1	3	2	3	2	0	1	3	2	0	1	5	5			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr10:69918255T>A	ENST00000358913.5	+	7	1818	c.1330T>A	c.(1330-1332)Ttg>Atg	p.L444M	RN7SKP202_ENST00000410439.1_RNA|MYPN_ENST00000373675.3_Missense_Mutation_p.L444M|MYPN_ENST00000354393.2_Missense_Mutation_p.L169M|MYPN_ENST00000540630.1_Missense_Mutation_p.L444M	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	444	Ig-like 2.|Interaction with CARP.				sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						GCTACAAAATTTGTCAGCTTC	0.358																																					p.L444M		Atlas-SNP	.											.	MYPN	189	.	0			c.T1330A						PASS	.						87	86	86					10																	69918255		2203	4300	6503	SO:0001583	missense	84665	exon7			CAAAATTTGTCAG	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.1330T>A	chr10.hg19:g.69918255T>A	ENSP00000351790:p.Leu444Met	84.0	0.0	.		91.0	34.0	.	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	hg19	CCDS7275.1	.	.	.	.	.	.	.	.	.	.	T	16.03	3.007533	0.54361	.	.	ENSG00000138347	ENST00000354393;ENST00000542332;ENST00000358913;ENST00000540630;ENST00000373675	T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34	5.62	2.08	0.27032	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.181068	0.36482	N	0.002568	T	0.64249	0.2581	L	0.32530	0.975	0.37395	D	0.912605	D;D;D;D	0.67145	0.989;0.996;0.973;0.991	P;D;P;P	0.65010	0.847;0.931;0.822;0.906	T	0.63269	-0.6675	9	.	.	.	.	3.9856	0.09514	0.196:0.3257:0.0:0.4783	.	444;444;169;444	F5GWA6;Q86TC9-3;Q86TC9-2;Q86TC9	.;.;.;MYPN_HUMAN	M	169;169;444;444;444	ENSP00000346369:L169M;ENSP00000351790:L444M;ENSP00000441668:L444M;ENSP00000362779:L444M	.	L	+	1	2	MYPN	69588261	0.367000	0.25023	1.000000	0.80357	0.991000	0.79684	-0.022000	0.12480	0.427000	0.26145	-0.250000	0.11733	TTG	.	.	.	none		0.358	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578		A	69918255	T	A	69918255	3	1	264	1	0	0	0	0	1	0	0	0	10105	1838	64	5	1352	5	MYPN	10	69918255	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	19239110	69918255	65616492	82	16587											
TET1	80312	hgsc.bcm.edu	37	chr10	70451494	70451494	+	Missense_Mutation	SNP	T	T	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	cttctcataaagcattaacaTtaacccatgacaatgttgtc	14	13	4	10	0	1	1	1	1	1	0	3	1	1	1	1	0	3	2	1	0	5	5			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr10:70451494T>G	ENST00000373644.4	+	12	6543	c.6334T>G	c.(6334-6336)Tta>Gta	p.L2112V		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	2112					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						AGCATTAACATTAACCCATGA	0.458																																					p.L2112V		Atlas-SNP	.											.	TET1	255	.	0			c.T6334G						PASS	.						117	120	119					10																	70451494		2203	4300	6503	SO:0001583	missense	80312	exon12			TTAACATTAACCC	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.6334T>G	chr10.hg19:g.70451494T>G	ENSP00000362748:p.Leu2112Val	96.0	0.0	.		92.0	36.0	.	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	hg19	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	T	14.99	2.698882	0.48307	.	.	ENSG00000138336	ENST00000373644	T	0.06218	3.33	5.59	3.33	0.38152	.	1.030220	0.07660	N	0.933448	T	0.03136	0.0092	N	0.11870	0.19	0.26401	N	0.976415	B	0.24823	0.112	B	0.24006	0.05	T	0.45789	-0.9237	10	0.07325	T	0.83	.	2.4588	0.04536	0.1167:0.0943:0.2833:0.5057	.	2112	Q8NFU7	TET1_HUMAN	V	2112	ENSP00000362748:L2112V	ENSP00000362748:L2112V	L	+	1	2	TET1	70121500	1.000000	0.71417	0.992000	0.48379	0.967000	0.64934	0.736000	0.26130	0.966000	0.38159	0.460000	0.39030	TTA	.	.	.	none		0.458	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		G	70451494	T	G	70451494	3	3	264	1	0	0	0	0	1	0	0	0	15781	1490	52	5	6376	5	TET1	10	70451494	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	533239	70451494	65083253	83	16588											
C10orf11	83938	hgsc.bcm.edu	37	chr10	77795776	77795776	+	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	gtcattgcaggtcactggaaGgactgagcgcattcaggagc	10	8	14	9	1	3	1	3	1	0	0	3	4	3	4	0	4	3	2	0	4	1	2			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr10:77795776G>A	ENST00000372499.1	+	2	273	c.58G>A	c.(58-60)Gga>Aga	p.G20R	C10orf11_ENST00000593699.1_3'UTR	NM_032024.3	NP_114413.1	Q9H2I8	CJ011_HUMAN	chromosome 10 open reading frame 11	20					melanocyte differentiation (GO:0030318)					endometrium(1)|large_intestine(4)|lung(4)|stomach(1)	10	Prostate(51;0.0095)|all_epithelial(25;0.0221)					GTCACTGGAAGGACTGAGCGC	0.478											OREG0020279	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G20R		Atlas-SNP	.											.	C10orf11	19	.	0			c.G58A						PASS	.						171	149	156					10																	77795776		2203	4300	6503	SO:0001583	missense	83938	exon2			CTGGAAGGACTGA	AF267860	CCDS7351.1	10q22.3	2013-08-22			ENSG00000148655	ENSG00000148655			23405	protein-coding gene	gene with protein product	"oculocutaneous albinism 7, autosomal recessive"	614537				23395477	Standard	NM_032024		Approved	CDA017, OCA7	uc001jxi.3	Q9H2I8	OTTHUMG00000018532	ENST00000372499.1:c.58G>A	chr10.hg19:g.77795776G>A	ENSP00000361577:p.Gly20Arg	83.0	0.0	.	1178	53.0	17.0	.	NM_032024	B1AVW6	Missense_Mutation	SNP	ENST00000372499.1	hg19	CCDS7351.1	.	.	.	.	.	.	.	.	.	.	G	19.57	3.852066	0.71719	.	.	ENSG00000148655	ENST00000354343;ENST00000372499	T	0.66460	-0.21	4.39	4.39	0.52855	.	0.000000	0.85682	D	0.000000	D	0.83982	0.5372	M	0.87456	2.885	0.58432	D	0.999994	D	0.71674	0.998	D	0.75484	0.986	D	0.87143	0.2204	10	0.62326	D	0.03	0.031	17.848	0.88736	0.0:0.0:1.0:0.0	.	20	Q9H2I8	CJ011_HUMAN	R	48;20	ENSP00000361577:G20R	ENSP00000346310:G48R	G	+	1	0	C10orf11	77465782	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.167000	0.94773	2.382000	0.81193	0.455000	0.32223	GGA	.	.	.	none		0.478	C10orf11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048839.1	NM_032024		A	77795776	G	A	77795776	3	1	264	1	0	0	0	0	1	0	0	0	1584	1001	35	2	64	2	C10orf11	10	77795776	Missense_Mutation	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10	7344282	77795776	57738971	84	16589											
PIK3AP1	118788	hgsc.bcm.edu	37	chr10	98380246	98380246	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagctgccgctggcctggcgTtttcattcccgcaaaagggt	7	10	12	12	3	1	0	1	0	0	0	2	0	2	0	3	3	2	4	3	3	3	3			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr10:98380246T>C	ENST00000339364.5	-	12	1923	c.1804A>G	c.(1804-1806)Acg>Gcg	p.T602A	PIK3AP1_ENST00000371110.2_Missense_Mutation_p.T424A|PIK3AP1_ENST00000371109.3_Missense_Mutation_p.T201A|RNA5SP324_ENST00000365177.1_RNA	NM_152309.2	NP_689522.2	Q6ZUJ8	BCAP_HUMAN	phosphoinositide-3-kinase adaptor protein 1	602					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)		TGGCCTGGCGTTTTCATTCCC	0.567																																					p.T602A		Atlas-SNP	.											.	PIK3AP1	111	.	0			c.A1804G						PASS	.						83	76	79					10																	98380246		2203	4300	6503	SO:0001583	missense	118788	exon12			CTGGCGTTTTCAT	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.1804A>G	chr10.hg19:g.98380246T>C	ENSP00000339826:p.Thr602Ala	104.0	0.0	.		100.0	41.0	.	NM_152309	Q5TB56|Q5VXJ9|Q8N6J6|Q8NAC8	Missense_Mutation	SNP	ENST00000339364.5	hg19	CCDS31259.1	.	.	.	.	.	.	.	.	.	.	T	27.2	4.806745	0.90623	.	.	ENSG00000155629	ENST00000339364;ENST00000371110;ENST00000371109	T;T;T	0.48522	0.81;0.81;0.81	5.89	5.89	0.94794	.	0.047516	0.85682	D	0.000000	T	0.58878	0.2153	L	0.52759	1.655	0.80722	D	1	P;D	0.65815	0.948;0.995	P;P	0.57371	0.562;0.819	T	0.60611	-0.7229	10	0.59425	D	0.04	-15.0229	15.4934	0.75629	0.0:0.0:0.0:1.0	.	602;201	Q6ZUJ8;Q6ZUJ8-3	BCAP_HUMAN;.	A	602;424;201	ENSP00000339826:T602A;ENSP00000360151:T424A;ENSP00000360150:T201A	ENSP00000339826:T602A	T	-	1	0	PIK3AP1	98370236	1.000000	0.71417	0.805000	0.32314	0.787000	0.44495	7.972000	0.88022	2.254000	0.74563	0.459000	0.35465	ACG	.	.	.	none		0.567	PIK3AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049619.2	NM_152309		C	98380246	T	C	98380246	3	2	264	1	0	0	0	0	1	0	0	0	11915	1725	60	3	637	3	PIK3AP1	10	98380246	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	20584470	98380246	37154501	85	16590											
TDRD1	56165	hgsc.bcm.edu	37	chr10	115964611	115964611	+	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	tgtcgacatcttggaagaggAagtggttacctttgctgtag	9	13	13	6	1	1	1	0	0	1	1	2	4	1	3	1	3	2	3	1	3	4	4			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr10:115964611A>T	ENST00000369280.1	+	10	1716	c.1256A>T	c.(1255-1257)gAa>gTa	p.E419V	TDRD1_ENST00000369282.1_Missense_Mutation_p.E419V|TDRD1_ENST00000422662.1_Missense_Mutation_p.E80V|TDRD1_ENST00000251864.2_Missense_Mutation_p.E419V|TDRD1_ENST00000369281.2_Missense_Mutation_p.E419V			Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	419					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ cell development (GO:0007281)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)	metal ion binding (GO:0046872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(5)	48		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		TTGGAAGAGGAAGTGGTTACC	0.398																																					p.E419V		Atlas-SNP	.											.	TDRD1	126	.	0			c.A1256T						PASS	.						143	124	130					10																	115964611		2203	4300	6503	SO:0001583	missense	56165	exon10			AAGAGGAAGTGGT	AF285606	CCDS7588.1	10q26.11	2013-01-23			ENSG00000095627	ENSG00000095627		"Tudor domain containing"	11712	protein-coding gene	gene with protein product	"cancer/testis antigen 41.1"	605796				11279525	Standard	NM_198795		Approved	CT41.1	uc001lbg.1	Q9BXT4	OTTHUMG00000019083	ENST00000369280.1:c.1256A>T	chr10.hg19:g.115964611A>T	ENSP00000358286:p.Glu419Val	114.0	0.0	.		139.0	53.0	.	NM_198795	A6NEN3|A6NMN2|B3KVI4|B4E2L5|D3DRC2|Q4G0Y8|Q6P518|Q9H7B3	Missense_Mutation	SNP	ENST00000369280.1	hg19		.	.	.	.	.	.	.	.	.	.	A	7.940	0.742555	0.15642	.	.	ENSG00000095627	ENST00000369282;ENST00000251864;ENST00000369281;ENST00000422662;ENST00000369280	T;T;T;T;T	0.20463	2.91;2.89;2.07;2.07;2.92	6.03	4.89	0.63831	.	0.870569	0.10238	N	0.698731	T	0.19366	0.0465	L	0.35854	1.095	0.34876	D	0.74407	B;B;B;B;B	0.14805	0.001;0.004;0.011;0.007;0.003	B;B;B;B;B	0.16289	0.012;0.007;0.007;0.015;0.008	T	0.09509	-1.0671	10	0.40728	T	0.16	-3.9984	10.6134	0.45436	0.8567:0.0:0.0:0.1433	.	80;419;419;419;419	Q9BXT4-4;Q9BXT4;B7WPM2;Q9BXT4-3;Q9BXT4-2	.;TDRD1_HUMAN;.;.;.	V	419;419;419;80;419	ENSP00000358288:E419V;ENSP00000251864:E419V;ENSP00000358287:E419V;ENSP00000402794:E80V;ENSP00000358286:E419V	ENSP00000251864:E419V	E	+	2	0	TDRD1	115954601	0.998000	0.40836	0.167000	0.22817	0.038000	0.13279	3.088000	0.50175	1.089000	0.41292	-0.301000	0.09380	GAA	.	.	.	none		0.398	TDRD1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050457.2			T	115964611	A	T	115964611	3	4	264	1	0	0	0	0	1	0	0	0	15742	246	9	5	1290	5	TDRD1	10	115964611	Missense_Mutation	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	17584365	115964611	19570136	86	16591											
CALCA	796	hgsc.bcm.edu	37	chr11	14991618	14991618	+	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	gctgggctgctctccagggcAgacctgtggaggggaagcaa	8	6	17	10	0	1	1	0	0	1	1	2	3	1	3	2	5	2	5	2	5	2	0	rs528241428		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr11:14991618A>T	ENST00000486207.1	-	2	98	c.90T>A	c.(88-90)tcT>tcA	p.S30S	CALCA_ENST00000359642.3_Silent_p.S30S|CALCA_ENST00000396372.2_Silent_p.S30S|CALCA_ENST00000361010.3_Silent_p.S30S|CALCB_ENST00000523376.1_Intron|CALCA_ENST00000331587.4_Silent_p.S30S			P06881	CALCA_HUMAN	calcitonin-related polypeptide alpha	30					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						TCTCCAGGGCAGACCTGTGGA	0.632																																					p.S30S		Atlas-SNP	.											.	CALCA	30	.	0			c.T90A						PASS	.						34	34	34					11																	14991618		2200	4294	6494	SO:0001819	synonymous_variant	796	exon3			CAGGGCAGACCTG	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.90T>A	chr11.hg19:g.14991618A>T		210.0	0.0	.		226.0	86.0	.	NM_001033953	Q93048|Q9UCP0	Silent	SNP	ENST00000486207.1	hg19	CCDS31432.1																																																																																			.	.	.	none		0.632	CALCA-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357068.1	NM_001741		T	14991618	A	T	14991618	2	4	264	1	0	0	0	0	0	0	0	1	2577	175	7	5		5	CALCA	11	14991618	Silent	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10		14991618	120014898	87	16592											
IMMP1L	196294	hgsc.bcm.edu	37	chr11	31454087	31454087	+	Frame_Shift_Del	DEL	A	A	-																															ggccattagggctggcacgtAaaaatccaaaatcactcaga																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr11:31454087delA	ENST00000278200.1	-	7	656	c.461delT	c.(460-462)ttafs	p.L154fs	IMMP1L_ENST00000534812.1_Frame_Shift_Del_p.L45fs|IMMP1L_ENST00000533642.1_Frame_Shift_Del_p.L45fs|AC108456.1_ENST00000408411.1_RNA|IMMP1L_ENST00000532287.1_Frame_Shift_Del_p.L154fs|IMMP1L_ENST00000526776.1_Frame_Shift_Del_p.L82fs	NM_144981.1	NP_659418.1	Q96LU5	IMP1L_HUMAN	IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae)	154					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)					GCTGGCACGTAAAAATCCAAA	0.338																																					p.L154fs		Atlas-Indel,Pindel	.											.	IMMP1L	16	.	0			c.462delA						PASS	.						71	67	69					11																	31454087		2202	4298	6500	SO:0001589	frameshift_variant	196294	exon7			.		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.461delT	chr11.hg19:g.31454087delA	ENSP00000278200:p.Leu154fs	374.0	0.0	0		400.0	141.0	0.3525	NM_144981	D3DQZ7|Q96SH9	Frame_Shift_Del	DEL	ENST00000278200.1	hg19	CCDS7874.1																																																																																			.	.	.	none		0.338	IMMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388496.1	NM_144981		-	31454087	A	-	31454087	7	5	264	1	0	1	0	1	0	0	0	0	7723	372	13	0	43	0	IMMP1L	11	31454087	Frame_Shift_Del	DEL	A	TCGA-UZ-A9PS-01A-11D-A42J-10	16462469	31454087	103552429	88	16593											
CPSF7	79869	hgsc.bcm.edu	37	chr11	61183972	61183972	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaatcactagaatctcgggaAtgggcccgtggaggtattcc	10	9	13	9	2	2	1	1	0	1	1	4	4	3	3	2	4	0	1	2	4	5	3			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr11:61183972A>G	ENST00000394888.4	-	6	742	c.570T>C	c.(568-570)caT>caC	p.H190H	CPSF7_ENST00000340437.4_Silent_p.H233H|CPSF7_ENST00000439958.3_Silent_p.H181H|CPSF7_ENST00000448745.1_Silent_p.H181H	NM_001136040.2	NP_001129512.1	Q8N684	CPSF7_HUMAN	cleavage and polyadenylation specific factor 7, 59kDa	190					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|protein tetramerization (GO:0051262)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	22						AATCTCGGGAATGGGCCCGTG	0.517																																					p.H233H		Atlas-SNP	.											.	CPSF7	46	.	0			c.T699C						PASS	.						77	77	77					11																	61183972		2202	4299	6501	SO:0001819	synonymous_variant	79869	exon6			TCGGGAATGGGCC		CCDS8006.2, CCDS44619.1, CCDS44620.1	11q12.2	2013-06-18			ENSG00000149532	ENSG00000149532		"RNA binding motif (RRM) containing"	30098	protein-coding gene	gene with protein product	"pre mRNA cleavage factor I, 59 kDa subunit", "cleavage factor Im complex 59 kDa subunit"					12477932	Standard	NM_024811		Approved	FLJ12529	uc001nrp.3	Q8N684	OTTHUMG00000168198	ENST00000394888.4:c.570T>C	chr11.hg19:g.61183972A>G		94.0	0.0	.		89.0	32.0	.	NM_024811	B3KU04|C9K0Q4|Q7Z3H9|Q9H025|Q9H9V1	Silent	SNP	ENST00000394888.4	hg19	CCDS44619.1																																																																																			.	.	.	none		0.517	CPSF7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347835.2	NM_024811		G	61183972	A	G	61183972	2	3	264	1	0	0	0	0	0	0	0	1	3832	98	4	3		3	CPSF7	11	61183972	Silent	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	29729885	61183972	73822544	89	16594											
SLC3A2	6520	hgsc.bcm.edu	37	chr11	62648555	62648556	+	Frame_Shift_Ins	INS	-	-	A																															tgaatgagttagagcccgagINSaagcagccgatgaacgcggc																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr11:62648555_62648556insA	ENST00000377890.2	+	4	531_532	c.363_364insA	c.(364-366)aagfs	p.K122fs	SLC3A2_ENST00000535296.1_Frame_Shift_Ins_p.K91fs|SLC3A2_ENST00000377892.1_Frame_Shift_Ins_p.K153fs|SLC3A2_ENST00000536981.1_5'Flank|SLC3A2_ENST00000338663.7_Frame_Shift_Ins_p.K21fs|SLC3A2_ENST00000377889.2_Frame_Shift_Ins_p.K60fs|SLC3A2_ENST00000377891.2_Frame_Shift_Ins_p.K123fs	NM_002394.5	NP_002385.3	P08195	4F2_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 2	122					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						TAGAGCCCGAGAAGCAGCCGAT	0.629											OREG0021031	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E122fs		Atlas-Indel,Pindel	.											.	SLC3A2	55	.	0			c.366_367insA						PASS	.																																			SO:0001589	frameshift_variant	6520	exon4			.		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.365dupA	chr11.hg19:g.62648557_62648557dupA	ENSP00000367122:p.Lys122fs	127.0	0.0	0	1062	129.0	49.0	0.379845	NM_001012662	Q13543	Frame_Shift_Ins	INS	ENST00000377890.2	hg19	CCDS8039.2																																																																																			.	.	.	none		0.629	SLC3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157306.1	NM_001012661		A	62648556	-	A	62648555	7	5	264	1	0	1	1	0	0	0	0	0	14640	933	33	0	477	0	SLC3A2	11	62648555	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PS-01A-11D-A42J-10	1464583	62648555	72357961	90	16595											
PAAF1	80227	hgsc.bcm.edu	37	chr11	73602239	73602239	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tactttttccagaattcataCaaagagtgtaagtattttga	14	16	6	5	0	1	3	1	1	0	2	2	3	2	3	1	0	2	2	1	0	6	9	rs369473709	byFrequency	TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr11:73602239C>T	ENST00000310571.3	+	4	328	c.275C>T	c.(274-276)aCa>aTa	p.T92I	PAAF1_ENST00000536003.1_Missense_Mutation_p.T75I|PAAF1_ENST00000544909.1_Missense_Mutation_p.T93I|PAAF1_ENST00000376384.5_Missense_Mutation_p.T75I|PAAF1_ENST00000543079.1_3'UTR|PAAF1_ENST00000544552.1_Missense_Mutation_p.T75I|PAAF1_ENST00000541951.1_5'UTR|PAAF1_ENST00000535604.1_5'UTR	NM_025155.2	NP_079431.1	Q9BRP4	PAAF1_HUMAN	proteasomal ATPase-associated factor 1	92					viral process (GO:0016032)	proteasome complex (GO:0000502)				breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Breast(11;7.42e-05)					AGAATTCATACAAAGAGTGTA	0.269																																					p.T92I		Atlas-SNP	.											.	PAAF1	39	.	0			c.C275T						PASS	.						72	68	70					11																	73602239		2197	4288	6485	SO:0001583	missense	80227	exon4			TTCATACAAAGAG	BC006142	CCDS8226.1, CCDS58157.1, CCDS58158.1	11q13.4	2013-05-21	2007-08-16	2007-08-16	ENSG00000175575	ENSG00000175575		"WD repeat domain containing"	25687	protein-coding gene	gene with protein product			"WD repeat domain 71"	WDR71		15831487, 17317272, 17289585	Standard	NM_001267803		Approved	FLJ11848, Rpn14	uc001ouk.2	Q9BRP4	OTTHUMG00000168062	ENST00000310571.3:c.275C>T	chr11.hg19:g.73602239C>T	ENSP00000311665:p.Thr92Ile	55.0	0.0	.		70.0	24.0	.	NM_025155	A6NDR5|B4DPB0|B7ZAS9|Q4G165|Q53HS9|Q7Z500|Q8TBU6|Q9HAB6	Missense_Mutation	SNP	ENST00000310571.3	hg19	CCDS8226.1	.	.	.	.	.	.	.	.	.	.	C	10.38	1.333327	0.24167	.	.	ENSG00000175575	ENST00000310571;ENST00000504441;ENST00000543814;ENST00000536003;ENST00000544552;ENST00000376384;ENST00000536582;ENST00000544909	T;T;T;T;T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14	5.96	1.58	0.23477	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	1.146690	0.06484	N	0.733427	T	0.57989	0.2091	M	0.66939	2.045	0.09310	N	1	B;B	0.13145	0.007;0.001	B;B	0.11329	0.005;0.006	T	0.49173	-0.8967	10	0.52906	T	0.07	0.3313	4.2156	0.10533	0.2415:0.3916:0.2938:0.0731	.	75;92	Q9BRP4-2;Q9BRP4	.;PAAF1_HUMAN	I	92;75;75;75;75;75;70;93	ENSP00000311665:T92I;ENSP00000439747:T75I;ENSP00000438894:T75I;ENSP00000438124:T75I;ENSP00000441494:T75I;ENSP00000365564:T75I;ENSP00000443473:T70I;ENSP00000438071:T93I	ENSP00000311665:T92I	T	+	2	0	PAAF1	73279887	0.009000	0.17119	0.929000	0.37066	0.836000	0.47400	0.864000	0.27926	0.314000	0.23086	-0.182000	0.12963	ACA	.	.	.	none		0.269	PAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397885.1	NM_025155		T	73602239	C	T	73602239	3	4	264	1	0	0	0	0	1	0	0	0	11369	478	17	2	289	2	PAAF1	11	73602239	Missense_Mutation	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	10953684	73602239	61404277	91	16596											
SLCO2B1	11309	hgsc.bcm.edu	37	chr11	74915579	74915579	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctgccgtagagcagcaatTgctagtgtcggggccaggga	8	7	15	11	2	0	1	0	0	0	1	1	2	0	2	3	3	4	4	3	3	3	3			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr11:74915579T>C	ENST00000289575.5	+	14	2479	c.2084T>C	c.(2083-2085)tTg>tCg	p.L695S	SLCO2B1_ENST00000525650.1_Missense_Mutation_p.L551S|SLCO2B1_ENST00000341411.4_Missense_Mutation_p.L468S|SLCO2B1_ENST00000454962.2_Missense_Mutation_p.L468S|SLCO2B1_ENST00000428359.2_Missense_Mutation_p.L673S|SLCO2B1_ENST00000532236.1_Missense_Mutation_p.L579S	NM_007256.4	NP_009187	O94956	SO2B1_HUMAN	solute carrier organic anion transporter family, member 2B1	695					liver development (GO:0001889)|sodium-independent icosanoid transport (GO:0071718)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid transmembrane transporter activity (GO:0015125)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(2)|endometrium(1)|large_intestine(7)|lung(20)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	39					Acetic acid(DB03166)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Digoxin(DB00390)|Dinoprostone(DB00917)|Ergoloid mesylate(DB01049)|Estradiol(DB00783)|Estrone(DB00655)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Glyburide(DB01016)|Ibuprofen(DB01050)|Iloprost(DB01088)|Latanoprost(DB00654)|Montelukast(DB00471)|Niacin(DB00627)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Tolbutamide(DB01124)	GAGCAGCAATTGCTAGTGTCG	0.577																																					p.L695S		Atlas-SNP	.											.	SLCO2B1	84	.	0			c.T2084C						PASS	.						84	74	78					11																	74915579		2200	4293	6493	SO:0001583	missense	11309	exon14			AGCAATTGCTAGT	AB026256	CCDS8235.1, CCDS44683.1, CCDS53679.1	11q13	2013-05-22	2003-11-25	2003-11-26				"Solute carriers"	10962	protein-coding gene	gene with protein product		604988	"solute carrier family 21 (organic anion transporter), member 9"	SLC21A9			Standard	NM_007256		Approved	OATP-B, OATP2B1	uc001owb.3	O94956		ENST00000289575.5:c.2084T>C	chr11.hg19:g.74915579T>C	ENSP00000289575:p.Leu695Ser	91.0	0.0	.		78.0	27.0	.	NM_007256	A8K2G9|B4DGA9|B4DTB0|E7ERN5|E9PPU8|Q9H2Z0|Q9UFU1	Missense_Mutation	SNP	ENST00000289575.5	hg19	CCDS8235.1	.	.	.	.	.	.	.	.	.	.	T	12.95	2.092879	0.36952	.	.	ENSG00000137491	ENST00000289575;ENST00000341411;ENST00000532236;ENST00000525650;ENST00000454962;ENST00000428359	T;T;T;T;T;T	0.42900	1.13;1.14;1.26;0.96;1.14;1.13	5.34	-3.38	0.04883	.	8.866070	0.00166	N	0.000000	T	0.15478	0.0373	N	0.08118	0	0.09310	N	1	P;B;B	0.34462	0.454;0.053;0.031	B;B;B	0.24974	0.057;0.022;0.004	T	0.06752	-1.0809	10	0.09084	T	0.74	.	1.9229	0.03311	0.1969:0.4011:0.1263:0.2757	.	551;468;695	E9PPU8;O94956-2;O94956	.;.;SO2B1_HUMAN	S	695;468;579;551;468;673	ENSP00000289575:L695S;ENSP00000341286:L468S;ENSP00000434112:L579S;ENSP00000436324:L551S;ENSP00000389653:L468S;ENSP00000388912:L673S	ENSP00000289575:L695S	L	+	2	0	SLCO2B1	74593227	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-0.363000	0.07593	-0.519000	0.06444	0.460000	0.39030	TTG	.	.	.	none		0.577	SLCO2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383933.1	NM_007256		C	74915579	T	C	74915579	3	2	264	1	0	0	0	0	1	0	0	0	14740	1821	63	3	2138	3	SLCO2B1	11	74915579	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	1313340	74915579	60090937	92	16597											
BIRC3	330	hgsc.bcm.edu	37	chr11	102195478	102195478	+	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	tggataactggaaaagaggaGacagtcctactgaaaagcat	17	7	11	6	0	0	3	0	1	0	2	1	6	1	5	1	3	3	1	1	3	6	2			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr11:102195478G>T	ENST00000263464.3	+	2	2988	c.238G>T	c.(238-240)Gac>Tac	p.D80Y	BIRC3_ENST00000532808.1_Missense_Mutation_p.D80Y	NM_001165.4	NP_001156.1	Q13489	BIRC3_HUMAN	baculoviral IAP repeat containing 3	80					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)		GAAAAGAGGAGACAGTCCTAC	0.428			T	MALT1	MALT																																p.D80Y		Atlas-SNP	.		Dom	yes		11	11q22-q23	330	baculoviral IAP repeat-containing 3		L	.	BIRC3	56	.	0			c.G238T						PASS	.						139	140	139					11																	102195478		2203	4299	6502	SO:0001583	missense	330	exon2			AGAGGAGACAGTC	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.238G>T	chr11.hg19:g.102195478G>T	ENSP00000263464:p.Asp80Tyr	137.0	0.0	.		100.0	11.0	.	NM_001165	Q16628|Q9HC27|Q9UP46	Missense_Mutation	SNP	ENST00000263464.3	hg19	CCDS8315.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.040615	0.75732	.	.	ENSG00000023445	ENST00000263464;ENST00000532808	T;T	0.09723	2.95;2.95	5.93	5.93	0.95920	Baculoviral inhibition of apoptosis protein repeat (5);	0.000000	0.85682	D	0.000000	T	0.53174	0.1780	H	0.98238	4.18	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.70710	-0.4797	10	0.87932	D	0	.	20.3334	0.98727	0.0:0.0:1.0:0.0	.	80	Q13489	BIRC3_HUMAN	Y	80	ENSP00000263464:D80Y;ENSP00000432907:D80Y	ENSP00000263464:D80Y	D	+	1	0	BIRC3	101700688	1.000000	0.71417	1.000000	0.80357	0.546000	0.35178	9.869000	0.99810	2.818000	0.97014	0.591000	0.81541	GAC	.	.	.	none		0.428	BIRC3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394159.1	NM_001165		T	102195478	G	T	102195478	3	4	264	1	0	0	0	0	1	0	0	0	1436	942	33	4	240	4	BIRC3	11	102195478	Missense_Mutation	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10	27279899	102195478	32811038	93	16598											
ATM	472	hgsc.bcm.edu	37	chr11	108236079	108236079	+	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	gaccagagtttcaacaaagtAgctgaacgtgtcttaatgag	14	10	10	7	1	2	3	1	2	1	1	2	4	2	3	1	0	3	3	1	0	5	3			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr11:108236079A>T	ENST00000452508.2	+	64	9204	c.9015A>T	c.(9013-9015)gtA>gtT	p.V3005V	C11orf65_ENST00000526725.1_Intron|ATM_ENST00000525178.1_3'UTR|ATM_ENST00000278616.4_Silent_p.V3005V|C11orf65_ENST00000525729.1_Intron			Q13315	ATM_HUMAN	ATM serine/threonine kinase	3005					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)	TCAACAAAGTAGCTGAACGTG	0.403			"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.V3005V		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	.	ATM	1657	.	0			c.A9015T						PASS	.						122	119	120					11																	108236079		2201	4298	6499	SO:0001819	synonymous_variant	472	exon63	Familial Cancer Database	AT, Louis-Bar syndrome	CAAAGTAGCTGAA	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.9015A>T	chr11.hg19:g.108236079A>T		113.0	0.0	.		67.0	48.0	.	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Silent	SNP	ENST00000452508.2	hg19	CCDS31669.1																																																																																			.	.	.	none		0.403	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		T	108236079	A	T	108236079	2	4	264	1	0	0	0	0	0	0	0	1	1109	407	15	5		5	ATM	11	108236079	Silent	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	6040601	108236079	26770437	94	16599											
JAM3	83700	hgsc.bcm.edu	37	chr11	134014786	134014786	+	Missense_Mutation	SNP	A	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	tgagggccacccccggcctcActacagctggtatcgcaatg	8	7	11	15	2	1	1	1	1	0	0	2	1	1	1	4	3	2	3	4	3	3	2			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr11:134014786A>C	ENST00000299106.4	+	5	668	c.509A>C	c.(508-510)cAc>cCc	p.H170P	JAM3_ENST00000524969.1_3'UTR|JAM3_ENST00000529443.2_Missense_Mutation_p.H215P|JAM3_ENST00000441717.3_Missense_Mutation_p.H119P			Q9BX67	JAM3_HUMAN	junctional adhesion molecule 3	170	Ig-like C2-type.				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)		CCCCGGCCTCACTACAGCTGG	0.542																																					p.H170P		Atlas-SNP	.											.	JAM3	41	.	0			c.A509C						PASS	.						123	105	111					11																	134014786		2201	4297	6498	SO:0001583	missense	83700	exon5			GGCCTCACTACAG	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.509A>C	chr11.hg19:g.134014786A>C	ENSP00000299106:p.His170Pro	154.0	0.0	.		136.0	58.0	.	NM_032801	B3KWG9|Q8WWL8|Q96FL1	Missense_Mutation	SNP	ENST00000299106.4	hg19	CCDS8494.2	.	.	.	.	.	.	.	.	.	.	A	15.40	2.822437	0.50739	.	.	ENSG00000166086	ENST00000299106;ENST00000441717;ENST00000532165	T	0.12147	2.71	5.1	2.59	0.31030	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.712485	0.14249	N	0.331596	T	0.13415	0.0325	L	0.35341	1.055	0.09310	N	0.999991	P;P	0.41524	0.753;0.753	P;P	0.48089	0.566;0.566	T	0.15178	-1.0446	10	0.30854	T	0.27	.	4.8908	0.13726	0.4689:0.2664:0.0:0.2647	.	119;170	B3KWG9;Q9BX67	.;JAM3_HUMAN	P	215;119;16	ENSP00000395742:H119P	ENSP00000299106:H215P	H	+	2	0	JAM3	133519996	0.001000	0.12720	0.703000	0.30354	0.829000	0.46940	1.746000	0.38288	0.763000	0.33175	0.533000	0.62120	CAC	.	.	.	none		0.542	JAM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393303.4	NM_032801		C	134014786	A	C	134014786	3	2	264	1	0	0	0	0	1	0	0	0	7951	159	6	5	662	5	JAM3	11	134014786	Missense_Mutation	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	25778707	134014786	991730	95	16600											
CNTN1	1272	hgsc.bcm.edu	37	chr12	41387017	41387017	+	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	gcgtggtagcaaccaatacaCtgggtagaggagagcccagt	12	6	14	9	1	0	2	0	0	0	2	0	3	0	2	2	3	4	3	2	3	5	3	rs377022967		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr12:41387017C>G	ENST00000551295.2	+	17	2176	c.2059C>G	c.(2059-2061)Ctg>Gtg	p.L687V	CNTN1_ENST00000347616.1_Missense_Mutation_p.L687V|CNTN1_ENST00000348761.2_Missense_Mutation_p.L676V	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	687	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.			L -> P (in Ref. 5; AA sequence). {ECO:0000305}.	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)				AACCAATACACTGGGTAGAGG	0.398																																					p.L687V		Atlas-SNP	.											.	CNTN1	207	.	0			c.C2059G						PASS	.						86	87	87					12																	41387017		2203	4300	6503	SO:0001583	missense	1272	exon17			AATACACTGGGTA	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.2059C>G	chr12.hg19:g.41387017C>G	ENSP00000447006:p.Leu687Val	145.0	0.0	.		127.0	44.0	.	NM_001843	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Missense_Mutation	SNP	ENST00000551295.2	hg19	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	C	14.11	2.439004	0.43326	.	.	ENSG00000018236	ENST00000551295;ENST00000347616;ENST00000348761	T;T;T	0.55052	0.54;0.54;0.54	5.2	0.159	0.14968	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	T	0.41396	0.1157	N	0.03281	-0.365	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.74348	0.971;0.983	T	0.18681	-1.0329	10	0.15952	T	0.53	.	10.3176	0.43747	0.0:0.3385:0.0:0.6615	.	676;687	Q12860-2;Q12860	.;CNTN1_HUMAN	V	687;687;676	ENSP00000447006:L687V;ENSP00000325660:L687V;ENSP00000261160:L676V	ENSP00000325660:L687V	L	+	1	2	CNTN1	39673284	0.003000	0.15002	0.249000	0.24280	0.929000	0.56500	-0.024000	0.12435	0.071000	0.16664	-0.351000	0.07748	CTG	.	.	.	alt		0.398	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		G	41387017	C	G	41387017	3	3	264	1	0	0	0	0	1	0	0	0	3642	564	20	4	2121	4	CNTN1	12	41387017	Missense_Mutation	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10		41387017	92464878	96	16601											
KRT86	3892	hgsc.bcm.edu	37	chr12	52702335	52702335	+	Frame_Shift_Del	DEL	T	T	-																															ctgcgccccctccgcccgggTtggcgtctgcggcggcagct																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr12:52702335delT	ENST00000423955.2	+	11	1605	c.1427delT	c.(1426-1428)gttfs	p.V476fs	RP11-845M18.6_ENST00000552441.1_RNA|KRT86_ENST00000293525.5_Frame_Shift_Del_p.V476fs|KRT86_ENST00000544024.1_Frame_Shift_Del_p.V476fs			O43790	KRT86_HUMAN	keratin 86	476	Tail.					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)		TCCGCCCGGGTTGGCGTCTGC	0.672																																					p.V476fs		Pindel	.											.	KRT86	33	.	0			c.1426delG						PASS	.						21	27	25					12																	52702335		2075	4201	6276	SO:0001589	frameshift_variant	3892	exon9			.	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.1427delT	chr12.hg19:g.52702335delT	ENSP00000444533:p.Val476fs	9.0	0.0	.		21.0	12.0	0.571	NM_002284	P78387	Frame_Shift_Del	DEL	ENST00000423955.2	hg19	CCDS41785.1																																																																																			.	.	.	none		0.672	KRT86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404911.1	NM_002284		-	52702335	T	-	52702335	7	5	264	1	0	1	0	1	0	0	0	0	8507	1725	60	0	1461	0	KRT86	12	52702335	Frame_Shift_Del	DEL	T	TCGA-UZ-A9PS-01A-11D-A42J-10	11315318	52702335	81149560	97	16602											
KRT3	3850	hgsc.bcm.edu	37	chr12	53188110	53188110	+	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	ttgttctgttgctccaggaaCcgcacctgcaatggttgcag	7	12	11	11	1	1	0	0	0	1	0	2	1	2	1	3	2	4	7	3	2	2	4			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr12:53188110C>A	ENST00000417996.2	-	2	725	c.651G>T	c.(649-651)cgG>cgT	p.R217R	KRT3_ENST00000309505.3_Silent_p.R217R	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	217	Coil 1A.|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						GCTCCAGGAACCGCACCTGCA	0.542																																					p.R217R		Atlas-SNP	.											.	KRT3	65	.	0			c.G651T						PASS	.						90	99	96					12																	53188110		2199	4299	6498	SO:0001819	synonymous_variant	3850	exon2			CAGGAACCGCACC		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.651G>T	chr12.hg19:g.53188110C>A		122.0	0.0	.		98.0	45.0	.	NM_057088	A6NIS2|Q701L8	Silent	SNP	ENST00000417996.2	hg19	CCDS44895.1																																																																																			.	.	.	none		0.542	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1	NM_057088		A	53188110	C	A	53188110	2	1	264	1	0	0	0	0	0	0	0	1	8473	494	18	4		4	KRT3	12	53188110	Silent	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	485775	53188110	80663785	98	16603											
ATP5G2	517	hgsc.bcm.edu	37	chr12	54059109	54059109	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acggctccttcacatggcaaAgaggatgagaaaggctacca	14	6	11	10	1	1	2	1	1	0	2	2	4	2	3	2	4	1	3	2	4	3	2			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr12:54059109A>G	ENST00000549164.1	-	5	602	c.415T>C	c.(415-417)Ttt>Ctt	p.F139L	ATP5G2_ENST00000338662.5_Missense_Mutation_p.F155L|ATP5G2_ENST00000550241.1_Intron|ATP5G2_ENST00000394349.3_Missense_Mutation_p.F196L|ATP5G2_ENST00000602871.1_Missense_Mutation_p.F139L			Q06055	AT5G2_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C2 (subunit 9)	139					ATP hydrolysis coupled proton transport (GO:0015991)|ATP synthesis coupled proton transport (GO:0015986)|response to ethanol (GO:0045471)	integral component of membrane (GO:0016021)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045263)	hydrogen ion transmembrane transporter activity (GO:0015078)|lipid binding (GO:0008289)|transporter activity (GO:0005215)			kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	6						CACATGGCAAAGAGGATGAGA	0.572																																					p.F196L		Atlas-SNP	.											.	ATP5G2	16	.	0			c.T586C						PASS	.						58	57	58					12																	54059109		2203	4300	6503	SO:0001583	missense	517	exon5			TGGCAAAGAGGAT	X69908	CCDS8863.2, CCDS31812.1	12q13.13	2012-10-12	2010-06-11		ENSG00000135390	ENSG00000135390		"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	842	protein-coding gene	gene with protein product		603193	"ATP synthase, H+ transporting, mitochondrial F0 complex, subunit c (subunit 9), isoform 2", "ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C2 (subunit 9)"			8328972	Standard	NM_005176		Approved		uc001sec.3	Q06055	OTTHUMG00000133442	ENST00000549164.1:c.415T>C	chr12.hg19:g.54059109A>G	ENSP00000447317:p.Phe139Leu	128.0	0.0	.		167.0	60.0	.	NM_005176	B3KQQ6	Missense_Mutation	SNP	ENST00000549164.1	hg19		.	.	.	.	.	.	.	.	.	.	A	35	5.594874	0.96602	.	.	ENSG00000135390	ENST00000394349;ENST00000549164;ENST00000338662	T;T;T	0.53857	0.6;0.6;0.6	5.32	5.32	0.75619	ATPase, F0/V0 complex, subunit C (3);	0.000000	0.85682	D	0.000000	T	0.68081	0.2962	M	0.85197	2.74	0.53688	D	0.999978	P;P;D	0.56968	0.891;0.945;0.978	P;P;P	0.52627	0.704;0.547;0.57	T	0.75007	-0.3469	10	0.72032	D	0.01	-18.2017	14.7093	0.69215	1.0:0.0:0.0:0.0	.	139;155;196	Q06055;Q06055-3;Q06055-2	AT5G2_HUMAN;.;.	L	196;139;155	ENSP00000377878:F196L;ENSP00000447317:F139L;ENSP00000340315:F155L	ENSP00000340315:F155L	F	-	1	0	ATP5G2	52345376	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.051000	0.93849	2.371000	0.80710	0.533000	0.62120	TTT	.	.	.	none		0.572	ATP5G2-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000407403.1	NM_005176		G	54059109	A	G	54059109	3	3	264	1	0	0	0	0	1	0	0	0	1154	72	3	3	14	3	ATP5G2	12	54059109	Missense_Mutation	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	870999	54059109	79792786	99	16604											
TBK1	29110	hgsc.bcm.edu	37	chr12	64860793	64860793	+	Missense_Mutation	SNP	T	T	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	tctgtgtacaaactcacagaTtttggtgcagctagagaatt	12	13	9	7	0	2	2	1	0	1	2	2	3	2	2	0	1	4	3	0	1	4	5			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr12:64860793T>G	ENST00000331710.5	+	5	810	c.471T>G	c.(469-471)gaT>gaG	p.D157E		NM_013254.3	NP_037386.1	Q9UHD2	TBK1_HUMAN	TANK-binding kinase 1	157	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|dendritic cell proliferation (GO:0044565)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of gene expression (GO:0010629)|negative regulation of type I interferon production (GO:0032480)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to virus (GO:0009615)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|type I interferon production (GO:0032606)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)	ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)|phosphoprotein binding (GO:0051219)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)	20				GBM - Glioblastoma multiforme(28;0.0386)		AACTCACAGATTTTGGTGCAG	0.378																																					p.D157E		Atlas-SNP	.											.	TBK1	149	.	0			c.T471G						PASS	.						196	183	188					12																	64860793		2203	4300	6503	SO:0001583	missense	29110	exon5			CACAGATTTTGGT	AF191838	CCDS8968.1	12q14.2	2006-06-10			ENSG00000183735	ENSG00000183735			11584	protein-coding gene	gene with protein product		604834				10581243, 10783893	Standard	NM_013254		Approved	NAK	uc001ssc.2	Q9UHD2	OTTHUMG00000168796	ENST00000331710.5:c.471T>G	chr12.hg19:g.64860793T>G	ENSP00000329967:p.Asp157Glu	93.0	0.0	.		94.0	31.0	.	NM_013254	A8K4S4|Q8IYV3|Q9NUJ5	Missense_Mutation	SNP	ENST00000331710.5	hg19	CCDS8968.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.937682	0.73557	.	.	ENSG00000183735	ENST00000331710	D	0.92911	-3.13	5.34	0.168	0.15012	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.97353	0.9134	H	0.99090	4.425	0.50467	D	0.99987	D	0.63046	0.992	D	0.79108	0.992	D	0.96021	0.9009	9	.	.	.	-13.1372	10.9578	0.47368	0.0:0.3822:0.0:0.6178	.	157	Q9UHD2	TBK1_HUMAN	E	157	ENSP00000329967:D157E	.	D	+	3	2	TBK1	63147060	0.998000	0.40836	0.997000	0.53966	0.836000	0.47400	0.527000	0.22987	-0.117000	0.11872	-0.326000	0.08463	GAT	.	.	.	none		0.378	TBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401130.1	NM_013254		G	64860793	T	G	64860793	3	3	264	1	0	0	0	0	1	0	0	0	15649	1490	52	5	485	5	TBK1	12	64860793	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	10801684	64860793	68991102	100	16605											
GLTP	51228	hgsc.bcm.edu	37	chr12	110295370	110295370	+	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	ccagtgtggcccctactttgGgccactctgctccatacatt	6	12	8	15	0	1	0	0	0	1	0	2	0	2	0	5	2	3	1	5	2	2	4			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr12:110295370G>A	ENST00000318348.4	-	3	370	c.257C>T	c.(256-258)cCc>cTc	p.P86L	GLTP_ENST00000544393.1_Intron	NM_016433.3	NP_057517.1	Q9NZD2	GLTP_HUMAN	glycolipid transfer protein	86					glycolipid transport (GO:0046836)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)|lipid binding (GO:0008289)			endometrium(1)|kidney(1)|lung(1)|upper_aerodigestive_tract(1)	4		Lung NSC(355;2.38e-06)|Breast(359;0.00354)|Myeloproliferative disorder(1001;0.0122)		BRCA - Breast invasive adenocarcinoma(302;0.0025)		CCCTACTTTGGGCCACTCTGC	0.552																																					p.P86L		Atlas-SNP	.											.	GLTP	15	.	0			c.C257T						PASS	.						89	85	86					12																	110295370		2203	4300	6503	SO:0001583	missense	51228	exon3			ACTTTGGGCCACT	AF209704, AY372530	CCDS9136.1	12q24.11	2008-08-08			ENSG00000139433	ENSG00000139433			24867	protein-coding gene	gene with protein product		608949				15287756, 15901739	Standard	NM_016433		Approved		uc001tpm.3	Q9NZD2	OTTHUMG00000169278	ENST00000318348.4:c.257C>T	chr12.hg19:g.110295370G>A	ENSP00000315263:p.Pro86Leu	63.0	0.0	.		51.0	30.0	.	NM_016433	Q53Z13|Q96J68	Missense_Mutation	SNP	ENST00000318348.4	hg19	CCDS9136.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.77|16.77	3.214772|3.214772	0.58452|0.58452	.|.	.|.	ENSG00000139433|ENSG00000139433	ENST00000318348|ENST00000540772	.|.	.|.	.|.	4.65|4.65	4.65|4.65	0.58169|0.58169	Glycolipid transfer protein domain (3);|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.70343|0.70343	0.3213|0.3213	L|L	0.57536|0.57536	1.79|1.79	0.80722|0.80722	D|D	1|1	B|.	0.22604|.	0.072|.	B|.	0.25405|.	0.06|.	T|T	0.69405|0.69405	-0.5154|-0.5154	9|6	0.38643|.	T|.	0.18|.	.|.	16.5324|16.5324	0.84365|0.84365	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	86|.	Q9NZD2|.	GLTP_HUMAN|.	L|S	86|70	.|.	ENSP00000315263:P86L|.	P|P	-|-	2|1	0|0	GLTP|GLTP	108779753|108779753	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	8.981000|8.981000	0.93465|0.93465	2.312000|2.312000	0.78011|0.78011	0.585000|0.585000	0.79938|0.79938	CCC|CCA	.	.	.	none		0.552	GLTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403278.2	NM_016433		A	110295370	G	A	110295370	3	1	264	1	0	0	0	0	1	0	0	0	6478	1232	43	2	384	2	GLTP	12	110295370	Missense_Mutation	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10	45434577	110295370	23556525	101	16606											
HNF1A	6927	hgsc.bcm.edu	37	chr12	121434509	121434509	+	Missense_Mutation	SNP	A	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	agcctgcctccctgggtcctAcgttcaccaacacaggtgcc	7	8	9	17	1	1	0	1	0	0	0	3	0	3	0	6	2	5	1	6	2	2	2			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr12:121434509A>C	ENST00000257555.6	+	6	1499	c.1273A>C	c.(1273-1275)Acg>Ccg	p.T425P	HNF1A_ENST00000543427.1_Missense_Mutation_p.T308P|HNF1A_ENST00000538626.1_Intron|HNF1A_ENST00000544413.1_Missense_Mutation_p.T425P|HNF1A_ENST00000400024.2_Missense_Mutation_p.T425P|HNF1A_ENST00000402929.1_Missense_Mutation_p.T425P|HNF1A_ENST00000541395.1_Missense_Mutation_p.T425P			P20823	HNF1A_HUMAN	HNF1 homeobox A	425					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)					CCTGGGTCCTACGTTCACCAA	0.637									Hepatic Adenoma, Familial Clustering of																												p.T425P		Atlas-SNP	.											.	HNF1A	302	.	0			c.A1273C						PASS	.						95	74	81					12																	121434509		2203	4300	6503	SO:0001583	missense	6927	exon6	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	GGTCCTACGTTCA	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.1273A>C	chr12.hg19:g.121434509A>C	ENSP00000257555:p.Thr425Pro	80.0	0.0	.		104.0	36.0	.	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Missense_Mutation	SNP	ENST00000257555.6	hg19	CCDS9209.1	.	.	.	.	.	.	.	.	.	.	A	17.32	3.360841	0.61403	.	.	ENSG00000135100	ENST00000257555;ENST00000535125;ENST00000544680;ENST00000537424;ENST00000543027;ENST00000543427;ENST00000545458;ENST00000541395;ENST00000340577;ENST00000344370;ENST00000544413	D;D;D;D	0.99893	-5.42;-7.57;-5.41;-5.42	4.81	4.81	0.61882	Hepatocyte nuclear factor 1, beta isoform, C-terminal (1);	0.100353	0.45126	D	0.000390	D	0.99390	0.9785	L	0.36672	1.1	0.30828	N	0.73707	P;P;P;D	0.55172	0.531;0.761;0.761;0.97	B;B;P;P	0.50314	0.259;0.312;0.582;0.637	D	0.99963	1.1771	10	0.33940	T	0.23	-13.874	5.8526	0.18701	0.8058:0.0:0.1942:0.0	.	425;425;425;425	F5H0K0;P20823;E7EUQ4;E7EMR0	.;HNF1A_HUMAN;.;.	P	425;317;425;425;246;308;425;425;425;425;425	ENSP00000257555:T425P;ENSP00000439721:T308P;ENSP00000443112:T425P;ENSP00000438804:T425P	ENSP00000257555:T425P	T	+	1	0	HNF1A	119918892	1.000000	0.71417	0.997000	0.53966	0.977000	0.68977	2.436000	0.44819	1.823000	0.53134	0.451000	0.29950	ACG	.	.	.	none		0.637	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		C	121434509	A	C	121434509	3	2	264	1	0	0	0	0	1	0	0	0	7258	391	14	5	1295	5	HNF1A	12	121434509	Missense_Mutation	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	11139139	121434509	12417386	102	16607											
PSMD9	5715	hgsc.bcm.edu	37	chr12	122340948	122340948	+	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	atgagattgtggagttcggcTctgtgaacacccagaacttc	10	11	11	9	1	1	3	0	2	1	2	3	5	1	4	1	2	2	2	1	2	2	3			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr12:122340948T>A	ENST00000541212.1	+	4	616	c.490T>A	c.(490-492)Tct>Act	p.S164T	PSMD9_ENST00000261817.2_Missense_Mutation_p.S164T|PSMD9_ENST00000340175.5_Missense_Mutation_p.S164T|RP11-87C12.2_ENST00000546333.1_3'UTR|PSMD9_ENST00000542602.1_Missense_Mutation_p.S59T			O00233	PSMD9_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 9	164	PDZ.				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 insulin secretion (GO:0046676)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of insulin secretion (GO:0032024)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome regulatory particle assembly (GO:0070682)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome regulatory particle (GO:0005838)	bHLH transcription factor binding (GO:0043425)|transcription coactivator activity (GO:0003713)			endometrium(1)|large_intestine(1)|lung(1)	3	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000117)|Epithelial(86;0.000415)|BRCA - Breast invasive adenocarcinoma(302;0.231)		GGAGTTCGGCTCTGTGAACAC	0.527																																					p.S164T		Atlas-SNP	.											.	PSMD9	8	.	0			c.T490A						PASS	.						169	134	146					12																	122340948		2203	4300	6503	SO:0001583	missense	5715	exon4			TTCGGCTCTGTGA	AB003177	CCDS9225.1, CCDS58284.1	12q24.31-q24.32	2008-05-22			ENSG00000110801	ENSG00000110801		"Proteasome (prosome, macropain) subunits"	9567	protein-coding gene	gene with protein product		603146				9653651	Standard	NM_002813		Approved	p27, Rpn4	uc001ubl.4	O00233	OTTHUMG00000168945	ENST00000541212.1:c.490T>A	chr12.hg19:g.122340948T>A	ENSP00000440485:p.Ser164Thr	113.0	0.0	.		148.0	90.0	.	NM_002813	B2RD35|G3V1Q6|Q9BQ42	Missense_Mutation	SNP	ENST00000541212.1	hg19	CCDS9225.1	.	.	.	.	.	.	.	.	.	.	T	17.83	3.485602	0.63962	.	.	ENSG00000110801;ENSG00000110801;ENSG00000110801;ENSG00000110801;ENSG00000256950	ENST00000541212;ENST00000340175;ENST00000261817;ENST00000544724;ENST00000542602	T;T;T;T;T	0.30182	1.54;2.39;1.69;1.54;2.39	5.6	5.6	0.85130	PDZ/DHR/GLGF (2);	0.054713	0.85682	D	0.000000	T	0.35008	0.0917	L	0.43923	1.385	0.58432	D	0.999995	B;D	0.57899	0.313;0.981	B;P	0.53360	0.279;0.724	T	0.05599	-1.0875	10	0.20046	T	0.44	-10.8784	10.947	0.47306	0.1396:0.0:0.0:0.8604	.	164;164	F8W7V8;O00233	.;PSMD9_HUMAN	T	164;164;164;75;59	ENSP00000440485:S164T;ENSP00000340847:S164T;ENSP00000261817:S164T;ENSP00000443929:S75T;ENSP00000443772:S59T	ENSP00000261817:S164T	S	+	1	0	RP11-87C12.2;PSMD9	120825331	1.000000	0.71417	1.000000	0.80357	0.657000	0.38888	4.346000	0.59367	2.129000	0.65627	0.533000	0.62120	TCT	.	.	.	none		0.527	PSMD9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401686.1	NM_002813		A	122340948	T	A	122340948	3	1	264	1	0	0	0	0	1	0	0	0	12715	1551	54	5	504	5	PSMD9	12	122340948	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	906439	122340948	11510947	103	16608											
RILPL1	353116	hgsc.bcm.edu	37	chr12	123984011	123984011	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagctccctgtccttggcgCggatctcgtcgcgttgtttg	2	13	12	14	5	1	0	0	0	1	0	5	1	3	1	3	2	1	3	3	2	0	3			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr12:123984011C>T	ENST00000376874.4	-	3	768	c.533G>A	c.(532-534)cGc>cAc	p.R178H	RILPL1_ENST00000340724.6_Missense_Mutation_p.R26H	NM_178314.3	NP_847884.2	Q5EBL4	RIPL1_HUMAN	Rab interacting lysosomal protein-like 1	178					epithelial cell morphogenesis (GO:0003382)|intracellular protein transport (GO:0006886)|regulation of neuron death (GO:1901214)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)				endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.00067)|all cancers(50;0.00836)|BRCA - Breast invasive adenocarcinoma(302;0.197)		GTCCTTGGCGCGGATCTCGTC	0.617																																					p.R178H		Atlas-SNP	.											.	RILPL1	23	.	0			c.G533A						PASS	.						139	155	150					12																	123984011		2155	4245	6400	SO:0001583	missense	353116	exon3			TTGGCGCGGATCT	AK097550	CCDS45006.1	12q24.31	2007-11-27			ENSG00000188026	ENSG00000188026			26814	protein-coding gene	gene with protein product		614092				14668488	Standard	NM_178314		Approved	FLJ39378	uc001ufe.2	Q5EBL4	OTTHUMG00000168686	ENST00000376874.4:c.533G>A	chr12.hg19:g.123984011C>T	ENSP00000366070:p.Arg178His	59.0	0.0	.		87.0	43.0	.	NM_178314	Q66K36|Q8N1M0	Missense_Mutation	SNP	ENST00000376874.4	hg19	CCDS45006.1	.	.	.	.	.	.	.	.	.	.	C	16.97	3.268272	0.59540	.	.	ENSG00000188026	ENST00000376874;ENST00000340724	T;T	0.30182	1.54;1.54	5.07	4.18	0.49190	.	0.000000	0.85682	D	0.000000	T	0.56949	0.2020	M	0.81802	2.56	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	0.63033	-0.6727	10	0.72032	D	0.01	-1.0E-4	13.638	0.62233	0.0:0.9246:0.0:0.0754	.	154;178;27	Q5EBL4-2;Q5EBL4;Q5EBL4-3	.;RIPL1_HUMAN;.	H	178;26	ENSP00000366070:R178H;ENSP00000345874:R26H	ENSP00000345874:R26H	R	-	2	0	RILPL1	122549964	1.000000	0.71417	0.816000	0.32577	0.005000	0.04900	7.818000	0.86416	1.125000	0.41998	-0.291000	0.09656	CGC	.	.	.	none		0.617	RILPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400595.1	NM_178314		T	123984011	C	T	123984011	3	4	264	1	0	0	0	0	1	0	0	0	13374	768	27	1	698	1	RILPL1	12	123984011	Missense_Mutation	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	1643063	123984011	9867884	104	16609											
NCOR2	9612	hgsc.bcm.edu	37	chr12	124887084	124887084	+	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	tgctgctgctgctgctgctgCtgctgctgctgttgttgctg	0	16	14	11	0	0	0	0	0	0	0	0	0	0	0	0	0	11	13	0	0	0	2			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr12:124887084C>T	ENST00000405201.1	-	14	1506	c.1506G>A	c.(1504-1506)caG>caA	p.Q502Q	NCOR2_ENST00000356219.3_Silent_p.Q502Q|NCOR2_ENST00000397355.1_Silent_p.Q502Q|NCOR2_ENST00000404621.1_Silent_p.Q501Q|NCOR2_ENST00000429285.2_Silent_p.Q501Q|NCOR2_ENST00000404121.2_Silent_p.Q72Q			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	502	Poly-Gln.				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)		gctgctgctgctgctgctgct	0.617																																					p.Q502Q		Atlas-SNP	.											.	NCOR2	475	.	0			c.G1506A						PASS	.						9	12	11					12																	124887084		2067	4185	6252	SO:0001819	synonymous_variant	9612	exon16			CTGCTGCTGCTGC	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.1506G>A	chr12.hg19:g.124887084C>T		29.0	0.0	.		57.0	6.0	.	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	hg19	CCDS41858.2																																																																																			.	.	.	none		0.617	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		T	124887084	C	T	124887084	2	4	264	1	0	0	0	0	0	0	0	1	10243	796	28	2		2	NCOR2	12	124887084	Silent	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	903073	124887084	8964811	105	16610											
RIMBP2	23504	hgsc.bcm.edu	37	chr12	130921476	130921476	+	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	ggtgccctgtggctgtggcaGgatgcggctgggtgagggcg	3	8	22	8	2	0	1	0	1	0	0	0	2	0	2	1	7	2	3	1	7	0	0			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr12:130921476G>T	ENST00000261655.4	-	10	2129	c.1966C>A	c.(1966-1968)Ctg>Atg	p.L656M	RIMBP2_ENST00000535703.1_Missense_Mutation_p.L564M|RIMBP2_ENST00000536002.1_Missense_Mutation_p.L564M	NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	656	Pro-rich.				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)		GGCTGTGGCAGGATGCGGCTG	0.731																																					p.L656M		Atlas-SNP	.											.	RIMBP2	220	.	0			c.C1966A						PASS	.						12	17	15					12																	130921476		2182	4275	6457	SO:0001583	missense	23504	exon10			GTGGCAGGATGCG	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.1966C>A	chr12.hg19:g.130921476G>T	ENSP00000261655:p.Leu656Met	92.0	0.0	.		100.0	60.0	.	NM_015347	Q96ID2	Missense_Mutation	SNP	ENST00000261655.4	hg19	CCDS31925.1	.	.	.	.	.	.	.	.	.	.	G	16.87	3.240944	0.58995	.	.	ENSG00000060709	ENST00000261655;ENST00000392375;ENST00000535703;ENST00000536002	T;T;T	0.22336	1.96;2.46;2.46	4.63	3.75	0.43078	.	0.084015	0.49305	D	0.000146	T	0.42944	0.1225	M	0.66939	2.045	0.47094	D	0.999317	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.97110	0.997;1.0;0.997	T	0.28776	-1.0033	10	0.49607	T	0.09	-23.8929	12.9334	0.58301	0.0794:0.0:0.9206:0.0	.	564;564;656	C9JWN3;O15034-2;O15034	.;.;RIMB2_HUMAN	M	656;564;564;564	ENSP00000261655:L656M;ENSP00000440347:L564M;ENSP00000439159:L564M	ENSP00000261655:L656M	L	-	1	2	RIMBP2	129487429	1.000000	0.71417	1.000000	0.80357	0.503000	0.33858	6.415000	0.73328	0.952000	0.37798	-0.224000	0.12420	CTG	.	.	.	none		0.731	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347		T	130921476	G	T	130921476	3	4	264	1	0	0	0	0	1	0	0	0	13376	991	35	4	1232	4	RIMBP2	12	130921476	Missense_Mutation	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10	6034392	130921476	2930419	106	16611											
PGAM5	192111	hgsc.bcm.edu	37	chr12	133291557	133291557	+	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	ggccacgcggcacatcttccTcatcaggcattcccagtacc	8	8	8	17	2	3	0	2	0	1	0	5	0	5	0	4	3	1	3	4	3	1	3			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr12:133291557T>A	ENST00000498926.2	+	2	363	c.305T>A	c.(304-306)cTc>cAc	p.L102H	PGAM5_ENST00000317555.2_Missense_Mutation_p.L102H|PGAM5_ENST00000454808.2_5'UTR|PXMP2_ENST00000545677.1_Silent_p.P141P|PGAM5_ENST00000543955.1_5'UTR	NM_001170543.1|NM_001170544.1	NP_001164014.1|NP_001164015.1	Q96HS1	PGAM5_HUMAN	phosphoglycerate mutase family member 5	102					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)		CACATCTTCCTCATCAGGCAT	0.587																																					p.L102H		Atlas-SNP	.											.	PGAM5	18	.	0			c.T305A						PASS	.						138	92	108					12																	133291557		2202	4300	6502	SO:0001583	missense	192111	exon2			TCTTCCTCATCAG	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.305T>A	chr12.hg19:g.133291557T>A	ENSP00000438465:p.Leu102His	105.0	0.0	.		162.0	40.0	.	NM_138575	A9LN06|C9IZY7|Q96JB0	Missense_Mutation	SNP	ENST00000498926.2	hg19	CCDS53845.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.609079	0.87258	.	.	ENSG00000247077	ENST00000317555;ENST00000498926	T;T	0.80738	0.33;-1.41	4.64	4.64	0.57946	Histidine phosphatase superfamily, clade-1 (2);	0.000000	0.85682	D	0.000000	D	0.93539	0.7938	H	0.98333	4.205	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.996	D	0.95728	0.8772	10	0.87932	D	0	-4.5906	14.0667	0.64834	0.0:0.0:0.0:1.0	.	102;102	Q96HS1;Q96HS1-2	PGAM5_HUMAN;.	H	102	ENSP00000321503:L102H;ENSP00000438465:L102H	ENSP00000321503:L102H	L	+	2	0	PGAM5	131801630	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.658000	0.83755	1.735000	0.51646	0.379000	0.24179	CTC	.	.	.	none		0.587	PGAM5-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397562.1	NM_138575		A	133291557	T	A	133291557	3	1	264	1	0	0	0	0	1	0	0	0	11783	1551	54	5	311	5	PGAM5	12	133291557	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	2370081	133291557	560338	107	16612											
TM9SF2	9375	hgsc.bcm.edu	37	chr13	100172311	100172311	+	Frame_Shift_Del	DEL	A	A	-																															tttgatttttgccaagcatcAgaaggaaagcgcccatctga																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr13:100172311delA	ENST00000376387.4	+	3	451	c.261delA	c.(259-261)tcafs	p.S87fs	TM9SF2_ENST00000463709.1_3'UTR	NM_004800.1	NP_004791.1	Q99805	TM9S2_HUMAN	transmembrane 9 superfamily member 2	87					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)					GCCAAGCATCAGAAGGAAAGC	0.353																																					p.S87X		Pindel	.											.	TM9SF2	52	.	0			c.260delC						PASS	.						75	75	75					13																	100172311		2203	4300	6503	SO:0001589	frameshift_variant	9375	exon3			.	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.261delA	chr13.hg19:g.100172311delA	ENSP00000365567:p.Ser87fs	108.0	0.0	.		119.0	10.0	0.084	NM_004800	A8K399|Q2TAY5	Frame_Shift_Del	DEL	ENST00000376387.4	hg19	CCDS9493.1																																																																																			.	.	.	none		0.353	TM9SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045602.3			-	100172311	A	-	100172311	7	5	264	1	0	1	0	1	0	0	0	0	15990	175	7	0	271	0	TM9SF2	13	100172311	Frame_Shift_Del	DEL	A	TCGA-UZ-A9PS-01A-11D-A42J-10		100172311	14997567	108	16613											
MDP1	145553	hgsc.bcm.edu	37	chr14	24683307	24683307	+	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	cgcaaatgtctctaacccttGacttagagtttgaagattca	12	13	7	9	1	2	4	1	2	1	2	3	4	2	4	1	0	1	2	1	0	4	5			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr14:24683307G>C	ENST00000288087.7	-	6	565	c.454C>G	c.(454-456)Caa>Gaa	p.Q152E	CHMP4A_ENST00000609024.1_5'Flank|CHMP4A_ENST00000530996.1_5'Flank|MDP1_ENST00000396833.2_Nonsense_Mutation_p.S105*|NEDD8-MDP1_ENST00000534348.1_Missense_Mutation_p.Q169E|MDP1_ENST00000532557.1_5'UTR|AL136419.6_ENST00000565988.1_RNA|NEDD8-MDP1_ENST00000604306.1_5'Flank|CHMP4A_ENST00000347519.6_5'Flank|CHMP4A_ENST00000542700.2_5'Flank|TM9SF1_ENST00000530611.1_5'Flank|TM9SF1_ENST00000556387.1_5'Flank	NM_001199822.1|NM_138476.3	NP_001186751.1|NP_612485.2	Q86V88	MGDP1_HUMAN	magnesium-dependent phosphatase 1	152						extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|large_intestine(2)|lung(3)	7						TCTAACCCTTGACTTAGAGTT	0.433																																					p.S105X		Atlas-SNP	.											.	MDP1	13	.	0			c.C314G						PASS	.						82	82	82					14																	24683307		2203	4300	6503	SO:0001583	missense	145553	exon5			ACCCTTGACTTAG	BC046912	CCDS9620.1, CCDS55908.1	14q12	2009-07-09			ENSG00000213920	ENSG00000213920			28781	protein-coding gene	gene with protein product	"fructosamine-6-phosphatase"					10889041, 16670083	Standard	NM_138476		Approved	MGC5987, FN6Pase		Q86V88	OTTHUMG00000133477	ENST00000288087.7:c.454C>G	chr14.hg19:g.24683307G>C	ENSP00000288087:p.Gln152Glu	77.0	0.0	.		77.0	38.0	.	NM_001199821	Q86Y84|Q8NAD9	Nonsense_Mutation	SNP	ENST00000288087.7	hg19	CCDS9620.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.69|18.69	3.677241|3.677241	0.68042|0.68042	.|.	.|.	ENSG00000213920;ENSG00000255526|ENSG00000213920	ENST00000288087;ENST00000534348|ENST00000396833	D|.	0.97114|.	-4.25|.	5.25|5.25	3.22|3.22	0.36961|0.36961	HAD-like domain (1);|.	0.317545|.	0.17362|.	U|.	0.177013|.	T|.	0.27663|.	0.0680|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|.	0.13495|.	-1.0507|.	9|.	0.06365|0.02654	T|T	0.9|1	-8.3948|-8.3948	7.5144|7.5144	0.27592|0.27592	0.0:0.1719:0.6255:0.2025|0.0:0.1719:0.6255:0.2025	.|.	152|.	Q86V88|.	MGDP1_HUMAN|.	E|X	152;169|105	ENSP00000288087:Q152E|.	ENSP00000288087:Q152E|ENSP00000380045:S105X	Q|S	-|-	1|2	0|0	MDP1;NEDD8-MDP1|MDP1	23753147|23753147	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	1.295000|1.295000	0.33377|0.33377	1.398000|1.398000	0.46701|0.46701	0.655000|0.655000	0.94253|0.94253	CAA|TCA	.	.	.	none		0.433	MDP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257367.1	NM_138476		C	24683307	G	C	24683307	3	2	264	1	0	0	0	0	1	0	0	0	9423	1299	45	4	80	4	MDP1	14	24683307	Missense_Mutation	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10		24683307	82666233	109	16614											
COQ6	51004	hgsc.bcm.edu	37	chr14	74426189	74426189	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagagctagttagcatggaTgaggaaaaatttgtggatgc	13	10	14	4	0	0	2	0	1	0	1	0	5	0	5	0	3	3	4	0	3	4	3			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr14:74426189T>C	ENST00000334571.2	+	8	895	c.855T>C	c.(853-855)gaT>gaC	p.D285D	ENTPD5_ENST00000557325.1_3'UTR|COQ6_ENST00000554920.1_Intron|COQ6_ENST00000238709.4_Silent_p.D210D|COQ6_ENST00000394026.4_Silent_p.D260D	NM_182476.2	NP_872282.1	Q9Y2Z9	COQ6_HUMAN	coenzyme Q6 monooxygenase	285					small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(234;0.00337)		TTAGCATGGATGAGGAAAAAT	0.458																																					p.D285D		Atlas-SNP	.											.	COQ6	27	.	0			c.T855C						PASS	.						256	224	235					14																	74426189		2203	4300	6503	SO:0001819	synonymous_variant	51004	exon8			CATGGATGAGGAA	AF132944	CCDS9823.1, CCDS9824.1, CCDS9824.2	14q24.1	2013-05-01	2013-05-01		ENSG00000119723	ENSG00000119723			20233	protein-coding gene	gene with protein product		614647	"coenzyme Q6 homolog (yeast)", "coenzyme Q6 homolog, monooxygenase (yeast)", "coenzyme Q6 homolog, monooxygenase (S. cerevisiae)"			21540551	Standard	NM_182476		Approved	CGI-10	uc001xph.3	Q9Y2Z9	OTTHUMG00000171260	ENST00000334571.2:c.855T>C	chr14.hg19:g.74426189T>C		102.0	0.0	.		103.0	46.0	.	NM_182476	B7Z3K8|Q53GG6|Q86U30|Q96CA1|Q96CK2	Silent	SNP	ENST00000334571.2	hg19	CCDS9823.1																																																																																			.	.	.	none		0.458	COQ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412616.1			C	74426189	T	C	74426189	2	2	264	1	0	0	0	0	0	0	0	1	3751	1461	51	3		3	COQ6	14	74426189	Silent	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	49742882	74426189	32923351	110	16615											
PPP4R4	57718	hgsc.bcm.edu	37	chr14	94722854	94722854	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actctgaagattcctgctgaTaagcatctacttcagcagtt	11	13	7	10	0	3	3	1	2	2	1	4	3	4	3	1	0	4	4	1	0	3	5			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr14:94722854T>C	ENST00000304338.3	+	17	2077	c.1923T>C	c.(1921-1923)gaT>gaC	p.D641D		NM_058237.1	NP_478144.1	Q6NUP7	PP4R4_HUMAN	protein phosphatase 4, regulatory subunit 4	641					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						TTCCTGCTGATAAGCATCTAC	0.343																																					p.D641D		Atlas-SNP	.											.	PPP4R4	107	.	0			c.T1923C						PASS	.						102	107	105					14																	94722854		2203	4300	6503	SO:0001819	synonymous_variant	57718	exon17			TGCTGATAAGCAT	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.1923T>C	chr14.hg19:g.94722854T>C		88.0	0.0	.		81.0	35.0	.	NM_058237	Q9BUF8|Q9HCF0	Silent	SNP	ENST00000304338.3	hg19	CCDS9921.1																																																																																			.	.	.	none		0.343	PPP4R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413056.1	NM_058237		C	94722854	T	C	94722854	2	2	264	1	0	0	0	0	0	0	0	1	12415	1403	49	3		3	PPP4R4	14	94722854	Silent	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	20296665	94722854	12626686	111	16616											
TP53BP1	7158	hgsc.bcm.edu	37	chr15	43714077	43714077	+	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	gttttcctgggcctcctcggGagctgggtaaggcaaaatct	7	11	13	10	1	1	0	0	0	1	0	4	1	3	1	3	4	1	4	3	4	3	3			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr15:43714077G>C	ENST00000263801.3	-	19	4313	c.4061C>G	c.(4060-4062)tCc>tGc	p.S1354C	TP53BP1_ENST00000382044.4_Missense_Mutation_p.S1359C|TP53BP1_ENST00000450115.2_Missense_Mutation_p.S1359C|TP53BP1_ENST00000382039.3_Missense_Mutation_p.S1359C	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	1354					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)		GCCTCCTCGGGAGCTGGGTAA	0.562								Other conserved DNA damage response genes																													p.S1359C		Atlas-SNP	.											.	TP53BP1	157	.	0			c.C4076G						PASS	.						63	66	65					15																	43714077		2201	4298	6499	SO:0001583	missense	7158	exon19			CCTCGGGAGCTGG	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.4061C>G	chr15.hg19:g.43714077G>C	ENSP00000263801:p.Ser1354Cys	86.0	0.0	.		79.0	39.0	.	NM_001141980	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Missense_Mutation	SNP	ENST00000263801.3	hg19	CCDS10096.1	.	.	.	.	.	.	.	.	.	.	G	16.13	3.034770	0.54896	.	.	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115	T;T;T;T	0.04917	3.58;3.58;3.53;3.58	5.71	5.71	0.89125	.	0.308734	0.33670	N	0.004678	T	0.10337	0.0253	N	0.19112	0.55	0.33853	D	0.63282	D;D;D;D	0.76494	0.997;0.993;0.999;0.996	P;P;P;P	0.56216	0.781;0.628;0.794;0.794	T	0.05484	-1.0882	10	0.59425	D	0.04	-8.8598	14.0939	0.65008	0.0:0.2469:0.7531:0.0	.	1359;1354;1359;1359	B7Z3E7;Q12888;Q12888-2;F8VY86	.;TP53B_HUMAN;.;.	C	1354;1359;1359;1359	ENSP00000263801:S1354C;ENSP00000371475:S1359C;ENSP00000371470:S1359C;ENSP00000393497:S1359C	ENSP00000263801:S1354C	S	-	2	0	TP53BP1	41501369	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.367000	0.44213	2.860000	0.98153	0.655000	0.94253	TCC	.	.	.	none		0.562	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			C	43714077	G	C	43714077	3	2	264	1	0	0	0	0	1	0	0	0	16395	1174	41	4	1897	4	TP53BP1	15	43714077	Missense_Mutation	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10		43714077	58817315	112	16617											
GOLGA6A	342096	hgsc.bcm.edu	37	chr15	74367328	74367328	+	Frame_Shift_Del	DEL	G	G	-																															ggtcactgctgggggcgccaGggatgggggctcagctgaga																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr15:74367328delG	ENST00000290438.3	-	11	902	c.862delC	c.(862-864)ctgfs	p.L288fs	RN7SL429P_ENST00000479090.2_RNA	NM_001038640.2	NP_001033729.2	Q9NYA3	GOG6A_HUMAN	golgin A6 family, member A	288						Golgi apparatus (GO:0005794)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|liver(1)|lung(6)|prostate(1)|urinary_tract(1)	16						GGGGGCGCCAGGGATGGGGGC	0.547																																					p.L288fs		Atlas-INDEL	.											.	GOLGA6A	28	.	0			c.863delT						PASS	.						7	10	9					15																	74367328		1445	3996	5441	SO:0001589	frameshift_variant	342096	exon11			.	AF263742	CCDS32290.1	15q24.1	2013-05-10	2010-02-12	2009-09-28	ENSG00000159289	ENSG00000159289			13567	protein-coding gene	gene with protein product		610288	"golgi autoantigen, golgin subfamily a, member 6", "golgi autoantigen, golgin subfamily a, 6", "golgi autoantigen, golgin subfamily a, 6A"	GOLGA6		11161787	Standard	NM_001038640		Approved	GLP	uc002axa.1	Q9NYA3	OTTHUMG00000173035	ENST00000290438.3:c.862delC	chr15.hg19:g.74367328delG	ENSP00000290438:p.Leu288fs	86.0	0.0	0		45.0	23.0	0.511111	NM_001038640	A8K959|Q9NYA7	Frame_Shift_Del	DEL	ENST00000290438.3	hg19	CCDS32290.1																																																																																			.	.	.	none		0.547	GOLGA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421835.1	XM_292357		-	74367328	G	-	74367328	7	5	264	1	0	1	0	1	0	0	0	0	6564	991	35	0	1251	0	GOLGA6A	15	74367328	Frame_Shift_Del	DEL	G	TCGA-UZ-A9PS-01A-11D-A42J-10	30653251	74367328	28164064	113	16618	173	2									
GOLGA6A	342096	hgsc.bcm.edu	37	chr15	74367333	74367333	+	Frame_Shift_Del	DEL	G	G	-																															ctgctgggggcgccagggatGggggctcagctgagaaatga																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr15:74367333delG	ENST00000290438.3	-	11	897	c.857delC	c.(856-858)ccafs	p.P286fs	RN7SL429P_ENST00000479090.2_RNA	NM_001038640.2	NP_001033729.2	Q9NYA3	GOG6A_HUMAN	golgin A6 family, member A	286						Golgi apparatus (GO:0005794)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|liver(1)|lung(6)|prostate(1)|urinary_tract(1)	16						CGCCAGGGATGGGGGCTCAGC	0.542																																					p.P286fs		Atlas-INDEL	.											.	GOLGA6A	28	.	0			c.858delA						PASS	.						7	10	9					15																	74367333		1445	3996	5441	SO:0001589	frameshift_variant	342096	exon11			.	AF263742	CCDS32290.1	15q24.1	2013-05-10	2010-02-12	2009-09-28	ENSG00000159289	ENSG00000159289			13567	protein-coding gene	gene with protein product		610288	"golgi autoantigen, golgin subfamily a, member 6", "golgi autoantigen, golgin subfamily a, 6", "golgi autoantigen, golgin subfamily a, 6A"	GOLGA6		11161787	Standard	NM_001038640		Approved	GLP	uc002axa.1	Q9NYA3	OTTHUMG00000173035	ENST00000290438.3:c.857delC	chr15.hg19:g.74367333delG	ENSP00000290438:p.Pro286fs	85.0	0.0	0		40.0	22.0	0.55	NM_001038640	A8K959|Q9NYA7	Frame_Shift_Del	DEL	ENST00000290438.3	hg19	CCDS32290.1																																																																																			.	.	.	none		0.542	GOLGA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421835.1	XM_292357		-	74367333	G	-	74367333	7	5	264	1	0	1	0	1	0	0	0	0	6564	1348	47	0	1256	0	GOLGA6A	15	74367333	Frame_Shift_Del	DEL	G	TCGA-UZ-A9PS-01A-11D-A42J-10	5	74367333	28164059	114	16619	173	2									
POLG	5428	hgsc.bcm.edu	37	chr15	89861981	89861981	+	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	ttcacacggctggtcataaaCtgggaagggaaggtgggcag	11	7	16	7	1	2	0	2	0	0	0	2	2	2	2	0	6	1	2	0	6	4	2			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr15:89861981C>G	ENST00000268124.5	-	21	3607		c.e21-1		POLG_ENST00000442287.2_Splice_Site	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma						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)			TGGTCATAAACTGGGAAGGGA	0.507								DNA polymerases (catalytic subunits)																													.	Colon(73;648 1203 11348 18386 27782)	Atlas-SNP	.											.	POLG	75	.	0			c.3274-1G>C						PASS	.						71	68	69					15																	89861981		2200	4299	6499	SO:0001630	splice_region_variant	5428	exon22			CATAAACTGGGAA	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.3274-1G>C	chr15.hg19:g.89861981C>G		30.0	0.0	.		44.0	13.0	.	NM_002693	Q8NFM2|Q92515	Splice_Site	SNP	ENST00000268124.5	hg19	CCDS10350.1	.	.	.	.	.	.	.	.	.	.	C	17.15	3.315677	0.60524	.	.	ENSG00000140521	ENST00000268124;ENST00000442287	.	.	.	5.25	5.25	0.73442	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.037	0.92983	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	POLG	87662985	1.000000	0.71417	0.999000	0.59377	0.663000	0.39108	7.320000	0.79064	2.738000	0.93877	0.655000	0.94253	.	.	.	.	none		0.507	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000312854.2	NM_002693	Intron	G	89861981	C	G	89861981	5	3	264	1	0	0	0	0	0	0	1	0	12207	579	20	4	458	4	POLG	15	89861981	Splice_Site	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	15494648	89861981	12669411	115	16620											
RGMA	56963	hgsc.bcm.edu	37	chr15	93595536	93595536	+	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	ccttggagcagttgtgctggCtcatgaggtcctctatgcca	6	12	12	11	0	2	1	1	1	1	0	3	2	3	2	3	3	3	4	3	3	1	3			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr15:93595536C>G	ENST00000329082.7	-	3	603	c.332G>C	c.(331-333)aGc>aCc	p.S111T	RGMA_ENST00000543599.1_Missense_Mutation_p.S95T|RGMA_ENST00000556087.1_Missense_Mutation_p.S95T|RGMA_ENST00000538818.1_Missense_Mutation_p.S2T|RGMA_ENST00000556658.1_Missense_Mutation_p.S2T|RGMA_ENST00000555584.1_5'UTR|RGMA_ENST00000425933.2_Missense_Mutation_p.S95T|RGMA_ENST00000557301.1_Missense_Mutation_p.S119T|RGMA_ENST00000557420.1_Intron|RGMA_ENST00000542321.2_Missense_Mutation_p.S95T	NM_020211.2	NP_064596	Q96B86	RGMA_HUMAN	repulsive guidance molecule family member a	111					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)			GTTGTGCTGGCTCATGAGGTC	0.706																																					p.S119T		Atlas-SNP	.											.	RGMA	49	.	0			c.G356C						PASS	.						24	29	27					15																	93595536		2185	4291	6476	SO:0001583	missense	56963	exon3			TGCTGGCTCATGA	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.332G>C	chr15.hg19:g.93595536C>G	ENSP00000330005:p.Ser111Thr	41.0	0.0	.		37.0	16.0	.	NM_001166283	B2RTW1|B7Z5S8|F5GXQ7|F5GZU6|G3V518|Q0JV97|Q8NC80|Q9H0E6|Q9NPM3	Missense_Mutation	SNP	ENST00000329082.7	hg19	CCDS45357.1	.	.	.	.	.	.	.	.	.	.	C	8.229	0.804169	0.16467	.	.	ENSG00000182175	ENST00000543599;ENST00000425933;ENST00000329082;ENST00000542321;ENST00000538818;ENST00000557301	D;D;D;D;D;D	0.97455	-4.39;-4.39;-4.39;-4.39;-4.39;-4.39	5.15	4.23	0.50019	Repulsive guidance molecule, N-terminal (1);	0.091755	0.85682	D	0.000000	D	0.94318	0.8174	L	0.49126	1.545	0.41814	D	0.989988	P;P	0.36438	0.498;0.553	B;B	0.40782	0.23;0.34	D	0.90471	0.4453	10	0.22109	T	0.4	-1.9022	5.7538	0.18162	0.1399:0.6452:0.1359:0.079	.	119;111	G3V518;Q96B86	.;RGMA_HUMAN	T	95;95;111;95;2;119	ENSP00000442498:S95T;ENSP00000404442:S95T;ENSP00000330005:S111T;ENSP00000440025:S95T;ENSP00000442546:S2T;ENSP00000452126:S119T	ENSP00000330005:S111T	S	-	2	0	RGMA	91396540	0.997000	0.39634	1.000000	0.80357	0.997000	0.91878	0.555000	0.23422	1.175000	0.42826	0.462000	0.41574	AGC	.	.	.	none		0.706	RGMA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415091.1	NM_020211		G	93595536	C	G	93595536	3	3	264	1	0	0	0	0	1	0	0	0	13293	797	28	4	1028	4	RGMA	15	93595536	Missense_Mutation	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	3733555	93595536	8935856	116	16621											
SMPD3	55512	hgsc.bcm.edu	37	chr16	68405641	68405641	+	Silent	SNP	T	T	C																															ccgatctccttggcccgcgcTtgggtgttaaaaaggttgtt																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr16:68405641T>C	ENST00000219334.5	-	3	1047	c.444A>G	c.(442-444)caA>caG	p.Q148Q	SMPD3_ENST00000566009.1_5'Flank|SMPD3_ENST00000563226.1_Silent_p.Q148Q|SMPD3_ENST00000568373.1_Silent_p.Q148Q	NM_018667.3	NP_061137.1	Q9NY59	NSMA2_HUMAN	sphingomyelin phosphodiesterase 3, neutral membrane (neutral sphingomyelinase II)	148					cell cycle (GO:0007049)|glycosphingolipid metabolic process (GO:0006687)|hematopoietic progenitor cell differentiation (GO:0002244)|peptide hormone secretion (GO:0030072)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	Golgi cis cisterna (GO:0000137)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0184)|Epithelial(162;0.0785)	Phosphatidylserine(DB00144)	TGGCCCGCGCTTGGGTGTTAA	0.607																																					p.Q148Q		Atlas-SNP	.											.	SMPD3	52	.	0			c.A444G						PASS	.						23	27	26					16																	68405641		2198	4300	6498	SO:0001819	synonymous_variant	55512	exon3			CCGCGCTTGGGTG	AJ250460	CCDS10867.1	16q22.1	2008-02-05			ENSG00000103056	ENSG00000103056			14240	protein-coding gene	gene with protein product		605777				10823942	Standard	NM_018667		Approved	NSMASE2	uc002ewa.3	Q9NY59	OTTHUMG00000137559	ENST00000219334.5:c.444A>G	chr16.hg19:g.68405641T>C		73.0	0.0	.		86.0	42.0	.	NM_018667	B7ZL82|Q2M1S8	Silent	SNP	ENST00000219334.5	hg19	CCDS10867.1																																																																																			.	.	.	none		0.607	SMPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268895.3	NM_018667		C	68405641	T	C	68405641	2	2	264	1	0	0	0	0	0	0	0	1	14819	1606	56	3		3	SMPD3	16	68405641	Silent	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10		68405641	21949112	117	16622	174	2									
SMPD3	55512	hgsc.bcm.edu	37	chr16	68405649	68405649	+	Missense_Mutation	SNP	T	T	G																															cttggcccgcgcttgggtgtTaaaaaggttgttgaccctgg																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr16:68405649T>G	ENST00000219334.5	-	3	1039	c.436A>C	c.(436-438)Aac>Cac	p.N146H	SMPD3_ENST00000566009.1_5'Flank|SMPD3_ENST00000563226.1_Missense_Mutation_p.N146H|SMPD3_ENST00000568373.1_Missense_Mutation_p.N146H	NM_018667.3	NP_061137.1	Q9NY59	NSMA2_HUMAN	sphingomyelin phosphodiesterase 3, neutral membrane (neutral sphingomyelinase II)	146					cell cycle (GO:0007049)|glycosphingolipid metabolic process (GO:0006687)|hematopoietic progenitor cell differentiation (GO:0002244)|peptide hormone secretion (GO:0030072)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	Golgi cis cisterna (GO:0000137)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0184)|Epithelial(162;0.0785)	Phosphatidylserine(DB00144)	GCTTGGGTGTTAAAAAGGTTG	0.587																																					p.N146H		Atlas-SNP	.											.	SMPD3	52	.	0			c.A436C						PASS	.						21	25	24					16																	68405649		2198	4300	6498	SO:0001583	missense	55512	exon3			GGGTGTTAAAAAG	AJ250460	CCDS10867.1	16q22.1	2008-02-05			ENSG00000103056	ENSG00000103056			14240	protein-coding gene	gene with protein product		605777				10823942	Standard	NM_018667		Approved	NSMASE2	uc002ewa.3	Q9NY59	OTTHUMG00000137559	ENST00000219334.5:c.436A>C	chr16.hg19:g.68405649T>G	ENSP00000219334:p.Asn146His	69.0	0.0	.		85.0	45.0	.	NM_018667	B7ZL82|Q2M1S8	Missense_Mutation	SNP	ENST00000219334.5	hg19	CCDS10867.1	.	.	.	.	.	.	.	.	.	.	T	7.498	0.651973	0.14516	.	.	ENSG00000103056	ENST00000219334	T	0.50001	0.76	5.24	4.11	0.48088	.	0.170687	0.64402	N	0.000005	T	0.31327	0.0793	N	0.20881	0.62	0.40830	D	0.983588	B;B;B	0.12630	0.006;0.006;0.006	B;B;B	0.08055	0.003;0.003;0.003	T	0.07947	-1.0746	10	0.23891	T	0.37	-22.7541	10.5661	0.45173	0.0:0.0:0.1623:0.8377	.	146;146;146	B7ZL82;B7ZL84;Q9NY59	.;.;NSMA2_HUMAN	H	146	ENSP00000219334:N146H	ENSP00000219334:N146H	N	-	1	0	SMPD3	66963150	1.000000	0.71417	0.879000	0.34478	0.943000	0.58893	1.979000	0.40608	0.898000	0.36418	0.533000	0.62120	AAC	.	.	.	none		0.587	SMPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268895.3	NM_018667		G	68405649	T	G	68405649	3	3	264	1	0	0	0	0	1	0	0	0	14819	1754	61	5	1559	5	SMPD3	16	68405649	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	8	68405649	21949104	118	16623	174	2									
PKD1L2	114780	hgsc.bcm.edu	37	chr16	81219237	81219237	+	RNA	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	aggcaggatgctggaaccacCagctccctctggtctgtgcg	7	8	13	13	1	2	0	0	0	2	0	3	2	3	2	3	4	4	3	3	4	1	0			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr16:81219237C>A	ENST00000525539.1	-	0	1856				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						CTGGAACCACCAGCTCCCTCT	0.602																																					p.L619L		Atlas-SNP	.											.	PKD1L2	361	.	0			c.G1857T						PASS	.						28	37	34					16																	81219237		2054	4211	6265			114780	exon11			AACCACCAGCTCC	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		chr16.hg19:g.81219237C>A		76.0	0.0	.		112.0	64.0	.	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Silent	SNP	ENST00000525539.1	hg19		.	.	.	.	.	.	.	.	.	.	C	2.794	-0.250742	0.05867	.	.	ENSG00000166473	ENST00000526632	.	.	.	4.83	4.83	0.62350	.	.	.	.	.	T	0.63977	0.2557	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62817	-0.6774	4	.	.	.	-11.14	12.4984	0.55942	0.0:0.832:0.168:0.0	.	.	.	.	C	147	.	.	G	-	1	0	PKD1L2	79776738	0.992000	0.36948	0.998000	0.56505	0.243000	0.25628	1.525000	0.35953	2.241000	0.73720	0.551000	0.68910	GGT	.	.	.	none		0.602	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2			A	81219237	C	A	81219237	1	1	264	0	1	0	0	0	0	0	0	0	11972	581	21	4		4	PKD1L2	16	81219237	RNA	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	12813588	81219237	9135516	119	16624											
SPNS3	201305	hgsc.bcm.edu	37	chr17	4343008	4343008	+	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	agtgacaaccatgctggtttGcttcagactggtaaggagga	11	10	13	7	0	1	2	1	1	0	1	1	4	1	4	1	4	3	4	1	4	2	3			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr17:4343008G>C	ENST00000355530.2	+	2	535	c.255G>C	c.(253-255)ttG>ttC	p.L85F	SPNS3_ENST00000576069.1_3'UTR|SPNS3_ENST00000333476.2_Missense_Mutation_p.C4S	NM_182538.4	NP_872344.3	Q6ZMD2	SPNS3_HUMAN	spinster homolog 3 (Drosophila)	85					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						ATGCTGGTTTGCTTCAGACTG	0.582																																					p.L85F		Atlas-SNP	.											.	SPNS3	52	.	0			c.G255C						PASS	.						58	49	52					17																	4343008		2203	4300	6503	SO:0001583	missense	201305	exon2			TGGTTTGCTTCAG		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.255G>C	chr17.hg19:g.4343008G>C	ENSP00000347721:p.Leu85Phe	45.0	0.0	.		42.0	14.0	.	NM_182538	Q8IZ31	Missense_Mutation	SNP	ENST00000355530.2	hg19	CCDS11045.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.05|17.05	3.289082|3.289082	0.59976|0.59976	.|.	.|.	ENSG00000182557|ENSG00000182557	ENST00000333476|ENST00000355530	T|T	0.25579|0.61980	1.79|0.06	4.31|4.31	3.33|3.33	0.38152|0.38152	.|Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	.|0.161988	.|0.40554	.|N	.|0.001061	T|T	0.74680|0.74680	0.3748|0.3748	M|M	0.75777|0.75777	2.31|2.31	0.24745|0.24745	N|N	0.993014|0.993014	B|D	0.18013|0.67145	0.025|0.996	B|D	0.16289|0.74023	0.015|0.982	T|T	0.65010|0.65010	-0.6272|-0.6272	9|10	0.07813|0.87932	T|D	0.8|0	-8.5223|-8.5223	8.7516|8.7516	0.34620|0.34620	0.1093:0.0:0.8907:0.0|0.1093:0.0:0.8907:0.0	.|.	4|85	Q6ZMD2-2|Q6ZMD2	.|SPNS3_HUMAN	S|F	4|85	ENSP00000333207:C4S|ENSP00000347721:L85F	ENSP00000333207:C4S|ENSP00000347721:L85F	C|L	+|+	2|3	0|2	SPNS3|SPNS3	4289757|4289757	0.836000|0.836000	0.29430|0.29430	1.000000|1.000000	0.80357|0.80357	0.959000|0.959000	0.62525|0.62525	-0.176000|-0.176000	0.09811|0.09811	1.115000|1.115000	0.41800|0.41800	0.650000|0.650000	0.86243|0.86243	TGC|TTG	.	.	.	none		0.582	SPNS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438793.1	NM_182538		C	4343008	G	C	4343008	3	2	264	1	0	0	0	0	1	0	0	0	15088	1310	46	4	261	4	SPNS3	17	4343008	Missense_Mutation	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10		4343008	76852202	120	16625											
MED9	55090	hgsc.bcm.edu	37	chr17	17380470	17380470	+	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	ctcctcagccgccgccggtcCctgcgcctcaaccgcagcag	5	5	10	21	5	2	0	2	0	0	0	4	0	4	0	7	1	4	2	7	1	1	0			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr17:17380470C>T	ENST00000268711.3	+	1	171	c.115C>T	c.(115-117)Cct>Tct	p.P39S	MED9_ENST00000585041.1_3'UTR|MED9_ENST00000580462.1_Missense_Mutation_p.P39S	NM_018019.2	NP_060489.1	Q9NWA0	MED9_HUMAN	mediator complex subunit 9	39	Pro-rich.					mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			cervix(1)|endometrium(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						gccgccggtccctgcgcctca	0.672																																					p.P39S		Atlas-SNP	.											.	MED9	11	.	0			c.C115T						PASS	.						15	16	16					17																	17380470		2199	4293	6492	SO:0001583	missense	55090	exon1			CCGGTCCCTGCGC	BC000647	CCDS11184.1	17p11.2	2007-07-30	2007-07-30		ENSG00000141026	ENSG00000141026			25487	protein-coding gene	gene with protein product		609878	"mediator of RNA polymerase II transcription, subunit 9 homolog (S. cerevisiae)"			11997338	Standard	NM_018019		Approved	FLJ10193, MED25	uc002grh.1	Q9NWA0	OTTHUMG00000059293	ENST00000268711.3:c.115C>T	chr17.hg19:g.17380470C>T	ENSP00000268711:p.Pro39Ser	69.0	0.0	.		103.0	48.0	.	NM_018019		Missense_Mutation	SNP	ENST00000268711.3	hg19	CCDS11184.1	.	.	.	.	.	.	.	.	.	.	C	2.166	-0.390952	0.04932	.	.	ENSG00000141026	ENST00000268711	.	.	.	5.5	2.19	0.27852	.	0.724378	0.12016	N	0.507437	T	0.22282	0.0537	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.17868	-1.0355	9	0.44086	T	0.13	-8.2254	8.2274	0.31577	0.0:0.3189:0.5081:0.1731	.	39	Q9NWA0	MED9_HUMAN	S	39	.	ENSP00000268711:P39S	P	+	1	0	MED9	17321195	0.067000	0.21026	0.021000	0.16686	0.292000	0.27327	1.046000	0.30354	0.668000	0.31126	-0.226000	0.12346	CCT	.	.	.	none		0.672	MED9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131669.2	NM_018019		T	17380470	C	T	17380470	3	4	264	1	0	0	0	0	1	0	0	0	9461	623	22	2	117	2	MED9	17	17380470	Missense_Mutation	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	13037462	17380470	63814740	121	16626											
MYO18A	399687	hgsc.bcm.edu	37	chr17	27447772	27447772	+	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	gtgtacagagcctgccacttCtccactgcagaatacaggcc	10	8	9	14	0	1	2	0	0	1	2	2	2	1	2	4	1	5	2	4	1	3	3			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr17:27447772C>T	ENST00000527372.1	-	7	1770	c.1590G>A	c.(1588-1590)gaG>gaA	p.E530E	MYO18A_ENST00000354329.4_Silent_p.E530E|MYO18A_ENST00000531253.1_Silent_p.E530E|MYO18A_ENST00000533112.1_Silent_p.E530E	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	530	Myosin motor.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			CCTGCCACTTCTCCACTGCAG	0.572																																					p.E530E	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.G1590A						PASS	.						57	65	62					17																	27447772		2043	4187	6230	SO:0001819	synonymous_variant	399687	exon7			CCACTTCTCCACT	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.1590G>A	chr17.hg19:g.27447772C>T		96.0	0.0	.		102.0	27.0	.	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Silent	SNP	ENST00000527372.1	hg19	CCDS45642.1																																																																																			.	.	.	none		0.572	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		T	27447772	C	T	27447772	2	4	264	1	0	0	0	0	0	0	0	1	10072	912	32	2		2	MYO18A	17	27447772	Silent	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	10067302	27447772	53747438	122	16627											
GPR179	440435	hgsc.bcm.edu	37	chr17	36482812	36482812	+	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	ctctgccatcctgcttcccaTgctgcctgcttccttggggc	2	13	9	17	0	1	0	0	0	1	0	4	0	4	0	5	2	5	3	5	2	0	3			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr17:36482812T>A	ENST00000342292.4	-	11	6660	c.6640A>T	c.(6640-6642)Atg>Ttg	p.M2214L	GPR179_ENST00000584976.1_Intron	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	2214					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)				CTGCTTCCCATGCTGCCTGCT	0.567																																					p.M2214L		Atlas-SNP	.											.	GPR179	170	.	0			c.A6640T						PASS	.						96	95	95					17																	36482812		2057	4211	6268	SO:0001583	missense	440435	exon11			TTCCCATGCTGCC		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.6640A>T	chr17.hg19:g.36482812T>A	ENSP00000345060:p.Met2214Leu	63.0	0.0	.		83.0	48.0	.	NM_001004334		Missense_Mutation	SNP	ENST00000342292.4	hg19	CCDS42308.1	.	.	.	.	.	.	.	.	.	.	T	12.05	1.822812	0.32237	.	.	ENSG00000188888	ENST00000342292	T	0.47869	0.83	4.85	-7.67	0.01272	.	2.213480	0.02200	N	0.062151	T	0.35278	0.0926	L	0.40543	1.245	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.12760	-1.0535	10	0.27082	T	0.32	2.8526	9.3478	0.38120	0.0:0.4802:0.2389:0.2809	.	2214	Q6PRD1	GP179_HUMAN	L	2214	ENSP00000345060:M2214L	ENSP00000345060:M2214L	M	-	1	0	GPR179	33736338	0.000000	0.05858	0.000000	0.03702	0.273000	0.26683	-2.919000	0.00694	-1.922000	0.01067	-0.621000	0.04028	ATG	.	.	.	none		0.567	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			A	36482812	T	A	36482812	3	1	264	1	0	0	0	0	1	0	0	0	6681	1464	51	5	467	5	GPR179	17	36482812	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	9035040	36482812	44712398	123	16628											
MED13	9969	hgsc.bcm.edu	37	chr17	60033103	60033103	+	Frame_Shift_Del	DEL	G	G	-																															agcaagcactgagaatgctaGgggagtctgcagcagatata																								rs74792573		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr17:60033103delG	ENST00000397786.2	-	25	5796	c.5720delC	c.(5719-5721)cctfs	p.P1907fs		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1907					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						GAGAATGCTAGGGGAGTCTGC	0.418																																					p.P1907fs		Atlas-Indel,Pindel	.											.	MED13	181	.	0			c.5721delT						PASS	.						96	97	97					17																	60033103		1894	4134	6028	SO:0001589	frameshift_variant	9969	exon25			.	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.5720delC	chr17.hg19:g.60033103delG	ENSP00000380888:p.Pro1907fs	186.0	0.0	0		291.0	24.0	0.0824742	NM_005121	B2RU05|O60334	Frame_Shift_Del	DEL	ENST00000397786.2	hg19	CCDS42366.1																																																																																			.	.	.	none		0.418	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		-	60033103	G	-	60033103	7	5	264	1	0	1	0	1	0	0	0	0	9437	1000	35	0	828	0	MED13	17	60033103	Frame_Shift_Del	DEL	G	TCGA-UZ-A9PS-01A-11D-A42J-10	23550291	60033103	21162107	124	16629											
TEX2	55852	hgsc.bcm.edu	37	chr17	62271048	62271048	+	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	gagatagagtatctgatctcGctggctagatcttgttccct	8	14	10	9	1	3	4	0	1	3	3	5	5	4	4	1	1	0	4	1	1	3	5			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr17:62271048G>T	ENST00000583097.1	-	4	2219	c.2047C>A	c.(2047-2049)Cga>Aga	p.R683R	TEX2_ENST00000584379.1_Silent_p.R683R|TEX2_ENST00000258991.3_Silent_p.R683R			Q8IWB9	TEX2_HUMAN	testis expressed 2	683					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)		ATCTGATCTCGCTGGCTAGAT	0.483																																					p.R683R		Atlas-SNP	.											.	TEX2	89	.	0			c.C2047A						PASS	.						127	121	123					17																	62271048		2203	4300	6503	SO:0001819	synonymous_variant	55852	exon4			GATCTCGCTGGCT	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.2047C>A	chr17.hg19:g.62271048G>T		107.0	0.0	.		180.0	116.0	.	NM_018469	Q6AHZ5|Q8N3L0|Q9C0C5	Silent	SNP	ENST00000583097.1	hg19																																																																																				.	.	.	none		0.483	TEX2-003	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000443745.1	NM_018469		T	62271048	G	T	62271048	2	4	264	1	0	0	0	0	0	0	0	1	15793	1095	38	4		4	TEX2	17	62271048	Silent	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10	2237945	62271048	18924162	125	16630											
PRKCA	5578	hgsc.bcm.edu	37	chr17	64728827	64728827	+	Frame_Shift_Del	DEL	G	G	-																															aagccaaacttggccctgctGgcaacaaagtcatcagtccc																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr17:64728827delG	ENST00000413366.3	+	9	966	c.940delG	c.(940-942)ggcfs	p.G314fs		NM_002737.2	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha	314					activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|chondrocyte differentiation (GO:0002062)|desmosome assembly (GO:0002159)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|histone H3-T6 phosphorylation (GO:0035408)|inactivation of MAPK activity (GO:0000188)|induction of positive chemotaxis (GO:0050930)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA metabolic process (GO:0016071)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|peptidyl-serine autophosphorylation (GO:0036289)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of dense core granule biogenesis (GO:2000707)|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 inflammatory response (GO:0050729)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein phosphorylation (GO:0001934)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of muscle contraction (GO:0006937)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of the force of heart contraction (GO:0002026)|response to interleukin-1 (GO:0070555)|rhodopsin mediated signaling pathway (GO:0016056)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|enzyme binding (GO:0019899)|histone kinase activity (H3-T6 specific) (GO:0035403)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Ingenol Mebutate(DB05013)|Phosphatidylserine(DB00144)|Tamoxifen(DB00675)|Vitamin E(DB00163)	TGGCCCTGCTGGCAACAAAGT	0.458																																					p.A313fs		Atlas-Indel,Pindel	.											.	PRKCA	82	.	0			c.939delT						PASS	.						189	194	192					17																	64728827		2203	4300	6503	SO:0001589	frameshift_variant	5578	exon9			.		CCDS11664.1	17q22-q24	2009-07-10				ENSG00000154229	2.7.11.1		9393	protein-coding gene	gene with protein product		176960		PKCA			Standard	NM_002737		Approved		uc002jfp.1	P17252		ENST00000413366.3:c.940delG	chr17.hg19:g.64728827delG	ENSP00000408695:p.Gly314fs	145.0	0.0	0		215.0	65.0	0.302326	NM_002737	B5BU22|Q15137|Q32M72|Q96RE4	Frame_Shift_Del	DEL	ENST00000413366.3	hg19	CCDS11664.1																																																																																			.	.	.	none		0.458	PRKCA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446976.1			-	64728827	G	-	64728827	7	5	264	1	0	1	0	1	0	0	0	0	12517	1348	47	0	974	0	PRKCA	17	64728827	Frame_Shift_Del	DEL	G	TCGA-UZ-A9PS-01A-11D-A42J-10	2457779	64728827	16466383	126	16631											
ABCA8	10351	hgsc.bcm.edu	37	chr17	66918423	66918423	+	Missense_Mutation	SNP	T	T	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	tcaggctttcctttatattcTtttgtaacatttctgattct	7	22	4	8	0	4	1	1	1	3	0	5	1	5	1	1	1	1	2	1	1	3	10			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr17:66918423T>G	ENST00000269080.2	-	11	1598	c.1461A>C	c.(1459-1461)aaA>aaC	p.K487N	ABCA8_ENST00000430352.2_Missense_Mutation_p.K487N|ABCA8_ENST00000586539.1_Missense_Mutation_p.K487N	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	487	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					CTTTATATTCTTTTGTAACAT	0.244																																					p.K487N		Atlas-SNP	.											.	ABCA8	213	.	0			c.A1461C						PASS	.						37	40	39					17																	66918423		2187	4289	6476	SO:0001583	missense	10351	exon11			ATATTCTTTTGTA	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.1461A>C	chr17.hg19:g.66918423T>G	ENSP00000269080:p.Lys487Asn	164.0	0.0	.		253.0	75.0	.	NM_007168	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	hg19	CCDS11680.1	.	.	.	.	.	.	.	.	.	.	T	17.21	3.332251	0.60853	.	.	ENSG00000141338	ENST00000269080;ENST00000430352;ENST00000541225;ENST00000542396	T;T	0.46819	0.86;0.86	4.74	1.29	0.21616	ABC transporter-like (1);	0.000000	0.56097	D	0.000033	T	0.68705	0.3030	M	0.92219	3.285	0.51012	D	0.999901	D;D;D;D;D	0.89917	0.999;0.991;1.0;0.998;0.996	D;D;D;D;D	0.79784	0.984;0.938;0.993;0.984;0.963	T	0.67007	-0.5779	10	0.87932	D	0	.	5.0198	0.14356	0.1396:0.164:0.0:0.6964	.	426;487;487;487;487	F5H6Z4;A1L3U3;B4DJ11;C9JQE6;O94911	.;.;.;.;ABCA8_HUMAN	N	487;487;426;118	ENSP00000269080:K487N;ENSP00000402814:K487N	ENSP00000269080:K487N	K	-	3	2	ABCA8	64430018	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.679000	0.37597	0.382000	0.24878	0.477000	0.44152	AAA	.	.	.	none		0.244	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		G	66918423	T	G	66918423	3	3	264	1	0	0	0	0	1	0	0	0	38	1606	56	5	3396	5	ABCA8	17	66918423	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	2189596	66918423	14276787	127	16632											
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2728547	2728547	+	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	ttcaggtggaagttttagatGaatcagacaacataacagca	16	10	9	6	0	2	3	2	1	0	2	2	4	2	4	0	2	3	2	0	2	5	4			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr18:2728547G>A	ENST00000320876.6	+	23	3204	c.2866G>A	c.(2866-2868)Gaa>Aaa	p.E956K	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000609587.1_3'UTR|SMCHD1_ENST00000261598.8_Missense_Mutation_p.E956K	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	956					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						AGTTTTAGATGAATCAGACAA	0.363																																					p.E956K		Atlas-SNP	.											.	SMCHD1	88	.	0			c.G2866A						PASS	.						106	100	101					18																	2728547		1849	4098	5947	SO:0001583	missense	23347	exon23			TTAGATGAATCAG	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.2866G>A	chr18.hg19:g.2728547G>A	ENSP00000326603:p.Glu956Lys	115.0	0.0	.		103.0	47.0	.	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	hg19	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	G	15.65	2.895482	0.52121	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	T;T	0.23754	1.89;1.89	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.21103	0.0508	L	0.39633	1.23	0.38058	D	0.935997	B	0.28512	0.214	B	0.20767	0.031	T	0.06643	-1.0815	10	0.23891	T	0.37	-26.3497	14.3232	0.66502	0.0705:0.0:0.9295:0.0	.	956	A6NHR9	SMHD1_HUMAN	K	956	ENSP00000326603:E956K;ENSP00000261598:E956K	ENSP00000261598:E956K	E	+	1	0	SMCHD1	2718547	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.430000	0.66501	2.764000	0.94973	0.650000	0.86243	GAA	.	.	.	none		0.363	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			A	2728547	G	A	2728547	3	1	264	1	0	0	0	0	1	0	0	0	14801	1291	45	2	2956	2	SMCHD1	18	2728547	Missense_Mutation	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10		2728547	75348701	128	16633											
CABLES1	91768	hgsc.bcm.edu	37	chr18	20815956	20815956	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctcccagttccgtaaccTgagccaccgcagcctctcca	7	10	6	18	2	2	1	0	1	2	0	5	1	3	1	7	0	3	3	7	0	1	3			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr18:20815956T>C	ENST00000256925.7	+	6	1283	c.1283T>C	c.(1282-1284)cTg>cCg	p.L428P	CABLES1_ENST00000420687.2_Missense_Mutation_p.L163P|TMEM241_ENST00000450466.2_Intron|CABLES1_ENST00000400473.2_Missense_Mutation_p.L101P|CABLES1_ENST00000585061.1_Intron	NM_001100619.2	NP_001094089.1	Q8TDN4	CABL1_HUMAN	Cdk5 and Abl enzyme substrate 1	428	Interacts with CDK3. {ECO:0000250}.				blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|nervous system development (GO:0007399)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)	cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			breast(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|stomach(1)	11	all_cancers(21;0.000102)|all_epithelial(16;2.48e-06)|Lung NSC(20;0.00696)|all_lung(20;0.0197)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TTCCGTAACCTGAGCCACCGC	0.572																																					p.L428P		Atlas-SNP	.											.	CABLES1	32	.	0			c.T1283C						PASS	.						79	83	82					18																	20815956		1895	4107	6002	SO:0001583	missense	91768	exon6			GTAACCTGAGCCA	BC037218	CCDS42417.1, CCDS42418.1, CCDS58615.1	18q11.2	2005-08-16				ENSG00000134508			25097	protein-coding gene	gene with protein product		609194				12477932	Standard	NM_138375		Approved	HsT2563, FLJ35924	uc002kuc.2	Q8TDN4		ENST00000256925.7:c.1283T>C	chr18.hg19:g.20815956T>C	ENSP00000256925:p.Leu428Pro	63.0	0.0	.		76.0	23.0	.	NM_001100619	B4DK60|Q8N3Y8|Q8NA22|Q9BTG1	Missense_Mutation	SNP	ENST00000256925.7	hg19	CCDS42417.1	.	.	.	.	.	.	.	.	.	.	T	15.05	2.717455	0.48622	.	.	ENSG00000134508	ENST00000400473;ENST00000256925;ENST00000420687	T;T;T	0.46063	0.93;0.88;0.89	5.47	4.34	0.51931	.	0.175925	0.48767	D	0.000177	T	0.18383	0.0441	N	0.14661	0.345	0.80722	D	1	B;P	0.46395	0.343;0.877	B;B	0.36030	0.134;0.216	T	0.02721	-1.1119	10	0.34782	T	0.22	-26.8928	3.1763	0.06570	0.0:0.357:0.0:0.643	.	163;428	Q8TDN4-2;Q8TDN4	.;CABL1_HUMAN	P	101;428;163	ENSP00000383321:L101P;ENSP00000256925:L428P;ENSP00000413851:L163P	ENSP00000256925:L428P	L	+	2	0	CABLES1	19069954	1.000000	0.71417	0.996000	0.52242	0.986000	0.74619	4.678000	0.61641	2.080000	0.62538	0.533000	0.62120	CTG	.	.	.	none		0.572	CABLES1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445198.2	NM_138375		C	20815956	T	C	20815956	3	2	264	1	0	0	0	0	1	0	0	0	2531	1580	55	3	1359	3	CABLES1	18	20815956	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	18087409	20815956	57261292	129	16634											
TTR	7276	hgsc.bcm.edu	37	chr18	29178600	29178600	+	Missense_Mutation	SNP	T	T	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	ccctgctgagcccctactccTattccaccacggctgtcgtc	5	10	7	19	2	0	1	0	1	0	0	4	1	2	1	6	1	3	2	6	1	2	3			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr18:29178600T>G	ENST00000237014.3	+	4	583	c.406T>G	c.(406-408)Tat>Gat	p.Y136D		NM_000371.3	NP_000362.1	P02766	TTHY_HUMAN	transthyretin	136	Thyroid hormone binding.		Y -> S (in AMYL-TTR; amyloid polyneuropathy). {ECO:0000269|PubMed:10627135}.|Y -> V (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:3675594}.		extracellular matrix organization (GO:0030198)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	hormone binding (GO:0042562)|identical protein binding (GO:0042802)			cervix(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)	13			OV - Ovarian serous cystadenocarcinoma(10;0.00523)		Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diflunisal(DB00861)|Dimethyl sulfoxide(DB01093)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	CCCCTACTCCTATTCCACCAC	0.547																																					p.Y136D		Atlas-SNP	.											TTR,NS,carcinoma,0,1	TTR	21	.	0			c.T406G						PASS	.						80	67	71					18																	29178600		2203	4300	6503	SO:0001583	missense	7276	exon4			TACTCCTATTCCA	M10605	CCDS11899.1	18q12.1	2014-09-17	2008-07-31		ENSG00000118271	ENSG00000118271			12405	protein-coding gene	gene with protein product		176300	"prealbumin, amyloidosis type I", "carpal tunnel syndrome 1"	PALB, CTS1		8309582	Standard	NM_000371		Approved	HsT2651, CTS	uc002kwx.4	P02766	OTTHUMG00000131984	ENST00000237014.3:c.406T>G	chr18.hg19:g.29178600T>G	ENSP00000237014:p.Tyr136Asp	71.0	2.0	.		60.0	20.0	.	NM_000371	Q549C7|Q6IB96|Q9UBZ6|Q9UCM9	Missense_Mutation	SNP	ENST00000237014.3	hg19	CCDS11899.1	.	.	.	.	.	.	.	.	.	.	T	17.49	3.403205	0.62288	.	.	ENSG00000118271	ENST00000237014;ENST00000432547;ENST00000541025	D	0.98120	-4.73	6.08	6.08	0.98989	Transthyretin, conserved site (1);Transthyretin/hydroxyisourate hydrolase, superfamily (4);	0.246709	0.42294	D	0.000722	D	0.99064	0.9679	H	0.96301	3.8	0.53688	D	0.99997	D	0.89917	1.0	D	0.97110	1.0	D	0.99497	1.0952	10	0.87932	D	0	-18.6558	11.4063	0.49900	0.1349:0.0:0.0:0.8651	.	136	P02766	TTHY_HUMAN	D	136;173;128	ENSP00000237014:Y136D	ENSP00000237014:Y136D	Y	+	1	0	TTR	27432598	0.997000	0.39634	0.892000	0.35008	0.476000	0.33039	4.452000	0.60054	2.333000	0.79357	0.482000	0.46254	TAT	.	.	.	none		0.547	TTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254948.1	NM_000371		G	29178600	T	G	29178600	3	3	264	1	0	0	0	0	1	0	0	0	16750	1522	53	5	420	5	TTR	18	29178600	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	8362644	29178600	48898648	130	16635											
WDR18	57418	hgsc.bcm.edu	37	chr19	984377	984377	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggcgcccatggaggtggcCgtgtgtacggactcggcggc	4	6	19	12	6	0	0	0	0	0	0	1	2	0	2	2	7	1	1	2	7	1	1			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr19:984377C>T	ENST00000251289.5	+	1	47	c.24C>T	c.(22-24)gcC>gcT	p.A8A	WDR18_ENST00000591997.1_Intron|WDR18_ENST00000587001.2_Silent_p.A8A	NM_024100.3	NP_077005.2	Q9BV38	WDR18_HUMAN	WD repeat domain 18	8					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|lung(2)|skin(2)	7		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGGAGGTGGCCGTGTGTACGG	0.716																																					p.A8A		Atlas-SNP	.											.	WDR18	20	.	0			c.C24T						PASS	.						20	22	21					19																	984377		2200	4296	6496	SO:0001819	synonymous_variant	57418	exon1			GGTGGCCGTGTGT		CCDS12051.1	19p13.3	2013-01-09				ENSG00000065268		"WD repeat domain containing"	17956	protein-coding gene	gene with protein product	"Involved in Processing ITS2 3 homolog (S. cerevisiae)"					22190735	Standard	NM_024100		Approved	Ipi3	uc002lqm.1	Q9BV38		ENST00000251289.5:c.24C>T	chr19.hg19:g.984377C>T		157.0	0.0	.		179.0	8.0	.	NM_024100	O60390|Q9BWR2	Silent	SNP	ENST00000251289.5	hg19	CCDS12051.1																																																																																			.	.	.	none		0.716	WDR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458225.2			T	984377	C	T	984377	2	4	264	1	0	0	0	0	0	0	0	1	17290	639	23	1		1	WDR18	19	984377	Silent	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10		984377	58144606	131	16636											
DOT1L	84444	hgsc.bcm.edu	37	chr19	2216297	2216297	+	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	cagatcagcattgtggagctAgagaagagccagcggcagca	13	5	14	9	1	1	3	1	0	0	3	1	5	1	4	1	2	5	4	1	2	2	2			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr19:2216297A>T	ENST00000398665.3	+	20	1977	c.1941A>T	c.(1939-1941)ctA>ctT	p.L647L	AC004490.1_ENST00000585593.1_RNA|DOT1L_ENST00000608122.1_3'UTR	NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	647					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)		TTGTGGAGCTAGAGAAGAGCC	0.662																																					p.L647L		Atlas-SNP	.											.	DOT1L	205	.	0			c.A1941T						PASS	.						38	44	42					19																	2216297		2012	4155	6167	SO:0001819	synonymous_variant	84444	exon20			GGAGCTAGAGAAG	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.1941A>T	chr19.hg19:g.2216297A>T		60.0	0.0	.		64.0	30.0	.	NM_032482	O60379|Q96JL1	Silent	SNP	ENST00000398665.3	hg19	CCDS42460.1	.	.	.	.	.	.	.	.	.	.	A	10.49	1.364766	0.24684	.	.	ENSG00000104885	ENST00000440640	.	.	.	5.13	-2.15	0.07102	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-18.8059	1.5698	0.02612	0.2261:0.288:0.3288:0.1572	.	.	.	.	L	434	.	.	X	+	2	0	DOT1L	2167297	0.994000	0.37717	0.998000	0.56505	0.938000	0.57974	0.207000	0.17395	-0.059000	0.13154	-0.132000	0.14878	TAG	.	.	.	none		0.662	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482		T	2216297	A	T	2216297	2	4	264	1	0	0	0	0	0	0	0	1	4711	407	15	5		5	DOT1L	19	2216297	Silent	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	1231920	2216297	56912686	132	16637											
RANBP3	8498	hgsc.bcm.edu	37	chr19	5921298	5921298	+	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	ctctctccacccaggactgtGaggtcttgtcaaagacaaac	11	9	8	13	0	3	2	1	1	2	1	5	3	4	3	2	2	1	0	2	2	2	1			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr19:5921298G>A	ENST00000340578.6	-	14	1301	c.1244C>T	c.(1243-1245)tCa>tTa	p.S415L	RANBP3_ENST00000591092.1_Missense_Mutation_p.S342L|RANBP3_ENST00000034275.8_Missense_Mutation_p.S347L|RANBP3_ENST00000439268.2_Missense_Mutation_p.S410L|RANBP3_ENST00000541471.1_Missense_Mutation_p.S287L	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	415	RanBD1. {ECO:0000255|PROSITE- ProRule:PRU00164}.				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						CCAGGACTGTGAGGTCTTGTC	0.612																																					p.S415L		Atlas-SNP	.											.	RANBP3	36	.	0			c.C1244T						PASS	.						58	66	63					19																	5921298		2009	4184	6193	SO:0001583	missense	8498	exon14			GACTGTGAGGTCT	Y08698	CCDS42477.1, CCDS42478.1, CCDS45935.1, CCDS74268.1	19p13.3	2008-02-05							9850	protein-coding gene	gene with protein product		603327				9637251	Standard	NM_007322		Approved		uc002mdw.3	Q9H6Z4		ENST00000340578.6:c.1244C>T	chr19.hg19:g.5921298G>A	ENSP00000341483:p.Ser415Leu	92.0	0.0	.		55.0	23.0	.	NM_007322	B2RAT8|O60405|O75759|O75760|Q9BT47|Q9UG74	Missense_Mutation	SNP	ENST00000340578.6	hg19	CCDS42478.1	.	.	.	.	.	.	.	.	.	.	G	34	5.360198	0.95877	.	.	ENSG00000031823	ENST00000340578;ENST00000439268;ENST00000034275;ENST00000324807;ENST00000541471	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	5.28	5.28	0.74379	Pleckstrin homology-type (1);Ran binding protein 1 (3);	0.191591	0.46442	D	0.000294	T	0.57460	0.2055	M	0.67569	2.06	0.58432	D	0.999995	P;D;D;D;D;D;D	0.59357	0.924;0.985;0.971;0.971;0.964;0.982;0.985	P;P;P;P;P;P;P	0.57548	0.505;0.823;0.714;0.714;0.591;0.729;0.823	T	0.54886	-0.8226	10	0.34782	T	0.22	-13.0523	16.4424	0.83906	0.0:0.0:1.0:0.0	.	287;410;287;342;347;410;415	F5H4C2;Q53GE1;B7Z5P4;B7Z7F3;Q9H6Z4-3;Q9H6Z4-2;Q9H6Z4	.;.;.;.;.;.;RANB3_HUMAN	L	415;410;347;346;287	ENSP00000341483:S415L;ENSP00000404837:S410L;ENSP00000034275:S347L;ENSP00000445071:S287L	ENSP00000034275:S347L	S	-	2	0	RANBP3	5872298	1.000000	0.71417	0.998000	0.56505	0.971000	0.66376	7.498000	0.81546	2.479000	0.83701	0.655000	0.94253	TCA	.	.	.	none		0.612	RANBP3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452304.1	NM_007322		A	5921298	G	A	5921298	3	1	264	1	0	0	0	0	1	0	0	0	13042	1294	45	2	475	2	RANBP3	19	5921298	Missense_Mutation	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10	3705001	5921298	53207685	133	16638											
MUC16	94025	hgsc.bcm.edu	37	chr19	9049050	9049050	+	Missense_Mutation	SNP	A	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	agttggaacagctgaactggAttctgccccatgactggtgg	9	10	13	9	0	1	2	0	2	1	0	1	4	1	4	2	4	4	2	2	4	2	2	rs554642180		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr19:9049050A>C	ENST00000397910.4	-	5	32784	c.32581T>G	c.(32581-32583)Tcc>Gcc	p.S10861A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10863	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						GCTGAACTGGATTCTGCCCCA	0.483													A|||	1	0.000199681	0	0	5008	,	,		23708	0.001		0	False		,,,				2504	0				p.S10861A		Atlas-SNP	.											.	MUC16	4315	.	0			c.T32581G						PASS	.						110	99	102					19																	9049050		1929	4137	6066	SO:0001583	missense	94025	exon5			AACTGGATTCTGC	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.32581T>G	chr19.hg19:g.9049050A>C	ENSP00000381008:p.Ser10861Ala	115.0	0.0	.		125.0	49.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	a	3.311	-0.140758	0.06669	.	.	ENSG00000181143	ENST00000397910	T	0.02395	4.31	3.2	-6.4	0.01944	.	.	.	.	.	T	0.01320	0.0043	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.04013	0.001	T	0.48055	-0.9068	8	0.87932	D	0	.	0.8056	0.01083	0.3995:0.1925:0.1073:0.3007	.	10861	B5ME49	.	A	10861	ENSP00000381008:S10861A	ENSP00000381008:S10861A	S	-	1	0	MUC16	8910050	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.603000	0.00890	-2.560000	0.00474	-2.063000	0.00397	TCC	.	.	.	none		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9049050	A	C	9049050	3	2	264	1	0	0	0	0	1	0	0	0	9980	333	12	5	11262	5	MUC16	19	9049050	Missense_Mutation	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	3127752	9049050	50079933	134	16639											
ZNF490	57474	hgsc.bcm.edu	37	chr19	12693704	12693704	+	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	tttgtgttcatcttcaatatCctggtctttccatttttccc	5	21	4	11	0	4	0	2	0	2	0	7	0	7	0	3	1	0	1	3	1	2	7			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr19:12693704C>G	ENST00000311437.6	-	4	432	c.310G>C	c.(310-312)Gat>Cat	p.D104H	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	104	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	18						TCTTCAATATCCTGGTCTTTC	0.313																																					p.D104H		Atlas-SNP	.											.	ZNF490	42	.	0			c.G310C						PASS	.						119	124	122					19																	12693704		2203	4299	6502	SO:0001583	missense	57474	exon4			CAATATCCTGGTC	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.310G>C	chr19.hg19:g.12693704C>G	ENSP00000311521:p.Asp104His	56.0	0.0	.		90.0	10.0	.	NM_020714		Missense_Mutation	SNP	ENST00000311437.6	hg19	CCDS12272.1	.	.	.	.	.	.	.	.	.	.	C	4.469	0.086965	0.08583	.	.	ENSG00000188033	ENST00000311437;ENST00000440366	T;T	0.00949	5.51;5.51	0.93	-0.166	0.13351	Krueppel-associated box (3);	.	.	.	.	T	0.00784	0.0026	N	0.26042	0.785	0.09310	N	1	B	0.10296	0.003	B	0.01281	0.0	T	0.46748	-0.9169	9	0.40728	T	0.16	.	3.172	0.06555	0.0:0.6767:0.0:0.3233	.	104	Q9ULM2	ZN490_HUMAN	H	104;51	ENSP00000311521:D104H;ENSP00000404112:D51H	ENSP00000311521:D104H	D	-	1	0	ZNF490	12554704	0.000000	0.05858	0.001000	0.08648	0.060000	0.15804	-1.188000	0.03064	-0.024000	0.13941	0.436000	0.28706	GAT	.	.	.	none		0.313	ZNF490-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344073.1	NM_020714		G	12693704	C	G	12693704	3	3	264	1	0	0	0	0	1	0	0	0	17953	855	30	4	1287	4	ZNF490	19	12693704	Missense_Mutation	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	3644654	12693704	46435279	135	16640											
UPF1	5976	hgsc.bcm.edu	37	chr19	18960968	18960968	+	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	ctgggggagacagtcctggaGtgctacaactgcggctgtcg	7	8	16	10	2	0	1	0	0	0	1	2	3	1	2	1	4	4	2	1	4	2	1			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr19:18960968G>T	ENST00000599848.1	+	4	755	c.546G>T	c.(544-546)gaG>gaT	p.E182D	UPF1_ENST00000600310.1_3'UTR|UPF1_ENST00000262803.5_Missense_Mutation_p.E182D			Q92900	RENT1_HUMAN	UPF1 regulator of nonsense transcripts homolog (yeast)	182	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						CAGTCCTGGAGTGCTACAACT	0.572																																					p.E182D		Atlas-SNP	.											.	UPF1	88	.	0			c.G546T						PASS	.						106	100	102					19																	18960968		2203	4300	6503	SO:0001583	missense	5976	exon4			CCTGGAGTGCTAC	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.546G>T	chr19.hg19:g.18960968G>T	ENSP00000470142:p.Glu182Asp	68.0	0.0	.		61.0	29.0	.	NM_002911	O00239|O43343|Q86Z25|Q92842	Missense_Mutation	SNP	ENST00000599848.1	hg19		.	.	.	.	.	.	.	.	.	.	G	21.7	4.189383	0.78789	.	.	ENSG00000005007	ENST00000262803	D	0.91843	-2.92	4.89	1.59	0.23543	RNA helicase UPF1, UPF2-interacting domain (1);	0.000000	0.85682	D	0.000000	D	0.96762	0.8943	H	0.97415	4	0.58432	D	0.999999	D;D	0.89917	1.0;0.999	D;D	0.79108	0.992;0.987	D	0.95078	0.8210	10	0.87932	D	0	-47.5877	7.77	0.29001	0.4208:0.0:0.5792:0.0	.	182;182	Q92900;Q92900-2	RENT1_HUMAN;.	D	182	ENSP00000262803:E182D	ENSP00000262803:E182D	E	+	3	2	UPF1	18821968	1.000000	0.71417	0.994000	0.49952	0.996000	0.88848	2.236000	0.43052	0.472000	0.27344	0.467000	0.42956	GAG	.	.	.	none		0.572	UPF1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464684.1	NM_002911		T	18960968	G	T	18960968	3	4	264	1	0	0	0	0	1	0	0	0	17015	1020	36	4	560	4	UPF1	19	18960968	Missense_Mutation	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10	6267264	18960968	40168015	136	16641											
ZNF529	57711	hgsc.bcm.edu	37	chr19	37038652	37038652	+	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	atgaactctttgaagtggagTaacttttccaactctttcaa	12	15	6	8	0	3	2	1	2	2	0	4	3	4	3	1	1	3	1	1	1	5	5			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr19:37038652T>A	ENST00000591340.1	-	5	966	c.808A>T	c.(808-810)Act>Tct	p.T270S	ZNF529_ENST00000334116.7_Missense_Mutation_p.T165S	NM_020951.4	NP_066002.3	Q6P280	ZN529_HUMAN	zinc finger protein 529	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(1)	1	Esophageal squamous(110;0.198)					TGAAGTGGAGTAACTTTTCCA	0.333																																					p.T270S		Atlas-SNP	.											.	ZNF529	82	.	0			c.A808T						PASS	.						143	141	141					19																	37038652		1875	4122	5997	SO:0001583	missense	57711	exon6			GTGGAGTAACTTT	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.808A>T	chr19.hg19:g.37038652T>A	ENSP00000465578:p.Thr270Ser	72.0	0.0	.		77.0	36.0	.	NM_001145649	K7EKE1|Q9H731|Q9HCF7	Missense_Mutation	SNP	ENST00000591340.1	hg19	CCDS54256.1	.	.	.	.	.	.	.	.	.	.	T	7.954	0.745517	0.15710	.	.	ENSG00000186020	ENST00000334116	.	.	.	3.68	2.66	0.31614	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.30070	0.0753	L	0.37800	1.135	0.09310	N	1	B;B	0.15719	0.014;0.008	B;B	0.15484	0.013;0.004	T	0.22034	-1.0228	8	0.42905	T	0.14	.	5.3337	0.15945	0.0:0.3507:0.0:0.6492	.	165;237	Q6P280-2;Q6P280	.;ZN529_HUMAN	S	270	.	ENSP00000334695:T270S	T	-	1	0	ZNF529	41730492	0.000000	0.05858	0.022000	0.16811	0.636000	0.38137	0.098000	0.15189	0.486000	0.27676	0.482000	0.46254	ACT	.	.	.	none		0.333	ZNF529-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452730.1	NM_020951		A	37038652	T	A	37038652	3	1	264	1	0	0	0	0	1	0	0	0	17982	1638	57	5	887	5	ZNF529	19	37038652	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	18077684	37038652	22090331	137	16642											
ZNF585B	92285	hgsc.bcm.edu	37	chr19	37677880	37677880	+	Missense_Mutation	SNP	T	T	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	ttttccacattcattgcactTatagggcttctctctcatat	8	18	4	11	0	3	0	2	0	2	0	6	0	4	0	1	1	1	2	1	1	3	8			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr19:37677880T>G	ENST00000532828.2	-	5	810	c.559A>C	c.(559-561)Aag>Cag	p.K187Q	CTC-454I21.3_ENST00000585860.2_Intron|ZNF585B_ENST00000527838.1_Intron|ZNF585B_ENST00000312908.5_Intron|ZNF585B_ENST00000531805.1_Missense_Mutation_p.K132Q	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	187					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)			TCATTGCACTTATAGGGCTTC	0.378																																					p.K187Q	Melanoma(93;882 1454 18863 28917 48427)	Atlas-SNP	.											.	ZNF585B	91	.	0			c.A559C						PASS	.						131	132	132					19																	37677880		2203	4300	6503	SO:0001583	missense	92285	exon5			TGCACTTATAGGG	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.559A>C	chr19.hg19:g.37677880T>G	ENSP00000433773:p.Lys187Gln	80.0	0.0	.		91.0	39.0	.	NM_152279	Q8IZD3|Q96JW6	Missense_Mutation	SNP	ENST00000532828.2	hg19	CCDS12500.1	.	.	.	.	.	.	.	.	.	.	T	6.257	0.415489	0.11870	.	.	ENSG00000245680	ENST00000531805;ENST00000532828	T;T	0.18810	2.19;2.19	2.41	0.0526	0.14303	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.398528	0.18240	N	0.147278	T	0.08891	0.0220	N	0.17838	0.53	0.22571	N	0.998976	P	0.42620	0.785	B	0.33521	0.165	T	0.22695	-1.0209	10	0.42905	T	0.14	.	4.7311	0.12964	0.0:0.1276:0.1936:0.6789	.	187	Q52M93	Z585B_HUMAN	Q	132;187	ENSP00000436774:K132Q;ENSP00000433773:K187Q	ENSP00000436774:K132Q	K	-	1	0	ZNF585B	42369720	0.000000	0.05858	0.916000	0.36221	0.699000	0.40488	-0.527000	0.06200	0.126000	0.18424	0.374000	0.22700	AAG	.	.	.	none		0.378	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279		G	37677880	T	G	37677880	3	3	264	1	0	0	0	0	1	0	0	0	18030	1763	61	5	1754	5	ZNF585B	19	37677880	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10	639228	37677880	21451103	138	16643											
PLEKHA4	57664	hgsc.bcm.edu	37	chr19	49364695	49364695	+	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	gccctcggggggctcccggcCcatctggtctaatattgtag	5	10	13	13	2	2	0	0	0	2	0	4	0	3	0	3	5	0	2	3	5	3	4	rs201822487		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr19:49364695C>T	ENST00000263265.6	-	5	884	c.329G>A	c.(328-330)gGg>gAg	p.G110E	PLEKHA4_ENST00000355496.5_Missense_Mutation_p.G110E|PLEKHA4_ENST00000596713.1_5'Flank	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	110	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		GGCTCCCGGCCCATCTGGTCT	0.612																																					p.G110E		Atlas-SNP	.											.	PLEKHA4	70	.	0			c.G329A						PASS	.						47	61	56					19																	49364695		2203	4300	6503	SO:0001583	missense	57664	exon5			CCCGGCCCATCTG	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.329G>A	chr19.hg19:g.49364695C>T	ENSP00000263265:p.Gly110Glu	56.0	0.0	.		98.0	51.0	.	NM_001161354	Q8N4M8|Q8N658	Missense_Mutation	SNP	ENST00000263265.6	hg19	CCDS12737.1	.	.	.	.	.	.	.	.	.	.	c	19.98	3.926443	0.73327	.	.	ENSG00000105559	ENST00000263265;ENST00000355496	T;T	0.74209	-0.82;-0.82	4.56	4.56	0.56223	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.424077	0.22724	N	0.056413	T	0.76849	0.4045	N	0.20357	0.565	0.31463	N	0.669357	D;P	0.89917	1.0;0.685	D;P	0.75020	0.985;0.624	T	0.78802	-0.2061	10	0.66056	D	0.02	.	15.2385	0.73450	0.0:1.0:0.0:0.0	.	110;110	Q9H4M7-2;Q9H4M7	.;PKHA4_HUMAN	E	110	ENSP00000263265:G110E;ENSP00000347683:G110E	ENSP00000263265:G110E	G	-	2	0	PLEKHA4	54056507	0.877000	0.30153	1.000000	0.80357	0.992000	0.81027	2.412000	0.44609	2.548000	0.85928	0.457000	0.33378	GGG	.	C|0.999;T|0.001	0.001	weak		0.612	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466216.1			T	49364695	C	T	49364695	3	4	264	1	0	0	0	0	1	0	0	0	12065	623	22	2	2074	2	PLEKHA4	19	49364695	Missense_Mutation	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	11686815	49364695	9764288	139	16644											
AP2A1	160	hgsc.bcm.edu	37	chr19	50304776	50304776	+	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	accaaggccaccatccagggCgtcctgcgggccggctccca	7	4	12	18	3	0	0	0	0	0	0	3	0	3	0	7	4	1	1	7	4	1	0			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr19:50304776C>T	ENST00000359032.5	+	13	1683	c.1683C>T	c.(1681-1683)ggC>ggT	p.G561G	AP2A1_ENST00000354293.5_Silent_p.G561G	NM_014203.2	NP_055018.2	O95782	AP2A1_HUMAN	adaptor-related protein complex 2, alpha 1 subunit	561					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	AP-2 adaptor complex (GO:0030122)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)	19		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0023)|GBM - Glioblastoma multiforme(134;0.0157)		CCATCCAGGGCGTCCTGCGGG	0.652																																					p.G561G		Atlas-SNP	.											.	AP2A1	108	.	0			c.C1683T						PASS	.						50	53	52					19																	50304776		2111	4233	6344	SO:0001819	synonymous_variant	160	exon13			CCAGGGCGTCCTG	AA993745	CCDS46148.1, CCDS46149.1	19q13.3	2008-05-23				ENSG00000196961			561	protein-coding gene	gene with protein product		601026		CLAPA1, ADTAA		2564002	Standard	NM_014203		Approved		uc002ppn.3	O95782		ENST00000359032.5:c.1683C>T	chr19.hg19:g.50304776C>T		138.0	0.0	.		156.0	20.0	.	NM_130787	Q96CI7|Q96PP6|Q96PP7|Q9H070	Silent	SNP	ENST00000359032.5	hg19	CCDS46148.1																																																																																			.	.	.	none		0.652	AP2A1-008	NOVEL	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465809.1			T	50304776	C	T	50304776	2	4	264	1	0	0	0	0	0	0	0	1	739	755	27	1		1	AP2A1	19	50304776	Silent	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	940081	50304776	8824207	140	16645											
ZNF749	388567	hgsc.bcm.edu	37	chr19	57955392	57955392	+	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	attgaacatcaggagattctCagtagaccaacaccttatga	15	10	7	9	0	2	4	2	2	1	2	3	5	2	4	2	1	2	1	2	1	4	4			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr19:57955392C>T	ENST00000334181.4	+	3	1126	c.876C>T	c.(874-876)ctC>ctT	p.L292L	AC004076.9_ENST00000596831.1_Intron	NM_001023561.2	NP_001018855.2	O43361	ZN749_HUMAN	zinc finger protein 749	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)|endometrium(6)|kidney(2)|lung(3)|prostate(1)	13		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;0.0264)|Lung(386;0.177)		AGGAGATTCTCAGTAGACCAA	0.453																																					p.L292L		Atlas-SNP	.											.	ZNF749	75	.	0			c.C876T						PASS	.						74	75	75					19																	57955392		2203	4300	6503	SO:0001819	synonymous_variant	388567	exon3			GATTCTCAGTAGA	AK122740	CCDS33132.2	19q13.43	2013-01-08			ENSG00000186230	ENSG00000186230		"Zinc fingers, C2H2-type", "-"	32783	protein-coding gene	gene with protein product							Standard	NM_001023561		Approved	FLJ16360	uc002qoq.2	O43361	OTTHUMG00000150372	ENST00000334181.4:c.876C>T	chr19.hg19:g.57955392C>T		118.0	0.0	.		123.0	49.0	.	NM_001023561		Silent	SNP	ENST00000334181.4	hg19	CCDS33132.2																																																																																			.	.	.	none		0.453	ZNF749-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317879.1	NM_001023561		T	57955392	C	T	57955392	2	4	264	1	0	0	0	0	0	0	0	1	18143	813	29	2		2	ZNF749	19	57955392	Silent	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	7650616	57955392	1173591	141	16646											
NINL	22981	hgsc.bcm.edu	37	chr20	25460838	25460838	+	Missense_Mutation	SNP	T	T	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	gaggtcttggtaatgctcctTtacctgctccatcatcagct	7	14	8	12	0	3	0	2	0	1	0	5	1	5	0	3	2	4	4	3	2	2	4			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr20:25460838T>G	ENST00000278886.6	-	15	1949	c.1876A>C	c.(1876-1878)Aag>Cag	p.K626Q	NINL_ENST00000422516.1_Missense_Mutation_p.K626Q	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	626					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						TAATGCTCCTTTACCTGCTCC	0.542																																					p.K626Q		Atlas-SNP	.											.	NINL	148	.	0			c.A1876C						PASS	.						167	142	150					20																	25460838		2203	4300	6503	SO:0001583	missense	22981	exon15			GCTCCTTTACCTG		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.1876A>C	chr20.hg19:g.25460838T>G	ENSP00000278886:p.Lys626Gln	97.0	0.0	.		132.0	48.0	.	NM_025176	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	ENST00000278886.6	hg19	CCDS33452.1	.	.	.	.	.	.	.	.	.	.	T	12.63	1.994822	0.35226	.	.	ENSG00000101004	ENST00000278886;ENST00000422516	T;T	0.41758	0.99;1.04	4.83	3.7	0.42460	.	0.285870	0.26460	N	0.024250	T	0.60971	0.2310	M	0.79258	2.445	0.25995	N	0.982195	D;D	0.76494	0.999;0.997	D;D	0.69479	0.964;0.953	T	0.54596	-0.8270	10	0.48119	T	0.1	-33.9293	10.6943	0.45890	0.0:0.0:0.1609:0.8391	.	626;626	Q9Y2I6-2;Q9Y2I6	.;NINL_HUMAN	Q	626	ENSP00000278886:K626Q;ENSP00000410431:K626Q	ENSP00000278886:K626Q	K	-	1	0	NINL	25408838	1.000000	0.71417	0.918000	0.36340	0.002000	0.02628	3.465000	0.53064	0.838000	0.34948	0.460000	0.39030	AAG	.	.	.	none		0.542	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176		G	25460838	T	G	25460838	3	3	264	1	0	0	0	0	1	0	0	0	10427	1850	64	5	2312	5	NINL	20	25460838	Missense_Mutation	SNP	T	TCGA-UZ-A9PS-01A-11D-A42J-10		25460838	37564682	142	16647											
MAPRE1	22919	hgsc.bcm.edu	37	chr20	31413759	31413764	+	In_Frame_Del	DEL	CAGTGA	CAGTGA	-																															agtgaacgtatactcaacgtCagtgaccagtgataacctaa																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	CAGTGA	CAGTGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr20:31413759_31413764delCAGTGA	ENST00000375571.5	+	2	165_170	c.26_31delCAGTGA	c.(25-33)tcagtgacc>tcc	p.VT10del		NM_012325.2	NP_036457.1	Q15691	MARE1_HUMAN	microtubule-associated protein, RP/EB family, member 1	10					cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of microtubule plus-end binding (GO:1903033)|protein localization to microtubule (GO:0035372)	cell projection membrane (GO:0031253)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule plus-end (GO:0035371)	microtubule plus-end binding (GO:0051010)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			endometrium(2)|large_intestine(1)|lung(3)|prostate(2)	8						TACTCAACGTCAGTGACCAGTGATAA	0.442																																					p.9_10del		Atlas-Indel,Pindel	.											.	MAPRE1	17	.	0			c.25_30del						PASS	.																																			SO:0001651	inframe_deletion	22919	exon2			.	U24166	CCDS13208.1	20q11.1-q11.3	2013-01-17			ENSG00000101367	ENSG00000101367			6890	protein-coding gene	gene with protein product	"adenomatous polyposis coli-binding protein EB1"	603108				7606712, 9724749, 11470413	Standard	NM_012325		Approved	EB1	uc002wyh.3	Q15691	OTTHUMG00000032228	ENST00000375571.5:c.26_31delCAGTGA	chr20.hg19:g.31413759_31413764delCAGTGA	ENSP00000364721:p.Val10_Thr11del	62.0	0.0	0		80.0	42.0	0.525	NM_012325	B2R6I7|E1P5M8|Q3KQS8	In_Frame_Del	DEL	ENST00000375571.5	hg19	CCDS13208.1																																																																																			.	.	.	none		0.442	MAPRE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078647.2	NM_012325		-	31413764	CAGTGA	-	31413759	7	5	264	1	0	1	0	1	0	0	0	0	9301	838	29	0	28	0	MAPRE1	20	31413759	In_Frame_Del	DEL	CAGTGA	TCGA-UZ-A9PS-01A-11D-A42J-10	5952921	31413759	31611761	143	16648											
EDEM2	55741	hgsc.bcm.edu	37	chr20	33730267	33730267	+	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	accactctttggaattctgaGacattccccaaaatctggaa	13	11	6	11	0	3	1	0	1	3	1	4	4	4	3	3	2	0	0	3	2	4	3	rs375028628		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr20:33730267G>T	ENST00000374492.3	-	4	378	c.273C>A	c.(271-273)gtC>gtA	p.V91V	EDEM2_ENST00000374491.3_Silent_p.V54V|EDEM2_ENST00000540582.1_Silent_p.V50V|EDEM2_ENST00000541621.1_5'UTR|EDEM2_ENST00000542871.1_5'UTR	NM_018217.2	NP_060687.2	Q9BV94	EDEM2_HUMAN	ER degradation enhancer, mannosidase alpha-like 2	91					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	22			BRCA - Breast invasive adenocarcinoma(18;0.00936)			GGAATTCTGAGACATTCCCCA	0.453																																					p.V91V	Esophageal Squamous(51;906 1021 24535 36410 39145)	Atlas-SNP	.											.	EDEM2	46	.	0			c.C273A						PASS	.						66	60	62					20																	33730267		2203	4300	6503	SO:0001819	synonymous_variant	55741	exon4			TTCTGAGACATTC	AK001645	CCDS13247.1, CCDS46592.1	20q11.22	2006-03-31	2006-03-31	2006-03-31	ENSG00000088298	ENSG00000088298			15877	protein-coding gene	gene with protein product		610302	"chromosome 20 open reading frame 31"	C20orf49, C20orf31		15537790, 15579471	Standard	NM_018217		Approved	FLJ10783, bA4204.1	uc002xbo.2	Q9BV94	OTTHUMG00000032322	ENST00000374492.3:c.273C>A	chr20.hg19:g.33730267G>T		56.0	0.0	.		103.0	55.0	.	NM_018217	B4DTG9|Q6GU33|Q6IA89|Q6UWZ4|Q9H4U0|Q9H886|Q9NTL9|Q9NVE6	Silent	SNP	ENST00000374492.3	hg19	CCDS13247.1																																																																																			.	.	.	alt		0.453	EDEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078842.2	NM_018217		T	33730267	G	T	33730267	2	4	264	1	0	0	0	0	0	0	0	1	4914	929	33	4		4	EDEM2	20	33730267	Silent	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10	2316508	33730267	29295253	144	16649											
SLC32A1	140679	hgsc.bcm.edu	37	chr20	37356467	37356468	+	Frame_Shift_Ins	INS	-	-	C																															ggccgtgctgctgccttgcgINSccttccttaagaacctcaag																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr20:37356467_37356468insC	ENST00000217420.1	+	2	1026_1027	c.763_764insC	c.(763-765)gccfs	p.A255fs		NM_080552.2	NP_542119.1	Q9H598	VIAAT_HUMAN	solute carrier family 32 (GABA vesicular transporter), member 1	255					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)	GCTGCCTTGCGCCTTCCTTAAG	0.579																																					p.A255fs		Atlas-Indel,Pindel	.											.	SLC32A1	81	.	0			c.763_764insC						PASS	.																																			SO:0001589	frameshift_variant	140679	exon2			.	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.765dupC	chr20.hg19:g.37356469_37356469dupC	ENSP00000217420:p.Ala255fs	84.0	0.0	0		73.0	30.0	0.410959	NM_080552	Q8N489	Frame_Shift_Ins	INS	ENST00000217420.1	hg19	CCDS13307.1																																																																																			.	.	.	none		0.579	SLC32A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079206.1	NM_080552		C	37356468	-	C	37356467	7	5	264	1	0	1	1	0	0	0	0	0	14578	1087	38	0	769	0	SLC32A1	20	37356467	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PS-01A-11D-A42J-10	3626200	37356467	25669053	145	16650											
TOMM34	10953	hgsc.bcm.edu	37	chr20	43580553	43580553	+	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	tccgaaggcaaggaattccaCctcttctgagctgaaacagg	12	8	10	11	1	2	2	0	2	2	0	4	4	4	3	3	3	2	2	3	3	4	2			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr20:43580553C>T	ENST00000372813.3	-	4	623	c.471G>A	c.(469-471)agG>agA	p.R157R	PABPC1L_ENST00000372819.1_Intron|PABPC1L_ENST00000490798.1_Intron	NM_006809.4	NP_006800.2	Q15785	TOM34_HUMAN	translocase of outer mitochondrial membrane 34	157					protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	heat shock protein binding (GO:0031072)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)	11		Myeloproliferative disorder(115;0.0122)				AGGAATTCCACCTCTTCTGAG	0.522																																					p.R157R		Atlas-SNP	.											.	TOMM34	16	.	0			c.G471A						PASS	.						157	125	135					20																	43580553		2203	4300	6503	SO:0001819	synonymous_variant	10953	exon4			ATTCCACCTCTTC	U58970	CCDS13340.1	20q12-q13.1	2013-01-10			ENSG00000025772	ENSG00000025772		"Tetratricopeptide (TTC) repeat domain containing"	15746	protein-coding gene	gene with protein product	"outer mitochondrial membrane translocase (34kD)"					9324309	Standard	NM_006809		Approved	TOM34, HTOM34P	uc002xmy.3	Q15785	OTTHUMG00000032552	ENST00000372813.3:c.471G>A	chr20.hg19:g.43580553C>T		71.0	0.0	.		73.0	29.0	.	NM_006809	Q53GH9|Q6IBN7|Q9NTZ3	Silent	SNP	ENST00000372813.3	hg19	CCDS13340.1																																																																																			.	.	.	none		0.522	TOMM34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079390.3	NM_006809		T	43580553	C	T	43580553	2	4	264	1	0	0	0	0	0	0	0	1	16369	506	18	2		2	TOMM34	20	43580553	Silent	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	6224086	43580553	19444967	146	16651											
NRIP1	8204	hgsc.bcm.edu	37	chr21	16337481	16337482	+	Missense_Mutation	DNP	AC	AC	TA																															aagtgctcagggaaagtaggActcacaggagtttttactac																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr21:16337481_16337482AC>TA	ENST00000400202.1	-	3	3744_3745	c.3032_3033GT>TA	c.(3031-3033)aGT>aTA	p.S1011I	NRIP1_ENST00000400199.1_Missense_Mutation_p.S1011I|NRIP1_ENST00000318948.4_Missense_Mutation_p.S1011I|AF127577.10_ENST00000446301.1_RNA			P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	1011	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)		GGAAAGTAGGACTCACAGGAGT	0.47																																					p.S1011R|p.S1011I		Atlas-SNP	.											.	NRIP1	103	.	0			c.T3033A|c.G3032T						PASS	.																																			SO:0001583	missense	8204	exon4			AGTAGGACTCACA|GTAGGACTCACAG	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.3032_3033delinsTA	chr21.hg19:g.16337481_16337482delinsTA	ENSP00000383063:p.Ser1011Ile	35.0|34.0	0.0	.		53.0|52.0	26.0|25.0	.	NM_003489	Q8IWE8	Missense_Mutation	SNP	ENST00000400202.1	hg19	CCDS13568.1																																																																																			.	.	.	none		0.47	NRIP1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157926.1	NM_003489		TA	16337482	AC	TA	16337481	3	4	264	1	0	0	0	0	1	0	0	0	10659	272	10	5	447	5	NRIP1	21	16337481	Missense_Mutation	DNP	AC	TCGA-UZ-A9PS-01A-11D-A42J-10		16337481	31792414	147	16652											
MORC3	23515	hgsc.bcm.edu	37	chr21	37732306	37732306	+	Missense_Mutation	SNP	A	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	tgcctgtctaaagtggcggaAattacctgatgggatggatc	10	11	13	7	1	1	1	0	1	1	0	2	4	1	4	2	4	2	0	2	4	4	2			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr21:37732306A>C	ENST00000400485.1	+	11	1338	c.1262A>C	c.(1261-1263)aAa>aCa	p.K421T	AP000692.9_ENST00000397184.2_RNA|MORC3_ENST00000487909.1_3'UTR	NM_015358.2	NP_056173.1	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	421					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						AAGTGGCGGAAATTACCTGAT	0.428																																					p.K421T		Atlas-SNP	.											.	MORC3	78	.	0			c.A1262C						PASS	.						194	186	188					21																	37732306		2049	4224	6273	SO:0001583	missense	23515	exon11			GGCGGAAATTACC	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.1262A>C	chr21.hg19:g.37732306A>C	ENSP00000383333:p.Lys421Thr	171.0	0.0	.		142.0	55.0	.	NM_015358	A8KA92|Q9UEZ2	Missense_Mutation	SNP	ENST00000400485.1	hg19	CCDS42924.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.096626	0.76870	.	.	ENSG00000159256	ENST00000400485	T	0.15256	2.44	5.68	5.68	0.88126	Zinc finger, CW-type (2);	0.000000	0.85682	D	0.000000	T	0.31420	0.0796	L	0.57130	1.785	0.58432	D	0.999995	P	0.46020	0.871	P	0.52343	0.696	T	0.01093	-1.1454	10	0.45353	T	0.12	-32.2775	15.9418	0.79758	1.0:0.0:0.0:0.0	.	421	Q14149	MORC3_HUMAN	T	421	ENSP00000383333:K421T	ENSP00000383333:K421T	K	+	2	0	MORC3	36654176	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	6.056000	0.71111	2.158000	0.67659	0.455000	0.32223	AAA	.	.	.	none		0.428	MORC3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000194640.1	NM_015358		C	37732306	A	C	37732306	3	2	264	1	0	0	0	0	1	0	0	0	9710	14	1	5	1304	5	MORC3	21	37732306	Missense_Mutation	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	21394825	37732306	10397589	148	16653											
COL6A2	1292	hgsc.bcm.edu	37	chr21	47545867	47545867	+	Frame_Shift_Del	DEL	G	G	-																															cctcaagtttgcctacgaccGcctcatcaaggagagccggc																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr21:47545867delG	ENST00000300527.4	+	26	2242	c.2138delG	c.(2137-2139)cgcfs	p.R713fs	COL6A2_ENST00000357838.4_Frame_Shift_Del_p.R713fs|COL6A2_ENST00000397763.1_Frame_Shift_Del_p.R713fs|COL6A2_ENST00000310645.5_Frame_Shift_Del_p.R713fs|COL6A2_ENST00000409416.1_Frame_Shift_Del_p.R713fs	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	713	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)		GCCTACGACCGCCTCATCAAG	0.627																																					p.R713fs		Atlas-INDEL	.											COL6A2_ENST00000357838,NS,carcinoma,0,5	COL6A2	351	.	0			c.2137delC						PASS	.						64	63	63					21																	47545867		2202	4300	6502	SO:0001589	frameshift_variant	1292	exon26			.	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.2138delG	chr21.hg19:g.47545867delG	ENSP00000300527:p.Arg713fs	192.0	0.0	0		136.0	31.0	0.227941	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Frame_Shift_Del	DEL	ENST00000300527.4	hg19	CCDS13728.1																																																																																			.	.	.	none		0.627	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1			-	47545867	G	-	47545867	7	5	264	1	0	1	0	1	0	0	0	0	3702	1087	38	0	2236	0	COL6A2	21	47545867	Frame_Shift_Del	DEL	G	TCGA-UZ-A9PS-01A-11D-A42J-10	9813561	47545867	584028	149	16654	175	2									
COL6A2	1292	hgsc.bcm.edu	37	chr21	47545869	47545879	+	Frame_Shift_Del	DEL	CTCATCAAGGA	CTCATCAAGGA	-																															tcaagtttgcctacgaccgcCtcatcaaggagagccggcgc																										TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	CTCATCAAGGA	CTCATCAAGGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr21:47545869_47545879delCTCATCAAGGA	ENST00000300527.4	+	26	2244_2254	c.2140_2150delCTCATCAAGGA	c.(2140-2151)ctcatcaaggagfs	p.LIKE714fs	COL6A2_ENST00000357838.4_Frame_Shift_Del_p.LIKE714fs|COL6A2_ENST00000397763.1_Frame_Shift_Del_p.LIKE714fs|COL6A2_ENST00000310645.5_Frame_Shift_Del_p.LIKE714fs|COL6A2_ENST00000409416.1_Frame_Shift_Del_p.LIKE714fs	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	714	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)		p.I715M(3)		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)		CTACGACCGCCTCATCAAGGAGAGCCGGCGC	0.63																																					p.713_717del		Atlas-INDEL	.											.	COL6A2	351	.	3	Substitution - Missense(3)	lung(3)	c.2139_2149del						PASS	.																																			SO:0001589	frameshift_variant	1292	exon26			.	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.2140_2150delCTCATCAAGGA	chr21.hg19:g.47545869_47545879delCTCATCAAGGA	ENSP00000300527:p.Leu714fs	190.0	0.0	0		131.0	31.0	0.236641	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Frame_Shift_Del	DEL	ENST00000300527.4	hg19	CCDS13728.1																																																																																			.	.	.	none		0.63	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1			-	47545879	CTCATCAAGGA	-	47545869	7	5	264	1	0	1	0	1	0	0	0	0	3702	681	24	0	2238	0	COL6A2	21	47545869	Frame_Shift_Del	DEL	CTCATCAAGGA	TCGA-UZ-A9PS-01A-11D-A42J-10	2	47545869	584026	150	16655	175	2									
A4GALT	53947	hgsc.bcm.edu	37	chr22	43089135	43089143	+	In_Frame_Del	DEL	CGCGGCAGG	CGCGGCAGG	-																															agggggcagggtggtgacgcCgcggcaggcgcggctctcgg																								rs577646955|rs372559008		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	CGCGGCAGG	CGCGGCAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr22:43089135_43089143delCGCGGCAGG	ENST00000401850.1	-	2	1304_1312	c.815_823delCCTGCCGCG	c.(814-825)gcctgccgcggc>ggc	p.ACR272del	A4GALT_ENST00000381278.3_In_Frame_Del_p.ACR272del|A4GALT_ENST00000465765.2_5'Flank|A4GALT_ENST00000249005.2_In_Frame_Del_p.ACR272del			Q9NPC4	A4GAT_HUMAN	alpha 1,4-galactosyltransferase	272					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)	p.R274R(1)		NS(1)|central_nervous_system(2)|large_intestine(6)|skin(1)|urinary_tract(1)	11						GTGGTGACGCCGCGGCAGGCGCGGCTCTC	0.66																																					p.272_275del		Atlas-Indel,Pindel	.											.	A4GALT	35	.	1	Substitution - coding silent(1)	large_intestine(1)	c.816_824del						PASS	.																																			SO:0001651	inframe_deletion	53947	exon3			.		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.815_823delCCTGCCGCG	chr22.hg19:g.43089135_43089143delCGCGGCAGG	ENSP00000384794:p.Ala272_Arg274del	57.0	0.0	0		46.0	11.0	0.23913	NM_017436	B2R7C4|Q9P1X5	In_Frame_Del	DEL	ENST00000401850.1	hg19	CCDS14041.1																																																																																			.	.	.	none		0.66	A4GALT-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319917.1	NM_017436		-	43089143	CGCGGCAGG	-	43089135	7	5	264	1	0	1	0	1	0	0	0	0	6	652	23	0	242	0	A4GALT	22	43089135	In_Frame_Del	DEL	CGCGGCAGG	TCGA-UZ-A9PS-01A-11D-A42J-10		43089135	8215431	151	16656											
TBC1D22A	25771	hgsc.bcm.edu	37	chr22	47507468	47507468	+	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	tgcttttctcgtgagatggaGgaaggaaatactagaagaaa	15	10	12	4	1	1	3	0	1	1	3	2	7	1	6	0	3	2	1	0	3	6	4			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr22:47507468G>C	ENST00000337137.4	+	12	1560	c.1394G>C	c.(1393-1395)aGg>aCg	p.R465T	TBC1D22A_ENST00000355704.3_Missense_Mutation_p.R387T|TBC1D22A_ENST00000407381.3_Missense_Mutation_p.R406T|TBC1D22A_ENST00000406733.1_Missense_Mutation_p.R418T	NM_001284304.1|NM_001284305.1|NM_014346.2	NP_001271233.1|NP_001271234.1|NP_055161.1	Q8WUA7	TB22A_HUMAN	TBC1 domain family, member 22A	465							protein homodimerization activity (GO:0042803)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(3)|large_intestine(10)|lung(5)|ovary(2)|prostate(1)	22		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)		GTGAGATGGAGGAAGGAAATA	0.348																																					p.R465T		Atlas-SNP	.											.	TBC1D22A	54	.	0			c.G1394C						PASS	.						102	100	101					22																	47507468		2203	4300	6503	SO:0001583	missense	25771	exon12			GATGGAGGAAGGA	AK125705	CCDS14078.1, CCDS63511.1, CCDS63512.1, CCDS74877.1	22q13	2008-01-22	2005-01-05	2005-01-05	ENSG00000054611	ENSG00000054611			1309	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 4"	C22orf4			Standard	XM_005261496		Approved		uc003bib.3	Q8WUA7	OTTHUMG00000150332	ENST00000337137.4:c.1394G>C	chr22.hg19:g.47507468G>C	ENSP00000336724:p.Arg465Thr	107.0	0.0	.		101.0	34.0	.	NM_014346	B0QYI2|B0QYI3|B9A6M3|Q5TE47|Q6ZUH2|Q92680|Q9BVD6|Q9UGG0|Q9UGT2|Q9UGU6|Q9UH25|Q9Y4W5	Missense_Mutation	SNP	ENST00000337137.4	hg19	CCDS14078.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.775821	0.90195	.	.	ENSG00000054611	ENST00000337137;ENST00000407381;ENST00000355704;ENST00000406733	T;T;T;T	0.28069	1.63;1.63;1.63;1.63	5.3	5.3	0.74995	Rab-GAP/TBC domain (3);	0.000000	0.85682	D	0.000000	T	0.46014	0.1371	M	0.77406	2.37	0.80722	D	1	B;D;P;B	0.57257	0.14;0.979;0.953;0.14	B;P;P;B	0.50352	0.059;0.638;0.54;0.059	T	0.42949	-0.9421	10	0.32370	T	0.25	.	16.4417	0.83903	0.0:0.0:1.0:0.0	.	465;387;406;465	B9A6M3;Q8WUA7-2;B0QYI1;Q8WUA7	.;.;.;TB22A_HUMAN	T	465;406;387;418	ENSP00000336724:R465T;ENSP00000384036:R406T;ENSP00000347932:R387T;ENSP00000385634:R418T	ENSP00000336724:R465T	R	+	2	0	TBC1D22A	45886132	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.438000	0.66550	2.462000	0.83206	0.655000	0.94253	AGG	.	.	.	none		0.348	TBC1D22A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317600.3	NM_014346		C	47507468	G	C	47507468	3	2	264	1	0	0	0	0	1	0	0	0	15623	1000	35	4	1440	4	TBC1D22A	22	47507468	Missense_Mutation	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10	4418333	47507468	3797098	152	16657											
BRD1	23774	hgsc.bcm.edu	37	chr22	50187854	50187854	+	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	gagccgctggacttcatagcGcaggtgaggtcgagcatgtc	8	8	15	10	3	1	1	1	1	0	0	3	4	1	2	1	3	3	3	1	3	1	2	rs369329207		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chr22:50187854G>C	ENST00000216267.8	-	6	2673	c.2187C>G	c.(2185-2187)tgC>tgG	p.C729W	BRD1_ENST00000542442.1_Missense_Mutation_p.C417W|BRD1_ENST00000404760.1_Missense_Mutation_p.C729W|BRD1_ENST00000342989.5_Missense_Mutation_p.C324W|BRD1_ENST00000404034.1_Missense_Mutation_p.C729W|BRD1_ENST00000457780.2_Missense_Mutation_p.C729W	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	729					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)		ACTTCATAGCGCAGGTGAGGT	0.612																																					p.C729W		Atlas-SNP	.											.	BRD1	144	.	0			c.C2187G						PASS	.						60	64	62					22																	50187854		2203	4300	6503	SO:0001583	missense	23774	exon6			CATAGCGCAGGTG	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.2187C>G	chr22.hg19:g.50187854G>C	ENSP00000216267:p.Cys729Trp	69.0	0.0	.		61.0	30.0	.	NM_014577	A6ZJA4	Missense_Mutation	SNP	ENST00000216267.8	hg19	CCDS14080.1	.	.	.	.	.	.	.	.	.	.	G	11.72	1.723195	0.30503	.	.	ENSG00000100425	ENST00000216267;ENST00000404034;ENST00000404760;ENST00000457780;ENST00000542442;ENST00000342989;ENST00000419212	T;T;T;T;T;T	0.27256	2.61;2.61;2.58;2.43;1.68;2.02	5.4	-1.65	0.08291	.	0.088754	0.85682	D	0.000000	T	0.37073	0.0990	L	0.59436	1.845	0.49051	D	0.999745	D;D;D;D	0.76494	0.998;0.996;0.996;0.999	P;P;P;P	0.60415	0.752;0.817;0.752;0.874	T	0.13710	-1.0499	10	0.66056	D	0.02	.	11.3583	0.49627	0.6417:0.0:0.3583:0.0	.	729;324;729;729	Q86X06;B7Z926;O95696;O95696-2	.;.;BRD1_HUMAN;.	W	729;729;729;729;417;324;189	ENSP00000216267:C729W;ENSP00000384076:C729W;ENSP00000385858:C729W;ENSP00000410042:C729W;ENSP00000437514:C417W;ENSP00000345886:C324W	ENSP00000216267:C729W	C	-	3	2	BRD1	48573858	0.040000	0.19996	0.370000	0.25965	0.975000	0.68041	-0.140000	0.10342	-0.460000	0.07003	-1.202000	0.01658	TGC	.	.	.	alt		0.612	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577		C	50187854	G	C	50187854	3	2	264	1	0	0	0	0	1	0	0	0	1503	1079	38	4	1017	4	BRD1	22	50187854	Missense_Mutation	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10	2680386	50187854	1116712	153	16658											
ZRSR2	8233	hgsc.bcm.edu	37	chrX	15841227	15841227	+	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	agggaccgcagccggggccgGggcagccggagccggagccg	6	0	21	14	6	0	0	0	0	0	0	0	3	0	3	6	7	4	2	6	7	0	0			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chrX:15841227G>C	ENST00000307771.7	+	11	1335	c.1311G>C	c.(1309-1311)cgG>cgC	p.R437R		NM_005089.3	NP_005080.1	Q15696	U2AFM_HUMAN	zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2	437	Arg/Ser-rich (RS domain).				mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	U12-type spliceosomal complex (GO:0005689)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|pre-mRNA 3'-splice site binding (GO:0030628)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(38)|kidney(1)|large_intestine(2)|ovary(2)	48	Hepatocellular(33;0.183)					GCCGGGGCCGGGGCagccgga	0.647			"F, S, Mis"		"MDS, CLL"																																p.R437R	NSCLC(197;1631 3042 5741 31152)	Atlas-SNP	.		Rec	yes		X	Xp22.1	8233	"zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2"		L	.	ZRSR2	78	.	0			c.G1311C						PASS	.						9	10	10					X																	15841227		2136	4121	6257	SO:0001819	synonymous_variant	8233	exon11			GGGCCGGGGCAGC	BC050451	CCDS14172.1	Xp22.1	2014-09-17	2006-09-26	2006-09-26	ENSG00000169249	ENSG00000169249		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	23019	protein-coding gene	gene with protein product		300028	"U2(RNU2) small nuclear RNA auxiliary factor 1-like 2", "U2 small nuclear RNA auxiliary factor 1-like 2"	U2AF1L2		8586425, 9237760, 15146077	Standard	NM_005089		Approved	U2AF1-RS2, URP	uc004cxg.4	Q15696	OTTHUMG00000021184	ENST00000307771.7:c.1311G>C	chrX.hg19:g.15841227G>C		334.0	0.0	.		338.0	14.0	.	NM_005089	Q14D69	Silent	SNP	ENST00000307771.7	hg19	CCDS14172.1																																																																																			.	.	.	none		0.647	ZRSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055889.1	NM_005089		C	15841227	G	C	15841227	2	2	264	1	0	0	0	0	0	0	0	1	18237	1219	43	4		4	ZRSR2	23	15841227	Silent	SNP	G	TCGA-UZ-A9PS-01A-11D-A42J-10		15841227	139429333	154	16659											
ZRSR2	8233	hgsc.bcm.edu	37	chrX	15841260	15841260	+	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	cggagccggagccggagccgCaggagccgccgcagccggag	7	0	19	15	7	0	0	0	0	0	0	0	5	0	5	6	5	5	2	6	5	0	0			TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chrX:15841260C>G	ENST00000307771.7	+	11	1368	c.1344C>G	c.(1342-1344)cgC>cgG	p.R448R		NM_005089.3	NP_005080.1	Q15696	U2AFM_HUMAN	zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2	448	Arg/Ser-rich (RS domain).				mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	U12-type spliceosomal complex (GO:0005689)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|pre-mRNA 3'-splice site binding (GO:0030628)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(38)|kidney(1)|large_intestine(2)|ovary(2)	48	Hepatocellular(33;0.183)					gccggagccgCAGGAGCCGCC	0.647			"F, S, Mis"		"MDS, CLL"																																p.R448R	NSCLC(197;1631 3042 5741 31152)	Atlas-SNP	.		Rec	yes		X	Xp22.1	8233	"zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2"		L	.	ZRSR2	78	.	0			c.C1344G						PASS	.						7	9	9					X																	15841260		1924	3790	5714	SO:0001819	synonymous_variant	8233	exon11			GAGCCGCAGGAGC	BC050451	CCDS14172.1	Xp22.1	2014-09-17	2006-09-26	2006-09-26	ENSG00000169249	ENSG00000169249		"Zinc fingers, CCCH-type domain containing", "RNA binding motif (RRM) containing"	23019	protein-coding gene	gene with protein product		300028	"U2(RNU2) small nuclear RNA auxiliary factor 1-like 2", "U2 small nuclear RNA auxiliary factor 1-like 2"	U2AF1L2		8586425, 9237760, 15146077	Standard	NM_005089		Approved	U2AF1-RS2, URP	uc004cxg.4	Q15696	OTTHUMG00000021184	ENST00000307771.7:c.1344C>G	chrX.hg19:g.15841260C>G		328.0	0.0	.		336.0	18.0	.	NM_005089	Q14D69	Silent	SNP	ENST00000307771.7	hg19	CCDS14172.1																																																																																			.	.	.	none		0.647	ZRSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055889.1	NM_005089		G	15841260	C	G	15841260	2	3	264	1	0	0	0	0	0	0	0	1	18237	697	25	4		4	ZRSR2	23	15841260	Silent	SNP	C	TCGA-UZ-A9PS-01A-11D-A42J-10	33	15841260	139429300	155	16660											
F9	2158	hgsc.bcm.edu	37	chrX	138643733	138643760	+	Frame_Shift_Del	DEL	ATTCGAATTATTCCTCACCACAACTACA	ATTCGAATTATTCCTCACCACAACTACA	-																															cagagcaaaagcgaaatgtgAttcgaattattcctcaccac																								rs1801202|rs137852250|rs369841886	byFrequency	TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	ATTCGAATTATTCCTCACCACAACTACA	ATTCGAATTATTCCTCACCACAACTACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chrX:138643733_138643760delATTCGAATTATTCCTCACCACAACTACA	ENST00000218099.2	+	8	896_923	c.889_916delATTCGAATTATTCCTCACCACAACTACA	c.(889-918)attcgaattattcctcaccacaactacaatfs	p.IRIIPHHNYN297fs	F9_ENST00000394090.2_Frame_Shift_Del_p.IRIIPHHNYN259fs	NM_000133.3	NP_000124.1	P00740	FA9_HUMAN	coagulation factor IX	297	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)	GCGAAATGTGATTCGAATTATTCCTCACCACAACTACAATGCAGCTAT	0.36																																					p.296_305del		Atlas-Indel,Pindel	.											.	F9	107	.	0			c.888_915del	GRCh37	CD010615|CD920994|CD951701|CM001680|CM940594|CM940595|CM940596|CM940597|CM940598|CM960592	F9	D|M	rs137852250|rs1801202	PASS	.																																			SO:0001589	frameshift_variant	2158	exon8			.	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.889_916delATTCGAATTATTCCTCACCACAACTACA	chrX.hg19:g.138643733_138643760delATTCGAATTATTCCTCACCACAACTACA	ENSP00000218099:p.Ile297fs	184.0	0.0	0		190.0	44.0	0.231579	NM_000133	A8K9N4|F2RM36|Q5FBE1|Q5JYJ8	Frame_Shift_Del	DEL	ENST00000218099.2	hg19	CCDS14666.1																																																																																			.	.	.	none		0.36	F9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058557.1			-	138643760	ATTCGAATTATTCCTCACCACAACTACA	-	138643733	7	5	264	1	0	1	0	1	0	0	0	0	5355	333	12	0	919	0	F9	23	138643733	Frame_Shift_Del	DEL	ATTCGAATTATTCCTCACCACAACTACA	TCGA-UZ-A9PS-01A-11D-A42J-10	122802473	138643733	16626827	156	16661											
MAGEC3	139081	hgsc.bcm.edu	37	chrX	140967157	140967157	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atggaggagaggcacaggctAcaccctttcccttcctgccg	8	8	11	14	1	0	1	0	0	0	1	2	3	2	2	4	4	2	2	4	4	1	3	rs200403296|rs372869684		TCGA-UZ-A9PS-01A-11D-A42J-10	TCGA-UZ-A9PS-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	acba931b-e52d-4487-b13a-7d8c91981263	57691588-0681-41ba-b333-4d612c7f0542	g.chrX:140967157A>G	ENST00000298296.1	+	3	455	c.455A>G	c.(454-456)tAc>tGc	p.Y152C	MAGEC3_ENST00000443323.2_5'Flank|MAGEC3_ENST00000448920.1_5'Flank|MAGEC3_ENST00000536088.1_5'Flank	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	152										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)					GGCACAGGCTACACCCTTTCC	0.567																																					p.Y152C		Atlas-SNP	.											.	MAGEC3	228	.	0			c.A455G						PASS	.						40	35	37					X																	140967157		2130	4297	6427	SO:0001583	missense	139081	exon3			CAGGCTACACCCT	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.455A>G	chrX.hg19:g.140967157A>G	ENSP00000298296:p.Tyr152Cys	261.0	0.0	.		271.0	13.0	.	NM_138702	Q3SYA7|Q5JZ43|Q9BZ80	Missense_Mutation	SNP	ENST00000298296.1	hg19	CCDS14676.1	.	.	.	.	.	.	.	.	.	.	G	0.001	-3.107554	0.00033	.	.	ENSG00000165509	ENST00000298296	T	0.06449	3.3	0.588	-0.678	0.11353	.	.	.	.	.	T	0.02571	0.0078	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45571	-0.9252	8	0.23891	T	0.37	.	.	.	.	.	152	Q8TD91	MAGC3_HUMAN	C	152	ENSP00000298296:Y152C	ENSP00000298296:Y152C	Y	+	2	0	MAGEC3	140794823	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.178000	0.03093	-1.244000	0.02516	-1.723000	0.00705	TAC	.	.	.	weak		0.567	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702		G	140967157	A	G	140967157	3	3	264	1	0	0	0	0	1	0	0	0	9189	391	14	3	465	3	MAGEC3	23	140967157	Missense_Mutation	SNP	A	TCGA-UZ-A9PS-01A-11D-A42J-10	2323424	140967157	14303403	157	16662											
KIAA2013	90231	hgsc.bcm.edu	37	chr1	11983151	11983151	+	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	caatgcatagctgttgtgcaGcacgtcggggtcggcctgga	7	9	15	10	3	0	0	0	0	0	0	2	1	0	1	1	4	4	5	1	4	2	2			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr1:11983151G>A	ENST00000376572.3	-	2	1614	c.1429C>T	c.(1429-1431)Ctg>Ttg	p.L477L	KIAA2013_ENST00000376576.3_Silent_p.L477L	NM_138346.2	NP_612355.1	Q8IYS2	K2013_HUMAN	KIAA2013	477						integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	7	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00149)|all_lung(284;0.00189)|Breast(348;0.00586)|Colorectal(325;0.0062)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0556)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CTGTTGTGCAGCACGTCGGGG	0.612																																					p.L477L		Atlas-SNP	.											.	KIAA2013	25	.	0			c.C1429T						PASS	.						45	42	43					1																	11983151		2202	4299	6501	SO:0001819	synonymous_variant	90231	exon2			TGTGCAGCACGTC	AB095933	CCDS141.1	1p36.22	2011-02-09			ENSG00000116685	ENSG00000116685			28513	protein-coding gene	gene with protein product						12477932	Standard	NM_138346		Approved	MGC33867, RP5-1077B9.1	uc001atk.3	Q8IYS2	OTTHUMG00000002391	ENST00000376572.3:c.1429C>T	chr1.hg19:g.11983151G>A		180.0	0.0	.		133.0	48.0	.	NM_138346	Q5JXC1|Q8IVF8|Q8NDI7|Q9BSY1	Silent	SNP	ENST00000376572.3	hg19	CCDS141.1																																																																																			.	.	.	none		0.612	KIAA2013-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006858.1	NM_138346		A	11983151	G	A	11983151	2	1	265	1	0	0	0	0	0	0	0	1	8274	962	34	2		2	KIAA2013	1	11983151	Silent	SNP	G	TCGA-UZ-A9PU-01A-11D-A42J-10		11983151	237267470	1	16663											
SPEN	23013	hgsc.bcm.edu	37	chr1	16257405	16257405	+	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	ggaagattctgacttcatttCtggtaggatctatgggaagc	10	13	12	6	0	4	2	1	1	3	1	4	5	4	5	0	4	1	1	0	4	4	5			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr1:16257405C>T	ENST00000375759.3	+	11	4874	c.4670C>T	c.(4669-4671)tCt>tTt	p.S1557F		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1557					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)		GACTTCATTTCTGGTAGGATC	0.413																																					p.S1557F		Atlas-SNP	.											.	SPEN	374	.	0			c.C4670T						PASS	.						91	94	93					1																	16257405		2203	4300	6503	SO:0001583	missense	23013	exon11			TCATTTCTGGTAG		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.4670C>T	chr1.hg19:g.16257405C>T	ENSP00000364912:p.Ser1557Phe	184.0	0.0	.		152.0	72.0	.	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	hg19	CCDS164.1	.	.	.	.	.	.	.	.	.	.	C	11.26	1.586812	0.28268	.	.	ENSG00000065526	ENST00000375759	T	0.09163	3.01	5.03	4.1	0.47936	.	.	.	.	.	T	0.08088	0.0202	N	0.19112	0.55	0.09310	N	1	B	0.29716	0.255	B	0.30029	0.11	T	0.28299	-1.0048	9	0.59425	D	0.04	-0.2817	9.0566	0.36410	0.0:0.7735:0.1492:0.0774	.	1557	Q96T58	MINT_HUMAN	F	1557	ENSP00000364912:S1557F	ENSP00000364912:S1557F	S	+	2	0	SPEN	16129992	0.083000	0.21467	0.063000	0.19743	0.447000	0.32167	1.805000	0.38883	1.295000	0.44724	0.563000	0.77884	TCT	.	.	.	none		0.413	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		T	16257405	C	T	16257405	3	4	265	1	0	0	0	0	1	0	0	0	15050	913	32	2	4712	2	SPEN	1	16257405	Missense_Mutation	SNP	C	TCGA-UZ-A9PU-01A-11D-A42J-10	4274254	16257405	232993216	2	16664											
PADI1	29943	hgsc.bcm.edu	37	chr1	17555524	17555524	+	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	tgacgcccaacactcagcctCctgaggagctgtatgtgtgc	8	9	11	13	1	1	2	1	2	0	0	2	3	2	3	3	1	4	2	3	1	2	1			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr1:17555524C>G	ENST00000375471.4	+	8	999	c.907C>G	c.(907-909)Cct>Gct	p.P303A		NM_013358.2	NP_037490.2	Q9ULC6	PADI1_HUMAN	peptidyl arginine deiminase, type I	303					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)	CACTCAGCCTCCTGAGGAGCT	0.632																																					p.P303A	Esophageal Squamous(80;414 1257 4580 27746 50832)	Atlas-SNP	.											.	PADI1	77	.	0			c.C907G						PASS	.						38	29	32					1																	17555524		2202	4298	6500	SO:0001583	missense	29943	exon8			CAGCCTCCTGAGG	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.907C>G	chr1.hg19:g.17555524C>G	ENSP00000364620:p.Pro303Ala	25.0	0.0	.		21.0	9.0	.	NM_013358	A1L4K6|Q70SX6	Missense_Mutation	SNP	ENST00000375471.4	hg19	CCDS178.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.990531	0.74589	.	.	ENSG00000142623	ENST00000375471	T	0.38560	1.13	4.93	4.93	0.64822	Protein-arginine deiminase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.62539	0.2436	M	0.67625	2.065	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.60885	-0.7174	10	0.34782	T	0.22	-26.2146	16.7057	0.85371	0.0:1.0:0.0:0.0	.	303	Q9ULC6	PADI1_HUMAN	A	303	ENSP00000364620:P303A	ENSP00000364620:P303A	P	+	1	0	PADI1	17428111	1.000000	0.71417	0.974000	0.42286	0.908000	0.53690	5.529000	0.67135	2.280000	0.76307	0.555000	0.69702	CCT	.	.	.	none		0.632	PADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006621.1	NM_013358		G	17555524	C	G	17555524	3	3	265	1	0	0	0	0	1	0	0	0	11384	855	30	4	937	4	PADI1	1	17555524	Missense_Mutation	SNP	C	TCGA-UZ-A9PU-01A-11D-A42J-10	1298119	17555524	231695097	3	16665											
LCE4A	199834	hgsc.bcm.edu	37	chr1	152681648	152681648	+	Frame_Shift_Del	DEL	T	T	-																															cctcaaagtgtgcatcctcaTgcccacctccaatctcttcc																										TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr1:152681648delT	ENST00000368777.1	+	2	353	c.97delT	c.(97-99)tgcfs	p.C33fs	LCE4A_ENST00000335535.3_Frame_Shift_Del_p.C33fs			Q5TA78	LCE4A_HUMAN	late cornified envelope 4A	33	Cys-rich.				keratinization (GO:0031424)					endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.116)			TGCATCCTCATGCCCACCTCC	0.592																																					p.S32fs		Atlas-Indel,Pindel	.											.	LCE4A	37	.	0			c.96delA						PASS	.						121	135	130					1																	152681648		2203	4300	6503	SO:0001589	frameshift_variant	199834	exon1			.	BI670517	CCDS1022.1	1q22	2008-02-05	2004-10-11	2004-10-15	ENSG00000187170	ENSG00000187170		"Late cornified envelopes"	16613	protein-coding gene	gene with protein product		612618	"small proline rich-like (epidermal differentiation complex) 4A"	SPRL4A		11698679	Standard	NM_178356		Approved	LEP8	uc001fak.2	Q5TA78	OTTHUMG00000014394	ENST00000368777.1:c.97delT	chr1.hg19:g.152681648delT	ENSP00000357766:p.Cys33fs	250.0	0.0	0		168.0	81.0	0.482143	NM_178356	Q14D97	Frame_Shift_Del	DEL	ENST00000368777.1	hg19	CCDS1022.1																																																																																			.	.	.	none		0.592	LCE4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040048.1	NM_178356		-	152681648	T	-	152681648	7	5	265	1	0	1	0	1	0	0	0	0	8681	1464	51	0	99	0	LCE4A	1	152681648	Frame_Shift_Del	DEL	T	TCGA-UZ-A9PU-01A-11D-A42J-10	135126124	152681648	96568973	4	16666											
OR10K1	391109	hgsc.bcm.edu	37	chr1	158436100	158436100	+	Missense_Mutation	SNP	T	T	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	ccatctcattgtggtaactgTtcactacagttgtgcctctt	7	16	7	11	0	3	0	2	0	2	0	4	0	3	0	2	1	3	3	2	1	2	6	rs202043017		TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr1:158436100T>G	ENST00000289451.2	+	1	829	c.749T>G	c.(748-750)gTt>gGt	p.V250G		NM_001004473.1	NP_001004473.1	Q8NGX5	O10K1_HUMAN	olfactory receptor, family 10, subfamily K, 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)			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)					GTGGTAACTGTTCACTACAGT	0.453																																					p.V250G		Atlas-SNP	.											.	OR10K1	80	.	0			c.T749G						PASS	.						172	148	156					1																	158436100		2203	4300	6503	SO:0001583	missense	391109	exon1			TAACTGTTCACTA	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.749T>G	chr1.hg19:g.158436100T>G	ENSP00000289451:p.Val250Gly	96.0	0.0	.		60.0	28.0	.	NM_001004473	Q6IFS2	Missense_Mutation	SNP	ENST00000289451.2	hg19	CCDS30897.1	.	.	.	.	.	.	.	.	.	.	t	14.94	2.684253	0.47991	.	.	ENSG00000173285	ENST00000289451	T	0.00202	8.56	4.24	4.24	0.50183	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36740	N	0.002436	T	0.00241	0.0007	M	0.75150	2.29	0.42767	D	0.993828	D	0.63880	0.993	D	0.65140	0.932	T	0.73183	-0.4063	10	0.87932	D	0	.	7.3876	0.26891	0.0:0.1011:0.0:0.8989	.	250	Q8NGX5	O10K1_HUMAN	G	250	ENSP00000289451:V250G	ENSP00000289451:V250G	V	+	2	0	OR10K1	156702724	0.016000	0.18221	0.728000	0.30774	0.644000	0.38419	2.073000	0.41519	1.753000	0.51906	0.455000	0.32223	GTT	.	T|1.000;C|0.000	.	alt		0.453	OR10K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046367.1			G	158436100	T	G	158436100	3	3	265	1	0	0	0	0	1	0	0	0	10920	1725	60	5	751	5	OR10K1	1	158436100	Missense_Mutation	SNP	T	TCGA-UZ-A9PU-01A-11D-A42J-10	5754452	158436100	90814521	5	16667											
C1orf49	84066	hgsc.bcm.edu	37	chr1	178483864	178483864	+	Missense_Mutation	SNP	A	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	tacaaagcagttaaacaagaAgggcggtttaccaaagcagg	17	6	11	7	1	0	1	0	0	0	1	0	1	0	1	1	3	5	4	1	3	8	4			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr1:178483864A>C	ENST00000319416.2	+	3	232	c.120A>C	c.(118-120)gaA>gaC	p.E40D	TEX35_ENST00000367639.1_Missense_Mutation_p.E48D|TEX35_ENST00000258298.2_5'UTR|TEX35_ENST00000367643.3_Missense_Mutation_p.E40D|TEX35_ENST00000367642.3_Missense_Mutation_p.E76D|TEX35_ENST00000367641.3_Missense_Mutation_p.E40D	NM_032126.4	NP_115502.2			testis expressed 35																		TTAAACAAGAAGGGCGGTTTA	0.473																																					p.E48D		Atlas-SNP	.											.	TEX35	15	.	0			c.A144C						PASS	.						144	106	119					1																	178483864		2203	4300	6503	SO:0001583	missense	84066	exon3			ACAAGAAGGGCGG	AL136694	CCDS1323.1, CCDS53433.1, CCDS53434.1	1q25.2	2014-01-28	2012-06-29	2012-06-29	ENSG00000240021	ENSG00000240021			25366	protein-coding gene	gene with protein product	"Testis-Specific Conserved gene 24kDa"		"chromosome 1 open reading frame 49"	C1orf49		11230166, 17077512	Standard	NM_032126		Approved	DKFZP564J047, TSC24	uc001glt.2	Q5T0J7	OTTHUMG00000035023	ENST00000319416.2:c.120A>C	chr1.hg19:g.178483864A>C	ENSP00000323795:p.Glu40Asp	135.0	0.0	.		107.0	55.0	.	NM_001170722		Missense_Mutation	SNP	ENST00000319416.2	hg19	CCDS1323.1	.	.	.	.	.	.	.	.	.	.	A	11.45	1.643611	0.29246	.	.	ENSG00000240021	ENST00000319416;ENST00000367643;ENST00000367642;ENST00000367641;ENST00000367639	T;T;T;T;T	0.51574	2.1;2.1;0.7;2.1;2.1	3.72	-1.68	0.08212	.	0.176851	0.27397	N	0.019551	T	0.28499	0.0705	L	0.40543	1.245	0.41184	D	0.986258	B;B;B	0.19073	0.033;0.033;0.033	B;B;B	0.19946	0.027;0.018;0.018	T	0.05920	-1.0856	10	0.45353	T	0.12	-12.1642	0.5174	0.00605	0.4397:0.1788:0.2082:0.1732	.	48;40;40	Q5T0J7-2;Q5T0J7-3;Q5T0J7	.;.;CA049_HUMAN	D	40;40;76;40;48	ENSP00000323795:E40D;ENSP00000356615:E40D;ENSP00000356614:E76D;ENSP00000356613:E40D;ENSP00000356611:E48D	ENSP00000323795:E40D	E	+	3	2	C1orf49	176750487	1.000000	0.71417	0.429000	0.26710	0.053000	0.15095	0.445000	0.21677	-0.316000	0.08690	0.459000	0.35465	GAA	.	.	.	none		0.473	TEX35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084917.1	NM_032126		C	178483864	A	C	178483864	3	2	265	1	0	0	0	0	1	0	0	0	2043	69	3	5	154	5	C1orf49	1	178483864	Missense_Mutation	SNP	A	TCGA-UZ-A9PU-01A-11D-A42J-10	20047764	178483864	70766757	6	16668											
HMCN1	83872	hgsc.bcm.edu	37	chr1	186099715	186099715	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aatgcaatcctgaattgtgaGgtgaaaggagaccccacccc	13	7	10	11	0	0	4	0	3	0	1	1	5	1	4	5	2	1	1	5	2	4	1			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr1:186099715G>A	ENST00000271588.4	+	85	13345	c.13116G>A	c.(13114-13116)gaG>gaA	p.E4372E	HMCN1_ENST00000367492.2_Silent_p.E4372E	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4372	Ig-like C2-type 43.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TGAATTGTGAGGTGAAAGGAG	0.478																																					p.E4372E		Atlas-SNP	.											.	HMCN1	797	.	0			c.G13116A						PASS	.						110	106	108					1																	186099715		2203	4300	6503	SO:0001819	synonymous_variant	83872	exon85			TTGTGAGGTGAAA	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.13116G>A	chr1.hg19:g.186099715G>A		147.0	0.0	.		112.0	53.0	.	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.	.	none		0.478	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186099715	G	A	186099715	2	1	265	1	0	0	0	0	0	0	0	1	7227	991	35	2		2	HMCN1	1	186099715	Silent	SNP	G	TCGA-UZ-A9PU-01A-11D-A42J-10	7615851	186099715	63150906	7	16669											
PLXNA2	5362	hgsc.bcm.edu	37	chr1	208215625	208215625	+	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	tgcagctccagggtgcggatGaaggtcagcaggaacacctt	10	7	14	10	1	1	1	1	1	0	0	2	3	2	3	2	4	5	3	2	4	2	1			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr1:208215625G>C	ENST00000367033.3	-	22	4861	c.4104C>G	c.(4102-4104)ttC>ttG	p.F1368L		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	1368					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)		GGGTGCGGATGAAGGTCAGCA	0.612																																					p.F1368L		Atlas-SNP	.											.	PLXNA2	178	.	0			c.C4104G						PASS	.						118	117	117					1																	208215625		2203	4300	6503	SO:0001583	missense	5362	exon22			GCGGATGAAGGTC	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.4104C>G	chr1.hg19:g.208215625G>C	ENSP00000356000:p.Phe1368Leu	101.0	0.0	.		66.0	26.0	.	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	hg19	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.825465	0.90955	.	.	ENSG00000076356	ENST00000367033	T	0.11169	2.8	5.15	4.24	0.50183	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.27798	0.0684	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.00849	-1.1541	10	0.54805	T	0.06	.	10.7984	0.46474	0.1524:0.0:0.8476:0.0	.	1368	O75051	PLXA2_HUMAN	L	1368	ENSP00000356000:F1368L	ENSP00000356000:F1368L	F	-	3	2	PLXNA2	206282248	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.436000	0.59948	1.169000	0.42739	0.455000	0.32223	TTC	.	.	.	none		0.612	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		C	208215625	G	C	208215625	3	2	265	1	0	0	0	0	1	0	0	0	12127	1281	45	4	1624	4	PLXNA2	1	208215625	Missense_Mutation	SNP	G	TCGA-UZ-A9PU-01A-11D-A42J-10	22115910	208215625	41034996	8	16670											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228404296	228404297	+	Frame_Shift_Ins	INS	-	-	A																															aagtatgaggtgcaggcatcINSggccgggcggcgggtgctcc																								rs116554705	byFrequency	TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr1:228404296_228404297insA	ENST00000422127.1	+	7	2314_2315	c.2270_2271insA	c.(2269-2274)tcggccfs	p.A758fs	OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Frame_Shift_Ins_p.A758fs|C1orf145_ENST00000295012.5_5'Flank|OBSCN_ENST00000570156.2_Frame_Shift_Ins_p.A758fs	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	758	Ig-like 7.				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)				GTGCAGGCATCGGCCGGGCGGC	0.683																																					p.S757fs		Atlas-Indel,Pindel	.											.	OBSCN	2142	.	0			c.2270_2271insA						PASS	.																																			SO:0001589	frameshift_variant	84033	exon7			.	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	Exception_encountered	chr1.hg19:g.228404296_228404297insA	ENSP00000409493:p.Ala758fs	151.0	0.0	0		127.0	52.0	0.409449	NM_001098623	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Frame_Shift_Ins	INS	ENST00000422127.1	hg19	CCDS58065.1																																																																																			.	.	.	none		0.683	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228404297	-	A	228404296	7	5	265	1	0	1	1	0	0	0	0	0	10819	893	31	0	2292	0	OBSCN	1	228404296	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PU-01A-11D-A42J-10	20188671	228404296	20846325	9	16671											
FOSL2	2355	hgsc.bcm.edu	37	chr2	28634997	28634997	+	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	tcggtgggcgctgtagtggtGaaacaggagcccctggaaga	9	7	17	8	2	0	2	0	1	0	1	1	4	0	4	2	5	2	2	2	5	3	1			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:28634997G>C	ENST00000264716.4	+	4	1526	c.663G>C	c.(661-663)gtG>gtC	p.V221V	FOSL2_ENST00000545753.1_Silent_p.V182V|FOSL2_ENST00000379619.1_Silent_p.V213V	NM_005253.3	NP_005244.1	P15408	FOSL2_HUMAN	FOS-like antigen 2	221					cell death (GO:0008219)|cellular response to hormone stimulus (GO:0032870)|female pregnancy (GO:0007565)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to progesterone (GO:0032570)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	14	Acute lymphoblastic leukemia(172;0.155)					CTGTAGTGGTGAAACAGGAGC	0.682																																					p.V221V		Atlas-SNP	.											.	FOSL2	39	.	0			c.G663C						PASS	.						33	37	36					2																	28634997		2203	4297	6500	SO:0001819	synonymous_variant	2355	exon4			AGTGGTGAAACAG		CCDS1766.1	2p23.3	2013-01-10			ENSG00000075426	ENSG00000075426		"basic leucine zipper proteins"	3798	protein-coding gene	gene with protein product		601575					Standard	NM_005253		Approved	FRA2, FLJ23306	uc002rma.3	P15408	OTTHUMG00000097832	ENST00000264716.4:c.663G>C	chr2.hg19:g.28634997G>C		87.0	0.0	.		80.0	28.0	.	NM_005253	B2RD58|B3KP27|B4DYV4|Q6FG46	Silent	SNP	ENST00000264716.4	hg19	CCDS1766.1																																																																																			.	.	.	none		0.682	FOSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215116.2	NM_005253		C	28634997	G	C	28634997	2	2	265	1	0	0	0	0	0	0	0	1	5995	1277	45	4		4	FOSL2	2	28634997	Silent	SNP	G	TCGA-UZ-A9PU-01A-11D-A42J-10		28634997	214564376	10	16672											
BIRC6	57448	hgsc.bcm.edu	37	chr2	32824826	32824826	+	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	gttctaataactggtccagcGgacaccccttatgcaaatgg	11	10	9	11	1	1	0	0	0	1	0	2	1	2	1	3	3	3	2	3	3	4	4	rs144649481		TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:32824826G>T	ENST00000421745.2	+	70	13985	c.13851G>T	c.(13849-13851)gcG>gcT	p.A4617A		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	4617	Ubiquitin-conjugating.				apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					CTGGTCCAGCGGACACCCCTT	0.373																																					p.A4617A	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											BIRC6_ENST00000421745,colon,carcinoma,0,2	BIRC6	838	.	0			c.G13851T						PASS	.						117	113	114					2																	32824826		2203	4300	6503	SO:0001819	synonymous_variant	57448	exon70			TCCAGCGGACACC	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.13851G>T	chr2.hg19:g.32824826G>T		71.0	0.0	.		68.0	3.0	.	NM_016252	Q9ULD1	Silent	SNP	ENST00000421745.2	hg19	CCDS33175.2																																																																																			.	G|1.000;A|0.000	.	alt		0.373	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		T	32824826	G	T	32824826	2	4	265	1	0	0	0	0	0	0	0	1	1438	1103	39	4		4	BIRC6	2	32824826	Silent	SNP	G	TCGA-UZ-A9PU-01A-11D-A42J-10	4189829	32824826	210374547	11	16673											
LHCGR	3973	hgsc.bcm.edu	37	chr2	48982764	48982764	+	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	gtggcagcggcggctgcagcAgcagcagcagcttcagcagc	8	4	16	13	2	1	0	1	0	0	0	1	0	1	0	0	3	9	9	0	3	0	1	rs4539842		TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:48982764A>T	ENST00000294954.7	-	1	68	c.47T>A	c.(46-48)cTg>cAg	p.L16Q	LHCGR_ENST00000403273.1_Missense_Mutation_p.L16Q|STON1-GTF2A1L_ENST00000402114.2_Intron|LHCGR_ENST00000405626.1_Missense_Mutation_p.L16Q|LHCGR_ENST00000344775.3_Missense_Mutation_p.L16Q|LHCGR_ENST00000401907.1_Missense_Mutation_p.L16Q	NM_000233.3	NP_000224.2	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor	16					activation of adenylate cyclase activity (GO:0007190)|cellular response to gonadotropin stimulus (GO:0071371)|cognition (GO:0050890)|development of secondary male sexual characteristics (GO:0046544)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|ovarian follicle development (GO:0001541)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|regulation of steroid hormone biosynthetic process (GO:0090030)|seminiferous tubule development (GO:0072520)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	choriogonadotropin hormone binding (GO:0038106)|choriogonadotropin hormone receptor activity (GO:0035472)|luteinizing hormone receptor activity (GO:0004964)			NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(3)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	56		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Buserelin(DB06719)|Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)	cggctgcagcagcagcagcag	0.721																																					p.L16Q		Atlas-SNP	.											.	LHCGR	154	.	0			c.T47A						PASS	.						1	3	2					2																	48982764		911	1841	2752	SO:0001583	missense	3973	exon1			TGCAGCAGCAGCA		CCDS1842.1	2p21	2012-08-10			ENSG00000138039	ENSG00000138039		"GPCR / Class A : Gonadotropin and TSH receptors"	6585	protein-coding gene	gene with protein product		152790	"hypergonadotropic hypogonadism"	HHG			Standard	NM_000233		Approved	LHR, LCGR, LGR2, ULG5	uc002rwu.4	P22888	OTTHUMG00000129257	ENST00000294954.7:c.47T>A	chr2.hg19:g.48982764A>T	ENSP00000294954:p.Leu16Gln	54.0	0.0	.		23.0	5.0	.	NM_000233	Q14751|Q15996|Q9UEW9	Missense_Mutation	SNP	ENST00000294954.7	hg19	CCDS1842.1	.	.	.	.	.	.	.	.	.	.	A	16.68	3.191104	0.58017	.	.	ENSG00000138039	ENST00000344775;ENST00000294954;ENST00000405626;ENST00000403273;ENST00000401907	D;D;D;D;D	0.85702	-2.02;-2.02;-2.02;-2.02;-2.02	4.18	4.18	0.49190	.	1.158800	0.06471	N	0.731104	D	0.83594	0.5288	L	0.29908	0.895	0.28253	N	0.925194	D	0.55172	0.97	P	0.51453	0.67	T	0.72527	-0.4266	9	.	.	.	.	9.5009	0.39017	1.0:0.0:0.0:0.0	rs4539842	16	P22888	LSHR_HUMAN	Q	16	ENSP00000344301:L16Q;ENSP00000294954:L16Q;ENSP00000386033:L16Q;ENSP00000385847:L16Q;ENSP00000385406:L16Q	.	L	-	2	0	LHCGR	48836268	0.561000	0.26578	0.862000	0.33874	0.243000	0.25628	1.821000	0.39041	1.736000	0.51660	0.421000	0.28195	CTG	.	.	.	weak		0.721	LHCGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251364.4	NM_000233.3		T	48982764	A	T	48982764	3	4	265	1	0	0	0	0	1	0	0	0	8769	188	7	5	2096	5	LHCGR	2	48982764	Missense_Mutation	SNP	A	TCGA-UZ-A9PU-01A-11D-A42J-10	16157938	48982764	194216609	12	16674											
NRXN1	9378	hgsc.bcm.edu	37	chr2	50850545	50850545	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgcttcaaaggcccctgaTcccaaattaatgaccagaga	14	8	8	11	0	1	3	1	2	0	1	2	4	2	3	4	1	1	1	4	1	3	2			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:50850545T>C	ENST00000406316.2	-	6	2517	c.1041A>G	c.(1039-1041)ggA>ggG	p.G347G	NRXN1_ENST00000402717.3_Silent_p.G347G|NRXN1_ENST00000404971.1_Silent_p.G380G|NRXN1_ENST00000406859.3_Silent_p.G347G|NRXN1_ENST00000401669.2_Silent_p.G347G|NRXN1_ENST00000405472.3_Silent_p.G347G|NRXN1_ENST00000331040.5_5'UTR	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	347	Laminin G-like 2. {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)			AGGCCCCTGATCCCAAATTAA	0.463																																					p.G380G		Atlas-SNP	.											.	NRXN1	1118	.	0			c.A1140G						PASS	.						117	111	113					2																	50850545		1897	4128	6025	SO:0001819	synonymous_variant	9378	exon7			CCCTGATCCCAAA	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.1041A>G	chr2.hg19:g.50850545T>C		91.0	0.0	.		67.0	25.0	.	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	hg19	CCDS54360.1																																																																																			.	.	.	none		0.463	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			C	50850545	T	C	50850545	2	2	265	1	0	0	0	0	0	0	0	1	10672	1422	50	3		3	NRXN1	2	50850545	Silent	SNP	T	TCGA-UZ-A9PU-01A-11D-A42J-10	1867781	50850545	192348828	13	16675											
ALMS1	7840	hgsc.bcm.edu	37	chr2	73676852	73676852	+	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	tacccacaggtgttatcagaCagtcatctacctgaagagag	13	9	9	10	0	3	3	2	1	1	2	3	4	3	3	2	1	2	1	2	1	4	3			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:73676852C>G	ENST00000264448.6	+	8	3306	c.3195C>G	c.(3193-3195)gaC>gaG	p.D1065E	ALMS1_ENST00000377715.1_Missense_Mutation_p.D1065E|ALMS1_ENST00000409009.1_Missense_Mutation_p.D1023E	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	1065	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						TGTTATCAGACAGTCATCTAC	0.488																																					p.D1065E		Atlas-SNP	.											.	ALMS1	384	.	0			c.C3195G						PASS	.						122	124	123					2																	73676852		1911	4127	6038	SO:0001583	missense	7840	exon8			ATCAGACAGTCAT	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.3195C>G	chr2.hg19:g.73676852C>G	ENSP00000264448:p.Asp1065Glu	176.0	0.0	.		150.0	48.0	.	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	C	13.96	2.393036	0.42410	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.20200	2.97;2.96;2.09	4.49	-6.07	0.02158	.	0.685138	0.13351	N	0.394421	T	0.31263	0.0791	L	0.52573	1.65	0.09310	N	1	D;P;D	0.76494	0.982;0.566;0.999	P;B;D	0.67548	0.802;0.138;0.952	T	0.10405	-1.0631	10	0.29301	T	0.29	.	13.7332	0.62802	0.0:0.1772:0.0:0.8228	.	1065;1023;1065	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	E	1023;1065;1065	ENSP00000386627:D1023E;ENSP00000264448:D1065E;ENSP00000366944:D1065E	ENSP00000264448:D1065E	D	+	3	2	ALMS1	73530360	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	-3.161000	0.00577	-1.296000	0.02353	0.591000	0.81541	GAC	.	.	.	none		0.488	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		G	73676852	C	G	73676852	3	3	265	1	0	0	0	0	1	0	0	0	535	477	17	4	3225	4	ALMS1	2	73676852	Missense_Mutation	SNP	C	TCGA-UZ-A9PU-01A-11D-A42J-10	22826307	73676852	169522521	14	16676			1	39		3	3	4073	N	GG_C_AGTGATGCC	3.201149e-05
ALMS1	7840	hgsc.bcm.edu	37	chr2	73680903	73680911	+	In_Frame_Del	DEL	AGTGATGCC	AGTGATGCC	-																															tcataaaaagtgattcaagtAgtgatgccagtgatggaaat																										TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	AGTGATGCC	AGTGATGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:73680903_73680911delAGTGATGCC	ENST00000264448.6	+	8	7357_7365	c.7246_7254delAGTGATGCC	c.(7246-7254)agtgatgccdel	p.SDA2416del	ALMS1-IT1_ENST00000441587.2_RNA|ALMS1_ENST00000377715.1_In_Frame_Del_p.SDA2416del|ALMS1_ENST00000409009.1_In_Frame_Del_p.SDA2374del	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2416					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						TGATTCAAGTAGTGATGCCAGTGATGGAA	0.392																																					p.2415_2418del		Atlas-Indel,Pindel	.											.	ALMS1	384	.	0			c.7245_7253del						PASS	.																																			SO:0001651	inframe_deletion	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.7246_7254delAGTGATGCC	chr2.hg19:g.73680903_73680911delAGTGATGCC	ENSP00000264448:p.Ser2416_Ala2418del	122.0	0.0	0		77.0	23.0	0.298701	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	In_Frame_Del	DEL	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.	.	none		0.392	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		-	73680911	AGTGATGCC	-	73680903	7	5	265	1	0	1	0	1	0	0	0	0	535	420	15	0	7276	0	ALMS1	2	73680903	In_Frame_Del	DEL	AGTGATGCC	TCGA-UZ-A9PU-01A-11D-A42J-10	4051	73680903	169518470	15	16677			1	39		3	3	4073	N	GG_C_AGTGATGCC	3.201149e-05
ALMS1	7840	hgsc.bcm.edu	37	chr2	73680924	73680925	+	Missense_Mutation	DNP	GG	GG	TT																															gtgatgccagtgatggaaatGgttcctgctcgtgggacagt																										TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:73680924_73680925GG>TT	ENST00000264448.6	+	8	7378_7379	c.7267_7268GG>TT	c.(7267-7269)GGt>TTt	p.G2423F	ALMS1-IT1_ENST00000441587.2_RNA|ALMS1_ENST00000377715.1_Missense_Mutation_p.G2423F|ALMS1_ENST00000409009.1_Missense_Mutation_p.G2381F	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2423					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						TGATGGAAATGGTTCCTGCTCG	0.381																																					p.G2423C|p.G2423V		Atlas-SNP	.											.	ALMS1	384	.	0			c.G7267T|c.G7268T						PASS	.																																			SO:0001583	missense	7840	exon8			GGAAATGGTTCCT|GAAATGGTTCCTG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	Exception_encountered	chr2.hg19:g.73680924_73680925delinsTT	ENSP00000264448:p.Gly2423Phe	136.0	0.0	.		78.0	30.0	.	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.	.	none		0.381	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		TT	73680925	GG	TT	73680924	3	4	265	1	0	0	0	0	1	0	0	0	535	1348	47	4	7297	4	ALMS1	2	73680924	Missense_Mutation	DNP	GG	TCGA-UZ-A9PU-01A-11D-A42J-10	21	73680924	169518449	16	16678			1	39		3	3	4073	N	GG_C_AGTGATGCC	3.201149e-05
POLR1A	25885	hgsc.bcm.edu	37	chr2	86302371	86302371	+	Missense_Mutation	SNP	T	T	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	tggctgtgggtaggtcagttTtgtggcaaacacctggaaat	9	12	14	6	0	1	0	1	0	0	0	1	1	1	1	1	5	1	4	1	5	3	3			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:86302371T>G	ENST00000263857.6	-	12	1771	c.1393A>C	c.(1393-1395)Aaa>Caa	p.K465Q	POLR1A_ENST00000409681.1_Missense_Mutation_p.K465Q			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	465					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						TAGGTCAGTTTTGTGGCAAAC	0.493																																					p.K465Q		Atlas-SNP	.											.	POLR1A	137	.	0			c.A1393C						PASS	.						22	22	22					2																	86302371		1939	4127	6066	SO:0001583	missense	25885	exon12			TCAGTTTTGTGGC	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.1393A>C	chr2.hg19:g.86302371T>G	ENSP00000263857:p.Lys465Gln	74.0	0.0	.		63.0	23.0	.	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	hg19	CCDS42706.1	.	.	.	.	.	.	.	.	.	.	T	18.61	3.660500	0.67586	.	.	ENSG00000068654	ENST00000263857;ENST00000409681	T;T	0.69306	-0.39;-0.39	5.01	5.01	0.66863	RNA polymerase, alpha subunit (1);RNA polymerase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.80308	0.4599	M	0.70275	2.135	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.82717	-0.0319	10	0.72032	D	0.01	-24.511	14.5645	0.68165	0.0:0.0:0.0:1.0	.	465	O95602	RPA1_HUMAN	Q	465	ENSP00000263857:K465Q;ENSP00000386300:K465Q	ENSP00000263857:K465Q	K	-	1	0	POLR1A	86155882	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.448000	0.80631	2.107000	0.64212	0.533000	0.62120	AAA	.	.	.	none		0.493	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425		G	86302371	T	G	86302371	3	3	265	1	0	0	0	0	1	0	0	0	12216	1850	64	5	3861	5	POLR1A	2	86302371	Missense_Mutation	SNP	T	TCGA-UZ-A9PU-01A-11D-A42J-10	12621447	86302371	156897002	17	16679											
XIRP2	129446	hgsc.bcm.edu	37	chr2	168106667	168106667	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcaaagcaagagattacacAgaacaaatctttcttttcct	15	13	4	9	0	3	2	1	0	2	2	4	3	4	2	1	0	3	1	1	0	5	5			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:168106667A>G	ENST00000409195.1	+	9	8854	c.8765A>G	c.(8764-8766)cAg>cGg	p.Q2922R	XIRP2_ENST00000409273.1_Missense_Mutation_p.Q2700R|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.Q2922R|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409605.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2747					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						GAGATTACACAGAACAAATCT	0.373																																					p.Q2922R		Atlas-SNP	.											XIRP2,colon,carcinoma,0,1	XIRP2	914	.	0			c.A8765G						PASS	.						81	77	78					2																	168106667		1824	4081	5905	SO:0001583	missense	129446	exon9			TTACACAGAACAA	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.8765A>G	chr2.hg19:g.168106667A>G	ENSP00000386840:p.Gln2922Arg	355.0	0.0	.		254.0	110.0	.	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	A	13.30	2.196928	0.38806	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.02472	4.28;4.28;4.29	6.02	4.86	0.63082	.	0.687182	0.14362	N	0.324364	T	0.05960	0.0155	L	0.60455	1.87	0.32557	N	0.531638	P;P;P	0.46142	0.799;0.873;0.873	B;P;P	0.44990	0.276;0.466;0.466	T	0.19910	-1.0291	10	0.28530	T	0.3	-0.7943	12.6473	0.56742	0.8617:0.1383:0.0:0.0	.	2747;2747;2700	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	R	2922;2922;2700;336	ENSP00000386840:Q2922R;ENSP00000295237:Q2922R;ENSP00000387255:Q2700R	ENSP00000295237:Q2922R	Q	+	2	0	XIRP2	167814913	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.353000	0.59411	1.082000	0.41137	0.533000	0.62120	CAG	.	.	.	none		0.373	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		G	168106667	A	G	168106667	3	3	265	1	0	0	0	0	1	0	0	0	17442	188	7	3	8795	3	XIRP2	2	168106667	Missense_Mutation	SNP	A	TCGA-UZ-A9PU-01A-11D-A42J-10	81804296	168106667	75092706	18	16680											
SLC40A1	30061	hgsc.bcm.edu	37	chr2	190439896	190439896	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acaacactcacctttaagtcTagcattcttgtccacccagt	11	12	4	14	0	3	0	1	0	2	0	4	0	4	0	3	0	2	1	3	0	3	5	rs387907374		TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:190439896T>C	ENST00000261024.2	-	3	688	c.262A>G	c.(262-264)Aga>Gga	p.R88G	SLC40A1_ENST00000418714.1_5'UTR	NM_014585.5	NP_055400.1	Q9NP59	S40A1_HUMAN	solute carrier family 40 (iron-regulated transporter), member 1	88					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)			CCTTTAAGTCTAGCATTCTTG	0.478																																					p.R88G		Atlas-SNP	.											.	SLC40A1	51	.	0			c.A262G	GRCh37	CM076533	SLC40A1	M		PASS	.						258	271	267					2																	190439896		2203	4300	6503	SO:0001583	missense	30061	exon3			TAAGTCTAGCATT	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.262A>G	chr2.hg19:g.190439896T>C	ENSP00000261024:p.Arg88Gly	142.0	0.0	.		113.0	41.0	.	NM_014585	Q6FI62|Q7Z4F8|Q8IVB2|Q9NRL0	Missense_Mutation	SNP	ENST00000261024.2	hg19	CCDS2299.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.628792	0.87560	.	.	ENSG00000138449	ENST00000261024;ENST00000427241	D;D	0.96041	-3.89;-3.89	5.16	3.95	0.45737	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.97399	0.9149	M	0.82323	2.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.97680	1.0172	10	0.87932	D	0	-28.426	12.2975	0.54857	0.0:0.0:0.141:0.859	.	88;88	A8K7Y1;Q9NP59	.;S40A1_HUMAN	G	88	ENSP00000261024:R88G;ENSP00000390005:R88G	ENSP00000261024:R88G	R	-	1	2	SLC40A1	190148141	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.987000	0.56944	2.177000	0.69029	0.533000	0.62120	AGA	.	.	.	none		0.478	SLC40A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255916.2			C	190439896	T	C	190439896	3	2	265	1	0	0	0	0	1	0	0	0	14641	1530	53	3	1477	3	SLC40A1	2	190439896	Missense_Mutation	SNP	T	TCGA-UZ-A9PU-01A-11D-A42J-10	22333229	190439896	52759477	19	16681											
BMPR2	659	hgsc.bcm.edu	37	chr2	203420241	203420241	+	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	cacaacaaccacaaacaccaCaggactcacgccaagtactg	17	3	5	16	1	1	0	1	0	0	0	1	1	1	1	3	1	4	1	3	1	5	1			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:203420241C>T	ENST00000374580.4	+	12	2392	c.1853C>T	c.(1852-1854)aCa>aTa	p.T618I	BMPR2_ENST00000374574.2_Intron	NM_001204.6	NP_001195.2	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)	618	Poly-Thr.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						ACAAACACCACAGGACTCACG	0.463																																					p.T618I		Atlas-SNP	.											.	BMPR2	142	.	0			c.C1853T						PASS	.						159	137	144					2																	203420241		2203	4300	6503	SO:0001583	missense	659	exon12			ACACCACAGGACT	Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217			1078	protein-coding gene	gene with protein product		600799	"primary pulmonary hypertension 1"	PPH1		7791754	Standard	NM_001204		Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374580.4:c.1853C>T	chr2.hg19:g.203420241C>T	ENSP00000363708:p.Thr618Ile	93.0	0.0	.		95.0	29.0	.	NM_001204	Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	Missense_Mutation	SNP	ENST00000374580.4	hg19	CCDS33361.1	.	.	.	.	.	.	.	.	.	.	C	14.47	2.545630	0.45280	.	.	ENSG00000204217	ENST00000374580	D	0.81908	-1.55	5.74	5.74	0.90152	.	0.070435	0.64402	D	0.000018	T	0.74711	0.3752	L	0.27053	0.805	0.80722	D	1	P	0.41313	0.745	B	0.34301	0.179	T	0.76195	-0.3048	10	0.44086	T	0.13	.	19.9329	0.97127	0.0:1.0:0.0:0.0	.	618	Q13873	BMPR2_HUMAN	I	618	ENSP00000363708:T618I	ENSP00000363708:T618I	T	+	2	0	BMPR2	203128486	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.062000	0.57492	2.714000	0.92807	0.650000	0.86243	ACA	.	.	.	none		0.463	BMPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257743.1	NM_001204		T	203420241	C	T	203420241	3	4	265	1	0	0	0	0	1	0	0	0	1471	478	17	2	1899	2	BMPR2	2	203420241	Missense_Mutation	SNP	C	TCGA-UZ-A9PU-01A-11D-A42J-10	12980345	203420241	39779132	20	16682											
CPS1	1373	hgsc.bcm.edu	37	chr2	211523412	211523412	+	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	gtcaaaggaaatgatgtcttGgtaagaaatgccaaggtgcc	14	9	12	6	0	2	2	1	1	1	1	2	3	2	3	2	3	2	1	2	3	5	2			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:211523412G>C	ENST00000233072.5	+	31	3952	c.3756G>C	c.(3754-3756)ttG>ttC	p.L1252F	CPS1_ENST00000430249.2_Splice_Site_p.L1258F|CPS1_ENST00000451903.2_Splice_Site_p.L801F	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	1252	ATP-grasp 2.				anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	ATGATGTCTTGGTAAGAAATG	0.443																																					p.L1258F		Atlas-SNP	.											.	CPS1	485	.	0			c.G3774C						PASS	.						93	85	88					2																	211523412		2203	4300	6503	SO:0001630	splice_region_variant	1373	exon32			TGTCTTGGTAAGA	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.3756+1G>C	chr2.hg19:g.211523412G>C		53.0	0.0	.		42.0	10.0	.	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	hg19	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.612712	0.87258	.	.	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	D;D;D	0.97256	-4.31;-4.31;-4.31	5.76	5.76	0.90799	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);	0.056700	0.64402	D	0.000001	D	0.94066	0.8098	N	0.04203	-0.255	0.80722	D	1	P;P	0.41080	0.737;0.737	P;P	0.46144	0.505;0.505	D	0.95123	0.8248	10	0.87932	D	0	-6.542	19.9595	0.97236	0.0:0.0:1.0:0.0	.	1262;1252	Q59HF8;P31327	.;CPSM_HUMAN	F	1258;1260;1252;801	ENSP00000402608:L1258F;ENSP00000233072:L1252F;ENSP00000406136:L801F	ENSP00000233072:L1252F	L	+	3	2	CPS1	211231657	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	9.118000	0.94355	2.706000	0.92434	0.563000	0.77884	TTG	.	.	.	none		0.443	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5		Missense_Mutation	C	211523412	G	C	211523412	5	2	265	1	0	0	0	0	0	0	1	0	3825	1362	47	4	3900	4	CPS1	2	211523412	Splice_Site	SNP	G	TCGA-UZ-A9PU-01A-11D-A42J-10	8103171	211523412	31675961	21	16683											
KIAA1486	57624	hgsc.bcm.edu	37	chr2	226491661	226491661	+	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	gaggaactgaaagtccgaagCcacagcacggagccattacc	14	4	11	12	2	0	1	0	1	0	0	1	5	1	3	4	2	5	1	4	2	4	1			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:226491661C>A	ENST00000272907.6	+	5	2060	c.1647C>A	c.(1645-1647)agC>agA	p.S549R	NYAP2_ENST00000409269.2_Missense_Mutation_p.P84T	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	549					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												AAGTCCGAAGCCACAGCACGG	0.433																																					p.S549R		Atlas-SNP	.											.	.	.	.	0			c.C1647A						PASS	.						26	28	27					2																	226491661		1893	4105	5998	SO:0001583	missense	57624	exon5			CCGAAGCCACAGC	AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"KIAA1486"	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.1647C>A	chr2.hg19:g.226491661C>A	ENSP00000272907:p.Ser549Arg	335.0	0.0	.		221.0	96.0	.	NM_020864	A2RRN4|Q96NL2	Missense_Mutation	SNP	ENST00000272907.6	hg19	CCDS46529.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.16|13.16	2.155070|2.155070	0.38021|0.38021	.|.	.|.	ENSG00000144460|ENSG00000144460	ENST00000409269|ENST00000272907	.|T	.|0.33438	.|1.41	5.78|5.78	2.04|2.04	0.26737|0.26737	.|.	.|0.224065	.|0.48286	.|D	.|0.000186	T|T	0.42040|0.42040	0.1185|0.1185	L|L	0.40543|0.40543	1.245|1.245	0.24652|0.24652	N|N	0.993512|0.993512	P|D;P	0.39326|0.71674	0.668|0.998;0.822	B|D;B	0.43867|0.76575	0.434|0.988;0.359	T|T	0.23013|0.23013	-1.0200|-1.0200	8|10	0.21014|0.66056	T|D	0.42|0.02	-24.7943|-24.7943	9.9677|9.9677	0.41734|0.41734	0.0:0.6438:0.0:0.3562|0.0:0.6438:0.0:0.3562	.|.	84|63;549	Q9P242-2|Q9P242-3;Q9P242	.|.;K1486_HUMAN	T|R	84|549	.|ENSP00000272907:S549R	ENSP00000386437:P84T|ENSP00000272907:S549R	P|S	+|+	1|3	0|2	KIAA1486|KIAA1486	226199905|226199905	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.995000|0.995000	0.86356|0.86356	0.765000|0.765000	0.26546|0.26546	0.095000|0.095000	0.17434|0.17434	-0.136000|-0.136000	0.14681|0.14681	CCA|AGC	.	.	.	none		0.433	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864		A	226491661	C	A	226491661	3	1	265	1	0	0	0	0	1	0	0	0	8244	738	26	4	1661	4	KIAA1486	2	226491661	Missense_Mutation	SNP	C	TCGA-UZ-A9PU-01A-11D-A42J-10	14968249	226491661	16707712	22	16684											
PID1	55022	hgsc.bcm.edu	37	chr2	229890502	229890502	+	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	cgagcttgctctcgcactccAcggcgtggcagtccatctgg	5	9	12	15	4	2	0	0	0	2	0	5	1	4	0	2	3	2	4	2	3	0	1			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:229890502A>T	ENST00000354069.6	-	3	629	c.599T>A	c.(598-600)gTg>gAg	p.V200E	PID1_ENST00000392054.3_Missense_Mutation_p.V198E|PID1_ENST00000392055.3_Missense_Mutation_p.V167E|PID1_ENST00000482518.2_Intron|PID1_ENST00000409462.1_Missense_Mutation_p.V118E			Q7Z2X4	PCLI1_HUMAN	phosphotyrosine interaction domain containing 1	200	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				cellular response to cytokine stimulus (GO:0071345)|cellular response to fatty acid (GO:0071398)|cellular response to interleukin-6 (GO:0071354)|cellular response to leptin stimulus (GO:0044320)|cellular response to tumor necrosis factor (GO:0071356)|energy reserve metabolic process (GO:0006112)|mitochondrion morphogenesis (GO:0070584)|negative regulation of ATP biosynthetic process (GO:2001170)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of glucose import in response to insulin stimulus (GO:2001274)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of mitochondrial DNA replication (GO:0090298)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of fat cell proliferation (GO:0070346)|positive regulation of gene expression (GO:0010628)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of mitochondrial fusion (GO:0010635)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of reactive oxygen species metabolic process (GO:2000377)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(4)|endometrium(3)|large_intestine(5)|lung(8)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	26		Renal(207;0.0112)|all_lung(227;0.0191)|Lung NSC(271;0.0851)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.171)		Epithelial(121;3.08e-11)|all cancers(144;2.28e-08)|LUSC - Lung squamous cell carcinoma(224;0.0145)|Lung(261;0.0189)		CTCGCACTCCACGGCGTGGCA	0.592																																					p.V198E		Atlas-SNP	.											.	PID1	43	.	0			c.T593A						PASS	.						132	115	121					2																	229890502		2203	4300	6503	SO:0001583	missense	55022	exon4			CACTCCACGGCGT	AK096636	CCDS2471.1, CCDS42830.1	2q36.3	2007-02-02			ENSG00000153823	ENSG00000153823			26084	protein-coding gene	gene with protein product		612930				17124247, 16815647, 15221005	Standard	NM_001100818		Approved	NYGGF4, FLJ20701	uc002vps.4	Q7Z2X4	OTTHUMG00000133191	ENST00000354069.6:c.599T>A	chr2.hg19:g.229890502A>T	ENSP00000283937:p.Val200Glu	108.0	0.0	.		82.0	30.0	.	NM_017933	B3KU82|Q68CJ2|Q6ZUS3|Q8IXL0|Q9NWP6	Missense_Mutation	SNP	ENST00000354069.6	hg19		.	.	.	.	.	.	.	.	.	.	A	25.7	4.667104	0.88251	.	.	ENSG00000153823	ENST00000392054;ENST00000409462;ENST00000392055;ENST00000542363;ENST00000354069	.	.	.	6.07	6.07	0.98685	Phosphotyrosine interaction domain (2);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	T	0.78266	0.4256	M	0.69823	2.125	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;1.0;1.0	D;D;D;D	0.87578	0.991;0.991;0.998;0.998	T	0.78183	-0.2303	8	.	.	.	-38.6448	15.8218	0.78654	1.0:0.0:0.0:0.0	.	118;167;198;200	Q7Z2X4-3;Q7Z2X4-4;Q7Z2X4-2;Q7Z2X4	.;.;.;PCLI1_HUMAN	E	198;118;167;200;200	.	.	V	-	2	0	PID1	229598746	1.000000	0.71417	0.906000	0.35671	0.997000	0.91878	8.854000	0.92228	2.326000	0.78906	0.533000	0.62120	GTG	.	.	.	none		0.592	PID1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000331810.2	NM_017933		T	229890502	A	T	229890502	3	4	265	1	0	0	0	0	1	0	0	0	11889	159	6	5	157	5	PID1	2	229890502	Missense_Mutation	SNP	A	TCGA-UZ-A9PU-01A-11D-A42J-10	3398841	229890502	13308871	23	16685											
DHX30	22907	hgsc.bcm.edu	37	chr3	47891247	47891253	+	Frame_Shift_Del	DEL	GTGCACA	GTGCACA	-																															tgctgctgaccgacggggacGtgcacatccgtggtgggtgc																										TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	GTGCACA	GTGCACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr3:47891247_47891253delGTGCACA	ENST00000445061.1	+	21	3726_3732	c.3319_3325delGTGCACA	c.(3319-3327)gtgcacatcfs	p.VHI1107fs	MIR1226_ENST00000408658.1_RNA|DHX30_ENST00000348968.4_Frame_Shift_Del_p.VHI1079fs|DHX30_ENST00000457607.1_Frame_Shift_Del_p.VHI1135fs|DHX30_ENST00000446256.2_Frame_Shift_Del_p.VHI1068fs	NM_138615.2	NP_619520.1	Q7L2E3	DHX30_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 30	1107						cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|large_intestine(11)|lung(13)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	37				BRCA - Breast invasive adenocarcinoma(193;0.000696)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		CGACGGGGACGTGCACATCCGTGGTGG	0.643											OREG0015550	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.1106_1108del		Atlas-Indel,Pindel	.											.	DHX30	101	.	0			c.3318_3324del						PASS	.																																			SO:0001589	frameshift_variant	22907	exon21			.	AB020697	CCDS2759.1	3p24.3-p22.1	2013-07-16	2013-07-16	2003-06-13	ENSG00000132153	ENSG00000132153		"DEAH-boxes"	16716	protein-coding gene	gene with protein product			"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 30", "DEAH (Asp-Glu-Ala-His) box polypeptide 30"	DDX30		10048485, 18022663	Standard	NM_138615		Approved	KIAA0890, FLJ11214	uc003cru.3	Q7L2E3	OTTHUMG00000133522	ENST00000445061.1:c.3319_3325delGTGCACA	chr3.hg19:g.47891247_47891253delGTGCACA	ENSP00000405620:p.Val1107fs	80.0	0.0	0	950	62.0	27.0	0.435484	NM_138615	A8K5F1|O94965|Q7Z753|Q96CH4|Q9NUQ0	Frame_Shift_Del	DEL	ENST00000445061.1	hg19	CCDS2759.1																																																																																			.	.	.	none		0.643	DHX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257495.2	NM_138615		-	47891253	GTGCACA	-	47891247	7	5	265	1	0	1	0	1	0	0	0	0	4506	1145	40	0	3404	0	DHX30	3	47891247	Frame_Shift_Del	DEL	GTGCACA	TCGA-UZ-A9PU-01A-11D-A42J-10		47891247	150131183	24	16686											
FAM107A	11170	hgsc.bcm.edu	37	chr3	58555533	58555533	+	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	attccactctctgtattctgGccgggccatcaggcccccaa	7	10	8	16	1	3	0	1	0	2	0	5	0	4	0	5	3	0	1	5	3	2	3			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr3:58555533G>C	ENST00000394481.1	-	3	613	c.55C>G	c.(55-57)Cca>Gca	p.P19A	FAM107A_ENST00000360997.2_Missense_Mutation_p.P19A|FAM107A_ENST00000464064.1_Missense_Mutation_p.P19A|RP11-475O23.2_ENST00000472513.1_RNA|FAM107A_ENST00000447756.2_Missense_Mutation_p.P47A|FAM107A_ENST00000474531.1_Missense_Mutation_p.P50A	NM_001282713.1|NM_007177.2	NP_001269642.1|NP_009108.1	O95990	F107A_HUMAN	family with sequence similarity 107, member A	19			P -> L (in renal cell carcinoma cell line). {ECO:0000269|PubMed:10564580}.		regulation of cell growth (GO:0001558)	neuron projection (GO:0043005)|nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				BRCA - Breast invasive adenocarcinoma(55;0.000189)|Kidney(10;0.000536)|KIRC - Kidney renal clear cell carcinoma(10;0.000716)|OV - Ovarian serous cystadenocarcinoma(275;0.154)		CTGTATTCTGGCCGGGCCATC	0.607																																					p.P19A		Atlas-SNP	.											.	FAM107A	33	.	0			c.C55G						PASS	.						69	73	72					3																	58555533		2203	4300	6503	SO:0001583	missense	11170	exon2			ATTCTGGCCGGGC	AF089854	CCDS2892.1, CCDS63672.1, CCDS63673.1	3p14.2	2006-02-03			ENSG00000168309	ENSG00000168309			30827	protein-coding gene	gene with protein product		608295				10564580, 10702698	Standard	XM_005264835		Approved	DRR1, TU3A	uc003dkn.3	O95990	OTTHUMG00000159159	ENST00000394481.1:c.55C>G	chr3.hg19:g.58555533G>C	ENSP00000377991:p.Pro19Ala	48.0	0.0	.		42.0	12.0	.	NM_001076778	B3KNQ4|B7ZAY5|J3KR61|Q96NH4	Missense_Mutation	SNP	ENST00000394481.1	hg19	CCDS2892.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.112146	0.77210	.	.	ENSG00000168309	ENST00000360997;ENST00000394481;ENST00000464064;ENST00000474531;ENST00000447756;ENST00000465970	T;T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83;0.83	4.68	2.87	0.33458	.	0.000000	0.85682	D	0.000000	T	0.67173	0.2865	M	0.80028	2.48	0.53688	D	0.999974	P;D;B;D	0.89917	0.477;1.0;0.262;0.999	B;D;B;D	0.87578	0.187;0.987;0.135;0.998	T	0.68891	-0.5289	10	0.72032	D	0.01	-5.4675	10.9672	0.47418	0.1515:0.0:0.8485:0.0	.	47;19;50;19	B7ZAY5;O95990-2;B3KNQ4;O95990	.;.;.;F107A_HUMAN	A	19;19;19;50;47;19	ENSP00000354270:P19A;ENSP00000377991:P19A;ENSP00000419529:P19A;ENSP00000419124:P50A;ENSP00000400858:P47A;ENSP00000418038:P19A	ENSP00000354270:P19A	P	-	1	0	FAM107A	58530573	1.000000	0.71417	0.989000	0.46669	0.992000	0.81027	7.884000	0.87274	0.517000	0.28361	0.655000	0.94253	CCA	.	.	.	none		0.607	FAM107A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353585.1	NM_007177		C	58555533	G	C	58555533	3	2	265	1	0	0	0	0	1	0	0	0	5393	1203	42	4	391	4	FAM107A	3	58555533	Missense_Mutation	SNP	G	TCGA-UZ-A9PU-01A-11D-A42J-10	10664286	58555533	139466897	25	16687											
NAA50	80218	hgsc.bcm.edu	37	chr3	113441795	113441795	+	Frame_Shift_Del	DEL	A	A	-																															catctttttcacagatgtttAagacatgatttaacatttta																										TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr3:113441795delA	ENST00000240922.3	-	4	614	c.290delT	c.(289-291)ttafs	p.L97fs	NAA50_ENST00000497525.1_Frame_Shift_Del_p.L23fs|NAA50_ENST00000497255.1_Intron|NAA50_ENST00000477813.1_Frame_Shift_Del_p.L57fs|NAA50_ENST00000467022.1_5'Flank|NAA50_ENST00000493454.1_Frame_Shift_Del_p.L23fs|NAA50_ENST00000493900.1_Frame_Shift_Del_p.L96fs	NM_025146.2	NP_079422.1	Q9GZZ1	NAA50_HUMAN	N(alpha)-acetyltransferase 50, NatE catalytic subunit	97	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				histone H4 acetylation (GO:0043967)|mitotic sister chromatid cohesion, centromeric (GO:0071962)|N-terminal protein amino acid acetylation (GO:0006474)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	H4 histone acetyltransferase activity (GO:0010485)|peptide alpha-N-acetyltransferase activity (GO:0004596)|peptidyl-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0052858)			large_intestine(2)|lung(2)|skin(1)	5						ACAGATGTTTAAGACATGATT	0.274																																					p.L97fs		Atlas-Indel,Pindel	.											.	NAA50	10	.	0			c.291delA						PASS	.						21	20	20					3																	113441795		2154	4192	6346	SO:0001589	frameshift_variant	80218	exon4			.	AK023256	CCDS2975.1	3q13.31	2010-05-07	2010-01-14	2010-01-14	ENSG00000121579	ENSG00000121579	2.3.1.-	"N(alpha)-acetyltransferase subunits"	29533	protein-coding gene	gene with protein product		610834	"Mak3 homolog (S. cerevisiae)", "N-acetyltransferase 13", "N-acetyltransferase 13 (GCN5-related)"	MAK3, NAT13		16507339, 17502424, 19660095	Standard	NM_025146		Approved	FLJ13194, NAT5, San	uc003ean.2	Q9GZZ1	OTTHUMG00000159294	ENST00000240922.3:c.290delT	chr3.hg19:g.113441795delA	ENSP00000240922:p.Leu97fs	536.0	0.0	0		522.0	145.0	0.277778	NM_025146	D3DN74|Q68DQ1	Frame_Shift_Del	DEL	ENST00000240922.3	hg19	CCDS2975.1																																																																																			.	.	.	none		0.274	NAA50-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354446.2	NM_025146		-	113441795	A	-	113441795	7	5	265	1	0	1	0	1	0	0	0	0	10133	372	13	0	227	0	NAA50	3	113441795	Frame_Shift_Del	DEL	A	TCGA-UZ-A9PU-01A-11D-A42J-10	54886262	113441795	84580635	26	16688											
MAGEF1	64110	hgsc.bcm.edu	37	chr3	184429221	184429221	+	Missense_Mutation	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	caaactgtttcagctcaaaaCcaaagacataccgcagatgc	16	7	6	12	1	2	2	2	0	0	2	2	2	2	2	2	0	5	3	2	0	5	2			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr3:184429221C>T	ENST00000317897.3	-	1	615	c.389G>A	c.(388-390)gGt>gAt	p.G130D		NM_022149.4	NP_071432.2	Q9HAY2	MAGF1_HUMAN	melanoma antigen family F, 1	130	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.					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)			CAGCTCAAAACCAAAGACATA	0.493																																					p.G130D		Atlas-SNP	.											.	MAGEF1	27	.	0			c.G389A						PASS	.						114	120	118					3																	184429221		2203	4300	6503	SO:0001583	missense	64110	exon1			TCAAAACCAAAGA	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.389G>A	chr3.hg19:g.184429221C>T	ENSP00000315064:p.Gly130Asp	76.0	0.0	.		80.0	24.0	.	NM_022149	Q9H215	Missense_Mutation	SNP	ENST00000317897.3	hg19	CCDS3269.1	.	.	.	.	.	.	.	.	.	.	C	17.53	3.411928	0.62511	.	.	ENSG00000177383	ENST00000317897	T	0.24151	1.87	4.62	1.74	0.24563	.	0.119020	0.56097	D	0.000024	T	0.53867	0.1823	H	0.94771	3.58	0.09310	N	0.999993	D	0.89917	1.0	D	0.80764	0.994	T	0.47509	-0.9112	10	0.87932	D	0	.	4.5619	0.12165	0.0:0.6151:0.1833:0.2016	.	130	Q9HAY2	MAGF1_HUMAN	D	130	ENSP00000315064:G130D	ENSP00000315064:G130D	G	-	2	0	MAGEF1	185911915	0.491000	0.26019	0.110000	0.21437	0.956000	0.61745	0.575000	0.23729	0.259000	0.21709	0.655000	0.94253	GGT	.	.	.	none		0.493	MAGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345417.1	NM_022149		T	184429221	C	T	184429221	3	4	265	1	0	0	0	0	1	0	0	0	9194	507	18	2	538	2	MAGEF1	3	184429221	Missense_Mutation	SNP	C	TCGA-UZ-A9PU-01A-11D-A42J-10	70987426	184429221	13593209	27	16689											
SLC2A9	56606	hgsc.bcm.edu	37	chr4	10020642	10020642	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaggttgtagccgtagaggAaggaggagccgaaggcgccc	11	4	17	9	3	0	1	0	0	0	1	0	5	0	4	3	5	2	3	3	5	4	3			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr4:10020642A>G	ENST00000264784.3	-	2	259	c.206T>C	c.(205-207)tTc>tCc	p.F69S	SLC2A9_ENST00000506583.1_Missense_Mutation_p.F40S|SLC2A9_ENST00000309065.3_Missense_Mutation_p.F40S	NM_020041.2	NP_064425.2	Q9NRM0	GTR9_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 9	69					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)	GCCGTAGAGGAAGGAGGAGCC	0.706																																					p.F69S		Atlas-SNP	.											.	SLC2A9	158	.	0			c.T206C						PASS	.						16	17	17					4																	10020642		1947	3904	5851	SO:0001583	missense	56606	exon2			TAGAGGAAGGAGG	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.206T>C	chr4.hg19:g.10020642A>G	ENSP00000264784:p.Phe69Ser	266.0	0.0	.		188.0	60.0	.	NM_020041	Q0VGC4|Q4W5D1|Q8WV30|Q96P00	Missense_Mutation	SNP	ENST00000264784.3	hg19	CCDS3407.1	.	.	.	.	.	.	.	.	.	.	a	19.38	3.816535	0.70912	.	.	ENSG00000109667	ENST00000506583;ENST00000264784;ENST00000309065;ENST00000513129	T;T;T;D	0.83914	-0.01;-1.06;-0.01;-1.78	4.89	4.89	0.63831	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.91496	0.7315	M	0.89715	3.055	0.34693	D	0.725902	D;D	0.76494	0.996;0.999	D;D	0.74023	0.969;0.982	D	0.95063	0.8197	9	.	.	.	.	10.8133	0.46559	1.0:0.0:0.0:0.0	.	40;69	Q9NRM0-2;Q9NRM0	.;GTR9_HUMAN	S	40;69;40;40	ENSP00000422209:F40S;ENSP00000264784:F69S;ENSP00000311383:F40S;ENSP00000426800:F40S	.	F	-	2	0	SLC2A9	9629740	1.000000	0.71417	1.000000	0.80357	0.458000	0.32498	3.598000	0.54038	2.068000	0.61886	0.454000	0.30748	TTC	.	.	.	none		0.706	SLC2A9-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207055.1			G	10020642	A	G	10020642	3	3	265	1	0	0	0	0	1	0	0	0	14565	246	9	3	1460	3	SLC2A9	4	10020642	Missense_Mutation	SNP	A	TCGA-UZ-A9PU-01A-11D-A42J-10		10020642	181133634	28	16690											
SDAD1	55153	hgsc.bcm.edu	37	chr4	76896925	76896925	+	Missense_Mutation	SNP	T	T	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	ccttctgtagagttcaatcaTtacatctaaagacatcttgg	12	14	6	9	0	5	2	2	0	3	2	5	2	5	2	1	1	1	2	1	1	5	6			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr4:76896925T>G	ENST00000356260.5	-	6	668	c.550A>C	c.(550-552)Atg>Ctg	p.M184L	SDAD1_ENST00000513089.1_5'Flank|SDAD1_ENST00000395711.4_Missense_Mutation_p.M147L	NM_018115.2	NP_060585.2	Q9NVU7	SDA1_HUMAN	SDA1 domain containing 1	184					actin cytoskeleton organization (GO:0030036)|protein transport (GO:0015031)|ribosomal large subunit biogenesis (GO:0042273)|ribosomal large subunit export from nucleus (GO:0000055)	nucleolus (GO:0005730)				breast(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	19			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			AGTTCAATCATTACATCTAAA	0.348																																					p.M184L		Atlas-SNP	.											.	SDAD1	47	.	0			c.A550C						PASS	.						123	118	120					4																	76896925		2203	4300	6503	SO:0001583	missense	55153	exon6			CAATCATTACATC	AF132198	CCDS3573.2, CCDS75147.1	4q21.21	2010-11-24			ENSG00000198301	ENSG00000198301			25537	protein-coding gene	gene with protein product						11483580	Standard	NM_001288984		Approved	FLJ10498	uc003hje.4	Q9NVU7	OTTHUMG00000130111	ENST00000356260.5:c.550A>C	chr4.hg19:g.76896925T>G	ENSP00000348596:p.Met184Leu	140.0	0.0	.		93.0	42.0	.	NM_018115	Q32Q11|Q68D52|Q7Z5U4|Q9H831|Q9H9P6	Missense_Mutation	SNP	ENST00000356260.5	hg19	CCDS3573.2	.	.	.	.	.	.	.	.	.	.	T	15.91	2.972226	0.53614	.	.	ENSG00000198301	ENST00000356260;ENST00000395711	T;T	0.04862	3.71;3.54	5.2	5.2	0.72013	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.08802	0.0218	L	0.51853	1.615	0.58432	D	0.999995	B;P	0.42337	0.075;0.776	B;P	0.44518	0.081;0.452	T	0.25984	-1.0116	10	0.09084	T	0.74	-17.1439	13.2882	0.60255	0.0:0.0:0.0:1.0	.	147;184	E7EW05;Q9NVU7	.;SDA1_HUMAN	L	184;147	ENSP00000348596:M184L;ENSP00000379061:M147L	ENSP00000348596:M184L	M	-	1	0	SDAD1	77115949	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.665000	0.83852	2.081000	0.62600	0.533000	0.62120	ATG	.	.	.	none		0.348	SDAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252418.3	NM_018115		G	76896925	T	G	76896925	3	3	265	1	0	0	0	0	1	0	0	0	13963	1493	52	5	1581	5	SDAD1	4	76896925	Missense_Mutation	SNP	T	TCGA-UZ-A9PU-01A-11D-A42J-10	66876283	76896925	114257351	29	16691											
IL2	3558	hgsc.bcm.edu	37	chr4	123377451	123377451	+	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	gaaaggaaatatacttacatTaattccattcaaaatcatct	18	13	3	7	0	3	0	2	0	1	0	4	2	4	1	1	1	2	0	1	1	8	6			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr4:123377451T>A	ENST00000226730.4	-	1	429	c.145A>T	c.(145-147)Aat>Tat	p.N49Y		NM_000586.3	NP_000577.2	P60568	IL2_HUMAN	interleukin 2	49					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|immune response (GO:0006955)|natural killer cell activation (GO:0030101)|negative regulation of apoptotic process (GO:0043066)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of heart contraction (GO:0045822)|negative regulation of inflammatory response (GO:0050728)|negative regulation of lymphocyte proliferation (GO:0050672)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dendritic spine development (GO:0060999)|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-17 production (GO:0032740)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of tissue remodeling (GO:0034105)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of T cell homeostatic proliferation (GO:0046013)|T cell differentiation (GO:0030217)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|cytokine activity (GO:0005125)|glycosphingolipid binding (GO:0043208)|growth factor activity (GO:0008083)|interleukin-2 receptor binding (GO:0005134)|kinase activator activity (GO:0019209)			endometrium(2)|large_intestine(4)|lung(6)|skin(1)	13				LUSC - Lung squamous cell carcinoma(721;0.185)	Pseudoephedrine(DB00852)	ATACTTACATTAATTCCATTC	0.299			T	TNFRSF17	intestinal T-cell lymphoma																																p.N49Y		Atlas-SNP	.		Dom	yes		4	4q26-q27	3558	interleukin 2		L	.	IL2	23	.	0			c.A145T						PASS	.						86	83	84					4																	123377451		2203	4299	6502	SO:0001583	missense	3558	exon1			TTACATTAATTCC	U25676	CCDS3726.1	4q26-q27	2011-07-14			ENSG00000109471	ENSG00000109471		"Interleukins and interleukin receptors"	6001	protein-coding gene	gene with protein product	"T cell growth factor"	147680				3260003	Standard	NM_000586		Approved	IL-2, TCGF	uc003ier.3	P60568	OTTHUMG00000133075	ENST00000226730.4:c.145A>T	chr4.hg19:g.123377451T>A	ENSP00000226730:p.Asn49Tyr	178.0	0.0	.		99.0	38.0	.	NM_000586	P01585	Missense_Mutation	SNP	ENST00000226730.4	hg19	CCDS3726.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.634791	0.87760	.	.	ENSG00000109471	ENST00000226730	.	.	.	6.17	2.06	0.26882	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	1.224380	0.05498	N	0.557971	T	0.56978	0.2022	M	0.71036	2.16	0.09310	N	1	D	0.65815	0.995	P	0.60012	0.867	T	0.28106	-1.0054	9	0.72032	D	0.01	0.0199	3.7496	0.08561	0.0:0.2335:0.1858:0.5806	.	49	P60568	IL2_HUMAN	Y	49	.	ENSP00000226730:N49Y	N	-	1	0	IL2	123596901	0.001000	0.12720	0.012000	0.15200	0.964000	0.63967	0.806000	0.27126	0.478000	0.27488	0.533000	0.62120	AAT	.	.	.	none		0.299	IL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256715.2			A	123377451	T	A	123377451	3	1	265	1	0	0	0	0	1	0	0	0	7673	1754	61	5	332	5	IL2	4	123377451	Missense_Mutation	SNP	T	TCGA-UZ-A9PU-01A-11D-A42J-10	46480526	123377451	67776825	30	16692											
ITPR3	3710	hgsc.bcm.edu	37	chr6	33632875	33632875	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaaggaggcctttgccatcGtgtcagtgcccgtgtctgag	7	10	13	11	2	2	1	1	1	1	0	3	2	2	2	3	2	2	0	3	2	1	1			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr6:33632875G>A	ENST00000374316.5	+	14	2354	c.1294G>A	c.(1294-1296)Gtg>Atg	p.V432M	ITPR3_ENST00000605930.1_Missense_Mutation_p.V432M			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	432	MIR 5. {ECO:0000255|PROSITE- ProRule:PRU00131}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	CTTTGCCATCGTGTCAGTGCC	0.627																																					p.V432M		Atlas-SNP	.											ITPR3_ENST00000374316,colon,carcinoma,0,2	ITPR3	409	.	0			c.G1294A						PASS	.						88	84	85					6																	33632875		2203	4300	6503	SO:0001583	missense	3710	exon13			GCCATCGTGTCAG	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.1294G>A	chr6.hg19:g.33632875G>A	ENSP00000363435:p.Val432Met	52.0	0.0	.		46.0	34.0	.	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	hg19	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.305299	0.60305	.	.	ENSG00000096433	ENST00000374316	D	0.91894	-2.93	4.89	4.89	0.63831	MIR motif (1);MIR (1);	0.068603	0.64402	N	0.000018	D	0.96071	0.8720	M	0.84511	2.7	0.58432	D	0.999999	D	0.89917	1.0	D	0.78314	0.991	D	0.96757	0.9558	10	0.87932	D	0	-22.0431	18.0608	0.89377	0.0:0.0:1.0:0.0	.	432	Q14573	ITPR3_HUMAN	M	432	ENSP00000363435:V432M	ENSP00000363435:V432M	V	+	1	0	ITPR3	33740853	1.000000	0.71417	0.964000	0.40570	0.004000	0.04260	9.735000	0.98825	2.260000	0.74910	0.557000	0.71058	GTG	.	.	.	none		0.627	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224		A	33632875	G	A	33632875	3	1	265	1	0	0	0	0	1	0	0	0	7929	1145	40	1	1344	1	ITPR3	6	33632875	Missense_Mutation	SNP	G	TCGA-UZ-A9PU-01A-11D-A42J-10		33632875	137482192	31	16693											
FOXP4	116113	hgsc.bcm.edu	37	chr6	41555205	41555205	+	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	accccccctctcccaccataCcctgcccaacggacagccta	9	5	4	23	1	1	0	0	0	1	0	2	1	1	1	8	1	4	0	8	1	3	2			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr6:41555205C>G	ENST00000307972.4	+	6	839	c.827C>G	c.(826-828)aCc>aGc	p.T276S	FOXP4_ENST00000409208.1_Missense_Mutation_p.T276S|FOXP4_ENST00000373063.3_Missense_Mutation_p.T275S|FOXP4_ENST00000373057.3_Missense_Mutation_p.T274S|FOXP4_ENST00000373060.1_Missense_Mutation_p.T276S			Q8IVH2	FOXP4_HUMAN	forkhead box P4	276					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)					TCCCACCATACCCTGCCCAAC	0.662											OREG0004065	type=REGULATORY REGION|Gene=FOXP4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.T276S		Atlas-SNP	.											.	FOXP4	83	.	0			c.C827G						PASS	.						68	73	71					6																	41555205		2203	4300	6503	SO:0001583	missense	116113	exon7			ACCATACCCTGCC	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.827C>G	chr6.hg19:g.41555205C>G	ENSP00000309823:p.Thr276Ser	171.0	0.0	.	902	137.0	114.0	.	NM_001012426	Q5W098|Q7Z7F8|Q8IW55|Q96E19	Missense_Mutation	SNP	ENST00000307972.4	hg19	CCDS34447.1	.	.	.	.	.	.	.	.	.	.	C	0.010	-1.757679	0.00657	.	.	ENSG00000137166	ENST00000373060;ENST00000373063;ENST00000409208;ENST00000373057;ENST00000307972	T;D;T;T;T	0.88431	1.09;-2.38;1.39;1.09;1.09	4.83	3.96	0.45880	.	0.359243	0.29383	N	0.012302	T	0.43743	0.1261	N	0.00841	-1.15	0.22629	N	0.998918	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.43048	-0.9415	10	0.02654	T	1	.	12.8987	0.58113	0.0:0.9209:0.0:0.0791	.	275;274;276	Q8IW55;Q7Z7F8;Q8IVH2	.;.;FOXP4_HUMAN	S	276;275;276;274;276	ENSP00000362151:T276S;ENSP00000362154:T275S;ENSP00000386958:T276S;ENSP00000362148:T274S;ENSP00000309823:T276S	ENSP00000309823:T276S	T	+	2	0	FOXP4	41663183	1.000000	0.71417	1.000000	0.80357	0.034000	0.12701	3.485000	0.53208	1.241000	0.43820	0.591000	0.81541	ACC	.	.	.	none		0.662	FOXP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106767.1	NM_138457		G	41555205	C	G	41555205	3	3	265	1	0	0	0	0	1	0	0	0	6036	507	18	4	849	4	FOXP4	6	41555205	Missense_Mutation	SNP	C	TCGA-UZ-A9PU-01A-11D-A42J-10	7922330	41555205	129559862	32	16694											
PCLO	27445	hgsc.bcm.edu	37	chr7	82508768	82508768	+	Missense_Mutation	SNP	T	T	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	ccacccacaattctaattccTaatccattacctgtattaaa	14	13	1	13	0	1	0	0	0	1	0	3	0	3	0	5	0	1	1	5	0	7	7			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr7:82508768T>G	ENST00000333891.9	-	10	13876	c.13539A>C	c.(13537-13539)ttA>ttC	p.L4513F	PCLO_ENST00000423517.2_Missense_Mutation_p.L4513F|PCLO_ENST00000426442.2_5'UTR	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						TTCTAATTCCTAATCCATTAC	0.393																																					p.L4513F		Atlas-SNP	.											.	PCLO	1506	.	0			c.A13539C						PASS	.						71	61	64					7																	82508768		1808	4075	5883	SO:0001583	missense	27445	exon10			AATTCCTAATCCA	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.13539A>C	chr7.hg19:g.82508768T>G	ENSP00000334319:p.Leu4513Phe	165.0	0.0	.		210.0	51.0	.	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	10.10	1.256665	0.22965	.	.	ENSG00000186472	ENST00000333891;ENST00000423517;ENST00000380195	T;T	0.35973	1.28;1.28	4.91	4.91	0.64330	.	.	.	.	.	T	0.34978	0.0916	L	0.48986	1.54	0.80722	D	1	B;B	0.32350	0.366;0.366	B;B	0.40329	0.191;0.326	T	0.39440	-0.9614	9	0.87932	D	0	.	4.3636	0.11213	0.2927:0.0856:0.0:0.6217	.	4513;4513	Q9Y6V0-5;Q9Y6V0-6	.;.	F	4513;4513;9	ENSP00000334319:L4513F;ENSP00000388393:L4513F	ENSP00000334319:L4513F	L	-	3	2	PCLO	82346704	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.672000	0.25187	1.961000	0.56991	0.482000	0.46254	TTA	.	.	.	none		0.393	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		G	82508768	T	G	82508768	3	3	265	1	0	0	0	0	1	0	0	0	11590	1519	53	5	1970	5	PCLO	7	82508768	Missense_Mutation	SNP	T	TCGA-UZ-A9PU-01A-11D-A42J-10		82508768	76629895	33	16695											
AP4M1	9179	hgsc.bcm.edu	37	chr7	99703890	99703890	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcaatgtcaggctgcaccTccccctgcctcgaggggtgg	5	8	12	16	1	2	0	2	0	0	0	4	1	3	0	5	4	2	2	5	4	1	0			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr7:99703890T>C	ENST00000359593.4	+	13	1159	c.1001T>C	c.(1000-1002)cTc>cCc	p.L334P	AP4M1_ENST00000429084.1_Missense_Mutation_p.L341P|AP4M1_ENST00000421755.1_Missense_Mutation_p.L334P|AP4M1_ENST00000422582.1_Missense_Mutation_p.L206P	NM_004722.3	NP_004713.2	O00189	AP4M1_HUMAN	adaptor-related protein complex 4, mu 1 subunit	334	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)					AGGCTGCACCTCCCCCTGCCT	0.587																																					p.L334P	Pancreas(174;1182 2812 29595 49511)	Atlas-SNP	.											.	AP4M1	39	.	0			c.T1001C						PASS	.						74	56	62					7																	99703890		2203	4300	6503	SO:0001583	missense	9179	exon13			TGCACCTCCCCCT	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.1001T>C	chr7.hg19:g.99703890T>C	ENSP00000352603:p.Leu334Pro	52.0	0.0	.		77.0	4.0	.	NM_004722	D6W5U1|Q8WV65|Q9UHK9	Missense_Mutation	SNP	ENST00000359593.4	hg19	CCDS5685.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.53|19.53	3.845106|3.845106	0.71603|0.71603	.|.	.|.	ENSG00000221838|ENSG00000221838	ENST00000438383;ENST00000429084;ENST00000359593;ENST00000421755;ENST00000422582;ENST00000450807|ENST00000445295	T;T;T;T;T;T|.	0.21543|.	2.0;2.0;2.0;2.0;2.0;2.0|.	4.96|4.96	4.96|4.96	0.65561|0.65561	Clathrin adaptor, mu subunit, C-terminal (3);|.	0.195814|.	0.43747|.	D|.	0.000522|.	T|T	0.60235|0.60235	0.2253|0.2253	L|L	0.48642|0.48642	1.525|1.525	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.87578|.	0.997;0.998;0.998|.	T|T	0.58160|0.58160	-0.7685|-0.7685	10|5	0.87932|.	D|.	0|.	-12.5702|-12.5702	12.6235|12.6235	0.56616|0.56616	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	286;341;334|.	B4DKN7;C9JC87;O00189|.	.;.;AP4M1_HUMAN|.	P|P	266;341;334;334;206;86|60	ENSP00000401613:L266P;ENSP00000403663:L341P;ENSP00000352603:L334P;ENSP00000412185:L334P;ENSP00000406676:L206P;ENSP00000391585:L86P|.	ENSP00000352603:L334P|.	L|S	+|+	2|1	0|0	AP4M1|AP4M1	99541826|99541826	0.998000|0.998000	0.40836|0.40836	0.995000|0.995000	0.50966|0.50966	0.650000|0.650000	0.38633|0.38633	3.616000|3.616000	0.54174|0.54174	2.079000|2.079000	0.62486|0.62486	0.459000|0.459000	0.35465|0.35465	CTC|TCC	.	.	.	none		0.587	AP4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336772.4	NM_004722		C	99703890	T	C	99703890	3	2	265	1	0	0	0	0	1	0	0	0	753	1551	54	3	1051	3	AP4M1	7	99703890	Missense_Mutation	SNP	T	TCGA-UZ-A9PU-01A-11D-A42J-10	17195122	99703890	59434773	34	16696											
POT1	25913	hgsc.bcm.edu	37	chr7	124493170	124493170	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaagtttggtatgaaggctaTagattctaagaaagcttcca	14	12	10	5	0	1	3	0	1	1	2	2	4	2	3	1	2	1	4	1	2	7	7			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr7:124493170T>C	ENST00000357628.3	-	10	1323	c.725A>G	c.(724-726)tAt>tGt	p.Y242C	POT1_ENST00000393329.1_Missense_Mutation_p.Y111C	NM_015450.2	NP_056265.2	Q9NUX5	POTE1_HUMAN	protection of telomeres 1	242					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						ATGAAGGCTATAGATTCTAAG	0.313																																					p.Y242C	Esophageal Squamous(149;1032 1141 16047 36610 40540 42429 44687 51642)	Atlas-SNP	.											POT1_ENST00000357628,NS,NS,0,2	POT1	186	.	0			c.A725G						PASS	.						63	60	61					7																	124493170		2203	4300	6503	SO:0001583	missense	25913	exon10			AGGCTATAGATTC	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.725A>G	chr7.hg19:g.124493170T>C	ENSP00000350249:p.Tyr242Cys	133.0	0.0	.		131.0	83.0	.	NM_015450	O95018|Q5MJ36|Q9H662|Q9NW19|Q9UG95	Missense_Mutation	SNP	ENST00000357628.3	hg19	CCDS5793.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.073572	0.76415	.	.	ENSG00000128513	ENST00000357628;ENST00000393329;ENST00000451720;ENST00000440969;ENST00000393326;ENST00000265391	T;T	0.49720	0.78;0.77	6.07	6.07	0.98685	Nucleic acid-binding, OB-fold-like (1);	0.178639	0.50627	D	0.000103	T	0.68384	0.2995	M	0.76002	2.32	0.48696	D	0.999696	D	0.89917	1.0	D	0.87578	0.998	T	0.69537	-0.5119	10	0.48119	T	0.1	-0.6297	14.5927	0.68378	0.0:0.0:0.0:1.0	.	242	Q9NUX5	POTE1_HUMAN	C	242;111;242;242;242;241	ENSP00000350249:Y242C;ENSP00000377002:Y111C	ENSP00000265391:Y241C	Y	-	2	0	POT1	124280406	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.512000	0.53407	2.326000	0.78906	0.533000	0.62120	TAT	.	.	.	none		0.313	POT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347861.1			C	124493170	T	C	124493170	3	2	265	1	0	0	0	0	1	0	0	0	12267	1406	49	3	1219	3	POT1	7	124493170	Missense_Mutation	SNP	T	TCGA-UZ-A9PU-01A-11D-A42J-10	24789280	124493170	34645493	35	16697											
PTPRD	5789	hgsc.bcm.edu	37	chr9	8460470	8460470	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaccactgcaaggacaggAcctacaacccagatcaagcc	16	3	8	14	0	1	2	1	0	0	2	1	4	1	4	4	2	4	1	4	2	5	1			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr9:8460470A>G	ENST00000381196.4	-	30	4359	c.3816T>C	c.(3814-3816)ggT>ggC	p.G1272G	PTPRD_ENST00000360074.4_Silent_p.G1259G|PTPRD_ENST00000397617.3_Silent_p.G851G|PTPRD_ENST00000358503.5_Silent_p.G1250G|PTPRD_ENST00000355233.5_Silent_p.G861G|PTPRD_ENST00000486161.1_Silent_p.G861G|PTPRD_ENST00000540109.1_Silent_p.G1272G|PTPRD_ENST00000397606.3_Silent_p.G851G|PTPRD_ENST00000356435.5_Silent_p.G1272G|PTPRD_ENST00000397611.3_Silent_p.G858G|PTPRD_ENST00000537002.1_Silent_p.G858G	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1272					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)		CAAGGACAGGACCTACAACCC	0.458										TSP Lung(15;0.13)																											p.G1272G		Atlas-SNP	.											.	PTPRD	1348	.	0			c.T3816C						PASS	.						180	158	165					9																	8460470		2203	4300	6503	SO:0001819	synonymous_variant	5789	exon33			GACAGGACCTACA	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.3816T>C	chr9.hg19:g.8460470A>G		99.0	0.0	.		90.0	28.0	.	NM_002839	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Silent	SNP	ENST00000381196.4	hg19	CCDS43786.1																																																																																			.	.	.	none		0.458	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			G	8460470	A	G	8460470	2	3	265	1	0	0	0	0	0	0	0	1	12812	262	10	3		3	PTPRD	9	8460470	Silent	SNP	A	TCGA-UZ-A9PU-01A-11D-A42J-10		8460470	132752961	36	16698											
BAAT	570	hgsc.bcm.edu	37	chr9	104130573	104130573	+	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	agcccacccaaaccaccaaaCaaatcaattacccctgggaa	17	4	4	16	0	1	0	1	0	0	0	1	1	1	1	6	1	4	0	6	1	6	1			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr9:104130573C>G	ENST00000395051.3	-	2	568	c.498G>C	c.(496-498)ttG>ttC	p.L166F	BAAT_ENST00000259407.2_Missense_Mutation_p.L166F			Q14032	BAAT_HUMAN	bile acid CoA:amino acid N-acyltransferase	166					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)	AACCACCAAACAAATCAATTA	0.458																																					p.L166F		Atlas-SNP	.											.	BAAT	52	.	0			c.G498C						PASS	.						55	50	51					9																	104130573		2203	4300	6503	SO:0001583	missense	570	exon3			ACCAAACAAATCA	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.498G>C	chr9.hg19:g.104130573C>G	ENSP00000378491:p.Leu166Phe	213.0	0.0	.		157.0	64.0	.	NM_001127610	Q3B7W9|Q96L31	Missense_Mutation	SNP	ENST00000395051.3	hg19	CCDS6752.1	.	.	.	.	.	.	.	.	.	.	C	15.55	2.865397	0.51588	.	.	ENSG00000136881	ENST00000259407;ENST00000395051	T;T	0.52754	0.65;0.65	4.76	2.76	0.32466	.	0.343871	0.22294	N	0.061953	T	0.67683	0.2919	M	0.89353	3.025	0.33048	D	0.532319	D	0.65815	0.995	D	0.65443	0.935	T	0.76710	-0.2859	10	0.87932	D	0	-8.5624	8.4628	0.32938	0.0:0.795:0.0:0.205	.	166	Q14032	BAAT_HUMAN	F	166	ENSP00000259407:L166F;ENSP00000378491:L166F	ENSP00000259407:L166F	L	-	3	2	BAAT	103170394	0.998000	0.40836	0.976000	0.42696	0.449000	0.32228	0.773000	0.26661	1.235000	0.43724	0.655000	0.94253	TTG	.	.	.	none		0.458	BAAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053433.1			G	104130573	C	G	104130573	3	3	265	1	0	0	0	0	1	0	0	0	1280	477	17	4	766	4	BAAT	9	104130573	Missense_Mutation	SNP	C	TCGA-UZ-A9PU-01A-11D-A42J-10	95670103	104130573	37082858	37	16699											
UVRAG	7405	hgsc.bcm.edu	37	chr11	75826995	75826995	+	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	atcaacatggactagggactCcagacttgcggcaaaccctt	12	8	9	12	1	1	1	1	0	0	1	2	3	2	3	2	3	3	1	2	3	3	3			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr11:75826995C>A	ENST00000356136.3	+	14	1574	c.1333C>A	c.(1333-1335)Cca>Aca	p.P445T	UVRAG_ENST00000533454.1_Missense_Mutation_p.P73T|UVRAG_ENST00000538870.1_5'UTR|UVRAG_ENST00000532130.1_Missense_Mutation_p.P73T|UVRAG_ENST00000528420.1_Missense_Mutation_p.P344T|UVRAG_ENST00000539288.1_Missense_Mutation_p.P73T|UVRAG_ENST00000531818.1_Missense_Mutation_p.P73T	NM_003369.3	NP_003360.2	Q9P2Y5	UVRAG_HUMAN	UV radiation resistance associated	445					DNA repair (GO:0006281)|positive regulation of autophagy (GO:0010508)|SNARE complex assembly (GO:0035493)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)|phagocytic vesicle (GO:0045335)|protein complex (GO:0043234)				central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(15)|skin(5)|urinary_tract(2)	32						ACTAGGGACTCCAGACTTGCG	0.393																																					p.P445T		Atlas-SNP	.											.	UVRAG	69	.	0			c.C1333A						PASS	.						93	81	85					11																	75826995		2200	4293	6493	SO:0001583	missense	7405	exon14			GGGACTCCAGACT	X99050, AB012958	CCDS8241.1	11q13	2012-11-15	2012-11-15		ENSG00000198382	ENSG00000198382			12640	protein-coding gene	gene with protein product	"beclin 1 binding protein"	602493	"UV radiation resistance associated gene"			9169138, 16799551, 18843052	Standard	NM_003369		Approved	VPS38	uc001oxc.3	Q9P2Y5	OTTHUMG00000165319	ENST00000356136.3:c.1333C>A	chr11.hg19:g.75826995C>A	ENSP00000348455:p.Pro445Thr	94.0	0.0	.		69.0	22.0	.	NM_003369	B3KTC1|O00392	Missense_Mutation	SNP	ENST00000356136.3	hg19	CCDS8241.1	.	.	.	.	.	.	.	.	.	.	C	18.00	3.524781	0.64747	.	.	ENSG00000198382	ENST00000356136;ENST00000528420;ENST00000533454;ENST00000531818;ENST00000532130;ENST00000539288	T;T	0.32023	1.47;1.47	5.69	5.69	0.88448	.	0.099426	0.64402	D	0.000001	T	0.24967	0.0606	L	0.41573	1.285	0.80722	D	1	B	0.32324	0.364	B	0.31016	0.123	T	0.03608	-1.1020	10	0.06891	T	0.86	-9.8812	17.6702	0.88214	0.0:1.0:0.0:0.0	.	445	Q9P2Y5	UVRAG_HUMAN	T	445;344;73;73;73;73	ENSP00000348455:P445T;ENSP00000436039:P344T	ENSP00000348455:P445T	P	+	1	0	UVRAG	75504643	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.753000	0.74904	2.840000	0.97914	0.655000	0.94253	CCA	.	.	.	none		0.393	UVRAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383430.1	NM_003369		A	75826995	C	A	75826995	3	1	265	1	0	0	0	0	1	0	0	0	17120	855	30	4	1387	4	UVRAG	11	75826995	Missense_Mutation	SNP	C	TCGA-UZ-A9PU-01A-11D-A42J-10		75826995	59179521	38	16700											
CALCOCO1	57658	hgsc.bcm.edu	37	chr12	54115291	54115291	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtcagcactttctcactgaTggtctggatgtcatcctcta	7	14	8	12	1	5	1	3	1	3	0	7	2	6	2	1	2	1	1	1	2	1	2	rs545468025		TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr12:54115291T>C	ENST00000550804.1	-	6	778	c.718A>G	c.(718-720)Atc>Gtc	p.I240V	CALCOCO1_ENST00000430117.2_Missense_Mutation_p.I207V|CALCOCO1_ENST00000262059.4_Missense_Mutation_p.I240V|CALCOCO1_ENST00000548263.1_Missense_Mutation_p.I240V|CALCOCO1_ENST00000547885.1_5'Flank			Q9P1Z2	CACO1_HUMAN	calcium binding and coiled-coil domain 1	240					intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	28						TTCTCACTGATGGTCTGGATG	0.597																																					p.I240V		Atlas-SNP	.											.	CALCOCO1	50	.	0			c.A718G						PASS	.						336	283	301					12																	54115291		2203	4300	6503	SO:0001583	missense	57658	exon6			CACTGATGGTCTG	AL136895	CCDS8864.1, CCDS44908.1	12q13.13	2014-01-02			ENSG00000012822	ENSG00000012822			29306	protein-coding gene	gene with protein product	"coiled-coil leucine zipper coactivator 1", "inorganic pyrophosphatase activator"					10819331, 11230166	Standard	NM_020898		Approved	KIAA1536, calphoglin, Cocoa	uc001sef.3	Q9P1Z2	OTTHUMG00000170095	ENST00000550804.1:c.718A>G	chr12.hg19:g.54115291T>C	ENSP00000449960:p.Ile240Val	79.0	0.0	.		63.0	25.0	.	NM_020898	B3KVA8|Q6FI59|Q71RC3|Q86WF8|Q96JU3|Q9H090	Missense_Mutation	SNP	ENST00000550804.1	hg19	CCDS8864.1	.	.	.	.	.	.	.	.	.	.	T	13.89	2.373295	0.42105	.	.	ENSG00000012822	ENST00000430117;ENST00000262059;ENST00000413257;ENST00000548263;ENST00000550804;ENST00000549935;ENST00000454332	T;T;T;T	0.10573	2.86;2.86;2.86;2.86	5.0	5.0	0.66597	.	0.157519	0.30201	N	0.010164	T	0.04272	0.0118	N	0.01761	-0.735	0.24470	N	0.994392	B;B;B;B;B;B	0.15930	0.008;0.007;0.007;0.015;0.007;0.008	B;B;B;B;B;B	0.22152	0.038;0.018;0.023;0.023;0.026;0.038	T	0.39251	-0.9623	10	0.10377	T	0.69	-7.9671	12.5553	0.56250	0.0:0.0:0.0:1.0	.	233;207;240;240;207;240	B4DG60;E9PAU0;Q9P1Z2-3;Q9P1Z2-2;E7EPK7;Q9P1Z2	.;.;.;.;.;CACO1_HUMAN	V	207;240;178;240;240;233;117	ENSP00000397189:I207V;ENSP00000262059:I240V;ENSP00000447647:I240V;ENSP00000449960:I240V	ENSP00000262059:I240V	I	-	1	0	CALCOCO1	52401558	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.902000	0.39848	2.009000	0.58944	0.460000	0.39030	ATC	.	.	.	none		0.597	CALCOCO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407233.2	NM_020898		C	54115291	T	C	54115291	3	2	265	1	0	0	0	0	1	0	0	0	2579	1464	51	3	1397	3	CALCOCO1	12	54115291	Missense_Mutation	SNP	T	TCGA-UZ-A9PU-01A-11D-A42J-10		54115291	79736604	39	16701											
CDK4	1019	hgsc.bcm.edu	37	chr12	58145350	58145350	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacctcacgaactgtgctgaTgggaaggcctcctccacctc	8	8	9	16	1	1	1	1	1	0	0	4	3	3	2	5	2	2	1	5	2	2	0			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr12:58145350T>C	ENST00000257904.6	-	2	516	c.151A>G	c.(151-153)Atc>Gtc	p.I51V	CDK4_ENST00000312990.6_Missense_Mutation_p.I51V|CDK4_ENST00000540325.1_5'UTR|CDK4_ENST00000549606.1_Intron|CDK4_ENST00000551888.1_5'UTR	NM_000075.3	NP_000066.1	P11802	CDK4_HUMAN	cyclin-dependent kinase 4	51	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|Required for binding D-type cyclins.				cell division (GO:0051301)|circadian rhythm (GO:0007623)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell cycle arrest (GO:0071157)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell size (GO:0045793)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of translation (GO:0045727)|protein phosphorylation (GO:0006468)|regulation of gene expression (GO:0010468)|response to drug (GO:0042493)|response to hyperoxia (GO:0055093)|response to lead ion (GO:0010288)|response to testosterone (GO:0033574)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)	chromatin (GO:0000785)|cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(2)	21	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)			ACTGTGCTGATGGGAAGGCCT	0.592			Mis			melanoma			Hereditary Melanoma																												p.I51V		Atlas-SNP	.	yes	Dom		Familial malignant melanoma	12	12q14	1019	cyclin-dependent kinase 4		E	.	CDK4	36	.	0			c.A151G						PASS	.						113	98	103					12																	58145350		2203	4300	6503	SO:0001583	missense	1019	exon2	Familial Cancer Database	Familial Atypical Multiple Mole Melanoma sydrome, FAMMM, Familial Dysplastic Nevus syndrome	TGCTGATGGGAAG	M14505	CCDS8953.1	12q13	2014-09-17				ENSG00000135446		"Cyclin-dependent kinases"	1773	protein-coding gene	gene with protein product		123829				8275715	Standard	NM_000075		Approved	PSK-J3	uc001spv.3	P11802		ENST00000257904.6:c.151A>G	chr12.hg19:g.58145350T>C	ENSP00000257904:p.Ile51Val	120.0	0.0	.		96.0	34.0	.	NM_000075	B2R9A0|B4DNF9|O00576|Q6FG61	Missense_Mutation	SNP	ENST00000257904.6	hg19	CCDS8953.1	.	.	.	.	.	.	.	.	.	.	T	0.310	-0.968185	0.02232	.	.	ENSG00000135446	ENST00000257904;ENST00000312990;ENST00000552254;ENST00000552388;ENST00000552862	T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16	5.23	-0.832	0.10785	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.292238	0.33144	N	0.005225	T	0.39489	0.1080	N	0.20685	0.6	0.28252	N	0.925209	B	0.02656	0.0	B	0.01281	0.0	T	0.19679	-1.0298	10	0.45353	T	0.12	.	6.7259	0.23357	0.0:0.3783:0.1311:0.4906	.	51	P11802	CDK4_HUMAN	V	51	ENSP00000257904:I51V;ENSP00000316889:I51V;ENSP00000449179:I51V;ENSP00000448963:I51V;ENSP00000446763:I51V	ENSP00000257904:I51V	I	-	1	0	CDK4	56431617	0.979000	0.34478	0.997000	0.53966	0.730000	0.41778	0.454000	0.21827	-0.025000	0.13918	-0.993000	0.02533	ATC	.	.	.	none		0.592	CDK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408790.2	NM_000075		C	58145350	T	C	58145350	3	2	265	1	0	0	0	0	1	0	0	0	3143	1464	51	3	788	3	CDK4	12	58145350	Missense_Mutation	SNP	T	TCGA-UZ-A9PU-01A-11D-A42J-10	4030059	58145350	75706545	40	16702											
FLT1	2321	hgsc.bcm.edu	37	chr13	28880844	28880844	+	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	agcgaggccttgggtttgctGtcagtccaggtgaagcgctt	6	11	15	9	2	1	1	1	1	0	0	2	2	2	1	2	3	3	3	2	3	1	3			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr13:28880844G>C	ENST00000282397.4	-	29	4037	c.3786C>G	c.(3784-3786)gaC>gaG	p.D1262E	FLT1_ENST00000543394.1_Missense_Mutation_p.D285E|FLT1_ENST00000540678.1_Missense_Mutation_p.D480E	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	1262					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)	TGGGTTTGCTGTCAGTCCAGG	0.537																																					p.D1262E		Atlas-SNP	.											.	FLT1	393	.	0			c.C3786G						PASS	.						98	91	93					13																	28880844		2203	4300	6503	SO:0001583	missense	2321	exon29			TTTGCTGTCAGTC	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.3786C>G	chr13.hg19:g.28880844G>C	ENSP00000282397:p.Asp1262Glu	67.0	0.0	.		59.0	29.0	.	NM_002019	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Missense_Mutation	SNP	ENST00000282397.4	hg19	CCDS9330.1	.	.	.	.	.	.	.	.	.	.	G	2.348	-0.349552	0.05173	.	.	ENSG00000102755	ENST00000282397;ENST00000543394;ENST00000540678	T;T;T	0.75938	-0.74;-0.94;-0.98	5.23	-0.809	0.10864	.	0.437579	0.23416	N	0.048409	T	0.28532	0.0706	N	0.00377	-1.585	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42882	-0.9425	10	0.02654	T	1	.	5.9864	0.19436	0.0:0.2813:0.2785:0.4402	.	1262	P17948	VGFR1_HUMAN	E	1262;285;480	ENSP00000282397:D1262E;ENSP00000437841:D285E;ENSP00000443311:D480E	ENSP00000282397:D1262E	D	-	3	2	FLT1	27778844	0.303000	0.24463	0.975000	0.42487	0.967000	0.64934	-0.392000	0.07314	-0.200000	0.10300	-0.219000	0.12488	GAC	.	.	.	none		0.537	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			C	28880844	G	C	28880844	3	2	265	1	0	0	0	0	1	0	0	0	5948	1368	48	4	238	4	FLT1	13	28880844	Missense_Mutation	SNP	G	TCGA-UZ-A9PU-01A-11D-A42J-10		28880844	86289034	41	16703											
NBEA	26960	hgsc.bcm.edu	37	chr13	35644191	35644191	+	Frame_Shift_Del	DEL	A	A	-																															ctctgcctggaatcatcaccAaaagagaatgcatcaatttt																										TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr13:35644191delA	ENST00000400445.3	+	9	1920	c.1386delA	c.(1384-1386)ccafs	p.P462fs	NBEA_ENST00000540320.1_Frame_Shift_Del_p.P462fs|NBEA_ENST00000379939.2_Frame_Shift_Del_p.P462fs|NBEA_ENST00000310336.4_Frame_Shift_Del_p.P462fs	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	462					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)		AATCATCACCAAAAGAGAATG	0.408																																					p.P462fs		Atlas-Indel,Pindel	.											.	NBEA	340	.	0			c.1385delC						PASS	.						50	44	46					13																	35644191		1908	4132	6040	SO:0001589	frameshift_variant	26960	exon9			.	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.1386delA	chr13.hg19:g.35644191delA	ENSP00000383295:p.Pro462fs	133.0	0.0	0		96.0	40.0	0.416667	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Frame_Shift_Del	DEL	ENST00000400445.3	hg19	CCDS45026.1																																																																																			.	.	.	none		0.408	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		-	35644191	A	-	35644191	7	5	265	1	0	1	0	1	0	0	0	0	10194	117	5	0	1420	0	NBEA	13	35644191	Frame_Shift_Del	DEL	A	TCGA-UZ-A9PU-01A-11D-A42J-10	6763347	35644191	79525687	42	16704											
SETDB2	83852	hgsc.bcm.edu	37	chr13	50041999	50041999	+	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	tcacattatttttttgtgtaGatcctatgcctgtgactcag	8	18	7	8	0	2	2	2	1	0	1	3	2	3	2	2	0	1	1	2	0	3	6			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr13:50041999G>A	ENST00000317257.8	+	6	1069		c.e6-1		SETDB2_ENST00000354234.4_Splice_Site|SETDB2_ENST00000258672.5_Splice_Site	NM_031915.2	NP_114121.2	Q96T68	SETB2_HUMAN	SET domain, bifurcated 2						chromosome segregation (GO:0007059)|heart looping (GO:0001947)|histone H3-K9 methylation (GO:0051567)|left/right axis specification (GO:0070986)|mitotic nuclear division (GO:0007067)|negative regulation of transcription, DNA-templated (GO:0045892)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	15		Lung NSC(96;0.000408)|Breast(56;0.00131)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;3.1e-09)		TTTTTGTGTAGATCCTATGCC	0.363																																					.		Atlas-SNP	.											.	SETDB2	48	.	0			c.245-1G>A						PASS	.						82	76	78					13																	50041999		2203	4298	6501	SO:0001630	splice_region_variant	83852	exon6			TGTGTAGATCCTA	AF334407	CCDS9417.1, CCDS53868.1	13q14	2011-07-01	2003-05-06	2003-05-09	ENSG00000136169	ENSG00000136169		"Chromatin-modifying enzymes / K-methyltransferases"	20263	protein-coding gene	gene with protein product		607865	"chromosome 13 open reading frame 4"	C13orf4		11306461	Standard	NM_031915		Approved	CLLD8, CLLL8, KMT1F	uc001vda.3	Q96T68	OTTHUMG00000016918	ENST00000317257.8:c.245-1G>A	chr13.hg19:g.50041999G>A		32.0	0.0	.		35.0	17.0	.	NM_031915	Q5TC65|Q5TC66|Q5W0A7|Q659A7|Q86UD6|Q96AI6	Splice_Site	SNP	ENST00000317257.8	hg19	CCDS9417.1	.	.	.	.	.	.	.	.	.	.	G	14.14	2.446781	0.43429	.	.	ENSG00000136169	ENST00000354234;ENST00000317257;ENST00000258672	.	.	.	4.96	4.96	0.65561	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8987	0.63790	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SETDB2	48940000	1.000000	0.71417	0.787000	0.31911	0.547000	0.35210	4.071000	0.57556	2.707000	0.92482	0.655000	0.94253	.	.	.	.	none		0.363	SETDB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044925.1	NM_031915	Intron	A	50041999	G	A	50041999	5	1	265	1	0	0	0	0	0	0	1	0	14152	956	33	2	262	2	SETDB2	13	50041999	Splice_Site	SNP	G	TCGA-UZ-A9PU-01A-11D-A42J-10	14397808	50041999	65127879	43	16705											
SYNE2	23224	hgsc.bcm.edu	37	chr14	64519388	64519388	+	Frame_Shift_Del	DEL	T	T	-																															ctggaagatcagttgaaaaaTcttaagattaggaccaacag																										TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr14:64519388delT	ENST00000344113.4	+	48	8969	c.8757delT	c.(8755-8757)aatfs	p.N2919fs	SYNE2_ENST00000358025.3_Frame_Shift_Del_p.N2919fs|SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Frame_Shift_Del_p.N2952fs	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2919					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)		AGTTGAAAAATCTTAAGATTA	0.328																																					p.N2919fs		Atlas-Indel,Pindel	.											.	SYNE2	577	.	0			c.8756delA						PASS	.						31	29	30					14																	64519388		1834	4083	5917	SO:0001589	frameshift_variant	23224	exon48			.	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"nuclear envelope spectrin repeat-2", "nucleus and actin connecting element"	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.8757delT	chr14.hg19:g.64519388delT	ENSP00000341781:p.Asn2919fs	146.0	0.0	0		120.0	52.0	0.433333	NM_015180	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Frame_Shift_Del	DEL	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.	.	none		0.328	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		-	64519388	T	-	64519388	7	5	265	1	0	1	0	1	0	0	0	0	15458	1432	50	0	8943	0	SYNE2	14	64519388	Frame_Shift_Del	DEL	T	TCGA-UZ-A9PU-01A-11D-A42J-10		64519388	42830152	44	16706											
SYNE2	23224	hgsc.bcm.edu	37	chr14	64669618	64669618	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaattgagtctgagctttcCaagcctgttgtttatgatgt	8	16	10	7	1	1	3	0	3	1	0	2	4	2	3	2	0	2	3	2	0	3	5			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr14:64669618C>T	ENST00000344113.4	+	100	18350	c.18138C>T	c.(18136-18138)tcC>tcT	p.S6046S	ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Silent_p.S2680S|SYNE2_ENST00000358025.3_Silent_p.S6046S|SYNE2_ENST00000357395.3_Silent_p.S2431S|SYNE2_ENST00000394768.2_Silent_p.S2431S|SYNE2_ENST00000555022.1_5'Flank|SYNE2_ENST00000554584.1_Silent_p.S6008S	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	6046					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)		CTGAGCTTTCCAAGCCTGTTG	0.483																																					p.S6046S		Atlas-SNP	.											.	SYNE2	577	.	0			c.C18138T						PASS	.						142	124	130					14																	64669618		2203	4300	6503	SO:0001819	synonymous_variant	23224	exon100			GCTTTCCAAGCCT	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.18138C>T	chr14.hg19:g.64669618C>T		87.0	0.0	.		65.0	31.0	.	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.	.	none		0.483	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		T	64669618	C	T	64669618	2	4	265	1	0	0	0	0	0	0	0	1	15458	581	21	2		2	SYNE2	14	64669618	Silent	SNP	C	TCGA-UZ-A9PU-01A-11D-A42J-10	150230	64669618	42679922	45	16707											
SNW1	22938	hgsc.bcm.edu	37	chr14	78203382	78203382	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataaccctctgtttagctccAgagttgaatgccactccttg	9	13	7	12	0	1	2	0	1	1	1	3	2	3	2	4	0	3	3	4	0	3	5			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr14:78203382A>G	ENST00000261531.7	-	6	632	c.570T>C	c.(568-570)tcT>tcC	p.S190S	SNW1_ENST00000554775.1_Silent_p.S28S|SLIRP_ENST00000557431.1_Intron|SNW1_ENST00000555761.1_Silent_p.S190S	NM_012245.2	NP_036377.1	Q13573	SNW1_HUMAN	SNW domain containing 1	190	SNW.				cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of vitamin D receptor signaling pathway (GO:0070564)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of vitamin D receptor signaling pathway (GO:0070562)|retinoic acid receptor signaling pathway (GO:0048384)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|chromatin (GO:0000785)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	Notch binding (GO:0005112)|nuclear hormone receptor binding (GO:0035257)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)|SMAD binding (GO:0046332)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|vitamin D receptor binding (GO:0042809)			NS(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		GTTTAGCTCCAGAGTTGAATG	0.398																																					p.S190S		Atlas-SNP	.											.	SNW1	44	.	0			c.T570C						PASS	.						156	140	145					14																	78203382		2203	4300	6503	SO:0001819	synonymous_variant	22938	exon6			AGCTCCAGAGTTG	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.570T>C	chr14.hg19:g.78203382A>G		24.0	0.0	.		22.0	13.0	.	NM_012245	A8K8A9|Q13483|Q32N03|Q5D0D6	Silent	SNP	ENST00000261531.7	hg19	CCDS9867.1																																																																																			.	.	.	none		0.398	SNW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413912.1	NM_012245		G	78203382	A	G	78203382	2	3	265	1	0	0	0	0	0	0	0	1	14892	175	7	3		3	SNW1	14	78203382	Silent	SNP	A	TCGA-UZ-A9PU-01A-11D-A42J-10	13533764	78203382	29146158	46	16708											
ZWILCH	55055	hgsc.bcm.edu	37	chr15	66838985	66838985	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaggatattctttactaacAtggttacctgcagccaggtg	12	12	9	8	0	1	0	0	0	1	0	1	1	1	1	2	3	5	2	2	3	5	6			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr15:66838985A>G	ENST00000307897.5	+	18	2124	c.1744A>G	c.(1744-1746)Atg>Gtg	p.M582V	ZWILCH_ENST00000446801.2_Missense_Mutation_p.M468V|ZWILCH_ENST00000535141.2_Missense_Mutation_p.M468V|ZWILCH_ENST00000565627.1_Missense_Mutation_p.M468V	NM_017975.3	NP_060445.3	Q9H900	ZWILC_HUMAN	zwilch kinetochore protein	582					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|kinetochore (GO:0000776)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(1)|lung(6)|ovary(1)	18						CTTTACTAACATGGTTACCTG	0.368																																					p.M582V		Atlas-SNP	.											.	ZWILCH	46	.	0			c.A1744G						PASS	.						108	105	106					15																	66838985		2201	4299	6500	SO:0001583	missense	55055	exon18			ACTAACATGGTTA	AK023175	CCDS10219.1, CCDS73746.1	15q22.31	2013-01-17	2012-12-13		ENSG00000174442	ENSG00000174442			25468	protein-coding gene	gene with protein product		609984	"Zwilch, kinetochore associated, homolog (Drosophila)"			12686595	Standard	NM_017975		Approved	FLJ10036, KNTC1AP	uc002aqb.3	Q9H900	OTTHUMG00000133194	ENST00000307897.5:c.1744A>G	chr15.hg19:g.66838985A>G	ENSP00000311429:p.Met582Val	76.0	0.0	.		50.0	21.0	.	NM_017975	B3KVB8|Q6N049|Q8N404|Q96SY7|Q9NWG7	Missense_Mutation	SNP	ENST00000307897.5	hg19	CCDS10219.1	.	.	.	.	.	.	.	.	.	.	A	15.98	2.993504	0.54041	.	.	ENSG00000174442	ENST00000307897;ENST00000446801;ENST00000535141	T;T;T	0.40756	1.02;1.02;1.02	5.63	-7.38	0.01407	.	0.476664	0.26539	N	0.023813	T	0.28699	0.0711	M	0.64997	1.995	0.09310	N	1	B	0.25809	0.135	B	0.23852	0.049	T	0.09574	-1.0668	10	0.62326	D	0.03	-4.3179	4.9984	0.14251	0.2239:0.5001:0.1786:0.0973	.	582	Q9H900	ZWILC_HUMAN	V	582;468;468	ENSP00000311429:M582V;ENSP00000402217:M468V;ENSP00000437749:M468V	ENSP00000311429:M582V	M	+	1	0	ZWILCH	64626039	0.001000	0.12720	0.000000	0.03702	0.948000	0.59901	-0.202000	0.09451	-1.637000	0.01531	-1.883000	0.00544	ATG	.	.	.	none		0.368	ZWILCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256904.4	NM_017975		G	66838985	A	G	66838985	3	3	265	1	0	0	0	0	1	0	0	0	18260	217	8	3	1814	3	ZWILCH	15	66838985	Missense_Mutation	SNP	A	TCGA-UZ-A9PU-01A-11D-A42J-10		66838985	35692407	47	16709											
CYP1A2	1544	hgsc.bcm.edu	37	chr15	75042609	75042609	+	Missense_Mutation	SNP	A	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	ggccctgatcagcaggttgcAggagctgatggcagggcctg	7	7	17	10	0	1	2	1	2	0	0	1	3	1	3	2	5	3	5	2	5	0	1			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr15:75042609A>C	ENST00000343932.4	+	2	593	c.530A>C	c.(529-531)cAg>cCg	p.Q177P		NM_000761.3	NP_000752.2	P05177	CP1A2_HUMAN	cytochrome P450, family 1, subfamily A, polypeptide 2	177					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)"	AGCAGGTTGCAGGAGCTGATG	0.582																																					p.Q177P		Atlas-SNP	.											.	CYP1A2	70	.	0			c.A530C						PASS	.						157	129	138					15																	75042609		2197	4296	6493	SO:0001583	missense	1544	exon2			GGTTGCAGGAGCT	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.530A>C	chr15.hg19:g.75042609A>C	ENSP00000342007:p.Gln177Pro	53.0	0.0	.		58.0	22.0	.	NM_000761	Q16754|Q6NWU5|Q9BXX7|Q9UK49	Missense_Mutation	SNP	ENST00000343932.4	hg19	CCDS32293.1	.	.	.	.	.	.	.	.	.	.	A	13.97	2.395368	0.42512	.	.	ENSG00000140505	ENST00000343932	T	0.70045	-0.45	4.98	3.82	0.43975	.	0.467933	0.25916	N	0.027474	D	0.82586	0.5069	M	0.92649	3.33	0.30278	N	0.791562	D	0.69078	0.997	D	0.70227	0.968	T	0.79804	-0.1649	10	0.30854	T	0.27	.	9.8555	0.41084	0.7119:0.0:0.0:0.2881	.	177	P05177-2	.	P	177	ENSP00000342007:Q177P	ENSP00000342007:Q177P	Q	+	2	0	CYP1A2	72829662	0.026000	0.19158	0.926000	0.36857	0.943000	0.58893	1.348000	0.33987	0.879000	0.35944	0.459000	0.35465	CAG	.	.	.	none		0.582	CYP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421263.2	NM_000761		C	75042609	A	C	75042609	3	2	265	1	0	0	0	0	1	0	0	0	4152	188	7	5	532	5	CYP1A2	15	75042609	Missense_Mutation	SNP	A	TCGA-UZ-A9PU-01A-11D-A42J-10	8203624	75042609	27488783	48	16710											
IL16	3603	hgsc.bcm.edu	37	chr15	81598444	81598444	+	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	ctccagaggccatgcccgacCtcaactcctccactgactct	8	8	6	19	1	2	2	1	1	1	1	5	3	5	2	6	1	2	0	6	1	1	0			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr15:81598444C>G	ENST00000302987.4	+	16	3616	c.3616C>G	c.(3616-3618)Ctc>Gtc	p.L1206V	RP11-761I4.4_ENST00000607019.1_RNA|IL16_ENST00000394660.2_Missense_Mutation_p.L1206V|IL16_ENST00000394652.2_Missense_Mutation_p.L505V			Q14005	IL16_HUMAN	interleukin 16	1206					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						CATGCCCGACCTCAACTCCTC	0.567																																					p.L1206V		Atlas-SNP	.											.	IL16	254	.	0			c.C3616G						PASS	.						89	92	91					15																	81598444		2203	4300	6503	SO:0001583	missense	3603	exon17			CCCGACCTCAACT	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.3616C>G	chr15.hg19:g.81598444C>G	ENSP00000302935:p.Leu1206Val	43.0	0.0	.		32.0	10.0	.	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Missense_Mutation	SNP	ENST00000302987.4	hg19	CCDS42069.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.66|13.66	2.303149|2.303149	0.40795|0.40795	.|.	.|.	ENSG00000172349|ENSG00000172349	ENST00000394660;ENST00000355368;ENST00000302987;ENST00000394653;ENST00000394652;ENST00000394656|ENST00000329842	T;T;T|.	0.39229|.	2.64;1.09;1.09|.	5.03|5.03	3.04|3.04	0.35103|0.35103	PDZ/DHR/GLGF (2);|.	0.206204|.	0.24341|.	N|.	0.039367|.	T|T	0.55955|0.55955	0.1953|0.1953	M|M	0.75447|0.75447	2.3|2.3	0.09310|0.09310	N|N	1|1	D;P;P;P;B|.	0.57571|.	0.98;0.601;0.843;0.601;0.029|.	P;B;D;B;B|.	0.68192|.	0.815;0.425;0.956;0.242;0.099|.	T|T	0.50259|0.50259	-0.8849|-0.8849	10|6	0.29301|0.72032	T|D	0.29|0.01	.|.	8.2659|8.2659	0.31813|0.31813	0.152:0.7674:0.0:0.0806|0.152:0.7674:0.0:0.0806	.|.	1038;699;596;1206;1206|.	F8W7Z5;Q6ZTT5;B3KY62;Q14005;Q14005-2|.	.;.;.;IL16_HUMAN;.|.	V|R	1206;1038;1206;596;505;505|716	ENSP00000378155:L1206V;ENSP00000302935:L1206V;ENSP00000378147:L505V|.	ENSP00000302935:L1206V|ENSP00000329317:P716R	L|P	+|+	1|2	0|0	IL16|IL16	79385499|79385499	0.766000|0.766000	0.28496|0.28496	0.148000|0.148000	0.22405|0.22405	0.023000|0.023000	0.10783|0.10783	1.183000|1.183000	0.32041|0.32041	1.027000|1.027000	0.39758|0.39758	0.561000|0.561000	0.74099|0.74099	CTC|CCT	.	.	.	none		0.567	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217		G	81598444	C	G	81598444	3	3	265	1	0	0	0	0	1	0	0	0	7640	681	24	4	3678	4	IL16	15	81598444	Missense_Mutation	SNP	C	TCGA-UZ-A9PU-01A-11D-A42J-10	6555835	81598444	20932948	49	16711											
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1270632	1270632	+	Frame_Shift_Del	DEL	C	C	-																															ctcacagggactccctggagCccacagagggctcaggcgcc																								rs532352517		TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr16:1270632delC	ENST00000348261.5	+	35	6948	c.6700delC	c.(6700-6702)cccfs	p.P2234fs	CACNA1H_ENST00000565831.1_Frame_Shift_Del_p.P2228fs|CACNA1H_ENST00000358590.4_Frame_Shift_Del_p.P2228fs	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	2234					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)	CTCCCTGGAGCCCACAGAGGG	0.746																																					p.E2233fs		Atlas-Indel,Pindel	.											.	CACNA1H	317	.	0			c.6699delG						PASS	.						7	8	8					16																	1270632		1700	3835	5535	SO:0001589	frameshift_variant	8912	exon35			.	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.6700delC	chr16.hg19:g.1270632delC	ENSP00000334198:p.Pro2234fs	52.0	0.0	0		74.0	21.0	0.283784	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Frame_Shift_Del	DEL	ENST00000348261.5	hg19	CCDS45375.1																																																																																			.	.	.	none		0.746	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		-	1270632	C	-	1270632	7	5	265	1	0	1	0	1	0	0	0	0	2547	739	26	0	6834	0	CACNA1H	16	1270632	Frame_Shift_Del	DEL	C	TCGA-UZ-A9PU-01A-11D-A42J-10		1270632	89084121	50	16712											
NLRP1	22861	hgsc.bcm.edu	37	chr17	5445303	5445303	+	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	ggttggctctcagcccaaagGcaaggtccttgcagtcctca	8	9	11	13	0	2	0	2	0	1	0	5	0	4	0	3	4	2	4	3	4	2	2			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr17:5445303G>T	ENST00000572272.1	-	6	2572	c.2573C>A	c.(2572-2574)gCc>gAc	p.A858D	NLRP1_ENST00000345221.3_Missense_Mutation_p.A858D|NLRP1_ENST00000577119.1_Missense_Mutation_p.A858D|NLRP1_ENST00000354411.3_Missense_Mutation_p.A858D|NLRP1_ENST00000269280.4_Missense_Mutation_p.A858D|NLRP1_ENST00000262467.5_Missense_Mutation_p.A858D|NLRP1_ENST00000571307.1_5'UTR			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	858					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)				CAGCCCAAAGGCAAGGTCCTT	0.557																																					p.A858D		Atlas-SNP	.											.	NLRP1	358	.	0			c.C2573A						PASS	.						81	62	68					17																	5445303		2203	4300	6503	SO:0001583	missense	22861	exon6			CCAAAGGCAAGGT	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.2573C>A	chr17.hg19:g.5445303G>T	ENSP00000460475:p.Ala858Asp	50.0	0.0	.		51.0	17.0	.	NM_033007	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	hg19	CCDS42246.1	.	.	.	.	.	.	.	.	.	.	G	12.85	2.061098	0.36373	.	.	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221;ENST00000537069	T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96	2.13	1.13	0.20643	.	0.496363	0.15148	N	0.277896	T	0.65015	0.2651	M	0.93638	3.44	0.09310	N	1	D;D;D;D;D;D	0.76494	0.999;0.998;0.998;0.998;0.999;0.997	D;D;D;P;D;D	0.66351	0.929;0.943;0.943;0.852;0.929;0.925	T	0.53493	-0.8431	10	0.66056	D	0.02	.	4.7785	0.13190	0.1885:0.0:0.8115:0.0	.	124;858;858;858;858;858	F5H042;Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;.;NALP1_HUMAN;.;.	D	858;858;858;858;858;124	ENSP00000442029:A858D;ENSP00000262467:A858D;ENSP00000269280:A858D;ENSP00000346390:A858D;ENSP00000324366:A858D	ENSP00000262467:A858D	A	-	2	0	NLRP1	5386027	0.049000	0.20398	0.014000	0.15608	0.010000	0.07245	2.010000	0.40913	0.494000	0.27859	-0.266000	0.10368	GCC	.	.	.	none		0.557	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004		T	5445303	G	T	5445303	3	4	265	1	0	0	0	0	1	0	0	0	10478	1203	42	4	1971	4	NLRP1	17	5445303	Missense_Mutation	SNP	G	TCGA-UZ-A9PU-01A-11D-A42J-10		5445303	75749907	51	16713											
SENP3	26168	hgsc.bcm.edu	37	chr17	7474732	7474733	+	In_Frame_Ins	INS	-	-	CAA																															ctcagccattcagcttcaccINScagcaggacatgcccaaact																										TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr17:7474732_7474733insCAA	ENST00000429205.2	+	12	1705_1706	c.1656_1657insCAA	c.(1657-1659)cag>CAAcag	p.553_553Q>QQ	SENP3_ENST00000578868.1_3'UTR|SENP3_ENST00000321337.7_In_Frame_Ins_p.552_552Q>QQ|SENP3-EIF4A1_ENST00000579777.1_RNA|EIF4A1_ENST00000582746.1_5'Flank|EIF4A1_ENST00000380512.5_5'Flank|EIF4A1_ENST00000293831.8_5'Flank|EIF4A1_ENST00000577269.1_5'Flank			Q9H4L4	SENP3_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 3	553						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)				TCAGCTTCACCCAGCAGGACAT	0.54																																					p.T552delinsTQ		Atlas-INDEL	.											.	SENP3	18	.	0			c.1656_1657insCAA						PASS	.																																			SO:0001652	inframe_insertion	26168	exon12			.	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		Exception_encountered	chr17.hg19:g.7474732_7474733insCAA	ENSP00000403712:p.Gln554dup	70.0	0.0	0		52.0	18.0	0.346154	NM_015670	Q66K15|Q86VS7|Q96PS4|Q9Y3W9	In_Frame_Ins	INS	ENST00000429205.2	hg19																																																																																				.	.	.	none		0.54	SENP3-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015670		CAA	7474733	-	CAA	7474732	7	5	265	1	0	1	1	0	0	0	0	0	14061	610	22	0	1695	0	SENP3	17	7474732	In_Frame_Ins	INS	-	TCGA-UZ-A9PU-01A-11D-A42J-10	2029429	7474732	73720478	52	16714	176	2									
SENP3	26168	hgsc.bcm.edu	37	chr17	7474735	7474735	+	Silent	SNP	G	G	A																															cagccattcagcttcacccaGcaggacatgcccaaacttcg																										TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr17:7474735G>A	ENST00000429205.2	+	12	1708	c.1659G>A	c.(1657-1659)caG>caA	p.Q553Q	SENP3_ENST00000578868.1_3'UTR|SENP3_ENST00000321337.7_Silent_p.Q552Q|SENP3-EIF4A1_ENST00000579777.1_RNA|EIF4A1_ENST00000582746.1_5'Flank|EIF4A1_ENST00000380512.5_5'Flank|EIF4A1_ENST00000293831.8_5'Flank|EIF4A1_ENST00000577269.1_5'Flank			Q9H4L4	SENP3_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 3	553						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)				GCTTCACCCAGCAGGACATGC	0.547																																					p.Q553Q		Atlas-SNP	.											.	SENP3	18	.	0			c.G1659A						PASS	.						102	101	102					17																	7474735		1987	4188	6175	SO:0001819	synonymous_variant	26168	exon12			CACCCAGCAGGAC	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.1659G>A	chr17.hg19:g.7474735G>A		69.0	0.0	.		52.0	9.0	.	NM_015670	Q66K15|Q86VS7|Q96PS4|Q9Y3W9	Silent	SNP	ENST00000429205.2	hg19																																																																																				.	.	.	none		0.547	SENP3-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015670		A	7474735	G	A	7474735	2	1	265	1	0	0	0	0	0	0	0	1	14061	962	34	2		2	SENP3	17	7474735	Silent	SNP	G	TCGA-UZ-A9PU-01A-11D-A42J-10	3	7474735	73720475	53	16715	176	2									
MAPT	4137	hgsc.bcm.edu	37	chr17	44073780	44073780	+	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	cccaggtgaacctccaaaatCaggggatcgcagcggctaca	12	5	11	13	2	1	1	1	1	0	0	3	2	2	2	3	4	3	2	3	4	4	1			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr17:44073780C>A	ENST00000571987.1	+	9	1523	c.1523C>A	c.(1522-1524)tCa>tAa	p.S508*	MAPT_ENST00000431008.3_Nonsense_Mutation_p.S191*|MAPT_ENST00000446361.3_Nonsense_Mutation_p.S133*|MAPT_ENST00000420682.2_Nonsense_Mutation_p.S162*|MAPT_ENST00000347967.5_Nonsense_Mutation_p.S97*|MAPT_ENST00000334239.8_Nonsense_Mutation_p.S133*|STH_ENST00000537309.1_5'Flank|MAPT_ENST00000262410.5_Nonsense_Mutation_p.S508*|MAPT_ENST00000344290.5_Nonsense_Mutation_p.S526*|MAPT_ENST00000351559.5_Nonsense_Mutation_p.S191*|MAPT_ENST00000570299.1_3'UTR|MAPT_ENST00000574436.1_Nonsense_Mutation_p.S191*|MAPT_ENST00000535772.1_Nonsense_Mutation_p.S191*|MAPT_ENST00000576518.1_Nonsense_Mutation_p.S122*|MAPT_ENST00000340799.5_Nonsense_Mutation_p.S162*|MAPT_ENST00000415613.2_Nonsense_Mutation_p.S526*			P10636	TAU_HUMAN	microtubule-associated protein tau	508					adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	CCTCCAAAATCAGGGGATCGC	0.682																																					p.S526X		Atlas-SNP	.											.	MAPT	135	.	0			c.C1577A						PASS	.						18	23	21					17																	44073780		2179	4264	6443	SO:0001587	stop_gained	4137	exon11			CAAAATCAGGGGA	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"G protein beta1/gamma2 subunit-interacting factor 1", "microtubule-associated protein tau, isoform 4", "protein phosphatase 1, regulatory subunit 103"	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.1523C>A	chr17.hg19:g.44073780C>A	ENSP00000458742:p.Ser508*	56.0	0.0	.		59.0	32.0	.	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Nonsense_Mutation	SNP	ENST00000571987.1	hg19	CCDS11501.1	.	.	.	.	.	.	.	.	.	.	C	36	5.672474	0.96754	.	.	ENSG00000186868	ENST00000344290;ENST00000262410;ENST00000351559;ENST00000340799;ENST00000535772;ENST00000347967;ENST00000354326;ENST00000446361;ENST00000334239;ENST00000420682;ENST00000415613;ENST00000431008	.	.	.	5.62	5.62	0.85841	.	0.000000	0.39985	N	0.001217	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.1915	18.2196	0.89897	0.0:1.0:0.0:0.0	.	.	.	.	X	526;508;191;162;191;97;140;133;133;162;526;45	.	ENSP00000262410:S508X	S	+	2	0	MAPT	41429617	1.000000	0.71417	0.996000	0.52242	0.796000	0.44982	5.434000	0.66526	2.651000	0.90000	0.561000	0.74099	TCA	.	.	.	none		0.682	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835		A	44073780	C	A	44073780	4	1	265	1	0	0	0	0	0	1	0	0	9304	838	29	4	1615	4	MAPT	17	44073780	Nonsense_Mutation	SNP	C	TCGA-UZ-A9PU-01A-11D-A42J-10	36599045	44073780	37121430	54	16716											
BZRAP1	9256	hgsc.bcm.edu	37	chr17	56405116	56405116	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttggaactctcctcagaccTcagttcttgaagctgcagag	9	11	9	12	0	4	3	2	1	2	2	5	4	4	4	2	1	3	3	2	1	2	3			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr17:56405116T>C	ENST00000343736.4	-	1	329	c.166A>G	c.(166-168)Agg>Ggg	p.R56G	BZRAP1-AS1_ENST00000579527.1_RNA|BZRAP1_ENST00000355701.3_Missense_Mutation_p.R56G|BZRAP1_ENST00000268893.6_Missense_Mutation_p.R56G|BZRAP1-AS1_ENST00000580515.1_RNA|BZRAP1-AS1_ENST00000578334.1_RNA|BZRAP1-AS1_ENST00000580633.1_RNA			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	56						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)					TCCTCAGACCTCAGTTCTTGA	0.622																																					p.R56G		Atlas-SNP	.											.	BZRAP1	287	.	0			c.A166G						PASS	.						72	65	67					17																	56405116		2203	4300	6503	SO:0001583	missense	9256	exon1			CAGACCTCAGTTC	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.166A>G	chr17.hg19:g.56405116T>C	ENSP00000345824:p.Arg56Gly	50.0	0.0	.		59.0	16.0	.	NM_024418	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	hg19	CCDS11605.1	.	.	.	.	.	.	.	.	.	.	T	9.117	1.008075	0.19199	.	.	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	T;T;T	0.05447	3.57;3.57;3.44	4.87	0.943	0.19531	.	0.624206	0.15757	N	0.246132	T	0.03827	0.0108	L	0.31294	0.92	0.09310	N	1	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.08055	0.0;0.001;0.003	T	0.47156	-0.9139	10	0.09084	T	0.74	.	6.0457	0.19758	0.0:0.3872:0.0:0.6128	.	56;56;56	B7ZVZ7;O95153-2;O95153	.;.;RIMB1_HUMAN	G	56	ENSP00000347929:R56G;ENSP00000345824:R56G;ENSP00000268893:R56G	ENSP00000268893:R56G	R	-	1	2	BZRAP1	53760115	0.001000	0.12720	0.004000	0.12327	0.106000	0.19336	0.525000	0.22956	0.299000	0.22661	0.379000	0.24179	AGG	.	.	.	none		0.622	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758		C	56405116	T	C	56405116	3	2	265	1	0	0	0	0	1	0	0	0	1579	1550	54	3	5531	3	BZRAP1	17	56405116	Missense_Mutation	SNP	T	TCGA-UZ-A9PU-01A-11D-A42J-10	12331336	56405116	24790094	55	16717											
CLUL1	27098	hgsc.bcm.edu	37	chr18	619309	619309	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catgatggaaagaaaagagaAggaacacaccaatctaatga	21	5	9	6	0	1	4	0	2	1	2	1	7	1	6	1	2	1	0	1	2	7	1			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr18:619309A>G	ENST00000400606.2	+	3	348	c.203A>G	c.(202-204)aAg>aGg	p.K68R	CLUL1_ENST00000579494.1_Missense_Mutation_p.K68R|CLUL1_ENST00000338387.7_Missense_Mutation_p.K68R|CLUL1_ENST00000580436.1_3'UTR|CLUL1_ENST00000540035.1_Missense_Mutation_p.K120R|CLUL1_ENST00000581619.1_Missense_Mutation_p.K93R	NM_014410.4	NP_055225.1	Q15846	CLUL1_HUMAN	clusterin-like 1 (retinal)	68					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						AGAAAAGAGAAGGAACACACC	0.398																																					p.K68R		Atlas-SNP	.											.	CLUL1	57	.	0			c.A203G						PASS	.						143	133	136					18																	619309		1903	4129	6032	SO:0001583	missense	27098	exon3			AAGAGAAGGAACA	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.203A>G	chr18.hg19:g.619309A>G	ENSP00000383449:p.Lys68Arg	215.0	0.0	.		146.0	59.0	.	NM_199167	A0FDN7	Missense_Mutation	SNP	ENST00000400606.2	hg19	CCDS42405.1	.	.	.	.	.	.	.	.	.	.	A	12.97	2.096911	0.37048	.	.	ENSG00000079101	ENST00000400606;ENST00000540035;ENST00000338387	T;T;T	0.24151	1.87;1.87;1.87	5.26	3.97	0.46021	Clusterin, N-terminal (1);	0.286892	0.38663	N	0.001609	T	0.17789	0.0427	N	0.22421	0.69	0.21325	N	0.999722	B;B	0.30973	0.257;0.302	B;B	0.30855	0.074;0.121	T	0.19484	-1.0304	10	0.54805	T	0.06	-9.7385	11.7298	0.51730	0.8008:0.0:0.0:0.1991	.	120;68	F5GWQ8;Q15846	.;CLUL1_HUMAN	R	68;120;68	ENSP00000383449:K68R;ENSP00000441726:K120R;ENSP00000341128:K68R	ENSP00000341128:K68R	K	+	2	0	CLUL1	609309	1.000000	0.71417	1.000000	0.80357	0.794000	0.44872	3.195000	0.51013	1.989000	0.58080	0.528000	0.53228	AAG	.	.	.	none		0.398	CLUL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441183.1			G	619309	A	G	619309	3	3	265	1	0	0	0	0	1	0	0	0	3572	72	3	3	209	3	CLUL1	18	619309	Missense_Mutation	SNP	A	TCGA-UZ-A9PU-01A-11D-A42J-10		619309	77457939	56	16718											
CLIP3	25999	hgsc.bcm.edu	37	chr19	36510103	36510103	+	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	agggcagatgaagtaccgaaCgcccccaacgctgccatcgt	11	5	11	14	4	0	2	0	1	0	1	1	3	0	2	4	1	4	3	4	1	4	1			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr19:36510103C>T	ENST00000360535.4	-	8	1251	c.1024G>A	c.(1024-1026)Gtt>Att	p.V342I	AC002116.7_ENST00000586962.1_RNA|CLIP3_ENST00000593074.1_Missense_Mutation_p.V342I	NM_015526.2	NP_056341.1	Q96DZ5	CLIP3_HUMAN	CAP-GLY domain containing linker protein 3	342	CAP-Gly 1. {ECO:0000255|PROSITE- ProRule:PRU00045}.				chaperone-mediated protein transport (GO:0072321)|fat cell differentiation (GO:0045444)|membrane biogenesis (GO:0044091)|negative regulation of microtubule polymerization (GO:0031115)|peptidyl-L-cysteine S-palmitoylation (GO:0018230)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endocytosis (GO:0045807)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein phosphorylation (GO:0001934)	early endosome membrane (GO:0031901)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|trans-Golgi network (GO:0005802)|trans-Golgi network membrane (GO:0032588)	ganglioside binding (GO:0035594)|microtubule binding (GO:0008017)			cervix(1)|endometrium(6)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	23	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			AAGTACCGAACGCCCCCAACG	0.637																																					p.V342I		Atlas-SNP	.											.	CLIP3	53	.	0			c.G1024A						PASS	.						109	92	98					19																	36510103		2203	4300	6503	SO:0001583	missense	25999	exon7			ACCGAACGCCCCC	AJ427922	CCDS12486.1	19q13.12	2014-08-12			ENSG00000105270	ENSG00000105270		"Ankyrin repeat domain containing"	24314	protein-coding gene	gene with protein product	"CLIP-170-related", "restin-like 1"	607382				11854307	Standard	NM_015526		Approved	CLIPR-59, RSNL1	uc002ocz.2	Q96DZ5	OTTHUMG00000181747	ENST00000360535.4:c.1024G>A	chr19.hg19:g.36510103C>T	ENSP00000353732:p.Val342Ile	35.0	0.0	.		26.0	11.0	.	NM_001199570	A8K0E4|Q8WWL1|Q96C99|Q9UFT7	Missense_Mutation	SNP	ENST00000360535.4	hg19	CCDS12486.1	.	.	.	.	.	.	.	.	.	.	c	13.77	2.336043	0.41398	.	.	ENSG00000105270	ENST00000360535;ENST00000544037;ENST00000534959	T	0.75477	-0.94	5.25	4.21	0.49690	Cytoskeleton-associated protein, Gly-rich domain (4);Cytoskeleton-associated protein, Gly-rich conserved site (1);	0.158804	0.47852	D	0.000220	T	0.55705	0.1937	N	0.25060	0.705	0.32427	N	0.548523	B	0.14805	0.011	B	0.12837	0.008	T	0.55528	-0.8127	10	0.23891	T	0.37	-29.9258	7.0873	0.25264	0.0:0.8131:0.0:0.1869	.	342	Q96DZ5	CLIP3_HUMAN	I	342;224;318	ENSP00000353732:V342I	ENSP00000353732:V342I	V	-	1	0	CLIP3	41201943	0.638000	0.27225	0.983000	0.44433	0.899000	0.52679	1.249000	0.32839	2.478000	0.83669	0.580000	0.79431	GTT	.	.	.	none		0.637	CLIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457426.1	NM_015526		T	36510103	C	T	36510103	3	4	265	1	0	0	0	0	1	0	0	0	3536	536	19	1	647	1	CLIP3	19	36510103	Missense_Mutation	SNP	C	TCGA-UZ-A9PU-01A-11D-A42J-10		36510103	22618880	57	16719											
PRR12	57479	hgsc.bcm.edu	37	chr19	50105116	50105116	+	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	ccggcgagagtggcggagagGgcatcttccgggaacgggac	8	4	19	10	5	1	2	0	0	1	2	2	6	2	4	2	6	1	1	2	6	1	1			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr19:50105116G>C	ENST00000418929.2	+	6	4726	c.4714G>C	c.(4714-4716)Ggc>Cgc	p.G1572R		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	751							DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		TGGCGGAGAGGGCATCTTCCG	0.642																																					p.G1572R		Atlas-SNP	.											.	PRR12	157	.	0			c.G4714C						PASS	.						23	32	29					19																	50105116		2055	4175	6230	SO:0001583	missense	57479	exon6			GGAGAGGGCATCT	AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"KIAA1205"	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.4714G>C	chr19.hg19:g.50105116G>C	ENSP00000394510:p.Gly1572Arg	122.0	0.0	.		69.0	27.0	.	NM_020719	E9PB06|Q8N4J6	Missense_Mutation	SNP	ENST00000418929.2	hg19	CCDS46143.1	.	.	.	.	.	.	.	.	.	.	G	8.279	0.815113	0.16607	.	.	ENSG00000126464	ENST00000418929;ENST00000246798;ENST00000314734	.	.	.	3.72	3.72	0.42706	.	0.200317	0.24566	N	0.037429	T	0.68897	0.3051	L	0.48642	1.525	0.47407	D	0.999416	D	0.89917	1.0	D	0.76575	0.988	T	0.73094	-0.4091	9	0.87932	D	0	-14.9557	14.4198	0.67175	0.0:0.0:1.0:0.0	.	1572	Q9ULL5-3	.	R	1572;752;752	.	ENSP00000246798:G752R	G	+	1	0	PRR12	54796928	1.000000	0.71417	1.000000	0.80357	0.369000	0.29798	7.892000	0.87324	1.902000	0.55061	0.305000	0.20034	GGC	.	.	.	none		0.642	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719		C	50105116	G	C	50105116	3	2	265	1	0	0	0	0	1	0	0	0	12594	1232	43	4	4736	4	PRR12	19	50105116	Missense_Mutation	SNP	G	TCGA-UZ-A9PU-01A-11D-A42J-10	13595013	50105116	9023867	58	16720											
ZNF616	90317	hgsc.bcm.edu	37	chr19	52618903	52618903	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgcactgcaagacgtgaaTgttgactgaagaccttgcca	12	9	11	9	1	0	5	0	3	0	2	0	6	0	5	2	0	3	3	2	0	3	2			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr19:52618903T>C	ENST00000600228.1	-	4	1775	c.1514A>G	c.(1513-1515)cAt>cGt	p.H505R	ZNF616_ENST00000330123.5_3'UTR	NM_178523.3	NP_848618.2	Q08AN1	ZN616_HUMAN	zinc finger protein 616	505					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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)		AAGACGTGAATGTTGACTGAA	0.423																																					p.H505R		Atlas-SNP	.											.	ZNF616	109	.	0			c.A1514G						PASS	.						114	106	109					19																	52618903		2203	4300	6503	SO:0001583	missense	90317	exon4			CGTGAATGTTGAC	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.1514A>G	chr19.hg19:g.52618903T>C	ENSP00000471000:p.His505Arg	57.0	0.0	.		55.0	21.0	.	NM_178523	B3KRV1|Q0P658|Q658V7	Missense_Mutation	SNP	ENST00000600228.1	hg19	CCDS33090.1	.	.	.	.	.	.	.	.	.	.	T	0.097	-1.157827	0.01686	.	.	ENSG00000204611	ENST00000330123	.	.	.	1.08	-1.23	0.09465	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08313	0.0207	N	0.00980	-1.08	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.37150	-0.9718	8	0.14252	T	0.57	.	6.2605	0.20897	0.0:0.5161:0.0:0.4839	.	505	Q08AN1	ZN616_HUMAN	R	505	.	ENSP00000328722:H505R	H	-	2	0	ZNF616	57310715	0.000000	0.05858	0.000000	0.03702	0.130000	0.20726	-4.154000	0.00284	-0.563000	0.06078	0.254000	0.18369	CAT	.	.	.	none		0.423	ZNF616-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462451.1	XM_030892		C	52618903	T	C	52618903	3	2	265	1	0	0	0	0	1	0	0	0	18053	1464	51	3	835	3	ZNF616	19	52618903	Missense_Mutation	SNP	T	TCGA-UZ-A9PU-01A-11D-A42J-10	2513787	52618903	6510080	59	16721											
ZNF256	10172	hgsc.bcm.edu	37	chr19	58452978	58452978	+	Frame_Shift_Del	DEL	G	G	-																															aggcccttctccaatgtgaaGtctccggtgtttaatgaggt																										TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr19:58452978delG	ENST00000282308.3	-	3	1394	c.1198delC	c.(1198-1200)cttfs	p.L400fs	ZNF256_ENST00000598928.1_3'UTR	NM_005773.2	NP_005764.2	Q9Y2P7	ZN256_HUMAN	zinc finger protein 256	400					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0155)		CCAATGTGAAGTCTCCGGTGT	0.428																																					p.L400fs	NSCLC(55;1313 1552 8040 11996)	Atlas-Indel,Pindel	.											.	ZNF256	117	.	0			c.1199delT						PASS	.						71	68	69					19																	58452978		2203	4300	6503	SO:0001589	frameshift_variant	10172	exon3			.	AF067165	CCDS12966.1	19q13	2013-01-08				ENSG00000152454		"Zinc fingers, C2H2-type", "-"	13049	protein-coding gene	gene with protein product		606956					Standard	NM_005773		Approved	BMZF-3	uc002qqu.3	Q9Y2P7		ENST00000282308.3:c.1198delC	chr19.hg19:g.58452978delG	ENSP00000282308:p.Leu400fs	66.0	0.0	0		61.0	27.0	0.442623	NM_005773	B2RA92|Q53Y85|Q9BV71	Frame_Shift_Del	DEL	ENST00000282308.3	hg19	CCDS12966.1																																																																																			.	.	.	none		0.428	ZNF256-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466702.1			-	58452978	G	-	58452978	7	5	265	1	0	1	0	1	0	0	0	0	17811	1029	36	0	689	0	ZNF256	19	58452978	Frame_Shift_Del	DEL	G	TCGA-UZ-A9PU-01A-11D-A42J-10	5834075	58452978	676005	60	16722											
NPEPL1	79716	hgsc.bcm.edu	37	chr20	57268875	57268875	+	Frame_Shift_Del	DEL	C	C	-																															gaactacgccaccgtggctgCcctgccctgcagggtgagcc																										TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr20:57268875delC	ENST00000356091.6	+	2	521	c.233delC	c.(232-234)gccfs	p.A78fs	NPEPL1_ENST00000525817.1_Frame_Shift_Del_p.A30fs|STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525967.1_Frame_Shift_Del_p.A50fs	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	78						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)			ACCGTGGCTGCCCTGCCCTGC	0.677																																					p.A78fs		Atlas-INDEL	.											.	NPEPL1	36	.	0			c.232delG						PASS	.						36	44	41					20																	57268875		2088	4197	6285	SO:0001589	frameshift_variant	79716	exon2			.	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.233delC	chr20.hg19:g.57268875delC	ENSP00000348395:p.Ala78fs	174.0	0.0	0		107.0	23.0	0.214953	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Frame_Shift_Del	DEL	ENST00000356091.6	hg19	CCDS46621.1																																																																																			.	.	.	none		0.677	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663		-	57268875	C	-	57268875	7	5	265	1	0	1	0	1	0	0	0	0	10581	739	26	0	85	0	NPEPL1	20	57268875	Frame_Shift_Del	DEL	C	TCGA-UZ-A9PU-01A-11D-A42J-10		57268875	5756645	61	16723	177	4									
NPEPL1	79716	hgsc.bcm.edu	37	chr20	57268877	57268883	+	Frame_Shift_Del	DEL	CTGCCCT	CTGCCCT	-																															actacgccaccgtggctgccCtgccctgcagggtgagccgg																										TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	CTGCCCT	CTGCCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr20:57268877_57268883delCTGCCCT	ENST00000356091.6	+	2	523_529	c.235_241delCTGCCCT	c.(235-243)ctgccctgcfs	p.LPC79fs	NPEPL1_ENST00000525817.1_Frame_Shift_Del_p.LPC31fs|STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525967.1_Frame_Shift_Del_p.LPC51fs	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	79						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)			CGTGGCTGCCCTGCCCTGCAGGGTGAG	0.676																																					p.78_80del		Pindel	.											.	NPEPL1	36	.	0			c.234_240del						PASS	.																																			SO:0001589	frameshift_variant	79716	exon2			.	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.235_241delCTGCCCT	chr20.hg19:g.57268877_57268883delCTGCCCT	ENSP00000348395:p.Leu79fs	171.0	0.0	.		106.0	19.0	0.179	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Frame_Shift_Del	DEL	ENST00000356091.6	hg19	CCDS46621.1																																																																																			.	.	.	none		0.676	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663		-	57268883	CTGCCCT	-	57268877	7	5	265	1	0	1	0	1	0	0	0	0	10581	680	24	0	87	0	NPEPL1	20	57268877	Frame_Shift_Del	DEL	CTGCCCT	TCGA-UZ-A9PU-01A-11D-A42J-10	2	57268877	5756643	62	16724	177	4									
NPEPL1	79716	hgsc.bcm.edu	37	chr20	57268881	57268881	+	Missense_Mutation	SNP	C	C	G																															cgccaccgtggctgccctgcCctgcagggtgagccggcaca																										TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr20:57268881C>G	ENST00000356091.6	+	2	527	c.239C>G	c.(238-240)cCc>cGc	p.P80R	NPEPL1_ENST00000525817.1_Missense_Mutation_p.P32R|STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525967.1_Missense_Mutation_p.P52R	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	80						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)			GCTGCCCTGCCCTGCAGGGTG	0.677																																					p.P80R		Atlas-SNP	.											.	NPEPL1	36	.	0			c.C239G						PASS	.						32	39	37					20																	57268881		2084	4196	6280	SO:0001583	missense	79716	exon2			CCCTGCCCTGCAG	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.239C>G	chr20.hg19:g.57268881C>G	ENSP00000348395:p.Pro80Arg	166.0	0.0	.		97.0	25.0	.	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Missense_Mutation	SNP	ENST00000356091.6	hg19	CCDS46621.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.976448	0.92982	.	.	ENSG00000215440	ENST00000525967;ENST00000525817;ENST00000356091	T;T;T	0.39592	1.13;1.15;1.07	4.97	4.97	0.65823	.	0.000000	0.85682	D	0.000000	T	0.68044	0.2958	M	0.83384	2.64	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79784	0.984;0.993;0.984	T	0.74003	-0.3804	10	0.72032	D	0.01	-36.5305	17.2194	0.86953	0.0:1.0:0.0:0.0	.	80;32;52	Q8NDH3;G5EA34;E9PN47	PEPL1_HUMAN;.;.	R	52;32;80	ENSP00000434810:P52R;ENSP00000437112:P32R;ENSP00000348395:P80R	ENSP00000348395:P80R	P	+	2	0	NPEPL1	56702288	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	5.622000	0.67750	2.304000	0.77564	0.505000	0.49811	CCC	.	.	.	none		0.677	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663		G	57268881	C	G	57268881	3	3	265	1	0	0	0	0	1	0	0	0	10581	623	22	4	91	4	NPEPL1	20	57268881	Missense_Mutation	SNP	C	TCGA-UZ-A9PU-01A-11D-A42J-10	4	57268881	5756639	63	16725	177	4									
NPEPL1	79716	hgsc.bcm.edu	37	chr20	57268883	57268883	+	Frame_Shift_Del	DEL	T	T	-																															ccaccgtggctgccctgcccTgcagggtgagccggcacaac																										TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr20:57268883delT	ENST00000356091.6	+	2	529	c.241delT	c.(241-243)tgcfs	p.C81fs	NPEPL1_ENST00000525817.1_Frame_Shift_Del_p.C33fs|STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525967.1_Frame_Shift_Del_p.C53fs	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	81						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)			TGCCCTGCCCTGCAGGGTGAG	0.677																																					p.P80fs		Atlas-INDEL	.											.	NPEPL1	36	.	0			c.240delC						PASS	.						31	38	36					20																	57268883		2083	4195	6278	SO:0001589	frameshift_variant	79716	exon2			.	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.241delT	chr20.hg19:g.57268883delT	ENSP00000348395:p.Cys81fs	166.0	0.0	0		96.0	26.0	0.270833	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Frame_Shift_Del	DEL	ENST00000356091.6	hg19	CCDS46621.1																																																																																			.	.	.	none		0.677	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663		-	57268883	T	-	57268883	7	5	265	1	0	1	0	1	0	0	0	0	10581	1580	55	0	93	0	NPEPL1	20	57268883	Frame_Shift_Del	DEL	T	TCGA-UZ-A9PU-01A-11D-A42J-10	2	57268883	5756637	64	16726	177	4									
POLR3H	171568	hgsc.bcm.edu	37	chr22	41926870	41926871	+	Frame_Shift_Del	DEL	CC	CC	-																															ctccgtctcgtactcccacaCccacacctgctccgcttcgt																										TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr22:41926870_41926871delCC	ENST00000355209.4	-	5	724_725	c.381_382delGG	c.(379-384)tgggtgfs	p.WV127fs	POLR3H_ENST00000396504.2_Frame_Shift_Del_p.WV127fs|POLR3H_ENST00000337566.5_Frame_Shift_Del_p.WV98fs|POLR3H_ENST00000407461.1_Frame_Shift_Del_p.WV127fs|POLR3H_ENST00000420561.1_5'Flank	NM_001018050.2	NP_001018060.1	Q9Y535	RPC8_HUMAN	polymerase (RNA) III (DNA directed) polypeptide H (22.9kD)	127					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|nucleobase-containing compound metabolic process (GO:0006139)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)	centrosome (GO:0005813)|cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			breast(1)|lung(5)|skin(1)|urinary_tract(1)	8						TACTCCCACACCCACACCTGCT	0.639																																					p.128_128del		Atlas-Indel,Pindel	.											.	POLR3H	30	.	0			c.382_383del						PASS	.																																			SO:0001589	frameshift_variant	171568	exon5			.	AB051452	CCDS14018.1, CCDS33651.1	22q13	2013-01-21			ENSG00000100413	ENSG00000100413		"RNA polymerase subunits"	30349	protein-coding gene	gene with protein product						11258795, 12391170	Standard	XR_244356		Approved	RPC8, KIAA1665	uc003baf.3	Q9Y535	OTTHUMG00000150971	ENST00000355209.4:c.381_382delGG	chr22.hg19:g.41926870_41926871delCC	ENSP00000347345:p.Trp127fs	84.0	0.0	0		69.0	34.0	0.492754	NM_001018050	B0QYH9|Q5M7Y8|Q96AE3|Q9BY95	Frame_Shift_Del	DEL	ENST00000355209.4	hg19	CCDS14018.1																																																																																			.	.	.	none		0.639	POLR3H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320701.1	NM_138338		-	41926871	CC	-	41926870	7	5	265	1	0	1	0	1	0	0	0	0	12243	507	18	0	240	0	POLR3H	22	41926870	Frame_Shift_Del	DEL	CC	TCGA-UZ-A9PU-01A-11D-A42J-10		41926870	9377696	65	16727											
MRPL37	51253	hgsc.bcm.edu	37	chr1	54671037	54671037	+	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	aagcatccttctctggccagGaggatctgtgtccaaaactc	10	10	9	12	0	2	0	0	0	2	0	6	2	4	2	3	3	2	1	3	3	3	1			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr1:54671037G>A	ENST00000360840.5	+	3	677	c.600G>A	c.(598-600)agG>agA	p.R200R	MRPL37_ENST00000336230.6_Intron|MRPL37_ENST00000487096.1_3'UTR|MRPL37_ENST00000605337.1_Silent_p.R200R	NM_016491.3	NP_057575.2	Q9BZE1	RM37_HUMAN	mitochondrial ribosomal protein L37	200					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(4)|skin(2)	19						CTCTGGCCAGGAGGATCTGTG	0.458																																					p.R200R		Atlas-SNP	.											.	MRPL37	36	.	0			c.G600A						PASS	.						153	140	144					1																	54671037		2203	4300	6503	SO:0001819	synonymous_variant	51253	exon3			GGCCAGGAGGATC	AB051344	CCDS589.1	1p32.1	2012-09-13			ENSG00000116221	ENSG00000116221		"Mitochondrial ribosomal proteins / large subunits"	14034	protein-coding gene	gene with protein product		611843				10600119	Standard	NM_016491		Approved	RPML2, MRP-L2	uc001cxa.4	Q9BZE1	OTTHUMG00000008118	ENST00000360840.5:c.600G>A	chr1.hg19:g.54671037G>A		180.0	0.0	.		82.0	40.0	.	NM_016491	Q96Q67|Q9BWR1|Q9P0P3	Silent	SNP	ENST00000360840.5	hg19	CCDS589.1																																																																																			.	.	.	none		0.458	MRPL37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022224.1	NM_016491		A	54671037	G	A	54671037	2	1	266	1	0	0	0	0	0	0	0	1	9807	1165	41	2		2	MRPL37	1	54671037	Silent	SNP	G	TCGA-UZ-A9PV-01A-11D-A42J-10		54671037	194579584	1	16728											
ABCA4	24	hgsc.bcm.edu	37	chr1	94522185	94522185	+	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	tcttcagctcagcggtcatgCggtcctgccaggcgaagcac	7	8	12	14	3	4	0	3	0	1	0	5	1	5	0	2	3	5	2	2	3	1	1	rs368457541		TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr1:94522185C>T	ENST00000370225.3	-	15	2440	c.2354G>A	c.(2353-2355)cGc>cAc	p.R785H	ABCA4_ENST00000535735.1_Intron	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	785					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)		AGCGGTCATGCGGTCCTGCCA	0.597													C|||	1	0.000199681	8e-04	0	5008	,	,		20408	0		0	False		,,,				2504	0				p.R785H		Atlas-SNP	.											ABCA4,colon,carcinoma,0,1	ABCA4	275	.	0			c.G2354A						PASS	.	C	HIS/ARG	2,4404	4.2+/-10.8	0,2,2201	67	56	60		2354	2.3	0.5	1		60	0,8600		0,0,4300	no	missense	ABCA4	NM_000350.2	29	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging	785/2274	94522185	2,13004	2203	4300	6503	SO:0001583	missense	24	exon15			GTCATGCGGTCCT	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.2354G>A	chr1.hg19:g.94522185C>T	ENSP00000359245:p.Arg785His	171.0	0.0	.		97.0	55.0	.	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	hg19	CCDS747.1	.	.	.	.	.	.	.	.	.	.	C	7.992	0.753505	0.15778	4.54E-4	0.0	ENSG00000198691	ENST00000370225	T	0.74632	-0.86	5.36	2.35	0.29111	.	0.172435	0.52532	D	0.000069	T	0.53302	0.1788	M	0.67397	2.05	0.80722	D	1	B	0.11235	0.004	B	0.18561	0.022	T	0.49214	-0.8963	10	0.28530	T	0.3	.	9.4895	0.38951	0.0:0.7563:0.0:0.2437	.	785	P78363	ABCA4_HUMAN	H	785	ENSP00000359245:R785H	ENSP00000359245:R785H	R	-	2	0	ABCA4	94294773	0.028000	0.19301	0.521000	0.27850	0.176000	0.22953	0.407000	0.21049	0.301000	0.22738	-0.258000	0.10820	CGC	.	.	.	none		0.597	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		T	94522185	C	T	94522185	3	4	266	1	0	0	0	0	1	0	0	0	34	768	27	1	4611	1	ABCA4	1	94522185	Missense_Mutation	SNP	C	TCGA-UZ-A9PV-01A-11D-A42J-10	39851148	94522185	154728436	2	16729											
DPH5	51611	hgsc.bcm.edu	37	chr1	101456156	101456156	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcgtcggctccaaccctggcTaagccaacacaaagtgtctc	10	8	8	15	2	1	0	0	0	1	0	5	0	2	0	3	2	3	2	3	2	4	1			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr1:101456156T>C	ENST00000370109.3	-	8	778	c.666A>G	c.(664-666)ttA>ttG	p.L222L	DPH5_ENST00000488176.1_Silent_p.L222L|DPH5_ENST00000370105.3_5'UTR|DPH5_ENST00000342173.7_Silent_p.L221L|AC093157.1_ENST00000593496.1_Silent_p.A50A|DPH5_ENST00000427040.2_5'UTR	NM_001077394.1|NM_001077395.1|NM_015958.2	NP_001070862.1|NP_001070863.1|NP_057042.2	Q9H2P9	DPH5_HUMAN	diphthamide biosynthesis 5	222					peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)		diphthine synthase activity (GO:0004164)			endometrium(2)|large_intestine(1)|lung(4)	7		all_epithelial(167;3.1e-06)|all_lung(203;0.000414)|Lung NSC(277;0.000946)		Epithelial(280;0.0385)|all cancers(265;0.043)|COAD - Colon adenocarcinoma(174;0.151)|Colorectal(144;0.173)|Lung(183;0.198)		CAACCCTGGCTAAGCCAACAC	0.433																																					p.L222L		Atlas-SNP	.											.	DPH5	14	.	0			c.A666G						PASS	.						82	80	81					1																	101456156		1943	4135	6078	SO:0001819	synonymous_variant	51611	exon8			CCTGGCTAAGCCA	AF132964	CCDS41358.1, CCDS41359.1	1p21.2	2013-05-02	2013-05-02		ENSG00000117543	ENSG00000117543			24270	protein-coding gene	gene with protein product		611075	"DPH5 homolog (S. cerevisiae)"			15485916, 23486472	Standard	NM_015958		Approved	CGI-30	uc001dtt.2	Q9H2P9	OTTHUMG00000010829	ENST00000370109.3:c.666A>G	chr1.hg19:g.101456156T>C		103.0	0.0	.		86.0	39.0	.	NM_015958	A8JZY6|D3DT62|Q9P017|Q9P0I4|Q9Y319	Silent	SNP	ENST00000370109.3	hg19	CCDS41358.1																																																																																			.	.	.	none		0.433	DPH5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000029881.1	NM_015958		C	101456156	T	C	101456156	2	2	266	1	0	0	0	0	0	0	0	1	4725	1519	53	3		3	DPH5	1	101456156	Silent	SNP	T	TCGA-UZ-A9PV-01A-11D-A42J-10	6933971	101456156	147794465	3	16730											
ALX3	257	hgsc.bcm.edu	37	chr1	110603552	110603552	+	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	catgaagccagccacactccCatgggggtgggaatatggag	11	6	14	10	0	0	1	0	1	0	0	1	3	1	3	3	4	2	0	3	4	3	1			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr1:110603552C>A	ENST00000369792.4	-	4	922	c.835G>T	c.(835-837)Ggg>Tgg	p.G279W	RP4-773N10.4_ENST00000596959.1_RNA|RP4-773N10.4_ENST00000554749.1_RNA	NM_006492.2	NP_006483.2	O95076	ALX3_HUMAN	ALX homeobox 3	279					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)		GCCACACTCCCATGGGGGTGG	0.652																																					p.G279W		Atlas-SNP	.											.	ALX3	16	.	0			c.G835T						PASS	.						15	19	18					1																	110603552		2200	4297	6497	SO:0001583	missense	257	exon4			CACTCCCATGGGG	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.835G>T	chr1.hg19:g.110603552C>A	ENSP00000358807:p.Gly279Trp	195.0	0.0	.		146.0	68.0	.	NM_006492	O95075|Q5T8M4	Missense_Mutation	SNP	ENST00000369792.4	hg19	CCDS819.1	.	.	.	.	.	.	.	.	.	.	C	11.93	1.784499	0.31593	.	.	ENSG00000156150	ENST00000369792	D	0.92752	-3.1	5.51	3.3	0.37823	.	0.149286	0.43747	D	0.000537	D	0.91872	0.7427	M	0.71581	2.175	0.43199	D	0.995046	D	0.69078	0.997	P	0.61328	0.887	D	0.91501	0.5219	10	0.59425	D	0.04	.	6.8466	0.23992	0.0:0.666:0.0:0.334	.	279	O95076	ALX3_HUMAN	W	279	ENSP00000358807:G279W	ENSP00000358807:G279W	G	-	1	0	ALX3	110405075	0.482000	0.25948	0.212000	0.23672	0.147000	0.21601	0.852000	0.27764	1.340000	0.45581	0.655000	0.94253	GGG	.	.	.	none		0.652	ALX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032232.2	NM_006492		A	110603552	C	A	110603552	3	1	266	1	0	0	0	0	1	0	0	0	557	594	21	4	200	4	ALX3	1	110603552	Missense_Mutation	SNP	C	TCGA-UZ-A9PV-01A-11D-A42J-10	9147396	110603552	138647069	4	16731											
RAB7L1	8934	hgsc.bcm.edu	37	chr1	205739969	205739969	+	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	ggtcccggctcactgcccaaGgggacagatcacactagcaa	11	5	11	14	1	2	1	2	0	0	1	3	2	3	2	2	4	2	2	2	4	3	1			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr1:205739969G>T	ENST00000367139.3	-	5	695	c.392C>A	c.(391-393)cCt>cAt	p.P131H	RAB7L1_ENST00000468887.1_5'UTR|RAB7L1_ENST00000437324.2_Missense_Mutation_p.P59H|RAB7L1_ENST00000414729.1_Missense_Mutation_p.P131H|RAB7L1_ENST00000446390.2_Missense_Mutation_p.P107H|RAB7L1_ENST00000235932.4_Missense_Mutation_p.P131H	NM_003929.2	NP_003920.1	O14966	RAB7L_HUMAN		131					cell differentiation (GO:0030154)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|positive regulation of intracellular protein transport (GO:0090316)|protein transport (GO:0015031)|retrograde transport, plasma membrane to Golgi (GO:0035526)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|vacuole (GO:0005773)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|urinary_tract(1)	10	Breast(84;0.0799)		BRCA - Breast invasive adenocarcinoma(75;0.0194)			CACTGCCCAAGGGGACAGATC	0.403																																					p.P131H	Pancreas(25;658 872 27763 34889 38531)	Atlas-SNP	.											.	RAB7L1	19	.	0			c.C392A						PASS	.						84	76	79					1																	205739969		2203	4300	6503	SO:0001583	missense	8934	exon5			GCCCAAGGGGACA																												ENST00000367139.3:c.392C>A	chr1.hg19:g.205739969G>T	ENSP00000356107:p.Pro131His	77.0	0.0	.		57.0	4.0	.	NM_001135662	B4E1K3|C9JE77	Missense_Mutation	SNP	ENST00000367139.3	hg19	CCDS1459.1	.	.	.	.	.	.	.	.	.	.	G	15.80	2.940484	0.52972	.	.	ENSG00000117280	ENST00000367139;ENST00000235932;ENST00000437324;ENST00000446390;ENST00000414729	T;T;T;T;T	0.79653	-1.29;-1.29;-0.42;-1.29;-1.29	5.27	5.27	0.74061	Small GTP-binding protein domain (1);	0.121659	0.56097	D	0.000026	T	0.69602	0.3129	N	0.04820	-0.15	0.39116	D	0.96156	B;B	0.29378	0.243;0.24	B;B	0.36464	0.092;0.225	T	0.73908	-0.3834	10	0.87932	D	0	-7.8433	17.0021	0.86384	0.0:0.0:1.0:0.0	.	107;131	B4E1K3;O14966	.;RAB7L_HUMAN	H	131;131;59;107;131	ENSP00000356107:P131H;ENSP00000235932:P131H;ENSP00000416613:P59H;ENSP00000389899:P107H;ENSP00000402910:P131H	ENSP00000235932:P131H	P	-	2	0	RAB7L1	204006592	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.213000	0.65230	2.619000	0.88677	0.561000	0.74099	CCT	.	.	.	none		0.403	RAB7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087732.1			T	205739969	G	T	205739969	3	4	266	1	0	0	0	0	1	0	0	0	12968	1000	35	4	227	4	RAB7L1	1	205739969	Missense_Mutation	SNP	G	TCGA-UZ-A9PV-01A-11D-A42J-10	95136417	205739969	43510652	5	16732											
OR2T33	391195	hgsc.bcm.edu	37	chr1	248436732	248436732	+	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	gctcatgagagtgggatatcGgagtgggtggcagacagccg	9	7	18	7	2	1	2	1	1	0	2	2	5	1	4	1	4	1	2	1	4	1	1			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr1:248436732G>A	ENST00000318021.2	-	1	406	c.385C>T	c.(385-387)Cga>Tga	p.R129*		NM_001004695.1	NP_001004695.1	Q8NG76	O2T33_HUMAN	olfactory receptor, family 2, subfamily T, member 33	129						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(41)|ovary(1)|prostate(1)|skin(4)	67	all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			GTGGGATATCGGAGTGGGTGG	0.592																																					p.R129X		Atlas-SNP	.											.	OR2T33	133	.	0			c.C385T						PASS	.						60	61	60					1																	248436732		2197	4289	6486	SO:0001587	stop_gained	391195	exon1			GATATCGGAGTGG		CCDS31109.1	1q44	2012-08-09			ENSG00000177212	ENSG00000177212		"GPCR / Class A : Olfactory receptors"	31255	protein-coding gene	gene with protein product							Standard	NM_001004695		Approved		uc010pzi.2	Q8NG76	OTTHUMG00000040458	ENST00000318021.2:c.385C>T	chr1.hg19:g.248436732G>A	ENSP00000324687:p.Arg129*	654.0	0.0	.		472.0	28.0	.	NM_001004695	B2RNN0	Nonsense_Mutation	SNP	ENST00000318021.2	hg19	CCDS31109.1	.	.	.	.	.	.	.	.	.	.	-	9.949	1.219752	0.22373	.	.	ENSG00000177212	ENST00000318021	.	.	.	2.7	0.405	0.16361	.	0.000000	0.30126	U	0.010346	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.3142	0.43727	0.0:0.0:0.6163:0.3837	.	.	.	.	X	129	.	ENSP00000324687:R129X	R	-	1	2	OR2T33	246503355	0.005000	0.15991	0.021000	0.16686	0.001000	0.01503	0.673000	0.25203	-0.062000	0.13088	-0.599000	0.04106	CGA	.	.	.	none		0.592	OR2T33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097354.1	NM_001004695		A	248436732	G	A	248436732	4	1	266	1	0	0	0	0	0	1	0	0	11031	1124	39	1	580	1	OR2T33	1	248436732	Nonsense_Mutation	SNP	G	TCGA-UZ-A9PV-01A-11D-A42J-10	42696763	248436732	813889	6	16733											
SCN9A	6335	hgsc.bcm.edu	37	chr2	167055908	167055908	+	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	atgttcaccacaaccaggaaGgatatgatgatataactaac	17	9	7	8	0	1	2	1	2	0	0	1	4	1	4	2	2	3	1	2	2	6	5			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr2:167055908G>T	ENST00000409435.1	-	26	5240	c.5241C>A	c.(5239-5241)tcC>tcA	p.S1747S	SCN9A_ENST00000375387.4_Silent_p.S1748S|AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000409672.1_Silent_p.S1736S|SCN9A_ENST00000303354.6_Silent_p.S1748S			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	1747					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)	CAACCAGGAAGGATATGATGA	0.398																																					p.S1736S		Atlas-SNP	.											SCN9A,NS,carcinoma,0,1	SCN9A	296	.	0			c.C5208A						PASS	.						187	198	194					2																	167055908		2203	4300	6503	SO:0001819	synonymous_variant	6335	exon27			CAGGAAGGATATG	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.5241C>A	chr2.hg19:g.167055908G>T		131.0	0.0	.		107.0	48.0	.	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Silent	SNP	ENST00000409435.1	hg19	CCDS46441.1																																																																																			.	.	.	none		0.398	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		T	167055908	G	T	167055908	2	4	266	1	0	0	0	0	0	0	0	1	13938	987	35	4		4	SCN9A	2	167055908	Silent	SNP	G	TCGA-UZ-A9PV-01A-11D-A42J-10		167055908	76143465	7	16734											
VILL	50853	hgsc.bcm.edu	37	chr3	38043001	38043001	+	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	tggaccccaagcgtcatggaCagctgtgtgcaggcaactgc	9	7	13	12	1	1	0	1	0	0	0	1	2	1	2	2	3	5	3	2	3	2	0			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr3:38043001C>G	ENST00000283713.6	+	12	1503	c.1237C>G	c.(1237-1239)Cag>Gag	p.Q413E	VILL_ENST00000465644.1_Missense_Mutation_p.Q131E|VILL_ENST00000383759.2_Missense_Mutation_p.Q413E			O15195	VILL_HUMAN	villin-like	413					actin filament capping (GO:0051693)|cytoskeleton organization (GO:0007010)	actin cytoskeleton (GO:0015629)	structural constituent of cytoskeleton (GO:0005200)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|urinary_tract(2)	28				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		GCGTCATGGACAGCTGTGTGC	0.587																																					p.Q413E		Atlas-SNP	.											.	VILL	61	.	0			c.C1237G						PASS	.						116	101	106					3																	38043001		2203	4300	6503	SO:0001583	missense	50853	exon11			CATGGACAGCTGT		CCDS2670.2	3p21	2004-07-28			ENSG00000136059	ENSG00000136059			30906	protein-coding gene	gene with protein product						9179494	Standard	XM_005265191		Approved		uc003chl.3	O15195	OTTHUMG00000130814	ENST00000283713.6:c.1237C>G	chr3.hg19:g.38043001C>G	ENSP00000283713:p.Gln413Glu	65.0	0.0	.		76.0	31.0	.	NM_015873	A8MZP1|Q9BT80|Q9BWH7	Missense_Mutation	SNP	ENST00000283713.6	hg19	CCDS2670.2	.	.	.	.	.	.	.	.	.	.	C	11.51	1.660433	0.29515	.	.	ENSG00000136059	ENST00000283713;ENST00000383759;ENST00000356246;ENST00000465644	T;T;T	0.55234	0.53;0.53;0.53	4.04	3.16	0.36331	Gelsolin domain (1);	0.108661	0.64402	D	0.000004	T	0.61961	0.2389	M	0.75150	2.29	0.37472	D	0.915635	P;P	0.41569	0.712;0.755	B;P	0.51945	0.373;0.685	T	0.64330	-0.6433	10	0.30078	T	0.28	-6.8034	10.8824	0.46946	0.0:0.9052:0.0:0.0948	.	399;413	O15195-2;O15195	.;VILL_HUMAN	E	413;413;399;131	ENSP00000283713:Q413E;ENSP00000373266:Q413E;ENSP00000422096:Q131E	ENSP00000283713:Q413E	Q	+	1	0	VILL	38018005	0.801000	0.28930	0.007000	0.13788	0.022000	0.10575	1.593000	0.36686	1.054000	0.40438	0.455000	0.32223	CAG	.	.	.	none		0.587	VILL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253360.3	NM_015873		G	38043001	C	G	38043001	3	3	266	1	0	0	0	0	1	0	0	0	17177	479	17	4	1279	4	VILL	3	38043001	Missense_Mutation	SNP	C	TCGA-UZ-A9PV-01A-11D-A42J-10		38043001	159979429	8	16735											
ZPLD1	131368	hgsc.bcm.edu	37	chr3	102187928	102187929	+	Frame_Shift_Del	DEL	GC	GC	-																															aaaatgtccactgtcttcttGcactgcgttaccaagctctg																										TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr3:102187928_102187929delGC	ENST00000491959.1	+	15	1764_1765	c.882_883delGC	c.(880-885)ttgcacfs	p.H295fs	ZPLD1_ENST00000306176.1_Frame_Shift_Del_p.H311fs|ZPLD1_ENST00000466937.1_Frame_Shift_Del_p.H295fs			Q8TCW7	ZPLD1_HUMAN	zona pellucida-like domain containing 1	295	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						CTGTCTTCTTGCACTGCGTTAC	0.45																																					p.310_310del		Atlas-Indel,Pindel	.											.	ZPLD1	82	.	0			c.929_930del						PASS	.																																			SO:0001589	frameshift_variant	131368	exon8			.	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.882_883delGC	chr3.hg19:g.102187928_102187929delGC	ENSP00000420265:p.His295fs	74.0	0.0	0		71.0	44.0	0.619718	NM_175056	Q49AS1|Q8WU36	Frame_Shift_Del	DEL	ENST00000491959.1	hg19																																																																																				.	.	.	none		0.45	ZPLD1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353984.1	NM_175056		-	102187929	GC	-	102187928	7	5	266	1	0	1	0	1	0	0	0	0	18233	1310	46	0	960	0	ZPLD1	3	102187928	Frame_Shift_Del	DEL	GC	TCGA-UZ-A9PV-01A-11D-A42J-10	64144927	102187928	95834502	9	16736											
ASTE1	28990	hgsc.bcm.edu	37	chr3	130743519	130743519	+	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	agagaggtagtagagctttaTtcatattgctgaagtgatgg	12	13	13	3	0	1	4	1	2	0	2	1	5	1	4	0	2	2	4	0	2	5	7			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr3:130743519T>A	ENST00000264992.3	-	3	1073	c.632A>T	c.(631-633)aAt>aTt	p.N211I	NEK11_ENST00000356918.4_5'Flank|ASTE1_ENST00000514044.1_Missense_Mutation_p.N211I|NEK11_ENST00000510769.1_5'Flank|NEK11_ENST00000412440.2_5'Flank|NEK11_ENST00000429253.2_5'Flank|NEK11_ENST00000510688.1_5'Flank|NEK11_ENST00000511262.1_5'Flank|NEK11_ENST00000383366.4_5'Flank	NM_014065.2	NP_054784.2	Q2TB18	ASTE1_HUMAN	asteroid homolog 1 (Drosophila)	211					DNA repair (GO:0006281)		nuclease activity (GO:0004518)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)	22						TAGAGCTTTATTCATATTGCT	0.408																																					p.N211I		Atlas-SNP	.											.	ASTE1	67	.	0			c.A632T						PASS	.						105	99	101					3																	130743519		2203	4300	6503	SO:0001583	missense	28990	exon3			GCTTTATTCATAT	AF113539	CCDS3068.1, CCDS75007.1	3q21.3	2005-11-17			ENSG00000034533	ENSG00000034533			25021	protein-coding gene	gene with protein product							Standard	NM_014065		Approved	HT001	uc003env.1	Q2TB18	OTTHUMG00000159644	ENST00000264992.3:c.632A>T	chr3.hg19:g.130743519T>A	ENSP00000264992:p.Asn211Ile	83.0	0.0	.		100.0	44.0	.	NM_014065	B4DFL9|Q3MIB6|Q8N6G4|Q96JY1|Q9UHX6	Missense_Mutation	SNP	ENST00000264992.3	hg19	CCDS3068.1	.	.	.	.	.	.	.	.	.	.	T	18.11	3.551442	0.65311	.	.	ENSG00000034533	ENST00000514044;ENST00000264992;ENST00000446270	.	.	.	5.54	4.38	0.52667	.	0.081556	0.85682	D	0.000000	T	0.71728	0.3374	M	0.71581	2.175	0.41819	D	0.990011	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	T	0.73040	-0.4108	9	0.66056	D	0.02	-14.7581	9.4519	0.38731	0.0:0.1477:0.0:0.8523	.	211;211	D6RG30;Q2TB18	.;ASTE1_HUMAN	I	211	.	ENSP00000264992:N211I	N	-	2	0	ASTE1	132226209	0.937000	0.31787	0.570000	0.28473	0.980000	0.70556	1.749000	0.38319	0.933000	0.37291	0.459000	0.35465	AAT	.	.	.	none		0.408	ASTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356659.1	NM_014065		A	130743519	T	A	130743519	3	1	266	1	0	0	0	0	1	0	0	0	1062	1493	52	5	1423	5	ASTE1	3	130743519	Missense_Mutation	SNP	T	TCGA-UZ-A9PV-01A-11D-A42J-10	28555591	130743519	67278911	10	16737											
WWTR1	25937	hgsc.bcm.edu	37	chr3	149243902	149243902	+	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	agtgctctgctccctcgaatGatatggccctctgcaaagca	9	10	9	13	1	2	1	0	1	2	0	4	2	3	1	2	1	4	4	2	1	3	1			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr3:149243902G>A	ENST00000465804.1	-	7	1172	c.916C>T	c.(916-918)Cat>Tat	p.H306Y	RNU6-1098P_ENST00000516772.1_RNA|WWTR1_ENST00000467467.1_Missense_Mutation_p.H306Y|WWTR1_ENST00000360632.3_Missense_Mutation_p.H306Y	NM_001168278.1	NP_001161750.1	Q9GZV5	WWTR1_HUMAN	WW domain containing transcription regulator 1	306					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)			TCCCTCGAATGATATGGCCCT	0.458			T	CAMTA1	epitheliod hemangioendothelioma																																p.H306Y		Atlas-SNP	.		Dom	yes		3	3q23-q24	607392	WW domain containing transcription regulator 1		M	WWTR1,NS,carcinoma,0,1	WWTR1	42	.	0			c.C916T						PASS	.						102	92	95					3																	149243902		2203	4300	6503	SO:0001583	missense	25937	exon7			TCGAATGATATGG	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.916C>T	chr3.hg19:g.149243902G>A	ENSP00000419465:p.His306Tyr	88.0	0.0	.		68.0	20.0	.	NM_001168278	D3DNH7|Q8N3P2|Q9Y3W6	Missense_Mutation	SNP	ENST00000465804.1	hg19	CCDS3144.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.649621	0.87958	.	.	ENSG00000018408	ENST00000465804;ENST00000360632;ENST00000467467;ENST00000472417	D;D;D	0.82619	-1.63;-1.63;-1.63	5.71	5.71	0.89125	.	0.103999	0.64402	D	0.000004	D	0.85665	0.5749	M	0.81497	2.545	0.80722	D	1	P	0.46621	0.881	B	0.41332	0.354	D	0.88133	0.2839	10	0.87932	D	0	-29.8014	19.846	0.96707	0.0:0.0:1.0:0.0	.	306	Q9GZV5	WWTR1_HUMAN	Y	306;306;306;164	ENSP00000419465:H306Y;ENSP00000353847:H306Y;ENSP00000419234:H306Y	ENSP00000353847:H306Y	H	-	1	0	WWTR1	150726592	1.000000	0.71417	0.615000	0.29064	0.887000	0.51463	9.467000	0.97671	2.683000	0.91414	0.563000	0.77884	CAT	.	.	.	none		0.458	WWTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356498.1	NM_015472		A	149243902	G	A	149243902	3	1	266	1	0	0	0	0	1	0	0	0	17429	1290	45	2	294	2	WWTR1	3	149243902	Missense_Mutation	SNP	G	TCGA-UZ-A9PV-01A-11D-A42J-10	18500383	149243902	48778528	11	16738											
ZNF639	51193	hgsc.bcm.edu	37	chr3	179051889	179051926	+	Frame_Shift_Del	DEL	TGGTTTTCGGAGTAGACTTCACACAAATGTTAACAGGC	TGGTTTTCGGAGTAGACTTCACACAAATGTTAACAGGC	-																															ttctttgtatgtcaagtatgTggttttcggagtagacttca																								rs61741048	byFrequency	TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	TGGTTTTCGGAGTAGACTTCACACAAATGTTAACAGGC	TGGTTTTCGGAGTAGACTTCACACAAATGTTAACAGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr3:179051889_179051926delTGGTTTTCGGAGTAGACTTCACACAAATGTTAACAGGC	ENST00000326361.3	+	7	1582_1619	c.1137_1174delTGGTTTTCGGAGTAGACTTCACACAAATGTTAACAGGC	c.(1135-1176)tgtggttttcggagtagacttcacacaaatgttaacaggcatfs	p.CGFRSRLHTNVNRH379fs	ZNF639_ENST00000484866.1_Frame_Shift_Del_p.CGFRSRLHTNVNRH379fs|ZNF639_ENST00000496856.1_Frame_Shift_Del_p.CGFRSRLHTNVNRH379fs	NM_016331.1	NP_057415.1	Q9UID6	ZN639_HUMAN	zinc finger protein 639	379	Interaction with CTNNA2.				negative regulation by host of viral transcription (GO:0043922)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of cell growth (GO:0030307)|transcription, DNA-templated (GO:0006351)|viral entry into host cell (GO:0046718)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein self-association (GO:0043621)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(10)|urinary_tract(1)	16	all_cancers(143;7.9e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			GTCAAGTATGTGGTTTTCGGAGTAGACTTCACACAAATGTTAACAGGCATGTTGCTAT	0.332																																					p.379_391del		Pindel	.											.	ZNF639	45	.	0			c.1136_1173del						PASS	.																																			SO:0001589	frameshift_variant	51193	exon7			.	BC020500	CCDS3227.1	3q27.1	2010-03-26			ENSG00000121864	ENSG00000121864		"Zinc fingers, C2H2-type"	30950	protein-coding gene	gene with protein product	"zinc finger amplified in esophageal squamous cell carcinomas 1"					14522885	Standard	NM_016331		Approved	ANC-2H01, ZASC1	uc003fjr.1	Q9UID6	OTTHUMG00000157439	ENST00000326361.3:c.1137_1174delTGGTTTTCGGAGTAGACTTCACACAAATGTTAACAGGC	chr3.hg19:g.179051889_179051926delTGGTTTTCGGAGTAGACTTCACACAAATGTTAACAGGC	ENSP00000325634:p.Cys379fs	170.0	0.0	.		160.0	18.0	0.112	NM_016331	A9X3Z9|D3DNR3	Frame_Shift_Del	DEL	ENST00000326361.3	hg19	CCDS3227.1																																																																																			.	.	.	none		0.332	ZNF639-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348855.1	NM_016331		-	179051926	TGGTTTTCGGAGTAGACTTCACACAAATGTTAACAGGC	-	179051889	7	5	266	1	0	1	0	1	0	0	0	0	18068	1702	59	0	1151	0	ZNF639	3	179051889	Frame_Shift_Del	DEL	TGGTTTTCGGAGTAGACTTCACACAAATGTTAACAGGC	TCGA-UZ-A9PV-01A-11D-A42J-10	29807987	179051889	18970541	12	16739											
MRFAP1	93621	hgsc.bcm.edu	37	chr4	6642705	6642705	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacgagatgcgcgaggacaTcgcgtcgctgacgcgcgagc	9	4	15	13	9	0	2	0	1	0	1	2	6	0	3	0	1	3	1	0	1	1	0			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr4:6642705T>C	ENST00000320912.4	+	2	769	c.116T>C	c.(115-117)aTc>aCc	p.I39T	MRFAP1_ENST00000382581.4_Missense_Mutation_p.I39T|MRFAP1_ENST00000507420.1_Missense_Mutation_p.I39T	NM_001272053.1	NP_001258982.1			Morf4 family associated protein 1											lung(1)	1						CGCGAGGACATCGCGTCGCTG	0.617																																					p.I39T		Atlas-SNP	.											.	MRFAP1	10	.	0			c.T116C						PASS	.						76	75	75					4																	6642705		2203	4300	6503	SO:0001583	missense	93621	exon2			AGGACATCGCGTC	AF116272	CCDS3389.1	4p16.1	2011-01-27	2011-01-27		ENSG00000179010	ENSG00000179010			24549	protein-coding gene	gene with protein product						15367658	Standard	NM_033296		Approved	PAM14, PGR1	uc003gjh.2	Q9Y605	OTTHUMG00000125504	ENST00000320912.4:c.116T>C	chr4.hg19:g.6642705T>C	ENSP00000318352:p.Ile39Thr	144.0	0.0	.		109.0	40.0	.	NM_001272053		Missense_Mutation	SNP	ENST00000320912.4	hg19	CCDS3389.1	.	.	.	.	.	.	.	.	.	.	T	19.09	3.759842	0.69763	.	.	ENSG00000179010	ENST00000320912;ENST00000507420;ENST00000382581	.	.	.	3.35	3.35	0.38373	.	0.000000	0.33040	N	0.005353	T	0.28366	0.0701	N	0.24115	0.695	0.23010	N	0.998433	B	0.30889	0.299	B	0.33121	0.158	T	0.26018	-1.0115	9	0.72032	D	0.01	-23.1149	8.4138	0.32659	0.0:0.0:0.0:1.0	.	39	Q9Y605	MOFA1_HUMAN	T	39	.	ENSP00000318352:I39T	I	+	2	0	MRFAP1	6693606	1.000000	0.71417	0.533000	0.28001	0.966000	0.64601	1.122000	0.31295	1.771000	0.52183	0.459000	0.35465	ATC	.	.	.	none		0.617	MRFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246831.1	NM_033296		C	6642705	T	C	6642705	3	2	266	1	0	0	0	0	1	0	0	0	9768	1435	50	3	118	3	MRFAP1	4	6642705	Missense_Mutation	SNP	T	TCGA-UZ-A9PV-01A-11D-A42J-10		6642705	184511571	13	16740											
SLC4A4	8671	hgsc.bcm.edu	37	chr4	72215763	72215763	+	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	atccatcatgcttgatcgggAggcttcttctctcccacagt	7	13	8	13	1	3	1	1	1	2	0	7	2	5	2	2	2	1	2	2	2	0	3			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr4:72215763A>T	ENST00000264485.5	+	5	641	c.524A>T	c.(523-525)gAg>gTg	p.E175V	SLC4A4_ENST00000514331.1_3'UTR|SLC4A4_ENST00000340595.3_Missense_Mutation_p.E131V|SLC4A4_ENST00000425175.1_Missense_Mutation_p.E175V|SLC4A4_ENST00000512686.1_Missense_Mutation_p.E131V|SLC4A4_ENST00000351898.6_Missense_Mutation_p.E175V	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	175					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)	CTTGATCGGGAGGCTTCTTCT	0.463																																					p.E175V		Atlas-SNP	.											.	SLC4A4	269	.	0			c.A524T						PASS	.						180	166	171					4																	72215763		2203	4300	6503	SO:0001583	missense	8671	exon5			ATCGGGAGGCTTC	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.524A>T	chr4.hg19:g.72215763A>T	ENSP00000264485:p.Glu175Val	69.0	0.0	.		37.0	21.0	.	NM_001098484	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	hg19	CCDS43236.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.716296	0.89205	.	.	ENSG00000080493	ENST00000264485;ENST00000425175;ENST00000351898;ENST00000512686;ENST00000340595	T;T;T;T;T	0.81078	-1.45;-1.45;-1.45;-1.45;-1.45	5.64	5.64	0.86602	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.000000	0.85682	D	0.000000	D	0.90024	0.6885	M	0.85710	2.77	0.80722	D	1	P;D;D;D;P;D	0.65815	0.956;0.995;0.974;0.995;0.956;0.979	P;D;P;D;P;P	0.66847	0.864;0.923;0.848;0.947;0.864;0.901	D	0.90840	0.4723	10	0.51188	T	0.08	.	15.8582	0.79000	1.0:0.0:0.0:0.0	.	175;175;131;131;155;175	A5JJ20;Q9Y6R1-4;Q9Y6R1-2;Q9Y6R1-3;Q9Y6R3;Q9Y6R1	.;.;.;.;.;S4A4_HUMAN	V	175;175;175;131;131	ENSP00000264485:E175V;ENSP00000393557:E175V;ENSP00000307349:E175V;ENSP00000422400:E131V;ENSP00000344272:E131V	ENSP00000264485:E175V	E	+	2	0	SLC4A4	72434627	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.307000	0.96226	2.136000	0.66102	0.455000	0.32223	GAG	.	.	.	none		0.463	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		T	72215763	A	T	72215763	3	4	266	1	0	0	0	0	1	0	0	0	14669	304	11	5	659	5	SLC4A4	4	72215763	Missense_Mutation	SNP	A	TCGA-UZ-A9PV-01A-11D-A42J-10	65573058	72215763	118938513	14	16741											
AGPAT9	84803	hgsc.bcm.edu	37	chr4	84516012	84516012	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctaggttggccaggttcaTggcggcttgatgggaattat	7	14	14	6	1	2	1	1	1	1	0	2	2	2	2	1	6	0	3	1	6	3	6			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr4:84516012T>C	ENST00000395226.2	+	8	971	c.753T>C	c.(751-753)caT>caC	p.H251H	AGPAT9_ENST00000264409.4_Silent_p.H251H	NM_001256421.1	NP_001243350.1	Q53EU6	GPAT3_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 9	251					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|regulation of TOR signaling (GO:0032006)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(3)	13		Hepatocellular(203;0.114)				GCCAGGTTCATGGCGGCTTGA	0.413																																					p.H251H		Atlas-SNP	.											.	AGPAT9	41	.	0			c.T753C						PASS	.						162	165	164					4																	84516012		2203	4300	6503	SO:0001819	synonymous_variant	84803	exon8			GGTTCATGGCGGC	AK055749	CCDS3606.1	4q21.23	2014-02-13	2008-01-29		ENSG00000138678	ENSG00000138678	2.3.1.15	"1-acylglycerol-3-phosphate O-acyltransferases"	28157	protein-coding gene	gene with protein product	"lysophosphatidic acid acyltransferase, theta"	610958	"1-acylglycerol-3-phosphate O-acyltransferase 9 (lysophosphatidic acid acyltransferase, theta)"			12975309	Standard	NM_001256421		Approved	MGC11324, LPAAT-theta, MAG1, HMFN0839	uc003how.4	Q53EU6	OTTHUMG00000130431	ENST00000395226.2:c.753T>C	chr4.hg19:g.84516012T>C		80.0	0.0	.		58.0	24.0	.	NM_001256421	Q68CJ4|Q6GPI6|Q96NA3	Silent	SNP	ENST00000395226.2	hg19	CCDS3606.1																																																																																			.	.	.	none		0.413	AGPAT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252821.3	NM_032717		C	84516012	T	C	84516012	2	2	266	1	0	0	0	0	0	0	0	1	392	1461	51	3		3	AGPAT9	4	84516012	Silent	SNP	T	TCGA-UZ-A9PV-01A-11D-A42J-10	12300249	84516012	106638264	15	16742											
CLCN3	1182	hgsc.bcm.edu	37	chr4	170610219	170610219	+	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	ctggccggattaatagacatTgctgccgattggatgactga	10	11	12	8	2	0	3	0	2	0	1	0	6	0	5	2	3	2	1	2	3	2	4			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr4:170610219T>A	ENST00000513761.1	+	5	1003	c.444T>A	c.(442-444)atT>atA	p.I148I	CLCN3_ENST00000504131.2_Silent_p.I131I|CLCN3_ENST00000347613.4_Silent_p.I148I|CLCN3_ENST00000360642.3_Silent_p.I148I	NM_001829.3	NP_001820.2	P51790	CLCN3_HUMAN	chloride channel, voltage-sensitive 3	148					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)		TAATAGACATTGCTGCCGATT	0.418																																					p.I148I		Atlas-SNP	.											.	CLCN3	85	.	0			c.T444A						PASS	.						155	152	153					4																	170610219		2203	4300	6503	SO:0001819	synonymous_variant	1182	exon5			AGACATTGCTGCC	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.444T>A	chr4.hg19:g.170610219T>A		89.0	0.0	.		66.0	33.0	.	NM_001243372	B7Z932|B9EGJ9|D3DP34|E9PB97|O14918|Q86Z21	Silent	SNP	ENST00000513761.1	hg19	CCDS34101.1																																																																																			.	.	.	none		0.418	CLCN3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363210.2			A	170610219	T	A	170610219	2	1	266	1	0	0	0	0	0	0	0	1	3466	1800	63	5		5	CLCN3	4	170610219	Silent	SNP	T	TCGA-UZ-A9PV-01A-11D-A42J-10	86094207	170610219	20544057	16	16743											
MED10	84246	hgsc.bcm.edu	37	chr5	6372638	6372638	+	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	aagaaggcgggtgatcctccCcccggatgcttcgatactta	9	9	11	12	3	0	2	0	1	0	1	3	4	2	3	4	3	2	1	4	3	4	3	rs145638352		TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr5:6372638C>A	ENST00000255764.3	-	4	496	c.386G>T	c.(385-387)gGg>gTg	p.G129V		NM_032286.2	NP_115662.2	Q9BTT4	MED10_HUMAN	mediator complex subunit 10	129					gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)	RNA polymerase II transcription cofactor activity (GO:0001104)			kidney(1)|large_intestine(1)|ovary(1)|prostate(1)|urinary_tract(1)	5						GTGATCCTCCCCCCGGATGCT	0.493																																					p.G129V		Atlas-SNP	.											.	MED10	7	.	0			c.G386T						PASS	.	C	VAL/GLY	2,4404	4.2+/-10.8	0,2,2201	114	114	114		386	6	1	5	dbSNP_134	114	0,8600		0,0,4300	no	missense	MED10	NM_032286.2	109	0,2,6501	AA,AC,CC		0.0,0.0454,0.0154	probably-damaging	129/136	6372638	2,13004	2203	4300	6503	SO:0001583	missense	84246	exon4			TCCTCCCCCCGGA		CCDS34134.1	5p15.31	2008-02-05	2007-07-30		ENSG00000133398	ENSG00000133398			28760	protein-coding gene	gene with protein product	"NUT2 homolog (S. cerevisiae)"	612382	"mediator of RNA polymerase II transcription, subunit 10 homolog (NUT2, S. cerevisiae)"			15657623, 15175163	Standard	NM_032286		Approved	TRG20, L6, MGC5309, NUT2	uc003jdo.3	Q9BTT4	OTTHUMG00000161682	ENST00000255764.3:c.386G>T	chr5.hg19:g.6372638C>A	ENSP00000255764:p.Gly129Val	115.0	0.0	.		99.0	48.0	.	NM_032286	C6G491	Missense_Mutation	SNP	ENST00000255764.3	hg19	CCDS34134.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.560514	0.86335	4.54E-4	0.0	ENSG00000133398	ENST00000255764	.	.	.	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.76786	0.4036	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.74797	-0.3543	9	0.49607	T	0.09	-30.6001	19.4269	0.94746	0.0:1.0:0.0:0.0	.	129	Q9BTT4	MED10_HUMAN	V	129	.	ENSP00000255764:G129V	G	-	2	0	MED10	6425638	1.000000	0.71417	0.996000	0.52242	0.655000	0.38815	4.489000	0.60309	2.836000	0.97738	0.655000	0.94253	GGG	.	C|1.000;A|0.000	0.000	weak		0.493	MED10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365714.1	NM_032286		A	6372638	C	A	6372638	3	1	266	1	0	0	0	0	1	0	0	0	9433	623	22	4	25	4	MED10	5	6372638	Missense_Mutation	SNP	C	TCGA-UZ-A9PV-01A-11D-A42J-10		6372638	174542622	17	16744											
FAM105A	54491	hgsc.bcm.edu	37	chr5	14608915	14608915	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggaagtatgtgcaacacccTtttttcagatgccattctgg	10	13	9	9	0	2	1	1	0	1	1	2	2	2	2	2	2	3	2	2	2	3	5			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr5:14608915T>C	ENST00000274217.3	+	7	806	c.686T>C	c.(685-687)cTt>cCt	p.L229P		NM_019018.2	NP_061891.1	Q9NUU6	F105A_HUMAN	family with sequence similarity 105, member A	229	OTU.							p.S231fs*13(1)		large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	Lung NSC(4;0.00592)					TGCAACACCCTTTTTTCAGAT	0.328																																					p.L229P		Atlas-SNP	.											.,1	FAM105A	32	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.T686C						PASS	.						77	77	77					5																	14608915		2203	4300	6503	SO:0001583	missense	54491	exon7			ACACCCTTTTTTC		CCDS3884.1	5p15.2	2014-02-24			ENSG00000145569	ENSG00000145569		"OTU domain containing"	25629	protein-coding gene	gene with protein product						12477932	Standard	NM_019018		Approved	FLJ11127, NET20	uc003jfj.3	Q9NUU6	OTTHUMG00000131056	ENST00000274217.3:c.686T>C	chr5.hg19:g.14608915T>C	ENSP00000274217:p.Leu229Pro	86.0	0.0	.		59.0	3.0	.	NM_019018	Q53H50|Q9H037	Missense_Mutation	SNP	ENST00000274217.3	hg19	CCDS3884.1	.	.	.	.	.	.	.	.	.	.	T	16.58	3.162069	0.57368	.	.	ENSG00000145569	ENST00000274217	T	0.16597	2.33	4.89	4.89	0.63831	.	0.109676	0.40064	N	0.001185	T	0.41213	0.1149	M	0.72894	2.215	0.58432	D	0.999999	D	0.89917	1.0	D	0.76575	0.988	T	0.37454	-0.9705	10	0.87932	D	0	-8.3487	14.4858	0.67616	0.0:0.0:0.0:1.0	.	229	Q9NUU6	F105A_HUMAN	P	229	ENSP00000274217:L229P	ENSP00000274217:L229P	L	+	2	0	FAM105A	14661915	0.991000	0.36638	0.996000	0.52242	0.879000	0.50718	4.189000	0.58358	1.819000	0.53055	0.477000	0.44152	CTT	.	.	.	none		0.328	FAM105A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253710.1	NM_019018		C	14608915	T	C	14608915	3	2	266	1	0	0	0	0	1	0	0	0	5391	1609	56	3	712	3	FAM105A	5	14608915	Missense_Mutation	SNP	T	TCGA-UZ-A9PV-01A-11D-A42J-10	8236277	14608915	166306345	18	16745											
AQPEP	206338	hgsc.bcm.edu	37	chr5	115351418	115351418	+	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	tctgaagttggccggtatgtCgcaaaagacttcttagtcaa	11	12	10	8	2	3	2	1	1	2	1	4	2	3	2	1	2	0	3	1	2	6	4	rs143698388		TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr5:115351418C>G	ENST00000357872.4	+	18	2836	c.2712C>G	c.(2710-2712)gtC>gtG	p.V904V	AQPEP_ENST00000515454.1_3'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		904						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.V904V(1)									GCCGGTATGTCGCAAAAGACT	0.413																																					p.V904V		Atlas-SNP	.											FLJ90650,colon,carcinoma,0,1	.	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2712G						PASS	.						78	76	77					5																	115351418		2202	4300	6502	SO:0001819	synonymous_variant	0	exon18			GTATGTCGCAAAA																												ENST00000357872.4:c.2712C>G	chr5.hg19:g.115351418C>G		147.0	0.0	.		122.0	67.0	.	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Silent	SNP	ENST00000357872.4	hg19	CCDS4124.1																																																																																			.	C|1.000;T|0.000	.	alt		0.413	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1			G	115351418	C	G	115351418	2	3	266	1	0	0	0	0	0	0	0	1	834	871	31	4		4	AQPEP	5	115351418	Silent	SNP	C	TCGA-UZ-A9PV-01A-11D-A42J-10	100742503	115351418	65563842	19	16746											
MARCH3	115123	hgsc.bcm.edu	37	chr5	126253785	126253785	+	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	taggctgccacaatcctccaCcgtcttcaccacgggtgcag	8	8	9	16	2	2	0	1	0	1	0	4	0	4	0	5	2	2	2	5	2	2	2			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr5:126253785C>G	ENST00000308660.5	-	2	593	c.79G>C	c.(79-81)Gtg>Ctg	p.V27L	MARCH3_ENST00000502289.1_5'UTR|MARCH3_ENST00000515241.1_Missense_Mutation_p.V27L	NM_178450.3	NP_848545.1	Q86UD3	MARH3_HUMAN	membrane-associated ring finger (C3HC4) 3, E3 ubiquitin protein ligase	27					endocytosis (GO:0006897)|protein ubiquitination (GO:0016567)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	6		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.074)|OV - Ovarian serous cystadenocarcinoma(64;0.0793)		CAATCCTCCACCGTCTTCACC	0.572																																					p.V27L		Atlas-SNP	.											.	MARCH3	14	.	0			c.G79C						PASS	.						65	59	61					5																	126253785		2203	4300	6503	SO:0001583	missense	115123	exon2			CCTCCACCGTCTT	AF055007	CCDS4141.1	5q23.2	2013-01-09	2012-02-23		ENSG00000173926	ENSG00000173926		"MARCH membrane-associated ring fingers", "RING-type (C3HC4) zinc fingers"	28728	protein-coding gene	gene with protein product		613333	"membrane-associated ring finger (C3HC4) 3"			14722266, 8619474	Standard	NM_178450		Approved	MGC48332, MARCH-III, RNF173	uc003kuf.4	Q86UD3	OTTHUMG00000128968	ENST00000308660.5:c.79G>C	chr5.hg19:g.126253785C>G	ENSP00000309141:p.Val27Leu	118.0	0.0	.		101.0	42.0	.	NM_178450	A8K264|B9EJE7	Missense_Mutation	SNP	ENST00000308660.5	hg19	CCDS4141.1	.	.	.	.	.	.	.	.	.	.	C	16.59	3.166917	0.57476	.	.	ENSG00000173926	ENST00000308660;ENST00000515241	T;T	0.24908	2.14;1.83	4.58	4.58	0.56647	.	0.206119	0.32769	N	0.005671	T	0.18923	0.0454	N	0.25485	0.75	0.48040	D	0.999578	B;B	0.16802	0.019;0.003	B;B	0.15052	0.012;0.006	T	0.03296	-1.1051	10	0.25751	T	0.34	-10.0037	15.0423	0.71799	0.0:0.8565:0.1435:0.0	.	27;27	B9EJE7;Q86UD3	.;MARH3_HUMAN	L	27	ENSP00000309141:V27L;ENSP00000421979:V27L	ENSP00000309141:V27L	V	-	1	0	MARCH3	126281684	1.000000	0.71417	0.980000	0.43619	0.988000	0.76386	5.656000	0.67988	2.833000	0.97629	0.650000	0.86243	GTG	.	.	.	none		0.572	MARCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250955.2	NM_178450		G	126253785	C	G	126253785	3	3	266	1	0	0	0	0	1	0	0	0	9309	507	18	4	698	4	MARCH3	5	126253785	Missense_Mutation	SNP	C	TCGA-UZ-A9PV-01A-11D-A42J-10	10902367	126253785	54661475	20	16747											
GRXCR2	643226	hgsc.bcm.edu	37	chr5	145246288	145246288	+	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	tccaaaatctataataggtaGgggctagagaaatggagaat	17	9	11	4	0	1	2	0	0	1	2	2	4	2	2	1	4	0	2	1	4	9	5			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr5:145246288G>T	ENST00000377976.1	-	2	339	c.340C>A	c.(340-342)Cta>Ata	p.L114I		NM_001080516.1	NP_001073985.1	A6NFK2	GRCR2_HUMAN	glutaredoxin, cysteine rich 2	114						cell projection (GO:0042995)				breast(1)|endometrium(1)|large_intestine(2)|lung(1)|urinary_tract(2)	7						ATAATAGGTAGGGGCTAGAGA	0.408																																					p.L114I		Atlas-SNP	.											.	GRXCR2	32	.	0			c.C340A						PASS	.						55	58	57					5																	145246288		2203	4300	6503	SO:0001583	missense	643226	exon2			TAGGTAGGGGCTA		CCDS34263.1	5q32	2014-03-14			ENSG00000204928	ENSG00000204928			33862	protein-coding gene	gene with protein product		615762				24619944	Standard	NM_001080516		Approved	DFNB101	uc003lns.1	A6NFK2	OTTHUMG00000163417	ENST00000377976.1:c.340C>A	chr5.hg19:g.145246288G>T	ENSP00000367214:p.Leu114Ile	74.0	0.0	.		39.0	17.0	.	NM_001080516		Missense_Mutation	SNP	ENST00000377976.1	hg19	CCDS34263.1	.	.	.	.	.	.	.	.	.	.	G	14.25	2.478994	0.44044	.	.	ENSG00000204928	ENST00000377976	T	0.22539	1.95	5.43	4.51	0.55191	.	0.330758	0.33772	N	0.004562	T	0.10594	0.0259	N	0.08118	0	0.22435	N	0.999101	B	0.22909	0.077	B	0.23018	0.043	T	0.12708	-1.0537	10	0.62326	D	0.03	-0.8771	7.9992	0.30286	0.0913:0.1642:0.7445:0.0	.	114	A6NFK2	GRCR2_HUMAN	I	114	ENSP00000367214:L114I	ENSP00000367214:L114I	L	-	1	2	GRXCR2	145226481	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	2.602000	0.46257	2.540000	0.85666	0.462000	0.41574	CTA	.	.	.	none		0.408	GRXCR2-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373289.2			T	145246288	G	T	145246288	3	4	266	1	0	0	0	0	1	0	0	0	6820	991	35	4	414	4	GRXCR2	5	145246288	Missense_Mutation	SNP	G	TCGA-UZ-A9PV-01A-11D-A42J-10	18992503	145246288	35668972	21	16748											
CDHR2	54825	hgsc.bcm.edu	37	chr5	176008530	176008530	+	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	tgctgacagtgcttgtgtctGactgcggcgagcctgtcctc	4	12	13	12	2	1	2	0	2	1	0	3	3	2	2	2	1	4	2	2	1	0	1			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr5:176008530G>A	ENST00000510636.1	+	17	2279	c.2005G>A	c.(2005-2007)Gac>Aac	p.D669N	CDHR2_ENST00000261944.5_Missense_Mutation_p.D669N|CDHR2_ENST00000506348.1_Missense_Mutation_p.D669N	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	669	Cadherin 6. {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						GCTTGTGTCTGACTGCGGCGA	0.642																																					p.D669N		Atlas-SNP	.											.	CDHR2	152	.	0			c.G2005A						PASS	.						51	53	52					5																	176008530		2203	4300	6503	SO:0001583	missense	54825	exon17			GTGTCTGACTGCG	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.2005G>A	chr5.hg19:g.176008530G>A	ENSP00000424565:p.Asp669Asn	51.0	0.0	.		40.0	20.0	.	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	hg19	CCDS34297.1	.	.	.	.	.	.	.	.	.	.	G	19.61	3.860050	0.71834	.	.	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.65364	-0.15;-0.15;-0.15	5.47	5.47	0.80525	Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.85128	0.5626	M	0.93763	3.455	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88812	0.3292	9	0.87932	D	0	-43.5559	18.9133	0.92494	0.0:0.0:1.0:0.0	.	669	Q9BYE9	CDHR2_HUMAN	N	669	ENSP00000424565:D669N;ENSP00000261944:D669N;ENSP00000421078:D669N	ENSP00000261944:D669N	D	+	1	0	CDHR2	175941136	1.000000	0.71417	0.114000	0.21550	0.152000	0.21847	8.137000	0.89612	2.575000	0.86900	0.549000	0.68633	GAC	.	.	.	none		0.642	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675		A	176008530	G	A	176008530	3	1	266	1	0	0	0	0	1	0	0	0	3121	1290	45	2	2067	2	CDHR2	5	176008530	Missense_Mutation	SNP	G	TCGA-UZ-A9PV-01A-11D-A42J-10	30762242	176008530	4906730	22	16749											
AGPAT1	10554	hgsc.bcm.edu	37	chr6	32139113	32139113	+	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	gtcctcgcacggcacacacaGggatggcgagcacagccagg	10	3	14	14	3	0	0	0	0	0	0	2	2	1	1	2	4	2	3	2	4	0	0			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr6:32139113G>T	ENST00000395499.1	-	2	740	c.161C>A	c.(160-162)cCt>cAt	p.P54H	AGPAT1_ENST00000395496.1_Missense_Mutation_p.P54H|AGPAT1_ENST00000336984.6_Missense_Mutation_p.P54H|AGPAT1_ENST00000490711.1_5'UTR|AGPAT1_ENST00000395497.1_Missense_Mutation_p.P54H|AGPAT1_ENST00000375107.3_Missense_Mutation_p.P54H|AGPAT1_ENST00000412465.2_De_novo_Start_InFrame|AGPAT1_ENST00000375104.2_Missense_Mutation_p.P54H|PPT2-EGFL8_ENST00000422437.1_3'UTR			Q99943	PLCA_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 1	54					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						GGCACACACAGGGATGGCGAG	0.562																																					p.P54H		Atlas-SNP	.											.	AGPAT1	22	.	0			c.C161A						PASS	.						171	143	153					6																	32139113		1511	2708	4219	SO:0001583	missense	10554	exon2			CACACAGGGATGG	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.161C>A	chr6.hg19:g.32139113G>T	ENSP00000378877:p.Pro54His	139.0	0.0	.		93.0	42.0	.	NM_006411	A2BFI5|Q5BL03	Missense_Mutation	SNP	ENST00000395499.1	hg19	CCDS4744.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.425097	0.83667	.	.	ENSG00000204310	ENST00000395496;ENST00000375107;ENST00000395499;ENST00000375104;ENST00000395497;ENST00000336984	T;T;T;T;T;T	0.70869	-0.52;-0.52;-0.52;-0.52;-0.52;-0.52	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.75428	0.3848	L	0.53249	1.67	0.80722	D	1	D	0.76494	0.999	D	0.64144	0.922	T	0.78542	-0.2164	10	0.72032	D	0.01	-8.6989	16.0303	0.80572	0.0:0.0:1.0:0.0	.	54	Q99943	PLCA_HUMAN	H	54	ENSP00000378874:P54H;ENSP00000364248:P54H;ENSP00000378877:P54H;ENSP00000364245:P54H;ENSP00000378875:P54H;ENSP00000337463:P54H	ENSP00000337463:P54H	P	-	2	0	AGPAT1	32247091	0.990000	0.36364	1.000000	0.80357	0.982000	0.71751	1.946000	0.40283	2.392000	0.81423	0.561000	0.74099	CCT	.	.	.	none		0.562	AGPAT1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268941.1	NM_006411		T	32139113	G	T	32139113	3	4	266	1	0	0	0	0	1	0	0	0	386	1000	35	4	714	4	AGPAT1	6	32139113	Missense_Mutation	SNP	G	TCGA-UZ-A9PV-01A-11D-A42J-10		32139113	138975954	23	16750											
OOEP	441161	hgsc.bcm.edu	37	chr6	74078985	74078985	+	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	acaggagcatgctcttcaccCgattctgtacacggggccgc	8	8	11	14	3	3	0	1	0	2	0	3	2	3	1	2	3	3	3	2	3	1	3	rs199988719		TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr6:74078985C>A	ENST00000370359.5	-	2	313	c.314G>T	c.(313-315)cGg>cTg	p.R105L	OOEP_ENST00000370363.1_Missense_Mutation_p.R50L|OOEP-AS1_ENST00000445350.2_RNA	NM_001080507.2	NP_001073976.1	A6NGQ2	OOEP_HUMAN	oocyte expressed protein	105	KH; atypical.				cellular protein complex assembly (GO:0043623)|embryo implantation (GO:0007566)|embryonic pattern specification (GO:0009880)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|protein phosphorylation (GO:0006468)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|protein complex (GO:0043234)	RNA binding (GO:0003723)			large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	8						GCTCTTCACCCGATTCTGTAC	0.567																																					p.R105L		Atlas-SNP	.											.	OOEP	18	.	0			c.G314T						PASS	.						62	61	61					6																	74078985		1987	4163	6150	SO:0001583	missense	441161	exon2			TTCACCCGATTCT	BC024931	CCDS47451.1	6q13	2012-02-22	2012-02-22	2007-11-13	ENSG00000203907	ENSG00000203907			21382	protein-coding gene	gene with protein product	"KH homology domain containing 2"	611689	"chromosome 6 open reading frame 156", "oocyte expressed protein homolog (dog)"	C6orf156		17913455	Standard	NM_001080507		Approved	Em:AC019205.2, KHDC2	uc003pgu.4	A6NGQ2	OTTHUMG00000150057	ENST00000370359.5:c.314G>T	chr6.hg19:g.74078985C>A	ENSP00000359384:p.Arg105Leu	178.0	0.0	.		124.0	52.0	.	NM_001080507	A6NIN5|A9UIB7	Missense_Mutation	SNP	ENST00000370359.5	hg19	CCDS47451.1	.	.	.	.	.	.	.	.	.	.	C	13.79	2.343145	0.41498	.	.	ENSG00000203907	ENST00000370363;ENST00000370359;ENST00000441145	T;T;T	0.13089	2.62;2.62;2.62	3.93	-2.22	0.06952	.	0.730725	0.11792	N	0.529109	T	0.04861	0.0131	M	0.65498	2.005	0.09310	N	1	P;P	0.47841	0.901;0.872	B;B	0.40782	0.303;0.34	T	0.17930	-1.0353	10	0.54805	T	0.06	-15.2063	4.2812	0.10833	0.1618:0.3562:0.0:0.4819	.	50;105	F2Z364;A6NGQ2	.;OOEP_HUMAN	L	50;105;50	ENSP00000359388:R50L;ENSP00000359384:R105L;ENSP00000397430:R50L	ENSP00000359384:R105L	R	-	2	0	OOEP	74135706	0.152000	0.22762	0.000000	0.03702	0.118000	0.20060	0.038000	0.13862	-0.521000	0.06426	-0.150000	0.13652	CGG	.	.	.	alt		0.567	OOEP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108414.2	NM_001080507		A	74078985	C	A	74078985	3	1	266	1	0	0	0	0	1	0	0	0	10877	652	23	4	143	4	OOEP	6	74078985	Missense_Mutation	SNP	C	TCGA-UZ-A9PV-01A-11D-A42J-10	41939872	74078985	97036082	24	16751											
ROS1	6098	hgsc.bcm.edu	37	chr6	117686779	117686779	+	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	aaattctacactgtagaaaaCtacaccccagtctaccgcag	15	8	5	13	1	2	1	0	0	2	1	2	1	2	1	3	0	4	2	3	0	7	5			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr6:117686779C>G	ENST00000368508.3	-	19	3136	c.2938G>C	c.(2938-2940)Gtt>Ctt	p.V980L	GOPC_ENST00000467125.1_Intron|ROS1_ENST00000368507.3_Missense_Mutation_p.V975L	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	980	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)		CTGTAGAAAACTACACCCCAG	0.418			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																p.V980L		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	.	ROS1	728	.	0			c.G2938C						PASS	.						78	69	72					6																	117686779		2203	4300	6503	SO:0001583	missense	6098	exon19			AGAAAACTACACC	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.2938G>C	chr6.hg19:g.117686779C>G	ENSP00000357494:p.Val980Leu	275.0	0.0	.		213.0	101.0	.	NM_002944	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	hg19	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	C	12.74	2.029959	0.35797	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	T;T	0.51817	0.69;0.69	4.98	1.7	0.24286	.	0.512100	0.17556	N	0.169963	T	0.15176	0.0366	N	0.24115	0.695	0.35341	D	0.786462	B	0.21452	0.056	B	0.18871	0.023	T	0.03545	-1.1026	10	0.72032	D	0.01	.	7.7926	0.29129	0.0:0.4713:0.0:0.5287	.	980	P08922	ROS1_HUMAN	L	980;975	ENSP00000357494:V980L;ENSP00000357493:V975L	ENSP00000357493:V975L	V	-	1	0	ROS1	117793472	0.745000	0.28261	0.167000	0.22817	0.993000	0.82548	1.022000	0.30052	0.123000	0.18342	0.650000	0.86243	GTT	.	.	.	none		0.418	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			G	117686779	C	G	117686779	3	3	266	1	0	0	0	0	1	0	0	0	13544	565	20	4	4205	4	ROS1	6	117686779	Missense_Mutation	SNP	C	TCGA-UZ-A9PV-01A-11D-A42J-10	43607794	117686779	53428288	25	16752											
TXLNB	167838	hgsc.bcm.edu	37	chr6	139563669	139563669	+	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	aggcacggtgaggcttagtcGacgccttccagattggtgtc	7	10	14	10	3	0	2	0	1	0	1	3	3	1	2	2	4	0	2	2	4	1	3	rs202149819	byFrequency	TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr6:139563669G>T	ENST00000358430.3	-	10	2281	c.2049C>A	c.(2047-2049)gtC>gtA	p.V683V	RP1-225E12.3_ENST00000585874.1_RNA	NM_153235.3	NP_694967.3	Q8N3L3	TXLNB_HUMAN	taxilin beta	683						cytoplasm (GO:0005737)				breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)		AGGCTTAGTCGACGCCTTCCA	0.582																																					p.V683V		Atlas-SNP	.											.	TXLNB	96	.	0			c.C2049A						PASS	.						39	45	43					6																	139563669		2202	4300	6502	SO:0001819	synonymous_variant	167838	exon10			TTAGTCGACGCCT		CCDS34545.1	6q23.3	2008-02-05	2005-07-29	2005-07-29	ENSG00000164440	ENSG00000164440			21617	protein-coding gene	gene with protein product		611438	"chromosome 6 open reading frame 198"	C6orf198		15184072	Standard	NM_153235		Approved	DKFZp451A175, MDP77, dJ522B19.2	uc021zfy.1	Q8N3L3	OTTHUMG00000015688	ENST00000358430.3:c.2049C>A	chr6.hg19:g.139563669G>T		126.0	0.0	.		83.0	32.0	.	NM_153235	Q5VTF3|Q76L25|Q86T52|Q8N3S2	Silent	SNP	ENST00000358430.3	hg19	CCDS34545.1																																																																																			.	G|0.999;A|0.001	.	alt		0.582	TXLNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042458.1	NM_153235		T	139563669	G	T	139563669	2	4	266	1	0	0	0	0	0	0	0	1	16800	1045	37	4		4	TXLNB	6	139563669	Silent	SNP	G	TCGA-UZ-A9PV-01A-11D-A42J-10	21876890	139563669	31551398	26	16753											
HECW1	23072	hgsc.bcm.edu	37	chr7	43485157	43485157	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccccgtggcaggtccaagcAatcggagagaaggttagacc	11	5	13	12	2	0	2	0	0	0	2	2	4	1	3	4	4	1	3	4	4	4	1			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr7:43485157A>G	ENST00000395891.2	+	11	2991	c.2386A>G	c.(2386-2388)Aat>Gat	p.N796D	HECW1_ENST00000453890.1_Missense_Mutation_p.N796D	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	796					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						AGGTCCAAGCAATCGGAGAGA	0.587																																					p.N796D		Atlas-SNP	.											.	HECW1	540	.	0			c.A2386G						PASS	.						8	9	9					7																	43485157		1779	3853	5632	SO:0001583	missense	23072	exon11			CCAAGCAATCGGA	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.2386A>G	chr7.hg19:g.43485157A>G	ENSP00000379228:p.Asn796Asp	233.0	0.0	.		232.0	133.0	.	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Missense_Mutation	SNP	ENST00000395891.2	hg19	CCDS5469.2	.	.	.	.	.	.	.	.	.	.	A	0.231	-1.021230	0.02061	.	.	ENSG00000002746	ENST00000395891;ENST00000453890;ENST00000265522	T;T	0.30981	1.51;1.51	5.33	-4.08	0.03963	.	1.229190	0.05172	N	0.499662	T	0.19087	0.0458	N	0.19112	0.55	0.19300	N	0.999974	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.30475	-0.9977	10	0.17832	T	0.49	.	12.2128	0.54389	0.3522:0.5858:0.062:0.0	.	796;796	B4DH42;Q76N89	.;HECW1_HUMAN	D	796	ENSP00000379228:N796D;ENSP00000407774:N796D	ENSP00000265522:N796D	N	+	1	0	HECW1	43451682	0.001000	0.12720	0.000000	0.03702	0.195000	0.23768	-0.115000	0.10741	-1.064000	0.03172	-1.243000	0.01532	AAT	.	.	.	none		0.587	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		G	43485157	A	G	43485157	3	3	266	1	0	0	0	0	1	0	0	0	7049	130	5	3	2420	3	HECW1	7	43485157	Missense_Mutation	SNP	A	TCGA-UZ-A9PV-01A-11D-A42J-10		43485157	115653506	27	16754											
LRRC17	10234	hgsc.bcm.edu	37	chr7	102584947	102584947	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccccaaagacaagttaccaGcatatcctgagtcatttgac	13	9	7	12	0	1	3	1	2	0	1	2	3	2	3	4	0	2	2	4	0	4	3			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr7:102584947G>A	ENST00000339431.4	+	4	1514	c.1219G>A	c.(1219-1221)Gca>Aca	p.A407T	FBXL13_ENST00000393772.2_Intron|LRRC17_ENST00000485478.1_3'UTR|FBXL13_ENST00000379308.3_Intron|LRRC17_ENST00000249377.4_3'UTR|FBXL13_ENST00000436908.1_Intron|FBXL13_ENST00000379306.3_Intron|FBXL13_ENST00000379305.3_Intron|FBXL13_ENST00000313221.4_Intron|FBXL13_ENST00000455112.2_Intron|FBXL13_ENST00000456695.1_Intron	NM_001031692.2	NP_001026862.1	Q8N6Y2	LRC17_HUMAN	leucine rich repeat containing 17	407					bone marrow development (GO:0048539)|negative regulation of osteoclast differentiation (GO:0045671)|ossification (GO:0001503)	extracellular space (GO:0005615)				NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	17						CAAGTTACCAGCATATCCTGA	0.378																																					p.A407T		Atlas-SNP	.											.	LRRC17	45	.	0			c.G1219A						PASS	.						88	84	85					7																	102584947		2203	4300	6503	SO:0001583	missense	10234	exon4			TTACCAGCATATC	U32907	CCDS5727.1, CCDS34721.1	7q22.1	2009-05-26			ENSG00000128606	ENSG00000128606			16895	protein-coding gene	gene with protein product						8982252, 19336404	Standard	NM_005824		Approved	P37NB, H_RG318M05.3	uc003vau.3	Q8N6Y2	OTTHUMG00000157210	ENST00000339431.4:c.1219G>A	chr7.hg19:g.102584947G>A	ENSP00000344242:p.Ala407Thr	141.0	0.0	.		118.0	5.0	.	NM_001031692	Q13288|Q6UWA7|Q75MG5	Missense_Mutation	SNP	ENST00000339431.4	hg19	CCDS34721.1	.	.	.	.	.	.	.	.	.	.	G	11.22	1.574748	0.28092	.	.	ENSG00000128606	ENST00000339431	T	0.57752	0.38	5.79	1.59	0.23543	.	0.701797	0.12953	N	0.425685	T	0.36936	0.0985	L	0.44542	1.39	0.09310	N	0.999995	B	0.02656	0.0	B	0.04013	0.001	T	0.23332	-1.0191	10	0.14656	T	0.56	-5.854	4.826	0.13416	0.3778:0.0:0.449:0.1732	.	407	Q8N6Y2	LRC17_HUMAN	T	407	ENSP00000344242:A407T	ENSP00000344242:A407T	A	+	1	0	LRRC17	102372183	0.002000	0.14202	0.715000	0.30552	0.984000	0.73092	0.041000	0.13927	0.380000	0.24823	0.655000	0.94253	GCA	.	.	.	none		0.378	LRRC17-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347930.1	NM_005824		A	102584947	G	A	102584947	3	1	266	1	0	0	0	0	1	0	0	0	8980	971	34	2	1247	2	LRRC17	7	102584947	Missense_Mutation	SNP	G	TCGA-UZ-A9PV-01A-11D-A42J-10	59099790	102584947	56553716	28	16755											
WASL	8976	hgsc.bcm.edu	37	chr7	123329152	123329152	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttccattaatgcacccacaAttcctgaagtgggtgcaggt	10	11	9	11	0	0	1	0	1	0	0	2	1	2	1	3	2	2	2	3	2	3	3			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr7:123329152A>G	ENST00000223023.4	-	10	1732	c.1400T>C	c.(1399-1401)aTt>aCt	p.I467T		NM_003941.2	NP_003932.3	O00401	WASL_HUMAN	Wiskott-Aldrich syndrome-like	467					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						TGCACCCACAATTCCTGAAGT	0.448																																					p.I467T		Atlas-SNP	.											.	WASL	70	.	0			c.T1400C						PASS	.						178	183	182					7																	123329152		2203	4300	6503	SO:0001583	missense	8976	exon10			CCCACAATTCCTG	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.1400T>C	chr7.hg19:g.123329152A>G	ENSP00000223023:p.Ile467Thr	81.0	0.0	.		68.0	26.0	.	NM_003941	A1JUI9|Q7Z746	Missense_Mutation	SNP	ENST00000223023.4	hg19	CCDS34743.1	.	.	.	.	.	.	.	.	.	.	A	17.89	3.499369	0.64298	.	.	ENSG00000106299	ENST00000223023	D	0.95949	-3.86	5.29	5.29	0.74685	Wiscott-Aldrich syndrome, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.93549	0.7941	L	0.47016	1.485	0.80722	D	1	P	0.41748	0.761	B	0.40982	0.345	D	0.94194	0.7444	10	0.87932	D	0	-15.0061	15.2082	0.73195	1.0:0.0:0.0:0.0	.	467	O00401	WASL_HUMAN	T	467	ENSP00000223023:I467T	ENSP00000223023:I467T	I	-	2	0	WASL	123116388	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.310000	0.96267	1.983000	0.57843	0.477000	0.44152	ATT	.	.	.	none		0.448	WASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348522.1	NM_003941		G	123329152	A	G	123329152	3	3	266	1	0	0	0	0	1	0	0	0	17268	101	4	3	125	3	WASL	7	123329152	Missense_Mutation	SNP	A	TCGA-UZ-A9PV-01A-11D-A42J-10	20744205	123329152	35809511	29	16756											
SLC13A4	26266	hgsc.bcm.edu	37	chr7	135412241	135412241	+	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	gagcaggccctgcagcaggcCcatcgcgcctctgtcctctc	5	7	11	18	2	2	0	0	0	2	0	5	1	3	0	4	2	3	3	4	2	0	0			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr7:135412241C>A	ENST00000354042.4	-	1	693	c.4G>T	c.(4-6)Ggc>Tgc	p.G2C	FAM180A_ENST00000435869.1_5'Flank	NM_012450.2	NP_036582.2	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 4	2					sodium ion transmembrane transport (GO:0035725)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	24						TGCAGCAGGCCCATCGCGCCT	0.652																																					p.G2C		Atlas-SNP	.											.	SLC13A4	56	.	0			c.G4T						PASS	.						28	26	27					7																	135412241		1839	3433	5272	SO:0001583	missense	26266	exon1			GCAGGCCCATCGC	AF169301	CCDS5840.1	7q33	2013-07-18	2013-07-18		ENSG00000164707	ENSG00000164707		"Solute carriers"	15827	protein-coding gene	gene with protein product	"sulphate transporter 1"	604309	"solute carrier family 13 (sodium/sulphate symporters), member 4"			10535998	Standard	NM_012450		Approved	SUT-1, SUT1	uc003vta.3	Q9UKG4	OTTHUMG00000155539	ENST00000354042.4:c.4G>T	chr7.hg19:g.135412241C>A	ENSP00000297282:p.Gly2Cys	139.0	0.0	.		152.0	54.0	.	NM_012450	A4D1Q4|Q8N631	Missense_Mutation	SNP	ENST00000354042.4	hg19	CCDS5840.1	.	.	.	.	.	.	.	.	.	.	C	13.88	2.369767	0.42003	.	.	ENSG00000164707	ENST00000354042	T	0.69435	-0.4	5.67	5.67	0.87782	.	0.175722	0.48767	D	0.000168	T	0.64983	0.2648	L	0.38175	1.15	0.37736	D	0.925466	P	0.49635	0.926	P	0.46718	0.525	T	0.70757	-0.4785	10	0.56958	D	0.05	.	17.2665	0.87088	0.0:1.0:0.0:0.0	.	2	Q9UKG4	S13A4_HUMAN	C	2	ENSP00000297282:G2C	ENSP00000297282:G2C	G	-	1	0	SLC13A4	135062781	1.000000	0.71417	0.999000	0.59377	0.231000	0.25187	4.087000	0.57671	2.679000	0.91253	0.655000	0.94253	GGC	.	.	.	none		0.652	SLC13A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340558.1	NM_012450		A	135412241	C	A	135412241	3	1	266	1	0	0	0	0	1	0	0	0	14407	623	22	4	1940	4	SLC13A4	7	135412241	Missense_Mutation	SNP	C	TCGA-UZ-A9PV-01A-11D-A42J-10	12083089	135412241	23726422	30	16757											
KCNU1	157855	hgsc.bcm.edu	37	chr8	36788664	36788664	+	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	ccattttatcagacgttaatGtgagtctactcttctcagaa	11	15	6	9	1	4	3	2	1	3	2	5	3	4	3	1	0	1	1	1	0	4	5			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr8:36788664G>A	ENST00000399881.3	+	25	2968		c.e25+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)		AGACGTTAATGTGAGTCTACT	0.448																																					.		Atlas-SNP	.											.	KCNU1	359	.	0			c.2931+1G>A						PASS	.						116	110	112					8																	36788664		1873	4109	5982	SO:0001630	splice_region_variant	157855	exon25			GTTAATGTGAGTC	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.2931+1G>A	chr8.hg19:g.36788664G>A		100.0	0.0	.		60.0	25.0	.	NM_001031836		Splice_Site	SNP	ENST00000399881.3	hg19	CCDS55220.1	.	.	.	.	.	.	.	.	.	.	G	8.145	0.786059	0.16189	.	.	ENSG00000215262	ENST00000399881	.	.	.	5.41	4.54	0.55810	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.1602	0.48512	0.0858:0.0:0.9142:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KCNU1	36907822	1.000000	0.71417	0.921000	0.36526	0.007000	0.05969	4.717000	0.61923	1.287000	0.44583	-0.142000	0.14014	.	.	.	.	none		0.448	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836	Intron	A	36788664	G	A	36788664	5	1	266	1	0	0	0	0	0	0	1	0	8100	1391	48	2	3030	2	KCNU1	8	36788664	Splice_Site	SNP	G	TCGA-UZ-A9PV-01A-11D-A42J-10		36788664	109575358	31	16758											
FER1L6	654463	hgsc.bcm.edu	37	chr8	125061887	125061887	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgccacagtggctgctcctGttgtgaagctggctgaccag	6	10	14	11	0	0	2	0	2	0	0	1	2	1	2	3	2	3	5	3	2	1	1			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr8:125061887G>A	ENST00000522917.1	+	22	2970	c.2764G>A	c.(2764-2766)Gtt>Att	p.V922I	FER1L6-AS2_ENST00000601180.1_RNA|FER1L6_ENST00000399018.1_Missense_Mutation_p.V922I|FER1L6-AS2_ENST00000520031.1_RNA	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	922						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)			GGCTGCTCCTGTTGTGAAGCT	0.468																																					p.V922I		Atlas-SNP	.											.	FER1L6	268	.	0			c.G2764A						PASS	.						65	73	70					8																	125061887		1949	4156	6105	SO:0001583	missense	654463	exon22			GCTCCTGTTGTGA	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.2764G>A	chr8.hg19:g.125061887G>A	ENSP00000428280:p.Val922Ile	103.0	0.0	.		64.0	32.0	.	NM_001039112		Missense_Mutation	SNP	ENST00000522917.1	hg19	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	G	6.965	0.547952	0.13312	.	.	ENSG00000214814	ENST00000522917;ENST00000399018	T;T	0.67171	-0.25;-0.25	5.91	4.12	0.48240	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.431030	0.22316	U	0.061665	T	0.55481	0.1923	L	0.47716	1.5	0.44162	D	0.996969	B	0.13145	0.007	B	0.17433	0.018	T	0.44817	-0.9303	10	0.19590	T	0.45	.	8.7432	0.34569	0.2874:0.0:0.7126:0.0	.	922	Q2WGJ9	FR1L6_HUMAN	I	922	ENSP00000428280:V922I;ENSP00000381982:V922I	ENSP00000381982:V922I	V	+	1	0	FER1L6	125131068	0.005000	0.15991	0.750000	0.31169	0.248000	0.25809	1.150000	0.31639	0.835000	0.34877	-0.150000	0.13652	GTT	.	.	.	none		0.468	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		A	125061887	G	A	125061887	3	1	266	1	0	0	0	0	1	0	0	0	5822	1377	48	2	2846	2	FER1L6	8	125061887	Missense_Mutation	SNP	G	TCGA-UZ-A9PV-01A-11D-A42J-10	88273223	125061887	21302135	32	16759											
RASEF	158158	hgsc.bcm.edu	37	chr9	85630731	85630731	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catgcctacctttcttagctTtttaatggtcacctgcagat	8	16	6	11	0	2	1	1	0	1	1	2	1	2	1	3	1	4	2	3	1	3	6			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr9:85630731T>C	ENST00000376447.3	-	4	1014	c.754A>G	c.(754-756)Aag>Gag	p.K252E		NM_152573.2	NP_689786.2	Q8IZ41	RASEF_HUMAN	RAS and EF-hand domain containing	252					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						TTTCTTAGCTTTTTAATGGTC	0.423																																					p.K252E		Atlas-SNP	.											.	RASEF	69	.	0			c.A754G						PASS	.						298	275	283					9																	85630731		2203	4300	6503	SO:0001583	missense	158158	exon4			TTAGCTTTTTAAT	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.754A>G	chr9.hg19:g.85630731T>C	ENSP00000365630:p.Lys252Glu	56.0	0.0	.		45.0	22.0	.	NM_152573	A6NC29|Q96N04	Missense_Mutation	SNP	ENST00000376447.3	hg19	CCDS6662.1	.	.	.	.	.	.	.	.	.	.	T	16.30	3.085637	0.55861	.	.	ENSG00000165105	ENST00000376447	T	0.68479	-0.33	6.16	6.16	0.99307	.	0.144833	0.64402	N	0.000007	T	0.63129	0.2485	L	0.59436	1.845	0.80722	D	1	P	0.44429	0.835	B	0.35813	0.211	T	0.69621	-0.5096	10	0.87932	D	0	.	16.8061	0.85666	0.0:0.0:0.0:1.0	.	252	Q8IZ41	RASEF_HUMAN	E	252	ENSP00000365630:K252E	ENSP00000365630:K252E	K	-	1	0	RASEF	84820551	1.000000	0.71417	1.000000	0.80357	0.421000	0.31385	6.427000	0.73378	2.367000	0.80283	0.528000	0.53228	AAG	.	.	.	none		0.423	RASEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052825.1	NM_152573		C	85630731	T	C	85630731	3	2	266	1	0	0	0	0	1	0	0	0	13081	1850	64	3	1524	3	RASEF	9	85630731	Missense_Mutation	SNP	T	TCGA-UZ-A9PV-01A-11D-A42J-10		85630731	55582700	33	16760											
PARG	119016	hgsc.bcm.edu	37	chr10	51363332	51363333	+	Intron	INS	-	-	A																															atcttgctgacaacttgcacINSagtcttccccaggatggcaa																										TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr10:51363332_51363333insA	ENST00000602930.1	-	1	468				RP11-592B15.3_ENST00000432221.2_RNA	NM_001276343.1	NP_001263272.1	Q5SRD3	AGAP8_HUMAN							regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|lung(2)|ovary(2)	6						ACAACTTGCACAGTCTTCCCCA	0.47																																					p.C247fs		Atlas-INDEL	.											.	PARG	46	.	0			c.740_741insT						PASS	.																																			SO:0001627	intron_variant	8505	exon3			.																												ENST00000602930.1:c.81+7520->T	chr10.hg19:g.51363333_51363333dupA		328.0	0.0	0		189.0	29.0	0.153439	NM_003631		Frame_Shift_Ins	INS	ENST00000602930.1	hg19																																																																																				.	.	.	none		0.47	AGAP8-006	PUTATIVE	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000467541.1			A	51363333	-	A	51363332	6	5	266	0	1	1	1	0	0	0	0	0	11455	478	17	0		0	PARG	10	51363332	Intron	INS	-	TCGA-UZ-A9PV-01A-11D-A42J-10		51363332	84171415	34	16761											
LGR4	55366	hgsc.bcm.edu	37	chr11	27413998	27413999	+	Frame_Shift_Ins	INS	-	-	T																															aattgcattacttacagaacINStttgagttctttcaacccag																										TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr11:27413998_27413999insT	ENST00000379214.4	-	3	767_768	c.324_325insA	c.(322-327)aaagttfs	p.V109fs	LGR4_ENST00000389858.4_Frame_Shift_Ins_p.V85fs|LGR4_ENST00000480977.2_Intron	NM_018490.2	NP_060960.2	Q9BXB1	LGR4_HUMAN	leucine-rich repeat containing G protein-coupled receptor 4	109					bone mineralization (GO:0030282)|bone remodeling (GO:0046849)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cell differentiation involved in metanephros development (GO:0072202)|epithelial cell proliferation (GO:0050673)|innate immune response (GO:0045087)|male genitalia development (GO:0030539)|metanephric glomerulus development (GO:0072224)|metanephric nephron tubule morphogenesis (GO:0072282)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(10)|ovary(1)	32						ACTTACAGAACTTTGAGTTCTT	0.376																																					p.V109fs		Atlas-Indel,Pindel	.											.	LGR4	87	.	0			c.325_326insA						PASS	.																																			SO:0001589	frameshift_variant	55366	exon3			.	AF257182	CCDS31449.1	11p14-p13	2012-08-21	2011-01-25	2004-11-12	ENSG00000205213	ENSG00000205213		"GPCR / Class A : Orphans"	13299	protein-coding gene	gene with protein product		606666	"G protein-coupled receptor 48", "leucine-rich repeat-containing G protein-coupled receptor 4"	GPR48		10894923	Standard	NM_018490		Approved		uc001mrj.4	Q9BXB1	OTTHUMG00000133508	ENST00000379214.4:c.325dupA	chr11.hg19:g.27414001_27414001dupT	ENSP00000368516:p.Val109fs	255.0	0.0	0		188.0	91.0	0.484043	NM_018490	A6NCH3|G5E9B3|Q8N537|Q9NYD1	Frame_Shift_Ins	INS	ENST00000379214.4	hg19	CCDS31449.1																																																																																			.	.	.	none		0.376	LGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257467.1	NM_018490		T	27413999	-	T	27413998	7	5	266	1	0	1	1	0	0	0	0	0	8763	565	20	0	2594	0	LGR4	11	27413998	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PV-01A-11D-A42J-10		27413998	107592518	35	16762											
DNAJC24	196294	hgsc.bcm.edu	37	chr11	31451825	31451825	+	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	0	0	0	0	0	0	0	0	0	0	ttttcttttgcaggtgatcaCtctttttatctgagttgcag	6	20	8	7	0	4	2	1	2	3	0	4	2	4	2	0	1	2	3	0	1	1	8			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr11:31451825C>A	ENST00000278200.1	-	0	795				DNAJC24_ENST00000465995.1_Missense_Mutation_p.H109Q	NM_144981.1	NP_659418.1	Q96LU5	IMP1L_HUMAN	IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae)						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)					CAGGTGATCACTCTTTTTATC	0.353																																					p.H109Q		Atlas-SNP	.											.	DNAJC24	23	.	0			c.C327A						PASS	.						155	145	148					11																	31451825		1835	4085	5920	SO:0001628	intergenic_variant	120526	exon5			TGATCACTCTTTT		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		chr11.hg19:g.31451825C>A		50.0	0.0	.		48.0	24.0	.	NM_181706	D3DQZ7|Q96SH9	Missense_Mutation	SNP	ENST00000278200.1	hg19	CCDS7874.1	.	.	.	.	.	.	.	.	.	.	C	1.616	-0.522774	0.04141	.	.	ENSG00000170946	ENST00000465995	T	0.28069	1.63	5.12	-10.2	0.00374	Zinc finger, DPH-type (2);	1.167550	0.05911	N	0.631602	T	0.06508	0.0167	N	0.01624	-0.795	0.09310	N	0.999996	B	0.06786	0.001	B	0.04013	0.001	T	0.17077	-1.0381	10	0.12766	T	0.61	.	0.9969	0.01469	0.1957:0.1745:0.2441:0.3857	.	108	Q6P3W2	DJC24_HUMAN	Q	109	ENSP00000417548:H109Q	ENSP00000417548:H109Q	H	+	3	2	DNAJC24	31408401	0.000000	0.05858	0.130000	0.21974	0.410000	0.31052	-1.536000	0.02208	-2.076000	0.00875	-0.259000	0.10710	CAC	.	.	.	none		0.353	IMMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388496.1	NM_144981		A	31451825	C	A	31451825	1	1	266	0	1	0	0	0	0	0	0	0	4644	564	20	4		4	DNAJC24	11	31451825	IGR	SNP	C	TCGA-UZ-A9PV-01A-11D-A42J-10	4037827	31451825	103554691	36	16763											
C11orf24	53838	hgsc.bcm.edu	37	chr11	68031211	68031211	+	Frame_Shift_Del	DEL	A	A	-																															taaggacaaggagaaaatccAaatgagcacaagagctgtcc																										TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr11:68031211delA	ENST00000304271.6	-	3	427	c.25delT	c.(25-27)tggfs	p.W9fs	C11orf24_ENST00000530166.1_Intron|C11orf24_ENST00000533310.1_Frame_Shift_Del_p.W9fs	NM_022338.3	NP_071733.1	Q96F05	CK024_HUMAN	chromosome 11 open reading frame 24	9						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						GAGAAAATCCAAATGAGCACA	0.572																																					p.W9X	NSCLC(21;855 905 4198 36694)	Atlas-Indel,Pindel	.											C11orf24,NS,carcinoma,0,1	C11orf24	35	.	0			c.26delG						PASS	.						67	61	63					11																	68031211		2200	4294	6494	SO:0001589	frameshift_variant	53838	exon3			.	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.25delT	chr11.hg19:g.68031211delA	ENSP00000307264:p.Trp9fs	55.0	0.0	0		46.0	21.0	0.456522	NM_022338	Q9H2K4	Frame_Shift_Del	DEL	ENST00000304271.6	hg19	CCDS8180.1																																																																																			.	.	.	none		0.572	C11orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394750.1	NM_022338		-	68031211	A	-	68031211	7	5	266	1	0	1	0	1	0	0	0	0	1637	130	5	0	1332	0	C11orf24	11	68031211	Frame_Shift_Del	DEL	A	TCGA-UZ-A9PV-01A-11D-A42J-10	36579386	68031211	66975305	37	16764											
CEP57	9702	hgsc.bcm.edu	37	chr11	95564230	95564230	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaagcagaagaaggaattaaAagctaccaaaaagactcttg	20	6	9	6	0	1	3	0	0	1	3	1	5	1	4	1	1	3	2	1	1	9	3			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr11:95564230A>G	ENST00000325542.5	+	11	1551	c.1313A>G	c.(1312-1314)aAa>aGa	p.K438R	CEP57_ENST00000325486.5_Missense_Mutation_p.K412R|CEP57_ENST00000541150.1_Missense_Mutation_p.K429R|CEP57_ENST00000537677.1_Missense_Mutation_p.K411R	NM_001243776.1|NM_014679.4	NP_001230705.1|NP_055494.2	Q86XR8	CEP57_HUMAN	centrosomal protein 57kDa	438	Mediates interaction with microtubules. {ECO:0000250}.				fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|mitotic cell cycle (GO:0000278)|protein homooligomerization (GO:0051260)|protein import into nucleus, translocation (GO:0000060)|spermatid development (GO:0007286)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	fibroblast growth factor binding (GO:0017134)|protein homodimerization activity (GO:0042803)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	13		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				AAGGAATTAAAAGCTACCAAA	0.363									Mosaic Variegated Aneuploidy Syndrome																												p.K438R		Atlas-SNP	.											.	CEP57	40	.	0			c.A1313G						PASS	.						57	58	58					11																	95564230		2201	4298	6499	SO:0001583	missense	9702	exon11	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	AATTAAAAGCTAC	D42054	CCDS8304.1, CCDS58166.1, CCDS58167.1	11q21	2014-09-17			ENSG00000166037	ENSG00000166037			30794	protein-coding gene	gene with protein product		607951				7788527	Standard	NM_014679		Approved	Translokin, TSP57, KIAA0092	uc001pfp.2	Q86XR8	OTTHUMG00000167740	ENST00000325542.5:c.1313A>G	chr11.hg19:g.95564230A>G	ENSP00000317902:p.Lys438Arg	279.0	0.0	.		212.0	104.0	.	NM_014679	A0PJH1|A8K5D0|B4DDP5|F5H5F7|Q14704|Q5JB46|Q8IXP0|Q9BVF9	Missense_Mutation	SNP	ENST00000325542.5	hg19	CCDS8304.1	.	.	.	.	.	.	.	.	.	.	A	7.425	0.637565	0.14386	.	.	ENSG00000166037	ENST00000537677;ENST00000325542;ENST00000325486;ENST00000541150	T;T;T;T	0.31510	1.49;1.49;1.5;1.49	5.89	-1.61	0.08399	.	0.694506	0.13726	N	0.367032	T	0.16896	0.0406	N	0.12746	0.255	0.09310	N	1	B;B;B	0.12013	0.005;0.0;0.003	B;B;B	0.11329	0.006;0.001;0.004	T	0.26360	-1.0105	10	0.87932	D	0	2.5484	11.7546	0.51868	0.8287:0.0:0.1713:0.0	.	429;412;438	F5H5F7;Q86XR8-2;Q86XR8	.;.;CEP57_HUMAN	R	411;438;412;429	ENSP00000441392:K411R;ENSP00000317902:K438R;ENSP00000317487:K412R;ENSP00000443436:K429R	ENSP00000317487:K412R	K	+	2	0	CEP57	95203878	0.971000	0.33674	0.007000	0.13788	0.813000	0.45954	1.442000	0.35046	-0.125000	0.11703	0.455000	0.32223	AAA	.	.	.	none		0.363	CEP57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395983.1	NM_014679		G	95564230	A	G	95564230	3	3	266	1	0	0	0	0	1	0	0	0	3258	14	1	3	1355	3	CEP57	11	95564230	Missense_Mutation	SNP	A	TCGA-UZ-A9PV-01A-11D-A42J-10	27533019	95564230	39442286	38	16765											
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103126956	103126956	+	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	agaatcttacaaactccaaaTttcccttgatcaagtaatta	16	13	3	9	0	2	2	1	1	1	1	4	2	4	2	2	0	2	1	2	0	7	5			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr11:103126956T>A	ENST00000375735.2	+	68	10592	c.10448T>A	c.(10447-10449)aTt>aAt	p.I3483N	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.I3490N|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	3483					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)		AAACTCCAAATTTCCCTTGAT	0.299																																					p.I3490N		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T10469A						PASS	.						42	41	41					11																	103126956		1802	4066	5868	SO:0001583	missense	79659	exon69			TCCAAATTTCCCT	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.10448T>A	chr11.hg19:g.103126956T>A	ENSP00000364887:p.Ile3483Asn	128.0	0.0	.		97.0	50.0	.	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	T	8.238	0.806220	0.16467	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.48201	0.82;0.82	5.32	2.77	0.32553	.	0.485095	0.23779	N	0.044650	T	0.41743	0.1172	L	0.57536	1.79	0.30134	N	0.804506	B;B	0.10296	0.0;0.003	B;B	0.13407	0.002;0.009	T	0.39078	-0.9631	10	0.18710	T	0.47	.	12.8549	0.57880	0.0:0.0:0.3632:0.6368	.	3483;3490	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	N	3483;3490	ENSP00000364887:I3483N;ENSP00000381167:I3490N	ENSP00000364887:I3483N	I	+	2	0	DYNC2H1	102632166	1.000000	0.71417	0.987000	0.45799	0.945000	0.59286	1.972000	0.40540	0.934000	0.37316	0.454000	0.30748	ATT	.	.	.	none		0.299	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		A	103126956	T	A	103126956	3	1	266	1	0	0	0	0	1	0	0	0	4848	1493	52	5	10743	5	DYNC2H1	11	103126956	Missense_Mutation	SNP	T	TCGA-UZ-A9PV-01A-11D-A42J-10	7562726	103126956	31879560	39	16766											
EXPH5	23086	hgsc.bcm.edu	37	chr11	108384989	108384989	+	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	ttctgtgaatggtacgattcAtatctcttattctcctgaaa	10	17	6	8	1	4	2	1	2	3	0	6	3	4	2	1	1	1	1	1	1	5	6			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr11:108384989A>T	ENST00000265843.4	-	6	1355	c.1245T>A	c.(1243-1245)taT>taA	p.Y415*	EXPH5_ENST00000525344.1_Nonsense_Mutation_p.Y408*|EXPH5_ENST00000524840.1_5'UTR|EXPH5_ENST00000428840.1_Nonsense_Mutation_p.Y339*|EXPH5_ENST00000443411.1_Nonsense_Mutation_p.Y227*	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	415					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)		GGTACGATTCATATCTCTTAT	0.448																																					p.Y415X		Atlas-SNP	.											.	EXPH5	193	.	0			c.T1245A						PASS	.						148	155	152					11																	108384989		2201	4298	6499	SO:0001587	stop_gained	23086	exon6			CGATTCATATCTC		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.1245T>A	chr11.hg19:g.108384989A>T	ENSP00000265843:p.Tyr415*	126.0	0.0	.		78.0	40.0	.	NM_015065	Q2KHM1|Q9Y4D6	Nonsense_Mutation	SNP	ENST00000265843.4	hg19	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.134773	0.77662	.	.	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000439956;ENST00000526312;ENST00000533052	.	.	.	5.66	3.36	0.38483	.	0.383998	0.22411	N	0.060404	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.4969	6.9989	0.24799	0.6913:0.0:0.3087:0.0	.	.	.	.	X	415;339;227;408;259;339;227	.	ENSP00000265843:Y415X	Y	-	3	2	EXPH5	107890199	0.149000	0.22717	0.645000	0.29479	0.110000	0.19582	0.320000	0.19540	0.439000	0.26476	-0.415000	0.06103	TAT	.	.	.	none		0.448	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		T	108384989	A	T	108384989	4	4	266	1	0	0	0	0	0	1	0	0	5324	224	8	5	4728	5	EXPH5	11	108384989	Nonsense_Mutation	SNP	A	TCGA-UZ-A9PV-01A-11D-A42J-10	5258033	108384989	26621527	40	16767											
TULP3	7289	hgsc.bcm.edu	37	chr12	3000145	3000145	+	Missense_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	gcgctgccggctcagtcccaGcggcgacaggtcagacaggg	7	4	16	14	4	2	1	2	0	0	1	3	2	3	1	2	4	2	2	2	4	0	0			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr12:3000145G>A	ENST00000448120.2	+	1	83	c.32G>A	c.(31-33)aGc>aAc	p.S11N	TULP3_ENST00000397132.2_Missense_Mutation_p.S11N	NM_003324.4	NP_003315.2	O75386	TULP3_HUMAN	tubby like protein 3	11					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)			CTCAGTCCCAGCGGCGACAGG	0.706																																					p.S11N		Atlas-SNP	.											.	TULP3	45	.	0			c.G32A						PASS	.						22	24	23					12																	3000145		2194	4298	6492	SO:0001583	missense	7289	exon1			GTCCCAGCGGCGA	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.32G>A	chr12.hg19:g.3000145G>A	ENSP00000410051:p.Ser11Asn	85.0	0.0	.		79.0	43.0	.	NM_003324	B3KNB7|B7Z6A2|D3DUQ4|F8WBZ9|Q8N5B0	Missense_Mutation	SNP	ENST00000448120.2	hg19	CCDS8519.1	.	.	.	.	.	.	.	.	.	.	G	12.04	1.817250	0.32145	.	.	ENSG00000078246	ENST00000228245;ENST00000448120;ENST00000397132	D;D	0.92495	-3.0;-3.05	4.31	2.45	0.29901	.	2.190990	0.01553	N	0.019778	D	0.87970	0.6312	L	0.38175	1.15	0.80722	D	1	B;B	0.27732	0.118;0.187	B;B	0.24155	0.017;0.051	T	0.71629	-0.4535	10	0.31617	T	0.26	-25.0169	7.0328	0.24977	0.2121:0.0:0.7879:0.0	.	11;11	O75386;F8WBZ9	TULP3_HUMAN;.	N	11	ENSP00000410051:S11N;ENSP00000380321:S11N	ENSP00000228245:S11N	S	+	2	0	TULP3	2870406	0.904000	0.30761	0.543000	0.28128	0.230000	0.25150	1.285000	0.33261	0.547000	0.28938	0.561000	0.74099	AGC	.	.	.	none		0.706	TULP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398468.1	NM_003324		A	3000145	G	A	3000145	3	1	266	1	0	0	0	0	1	0	0	0	16787	971	34	2	34	2	TULP3	12	3000145	Missense_Mutation	SNP	G	TCGA-UZ-A9PV-01A-11D-A42J-10		3000145	130851750	41	16768											
VWF	7450	hgsc.bcm.edu	37	chr12	6061618	6061618	+	Frame_Shift_Del	DEL	A	A	-																															ctgtgaccctcttctcccagAagtactctcctctctcattg																										TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr12:6061618delA	ENST00000261405.5	-	49	8308	c.8054delT	c.(8053-8055)ttcfs	p.F2685fs		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	2685					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)	CTTCTCCCAGAAGTACTCTCC	0.502																																					p.F2685fs		Atlas-Indel,Pindel	.											.	VWF	338	.	0			c.8055delC						PASS	.						148	126	134					12																	6061618		2203	4300	6503	SO:0001589	frameshift_variant	7450	exon49			.		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.8054delT	chr12.hg19:g.6061618delA	ENSP00000261405:p.Phe2685fs	115.0	0.0	0		77.0	32.0	0.415584	NM_000552	Q8TCE8|Q99806	Frame_Shift_Del	DEL	ENST00000261405.5	hg19	CCDS8539.1																																																																																			.	.	.	none		0.502	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		-	6061618	A	-	6061618	7	5	266	1	0	1	0	1	0	0	0	0	17258	246	9	0	403	0	VWF	12	6061618	Frame_Shift_Del	DEL	A	TCGA-UZ-A9PV-01A-11D-A42J-10	3061473	6061618	127790277	42	16769											
DENND5B	160518	hgsc.bcm.edu	37	chr12	31632918	31632918	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtatcgctggagtttcaaaAgggaagttgtatctccttca	10	14	10	7	1	3	0	2	0	1	0	5	2	3	2	1	2	0	5	1	2	5	5			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr12:31632918A>G	ENST00000389082.5	-	3	773	c.509T>C	c.(508-510)cTt>cCt	p.L170P	DENND5B_ENST00000354285.4_Missense_Mutation_p.L192P|DENND5B_ENST00000536562.1_Missense_Mutation_p.L205P|DENND5B_ENST00000545147.1_Intron|DENND5B_ENST00000306833.6_Missense_Mutation_p.L205P	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	170					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						GAGTTTCAAAAGGGAAGTTGT	0.433																																					p.L170P		Atlas-SNP	.											.	DENND5B	114	.	0			c.T509C						PASS	.						158	149	152					12																	31632918		1970	4164	6134	SO:0001583	missense	160518	exon3			TTCAAAAGGGAAG	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.509T>C	chr12.hg19:g.31632918A>G	ENSP00000373734:p.Leu170Pro	104.0	0.0	.		100.0	4.0	.	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Missense_Mutation	SNP	ENST00000389082.5	hg19	CCDS44857.1	.	.	.	.	.	.	.	.	.	.	A	9.787	1.176857	0.21704	.	.	ENSG00000170456	ENST00000389082;ENST00000306833;ENST00000536562;ENST00000354285;ENST00000546299	T;T;T;T;T	0.08807	3.57;3.67;3.67;3.05;3.07	4.65	3.49	0.39957	.	0.357740	0.26582	N	0.023567	T	0.09862	0.0242	L	0.44542	1.39	0.80722	D	1	B;B;B;B;B	0.27192	0.171;0.066;0.171;0.107;0.171	B;B;B;B;B	0.34991	0.193;0.048;0.059;0.065;0.137	T	0.15350	-1.0440	10	0.30078	T	0.28	-26.6622	11.5172	0.50529	0.8497:0.1502:0.0:0.0	.	205;92;192;170;205	Q6ZUT9-2;Q6ZUT9-3;Q6ZUT9-4;Q6ZUT9;G3V1S3	.;.;.;DEN5B_HUMAN;.	P	170;205;205;192;122	ENSP00000373734:L170P;ENSP00000306482:L205P;ENSP00000444889:L205P;ENSP00000346238:L192P;ENSP00000442938:L122P	ENSP00000306482:L205P	L	-	2	0	DENND5B	31524185	1.000000	0.71417	0.730000	0.30809	0.950000	0.60333	6.419000	0.73345	0.795000	0.33922	0.533000	0.62120	CTT	.	.	.	none		0.433	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973		G	31632918	A	G	31632918	3	3	266	1	0	0	0	0	1	0	0	0	4439	72	3	3	3391	3	DENND5B	12	31632918	Missense_Mutation	SNP	A	TCGA-UZ-A9PV-01A-11D-A42J-10	25571300	31632918	102218977	43	16770											
PTPRB	5787	hgsc.bcm.edu	37	chr12	71016227	71016227	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaacccatgatgtgtctgtAattccagtcatgtgcagatt	12	13	8	8	0	2	2	1	1	1	1	3	2	3	2	2	0	2	2	2	0	3	3			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr12:71016227A>G	ENST00000550358.1	-	3	676	c.651T>C	c.(649-651)atT>atC	p.I217I	PTPRB_ENST00000551525.1_Silent_p.I216I|PTPRB_ENST00000334414.6_Silent_p.I217I|PTPRB_ENST00000538174.2_5'UTR			P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	0	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			ATGTGTCTGTAATTCCAGTCA	0.493																																					p.I217I		Atlas-SNP	.											.	PTPRB	676	.	0			c.T651C						PASS	.						164	177	172					12																	71016227		2050	4203	6253	SO:0001819	synonymous_variant	5787	exon3			GTCTGTAATTCCA	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like", "Fibronectin type III domain containing"	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000550358.1:c.651T>C	chr12.hg19:g.71016227A>G		74.0	0.0	.		60.0	27.0	.	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Silent	SNP	ENST00000550358.1	hg19																																																																																				.	.	.	none		0.493	PTPRB-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404436.1			G	71016227	A	G	71016227	2	3	266	1	0	0	0	0	0	0	0	1	12809	358	13	3		3	PTPRB	12	71016227	Silent	SNP	A	TCGA-UZ-A9PV-01A-11D-A42J-10	39383309	71016227	62835668	44	16771											
LHX5	64211	hgsc.bcm.edu	37	chr12	113909298	113909298	+	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	tcgcaaccggcgcagtgcacCatcatagccccgcgccccgg	7	4	11	19	6	1	0	1	0	0	0	2	0	1	0	6	2	3	3	6	2	2	1			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr12:113909298C>T	ENST00000261731.3	-	1	579	c.6G>A	c.(4-6)atG>atA	p.M2I	LHX5_ENST00000557836.1_5'UTR|RP11-82C23.2_ENST00000551357.2_RNA	NM_022363.2	NP_071758.1	Q9H2C1	LHX5_HUMAN	LIM homeobox 5	2					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						CGCAGTGCACCATCATAGCCC	0.697																																					p.M2I		Atlas-SNP	.											.	LHX5	39	.	0			c.G6A						PASS	.						22	19	20					12																	113909298		2201	4297	6498	SO:0001583	missense	64211	exon1			GTGCACCATCATA	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.6G>A	chr12.hg19:g.113909298C>T	ENSP00000261731:p.Met2Ile	76.0	0.0	.		79.0	41.0	.	NM_022363	Q32MA4	Missense_Mutation	SNP	ENST00000261731.3	hg19	CCDS9171.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.207726	0.79240	.	.	ENSG00000089116	ENST00000261731	D	0.90676	-2.71	4.04	4.04	0.47022	.	0.000000	0.64402	D	0.000012	D	0.83635	0.5297	L	0.33339	1.005	0.80722	D	1	P	0.41929	0.765	B	0.34180	0.177	T	0.83273	-0.0042	10	0.25106	T	0.35	.	16.3982	0.83630	0.0:1.0:0.0:0.0	.	2	Q9H2C1	LHX5_HUMAN	I	2	ENSP00000261731:M2I	ENSP00000261731:M2I	M	-	3	0	LHX5	112393681	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	4.722000	0.61958	2.084000	0.62774	0.491000	0.48974	ATG	.	.	.	none		0.697	LHX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404788.3	NM_022363		T	113909298	C	T	113909298	3	4	266	1	0	0	0	0	1	0	0	0	8781	594	21	2	1222	2	LHX5	12	113909298	Missense_Mutation	SNP	C	TCGA-UZ-A9PV-01A-11D-A42J-10	42893071	113909298	19942597	45	16772											
WDR25	79446	hgsc.bcm.edu	37	chr14	100847806	100847806	+	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	ctatactcccagaagactaaGacagcggcaggcattaagca	15	6	9	11	1	0	3	0	0	0	3	1	3	1	3	1	2	3	3	1	2	5	4			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr14:100847806G>T	ENST00000335290.6	+	2	771	c.545G>T	c.(544-546)aGa>aTa	p.R182I	WDR25_ENST00000402312.3_Missense_Mutation_p.R182I|WDR25_ENST00000542471.2_5'Flank|WDR25_ENST00000554998.1_Missense_Mutation_p.R182I|WDR25_ENST00000554175.1_Missense_Mutation_p.R182I	NM_024515.4	NP_078791.3	Q64LD2	WDR25_HUMAN	WD repeat domain 25	182										central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|skin(1)	20		Melanoma(154;0.212)				AGAAGACTAAGACAGCGGCAG	0.552																																					p.R182I		Atlas-SNP	.											.	WDR25	37	.	0			c.G545T						PASS	.						81	90	87					14																	100847806		2203	4300	6503	SO:0001583	missense	79446	exon2			GACTAAGACAGCG	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.545G>T	chr14.hg19:g.100847806G>T	ENSP00000334148:p.Arg182Ile	63.0	0.0	.		33.0	20.0	.	NM_001161476	A8K7E5|Q6NVV6|Q86TQ4|Q9BTK5	Missense_Mutation	SNP	ENST00000335290.6	hg19	CCDS32157.1	.	.	.	.	.	.	.	.	.	.	G	19.98	3.926450	0.73327	.	.	ENSG00000176473	ENST00000554998;ENST00000402312;ENST00000335290;ENST00000554175	T;T;T;T	0.67523	-0.27;-0.27;-0.27;1.59	5.75	5.75	0.90469	.	0.000000	0.56097	D	0.000030	T	0.80352	0.4607	M	0.63843	1.955	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.81221	-0.1031	10	0.72032	D	0.01	-27.8569	16.8544	0.86002	0.0:0.0:1.0:0.0	.	182	Q64LD2	WDR25_HUMAN	I	182	ENSP00000450661:R182I;ENSP00000385540:R182I;ENSP00000334148:R182I;ENSP00000450727:R182I	ENSP00000334148:R182I	R	+	2	0	WDR25	99917559	0.490000	0.26012	0.008000	0.14137	0.041000	0.13682	5.365000	0.66116	2.711000	0.92665	0.655000	0.94253	AGA	.	.	.	none		0.552	WDR25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414312.1	NM_024515		T	100847806	G	T	100847806	3	4	266	1	0	0	0	0	1	0	0	0	17294	942	33	4	547	4	WDR25	14	100847806	Missense_Mutation	SNP	G	TCGA-UZ-A9PV-01A-11D-A42J-10		100847806	6501734	46	16773											
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102452422	102452422	+	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	gatgacattgagtctcttcaCgacaagttcaaggtccagta	12	11	9	9	1	3	2	2	2	1	0	5	4	4	2	1	1	0	2	1	1	3	4			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr14:102452422C>G	ENST00000360184.4	+	8	2024	c.1860C>G	c.(1858-1860)caC>caG	p.H620Q		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	620	Interaction with DYNC1I2. {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						AGTCTCTTCACGACAAGTTCA	0.517																																					p.H620Q		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.C1860G						PASS	.						68	57	61					14																	102452422		2203	4300	6503	SO:0001583	missense	1778	exon8			TCTTCACGACAAG	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.1860C>G	chr14.hg19:g.102452422C>G	ENSP00000348965:p.His620Gln	78.0	0.0	.		80.0	34.0	.	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	hg19	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	C	12.10	1.836491	0.32421	.	.	ENSG00000197102	ENST00000360184	T	0.52754	0.65	5.85	-4.23	0.03789	Dynein heavy chain, domain-1 (1);	0.000000	0.85682	D	0.000000	T	0.41328	0.1154	L	0.38953	1.18	0.58432	D	0.999998	P	0.47604	0.898	P	0.49528	0.614	T	0.39057	-0.9632	10	0.29301	T	0.29	.	15.3766	0.74610	0.0:0.2162:0.0:0.7838	.	620	Q14204	DYHC1_HUMAN	Q	620	ENSP00000348965:H620Q	ENSP00000348965:H620Q	H	+	3	2	DYNC1H1	101522175	0.035000	0.19736	0.804000	0.32291	0.988000	0.76386	-0.917000	0.04025	-0.650000	0.05423	0.655000	0.94253	CAC	.	.	.	none		0.517	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		G	102452422	C	G	102452422	3	3	266	1	0	0	0	0	1	0	0	0	4843	535	19	4	1890	4	DYNC1H1	14	102452422	Missense_Mutation	SNP	C	TCGA-UZ-A9PV-01A-11D-A42J-10	1604616	102452422	4897118	47	16774											
LOXL1	4016	hgsc.bcm.edu	37	chr15	74241804	74241804	+	Missense_Mutation	SNP	A	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	ttctcttcttcctcaggtgcAcgtgaacccaaagtatattg	9	14	7	11	1	3	1	1	1	2	0	5	1	4	1	2	1	2	2	2	1	4	6			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr15:74241804A>C	ENST00000261921.7	+	6	1933	c.1607A>C	c.(1606-1608)cAc>cCc	p.H536P	LOXL1_ENST00000567675.1_3'UTR	NM_005576.2	NP_005567.2	Q08397	LOXL1_HUMAN	lysyl oxidase-like 1	536	Lysyl-oxidase like.				extracellular matrix organization (GO:0030198)|oxidation-reduction process (GO:0055114)|protein deamination (GO:0018277)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor (GO:0016641)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10						CCTCAGGTGCACGTGAACCCA	0.498																																					p.H536P		Atlas-SNP	.											.	LOXL1	25	.	0			c.A1607C						PASS	.						187	180	182					15																	74241804		2198	4297	6495	SO:0001583	missense	4016	exon6			AGGTGCACGTGAA	L21186	CCDS10253.1	15q24-q25	2008-07-18			ENSG00000129038	ENSG00000129038			6665	protein-coding gene	gene with protein product		153456				7689553	Standard	NM_005576		Approved	LOXL, LOL	uc002awc.1	Q08397	OTTHUMG00000137595	ENST00000261921.7:c.1607A>C	chr15.hg19:g.74241804A>C	ENSP00000261921:p.His536Pro	94.0	0.0	.		70.0	34.0	.	NM_005576	Q6NUL3|Q96BW7	Missense_Mutation	SNP	ENST00000261921.7	hg19	CCDS10253.1	.	.	.	.	.	.	.	.	.	.	A	11.75	1.732848	0.30684	.	.	ENSG00000129038	ENST00000261921;ENST00000395162	T	0.30182	1.54	5.02	5.02	0.67125	.	0.361157	0.29002	N	0.013455	T	0.18425	0.0442	N	0.14661	0.345	0.31393	N	0.677542	P	0.42584	0.784	B	0.39562	0.303	T	0.12656	-1.0539	10	0.59425	D	0.04	.	9.0722	0.36500	0.8362:0.0:0.0:0.1638	.	536	Q08397	LOXL1_HUMAN	P	536;398	ENSP00000261921:H536P	ENSP00000261921:H536P	H	+	2	0	LOXL1	72028857	0.545000	0.26449	1.000000	0.80357	0.590000	0.36582	3.250000	0.51445	1.880000	0.54463	0.460000	0.39030	CAC	.	.	.	none		0.498	LOXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268995.2	NM_005576		C	74241804	A	C	74241804	3	2	266	1	0	0	0	0	1	0	0	0	8906	159	6	5	1629	5	LOXL1	15	74241804	Missense_Mutation	SNP	A	TCGA-UZ-A9PV-01A-11D-A42J-10		74241804	28289588	48	16775											
NUDT21	11051	hgsc.bcm.edu	37	chr16	56473585	56473585	+	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	tgacctgaggaggttcaaaaTttggtctccaccagttacca	11	11	9	10	0	2	2	1	2	1	0	3	3	2	3	4	3	1	2	4	3	3	3			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr16:56473585T>A	ENST00000300291.5	-	4	627	c.455A>T	c.(454-456)aAt>aTt	p.N152I		NM_007006.2	NP_008937.1	O43809	CPSF5_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 21	152	Necessary for interactions with PAPOLA and PABPN1.|Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA polyadenylation (GO:0006378)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein tetramerization (GO:0051262)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	AU-rich element binding (GO:0017091)|histone deacetylase binding (GO:0042826)|hydrolase activity (GO:0016787)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)	7						AGGTTCAAAATTTGGTCTCCA	0.403																																					p.N152I		Atlas-SNP	.											.	NUDT21	12	.	0			c.A455T						PASS	.						185	189	187					16																	56473585		2198	4300	6498	SO:0001583	missense	11051	exon4			TCAAAATTTGGTC	AJ001810	CCDS10760.1	16q12.2	2013-06-18	2005-07-11	2005-07-11	ENSG00000167005	ENSG00000167005		"Nudix motif containing"	13870	protein-coding gene	gene with protein product	"cleavage factor Im complex 25 kDa subunit"	604978	"cleavage and polyadenylation specific factor 5, 25 kDa", "cleavage and polyadenylation specific factor 5, 25 kD subunit"	CPSF5		9659921	Standard	NM_007006		Approved	CFIM25	uc002eja.3	O43809	OTTHUMG00000133240	ENST00000300291.5:c.455A>T	chr16.hg19:g.56473585T>A	ENSP00000300291:p.Asn152Ile	119.0	0.0	.		163.0	85.0	.	NM_007006	Q6IB85|Q6NE84	Missense_Mutation	SNP	ENST00000300291.5	hg19	CCDS10760.1	.	.	.	.	.	.	.	.	.	.	T	29.9	5.044654	0.93685	.	.	ENSG00000167005	ENST00000300291	.	.	.	5.78	5.78	0.91487	NUDIX hydrolase domain (1);	0.040554	0.85682	D	0.000000	D	0.85669	0.5750	M	0.92219	3.285	0.80722	D	1	D	0.71674	0.998	D	0.71870	0.975	D	0.89235	0.3580	9	0.87932	D	0	.	16.1205	0.81351	0.0:0.0:0.0:1.0	.	152	O43809	CPSF5_HUMAN	I	152	.	ENSP00000300291:N152I	N	-	2	0	NUDT21	55031086	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.027000	0.88791	2.205000	0.71048	0.533000	0.62120	AAT	.	.	.	none		0.403	NUDT21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256980.3	NM_007006		A	56473585	T	A	56473585	3	1	266	1	0	0	0	0	1	0	0	0	10745	1493	52	5	244	5	NUDT21	16	56473585	Missense_Mutation	SNP	T	TCGA-UZ-A9PV-01A-11D-A42J-10		56473585	33881168	49	16776											
FOXL1	2300	hgsc.bcm.edu	37	chr16	86612503	86612503	+	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	tacagctacatcgcgctcatCgccatggcgatccaggacgc	9	7	10	15	5	1	0	1	0	0	0	4	2	2	1	2	2	3	2	2	2	2	2			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr16:86612503C>A	ENST00000320241.3	+	1	389	c.174C>A	c.(172-174)atC>atA	p.I58I		NM_005250.2	NP_005241.1	Q12952	FOXL1_HUMAN	forkhead box L1	58					heart development (GO:0007507)|multicellular organismal development (GO:0007275)|organ morphogenesis (GO:0009887)|Peyer's patch morphogenesis (GO:0061146)|proteoglycan biosynthetic process (GO:0030166)|regulation of Wnt signaling pathway (GO:0030111)|transcription, DNA-templated (GO:0006351)|visceral mesoderm-endoderm interaction involved in midgut development (GO:0007495)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(2)|prostate(3)|skin(1)|urinary_tract(1)	15						TCGCGCTCATCGCCATGGCGA	0.677																																					p.I58I	NSCLC(163;308 2020 10889 11476 18208)	Atlas-SNP	.											.	FOXL1	39	.	0			c.C174A						PASS	.						60	61	61					16																	86612503		2198	4300	6498	SO:0001819	synonymous_variant	2300	exon1			GCTCATCGCCATG	AF315075	CCDS10959.1	16q24	2014-07-15			ENSG00000176678	ENSG00000176678		"Forkhead boxes"	3817	protein-coding gene	gene with protein product		603252		FKHL11		7957066	Standard	NM_005250		Approved	FREAC7, FKH6	uc002fjr.3	Q12952	OTTHUMG00000137653	ENST00000320241.3:c.174C>A	chr16.hg19:g.86612503C>A		150.0	0.0	.		189.0	80.0	.	NM_005250	Q17RR1|Q9H242	Silent	SNP	ENST00000320241.3	hg19	CCDS10959.1																																																																																			.	.	.	none		0.677	FOXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269105.2	NM_005250		A	86612503	C	A	86612503	2	1	266	1	0	0	0	0	0	0	0	1	6023	874	31	4		4	FOXL1	16	86612503	Silent	SNP	C	TCGA-UZ-A9PV-01A-11D-A42J-10	30138918	86612503	3742250	50	16777											
SMG6	23293	hgsc.bcm.edu	37	chr17	2185973	2185973	+	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	caggctgcccagcccattctCttgctcagaatccttcccag	7	10	7	17	0	2	1	1	0	1	1	5	1	4	1	4	1	3	2	4	1	1	3			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr17:2185973C>T	ENST00000263073.6	-	8	2679	c.2629G>A	c.(2629-2631)Gag>Aag	p.E877K	SMG6_ENST00000544865.1_Missense_Mutation_p.E846K	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	877					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						AGCCCATTCTCTTGCTCAGAA	0.542																																					p.E877K	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.G2629A						PASS	.						159	144	149					17																	2185973		2203	4300	6503	SO:0001583	missense	23293	exon8			CATTCTCTTGCTC	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.2629G>A	chr17.hg19:g.2185973C>T	ENSP00000263073:p.Glu877Lys	84.0	0.0	.		99.0	27.0	.	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Missense_Mutation	SNP	ENST00000263073.6	hg19	CCDS11016.1	.	.	.	.	.	.	.	.	.	.	C	14.29	2.490176	0.44249	.	.	ENSG00000070366	ENST00000263073;ENST00000544865	T;T	0.27256	1.68;1.68	5.55	5.55	0.83447	.	0.062061	0.64402	D	0.000004	T	0.22475	0.0542	L	0.38175	1.15	0.37547	D	0.918554	P	0.38677	0.642	B	0.37508	0.252	T	0.07849	-1.0751	10	0.36615	T	0.2	-12.2888	14.4148	0.67142	0.1475:0.8525:0.0:0.0	.	877	Q86US8	EST1A_HUMAN	K	877;846	ENSP00000263073:E877K;ENSP00000443920:E846K	ENSP00000263073:E877K	E	-	1	0	SMG6	2132723	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.269000	0.65542	2.615000	0.88500	0.555000	0.69702	GAG	.	.	.	none		0.542	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3			T	2185973	C	T	2185973	3	4	266	1	0	0	0	0	1	0	0	0	14810	922	32	2	1678	2	SMG6	17	2185973	Missense_Mutation	SNP	C	TCGA-UZ-A9PV-01A-11D-A42J-10		2185973	79009237	51	16778											
OR1A1	8383	hgsc.bcm.edu	37	chr17	3119607	3119607	+	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	ttccaggttccttccaccaaGggcgtgctcaaggccttctc	6	11	9	15	1	2	0	1	0	1	0	6	0	5	0	5	3	1	2	5	3	2	4			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr17:3119607G>T	ENST00000304094.1	+	1	693	c.693G>T	c.(691-693)aaG>aaT	p.K231N		NM_014565.2	NP_055380.2	Q9P1Q5	OR1A1_HUMAN	olfactory receptor, family 1, subfamily A, member 1	231						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	23						CTTCCACCAAGGGCGTGCTCA	0.488																																					p.K231N		Atlas-SNP	.											.	OR1A1	54	.	0			c.G693T						PASS	.						217	191	199					17																	3119607		2203	4300	6503	SO:0001583	missense	8383	exon1			CACCAAGGGCGTG	AF087918	CCDS11022.1	17p13.3	2012-08-09			ENSG00000172146	ENSG00000172146		"GPCR / Class A : Olfactory receptors"	8179	protein-coding gene	gene with protein product						10673334	Standard	NM_014565		Approved	OR17-7	uc010vrc.2	Q9P1Q5	OTTHUMG00000090637	ENST00000304094.1:c.693G>T	chr17.hg19:g.3119607G>T	ENSP00000305207:p.Lys231Asn	91.0	0.0	.		94.0	68.0	.	NM_014565	A5D914|Q6IFM1|Q6NTA9|Q96R87	Missense_Mutation	SNP	ENST00000304094.1	hg19	CCDS11022.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.693103	0.30052	.	.	ENSG00000172146	ENST00000304094	T	0.00145	8.67	4.96	-0.611	0.11601	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	D	0.000052	T	0.00271	0.0008	M	0.65320	2	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.51276	-0.8726	10	0.46703	T	0.11	.	4.3539	0.11169	0.3002:0.0:0.4654:0.2344	.	231	Q9P1Q5	OR1A1_HUMAN	N	231	ENSP00000305207:K231N	ENSP00000305207:K231N	K	+	3	2	OR1A1	3066357	0.998000	0.40836	0.960000	0.40013	0.312000	0.27988	0.687000	0.25407	0.303000	0.22785	0.436000	0.28706	AAG	.	.	.	none		0.488	OR1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207292.1	NM_014565		T	3119607	G	T	3119607	3	4	266	1	0	0	0	0	1	0	0	0	10956	991	35	4	695	4	OR1A1	17	3119607	Missense_Mutation	SNP	G	TCGA-UZ-A9PV-01A-11D-A42J-10	933634	3119607	78075603	52	16779											
CAMKK1	84254	hgsc.bcm.edu	37	chr17	3786457	3786457	+	Frame_Shift_Del	DEL	G	G	-																															gggcagcctgggaccctctcGggggagggcgacctgtgacc																										TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr17:3786457delG	ENST00000348335.2	-	6	675	c.527delC	c.(526-528)ccgfs	p.P176fs	CAMKK1_ENST00000158166.5_Frame_Shift_Del_p.P176fs|CAMKK1_ENST00000381771.2_Frame_Shift_Del_p.P176fs|CAMKK1_ENST00000381769.2_Frame_Shift_Del_p.P203fs	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)		GGACCCTCTCGGGGGAGGGCG	0.627																																					p.P176fs		Atlas-Indel,Pindel	.											.	CAMKK1	70	.	0			c.528delG						PASS	.						60	59	59					17																	3786457		2203	4300	6503	SO:0001589	frameshift_variant	84254	exon6			.	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.527delC	chr17.hg19:g.3786457delG	ENSP00000323118:p.Pro176fs	30.0	0.0	0		29.0	21.0	0.724138	NM_172207	Q9BQH3	Frame_Shift_Del	DEL	ENST00000348335.2	hg19	CCDS11038.1																																																																																			.	.	.	none		0.627	CAMKK1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207456.1	NM_032294, NM_172206, NM_172207		-	3786457	G	-	3786457	7	5	266	1	0	1	0	1	0	0	0	0	2608	1116	39	0	1156	0	CAMKK1	17	3786457	Frame_Shift_Del	DEL	G	TCGA-UZ-A9PV-01A-11D-A42J-10	666850	3786457	77408753	53	16780											
ACACA	31	hgsc.bcm.edu	37	chr17	35549238	35549238	+	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	agatgacgatagatacgatcCtcctcaaactgagtacaaga	16	8	8	9	2	1	5	1	2	0	3	3	7	3	5	2	0	3	1	2	0	5	3			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr17:35549238C>A	ENST00000394406.2	-	37	4288	c.4098G>T	c.(4096-4098)gaG>gaT	p.E1366D	ACACA_ENST00000335166.5_Missense_Mutation_p.E1288D|ACACA_ENST00000353139.5_Missense_Mutation_p.E1403D|ACACA_ENST00000360679.3_Missense_Mutation_p.E1308D	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	1366					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)	AGATACGATCCTCCTCAAACT	0.403																																					p.E1403D	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-SNP	.											.	ACACA	395	.	0			c.G4209T						PASS	.						48	44	46					17																	35549238		2203	4300	6503	SO:0001583	missense	31	exon37			ACGATCCTCCTCA	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.4098G>T	chr17.hg19:g.35549238C>A	ENSP00000377928:p.Glu1366Asp	56.0	0.0	.		72.0	25.0	.	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	hg19	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	C	18.68	3.676844	0.67928	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166;ENST00000427330	D;D;D;D	0.83250	-1.7;-1.7;-1.7;-1.7	5.68	-0.978	0.10279	Acetyl-CoA carboxylase, central domain (1);	0.048932	0.85682	D	0.000000	D	0.90851	0.7126	M	0.91872	3.25	0.80722	D	1	D;D;D;D	0.89917	0.999;0.99;1.0;0.999	D;D;D;D	0.79784	0.98;0.911;0.993;0.982	D	0.90220	0.4271	10	0.87932	D	0	-18.278	10.9907	0.47547	0.0:0.4713:0.0:0.5287	.	114;1403;1366;1308	F8W6G0;Q13085-4;Q13085;Q13085-2	.;.;ACACA_HUMAN;.	D	1403;1308;1366;1390;1288;114	ENSP00000344789:E1403D;ENSP00000353898:E1308D;ENSP00000377928:E1366D;ENSP00000335323:E1288D	ENSP00000335323:E1288D	E	-	3	2	ACACA	32623351	0.976000	0.34144	1.000000	0.80357	0.992000	0.81027	0.180000	0.16860	-0.026000	0.13895	-0.355000	0.07637	GAG	.	.	.	none		0.403	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		A	35549238	C	A	35549238	3	1	266	1	0	0	0	0	1	0	0	0	106	680	24	4	3022	4	ACACA	17	35549238	Missense_Mutation	SNP	C	TCGA-UZ-A9PV-01A-11D-A42J-10	31762781	35549238	45645972	54	16781											
BPTF	2186	hgsc.bcm.edu	37	chr17	65919081	65919082	+	Frame_Shift_Ins	INS	-	-	G																															agaagaagaactggaattgtINSgggagatcagggcatttgct																										TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr17:65919081_65919082insG	ENST00000321892.4	+	16	6122_6123	c.6061_6062insG	c.(6061-6063)tggfs	p.W2021fs	BPTF_ENST00000424123.3_Frame_Shift_Ins_p.W1882fs|BPTF_ENST00000306378.6_Frame_Shift_Ins_p.W1895fs|BPTF_ENST00000335221.5_Frame_Shift_Ins_p.W2021fs			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2021					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)			ACTGGAATTGTGGGAGATCAGG	0.411																																					p.W2021fs		Atlas-Indel,Pindel	.											.	BPTF	415	.	0			c.6061_6062insG						PASS	.																																			SO:0001589	frameshift_variant	2186	exon16			.	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.6064dupG	chr17.hg19:g.65919084_65919084dupG	ENSP00000315454:p.Trp2021fs	130.0	0.0	0		114.0	72.0	0.631579	NM_004459	Q6NX67|Q7Z7D6|Q9UIG2	Frame_Shift_Ins	INS	ENST00000321892.4	hg19																																																																																				.	.	.	none		0.411	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		G	65919082	-	G	65919081	7	5	266	1	0	1	1	0	0	0	0	0	1497	1696	59	0	6123	0	BPTF	17	65919081	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PV-01A-11D-A42J-10	30369843	65919081	15276129	55	16782											
CACNA1A	773	hgsc.bcm.edu	37	chr19	13409851	13409851	+	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	gctggggtcccgggcccgatCgtggtagcgggcctgtttcc	2	9	17	13	4	0	0	0	0	0	0	3	1	2	0	4	5	1	3	4	5	1	2			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr19:13409851C>G	ENST00000360228.5	-	19	2595	c.2596G>C	c.(2596-2598)Gat>Cat	p.D866H	CACNA1A_ENST00000573710.2_Missense_Mutation_p.D867H	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	867					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)	CGGGCCCGATCGTGGTAGCGG	0.741																																					p.D867H		Atlas-SNP	.											.	CACNA1A	715	.	0			c.G2599C						PASS	.						10	13	12					19																	13409851		1849	4035	5884	SO:0001583	missense	773	exon19			CCCGATCGTGGTA	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.2596G>C	chr19.hg19:g.13409851C>G	ENSP00000353362:p.Asp866His	518.0	0.0	.		297.0	139.0	.	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	hg19	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	C	5.552	0.286812	0.10513	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.95724	-3.79	3.09	2.04	0.26737	.	3.396480	0.00857	N	0.001886	D	0.95043	0.8395	N	0.14661	0.345	0.21105	N	0.999782	P;P;D	0.76494	0.929;0.946;0.999	B;P;D	0.69654	0.414;0.667;0.965	D	0.87123	0.2192	10	0.46703	T	0.11	.	8.9031	0.35507	0.0:0.8807:0.0:0.1193	.	867;870;866	O00555;E9PD31;Q9NS88	CAC1A_HUMAN;.;.	H	866;870;867;867	ENSP00000353362:D866H	ENSP00000317661:D867H	D	-	1	0	CACNA1A	13270851	0.893000	0.30496	0.385000	0.26158	0.002000	0.02628	1.730000	0.38125	0.296000	0.22592	-0.481000	0.04817	GAT	.	.	.	none		0.741	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		G	13409851	C	G	13409851	3	3	266	1	0	0	0	0	1	0	0	0	2540	884	31	4	5142	4	CACNA1A	19	13409851	Missense_Mutation	SNP	C	TCGA-UZ-A9PV-01A-11D-A42J-10		13409851	45719132	56	16783											
KCNN1	3780	hgsc.bcm.edu	37	chr19	18096236	18096240	+	Frame_Shift_Del	DEL	GGTGT	GGTGT	-																															cccacacctactgcgggaagGgtgtgtgcctgctcactggc																										TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	GGTGT	GGTGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr19:18096236_18096240delGGTGT	ENST00000222249.9	+	6	1352_1356	c.1033_1037delGGTGT	c.(1033-1038)ggtgtgfs	p.GV345fs		NM_002248.3	NP_002239.2	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	345					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)	CTGCGGGAAGGGTGTGTGCCTGCTC	0.6																																					p.344_346del		Atlas-Indel,Pindel	.											.	KCNN1	74	.	0			c.1032_1036del						PASS	.																																			SO:0001589	frameshift_variant	3780	exon6			.	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.1033_1037delGGTGT	chr19.hg19:g.18096236_18096240delGGTGT	ENSP00000476519:p.Gly345fs	67.0	0.0	0		34.0	15.0	0.441176	NM_002248	Q5KR10|Q6DJU4	Frame_Shift_Del	DEL	ENST00000222249.9	hg19																																																																																				.	.	.	none		0.6	KCNN1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471896.2	NM_002248		-	18096240	GGTGT	-	18096236	7	5	266	1	0	1	0	1	0	0	0	0	8085	1232	43	0	1047	0	KCNN1	19	18096236	Frame_Shift_Del	DEL	GGTGT	TCGA-UZ-A9PV-01A-11D-A42J-10	4686385	18096236	41032747	57	16784											
ZNF792	126375	hgsc.bcm.edu	37	chr19	35450319	35450319	+	Frame_Shift_Del	DEL	A	A	-																															gtgttgtctggtgttcagccAaatgcaaaatgtctttcaaa																										TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr19:35450319delA	ENST00000404801.1	-	4	826	c.440delT	c.(439-441)ttgfs	p.L147fs	ZNF792_ENST00000605484.1_Frame_Shift_Del_p.L80fs	NM_175872.4	NP_787068.3	Q3KQV3	ZN792_HUMAN	zinc finger protein 792	147					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(4)|kidney(1)|large_intestine(1)|lung(5)	12	all_lung(56;4.18e-08)|Lung NSC(56;6.62e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			GTGTTCAGCCAAATGCAAAAT	0.522																																					p.L147fs	GBM(1;7 183 21053 22581 22847)	Atlas-Indel,Pindel	.											.	ZNF792	46	.	0			c.441delG						PASS	.						196	188	191					19																	35450319		2203	4300	6503	SO:0001589	frameshift_variant	126375	exon4			.	AK095770	CCDS12440.2	19q13.11	2013-01-08			ENSG00000180884	ENSG00000180884		"Zinc fingers, C2H2-type", "-"	24751	protein-coding gene	gene with protein product						8889548	Standard	NM_175872		Approved	FLJ38451	uc002nxh.1	Q3KQV3	OTTHUMG00000150339	ENST00000404801.1:c.440delT	chr19.hg19:g.35450319delA	ENSP00000385099:p.Leu147fs	138.0	0.0	0		88.0	45.0	0.511364	NM_175872	B4E333|Q495L1|Q495L3|Q8N932	Frame_Shift_Del	DEL	ENST00000404801.1	hg19	CCDS12440.2																																																																																			.	.	.	none		0.522	ZNF792-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317673.1	NM_175872		-	35450319	A	-	35450319	7	5	266	1	0	1	0	1	0	0	0	0	18176	131	5	0	1462	0	ZNF792	19	35450319	Frame_Shift_Del	DEL	A	TCGA-UZ-A9PV-01A-11D-A42J-10	17354083	35450319	23678664	58	16785											
FBL	2091	hgsc.bcm.edu	37	chr19	40328472	40328472	+	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	tgggagaactcgactgcataGactagaccatcctaaaataa	16	8	8	9	1	0	3	0	0	0	3	2	5	1	3	2	1	2	1	2	1	6	4			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr19:40328472G>A	ENST00000221801.3	-	6	674	c.561C>T	c.(559-561)gtC>gtT	p.V187V	FBL_ENST00000593503.1_5'UTR	NM_001436.3	NP_001427.2	P22087	FBRL_HUMAN	fibrillarin	187					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)		CGACTGCATAGACTAGACCAT	0.458																																					p.V187V		Atlas-SNP	.											.	FBL	37	.	0			c.C561T						PASS	.						92	74	80					19																	40328472		2203	4300	6503	SO:0001819	synonymous_variant	2091	exon6			TGCATAGACTAGA	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.561C>T	chr19.hg19:g.40328472G>A		114.0	0.0	.		90.0	41.0	.	NM_001436	B5BUE8|O75259|Q6IAT5|Q9UPI6	Silent	SNP	ENST00000221801.3	hg19	CCDS12545.1																																																																																			.	.	.	none		0.458	FBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462509.4	NM_001436		A	40328472	G	A	40328472	2	1	266	1	0	0	0	0	0	0	0	1	5703	929	33	2		2	FBL	19	40328472	Silent	SNP	G	TCGA-UZ-A9PV-01A-11D-A42J-10	4878153	40328472	18800511	59	16786											
CNOT3	4849	hgsc.bcm.edu	37	chr19	54647753	54647753	+	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	tctctacagcaaatggaacgGttcaaagttgtggaacgaga	14	9	11	7	2	2	1	1	0	1	1	3	4	2	3	0	3	4	3	0	3	5	3			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr19:54647753G>C	ENST00000406403.1	+	5	1873	c.270G>C	c.(268-270)cgG>cgC	p.R90R	CNOT3_ENST00000221232.5_Silent_p.R90R|CNOT3_ENST00000358389.3_5'UTR			O75175	CNOT3_HUMAN	CCR4-NOT transcription complex, subunit 3	90					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)					AAATGGAACGGTTCAAAGTTG	0.557																																					p.R90R		Atlas-SNP	.											.	CNOT3	133	.	0			c.G270C						PASS	.						84	85	85					19																	54647753		2203	4300	6503	SO:0001819	synonymous_variant	4849	exon6			GGAACGGTTCAAA	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.270G>C	chr19.hg19:g.54647753G>C		169.0	0.0	.		125.0	56.0	.	NM_014516	Q9NZN7|Q9UF76	Silent	SNP	ENST00000406403.1	hg19	CCDS12880.1	.	.	.	.	.	.	.	.	.	.	G	8.775	0.926919	0.18056	.	.	ENSG00000088038	ENST00000440571	.	.	.	5.28	3.09	0.35607	.	.	.	.	.	T	0.59797	0.2220	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57376	-0.7822	4	.	.	.	-32.5338	10.2659	0.43455	0.0767:0.0:0.7851:0.1382	.	.	.	.	A	11	.	.	G	+	2	0	CNOT3	59339565	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	0.712000	0.25779	1.349000	0.45751	-0.182000	0.12963	GGT	.	.	.	none		0.557	CNOT3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142130.3	NM_014516		C	54647753	G	C	54647753	2	2	266	1	0	0	0	0	0	0	0	1	3622	1248	44	4		4	CNOT3	19	54647753	Silent	SNP	G	TCGA-UZ-A9PV-01A-11D-A42J-10	14319281	54647753	4481230	60	16787											
ZNF335	63925	hgsc.bcm.edu	37	chr20	44581108	44581108	+	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	gcagcaggggccatttggcaCcagaggccagagcatctgga	10	5	15	11	0	1	2	0	0	1	2	1	3	1	3	3	5	2	4	3	5	0	1			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr20:44581108C>A	ENST00000322927.2	-	20	2967	c.2867G>T	c.(2866-2868)gGt>gTt	p.G956V	ZNF335_ENST00000426788.1_Missense_Mutation_p.G801V	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	956					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				CCATTTGGCACCAGAGGCCAG	0.627																																					p.G956V		Atlas-SNP	.											.	ZNF335	115	.	0			c.G2867T						PASS	.						50	55	53					20																	44581108		2203	4300	6503	SO:0001583	missense	63925	exon20			TTGGCACCAGAGG	AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"Zinc fingers, C2H2-type"	15807	protein-coding gene	gene with protein product	"NRC-interacting factor 1"	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.2867G>T	chr20.hg19:g.44581108C>A	ENSP00000325326:p.Gly956Val	86.0	0.0	.		84.0	57.0	.	NM_022095	B4DLG7|Q548D0|Q9H684	Missense_Mutation	SNP	ENST00000322927.2	hg19	CCDS13389.1	.	.	.	.	.	.	.	.	.	.	C	16.52	3.145579	0.57044	.	.	ENSG00000198026	ENST00000322927;ENST00000243961;ENST00000426788	T;T	0.09255	3.14;3.0	4.7	3.74	0.42951	.	0.181866	0.38663	N	0.001613	T	0.18800	0.0451	N	0.24115	0.695	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.996	T	0.01988	-1.1234	10	0.52906	T	0.07	-8.9973	12.4133	0.55480	0.0:0.831:0.169:0.0	.	801;956	Q9H4Z2-2;Q9H4Z2	.;ZN335_HUMAN	V	956;733;801	ENSP00000325326:G956V;ENSP00000397098:G801V	ENSP00000243961:G733V	G	-	2	0	ZNF335	44014515	0.009000	0.17119	0.998000	0.56505	0.975000	0.68041	1.170000	0.31883	1.164000	0.42652	0.561000	0.74099	GGT	.	.	.	none		0.627	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095		A	44581108	C	A	44581108	3	1	266	1	0	0	0	0	1	0	0	0	17864	507	18	4	1197	4	ZNF335	20	44581108	Missense_Mutation	SNP	C	TCGA-UZ-A9PV-01A-11D-A42J-10		44581108	18444412	61	16788											
ITSN1	6453	hgsc.bcm.edu	37	chr21	35208937	35208937	+	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	catggacccaagccagcaatGtaagtgccctggtggctctg	9	8	12	12	0	1	0	0	0	1	0	1	1	1	1	3	3	3	3	3	3	3	1			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr21:35208937G>A	ENST00000381318.3	+	29	3949		c.e29+1		AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000381285.4_Splice_Site|ITSN1_ENST00000399326.3_Splice_Site|ITSN1_ENST00000399352.1_Splice_Site|ITSN1_ENST00000399353.1_Splice_Site|ITSN1_ENST00000399349.1_Splice_Site|ITSN1_ENST00000399367.3_Splice_Site|ITSN1_ENST00000437442.2_Splice_Site|ITSN1_ENST00000379960.5_Splice_Site|ITSN1_ENST00000381291.4_Splice_Site|ITSN1_ENST00000399355.2_Splice_Site	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)						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						AGCCAGCAATGTAAGTGCCCT	0.507																																					.		Atlas-SNP	.											.	ITSN1	166	.	0			c.3661+1G>A						PASS	.						90	81	84					21																	35208937		2203	4300	6503	SO:0001630	splice_region_variant	6453	exon29			AGCAATGTAAGTG	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.3661+1G>A	chr21.hg19:g.35208937G>A		201.0	0.0	.		144.0	55.0	.	NM_003024	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Splice_Site	SNP	ENST00000381318.3	hg19	CCDS33545.1	.	.	.	.	.	.	.	.	.	.	G	17.71	3.456766	0.63401	.	.	ENSG00000205726	ENST00000381318;ENST00000381285;ENST00000381288;ENST00000399367;ENST00000437442	.	.	.	4.51	4.51	0.55191	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.2445	0.87023	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ITSN1	34130807	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.278000	0.95766	2.059000	0.61396	0.637000	0.83480	.	.	.	.	none		0.507	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024	Intron	A	35208937	G	A	35208937	5	1	266	1	0	0	0	0	0	0	1	0	7933	1391	48	2	3772	2	ITSN1	21	35208937	Splice_Site	SNP	G	TCGA-UZ-A9PV-01A-11D-A42J-10		35208937	12920958	62	16789											
CCT8L2	150160	hgsc.bcm.edu	37	chr22	17073027	17073027	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaggacctctgcagtggcCgtggcgtaggcctcccggag	5	6	16	14	3	1	0	0	0	1	0	2	2	2	2	5	5	1	2	5	5	1	1			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chr22:17073027C>T	ENST00000359963.3	-	1	673	c.414G>A	c.(412-414)acG>acA	p.T138T		NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2	138					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)				CTGCAGTGGCCGTGGCGTAGG	0.637																																					p.T138T		Atlas-SNP	.											CCT8L2,NS,adenocarcinoma,0,2	CCT8L2	150	.	0			c.G414A						PASS	.						46	43	44					22																	17073027		2203	4300	6503	SO:0001819	synonymous_variant	150160	exon1			AGTGGCCGTGGCG	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.414G>A	chr22.hg19:g.17073027C>T		86.0	1.0	.		58.0	5.0	.	NM_014406	A4QPH3|Q9UJS3	Silent	SNP	ENST00000359963.3	hg19	CCDS13738.1																																																																																			.	.	.	none		0.637	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280580.1			T	17073027	C	T	17073027	2	4	266	1	0	0	0	0	0	0	0	1	2963	639	23	1		1	CCT8L2	22	17073027	Silent	SNP	C	TCGA-UZ-A9PV-01A-11D-A42J-10		17073027	34231539	63	16790											
FOXO4	4303	hgsc.bcm.edu	37	chrX	70316598	70316598	+	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	tcctgttgccctctcggctcCcagagccggccgggggcccc	2	7	13	19	3	1	1	0	0	1	1	4	1	3	1	7	4	2	2	7	4	0	1			TCGA-UZ-A9PV-01A-11D-A42J-10	TCGA-UZ-A9PV-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b0d2ed48-20a7-461b-a05b-356f5c192282	4c8c47c9-9ba8-4f00-a029-5d6e48a25489	g.chrX:70316598C>A	ENST00000374259.3	+	1	552	c.220C>A	c.(220-222)Cca>Aca	p.P74T	FOXO4_ENST00000341558.3_Intron|FOXO4_ENST00000466874.1_Intron	NM_001170931.1|NM_005938.3	NP_001164402.1|NP_005929.2	P98177	FOXO4_HUMAN	forkhead box O4	74				P -> S (in Ref. 2; CAA63819). {ECO:0000305}.	cell cycle arrest (GO:0007050)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|mitotic G2 DNA damage checkpoint (GO:0007095)|muscle organ development (GO:0007517)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of smooth muscle cell differentiation (GO:0051151)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)	18	Renal(35;0.156)					CTCTCGGCTCCCAGAGCCGGC	0.677																																					p.P74T		Atlas-SNP	.											.	FOXO4	60	.	0			c.C220A						PASS	.						9	10	10					X																	70316598		1789	4009	5798	SO:0001583	missense	4303	exon1			CGGCTCCCAGAGC		CCDS43969.1, CCDS55440.1	Xq13.1	2008-02-05	2007-05-02	2007-05-02	ENSG00000184481	ENSG00000184481		"Forkhead boxes"	7139	protein-coding gene	gene with protein product		300033	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 7", "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 7"	MLLT7		7529552	Standard	NM_005938		Approved	AFX1	uc004dys.2	P98177	OTTHUMG00000021789	ENST00000374259.3:c.220C>A	chrX.hg19:g.70316598C>A	ENSP00000363377:p.Pro74Thr	183.0	0.0	.		117.0	114.0	.	NM_005938	B7WPJ7|O43821|Q13720|Q3KPF1|Q8TDK9	Missense_Mutation	SNP	ENST00000374259.3	hg19	CCDS43969.1	.	.	.	.	.	.	.	.	.	.	C	6.735	0.504472	0.12822	.	.	ENSG00000184481	ENST00000374259	D	0.94862	-3.54	4.83	4.83	0.62350	.	0.677789	0.13613	N	0.374986	D	0.90469	0.7015	L	0.43152	1.355	0.80722	D	1	P;P	0.39809	0.689;0.509	B;B	0.34590	0.186;0.04	D	0.87734	0.2581	10	0.15499	T	0.54	-3.4079	14.6543	0.68823	0.0:1.0:0.0:0.0	.	74;74	B4DTB6;P98177	.;FOXO4_HUMAN	T	74	ENSP00000363377:P74T	ENSP00000363377:P74T	P	+	1	0	FOXO4	70233323	0.976000	0.34144	1.000000	0.80357	0.137000	0.21094	2.530000	0.45641	2.130000	0.65690	0.594000	0.82650	CCA	.	.	.	none		0.677	FOXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057115.1	NM_005938		A	70316598	C	A	70316598	3	1	266	1	0	0	0	0	1	0	0	0	6032	623	22	4	222	4	FOXO4	23	70316598	Missense_Mutation	SNP	C	TCGA-UZ-A9PV-01A-11D-A42J-10		70316598	84953962	64	16791											
GMEB1	10691	hgsc.bcm.edu	37	chr1	29037152	29037152	+	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	acagtttctctatactctgaCaggtatgtataagttatcgc	11	15	7	8	1	2	1	0	1	2	0	4	1	2	1	0	1	1	4	0	1	6	7			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr1:29037152C>A	ENST00000294409.2	+	9	1109	c.1019C>A	c.(1018-1020)aCa>aAa	p.T340K	GMEB1_ENST00000480454.1_3'UTR|GMEB1_ENST00000373816.1_Missense_Mutation_p.T330K|GMEB1_ENST00000361872.4_Missense_Mutation_p.T330K	NM_006582.3	NP_006573.2	Q9Y692	GMEB1_HUMAN	glucocorticoid modulatory element binding protein 1	340					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)	11		Colorectal(325;3.46e-05)|Lung NSC(340;0.000451)|all_lung(284;0.00063)|Breast(348;0.00502)|Renal(390;0.00555)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)		TATACTCTGACAGGTATGTAT	0.378																																					p.T340K		Atlas-SNP	.											.	GMEB1	28	.	0			c.C1019A						PASS	.						162	144	150					1																	29037152		2203	4300	6503	SO:0001583	missense	10691	exon9			CTCTGACAGGTAT	AF099013	CCDS327.1, CCDS328.1	1p35	2008-02-05			ENSG00000162419	ENSG00000162419			4370	protein-coding gene	gene with protein product		604409				10386584, 10523663	Standard	NM_006582		Approved	P96PIF, PIF96	uc001bra.3	Q9Y692	OTTHUMG00000003647	ENST00000294409.2:c.1019C>A	chr1.hg19:g.29037152C>A	ENSP00000294409:p.Thr340Lys	201.0	0.0	.		85.0	32.0	.	NM_006582	B1AT48|Q9NWH1|Q9UKD0	Missense_Mutation	SNP	ENST00000294409.2	hg19	CCDS327.1	.	.	.	.	.	.	.	.	.	.	C	17.10	3.303791	0.60305	.	.	ENSG00000162419	ENST00000373816;ENST00000456852;ENST00000361872;ENST00000294409	T;T;T	0.54279	0.58;0.58;0.58	5.52	5.52	0.82312	.	0.273025	0.41500	D	0.000870	T	0.48995	0.1531	L	0.50333	1.59	0.29901	N	0.824419	B;B	0.27498	0.023;0.18	B;B	0.19946	0.015;0.027	T	0.48864	-0.8997	10	0.36615	T	0.2	-8.9719	18.278	0.90089	0.0:1.0:0.0:0.0	.	340;330	Q9Y692;B1AT47	GMEB1_HUMAN;.	K	330;306;330;340	ENSP00000362922:T330K;ENSP00000355186:T330K;ENSP00000294409:T340K	ENSP00000294409:T340K	T	+	2	0	GMEB1	28909739	1.000000	0.71417	1.000000	0.80357	0.764000	0.43329	4.712000	0.61888	2.609000	0.88269	0.650000	0.86243	ACA	.	.	.	none		0.378	GMEB1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000010333.1	NM_006582		A	29037152	C	A	29037152	3	1	267	1	0	0	0	0	1	0	0	0	6494	478	17	4	1049	4	GMEB1	1	29037152	Missense_Mutation	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10		29037152	220213469	1	16792											
ZMYM6	9204	hgsc.bcm.edu	37	chr1	35457924	35457924	+	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	atgatatgcctttgttctttAaaagcctggaaggctgggaa	11	13	11	6	0	1	1	0	1	1	0	1	3	1	3	2	3	2	2	2	3	5	5			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr1:35457924A>C	ENST00000357182.4	-	15	2284	c.2057T>G	c.(2056-2058)tTa>tGa	p.L686*	ZMYM6_ENST00000487874.1_Nonsense_Mutation_p.L686*|ZMYM6_ENST00000373340.2_Nonsense_Mutation_p.L686*|ZMYM6_ENST00000493328.1_5'UTR	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6	686					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)				TTTGTTCTTTAAAAGCCTGGA	0.408																																					p.L686X		Atlas-SNP	.											.	ZMYM6	110	.	0			c.T2057G						PASS	.						209	193	198					1																	35457924		2203	4300	6503	SO:0001587	stop_gained	9204	exon15			TTCTTTAAAAGCC	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.2057T>G	chr1.hg19:g.35457924A>C	ENSP00000349708:p.Leu686*	188.0	0.0	.		95.0	46.0	.	NM_007167	B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	Nonsense_Mutation	SNP	ENST00000357182.4	hg19	CCDS387.2	.	.	.	.	.	.	.	.	.	.	A	39	7.609622	0.98387	.	.	ENSG00000163867	ENST00000373340;ENST00000357182	.	.	.	4.47	4.47	0.54385	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.6736	13.8694	0.63610	1.0:0.0:0.0:0.0	.	.	.	.	X	686	.	ENSP00000349708:L686X	L	-	2	0	ZMYM6	35230511	1.000000	0.71417	0.941000	0.38009	0.897000	0.52465	3.726000	0.54977	2.009000	0.58944	0.477000	0.44152	TTA	.	.	.	none		0.408	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011999.1	NM_007167		C	35457924	A	C	35457924	4	2	267	1	0	0	0	0	0	1	0	0	17716	372	13	5	1928	5	ZMYM6	1	35457924	Nonsense_Mutation	SNP	A	TCGA-UZ-A9PX-01A-11D-A42J-10	6420772	35457924	213792697	2	16793											
NFYC	4802	hgsc.bcm.edu	37	chr1	41228712	41228712	+	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	aacacaggagagatccagcaGatcccggtgagtcctgccct	11	6	11	13	1	0	3	0	1	0	2	3	5	3	4	4	2	3	1	4	2	1	0			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr1:41228712G>C	ENST00000308733.5	+	6	720	c.714G>C	c.(712-714)caG>caC	p.Q238H	NFYC_ENST00000447388.3_Missense_Mutation_p.Q238H|NFYC_ENST00000372651.1_Missense_Mutation_p.Q238H|NFYC_ENST00000427410.2_Missense_Mutation_p.Q200H|NFYC_ENST00000456393.2_Missense_Mutation_p.Q238H|NFYC_ENST00000425457.2_Missense_Mutation_p.Q238H|NFYC_ENST00000440226.3_Missense_Mutation_p.Q238H|NFYC_ENST00000372652.1_Missense_Mutation_p.Q238H|NFYC_ENST00000372654.1_Missense_Mutation_p.Q238H|NFYC_ENST00000372653.1_Missense_Mutation_p.Q204H			Q13952	NFYC_HUMAN	nuclear transcription factor Y, gamma	238					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)			AGATCCAGCAGATCCCGGTGA	0.448																																					p.Q238H		Atlas-SNP	.											.	NFYC	39	.	0			c.G714C						PASS	.						58	54	56					1																	41228712		2203	4300	6503	SO:0001583	missense	4802	exon7			CCAGCAGATCCCG	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.714G>C	chr1.hg19:g.41228712G>C	ENSP00000312617:p.Gln238His	189.0	0.0	.		109.0	41.0	.	NM_001142587	B4DUS6|B4DW63|D3DPV9|F8VWM3|Q59GY4|Q5T6K8|Q5T6K9|Q5T6L1|Q5TZR6|Q92869|Q9HBX1|Q9NXB5|Q9UM67|Q9UML0|Q9UMT7	Missense_Mutation	SNP	ENST00000308733.5	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.22|16.22	3.060411|3.060411	0.55432|0.55432	.|.	.|.	ENSG00000066136|ENSG00000066136	ENST00000414185|ENST00000427410;ENST00000447388;ENST00000425457;ENST00000456393;ENST00000372658;ENST00000372655;ENST00000372654;ENST00000372653;ENST00000372669;ENST00000372652;ENST00000372651;ENST00000440226;ENST00000308733	.|T;T;T;T;T;T;T;T;T;T;T	.|0.48201	.|0.82;0.82;0.82;0.82;0.82;1.32;0.82;0.82;0.82;0.82;0.82	5.69|5.69	4.59|4.59	0.56863|0.56863	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.57814|0.57814	0.2079|0.2079	L|L	0.41236|0.41236	1.265|1.265	0.52501|0.52501	D|D	0.99995|0.99995	.|D;D;B;B;B;D;D;D	.|0.71674	.|0.994;0.996;0.053;0.006;0.089;0.998;0.998;0.997	.|P;D;B;B;B;D;D;D	.|0.79108	.|0.808;0.992;0.028;0.007;0.035;0.933;0.933;0.989	T|T	0.56541|0.56541	-0.7962|-0.7962	5|10	.|0.51188	.|T	.|0.08	.|.	12.8221|12.8221	0.57698|0.57698	0.0927:0.0:0.9073:0.0|0.0927:0.0:0.9073:0.0	.|.	.|200;144;238;204;238;238;238;238	.|B4DW63;B4DVS8;Q13952;Q5T6K9;Q13952-3;F8VWM3;Q13952-2;B4DUS6	.|.;.;NFYC_HUMAN;.;.;.;.;.	H|H	121|200;238;238;238;136;136;238;204;238;238;238;238;238	.|ENSP00000408315:Q200H;ENSP00000404427:Q238H;ENSP00000396620:Q238H;ENSP00000408867:Q238H;ENSP00000361738:Q238H;ENSP00000361737:Q204H;ENSP00000361754:Q238H;ENSP00000361736:Q238H;ENSP00000361734:Q238H;ENSP00000414299:Q238H;ENSP00000312617:Q238H	.|ENSP00000312617:Q238H	D|Q	+|+	1|3	0|2	NFYC|NFYC	41001299|41001299	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	1.519000|1.519000	0.35888|0.35888	2.686000|2.686000	0.91538|0.91538	0.603000|0.603000	0.83216|0.83216	GAT|CAG	.	.	.	none		0.448	NFYC-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000020802.1	NM_014223		C	41228712	G	C	41228712	3	2	267	1	0	0	0	0	1	0	0	0	10398	933	33	4	736	4	NFYC	1	41228712	Missense_Mutation	SNP	G	TCGA-UZ-A9PX-01A-11D-A42J-10	5770788	41228712	208021909	3	16794											
LRIG2	9860	hgsc.bcm.edu	37	chr1	113642882	113642882	+	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	ttacaaagaaagcattcattGgtcttgaatcccttgagcat	13	13	7	8	0	2	3	1	2	1	1	3	3	3	3	1	1	3	2	1	1	4	5			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr1:113642882G>T	ENST00000361127.5	+	10	1420	c.1222G>T	c.(1222-1224)Ggt>Tgt	p.G408C		NM_014813.1	NP_055628.1	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like domains 2	408					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)		AGCATTCATTGGTCTTGAATC	0.308																																					p.G408C		Atlas-SNP	.											.	LRIG2	67	.	0			c.G1222T						PASS	.						84	89	87					1																	113642882		2203	4293	6496	SO:0001583	missense	9860	exon10			TTCATTGGTCTTG	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.1222G>T	chr1.hg19:g.113642882G>T	ENSP00000355396:p.Gly408Cys	506.0	0.0	.		325.0	145.0	.	NM_014813	Q9NSN2	Missense_Mutation	SNP	ENST00000361127.5	hg19	CCDS30808.1	.	.	.	.	.	.	.	.	.	.	g	20.3	3.966927	0.74131	.	.	ENSG00000198799	ENST00000361127	T	0.25912	1.77	5.81	4.9	0.64082	.	0.049680	0.85682	D	0.000000	T	0.49098	0.1537	M	0.88979	2.995	0.58432	D	0.99999	D	0.89917	1.0	D	0.87578	0.998	T	0.62258	-0.6892	10	0.87932	D	0	.	14.7602	0.69600	0.0694:0.0:0.9306:0.0	.	408	O94898	LRIG2_HUMAN	C	408	ENSP00000355396:G408C	ENSP00000355396:G408C	G	+	1	0	LRIG2	113444405	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.124000	0.71620	1.457000	0.47850	0.655000	0.94253	GGT	.	.	.	none		0.308	LRIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033549.2	NM_014813		T	113642882	G	T	113642882	3	4	267	1	0	0	0	0	1	0	0	0	8952	1348	47	4	1260	4	LRIG2	1	113642882	Missense_Mutation	SNP	G	TCGA-UZ-A9PX-01A-11D-A42J-10	72414170	113642882	135607739	4	16795											
DCLRE1B	64858	hgsc.bcm.edu	37	chr1	114454066	114454066	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttactccgagcttcgtgcCtttgtcgcagcactgaagcc	6	12	9	14	3	1	1	0	1	1	0	4	2	2	1	3	0	5	3	3	0	2	3			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr1:114454066C>T	ENST00000369563.3	+	4	1298	c.852C>T	c.(850-852)gcC>gcT	p.A284A	DCLRE1B_ENST00000466480.1_3'UTR	NM_022836.3	NP_073747.1	Q9H816	DCR1B_HUMAN	DNA cross-link repair 1B	284					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|protection from non-homologous end joining at telomere (GO:0031848)|telomere maintenance (GO:0000723)|telomeric 3' overhang formation (GO:0031860)|telomeric loop formation (GO:0031627)	centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)			breast(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(6)|stomach(1)	18	Lung SC(450;0.184)	all_cancers(81;1.46e-05)|all_epithelial(167;2.42e-05)|all_lung(203;0.000353)|Lung NSC(69;0.000518)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGCTTCGTGCCTTTGTCGCAG	0.572								Other identified genes with known or suspected DNA repair function																													p.A284A		Atlas-SNP	.											.	DCLRE1B	36	.	0			c.C852T						PASS	.						123	105	111					1																	114454066		2203	4300	6503	SO:0001819	synonymous_variant	64858	exon4			TCGTGCCTTTGTC	BC029687	CCDS866.1	1p11.1	2010-06-24	2010-06-24		ENSG00000118655	ENSG00000118655			17641	protein-coding gene	gene with protein product	"APOLLO", "PSO2 homolog (S. cerevisiae)"	609683	"DNA cross-link repair 1B (PSO2 homolog, S. cerevisiae)"				Standard	NM_022836		Approved	SNM1B, FLJ12810, FLJ13998	uc001eeg.3	Q9H816	OTTHUMG00000011937	ENST00000369563.3:c.852C>T	chr1.hg19:g.114454066C>T		75.0	0.0	.		52.0	22.0	.	NM_022836	Q9H9E5	Silent	SNP	ENST00000369563.3	hg19	CCDS866.1																																																																																			.	.	.	none		0.572	DCLRE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033020.2	NM_022836		T	114454066	C	T	114454066	2	4	267	1	0	0	0	0	0	0	0	1	4297	668	24	2		2	DCLRE1B	1	114454066	Silent	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	811184	114454066	134796555	5	16796											
UBAP2L	9898	hgsc.bcm.edu	37	chr1	154221875	154221875	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccacctcctcttgggacaTgggctcgacgacacaatccc	9	7	8	17	2	1	0	0	0	1	0	4	3	3	1	4	2	0	1	4	2	1	1			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr1:154221875T>C	ENST00000361546.2	+	11	1217	c.1175T>C	c.(1174-1176)aTg>aCg	p.M392T	UBAP2L_ENST00000343815.6_Missense_Mutation_p.M392T|UBAP2L_ENST00000271877.7_Missense_Mutation_p.M403T|UBAP2L_ENST00000428931.1_Missense_Mutation_p.M392T			Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like	392					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)			TCTTGGGACATGGGCTCGACG	0.517																																					p.M392T		Atlas-SNP	.											.	UBAP2L	197	.	0			c.T1175C						PASS	.						133	121	125					1																	154221875		2203	4300	6503	SO:0001583	missense	9898	exon12			GGGACATGGGCTC	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.1175T>C	chr1.hg19:g.154221875T>C	ENSP00000355343:p.Met392Thr	163.0	0.0	.		93.0	40.0	.	NM_001127320	B4E0U8|Q5VU75|Q5VU76|Q9BTU3|Q9UGL2|Q9UGL3|Q9UGL4|Q9UGL5	Missense_Mutation	SNP	ENST00000361546.2	hg19	CCDS1063.1	.	.	.	.	.	.	.	.	.	.	T	14.70	2.614833	0.46631	.	.	ENSG00000143569	ENST00000343815;ENST00000428931;ENST00000271877;ENST00000361546	T;T;T;T	0.10860	2.83;2.84;2.83;2.84	5.1	5.1	0.69264	.	0.045985	0.85682	D	0.000000	T	0.02083	0.0065	N	0.02011	-0.69	0.32303	N	0.564825	B;B;B;B;B	0.17465	0.0;0.022;0.0;0.0;0.0	B;B;B;B;B	0.24541	0.0;0.054;0.001;0.001;0.0	T	0.36720	-0.9736	10	0.72032	D	0.01	-3.987	14.5124	0.67797	0.0:0.0:0.0:1.0	.	306;403;385;392;392	B4DZJ6;F8W726;Q14157-4;Q14157-1;Q14157	.;.;.;.;UBP2L_HUMAN	T	392;392;403;392	ENSP00000345308:M392T;ENSP00000389445:M392T;ENSP00000271877:M403T;ENSP00000355343:M392T	ENSP00000271877:M403T	M	+	2	0	UBAP2L	152488499	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.269000	0.65542	2.263000	0.75096	0.533000	0.62120	ATG	.	.	.	none		0.517	UBAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087673.1	NM_014847		C	154221875	T	C	154221875	3	2	267	1	0	0	0	0	1	0	0	0	16850	1464	51	3	1217	3	UBAP2L	1	154221875	Missense_Mutation	SNP	T	TCGA-UZ-A9PX-01A-11D-A42J-10	39767809	154221875	95028746	6	16797											
TTC24	164118	hgsc.bcm.edu	37	chr1	156551345	156551345	+	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	aacaacttccagagggccttCcttctggcctccaaggcccc	8	8	8	17	0	1	1	0	0	1	1	4	1	4	1	7	3	2	0	7	3	3	3	rs12729118		TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr1:156551345C>T	ENST00000368237.3	+	1	189	c.189C>T	c.(187-189)ttC>ttT	p.F63F	TTC24_ENST00000368236.3_Silent_p.F63F			A2A3L6	TTC24_HUMAN	tetratricopeptide repeat domain 24	63										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)					AGAGGGCCTTCCTTCTGGCCT	0.632																																					p.F63F		Atlas-SNP	.											.	TTC24	46	.	0			c.C189T						PASS	.						34	36	35					1																	156551345		692	1591	2283	SO:0001819	synonymous_variant	164118	exon2			GGCCTTCCTTCTG		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.189C>T	chr1.hg19:g.156551345C>T		186.0	0.0	.		97.0	40.0	.	NM_001105669	Q5T3H7	Silent	SNP	ENST00000368237.3	hg19	CCDS53379.1																																																																																			.	.	.	weak		0.632	TTC24-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158547.1	XM_089384		T	156551345	C	T	156551345	2	4	267	1	0	0	0	0	0	0	0	1	16704	854	30	2		2	TTC24	1	156551345	Silent	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	2329470	156551345	92699276	7	16798											
MYOC	4653	hgsc.bcm.edu	37	chr1	171621388	171621388	+	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	ccgctcccgcctcagggtgcCcagctccctctgcagcccct	3	7	9	22	2	2	0	1	0	1	0	4	0	4	0	7	1	4	3	7	1	0	0			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr1:171621388C>G	ENST00000037502.6	-	1	435	c.364G>C	c.(364-366)Ggc>Cgc	p.G122R		NM_000261.1	NP_000252.1	Q99972	MYOC_HUMAN	myocilin, trabecular meshwork inducible glucocorticoid response	122					bone development (GO:0060348)|clustering of voltage-gated sodium channels (GO:0045162)|ERBB2-ERBB3 signaling pathway (GO:0038133)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neuron projection development (GO:0031175)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|osteoblast differentiation (GO:0001649)|positive regulation of cell migration (GO:0030335)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of MAPK cascade (GO:0043408)|skeletal muscle hypertrophy (GO:0014734)	cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|node of Ranvier (GO:0033268)|proteinaceous extracellular matrix (GO:0005578)	fibronectin binding (GO:0001968)|frizzled binding (GO:0005109)|myosin light chain binding (GO:0032027)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|prostate(1)|urinary_tract(2)	28	all_cancers(6;5.47e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					CTCAGGGTGCCCAGCTCCCTC	0.622																																					p.G122R		Atlas-SNP	.											.	MYOC	69	.	0			c.G364C						PASS	.						53	59	57					1																	171621388		2203	4300	6503	SO:0001583	missense	4653	exon1			GGGTGCCCAGCTC	BC029261	CCDS1297.1	1q23-q24	2008-02-05			ENSG00000034971	ENSG00000034971			7610	protein-coding gene	gene with protein product		601652		GLC1A		9169133, 9005853	Standard	NM_000261		Approved	TIGR, JOAG1	uc001ghu.3	Q99972	OTTHUMG00000034789	ENST00000037502.6:c.364G>C	chr1.hg19:g.171621388C>G	ENSP00000037502:p.Gly122Arg	98.0	0.0	.		57.0	20.0	.	NM_000261	B2RD84|O00620|Q7Z6Q9	Missense_Mutation	SNP	ENST00000037502.6	hg19	CCDS1297.1	.	.	.	.	.	.	.	.	.	.	C	0.034	-1.318487	0.01320	.	.	ENSG00000034971	ENST00000037502;ENST00000536591;ENST00000537133	T	0.57273	0.41	5.25	2.99	0.34606	.	0.913959	0.09386	N	0.809260	T	0.22166	0.0534	L	0.57536	1.79	0.33371	D	0.573529	B	0.34015	0.435	B	0.28305	0.088	T	0.10064	-1.0646	10	0.14252	T	0.57	.	6.6244	0.22820	0.0:0.7184:0.0:0.2816	.	122	Q99972	MYOC_HUMAN	R	122;55;122	ENSP00000037502:G122R	ENSP00000037502:G122R	G	-	1	0	MYOC	169888011	0.075000	0.21258	0.056000	0.19401	0.003000	0.03518	0.213000	0.17521	0.446000	0.26666	-0.345000	0.07892	GGC	.	.	.	none		0.622	MYOC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084178.2	NM_000261		G	171621388	C	G	171621388	3	3	267	1	0	0	0	0	1	0	0	0	10093	623	22	4	1162	4	MYOC	1	171621388	Missense_Mutation	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	15070043	171621388	77629233	8	16799											
KLHL20	27252	hgsc.bcm.edu	37	chr1	173703270	173703270	+	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	ttctgccagctgcttgcctcCtccagctggcagaaatacag	8	10	9	14	0	1	1	0	0	1	1	3	1	3	1	4	1	6	4	4	1	2	3			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr1:173703270C>A	ENST00000209884.4	+	3	578	c.442C>A	c.(442-444)Ctc>Atc	p.L148I	KLHL20_ENST00000493170.1_3'UTR|KLHL20_ENST00000546011.1_Intron	NM_014458.3	NP_055273.2	Q9Y2M5	KLH20_HUMAN	kelch-like family member 20	148					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						TGCTTGCCTCCTCCAGCTGGC	0.473																																					p.L148I	GBM(159;862 2695 6559 23041)	Atlas-SNP	.											.	KLHL20	54	.	0			c.C442A						PASS	.						68	66	66					1																	173703270		2203	4300	6503	SO:0001583	missense	27252	exon3			TGCCTCCTCCAGC	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.442C>A	chr1.hg19:g.173703270C>A	ENSP00000209884:p.Leu148Ile	108.0	0.0	.		72.0	28.0	.	NM_014458	B3KMA0|B4DUR0|Q5TZF2|Q5ZF45|Q9H457	Missense_Mutation	SNP	ENST00000209884.4	hg19	CCDS1310.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.307687	0.81247	.	.	ENSG00000076321	ENST00000209884	T	0.74421	-0.84	5.63	4.72	0.59763	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.86385	0.5920	M	0.93106	3.38	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.989	D	0.89802	0.3976	9	.	.	.	.	13.2837	0.60230	0.0:0.9226:0.0:0.0774	.	148;148	Q9BS75;Q9Y2M5	.;KLH20_HUMAN	I	148	ENSP00000209884:L148I	.	L	+	1	0	KLHL20	171969893	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.951000	0.70273	1.382000	0.46385	0.644000	0.83932	CTC	.	.	.	none		0.473	KLHL20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097582.1	NM_014458		A	173703270	C	A	173703270	3	1	267	1	0	0	0	0	1	0	0	0	8382	681	24	4	448	4	KLHL20	1	173703270	Missense_Mutation	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	2081882	173703270	75547351	9	16800											
RYR2	6262	hgsc.bcm.edu	37	chr1	237550598	237550598	+	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	cagcacttgtcttatggcaaCggcagcttacacgtggatgc	9	10	11	11	2	1	0	0	0	1	0	1	1	1	1	0	3	5	4	0	3	3	3			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr1:237550598C>T	ENST00000366574.2	+	9	911	c.594C>T	c.(592-594)aaC>aaT	p.N198N	RYR2_ENST00000360064.6_Silent_p.N196N|RYR2_ENST00000542537.1_Silent_p.N182N	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	198	MIR 2. {ECO:0000255|PROSITE- ProRule:PRU00131}.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CTTATGGCAACGGCAGCTTAC	0.498																																					p.N198N		Atlas-SNP	.											RYR2,colon,carcinoma,0,1	RYR2	1273	.	0			c.C594T						PASS	.						113	114	114					1																	237550598		2003	4178	6181	SO:0001819	synonymous_variant	6262	exon9			TGGCAACGGCAGC	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.594C>T	chr1.hg19:g.237550598C>T		120.0	0.0	.		72.0	6.0	.	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.	.	none		0.498	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		T	237550598	C	T	237550598	2	4	267	1	0	0	0	0	0	0	0	1	13782	535	19	1		1	RYR2	1	237550598	Silent	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	63847328	237550598	11700023	10	16801											
APOB	338	hgsc.bcm.edu	37	chr2	21238299	21238299	+	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	ataagctgtagcagatgagtCcatttggagaagcagtttgg	12	11	13	5	0	0	3	0	1	0	2	1	4	1	3	1	2	3	5	1	2	3	4			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr2:21238299C>T	ENST00000233242.1	-	22	3578	c.3451G>A	c.(3451-3453)Gac>Aac	p.D1151N		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1151					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)					GCAGATGAGTCCATTTGGAGA	0.488																																					p.D1151N		Atlas-SNP	.											.	APOB	761	.	0			c.G3451A						PASS	.						147	128	134					2																	21238299		2203	4300	6503	SO:0001583	missense	338	exon22			ATGAGTCCATTTG	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.3451G>A	chr2.hg19:g.21238299C>T	ENSP00000233242:p.Asp1151Asn	156.0	0.0	.		77.0	29.0	.	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.225393	0.79576	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.00816	5.66	5.49	4.6	0.57074	.	0.185608	0.38272	N	0.001754	T	0.03434	0.0099	M	0.67953	2.075	0.80722	D	1	D	0.69078	0.997	D	0.64042	0.921	T	0.43163	-0.9408	10	0.72032	D	0.01	.	8.2055	0.31452	0.1578:0.7577:0.0:0.0845	.	1151	P04114	APOB_HUMAN	N	1151	ENSP00000233242:D1151N	ENSP00000233242:D1151N	D	-	1	0	APOB	21091804	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.251000	0.43187	1.441000	0.47550	0.655000	0.94253	GAC	.	.	.	none		0.488	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			T	21238299	C	T	21238299	3	4	267	1	0	0	0	0	1	0	0	0	785	855	30	2	10272	2	APOB	2	21238299	Missense_Mutation	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10		21238299	221961074	11	16802											
ITSN2	50618	hgsc.bcm.edu	37	chr2	24524074	24524074	+	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	cattttctgatatgaaggcaGagttccattaatggaatcaa	14	13	8	6	0	2	3	1	2	1	1	3	4	3	4	1	2	0	2	1	2	5	5			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr2:24524074G>C	ENST00000355123.4	-	11	1473	c.1030C>G	c.(1030-1032)Ctg>Gtg	p.L344V	ITSN2_ENST00000361999.3_Missense_Mutation_p.L344V|ITSN2_ENST00000406921.3_Missense_Mutation_p.L344V	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	344					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)					TATGAAGGCAGAGTTCCATTA	0.338																																					p.L344V		Atlas-SNP	.											.	ITSN2	224	.	0			c.C1030G						PASS	.						94	93	93					2																	24524074		2203	4299	6502	SO:0001583	missense	50618	exon11			AAGGCAGAGTTCC	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.1030C>G	chr2.hg19:g.24524074G>C	ENSP00000347244:p.Leu344Val	342.0	1.0	.		203.0	77.0	.	NM_147152	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Missense_Mutation	SNP	ENST00000355123.4	hg19	CCDS1710.2	.	.	.	.	.	.	.	.	.	.	G	11.47	1.649174	0.29336	.	.	ENSG00000198399	ENST00000361999;ENST00000355123;ENST00000380868;ENST00000445614;ENST00000406921;ENST00000412011	T;T;T;T;T	0.60424	0.2;0.19;0.2;0.69;1.02	5.36	4.48	0.54585	.	0.000000	0.27927	U	0.017293	T	0.46678	0.1405	L	0.38838	1.175	0.32270	N	0.568969	B;B;B;B	0.29805	0.147;0.147;0.257;0.107	B;B;B;B	0.34093	0.141;0.13;0.175;0.159	T	0.54330	-0.8310	10	0.25106	T	0.35	.	10.1709	0.42908	0.1543:0.0:0.8457:0.0	.	344;344;344;344	Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3	.;.;.;ITSN2_HUMAN	V	344;344;344;368;344;369	ENSP00000354561:L344V;ENSP00000347244:L344V;ENSP00000370250:L344V;ENSP00000384499:L344V;ENSP00000391224:L369V	ENSP00000347244:L344V	L	-	1	2	ITSN2	24377578	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.457000	0.45005	1.413000	0.46997	0.491000	0.48974	CTG	.	.	.	none		0.338	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277		C	24524074	G	C	24524074	3	2	267	1	0	0	0	0	1	0	0	0	7934	933	33	4	4234	4	ITSN2	2	24524074	Missense_Mutation	SNP	G	TCGA-UZ-A9PX-01A-11D-A42J-10	3285775	24524074	218675299	12	16803											
MTIF2	4528	hgsc.bcm.edu	37	chr2	55473542	55473542	+	Missense_Mutation	SNP	T	T	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	cattgggatctgctttcaatTctaacatttctgcaagagca	11	14	7	9	0	4	1	1	0	3	1	4	2	4	2	0	1	4	3	0	1	3	5			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr2:55473542T>G	ENST00000263629.4	-	10	1352	c.1037A>C	c.(1036-1038)gAa>gCa	p.E346A	MTIF2_ENST00000394600.3_Missense_Mutation_p.E346A|MTIF2_ENST00000403721.1_Missense_Mutation_p.E346A	NM_002453.2	NP_002444.2	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2	346	tr-type G.				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						TGCTTTCAATTCTAACATTTC	0.363																																					p.E346A		Atlas-SNP	.											.	MTIF2	64	.	0			c.A1037C						PASS	.						167	153	158					2																	55473542		2203	4300	6503	SO:0001583	missense	4528	exon10			TTCAATTCTAACA	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.1037A>C	chr2.hg19:g.55473542T>G	ENSP00000263629:p.Glu346Ala	133.0	0.0	.		90.0	41.0	.	NM_002453	D6W5D0	Missense_Mutation	SNP	ENST00000263629.4	hg19	CCDS1853.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.368297	0.82463	.	.	ENSG00000085760	ENST00000403721;ENST00000263629;ENST00000394600;ENST00000418823;ENST00000535023	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.75997	0.3926	H	0.97315	3.98	0.80722	D	1	P	0.39094	0.659	P	0.51701	0.677	D	0.83541	0.0096	10	0.87932	D	0	-25.932	15.3048	0.73985	0.0:0.0:0.0:1.0	.	346	P46199	IF2M_HUMAN	A	346;346;346;66;346	ENSP00000384481:E346A;ENSP00000263629:E346A;ENSP00000378099:E346A;ENSP00000403492:E66A	ENSP00000263629:E346A	E	-	2	0	MTIF2	55327046	1.000000	0.71417	0.999000	0.59377	0.758000	0.43043	7.472000	0.80996	2.027000	0.59764	0.533000	0.62120	GAA	.	.	.	none		0.363	MTIF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251486.4	NM_002453		G	55473542	T	G	55473542	3	3	267	1	0	0	0	0	1	0	0	0	9941	1783	62	5	1174	5	MTIF2	2	55473542	Missense_Mutation	SNP	T	TCGA-UZ-A9PX-01A-11D-A42J-10	30949468	55473542	187725831	13	16804											
NFU1	27247	hgsc.bcm.edu	37	chr2	69650823	69650823	+	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	gctgtttggatttggggtatCttgtgtttgaataaacatgt	8	18	12	3	0	1	1	0	1	1	0	1	2	1	2	0	3	1	4	0	3	4	6			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr2:69650823C>T	ENST00000410022.2	-	3	398	c.193G>A	c.(193-195)Gat>Aat	p.D65N	NFU1_ENST00000394305.1_Intron|NFU1_ENST00000303698.3_Missense_Mutation_p.D41N|NFU1_ENST00000471185.1_Intron	NM_001002755.2	NP_001002755.1	Q9UMS0	NFU1_HUMAN	NFU1 iron-sulfur cluster scaffold	65					iron-sulfur cluster assembly (GO:0016226)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|iron ion binding (GO:0005506)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)	7						TTTGGGGTATCTTGTGTTTGA	0.368																																					p.D65N		Atlas-SNP	.											.	NFU1	19	.	0			c.G193A						PASS	.						74	72	73					2																	69650823		2203	4300	6503	SO:0001583	missense	27247	exon3			GGGTATCTTGTGT	AJ132584	CCDS33217.1, CCDS42694.1, CCDS46315.1	2p15-p13	2014-07-03	2014-07-03	2006-10-24	ENSG00000169599	ENSG00000169599			16287	protein-coding gene	gene with protein product		608100	"HIRA interacting protein 5", "NFU1 iron-sulfur cluster scaffold homolog (S. cerevisiae)"	HIRIP5		11342215, 12886008	Standard	NR_045631		Approved	CGI-33, NifU, NIFUC	uc002sfk.3	Q9UMS0	OTTHUMG00000152668	ENST00000410022.2:c.193G>A	chr2.hg19:g.69650823C>T	ENSP00000387219:p.Asp65Asn	128.0	0.0	.		61.0	21.0	.	NM_001002755	B4DUL9|Q53QE5|Q6VNZ8|Q7Z5B1|Q7Z5B2|Q9Y322	Missense_Mutation	SNP	ENST00000410022.2	hg19	CCDS33217.1	.	.	.	.	.	.	.	.	.	.	C	18.66	3.671512	0.67814	.	.	ENSG00000169599	ENST00000410022;ENST00000303698	T;T	0.63417	-0.04;-0.02	5.18	5.18	0.71444	NIF system FeS cluster assembly, NifU-like scaffold, N-terminal (4);	0.091423	0.64402	D	0.000001	T	0.76335	0.3973	M	0.75884	2.315	0.80722	D	1	D;P	0.65815	0.995;0.571	P;B	0.61800	0.894;0.378	T	0.74450	-0.3661	10	0.29301	T	0.29	3.0E-4	17.7387	0.88402	0.0:1.0:0.0:0.0	.	41;65	Q9UMS0-3;Q9UMS0	.;NFU1_HUMAN	N	65;41	ENSP00000387219:D65N;ENSP00000306965:D41N	ENSP00000306965:D41N	D	-	1	0	NFU1	69504327	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.121000	0.77160	2.421000	0.82119	0.591000	0.81541	GAT	.	.	.	none		0.368	NFU1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327279.3	NM_015700		T	69650823	C	T	69650823	3	4	267	1	0	0	0	0	1	0	0	0	10393	913	32	2	595	2	NFU1	2	69650823	Missense_Mutation	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	14177281	69650823	173548550	14	16805											
TTC21B	79809	hgsc.bcm.edu	37	chr2	166737187	166737187	+	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	tctaggtgattgccaaactcAcctactgccggatttgtccg	8	12	9	12	2	2	1	1	1	1	0	3	2	3	2	4	2	4	0	4	2	3	4			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr2:166737187A>T	ENST00000243344.7	-	27	3943		c.e27+1		TTC21B_ENST00000536175.1_Splice_Site	NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B						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						TGCCAAACTCACCTACTGCCG	0.313																																					.		Atlas-SNP	.											.	TTC21B	130	.	0			c.3805+2T>A						PASS	.						107	99	102					2																	166737187		2203	4300	6503	SO:0001630	splice_region_variant	79809	exon28			AAACTCACCTACT	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.3805+1T>A	chr2.hg19:g.166737187A>T		55.0	0.0	.		24.0	11.0	.	NM_024753	A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Splice_Site	SNP	ENST00000243344.7	hg19	CCDS33315.1	.	.	.	.	.	.	.	.	.	.	A	11.57	1.677877	0.29783	.	.	ENSG00000123607	ENST00000536175;ENST00000243344	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.9431	0.47285	0.9214:0.0:0.0786:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TTC21B	166445433	1.000000	0.71417	1.000000	0.80357	0.048000	0.14542	6.088000	0.71371	2.311000	0.77944	0.533000	0.62120	.	.	.	.	none		0.313	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333770.1	NM_024753	Intron	T	166737187	A	T	166737187	5	4	267	1	0	0	0	0	0	0	1	0	16700	173	6	5	155	5	TTC21B	2	166737187	Splice_Site	SNP	A	TCGA-UZ-A9PX-01A-11D-A42J-10	97086364	166737187	76462186	15	16806											
DYNC1I2	1781	hgsc.bcm.edu	37	chr2	172582207	172582208	+	Frame_Shift_Ins	INS	-	-	GA																															aaactttaaagaaagatgagINSgaaaatgatagtaaaggtat																										TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr2:172582207_172582208insGA	ENST00000397119.3	+	8	758_759	c.591_592insGA	c.(592-594)gaafs	p.E198fs	DYNC1I2_ENST00000409197.1_Frame_Shift_Ins_p.E172fs|DYNC1I2_ENST00000409453.1_Frame_Shift_Ins_p.E198fs|DYNC1I2_ENST00000263811.4_Frame_Shift_Ins_p.E192fs|DYNC1I2_ENST00000508530.1_Frame_Shift_Ins_p.E172fs|DYNC1I2_ENST00000534253.2_Frame_Shift_Ins_p.E198fs|DYNC1I2_ENST00000340296.4_Frame_Shift_Ins_p.E172fs|DYNC1I2_ENST00000409773.1_Frame_Shift_Ins_p.E198fs|DYNC1I2_ENST00000409317.1_Frame_Shift_Ins_p.E192fs|DYNC1I2_ENST00000358002.6_Frame_Shift_Ins_p.E190fs|DYNC1I2_ENST00000410079.3_Frame_Shift_Ins_p.E190fs	NM_001378.1	NP_001369.1	Q13409	DC1I2_HUMAN	dynein, cytoplasmic 1, intermediate chain 2	198					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|G2/M transition of mitotic cell cycle (GO:0000086)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|transport (GO:0006810)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|microtubule (GO:0005874)|vesicle (GO:0031982)	microtubule motor activity (GO:0003777)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)	15			OV - Ovarian serous cystadenocarcinoma(117;0.198)			AGAAAGATGAGGAAAATGATAG	0.282																																					p.E197fs		Atlas-Indel,Pindel	.											.	DYNC1I2	43	.	0			c.591_592insGA						PASS	.																																			SO:0001589	frameshift_variant	1781	exon8			.	AK055491	CCDS46450.1, CCDS63054.1, CCDS63056.1, CCDS63057.1	2q31.1	2013-01-10	2005-11-24	2005-11-24	ENSG00000077380	ENSG00000077380		"Cytoplasmic dyneins", "WD repeat domain containing"	2964	protein-coding gene	gene with protein product		603331	"dynein, cytoplasmic, intermediate polypeptide 2"	DNCI2		10049579, 16260502	Standard	NM_001378		Approved		uc002uha.2	Q13409	OTTHUMG00000154061	ENST00000397119.3:c.592_593dupGA	chr2.hg19:g.172582208_172582209dupGA	ENSP00000380308:p.Glu198fs	260.0	0.0	0		147.0	60.0	0.408163	NM_001378	B7ZA04|D3DPD4|D3DPD5|D3DPD6|Q32LY9|Q53S84|Q5BJF8|Q7Z4X1|Q96NG7|Q96S87|Q9BXZ5|Q9NT58	Frame_Shift_Ins	INS	ENST00000397119.3	hg19	CCDS46450.1																																																																																			.	.	.	none		0.282	DYNC1I2-001	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333683.2	NM_001378		GA	172582208	-	GA	172582207	7	5	267	1	0	1	1	0	0	0	0	0	4845	991	35	0	617	0	DYNC1I2	2	172582207	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PX-01A-11D-A42J-10	5845020	172582207	70617166	16	16807											
CAB39	51719	hgsc.bcm.edu	37	chr2	231663533	231663533	+	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	tgcaaaaatcattttgtggtCggaacagttttatgatttct	11	17	8	5	1	2	1	1	1	1	0	3	2	2	2	0	2	2	2	0	2	4	5			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr2:231663533C>T	ENST00000258418.5	+	5	917	c.488C>T	c.(487-489)tCg>tTg	p.S163L	CAB39_ENST00000409788.3_Missense_Mutation_p.S163L|CAB39_ENST00000410084.3_Missense_Mutation_p.S163L	NM_016289.3	NP_057373.1	Q9Y376	CAB39_HUMAN	calcium binding protein 39	163					activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|cellular hypotonic response (GO:0071476)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of rubidium ion transmembrane transporter activity (GO:2000687)|negative regulation of rubidium ion transport (GO:2000681)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein heterooligomerization (GO:0051291)|signal transduction by phosphorylation (GO:0023014)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	kinase binding (GO:0019900)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activator activity (GO:0043539)			central_nervous_system(1)|large_intestine(1)|skin(1)	3		all_lung(227;4.63e-07)|all_hematologic(139;1.83e-06)|Lung NSC(271;2.11e-05)|Acute lymphoblastic leukemia(138;5.51e-05)|Hepatocellular(293;0.0207)|Lung SC(224;0.187)		all cancers(144;1.64e-12)|Epithelial(121;5.29e-11)|LUSC - Lung squamous cell carcinoma(224;0.0154)|Lung(119;0.0177)|COAD - Colon adenocarcinoma(134;0.226)		ATTTTGTGGTCGGAACAGTTT	0.343																																					p.S163L		Atlas-SNP	.											CAB39_ENST00000258418,NS,carcinoma,0,1	CAB39	30	.	0			c.C488T						PASS	.						88	86	87					2																	231663533		2203	4300	6503	SO:0001583	missense	51719	exon5			TGTGGTCGGAACA	AF113536	CCDS2478.1	2q37.1	2008-02-05			ENSG00000135932	ENSG00000135932			20292	protein-coding gene	gene with protein product		612174					Standard	NM_016289		Approved	CGI-66, MO25	uc002vqx.3	Q9Y376	OTTHUMG00000133220	ENST00000258418.5:c.488C>T	chr2.hg19:g.231663533C>T	ENSP00000258418:p.Ser163Leu	319.0	1.0	.		164.0	66.0	.	NM_001130849	A8K8L7	Missense_Mutation	SNP	ENST00000258418.5	hg19	CCDS2478.1	.	.	.	.	.	.	.	.	.	.	C	32	5.161225	0.94727	.	.	ENSG00000135932	ENST00000258418;ENST00000409788;ENST00000410084	T;T;T	0.35236	1.32;1.32;1.32	5.58	5.58	0.84498	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.67078	0.2855	M	0.90542	3.125	0.80722	D	1	D	0.89917	1.0	D	0.70935	0.971	T	0.72478	-0.4281	10	0.52906	T	0.07	.	17.0555	0.86532	0.0:1.0:0.0:0.0	.	163	Q9Y376	CAB39_HUMAN	L	163	ENSP00000258418:S163L;ENSP00000386238:S163L;ENSP00000386642:S163L	ENSP00000258418:S163L	S	+	2	0	CAB39	231371777	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	7.818000	0.86416	2.616000	0.88540	0.467000	0.42956	TCG	.	.	.	none		0.343	CAB39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256955.2	NM_016289		T	231663533	C	T	231663533	3	4	267	1	0	0	0	0	1	0	0	0	2527	893	31	1	502	1	CAB39	2	231663533	Missense_Mutation	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	59081326	231663533	11535840	17	16808											
GOLGA4	2803	hgsc.bcm.edu	37	chr3	37369055	37369056	+	Frame_Shift_Ins	INS	-	-	AAAT																															ttacaacagatggatggaagINSaaataaacccacagaacttt																										TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr3:37369055_37369056insAAAT	ENST00000361924.2	+	14	6052_6053	c.5678_5679insAAAT	c.(5677-5682)agaaatfs	p.-1895fs	GOLGA4_ENST00000356847.4_Frame_Shift_Ins_p.-1917fs|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4						Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						ATGGATGGAAGAAATAAACCCA	0.371																																					p.R1915fs		Atlas-Indel,Pindel	.											.	GOLGA4	173	.	0			c.5744_5745insAAAT						PASS	.																																			SO:0001589	frameshift_variant	2803	exon15			.	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.5679_5682dupAAAT	chr3.hg19:g.37369056_37369059dupAAAT	ENSP00000354486:p.Lys1895fs	401.0	0.0	0		217.0	88.0	0.40553	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Frame_Shift_Ins	INS	ENST00000361924.2	hg19	CCDS2666.1																																																																																			.	.	.	none		0.371	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		AAAT	37369056	-	AAAT	37369055	7	5	267	1	0	1	1	0	0	0	0	0	6562	942	33	0	5802	0	GOLGA4	3	37369055	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PX-01A-11D-A42J-10		37369055	160653375	18	16809											
CTNNB1	1499	hgsc.bcm.edu	37	chr3	41267192	41267192	+	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	gttttatgccattacaactcTccacaaccttttattacatc	11	16	2	12	0	1	0	0	0	1	0	3	0	1	0	3	0	5	1	3	0	6	6			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr3:41267192T>A	ENST00000349496.5	+	6	1056	c.776T>A	c.(775-777)cTc>cAc	p.L259H	CTNNB1_ENST00000396183.3_Missense_Mutation_p.L259H|CTNNB1_ENST00000405570.1_Missense_Mutation_p.L259H|CTNNB1_ENST00000396185.3_Missense_Mutation_p.L259H|CTNNB1_ENST00000453024.1_Missense_Mutation_p.L252H	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	259					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		ATTACAACTCTCCACAACCTT	0.383		15	"H, Mis, T"	PLAG1	"colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"				Pilomatrixoma, Familial Clustering of																												p.L259H	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"catenin (cadherin-associated protein), beta 1"		"E, M, O"	.	CTNNB1	4904	.	0			c.T776A						PASS	.						93	99	97					3																	41267192		2203	4300	6503	SO:0001583	missense	1499	exon6	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	CAACTCTCCACAA	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"Armadillo repeat containing"	2514	protein-coding gene	gene with protein product		116806	"catenin (cadherin-associated protein), beta 1 (88kD)"	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.776T>A	chr3.hg19:g.41267192T>A	ENSP00000344456:p.Leu259His	237.0	0.0	.		115.0	49.0	.	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.007483	0.75046	.	.	ENSG00000168036	ENST00000405570;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185	D;D;D;D;D	0.85955	-2.05;-2.05;-2.05;-2.05;-2.05	5.51	5.51	0.81932	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.92941	0.7754	M	0.84511	2.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.94038	0.7307	10	0.87932	D	0	-18.0393	15.6183	0.76784	0.0:0.0:0.0:1.0	.	187;259	B4DSW9;P35222	.;CTNB1_HUMAN	H	259;259;259;252;259	ENSP00000385604:L259H;ENSP00000379486:L259H;ENSP00000344456:L259H;ENSP00000411226:L252H;ENSP00000379488:L259H	ENSP00000344456:L259H	L	+	2	0	CTNNB1	41242196	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.092000	0.63282	0.482000	0.46254	CTC	.	.	.	none		0.383	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210		A	41267192	T	A	41267192	3	1	267	1	0	0	0	0	1	0	0	0	4018	1551	54	5	794	5	CTNNB1	3	41267192	Missense_Mutation	SNP	T	TCGA-UZ-A9PX-01A-11D-A42J-10	3898137	41267192	156755238	19	16810											
RBM15B	29890	hgsc.bcm.edu	37	chr3	51429622	51429622	+	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	ggctaccagtacaagcagcgCtcgctgtcccccgtcgctgc	6	7	11	17	4	0	0	0	0	0	0	3	0	1	0	3	1	5	6	3	1	3	2			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr3:51429622C>A	ENST00000323686.4	+	1	892	c.792C>A	c.(790-792)cgC>cgA	p.R264R		NM_013286.4	NP_037418.3	Q8NDT2	RB15B_HUMAN	RNA binding motif protein 15B	264					mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|large_intestine(5)|lung(3)	12				BRCA - Breast invasive adenocarcinoma(193;0.000224)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		ACAAGCAGCGCTCGCTGTccc	0.781																																					p.R264R		Atlas-SNP	.											.	RBM15B	47	.	0			c.C792A						PASS	.						3	3	3					3																	51429622		1417	2994	4411	SO:0001819	synonymous_variant	29890	exon1			GCAGCGCTCGCTG	AL831838	CCDS33764.1	3p21.1	2013-02-12			ENSG00000179837	ENSG00000259956		"RNA binding motif (RRM) containing"	24303	protein-coding gene	gene with protein product		612602				16129689	Standard	NM_013286		Approved	HUMAGCGB, OTT3	uc003dbd.3	Q8NDT2	OTTHUMG00000156896	ENST00000323686.4:c.792C>A	chr3.hg19:g.51429622C>A		60.0	0.0	.		28.0	10.0	.	NM_013286	A4QPG7|Q6QE19|Q9BV96	Silent	SNP	ENST00000323686.4	hg19	CCDS33764.1																																																																																			.	.	.	none		0.781	RBM15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346489.1	NM_013286		A	51429622	C	A	51429622	2	1	267	1	0	0	0	0	0	0	0	1	13130	784	28	4		4	RBM15B	3	51429622	Silent	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	10162430	51429622	146592808	20	16811											
TMF1	7110	hgsc.bcm.edu	37	chr3	69096518	69096518	+	Missense_Mutation	SNP	A	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	actagagttaccttgcaaacAtcttccttctcagaaagtgc	12	12	6	11	0	2	2	1	0	2	2	4	2	3	2	2	0	4	2	2	0	4	5			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr3:69096518A>C	ENST00000398559.2	-	2	1554	c.1338T>G	c.(1336-1338)gaT>gaG	p.D446E	MIR3136_ENST00000583498.1_RNA|CTD-2013N24.2_ENST00000596732.1_RNA|CTD-2013N24.2_ENST00000596274.1_RNA|CTD-2013N24.2_ENST00000598783.1_RNA|CTD-2013N24.2_ENST00000595925.1_RNA|CTD-2013N24.2_ENST00000601735.1_RNA|CTD-2013N24.2_ENST00000596523.1_RNA|CTD-2013N24.2_ENST00000482368.2_RNA|CTD-2013N24.2_ENST00000597950.1_RNA|TMF1_ENST00000543976.1_Missense_Mutation_p.D446E			P82094	TMF1_HUMAN	TATA element modulatory factor 1	446					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)		CCTTGCAAACATCTTCCTTCT	0.373																																					p.D446E		Atlas-SNP	.											.	TMF1	77	.	0			c.T1338G						PASS	.						117	113	114					3																	69096518		1877	4104	5981	SO:0001583	missense	7110	exon2			GCAAACATCTTCC		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.1338T>G	chr3.hg19:g.69096518A>C	ENSP00000381567:p.Asp446Glu	83.0	0.0	.		48.0	20.0	.	NM_007114	B7ZLJ2|Q17R87|Q59GK0	Missense_Mutation	SNP	ENST00000398559.2	hg19	CCDS43105.1	.	.	.	.	.	.	.	.	.	.	A	8.573	0.880464	0.17467	.	.	ENSG00000144747	ENST00000398559;ENST00000543976;ENST00000356248;ENST00000438636	T;T	0.81247	-1.47;-1.31	5.86	-2.1	0.07210	.	0.177079	0.64402	D	0.000012	T	0.63367	0.2505	L	0.41824	1.3	0.23210	N	0.998115	B;B	0.15141	0.012;0.007	B;B	0.11329	0.006;0.003	T	0.51387	-0.8712	10	0.02654	T	1	-12.2902	9.5763	0.39459	0.3454:0.155:0.4996:0.0	.	446;446	P82094-2;P82094	.;TMF1_HUMAN	E	446;446;359;446	ENSP00000381567:D446E;ENSP00000438706:D446E	ENSP00000348582:D359E	D	-	3	2	TMF1	69179208	0.978000	0.34361	0.568000	0.28447	0.499000	0.33736	0.418000	0.21230	-0.266000	0.09339	-0.297000	0.09499	GAT	.	.	.	none		0.373	TMF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352106.1	NM_007114		C	69096518	A	C	69096518	3	2	267	1	0	0	0	0	1	0	0	0	16240	214	8	5	2007	5	TMF1	3	69096518	Missense_Mutation	SNP	A	TCGA-UZ-A9PX-01A-11D-A42J-10	17666896	69096518	128925912	21	16812											
CRYBG3	131544	hgsc.bcm.edu	37	chr3	97596113	97596114	+	Frame_Shift_Ins	INS	-	-	T																															gacaaacacagtctgtcttgINStttcatgatacgtccgctga																										TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr3:97596113_97596114insT	ENST00000182096.4	+	1	295_296	c.231_232insT	c.(232-234)tttfs	p.F78fs		NM_153605.3	NP_705833.3	Q68DQ2	CRBG3_HUMAN	beta-gamma crystallin domain containing 3	2026							carbohydrate binding (GO:0030246)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(10)|stomach(1)|upper_aerodigestive_tract(2)	32						AGTCTGTCTTGTTTCATGATAC	0.421																																					p.L2025fs		Atlas-Indel,Pindel	.											.	CRYBG3	86	.	0			c.6075_6076insT						PASS	.																																			SO:0001589	frameshift_variant	131544	exon4			.			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.234dupT	chr3.hg19:g.97596116_97596116dupT	ENSP00000182096:p.Phe78fs	215.0	0.0	0		141.0	54.0	0.382979	NM_153605	B4DLE8|F6VHI2|Q4G0V8|Q7Z4R9|Q86VD0|Q8N262|Q8N7F1|Q8NDQ8	Frame_Shift_Ins	INS	ENST00000182096.4	hg19																																																																																				.	.	.	none		0.421	CRYBG3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353751.1	NM_153605		T	97596114	-	T	97596113	7	5	267	1	0	1	1	0	0	0	0	0	3915	1368	48	0	233	0	CRYBG3	3	97596113	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PX-01A-11D-A42J-10	28499595	97596113	100426317	22	16813											
LETM1	3954	hgsc.bcm.edu	37	chr4	1836665	1836665	+	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	atggtgtcctggaggaacttGgccagctccagcttgacccg	7	9	13	12	1	0	1	0	1	0	0	2	3	2	3	4	4	3	2	4	4	1	2	rs145939138		TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr4:1836665G>T	ENST00000302787.2	-	5	1079	c.783C>A	c.(781-783)gcC>gcA	p.A261A		NM_012318.2	NP_036450.1	O95202	LETM1_HUMAN	leucine zipper-EF-hand containing transmembrane protein 1	261	LETM1.				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)			GGAGGAACTTGGCCAGCTCCA	0.567																																					p.A261A		Atlas-SNP	.											.	LETM1	48	.	0			c.C783A						PASS	.						102	82	89					4																	1836665		2203	4300	6503	SO:0001819	synonymous_variant	3954	exon5			GAACTTGGCCAGC	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.783C>A	chr4.hg19:g.1836665G>T		52.0	0.0	.		35.0	21.0	.	NM_012318	B4DED2|Q9UF65	Silent	SNP	ENST00000302787.2	hg19	CCDS3355.1																																																																																			.	G|1.000;A|0.000	.	alt		0.567	LETM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241634.1			T	1836665	G	T	1836665	2	4	267	1	0	0	0	0	0	0	0	1	8741	1335	47	4		4	LETM1	4	1836665	Silent	SNP	G	TCGA-UZ-A9PX-01A-11D-A42J-10		1836665	189317611	23	16814											
PPARGC1A	10891	hgsc.bcm.edu	37	chr4	23833339	23833339	+	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	tctagtgtctctgtgaggacTgctagcaagtttgcctcatt	7	15	10	9	0	3	1	1	1	2	0	4	2	3	2	1	1	3	3	1	1	3	4			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr4:23833339T>A	ENST00000264867.2	-	3	389	c.270A>T	c.(268-270)gcA>gcT	p.A90A	PPARGC1A_ENST00000509702.1_5'UTR	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	90					androgen metabolic process (GO:0008209)|androgen receptor signaling pathway (GO:0030521)|brown fat cell differentiation (GO:0050873)|cellular glucose homeostasis (GO:0001678)|cellular respiration (GO:0045333)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to nitrite (GO:0071250)|cellular response to oxidative stress (GO:0034599)|cellular response to thyroid hormone stimulus (GO:0097067)|cellular response to tumor necrosis factor (GO:0071356)|circadian regulation of gene expression (GO:0032922)|digestion (GO:0007586)|fatty acid oxidation (GO:0019395)|flavone metabolic process (GO:0051552)|galactose metabolic process (GO:0006012)|gluconeogenesis (GO:0006094)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of receptor activity (GO:2000272)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of cellular respiration (GO:1901857)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of histone acetylation (GO:0035066)|positive regulation of mitochondrial DNA metabolic process (GO:1901860)|positive regulation of mitochondrion organization (GO:0010822)|positive regulation of muscle tissue development (GO:1901863)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|regulation of circadian rhythm (GO:0042752)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|response to cold (GO:0009409)|response to epinephrine (GO:0071871)|response to leucine (GO:0043201)|response to muscle activity (GO:0014850)|response to norepinephrine (GO:0071873)|response to starvation (GO:0042594)|response to statin (GO:0036273)|RNA splicing (GO:0008380)|temperature homeostasis (GO:0001659)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytosol (GO:0005829)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|liver(1)|lung(24)|ovary(3)|skin(5)	51		Breast(46;0.0503)				CTGTGAGGACTGCTAGCAAGT	0.473																																					p.A90A	Esophageal Squamous(29;694 744 13796 34866 44181)	Atlas-SNP	.											.	PPARGC1A	129	.	0			c.A270T						PASS	.						335	275	295					4																	23833339		2203	4300	6503	SO:0001819	synonymous_variant	10891	exon3			GAGGACTGCTAGC	AF106698	CCDS3429.1	4p15.1	2013-02-12	2006-10-17	2004-02-04	ENSG00000109819	ENSG00000109819		"RNA binding motif (RRM) containing"	9237	protein-coding gene	gene with protein product		604517	"peroxisome proliferative activated receptor, gamma, coactivator 1", "peroxisome proliferative activated receptor, gamma, coactivator 1, alpha"	PPARGC1		10585775	Standard	NM_013261		Approved	PGC1, PGC1A	uc003gqs.3	Q9UBK2	OTTHUMG00000097747	ENST00000264867.2:c.270A>T	chr4.hg19:g.23833339T>A		112.0	0.0	.		52.0	21.0	.	NM_013261	B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	Silent	SNP	ENST00000264867.2	hg19	CCDS3429.1																																																																																			.	.	.	none		0.473	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1	NM_013261		A	23833339	T	A	23833339	2	1	267	1	0	0	0	0	0	0	0	1	12307	1567	55	5		5	PPARGC1A	4	23833339	Silent	SNP	T	TCGA-UZ-A9PX-01A-11D-A42J-10	21996674	23833339	167320937	24	16815											
KLB	152831	hgsc.bcm.edu	37	chr4	39409127	39409127	+	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	gacgctctagtgcttagaaaCattgaacctatagttacttt	12	14	7	8	1	1	2	0	1	1	1	1	3	1	2	1	0	4	3	1	0	7	7			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr4:39409127C>A	ENST00000257408.4	+	1	655	c.558C>A	c.(556-558)aaC>aaA	p.N186K		NM_175737.3	NP_783864.1	Q86Z14	KLOTB_HUMAN	klotho beta	186	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						TGCTTAGAAACATTGAACCTA	0.413																																					p.N186K		Atlas-SNP	.											.	KLB	95	.	0			c.C558A						PASS	.						77	80	79					4																	39409127		2203	4299	6502	SO:0001583	missense	152831	exon1			TAGAAACATTGAA	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.558C>A	chr4.hg19:g.39409127C>A	ENSP00000257408:p.Asn186Lys	175.0	0.0	.		71.0	35.0	.	NM_175737	Q2M3K8	Missense_Mutation	SNP	ENST00000257408.4	hg19	CCDS3451.1	.	.	.	.	.	.	.	.	.	.	C	3.801	-0.041733	0.07452	.	.	ENSG00000134962	ENST00000257408	T	0.32272	1.46	5.33	3.58	0.41010	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.257041	0.43416	D	0.000578	T	0.29256	0.0728	L	0.55103	1.725	0.18873	N	0.999985	B;B	0.26483	0.15;0.15	B;B	0.32624	0.149;0.149	T	0.21793	-1.0235	10	0.41790	T	0.15	-11.7505	7.8899	0.29672	0.0:0.6521:0.0:0.3479	.	186;186	B7ZL50;Q86Z14	.;KLOTB_HUMAN	K	186	ENSP00000257408:N186K	ENSP00000257408:N186K	N	+	3	2	KLB	39085522	0.996000	0.38824	0.004000	0.12327	0.405000	0.30901	0.343000	0.19944	0.607000	0.29982	-0.373000	0.07131	AAC	.	.	.	none		0.413	KLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250429.1	NM_175737		A	39409127	C	A	39409127	3	1	267	1	0	0	0	0	1	0	0	0	8339	477	17	4	560	4	KLB	4	39409127	Missense_Mutation	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	15575788	39409127	151745149	25	16816											
PRKG2	5593	hgsc.bcm.edu	37	chr4	82126083	82126083	+	Missense_Mutation	SNP	T	T	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	gctcctggatctcagcatccTtcctcctcaactctctctcc	5	13	4	19	0	4	0	2	0	3	0	11	1	8	1	5	1	2	2	5	1	1	1			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr4:82126083T>G	ENST00000395578.1	-	2	235	c.119A>C	c.(118-120)aAg>aCg	p.K40T	PRKG2_ENST00000264399.1_Missense_Mutation_p.K40T|PRKG2_ENST00000418486.2_Missense_Mutation_p.K40T			Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	40					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						CTCAGCATCCTTCCTCCTCAA	0.542																																					p.K40T		Atlas-SNP	.											.	PRKG2	195	.	0			c.A119C						PASS	.						114	108	110					4																	82126083		2203	4300	6503	SO:0001583	missense	5593	exon1			GCATCCTTCCTCC	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.119A>C	chr4.hg19:g.82126083T>G	ENSP00000378945:p.Lys40Thr	106.0	0.0	.		66.0	28.0	.	NM_006259	B4DMX3|E7EPE6|O00125|O60916	Missense_Mutation	SNP	ENST00000395578.1	hg19	CCDS3589.1	.	.	.	.	.	.	.	.	.	.	T	14.64	2.594584	0.46214	.	.	ENSG00000138669	ENST00000395578;ENST00000264399;ENST00000418486	D;D;D	0.82433	-1.61;-1.61;-1.61	5.1	3.88	0.44766	.	0.098784	0.64402	D	0.000002	T	0.68677	0.3027	N	0.24115	0.695	0.80722	D	1	B;P	0.36465	0.411;0.554	B;B	0.33196	0.111;0.159	T	0.63001	-0.6734	10	0.20519	T	0.43	-22.8646	10.7529	0.46219	0.0:0.076:0.0:0.924	.	40;40	E7EPE6;Q13237	.;KGP2_HUMAN	T	40	ENSP00000378945:K40T;ENSP00000264399:K40T;ENSP00000389038:K40T	ENSP00000264399:K40T	K	-	2	0	PRKG2	82345107	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.387000	0.44389	0.940000	0.37473	0.477000	0.44152	AAG	.	.	.	none		0.542	PRKG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252639.1	NM_006259		G	82126083	T	G	82126083	3	3	267	1	0	0	0	0	1	0	0	0	12533	1609	56	5	2241	5	PRKG2	4	82126083	Missense_Mutation	SNP	T	TCGA-UZ-A9PX-01A-11D-A42J-10	42716956	82126083	109028193	26	16817											
SEC31A	22872	hgsc.bcm.edu	37	chr4	83765635	83765635	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attaacatttccatgcattaTgaaacccggaggtggaggat	13	11	10	7	1	0	1	0	1	0	0	1	4	1	4	2	4	3	1	2	4	3	3	rs375945567		TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr4:83765635T>C	ENST00000395310.2	-	21	2712	c.2530A>G	c.(2530-2532)Ata>Gta	p.I844V	SEC31A_ENST00000348405.4_Missense_Mutation_p.I805V|SEC31A_ENST00000508502.1_Missense_Mutation_p.I844V|SEC31A_ENST00000500777.2_Missense_Mutation_p.I805V|SEC31A_ENST00000509142.1_Missense_Mutation_p.I844V|SEC31A_ENST00000355196.2_Missense_Mutation_p.I844V|SEC31A_ENST00000505984.1_Missense_Mutation_p.I805V|SEC31A_ENST00000505472.1_Missense_Mutation_p.I875V|SEC31A_ENST00000311785.7_Missense_Mutation_p.I844V|SEC31A_ENST00000448323.1_Missense_Mutation_p.I844V|SEC31A_ENST00000513858.1_Missense_Mutation_p.I805V|SEC31A_ENST00000432794.1_Missense_Mutation_p.I844V|SEC31A_ENST00000264405.5_Missense_Mutation_p.I608V|SEC31A_ENST00000508479.1_Missense_Mutation_p.I844V|SEC31A_ENST00000326950.5_Missense_Mutation_p.I805V|SEC31A_ENST00000443462.2_Missense_Mutation_p.I839V	NM_001077207.2|NM_001077208.2|NM_014933.3	NP_001070675.1|NP_001070676.1|NP_055748.2	O94979	SC31A_HUMAN	SEC31 homolog A (S. cerevisiae)	844	Interaction with PDCD6.|Pro-rich.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|response to calcium ion (GO:0051592)	COPII vesicle coat (GO:0030127)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|vesicle coat (GO:0030120)	calcium-dependent protein binding (GO:0048306)		SEC31A/ALK(3)|SEC31A/JAK2(4)	breast(1)	1		Hepatocellular(203;0.114)				CCATGCATTATGAAACCCGGA	0.458																																					p.I844V		Atlas-SNP	.											.	SEC31A	227	.	0			c.A2530G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	1,4405	2.1+/-5.4	0,1,2202	125	120	122		2530,2530,2530,2515,2530,2413	-1.9	1	4		122	0,8600		0,0,4300	no	missense,missense,missense,missense,missense,missense	SEC31A	NM_001077206.2,NM_001077207.2,NM_001077208.2,NM_001191049.1,NM_014933.3,NM_016211.3	29,29,29,29,29,29	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign,benign,benign,benign,benign,benign	844/1107,844/1221,844/1206,839/1201,844/1221,805/1182	83765635	1,13005	2203	4300	6503	SO:0001583	missense	22872	exon21			GCATTATGAAACC	AB018358	CCDS3596.1, CCDS3597.1, CCDS43244.1, CCDS47088.1, CCDS54773.1, CCDS75155.1, CCDS75156.1	4q21.3	2013-01-10	2006-10-05	2006-09-07	ENSG00000138674	ENSG00000138674		"WD repeat domain containing"	17052	protein-coding gene	gene with protein product		610257	"SEC31-like 1 (S. cerevisiae)", "Sec31 homolog A (S. cerevisiae)"	SEC31L1		10048485, 10788476	Standard	NM_001077206		Approved	KIAA0905, ABP125, ABP130	uc003hnh.3	O94979	OTTHUMG00000130297	ENST00000395310.2:c.2530A>G	chr4.hg19:g.83765635T>C	ENSP00000378721:p.Ile844Val	190.0	0.0	.		85.0	32.0	.	NM_001077206	B4DIW6|B7ZKZ7|B7ZL00|H7C2W3|Q17RR5|Q5H9P6|Q5XG74|Q659G7|Q6ZU90|Q7LCX9|Q86TJ0|Q8IZH4|Q9P048|Q9P0A6|Q9UM05|Q9UM06	Missense_Mutation	SNP	ENST00000395310.2	hg19	CCDS3596.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.116|9.116	1.007818|1.007818	0.19199|0.19199	2.27E-4|2.27E-4	0.0|0.0	ENSG00000138674|ENSG00000138674	ENST00000511338|ENST00000348405;ENST00000513858;ENST00000395310;ENST00000443462;ENST00000509142;ENST00000432794;ENST00000448323;ENST00000326950;ENST00000311785;ENST00000505472;ENST00000500777;ENST00000508502;ENST00000355196;ENST00000264405;ENST00000505984;ENST00000508479	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.35789	.|1.48;1.32;2.52;2.52;1.38;2.41;2.52;1.48;1.38;1.29;1.32;2.52;2.52;3.35;2.47;2.4	5.52|5.52	-1.9|-1.9	0.07665|0.07665	.|.	.|0.490823	.|0.23787	.|N	.|0.044567	T|T	0.16214|0.16214	0.0390|0.0390	L|L	0.29908|0.29908	0.895|0.895	0.29715|0.29715	N|N	0.839122|0.839122	.|B;B;B;B;B;B;B;B;B	.|0.12013	.|0.001;0.0;0.0;0.005;0.0;0.003;0.0;0.0;0.002	.|B;B;B;B;B;B;B;B;B	.|0.16289	.|0.001;0.0;0.001;0.015;0.0;0.009;0.001;0.001;0.002	T|T	0.15321|0.15321	-1.0441|-1.0441	5|10	.|0.13853	.|T	.|0.58	-1.5149|-1.5149	0.9936|0.9936	0.01462|0.01462	0.1356:0.2089:0.246:0.4096|0.1356:0.2089:0.246:0.4096	.|.	.|839;805;844;805;805;844;844;844;608	.|B4DIW6;B7ZL00;D6RHZ5;O94979-6;O94979-4;O94979-3;O94979-2;O94979;O94979-7	.|.;.;.;.;.;.;.;SC31A_HUMAN;.	R|V	54|805;805;844;839;844;844;844;805;844;875;805;844;844;608;805;844	.|ENSP00000337602:I805V;ENSP00000426886:I805V;ENSP00000378721:I844V;ENSP00000408027:I839V;ENSP00000426569:I844V;ENSP00000407944:I844V;ENSP00000400926:I844V;ENSP00000325087:I805V;ENSP00000309070:I844V;ENSP00000421633:I875V;ENSP00000421464:I805V;ENSP00000424635:I844V;ENSP00000347329:I844V;ENSP00000264405:I608V;ENSP00000424451:I805V;ENSP00000425999:I844V	.|ENSP00000264405:I608V	H|I	-|-	2|1	0|0	SEC31A|SEC31A	83984659|83984659	0.978000|0.978000	0.34361|0.34361	0.958000|0.958000	0.39756|0.39756	0.867000|0.867000	0.49689|0.49689	-0.068000|-0.068000	0.11561|0.11561	-0.543000|-0.543000	0.06240|0.06240	-0.707000|-0.707000	0.03653|0.03653	CAT|ATA	.	.	.	weak		0.458	SEC31A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252640.1	NM_016211		C	83765635	T	C	83765635	3	2	267	1	0	0	0	0	1	0	0	0	14011	1464	51	3	1160	3	SEC31A	4	83765635	Missense_Mutation	SNP	T	TCGA-UZ-A9PX-01A-11D-A42J-10	1639552	83765635	107388641	27	16818											
WDFY3	23001	hgsc.bcm.edu	37	chr4	85729530	85729531	+	Frame_Shift_Ins	INS	-	-	AG																															ccccaaggagaggggagagaINSagactcacttgtcaggcaag																										TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr4:85729530_85729531insAG	ENST00000295888.4	-	15	2792_2793	c.2385_2386insCT	c.(2383-2388)tcttctfs	p.S796fs	WDFY3-AS1_ENST00000510449.1_RNA|WDFY3_ENST00000322366.6_Frame_Shift_Ins_p.S796fs	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	796					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)		GAGGGGAGAGAAGACTCACTTG	0.46																																					p.S796fs		Atlas-Indel,Pindel	.											.	WDFY3	314	.	0			c.2386_2387insCT						PASS	.																																			SO:0001589	frameshift_variant	23001	exon15			.	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.2384_2385dupCT	chr4.hg19:g.85729531_85729532dupAG	ENSP00000295888:p.Ser796fs	349.0	0.0	0		204.0	84.0	0.411765	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Frame_Shift_Ins	INS	ENST00000295888.4	hg19	CCDS3609.1																																																																																			.	.	.	none		0.46	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		AG	85729531	-	AG	85729530	7	5	267	1	0	1	1	0	0	0	0	0	17282	246	9	0	8410	0	WDFY3	4	85729530	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PX-01A-11D-A42J-10	1963895	85729530	105424746	28	16819											
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123150305	123150305	+	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	attcctgggccttgtccaacTtcagatgatttgaaatatac	11	14	7	9	0	1	3	1	2	0	1	3	3	3	3	3	1	2	0	3	1	4	6			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr4:123150305T>A	ENST00000264501.4	+	25	3325	c.2952T>A	c.(2950-2952)acT>acA	p.T984T	KIAA1109_ENST00000455637.1_Silent_p.T984T|KIAA1109_ENST00000388738.3_Silent_p.T984T|KIAA1109_ENST00000495260.1_3'UTR			Q2LD37	K1109_HUMAN	KIAA1109	984					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.T984T(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CTTGTCCAACTTCAGATGATT	0.323																																					p.T984T		Atlas-SNP	.											KIAA1109,NS,carcinoma,0,1	KIAA1109	424	.	1	Substitution - coding silent(1)	kidney(1)	c.T2952A						PASS	.						207	193	198					4																	123150305		1864	4109	5973	SO:0001819	synonymous_variant	84162	exon23			TCCAACTTCAGAT	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.2952T>A	chr4.hg19:g.123150305T>A		120.0	0.0	.		60.0	25.0	.	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Silent	SNP	ENST00000264501.4	hg19	CCDS43267.1	.	.	.	.	.	.	.	.	.	.	T	9.845	1.191962	0.21954	.	.	ENSG00000138688	ENST00000424425	.	.	.	5.33	-0.0113	0.13993	.	.	.	.	.	T	0.39989	0.1099	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.22521	-1.0214	4	.	.	.	.	0.9972	0.01470	0.4442:0.207:0.1147:0.2341	.	.	.	.	I	816	.	.	F	+	1	0	KIAA1109	123369755	0.878000	0.30173	1.000000	0.80357	0.992000	0.81027	-0.019000	0.12546	0.060000	0.16281	-0.496000	0.04628	TTC	.	.	.	none		0.323	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		A	123150305	T	A	123150305	2	1	267	1	0	0	0	0	0	0	0	1	8215	1596	56	5		5	KIAA1109	4	123150305	Silent	SNP	T	TCGA-UZ-A9PX-01A-11D-A42J-10	37420775	123150305	68003971	29	16820											
SAP30	8819	hgsc.bcm.edu	37	chr4	174294597	174294597	+	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	ttaattcagagtgttcgaaaCagaagaaagagaaaagggag	19	7	12	3	1	1	4	1	0	0	4	2	7	1	5	0	1	1	1	0	1	6	3			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr4:174294597C>G	ENST00000296504.3	+	2	612	c.372C>G	c.(370-372)aaC>aaG	p.N124K	RP11-798M19.6_ENST00000609153.1_RNA	NM_003864.3	NP_003855.1			Sin3A-associated protein, 30kDa											large_intestine(1)|lung(2)|ovary(1)	4		Prostate(90;0.00601)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_neural(102;0.0837)|all_hematologic(60;0.107)		all cancers(43;1.15e-17)|Epithelial(43;4.33e-16)|OV - Ovarian serous cystadenocarcinoma(60;6.62e-09)|STAD - Stomach adenocarcinoma(60;0.00278)|GBM - Glioblastoma multiforme(59;0.00659)|LUSC - Lung squamous cell carcinoma(193;0.0919)		GTGTTCGAAACAGAAGAAAGA	0.338																																					p.N124K		Atlas-SNP	.											.	SAP30	9	.	0			c.C372G						PASS	.						143	139	141					4																	174294597		2203	4300	6503	SO:0001583	missense	8819	exon2			TCGAAACAGAAGA	AF055993	CCDS3817.1	4q34.1	2008-02-05	2006-02-02		ENSG00000164105	ENSG00000164105			10532	protein-coding gene	gene with protein product		603378	"sin3A-associated protein, 30kDa"			9651585	Standard	NM_003864		Approved		uc003itd.3	O75446	OTTHUMG00000160798	ENST00000296504.3:c.372C>G	chr4.hg19:g.174294597C>G	ENSP00000296504:p.Asn124Lys	247.0	1.0	.		105.0	47.0	.	NM_003864		Missense_Mutation	SNP	ENST00000296504.3	hg19	CCDS3817.1	.	.	.	.	.	.	.	.	.	.	C	14.96	2.692434	0.48202	.	.	ENSG00000164105	ENST00000296504	.	.	.	5.62	4.78	0.61160	.	0.301984	0.31415	N	0.007686	T	0.67730	0.2924	L	0.50333	1.59	0.52501	D	0.999957	D	0.76494	0.999	D	0.87578	0.998	T	0.69075	-0.5241	9	0.66056	D	0.02	-17.9972	8.8041	0.34927	0.0:0.7598:0.0:0.2402	.	124	O75446	SAP30_HUMAN	K	124	.	ENSP00000296504:N124K	N	+	3	2	SAP30	174531172	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.014000	0.57145	1.353000	0.45828	0.655000	0.94253	AAC	.	.	.	none		0.338	SAP30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362360.1	NM_003864		G	174294597	C	G	174294597	3	3	267	1	0	0	0	0	1	0	0	0	13846	477	17	4	378	4	SAP30	4	174294597	Missense_Mutation	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	51144292	174294597	16859679	30	16821											
TRIO	7204	hgsc.bcm.edu	37	chr5	14401112	14401112	+	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	agaacatgttgaaggagaccCttgcaaatttgcactgtggg	12	10	12	7	0	0	3	0	1	0	2	0	4	0	3	1	2	3	3	1	2	3	3			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr5:14401112C>A	ENST00000344204.4	+	31	4679	c.4655C>A	c.(4654-4656)cCt>cAt	p.P1552H	TRIO_ENST00000537187.1_Missense_Mutation_p.P1552H	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	1552	PH 1. {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 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)					GAAGGAGACCCTTGCAAATTT	0.393																																					p.P1552H		Atlas-SNP	.											.	TRIO	305	.	0			c.C4655A						PASS	.						90	87	88					5																	14401112		2203	4300	6503	SO:0001583	missense	7204	exon31			GAGACCCTTGCAA	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.4655C>A	chr5.hg19:g.14401112C>A	ENSP00000339299:p.Pro1552His	127.0	0.0	.		72.0	32.0	.	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	hg19	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	C	18.24	3.579193	0.65878	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000513206	T;T	0.31769	1.48;1.48	5.8	5.8	0.92144	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.053023	0.85682	D	0.000000	T	0.40815	0.1132	M	0.69823	2.125	0.58432	D	0.999999	B;B	0.25809	0.135;0.005	B;B	0.30029	0.11;0.006	T	0.18840	-1.0324	10	0.42905	T	0.14	.	20.063	0.97692	0.0:1.0:0.0:0.0	.	1552;1552	O75962-5;O75962	.;TRIO_HUMAN	H	1552;1552;1239	ENSP00000339299:P1552H;ENSP00000446348:P1552H	ENSP00000339299:P1552H	P	+	2	0	TRIO	14454112	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.986000	0.70563	2.735000	0.93741	0.655000	0.94253	CCT	.	.	.	none		0.393	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		A	14401112	C	A	14401112	3	1	267	1	0	0	0	0	1	0	0	0	16564	681	24	4	4777	4	TRIO	5	14401112	Missense_Mutation	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10		14401112	166514148	31	16822											
MAP3K1	4214	hgsc.bcm.edu	37	chr5	56178645	56178645	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgccctccccatagttccTcagctgcaggttgaaaatgg	9	10	10	12	0	1	1	1	1	0	0	3	2	3	1	4	2	3	4	4	2	3	3			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr5:56178645T>C	ENST00000399503.3	+	14	3618	c.3618T>C	c.(3616-3618)ccT>ccC	p.P1206P		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	1206					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)		CCATAGTTCCTCAGCTGCAGG	0.423																																					p.P1206P		Atlas-SNP	.											.	MAP3K1	355	.	0			c.T3618C						PASS	.						77	78	78					5																	56178645		2084	4234	6318	SO:0001819	synonymous_variant	4214	exon14			AGTTCCTCAGCTG	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.3618T>C	chr5.hg19:g.56178645T>C		61.0	0.0	.		34.0	12.0	.	NM_005921		Silent	SNP	ENST00000399503.3	hg19	CCDS43318.1																																																																																			.	.	.	none		0.423	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066		C	56178645	T	C	56178645	2	2	267	1	0	0	0	0	0	0	0	1	9250	1538	54	3		3	MAP3K1	5	56178645	Silent	SNP	T	TCGA-UZ-A9PX-01A-11D-A42J-10	41777533	56178645	124736615	32	16823											
DEPDC1B	55789	hgsc.bcm.edu	37	chr5	59901536	59901536	+	Missense_Mutation	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	ccagtgttcgggtaccaaagCcatcacacaggggtggcatc	10	7	12	12	1	1	0	1	0	0	0	3	0	1	0	3	4	2	3	3	4	2	2			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr5:59901536C>T	ENST00000265036.5	-	8	1113	c.1046G>A	c.(1045-1047)gGc>gAc	p.G349D	DEPDC1B_ENST00000509006.1_5'UTR|DEPDC1B_ENST00000545085.1_Missense_Mutation_p.G322D|DEPDC1B_ENST00000453022.2_Missense_Mutation_p.G349D	NM_018369.2	NP_060839.2	Q8WUY9	DEP1B_HUMAN	DEP domain containing 1B	349	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(2)|skin(2)	17		Lung NSC(810;0.000214)|Prostate(74;0.0147)|Breast(144;0.0991)|Ovarian(174;0.17)				GGTACCAAAGCCATCACACAG	0.423																																					p.G349D		Atlas-SNP	.											.	DEPDC1B	56	.	0			c.G1046A						PASS	.						178	157	164					5																	59901536		2203	4300	6503	SO:0001583	missense	55789	exon8			CCAAAGCCATCAC	AF303178	CCDS3977.1, CCDS47214.1	5q12	2008-02-05			ENSG00000035499	ENSG00000035499			24902	protein-coding gene	gene with protein product	"breast cancer cell 3"					12477932	Standard	NM_001145208		Approved	XTP1, BRCC3	uc003jsh.3	Q8WUY9	OTTHUMG00000097083	ENST00000265036.5:c.1046G>A	chr5.hg19:g.59901536C>T	ENSP00000265036:p.Gly349Asp	125.0	0.0	.		53.0	22.0	.	NM_001145208	A8K3R9|B4DUT4|Q86WJ3|Q8IZY6|Q9NUN3|Q9NW57	Missense_Mutation	SNP	ENST00000265036.5	hg19	CCDS3977.1	.	.	.	.	.	.	.	.	.	.	C	13.16	2.155593	0.38021	.	.	ENSG00000035499	ENST00000265036;ENST00000453022;ENST00000545085	T;T;T	0.41400	1.0;1.0;1.0	4.18	4.18	0.49190	Rho GTPase-activating protein domain (2);Rho GTPase activation protein (1);	0.363482	0.31167	N	0.008126	T	0.21103	0.0508	N	0.08118	0	0.33818	D	0.628647	B;B	0.24823	0.112;0.088	B;B	0.20184	0.028;0.028	T	0.25047	-1.0143	9	.	.	.	-7.9597	11.4426	0.50105	0.0:0.6472:0.3528:0.0	.	349;349	B4DUT4;Q8WUY9	.;DEP1B_HUMAN	D	349;349;322	ENSP00000265036:G349D;ENSP00000389101:G349D;ENSP00000438320:G322D	.	G	-	2	0	DEPDC1B	59937293	0.062000	0.20869	0.939000	0.37840	0.962000	0.63368	2.567000	0.45956	2.166000	0.68216	0.655000	0.94253	GGC	.	.	.	none		0.423	DEPDC1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214207.1	NM_018369		T	59901536	C	T	59901536	3	4	267	1	0	0	0	0	1	0	0	0	4442	739	26	2	559	2	DEPDC1B	5	59901536	Missense_Mutation	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	3722891	59901536	121013724	33	16824											
THBS4	7060	hgsc.bcm.edu	37	chr5	79375049	79375049	+	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	attggcaagccaccccattcCgagcagttgcagaacctggc	10	7	10	14	1	0	1	0	0	0	1	1	2	1	1	5	2	4	4	5	2	2	3			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr5:79375049C>T	ENST00000350881.2	+	19	2669	c.2479C>T	c.(2479-2481)Cga>Tga	p.R827*	CTD-2201I18.1_ENST00000514042.1_RNA|CTD-2201I18.1_ENST00000503007.1_RNA|THBS4_ENST00000511733.1_Nonsense_Mutation_p.R736*|THBS4_ENST00000504720.1_3'UTR	NM_003248.4	NP_003239.2	P35443	TSP4_HUMAN	thrombospondin 4	827	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)		CACCCCATTCCGAGCAGTTGC	0.468																																					p.R827X		Atlas-SNP	.											.	THBS4	82	.	0			c.C2479T						PASS	.						88	77	81					5																	79375049		2203	4300	6503	SO:0001587	stop_gained	7060	exon19			CCATTCCGAGCAG		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.2479C>T	chr5.hg19:g.79375049C>T	ENSP00000339730:p.Arg827*	83.0	0.0	.		47.0	23.0	.	NM_003248	B2R909|Q86TG2	Nonsense_Mutation	SNP	ENST00000350881.2	hg19	CCDS4049.1	.	.	.	.	.	.	.	.	.	.	C	40	8.514351	0.98843	.	.	ENSG00000113296	ENST00000350881;ENST00000511733	.	.	.	5.08	3.24	0.37175	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.6578	14.4118	0.67119	0.5359:0.4641:0.0:0.0	.	.	.	.	X	827;736	.	ENSP00000339730:R827X	R	+	1	2	THBS4	79410805	1.000000	0.71417	0.998000	0.56505	0.669000	0.39330	1.437000	0.34991	0.789000	0.33779	0.650000	0.86243	CGA	.	.	.	none		0.468	THBS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226977.1			T	79375049	C	T	79375049	4	4	267	1	0	0	0	0	0	1	0	0	15868	644	23	1	2553	1	THBS4	5	79375049	Nonsense_Mutation	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	19473513	79375049	101540211	34	16825											
ST8SIA4	7903	hgsc.bcm.edu	37	chr5	100231400	100231400	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aattgattttccaaccttctAcattgtgctggaagattgaa	12	15	7	7	0	1	3	0	2	1	1	2	4	2	4	2	1	3	1	2	1	5	7			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr5:100231400A>G	ENST00000231461.5	-	2	513	c.203T>C	c.(202-204)gTa>gCa	p.V68A	ST8SIA4_ENST00000451528.2_Missense_Mutation_p.V68A	NM_005668.4	NP_005659.1	Q92187	SIA8D_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	68					axon guidance (GO:0007411)|cellular protein modification process (GO:0006464)|ganglioside biosynthetic process (GO:0001574)|N-glycan processing (GO:0006491)|nervous system development (GO:0007399)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(11)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)	25		all_cancers(142;1.5e-07)|all_epithelial(76;1.43e-10)|Prostate(80;0.000644)|Lung NSC(167;0.0059)|all_lung(232;0.00914)|Ovarian(225;0.024)|Colorectal(57;0.09)|Breast(839;0.203)		COAD - Colon adenocarcinoma(37;0.00402)		CCAACCTTCTACATTGTGCTG	0.378																																					p.V68A		Atlas-SNP	.											.	ST8SIA4	77	.	0			c.T203C						PASS	.						121	116	117					5																	100231400		2203	4299	6502	SO:0001583	missense	7903	exon2			CCTTCTACATTGT	L41680	CCDS4091.1, CCDS47252.1	5q21	2013-03-01	2003-01-14	2005-02-07	ENSG00000113532	ENSG00000113532		"Sialyltransferases"	10871	protein-coding gene	gene with protein product	"ST8Sia IV"	602547	"sialyltransferase 8 (alpha-2, 8-polysialytransferase) D"	SIAT8D		7624364	Standard	NM_005668		Approved	PST, PST1	uc003knk.3	Q92187	OTTHUMG00000128727	ENST00000231461.5:c.203T>C	chr5.hg19:g.100231400A>G	ENSP00000231461:p.Val68Ala	135.0	0.0	.		82.0	33.0	.	NM_175052	A8KA07|G3V104|Q8N1F4|Q92693	Missense_Mutation	SNP	ENST00000231461.5	hg19	CCDS4091.1	.	.	.	.	.	.	.	.	.	.	A	13.16	2.154860	0.38021	.	.	ENSG00000113532	ENST00000231461;ENST00000451528	T;T	0.30448	2.29;1.53	6.07	4.92	0.64577	.	0.093065	0.46758	D	0.000265	T	0.16171	0.0389	N	0.24115	0.695	0.29429	N	0.859974	B	0.02656	0.0	B	0.01281	0.0	T	0.26292	-1.0107	10	0.08837	T	0.75	.	6.0554	0.19809	0.7189:0.1383:0.1427:0.0	.	68	Q92187	SIA8D_HUMAN	A	68	ENSP00000231461:V68A;ENSP00000428914:V68A	ENSP00000231461:V68A	V	-	2	0	ST8SIA4	100259299	1.000000	0.71417	0.997000	0.53966	0.966000	0.64601	2.363000	0.44178	1.122000	0.41944	0.533000	0.62120	GTA	.	.	.	none		0.378	ST8SIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250632.3	NM_005668		G	100231400	A	G	100231400	3	3	267	1	0	0	0	0	1	0	0	0	15246	391	14	3	896	3	ST8SIA4	5	100231400	Missense_Mutation	SNP	A	TCGA-UZ-A9PX-01A-11D-A42J-10	20856351	100231400	80683860	35	16826											
ATXN1	6310	hgsc.bcm.edu	37	chr6	16327864	16327864	+	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	agccccggagccctgctgagGtgctgctgctgctgctgctg	3	9	15	14	1	0	1	0	1	0	0	0	2	0	2	3	2	9	7	3	2	0	0			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr6:16327864G>C	ENST00000244769.4	-	8	1614	c.678C>G	c.(676-678)caC>caG	p.H226Q	ATXN1_ENST00000436367.1_Missense_Mutation_p.H226Q	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	226					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				CCCTGCTGAGGtgctgctgct	0.652																																					p.H226Q		Atlas-SNP	.											.,1	ATXN1	117	.	0			c.C678G						PASS	.						11	15	13					6																	16327864		2150	4194	6344	SO:0001583	missense	6310	exon7			GCTGAGGTGCTGC	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"Ataxins"	10548	protein-coding gene	gene with protein product		601556	"spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.678C>G	chr6.hg19:g.16327864G>C	ENSP00000244769:p.His226Gln	80.0	1.0	.		29.0	5.0	.	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	hg19	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	G	1.926	-0.447046	0.04572	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.27256	1.68;1.68	4.74	0.503	0.16940	.	0.308295	0.34291	N	0.004091	T	0.05686	0.0149	L	0.39397	1.21	0.09310	N	0.999995	B	0.32245	0.361	B	0.28638	0.092	T	0.23976	-1.0173	10	0.48119	T	0.1	-16.8942	3.2876	0.06937	0.3032:0.0:0.385:0.3119	.	226	P54253	ATX1_HUMAN	Q	226	ENSP00000244769:H226Q;ENSP00000416360:H226Q	ENSP00000244769:H226Q	H	-	3	2	ATXN1	16435843	0.437000	0.25593	0.006000	0.13384	0.009000	0.06853	0.925000	0.28791	0.191000	0.20236	0.563000	0.77884	CAC	.	.	.	none		0.652	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332		C	16327864	G	C	16327864	3	2	267	1	0	0	0	0	1	0	0	0	1209	1252	44	4	1777	4	ATXN1	6	16327864	Missense_Mutation	SNP	G	TCGA-UZ-A9PX-01A-11D-A42J-10		16327864	154787203	36	16827											
GRM4	2914	hgsc.bcm.edu	37	chr6	34004335	34004335	+	Missense_Mutation	SNP	A	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	gcagggcaggctgcagatggAgcggggcagctgctgcccgc	6	4	19	12	2	0	1	0	0	0	1	0	2	0	2	1	5	5	7	1	5	0	0			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr6:34004335A>C	ENST00000538487.2	-	9	1995	c.1552T>G	c.(1552-1554)Tcc>Gcc	p.S518A	GRM4_ENST00000374181.4_Missense_Mutation_p.S518A|GRM4_ENST00000455714.2_Missense_Mutation_p.S378A|GRM4_ENST00000609222.1_Missense_Mutation_p.S385A|GRM4_ENST00000374177.3_Missense_Mutation_p.S402A|GRM4_ENST00000545715.1_5'UTR|GRM4_ENST00000535756.1_Missense_Mutation_p.S385A|GRM4_ENST00000544773.2_Missense_Mutation_p.S349A	NM_000841.2|NM_001256811.1	NP_000832.1|NP_001243740.1	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4	518					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						CTGCAGATGGAGCGGGGCAGC	0.647																																					p.S518A		Atlas-SNP	.											.	GRM4	317	.	0			c.T1552G						PASS	.						35	32	33					6																	34004335		2201	4299	6500	SO:0001583	missense	2914	exon9			AGATGGAGCGGGG	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.1552T>G	chr6.hg19:g.34004335A>C	ENSP00000440556:p.Ser518Ala	63.0	0.0	.		23.0	14.0	.	NM_000841	B3KVL9|B7Z1T9|B7Z1U6|F5GXM5|Q5SZ84|Q6ZMQ2	Missense_Mutation	SNP	ENST00000538487.2	hg19	CCDS4787.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.236349	0.79800	.	.	ENSG00000124493	ENST00000374181;ENST00000374177;ENST00000545715;ENST00000535756;ENST00000544773;ENST00000538487;ENST00000455714	D;D;D;D;D;D;D	0.97089	-4.24;-4.24;-4.24;-4.24;-4.24;-4.24;-4.24	4.79	4.79	0.61399	GPCR, family 3, nine cysteines domain (1);	0.000000	0.85682	D	0.000000	D	0.98172	0.9396	M	0.85542	2.76	0.58432	D	0.999997	D;D;D;D;D	0.89917	1.0;1.0;0.99;0.997;1.0	D;D;D;D;D	0.91635	0.999;0.997;0.979;0.992;0.997	D	0.98468	1.0599	10	0.49607	T	0.09	.	14.1617	0.65450	1.0:0.0:0.0:0.0	.	471;349;378;518;385	B7ZLU9;B7Z1T9;F5GXM5;Q14833;B3KVL9	.;.;.;GRM4_HUMAN;.	A	518;402;210;385;349;518;378	ENSP00000363296:S518A;ENSP00000363292:S402A;ENSP00000445533:S210A;ENSP00000437925:S385A;ENSP00000437730:S349A;ENSP00000440556:S518A;ENSP00000398456:S378A	ENSP00000363292:S402A	S	-	1	0	GRM4	34112313	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.130000	0.94437	2.008000	0.58898	0.450000	0.29827	TCC	.	.	.	none		0.647	GRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040213.2			C	34004335	A	C	34004335	3	2	267	1	0	0	0	0	1	0	0	0	6806	304	11	5	1198	5	GRM4	6	34004335	Missense_Mutation	SNP	A	TCGA-UZ-A9PX-01A-11D-A42J-10	17676471	34004335	137110732	37	16828											
SPDEF	25803	hgsc.bcm.edu	37	chr6	34508954	34508954	+	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	ttgctggggctccagtccatGggatctgggcaagaggcatc	7	9	15	10	0	1	1	0	0	1	1	4	2	3	2	2	5	1	4	2	5	1	1			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr6:34508954G>T	ENST00000374037.3	-	3	855	c.441C>A	c.(439-441)ccC>ccA	p.P147P	SPDEF_ENST00000544425.1_Silent_p.P147P	NM_012391.2	NP_036523.1	O95238	SPDEF_HUMAN	SAM pointed domain containing ETS transcription factor	147	PNT. {ECO:0000255|PROSITE- ProRule:PRU00762}.				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						TCCAGTCCATGGGATCTGGGC	0.642																																					p.P147P		Atlas-SNP	.											.	SPDEF	34	.	0			c.C441A						PASS	.						34	33	33					6																	34508954		2203	4299	6502	SO:0001819	synonymous_variant	25803	exon3			GTCCATGGGATCT	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.441C>A	chr6.hg19:g.34508954G>T		59.0	0.0	.		27.0	12.0	.	NM_001252294	B4DWH8|F5H778	Silent	SNP	ENST00000374037.3	hg19	CCDS4794.1																																																																																			.	.	.	none		0.642	SPDEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040246.1	NM_012391		T	34508954	G	T	34508954	2	4	267	1	0	0	0	0	0	0	0	1	15038	1335	47	4		4	SPDEF	6	34508954	Silent	SNP	G	TCGA-UZ-A9PX-01A-11D-A42J-10	504619	34508954	136606113	38	16829											
C6orf223	221416	hgsc.bcm.edu	37	chr6	43969793	43969793	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtttttatttgccagatcTggtaaccctaggtgcctcca	7	15	9	10	0	1	1	0	0	1	1	2	1	2	1	4	2	3	2	4	2	3	6			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr6:43969793T>C	ENST00000336600.5	+	3	232	c.212T>C	c.(211-213)cTg>cCg	p.L71P	RP5-1120P11.1_ENST00000607590.1_RNA|C6orf223_ENST00000442114.2_Missense_Mutation_p.L51P|C6orf223_ENST00000448947.2_3'UTR|C6orf223_ENST00000439969.2_Silent_p.S85S|RP5-1120P11.1_ENST00000422059.1_RNA	NM_001171992.1|NM_153246.4	NP_001165463.1|NP_694978.2	Q8N319	CF223_HUMAN	chromosome 6 open reading frame 223	71										central_nervous_system(1)|lung(2)|pancreas(1)|prostate(1)|urinary_tract(1)	6	all_cancers(18;2.28e-07)|all_epithelial(2;1.62e-08)|Lung NSC(15;0.000172)|all_lung(25;0.000533)|Hepatocellular(11;0.00309)|Ovarian(13;0.0437)		all cancers(41;0.00141)|Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.217)			ttgccagatctggtaacccta	0.463																																					p.L71P		Atlas-SNP	.											.	C6orf223	14	.	0			c.T212C						PASS	.						88	87	87					6																	43969793		2156	4227	6383	SO:0001583	missense	221416	exon3			CAGATCTGGTAAC	BC032706	CCDS34459.1, CCDS55016.1	6p21.1	2012-09-05			ENSG00000181577	ENSG00000181577			28692	protein-coding gene	gene with protein product						12477932	Standard	NM_153246		Approved	MGC45491	uc003own.3	Q8N319	OTTHUMG00000014753	ENST00000336600.5:c.212T>C	chr6.hg19:g.43969793T>C	ENSP00000426159:p.Leu71Pro	98.0	0.0	.		58.0	22.0	.	NM_153246	E9PB59|Q8N575	Missense_Mutation	SNP	ENST00000336600.5	hg19	CCDS34459.1	.	.	.	.	.	.	.	.	.	.	T	4.326	0.059826	0.08339	.	.	ENSG00000181577	ENST00000336600	T	0.44482	0.92	3.87	-0.527	0.11909	.	1.108720	0.07254	N	0.866419	T	0.38268	0.1034	.	.	.	0.22127	N	0.999349	D	0.71674	0.998	D	0.66351	0.943	T	0.14868	-1.0457	9	0.87932	D	0	.	4.1088	0.10049	0.4521:0.0:0.1694:0.3784	.	71	Q8N319	CF223_HUMAN	P	71	ENSP00000426159:L71P	ENSP00000426159:L71P	L	+	2	0	C6orf223	44077771	0.330000	0.24705	0.001000	0.08648	0.005000	0.04900	0.534000	0.23098	-0.065000	0.13021	0.459000	0.35465	CTG	.	.	.	none		0.463	C6orf223-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040702.3	NM_153246		C	43969793	T	C	43969793	3	2	267	1	0	0	0	0	1	0	0	0	2359	1580	55	3	265	3	C6orf223	6	43969793	Missense_Mutation	SNP	T	TCGA-UZ-A9PX-01A-11D-A42J-10	9460839	43969793	127145274	39	16830											
LTV1	84946	hgsc.bcm.edu	37	chr6	144179108	144179108	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcagtcatgaggagaaaTgaacagctgaccctacatga	14	8	9	10	0	2	5	2	4	0	1	3	6	3	5	2	1	3	1	2	1	3	1			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr6:144179108T>C	ENST00000367576.5	+	6	893	c.759T>C	c.(757-759)aaT>aaC	p.N253N		NM_032860.3	NP_116249.2	Q96GA3	LTV1_HUMAN	LTV1 ribosome biogenesis factor	253						cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)	13				OV - Ovarian serous cystadenocarcinoma(155;2.72e-06)|GBM - Glioblastoma multiforme(68;0.0372)		TGAGGAGAAATGAACAGCTGA	0.398																																					p.N253N		Atlas-SNP	.											.	LTV1	48	.	0			c.T759C						PASS	.						73	73	73					6																	144179108		2203	4300	6503	SO:0001819	synonymous_variant	84946	exon6			GAGAAATGAACAG	BC009855	CCDS5201.1	6q24.2	2014-02-03	2014-02-03	2006-02-06	ENSG00000135521	ENSG00000135521			21173	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 93", "LTV1 homolog (S. cerevisiae)"	C6orf93			Standard	NM_032860		Approved	FLJ14909, dJ468K18.4	uc003qjs.3	Q96GA3	OTTHUMG00000015733	ENST00000367576.5:c.759T>C	chr6.hg19:g.144179108T>C		110.0	0.0	.		47.0	20.0	.	NM_032860	Q96JX8	Silent	SNP	ENST00000367576.5	hg19	CCDS5201.1																																																																																			.	.	.	none		0.398	LTV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042532.1	NM_032860		C	144179108	T	C	144179108	2	2	267	1	0	0	0	0	0	0	0	1	9088	1461	51	3		3	LTV1	6	144179108	Silent	SNP	T	TCGA-UZ-A9PX-01A-11D-A42J-10	100209315	144179108	26935959	40	16831											
TNRC18	84629	hgsc.bcm.edu	37	chr7	5354660	5354669	+	Frame_Shift_Del	DEL	TGGCTCCTGG	TGGCTCCTGG	-																															ccgcccacgcccacgggcctTggctcctggctcctccgacc																								rs10250456		TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	TGGCTCCTGG	TGGCTCCTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr7:5354660_5354669delTGGCTCCTGG	ENST00000430969.1	-	26	7321_7330	c.6973_6982delCCAGGAGCCA	c.(6973-6984)ccaggagccaagfs	p.PGAK2325fs	TNRC18_ENST00000399537.4_Frame_Shift_Del_p.PGAK2325fs	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2325							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)		CCACGGGCCTTGGCTCCTGGCTCCTCCGAC	0.69																																					p.2325_2328del		Atlas-Indel,Pindel	.											.	TNRC18	311	.	0			c.6974_6983del						PASS	.																																			SO:0001589	frameshift_variant	84629	exon26			.	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.6973_6982delCCAGGAGCCA	chr7.hg19:g.5354660_5354669delTGGCTCCTGG	ENSP00000395538:p.Pro2325fs	144.0	0.0	0		123.0	42.0	0.341463	NM_001080495	A8MX41|Q96JH1|Q96K91	Frame_Shift_Del	DEL	ENST00000430969.1	hg19	CCDS47534.1																																																																																			.	.	.	none		0.69	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				-	5354669	TGGCTCCTGG	-	5354660	7	5	267	1	0	1	0	1	0	0	0	0	16351	1821	63	0	1944	0	TNRC18	7	5354660	Frame_Shift_Del	DEL	TGGCTCCTGG	TCGA-UZ-A9PX-01A-11D-A42J-10		5354660	153784003	41	16832											
ZNF3	7551	hgsc.bcm.edu	37	chr7	99669236	99669236	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagctccagctgaaggtctTcccacactcattacattcat	10	11	7	13	0	3	1	2	1	1	0	5	2	5	2	2	2	3	2	2	2	2	3			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr7:99669236T>C	ENST00000424697.1	-	6	1177	c.871A>G	c.(871-873)Aag>Gag	p.K291E	ZNF3_ENST00000303915.6_Missense_Mutation_p.K291E|ZNF3_ENST00000299667.4_Missense_Mutation_p.K291E|ZNF3_ENST00000413658.2_Intron	NM_001278284.1|NM_001278287.1|NM_001278290.1|NM_001278291.1|NM_001278292.1|NM_032924.3	NP_001265213.1|NP_001265216.1|NP_001265219.1|NP_001265220.1|NP_001265221.1|NP_116313.3	P17036	ZNF3_HUMAN	zinc finger protein 3	291					cell differentiation (GO:0030154)|leukocyte activation (GO:0045321)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	25	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)	Ovarian(593;2.06e-05)|Myeloproliferative disorder(862;0.0122)|Breast(660;0.029)	STAD - Stomach adenocarcinoma(171;0.129)			CTGAAGGTCTTCCCACACTCA	0.527																																					p.K291E		Atlas-SNP	.											.	ZNF3	54	.	0			c.A871G						PASS	.						57	64	62					7																	99669236		2202	4300	6502	SO:0001583	missense	7551	exon6			AGGTCTTCCCACA	AF027136	CCDS43618.1, CCDS43619.1	7q22.1	2013-01-08	2006-05-05					"Zinc fingers, C2H2-type", "-"	13089	protein-coding gene	gene with protein product		194510	"zinc finger protein 3 (A8-51)"				Standard	NM_032924		Approved	A8-51, KOX25, PP838, FLJ20216, HF.12, Zfp113	uc003usr.4	P17036		ENST00000424697.1:c.871A>G	chr7.hg19:g.99669236T>C	ENSP00000415358:p.Lys291Glu	99.0	0.0	.		100.0	49.0	.	NM_032924	D6W5U0|P13683|Q9HBR4|Q9NNX8|Q9NXJ1|Q9UC15|Q9UC16	Missense_Mutation	SNP	ENST00000424697.1	hg19	CCDS43619.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.498565	0.85069	.	.	ENSG00000166526	ENST00000424697;ENST00000303915;ENST00000299667	T;T;T	0.35973	1.28;1.28;1.28	4.6	4.6	0.57074	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.56097	D	0.000028	T	0.60547	0.2277	M	0.80028	2.48	0.53005	D	0.99996	D;D	0.89917	0.998;1.0	D;D	0.91635	0.991;0.999	T	0.66172	-0.5990	10	0.87932	D	0	-36.512	12.2643	0.54668	0.0:0.0:0.0:1.0	.	274;291	B3KRP4;P17036	.;ZNF3_HUMAN	E	291	ENSP00000415358:K291E;ENSP00000306372:K291E;ENSP00000299667:K291E	ENSP00000299667:K291E	K	-	1	0	ZNF3	99507172	0.994000	0.37717	1.000000	0.80357	0.995000	0.86356	2.522000	0.45572	2.075000	0.62263	0.533000	0.62120	AAG	.	.	.	none		0.527	ZNF3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336247.3	NM_017715		C	99669236	T	C	99669236	3	2	267	1	0	0	0	0	1	0	0	0	17841	1792	62	3	602	3	ZNF3	7	99669236	Missense_Mutation	SNP	T	TCGA-UZ-A9PX-01A-11D-A42J-10	94314576	99669236	59469427	42	16833											
HIPK2	28996	hgsc.bcm.edu	37	chr7	139311504	139311504	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttttctaccaacatgtcgcTcccttccaaatctgtcgtca	8	14	4	15	2	3	0	1	0	2	0	7	0	5	0	3	0	2	1	3	0	3	4			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr7:139311504T>C	ENST00000406875.3	-	6	1556	c.1462A>G	c.(1462-1464)Agc>Ggc	p.S488G	HIPK2_ENST00000342645.6_Missense_Mutation_p.S488G|HIPK2_ENST00000428878.2_Missense_Mutation_p.S488G	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	488	Interaction with DAXX.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)			breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					AACATGTCGCTCCCTTCCAAA	0.507																																					p.S488G		Atlas-SNP	.											.	HIPK2	192	.	0			c.A1462G						PASS	.						174	175	175					7																	139311504		2001	4177	6178	SO:0001583	missense	28996	exon6			TGTCGCTCCCTTC	AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"homeodomain-interacting protein kinase 2"			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.1462A>G	chr7.hg19:g.139311504T>C	ENSP00000385571:p.Ser488Gly	98.0	0.0	.		106.0	46.0	.	NM_022740	Q75MR7|Q8WWI4|Q9H2Y1	Missense_Mutation	SNP	ENST00000406875.3	hg19		.	.	.	.	.	.	.	.	.	.	T	15.60	2.880967	0.51801	.	.	ENSG00000064393	ENST00000406875;ENST00000428878;ENST00000342645	T;T;T	0.20598	2.06;2.06;2.06	5.67	5.67	0.87782	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.41442	0.1159	.	.	.	0.52501	D	0.999952	D;P	0.63046	0.992;0.525	D;B	0.76071	0.987;0.158	T	0.11084	-1.0602	8	0.19590	T	0.45	.	15.9026	0.79392	0.0:0.0:0.0:1.0	.	488;488	Q9H2X6;Q9H2X6-3	HIPK2_HUMAN;.	G	488	ENSP00000385571:S488G;ENSP00000413724:S488G;ENSP00000343108:S488G	ENSP00000343108:S488G	S	-	1	0	HIPK2	138962044	1.000000	0.71417	0.844000	0.33320	0.847000	0.48162	7.986000	0.88173	2.163000	0.67991	0.368000	0.22195	AGC	.	.	.	none		0.507	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740		C	139311504	T	C	139311504	3	2	267	1	0	0	0	0	1	0	0	0	7124	1551	54	3	2174	3	HIPK2	7	139311504	Missense_Mutation	SNP	T	TCGA-UZ-A9PX-01A-11D-A42J-10	39642268	139311504	19827159	43	16834											
OR2F1	26211	hgsc.bcm.edu	37	chr7	143657752	143657752	+	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	caccatcctaaagatccagtCcagagaaggaagaaagaaag	19	4	9	9	0	0	4	0	0	0	4	3	6	3	5	4	1	0	0	4	1	6	1			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr7:143657752C>G	ENST00000392899.1	+	1	726	c.689C>G	c.(688-690)tCc>tGc	p.S230C	RP4-669B10.3_ENST00000466281.1_lincRNA	NM_012369.2	NP_036501.2	Q13607	OR2F1_HUMAN	olfactory receptor, family 2, subfamily F, member 1 (gene/pseudogene)	230					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|skin(4)	34	Melanoma(164;0.0903)					AAGATCCAGTCCAGAGAAGGA	0.493																																					p.S230C		Atlas-SNP	.											.	OR2F1	71	.	0			c.C689G						PASS	.						183	161	168					7																	143657752		2203	4300	6503	SO:0001583	missense	26211	exon1			TCCAGTCCAGAGA	U56421	CCDS5887.1	7q35	2013-06-03	2013-06-03		ENSG00000213215	ENSG00000213215		"GPCR / Class A : Olfactory receptors"	8246	protein-coding gene	gene with protein product		608497	"olfactory receptor, family 2, subfamily F, member 1"	OR2F4, OR2F5, OR2F3, OR2F3P		9500546	Standard	NM_012369		Approved	OLF3, OR7-140, OR7-139, OR14-60	uc003wds.1	Q13607	OTTHUMG00000157771	ENST00000392899.1:c.689C>G	chr7.hg19:g.143657752C>G	ENSP00000376633:p.Ser230Cys	150.0	0.0	.		156.0	68.0	.	NM_012369	A4D2G1|Q6IFP7|Q96R49|Q9UDX1	Missense_Mutation	SNP	ENST00000392899.1	hg19	CCDS5887.1	.	.	.	.	.	.	.	.	.	.	C	15.75	2.925090	0.52759	.	.	ENSG00000213215	ENST00000392899	T	0.00575	6.46	5.53	5.53	0.82687	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000064	T	0.04407	0.0121	M	0.91354	3.2	0.43913	D	0.996555	D	0.89917	1.0	D	0.91635	0.999	T	0.01608	-1.1313	10	0.87932	D	0	-33.0786	17.0114	0.86407	0.0:1.0:0.0:0.0	.	230	Q13607	OR2F1_HUMAN	C	230	ENSP00000376633:S230C	ENSP00000376633:S230C	S	+	2	0	OR2F1	143288685	0.411000	0.25384	0.245000	0.24217	0.417000	0.31264	2.968000	0.49224	2.871000	0.98454	0.655000	0.94253	TCC	.	.	.	none		0.493	OR2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349581.1			G	143657752	C	G	143657752	3	3	267	1	0	0	0	0	1	0	0	0	11003	855	30	4	691	4	OR2F1	7	143657752	Missense_Mutation	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	4346248	143657752	15480911	44	16835											
ATP6V1B2	526	hgsc.bcm.edu	37	chr8	20077779	20077779	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctcaattttttaaggtcctTacgaaaatcgcactgtcttt	10	17	5	9	2	2	0	1	0	2	0	5	1	3	0	1	1	1	1	1	1	5	5			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr8:20077779T>C	ENST00000276390.2	+	14	1442	c.1402T>C	c.(1402-1404)Tac>Cac	p.Y468H		NM_001693.3	NP_001684.2	P21281	VATB2_HUMAN	ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B2	468					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|ruffle (GO:0001726)	ATP binding (GO:0005524)|hydrogen ion transmembrane transporter activity (GO:0015078)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			endometrium(1)|kidney(2)|lung(5)|prostate(1)	9				Colorectal(74;0.0535)|COAD - Colon adenocarcinoma(73;0.211)	Gallium nitrate(DB05260)	TTAAGGTCCTTACGAAAATCG	0.388																																					p.Y468H	Pancreas(119;1230 1726 3901 4036 31644)	Atlas-SNP	.											.	ATP6V1B2	34	.	0			c.T1402C						PASS	.						102	99	100					8																	20077779		2203	4300	6503	SO:0001583	missense	526	exon14			GGTCCTTACGAAA	L35249	CCDS6014.1	8p21.3	2010-04-21	2006-01-13	2002-05-10	ENSG00000147416	ENSG00000147416	3.6.3.14	"ATPases / V-type"	854	protein-coding gene	gene with protein product		606939	"ATPase, H+ transporting, lysosomal (vacuolar proton pump), beta polypeptide, 56/58kD, isoform 2", "ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B, isoform 2"	VPP3, ATP6B2		2145275, 14580332	Standard	NM_001693		Approved	VATB, Vma2, HO57	uc003wzp.3	P21281	OTTHUMG00000131073	ENST00000276390.2:c.1402T>C	chr8.hg19:g.20077779T>C	ENSP00000276390:p.Tyr468His	140.0	0.0	.		81.0	36.0	.	NM_001693	B2R5Z3|D3DSQ5|Q14544|Q15859|Q96IR0	Missense_Mutation	SNP	ENST00000276390.2	hg19	CCDS6014.1	.	.	.	.	.	.	.	.	.	.	T	16.87	3.242329	0.58995	.	.	ENSG00000147416	ENST00000276390;ENST00000542368	T	0.79554	-1.28	5.32	5.32	0.75619	ATPase, F1/V1/A1 complex, alpha/beta subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.83220	0.5207	M	0.70108	2.13	0.80722	D	1	B	0.32507	0.373	B	0.41202	0.35	D	0.84288	0.0498	10	0.66056	D	0.02	-15.2107	14.392	0.66986	0.0:0.0:0.0:1.0	.	468	P21281	VATB2_HUMAN	H	468;342	ENSP00000276390:Y468H	ENSP00000276390:Y468H	Y	+	1	0	ATP6V1B2	20122059	1.000000	0.71417	0.990000	0.47175	0.969000	0.65631	8.040000	0.89188	2.134000	0.65973	0.460000	0.39030	TAC	.	.	.	none		0.388	ATP6V1B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253732.1	NM_001693		C	20077779	T	C	20077779	3	2	267	1	0	0	0	0	1	0	0	0	1179	1754	61	3	1456	3	ATP6V1B2	8	20077779	Missense_Mutation	SNP	T	TCGA-UZ-A9PX-01A-11D-A42J-10		20077779	126286243	45	16836											
PLEC	5339	hgsc.bcm.edu	37	chr8	144995292	144995292	+	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	tcaaagacgtcccgggcctcGgagtcagtgtagaccagctc	9	7	12	13	3	2	2	2	0	0	2	5	3	3	3	3	2	1	2	3	2	2	1	rs200383203	byFrequency	TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr8:144995292G>T	ENST00000322810.4	-	32	9277	c.9108C>A	c.(9106-9108)tcC>tcA	p.S3036S	PLEC_ENST00000356346.3_Silent_p.S2885S|PLEC_ENST00000398774.2_Silent_p.S2867S|PLEC_ENST00000354958.2_Silent_p.S2877S|PLEC_ENST00000436759.2_Silent_p.S2926S|PLEC_ENST00000345136.3_Silent_p.S2899S|PLEC_ENST00000527096.1_Silent_p.S2922S|PLEC_ENST00000354589.3_Silent_p.S2899S|PLEC_ENST00000357649.2_Silent_p.S2903S	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3036	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						CCCGGGCCTCGGAGTCAGTGT	0.617																																					p.S3036S		Atlas-SNP	.											PLEC_ENST00000436759,NS,carcinoma,0,4	PLEC	1144	.	0			c.C9108A						PASS	.						58	66	63					8																	144995292		2203	4300	6503	SO:0001819	synonymous_variant	5339	exon32			GGCCTCGGAGTCA	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.9108C>A	chr8.hg19:g.144995292G>T		64.0	0.0	.		28.0	14.0	.	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	hg19	CCDS43772.1																																																																																			.	G|1.000;A|0.000	.	alt		0.617	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		T	144995292	G	T	144995292	2	4	267	1	0	0	0	0	0	0	0	1	12059	1103	39	4		4	PLEC	8	144995292	Silent	SNP	G	TCGA-UZ-A9PX-01A-11D-A42J-10	124917513	144995292	1368730	46	16837											
C9orf93	203238	hgsc.bcm.edu	37	chr9	15724954	15724954	+	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	aactgcagaagctttcccagGctttccataaggatgcagag	12	9	10	10	0	0	2	0	0	0	2	2	3	2	3	2	2	4	4	2	2	3	3			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr9:15724954G>C	ENST00000380701.3	+	14	2000	c.1672G>C	c.(1672-1674)Gct>Cct	p.A558P	CCDC171_ENST00000297641.3_Missense_Mutation_p.A558P	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	558																	GCTTTCCCAGGCTTTCCATAA	0.428																																					p.A558P		Atlas-SNP	.											.	.	.	.	0			c.G1672C						PASS	.						76	78	78					9																	15724954		2203	4300	6503	SO:0001583	missense	203238	exon14			TCCCAGGCTTTCC	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.1672G>C	chr9.hg19:g.15724954G>C	ENSP00000370077:p.Ala558Pro	247.0	0.0	.		126.0	59.0	.	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Missense_Mutation	SNP	ENST00000380701.3	hg19	CCDS6481.1	.	.	.	.	.	.	.	.	.	.	G	18.24	3.580851	0.65992	.	.	ENSG00000164989	ENST00000297641;ENST00000380701	T;T	0.56103	0.48;0.48	5.63	3.81	0.43845	.	0.436641	0.26773	N	0.022576	T	0.52789	0.1756	L	0.27053	0.805	0.80722	D	1	P;P;P	0.48589	0.912;0.912;0.912	P;P;P	0.54759	0.76;0.696;0.76	T	0.47812	-0.9088	10	0.31617	T	0.26	-0.6344	15.1024	0.72292	0.0788:0.0:0.9212:0.0	.	566;558;558	B7ZM22;Q6TFL3-3;Q6TFL3	.;.;CI093_HUMAN	P	558	ENSP00000297641:A558P;ENSP00000370077:A558P	ENSP00000297641:A558P	A	+	1	0	C9orf93	15714954	1.000000	0.71417	0.997000	0.53966	0.951000	0.60555	3.772000	0.55325	0.872000	0.35775	0.655000	0.94253	GCT	.	.	.	none		0.428	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550		C	15724954	G	C	15724954	3	2	267	1	0	0	0	0	1	0	0	0	2508	1203	42	4	1722	4	C9orf93	9	15724954	Missense_Mutation	SNP	G	TCGA-UZ-A9PX-01A-11D-A42J-10		15724954	125488477	47	16838											
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79322239	79322239	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagattgctttcctgatgtgTccctgaatgttcagaatatt	9	17	8	7	0	1	4	1	2	0	2	3	4	3	4	2	0	1	2	2	0	4	6			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr9:79322239T>C	ENST00000376718.3	-	8	5074	c.4951A>G	c.(4951-4953)Aca>Gca	p.T1651A	PRUNE2_ENST00000428286.1_Missense_Mutation_p.T1292A	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	1651					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						TCCTGATGTGTCCCTGAATGT	0.413																																					p.T1651A		Atlas-SNP	.											.	PRUNE2	331	.	0			c.A4951G						PASS	.						60	51	53					9																	79322239		1568	3582	5150	SO:0001583	missense	158471	exon8			GATGTGTCCCTGA	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.4951A>G	chr9.hg19:g.79322239T>C	ENSP00000365908:p.Thr1651Ala	139.0	0.0	.		75.0	24.0	.	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	hg19	CCDS47982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.001|0.001	-2.928036|-2.928036	0.00054|0.00054	.|.	.|.	ENSG00000106772|ENSG00000106772	ENST00000426088|ENST00000376718;ENST00000428286;ENST00000422033	.|T;T	.|0.36520	.|1.27;1.25	4.88|4.88	0.901|0.901	0.19284|0.19284	.|.	.|0.433490	.|0.19678	.|N	.|0.108589	T|T	0.09158|0.09158	0.0226|0.0226	N|N	0.01109|0.01109	-1.01|-1.01	0.09310|0.09310	N|N	1|1	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.38090|0.38090	-0.9677|-0.9677	5|10	.|0.02654	.|T	.|1	-0.1643|-0.1643	7.7278|7.7278	0.28769|0.28769	0.0:0.6452:0.0:0.3548|0.0:0.6452:0.0:0.3548	.|.	.|1651	.|Q8WUY3	.|PRUN2_HUMAN	G|A	972|1651;1292;1650	.|ENSP00000365908:T1651A;ENSP00000397425:T1292A	.|ENSP00000365908:T1651A	D|T	-|-	2|1	0|0	PRUNE2|PRUNE2	78512059|78512059	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.026000|0.026000	0.11368|0.11368	-0.115000|-0.115000	0.10741|0.10741	0.049000|0.049000	0.15920|0.15920	-0.242000|-0.242000	0.12053|0.12053	GAC|ACA	.	.	.	none		0.413	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		C	79322239	T	C	79322239	3	2	267	1	0	0	0	0	1	0	0	0	12651	1667	58	3	4363	3	PRUNE2	9	79322239	Missense_Mutation	SNP	T	TCGA-UZ-A9PX-01A-11D-A42J-10	63597285	79322239	61891192	48	16839											
RNF20	56254	hgsc.bcm.edu	37	chr9	104309714	104309714	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcagagcttgaggagaacAaagagttggctcagaaccgt	14	7	13	7	1	1	5	1	1	0	4	1	6	1	5	1	2	4	4	1	2	3	2			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr9:104309714A>G	ENST00000389120.3	+	9	1096	c.1006A>G	c.(1006-1008)Aaa>Gaa	p.K336E	AL591377.1_ENST00000584534.1_RNA	NM_019592.5	NP_062538.5	Q5VTR2	BRE1A_HUMAN	ring finger protein 20, E3 ubiquitin protein ligase	336					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|negative regulation of cell migration (GO:0030336)|positive regulation of histone methylation (GO:0031062)|positive regulation of transcription, DNA-templated (GO:0045893)|protein polyubiquitination (GO:0000209)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(6)|large_intestine(7)|lung(23)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)		TGAGGAGAACAAAGAGTTGGC	0.408																																					p.K336E		Atlas-SNP	.											.	RNF20	110	.	0			c.A1006G						PASS	.						73	74	74					9																	104309714		2203	4300	6503	SO:0001583	missense	56254	exon9			GAGAACAAAGAGT	AF265230	CCDS35084.1	9q22	2012-02-23	2012-02-23	2008-12-12	ENSG00000155827	ENSG00000155827		"RING-type (C3HC4) zinc fingers"	10062	protein-coding gene	gene with protein product	"BRE1 E3 ubiquitin ligase homolog (S. cerevisiae)"	607699	"ring finger protein 20"			16337599, 12876294, 18832071, 19037095	Standard	NM_019592		Approved	FLJ20382, FLJ11189, KAIA2779, BRE1A, hBRE1, BRE1	uc004bbn.3	Q5VTR2	OTTHUMG00000020385	ENST00000389120.3:c.1006A>G	chr9.hg19:g.104309714A>G	ENSP00000373772:p.Lys336Glu	236.0	0.0	.		151.0	57.0	.	NM_019592	A7MCT5|Q2TB34|Q69YL5|Q6P527|Q8N3J4|Q96JD3|Q9H9Y7|Q9HA51|Q9NUR4|Q9NWQ3|Q9NX83	Missense_Mutation	SNP	ENST00000389120.3	hg19	CCDS35084.1	.	.	.	.	.	.	.	.	.	.	A	16.80	3.222742	0.58668	.	.	ENSG00000155827	ENST00000389120	T	0.39592	1.07	5.41	5.41	0.78517	.	0.130255	0.64402	D	0.000001	T	0.33000	0.0848	L	0.46157	1.445	0.46416	D	0.999031	B	0.16603	0.018	B	0.11329	0.006	T	0.12243	-1.0555	10	0.08381	T	0.77	-24.3341	12.0138	0.53303	0.8558:0.1442:0.0:0.0	.	336	Q5VTR2	BRE1A_HUMAN	E	336	ENSP00000373772:K336E	ENSP00000373772:K336E	K	+	1	0	RNF20	103349535	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.562000	0.60816	2.174000	0.68829	0.460000	0.39030	AAA	.	.	.	none		0.408	RNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356402.1	NM_019592		G	104309714	A	G	104309714	3	3	267	1	0	0	0	0	1	0	0	0	13486	131	5	3	1036	3	RNF20	9	104309714	Missense_Mutation	SNP	A	TCGA-UZ-A9PX-01A-11D-A42J-10	24987475	104309714	36903717	49	16840											
SVEP1	79987	hgsc.bcm.edu	37	chr9	113241924	113241924	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tattgatgtaccatttttccCagggtcgtctcaaatgcttc	8	16	7	10	1	1	1	1	1	1	0	5	1	2	1	2	1	2	2	2	1	3	6			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr9:113241924C>T	ENST00000401783.2	-	13	2814	c.2478G>A	c.(2476-2478)ctG>ctA	p.L826L	SVEP1_ENST00000374469.1_Silent_p.L803L|SVEP1_ENST00000374461.1_Silent_p.L803L|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000302728.8_Silent_p.L826L	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	826					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						CCATTTTTCCCAGGGTCGTCT	0.388																																					p.L826L		Atlas-SNP	.											.	SVEP1	326	.	0			c.G2478A						PASS	.						242	234	236					9																	113241924		1844	4091	5935	SO:0001819	synonymous_variant	79987	exon13			TTTTCCCAGGGTC	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.2478G>A	chr9.hg19:g.113241924C>T		130.0	0.0	.		56.0	27.0	.	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	hg19	CCDS48004.1																																																																																			.	.	.	none		0.388	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	113241924	C	T	113241924	2	4	267	1	0	0	0	0	0	0	0	1	15432	581	21	2		2	SVEP1	9	113241924	Silent	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	8932210	113241924	27971507	50	16841											
C9orf84	158401	hgsc.bcm.edu	37	chr9	114484785	114484785	+	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	aaatttccaattagcagtagGgagggtacacaaggatacaa	17	8	10	6	0	0	0	0	0	0	0	1	2	1	2	1	3	3	3	1	3	8	5			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr9:114484785G>C	ENST00000318737.4	-	13	1971	c.1843C>G	c.(1843-1845)Cct>Gct	p.P615A	C9orf84_ENST00000394779.3_Missense_Mutation_p.P576A|C9orf84_ENST00000394777.4_Missense_Mutation_p.P576A|C9orf84_ENST00000374287.3_Missense_Mutation_p.P615A	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	615										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						TTAGCAGTAGGGAGGGTACAC	0.398																																					p.P615A		Atlas-SNP	.											.	C9orf84	207	.	0			c.C1843G						PASS	.						110	108	108					9																	114484785		2203	4300	6503	SO:0001583	missense	158401	exon13			CAGTAGGGAGGGT	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.1843C>G	chr9.hg19:g.114484785G>C	ENSP00000322108:p.Pro615Ala	141.0	0.0	.		71.0	27.0	.	NM_173521	A2A2V3|Q2M1H8|Q96M73	Missense_Mutation	SNP	ENST00000318737.4	hg19	CCDS6781.3	.	.	.	.	.	.	.	.	.	.	G	11.93	1.785821	0.31593	.	.	ENSG00000165181	ENST00000394779;ENST00000394777;ENST00000394778;ENST00000374287;ENST00000318737	T;T;T;T	0.05382	3.58;3.45;3.58;3.58	5.8	4.91	0.64330	.	0.253301	0.28630	N	0.014667	T	0.06690	0.0171	L	0.32530	0.975	0.09310	N	1	P;P;P	0.40970	0.734;0.734;0.734	B;B;B	0.43478	0.421;0.421;0.421	T	0.33137	-0.9880	10	0.22706	T	0.39	-8.4088	9.0522	0.36383	0.079:0.2432:0.6777:0.0	.	576;615;576	A6PVK7;Q5VXU9;A2A2V3	.;CI084_HUMAN;.	A	576;576;229;615;615	ENSP00000378259:P576A;ENSP00000378257:P576A;ENSP00000363405:P615A;ENSP00000322108:P615A	ENSP00000322108:P615A	P	-	1	0	C9orf84	113524606	0.993000	0.37304	0.590000	0.28732	0.735000	0.41995	2.883000	0.48554	1.478000	0.48253	0.561000	0.74099	CCT	.	.	.	none		0.398	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521		C	114484785	G	C	114484785	3	2	267	1	0	0	0	0	1	0	0	0	2502	1232	43	4	2547	4	C9orf84	9	114484785	Missense_Mutation	SNP	G	TCGA-UZ-A9PX-01A-11D-A42J-10	1242861	114484785	26728646	51	16842											
ARHGAP22	58504	hgsc.bcm.edu	37	chr10	49659125	49659127	+	In_Frame_Del	DEL	GAA	GAA	-																															ccttccgggaccggtgccgtGaagagctggctgtgtttgcg																										TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr10:49659125_49659127delGAA	ENST00000249601.4	-	9	1341_1343	c.1045_1047delTTC	c.(1045-1047)ttcdel	p.F349del	ARHGAP22_ENST00000374170.1_In_Frame_Del_p.F190del|ARHGAP22_ENST00000417912.2_In_Frame_Del_p.F365del|ARHGAP22_ENST00000477708.2_In_Frame_Del_p.F182del|ARHGAP22_ENST00000435790.2_In_Frame_Del_p.F355del|ARHGAP22_ENST00000374172.1_In_Frame_Del_p.F240del|ARHGAP22_ENST00000417247.2_In_Frame_Del_p.F259del	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	349	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CCGGTGCCGTGAAGAGCTGGCTG	0.685																																					p.365_366del		Atlas-Indel,Pindel	.											.	ARHGAP22	94	.	0			c.1094_1096del						PASS	.																																			SO:0001651	inframe_deletion	58504	exon9			.	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.1045_1047delTTC	chr10.hg19:g.49659125_49659127delGAA	ENSP00000249601:p.Phe349del	197.0	0.0	0		94.0	34.0	0.361702	NM_001256024	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	In_Frame_Del	DEL	ENST00000249601.4	hg19	CCDS7227.1																																																																																			.	.	.	none		0.685	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226		-	49659127	GAA	-	49659125	7	5	267	1	0	1	0	1	0	0	0	0	872	1281	45	0	1057	0	ARHGAP22	10	49659125	In_Frame_Del	DEL	GAA	TCGA-UZ-A9PX-01A-11D-A42J-10		49659125	85875622	52	16843											
TTC18	118491	hgsc.bcm.edu	37	chr10	75051507	75051507	+	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	acagccaggacaccacacagCaacaagctgagaaaagatca	19	2	8	12	0	1	2	1	1	0	2	1	4	1	3	2	1	4	2	2	1	4	0			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr10:75051507C>T	ENST00000310715.3	-	19	2241	c.2121G>A	c.(2119-2121)ttG>ttA	p.L707L	TTC18_ENST00000340329.3_Intron|TTC18_ENST00000493787.1_5'UTR|TTC18_ENST00000401621.2_Silent_p.L707L|TTC18_ENST00000394865.1_Silent_p.L707L|TTC18_ENST00000355577.3_Silent_p.L176L	NM_145170.3	NP_660153.3	Q5T0N1	TTC18_HUMAN		707						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)					CACCACACAGCAACAAGCTGA	0.428																																					p.L707L		Atlas-SNP	.											.	TTC18	106	.	0			c.G2121A						PASS	.						111	88	96					10																	75051507		2203	4300	6503	SO:0001819	synonymous_variant	118491	exon19			ACACAGCAACAAG																												ENST00000310715.3:c.2121G>A	chr10.hg19:g.75051507C>T		166.0	0.0	.		96.0	35.0	.	NM_145170	C9JIZ9|Q5T0M4|Q5T0M9|Q5T0N0|Q69YH9|Q8IYZ8|Q8N7D5|Q8NI30|Q8NI31	Silent	SNP	ENST00000310715.3	hg19	CCDS7324.3																																																																																			.	.	.	none		0.428	TTC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	75051507	C	T	75051507	2	4	267	1	0	0	0	0	0	0	0	1	16697	709	25	2		2	TTC18	10	75051507	Silent	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	25392382	75051507	60483240	53	16844											
MYOF	26509	hgsc.bcm.edu	37	chr10	95076511	95076511	+	Frame_Shift_Del	DEL	C	C	-																															aacttgtcattgtcccatatCtgaatgatcagcctgggtgg																										TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr10:95076511delC	ENST00000359263.4	-	50	5657	c.5658delG	c.(5656-5658)cagfs	p.Q1886fs	MYOF_ENST00000371501.4_Frame_Shift_Del_p.Q1886fs|MYOF_ENST00000371502.4_Frame_Shift_Del_p.Q1876fs|MYOF_ENST00000358334.5_Frame_Shift_Del_p.Q1873fs	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	1886					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						TGTCCCATATCTGAATGATCA	0.398																																					p.I1887fs		Pindel	.											.	MYOF	177	.	0			c.5659delA						PASS	.						141	130	134					10																	95076511		1854	4095	5949	SO:0001589	frameshift_variant	26509	exon50			.	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.5658delG	chr10.hg19:g.95076511delC	ENSP00000352208:p.Gln1886fs	190.0	0.0	.		90.0	28.0	0.311	NM_013451	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Frame_Shift_Del	DEL	ENST00000359263.4	hg19	CCDS41551.1																																																																																			.	.	.	none		0.398	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451		-	95076511	C	-	95076511	7	5	267	1	0	1	0	1	0	0	0	0	10096	912	32	0	547	0	MYOF	10	95076511	Frame_Shift_Del	DEL	C	TCGA-UZ-A9PX-01A-11D-A42J-10	20025004	95076511	40458236	54	16845											
ZDHHC16	84287	hgsc.bcm.edu	37	chr10	99213325	99213327	+	In_Frame_Del	DEL	TAC	TAC	-																															tgggccactataaccatcggTacttcttctctttctgcttt																										TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	TAC	TAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr10:99213325_99213327delTAC	ENST00000370854.3	+	6	784_786	c.595_597delTAC	c.(595-597)tacdel	p.Y199del	ZDHHC16_ENST00000352634.4_In_Frame_Del_p.Y199del|ZDHHC16_ENST00000370842.2_In_Frame_Del_p.Y199del|ZDHHC16_ENST00000370846.4_Intron|ZDHHC16_ENST00000495735.1_3'UTR|ZDHHC16_ENST00000353979.3_Intron|ZDHHC16_ENST00000393760.1_In_Frame_Del_p.Y199del|ZDHHC16_ENST00000345745.5_In_Frame_Del_p.Y134del	NM_032327.2	NP_115703.2	Q969W1	ZDH16_HUMAN	zinc finger, DHHC-type containing 16	199					apoptotic process (GO:0006915)|protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			kidney(4)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	14		Colorectal(252;0.0846)		Epithelial(162;5.81e-10)|all cancers(201;4.19e-08)		TAACCATCGGTACTTCTTCTCTT	0.488																																					p.198_199del		Atlas-Indel,Pindel	.											.	ZDHHC16	25	.	0			c.594_596del						PASS	.																																			SO:0001651	inframe_deletion	84287	exon6			.	AF258563	CCDS7460.1, CCDS7461.1, CCDS7462.1, CCDS7463.1, CCDS73176.1	10q24.1	2008-05-02			ENSG00000171307	ENSG00000171307		"Zinc fingers, DHHC-type"	20714	protein-coding gene	gene with protein product						12021275	Standard	NM_198043		Approved	APH2	uc001knk.3	Q969W1	OTTHUMG00000018847	ENST00000370854.3:c.595_597delTAC	chr10.hg19:g.99213325_99213327delTAC	ENSP00000359891:p.Tyr199del	109.0	0.0	0		55.0	22.0	0.4	NM_032327	D3DR52|D3DR53|D3DR54|Q5JTG7|Q5JTH0|Q8N4Z6|Q8WY84|Q9BSV3	In_Frame_Del	DEL	ENST00000370854.3	hg19	CCDS7460.1																																																																																			.	.	.	none		0.488	ZDHHC16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049658.2	NM_032327		-	99213327	TAC	-	99213325	7	5	267	1	0	1	0	1	0	0	0	0	17618	1638	57	0	613	0	ZDHHC16	10	99213325	In_Frame_Del	DEL	TAC	TCGA-UZ-A9PX-01A-11D-A42J-10	4136814	99213325	36321422	55	16846			1	40		2	2	14	N	TC_TAC	4.451277e-05
ZDHHC16	84287	hgsc.bcm.edu	37	chr10	99213338	99213339	+	Missense_Mutation	DNP	TC	TC	CT																															ccatcggtacttcttctcttTctgctttttcatgactctgg																										TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr10:99213338_99213339TC>CT	ENST00000370854.3	+	6	797_798	c.608_609TC>CT	c.(607-609)tTC>tCT	p.F203S	ZDHHC16_ENST00000352634.4_Missense_Mutation_p.F203S|ZDHHC16_ENST00000370842.2_Missense_Mutation_p.F203S|ZDHHC16_ENST00000370846.4_Intron|ZDHHC16_ENST00000495735.1_3'UTR|ZDHHC16_ENST00000353979.3_Intron|ZDHHC16_ENST00000393760.1_Missense_Mutation_p.F203S|ZDHHC16_ENST00000345745.5_Missense_Mutation_p.F138S	NM_032327.2	NP_115703.2	Q969W1	ZDH16_HUMAN	zinc finger, DHHC-type containing 16	203					apoptotic process (GO:0006915)|protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			kidney(4)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	14		Colorectal(252;0.0846)		Epithelial(162;5.81e-10)|all cancers(201;4.19e-08)		TTCTTCTCTTTCTGCTTTTTCA	0.47																																					p.F203S|p.F203F		Atlas-SNP	.											.	ZDHHC16	25	.	0			c.T608C|c.C609T						PASS	.																																			SO:0001583	missense	84287	exon7			TCTCTTTCTGCTT|CTCTTTCTGCTTT	AF258563	CCDS7460.1, CCDS7461.1, CCDS7462.1, CCDS7463.1, CCDS73176.1	10q24.1	2008-05-02			ENSG00000171307	ENSG00000171307		"Zinc fingers, DHHC-type"	20714	protein-coding gene	gene with protein product						12021275	Standard	NM_198043		Approved	APH2	uc001knk.3	Q969W1	OTTHUMG00000018847	Exception_encountered	chr10.hg19:g.99213338_99213339delinsCT	ENSP00000359891:p.Phe203Ser	121.0	0.0	.		58.0	23.0	.	NM_198046	D3DR52|D3DR53|D3DR54|Q5JTG7|Q5JTH0|Q8N4Z6|Q8WY84|Q9BSV3	Missense_Mutation|Silent	SNP	ENST00000370854.3	hg19	CCDS7460.1																																																																																			.	.	.	none		0.47	ZDHHC16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049658.2	NM_032327		CT	99213339	TC	CT	99213338	3	2	267	1	0	0	0	0	1	0	0	0	17618	1783	62	3	626	3	ZDHHC16	10	99213338	Missense_Mutation	DNP	TC	TCGA-UZ-A9PX-01A-11D-A42J-10	13	99213338	36321409	56	16847			1	40		2	2	14	N	TC_TAC	4.451277e-05
FAM160B1	57700	hgsc.bcm.edu	37	chr10	116606357	116606357	+	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	gaatgtttgaacatcttttaCaaaaacccaatgagcacatt	16	12	5	8	0	1	2	0	2	1	0	1	3	1	2	1	0	4	2	1	0	6	4			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr10:116606357C>A	ENST00000369248.4	+	11	1773	c.1438C>A	c.(1438-1440)Caa>Aaa	p.Q480K	FAM160B1_ENST00000369250.3_Missense_Mutation_p.Q480K	NM_020940.3	NP_065991.3	Q5W0V3	F16B1_HUMAN	family with sequence similarity 160, member B1	480										NS(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)	25						ACATCTTTTACAAAAACCCAA	0.299																																					p.Q480K		Atlas-SNP	.											.	FAM160B1	107	.	0			c.C1438A						PASS	.						70	69	69					10																	116606357		2203	4300	6503	SO:0001583	missense	57700	exon11			CTTTTACAAAAAC	AB046820	CCDS31290.1, CCDS44480.1	10q26.11	2008-06-05	2008-06-05	2008-06-05	ENSG00000151553	ENSG00000151553			29320	protein-coding gene	gene with protein product			"KIAA1600"	KIAA1600		10997877	Standard	NM_020940		Approved	bA106M7.3	uc001lcb.3	Q5W0V3	OTTHUMG00000019092	ENST00000369248.4:c.1438C>A	chr10.hg19:g.116606357C>A	ENSP00000358251:p.Gln480Lys	120.0	0.0	.		104.0	44.0	.	NM_020940	Q5H9P7|Q5W0V2|Q8IY76|Q9HCH2	Missense_Mutation	SNP	ENST00000369248.4	hg19	CCDS31290.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.722985	0.89298	.	.	ENSG00000151553	ENST00000369248;ENST00000369250	T;T	0.30448	1.53;1.53	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.49201	0.1543	M	0.76574	2.34	0.80722	D	1	P;P	0.48911	0.917;0.734	P;B	0.55508	0.777;0.325	T	0.38564	-0.9655	10	0.07990	T	0.79	-24.5865	20.1338	0.98010	0.0:1.0:0.0:0.0	.	480;480	Q5W0V3-2;Q5W0V3	.;F16B1_HUMAN	K	480	ENSP00000358251:Q480K;ENSP00000358253:Q480K	ENSP00000358251:Q480K	Q	+	1	0	FAM160B1	116596347	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.500000	0.81588	2.770000	0.95276	0.655000	0.94253	CAA	.	.	.	none		0.299	FAM160B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050499.1	XM_049351		A	116606357	C	A	116606357	3	1	267	1	0	0	0	0	1	0	0	0	5474	479	17	4	1480	4	FAM160B1	10	116606357	Missense_Mutation	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	17393019	116606357	18928390	57	16848											
MKI67	4288	hgsc.bcm.edu	37	chr10	129904535	129904535	+	Frame_Shift_Del	DEL	T	T	-																															ttgcggagatttgcagagtaTttttttggtagttttctcat																										TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr10:129904535delT	ENST00000368654.3	-	13	5944	c.5569delA	c.(5569-5571)atafs	p.I1857fs	MKI67_ENST00000368653.3_Frame_Shift_Del_p.I1497fs	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1857	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)				TTGCAGAGTATTTTTTTGGTA	0.483																																					p.I1857fs		Atlas-Indel,Pindel	.											.	MKI67	363	.	0			c.5570delT						PASS	.						237	241	240					10																	129904535		2203	4300	6503	SO:0001589	frameshift_variant	4288	exon13			.	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.5569delA	chr10.hg19:g.129904535delT	ENSP00000357643:p.Ile1857fs	168.0	0.0	0		107.0	43.0	0.401869	NM_002417	Q5VWH2	Frame_Shift_Del	DEL	ENST00000368654.3	hg19	CCDS7659.1																																																																																			.	.	.	none		0.483	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		-	129904535	T	-	129904535	7	5	267	1	0	1	0	1	0	0	0	0	9605	1493	52	0	4213	0	MKI67	10	129904535	Frame_Shift_Del	DEL	T	TCGA-UZ-A9PX-01A-11D-A42J-10	13298178	129904535	5630212	58	16849											
OR52B6	340980	hgsc.bcm.edu	37	chr11	5602863	5602863	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctcctttctcaagatgccCgctccaaggccctgagtacc	7	9	8	17	1	1	2	1	1	1	1	4	2	3	2	6	1	2	2	6	1	3	2	rs375173605		TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr11:5602863C>T	ENST00000345043.2	+	1	757	c.757C>T	c.(757-759)Cgc>Tgc	p.R253C	HBG2_ENST00000380259.2_Intron|AC015691.13_ENST00000394793.2_RNA	NM_001005162.2	NP_001005162.2	Q8NGF0	O52B6_HUMAN	olfactory receptor, family 52, subfamily B, member 6	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)|kidney(2)|lung(7)|ovary(1)|prostate(1)	12		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;3.56e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCAAGATGCCCGCTCCAAGGC	0.512																																					p.R253C		Atlas-SNP	.											.	OR52B6	37	.	0			c.C757T						PASS	.	C	CYS/ARG	1,4041		0,1,2020	217	232	227		757	3	0.5	11		227	0,8354		0,0,4177	no	missense	OR52B6	NM_001005162.2	180	0,1,6197	TT,TC,CC		0.0,0.0247,0.0081	benign	253/336	5602863	1,12395	2021	4177	6198	SO:0001583	missense	340980	exon1			GATGCCCGCTCCA	AB065858	CCDS41611.1	11p15.4	2012-08-09			ENSG00000187747	ENSG00000187747		"GPCR / Class A : Olfactory receptors"	15211	protein-coding gene	gene with protein product							Standard	NM_001005162		Approved		uc010qzi.2	Q8NGF0	OTTHUMG00000066906	ENST00000345043.2:c.757C>T	chr11.hg19:g.5602863C>T	ENSP00000341581:p.Arg253Cys	143.0	0.0	.		89.0	42.0	.	NM_001005162	Q6IFI7	Missense_Mutation	SNP	ENST00000345043.2	hg19	CCDS41611.1	.	.	.	.	.	.	.	.	.	.	C	8.515	0.867481	0.17250	2.47E-4	0.0	ENSG00000187747	ENST00000345043	T	0.00337	8.05	4.99	3.05	0.35203	GPCR, rhodopsin-like superfamily (1);	0.218860	0.22458	U	0.059787	T	0.00328	0.0010	M	0.78637	2.42	0.21220	N	0.999759	P	0.35011	0.48	B	0.34346	0.18	T	0.36016	-0.9765	10	0.72032	D	0.01	.	7.8717	0.29569	0.325:0.5173:0.1577:0.0	.	253	Q8NGF0	O52B6_HUMAN	C	253	ENSP00000341581:R253C	ENSP00000341581:R253C	R	+	1	0	OR52B6	5559439	0.000000	0.05858	0.478000	0.27316	0.464000	0.32679	-1.090000	0.03372	0.638000	0.30545	0.650000	0.86243	CGC	.	.	.	weak		0.512	OR52B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143397.1	NM_001005162		T	5602863	C	T	5602863	3	4	267	1	0	0	0	0	1	0	0	0	11120	652	23	1	759	1	OR52B6	11	5602863	Missense_Mutation	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10		5602863	129403653	59	16850											
F2	2147	hgsc.bcm.edu	37	chr11	46747489	46747489	+	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	cacctccattggagcagtgtGtccctgatcgggggcagcag	7	8	14	12	1	0	1	0	1	0	0	3	2	2	2	3	3	2	3	3	3	0	1			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr11:46747489G>C	ENST00000311907.5	+	7	696	c.640G>C	c.(640-642)Gtc>Ctc	p.V214L	F2_ENST00000530231.1_Missense_Mutation_p.V214L	NM_000506.3	NP_000497.1	P00734	THRB_HUMAN	coagulation factor II (thrombin)	214	Kringle 2. {ECO:0000255|PROSITE- ProRule:PRU00121}.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell surface receptor signaling pathway (GO:0007166)|cellular protein metabolic process (GO:0044267)|cytosolic calcium ion homeostasis (GO:0051480)|fibrinolysis (GO:0042730)|leukocyte migration (GO:0050900)|multicellular organismal development (GO:0007275)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of platelet activation (GO:0010544)|negative regulation of proteolysis (GO:0045861)|peptidyl-glutamic acid carboxylation (GO:0017187)|platelet activation (GO:0030168)|positive regulation of blood coagulation (GO:0030194)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900738)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|regulation of blood coagulation (GO:0030193)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)	blood microparticle (GO:0072562)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|receptor binding (GO:0005102)|serine-type endopeptidase activity (GO:0004252)|thrombospondin receptor activity (GO:0070053)			endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	27		all_lung(304;0.000414)|Lung NSC(402;0.0011)		BRCA - Breast invasive adenocarcinoma(625;0.146)	Antihemophilic Factor(DB00025)|Argatroban(DB00278)|ART-123(DB05777)|Bivalirudin(DB00006)|Coagulation Factor IX(DB00100)|Dabigatran etexilate(DB06695)|Drotrecogin alfa(DB00055)|Lepirudin(DB00001)|Menadione(DB00170)|Proflavine(DB01123)|Suramin(DB04786)|Ximelagatran(DB04898)	GGAGCAGTGTGTCCCTGATCG	0.647																																					p.V214L	Esophageal Squamous(147;1147 1808 2148 38609 51144)	Atlas-SNP	.											.	F2	75	.	0			c.G640C						PASS	.						67	61	63					11																	46747489		2201	4299	6500	SO:0001583	missense	2147	exon7			CAGTGTGTCCCTG	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.640G>C	chr11.hg19:g.46747489G>C	ENSP00000308541:p.Val214Leu	181.0	0.0	.		79.0	35.0	.	NM_000506	B2R7F7|B4E1A7|Q4QZ40|Q53H04|Q53H06|Q69EZ7|Q7Z7P3|Q9UCA1	Missense_Mutation	SNP	ENST00000311907.5	hg19	CCDS31476.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	2.143|2.143	-0.396352|-0.396352	0.04899|0.04899	.|.	.|.	ENSG00000180210|ENSG00000180210	ENST00000446804|ENST00000311907;ENST00000530231;ENST00000442468	.|T;T;T	.|0.65549	.|-0.16;-0.16;-0.16	5.2|5.2	-3.55|-3.55	0.04639|0.04639	.|Kringle (4);Kringle-like fold (1);	.|0.978143	.|0.08402	.|N	.|0.951286	T|T	0.43919|0.43919	0.1269|0.1269	N|N	0.26042|0.26042	0.785|0.785	0.09310|0.09310	N|N	1|1	.|B	.|0.06786	.|0.001	.|B	.|0.12156	.|0.007	T|T	0.38714|0.38714	-0.9648|-0.9648	6|10	0.87932|0.87932	D|D	0|0	.|.	5.8666|5.8666	0.18779|0.18779	0.3517:0.2302:0.4182:0.0|0.3517:0.2302:0.4182:0.0	.|.	.|214	.|P00734	.|THRB_HUMAN	S|L	63|214;214;204	.|ENSP00000308541:V214L;ENSP00000433907:V214L;ENSP00000387413:V204L	ENSP00000406403:C63S|ENSP00000308541:V214L	C|V	+|+	2|1	0|0	F2|F2	46704065|46704065	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.045000|0.045000	0.14185|0.14185	-0.127000|-0.127000	0.10547|0.10547	-0.660000|-0.660000	0.05352|0.05352	-0.218000|-0.218000	0.12543|0.12543	TGT|GTC	.	.	.	none		0.647	F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317706.1			C	46747489	G	C	46747489	3	2	267	1	0	0	0	0	1	0	0	0	5344	1377	48	4	666	4	F2	11	46747489	Missense_Mutation	SNP	G	TCGA-UZ-A9PX-01A-11D-A42J-10	41144626	46747489	88259027	60	16851											
CARNS1	57571	hgsc.bcm.edu	37	chr11	67191541	67191541	+	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	cccaccgggctggcaccagaGcaggaggcacagatggttca	10	4	14	13	1	1	2	1	0	0	2	1	3	1	3	3	5	1	5	3	5	0	1			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr11:67191541G>T	ENST00000307823.3	+	9	2405	c.1953G>T	c.(1951-1953)gaG>gaT	p.E651D	CARNS1_ENST00000531040.1_Missense_Mutation_p.E748D|CARNS1_ENST00000445895.2_Missense_Mutation_p.E774D|CARNS1_ENST00000423745.2_Missense_Mutation_p.E651D	NM_020811.1	NP_065862.1	A5YM72	CRNS1_HUMAN	carnosine synthase 1	651	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.				ATP catabolic process (GO:0006200)|carnosine biosynthetic process (GO:0035499)		ATP binding (GO:0005524)|ATPase activity (GO:0016887)|carnosine synthase activity (GO:0047730)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)	11						TGGCACCAGAGCAGGAGGCAC	0.657																																					p.E774D		Atlas-SNP	.											.	CARNS1	60	.	0			c.G2322T						PASS	.						50	55	53					11																	67191541		2090	4206	6296	SO:0001583	missense	57571	exon10			ACCAGAGCAGGAG		CCDS44658.1, CCDS53667.1	11q13.1	2010-03-25	2010-03-25	2010-03-25	ENSG00000172508	ENSG00000172508			29268	protein-coding gene	gene with protein product		613368	"ATP-grasp domain containing 1"	ATPGD1		20097752	Standard	NM_020811		Approved	KIAA1394	uc010rpr.2	A5YM72		ENST00000307823.3:c.1953G>T	chr11.hg19:g.67191541G>T	ENSP00000308268:p.Glu651Asp	51.0	0.0	.		24.0	9.0	.	NM_001166222	A8K1M3|B4DFC6|E9PK38|F5H427|Q8N467|Q9P2F3	Missense_Mutation	SNP	ENST00000307823.3	hg19	CCDS44658.1	.	.	.	.	.	.	.	.	.	.	G	7.607	0.674003	0.14841	.	.	ENSG00000172508	ENST00000531040;ENST00000307823;ENST00000542831;ENST00000423745;ENST00000445895	D;D;D;D	0.97831	-4.56;-4.56;-4.56;-4.56	5.07	5.07	0.68467	ATP-grasp fold (1);ATP-grasp fold, DUF201-type (1);ATP-grasp fold, subdomain 2 (1);	0.000000	0.64402	D	0.000017	D	0.91175	0.7220	N	0.11255	0.115	0.37414	D	0.913347	B;B	0.20988	0.015;0.05	B;B	0.17722	0.013;0.019	D	0.87313	0.2313	10	0.10902	T	0.67	-26.1766	7.3509	0.26691	0.0902:0.1717:0.7382:0.0	.	651;790	A5YM72;A5YM72-3	CRNS1_HUMAN;.	D	748;651;748;651;774	ENSP00000431670:E748D;ENSP00000308268:E651D;ENSP00000401519:E651D;ENSP00000389009:E774D	ENSP00000308268:E651D	E	+	3	2	CARNS1	66948117	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	1.888000	0.39708	2.364000	0.80123	0.549000	0.68633	GAG	.	.	.	none		0.657	CARNS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395501.1	NM_020811		T	67191541	G	T	67191541	3	4	267	1	0	0	0	0	1	0	0	0	2658	962	34	4	2356	4	CARNS1	11	67191541	Missense_Mutation	SNP	G	TCGA-UZ-A9PX-01A-11D-A42J-10	20444052	67191541	67814975	61	16852											
CWF19L2	143884	hgsc.bcm.edu	37	chr11	107326471	107326471	+	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	gaagtcgcttaagttctttaCgcctttcttctttttcaaaa	9	18	5	9	2	4	0	1	0	3	0	5	1	4	0	1	0	1	2	1	0	5	8			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr11:107326471C>G	ENST00000282251.5	-	2	164	c.137G>C	c.(136-138)cGt>cCt	p.R46P	CWF19L2_ENST00000433523.1_Missense_Mutation_p.R46P	NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	46							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)		AAGTTCTTTACGCCTTTCTTC	0.388																																					p.R46P		Atlas-SNP	.											.	CWF19L2	135	.	0			c.G137C						PASS	.						266	214	230					11																	107326471		692	1591	2283	SO:0001583	missense	143884	exon2			TCTTTACGCCTTT	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.137G>C	chr11.hg19:g.107326471C>G	ENSP00000282251:p.Arg46Pro	101.0	0.0	.		42.0	16.0	.	NM_152434	A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	Missense_Mutation	SNP	ENST00000282251.5	hg19	CCDS8336.2	.	.	.	.	.	.	.	.	.	.	C	16.65	3.180931	0.57800	.	.	ENSG00000152404	ENST00000282251;ENST00000433523	T;T	0.25085	1.82;1.82	5.4	1.37	0.22104	.	.	.	.	.	T	0.29817	0.0745	M	0.77103	2.36	0.19945	N	0.999941	P	0.48503	0.911	B	0.43301	0.415	T	0.18335	-1.0340	9	0.72032	D	0.01	.	5.946	0.19219	0.1335:0.6434:0.0:0.2231	.	46	Q2TBE0	C19L2_HUMAN	P	46	ENSP00000282251:R46P;ENSP00000387533:R46P	ENSP00000282251:R46P	R	-	2	0	CWF19L2	106831681	0.116000	0.22171	0.120000	0.21714	0.983000	0.72400	1.251000	0.32862	0.007000	0.14760	-0.237000	0.12165	CGT	.	.	.	none		0.388	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328825.2	NM_152434		G	107326471	C	G	107326471	3	3	267	1	0	0	0	0	1	0	0	0	4074	536	19	4	2615	4	CWF19L2	11	107326471	Missense_Mutation	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	40134930	107326471	27680045	62	16853											
OR8D2	283160	hgsc.bcm.edu	37	chr11	124190009	124190009	+	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	atatattccaaggaacaggaGgaagagtggcagttgaagtt	15	9	13	4	0	0	2	0	1	0	1	1	5	1	5	1	4	1	3	1	4	6	5			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr11:124190009G>A	ENST00000357438.2	-	1	175	c.85C>T	c.(85-87)Ctc>Ttc	p.L29F		NM_001002918.1	NP_001002918.1	Q9GZM6	OR8D2_HUMAN	olfactory receptor, family 8, subfamily D, member 2	29						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)		AGGAACAGGAGGAAGAGTGGC	0.448																																					p.L29F		Atlas-SNP	.											.	OR8D2	65	.	0			c.C85T						PASS	.						86	84	84					11																	124190009		2201	4299	6500	SO:0001583	missense	283160	exon1			ACAGGAGGAAGAG	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.85C>T	chr11.hg19:g.124190009G>A	ENSP00000350022:p.Leu29Phe	117.0	0.0	.		50.0	19.0	.	NM_001002918	B9EH49|Q6IFR0	Missense_Mutation	SNP	ENST00000357438.2	hg19	CCDS31707.1	.	.	.	.	.	.	.	.	.	.	g	0.212	-1.036091	0.02029	.	.	ENSG00000197263	ENST00000357438	T	0.00455	7.31	3.42	-2.06	0.07298	.	0.369536	0.19376	N	0.115781	T	0.00178	0.0005	L	0.37466	1.105	0.09310	N	1	B	0.13145	0.007	B	0.10450	0.005	T	0.49835	-0.8897	10	0.05436	T	0.98	.	0.4285	0.00467	0.3664:0.1321:0.2334:0.2681	.	29	Q9GZM6	OR8D2_HUMAN	F	29	ENSP00000350022:L29F	ENSP00000350022:L29F	L	-	1	0	OR8D2	123695219	0.000000	0.05858	0.011000	0.14972	0.500000	0.33767	-3.943000	0.00329	-0.405000	0.07599	0.395000	0.25975	CTC	.	.	.	none		0.448	OR8D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387286.1	NM_001002918		A	124190009	G	A	124190009	3	1	267	1	0	0	0	0	1	0	0	0	11239	1000	35	2	853	2	OR8D2	11	124190009	Missense_Mutation	SNP	G	TCGA-UZ-A9PX-01A-11D-A42J-10	16863538	124190009	10816507	63	16854											
ERC1	23085	hgsc.bcm.edu	37	chr12	1137356	1137356	+	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	gacacttggccgttctggggGacgtctgccttacggtgttc	4	12	14	11	3	2	0	0	0	2	0	3	2	2	1	2	4	2	2	2	4	1	4			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr12:1137356G>A	ENST00000397203.2	+	2	693	c.287G>A	c.(286-288)gGa>gAa	p.G96E	ERC1_ENST00000543086.3_Missense_Mutation_p.G96E|ERC1_ENST00000546231.2_Missense_Mutation_p.G96E|ERC1_ENST00000355446.5_Missense_Mutation_p.G96E|ERC1_ENST00000360905.4_Missense_Mutation_p.G96E|ERC1_ENST00000589028.1_Missense_Mutation_p.G96E			Q8IUD2	RB6I2_HUMAN	ELKS/RAB6-interacting/CAST family member 1	96					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)			CGTTCTGGGGGACGTCTGCCT	0.502																																					p.G96E		Atlas-SNP	.											.	ERC1	95	.	0			c.G287A						PASS	.						130	123	125					12																	1137356		2203	4300	6503	SO:0001583	missense	23085	exon2			CTGGGGGACGTCT	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.287G>A	chr12.hg19:g.1137356G>A	ENSP00000380386:p.Gly96Glu	103.0	0.0	.		68.0	39.0	.	NM_178039	A2RU77|A7E295|D3DUP7|D3DUP8|Q6NVK2|Q8IUD3|Q8IUD4|Q8IUD5|Q8NAS1|Q9NXN5|Q9UIK7|Q9UPS1	Missense_Mutation	SNP	ENST00000397203.2	hg19	CCDS8508.1	.	.	.	.	.	.	.	.	.	.	G	17.94	3.510591	0.64522	.	.	ENSG00000082805	ENST00000347735;ENST00000397203;ENST00000454194;ENST00000537890;ENST00000299183;ENST00000543086;ENST00000542302;ENST00000545948;ENST00000546231;ENST00000355446;ENST00000360905;ENST00000440394	D;D;D;D;D;D;D;D;D	0.87809	-2.3;-2.3;-2.3;-2.3;-2.3;-2.3;-2.3;-2.3;-2.3	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	D	0.82637	0.5080	N	0.24115	0.695	0.47778	D	0.999516	P;P;B	0.39424	0.617;0.673;0.399	B;B;B	0.39738	0.308;0.307;0.206	T	0.82575	-0.0389	10	0.45353	T	0.12	-21.4162	20.0621	0.97678	0.0:0.0:1.0:0.0	.	96;96;96	Q8IUD2-2;Q8IUD2-3;Q8IUD2	.;.;RB6I2_HUMAN	E	96	ENSP00000340054:G96E;ENSP00000380386:G96E;ENSP00000438546:G96E;ENSP00000445336:G96E;ENSP00000442976:G96E;ENSP00000442739:G96E;ENSP00000347621:G96E;ENSP00000354158:G96E;ENSP00000410064:G96E	ENSP00000299183:G96E	G	+	2	0	ERC1	1007617	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.334000	0.72944	2.750000	0.94351	0.655000	0.94253	GGA	.	.	.	none		0.502	ERC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398380.2	NM_015064		A	1137356	G	A	1137356	3	1	267	1	0	0	0	0	1	0	0	0	5212	1174	41	2	289	2	ERC1	12	1137356	Missense_Mutation	SNP	G	TCGA-UZ-A9PX-01A-11D-A42J-10		1137356	132714539	64	16855											
DCP1B	196513	hgsc.bcm.edu	37	chr12	2061663	2061663	+	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	ttccctgttccagagctctgAgcgagcacaggaaacttagc	10	9	10	12	1	1	2	0	1	1	1	3	4	3	3	2	1	5	3	2	1	2	3			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr12:2061663A>T	ENST00000280665.6	-	7	1522	c.1443T>A	c.(1441-1443)gcT>gcA	p.A481A	DCP1B_ENST00000540622.1_Silent_p.A355A|DCP1B_ENST00000541700.1_5'Flank|DCP1B_ENST00000397173.4_Silent_p.A379A	NM_152640.3	NP_689853.3	Q8IZD4	DCP1B_HUMAN	decapping mRNA 1B	481					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)			CAGAGCTCTGAGCGAGCACAG	0.527																																					p.A481A		Atlas-SNP	.											.	DCP1B	63	.	0			c.T1443A						PASS	.						81	83	82					12																	2061663		2203	4300	6503	SO:0001819	synonymous_variant	196513	exon7			GCTCTGAGCGAGC	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.1443T>A	chr12.hg19:g.2061663A>T		105.0	0.0	.		88.0	52.0	.	NM_152640	B4DRD1|Q86XH9|Q96BP8|Q96MZ8	Silent	SNP	ENST00000280665.6	hg19	CCDS31727.1																																																																																			.	.	.	none		0.527	DCP1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398244.1	NM_152640		T	2061663	A	T	2061663	2	4	267	1	0	0	0	0	0	0	0	1	4301	291	11	5		5	DCP1B	12	2061663	Silent	SNP	A	TCGA-UZ-A9PX-01A-11D-A42J-10	924307	2061663	131790232	65	16856											
ACVR1B	91	hgsc.bcm.edu	37	chr12	52379093	52379093	+	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	tcatgatgcagtcactgacaCcattgacattgccccgaatc	11	10	7	13	1	2	3	2	3	0	0	3	4	2	3	3	0	2	1	3	0	1	2			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr12:52379093C>T	ENST00000257963.4	+	6	1174	c.1097C>T	c.(1096-1098)aCc>aTc	p.T366I	ACVR1B_ENST00000415850.2_Missense_Mutation_p.T366I|ACVR1B_ENST00000542485.1_Missense_Mutation_p.T314I|RNU6-574P_ENST00000384265.1_RNA|ACVR1B_ENST00000563121.1_3'UTR|ACVR1B_ENST00000426655.2_Missense_Mutation_p.T366I|ACVR1B_ENST00000541224.1_Missense_Mutation_p.T407I	NM_004302.4|NM_020328.3	NP_004293.1|NP_064733.3	P36896	ACV1B_HUMAN	activin A receptor, type IB	366	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|central nervous system development (GO:0007417)|development of primary female sexual characteristics (GO:0046545)|extrinsic apoptotic signaling pathway (GO:0097191)|G1/S transition of mitotic cell cycle (GO:0000082)|hair follicle development (GO:0001942)|in utero embryonic development (GO:0001701)|negative regulation of cell growth (GO:0030308)|nodal signaling pathway (GO:0038092)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of trophoblast cell migration (GO:1901165)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|inhibin binding (GO:0034711)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|ubiquitin protein ligase binding (GO:0031625)			breast(5)|endometrium(4)|kidney(5)|large_intestine(12)|lung(10)|ovary(1)|pancreas(6)|prostate(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.104)	Adenosine triphosphate(DB00171)	GTCACTGACACCATTGACATT	0.527																																					p.T407I		Atlas-SNP	.											.	ACVR1B	167	.	0			c.C1220T						PASS	.						146	132	137					12																	52379093		2203	4300	6503	SO:0001583	missense	91	exon7			CTGACACCATTGA		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.1097C>T	chr12.hg19:g.52379093C>T	ENSP00000257963:p.Thr366Ile	173.0	0.0	.		112.0	72.0	.	NM_020328	B7Z5L8|B7Z5W5|Q15479|Q15480|Q15481|Q15482	Missense_Mutation	SNP	ENST00000257963.4	hg19	CCDS8816.1	.	.	.	.	.	.	.	.	.	.	C	17.15	3.315896	0.60524	.	.	ENSG00000135503	ENST00000257963;ENST00000541224;ENST00000426655;ENST00000415850;ENST00000542485	T;T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19;-0.19	4.76	3.83	0.44106	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.051038	0.85682	D	0.000000	T	0.70684	0.3252	L	0.48260	1.515	0.80722	D	1	P;D;B;B	0.58268	0.919;0.982;0.372;0.344	P;D;B;B	0.64237	0.706;0.923;0.181;0.203	T	0.72418	-0.4300	10	0.51188	T	0.08	.	14.3487	0.66685	0.1493:0.8507:0.0:0.0	.	407;366;366;366	P36896-4;P36896;P36896-2;P36896-3	.;ACV1B_HUMAN;.;.	I	366;407;366;366;314	ENSP00000257963:T366I;ENSP00000442656:T407I;ENSP00000390477:T366I;ENSP00000397550:T366I;ENSP00000442885:T314I	ENSP00000257963:T366I	T	+	2	0	ACVR1B	50665360	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.651000	0.83577	1.302000	0.44855	0.563000	0.77884	ACC	.	.	.	none		0.527	ACVR1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397000.1	NM_020328		T	52379093	C	T	52379093	3	4	267	1	0	0	0	0	1	0	0	0	221	507	18	2	1246	2	ACVR1B	12	52379093	Missense_Mutation	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	50317430	52379093	81472802	66	16857											
SLC25A3	5250	hgsc.bcm.edu	37	chr12	98993879	98993879	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcaaagccagagcagctggTtgtaacatttgtagcaggtt	11	12	11	7	0	1	1	1	0	0	1	1	1	1	1	1	2	5	7	1	2	3	6			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr12:98993879T>C	ENST00000228318.3	+	6	911	c.791T>C	c.(790-792)gTt>gCt	p.V264A	SLC25A3_ENST00000552981.1_Missense_Mutation_p.V263A|SLC25A3_ENST00000401722.3_Missense_Mutation_p.V263A|SNORA53_ENST00000391141.1_RNA|SLC25A3_ENST00000188376.5_Missense_Mutation_p.V263A|SLC25A3_ENST00000548847.1_Missense_Mutation_p.V263A|SLC25A3_ENST00000549338.1_Missense_Mutation_p.V263A|SLC25A3_ENST00000551917.1_Missense_Mutation_p.V264A	NM_005888.3	NP_005879.1	Q00325	MPCP_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 3	264					generation of precursor metabolites and energy (GO:0006091)|phosphate ion transmembrane transport (GO:0035435)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	phosphate ion carrier activity (GO:0015320)|protein complex binding (GO:0032403)|symporter activity (GO:0015293)			breast(1)|endometrium(2)|large_intestine(4)|lung(8)|prostate(1)	16		Lung NSC(355;4.08e-05)|Breast(359;0.00191)|Colorectal(145;0.00205)|Myeloproliferative disorder(1001;0.0255)		GBM - Glioblastoma multiforme(134;1.36e-23)|BRCA - Breast invasive adenocarcinoma(302;0.000115)		GAGCAGCTGGTTGTAACATTT	0.398																																					p.V264A		Atlas-SNP	.											.	SLC25A3	95	.	0			c.T791C						PASS	.						117	99	105					12																	98993879		2203	4300	6503	SO:0001583	missense	5250	exon6			AGCTGGTTGTAAC		CCDS9065.1, CCDS9066.1	12q23.1	2013-05-22			ENSG00000075415	ENSG00000075415		"Solute carriers"	10989	protein-coding gene	gene with protein product		600370		PHC		8168843	Standard	NM_213611		Approved		uc001tfo.3	Q00325	OTTHUMG00000170212	ENST00000228318.3:c.791T>C	chr12.hg19:g.98993879T>C	ENSP00000228318:p.Val264Ala	80.0	0.0	.		89.0	52.0	.	NM_005888	B3KS34|Q7Z7N7|Q96A03	Missense_Mutation	SNP	ENST00000228318.3	hg19	CCDS9066.1	.	.	.	.	.	.	.	.	.	.	T	9.522	1.108656	0.20714	.	.	ENSG00000075415	ENST00000401722;ENST00000188376;ENST00000228318;ENST00000551917;ENST00000552981;ENST00000549338;ENST00000548847	T;T;T;T;T;T;T	0.79749	-1.3;-1.3;-1.3;-1.3;-1.3;-1.3;-1.17	5.34	4.2	0.49525	Mitochondrial carrier domain (2);	0.219986	0.46758	N	0.000266	T	0.67363	0.2885	N	0.25647	0.755	0.58432	D	0.999999	B;B;B;B	0.09022	0.002;0.0;0.001;0.001	B;B;B;B	0.17979	0.012;0.006;0.02;0.005	T	0.58267	-0.7666	10	0.21014	T	0.42	-9.264	9.8807	0.41231	0.0:0.0779:0.0:0.9221	.	263;263;264;263	F8VVM2;B2RE88;Q00325;Q00325-2	.;.;MPCP_HUMAN;.	A	263;263;264;264;263;263;263	ENSP00000383898:V263A;ENSP00000188376:V263A;ENSP00000228318:V264A;ENSP00000447310:V264A;ENSP00000448708:V263A;ENSP00000447740:V263A;ENSP00000449166:V263A	ENSP00000188376:V263A	V	+	2	0	SLC25A3	97518010	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.469000	0.80959	0.986000	0.38683	0.533000	0.62120	GTT	.	.	.	none		0.398	SLC25A3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407989.1	NM_005888		C	98993879	T	C	98993879	3	2	267	1	0	0	0	0	1	0	0	0	14506	1725	60	3	935	3	SLC25A3	12	98993879	Missense_Mutation	SNP	T	TCGA-UZ-A9PX-01A-11D-A42J-10	46614786	98993879	34858016	67	16858											
HSPB8	26353	hgsc.bcm.edu	37	chr12	119617127	119617127	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagcagccaccatggctgacGgtcagatgcccttctcctgc	7	8	11	15	1	2	2	1	1	1	1	3	3	2	2	4	2	4	2	4	2	0	1			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr12:119617127G>A	ENST00000281938.2	+	1	681	c.10G>A	c.(10-12)Ggt>Agt	p.G4S	RP11-64B16.3_ENST00000538405.1_RNA|RP11-64B16.4_ENST00000535921.1_RNA	NM_014365.2	NP_055180.1	Q9UJY1	HSPB8_HUMAN	heat shock 22kDa protein 8	4					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)					CATGGCTGACGGTCAGATGCC	0.612																																					p.G4S		Atlas-SNP	.											.	HSPB8	45	.	0			c.G10A						PASS	.						50	61	57					12																	119617127		2203	4300	6503	SO:0001583	missense	26353	exon1			GCTGACGGTCAGA	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.10G>A	chr12.hg19:g.119617127G>A	ENSP00000281938:p.Gly4Ser	41.0	0.0	.		20.0	7.0	.	NM_014365	B2R6A6|Q6FIH3|Q9UKS3	Missense_Mutation	SNP	ENST00000281938.2	hg19	CCDS9189.1	.	.	.	.	.	.	.	.	.	.	G	9.471	1.095576	0.20471	.	.	ENSG00000152137	ENST00000281938	D	0.85556	-2.0	4.42	4.42	0.53409	.	0.256618	0.33631	N	0.004719	T	0.71187	0.3310	L	0.31664	0.95	0.42229	D	0.991888	B	0.27264	0.173	B	0.13407	0.009	T	0.65697	-0.6105	9	.	.	.	.	5.2215	0.15371	0.2542:0.0:0.7458:0.0	.	4	Q9UJY1	HSPB8_HUMAN	S	4	ENSP00000281938:G4S	.	G	+	1	0	HSPB8	118101510	0.981000	0.34729	0.940000	0.37924	0.516000	0.34256	2.064000	0.41432	2.294000	0.77228	0.563000	0.77884	GGT	.	.	.	none		0.612	HSPB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401647.1	NM_014365		A	119617127	G	A	119617127	3	1	267	1	0	0	0	0	1	0	0	0	7430	1116	39	1	12	1	HSPB8	12	119617127	Missense_Mutation	SNP	G	TCGA-UZ-A9PX-01A-11D-A42J-10	20623248	119617127	14234768	68	16859											
KL	9365	hgsc.bcm.edu	37	chr13	33628024	33628024	+	Frame_Shift_Del	DEL	A	A	-																															gaatgaccgaccacagcatcAaagaatgtcaaaaatctctg																										TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr13:33628024delA	ENST00000380099.3	+	2	948	c.940delA	c.(940-942)aaafs	p.K314fs	KL_ENST00000487852.1_3'UTR|KL_ENST00000426690.2_Frame_Shift_Del_p.K7fs	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	314	Glycosyl hydrolase-1 1.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)			breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		CCACAGCATCAAAGAATGTCA	0.448																																					p.I313fs		Atlas-Indel,Pindel	.											.	KL	106	.	0			c.939delC						PASS	.						167	159	162					13																	33628024		2203	4300	6503	SO:0001589	frameshift_variant	9365	exon2			.	AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.940delA	chr13.hg19:g.33628024delA	ENSP00000369442:p.Lys314fs	185.0	0.0	0		150.0	60.0	0.4	NM_004795	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Frame_Shift_Del	DEL	ENST00000380099.3	hg19	CCDS9347.1																																																																																			.	.	.	none		0.448	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1			-	33628024	A	-	33628024	7	5	267	1	0	1	0	1	0	0	0	0	8338	131	5	0	946	0	KL	13	33628024	Frame_Shift_Del	DEL	A	TCGA-UZ-A9PX-01A-11D-A42J-10		33628024	81541854	69	16860											
DZIP1	22873	hgsc.bcm.edu	37	chr13	96293651	96293651	+	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	gtcttgatctcccccgcctgCttggtgagcagcttcttgct	3	14	10	14	1	3	2	0	2	3	0	4	2	3	2	3	1	4	4	3	1	0	4			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr13:96293651C>T	ENST00000376829.2	-	5	1346	c.495G>A	c.(493-495)aaG>aaA	p.K165K	DZIP1_ENST00000466027.1_5'UTR|DZIP1_ENST00000347108.3_Silent_p.K165K|DZIP1_ENST00000361156.3_Silent_p.K165K|DZIP1_ENST00000361396.2_Silent_p.K165K	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	165					cilium assembly (GO:0042384)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(20)|lung(11)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	38	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			CCCCCGCCTGCTTGGTGAGCA	0.592																																					p.K165K		Atlas-SNP	.											.	DZIP1	195	.	0			c.G495A						PASS	.						83	54	64					13																	96293651		2203	4300	6503	SO:0001819	synonymous_variant	22873	exon5			CGCCTGCTTGGTG	AB023213	CCDS9477.1, CCDS9478.1	13q32.1	2013-05-22	2013-05-22		ENSG00000134874	ENSG00000134874		"Zinc fingers, C2H2-type"	20908	protein-coding gene	gene with protein product		608671	"DAZ interacting protein 1"				Standard	NM_014934		Approved	KIAA0996, DZIP	uc001vmk.4	Q86YF9	OTTHUMG00000017224	ENST00000376829.2:c.495G>A	chr13.hg19:g.96293651C>T		82.0	0.0	.		53.0	35.0	.	NM_014934	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Silent	SNP	ENST00000376829.2	hg19	CCDS9478.1																																																																																			.	.	.	none		0.592	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934		T	96293651	C	T	96293651	2	4	267	1	0	0	0	0	0	0	0	1	4865	796	28	2		2	DZIP1	13	96293651	Silent	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	62665627	96293651	18876227	70	16861											
MUDENG	55745	hgsc.bcm.edu	37	chr14	57747111	57747111	+	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	cattcactccacctttagagTcattcaacttatgcttctac	10	15	3	13	0	4	1	3	0	1	1	5	1	5	1	2	0	3	1	2	0	4	7			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr14:57747111T>A	ENST00000261558.3	+	3	1325	c.919T>A	c.(919-921)Tca>Aca	p.S307T	AP5M1_ENST00000431972.2_Missense_Mutation_p.S321T|AP5M1_ENST00000556723.1_3'UTR	NM_018229.3	NP_060699.3	Q9H0R1	AP5M1_HUMAN	adaptor-related protein complex 5, mu 1 subunit	307	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|cytosol (GO:0005829)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)											ACCTTTAGAGTCATTCAACTT	0.353																																					p.S307T		Atlas-SNP	.											.	.	.	.	0			c.T919A						PASS	.						141	125	130					14																	57747111		2203	4300	6503	SO:0001583	missense	55745	exon3			TTAGAGTCATTCA	AF094583	CCDS9729.1	14q22.2	2012-03-20	2012-03-20	2012-03-20	ENSG00000053770	ENSG00000053770			20192	protein-coding gene	gene with protein product	"Mu-2 related death-inducing gene"	614368	"chromosome 14 open reading frame 108", "MU-2/AP1M2 domain containing, death-inducing"	C14orf108, MUDENG		18395520	Standard	NM_018229		Approved	FLJ10813, MuD, mu5	uc001xcv.3	Q9H0R1	OTTHUMG00000140318	ENST00000261558.3:c.919T>A	chr14.hg19:g.57747111T>A	ENSP00000261558:p.Ser307Thr	178.0	0.0	.		86.0	35.0	.	NM_018229	O95354|Q6ZMD7|Q96DX3|Q9NVC5	Missense_Mutation	SNP	ENST00000261558.3	hg19	CCDS9729.1	.	.	.	.	.	.	.	.	.	.	T	7.432	0.638915	0.14386	.	.	ENSG00000053770	ENST00000261558;ENST00000431972	T;T	0.20200	2.09;2.09	5.96	3.58	0.41010	Clathrin adaptor, mu subunit, C-terminal (3);	0.377447	0.30901	N	0.008651	T	0.09992	0.0245	N	0.20685	0.6	0.40343	D	0.979055	B	0.02656	0.0	B	0.10450	0.005	T	0.19128	-1.0315	10	0.19147	T	0.46	.	2.013	0.03492	0.1366:0.1307:0.1425:0.5903	.	307	Q9H0R1	MUDEN_HUMAN	T	307;321	ENSP00000261558:S307T;ENSP00000390531:S321T	ENSP00000261558:S307T	S	+	1	0	MUDENG	56816864	0.995000	0.38212	0.999000	0.59377	0.983000	0.72400	1.162000	0.31786	1.044000	0.40200	0.496000	0.49642	TCA	.	.	.	none		0.353	AP5M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276922.1	NM_018229		A	57747111	T	A	57747111	3	1	267	1	0	0	0	0	1	0	0	0	9990	1667	58	5	929	5	MUDENG	14	57747111	Missense_Mutation	SNP	T	TCGA-UZ-A9PX-01A-11D-A42J-10		57747111	49602429	71	16862											
TSHR	7253	hgsc.bcm.edu	37	chr14	81610606	81610606	+	Frame_Shift_Del	DEL	T	T	-																															gaggcagggtctccacaacaTggaagatgtctatgaactga																										TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr14:81610606delT	ENST00000541158.2	+	11	2526	c.2204delT	c.(2203-2205)atgfs	p.M735fs	TSHR_ENST00000298171.2_Frame_Shift_Del_p.M735fs|RP11-114N19.3_ENST00000557775.1_RNA			P16473	TSHR_HUMAN	thyroid stimulating hormone receptor	735					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)	CTCCACAACATGGAAGATGTC	0.463			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism																														p.M735fs		Pindel	.	yes	Dom	yes		14	14q31	7253	thyroid stimulating hormone receptor	yes	E	.	TSHR	462	.	0			c.2203delA						PASS	.						116	107	110					14																	81610606		2203	4300	6503	SO:0001589	frameshift_variant	7253	exon10			.	AY429111	CCDS9872.1, CCDS32131.1, CCDS55935.1	14q24-q31	2014-09-17			ENSG00000165409	ENSG00000165409		"GPCR / Class A : Gonadotropin and TSH receptors"	12373	protein-coding gene	gene with protein product		603372				2558651, 2610690	Standard	NM_001018036		Approved	LGR3	uc001xvd.1	P16473		ENST00000541158.2:c.2204delT	chr14.hg19:g.81610606delT	ENSP00000441235:p.Met735fs	193.0	0.0	.		113.0	31.0	0.274	NM_000369	A0PJU7|F5GYU5|G3V2A9|Q16503|Q8TB90|Q96GT6|Q9P1V4|Q9ULA3|Q9UPH3	Frame_Shift_Del	DEL	ENST00000541158.2	hg19	CCDS9872.1																																																																																			.	.	.	none		0.463	TSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413364.1	NM_000369		-	81610606	T	-	81610606	7	5	267	1	0	1	0	1	0	0	0	0	16634	1464	51	0	2379	0	TSHR	14	81610606	Frame_Shift_Del	DEL	T	TCGA-UZ-A9PX-01A-11D-A42J-10	23863495	81610606	25738934	72	16863											
ADSSL1	122622	hgsc.bcm.edu	37	chr14	105208271	105208271	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccgcagaacataggtgacGtgtatggcgtggtgaaagcc	10	7	14	10	3	0	3	0	2	0	1	0	3	0	3	3	3	2	2	3	3	4	2			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr14:105208271G>A	ENST00000330877.2	+	9	965	c.880G>A	c.(880-882)Gtg>Atg	p.V294M	ADSSL1_ENST00000332972.5_Missense_Mutation_p.V337M	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)		CATAGGTGACGTGTATGGCGT	0.632																																					p.V337M		Atlas-SNP	.											.	ADSSL1	37	.	0			c.G1009A						PASS	.						164	143	150					14																	105208271		2203	4300	6503	SO:0001583	missense	122622	exon9			GGTGACGTGTATG	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.880G>A	chr14.hg19:g.105208271G>A	ENSP00000331260:p.Val294Met	128.0	0.0	.		76.0	28.0	.	NM_199165		Missense_Mutation	SNP	ENST00000330877.2	hg19	CCDS9990.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.377953	0.82682	.	.	ENSG00000185100	ENST00000330877;ENST00000332972	T;T	0.55052	0.54;0.54	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.80649	0.4663	M	0.93678	3.445	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.85997	0.1492	10	0.87932	D	0	-2.253	18.9013	0.92443	0.0:0.0:1.0:0.0	.	337;294	Q8N142-2;Q8N142	.;PURA1_HUMAN	M	294;337	ENSP00000331260:V294M;ENSP00000333019:V337M	ENSP00000331260:V294M	V	+	1	0	ADSSL1	104279316	1.000000	0.71417	0.417000	0.26559	0.561000	0.35649	9.655000	0.98512	2.534000	0.85438	0.655000	0.94253	GTG	.	.	.	none		0.632	ADSSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410529.1			A	105208271	G	A	105208271	3	1	267	1	0	0	0	0	1	0	0	0	348	1145	40	1	1239	1	ADSSL1	14	105208271	Missense_Mutation	SNP	G	TCGA-UZ-A9PX-01A-11D-A42J-10	23597665	105208271	2141269	73	16864											
SNURF	8926	hgsc.bcm.edu	37	chr15	25207312	25207312	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagcacgtaccagaggtggaAgtccaagtcaaacgcagaag	15	4	12	10	2	1	2	1	0	0	2	2	3	2	3	2	2	3	3	2	2	5	1			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr15:25207312A>G	ENST00000577949.1	+	2	129	c.66A>G	c.(64-66)gaA>gaG	p.E22E	SNRPN_ENST00000577565.1_5'UTR|SNRPN_ENST00000400098.1_5'UTR|SNRPN_ENST00000553597.1_3'UTR|SNRPN_ENST00000400097.1_5'UTR|SNURF_ENST00000338094.6_Silent_p.E22E|SNURF_ENST00000338327.4_Silent_p.E22E|SNURF_ENST00000551312.2_Silent_p.E22E|SNRPN_ENST00000346403.6_5'UTR|SNRPN_ENST00000390687.4_5'UTR|SNRPN_ENST00000554227.2_5'UTR|SNRPN_ENST00000400100.1_5'UTR			Q9Y675	SNURF_HUMAN	SNRPN upstream reading frame	22						nucleus (GO:0005634)				breast(2)|large_intestine(2)|lung(1)	5		all_cancers(20;1.4e-21)|Breast(32;0.000625)		all cancers(64;3.48e-07)|Epithelial(43;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0142)		CAGAGGTGGAAGTCCAAGTCA	0.458																																					p.E22E		Atlas-SNP	.											.	SNURF	17	.	0			c.A66G						PASS	.						154	121	132					15																	25207312		2203	4300	6503	SO:0001819	synonymous_variant	8926	exon2			GGTGGAAGTCCAA		CCDS10016.1	15q11.2	2013-08-27			ENSG00000214265	ENSG00000214265			11171	protein-coding gene	gene with protein product						10318933	Standard	NM_022804		Approved		uc001ywu.3	Q9Y675	OTTHUMG00000129181	ENST00000577949.1:c.66A>G	chr15.hg19:g.25207312A>G		152.0	0.0	.		75.0	30.0	.	NM_005678	A6NCW2	Silent	SNP	ENST00000577949.1	hg19	CCDS10016.1																																																																																			.	.	.	none		0.458	SNURF-005	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446300.1	NM_005678		G	25207312	A	G	25207312	2	3	267	1	0	0	0	0	0	0	0	1	14891	69	3	3		3	SNURF	15	25207312	Silent	SNP	A	TCGA-UZ-A9PX-01A-11D-A42J-10		25207312	77324080	74	16865											
HERC2	8924	hgsc.bcm.edu	37	chr15	28369256	28369256	+	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	cgagtccagtttcgtcgagcGagccttccaggtcgaacatg	8	9	12	12	5	0	0	0	0	0	0	5	4	2	0	3	1	3	1	3	1	1	2	rs371676185		TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr15:28369256G>A	ENST00000261609.7	-	85	13223	c.13115C>T	c.(13114-13116)tCg>tTg	p.S4372L		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)		TTCGTCGAGCGAGCCTTCCAG	0.562																																					p.S4372L		Atlas-SNP	.											.	HERC2	501	.	0			c.C13115T						PASS	.	G	LEU/SER	0,4406		0,0,2203	105	95	98		13115	2.5	0.6	15		98	1,8599	1.2+/-3.3	0,1,4299	no	missense	HERC2	NM_004667.4	145	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	4372/4835	28369256	1,13005	2203	4300	6503	SO:0001583	missense	8924	exon85			TCGAGCGAGCCTT	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.13115C>T	chr15.hg19:g.28369256G>A	ENSP00000261609:p.Ser4372Leu	123.0	0.0	.		73.0	31.0	.	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	G	9.737	1.163853	0.21538	0.0	1.16E-4	ENSG00000128731	ENST00000261609	T	0.38401	1.14	5.55	2.51	0.30379	.	0.314292	0.32687	N	0.005768	T	0.25531	0.0621	L	0.38175	1.15	0.28428	N	0.917401	B	0.25105	0.118	B	0.14578	0.011	T	0.11916	-1.0568	10	0.27785	T	0.31	.	11.1638	0.48531	0.0:0.637:0.2573:0.1058	.	4372	O95714	HERC2_HUMAN	L	4372	ENSP00000261609:S4372L	ENSP00000261609:S4372L	S	-	2	0	HERC2	26042851	1.000000	0.71417	0.580000	0.28601	0.161000	0.22273	3.800000	0.55537	0.253000	0.21552	-0.150000	0.13652	TCG	.	.	.	weak		0.562	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		A	28369256	G	A	28369256	3	1	267	1	0	0	0	0	1	0	0	0	7065	1059	37	1	1425	1	HERC2	15	28369256	Missense_Mutation	SNP	G	TCGA-UZ-A9PX-01A-11D-A42J-10	3161944	28369256	74162136	75	16866											
RYR3	6263	hgsc.bcm.edu	37	chr15	34127190	34127190	+	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	gcccttgcattggtaatcaaCagagcctggctcacagcagg	10	8	11	12	0	2	1	2	0	0	1	2	1	2	1	2	3	4	4	2	3	2	3			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr15:34127190C>A	ENST00000389232.4	+	87	11555	c.11485C>A	c.(11485-11487)Cag>Aag	p.Q3829K	RYR3_ENST00000415757.3_Missense_Mutation_p.Q3824K	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3829					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)		TGGTAATCAACAGAGCCTGGC	0.488																																					p.Q3829K		Atlas-SNP	.											.	RYR3	760	.	0			c.C11485A						PASS	.						101	98	99					15																	34127190		1992	4183	6175	SO:0001583	missense	6263	exon87			AATCAACAGAGCC		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.11485C>A	chr15.hg19:g.34127190C>A	ENSP00000373884:p.Gln3829Lys	68.0	0.0	.		29.0	10.0	.	NM_001036	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	hg19	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.485309	0.84854	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D	0.94931	-3.56	4.66	4.66	0.58398	RyR/IP3R Homology associated domain (1);	0.000000	0.85682	D	0.000000	D	0.95931	0.8675	L	0.58969	1.84	0.58432	D	0.999998	P;D	0.55172	0.955;0.97	P;P	0.60068	0.725;0.868	D	0.95788	0.8822	10	0.49607	T	0.09	.	17.7356	0.88391	0.0:1.0:0.0:0.0	.	3824;3829	Q15413-2;Q15413	.;RYR3_HUMAN	K	3829;3828;3825	ENSP00000373884:Q3829K	ENSP00000354735:Q3825K	Q	+	1	0	RYR3	31914482	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	7.470000	0.80973	2.423000	0.82170	0.650000	0.86243	CAG	.	.	.	none		0.488	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			A	34127190	C	A	34127190	3	1	267	1	0	0	0	0	1	0	0	0	13783	479	17	4	11831	4	RYR3	15	34127190	Missense_Mutation	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	5757934	34127190	68404202	76	16867											
GNB5	10681	hgsc.bcm.edu	37	chr15	52425644	52425644	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccggagcgcatgtcccacAccatggctttcttgtcacat	7	10	10	14	2	2	0	1	0	1	0	3	1	3	1	3	3	1	2	3	3	0	2			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr15:52425644A>G	ENST00000261837.7	-	9	859	c.794T>C	c.(793-795)gTg>gCg	p.V265A	GNB5_ENST00000396335.4_Missense_Mutation_p.V153A|CTD-2184D3.7_ENST00000557898.1_RNA|GNB5_ENST00000358784.7_Missense_Mutation_p.V223A|GNB5_ENST00000559348.1_5'UTR	NM_016194.3	NP_057278.2	O14775	GBB5_HUMAN	guanine nucleotide binding protein (G protein), beta 5	265					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)		CATGTCCCACACCATGGCTTT	0.473																																					p.V265A		Atlas-SNP	.											.	GNB5	28	.	0			c.T794C						PASS	.						151	122	132					15																	52425644		2195	4293	6488	SO:0001583	missense	10681	exon9			TCCCACACCATGG	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.794T>C	chr15.hg19:g.52425644A>G	ENSP00000261837:p.Val265Ala	95.0	0.0	.		55.0	21.0	.	NM_016194	B2RBR5|Q9HAU9|Q9UFT3	Missense_Mutation	SNP	ENST00000261837.7	hg19	CCDS10149.1	.	.	.	.	.	.	.	.	.	.	A	28.8	4.952064	0.92660	.	.	ENSG00000069966	ENST00000261837;ENST00000396335;ENST00000544480;ENST00000358784	T	0.66280	-0.2	5.78	5.78	0.91487	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.80444	0.4624	M	0.79693	2.465	0.80722	D	1	D;D	0.62365	0.991;0.986	D;P	0.80764	0.994;0.839	T	0.83227	-0.0065	10	0.87932	D	0	-28.0646	16.1146	0.81295	1.0:0.0:0.0:0.0	.	265;153	O14775;O14775-3	GBB5_HUMAN;.	A	265;223;63;153	ENSP00000261837:V265A	ENSP00000261837:V265A	V	-	2	0	GNB5	50212936	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.720000	0.91442	2.200000	0.70718	0.460000	0.39030	GTG	.	.	.	none		0.473	GNB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254842.1			G	52425644	A	G	52425644	3	3	267	1	0	0	0	0	1	0	0	0	6528	159	6	3	413	3	GNB5	15	52425644	Missense_Mutation	SNP	A	TCGA-UZ-A9PX-01A-11D-A42J-10	18298454	52425644	50105748	77	16868											
RASGRF1	5923	hgsc.bcm.edu	37	chr15	79294058	79294058	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttggagatttagttggtgAtgtttcagtatcaccatcat	9	17	10	5	0	3	2	3	1	0	1	3	3	3	2	1	2	0	4	1	2	2	6			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr15:79294058A>G	ENST00000419573.3	-	17	2843	c.2569T>C	c.(2569-2571)Tca>Cca	p.S857P	RASGRF1_ENST00000394745.3_Missense_Mutation_p.S73P|RASGRF1_ENST00000558480.2_Missense_Mutation_p.S841P|RASGRF1_ENST00000560334.1_5'UTR	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	857					activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						TTAGTTGGTGATGTTTCAGTA	0.363																																					p.S857P		Atlas-SNP	.											.	RASGRF1	168	.	0			c.T2569C						PASS	.						237	215	222					15																	79294058		2196	4293	6489	SO:0001583	missense	5923	exon17			TTGGTGATGTTTC	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing"	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.2569T>C	chr15.hg19:g.79294058A>G	ENSP00000405963:p.Ser857Pro	161.0	0.0	.		79.0	4.0	.	NM_002891	F8VPA5|H0YKF2|J3KQP9|Q16027	Missense_Mutation	SNP	ENST00000419573.3	hg19	CCDS10309.1	.	.	.	.	.	.	.	.	.	.	A	19.13	3.767238	0.69878	.	.	ENSG00000058335	ENST00000419573;ENST00000394741;ENST00000394745	T;T	0.67698	-0.28;-0.28	4.97	4.97	0.65823	Ras guanine nucleotide exchange factor, domain (1);	0.227415	0.38272	N	0.001742	T	0.80025	0.4548	M	0.77820	2.39	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;0.967;0.973;0.987;0.987	D;D;P;P;P	0.74348	0.983;0.91;0.694;0.83;0.833	T	0.82112	-0.0618	10	0.66056	D	0.02	.	11.0365	0.47804	1.0:0.0:0.0:0.0	.	253;857;841;859;841	B7Z6Z6;A8K270;Q8IUU5;Q13972;F8VPA5	.;.;.;RGRF1_HUMAN;.	P	857;841;73	ENSP00000405963:S857P;ENSP00000378228:S73P	ENSP00000378224:S841P	S	-	1	0	RASGRF1	77081113	1.000000	0.71417	0.036000	0.18154	0.910000	0.53928	6.239000	0.72356	1.871000	0.54225	0.402000	0.26972	TCA	.	.	.	none		0.363	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891		G	79294058	A	G	79294058	3	3	267	1	0	0	0	0	1	0	0	0	13085	333	12	3	1300	3	RASGRF1	15	79294058	Missense_Mutation	SNP	A	TCGA-UZ-A9PX-01A-11D-A42J-10	26868414	79294058	23237334	78	16869											
WDR93	56964	hgsc.bcm.edu	37	chr15	90260171	90260171	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtcccatttctgcagatccTttagaaatggtaagaaactt	12	13	8	8	0	1	3	0	0	1	3	3	3	3	3	2	2	2	2	2	2	4	5			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr15:90260171T>C	ENST00000268130.7	+	7	887	c.786T>C	c.(784-786)ccT>ccC	p.P262P	RNU6-132P_ENST00000383863.1_RNA|WDR93_ENST00000560294.1_Silent_p.P262P	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	262					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)			CTGCAGATCCTTTAGAAATGG	0.294																																					p.P262P		Atlas-SNP	.											.	WDR93	63	.	0			c.T786C						PASS	.						81	86	84					15																	90260171		2200	4299	6499	SO:0001819	synonymous_variant	56964	exon7			AGATCCTTTAGAA		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.786T>C	chr15.hg19:g.90260171T>C		151.0	0.0	.		104.0	46.0	.	NM_020212	Q8N7Y8|Q9NP89	Silent	SNP	ENST00000268130.7	hg19	CCDS32326.1																																																																																			.	.	.	none		0.294	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212		C	90260171	T	C	90260171	2	2	267	1	0	0	0	0	0	0	0	1	17352	1596	56	3		3	WDR93	15	90260171	Silent	SNP	T	TCGA-UZ-A9PX-01A-11D-A42J-10	10966113	90260171	12271221	79	16870											
TTLL13	440307	hgsc.bcm.edu	37	chr15	90796537	90796540	+	Frame_Shift_Del	DEL	ACTC	ACTC	-																															tgggggaggatgaagagtggActctgtactggacagactgc																										TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	ACTC	ACTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr15:90796537_90796540delACTC	ENST00000561573.1	+	4	619_622	c.355_358delACTC	c.(355-360)actctgfs	p.TL119fs	TTLL13_ENST00000438251.1_Frame_Shift_Del_p.TL119fs|TTLL13_ENST00000339615.5_Frame_Shift_Del_p.TL119fs																							TGAAGAGTGGACTCTGTACTGGAC	0.583																																					p.118_119del		Atlas-Indel,Pindel	.											.	TTLL13	44	.	0			c.354_357del						PASS	.																																			SO:0001589	frameshift_variant	440307	exon4			.																												ENST00000561573.1:c.355_358delACTC	chr15.hg19:g.90796537_90796540delACTC	ENSP00000456615:p.Thr119fs	129.0	0.0	0		87.0	25.0	0.287356	NM_001029964		Frame_Shift_Del	DEL	ENST00000561573.1	hg19																																																																																				.	.	.	none		0.583	RP11-697E2.6-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	protein_coding	OTTHUMT00000435855.1			-	90796540	ACTC	-	90796537	7	5	267	1	0	1	0	1	0	0	0	0	16738	275	10	0	365	0	TTLL13	15	90796537	Frame_Shift_Del	DEL	ACTC	TCGA-UZ-A9PX-01A-11D-A42J-10	536366	90796537	11734855	80	16871											
CLN3	1201	hgsc.bcm.edu	37	chr16	28497728	28497728	+	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	gggtctgctgaggggagaggCcggcctgggtgaggcccagg	5	5	22	9	1	1	3	0	2	1	1	1	4	1	3	3	8	1	1	3	8	0	0			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr16:28497728C>A	ENST00000569430.1	-	10	1436	c.617G>T	c.(616-618)gGc>gTc	p.G206V	CLN3_ENST00000535392.1_Missense_Mutation_p.G128V|CLN3_ENST00000568224.1_Missense_Mutation_p.G128V|CLN3_ENST00000359984.7_Missense_Mutation_p.G206V|CLN3_ENST00000357076.5_Intron|CLN3_ENST00000360019.2_Missense_Mutation_p.G206V|CLN3_ENST00000355477.5_Intron|CLN3_ENST00000395653.4_Missense_Mutation_p.G106V|CLN3_ENST00000357806.7_Intron|CLN3_ENST00000565316.1_Missense_Mutation_p.G206V|CLN3_ENST00000357857.9_Missense_Mutation_p.G152V|CLN3_ENST00000354630.5_Missense_Mutation_p.G206V|CLN3_ENST00000333496.9_Missense_Mutation_p.G182V|CLN3_ENST00000567963.1_Missense_Mutation_p.G206V			Q13286	CLN3_HUMAN	ceroid-lipofuscinosis, neuronal 3	206					action potential (GO:0001508)|amyloid precursor protein catabolic process (GO:0042987)|arginine transport (GO:0015809)|associative learning (GO:0008306)|autophagic vacuole fusion (GO:0000046)|cell death (GO:0008219)|cellular amino acid metabolic process (GO:0006520)|ceramide metabolic process (GO:0006672)|cytosolic calcium ion homeostasis (GO:0051480)|galactosylceramide metabolic process (GO:0006681)|globoside metabolic process (GO:0001575)|glucosylceramide metabolic process (GO:0006678)|ionotropic glutamate receptor signaling pathway (GO:0035235)|lysosomal lumen acidification (GO:0007042)|lysosomal lumen pH elevation (GO:0035752)|lysosome organization (GO:0007040)|macroautophagy (GO:0016236)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of macroautophagy (GO:0016242)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of proteolysis (GO:0045861)|neuromuscular process controlling balance (GO:0050885)|neurotransmitter metabolic process (GO:0042133)|protein catabolic process (GO:0030163)|protein processing (GO:0016485)|receptor-mediated endocytosis (GO:0006898)|sphingomyelin metabolic process (GO:0006684)|vacuolar transport (GO:0007034)|vesicle transport along microtubule (GO:0047496)	autophagic vacuole (GO:0005776)|caveola (GO:0005901)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|trans-Golgi network (GO:0005802)	unfolded protein binding (GO:0051082)			breast(1)|large_intestine(2)|lung(11)|upper_aerodigestive_tract(1)	15						AGGGGAGAGGCCGGCCTGGGT	0.687																																					p.G206V		Atlas-SNP	.											.	CLN3	33	.	0			c.G617T						PASS	.						25	28	27					16																	28497728		2195	4300	6495	SO:0001583	missense	1201	exon9			GAGAGGCCGGCCT	U32680	CCDS10632.1, CCDS73852.1, CCDS73853.1, CCDS73854.1, CCDS73855.1	16p12	2014-09-17	2008-07-29		ENSG00000188603	ENSG00000188603			2074	protein-coding gene	gene with protein product	"juvenile neuronal ceroid lipofuscinosis"	607042	"Batten, Spielmeyer-Vogt disease"	BTS		18317235	Standard	NM_001042432		Approved	JNCL	uc002dpp.3	Q13286	OTTHUMG00000097024	ENST00000569430.1:c.617G>T	chr16.hg19:g.28497728C>A	ENSP00000454229:p.Gly206Val	180.0	0.0	.		144.0	46.0	.	NM_001042432	B2R7J1|O00668|O95089|Q549S9|Q9UP09|Q9UP11|Q9UP12|Q9UP13|Q9UP14	Missense_Mutation	SNP	ENST00000569430.1	hg19	CCDS10632.1	.	.	.	.	.	.	.	.	.	.	C	18.75	3.691246	0.68271	.	.	ENSG00000188603	ENST00000535392;ENST00000359984;ENST00000360019;ENST00000354630;ENST00000357857;ENST00000395653	T;T;T;T;T;T	0.61158	0.13;0.13;0.13;0.13;0.13;0.13	5.6	5.6	0.85130	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	T	0.81922	0.4925	M	0.92169	3.28	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;0.992	D	0.85590	0.1245	10	0.62326	D	0.03	-20.6091	17.1168	0.86691	0.0:1.0:0.0:0.0	.	106;182;206;206;257;106;206	B4DFT5;B4DXL3;Q13286-3;Q13286-4;B4DIA8;B4DMY6;Q13286	.;.;.;.;.;.;CLN3_HUMAN	V	128;206;206;206;152;106	ENSP00000443221:G128V;ENSP00000353073:G206V;ENSP00000353116:G206V;ENSP00000346650:G206V;ENSP00000350523:G152V;ENSP00000379014:G106V	ENSP00000346650:G206V	G	-	2	0	CLN3	28405229	1.000000	0.71417	1.000000	0.80357	0.240000	0.25518	6.412000	0.73303	2.654000	0.90174	0.651000	0.88453	GGC	.	.	.	none		0.687	CLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214115.2			A	28497728	C	A	28497728	3	1	267	1	0	0	0	0	1	0	0	0	3545	739	26	4	731	4	CLN3	16	28497728	Missense_Mutation	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10		28497728	61857025	81	16872											
TERF2IP	54386	hgsc.bcm.edu	37	chr16	75690303	75690303	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttaacttggatctatcaacaGttacacaggccttcctaaaa	14	12	5	10	0	2	0	1	0	1	0	3	1	3	1	2	2	3	1	2	2	6	6			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr16:75690303G>A	ENST00000300086.4	+	3	1091	c.994G>A	c.(994-996)Gtt>Att	p.V332I		NM_018975.3	NP_061848.2	Q9NYB0	TE2IP_HUMAN	telomeric repeat binding factor 2, interacting protein	332					negative regulation of DNA recombination at telomere (GO:0048239)|negative regulation of telomere maintenance (GO:0032205)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protection from non-homologous end joining at telomere (GO:0031848)|protein localization to chromosome, telomeric region (GO:0070198)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of transcription, DNA-templated (GO:0006355)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere lengthening (GO:0010833)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear chromosome (GO:0000228)|nuclear chromosome, telomeric region (GO:0000784)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)	5						TCTATCAACAGTTACACAGGC	0.453																																					p.V332I		Atlas-SNP	.											.	TERF2IP	17	.	0			c.G994A						PASS	.						159	161	160					16																	75690303		2198	4300	6498	SO:0001583	missense	54386	exon3			TCAACAGTTACAC	AK000669	CCDS32491.1	16q23.1	2012-10-03			ENSG00000166848	ENSG00000166848			19246	protein-coding gene	gene with protein product		605061				10850490	Standard	NM_018975		Approved	RAP1	uc002fet.2	Q9NYB0	OTTHUMG00000177136	ENST00000300086.4:c.994G>A	chr16.hg19:g.75690303G>A	ENSP00000300086:p.Val332Ile	214.0	0.0	.		181.0	45.0	.	NM_018975	B4DQN4|Q4W4Y2|Q8WYZ3|Q9NWR2	Missense_Mutation	SNP	ENST00000300086.4	hg19	CCDS32491.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.392384	0.83011	.	.	ENSG00000166848	ENST00000300086	T	0.45276	0.9	5.75	4.79	0.61399	.	0.055638	0.64402	N	0.000001	T	0.34454	0.0898	L	0.34521	1.04	0.44890	D	0.997905	B	0.21225	0.053	B	0.19666	0.026	T	0.16778	-1.0391	10	0.87932	D	0	-10.2609	13.2667	0.60137	0.0769:0.0:0.9231:0.0	.	332	Q9NYB0	TE2IP_HUMAN	I	332	ENSP00000300086:V332I	ENSP00000300086:V332I	V	+	1	0	TERF2IP	74247804	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.919000	0.56439	1.426000	0.47256	0.591000	0.81541	GTT	.	.	.	none		0.453	TERF2IP-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000435519.1	NM_018975		A	75690303	G	A	75690303	3	1	267	1	0	0	0	0	1	0	0	0	15775	1029	36	2	1004	2	TERF2IP	16	75690303	Missense_Mutation	SNP	G	TCGA-UZ-A9PX-01A-11D-A42J-10	47192575	75690303	14664450	82	16873											
STAT5A	6776	hgsc.bcm.edu	37	chr17	40461463	40461482	+	Frame_Shift_Del	DEL	CTGTGTGCCCCCAGGCTCCC	CTGTGTGCCCCCAGGCTCCC	-																															ggaccaggccccctccccagCtgtgtgcccccaggctccct																								rs552732197		TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	CTGTGTGCCCCCAGGCTCCC	CTGTGTGCCCCCAGGCTCCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr17:40461463_40461482delCTGTGTGCCCCCAGGCTCCC	ENST00000345506.4	+	19	2825_2844	c.2183_2202delCTGTGTGCCCCCAGGCTCCC	c.(2182-2202)gctgtgtgcccccaggctcccfs	p.AVCPQAP728fs	STAT5A_ENST00000588868.1_Frame_Shift_Del_p.AVCPQAP697fs|STAT5A_ENST00000546010.2_Frame_Shift_Del_p.AVCPQAP698fs|STAT5A_ENST00000587646.1_Frame_Shift_Del_p.AVCPQAP216fs|STAT5A_ENST00000590949.1_Frame_Shift_Del_p.AVCPQAP728fs|STAT5A_ENST00000452307.2_Frame_Shift_Del_p.AVCPQAP725fs	NM_003152.3	NP_003143.2	P42229	STA5A_HUMAN	signal transducer and activator of transcription 5A	728					2-oxoglutarate metabolic process (GO:0006103)|allantoin metabolic process (GO:0000255)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|citrate metabolic process (GO:0006101)|creatine metabolic process (GO:0006600)|creatinine metabolic process (GO:0046449)|development of secondary female sexual characteristics (GO:0046543)|development of secondary male sexual characteristics (GO:0046544)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|fatty acid metabolic process (GO:0006631)|female pregnancy (GO:0007565)|isoleucine metabolic process (GO:0006549)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|lipid storage (GO:0019915)|luteinization (GO:0001553)|mammary gland epithelium development (GO:0061180)|natural killer cell differentiation (GO:0001779)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of mast cell apoptotic process (GO:0033026)|oxaloacetate metabolic process (GO:0006107)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch development (GO:0048541)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mast cell differentiation (GO:0060376)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prolactin signaling pathway (GO:0038161)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of cell adhesion (GO:0030155)|regulation of epithelial cell differentiation (GO:0030856)|regulation of multicellular organism growth (GO:0040014)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|succinate metabolic process (GO:0006105)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|taurine metabolic process (GO:0019530)|transcription, DNA-templated (GO:0006351)|valine metabolic process (GO:0006573)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	calcium ion binding (GO:0005509)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	14		all_cancers(22;1.56e-06)|all_epithelial(22;3.17e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.128)		CCCTCCCCAGCTGTGTGCCCCCAGGCTCCCTATAACATGT	0.618																																					p.728_734del		Pindel	.											.	STAT5A	49	.	0			c.2182_2201del						PASS	.																																			SO:0001589	frameshift_variant	6776	exon19			.	U43185	CCDS11424.1, CCDS74066.1, CCDS74067.1	17q11.2	2013-02-14			ENSG00000126561	ENSG00000126561		"SH2 domain containing"	11366	protein-coding gene	gene with protein product		601511		STAT5		7719937, 8631883	Standard	NM_003152		Approved	MGF	uc002hzj.2	P42229	OTTHUMG00000150725	ENST00000345506.4:c.2183_2202delCTGTGTGCCCCCAGGCTCCC	chr17.hg19:g.40461463_40461482delCTGTGTGCCCCCAGGCTCCC	ENSP00000341208:p.Ala728fs	181.0	0.0	.		112.0	10.0	0.089	NM_003152	Q1KLZ6	Frame_Shift_Del	DEL	ENST00000345506.4	hg19	CCDS11424.1																																																																																			.	.	.	none		0.618	STAT5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319804.1	NM_003152		-	40461482	CTGTGTGCCCCCAGGCTCCC	-	40461463	7	5	267	1	0	1	0	1	0	0	0	0	15280	797	28	0	2249	0	STAT5A	17	40461463	Frame_Shift_Del	DEL	CTGTGTGCCCCCAGGCTCCC	TCGA-UZ-A9PX-01A-11D-A42J-10		40461463	40733747	83	16874											
UTP18	51096	hgsc.bcm.edu	37	chr17	49357809	49357809	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gttgcagcatccacattctcTtcagatagtaagaaagtata	14	12	7	8	0	2	2	1	0	1	2	4	2	3	2	1	0	2	5	1	0	5	7			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr17:49357809T>C	ENST00000225298.7	+	9	1230	c.1173T>C	c.(1171-1173)tcT>tcC	p.S391S		NM_016001.2	NP_057085.2	Q9Y5J1	UTP18_HUMAN	UTP18 small subunit (SSU) processome component homolog (yeast)	391					rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(3)|kidney(2)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16			BRCA - Breast invasive adenocarcinoma(22;2.09e-07)			CCACATTCTCTTCAGATAGTA	0.353																																					p.S391S		Atlas-SNP	.											.	UTP18	28	.	0			c.T1173C						PASS	.						72	66	68					17																	49357809		1846	4094	5940	SO:0001819	synonymous_variant	51096	exon9			ATTCTCTTCAGAT	AF151806	CCDS42362.1	17q21.33	2013-05-21	2011-12-09	2006-05-16	ENSG00000011260	ENSG00000011260		"WD repeat domain containing"	24274	protein-coding gene	gene with protein product		612816	"WD repeat domain 50"	WDR50		10810093, 8619474, 15590835	Standard	NM_016001		Approved	CGI-48	uc002its.3	Q9Y5J1	OTTHUMG00000162370	ENST00000225298.7:c.1173T>C	chr17.hg19:g.49357809T>C		403.0	0.0	.		356.0	87.0	.	NM_016001	Q9H4N6	Silent	SNP	ENST00000225298.7	hg19	CCDS42362.1																																																																																			.	.	.	none		0.353	UTP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368654.1	NM_016001		C	49357809	T	C	49357809	2	2	267	1	0	0	0	0	0	0	0	1	17110	1596	56	3		3	UTP18	17	49357809	Silent	SNP	T	TCGA-UZ-A9PX-01A-11D-A42J-10	8896346	49357809	31837401	84	16875											
DDX5	1655	hgsc.bcm.edu	37	chr17	62496750	62496750	+	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	gcacagagataaggtcgctcActtgctttatgttattaggt	10	14	10	7	1	1	1	1	0	0	1	2	2	1	1	0	2	1	4	0	2	4	6			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr17:62496750A>T	ENST00000225792.5	-	12	1759	c.1358T>A	c.(1357-1359)gTg>gAg	p.V453E	DDX5_ENST00000580026.1_5'UTR|DDX5_ENST00000578804.1_Missense_Mutation_p.V453E|DDX5_ENST00000450599.2_Missense_Mutation_p.V374E|MIR5047_ENST00000579212.1_RNA|MIR3064_ENST00000581130.1_RNA	NM_004396.3	NP_004387.1	P17844	DDX5_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 5	453	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cell growth (GO:0016049)|circadian rhythm (GO:0007623)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of osteoblast differentiation (GO:0045667)|regulation of skeletal muscle cell differentiation (GO:2001014)|regulation of viral genome replication (GO:0045069)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA helicase activity (GO:0003724)|transcription coactivator activity (GO:0003713)	p.V453A(2)		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)			AAGGTCGCTCACTTGCTTTAT	0.418			T	ETV4	prostate																																p.V453E	NSCLC(22;406 813 4871 19580 40307)	Atlas-SNP	.		Dom	yes		17	17q21	1655	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5		E	DDX5_ENST00000540698,colon,carcinoma,0,2	DDX5	101	.	2	Substitution - Missense(2)	large_intestine(2)	c.T1358A						PASS	.						159	141	147					17																	62496750		2203	4300	6503	SO:0001583	missense	1655	exon12			TCGCTCACTTGCT	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.1358T>A	chr17.hg19:g.62496750A>T	ENSP00000225792:p.Val453Glu	176.0	0.0	.		126.0	68.0	.	NM_004396	B4DLW8|B5BU21|D3DU32|E7ETL9|O75681|Q53Y61	Missense_Mutation	SNP	ENST00000225792.5	hg19	CCDS11659.1	.	.	.	.	.	.	.	.	.	.	A	8.939	0.965316	0.18583	.	.	ENSG00000108654	ENST00000540698;ENST00000450599;ENST00000225792	.	.	.	5.73	5.73	0.89815	Helicase, C-terminal (1);	0.103387	0.64402	D	0.000003	T	0.53384	0.1793	L	0.51914	1.62	0.80722	D	1	P;P;P	0.39576	0.471;0.679;0.679	B;B;B	0.35859	0.191;0.212;0.212	T	0.60229	-0.7304	9	0.87932	D	0	-5.3751	16.3123	0.82883	1.0:0.0:0.0:0.0	.	374;453;453	B4DLW8;B5BUE6;P17844	.;.;DDX5_HUMAN	E	453;383;442	.	ENSP00000225792:V442E	V	-	2	0	DDX5	59927212	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.406000	0.73276	2.308000	0.77769	0.533000	0.62120	GTG	.	.	.	none		0.418	DDX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444030.1	NM_004396		T	62496750	A	T	62496750	3	4	267	1	0	0	0	0	1	0	0	0	4369	159	6	5	494	5	DDX5	17	62496750	Missense_Mutation	SNP	A	TCGA-UZ-A9PX-01A-11D-A42J-10	13138941	62496750	18698460	85	16876											
SLC25A19	60386	hgsc.bcm.edu	37	chr17	73273495	73273495	+	Missense_Mutation	SNP	T	T	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	gtagccgcttcttgaagaggTccagcggatatgtcagggtc	8	10	14	9	2	2	2	1	1	1	1	4	3	3	3	2	3	2	2	2	3	3	4			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr17:73273495T>G	ENST00000402418.3	-	5	1622	c.713A>C	c.(712-714)gAc>gCc	p.D238A	SLC25A19_ENST00000442286.2_Missense_Mutation_p.D238A|SLC25A19_ENST00000580994.1_Missense_Mutation_p.D238A|SLC25A19_ENST00000375261.4_Missense_Mutation_p.D181A|SLC25A19_ENST00000416858.2_Missense_Mutation_p.D238A|SLC25A19_ENST00000320362.3_Missense_Mutation_p.D238A			Q9HC21	TPC_HUMAN	solute carrier family 25 (mitochondrial thiamine pyrophosphate carrier), member 19	238					deoxynucleotide transport (GO:0030302)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	deoxynucleotide transmembrane transporter activity (GO:0030233)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9	all_cancers(13;5.98e-08)|all_epithelial(9;1.16e-08)|Breast(9;3.1e-08)		all cancers(21;6.82e-07)|Epithelial(20;6.86e-06)			CTTGAAGAGGTCCAGCGGATA	0.557																																					p.D238A		Atlas-SNP	.											.	SLC25A19	25	.	0			c.A713C						PASS	.						101	85	90					17																	73273495		2203	4300	6503	SO:0001583	missense	60386	exon6			AAGAGGTCCAGCG		CCDS11720.1	17q25.1	2013-05-22	2007-03-08		ENSG00000125454	ENSG00000125454		"Solute carriers"	14409	protein-coding gene	gene with protein product		606521	"solute carrier family 25 (mitochondrial deoxynucleotide carrier), member 19", "microcephaly, Amish"	MCPHA		11474176, 11226231, 19798730	Standard	NM_021734		Approved	DNC, MUP1, TPC	uc002jnw.4	Q9HC21		ENST00000402418.3:c.713A>C	chr17.hg19:g.73273495T>G	ENSP00000385312:p.Asp238Ala	103.0	0.0	.		56.0	13.0	.	NM_001126122	E9PF74|Q6V9R7	Missense_Mutation	SNP	ENST00000402418.3	hg19	CCDS11720.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.511535	0.85389	.	.	ENSG00000125454	ENST00000416858;ENST00000442286;ENST00000320362;ENST00000402418;ENST00000375261	D;D;D;D;D	0.84370	-1.84;-1.84;-1.84;-1.84;-1.84	5.35	5.35	0.76521	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.94486	0.8225	H	0.95884	3.735	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94730	0.7909	10	0.31617	T	0.26	-39.7112	15.0367	0.71754	0.0:0.0:0.0:1.0	.	181;238	E9PF74;Q9HC21	.;TPC_HUMAN	A	238;238;238;238;181	ENSP00000397818:D238A;ENSP00000402202:D238A;ENSP00000319574:D238A;ENSP00000385312:D238A;ENSP00000364410:D181A	ENSP00000319574:D238A	D	-	2	0	SLC25A19	70785090	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	7.698000	0.84413	2.033000	0.60031	0.528000	0.53228	GAC	.	.	.	none		0.557	SLC25A19-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447282.1	NM_021734		G	73273495	T	G	73273495	3	3	267	1	0	0	0	0	1	0	0	0	14494	1667	58	5	257	5	SLC25A19	17	73273495	Missense_Mutation	SNP	T	TCGA-UZ-A9PX-01A-11D-A42J-10	10776745	73273495	7921715	86	16877											
ALPK2	115701	hgsc.bcm.edu	37	chr18	56202906	56202906	+	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	gcctatgctacatccacttgGaattctttcaccgccttcgc	7	13	6	15	2	2	0	1	0	1	0	4	1	3	1	4	1	2	1	4	1	3	6			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr18:56202906G>C	ENST00000361673.3	-	5	4726	c.4513C>G	c.(4513-4515)Cca>Gca	p.P1505A	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1505						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						CATCCACTTGGAATTCTTTCA	0.483																																					p.P1505A		Atlas-SNP	.											.	ALPK2	487	.	0			c.C4513G						PASS	.						86	88	88					18																	56202906		2203	4300	6503	SO:0001583	missense	115701	exon5			CACTTGGAATTCT	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.4513C>G	chr18.hg19:g.56202906G>C	ENSP00000354991:p.Pro1505Ala	172.0	0.0	.		90.0	31.0	.	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	hg19	CCDS11966.2	.	.	.	.	.	.	.	.	.	.	G	16.71	3.199585	0.58126	.	.	ENSG00000198796	ENST00000361673	T	0.68624	-0.34	5.68	3.88	0.44766	.	10.063900	0.00166	N	0.000004	T	0.68495	0.3007	L	0.43152	1.355	0.23468	N	0.997617	D;P	0.54047	0.964;0.952	P;B	0.48873	0.593;0.335	T	0.54153	-0.8336	10	0.72032	D	0.01	-9.3927	7.1825	0.25780	0.0892:0.1733:0.7374:0.0	.	1500;1505	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	A	1505	ENSP00000354991:P1505A	ENSP00000354991:P1505A	P	-	1	0	ALPK2	54353886	0.353000	0.24904	0.156000	0.22583	0.066000	0.16364	1.417000	0.34770	1.385000	0.46445	0.563000	0.77884	CCA	.	.	.	none		0.483	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		C	56202906	G	C	56202906	3	2	267	1	0	0	0	0	1	0	0	0	545	1174	41	4	2035	4	ALPK2	18	56202906	Missense_Mutation	SNP	G	TCGA-UZ-A9PX-01A-11D-A42J-10		56202906	21874342	87	16878											
ADAMTS10	81794	hgsc.bcm.edu	37	chr19	8661948	8661948	+	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	ccatggccgctgtggttcacGatggatttctgccacttaca	7	12	10	12	2	2	0	1	0	1	0	2	2	2	1	3	3	2	2	3	3	1	3			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr19:8661948G>A	ENST00000597188.1	-	8	1233	c.963C>T	c.(961-963)atC>atT	p.I321I	ADAMTS10_ENST00000596709.1_5'Flank|ADAMTS10_ENST00000270328.4_Silent_p.I321I	NM_030957.2	NP_112219.3	Q9H324	ATS10_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 10	321	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					extracellular matrix (GO:0031012)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(16)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(3)|skin(10)|urinary_tract(1)	53						TGTGGTTCACGATGGATTTCT	0.572																																					p.I321I		Atlas-SNP	.											.	ADAMTS10	132	.	0			c.C963T						PASS	.						102	89	94					19																	8661948		2203	4300	6503	SO:0001819	synonymous_variant	81794	exon8			GTTCACGATGGAT	AF163762	CCDS12206.1, CCDS62529.1	19p13.2	2014-08-12	2005-08-19		ENSG00000142303	ENSG00000142303		"ADAM metallopeptidases with thrombospondin type 1 motif"	13201	protein-coding gene	gene with protein product		608990	"a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 10"				Standard	XM_005272499		Approved	ADAM-TS10	uc002mkj.1	Q9H324	OTTHUMG00000182216	ENST00000597188.1:c.963C>T	chr19.hg19:g.8661948G>A		79.0	0.0	.		63.0	28.0	.	NM_030957	M0QZE4	Silent	SNP	ENST00000597188.1	hg19	CCDS12206.1																																																																																			.	.	.	none		0.572	ADAMTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460085.3	NM_030957		A	8661948	G	A	8661948	2	1	267	1	0	0	0	0	0	0	0	1	256	1048	37	1		1	ADAMTS10	19	8661948	Silent	SNP	G	TCGA-UZ-A9PX-01A-11D-A42J-10		8661948	50467035	88	16879											
KLF1	10661	hgsc.bcm.edu	37	chr19	12996546	12996546	+	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	ggccccgggtacaccggttgCagcgccagcgccttgggctc	4	6	15	16	4	0	0	0	0	0	0	1	0	0	0	5	4	4	4	5	4	1	3			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr19:12996546C>A	ENST00000264834.4	-	2	538	c.498G>T	c.(496-498)ctG>ctT	p.L166L	CTD-2265O21.7_ENST00000592400.1_RNA	NM_006563.3	NP_006554.1	Q13351	KLF1_HUMAN	Kruppel-like factor 1 (erythroid)	166	Pro-rich.				cellular response to peptide (GO:1901653)|chromatin remodeling (GO:0006338)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|erythrocyte maturation (GO:0043249)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(3)|large_intestine(1)|skin(1)	5		Hepatocellular(1079;0.137)		GBM - Glioblastoma multiforme(1328;0.00016)|Lung(535;0.171)|STAD - Stomach adenocarcinoma(1328;0.18)		ACACCGGTTGCAGCGCCAGCG	0.781																																					p.L166L		Atlas-SNP	.											.	KLF1	15	.	0			c.G498T						PASS	.						1	1	1					19																	12996546		684	1693	2377	SO:0001819	synonymous_variant	10661	exon2			CGGTTGCAGCGCC	U37106	CCDS12285.1	19p13.2	2014-07-18			ENSG00000105610	ENSG00000105610		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	6345	protein-coding gene	gene with protein product	"erythroid Kruppel-like factor"	600599				8924208, 9119377	Standard	NM_006563		Approved	EKLF	uc002mvo.3	Q13351	OTTHUMG00000180536	ENST00000264834.4:c.498G>T	chr19.hg19:g.12996546C>A		61.0	0.0	.		37.0	18.0	.	NM_006563	Q6PIJ5|Q92899	Silent	SNP	ENST00000264834.4	hg19	CCDS12285.1																																																																																			.	.	.	none		0.781	KLF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451794.1	NM_006563		A	12996546	C	A	12996546	2	1	267	1	0	0	0	0	0	0	0	1	8344	697	25	4		4	KLF1	19	12996546	Silent	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	4334598	12996546	46132437	89	16880											
CYP4F2	8529	hgsc.bcm.edu	37	chr19	16006325	16006325	+	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	ccagatggtacctgaggcgtTgatgacagaccggatgatgt	10	9	14	8	2	0	6	0	4	0	2	0	7	0	7	3	3	1	2	3	3	1	2			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr19:16006325T>A	ENST00000221700.6	-	3	429	c.334A>T	c.(334-336)Aac>Tac	p.N112Y	CYP4F2_ENST00000011989.7_Intron	NM_001082.3	NP_001073.3			cytochrome P450, family 4, subfamily F, polypeptide 2											NS(2)|breast(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						CCTGAGGCGTTGATGACAGAC	0.607																																					p.N112Y		Atlas-SNP	.											.	CYP4F2	97	.	0			c.A334T						PASS	.						124	134	131					19																	16006325		2203	4300	6503	SO:0001583	missense	8529	exon3			AGGCGTTGATGAC	U02388	CCDS12336.1	19p13.12	2013-11-11	2003-01-14		ENSG00000186115	ENSG00000186115		"Cytochrome P450s"	2645	protein-coding gene	gene with protein product		604426	"cytochrome P450, subfamily IVF, polypeptide 2"			8424651, 8026587	Standard	NM_001082		Approved		uc002nbs.1	P78329	OTTHUMG00000185995	ENST00000221700.6:c.334A>T	chr19.hg19:g.16006325T>A	ENSP00000221700:p.Asn112Tyr	69.0	0.0	.		34.0	15.0	.	NM_001082		Missense_Mutation	SNP	ENST00000221700.6	hg19	CCDS12336.1	.	.	.	.	.	.	.	.	.	.	t	10.88	1.475353	0.26511	.	.	ENSG00000186115	ENST00000221700	D	0.95171	-3.63	3.13	2.1	0.27182	.	0.598081	0.13811	U	0.361135	D	0.90642	0.7065	M	0.62209	1.925	0.09310	N	1	B	0.02656	0.0	B	0.12837	0.008	T	0.80211	-0.1476	10	0.32370	T	0.25	.	3.9592	0.09403	0.0:0.2815:0.0:0.7185	.	112	P78329	CP4F2_HUMAN	Y	112	ENSP00000221700:N112Y	ENSP00000221700:N112Y	N	-	1	0	CYP4F2	15867325	0.008000	0.16893	0.003000	0.11579	0.625000	0.37756	1.889000	0.39718	1.414000	0.47017	0.254000	0.18369	AAC	.	.	.	none		0.607	CYP4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460372.3	NM_001082		A	16006325	T	A	16006325	3	1	267	1	0	0	0	0	1	0	0	0	4190	1812	63	5	1272	5	CYP4F2	19	16006325	Missense_Mutation	SNP	T	TCGA-UZ-A9PX-01A-11D-A42J-10	3009779	16006325	43122658	90	16881											
UNC13A	23025	hgsc.bcm.edu	37	chr19	17722656	17722656	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcacccacagggtcttctaCacccaagcctgggcagggca	9	7	10	15	0	3	0	1	0	2	0	3	0	3	0	3	3	2	2	3	3	2	3			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr19:17722656C>T	ENST00000519716.2	-	42	4566	c.4567G>A	c.(4567-4569)Gta>Ata	p.V1523I	UNC13A_ENST00000252773.7_Missense_Mutation_p.V1523I|UNC13A_ENST00000552293.1_Missense_Mutation_p.V1517I|UNC13A_ENST00000428389.2_Missense_Mutation_p.V1611I|UNC13A_ENST00000551649.1_Missense_Mutation_p.V1542I|UNC13A_ENST00000550896.1_Missense_Mutation_p.V1496I|CTD-3149D2.3_ENST00000600512.1_RNA	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	1523					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						GGGTCTTCTACACCCAAGCCT	0.587																																					p.V1523I		Atlas-SNP	.											.	UNC13A	299	.	0			c.G4567A						PASS	.						102	101	102					19																	17722656		2111	4245	6356	SO:0001583	missense	23025	exon40			CTTCTACACCCAA	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.4567G>A	chr19.hg19:g.17722656C>T	ENSP00000429562:p.Val1523Ile	119.0	0.0	.		59.0	22.0	.	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	hg19	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	C	17.36	3.371221	0.61624	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	T;T;T;T;T;T	0.80824	-1.41;-1.42;-1.41;-1.29;-1.27;-1.38	4.75	4.75	0.60458	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.64402	U	0.000002	T	0.72614	0.3482	L	0.32530	0.975	0.43761	D	0.996277	B	0.15719	0.014	B	0.20384	0.029	T	0.67952	-0.5537	10	0.32370	T	0.25	-16.2067	15.3216	0.74126	0.0:1.0:0.0:0.0	.	1523	Q9UPW8	UN13A_HUMAN	I	1523;1611;1523;1542;1517;1496	ENSP00000429562:V1523I;ENSP00000400409:V1611I;ENSP00000252773:V1523I;ENSP00000447236:V1542I;ENSP00000447572:V1517I;ENSP00000446831:V1496I	ENSP00000252773:V1523I	V	-	1	0	UNC13A	17583656	0.982000	0.34865	0.962000	0.40283	0.916000	0.54674	3.975000	0.56859	2.209000	0.71365	0.549000	0.68633	GTA	.	.	.	none		0.587	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		T	17722656	C	T	17722656	3	4	267	1	0	0	0	0	1	0	0	0	16996	478	17	2	556	2	UNC13A	19	17722656	Missense_Mutation	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	1716331	17722656	41406327	91	16882											
SLC25A42	284439	hgsc.bcm.edu	37	chr19	19217183	19217183	+	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	agagcgcggatggccgtaacCccgaaggaaatgtgagtcct	11	6	14	10	4	0	2	0	1	0	1	1	5	1	4	4	3	2	1	4	3	3	1			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr19:19217183C>A	ENST00000318596.7	+	6	637	c.486C>A	c.(484-486)acC>acA	p.T162T	SLC25A42_ENST00000600275.1_3'UTR	NM_178526.4	NP_848621.2	Q86VD7	S2542_HUMAN	solute carrier family 25, member 42	162					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)			TGGCCGTAACCCCGAAGGAAA	0.657																																					p.T162T		Atlas-SNP	.											.	SLC25A42	18	.	0			c.C486A						PASS	.						67	64	65					19																	19217183		2203	4300	6503	SO:0001819	synonymous_variant	284439	exon6			CGTAACCCCGAAG		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.486C>A	chr19.hg19:g.19217183C>A		55.0	0.0	.		24.0	10.0	.	NM_178526	D2T2J5|O14553|O43378	Silent	SNP	ENST00000318596.7	hg19	CCDS32966.1																																																																																			.	.	.	none		0.657	SLC25A42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465931.1	NM_178526		A	19217183	C	A	19217183	2	1	267	1	0	0	0	0	0	0	0	1	14520	610	22	4		4	SLC25A42	19	19217183	Silent	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	1494527	19217183	39911800	92	16883											
MAG	4099	hgsc.bcm.edu	37	chr19	35800864	35800864	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgaagtccaacccggagcCgtccgtggcctttgagctgc	6	8	14	13	3	0	2	0	2	0	0	2	3	2	3	5	3	4	1	5	3	2	1			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr19:35800864C>T	ENST00000392213.3	+	8	1478	c.1319C>T	c.(1318-1320)cCg>cTg	p.P440L	MAG_ENST00000361922.4_Missense_Mutation_p.P440L|MAG_ENST00000593348.1_3'UTR|MAG_ENST00000537831.2_Missense_Mutation_p.P415L	NM_002361.3	NP_002352.1	P20916	MAG_HUMAN	myelin associated glycoprotein	440	Ig-like C2-type 4.				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)			AACCCGGAGCCGTCCGTGGCC	0.662																																					p.P440L		Atlas-SNP	.											.	MAG	172	.	0			c.C1319T						PASS	.						78	73	75					19																	35800864		2203	4300	6503	SO:0001583	missense	4099	exon8			CGGAGCCGTCCGT	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.1319C>T	chr19.hg19:g.35800864C>T	ENSP00000376048:p.Pro440Leu	121.0	0.0	.		77.0	32.0	.	NM_080600	B7Z2E5|F5GYC0|Q567S4	Missense_Mutation	SNP	ENST00000392213.3	hg19	CCDS12455.1	.	.	.	.	.	.	.	.	.	.	C	17.25	3.342867	0.61073	.	.	ENSG00000105695	ENST00000262624;ENST00000361922;ENST00000392213;ENST00000537831	T;T;T	0.18338	2.22;2.22;2.22	4.8	3.74	0.42951	.	0.056265	0.64402	D	0.000001	T	0.24122	0.0584	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	0.981;1.0;0.999	B;P;P	0.61132	0.373;0.884;0.78	T	0.02345	-1.1173	10	0.87932	D	0	.	12.0011	0.53230	0.1744:0.8256:0.0:0.0	.	477;440;440	Q59GD9;P20916;Q567S4	.;MAG_HUMAN;.	L	477;440;440;415	ENSP00000355234:P440L;ENSP00000376048:P440L;ENSP00000440695:P415L	ENSP00000262624:P477L	P	+	2	0	MAG	40492704	0.999000	0.42202	0.772000	0.31596	0.697000	0.40408	5.287000	0.65645	1.212000	0.43366	0.462000	0.41574	CCG	.	.	.	none		0.662	MAG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466071.1	NM_080600		T	35800864	C	T	35800864	3	4	267	1	0	0	0	0	1	0	0	0	9169	652	23	1	1341	1	MAG	19	35800864	Missense_Mutation	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	16583681	35800864	23328119	93	16884											
LTBP4	8425	hgsc.bcm.edu	37	chr19	41117892	41117892	+	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	gctggctccgagtgcgagggTgaggccggggagggagggag	6	4	24	7	3	0	1	0	1	0	0	1	6	1	4	2	7	1	2	2	7	0	0	rs1131621		TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr19:41117892T>A	ENST00000602240.1	+	17	2269		c.e17+2		LTBP4_ENST00000545697.1_Splice_Site|LTBP4_ENST00000204005.9_Splice_Site|LTBP4_ENST00000396819.3_Splice_Site|LTBP4_ENST00000243562.9_5'Flank|LTBP4_ENST00000308370.7_Splice_Site			Q8N2S1	LTBP4_HUMAN	latent transforming growth factor beta binding protein 4						extracellular matrix organization (GO:0030198)|growth hormone secretion (GO:0030252)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|regulation of cell differentiation (GO:0045595)|regulation of cell growth (GO:0001558)|regulation of proteolysis (GO:0030162)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|integrin binding (GO:0005178)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			central_nervous_system(1)	1			Lung(22;0.000158)|LUSC - Lung squamous cell carcinoma(20;0.000384)			AGTGCGAGGGTGAGGCCGGGG	0.637																																					.		Atlas-SNP	.											.	LTBP4	101	.	0			c.2269+2T>A						PASS	.						30	35	33					19																	41117892		2099	4214	6313	SO:0001630	splice_region_variant	8425	exon17			CGAGGGTGAGGCC	Y13622	CCDS74368.1, CCDS74369.1, CCDS74370.1	19q13.1-q13.2	2011-10-20				ENSG00000090006		"Latent transforming growth factor, beta binding proteins"	6717	protein-coding gene	gene with protein product		604710				9660815, 9271198	Standard	NM_003573		Approved	LTBP-4, LTBP-4L, FLJ46318, FLJ90018	uc002ooh.1	Q8N2S1		ENST00000602240.1:c.2269+2T>A	chr19.hg19:g.41117892T>A		79.0	0.0	.		67.0	33.0	.	NM_003573	O00508|O75412|O75413	Splice_Site	SNP	ENST00000602240.1	hg19		.	.	.	.	.	.	.	.	.	.	T	16.01	3.000075	0.54147	.	.	ENSG00000090006	ENST00000204005;ENST00000545697;ENST00000308370;ENST00000396819	.	.	.	4.5	4.5	0.54988	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.0527	0.58964	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	LTBP4	45809732	1.000000	0.71417	1.000000	0.80357	0.626000	0.37791	4.489000	0.60309	1.800000	0.52685	0.459000	0.35465	.	.	.	.	none		0.637	LTBP4-002	KNOWN	sequence_error|basic	processed_transcript	protein_coding	OTTHUMT00000462815.2	NM_003573	Intron	A	41117892	T	A	41117892	5	1	267	1	0	0	0	0	0	0	1	0	9083	1710	59	5	2741	5	LTBP4	19	41117892	Splice_Site	SNP	T	TCGA-UZ-A9PX-01A-11D-A42J-10	5317028	41117892	18011091	94	16885											
ESF1	51575	hgsc.bcm.edu	37	chr20	13756539	13756540	+	Frame_Shift_Ins	INS	-	-	T																															tcatcagcacgaggagcatcINStttatctaattctctccaag																								rs138569918	byFrequency	TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr20:13756539_13756540insT	ENST00000202816.1	-	3	1121_1122	c.1014_1015insA	c.(1012-1017)aaagatfs	p.D339fs		NM_001276380.1|NM_016649.3	NP_001263309.1|NP_057733.2	Q9H501	ESF1_HUMAN	ESF1, nucleolar pre-rRNA processing protein, homolog (S. cerevisiae)	339					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|skin(1)|stomach(1)	31						CGAGGAGCATCTTTATCTAATT	0.361																																					p.D339fs		Atlas-Indel,Pindel	.											.	ESF1	77	.	0			c.1015_1016insA						PASS	.																																			SO:0001589	frameshift_variant	51575	exon3			.		CCDS13117.1	20p12.1	2007-02-12	2006-11-13	2006-11-13	ENSG00000089048	ENSG00000089048			15898	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 6"	C20orf6			Standard	NM_016649		Approved	bA526K24.1	uc002wok.2	Q9H501	OTTHUMG00000031906	ENST00000202816.1:c.1015dupA	chr20.hg19:g.13756542_13756542dupT	ENSP00000202816:p.Asp339fs	134.0	0.0	0		76.0	28.0	0.368421	NM_016649	Q86X92|Q9H9Q5|Q9HA35|Q9NX93|Q9P1S6	Frame_Shift_Ins	INS	ENST00000202816.1	hg19	CCDS13117.1																																																																																			.	.	.	none		0.361	ESF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078049.1	NM_016649		T	13756540	-	T	13756539	7	5	267	1	0	1	1	0	0	0	0	0	5253	913	32	0	1588	0	ESF1	20	13756539	Frame_Shift_Ins	INS	-	TCGA-UZ-A9PX-01A-11D-A42J-10		13756539	49268981	95	16886											
ACSS2	55902	hgsc.bcm.edu	37	chr20	33470621	33470621	+	Frame_Shift_Del	DEL	A	A	-																															ctggggagacattgccaaggAattttactggaagactccat																										TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr20:33470621delA	ENST00000360596.2	+	2	414	c.203delA	c.(202-204)gaafs	p.E68fs	ACSS2_ENST00000476922.1_3'UTR|ACSS2_ENST00000336325.4_Frame_Shift_Del_p.E18fs|ACSS2_ENST00000253382.5_Frame_Shift_Del_p.E68fs	NM_018677.3	NP_061147.1	Q9NR19	ACSA_HUMAN	acyl-CoA synthetase short-chain family member 2	68					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)	ATTGCCAAGGAATTTTACTGG	0.428																																					p.E68fs		Atlas-Indel,Pindel	.											.	ACSS2	75	.	0			c.202delG						PASS	.						105	100	102					20																	33470621		2203	4300	6503	SO:0001589	frameshift_variant	55902	exon2			.	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.203delA	chr20.hg19:g.33470621delA	ENSP00000353804:p.Glu68fs	171.0	0.0	0		90.0	33.0	0.366667	NM_001076552	A6NE90|Q5QPH2|Q5QPH3|Q8N238|Q96EL0|Q9NQP7|Q9UJ15	Frame_Shift_Del	DEL	ENST00000360596.2	hg19	CCDS13243.1																																																																																			.	.	.	none		0.428	ACSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078823.3	NM_018677		-	33470621	A	-	33470621	7	5	267	1	0	1	0	1	0	0	0	0	189	246	9	0	209	0	ACSS2	20	33470621	Frame_Shift_Del	DEL	A	TCGA-UZ-A9PX-01A-11D-A42J-10	19714082	33470621	29554899	96	16887											
LSM14B	149986	hgsc.bcm.edu	37	chr20	60705652	60705652	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taacgttaaggaaaacacaaTcaaatttgagggtgactttg	16	11	9	5	1	1	2	1	2	0	0	1	3	1	3	0	2	2	1	0	2	6	4			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr20:60705652T>C	ENST00000279068.6	+	6	900	c.740T>C	c.(739-741)aTc>aCc	p.I247T	LSM14B_ENST00000253001.4_Missense_Mutation_p.I247T	NM_144703.2	NP_653304.2	Q9BX40	LS14B_HUMAN	LSM14B, SCD6 homolog B (S. cerevisiae)	247	DFDF. {ECO:0000255|PROSITE- ProRule:PRU00845}.				multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)	ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|lung(4)	8	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.28e-07)			GAAAACACAATCAAATTTGAG	0.438																																					p.I247T		Atlas-SNP	.											.	LSM14B	62	.	0			c.T740C						PASS	.						93	89	90					20																	60705652		1896	4113	6009	SO:0001583	missense	149986	exon6			ACACAATCAAATT	AF172328	CCDS46626.1	20q13.33	2010-01-27	2006-12-21	2006-01-24	ENSG00000149657	ENSG00000149657			15887	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 40", "family with sequence similarity 61, member B", "LSM14 homolog B (SCD6, S. cerevisiae)"	C20orf40, FAM61B			Standard	NM_144703		Approved	FT005, bA11M20.3, FLJ25473, LSM13, RAP55B	uc010gjy.1	Q9BX40	OTTHUMG00000032901	ENST00000279068.6:c.740T>C	chr20.hg19:g.60705652T>C	ENSP00000279068:p.Ile247Thr	220.0	0.0	.		110.0	44.0	.	NM_144703	Q6PFW8|Q96LH8	Missense_Mutation	SNP	ENST00000279068.6	hg19	CCDS46626.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.657274	0.88154	.	.	ENSG00000149657	ENST00000279068;ENST00000253001;ENST00000444156;ENST00000400318;ENST00000279069;ENST00000370906;ENST00000361670	T;T;T;T	0.44881	0.98;0.93;0.96;0.91	5.59	5.59	0.84812	.	0.055865	0.64402	D	0.000001	T	0.55705	0.1937	L	0.36672	1.1	0.51233	D	0.999912	D;D;D;D;D	0.69078	0.997;0.997;0.997;0.997;0.974	D;D;D;D;P	0.83275	0.994;0.994;0.994;0.996;0.647	T	0.58719	-0.7587	10	0.72032	D	0.01	.	15.4482	0.75248	0.0:0.0:0.0:1.0	.	167;203;247;273;247	E9PG81;C9J454;Q9BX40;Q5TBQ0;Q9BX40-2	.;.;LS14B_HUMAN;.;.	T	247;247;203;273;221;203;167	ENSP00000279068:I247T;ENSP00000253001:I247T;ENSP00000383172:I273T;ENSP00000355209:I167T	ENSP00000253001:I247T	I	+	2	0	LSM14B	60139047	1.000000	0.71417	0.999000	0.59377	0.910000	0.53928	7.768000	0.85345	2.125000	0.65367	0.454000	0.30748	ATC	.	.	.	none		0.438	LSM14B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079996.4	NM_144703		C	60705652	T	C	60705652	3	2	267	1	0	0	0	0	1	0	0	0	9062	1435	50	3	762	3	LSM14B	20	60705652	Missense_Mutation	SNP	T	TCGA-UZ-A9PX-01A-11D-A42J-10	27235031	60705652	2319868	97	16888											
BCL2L13	23786	hgsc.bcm.edu	37	chr22	18185096	18185096	+	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	tgagcgcactgctgcagtttGgcgtgacatacctggaggac	8	9	14	10	2	0	2	0	2	0	0	0	4	0	4	1	3	4	4	1	3	1	2			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr22:18185096G>A	ENST00000317582.5	+	6	891	c.544G>A	c.(544-546)Ggc>Agc	p.G182S	BCL2L13_ENST00000355028.3_Intron|BCL2L13_ENST00000543133.1_Missense_Mutation_p.G20S|BCL2L13_ENST00000399782.1_Missense_Mutation_p.G182S|BCL2L13_ENST00000337612.5_Missense_Mutation_p.G20S|BCL2L13_ENST00000538149.1_Missense_Mutation_p.G58S|BCL2L13_ENST00000493680.1_Missense_Mutation_p.G182S|BCL2L13_ENST00000418951.2_Intron	NM_015367.3	NP_056182.2	Q9BXK5	B2L13_HUMAN	BCL2-like 13 (apoptosis facilitator)	182					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			breast(2)|central_nervous_system(1)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|skin(3)|urinary_tract(2)	15		all_epithelial(15;0.123)		Lung(27;0.199)		GCTGCAGTTTGGCGTGACATA	0.408																																					p.W106X		Atlas-SNP	.											.	BCL2L13	27	.	0			c.G317A						PASS	.						115	108	110					22																	18185096		2203	4300	6503	SO:0001583	missense	23786	exon4			CAGTTTGGCGTGA	AF146568	CCDS13746.1, CCDS59447.1, CCDS59448.1, CCDS74810.1, CCDS74811.1, CCDS74812.1, CCDS74813.1, CCDS74814.1	22q11	2014-03-07			ENSG00000099968	ENSG00000099968			17164	protein-coding gene	gene with protein product						11262395, 11381032	Standard	NM_015367		Approved	MIL1, BCL-RAMBO	uc002zmw.4	Q9BXK5	OTTHUMG00000150088	ENST00000317582.5:c.544G>A	chr22.hg19:g.18185096G>A	ENSP00000318883:p.Gly182Ser	173.0	0.0	.		88.0	35.0	.	NM_001270732	B3KPE7|Q96B37|Q96IB7|Q9BY01|Q9HC05|Q9UFE0|Q9UKN3	Nonsense_Mutation	SNP	ENST00000317582.5	hg19	CCDS13746.1	.	.	.	.	.	.	.	.	.	.	G	34	5.326602	0.95708	.	.	ENSG00000099968	ENST00000399782;ENST00000317582;ENST00000543133;ENST00000538149;ENST00000337612;ENST00000493680	T;T;T;T;T;T	0.04551	3.6;3.6;3.6;3.6;3.6;3.6	5.95	5.95	0.96441	Apoptosis regulator, Bcl2-like (1);Apoptosis regulator, Bcl-2, BH (2);	0.000000	0.85682	D	0.000000	T	0.22282	0.0537	M	0.69823	2.125	0.58432	D	0.999991	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	T	0.00008	-1.2486	10	0.54805	T	0.06	-13.5484	18.1662	0.89727	0.0:0.0:1.0:0.0	.	58;182;182	B7Z238;Q9BXK5;Q9BXK5-2	.;B2L13_HUMAN;.	S	182;182;20;58;20;182	ENSP00000382682:G182S;ENSP00000318883:G182S;ENSP00000437667:G20S;ENSP00000441344:G58S;ENSP00000338932:G20S;ENSP00000434764:G182S	ENSP00000318883:G182S	G	+	1	0	BCL2L13	16565096	1.000000	0.71417	0.994000	0.49952	0.868000	0.49771	5.477000	0.66799	2.824000	0.97209	0.655000	0.94253	GGC	.	.	.	none		0.408	BCL2L13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316184.1	NM_015367		A	18185096	G	A	18185096	3	1	267	1	0	0	0	0	1	0	0	0	1371	1348	47	2	562	2	BCL2L13	22	18185096	Missense_Mutation	SNP	G	TCGA-UZ-A9PX-01A-11D-A42J-10		18185096	33119470	98	16889											
TCN2	6948	hgsc.bcm.edu	37	chr22	31011613	31011613	+	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	catgacttcccccatgcgtgGggcagaactgggaacagcat	10	7	12	12	1	0	2	0	1	0	1	1	3	1	3	2	3	4	2	2	3	2	1			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr22:31011613G>A	ENST00000215838.3	+	6	1273	c.779G>A	c.(778-780)gGg>gAg	p.G260E	TCN2_ENST00000405742.3_Missense_Mutation_p.G256E|TCN2_ENST00000407817.3_Missense_Mutation_p.G233E			P20062	TCO2_HUMAN	transcobalamin II	260					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)	CCCATGCGTGGGGCAGAACTG	0.572																																					p.G260E		Atlas-SNP	.											.	TCN2	44	.	0			c.G779A						PASS	.						71	63	66					22																	31011613		2203	4300	6503	SO:0001583	missense	6948	exon6			TGCGTGGGGCAGA		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.779G>A	chr22.hg19:g.31011613G>A	ENSP00000215838:p.Gly260Glu	102.0	0.0	.		46.0	15.0	.	NM_000355	Q96FD4|Q9BVI8|Q9UCI5|Q9UCI6|Q9UDM0	Missense_Mutation	SNP	ENST00000215838.3	hg19	CCDS13881.1	.	.	.	.	.	.	.	.	.	.	G	0.301	-0.974151	0.02215	.	.	ENSG00000185339	ENST00000215838;ENST00000405742;ENST00000407817	T;T;T	0.24908	1.83;1.83;1.83	5.33	-0.87	0.10646	.	0.953276	0.08911	N	0.875895	T	0.17365	0.0417	L	0.46157	1.445	0.09310	N	1	B;B;B	0.17465	0.022;0.017;0.017	B;B;B	0.17433	0.018;0.007;0.007	T	0.39961	-0.9588	10	0.02654	T	1	-0.0037	7.6817	0.28518	0.1555:0.4063:0.4382:0.0	.	233;256;260	Q96FD4;B5MBX2;P20062	.;.;TCO2_HUMAN	E	260;256;233	ENSP00000215838:G260E;ENSP00000385914:G256E;ENSP00000384914:G233E	ENSP00000215838:G260E	G	+	2	0	TCN2	29341613	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.178000	0.16820	0.147000	0.19030	-0.150000	0.13652	GGG	.	.	.	none		0.572	TCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321282.2	NM_000355		A	31011613	G	A	31011613	3	1	267	1	0	0	0	0	1	0	0	0	15719	1232	43	2	801	2	TCN2	22	31011613	Missense_Mutation	SNP	G	TCGA-UZ-A9PX-01A-11D-A42J-10	12826517	31011613	20292953	99	16890											
RNF185	91445	hgsc.bcm.edu	37	chr22	31600511	31600511	+	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	ccagtatgtggacgagcagtTcctgtcacgcctcttcctat	7	12	9	13	2	2	0	1	0	1	0	4	2	4	1	4	1	1	3	4	1	2	4			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr22:31600511T>A	ENST00000326132.6	+	7	677	c.518T>A	c.(517-519)tTc>tAc	p.F173Y	RNF185-AS1_ENST00000526089.1_RNA|RNF185_ENST00000266252.7_Missense_Mutation_p.F117Y|RNF185_ENST00000426256.2_Missense_Mutation_p.F111Y	NM_152267.3	NP_689480.2	Q96GF1	RN185_HUMAN	ring finger protein 185	173					autophagy (GO:0006914)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(3)|skin(1)	6						GACGAGCAGTTCCTGTCACGC	0.552																																					p.F173Y		Atlas-SNP	.											.	RNF185	14	.	0			c.T518A						PASS	.						139	119	125					22																	31600511		2203	4298	6501	SO:0001583	missense	91445	exon7			AGCAGTTCCTGTC		CCDS13890.1, CCDS46689.1	22q12.2	2013-01-09			ENSG00000138942	ENSG00000138942		"RING-type (C3HC4) zinc fingers"	26783	protein-coding gene	gene with protein product	"hypothetical protein FLJ38628"					12477932	Standard	NM_152267		Approved	FLJ38628	uc003akb.3	Q96GF1	OTTHUMG00000151253	ENST00000326132.6:c.518T>A	chr22.hg19:g.31600511T>A	ENSP00000320508:p.Phe173Tyr	71.0	0.0	.		42.0	21.0	.	NM_152267	A8K5C1|A9X3T8|Q8N900	Missense_Mutation	SNP	ENST00000326132.6	hg19	CCDS13890.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.241643	0.79912	.	.	ENSG00000138942	ENST00000426256;ENST00000326132;ENST00000266252	D	0.95554	-3.74	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	D	0.95733	0.8612	L	0.37561	1.115	0.54753	D	0.999989	P;D;P	0.61080	0.877;0.989;0.805	D;D;P	0.67725	0.916;0.953;0.827	D	0.94992	0.8135	10	0.33940	T	0.23	.	14.9068	0.70727	0.0:0.0:0.0:1.0	.	117;111;173	Q96GF1-2;B4DMD6;Q96GF1	.;.;RN185_HUMAN	Y	111;173;117	ENSP00000320508:F173Y	ENSP00000266252:F117Y	F	+	2	0	RNF185	29930511	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.454000	0.80714	2.169000	0.68431	0.528000	0.53228	TTC	.	.	.	none		0.552	RNF185-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321927.2	NM_152267		A	31600511	T	A	31600511	3	1	267	1	0	0	0	0	1	0	0	0	13481	1783	62	5	540	5	RNF185	22	31600511	Missense_Mutation	SNP	T	TCGA-UZ-A9PX-01A-11D-A42J-10	588898	31600511	19704055	100	16891											
SMC1B	26150	hgsc.bcm.edu	37	chr22	45809422	45809422	+	5'Flank	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	cgccacgacttgaaattttcCacaagcagcagctccaggtg	11	8	9	13	2	0	1	0	1	0	0	2	2	2	1	3	1	3	3	3	1	2	3			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chr22:45809422C>G	ENST00000342894.3	+	0	0				SMC1B_ENST00000404354.3_Silent_p.V9V|SMC1B_ENST00000357450.4_Silent_p.V9V|RIBC2_ENST00000538017.1_5'Flank			Q9H4K1	RIBC2_HUMAN	RIB43A domain with coiled-coils 2							nucleus (GO:0005634)				NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|skin(2)|urinary_tract(1)	10		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		TGAAATTTTCCACAAGCAGCA	0.637																																					p.V9V		Atlas-SNP	.											.	SMC1B	215	.	0			c.G27C						PASS	.						21	27	25					22																	45809422		1935	4141	6076	SO:0001631	upstream_gene_variant	27127	exon1			ATTTTCCACAAGC	AK098586		22q13.3	2004-08-18	2004-08-18	2004-08-18	ENSG00000128408	ENSG00000128408			13241	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 11"	C22orf11		12477932	Standard	NM_015653		Approved	DKFZp566F0546, FLJ25720	uc011aqs.3	Q9H4K1	OTTHUMG00000151332		chr22.hg19:g.45809422C>G	Exception_encountered	169.0	0.0	.		104.0	50.0	.	NM_148674	Q6ICD0|Q9Y413	Silent	SNP	ENST00000342894.3	hg19																																																																																				.	.	.	none		0.637	RIBC2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000322250.1	NM_015653		G	45809422	C	G	45809422	1	3	267	0	1	0	0	0	0	0	0	0	14795	581	21	4		4	SMC1B	22	45809422	5'Flank	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	14208911	45809422	5495144	101	16892											
PTCHD1	139411	hgsc.bcm.edu	37	chrX	23353163	23353163	+	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	agcgtggagcacctgctggcGccccagcacagcctggccaa	8	4	13	16	2	0	0	0	0	0	0	0	1	0	1	5	3	5	3	5	3	1	0			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chrX:23353163G>A	ENST00000379361.4	+	1	1031	c.171G>A	c.(169-171)gcG>gcA	p.A57A		NM_173495.2	NP_775766.2	Q96NR3	PTHD1_HUMAN	patched domain containing 1	57					cognition (GO:0050890)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(4)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(4)|skin(2)|urinary_tract(2)	42						ACCTGCTGGCGCCCCAGCACA	0.657																																					p.A57A		Atlas-SNP	.											.	PTCHD1	213	.	0			c.G171A						PASS	.						48	52	50					X																	23353163		2202	4298	6500	SO:0001819	synonymous_variant	139411	exon1			GCTGGCGCCCCAG	AK054858	CCDS35215.2	Xp22.13	2008-02-05			ENSG00000165186	ENSG00000165186			26392	protein-coding gene	gene with protein product		300828					Standard	NM_173495		Approved	FLJ30296	uc004dal.4	Q96NR3	OTTHUMG00000021251	ENST00000379361.4:c.171G>A	chrX.hg19:g.23353163G>A		78.0	0.0	.		47.0	41.0	.	NM_173495	B4DQH0|Q0IJ60|Q6P6B8	Silent	SNP	ENST00000379361.4	hg19	CCDS35215.2																																																																																			.	.	.	none		0.657	PTCHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056047.2	NM_173495		A	23353163	G	A	23353163	2	1	267	1	0	0	0	0	0	0	0	1	12742	1074	38	1		1	PTCHD1	23	23353163	Silent	SNP	G	TCGA-UZ-A9PX-01A-11D-A42J-10		23353163	131917397	102	16893											
FAM48B1	100130302	hgsc.bcm.edu	37	chrX	24382400	24382401	+	IGR	INS	-	-	TAT																															gctgctgctgctgctgctgcINStgctgctgctgctgctgctg																										TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chrX:24382400_24382401insTAT								AC004552.1 (15377 upstream) : PDK3 (100936 downstream)																							gctgctgctgctgctgctgctg	0.599																																					p.A508delinsAI		Atlas-INDEL	.											.	.	.	.	0			c.1523_1524insTAT						PASS	.																																			SO:0001628	intergenic_variant	100130302	exon1			.																													chrX.hg19:g.24382400_24382401insTAT		90.0	0.0	0		56.0	24.0	0.428571	NM_001136234		In_Frame_Ins	INS		hg19																																																																																				.	.	.	none	0	0.599									TAT	24382401	-	TAT	24382400	6	5	267	0	1	1	1	0	0	0	0	0	5580	797	28	0		0	FAM48B1	23	24382400	IGR	INS	-	TCGA-UZ-A9PX-01A-11D-A42J-10	1029237	24382400	130888160	103	16894											
ELK1	2002	hgsc.bcm.edu	37	chrX	47497265	47497265	+	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	gcccacctagcaggctcgggCtgagtggaagctctaggtcc	7	7	14	13	1	1	1	0	1	1	0	3	2	2	2	3	4	2	4	3	4	3	2			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chrX:47497265C>T	ENST00000247161.3	-	4	1070	c.971G>A	c.(970-972)aGc>aAc	p.S324N	ELK1_ENST00000376983.3_Missense_Mutation_p.S324N|ELK1_ENST00000592066.1_Missense_Mutation_p.S270N|ELK1_ENST00000343894.4_Intron	NM_005229.4	NP_005220.2	P19419	ELK1_HUMAN	ELK1, member of ETS oncogene family	324					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						CAGGCTCGGGCTGAGTGGAAG	0.716																																					p.S324N		Atlas-SNP	.											.	ELK1	54	.	0			c.G971A						PASS	.						6	7	7					X																	47497265		2104	4101	6205	SO:0001583	missense	2002	exon5			CTCGGGCTGAGTG	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.971G>A	chrX.hg19:g.47497265C>T	ENSP00000247161:p.Ser324Asn	60.0	0.0	.		29.0	26.0	.	NM_001114123	B2R7H4|O75606|O95058|Q969X8|Q9UJM4	Missense_Mutation	SNP	ENST00000247161.3	hg19	CCDS14283.1	.	.	.	.	.	.	.	.	.	.	c	23.9	4.467119	0.84533	.	.	ENSG00000126767	ENST00000247161;ENST00000542746;ENST00000376983	T;T	0.26223	1.75;1.75	5.09	4.15	0.48705	.	0.240251	0.45361	D	0.000377	T	0.27629	0.0679	L	0.48642	1.525	0.80722	D	1	P	0.51791	0.948	P	0.48738	0.588	T	0.00842	-1.1544	10	0.37606	T	0.19	.	9.4929	0.38971	0.0:0.7904:0.2096:0.0	.	324	P19419	ELK1_HUMAN	N	324;34;324	ENSP00000247161:S324N;ENSP00000366182:S324N	ENSP00000247161:S324N	S	-	2	0	ELK1	47382209	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	2.433000	0.44793	2.447000	0.82792	0.597000	0.82753	AGC	.	.	.	none		0.716	ELK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056436.1	NM_005229		T	47497265	C	T	47497265	3	4	267	1	0	0	0	0	1	0	0	0	5061	797	28	2	327	2	ELK1	23	47497265	Missense_Mutation	SNP	C	TCGA-UZ-A9PX-01A-11D-A42J-10	23114865	47497265	107773295	104	16895											
CLCN5	1184	hgsc.bcm.edu	37	chrX	49846494	49846494	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atacaggaagaatgaagccaAgcgcagagaggtaataatga	19	5	12	5	1	0	4	0	2	0	2	0	6	0	5	1	2	3	2	1	2	7	3			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chrX:49846494A>G	ENST00000307367.2	+	6	1004	c.713A>G	c.(712-714)aAg>aGg	p.K238R	CLCN5_ENST00000376088.3_Missense_Mutation_p.K308R|CLCN5_ENST00000376091.3_Missense_Mutation_p.K308R|CLCN5_ENST00000376108.3_Missense_Mutation_p.K238R			P51795	CLCN5_HUMAN	chloride channel, voltage-sensitive 5	238					chloride transmembrane transport (GO:1902476)|endocytosis (GO:0006897)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)	30	Ovarian(276;0.236)					AATGAAGCCAAGCGCAGAGAG	0.468																																					p.K308R		Atlas-SNP	.											.	CLCN5	137	.	0			c.A923G						PASS	.						98	77	84					X																	49846494		2203	4300	6503	SO:0001583	missense	1184	exon9			AAGCCAAGCGCAG	X91906	CCDS14328.1, CCDS48115.1, CCDS69763.1	Xp11.23-p11.22	2012-09-26	2012-02-23		ENSG00000171365	ENSG00000171365		"Ion channels / Chloride channels : Voltage-sensitive"	2023	protein-coding gene	gene with protein product	"Dent disease"	300008	"nephrolithiasis 2, X-linked", "nephrolithiasis 1 (X-linked)", "chloride channel 5"	NPHL2, NPHL1		7874126, 8111383, 8099916, 8559248, 9602200	Standard	NM_001272102		Approved	DENTS, XLRH, hClC-K2, hCIC-K2, CLC5, XRN, ClC-5	uc004doq.1	P51795	OTTHUMG00000021514	ENST00000307367.2:c.713A>G	chrX.hg19:g.49846494A>G	ENSP00000304257:p.Lys238Arg	65.0	0.0	.		28.0	21.0	.	NM_001127898	A1L475|B3KPN6|Q5JQD5|Q7RTN8	Missense_Mutation	SNP	ENST00000307367.2	hg19	CCDS14328.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.684586	0.88639	.	.	ENSG00000171365	ENST00000376088;ENST00000450422;ENST00000376091;ENST00000376108;ENST00000307367	D;D;D;D	0.93763	-3.28;-3.28;-3.28;-3.28	6.08	6.08	0.98989	Chloride channel, core (2);	0.000000	0.85682	D	0.000000	D	0.94823	0.8328	L	0.43757	1.38	0.80722	D	1	P;D	0.67145	0.932;0.996	P;D	0.76071	0.718;0.987	D	0.94286	0.7524	10	0.39692	T	0.17	-2.9127	14.3879	0.66958	1.0:0.0:0.0:0.0	.	238;308	P51795;P51795-2	CLCN5_HUMAN;.	R	308;140;308;238;238	ENSP00000365256:K308R;ENSP00000365259:K308R;ENSP00000365276:K238R;ENSP00000304257:K238R	ENSP00000304257:K238R	K	+	2	0	CLCN5	49733234	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	9.185000	0.94900	2.044000	0.60594	0.486000	0.48141	AAG	.	.	.	none		0.468	CLCN5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056544.1			G	49846494	A	G	49846494	3	3	267	1	0	0	0	0	1	0	0	0	3468	72	3	3	949	3	CLCN5	23	49846494	Missense_Mutation	SNP	A	TCGA-UZ-A9PX-01A-11D-A42J-10	2349229	49846494	105424066	105	16896											
NAA10	8260	hgsc.bcm.edu	37	chrX	153199832	153199832	+	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	aattcagaagctgcccacctGgggccaggaaaggccatggt	11	6	13	11	0	1	1	1	0	0	1	1	2	1	2	4	5	2	1	4	5	3	1			TCGA-UZ-A9PX-01A-11D-A42J-10	TCGA-UZ-A9PX-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b648818d-4e4e-47da-a20b-366ef8d54eaf	bd3cecf6-5961-4472-b1dc-a7d96c6da4a1	g.chrX:153199832G>T	ENST00000464845.1	-	2	436	c.118C>A	c.(118-120)Cag>Aag	p.Q40K	NAA10_ENST00000370009.1_Missense_Mutation_p.Q40K|NAA10_ENST00000370015.4_Missense_Mutation_p.Q40K|NAA10_ENST00000393712.3_Missense_Mutation_p.Q40K|NAA10_ENST00000393710.3_5'UTR	NM_001256120.1|NM_003491.3	NP_001243049.1|NP_003482.1	P41227	NAA10_HUMAN	N(alpha)-acetyltransferase 10, NatA catalytic subunit	40	Interaction with NAA15.|N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				DNA packaging (GO:0006323)|internal protein amino acid acetylation (GO:0006475)|N-terminal protein amino acid acetylation (GO:0006474)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)|NatA complex (GO:0031415)|nucleolus (GO:0005730)|nucleus (GO:0005634)	N-acetyltransferase activity (GO:0008080)|peptide alpha-N-acetyltransferase activity (GO:0004596)			breast(1)|endometrium(3)|kidney(1)|lung(3)|ovary(1)|prostate(1)	10						CTGCCCACCTGGGGCCAGGAA	0.562																																					p.Q40K	Ovarian(94;1099 1433 38814 45882 51063)	Atlas-SNP	.											.	NAA10	18	.	0			c.C118A						PASS	.						66	51	56					X																	153199832		2200	4299	6499	SO:0001583	missense	8260	exon2			CCACCTGGGGCCA	BC000308	CCDS14737.1, CCDS59179.1	Xq28	2010-05-07	2010-01-14	2010-01-14	ENSG00000102030	ENSG00000102030	2.3.1.88	"N(alpha)-acetyltransferase subunits"	18704	protein-coding gene	gene with protein product		300013	"ARD1 homolog, N-acetyltransferase (S. cerevisiae)", "ARD1 homolog A, N-acetyltransferase (S. cerevisiae)"	ARD1, ARD1A		7981673, 19660095	Standard	NM_003491		Approved	DXS707, TE2	uc004fjm.2	P41227	OTTHUMG00000024225	ENST00000464845.1:c.118C>A	chrX.hg19:g.153199832G>T	ENSP00000417763:p.Gln40Lys	73.0	0.0	.		41.0	36.0	.	NM_001256119	A6NM98	Missense_Mutation	SNP	ENST00000464845.1	hg19	CCDS14737.1	.	.	.	.	.	.	.	.	.	.	G	34	5.294637	0.95546	.	.	ENSG00000102030	ENST00000464845;ENST00000370015;ENST00000393712;ENST00000370009;ENST00000545734;ENST00000370011;ENST00000432089	T;T;T;T;T;T	0.33654	1.4;1.4;1.4;1.4;1.4;1.4	4.66	4.66	0.58398	GCN5-related N-acetyltransferase (GNAT) domain (1);Acyl-CoA N-acyltransferase (2);	0.065490	0.64402	D	0.000006	T	0.47948	0.1473	M	0.77712	2.385	0.80722	D	1	B;B;P	0.42375	0.417;0.227;0.778	B;P;P	0.44732	0.356;0.459;0.459	T	0.57866	-0.7737	10	0.87932	D	0	-14.9532	15.5532	0.76170	0.0:0.0:1.0:0.0	.	40;40;40	B7Z9N2;A6NM98;P41227	.;.;NAA10_HUMAN	K	40	ENSP00000417763:Q40K;ENSP00000359032:Q40K;ENSP00000377315:Q40K;ENSP00000359026:Q40K;ENSP00000359028:Q40K;ENSP00000413668:Q40K	ENSP00000359026:Q40K	Q	-	1	0	NAA10	152853026	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.859000	0.92264	1.911000	0.55334	0.529000	0.55759	CAG	.	.	.	none		0.562	NAA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061108.2	NM_003491		T	153199832	G	T	153199832	3	4	267	1	0	0	0	0	1	0	0	0	10123	1357	47	4	617	4	NAA10	23	153199832	Missense_Mutation	SNP	G	TCGA-UZ-A9PX-01A-11D-A42J-10	103353338	153199832	2070728	106	16897											
MUTYH	4595	hgsc.bcm.edu	37	chr1	45797352	45797352	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgagttgggcctctgcacCagcagaatttgggccccaag	8	8	12	13	0	1	2	0	1	1	1	1	2	1	2	5	2	2	3	5	2	2	2			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr1:45797352C>T	ENST00000372098.3	-	12	1291	c.1158G>A	c.(1156-1158)ctG>ctA	p.L386L	MUTYH_ENST00000488731.2_Intron|MUTYH_ENST00000372110.3_Silent_p.L376L|MUTYH_ENST00000372100.5_Silent_p.L372L|MUTYH_ENST00000355498.2_Silent_p.L361L|MUTYH_ENST00000372115.3_Silent_p.L375L|MUTYH_ENST00000354383.6_Silent_p.L362L|MUTYH_ENST00000450313.1_Silent_p.L389L|MUTYH_ENST00000528013.2_Silent_p.L375L|MUTYH_ENST00000529984.1_Intron|MUTYH_ENST00000528332.2_Intron|MUTYH_ENST00000372104.1_Silent_p.L361L|MUTYH_ENST00000531105.1_Intron|MUTYH_ENST00000448481.1_Silent_p.L372L|MUTYH_ENST00000456914.2_Silent_p.L361L			Q9UIF7	MUTYH_HUMAN	mutY homolog	386	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA repair (GO:0006281)|mismatch repair (GO:0006298)	mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|metal ion binding (GO:0046872)|MutSalpha complex binding (GO:0032407)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					GCCTCTGCACCAGCAGAATTT	0.617			Mis			colorectal		Base excision repair (BER), DNA glycosylases	MUTYH-associated polyposis																												p.L389L		Atlas-SNP	.	yes	Rec		Adenomatous polyposis coli	1	1p34.3-1p32.1	4595	mutY homolog (E. coli)		E	.	MUTYH	38	.	0			c.G1167A						PASS	.						36	41	40					1																	45797352		2199	4299	6498	SO:0001819	synonymous_variant	4595	exon12	Familial Cancer Database	MAP, MYH-associated polyposis	CTGCACCAGCAGA	U63329	CCDS520.1, CCDS41320.1, CCDS41321.1, CCDS41322.1, CCDS72776.1, CCDS72777.1	1p34.1	2014-09-17	2013-09-12		ENSG00000132781	ENSG00000132781			7527	protein-coding gene	gene with protein product		604933	"mutY (E. coli) homolog", "mutY homolog (E. coli)"			7823963, 10684930	Standard	NM_012222		Approved	MYH	uc009vxp.3	Q9UIF7	OTTHUMG00000007682	ENST00000372098.3:c.1158G>A	chr1.hg19:g.45797352C>T		49.0	0.0	.		31.0	11.0	.	NM_001128425	D3DPZ4|Q15830|Q9UBP2|Q9UBS7|Q9UIF4|Q9UIF5|Q9UIF6	Silent	SNP	ENST00000372098.3	hg19	CCDS520.1																																																																																			.	.	.	none		0.617	MUTYH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020529.1	NM_012222		T	45797352	C	T	45797352	2	4	268	1	0	0	0	0	0	0	0	1	10000	581	21	2		2	MUTYH	1	45797352	Silent	SNP	C	TCGA-UZ-A9PZ-01A-11D-A42J-10		45797352	203453269	1	16898											
LRRC42	115353	hgsc.bcm.edu	37	chr1	54433526	54433526	+	Frame_Shift_Del	DEL	A	A	-																															gaccttttgaggagtcagagAcagaacagaataactcttca																										TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr1:54433526delA	ENST00000371370.3	+	9	1722	c.1201delA	c.(1201-1203)acafs	p.T401fs	LRRC42_ENST00000319223.4_Frame_Shift_Del_p.T401fs	NM_001256409.1	NP_001243338.1	Q9Y546	LRC42_HUMAN	leucine rich repeat containing 42	401										breast(2)|kidney(1)|large_intestine(1)|lung(5)	9						GGAGTCAGAGACAGAACAGAA	0.423																																					p.E400fs		Atlas-INDEL	.											.	LRRC42	29	.	0			c.1200delG						PASS	.						93	93	93					1																	54433526		2203	4300	6503	SO:0001589	frameshift_variant	115353	exon8			.	AK075201	CCDS585.1	1p33-p32.1	2014-02-12			ENSG00000116212	ENSG00000116212			28792	protein-coding gene	gene with protein product						12477932	Standard	NM_001256409		Approved	MGC8974	uc001cwj.2	Q9Y546	OTTHUMG00000008436	ENST00000371370.3:c.1201delA	chr1.hg19:g.54433526delA	ENSP00000360421:p.Thr401fs	171.0	0.0	0		116.0	49.0	0.422414	NM_052940	D3DQ46|Q8N2Q8	Frame_Shift_Del	DEL	ENST00000371370.3	hg19	CCDS585.1																																																																																			.	.	.	none		0.423	LRRC42-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023250.1	NM_052940		-	54433526	A	-	54433526	7	5	268	1	0	1	0	1	0	0	0	0	9007	275	10	0	1227	0	LRRC42	1	54433526	Frame_Shift_Del	DEL	A	TCGA-UZ-A9PZ-01A-11D-A42J-10	8636174	54433526	194817095	2	16899											
RAG1AP1	55974	hgsc.bcm.edu	37	chr1	155110120	155110120	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggctcctggtacccaacccTgaggcccggcttcagcagtt	6	9	11	15	1	1	1	1	1	0	0	2	1	2	1	4	4	3	5	4	4	2	3			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr1:155110120T>C	ENST00000368404.4	+	4	428	c.366T>C	c.(364-366)ccT>ccC	p.P122P	SLC50A1_ENST00000368401.5_Silent_p.P67P|SLC50A1_ENST00000368405.3_Intron|SLC50A1_ENST00000484157.1_Silent_p.P57P|SLC50A1_ENST00000303343.8_Intron	NM_018845.3	NP_061333.2	Q9BRV3	SWET1_HUMAN	solute carrier family 50 (sugar efflux transporter), member 1	122					carbohydrate transport (GO:0008643)|DNA recombination (GO:0006310)|glucoside transport (GO:0042946)|positive regulation of gene expression, epigenetic (GO:0045815)	endomembrane system (GO:0012505)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glucoside transmembrane transporter activity (GO:0042947)			endometrium(1)|lung(1)|ovary(1)|skin(1)	4						TACCCAACCCTGAGGCCCGGC	0.577																																					p.P122P		Atlas-SNP	.											.	SLC50A1	16	.	0			c.T366C						PASS	.						75	77	76					1																	155110120		2203	4300	6503	SO:0001819	synonymous_variant	55974	exon4			CAACCCTGAGGCC	AF126023, AF126024	CCDS1093.1, CCDS44238.1, CCDS44239.1, CCDS72929.1, CCDS72930.1	1q22	2013-07-17	2013-07-17	2010-11-30	ENSG00000169241	ENSG00000169241		"Solute carriers"	30657	protein-coding gene	gene with protein product	"stromal cell protein"	613683	"recombination activating gene 1 activating protein 1"	RAG1AP1		21107422	Standard	NM_018845		Approved	SCP, RP11-540D14.5, slv, RZPDo834D038D, HsSWEET1, SWEET1	uc001fhj.4	Q9BRV3	OTTHUMG00000035333	ENST00000368404.4:c.366T>C	chr1.hg19:g.155110120T>C		92.0	0.0	.		44.0	24.0	.	NM_018845	Q5SR64|Q6IAK6|Q96DC5|Q9UHQ2|Q9UHQ3	Silent	SNP	ENST00000368404.4	hg19	CCDS1093.1																																																																																			.	.	.	none		0.577	SLC50A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085505.1	NM_018845		C	155110120	T	C	155110120	2	2	268	1	0	0	0	0	0	0	0	1	13017	1567	55	3		3	RAG1AP1	1	155110120	Silent	SNP	T	TCGA-UZ-A9PZ-01A-11D-A42J-10	100676594	155110120	94140501	3	16900											
ATP1A4	480	hgsc.bcm.edu	37	chr1	160146320	160146320	+	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	ctgaaagcgacatcatgaagAggcttccaaggaacccaaag	16	5	10	10	1	1	3	1	2	0	1	2	5	2	4	2	2	2	1	2	2	5	1			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr1:160146320A>C	ENST00000368081.4	+	17	2989	c.2518A>C	c.(2518-2520)Agg>Cgg	p.R840R	ATP1A4_ENST00000470705.1_5'Flank|ATP1A4_ENST00000418334.1_3'UTR	NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	840					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)			CATCATGAAGAGGCTTCCAAG	0.542																																					p.R840R		Atlas-SNP	.											.	ATP1A4	167	.	0			c.A2518C						PASS	.						77	67	70					1																	160146320		2203	4300	6503	SO:0001819	synonymous_variant	480	exon17			ATGAAGAGGCTTC	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.2518A>C	chr1.hg19:g.160146320A>C		135.0	0.0	.		75.0	27.0	.	NM_144699	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Silent	SNP	ENST00000368081.4	hg19	CCDS1197.1																																																																																			.	.	.	none		0.542	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699		C	160146320	A	C	160146320	2	2	268	1	0	0	0	0	0	0	0	1	1131	295	11	5		5	ATP1A4	1	160146320	Silent	SNP	A	TCGA-UZ-A9PZ-01A-11D-A42J-10	5036200	160146320	89104301	4	16901											
GREB1	9687	hgsc.bcm.edu	37	chr2	11755338	11755338	+	Missense_Mutation	SNP	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	aggttcccttggagaaggggGctaggaacgaggccttggag	9	7	18	7	1	0	1	0	0	0	1	1	5	1	3	2	7	1	2	2	7	3	4			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr2:11755338G>A	ENST00000381486.2	+	20	3544	c.3244G>A	c.(3244-3246)Gct>Act	p.A1082T	GREB1_ENST00000234142.5_Missense_Mutation_p.A1082T|GREB1_ENST00000396123.1_Missense_Mutation_p.A80T	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1082						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)		GGAGAAGGGGGCTAGGAACGA	0.582																																					p.A1082T	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.G3244A						PASS	.						75	80	78					2																	11755338		2094	4224	6318	SO:0001583	missense	9687	exon20			AAGGGGGCTAGGA		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.3244G>A	chr2.hg19:g.11755338G>A	ENSP00000370896:p.Ala1082Thr	126.0	0.0	.		74.0	29.0	.	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	hg19	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	G	9.541	1.113334	0.20795	.	.	ENSG00000196208	ENST00000381486;ENST00000234142;ENST00000396123	T;T;T	0.22336	3.27;3.27;1.96	5.12	-2.51	0.06365	.	1.032170	0.07616	N	0.926316	T	0.06735	0.0172	N	0.04203	-0.255	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.37663	-0.9696	10	0.07990	T	0.79	-38.687	3.2282	0.06739	0.2075:0.3012:0.3892:0.1021	.	1082	Q4ZG55	GREB1_HUMAN	T	1082;1082;80	ENSP00000370896:A1082T;ENSP00000234142:A1082T;ENSP00000379429:A80T	ENSP00000234142:A1082T	A	+	1	0	GREB1	11672789	0.000000	0.05858	0.001000	0.08648	0.962000	0.63368	-0.227000	0.09126	-0.373000	0.07979	-0.254000	0.11334	GCT	.	.	.	none		0.582	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		A	11755338	G	A	11755338	3	1	268	1	0	0	0	0	1	0	0	0	6767	1203	42	2	3426	2	GREB1	2	11755338	Missense_Mutation	SNP	G	TCGA-UZ-A9PZ-01A-11D-A42J-10		11755338	231444035	5	16902											
NAT8	9027	hgsc.bcm.edu	37	chr2	73868455	73868455	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggagccacgctcactcaggtAggatttggtaatgtcagaca	11	9	12	9	1	3	1	3	0	0	1	3	3	3	3	1	4	1	3	1	4	2	3			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr2:73868455A>G	ENST00000272425.3	-	2	450	c.301T>C	c.(301-303)Tac>Cac	p.Y101H		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						TCACTCAGGTAGGATTTGGTA	0.537																																					p.Y101H		Atlas-SNP	.											.	NAT8	26	.	0			c.T301C						PASS	.						126	119	122					2																	73868455		2203	4300	6503	SO:0001583	missense	9027	exon2			TCAGGTAGGATTT	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.301T>C	chr2.hg19:g.73868455A>G	ENSP00000272425:p.Tyr101His	134.0	0.0	.		107.0	45.0	.	NM_003960		Missense_Mutation	SNP	ENST00000272425.3	hg19	CCDS1926.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.108127	0.77096	.	.	ENSG00000144035	ENST00000272425	T	0.30714	1.52	3.86	3.86	0.44501	GCN5-related N-acetyltransferase (GNAT) domain (1);Acyl-CoA N-acyltransferase (2);	0.000000	0.85682	D	0.000000	T	0.57784	0.2077	M	0.86420	2.815	0.44061	D	0.996801	D	0.89917	1.0	D	0.80764	0.994	T	0.65384	-0.6181	10	0.87932	D	0	-39.9926	11.3146	0.49383	1.0:0.0:0.0:0.0	.	101	Q9UHE5	NAT8_HUMAN	H	101	ENSP00000272425:Y101H	ENSP00000272425:Y101H	Y	-	1	0	NAT8	73721963	1.000000	0.71417	0.423000	0.26634	0.335000	0.28730	5.761000	0.68801	1.715000	0.51383	0.524000	0.50904	TAC	.	.	.	none		0.537	NAT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327854.1	NM_003960		G	73868455	A	G	73868455	3	3	268	1	0	0	0	0	1	0	0	0	10186	420	15	3	386	3	NAT8	2	73868455	Missense_Mutation	SNP	A	TCGA-UZ-A9PZ-01A-11D-A42J-10	62113117	73868455	169330918	6	16903											
SCTR	6344	hgsc.bcm.edu	37	chr2	120221714	120221714	+	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	attaccctgtgggcatcgcaGtaggtgacatcatctgagga	10	10	12	9	1	2	2	1	2	1	0	3	3	2	3	1	3	1	3	1	3	2	2			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr2:120221714G>A	ENST00000019103.5	-	6	888	c.621C>T	c.(619-621)taC>taT	p.Y207Y		NM_002980.2	NP_002971.2	P47872	SCTR_HUMAN	secretin receptor	207					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)	GGGCATCGCAGTAGGTGACAT	0.572																																					p.Y207Y		Atlas-SNP	.											.	SCTR	45	.	0			c.C621T						PASS	.						176	152	160					2																	120221714		2203	4300	6503	SO:0001819	synonymous_variant	6344	exon6			ATCGCAGTAGGTG		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.621C>T	chr2.hg19:g.120221714G>A		122.0	0.0	.		97.0	39.0	.	NM_002980	Q12961|Q13213|Q53T00	Silent	SNP	ENST00000019103.5	hg19	CCDS2127.1																																																																																			.	.	.	none		0.572	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2			A	120221714	G	A	120221714	2	1	268	1	0	0	0	0	0	0	0	1	13956	1024	36	2		2	SCTR	2	120221714	Silent	SNP	G	TCGA-UZ-A9PZ-01A-11D-A42J-10	46353259	120221714	122977659	7	16904											
GPR155	151556	hgsc.bcm.edu	37	chr2	175304729	175304729	+	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	aacaggagaatccctgttttCtgctgtgtctttattgttcc	7	17	8	9	0	2	1	0	0	2	1	4	2	4	1	2	1	2	3	2	1	3	6			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr2:175304729C>G	ENST00000392552.2	-	15	2447	c.2209G>C	c.(2209-2211)Gaa>Caa	p.E737Q	GPR155_ENST00000459996.1_5'UTR|GPR155_ENST00000295500.4_Missense_Mutation_p.E737Q|GPR155_ENST00000392551.2_Missense_Mutation_p.E737Q	NM_001267051.1|NM_152529.6	NP_001253980.1|NP_689742.4	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155	737					cognition (GO:0050890)|intracellular signal transduction (GO:0035556)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	26						TCCCTGTTTTCTGCTGTGTCT	0.373																																					p.E737Q		Atlas-SNP	.											.	GPR155	76	.	0			c.G2209C						PASS	.						126	124	124					2																	175304729		2203	4300	6503	SO:0001583	missense	151556	exon16			TGTTTTCTGCTGT	AY255528	CCDS2259.1, CCDS74605.1	2q31.1	2012-04-10			ENSG00000163328	ENSG00000163328			22951	protein-coding gene	gene with protein product						12679517	Standard	NM_001033045		Approved	DEPDC3, DEP.7, FLJ31819, PGR22	uc002uiu.4	Q7Z3F1	OTTHUMG00000132336	ENST00000392552.2:c.2209G>C	chr2.hg19:g.175304729C>G	ENSP00000376335:p.Glu737Gln	81.0	0.0	.		59.0	31.0	.	NM_001033045	B2RCI2|D3DPE2|Q4G0Y6|Q53SJ3|Q53TA8|Q69YG8|Q86SP9|Q8N261|Q8N639|Q8N8K3|Q96MV6	Missense_Mutation	SNP	ENST00000392552.2	hg19	CCDS2259.1	.	.	.	.	.	.	.	.	.	.	C	10.74	1.434272	0.25813	.	.	ENSG00000163328	ENST00000392552;ENST00000510236;ENST00000392551;ENST00000295500	T;T;T	0.44083	0.93;0.93;0.93	5.59	5.59	0.84812	.	0.587930	0.19501	N	0.112740	T	0.37598	0.1009	L	0.38838	1.175	0.24898	N	0.992127	B;B	0.26258	0.145;0.003	B;B	0.27887	0.084;0.009	T	0.15752	-1.0426	10	0.18276	T	0.48	-0.5171	19.5907	0.95509	0.0:1.0:0.0:0.0	.	217;737	F5H464;Q7Z3F1	.;GP155_HUMAN	Q	737;217;737;737	ENSP00000376335:E737Q;ENSP00000376334:E737Q;ENSP00000295500:E737Q	ENSP00000295500:E737Q	E	-	1	0	GPR155	175012975	1.000000	0.71417	0.991000	0.47740	0.931000	0.56810	4.009000	0.57110	2.640000	0.89533	0.655000	0.94253	GAA	.	.	.	none		0.373	GPR155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255455.1	NM_152529		G	175304729	C	G	175304729	3	3	268	1	0	0	0	0	1	0	0	0	6667	922	32	4	411	4	GPR155	2	175304729	Missense_Mutation	SNP	C	TCGA-UZ-A9PZ-01A-11D-A42J-10	55083015	175304729	67894644	8	16905											
HSPD1	3329	hgsc.bcm.edu	37	chr2	198362107	198362108	+	Frame_Shift_Del	DEL	CT	CT	-																															ccaactctgctcaataatcaCtgttcttccctagaagaaaa																										TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr2:198362107_198362108delCT	ENST00000388968.3	-	3	450_451	c.183_184delAG	c.(181-186)acagtgfs	p.V62fs	HSPD1_ENST00000345042.2_Frame_Shift_Del_p.V62fs|HSPD1_ENST00000544407.1_Frame_Shift_Del_p.V62fs|HSPE1_ENST00000409468.1_5'Flank|HSPE1_ENST00000409729.1_5'Flank|HSPE1_ENST00000233893.5_5'Flank	NM_002156.4	NP_002147.2	P10809	CH60_HUMAN	heat shock 60kDa protein 1 (chaperonin)	62					'de novo' protein folding (GO:0006458)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|ATP catabolic process (GO:0006200)|B cell activation (GO:0042113)|B cell cytokine production (GO:0002368)|B cell proliferation (GO:0042100)|chaperone-mediated protein complex assembly (GO:0051131)|isotype switching to IgG isotypes (GO:0048291)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell mediated immune response to tumor cell (GO:0002842)|protein maturation (GO:0051604)|protein refolding (GO:0042026)|protein stabilization (GO:0050821)|response to unfolded protein (GO:0006986)|T cell activation (GO:0042110)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lipopolysaccharide receptor complex (GO:0046696)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|secretory granule (GO:0030141)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chaperone binding (GO:0051087)|DNA replication origin binding (GO:0003688)|double-stranded RNA binding (GO:0003725)|lipopolysaccharide binding (GO:0001530)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)|unfolded protein binding (GO:0051082)			NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(7)|skin(1)	17			Epithelial(96;0.225)			TCAATAATCACTGTTCTTCCCT	0.342																																					p.62_62del		Atlas-Indel,Pindel	.											.	HSPD1	68	.	0			c.184_185del						PASS	.																																			SO:0001589	frameshift_variant	3329	exon3			.	M34664	CCDS33357.1	2q33.1	2011-09-02	2002-08-29		ENSG00000144381	ENSG00000144381		"Heat Shock Proteins / Chaperonins"	5261	protein-coding gene	gene with protein product		118190	"heat shock 60kD protein 1 (chaperonin)", "spastic paraplegia 13 (autosomal dominant)"	SPG13		1980192, 11898127	Standard	NM_002156		Approved	GROEL, HSP60	uc002uui.3	P10809	OTTHUMG00000154463	ENST00000388968.3:c.183_184delAG	chr2.hg19:g.198362107_198362108delCT	ENSP00000373620:p.Val62fs	271.0	0.0	0		143.0	50.0	0.34965	NM_002156	B2R5M6|B7Z712|Q38L19|Q9UCR6	Frame_Shift_Del	DEL	ENST00000388968.3	hg19	CCDS33357.1																																																																																			.	.	.	none		0.342	HSPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335324.2	NM_002156		-	198362108	CT	-	198362107	7	5	268	1	0	1	0	1	0	0	0	0	7435	565	20	0	1577	0	HSPD1	2	198362107	Frame_Shift_Del	DEL	CT	TCGA-UZ-A9PZ-01A-11D-A42J-10	23057378	198362107	44837266	9	16906											
GIGYF2	26058	hgsc.bcm.edu	37	chr2	233612395	233612395	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagcattgccgaagtataaaTtagcagattatcgttacggc	13	11	9	8	3	0	1	0	0	0	1	1	2	0	1	1	1	4	4	1	1	7	6			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr2:233612395T>C	ENST00000409547.1	+	6	423	c.112T>C	c.(112-114)Tta>Cta	p.L38L	GIGYF2_ENST00000373563.4_Silent_p.L38L|GIGYF2_ENST00000409451.3_Silent_p.L38L|GIGYF2_ENST00000409196.3_Silent_p.L38L|GIGYF2_ENST00000409480.1_Silent_p.L38L|GIGYF2_ENST00000373566.3_Silent_p.L38L	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	38					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)		GAAGTATAAATTAGCAGATTA	0.398																																					p.L38L		Atlas-SNP	.											.	GIGYF2	288	.	0			c.T112C						PASS	.						124	123	123					2																	233612395		2203	4300	6503	SO:0001819	synonymous_variant	26058	exon4			TATAAATTAGCAG	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.112T>C	chr2.hg19:g.233612395T>C		96.0	0.0	.		68.0	28.0	.	NM_001103146	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Silent	SNP	ENST00000409547.1	hg19	CCDS33401.1																																																																																			.	.	.	none		0.398	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		C	233612395	T	C	233612395	2	2	268	1	0	0	0	0	0	0	0	1	6385	1490	52	3		3	GIGYF2	2	233612395	Silent	SNP	T	TCGA-UZ-A9PZ-01A-11D-A42J-10	35250288	233612395	9586978	10	16907											
OR6B2	389090	hgsc.bcm.edu	37	chr2	240969002	240969002	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaaagggttaattattggcGtgacaacagtgtacacggca	13	10	11	7	2	1	1	1	1	0	0	1	1	1	1	0	3	2	3	0	3	5	4			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr2:240969002G>A	ENST00000402971.2	-	1	904	c.845C>T	c.(844-846)aCg>aTg	p.T282M		NM_001005853.1	NP_001005853.1	Q6IFH4	OR6B2_HUMAN	olfactory receptor, family 6, subfamily B, member 2	282						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(4)|lung(9)|prostate(1)	15		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;3.4e-29)|all cancers(36;2.08e-27)|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)		AATTATTGGCGTGACAACAGT	0.468																																					p.T282M		Atlas-SNP	.											.	OR6B2	30	.	0			c.C845T						PASS	.						119	116	117					2																	240969002		1917	4130	6047	SO:0001583	missense	389090	exon1			ATTGGCGTGACAA		CCDS46559.1	2q37.3	2012-08-09	2004-10-07	2004-10-07	ENSG00000182083	ENSG00000182083		"GPCR / Class A : Olfactory receptors"	15041	protein-coding gene	gene with protein product			"olfactory receptor, family 6, subfamily B, member 2 pseudogene"	OR6B2P			Standard	XM_005247004		Approved		uc010zoc.2	Q6IFH4	OTTHUMG00000152400	ENST00000402971.2:c.845C>T	chr2.hg19:g.240969002G>A	ENSP00000384563:p.Thr282Met	229.0	0.0	.		146.0	7.0	.	NM_001005853	B2RPR3|Q8NGW0	Missense_Mutation	SNP	ENST00000402971.2	hg19	CCDS46559.1	.	.	.	.	.	.	.	.	.	.	G	11.24	1.581713	0.28180	.	.	ENSG00000182083	ENST00000402971	T	0.38401	1.14	4.36	3.48	0.39840	GPCR, rhodopsin-like superfamily (1);	0.135419	0.33075	N	0.005308	T	0.54615	0.1869	M	0.88906	2.99	0.29521	N	0.8535	P	0.52577	0.954	P	0.55391	0.775	T	0.58696	-0.7591	10	0.87932	D	0	.	7.0844	0.25249	0.2031:0.0:0.7969:0.0	.	282	Q6IFH4	OR6B2_HUMAN	M	282	ENSP00000384563:T282M	ENSP00000384563:T282M	T	-	2	0	OR6B2	240617675	0.008000	0.16893	0.457000	0.27056	0.032000	0.12392	1.620000	0.36976	1.174000	0.42811	-0.194000	0.12790	ACG	.	.	.	none		0.468	OR6B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326079.1	NM_001005853		A	240969002	G	A	240969002	3	1	268	1	0	0	0	0	1	0	0	0	11195	1145	40	1	95	1	OR6B2	2	240969002	Missense_Mutation	SNP	G	TCGA-UZ-A9PZ-01A-11D-A42J-10	7356607	240969002	2230371	11	16908											
LRPAP1	4043	hgsc.bcm.edu	37	chr4	3533995	3533995	+	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	gcggaactcctctccggactCgcgtttcggggacggcttgg	4	9	15	13	6	1	0	0	0	1	0	5	3	2	3	2	6	1	2	2	6	1	2	rs539416757		TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr4:3533995C>T	ENST00000500728.2	-	1	291	c.145G>A	c.(145-147)Gag>Aag	p.E49K	LRPAP1_ENST00000296325.5_5'Flank	NM_002337.3	NP_002328.1	P30533	AMRP_HUMAN	low density lipoprotein receptor-related protein associated protein 1	49					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)		TCTCCGGACTCGCGTTTCGGG	0.697													c|||	1	0.000199681	0	0.0014	5008	,	,		9728	0		0	False		,,,				2504	0				p.E49K		Atlas-SNP	.											.	LRPAP1	29	.	0			c.G145A						PASS	.						30	28	29					4																	3533995		2137	4234	6371	SO:0001583	missense	4043	exon1			CGGACTCGCGTTT		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.145G>A	chr4.hg19:g.3533995C>T	ENSP00000421922:p.Glu49Lys	158.0	0.0	.		99.0	41.0	.	NM_002337	D3DVR9|Q2M310|Q53HQ3|Q53HS6	Missense_Mutation	SNP	ENST00000500728.2	hg19	CCDS3371.1	.	.	.	.	.	.	.	.	.	.	C	11.08	1.532771	0.27387	.	.	ENSG00000163956	ENST00000500728	T	0.43688	0.94	3.59	3.59	0.41128	Alpha-2-macroglobulin receptor-associated protein, domain 1 (1);	0.744185	0.12472	N	0.465930	T	0.35480	0.0933	L	0.46741	1.465	0.27557	N	0.950308	P	0.41008	0.735	B	0.38056	0.264	T	0.16158	-1.0412	10	0.38643	T	0.18	-15.3408	10.5987	0.45354	0.0:1.0:0.0:0.0	.	49	P30533	AMRP_HUMAN	K	49	ENSP00000421922:E49K	ENSP00000421922:E49K	E	-	1	0	LRPAP1	3503793	0.445000	0.25657	0.659000	0.29680	0.054000	0.15201	0.827000	0.27421	1.823000	0.53134	0.591000	0.81541	GAG	.	.	.	none		0.697	LRPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206659.4			T	3533995	C	T	3533995	3	4	268	1	0	0	0	0	1	0	0	0	8971	893	31	1	960	1	LRPAP1	4	3533995	Missense_Mutation	SNP	C	TCGA-UZ-A9PZ-01A-11D-A42J-10		3533995	187620281	12	16909											
LRRC66	339977	hgsc.bcm.edu	37	chr4	52861561	52861562	+	Missense_Mutation	DNP	CC	CC	TG																															actgagaggctcttcctgggCcacagtttcataagtccatt																										TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr4:52861561_52861562CC>TG	ENST00000343457.3	-	4	1632_1633	c.1626_1627GG>CA	c.(1624-1629)gtGGcc>gtCAcc	p.A543T		NM_001024611.1	NP_001019782.1	Q68CR7	LRC66_HUMAN	leucine rich repeat containing 66	543						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						TCTTCCTGGGCCACAGTTTCAT	0.505																																					p.A543T|p.V542V		Atlas-SNP	.											.	LRRC66	128	.	0			c.G1627A|c.G1626C						PASS	.																																			SO:0001583	missense	339977	exon4			CCTGGGCCACAGT|CTGGGCCACAGTT	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.1626_1627delinsTG	chr4.hg19:g.52861561_52861562delinsTG	ENSP00000341944:p.Ala543Thr	114.0|117.0	0.0	.		77.0|76.0	24.0|23.0	.	NM_001024611		Missense_Mutation|Silent	SNP	ENST00000343457.3	hg19	CCDS43229.1																																																																																			.	.	.	none		0.505	LRRC66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361473.1	NM_001024611		TG	52861562	CC	TG	52861561	3	4	268	1	0	0	0	0	1	0	0	0	9025	739	26	2	1019	2	LRRC66	4	52861561	Missense_Mutation	DNP	CC	TCGA-UZ-A9PZ-01A-11D-A42J-10	49327566	52861561	138292715	13	16910											
GRIA2	2891	hgsc.bcm.edu	37	chr4	158257702	158257702	+	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	gcctatgagatctggatgtgCattgtttttgcctacattgg	7	16	11	7	0	1	1	0	1	1	1	1	3	1	2	2	2	3	2	2	2	2	6			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr4:158257702C>A	ENST00000264426.9	+	11	1926	c.1647C>A	c.(1645-1647)tgC>tgA	p.C549*	GRIA2_ENST00000296526.7_Nonsense_Mutation_p.C549*|GRIA2_ENST00000393815.2_Nonsense_Mutation_p.C502*|GRIA2_ENST00000507898.1_Nonsense_Mutation_p.C502*|GRIA2_ENST00000449365.1_Nonsense_Mutation_p.C502*	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	549					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)	TCTGGATGTGCATTGTTTTTG	0.443																																					p.C549X		Atlas-SNP	.											.	GRIA2	358	.	0			c.C1647A						PASS	.						234	219	224					4																	158257702		2203	4300	6503	SO:0001587	stop_gained	2891	exon11			GATGTGCATTGTT		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.1647C>A	chr4.hg19:g.158257702C>A	ENSP00000264426:p.Cys549*	247.0	0.0	.		128.0	39.0	.	NM_000826	A8MT92|I6L997|Q96FP6	Nonsense_Mutation	SNP	ENST00000264426.9	hg19	CCDS43274.1	.	.	.	.	.	.	.	.	.	.	C	39	7.595898	0.98381	.	.	ENSG00000120251	ENST00000507898;ENST00000393815;ENST00000296526;ENST00000264426;ENST00000449365	.	.	.	5.46	4.62	0.57501	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	.	14.5219	0.67856	0.0:0.9291:0.0:0.0709	.	.	.	.	X	502;502;549;549;502	.	ENSP00000264426:C549X	C	+	3	2	GRIA2	158477152	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.561000	0.45905	1.442000	0.47568	0.655000	0.94253	TGC	.	.	.	none		0.443	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2			A	158257702	C	A	158257702	4	1	268	1	0	0	0	0	0	1	0	0	6775	718	25	4	1689	4	GRIA2	4	158257702	Nonsense_Mutation	SNP	C	TCGA-UZ-A9PZ-01A-11D-A42J-10	105396141	158257702	32896574	14	16911											
ODZ3	55714	hgsc.bcm.edu	37	chr4	183696133	183696133	+	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	tcagaattatctacgccagtGgcctggactcacactaccaa	12	9	7	13	1	3	1	2	0	1	1	3	2	3	2	3	2	2	0	3	2	5	3			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr4:183696133G>A	ENST00000511685.1	+	24	5254	c.5131G>A	c.(5131-5133)Ggc>Agc	p.G1711S	RP11-18D7.2_ENST00000513255.1_RNA|TENM3_ENST00000406950.2_Missense_Mutation_p.G1711S			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1711					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)										CTACGCCAGTGGCCTGGACTC	0.473																																					p.G1711S		Atlas-SNP	.											.	.	.	.	0			c.G5131A						PASS	.						42	43	43					4																	183696133		1907	4124	6031	SO:0001583	missense	55714	exon23			GCCAGTGGCCTGG	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.5131G>A	chr4.hg19:g.183696133G>A	ENSP00000424226:p.Gly1711Ser	189.0	0.0	.		141.0	57.0	.	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	hg19	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.404306	0.83230	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.87966	-2.32;-2.32	4.77	4.77	0.60923	.	.	.	.	.	D	0.93706	0.7989	M	0.80847	2.515	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.94287	0.7525	9	0.72032	D	0.01	.	18.3535	0.90348	0.0:0.0:1.0:0.0	.	1711	Q9P273	TEN3_HUMAN	S	1711	ENSP00000424226:G1711S;ENSP00000385276:G1711S	ENSP00000385276:G1711S	G	+	1	0	ODZ3	183933127	1.000000	0.71417	0.835000	0.33067	0.392000	0.30506	9.601000	0.98297	2.627000	0.88993	0.650000	0.86243	GGC	.	.	.	none		0.473	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			A	183696133	G	A	183696133	3	1	268	1	0	0	0	0	1	0	0	0	10843	1348	47	2	5221	2	ODZ3	4	183696133	Missense_Mutation	SNP	G	TCGA-UZ-A9PZ-01A-11D-A42J-10	25438431	183696133	7458143	15	16912											
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5465025	5465025	+	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	ggtccccagaaccagaaaccAggggagtcactgcagaagga	14	3	13	11	0	1	3	1	0	0	3	2	5	2	5	4	4	3	1	4	4	3	0			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr5:5465025A>T	ENST00000296564.7	+	13	5800	c.5578A>T	c.(5578-5580)Agg>Tgg	p.R1860W		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		1860					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						ACCAGAAACCAGGGGAGTCAC	0.507																																					p.R1860W		Atlas-SNP	.											.	KIAA0947	301	.	0			c.A5578T						PASS	.						59	63	62					5																	5465025		1889	4124	6013	SO:0001583	missense	23379	exon13			GAAACCAGGGGAG																												ENST00000296564.7:c.5578A>T	chr5.hg19:g.5465025A>T	ENSP00000296564:p.Arg1860Trp	303.0	0.0	.		229.0	108.0	.	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	hg19	CCDS47187.1	.	.	.	.	.	.	.	.	.	.	A	18.28	3.588195	0.66105	.	.	ENSG00000164151	ENST00000296564	T	0.10668	2.85	5.24	-3.67	0.04476	.	.	.	.	.	T	0.09818	0.0241	N	0.22421	0.69	0.09310	N	1	D	0.59767	0.986	P	0.55455	0.776	T	0.13522	-1.0506	9	0.66056	D	0.02	-0.8027	1.3306	0.02134	0.1867:0.3863:0.1747:0.2523	.	1860	Q9Y2F5	K0947_HUMAN	W	1860	ENSP00000296564:R1860W	ENSP00000296564:R1860W	R	+	1	2	KIAA0947	5518025	0.000000	0.05858	0.000000	0.03702	0.137000	0.21094	-0.142000	0.10311	-0.636000	0.05524	-0.644000	0.03951	AGG	.	.	.	none		0.507	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			T	5465025	A	T	5465025	3	4	268	1	0	0	0	0	1	0	0	0	8209	179	7	5	5628	5	KIAA0947	5	5465025	Missense_Mutation	SNP	A	TCGA-UZ-A9PZ-01A-11D-A42J-10		5465025	175450235	16	16913											
FAM173B	134145	hgsc.bcm.edu	37	chr5	10227716	10227716	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaagcaataactcgtgcaTcatcctcaagttcacgttca	12	10	7	12	2	4	0	4	0	0	0	6	0	5	0	1	1	3	5	1	1	4	3			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr5:10227716T>C	ENST00000511437.1	-	5	551	c.539A>G	c.(538-540)gAt>gGt	p.D180G	FAM173B_ENST00000510047.1_Missense_Mutation_p.D163G|FAM173B_ENST00000510052.1_5'UTR|FAM173B_ENST00000280330.8_Missense_Mutation_p.D16G	NM_199133.3	NP_954584.2	Q6P4H8	F173B_HUMAN	family with sequence similarity 173, member B	180						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	16						AACTCGTGCATCATCCTCAAG	0.488																																					p.D180G		Atlas-SNP	.											.	FAM173B	24	.	0			c.A539G						PASS	.						117	111	112					5																	10227716		1974	4158	6132	SO:0001583	missense	134145	exon5			CGTGCATCATCCT		CCDS43301.1, CCDS58942.1	5p15.2	2008-08-08			ENSG00000150756	ENSG00000150756			27029	protein-coding gene	gene with protein product						12477932	Standard	NM_199133		Approved		uc003jeo.3	Q6P4H8	OTTHUMG00000161771	ENST00000511437.1:c.539A>G	chr5.hg19:g.10227716T>C	ENSP00000422338:p.Asp180Gly	82.0	0.0	.		83.0	4.0	.	NM_199133	B4DT41|B4DXK2|E9PBZ4	Missense_Mutation	SNP	ENST00000511437.1	hg19	CCDS43301.1	.	.	.	.	.	.	.	.	.	.	T	5.398	0.258646	0.10239	.	.	ENSG00000150756	ENST00000280330;ENST00000511437;ENST00000510047	T;T;T	0.16897	2.31;3.03;3.03	5.17	2.75	0.32379	.	0.481441	0.24198	N	0.040649	T	0.04907	0.0132	N	0.01809	-0.71	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.13407	0.004;0.009	T	0.40905	-0.9538	10	0.12430	T	0.62	-6.4801	4.8377	0.13473	0.0:0.1713:0.1582:0.6705	.	163;180	E9PBZ4;Q6P4H8	.;F173B_HUMAN	G	16;180;163	ENSP00000280330:D16G;ENSP00000422338:D180G;ENSP00000420876:D163G	ENSP00000280330:D16G	D	-	2	0	FAM173B	10280716	0.020000	0.18652	0.000000	0.03702	0.368000	0.29767	1.126000	0.31344	0.381000	0.24851	0.528000	0.53228	GAT	.	.	.	none		0.488	FAM173B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000366048.2	NM_199133		C	10227716	T	C	10227716	3	2	268	1	0	0	0	0	1	0	0	0	5498	1435	50	3	166	3	FAM173B	5	10227716	Missense_Mutation	SNP	T	TCGA-UZ-A9PZ-01A-11D-A42J-10	4762691	10227716	170687544	17	16914											
ZNF622	90441	hgsc.bcm.edu	37	chr5	16463842	16463842	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attcttcatcagaatcaataTcttcccaatctgcaagccag	13	12	4	12	0	6	1	3	0	3	1	7	1	7	1	2	0	2	1	2	0	5	4			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr5:16463842T>C	ENST00000308683.2	-	2	761	c.635A>G	c.(634-636)gAt>gGt	p.D212G		NM_033414.2	NP_219482.1	Q969S3	ZN622_HUMAN	zinc finger protein 622	212	Glu-rich.				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						AGAATCAATATCTTCCCAATC	0.413																																					p.D212G		Atlas-SNP	.											ZNF622,NS,carcinoma,0,1	ZNF622	49	.	0			c.A635G						PASS	.						152	164	160					5																	16463842		2203	4300	6503	SO:0001583	missense	90441	exon2			TCAATATCTTCCC	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.635A>G	chr5.hg19:g.16463842T>C	ENSP00000310042:p.Asp212Gly	91.0	0.0	.		78.0	30.0	.	NM_033414		Missense_Mutation	SNP	ENST00000308683.2	hg19	CCDS3886.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.407580	0.83340	.	.	ENSG00000173545	ENST00000308683	.	.	.	5.18	5.18	0.71444	.	0.092716	0.64402	N	0.000001	T	0.61553	0.2356	M	0.78049	2.395	0.80722	D	1	P	0.48294	0.908	B	0.43754	0.43	T	0.63664	-0.6586	9	0.27082	T	0.32	-3.0532	15.3358	0.74250	0.0:0.0:0.0:1.0	.	212	Q969S3	ZN622_HUMAN	G	212	.	ENSP00000310042:D212G	D	-	2	0	ZNF622	16516842	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.193000	0.77780	2.068000	0.61886	0.459000	0.35465	GAT	.	.	.	none		0.413	ZNF622-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207105.1	NM_033414		C	16463842	T	C	16463842	3	2	268	1	0	0	0	0	1	0	0	0	18058	1435	50	3	818	3	ZNF622	5	16463842	Missense_Mutation	SNP	T	TCGA-UZ-A9PZ-01A-11D-A42J-10	6236126	16463842	164451418	18	16915											
RXFP3	51289	hgsc.bcm.edu	37	chr5	33937725	33937725	+	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	acctgctgctggtgcgcttcAtcgccgaccgccgcgcggcg	3	7	14	17	8	1	0	1	0	0	0	2	1	1	0	4	2	3	3	4	2	0	1			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr5:33937725A>T	ENST00000330120.3	+	1	1235	c.880A>T	c.(880-882)Atc>Ttc	p.I294F		NM_016568.3	NP_057652.1	Q9NSD7	RL3R1_HUMAN	relaxin/insulin-like family peptide receptor 3	294					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						GGTGCGCTTCATCGCCGACCG	0.672																																					p.I294F		Atlas-SNP	.											.	RXFP3	114	.	0			c.A880T						PASS	.						33	25	28					5																	33937725		2190	4272	6462	SO:0001583	missense	51289	exon1			CGCTTCATCGCCG	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.880A>T	chr5.hg19:g.33937725A>T	ENSP00000328708:p.Ile294Phe	75.0	0.0	.		53.0	31.0	.	NM_016568	Q14DA5	Missense_Mutation	SNP	ENST00000330120.3	hg19	CCDS3900.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.991457	0.74703	.	.	ENSG00000182631	ENST00000330120	T	0.41758	0.99	5.74	4.55	0.56014	GPCR, rhodopsin-like superfamily (1);	0.108059	0.64402	D	0.000008	T	0.63343	0.2503	M	0.78285	2.405	0.48632	D	0.999689	D	0.63046	0.992	D	0.68483	0.958	T	0.66352	-0.5945	10	0.62326	D	0.03	-23.9733	12.8323	0.57752	0.8636:0.1364:0.0:0.0	.	294	Q9NSD7	RL3R1_HUMAN	F	294	ENSP00000328708:I294F	ENSP00000328708:I294F	I	+	1	0	RXFP3	33973482	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.969000	0.40510	0.944000	0.37579	0.533000	0.62120	ATC	.	.	.	none		0.672	RXFP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207369.1	NM_016568		T	33937725	A	T	33937725	3	4	268	1	0	0	0	0	1	0	0	0	13774	217	8	5	882	5	RXFP3	5	33937725	Missense_Mutation	SNP	A	TCGA-UZ-A9PZ-01A-11D-A42J-10	17473883	33937725	146977535	19	16916											
RASA1	5921	hgsc.bcm.edu	37	chr5	86659213	86659213	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttatcttagagggtagtgAtgcccaacttatttattttg	9	19	8	5	0	1	2	0	1	1	1	1	2	1	2	1	1	2	1	1	1	6	9			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr5:86659213A>G	ENST00000274376.6	+	11	2066	c.1502A>G	c.(1501-1503)gAt>gGt	p.D501G	RASA1_ENST00000506290.1_Missense_Mutation_p.D335G|RASA1_ENST00000512763.1_Missense_Mutation_p.D334G|RASA1_ENST00000456692.2_Missense_Mutation_p.D324G	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	501	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)			NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		GAGGGTAGTGATGCCCAACTT	0.318																																					p.D501G		Atlas-SNP	.											.	RASA1	213	.	0			c.A1502G						PASS	.						76	77	77					5																	86659213		2203	4300	6503	SO:0001583	missense	5921	exon11			GTAGTGATGCCCA		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.1502A>G	chr5.hg19:g.86659213A>G	ENSP00000274376:p.Asp501Gly	102.0	0.0	.		78.0	31.0	.	NM_002890	B2R6W3|Q9UDI1	Missense_Mutation	SNP	ENST00000274376.6	hg19	CCDS34200.1	.	.	.	.	.	.	.	.	.	.	A	26.7	4.763741	0.89932	.	.	ENSG00000145715	ENST00000274376;ENST00000534133;ENST00000456692;ENST00000512763;ENST00000506290	T;T;T;T	0.12255	2.7;2.7;2.7;2.7	5.58	5.58	0.84498	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.31827	0.0809	L	0.49571	1.57	0.80722	D	1	D;D;D;D;D	0.67145	0.996;0.996;0.996;0.995;0.992	D;D;D;D;D	0.69479	0.964;0.935;0.964;0.939;0.947	T	0.01858	-1.1259	10	0.72032	D	0.01	.	15.754	0.78011	1.0:0.0:0.0:0.0	.	335;334;335;324;501	E9PGC0;B4DTL2;B4DTX4;P20936-2;P20936	.;.;.;.;RASA1_HUMAN	G	501;534;324;334;335	ENSP00000274376:D501G;ENSP00000411221:D324G;ENSP00000422008:D334G;ENSP00000420905:D335G	ENSP00000274376:D501G	D	+	2	0	RASA1	86694969	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	9.305000	0.96197	2.118000	0.64928	0.383000	0.25322	GAT	.	.	.	none		0.318	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890		G	86659213	A	G	86659213	3	3	268	1	0	0	0	0	1	0	0	0	13073	333	12	3	1556	3	RASA1	5	86659213	Missense_Mutation	SNP	A	TCGA-UZ-A9PZ-01A-11D-A42J-10	52721488	86659213	94256047	20	16917											
DST	667	hgsc.bcm.edu	37	chr6	56464935	56464935	+	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	catgaaggcttcttggtgacCaattaggcggttttcagttt	8	15	11	7	1	2	2	1	2	1	0	2	2	2	2	1	4	0	3	1	4	3	6			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr6:56464935C>G	ENST00000361203.3	-	41	11000	c.10993G>C	c.(10993-10995)Ggt>Cgt	p.G3665R	DST_ENST00000421834.2_Missense_Mutation_p.G1579R|DST_ENST00000244364.6_Missense_Mutation_p.G1253R|DST_ENST00000370788.2_Missense_Mutation_p.G1579R|DST_ENST00000370769.4_Missense_Mutation_p.G3667R|DST_ENST00000446842.2_Missense_Mutation_p.G3341R|DST_ENST00000370754.5_Missense_Mutation_p.G3845R|DST_ENST00000312431.6_Missense_Mutation_p.G3665R			Q03001	DYST_HUMAN	dystonin	3665					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)			TCTTGGTGACCAATTAGGCGG	0.403																																					p.G1253R		Atlas-SNP	.											.	DST	1427	.	0			c.G3757C						PASS	.						168	156	160					6																	56464935		1847	4102	5949	SO:0001583	missense	667	exon26			GGTGACCAATTAG	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.10993G>C	chr6.hg19:g.56464935C>G	ENSP00000354508:p.Gly3665Arg	124.0	0.0	.		74.0	27.0	.	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	hg19		.	.	.	.	.	.	.	.	.	.	C	17.41	3.383400	0.61845	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73	6.05	5.17	0.71159	.	0.113109	0.39341	N	0.001390	T	0.48624	0.1510	L	0.50333	1.59	0.29604	N	0.847445	D;D;D;D;B	0.69078	0.974;0.997;0.997;0.976;0.439	P;D;D;P;B	0.71184	0.726;0.972;0.972;0.788;0.209	T	0.46871	-0.9160	9	0.21540	T	0.41	.	14.4473	0.67359	0.0:0.9289:0.0:0.0711	.	1579;3667;3845;3665;1253	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	R	1253;3845;3667;1579;3341;3665;1579;3665	ENSP00000244364:G1253R;ENSP00000359790:G3845R;ENSP00000359805:G3667R;ENSP00000400883:G1579R;ENSP00000393645:G3341R;ENSP00000307959:G3665R;ENSP00000359824:G1579R;ENSP00000354508:G3665R	ENSP00000244364:G1253R	G	-	1	0	DST	56572894	0.999000	0.42202	0.887000	0.34795	0.994000	0.84299	4.339000	0.59322	1.543000	0.49345	0.650000	0.86243	GGT	.	.	.	none		0.403	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		G	56464935	C	G	56464935	3	3	268	1	0	0	0	0	1	0	0	0	4785	594	21	4	11994	4	DST	6	56464935	Missense_Mutation	SNP	C	TCGA-UZ-A9PZ-01A-11D-A42J-10		56464935	114650132	21	16918											
ZBTB24	9841	hgsc.bcm.edu	37	chr6	109796655	109796655	+	Missense_Mutation	SNP	T	T	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	acacatccatgaatttgcgaTggcagtctttgcattccggt	9	13	9	10	2	1	1	0	1	1	0	3	2	3	1	2	2	2	2	2	2	1	3	rs548726702		TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr6:109796655T>G	ENST00000230122.3	-	5	1402	c.1235A>C	c.(1234-1236)cAt>cCt	p.H412P		NM_001164313.1|NM_014797.2	NP_001157785.1|NP_055612.2	O43167	ZBT24_HUMAN	zinc finger and BTB domain containing 24	412					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)		GAATTTGCGATGGCAGTCTTT	0.453																																					p.H412P		Atlas-SNP	.											.	ZBTB24	64	.	0			c.A1235C						PASS	.						214	175	188					6																	109796655		2203	4300	6503	SO:0001583	missense	9841	exon5			TTGCGATGGCAGT	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.1235A>C	chr6.hg19:g.109796655T>G	ENSP00000230122:p.His412Pro	115.0	0.0	.		65.0	26.0	.	NM_014797	Q17RC6|Q5TED5|Q8N455	Missense_Mutation	SNP	ENST00000230122.3	hg19	CCDS34509.1	.	.	.	.	.	.	.	.	.	.	T	18.54	3.645420	0.67358	.	.	ENSG00000112365	ENST00000230122	T	0.07327	3.2	6.17	3.82	0.43975	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.047154	0.85682	D	0.000000	T	0.01765	0.0056	N	0.03948	-0.315	0.41015	D	0.985037	B	0.31009	0.303	B	0.34038	0.174	T	0.49707	-0.8911	10	0.72032	D	0.01	-13.7104	11.4813	0.50326	0.0:0.1436:0.0:0.8564	.	412	O43167	ZBT24_HUMAN	P	412	ENSP00000230122:H412P	ENSP00000230122:H412P	H	-	2	0	ZBTB24	109903348	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	2.512000	0.45485	0.579000	0.29504	0.533000	0.62120	CAT	.	.	.	none		0.453	ZBTB24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041758.1	NM_014797		G	109796655	T	G	109796655	3	3	268	1	0	0	0	0	1	0	0	0	17543	1464	51	5	870	5	ZBTB24	6	109796655	Missense_Mutation	SNP	T	TCGA-UZ-A9PZ-01A-11D-A42J-10	53331720	109796655	61318412	22	16919											
IGF2BP3	10643	hgsc.bcm.edu	37	chr7	23357270	23357270	+	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	gcacataccttgaactgagcCtctggtggtccagtgataat	10	11	10	10	0	1	3	0	3	1	0	2	3	2	3	3	2	3	1	3	2	3	3			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr7:23357270C>A	ENST00000258729.3	-	12	1739	c.1383G>T	c.(1381-1383)gaG>gaT	p.E461D		NM_006547.2	NP_006538.2	O00425	IF2B3_HUMAN	insulin-like growth factor 2 mRNA binding protein 3	461	KH 3. {ECO:0000255|PROSITE- ProRule:PRU00117}.				anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation regulator activity (GO:0045182)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(2)|prostate(2)|skin(4)|stomach(1)	34						TGAACTGAGCCTCTGGTGGTC	0.448																																					p.E461D		Atlas-SNP	.											.	IGF2BP3	71	.	0			c.G1383T						PASS	.						246	192	210					7																	23357270		2203	4300	6503	SO:0001583	missense	10643	exon12			CTGAGCCTCTGGT	AF117108	CCDS5382.1	7p15.3	2014-02-19			ENSG00000136231	ENSG00000136231		"RNA binding motif (RRM) containing"	28868	protein-coding gene	gene with protein product	"IGF II mRNA binding protein 3", "cancer/testis antigen 98"	608259				9891060, 9178771	Standard	NM_006547		Approved	IMP-3, CT98, IMP3	uc003swg.3	O00425	OTTHUMG00000128445	ENST00000258729.3:c.1383G>T	chr7.hg19:g.23357270C>A	ENSP00000258729:p.Glu461Asp	78.0	0.0	.		108.0	45.0	.	NM_006547	A0A4Z5|Q63HM0|Q6MZZ2|Q86VB1	Missense_Mutation	SNP	ENST00000258729.3	hg19	CCDS5382.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.931823	0.73442	.	.	ENSG00000136231	ENST00000258729	T	0.35236	1.32	5.52	4.62	0.57501	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.000000	0.85682	D	0.000000	T	0.33440	0.0863	L	0.37800	1.135	0.80722	D	1	B	0.32160	0.358	B	0.42625	0.393	T	0.05582	-1.0876	10	0.25751	T	0.34	-21.5421	9.7329	0.40372	0.0:0.8035:0.0:0.1965	.	461	O00425	IF2B3_HUMAN	D	461	ENSP00000258729:E461D	ENSP00000258729:E461D	E	-	3	2	IGF2BP3	23323795	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.113000	0.31184	2.767000	0.95098	0.655000	0.94253	GAG	.	.	.	none		0.448	IGF2BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250243.2	NM_006547		A	23357270	C	A	23357270	3	1	268	1	0	0	0	0	1	0	0	0	7582	680	24	4	372	4	IGF2BP3	7	23357270	Missense_Mutation	SNP	C	TCGA-UZ-A9PZ-01A-11D-A42J-10		23357270	135781393	23	16920											
AQP1	358	hgsc.bcm.edu	37	chr7	30963176	30963176	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgtgaaggtgtggaccagcGgccaggtggaggagtatgac	9	6	19	7	2	0	2	0	2	0	0	0	5	0	5	2	6	1	1	2	6	2	1	rs149637560		TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr7:30963176G>A	ENST00000311813.4	+	4	797	c.742G>A	c.(742-744)Ggc>Agc	p.G248S	AQP1_ENST00000409611.1_Missense_Mutation_p.G197S|AQP1_ENST00000409899.1_Missense_Mutation_p.G133S|AQP1_ENST00000434909.2_Missense_Mutation_p.G308S|AQP1_ENST00000509504.1_Missense_Mutation_p.G425S|AQP1_ENST00000441328.2_Missense_Mutation_p.G165S|AQP1_ENST00000482461.1_3'UTR	NM_198098.2	NP_932766.1	P29972	AQP1_HUMAN	aquaporin 1 (Colton blood group)	248					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|bicarbonate transport (GO:0015701)|camera-type eye morphogenesis (GO:0048593)|carbon dioxide transmembrane transport (GO:0035378)|carbon dioxide transport (GO:0015670)|cation transmembrane transport (GO:0098655)|cell volume homeostasis (GO:0006884)|cellular homeostasis (GO:0019725)|cellular hyperosmotic response (GO:0071474)|cellular response to cAMP (GO:0071320)|cellular response to copper ion (GO:0071280)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to inorganic substance (GO:0071241)|cellular response to mechanical stimulus (GO:0071260)|cellular response to mercury ion (GO:0071288)|cellular response to nitric oxide (GO:0071732)|cellular response to retinoic acid (GO:0071300)|cellular response to salt stress (GO:0071472)|cellular response to stress (GO:0033554)|cellular response to UV (GO:0034644)|cerebrospinal fluid secretion (GO:0033326)|cGMP biosynthetic process (GO:0006182)|corticotropin secretion (GO:0051458)|establishment or maintenance of actin cytoskeleton polarity (GO:0030950)|glomerular filtration (GO:0003094)|glycerol transport (GO:0015793)|hyperosmotic salinity response (GO:0042538)|lateral ventricle development (GO:0021670)|lipid digestion (GO:0044241)|maintenance of symbiont-containing vacuole by host (GO:0085018)|metanephric descending thin limb development (GO:0072220)|metanephric glomerulus vasculature development (GO:0072239)|metanephric proximal convoluted tubule segment 2 development (GO:0072232)|metanephric proximal straight tubule development (GO:0072230)|multicellular organismal water homeostasis (GO:0050891)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|nitric oxide transport (GO:0030185)|odontogenesis (GO:0042476)|pancreatic juice secretion (GO:0030157)|positive regulation of angiogenesis (GO:0045766)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of saliva secretion (GO:0046878)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|renal water absorption (GO:0070295)|renal water transport (GO:0003097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|secretory granule organization (GO:0033363)|sensory perception of pain (GO:0019233)|small molecule metabolic process (GO:0044281)|transepithelial water transport (GO:0035377)|transmembrane transport (GO:0055085)|water transport (GO:0006833)|wound healing (GO:0042060)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|axon terminus (GO:0043679)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|symbiont-containing vacuole (GO:0020003)	ammonium transmembrane transporter activity (GO:0008519)|carbon dioxide transmembrane transporter activity (GO:0035379)|glycerol transmembrane transporter activity (GO:0015168)|intracellular cGMP activated cation channel activity (GO:0005223)|nitric oxide transmembrane transporter activity (GO:0030184)|potassium channel activity (GO:0005267)|potassium ion transmembrane transporter activity (GO:0015079)|transmembrane transporter activity (GO:0022857)|water channel activity (GO:0015250)|water transmembrane transporter activity (GO:0005372)			kidney(1)|large_intestine(2)|lung(9)	12		Melanoma(862;0.16)			Acetazolamide(DB00819)	GTGGACCAGCGGCCAGGTGGA	0.622																																					p.G248S		Atlas-SNP	.											.	AQP1	38	.	0			c.G742A						PASS	.	G	SER/GLY,SER/GLY,SER/GLY,SER/GLY	0,4406		0,0,2203	51	43	46		493,589,397,742	5.1	1	7	dbSNP_134	46	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	AQP1	NM_001185060.1,NM_001185061.1,NM_001185062.1,NM_198098.2	56,56,56,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,	165/187,197/219,133/155,248/270	30963176	1,13005	2203	4300	6503	SO:0001583	missense	358	exon4			ACCAGCGGCCAGG	M77829	CCDS5431.1, CCDS55096.1, CCDS55097.1, CCDS55098.1	7p14	2014-07-19	2014-01-02		ENSG00000240583	ENSG00000240583		"Ion channels / Aquaporins", "Blood group antigens"	633	protein-coding gene	gene with protein product		107776	"Colton blood group", "aquaporin 1 (channel-forming integral protein, 28kDa)", "aquaporin 1 (channel-forming integral protein, 28kDa, CO blood group)", "aquaporin 1"	CO		1722319, 3166547	Standard	NM_198098		Approved	CHIP28		P29972	OTTHUMG00000023944	ENST00000311813.4:c.742G>A	chr7.hg19:g.30963176G>A	ENSP00000311165:p.Gly248Ser	228.0	0.0	.		252.0	116.0	.	NM_198098	B5BU39|E7EM69|E9PC21|F5GY19|Q8TBI5|Q8TDC1	Missense_Mutation	SNP	ENST00000311813.4	hg19	CCDS5431.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.419918	0.83559	0.0	1.16E-4	ENSG00000240583;ENSG00000240583;ENSG00000240583;ENSG00000240583;ENSG00000240583;ENSG00000240583;ENSG00000240583;ENSG00000250424	ENST00000434909;ENST00000265298;ENST00000311813;ENST00000413400;ENST00000441328;ENST00000409899;ENST00000409611;ENST00000509504	D;D;D;D;D;D	0.93953	-2.27;-1.97;-2.93;-3.32;-2.95;-2.27	5.07	5.07	0.68467	.	0.050340	0.85682	N	0.000000	D	0.95589	0.8566	L	0.61218	1.895	0.51233	D	0.99991	P;D;D;D	0.89917	0.774;1.0;1.0;1.0	B;D;D;D	0.91635	0.099;0.999;0.998;0.999	D	0.94980	0.8125	10	0.42905	T	0.14	0.8519	13.9555	0.64144	0.0:0.0:1.0:0.0	.	308;197;133;248	B4E220;E7EM69;E9PC21;P29972	.;.;.;AQP1_HUMAN	S	308;153;248;233;165;133;197;425	ENSP00000395059:G308S;ENSP00000311165:G248S;ENSP00000405698:G165S;ENSP00000386712:G133S;ENSP00000387178:G197S;ENSP00000421315:G425S	ENSP00000265298:G153S	G	+	1	0	RP5-877J2.1;AQP1	30929701	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.861000	0.75478	2.345000	0.79718	0.549000	0.68633	GGC	.	G|1.000;A|0.000	0.000	weak		0.622	AQP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215002.3	NM_000385		A	30963176	G	A	30963176	3	1	268	1	0	0	0	0	1	0	0	0	821	1116	39	1	1013	1	AQP1	7	30963176	Missense_Mutation	SNP	G	TCGA-UZ-A9PZ-01A-11D-A42J-10	7605906	30963176	128175487	24	16921											
SLC25A13	10165	hgsc.bcm.edu	37	chr7	95750615	95750615	+	Frame_Shift_Del	DEL	C	C	-																															tagcaactgccagtttgtagCccccaacgtgatcaggattc																										TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr7:95750615delC	ENST00000265631.5	-	18	2052	c.1916delG	c.(1915-1917)ggcfs	p.G639fs	SLC25A13_ENST00000416240.2_Frame_Shift_Del_p.G640fs|SLC25A13_ENST00000542654.1_Frame_Shift_Del_p.G531fs|SLC25A13_ENST00000494085.1_5'UTR			Q9UJS0	CMC2_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 13	639					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)	CAGTTTGTAGCCCCCAACGTG	0.448																																					p.G640fs		Atlas-Indel,Pindel	.											.	SLC25A13	131	.	0			c.1920delC						PASS	.						87	84	85					7																	95750615		2203	4300	6503	SO:0001589	frameshift_variant	10165	exon18			.	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.1916delG	chr7.hg19:g.95750615delC	ENSP00000265631:p.Gly639fs	174.0	0.0	0		194.0	88.0	0.453608	NM_001160210	O14566|O14575|Q546F9|Q9NZW1|Q9UNI7	Frame_Shift_Del	DEL	ENST00000265631.5	hg19	CCDS5645.1																																																																																			.	.	.	none		0.448	SLC25A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059395.2	NM_014251		-	95750615	C	-	95750615	7	5	268	1	0	1	0	1	0	0	0	0	14488	739	26	0	115	0	SLC25A13	7	95750615	Frame_Shift_Del	DEL	C	TCGA-UZ-A9PZ-01A-11D-A42J-10	64787439	95750615	63388048	25	16922											
C8orf74	203076	hgsc.bcm.edu	37	chr8	10555296	10555296	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgaccgttgcccacctggaGgtgtgcatgccaccccatcc	6	8	10	17	1	0	1	0	1	0	0	1	2	1	2	7	2	3	2	7	2	0	1			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr8:10555296G>A	ENST00000304519.5	+	3	458	c.429G>A	c.(427-429)gaG>gaA	p.E143E	RP1L1_ENST00000329335.3_Intron	NM_001040032.1	NP_001035121	Q6P047	CH074_HUMAN	chromosome 8 open reading frame 74	143										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	13				COAD - Colon adenocarcinoma(149;0.0811)		CCCACCTGGAGGTGTGCATGC	0.627																																					p.E143E		Atlas-SNP	.											.	C8orf74	28	.	0			c.G429A						PASS	.						125	129	128					8																	10555296		2143	4230	6373	SO:0001819	synonymous_variant	203076	exon3			CCTGGAGGTGTGC	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.429G>A	chr8.hg19:g.10555296G>A		102.0	0.0	.		69.0	25.0	.	NM_001040032	A2RUD6	Silent	SNP	ENST00000304519.5	hg19	CCDS47800.1																																																																																			.	.	.	none		0.627	C8orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375675.1	NM_001040032		A	10555296	G	A	10555296	2	1	268	1	0	0	0	0	0	0	0	1	2438	991	35	2		2	C8orf74	8	10555296	Silent	SNP	G	TCGA-UZ-A9PZ-01A-11D-A42J-10		10555296	135808726	26	16923											
SLC7A2	6542	hgsc.bcm.edu	37	chr8	17409383	17409383	+	Missense_Mutation	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	cagctttaacacttatgatgCcgtactacctcctcgatgaa	11	12	6	12	2	0	2	0	2	0	0	2	3	1	2	3	0	5	2	3	0	5	5			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr8:17409383C>T	ENST00000494857.1	+	7	1161	c.943C>T	c.(943-945)Ccg>Tcg	p.P315S	SLC7A2_ENST00000004531.10_Missense_Mutation_p.P355S|SLC7A2_ENST00000522656.1_Missense_Mutation_p.P315S|SLC7A2_ENST00000398090.3_Missense_Mutation_p.P355S|SLC7A2_ENST00000470360.1_Missense_Mutation_p.P355S	NM_001008539.3	NP_001008539.3	P52569	CTR2_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	315					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)	ACTTATGATGCCGTACTACCT	0.483																																					p.P355S		Atlas-SNP	.											.	SLC7A2	157	.	0			c.C1063T						PASS	.						220	203	208					8																	17409383		2203	4300	6503	SO:0001583	missense	6542	exon6			ATGATGCCGTACT	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.943C>T	chr8.hg19:g.17409383C>T	ENSP00000419140:p.Pro315Ser	186.0	0.0	.		120.0	50.0	.	NM_001164771	B7ZL54|O15291|O15292|Q14CQ6|Q6NSZ7|Q86TC6	Missense_Mutation	SNP	ENST00000494857.1	hg19	CCDS34852.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.660463	0.88154	.	.	ENSG00000003989	ENST00000494857;ENST00000522656;ENST00000470360;ENST00000004531;ENST00000398090	D;D;D;D;D	0.91843	-2.92;-2.92;-2.92;-2.92;-2.92	5.4	5.4	0.78164	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.96466	0.8847	M	0.82433	2.59	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	0.96575	0.9426	10	0.72032	D	0.01	.	19.5642	0.95386	0.0:1.0:0.0:0.0	.	355;355;315	P52569-3;P52569-2;P52569	.;.;CTR2_HUMAN	S	315;315;355;355;355	ENSP00000419140:P315S;ENSP00000430464:P315S;ENSP00000419873:P355S;ENSP00000004531:P355S;ENSP00000381164:P355S	ENSP00000004531:P355S	P	+	1	0	SLC7A2	17453761	1.000000	0.71417	0.999000	0.59377	0.723000	0.41478	7.818000	0.86416	2.702000	0.92279	0.655000	0.94253	CCG	.	.	.	none		0.483	SLC7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253367.3	NM_003046		T	17409383	C	T	17409383	3	4	268	1	0	0	0	0	1	0	0	0	14710	739	26	2	1085	2	SLC7A2	8	17409383	Missense_Mutation	SNP	C	TCGA-UZ-A9PZ-01A-11D-A42J-10	6854087	17409383	128954639	27	16924											
PEX2	5828	hgsc.bcm.edu	37	chr8	77896129	77896129	+	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	ttgatttttactgggtggctGatatctcaggttaggggaaa	9	15	13	4	0	1	2	1	2	1	0	2	3	1	3	0	5	1	2	0	5	4	6			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr8:77896129G>A	ENST00000419564.2	-	4	750	c.286C>T	c.(286-288)Cag>Tag	p.Q96*	PEX2_ENST00000357039.4_Nonsense_Mutation_p.Q96*|PEX2_ENST00000522527.1_Nonsense_Mutation_p.Q96*|PEX2_ENST00000520103.1_Nonsense_Mutation_p.Q96*	NM_001172087.1	NP_001165558.1	P28328	PEX2_HUMAN	peroxisomal biogenesis factor 2	96					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						CTGGGTGGCTGATATCTCAGG	0.373																																					p.Q96X		Atlas-SNP	.											.	PEX2	44	.	0			c.C286T						PASS	.						48	47	47					8																	77896129		2203	4300	6503	SO:0001587	stop_gained	5828	exon4			GTGGCTGATATCT	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.286C>T	chr8.hg19:g.77896129G>A	ENSP00000400984:p.Gln96*	154.0	0.0	.		103.0	35.0	.	NM_000318	Q567S6|Q9BW41	Nonsense_Mutation	SNP	ENST00000419564.2	hg19	CCDS6221.1	.	.	.	.	.	.	.	.	.	.	G	37	6.549895	0.97654	.	.	ENSG00000164751	ENST00000357039;ENST00000419564;ENST00000520103;ENST00000522527;ENST00000518986	.	.	.	5.04	5.04	0.67666	.	0.183165	0.46442	D	0.000298	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	-1.9694	13.5869	0.61937	0.0:0.0:0.8448:0.1552	.	.	.	.	X	96	.	ENSP00000349543:Q96X	Q	-	1	0	PEX2	78058684	1.000000	0.71417	0.304000	0.25085	0.816000	0.46133	3.661000	0.54503	2.625000	0.88918	0.558000	0.71614	CAG	.	.	.	none		0.373	PEX2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379122.1	NM_000318		A	77896129	G	A	77896129	4	1	268	1	0	0	0	0	0	1	0	0	11752	1299	45	2	635	2	PEX2	8	77896129	Nonsense_Mutation	SNP	G	TCGA-UZ-A9PZ-01A-11D-A42J-10	60486746	77896129	68467893	28	16925											
PHF2	5253	hgsc.bcm.edu	37	chr9	96435951	96435951	+	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	0	0	0	0	0	0	0	0	0	caggcctccgactcctgcctGcagaccacgtggggagctgg	6	6	14	15	2	0	1	0	0	0	1	2	3	2	2	5	4	3	2	5	4	0	0			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr9:96435951G>C	ENST00000359246.4	+	18	2800	c.2433G>C	c.(2431-2433)ctG>ctC	p.L811L	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	811					liver development (GO:0001889)|negative regulation of chromatin silencing at rDNA (GO:0061188)|protein demethylation (GO:0006482)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K9 specific) (GO:0032454)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		ACTCCTGCCTGCAGACCACGT	0.667																																					p.L811L		Atlas-SNP	.											.	PHF2	113	.	0			c.G2433C						PASS	.						34	37	36					9																	96435951		2203	4300	6503	SO:0001819	synonymous_variant	5253	exon18			CTGCCTGCAGACC	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.2433G>C	chr9.hg19:g.96435951G>C		150.0	0.0	.		116.0	47.0	.	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Silent	SNP	ENST00000359246.4	hg19	CCDS35069.1																																																																																			.	.	.	none		0.667	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392		C	96435951	G	C	96435951	2	2	268	1	0	0	0	0	0	0	0	1	11837	1306	46	4		4	PHF2	9	96435951	Silent	SNP	G	TCGA-UZ-A9PZ-01A-11D-A42J-10		96435951	44777480	29	16926											
CUBN	8029	hgsc.bcm.edu	37	chr10	16941122	16941122	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atctgctgttttcgggaaaaTtctgaggccagtgaggggat	9	12	14	6	1	2	2	0	2	2	0	3	4	2	4	1	4	1	2	1	4	2	3	rs141773881		TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr10:16941122T>C	ENST00000377833.4	-	54	8536	c.8471A>G	c.(8470-8472)aAt>aGt	p.N2824S		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2824	CUB 21. {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)	TTCGGGAAAATTCTGAGGCCA	0.428																																					p.N2824S		Atlas-SNP	.											.	CUBN	515	.	0			c.A8471G						PASS	.	T	SER/ASN	0,4406		0,0,2203	140	131	134		8471	1.6	0.7	10	dbSNP_134	134	1,8599	1.2+/-3.3	0,1,4299	no	missense	CUBN	NM_001081.3	46	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	possibly-damaging	2824/3624	16941122	1,13005	2203	4300	6503	SO:0001583	missense	8029	exon54			GGAAAATTCTGAG	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.8471A>G	chr10.hg19:g.16941122T>C	ENSP00000367064:p.Asn2824Ser	130.0	0.0	.		96.0	78.0	.	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	hg19	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	T	10.93	1.490599	0.26686	0.0	1.16E-4	ENSG00000107611	ENST00000377833	T	0.28666	1.6	5.63	1.6	0.23607	CUB (5);	0.653650	0.13545	N	0.379921	T	0.33789	0.0875	L	0.53729	1.69	0.80722	D	1	P	0.41366	0.747	B	0.43386	0.418	T	0.17992	-1.0351	10	0.45353	T	0.12	.	13.0134	0.58743	0.0:0.0:0.3986:0.6014	.	2824	O60494	CUBN_HUMAN	S	2824	ENSP00000367064:N2824S	ENSP00000367064:N2824S	N	-	2	0	CUBN	16981128	1.000000	0.71417	0.713000	0.30519	0.079000	0.17450	3.883000	0.56168	0.452000	0.26830	0.459000	0.35465	AAT	.	T|1.000;C|0.000	0.000	weak		0.428	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		C	16941122	T	C	16941122	3	2	268	1	0	0	0	0	1	0	0	0	4053	1493	52	3	2456	3	CUBN	10	16941122	Missense_Mutation	SNP	T	TCGA-UZ-A9PZ-01A-11D-A42J-10		16941122	118593625	30	16927											
NLRP14	338323	hgsc.bcm.edu	37	chr11	7064285	7064285	+	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	ggagtatatttaccagttttTtgaagataagaggtgggcca	12	13	12	4	0	0	3	0	1	0	2	0	4	0	4	2	3	1	2	2	3	5	8			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr11:7064285T>A	ENST00000299481.4	+	4	1374	c.1028T>A	c.(1027-1029)tTt>tAt	p.F343Y		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	343	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)		TACCAGTTTTTTGAAGATAAG	0.418																																					p.F343Y		Atlas-SNP	.											.	NLRP14	187	.	0			c.T1028A						PASS	.						93	98	96					11																	7064285		2201	4296	6497	SO:0001583	missense	338323	exon4			AGTTTTTTGAAGA	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.1028T>A	chr11.hg19:g.7064285T>A	ENSP00000299481:p.Phe343Tyr	128.0	0.0	.		83.0	30.0	.	NM_176822	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	hg19	CCDS7776.1	.	.	.	.	.	.	.	.	.	.	T	16.50	3.140789	0.56936	.	.	ENSG00000158077	ENST00000299481	T	0.81330	-1.48	4.51	3.34	0.38264	NACHT nucleoside triphosphatase (1);	0.272209	0.26840	N	0.022228	D	0.88905	0.6564	M	0.86740	2.835	0.27111	N	0.962373	D	0.76494	0.999	D	0.69824	0.966	T	0.81604	-0.0857	10	0.62326	D	0.03	.	9.4923	0.38967	0.0:0.0:0.1784:0.8216	.	343	Q86W24	NAL14_HUMAN	Y	343	ENSP00000299481:F343Y	ENSP00000299481:F343Y	F	+	2	0	NLRP14	7020861	0.997000	0.39634	0.149000	0.22428	0.663000	0.39108	3.745000	0.55119	0.842000	0.35045	0.533000	0.62120	TTT	.	.	.	none		0.418	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822		A	7064285	T	A	7064285	3	1	268	1	0	0	0	0	1	0	0	0	10483	1841	64	5	1038	5	NLRP14	11	7064285	Missense_Mutation	SNP	T	TCGA-UZ-A9PZ-01A-11D-A42J-10		7064285	127942231	31	16928											
FAR1	84188	hgsc.bcm.edu	37	chr11	13729613	13729613	+	Missense_Mutation	SNP	A	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	ctgtggatcccaagaagctgAttgattctttagagtatgtt	10	15	10	6	0	1	4	0	2	1	2	2	5	2	5	1	1	1	3	1	1	4	6			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr11:13729613A>C	ENST00000354817.3	+	4	676	c.532A>C	c.(532-534)Att>Ctt	p.I178L		NM_032228.5	NP_115604.1	Q8WVX9	FACR1_HUMAN	fatty acyl CoA reductase 1	178					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						CAAGAAGCTGATTGATTCTTT	0.413																																					p.I178L		Atlas-SNP	.											.	FAR1	40	.	0			c.A532C						PASS	.						134	131	132					11																	13729613		2200	4294	6494	SO:0001583	missense	84188	exon4			AAGCTGATTGATT	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.532A>C	chr11.hg19:g.13729613A>C	ENSP00000346874:p.Ile178Leu	80.0	0.0	.		47.0	23.0	.	NM_032228	D3DQW8|Q5CZA3	Missense_Mutation	SNP	ENST00000354817.3	hg19	CCDS7813.1	.	.	.	.	.	.	.	.	.	.	A	16.79	3.219145	0.58560	.	.	ENSG00000197601	ENST00000354817;ENST00000532701;ENST00000355107	T;T	0.28895	2.03;1.59	5.83	5.83	0.93111	NAD(P)-binding domain (1);Male sterility, NAD-binding (1);	0.044587	0.85682	D	0.000000	T	0.24005	0.0581	L	0.31578	0.945	0.80722	D	1	B;B	0.12013	0.005;0.001	B;B	0.17979	0.02;0.012	T	0.07404	-1.0774	10	0.13853	T	0.58	-16.2928	15.8464	0.78895	1.0:0.0:0.0:0.0	.	178;178	E7ETC1;Q8WVX9	.;FACR1_HUMAN	L	178	ENSP00000346874:I178L;ENSP00000437111:I178L	ENSP00000346874:I178L	I	+	1	0	FAR1	13686189	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.011000	0.70760	2.216000	0.71823	0.477000	0.44152	ATT	.	.	.	none		0.413	FAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385990.2	NM_032228		C	13729613	A	C	13729613	3	2	268	1	0	0	0	0	1	0	0	0	5681	333	12	5	542	5	FAR1	11	13729613	Missense_Mutation	SNP	A	TCGA-UZ-A9PZ-01A-11D-A42J-10	6665328	13729613	121276903	32	16929											
TSPAN11	441631	hgsc.bcm.edu	37	chr12	31135568	31135568	+	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	gtgcccgacagctgctgcaaGacagtggtggtgcgctgcgg	6	7	17	11	3	0	1	0	0	0	1	0	2	0	1	1	3	6	4	1	3	1	0			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr12:31135568G>C	ENST00000261177.9	+	6	617	c.558G>C	c.(556-558)aaG>aaC	p.K186N	TSPAN11_ENST00000535215.1_Missense_Mutation_p.K115N|TSPAN11_ENST00000544427.1_Missense_Mutation_p.K176N|TSPAN11_ENST00000546076.1_Missense_Mutation_p.K186N	NM_001080509.2	NP_001073978.1	A1L157	TSN11_HUMAN	tetraspanin 11	186						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)	11	all_lung(12;3.11e-10)|Lung NSC(12;5.24e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					GCTGCTGCAAGACAGTGGTGG	0.647																																					p.K186N		Atlas-SNP	.											.	TSPAN11	30	.	0			c.G558C						PASS	.						19	21	20					12																	31135568		2198	4296	6494	SO:0001583	missense	441631	exon6			CTGCAAGACAGTG		CCDS31765.1	12p11.21	2013-02-14				ENSG00000110900		"Tetraspanins"	30795	protein-coding gene	gene with protein product							Standard	NM_001080509		Approved		uc001rjp.3	A1L157		ENST00000261177.9:c.558G>C	chr12.hg19:g.31135568G>C	ENSP00000261177:p.Lys186Asn	208.0	0.0	.		134.0	59.0	.	NM_001080509	A1L158|B2RUX6	Missense_Mutation	SNP	ENST00000261177.9	hg19	CCDS31765.1	.	.	.	.	.	.	.	.	.	.	G	15.37	2.814257	0.50527	.	.	ENSG00000110900	ENST00000546076;ENST00000535215;ENST00000544427;ENST00000261177	D;D;D;D	0.87334	-2.24;-2.24;-2.24;-2.24	4.01	4.01	0.46588	Tetraspanin, EC2 domain (1);	0.446856	0.20497	U	0.091161	D	0.91418	0.7292	M	0.69185	2.1	0.49798	D	0.999823	D;D	0.89917	0.999;1.0	D;D	0.81914	0.986;0.995	D	0.89311	0.3633	10	0.24483	T	0.36	.	13.6064	0.62050	0.0:0.0:1.0:0.0	.	176;186	F5H0F0;A1L157	.;TSN11_HUMAN	N	186;115;176;186	ENSP00000437403:K186N;ENSP00000445503:K115N;ENSP00000439895:K176N;ENSP00000261177:K186N	ENSP00000261177:K186N	K	+	3	2	TSPAN11	31026835	1.000000	0.71417	1.000000	0.80357	0.334000	0.28698	1.524000	0.35942	1.752000	0.51891	0.313000	0.20887	AAG	.	.	.	none		0.647	TSPAN11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399888.1	XM_497334		C	31135568	G	C	31135568	3	2	268	1	0	0	0	0	1	0	0	0	16647	933	33	4	576	4	TSPAN11	12	31135568	Missense_Mutation	SNP	G	TCGA-UZ-A9PZ-01A-11D-A42J-10		31135568	102716327	33	16930											
ZFC3H1	196441	hgsc.bcm.edu	37	chr12	72056805	72056805	+	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	aaggatacagctcttccgagGtggagagggctctcgccagc	9	7	14	11	2	2	1	0	0	2	1	4	4	3	2	2	4	3	2	2	4	2	2			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr12:72056805G>T	ENST00000378743.3	-	1	944	c.586C>A	c.(586-588)Cct>Act	p.P196T	ZFC3H1_ENST00000552037.1_Missense_Mutation_p.P196T|THAP2_ENST00000547843.1_5'Flank|THAP2_ENST00000308086.2_5'UTR|ZFC3H1_ENST00000549407.1_5'UTR|ZFC3H1_ENST00000548100.1_Missense_Mutation_p.P196T	NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	196					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						CTCTTCCGAGGTGGAGAGGGC	0.587																																					p.P196T		Atlas-SNP	.											.	ZFC3H1	172	.	0			c.C586A						PASS	.						136	151	147					12																	72056805		2010	4169	6179	SO:0001583	missense	196441	exon1			TCCGAGGTGGAGA	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.586C>A	chr12.hg19:g.72056805G>T	ENSP00000368017:p.Pro196Thr	35.0	0.0	.		32.0	13.0	.	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Missense_Mutation	SNP	ENST00000378743.3	hg19	CCDS41813.1	.	.	.	.	.	.	.	.	.	.	G	12.00	1.805554	0.31961	.	.	ENSG00000133858	ENST00000378743;ENST00000548100;ENST00000552037	T	0.29142	1.58	3.73	3.73	0.42828	.	0.434461	0.21170	N	0.078982	T	0.23532	0.0569	N	0.08118	0	0.80722	D	1	B;D;P	0.54207	0.361;0.965;0.849	B;P;B	0.49708	0.141;0.62;0.227	T	0.08371	-1.0725	10	0.34782	T	0.22	.	14.9879	0.71362	0.0:0.0:1.0:0.0	.	196;196;196	G3V1X1;O60293-4;O60293	.;.;ZC3H1_HUMAN	T	196	ENSP00000368017:P196T	ENSP00000368017:P196T	P	-	1	0	ZFC3H1	70343072	0.997000	0.39634	1.000000	0.80357	0.996000	0.88848	2.062000	0.41413	2.384000	0.81235	0.650000	0.86243	CCT	.	.	.	none		0.587	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		T	72056805	G	T	72056805	3	4	268	1	0	0	0	0	1	0	0	0	17645	1261	44	4	5523	4	ZFC3H1	12	72056805	Missense_Mutation	SNP	G	TCGA-UZ-A9PZ-01A-11D-A42J-10	40921237	72056805	61795090	34	16931											
VPS36	51028	hgsc.bcm.edu	37	chr13	52992189	52992189	+	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	actaaatcttctggtgagagCaactaatagggaaaaaaaat	19	9	8	5	0	2	1	0	1	2	1	2	3	2	2	0	2	2	1	0	2	9	4			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr13:52992189C>A	ENST00000378060.4	-	11	870	c.843G>T	c.(841-843)ttG>ttT	p.L281F		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)	281					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)		CTGGTGAGAGCAACTAATAGG	0.363																																					p.L281F		Atlas-SNP	.											.	VPS36	38	.	0			c.G843T						PASS	.						78	71	73					13																	52992189		2203	4300	6503	SO:0001583	missense	51028	exon11			TGAGAGCAACTAA	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.843G>T	chr13.hg19:g.52992189C>A	ENSP00000367299:p.Leu281Phe	90.0	0.0	.		55.0	12.0	.	NM_016075	A8K125|Q3ZCV7|Q5H9S1|Q5VXB6|Q9H8Z5|Q9Y3E3	Missense_Mutation	SNP	ENST00000378060.4	hg19	CCDS9434.1	.	.	.	.	.	.	.	.	.	.	.	20.4	3.978040	0.74360	.	.	ENSG00000136100	ENST00000378060	.	.	.	5.36	4.5	0.54988	.	0.000000	0.85682	D	0.000000	D	0.85102	0.5620	M	0.93594	3.435	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88191	0.2877	9	0.87932	D	0	-9.0496	12.9041	0.58141	0.0:0.9216:0.0:0.0783	.	281	Q86VN1	VPS36_HUMAN	F	281	.	ENSP00000367299:L281F	L	-	3	2	VPS36	51890190	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.228000	0.32588	2.653000	0.90120	0.561000	0.74099	TTG	.	.	.	none		0.363	VPS36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045059.3			A	52992189	C	A	52992189	3	1	268	1	0	0	0	0	1	0	0	0	17216	709	25	4	333	4	VPS36	13	52992189	Missense_Mutation	SNP	C	TCGA-UZ-A9PZ-01A-11D-A42J-10		52992189	62177689	35	16932											
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77657271	77657272	+	Missense_Mutation	DNP	TT	TT	CG																															tgtggtaaaggatgagcagcTtccccggcaatcactatgtc																										TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr13:77657271_77657272TT>CG	ENST00000544440.2	-	63	10834_10835	c.10817_10818AA>CG	c.(10816-10818)gAA>gCG	p.E3606A	MYCBP2-AS1_ENST00000448470.2_RNA|MYCBP2-AS1_ENST00000450627.2_RNA|MYCBP2-AS1_ENST00000422231.2_RNA|MYCBP2-AS1_ENST00000593933.1_RNA|MYCBP2-AS2_ENST00000428716.2_RNA|MYCBP2_ENST00000407578.2_Missense_Mutation_p.E3644A|MYCBP2_ENST00000357337.6_Missense_Mutation_p.E3606A					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)		GATGAGCAGCTTCCCCGGCAAT	0.47																																					p.E3644E|p.E3644A		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.A10932G|c.A10931C						PASS	.																																			SO:0001583	missense	23077	exon63			AGCAGCTTCCCCG|GCAGCTTCCCCGG	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.10817_10818delinsCG	chr13.hg19:g.77657271_77657272delinsCG	ENSP00000444596:p.Glu3606Ala	102.0|99.0	0.0	.		60.0|59.0	20.0|18.0	.	NM_015057		Silent|Missense_Mutation	SNP	ENST00000544440.2	hg19																																																																																				.	.	.	none		0.47	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		CG	77657272	TT	CG	77657271	3	2	268	1	0	0	0	0	1	0	0	0	10025	1606	56	3	3188	3	MYCBP2	13	77657271	Missense_Mutation	DNP	TT	TCGA-UZ-A9PZ-01A-11D-A42J-10	24665082	77657271	37512607	36	16933											
KCNH5	27133	hgsc.bcm.edu	37	chr14	63468086	63468086	+	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	tctattggctgtttgaacaaCgtaatatccttgaaagtaca	13	14	7	7	1	1	2	0	2	1	0	2	2	2	2	1	1	3	4	1	1	7	7	rs143574473		TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr14:63468086C>T	ENST00000322893.7	-	4	664	c.396G>A	c.(394-396)acG>acA	p.T132T	KCNH5_ENST00000420622.2_Silent_p.T132T|KCNH5_ENST00000394964.2_Silent_p.T74T|KCNH5_ENST00000394968.1_Silent_p.T74T	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	132	PAC. {ECO:0000255|PROSITE- ProRule:PRU00141}.				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)		GTTTGAACAACGTAATATCCT	0.343													C|||	1	0.000199681	0	0	5008	,	,		18984	0		0	False		,,,				2504	0.001				p.T132T		Atlas-SNP	.											.	KCNH5	320	.	0			c.G396A						PASS	.	C	,,	0,4406		0,0,2203	113	101	105		396,396,222	-11.3	0.1	14	dbSNP_134	105	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	KCNH5	NM_139318.3,NM_172375.1,NM_172376.1	,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,	132/989,132/612,74/625	63468086	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	27133	exon4			GAACAACGTAATA	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.396G>A	chr14.hg19:g.63468086C>T		130.0	0.0	.		102.0	32.0	.	NM_172375	C9JP98	Silent	SNP	ENST00000322893.7	hg19	CCDS9756.1																																																																																			.	C|1.000;T|0.000	0.000	weak		0.343	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		T	63468086	C	T	63468086	2	4	268	1	0	0	0	0	0	0	0	1	8042	523	19	1		1	KCNH5	14	63468086	Silent	SNP	C	TCGA-UZ-A9PZ-01A-11D-A42J-10		63468086	43881454	37	16934											
SLC28A1	9154	hgsc.bcm.edu	37	chr15	85488365	85488365	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctttttagcgtcaatccAgagttcagcccagaggccct	8	13	8	12	1	3	2	2	0	1	2	4	2	4	2	3	1	2	1	3	1	2	5			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr15:85488365A>G	ENST00000286749.3	+	18	1974	c.1884A>G	c.(1882-1884)ccA>ccG	p.P628P	SLC28A1_ENST00000538177.1_Silent_p.P462P|SLC28A1_ENST00000394573.1_Silent_p.P628P|SLC28A1_ENST00000537624.1_Intron|SLC28A1_ENST00000537216.1_Intron			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	628					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)	GCGTCAATCCAGAGTTCAGCC	0.547																																					p.P628P		Atlas-SNP	.											.	SLC28A1	118	.	0			c.A1884G						PASS	.						141	124	130					15																	85488365		2203	4299	6502	SO:0001819	synonymous_variant	9154	exon19			CAATCCAGAGTTC	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.1884A>G	chr15.hg19:g.85488365A>G		124.0	0.0	.		81.0	35.0	.	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Silent	SNP	ENST00000286749.3	hg19	CCDS10334.1																																																																																			.	.	.	none		0.547	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2			G	85488365	A	G	85488365	2	3	268	1	0	0	0	0	0	0	0	1	14544	175	7	3		3	SLC28A1	15	85488365	Silent	SNP	A	TCGA-UZ-A9PZ-01A-11D-A42J-10		85488365	17043027	38	16935											
SHMT1	6470	hgsc.bcm.edu	37	chr17	18232672	18232672	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctggggtccccagccgcAgtccactgggccgcagagcg	5	5	16	15	3	0	1	0	0	0	1	2	1	2	1	5	3	3	3	5	3	0	0			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr17:18232672A>G	ENST00000316694.3	-	11	1336	c.1202T>C	c.(1201-1203)cTg>cCg	p.L401P	SHMT1_ENST00000354098.3_Missense_Mutation_p.L362P|SHMT1_ENST00000539052.1_Missense_Mutation_p.L263P|SHMT1_ENST00000352886.6_Missense_Mutation_p.L321P	NM_004169.3	NP_004160.3	P34896	GLYC_HUMAN	serine hydroxymethyltransferase 1 (soluble)	401					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)	CCCCAGCCGCAGTCCACTGGG	0.498																																					p.L401P		Atlas-SNP	.											.	SHMT1	36	.	0			c.T1202C						PASS	.						41	43	42					17																	18232672		2203	4300	6503	SO:0001583	missense	6470	exon11			AGCCGCAGTCCAC		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.1202T>C	chr17.hg19:g.18232672A>G	ENSP00000318868:p.Leu401Pro	57.0	0.0	.		57.0	18.0	.	NM_004169	B4DPM9|D3DXD0|Q96HY0|Q9UMD1|Q9UMD2	Missense_Mutation	SNP	ENST00000316694.3	hg19	CCDS11196.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.193981	0.78902	.	.	ENSG00000176974	ENST00000316694;ENST00000395684;ENST00000352886;ENST00000539052;ENST00000354098	T;T;T;T	0.39592	1.07;1.07;1.07;1.07	5.52	5.52	0.82312	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	T	0.75838	0.3904	H	0.96048	3.76	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.91635	0.979;0.999	D	0.84338	0.0525	10	0.87932	D	0	-15.5184	15.9269	0.79624	1.0:0.0:0.0:0.0	.	362;401	P34896-2;P34896	.;GLYC_HUMAN	P	401;176;321;263;362	ENSP00000318868:L401P;ENSP00000345881:L321P;ENSP00000440089:L263P;ENSP00000318805:L362P	ENSP00000318868:L401P	L	-	2	0	SHMT1	18173397	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	6.913000	0.75759	2.228000	0.72767	0.533000	0.62120	CTG	.	.	.	none		0.498	SHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130831.2	NM_004169		G	18232672	A	G	18232672	3	3	268	1	0	0	0	0	1	0	0	0	14298	188	7	3	257	3	SHMT1	17	18232672	Missense_Mutation	SNP	A	TCGA-UZ-A9PZ-01A-11D-A42J-10		18232672	62962538	39	16936											
TBCD	6904	hgsc.bcm.edu	37	chr17	80714073	80714073	+	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	aataccaggagcagcctcatCtgttggacccgcaccttggt	9	9	10	13	1	2	0	1	0	1	0	2	2	2	2	4	3	3	3	4	3	2	3			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr17:80714073C>A	ENST00000355528.4	+	2	347	c.217C>A	c.(217-219)Ctg>Atg	p.L73M	TBCD_ENST00000397466.2_5'UTR|TBCD_ENST00000539345.2_Missense_Mutation_p.L73M	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	73					'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)			GCAGCCTCATCTGTTGGACCC	0.433																																					p.L73M		Atlas-SNP	.											.	TBCD	94	.	0			c.C217A						PASS	.						96	91	92					17																	80714073		1904	4125	6029	SO:0001583	missense	6904	exon2			CCTCATCTGTTGG	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.217C>A	chr17.hg19:g.80714073C>A	ENSP00000347719:p.Leu73Met	100.0	0.0	.		78.0	42.0	.	NM_005993	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Missense_Mutation	SNP	ENST00000355528.4	hg19	CCDS45818.1	.	.	.	.	.	.	.	.	.	.	C	19.26	3.793621	0.70452	.	.	ENSG00000141556	ENST00000355528;ENST00000536182	T	0.69926	-0.44	4.84	4.84	0.62591	Armadillo-type fold (1);	.	.	.	.	D	0.85835	0.5789	M	0.92507	3.315	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.89585	0.3823	8	.	.	.	.	16.5397	0.84382	0.0:1.0:0.0:0.0	.	73;73	Q9BTW9;Q9BTW9-4	TBCD_HUMAN;.	M	73	ENSP00000347719:L73M	.	L	+	1	2	TBCD	78307362	0.982000	0.34865	1.000000	0.80357	0.728000	0.41692	0.757000	0.26433	2.231000	0.72958	0.655000	0.94253	CTG	.	.	.	none		0.433	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993		A	80714073	C	A	80714073	3	1	268	1	0	0	0	0	1	0	0	0	15645	912	32	4	223	4	TBCD	17	80714073	Missense_Mutation	SNP	C	TCGA-UZ-A9PZ-01A-11D-A42J-10	62481401	80714073	481137	40	16937											
DSG1	1828	hgsc.bcm.edu	37	chr18	28935300	28935300	+	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	aagtatagtaccgtgcaataTagcaagtagtcaggacccca	15	8	9	9	1	1	0	1	0	0	0	1	1	1	1	3	1	3	5	3	1	9	6			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr18:28935300T>A	ENST00000257192.4	+	15	3353	c.3141T>A	c.(3139-3141)taT>taA	p.Y1047*	RP11-534N16.1_ENST00000578119.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000581452.1_RNA|RP11-534N16.1_ENST00000578477.1_RNA|DSG1_ENST00000462981.2_Nonsense_Mutation_p.Y406*	NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	1047					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)			CCGTGCAATATAGCAAGTAGT	0.438																																					p.Y1047X		Atlas-SNP	.											.	DSG1	176	.	0			c.T3141A						PASS	.						50	47	48					18																	28935300		2203	4300	6503	SO:0001587	stop_gained	1828	exon15			GCAATATAGCAAG	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.3141T>A	chr18.hg19:g.28935300T>A	ENSP00000257192:p.Tyr1047*	89.0	0.0	.		63.0	26.0	.	NM_001942	B7Z845	Nonsense_Mutation	SNP	ENST00000257192.4	hg19	CCDS11896.1	.	.	.	.	.	.	.	.	.	.	T	32	5.188195	0.94923	.	.	ENSG00000134760	ENST00000257192	.	.	.	6.17	-5.88	0.02290	.	0.000000	0.64402	D	0.000009	.	.	.	.	.	.	0.41102	D	0.985674	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.1241	0.97973	0.0:0.6843:0.0:0.3157	.	.	.	.	X	1047	.	ENSP00000257192:Y1047X	Y	+	3	2	DSG1	27189298	0.110000	0.22057	0.666000	0.29783	0.810000	0.45777	-1.057000	0.03486	-1.021000	0.03350	-0.242000	0.12053	TAT	.	.	.	none		0.438	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942		A	28935300	T	A	28935300	4	1	268	1	0	0	0	0	0	1	0	0	4778	1413	49	5	3199	5	DSG1	18	28935300	Nonsense_Mutation	SNP	T	TCGA-UZ-A9PZ-01A-11D-A42J-10		28935300	49141948	41	16938											
ZNF429	353088	hgsc.bcm.edu	37	chr19	21712584	21712584	+	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	ctacagaaacttggtcttccTgggtgagaataacttcaata	13	12	8	8	0	2	2	1	1	1	2	3	3	3	2	1	2	3	0	1	2	6	6			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr19:21712584T>A	ENST00000358491.4	+	2	336	c.128T>A	c.(127-129)cTg>cAg	p.L43Q	ZNF429_ENST00000597078.1_Missense_Mutation_p.L43Q|ZNF429_ENST00000594022.1_3'UTR	NM_001001415.2	NP_001001415.2	Q86V71	ZN429_HUMAN	zinc finger protein 429	43	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(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						TTGGTCTTCCTGGGTGAGAAT	0.373																																					p.L43Q		Atlas-SNP	.											.	ZNF429	338	.	0			c.T128A						PASS	.						100	111	107					19																	21712584		2201	4299	6500	SO:0001583	missense	353088	exon2			TCTTCCTGGGTGA	AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013		"Zinc fingers, C2H2-type", "-"	20817	protein-coding gene	gene with protein product							Standard	NM_001001415		Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000358491.4:c.128T>A	chr19.hg19:g.21712584T>A	ENSP00000351280:p.Leu43Gln	194.0	0.0	.		108.0	43.0	.	NM_001001415	A6NLV7|Q9BZE6	Missense_Mutation	SNP	ENST00000358491.4	hg19	CCDS42537.1	.	.	.	.	.	.	.	.	.	.	.	10.30	1.312394	0.23908	.	.	ENSG00000197013	ENST00000358491	T	0.02763	4.17	0.926	0.926	0.19430	Krueppel-associated box (4);	.	.	.	.	T	0.23014	0.0556	H	0.98682	4.3	0.24819	N	0.992593	D	0.89917	1.0	D	0.97110	1.0	T	0.05533	-1.0879	9	0.87932	D	0	.	6.7513	0.23489	0.0:0.0:0.0:1.0	.	43	Q86V71	ZN429_HUMAN	Q	43	ENSP00000351280:L43Q	ENSP00000351280:L43Q	L	+	2	0	ZNF429	21504424	0.948000	0.32251	0.353000	0.25747	0.357000	0.29423	2.617000	0.46385	0.263000	0.21812	0.260000	0.18958	CTG	.	.	.	none		0.373	ZNF429-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463981.1	NM_001001415		A	21712584	T	A	21712584	3	1	268	1	0	0	0	0	1	0	0	0	17914	1580	55	5	134	5	ZNF429	19	21712584	Missense_Mutation	SNP	T	TCGA-UZ-A9PZ-01A-11D-A42J-10		21712584	37416399	42	16939											
SLC1A5	6510	hgsc.bcm.edu	37	chr19	47278876	47278876	+	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	ggactggcagcggatccaggGgcagctcactcttcacttgt	7	9	13	12	1	3	0	2	0	1	0	4	2	4	2	1	5	2	3	1	5	0	2			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr19:47278876G>C	ENST00000542575.2	-	8	2145	c.1517C>G	c.(1516-1518)cCc>cGc	p.P506R	SLC1A5_ENST00000412532.2_Missense_Mutation_p.P278R|SLC1A5_ENST00000594991.1_Missense_Mutation_p.P330R|FKRP_ENST00000600646.1_Intron|SLC1A5_ENST00000434726.2_Missense_Mutation_p.P304R	NM_005628.2	NP_005619.1	Q15758	AAAT_HUMAN	solute carrier family 1 (neutral amino acid transporter), member 5	506					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)	CGGATCCAGGGGCAGCTCACT	0.592																																					p.P506R		Atlas-SNP	.											.	SLC1A5	31	.	0			c.C1517G						PASS	.						153	146	148					19																	47278876		2203	4300	6503	SO:0001583	missense	6510	exon8			TCCAGGGGCAGCT	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.1517C>G	chr19.hg19:g.47278876G>C	ENSP00000444408:p.Pro506Arg	141.0	0.0	.		98.0	48.0	.	NM_005628	A8K9H5|B4DR77|B4DWS4|B7ZB81|D0EYG6|E9PC01|O95720|Q96RL9|Q9BWQ3|Q9UNP2	Missense_Mutation	SNP	ENST00000542575.2	hg19	CCDS12692.1	.	.	.	.	.	.	.	.	.	.	-	12.62	1.992493	0.35131	.	.	ENSG00000105281	ENST00000542575;ENST00000434726;ENST00000412532;ENST00000306894	T;T;T	0.63255	0.77;-0.03;-0.02	4.88	2.72	0.32119	.	0.616112	0.14575	N	0.311214	T	0.50565	0.1623	L	0.36672	1.1	0.09310	N	1	P;P;P	0.43477	0.808;0.664;0.664	B;B;B	0.42555	0.391;0.168;0.168	T	0.28170	-1.0052	10	0.23302	T	0.38	-16.5459	9.1558	0.36992	0.0824:0.1484:0.7692:0.0	.	304;506;506	E9PC01;Q15758;Q71UA6	.;AAAT_HUMAN;.	R	506;304;278;513	ENSP00000444408:P506R;ENSP00000406532:P304R;ENSP00000397924:P278R	ENSP00000303623:P513R	P	-	2	0	SLC1A5	51970716	0.000000	0.05858	0.003000	0.11579	0.158000	0.22134	0.648000	0.24828	0.638000	0.30545	0.550000	0.68814	CCC	.	.	.	none		0.592	SLC1A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466630.1			C	47278876	G	C	47278876	3	2	268	1	0	0	0	0	1	0	0	0	14448	1232	43	4	112	4	SLC1A5	19	47278876	Missense_Mutation	SNP	G	TCGA-UZ-A9PZ-01A-11D-A42J-10	25566292	47278876	11850107	43	16940											
PIH1D1	55011	hgsc.bcm.edu	37	chr19	49950663	49950663	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggatccgaggacgctgctcCgagcggatgttctgctgcga	6	9	15	11	5	1	0	0	0	1	0	3	6	3	3	2	3	4	4	2	3	0	1			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr19:49950663C>T	ENST00000262265.5	-	6	778	c.543G>A	c.(541-543)tcG>tcA	p.S181S	PIH1D1_ENST00000596049.1_Silent_p.S181S|PIH1D1_ENST00000602226.1_5'Flank	NM_017916.2	NP_060386.1	Q9NWS0	PIHD1_HUMAN	PIH1 domain containing 1	181					box C/D snoRNP assembly (GO:0000492)|epithelial cell differentiation (GO:0030855)	pre-snoRNP complex (GO:0070761)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)|urinary_tract(1)	11		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00152)|GBM - Glioblastoma multiforme(486;0.0244)		GACGCTGCTCCGAGCGGATGT	0.622																																					p.S181S		Atlas-SNP	.											.	PIH1D1	23	.	0			c.G543A						PASS	.						69	72	71					19																	49950663		2203	4300	6503	SO:0001819	synonymous_variant	55011	exon6			CTGCTCCGAGCGG	AK000650	CCDS12765.1	19q13.33	2012-07-18	2007-01-31	2007-01-31	ENSG00000104872	ENSG00000104872			26075	protein-coding gene	gene with protein product		611480		NOP17		12477932	Standard	NM_017916		Approved	FLJ20643	uc002pns.2	Q9NWS0		ENST00000262265.5:c.543G>A	chr19.hg19:g.49950663C>T		51.0	0.0	.		29.0	9.0	.	NM_017916	B4DGN7|B4E2X7|Q9BVL0	Silent	SNP	ENST00000262265.5	hg19	CCDS12765.1																																																																																			.	.	.	none		0.622	PIH1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465389.2	NM_017916		T	49950663	C	T	49950663	2	4	268	1	0	0	0	0	0	0	0	1	11913	639	23	1		1	PIH1D1	19	49950663	Silent	SNP	C	TCGA-UZ-A9PZ-01A-11D-A42J-10	2671787	49950663	9178320	44	16941											
BMP7	655	hgsc.bcm.edu	37	chr20	55748287	55748287	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgatggcgtggttggtggcgTtcatgtaggagttcagaggg	6	11	19	5	3	2	1	2	0	0	1	2	3	2	2	0	6	0	4	0	6	1	4			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr20:55748287T>C	ENST00000395863.3	-	6	1620	c.1115A>G	c.(1114-1116)aAc>aGc	p.N372S	BMP7_ENST00000450594.2_Missense_Mutation_p.N372S|BMP7_ENST00000395864.3_Missense_Mutation_p.N306S|BMP7_ENST00000460817.1_5'UTR	NM_001719.2	NP_001710.1	P18075	BMP7_HUMAN	bone morphogenetic protein 7	372					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)			GTTGGTGGCGTTCATGTAGGA	0.627																																					p.N372S		Atlas-SNP	.											.	BMP7	60	.	0			c.A1115G						PASS	.						212	131	158					20																	55748287		2203	4300	6503	SO:0001583	missense	655	exon6			GTGGCGTTCATGT		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.1115A>G	chr20.hg19:g.55748287T>C	ENSP00000379204:p.Asn372Ser	74.0	0.0	.		84.0	25.0	.	NM_001719	Q9H512|Q9NTQ7	Missense_Mutation	SNP	ENST00000395863.3	hg19	CCDS13455.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.760251	0.89932	.	.	ENSG00000101144	ENST00000395863;ENST00000395864;ENST00000450594	D;D;D	0.88818	-2.43;-2.43;-2.43	4.68	4.68	0.58851	Transforming growth factor-beta, C-terminal (3);	0.082917	0.85682	D	0.000000	D	0.93989	0.8075	M	0.78344	2.41	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;P;D	0.97110	0.999;0.906;1.0	D	0.94769	0.7943	10	0.87932	D	0	.	14.4246	0.67207	0.0:0.0:0.0:1.0	.	306;372;372	B1AKZ9;P18075;B1AL00	.;BMP7_HUMAN;.	S	372;306;372	ENSP00000379204:N372S;ENSP00000379205:N306S;ENSP00000398687:N372S	ENSP00000379204:N372S	N	-	2	0	BMP7	55181694	1.000000	0.71417	0.991000	0.47740	0.978000	0.69477	7.930000	0.87610	1.878000	0.54408	0.383000	0.25322	AAC	.	.	.	none		0.627	BMP7-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079831.2			C	55748287	T	C	55748287	3	2	268	1	0	0	0	0	1	0	0	0	1465	1725	60	3	188	3	BMP7	20	55748287	Missense_Mutation	SNP	T	TCGA-UZ-A9PZ-01A-11D-A42J-10		55748287	7277233	45	16942											
PRIC285	85441	hgsc.bcm.edu	37	chr20	62195231	62195231	+	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	tggtggccccgggcgcagcgGccgaacgccgagcgctccag	5	3	17	16	7	0	0	0	0	0	0	1	2	1	0	5	4	3	2	5	4	1	0			TCGA-UZ-A9PZ-01A-11D-A42J-10	TCGA-UZ-A9PZ-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	d803a908-b844-4475-8169-a7139df2f89e	027f6901-bb89-4fb7-8e82-7dd1ba7fcaf3	g.chr20:62195231G>A	ENST00000467148.1	-	8	5013	c.4944C>T	c.(4942-4944)ggC>ggT	p.G1648G	HELZ2_ENST00000427522.2_Silent_p.G1079G	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	1648					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)										GGGCGCAGCGGCCGAACGCCG	0.692																																					p.G1648G		Atlas-SNP	.											.	.	.	.	0			c.C4944T						PASS	.						15	14	14					20																	62195231		2162	4271	6433	SO:0001819	synonymous_variant	85441	exon9			GCAGCGGCCGAAC	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.4944C>T	chr20.hg19:g.62195231G>A		51.0	0.0	.		56.0	16.0	.	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	hg19	CCDS33508.1																																																																																			.	.	.	none		0.692	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		A	62195231	G	A	62195231	2	1	268	1	0	0	0	0	0	0	0	1	12495	1190	42	2		2	PRIC285	20	62195231	Silent	SNP	G	TCGA-UZ-A9PZ-01A-11D-A42J-10	6446944	62195231	830289	46	16943											
ARID1A	8289	hgsc.bcm.edu	37	chr1	27105645	27105645	+	Frame_Shift_Del	DEL	G	G	-																															gatcctgggaggttcagcaaGgtgtctagtccagctcccat																										TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr1:27105645delG	ENST00000324856.7	+	20	5627	c.5256delG	c.(5254-5256)aagfs	p.K1752fs	ARID1A_ENST00000540690.1_Frame_Shift_Del_p.K80fs|ARID1A_ENST00000457599.2_Frame_Shift_Del_p.K1535fs|ARID1A_ENST00000374152.2_Frame_Shift_Del_p.K1369fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1752					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)		GGTTCAGCAAGGTGTCTAGTC	0.473			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.K1752fs		Atlas-Indel,Pindel	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.5255delA						PASS	.						84	88	87					1																	27105645		2203	4300	6503	SO:0001589	frameshift_variant	8289	exon20			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"-"	11110	protein-coding gene	gene with protein product		603024	"SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1", "AT rich interactive domain 1A (SWI- like)"	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.5256delG	chr1.hg19:g.27105645delG	ENSP00000320485:p.Lys1752fs	136.0	0.0	0		130.0	55.0	0.423077	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Del	DEL	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.	.	none		0.473	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		-	27105645	G	-	27105645	7	5	269	1	0	1	0	1	0	0	0	0	913	991	35	0	5334	0	ARID1A	1	27105645	Frame_Shift_Del	DEL	G	TCGA-UZ-A9Q0-01A-12D-A42J-10		27105645	222144976	1	16944											
ZC3H12A	80149	hgsc.bcm.edu	37	chr1	37948519	37948519	+	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	cagtccagctctctgctaacAgagagtgagcagtgcagcct	10	8	11	12	0	1	2	0	1	1	1	3	3	2	2	2	0	6	4	2	0	1	1			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr1:37948519A>T	ENST00000373087.6	+	6	1223	c.1107A>T	c.(1105-1107)acA>acT	p.T369T		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)				CTCTGCTAACAGAGAGTGAGC	0.612																																					p.T369T		Atlas-SNP	.											.	ZC3H12A	58	.	0			c.A1107T						PASS	.						23	25	25					1																	37948519		2203	4300	6503	SO:0001819	synonymous_variant	80149	exon6			GCTAACAGAGAGT		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.1107A>T	chr1.hg19:g.37948519A>T		196.0	0.0	.		159.0	76.0	.	NM_025079		Silent	SNP	ENST00000373087.6	hg19	CCDS417.1																																																																																			.	.	.	none		0.612	ZC3H12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012154.2	NM_025079		T	37948519	A	T	37948519	2	4	269	1	0	0	0	0	0	0	0	1	17573	175	7	5		5	ZC3H12A	1	37948519	Silent	SNP	A	TCGA-UZ-A9Q0-01A-12D-A42J-10	10842874	37948519	211302102	2	16945											
PRPF3	9129	hgsc.bcm.edu	37	chr1	150325324	150325324	+	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	tctagggtacagccaaagacCggagctttggagagatgaag	13	7	14	7	1	1	3	0	1	1	2	1	6	1	5	2	3	3	2	2	3	4	3			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr1:150325324C>A	ENST00000324862.6	+	16	2086	c.1921C>A	c.(1921-1923)Cgg>Agg	p.R641R	PRPF3_ENST00000414970.2_Silent_p.R592R|PRPF3_ENST00000467329.1_3'UTR	NM_004698.2	NP_004689.1	O43395	PRPF3_HUMAN	pre-mRNA processing factor 3	641					mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U4/U6 x U5 tri-snRNP complex (GO:0046540)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Lung NSC(24;5.57e-29)|Breast(34;0.000844)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)	Colorectal(1306;0.0149)		AGCCAAAGACCGGAGCTTTGG	0.368																																					p.R641R	Ovarian(168;1070 2670 5178 20729)	Atlas-SNP	.											.	PRPF3	55	.	0			c.C1921A						PASS	.						82	84	83					1																	150325324		2203	4300	6503	SO:0001819	synonymous_variant	9129	exon16			AAAGACCGGAGCT	AF001947	CCDS951.1	1q21.1	2013-07-16	2013-06-10		ENSG00000117360	ENSG00000117360			17348	protein-coding gene	gene with protein product		607301	"retinitis pigmentosa 18 (autosomal dominant)", "PRP3 pre-mRNA processing factor 3 homolog (yeast)", "PRP3 pre-mRNA processing factor 3 homolog (S. cerevisiae)"	RP18			Standard	NM_004698		Approved	Prp3, hPrp3, SNRNP90	uc001eum.4	O43395	OTTHUMG00000012807	ENST00000324862.6:c.1921C>A	chr1.hg19:g.150325324C>A		460.0	1.0	.		438.0	180.0	.	NM_004698	B4DSY9|O43446|Q5VT54	Silent	SNP	ENST00000324862.6	hg19	CCDS951.1																																																																																			.	.	.	none		0.368	PRPF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035836.1	NM_004698		A	150325324	C	A	150325324	2	1	269	1	0	0	0	0	0	0	0	1	12575	643	23	4		4	PRPF3	1	150325324	Silent	SNP	C	TCGA-UZ-A9Q0-01A-12D-A42J-10	112376805	150325324	98925297	3	16946											
MCL1	4170	hgsc.bcm.edu	37	chr1	150551933	150551933	+	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	ccgggcgggtggcgccgccgCtgccggcccccaagccggcc	2	2	17	20	7	0	0	0	0	0	0	0	0	0	0	8	5	2	1	8	5	1	0			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr1:150551933C>A	ENST00000369026.2	-	1	133	c.74G>T	c.(73-75)aGc>aTc	p.S25I	MCL1_ENST00000464132.1_5'Flank|MCL1_ENST00000307940.3_Missense_Mutation_p.S25I	NM_001197320.1|NM_021960.4	NP_001184249.1|NP_068779.1	Q07820	MCL1_HUMAN	myeloid cell leukemia 1	25					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)			GGCGCCGCCGCTGCCGGCCCC	0.701																																					p.S25I		Atlas-SNP	.											.	MCL1	27	.	0			c.G74T						PASS	.						8	12	11					1																	150551933		1186	2513	3699	SO:0001583	missense	4170	exon1			CCGCCGCTGCCGG	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.74G>T	chr1.hg19:g.150551933C>A	ENSP00000358022:p.Ser25Ile	181.0	0.0	.		205.0	83.0	.	NM_021960	B2R6B2|D3DV03|D3DV04|Q9HD91|Q9NRQ3|Q9NRQ4|Q9UHR7|Q9UHR8|Q9UHR9|Q9UNJ1	Missense_Mutation	SNP	ENST00000369026.2	hg19	CCDS957.1	.	.	.	.	.	.	.	.	.	.	C	10.38	1.333131	0.24167	.	.	ENSG00000143384	ENST00000369026;ENST00000307940;ENST00000439749	T;T	0.27720	2.8;1.65	4.72	2.75	0.32379	.	0.757532	0.11269	N	0.581776	T	0.08313	0.0207	N	0.19112	0.55	0.24195	N	0.995532	P;B	0.36249	0.545;0.119	B;B	0.32533	0.147;0.07	T	0.16012	-1.0417	10	0.62326	D	0.03	-0.9013	11.0335	0.47787	0.0:0.6369:0.3631:0.0	.	25;25	Q07820-2;Q07820	.;MCL1_HUMAN	I	25	ENSP00000358022:S25I;ENSP00000309973:S25I	ENSP00000309973:S25I	S	-	2	0	MCL1	148818557	0.045000	0.20229	0.618000	0.29105	0.094000	0.18550	0.869000	0.27996	0.549000	0.28973	0.561000	0.74099	AGC	.	.	.	none		0.701	MCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084402.1	NM_021960		A	150551933	C	A	150551933	3	1	269	1	0	0	0	0	1	0	0	0	9391	797	28	4	1001	4	MCL1	1	150551933	Missense_Mutation	SNP	C	TCGA-UZ-A9Q0-01A-12D-A42J-10	226609	150551933	98698688	4	16947											
TDRKH	11022	hgsc.bcm.edu	37	chr1	151748012	151748012	+	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	tccaaagcttcctcttcccaCtggtcacctggcaaaagatt	10	11	6	14	0	2	1	1	0	1	1	5	1	5	1	4	2	1	2	4	2	3	3			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr1:151748012C>G	ENST00000368822.1	-	10	1923	c.1290G>C	c.(1288-1290)caG>caC	p.Q430H	TDRKH_ENST00000368825.3_Missense_Mutation_p.Q385H|TDRKH_ENST00000368824.3_Missense_Mutation_p.Q430H|TDRKH_ENST00000368823.1_Missense_Mutation_p.Q426H|TDRKH_ENST00000440583.2_Missense_Mutation_p.Q206H|TDRKH_ENST00000458431.2_Missense_Mutation_p.Q430H|TDRKH_ENST00000368827.6_Missense_Mutation_p.Q430H			Q9Y2W6	TDRKH_HUMAN	tudor and KH domain containing	430					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	mitochondrion (GO:0005739)|pi-body (GO:0071546)|piP-body (GO:0071547)	RNA binding (GO:0003723)			breast(5)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			CCTCTTCCCACTGGTCACCTG	0.502																																					p.Q430H		Atlas-SNP	.											.	TDRKH	45	.	0			c.G1290C						PASS	.						84	79	81					1																	151748012		1909	4121	6030	SO:0001583	missense	11022	exon10			TTCCCACTGGTCA	AF227192	CCDS41394.1, CCDS41395.1	1q21	2013-01-23	2003-11-07		ENSG00000182134	ENSG00000182134		"Tudor domain containing"	11713	protein-coding gene	gene with protein product		609501	"tudor and KH domain containing"			10767542	Standard	NM_001083964		Approved	TDRD2	uc001eza.4	Q9Y2W6	OTTHUMG00000013062	ENST00000368822.1:c.1290G>C	chr1.hg19:g.151748012C>G	ENSP00000357812:p.Gln430His	137.0	0.0	.		120.0	59.0	.	NM_001083965	D3DV24|Q5SZR3|Q5SZR5|Q8N582|Q9NYV5	Missense_Mutation	SNP	ENST00000368822.1	hg19	CCDS41394.1	.	.	.	.	.	.	.	.	.	.	C	10.12	1.263143	0.23051	.	.	ENSG00000182134	ENST00000368827;ENST00000368825;ENST00000368824;ENST00000368823;ENST00000368822;ENST00000458431;ENST00000440583	T;T;T;T;T;T;T	0.23950	2.21;1.88;2.21;2.21;2.21;2.21;1.88	5.92	-9.61	0.00550	.	0.718421	0.14138	N	0.338922	T	0.03827	0.0108	N	0.22421	0.69	0.19775	N	0.999958	B;B;B	0.09022	0.002;0.002;0.001	B;B;B	0.06405	0.002;0.002;0.001	T	0.39941	-0.9589	10	0.17832	T	0.49	-3.0131	12.7851	0.57500	0.0:0.3884:0.0756:0.536	.	385;426;430	Q5SZR5;Q5SZR4;Q9Y2W6	.;.;TDRKH_HUMAN	H	430;385;430;426;430;430;206	ENSP00000357819:Q430H;ENSP00000357817:Q385H;ENSP00000357815:Q430H;ENSP00000357813:Q426H;ENSP00000357812:Q430H;ENSP00000395718:Q430H;ENSP00000416645:Q206H	ENSP00000357812:Q430H	Q	-	3	2	TDRKH	150014636	0.000000	0.05858	0.228000	0.23943	0.945000	0.59286	-1.669000	0.01958	-1.556000	0.01695	-1.149000	0.01842	CAG	.	.	.	none		0.502	TDRKH-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000036648.2	NM_006862		G	151748012	C	G	151748012	3	3	269	1	0	0	0	0	1	0	0	0	15749	564	20	4	411	4	TDRKH	1	151748012	Missense_Mutation	SNP	C	TCGA-UZ-A9Q0-01A-12D-A42J-10	1196079	151748012	97502609	5	16948											
ASTN1	460	hgsc.bcm.edu	37	chr1	176863825	176863825	+	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	gggggcaggacgaggggcatCgtcccttgctgtggcactcc	5	7	17	12	2	0	0	0	0	0	0	3	2	2	1	2	6	1	4	2	6	0	1	rs377472669		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr1:176863825C>G	ENST00000367654.3	-	17	3048	c.2837G>C	c.(2836-2838)cGa>cCa	p.R946P	ASTN1_ENST00000361833.2_Missense_Mutation_p.R938P|ASTN1_ENST00000424564.2_Missense_Mutation_p.R938P|ASTN1_ENST00000367657.3_Missense_Mutation_p.R938P	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	946					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						CGAGGGGCATCGTCCCTTGCT	0.602																																					p.R938P		Atlas-SNP	.											.	ASTN1	314	.	0			c.G2813C						PASS	.						99	97	97					1																	176863825		2203	4300	6503	SO:0001583	missense	460	exon17			GGGCATCGTCCCT	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.2837G>C	chr1.hg19:g.176863825C>G	ENSP00000356626:p.Arg946Pro	75.0	0.0	.		73.0	31.0	.	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	hg19		.	.	.	.	.	.	.	.	.	.	C	22.4	4.284468	0.80803	.	.	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	T;T;T;T	0.33865	1.39;1.39;1.39;1.39	5.26	5.26	0.73747	.	0.056729	0.64402	D	0.000001	T	0.45736	0.1357	L	0.39898	1.24	0.58432	D	0.999999	D;D	0.53151	0.958;0.958	P;P	0.52881	0.712;0.712	T	0.43718	-0.9374	10	0.87932	D	0	-14.8582	18.8334	0.92150	0.0:1.0:0.0:0.0	.	938;938	O14525-2;B1AJS1	.;.	P	938;938;946;938;938	ENSP00000356629:R938P;ENSP00000354536:R938P;ENSP00000356626:R946P;ENSP00000395041:R938P	ENSP00000354536:R938P	R	-	2	0	ASTN1	175130448	1.000000	0.71417	0.971000	0.41717	0.999000	0.98932	5.330000	0.65899	2.640000	0.89533	0.655000	0.94253	CGA	.	.	.	none		0.602	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		G	176863825	C	G	176863825	3	3	269	1	0	0	0	0	1	0	0	0	1064	884	31	4	1103	4	ASTN1	1	176863825	Missense_Mutation	SNP	C	TCGA-UZ-A9Q0-01A-12D-A42J-10	25115813	176863825	72386796	6	16949											
RASAL2	9462	hgsc.bcm.edu	37	chr1	178063695	178063695	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccggagatgttcccggcgcTggagtccgactcgccgctgc	4	7	15	15	6	0	1	0	0	0	1	3	4	2	2	4	3	1	3	4	3	0	1			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr1:178063695T>C	ENST00000367649.3	+	1	420	c.68T>C	c.(67-69)cTg>cCg	p.L23P	RASAL2_ENST00000448150.3_Missense_Mutation_p.L5P|RASAL2-AS1_ENST00000421505.1_lincRNA			Q9UJF2	NGAP_HUMAN	RAS protein activator like 2	0					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						TTCCCGGCGCTGGAGTCCGAC	0.716																																					p.L23P		Atlas-SNP	.											.	RASAL2	334	.	0			c.T68C						PASS	.						17	16	16					1																	178063695		2197	4292	6489	SO:0001583	missense	9462	exon1			CGGCGCTGGAGTC	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	ENST00000367649.3:c.68T>C	chr1.hg19:g.178063695T>C	ENSP00000356621:p.Leu23Pro	148.0	0.0	.		124.0	58.0	.	NM_170692	F8W755|O95174|Q2TB22|Q5TFU9	Missense_Mutation	SNP	ENST00000367649.3	hg19	CCDS1321.2	.	.	.	.	.	.	.	.	.	.	T	21.2	4.119866	0.77323	.	.	ENSG00000075391	ENST00000448150;ENST00000367649	T;T	0.23754	1.89;2.02	4.69	3.55	0.40652	.	0.203901	0.23740	N	0.045038	T	0.16557	0.0398	N	0.08118	0	0.44515	D	0.997463	P	0.39131	0.661	P	0.45232	0.474	T	0.05037	-1.0910	10	0.87932	D	0	.	7.6777	0.28494	0.0:0.1:0.0:0.9	.	23	F8W755	.	P	5;23	ENSP00000407768:L5P;ENSP00000356621:L23P	ENSP00000356621:L23P	L	+	2	0	RASAL2	176330318	0.972000	0.33761	0.949000	0.38748	0.887000	0.51463	1.179000	0.31993	1.860000	0.53959	0.402000	0.26972	CTG	.	.	.	none		0.716	RASAL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352415.1	NM_170692		C	178063695	T	C	178063695	3	2	269	1	0	0	0	0	1	0	0	0	13077	1580	55	3	70	3	RASAL2	1	178063695	Missense_Mutation	SNP	T	TCGA-UZ-A9Q0-01A-12D-A42J-10	1199870	178063695	71186926	7	16950											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228528466	228528466	+	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	cggaacagacagaactgcgcGctgctggagcaggcctatgc	10	5	14	12	3	0	2	0	0	0	2	0	4	0	4	1	3	6	3	1	3	3	1	rs558801538		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr1:228528466G>A	ENST00000422127.1	+	72	17618	c.17574G>A	c.(17572-17574)gcG>gcA	p.A5858A	OBSCN_ENST00000284548.11_Silent_p.A5858A|OBSCN_ENST00000570156.2_Silent_p.A6815A|OBSCN_ENST00000366709.4_Silent_p.A2977A|OBSCN_ENST00000366707.4_Silent_p.A3492A	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5858	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AGAACTGCGCGCTGCTGGAGC	0.637													G|||	1	0.000199681	0	0	5008	,	,		15267	0		0.001	False		,,,				2504	0				p.A6815A		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G20445A						PASS	.						18	22	21					1																	228528466		1999	4162	6161	SO:0001819	synonymous_variant	84033	exon83			CTGCGCGCTGCTG	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.17574G>A	chr1.hg19:g.228528466G>A		225.0	1.0	.		190.0	87.0	.	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	10.95	1.494467	0.26774	.	.	ENSG00000154358	ENST00000441106	T	0.63096	-0.02	5.04	-7.86	0.01187	.	0.247869	0.35466	N	0.003192	T	0.40222	0.1108	.	.	.	0.53688	D	0.999977	.	.	.	.	.	.	T	0.35525	-0.9785	7	0.18276	T	0.48	.	3.5033	0.07681	0.3257:0.3274:0.2639:0.0831	.	.	.	.	T	475	ENSP00000388554:A475T	ENSP00000388554:A475T	A	+	1	0	OBSCN	226595089	0.000000	0.05858	0.146000	0.22360	0.269000	0.26545	-1.982000	0.01489	-1.315000	0.02297	-0.266000	0.10368	GCT	.	.	.	none		0.637	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228528466	G	A	228528466	2	1	269	1	0	0	0	0	0	0	0	1	10819	1074	38	1		1	OBSCN	1	228528466	Silent	SNP	G	TCGA-UZ-A9Q0-01A-12D-A42J-10	50464771	228528466	20722155	8	16951											
ITPRIPL1	150771	hgsc.bcm.edu	37	chr2	96993651	96993651	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtgcctccagatcattttaAgtctccggcagcatcagagc	10	10	9	12	1	3	2	2	0	1	2	5	2	4	2	3	1	3	2	3	1	1	2	rs35855657	byFrequency	TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr2:96993651A>G	ENST00000439118.2	+	3	1533	c.1282A>G	c.(1282-1284)Agt>Ggt	p.S428G	ITPRIPL1_ENST00000536814.1_Missense_Mutation_p.S420G|ITPRIPL1_ENST00000542887.1_Missense_Mutation_p.S420G|ITPRIPL1_ENST00000361124.4_Missense_Mutation_p.S436G	NM_001008949.2	NP_001008949.1	Q6GPH6	IPIL1_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein-like 1	428			S -> C (in dbSNP:rs35855657).			integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GATCATTTTAAGTCTCCGGCA	0.557																																					p.S436G		Atlas-SNP	.											.	ITPRIPL1	58	.	0			c.A1306G						PASS	.						93	94	93					2																	96993651		2203	4300	6503	SO:0001583	missense	150771	exon1			ATTTTAAGTCTCC		CCDS33250.1, CCDS46360.1, CCDS54378.1	2q11.2	2011-04-28	2011-04-28	2008-08-11	ENSG00000198885	ENSG00000198885			29371	protein-coding gene	gene with protein product			"KIAA1754-like", "inositol 1,4,5-triphosphate receptor interacting protein-like 1"	KIAA1754L		12477932	Standard	NM_178495		Approved		uc010yul.2	Q6GPH6	OTTHUMG00000155230	ENST00000439118.2:c.1282A>G	chr2.hg19:g.96993651A>G	ENSP00000389308:p.Ser428Gly	91.0	0.0	.		93.0	35.0	.	NM_178495	F5H1L8|Q8NE61	Missense_Mutation	SNP	ENST00000439118.2	hg19	CCDS46360.1	.	.	.	.	.	.	.	.	.	.	A	14.17	2.456320	0.43634	.	.	ENSG00000198885	ENST00000536814;ENST00000439118;ENST00000361124;ENST00000542887	T;T;T;T	0.08458	3.09;3.09;3.09;3.09	5.5	4.29	0.51040	.	0.374013	0.22795	N	0.055547	T	0.04815	0.0130	N	0.03608	-0.345	0.29897	N	0.824686	P;P	0.43578	0.774;0.811	B;B	0.44315	0.318;0.446	T	0.08310	-1.0728	10	0.52906	T	0.07	-1.8867	8.2792	0.31889	0.7022:0.0:0.0:0.2977	.	436;428	Q6GPH6-2;Q6GPH6	.;IPIL1_HUMAN	G	420;428;436;420	ENSP00000439566:S420G;ENSP00000389308:S428G;ENSP00000355121:S436G;ENSP00000438212:S420G	ENSP00000355121:S436G	S	+	1	0	ITPRIPL1	96357378	1.000000	0.71417	0.981000	0.43875	0.824000	0.46624	4.036000	0.57304	2.308000	0.77769	0.533000	0.62120	AGT	.	A|0.643;T|0.357	.	alt		0.557	ITPRIPL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338896.1	NM_178495		G	96993651	A	G	96993651	3	3	269	1	0	0	0	0	1	0	0	0	7931	72	3	3	1322	3	ITPRIPL1	2	96993651	Missense_Mutation	SNP	A	TCGA-UZ-A9Q0-01A-12D-A42J-10		96993651	146205722	9	16952											
CFC1	653275	hgsc.bcm.edu	37	chr2	131279604	131279604	+	Frame_Shift_Del	DEL	C	C	-																															ctcagaagcaccgacagtcaCcgctcaactggacctccagt																										TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr2:131279604delC	ENST00000281882.3	+	3	436	c.148delC	c.(148-150)ccgfs	p.P50fs	AC013269.3_ENST00000450486.1_RNA	NM_001079530.1	NP_001072998.1	P0CG36	CFC1B_HUMAN	cripto, FRL-1, cryptic family 1B	50					gastrulation (GO:0007369)	extracellular region (GO:0005576)						Colorectal(110;0.1)					CCGACAGTCACCGCTCAACTG	0.547																																					p.S49fs		Pindel	.											.	.	.	.	0			c.147delA						PASS	.						5	1	5					2																	131279604		353	34	387	SO:0001589	frameshift_variant	653275	exon3			.		CCDS33286.1	2q21.1	2008-09-04			ENSG00000152093	ENSG00000152093			33983	protein-coding gene	gene with protein product							Standard	NM_001079530		Approved		uc002trl.2	P0CG36	OTTHUMG00000153959	ENST00000281882.3:c.148delC	chr2.hg19:g.131279604delC	ENSP00000281882:p.Pro50fs	396.0	0.0	.		381.0	39.0	0.102	NM_001079530	B2RCY0|B9EJD3|Q53T05|Q9GZR3	Frame_Shift_Del	DEL	ENST00000281882.3	hg19	CCDS33286.1																																																																																			.	.	.	none		0.547	CFC1B-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254521.1	NM_001079530		-	131279604	C	-	131279604	7	5	269	1	0	1	0	1	0	0	0	0	3281	507	18	0	158	0	CFC1	2	131279604	Frame_Shift_Del	DEL	C	TCGA-UZ-A9Q0-01A-12D-A42J-10	34285953	131279604	111919769	10	16953											
CFC1	55997	hgsc.bcm.edu	37	chr2	131356313	131356313	+	Frame_Shift_Del	DEL	G	G	-																															gactggaggtccagttgagcGgtgactgtcggtgcttctga																										TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr2:131356313delG	ENST00000259216.4	-	3	411	c.149delC	c.(148-150)ccgfs	p.P50fs		NM_032545.3	NP_115934.1	P0CG37	CFC1_HUMAN	cripto, FRL-1, cryptic family 1	50					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)					CCAGTTGAGCGGTGACTGTCG	0.557																																					p.P50fs		Pindel	.											.	CFC1	14	.	0			c.150delG						PASS	.						13	20	18					2																	131356313		2172	4248	6420	SO:0001589	frameshift_variant	55997	exon3			.	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.149delC	chr2.hg19:g.131356313delG	ENSP00000259216:p.Pro50fs	957.0	0.0	.		1015.0	120.0	0.118	NM_001270420	B2RCY0|B9EJD3|Q53T05|Q9GZR3	Frame_Shift_Del	DEL	ENST00000259216.4	hg19	CCDS2162.1																																																																																			.	.	.	none		0.557	CFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333367.1	NM_032545		-	131356313	G	-	131356313	7	5	269	1	0	1	0	1	0	0	0	0	3281	1116	39	0	1234	0	CFC1	2	131356313	Frame_Shift_Del	DEL	G	TCGA-UZ-A9Q0-01A-12D-A42J-10	76709	131356313	111843060	11	16954											
CCNT2	905	hgsc.bcm.edu	37	chr2	135710229	135710229	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agagctaacacatgagtttcTacaaatattggagaaaacgc	17	9	8	7	1	1	3	0	1	1	2	1	4	1	3	0	1	4	2	0	1	6	5			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr2:135710229T>C	ENST00000264157.5	+	8	752	c.722T>C	c.(721-723)cTa>cCa	p.L241P	CCNT2_ENST00000537343.1_Missense_Mutation_p.L66P|CCNT2_ENST00000295238.6_Missense_Mutation_p.L241P	NM_001241.3|NM_058241.2	NP_001232.1|NP_490595.1	O60583	CCNT2_HUMAN	cyclin T2	241					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(2)|kidney(3)|large_intestine(10)|lung(6)|ovary(2)|prostate(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.107)		CATGAGTTTCTACAAATATTG	0.313																																					p.L241P		Atlas-SNP	.											.	CCNT2	98	.	0			c.T722C						PASS	.						63	69	67					2																	135710229		2203	4300	6503	SO:0001583	missense	905	exon8			AGTTTCTACAAAT	AF048731	CCDS2174.1, CCDS2175.1	2q21.3	2010-11-15			ENSG00000082258	ENSG00000082258			1600	protein-coding gene	gene with protein product		603862				9499409, 10465067	Standard	NM_001241		Approved		uc002tuc.2	O60583	OTTHUMG00000131712	ENST00000264157.5:c.722T>C	chr2.hg19:g.135710229T>C	ENSP00000264157:p.Leu241Pro	346.0	0.0	.		287.0	126.0	.	NM_058241	A8KA48|D3DP73|D3DP74|O60582|Q29R66|Q53SR4|Q5I1Y0	Missense_Mutation	SNP	ENST00000264157.5	hg19	CCDS2174.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.486977	0.84854	.	.	ENSG00000082258	ENST00000446247;ENST00000537343;ENST00000295238;ENST00000264157	T;T;T;T	0.54479	0.57;0.57;0.57;0.57	5.7	5.7	0.88788	Cyclin-like (1);	0.000000	0.85682	D	0.000000	T	0.78566	0.4303	M	0.91612	3.225	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.991;0.996	D	0.83854	0.0264	10	0.87932	D	0	.	15.6442	0.77036	0.0:0.0:0.0:1.0	.	66;241;241	B4DH21;O60583;O60583-2	.;CCNT2_HUMAN;.	P	82;66;241;241	ENSP00000399497:L82P;ENSP00000439506:L66P;ENSP00000295238:L241P;ENSP00000264157:L241P	ENSP00000264157:L241P	L	+	2	0	CCNT2	135426699	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.281000	0.72632	2.167000	0.68274	0.528000	0.53228	CTA	.	.	.	none		0.313	CCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254629.1	NM_058241		C	135710229	T	C	135710229	3	2	269	1	0	0	0	0	1	0	0	0	2937	1522	53	3	752	3	CCNT2	2	135710229	Missense_Mutation	SNP	T	TCGA-UZ-A9Q0-01A-12D-A42J-10	4353916	135710229	107489144	12	16955											
MAGI1	9223	hgsc.bcm.edu	37	chr3	65342733	65342733	+	Frame_Shift_Del	DEL	G	G	-																															ctccaatgacggatgctgccGgcggtcgggcccggccctca																										TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr3:65342733delG	ENST00000402939.2	-	23	3708	c.3709delC	c.(3709-3711)cggfs	p.R1237fs	RP11-88H12.2_ENST00000602316.1_RNA|MAGI1_ENST00000330909.8_3'UTR	NM_001033057.1	NP_001028229.1	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	1266					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)		GGATGCTGCCGGCGGTCGGGC	0.622																																					p.R1237fs		Atlas-Indel,Pindel	.											.	MAGI1	481	.	0			c.3710delG						PASS	.						70	73	72					3																	65342733		2203	4300	6503	SO:0001589	frameshift_variant	9223	exon23			.	AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"BAI1-associated protein 1"	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000402939.2:c.3709delC	chr3.hg19:g.65342733delG	ENSP00000385450:p.Arg1237fs	93.0	0.0	0		107.0	40.0	0.373832	NM_001033057	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Frame_Shift_Del	DEL	ENST00000402939.2	hg19	CCDS33780.1																																																																																			.	.	.	none		0.622	MAGI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349126.1	NM_004742		-	65342733	G	-	65342733	7	5	269	1	0	1	0	1	0	0	0	0	9197	1115	39	0	683	0	MAGI1	3	65342733	Frame_Shift_Del	DEL	G	TCGA-UZ-A9Q0-01A-12D-A42J-10		65342733	132679697	13	16956											
STXBP5L	9515	hgsc.bcm.edu	37	chr3	121100364	121100367	+	Frame_Shift_Del	DEL	ATGG	ATGG	-																															aaaggtttacagagccagtcAtggtattgccaagtggtaag																										TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	ATGG	ATGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr3:121100364_121100367delATGG	ENST00000273666.6	+	23	2915_2918	c.2644_2647delATGG	c.(2644-2649)atggtafs	p.MV882fs	STXBP5L_ENST00000471454.1_Frame_Shift_Del_p.MV858fs|STXBP5L_ENST00000497029.1_Frame_Shift_Del_p.MV856fs|STXBP5L_ENST00000472879.1_Frame_Shift_Del_p.MV858fs|STXBP5L_ENST00000492541.1_Frame_Shift_Del_p.MV882fs	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	882					exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|negative regulation of insulin secretion (GO:0046676)|positive regulation of protein secretion (GO:0050714)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(12)|lung(28)|ovary(7)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				GBM - Glioblastoma multiforme(114;0.0694)		AGAGCCAGTCATGGTATTGCCAAG	0.353																																					p.881_882del		Atlas-Indel,Pindel	.											.	STXBP5L	159	.	0			c.2643_2646del						PASS	.																																			SO:0001589	frameshift_variant	9515	exon23			.	AB023223	CCDS43137.1	3q13.33-q21.1	2013-01-10			ENSG00000145087	ENSG00000145087		"WD repeat domain containing"	30757	protein-coding gene	gene with protein product		609381				10231032, 14767561	Standard	NM_014980		Approved	KIAA1006, LLGL4	uc003eec.4	Q9Y2K9	OTTHUMG00000159426	ENST00000273666.6:c.2644_2647delATGG	chr3.hg19:g.121100364_121100367delATGG	ENSP00000273666:p.Met882fs	75.0	0.0	0		118.0	31.0	0.262712	NM_014980	Q4G1B4|Q6PIC3	Frame_Shift_Del	DEL	ENST00000273666.6	hg19	CCDS43137.1																																																																																			.	.	.	none		0.353	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3			-	121100367	ATGG	-	121100364	7	5	269	1	0	1	0	1	0	0	0	0	15369	217	8	0	2730	0	STXBP5L	3	121100364	Frame_Shift_Del	DEL	ATGG	TCGA-UZ-A9Q0-01A-12D-A42J-10	55757631	121100364	76922066	14	16957											
MUC13	56667	hgsc.bcm.edu	37	chr3	124632081	124632081	+	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	aggcatcaggacacttgagaCtggaagcttcaaaacagaat	16	7	10	8	0	2	2	2	1	0	2	2	5	2	4	0	3	2	2	0	3	4	2			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr3:124632081C>T	ENST00000311075.3	-	8	1126	c.1088G>A	c.(1087-1089)aGt>aAt	p.S363N		NM_033049.3	NP_149038	Q9H3R2	MUC13_HUMAN	mucin 13, cell surface associated	364	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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						ACACTTGAGACTGGAAGCTTC	0.468																																					p.S363N		Atlas-SNP	.											.	MUC13	57	.	0			c.G1088A						PASS	.						59	58	58					3																	124632081		2203	4300	6503	SO:0001583	missense	56667	exon8			TTGAGACTGGAAG	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.1088G>A	chr3.hg19:g.124632081C>T	ENSP00000312235:p.Ser363Asn	84.0	0.0	.		112.0	28.0	.	NM_033049	Q6UWD9|Q9NXT5	Missense_Mutation	SNP	ENST00000311075.3	hg19		.	.	.	.	.	.	.	.	.	.	C	8.737	0.918083	0.17982	.	.	ENSG00000173702	ENST00000311075	D	0.87334	-2.24	2.5	-2.08	0.07254	.	3.688240	0.00702	N	0.000787	T	0.76948	0.4059	N	0.22421	0.69	0.09310	N	1	D	0.53885	0.963	P	0.44359	0.447	T	0.67465	-0.5664	10	0.17369	T	0.5	0.23	2.0258	0.03519	0.1747:0.2503:0.4354:0.1396	.	363	Q9H3R2	MUC13_HUMAN	N	363	ENSP00000312235:S363N	ENSP00000312235:S363N	S	-	2	0	MUC13	126114771	0.000000	0.05858	0.000000	0.03702	0.442000	0.32017	-0.169000	0.09911	-0.549000	0.06191	0.462000	0.41574	AGT	.	.	.	none		0.468	MUC13-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000355714.1	NM_033049		T	124632081	C	T	124632081	3	4	269	1	0	0	0	0	1	0	0	0	9978	565	20	2	463	2	MUC13	3	124632081	Missense_Mutation	SNP	C	TCGA-UZ-A9Q0-01A-12D-A42J-10	3531717	124632081	73390349	15	16958											
ISY1	57461	hgsc.bcm.edu	37	chr3	128852942	128852942	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctcggtgactgcatagatgTtgatctcttcctcctcttcc	5	15	7	14	1	2	3	0	2	2	1	7	3	5	3	4	1	1	2	4	1	1	4			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr3:128852942T>C	ENST00000393295.3	-	9	955	c.638A>G	c.(637-639)aAc>aGc	p.N213S	ISY1-RAB43_ENST00000418265.1_Missense_Mutation_p.N213S|ISY1_ENST00000273541.8_Missense_Mutation_p.N235S|ISY1_ENST00000393292.3_Silent_p.Q214Q|ISY1_ENST00000471497.1_Intron	NM_001199469.1|NM_020701.3	NP_001186398.1|NP_065752.1	Q9ULR0	ISY1_HUMAN	ISY1 splicing factor homolog (S. cerevisiae)	213					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|prostate(1)|skin(1)	15						TGCATAGATGTTGATctcttc	0.542																																					p.N235S		Atlas-SNP	.											.	ISY1	36	.	0			c.A704G						PASS	.						117	122	120					3																	128852942		2055	4200	6255	SO:0001583	missense	57461	exon10			TAGATGTTGATCT		CCDS43149.1, CCDS56277.1	3q21.3	2008-11-25			ENSG00000240682	ENSG00000240682			29201	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 33"	612764				16103217	Standard	NM_020701		Approved	KIAA1160, fSAP33		Q9ULR0	OTTHUMG00000137365	ENST00000393295.3:c.638A>G	chr3.hg19:g.128852942T>C	ENSP00000376973:p.Asn213Ser	57.0	0.0	.		92.0	54.0	.	NM_001199469	Q96IL2|Q9BT05	Missense_Mutation	SNP	ENST00000393295.3	hg19	CCDS43149.1	.	.	.	.	.	.	.	.	.	.	T	14.97	2.694987	0.48202	.	.	ENSG00000240682	ENST00000418265;ENST00000393295;ENST00000273541	T	0.30182	1.54	5.64	5.64	0.86602	.	0.211897	0.49916	D	0.000137	T	0.23054	0.0557	L	0.33485	1.01	0.80722	D	1	B;B;B	0.18610	0.016;0.02;0.029	B;B;B	0.23852	0.049;0.044;0.045	T	0.07443	-1.0772	10	0.11794	T	0.64	.	12.2414	0.54544	0.0:0.0:0.0:1.0	.	235;213;213	Q9ULR0-2;Q9ULR0;Q9ULR0-1	.;ISY1_HUMAN;.	S	213;213;235	ENSP00000273541:N235S	ENSP00000273541:N235S	N	-	2	0	ISY1	130335632	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.228000	0.58619	2.141000	0.66446	0.477000	0.44152	AAC	.	.	.	none		0.542	ISY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000267856.1	NM_020701		C	128852942	T	C	128852942	3	2	269	1	0	0	0	0	1	0	0	0	7873	1725	60	3	231	3	ISY1	3	128852942	Missense_Mutation	SNP	T	TCGA-UZ-A9Q0-01A-12D-A42J-10	4220861	128852942	69169488	16	16959											
HTR3D	200909	hgsc.bcm.edu	37	chr3	183756384	183756384	+	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	ccccagaagggaaataagggCccgggtctcacccccaccca	11	3	10	17	1	1	1	1	0	1	1	2	2	1	2	6	3	0	0	6	3	3	1			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr3:183756384C>T	ENST00000382489.3	+	7	1107	c.1107C>T	c.(1105-1107)ggC>ggT	p.G369G	HTR3D_ENST00000453435.1_Silent_p.G148G|HTR3D_ENST00000334128.2_Silent_p.G194G|HTR3D_ENST00000428798.2_Silent_p.G319G	NM_001163646.1	NP_001157118.1	Q70Z44	5HT3D_HUMAN	5-hydroxytryptamine (serotonin) receptor 3D, ionotropic	369					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)			large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)	10	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;6.23e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Ergoloid mesylate(DB01049)	GAAATAAGGGCCCGGGTCTCA	0.657																																					p.G369G		Atlas-SNP	.											.	HTR3D	65	.	0			c.C1107T						PASS	.						27	32	30					3																	183756384		2202	4300	6502	SO:0001819	synonymous_variant	200909	exon7			TAAGGGCCCGGGT	AY159812	CCDS3249.1, CCDS46966.1, CCDS54685.1	3q27	2012-05-22	2012-02-03		ENSG00000186090	ENSG00000186090		"5-HT (serotonin) receptors", "Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"	24004	protein-coding gene	gene with protein product		610122	"5-hydroxytryptamine (serotonin) receptor 3 family member D"			12801637	Standard	NM_001145143		Approved		uc011bqv.2	Q70Z44	OTTHUMG00000156858	ENST00000382489.3:c.1107C>T	chr3.hg19:g.183756384C>T		150.0	0.0	.		234.0	60.0	.	NM_001163646	C9J2I6|J3QT78|Q495N5|Q495N6|Q7Z6B3	Silent	SNP	ENST00000382489.3	hg19	CCDS54685.1																																																																																			.	.	.	none		0.657	HTR3D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346289.1	NM_182537		T	183756384	C	T	183756384	2	4	269	1	0	0	0	0	0	0	0	1	7454	726	26	2		2	HTR3D	3	183756384	Silent	SNP	C	TCGA-UZ-A9Q0-01A-12D-A42J-10	54903442	183756384	14266046	17	16960											
FAM131A	131408	hgsc.bcm.edu	37	chr3	184062687	184062687	+	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	gcagctgggaacggcagcggCaagcctctgacctggcctct	7	6	14	14	2	2	1	0	1	2	0	2	2	2	2	3	4	4	4	3	4	2	0			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr3:184062687C>A	ENST00000310585.4	+	3	2301	c.937C>A	c.(937-939)Caa>Aaa	p.Q313K	FAM131A_ENST00000453072.1_Missense_Mutation_p.Q259K|FAM131A_ENST00000340957.5_Missense_Mutation_p.Q259K|FAM131A_ENST00000450976.1_Missense_Mutation_p.Q259K|EIF2B5_ENST00000444495.1_Intron|FAM131A_ENST00000383847.2_Missense_Mutation_p.Q344K|FAM131A_ENST00000418281.1_Intron			Q6UXB0	F131A_HUMAN	family with sequence similarity 131, member A	313						extracellular region (GO:0005576)				breast(1)|endometrium(1)|large_intestine(2)|lung(9)|skin(1)	14	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			ACGGCAGCGGCAAGCCTCTGA	0.632																																					p.Q344K		Atlas-SNP	.											.	FAM131A	37	.	0			c.C1030A						PASS	.						23	19	21					3																	184062687		2200	4298	6498	SO:0001583	missense	131408	exon6			CAGCGGCAAGCCT	BC026221	CCDS3262.1, CCDS3262.2, CCDS54689.1	3q27.1	2007-03-20	2007-03-20	2007-03-20	ENSG00000175182	ENSG00000175182			28308	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 40"	C3orf40		12975309	Standard	NM_144635		Approved	MGC21688	uc003foe.3	Q6UXB0	OTTHUMG00000156206	ENST00000310585.4:c.937C>A	chr3.hg19:g.184062687C>A	ENSP00000310135:p.Gln313Lys	59.0	0.0	.		90.0	46.0	.	NM_144635	D3DNT6|G5E9B1|Q8TA84	Missense_Mutation	SNP	ENST00000310585.4	hg19		.	.	.	.	.	.	.	.	.	.	c	0.020	-1.434094	0.01108	.	.	ENSG00000175182	ENST00000450976;ENST00000340957;ENST00000383847;ENST00000453072;ENST00000310585	T;T;T;T;T	0.19394	2.15;2.15;2.15;2.15;2.15	4.63	2.58	0.30949	.	0.322570	0.28600	N	0.014777	T	0.06005	0.0156	N	0.01505	-0.83	0.31769	N	0.632341	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.001	T	0.26710	-1.0095	10	0.02654	T	1	-26.278	11.3787	0.49743	0.4075:0.5925:0.0:0.0	.	313;344	Q6UXB0;G5E9B1	F131A_HUMAN;.	K	259;259;344;259;313	ENSP00000388551:Q259K;ENSP00000340974:Q259K;ENSP00000373360:Q344K;ENSP00000390588:Q259K;ENSP00000310135:Q313K	ENSP00000310135:Q313K	Q	+	1	0	FAM131A	185545381	1.000000	0.71417	0.998000	0.56505	0.290000	0.27261	6.309000	0.72825	2.122000	0.65172	0.591000	0.81541	CAA	.	.	.	none		0.632	FAM131A-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000343462.1	NM_144635		A	184062687	C	A	184062687	3	1	269	1	0	0	0	0	1	0	0	0	5443	711	25	4	1052	4	FAM131A	3	184062687	Missense_Mutation	SNP	C	TCGA-UZ-A9Q0-01A-12D-A42J-10	306303	184062687	13959743	18	16961											
IDUA	3425	hgsc.bcm.edu	37	chr4	995927	995927	+	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	gccgtggagggcggacgtgaCctacgcggccatggtggtga	6	6	19	10	5	0	2	0	2	0	0	0	4	0	4	3	6	1	0	3	6	1	1			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr4:995927C>T	ENST00000247933.4	+	7	1038	c.950C>T	c.(949-951)aCc>aTc	p.T317I	IDUA_ENST00000453894.1_Silent_p.D303D|IDUA_ENST00000514224.1_Missense_Mutation_p.T185I	NM_000203.3	NP_000194.2	P35475	IDUA_HUMAN	iduronidase, alpha-L-	317					carbohydrate metabolic process (GO:0005975)|cell morphogenesis (GO:0000902)|chemical homeostasis (GO:0048878)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate catabolic process (GO:0030209)|disaccharide metabolic process (GO:0005984)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|limb morphogenesis (GO:0035108)|lysosome organization (GO:0007040)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)	coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	L-iduronidase activity (GO:0003940)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GCGGACGTGACCTACGCGGCC	0.726																																					p.T317I		Atlas-SNP	.											.	IDUA	33	.	0			c.C950T						PASS	.						17	19	18					4																	995927		2143	4218	6361	SO:0001583	missense	3425	exon7			ACGTGACCTACGC	M74715	CCDS3343.1	4p16.3	2012-10-02			ENSG00000127415	ENSG00000127415	3.2.1.76		5391	protein-coding gene	gene with protein product		252800				1832239	Standard	NM_000203		Approved	MPS1	uc003gby.3	P35475	OTTHUMG00000088901	ENST00000247933.4:c.950C>T	chr4.hg19:g.995927C>T	ENSP00000247933:p.Thr317Ile	107.0	0.0	.		120.0	55.0	.	NM_000203	B3KWK6	Missense_Mutation	SNP	ENST00000247933.4	hg19	CCDS3343.1	.	.	.	.	.	.	.	.	.	.	C	17.69	3.451756	0.63290	.	.	ENSG00000127415	ENST00000247933;ENST00000514224	D;D	0.95035	-3.59;-3.59	4.91	4.91	0.64330	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.96821	0.8962	M	0.79805	2.47	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	D	0.95631	0.8689	10	0.22706	T	0.39	.	15.936	0.79707	0.0:1.0:0.0:0.0	.	317	P35475	IDUA_HUMAN	I	317;185	ENSP00000247933:T317I;ENSP00000425081:T185I	ENSP00000247933:T317I	T	+	2	0	IDUA	985927	1.000000	0.71417	0.993000	0.49108	0.033000	0.12548	4.700000	0.61803	2.450000	0.82876	0.561000	0.74099	ACC	.	.	.	none		0.726	IDUA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000201812.1	NM_000203		T	995927	C	T	995927	3	4	269	1	0	0	0	0	1	0	0	0	7511	507	18	2	976	2	IDUA	4	995927	Missense_Mutation	SNP	C	TCGA-UZ-A9Q0-01A-12D-A42J-10		995927	190158349	19	16962											
HTT	3064	hgsc.bcm.edu	37	chr4	3076668	3076668	+	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	gcagcagcagcagcaacagcCgccaccgccgccgccgccgc	8	0	12	21	6	0	0	0	0	0	0	0	0	0	0	7	0	6	5	7	0	1	0			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr4:3076668C>A	ENST00000355072.5	+	1	261	c.116C>A	c.(115-117)cCg>cAg	p.P39Q	HTT-AS_ENST00000503893.1_RNA	NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	39	Poly-Pro.				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)		cagcaacagccgccaccgccg	0.726																																					p.P39Q		Atlas-SNP	.											.	HTT	221	.	0			c.C116A						PASS	.						1	2	2					4																	3076668		374	1244	1618	SO:0001583	missense	3064	exon1			AACAGCCGCCACC	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.116C>A	chr4.hg19:g.3076668C>A	ENSP00000347184:p.Pro39Gln	11.0	0.0	.		16.0	4.0	.	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	C	0.023	-1.397978	0.01175	.	.	ENSG00000197386	ENST00000355072	T	0.22743	1.94	1.58	1.58	0.23477	.	.	.	.	.	T	0.12518	0.0304	N	0.22421	0.69	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.25710	-1.0124	9	0.32370	T	0.25	.	6.4693	0.21999	0.0:1.0:0.0:0.0	.	39	P42858	HD_HUMAN	Q	39	ENSP00000347184:P39Q	ENSP00000347184:P39Q	P	+	2	0	HTT	3046466	0.949000	0.32298	0.001000	0.08648	0.004000	0.04260	0.435000	0.21510	0.829000	0.34733	0.305000	0.20034	CCG	.	.	.	none		0.726	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		A	3076668	C	A	3076668	3	1	269	1	0	0	0	0	1	0	0	0	7464	652	23	4	118	4	HTT	4	3076668	Missense_Mutation	SNP	C	TCGA-UZ-A9Q0-01A-12D-A42J-10	2080741	3076668	188077608	20	16963											
SPINK5	11005	hgsc.bcm.edu	37	chr5	147484531	147484531	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaagtcaacaagaagaaagaGcaagagcaaaggctaaaaga	24	2	10	5	0	1	5	1	0	0	5	1	5	1	5	0	1	3	3	0	1	9	1			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr5:147484531G>A	ENST00000256084.7	+	16	1489	c.1447G>A	c.(1447-1449)Gca>Aca	p.A483T	SPINK5_ENST00000359874.3_Missense_Mutation_p.A483T|SPINK5_ENST00000398454.1_Missense_Mutation_p.A483T	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	483	Kazal-like 7. {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)			AGAAGAAAGAGCAAGAGCAAA	0.358																																					p.A483T		Atlas-SNP	.											.	SPINK5	245	.	0			c.G1447A						PASS	.						90	91	90					5																	147484531		1808	4088	5896	SO:0001583	missense	11005	exon16			GAAAGAGCAAGAG	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.1447G>A	chr5.hg19:g.147484531G>A	ENSP00000256084:p.Ala483Thr	332.0	1.0	.		323.0	146.0	.	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	hg19	CCDS43382.1	.	.	.	.	.	.	.	.	.	.	G	15.03	2.712874	0.48517	.	.	ENSG00000133710	ENST00000398454;ENST00000359874;ENST00000508733;ENST00000256084	T;T;T;T	0.03889	3.77;3.77;3.77;3.77	3.91	0.0124	0.14091	Proteinase inhibitor I1, Kazal (1);Protease inhibitor, Kazal-type (1);	0.480204	0.17596	N	0.168583	T	0.08492	0.0211	L	0.44542	1.39	0.23107	N	0.998281	D;P;D;D	0.76494	0.999;0.911;0.997;0.998	D;P;D;D	0.79108	0.992;0.55;0.98;0.966	T	0.30119	-0.9989	10	0.13108	T	0.6	-3.4513	3.0931	0.06301	0.3199:0.0:0.4907:0.1894	.	464;483;483;483	B4DWS3;Q9NQ38-3;Q9NQ38;Q9NQ38-2	.;.;ISK5_HUMAN;.	T	483;483;464;483	ENSP00000381472:A483T;ENSP00000352936:A483T;ENSP00000421519:A464T;ENSP00000256084:A483T	ENSP00000256084:A483T	A	+	1	0	SPINK5	147464724	1.000000	0.71417	0.925000	0.36789	0.678000	0.39670	1.527000	0.35975	-0.013000	0.14199	0.313000	0.20887	GCA	.	.	.	none		0.358	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698		A	147484531	G	A	147484531	3	1	269	1	0	0	0	0	1	0	0	0	15074	971	34	2	1509	2	SPINK5	5	147484531	Missense_Mutation	SNP	G	TCGA-UZ-A9Q0-01A-12D-A42J-10		147484531	33430729	21	16964											
SLU7	10569	hgsc.bcm.edu	37	chr5	159831848	159831848	+	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	ttgaggttttttcacagattCttccccagttatctcattta	8	19	5	9	0	3	2	2	1	2	1	5	2	4	2	2	1	0	2	2	1	2	9			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr5:159831848C>A	ENST00000297151.4	-	14	1819	c.1432G>T	c.(1432-1434)Gaa>Taa	p.E478*		NM_006425.4	NP_006416.3	O95391	SLU7_HUMAN	SLU7 splicing factor homolog (S. cerevisiae)	478					alternative mRNA splicing, via spliceosome (GO:0000380)|cellular response to heat (GO:0034605)|intracellular protein transport (GO:0006886)|mRNA 3'-splice site recognition (GO:0000389)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)	pre-mRNA 3'-splice site binding (GO:0030628)|second spliceosomal transesterification activity (GO:0000386)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(4)|lung(6)|ovary(1)	20	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TTCACAGATTCTTCCCCAGTT	0.378																																					p.E478X		Atlas-SNP	.											.	SLU7	35	.	0			c.G1432T						PASS	.						73	72	72					5																	159831848		2202	4300	6502	SO:0001587	stop_gained	10569	exon14			CAGATTCTTCCCC	AF101074	CCDS4352.1	5q33.3	2010-04-13			ENSG00000164609	ENSG00000164609			16939	protein-coding gene	gene with protein product	zinc knuckle motif containing	605974				10197984, 15728250	Standard	NM_006425		Approved	9G8	uc003lyg.3	O95391	OTTHUMG00000130324	ENST00000297151.4:c.1432G>T	chr5.hg19:g.159831848C>A	ENSP00000297151:p.Glu478*	74.0	0.0	.		94.0	36.0	.	NM_006425	D3DQK2|Q3LUJ0|Q3LUJ1|Q6RXQ5|Q96FM9	Nonsense_Mutation	SNP	ENST00000297151.4	hg19	CCDS4352.1	.	.	.	.	.	.	.	.	.	.	C	39	7.866543	0.98534	.	.	ENSG00000164609	ENST00000297151	.	.	.	5.68	4.81	0.61882	.	0.163071	0.53938	D	0.000051	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	-1.6375	15.3992	0.74823	0.0:0.8614:0.1385:0.0	.	.	.	.	X	478	.	ENSP00000297151:E478X	E	-	1	0	SLU7	159764426	1.000000	0.71417	0.968000	0.41197	0.313000	0.28021	4.521000	0.60532	1.522000	0.49001	0.591000	0.81541	GAA	.	.	.	none		0.378	SLU7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252673.1	NM_006425		A	159831848	C	A	159831848	4	1	269	1	0	0	0	0	0	1	0	0	14768	922	32	4	340	4	SLU7	5	159831848	Nonsense_Mutation	SNP	C	TCGA-UZ-A9Q0-01A-12D-A42J-10	12347317	159831848	21083412	22	16965											
F12	2161	hgsc.bcm.edu	37	chr5	176831333	176831333	+	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	gcctgggttggggtctggcaCtgtgccaggtcgcagtactc	4	10	16	11	1	1	0	0	0	1	0	3	0	1	0	2	5	2	4	2	5	1	2			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr5:176831333C>T	ENST00000253496.3	-	9	930	c.882G>A	c.(880-882)caG>caA	p.Q294Q	F12_ENST00000514943.1_5'Flank	NM_000505.3	NP_000496.2	P00748	FA12_HUMAN	coagulation factor XII (Hageman factor)	294	Kringle. {ECO:0000255|PROSITE- ProRule:PRU00121}.				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)	p.Q294H(1)		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)	GGGTCTGGCACTGTGCCAGGT	0.692									Hereditary Angioedema		OREG0017088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q294Q		Atlas-SNP	.											F12,NS,carcinoma,0,1	F12	35	.	1	Substitution - Missense(1)	kidney(1)	c.G882A						PASS	.						17	21	20					5																	176831333		2200	4295	6495	SO:0001819	synonymous_variant	2161	exon9	Familial Cancer Database	HAE, type I-III, Hereditary Angioneurotic Edema, HANE,	CTGGCACTGTGCC	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.882G>A	chr5.hg19:g.176831333C>T		204.0	0.0	.	1934	160.0	81.0	.	NM_000505	P78339	Silent	SNP	ENST00000253496.3	hg19	CCDS34302.1																																																																																			.	.	.	none		0.692	F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373217.1			T	176831333	C	T	176831333	2	4	269	1	0	0	0	0	0	0	0	1	5341	564	20	2		2	F12	5	176831333	Silent	SNP	C	TCGA-UZ-A9Q0-01A-12D-A42J-10	16999485	176831333	4083927	23	16966											
SCGN	10590	hgsc.bcm.edu	37	chr6	25665199	25665199	+	Missense_Mutation	SNP	A	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	tatgttcttatctgaggatgAaaactttcttctgctctttc	8	19	6	8	0	5	2	0	2	5	0	6	3	5	3	0	1	2	2	0	1	4	6			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr6:25665199A>C	ENST00000377961.2	+	4	443	c.275A>C	c.(274-276)gAa>gCa	p.E92A	SCGN_ENST00000334979.6_3'UTR	NM_006998.3	NP_008929.2	O76038	SEGN_HUMAN	secretagogin, EF-hand calcium binding protein	92	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.					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						TCTGAGGATGAAAACTTTCTT	0.478																																					p.E92A		Atlas-SNP	.											.	SCGN	57	.	0			c.A275C						PASS	.						161	140	147					6																	25665199		2203	4300	6503	SO:0001583	missense	10590	exon4			AGGATGAAAACTT	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.275A>C	chr6.hg19:g.25665199A>C	ENSP00000367197:p.Glu92Ala	33.0	0.0	.		40.0	15.0	.	NM_006998	A8K0B2|Q5VV44|Q96QV7|Q9UJF6	Missense_Mutation	SNP	ENST00000377961.2	hg19	CCDS4561.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.147340	0.77888	.	.	ENSG00000079689	ENST00000377961	D	0.88431	-2.38	5.19	5.19	0.71726	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.92977	0.7765	M	0.78344	2.41	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94009	0.7282	10	0.72032	D	0.01	.	14.0409	0.64674	1.0:0.0:0.0:0.0	.	92	O76038	SEGN_HUMAN	A	92	ENSP00000367197:E92A	ENSP00000367197:E92A	E	+	2	0	SCGN	25773178	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	6.810000	0.75216	1.938000	0.56188	0.528000	0.53228	GAA	.	.	.	none		0.478	SCGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040067.1			C	25665199	A	C	25665199	3	2	269	1	0	0	0	0	1	0	0	0	13916	246	9	5	289	5	SCGN	6	25665199	Missense_Mutation	SNP	A	TCGA-UZ-A9Q0-01A-12D-A42J-10		25665199	145449868	24	16967											
HIST1H2AD	3013	hgsc.bcm.edu	37	chr6	26199103	26199103	+	Missense_Mutation	SNP	A	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	ttgcccttggccttgtggtgActctcagtcttcttggggag	3	15	13	10	0	3	1	1	1	3	0	4	2	3	2	2	4	1	0	2	4	0	5			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr6:26199103A>C	ENST00000341023.1	-	1	368	c.369T>G	c.(367-369)agT>agG	p.S123R	HIST1H3D_ENST00000356476.2_5'Flank|HIST1H3D_ENST00000377831.5_5'UTR|HIST1H2BF_ENST00000359985.1_5'Flank	NM_021065.2	NP_066409.1	P20671	H2A1D_HUMAN	histone cluster 1, H2ad	123						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6		all_hematologic(11;0.196)				CCTTGTGGTGACTCTCAGTCT	0.478																																					p.S123R		Atlas-SNP	.											.	HIST1H2AD	20	.	0			c.T369G						PASS	.						117	103	107					6																	26199103		2203	4300	6503	SO:0001583	missense	3013	exon1			GTGGTGACTCTCA	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.369T>G	chr6.hg19:g.26199103A>C	ENSP00000341094:p.Ser123Arg	151.0	0.0	.		131.0	58.0	.	NM_021065	A0PK91|P57754|Q6FGY6	Missense_Mutation	SNP	ENST00000341023.1	hg19	CCDS4591.1	.	.	.	.	.	.	.	.	.	.	.	5.438	0.265913	0.10294	.	.	ENSG00000196866	ENST00000341023	T	0.40756	1.02	4.5	0.596	0.17496	Histone-fold (2);Histone H2A (1);	0.000000	0.51477	U	0.000097	T	0.08492	0.0211	N	0.10916	0.065	0.24754	N	0.992963	B	0.06786	0.001	B	0.04013	0.001	T	0.30765	-0.9967	10	0.51188	T	0.08	.	9.3362	0.38051	0.4304:0.0:0.5696:0.0	.	123	P20671	H2A1D_HUMAN	R	123	ENSP00000341094:S123R	ENSP00000341094:S123R	S	-	3	2	HIST1H2AD	26307082	0.996000	0.38824	0.997000	0.53966	0.146000	0.21551	0.211000	0.17474	-0.102000	0.12197	-0.726000	0.03593	AGT	.	.	.	none		0.478	HIST1H2AD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040100.1	NM_021065		C	26199103	A	C	26199103	3	2	269	1	0	0	0	0	1	0	0	0	7138	272	10	5	27	5	HIST1H2AD	6	26199103	Missense_Mutation	SNP	A	TCGA-UZ-A9Q0-01A-12D-A42J-10	533904	26199103	144915964	25	16968											
HSD17B8	7923	hgsc.bcm.edu	37	chr6	33173455	33173455	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acaaactatgcagcatccaaGgctggagtgattgggctgac	12	8	12	9	0	0	2	0	2	0	0	1	3	1	3	1	3	3	4	1	3	3	2			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr6:33173455G>A	ENST00000374662.3	+	5	546	c.519G>A	c.(517-519)aaG>aaA	p.K173K	RING1_ENST00000374656.4_5'Flank|HSD17B8_ENST00000469186.1_3'UTR|MIR219-1_ENST00000362166.1_RNA	NM_014234.4	NP_055049.1	Q92506	DHB8_HUMAN	hydroxysteroid (17-beta) dehydrogenase 8	173					androgen metabolic process (GO:0008209)|estrogen biosynthetic process (GO:0006703)|fatty acid biosynthetic process (GO:0006633)	mitochondrial envelope (GO:0005740)|mitochondrial matrix (GO:0005759)|plasma membrane (GO:0005886)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone dehydrogenase (NAD+) activity (GO:0047035)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(1)|urinary_tract(2)	9						CAGCATCCAAGGCTGGAGTGA	0.587																																					p.K173K		Atlas-SNP	.											.	HSD17B8	20	.	0			c.G519A						PASS	.						46	47	47					6																	33173455		1508	2707	4215	SO:0001819	synonymous_variant	7923	exon5			ATCCAAGGCTGGA	D82061	CCDS4769.1	6p21.3	2011-09-14	2002-02-19	2002-02-22	ENSG00000204228	ENSG00000204228	1.1.1.62	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	3554	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 30C, member 1"	601417	"FabG (beta-ketoacyl-[acyl-carrier-protein] reductase, E coli) like (E. coli)"	FABGL		8812499, 19027726	Standard	NM_014234		Approved	HKE6, D6S2245E, RING2, KE6, H2-KE6, SDR30C1	uc003odi.2	Q92506	OTTHUMG00000031117	ENST00000374662.3:c.519G>A	chr6.hg19:g.33173455G>A		80.0	0.0	.		101.0	42.0	.	NM_014234	A6NLX7|Q5STP7|Q9UIQ1	Silent	SNP	ENST00000374662.3	hg19	CCDS4769.1																																																																																			.	.	.	none		0.587	HSD17B8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076196.1	NM_014234		A	33173455	G	A	33173455	2	1	269	1	0	0	0	0	0	0	0	1	7396	991	35	2		2	HSD17B8	6	33173455	Silent	SNP	G	TCGA-UZ-A9Q0-01A-12D-A42J-10	6974352	33173455	137941612	26	16969											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152462387	152462387	+	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	ttaacaaagccaggaaggctCtcctcttcctccttcagttt	9	13	6	13	0	3	0	1	0	2	0	6	1	5	1	4	2	2	2	4	2	3	4			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr6:152462387C>T	ENST00000367255.5	-	139	25798	c.25197G>A	c.(25195-25197)gaG>gaA	p.E8399E	SYNE1_ENST00000356820.4_Silent_p.E2923E|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000448038.1_Silent_p.E8351E|SYNE1_ENST00000354674.4_Silent_p.E577E|SYNE1_ENST00000423061.1_Silent_p.E8351E|SYNE1_ENST00000539504.1_Silent_p.E554E|SYNE1_ENST00000341594.5_Silent_p.E8011E|SYNE1_ENST00000265368.4_Silent_p.E8399E	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8399					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)		CAGGAAGGCTCTCCTCTTCCT	0.478										HNSCC(10;0.0054)																											p.E8399E		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G25197A						PASS	.						180	152	162					6																	152462387		2203	4300	6503	SO:0001819	synonymous_variant	23345	exon139			AAGGCTCTCCTCT	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.25197G>A	chr6.hg19:g.152462387C>T		92.0	0.0	.		82.0	36.0	.	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	hg19	CCDS5236.2																																																																																			.	.	.	none		0.478	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152462387	C	T	152462387	2	4	269	1	0	0	0	0	0	0	0	1	15457	912	32	2		2	SYNE1	6	152462387	Silent	SNP	C	TCGA-UZ-A9Q0-01A-12D-A42J-10	119288932	152462387	18652680	27	16970											
DFNA5	1687	hgsc.bcm.edu	37	chr7	24742409	24742409	+	Frame_Shift_Del	DEL	T	T	-																															agtgtgggaatgatctggagTttgcagcaagtgcccagcag																										TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr7:24742409delT	ENST00000342947.3	-	9	1652	c.1227delA	c.(1225-1227)aaafs	p.K409fs	DFNA5_ENST00000545231.1_Frame_Shift_Del_p.K245fs|DFNA5_ENST00000409775.3_Frame_Shift_Del_p.K409fs|DFNA5_ENST00000419307.1_Frame_Shift_Del_p.K245fs|DFNA5_ENST00000409970.1_Frame_Shift_Del_p.K245fs	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	409					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						TGATCTGGAGTTTGCAGCAAG	0.502																																					p.L410fs	GBM(78;184 1250 20134 20900 23600)	Atlas-Indel,Pindel	.											.	DFNA5	51	.	0			c.1228delC						PASS	.						117	111	113					7																	24742409		2203	4300	6503	SO:0001589	frameshift_variant	1687	exon9			.	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.1227delA	chr7.hg19:g.24742409delT	ENSP00000339587:p.Lys409fs	70.0	0.0	0		120.0	75.0	0.625	NM_001127453	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Frame_Shift_Del	DEL	ENST00000342947.3	hg19	CCDS5389.1																																																																																			.	.	.	none		0.502	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403		-	24742409	T	-	24742409	7	5	269	1	0	1	0	1	0	0	0	0	4456	1722	60	0	271	0	DFNA5	7	24742409	Frame_Shift_Del	DEL	T	TCGA-UZ-A9Q0-01A-12D-A42J-10		24742409	134396254	28	16971											
SSPO	23145	hgsc.bcm.edu	37	chr7	149499004	149499004	+	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	ctgagcggcgctgtgacctgCggcctgactgccaggatggc	5	7	16	13	3	0	3	0	3	0	0	0	4	0	4	3	4	3	1	3	4	0	0	rs376985175		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr7:149499004C>T	ENST00000378016.2	+	0	7456							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)			CTGTGACCTGCGGCCTGACTG	0.687													C|||	1	0.000199681	0	0.0014	5008	,	,		17106	0		0	False		,,,				2504	0				p.R2486W		Atlas-SNP	.											.	.	.	.	0			c.C7456T						PASS	.	C		1,4285		0,1,2142	26	28	27		7460	3.5	0	7		27	0,8482		0,0,4241	no	coding-notMod3	SSPO	NM_198455.2		0,1,6383	TT,TC,CC		0.0,0.0233,0.0078			149499004	1,12767	2143	4241	6384			23145	exon50			GACCTGCGGCCTG	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"subcommissural organ spondin", "SCO protein, thrombospondin domain containing"		"SCO-spondin homolog (Bos taurus)"			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149499004C>T		40.0	0.0	.		70.0	27.0	.	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	hg19																																																																																				.	.	.	weak		0.687	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				T	149499004	C	T	149499004	1	4	269	0	1	0	0	0	0	0	0	0	15201	759	27	1		1	SSPO	7	149499004	RNA	SNP	C	TCGA-UZ-A9Q0-01A-12D-A42J-10	124756595	149499004	9639659	29	16972											
FPGS	2356	hgsc.bcm.edu	37	chr9	130570589	130570589	+	Splice_Site	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	ggaccgagcccagcagatctCagtaagtctgattggaatgg	11	8	13	9	1	2	2	1	1	2	1	3	5	2	4	2	3	2	2	2	3	2	2			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr9:130570589C>A	ENST00000373247.2	+	9	871	c.821C>A	c.(820-822)tCa>tAa	p.S274*	FPGS_ENST00000373225.3_Splice_Site_p.S224*|FPGS_ENST00000393706.2_Splice_Site_p.S248*|FPGS_ENST00000460181.1_3'UTR|FPGS_ENST00000373245.1_Splice_Site_p.S274*	NM_004957.4	NP_004948.4	Q05932	FOLC_HUMAN	folylpolyglutamate synthase	274					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)	CAGCAGATCTCAGTAAGTCTG	0.592																																					p.S274X		Atlas-SNP	.											.	FPGS	30	.	0			c.C821A						PASS	.						84	76	79					9																	130570589		2203	4300	6503	SO:0001630	splice_region_variant	2356	exon9			AGATCTCAGTAAG		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.822+1C>A	chr9.hg19:g.130570589C>A		52.0	0.0	.		48.0	18.0	.	NM_004957	B3KPW4|B7Z2Z3|F5H0K6|Q5JU19|Q5JU22|Q6P2P6	Nonsense_Mutation	SNP	ENST00000373247.2	hg19	CCDS35148.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.709436	0.89018	.	.	ENSG00000136877	ENST00000373247;ENST00000373245;ENST00000393706;ENST00000373228;ENST00000373225;ENST00000431857	.	.	.	5.06	3.12	0.35913	.	0.769059	0.12103	N	0.499303	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	-8.0083	4.8255	0.13414	0.1505:0.62:0.1462:0.0833	.	.	.	.	X	274;274;248;274;224;224	.	ENSP00000362322:S224X	S	+	2	0	FPGS	129610410	0.000000	0.05858	0.996000	0.52242	0.900000	0.52787	0.615000	0.24329	1.084000	0.41184	0.462000	0.41574	TCA	.	.	.	none		0.592	FPGS-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054251.1		Nonsense_Mutation	A	130570589	C	A	130570589	5	1	269	1	0	0	0	0	0	0	1	0	6043	840	29	4	855	4	FPGS	9	130570589	Splice_Site	SNP	C	TCGA-UZ-A9Q0-01A-12D-A42J-10		130570589	10642842	30	16973											
PRKG1	5592	hgsc.bcm.edu	37	chr10	54053646	54053646	+	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	ctgatgacaactcaggatggGatatagacttctaatgtatt	13	13	9	6	0	2	3	1	2	1	1	2	5	2	5	0	2	1	1	0	2	5	6			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr10:54053646G>T	ENST00000401604.2	+	18	2196	c.2002G>T	c.(2002-2004)Gat>Tat	p.D668Y	PRKG1_ENST00000373985.1_Missense_Mutation_p.D656Y|PRKG1_ENST00000373975.2_Missense_Mutation_p.D386Y|PRKG1-AS1_ENST00000452247.2_RNA|PRKG1_ENST00000373980.4_Missense_Mutation_p.D683Y|PRKG1-AS1_ENST00000426785.2_RNA			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	668	AGC-kinase C-terminal.				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)		CTCAGGATGGGATATAGACTT	0.443																																					p.D683Y		Atlas-SNP	.											.	PRKG1	167	.	0			c.G2047T						PASS	.						153	136	142					10																	54053646		2203	4300	6503	SO:0001583	missense	5592	exon18			GGATGGGATATAG		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.2002G>T	chr10.hg19:g.54053646G>T	ENSP00000384200:p.Asp668Tyr	69.0	0.0	.		70.0	34.0	.	NM_006258	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Missense_Mutation	SNP	ENST00000401604.2	hg19	CCDS44399.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.976705	0.74360	.	.	ENSG00000185532	ENST00000401604;ENST00000373985;ENST00000373980;ENST00000332193;ENST00000373975	T;T;T	0.72835	-0.69;-0.68;-0.69	5.99	5.99	0.97316	AGC-kinase, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.87653	0.6231	M	0.89163	3.01	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	0.88702	0.3216	10	0.87932	D	0	-21.0641	20.0728	0.97731	0.0:0.0:1.0:0.0	.	386;683;668	B3KSF3;Q13976-2;Q13976	.;.;KGP1_HUMAN	Y	668;656;683;386;280	ENSP00000384200:D668Y;ENSP00000363097:D656Y;ENSP00000363092:D683Y	ENSP00000327642:D386Y	D	+	1	0	PRKG1	53723652	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.476000	0.97823	2.840000	0.97914	0.655000	0.94253	GAT	.	.	.	none		0.443	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	54053646	G	T	54053646	3	4	269	1	0	0	0	0	1	0	0	0	12532	1174	41	4	2387	4	PRKG1	10	54053646	Missense_Mutation	SNP	G	TCGA-UZ-A9Q0-01A-12D-A42J-10		54053646	81481101	31	16974											
KIAA0913	23053	hgsc.bcm.edu	37	chr10	75548546	75548546	+	Frame_Shift_Del	DEL	T	T	-																															cagctacagctccgaattgcTttttggagcttccctgagaa																										TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr10:75548546delT	ENST00000605216.1	+	2	544	c.327delT	c.(325-327)gctfs	p.A109fs	ZSWIM8_ENST00000603114.1_Frame_Shift_Del_p.A109fs|ZSWIM8_ENST00000604729.1_Frame_Shift_Del_p.A109fs|ZSWIM8_ENST00000398706.2_Frame_Shift_Del_p.A109fs|ZSWIM8_ENST00000604524.1_Frame_Shift_Del_p.A109fs	NM_001242487.1	NP_001229416.1	A7E2V4	ZSWM8_HUMAN	zinc finger, SWIM-type containing 8	109							zinc ion binding (GO:0008270)										TCCGAATTGCTTTTTGGAGCT	0.527																																					p.A109fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.326delC						PASS	.						71	69	70					10																	75548546		1931	4131	6062	SO:0001589	frameshift_variant	23053	exon2			.	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.327delT	chr10.hg19:g.75548546delT	ENSP00000474748:p.Ala109fs	56.0	0.0	0		56.0	19.0	0.339286	NM_015037	B2RP37|O94987|Q17RS8|Q2TAB8|Q6P439|Q8IW81|Q8NB34|Q9H8F3	Frame_Shift_Del	DEL	ENST00000605216.1	hg19																																																																																				.	.	.	none		0.527	ZSWIM8-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000468545.1	NM_001242487		-	75548546	T	-	75548546	7	5	269	1	0	1	0	1	0	0	0	0	8207	1596	56	0	333	0	KIAA0913	10	75548546	Frame_Shift_Del	DEL	T	TCGA-UZ-A9Q0-01A-12D-A42J-10	21494900	75548546	59986201	32	16975											
SMPD1	6609	hgsc.bcm.edu	37	chr11	6411941	6411941	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggatgggcctggtgctggCgctggcgctggcgctggcgc	1	9	20	11	4	0	0	0	0	0	0	0	1	0	1	1	7	1	4	1	7	0	1	rs550365194|rs550067660|rs71467507|rs78250081|rs558809956|rs3838786	byFrequency	TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr11:6411941C>T	ENST00000342245.4	+	1	281	c.113C>T	c.(112-114)gCg>gTg	p.A38V	SMPD1_ENST00000527275.1_Missense_Mutation_p.A38V|SMPD1_ENST00000533196.1_3'UTR|SMPD1_ENST00000356761.2_Missense_Mutation_p.A38V|SMPD1_ENST00000299397.3_Missense_Mutation_p.A38V	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	38					cell death (GO:0008219)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of MAP kinase activity (GO:0043407)|nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein dephosphorylation (GO:0035307)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)|sphingomyelin metabolic process (GO:0006684)|termination of signal transduction (GO:0023021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lamellar body (GO:0042599)|lysosomal lumen (GO:0043202)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(3)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Amlodipine(DB00381)|Chlorpromazine(DB00477)|Desipramine(DB01151)	ctggtgctggcgctggcgctg	0.711																																					p.A38V		Atlas-SNP	.											.	SMPD1	108	.	0			c.C113T						PASS	.						11	14	13					11																	6411941		2185	4258	6443	SO:0001583	missense	6609	exon1			TGCTGGCGCTGGC	AB209775	CCDS31409.1, CCDS44531.1, CCDS31409.2	11p15.4-p15.1	2010-04-28	2008-02-04		ENSG00000166311	ENSG00000166311	3.1.4.12		11120	protein-coding gene	gene with protein product	"acid sphingomyelinase"	607608				1711683	Standard	NM_000543		Approved	ASM	uc001mcw.3	P17405	OTTHUMG00000165453	ENST00000342245.4:c.113C>T	chr11.hg19:g.6411941C>T	ENSP00000340409:p.Ala38Val	74.0	0.0	.		102.0	11.0	.	NM_000543	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Missense_Mutation	SNP	ENST00000342245.4	hg19	CCDS44531.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.234305	0.39498	.	.	ENSG00000166311	ENST00000299397;ENST00000356761;ENST00000342245;ENST00000527275	T;T;T;T	0.09723	2.95;2.95;2.95;2.95	4.54	-1.08	0.09936	.	.	.	.	.	T	0.04363	0.0120	N	0.08118	0	0.09310	N	1	B;B	0.15473	0.002;0.013	B;B	0.10450	0.002;0.005	T	0.47275	-0.9130	9	0.12103	T	0.63	.	6.8659	0.24093	0.0:0.5614:0.262:0.1766	.	38;38	E9PKS3;G3XAB5	.;.	V	38	ENSP00000299397:A38V;ENSP00000349203:A38V;ENSP00000340409:A38V;ENSP00000435350:A38V	ENSP00000299397:A38V	A	+	2	0	SMPD1	6368517	0.000000	0.05858	0.130000	0.21974	0.033000	0.12548	-2.110000	0.01334	-0.479000	0.06813	-1.305000	0.01319	GCG	.	.	.	weak		0.711	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543		T	6411941	C	T	6411941	3	4	269	1	0	0	0	0	1	0	0	0	14817	768	27	1	115	1	SMPD1	11	6411941	Missense_Mutation	SNP	C	TCGA-UZ-A9Q0-01A-12D-A42J-10		6411941	128594575	33	16976											
PLEKHA7	144100	hgsc.bcm.edu	37	chr11	16816490	16816490	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgactccactagaattctgaAgttctctttatttgcactca	10	16	5	10	0	3	3	1	2	2	1	5	3	4	3	1	0	1	2	1	0	4	6			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr11:16816490A>G	ENST00000355661.3	-	18	2495	c.2485T>C	c.(2485-2487)Ttc>Ctc	p.F829L	PLEKHA7_ENST00000532079.1_Intron|PLEKHA7_ENST00000531066.1_Missense_Mutation_p.F829L|PLEKHA7_ENST00000448080.2_Missense_Mutation_p.F829L			Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A member 7	829					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						AGAATTCTGAAGTTCTCTTTA	0.483																																					p.F829L		Atlas-SNP	.											.	PLEKHA7	120	.	0			c.T2485C						PASS	.						197	190	193					11																	16816490		2200	4294	6494	SO:0001583	missense	144100	exon18			TTCTGAAGTTCTC	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.2485T>C	chr11.hg19:g.16816490A>G	ENSP00000347883:p.Phe829Leu	77.0	0.0	.		94.0	42.0	.	NM_175058	B4DK33|B4DWC3|Q86VZ7	Missense_Mutation	SNP	ENST00000355661.3	hg19	CCDS31434.1	.	.	.	.	.	.	.	.	.	.	A	15.76	2.928012	0.52759	.	.	ENSG00000166689	ENST00000531066;ENST00000355661;ENST00000448080	T;T;T	0.17370	2.28;2.28;2.28	5.57	5.57	0.84162	.	0.210963	0.50627	D	0.000109	T	0.16471	0.0396	L	0.42245	1.32	0.41172	D	0.986176	B;B;B;B	0.20368	0.026;0.031;0.044;0.043	B;B;B;B	0.24541	0.036;0.05;0.024;0.054	T	0.06844	-1.0804	10	0.10636	T	0.68	-10.738	16.0108	0.80402	1.0:0.0:0.0:0.0	.	403;829;829;829	Q6IQ23-3;E9PKC0;Q6IQ23;Q6IQ23-2	.;.;PKHA7_HUMAN;.	L	829	ENSP00000435389:F829L;ENSP00000347883:F829L;ENSP00000416895:F829L	ENSP00000347883:F829L	F	-	1	0	PLEKHA7	16773066	1.000000	0.71417	1.000000	0.80357	0.858000	0.48976	8.870000	0.92336	2.242000	0.73789	0.482000	0.46254	TTC	.	.	.	none		0.483	PLEKHA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000387242.2	NM_175058		G	16816490	A	G	16816490	3	3	269	1	0	0	0	0	1	0	0	0	12068	72	3	3	904	3	PLEKHA7	11	16816490	Missense_Mutation	SNP	A	TCGA-UZ-A9Q0-01A-12D-A42J-10	10404549	16816490	118190026	34	16977											
ARFGAP2	84364	hgsc.bcm.edu	37	chr11	47198367	47198367	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgcgcgaagcctcttaaaaAgagtctggatttcggtcttg	9	12	11	9	3	3	1	0	0	3	1	4	3	3	2	1	2	2	0	1	2	4	3			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr11:47198367A>G	ENST00000524782.1	-	1	266	c.38T>C	c.(37-39)cTt>cCt	p.L13P	ARFGAP2_ENST00000319543.6_5'UTR|ARFGAP2_ENST00000419701.2_5'UTR|ARFGAP2_ENST00000426335.2_Missense_Mutation_p.L13P|ARFGAP2_ENST00000395449.3_5'UTR	NM_001242832.1|NM_032389.4	NP_001229761.1|NP_115765.2	Q8N6H7	ARFG2_HUMAN	ADP-ribosylation factor GTPase activating protein 2	13	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			breast(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						CCTCTTAAAAAGAGTCTGGAT	0.652																																					p.L13P		Atlas-SNP	.											.	ARFGAP2	43	.	0			c.T38C						PASS	.						52	55	54					11																	47198367		2201	4298	6499	SO:0001583	missense	84364	exon1			TTAAAAAGAGTCT	AK027482	CCDS7926.1, CCDS73283.1	11p11.2-p11.12	2012-10-05	2008-01-09	2008-01-09	ENSG00000149182	ENSG00000149182		"ADP-ribosylation factor GTPase activating proteins"	13504	protein-coding gene	gene with protein product		606908	"zinc finger protein 289, ID1 regulated"	ZNF289		11278321, 14690497	Standard	NM_032389		Approved	IRZ, Zfp289, FLJ14576	uc001ndt.3	Q8N6H7	OTTHUMG00000166773	ENST00000524782.1:c.38T>C	chr11.hg19:g.47198367A>G	ENSP00000434442:p.Leu13Pro	57.0	0.0	.		79.0	40.0	.	NM_001242832	B4DX29|B7Z9M7|D3DQQ9|Q3LIF2|Q8N3I1|Q96SX7	Missense_Mutation	SNP	ENST00000524782.1	hg19	CCDS7926.1	.	.	.	.	.	.	.	.	.	.	A	32	5.139315	0.94560	.	.	ENSG00000149182	ENST00000426335;ENST00000524782;ENST00000526342;ENST00000527927;ENST00000525398;ENST00000525314;ENST00000528444;ENST00000530596	T;T;T;T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86;0.86;0.86;0.86	5.54	5.54	0.83059	.	0.251453	0.32533	N	0.005971	T	0.60996	0.2312	L	0.39467	1.215	0.80722	D	1	D;D;D;P	0.76494	0.998;0.999;0.999;0.874	D;D;D;P	0.76575	0.969;0.985;0.988;0.756	T	0.64283	-0.6444	10	0.87932	D	0	-3.7774	15.6714	0.77279	1.0:0.0:0.0:0.0	.	13;13;13;13	B7Z6H9;B3KV00;G5E9L0;Q8N6H7	.;.;.;ARFG2_HUMAN	P	13	ENSP00000400226:L13P;ENSP00000434442:L13P;ENSP00000437305:L13P;ENSP00000434433:L13P;ENSP00000431939:L13P;ENSP00000434809:L13P;ENSP00000431684:L13P;ENSP00000435488:L13P	ENSP00000400226:L13P	L	-	2	0	ARFGAP2	47154943	0.987000	0.35691	0.974000	0.42286	0.983000	0.72400	6.783000	0.75078	2.107000	0.64212	0.459000	0.35465	CTT	.	.	.	none		0.652	ARFGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391425.1	NM_032389		G	47198367	A	G	47198367	3	3	269	1	0	0	0	0	1	0	0	0	850	72	3	3	1591	3	ARFGAP2	11	47198367	Missense_Mutation	SNP	A	TCGA-UZ-A9Q0-01A-12D-A42J-10	30381877	47198367	87808149	35	16978											
BCL9L	283149	hgsc.bcm.edu	37	chr11	118772132	118772132	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgttcatgttgacattcaTgttcatgttgaggttgcctg	7	17	10	7	0	3	2	3	2	0	0	3	2	3	2	1	1	1	5	1	1	0	6			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr11:118772132T>C	ENST00000334801.3	-	6	3284	c.2320A>G	c.(2320-2322)Atg>Gtg	p.M774V	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	774	Met-rich.				canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		ttgacattcatgttcatgttG	0.597																																					p.M774V		Atlas-SNP	.											.	BCL9L	254	.	0			c.A2320G						PASS	.						170	97	122					11																	118772132		2200	4294	6494	SO:0001583	missense	283149	exon6			CATTCATGTTCAT	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.2320A>G	chr11.hg19:g.118772132T>C	ENSP00000335320:p.Met774Val	34.0	0.0	.		43.0	22.0	.	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Missense_Mutation	SNP	ENST00000334801.3	hg19	CCDS8403.1	.	.	.	.	.	.	.	.	.	.	T	12.07	1.827150	0.32329	.	.	ENSG00000186174	ENST00000334801;ENST00000526143;ENST00000525300;ENST00000392849;ENST00000431085	T	0.78364	-1.17	5.24	4.12	0.48240	.	0.000000	0.64402	D	0.000011	T	0.69967	0.3170	L	0.42245	1.32	0.41065	D	0.985405	P;B	0.36837	0.571;0.435	B;B	0.39503	0.301;0.158	T	0.68606	-0.5364	10	0.32370	T	0.25	-11.8278	10.1544	0.42814	0.0:0.0794:0.0:0.9206	.	769;774	Q86UU0-2;Q86UU0	.;BCL9L_HUMAN	V	774;737;67;774;774	ENSP00000335320:M774V	ENSP00000335320:M774V	M	-	1	0	BCL9L	118277342	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.585000	0.60977	1.974000	0.57490	0.379000	0.24179	ATG	.	.	.	none		0.597	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557		C	118772132	T	C	118772132	3	2	269	1	0	0	0	0	1	0	0	0	1382	1464	51	3	2191	3	BCL9L	11	118772132	Missense_Mutation	SNP	T	TCGA-UZ-A9Q0-01A-12D-A42J-10	71573765	118772132	16234384	36	16979											
NCAPD3	23310	hgsc.bcm.edu	37	chr11	134038058	134038058	+	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	gagtaactcactggcgtccaGgtccaggggtaggatgccat	9	8	14	10	1	1	0	1	0	0	0	3	2	3	1	3	5	2	2	3	5	2	2			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr11:134038058G>C	ENST00000534548.2	-	27	3470	c.3406C>G	c.(3406-3408)Ctg>Gtg	p.L1136V		NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	1136					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)		CTGGCGTCCAGGTCCAGGGGT	0.493																																					p.L1136V		Atlas-SNP	.											.	NCAPD3	141	.	0			c.C3406G						PASS	.						89	80	83					11																	134038058		2201	4297	6498	SO:0001583	missense	23310	exon27			CGTCCAGGTCCAG	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.3406C>G	chr11.hg19:g.134038058G>C	ENSP00000433681:p.Leu1136Val	71.0	0.0	.		70.0	43.0	.	NM_015261	A6NFS2|Q4KMQ9	Missense_Mutation	SNP	ENST00000534548.2	hg19	CCDS31723.1	.	.	.	.	.	.	.	.	.	.	g	8.791	0.930650	0.18131	.	.	ENSG00000151503	ENST00000534548;ENST00000527944;ENST00000530396	T;T	0.41758	0.99;0.99	5.52	3.25	0.37280	Armadillo-type fold (1);	0.321794	0.43416	D	0.000563	T	0.18923	0.0454	N	0.03608	-0.345	0.80722	D	1	B;B	0.16802	0.012;0.019	B;B	0.21151	0.033;0.02	T	0.04029	-1.0983	10	0.30078	T	0.28	-16.907	8.1785	0.31296	0.0:0.0704:0.2849:0.6447	.	1136;196	P42695;Q96FA6	CNDD3_HUMAN;.	V	1136;41;172	ENSP00000433681:L1136V;ENSP00000435173:L172V	ENSP00000432532:L41V	L	-	1	2	NCAPD3	133543268	1.000000	0.71417	0.996000	0.52242	0.523000	0.34469	1.122000	0.31295	0.430000	0.26230	0.586000	0.80456	CTG	.	.	.	none		0.493	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261		C	134038058	G	C	134038058	3	2	269	1	0	0	0	0	1	0	0	0	10213	991	35	4	1126	4	NCAPD3	11	134038058	Missense_Mutation	SNP	G	TCGA-UZ-A9Q0-01A-12D-A42J-10	15265926	134038058	968458	37	16980											
KRT82	3888	hgsc.bcm.edu	37	chr12	52789833	52789833	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcaggcgcctgtaggtggCgatctcgatgtccaggccca	7	7	14	13	3	1	0	0	0	1	0	3	2	2	0	3	4	1	2	3	4	1	1	rs377127392		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr12:52789833C>T	ENST00000257974.2	-	7	1329	c.1252G>A	c.(1252-1254)Gcc>Acc	p.A418T	RP3-416H24.4_ENST00000547174.1_RNA	NM_033033.3	NP_149022.3	Q9NSB4	KRT82_HUMAN	keratin 82	418	Coil 2.|Rod.					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)		CTGTAGGTGGCGATCTCGATG	0.602																																					p.A418T		Atlas-SNP	.											.	KRT82	45	.	0			c.G1252A						PASS	.						80	74	76					12																	52789833		2203	4300	6503	SO:0001583	missense	3888	exon7			AGGTGGCGATCTC	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.1252G>A	chr12.hg19:g.52789833C>T	ENSP00000257974:p.Ala418Thr	91.0	0.0	.		76.0	32.0	.	NM_033033		Missense_Mutation	SNP	ENST00000257974.2	hg19	CCDS8826.1	.	.	.	.	.	.	.	.	.	.	C	35	5.503534	0.96371	.	.	ENSG00000161850	ENST00000257974	D	0.90900	-2.75	4.93	4.93	0.64822	Filament (1);Intermediate filament protein, conserved site (1);	0.000000	0.48767	D	0.000169	D	0.95255	0.8461	M	0.77616	2.38	0.51233	D	0.999916	D	0.89917	1.0	D	0.75484	0.986	D	0.95515	0.8589	10	0.66056	D	0.02	.	18.3396	0.90300	0.0:1.0:0.0:0.0	.	418	Q9NSB4	KRT82_HUMAN	T	418	ENSP00000257974:A418T	ENSP00000257974:A418T	A	-	1	0	KRT82	51076100	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.724000	0.68500	2.566000	0.86566	0.561000	0.74099	GCC	.	.	.	weak		0.602	KRT82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405189.1	NM_033033		T	52789833	C	T	52789833	3	4	269	1	0	0	0	0	1	0	0	0	8503	768	27	1	301	1	KRT82	12	52789833	Missense_Mutation	SNP	C	TCGA-UZ-A9Q0-01A-12D-A42J-10		52789833	81062062	38	16981											
RDH5	5959	hgsc.bcm.edu	37	chr12	56115699	56115699	+	Missense_Mutation	SNP	A	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	gggggctactgtgtctccaaAtttggcctggaggccttctc	5	12	13	11	0	2	0	0	0	2	0	4	1	2	1	3	5	1	1	3	5	2	3			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr12:56115699A>C	ENST00000257895.5	+	3	689	c.537A>C	c.(535-537)aaA>aaC	p.K179N	RDH5_ENST00000548082.1_Missense_Mutation_p.K179N|RDH5_ENST00000553160.1_Intron|RP11-644F5.10_ENST00000550412.1_3'UTR|RDH5_ENST00000547072.1_Missense_Mutation_p.K82N	NM_001199771.1|NM_002905.3	NP_001186700.1|NP_002896.2	Q92781	RDH1_HUMAN	retinol dehydrogenase 5 (11-cis/9-cis)	179					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	cell body (GO:0044297)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	retinol dehydrogenase activity (GO:0004745)			breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|skin(1)	12					Vitamin A(DB00162)	GTGTCTCCAAATTTGGCCTGG	0.627																																					p.K179N		Atlas-SNP	.											.	RDH5	25	.	0			c.A537C						PASS	.						25	27	26					12																	56115699		2203	4300	6503	SO:0001583	missense	5959	exon3			CTCCAAATTTGGC	U89717	CCDS31829.1	12q13-q14	2013-06-03	2006-05-09			ENSG00000135437	1.1.1.105	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	9940	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 9C, member 5"	601617	"retinol dehydrogenase 5 (11-cis and 9-cis)"	RDH1		9115228, 8884265, 19027726	Standard	NM_002905		Approved	HSD17B9, SDR9C5	uc001shl.3	Q92781	OTTHUMG00000170126	ENST00000257895.5:c.537A>C	chr12.hg19:g.56115699A>C	ENSP00000257895:p.Lys179Asn	345.0	0.0	.		365.0	142.0	.	NM_001199771	O00179|Q8TAI2	Missense_Mutation	SNP	ENST00000257895.5	hg19	CCDS31829.1	.	.	.	.	.	.	.	.	.	.	A	14.75	2.627250	0.46944	.	.	ENSG00000135437	ENST00000547072;ENST00000257895;ENST00000548082	D;D;D	0.98958	-5.27;-5.27;-5.27	5.36	2.02	0.26589	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99339	0.9768	H	0.98466	4.24	0.51482	D	0.999926	D	0.89917	1.0	D	0.97110	1.0	D	0.98368	1.0552	10	0.87932	D	0	.	7.5049	0.27538	0.3471:0.0:0.6529:0.0	.	179	Q92781	RDH1_HUMAN	N	82;179;179	ENSP00000449927:K82N;ENSP00000257895:K179N;ENSP00000447128:K179N	ENSP00000257895:K179N	K	+	3	2	RDH5	54401966	1.000000	0.71417	1.000000	0.80357	0.057000	0.15508	1.727000	0.38095	0.738000	0.32606	-0.242000	0.12053	AAA	.	.	.	none		0.627	RDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407493.1	NM_002905		C	56115699	A	C	56115699	3	2	269	1	0	0	0	0	1	0	0	0	13208	98	4	5	543	5	RDH5	12	56115699	Missense_Mutation	SNP	A	TCGA-UZ-A9Q0-01A-12D-A42J-10	3325866	56115699	77736196	39	16982											
PAN2	9924	hgsc.bcm.edu	37	chr12	56720417	56720417	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacctgggagctggagcagAgttggcagcaggccaatcag	11	5	15	10	0	1	1	1	0	0	1	1	3	1	3	2	4	4	5	2	4	2	1			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr12:56720417A>G	ENST00000425394.2	-	7	1622	c.1246T>C	c.(1246-1248)Tct>Cct	p.S416P	PAN2_ENST00000548043.1_Missense_Mutation_p.S416P|PAN2_ENST00000440411.3_Missense_Mutation_p.S416P|PAN2_ENST00000257931.5_Missense_Mutation_p.S416P	NM_001127460.2	NP_001120932	Q9HBH5	RDH14_HUMAN	PAN2 poly(A) specific ribonuclease subunit	0					osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	41					Vitamin A(DB00162)	GCTGGAGCAGAGTTGGCAGCA	0.572																																					p.S416P		Atlas-SNP	.											.	PAN2	107	.	0			c.T1246C						PASS	.						42	37	39					12																	56720417		2203	4299	6502	SO:0001583	missense	9924	exon7			GAGCAGAGTTGGC	AB014610	CCDS8915.1, CCDS44922.1, CCDS53802.1	12q13.2	2014-03-27	2014-03-27	2008-01-08		ENSG00000135473		"Ubiquitin-specific peptidases"	20074	protein-coding gene	gene with protein product	"PAN2 homolog, PABP1 dependent poly A specific ribonuclease subunit (S. cerevisiae)"		"ubiquitin specific protease 52", "ubiquitin specific peptidase 52", "PAN2 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"	USP52		12838346, 14583602	Standard	NM_014871		Approved	KIAA0710, hPAN2	uc001skx.3	Q504Q3	OTTHUMG00000170412	ENST00000425394.2:c.1246T>C	chr12.hg19:g.56720417A>G	ENSP00000401721:p.Ser416Pro	131.0	0.0	.		127.0	53.0	.	NM_014871		Missense_Mutation	SNP	ENST00000425394.2	hg19	CCDS44922.1	.	.	.	.	.	.	.	.	.	.	A	14.28	2.488292	0.44249	.	.	ENSG00000135473	ENST00000425394;ENST00000440411;ENST00000257931;ENST00000548043	T;T;T;T	0.05717	3.4;3.4;3.4;3.4	5.08	3.91	0.45181	.	0.201660	0.45867	D	0.000336	T	0.05364	0.0142	N	0.17082	0.46	0.36821	D	0.886405	P;P;P	0.43885	0.82;0.727;0.733	B;B;B	0.43103	0.408;0.408;0.177	T	0.51116	-0.8746	10	0.34782	T	0.22	-11.6206	11.3926	0.49824	0.8479:0.152:0.0:0.0	.	416;416;416	Q504Q3-3;Q504Q3-2;Q504Q3	.;.;PAN2_HUMAN	P	416	ENSP00000401721:S416P;ENSP00000388231:S416P;ENSP00000257931:S416P;ENSP00000449861:S416P	ENSP00000257931:S416P	S	-	1	0	PAN2	55006684	1.000000	0.71417	0.995000	0.50966	0.997000	0.91878	2.711000	0.47177	1.033000	0.39918	0.477000	0.44152	TCT	.	.	.	none		0.572	PAN2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409024.1	NM_014871		G	56720417	A	G	56720417	3	3	269	1	0	0	0	0	1	0	0	0	11421	304	11	3	2442	3	PAN2	12	56720417	Missense_Mutation	SNP	A	TCGA-UZ-A9Q0-01A-12D-A42J-10	604718	56720417	77131478	40	16983											
ATP5B	506	hgsc.bcm.edu	37	chr12	57033773	57033773	+	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	aatatactcacctgcaggatCttttgcaccccacgggcaac	11	9	7	14	1	2	0	1	0	1	0	2	1	2	1	3	2	4	3	3	2	4	4			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr12:57033773C>A	ENST00000262030.3	-	8	1328	c.1278G>T	c.(1276-1278)aaG>aaT	p.K426N	ATP5B_ENST00000550162.1_5'UTR|ATP5B_ENST00000552919.1_Missense_Mutation_p.K415N	NM_001686.3	NP_001677.2	P06576	ATPB_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide	426					angiogenesis (GO:0001525)|ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular metabolic process (GO:0044237)|generation of precursor metabolites and energy (GO:0006091)|lipid metabolic process (GO:0006629)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|osteoblast differentiation (GO:0001649)|proton transport (GO:0015992)|regulation of intracellular pH (GO:0051453)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial nucleoid (GO:0042645)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase, catalytic core (GO:0005754)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MHC class I protein binding (GO:0042288)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)|transporter activity (GO:0005215)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CCTGCAGGATCTTTTGCACCC	0.478																																					p.K426N		Atlas-SNP	.											.	ATP5B	48	.	0			c.G1278T						PASS	.						80	71	74					12																	57033773		2203	4300	6503	SO:0001583	missense	506	exon8			CAGGATCTTTTGC	M27132	CCDS8924.1	12p13.3	2012-10-12			ENSG00000110955	ENSG00000110955	3.6.3.14	"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	830	protein-coding gene	gene with protein product		102910		ATPSB		2687158	Standard	NM_001686		Approved		uc001slr.3	P06576	OTTHUMG00000170291	ENST00000262030.3:c.1278G>T	chr12.hg19:g.57033773C>A	ENSP00000262030:p.Lys426Asn	74.0	0.0	.		85.0	31.0	.	NM_001686	A8K4X0|Q14283	Missense_Mutation	SNP	ENST00000262030.3	hg19	CCDS8924.1	.	.	.	.	.	.	.	.	.	.	C	17.49	3.403225	0.62288	.	.	ENSG00000110955	ENST00000262030;ENST00000552919;ENST00000552104	T;T;T	0.76839	-1.05;-1.05;-1.05	5.77	2.93	0.34026	ATPase, F1/V1/A1 complex, alpha/beta subunit, C-terminal (2);ATPase, F1 complex beta subunit/V1 complex, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.79592	0.4472	M	0.82923	2.615	0.58432	D	0.999999	B	0.20368	0.044	B	0.29077	0.098	T	0.74393	-0.3680	10	0.72032	D	0.01	-20.7654	11.5714	0.50836	0.0:0.7302:0.0:0.2698	.	426	P06576	ATPB_HUMAN	N	426;415;129	ENSP00000262030:K426N;ENSP00000450297:K415N;ENSP00000450233:K129N	ENSP00000262030:K426N	K	-	3	2	ATP5B	55320040	0.994000	0.37717	0.999000	0.59377	0.958000	0.62258	0.429000	0.21412	0.086000	0.17137	-0.797000	0.03246	AAG	.	.	.	none		0.478	ATP5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408380.1	NM_001686		A	57033773	C	A	57033773	3	1	269	1	0	0	0	0	1	0	0	0	1148	912	32	4	323	4	ATP5B	12	57033773	Missense_Mutation	SNP	C	TCGA-UZ-A9Q0-01A-12D-A42J-10	313356	57033773	76818122	41	16984											
SCYL2	55681	hgsc.bcm.edu	37	chr12	100717393	100717393	+	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	taccaagaattaaaaatgctTgtctacaaacatcttccctt	15	13	3	10	0	2	1	0	0	2	1	3	1	3	1	2	0	4	1	2	0	8	6			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr12:100717393T>A	ENST00000360820.2	+	11	1923	c.1486T>A	c.(1486-1488)Tgt>Agt	p.C496S		NM_017988.4	NP_060458.3	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 (S. cerevisiae)	496					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						TAAAAATGCTTGTCTACAAAC	0.308																																					p.C496S		Atlas-SNP	.											.	SCYL2	99	.	0			c.T1486A						PASS	.						83	79	81					12																	100717393		2203	4297	6500	SO:0001583	missense	55681	exon11			AATGCTTGTCTAC	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.1486T>A	chr12.hg19:g.100717393T>A	ENSP00000354061:p.Cys496Ser	73.0	0.0	.		80.0	30.0	.	NM_017988	A8KAB5|Q96EF4|Q96ST4|Q9H7V5|Q9NVH3|Q9P2I7	Missense_Mutation	SNP	ENST00000360820.2	hg19	CCDS9076.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.933340	0.92458	.	.	ENSG00000136021	ENST00000549687;ENST00000258506;ENST00000360820	T;T	0.32272	1.46;1.46	5.68	5.68	0.88126	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.54447	0.1859	M	0.78637	2.42	0.80722	D	1	D	0.59767	0.986	P	0.60886	0.88	T	0.58120	-0.7692	10	0.56958	D	0.05	.	16.2237	0.82280	0.0:0.0:0.0:1.0	.	496	Q6P3W7	SCYL2_HUMAN	S	496;323;496	ENSP00000448366:C496S;ENSP00000354061:C496S	ENSP00000258506:C323S	C	+	1	0	SCYL2	99241524	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.901000	0.87382	2.289000	0.77006	0.482000	0.46254	TGT	.	.	.	none		0.308	SCYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408493.2	NM_017988		A	100717393	T	A	100717393	3	1	269	1	0	0	0	0	1	0	0	0	13961	1812	63	5	1524	5	SCYL2	12	100717393	Missense_Mutation	SNP	T	TCGA-UZ-A9Q0-01A-12D-A42J-10	43683620	100717393	33134502	42	16985											
HPD	3242	hgsc.bcm.edu	37	chr12	122295709	122295709	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacagagtggaagtggaggAatcggcctctctcaggctgc	9	8	14	10	1	3	1	2	0	1	1	5	4	3	4	1	5	1	1	1	5	2	0			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr12:122295709A>G	ENST00000289004.4	-	3	82	c.47T>C	c.(46-48)tTc>tCc	p.F16S	HPD_ENST00000543163.1_5'UTR|RP11-7M8.2_ENST00000543848.1_RNA	NM_002150.2	NP_002141	P32754	HPPD_HUMAN	4-hydroxyphenylpyruvate dioxygenase	16					cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	4-hydroxyphenylpyruvate dioxygenase activity (GO:0003868)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(8)|urinary_tract(1)	18	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000105)|Epithelial(86;0.000352)|BRCA - Breast invasive adenocarcinoma(302;0.225)	Nitisinone(DB00348)	GAAGTGGAGGAATCGGCCTCT	0.597																																					p.F16S		Atlas-SNP	.											.	HPD	46	.	0			c.T47C						PASS	.						61	55	57					12																	122295709		2203	4300	6503	SO:0001583	missense	3242	exon3			TGGAGGAATCGGC	BC014790	CCDS9224.1, CCDS53839.1	12q24.31	2013-09-19			ENSG00000158104	ENSG00000158104	1.13.11.27		5147	protein-coding gene	gene with protein product	"glyoxalase domain containing 3"	609695		PPD			Standard	NM_001171993		Approved	4-HPPD, 4HPPD, GLOD3	uc001ubj.3	P32754	OTTHUMG00000169081	ENST00000289004.4:c.47T>C	chr12.hg19:g.122295709A>G	ENSP00000289004:p.Phe16Ser	168.0	0.0	.		160.0	68.0	.	NM_002150	A8K461|B3KQ63|Q13234	Missense_Mutation	SNP	ENST00000289004.4	hg19	CCDS9224.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.002646	0.74932	.	.	ENSG00000158104	ENST00000289004;ENST00000545969	T	0.63417	-0.04	5.28	5.28	0.74379	.	0.200575	0.49916	D	0.000131	T	0.75583	0.3869	M	0.84082	2.675	0.80722	D	1	D	0.62365	0.991	P	0.59424	0.857	T	0.79225	-0.1891	10	0.72032	D	0.01	-30.6711	9.6882	0.40111	0.8256:0.1744:0.0:0.0	.	16	P32754	HPPD_HUMAN	S	16;13	ENSP00000289004:F16S	ENSP00000289004:F16S	F	-	2	0	HPD	120780092	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.648000	0.83479	2.107000	0.64212	0.533000	0.62120	TTC	.	.	.	none		0.597	HPD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402184.1	NM_002150		G	122295709	A	G	122295709	3	3	269	1	0	0	0	0	1	0	0	0	7339	246	9	3	1182	3	HPD	12	122295709	Missense_Mutation	SNP	A	TCGA-UZ-A9Q0-01A-12D-A42J-10	21578316	122295709	11556186	43	16986											
B3GNT4	79369	hgsc.bcm.edu	37	chr12	122691299	122691299	+	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	gtggcaggatccgctcccccAgcccagctgctggcctatga	6	7	12	16	1	0	1	0	1	0	0	2	2	2	2	5	3	3	4	5	3	1	1			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr12:122691299A>T	ENST00000324189.4	+	3	857	c.501A>T	c.(499-501)ccA>ccT	p.P167P	B3GNT4_ENST00000545141.1_Intron|B3GNT4_ENST00000546192.1_Silent_p.P142P|B3GNT4_ENST00000535274.1_Silent_p.P142P	NM_030765.2	NP_110392.1	Q9C0J1	B3GN4_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4	167					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)		CCGCTCCCCCAGCCCAGCTGC	0.632																																					p.P167P		Atlas-SNP	.											.	B3GNT4	35	.	0			c.A501T						PASS	.						25	28	27					12																	122691299		2203	4300	6503	SO:0001819	synonymous_variant	79369	exon3			TCCCCCAGCCCAG	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.501A>T	chr12.hg19:g.122691299A>T		37.0	0.0	.		43.0	17.0	.	NM_030765	Q8N5W4|Q8N934|Q8ND21|Q8WWR5|Q8WY02|Q96QH5	Silent	SNP	ENST00000324189.4	hg19	CCDS9227.1																																																																																			.	.	.	none		0.632	B3GNT4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401595.1	NM_030765		T	122691299	A	T	122691299	2	4	269	1	0	0	0	0	0	0	0	1	1259	175	7	5		5	B3GNT4	12	122691299	Silent	SNP	A	TCGA-UZ-A9Q0-01A-12D-A42J-10	395590	122691299	11160596	44	16987											
GOLGA3	2802	hgsc.bcm.edu	37	chr12	133385055	133385055	+	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	gtcatagccagggtactggcCcttggtaagttttctgggtt	6	14	13	8	0	2	0	1	0	1	0	2	0	2	0	2	4	2	4	2	4	3	7			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr12:133385055C>A	ENST00000450791.2	-	4	783	c.600G>T	c.(598-600)agG>agT	p.R200S	GOLGA3_ENST00000204726.3_Missense_Mutation_p.R200S|GOLGA3_ENST00000456883.2_Missense_Mutation_p.R200S|GOLGA3_ENST00000537452.1_Missense_Mutation_p.R200S|GOLGA3_ENST00000545875.1_Missense_Mutation_p.R200S			Q08378	GOGA3_HUMAN	golgin A3	200	Golgi-targeting domain.				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)		GGGTACTGGCCCTTGGTAAGT	0.512																																					p.R200S		Atlas-SNP	.											.	GOLGA3	234	.	0			c.G600T						PASS	.						205	228	220					12																	133385055		2203	4300	6503	SO:0001583	missense	2802	exon5			ACTGGCCCTTGGT	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.600G>T	chr12.hg19:g.133385055C>A	ENSP00000410378:p.Arg200Ser	95.0	0.0	.		110.0	54.0	.	NM_001172557	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Missense_Mutation	SNP	ENST00000450791.2	hg19	CCDS9281.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.987682	0.74589	.	.	ENSG00000090615	ENST00000204726;ENST00000450791;ENST00000456883;ENST00000537452;ENST00000545875	T;T;T;T;T	0.28454	1.61;1.61;1.61;1.61;1.61	5.34	0.246	0.15516	.	0.086607	0.85682	D	0.000000	T	0.42040	0.1185	M	0.66939	2.045	0.80722	D	1	D;P;D	0.64830	0.972;0.925;0.994	P;P;P	0.60068	0.742;0.621;0.868	T	0.27606	-1.0069	10	0.87932	D	0	.	6.2402	0.20787	0.1205:0.4387:0.0:0.4408	.	200;200;200	Q08378-4;Q08378-2;Q08378	.;.;GOGA3_HUMAN	S	200	ENSP00000204726:R200S;ENSP00000410378:R200S;ENSP00000409303:R200S;ENSP00000442143:R200S;ENSP00000442603:R200S	ENSP00000204726:R200S	R	-	3	2	GOLGA3	131895128	0.974000	0.33945	0.998000	0.56505	0.895000	0.52256	0.129000	0.15830	0.060000	0.16281	0.585000	0.79938	AGG	.	.	.	none		0.512	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895		A	133385055	C	A	133385055	3	1	269	1	0	0	0	0	1	0	0	0	6561	622	22	4	4114	4	GOLGA3	12	133385055	Missense_Mutation	SNP	C	TCGA-UZ-A9Q0-01A-12D-A42J-10	10693756	133385055	466840	45	16988											
COG3	83548	hgsc.bcm.edu	37	chr13	46066332	46066332	+	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	ttcatggttcatgtctgccaGgatgaacaccaactttacaa	12	12	7	10	0	3	1	2	1	1	0	3	2	3	2	2	2	4	1	2	2	4	4			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr13:46066332G>T	ENST00000349995.5	+	11	1246	c.1134G>T	c.(1132-1134)caG>caT	p.Q378H	COG3_ENST00000465942.1_3'UTR	NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	378					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)		ATGTCTGCCAGGATGAACACC	0.373																																					p.Q378H	Ovarian(150;1048 1859 18083 21577 42700)	Atlas-SNP	.											.	COG3	52	.	0			c.G1134T						PASS	.						195	157	170					13																	46066332		2203	4300	6503	SO:0001583	missense	83548	exon11			CTGCCAGGATGAA	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.1134G>T	chr13.hg19:g.46066332G>T	ENSP00000258654:p.Gln378His	107.0	0.0	.		106.0	5.0	.	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Missense_Mutation	SNP	ENST00000349995.5	hg19	CCDS9398.1	.	.	.	.	.	.	.	.	.	.	g	13.99	2.401591	0.42613	.	.	ENSG00000136152	ENST00000349995	T	0.48201	0.82	5.87	1.67	0.24075	.	0.000000	0.85682	D	0.000000	T	0.57475	0.2056	M	0.63843	1.955	0.80722	D	1	B;D;P	0.71674	0.052;0.998;0.539	B;P;B	0.61940	0.035;0.896;0.188	T	0.53315	-0.8456	10	0.31617	T	0.26	-12.2902	10.952	0.47334	0.3066:0.0:0.6934:0.0	.	215;378;378	B4E2F3;Q96JB2;Q96JB2-2	.;COG3_HUMAN;.	H	378	ENSP00000258654:Q378H	ENSP00000258654:Q378H	Q	+	3	2	COG3	44964333	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.694000	0.47035	0.386000	0.24997	-0.119000	0.15052	CAG	.	.	.	none		0.373	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2			T	46066332	G	T	46066332	3	4	269	1	0	0	0	0	1	0	0	0	3661	991	35	4	1176	4	COG3	13	46066332	Missense_Mutation	SNP	G	TCGA-UZ-A9Q0-01A-12D-A42J-10		46066332	69103546	46	16989											
ACTR10	55860	hgsc.bcm.edu	37	chr14	58675768	58675768	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttgtgattatcgaatcggtAttatgtccttctcacttcag	8	17	8	8	2	2	1	2	1	1	0	6	2	3	1	1	1	0	2	1	1	4	6			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr14:58675768A>G	ENST00000254286.4	+	4	365	c.285A>G	c.(283-285)gtA>gtG	p.V95V		NM_018477.2	NP_060947.1	Q9NZ32	ARP10_HUMAN	actin-related protein 10 homolog (S. cerevisiae)	95					microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|dynactin complex (GO:0005869)				central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	13						TCGAATCGGTATTATGTCCTT	0.328																																					p.V95V		Atlas-SNP	.											.	ACTR10	33	.	0			c.A285G						PASS	.						122	123	122					14																	58675768		2203	4300	6503	SO:0001819	synonymous_variant	55860	exon4			ATCGGTATTATGT	AF220190	CCDS32090.1	14q23.1	2014-08-08			ENSG00000131966	ENSG00000131966			17372	protein-coding gene	gene with protein product						12857853	Standard	NM_018477		Approved	HARP11, ACTR11, Arp11	uc001xdf.3	Q9NZ32	OTTHUMG00000171049	ENST00000254286.4:c.285A>G	chr14.hg19:g.58675768A>G		86.0	0.0	.		62.0	21.0	.	NM_018477	Q9H9Y5|Q9NWY2	Silent	SNP	ENST00000254286.4	hg19	CCDS32090.1																																																																																			.	.	.	none		0.328	ACTR10-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411405.1			G	58675768	A	G	58675768	2	3	269	1	0	0	0	0	0	0	0	1	208	436	16	3		3	ACTR10	14	58675768	Silent	SNP	A	TCGA-UZ-A9Q0-01A-12D-A42J-10		58675768	48673772	47	16990											
SNAPC1	6617	hgsc.bcm.edu	37	chr14	62229244	62229244	+	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	agccgcttccaggagacggaCagtgtacgcttcgaggactt	9	8	13	11	4	0	1	0	0	0	1	2	5	1	3	2	3	2	3	2	3	1	4			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr14:62229244C>T	ENST00000216294.4	+	1	170	c.66C>T	c.(64-66)gaC>gaT	p.D22D	RP11-618G20.1_ENST00000555937.1_RNA	NM_003082.3	NP_003073.1	Q16533	SNPC1_HUMAN	small nuclear RNA activating complex, polypeptide 1, 43kDa	22	SNAPC3-binding.				gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)	13				OV - Ovarian serous cystadenocarcinoma(108;0.0639)|BRCA - Breast invasive adenocarcinoma(234;0.186)		AGGAGACGGACAGTGTACGCT	0.642																																					p.D22D	NSCLC(27;223 907 37180 39193 46568)	Atlas-SNP	.											.	SNAPC1	32	.	0			c.C66T						PASS	.						124	116	119					14																	62229244		2203	4300	6503	SO:0001819	synonymous_variant	6617	exon1			GACGGACAGTGTA	Z47542	CCDS9755.1	14q22	2008-08-11	2002-08-29		ENSG00000023608	ENSG00000023608			11134	protein-coding gene	gene with protein product		600591	"small nuclear RNA activating complex, polypeptide 1, 43kD"			9644240	Standard	NM_003082		Approved	SNAP43, PTFgamma	uc001xft.3	Q16533	OTTHUMG00000140343	ENST00000216294.4:c.66C>T	chr14.hg19:g.62229244C>T		66.0	0.0	.		61.0	20.0	.	NM_003082		Silent	SNP	ENST00000216294.4	hg19	CCDS9755.1																																																																																			.	.	.	none		0.642	SNAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276976.2	NM_003082		T	62229244	C	T	62229244	2	4	269	1	0	0	0	0	0	0	0	1	14847	477	17	2		2	SNAPC1	14	62229244	Silent	SNP	C	TCGA-UZ-A9Q0-01A-12D-A42J-10	3553476	62229244	45120296	48	16991											
SYNE2	23224	hgsc.bcm.edu	37	chr14	64595265	64595265	+	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	gggcagagtgttgctgaacaGcttcaggtaatcaagtcaaa	13	9	12	7	0	3	2	3	1	0	1	3	2	3	2	0	2	3	5	0	2	4	3			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr14:64595265G>A	ENST00000344113.4	+	74	14225	c.14013G>A	c.(14011-14013)caG>caA	p.Q4671Q	SYNE2_ENST00000555002.1_Silent_p.Q1305Q|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000357395.3_Silent_p.Q1056Q|SYNE2_ENST00000394768.2_Silent_p.Q1056Q|SYNE2_ENST00000358025.3_Silent_p.Q4671Q|SYNE2_ENST00000554584.1_Intron	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	4671					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)		TTGCTGAACAGCTTCAGGTAA	0.368																																					p.Q4671Q		Atlas-SNP	.											.	SYNE2	577	.	0			c.G14013A						PASS	.						86	84	84					14																	64595265		2203	4300	6503	SO:0001819	synonymous_variant	23224	exon74			TGAACAGCTTCAG	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.14013G>A	chr14.hg19:g.64595265G>A		151.0	0.0	.		143.0	55.0	.	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.	.	none		0.368	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		A	64595265	G	A	64595265	2	1	269	1	0	0	0	0	0	0	0	1	15458	962	34	2		2	SYNE2	14	64595265	Silent	SNP	G	TCGA-UZ-A9Q0-01A-12D-A42J-10	2366021	64595265	42754275	49	16992											
GPHN	10243	hgsc.bcm.edu	37	chr14	67646373	67646373	+	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	ggcatcaccaagaaccactaCcttgggcacagagtacaggt	13	6	10	12	0	1	2	1	0	0	2	1	2	1	2	3	3	3	3	3	3	4	3			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr14:67646373C>A	ENST00000315266.5	+	21	3180	c.2059C>A	c.(2059-2061)Cct>Act	p.P687T	GPHN_ENST00000543237.1_Missense_Mutation_p.P733T|GPHN_ENST00000478722.1_Missense_Mutation_p.P720T|GPHN_ENST00000305960.9_Missense_Mutation_p.P656T|GPHN_ENST00000544752.2_3'UTR	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	687	MPT adenylyltransferase.				establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycine receptor clustering (GO:0072579)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|molybdopterin adenylyltransferase activity (GO:0061598)|molybdopterin molybdotransferase activity (GO:0061599)|transferase activity (GO:0016740)			large_intestine(8)|liver(1)|ovary(2)|stomach(1)	12		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		AGAACCACTACCTTGGGCACA	0.368			T	MLL	AL																																p.P720T		Atlas-SNP	.		Dom	yes		14	14q24	10243	gephyrin (GPH)		L	.	GPHN	79	.	0			c.C2158A						PASS	.						124	103	110					14																	67646373		2203	4300	6503	SO:0001583	missense	10243	exon22			CCACTACCTTGGG	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.2059C>A	chr14.hg19:g.67646373C>A	ENSP00000312771:p.Pro687Thr	96.0	0.0	.		77.0	41.0	.	NM_020806	Q9H4E9|Q9P2G2	Missense_Mutation	SNP	ENST00000315266.5	hg19	CCDS32103.1	.	.	.	.	.	.	.	.	.	.	C	18.33	3.599845	0.66332	.	.	ENSG00000171723	ENST00000315266;ENST00000478722;ENST00000543237;ENST00000305960	.	.	.	5.79	5.79	0.91817	MoeA, C-terminal, domain IV (3);	0.000000	0.85682	D	0.000000	D	0.83885	0.5351	M	0.86028	2.79	0.80722	D	1	D;D;D;D	0.71674	0.998;0.997;0.989;0.994	D;D;D;D	0.74023	0.982;0.97;0.964;0.961	T	0.82086	-0.0631	9	0.33940	T	0.23	-6.8827	20.0417	0.97594	0.0:1.0:0.0:0.0	.	656;733;687;720	F8W7D6;F5H039;Q9NQX3;Q9NQX3-2	.;.;GEPH_HUMAN;.	T	687;720;733;656	.	ENSP00000303019:P656T	P	+	1	0	GPHN	66716126	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.734000	0.84928	2.736000	0.93811	0.655000	0.94253	CCT	.	.	.	none		0.368	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806		A	67646373	C	A	67646373	3	1	269	1	0	0	0	0	1	0	0	0	6617	507	18	4	2244	4	GPHN	14	67646373	Missense_Mutation	SNP	C	TCGA-UZ-A9Q0-01A-12D-A42J-10	3051108	67646373	39703167	50	16993											
C14orf115	55237	hgsc.bcm.edu	37	chr14	74824607	74824607	+	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	ggtgctgggcatggaggagcTagagaagctgccggaggagc	9	5	20	7	1	0	1	0	0	0	1	0	6	0	5	1	6	5	4	1	6	2	1			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr14:74824607T>A	ENST00000256362.4	+	2	1362	c.1121T>A	c.(1120-1122)cTa>cAa	p.L374Q		NM_018228.2	NP_060698.2	Q9H8Y1	VRTN_HUMAN	vertebrae development associated	374					transposition, DNA-mediated (GO:0006313)		sequence-specific DNA binding (GO:0043565)|transposase activity (GO:0004803)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(15)|ovary(5)|prostate(2)|skin(1)|urinary_tract(1)	41						ATGGAGGAGCTAGAGAAGCTG	0.637																																					p.L374Q		Atlas-SNP	.											.	VRTN	79	.	0			c.T1121A						PASS	.						41	40	41					14																	74824607		2203	4300	6503	SO:0001583	missense	55237	exon2			AGGAGCTAGAGAA	AK001673	CCDS9830.1	14q24.2	2012-12-07	2012-12-07	2010-10-20	ENSG00000133980	ENSG00000133980			20223	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 115", "vertebrae development homolog (pig)"	C14orf115		21232157	Standard	NM_018228		Approved	FLJ10811, vertnin	uc001xpw.4	Q9H8Y1	OTTHUMG00000171208	ENST00000256362.4:c.1121T>A	chr14.hg19:g.74824607T>A	ENSP00000256362:p.Leu374Gln	61.0	0.0	.		55.0	23.0	.	NM_018228	Q9NVC7	Missense_Mutation	SNP	ENST00000256362.4	hg19	CCDS9830.1	.	.	.	.	.	.	.	.	.	.	T	11.39	1.625234	0.28889	.	.	ENSG00000133980	ENST00000256362	T	0.47177	0.85	4.53	2.07	0.26955	.	0.926239	0.09176	N	0.838183	T	0.30823	0.0777	N	0.24115	0.695	0.24060	N	0.996016	B	0.15473	0.013	B	0.08055	0.003	T	0.29458	-1.0011	10	0.72032	D	0.01	-8.4468	3.2816	0.06917	0.1707:0.2001:0.0:0.6292	.	374	Q9H8Y1	VRTN_HUMAN	Q	374	ENSP00000256362:L374Q	ENSP00000256362:L374Q	L	+	2	0	VRTN	73894360	0.947000	0.32204	0.681000	0.30009	0.154000	0.21943	0.153000	0.16323	0.238000	0.21222	0.459000	0.35465	CTA	.	.	.	none		0.637	VRTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412339.1	NM_018228		A	74824607	T	A	74824607	3	1	269	1	0	0	0	0	1	0	0	0	1742	1522	53	5	1123	5	C14orf115	14	74824607	Missense_Mutation	SNP	T	TCGA-UZ-A9Q0-01A-12D-A42J-10	7178234	74824607	32524933	51	16994											
PLA2G4E	123745	hgsc.bcm.edu	37	chr15	42298282	42298282	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagatggtcatctggtgtcActgtgtcttcatcacagaca	9	12	11	9	0	6	2	4	0	2	2	6	3	6	2	0	3	0	0	0	3	0	1			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr15:42298282A>G	ENST00000399518.3	-	4	917	c.431T>C	c.(430-432)gTg>gCg	p.V144A	CTD-2382E5.2_ENST00000552704.1_RNA|PLA2G4E_ENST00000413860.2_Missense_Mutation_p.V115A	NM_001206670.1	NP_001193599.1	Q3MJ16	PA24E_HUMAN	phospholipase A2, group IVE	126					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)		ATCTGGTGTCACTGTGTCTTC	0.507																																					p.V144A		Atlas-SNP	.											.	PLA2G4E	60	.	0			c.T431C						PASS	.						133	140	138					15																	42298282		2138	4259	6397	SO:0001583	missense	123745	exon4			GGTGTCACTGTGT		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.431T>C	chr15.hg19:g.42298282A>G	ENSP00000382434:p.Val144Ala	106.0	0.0	.		101.0	52.0	.	NM_001206670	Q6ZSC0	Missense_Mutation	SNP	ENST00000399518.3	hg19	CCDS55962.1	.	.	.	.	.	.	.	.	.	.	A	15.16	2.750182	0.49257	.	.	ENSG00000188089	ENST00000399518;ENST00000413860	T;T	0.40476	1.03;2.9	5.66	5.66	0.87406	.	1.275240	0.06088	U	0.663186	T	0.48502	0.1503	M	0.67517	2.055	0.19775	N	0.999954	B	0.29232	0.238	B	0.35353	0.201	T	0.43861	-0.9365	10	0.41790	T	0.15	-0.4635	8.9392	0.35720	0.735:0.0:0.0:0.265	.	115	C9JK77	.	A	144;115	ENSP00000382434:V144A;ENSP00000413897:V115A	ENSP00000382434:V144A	V	-	2	0	PLA2G4E	40085574	0.205000	0.23458	0.884000	0.34674	0.976000	0.68499	2.142000	0.42177	2.153000	0.67306	0.460000	0.39030	GTG	.	.	.	none		0.507	PLA2G4E-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252738.2	NM_198442		G	42298282	A	G	42298282	3	3	269	1	0	0	0	0	1	0	0	0	12012	159	6	3	2243	3	PLA2G4E	15	42298282	Missense_Mutation	SNP	A	TCGA-UZ-A9Q0-01A-12D-A42J-10		42298282	60233110	52	16995											
SLC24A1	9187	hgsc.bcm.edu	37	chr15	65943100	65943100	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaggaggaagagcaggaggaAgaggaggaggaggaagagca	17	0	22	2	0	0	3	0	0	0	3	0	12	0	11	0	8	2	2	0	8	3	0	rs574760946		TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr15:65943100A>G	ENST00000261892.6	+	7	2900	c.2613A>G	c.(2611-2613)gaA>gaG	p.E871E	SLC24A1_ENST00000546330.1_Silent_p.E853E|SLC24A1_ENST00000449142.2_3'UTR|SLC24A1_ENST00000544319.2_Silent_p.E757E|SLC24A1_ENST00000537259.1_Silent_p.E853E|SLC24A1_ENST00000399033.4_Silent_p.E871E|SLC24A1_ENST00000339868.6_Silent_p.E853E	NM_001254740.1|NM_004727.2	NP_001241669.1|NP_004718.1	O60721	NCKX1_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 1	871	Poly-Glu.				calcium ion transport (GO:0006816)|ion transport (GO:0006811)|phototransduction, visible light (GO:0007603)|response to light intensity (GO:0009642)|rhodopsin mediated signaling pathway (GO:0016056)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|outer membrane (GO:0019867)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						agcaggaggaagaggaggagg	0.547																																					p.E871E		Atlas-SNP	.											.	SLC24A1	58	.	0			c.A2613G						PASS	.						28	32	30					15																	65943100		2182	4274	6456	SO:0001819	synonymous_variant	9187	exon7			GGAGGAAGAGGAG	AF062922	CCDS45284.1, CCDS73742.1, CCDS73743.1, CCDS73744.1	15q22.31	2014-01-28			ENSG00000074621	ENSG00000074621		"Solute carriers"	10975	protein-coding gene	gene with protein product		603617				9856482	Standard	NM_004727		Approved	NCKX1, NCKX, RODX, KIAA0702, HsT17412, CSNB1D	uc010ujf.2	O60721	OTTHUMG00000167960	ENST00000261892.6:c.2613A>G	chr15.hg19:g.65943100A>G		84.0	0.0	.		79.0	10.0	.	NM_004727	O43485|O75184|Q17RM9	Silent	SNP	ENST00000261892.6	hg19	CCDS45284.1																																																																																			.	.	.	none		0.547	SLC24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397304.1	NM_004727		G	65943100	A	G	65943100	2	3	269	1	0	0	0	0	0	0	0	1	14478	69	3	3		3	SLC24A1	15	65943100	Silent	SNP	A	TCGA-UZ-A9Q0-01A-12D-A42J-10	23644818	65943100	36588292	53	16996											
NR2F2	7026	hgsc.bcm.edu	37	chr15	96875660	96875660	+	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	cttcaagcgcagcgtgcggaGgaacctgagctacacgtgcc	9	6	13	13	4	1	1	1	1	0	0	1	3	1	3	2	2	7	2	2	2	3	2			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr15:96875660G>T	ENST00000394166.3	+	1	1715	c.326G>T	c.(325-327)aGg>aTg	p.R109M	NR2F2_ENST00000394171.2_5'Flank|MIR1469_ENST00000410719.1_RNA|NR2F2_ENST00000453270.2_5'Flank|NR2F2_ENST00000421109.2_Intron	NM_021005.3	NP_066285.1	P24468	COT2_HUMAN	nuclear receptor subfamily 2, group F, member 2	109					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)			AGCGTGCGGAGGAACCTGAGC	0.607																																					p.R109M		Atlas-SNP	.											.	NR2F2	35	.	0			c.G326T						PASS	.						83	69	73					15																	96875660		2197	4298	6495	SO:0001583	missense	7026	exon1			TGCGGAGGAACCT	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.326G>T	chr15.hg19:g.96875660G>T	ENSP00000377721:p.Arg109Met	100.0	0.0	.		86.0	32.0	.	NM_021005	B4DQJ2|B6ZGU1|Q03754|Q3KQR7	Missense_Mutation	SNP	ENST00000394166.3	hg19	CCDS10375.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.687254	0.88639	.	.	ENSG00000185551	ENST00000394166	D	0.97455	-4.39	4.61	4.61	0.57282	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (4);	0.000000	0.64402	D	0.000001	D	0.98096	0.9372	M	0.73319	2.225	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99327	1.0908	10	0.87932	D	0	.	16.0226	0.80509	0.0:0.0:1.0:0.0	.	109	P24468	COT2_HUMAN	M	109	ENSP00000377721:R109M	ENSP00000377721:R109M	R	+	2	0	NR2F2	94676664	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.728000	0.74769	2.097000	0.63578	0.462000	0.41574	AGG	.	.	.	none		0.607	NR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313534.1			T	96875660	G	T	96875660	3	4	269	1	0	0	0	0	1	0	0	0	10635	1000	35	4	375	4	NR2F2	15	96875660	Missense_Mutation	SNP	G	TCGA-UZ-A9Q0-01A-12D-A42J-10	30932560	96875660	5655732	54	16997											
NTN3	4917	hgsc.bcm.edu	37	chr16	2522514	2522514	+	Missense_Mutation	SNP	A	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	cctgctggacacacagggccAcctgatctgcgactgtcggc	7	7	12	15	2	1	1	0	1	1	0	2	3	1	2	3	3	2	1	3	3	0	0			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr16:2522514A>C	ENST00000293973.1	+	1	1015	c.812A>C	c.(811-813)cAc>cCc	p.H271P	TBC1D24_ENST00000567020.1_5'Flank|TBC1D24_ENST00000293970.5_5'Flank	NM_006181.2	NP_006172.1	O00634	NET3_HUMAN	netrin 3	271	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						ACACAGGGCCACCTGATCTGC	0.677																																					p.H271P		Atlas-SNP	.											.	NTN3	28	.	0			c.A812C						PASS	.						33	32	32					16																	2522514		2195	4291	6486	SO:0001583	missense	4917	exon1			AGGGCCACCTGAT	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.812A>C	chr16.hg19:g.2522514A>C	ENSP00000293973:p.His271Pro	41.0	0.0	.		47.0	5.0	.	NM_006181		Missense_Mutation	SNP	ENST00000293973.1	hg19	CCDS10469.1	.	.	.	.	.	.	.	.	.	.	A	9.869	1.198347	0.22037	.	.	ENSG00000162068	ENST00000293973	T	0.61158	0.13	4.09	-0.489	0.12052	EGF-like, laminin (3);	0.412612	0.24350	N	0.039292	T	0.34832	0.0911	N	0.21240	0.645	0.28172	N	0.928542	P	0.42357	0.777	B	0.35655	0.207	T	0.29150	-1.0021	10	0.44086	T	0.13	.	8.7149	0.34405	0.5211:0.0:0.4789:0.0	.	271	O00634	NET3_HUMAN	P	271	ENSP00000293973:H271P	ENSP00000293973:H271P	H	+	2	0	NTN3	2462515	0.000000	0.05858	0.988000	0.46212	0.933000	0.57130	0.208000	0.17415	-0.098000	0.12285	0.254000	0.18369	CAC	.	.	.	none		0.677	NTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250812.1	NM_006181		C	2522514	A	C	2522514	3	2	269	1	0	0	0	0	1	0	0	0	10708	159	6	5	814	5	NTN3	16	2522514	Missense_Mutation	SNP	A	TCGA-UZ-A9Q0-01A-12D-A42J-10		2522514	87832239	55	16998											
TMCO7	79613	hgsc.bcm.edu	37	chr16	68914532	68914532	+	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	atgcattgaggatgtgtttaAggttggtaatctgagtcact	10	15	12	4	0	2	2	1	2	1	0	2	3	2	3	0	3	1	4	0	3	2	5			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr16:68914532A>C	ENST00000261778.1	+	7	1388	c.1376A>C	c.(1375-1377)aAg>aCg	p.K459T		NM_024562.1	NP_078838.1	Q9C0B7	TNG6_HUMAN	transport and golgi organization 6 homolog (Drosophila)	459						integral component of membrane (GO:0016021)											GATGTGTTTAAGGTTGGTAAT	0.323																																					p.K459T		Atlas-SNP	.											.	.	.	.	0			c.A1376C						PASS	.						192	175	181					16																	68914532		1823	4084	5907	SO:0001630	splice_region_variant	79613	exon7			TGTTTAAGGTTGG		CCDS45516.1	16q22.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000103047	ENSG00000103047			25749	protein-coding gene	gene with protein product			"transmembrane and coiled-coil domains 7"	TMCO7		11214970	Standard	NM_024562		Approved	FLJ12688, KIAA1746	uc002ewi.4	Q9C0B7	OTTHUMG00000176743	ENST00000261778.1:c.1377+1A>C	chr16.hg19:g.68914532A>C		115.0	0.0	.		163.0	41.0	.	NM_024562	Q569F9|Q9H9K1	Missense_Mutation	SNP	ENST00000261778.1	hg19	CCDS45516.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.952009	0.73787	.	.	ENSG00000103047	ENST00000261778	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	T	0.76047	0.3933	M	0.72894	2.215	0.49299	D	0.999779	D	0.89917	1.0	D	0.85130	0.997	T	0.74460	-0.3658	8	0.29301	T	0.29	-10.3412	12.9949	0.58640	1.0:0.0:0.0:0.0	.	459	Q9C0B7	TMCO7_HUMAN	T	459	.	ENSP00000261778:K459T	K	+	2	0	TMCO7	67472033	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	5.339000	0.65953	2.053000	0.61076	0.533000	0.62120	AAG	.	.	.	none		0.323	TANGO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433471.2	XM_928235.2	Missense_Mutation	C	68914532	A	C	68914532	5	2	269	1	0	0	0	0	0	0	1	0	16013	86	3	5	1402	5	TMCO7	16	68914532	Splice_Site	SNP	A	TCGA-UZ-A9Q0-01A-12D-A42J-10	66392018	68914532	21440221	56	16999											
BANP	54971	hgsc.bcm.edu	37	chr16	88039824	88039824	+	Missense_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	cagctgtgggcaggcgggcaGtcagagcatcgggagcaacg	9	4	18	10	3	1	1	1	0	0	1	2	2	1	2	0	4	4	5	0	4	1	0			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr16:88039824G>A	ENST00000393207.1	+	6	805	c.584G>A	c.(583-585)aGt>aAt	p.S195N	BANP_ENST00000355163.5_Missense_Mutation_p.S170N|BANP_ENST00000538234.1_Missense_Mutation_p.S203N|BANP_ENST00000355022.4_Missense_Mutation_p.S164N|BANP_ENST00000393208.2_Missense_Mutation_p.S164N|BANP_ENST00000479780.2_Missense_Mutation_p.S164N|BANP_ENST00000286122.7_Missense_Mutation_p.S195N	NM_001173543.1	NP_001167014.1	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein	195	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)		CAGGCGGGCAGTCAGAGCATC	0.627																																					p.S203N		Atlas-SNP	.											.	BANP	67	.	0			c.G608A						PASS	.						84	83	83					16																	88039824		2198	4300	6498	SO:0001583	missense	54971	exon6			CGGGCAGTCAGAG	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.584G>A	chr16.hg19:g.88039824G>A	ENSP00000376902:p.Ser195Asn	49.0	0.0	.		58.0	31.0	.	NM_001173542	A8MU25|A8MX25|B2RCF7|B4DNJ9|F5GZM0|Q96GJ7|Q9NWY1	Missense_Mutation	SNP	ENST00000393207.1	hg19	CCDS54054.1	.	.	.	.	.	.	.	.	.	.	G	8.683	0.905509	0.17760	.	.	ENSG00000172530	ENST00000439677;ENST00000286122;ENST00000355163;ENST00000289484;ENST00000479780;ENST00000393208;ENST00000540932;ENST00000355022;ENST00000538234;ENST00000393207	T;T;T;T;T;T;T;T	0.25912	1.77;1.77;1.77;1.77;1.77;1.77;1.77;1.77	5.43	5.43	0.79202	.	0.141405	0.64402	D	0.000002	T	0.12050	0.0293	N	0.03608	-0.345	0.31704	N	0.64034	B;B;B;B;B;B	0.26258	0.002;0.002;0.001;0.145;0.002;0.001	B;B;B;B;B;B	0.25884	0.004;0.003;0.001;0.064;0.003;0.005	T	0.10245	-1.0638	10	0.29301	T	0.29	.	11.9944	0.53194	0.0791:0.0:0.9209:0.0	.	203;170;164;195;164;164	B4DE54;B4DNJ9;B2RCF7;Q8N9N5;Q8N9N5-2;Q8N9N5-4	.;.;.;BANP_HUMAN;.;.	N	170;195;170;160;164;164;164;164;203;195	ENSP00000411479:S170N;ENSP00000286122:S195N;ENSP00000347290:S170N;ENSP00000432508:S164N;ENSP00000376903:S164N;ENSP00000347125:S164N;ENSP00000444352:S203N;ENSP00000376902:S195N	ENSP00000286122:S195N	S	+	2	0	BANP	86597325	0.981000	0.34729	0.229000	0.23960	0.201000	0.24016	2.542000	0.45744	2.706000	0.92434	0.655000	0.94253	AGT	.	.	.	none		0.627	BANP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269166.1	NM_017869		A	88039824	G	A	88039824	3	1	269	1	0	0	0	0	1	0	0	0	1310	1029	36	2	644	2	BANP	16	88039824	Missense_Mutation	SNP	G	TCGA-UZ-A9Q0-01A-12D-A42J-10	19125292	88039824	2314929	57	17000											
NTN1	9423	hgsc.bcm.edu	37	chr17	9066277	9066277	+	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	ctgcaaggagggctactaccGcgacatgggcaagcccatca	11	5	12	13	2	1	0	1	0	0	0	1	2	1	1	2	3	4	3	2	3	4	2			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr17:9066277G>T	ENST00000173229.2	+	3	1273	c.1166G>T	c.(1165-1167)cGc>cTc	p.R389L	NTN1_ENST00000546090.1_Missense_Mutation_p.R389L|NTN1_ENST00000538852.1_Missense_Mutation_p.R389L	NM_004822.2	NP_004813.2	O95631	NET1_HUMAN	netrin 1	389	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|establishment of nucleus localization (GO:0040023)|inner ear morphogenesis (GO:0042472)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of axon extension (GO:0030517)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of cell proliferation (GO:0008284)|regulation of cell migration (GO:0030334)|single organismal cell-cell adhesion (GO:0016337)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)			NTN1/ACLY(2)	central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|lung(5)	13						GGCTACTACCGCGACATGGGC	0.662																																					p.R389L		Atlas-SNP	.											.	NTN1	31	.	0			c.G1166T						PASS	.						33	25	28					17																	9066277		2203	4300	6503	SO:0001583	missense	9423	exon3			ACTACCGCGACAT	U75586	CCDS11148.1	17p13-p12	2013-03-01			ENSG00000065320	ENSG00000065320		"Netrins"	8029	protein-coding gene	gene with protein product	"Netrin-1"	601614				9950216	Standard	NM_004822		Approved	NTN1L	uc002glw.4	O95631	OTTHUMG00000130257	ENST00000173229.2:c.1166G>T	chr17.hg19:g.9066277G>T	ENSP00000173229:p.Arg389Leu	83.0	0.0	.		139.0	87.0	.	NM_004822	E9KL51	Missense_Mutation	SNP	ENST00000173229.2	hg19	CCDS11148.1	.	.	.	.	.	.	.	.	.	.	G	34	5.334742	0.95758	.	.	ENSG00000065320	ENST00000173229;ENST00000538852;ENST00000546090;ENST00000436734	T;T;T;T	0.64438	-0.1;-0.1;-0.1;2.47	4.89	4.89	0.63831	EGF-like, laminin (4);	0.000000	0.85682	D	0.000000	D	0.84188	0.5417	M	0.92317	3.295	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.88486	0.3072	10	0.87932	D	0	.	18.4101	0.90549	0.0:0.0:1.0:0.0	.	389	O95631	NET1_HUMAN	L	389;389;389;9	ENSP00000173229:R389L;ENSP00000443259:R389L;ENSP00000441611:R389L;ENSP00000389375:R9L	ENSP00000173229:R389L	R	+	2	0	NTN1	9007002	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.365000	0.97139	2.437000	0.82529	0.650000	0.86243	CGC	.	.	.	none		0.662	NTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252583.1			T	9066277	G	T	9066277	3	4	269	1	0	0	0	0	1	0	0	0	10707	1087	38	4	1172	4	NTN1	17	9066277	Missense_Mutation	SNP	G	TCGA-UZ-A9Q0-01A-12D-A42J-10		9066277	72128933	58	17001											
ACACA	31	hgsc.bcm.edu	37	chr17	35609953	35609953	+	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	gacagctccttcaaagccacCaccatgtttctgggagaaca	12	8	8	13	0	2	1	1	0	1	1	3	3	3	1	4	1	3	2	4	1	2	2			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr17:35609953C>A	ENST00000394406.2	-	15	1915	c.1725G>T	c.(1723-1725)gtG>gtT	p.V575V	ACACA_ENST00000360679.3_Silent_p.V517V|ACACA_ENST00000353139.5_Silent_p.V612V|ACACA_ENST00000335166.5_Silent_p.V497V	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	575	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)	TCAAAGCCACCACCATGTTTC	0.403																																					p.V612V	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-SNP	.											.	ACACA	395	.	0			c.G1836T						PASS	.						103	101	102					17																	35609953		2203	4300	6503	SO:0001819	synonymous_variant	31	exon15			AGCCACCACCATG	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.1725G>T	chr17.hg19:g.35609953C>A		88.0	0.0	.		93.0	59.0	.	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Silent	SNP	ENST00000394406.2	hg19	CCDS11317.1																																																																																			.	.	.	none		0.403	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		A	35609953	C	A	35609953	2	1	269	1	0	0	0	0	0	0	0	1	106	581	21	4		4	ACACA	17	35609953	Silent	SNP	C	TCGA-UZ-A9Q0-01A-12D-A42J-10	26543676	35609953	45585257	59	17002											
UBE2O	63893	hgsc.bcm.edu	37	chr17	74398143	74398143	+	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	tggcctggatggagcacactAccgagtcgctgacgtgcggg	7	7	16	11	4	0	1	0	1	0	0	1	4	0	3	2	4	3	2	2	4	1	1			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr17:74398143A>G	ENST00000319380.7	-	5	815		c.e5+1		UBE2O_ENST00000587581.1_5'Flank	NM_022066.3	NP_071349.3	Q9C0C9	UBE2O_HUMAN	ubiquitin-conjugating enzyme E2O						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						GGAGCACACTACCGAGTCGCT	0.562																																					.		Atlas-SNP	.											.	UBE2O	207	.	0			c.750+2T>C						PASS	.						86	61	70					17																	74398143		2203	4300	6503	SO:0001630	splice_region_variant	63893	exon6			CACACTACCGAGT	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.750+1T>C	chr17.hg19:g.74398143A>G		76.0	0.0	.		135.0	85.0	.	NM_022066	A6NDU5|Q69YP4|Q6PIZ2|Q86UA4|Q8N425|Q8TBN1|Q9BSW1|Q9H6E6|Q9H7E4|Q9H9B2	Splice_Site	SNP	ENST00000319380.7	hg19	CCDS32742.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.810257	0.90707	.	.	ENSG00000175931	ENST00000319380	.	.	.	5.73	5.73	0.89815	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5935	0.68386	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	UBE2O	71909738	1.000000	0.71417	0.995000	0.50966	0.970000	0.65996	8.917000	0.92751	2.198000	0.70561	0.533000	0.62120	.	.	.	.	none		0.562	UBE2O-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450123.1	NM_022066	Intron	G	74398143	A	G	74398143	5	3	269	1	0	0	0	0	0	0	1	0	16880	405	14	3	3182	3	UBE2O	17	74398143	Splice_Site	SNP	A	TCGA-UZ-A9Q0-01A-12D-A42J-10	38788190	74398143	6797067	60	17003											
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11138579	11138579	+	Missense_Mutation	SNP	T	T	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	gacctccctcatgaccatcaTggaagattactttgcgtatc	10	12	7	12	1	2	2	2	1	0	1	4	4	3	3	3	1	2	1	3	1	3	3			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr19:11138579T>G	ENST00000429416.3	+	25	3616	c.3335T>G	c.(3334-3336)aTg>aGg	p.M1112R	SMARCA4_ENST00000450717.3_Missense_Mutation_p.M1112R|SMARCA4_ENST00000344626.4_Missense_Mutation_p.M1112R|SMARCA4_ENST00000358026.2_Missense_Mutation_p.M1112R|SMARCA4_ENST00000541122.2_Missense_Mutation_p.M1112R|SMARCA4_ENST00000444061.3_Missense_Mutation_p.M1112R|SMARCA4_ENST00000589677.1_Missense_Mutation_p.M1112R|SMARCA4_ENST00000413806.3_Missense_Mutation_p.M1112R|SMARCA4_ENST00000590574.1_Missense_Mutation_p.M1112R	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1112	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(2)		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)				ATGACCATCATGGAAGATTAC	0.468			"F, N, Mis"		NSCLC																																p.M1112R		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	.	2	Unknown(2)	lung(2)	c.T3335G						PASS	.						181	176	177					19																	11138579		2203	4300	6503	SO:0001583	missense	6597	exon24			CCATCATGGAAGA	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.3335T>G	chr19.hg19:g.11138579T>G	ENSP00000395654:p.Met1112Arg	151.0	0.0	.		145.0	71.0	.	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.536828	0.85812	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	T;T;T;T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97;-0.97;-0.97;-0.97	5.04	5.04	0.67666	Helicase, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.85978	0.5823	M	0.87758	2.905	0.58432	D	0.999999	D;D;D;D;D;D;D;D	0.61080	0.989;0.989;0.989;0.988;0.981;0.969;0.989;0.989	P;P;P;P;P;P;P;P	0.61201	0.862;0.862;0.862;0.885;0.716;0.832;0.862;0.862	D	0.88680	0.3201	10	0.87932	D	0	-42.4872	13.9052	0.63831	0.0:0.0:0.0:1.0	.	1112;1112;1112;1112;1112;332;1112;1112	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;A7E2E1;P51532	.;.;.;.;.;.;.;SMCA4_HUMAN	R	1112;1112;1176;1112;1112;1112;1112;1112	ENSP00000395654:M1112R;ENSP00000350720:M1112R;ENSP00000343896:M1112R;ENSP00000445036:M1112R;ENSP00000392837:M1112R;ENSP00000397783:M1112R;ENSP00000414727:M1112R	ENSP00000343896:M1112R	M	+	2	0	SMARCA4	10999579	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.575000	0.82447	2.115000	0.64714	0.533000	0.62120	ATG	.	.	.	none		0.468	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		G	11138579	T	G	11138579	3	3	269	1	0	0	0	0	1	0	0	0	14783	1464	51	5	3425	5	SMARCA4	19	11138579	Missense_Mutation	SNP	T	TCGA-UZ-A9Q0-01A-12D-A42J-10		11138579	47990404	61	17004											
PAK4	10298	hgsc.bcm.edu	37	chr19	39664225	39664225	+	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	ttctgtttcagggggagcctCatgacgtggcccctaacggg	6	10	14	11	2	3	1	2	1	1	0	3	2	3	2	3	4	2	1	3	4	1	3			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr19:39664225C>A	ENST00000593690.1	+	6	1100	c.673C>A	c.(673-675)Cat>Aat	p.H225N	PAK4_ENST00000321944.4_Missense_Mutation_p.H135N|PAK4_ENST00000599470.1_Missense_Mutation_p.H72N|PAK4_ENST00000358301.3_Missense_Mutation_p.H225N|PAK4_ENST00000435673.2_Missense_Mutation_p.H225N|PAK4_ENST00000599386.1_Missense_Mutation_p.H72N|PAK4_ENST00000360442.3_Missense_Mutation_p.H225N	NM_001014831.2	NP_001014831.1	O96013	PAK4_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 4	225	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)			GGGGGAGCCTCATGACGTGGC	0.667																																					p.H225N		Atlas-SNP	.											.	PAK4	40	.	0			c.C673A						PASS	.						13	15	14					19																	39664225		2145	4193	6338	SO:0001583	missense	10298	exon4			GAGCCTCATGACG	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.673C>A	chr19.hg19:g.39664225C>A	ENSP00000469413:p.His225Asn	65.0	0.0	.		66.0	22.0	.	NM_001014832	B4DGG6|Q8N4E1|Q8NCH5|Q8NDE3|Q9BU33|Q9ULS8	Missense_Mutation	SNP	ENST00000593690.1	hg19	CCDS12528.1	.	.	.	.	.	.	.	.	.	.	C	0.108	-1.142902	0.01728	.	.	ENSG00000130669	ENST00000358301;ENST00000321944;ENST00000358801;ENST00000435673;ENST00000360442	T;T;T	0.70986	-0.53;-0.53;-0.53	4.25	3.22	0.36961	.	1.326000	0.04874	N	0.446555	T	0.65249	0.2673	L	0.53249	1.67	0.30292	N	0.790288	B;B;B	0.16166	0.016;0.016;0.009	B;B;B	0.16289	0.01;0.015;0.005	T	0.51188	-0.8737	10	0.16896	T	0.51	.	7.9058	0.29761	0.0:0.887:0.0:0.113	.	135;72;225	O96013-4;O96013-3;O96013	.;.;PAK4_HUMAN	N	225;72;29;225;225	ENSP00000351049:H225N;ENSP00000392753:H225N;ENSP00000353625:H225N	ENSP00000326864:H72N	H	+	1	0	PAK4	44356065	0.020000	0.18652	0.427000	0.26684	0.020000	0.10135	0.211000	0.17474	1.008000	0.39264	0.462000	0.41574	CAT	.	.	.	none		0.667	PAK4-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463823.1			A	39664225	C	A	39664225	3	1	269	1	0	0	0	0	1	0	0	0	11410	826	29	4	683	4	PAK4	19	39664225	Missense_Mutation	SNP	C	TCGA-UZ-A9Q0-01A-12D-A42J-10	28525646	39664225	19464758	62	17005											
ZNF582	147948	hgsc.bcm.edu	37	chr19	56895643	56895643	+	Frame_Shift_Del	DEL	T	T	-																															attctctgatgttgcttgagTtgtgagctcactctaaaggc																										TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr19:56895643delT	ENST00000301310.4	-	5	1301	c.1143delA	c.(1141-1143)caafs	p.Q381fs	ZNF582_ENST00000586929.1_Frame_Shift_Del_p.Q381fs	NM_144690.1	NP_653291.1	Q96NG8	ZN582_HUMAN	zinc finger protein 582	381					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)		GTTGCTTGAGTTGTGAGCTCA	0.428																																					p.L382fs	Ovarian(183;1887 2032 4349 30507 51343)	Atlas-Indel,Pindel	.											.	ZNF582	56	.	0			c.1144delC						PASS	.						99	97	97					19																	56895643		2203	4300	6503	SO:0001589	frameshift_variant	147948	exon5			.	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.1143delA	chr19.hg19:g.56895643delT	ENSP00000301310:p.Gln381fs	125.0	0.0	0		93.0	46.0	0.494624	NM_144690	B4DQZ9|B7Z9R3|Q6PJT6	Frame_Shift_Del	DEL	ENST00000301310.4	hg19	CCDS33121.1																																																																																			.	.	.	none		0.428	ZNF582-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458387.2	NM_144690		-	56895643	T	-	56895643	7	5	269	1	0	1	0	1	0	0	0	0	18026	1722	60	0	414	0	ZNF582	19	56895643	Frame_Shift_Del	DEL	T	TCGA-UZ-A9Q0-01A-12D-A42J-10	17231418	56895643	2233340	63	17006											
C20orf144	128864	hgsc.bcm.edu	37	chr20	32251357	32251357	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccaggatcgtgctgattcTccccctggacaagcggcagc	8	7	12	14	2	1	1	0	1	1	0	3	4	1	3	3	3	3	2	3	3	1	1			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr20:32251357T>C	ENST00000375222.3	+	2	208	c.146T>C	c.(145-147)cTc>cCc	p.L49P	ACTL10_ENST00000330271.4_5'Flank|NECAB3_ENST00000375238.4_Intron|NECAB3_ENST00000246190.6_Intron|NECAB3_ENST00000606525.1_5'Flank	NM_080825.3	NP_543015.1	Q9BQM9	CT144_HUMAN	chromosome 20 open reading frame 144	49										lung(1)	1						GTGCTGATTCTCCCCCTGGAC	0.721																																					p.L49P		Atlas-SNP	.											.	C20orf144	4	.	0			c.T146C						PASS	.						14	17	16					20																	32251357		1788	3701	5489	SO:0001583	missense	128864	exon2			TGATTCTCCCCCT	AL121906	CCDS13223.1	20q11.22	2012-07-17			ENSG00000149609	ENSG00000149609			16137	protein-coding gene	gene with protein product	"bcl-2-like protein from testis"					11780052	Standard	NM_080825		Approved	dJ63M2.6, bclt	uc002wzs.2	Q9BQM9	OTTHUMG00000032263	ENST00000375222.3:c.146T>C	chr20.hg19:g.32251357T>C	ENSP00000364370:p.Leu49Pro	106.0	0.0	.		141.0	7.0	.	NM_080825	Q1AHR2	Missense_Mutation	SNP	ENST00000375222.3	hg19	CCDS13223.1	.	.	.	.	.	.	.	.	.	.	T	17.28	3.349754	0.61183	.	.	ENSG00000149609	ENST00000375222	T	0.55413	0.52	4.08	4.08	0.47627	.	0.272630	0.26366	N	0.024800	T	0.51160	0.1658	N	0.24115	0.695	0.18873	N	0.999984	D	0.60160	0.987	P	0.58391	0.838	T	0.41484	-0.9506	10	0.72032	D	0.01	-9.1117	9.636	0.39809	0.0:0.0:0.0:1.0	.	49	Q9BQM9	CT144_HUMAN	P	49	ENSP00000364370:L49P	ENSP00000364370:L49P	L	+	2	0	C20orf144	31715018	0.001000	0.12720	0.013000	0.15412	0.002000	0.02628	0.816000	0.27267	1.842000	0.53543	0.379000	0.24179	CTC	.	.	.	none		0.721	C20orf144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078714.2	NM_080825		C	32251357	T	C	32251357	3	2	269	1	0	0	0	0	1	0	0	0	2092	1551	54	3	152	3	C20orf144	20	32251357	Missense_Mutation	SNP	T	TCGA-UZ-A9Q0-01A-12D-A42J-10		32251357	30774163	64	17007											
USP25	29761	hgsc.bcm.edu	37	chr21	17214827	17214829	+	In_Frame_Del	DEL	GAA	GAA	-																															ccaaggcatcacatgagcatGaagataaaagtcctgaaaca																										TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr21:17214827_17214829delGAA	ENST00000285679.6	+	18	2674_2676	c.2305_2307delGAA	c.(2305-2307)gaadel	p.E769del	USP25_ENST00000351097.5_Intron|USP25_ENST00000400183.2_In_Frame_Del_p.E769del|USP25_ENST00000285681.2_In_Frame_Del_p.E769del	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	769					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)		ACATGAGCATGAAGATAAAAGTC	0.404																																					p.768_769del		Atlas-Indel,Pindel	.											.	USP25	156	.	0			c.2304_2306del						PASS	.																																			SO:0001651	inframe_deletion	29761	exon18			.	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.2305_2307delGAA	chr21.hg19:g.17214827_17214829delGAA	ENSP00000285679:p.Glu769del	178.0	0.0	0		217.0	125.0	0.576037	NM_013396	C0LSZ0|Q6DHZ9|Q9H9W1	In_Frame_Del	DEL	ENST00000285679.6	hg19	CCDS33515.1																																																																																			.	.	.	none		0.404	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			-	17214829	GAA	-	17214827	7	5	269	1	0	1	0	1	0	0	0	0	17068	1291	45	0	2375	0	USP25	21	17214827	In_Frame_Del	DEL	GAA	TCGA-UZ-A9Q0-01A-12D-A42J-10		17214827	30915068	65	17008											
SDF2L1	23753	hgsc.bcm.edu	37	chr22	21996638	21996638	+	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	ccggggcgatgtggagcgcgGgccgcggcggggctgcctgg	2	4	23	12	7	0	0	0	0	0	0	0	2	0	1	3	8	2	1	3	8	0	0			TCGA-UZ-A9Q0-01A-12D-A42J-10	TCGA-UZ-A9Q0-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1ade8c1b-f1d7-49ad-a7f1-d7b91dd79670	43bffa96-ab4f-4ba3-b15b-918e180d7be6	g.chr22:21996638G>A	ENST00000248958.4	+	1	89	c.13G>A	c.(13-15)Ggc>Agc	p.G5S	KB-1440D3.14_ENST00000609038.1_lincRNA	NM_022044.2	NP_071327.2	Q9HCN8	SDF2L_HUMAN	stromal cell-derived factor 2-like 1	5						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				prostate(1)	1	Colorectal(54;0.105)					GTGGAGCGCGGGCCGCGGCGG	0.771																																					p.G5S		Atlas-SNP	.											.	SDF2L1	5	.	0			c.G13A						PASS	.						4	6	5					22																	21996638		1658	3214	4872	SO:0001583	missense	23753	exon1			AGCGCGGGCCGCG		CCDS13792.1	22q11.21	2008-07-01			ENSG00000128228	ENSG00000128228			10676	protein-coding gene	gene with protein product	"dihydropyrimidinase-like 2", "PWP1-interacting protein 8"	607551				10591208, 11162531	Standard	NM_022044		Approved	AP000553.C22.4, OTTHUMT00000075032	uc002zvf.3	Q9HCN8	OTTHUMG00000150820	ENST00000248958.4:c.13G>A	chr22.hg19:g.21996638G>A	ENSP00000248958:p.Gly5Ser	46.0	0.0	.		49.0	24.0	.	NM_022044	A2RUD3|Q9BRI5	Missense_Mutation	SNP	ENST00000248958.4	hg19	CCDS13792.1	.	.	.	.	.	.	.	.	.	.	G	17.19	3.327679	0.60743	.	.	ENSG00000128228	ENST00000248958	T	0.79247	-1.25	4.86	3.84	0.44239	.	0.284658	0.24713	N	0.036213	T	0.66839	0.2830	L	0.36672	1.1	0.24093	N	0.995908	B	0.02656	0.0	B	0.10450	0.005	T	0.54840	-0.8233	10	0.30854	T	0.27	-18.1036	10.7972	0.46468	0.0977:0.0:0.9023:0.0	.	5	Q9HCN8	SDF2L_HUMAN	S	5	ENSP00000248958:G5S	ENSP00000248958:G5S	G	+	1	0	SDF2L1	20326638	0.052000	0.20516	0.997000	0.53966	0.628000	0.37860	0.117000	0.15583	1.332000	0.45431	0.655000	0.94253	GGC	.	.	.	none		0.771	SDF2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320197.1	NM_022044		A	21996638	G	A	21996638	3	1	269	1	0	0	0	0	1	0	0	0	13974	1232	43	2	15	2	SDF2L1	22	21996638	Missense_Mutation	SNP	G	TCGA-UZ-A9Q0-01A-12D-A42J-10		21996638	29307928	66	17009											
OR4F5	79501	hgsc.bcm.edu	37	chr1	69618	69629	+	In_Frame_Del	DEL	GGTAATCAAACT	GGTAATCAAACT	-																															ttttattgtgaccttcctagGgtaatcaaacttgcctgtac																										TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	GGTAATCAAACT	GGTAATCAAACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr1:69618_69629delGGTAATCAAACT	ENST00000335137.3	+	1	528_539	c.528_539delGGTAATCAAACT	c.(526-540)agggtaatcaaactt>agt	p.176_180RVIKL>S		NM_001005484.1	NP_001005484.1	Q8NH21	OR4F5_HUMAN	olfactory receptor, family 4, subfamily F, member 5	176						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			lung(1)|ovary(1)	2	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;3.48e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.21e-22)|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)		ACCTTCCTAGGGTAATCAAACTTGCCTGTACA	0.434																																					p.176_180del		Pindel	.											.	OR4F5	7	.	0			c.527_538del						PASS	.																																			SO:0001651	inframe_deletion	79501	exon1			.	AB065592	CCDS30547.1	1p36.33	2012-08-09			ENSG00000186092	ENSG00000186092		"GPCR / Class A : Olfactory receptors"	14825	protein-coding gene	gene with protein product							Standard	NM_001005484		Approved		uc001aal.1	Q8NH21	OTTHUMG00000001094	ENST00000335137.3:c.528_539delGGTAATCAAACT	chr1.hg19:g.69618_69629delGGTAATCAAACT	ENSP00000334393:p.Arg176_Leu180delinsSer	276.0	0.0	.		365.0	20.0	0.055	NM_001005484	Q5VT22	In_Frame_Del	DEL	ENST00000335137.3	hg19	CCDS30547.1																																																																																			.	.	.	none		0.434	OR4F5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003223.1	NM_001005484		-	69629	GGTAATCAAACT	-	69618	7	5	270	1	0	1	0	1	0	0	0	0	11072	1223	43	0	530	0	OR4F5	1	69618	In_Frame_Del	DEL	GGTAATCAAACT	TCGA-UZ-A9Q1-01A-11D-A42J-10		69618	249181003	1	17010											
PLEKHG5	57449	hgsc.bcm.edu	37	chr1	6556604	6556604	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggttctgacagcgcagtccCttcttttcagcggggctctg	4	12	13	12	2	4	1	1	1	3	0	5	1	5	1	1	3	2	3	1	3	0	4			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr1:6556604C>T	ENST00000400915.3	-	2	96	c.30G>A	c.(28-30)aaG>aaA	p.K10K	PLEKHG5_ENST00000537245.1_Silent_p.K33K|PLEKHG5_ENST00000377740.3_Silent_p.K31K|PLEKHG5_ENST00000377732.1_5'UTR|PLEKHG5_ENST00000377748.1_Silent_p.K31K|PLEKHG5_ENST00000377737.2_5'UTR|PLEKHG5_ENST00000544978.1_5'UTR	NM_001042663.1	NP_001036128.1	O94827	PKHG5_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 5	10					apoptotic signaling pathway (GO:0097190)|endothelial cell chemotaxis (GO:0035767)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			liver(1)	1	Ovarian(185;0.02)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;5.51e-35)|GBM - Glioblastoma multiforme(13;3.57e-27)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419)		AGCGCAGTCCCTTCTTTTCAG	0.711																																					p.K33K		Atlas-SNP	.											.	PLEKHG5	66	.	0			c.G99A						PASS	.						36	40	39					1																	6556604		1918	4113	6031	SO:0001819	synonymous_variant	57449	exon2			CAGTCCCTTCTTT	AK024676	CCDS79.1, CCDS41240.1, CCDS41241.1, CCDS57967.1, CCDS57968.1, CCDS57969.1	1p36.31	2014-09-17		2005-08-09	ENSG00000171680	ENSG00000171680		"Pleckstrin homology (PH) domain containing"	29105	protein-coding gene	gene with protein product	"synectin-binding guanine exchange factor"	611101				17564964	Standard	NM_001042663		Approved	KIAA0720, Syx, GEF720, Tech	uc010nzr.1	O94827	OTTHUMG00000000905	ENST00000400915.3:c.30G>A	chr1.hg19:g.6556604C>T		174.0	0.0	.		214.0	82.0	.	NM_001265592	B3KU07|B7Z2M3|B7Z5X2|F5GZ21|F5H1I0|Q5SY17|Q5T8W5|Q5T8W9|Q6ZNM0|Q7Z436|Q86YD8|Q96BS1	Silent	SNP	ENST00000400915.3	hg19	CCDS41241.1																																																																																			.	.	.	none		0.711	PLEKHG5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002631.1	NM_020631		T	6556604	C	T	6556604	2	4	270	1	0	0	0	0	0	0	0	1	12080	680	24	2		2	PLEKHG5	1	6556604	Silent	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10	6486986	6556604	242694017	2	17011											
KAZ	23254	hgsc.bcm.edu	37	chr1	15438985	15438985	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcagggcctccagcgtcaCgcgggcaggaaaggaggaga	10	3	18	10	3	1	1	1	0	0	1	2	4	2	3	2	6	1	2	2	6	1	0			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr1:15438985C>T	ENST00000376030.2	+	14	2405	c.2111C>T	c.(2110-2112)aCg>aTg	p.T704M		NM_201628.2	NP_963922.2	Q674X7	KAZRN_HUMAN	kazrin, periplakin interacting protein	704					keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(1)|prostate(2)	25						TCCAGCGTCACGCGGGCAGGA	0.602																																					p.T704M		Atlas-SNP	.											.	KAZN	57	.	0			c.C2111T						PASS	.						35	34	34					1																	15438985		2203	4298	6501	SO:0001583	missense	23254	exon14			GCGTCACGCGGGC	AY505119	CCDS30604.1, CCDS41267.1, CCDS152.2, CCDS41268.1	1p36.21	2014-02-12	2011-01-31		ENSG00000189337	ENSG00000189337		"Sterile alpha motif (SAM) domain containing"	29173	protein-coding gene	gene with protein product						15337775, 18840647	Standard	NM_015209		Approved	KIAA1026, KAZRIN, FLJ43806	uc001avm.4	Q674X7	OTTHUMG00000002042	ENST00000376030.2:c.2111C>T	chr1.hg19:g.15438985C>T	ENSP00000365198:p.Thr704Met	284.0	0.0	.		349.0	137.0	.	NM_201628	B0QYQ0|B1AK78|Q5TGF1|Q674X4|Q674X6|Q6ZUD1|Q8IYN7|Q8N409|Q9UIL2|Q9UPX4	Missense_Mutation	SNP	ENST00000376030.2	hg19	CCDS152.2	.	.	.	.	.	.	.	.	.	.	C	15.00	2.704557	0.48412	.	.	ENSG00000189337	ENST00000376030	T	0.18174	2.23	5.52	5.52	0.82312	.	0.568180	0.15933	N	0.237585	T	0.16171	0.0389	N	0.19112	0.55	0.80722	D	1	D	0.65815	0.995	P	0.46339	0.513	T	0.02294	-1.1181	10	0.46703	T	0.11	-15.1435	14.97	0.71226	0.0:1.0:0.0:0.0	.	704	Q674X7	KAZRN_HUMAN	M	704	ENSP00000365198:T704M	ENSP00000365198:T704M	T	+	2	0	KAZN	15311572	0.897000	0.30589	0.951000	0.38953	0.622000	0.37654	3.734000	0.55037	2.591000	0.87537	0.650000	0.86243	ACG	.	.	.	none		0.602	KAZN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005690.2	NM_001017999		T	15438985	C	T	15438985	3	4	270	1	0	0	0	0	1	0	0	0	7995	536	19	1	2421	1	KAZ	1	15438985	Missense_Mutation	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10	8882381	15438985	233811636	3	17012											
XPR1	9213	hgsc.bcm.edu	37	chr1	180843044	180843044	+	Missense_Mutation	SNP	A	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	tgcctcattctggggacatcAttgctactgtctttgcccca	6	14	8	13	0	4	0	2	0	2	0	4	1	4	1	3	2	4	1	3	2	1	4			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr1:180843044A>C	ENST00000367590.4	+	13	1972	c.1774A>C	c.(1774-1776)Att>Ctt	p.I592L	XPR1_ENST00000367589.3_Missense_Mutation_p.I527L	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1	592	EXS. {ECO:0000255|PROSITE- ProRule:PRU00712}.				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						TGGGGACATCATTGCTACTGT	0.393																																					p.I592L		Atlas-SNP	.											.	XPR1	76	.	0			c.A1774C						PASS	.						128	111	116					1																	180843044		2203	4300	6503	SO:0001583	missense	9213	exon13			GACATCATTGCTA	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.1774A>C	chr1.hg19:g.180843044A>C	ENSP00000356562:p.Ile592Leu	74.0	0.0	.		72.0	32.0	.	NM_004736	O95719|Q7L8K9|Q8IW20|Q9NT19|Q9UFB9	Missense_Mutation	SNP	ENST00000367590.4	hg19	CCDS1340.1	.	.	.	.	.	.	.	.	.	.	A	10.13	1.266946	0.23136	.	.	ENSG00000143324	ENST00000367590;ENST00000367589	T;T	0.39787	1.06;1.06	5.43	4.31	0.51392	EXS, C-terminal (2);	0.170586	0.51477	D	0.000092	T	0.19604	0.0471	N	0.04636	-0.2	0.27836	N	0.941287	B;B	0.11235	0.001;0.004	B;B	0.11329	0.003;0.006	T	0.17319	-1.0373	10	0.14656	T	0.56	-10.892	10.5361	0.45004	0.9236:0.0:0.0764:0.0	.	527;592	Q9UBH6-2;Q9UBH6	.;XPR1_HUMAN	L	592;527	ENSP00000356562:I592L;ENSP00000356561:I527L	ENSP00000356561:I527L	I	+	1	0	XPR1	179109667	1.000000	0.71417	1.000000	0.80357	0.680000	0.39746	1.548000	0.36201	0.925000	0.37094	0.528000	0.53228	ATT	.	.	.	none		0.393	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084996.2	NM_004736		C	180843044	A	C	180843044	3	2	270	1	0	0	0	0	1	0	0	0	17463	217	8	5	1824	5	XPR1	1	180843044	Missense_Mutation	SNP	A	TCGA-UZ-A9Q1-01A-11D-A42J-10	165404059	180843044	68407577	4	17013											
SYT2	127833	hgsc.bcm.edu	37	chr1	202572220	202572220	+	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	ccttcaccttccccctcagtCaggcctgtctctgcgtcgtc	3	12	7	19	2	4	0	3	0	1	0	8	0	5	0	5	1	1	0	5	1	0	2			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr1:202572220C>G	ENST00000367267.1	-	4	564	c.372G>C	c.(370-372)ctG>ctC	p.L124L	SYT2_ENST00000367268.4_Silent_p.L124L|RP11-569A11.1_ENST00000428573.1_RNA	NM_001136504.1	NP_001129976.1	Q8N9I0	SYT2_HUMAN	synaptotagmin II	124					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)	CCCCCTCAGTCAGGCCTGTCT	0.547																																					p.L124L		Atlas-SNP	.											.	SYT2	51	.	0			c.G372C						PASS	.						128	111	117					1																	202572220		2203	4300	6503	SO:0001819	synonymous_variant	127833	exon4			CTCAGTCAGGCCT	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.372G>C	chr1.hg19:g.202572220C>G		68.0	0.0	.		100.0	41.0	.	NM_177402	Q496K5|Q8NBE5	Silent	SNP	ENST00000367267.1	hg19	CCDS1427.1																																																																																			.	.	.	none		0.547	SYT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099157.1	NM_177402		G	202572220	C	G	202572220	2	3	270	1	0	0	0	0	0	0	0	1	15486	813	29	4		4	SYT2	1	202572220	Silent	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10	21729176	202572220	46678401	5	17014											
ADAM17	6868	hgsc.bcm.edu	37	chr2	9666345	9666345	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcttcatgggatctgggtcAgctcttcttttcactcgatg	5	17	9	10	1	7	0	3	0	4	0	8	2	7	1	0	2	1	1	0	2	0	5			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr2:9666345A>G	ENST00000310823.3	-	6	830	c.648T>C	c.(646-648)gcT>gcC	p.A216A	ADAM17_ENST00000497134.1_Silent_p.A216A	NM_003183.4	NP_003174.3	P78536	ADA17_HUMAN	ADAM metallopeptidase domain 17	216					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell motility (GO:0048870)|collagen catabolic process (GO:0030574)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|germinal center formation (GO:0002467)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil mediated immunity (GO:0002446)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of chemokine production (GO:0032722)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|proteolysis (GO:0006508)|regulation of mast cell apoptotic process (GO:0033025)|response to drug (GO:0042493)|response to high density lipoprotein particle (GO:0055099)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|wound healing, spreading of epidermal cells (GO:0035313)	actin cytoskeleton (GO:0015629)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|interleukin-6 receptor binding (GO:0005138)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|Notch binding (GO:0005112)|PDZ domain binding (GO:0030165)|zinc ion binding (GO:0008270)			breast(1)|cervix(4)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	28	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.225)		GATCTGGGTCAGCTCTTCTTT	0.368																																					p.A216A		Atlas-SNP	.											.	ADAM17	61	.	0			c.T648C						PASS	.						173	153	160					2																	9666345		2203	4300	6503	SO:0001819	synonymous_variant	6868	exon6			TGGGTCAGCTCTT	U69611	CCDS1665.1	2p25	2010-08-05	2008-07-31		ENSG00000151694	ENSG00000151694		"ADAM metallopeptidase domain containing", "CD molecules"	195	protein-coding gene	gene with protein product		603639	"tumor necrosis factor, alpha, converting enzyme"	TACE		9034190, 9574564	Standard	NM_003183		Approved	cSVP, CD156B	uc002qzu.3	P78536	OTTHUMG00000090425	ENST00000310823.3:c.648T>C	chr2.hg19:g.9666345A>G		54.0	0.0	.		77.0	21.0	.	NM_003183	O60226	Silent	SNP	ENST00000310823.3	hg19	CCDS1665.1																																																																																			.	.	.	none		0.368	ADAM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206857.1			G	9666345	A	G	9666345	2	3	270	1	0	0	0	0	0	0	0	1	238	175	7	3		3	ADAM17	2	9666345	Silent	SNP	A	TCGA-UZ-A9Q1-01A-11D-A42J-10		9666345	233533028	6	17015											
ATP6V1C2	245973	hgsc.bcm.edu	37	chr2	10922432	10922436	+	Frame_Shift_Del	DEL	GCGTT	GCGTT	-																															cataagaagtcatccaccaaGcgtttaagagaggttctaaa																								rs377277646		TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	GCGTT	GCGTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr2:10922432_10922436delGCGTT	ENST00000272238.4	+	13	1234_1238	c.1125_1129delGCGTT	c.(1123-1131)aagcgtttafs	p.KRL375fs	ATP6V1C2_ENST00000381661.3_Frame_Shift_Del_p.KRL329fs	NM_001039362.1	NP_001034451.1	Q8NEY4	VATC2_HUMAN	ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C2	375					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of Wnt signaling pathway (GO:0030177)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)|protein dimerization activity (GO:0046983)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.15)|OV - Ovarian serous cystadenocarcinoma(76;0.152)		CATCCACCAAGCGTTTAAGAGAGGT	0.449																																					p.375_376del	NSCLC(188;1042 2136 10807 16813 47705)	Atlas-Indel,Pindel	.											.	ATP6V1C2	73	.	0			c.1124_1128del						PASS	.																																			SO:0001589	frameshift_variant	245973	exon13			.	AY039759	CCDS1674.1, CCDS42653.1	2p25.1	2010-04-21	2006-01-13		ENSG00000143882	ENSG00000143882		"ATPases / V-type"	18264	protein-coding gene	gene with protein product			"ATPase, H+ transporting, lysosomal 42kD, V1 subunit C isoform 2", "ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C isoform 2"			12384298	Standard	XR_426949		Approved	VMA5, ATP6C2	uc002ras.3	Q8NEY4	OTTHUMG00000090459	ENST00000272238.4:c.1125_1129delGCGTT	chr2.hg19:g.10922432_10922436delGCGTT	ENSP00000272238:p.Lys375fs	123.0	0.0	0		103.0	32.0	0.31068	NM_001039362	Q96EL8	Frame_Shift_Del	DEL	ENST00000272238.4	hg19	CCDS42653.1																																																																																			.	.	.	none		0.449	ATP6V1C2-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323555.1	NM_144583		-	10922436	GCGTT	-	10922432	7	5	270	1	0	1	0	1	0	0	0	0	1181	962	34	0	1171	0	ATP6V1C2	2	10922432	Frame_Shift_Del	DEL	GCGTT	TCGA-UZ-A9Q1-01A-11D-A42J-10	1256087	10922432	232276941	7	17016											
ARID5A	10865	hgsc.bcm.edu	37	chr2	97217448	97217448	+	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	tgtggggcggagacgctaacCgcccttctgcgttccataaa	8	9	12	12	4	1	1	0	0	1	1	2	2	2	1	3	3	2	2	3	3	3	4			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr2:97217448C>A	ENST00000357485.3	+	7	1261	c.1183C>A	c.(1183-1185)Cgc>Agc	p.R395S	ARID5A_ENST00000454558.2_Missense_Mutation_p.R327S	NM_212481.1	NP_997646.1	Q03989	ARI5A_HUMAN	AT rich interactive domain 5A (MRF1-like)	395					chondrocyte differentiation (GO:0002062)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)|skin(1)|urinary_tract(2)	14						AGACGCTAACCGCCCTTCTGC	0.597																																					p.R395S		Atlas-SNP	.											.	ARID5A	31	.	0			c.C1183A						PASS	.						37	33	35					2																	97217448		2203	4299	6502	SO:0001583	missense	10865	exon7			GCTAACCGCCCTT	M62324	CCDS33251.1	2p11.1	2013-02-07			ENSG00000196843	ENSG00000196843		"-"	17361	protein-coding gene	gene with protein product	"modulator recognition factor 1"	611583				8649988	Standard	NM_212481		Approved	MRF-1, RP11-363D14	uc002swe.3	Q03989	OTTHUMG00000155229	ENST00000357485.3:c.1183C>A	chr2.hg19:g.97217448C>A	ENSP00000350078:p.Arg395Ser	153.0	0.0	.		159.0	64.0	.	NM_212481	Q6NX37	Missense_Mutation	SNP	ENST00000357485.3	hg19	CCDS33251.1	.	.	.	.	.	.	.	.	.	.	C	14.75	2.628516	0.46944	.	.	ENSG00000196843	ENST00000357485;ENST00000359765;ENST00000454558	T	0.66638	-0.22	5.22	5.22	0.72569	.	0.267002	0.27193	N	0.020484	T	0.63954	0.2555	L	0.57536	1.79	0.30657	N	0.754762	P;B;B	0.44090	0.826;0.36;0.135	B;B;B	0.43155	0.41;0.04;0.081	T	0.64101	-0.6486	10	0.17369	T	0.5	-20.5478	14.6192	0.68572	0.0:1.0:0.0:0.0	.	395;327;395	A6NM59;C9J1Q0;Q03989	.;.;ARI5A_HUMAN	S	395;395;327	ENSP00000350078:R395S	ENSP00000350078:R395S	R	+	1	0	ARID5A	96581175	0.057000	0.20700	0.976000	0.42696	0.578000	0.36192	3.330000	0.52068	2.588000	0.87417	0.655000	0.94253	CGC	.	.	.	none		0.597	ARID5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338888.2	NM_212481		A	97217448	C	A	97217448	3	1	270	1	0	0	0	0	1	0	0	0	921	652	23	4	1209	4	ARID5A	2	97217448	Missense_Mutation	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10	86295016	97217448	145981925	8	17017											
ACVR2A	92	hgsc.bcm.edu	37	chr2	148683732	148683732	+	Splice_Site	DEL	T	T	-																															ttattggcagaaacatgctgTaagttatccagttagctttt																										TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr2:148683732delT	ENST00000241416.7	+	10	1983		c.e10+2		ACVR2A_ENST00000535787.1_Splice_Site|ACVR2A_ENST00000495775.1_Splice_Site|ACVR2A_ENST00000404590.1_Splice_Site	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA						activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		AAACATGCTGTAAGTTATCCA	0.353																																					.		Atlas-Indel,Pindel	.											.,1	ACVR2A	125	.	0			c.1347+1T>-						PASS	.						115	95	102					2																	148683732		2203	4299	6502	SO:0001630	splice_region_variant	92	exon10			.		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.1347+2T>-	chr2.hg19:g.148683732delT		66.0	0.0	0		70.0	22.0	0.314286	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Splice_Site	DEL	ENST00000241416.7	hg19	CCDS33301.1																																																																																			.	.	.	none		0.353	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616	Intron	-	148683732	T	-	148683732	8	5	270	1	0	1	0	1	0	0	1	0	223	1652	57	0	1387	0	ACVR2A	2	148683732	Splice_Site	DEL	T	TCGA-UZ-A9Q1-01A-11D-A42J-10	51466284	148683732	94515641	9	17018											
BOLL	66037	hgsc.bcm.edu	37	chr2	198643755	198643755	+	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	acttctttcacagacccataCtgggaaaaaaattttcttaa	15	13	4	9	0	3	1	1	0	2	1	3	2	3	2	1	1	1	0	1	1	5	6			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr2:198643755C>T	ENST00000392296.4	-	3	474	c.165G>A	c.(163-165)caG>caA	p.Q55Q	BOLL_ENST00000433157.1_Silent_p.Q55Q|BOLL_ENST00000321801.7_Silent_p.Q67Q|BOLL_ENST00000430004.1_Silent_p.Q55Q|BOLL_ENST00000282278.8_5'UTR	NM_033030.5	NP_149019.1	Q8N9W6	BOLL_HUMAN	boule-like RNA-binding protein	55	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell differentiation (GO:0030154)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|positive regulation of translational initiation (GO:0045948)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|translation activator activity (GO:0008494)			central_nervous_system(1)|endometrium(2)|lung(6)|ovary(3)|prostate(1)	13						CAGACCCATACTGGGAAAAAA	0.308																																					p.Q67Q		Atlas-SNP	.											.	BOLL	67	.	0			c.G201A						PASS	.						90	91	91					2																	198643755		2202	4299	6501	SO:0001819	synonymous_variant	66037	exon3			CCCATACTGGGAA		CCDS2324.1, CCDS2325.1, CCDS63081.1	2q33	2013-10-17	2013-10-17		ENSG00000152430	ENSG00000152430		"RNA binding motif (RRM) containing"	14273	protein-coding gene	gene with protein product		606165	"bol (Drosophila boule homolog)-like", "bol, boule-like (Drosophila)"			11390979, 16001084	Standard	NM_197970		Approved	BOULE	uc002uut.2	Q8N9W6	OTTHUMG00000132747	ENST00000392296.4:c.165G>A	chr2.hg19:g.198643755C>T		73.0	0.0	.		79.0	32.0	.	NM_197970	B4DZA4|Q0JW32|Q53T62|Q969U3	Silent	SNP	ENST00000392296.4	hg19	CCDS2325.1																																																																																			.	.	.	none		0.308	BOLL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256107.3	NM_033030		T	198643755	C	T	198643755	2	4	270	1	0	0	0	0	0	0	0	1	1489	564	20	2		2	BOLL	2	198643755	Silent	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10	49960023	198643755	44555618	10	17019											
CCR9	10803	hgsc.bcm.edu	37	chr3	45942933	45942933	+	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	gtcagctgtcttgaccctgaAggtcattctggggttcttcc	5	14	11	11	0	5	2	2	2	3	0	6	2	6	2	2	3	1	2	2	3	1	4			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr3:45942933A>T	ENST00000357632.2	+	3	833	c.653A>T	c.(652-654)aAg>aTg	p.K218M	CCR9_ENST00000355983.2_Missense_Mutation_p.K206M|CCR9_ENST00000422395.1_3'UTR|LZTFL1_ENST00000536047.1_Intron|Y_RNA_ENST00000364765.1_RNA|CCR9_ENST00000395963.2_Missense_Mutation_p.K206M|LZTFL1_ENST00000539217.1_Intron	NM_001256369.1|NM_031200.2	NP_001243298.1|NP_112477.1	P51686	CCR9_HUMAN	chemokine (C-C motif) receptor 9	218					cellular defense response (GO:0006968)|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)	cell surface (GO:0009986)|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(4)|large_intestine(8)|lung(2)|ovary(2)|prostate(2)|skin(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.00118)|KIRC - Kidney renal clear cell carcinoma(197;0.0182)|Kidney(197;0.0214)		TTGACCCTGAAGGTCATTCTG	0.478																																					p.K218M		Atlas-SNP	.											.	CCR9	45	.	0			c.A653T						PASS	.						190	169	176					3																	45942933		2203	4300	6503	SO:0001583	missense	10803	exon3			CCCTGAAGGTCAT	AJ132337	CCDS2732.1, CCDS2733.1	3p21.31	2012-09-20			ENSG00000173585	ENSG00000173585		"GPCR / Class A : Chemokine receptors : C-C motif", "CD molecules"	1610	protein-coding gene	gene with protein product		604738		GPR28		10229797	Standard	NM_006641		Approved	GPR-9-6, CDw199	uc003coz.2	P51686	OTTHUMG00000133450	ENST00000357632.2:c.653A>T	chr3.hg19:g.45942933A>T	ENSP00000350256:p.Lys218Met	86.0	0.0	.		124.0	51.0	.	NM_031200	Q4VBM3|Q549E0|Q9UQQ6	Missense_Mutation	SNP	ENST00000357632.2	hg19	CCDS2732.1	.	.	.	.	.	.	.	.	.	.	A	19.70	3.876744	0.72180	.	.	ENSG00000173585	ENST00000357632;ENST00000395963;ENST00000355983	T;T;T	0.72051	-0.62;-0.62;-0.62	4.96	3.82	0.43975	GPCR, rhodopsin-like superfamily (1);	8.991370	0.00357	N	0.000032	T	0.72495	0.3467	N	0.12853	0.265	0.46609	D	0.999123	P	0.49961	0.93	P	0.62014	0.897	T	0.64478	-0.6398	10	0.41790	T	0.15	.	10.0158	0.42014	0.9208:0.0:0.0792:0.0	.	218	P51686	CCR9_HUMAN	M	218;206;206	ENSP00000350256:K218M;ENSP00000379292:K206M;ENSP00000348260:K206M	ENSP00000348260:K206M	K	+	2	0	CCR9	45917937	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.324000	0.72896	1.858000	0.53909	0.460000	0.39030	AAG	.	.	.	none		0.478	CCR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257323.2			T	45942933	A	T	45942933	3	4	270	1	0	0	0	0	1	0	0	0	2950	72	3	5	659	5	CCR9	3	45942933	Missense_Mutation	SNP	A	TCGA-UZ-A9Q1-01A-11D-A42J-10		45942933	152079497	11	17020											
PTH1R	5745	hgsc.bcm.edu	37	chr3	46935466	46935467	+	Frame_Shift_Ins	INS	-	-	A																															ccgtgctcaggcccagtgcgINSaaaaacggctcaaggaggtc																										TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr3:46935466_46935467insA	ENST00000313049.5	+	2	348_349	c.145_146insA	c.(145-147)gaafs	p.E49fs	PTH1R_ENST00000490109.1_3'UTR|PTH1R_ENST00000418619.1_Frame_Shift_Ins_p.E49fs|PTH1R_ENST00000430002.2_Frame_Shift_Ins_p.E49fs|PTH1R_ENST00000449590.1_Frame_Shift_Ins_p.E49fs			Q03431	PTH1R_HUMAN	parathyroid hormone 1 receptor	49					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)	GGCCCAGTGCGAAAAACGGCTC	0.609																																					p.E49fs		Pindel	.											.	PTH1R	49	.	0			c.145_146insA						PASS	.																																			SO:0001589	frameshift_variant	5745	exon3			.		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.150dupA	chr3.hg19:g.46935471_46935471dupA	ENSP00000321999:p.Glu49fs	190.0	0.0	.		281.0	86.0	0.306	NM_001184744	Q2M1U3	Frame_Shift_Ins	INS	ENST00000313049.5	hg19	CCDS2747.1																																																																																			.	.	.	none		0.609	PTH1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257481.1	NM_000316		A	46935467	-	A	46935466	7	5	270	1	0	1	1	0	0	0	0	0	12769	1059	37	0	151	0	PTH1R	3	46935466	Frame_Shift_Ins	INS	-	TCGA-UZ-A9Q1-01A-11D-A42J-10	992533	46935466	151086964	12	17021											
CEP135	9662	hgsc.bcm.edu	37	chr4	56818348	56818348	+	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	atattaggaaaaggctggatCagctgggataccgccagact	13	8	12	8	1	1	1	1	0	0	1	1	4	1	4	2	4	2	2	2	4	5	3			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr4:56818348C>T	ENST00000257287.4	+	2	176	c.52C>T	c.(52-54)Cag>Tag	p.Q18*	CEP135_ENST00000422247.2_Nonsense_Mutation_p.Q18*	NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	18					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)					AAGGCTGGATCAGCTGGGATA	0.363																																					p.Q18X		Atlas-SNP	.											.	CEP135	115	.	0			c.C52T						PASS	.						62	66	64					4																	56818348		2203	4300	6503	SO:0001587	stop_gained	9662	exon2			CTGGATCAGCTGG	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.52C>T	chr4.hg19:g.56818348C>T	ENSP00000257287:p.Gln18*	413.0	0.0	.		463.0	172.0	.	NM_025009	B2RMY0|O75130|Q58F25|Q9H8H7	Nonsense_Mutation	SNP	ENST00000257287.4	hg19	CCDS33986.1	.	.	.	.	.	.	.	.	.	.	C	36	5.700451	0.96802	.	.	ENSG00000174799	ENST00000422247;ENST00000257287	.	.	.	5.88	5.03	0.67393	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	.	16.9683	0.86293	0.0:0.8722:0.1278:0.0	.	.	.	.	X	18	.	ENSP00000257287:Q18X	Q	+	1	0	CEP135	56513105	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.794000	0.85869	1.471000	0.48121	0.655000	0.94253	CAG	.	.	.	none		0.363	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009		T	56818348	C	T	56818348	4	4	270	1	0	0	0	0	0	1	0	0	3249	827	29	2	54	2	CEP135	4	56818348	Nonsense_Mutation	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10		56818348	134335928	13	17022											
SEC24B	10427	hgsc.bcm.edu	37	chr4	110433149	110433169	+	In_Frame_Del	DEL	TGCCGATCCTGTCGAACGTAT	TGCCGATCCTGTCGAACGTAT	-																															catcaaataccattgtgaggTgccgatcctgtcgaacgtat																								rs534235016|rs574648225		TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	TGCCGATCCTGTCGAACGTAT	TGCCGATCCTGTCGAACGTAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr4:110433149_110433169delTGCCGATCCTGTCGAACGTAT	ENST00000265175.5	+	9	1868_1888	c.1813_1833delTGCCGATCCTGTCGAACGTAT	c.(1813-1833)tgccgatcctgtcgaacgtatdel	p.CRSCRTY605del	SEC24B_ENST00000504968.2_In_Frame_Del_p.CRSCRTY635del|SEC24B_ENST00000399100.2_In_Frame_Del_p.CRSCRTY570del	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B	605	Zinc finger-like.				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)		CATTGTGAGGTGCCGATCCTGTCGAACGTATATTAACCCCT	0.367																																					p.604_611del		Atlas-Indel,Pindel	.											.	SEC24B	186	.	0			c.1812_1832del						PASS	.																																			SO:0001651	inframe_deletion	10427	exon9			.	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.1813_1833delTGCCGATCCTGTCGAACGTAT	chr4.hg19:g.110433149_110433169delTGCCGATCCTGTCGAACGTAT	ENSP00000265175:p.Cys605_Tyr611del	104.0	0.0	0		70.0	15.0	0.214286	NM_006323	B7ZKM8|B7ZKN4|Q0VG08	In_Frame_Del	DEL	ENST00000265175.5	hg19	CCDS47124.1																																																																																			.	.	.	none		0.367	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364693.2			-	110433169	TGCCGATCCTGTCGAACGTAT	-	110433149	7	5	270	1	0	1	0	1	0	0	0	0	14008	1696	59	0	1847	0	SEC24B	4	110433149	In_Frame_Del	DEL	TGCCGATCCTGTCGAACGTAT	TCGA-UZ-A9Q1-01A-11D-A42J-10	53614801	110433149	80721127	14	17023											
RPS3A	6189	hgsc.bcm.edu	37	chr4	152021725	152021725	+	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	ttggaaagacgctcgtcaccAggacccaaggaaccagtaag	14	5	11	11	2	1	1	1	0	0	1	2	4	1	4	3	3	1	2	3	3	4	2			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr4:152021725A>C	ENST00000274065.4	+	2	231	c.151A>C	c.(151-153)Agg>Cgg	p.R51R	SNORD73_ENST00000364394.1_RNA|RPS3A_ENST00000506126.1_Silent_p.R14R|RPS3A_ENST00000509736.1_Intron|RPS3A_ENST00000514682.1_Silent_p.R14R|RPS3A_ENST00000512690.1_Silent_p.R51R|RPS3A_ENST00000322686.6_Silent_p.R38R	NM_001006.4	NP_000997.1			ribosomal protein S3A											endometrium(1)|lung(1)|ovary(1)|pancreas(1)	4	all_hematologic(180;0.093)					GCTCGTCACCAGGACCCAAGG	0.398																																					p.R51R		Atlas-SNP	.											.	RPS3A	11	.	0			c.A151C						PASS	.						72	78	76					4																	152021725		2203	4300	6503	SO:0001819	synonymous_variant	6189	exon2			GTCACCAGGACCC	X87373	CCDS3775.1	4q31.2-q31.3	2011-04-05			ENSG00000145425	ENSG00000145425		"S ribosomal proteins"	10421	protein-coding gene	gene with protein product		180478		MFTL		8647443, 1398113	Standard	NM_001006		Approved	S3A	uc003ilz.4	P61247	OTTHUMG00000161445	ENST00000274065.4:c.151A>C	chr4.hg19:g.152021725A>C		45.0	0.0	.		72.0	33.0	.	NM_001006		Silent	SNP	ENST00000274065.4	hg19	CCDS3775.1																																																																																			.	.	.	none		0.398	RPS3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364957.1			C	152021725	A	C	152021725	2	2	270	1	0	0	0	0	0	0	0	1	13657	179	7	5		5	RPS3A	4	152021725	Silent	SNP	A	TCGA-UZ-A9Q1-01A-11D-A42J-10	41588576	152021725	39132551	15	17024											
RXFP1	59350	hgsc.bcm.edu	37	chr4	159573058	159573058	+	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	gaaaatctatggacagcaaaGgtcagaaaacatatgctcca	18	7	8	8	0	2	1	1	0	1	1	3	3	3	2	1	2	3	2	1	2	7	2			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr4:159573058G>T	ENST00000307765.5	+	18	2376	c.2125G>T	c.(2125-2127)Ggt>Tgt	p.G709C	RXFP1_ENST00000470033.1_Missense_Mutation_p.G676C|RXFP1_ENST00000448688.2_Missense_Mutation_p.G604C|RXFP1_ENST00000460056.2_Missense_Mutation_p.G628C|RXFP1_ENST00000343542.5_Missense_Mutation_p.G661C	NM_001253727.1|NM_001253728.1|NM_001253730.1|NM_001253732.1|NM_001253733.1|NM_021634.3	NP_001240656.1|NP_001240657.1|NP_001240659.1|NP_001240661.1|NP_001240662.1|NP_067647.2	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1	709					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|lung connective tissue development (GO:0060427)|nipple morphogenesis (GO:0060658)|parturition (GO:0007567)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)	p.G709C(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|liver(2)|lung(22)|prostate(1)|skin(10)	49	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)		GGACAGCAAAGGTCAGAAAAC	0.418																																					p.G736C		Atlas-SNP	.											RXFP1,NS,carcinoma,0,1	RXFP1	98	.	1	Substitution - Missense(1)	lung(1)	c.G2206T						PASS	.						121	113	115					4																	159573058		1903	4111	6014	SO:0001583	missense	59350	exon18			AGCAAAGGTCAGA	AF190500	CCDS43276.1, CCDS58929.1, CCDS58930.1, CCDS75204.1, CCDS75205.1, CCDS75206.1	4q31.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000171509	ENSG00000171509		"GPCR / Class A : Relaxin family peptide receptors"	19718	protein-coding gene	gene with protein product		606654	"leucine-rich repeat-containing G protein-coupled receptor 7"	LGR7		15956688, 16507880	Standard	NM_021634		Approved	RXFPR1	uc003ipz.3	Q9HBX9	OTTHUMG00000149973	ENST00000307765.5:c.2125G>T	chr4.hg19:g.159573058G>T	ENSP00000303248:p.Gly709Cys	97.0	0.0	.		82.0	30.0	.	NM_001253727	B4DHD1|B4DTV2|Q2M215|Q3KU24|Q3KU25|Q3KU26	Missense_Mutation	SNP	ENST00000307765.5	hg19	CCDS43276.1	.	.	.	.	.	.	.	.	.	.	G	13.42	2.232792	0.39498	.	.	ENSG00000171509	ENST00000460056;ENST00000307765;ENST00000448688;ENST00000343542;ENST00000470033;ENST00000440678	T;T;T;T;T	0.70869	-0.37;-0.47;-0.33;-0.52;-0.47	5.75	3.11	0.35812	.	0.407867	0.26279	N	0.025297	T	0.65770	0.2723	L	0.51422	1.61	0.24866	N	0.992319	P;P;P;P;P;P;P;P	0.50617	0.896;0.883;0.896;0.616;0.937;0.88;0.896;0.482	B;B;B;B;P;B;B;B	0.45913	0.302;0.417;0.395;0.393;0.497;0.376;0.321;0.28	T	0.60005	-0.7347	10	0.66056	D	0.02	.	8.488	0.33082	0.2892:0.0:0.7108:0.0	.	720;736;604;661;676;628;579;709	B3KV27;B4DGP2;B4DHD1;Q9HBX9-4;Q9HBX9-2;E9PCA3;Q59H16;Q9HBX9	.;.;.;.;.;.;.;RXFP1_HUMAN	C	628;709;604;661;676;579	ENSP00000423306:G628C;ENSP00000303248:G709C;ENSP00000414885:G604C;ENSP00000345889:G661C;ENSP00000420712:G676C	ENSP00000303248:G709C	G	+	1	0	RXFP1	159792508	0.580000	0.26733	0.981000	0.43875	0.525000	0.34531	0.400000	0.20932	0.779000	0.33543	0.655000	0.94253	GGT	.	.	.	none		0.418	RXFP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314865.1	NM_021634		T	159573058	G	T	159573058	3	4	270	1	0	0	0	0	1	0	0	0	13772	1000	35	4	2195	4	RXFP1	4	159573058	Missense_Mutation	SNP	G	TCGA-UZ-A9Q1-01A-11D-A42J-10	7551333	159573058	31581218	16	17025											
FNIP2	57600	hgsc.bcm.edu	37	chr4	159753052	159753054	+	In_Frame_Del	DEL	ATG	ATG	-																															atgtcaacatgttaggggaaAtgatgtttggctcagttgcc																										TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	ATG	ATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr4:159753052_159753054delATG	ENST00000264433.6	+	4	496_498	c.421_423delATG	c.(421-423)atgdel	p.M142del	FNIP2_ENST00000379346.3_In_Frame_Del_p.M165del	NM_020840.1	NP_065891.1	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	142					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)		GTTAGGGGAAATGATGTTTGGCT	0.409																																					p.140_141del		Atlas-Indel,Pindel	.											.	FNIP2	90	.	0			c.420_422del						PASS	.																																			SO:0001651	inframe_deletion	57600	exon4			.	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.421_423delATG	chr4.hg19:g.159753055_159753057delATG	ENSP00000264433:p.Met142del	135.0	0.0	0		151.0	60.0	0.397351	NM_020840	Q05DC3|Q96I31|Q9H994	In_Frame_Del	DEL	ENST00000264433.6	hg19	CCDS47155.1																																																																																			.	.	.	none		0.409	FNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366602.1	NM_020840		-	159753054	ATG	-	159753052	7	5	270	1	0	1	0	1	0	0	0	0	5983	101	4	0	435	0	FNIP2	4	159753052	In_Frame_Del	DEL	ATG	TCGA-UZ-A9Q1-01A-11D-A42J-10	179994	159753052	31401224	17	17026											
SGTB	54557	hgsc.bcm.edu	37	chr5	65016544	65016544	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagatgcataccttccaaacTttcttgttcatccgaggtgt	9	14	7	11	1	2	1	1	0	1	1	4	2	4	1	3	1	3	2	3	1	2	5			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr5:65016544T>C	ENST00000381007.4	-	2	326	c.91A>G	c.(91-93)Agt>Ggt	p.S31G	NLN_ENST00000502464.1_5'Flank|NLN_ENST00000380985.5_5'Flank	NM_019072.2	NP_061945.1	Q96EQ0	SGTB_HUMAN	small glutamine-rich tetratricopeptide repeat (TPR)-containing, beta	31										large_intestine(3)|lung(3)|skin(3)	9		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Ovarian(174;0.0545)|Breast(144;0.174)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0657)|Lung(70;0.00487)		CCTTCCAAACTTTCTTGTTCA	0.353																																					p.S31G		Atlas-SNP	.											.	SGTB	22	.	0			c.A91G						PASS	.						105	106	105					5																	65016544		2203	4300	6503	SO:0001583	missense	54557	exon2			CCAAACTTTCTTG	AK096321	CCDS3988.1	5q12.3	2013-01-10			ENSG00000197860	ENSG00000197860		"Tetratricopeptide (TTC) repeat domain containing"	23567	protein-coding gene	gene with protein product						12477932	Standard	XM_005248548		Approved	Sgt2, FLJ39002	uc003jud.3	Q96EQ0	OTTHUMG00000097801	ENST00000381007.4:c.91A>G	chr5.hg19:g.65016544T>C	ENSP00000370395:p.Ser31Gly	73.0	0.0	.		103.0	49.0	.	NM_019072		Missense_Mutation	SNP	ENST00000381007.4	hg19	CCDS3988.1	.	.	.	.	.	.	.	.	.	.	T	13.30	2.197350	0.38806	.	.	ENSG00000197860	ENST00000381007;ENST00000506816	T;T	0.68181	-0.31;-0.23	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.66713	0.2817	M	0.62723	1.935	0.80722	D	1	B	0.27679	0.185	B	0.32342	0.144	T	0.67393	-0.5682	10	0.56958	D	0.05	-12.5719	14.3443	0.66649	0.0:0.0:0.0:1.0	.	31	Q96EQ0	SGTB_HUMAN	G	31	ENSP00000370395:S31G;ENSP00000421447:S31G	ENSP00000370395:S31G	S	-	1	0	SGTB	65052300	1.000000	0.71417	1.000000	0.80357	0.490000	0.33462	6.128000	0.71650	2.020000	0.59435	0.455000	0.32223	AGT	.	.	.	none		0.353	SGTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215057.2	NM_019072		C	65016544	T	C	65016544	3	2	270	1	0	0	0	0	1	0	0	0	14239	1609	56	3	863	3	SGTB	5	65016544	Missense_Mutation	SNP	T	TCGA-UZ-A9Q1-01A-11D-A42J-10		65016544	115898716	18	17027											
OTP	23440	hgsc.bcm.edu	37	chr5	76926470	76926470	+	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	tcgttggcgtggaaagagcaCaggctgtcgcccatggcggc	7	7	16	11	4	0	1	0	0	0	1	2	2	0	2	1	5	1	3	1	5	1	1			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr5:76926470C>T	ENST00000306422.3	-	3	1735	c.597G>A	c.(595-597)ctG>ctA	p.L199L		NM_032109.2	NP_115485.1	Q5XKR4	OTP_HUMAN	orthopedia homeobox	199					forebrain neuron differentiation (GO:0021879)|hypothalamus cell differentiation (GO:0021979)|neurohypophysis development (GO:0021985)|positive regulation of neuroblast proliferation (GO:0002052)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|pancreas(1)	13		all_lung(232;0.00051)|Lung NSC(167;0.000601)|Ovarian(174;0.0105)|Prostate(461;0.214)		OV - Ovarian serous cystadenocarcinoma(54;9.04e-51)|Epithelial(54;1.62e-45)|all cancers(79;4.4e-41)		GGAAAGAGCACAGGCTGTCGC	0.741																																					p.L199L		Atlas-SNP	.											.	OTP	29	.	0			c.G597A						PASS	.						4	5	5					5																	76926470		1672	3596	5268	SO:0001819	synonymous_variant	23440	exon3			AGAGCACAGGCTG		CCDS4039.1	5q14.1	2011-06-20	2007-02-15		ENSG00000171540	ENSG00000171540		"Homeoboxes / PRD class"	8518	protein-coding gene	gene with protein product		604529	"orthopedia homolog (Drosophila)"			10458915	Standard	NM_032109		Approved		uc003kfg.3	Q5XKR4	OTTHUMG00000102171	ENST00000306422.3:c.597G>A	chr5.hg19:g.76926470C>T		46.0	0.0	.		61.0	23.0	.	NM_032109		Silent	SNP	ENST00000306422.3	hg19	CCDS4039.1																																																																																			.	.	.	none		0.741	OTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220016.2			T	76926470	C	T	76926470	2	4	270	1	0	0	0	0	0	0	0	1	11317	465	17	2		2	OTP	5	76926470	Silent	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10	11909926	76926470	103988790	19	17028											
ZFYVE16	9765	hgsc.bcm.edu	37	chr5	79743873	79743873	+	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	cacagtggatcattcccattCtactacagtggaaaagccaa	14	9	7	11	0	2	0	1	0	1	0	3	2	3	2	2	2	3	0	2	2	5	4			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr5:79743873C>T	ENST00000338008.5	+	7	2933	c.2753C>T	c.(2752-2754)tCt>tTt	p.S918F	ZFYVE16_ENST00000505560.1_Missense_Mutation_p.S918F|ZFYVE16_ENST00000510158.1_Missense_Mutation_p.S918F	NM_001284236.1|NM_014733.3	NP_001271165.1|NP_055548	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	918					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)		CATTCCCATTCTACTACAGTG	0.323																																					p.S918F	Melanoma(150;1452 1854 16018 17851 37292)	Atlas-SNP	.											.	ZFYVE16	100	.	0			c.C2753T						PASS	.						71	70	70					5																	79743873		2203	4300	6503	SO:0001583	missense	9765	exon8			CCCATTCTACTAC	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.2753C>T	chr5.hg19:g.79743873C>T	ENSP00000337159:p.Ser918Phe	117.0	0.0	.		116.0	43.0	.	NM_001105251	O15023|Q5H9U2|Q7LAU7|Q86T69|Q8N5L3|Q8NEK3	Missense_Mutation	SNP	ENST00000338008.5	hg19	CCDS4050.1	.	.	.	.	.	.	.	.	.	.	C	12.75	2.031051	0.35797	.	.	ENSG00000039319	ENST00000338008;ENST00000510158;ENST00000505560	T;T;T	0.40476	1.03;1.03;1.03	5.43	4.56	0.56223	.	0.218052	0.32901	N	0.005502	T	0.38746	0.1052	M	0.62723	1.935	0.24063	N	0.996004	B	0.15473	0.013	B	0.10450	0.005	T	0.39881	-0.9592	10	0.66056	D	0.02	-5.2169	7.9596	0.30064	0.0:0.7529:0.161:0.0861	.	918	Q7Z3T8	ZFY16_HUMAN	F	918	ENSP00000337159:S918F;ENSP00000423663:S918F;ENSP00000426848:S918F	ENSP00000337159:S918F	S	+	2	0	ZFYVE16	79779629	0.001000	0.12720	0.770000	0.31555	0.998000	0.95712	0.510000	0.22723	1.440000	0.47531	0.650000	0.86243	TCT	.	.	.	none		0.323	ZFYVE16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226982.2	NM_014733		T	79743873	C	T	79743873	3	4	270	1	0	0	0	0	1	0	0	0	17676	913	32	2	2775	2	ZFYVE16	5	79743873	Missense_Mutation	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10	2817403	79743873	101171387	20	17029											
MRS2	57380	hgsc.bcm.edu	37	chr6	24423170	24423170	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtgttctcttttaggaccaTagaattttttggctgattac	8	19	8	6	0	1	2	0	1	1	1	2	3	1	3	1	2	1	2	1	2	4	8			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr6:24423170T>C	ENST00000378386.3	+	10	1206	c.1113T>C	c.(1111-1113)caT>caC	p.H371H	MRS2_ENST00000378353.1_Silent_p.H371H|MRS2_ENST00000274747.7_3'UTR|MRS2_ENST00000543597.1_Silent_p.H80H|MRS2_ENST00000443868.2_Silent_p.H374H|MRS2_ENST00000535061.1_Silent_p.H321H	NM_020662.2	NP_065713.1	Q9HD23	MRS2_HUMAN	MRS2 magnesium transporter	371						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						TTTAGGACCATAGAATTTTTT	0.443																																					p.H371H		Atlas-SNP	.											.	MRS2	31	.	0			c.T1113C						PASS	.						146	136	139					6																	24423170		2203	4300	6503	SO:0001819	synonymous_variant	57380	exon10			GGACCATAGAATT	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.1113T>C	chr6.hg19:g.24423170T>C		54.0	0.0	.		47.0	16.0	.	NM_020662	A8K4U3|B3KNN2|B4DQL2|Q5T3Y1|Q6NTG4|Q96KF8|Q9BVP1	Silent	SNP	ENST00000378386.3	hg19	CCDS4552.1																																																																																			.	.	.	none		0.443	MRS2-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040002.1			C	24423170	T	C	24423170	2	2	270	1	0	0	0	0	0	0	0	1	9858	1403	49	3		3	MRS2	6	24423170	Silent	SNP	T	TCGA-UZ-A9Q1-01A-11D-A42J-10		24423170	146691897	21	17030											
PCMT1	5110	hgsc.bcm.edu	37	chr6	150070882	150070883	+	5'UTR	INS	-	-	GCGGCA																															gatgccgggagcgcgcagtgINSgcggcagcggcggcgacggc																										TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr6:150070882_150070883insGCGGCA	ENST00000367380.5	+	0	52_53				PCMT1_ENST00000367378.1_In_Frame_Ins_p.9_10insGS|PCMT1_ENST00000464889.1_In_Frame_Ins_p.9_10insGS|NUP43_ENST00000463048.3_5'Flank|PCMT1_ENST00000367384.2_In_Frame_Ins_p.9_10insGS|PCMT1_ENST00000544496.1_5'Flank	NM_001252049.1|NM_001252050.1|NM_001252051.1|NM_001252052.1|NM_005389.2	NP_001238978.1|NP_001238979.1|NP_001238980.1|NP_001238981.1|NP_005380.2	P22061	PIMT_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase						protein methylation (GO:0006479)|protein repair (GO:0030091)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			kidney(1)|large_intestine(2)|lung(4)|ovary(1)	8		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.221)	OV - Ovarian serous cystadenocarcinoma(155;5.63e-13)|GBM - Glioblastoma multiforme(68;0.207)		AGCGCgcagtggcggcagcggc	0.743																																					p.G7delinsGGS		Atlas-Indel,Pindel	.											.	PCMT1	27	.	0			c.19_20insGCGGCA						PASS	.																																			SO:0001623	5_prime_UTR_variant	5110	exon1			.		CCDS5219.1, CCDS5219.2, CCDS59041.1, CCDS75533.1, CCDS75534.1	6q22.3-q24	2008-02-05			ENSG00000120265	ENSG00000120265	2.1.1.77		8728	protein-coding gene	gene with protein product		176851				1478665, 10343128	Standard	NM_005389		Approved		uc003qne.3	P22061	OTTHUMG00000015794	ENST00000367380.5:c.-155->GCGGCA	chr6.hg19:g.150070883_150070888dupGCGGCA		28.0	0.0	0		47.0	13.0	0.276596	NM_001252050	A8K109|J3KP72|Q14661|Q16556|Q5VYC1|Q5VYC2|Q93061|Q96II9|Q99625|Q9BQV7|Q9BQV8|Q9NP03	In_Frame_Ins	INS	ENST00000367380.5	hg19																																																																																				.	.	.	none		0.743	PCMT1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				GCGGCA	150070883	-	GCGGCA	150070882	6	5	270	0	1	1	1	0	0	0	0	0	11592	1348	47	0		0	PCMT1	6	150070882	5'UTR	INS	-	TCGA-UZ-A9Q1-01A-11D-A42J-10	125647712	150070882	21044185	22	17031											
OPRM1	4988	hgsc.bcm.edu	37	chr6	154360579	154360579	+	De_novo_Start_OutOfFrame	SNP	T	T	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	ctgtaagaaacagcaggagcTgtggcagcggcgaaaggaag	14	4	16	7	2	0	1	0	0	0	1	0	4	0	3	0	4	4	4	0	4	4	1			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr6:154360579T>A	ENST00000330432.7	+	0	137				OPRM1_ENST00000452687.2_5'Flank|OPRM1_ENST00000360422.4_De_novo_Start_OutOfFrame|OPRM1_ENST00000414028.2_5'Flank|OPRM1_ENST00000435918.2_5'Flank|OPRM1_ENST00000428397.2_De_novo_Start_OutOfFrame|OPRM1_ENST00000434900.2_Missense_Mutation_p.L60Q|OPRM1_ENST00000520708.1_Intron|OPRM1_ENST00000337049.4_5'Flank|OPRM1_ENST00000523520.1_3'UTR|OPRM1_ENST00000518759.1_Intron|OPRM1_ENST00000229768.5_5'Flank|OPRM1_ENST00000524163.1_5'Flank|OPRM1_ENST00000419506.2_5'Flank	NM_000914.3	NP_000905.3	P35372	OPRM_HUMAN	opioid receptor, mu 1						adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral response to ethanol (GO:0048149)|calcium ion transmembrane transport (GO:0070588)|cellular response to stress (GO:0033554)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|locomotory behavior (GO:0007626)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of Wnt protein secretion (GO:0061358)|neuropeptide signaling pathway (GO:0007218)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neurogenesis (GO:0050769)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-endorphin receptor activity (GO:0004979)|G-protein alpha-subunit binding (GO:0001965)|G-protein coupled receptor activity (GO:0004930)|morphine receptor activity (GO:0038047)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	33		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	Alfentanil(DB00802)|Alvimopan(DB06274)|Amitriptyline(DB00321)|Anileridine(DB00913)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Diphenoxylate(DB01081)|Ethylmorphine(DB01466)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levallorphan(DB00504)|Levomethadyl Acetate(DB01227)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Methadyl Acetate(DB01433)|Methylnaltrexone(DB06800)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Ondansetron(DB00904)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Pentazocine(DB00652)|Pethidine(DB00454)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	CAGCAGGAGCTGTGGCAGCGG	0.617																																					p.L60Q		Atlas-SNP	.											.	OPRM1	241	.	0			c.T179A						PASS	.						27	40	36					6																	154360579		692	1591	2283			4988	exon3			AGGAGCTGTGGCA	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.-101T>A	chr6.hg19:g.154360579T>A		68.0	0.0	.		86.0	33.0	.	NM_001145279	B0FXJ1|B2R9S7|B8Q1L7|B8Q1L8|B8Q1L9|E7EWZ3|G8XRH6|G8XRH8|Q12930|Q4VWM1|Q4VWM2|Q4VWM3|Q4VWM4|Q4VWM6|Q4VWX6|Q5TDA1|Q6UPP1|Q6UQ80|Q7Z2D8|Q86V80|Q8IWW3|Q8IWW4|Q9UCZ4|Q9UN57	Missense_Mutation	SNP	ENST00000330432.7	hg19	CCDS55070.1	.	.	.	.	.	.	.	.	.	.	T	13.40	2.225525	0.39300	.	.	ENSG00000112038	ENST00000520282;ENST00000434900	T;T	0.74632	3.71;-0.86	5.53	-5.34	0.02705	.	6.095000	0.00166	N	0.000003	T	0.28067	0.0692	N	0.08118	0	0.21020	N	0.999808	B	0.06786	0.001	B	0.08055	0.003	T	0.28650	-1.0037	10	0.72032	D	0.01	.	2.5601	0.04770	0.2319:0.4117:0.1184:0.2379	.	60	P35372-10	.	Q	15;60	ENSP00000430247:L15Q;ENSP00000394624:L60Q	ENSP00000394624:L60Q	L	+	2	0	OPRM1	154402272	0.000000	0.05858	0.005000	0.12908	0.091000	0.18340	-1.532000	0.02217	-0.475000	0.06852	0.528000	0.53228	CTG	.	.	.	none		0.617	OPRM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042786.2	NM_000914		A	154360579	T	A	154360579	1	1	270	1	0	1	0	0	0	0	0	0	10894	1580	55	5		5	OPRM1	6	154360579	De_novo_Start_OutOfFrame	SNP	T	TCGA-UZ-A9Q1-01A-11D-A42J-10	4289697	154360579	16754488	23	17032											
CNKSR3	154043	hgsc.bcm.edu	37	chr6	154732219	154732219	+	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	gactctgaacccttaggaccAggcaatggttgtttgcactt	9	12	10	10	0	1	1	0	1	1	0	1	3	1	2	2	3	2	4	2	3	3	4			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr6:154732219A>C	ENST00000607772.1	-	11	1672	c.1128T>G	c.(1126-1128)ccT>ccG	p.P376P	CNKSR3_ENST00000479339.1_Silent_p.P296P|CNKSR3_ENST00000433165.2_Silent_p.P201P	NM_173515.2	NP_775786.2	Q6P9H4	CNKR3_HUMAN	CNKSR family member 3	376	DUF1170.				negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)	cytoplasm (GO:0005737)|membrane (GO:0016020)				breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	15		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;5.03e-11)|BRCA - Breast invasive adenocarcinoma(81;0.00627)		CCTTAGGACCAGGCAATGGTT	0.463																																					p.P376P		Atlas-SNP	.											.	CNKSR3	56	.	0			c.T1128G						PASS	.						95	95	95					6																	154732219		2203	4300	6503	SO:0001819	synonymous_variant	154043	exon11			AGGACCAGGCAAT	AK055911	CCDS5246.1	6q25.2	2013-01-10	2005-04-11	2005-04-11	ENSG00000153721	ENSG00000153721		"Sterile alpha motif (SAM) domain containing"	23034	protein-coding gene	gene with protein product			"membrane associated guanylate kinase interacting protein-like 1"	MAGI1			Standard	NM_173515		Approved	FLJ31349		Q6P9H4	OTTHUMG00000015873	ENST00000607772.1:c.1128T>G	chr6.hg19:g.154732219A>C		78.0	0.0	.		119.0	48.0	.	NM_173515	Q5SGD5|Q96N65	Silent	SNP	ENST00000607772.1	hg19	CCDS5246.1																																																																																			.	.	.	none		0.463	CNKSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042792.2	NM_173515		C	154732219	A	C	154732219	2	2	270	1	0	0	0	0	0	0	0	1	3610	175	7	5		5	CNKSR3	6	154732219	Silent	SNP	A	TCGA-UZ-A9Q1-01A-11D-A42J-10	371640	154732219	16382848	24	17033											
FGFR1OP	11116	hgsc.bcm.edu	37	chr6	167438317	167438317	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtctggcctcgctctcggAtgcaccccccttaaaaagtg	9	9	9	14	2	2	0	0	0	2	0	4	1	2	1	4	2	1	2	4	2	4	1			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr6:167438317A>G	ENST00000366847.4	+	9	1085	c.854A>G	c.(853-855)gAt>gGt	p.D285G	FGFR1OP_ENST00000349556.4_Missense_Mutation_p.D265G|RP11-517H2.6_ENST00000609590.1_RNA	NM_007045.2	NP_008976.1	O95684	FR1OP_HUMAN	FGFR1 oncogene partner	285					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|mitotic cell cycle (GO:0000278)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein tyrosine kinase activity (GO:0061099)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|protein tyrosine kinase inhibitor activity (GO:0030292)			large_intestine(2)|ovary(1)|stomach(1)	4		Breast(66;1.48e-05)|Ovarian(120;0.0607)		OV - Ovarian serous cystadenocarcinoma(33;1.73e-19)|BRCA - Breast invasive adenocarcinoma(81;5.1e-06)|GBM - Glioblastoma multiforme(31;0.00231)		TCGCTCTCGGATGCACCCCCC	0.502			T	FGFR1	"MPD, NHL"																																p.D285G		Atlas-SNP	.		Dom	yes		6	6q27	11116	FGFR1 oncogene partner (FOP)		L	.	FGFR1OP	24	.	0			c.A854G						PASS	.						132	146	141					6																	167438317		2203	4300	6503	SO:0001583	missense	11116	exon9			TCTCGGATGCACC	Y18046	CCDS5296.1, CCDS5297.1, CCDS75550.1	6q27	2008-02-05			ENSG00000213066	ENSG00000213066			17012	protein-coding gene	gene with protein product		605392				9949182, 10373756	Standard	NM_007045		Approved	FOP	uc003qvj.3	O95684	OTTHUMG00000016011	ENST00000366847.4:c.854A>G	chr6.hg19:g.167438317A>G	ENSP00000355812:p.Asp285Gly	243.0	1.0	.		285.0	119.0	.	NM_007045	A8K1D1|B2R705|Q49AI0|Q5R3F6|Q96EW1	Missense_Mutation	SNP	ENST00000366847.4	hg19	CCDS5296.1	.	.	.	.	.	.	.	.	.	.	A	13.53	2.266096	0.40095	.	.	ENSG00000213066	ENST00000366847;ENST00000420493;ENST00000349556	T;T	0.31247	1.5;1.5	5.3	4.11	0.48088	.	0.629098	0.17100	N	0.187033	T	0.32823	0.0842	M	0.65975	2.015	0.09310	N	1	D;D;D	0.67145	0.996;0.984;0.973	P;P;P	0.62649	0.905;0.857;0.767	T	0.13899	-1.0492	10	0.41790	T	0.15	-15.1292	10.3254	0.43790	0.6821:0.3179:0.0:0.0	.	238;265;285	E7ET71;O95684-2;O95684	.;.;FR1OP_HUMAN	G	285;238;265	ENSP00000355812:D285G;ENSP00000230248:D265G	ENSP00000230248:D265G	D	+	2	0	FGFR1OP	167358307	0.945000	0.32115	0.000000	0.03702	0.262000	0.26303	3.526000	0.53509	0.813000	0.34350	0.443000	0.29094	GAT	.	.	.	none		0.502	FGFR1OP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043099.2	NM_007045		G	167438317	A	G	167438317	3	3	270	1	0	0	0	0	1	0	0	0	5871	333	12	3	888	3	FGFR1OP	6	167438317	Missense_Mutation	SNP	A	TCGA-UZ-A9Q1-01A-11D-A42J-10	12706098	167438317	3676750	25	17034											
AEBP1	165	hgsc.bcm.edu	37	chr7	44150559	44150559	+	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	acacccgtgctgagtgagctCccagagccggtggtggctcg	6	7	15	13	3	0	3	0	2	0	1	2	3	1	3	3	3	3	3	3	3	0	0			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr7:44150559C>A	ENST00000223357.3	+	13	1838	c.1533C>A	c.(1531-1533)ctC>ctA	p.L511L	MIR4649_ENST00000582839.1_RNA|AEBP1_ENST00000450684.2_Silent_p.L54L	NM_001129.3	NP_001120.3	Q8IUX7	AEBP1_HUMAN	AE binding protein 1	511	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.|Interaction with MAPK1 and MAPK3. {ECO:0000250}.|Required for DNA-binding and interaction with NFKBIA. {ECO:0000250}.				cell adhesion (GO:0007155)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(13)|upper_aerodigestive_tract(2)	33						TGAGTGAGCTCCCAGAGCCGG	0.637																																					p.L511L		Atlas-SNP	.											.	AEBP1	102	.	0			c.C1533A						PASS	.						93	85	87					7																	44150559		2203	4300	6503	SO:0001819	synonymous_variant	165	exon13			TGAGCTCCCAGAG	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.1533C>A	chr7.hg19:g.44150559C>A		88.0	0.0	.		134.0	80.0	.	NM_001129	Q14113|Q59ER7|Q6ZSC7|Q7KZ79	Silent	SNP	ENST00000223357.3	hg19	CCDS5476.1																																																																																			.	.	.	none		0.637	AEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250993.2	NM_001129		A	44150559	C	A	44150559	2	1	270	1	0	0	0	0	0	0	0	1	349	842	30	4		4	AEBP1	7	44150559	Silent	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10		44150559	114988104	26	17035											
PTPN12	5782	hgsc.bcm.edu	37	chr7	77256523	77256523	+	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	tcaaacaaagtttcagttacTccaccagaagaatcccagaa	17	8	5	11	0	2	3	2	0	0	3	4	3	4	3	3	0	2	2	3	0	6	2			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr7:77256523T>A	ENST00000248594.6	+	13	1799	c.1527T>A	c.(1525-1527)acT>acA	p.T509T	PTPN12_ENST00000415482.2_Silent_p.T390T|PTPN12_ENST00000435495.2_Silent_p.T379T	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	509					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						TTTCAGTTACTCCACCAGAAG	0.438																																					p.T509T		Atlas-SNP	.											.	PTPN12	83	.	0			c.T1527A						PASS	.						71	67	68					7																	77256523		2203	4300	6503	SO:0001819	synonymous_variant	5782	exon13			AGTTACTCCACCA		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.1527T>A	chr7.hg19:g.77256523T>A		103.0	0.0	.		217.0	124.0	.	NM_002835	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	Silent	SNP	ENST00000248594.6	hg19	CCDS5592.1																																																																																			.	.	.	none		0.438	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3			A	77256523	T	A	77256523	2	1	270	1	0	0	0	0	0	0	0	1	12792	1538	54	5		5	PTPN12	7	77256523	Silent	SNP	T	TCGA-UZ-A9Q1-01A-11D-A42J-10	33105964	77256523	81882140	27	17036											
STEAP4	79689	hgsc.bcm.edu	37	chr7	87913338	87913349	+	In_Frame_Del	DEL	TGTGGATTGCTA	TGTGGATTGCTA	-																															gagaaaatcataatgctctcTgtggattgctatgattatga																								rs149348409	byFrequency	TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	TGTGGATTGCTA	TGTGGATTGCTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr7:87913338_87913349delTGTGGATTGCTA	ENST00000380079.4	-	2	337_348	c.236_247delTAGCAATCCACA	c.(235-249)atagcaatccacaga>aga	p.IAIH79del	AC003991.3_ENST00000595121.1_RNA|AC003991.3_ENST00000434733.1_RNA|AC003991.3_ENST00000447758.1_RNA|STEAP4_ENST00000414498.1_In_Frame_Del_p.IAIH79del|STEAP4_ENST00000301959.5_In_Frame_Del_p.IAIH79del|AC003991.3_ENST00000600908.1_RNA	NM_001205315.1|NM_024636.3	NP_001192244.1|NP_078912.2	Q687X5	STEA4_HUMAN	STEAP family member 4	79					copper ion import (GO:0015677)|fat cell differentiation (GO:0045444)|ferric iron import into cell (GO:0097461)|iron ion homeostasis (GO:0055072)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cupric reductase activity (GO:0008823)|ferric-chelate reductase (NADPH) activity (GO:0052851)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(3)	15	Esophageal squamous(14;0.00802)					TAATGCTCTCTGTGGATTGCTATGATTATGAT	0.415																																					p.79_83del		Pindel	.											.	STEAP4	54	.	0			c.237_248del						PASS	.																																			SO:0001651	inframe_deletion	79689	exon3			.	AK026806	CCDS43611.1, CCDS56494.1	7q21.13	2014-01-28	2005-06-15	2005-06-15	ENSG00000127954	ENSG00000127954			21923	protein-coding gene	gene with protein product		611098	"tumor necrosis factor, alpha-induced protein 9"	TNFAIP9		11443137, 15897894	Standard	NM_024636		Approved	FLJ23153, TIARP, STAMP2	uc003ujs.3	Q687X5	OTTHUMG00000153853	ENST00000380079.4:c.236_247delTAGCAATCCACA	chr7.hg19:g.87913338_87913349delTGTGGATTGCTA	ENSP00000369419:p.Ile79_His82del	80.0	0.0	.		131.0	18.0	0.137	NM_001205315	Q658Q9|Q687X4|Q8WWB0|Q9H5R1	In_Frame_Del	DEL	ENST00000380079.4	hg19	CCDS43611.1																																																																																			.	.	.	none		0.415	STEAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332712.4	NM_024636		-	87913349	TGTGGATTGCTA	-	87913338	7	5	270	1	0	1	0	1	0	0	0	0	15292	1588	55	0	1148	0	STEAP4	7	87913338	In_Frame_Del	DEL	TGTGGATTGCTA	TCGA-UZ-A9Q1-01A-11D-A42J-10	10656815	87913338	71225325	28	17037											
CCDC132	55610	hgsc.bcm.edu	37	chr7	92885845	92885845	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctaaaaaagtggcagatttaAtccttgaaaaacagcctgct	16	10	7	8	0	0	2	0	1	0	1	1	2	1	2	2	1	3	2	2	1	6	4			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr7:92885845A>G	ENST00000305866.5	+	5	450	c.322A>G	c.(322-324)Atc>Gtc	p.I108V	CCDC132_ENST00000251739.5_Missense_Mutation_p.I108V|CCDC132_ENST00000541136.1_5'UTR|CCDC132_ENST00000317751.6_5'UTR|CCDC132_ENST00000535481.1_Intron|CCDC132_ENST00000544910.1_Missense_Mutation_p.I78V	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	108						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)			GGCAGATTTAATCCTTGAAAA	0.254																																					p.I108V		Atlas-SNP	.											.	CCDC132	136	.	0			c.A322G						PASS	.						52	58	56					7																	92885845		2199	4281	6480	SO:0001583	missense	55610	exon5			GATTTAATCCTTG	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.322A>G	chr7.hg19:g.92885845A>G	ENSP00000307666:p.Ile108Val	58.0	0.0	.		93.0	20.0	.	NM_024553	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	hg19	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	A	15.49	2.847997	0.51164	.	.	ENSG00000004766	ENST00000251739;ENST00000305866;ENST00000544910;ENST00000458530	.	.	.	5.52	5.52	0.82312	Vacuolar protein sorting-associated protein 54 (1);	0.000000	0.85682	D	0.000000	T	0.56848	0.2013	N	0.25426	0.745	0.80722	D	1	P;P;P	0.48407	0.65;0.699;0.91	P;P;B	0.58130	0.743;0.833;0.377	T	0.50617	-0.8807	9	0.06365	T	0.9	-9.0769	15.9527	0.79855	1.0:0.0:0.0:0.0	.	78;108;108	F5H5U7;Q96JG6;Q96JG6-2	.;CC132_HUMAN;.	V	108;108;78;107	.	ENSP00000251739:I108V	I	+	1	0	CCDC132	92723781	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.183000	0.89700	2.234000	0.73211	0.460000	0.39030	ATC	.	.	.	none		0.254	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667		G	92885845	A	G	92885845	3	3	270	1	0	0	0	0	1	0	0	0	2769	101	4	3	340	3	CCDC132	7	92885845	Missense_Mutation	SNP	A	TCGA-UZ-A9Q1-01A-11D-A42J-10	4972507	92885845	66252818	29	17038											
TMUB1	83590	hgsc.bcm.edu	37	chr7	150779559	150779559	+	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	ccccgccctcagcggtgtgcGttgagacccaggcaagggcc	6	5	14	16	3	1	1	1	1	0	1	1	2	1	1	5	3	2	2	5	3	1	1			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr7:150779559G>C	ENST00000392818.3	-	2	449	c.92C>G	c.(91-93)aCg>aGg	p.T31R	FASTK_ENST00000540185.1_5'Flank|FASTK_ENST00000482571.1_5'Flank|FASTK_ENST00000353841.2_5'Flank|FASTK_ENST00000297532.6_5'Flank|FASTK_ENST00000489884.1_5'Flank|TMUB1_ENST00000476627.1_Missense_Mutation_p.T31R|TMUB1_ENST00000462940.1_Missense_Mutation_p.T31R|TMUB1_ENST00000482202.1_Missense_Mutation_p.T31R|TMUB1_ENST00000297533.4_Missense_Mutation_p.T31R	NM_031434.3	NP_113622.1	Q9BVT8	TMUB1_HUMAN	transmembrane and ubiquitin-like domain containing 1	31						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				endometrium(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(82;0.00989)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AGCGGTGTGCGTTGAGACCCA	0.662																																					p.T31R		Atlas-SNP	.											.	TMUB1	7	.	0			c.C92G						PASS	.						62	64	63					7																	150779559		2203	4300	6503	SO:0001583	missense	83590	exon2			GTGTGCGTTGAGA	BC000936	CCDS5920.1	7q36.1	2006-06-27	2006-06-27	2006-06-27	ENSG00000164897	ENSG00000164897			21709	protein-coding gene	gene with protein product		614792	"chromosome 7 open reading frame 21"	C7orf21			Standard	NM_001136044		Approved	SB144	uc003wjd.3	Q9BVT8	OTTHUMG00000158621	ENST00000392818.3:c.92C>G	chr7.hg19:g.150779559G>C	ENSP00000376565:p.Thr31Arg	131.0	0.0	.		201.0	118.0	.	NM_031434	D3DX06|Q53AQ2	Missense_Mutation	SNP	ENST00000392818.3	hg19	CCDS5920.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.129878	0.77549	.	.	ENSG00000164897	ENST00000297533;ENST00000392818;ENST00000462940;ENST00000482202;ENST00000476627;ENST00000488752;ENST00000492838	T;T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91;0.91	4.83	3.95	0.45737	.	0.067439	0.64402	D	0.000018	T	0.58235	0.2108	M	0.74467	2.265	0.51767	D	0.999931	D	0.63880	0.993	P	0.60236	0.871	T	0.62215	-0.6901	10	0.87932	D	0	.	10.8464	0.46744	0.0934:0.0:0.9066:0.0	.	31	Q9BVT8	TMUB1_HUMAN	R	31	ENSP00000297533:T31R;ENSP00000376565:T31R;ENSP00000417519:T31R;ENSP00000418709:T31R;ENSP00000419214:T31R;ENSP00000420692:T31R;ENSP00000420516:T31R	ENSP00000297533:T31R	T	-	2	0	TMUB1	150410492	1.000000	0.71417	0.983000	0.44433	0.969000	0.65631	6.693000	0.74582	1.035000	0.39972	0.305000	0.20034	ACG	.	.	.	none		0.662	TMUB1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351485.1	NM_031434		C	150779559	G	C	150779559	3	2	270	1	0	0	0	0	1	0	0	0	16276	1145	40	4	656	4	TMUB1	7	150779559	Missense_Mutation	SNP	G	TCGA-UZ-A9Q1-01A-11D-A42J-10	57893714	150779559	8359104	30	17039											
MLL3	58508	hgsc.bcm.edu	37	chr7	151853289	151853289	+	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	atttggaggctataatcataCcttcatggctcactaacact	12	13	6	10	0	3	0	3	0	0	0	3	1	3	1	1	3	2	2	1	3	4	6			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr7:151853289C>T	ENST00000262189.6	-	45	12031		c.e45+1		KMT2C_ENST00000485241.1_5'Flank|KMT2C_ENST00000355193.2_Splice_Site	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C						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)										TATAATCATACCTTCATGGCT	0.438																																					.		Atlas-SNP	.											.	MLL3	1564	.	0			c.11812+1G>A						PASS	.						137	139	138					7																	151853289		2203	4300	6503	SO:0001630	splice_region_variant	58508	exon46			ATCATACCTTCAT	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.11812+1G>A	chr7.hg19:g.151853289C>T		68.0	0.0	.		81.0	52.0	.	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Splice_Site	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	19.17	3.775125	0.70107	.	.	ENSG00000055609	ENST00000360104;ENST00000262189;ENST00000355193;ENST00000424877;ENST00000418061	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.077	0.89430	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MLL3	151484222	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	4.000000	0.57039	2.717000	0.92951	0.655000	0.94253	.	.	.	.	none		0.438	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		Intron	T	151853289	C	T	151853289	5	4	270	1	0	0	0	0	0	0	1	0	9629	521	18	2	2982	2	MLL3	7	151853289	Splice_Site	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10	1073730	151853289	7285374	31	17040											
SORBS3	10174	hgsc.bcm.edu	37	chr8	22432205	22432205	+	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	tcccggaggacccagaaattCggaacgttccctggaaatta	12	8	10	11	3	0	1	0	0	0	1	3	5	2	5	3	4	1	1	3	4	4	3			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr8:22432205C>T	ENST00000240123.7	+	21	2363	c.1980C>T	c.(1978-1980)ttC>ttT	p.F660F	SORBS3_ENST00000428103.1_Silent_p.F318F	NM_005775.4	NP_005766.3	O60504	VINEX_HUMAN	sorbin and SH3 domain containing 3	660	Binds to SOS.|SH3 3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|muscle contraction (GO:0006936)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cytoskeleton organization (GO:0051495)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of stress fiber assembly (GO:0051496)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(9)	18		Prostate(55;0.0421)|Breast(100;0.102)		BRCA - Breast invasive adenocarcinoma(99;0.00566)|Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)		CCCAGAAATTCGGAACGTTCC	0.607											OREG0018613	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F660F		Atlas-SNP	.											.	SORBS3	45	.	0			c.C1980T						PASS	.						141	137	138					8																	22432205		2203	4300	6503	SO:0001819	synonymous_variant	10174	exon21			GAAATTCGGAACG		CCDS6031.1	8p21.3	2008-02-05			ENSG00000120896	ENSG00000120896			30907	protein-coding gene	gene with protein product		610795				9885244, 12510380	Standard	NM_001018003		Approved	SCAM-1, SH3D4, vinexin	uc003xbv.3	O60504	OTTHUMG00000131728	ENST00000240123.7:c.1980C>T	chr8.hg19:g.22432205C>T		83.0	0.0	.	756	115.0	47.0	.	NM_005775	Q5BJE4|Q6NX54|Q96FY4|Q9UQE4	Silent	SNP	ENST00000240123.7	hg19	CCDS6031.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.883|9.883	1.202193|1.202193	0.22121|0.22121	.|.	.|.	ENSG00000120896|ENSG00000120896	ENST00000519127|ENST00000517962;ENST00000520207	.|.	.|.	.|.	5.4|5.4	-0.357|-0.357	0.12579|0.12579	.|.	.|.	.|.	.|.	.|.	T|T	0.55970|0.55970	0.1954|0.1954	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.50955|0.50955	-0.8766|-0.8766	5|4	0.87932|.	D|.	0|.	-9.7988|-9.7988	9.8167|9.8167	0.40858|0.40858	0.0:0.3502:0.0:0.6498|0.0:0.3502:0.0:0.6498	.|.	.|.	.|.	.|.	W|L	38|172;88	.|.	ENSP00000428930:R38W|.	R|S	+|+	1|2	2|0	SORBS3|SORBS3	22488150|22488150	0.993000|0.993000	0.37304|0.37304	1.000000|1.000000	0.80357|0.80357	0.439000|0.439000	0.31926|0.31926	0.168000|0.168000	0.16622|0.16622	0.093000|0.093000	0.17368|0.17368	-0.982000|-0.982000	0.02568|0.02568	CGG|TCG	.	.	.	none		0.607	SORBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254647.3	NM_005775		T	22432205	C	T	22432205	2	4	270	1	0	0	0	0	0	0	0	1	14942	883	31	1		1	SORBS3	8	22432205	Silent	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10		22432205	123931817	32	17041											
GSR	2936	hgsc.bcm.edu	37	chr8	30537066	30537066	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgaccagctcttctgaagAggtagggtgaatggcgactg	9	10	15	7	1	2	4	0	3	2	1	2	5	2	4	1	3	1	2	1	3	3	2			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr8:30537066A>G	ENST00000221130.5	-	13	1630	c.1540T>C	c.(1540-1542)Tct>Cct	p.S514P	GSR_ENST00000414019.1_Missense_Mutation_p.S471P|GSR_ENST00000541648.1_Missense_Mutation_p.S461P|GSR_ENST00000537535.1_Missense_Mutation_p.S432P|GSR_ENST00000546342.1_Missense_Mutation_p.S485P	NM_000637.3|NM_001195102.1|NM_001195103.1	NP_000628.2|NP_001182031.1|NP_001182032.1	P00390	GSHR_HUMAN	glutathione reductase	514					cell redox homeostasis (GO:0045454)|glutathione metabolic process (GO:0006749)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|glutathione-disulfide reductase activity (GO:0004362)|NADP binding (GO:0050661)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	23				KIRC - Kidney renal clear cell carcinoma(542;0.105)|Kidney(114;0.125)	Carmustine(DB00262)|Flavin adenine dinucleotide(DB03147)|Glutathione(DB00143)	TCTTCTGAAGAGGTAGGGTGA	0.493																																					p.S514P		Atlas-SNP	.											.	GSR	53	.	0			c.T1540C						PASS	.						170	132	145					8																	30537066		2203	4300	6503	SO:0001583	missense	2936	exon13			CTGAAGAGGTAGG		CCDS34877.1, CCDS56530.1, CCDS56531.1, CCDS56532.1	8p21.1	2012-10-02			ENSG00000104687	ENSG00000104687	1.8.1.7		4623	protein-coding gene	gene with protein product		138300					Standard	NM_000637		Approved		uc003xih.2	P00390	OTTHUMG00000163946	ENST00000221130.5:c.1540T>C	chr8.hg19:g.30537066A>G	ENSP00000221130:p.Ser514Pro	104.0	0.0	.		120.0	46.0	.	NM_000637	C8KIL8|C8KIL9|C8KIM0|D3DSV3|Q7Z5C9|Q9NP63	Missense_Mutation	SNP	ENST00000221130.5	hg19	CCDS34877.1	.	.	.	.	.	.	.	.	.	.	A	29.1	4.976636	0.92982	.	.	ENSG00000104687	ENST00000221130;ENST00000414019;ENST00000546342;ENST00000541648;ENST00000537535	D;D;D;D;D	0.92752	-3.1;-3.1;-3.1;-3.1;-3.1	5.34	5.34	0.76211	FAD/NAD-linked reductase, dimerisation (1);Pyridine nucleotide-disulphide oxidoreductase, dimerisation (2);	0.000000	0.85682	D	0.000000	D	0.97117	0.9058	H	0.95470	3.675	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97953	1.0333	10	0.66056	D	0.02	-17.0472	13.5686	0.61832	1.0:0.0:0.0:0.0	.	514	P00390	GSHR_HUMAN	P	514;471;485;461;432	ENSP00000221130:S514P;ENSP00000390065:S471P;ENSP00000445516:S485P;ENSP00000444559:S461P;ENSP00000438845:S432P	ENSP00000221130:S514P	S	-	1	0	GSR	30656608	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.577000	0.90773	2.160000	0.67779	0.454000	0.30748	TCT	.	.	.	none		0.493	GSR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376519.1			G	30537066	A	G	30537066	3	3	270	1	0	0	0	0	1	0	0	0	6835	304	11	3	32	3	GSR	8	30537066	Missense_Mutation	SNP	A	TCGA-UZ-A9Q1-01A-11D-A42J-10	8104861	30537066	115826956	33	17042											
RORB	6096	hgsc.bcm.edu	37	chr9	77300383	77300383	+	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	tctctccgttctgcagttaaTagccaagataccaaccatca	12	11	5	13	1	3	1	1	0	2	1	5	1	4	1	4	0	4	3	4	0	5	4			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr9:77300383T>A	ENST00000396204.2	+	10	1262	c.1262T>A	c.(1261-1263)aTa>aAa	p.I421K	RORB_ENST00000376896.3_Missense_Mutation_p.I410K			Q92753	RORB_HUMAN	RAR-related orphan receptor B	421	Ligand-binding. {ECO:0000255}.				amacrine cell differentiation (GO:0035881)|cellular response to retinoic acid (GO:0071300)|eye photoreceptor cell development (GO:0042462)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|rhythmic process (GO:0048511)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(2)|large_intestine(4)|lung(1)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	12					Melatonin(DB01065)	CTGCAGTTAATAGCCAAGATA	0.478																																					p.I410K		Atlas-SNP	.											.	RORB	89	.	0			c.T1229A						PASS	.						158	148	151					9																	77300383		2203	4300	6503	SO:0001583	missense	6096	exon10			AGTTAATAGCCAA	Y08639	CCDS6646.1	9q22	2013-01-16			ENSG00000198963	ENSG00000198963		"Nuclear hormone receptors"	10259	protein-coding gene	gene with protein product		601972				7926749	Standard	NM_006914		Approved	RZRB, NR1F2, ROR-BETA	uc004ajh.3	Q92753	OTTHUMG00000020026	ENST00000396204.2:c.1262T>A	chr9.hg19:g.77300383T>A	ENSP00000379507:p.Ile421Lys	64.0	0.0	.		86.0	37.0	.	NM_006914	Q8WX73	Missense_Mutation	SNP	ENST00000396204.2	hg19		.	.	.	.	.	.	.	.	.	.	T	17.09	3.301008	0.60195	.	.	ENSG00000198963	ENST00000376896;ENST00000396204	D;D	0.96913	-4.17;-4.17	5.45	5.45	0.79879	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.083997	0.85682	D	0.000000	D	0.97210	0.9088	M	0.70275	2.135	0.80722	D	1	B;B	0.33748	0.423;0.353	P;P	0.48795	0.486;0.59	D	0.97590	1.0116	10	0.72032	D	0.01	.	16.226	0.82293	0.0:0.0:0.0:1.0	.	421;410	Q92753;Q58EY0	RORB_HUMAN;.	K	410;421	ENSP00000366093:I410K;ENSP00000379507:I421K	ENSP00000366093:I410K	I	+	2	0	RORB	76490203	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.564000	0.82326	2.371000	0.80710	0.533000	0.62120	ATA	.	.	.	none		0.478	RORB-201	KNOWN	basic	protein_coding	protein_coding				A	77300383	T	A	77300383	3	1	270	1	0	0	0	0	1	0	0	0	13542	1406	49	5	1267	5	RORB	9	77300383	Missense_Mutation	SNP	T	TCGA-UZ-A9Q1-01A-11D-A42J-10		77300383	63913048	34	17043											
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84609332	84609332	+	Missense_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	agggctggggacatcccaacGcaggagaaagagcctccctg	11	4	14	12	1	0	2	0	0	0	2	2	4	2	3	3	4	2	2	3	4	2	0			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr9:84609332G>A	ENST00000344803.2	+	4	3994	c.3947G>A	c.(3946-3948)cGc>cAc	p.R1316H		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	1316					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											ACATCCCAACGCAGGAGAAAG	0.522																																					p.R1316H		Atlas-SNP	.											FAM75D4,NS,carcinoma,0,2	.	.	.	0			c.G3947A						PASS	.						27	27	27					9																	84609332		1915	4114	6029	SO:0001583	missense	389763	exon4			CCCAACGCAGGAG		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.3947G>A	chr9.hg19:g.84609332G>A	ENSP00000341988:p.Arg1316His	129.0	1.0	.		123.0	50.0	.	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	hg19	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.100997	0.00360	.	.	ENSG00000214929	ENST00000344803	T	0.04917	3.53	3.17	-6.34	0.01982	.	.	.	.	.	T	0.02119	0.0066	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.35450	-0.9788	9	0.39692	T	0.17	3.2905	2.1019	0.03682	0.3168:0.1206:0.0935:0.4691	.	1316	Q6ZQQ2	F75D1_HUMAN	H	1316	ENSP00000341988:R1316H	ENSP00000341988:R1316H	R	+	2	0	FAM75D1	83799152	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.252000	0.00074	-4.681000	0.00036	-4.324000	0.00007	CGC	.	.	.	none		0.522	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		A	84609332	G	A	84609332	3	1	270	1	0	0	0	0	1	0	0	0	5939	1087	38	1	3961	1	FLJ46321	9	84609332	Missense_Mutation	SNP	G	TCGA-UZ-A9Q1-01A-11D-A42J-10	7308949	84609332	56604099	35	17044											
IARS	3376	hgsc.bcm.edu	37	chr9	95027351	95027351	+	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	caacagtcaaacacttcagaGatgcggtgcaaggatccctt	13	8	9	11	1	2	1	2	0	0	1	3	3	3	2	1	2	4	1	1	2	3	2			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr9:95027351G>A	ENST00000375643.3	-	16	1826	c.1560C>T	c.(1558-1560)atC>atT	p.I520I	IARS_ENST00000375629.3_5'UTR|IARS_ENST00000443024.2_Silent_p.I520I|IARS_ENST00000447699.2_Silent_p.I410I	NM_013417.2	NP_038203.2	P41252	SYIC_HUMAN	isoleucyl-tRNA synthetase	520					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)	ACACTTCAGAGATGCGGTGCA	0.448																																					p.I520I		Atlas-SNP	.											.	IARS	74	.	0			c.C1560T						PASS	.						83	69	74					9																	95027351		2203	4300	6503	SO:0001819	synonymous_variant	3376	exon16			TTCAGAGATGCGG	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.1560C>T	chr9.hg19:g.95027351G>A		140.0	0.0	.		157.0	62.0	.	NM_013417	A8KAE9|Q5TCD0|Q7Z3T4|Q9H588	Silent	SNP	ENST00000375643.3	hg19	CCDS6694.1																																																																																			.	.	.	none		0.448	IARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053059.2	NM_002161		A	95027351	G	A	95027351	2	1	270	1	0	0	0	0	0	0	0	1	7480	932	33	2		2	IARS	9	95027351	Silent	SNP	G	TCGA-UZ-A9Q1-01A-11D-A42J-10	10418019	95027351	46186080	36	17045											
FAM73B	84895	hgsc.bcm.edu	37	chr9	131832215	131832215	+	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	gcttccttggacccaagcctCagcttgctgaagtctgtgct	6	12	10	13	0	2	1	1	1	1	0	3	2	3	2	3	1	4	4	3	1	2	3			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr9:131832215C>T	ENST00000358369.4	+	15	1772	c.1546C>T	c.(1546-1548)Cag>Tag	p.Q516*	FAM73B_ENST00000277475.5_3'UTR|FAM73B_ENST00000406926.2_3'UTR	NM_032809.2	NP_116198.2	Q7L4E1	FA73B_HUMAN	family with sequence similarity 73, member B	516					bone development (GO:0060348)	integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(1)	13						ACCCAAGCCTCAGCTTGCTGA	0.572																																					p.Q516X		Atlas-SNP	.											.	FAM73B	37	.	0			c.C1546T						PASS	.						214	204	208					9																	131832215		2203	4300	6503	SO:0001587	stop_gained	84895	exon15			AAGCCTCAGCTTG	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.1546C>T	chr9.hg19:g.131832215C>T	ENSP00000351138:p.Gln516*	60.0	0.0	.		60.0	16.0	.	NM_032809	Q8NBM3|Q8TEJ6|Q969E6	Nonsense_Mutation	SNP	ENST00000358369.4	hg19	CCDS6917.1	.	.	.	.	.	.	.	.	.	.	C	38	7.196286	0.98129	.	.	ENSG00000148343	ENST00000358369	.	.	.	5.74	5.74	0.90152	.	0.050861	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	.	18.9022	0.92448	0.0:1.0:0.0:0.0	.	.	.	.	X	516	.	ENSP00000351138:Q516X	Q	+	1	0	FAM73B	130872036	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.736000	0.68597	2.700000	0.92200	0.655000	0.94253	CAG	.	.	.	none		0.572	FAM73B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054542.7	NM_032809		T	131832215	C	T	131832215	4	4	270	1	0	0	0	0	0	1	0	0	5625	827	29	2	1600	2	FAM73B	9	131832215	Nonsense_Mutation	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10	36804864	131832215	9381216	37	17046											
RAPGEF1	2889	hgsc.bcm.edu	37	chr9	134464315	134464315	+	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	gctcagctccccattgcacaCcaggcggaagaccagttcca	10	6	9	16	1	1	1	1	0	0	1	3	2	3	2	5	2	2	4	5	2	1	2			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr9:134464315C>T	ENST00000372189.3	-	17	2491	c.2368G>A	c.(2368-2370)Gtg>Atg	p.V790M	RAPGEF1_ENST00000372190.3_Missense_Mutation_p.V808M|RAPGEF1_ENST00000372195.1_Missense_Mutation_p.V807M	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1	790	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				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)		CCATTGCACACCAGGCGGAAG	0.577																																					p.V808M		Atlas-SNP	.											.	RAPGEF1	126	.	0			c.G2422A						PASS	.						75	81	79					9																	134464315		2106	4237	6343	SO:0001583	missense	2889	exon17			TGCACACCAGGCG	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.2368G>A	chr9.hg19:g.134464315C>T	ENSP00000361263:p.Val790Met	41.0	0.0	.		74.0	35.0	.	NM_198679	Q5JUE4|Q8IV73	Missense_Mutation	SNP	ENST00000372189.3	hg19	CCDS48047.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.9|23.9	4.472039|4.472039	0.84533|0.84533	.|.	.|.	ENSG00000107263|ENSG00000107263	ENST00000414781|ENST00000266110;ENST00000372195;ENST00000429421;ENST00000372189;ENST00000372190;ENST00000411834;ENST00000337036;ENST00000398415;ENST00000357686	.|T;T;T	.|0.30981	.|1.51;1.51;1.51	5.45|5.45	5.45|5.45	0.79879|0.79879	.|Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (2);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.51346|0.51346	0.1669|0.1669	L|L	0.49126|0.49126	1.545|1.545	0.53005|0.53005	D|D	0.999961|0.999961	.|D;D	.|0.76494	.|0.995;0.999	.|P;D	.|0.71414	.|0.901;0.973	T|T	0.51426|0.51426	-0.8707|-0.8707	5|10	.|0.87932	.|D	.|0	.|.	18.2518|18.2518	0.90006|0.90006	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|790;808	.|Q13905;Q13905-3	.|RPGF1_HUMAN;.	D|M	217|790;807;736;790;808;770;768;235;807	.|ENSP00000361269:V807M;ENSP00000361263:V790M;ENSP00000361264:V808M	.|ENSP00000266110:V790M	G|V	-|-	2|1	0|0	RAPGEF1|RAPGEF1	133454136|133454136	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	4.538000|4.538000	0.60650|0.60650	2.546000|2.546000	0.85860|0.85860	0.462000|0.462000	0.41574|0.41574	GGT|GTG	.	.	.	none		0.577	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312		T	134464315	C	T	134464315	3	4	270	1	0	0	0	0	1	0	0	0	13056	507	18	2	897	2	RAPGEF1	9	134464315	Missense_Mutation	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10	2632100	134464315	6749116	38	17047											
PTEN	5728	hgsc.bcm.edu	37	chr10	89653783	89653783	+	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	ccttaactaaagtactcagaTatttatccaaacattattgc	15	14	3	9	0	1	1	1	0	0	1	2	1	2	1	2	0	4	1	2	0	8	8			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr10:89653783T>A	ENST00000371953.3	+	2	1438	c.81T>A	c.(79-81)taT>taA	p.Y27*		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	27	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.		Y -> S (loss of phosphatase activity towards Ins(1,3,4,5)P4).		activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(8)|p.Y27fs*1(3)|p.Y27fs*16(1)|p.Y27*(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)		AGTACTCAGATATTTATCCAA	0.294		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.Y27X		Atlas-SNP	.	yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	PTEN,colon,carcinoma,+1,2	PTEN	3652	.	50	Whole gene deletion(37)|Unknown(8)|Deletion - Frameshift(4)|Substitution - Nonsense(1)	prostate(14)|central_nervous_system(9)|skin(8)|haematopoietic_and_lymphoid_tissue(4)|lung(4)|ovary(3)|endometrium(2)|breast(2)|soft_tissue(1)|urinary_tract(1)|NS(1)|kidney(1)	c.T81A						PASS	.						98	98	98					10																	89653783		2203	4292	6495	SO:0001630	splice_region_variant	5728	exon2	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	CTCAGATATTTAT	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.80-1T>A	chr10.hg19:g.89653783T>A		52.0	0.0	.		69.0	55.0	.	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Nonsense_Mutation	SNP	ENST00000371953.3	hg19	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	T	47	13.707906	0.99758	.	.	ENSG00000171862	ENST00000371953	.	.	.	5.19	5.19	0.71726	.	0.071107	0.64402	D	0.000018	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0135	0.64511	0.0:0.0:0.0:1.0	.	.	.	.	X	27	.	.	Y	+	3	2	PTEN	89643763	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.599000	0.67592	1.959000	0.56917	0.533000	0.62120	TAT	.	.	.	none		0.294	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	Nonsense_Mutation	A	89653783	T	A	89653783	5	1	270	1	0	0	0	0	0	0	1	0	12748	1420	49	5	87	5	PTEN	10	89653783	Splice_Site	SNP	T	TCGA-UZ-A9Q1-01A-11D-A42J-10		89653783	45880964	39	17048											
EEF1G	1937	hgsc.bcm.edu	37	chr11	62327757	62327757	+	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	cagacccactctcttaccagTgatgagattgcagctcatga	11	10	8	12	0	2	4	1	3	1	2	3	5	2	4	2	0	3	2	2	0	1	2			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr11:62327757T>A	ENST00000329251.4	-	8	1157	c.1027A>T	c.(1027-1029)Act>Tct	p.T343S	EEF1G_ENST00000378019.3_Missense_Mutation_p.T393S|MIR3654_ENST00000496634.2_3'UTR	NM_001404.4	NP_001395.1	P26641	EF1G_HUMAN	eukaryotic translation elongation factor 1 gamma	343	EF-1-gamma C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00519}.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to virus (GO:0009615)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	translation elongation factor activity (GO:0003746)			breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						CTCTTACCAGTGATGAGATTG	0.498																																					p.T343S		Atlas-SNP	.											.	EEF1G	33	.	0			c.A1027T						PASS	.						34	31	32					11																	62327757		1982	4164	6146	SO:0001583	missense	1937	exon8			TACCAGTGATGAG	X63526	CCDS44626.1	11q12.3	2008-02-05			ENSG00000254772	ENSG00000254772			3213	protein-coding gene	gene with protein product		130593				1598220, 1461723	Standard	NM_001404		Approved	EF1G	uc001ntm.1	P26641	OTTHUMG00000167567	ENST00000329251.4:c.1027A>T	chr11.hg19:g.62327757T>A	ENSP00000331901:p.Thr343Ser	108.0	0.0	.		107.0	39.0	.	NM_001404	B4DTG2|Q6PJ62|Q6PK31|Q96CU2|Q9P196	Missense_Mutation	SNP	ENST00000329251.4	hg19	CCDS44626.1	.	.	.	.	.	.	.	.	.	.	T	8.114	0.779396	0.16120	.	.	ENSG00000254772	ENST00000329251;ENST00000378019;ENST00000424909	T;T	0.21932	2.01;1.98	4.7	4.7	0.59300	Translation elongation factor EF1B, gamma chain, conserved (4);	0.158521	0.53938	D	0.000048	T	0.14098	0.0341	N	0.19112	0.55	0.46542	D	0.999093	B;B;B	0.12013	0.005;0.0;0.0	B;B;B	0.22753	0.041;0.005;0.002	T	0.09684	-1.0663	10	0.22706	T	0.39	.	12.1911	0.54273	0.0:0.0:0.0:1.0	.	393;112;343	B4DTG2;B4DUP0;P26641	.;.;EF1G_HUMAN	S	343;393;112	ENSP00000331901:T343S;ENSP00000367258:T393S	ENSP00000331901:T343S	T	-	1	0	EEF1G	62084333	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	2.991000	0.49409	1.995000	0.58328	0.449000	0.29647	ACT	.	.	.	none		0.498	EEF1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395047.1	NM_001404		A	62327757	T	A	62327757	3	1	270	1	0	0	0	0	1	0	0	0	4930	1696	59	5	298	5	EEF1G	11	62327757	Missense_Mutation	SNP	T	TCGA-UZ-A9Q1-01A-11D-A42J-10		62327757	72678759	40	17049											
GPR152	390212	hgsc.bcm.edu	37	chr11	67219103	67219103	+	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	tgtgggatccgatcgtggctGgagtgtggggttcacctgag	5	11	18	7	2	1	1	1	1	0	0	3	4	2	3	2	5	0	2	2	5	0	1			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr11:67219103G>C	ENST00000312457.2	-	1	1097	c.1093C>G	c.(1093-1095)Cag>Gag	p.Q365E	CABP4_ENST00000438189.2_5'Flank	NM_206997.1	NP_996880.1	Q8TDT2	GP152_HUMAN	G protein-coupled receptor 152	365						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)			GATCGTGGCTGGAGTGTGGGG	0.632																																					p.Q365E	Pancreas(102;800 1581 2723 7382 33622)	Atlas-SNP	.											.	GPR152	41	.	0			c.C1093G						PASS	.						46	44	45					11																	67219103		2200	4295	6495	SO:0001583	missense	390212	exon1			GTGGCTGGAGTGT	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.1093C>G	chr11.hg19:g.67219103G>C	ENSP00000310255:p.Gln365Glu	49.0	0.0	.		55.0	23.0	.	NM_206997	Q0VD88|Q86SM0	Missense_Mutation	SNP	ENST00000312457.2	hg19	CCDS8165.1	.	.	.	.	.	.	.	.	.	.	G	15.14	2.744684	0.49151	.	.	ENSG00000175514	ENST00000312457	T	0.07021	3.23	4.43	1.43	0.22495	.	0.186743	0.26133	N	0.026147	T	0.09423	0.0232	M	0.68952	2.095	0.22305	N	0.99922	P	0.34662	0.462	B	0.33960	0.173	T	0.16660	-1.0395	10	0.72032	D	0.01	.	6.2505	0.20843	0.0912:0.0:0.5823:0.3265	.	365	Q8TDT2	GP152_HUMAN	E	365	ENSP00000310255:Q365E	ENSP00000310255:Q365E	Q	-	1	0	GPR152	66975679	0.005000	0.15991	0.003000	0.11579	0.008000	0.06430	0.904000	0.28491	0.114000	0.18032	0.491000	0.48974	CAG	.	.	.	none		0.632	GPR152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397623.1			C	67219103	G	C	67219103	3	2	270	1	0	0	0	0	1	0	0	0	6665	1357	47	4	323	4	GPR152	11	67219103	Missense_Mutation	SNP	G	TCGA-UZ-A9Q1-01A-11D-A42J-10	4891346	67219103	67787413	41	17050											
KRTAP5-8	57830	hgsc.bcm.edu	37	chr11	71249532	71249532	+	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	ctgctgcaagccctgctgttCccagtccagctgctgtaagc	6	10	10	15	0	0	0	0	0	0	0	2	0	2	0	3	0	7	7	3	0	2	2	rs532438179|rs11234084|rs369043826	byFrequency	TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	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	chr11.hg19:g.71249532C>G	ENSP00000420723:p.Ser144Cys	66.0	0.0	.		99.0	6.0	.	NM_021046	Q6L8G7|Q6UTX6	Missense_Mutation	SNP	ENST00000398534.3	hg19	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	270	1	0	0	0	0	1	0	0	0	8574	855	30	4	433	4	KRTAP5-8	11	71249532	Missense_Mutation	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10	4030429	71249532	63756984	42	17051											
C11orf63	79864	hgsc.bcm.edu	37	chr11	122830003	122830007	+	Frame_Shift_Del	DEL	GACTC	GACTC	-																															aaacccaaaccatcaaatctGactcatcaagcatcaaagga																								rs369261311		TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	GACTC	GACTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr11:122830003_122830007delGACTC	ENST00000531316.1	+	8	2279_2283	c.2187_2191delGACTC	c.(2185-2193)ctgactcatfs	p.TH730fs	C11orf63_ENST00000227349.2_Frame_Shift_Del_p.TH730fs			Q6NUN7	CK063_HUMAN	chromosome 11 open reading frame 63	730					axoneme assembly (GO:0035082)|brain development (GO:0007420)|cerebrospinal fluid secretion (GO:0033326)|ciliary basal body organization (GO:0032053)					breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(13)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	47		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.018)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.34e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0311)		CATCAAATCTGACTCATCAAGCATC	0.4																																					p.729_730del		Atlas-Indel,Pindel	.											.	C11orf63	116	.	0			c.2186_2190del						PASS	.																																			SO:0001589	frameshift_variant	79864	exon9			.	BC068507	CCDS8438.1, CCDS8439.1	11q24.1	2012-05-25			ENSG00000109944	ENSG00000109944			26288	protein-coding gene	gene with protein product						12477932	Standard	NM_024806		Approved	FLJ23554	uc001pym.4	Q6NUN7	OTTHUMG00000166027	ENST00000531316.1:c.2187_2191delGACTC	chr11.hg19:g.122830003_122830007delGACTC	ENSP00000431669:p.Thr730fs	283.0	0.0	0		289.0	118.0	0.408305	NM_024806	A8K6G0|Q96GB5|Q9H5D6	Frame_Shift_Del	DEL	ENST00000531316.1	hg19	CCDS8438.1																																																																																			.	.	.	none		0.4	C11orf63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387511.1	NM_024806		-	122830007	GACTC	-	122830003	7	5	270	1	0	1	0	1	0	0	0	0	1656	1277	45	0	2281	0	C11orf63	11	122830003	Frame_Shift_Del	DEL	GACTC	TCGA-UZ-A9Q1-01A-11D-A42J-10	51580471	122830003	12176513	43	17052											
HSPA8	3312	hgsc.bcm.edu	37	chr11	122930962	122930962	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taagctggcactgtgaccacAgcattggtaacagtctagga	12	9	11	9	0	1	1	0	1	1	0	1	2	1	2	1	3	3	4	1	3	3	4			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr11:122930962A>G	ENST00000532636.1	-	4	545	c.426T>C	c.(424-426)gcT>gcC	p.A142A	HSPA8_ENST00000227378.3_Silent_p.A142A|SNORD14E_ENST00000364009.1_RNA|HSPA8_ENST00000533540.1_Intron|HSPA8_ENST00000534624.1_Silent_p.A142A|SNORD14C_ENST00000365382.1_RNA|HSPA8_ENST00000453788.2_Silent_p.A142A|HSPA8_ENST00000526110.1_Intron|HSPA8_ENST00000534319.1_5'UTR|SNORD14D_ENST00000384390.1_RNA|HSPA8_ENST00000526862.1_5'Flank			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	142					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)		CTGTGACCACAGCATTGGTAA	0.393																																					p.A142A	Colon(21;486 594 5900 6733 14272)	Atlas-SNP	.											.	HSPA8	168	.	0			c.T426C						PASS	.						64	62	62					11																	122930962		2202	4299	6501	SO:0001819	synonymous_variant	3312	exon4			GACCACAGCATTG	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.426T>C	chr11.hg19:g.122930962A>G		28.0	0.0	.		35.0	19.0	.	NM_006597	Q9H3R6	Silent	SNP	ENST00000532636.1	hg19	CCDS8440.1																																																																																			.	.	.	none		0.393	HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1			G	122930962	A	G	122930962	2	3	270	1	0	0	0	0	0	0	0	1	7423	175	7	3		3	HSPA8	11	122930962	Silent	SNP	A	TCGA-UZ-A9Q1-01A-11D-A42J-10	100959	122930962	12075554	44	17053											
ARHGAP32	9743	hgsc.bcm.edu	37	chr11	128840378	128840379	+	Frame_Shift_Ins	INS	-	-	AGCTCAAAGA																															acaggtattcctgacagaggINSagctcaaagaagacacatac																										TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr11:128840378_128840379insAGCTCAAAGA	ENST00000310343.9	-	22	4686_4687	c.4687_4688insTCTTTGAGCT	c.(4687-4689)tccfs	p.S1563fs	ARHGAP32_ENST00000524655.1_3'UTR|ARHGAP32_ENST00000527272.1_Frame_Shift_Ins_p.S1214fs|ARHGAP32_ENST00000392657.3_Frame_Shift_Ins_p.S1214fs	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	1563	Interaction with GAB2.				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						CCTGACAGAGGAGCTCAAAGAA	0.535																																					p.S1563fs		Atlas-Indel,Pindel	.											.	ARHGAP32	307	.	0			c.4688_4689insTCTTTGAGCT						PASS	.																																			SO:0001589	frameshift_variant	9743	exon22			.	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.4678_4687dupTCTTTGAGCT	chr11.hg19:g.128840379_128840388dupAGCTCAAAGA	ENSP00000310561:p.Ser1563fs	135.0	0.0	0		133.0	21.0	0.157895	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Frame_Shift_Ins	INS	ENST00000310343.9	hg19	CCDS44769.1																																																																																			.	.	.	none		0.535	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		AGCTCAAAGA	128840379	-	AGCTCAAAGA	128840378	7	5	270	1	0	1	1	0	0	0	0	0	881	1174	41	0	1579	0	ARHGAP32	11	128840378	Frame_Shift_Ins	INS	-	TCGA-UZ-A9Q1-01A-11D-A42J-10	5909416	128840378	6166138	45	17054											
EPS8	2059	hgsc.bcm.edu	37	chr12	15776128	15776128	+	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	tgtacagtgatttggctataGactctcgccccttcagggca	8	12	10	11	1	2	2	1	1	1	1	3	2	2	2	2	2	1	3	2	2	3	5			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr12:15776128G>C	ENST00000281172.5	-	20	2755	c.2319C>G	c.(2317-2319)gtC>gtG	p.V773V	EPS8_ENST00000542903.1_Silent_p.V513V|EPS8_ENST00000543612.1_Silent_p.V773V|EPS8_ENST00000540613.1_Silent_p.V513V|EPS8_ENST00000543523.1_Silent_p.V773V	NM_004447.5	NP_004438.3	Q12929	EPS8_HUMAN	epidermal growth factor receptor pathway substrate 8	773	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)		TTTGGCTATAGACTCTCGCCC	0.403																																					p.V773V		Atlas-SNP	.											.	EPS8	70	.	0			c.C2319G						PASS	.						130	133	132					12																	15776128		2203	4300	6503	SO:0001819	synonymous_variant	2059	exon20			GCTATAGACTCTC	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.2319C>G	chr12.hg19:g.15776128G>C		60.0	0.0	.		149.0	81.0	.	NM_004447	A6NMC3|A8K6W2|A8KA66|B4DX66|Q8N6J0	Silent	SNP	ENST00000281172.5	hg19	CCDS31753.1																																																																																			.	.	.	none		0.403	EPS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401093.1			C	15776128	G	C	15776128	2	2	270	1	0	0	0	0	0	0	0	1	5196	929	33	4		4	EPS8	12	15776128	Silent	SNP	G	TCGA-UZ-A9Q1-01A-11D-A42J-10		15776128	118075767	46	17055											
PDZRN4	29951	hgsc.bcm.edu	37	chr12	41966314	41966314	+	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	gaatgcagccgaggaccccaAtagcacatctttgaagagca	14	6	10	11	1	1	2	0	1	1	1	1	5	1	3	3	1	4	3	3	1	4	2	rs370916106		TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr12:41966314A>T	ENST00000402685.2	+	10	1741	c.1733A>T	c.(1732-1734)aAt>aTt	p.N578I	PDZRN4_ENST00000539469.2_Missense_Mutation_p.N320I|PDZRN4_ENST00000298919.7_Missense_Mutation_p.N318I	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	578							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)				GAGGACCCCAATAGCACATCT	0.493																																					p.N578I		Atlas-SNP	.											.	PDZRN4	346	.	0			c.A1733T						PASS	.						93	84	87					12																	41966314		2203	4300	6503	SO:0001583	missense	29951	exon10			ACCCCAATAGCAC	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.1733A>T	chr12.hg19:g.41966314A>T	ENSP00000384197:p.Asn578Ile	187.0	0.0	.		291.0	82.0	.	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Missense_Mutation	SNP	ENST00000402685.2	hg19	CCDS53777.1	.	.	.	.	.	.	.	.	.	.	A	4.527	0.097859	0.08681	.	.	ENSG00000165966	ENST00000402685;ENST00000539469;ENST00000298919	T;T;T	0.73363	-0.74;3.76;3.76	4.2	1.65	0.23941	.	2.717730	0.00792	N	0.001341	T	0.64811	0.2632	L	0.40543	1.245	0.25084	N	0.990904	P;B;B	0.34462	0.454;0.037;0.01	B;B;B	0.26202	0.067;0.062;0.038	T	0.52675	-0.8544	10	0.51188	T	0.08	-1.7376	5.993	0.19478	0.7343:0.1583:0.1074:0.0	.	578;318;320	Q6ZMN7;Q6ZMN7-4;Q6ZMN7-2	PZRN4_HUMAN;.;.	I	578;320;318	ENSP00000384197:N578I;ENSP00000439990:N320I;ENSP00000298919:N318I	ENSP00000298919:N318I	N	+	2	0	PDZRN4	40252581	0.596000	0.26866	0.155000	0.22561	0.696000	0.40369	1.314000	0.33597	0.195000	0.20347	0.528000	0.53228	AAT	.	.	.	alt		0.493	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377		T	41966314	A	T	41966314	3	4	270	1	0	0	0	0	1	0	0	0	11717	101	4	5	1844	5	PDZRN4	12	41966314	Missense_Mutation	SNP	A	TCGA-UZ-A9Q1-01A-11D-A42J-10	26190186	41966314	91885581	47	17056											
TARBP2	8620	hgsc.bcm.edu	37	chr12	53899550	53899550	+	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	gcagttgctccctgggctccCtgggtgccctgggccctgcc	1	9	14	17	0	0	0	0	0	0	0	2	0	2	0	5	3	3	4	5	3	0	1			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr12:53899550C>T	ENST00000267017.3	-	0	592				TARBP2_ENST00000266987.2_Silent_p.L287L|TARBP2_ENST00000456234.2_Silent_p.L266L|TARBP2_ENST00000552857.1_Missense_Mutation_p.P153L|TARBP2_ENST00000394357.2_Silent_p.L266L	NM_003717.2	NP_003708.1	O15130	NPFF_HUMAN	neuropeptide FF-amide peptide precursor						acute inflammatory response to antigenic stimulus (GO:0002438)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of appetite (GO:0032099)|negative regulation of heart rate (GO:0010459)|negative regulation of insulin secretion (GO:0046676)|neuropeptide signaling pathway (GO:0007218)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane depolarization (GO:0003254)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|response to morphine (GO:0043278)|somatostatin secretion (GO:0070253)|spinal cord development (GO:0021510)|synaptic transmission (GO:0007268)|vasopressin secretion (GO:0030103)	axon terminus (GO:0043679)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|perikaryon (GO:0043204)|vesicle (GO:0031982)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(1)|prostate(1)|urinary_tract(1)	3						CCTGGGCTCCCTGGGTGCCCT	0.602																																					p.L287L		Atlas-SNP	.											.	TARBP2	35	.	0			c.C859T						PASS	.						77	79	78					12																	53899550		2203	4300	6503	SO:0001628	intergenic_variant	6895	exon8			GGCTCCCTGGGTG	AF005271	CCDS8862.1	12q13.13	2013-02-26			ENSG00000139574	ENSG00000139574		"Endogenous ligands"	7901	protein-coding gene	gene with protein product		604643				9224703	Standard	NM_003717		Approved	FMRFAL	uc001sdw.1	O15130	OTTHUMG00000169856		chr12.hg19:g.53899550C>T		57.0	0.0	.		77.0	17.0	.	NM_134323	Q3SXL4	Silent	SNP	ENST00000267017.3	hg19	CCDS8862.1	.	.	.	.	.	.	.	.	.	.	C	9.318	1.057290	0.19907	.	.	ENSG00000139546	ENST00000552857;ENST00000550407	.	.	.	4.45	-0.875	0.10628	.	.	.	.	.	T	0.34279	0.0892	.	.	.	0.23533	N	0.997471	.	.	.	.	.	.	T	0.34030	-0.9845	4	.	.	.	-15.6952	9.7019	0.40192	0.0:0.6534:0.0:0.3466	.	.	.	.	L	153;145	.	.	P	+	2	0	TARBP2	52185817	0.000000	0.05858	0.105000	0.21289	0.991000	0.79684	0.070000	0.14573	-0.157000	0.11059	0.561000	0.74099	CCT	.	.	.	none		0.602	NPFF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406301.1	NM_003717		T	53899550	C	T	53899550	1	4	270	0	1	0	0	0	0	0	0	0	15568	680	24	2		2	TARBP2	12	53899550	IGR	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10	11933236	53899550	79952345	48	17057											
NAV3	89795	hgsc.bcm.edu	37	chr12	78516178	78516178	+	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	ccagagcctgctcatgagaaCgggtagtgtgagatctactc	10	9	12	10	1	2	3	1	2	1	3	3	5	2	3	2	1	4	2	2	1	3	2			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr12:78516178C>T	ENST00000397909.2	+	16	4381	c.4208C>T	c.(4207-4209)aCg>aTg	p.T1403M	NAV3_ENST00000536525.2_Missense_Mutation_p.T1403M|NAV3_ENST00000228327.6_Missense_Mutation_p.T1403M|NAV3_ENST00000266692.7_Intron			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1403	Ser-rich.					membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.T1403M(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						CTCATGAGAACGGGTAGTGTG	0.552										HNSCC(70;0.22)																											p.T1403M		Atlas-SNP	.											NAV3,NS,carcinoma,0,2	NAV3	506	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4208T						PASS	.						104	96	99					12																	78516178		2021	4186	6207	SO:0001583	missense	89795	exon16			TGAGAACGGGTAG	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.4208C>T	chr12.hg19:g.78516178C>T	ENSP00000381007:p.Thr1403Met	36.0	0.0	.		60.0	5.0	.	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	hg19		.	.	.	.	.	.	.	.	.	.	C	22.2	4.260794	0.80246	.	.	ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000378640;ENST00000550788	T;T;T;T	0.30981	1.53;1.54;1.51;2.25	5.97	5.97	0.96955	.	0.000000	0.41294	U	0.000916	T	0.57961	0.2089	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.99;0.998;0.999	T	0.56860	-0.7909	10	0.87932	D	0	-13.975	20.4239	0.99064	0.0:1.0:0.0:0.0	.	1403;1403;1403	E7EUC6;Q8IVL0;Q8IVL0-2	.;NAV3_HUMAN;.	M	1403;1403;1403;38;46	ENSP00000446132:T1403M;ENSP00000381007:T1403M;ENSP00000228327:T1403M;ENSP00000448303:T46M	ENSP00000228327:T1403M	T	+	2	0	NAV3	77040309	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.594000	0.82698	2.828000	0.97474	0.655000	0.94253	ACG	.	.	.	none		0.552	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		T	78516178	C	T	78516178	3	4	270	1	0	0	0	0	1	0	0	0	10192	536	19	1	4270	1	NAV3	12	78516178	Missense_Mutation	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10	24616628	78516178	55335717	49	17058											
NUPL1	9818	hgsc.bcm.edu	37	chr13	25895072	25895072	+	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	tttaggaaatttgtgaaggaGcagaaacaagttcaagaaga	18	9	11	3	0	1	4	1	1	0	3	1	6	1	6	0	2	2	2	0	2	7	4			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr13:25895072G>C	ENST00000381736.3	+	9	1042	c.792G>C	c.(790-792)gaG>gaC	p.E264D	NUPL1_ENST00000381718.3_Missense_Mutation_p.E252D|NUPL1_ENST00000466694.1_3'UTR|NUPL1_ENST00000463407.1_Missense_Mutation_p.E264D	NM_001008564.1|NM_014089.3	NP_001008564.1|NP_054808.1	Q9BVL2	NUPL1_HUMAN	nucleoporin like 1	264	14 X 2 AA repeats of F-G.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)	nucleocytoplasmic transporter activity (GO:0005487)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|stomach(1)|urinary_tract(1)	16		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.0092)|Epithelial(112;0.0477)|OV - Ovarian serous cystadenocarcinoma(117;0.165)|GBM - Glioblastoma multiforme(144;0.244)		TTGTGAAGGAGCAGAAACAAG	0.308																																					p.E264D	Pancreas(166;1040 2004 4560 4728 37041)|GBM(109;1045 1520 7614 9308 19618)	Atlas-SNP	.											.	NUPL1	37	.	0			c.G792C						PASS	.						35	39	37					13																	25895072		2197	4296	6493	SO:0001583	missense	9818	exon9			GAAGGAGCAGAAA	AB007870	CCDS9314.1, CCDS31949.1	13q12.12	2011-04-12			ENSG00000139496	ENSG00000139496			20261	protein-coding gene	gene with protein product		607615				9455477	Standard	NM_014089		Approved	KIAA0410	uc001uqi.3	Q9BVL2	OTTHUMG00000016608	ENST00000381736.3:c.792G>C	chr13.hg19:g.25895072G>C	ENSP00000371155:p.Glu264Asp	88.0	0.0	.		87.0	32.0	.	NM_014089	A6NI12|B4DZJ1|O43160|Q5JRG2|Q5JRG5	Missense_Mutation	SNP	ENST00000381736.3	hg19	CCDS9314.1	.	.	.	.	.	.	.	.	.	.	G	11.68	1.710839	0.30322	.	.	ENSG00000139496	ENST00000381736;ENST00000381745;ENST00000313619;ENST00000463407;ENST00000381718;ENST00000381747;ENST00000394327	T;T;T;T;T	0.49720	1.38;1.35;1.37;1.32;0.77	6.14	0.847	0.18961	.	0.180956	0.64402	D	0.000016	T	0.33000	0.0848	N	0.21448	0.665	0.44432	D	0.997351	B;B;P	0.46859	0.236;0.41;0.885	B;B;P	0.44946	0.07;0.07;0.465	T	0.03043	-1.1079	10	0.28530	T	0.3	-14.1628	9.5224	0.39143	0.6241:0.0:0.3759:0.0	.	252;264;264	A6NI12;Q9BVL2;Q9BVL2-2	.;NUPL1_HUMAN;.	D	264;252;241;264;252;264;211	ENSP00000371155:E264D;ENSP00000418555:E264D;ENSP00000371137:E252D;ENSP00000371166:E264D;ENSP00000408147:E211D	ENSP00000318459:E241D	E	+	3	2	NUPL1	24793072	0.990000	0.36364	0.997000	0.53966	0.927000	0.56198	0.394000	0.20834	-0.057000	0.13199	-0.355000	0.07637	GAG	.	.	.	none		0.308	NUPL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044228.2			C	25895072	G	C	25895072	3	2	270	1	0	0	0	0	1	0	0	0	10781	962	34	4	826	4	NUPL1	13	25895072	Missense_Mutation	SNP	G	TCGA-UZ-A9Q1-01A-11D-A42J-10		25895072	89274806	50	17059											
MYO16	23026	hgsc.bcm.edu	37	chr13	109379841	109379841	+	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	attctgattgacagaggagtCaacgtcaaccaccaggatga	14	8	10	9	1	3	4	2	3	1	1	3	6	3	6	2	2	2	0	2	2	2	2			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr13:109379841C>T	ENST00000357550.2	+	3	392	c.351C>T	c.(349-351)gtC>gtT	p.V117V	MYO16_ENST00000251041.5_Silent_p.V117V|MYO16_ENST00000356711.2_Silent_p.V117V	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)			ACAGAGGAGTCAACGTCAACC	0.403																																					p.V139V		Atlas-SNP	.											.	MYO16	285	.	0			c.C417T						PASS	.						206	184	191					13																	109379841		2203	4300	6503	SO:0001819	synonymous_variant	23026	exon4			AGGAGTCAACGTC		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.351C>T	chr13.hg19:g.109379841C>T		81.0	0.0	.		116.0	50.0	.	NM_001198950		Silent	SNP	ENST00000357550.2	hg19	CCDS32008.1																																																																																			.	.	.	none		0.403	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011		T	109379841	C	T	109379841	2	4	270	1	0	0	0	0	0	0	0	1	10071	813	29	2		2	MYO16	13	109379841	Silent	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10	83484769	109379841	5790037	51	17060											
SLC7A7	9056	hgsc.bcm.edu	37	chr14	23242825	23242825	+	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	attccagatggtgtttagttAgatttgggatcccgttgctt	7	17	11	6	1	0	2	0	0	0	2	2	3	2	3	2	2	1	4	2	2	2	7			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr14:23242825A>T	ENST00000397532.3	-	10	2055	c.1530T>A	c.(1528-1530)tcT>tcA	p.S510S	SLC7A7_ENST00000554061.1_5'UTR|SLC7A7_ENST00000397529.2_Silent_p.S510S|SLC7A7_ENST00000397528.4_Silent_p.S510S|SLC7A7_ENST00000555702.1_Silent_p.S510S|SLC7A7_ENST00000285850.7_Silent_p.S510S|SLC7A7_ENST00000554517.1_Silent_p.S244S			Q9UM01	YLAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, y+L system), member 7	510					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(2)	20	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.00741)		GTGTTTAGTTAGATTTGGGAT	0.488																																					p.S510S		Atlas-SNP	.											.	SLC7A7	36	.	0			c.T1530A						PASS	.						141	117	125					14																	23242825		2203	4300	6503	SO:0001819	synonymous_variant	9056	exon11			TTAGTTAGATTTG	AF092032	CCDS9574.1	14q11.2	2014-09-17	2011-07-12		ENSG00000155465	ENSG00000155465		"Solute carriers"	11065	protein-coding gene	gene with protein product		603593		LPI		9829974	Standard	NM_001126106		Approved	y+LAT-1	uc001wgs.4	Q9UM01	OTTHUMG00000028692	ENST00000397532.3:c.1530T>A	chr14.hg19:g.23242825A>T		89.0	0.0	.		88.0	41.0	.	NM_001126105	B2RAU0|D3DS26|O95984|Q53XC1|Q86U07|Q9P2V5	Silent	SNP	ENST00000397532.3	hg19	CCDS9574.1																																																																																			.	.	.	none		0.488	SLC7A7-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071636.3			T	23242825	A	T	23242825	2	4	270	1	0	0	0	0	0	0	0	1	14716	407	15	5		5	SLC7A7	14	23242825	Silent	SNP	A	TCGA-UZ-A9Q1-01A-11D-A42J-10		23242825	84106715	52	17061											
HECTD1	25831	hgsc.bcm.edu	37	chr14	31604218	31604218	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgaagtgtatatgctgatggTatcacccagagacccagatc	12	9	10	10	1	1	3	1	1	0	2	2	5	1	3	2	1	1	3	2	1	4	3			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr14:31604218T>C	ENST00000399332.1	-	22	3926	c.3438A>G	c.(3436-3438)atA>atG	p.I1146M	HECTD1_ENST00000553700.1_Missense_Mutation_p.I1146M	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	1146					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)		ATGCTGATGGTATCACCCAGA	0.418																																					p.I1146M		Atlas-SNP	.											.	HECTD1	159	.	0			c.A3438G						PASS	.						189	167	174					14																	31604218		1952	4139	6091	SO:0001583	missense	25831	exon22			TGATGGTATCACC	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.3438A>G	chr14.hg19:g.31604218T>C	ENSP00000382269:p.Ile1146Met	123.0	0.0	.		117.0	44.0	.	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	hg19	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	T	16.23	3.064792	0.55432	.	.	ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332;ENST00000553957	T;T;T	0.29917	1.55;1.55;1.55	5.91	3.45	0.39498	Galactose-binding domain-like (1);Sad1/UNC-like, C-terminal (1);	0.151756	0.43260	U	0.000599	T	0.20577	0.0495	L	0.43923	1.385	0.48571	D	0.999676	P;B	0.39022	0.655;0.225	B;B	0.34536	0.185;0.121	T	0.06075	-1.0847	10	0.87932	D	0	-6.2714	4.6526	0.12603	0.1194:0.0674:0.1242:0.689	.	1146;1146	D3DS86;Q9ULT8	.;HECD1_HUMAN	M	1146;1148;1146;620	ENSP00000450697:I1146M;ENSP00000382269:I1146M;ENSP00000451860:I620M	ENSP00000261312:I1148M	I	-	3	3	HECTD1	30673969	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.886000	0.28241	2.261000	0.74972	0.533000	0.62120	ATA	.	.	.	none		0.418	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			C	31604218	T	C	31604218	3	2	270	1	0	0	0	0	1	0	0	0	7046	1628	57	3	4482	3	HECTD1	14	31604218	Missense_Mutation	SNP	T	TCGA-UZ-A9Q1-01A-11D-A42J-10	8361393	31604218	75745322	53	17062											
DMXL2	23312	hgsc.bcm.edu	37	chr15	51783940	51783940	+	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	caggcaaaatggcatgtagaGacacctaaattggaaatata	18	8	9	6	0	0	1	0	0	0	1	0	3	0	2	1	3	0	3	1	3	8	5			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr15:51783940G>A	ENST00000251076.5	-	20	5075	c.4788C>T	c.(4786-4788)gtC>gtT	p.V1596V	DMXL2_ENST00000449909.3_Silent_p.V960V|RP11-707P17.1_ENST00000561007.1_RNA|DMXL2_ENST00000543779.2_Silent_p.V1596V	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	1596						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		GGCATGTAGAGACACCTAAAT	0.368																																					p.V1596V		Atlas-SNP	.											.	DMXL2	262	.	0			c.C4788T						PASS	.						68	74	72					15																	51783940		2195	4293	6488	SO:0001819	synonymous_variant	23312	exon20			TGTAGAGACACCT	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"WD repeat domain containing"	2938	protein-coding gene	gene with protein product	"rabconnectin 3"	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.4788C>T	chr15.hg19:g.51783940G>A		65.0	0.0	.		63.0	29.0	.	NM_001174116	B2RTR3|B7ZMH3|F5GWF1|O94938	Silent	SNP	ENST00000251076.5	hg19	CCDS10141.1																																																																																			.	.	.	none		0.368	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263		A	51783940	G	A	51783940	2	1	270	1	0	0	0	0	0	0	0	1	4597	929	33	2		2	DMXL2	15	51783940	Silent	SNP	G	TCGA-UZ-A9Q1-01A-11D-A42J-10		51783940	50747452	54	17063											
ADAMTS7	11173	hgsc.bcm.edu	37	chr15	79088990	79088991	+	Frame_Shift_Ins	INS	-	-	T																															ctgtccgtggtactccaccaINSttttggcatcagctactacc																										TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr15:79088990_79088991insT	ENST00000388820.4	-	4	970_971	c.760_761insA	c.(760-762)atgfs	p.M254fs	ADAMTS7_ENST00000566303.1_5'UTR	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	254	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						GTACTCCACCATTTTGGCATCA	0.614																																					p.M254fs		Atlas-Indel,Pindel	.											.	ADAMTS7	142	.	0			c.761_762insA						PASS	.																																			SO:0001589	frameshift_variant	11173	exon4			.	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.761dupA	chr15.hg19:g.79088994_79088994dupT	ENSP00000373472:p.Met254fs	70.0	0.0	0		75.0	34.0	0.453333	NM_014272	Q14F51|Q6P7J9	Frame_Shift_Ins	INS	ENST00000388820.4	hg19	CCDS32303.1																																																																																			.	.	.	none		0.614	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272		T	79088991	-	T	79088990	7	5	270	1	0	1	1	0	0	0	0	0	271	217	8	0	4383	0	ADAMTS7	15	79088990	Frame_Shift_Ins	INS	-	TCGA-UZ-A9Q1-01A-11D-A42J-10	27305050	79088990	23442402	55	17064											
ALPK3	57538	hgsc.bcm.edu	37	chr15	85360356	85360356	+	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	catgaccaggacacccgctgCgccttcctcccgaggcctcc	6	6	9	20	3	0	1	0	1	0	0	3	3	3	2	7	2	1	1	7	2	0	1			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr15:85360356C>T	ENST00000258888.5	+	1	446	c.279C>T	c.(277-279)tgC>tgT	p.C93C		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	93					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)			ACACCCGCTGCGCCTTCCTCC	0.731																																					p.C93C		Atlas-SNP	.											.	ALPK3	289	.	0			c.C279T						PASS	.						5	6	5					15																	85360356		2058	4100	6158	SO:0001819	synonymous_variant	57538	exon1			CCGCTGCGCCTTC	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.279C>T	chr15.hg19:g.85360356C>T		75.0	0.0	.		74.0	24.0	.	NM_020778	Q9P2L6	Silent	SNP	ENST00000258888.5	hg19	CCDS10333.1																																																																																			.	.	.	none		0.731	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778		T	85360356	C	T	85360356	2	4	270	1	0	0	0	0	0	0	0	1	546	776	27	1		1	ALPK3	15	85360356	Silent	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10	6271366	85360356	17171036	56	17065											
ANPEP	290	hgsc.bcm.edu	37	chr15	90340878	90340878	+	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	aggctgctcagggcggcctcCcagggcatgtactgtctctc	5	9	13	14	1	2	0	1	0	1	0	5	0	3	0	2	4	2	4	2	4	1	1			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr15:90340878C>A	ENST00000300060.6	-	15	2398	c.2085G>T	c.(2083-2085)tgG>tgT	p.W695C	ANPEP_ENST00000558177.1_5'UTR	NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	695	Metalloprotease.				angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	GGGCGGCCTCCCAGGGCATGT	0.562																																					p.W695C	NSCLC(30;827 977 2459 19669 26125)	Atlas-SNP	.											.	ANPEP	124	.	0			c.G2085T						PASS	.						135	127	130					15																	90340878		2200	4299	6499	SO:0001583	missense	290	exon15			GGCCTCCCAGGGC	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"CD molecules"	500	protein-coding gene	gene with protein product	"aminopeptidase N", "aminopeptidase M", "microsomal aminopeptidase"	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.2085G>T	chr15.hg19:g.90340878C>A	ENSP00000300060:p.Trp695Cys	96.0	0.0	.		145.0	70.0	.	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Missense_Mutation	SNP	ENST00000300060.6	hg19	CCDS10356.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.725444	0.89298	.	.	ENSG00000166825	ENST00000300060	T	0.07908	3.15	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.47525	0.1450	H	0.97806	4.08	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.67341	-0.5695	10	0.87932	D	0	.	18.2369	0.89952	0.0:1.0:0.0:0.0	.	695	P15144	AMPN_HUMAN	C	695	ENSP00000300060:W695C	ENSP00000300060:W695C	W	-	3	0	ANPEP	88141882	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	7.659000	0.83766	2.728000	0.93425	0.655000	0.94253	TGG	.	.	.	none		0.562	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1			A	90340878	C	A	90340878	3	1	270	1	0	0	0	0	1	0	0	0	710	624	22	4	846	4	ANPEP	15	90340878	Missense_Mutation	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10	4980522	90340878	12190514	57	17066											
ANPEP	290	hgsc.bcm.edu	37	chr15	90349261	90349261	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgccaggtcatctgccaacTccccctcgaactcgctgtcc	6	8	7	20	3	2	0	1	0	1	0	6	1	4	0	6	1	3	1	6	1	2	0			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr15:90349261T>C	ENST00000300060.6	-	2	867	c.554A>G	c.(553-555)gAg>gGg	p.E185G		NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	185	Metalloprotease.				angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	ATCTGCCAACTCCCCCTCGAA	0.617																																					p.E185G	NSCLC(30;827 977 2459 19669 26125)	Atlas-SNP	.											.	ANPEP	124	.	0			c.A554G						PASS	.						91	85	87					15																	90349261		2200	4299	6499	SO:0001583	missense	290	exon2			GCCAACTCCCCCT	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"CD molecules"	500	protein-coding gene	gene with protein product	"aminopeptidase N", "aminopeptidase M", "microsomal aminopeptidase"	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.554A>G	chr15.hg19:g.90349261T>C	ENSP00000300060:p.Glu185Gly	33.0	0.0	.		42.0	20.0	.	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Missense_Mutation	SNP	ENST00000300060.6	hg19	CCDS10356.1	.	.	.	.	.	.	.	.	.	.	T	17.47	3.397231	0.62177	.	.	ENSG00000166825	ENST00000300060	T	0.02974	4.09	4.8	4.8	0.61643	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.19446	0.0467	M	0.93854	3.465	0.52099	D	0.999947	D	0.89917	1.0	D	0.91635	0.999	T	0.08806	-1.0704	10	0.29301	T	0.29	.	12.3003	0.54870	0.0:0.0:0.0:1.0	.	185	P15144	AMPN_HUMAN	G	185	ENSP00000300060:E185G	ENSP00000300060:E185G	E	-	2	0	ANPEP	88150265	1.000000	0.71417	1.000000	0.80357	0.161000	0.22273	6.099000	0.71466	1.794000	0.52575	0.460000	0.39030	GAG	.	.	.	none		0.617	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1			C	90349261	T	C	90349261	3	2	270	1	0	0	0	0	1	0	0	0	710	1551	54	3	2429	3	ANPEP	15	90349261	Missense_Mutation	SNP	T	TCGA-UZ-A9Q1-01A-11D-A42J-10	8383	90349261	12182131	58	17067											
ST8SIA2	8128	hgsc.bcm.edu	37	chr15	92981704	92981704	+	Frame_Shift_Del	DEL	A	A	-																															gcaccatgaatgtgtcccagAacctctacgagctcctcccc																										TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr15:92981704delA	ENST00000268164.3	+	4	649	c.412delA	c.(412-414)aacfs	p.N138fs	ST8SIA2_ENST00000539113.1_Frame_Shift_Del_p.N117fs	NM_006011.3	NP_006002.1	Q92186	SIA8B_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	138					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|ganglioside biosynthetic process (GO:0001574)|N-glycan processing (GO:0006491)|nervous system development (GO:0007399)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	early endosome (GO:0005769)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|recycling endosome (GO:0055037)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			endometrium(2)|large_intestine(6)|lung(9)|skin(2)|urinary_tract(1)	20	Lung NSC(78;0.0893)|all_lung(78;0.125)		BRCA - Breast invasive adenocarcinoma(143;0.0355)|OV - Ovarian serous cystadenocarcinoma(32;0.203)			TGTGTCCCAGAACCTCTACGA	0.512																																					p.Q137fs		Atlas-Indel,Pindel	.											.	ST8SIA2	41	.	0			c.411delG						PASS	.						143	144	144					15																	92981704		2198	4298	6496	SO:0001589	frameshift_variant	8128	exon4			.	U33551	CCDS10372.1	15q26	2013-03-01	2003-01-14	2005-02-07	ENSG00000140557	ENSG00000140557		"Sialyltransferases"	10870	protein-coding gene	gene with protein product		602546	"sialyltransferase 8 (alpha-2, 8-sialytransferase) B"	SIAT8B		7559389	Standard	NM_006011		Approved	STX, ST8SIA-II, HsT19690	uc002bra.3	Q92186	OTTHUMG00000149843	ENST00000268164.3:c.412delA	chr15.hg19:g.92981704delA	ENSP00000268164:p.Asn138fs	123.0	0.0	0		155.0	54.0	0.348387	NM_006011	Q4VAZ0|Q92470|Q92746	Frame_Shift_Del	DEL	ENST00000268164.3	hg19	CCDS10372.1																																																																																			.	.	.	none		0.512	ST8SIA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313526.1	NM_006011		-	92981704	A	-	92981704	7	5	270	1	0	1	0	1	0	0	0	0	15244	246	9	0	426	0	ST8SIA2	15	92981704	Frame_Shift_Del	DEL	A	TCGA-UZ-A9Q1-01A-11D-A42J-10	2632443	92981704	9549688	59	17068											
ZNF597	146434	hgsc.bcm.edu	37	chr16	3487452	3487453	+	Frame_Shift_Ins	INS	-	-	A																															taagggacaaggggtgcagcINSaatggggtacttttctaagg																										TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr16:3487452_3487453insA	ENST00000301744.4	-	4	481_482	c.246_247insT	c.(244-249)attgctfs	p.A83fs		NM_152457.1	NP_689670.1	Q96LX8	ZN597_HUMAN	zinc finger protein 597	83	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						AGGGGTGCAGCAATGGGGTACT	0.45																																					p.A83fs		Pindel	.											.	ZNF597	41	.	0			c.247_248insT						PASS	.																																			SO:0001589	frameshift_variant	146434	exon4			.	AK057633	CCDS10505.1	16p13.3	2013-01-08			ENSG00000167981	ENSG00000167981		"Zinc fingers, C2H2-type", "-"	26573	protein-coding gene	gene with protein product		614685				12477932	Standard	NM_152457		Approved	FLJ33071	uc002cvd.3	Q96LX8	OTTHUMG00000129359	ENST00000301744.4:c.247dupT	chr16.hg19:g.3487454_3487454dupA	ENSP00000301744:p.Ala83fs	91.0	0.0	.		121.0	43.0	0.355	NM_152457		Frame_Shift_Ins	INS	ENST00000301744.4	hg19	CCDS10505.1																																																																																			.	.	.	none		0.45	ZNF597-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251511.2	NM_152457		A	3487453	-	A	3487452	7	5	270	1	0	1	1	0	0	0	0	0	18039	710	25	0	1031	0	ZNF597	16	3487452	Frame_Shift_Ins	INS	-	TCGA-UZ-A9Q1-01A-11D-A42J-10		3487452	86867301	60	17069											
NUDT16L1	84309	hgsc.bcm.edu	37	chr16	4745104	4745104	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caacatgatgcccgaggagaAgctggttgaggccctggctg	9	7	15	10	1	0	3	0	2	0	1	0	5	0	3	2	4	3	3	2	4	2	1			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr16:4745104A>G	ENST00000304301.6	+	3	593	c.560A>G	c.(559-561)aAg>aGg	p.K187R	NUDT16L1_ENST00000405142.1_3'UTR|NUDT16L1_ENST00000586252.1_Missense_Mutation_p.K147R|NUDT16L1_ENST00000586536.1_3'UTR	NM_032349.3	NP_115725.1	Q9BRJ7	SDOS_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 16-like 1	187	Interaction with PXN. {ECO:0000250}.					cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)|poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)			endometrium(1)|large_intestine(1)|lung(1)|skin(1)	4						CCCGAGGAGAAGCTGGTTGAG	0.622																																					p.K187R		Atlas-SNP	.											.	NUDT16L1	13	.	0			c.A560G						PASS	.						82	78	80					16																	4745104		2197	4300	6497	SO:0001583	missense	84309	exon3			AGGAGAAGCTGGT	BC006223	CCDS10519.1, CCDS59257.1	16p13.3	2008-02-05			ENSG00000168101	ENSG00000168101		"Nudix motif containing"	28154	protein-coding gene	gene with protein product						11805099	Standard	NM_032349		Approved	SDOS	uc002cxe.3	Q9BRJ7	OTTHUMG00000129471	ENST00000304301.6:c.560A>G	chr16.hg19:g.4745104A>G	ENSP00000306670:p.Lys187Arg	59.0	0.0	.		129.0	32.0	.	NM_032349	Q8NAI2	Missense_Mutation	SNP	ENST00000304301.6	hg19	CCDS10519.1	.	.	.	.	.	.	.	.	.	.	A	15.37	2.813806	0.50527	.	.	ENSG00000168101	ENST00000304301	T	0.50001	0.76	4.38	4.38	0.52667	NUDIX hydrolase domain-like (1);	4.226410	0.00639	N	0.000518	T	0.40979	0.1139	N	0.22421	0.69	0.80722	D	1	P	0.47484	0.896	B	0.41466	0.358	T	0.28964	-1.0027	10	0.23891	T	0.37	.	12.4484	0.55664	1.0:0.0:0.0:0.0	.	187	Q9BRJ7	SDOS_HUMAN	R	187	ENSP00000306670:K187R	ENSP00000306670:K187R	K	+	2	0	NUDT16L1	4685105	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.660000	0.61511	1.605000	0.50152	0.533000	0.62120	AAG	.	.	.	none		0.622	NUDT16L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251634.1	NM_032349		G	4745104	A	G	4745104	3	3	270	1	0	0	0	0	1	0	0	0	10740	72	3	3	570	3	NUDT16L1	16	4745104	Missense_Mutation	SNP	A	TCGA-UZ-A9Q1-01A-11D-A42J-10	1257652	4745104	85609649	61	17070											
GFOD2	81577	hgsc.bcm.edu	37	chr16	67719468	67719468	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtccggctggtgtagaaggCgatgttcatctcctcagcaa	9	10	12	10	2	3	1	2	0	1	1	5	2	4	1	2	3	1	4	2	3	3	2	rs145155253		TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr16:67719468C>T	ENST00000268797.7	-	2	496	c.151G>A	c.(151-153)Gcc>Acc	p.A51T	GFOD2_ENST00000602377.1_5'UTR	NM_030819.3	NP_110446.3	Q3B7J2	GFOD2_HUMAN	glucose-fructose oxidoreductase domain containing 2	51					extracellular matrix organization (GO:0030198)	proteinaceous extracellular matrix (GO:0005578)	oxidoreductase activity (GO:0016491)			breast(2)|endometrium(1)|large_intestine(4)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	19		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0151)|Epithelial(162;0.0505)|all cancers(182;0.242)		GTGTAGAAGGCGATGTTCATC	0.567																																					p.A51T		Atlas-SNP	.											.	GFOD2	36	.	0			c.G151A						PASS	.	C	THR/ALA	0,4396		0,0,2198	102	78	86		151	0.6	1	16	dbSNP_134	86	2,8598	2.2+/-6.3	0,2,4298	no	missense	GFOD2	NM_030819.3	58	0,2,6496	TT,TC,CC		0.0233,0.0,0.0154	benign	51/386	67719468	2,12994	2198	4300	6498	SO:0001583	missense	81577	exon2			AGAAGGCGATGTT	AK074382	CCDS10845.1, CCDS59268.1	16q22.1	2008-02-05			ENSG00000141098	ENSG00000141098			28159	protein-coding gene	gene with protein product						12975309	Standard	NM_030819		Approved	FLJ23802, MGC11335	uc002eub.3	Q3B7J2	OTTHUMG00000137537	ENST00000268797.7:c.151G>A	chr16.hg19:g.67719468C>T	ENSP00000268797:p.Ala51Thr	58.0	0.0	.		96.0	28.0	.	NM_001243650	Q69YL9|Q6UXX6|Q7L648|Q8TE86|Q9BQ07|R4GNG5	Missense_Mutation	SNP	ENST00000268797.7	hg19	CCDS10845.1	.	.	.	.	.	.	.	.	.	.	C	14.36	2.513067	0.44660	0.0	2.33E-4	ENSG00000141098	ENST00000268797	T	0.22743	1.94	5.58	0.555	0.17247	Oxidoreductase, N-terminal (1);NAD(P)-binding domain (1);	0.438834	0.26349	N	0.024890	T	0.13628	0.0330	L	0.48642	1.525	0.23293	N	0.997962	B	0.21452	0.056	B	0.17098	0.017	T	0.16928	-1.0386	10	0.41790	T	0.15	-9.6132	1.6318	0.02734	0.2087:0.3687:0.1169:0.3057	.	51	Q3B7J2	GFOD2_HUMAN	T	51	ENSP00000268797:A51T	ENSP00000268797:A51T	A	-	1	0	GFOD2	66276969	0.995000	0.38212	0.997000	0.53966	0.894000	0.52154	0.540000	0.23191	0.101000	0.17610	-0.367000	0.07326	GCC	.	C|1.000;T|0.000	0.000	weak		0.567	GFOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268868.2	NM_030819		T	67719468	C	T	67719468	3	4	270	1	0	0	0	0	1	0	0	0	6351	768	27	1	1014	1	GFOD2	16	67719468	Missense_Mutation	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10	62974364	67719468	22635285	62	17071											
SMG6	23293	hgsc.bcm.edu	37	chr17	1989066	1989066	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttcccatttcctttcccaTggtgtctgggacgggtgcca	4	13	11	13	1	1	0	0	0	1	0	4	1	4	1	4	3	1	1	4	3	0	3	rs369806279		TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr17:1989066T>C	ENST00000263073.6	-	14	3537	c.3487A>G	c.(3487-3489)Atg>Gtg	p.M1163V	SMG6_ENST00000354901.4_Missense_Mutation_p.M255V|SMG6_ENST00000573166.1_5'UTR|SMG6_ENST00000536871.2_Missense_Mutation_p.M255V|SMG6_ENST00000544865.1_Missense_Mutation_p.M1132V	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	1163					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						TCCTTTCCCATGGTGTCTGGG	0.547																																					p.M1163V	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.A3487G						PASS	.	T	VAL/MET,VAL/MET	0,4406		0,0,2203	278	263	268		3394,3487	5.9	1	17		268	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	SMG6	NM_001170957.1,NM_017575.4	21,21	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	benign,benign	1132/1389,1163/1420	1989066	1,13005	2203	4300	6503	SO:0001583	missense	23293	exon14			TTCCCATGGTGTC	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.3487A>G	chr17.hg19:g.1989066T>C	ENSP00000263073:p.Met1163Val	95.0	0.0	.		123.0	11.0	.	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Missense_Mutation	SNP	ENST00000263073.6	hg19	CCDS11016.1	.	.	.	.	.	.	.	.	.	.	T	10.57	1.388136	0.25118	0.0	1.16E-4	ENSG00000070366	ENST00000263073;ENST00000544865;ENST00000354901;ENST00000536871	T;T;T	0.16324	3.17;3.17;2.35	5.93	5.93	0.95920	.	0.243961	0.43260	D	0.000590	T	0.09905	0.0243	N	0.12182	0.205	0.44816	D	0.997822	B	0.27351	0.176	B	0.14023	0.01	T	0.24297	-1.0164	10	0.12430	T	0.62	-8.9459	16.3798	0.83452	0.0:0.0:0.0:1.0	.	1163	Q86US8	EST1A_HUMAN	V	1163;1132;74;255	ENSP00000263073:M1163V;ENSP00000443920:M1132V;ENSP00000440283:M255V	ENSP00000263073:M1163V	M	-	1	0	SMG6	1935816	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.867000	0.63013	2.271000	0.75665	0.533000	0.62120	ATG	.	.	.	weak		0.547	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3			C	1989066	T	C	1989066	3	2	270	1	0	0	0	0	1	0	0	0	14810	1464	51	3	796	3	SMG6	17	1989066	Missense_Mutation	SNP	T	TCGA-UZ-A9Q1-01A-11D-A42J-10		1989066	79206144	63	17072											
RAI1	10743	hgsc.bcm.edu	37	chr17	17699195	17699195	+	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	tctggcccagaagcccaacaAgcctgctgtgcccgaggcgc	8	5	12	16	2	1	1	0	0	1	1	1	2	1	1	4	2	5	1	4	2	3	0			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr17:17699195A>T	ENST00000353383.1	+	3	3402	c.2933A>T	c.(2932-2934)aAg>aTg	p.K978M	RAI1_ENST00000261641.6_Missense_Mutation_p.K978M	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	978					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)		AAGCCCAACAAGCCTGCTGTG	0.657																																					p.K978M		Atlas-SNP	.											.	RAI1	121	.	0			c.A2933T						PASS	.						29	30	30					17																	17699195		2203	4299	6502	SO:0001583	missense	10743	exon3			CCAACAAGCCTGC	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.2933A>T	chr17.hg19:g.17699195A>T	ENSP00000323074:p.Lys978Met	27.0	0.0	.		59.0	25.0	.	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Missense_Mutation	SNP	ENST00000353383.1	hg19	CCDS11188.1	.	.	.	.	.	.	.	.	.	.	A	14.60	2.582930	0.46006	.	.	ENSG00000108557	ENST00000353383;ENST00000395776;ENST00000261641;ENST00000315321	T;T	0.72282	-0.64;-0.04	4.59	3.49	0.39957	.	0.277855	0.30519	N	0.009444	T	0.70937	0.3281	L	0.57536	1.79	0.35405	D	0.791949	P	0.46395	0.877	P	0.47470	0.548	T	0.77789	-0.2456	10	0.62326	D	0.03	.	11.3935	0.49827	0.8486:0.1514:0.0:0.0	.	978	Q7Z5J4	RAI1_HUMAN	M	978;978;978;930	ENSP00000323074:K978M;ENSP00000261641:K978M	ENSP00000261641:K978M	K	+	2	0	RAI1	17639920	1.000000	0.71417	0.975000	0.42487	0.557000	0.35523	2.673000	0.46858	0.593000	0.29745	0.402000	0.26972	AAG	.	.	.	none		0.657	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665		T	17699195	A	T	17699195	3	4	270	1	0	0	0	0	1	0	0	0	13020	72	3	5	2935	5	RAI1	17	17699195	Missense_Mutation	SNP	A	TCGA-UZ-A9Q1-01A-11D-A42J-10	15710129	17699195	63496015	64	17073											
FAM83G	644815	hgsc.bcm.edu	37	chr17	18882130	18882130	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagacagcacagagatcacAttccggtccgtccgcgcggc	9	5	11	16	5	1	2	1	0	0	2	4	3	4	2	4	2	1	1	4	2	0	1			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr17:18882130A>G	ENST00000388995.6	-	5	1072	c.849T>C	c.(847-849)aaT>aaC	p.N283N	SLC5A10_ENST00000395647.2_Intron|SLC5A10_ENST00000417251.2_Intron|SLC5A10_ENST00000395643.2_Intron|FAM83G_ENST00000345041.4_Silent_p.N283N|FAM83G_ENST00000585154.2_Silent_p.N283N|SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000317977.6_Intron|SLC5A10_ENST00000395645.3_Intron			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	283					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						CAGAGATCACATTCCGGTCCG	0.632																																					p.N283N		Atlas-SNP	.											.	FAM83G	51	.	0			c.T849C						PASS	.						52	58	56					17																	18882130		2168	4253	6421	SO:0001819	synonymous_variant	644815	exon5			GATCACATTCCGG	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.849T>C	chr17.hg19:g.18882130A>G		165.0	0.0	.		158.0	73.0	.	NM_001039999	Q3KQZ4|Q6ZW60	Silent	SNP	ENST00000388995.6	hg19	CCDS42276.1																																																																																			.	.	.	none		0.632	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4			G	18882130	A	G	18882130	2	3	270	1	0	0	0	0	0	0	0	1	5646	214	8	3		3	FAM83G	17	18882130	Silent	SNP	A	TCGA-UZ-A9Q1-01A-11D-A42J-10	1182935	18882130	62313080	65	17074											
KIAA0100	9703	hgsc.bcm.edu	37	chr17	26961608	26961608	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctaatccctcagggggaaaAgggctgcctggatcaagctc	10	8	12	11	0	3	0	2	0	1	0	5	2	4	2	2	4	2	2	2	4	4	1			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr17:26961608A>G	ENST00000528896.2	-	16	3071	c.2997T>C	c.(2995-2997)ccT>ccC	p.P999P	KIAA0100_ENST00000544884.1_Silent_p.P856P|RP11-192H23.7_ENST00000583787.1_RNA|KIAA0100_ENST00000389003.3_Silent_p.P856P|RP11-192H23.7_ENST00000577814.1_RNA	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	999						extracellular region (GO:0005576)		p.P999P(1)		breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					CAGGGGGAAAAGGGCTGCCTG	0.493																																					p.P999P		Atlas-SNP	.											KIAA0100,NS,carcinoma,0,1	KIAA0100	175	.	1	Substitution - coding silent(1)	prostate(1)	c.T2997C						PASS	.						110	106	107					17																	26961608		2203	4300	6503	SO:0001819	synonymous_variant	9703	exon16			GGGAAAAGGGCTG	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.2997T>C	chr17.hg19:g.26961608A>G		79.0	0.0	.		97.0	4.0	.	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Silent	SNP	ENST00000528896.2	hg19	CCDS32595.1																																																																																			.	.	.	none		0.493	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		G	26961608	A	G	26961608	2	3	270	1	0	0	0	0	0	0	0	1	8161	59	3	3		3	KIAA0100	17	26961608	Silent	SNP	A	TCGA-UZ-A9Q1-01A-11D-A42J-10	8079478	26961608	54233602	66	17075											
KRTAP4-7	100132476	hgsc.bcm.edu	37	chr17	39240791	39240791	+	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	tgccagcccacctgctgccgCcccagctgctgccgcccctg	3	6	10	22	2	0	0	0	0	0	0	0	0	0	0	9	0	7	3	9	0	0	0	rs553572799	byFrequency	TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	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,0,2	KRTAP4-7	49	.	2	Unknown(1)|Deletion - In frame(1)	NS(2)	c.C333G						PASS	.																																			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	chr17.hg19:g.39240791C>G		19.0	0.0	.		42.0	6.0	.	NM_033061	A0AVM6|A8MQ08|A8MTL4	Silent	SNP	ENST00000391417.4	hg19	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	270	1	0	0	0	0	0	0	0	1	8562	726	26	4		4	KRTAP4-7	17	39240791	Silent	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10	12279183	39240791	41954419	67	17076											
KRT34	3885	hgsc.bcm.edu	37	chr17	39538610	39538610	+	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	ccattaattgtgggtgggggCttggcatacagcatagtttc	8	13	13	7	0	0	0	0	0	0	0	1	0	0	0	1	4	2	4	1	4	3	6			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr17:39538610C>T	ENST00000394001.1	-	1	45	c.15G>A	c.(13-15)aaG>aaA	p.K5K		NM_021013.3	NP_066293.2	O76011	KRT34_HUMAN	keratin 34	5	Head.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Breast(137;0.000496)				TGGGTGGGGGCTTGGCATACA	0.443																																					p.K5K		Atlas-SNP	.											.	KRT34	71	.	0			c.G15A						PASS	.						70	70	70					17																	39538610		2203	4300	6503	SO:0001819	synonymous_variant	3885	exon1			TGGGGGCTTGGCA	Y16790	CCDS11390.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000131737	ENSG00000131737		"-", "Intermediate filaments type I, keratins (acidic)"	6452	protein-coding gene	gene with protein product	"hard keratin type I 4"	602763	"keratin, hair, acidic, 4"	KRTHA4		2431943, 9756910, 16831889	Standard	NM_021013		Approved	Ha-4	uc002hwm.3	O76011	OTTHUMG00000133436	ENST00000394001.1:c.15G>A	chr17.hg19:g.39538610C>T		89.0	0.0	.		152.0	58.0	.	NM_021013	Q8IUT8|Q8N4W2	Silent	SNP	ENST00000394001.1	hg19	CCDS11390.1																																																																																			.	.	.	none		0.443	KRT34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257304.3	NM_021013		T	39538610	C	T	39538610	2	4	270	1	0	0	0	0	0	0	0	1	8478	796	28	2		2	KRT34	17	39538610	Silent	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10	297819	39538610	41656600	68	17077											
ATCAY	85300	hgsc.bcm.edu	37	chr19	3907799	3907799	+	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	gatctatttggggacggcacGacggaggacggcagcgccgc	8	5	17	11	6	1	0	0	0	1	0	1	5	1	3	1	6	1	2	1	6	1	2	rs373080859	byFrequency	TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr19:3907799G>C	ENST00000450849.2	+	5	893	c.426G>C	c.(424-426)acG>acC	p.T142T	ATCAY_ENST00000600960.1_Silent_p.T142T|ATCAY_ENST00000398448.3_Silent_p.T148T|ATCAY_ENST00000301260.6_Silent_p.T142T	NM_033064.4	NP_149053.1	Q86WG3	ATCAY_HUMAN	ataxia, cerebellar, Cayman type	142					apoptotic process (GO:0006915)|mitochondrion distribution (GO:0048311)|negative regulation of glutamate metabolic process (GO:2000212)|neuron projection development (GO:0031175)|regulation of protein localization (GO:0032880)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrial membrane (GO:0031966)|neuron projection (GO:0043005)|synapse (GO:0045202)	kinesin binding (GO:0019894)			breast(1)|endometrium(2)|kidney(2)|lung(2)	7		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00485)|STAD - Stomach adenocarcinoma(1328;0.183)		GGGACGGCACGACGGAGGACG	0.647																																					p.T142T		Atlas-SNP	.											.	ATCAY	84	.	0			c.G426C						PASS	.						48	58	55					19																	3907799		2075	4210	6285	SO:0001819	synonymous_variant	85300	exon5			CGGCACGACGGAG		CCDS45923.1	19p13.3	2014-06-24	2008-07-18		ENSG00000167654	ENSG00000167654			779	protein-coding gene	gene with protein product	"Cayman ataxia", "caytaxin"	608179				8845847, 14556008	Standard	NM_033064		Approved		uc002lyy.4	Q86WG3	OTTHUMG00000181836	ENST00000450849.2:c.426G>C	chr19.hg19:g.3907799G>C		208.0	0.0	.		257.0	114.0	.	NM_033064	Q8NAQ2|Q8TAQ3|Q96HC6|Q96JF5	Silent	SNP	ENST00000450849.2	hg19	CCDS45923.1																																																																																			.	.	.	alt		0.647	ATCAY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457872.2			C	3907799	G	C	3907799	2	2	270	1	0	0	0	0	0	0	0	1	1077	1045	37	4		4	ATCAY	19	3907799	Silent	SNP	G	TCGA-UZ-A9Q1-01A-11D-A42J-10		3907799	55221184	69	17078											
OR7A10	390892	hgsc.bcm.edu	37	chr19	14952156	14952157	+	Frame_Shift_Ins	INS	-	-	A																															ccacctgattaatttcacagINSaaaaaatgagggatttccat																										TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr19:14952156_14952157insA	ENST00000248058.1	-	1	532_533	c.533_534insT	c.(532-534)ttcfs	p.F178fs		NM_001005190.1	NP_001005190.1	O76100	OR7AA_HUMAN	olfactory receptor, family 7, subfamily A, member 10	178						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)					TAATTTCACAGAAAAAATGAGG	0.45																																					p.F178fs		Atlas-Indel,Pindel	.											.	OR7A10	33	.	0			c.534_535insT						PASS	.																																			SO:0001589	frameshift_variant	390892	exon1			.		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.534dupT	chr19.hg19:g.14952162_14952162dupA	ENSP00000248058:p.Phe178fs	140.0	0.0	0		181.0	68.0	0.375691	NM_001005190	Q6IFP0|Q96R97	Frame_Shift_Ins	INS	ENST00000248058.1	hg19	CCDS32936.1																																																																																			.	.	.	none		0.45	OR7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466520.1	NM_001005190		A	14952157	-	A	14952156	7	5	270	1	0	1	1	0	0	0	0	0	11221	933	33	0	399	0	OR7A10	19	14952156	Frame_Shift_Ins	INS	-	TCGA-UZ-A9Q1-01A-11D-A42J-10	11044357	14952156	44176827	70	17079											
BRD4	23476	hgsc.bcm.edu	37	chr19	15354087	15354087	+	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	accttctgcagctgctgcagGtacagctgcatctgcatgga	8	10	11	12	0	2	0	0	0	2	0	2	1	2	1	1	2	8	8	1	2	1	2			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr19:15354087G>A	ENST00000263377.2	-	14	3014	c.2793C>T	c.(2791-2793)taC>taT	p.Y931Y		NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	931					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)			GCTGCTGCAGGTACAGCTGCA	0.692			T	C15orf55	lethal midline carcinoma of young people																																p.Y931Y		Atlas-SNP	.		Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	.	BRD4	172	.	0			c.C2793T						PASS	.						9	9	9					19																	15354087		2151	4234	6385	SO:0001819	synonymous_variant	23476	exon14			CTGCAGGTACAGC	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.2793C>T	chr19.hg19:g.15354087G>A		44.0	0.0	.		32.0	18.0	.	NM_058243	O60433|Q4G0X8|Q86YS8|Q96PD3	Silent	SNP	ENST00000263377.2	hg19	CCDS12328.1																																																																																			.	.	.	none		0.692	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243		A	15354087	G	A	15354087	2	1	270	1	0	0	0	0	0	0	0	1	1506	1256	44	2		2	BRD4	19	15354087	Silent	SNP	G	TCGA-UZ-A9Q1-01A-11D-A42J-10	401931	15354087	43774896	71	17080											
GYS1	2997	hgsc.bcm.edu	37	chr19	49489290	49489290	+	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	ttctcctcactctgtgccagGaactgtgggcaacagggaca	9	9	11	12	0	3	0	1	0	2	0	4	2	3	2	2	3	3	1	2	3	2	1			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr19:49489290G>A	ENST00000323798.3	-	4	691	c.495C>T	c.(493-495)ttC>ttT	p.F165F	GYS1_ENST00000540532.1_Silent_p.F85F|GYS1_ENST00000541188.1_Silent_p.F85F|GYS1_ENST00000263276.6_Silent_p.F101F|GYS1_ENST00000457974.1_5'Flank|GYS1_ENST00000544287.1_Intron	NM_002103.4	NP_002094.2	P13807	GYS1_HUMAN	glycogen synthase 1 (muscle)	165					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|heart development (GO:0007507)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|inclusion body (GO:0016234)|membrane (GO:0016020)	glucose binding (GO:0005536)|glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000164)|all cancers(93;0.000226)|GBM - Glioblastoma multiforme(486;0.00561)|Epithelial(262;0.0286)		TCTGTGCCAGGAACTGTGGGC	0.582																																					p.F165F		Atlas-SNP	.											.	GYS1	59	.	0			c.C495T						PASS	.						52	43	46					19																	49489290		2203	4300	6503	SO:0001819	synonymous_variant	2997	exon4			TGCCAGGAACTGT		CCDS12747.1, CCDS54292.1	19q13.3	2013-02-22			ENSG00000104812	ENSG00000104812	2.4.1.11	"Glycosyltransferase group 1 domain containing"	4706	protein-coding gene	gene with protein product		138570		GYS			Standard	NM_002103		Approved	GSY	uc002plp.3	P13807	OTTHUMG00000150723	ENST00000323798.3:c.495C>T	chr19.hg19:g.49489290G>A		46.0	0.0	.		43.0	14.0	.	NM_002103	Q9BTT9	Silent	SNP	ENST00000323798.3	hg19	CCDS12747.1																																																																																			.	.	.	none		0.582	GYS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319791.1	NM_002103		A	49489290	G	A	49489290	2	1	270	1	0	0	0	0	0	0	0	1	6919	1165	41	2		2	GYS1	19	49489290	Silent	SNP	G	TCGA-UZ-A9Q1-01A-11D-A42J-10	34135203	49489290	9639693	72	17081											
PPFIA3	8541	hgsc.bcm.edu	37	chr19	49652538	49652538	+	Missense_Mutation	SNP	T	T	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	ggcagcttctggagaaggaaTtcagcaaccttatctcctta	11	11	9	10	0	3	1	1	0	2	1	4	3	3	2	2	3	3	3	2	3	5	4			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr19:49652538T>G	ENST00000334186.4	+	27	3659	c.3310T>G	c.(3310-3312)Ttc>Gtc	p.F1104V	PPFIA3_ENST00000602351.1_Missense_Mutation_p.F1095V	NM_003660.2	NP_003651.1	O75145	LIPA3_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 3	1104	SAM 3. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|presynaptic active zone (GO:0048786)				NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(16)|pancreas(1)|prostate(1)|skin(4)|urinary_tract(1)	35		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)		GGAGAAGGAATTCAGCAACCT	0.657																																					p.F1104V		Atlas-SNP	.											.	PPFIA3	71	.	0			c.T3310G						PASS	.						38	43	41					19																	49652538		2203	4300	6503	SO:0001583	missense	8541	exon27			AAGGAATTCAGCA	AF034800	CCDS12758.1	19q13.33	2013-09-23			ENSG00000177380	ENSG00000177380		"Sterile alpha motif (SAM) domain containing"	9247	protein-coding gene	gene with protein product	"protein tyrosine phosphatase, receptor type, f polypeptide, alpha 3", "liprin-alpha 3", "liprin"	603144				9624153, 9734811	Standard	NM_003660		Approved	KIAA0654, LPNA3, MGC126567, MGC126569	uc002pmr.3	O75145	OTTHUMG00000183213	ENST00000334186.4:c.3310T>G	chr19.hg19:g.49652538T>G	ENSP00000335614:p.Phe1104Val	168.0	0.0	.		167.0	68.0	.	NM_003660	A8K142|Q3MJA0|Q9H8B5|Q9UEW4	Missense_Mutation	SNP	ENST00000334186.4	hg19	CCDS12758.1	.	.	.	.	.	.	.	.	.	.	T	26.6	4.749161	0.89753	.	.	ENSG00000177380	ENST00000334186	D	0.83914	-1.78	4.29	4.29	0.51040	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (1);Sterile alpha motif, type 2 (1);	0.000000	0.50627	D	0.000111	D	0.88100	0.6346	M	0.78285	2.405	0.80722	D	1	P;D	0.53462	0.934;0.96	P;P	0.55615	0.78;0.699	D	0.89774	0.3956	10	0.87932	D	0	-18.5267	12.8314	0.57748	0.0:0.0:0.0:1.0	.	1095;1104	O75145-2;O75145	.;LIPA3_HUMAN	V	1104	ENSP00000335614:F1104V	ENSP00000335614:F1104V	F	+	1	0	PPFIA3	54344350	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.014000	0.70784	1.935000	0.56089	0.459000	0.35465	TTC	.	.	.	none		0.657	PPFIA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465688.1	NM_003660		G	49652538	T	G	49652538	3	3	270	1	0	0	0	0	1	0	0	0	12318	1493	52	5	3412	5	PPFIA3	19	49652538	Missense_Mutation	SNP	T	TCGA-UZ-A9Q1-01A-11D-A42J-10	163248	49652538	9476445	73	17082											
TSHZ2	128553	hgsc.bcm.edu	37	chr20	51871547	51871547	+	Missense_Mutation	SNP	T	T	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	aaagggtggaggggacatttTgaaatctttggaaaatactg	14	11	13	3	0	1	1	0	1	1	0	1	4	1	4	0	5	1	0	0	5	5	4			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr20:51871547T>G	ENST00000371497.5	+	2	2437	c.1550T>G	c.(1549-1551)tTg>tGg	p.L517W	TSHZ2_ENST00000329613.6_Missense_Mutation_p.L514W|TSHZ2_ENST00000603338.2_Missense_Mutation_p.L514W|RP4-678D15.1_ENST00000606932.1_RNA	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	517					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)			GGGGACATTTTGAAATCTTTG	0.483																																					p.L517W		Atlas-SNP	.											.	TSHZ2	209	.	0			c.T1550G						PASS	.						56	60	59					20																	51871547		2203	4300	6503	SO:0001583	missense	128553	exon2			ACATTTTGAAATC	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.1550T>G	chr20.hg19:g.51871547T>G	ENSP00000360552:p.Leu517Trp	98.0	0.0	.		126.0	66.0	.	NM_173485	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	hg19	CCDS33490.1	.	.	.	.	.	.	.	.	.	.	T	19.69	3.874271	0.72180	.	.	ENSG00000182463	ENST00000371497;ENST00000329613;ENST00000450262	T;T	0.54866	0.55;0.55	5.95	5.95	0.96441	.	0.000000	0.64402	D	0.000001	T	0.74015	0.3661	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.77437	-0.2588	10	0.87932	D	0	-12.7719	16.3964	0.83607	0.0:0.0:0.0:1.0	.	517	Q9NRE2	TSH2_HUMAN	W	517;514;43	ENSP00000360552:L517W;ENSP00000333114:L514W	ENSP00000333114:L514W	L	+	2	0	TSHZ2	51304954	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	7.693000	0.84214	2.275000	0.75901	0.523000	0.50628	TTG	.	.	.	none		0.483	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485		G	51871547	T	G	51871547	3	3	270	1	0	0	0	0	1	0	0	0	16636	1821	63	5	1556	5	TSHZ2	20	51871547	Missense_Mutation	SNP	T	TCGA-UZ-A9Q1-01A-11D-A42J-10		51871547	11153973	74	17083											
TH1L	51497	hgsc.bcm.edu	37	chr20	57568776	57568776	+	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	catccgaaagtgtctggagaAgctggacactgacatttcac	12	9	10	10	1	2	2	1	1	1	1	3	5	3	3	1	2	1	1	1	2	2	1			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr20:57568776A>T	ENST00000344018.3	+	13	1592	c.1565A>T	c.(1564-1566)aAg>aTg	p.K522M	NELFCD_ENST00000479207.1_Intron|NELFCD_ENST00000602795.1_Missense_Mutation_p.K531M			Q8IXH7	NELFD_HUMAN	negative elongation factor complex member C/D	522					gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	membrane (GO:0016020)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)											TGTCTGGAGAAGCTGGACACT	0.453																																					p.K531M		Atlas-SNP	.											.	.	.	.	0			c.A1592T						PASS	.						198	176	183					20																	57568776		2203	4300	6503	SO:0001583	missense	51497	exon13			TGGAGAAGCTGGA	AF161479	CCDS13473.1, CCDS13473.2	20q13	2013-01-31	2013-01-31	2013-01-31	ENSG00000101158	ENSG00000101158			15934	protein-coding gene	gene with protein product	"trihydrophobin 1"	605297	"TH1-like (Drosophila homolog)", "TH1-like (Drosophila)"	TH1L		11030415, 11042152	Standard	NM_198976		Approved	HSPC130, TH1, NELF-C, NELF-D	uc002yag.4	Q8IXH7	OTTHUMG00000032861	ENST00000344018.3:c.1565A>T	chr20.hg19:g.57568776A>T	ENSP00000342300:p.Lys522Met	80.0	0.0	.		74.0	35.0	.	NM_198976	B4DE06|Q9BYL2|Q9H405|Q9H888|Q9H8T3|Q9NVX5|Q9P029|Q9UGN1|Q9UGN2|Q9UGN3	Missense_Mutation	SNP	ENST00000344018.3	hg19		.	.	.	.	.	.	.	.	.	.	A	18.47	3.631340	0.67015	.	.	ENSG00000101158	ENST00000344018	.	.	.	4.35	4.35	0.52113	.	0.000000	0.85682	D	0.000000	T	0.65678	0.2714	L	0.47716	1.5	0.58432	D	0.999995	D	0.69078	0.997	P	0.60345	0.873	T	0.68519	-0.5387	9	0.56958	D	0.05	-49.9271	13.982	0.64310	1.0:0.0:0.0:0.0	.	522	Q8IXH7	NELFD_HUMAN	M	522	.	ENSP00000342300:K522M	K	+	2	0	TH1L	57002171	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.301000	0.78850	1.953000	0.56701	0.455000	0.32223	AAG	.	.	.	none		0.453	NELFCD-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198976		T	57568776	A	T	57568776	3	4	270	1	0	0	0	0	1	0	0	0	15851	72	3	5	1615	5	TH1L	20	57568776	Missense_Mutation	SNP	A	TCGA-UZ-A9Q1-01A-11D-A42J-10	5697229	57568776	5456744	75	17084											
C20orf151	140893	hgsc.bcm.edu	37	chr20	60992327	60992327	+	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	ttcagtgtcttctgctgttcCcggagctggtggttcttgga	3	16	13	9	1	4	0	1	0	3	0	5	2	5	2	1	4	2	4	1	4	0	5			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr20:60992327C>A	ENST00000252998.1	-	4	309	c.153G>T	c.(151-153)cgG>cgT	p.R51R		NM_080833.2	NP_543023.2	Q8NC74	RB8NL_HUMAN	RBBP8 N-terminal like	51						extracellular space (GO:0005615)											TCTGCTGTTCCCGGAGCTGGT	0.612																																					p.R51R		Atlas-SNP	.											.	.	.	.	0			c.G153T						PASS	.						108	75	86					20																	60992327		2203	4296	6499	SO:0001819	synonymous_variant	140893	exon4			CTGTTCCCGGAGC	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.153G>T	chr20.hg19:g.60992327C>A		59.0	0.0	.		46.0	17.0	.	NM_080833	B2RP98|Q8N4Z9|Q9BR75|Q9H0Y9	Silent	SNP	ENST00000252998.1	hg19	CCDS13498.1																																																																																			.	.	.	none		0.612	RBBP8NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080029.1	NM_080833		A	60992327	C	A	60992327	2	1	270	1	0	0	0	0	0	0	0	1	2093	610	22	4		4	C20orf151	20	60992327	Silent	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10	3423551	60992327	2033193	76	17085											
PTK6	5753	hgsc.bcm.edu	37	chr20	62168575	62168575	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccacgtggaagacgtccccCgcgcggaagctcagctcctc	7	5	12	17	5	1	1	1	0	0	1	4	3	3	3	4	2	2	2	4	2	2	0	rs370151198		TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr20:62168575C>T	ENST00000217185.2	-	1	120	c.93G>A	c.(91-93)gcG>gcA	p.A31A	PTK6_ENST00000542869.1_5'UTR	NM_005975.3	NP_005966.1	Q13882	PTK6_HUMAN	protein tyrosine kinase 6	31	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|intestinal epithelial cell differentiation (GO:0060575)|negative regulation of growth (GO:0045926)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of neuron projection development (GO:0010976)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|ruffle (GO:0001726)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			endometrium(3)|kidney(1)|lung(5)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	15	all_cancers(38;2.51e-11)		Epithelial(9;1.5e-08)|all cancers(9;8.67e-08)|BRCA - Breast invasive adenocarcinoma(10;6.43e-06)		Vandetanib(DB05294)	AGACGTCCCCCGCGCGGAAGC	0.701																																					p.A31A		Atlas-SNP	.											.	PTK6	33	.	0			c.G93A						PASS	.	A		1,4369	2.1+/-5.4	0,1,2184	33	28	30		93	-9	0	20		30	0,8580		0,0,4290	no	coding-synonymous	PTK6	NM_005975.2		0,1,6474	TT,TC,CC		0.0,0.0229,0.0077		31/452	62168575	1,12949	2185	4290	6475	SO:0001819	synonymous_variant	5753	exon1			GTCCCCCGCGCGG	U61412	CCDS13524.1, CCDS74750.1	20q13.3	2013-02-18	2013-02-18		ENSG00000101213	ENSG00000101213	2.7.10.1	"SH2 domain containing"	9617	protein-coding gene	gene with protein product		602004	"PTK6 protein tyrosine kinase 6"			8247543, 9284935	Standard	NM_005975		Approved	BRK	uc002yfg.4	Q13882	OTTHUMG00000033039	ENST00000217185.2:c.93G>A	chr20.hg19:g.62168575C>T		76.0	0.0	.		69.0	20.0	.	NM_001256358	B2RCR3|B4DW46|Q58F01	Silent	SNP	ENST00000217185.2	hg19	CCDS13524.1																																																																																			.	.	.	weak		0.701	PTK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080313.1			T	62168575	C	T	62168575	2	4	270	1	0	0	0	0	0	0	0	1	12775	639	23	1		1	PTK6	20	62168575	Silent	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10	1176248	62168575	856945	77	17086											
ZNF295	49854	hgsc.bcm.edu	37	chr21	43411959	43411959	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaggctgcagtaagggcagAcggccgcgttccggcacagc	8	5	16	12	4	0	2	0	1	0	1	1	2	1	2	2	4	2	6	2	4	1	2			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr21:43411959A>G	ENST00000310826.5	-	3	2429	c.2246T>C	c.(2245-2247)gTc>gCc	p.V749A	ZBTB21_ENST00000465968.1_5'UTR|ZBTB21_ENST00000398511.3_Missense_Mutation_p.V749A|ZBTB21_ENST00000398499.1_Missense_Mutation_p.V749A|ZBTB21_ENST00000398505.3_Missense_Mutation_p.V548A	NM_001098402.1	NP_001091872.1	Q9ULJ3	ZBT21_HUMAN	zinc finger and BTB domain containing 21	749					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)										GTAAGGGCAGACGGCCGCGTT	0.557																																					p.V749A		Atlas-SNP	.											.	.	.	.	0			c.T2246C						PASS	.						141	162	155					21																	43411959		2203	4300	6503	SO:0001583	missense	49854	exon3			GGGCAGACGGCCG	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.2246T>C	chr21.hg19:g.43411959A>G	ENSP00000308759:p.Val749Ala	59.0	0.0	.		79.0	38.0	.	NM_001098402	Q5R2W1|Q5R2W2|Q6P4R0	Missense_Mutation	SNP	ENST00000310826.5	hg19	CCDS13678.1	.	.	.	.	.	.	.	.	.	.	A	19.02	3.745708	0.69418	.	.	ENSG00000173276	ENST00000398505;ENST00000310826;ENST00000398499;ENST00000398511	T;T;T;T	0.07567	3.24;3.18;3.18;3.18	5.62	4.47	0.54385	Zinc finger, C2H2-like (1);	0.000000	0.64402	D	0.000003	T	0.21307	0.0513	L	0.58101	1.795	0.42558	D	0.993131	D;D	0.76494	0.999;0.989	D;P	0.75484	0.986;0.81	T	0.02683	-1.1124	10	0.21540	T	0.41	-20.3315	11.354	0.49605	0.9292:0.0:0.0708:0.0	.	548;749	Q9ULJ3-2;Q9ULJ3	.;ZN295_HUMAN	A	548;749;749;749	ENSP00000381517:V548A;ENSP00000308759:V749A;ENSP00000381512:V749A;ENSP00000381523:V749A	ENSP00000308759:V749A	V	-	2	0	ZNF295	42285028	1.000000	0.71417	0.838000	0.33150	0.895000	0.52256	8.724000	0.91462	0.964000	0.38108	0.460000	0.39030	GTC	.	.	.	none		0.557	ZBTB21-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195308.1	NM_020727		G	43411959	A	G	43411959	3	3	270	1	0	0	0	0	1	0	0	0	17839	275	10	3	958	3	ZNF295	21	43411959	Missense_Mutation	SNP	A	TCGA-UZ-A9Q1-01A-11D-A42J-10		43411959	4717936	78	17087											
PIM3	415116	hgsc.bcm.edu	37	chr22	50354605	50354605	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtcgcccgcgatgctgctcTccaagttcggctccctggcg	3	9	12	17	6	1	0	0	0	1	0	5	1	2	0	3	2	2	4	3	2	1	1			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chr22:50354605T>C	ENST00000360612.4	+	1	445	c.10T>C	c.(10-12)Tcc>Ccc	p.S4P		NM_001001852.3	NP_001001852.2	Q86V86	PIM3_HUMAN	Pim-3 proto-oncogene, serine/threonine kinase	4					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)		GATGCTGCTCTCCAAGTTCGG	0.796																																					p.S4P		Atlas-SNP	.											.	PIM3	15	.	0			c.T10C						PASS	.						2	3	3					22																	50354605		1697	3572	5269	SO:0001583	missense	415116	exon1			CTGCTCTCCAAGT	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.10T>C	chr22.hg19:g.50354605T>C	ENSP00000353824:p.Ser4Pro	11.0	0.0	.		16.0	8.0	.	NM_001001852	A5D8X8|A8K7J0|B1B0P0|Q68BM2	Missense_Mutation	SNP	ENST00000360612.4	hg19	CCDS33678.1	.	.	.	.	.	.	.	.	.	.	t	14.84	2.655437	0.47467	.	.	ENSG00000198355	ENST00000360612	T	0.58060	0.36	2.45	2.45	0.29901	.	0.370508	0.18727	U	0.132860	T	0.63248	0.2495	L	0.59436	1.845	0.46376	D	0.999016	D	0.71674	0.998	D	0.64877	0.93	T	0.64504	-0.6392	10	0.72032	D	0.01	.	9.6248	0.39743	0.0:0.0:0.0:1.0	.	4	Q86V86	PIM3_HUMAN	P	4	ENSP00000353824:S4P	ENSP00000353824:S4P	S	+	1	0	PIM3	48740609	0.997000	0.39634	0.992000	0.48379	0.091000	0.18340	1.814000	0.38972	1.031000	0.39867	0.382000	0.24955	TCC	.	.	.	none		0.796	PIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317406.1	NM_001001852		C	50354605	T	C	50354605	3	2	270	1	0	0	0	0	1	0	0	0	11936	1551	54	3	12	3	PIM3	22	50354605	Missense_Mutation	SNP	T	TCGA-UZ-A9Q1-01A-11D-A42J-10		50354605	949961	79	17088											
MAGEB16	139604	hgsc.bcm.edu	37	chrX	35821036	35821036	+	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	tattctgggaagaagcacttCatctttggagagcccagaat	12	11	10	8	0	3	3	1	0	2	3	3	5	3	4	1	2	2	1	1	2	4	4			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chrX:35821036C>T	ENST00000399989.1	+	2	1002	c.723C>T	c.(721-723)ttC>ttT	p.F241F	MAGEB16_ENST00000399988.1_Silent_p.F241F|MAGEB16_ENST00000399985.1_Silent_p.F241F|MAGEB16_ENST00000399987.1_Silent_p.F241F|MAGEB16_ENST00000399992.1_Silent_p.F273F	NM_001099921.1	NP_001093391.1	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	241	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						AGAAGCACTTCATCTTTGGAG	0.483																																					p.F241F		Atlas-SNP	.											.	MAGEB16	64	.	0			c.C723T						PASS	.						51	50	50					X																	35821036		2161	4280	6441	SO:0001819	synonymous_variant	139604	exon2			GCACTTCATCTTT		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.723C>T	chrX.hg19:g.35821036C>T		255.0	0.0	.		309.0	142.0	.	NM_001099921	A8MU30	Silent	SNP	ENST00000399989.1	hg19	CCDS43927.1																																																																																			.	.	.	none		0.483	MAGEB16-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251034.1			T	35821036	C	T	35821036	2	4	270	1	0	0	0	0	0	0	0	1	9181	825	29	2		2	MAGEB16	23	35821036	Silent	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10		35821036	119449524	80	17089											
AR	367	hgsc.bcm.edu	37	chrX	66765152	66765152	+	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	acctcccggcgccagtttgcTgctgctgcagcagcagcagc	6	7	12	16	2	0	0	0	0	0	0	1	0	1	0	3	1	8	8	3	1	0	1			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chrX:66765152T>A	ENST00000374690.3	+	1	688	c.164T>A	c.(163-165)cTg>cAg	p.L55Q	AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.L55Q|AR_ENST00000504326.1_Missense_Mutation_p.L55Q	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	55	Modulating.|Poly-Leu.				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)	GCCAGTTTGCTGCTGCTgcag	0.662									Androgen Insensitivity Syndrome																												p.L55Q		Atlas-SNP	.											.	AR	249	.	0			c.T164A						PASS	.						11	14	13					X																	66765152		2169	4252	6421	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	GTTTGCTGCTGCT	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.164T>A	chrX.hg19:g.66765152T>A	ENSP00000363822:p.Leu55Gln	217.0	0.0	.		278.0	13.0	.	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	N	7.392	0.630975	0.14322	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.58797	0.31;0.31;0.31	.	.	.	.	0.268702	0.26919	N	0.021823	T	0.26666	0.0652	N	0.08118	0	0.09310	N	0.999996	B;B	0.17852	0.006;0.024	B;B	0.04013	0.0;0.001	T	0.17107	-1.0380	8	0.10111	T	0.7	.	.	.	.	.	55;55	E7EVX6;D3YPQ2	.;.	Q	55	ENSP00000363822:L55Q;ENSP00000421155:L55Q;ENSP00000379359:L55Q	ENSP00000363822:L55Q	L	+	2	0	AR	66681877	0.998000	0.40836	0.922000	0.36590	0.480000	0.33159	0.009000	0.13219	0.000000	0.14550	0.000000	0.15137	CTG	.	.	.	none		0.662	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		A	66765152	T	A	66765152	3	1	270	1	0	0	0	0	1	0	0	0	836	1580	55	5	166	5	AR	23	66765152	Missense_Mutation	SNP	T	TCGA-UZ-A9Q1-01A-11D-A42J-10	30944116	66765152	88505408	81	17090											
ATP7A	538	hgsc.bcm.edu	37	chrX	77254011	77254011	+	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	ggtagtaatagctcagccttCatcggaaatgccgcttttga	10	12	10	9	2	2	1	2	1	0	0	3	2	2	2	2	2	3	4	2	2	4	6			TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chrX:77254011C>T	ENST00000341514.6	+	5	1528	c.1373C>T	c.(1372-1374)tCa>tTa	p.S458L	ATP7A_ENST00000350425.4_Intron|ATP7A_ENST00000343533.5_Missense_Mutation_p.S458L	NM_000052.5	NP_000043.4	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	458					blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cartilage development (GO:0051216)|catecholamine metabolic process (GO:0006584)|cellular copper ion homeostasis (GO:0006878)|central nervous system neuron development (GO:0021954)|cerebellar Purkinje cell differentiation (GO:0021702)|collagen fibril organization (GO:0030199)|copper ion export (GO:0060003)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detoxification of copper ion (GO:0010273)|dopamine metabolic process (GO:0042417)|elastic fiber assembly (GO:0048251)|elastin biosynthetic process (GO:0051542)|epinephrine metabolic process (GO:0042414)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|lung alveolus development (GO:0048286)|mitochondrion organization (GO:0007005)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of neuron apoptotic process (GO:0043524)|neuron projection morphogenesis (GO:0048812)|norepinephrine biosynthetic process (GO:0042421)|norepinephrine metabolic process (GO:0042415)|peptidyl-lysine modification (GO:0018205)|pigmentation (GO:0043473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|pyramidal neuron development (GO:0021860)|regulation of gene expression (GO:0010468)|regulation of oxidative phosphorylation (GO:0002082)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|response to iron(III) ion (GO:0010041)|response to zinc ion (GO:0010043)|serotonin metabolic process (GO:0042428)|skin development (GO:0043588)|T-helper cell differentiation (GO:0042093)|transmembrane transport (GO:0055085)|tryptophan metabolic process (GO:0006568)|tyrosine metabolic process (GO:0006570)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|copper-dependent protein binding (GO:0032767)|copper-exporting ATPase activity (GO:0004008)|superoxide dismutase copper chaperone activity (GO:0016532)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(26)|pancreas(1)|prostate(1)|urinary_tract(1)	53					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	GCTCAGCCTTCATCGGAAATG	0.393																																					p.S458L		Atlas-SNP	.											.	ATP7A	248	.	0			c.C1373T						PASS	.						166	155	158					X																	77254011		2203	4296	6499	SO:0001583	missense	538	exon5			AGCCTTCATCGGA	L06133	CCDS35339.1, CCDS75997.1	Xq21.1	2012-10-22	2008-07-31		ENSG00000165240	ENSG00000165240	3.6.3.4	"ATPases / P-type"	869	protein-coding gene	gene with protein product	"copper pump 1", "copper-transporting ATPase 1"	300011	"Menkes syndrome"	MNK		10079817	Standard	NM_000052		Approved		uc004ecx.4	Q04656	OTTHUMG00000021885	ENST00000341514.6:c.1373C>T	chrX.hg19:g.77254011C>T	ENSP00000345728:p.Ser458Leu	293.0	0.0	.		286.0	115.0	.	NM_000052	B1AT72|O00227|O00745|Q9BYY8	Missense_Mutation	SNP	ENST00000341514.6	hg19	CCDS35339.1	.	.	.	.	.	.	.	.	.	.	C	9.335	1.061539	0.19987	.	.	ENSG00000165240	ENST00000343533;ENST00000341514;ENST00000355691	D;D	0.96300	-3.97;-3.97	5.23	4.34	0.51931	.	0.427019	0.23409	N	0.048483	D	0.91061	0.7187	N	0.19112	0.55	0.39495	D	0.968115	B;B	0.17667	0.001;0.023	B;B	0.17098	0.002;0.017	D	0.87643	0.2523	10	0.29301	T	0.29	-6.2236	11.0442	0.47849	0.0:0.7938:0.1285:0.0777	.	458;468	Q04656;Q59HD1	ATP7A_HUMAN;.	L	458;458;468	ENSP00000343026:S458L;ENSP00000345728:S458L	ENSP00000345728:S458L	S	+	2	0	ATP7A	77140667	0.774000	0.28592	0.851000	0.33527	0.190000	0.23558	1.694000	0.37752	2.315000	0.78130	0.600000	0.82982	TCA	.	.	.	none		0.393	ATP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057306.1	NM_000052		T	77254011	C	T	77254011	3	4	270	1	0	0	0	0	1	0	0	0	1190	838	29	2	1387	2	ATP7A	23	77254011	Missense_Mutation	SNP	C	TCGA-UZ-A9Q1-01A-11D-A42J-10	10488859	77254011	78016549	82	17091											
MORF4L2	9643	hgsc.bcm.edu	37	chrX	102931211	102931211	+	Frame_Shift_Del	DEL	G	G	-																															atagcccaacaataatgcaaGgcttttctcatcaaggggcg																										TCGA-UZ-A9Q1-01A-11D-A42J-10	TCGA-UZ-A9Q1-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69f0f324-fc06-44ab-b056-8fb3fb4706ae	1a85c2bb-8b95-429a-b782-c05a44345d4c	g.chrX:102931211delG	ENST00000441076.2	-	4	1049	c.745delC	c.(745-747)cttfs	p.L249fs	MORF4L2_ENST00000360458.1_Frame_Shift_Del_p.L249fs|MORF4L2_ENST00000433176.2_Frame_Shift_Del_p.L249fs|MORF4L2_ENST00000492116.1_5'Flank|MORF4L2_ENST00000451301.1_Frame_Shift_Del_p.L249fs|MORF4L2_ENST00000423833.2_Frame_Shift_Del_p.L249fs|MORF4L2_ENST00000422154.2_Frame_Shift_Del_p.L249fs	NM_001142419.1|NM_012286.2	NP_001135891.1|NP_036418.1	Q15014	MO4L2_HUMAN	mortality factor 4 like 2	249	MRG. {ECO:0000255|PROSITE- ProRule:PRU00972}.				chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|DNA repair (GO:0006281)|positive regulation of striated muscle cell differentiation (GO:0051155)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)	13						AATAATGCAAGGCTTTTCTCA	0.418																																					p.L249fs		Pindel	.											.	MORF4L2	35	.	0			c.746delT						PASS	.						94	82	86					X																	102931211		2203	4300	6503	SO:0001589	frameshift_variant	9643	exon5			.	AF100620	CCDS14512.1	Xq22	2010-11-24			ENSG00000123562	ENSG00000123562			16849	protein-coding gene	gene with protein product	"MORF-related gene X"	300409				9891081, 7584026	Standard	NM_012286		Approved	KIAA0026, MRGX	uc011msa.2	Q15014	OTTHUMG00000022104	ENST00000441076.2:c.745delC	chrX.hg19:g.102931211delG	ENSP00000391969:p.Leu249fs	234.0	0.0	.		292.0	76.0	0.260	NM_001142422	B3KP92|D3DXA5|Q567V0|Q8J026	Frame_Shift_Del	DEL	ENST00000441076.2	hg19	CCDS14512.1																																																																																			.	.	.	none		0.418	MORF4L2-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057732.1	NM_012286		-	102931211	G	-	102931211	7	5	270	1	0	1	0	1	0	0	0	0	9714	1000	35	0	125	0	MORF4L2	23	102931211	Frame_Shift_Del	DEL	G	TCGA-UZ-A9Q1-01A-11D-A42J-10	25677200	102931211	52339349	83	17092											
LRP8	7804	hgsc.bcm.edu	37	chr1	53712713	53712713	+	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	gggtagtccatcatcttcaaGgcttaatgccactcgctggg	8	11	11	11	1	3	0	2	0	1	0	5	0	4	0	2	3	1	3	2	3	3	3			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr1:53712713G>A	ENST00000306052.6	-	19	2970	c.2869C>T	c.(2869-2871)Ctt>Ttt	p.L957F	LRP8_ENST00000354412.3_Missense_Mutation_p.L694F|LRP8_ENST00000465675.1_Missense_Mutation_p.L451F|LRP8_ENST00000371454.2_Missense_Mutation_p.L898F|LRP8_ENST00000347547.2_Missense_Mutation_p.L787F|RP5-1024G6.8_ENST00000602943.1_lincRNA	NM_004631.4	NP_004622.2	Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	957					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						TCATCTTCAAGGCTTAATGCC	0.433																																					p.L957F		Atlas-SNP	.											.	LRP8	58	.	0			c.C2869T						PASS	.						122	106	111					1																	53712713		2203	4300	6503	SO:0001583	missense	7804	exon19			CTTCAAGGCTTAA	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.2869C>T	chr1.hg19:g.53712713G>A	ENSP00000303634:p.Leu957Phe	91.0	0.0	.		64.0	10.0	.	NM_004631	B1AMT6|B1AMT7|B1AMT8|O14968|Q86V27|Q99876|Q9BR78	Missense_Mutation	SNP	ENST00000306052.6	hg19	CCDS578.1	.	.	.	.	.	.	.	.	.	.	G	19.15	3.771798	0.69992	.	.	ENSG00000157193	ENST00000306052;ENST00000371454;ENST00000465675;ENST00000354412;ENST00000347547	D;D;D;D;D	0.94092	-3.0;-2.84;-3.35;-2.86;-2.95	5.47	3.42	0.39159	.	.	.	.	.	D	0.92140	0.7508	N	0.19112	0.55	0.41755	D	0.989687	P;D;P;P;D	0.67145	0.928;0.992;0.928;0.954;0.996	P;P;P;B;D	0.70487	0.541;0.747;0.541;0.356;0.969	D	0.90630	0.4566	9	0.72032	D	0.01	.	7.9953	0.30265	0.0796:0.0:0.5688:0.3516	.	694;787;898;957;451	Q14114-2;Q14114-4;Q14114-3;Q14114;E9PP15	.;.;.;LRP8_HUMAN;.	F	957;898;451;694;787	ENSP00000303634:L957F;ENSP00000360509:L898F;ENSP00000437009:L451F;ENSP00000346391:L694F;ENSP00000334522:L787F	ENSP00000303634:L957F	L	-	1	0	LRP8	53485301	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.688000	0.46984	0.479000	0.27511	0.655000	0.94253	CTT	.	.	.	none		0.433	LRP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024699.1	NM_004631		A	53712713	G	A	53712713	3	1	271	1	0	0	0	0	1	0	0	0	8970	1000	35	2	26	2	LRP8	1	53712713	Missense_Mutation	SNP	G	TCGA-V9-A7HT-01A-11D-A33Q-10		53712713	195537908	1	17093											
ZNHIT6	54680	hgsc.bcm.edu	37	chr1	86167916	86167916	+	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	ttttaagttaataccttgccTccgggcacgatttttcataa	10	16	6	9	2	1	0	1	0	0	0	2	1	2	0	3	1	2	2	3	1	4	8			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr1:86167916T>A	ENST00000370574.3	-	5	1076	c.943A>T	c.(943-945)Agg>Tgg	p.R315W	ZNHIT6_ENST00000431532.2_Missense_Mutation_p.R276W			Q9NWK9	BCD1_HUMAN	zinc finger, HIT-type containing 6	315					box C/D snoRNP assembly (GO:0000492)|ribosome biogenesis (GO:0042254)	extracellular vesicular exosome (GO:0070062)|pre-snoRNP complex (GO:0070761)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|breast(2)|cervix(2)|large_intestine(10)|lung(1)|urinary_tract(1)	17						ATACCTTGCCTCCGGGCACGA	0.294																																					p.R315W		Atlas-SNP	.											.	ZNHIT6	42	.	0			c.A943T						PASS	.						67	67	67					1																	86167916		2202	4299	6501	SO:0001583	missense	54680	exon5			CTTGCCTCCGGGC	AL442074	CCDS707.1, CCDS53338.1	1p22.3	2013-01-17	2010-09-15	2008-06-23	ENSG00000117174	ENSG00000117174		"Zinc fingers, HIT-type"	26089	protein-coding gene	gene with protein product	"box C/D snoRNA essential 1 homolog (S. cerevisiae)"		"chromosome 1 open reading frame 181", "zinc finger, HIT type 6"	C1orf181		12747765	Standard	NM_017953		Approved	FLJ20729, NY-BR-75, BCD1	uc001dlh.3	Q9NWK9	OTTHUMG00000010576	ENST00000370574.3:c.943A>T	chr1.hg19:g.86167916T>A	ENSP00000359606:p.Arg315Trp	296.0	0.0	.		235.0	51.0	.	NM_017953	B2RBA1|B4DP13|D3DT20|Q9H278|Q9H3X3|Q9NWN0	Missense_Mutation	SNP	ENST00000370574.3	hg19	CCDS707.1	.	.	.	.	.	.	.	.	.	.	T	19.77	3.889819	0.72524	.	.	ENSG00000117174	ENST00000431532;ENST00000370574	T;T	0.54279	0.62;0.58	5.37	4.21	0.49690	.	0.240905	0.40302	N	0.001123	T	0.45518	0.1346	L	0.46157	1.445	0.34792	D	0.735819	D;D	0.61697	0.99;0.985	P;P	0.55667	0.781;0.715	T	0.53222	-0.8469	10	0.62326	D	0.03	-10.471	11.2031	0.48754	0.0:0.0:0.2929:0.7071	.	276;315	B4DP13;Q9NWK9	.;BCD1_HUMAN	W	276;315	ENSP00000414344:R276W;ENSP00000359606:R315W	ENSP00000359606:R315W	R	-	1	2	ZNHIT6	85940504	0.995000	0.38212	0.919000	0.36401	0.900000	0.52787	2.999000	0.49473	0.929000	0.37192	0.454000	0.30748	AGG	.	.	.	none		0.294	ZNHIT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029186.1	NM_017953		A	86167916	T	A	86167916	3	1	271	1	0	0	0	0	1	0	0	0	18221	1550	54	5	493	5	ZNHIT6	1	86167916	Missense_Mutation	SNP	T	TCGA-V9-A7HT-01A-11D-A33Q-10	32455203	86167916	163082705	2	17094											
FCRL6	343413	hgsc.bcm.edu	37	chr1	159778131	159778131	+	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	cagactctgtccatgggagcAgcaacagtgcagagccgtgg	10	6	14	11	1	1	2	0	0	1	2	2	3	2	3	2	2	5	3	2	2	1	0			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr1:159778131A>T	ENST00000368106.3	+	3	217	c.216A>T	c.(214-216)gcA>gcT	p.A72A	FCRL6_ENST00000392235.3_Silent_p.A72A|FCRL6_ENST00000339348.5_Silent_p.A72A|FCRL6_ENST00000321935.6_Silent_p.A79A	NM_001004310.2	NP_001004310.2	Q6DN72	FCRL6_HUMAN	Fc receptor-like 6	72	Ig-like C2-type 1.					external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	24	all_hematologic(112;0.0597)					CCATGGGAGCAGCAACAGTGC	0.483																																					p.A72A		Atlas-SNP	.											.	FCRL6	61	.	0			c.A216T						PASS	.						55	48	51					1																	159778131		2203	4300	6503	SO:0001819	synonymous_variant	343413	exon3			GGGAGCAGCAACA	AK131201	CCDS30912.1, CCDS60312.1	1q23.2	2013-01-11			ENSG00000181036	ENSG00000181036		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	31910	protein-coding gene	gene with protein product		613562					Standard	NM_001004310		Approved	IFGP6, FLJ16056, FcRH6	uc001fud.4	Q6DN72	OTTHUMG00000035351	ENST00000368106.3:c.216A>T	chr1.hg19:g.159778131A>T		297.0	0.0	.		203.0	41.0	.	NM_001004310	A1KXW6|A2A4D6|Q6DN73|Q6XRC3|Q6ZNI1	Silent	SNP	ENST00000368106.3	hg19	CCDS30912.1																																																																																			.	.	.	none		0.483	FCRL6-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276853.1	NM_001004310		T	159778131	A	T	159778131	2	4	271	1	0	0	0	0	0	0	0	1	5806	175	7	5		5	FCRL6	1	159778131	Silent	SNP	A	TCGA-V9-A7HT-01A-11D-A33Q-10	73610215	159778131	89472490	3	17095											
ARHGAP30	257106	hgsc.bcm.edu	37	chr1	161018636	161018638	+	In_Frame_Del	DEL	CTT	CTT	-																															ttagcctccatactgtcagcCttcttctgacctttggactt																								rs552705270|rs530896501		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr1:161018636_161018638delCTT	ENST00000368013.3	-	12	2493_2495	c.2173_2175delAAG	c.(2173-2175)aagdel	p.K725del	USF1_ENST00000368021.3_5'Flank|ARHGAP30_ENST00000368015.1_In_Frame_Del_p.K548del|ARHGAP30_ENST00000368016.3_Intron|USF1_ENST00000435396.1_5'Flank	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	725	Glu-rich.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			TACTGTCAGCCTTCTTCTGACCT	0.478																																					p.725_726del		Atlas-Indel,Pindel	.											.	ARHGAP30	105	.	0			c.2174_2176del						PASS	.		,	2,4264		1,0,2132					,	2.5	0		dbSNP_126	261	4,8248		0,4,4122	no	intron,coding	ARHGAP30	NM_181720.2,NM_001025598.1	,	1,4,6254	A1A1,A1R,RR		0.0485,0.0469,0.0479	,	,		6,12512				SO:0001651	inframe_deletion	257106	exon12			.	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.2173_2175delAAG	chr1.hg19:g.161018639_161018641delCTT	ENSP00000356992:p.Lys725del	128.0	0.0	0		102.0	13.0	0.127451	NM_001025598	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	In_Frame_Del	DEL	ENST00000368013.3	hg19	CCDS30918.1																																																																																			.	.	.	none		0.478	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720		-	161018638	CTT	-	161018636	7	5	271	1	0	1	0	1	0	0	0	0	879	680	24	0	1134	0	ARHGAP30	1	161018636	In_Frame_Del	DEL	CTT	TCGA-V9-A7HT-01A-11D-A33Q-10	1240505	161018636	88231985	4	17096											
DNM3	26052	hgsc.bcm.edu	37	chr1	171956839	171956839	+	Frame_Shift_Del	DEL	T	T	-																															aaaggaaagaaatttacagaTtttgatgaagttcgccttga																										TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr1:171956839delT	ENST00000355305.5	+	3	436	c.279delT	c.(277-279)gatfs	p.D93fs	DNM3_ENST00000358155.4_Frame_Shift_Del_p.D93fs|DNM3_ENST00000520906.1_Frame_Shift_Del_p.D93fs|DNM3_ENST00000367731.1_Frame_Shift_Del_p.D93fs|DNM3_ENST00000367733.2_Frame_Shift_Del_p.D93fs			Q9UQ16	DYN3_HUMAN	dynamin 3	93	Dynamin-type G.				endocytosis (GO:0006897)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|synapse assembly (GO:0007416)	dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(16)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						AATTTACAGATTTTGATGAAG	0.343																																					p.D93fs		Atlas-Indel,Pindel	.											.	DNM3	85	.	0			c.278delA						PASS	.						134	149	145					1																	171956839		1824	4086	5910	SO:0001589	frameshift_variant	26052	exon3			.	AL136712	CCDS44276.1, CCDS60356.1	1q24.1	2013-01-10			ENSG00000197959	ENSG00000197959		"Pleckstrin homology (PH) domain containing"	29125	protein-coding gene	gene with protein product	"Dyna III"	611445				10048485	Standard	NM_015569		Approved	KIAA0820	uc001gie.4	Q9UQ16	OTTHUMG00000034913	ENST00000355305.5:c.279delT	chr1.hg19:g.171956839delT	ENSP00000347457:p.Asp93fs	71.0	0.0	0		46.0	12.0	0.26087	NM_001136127	A9Z1Y1|O14982|O95555|Q1MTM8|Q5W129|Q6P2G1|Q9H0P3|Q9H548|Q9NQ68|Q9NQN6	Frame_Shift_Del	DEL	ENST00000355305.5	hg19																																																																																				.	.	.	none		0.343	DNM3-003	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000084531.1	NM_015569		-	171956839	T	-	171956839	7	5	271	1	0	1	0	1	0	0	0	0	4675	1490	52	0	289	0	DNM3	1	171956839	Frame_Shift_Del	DEL	T	TCGA-V9-A7HT-01A-11D-A33Q-10	10938203	171956839	77293782	5	17097											
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125547712	125547712	+	Frame_Shift_Del	DEL	A	A	-																															cttatgaagggcccttttgcAaaaaaggtaccttaggcgct																										TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr2:125547712delA	ENST00000431078.1	+	18	3347	c.2983delA	c.(2983-2985)aaafs	p.K996fs		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	996					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)		GCCCTTTTGCAAAAAAGGTAC	0.507																																					p.C994X		Atlas-Indel,Pindel	.											.,1	CNTNAP5	405	.	0			c.2982delC						PASS	.						46	51	49					2																	125547712		2015	4193	6208	SO:0001589	frameshift_variant	129684	exon18			.	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.2983delA	chr2.hg19:g.125547712delA	ENSP00000399013:p.Lys996fs	219.0	0.0	0		243.0	101.0	0.415638	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Frame_Shift_Del	DEL	ENST00000431078.1	hg19	CCDS46401.1																																																																																			.	.	.	none		0.507	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			-	125547712	A	-	125547712	7	5	271	1	0	1	0	1	0	0	0	0	3652	131	5	0	3053	0	CNTNAP5	2	125547712	Frame_Shift_Del	DEL	A	TCGA-V9-A7HT-01A-11D-A33Q-10		125547712	117651661	6	17098											
LRP2	4036	hgsc.bcm.edu	37	chr2	170058231	170058232	+	Frame_Shift_Ins	INS	-	-	A																															caccttctgttattgcacatINSaaactccgtggtggcattgc																										TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr2:170058231_170058232insA	ENST00000263816.3	-	44	8643_8644	c.8358_8359insT	c.(8356-8361)tttatgfs	p.M2787fs		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2787	LDL-receptor class A 18. {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)"	TTATTGCACATAAACTCCGTGG	0.45																																					p.M2787fs		Atlas-Indel,Pindel	.											.	LRP2	751	.	0			c.8359_8360insT						PASS	.																																			SO:0001589	frameshift_variant	4036	exon44			.		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.8359dupT	chr2.hg19:g.170058234_170058234dupA	ENSP00000263816:p.Met2787fs	71.0	0.0	0		87.0	26.0	0.298851	NM_004525	O00711|Q16215	Frame_Shift_Ins	INS	ENST00000263816.3	hg19	CCDS2232.1																																																																																			.	.	.	none		0.45	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		A	170058232	-	A	170058231	7	5	271	1	0	1	1	0	0	0	0	0	8963	1406	49	0	5752	0	LRP2	2	170058231	Frame_Shift_Ins	INS	-	TCGA-V9-A7HT-01A-11D-A33Q-10	44510519	170058231	73141142	7	17099											
TTN	7273	hgsc.bcm.edu	37	chr2	179397361	179397362	+	Frame_Shift_Ins	INS	-	-	A																															atggggaggagtaattcttcINSatcagagatgtccccaagag																										TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr2:179397361_179397362insA	ENST00000591111.1	-	308	99281_99282	c.99057_99058insT	c.(99055-99060)gatgaafs	p.E33020fs	TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN_ENST00000589042.1_Frame_Shift_Ins_p.E34661fs|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN_ENST00000342992.6_Frame_Shift_Ins_p.E32093fs|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN_ENST00000342175.6_Frame_Shift_Ins_p.E25788fs|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN_ENST00000460472.2_Frame_Shift_Ins_p.E25596fs|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN_ENST00000359218.5_Frame_Shift_Ins_p.E25721fs			Q8WZ42	TITIN_HUMAN	titin	33020					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)			AGTAATTCTTCATCAGAGATGT	0.455																																					p.E34661_E34662delinsX		Atlas-Indel,Pindel	.											.	TTN	18412	.	0			c.103981_103982insT						PASS	.																																			SO:0001589	frameshift_variant	7273	exon358			.	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.99058dupT	chr2.hg19:g.179397362_179397362dupA	ENSP00000465570:p.Glu33020fs	131.0	0.0	0		126.0	17.0	0.134921	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_Ins	INS	ENST00000591111.1	hg19																																																																																				.	.	.	none		0.455	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179397362	-	A	179397361	7	5	271	1	0	1	1	0	0	0	0	0	16747	835	29	0	4018	0	TTN	2	179397361	Frame_Shift_Ins	INS	-	TCGA-V9-A7HT-01A-11D-A33Q-10	9339130	179397361	63802012	8	17100											
TTN	7273	hgsc.bcm.edu	37	chr2	179456111	179456111	+	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	ttttaatctcactcccatcgGttgtccactttgcagtagga	8	15	7	11	1	1	0	1	0	1	0	5	1	3	1	2	2	1	3	2	2	2	5			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr2:179456111G>T	ENST00000591111.1	-	254	55642	c.55418C>A	c.(55417-55419)aCc>aAc	p.T18473N	TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.T20114N|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.T17546N|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T11241N|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.T11049N|TTN_ENST00000359218.5_Missense_Mutation_p.T11174N			Q8WZ42	TITIN_HUMAN	titin	18473	Ig-like 106.				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)			ACTCCCATCGGTTGTCCACTT	0.433																																					p.T20114N		Atlas-SNP	.											.	TTN	18412	.	0			c.C60341A						PASS	.						300	297	298					2																	179456111		1929	4129	6058	SO:0001583	missense	7273	exon304			CCATCGGTTGTCC	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.55418C>A	chr2.hg19:g.179456111G>T	ENSP00000465570:p.Thr18473Asn	51.0	0.0	.		65.0	22.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	13.04	2.118519	0.37436	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.40756	1.02;1.02;1.02;1.02	6.1	3.21	0.36854	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	0.41949	0.1181	L	0.49126	1.545	0.39154	D	0.962285	B;B;B;B	0.32653	0.379;0.379;0.379;0.379	B;B;B;B	0.33890	0.172;0.172;0.172;0.172	T	0.46569	-0.9182	9	0.87932	D	0	.	17.2594	0.87065	0.0:0.3531:0.6469:0.0	.	11049;11174;11241;18473	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	N	17546;11049;11241;11174;11047	ENSP00000343764:T17546N;ENSP00000434586:T11049N;ENSP00000340554:T11241N;ENSP00000352154:T11174N	ENSP00000340554:T11241N	T	-	2	0	TTN	179164357	0.992000	0.36948	0.447000	0.26932	0.882000	0.50991	2.447000	0.44917	0.396000	0.25283	0.650000	0.86243	ACC	.	.	.	none		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179456111	G	T	179456111	3	4	271	1	0	0	0	0	1	0	0	0	16747	1261	44	4	47874	4	TTN	2	179456111	Missense_Mutation	SNP	G	TCGA-V9-A7HT-01A-11D-A33Q-10	58750	179456111	63743262	9	17101											
GTF3C3	9330	hgsc.bcm.edu	37	chr2	197649653	197649653	+	Splice_Site	DEL	T	T	-																															tccagaaaaatctgtaattaTctaaaagaatgggaaagaag																										TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr2:197649653delT	ENST00000263956.3	-	8	1131	c.1042delA	c.(1042-1044)ata>ta	p.I349fs	GTF3C3_ENST00000409364.3_Splice_Site_p.I349fs|GTF3C3_ENST00000470386.1_5'Flank	NM_012086.4	NP_036218.1	Q9Y5Q9	TF3C3_HUMAN	general transcription factor IIIC, polypeptide 3, 102kDa	349					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(4)|endometrium(3)|kidney(1)|large_intestine(9)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						TCTGTAATTATCTAAAAGAAT	0.303																																					p.I348fs		Atlas-Indel,Pindel	.											.	GTF3C3	96	.	0			c.1043delT						PASS	.						48	49	49					2																	197649653		2202	4295	6497	SO:0001630	splice_region_variant	9330	exon8			.	AF133123	CCDS2316.1, CCDS56153.1	2q33.1	2013-01-10	2002-08-29		ENSG00000119041	ENSG00000119041		"General transcription factors", "Tetratricopeptide (TTC) repeat domain containing"	4666	protein-coding gene	gene with protein product		604888	"general transcription factor IIIC, polypeptide 3 (102kD)"			10373544	Standard	NM_001206774		Approved	TFiiiC2-102, TFIIIC102	uc002uts.3	Q9Y5Q9	OTTHUMG00000154633	ENST00000263956.3:c.1042-1A>-	chr2.hg19:g.197649653delT		39.0	0.0	0		68.0	17.0	0.25	NM_012086	Q4ZG48|Q86XJ8|Q8WX84|Q96B44|Q9H5I8|Q9NT97	Frame_Shift_Del	DEL	ENST00000263956.3	hg19	CCDS2316.1																																																																																			.	.	.	none		0.303	GTF3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256104.1		Frame_Shift_Del	-	197649653	T	-	197649653	8	5	271	1	0	1	0	1	0	0	1	0	6881	1449	50	0	1662	0	GTF3C3	2	197649653	Splice_Site	DEL	T	TCGA-V9-A7HT-01A-11D-A33Q-10	18193542	197649653	45549720	10	17102											
UGT1A3	54659	hgsc.bcm.edu	37	chr2	234638590	234638590	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggccaatcatgcccaacaTggtcttcattgggggcatca	10	9	10	12	0	4	0	3	0	1	0	4	0	4	0	2	4	2	1	2	4	2	2			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr2:234638590T>C	ENST00000482026.1	+	1	837	c.818T>C	c.(817-819)aTg>aCg	p.M273T	UGT1A5_ENST00000373414.3_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000609767.1_Missense_Mutation_p.M273T|UGT1A6_ENST00000480628.1_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A1_ENST00000373450.4_Intron			P35503	UD13_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A3	273					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)	ATGCCCAACATGGTCTTCATT	0.493																																					p.M273T		Atlas-SNP	.											.	UGT1A3	91	.	0			c.T818C						PASS	.						125	127	126					2																	234638590		2203	4300	6503	SO:0001583	missense	54659	exon1			CCAACATGGTCTT	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.818T>C	chr2.hg19:g.234638590T>C	ENSP00000418532:p.Met273Thr	125.0	0.0	.		91.0	34.0	.	NM_019093	B8K287	Missense_Mutation	SNP	ENST00000482026.1	hg19	CCDS2509.1	.	.	.	.	.	.	.	.	.	.	t	15.28	2.787614	0.49997	.	.	ENSG00000243135	ENST00000482026	T	0.61392	0.11	4.0	4.0	0.46444	.	.	.	.	.	T	0.64605	0.2613	M	0.74258	2.255	0.39951	D	0.974548	B;B	0.30686	0.29;0.29	B;B	0.41299	0.353;0.353	T	0.69146	-0.5222	9	0.54805	T	0.06	.	12.938	0.58327	0.0:0.0:0.0:1.0	.	273;273	Q5DT01;P35503	.;UD13_HUMAN	T	273	ENSP00000418532:M273T	ENSP00000418532:M273T	M	+	2	0	UGT1A3	234303329	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	3.500000	0.53318	1.457000	0.47850	0.373000	0.22412	ATG	.	.	.	none		0.493	UGT1A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130983.1	NM_019093		C	234638590	T	C	234638590	3	2	271	1	0	0	0	0	1	0	0	0	16958	1464	51	3	820	3	UGT1A3	2	234638590	Missense_Mutation	SNP	T	TCGA-V9-A7HT-01A-11D-A33Q-10	36988937	234638590	8560783	11	17103											
ESPNL	339768	hgsc.bcm.edu	37	chr2	239040220	239040220	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcccctgcctcacgccgcCgtcccctgcagcggccctga	3	5	12	21	4	1	1	1	1	0	0	2	1	2	1	8	2	3	1	8	2	0	0	rs190347409	byFrequency	TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr2:239040220C>T	ENST00000343063.3	+	9	3128	c.2865C>T	c.(2863-2865)gcC>gcT	p.A955A	ESPNL_ENST00000409506.1_Silent_p.A587A|ESPNL_ENST00000409169.1_Silent_p.A911A|ESPNL_ENST00000477241.1_3'UTR	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	955				A -> T (in Ref. 1; BAC85884). {ECO:0000305}.						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)		CTCACGCCGCCGTCCCCTGCA	0.687													C|||	9	0.00179712	0	0	5008	,	,		14478	0		0.001	False		,,,				2504	0.0082				p.A955A		Atlas-SNP	.											.	ESPNL	63	.	0			c.C2865T						PASS	.						17	18	18					2																	239040220		2196	4298	6494	SO:0001819	synonymous_variant	339768	exon9			CGCCGCCGTCCCC	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.2865C>T	chr2.hg19:g.239040220C>T		72.0	0.0	.		60.0	26.0	.	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Silent	SNP	ENST00000343063.3	hg19	CCDS2525.1																																																																																			.	C|1.000;G|0.000	.	alt		0.687	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312		T	239040220	C	T	239040220	2	4	271	1	0	0	0	0	0	0	0	1	5257	639	23	1		1	ESPNL	2	239040220	Silent	SNP	C	TCGA-V9-A7HT-01A-11D-A33Q-10	4401630	239040220	4159153	12	17104											
BRPF1	7862	hgsc.bcm.edu	37	chr3	9788110	9788110	+	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	cccgagagcatctctacctcGtcctcttctttgacaacaaa	10	11	5	15	2	3	2	0	1	3	1	6	3	4	2	3	0	3	1	3	0	3	3			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr3:9788110G>C	ENST00000457855.1	+	12	3444	c.3433G>C	c.(3433-3435)Gtc>Ctc	p.V1145L	BRPF1_ENST00000383829.2_Missense_Mutation_p.V1151L|BRPF1_ENST00000424362.1_Missense_Mutation_p.V1144L|BRPF1_ENST00000302054.3_Missense_Mutation_p.V1145L|BRPF1_ENST00000433861.2_Missense_Mutation_p.V1050L			P55201	BRPF1_HUMAN	bromodomain and PHD finger containing, 1	1145	PWWP. {ECO:0000255|PROSITE- ProRule:PRU00162}.				chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	49	Medulloblastoma(99;0.227)					TCTCTACCTCGTCCTCTTCTT	0.567																																					p.V1151L		Atlas-SNP	.											.	BRPF1	104	.	0			c.G3451C						PASS	.						80	75	77					3																	9788110		2203	4300	6503	SO:0001583	missense	7862	exon13			TACCTCGTCCTCT	M91585	CCDS2575.1, CCDS33692.1	3p26-p25	2008-07-18			ENSG00000156983	ENSG00000156983			14255	protein-coding gene	gene with protein product	"peregrin", "bromodomain-containing protein, 140kD"	602410				8946209, 7906940	Standard	NM_001003694		Approved	BR140	uc003bsf.3	P55201	OTTHUMG00000097033	ENST00000457855.1:c.3433G>C	chr3.hg19:g.9788110G>C	ENSP00000410210:p.Val1145Leu	87.0	0.0	.		68.0	25.0	.	NM_001003694	B4DEZ6|Q7Z6E0|Q8TCM6|Q9UHI0	Missense_Mutation	SNP	ENST00000457855.1	hg19	CCDS2575.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.237373	0.79800	.	.	ENSG00000156983	ENST00000433861;ENST00000424362;ENST00000383829;ENST00000302054;ENST00000457855	D;D;D;D;D	0.85702	-2.02;-2.02;-2.02;-2.02;-2.02	6.06	6.06	0.98353	PWWP (3);	0.000000	0.85682	D	0.000000	D	0.89694	0.6789	M	0.85197	2.74	0.80722	D	1	P;P;P;P	0.42735	0.676;0.788;0.788;0.723	B;B;B;B	0.43783	0.225;0.396;0.396;0.431	D	0.90510	0.4480	10	0.87932	D	0	.	20.6208	0.99490	0.0:0.0:1.0:0.0	.	1050;1144;1151;1145	P55201-4;P55201-3;P55201-2;P55201	.;.;.;BRPF1_HUMAN	L	1050;1144;1151;1145;1145	ENSP00000402485:V1050L;ENSP00000398863:V1144L;ENSP00000373340:V1151L;ENSP00000306297:V1145L;ENSP00000410210:V1145L	ENSP00000306297:V1145L	V	+	1	0	BRPF1	9763110	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.813000	0.99286	2.882000	0.98803	0.655000	0.94253	GTC	.	.	.	none		0.567	BRPF1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338485.1	NM_001003694		C	9788110	G	C	9788110	3	2	271	1	0	0	0	0	1	0	0	0	1522	1145	40	4	3497	4	BRPF1	3	9788110	Missense_Mutation	SNP	G	TCGA-V9-A7HT-01A-11D-A33Q-10		9788110	188234320	13	17105											
RARB	5915	hgsc.bcm.edu	37	chr3	25637915	25637915	+	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	tatctcttttgaaaaggtgcAgagcgtgtaattaccttgaa	12	14	9	6	1	1	3	0	2	1	1	2	3	1	3	1	1	3	2	1	1	6	6	rs61733682	byFrequency	TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr3:25637915A>T	ENST00000404969.1	+	8	1176	c.1176A>T	c.(1174-1176)gcA>gcT	p.A392A	RARB_ENST00000458646.1_Silent_p.A273A|RARB_ENST00000462272.1_3'UTR|RARB_ENST00000437042.2_Silent_p.A273A|RARB_ENST00000330688.4_Silent_p.A385A			P10826	RARB_HUMAN	retinoic acid receptor, beta	392	Ligand-binding.				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)	GAAAAGGTGCAGAGCGTGTAA	0.378																																					p.A385A		Atlas-SNP	.											.	RARB	123	.	0			c.A1155T						PASS	.						83	84	84					3																	25637915		2203	4300	6503	SO:0001819	synonymous_variant	5915	exon8			AGGTGCAGAGCGT	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.1176A>T	chr3.hg19:g.25637915A>T		178.0	0.0	.		153.0	66.0	.	NM_000965	P12891|Q00989|Q15298|Q9UN48	Silent	SNP	ENST00000404969.1	hg19																																																																																				.	A|0.979;G|0.021	.	alt		0.378	RARB-201	KNOWN	basic	protein_coding	protein_coding		NM_000965, NM_016152		T	25637915	A	T	25637915	2	4	271	1	0	0	0	0	0	0	0	1	13066	175	7	5		5	RARB	3	25637915	Silent	SNP	A	TCGA-V9-A7HT-01A-11D-A33Q-10	15849805	25637915	172384515	14	17106											
NEK10	152110	hgsc.bcm.edu	37	chr3	27346274	27346275	+	Frame_Shift_Ins	INS	-	-	A																															aagctgtttgatgcctccccINSaaatgcgaatttccacgctg																										TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr3:27346274_27346275insA	ENST00000429845.2	-	13	1353_1354	c.991_992insT	c.(991-993)tggfs	p.W331fs	NEK10_ENST00000341435.5_Frame_Shift_Ins_p.W331fs			Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10	331					positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein autophosphorylation (GO:0031954)|protein phosphorylation (GO:0006468)|regulation of cell cycle G2/M phase transition (GO:1902749)|regulation of ERK1 and ERK2 cascade (GO:0070372)	protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						GATGCCTCCCCAAATGCGAATT	0.49																																					p.W331fs		Atlas-Indel,Pindel	.											.	NEK10	271	.	0			c.992_993insT						PASS	.																																			SO:0001589	frameshift_variant	152110	exon13			.	AK123061, AK057247	CCDS46781.1	3p24.1	2012-11-15	2012-11-15		ENSG00000163491	ENSG00000163491			18592	protein-coding gene	gene with protein product			"NIMA (never in mitosis gene a)- related kinase 10"			15289607	Standard	NM_199347		Approved	FLJ32685	uc003cdt.2	Q6ZWH5	OTTHUMG00000130571	ENST00000429845.2:c.992dupT	chr3.hg19:g.27346277_27346277dupA	ENSP00000395849:p.Trp331fs	92.0	0.0	0		111.0	36.0	0.324324	NM_199347	A8MWG1|B9ZVR0|Q45VJ4|Q6ZR11|Q7Z671|Q86XB1|Q96MB3	Frame_Shift_Ins	INS	ENST00000429845.2	hg19																																																																																				.	.	.	none		0.49	NEK10-016	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000438156.1	NM_152534		A	27346275	-	A	27346274	7	5	271	1	0	1	1	0	0	0	0	0	10329	595	21	0	1198	0	NEK10	3	27346274	Frame_Shift_Ins	INS	-	TCGA-V9-A7HT-01A-11D-A33Q-10	1708359	27346274	170676156	15	17107											
FLNB	2317	hgsc.bcm.edu	37	chr3	58135898	58135898	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagcatcacccgcaccagtcGggccccgtccgtggccactg	6	5	12	18	4	1	0	1	0	0	0	3	1	2	0	6	2	1	2	6	2	0	0			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr3:58135898G>A	ENST00000295956.4	+	38	6476	c.6311G>A	c.(6310-6312)cGg>cAg	p.R2104Q	FLNB_ENST00000419752.2_Missense_Mutation_p.R1924Q|FLNB_ENST00000490882.1_Missense_Mutation_p.R2135Q|FLNB_ENST00000493452.1_Missense_Mutation_p.R1911Q|FLNB_ENST00000358537.3_Missense_Mutation_p.R2080Q|FLNB_ENST00000357272.4_Missense_Mutation_p.R2104Q|FLNB_ENST00000348383.5_Intron|FLNB_ENST00000429972.2_Missense_Mutation_p.R2093Q	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	2104	Interaction with FLNA 1.|Interaction with the cytoplasmic tail of GP1BA.				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)		CGCACCAGTCGGGCCCCGTCC	0.612																																					p.R2135Q		Atlas-SNP	.											.	FLNB	430	.	0			c.G6404A						PASS	.						101	111	107					3																	58135898		2203	4300	6503	SO:0001583	missense	2317	exon39			CCAGTCGGGCCCC	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.6311G>A	chr3.hg19:g.58135898G>A	ENSP00000295956:p.Arg2104Gln	113.0	0.0	.		101.0	6.0	.	NM_001164317	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	hg19	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	G	12.45	1.941726	0.34283	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000357272;ENST00000493452;ENST00000419752	D;D;D;D;D;D;D	0.85484	-1.92;-1.92;-1.93;-1.93;-1.99;-1.68;-1.67	6.17	6.17	0.99709	Immunoglobulin E-set (1);	0.113900	0.64402	D	0.000008	T	0.66268	0.2772	N	0.04880	-0.145	0.45477	D	0.998443	P;B;D;B;P;P	0.52996	0.808;0.22;0.957;0.359;0.922;0.922	B;B;B;B;B;B	0.39152	0.193;0.058;0.292;0.015;0.292;0.292	T	0.70930	-0.4738	10	0.06757	T	0.87	.	13.9957	0.64397	0.0685:0.0:0.9315:0.0	.	2080;2135;1911;1924;2093;2104	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	Q	2104;2135;2080;2093;2104;1911;1924	ENSP00000295956:R2104Q;ENSP00000420213:R2135Q;ENSP00000351339:R2080Q;ENSP00000415599:R2093Q;ENSP00000349819:R2104Q;ENSP00000418510:R1911Q;ENSP00000414532:R1924Q	ENSP00000295956:R2104Q	R	+	2	0	FLNB	58110938	1.000000	0.71417	1.000000	0.80357	0.691000	0.40173	2.419000	0.44671	2.941000	0.99782	0.655000	0.94253	CGG	.	.	.	none		0.612	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457		A	58135898	G	A	58135898	3	1	271	1	0	0	0	0	1	0	0	0	5941	1116	39	1	6558	1	FLNB	3	58135898	Missense_Mutation	SNP	G	TCGA-V9-A7HT-01A-11D-A33Q-10	30789624	58135898	139886532	16	17108											
SHQ1	55164	hgsc.bcm.edu	37	chr3	72881545	72881545	+	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	atgatcaggatcaaacttggCcagctcagcggccaggcgct	10	7	12	12	2	3	1	3	1	0	0	3	2	3	2	2	4	3	2	2	4	1	1			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr3:72881545C>T	ENST00000325599.8	-	5	713	c.574G>A	c.(574-576)Gcc>Acc	p.A192T	SHQ1_ENST00000463369.1_Missense_Mutation_p.A164T	NM_018130.2	NP_060600.2	Q6PI26	SHQ1_HUMAN	SHQ1, H/ACA ribonucleoprotein assembly factor	192					negative regulation of rRNA processing (GO:2000233)|positive regulation of apoptotic process (GO:0043065)|ribonucleoprotein complex assembly (GO:0022618)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	27		Prostate(10;0.00482)|Lung NSC(201;0.0339)|Myeloproliferative disorder(1037;0.204)		BRCA - Breast invasive adenocarcinoma(55;9.68e-05)|Epithelial(33;0.000563)|LUSC - Lung squamous cell carcinoma(21;0.00229)|Lung(16;0.00688)|KIRC - Kidney renal clear cell carcinoma(39;0.018)|Kidney(39;0.0213)		TCAAACTTGGCCAGCTCAGCG	0.383																																					p.A192T		Atlas-SNP	.											.	SHQ1	60	.	0			c.G574A						PASS	.						71	78	76					3																	72881545		2203	4300	6503	SO:0001583	missense	55164	exon5			ACTTGGCCAGCTC	BC025270	CCDS33788.1	3p13	2013-01-08	2013-01-08		ENSG00000144736	ENSG00000144736			25543	protein-coding gene	gene with protein product		613663	"SHQ1 homolog (S. cerevisiae)"			12477932	Standard	NM_018130		Approved	FLJ10539, Shq1p	uc003dpf.3	Q6PI26	OTTHUMG00000158814	ENST00000325599.8:c.574G>A	chr3.hg19:g.72881545C>T	ENSP00000315182:p.Ala192Thr	197.0	0.0	.		179.0	24.0	.	NM_018130	B4DL05|Q6MZJ4|Q7Z748|Q9H7E5|Q9NVS8	Missense_Mutation	SNP	ENST00000325599.8	hg19	CCDS33788.1	.	.	.	.	.	.	.	.	.	.	C	15.90	2.970048	0.53614	.	.	ENSG00000144736	ENST00000325599;ENST00000463369;ENST00000482785	T;T;T	0.46063	0.88;0.88;0.88	5.95	4.1	0.47936	.	0.237159	0.42548	N	0.000699	T	0.34193	0.0889	M	0.62016	1.91	0.47547	D	0.999451	P	0.40360	0.714	B	0.34180	0.177	T	0.13229	-1.0517	10	0.15952	T	0.53	-3.5238	10.9513	0.47332	0.0:0.7981:0.1303:0.0717	.	192	Q6PI26	SHQ1_HUMAN	T	192;164;103	ENSP00000315182:A192T;ENSP00000417452:A164T;ENSP00000418398:A103T	ENSP00000315182:A192T	A	-	1	0	SHQ1	72964235	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	1.403000	0.34612	1.519000	0.48950	0.585000	0.79938	GCC	.	.	.	none		0.383	SHQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352310.1	NM_018130		T	72881545	C	T	72881545	3	4	271	1	0	0	0	0	1	0	0	0	14305	739	26	2	1187	2	SHQ1	3	72881545	Missense_Mutation	SNP	C	TCGA-V9-A7HT-01A-11D-A33Q-10	14745647	72881545	125140885	17	17109											
MCF2L2	23101	hgsc.bcm.edu	37	chr3	183017880	183017880	+	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	atgaaatcgtcacagaggtgCctgagctccacacaccgggg	11	6	12	12	2	1	3	1	2	0	1	3	3	2	3	3	3	2	1	3	3	1	0			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr3:183017880C>T	ENST00000328913.3	-	11	1515	c.1218G>A	c.(1216-1218)agG>agA	p.R406R	MCF2L2_ENST00000473233.1_Silent_p.R406R|MCF2L2_ENST00000447025.2_Silent_p.R406R|MCF2L2_ENST00000414362.2_Silent_p.R406R	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	406							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)			CACAGAGGTGCCTGAGCTCCA	0.507																																					p.R406R		Atlas-SNP	.											.	MCF2L2	164	.	0			c.G1218A						PASS	.						104	98	100					3																	183017880		2203	4300	6503	SO:0001819	synonymous_variant	23101	exon11			GAGGTGCCTGAGC	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.1218G>A	chr3.hg19:g.183017880C>T		69.0	0.0	.		53.0	8.0	.	NM_015078	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Silent	SNP	ENST00000328913.3	hg19	CCDS3243.1																																																																																			.	.	.	none		0.507	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078		T	183017880	C	T	183017880	2	4	271	1	0	0	0	0	0	0	0	1	9387	738	26	2		2	MCF2L2	3	183017880	Silent	SNP	C	TCGA-V9-A7HT-01A-11D-A33Q-10	110136335	183017880	15004550	18	17110											
SLIT2	9353	hgsc.bcm.edu	37	chr4	20258328	20258328	+	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	aataacatcacaagaattacGaagacagattttgctggtct	16	11	7	7	1	2	3	1	0	1	3	2	4	2	3	0	1	3	1	0	1	6	4	rs377588103		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr4:20258328G>C	ENST00000504154.1	+	2	465	c.213G>C	c.(211-213)acG>acC	p.T71T	SLIT2_ENST00000273739.5_Silent_p.T71T|SLIT2_ENST00000503823.1_Silent_p.T71T|SLIT2_ENST00000503837.1_Silent_p.T71T	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	71					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						CAAGAATTACGAAGACAGATT	0.299																																					p.T71T		Atlas-SNP	.											SLIT2,colon,carcinoma,0,2	SLIT2	290	.	0			c.G213C						PASS	.						87	94	92					4																	20258328		2203	4297	6500	SO:0001819	synonymous_variant	9353	exon2			AATTACGAAGACA	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.213G>C	chr4.hg19:g.20258328G>C		158.0	0.0	.		139.0	16.0	.	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Silent	SNP	ENST00000504154.1	hg19	CCDS3426.1																																																																																			.	.	.	alt		0.299	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			C	20258328	G	C	20258328	2	2	271	1	0	0	0	0	0	0	0	1	14753	1045	37	4		4	SLIT2	4	20258328	Silent	SNP	G	TCGA-V9-A7HT-01A-11D-A33Q-10		20258328	170895948	19	17111											
SNCAIP	9627	hgsc.bcm.edu	37	chr5	121780389	121780389	+	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	gtggagacctgcatgtcgctGgcctctcaagtggtgaagtt	7	11	14	9	1	1	2	1	1	1	1	3	3	1	2	2	3	1	3	2	3	2	1			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr5:121780389G>T	ENST00000261368.8	+	8	1816	c.1554G>T	c.(1552-1554)ctG>ctT	p.L518L	CTC-210G5.1_ENST00000503529.1_RNA|SNCAIP_ENST00000504884.2_3'UTR|SNCAIP_ENST00000379533.2_Silent_p.L565L|SNCAIP_ENST00000503116.2_3'UTR|SNCAIP_ENST00000379536.2_Silent_p.L458L|CTC-210G5.1_ENST00000510972.1_RNA|SNCAIP_ENST00000542191.1_Silent_p.L76L|CTC-210G5.1_ENST00000506053.1_RNA|SNCAIP_ENST00000261367.7_Silent_p.L565L|SNCAIP_ENST00000379538.3_Silent_p.L152L|CTC-210G5.1_ENST00000505546.1_RNA|SNCAIP_ENST00000414317.2_Silent_p.L120L|CTC-210G5.1_ENST00000509993.1_RNA	NM_005460.2	NP_005451.2	Q9Y6H5	SNCAP_HUMAN	synuclein, alpha interacting protein	518					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)		GCATGTCGCTGGCCTCTCAAG	0.552																																					p.L518L		Atlas-SNP	.											.	SNCAIP	308	.	0			c.G1554T						PASS	.						80	77	78					5																	121780389		2203	4300	6503	SO:0001819	synonymous_variant	9627	exon8			GTCGCTGGCCTCT	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.1554G>T	chr5.hg19:g.121780389G>T		89.0	0.0	.		68.0	10.0	.	NM_005460	D3DSZ1|Q05BS1|Q1PSC2|Q49AC6|Q504U9|Q6L984|Q6L985|Q6L986|Q9HC59	Silent	SNP	ENST00000261368.8	hg19	CCDS4131.1																																																																																			.	.	.	none		0.552	SNCAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250888.1			T	121780389	G	T	121780389	2	4	271	1	0	0	0	0	0	0	0	1	14854	1335	47	4		4	SNCAIP	5	121780389	Silent	SNP	G	TCGA-V9-A7HT-01A-11D-A33Q-10		121780389	59134871	20	17112											
PCDHGB3	56102	hgsc.bcm.edu	37	chr5	140752308	140752308	+	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	caccacaagatcttctatgtGatgaagcctcttggtttgaa	11	13	8	9	0	3	4	0	3	3	1	3	4	3	4	2	1	1	1	2	1	4	4			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr5:140752308G>T	ENST00000576222.1	+	1	2478	c.2347G>T	c.(2347-2349)Gat>Tat	p.D783Y	PCDHGA3_ENST00000253812.6_Intron|PCDHGA6_ENST00000517434.1_5'Flank|PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3	783					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTTCTATGTGATGAAGCCTC	0.378																																					p.D783Y		Atlas-SNP	.											.	PCDHGB3	168	.	0			c.G2347T						PASS	.						58	53	55					5																	140752308		1866	4110	5976	SO:0001583	missense	56102	exon1			CTATGTGATGAAG	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.2347G>T	chr5.hg19:g.140752308G>T	ENSP00000461862:p.Asp783Tyr	99.0	0.0	.		68.0	22.0	.	NM_018924	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	hg19	CCDS58980.1																																																																																			.	.	.	none		0.378	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		T	140752308	G	T	140752308	3	4	271	1	0	0	0	0	1	0	0	0	11571	1290	45	4	2349	4	PCDHGB3	5	140752308	Missense_Mutation	SNP	G	TCGA-V9-A7HT-01A-11D-A33Q-10	18971919	140752308	40162952	21	17113											
XPO5	57510	hgsc.bcm.edu	37	chr6	43498437	43498437	+	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	aaaggatatgaagcatgggtCtgagtcggtagtcaggaata	14	9	14	4	1	2	2	1	2	1	0	3	4	2	4	0	4	1	2	0	4	6	3			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr6:43498437C>G	ENST00000265351.7	-	23	2876	c.2666G>C	c.(2665-2667)aGa>aCa	p.R889T		NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	889					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)			AAGCATGGGTCTGAGTCGGTA	0.453																																					p.R889T		Atlas-SNP	.											.	XPO5	79	.	0			c.G2666C						PASS	.						112	106	108					6																	43498437		1922	4141	6063	SO:0001583	missense	57510	exon23			ATGGGTCTGAGTC	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.2666G>C	chr6.hg19:g.43498437C>G	ENSP00000265351:p.Arg889Thr	81.0	0.0	.		59.0	20.0	.	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Missense_Mutation	SNP	ENST00000265351.7	hg19	CCDS47430.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.247509	0.80024	.	.	ENSG00000124571	ENST00000265351;ENST00000436943;ENST00000372258;ENST00000439465	T	0.70869	-0.52	5.83	5.83	0.93111	Armadillo-like helical (1);Armadillo-type fold (1);	0.052809	0.64402	D	0.000001	T	0.65554	0.2702	M	0.68593	2.085	0.58432	D	0.999996	P	0.46706	0.883	B	0.40375	0.327	T	0.72808	-0.4181	10	0.72032	D	0.01	-16.8308	20.1133	0.97917	0.0:1.0:0.0:0.0	.	889	Q9HAV4	XPO5_HUMAN	T	889;594;429;517	ENSP00000265351:R889T	ENSP00000265351:R889T	R	-	2	0	XPO5	43606415	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.630000	0.67805	2.762000	0.94881	0.591000	0.81541	AGA	.	.	.	none		0.453	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750		G	43498437	C	G	43498437	3	3	271	1	0	0	0	0	1	0	0	0	17459	913	32	4	988	4	XPO5	6	43498437	Missense_Mutation	SNP	C	TCGA-V9-A7HT-01A-11D-A33Q-10		43498437	127616630	22	17114											
HCRTR2	3062	hgsc.bcm.edu	37	chr6	55142245	55142245	+	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	gcctgtttcacagcctcgagGgccaggacagccaacgaagt	10	6	12	13	2	1	0	1	0	0	0	2	3	1	1	4	2	3	1	4	2	2	1			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr6:55142245G>A	ENST00000370862.3	+	5	1166	c.830G>A	c.(829-831)gGg>gAg	p.G277E		NM_001526.3	NP_001517.2	O43614	OX2R_HUMAN	hypocretin (orexin) receptor 2	277					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)			CAGCCTCGAGGGCCAGGACAG	0.517																																					p.G277E		Atlas-SNP	.											.	HCRTR2	112	.	0			c.G830A						PASS	.						72	75	74					6																	55142245		2203	4300	6503	SO:0001583	missense	3062	exon5			CTCGAGGGCCAGG	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.830G>A	chr6.hg19:g.55142245G>A	ENSP00000359899:p.Gly277Glu	161.0	0.0	.		125.0	26.0	.	NM_001526	Q5VTM0	Missense_Mutation	SNP	ENST00000370862.3	hg19	CCDS4956.1	.	.	.	.	.	.	.	.	.	.	G	19.39	3.818157	0.71028	.	.	ENSG00000137252	ENST00000370862	T	0.63255	-0.03	5.84	4.05	0.47172	GPCR, rhodopsin-like superfamily (1);	0.326969	0.35320	N	0.003299	T	0.55194	0.1905	M	0.78801	2.425	0.49582	D	0.999802	B	0.34241	0.444	B	0.41571	0.36	T	0.56968	-0.7891	10	0.38643	T	0.18	.	12.8874	0.58051	0.0:0.1242:0.7463:0.1294	.	277	O43614	OX2R_HUMAN	E	277	ENSP00000359899:G277E	ENSP00000359899:G277E	G	+	2	0	HCRTR2	55250204	0.973000	0.33851	0.621000	0.29145	0.603000	0.37013	1.636000	0.37144	0.802000	0.34089	0.650000	0.86243	GGG	.	.	.	none		0.517	HCRTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043392.1			A	55142245	G	A	55142245	3	1	271	1	0	0	0	0	1	0	0	0	7009	1232	43	2	848	2	HCRTR2	6	55142245	Missense_Mutation	SNP	G	TCGA-V9-A7HT-01A-11D-A33Q-10	11643808	55142245	115972822	23	17115											
KHDRBS2	202559	hgsc.bcm.edu	37	chr6	62604622	62604622	+	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	ccccccgggctcgaggggtaGggacacctcttgctacaggt	6	7	14	14	2	1	0	0	0	1	0	2	2	1	1	4	5	2	3	4	5	2	3			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr6:62604622G>A	ENST00000281156.4	-	6	1006	c.728C>T	c.(727-729)cCt>cTt	p.P243L		NM_152688.2	NP_689901.2	Q5VWX1	KHDR2_HUMAN	KH domain containing, RNA binding, signal transduction associated 2	243	Pro-rich.				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.P243L(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)		TCGAGGGGTAGGGACACCTCT	0.577																																					p.P243L		Atlas-SNP	.											KHDRBS2,NS,carcinoma,0,1	KHDRBS2	103	.	1	Substitution - Missense(1)	lung(1)	c.C728T						PASS	.						56	56	56					6																	62604622		2203	4300	6503	SO:0001583	missense	202559	exon6			GGGGTAGGGACAC	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.728C>T	chr6.hg19:g.62604622G>A	ENSP00000281156:p.Pro243Leu	69.0	0.0	.		65.0	10.0	.	NM_152688	A8K7M8|Q8N4I4|Q8TCZ4	Missense_Mutation	SNP	ENST00000281156.4	hg19	CCDS4963.1	.	.	.	.	.	.	.	.	.	.	G	11.42	1.634280	0.29068	.	.	ENSG00000112232	ENST00000281156;ENST00000539571	T	0.43688	0.94	5.52	5.52	0.82312	.	0.169262	0.52532	D	0.000068	T	0.21347	0.0514	N	0.25201	0.72	0.53688	D	0.99997	B	0.06786	0.001	B	0.06405	0.002	T	0.02358	-1.1171	10	0.42905	T	0.14	-0.0854	19.7889	0.96450	0.0:0.0:1.0:0.0	.	243	Q5VWX1	KHDR2_HUMAN	L	243	ENSP00000281156:P243L	ENSP00000281156:P243L	P	-	2	0	KHDRBS2	62662581	1.000000	0.71417	0.965000	0.40720	0.996000	0.88848	7.731000	0.84895	2.734000	0.93682	0.655000	0.94253	CCT	.	.	.	none		0.577	KHDRBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041066.2	NM_152688		A	62604622	G	A	62604622	3	1	271	1	0	0	0	0	1	0	0	0	8154	1000	35	2	337	2	KHDRBS2	6	62604622	Missense_Mutation	SNP	G	TCGA-V9-A7HT-01A-11D-A33Q-10	7462377	62604622	108510445	24	17116											
UTRN	7402	hgsc.bcm.edu	37	chr6	144811284	144811284	+	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	atgcgttctcagcccctgacCtccccagagagtaggactgc	8	8	10	15	1	1	2	1	1	1	1	3	4	2	3	5	1	3	2	5	1	1	2			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr6:144811284C>A	ENST00000367545.3	+	30	4212	c.4212C>A	c.(4210-4212)acC>acA	p.T1404T		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	1404	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)		AGCCCCTGACCTCCCCAGAGA	0.468																																					p.T1404T		Atlas-SNP	.											.	UTRN	327	.	0			c.C4212A						PASS	.						82	88	86					6																	144811284		2203	4300	6503	SO:0001819	synonymous_variant	7402	exon30			CCTGACCTCCCCA	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.4212C>A	chr6.hg19:g.144811284C>A		82.0	0.0	.		82.0	20.0	.	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Silent	SNP	ENST00000367545.3	hg19	CCDS34547.1																																																																																			.	.	.	none		0.468	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			A	144811284	C	A	144811284	2	1	271	1	0	0	0	0	0	0	0	1	17115	668	24	4		4	UTRN	6	144811284	Silent	SNP	C	TCGA-V9-A7HT-01A-11D-A33Q-10	82206662	144811284	26303783	25	17117											
AKAP12	9590	hgsc.bcm.edu	37	chr6	151674035	151674035	+	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	agttccgacctggaaggagaGaaaaccacatcactgaagtg	15	6	11	9	1	1	2	1	1	0	1	2	6	2	4	3	2	1	1	3	2	4	1			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr6:151674035G>T	ENST00000253332.1	+	3	4698	c.4509G>T	c.(4507-4509)gaG>gaT	p.E1503D	AKAP12_ENST00000402676.2_Missense_Mutation_p.E1503D|AKAP12_ENST00000359755.5_Missense_Mutation_p.E1398D|AKAP12_ENST00000354675.6_Missense_Mutation_p.E1405D			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	1503					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		TGGAAGGAGAGAAAACCACAT	0.483																																					p.E1503D	Melanoma(141;1616 1805 10049 24534 51979)	Atlas-SNP	.											.	AKAP12	170	.	0			c.G4509T						PASS	.						104	104	104					6																	151674035		2203	4300	6503	SO:0001583	missense	9590	exon4			AGGAGAGAAAACC	U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"A-kinase anchor proteins"	370	protein-coding gene	gene with protein product	"gravin", "Src-Suppressed C Kinase Substrate"	604698	"A kinase (PRKA) anchor protein (gravin) 12"			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.4509G>T	chr6.hg19:g.151674035G>T	ENSP00000253332:p.Glu1503Asp	53.0	0.0	.		54.0	16.0	.	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	hg19	CCDS5229.1	.	.	.	.	.	.	.	.	.	.	G	8.226	0.803473	0.16397	.	.	ENSG00000131016	ENST00000402676;ENST00000253332;ENST00000354675;ENST00000359755	T;T;T;T	0.06528	3.29;3.29;3.32;3.32	4.89	-7.41	0.01392	.	0.486247	0.15127	N	0.279075	T	0.00580	0.0019	N	0.11201	0.11	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.002;0.001	T	0.46652	-0.9176	10	0.20519	T	0.43	.	0.6764	0.00867	0.2365:0.3173:0.1924:0.2538	.	1398;1405;1503	Q02952-3;Q02952-2;Q02952	.;.;AKA12_HUMAN	D	1503;1503;1405;1398	ENSP00000384537:E1503D;ENSP00000253332:E1503D;ENSP00000346702:E1405D;ENSP00000352794:E1398D	ENSP00000253332:E1503D	E	+	3	2	AKAP12	151715728	0.000000	0.05858	0.002000	0.10522	0.478000	0.33099	-2.638000	0.00866	-0.945000	0.03681	0.650000	0.86243	GAG	.	.	.	none		0.483	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1			T	151674035	G	T	151674035	3	4	271	1	0	0	0	0	1	0	0	0	448	933	33	4	4548	4	AKAP12	6	151674035	Missense_Mutation	SNP	G	TCGA-V9-A7HT-01A-11D-A33Q-10	6862751	151674035	19441032	26	17118											
MLLT4	4301	hgsc.bcm.edu	37	chr6	168347513	168347513	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcagaatatagtgaaccaaAgaaattgcctggtgatgaca	16	8	11	6	0	0	5	0	3	0	2	0	5	0	5	2	2	2	1	2	2	6	3			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr6:168347513A>G	ENST00000447894.2	+	26	3464	c.3464A>G	c.(3463-3465)aAg>aGg	p.K1155R	MLLT4_ENST00000392108.3_Missense_Mutation_p.K1155R|MLLT4_ENST00000507679.1_3'UTR|MLLT4_ENST00000366806.2_Missense_Mutation_p.K1155R|MLLT4_ENST00000392112.1_Missense_Mutation_p.K1138R|MLLT4_ENST00000351017.4_Missense_Mutation_p.K1162R|MLLT4_ENST00000400822.3_Missense_Mutation_p.K1154R|MLLT4_ENST00000344191.4_Missense_Mutation_p.K1155R			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	1155					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)		AGTGAACCAAAGAAATTGCCT	0.448			T	MLL	AL																																p.K1155R		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.A3464G						PASS	.						122	126	125					6																	168347513		2203	4300	6503	SO:0001583	missense	4301	exon26			AACCAAAGAAATT	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.3464A>G	chr6.hg19:g.168347513A>G	ENSP00000404595:p.Lys1155Arg	93.0	0.0	.		76.0	17.0	.	NM_001040000	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Missense_Mutation	SNP	ENST00000447894.2	hg19		.	.	.	.	.	.	.	.	.	.	A	22.2	4.253254	0.80135	.	.	ENSG00000130396	ENST00000344191;ENST00000351017;ENST00000392108;ENST00000366806;ENST00000392112;ENST00000341575;ENST00000400822;ENST00000447894	T;T;T;T;T;T;T	0.04809	3.78;3.68;3.77;3.76;3.55;3.67;3.68	5.36	4.19	0.49359	.	0.056942	0.64402	D	0.000001	T	0.08670	0.0215	M	0.72479	2.2	0.53005	D	0.999969	P;D;P;P	0.76494	0.539;0.999;0.663;0.89	B;D;B;B	0.85130	0.132;0.997;0.159;0.374	T	0.28073	-1.0055	10	0.16896	T	0.51	-4.4903	11.4921	0.50387	0.929:0.0:0.071:0.0	.	1155;1154;1155;1139	P55196;P55196-5;P55196-6;P55196-2	AFAD_HUMAN;.;.;.	R	1155;1162;1155;1155;1138;1155;1154;1155	ENSP00000341118:K1155R;ENSP00000252692:K1162R;ENSP00000375956:K1155R;ENSP00000355771:K1155R;ENSP00000375960:K1138R;ENSP00000383623:K1154R;ENSP00000404595:K1155R	ENSP00000345834:K1155R	K	+	2	0	MLLT4	168090362	1.000000	0.71417	0.926000	0.36857	0.909000	0.53808	6.763000	0.74955	0.965000	0.38133	0.533000	0.62120	AAG	.	.	.	none		0.448	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936		G	168347513	A	G	168347513	3	3	271	1	0	0	0	0	1	0	0	0	9636	72	3	3	3566	3	MLLT4	6	168347513	Missense_Mutation	SNP	A	TCGA-V9-A7HT-01A-11D-A33Q-10	16673478	168347513	2767554	27	17119											
FGL2	10875	hgsc.bcm.edu	37	chr7	76826164	76826164	+	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	gacgtgcctgcagcactgtcCagcctccccccatggtctcc	5	8	9	19	1	1	0	0	0	1	0	4	1	3	0	7	1	4	2	7	1	0	0			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr7:76826164C>G	ENST00000248598.5	-	2	784	c.752G>C	c.(751-753)tGg>tCg	p.W251S	CCDC146_ENST00000285871.4_Intron|CCDC146_ENST00000431197.1_Intron|RP11-467H10.2_ENST00000459742.1_RNA	NM_006682.2	NP_006673.1	Q14314	FGL2_HUMAN	fibrinogen-like 2	251	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.					extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)				breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(2)	13						CAGCACTGTCCAGCCTCCCCC	0.493																																					p.W251S		Atlas-SNP	.											.	FGL2	40	.	0			c.G752C						PASS	.						112	107	108					7																	76826164		2203	4300	6503	SO:0001583	missense	10875	exon2			ACTGTCCAGCCTC	Z36531	CCDS5591.1	7q11.23	2013-02-06			ENSG00000127951	ENSG00000127951		"Fibrinogen C domain containing"	3696	protein-coding gene	gene with protein product		605351				7642106	Standard	NM_006682		Approved	pT49, T49	uc003ugb.3	Q14314	OTTHUMG00000130681	ENST00000248598.5:c.752G>C	chr7.hg19:g.76826164C>G	ENSP00000248598:p.Trp251Ser	125.0	0.0	.		136.0	38.0	.	NM_006682		Missense_Mutation	SNP	ENST00000248598.5	hg19	CCDS5591.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.215375	0.79352	.	.	ENSG00000127951	ENST00000248598	D	0.91686	-2.89	5.87	5.87	0.94306	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.000000	0.85682	D	0.000000	D	0.97739	0.9258	H	0.96889	3.9	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98417	1.0575	10	0.87932	D	0	.	19.8132	0.96556	0.0:1.0:0.0:0.0	.	251	Q14314	FGL2_HUMAN	S	251	ENSP00000248598:W251S	ENSP00000248598:W251S	W	-	2	0	FGL2	76664100	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.487000	0.81328	2.785000	0.95823	0.655000	0.94253	TGG	.	.	.	none		0.493	FGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253176.1	NM_006682		G	76826164	C	G	76826164	3	3	271	1	0	0	0	0	1	0	0	0	5880	595	21	4	571	4	FGL2	7	76826164	Missense_Mutation	SNP	C	TCGA-V9-A7HT-01A-11D-A33Q-10		76826164	82312499	28	17120											
SRPK2	6733	hgsc.bcm.edu	37	chr7	104783659	104783659	+	Missense_Mutation	SNP	T	T	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	tgatgttttcttctattattTtcctttcagcttctcgctcc	4	22	4	11	1	4	1	1	1	3	0	7	1	6	1	2	0	1	3	2	0	2	9			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr7:104783659T>G	ENST00000393651.3	-	10	1019	c.932A>C	c.(931-933)aAa>aCa	p.K311T	SRPK2_ENST00000489828.1_Missense_Mutation_p.K300T|SRPK2_ENST00000357311.3_Missense_Mutation_p.K300T	NM_182692.1	NP_872634.1			SRSF protein kinase 2											NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(11)|large_intestine(6)|lung(4)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	35						TTCTATTATTTTCCTTTCAGC	0.433																																					p.K311T		Atlas-SNP	.											.	SRPK2	76	.	0			c.A932C						PASS	.						132	117	122					7																	104783659		2203	4300	6503	SO:0001583	missense	6733	exon10			ATTATTTTCCTTT	U88666	CCDS5735.1, CCDS34724.1	7q22-q31.1	2010-06-23	2010-06-23		ENSG00000135250	ENSG00000135250			11306	protein-coding gene	gene with protein product	"SR protein kinase 2", "serine/arginine-rich splicing factor kinase 2"	602980	"SFRS protein kinase 2"			8208298, 9472028	Standard	NM_182692		Approved	SFRSK2	uc003vcv.4	P78362	OTTHUMG00000157405	ENST00000393651.3:c.932A>C	chr7.hg19:g.104783659T>G	ENSP00000377262:p.Lys311Thr	99.0	0.0	.		85.0	24.0	.	NM_182692		Missense_Mutation	SNP	ENST00000393651.3	hg19	CCDS34724.1	.	.	.	.	.	.	.	.	.	.	T	18.34	3.603271	0.66445	.	.	ENSG00000135250	ENST00000393651;ENST00000357311;ENST00000489828	T;T;T	0.31510	1.49;1.5;1.5	5.68	5.68	0.88126	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.191930	0.44483	D	0.000456	T	0.27063	0.0663	N	0.16478	0.41	0.51012	D	0.999906	P;P	0.51933	0.949;0.808	P;B	0.49085	0.6;0.201	T	0.03630	-1.1018	10	0.18710	T	0.47	-23.6027	15.9347	0.79694	0.0:0.0:0.0:1.0	.	311;300	P78362-2;P78362	.;SRPK2_HUMAN	T	311;300;300	ENSP00000377262:K311T;ENSP00000349863:K300T;ENSP00000419791:K300T	ENSP00000349863:K300T	K	-	2	0	SRPK2	104570895	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.834000	0.55798	2.167000	0.68274	0.454000	0.30748	AAA	.	.	.	none		0.433	SRPK2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348723.1	NM_182691		G	104783659	T	G	104783659	3	3	271	1	0	0	0	0	1	0	0	0	15172	1841	64	5	1195	5	SRPK2	7	104783659	Missense_Mutation	SNP	T	TCGA-V9-A7HT-01A-11D-A33Q-10	27957495	104783659	54355004	29	17121											
IQUB	154865	hgsc.bcm.edu	37	chr7	123152366	123152366	+	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	ttgaattgactatattctgaGcttcatacttctcctgttga	9	18	6	8	0	3	4	1	4	2	0	4	4	3	4	1	0	2	2	1	0	4	9			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr7:123152366G>T	ENST00000466202.1	-	2	605	c.29C>A	c.(28-30)gCt>gAt	p.A10D	IQUB_ENST00000324698.6_Missense_Mutation_p.A10D|IQUB_ENST00000488987.1_Intron|IQUB_ENST00000434450.1_Missense_Mutation_p.A10D	NM_001282855.1	NP_001269784.1	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	10					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						TATATTCTGAGCTTCATACTT	0.333																																					p.A10D		Atlas-SNP	.											.	IQUB	117	.	0			c.C29A						PASS	.						79	78	78					7																	123152366		2203	4300	6503	SO:0001583	missense	154865	exon2			TTCTGAGCTTCAT	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.29C>A	chr7.hg19:g.123152366G>T	ENSP00000417769:p.Ala10Asp	50.0	0.0	.		63.0	13.0	.	NM_178827	A4D0X0|Q49AL6|Q4G189|Q5BJD9|Q6NUH6|Q8N9Y2	Missense_Mutation	SNP	ENST00000466202.1	hg19	CCDS5787.1	.	.	.	.	.	.	.	.	.	.	G	8.113	0.779300	0.16120	.	.	ENSG00000164675	ENST00000466202;ENST00000324698;ENST00000434450	T;T;T	0.51071	1.75;1.75;0.72	4.04	-0.916	0.10489	.	5.141830	0.00397	N	0.000040	T	0.30355	0.0762	L	0.27053	0.805	0.09310	N	1	B;P;P	0.43701	0.392;0.815;0.718	B;B;B	0.36885	0.095;0.235;0.086	T	0.14839	-1.0458	10	0.29301	T	0.29	.	3.4549	0.07511	0.3929:0.0:0.4308:0.1763	.	10;10;10	A1A4Z1;Q8NA54-2;Q8NA54	.;.;IQUB_HUMAN	D	10	ENSP00000417769:A10D;ENSP00000324882:A10D;ENSP00000388498:A10D	ENSP00000324882:A10D	A	-	2	0	IQUB	122939602	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.095000	0.11077	-0.190000	0.10465	-0.262000	0.10625	GCT	.	.	.	none		0.333	IQUB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348529.1	NM_178827		T	123152366	G	T	123152366	3	4	271	1	0	0	0	0	1	0	0	0	7827	971	34	4	2394	4	IQUB	7	123152366	Missense_Mutation	SNP	G	TCGA-V9-A7HT-01A-11D-A33Q-10	18368707	123152366	35986297	30	17122											
CCDC136	64753	hgsc.bcm.edu	37	chr7	128452883	128452883	+	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	ggaaaagttactggccaagcAgaaagacctgaaggaagagc	17	4	13	7	0	0	4	0	1	0	3	0	6	0	6	2	3	3	2	2	3	7	1			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr7:128452883A>T	ENST00000297788.4	+	14	3030	c.2663A>T	c.(2662-2664)cAg>cTg	p.Q888L	CCDC136_ENST00000464832.1_Intron|CCDC136_ENST00000487361.1_Intron|CCDC136_ENST00000378685.4_Intron	NM_022742.4	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	888						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)	24						CTGGCCAAGCAGAAAGACCTG	0.527																																					p.Q888L		Atlas-SNP	.											.	CCDC136	170	.	0			c.A2663T						PASS	.						58	61	60					7																	128452883		1971	4163	6134	SO:0001583	missense	64753	exon14			CCAAGCAGAAAGA		CCDS47704.1, CCDS56510.1	7q33	2007-08-01			ENSG00000128596	ENSG00000128596			22225	protein-coding gene	gene with protein product		611902				15112360	Standard	NM_022742		Approved	KIAA1793, NAG6, DKFZP434G156	uc003vnv.2	Q96JN2	OTTHUMG00000158310	ENST00000297788.4:c.2663A>T	chr7.hg19:g.128452883A>T	ENSP00000297788:p.Gln888Leu	37.0	0.0	.		40.0	15.0	.	NM_022742	A4D1K1|A7MCY7|A8MYA7|Q6ZVK7|Q9H8M3|Q9UFE1	Missense_Mutation	SNP	ENST00000297788.4	hg19	CCDS47704.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.99|15.99	2.996429|2.996429	0.54147|0.54147	.|.	.|.	ENSG00000128596|ENSG00000128596	ENST00000297788;ENST00000397697;ENST00000320524;ENST00000464672|ENST00000494552	T|.	0.31769|.	1.48|.	5.6|5.6	4.38|4.38	0.52667|0.52667	.|.	0.105029|.	0.42821|.	D|.	0.000649|.	T|.	0.48857|.	0.1523|.	L|L	0.52126|0.52126	1.63|1.63	0.32437|0.32437	N|N	0.547286|0.547286	B;B;P|.	0.40638|.	0.297;0.129;0.725|.	B;B;P|.	0.48166|.	0.189;0.067;0.569|.	T|.	0.57388|.	-0.7820|.	10|.	0.21540|.	T|.	0.41|.	-30.5478|-30.5478	9.3378|9.3378	0.38060|0.38060	0.8402:0.0:0.0:0.1598|0.8402:0.0:0.0:0.1598	.|.	888;888;888|.	Q96JN2-4;Q96JN2-2;Q96JN2|.	.;.;CC136_HUMAN|.	L|X	888;888;888;479|765	ENSP00000297788:Q888L|.	ENSP00000297788:Q888L|.	Q|R	+|+	2|1	0|2	CCDC136|CCDC136	128240119|128240119	1.000000|1.000000	0.71417|0.71417	0.889000|0.889000	0.34880|0.34880	0.017000|0.017000	0.09413|0.09413	2.557000|2.557000	0.45871|0.45871	2.257000|2.257000	0.74773|0.74773	0.533000|0.533000	0.62120|0.62120	CAG|AGA	.	.	.	none		0.527	CCDC136-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350641.1	NM_022742		T	128452883	A	T	128452883	3	4	271	1	0	0	0	0	1	0	0	0	2772	188	7	5	2717	5	CCDC136	7	128452883	Missense_Mutation	SNP	A	TCGA-V9-A7HT-01A-11D-A33Q-10	5300517	128452883	30685780	31	17123											
KCNH2	3757	hgsc.bcm.edu	37	chr7	150649865	150649865	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggccttgaaggggctgtaaTgcaggatggtccagcggtgg	7	8	18	8	2	0	1	0	1	0	0	1	2	1	2	2	7	2	3	2	7	2	2	rs199473506		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr7:150649865T>C	ENST00000262186.5	-	6	1606	c.1205A>G	c.(1204-1206)cAt>cGt	p.H402R	KCNH2_ENST00000330883.4_Missense_Mutation_p.H62R|KCNH2_ENST00000430723.3_Missense_Mutation_p.H402R|KCNH2_ENST00000392968.2_Missense_Mutation_p.H306R	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	402					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)	GGGGCTGTAATGCAGGATGGT	0.642																																					p.H402R	GBM(137;110 1844 13671 20123 45161)	Atlas-SNP	.											.	KCNH2	157	.	0			c.A1205G						PASS	.						133	110	118					7																	150649865		2203	4300	6503	SO:0001583	missense	3757	exon6			CTGTAATGCAGGA	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.1205A>G	chr7.hg19:g.150649865T>C	ENSP00000262186:p.His402Arg	71.0	0.0	.		58.0	16.0	.	NM_000238	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Missense_Mutation	SNP	ENST00000262186.5	hg19	CCDS5910.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.546889	0.86022	.	.	ENSG00000055118	ENST00000330883;ENST00000392968;ENST00000262186;ENST00000350328;ENST00000430723	D;D;D;D	0.97378	-4.36;-4.36;-4.36;-4.36	4.82	4.82	0.62117	.	0.052173	0.85682	D	0.000000	D	0.98729	0.9573	H	0.94620	3.56	0.49798	D	0.999825	D;D;B;P;D	0.89917	0.993;1.0;0.2;0.691;0.963	D;D;B;B;P	0.80764	0.977;0.994;0.167;0.414;0.781	D	0.99497	1.0952	10	0.72032	D	0.01	.	12.3518	0.55153	0.0:0.0:0.0:1.0	.	306;402;62;402;62	C4PFH9;G5E9I0;Q708S9;Q12809;Q12809-2	.;.;.;KCNH2_HUMAN;.	R	62;306;402;62;402	ENSP00000328531:H62R;ENSP00000376695:H306R;ENSP00000262186:H402R;ENSP00000387657:H402R	ENSP00000262186:H402R	H	-	2	0	KCNH2	150280798	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.892000	0.87324	1.820000	0.53075	0.459000	0.35465	CAT	.	.	.	weak		0.642	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	NM_000238		C	150649865	T	C	150649865	3	2	271	1	0	0	0	0	1	0	0	0	8039	1464	51	3	2583	3	KCNH2	7	150649865	Missense_Mutation	SNP	T	TCGA-V9-A7HT-01A-11D-A33Q-10	22196982	150649865	8488798	32	17124											
MLL3	58508	hgsc.bcm.edu	37	chr7	151878422	151878422	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggggtttggggctgctgacTatatgggtcaacagtagtag	8	12	16	5	0	1	1	1	1	0	0	1	1	1	1	0	5	2	5	0	5	5	5			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr7:151878422T>C	ENST00000262189.6	-	36	6741	c.6523A>G	c.(6523-6525)Agt>Ggt	p.S2175G	KMT2C_ENST00000355193.2_Missense_Mutation_p.S2175G	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2175	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)										GGCTGCTGACTATATGGGTCA	0.468																																					p.S2175G		Atlas-SNP	.											.	MLL3	1564	.	0			c.A6523G						PASS	.						125	125	125					7																	151878422		2203	4300	6503	SO:0001583	missense	58508	exon36			GCTGACTATATGG	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.6523A>G	chr7.hg19:g.151878422T>C	ENSP00000262189:p.Ser2175Gly	196.0	0.0	.		206.0	64.0	.	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	T	9.208	1.030201	0.19512	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.84800	-1.89;-1.9	5.51	2.94	0.34122	.	0.600694	0.14603	N	0.309499	T	0.80618	0.4657	L	0.59436	1.845	0.51012	D	0.999901	B;B	0.19200	0.001;0.034	B;B	0.24394	0.001;0.053	T	0.74022	-0.3798	10	0.38643	T	0.18	.	6.6601	0.23009	0.2679:0.0:0.1394:0.5927	.	2175;1236	Q8NEZ4;Q8NEZ4-2	MLL3_HUMAN;.	G	2175	ENSP00000262189:S2175G;ENSP00000347325:S2175G	ENSP00000262189:S2175G	S	-	1	0	MLL3	151509355	0.026000	0.19158	0.794000	0.32065	0.870000	0.49936	0.688000	0.25422	0.892000	0.36259	0.533000	0.62120	AGT	.	.	.	none		0.468	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			C	151878422	T	C	151878422	3	2	271	1	0	0	0	0	1	0	0	0	9629	1522	53	3	8308	3	MLL3	7	151878422	Missense_Mutation	SNP	T	TCGA-V9-A7HT-01A-11D-A33Q-10	1228557	151878422	7260241	33	17125											
NEFL	4747	hgsc.bcm.edu	37	chr8	24813060	24813060	+	RNA	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	ctccagcgcttcattcatgcCccggcatgcttcgatttcca	6	12	7	16	3	2	0	2	0	0	0	5	1	4	0	4	1	3	3	4	1	0	4	rs267607537		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr8:24813060C>A	ENST00000221169.5	-	0	1564				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)		TCATTCATGCCCCGGCATGCT	0.642																																					p.G324C		Atlas-SNP	.											.	NEFL	47	.	0			c.G970T						PASS	.						51	53	52					8																	24813060		2088	4204	6292			4747	exon1			TCATGCCCCGGCA		CCDS75712.1	8p21.2	2014-09-17	2008-09-19		ENSG00000104725	ENSG00000277586		"Intermediate filaments type IV"	7739	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 110"	162280	"neurofilament, light polypeptide 68kDa"			17620486, 3145240	Standard	NM_006158		Approved	NFL, CMT1F, CMT2E, NF68, PPP1R110	uc003xee.4	P07196	OTTHUMG00000134284		chr8.hg19:g.24813060C>A		63.0	0.0	.		54.0	10.0	.	NM_006158	B9ZVN2|Q16154|Q8IU72	Missense_Mutation	SNP	ENST00000221169.5	hg19																																																																																				.	.	.	none		0.642	NEFL-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000258943.4	NM_006158		A	24813060	C	A	24813060	1	1	271	0	1	0	0	0	0	0	0	0	10322	623	22	4		4	NEFL	8	24813060	RNA	SNP	C	TCGA-V9-A7HT-01A-11D-A33Q-10		24813060	121550962	34	17126											
SULF1	23213	hgsc.bcm.edu	37	chr8	70515847	70515847	+	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	gctttcaggtttcgaacaaaCaagaaggccaaaatttggcg	14	9	10	8	2	1	1	1	0	0	1	2	2	1	1	1	3	2	2	1	3	6	3			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr8:70515847C>T	ENST00000260128.4	+	12	1920	c.1203C>T	c.(1201-1203)aaC>aaT	p.N401N	SULF1_ENST00000402687.4_Silent_p.N401N|SULF1_ENST00000419716.3_Silent_p.N401N|SULF1_ENST00000458141.2_Silent_p.N401N|SULF1_ENST00000521946.1_3'UTR	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	401					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)			TTCGAACAAACAAGAAGGCCA	0.418																																					p.N401N		Atlas-SNP	.											.	SULF1	153	.	0			c.C1203T						PASS	.						106	103	104					8																	70515847		2203	4300	6503	SO:0001819	synonymous_variant	23213	exon12			AACAAACAAGAAG	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.1203C>T	chr8.hg19:g.70515847C>T		119.0	0.0	.		116.0	18.0	.	NM_001128205	Q86YV8|Q8NCA2|Q9UPS5	Silent	SNP	ENST00000260128.4	hg19	CCDS6204.1																																																																																			.	.	.	none		0.418	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378885.2	NM_015170		T	70515847	C	T	70515847	2	4	271	1	0	0	0	0	0	0	0	1	15382	477	17	2		2	SULF1	8	70515847	Silent	SNP	C	TCGA-V9-A7HT-01A-11D-A33Q-10	45702787	70515847	75848175	35	17127											
UBR5	51366	hgsc.bcm.edu	37	chr8	103266727	103266727	+	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	ggctggcagtgatgggcttgAtgtccaaaagtaaacctgaa	12	9	13	7	0	0	3	0	3	0	0	1	3	1	3	2	3	1	4	2	3	5	2			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr8:103266727A>T	ENST00000520539.1	-	59	8809	c.8203T>A	c.(8203-8205)Tca>Aca	p.S2735T	UBR5_ENST00000518205.1_Missense_Mutation_p.S463T|UBR5_ENST00000521922.1_Missense_Mutation_p.S2728T|UBR5_ENST00000220959.4_Missense_Mutation_p.S2734T|KB-431C1.4_ENST00000520820.1_RNA|KB-431C1.5_ENST00000606361.1_RNA|KB-431C1.4_ENST00000499653.1_RNA	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	2735	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)			GATGGGCTTGATGTCCAAAAG	0.393																																					p.S2735T	Ovarian(131;96 1741 5634 7352 27489)	Atlas-SNP	.											.	UBR5	285	.	0			c.T8203A						PASS	.						125	114	118					8																	103266727		2203	4300	6503	SO:0001583	missense	51366	exon59			GGCTTGATGTCCA	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.8203T>A	chr8.hg19:g.103266727A>T	ENSP00000429084:p.Ser2735Thr	102.0	0.0	.		112.0	38.0	.	NM_015902	B2RP24|J3KMW7|O94970|Q9NPL3	Missense_Mutation	SNP	ENST00000520539.1	hg19	CCDS34933.1	.	.	.	.	.	.	.	.	.	.	A	19.37	3.814109	0.70912	.	.	ENSG00000104517	ENST00000520539;ENST00000220959;ENST00000518205;ENST00000521922	T;T;T;T	0.46063	0.88;0.88;0.88;0.88	5.64	5.64	0.86602	HECT (4);	0.000000	0.64402	D	0.000001	T	0.64702	0.2622	M	0.86097	2.795	0.58432	D	0.999999	D;D	0.53151	0.958;0.958	P;P	0.57283	0.817;0.817	T	0.71361	-0.4616	10	0.72032	D	0.01	.	15.8548	0.78968	1.0:0.0:0.0:0.0	.	2728;2735	E7EMW7;O95071	.;UBR5_HUMAN	T	2735;2734;463;2728	ENSP00000429084:S2735T;ENSP00000220959:S2734T;ENSP00000428693:S463T;ENSP00000427819:S2728T	ENSP00000220959:S2734T	S	-	1	0	UBR5	103335903	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.169000	0.94788	2.138000	0.66242	0.460000	0.39030	TCA	.	.	.	none		0.393	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902		T	103266727	A	T	103266727	3	4	271	1	0	0	0	0	1	0	0	0	16917	333	12	5	200	5	UBR5	8	103266727	Missense_Mutation	SNP	A	TCGA-V9-A7HT-01A-11D-A33Q-10	32750880	103266727	43097295	36	17128											
PTPRD	5789	hgsc.bcm.edu	37	chr9	8341221	8341221	+	Missense_Mutation	SNP	A	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	ttgaatttattacatggaagAttggcactgataaaccttga	14	14	8	5	0	0	4	0	3	0	1	0	5	0	5	1	2	2	1	1	2	6	7			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr9:8341221A>C	ENST00000381196.4	-	38	5538	c.4995T>G	c.(4993-4995)aaT>aaG	p.N1665K	PTPRD_ENST00000540109.1_Missense_Mutation_p.N1665K|PTPRD_ENST00000356435.5_Missense_Mutation_p.N1665K|PTPRD_ENST00000397611.3_Missense_Mutation_p.N1255K|PTPRD_ENST00000537002.1_Missense_Mutation_p.N1255K|PTPRD_ENST00000360074.4_Missense_Mutation_p.N1652K|PTPRD_ENST00000358503.5_Missense_Mutation_p.N1643K|PTPRD_ENST00000355233.5_Missense_Mutation_p.N1259K|PTPRD_ENST00000486161.1_Missense_Mutation_p.N1258K|PTPRD_ENST00000397606.3_Missense_Mutation_p.N1258K|PTPRD_ENST00000397617.3_Missense_Mutation_p.N1258K	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1665	Tyrosine-protein phosphatase 2. {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)		TACATGGAAGATTGGCACTGA	0.388										TSP Lung(15;0.13)																											p.N1665K		Atlas-SNP	.											.	PTPRD	1348	.	0			c.T4995G						PASS	.						177	194	188					9																	8341221		2203	4300	6503	SO:0001583	missense	5789	exon41			TGGAAGATTGGCA	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.4995T>G	chr9.hg19:g.8341221A>C	ENSP00000370593:p.Asn1665Lys	96.0	0.0	.		83.0	21.0	.	NM_002839	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	hg19	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	A	13.81	2.347906	0.41599	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606	T;T;T;T;T;T;T;T;T;T;T	0.10860	2.83;2.83;2.83;2.83;2.83;2.83;2.83;2.83;2.83;2.83;2.83	6.07	4.93	0.64822	Protein-tyrosine phosphatase, receptor/non-receptor type (2);	0.094396	0.64402	D	0.000001	T	0.11452	0.0279	L	0.41632	1.29	0.54753	D	0.999983	P;P;P;P;P;P;P;P;P	0.52842	0.525;0.525;0.525;0.525;0.58;0.656;0.956;0.892;0.615	B;B;B;B;B;B;B;B;B	0.43701	0.014;0.014;0.014;0.014;0.176;0.031;0.428;0.266;0.085	T	0.07139	-1.0788	9	.	.	.	.	12.3228	0.54993	0.9341:0.0:0.0659:0.0	.	1258;1249;1258;1259;1255;1255;1652;1665;1665	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	K	1665;1665;1652;1643;1259;1258;1255;1255;1136;1665;1258;1258	ENSP00000370593:N1665K;ENSP00000348812:N1665K;ENSP00000353187:N1652K;ENSP00000351293:N1643K;ENSP00000347373:N1259K;ENSP00000380741:N1258K;ENSP00000380735:N1255K;ENSP00000440515:N1255K;ENSP00000438164:N1665K;ENSP00000417093:N1258K;ENSP00000380731:N1258K	.	N	-	3	2	PTPRD	8331221	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.147000	0.58078	1.107000	0.41642	0.533000	0.62120	AAT	.	.	.	none		0.388	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			C	8341221	A	C	8341221	3	2	271	1	0	0	0	0	1	0	0	0	12812	330	12	5	767	5	PTPRD	9	8341221	Missense_Mutation	SNP	A	TCGA-V9-A7HT-01A-11D-A33Q-10		8341221	132872210	37	17129											
PSIP1	11168	hgsc.bcm.edu	37	chr9	15474059	15474060	+	Frame_Shift_Ins	INS	-	-	C																															agaatcggaggttgaagtaaINScccctgttttagctaaattt																										TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr9:15474059_15474060insC	ENST00000380733.4	-	9	1148_1149	c.805_806insG	c.(805-807)gttfs	p.V269fs	PSIP1_ENST00000380738.4_Frame_Shift_Ins_p.V269fs|PSIP1_ENST00000380716.4_Frame_Shift_Ins_p.V269fs|PSIP1_ENST00000397519.2_Frame_Shift_Ins_p.V269fs|PSIP1_ENST00000380715.1_Frame_Shift_Ins_p.V269fs			O75475	PSIP1_HUMAN	PC4 and SFRS1 interacting protein 1	269					establishment of integrated proviral latency (GO:0075713)|mRNA 5'-splice site recognition (GO:0000395)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to heat (GO:0009408)|response to oxidative stress (GO:0006979)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear heterochromatin (GO:0005720)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription coactivator activity (GO:0001105)|supercoiled DNA binding (GO:0097100)			breast(2)|endometrium(2)|kidney(1)|lung(3)|prostate(1)	9				GBM - Glioblastoma multiforme(50;2.38e-06)		GGTTGAAGTAACCCCTGTTTTA	0.351																																					p.V269fs		Atlas-Indel,Pindel	.											.	PSIP1	93	.	0			c.806_807insG						PASS	.																																			SO:0001589	frameshift_variant	11168	exon9			.	AF098482	CCDS6479.1, CCDS6480.1	9p22.2	2008-02-05	2004-02-24		ENSG00000164985	ENSG00000164985			9527	protein-coding gene	gene with protein product		603620	"PC4 and SFRS1 interacting protein 2"	PSIP2		9822615, 9885563	Standard	NM_033222		Approved	p52, LEDGF, p75	uc003zlw.4	O75475	OTTHUMG00000021021	ENST00000380733.4:c.806dupG	chr9.hg19:g.15474063_15474063dupC	ENSP00000370109:p.Val269fs	104.0	0.0	0		84.0	12.0	0.142857	NM_001128217	D3DRI9|O00256|O95368|Q6P391|Q86YB9|Q9NZI3|Q9UER6	Frame_Shift_Ins	INS	ENST00000380733.4	hg19	CCDS6479.1																																																																																			.	.	.	none		0.351	PSIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055445.1	NM_033222		C	15474060	-	C	15474059	7	5	271	1	0	1	1	0	0	0	0	0	12673	43	2	0	847	0	PSIP1	9	15474059	Frame_Shift_Ins	INS	-	TCGA-V9-A7HT-01A-11D-A33Q-10	7132838	15474059	125739372	38	17130											
ZNF782	158431	hgsc.bcm.edu	37	chr9	99581195	99581195	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atagagcaggatttcccacaTtcattatactcatagggttt	12	14	7	8	0	2	1	2	0	0	1	3	2	3	2	1	2	2	2	1	2	4	7			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr9:99581195T>C	ENST00000481138.1	-	6	1771	c.1110A>G	c.(1108-1110)gaA>gaG	p.E370E	ZNF782_ENST00000466833.1_5'Flank|ZNF782_ENST00000535338.1_Silent_p.E238E	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	370					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			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)				ATTTCCCACATTCATTATACT	0.433																																					p.E370E		Atlas-SNP	.											.	ZNF782	64	.	0			c.A1110G						PASS	.						154	148	150					9																	99581195		2203	4300	6503	SO:0001819	synonymous_variant	158431	exon6			CCCACATTCATTA	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.1110A>G	chr9.hg19:g.99581195T>C		114.0	0.0	.		93.0	23.0	.	NM_001001662	B2RNR0	Silent	SNP	ENST00000481138.1	hg19	CCDS35075.1	.	.	.	.	.	.	.	.	.	.	T	5.011	0.187743	0.09547	.	.	ENSG00000196597	ENST00000289032	.	.	.	3.18	0.829	0.18847	.	.	.	.	.	T	0.52354	0.1729	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39354	-0.9618	4	.	.	.	.	6.3014	0.21115	0.0:0.2311:0.0:0.7689	.	.	.	.	V	359	.	.	M	-	1	0	ZNF782	98621016	0.000000	0.05858	0.022000	0.16811	0.206000	0.24218	-1.332000	0.02670	0.154000	0.19237	-0.250000	0.11733	ATG	.	.	.	none		0.433	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356810.1	NM_001001662		C	99581195	T	C	99581195	2	2	271	1	0	0	0	0	0	0	0	1	18167	1490	52	3		3	ZNF782	9	99581195	Silent	SNP	T	TCGA-V9-A7HT-01A-11D-A33Q-10	84107136	99581195	41632236	39	17131											
C10orf18	54906	hgsc.bcm.edu	37	chr10	5788734	5788734	+	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	tccctctctagtagttgcagGacagaagggcactaagtacc	11	9	10	11	0	1	1	0	0	1	1	3	2	2	2	2	2	2	5	2	2	5	5			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr10:5788734G>T	ENST00000328090.5	+	15	3975	c.3350G>T	c.(3349-3351)gGa>gTa	p.G1117V	RP11-336A10.2_ENST00000411512.2_RNA	NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	1117																	GTAGTTGCAGGACAGAAGGGC	0.498																																					p.G1117V		Atlas-SNP	.											.	.	.	.	0			c.G3350T						PASS	.						121	117	119					10																	5788734		1998	4180	6178	SO:0001583	missense	54906	exon15			TTGCAGGACAGAA	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.3350G>T	chr10.hg19:g.5788734G>T	ENSP00000328426:p.Gly1117Val	74.0	0.0	.		42.0	23.0	.	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Missense_Mutation	SNP	ENST00000328090.5	hg19	CCDS41485.1	.	.	.	.	.	.	.	.	.	.	G	8.684	0.905742	0.17760	.	.	ENSG00000108021	ENST00000328090	T	0.04551	3.6	5.68	-2.81	0.05805	.	1.074830	0.07161	N	0.850789	T	0.04407	0.0121	L	0.46157	1.445	0.09310	N	1	B	0.25667	0.131	B	0.21546	0.035	T	0.46582	-0.9181	10	0.59425	D	0.04	.	2.0015	0.03468	0.4653:0.132:0.2681:0.1346	.	1117	Q5VWN6	F208B_HUMAN	V	1117	ENSP00000328426:G1117V	ENSP00000328426:G1117V	G	+	2	0	C10orf18	5828740	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-0.207000	0.09384	-0.015000	0.14150	0.591000	0.81541	GGA	.	.	.	none		0.498	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782		T	5788734	G	T	5788734	3	4	271	1	0	0	0	0	1	0	0	0	1598	1174	41	4	3396	4	C10orf18	10	5788734	Missense_Mutation	SNP	G	TCGA-V9-A7HT-01A-11D-A33Q-10		5788734	129746013	40	17132											
BAMBI	25805	hgsc.bcm.edu	37	chr10	28970452	28970452	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggctgcacgatgttctctcTcctcccaggggtgaggcctc	4	10	13	14	1	2	1	0	1	2	0	6	2	3	1	3	4	1	3	3	4	0	1			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr10:28970452T>C	ENST00000375533.3	+	2	898	c.342T>C	c.(340-342)tcT>tcC	p.S114S		NM_012342.2	NP_036474.1	Q13145	BAMBI_HUMAN	BMP and activin membrane-bound inhibitor	114					cell migration (GO:0016477)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell shape (GO:0008360)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|type II transforming growth factor beta receptor binding (GO:0005114)			central_nervous_system(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)	17						ATGTTCTCTCTCCTCCCAGGG	0.517																																					p.S114S		Atlas-SNP	.											.	BAMBI	31	.	0			c.T342C						PASS	.						85	93	90					10																	28970452		2203	4300	6503	SO:0001819	synonymous_variant	25805	exon2			TCTCTCTCCTCCC	U23070	CCDS7162.1	10p12.3-p11.2	2013-07-23	2013-07-23		ENSG00000095739	ENSG00000095739			30251	protein-coding gene	gene with protein product		604444	"BMP and activin membrane-bound inhibitor homolog (Xenopus laevis)"			8621228, 19758997	Standard	NM_012342		Approved	NMA	uc001iuj.1	Q13145	OTTHUMG00000017874	ENST00000375533.3:c.342T>C	chr10.hg19:g.28970452T>C		48.0	0.0	.		42.0	15.0	.	NM_012342		Silent	SNP	ENST00000375533.3	hg19	CCDS7162.1																																																																																			.	.	.	none		0.517	BAMBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047374.1	NM_012342		C	28970452	T	C	28970452	2	2	271	1	0	0	0	0	0	0	0	1	1306	1538	54	3		3	BAMBI	10	28970452	Silent	SNP	T	TCGA-V9-A7HT-01A-11D-A33Q-10	23181718	28970452	106564295	41	17133											
CWF19L1	55280	hgsc.bcm.edu	37	chr10	101996700	101996700	+	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	tctttaatgtcatcagtagtAgagcagctgattgggacagg	11	12	12	6	0	3	2	2	1	1	1	3	3	3	3	0	2	2	4	0	2	3	5			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr10:101996700A>C	ENST00000354105.4	-	12	1367	c.1281T>G	c.(1279-1281)tcT>tcG	p.S427S	CWF19L1_ENST00000478047.1_5'UTR|SNORA12_ENST00000391162.1_RNA|CWF19L1_ENST00000370379.1_Intron|RP11-316M21.6_ENST00000444359.1_RNA	NM_018294.4	NP_060764.3	Q69YN2	C19L1_HUMAN	CWF19-like 1, cell cycle control (S. pombe)	427							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)		CATCAGTAGTAGAGCAGCTGA	0.507																																					p.S427S		Atlas-SNP	.											.	CWF19L1	39	.	0			c.T1281G						PASS	.						164	158	160					10																	101996700		2203	4300	6503	SO:0001819	synonymous_variant	55280	exon12			AGTAGTAGAGCAG	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.1281T>G	chr10.hg19:g.101996700A>C		50.0	0.0	.		42.0	13.0	.	NM_018294	B4DHX1|D3DR66|Q5W0I3|Q96HC3|Q9H865|Q9NV13	Silent	SNP	ENST00000354105.4	hg19	CCDS7489.1																																																																																			.	.	.	none		0.507	CWF19L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018294		C	101996700	A	C	101996700	2	2	271	1	0	0	0	0	0	0	0	1	4073	407	15	5		5	CWF19L1	10	101996700	Silent	SNP	A	TCGA-V9-A7HT-01A-11D-A33Q-10	73026248	101996700	33538047	42	17134											
OR52R1	119695	hgsc.bcm.edu	37	chr11	4825301	4825301	+	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	aaaggcatggatgaagaacaCctggatgaggcaggcatggt	14	6	15	6	0	0	3	0	2	0	1	0	5	0	5	1	6	1	3	1	6	3	0			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr11:4825301C>A	ENST00000356069.2	-	1	309	c.310G>T	c.(310-312)Gtg>Ttg	p.V104L	MMP26_ENST00000477339.1_Intron|OR52R1_ENST00000380382.1_Missense_Mutation_p.V183L|MMP26_ENST00000380390.1_Intron	NM_001005177.3	NP_001005177.3	Q8NGF1	O52R1_HUMAN	olfactory receptor, family 52, subfamily R, member 1	104						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|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)		ATGAAGAACACCTGGATGAGG	0.522																																					p.V104L		Atlas-SNP	.											.	OR52R1	81	.	0			c.G310T						PASS	.						154	139	144					11																	4825301		2201	4298	6499	SO:0001583	missense	119695	exon1			AGAACACCTGGAT	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.310G>T	chr11.hg19:g.4825301C>A	ENSP00000348368:p.Val104Leu	66.0	0.0	.		69.0	29.0	.	NM_001005177	Q6IFI0	Missense_Mutation	SNP	ENST00000356069.2	hg19	CCDS31360.2	.	.	.	.	.	.	.	.	.	.	C	12.99	2.102095	0.37048	.	.	ENSG00000176937	ENST00000356069;ENST00000380382	T;T	0.00381	7.63;7.63	5.42	2.48	0.30137	GPCR, rhodopsin-like superfamily (1);	0.340919	0.20955	N	0.082663	T	0.00144	0.0004	N	0.02391	-0.57	0.24499	N	0.994261	B	0.11235	0.004	B	0.12837	0.008	T	0.42032	-0.9475	10	0.72032	D	0.01	.	3.7756	0.08659	0.2976:0.4713:0.0:0.231	.	104	Q8NGF1	O52R1_HUMAN	L	104;183	ENSP00000348368:V104L;ENSP00000369742:V183L	ENSP00000348368:V104L	V	-	1	0	OR52R1	4781877	0.871000	0.30034	1.000000	0.80357	0.974000	0.67602	-0.059000	0.11731	0.848000	0.35191	0.650000	0.86243	GTG	.	.	.	none		0.522	OR52R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142183.1	NM_001005177		A	4825301	C	A	4825301	3	1	271	1	0	0	0	0	1	0	0	0	11138	507	18	4	640	4	OR52R1	11	4825301	Missense_Mutation	SNP	C	TCGA-V9-A7HT-01A-11D-A33Q-10		4825301	130181215	43	17135											
ARHGAP32	9743	hgsc.bcm.edu	37	chr11	128844881	128844883	+	In_Frame_Del	DEL	GAA	GAA	-																															gatctgggtcttctgggtcgGaagagcttagaatcacctgg																										TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr11:128844881_128844883delGAA	ENST00000310343.9	-	20	2166_2168	c.2167_2169delTTC	c.(2167-2169)ttcdel	p.F723del	ARHGAP32_ENST00000524655.1_In_Frame_Del_p.F649del|ARHGAP32_ENST00000392657.3_In_Frame_Del_p.F374del|ARHGAP32_ENST00000527272.1_In_Frame_Del_p.F374del	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	723					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						TTCTGGGTCGGAAGAGCTTAGAA	0.443																																					p.723_724del		Atlas-Indel,Pindel	.											.	ARHGAP32	307	.	0			c.2168_2170del						PASS	.																																			SO:0001651	inframe_deletion	9743	exon20			.	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.2167_2169delTTC	chr11.hg19:g.128844881_128844883delGAA	ENSP00000310561:p.Phe723del	38.0	0.0	0		31.0	14.0	0.451613	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	In_Frame_Del	DEL	ENST00000310343.9	hg19	CCDS44769.1																																																																																			.	.	.	none		0.443	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		-	128844883	GAA	-	128844881	7	5	271	1	0	1	0	1	0	0	0	0	881	1165	41	0	4106	0	ARHGAP32	11	128844881	In_Frame_Del	DEL	GAA	TCGA-V9-A7HT-01A-11D-A33Q-10	124019580	128844881	6161635	44	17136											
EFCAB4B	84766	hgsc.bcm.edu	37	chr12	3747327	3747327	+	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	ttccaacaggctgccctcggGgggatgtgggggtgagtttc	5	10	17	9	1	0	1	0	1	0	0	3	2	1	2	2	6	2	2	2	6	1	2			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr12:3747327G>A	ENST00000440314.2	-	14	2038	c.1565C>T	c.(1564-1566)cCc>cTc	p.P522L		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)			CTGCCCTCGGGGGGATGTGGG	0.547																																					p.P522L		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.C1565T						PASS	.						7	9	8					12																	3747327		690	1588	2278	SO:0001583	missense	84766	exon14			CCTCGGGGGGATG																												ENST00000440314.2:c.1565C>T	chr12.hg19:g.3747327G>A	ENSP00000409382:p.Pro522Leu	75.0	0.0	.		66.0	23.0	.	NM_001144958	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000440314.2	hg19	CCDS44803.1	.	.	.	.	.	.	.	.	.	.	G	12.53	1.964657	0.34659	.	.	ENSG00000130038	ENST00000440314	T	0.62639	0.01	4.72	4.72	0.59763	.	.	.	.	.	T	0.56001	0.1956	.	.	.	0.80722	D	1	B	0.22346	0.068	B	0.19148	0.024	T	0.58301	-0.7660	8	0.87932	D	0	.	15.2134	0.73244	0.0:0.0:1.0:0.0	.	522	Q9BSW2-2	.	L	522	ENSP00000409382:P522L	ENSP00000409382:P522L	P	-	2	0	EFCAB4B	3617588	1.000000	0.71417	0.993000	0.49108	0.208000	0.24298	3.966000	0.56795	2.424000	0.82194	0.557000	0.71058	CCC	.	.	.	none		0.547	EFCAB4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398640.2			A	3747327	G	A	3747327	3	1	271	1	0	0	0	0	1	0	0	0	4939	1232	43	2	658	2	EFCAB4B	12	3747327	Missense_Mutation	SNP	G	TCGA-V9-A7HT-01A-11D-A33Q-10		3747327	130104568	45	17137											
C12orf41	54934	hgsc.bcm.edu	37	chr12	49062931	49062931	+	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	gccagcattctccgttccttCaactgcctatgcagtaaggc	8	11	8	14	1	2	0	1	0	1	0	4	0	3	0	4	1	4	4	4	1	3	5			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr12:49062931C>A	ENST00000420613.2	-	6	881	c.834G>T	c.(832-834)ttG>ttT	p.L278F	KANSL2_ENST00000553086.1_Missense_Mutation_p.L278F|SNORA2B_ENST00000384583.1_RNA|KANSL2_ENST00000357861.3_Missense_Mutation_p.L83F|KANSL2_ENST00000550347.1_Missense_Mutation_p.L461F	NM_017822.3	NP_060292.3	Q9H9L4	KANL2_HUMAN	KAT8 regulatory NSL complex subunit 2	278					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)											TCCGTTCCTTCAACTGCCTAT	0.428																																					p.L278F		Atlas-SNP	.											.	.	.	.	0			c.G834T						PASS	.						53	53	53					12																	49062931		1944	4082	6026	SO:0001583	missense	54934	exon6			TTCCTTCAACTGC	AK094528	CCDS44869.1	12q13.11	2011-10-31	2011-10-31	2011-10-31	ENSG00000139620	ENSG00000139620			26024	protein-coding gene	gene with protein product		615488	"chromosome 12 open reading frame 41"	C12orf41		12477932	Standard	NM_017822		Approved	FLJ20436, NSL2	uc001rrz.2	Q9H9L4	OTTHUMG00000170392	ENST00000420613.2:c.834G>T	chr12.hg19:g.49062931C>A	ENSP00000415436:p.Leu278Phe	64.0	0.0	.		66.0	23.0	.	NM_017822	Q8N3B5|Q96CV0|Q9NX51	Missense_Mutation	SNP	ENST00000420613.2	hg19	CCDS44869.1	.	.	.	.	.	.	.	.	.	.	C	13.12	2.141053	0.37825	.	.	ENSG00000139620	ENST00000550347;ENST00000420613;ENST00000547087;ENST00000553086;ENST00000357861	T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89	5.95	1.65	0.23941	.	0.142489	0.47093	D	0.000254	T	0.32793	0.0841	L	0.55743	1.74	0.45837	D	0.998708	P;B;P	0.41102	0.738;0.101;0.587	B;B;B	0.37267	0.233;0.039;0.245	T	0.06716	-1.0811	10	0.26408	T	0.33	-8.2093	9.9462	0.41611	0.0:0.6755:0.0:0.3245	.	461;278;83	F8VX10;Q9H9L4;Q9H9L4-2	.;CL041_HUMAN;.	F	461;278;26;278;83	ENSP00000449747:L461F;ENSP00000415436:L278F;ENSP00000447608:L26F;ENSP00000448833:L278F;ENSP00000350527:L83F	ENSP00000350527:L83F	L	-	3	2	C12orf41	47349198	0.998000	0.40836	1.000000	0.80357	0.976000	0.68499	0.558000	0.23469	0.432000	0.26286	-0.136000	0.14681	TTG	.	.	.	none		0.428	KANSL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408841.1	NM_017822		A	49062931	C	A	49062931	3	1	271	1	0	0	0	0	1	0	0	0	1689	825	29	4	664	4	C12orf41	12	49062931	Missense_Mutation	SNP	C	TCGA-V9-A7HT-01A-11D-A33Q-10	45315604	49062931	84788964	46	17138											
PRMT5	10419	hgsc.bcm.edu	37	chr14	23393691	23393691	+	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	gaggggaaagcactcactggAcattggtatccttctcctct	9	11	10	11	0	3	0	1	0	2	0	5	3	4	2	2	4	1	2	2	4	2	3			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr14:23393691A>T	ENST00000324366.8	-	10	1296	c.1073T>A	c.(1072-1074)gTc>gAc	p.V358D	PRMT5-AS1_ENST00000587245.2_RNA|PRMT5_ENST00000538452.1_Missense_Mutation_p.V252D|PRMT5_ENST00000553897.1_Missense_Mutation_p.V314D|PRMT5_ENST00000216350.8_Missense_Mutation_p.V297D|PRMT5_ENST00000397441.2_Missense_Mutation_p.V341D|PRMT5_ENST00000553641.1_5'Flank|PRMT5-AS1_ENST00000595662.1_RNA|PRMT5-AS1_ENST00000609885.1_RNA|PRMT5-AS1_ENST00000599580.2_RNA|PRMT5-AS1_ENST00000424245.2_RNA|PRMT5-AS1_ENST00000457443.2_RNA|PRMT5-AS1_ENST00000590290.1_RNA|PRMT5_ENST00000397440.4_Missense_Mutation_p.V187D	NM_006109.3	NP_006100.2	O14744	ANM5_HUMAN	protein arginine methyltransferase 5	358	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|endothelial cell activation (GO:0042118)|gene expression (GO:0010467)|histone H4-R3 methylation (GO:0043985)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|peptidyl-arginine N-methylation (GO:0035246)|regulation of mitosis (GO:0007088)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|methylosome (GO:0034709)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|histone-arginine N-methyltransferase activity (GO:0008469)|methyltransferase activity (GO:0008168)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|transcription corepressor activity (GO:0003714)			endometrium(4)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	25	all_cancers(95;2.76e-05)			GBM - Glioblastoma multiforme(265;0.0126)		CACTCACTGGACATTGGTATC	0.473																																					p.V358D		Atlas-SNP	.											.	PRMT5	101	.	0			c.T1073A						PASS	.						175	169	171					14																	23393691		2203	4300	6503	SO:0001583	missense	10419	exon10			CACTGGACATTGG	AF015913	CCDS9579.1, CCDS41922.1, CCDS61394.1, CCDS61395.1, CCDS61396.1	14q11.2	2014-06-12	2006-02-16	2006-02-16	ENSG00000100462	ENSG00000100462	2.1.1.125	"Protein arginine methyltransferases"	10894	protein-coding gene	gene with protein product		604045	"skb1 (S. pombe) homolog", "SKB1 homolog (S. pombe)"	HRMT1L5, SKB1		9843966	Standard	NM_001282955		Approved	SKB1Hs	uc001whm.1	O14744	OTTHUMG00000028709	ENST00000324366.8:c.1073T>A	chr14.hg19:g.23393691A>T	ENSP00000319169:p.Val358Asp	273.0	0.0	.		181.0	39.0	.	NM_006109	A8MTP3|A8MZ91|B4DX49|B4DY30|B5BU10|D3DS33|E2QRE7|Q6IBR1|Q9UKH1	Missense_Mutation	SNP	ENST00000324366.8	hg19	CCDS9579.1	.	.	.	.	.	.	.	.	.	.	A	16.44	3.125303	0.56721	.	.	ENSG00000100462	ENST00000324366;ENST00000397441;ENST00000397440;ENST00000216350;ENST00000538452;ENST00000553897;ENST00000553502;ENST00000555530	T;T;T;T;T;T	0.17691	2.26;2.26;2.26;2.26;2.26;2.26	5.36	5.36	0.76844	.	0.295026	0.37304	N	0.002160	T	0.16642	0.0400	L	0.45137	1.4	0.80722	D	1	B;B;B;B;B	0.30727	0.265;0.292;0.131;0.229;0.091	B;B;B;B;B	0.34242	0.142;0.178;0.091;0.079;0.094	T	0.05115	-1.0905	10	0.12103	T	0.63	.	14.4831	0.67597	1.0:0.0:0.0:0.0	.	314;297;187;358;341	G3V5W5;B4DX49;A8MTP3;O14744;A8MZ91	.;.;.;ANM5_HUMAN;.	D	358;341;187;297;252;314;101;253	ENSP00000319169:V358D;ENSP00000380583:V341D;ENSP00000380582:V187D;ENSP00000216350:V297D;ENSP00000444915:V252D;ENSP00000452555:V314D	ENSP00000216350:V297D	V	-	2	0	PRMT5	22463531	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.587000	0.82613	2.254000	0.74563	0.459000	0.35465	GTC	.	.	.	none		0.473	PRMT5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071674.3			T	23393691	A	T	23393691	3	4	271	1	0	0	0	0	1	0	0	0	12549	275	10	5	872	5	PRMT5	14	23393691	Missense_Mutation	SNP	A	TCGA-V9-A7HT-01A-11D-A33Q-10		23393691	83955849	47	17139											
NEO1	4756	hgsc.bcm.edu	37	chr15	73409078	73409079	+	Frame_Shift_Ins	INS	-	-	A																															tctcccggatggatctttatINSttatcagcaatgtggtgcat																										TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr15:73409078_73409079insA	ENST00000339362.5	+	3	775_776	c.328_329insA	c.(328-330)tttfs	p.F110fs	NEO1_ENST00000261908.6_Frame_Shift_Ins_p.F110fs|NEO1_ENST00000560262.1_Frame_Shift_Ins_p.F110fs|NEO1_ENST00000558964.1_Frame_Shift_Ins_p.F110fs			Q92859	NEO1_HUMAN	neogenin 1	110	Ig-like C2-type 1.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|iron ion homeostasis (GO:0055072)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						TGGATCTTTATTTATCAGCAAT	0.376																																					p.F110fs		Atlas-INDEL	.											.	NEO1	102	.	0			c.328_329insA						PASS	.																																			SO:0001589	frameshift_variant	4756	exon2			.	U61262	CCDS10247.1, CCDS53957.1, CCDS58378.1	15q22.3-q23	2014-06-20	2010-06-24		ENSG00000067141	ENSG00000067141		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing", "Fibronectin type III domain containing"	7754	protein-coding gene	gene with protein product	"immunoglobulin superfamily, DCC subclass, member 2"	601907	"neogenin (chicken) homolog 1"			9121761	Standard	NM_002499		Approved	NGN, HsT17534, IGDCC2, NTN1R2	uc002avm.4	Q92859	OTTHUMG00000133509	Exception_encountered	chr15.hg19:g.73409078_73409079insA	ENSP00000341198:p.Phe110fs	90.0	0.0	0		51.0	13.0	0.254902	NM_001172623	B7ZKM9|B7ZKN0|O00340|Q17RX1	Frame_Shift_Ins	INS	ENST00000339362.5	hg19	CCDS10247.1																																																																																			.	.	.	none		0.376	NEO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257472.2	NM_002499		A	73409079	-	A	73409078	7	5	271	1	0	1	1	0	0	0	0	0	10343	1493	52	0	334	0	NEO1	15	73409078	Frame_Shift_Ins	INS	-	TCGA-V9-A7HT-01A-11D-A33Q-10		73409078	29122314	48	17140											
CRTC3	64784	hgsc.bcm.edu	37	chr15	91172533	91172533	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagactgtgctttcctcttcCttaaataaccacccacagac	12	11	4	14	0	1	2	0	0	1	2	3	2	3	2	4	0	2	1	4	0	4	4			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr15:91172533C>T	ENST00000268184.6	+	11	1039	c.1035C>T	c.(1033-1035)tcC>tcT	p.S345S	RP11-387D10.2_ENST00000559531.1_RNA|CRTC3_ENST00000420329.2_Silent_p.S345S			Q6UUV7	CRTC3_HUMAN	CREB regulated transcription coactivator 3	345					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)			TTTCCTCTTCCTTAAATAACC	0.473			T	MAML2	salivary gland mucoepidermoid																																p.S345S		Atlas-SNP	.		Dom	yes		15	15q26.1	64784	CREB regulated transcription coactivator 3		E	.	CRTC3	47	.	0			c.C1035T						PASS	.						180	176	178					15																	91172533		2198	4298	6496	SO:0001819	synonymous_variant	64784	exon11			CTCTTCCTTAAAT		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.1035C>T	chr15.hg19:g.91172533C>T		182.0	0.0	.		112.0	21.0	.	NM_022769	Q6DK61|Q6DK62|Q8NF38|Q9H6U2	Silent	SNP	ENST00000268184.6	hg19	CCDS32331.1																																																																																			.	.	.	none		0.473	CRTC3-001	KNOWN	NAGNAG_splice_site|non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417716.2	NM_022769		T	91172533	C	T	91172533	2	4	271	1	0	0	0	0	0	0	0	1	3903	668	24	2		2	CRTC3	15	91172533	Silent	SNP	C	TCGA-V9-A7HT-01A-11D-A33Q-10	17763455	91172533	11358859	49	17141											
PDXDC1	23042	hgsc.bcm.edu	37	chr16	15129917	15129917	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgaggttcagatgctttgAgtgagaccagctcagtcagt	9	11	13	8	1	3	3	3	2	0	2	3	5	3	3	1	1	3	3	1	1	0	2			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr16:15129917A>G	ENST00000396410.4	+	23	2249	c.2152A>G	c.(2152-2154)Agt>Ggt	p.S718G	PDXDC1_ENST00000535621.2_Intron|PDXDC1_ENST00000563679.1_Missense_Mutation_p.S736G|PDXDC1_ENST00000325823.7_Missense_Mutation_p.S703G|PDXDC1_ENST00000569715.1_Missense_Mutation_p.S691G|PDXDC1_ENST00000450288.2_Missense_Mutation_p.S690G|PDXDC1_ENST00000447912.2_Missense_Mutation_p.S627G	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	718					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						AGATGCTTTGAGTGAGACCAG	0.537																																					p.S718G		Atlas-SNP	.											.	PDXDC1	59	.	0			c.A2152G						PASS	.						145	139	141					16																	15129917		2197	4300	6497	SO:0001583	missense	23042	exon23			GCTTTGAGTGAGA	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.2152A>G	chr16.hg19:g.15129917A>G	ENSP00000379691:p.Ser718Gly	53.0	0.0	.		47.0	6.0	.	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Missense_Mutation	SNP	ENST00000396410.4	hg19	CCDS32393.1	.	.	.	.	.	.	.	.	.	.	A	17.18	3.324586	0.60634	.	.	ENSG00000179889	ENST00000325823;ENST00000447912;ENST00000396410;ENST00000450288	T;T;T;T	0.34859	1.35;1.91;1.34;1.38	5.91	4.82	0.62117	.	0.038008	0.85682	D	0.000000	T	0.27349	0.0671	L	0.29908	0.895	0.58432	D	0.999998	B;B;B;B	0.19073	0.025;0.033;0.025;0.012	B;B;B;B	0.20184	0.022;0.028;0.022;0.016	T	0.07770	-1.0755	10	0.54805	T	0.06	-17.3828	10.7095	0.45975	0.9265:0.0:0.0735:0.0	.	690;627;690;718	E7EPL4;E7EMH5;B4DR55;Q6P996	.;.;.;PDXD1_HUMAN	G	703;627;718;690	ENSP00000322807:S703G;ENSP00000400310:S627G;ENSP00000379691:S718G;ENSP00000391147:S690G	ENSP00000322807:S703G	S	+	1	0	PDXDC1	15037418	1.000000	0.71417	0.945000	0.38365	0.998000	0.95712	6.045000	0.71020	2.254000	0.74563	0.533000	0.62120	AGT	.	.	.	none		0.537	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027		G	15129917	A	G	15129917	3	3	271	1	0	0	0	0	1	0	0	0	11703	304	11	3	2242	3	PDXDC1	16	15129917	Missense_Mutation	SNP	A	TCGA-V9-A7HT-01A-11D-A33Q-10		15129917	75224836	50	17142											
DPEP3	64180	hgsc.bcm.edu	37	chr16	68012250	68012250	+	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	cgcagcacagagaggctgctGtccagtgagtgaccaccctc	9	6	12	14	1	0	3	0	2	0	1	2	4	1	3	3	1	2	4	3	1	0	0	rs553819810		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr16:68012250G>C	ENST00000268793.4	-	4	1054	c.681C>G	c.(679-681)gaC>gaG	p.D227E	DPEP3_ENST00000574342.1_5'Flank	NM_001129758.1|NM_022357.3	NP_001123230.1|NP_071752.3	Q9H4B8	DPEP3_HUMAN	dipeptidase 3	202					male meiosis (GO:0007140)	anchored component of membrane (GO:0031225)	dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metalloexopeptidase activity (GO:0008235)			breast(4)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(2)	20		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0117)|Epithelial(162;0.0481)|all cancers(182;0.236)		AGAGGCTGCTGTCCAGTGAGT	0.552																																					p.D227E		Atlas-SNP	.											.	DPEP3	48	.	0			c.C681G						PASS	.						79	76	77					16																	68012250		2198	4300	6498	SO:0001583	missense	64180	exon4			GCTGCTGTCCAGT	AJ291679	CCDS10856.1	16q22.1	2011-07-22			ENSG00000141096	ENSG00000141096	3.4.13.19		23029	protein-coding gene	gene with protein product		609926					Standard	NM_022357		Approved		uc002evc.4	Q9H4B8	OTTHUMG00000137544	ENST00000268793.4:c.681C>G	chr16.hg19:g.68012250G>C	ENSP00000268793:p.Asp227Glu	84.0	0.0	.		84.0	23.0	.	NM_001129758	B3KQ48|Q6PEZ5|Q6UXE4	Missense_Mutation	SNP	ENST00000268793.4	hg19	CCDS10856.1	.	.	.	.	.	.	.	.	.	.	G	12.08	1.829864	0.32329	.	.	ENSG00000141096	ENST00000268793	T	0.19938	2.11	4.7	1.1	0.20463	.	0.050722	0.85682	D	0.000000	T	0.14917	0.0360	L	0.39397	1.21	0.42993	D	0.994498	B	0.33777	0.425	B	0.31101	0.124	T	0.07462	-1.0771	10	0.48119	T	0.1	.	9.1289	0.36833	0.3032:0.0:0.6968:0.0	.	202	Q9H4B8	DPEP3_HUMAN	E	227	ENSP00000268793:D227E	ENSP00000268793:D227E	D	-	3	2	DPEP3	66569751	1.000000	0.71417	1.000000	0.80357	0.435000	0.31806	5.324000	0.65863	0.420000	0.25954	0.561000	0.74099	GAC	.	.	.	none		0.552	DPEP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268875.3	NM_022357		C	68012250	G	C	68012250	3	2	271	1	0	0	0	0	1	0	0	0	4717	1368	48	4	888	4	DPEP3	16	68012250	Missense_Mutation	SNP	G	TCGA-V9-A7HT-01A-11D-A33Q-10	52882333	68012250	22342503	51	17143											
PRMT7	54496	hgsc.bcm.edu	37	chr16	68373404	68373404	+	Missense_Mutation	SNP	T	T	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	gcaccctctgtctgtgacatTcagctgaaccaggtgtcacc	8	10	9	14	0	4	2	2	2	2	0	4	2	4	2	3	1	2	2	3	1	1	1			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr16:68373404T>G	ENST00000339507.5	+	8	1514	c.684T>G	c.(682-684)atT>atG	p.I228M	PRMT7_ENST00000348497.4_Missense_Mutation_p.I154M|PRMT7_ENST00000441236.1_Missense_Mutation_p.I178M|PRMT7_ENST00000449359.3_Missense_Mutation_p.I178M|PRMT7_ENST00000564441.1_3'UTR			Q9NVM4	ANM7_HUMAN	protein arginine methyltransferase 7	228	SAM-dependent MTase PRMT-type 1. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|histone arginine methylation (GO:0034969)|histone methylation (GO:0016571)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of protein binding (GO:0043393)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	[myelin basic protein]-arginine N-methyltransferase activity (GO:0016277)|histone binding (GO:0042393)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|histone-arginine N-methyltransferase activity (GO:0008469)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			endometrium(3)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|urinary_tract(1)	20		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0155)|Epithelial(162;0.0629)		TCTGTGACATTCAGCTGAACC	0.582																																					p.I228M		Atlas-SNP	.											.	PRMT7	51	.	0			c.T684G						PASS	.						98	76	83					16																	68373404		2198	4300	6498	SO:0001583	missense	54496	exon8			TGACATTCAGCTG	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.684T>G	chr16.hg19:g.68373404T>G	ENSP00000343103:p.Ile228Met	52.0	0.0	.		57.0	21.0	.	NM_019023	B3KPR0|B3KUG9|B4E379|Q96PV5|Q9H9L0	Missense_Mutation	SNP	ENST00000339507.5	hg19	CCDS10866.1	.	.	.	.	.	.	.	.	.	.	T	17.98	3.520487	0.64747	.	.	ENSG00000132600	ENST00000449359;ENST00000441236;ENST00000348497;ENST00000339507	T;T	0.78481	-1.18;0.84	5.51	1.98	0.26296	.	0.087357	0.85682	D	0.000000	T	0.77624	0.4158	L	0.41906	1.305	0.51767	D	0.999933	D;D;P;D	0.76494	0.998;0.996;0.901;0.999	D;D;B;D	0.76575	0.963;0.988;0.387;0.984	T	0.71902	-0.4452	10	0.38643	T	0.18	-9.242	3.2342	0.06758	0.2932:0.163:0.0:0.5438	.	178;154;228;228	Q9NVM4-3;Q9NVM4-2;Q9NVM4;Q9NVM4-4	.;.;ANM7_HUMAN;.	M	178;178;154;228	ENSP00000345775:I154M;ENSP00000343103:I228M	ENSP00000343103:I228M	I	+	3	3	PRMT7	66930905	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.000000	0.29770	0.113000	0.18004	0.533000	0.62120	ATT	.	.	.	none		0.582	PRMT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268892.3	NM_019023		G	68373404	T	G	68373404	3	3	271	1	0	0	0	0	1	0	0	0	12551	1771	62	5	706	5	PRMT7	16	68373404	Missense_Mutation	SNP	T	TCGA-V9-A7HT-01A-11D-A33Q-10	361154	68373404	21981349	52	17144											
CDH3	1001	hgsc.bcm.edu	37	chr16	68716217	68716217	+	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	actgacagtacgaggcccatGtgcctgagaatgcagtgggc	10	7	14	10	1	0	2	0	2	0	1	0	4	0	2	2	2	3	2	2	2	2	1			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr16:68716217G>T	ENST00000264012.4	+	9	1553	c.1009G>T	c.(1009-1011)Gtg>Ttg	p.V337L	CDH3_ENST00000581171.1_Missense_Mutation_p.V282L|CDH3_ENST00000429102.2_Missense_Mutation_p.V337L	NM_001793.4	NP_001784.2	P22223	CADH3_HUMAN	cadherin 3, type 1, P-cadherin (placental)	337	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)		CGAGGCCCATGTGCCTGAGAA	0.577																																					p.V337L		Atlas-SNP	.											.	CDH3	68	.	2	Unknown(2)	breast(2)	c.G1009T						PASS	.						75	54	61					16																	68716217		2198	4300	6498	SO:0001583	missense	1001	exon9			GCCCATGTGCCTG	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.1009G>T	chr16.hg19:g.68716217G>T	ENSP00000264012:p.Val337Leu	73.0	0.0	.		65.0	13.0	.	NM_001793	B2R6F4|Q05DI6	Missense_Mutation	SNP	ENST00000264012.4	hg19	CCDS10868.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.509463	0.85282	.	.	ENSG00000062038	ENST00000429102;ENST00000264012;ENST00000542274	T;T	0.55234	0.53;0.53	5.56	5.56	0.83823	Cadherin (4);Cadherin-like (1);	0.000000	0.37483	N	0.002065	T	0.72463	0.3463	M	0.71581	2.175	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.75007	-0.3469	10	0.87932	D	0	.	17.0347	0.86471	0.0:0.0:1.0:0.0	.	337	P22223	CADH3_HUMAN	L	337;337;282	ENSP00000398485:V337L;ENSP00000264012:V337L	ENSP00000264012:V337L	V	+	1	0	CDH3	67273718	1.000000	0.71417	0.951000	0.38953	0.562000	0.35680	7.361000	0.79497	2.614000	0.88457	0.561000	0.74099	GTG	.	.	.	none		0.577	CDH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268896.2	NM_001793		T	68716217	G	T	68716217	3	4	271	1	0	0	0	0	1	0	0	0	3113	1377	48	4	1043	4	CDH3	16	68716217	Missense_Mutation	SNP	G	TCGA-V9-A7HT-01A-11D-A33Q-10	342813	68716217	21638536	53	17145											
ZNRF1	84937	hgsc.bcm.edu	37	chr16	75127548	75127548	+	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	tataatgtgtttgagcaaacCtcgcctctcctacaacggta	11	12	7	11	2	1	1	0	1	1	0	3	1	1	1	3	1	4	3	3	1	6	5			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr16:75127548C>G	ENST00000335325.4	+	2	1145	c.503C>G	c.(502-504)cCt>cGt	p.P168R	ZNRF1_ENST00000564320.1_3'UTR|ZNRF1_ENST00000566250.1_Missense_Mutation_p.P168R|ZNRF1_ENST00000320619.6_Missense_Mutation_p.P168R|ZNRF1_ENST00000567962.1_Missense_Mutation_p.P168R	NM_032268.4	NP_115644.1	Q8ND25	ZNRF1_HUMAN	zinc and ring finger 1, E3 ubiquitin protein ligase	168					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						TTGAGCAAACCTCGCCTCTCC	0.557																																					p.P168R		Atlas-SNP	.											.	ZNRF1	6	.	0			c.C503G						PASS	.						136	118	124					16																	75127548		2198	4300	6498	SO:0001583	missense	84937	exon2			GCAAACCTCGCCT	AF378524	CCDS10912.1	16q22.3	2013-01-09	2012-02-23		ENSG00000186187	ENSG00000186187		"RING-type (C3HC4) zinc fingers"	18452	protein-coding gene	gene with protein product		612060	"zinc and ring finger 1"				Standard	NM_032268		Approved	nin283, FLJ14846, DKFZp434E229	uc002fdl.1	Q8ND25	OTTHUMG00000137606	ENST00000335325.4:c.503C>G	chr16.hg19:g.75127548C>G	ENSP00000335091:p.Pro168Arg	157.0	0.0	.		109.0	39.0	.	NM_032268	D3DUJ9|Q9H083	Missense_Mutation	SNP	ENST00000335325.4	hg19	CCDS10912.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.834662	0.91036	.	.	ENSG00000186187	ENST00000320619;ENST00000335325	T	0.52057	0.68	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.70395	0.3219	M	0.70595	2.14	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.998	D;D;D	0.91635	0.994;0.999;0.987	T	0.71573	-0.4552	10	0.72032	D	0.01	-0.0544	19.9542	0.97213	0.0:1.0:0.0:0.0	.	168;168;168	B4DG67;Q8ND25-2;Q8ND25	.;.;ZNRF1_HUMAN	R	168	ENSP00000335091:P168R	ENSP00000323362:P168R	P	+	2	0	ZNRF1	73685049	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.414000	0.80117	2.728000	0.93425	0.650000	0.86243	CCT	.	.	.	none		0.557	ZNRF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269020.2			G	75127548	C	G	75127548	3	3	271	1	0	0	0	0	1	0	0	0	18223	681	24	4	509	4	ZNRF1	16	75127548	Missense_Mutation	SNP	C	TCGA-V9-A7HT-01A-11D-A33Q-10	6411331	75127548	15227205	54	17146											
FANCA	2175	hgsc.bcm.edu	37	chr16	89831438	89831439	+	In_Frame_Ins	INS	-	-	GGCCTCTGA																															tcctcagaaagaggctgtcgINSggcctctgagaacaatctga																								rs149435806	byFrequency	TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr16:89831438_89831439insGGCCTCTGA	ENST00000389301.3	-	28	2667_2668	c.2637_2638insTCAGAGGCC	c.(2635-2640)gcccga>gccTCAGAGGCCcga	p.878_879insASE	FANCA_ENST00000568369.1_In_Frame_Ins_p.878_879insASE	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	878					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)		AGAGGCTGTCGGGCCTCTGAGA	0.535			"D, Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.R880delinsSEAR		Pindel	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"Fanconi anemia, complementation group A"		L	.	FANCA	99	.	0			c.2638_2639insTCAGAGGCC	GRCh37	CM080346	FANCA	M		PASS	.																																			SO:0001652	inframe_insertion	2175	exon28	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	.	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.2629_2637dupTCAGAGGCC	chr16.hg19:g.89831439_89831447dupGGCCTCTGA	ENSP00000373952:p.Glu878_Ala879insAlaSerGlu	91.0	0.0	.		80.0	12.0	0.150	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	In_Frame_Ins	INS	ENST00000389301.3	hg19	CCDS32515.1																																																																																			.	.	.	none		0.535	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1			GGCCTCTGA	89831439	-	GGCCTCTGA	89831438	7	5	271	1	0	1	1	0	0	0	0	0	5669	1124	39	0	1793	0	FANCA	16	89831438	In_Frame_Ins	INS	-	TCGA-V9-A7HT-01A-11D-A33Q-10	14703890	89831438	523315	55	17147											
C17orf48	56985	hgsc.bcm.edu	37	chr17	10608320	10608320	+	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	ctttggcgtcatcgcagatgTtcaatttgcagacttagaag	10	13	10	8	2	2	3	2	0	0	3	3	3	2	3	0	1	1	3	0	1	3	4			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr17:10608320T>A	ENST00000379774.4	+	2	168	c.77T>A	c.(76-78)gTt>gAt	p.V26D	ADPRM_ENST00000609540.1_Missense_Mutation_p.V26D	NM_020233.4	NP_064618.3	Q3LIE5	ADPRM_HUMAN	ADP-ribose/CDP-alcohol diphosphatase, manganese-dependent	26							ADP-ribose diphosphatase activity (GO:0047631)|CDP-glycerol diphosphatase activity (GO:0047734)|metal ion binding (GO:0046872)										ATCGCAGATGTTCAATTTGCA	0.438																																					p.V26D		Atlas-SNP	.											.	.	.	.	0			c.T77A						PASS	.						148	144	145					17																	10608320		2203	4300	6503	SO:0001583	missense	56985	exon2			CAGATGTTCAATT	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.77T>A	chr17.hg19:g.10608320T>A	ENSP00000369099:p.Val26Asp	80.0	0.0	.		84.0	21.0	.	NM_020233	A8K9B4|D3DTS4|Q9BVD4|Q9NRU8	Missense_Mutation	SNP	ENST00000379774.4	hg19	CCDS11159.2	.	.	.	.	.	.	.	.	.	.	T	20.9	4.059631	0.76074	.	.	ENSG00000170222	ENST00000379774	D	0.94723	-3.5	5.38	5.38	0.77491	.	0.160556	0.53938	D	0.000044	D	0.96935	0.8999	M	0.78049	2.395	0.80722	D	1	D	0.76494	0.999	D	0.72338	0.977	D	0.97458	1.0032	10	0.72032	D	0.01	-22.0576	15.22	0.73303	0.0:0.0:0.0:1.0	.	26	Q3LIE5	ADPRM_HUMAN	D	26	ENSP00000369099:V26D	ENSP00000369099:V26D	V	+	2	0	C17orf48	10549045	1.000000	0.71417	1.000000	0.80357	0.696000	0.40369	7.096000	0.76960	2.248000	0.74166	0.460000	0.39030	GTT	.	.	.	none		0.438	ADPRM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252732.2	NM_020233		A	10608320	T	A	10608320	3	1	271	1	0	0	0	0	1	0	0	0	1861	1725	60	5	79	5	C17orf48	17	10608320	Missense_Mutation	SNP	T	TCGA-V9-A7HT-01A-11D-A33Q-10		10608320	70586890	56	17148											
SPAG5	10615	hgsc.bcm.edu	37	chr17	26906801	26906801	+	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	gggaaaccattgatgctactCgggtgaaagcactcttgtca	11	10	11	9	1	2	2	1	2	1	0	3	3	2	3	1	2	4	2	1	2	3	3	rs546549488		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr17:26906801C>G	ENST00000321765.5	-	17	3184	c.2852G>C	c.(2851-2853)cGa>cCa	p.R951P	ALDOC_ENST00000226253.4_5'Flank|ALDOC_ENST00000395319.3_5'Flank|ALDOC_ENST00000395321.2_5'Flank	NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	951					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)		p.R951L(1)		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)					TGATGCTACTCGGGTGAAAGC	0.502																																					p.R951P		Atlas-SNP	.											SPAG5,NS,carcinoma,0,1	SPAG5	92	.	1	Substitution - Missense(1)	lung(1)	c.G2852C						PASS	.						148	152	151					17																	26906801		2203	4300	6503	SO:0001583	missense	10615	exon17			GCTACTCGGGTGA	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.2852G>C	chr17.hg19:g.26906801C>G	ENSP00000323300:p.Arg951Pro	145.0	0.0	.		103.0	29.0	.	NM_006461	O95213|Q9BWE8|Q9NT17|Q9UFE6	Missense_Mutation	SNP	ENST00000321765.5	hg19	CCDS32594.1	.	.	.	.	.	.	.	.	.	.	c	17.07	3.293952	0.60086	.	.	ENSG00000076382	ENST00000321765	T	0.32753	1.44	5.4	4.41	0.53225	.	0.148155	0.30365	N	0.009799	T	0.40956	0.1138	L	0.34521	1.04	0.34124	D	0.664436	D	0.89917	1.0	D	0.75484	0.986	T	0.50224	-0.8853	10	0.62326	D	0.03	-7.7226	10.1832	0.42982	0.0:0.9085:0.0:0.0915	.	951	Q96R06	SPAG5_HUMAN	P	951	ENSP00000323300:R951P	ENSP00000323300:R951P	R	-	2	0	SPAG5	23930928	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.368000	0.34216	2.817000	0.96982	0.645000	0.84053	CGA	.	.	.	none		0.502	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461		G	26906801	C	G	26906801	3	3	271	1	0	0	0	0	1	0	0	0	14994	884	31	4	761	4	SPAG5	17	26906801	Missense_Mutation	SNP	C	TCGA-V9-A7HT-01A-11D-A33Q-10	16298481	26906801	54288409	57	17149											
ZNF830	91603	hgsc.bcm.edu	37	chr17	33289174	33289175	+	Missense_Mutation	DNP	TC	TC	AT																															aggagcactcagtttcctctTcacgggaggtaacaagtagt																										TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr17:33289174_33289175TC>AT	ENST00000361952.3	+	1	626_627	c.589_590TC>AT	c.(589-591)TCa>ATa	p.S197I	CCT6B_ENST00000436961.3_5'Flank|CCT6B_ENST00000421975.3_5'Flank|CCT6B_ENST00000314144.5_5'Flank	NM_052857.3	NP_443089.3	Q96NB3	ZN830_HUMAN	zinc finger protein 830	197					blastocyst growth (GO:0001832)|mitotic nuclear division (GO:0007067)|nuclear cell cycle DNA replication (GO:0033260)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|large_intestine(1)|liver(2)|lung(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Ovarian(249;0.17)				AGTTTCCTCTTCACGGGAGGTA	0.52																																					p.S197T|p.S197L		Atlas-SNP	.											.	ZNF830	26	.	0			c.T589A|c.C590T						PASS	.																																			SO:0001583	missense	91603	exon1			TCCTCTTCACGGG|CCTCTTCACGGGA	AK055707	CCDS32618.1	17q12	2013-10-23	2008-03-25	2008-03-25	ENSG00000198783	ENSG00000198783			28291	protein-coding gene	gene with protein product	"orphan maintenance of genome 1"		"coiled-coil domain containing 16"	CCDC16		23066043	Standard	NM_052857		Approved	MGC20398, OMCG1	uc002hih.4	Q96NB3	OTTHUMG00000179771	Exception_encountered	chr17.hg19:g.33289174_33289175delinsAT	ENSP00000354518:p.Ser197Ile	65.0|66.0	0.0	.		65.0	10.0	.	NM_052857	Q96F60|Q96GZ5|Q9BU38	Missense_Mutation	SNP	ENST00000361952.3	hg19	CCDS32618.1																																																																																			.	.	.	none		0.52	ZNF830-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448018.1	NM_052857		AT	33289175	TC	AT	33289174	3	1	271	1	0	0	0	0	1	0	0	0	18196	1783	62	5	591	5	ZNF830	17	33289174	Missense_Mutation	DNP	TC	TCGA-V9-A7HT-01A-11D-A33Q-10	6382373	33289174	47906036	58	17150											
TNRC6C	57690	hgsc.bcm.edu	37	chr17	76045429	76045429	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttccaactccaatgctggcAttaatcttaaccttaatcct	11	14	3	13	0	1	0	0	0	1	0	4	0	4	0	4	1	3	2	4	1	5	4			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr17:76045429A>G	ENST00000588061.1	+	5	1013	c.286A>G	c.(286-288)Att>Gtt	p.I96V	TNRC6C_ENST00000544502.1_Missense_Mutation_p.I96V|TNRC6C_ENST00000588847.1_Missense_Mutation_p.I96V|TNRC6C_ENST00000541771.1_Missense_Mutation_p.I96V|TNRC6C_ENST00000335749.4_Missense_Mutation_p.I96V|TNRC6C_ENST00000301624.4_Missense_Mutation_p.I96V			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	96	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)			CAATGCTGGCATTAATCTTAA	0.507																																					p.I96V		Atlas-SNP	.											.	TNRC6C	173	.	0			c.A286G						PASS	.						51	55	53					17																	76045429		2032	4182	6214	SO:0001583	missense	57690	exon4			GCTGGCATTAATC	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.286A>G	chr17.hg19:g.76045429A>G	ENSP00000468647:p.Ile96Val	156.0	0.0	.		120.0	10.0	.	NM_018996	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Missense_Mutation	SNP	ENST00000588061.1	hg19	CCDS45798.1	.	.	.	.	.	.	.	.	.	.	A	4.973	0.180743	0.09443	.	.	ENSG00000078687	ENST00000455761;ENST00000395801;ENST00000335749;ENST00000301624;ENST00000541771;ENST00000544502	T;T;T;T	0.14144	2.53;2.54;2.54;2.53	5.15	5.15	0.70609	.	0.333646	0.33217	N	0.005144	T	0.13114	0.0318	L	0.42245	1.32	0.42692	D	0.993588	B;B;B	0.29988	0.225;0.264;0.144	B;B;B	0.31101	0.078;0.124;0.035	T	0.08493	-1.0719	10	0.12430	T	0.62	-4.1759	15.1447	0.72641	1.0:0.0:0.0:0.0	.	96;96;96	G3XAB8;Q9HCJ0-2;Q9HCJ0	.;.;TNR6C_HUMAN	V	96	ENSP00000336783:I96V;ENSP00000301624:I96V;ENSP00000440310:I96V;ENSP00000442421:I96V	ENSP00000301624:I96V	I	+	1	0	TNRC6C	73557024	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.359000	0.59449	2.159000	0.67721	0.533000	0.62120	ATT	.	.	.	none		0.507	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996		G	76045429	A	G	76045429	3	3	271	1	0	0	0	0	1	0	0	0	16354	217	8	3	288	3	TNRC6C	17	76045429	Missense_Mutation	SNP	A	TCGA-V9-A7HT-01A-11D-A33Q-10	42756255	76045429	5149781	59	17151											
NPC1	4864	hgsc.bcm.edu	37	chr18	21116701	21116701	+	Missense_Mutation	SNP	T	T	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	ttcggtgacattactggctaTaagtcgggctttcttcagag	8	14	11	8	2	2	2	1	1	1	1	4	2	2	2	0	3	1	2	0	3	3	6			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr18:21116701T>G	ENST00000269228.5	-	21	3735	c.3181A>C	c.(3181-3183)Ata>Cta	p.I1061L	NPC1_ENST00000540608.1_5'Flank|NPC1_ENST00000412552.2_Missense_Mutation_p.I743L	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	1061			I -> T (in NPC1; late infantile form). {ECO:0000269|PubMed:10521290, ECO:0000269|PubMed:10521297, ECO:0000269|PubMed:11182931, ECO:0000269|PubMed:11333381, ECO:0000269|PubMed:11349231, ECO:0000269|PubMed:11479732, ECO:0000269|PubMed:11754101, ECO:0000269|PubMed:12401890, ECO:0000269|PubMed:16098014, ECO:0000269|PubMed:16126423}.		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)					TTACTGGCTATAAGTCGGGCT	0.522																																					p.I1061L		Atlas-SNP	.											.	NPC1	114	.	0			c.A3181C						PASS	.						109	94	99					18																	21116701		2203	4300	6503	SO:0001583	missense	4864	exon21			TGGCTATAAGTCG	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.3181A>C	chr18.hg19:g.21116701T>G	ENSP00000269228:p.Ile1061Leu	124.0	0.0	.		80.0	17.0	.	NM_000271	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	hg19	CCDS11878.1	.	.	.	.	.	.	.	.	.	.	T	13.92	2.380899	0.42207	.	.	ENSG00000141458	ENST00000269228;ENST00000412552	D;D	0.88354	-2.37;-2.37	6.04	-6.49	0.01890	.	0.632759	0.17408	N	0.175275	T	0.78291	0.4260	L	0.31065	0.9	0.24200	N	0.995511	B;B	0.10296	0.001;0.003	B;B	0.17722	0.019;0.012	T	0.58160	-0.7685	10	0.31617	T	0.26	-6.4466	11.8648	0.52486	0.0:0.5076:0.0856:0.4068	.	1072;1061	Q59GR1;O15118	.;NPC1_HUMAN	L	1061;743	ENSP00000269228:I1061L;ENSP00000408606:I743L	ENSP00000269228:I1061L	I	-	1	0	NPC1	19370699	0.002000	0.14202	0.000000	0.03702	0.637000	0.38172	-0.050000	0.11904	-1.525000	0.01762	-0.375000	0.07067	ATA	.	.	.	none		0.522	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271		G	21116701	T	G	21116701	3	3	271	1	0	0	0	0	1	0	0	0	10577	1406	49	5	675	5	NPC1	18	21116701	Missense_Mutation	SNP	T	TCGA-V9-A7HT-01A-11D-A33Q-10		21116701	56960547	60	17152											
ATP5A1	498	hgsc.bcm.edu	37	chr18	43666115	43666115	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcaactcagttagacgcaCgccacgactcaaaagttgtt	13	8	8	12	3	2	1	2	0	0	1	2	2	2	1	1	0	2	5	1	0	4	3			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr18:43666115C>T	ENST00000398752.6	-	10	1514	c.1393G>A	c.(1393-1395)Gtg>Atg	p.V465M	ATP5A1_ENST00000590665.1_Missense_Mutation_p.V443M|ATP5A1_ENST00000593152.2_Missense_Mutation_p.V415M|ATP5A1_ENST00000282050.2_Missense_Mutation_p.V465M	NM_001001935.2|NM_004046.5	NP_001001935.1|NP_004037.1	P25705	ATPA_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle	465					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular metabolic process (GO:0044237)|embryo development (GO:0009790)|lipid metabolic process (GO:0006629)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|negative regulation of endothelial cell proliferation (GO:0001937)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting ATP synthase complex, catalytic core F(1) (GO:0045261)	ATP binding (GO:0005524)|MHC class I protein binding (GO:0042288)|poly(A) RNA binding (GO:0044822)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)			breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|skin(1)|urinary_tract(1)	22						GTTAGACGCACGCCACGACTC	0.478																																					p.V465M		Atlas-SNP	.											.	ATP5A1	52	.	0			c.G1393A						PASS	.						87	76	80					18																	43666115		2203	4300	6503	SO:0001583	missense	498	exon10			GACGCACGCCACG	D14710	CCDS11927.1, CCDS58620.1, CCDS59315.1	18q21	2012-10-12	2006-01-13		ENSG00000152234	ENSG00000152234	3.6.1.14	"Mitochondrial respiratory chain complex / Complex V", "ATPases / F-type"	823	protein-coding gene	gene with protein product		164360	"ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 2, non-cardiac muscle-like 2", "ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscle"	ATP5AL2, ATPM		1830491	Standard	NM_001257334		Approved	ATP5A, hATP1, OMR, ORM	uc002lbr.2	P25705	OTTHUMG00000132637	ENST00000398752.6:c.1393G>A	chr18.hg19:g.43666115C>T	ENSP00000381736:p.Val465Met	95.0	0.0	.		87.0	11.0	.	NM_004046	A8K092|B4DY56|K7ENP3|Q53XX6|Q8IXV2|Q96FB4|Q96HW2|Q96IR6|Q9BTV8	Missense_Mutation	SNP	ENST00000398752.6	hg19	CCDS11927.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.018806	0.75275	.	.	ENSG00000152234	ENST00000282050;ENST00000398752;ENST00000542290	T;T	0.76448	-1.02;-1.02	4.93	4.93	0.64822	ATPase, F1/V1/A1 complex, alpha/beta subunit, C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.72053	0.3413	L	0.43757	1.38	0.80722	D	1	P	0.42757	0.789	B	0.37091	0.241	T	0.77629	-0.2516	10	0.72032	D	0.01	-13.5043	18.2285	0.89926	0.0:1.0:0.0:0.0	.	465	P25705	ATPA_HUMAN	M	465;465;415	ENSP00000282050:V465M;ENSP00000381736:V465M	ENSP00000282050:V465M	V	-	1	0	ATP5A1	41920113	1.000000	0.71417	0.999000	0.59377	0.965000	0.64279	7.693000	0.84214	2.304000	0.77564	0.650000	0.86243	GTG	.	.	.	none		0.478	ATP5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255884.1	NM_004046		T	43666115	C	T	43666115	3	4	271	1	0	0	0	0	1	0	0	0	1147	536	19	1	280	1	ATP5A1	18	43666115	Missense_Mutation	SNP	C	TCGA-V9-A7HT-01A-11D-A33Q-10	22549414	43666115	34411133	61	17153											
MUC16	94025	hgsc.bcm.edu	37	chr19	9086492	9086492	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgtctgaggtcataactgTggtgacctccttggtccaaa	9	12	11	9	0	2	2	1	2	1	0	4	3	4	2	3	3	1	0	3	3	2	2			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr19:9086492T>C	ENST00000397910.4	-	1	5526	c.5323A>G	c.(5323-5325)Aca>Gca	p.T1775A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1775	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						GTCATAACTGTGGTGACCTCC	0.488																																					p.T1775A		Atlas-SNP	.											.	MUC16	4315	.	0			c.A5323G						PASS	.						124	116	119					19																	9086492		1965	4142	6107	SO:0001583	missense	94025	exon1			TAACTGTGGTGAC	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.5323A>G	chr19.hg19:g.9086492T>C	ENSP00000381008:p.Thr1775Ala	82.0	0.0	.		67.0	12.0	.	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	2.556	-0.303013	0.05495	.	.	ENSG00000181143	ENST00000397910	T	0.02301	4.35	1.32	-2.02	0.07388	.	.	.	.	.	T	0.01254	0.0041	N	0.08118	0	.	.	.	B	0.27594	0.182	B	0.23852	0.049	T	0.45041	-0.9288	8	0.87932	D	0	.	4.3299	0.11059	0.4077:0.0:0.0:0.5923	.	1775	B5ME49	.	A	1775	ENSP00000381008:T1775A	ENSP00000381008:T1775A	T	-	1	0	MUC16	8947492	0.000000	0.05858	0.000000	0.03702	0.092000	0.18411	-0.813000	0.04491	-0.764000	0.04651	0.254000	0.18369	ACA	.	.	.	none		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	9086492	T	C	9086492	3	2	271	1	0	0	0	0	1	0	0	0	9980	1696	59	3	38536	3	MUC16	19	9086492	Missense_Mutation	SNP	T	TCGA-V9-A7HT-01A-11D-A33Q-10		9086492	50042491	62	17154											
KIAA1683	80726	hgsc.bcm.edu	37	chr19	18377324	18377324	+	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	gtcacggagaccactggataTgtctggagtagagtcttggt	9	11	14	7	1	3	2	1	0	2	2	3	5	3	4	1	4	0	1	1	4	2	3			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr19:18377324T>A	ENST00000600328.3	-	3	1219	c.1026A>T	c.(1024-1026)acA>acT	p.T342T	KIAA1683_ENST00000600359.3_Silent_p.T296T|KIAA1683_ENST00000392413.4_Silent_p.T342T			Q9H0B3	K1683_HUMAN	KIAA1683	342	Thr-rich.					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						CCACTGGATATGTCTGGAGTA	0.552																																					p.T342T		Atlas-SNP	.											.	KIAA1683	190	.	0			c.A1026T						PASS	.						68	63	65					19																	18377324		2203	4300	6503	SO:0001819	synonymous_variant	80726	exon3			TGGATATGTCTGG	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.1026A>T	chr19.hg19:g.18377324T>A		50.0	0.0	.		37.0	9.0	.	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Silent	SNP	ENST00000600328.3	hg19	CCDS32958.1																																																																																			.	.	.	none		0.552	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3			A	18377324	T	A	18377324	2	1	271	1	0	0	0	0	0	0	0	1	8258	1451	51	5		5	KIAA1683	19	18377324	Silent	SNP	T	TCGA-V9-A7HT-01A-11D-A33Q-10	9290832	18377324	40751659	63	17155											
RASGRP4	115727	hgsc.bcm.edu	37	chr19	38910519	38910519	+	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	ccgtgatagcctggaaggacCggaactccaggtaggtgagg	10	6	16	9	2	0	2	0	2	0	0	1	5	1	5	4	6	2	1	4	6	4	2			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr19:38910519C>G	ENST00000587738.1	-	6	714	c.644G>C	c.(643-645)cGg>cCg	p.R215P	RASGRP4_ENST00000426920.2_Missense_Mutation_p.R215P|RASGRP4_ENST00000293062.9_Missense_Mutation_p.R215P|RASGRP4_ENST00000586305.1_Missense_Mutation_p.R201P|RASGRP4_ENST00000454404.2_Missense_Mutation_p.R215P|RASGRP4_ENST00000433821.2_Missense_Mutation_p.R215P|RASGRP4_ENST00000587753.1_Missense_Mutation_p.R215P			Q8TDF6	GRP4_HUMAN	RAS guanyl releasing protein 4	215	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				activation of phospholipase C activity (GO:0007202)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|myeloid cell differentiation (GO:0030099)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|response to extracellular stimulus (GO:0009991)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|GTP-dependent protein binding (GO:0030742)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			cervix(1)|kidney(1)|large_intestine(4)|lung(12)|pancreas(1)|prostate(3)|skin(1)	23	all_cancers(60;4.21e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			CTGGAAGGACCGGAACTCCAG	0.622																																					p.R215P		Atlas-SNP	.											.	RASGRP4	54	.	0			c.G644C						PASS	.						28	29	29					19																	38910519		1960	4144	6104	SO:0001583	missense	115727	exon6			AAGGACCGGAACT	AY048119	CCDS46068.1, CCDS54262.1, CCDS54263.1, CCDS54264.1	19q13.1	2013-01-10						"EF-hand domain containing"	18958	protein-coding gene	gene with protein product		607320				11956218	Standard	NM_170604		Approved		uc021uub.1	Q8TDF6		ENST00000587738.1:c.644G>C	chr19.hg19:g.38910519C>G	ENSP00000465772:p.Arg215Pro	117.0	0.0	.		92.0	16.0	.	NM_001146206	A6H8M4|C0LTP2|C0LTP3|C0LTP4|C0LTP5|C0LTP7|C9J416|C9JHZ1|Q8N858|Q96QN5|Q96QN6|Q96QN7	Missense_Mutation	SNP	ENST00000587738.1	hg19	CCDS46068.1	.	.	.	.	.	.	.	.	.	.	C	15.36	2.809856	0.50421	.	.	ENSG00000171777	ENST00000433821;ENST00000293062;ENST00000426920;ENST00000405332;ENST00000454404	T;T;T;T	0.30448	1.53;1.56;1.56;1.56	4.78	3.75	0.43078	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.057267	0.64402	D	0.000002	T	0.37073	0.0990	L	0.27053	0.805	0.46521	D	0.999082	D;D;D;D;D;D;D	0.89917	0.997;0.99;0.994;0.999;0.987;0.999;1.0	P;P;D;D;D;D;D	0.76575	0.805;0.512;0.988;0.914;0.988;0.971;0.977	T	0.20174	-1.0283	10	0.72032	D	0.01	-28.4274	7.0414	0.25023	0.0:0.8014:0.0:0.1986	.	215;215;215;215;215;201;215	C0LTP5;C0LTP7;C0LTP2;C0LTP4;C0LTP3;Q8TDF6-2;Q8TDF6	.;.;.;.;.;.;GRP4_HUMAN	P	215	ENSP00000411878:R215P;ENSP00000293062:R215P;ENSP00000445966:R215P;ENSP00000416463:R215P	ENSP00000293062:R215P	R	-	2	0	RASGRP4	43602359	0.997000	0.39634	0.997000	0.53966	0.984000	0.73092	2.924000	0.48876	1.242000	0.43836	0.561000	0.74099	CGG	.	.	.	none		0.622	RASGRP4-013	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460540.1	NM_170604		G	38910519	C	G	38910519	3	3	271	1	0	0	0	0	1	0	0	0	13090	652	23	4	1425	4	RASGRP4	19	38910519	Missense_Mutation	SNP	C	TCGA-V9-A7HT-01A-11D-A33Q-10	20533195	38910519	20218464	64	17156											
MEGF8	1954	hgsc.bcm.edu	37	chr19	42879872	42879872	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatccgcctgacgctggacGtgaccttcggggccgtggac	6	7	14	14	5	0	2	0	2	0	0	2	4	1	4	4	4	0	1	4	4	0	1	rs376078071		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr19:42879872G>A	ENST00000251268.6	+	42	7483	c.7483G>A	c.(7483-7485)Gtg>Atg	p.V2495M	MEGF8_ENST00000378073.4_Missense_Mutation_p.V89M|MEGF8_ENST00000334370.4_Missense_Mutation_p.V2428M	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	2495					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)				GACGCTGGACGTGACCTTCGG	0.627																																					p.V2495M		Atlas-SNP	.											.	MEGF8	358	.	0			c.G7483A						PASS	.	G	MET/VAL	0,4406		0,0,2203	51	31	37		7282	4.9	1	19		37	1,8597	1.2+/-3.3	0,1,4298	no	missense	MEGF8	NM_001410.2	21	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	2428/2779	42879872	1,13003	2203	4299	6502	SO:0001583	missense	1954	exon42			CTGGACGTGACCT	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.7483G>A	chr19.hg19:g.42879872G>A	ENSP00000251268:p.Val2495Met	145.0	0.0	.		86.0	10.0	.	NM_001271938	A8KAY0|O75097	Missense_Mutation	SNP	ENST00000251268.6	hg19		.	.	.	.	.	.	.	.	.	.	g	24.6	4.550995	0.86127	0.0	1.16E-4	ENSG00000105429	ENST00000334370;ENST00000251268;ENST00000378073	T;T	0.38240	1.15;1.15	4.92	4.92	0.64577	.	0.000000	0.64402	D	0.000005	T	0.54743	0.1877	L	0.46819	1.47	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.997;0.998	T	0.57648	-0.7775	10	0.87932	D	0	-18.7745	17.2736	0.87109	0.0:0.0:1.0:0.0	.	89;2495;2428	F5GZG7;Q7Z7M0;Q7Z7M0-2	.;MEGF8_HUMAN;.	M	2428;2495;89	ENSP00000334219:V2428M;ENSP00000251268:V2495M	ENSP00000251268:V2495M	V	+	1	0	MEGF8	47571712	1.000000	0.71417	0.997000	0.53966	0.984000	0.73092	9.181000	0.94874	2.451000	0.82905	0.651000	0.88453	GTG	.	.	.	weak		0.627	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		A	42879872	G	A	42879872	3	1	271	1	0	0	0	0	1	0	0	0	9470	1145	40	1	7444	1	MEGF8	19	42879872	Missense_Mutation	SNP	G	TCGA-V9-A7HT-01A-11D-A33Q-10	3969353	42879872	16249111	65	17157											
C20orf85	128602	hgsc.bcm.edu	37	chr20	56730567	56730567	+	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	ccccaccccaaagcccaaaaTcgagcttcctgagcgtttcc	10	7	6	18	2	0	1	0	1	0	0	3	2	2	1	7	0	3	2	7	0	3	2			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr20:56730567T>A	ENST00000371168.3	+	3	255	c.194T>A	c.(193-195)aTc>aAc	p.I65N		NM_178456.2	NP_848551.1	Q9H1P6	CT085_HUMAN	chromosome 20 open reading frame 85	65										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)			AAGCCCAAAATCGAGCTTCCT	0.453																																					p.I65N		Atlas-SNP	.											.	C20orf85	35	.	0			c.T194A						PASS	.						88	88	88					20																	56730567		2203	4300	6503	SO:0001583	missense	128602	exon3			CCAAAATCGAGCT	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.194T>A	chr20.hg19:g.56730567T>A	ENSP00000360210:p.Ile65Asn	129.0	0.0	.		96.0	9.0	.	NM_178456		Missense_Mutation	SNP	ENST00000371168.3	hg19	CCDS13465.1	.	.	.	.	.	.	.	.	.	.	T	11.94	1.788735	0.31685	.	.	ENSG00000124237	ENST00000371168	T	0.24908	1.83	4.68	2.25	0.28309	.	1.023280	0.07799	N	0.956184	T	0.31857	0.0810	M	0.65975	2.015	0.09310	N	1	P	0.47191	0.891	P	0.45138	0.471	T	0.20438	-1.0275	10	0.87932	D	0	-8.7798	6.1898	0.20518	0.0:0.086:0.1606:0.7534	.	65	Q9H1P6	CT085_HUMAN	N	65	ENSP00000360210:I65N	ENSP00000360210:I65N	I	+	2	0	C20orf85	56163973	0.028000	0.19301	0.007000	0.13788	0.333000	0.28666	2.203000	0.42752	0.140000	0.18849	0.383000	0.25322	ATC	.	.	.	none		0.453	C20orf85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079866.2	NM_178456		A	56730567	T	A	56730567	3	1	271	1	0	0	0	0	1	0	0	0	2122	1435	50	5	204	5	C20orf85	20	56730567	Missense_Mutation	SNP	T	TCGA-V9-A7HT-01A-11D-A33Q-10		56730567	6294953	66	17158											
BCR	613	hgsc.bcm.edu	37	chr22	23653908	23653908	+	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	gagaggtccaaggtgccctaCatcgtgcgccagtgcgtgga	8	7	15	11	3	0	1	0	0	0	1	2	3	1	2	3	3	4	0	3	3	2	1	rs138762891		TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chr22:23653908C>T	ENST00000305877.8	+	19	3958	c.3207C>T	c.(3205-3207)taC>taT	p.Y1069Y	BCR_ENST00000436990.2_3'UTR|BCR_ENST00000359540.3_Silent_p.Y1025Y	NM_004327.3	NP_004318.3	P11274	BCR_HUMAN	breakpoint cluster region	1069	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				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)	AGGTGCCCTACATCGTGCGCC	0.612			T	"ABL1,  FGFR1, JAK2 "	"CML, ALL, AML"								.|||	1	0.000199681	8e-04	0	5008	,	,		24815	0		0	False		,,,				2504	0				p.Y1069Y		Atlas-SNP	.		Dom	yes		22	22q11.21	613	breakpoint cluster region		L	.	BCR	74	.	0			c.C3207T						PASS	.	C	,	1,4365		0,1,2182	23	16	18		3207,3075	1.2	1	22	dbSNP_134	18	0,8514		0,0,4257	no	coding-synonymous,coding-synonymous	BCR	NM_004327.3,NM_021574.2	,	0,1,6439	TT,TC,CC		0.0,0.0229,0.0078	,	1069/1272,1025/1228	23653908	1,12879	2183	4257	6440	SO:0001819	synonymous_variant	613	exon19			GCCCTACATCGTG		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.3207C>T	chr22.hg19:g.23653908C>T		84.0	0.0	.		62.0	10.0	.	NM_004327	P78501|Q12842|Q4LE80|Q6NZI3	Silent	SNP	ENST00000305877.8	hg19	CCDS13806.1																																																																																			.	C|1.000;T|0.000	0.000	weak		0.612	BCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075819.1	NM_004327		T	23653908	C	T	23653908	2	4	271	1	0	0	0	0	0	0	0	1	1388	489	17	2		2	BCR	22	23653908	Silent	SNP	C	TCGA-V9-A7HT-01A-11D-A33Q-10		23653908	27650658	67	17159											
P2RY4	5030	hgsc.bcm.edu	37	chrX	69478929	69478931	+	In_Frame_Del	DEL	GGT	GGT	-																															gtggtgtcatggcacaggacGgtggtccctttgttgctggt																										TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	GGT	GGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chrX:69478929_69478931delGGT	ENST00000374519.2	-	1	723_725	c.544_546delACC	c.(544-546)accdel	p.T182del		NM_002565.3	NP_002556.1	P51582	P2RY4_HUMAN	pyrimidinergic receptor P2Y, G-protein coupled, 4	182					phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|transepithelial chloride transport (GO:0030321)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|uridine nucleotide receptor activity (GO:0015065)|UTP-activated nucleotide receptor activity (GO:0045030)			cervix(2)|endometrium(2)|large_intestine(8)|lung(6)	18						GGCACAGGACGGTGGTCCCTTTG	0.606																																					p.182_183del		Atlas-Indel,Pindel	.											.	P2RY4	39	.	0			c.545_547del						PASS	.																																			SO:0001651	inframe_deletion	5030	exon1			.	X91852	CCDS14398.1	Xq13	2012-08-08			ENSG00000186912	ENSG00000186912		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8542	protein-coding gene	gene with protein product		300038				8537336	Standard	NM_002565		Approved	NRU, P2Y4, UNR, P2P	uc004dxz.1	P51582	OTTHUMG00000021769	ENST00000374519.2:c.544_546delACC	chrX.hg19:g.69478932_69478934delGGT	ENSP00000363643:p.Thr182del	61.0	0.0	0		51.0	28.0	0.54902	NM_002565	Q4VBB7|Q4VBB8|Q502W2|Q5JT22	In_Frame_Del	DEL	ENST00000374519.2	hg19	CCDS14398.1																																																																																			.	.	.	none		0.606	P2RY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057058.2	NM_002565		-	69478931	GGT	-	69478929	7	5	271	1	0	1	0	1	0	0	0	0	11360	1103	39	0	555	0	P2RY4	23	69478929	In_Frame_Del	DEL	GGT	TCGA-V9-A7HT-01A-11D-A33Q-10		69478929	85791631	68	17160											
MORC4	79710	hgsc.bcm.edu	37	chrX	106236528	106236528	+	Missense_Mutation	SNP	A	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	gtaaaggtcaaacaagatttAttcttgacctcctcaacatc	14	12	5	10	0	3	2	2	1	1	1	5	2	4	2	2	1	2	1	2	1	6	5			TCGA-V9-A7HT-01A-11D-A33Q-10	TCGA-V9-A7HT-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	45bfc21a-7f33-4ce5-aad0-3daef129ceeb	452a55d9-c5f9-495b-acf0-4bf10ff5e529	g.chrX:106236528A>C	ENST00000355610.4	-	3	514	c.240T>G	c.(238-240)aaT>aaG	p.N80K	MORC4_ENST00000255495.7_Missense_Mutation_p.N80K|MORC4_ENST00000535534.1_5'UTR	NM_001085354.2|NM_024657.4	NP_001078823.1|NP_078933.3	Q8TE76	MORC4_HUMAN	MORC family CW-type zinc finger 4	80						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						AACAAGATTTATTCTTGACCT	0.398																																					p.N80K		Atlas-SNP	.											.	MORC4	155	.	0			c.T240G						PASS	.						167	151	156					X																	106236528		1899	4108	6007	SO:0001583	missense	79710	exon3			AGATTTATTCTTG	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.240T>G	chrX.hg19:g.106236528A>C	ENSP00000347821:p.Asn80Lys	192.0	0.0	.		168.0	66.0	.	NM_001085354	A1YR23|A1YR24|H7BXF1|Q5JUK7|Q96MZ2|Q9HAI7	Missense_Mutation	SNP	ENST00000355610.4	hg19	CCDS14525.2	.	.	.	.	.	.	.	.	.	.	A	10.38	1.333030	0.24167	.	.	ENSG00000133131	ENST00000355610;ENST00000255495	T;T	0.74106	-0.81;-0.81	5.44	3.01	0.34805	ATPase-like, ATP-binding domain (4);	0.479943	0.23594	N	0.046517	T	0.55016	0.1894	N	0.21324	0.655	0.80722	D	1	B;B	0.10296	0.003;0.002	B;B	0.10450	0.005;0.004	T	0.39702	-0.9601	10	0.35671	T	0.21	-0.6851	4.0793	0.09919	0.6372:0.1767:0.1861:0.0	.	80;80	A1YR23;Q8TE76	.;MORC4_HUMAN	K	80	ENSP00000347821:N80K;ENSP00000255495:N80K	ENSP00000255495:N80K	N	-	3	2	MORC4	106123184	0.016000	0.18221	0.980000	0.43619	0.985000	0.73830	0.108000	0.15396	0.287000	0.22375	0.481000	0.45027	AAT	.	.	.	none		0.398	MORC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057816.3	NM_024657		C	106236528	A	C	106236528	3	2	271	1	0	0	0	0	1	0	0	0	9711	446	16	5	2633	5	MORC4	23	106236528	Missense_Mutation	SNP	A	TCGA-V9-A7HT-01A-11D-A33Q-10	36757599	106236528	49034032	69	17161											
ERRFI1	54206	hgsc.bcm.edu	37	chr1	8073471	8073472	+	Frame_Shift_Ins	INS	-	-	A																															atggtggtcgttcaggtagtINSaggtaataatgtgttgaact																										TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr1:8073471_8073472insA	ENST00000377482.5	-	4	1410_1411	c.1187_1188insT	c.(1186-1188)ctafs	p.L396fs	ERRFI1_ENST00000474874.1_Intron	NM_018948.3	NP_061821.1	Q9UJM3	ERRFI_HUMAN	ERBB receptor feedback inhibitor 1	396					lung alveolus development (GO:0048286)|lung epithelium development (GO:0060428)|lung vasculature development (GO:0060426)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of protein autophosphorylation (GO:0031953)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of keratinocyte differentiation (GO:0045616)|response to stress (GO:0006950)|skin morphogenesis (GO:0043589)	cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|Rho GTPase activator activity (GO:0005100)			breast(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(3)|ovary(1)|prostate(1)|skin(2)	16	Ovarian(185;0.06)|all_lung(157;0.151)	all_epithelial(116;1.76e-16)|all_lung(118;3.66e-05)|Lung NSC(185;0.000163)|Renal(390;0.000469)|Colorectal(325;0.0033)|Breast(348;0.0044)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.33e-70)|GBM - Glioblastoma multiforme(8;8.05e-37)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;6.9e-06)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.000985)|READ - Rectum adenocarcinoma(331;0.0642)		GTTCAGGTAGTAGGTAATAATG	0.431																																					p.L396fs		Atlas-Indel,Pindel	.											.	ERRFI1	42	.	0			c.1188_1189insT						PASS	.																																			SO:0001589	frameshift_variant	54206	exon4			.	BC025337	CCDS94.1	1p36.23	2008-02-05			ENSG00000116285	ENSG00000116285			18185	protein-coding gene	gene with protein product		608069				10749885, 2780291, 12226756, 11003669	Standard	NM_018948		Approved	MIG-6, GENE-33, RALT	uc001aoz.3	Q9UJM3	OTTHUMG00000001221	ENST00000377482.5:c.1188dupT	chr1.hg19:g.8073472_8073472dupA	ENSP00000366702:p.Leu396fs	161.0	0.0	0		181.0	21.0	0.116022	NM_018948	B2RDX9|Q9NTG9|Q9UD05	Frame_Shift_Ins	INS	ENST00000377482.5	hg19	CCDS94.1																																																																																			.	.	.	none		0.431	ERRFI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003617.1	NM_018948		A	8073472	-	A	8073471	7	5	272	1	0	1	1	0	0	0	0	0	5246	1625	57	0	204	0	ERRFI1	1	8073471	Frame_Shift_Ins	INS	-	TCGA-WN-A9G9-01A-12D-A36X-10		8073471	241177150	1	17162											
USP24	23358	hgsc.bcm.edu	37	chr1	55603533	55603533	+	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	acaggagagcacaactgcttGgctattttccaccggacact	11	9	9	12	1	0	1	0	0	0	1	1	3	1	2	2	3	3	3	2	3	2	4			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr1:55603533G>T	ENST00000294383.6	-	27	2972	c.2973C>A	c.(2971-2973)gcC>gcA	p.A991A	USP24_ENST00000407756.1_Silent_p.A831A	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	991					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						ACAACTGCTTGGCTATTTTCC	0.313																																					p.A991A		Atlas-SNP	.											.	USP24	323	.	0			c.C2973A						PASS	.						61	53	56					1																	55603533		1812	4077	5889	SO:0001819	synonymous_variant	23358	exon27			CTGCTTGGCTATT	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.2973C>A	chr1.hg19:g.55603533G>T		172.0	0.0	.		187.0	23.0	.	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Silent	SNP	ENST00000294383.6	hg19	CCDS44154.2																																																																																			.	.	.	none		0.313	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			T	55603533	G	T	55603533	2	4	272	1	0	0	0	0	0	0	0	1	17067	1335	47	4		4	USP24	1	55603533	Silent	SNP	G	TCGA-WN-A9G9-01A-12D-A36X-10	47530062	55603533	193647088	2	17163											
SYPL2	284612	hgsc.bcm.edu	37	chr1	110009739	110009739	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggagccgctgggcttcaTcaaagttctccagtgggtga	8	9	15	9	1	3	1	2	1	1	0	4	3	3	3	2	4	1	3	2	4	1	2			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr1:110009739T>C	ENST00000369872.3	+	2	329	c.113T>C	c.(112-114)aTc>aCc	p.I38T	SYPL2_ENST00000401021.3_Missense_Mutation_p.I38T	NM_001040709.1	NP_001035799.1	Q5VXT5	SYPL2_HUMAN	synaptophysin-like 2	38	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				cellular calcium ion homeostasis (GO:0006874)|substantia nigra development (GO:0021762)	integral component of synaptic vesicle membrane (GO:0030285)	transporter activity (GO:0005215)			breast(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	16		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Colorectal(144;0.0129)|Lung(183;0.0436)|READ - Rectum adenocarcinoma(129;0.0698)|Epithelial(280;0.0808)|all cancers(265;0.0869)|LUSC - Lung squamous cell carcinoma(189;0.231)		CTGGGCTTCATCAAAGTTCTC	0.701																																					p.I38T		Atlas-SNP	.											.	SYPL2	41	.	0			c.T113C						PASS	.						3	4	4					1																	110009739		1622	3533	5155	SO:0001583	missense	284612	exon2			GCTTCATCAAAGT	AK131459	CCDS41365.1	1p13.3	2008-02-05			ENSG00000143028	ENSG00000143028			27638	protein-coding gene	gene with protein product	"mitsugumin-29"					12975309	Standard	NM_001040709		Approved	Mg29	uc001dxp.3	Q5VXT5	OTTHUMG00000010969	ENST00000369872.3:c.113T>C	chr1.hg19:g.110009739T>C	ENSP00000358888:p.Ile38Thr	85.0	0.0	.		93.0	9.0	.	NM_001040709	A8K0E8|A8KAL7|I0IT67|Q6ZMX1	Missense_Mutation	SNP	ENST00000369872.3	hg19	CCDS41365.1	.	.	.	.	.	.	.	.	.	.	t	18.47	3.630048	0.67015	.	.	ENSG00000143028	ENST00000401021;ENST00000369872	T;T	0.28895	1.59;1.59	4.95	3.81	0.43845	Marvel (1);MARVEL-like domain (1);	0.166220	0.50627	D	0.000119	T	0.23370	0.0565	M	0.70842	2.15	0.42041	D	0.991071	P;P;P	0.43826	0.818;0.503;0.557	P;B;B	0.44561	0.453;0.404;0.167	T	0.04723	-1.0931	10	0.87932	D	0	.	9.711	0.40245	0.0:0.0844:0.0:0.9156	.	38;38;38	B4DYR7;Q5VXT5;Q5VXT5-2	.;SYPL2_HUMAN;.	T	38	ENSP00000383805:I38T;ENSP00000358888:I38T	ENSP00000358888:I38T	I	+	2	0	SYPL2	109811262	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.950000	0.63603	0.732000	0.32470	0.454000	0.30748	ATC	.	.	.	none		0.701	SYPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030191.1	NM_001006603		C	110009739	T	C	110009739	3	2	272	1	0	0	0	0	1	0	0	0	15475	1435	50	3	119	3	SYPL2	1	110009739	Missense_Mutation	SNP	T	TCGA-WN-A9G9-01A-12D-A36X-10	54406206	110009739	139240882	3	17164											
SPTA1	6708	hgsc.bcm.edu	37	chr1	158615036	158615047	+	In_Frame_Del	DEL	TCATCTCTCTCT	TCATCTCTCTCT	-																															tttcccaagccttctccaaaTcatctctctctagcttgaca																										TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	TCATCTCTCTCT	TCATCTCTCTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr1:158615036_158615047delTCATCTCTCTCT	ENST00000368147.4	-	29	4305_4316	c.4125_4136delAGAGAGAGATGA	c.(4123-4137)ctagagagagatgat>ctt	p.ERDD1376del		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1376					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)					CTTCTCCAAATCATCTCTCTCTAGCTTGACAG	0.472																																					p.1376_1379del		Atlas-Indel,Pindel	.											.	SPTA1	720	.	0			c.4126_4137del						PASS	.																																			SO:0001651	inframe_deletion	6708	exon29			.	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.4125_4136delAGAGAGAGATGA	chr1.hg19:g.158615036_158615047delTCATCTCTCTCT	ENSP00000357129:p.Glu1376_Asp1379del	95.0	0.0	0		78.0	13.0	0.166667	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	In_Frame_Del	DEL	ENST00000368147.4	hg19	CCDS41423.1																																																																																			.	.	.	none		0.472	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		-	158615047	TCATCTCTCTCT	-	158615036	7	5	272	1	0	1	0	1	0	0	0	0	15128	1435	50	0	3219	0	SPTA1	1	158615036	In_Frame_Del	DEL	TCATCTCTCTCT	TCGA-WN-A9G9-01A-12D-A36X-10	48605297	158615036	90635585	4	17165											
MNDA	4332	hgsc.bcm.edu	37	chr1	158815387	158815387	+	Frame_Shift_Del	DEL	C	C	-																															cccaacacagaatcaggaaaCccaggcccaacggcaggtgg																										TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr1:158815387delC	ENST00000368141.4	+	5	842	c.581delC	c.(580-582)accfs	p.T194fs		NM_002432.1	NP_002423.1	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	194					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)					AATCAGGAAACCCAGGCCCAA	0.512																																					p.T194fs		Atlas-Indel,Pindel	.											MNDA,NS,carcinoma,0,1	MNDA	147	.	0			c.580delA						PASS	.						43	44	44					1																	158815387		2203	4300	6503	SO:0001589	frameshift_variant	4332	exon5			.	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.581delC	chr1.hg19:g.158815387delC	ENSP00000357123:p.Thr194fs	255.0	0.0	0		338.0	31.0	0.091716	NM_002432		Frame_Shift_Del	DEL	ENST00000368141.4	hg19	CCDS1177.1																																																																																			.	.	.	none		0.512	MNDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059069.1	NM_002432		-	158815387	C	-	158815387	7	5	272	1	0	1	0	1	0	0	0	0	9683	507	18	0	595	0	MNDA	1	158815387	Frame_Shift_Del	DEL	C	TCGA-WN-A9G9-01A-12D-A36X-10	200351	158815387	90435234	5	17166											
TARBP1	6894	hgsc.bcm.edu	37	chr1	234541785	234541786	+	Frame_Shift_Ins	INS	-	-	AA																															aaagcatacagtcgaacactINSaaaattgtgattgaaacacc																										TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr1:234541785_234541786insAA	ENST00000040877.1	-	24	3851_3852	c.3852_3853insTT	c.(3850-3855)tttagtfs	p.S1285fs	TARBP1_ENST00000483404.1_5'UTR	NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	1285					regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA processing (GO:0006396)	nucleus (GO:0005634)	RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(7)|large_intestine(6)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	55	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			AGTCGAACACTAAAATTGTGAT	0.381																																					p.S1285fs		Atlas-Indel,Pindel	.											.	TARBP1	111	.	0			c.3853_3854insTT						PASS	.																																			SO:0001589	frameshift_variant	6894	exon24			.		CCDS1601.1	1q42.2	2012-06-12	2007-06-26		ENSG00000059588	ENSG00000059588			11568	protein-coding gene	gene with protein product	"tRNA methyltransferase 3 homolog (S. cerevisiae)"	605052	"Tar (HIV-1) RNA binding protein 1"			1936997	Standard	NM_005646		Approved	TRP-185, TRM3	uc001hwd.3	Q13395	OTTHUMG00000037947	ENST00000040877.1:c.3851_3852dupTT	chr1.hg19:g.234541788_234541789dupAA	ENSP00000040877:p.Ser1285fs	324.0	0.0	0		383.0	46.0	0.120104	NM_005646	Q9H581	Frame_Shift_Ins	INS	ENST00000040877.1	hg19	CCDS1601.1																																																																																			.	.	.	none		0.381	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646		AA	234541786	-	AA	234541785	7	5	272	1	0	1	1	0	0	0	0	0	15567	1522	53	0	1040	0	TARBP1	1	234541785	Frame_Shift_Ins	INS	-	TCGA-WN-A9G9-01A-12D-A36X-10	75726398	234541785	14708836	6	17167											
AHCTF1	25909	hgsc.bcm.edu	37	chr1	247063492	247063492	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtggagaagtcctacttacaAcagactccaatgaccacagt	14	8	8	11	0	0	3	0	1	0	2	2	4	2	3	3	1	3	0	3	1	5	2			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr1:247063492A>G	ENST00000391829.2	-	10	1430	c.1307T>C	c.(1306-1308)gTt>gCt	p.V436A	AHCTF1_ENST00000326225.3_Missense_Mutation_p.V445A|AHCTF1_ENST00000366508.1_Missense_Mutation_p.V471A|AHCTF1_ENST00000470300.1_5'Flank			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	436	Necessary for cytoplasmic localization. {ECO:0000250}.|Seven-bladed beta propeller repeats. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			CCTACTTACAACAGACTCCAA	0.378																																					p.V445A	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.T1334C						PASS	.						72	80	77					1																	247063492		2199	4295	6494	SO:0001583	missense	25909	exon10			CTTACAACAGACT		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.1307T>C	chr1.hg19:g.247063492A>G	ENSP00000375705:p.Val436Ala	463.0	0.0	.		539.0	103.0	.	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Missense_Mutation	SNP	ENST00000391829.2	hg19		.	.	.	.	.	.	.	.	.	.	A	14.85	2.658875	0.47467	.	.	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	T;T;T	0.35789	1.29;1.29;1.3	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.47040	0.1424	L	0.34521	1.04	0.53688	D	0.999974	D;D	0.69078	0.997;0.997	D;D	0.66351	0.941;0.943	T	0.43972	-0.9358	10	0.48119	T	0.1	-17.8272	14.752	0.69533	1.0:0.0:0.0:0.0	.	471;436	Q8WYP5-2;Q8WYP5	.;ELYS_HUMAN	A	471;445;436	ENSP00000355464:V471A;ENSP00000355465:V445A;ENSP00000375705:V436A	ENSP00000355465:V445A	V	-	2	0	AHCTF1	245130115	1.000000	0.71417	1.000000	0.80357	0.052000	0.14988	8.910000	0.92685	1.936000	0.56123	0.379000	0.24179	GTT	.	.	.	none		0.378	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446		G	247063492	A	G	247063492	3	3	272	1	0	0	0	0	1	0	0	0	408	43	2	3	5601	3	AHCTF1	1	247063492	Missense_Mutation	SNP	A	TCGA-WN-A9G9-01A-12D-A36X-10	12521707	247063492	2187129	7	17168											
OR2L8	391190	hgsc.bcm.edu	37	chr1	248112664	248112664	+	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	tactccatattccttattgcCgatccagggccatcaatcat	10	13	5	13	1	2	0	2	0	0	0	5	1	5	0	5	1	2	0	5	1	4	5			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr1:248112664C>T	ENST00000357191.3	+	1	505	c.505C>T	c.(505-507)Cga>Tga	p.R169*	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	169						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)			TCCTTATTGCCGATCCAGGGC	0.478																																					p.R169X		Atlas-SNP	.											.	OR2L8	92	.	0			c.C505T						PASS	.						224	146	173					1																	248112664		2203	4300	6503	SO:0001587	stop_gained	391190	exon1			TATTGCCGATCCA	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.505C>T	chr1.hg19:g.248112664C>T	ENSP00000349719:p.Arg169*	67.0	0.0	.		85.0	6.0	.	NM_001001963	Q6IF03	Nonsense_Mutation	SNP	ENST00000357191.3	hg19	CCDS31101.1	.	.	.	.	.	.	.	.	.	.	.	14.81	2.647421	0.47258	.	.	ENSG00000196936	ENST00000357191	.	.	.	1.79	-1.05	0.10036	.	1.479880	0.05398	U	0.540099	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	.	4.4365	0.11552	0.5017:0.364:0.0:0.1343	.	.	.	.	X	169	.	ENSP00000349719:R169X	R	+	1	2	OR2L8	246179287	0.000000	0.05858	0.615000	0.29064	0.832000	0.47134	-0.640000	0.05440	0.072000	0.16694	0.479000	0.44913	CGA	.	.	.	none		0.478	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2			T	248112664	C	T	248112664	4	4	272	1	0	0	0	0	0	1	0	0	11016	644	23	1	507	1	OR2L8	1	248112664	Nonsense_Mutation	SNP	C	TCGA-WN-A9G9-01A-12D-A36X-10	1049172	248112664	1137957	8	17169											
USP34	9736	hgsc.bcm.edu	37	chr2	61483604	61483604	+	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	gtcttttatagtaacttcatCaagagattcctgtgtataaa	13	16	6	6	0	3	1	2	0	1	1	4	2	4	1	1	0	1	2	1	0	7	8			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr2:61483604C>G	ENST00000398571.2	-	48	6212	c.6136G>C	c.(6136-6138)Gat>Cat	p.D2046H		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	2046	USP.				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)			GTAACTTCATCAAGAGATTCC	0.308																																					p.D2046H		Atlas-SNP	.											.	USP34	334	.	0			c.G6136C						PASS	.						72	67	68					2																	61483604		1803	4066	5869	SO:0001583	missense	9736	exon48			CTTCATCAAGAGA	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.6136G>C	chr2.hg19:g.61483604C>G	ENSP00000381577:p.Asp2046His	411.0	0.0	.		442.0	30.0	.	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	hg19	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.233804	0.79688	.	.	ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571;ENST00000453734	T;T	0.06608	3.28;3.28	5.66	5.66	0.87406	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.32526	0.0832	M	0.89658	3.05	0.80722	D	1	D	0.61697	0.99	D	0.79108	0.992	T	0.15178	-1.0446	10	0.87932	D	0	.	16.043	0.80698	0.1347:0.8653:0.0:0.0	.	2046	Q70CQ2	UBP34_HUMAN	H	1894;1894;2046;324	ENSP00000381577:D2046H;ENSP00000410559:D324H	ENSP00000263989:D1894H	D	-	1	0	USP34	61337108	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.070000	0.71220	2.645000	0.89757	0.650000	0.86243	GAT	.	.	.	none		0.308	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			G	61483604	C	G	61483604	3	3	272	1	0	0	0	0	1	0	0	0	17077	826	29	4	4636	4	USP34	2	61483604	Missense_Mutation	SNP	C	TCGA-WN-A9G9-01A-12D-A36X-10		61483604	181715769	9	17170											
CEP68	23177	hgsc.bcm.edu	37	chr2	65299733	65299733	+	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	ctggtttcgtatctaggatcCatttctaccttggttaccct	6	17	7	11	1	2	0	0	0	2	0	4	1	3	1	3	3	2	3	3	3	4	7			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr2:65299733C>A	ENST00000377990.2	+	3	1706	c.1503C>A	c.(1501-1503)tcC>tcA	p.S501S	CEP68_ENST00000260569.4_Intron|RAB1A_ENST00000494188.1_Intron|CEP68_ENST00000537589.1_Silent_p.S113S|CEP68_ENST00000546106.1_Silent_p.S501S|CEP68_ENST00000497039.1_Intron	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	501					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						ATCTAGGATCCATTTCTACCT	0.527																																					p.S501S		Atlas-SNP	.											.	CEP68	69	.	0			c.C1503A						PASS	.						98	108	104					2																	65299733		2203	4300	6503	SO:0001819	synonymous_variant	23177	exon3			AGGATCCATTTCT	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.1503C>A	chr2.hg19:g.65299733C>A		116.0	0.0	.		93.0	9.0	.	NM_015147	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Silent	SNP	ENST00000377990.2	hg19	CCDS1880.2																																																																																			.	.	.	none		0.527	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147		A	65299733	C	A	65299733	2	1	272	1	0	0	0	0	0	0	0	1	3260	581	21	4		4	CEP68	2	65299733	Silent	SNP	C	TCGA-WN-A9G9-01A-12D-A36X-10	3816129	65299733	177899640	10	17171											
MAT2A	4144	hgsc.bcm.edu	37	chr2	85768828	85768828	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatattgctcaaggtgttcAtcttgacagaaatgaagaag	15	11	10	5	0	3	5	2	2	1	3	3	5	3	5	0	1	1	2	0	1	5	4			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr2:85768828A>G	ENST00000306434.3	+	4	488	c.365A>G	c.(364-366)cAt>cGt	p.H122R	MAT2A_ENST00000409017.1_Missense_Mutation_p.H59R|MAT2A_ENST00000490878.1_3'UTR	NM_005911.5	NP_005902.1	P31153	METK2_HUMAN	methionine adenosyltransferase II, alpha	122					cellular nitrogen compound metabolic process (GO:0034641)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|methionine adenosyltransferase complex (GO:0048269)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methionine adenosyltransferase activity (GO:0004478)			breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	9					L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	CAAGGTGTTCATCTTGACAGA	0.403																																					p.H122R		Atlas-SNP	.											.	MAT2A	23	.	0			c.A365G						PASS	.						99	94	95					2																	85768828		2203	4300	6503	SO:0001583	missense	4144	exon4			GTGTTCATCTTGA		CCDS1977.1	2p11.2	2008-06-03			ENSG00000168906	ENSG00000168906			6904	protein-coding gene	gene with protein product		601468				1426236, 9703951	Standard	NM_005911		Approved	SAMS2, MATA2, MATII	uc002spr.3	P31153	OTTHUMG00000130174	ENST00000306434.3:c.365A>G	chr2.hg19:g.85768828A>G	ENSP00000303147:p.His122Arg	116.0	0.0	.		133.0	22.0	.	NM_005911	A8K511|B4DN45|D6W5L1|Q53SP5	Missense_Mutation	SNP	ENST00000306434.3	hg19	CCDS1977.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.326536	0.81690	.	.	ENSG00000168906	ENST00000306434;ENST00000409017	D;D	0.82433	-1.61;-1.61	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	D	0.90456	0.7011	M	0.86178	2.8	0.80722	D	1	D;D;D	0.62365	0.983;0.983;0.991	P;P;P	0.61397	0.598;0.809;0.888	D	0.91853	0.5493	10	0.72032	D	0.01	-20.5989	13.4153	0.60966	1.0:0.0:0.0:0.0	.	59;122;122	B4DN45;B4DEX8;P31153	.;.;METK2_HUMAN	R	122;59	ENSP00000303147:H122R;ENSP00000386353:H59R	ENSP00000303147:H122R	H	+	2	0	MAT2A	85622339	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.936000	0.92931	2.053000	0.61076	0.460000	0.39030	CAT	.	.	.	none		0.403	MAT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252491.2	NM_005911		G	85768828	A	G	85768828	3	3	272	1	0	0	0	0	1	0	0	0	9337	217	8	3	379	3	MAT2A	2	85768828	Missense_Mutation	SNP	A	TCGA-WN-A9G9-01A-12D-A36X-10	20469095	85768828	157430545	11	17172											
IMMT	10989	hgsc.bcm.edu	37	chr2	86385801	86385801	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcttggaccaccagctcaTgatactgagatacaacctta	13	9	8	11	0	1	2	1	2	0	1	1	5	1	3	3	1	5	2	3	1	4	4			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr2:86385801T>C	ENST00000410111.3	-	10	1463	c.1076A>G	c.(1075-1077)cAt>cGt	p.H359R	IMMT_ENST00000490238.1_5'UTR|IMMT_ENST00000442664.2_Missense_Mutation_p.H358R|IMMT_ENST00000409051.2_Missense_Mutation_p.H312R|IMMT_ENST00000449247.2_Missense_Mutation_p.H348R|IMMT_ENST00000254636.5_Missense_Mutation_p.H260R|Y_RNA_ENST00000363371.1_RNA	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	359					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						CACCAGCTCATGATACTGAGA	0.438																																					p.H359R		Atlas-SNP	.											.	IMMT	65	.	0			c.A1076G						PASS	.						62	56	58					2																	86385801		1878	4125	6003	SO:0001583	missense	10989	exon10			AGCTCATGATACT	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.1076A>G	chr2.hg19:g.86385801T>C	ENSP00000387262:p.His359Arg	120.0	0.0	.		107.0	15.0	.	NM_006839	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Missense_Mutation	SNP	ENST00000410111.3	hg19	CCDS46355.1	.	.	.	.	.	.	.	.	.	.	T	13.30	2.195826	0.38806	.	.	ENSG00000132305	ENST00000254636;ENST00000449247;ENST00000410111;ENST00000442664;ENST00000409051;ENST00000545283;ENST00000377310	T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59	5.76	5.76	0.90799	.	0.088283	0.85682	D	0.000000	T	0.32526	0.0832	L	0.39633	1.23	0.48830	D	0.999711	B;B;B;B;B;B;B	0.25486	0.127;0.118;0.034;0.043;0.097;0.097;0.043	B;B;B;B;B;B;B	0.41174	0.349;0.078;0.03;0.05;0.047;0.047;0.05	T	0.06373	-1.0830	10	0.02654	T	1	-17.6143	16.0709	0.80928	0.0:0.0:0.0:1.0	.	312;347;327;261;348;327;359	B9A067;B4DKR1;F8W9I1;B4DS66;Q16891-2;Q16891-3;Q16891	.;.;.;.;.;.;IMMT_HUMAN	R	260;348;359;358;312;348;327	ENSP00000254636:H260R;ENSP00000396899:H348R;ENSP00000387262:H359R;ENSP00000407788:H358R;ENSP00000387227:H312R	ENSP00000254636:H260R	H	-	2	0	IMMT	86239312	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	4.525000	0.60559	2.198000	0.70561	0.528000	0.53228	CAT	.	.	.	none		0.438	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839		C	86385801	T	C	86385801	3	2	272	1	0	0	0	0	1	0	0	0	7725	1464	51	3	1224	3	IMMT	2	86385801	Missense_Mutation	SNP	T	TCGA-WN-A9G9-01A-12D-A36X-10	616973	86385801	156813572	12	17173											
INPP4A	3631	hgsc.bcm.edu	37	chr2	99156012	99156012	+	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	gttcggtggtgccatctgccGcatgtaccggtttccaacca	6	11	11	13	3	1	0	0	0	1	0	3	0	2	0	5	3	4	4	5	3	2	3			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr2:99156012G>T	ENST00000523221.1	+	8	692	c.692G>T	c.(691-693)cGc>cTc	p.R231L	INPP4A_ENST00000409540.3_Missense_Mutation_p.R231L|INPP4A_ENST00000074304.5_Missense_Mutation_p.R231L|INPP4A_ENST00000409851.3_Missense_Mutation_p.R231L|INPP4A_ENST00000409463.1_Intron|INPP4A_ENST00000409016.4_Missense_Mutation_p.R231L|INPP4A_ENST00000545415.1_Missense_Mutation_p.R231L			Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type I, 107kDa	231					inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(1)|endometrium(9)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(4)|upper_aerodigestive_tract(4)	43						GCCATCTGCCGCATGTACCGG	0.602																																					p.R231L		Atlas-SNP	.											INPP4A_ENST00000409540,caecum,carcinoma,0,3	INPP4A	205	.	0			c.G692T						PASS	.						130	125	126					2																	99156012		2074	4209	6283	SO:0001583	missense	3631	exon10			TCTGCCGCATGTA	U26398	CCDS46369.1, CCDS46370.1, CCDS46371.1, CCDS46372.1	2q11.2	2008-05-27	2002-08-29		ENSG00000040933	ENSG00000040933			6074	protein-coding gene	gene with protein product		600916	"inositol polyphosphate-4-phosphatase, type I, 107kD"	INPP4		7608176, 9295334	Standard	NM_004027		Approved		uc002syy.3	Q96PE3	OTTHUMG00000153106	ENST00000523221.1:c.692G>T	chr2.hg19:g.99156012G>T	ENSP00000427722:p.Arg231Leu	60.0	0.0	.		59.0	7.0	.	NM_004027	O15326|Q13187|Q53TD8|Q8TC02	Missense_Mutation	SNP	ENST00000523221.1	hg19	CCDS46369.1	.	.	.	.	.	.	.	.	.	.	G	33	5.275491	0.95459	.	.	ENSG00000040933	ENST00000409016;ENST00000409851;ENST00000074304;ENST00000545415;ENST00000409540;ENST00000523221	T;T;T;T;T;T	0.34859	1.34;1.34;1.34;1.34;1.34;1.34	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.59004	0.2162	M	0.63843	1.955	0.80722	D	1	D;D;D;D	0.89917	0.998;0.999;1.0;1.0	D;D;D;D	0.91635	0.94;0.956;0.999;0.999	T	0.59553	-0.7433	10	0.59425	D	0.04	-22.292	17.811	0.88616	0.0:0.0:1.0:0.0	.	231;231;231;231	Q96PE3-2;Q96PE3-4;Q96PE3;Q96PE3-3	.;.;INP4A_HUMAN;.	L	231	ENSP00000386704:R231L;ENSP00000386777:R231L;ENSP00000074304:R231L;ENSP00000442149:R231L;ENSP00000387294:R231L;ENSP00000427722:R231L	ENSP00000074304:R231L	R	+	2	0	INPP4A	98522444	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.657000	0.98554	2.684000	0.91462	0.585000	0.79938	CGC	.	.	.	none		0.602	INPP4A-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376095.1	NM_001566		T	99156012	G	T	99156012	3	4	272	1	0	0	0	0	1	0	0	0	7759	1087	38	4	722	4	INPP4A	2	99156012	Missense_Mutation	SNP	G	TCGA-WN-A9G9-01A-12D-A36X-10	12770211	99156012	144043361	13	17174											
CFLAR	8837	hgsc.bcm.edu	37	chr2	202005084	202005084	+	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	ccttctgcttttatagttcaAggagcagggacaagttacag	11	12	10	8	0	2	0	1	0	1	0	2	2	2	2	1	2	3	4	1	2	5	6			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr2:202005084A>T	ENST00000309955.3	+	5	1043	c.528A>T	c.(526-528)caA>caT	p.Q176H	CFLAR_ENST00000423241.2_Missense_Mutation_p.Q176H|CFLAR-AS1_ENST00000474886.2_RNA|CFLAR-AS1_ENST00000415011.2_RNA|CFLAR_ENST00000340870.5_Missense_Mutation_p.Q176H|CFLAR_ENST00000341222.6_Missense_Mutation_p.Q176H|CFLAR_ENST00000443227.1_Missense_Mutation_p.Q80H|CFLAR_ENST00000342795.5_Missense_Mutation_p.Q176H|CFLAR_ENST00000355558.4_Missense_Mutation_p.Q176H|RNU7-45P_ENST00000459460.1_RNA|CFLAR_ENST00000494258.1_Missense_Mutation_p.Q80H|CFLAR_ENST00000341582.6_Missense_Mutation_p.Q176H|CFLAR_ENST00000457277.1_Missense_Mutation_p.Q176H|CFLAR_ENST00000479953.2_Missense_Mutation_p.Q80H|CFLAR_ENST00000440180.1_Missense_Mutation_p.Q176H	NM_001202515.1|NM_003879.5	NP_001189444.1|NP_003870.4	O15519	CFLAR_HUMAN	CASP8 and FADD-like apoptosis regulator	176	Interaction with FADD.|Interaction with caspase-8 propeptide.|Interaction with caspase-8.|Not proteolytically processed and involved in apoptosis inhibition.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of myoblast fusion (GO:1901740)|positive regulation of catalytic activity (GO:0043085)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of necroptotic process (GO:0060544)|regulation of satellite cell proliferation (GO:0014842)|skeletal muscle atrophy (GO:0014732)|skeletal muscle tissue development (GO:0007519)|skeletal muscle tissue regeneration (GO:0043403)|skeletal myofibril assembly (GO:0014866)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|ripoptosome (GO:0097342)	cysteine-type peptidase activity (GO:0008234)|death effector domain binding (GO:0035877)|enzyme activator activity (GO:0008047)|protease binding (GO:0002020)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|stomach(1)	13						TTATAGTTCAAGGAGCAGGGA	0.378																																					p.Q176H	Pancreas(16;548 657 22190 32864 42338)	Atlas-SNP	.											.	CFLAR	37	.	0			c.A528T						PASS	.						120	121	121					2																	202005084		2203	4300	6503	SO:0001583	missense	8837	exon5			AGTTCAAGGAGCA	AF005774	CCDS2337.1, CCDS46487.1, CCDS56157.1, CCDS56158.1, CCDS59436.1	2q33-q34	2014-01-30			ENSG00000003402	ENSG00000003402		"Endogenous ligands"	1876	protein-coding gene	gene with protein product		603599		CASP8AP1		9208847, 9217161	Standard	NM_003879		Approved	CASH, Casper, CLARP, FLAME, FLIP, I-FLICE, MRIT, c-FLIP	uc002uxb.4	O15519	OTTHUMG00000132819	ENST00000309955.3:c.528A>T	chr2.hg19:g.202005084A>T	ENSP00000312455:p.Gln176His	283.0	0.0	.		371.0	36.0	.	NM_001202516	B4DJE0|B7Z9F9|O14673|O14674|O14675|O15137|O15138|O15356|O15510|O43618|O43619|O43620|O60458|O60459|Q53TS6|Q54AF1|Q96TE4|Q9UEW1	Missense_Mutation	SNP	ENST00000309955.3	hg19	CCDS2337.1	.	.	.	.	.	.	.	.	.	.	A	12.71	2.020924	0.35606	.	.	ENSG00000003402	ENST00000309955;ENST00000443227;ENST00000341222;ENST00000355558;ENST00000340870;ENST00000343375;ENST00000341582;ENST00000342795;ENST00000423241;ENST00000440180;ENST00000457277	D;D;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;-1.7;-1.7	4.69	2.29	0.28610	DEATH-like (1);	0.935073	0.09112	N	0.846973	D	0.86234	0.5884	L	0.56769	1.78	0.80722	D	1	D;B;D;D;D;B;D	0.62365	0.964;0.253;0.989;0.989;0.991;0.202;0.966	P;B;P;P;P;B;P	0.60541	0.846;0.173;0.717;0.717;0.876;0.138;0.717	T	0.79918	-0.1600	10	0.56958	D	0.05	-9.6859	5.9993	0.19511	0.784:0.0:0.216:0.0	.	80;176;176;176;176;176;176	O15519-3;C9JK38;O15519-11;O15519-8;O15519;O15519-12;O15519-2	.;.;.;.;CFLAR_HUMAN;.;.	H	176;80;176;176;176;80;176;176;176;176;176	ENSP00000312455:Q176H;ENSP00000413270:Q80H;ENSP00000339335:Q176H;ENSP00000347757:Q176H;ENSP00000339326:Q176H;ENSP00000345807:Q176H;ENSP00000342809:Q176H;ENSP00000399420:Q176H;ENSP00000406775:Q176H;ENSP00000411535:Q176H	ENSP00000312455:Q176H	Q	+	3	2	CFLAR	201713329	0.463000	0.25799	0.485000	0.27403	0.215000	0.24574	0.514000	0.22786	0.521000	0.28445	0.528000	0.53228	CAA	.	.	.	none		0.378	CFLAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256276.3	NM_003879		T	202005084	A	T	202005084	3	4	272	1	0	0	0	0	1	0	0	0	3294	69	3	5	542	5	CFLAR	2	202005084	Missense_Mutation	SNP	A	TCGA-WN-A9G9-01A-12D-A36X-10	102849072	202005084	41194289	14	17175											
C2orf67	151050	hgsc.bcm.edu	37	chr2	210894559	210894559	+	Missense_Mutation	SNP	T	T	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	ctggattcttgataaaacgtTgacattggaaacagcagtaa	15	11	9	6	1	1	2	0	2	1	0	1	4	1	4	0	2	3	3	0	2	4	6			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr2:210894559T>G	ENST00000281772.9	-	10	2502	c.2239A>C	c.(2239-2241)Aac>Cac	p.N747H	KANSL1L_ENST00000418791.1_Missense_Mutation_p.N705H|AC007038.7_ENST00000452057.1_RNA|RP11-260M2.1_ENST00000608095.1_RNA	NM_152519.2	NP_689732.2	A0AUZ9	KAL1L_HUMAN	KAT8 regulatory NSL complex subunit 1-like	747						histone acetyltransferase complex (GO:0000123)											GATAAAACGTTGACATTGGAA	0.328																																					p.N747H		Atlas-SNP	.											.	.	.	.	0			c.A2239C						PASS	.						146	145	146					2																	210894559		2203	4300	6503	SO:0001583	missense	151050	exon10			AAACGTTGACATT	AK074441	CCDS33370.1	2q34	2012-02-20	2012-02-20	2012-02-20	ENSG00000144445	ENSG00000144445			26310	protein-coding gene	gene with protein product	"KIAA1267-like"	613833	"chromosome 2 open reading frame 67"	C2orf67		12477932	Standard	NM_152519		Approved	FLJ23861, FLJ32349, MSL1v2, KIAA1267L	uc002vds.3	A0AUZ9	OTTHUMG00000154697	ENST00000281772.9:c.2239A>C	chr2.hg19:g.210894559T>G	ENSP00000281772:p.Asn747His	115.0	0.0	.		91.0	13.0	.	NM_152519	B7ZLN1|I6L9A8|Q53TV8|Q53TW3|Q6IS05|Q8TCI1|Q96MI0|Q9UFC3	Missense_Mutation	SNP	ENST00000281772.9	hg19	CCDS33370.1	.	.	.	.	.	.	.	.	.	.	T	11.47	1.649295	0.29336	.	.	ENSG00000144445	ENST00000281772;ENST00000418791	.	.	.	5.5	2.91	0.33838	.	0.298177	0.30930	N	0.008587	T	0.39682	0.1087	L	0.56769	1.78	0.22280	N	0.999231	B;B	0.15930	0.015;0.015	B;B	0.13407	0.009;0.009	T	0.34601	-0.9822	9	0.49607	T	0.09	.	6.1909	0.20524	0.0:0.0811:0.313:0.6059	.	705;747	A0AUZ9-2;A0AUZ9	.;CB067_HUMAN	H	747;705	.	ENSP00000281772:N747H	N	-	1	0	C2orf67	210602804	0.988000	0.35896	0.660000	0.29694	0.791000	0.44710	1.629000	0.37071	0.890000	0.36211	0.533000	0.62120	AAC	.	.	.	none		0.328	KANSL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336633.3	NM_152519		G	210894559	T	G	210894559	3	3	272	1	0	0	0	0	1	0	0	0	2188	1812	63	5	748	5	C2orf67	2	210894559	Missense_Mutation	SNP	T	TCGA-WN-A9G9-01A-12D-A36X-10	8889475	210894559	32304814	15	17176											
VHL	7428	hgsc.bcm.edu	37	chr3	10183797	10183797	+	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	cgtcgtgctgcccgtatggcTcaacttcgacggcgagccgc	5	8	13	15	7	1	0	1	0	0	0	3	2	1	0	2	2	4	3	2	2	2	2	rs5030807		TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr3:10183797T>A	ENST00000256474.2	+	1	1106	c.266T>A	c.(265-267)cTc>cAc	p.L89H	VHL_ENST00000345392.2_Missense_Mutation_p.L89H|snoU13_ENST00000458986.1_RNA	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	89			L -> H (in lung cancer).|L -> P (in VHLD; type I; dbSNP:rs5030807). {ECO:0000269|PubMed:8956040}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|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)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.L89H(11)|p.L89P(6)|p.L89R(3)|p.R60fs*35(1)|p.V84_E94>E(1)|p.V84fs*69(1)|p.L89fs*67(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CCCGTATGGCTCAACTTCGAC	0.726	L89H(NCIH28_PLEURA)	1	"D, Mis, N, F, S"		"renal, hemangioma, pheochromocytoma"	"renal, hemangioma, pheochromocytoma"			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																												p.L89H		Atlas-SNP	.	yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"E, M, O"	VHL,NS,carcinoma,0,23	VHL	2192	.	24	Substitution - Missense(20)|Deletion - Frameshift(3)|Complex - deletion inframe(1)	kidney(22)|pancreas(1)|pleura(1)	c.T266A	GRCh37	CM941368	VHL	M	rs5030807	PASS	.						13	16	15					3																	10183797		2106	4156	6262	SO:0001583	missense	7428	exon1	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	TATGGCTCAACTT	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"von Hippel-Lindau syndrome", "von Hippel-Lindau tumor suppressor"			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.266T>A	chr3.hg19:g.10183797T>A	ENSP00000256474:p.Leu89His	87.0	1.0	.		46.0	7.0	.	NM_198156	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	hg19	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	T	29.2	4.986585	0.93106	.	.	ENSG00000134086	ENST00000256474;ENST00000345392	D;D	0.99815	-6.9;-6.9	5.06	5.06	0.68205	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.185584	0.46442	D	0.000292	D	0.99576	0.9847	L	0.41492	1.28	0.33129	D	0.542832	D;D	0.89917	1.0;1.0	D;D	0.76071	0.987;0.957	D	0.97755	1.0217	10	0.87932	D	0	-8.4916	12.8448	0.57823	0.0:0.0:0.0:1.0	.	89;89	P40337-2;P40337	.;VHL_HUMAN	H	89	ENSP00000256474:L89H;ENSP00000344757:L89H	ENSP00000256474:L89H	L	+	2	0	VHL	10158797	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	4.914000	0.63348	1.920000	0.55613	0.450000	0.29827	CTC	.	T|1.000	.	weak		0.726	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		A	10183797	T	A	10183797	3	1	272	1	0	0	0	0	1	0	0	0	17174	1551	54	5	268	5	VHL	3	10183797	Missense_Mutation	SNP	T	TCGA-WN-A9G9-01A-12D-A36X-10		10183797	187838633	16	17177											
TRIM71	131405	hgsc.bcm.edu	37	chr3	32859580	32859581	+	Missense_Mutation	DNP	CG	CG	TT																															ggctgggttgcaaatggcttCgttccccgagaccgatttcc																										TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	C|G	C|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr3:32859580_32859581CG>TT	ENST00000383763.5	+	1	71_72	c.8_9CG>TT	c.(7-9)tCG>tTT	p.S3F		NM_001039111.1	NP_001034200.1	Q2Q1W2	LIN41_HUMAN	tripartite motif containing 71, E3 ubiquitin protein ligase	3					fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|miRNA metabolic process (GO:0010586)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|positive regulation of gene silencing by miRNA (GO:2000637)|protein autoubiquitination (GO:0051865)|regulation of gene silencing by miRNA (GO:0060964)|regulation of neural precursor cell proliferation (GO:2000177)|stem cell proliferation (GO:0072089)	cytoplasmic mRNA processing body (GO:0000932)	ligase activity (GO:0016874)|miRNA binding (GO:0035198)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CAAATGGCTTCGTTCCCCGAGA	0.649																																					p.S3L|p.S3S		Atlas-SNP	.											.	TRIM71	73	.	0			c.C8T|c.G9T						PASS	.																																			SO:0001583	missense	131405	exon1			TGGCTTCGTTCCC|GGCTTCGTTCCCC		CCDS43060.1	3p22.3	2014-02-17	2012-02-29		ENSG00000206557	ENSG00000206557		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	32669	protein-coding gene	gene with protein product			"tripartite motif-containing 71", "tripartite motif containing 71"				Standard	NM_001039111		Approved	LIN41, LIN-41	uc003cff.3	Q2Q1W2	OTTHUMG00000155778	Exception_encountered	chr3.hg19:g.32859580_32859581delinsTT	ENSP00000373272:p.Ser3Phe	65.0|64.0	0.0	.		59.0|56.0	12.0|13.0	.	NM_001039111		Missense_Mutation|Silent	SNP	ENST00000383763.5	hg19	CCDS43060.1																																																																																			.	.	.	none		0.649	TRIM71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341565.3	NM_001039111		TT	32859581	CG	TT	32859580	3	4	272	1	0	0	0	0	1	0	0	0	16556	893	31	1	10	1	TRIM71	3	32859580	Missense_Mutation	DNP	CG	TCGA-WN-A9G9-01A-12D-A36X-10	22675783	32859580	165162850	17	17178											
OSBPL11	114885	hgsc.bcm.edu	37	chr3	125282684	125282684	+	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	gttctaaccactcgattgtcGttcctgatggagtaagagaa	11	12	10	8	2	1	2	0	1	1	1	4	5	2	3	2	1	1	3	2	1	3	5			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr3:125282684G>C	ENST00000296220.5	-	7	1161	c.872C>G	c.(871-873)aCg>aGg	p.T291R		NM_022776.4	NP_073613.2	Q9BXB4	OSB11_HUMAN	oxysterol binding protein-like 11	291					fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|positive regulation of sequestering of triglyceride (GO:0010890)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)			NS(1)|breast(1)|cervix(1)|kidney(2)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	27						CTCGATTGTCGTTCCTGATGG	0.413																																					p.T291R		Atlas-SNP	.											.	OSBPL11	64	.	0			c.C872G						PASS	.						69	70	70					3																	125282684		2203	4300	6503	SO:0001583	missense	114885	exon7			ATTGTCGTTCCTG	AF392454	CCDS3033.1	3q21	2013-01-10			ENSG00000144909	ENSG00000144909		"Oxysterol binding proteins", "Pleckstrin homology (PH) domain containing"	16397	protein-coding gene	gene with protein product		606739					Standard	NM_022776		Approved	ORP-11, ORP11, FLJ13012, FLJ13164	uc003eic.3	Q9BXB4	OTTHUMG00000159571	ENST00000296220.5:c.872C>G	chr3.hg19:g.125282684G>C	ENSP00000296220:p.Thr291Arg	46.0	0.0	.		53.0	9.0	.	NM_022776	A8K9I7	Missense_Mutation	SNP	ENST00000296220.5	hg19	CCDS3033.1	.	.	.	.	.	.	.	.	.	.	G	11.15	1.554856	0.27739	.	.	ENSG00000144909	ENST00000296220	T	0.17854	2.25	5.09	4.21	0.49690	.	0.231057	0.44483	D	0.000442	T	0.14960	0.0361	L	0.40543	1.245	0.44012	D	0.996725	B	0.17852	0.024	B	0.14578	0.011	T	0.04579	-1.0941	10	0.25751	T	0.34	-3.2492	13.4431	0.61125	0.0:0.0:0.8432:0.1568	.	291	Q9BXB4	OSB11_HUMAN	R	291	ENSP00000296220:T291R	ENSP00000296220:T291R	T	-	2	0	OSBPL11	126765374	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	6.916000	0.75776	1.349000	0.45751	0.467000	0.42956	ACG	.	.	.	none		0.413	OSBPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356295.1	NM_022776		C	125282684	G	C	125282684	3	2	272	1	0	0	0	0	1	0	0	0	11283	1145	40	4	1399	4	OSBPL11	3	125282684	Missense_Mutation	SNP	G	TCGA-WN-A9G9-01A-12D-A36X-10	92423104	125282684	72739746	18	17179											
CAMK2D	817	hgsc.bcm.edu	37	chr4	114378666	114378666	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcatcatcccctaccagatGtacatgagggtttagaataa	13	10	9	9	0	1	3	1	1	0	2	2	3	2	3	3	2	2	3	3	2	5	5			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr4:114378666G>A	ENST00000342666.5	-	17	1257	c.1258C>T	c.(1258-1260)Cat>Tat	p.H420Y	CAMK2D_ENST00000394524.3_Missense_Mutation_p.H420Y|CAMK2D_ENST00000296402.5_Missense_Mutation_p.H420Y|CAMK2D_ENST00000394526.2_Missense_Mutation_p.H431Y|CAMK2D_ENST00000394522.3_Missense_Mutation_p.H434Y|CAMK2D_ENST00000418639.2_Missense_Mutation_p.H434Y|CAMK2D_ENST00000379773.2_Missense_Mutation_p.H420Y|CAMK2D_ENST00000429180.1_Missense_Mutation_p.H440Y|CAMK2D_ENST00000511664.1_Missense_Mutation_p.H454Y|CAMK2D_ENST00000508738.1_Missense_Mutation_p.H431Y|CAMK2D_ENST00000505990.1_Missense_Mutation_p.H454Y|CAMK2D_ENST00000454265.2_Missense_Mutation_p.H445Y|CAMK2D_ENST00000515496.1_Missense_Mutation_p.H431Y|CAMK2D_ENST00000514328.1_Missense_Mutation_p.H419Y			Q13557	KCC2D_HUMAN	calcium/calmodulin-dependent protein kinase II delta	420					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)		CCTACCAGATGTACATGAGGG	0.403																																					p.H434Y		Atlas-SNP	.											.	CAMK2D	55	.	0			c.C1300T						PASS	.						187	185	186					4																	114378666		2203	4300	6503	SO:0001583	missense	817	exon18			CCAGATGTACATG	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.1258C>T	chr4.hg19:g.114378666G>A	ENSP00000339740:p.His420Tyr	114.0	0.0	.		164.0	15.0	.	NM_172114	A8MVS8|Q52PK4|Q59G21|Q8N553|Q9UGH6|Q9UQE9	Missense_Mutation	SNP	ENST00000342666.5	hg19	CCDS3703.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.2|25.2	4.618401|4.618401	0.87359|0.87359	.|.	.|.	ENSG00000145349|ENSG00000145349	ENST00000394524;ENST00000454265;ENST00000429180;ENST00000418639;ENST00000394526;ENST00000296402;ENST00000511664;ENST00000342666;ENST00000515496;ENST00000514328;ENST00000394522;ENST00000505990;ENST00000379773;ENST00000508738|ENST00000513132	T;T;T;T;T;T;T;T;T;T;T;T;T;T|.	0.48201|.	0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82|.	5.93|5.93	5.93|5.93	0.95920|0.95920	Protein kinase-like domain (1);Calcium/calmodulin-dependent protein kinase II, association-domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.85318|0.85318	0.5669|0.5669	M|M	0.88704|0.88704	2.975|2.975	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.76494|.	0.996;0.997;0.999;0.97;0.998|.	D;D;D;P;D|.	0.87578|.	0.963;0.995;0.998;0.782;0.997|.	D|D	0.86142|0.86142	0.1582|0.1582	10|5	0.32370|.	T|.	0.25|.	.|.	20.3396|20.3396	0.98756|0.98756	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	454;431;434;420;420|.	E9PF82;Q13557-3;Q13557-6;Q13557-12;Q13557|.	.;.;.;.;KCC2D_HUMAN|.	Y|I	420;445;440;434;431;420;454;420;431;419;434;454;420;431|123	ENSP00000378032:H420Y;ENSP00000415248:H445Y;ENSP00000415707:H440Y;ENSP00000406131:H434Y;ENSP00000378034:H431Y;ENSP00000296402:H420Y;ENSP00000425824:H454Y;ENSP00000339740:H420Y;ENSP00000423482:H431Y;ENSP00000423677:H419Y;ENSP00000378030:H434Y;ENSP00000424245:H454Y;ENSP00000369098:H420Y;ENSP00000422566:H431Y|.	ENSP00000296402:H420Y|.	H|T	-|-	1|2	0|0	CAMK2D|CAMK2D	114598115|114598115	1.000000|1.000000	0.71417|0.71417	0.243000|0.243000	0.24186|0.24186	0.679000|0.679000	0.39708|0.39708	9.409000|9.409000	0.97331|0.97331	2.812000|2.812000	0.96745|0.96745	0.555000|0.555000	0.69702|0.69702	CAT|ACA	.	.	.	none		0.403	CAMK2D-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256420.2			A	114378666	G	A	114378666	3	1	272	1	0	0	0	0	1	0	0	0	2603	1377	48	2	261	2	CAMK2D	4	114378666	Missense_Mutation	SNP	G	TCGA-WN-A9G9-01A-12D-A36X-10		114378666	76775610	19	17180											
SPOCK3	50859	hgsc.bcm.edu	37	chr4	167810344	167810344	+	Frame_Shift_Del	DEL	A	A	-																															acatgggcaatgtccttcacAtttgactgagatctgttttc																										TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr4:167810344delA	ENST00000357154.3	-	7	672	c.535delT	c.(535-537)tgtfs	p.C179fs	SPOCK3_ENST00000511531.1_Frame_Shift_Del_p.C179fs|SPOCK3_ENST00000541354.1_Frame_Shift_Del_p.C59fs|SPOCK3_ENST00000504953.1_Frame_Shift_Del_p.C176fs|SPOCK3_ENST00000421836.2_Frame_Shift_Del_p.C128fs|SPOCK3_ENST00000502330.1_Frame_Shift_Del_p.C179fs|SPOCK3_ENST00000507137.1_5'UTR|SPOCK3_ENST00000357545.4_Frame_Shift_Del_p.C176fs|SPOCK3_ENST00000511269.1_Frame_Shift_Del_p.C176fs|SPOCK3_ENST00000512681.1_Frame_Shift_Del_p.C81fs|SPOCK3_ENST00000534949.1_Frame_Shift_Del_p.C83fs|SPOCK3_ENST00000506886.1_Frame_Shift_Del_p.C179fs|SPOCK3_ENST00000541637.1_Frame_Shift_Del_p.C81fs|SPOCK3_ENST00000510741.1_Frame_Shift_Del_p.C176fs|SPOCK3_ENST00000512648.1_Frame_Shift_Del_p.C176fs|SPOCK3_ENST00000535728.1_Frame_Shift_Del_p.C87fs	NM_016950.2	NP_058646.2	Q9BQ16	TICN3_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3	179	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				negative regulation of endopeptidase activity (GO:0010951)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|metalloendopeptidase inhibitor activity (GO:0008191)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	38	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		TGTCCTTCACATTTGACTGAG	0.318																																					p.C179fs		Atlas-Indel,Pindel	.											.	SPOCK3	90	.	0			c.536delG						PASS	.						126	121	123					4																	167810344		2203	4300	6503	SO:0001589	frameshift_variant	50859	exon7			.	AJ001454	CCDS34095.1, CCDS54817.1, CCDS56343.1, CCDS56344.1, CCDS56346.1, CCDS56347.1, CCDS58931.1, CCDS75207.1	4q32.3	2011-10-10			ENSG00000196104	ENSG00000196104			13565	protein-coding gene	gene with protein product		607989				11751414	Standard	NM_001204352		Approved	testican-3	uc003iri.1	Q9BQ16	OTTHUMG00000161190	ENST00000357154.3:c.535delT	chr4.hg19:g.167810344delA	ENSP00000349677:p.Cys179fs	131.0	0.0	0		164.0	27.0	0.164634	NM_016950	B2R7M7|B3KR67|B4DGK5|B4DHB4|B4DHV3|B4DI46|B4DJY3|E7EP61|F5H099|O75705|Q6UW53|Q96Q26	Frame_Shift_Del	DEL	ENST00000357154.3	hg19	CCDS54817.1																																																																																			.	.	.	none		0.318	SPOCK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364091.1			-	167810344	A	-	167810344	7	5	272	1	0	1	0	1	0	0	0	0	15093	217	8	0	799	0	SPOCK3	4	167810344	Frame_Shift_Del	DEL	A	TCGA-WN-A9G9-01A-12D-A36X-10	53431678	167810344	23343932	20	17181											
ZFYVE16	9765	hgsc.bcm.edu	37	chr5	79745509	79745509	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcctaaatgctaatctacTcgtgaatgtcaaattcatat	13	15	5	8	1	3	1	2	1	1	0	5	1	4	1	1	0	2	1	1	0	7	5			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr5:79745509T>C	ENST00000338008.5	+	8	3383	c.3203T>C	c.(3202-3204)cTc>cCc	p.L1068P	ZFYVE16_ENST00000510158.1_Missense_Mutation_p.L1068P|ZFYVE16_ENST00000505560.1_Missense_Mutation_p.L1068P	NM_001284236.1|NM_014733.3	NP_001271165.1|NP_055548	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	1068					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)		GCTAATCTACTCGTGAATGTC	0.323																																					p.L1068P	Melanoma(150;1452 1854 16018 17851 37292)	Atlas-SNP	.											.	ZFYVE16	100	.	0			c.T3203C						PASS	.						131	121	124					5																	79745509		2202	4299	6501	SO:0001583	missense	9765	exon9			ATCTACTCGTGAA	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.3203T>C	chr5.hg19:g.79745509T>C	ENSP00000337159:p.Leu1068Pro	172.0	0.0	.		222.0	34.0	.	NM_001105251	O15023|Q5H9U2|Q7LAU7|Q86T69|Q8N5L3|Q8NEK3	Missense_Mutation	SNP	ENST00000338008.5	hg19	CCDS4050.1	.	.	.	.	.	.	.	.	.	.	T	18.88	3.718416	0.68844	.	.	ENSG00000039319	ENST00000338008;ENST00000510158;ENST00000505560	T;T;T	0.49139	0.79;0.79;0.79	5.91	5.91	0.95273	.	0.118100	0.38436	N	0.001681	T	0.68659	0.3025	M	0.72894	2.215	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.71712	-0.4510	10	0.72032	D	0.01	-11.6581	16.0084	0.80380	0.0:0.0:0.0:1.0	.	1068	Q7Z3T8	ZFY16_HUMAN	P	1068	ENSP00000337159:L1068P;ENSP00000423663:L1068P;ENSP00000426848:L1068P	ENSP00000337159:L1068P	L	+	2	0	ZFYVE16	79781265	1.000000	0.71417	0.364000	0.25888	0.571000	0.35966	7.286000	0.78671	2.263000	0.75096	0.528000	0.53228	CTC	.	.	.	none		0.323	ZFYVE16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226982.2	NM_014733		C	79745509	T	C	79745509	3	2	272	1	0	0	0	0	1	0	0	0	17676	1551	54	3	3229	3	ZFYVE16	5	79745509	Missense_Mutation	SNP	T	TCGA-WN-A9G9-01A-12D-A36X-10		79745509	101169751	21	17182											
PCDHB7	56129	hgsc.bcm.edu	37	chr5	140554081	140554081	+	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	gtgctggtgctggacgccaaCgacaactcgcccttcgtgct	6	9	12	14	4	0	0	0	0	0	0	2	2	0	1	2	2	5	3	2	2	2	1			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr5:140554081C>T	ENST00000231137.3	+	1	1839	c.1665C>T	c.(1663-1665)aaC>aaT	p.N555N		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	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)			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)			TGGACGCCAACGACAACTCGC	0.726																																					p.N555N		Atlas-SNP	.											.	PCDHB7	231	.	0			c.C1665T						PASS	.						28	32	31					5																	140554081		2192	4283	6475	SO:0001819	synonymous_variant	56129	exon1			CGCCAACGACAAC	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.1665C>T	chr5.hg19:g.140554081C>T		95.0	0.0	.		115.0	10.0	.	NM_018940	A1L3Y8	Silent	SNP	ENST00000231137.3	hg19	CCDS4249.1	.	.	.	.	.	.	.	.	.	.	c	7.905	0.735232	0.15574	.	.	ENSG00000113212	ENST00000543636	.	.	.	4.3	0.795	0.18643	.	.	.	.	.	T	0.60064	0.2240	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59648	-0.7415	5	0.87932	D	0	.	5.9973	0.19501	0.0:0.3365:0.0:0.6635	.	.	.	.	M	338	.	ENSP00000440828:T338M	T	+	2	0	PCDHB7	140534265	0.000000	0.05858	0.992000	0.48379	0.966000	0.64601	-2.009000	0.01455	0.355000	0.24131	0.449000	0.29647	ACG	.	.	.	none		0.726	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940		T	140554081	C	T	140554081	2	4	272	1	0	0	0	0	0	0	0	1	11554	535	19	1		1	PCDHB7	5	140554081	Silent	SNP	C	TCGA-WN-A9G9-01A-12D-A36X-10	60808572	140554081	40361179	22	17183											
RNF39	80352	hgsc.bcm.edu	37	chr6	30039171	30039172	+	Frame_Shift_Ins	INS	-	-	T																															ggcccccgcagggcacagccINSttacgcagcccttgcgttgc																										TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr6:30039171_30039172insT	ENST00000244360.6	-	4	1076_1077	c.979_980insA	c.(979-981)aggfs	p.R327fs	RNF39_ENST00000376751.3_Intron	NM_025236.3	NP_079512.2	Q9H2S5	RNF39_HUMAN	ring finger protein 39	327	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)										AGGGCACAGCCTTACGCAGCCC	0.718																																					p.R327fs	NSCLC(8;188 360 1520 20207 31481)	Atlas-INDEL	.											.	RNF39	27	.	0			c.980_981insA						PASS	.																																			SO:0001589	frameshift_variant	80352	exon4			.	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.980dupA	chr6.hg19:g.30039173_30039173dupT	ENSP00000244360:p.Arg327fs	67.0	0.0	0		61.0	10.0	0.163934	NM_025236	A2BEK3|A6NCD6|B0S858|Q5SPM8|Q5SPM9|Q5SPN0|Q5SRJ9|Q5SRK1|Q5SS29|Q9H2S3|Q9H2S4	Frame_Shift_Ins	INS	ENST00000244360.6	hg19	CCDS4673.1																																																																																			.	.	.	none		0.718	RNF39-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076625.3	NM_170769		T	30039172	-	T	30039171	7	5	272	1	0	1	1	0	0	0	0	0	13504	681	24	0	286	0	RNF39	6	30039171	Frame_Shift_Ins	INS	-	TCGA-WN-A9G9-01A-12D-A36X-10		30039171	141075896	23	17184											
DPCR1	135656	hgsc.bcm.edu	37	chr6	30919864	30919864	+	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	cacaccagtcccagaaaagcCtacagaaaacctggggaaca	17	3	8	13	0	0	2	0	0	0	2	1	3	1	3	4	2	4	0	4	2	6	1			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr6:30919864C>G	ENST00000462446.1	+	2	3651	c.3623C>G	c.(3622-3624)cCt>cGt	p.P1208R	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_Missense_Mutation_p.P50R			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	332						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						CCAGAAAAGCCTACAGAAAAC	0.463																																					p.P1208R		Atlas-SNP	.											.	DPCR1	99	.	0			c.C3623G						PASS	.						152	151	151					6																	30919864		2203	4300	6503	SO:0001583	missense	135656	exon2			AAAAGCCTACAGA	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.3623C>G	chr6.hg19:g.30919864C>G	ENSP00000417182:p.Pro1208Arg	91.0	0.0	.		128.0	19.0	.	NM_080870	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	hg19	CCDS4692.2	.	.	.	.	.	.	.	.	.	.	C	10.72	1.428353	0.25726	.	.	ENSG00000168631	ENST00000462446;ENST00000450344;ENST00000304311	T;T	0.31247	1.5;1.5	3.26	-0.882	0.10604	.	.	.	.	.	T	0.19685	0.0473	L	0.34521	1.04	0.09310	N	1	D	0.89917	1.0	D	0.68765	0.96	T	0.05068	-1.0908	9	0.66056	D	0.02	0.0343	3.7848	0.08695	0.3285:0.4587:0.0:0.2128	.	1208	E9PEI6	.	R	1208;332;50	ENSP00000417182:P1208R;ENSP00000305948:P50R	ENSP00000305948:P50R	P	+	2	0	DPCR1	31027843	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.083000	0.14871	-0.107000	0.12088	-0.279000	0.10071	CCT	.	.	.	none		0.463	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870		G	30919864	C	G	30919864	3	3	272	1	0	0	0	0	1	0	0	0	4714	681	24	4	3629	4	DPCR1	6	30919864	Missense_Mutation	SNP	C	TCGA-WN-A9G9-01A-12D-A36X-10	880693	30919864	140195203	24	17185											
PNRC1	10957	hgsc.bcm.edu	37	chr6	89793765	89793765	+	Missense_Mutation	SNP	T	T	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	gaagtgagccaaaaggaaaaTtatgctggggcaaagtttag	16	8	13	4	0	0	1	0	1	0	0	0	3	0	2	1	3	2	3	1	3	8	3			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr6:89793765T>G	ENST00000336032.3	+	2	951	c.834T>G	c.(832-834)aaT>aaG	p.N278K	PNRC1_ENST00000369472.1_Missense_Mutation_p.N93K|PNRC1_ENST00000354922.3_Missense_Mutation_p.N93K	NM_006813.2	NP_006804.1	Q12796	PNRC1_HUMAN	proline-rich nuclear receptor coactivator 1	278					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(1)|large_intestine(2)|lung(3)	6		all_cancers(76;3.64e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.102)		AAAAGGAAAATTATGCTGGGG	0.383										Multiple Myeloma(7;0.094)																											p.N278K		Atlas-SNP	.											.	PNRC1	17	.	0			c.T834G						PASS	.						74	79	77					6																	89793765		2203	4300	6503	SO:0001583	missense	10957	exon2			GGAAAATTATGCT	U03105	CCDS5018.1	6q16.1	2008-02-05	2003-09-25	2003-09-26	ENSG00000146278	ENSG00000146278			17278	protein-coding gene	gene with protein product		606714	"proline rich 2"	PROL2		7578250	Standard	NM_006813		Approved	B4-2, PRR2	uc003pmv.3	Q12796	OTTHUMG00000015191	ENST00000336032.3:c.834T>G	chr6.hg19:g.89793765T>G	ENSP00000336931:p.Asn278Lys	281.0	0.0	.		298.0	32.0	.	NM_006813	B2R6Q0|E1P515|Q5T7J6|Q7Z5N0	Missense_Mutation	SNP	ENST00000336032.3	hg19	CCDS5018.1	.	.	.	.	.	.	.	.	.	.	T	12.65	2.002264	0.35320	.	.	ENSG00000146278	ENST00000369472;ENST00000336032;ENST00000354922	T;T;T	0.49720	0.86;0.77;0.86	5.64	3.26	0.37387	.	0.098076	0.64402	D	0.000001	T	0.52613	0.1745	M	0.73962	2.25	0.38214	D	0.940557	D	0.76494	0.999	D	0.68943	0.961	T	0.58183	-0.7681	10	0.72032	D	0.01	-6.2751	8.7345	0.34519	0.0:0.2152:0.0:0.7848	.	278	Q12796	PNRC1_HUMAN	K	93;278;93	ENSP00000358484:N93K;ENSP00000336931:N278K;ENSP00000347000:N93K	ENSP00000336931:N278K	N	+	3	2	PNRC1	89850484	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.367000	0.44213	0.419000	0.25927	0.533000	0.62120	AAT	.	.	.	none		0.383	PNRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041471.1	NM_006813		G	89793765	T	G	89793765	3	3	272	1	0	0	0	0	1	0	0	0	12181	1490	52	5	840	5	PNRC1	6	89793765	Missense_Mutation	SNP	T	TCGA-WN-A9G9-01A-12D-A36X-10	58873901	89793765	81321302	25	17186											
GPR141	353345	hgsc.bcm.edu	37	chr7	37780739	37780739	+	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	cagttctttaggatctattaCttgaatgttgtgacgcattc	9	17	8	7	1	2	2	0	2	2	0	3	3	2	3	0	1	1	3	0	1	4	8			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr7:37780739C>T	ENST00000447769.1	+	4	1033	c.744C>T	c.(742-744)taC>taT	p.Y248Y	EPDR1_ENST00000476620.1_Intron|GPR141_ENST00000334425.1_Silent_p.Y248Y|GPR141_ENST00000461610.1_Intron			Q7Z602	GP141_HUMAN	G protein-coupled receptor 141	248						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(13)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						GGATCTATTACTTGAATGTTG	0.398																																					p.Y248Y		Atlas-SNP	.											.	GPR141	79	.	0			c.C744T						PASS	.						177	172	174					7																	37780739		2203	4300	6503	SO:0001819	synonymous_variant	353345	exon1			CTATTACTTGAAT	AY288420	CCDS5451.1	7p14.1	2012-08-21			ENSG00000187037	ENSG00000187037		"GPCR / Class A : Orphans"	19997	protein-coding gene	gene with protein product		609045				12679517, 14623098	Standard	NM_181791		Approved	PGR13	uc003tfm.1	Q7Z602	OTTHUMG00000102105	ENST00000447769.1:c.744C>T	chr7.hg19:g.37780739C>T		104.0	0.0	.		92.0	12.0	.	NM_181791	A4D1X7|Q0VAR5|Q86SP3	Silent	SNP	ENST00000447769.1	hg19	CCDS5451.1																																																																																			.	.	.	none		0.398	GPR141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219943.2	NM_181791		T	37780739	C	T	37780739	2	4	272	1	0	0	0	0	0	0	0	1	6656	576	20	2		2	GPR141	7	37780739	Silent	SNP	C	TCGA-WN-A9G9-01A-12D-A36X-10		37780739	121357924	26	17187											
C7orf36	57002	hgsc.bcm.edu	37	chr7	39612136	39612136	+	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	tgctgagtttaacaaaaactGtagcaagagccatagtggga	15	9	11	6	0	0	2	0	1	0	1	0	3	0	3	1	1	5	4	1	1	6	4			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr7:39612136G>C	ENST00000223273.2	+	3	555	c.512G>C	c.(511-513)tGt>tCt	p.C171S	YAE1D1_ENST00000432096.2_Intron	NM_020192.3	NP_064577.1	Q9NRH1	YAED1_HUMAN	Yae1 domain containing 1	171																	AACAAAAACTGTAGCAAGAGC	0.388																																					p.C171S		Atlas-SNP	.											.	YAE1D1	2	.	0			c.G512C						PASS	.						105	106	105					7																	39612136		2203	4300	6503	SO:0001583	missense	57002	exon3			AAAACTGTAGCAA	AF226046	CCDS5459.1, CCDS64630.1	7p14.1	2011-11-24	2011-11-24	2011-11-24	ENSG00000241127	ENSG00000241127			24857	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 36"	C7orf36		12477932	Standard	NM_020192		Approved	GK003	uc003thc.4	Q9NRH1	OTTHUMG00000128689	ENST00000223273.2:c.512G>C	chr7.hg19:g.39612136G>C	ENSP00000223273:p.Cys171Ser	180.0	0.0	.		139.0	16.0	.	NM_020192	A4D1W4|B4DE83|Q6IAF7|Q8WVZ5	Missense_Mutation	SNP	ENST00000223273.2	hg19	CCDS5459.1	.	.	.	.	.	.	.	.	.	.	G	9.647	1.140562	0.21205	.	.	ENSG00000241127	ENST00000223273	T	0.52295	0.67	5.93	4.1	0.47936	.	0.134009	0.64402	D	0.000001	T	0.31199	0.0789	L	0.31065	0.9	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.25745	-1.0123	10	0.62326	D	0.03	-3.9594	3.8091	0.08789	0.1436:0.1357:0.5882:0.1324	.	171	Q9NRH1	CG036_HUMAN	S	171	ENSP00000223273:C171S	ENSP00000223273:C171S	C	+	2	0	C7orf36	39578661	0.010000	0.17322	0.827000	0.32855	0.652000	0.38707	0.587000	0.23909	0.829000	0.34733	0.655000	0.94253	TGT	.	.	.	none		0.388	YAE1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250586.1	NM_020192		C	39612136	G	C	39612136	3	2	272	1	0	0	0	0	1	0	0	0	2392	1377	48	4	522	4	C7orf36	7	39612136	Missense_Mutation	SNP	G	TCGA-WN-A9G9-01A-12D-A36X-10	1831397	39612136	119526527	27	17188											
ABCA13	154664	hgsc.bcm.edu	37	chr7	48317734	48317734	+	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	tagaaattctgaaactggatCaatttcttaccctgatgata	14	14	6	7	0	3	4	1	3	2	1	3	5	3	5	1	1	2	0	1	1	6	5			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr7:48317734C>T	ENST00000435803.1	+	18	6967	c.6943C>T	c.(6943-6945)Caa>Taa	p.Q2315*		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2315					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						GAAACTGGATCAATTTCTTAC	0.239																																					p.Q2315X		Atlas-SNP	.											.	ABCA13	1192	.	0			c.C6943T						PASS	.						19	18	18					7																	48317734		1775	4024	5799	SO:0001587	stop_gained	154664	exon18			CTGGATCAATTTC	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.6943C>T	chr7.hg19:g.48317734C>T	ENSP00000411096:p.Gln2315*	366.0	0.0	.		435.0	43.0	.	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Nonsense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	C	46	12.263306	0.99651	.	.	ENSG00000179869	ENST00000435803	.	.	.	4.88	3.95	0.45737	.	0.651374	0.13231	N	0.403679	.	.	.	.	.	.	0.47183	D	0.999344	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	.	8.1462	0.31113	0.0:0.878:0.0:0.122	.	.	.	.	X	2315	.	ENSP00000411096:Q2315X	Q	+	1	0	ABCA13	48288280	0.090000	0.21635	0.028000	0.17463	0.343000	0.28985	0.786000	0.26844	1.097000	0.41459	0.650000	0.86243	CAA	.	.	.	none		0.239	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48317734	C	T	48317734	4	4	272	1	0	0	0	0	0	1	0	0	31	827	29	2	6842	2	ABCA13	7	48317734	Nonsense_Mutation	SNP	C	TCGA-WN-A9G9-01A-12D-A36X-10	8705598	48317734	110820929	28	17189											
CLIP2	7461	hgsc.bcm.edu	37	chr7	73791021	73791021	+	Frame_Shift_Del	DEL	T	T	-																															cgctggccgagaagaagatgTtggactacgagcggctgcag																										TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr7:73791021delT	ENST00000395060.1	+	9	2290	c.2290delT	c.(2290-2292)ttgfs	p.L764fs	CLIP2_ENST00000361545.5_Frame_Shift_Del_p.L729fs|CLIP2_ENST00000223398.6_Frame_Shift_Del_p.L764fs			Q9UDT6	CLIP2_HUMAN	CAP-GLY domain containing linker protein 2	764						cytoplasmic microtubule (GO:0005881)|microtubule associated complex (GO:0005875)|microtubule plus-end (GO:0035371)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|pancreas(1)|prostate(2)|skin(3)	30						GAAGAAGATGTTGGACTACGA	0.612																																					p.M763fs		Atlas-INDEL	.											.	CLIP2	134	.	0			c.2289delG						PASS	.						29	34	32					7																	73791021		2203	4300	6503	SO:0001589	frameshift_variant	7461	exon10			.	AB006629	CCDS5569.1, CCDS5570.1	7q11.23	2008-06-12	2007-01-04	2007-01-04	ENSG00000106665	ENSG00000106665			2586	protein-coding gene	gene with protein product		603432	"cytoplasmic linker 2", "Williams-Beuren syndrome chromosome region 3"	WBSCR4, CYLN2, WBSCR3		8812460, 9799601	Standard	NM_003388		Approved	CLIP-115, KIAA0291, WSCR4, CLIP, WSCR3	uc003uam.3	Q9UDT6	OTTHUMG00000022980	ENST00000395060.1:c.2290delT	chr7.hg19:g.73791021delT	ENSP00000378500:p.Leu764fs	204.0	0.0	0		185.0	16.0	0.0864865	NM_003388	O14527|O43611	Frame_Shift_Del	DEL	ENST00000395060.1	hg19	CCDS5569.1																																																																																			.	.	.	none		0.612	CLIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252556.1	NM_003388		-	73791021	T	-	73791021	7	5	272	1	0	1	0	1	0	0	0	0	3535	1722	60	0	2324	0	CLIP2	7	73791021	Frame_Shift_Del	DEL	T	TCGA-WN-A9G9-01A-12D-A36X-10	25473287	73791021	85347642	29	17190											
EPHB4	2050	hgsc.bcm.edu	37	chr7	100414914	100414914	+	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	tagctggctccccgcttcagCccccgcagctctgcccggtt	3	9	10	19	3	2	0	1	0	1	0	3	0	3	0	5	2	4	6	5	2	1	3			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr7:100414914C>A	ENST00000358173.3	-	8	1956	c.1488G>T	c.(1486-1488)ggG>ggT	p.G496G	EPHB4_ENST00000360620.3_Silent_p.G496G|EPHB4_ENST00000477446.1_5'UTR	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	496	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)					CCCGCTTCAGCCCCCGCAGCT	0.687																																					p.G496G	GBM(200;2113 3072 25865 52728)	Atlas-SNP	.											.	EPHB4	106	.	0			c.G1488T						PASS	.						18	19	18					7																	100414914		2200	4296	6496	SO:0001819	synonymous_variant	2050	exon8			CTTCAGCCCCCGC	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.1488G>T	chr7.hg19:g.100414914C>A		59.0	0.0	.		75.0	13.0	.	NM_004444	B5A970|B5A971|B5A972|Q7Z635|Q9BTA5|Q9BXP0	Silent	SNP	ENST00000358173.3	hg19	CCDS5706.1																																																																																			.	.	.	none		0.687	EPHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347222.1	NM_004444		A	100414914	C	A	100414914	2	1	272	1	0	0	0	0	0	0	0	1	5179	726	26	4		4	EPHB4	7	100414914	Silent	SNP	C	TCGA-WN-A9G9-01A-12D-A36X-10	26623893	100414914	58723749	30	17191											
MUC17	140453	hgsc.bcm.edu	37	chr7	100684959	100684959	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgaggttaacaccctttcaaCaactcctgtggactccaaca	12	10	6	13	0	1	1	1	1	0	0	3	2	3	2	3	2	4	1	3	2	4	2			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr7:100684959C>T	ENST00000306151.4	+	3	10326	c.10262C>T	c.(10261-10263)aCa>aTa	p.T3421I		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3421	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)					ACCCTTTCAACAACTCCTGTG	0.498																																					p.T3421I		Atlas-SNP	.											.	MUC17	804	.	0			c.C10262T						PASS	.						246	252	250					7																	100684959		2203	4300	6503	SO:0001583	missense	140453	exon3			TTTCAACAACTCC	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.10262C>T	chr7.hg19:g.100684959C>T	ENSP00000302716:p.Thr3421Ile	98.0	0.0	.		113.0	13.0	.	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	10.54	1.378183	0.24944	.	.	ENSG00000169876	ENST00000306151	T	0.03441	3.93	1.37	1.37	0.22104	.	.	.	.	.	T	0.05547	0.0146	N	0.24115	0.695	0.09310	N	0.999999	D	0.61697	0.99	P	0.56088	0.791	T	0.45818	-0.9235	9	0.36615	T	0.2	.	8.2792	0.31889	0.0:1.0:0.0:0.0	.	3421	Q685J3	MUC17_HUMAN	I	3421	ENSP00000302716:T3421I	ENSP00000302716:T3421I	T	+	2	0	MUC17	100471679	0.007000	0.16637	0.015000	0.15790	0.027000	0.11550	1.274000	0.33132	0.715000	0.32103	0.186000	0.17326	ACA	.	.	.	none		0.498	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		T	100684959	C	T	100684959	3	4	272	1	0	0	0	0	1	0	0	0	9981	478	17	2	10272	2	MUC17	7	100684959	Missense_Mutation	SNP	C	TCGA-WN-A9G9-01A-12D-A36X-10	270045	100684959	58453704	31	17192											
BRAF	673	hgsc.bcm.edu	37	chr7	140507773	140507774	+	Frame_Shift_Ins	INS	-	-	T																															acatacaaagttgtgtgttgINStaagtggaacattctccaac																										TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr7:140507773_140507774insT	ENST00000288602.6	-	5	757_758	c.697_698insA	c.(697-699)acafs	p.T233fs		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	233					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)	GTTGTGTGTTGTAAGTGGAACA	0.312		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.T233fs	Colon(40;35 892 2973 5743 27438)	Atlas-INDEL	.		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	.	BRAF	36346	.	0			c.698_699insA						PASS	.																																			SO:0001589	frameshift_variant	673	exon5	Familial Cancer Database	CFC, CFCS	.	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.698dupA	chr7.hg19:g.140507774_140507774dupT	ENSP00000288602:p.Thr233fs	90.0	0.0	0		90.0	10.0	0.111111	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Frame_Shift_Ins	INS	ENST00000288602.6	hg19	CCDS5863.1																																																																																			.	.	.	none		0.312	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		T	140507774	-	T	140507773	7	5	272	1	0	1	1	0	0	0	0	0	1498	1377	48	0	1658	0	BRAF	7	140507773	Frame_Shift_Ins	INS	-	TCGA-WN-A9G9-01A-12D-A36X-10	39822814	140507773	18630890	32	17193											
CSMD1	64478	hgsc.bcm.edu	37	chr8	2910077	2910077	+	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	ggattcaagcttgaagccctCatgacattcatagaccactt	12	11	7	11	0	3	3	3	2	0	1	3	4	3	4	2	1	2	1	2	1	3	5			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr8:2910077C>A	ENST00000520002.1	-	51	8125	c.7570G>T	c.(7570-7572)Gag>Tag	p.E2524*	CSMD1_ENST00000602557.1_Nonsense_Mutation_p.E2524*|CSMD1_ENST00000537824.1_Nonsense_Mutation_p.E2523*|CSMD1_ENST00000602723.1_Nonsense_Mutation_p.E2524*|CSMD1_ENST00000400186.3_Nonsense_Mutation_p.E2524*|CSMD1_ENST00000542608.1_Nonsense_Mutation_p.E2523*			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	2524	Sushi 15. {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)		TTGAAGCCCTCATGACATTCA	0.502																																					p.E2523X		Atlas-SNP	.											.	CSMD1	1469	.	0			c.G7567T						PASS	.						68	65	66					8																	2910077		1951	4141	6092	SO:0001587	stop_gained	64478	exon50			AGCCCTCATGACA			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.7570G>T	chr8.hg19:g.2910077C>A	ENSP00000430733:p.Glu2524*	135.0	0.0	.		129.0	20.0	.	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Nonsense_Mutation	SNP	ENST00000520002.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	48|48	14.850392|14.850392	0.99812|0.99812	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608|ENST00000335551	.|.	.|.	.|.	5.32|5.32	4.43|4.43	0.53597|0.53597	.|.	0.336188|.	0.27482|.	N|.	0.019168|.	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.24483|.	T|.	0.36|.	.|.	13.7213|13.7213	0.62728|0.62728	0.0:0.9254:0.0:0.0746|0.0:0.9254:0.0:0.0746	.|.	.|.	.|.	.|.	X|L	2524;2524;2385;2523;2523|1940	.|.	ENSP00000320445:E2385X|.	E|X	-|-	1|2	0|2	CSMD1|CSMD1	2897484|2897484	0.959000|0.959000	0.32827|0.32827	0.951000|0.951000	0.38953|0.38953	0.103000|0.103000	0.19146|0.19146	2.127000|2.127000	0.42035|0.42035	2.628000|2.628000	0.89032|0.89032	0.655000|0.655000	0.94253|0.94253	GAG|TGA	.	.	.	none		0.502	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	2910077	C	A	2910077	4	1	272	1	0	0	0	0	0	1	0	0	3946	835	29	4	3211	4	CSMD1	8	2910077	Nonsense_Mutation	SNP	C	TCGA-WN-A9G9-01A-12D-A36X-10		2910077	143453945	33	17194											
PTK2B	2185	hgsc.bcm.edu	37	chr8	27315863	27315863	+	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	cctggcagagctcatcaacaAgatgcggctggcacagcaga	12	5	12	12	1	2	3	2	0	0	3	2	3	2	3	1	3	4	5	1	3	2	0			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr8:27315863A>T	ENST00000397501.1	+	36	3675	c.2867A>T	c.(2866-2868)aAg>aTg	p.K956M	PTK2B_ENST00000346049.5_Missense_Mutation_p.K956M|PTK2B_ENST00000420218.2_Missense_Mutation_p.K914M|PTK2B_ENST00000544172.1_Missense_Mutation_p.K956M|PTK2B_ENST00000517339.1_Missense_Mutation_p.K914M|PTK2B_ENST00000338238.4_Missense_Mutation_p.K914M	NM_173174.2	NP_775266.1	Q14289	FAK2_HUMAN	protein tyrosine kinase 2 beta	956	Focal adhesion targeting (FAT).|Interaction with TGFB1I1. {ECO:0000250}.				activation of Janus kinase activity (GO:0042976)|activation of Rac GTPase activity (GO:0032863)|apoptotic process (GO:0006915)|blood vessel endothelial cell migration (GO:0043534)|bone resorption (GO:0045453)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|cellular response to retinoic acid (GO:0071300)|chemokine-mediated signaling pathway (GO:0070098)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|glial cell proliferation (GO:0014009)|integrin-mediated signaling pathway (GO:0007229)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term synaptic potentiation (GO:0060291)|MAPK cascade (GO:0000165)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of potassium ion transport (GO:0043267)|neuron projection development (GO:0031175)|oocyte maturation (GO:0001556)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell chemotaxis (GO:2000538)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of establishment of cell polarity (GO:2000114)|regulation of inositol trisphosphate biosynthetic process (GO:0032960)|regulation of macrophage chemotaxis (GO:0010758)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000058)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to hormone (GO:0009725)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|stress fiber assembly (GO:0043149)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	apical dendrite (GO:0097440)|axon (GO:0030424)|cell body (GO:0044297)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(17)|ovary(4)|skin(12)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)	Leflunomide(DB01097)	CTCATCAACAAGATGCGGCTG	0.562																																					p.K956M		Atlas-SNP	.											.	PTK2B	304	.	0			c.A2867T						PASS	.						77	57	64					8																	27315863		2203	4300	6503	SO:0001583	missense	2185	exon36			TCAACAAGATGCG	U33284	CCDS6057.1, CCDS6058.1	8p21.1	2013-02-18	2013-02-18		ENSG00000120899	ENSG00000120899			9612	protein-coding gene	gene with protein product		601212	"protein tyrosine kinase 2 beta", "PTK2B protein tyrosine kinase 2 beta"	FAK2		7544443, 7499242	Standard	NM_173174		Approved	CAKB, PYK2, RAFTK, PTK, CADTK	uc003xfp.2	Q14289	OTTHUMG00000102082	ENST00000397501.1:c.2867A>T	chr8.hg19:g.27315863A>T	ENSP00000380638:p.Lys956Met	116.0	0.0	.		166.0	19.0	.	NM_173174	D3DST0|Q13475|Q14290|Q16709|Q6PID4	Missense_Mutation	SNP	ENST00000397501.1	hg19	CCDS6057.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.500119	0.85176	.	.	ENSG00000120899	ENST00000397501;ENST00000338238;ENST00000544172;ENST00000346049;ENST00000420218;ENST00000517339	T;T;T;T;T;T	0.35789	1.29;1.29;1.29;1.29;1.29;1.29	4.91	4.91	0.64330	Focal adhesion kinase, targeting (FAT) domain (3);	0.000000	0.85682	D	0.000000	T	0.57577	0.2063	M	0.72118	2.19	0.80722	D	1	P;D	0.89917	0.915;1.0	P;D	0.87578	0.596;0.998	T	0.59883	-0.7370	10	0.52906	T	0.07	.	12.5376	0.56150	1.0:0.0:0.0:0.0	.	914;956	Q14289-2;Q14289	.;FAK2_HUMAN	M	956;914;956;956;914;914	ENSP00000380638:K956M;ENSP00000342242:K914M;ENSP00000440926:K956M;ENSP00000332816:K956M;ENSP00000391995:K914M;ENSP00000427931:K914M	ENSP00000342242:K914M	K	+	2	0	PTK2B	27371780	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.139000	0.94554	2.048000	0.60808	0.460000	0.39030	AAG	.	.	.	none		0.562	PTK2B-009	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219916.1	NM_004103		T	27315863	A	T	27315863	3	4	272	1	0	0	0	0	1	0	0	0	12774	72	3	5	2985	5	PTK2B	8	27315863	Missense_Mutation	SNP	A	TCGA-WN-A9G9-01A-12D-A36X-10	24405786	27315863	119048159	34	17195											
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77775451	77775451	+	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	actccaccacctccaccaccTcctcctcctcctcctccttc	5	10	0	26	0	0	0	0	0	0	0	9	0	8	0	12	0	0	0	12	0	0	1	rs199874527		TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr8:77775451T>A	ENST00000521891.2	+	11	9949	c.9501T>A	c.(9499-9501)ccT>ccA	p.P3167P	ZFHX4_ENST00000455469.2_Silent_p.P3122P|ZFHX4_ENST00000050961.6_Silent_p.P3118P|ZFHX4_ENST00000518282.1_Silent_p.P3141P	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	3118					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)			ctccaccacctcctcctcctc	0.522										HNSCC(33;0.089)																											p.P3167P		Atlas-SNP	.											ZFHX4,colon,carcinoma,0,2	ZFHX4	878	.	0			c.T9501A						PASS	.						52	53	53					8																	77775451		2064	4225	6289	SO:0001819	synonymous_variant	79776	exon11			ACCACCTCCTCCT		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.9501T>A	chr8.hg19:g.77775451T>A		75.0	1.0	.		83.0	5.0	.	NM_024721	G3V138|Q18PS0|Q6ZN20	Silent	SNP	ENST00000521891.2	hg19	CCDS47878.2																																																																																			.	.	.	none		0.522	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		A	77775451	T	A	77775451	2	1	272	1	0	0	0	0	0	0	0	1	17647	1538	54	5		5	ZFHX4	8	77775451	Silent	SNP	T	TCGA-WN-A9G9-01A-12D-A36X-10	50459588	77775451	68588571	35	17196											
S1PR3	1903	hgsc.bcm.edu	37	chr9	91616360	91616361	+	Frame_Shift_Del	DEL	CT	CT	-																															ctttttcattggcaacctggCtctctgcgacctgctggccg																										TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr9:91616360_91616361delCT	ENST00000375846.3	+	1	4940_4941	c.245_246delCT	c.(244-246)gctfs	p.A82fs	S1PR3_ENST00000358157.2_Frame_Shift_Del_p.A82fs			Q99500	S1PR3_HUMAN	sphingosine-1-phosphate receptor 3	82					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|anatomical structure morphogenesis (GO:0009653)|cytokine production (GO:0001816)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of establishment of endothelial barrier (GO:1903141)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of interleukin-1 beta production (GO:0032651)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|integrin binding (GO:0005178)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(1)	34						GGCAACCTGGCTCTCTGCGACC	0.495											OREG0019291	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.82_82del		Atlas-Indel,Pindel	.											.	S1PR3	49	.	0			c.244_245del						PASS	.																																			SO:0001589	frameshift_variant	1903	exon2			.	AF022139	CCDS6680.1	9q22.1-q22.2	2012-08-08	2008-04-30	2008-04-30	ENSG00000213694	ENSG00000213694		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"	3167	protein-coding gene	gene with protein product	"sphingosine-1-phosphate receptor 3"	601965	"endothelial differentiation, sphingolipid G-protein-coupled receptor, 3"	EDG3		8878560, 9409733	Standard	NM_005226		Approved	EDG-3	uc004aqe.4	Q99500	OTTHUMG00000020173	ENST00000375846.3:c.245_246delCT	chr9.hg19:g.91616364_91616365delCT	ENSP00000365006:p.Ala82fs	114.0	0.0	0	1283	138.0	14.0	0.101449	NM_005226	Q5SQD8|Q7Z5I2	Frame_Shift_Del	DEL	ENST00000375846.3	hg19	CCDS6680.1																																																																																			.	.	.	none		0.495	S1PR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052979.2	NM_005226		-	91616361	CT	-	91616360	7	5	272	1	0	1	0	1	0	0	0	0	13808	797	28	0	247	0	S1PR3	9	91616360	Frame_Shift_Del	DEL	CT	TCGA-WN-A9G9-01A-12D-A36X-10		91616360	49597071	36	17197											
FKTN	2218	hgsc.bcm.edu	37	chr9	108397413	108397413	+	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	ccctgtgaaaccctcgaataCattgaagccaactatggtaa	14	9	7	11	1	0	2	0	2	0	0	1	3	0	2	3	1	4	1	3	1	7	4			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr9:108397413C>A	ENST00000223528.2	+	10	1378	c.1254C>A	c.(1252-1254)taC>taA	p.Y418*	FKTN_ENST00000357998.5_Nonsense_Mutation_p.Y418*|FKTN_ENST00000540160.1_3'UTR|FKTN_ENST00000602661.1_Nonsense_Mutation_p.Y418*|FKTN_ENST00000448551.2_Nonsense_Mutation_p.Y418*	NM_006731.2	NP_006722.2	O75072	FKTN_HUMAN	fukutin	418					muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|negative regulation of JNK cascade (GO:0046329)|nervous system development (GO:0007399)|regulation of protein glycosylation (GO:0060049)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	transferase activity (GO:0016740)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	25						CCCTCGAATACATTGAAGCCA	0.473																																					p.Y418X		Atlas-SNP	.											.	FKTN	47	.	0			c.C1254A						PASS	.						203	181	188					9																	108397413		2203	4300	6503	SO:0001587	stop_gained	2218	exon10			CGAATACATTGAA		CCDS6766.1	9q31-q33	2014-09-17	2007-11-21	2007-11-21	ENSG00000106692	ENSG00000106692			3622	protein-coding gene	gene with protein product		607440	"Fukuyama type congenital muscular dystrophy (fukutin)"	FCMD		8275093, 17036286, 17044012	Standard	NM_001079802		Approved	LGMD2M	uc004bcs.3	O75072	OTTHUMG00000020425	ENST00000223528.2:c.1254C>A	chr9.hg19:g.108397413C>A	ENSP00000223528:p.Tyr418*	140.0	0.0	.		153.0	14.0	.	NM_006731	B4DUX9|J3KP13|Q3MIJ1|Q96TE1|Q9P295	Nonsense_Mutation	SNP	ENST00000223528.2	hg19	CCDS6766.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.282505|5.282505	0.95489|0.95489	.|.	.|.	ENSG00000106692|ENSG00000106692	ENST00000457847|ENST00000223528;ENST00000357998	.|.	.|.	.|.	6.04|6.04	1.09|1.09	0.20402|0.20402	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.29850|.	0.0746|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.17077|.	-1.0381|.	4|.	.|0.02654	.|T	.|1	1.15|1.15	10.5637|10.5637	0.45161|0.45161	0.0:0.5396:0.0:0.4604|0.0:0.5396:0.0:0.4604	.|.	.|.	.|.	.|.	K|X	115|418	.|.	.|ENSP00000223528:Y418X	T|Y	+|+	2|3	0|2	FKTN|FKTN	107437234|107437234	0.964000|0.964000	0.33143|0.33143	0.996000|0.996000	0.52242|0.52242	0.993000|0.993000	0.82548|0.82548	0.154000|0.154000	0.16343|0.16343	0.163000|0.163000	0.19507|0.19507	0.563000|0.563000	0.77884|0.77884	ACA|TAC	.	.	.	none		0.473	FKTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053505.1	NM_006731		A	108397413	C	A	108397413	4	1	272	1	0	0	0	0	0	1	0	0	5926	489	17	4	1288	4	FKTN	9	108397413	Nonsense_Mutation	SNP	C	TCGA-WN-A9G9-01A-12D-A36X-10	16781053	108397413	32816018	37	17198											
TOR1B	27348	hgsc.bcm.edu	37	chr9	132569640	132569640	+	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	aaagccatcttcatctttctCaggtcagcgggaggcggttt	8	12	11	10	2	5	0	3	0	3	0	6	1	5	1	1	4	2	1	1	4	1	3			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr9:132569640C>T	ENST00000259339.2	+	3	699	c.639C>T	c.(637-639)ctC>ctT	p.L213L		NM_014506.1	NP_055321.1	O14657	TOR1B_HUMAN	torsin family 1, member B (torsin B)	213					ATP catabolic process (GO:0006200)|chaperone mediated protein folding requiring cofactor (GO:0051085)|endoplasmic reticulum organization (GO:0007029)|nuclear membrane organization (GO:0071763)|protein homooligomerization (GO:0051260)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			endometrium(3)|kidney(1)|large_intestine(1)|lung(7)	12		Ovarian(14;0.0586)				TCATCTTTCTCAGGTCAGCGG	0.488																																					p.L213L		Atlas-SNP	.											.	TOR1B	20	.	0			c.C639T						PASS	.						172	167	169					9																	132569640		2203	4300	6503	SO:0001819	synonymous_variant	27348	exon3			CTTTCTCAGGTCA	AF007872	CCDS6929.1	9q34	2008-07-21			ENSG00000136816	ENSG00000136816			11995	protein-coding gene	gene with protein product		608050				9288096, 10644435	Standard	NM_014506		Approved	DQ1, MGC4386	uc004byk.1	O14657	OTTHUMG00000020795	ENST00000259339.2:c.639C>T	chr9.hg19:g.132569640C>T		95.0	0.0	.		85.0	7.0	.	NM_014506		Silent	SNP	ENST00000259339.2	hg19	CCDS6929.1																																																																																			.	.	.	none		0.488	TOR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054615.1	NM_014506		T	132569640	C	T	132569640	2	4	272	1	0	0	0	0	0	0	0	1	16386	813	29	2		2	TOR1B	9	132569640	Silent	SNP	C	TCGA-WN-A9G9-01A-12D-A36X-10	24172227	132569640	8643791	38	17199											
ERCC6	2074	hgsc.bcm.edu	37	chr10	50708590	50708590	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaggagcacttgcctgtaaTttgaaccacgagtcctgatc	11	10	10	10	1	0	3	0	2	0	1	2	5	1	4	3	1	3	2	3	1	2	3			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr10:50708590T>C	ENST00000355832.5	-	7	1757	c.1679A>G	c.(1678-1680)aAt>aGt	p.N560S	ERCC6_ENST00000542458.1_5'UTR	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	560	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)			breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						TTGCCTGTAATTTGAACCACG	0.458								Direct reversal of damage;Nucleotide excision repair (NER)																													p.V560G		Atlas-SNP	.											.	ERCC6	162	.	0			c.T1679G						PASS	.						148	129	135					10																	50708590		2203	4300	6503	SO:0001583	missense	2074	exon7			CTGTAATTTGAAC	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.1679A>G	chr10.hg19:g.50708590T>C	ENSP00000348089:p.Asn560Ser	58.0	0.0	.		62.0	9.0	.	NM_000124	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	hg19	CCDS7229.1	.	.	.	.	.	.	.	.	.	.	T	11.32	1.604045	0.28534	.	.	ENSG00000225830	ENST00000355832	D	0.92199	-2.99	5.87	5.87	0.94306	DEAD-like helicase (2);SNF2-related (1);	.	.	.	.	T	0.81230	0.4779	N	0.01800	-0.715	0.80722	D	1	B	0.27068	0.167	B	0.27608	0.081	T	0.78932	-0.2009	9	0.27785	T	0.31	-26.6076	16.5764	0.84681	0.0:0.0:0.0:1.0	.	560	Q03468	ERCC6_HUMAN	S	560	ENSP00000348089:N560S	ENSP00000348089:N560S	N	-	2	0	ERCC6	50378596	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.249000	0.72427	2.371000	0.80710	0.533000	0.62120	AAT	.	.	.	none		0.458	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124		C	50708590	T	C	50708590	3	2	272	1	0	0	0	0	1	0	0	0	5219	1493	52	3	2862	3	ERCC6	10	50708590	Missense_Mutation	SNP	T	TCGA-WN-A9G9-01A-12D-A36X-10		50708590	84826157	39	17200											
LRRC32	2615	hgsc.bcm.edu	37	chr11	76371485	76371485	+	Silent	SNP	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	agcgtccgcagagaccccagGgctctggcgcccagttccag	7	5	13	16	3	1	1	0	0	1	1	3	2	3	1	5	2	1	3	5	2	0	1			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr11:76371485G>A	ENST00000407242.2	-	3	1394	c.1152C>T	c.(1150-1152)gcC>gcT	p.A384A	LRRC32_ENST00000260061.5_Silent_p.A384A|AP001189.4_ENST00000447519.1_RNA|LRRC32_ENST00000464145.1_Intron|LRRC32_ENST00000404995.1_Silent_p.A384A	NM_005512.2	NP_005503.1	Q14392	LRC32_HUMAN	leucine rich repeat containing 32	384					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						GAGACCCCAGGGCTCTGGCGC	0.647																																					p.A384A		Atlas-SNP	.											.	LRRC32	74	.	0			c.C1152T						PASS	.						18	20	19					11																	76371485		2199	4289	6488	SO:0001819	synonymous_variant	2615	exon3			CCCCAGGGCTCTG	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.1152C>T	chr11.hg19:g.76371485G>A		112.0	0.0	.		125.0	7.0	.	NM_005512	Q86V06	Silent	SNP	ENST00000407242.2	hg19	CCDS8245.1																																																																																			.	.	.	none		0.647	LRRC32-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257926.2	NM_005512		A	76371485	G	A	76371485	2	1	272	1	0	0	0	0	0	0	0	1	8994	1219	43	2		2	LRRC32	11	76371485	Silent	SNP	G	TCGA-WN-A9G9-01A-12D-A36X-10		76371485	58635031	40	17201											
ATM	472	hgsc.bcm.edu	37	chr11	108143336	108143336	+	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	ccttaaaactttgcttgaggTgagtttttgcatttttttag	8	20	8	5	0	0	2	0	2	0	0	0	2	0	2	1	1	3	3	1	1	3	9			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr11:108143336T>A	ENST00000452508.2	+	22	3342		c.e22+2		ATM_ENST00000278616.4_Splice_Site			Q13315	ATM_HUMAN	ATM serine/threonine kinase						brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.?(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)	TTGCTTGAGGTGAGTTTTTGC	0.299			"D, Mis, N, F, S"		T-PLL	"leukemia, lymphoma, medulloblastoma, glioma"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																											.		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	ATM_ENST00000278616,caecum,carcinoma,0,3	ATM	1657	.	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.3153+2T>A						PASS	.						105	108	107					11																	108143336		2201	4298	6499	SO:0001630	splice_region_variant	472	exon21	Familial Cancer Database	AT, Louis-Bar syndrome	TTGAGGTGAGTTT	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.3153+2T>A	chr11.hg19:g.108143336T>A		199.0	0.0	.		237.0	24.0	.	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Splice_Site	SNP	ENST00000452508.2	hg19	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.163596	0.78226	.	.	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7767	0.78228	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ATM	107648546	1.000000	0.71417	0.976000	0.42696	0.907000	0.53573	4.461000	0.60115	2.174000	0.68829	0.533000	0.62120	.	.	.	.	none		0.299	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	Intron	A	108143336	T	A	108143336	5	1	272	1	0	0	0	0	0	0	1	0	1109	1710	59	5	3233	5	ATM	11	108143336	Splice_Site	SNP	T	TCGA-WN-A9G9-01A-12D-A36X-10	31771851	108143336	26863180	41	17202											
HNRNPA1	3178	hgsc.bcm.edu	37	chr12	54675583	54675583	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaacactgttctcaggtaaTgagagatccaaacaccaagc	15	9	7	10	0	1	2	1	1	1	1	3	3	2	2	2	1	3	2	2	1	4	3			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr12:54675583T>C	ENST00000340913.6	+	3	190	c.137T>C	c.(136-138)aTg>aCg	p.M46T	CBX5_ENST00000209875.4_5'Flank|RP11-968A15.2_ENST00000547177.1_RNA|RP11-968A15.8_ENST00000553061.1_RNA|HNRNPA1_ENST00000330752.8_Missense_Mutation_p.M46T|HNRNPA1_ENST00000547276.1_Missense_Mutation_p.M46T|HNRNPA1_ENST00000546500.1_Missense_Mutation_p.M46T	NM_002136.2|NM_031157.2	NP_002127.1|NP_112420.1	P09651	ROA1_HUMAN	heterogeneous nuclear ribonucleoprotein A1	46	Globular A domain.|RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				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						TCTCAGGTAATGAGAGATCCA	0.448																																					p.M46T	Colon(83;502 1289 8436 16406 24870)	Atlas-SNP	.											.	HNRNPA1	72	.	0			c.T137C						PASS	.						47	47	47					12																	54675583		1972	4195	6167	SO:0001583	missense	3178	exon3			AGGTAATGAGAGA	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.137T>C	chr12.hg19:g.54675583T>C	ENSP00000341826:p.Met46Thr	163.0	0.0	.		131.0	16.0	.	NM_002136	A8K4Z8|Q3MIB7|Q6PJZ7	Missense_Mutation	SNP	ENST00000340913.6	hg19	CCDS44909.1	.	.	.	.	.	.	.	.	.	.	T	16.89	3.248556	0.59103	.	.	ENSG00000135486	ENST00000546500;ENST00000547708;ENST00000547617;ENST00000552494;ENST00000340913;ENST00000330752;ENST00000552591;ENST00000551133;ENST00000547276;ENST00000548688;ENST00000550994	D;D;D;D;D;D;D	0.89552	-2.53;-2.53;-2.53;-2.53;-2.53;-2.53;-2.53	3.81	3.81	0.43845	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.64402	D	0.000002	D	0.94489	0.8226	M	0.89214	3.015	0.58432	D	0.999996	D;P;P;P;D;B;P;D	0.89917	0.981;0.453;0.749;0.893;0.99;0.164;0.749;1.0	P;B;P;P;D;B;P;D	0.83275	0.855;0.38;0.631;0.597;0.965;0.161;0.631;0.996	D	0.94901	0.8056	10	0.87932	D	0	.	11.1785	0.48614	0.0:0.0:0.0:1.0	.	24;46;46;46;46;46;46;46	Q9BSM5;F8VRQ1;F8W6I7;F8VSB5;F8VXY0;P09651-3;P09651-2;P09651	.;.;.;.;.;.;.;ROA1_HUMAN	T	46;46;46;46;46;46;46;46;46;65;1	ENSP00000448617:M46T;ENSP00000448229:M46T;ENSP00000341826:M46T;ENSP00000333504:M46T;ENSP00000447260:M46T;ENSP00000447782:M65T;ENSP00000448917:M1T	ENSP00000333504:M46T	M	+	2	0	HNRNPA1	52961850	1.000000	0.71417	1.000000	0.80357	0.459000	0.32528	7.892000	0.87324	1.698000	0.51180	0.260000	0.18958	ATG	.	.	.	none		0.448	HNRNPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000405480.1	NM_031157		C	54675583	T	C	54675583	3	2	272	1	0	0	0	0	1	0	0	0	7264	1464	51	3	147	3	HNRNPA1	12	54675583	Missense_Mutation	SNP	T	TCGA-WN-A9G9-01A-12D-A36X-10		54675583	79176312	42	17203											
GNPTAB	79158	hgsc.bcm.edu	37	chr12	102147264	102147264	+	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	ccctgagaacagccttcactGtctgagcatctttatgattg	9	13	8	11	0	3	3	1	3	2	1	3	4	3	3	2	0	3	1	2	0	2	4	rs281865020		TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr12:102147264G>T	ENST00000299314.7	-	19	3750	c.3488C>A	c.(3487-3489)aCa>aAa	p.T1163K		NM_024312.4	NP_077288.2	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	1163					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						AGCCTTCACTGTCTGAGCATC	0.408																																					p.T1163K		Atlas-SNP	.											.	GNPTAB	120	.	0			c.C3488A						PASS	.						129	116	120					12																	102147264		2203	4300	6503	SO:0001583	missense	79158	exon19			TTCACTGTCTGAG	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.3488C>A	chr12.hg19:g.102147264G>T	ENSP00000299314:p.Thr1163Lys	110.0	0.0	.		134.0	14.0	.	NM_024312	A2RRQ9|Q3ZQK2|Q6IPW5|Q86TQ2|Q96N13|Q9ULL2	Missense_Mutation	SNP	ENST00000299314.7	hg19	CCDS9088.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.654854	0.88056	.	.	ENSG00000111670	ENST00000299314	D	0.81996	-1.56	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	D	0.87128	0.6100	L	0.31664	0.95	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.87818	0.2636	10	0.54805	T	0.06	-19.2071	19.2587	0.93959	0.0:0.0:1.0:0.0	.	1163	Q3T906	GNPTA_HUMAN	K	1163	ENSP00000299314:T1163K	ENSP00000299314:T1163K	T	-	2	0	GNPTAB	100671395	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.471000	0.97696	2.547000	0.85894	0.591000	0.81541	ACA	.	.	.	none		0.408	GNPTAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409182.1			T	102147264	G	T	102147264	3	4	272	1	0	0	0	0	1	0	0	0	6552	1377	48	4	294	4	GNPTAB	12	102147264	Missense_Mutation	SNP	G	TCGA-WN-A9G9-01A-12D-A36X-10	47471681	102147264	31704631	43	17204											
MYH7	4625	hgsc.bcm.edu	37	chr14	23902759	23902759	+	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	accttgccatactcggtctcGgcagtgactttgccaccctc	6	11	8	16	2	1	1	0	1	1	0	4	1	1	1	4	2	3	1	4	2	1	3	rs370743876		TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr14:23902759G>T	ENST00000355349.3	-	3	345	c.183C>A	c.(181-183)gcC>gcA	p.A61A		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	61					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		ACTCGGTCTCGGCAGTGACTT	0.567																																					p.A61A		Atlas-SNP	.											MYH7,colon,carcinoma,0,1	MYH7	349	.	0			c.C183A						PASS	.						127	98	108					14																	23902759		2203	4300	6503	SO:0001819	synonymous_variant	4625	exon3			GGTCTCGGCAGTG	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"Myosins / Myosin superfamily : Class II"	7577	protein-coding gene	gene with protein product		160760	"myopathy, distal 1", "myosin, heavy polypeptide 7, cardiac muscle, beta"	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.183C>A	chr14.hg19:g.23902759G>T		62.0	0.0	.		42.0	2.0	.	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Silent	SNP	ENST00000355349.3	hg19	CCDS9601.1																																																																																			.	.	.	alt		0.567	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257		T	23902759	G	T	23902759	2	4	272	1	0	0	0	0	0	0	0	1	10046	1103	39	4		4	MYH7	14	23902759	Silent	SNP	G	TCGA-WN-A9G9-01A-12D-A36X-10		23902759	83446781	44	17205											
FAM98B	283742	hgsc.bcm.edu	37	chr15	38776812	38776812	+	IGR	SNP	T	T	A																															gatccatatggaggaggtggTggtggtggtggtggtggtgg																								rs201831942		TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr15:38776812T>A	ENST00000491535.1	+	0	3111				FAM98B_ENST00000397609.2_Silent_p.G418G	NM_001042429.1	NP_001035894.1	Q52LJ0	FA98B_HUMAN	family with sequence similarity 98, member B							cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-splicing ligase complex (GO:0072669)	poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|skin(1)	8		all_cancers(109;3.11e-17)|all_epithelial(112;2.64e-15)|Lung NSC(122;2.11e-11)|all_lung(180;5.61e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;9e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0209)		GAGGAggtggtggtggtggtg	0.463																																					p.G418G		Atlas-SNP	.											.	FAM98B	53	.	0			c.T1254A						PASS	.						24	23	23					15																	38776812		1552	3434	4986	SO:0001628	intergenic_variant	283742	exon8			AGGTGGTGGTGGT		CCDS10047.2	15q14	2006-11-29		2005-11-20	ENSG00000171262	ENSG00000171262			26773	protein-coding gene	gene with protein product						12477932	Standard	NM_173611		Approved	FLJ38426	uc001zkc.3	Q52LJ0	OTTHUMG00000129831		chr15.hg19:g.38776812T>A		62.0	0.0	.		82.0	7.0	.	NM_173611	A8MUW5|Q8N935	Silent	SNP	ENST00000491535.1	hg19	CCDS42015.1																																																																																			.	.	.	none		0.463	FAM98B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252071.2	NM_173611		A	38776812	T	A	38776812	1	1	272	0	1	0	0	0	0	0	0	0	5664	1683	59	5		5	FAM98B	15	38776812	IGR	SNP	T	TCGA-WN-A9G9-01A-12D-A36X-10		38776812	63754580	45	17206	178	2									
FAM98B	283742	hgsc.bcm.edu	37	chr15	38776815	38776815	+	IGR	SNP	T	T	A																															ccatatggaggaggtggtggTggtggtggtggtggtggtgg																								rs201831942		TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr15:38776815T>A	ENST00000491535.1	+	0	3111				FAM98B_ENST00000397609.2_Silent_p.G419G	NM_001042429.1	NP_001035894.1	Q52LJ0	FA98B_HUMAN	family with sequence similarity 98, member B							cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-splicing ligase complex (GO:0072669)	poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|skin(1)	8		all_cancers(109;3.11e-17)|all_epithelial(112;2.64e-15)|Lung NSC(122;2.11e-11)|all_lung(180;5.61e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;9e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0209)		GAggtggtggtggtggtggtg	0.458																																					p.G419G		Atlas-SNP	.											.	FAM98B	53	.	0			c.T1257A						PASS	.																																			SO:0001628	intergenic_variant	283742	exon8			TGGTGGTGGTGGT		CCDS10047.2	15q14	2006-11-29		2005-11-20	ENSG00000171262	ENSG00000171262			26773	protein-coding gene	gene with protein product						12477932	Standard	NM_173611		Approved	FLJ38426	uc001zkc.3	Q52LJ0	OTTHUMG00000129831		chr15.hg19:g.38776815T>A		59.0	0.0	.		76.0	10.0	.	NM_173611	A8MUW5|Q8N935	Silent	SNP	ENST00000491535.1	hg19	CCDS42015.1																																																																																			.	.	.	none		0.458	FAM98B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252071.2	NM_173611		A	38776815	T	A	38776815	1	1	272	0	1	0	0	0	0	0	0	0	5664	1683	59	5		5	FAM98B	15	38776815	IGR	SNP	T	TCGA-WN-A9G9-01A-12D-A36X-10	3	38776815	63754577	46	17207	178	2									
PDE8A	5151	hgsc.bcm.edu	37	chr15	85652313	85652313	+	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	caggcaaacataaagacaggAgaaaaggctcactagacgtc	18	4	10	9	1	1	3	1	0	0	3	2	4	1	3	0	3	1	2	0	3	6	2			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr15:85652313A>C	ENST00000310298.4	+	13	1318	c.1066A>C	c.(1066-1068)Aga>Cga	p.R356R	PDE8A_ENST00000557957.1_Silent_p.R284R|PDE8A_ENST00000339708.5_Silent_p.R310R|PDE8A_ENST00000394553.1_Silent_p.R356R|PDE8A_ENST00000557819.2_3'UTR			O60658	PDE8A_HUMAN	phosphodiesterase 8A	356					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)	TAAAGACAGGAGAAAAGGCTC	0.368																																					p.R356R		Atlas-SNP	.											.	PDE8A	50	.	0			c.A1066C						PASS	.						111	106	108					15																	85652313		2203	4299	6502	SO:0001819	synonymous_variant	5151	exon12			GACAGGAGAAAAG	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.1066A>C	chr15.hg19:g.85652313A>C		375.0	0.0	.		454.0	45.0	.	NM_002605	B3KXE6|H0YMZ7|Q6P9H3|Q969I1|Q96PC9|Q96PD0|Q96PD1|Q96T71|Q9UMB7|Q9UMC3	Silent	SNP	ENST00000310298.4	hg19	CCDS10336.1																																																																																			.	.	.	none		0.368	PDE8A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309018.1	NM_002605		C	85652313	A	C	85652313	2	2	272	1	0	0	0	0	0	0	0	1	11660	296	11	5		5	PDE8A	15	85652313	Silent	SNP	A	TCGA-WN-A9G9-01A-12D-A36X-10	46875498	85652313	16879079	47	17208											
ZNF771	51333	hgsc.bcm.edu	37	chr16	30419477	30419477	+	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	atgagggtgaggagaagtatGaggtggtgaaactcaagatc	14	8	16	3	0	1	6	1	4	0	2	2	7	1	6	0	4	1	1	0	4	4	1			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr16:30419477G>A	ENST00000319296.5	+	2	480	c.103G>A	c.(103-105)Gag>Aag	p.E35K	ZNF771_ENST00000566625.1_Missense_Mutation_p.E35K|ZNF771_ENST00000564550.1_Missense_Mutation_p.E35K|ZNF771_ENST00000434417.1_Missense_Mutation_p.E35K			Q7L3S4	ZN771_HUMAN	zinc finger protein 771	35	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)							Colorectal(24;0.193)			ggagaagtatgaggtggTGAA	0.582																																					p.E35K		Atlas-SNP	.											.	ZNF771	1	.	0			c.G103A						PASS	.						206	234	225					16																	30419477		2176	4264	6440	SO:0001583	missense	51333	exon2			AAGTATGAGGTGG	BC026192	CCDS45460.1	16p11.2	2013-01-08				ENSG00000179965		"Zinc fingers, C2H2-type"	29653	protein-coding gene	gene with protein product						12477932	Standard	NM_016643		Approved	DSC43	uc010ver.2	Q7L3S4		ENST00000319296.5:c.103G>A	chr16.hg19:g.30419477G>A	ENSP00000323945:p.Glu35Lys	119.0	0.0	.		156.0	10.0	.	NM_001142305	Q8TAQ7|Q9NYI6	Missense_Mutation	SNP	ENST00000319296.5	hg19	CCDS45460.1	.	.	.	.	.	.	.	.	.	.	G	18.37	3.608829	0.66558	.	.	ENSG00000179965	ENST00000434417;ENST00000319296	T;T	0.07444	3.19;3.19	4.86	3.82	0.43975	.	.	.	.	.	T	0.04003	0.0112	N	0.08118	0	0.28185	N	0.92801	B	0.23854	0.092	B	0.10450	0.005	T	0.30149	-0.9988	9	0.10377	T	0.69	-6.4062	10.3652	0.44019	0.0:0.1994:0.8006:0.0	.	35	Q7L3S4	ZN771_HUMAN	K	35	ENSP00000416197:E35K;ENSP00000323945:E35K	ENSP00000323945:E35K	E	+	1	0	ZNF771	30326978	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.857000	0.39399	2.634000	0.89283	0.491000	0.48974	GAG	.	.	.	none		0.582	ZNF771-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434612.2	NM_016643		A	30419477	G	A	30419477	3	1	272	1	0	0	0	0	1	0	0	0	18156	1291	45	2	105	2	ZNF771	16	30419477	Missense_Mutation	SNP	G	TCGA-WN-A9G9-01A-12D-A36X-10		30419477	59935276	48	17209											
NEURL4	84461	hgsc.bcm.edu	37	chr17	7225239	7225239	+	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	tgaagacaaggccatgagcaTagccagcggcacgcactgcc	12	4	12	13	2	0	3	0	2	0	1	0	3	0	3	3	2	4	3	3	2	3	1			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr17:7225239T>A	ENST00000399464.2	-	17	2831	c.2816A>T	c.(2815-2817)tAt>tTt	p.Y939F	RP11-542C16.2_ENST00000575474.1_5'Flank|NEURL4_ENST00000570460.1_Missense_Mutation_p.Y915F|NEURL4_ENST00000315614.7_Missense_Mutation_p.Y937F	NM_032442.2	NP_115818.2	Q96JN8	NEUL4_HUMAN	neuralized E3 ubiquitin protein ligase 4	939	NHR 5. {ECO:0000255|PROSITE- ProRule:PRU00400}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GCCATGAGCATAGCCAGCGGC	0.587																																					p.Y939F		Atlas-SNP	.											.	NEURL4	192	.	0			c.A2816T						PASS	.						102	103	103					17																	7225239		2139	4239	6378	SO:0001583	missense	84461	exon17			TGAGCATAGCCAG		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.2816A>T	chr17.hg19:g.7225239T>A	ENSP00000382390:p.Tyr939Phe	22.0	0.0	.		34.0	4.0	.	NM_032442	Q6GPI8|Q96IU9|Q9H0B0	Missense_Mutation	SNP	ENST00000399464.2	hg19	CCDS42251.1	.	.	.	.	.	.	.	.	.	.	T	15.17	2.752850	0.49362	.	.	ENSG00000215041	ENST00000315614;ENST00000399464	T;T	0.24723	1.87;1.84	5.87	5.87	0.94306	NEUZ (3);	0.066390	0.64402	D	0.000005	T	0.19765	0.0475	N	0.03294	-0.36	0.37210	D	0.904753	D;D	0.63046	0.99;0.992	P;P	0.61722	0.829;0.893	T	0.28586	-1.0039	10	0.12430	T	0.62	-12.3966	8.7135	0.34397	0.0:0.084:0.0:0.916	.	937;939	Q96JN8-2;Q96JN8	.;NEUL4_HUMAN	F	937;939	ENSP00000319826:Y937F;ENSP00000382390:Y939F	ENSP00000319826:Y937F	Y	-	2	0	NEURL4	7165963	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	4.145000	0.58065	2.244000	0.73946	0.533000	0.62120	TAT	.	.	.	none		0.587	NEURL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255434.2	NM_032442		A	7225239	T	A	7225239	3	1	272	1	0	0	0	0	1	0	0	0	10354	1406	49	5	1924	5	NEURL4	17	7225239	Missense_Mutation	SNP	T	TCGA-WN-A9G9-01A-12D-A36X-10		7225239	73969971	49	17210											
MED1	5469	hgsc.bcm.edu	37	chr17	37595435	37595435	+	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	caccttagctgctgtacaagCtccggacagctctgaaatca	11	9	8	13	1	2	1	1	1	1	0	3	2	3	2	2	1	5	5	2	1	4	2			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr17:37595435C>A	ENST00000394287.3	-	6	616	c.411G>T	c.(409-411)gaG>gaT	p.E137D	MED1_ENST00000300651.6_Missense_Mutation_p.E137D			O95243	MBD4_HUMAN	mediator complex subunit 1	0	MBD. {ECO:0000255|PROSITE- ProRule:PRU00338}.				base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)			NS(1)|breast(2)|cervix(3)|kidney(3)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(7)|urinary_tract(1)	59		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)		GCTGTACAAGCTCCGGACAGC	0.348										HNSCC(31;0.082)																											p.E137D	Pancreas(21;279 768 2492 4877 24026)	Atlas-SNP	.											.	MED1	123	.	0			c.G411T						PASS	.						92	90	90					17																	37595435		2203	4300	6503	SO:0001583	missense	5469	exon6			TACAAGCTCCGGA	L40366	CCDS11336.1	17q12	2007-07-30	2007-07-30	2007-07-30	ENSG00000125686	ENSG00000125686			9234	protein-coding gene	gene with protein product		604311	"PPAR binding protein"	TRIP2, PPARGBP, PPARBP		9325263, 10485914	Standard	NM_004774		Approved	PBP, TRAP220, RB18A, DRIP230, CRSP200, CRSP1	uc002hrv.4	Q15648	OTTHUMG00000133216	ENST00000394287.3:c.411G>T	chr17.hg19:g.37595435C>A	ENSP00000377828:p.Glu137Asp	58.0	0.0	.		63.0	7.0	.	NM_004774	B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Missense_Mutation	SNP	ENST00000394287.3	hg19		.	.	.	.	.	.	.	.	.	.	C	11.87	1.768760	0.31320	.	.	ENSG00000125686	ENST00000394287;ENST00000300651	T	0.36699	1.24	5.35	2.31	0.28768	Mediator complex, subunit Med1, metazoa/fungi (1);	.	.	.	.	T	0.48624	0.1510	M	0.70275	2.135	0.46222	D	0.998931	P;P	0.48089	0.905;0.724	P;B	0.55667	0.781;0.183	T	0.42732	-0.9434	9	0.56958	D	0.05	-15.0086	8.7576	0.34654	0.0:0.6417:0.0:0.3583	.	137;137	Q15648;Q15648-3	MED1_HUMAN;.	D	137	ENSP00000300651:E137D	ENSP00000300651:E137D	E	-	3	2	MED1	34848961	0.837000	0.29446	1.000000	0.80357	0.984000	0.73092	-0.167000	0.09940	0.340000	0.23745	0.591000	0.81541	GAG	.	.	.	none		0.348	MED1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000256944.1	NM_004774		A	37595435	C	A	37595435	3	1	272	1	0	0	0	0	1	0	0	0	9432	796	28	4	4382	4	MED1	17	37595435	Missense_Mutation	SNP	C	TCGA-WN-A9G9-01A-12D-A36X-10	30370196	37595435	43599775	50	17211											
TOB1	10140	hgsc.bcm.edu	37	chr17	48940877	48940877	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggctgagtggaccggggcaTgaaggtagggcttacagcag	10	6	18	7	1	0	2	0	2	0	0	0	3	0	3	1	6	2	5	1	6	3	2			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr17:48940877T>C	ENST00000268957.3	-	3	930	c.502A>G	c.(502-504)Atg>Gtg	p.M168V	TOB1_ENST00000509385.1_5'UTR|TOB1_ENST00000499247.2_Missense_Mutation_p.M168V	NM_001243877.1	NP_001230806.1	P50616	TOB1_HUMAN	transducer of ERBB2, 1	168					negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060212)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of translation (GO:0017148)|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 signal transduction (GO:0009967)|SMAD protein import into nucleus (GO:0007184)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	receptor tyrosine kinase binding (GO:0030971)|SH3/SH2 adaptor activity (GO:0005070)|transcription corepressor activity (GO:0003714)			breast(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			GACCGGGGCATGAAGGTAGGG	0.522											OREG0024576	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.M168V	NSCLC(144;643 1919 24513 29423 40686)	Atlas-SNP	.											.	TOB1	40	.	0			c.A502G						PASS	.						91	76	81					17																	48940877		2203	4300	6503	SO:0001583	missense	10140	exon2			GGGGCATGAAGGT	D38305	CCDS11576.1	17q21.33	2012-08-14			ENSG00000141232	ENSG00000141232			11979	protein-coding gene	gene with protein product		605523		TROB1		8632892, 17785442	Standard	NM_005749		Approved	TOB, TROB	uc002isw.3	P50616	OTTHUMG00000162277	ENST00000268957.3:c.502A>G	chr17.hg19:g.48940877T>C	ENSP00000268957:p.Met168Val	113.0	0.0	.	958	143.0	19.0	.	NM_005749	B2R9T0|D3DTY3|Q4KMQ0	Missense_Mutation	SNP	ENST00000268957.3	hg19	CCDS11576.1	.	.	.	.	.	.	.	.	.	.	T	5.997	0.367857	0.11352	.	.	ENSG00000141232	ENST00000499247;ENST00000268957	T;T	0.40225	1.04;1.04	5.67	4.58	0.56647	.	0.000000	0.85682	D	0.000000	T	0.37265	0.0997	L	0.52266	1.64	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.10405	-1.0631	10	0.29301	T	0.29	.	12.9615	0.58462	0.0:0.0:0.1352:0.8648	.	168	P50616	TOB1_HUMAN	V	168	ENSP00000427695:M168V;ENSP00000268957:M168V	ENSP00000268957:M168V	M	-	1	0	TOB1	46295876	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.903000	0.69877	0.964000	0.38108	0.533000	0.62120	ATG	.	.	.	none		0.522	TOB1-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000368364.1			C	48940877	T	C	48940877	3	2	272	1	0	0	0	0	1	0	0	0	16359	1464	51	3	539	3	TOB1	17	48940877	Missense_Mutation	SNP	T	TCGA-WN-A9G9-01A-12D-A36X-10	11345442	48940877	32254333	51	17212											
GNA13	10672	hgsc.bcm.edu	37	chr17	63049759	63049759	+	Frame_Shift_Del	DEL	G	G	-																															tgggggcccgggtatcaaacGacatcatcttatctccatgt																										TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr17:63049759delG	ENST00000439174.2	-	2	616	c.371delC	c.(370-372)tcgfs	p.S124fs	GNA13_ENST00000541118.1_Frame_Shift_Del_p.S29fs|RP11-583F2.5_ENST00000581796.1_RNA	NM_006572.4	NP_006563.2	Q14344	GNA13_HUMAN	guanine nucleotide binding protein (G protein), alpha 13	124					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						GGTATCAAACGACATCATCTT	0.468																																					p.S124fs		Atlas-INDEL	.											.	GNA13	69	.	0			c.372delG						PASS	.						148	144	146					17																	63049759		2203	4300	6503	SO:0001589	frameshift_variant	10672	exon2			.	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.371delC	chr17.hg19:g.63049759delG	ENSP00000400717:p.Ser124fs	106.0	0.0	0		122.0	12.0	0.0983607	NM_006572	B2R977|B7Z7R0|F5H1G8|Q8TD70	Frame_Shift_Del	DEL	ENST00000439174.2	hg19	CCDS11661.1																																																																																			.	.	.	none		0.468	GNA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445720.1	NM_006572		-	63049759	G	-	63049759	7	5	272	1	0	1	0	1	0	0	0	0	6508	1059	37	0	774	0	GNA13	17	63049759	Frame_Shift_Del	DEL	G	TCGA-WN-A9G9-01A-12D-A36X-10	14108882	63049759	18145451	52	17213											
HELZ	9931	hgsc.bcm.edu	37	chr17	65163789	65163789	+	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	cgtccagccaaagtatcttcAgaaagtgtttcagtaagctt	12	12	8	9	1	3	1	2	0	1	1	4	1	4	1	2	0	2	4	2	0	4	5			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr17:65163789A>T	ENST00000358691.5	-	14	1720	c.1554T>A	c.(1552-1554)tcT>tcA	p.S518S	HELZ_ENST00000580168.1_Silent_p.S518S	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	518						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)					AAGTATCTTCAGAAAGTGTTT	0.428																																					p.S518S		Atlas-SNP	.											.	HELZ	160	.	0			c.T1554A						PASS	.						112	100	103					17																	65163789		1862	4115	5977	SO:0001819	synonymous_variant	9931	exon14			ATCTTCAGAAAGT	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.1554T>A	chr17.hg19:g.65163789A>T		247.0	0.0	.		308.0	41.0	.	NM_014877	I6L9H4	Silent	SNP	ENST00000358691.5	hg19	CCDS42374.1																																																																																			.	.	.	none		0.428	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		T	65163789	A	T	65163789	2	4	272	1	0	0	0	0	0	0	0	1	7056	175	7	5		5	HELZ	17	65163789	Silent	SNP	A	TCGA-WN-A9G9-01A-12D-A36X-10	2114030	65163789	16031421	53	17214											
USH1G	124590	hgsc.bcm.edu	37	chr17	72915897	72915897	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgggggagctctgcagcCgaccccgcggcgctcccacc	4	4	15	18	4	1	0	0	0	1	0	2	2	2	1	5	4	3	4	5	4	0	0			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr17:72915897C>T	ENST00000319642.1	-	2	1216	c.1034G>A	c.(1033-1035)cGg>cAg	p.R345Q		NM_001282489.1|NM_173477.2	NP_001269418.1|NP_775748.2	Q495M9	USH1G_HUMAN	Usher syndrome 1G (autosomal recessive)	345					equilibrioception (GO:0050957)|inner ear morphogenesis (GO:0042472)|inner ear receptor cell differentiation (GO:0060113)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	spectrin binding (GO:0030507)		HN1/USH1G(2)	endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(1)|skin(3)	14	all_lung(278;0.172)|Lung NSC(278;0.207)					GCTCTGCAGCCGACCCCGCGG	0.672																																					p.R345Q		Atlas-SNP	.											.	USH1G	40	.	0			c.G1034A						PASS	.						34	42	39					17																	72915897		2202	4293	6495	SO:0001583	missense	124590	exon2			TGCAGCCGACCCC	AK091243	CCDS32725.1	17q25.1	2013-01-10			ENSG00000182040	ENSG00000182040		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	16356	protein-coding gene	gene with protein product		607696				12588794	Standard	NM_001282489		Approved	Sans, FLJ33924, ANKS4A	uc002jme.1	Q495M9	OTTHUMG00000178864	ENST00000319642.1:c.1034G>A	chr17.hg19:g.72915897C>T	ENSP00000320076:p.Arg345Gln	117.0	0.0	.		141.0	16.0	.	NM_173477	Q8N251	Missense_Mutation	SNP	ENST00000319642.1	hg19	CCDS32725.1	.	.	.	.	.	.	.	.	.	.	C	9.720	1.159540	0.21454	.	.	ENSG00000182040	ENST00000319642	T	0.70631	-0.5	4.34	4.34	0.51931	.	0.065307	0.64402	D	0.000009	T	0.53012	0.1770	L	0.34521	1.04	0.46499	D	0.999071	P	0.44006	0.824	B	0.27887	0.084	T	0.56842	-0.7912	10	0.20046	T	0.44	-24.1946	17.0851	0.86609	0.0:1.0:0.0:0.0	.	345	Q495M9	USH1G_HUMAN	Q	345	ENSP00000320076:R345Q	ENSP00000320076:R345Q	R	-	2	0	USH1G	70427492	1.000000	0.71417	0.999000	0.59377	0.901000	0.52897	1.950000	0.40323	2.275000	0.75901	0.555000	0.69702	CGG	.	.	.	none		0.672	USH1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443676.1	NM_173477		T	72915897	C	T	72915897	3	4	272	1	0	0	0	0	1	0	0	0	17047	652	23	1	359	1	USH1G	17	72915897	Missense_Mutation	SNP	C	TCGA-WN-A9G9-01A-12D-A36X-10	7752108	72915897	8279313	54	17215											
ABCA7	10347	hgsc.bcm.edu	37	chr19	1054009	1054009	+	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	cctgatggccctgcagatggCagctgcgggcagcacctatg	7	7	14	13	1	0	2	0	1	0	1	0	2	0	2	3	3	4	5	3	3	1	1			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr19:1054009C>T	ENST00000263094.6	+	26	3708	c.3477C>T	c.(3475-3477)ggC>ggT	p.G1159G	ABCA7_ENST00000435683.2_Silent_p.G1021G|ABCA7_ENST00000433129.1_Silent_p.G1159G	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1159					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)		CTGCAGATGGCAGCTGCGGGC	0.592																																					p.G1159G		Atlas-SNP	.											.	ABCA7	174	.	0			c.C3477T						PASS	.						75	85	82					19																	1054009		2203	4300	6503	SO:0001819	synonymous_variant	10347	exon26			AGATGGCAGCTGC	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.3477C>T	chr19.hg19:g.1054009C>T		136.0	0.0	.		150.0	6.0	.	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	hg19	CCDS12055.1																																																																																			.	.	.	none		0.592	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		T	1054009	C	T	1054009	2	4	272	1	0	0	0	0	0	0	0	1	37	697	25	2		2	ABCA7	19	1054009	Silent	SNP	C	TCGA-WN-A9G9-01A-12D-A36X-10		1054009	58074974	55	17216											
COL5A3	50509	hgsc.bcm.edu	37	chr19	10112281	10112281	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggaatcatctccttcttcAtcctccctggctgccttggt	4	15	8	14	0	4	0	2	0	2	0	7	1	6	1	4	3	1	1	4	3	1	3			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr19:10112281A>G	ENST00000264828.3	-	8	1114	c.1029T>C	c.(1027-1029)gaT>gaC	p.D343D		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	343	Nonhelical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			CTCCTTCTTCATCCTCCCTGG	0.542											OREG0025228	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D343D		Atlas-SNP	.											.	COL5A3	243	.	0			c.T1029C						PASS	.						103	99	100					19																	10112281		2203	4300	6503	SO:0001819	synonymous_variant	50509	exon8			TTCTTCATCCTCC	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.1029T>C	chr19.hg19:g.10112281A>G		121.0	0.0	.	662	122.0	10.0	.	NM_015719	Q9NZQ6	Silent	SNP	ENST00000264828.3	hg19	CCDS12222.1																																																																																			.	.	.	none		0.542	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719		G	10112281	A	G	10112281	2	3	272	1	0	0	0	0	0	0	0	1	3700	214	8	3		3	COL5A3	19	10112281	Silent	SNP	A	TCGA-WN-A9G9-01A-12D-A36X-10	9058272	10112281	49016702	56	17217											
RYR1	6261	hgsc.bcm.edu	37	chr19	38997149	38997149	+	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	gcagaaaattaccacaacacGtggggacggaagaagaagca	18	3	12	8	2	0	3	0	0	0	3	0	5	0	5	1	3	3	2	1	3	7	1			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr19:38997149G>A	ENST00000359596.3	+	56	8655	c.8655G>A	c.(8653-8655)acG>acA	p.T2885T	RYR1_ENST00000355481.4_Silent_p.T2885T|RYR1_ENST00000360985.3_Silent_p.T2885T			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2885	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.T2885T(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	ACCACAACACGTGGGGACGGA	0.587																																					p.T2885T		Atlas-SNP	.											.	RYR1	708	.	1	Substitution - coding silent(1)	lung(1)	c.G8655A						PASS	.						61	59	59					19																	38997149		2203	4300	6503	SO:0001819	synonymous_variant	6261	exon56			CAACACGTGGGGA	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.8655G>A	chr19.hg19:g.38997149G>A		182.0	0.0	.		175.0	15.0	.	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	hg19	CCDS33011.1																																																																																			.	.	.	none		0.587	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			A	38997149	G	A	38997149	2	1	272	1	0	0	0	0	0	0	0	1	13781	1132	40	1		1	RYR1	19	38997149	Silent	SNP	G	TCGA-WN-A9G9-01A-12D-A36X-10	28884868	38997149	20131834	57	17218											
NUMBL	9253	hgsc.bcm.edu	37	chr19	41192843	41192843	+	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	cgtcctgcaggtttctggggGccccggggccccacaggggg	3	6	18	14	2	1	0	0	0	1	0	2	0	2	0	5	7	1	2	5	7	0	1			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr19:41192843G>T	ENST00000252891.4	-	2	249	c.82C>A	c.(82-84)Ccc>Acc	p.P28T	NUMBL_ENST00000540131.1_Intron|NUMBL_ENST00000598779.1_Intron|NUMBL_ENST00000599594.1_5'UTR	NM_004756.3	NP_004747.1	Q9Y6R0	NUMBL_HUMAN	numb homolog (Drosophila)-like	28					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)			GTTTCTGGGGGCCCCGGGGCC	0.672																																					p.P28T		Atlas-SNP	.											.	NUMBL	49	.	0			c.C82A						PASS	.						3	4	4					19																	41192843		1692	3271	4963	SO:0001583	missense	9253	exon2			CTGGGGGCCCCGG	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.82C>A	chr19.hg19:g.41192843G>T	ENSP00000252891:p.Pro28Thr	166.0	0.0	.		148.0	24.0	.	NM_004756	Q7Z4J9	Missense_Mutation	SNP	ENST00000252891.4	hg19	CCDS12561.1	.	.	.	.	.	.	.	.	.	.	G	19.52	3.843968	0.71488	.	.	ENSG00000105245	ENST00000252891	T	0.54279	0.58	4.48	4.48	0.54585	.	0.369326	0.19810	N	0.105553	T	0.30103	0.0754	N	0.08118	0	0.80722	D	1	P;P	0.38395	0.629;0.629	B;B	0.33568	0.166;0.166	T	0.17592	-1.0364	10	0.34782	T	0.22	-8.0968	12.5039	0.55970	0.0:0.0:1.0:0.0	.	28;28	A8K033;Q9Y6R0	.;NUMBL_HUMAN	T	28	ENSP00000252891:P28T	ENSP00000252891:P28T	P	-	1	0	NUMBL	45884683	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	2.611000	0.46334	2.335000	0.79485	0.297000	0.19635	CCC	.	.	.	none		0.672	NUMBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462749.2	NM_004756		T	41192843	G	T	41192843	3	4	272	1	0	0	0	0	1	0	0	0	10759	1203	42	4	1783	4	NUMBL	19	41192843	Missense_Mutation	SNP	G	TCGA-WN-A9G9-01A-12D-A36X-10	2195694	41192843	17936140	58	17219											
ZNF226	7769	hgsc.bcm.edu	37	chr19	44680079	44680102	+	In_Frame_Del	DEL	AAATCTTATAGACCCAATGATTAT	AAATCTTATAGACCCAATGATTAT	-																															atagagtacacaaaagtgaaAaatcttatagacccaatgat																								rs376461816|rs371556470|rs533087898	byFrequency	TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	AAATCTTATAGACCCAATGATTAT	AAATCTTATAGACCCAATGATTAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr19:44680079_44680102delAAATCTTATAGACCCAATGATTAT	ENST00000590089.1	+	7	1031_1054	c.664_687delAAATCTTATAGACCCAATGATTAT	c.(664-687)aaatcttatagacccaatgattatdel	p.KSYRPNDY222del	ZNF226_ENST00000454662.2_In_Frame_Del_p.KSYRPNDY222del|ZNF226_ENST00000588883.1_3'UTR|ZNF226_ENST00000337433.5_In_Frame_Del_p.KSYRPNDY222del			Q9NYT6	ZN226_HUMAN	zinc finger protein 226	222					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)						Prostate(69;0.0352)|all_neural(266;0.202)				CAAAAGTGAAAAATCTTATAGACCCAATGATTATGAAAAAGACA	0.339																																					p.221_229del	Pancreas(115;581 1665 13228 19278 50070)	Pindel	.											.	.	.	.	0			c.663_686del						PASS	.																																			SO:0001651	inframe_deletion	7769	exon6			.	AF024707	CCDS46102.1, CCDS46103.1	19q13.31	2013-01-08	2012-09-11	2012-09-11	ENSG00000167380	ENSG00000167380		"Zinc fingers, C2H2-type", "-"	13019	protein-coding gene	gene with protein product							Standard	NM_001146220		Approved		uc002oyp.3	Q9NYT6		ENST00000590089.1:c.664_687delAAATCTTATAGACCCAATGATTAT	chr19.hg19:g.44680079_44680102delAAATCTTATAGACCCAATGATTAT	ENSP00000465121:p.Lys222_Tyr229del	75.0	0.0	.		87.0	10.0	0.115	NM_001032372	Q8WWE6|Q96TE6|Q9NS44	In_Frame_Del	DEL	ENST00000590089.1	hg19	CCDS46102.1																																																																																			.	.	.	none		0.339	ZNF226-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460712.1			-	44680102	AAATCTTATAGACCCAATGATTAT	-	44680079	7	5	272	1	0	1	0	1	0	0	0	0	17792	15	1	0	732	0	ZNF226	19	44680079	In_Frame_Del	DEL	AAATCTTATAGACCCAATGATTAT	TCGA-WN-A9G9-01A-12D-A36X-10	3487236	44680079	14448904	59	17220											
GEMIN7	79760	hgsc.bcm.edu	37	chr19	45593461	45593461	+	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	tggctttgcccctgatggacGcagagcccccttgaggccag	6	8	13	14	1	0	3	0	2	0	1	0	4	0	4	5	3	2	2	5	3	0	2			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr19:45593461G>T	ENST00000270257.4	+	3	336	c.89G>T	c.(88-90)cGc>cTc	p.R30L	PPP1R37_ENST00000221462.4_5'Flank|GEMIN7_ENST00000391951.2_Missense_Mutation_p.R30L|CTB-179K24.3_ENST00000586556.1_RNA|PPP1R37_ENST00000421905.1_5'Flank|GEMIN7_ENST00000591607.1_Missense_Mutation_p.R30L|GEMIN7_ENST00000591747.1_Missense_Mutation_p.R30L|CTB-179K24.3_ENST00000586744.1_RNA	NM_001007269.1|NM_001007270.1|NM_024707.2	NP_001007270.1|NP_001007271.1|NP_078983.1	Q9H840	GEMI7_HUMAN	gem (nuclear organelle) associated protein 7	30					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				endometrium(1)|kidney(1)|lung(4)|ovary(1)	7		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0131)		CCTGATGGACGCAGAGCCCCC	0.622																																					p.R30L		Atlas-SNP	.											GEMIN7,right_lower_lobe,carcinoma,0,1	GEMIN7	18	.	0			c.G89T						PASS	.						60	63	62					19																	45593461		2203	4300	6503	SO:0001583	missense	79760	exon3			ATGGACGCAGAGC	AK024018	CCDS12654.1	19q13.32	2008-02-05				ENSG00000142252			20045	protein-coding gene	gene with protein product		607419				12065586	Standard	NM_024707		Approved	FLJ13956	uc002pap.1	Q9H840		ENST00000270257.4:c.89G>T	chr19.hg19:g.45593461G>T	ENSP00000270257:p.Arg30Leu	66.0	0.0	.		71.0	3.0	.	NM_024707	Q6IA34	Missense_Mutation	SNP	ENST00000270257.4	hg19	CCDS12654.1	.	.	.	.	.	.	.	.	.	.	G	8.438	0.850206	0.17034	.	.	ENSG00000142252	ENST00000270257;ENST00000391951	.	.	.	4.33	3.19	0.36642	.	0.062984	0.64402	D	0.000006	T	0.47040	0.1424	L	0.51422	1.61	0.80722	D	1	B	0.31519	0.327	B	0.30572	0.117	T	0.41324	-0.9515	9	0.26408	T	0.33	0.2346	10.1352	0.42701	0.0:0.332:0.668:0.0	.	30	Q9H840	GEMI7_HUMAN	L	30	.	ENSP00000270257:R30L	R	+	2	0	GEMIN7	50285301	0.995000	0.38212	0.995000	0.50966	0.373000	0.29922	1.634000	0.37123	2.357000	0.79964	0.555000	0.69702	CGC	.	.	.	none		0.622	GEMIN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457533.1			T	45593461	G	T	45593461	3	4	272	1	0	0	0	0	1	0	0	0	6340	1087	38	4	91	4	GEMIN7	19	45593461	Missense_Mutation	SNP	G	TCGA-WN-A9G9-01A-12D-A36X-10	913382	45593461	13535522	60	17221											
TP53RK	112858	hgsc.bcm.edu	37	chr20	45315710	45315710	+	3'UTR	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgtgcattcgagccaaaacCtgcccaattgtcttggctaa	10	11	8	12	2	1	0	0	0	1	0	3	1	1	0	3	1	4	2	3	1	4	4			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr20:45315710C>T	ENST00000372102.3	-	0	474				RP1-28H20.3_ENST00000606362.1_lincRNA			Q96S44	PRPK_HUMAN	TP53 regulating kinase						lipopolysaccharide biosynthetic process (GO:0009103)|protein phosphorylation (GO:0006468)|tRNA processing (GO:0008033)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|hydrolase activity (GO:0016787)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|large_intestine(1)|lung(4)|skin(1)	7		Myeloproliferative disorder(115;0.0122)				GAGCCAAAACCTGCCCAATTG	0.478																																					p.Q148Q		Atlas-SNP	.											.	TP53RK	13	.	0			c.G444A						PASS	.						138	152	147					20																	45315710		2203	4300	6503	SO:0001624	3_prime_UTR_variant	112858	exon2			CAAAACCTGCCCA		CCDS13401.1	20q13.2	2014-05-14	2004-05-10	2004-05-12	ENSG00000172315	ENSG00000172315			16197	protein-coding gene	gene with protein product		608679	"chromosome 20 open reading frame 64"	C20orf64		11546806, 12914926	Standard	NM_033550		Approved	dJ101A2.2, prpk, Nori-2p, BUD32	uc002xsk.3	Q96S44	OTTHUMG00000085887	ENST00000372102.3:c.*83G>A	chr20.hg19:g.45315710C>T		92.0	0.0	.		149.0	15.0	.	NM_033550	B3KU44|Q3T977|Q5JZ01|Q6NZ60|Q96FM7|Q9NQE6	Silent	SNP	ENST00000372102.3	hg19																																																																																				.	.	.	none		0.478	TP53RK-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000193688.1	NM_033550		T	45315710	C	T	45315710	1	4	272	0	1	0	0	0	0	0	0	0	16402	680	24	2		2	TP53RK	20	45315710	3'UTR	SNP	C	TCGA-WN-A9G9-01A-12D-A36X-10		45315710	17709810	61	17222											
DOK5	55816	hgsc.bcm.edu	37	chr20	53205106	53205106	+	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	tagggatttatttcaatgacGatacctccaagacttttgct	11	15	7	8	1	1	2	1	1	0	1	2	4	2	3	2	1	2	1	2	1	5	7			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr20:53205106G>A	ENST00000262593.5	+	3	609	c.259G>A	c.(259-261)Gat>Aat	p.D87N	DOK5_ENST00000395939.1_5'UTR	NM_018431.3	NP_060901.2	Q9P104	DOK5_HUMAN	docking protein 5	87	PH.				MAPK cascade (GO:0000165)|nervous system development (GO:0007399)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)		receptor signaling protein activity (GO:0005057)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(2)|skin(1)	19			Colorectal(105;0.202)			TTTCAATGACGATACCTCCAA	0.418																																					p.D87N		Atlas-SNP	.											.	DOK5	54	.	0			c.G259A						PASS	.						156	150	152					20																	53205106		2203	4300	6503	SO:0001583	missense	55816	exon3			AATGACGATACCT	AF132732	CCDS13446.1, CCDS13447.1	20q13.2	2013-01-10	2002-11-28	2002-11-29	ENSG00000101134	ENSG00000101134		"Pleckstrin homology (PH) domain containing"	16173	protein-coding gene	gene with protein product		608334	"chromosome 20 open reading frame 180"	C20orf180		11470823	Standard	XM_005260451		Approved	dJ805C22.1	uc002xwy.3	Q9P104	OTTHUMG00000032778	ENST00000262593.5:c.259G>A	chr20.hg19:g.53205106G>A	ENSP00000262593:p.Asp87Asn	159.0	0.0	.		186.0	20.0	.	NM_018431	Q5T7Y0|Q5TE53|Q8TEW7|Q96H13|Q9BZ24|Q9NQF4|Q9Y411	Missense_Mutation	SNP	ENST00000262593.5	hg19	CCDS13446.1	.	.	.	.	.	.	.	.	.	.	G	16.03	3.006212	0.54361	.	.	ENSG00000101134	ENST00000262593	D	0.86164	-2.08	5.61	5.61	0.85477	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.044516	0.85682	D	0.000000	T	0.80571	0.4648	L	0.43152	1.355	0.80722	D	1	P	0.39250	0.665	B	0.24155	0.051	T	0.79374	-0.1830	10	0.25106	T	0.35	-18.4349	18.9956	0.92812	0.0:0.0:1.0:0.0	.	87	Q9P104	DOK5_HUMAN	N	87	ENSP00000262593:D87N	ENSP00000262593:D87N	D	+	1	0	DOK5	52638513	1.000000	0.71417	0.372000	0.25991	0.707000	0.40811	4.931000	0.63469	2.807000	0.96579	0.557000	0.71058	GAT	.	.	.	none		0.418	DOK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079777.2			A	53205106	G	A	53205106	3	1	272	1	0	0	0	0	1	0	0	0	4702	1058	37	1	269	1	DOK5	20	53205106	Missense_Mutation	SNP	G	TCGA-WN-A9G9-01A-12D-A36X-10	7889396	53205106	9820414	62	17223											
DDX17	11015	hgsc.bcm.edu	37	chr22	38882032	38882032	+	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	1	0	0	0	0	0	0	0	0	catattggtagctcccggagGctgtgcaaactgttgtgaca	9	11	12	9	1	0	1	0	1	0	0	1	2	1	2	1	3	3	5	1	3	3	4			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chr22:38882032G>T	ENST00000216014.4	+	0	1728				DDX17_ENST00000396821.3_Missense_Mutation_p.P702T|DDX17_ENST00000381633.3_Missense_Mutation_p.P623T|DDX17_ENST00000444597.1_Missense_Mutation_p.P152T	NM_006855.2	NP_006846.1	O43731	ERD23_HUMAN	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3						activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein retention in ER lumen (GO:0006621)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ER retention sequence binding (GO:0046923)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)	13	Melanoma(58;0.0286)					GCTCCCGGAGGCTGTGCAAAC	0.547																																					p.P702T	Ovarian(11;103 529 24120 28493 32980)	Atlas-SNP	.											.	DDX17	73	.	0			c.C2104A						PASS	.						170	154	160					22																	38882032		2203	4300	6503	SO:0001628	intergenic_variant	10521	exon13			CCGGAGGCTGTGC	AL035081	CCDS13972.1, CCDS46705.1	22q13	2008-05-02			ENSG00000100196	ENSG00000100196			6306	protein-coding gene	gene with protein product							Standard	NM_006855		Approved		uc003avu.3	O43731	OTTHUMG00000153520		chr22.hg19:g.38882032G>T		99.0	0.0	.		128.0	14.0	.	NM_001098504	A8K7T7|B8ZZ26|O95557|Q4V750|Q4V767|Q53FP4|Q53GK1	Missense_Mutation	SNP	ENST00000216014.4	hg19	CCDS13972.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.756221	0.49362	.	.	ENSG00000100201	ENST00000396821;ENST00000381633;ENST00000415748;ENST00000444597;ENST00000403230;ENST00000404499	T;T;T	0.27104	1.71;1.73;1.69	5.42	5.42	0.78866	.	0.214763	0.37577	N	0.002024	T	0.37019	0.0988	N	0.24115	0.695	0.58432	D	0.999996	P;P;D	0.71674	0.798;0.872;0.998	B;P;D	0.64687	0.284;0.476;0.928	T	0.08889	-1.0700	10	0.36615	T	0.2	-9.9176	19.2201	0.93793	0.0:0.0:1.0:0.0	.	704;700;154	Q59F66;Q92841-4;Q9UQL5	.;.;.	T	702;623;154;152;700;704	ENSP00000380033:P702T;ENSP00000371046:P623T;ENSP00000385536:P700T	ENSP00000371046:P623T	P	-	1	0	DDX17	37211978	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.900000	0.75687	2.524000	0.85096	0.655000	0.94253	CCT	.	.	.	none		0.547	KDELR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331474.1			T	38882032	G	T	38882032	1	4	272	0	1	0	0	0	0	0	0	0	4346	1203	42	4		4	DDX17	22	38882032	IGR	SNP	G	TCGA-WN-A9G9-01A-12D-A36X-10		38882032	12422534	63	17224											
RBM10	8241	hgsc.bcm.edu	37	chrX	47044733	47044733	+	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	gagagacagcacaccagcatGgatctcccgaaattggccag	13	5	11	12	1	1	1	0	0	1	1	2	5	1	2	3	2	2	2	3	2	1	1			TCGA-WN-A9G9-01A-12D-A36X-10	TCGA-WN-A9G9-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e78e2342-adb4-4c7b-96ae-4e2ccb668d49	394f018a-b0e0-40a9-afd2-2a1a4f552485	g.chrX:47044733G>C	ENST00000377604.3	+	19	2875	c.2133G>C	c.(2131-2133)atG>atC	p.M711I	RBM10_ENST00000345781.6_Missense_Mutation_p.M634I|RBM10_ENST00000329236.7_Missense_Mutation_p.M633I	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	711					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						ACACCAGCATGGATCTCCCGA	0.632																																					p.M776I	Melanoma(171;120 2705 19495 39241)	Atlas-SNP	.											.	RBM10	117	.	0			c.G2328C						PASS	.						37	34	35					X																	47044733		2203	4300	6503	SO:0001583	missense	8241	exon19			CAGCATGGATCTC	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.2133G>C	chrX.hg19:g.47044733G>C	ENSP00000366829:p.Met711Ile	77.0	0.0	.		72.0	18.0	.	NM_001204468	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Missense_Mutation	SNP	ENST00000377604.3	hg19	CCDS14274.1	.	.	.	.	.	.	.	.	.	.	G	8.375	0.836295	0.16891	.	.	ENSG00000182872	ENST00000377604;ENST00000329236;ENST00000345781	T;T;T	0.18174	2.91;2.23;2.5	5.63	5.63	0.86233	.	0.213638	0.43579	D	0.000543	T	0.16514	0.0397	L	0.48642	1.525	0.32547	N	0.532888	B;B;B;B;B	0.06786	0.001;0.001;0.0;0.0;0.0	B;B;B;B;B	0.10450	0.003;0.005;0.005;0.002;0.002	T	0.10776	-1.0615	10	0.17369	T	0.5	-11.0981	14.1672	0.65486	0.0:0.0:1.0:0.0	.	634;776;710;633;711	P98175-3;Q7Z3D7;P98175-2;P98175-4;P98175	.;.;.;.;RBM10_HUMAN	I	711;633;634	ENSP00000366829:M711I;ENSP00000328848:M633I;ENSP00000329659:M634I	ENSP00000328848:M633I	M	+	3	0	RBM10	46929677	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.567000	0.53813	2.509000	0.84616	0.600000	0.82982	ATG	.	.	.	none		0.632	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676		C	47044733	G	C	47044733	3	2	272	1	0	0	0	0	1	0	0	0	13124	1348	47	4	2203	4	RBM10	23	47044733	Missense_Mutation	SNP	G	TCGA-WN-A9G9-01A-12D-A36X-10		47044733	108225827	64	17225											
PRAMEF1	65121	hgsc.bcm.edu	37	chr1	12854245	12854246	+	Frame_Shift_Ins	INS	-	-	AA																															catagacatctgcctcaaggINSaaataccccaggatgaatgc																										TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr1:12854245_12854246insAA	ENST00000332296.7	+	3	572_573	c.469_470insAA	c.(469-471)gaafs	p.E157fs	PRAMEF1_ENST00000400814.3_5'Flank	NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	157					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)					cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35	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;0.00812)|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)		CTGCCTCAAGGAAATACCCCAG	0.495																																					p.E157fs		Atlas-Indel,Pindel	.											.	PRAMEF1	78	.	0			c.469_470insAA						PASS	.																																			SO:0001589	frameshift_variant	65121	exon3			.	AL049686	CCDS148.1	1p36.21	2013-01-17			ENSG00000116721	ENSG00000116721		"-"	28840	protein-coding gene	gene with protein product							Standard	NM_023013		Approved		uc001auj.2	O95521	OTTHUMG00000001928	ENST00000332296.7:c.470_471dupAA	chr1.hg19:g.12854246_12854247dupAA	ENSP00000332134:p.Glu157fs	165.0	0.0	0		168.0	12.0	0.0714286	NM_023013	Q9UQP2	Frame_Shift_Ins	INS	ENST00000332296.7	hg19	CCDS148.1																																																																																			.	.	.	none		0.495	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005458.1	NM_023013		AA	12854246	-	AA	12854245	7	5	273	1	0	1	1	0	0	0	0	0	12435	1175	41	0	475	0	PRAMEF1	1	12854245	Frame_Shift_Ins	INS	-	TCGA-WN-AB4C-01A-11D-A42J-10		12854245	236396376	1	17226											
PRAMEF13	400736	hgsc.bcm.edu	37	chr1	13449601	13449601	+	Frame_Shift_Del	DEL	T	T	-																															ccactgaagaaggtgatcaaTtttattttaagcaactggag																										TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr1:13449601delT	ENST00000376132.3	-	3	927	c.825delA	c.(823-825)aaafs	p.K275fs		NM_001024661.1	NP_001019832.1	Q5VWM6	PRA13_HUMAN	PRAME family member 13	275					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)|large_intestine(1)|lung(3)|skin(2)	7	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;9.86e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|COAD - Colon adenocarcinoma(227;0.000502)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AGGTGATCAATTTTATTTTAA	0.458																																					p.L276X		Atlas-Indel,Pindel	.											.	PRAMEF13	10	.	0			c.826delT						PASS	.																																			SO:0001589	frameshift_variant	400736	exon3			.			1p36.21	2013-01-17			ENSG00000204495			"-"	13262	protein-coding gene	gene with protein product							Standard	NG_005159		Approved	OTTHUMG00000008034	uc010obi.1	Q5VWM6	OTTHUMG00000008034	ENST00000376132.3:c.825delA	chr1.hg19:g.13449601delT	ENSP00000365302:p.Lys275fs	144.0	0.0	0		135.0	20.0	0.148148	NM_001024661		Frame_Shift_Del	DEL	ENST00000376132.3	hg19	CCDS41257.1																																																																																			.	.	.	none		0.458	PRAMEF13-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022040.1	XM_375688		-	13449601	T	-	13449601	7	5	273	1	0	1	0	1	0	0	0	0	12439	1490	52	0	607	0	PRAMEF13	1	13449601	Frame_Shift_Del	DEL	T	TCGA-WN-AB4C-01A-11D-A42J-10	595356	13449601	235801020	2	17227											
WDTC1	23038	hgsc.bcm.edu	37	chr1	27631607	27631607	+	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	agtccattgtcaactgcctgCagccacaccccagctactgc	9	8	7	17	0	1	0	1	0	0	0	2	0	2	0	5	0	7	2	5	0	2	2			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr1:27631607C>T	ENST00000319394.3	+	15	2294	c.1759C>T	c.(1759-1761)Cag>Tag	p.Q587*	WDTC1_ENST00000361771.3_Nonsense_Mutation_p.Q586*	NM_001276252.1|NM_015023.3	NP_001263181.1|NP_055838.2	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1	587					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)	p.Q586*(1)		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)		CAACTGCCTGCAGCCACACCC	0.597																																					p.Q587X		Atlas-SNP	.											WDTC1,NS,carcinoma,0,1	WDTC1	69	.	1	Substitution - Nonsense(1)	endometrium(1)	c.C1759T						PASS	.						101	73	82					1																	27631607		2203	4300	6503	SO:0001587	stop_gained	23038	exon15			TGCCTGCAGCCAC	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.1759C>T	chr1.hg19:g.27631607C>T	ENSP00000317971:p.Gln587*	69.0	0.0	.		86.0	19.0	.	NM_001276252	D3DPL5|Q5SSC5|Q9NV87|Q9UPW4	Nonsense_Mutation	SNP	ENST00000319394.3	hg19		.	.	.	.	.	.	.	.	.	.	C	42	9.774571	0.99260	.	.	ENSG00000142784	ENST00000319394;ENST00000361771	.	.	.	4.67	4.67	0.58626	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.24483	T	0.36	.	17.0891	0.86618	0.0:1.0:0.0:0.0	.	.	.	.	X	587;586	.	ENSP00000317971:Q587X	Q	+	1	0	WDTC1	27504194	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.589000	0.67523	2.581000	0.87130	0.455000	0.32223	CAG	.	.	.	none		0.597	WDTC1-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015023		T	27631607	C	T	27631607	4	4	273	1	0	0	0	0	0	1	0	0	17354	711	25	2	1810	2	WDTC1	1	27631607	Nonsense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	14182006	27631607	221619014	3	17228											
PHACTR4	65979	hgsc.bcm.edu	37	chr1	28792196	28792196	+	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	actcttctttcaccttgcagGtggtgaggatccaggaaagc	9	11	11	10	0	3	1	1	1	2	0	4	3	4	3	2	4	2	1	2	4	1	3			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr1:28792196G>A	ENST00000373839.3	+	5	533	c.272G>A	c.(271-273)gGt>gAt	p.G91D	PHACTR4_ENST00000373836.3_Splice_Site_p.G101D|PHACTR4_ENST00000493669.1_3'UTR	NM_001048183.1	NP_001041648.1	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	91					actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		CACCTTGCAGGTGGTGAGGAT	0.408																																					p.G101D		Atlas-SNP	.											.	PHACTR4	64	.	0			c.G302A						PASS	.						133	127	129					1																	28792196		1913	4126	6039	SO:0001630	splice_region_variant	65979	exon4			TTGCAGGTGGTGA	AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138		"Phosphatase and actin regulators"	25793	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 124"	608726				11483580, 15107502	Standard	NM_023923		Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373839.3:c.272-1G>A	chr1.hg19:g.28792196G>A		114.0	0.0	.		108.0	29.0	.	NM_023923	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	Missense_Mutation	SNP	ENST00000373839.3	hg19	CCDS41293.1	.	.	.	.	.	.	.	.	.	.	G	0.368	-0.935524	0.02340	.	.	ENSG00000204138	ENST00000373839;ENST00000373836;ENST00000373838	T;T	0.35421	1.31;1.31	5.11	1.1	0.20463	.	0.374471	0.29684	N	0.011468	T	0.17238	0.0414	N	0.17082	0.46	0.24318	N	0.995057	B;B;B	0.14805	0.011;0.007;0.011	B;B;B	0.16722	0.016;0.004;0.01	T	0.17961	-1.0352	9	.	.	.	.	4.5085	0.11899	0.3516:0.1562:0.4922:0.0	.	101;91;75	Q8IZ21-2;Q8IZ21;Q8IZ21-3	.;PHAR4_HUMAN;.	D	91;101;90	ENSP00000362945:G91D;ENSP00000362942:G101D	.	G	+	2	0	PHACTR4	28664783	0.981000	0.34729	0.336000	0.25522	0.672000	0.39443	1.242000	0.32755	-0.049000	0.13379	0.561000	0.74099	GGT	.	.	.	none		0.408	PHACTR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009868.4	NM_023923	Missense_Mutation	A	28792196	G	A	28792196	5	1	273	1	0	0	0	0	0	0	1	0	11819	1275	44	2	336	2	PHACTR4	1	28792196	Splice_Site	SNP	G	TCGA-WN-AB4C-01A-11D-A42J-10	1160589	28792196	220458425	4	17229											
CSMD2	114784	hgsc.bcm.edu	37	chr1	34008360	34008360	+	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	cctgtccaggtaccattgacCgagcagtgacggctgagcag	9	7	13	12	2	0	3	0	3	0	0	1	4	1	3	4	2	3	4	4	2	1	2	rs199932348		TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr1:34008360C>A	ENST00000373381.4	-	58	9413	c.9237G>T	c.(9235-9237)tcG>tcT	p.S3079S		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	3053	Sushi 24. {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)				TACCATTGACCGAGCAGTGAC	0.592																																					p.S2935S		Atlas-SNP	.											.	CSMD2	946	.	0			c.G8805T						PASS	.						64	53	57					1																	34008360		2203	4300	6503	SO:0001819	synonymous_variant	114784	exon57			ATTGACCGAGCAG	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.9237G>T	chr1.hg19:g.34008360C>A		83.0	0.0	.		85.0	28.0	.	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Silent	SNP	ENST00000373381.4	hg19																																																																																				.	C|0.999;T|0.001	.	alt		0.592	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		A	34008360	C	A	34008360	2	1	273	1	0	0	0	0	0	0	0	1	3947	639	23	4		4	CSMD2	1	34008360	Silent	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	5216164	34008360	215242261	5	17230											
EPS15	2060	hgsc.bcm.edu	37	chr1	51929372	51929372	+	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	aggatatccacaggtaacttAgagttgagcaacactggttt	13	11	10	7	0	0	2	0	1	0	1	1	3	1	3	1	3	3	4	1	3	4	5			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr1:51929372A>T	ENST00000371733.3	-	7	570	c.474T>A	c.(472-474)tcT>tcA	p.S158S	EPS15_ENST00000371730.2_Silent_p.S158S|RP11-253A20.1_ENST00000424246.1_RNA	NM_001981.2	NP_001972.1	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway substrate 15	158	EH 2. {ECO:0000255|PROSITE- ProRule:PRU00077}.|Interaction with DAB2. {ECO:0000250}.				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?(1)		endometrium(3)|kidney(5)|large_intestine(8)|lung(13)|prostate(2)|skin(1)|stomach(1)|urinary_tract(2)	35						CAGGTAACTTAGAGTTGAGCA	0.333			T	MLL	ALL																																p.S158S		Atlas-SNP	.		Dom	yes		1	1p32	2060	epidermal growth factor receptor pathway substrate 15 (AF1p)		L	.,1	EPS15	72	.	1	Whole gene deletion(1)	central_nervous_system(1)	c.T474A						PASS	.						68	66	67					1																	51929372		2203	4300	6503	SO:0001819	synonymous_variant	2060	exon7			TAACTTAGAGTTG	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.474T>A	chr1.hg19:g.51929372A>T		40.0	0.0	.		58.0	11.0	.	NM_001981	B2R8J7|D3DPJ2|Q5SRH4	Silent	SNP	ENST00000371733.3	hg19	CCDS557.1																																																																																			.	.	.	none		0.333	EPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022422.1	NM_001981		T	51929372	A	T	51929372	2	4	273	1	0	0	0	0	0	0	0	1	5194	407	15	5		5	EPS15	1	51929372	Silent	SNP	A	TCGA-WN-AB4C-01A-11D-A42J-10	17921012	51929372	197321249	6	17231											
TMED5	50999	hgsc.bcm.edu	37	chr1	93621899	93621899	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccaatatatctgtgccagtAatatatttcttccaatcttc	11	17	3	10	0	3	0	0	0	3	0	6	0	5	0	3	0	1	1	3	0	7	8			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr1:93621899A>G	ENST00000370282.3	-	3	914	c.429T>C	c.(427-429)atT>atC	p.I143I	TMED5_ENST00000479918.1_Silent_p.I143I|TMED5_ENST00000370280.1_Silent_p.I143I|TMED5_ENST00000483033.1_5'UTR	NM_016040.4	NP_057124.3	Q9Y3A6	TMED5_HUMAN	transmembrane emp24 protein transport domain containing 5	143					Golgi ribbon formation (GO:0090161)|protein transport (GO:0015031)	cis-Golgi network (GO:0005801)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)	6		all_lung(203;0.0223)|Lung NSC(277;0.071)|Melanoma(281;0.147)|Glioma(108;0.188)		all cancers(265;0.00108)|GBM - Glioblastoma multiforme(16;0.00407)|Epithelial(280;0.0797)		CTGTGCCAGTAATATATTTCT	0.348																																					p.I143I		Atlas-SNP	.											.	TMED5	16	.	0			c.T429C						PASS	.						180	171	174					1																	93621899		2203	4300	6503	SO:0001819	synonymous_variant	50999	exon3			GCCAGTAATATAT	BC070051	CCDS743.1, CCDS53342.1	1p22.1	2013-09-19			ENSG00000117500	ENSG00000117500			24251	protein-coding gene	gene with protein product						10810093	Standard	NM_016040		Approved	CGI-100	uc001dpn.3	Q9Y3A6	OTTHUMG00000010162	ENST00000370282.3:c.429T>C	chr1.hg19:g.93621899A>G		105.0	0.0	.		97.0	24.0	.	NM_001167830	B1AKT4|B2R703|D3DT38|Q96AX8	Silent	SNP	ENST00000370282.3	hg19	CCDS743.1																																																																																			.	.	.	none		0.348	TMED5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028076.3	NM_016040		G	93621899	A	G	93621899	2	3	273	1	0	0	0	0	0	0	0	1	16019	358	13	3		3	TMED5	1	93621899	Silent	SNP	A	TCGA-WN-AB4C-01A-11D-A42J-10	41692527	93621899	155628722	7	17232											
FMO5	2330	hgsc.bcm.edu	37	chr1	146658726	146658726	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttggggtcagtgaaggccAgagacagcagattgggcctg	9	7	17	8	0	1	3	1	1	0	2	1	4	1	3	2	4	1	2	2	4	1	2			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr1:146658726A>G	ENST00000254090.4	-	9	1743	c.1355T>C	c.(1354-1356)cTg>cCg	p.L452P	FMO5_ENST00000441068.2_Intron|RP11-337C18.8_ENST00000606757.1_RNA|FMO5_ENST00000369272.3_3'UTR|RP11-337C18.8_ENST00000607149.1_RNA|RP11-337C18.10_ENST00000606856.1_RNA	NM_001461.2	NP_001452.2	P49326	FMO5_HUMAN	flavin containing monooxygenase 5	452						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)					AGTGAAGGCCAGAGACAGCAG	0.537																																					p.L452P		Atlas-SNP	.											.	FMO5	94	.	0			c.T1355C						PASS	.						86	81	83					1																	146658726		2203	4300	6503	SO:0001583	missense	2330	exon9			AAGGCCAGAGACA	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	ENST00000254090.4:c.1355T>C	chr1.hg19:g.146658726A>G	ENSP00000254090:p.Leu452Pro	111.0	0.0	.		119.0	33.0	.	NM_001461	B2RBG1|C9JJD1|Q8IV22	Missense_Mutation	SNP	ENST00000254090.4	hg19	CCDS926.1	.	.	.	.	.	.	.	.	.	.	.	21.1	4.096346	0.76870	.	.	ENSG00000131781	ENST00000254090	T	0.61742	0.08	5.8	4.67	0.58626	.	0.078821	0.52532	D	0.000071	T	0.76535	0.4001	H	0.95187	3.635	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.82372	-0.0490	10	0.87932	D	0	-2.7964	10.1529	0.42805	0.9212:0.0:0.0788:0.0	.	452	P49326	FMO5_HUMAN	P	452	ENSP00000254090:L452P	ENSP00000254090:L452P	L	-	2	0	FMO5	145125350	1.000000	0.71417	0.967000	0.41034	0.997000	0.91878	8.981000	0.93465	1.011000	0.39340	0.533000	0.62120	CTG	.	.	.	none		0.537	FMO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040373.2	NM_001461		G	146658726	A	G	146658726	3	3	273	1	0	0	0	0	1	0	0	0	5965	188	7	3	393	3	FMO5	1	146658726	Missense_Mutation	SNP	A	TCGA-WN-AB4C-01A-11D-A42J-10	53036827	146658726	102591895	8	17233											
ATP1B1	481	hgsc.bcm.edu	37	chr1	169096621	169096621	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtgcattattataaagctcaAccgagttctaggcttcaaac	13	12	7	9	1	3	0	2	0	1	0	3	1	3	0	1	1	4	4	1	1	7	6			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr1:169096621A>G	ENST00000367816.1	+	5	1071	c.542A>G	c.(541-543)aAc>aGc	p.N181S	ATP1B1_ENST00000367813.3_Missense_Mutation_p.N173S|ATP1B1_ENST00000367815.4_Missense_Mutation_p.N181S|ATP1B1_ENST00000499679.3_Missense_Mutation_p.N125S			P05026	AT1B1_HUMAN	ATPase, Na+/K+ transporting, beta 1 polypeptide	181					blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular potassium ion homeostasis (GO:0030007)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|leukocyte migration (GO:0050900)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|positive regulation of ATP catabolic process (GO:1903291)|positive regulation of ATPase activity (GO:0032781)|positive regulation of calcium:sodium antiporter activity (GO:1903281)|positive regulation of potassium ion import (GO:1903288)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of sodium ion export from cell (GO:1903278)|potassium ion import (GO:0010107)|protein localization to plasma membrane (GO:0072659)|protein stabilization (GO:0050821)|protein transport into plasma membrane raft (GO:0044861)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression (GO:0010468)|relaxation of cardiac muscle (GO:0055119)|response to hypoxia (GO:0001666)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|vesicle (GO:0031982)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|MHC class II protein complex binding (GO:0023026)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	14	all_hematologic(923;0.208)					ATAAAGCTCAACCGAGTTCTA	0.358																																					p.N181S		Atlas-SNP	.											.	ATP1B1	29	.	0			c.A542G						PASS	.						89	87	88					1																	169096621		2203	4300	6503	SO:0001583	missense	481	exon4			AGCTCAACCGAGT	U16799	CCDS1276.1	1q24.2	2012-10-22			ENSG00000143153	ENSG00000143153		"ATPases / P-type"	804	protein-coding gene	gene with protein product	"sodium/potassium-transporting ATPase subunit beta-1", "sodium pump subunit beta-1", "sodium-potassium ATPase subunit beta 1 (non-catalytic)"	182330		ATP1B			Standard	NM_001677		Approved		uc001gfr.1	P05026	OTTHUMG00000034590	ENST00000367816.1:c.542A>G	chr1.hg19:g.169096621A>G	ENSP00000356790:p.Asn181Ser	111.0	0.0	.		79.0	22.0	.	NM_001677	Q5TGZ3	Missense_Mutation	SNP	ENST00000367816.1	hg19	CCDS1276.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.929242	0.92389	.	.	ENSG00000143153	ENST00000367816;ENST00000367815;ENST00000499679;ENST00000367813	T;T;T;T	0.36699	1.24;1.24;1.24;1.24	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.67021	0.2849	H	0.95328	3.655	0.54753	D	0.999982	D	0.89917	1.0	D	0.78314	0.991	T	0.78003	-0.2374	9	0.66056	D	0.02	-8.8621	16.5446	0.84426	1.0:0.0:0.0:0.0	.	181	P05026	AT1B1_HUMAN	S	181;181;125;173	ENSP00000356790:N181S;ENSP00000356789:N181S;ENSP00000423450:N125S;ENSP00000356787:N173S	ENSP00000356787:N173S	N	+	2	0	ATP1B1	167363245	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	8.600000	0.90860	2.311000	0.77944	0.533000	0.62120	AAC	.	.	.	none		0.358	ATP1B1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083696.1			G	169096621	A	G	169096621	3	3	273	1	0	0	0	0	1	0	0	0	1132	43	2	3	556	3	ATP1B1	1	169096621	Missense_Mutation	SNP	A	TCGA-WN-AB4C-01A-11D-A42J-10	22437895	169096621	80154000	9	17234											
PPP1R12B	4660	hgsc.bcm.edu	37	chr1	202464697	202464697	+	Splice_Site	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	ctttattttatctctggccaGagaatgaagaagcagatttg	12	14	9	6	0	1	4	0	1	1	3	2	5	1	4	1	1	1	1	1	1	5	5			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr1:202464697G>C	ENST00000608999.1	+	17	2488		c.e17-1		PPP1R12B_ENST00000391959.3_Splice_Site|PPP1R12B_ENST00000367270.4_Splice_Site|PPP1R12B_ENST00000336894.4_Splice_Site|PPP1R12B_ENST00000290419.5_Splice_Site	NM_001197131.1|NM_002481.3	NP_001184060.1|NP_002472.2	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory subunit 12B						G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)|regulation of muscle contraction (GO:0006937)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	enzyme activator activity (GO:0008047)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(17)|ovary(4)|skin(3)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(75;0.166)			TCTCTGGCCAGAGAATGAAGA	0.463																																					.		Atlas-SNP	.											.	PPP1R12B	100	.	0			c.2336-1G>C						PASS	.						51	52	52					1																	202464697		2203	4299	6502	SO:0001630	splice_region_variant	4660	exon17			TGGCCAGAGAATG	AB003062	CCDS1426.1, CCDS44294.1, CCDS44295.1, CCDS53458.1, CCDS53459.1, CCDS73005.1	1q32.1	2013-01-10	2011-10-04	2001-08-10	ENSG00000077157	ENSG00000077157		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	7619	protein-coding gene	gene with protein product	"myosin phosphatase regulatory subunit", "myosin phosphatase, target subunit 2"	603768	"protein phosphatase 1, regulatory (inhibitor) subunit 12B"	MYPT2		9570949	Standard	NM_002481		Approved	MGC87886, MGC131980, PP1bp55	uc001gya.2	O60237	OTTHUMG00000041393	ENST00000608999.1:c.2336-1G>C	chr1.hg19:g.202464697G>C		81.0	0.0	.		82.0	22.0	.	NM_002481	A8MYF5|B7ZMN6|Q2TAI8|Q5T506|Q5VUK2|Q8N179|Q9HCB7|Q9HCB8	Splice_Site	SNP	ENST00000608999.1	hg19	CCDS1426.1	.	.	.	.	.	.	.	.	.	.	G	18.85	3.710994	0.68730	.	.	ENSG00000077157	ENST00000406302;ENST00000336894;ENST00000391959;ENST00000367270	.	.	.	5.67	5.67	0.87782	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.0413	0.86490	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PPP1R12B	200731320	1.000000	0.71417	0.983000	0.44433	0.715000	0.41141	4.311000	0.59147	2.828000	0.97474	0.655000	0.94253	.	.	.	.	none		0.463	PPP1R12B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099166.3	NM_032105	Intron	C	202464697	G	C	202464697	5	2	273	1	0	0	0	0	0	0	1	0	12365	956	33	4	2491	4	PPP1R12B	1	202464697	Splice_Site	SNP	G	TCGA-WN-AB4C-01A-11D-A42J-10	33368076	202464697	46785924	10	17235											
FCAMR	83953	hgsc.bcm.edu	37	chr1	207131928	207131928	+	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	gaagagagtcatcctggagcAtctttctttccacatggggc	9	11	11	10	0	3	1	1	0	2	1	5	4	5	2	2	3	1	1	2	3	1	2			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr1:207131928A>T	ENST00000324852.4	-	8	2141	c.1667T>A	c.(1666-1668)aTg>aAg	p.M556K	FCAMR_ENST00000450945.2_3'UTR|FCAMR_ENST00000486178.1_5'UTR|FCAMR_ENST00000400962.3_3'UTR	NM_001170631.1	NP_001164102.1	Q8WWV6	FCAMR_HUMAN	Fc receptor, IgA, IgM, high affinity	511					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						ATCCTGGAGCATCTTTCTTTC	0.537																																					p.M556K	Ovarian(199;1883 2142 16966 44409 45154)	Atlas-SNP	.											.	FCAMR	125	.	0			c.T1667A						PASS	.						109	100	103					1																	207131928		692	1591	2283	SO:0001583	missense	83953	exon8			TGGAGCATCTTTC	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.1667T>A	chr1.hg19:g.207131928A>T	ENSP00000316491:p.Met556Lys	87.0	0.0	.		79.0	18.0	.	NM_001170631	Q32M82|Q8WWV5|Q96SA2	Missense_Mutation	SNP	ENST00000324852.4	hg19	CCDS53468.1	.	.	.	.	.	.	.	.	.	.	A	15.87	2.960491	0.53400	.	.	ENSG00000162897	ENST00000324852;ENST00000367087	T	0.05139	3.49	4.73	-0.538	0.11868	.	0.830835	0.10440	N	0.674376	T	0.04679	0.0127	L	0.48642	1.525	0.09310	N	1	P;P	0.39551	0.483;0.678	B;B	0.33690	0.118;0.168	T	0.38001	-0.9681	10	0.87932	D	0	0.0976	0.44	0.00484	0.4307:0.186:0.2041:0.1791	.	531;511	D2KTA8;Q8WWV6	.;FCAMR_HUMAN	K	556;514	ENSP00000316491:M556K	ENSP00000316491:M556K	M	-	2	0	FCAMR	205198551	0.000000	0.05858	0.001000	0.08648	0.564000	0.35744	-0.017000	0.12590	0.266000	0.21894	0.459000	0.35465	ATG	.	.	.	none		0.537	FCAMR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088969.2	NM_032029		T	207131928	A	T	207131928	3	4	273	1	0	0	0	0	1	0	0	0	5779	217	8	5	70	5	FCAMR	1	207131928	Missense_Mutation	SNP	A	TCGA-WN-AB4C-01A-11D-A42J-10	4667231	207131928	42118693	11	17236											
CDC42BPA	8476	hgsc.bcm.edu	37	chr1	227182594	227182594	+	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	cagaggacaaagagccctctGacggggagggcatgggctgc	10	4	17	10	1	1	3	0	1	1	2	1	5	1	5	1	5	2	2	1	5	1	0			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr1:227182594G>T	ENST00000366769.3	-	35	6249	c.4958C>A	c.(4957-4959)tCa>tAa	p.S1653*	RP5-1087E8.3_ENST00000433837.1_RNA|CDC42BPA_ENST00000366764.2_Nonsense_Mutation_p.S1625*|CDC42BPA_ENST00000366766.2_Nonsense_Mutation_p.S1688*|CDC42BPA_ENST00000334218.5_Nonsense_Mutation_p.S1715*|CDC42BPA_ENST00000535525.1_Nonsense_Mutation_p.S1633*|CDC42BPA_ENST00000366765.3_Nonsense_Mutation_p.S1666*|CDC42BPA_ENST00000366767.3_Nonsense_Mutation_p.S1572*	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)				AGAGCCCTCTGACGGGGAGGG	0.582																																					p.S1653X		Atlas-SNP	.											CDC42BPA_ENST00000366769,NS,carcinoma,0,3	CDC42BPA	528	.	0			c.C4958A						PASS	.						93	91	92					1																	227182594		2203	4300	6503	SO:0001587	stop_gained	8476	exon35			CCCTCTGACGGGG	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.4958C>A	chr1.hg19:g.227182594G>T	ENSP00000355731:p.Ser1653*	59.0	0.0	.		40.0	9.0	.	NM_003607		Nonsense_Mutation	SNP	ENST00000366769.3	hg19	CCDS1558.1	.	.	.	.	.	.	.	.	.	.	g	43	9.953409	0.99303	.	.	ENSG00000143776	ENST00000366769;ENST00000366767;ENST00000334218;ENST00000366766;ENST00000366764;ENST00000535525;ENST00000366765	.	.	.	5.09	5.09	0.68999	.	0.132428	0.52532	D	0.000065	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05525	T	0.97	.	18.5149	0.90933	0.0:0.0:1.0:0.0	.	.	.	.	X	1653;1572;1715;1688;1625;1633;1666	.	ENSP00000335341:S1715X	S	-	2	0	CDC42BPA	225249217	1.000000	0.71417	0.100000	0.21137	0.917000	0.54804	7.341000	0.79300	2.367000	0.80283	0.651000	0.88453	TCA	.	.	.	none		0.582	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826		T	227182594	G	T	227182594	4	4	273	1	0	0	0	0	0	1	0	0	3074	1294	45	4	209	4	CDC42BPA	1	227182594	Nonsense_Mutation	SNP	G	TCGA-WN-AB4C-01A-11D-A42J-10	20050666	227182594	22068027	12	17237											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228482711	228482711	+	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	agtactcgtgtgtgtgcgggCaggagaggacctcggccaca	8	7	16	10	3	0	1	0	0	0	1	2	3	0	2	2	4	2	2	2	4	1	1			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr1:228482711C>A	ENST00000422127.1	+	43	11670	c.11626C>A	c.(11626-11628)Cag>Aag	p.Q3876K	OBSCN_ENST00000366709.4_Missense_Mutation_p.Q995K|OBSCN_ENST00000366707.4_Missense_Mutation_p.Q995K|RP5-1139B12.4_ENST00000602778.1_RNA|OBSCN_ENST00000359599.6_Missense_Mutation_p.Q2723K|OBSCN_ENST00000284548.11_Missense_Mutation_p.Q3876K|OBSCN_ENST00000570156.2_Missense_Mutation_p.Q4305K	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3876	Ig-like 39.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TGTGTGCGGGCAGGAGAGGAC	0.582																																					p.Q4305K		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C12913A						PASS	.						120	122	121					1																	228482711		2147	4242	6389	SO:0001583	missense	84033	exon48			TGCGGGCAGGAGA	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.11626C>A	chr1.hg19:g.228482711C>A	ENSP00000409493:p.Gln3876Lys	161.0	0.0	.		117.0	29.0	.	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	hg19	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	C	16.58	3.163675	0.57476	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21	5.01	4.06	0.47325	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.406049	0.23692	N	0.045504	T	0.44307	0.1287	N	0.20304	0.555	0.30201	N	0.798588	B;B	0.23854	0.092;0.059	B;B	0.25987	0.065;0.018	T	0.35871	-0.9771	10	0.06494	T	0.89	.	8.1272	0.31005	0.1337:0.6027:0.2636:0.0	.	3876;3876	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	K	3876;3876;995;995;2723	ENSP00000284548:Q3876K;ENSP00000409493:Q3876K;ENSP00000355668:Q995K;ENSP00000355670:Q995K;ENSP00000352613:Q2723K	ENSP00000284548:Q3876K	Q	+	1	0	OBSCN	226549334	0.000000	0.05858	1.000000	0.80357	0.794000	0.44872	0.274000	0.18680	2.611000	0.88343	0.563000	0.77884	CAG	.	.	.	none		0.582	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228482711	C	A	228482711	3	1	273	1	0	0	0	0	1	0	0	0	10819	711	25	4	11792	4	OBSCN	1	228482711	Missense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	1300117	228482711	20767910	13	17238											
BIRC6	57448	hgsc.bcm.edu	37	chr2	32740159	32740160	+	Frame_Shift_Ins	INS	-	-	TC																															acgtacacccaaactattttINStctttgctcatgggctggat																										TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr2:32740159_32740160insTC	ENST00000421745.2	+	55	10805_10806	c.10671_10672insTC	c.(10672-10674)tctfs	p.S3558fs		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	3558					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)					CAAACTATTTTTCTTTGCTCAT	0.416																																					p.F3557fs	Pancreas(94;175 1509 16028 18060 45422)	Atlas-Indel,Pindel	.											.	BIRC6	838	.	0			c.10671_10672insTC						PASS	.																																			SO:0001589	frameshift_variant	57448	exon55			.	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.10672_10673dupTC	chr2.hg19:g.32740160_32740161dupTC	ENSP00000393596:p.Ser3558fs	87.0	0.0	0		74.0	15.0	0.202703	NM_016252	Q9ULD1	Frame_Shift_Ins	INS	ENST00000421745.2	hg19	CCDS33175.2																																																																																			.	.	.	none		0.416	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		TC	32740160	-	TC	32740159	7	5	273	1	0	1	1	0	0	0	0	0	1438	1838	64	0	10889	0	BIRC6	2	32740159	Frame_Shift_Ins	INS	-	TCGA-WN-AB4C-01A-11D-A42J-10		32740159	210459214	14	17239											
AAK1	22848	hgsc.bcm.edu	37	chr2	69732772	69732772	+	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	gaaagcctgggatcaaactcTcagctgagcctccaagcttc	11	8	9	13	0	2	1	2	1	1	0	5	3	3	2	3	1	5	2	3	1	3	1			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr2:69732772T>A	ENST00000409085.4	-	16	2574	c.2198A>T	c.(2197-2199)gAg>gTg	p.E733V	AAK1_ENST00000406297.3_Missense_Mutation_p.E733V|AAK1_ENST00000409068.1_Intron	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	733					endocytosis (GO:0006897)|positive regulation of Notch signaling pathway (GO:0045747)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of clathrin-mediated endocytosis (GO:2000369)|regulation of protein localization (GO:0032880)	cell leading edge (GO:0031252)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extrinsic component of plasma membrane (GO:0019897)|terminal bouton (GO:0043195)	AP-2 adaptor complex binding (GO:0035612)|ATP binding (GO:0005524)|Notch binding (GO:0005112)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)	17						GATCAAACTCTCAGCTGAGCC	0.493																																					p.E733V		Atlas-SNP	.											.	AAK1	121	.	0			c.A2198T						PASS	.						78	78	78					2																	69732772		1895	4114	6009	SO:0001583	missense	22848	exon16			AAACTCTCAGCTG	AB028971	CCDS1893.2	2p13.3	2012-07-10			ENSG00000115977	ENSG00000115977			19679	protein-coding gene	gene with protein product						11877461, 12471243	Standard	NM_014911		Approved	KIAA1048, DKFZp686K16132	uc002sfp.2	Q2M2I8	OTTHUMG00000129648	ENST00000409085.4:c.2198A>T	chr2.hg19:g.69732772T>A	ENSP00000386456:p.Glu733Val	85.0	0.0	.		87.0	29.0	.	NM_014911	Q4ZFZ3|Q53RX6|Q9UPV4	Missense_Mutation	SNP	ENST00000409085.4	hg19	CCDS1893.2	.	.	.	.	.	.	.	.	.	.	T	18.85	3.711046	0.68730	.	.	ENSG00000115977	ENST00000409085;ENST00000406297	T;T	0.36340	1.26;1.26	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.49558	0.1564	L	0.34521	1.04	0.49915	D	0.999833	D;D;P	0.76494	0.998;0.999;0.492	D;D;B	0.80764	0.987;0.994;0.219	T	0.51601	-0.8685	10	0.72032	D	0.01	-22.5886	14.7584	0.69588	0.0:0.0:0.0:1.0	.	733;733;733	B7ZLC4;Q2M2I8-2;Q2M2I8	.;.;AAK1_HUMAN	V	733	ENSP00000386456:E733V;ENSP00000385181:E733V	ENSP00000385181:E733V	E	-	2	0	AAK1	69586276	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.833000	0.55790	2.161000	0.67846	0.533000	0.62120	GAG	.	.	.	none		0.493	AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251847.4	NM_014911		A	69732772	T	A	69732772	3	1	273	1	0	0	0	0	1	0	0	0	16	1551	54	5	715	5	AAK1	2	69732772	Missense_Mutation	SNP	T	TCGA-WN-AB4C-01A-11D-A42J-10	36992613	69732772	173466601	15	17240											
FAM136A	84908	hgsc.bcm.edu	37	chr2	70529069	70529069	+	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	cccgctacctgcatcttccgGatgttctctctttccagact	5	14	6	16	2	3	1	0	0	3	1	6	2	5	2	4	1	2	3	4	1	1	4			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr2:70529069G>C	ENST00000037869.3	-	1	153	c.75C>G	c.(73-75)atC>atG	p.I25M	AC022201.5_ENST00000445084.1_RNA|FAM136A_ENST00000450256.1_Missense_Mutation_p.I25M|FAM136A_ENST00000430566.1_Missense_Mutation_p.I25M	NM_032822.2	NP_116211.2	Q96C01	F136A_HUMAN	family with sequence similarity 136, member A	25						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				breast(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	6						GCATCTTCCGGATGTTCTCTC	0.687											OREG0014676	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I25M		Atlas-SNP	.											.	FAM136A	14	.	0			c.C75G						PASS	.						62	52	56					2																	70529069		2203	4299	6502	SO:0001583	missense	84908	exon1			CTTCCGGATGTTC	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.75C>G	chr2.hg19:g.70529069G>C	ENSP00000037869:p.Ile25Met	95.0	0.0	.	1123	102.0	25.0	.	NM_032822	Q96SS3	Missense_Mutation	SNP	ENST00000037869.3	hg19	CCDS1904.1	.	.	.	.	.	.	.	.	.	.	G	13.70	2.315072	0.40996	.	.	ENSG00000035141	ENST00000037869;ENST00000450256;ENST00000430566;ENST00000438759	.	.	.	3.81	3.81	0.43845	.	0.000000	0.85682	D	0.000000	T	0.65512	0.2698	M	0.86178	2.8	0.25158	N	0.990371	D	0.64830	0.994	D	0.65773	0.938	T	0.56998	-0.7886	9	0.40728	T	0.16	.	8.7433	0.34571	0.1086:0.0:0.8914:0.0	.	25	Q96C01	F136A_HUMAN	M	25;25;25;10	.	ENSP00000037869:I25M	I	-	3	3	FAM136A	70382573	1.000000	0.71417	1.000000	0.80357	0.625000	0.37756	5.161000	0.64935	2.124000	0.65301	0.195000	0.17529	ATC	.	.	.	none		0.687	FAM136A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251869.2	NM_032822		C	70529069	G	C	70529069	3	2	273	1	0	0	0	0	1	0	0	0	5454	1164	41	4	353	4	FAM136A	2	70529069	Missense_Mutation	SNP	G	TCGA-WN-AB4C-01A-11D-A42J-10	796297	70529069	172670304	16	17241											
RTKN	6242	hgsc.bcm.edu	37	chr2	74657138	74657138	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccatacagctctaaccgcAgttcaaagtctggccccgcc	9	7	7	18	2	3	0	1	0	2	0	3	0	3	0	6	1	3	3	6	1	3	3			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr2:74657138A>G	ENST00000233330.6	-	6	739	c.422T>C	c.(421-423)cTg>cCg	p.L141P	RTKN_ENST00000272430.5_Missense_Mutation_p.L191P|RTKN_ENST00000305557.5_Missense_Mutation_p.L178P|RTKN_ENST00000484453.1_5'Flank	NM_001015056.1	NP_001015056.1			rhotekin											endometrium(3)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	16						CTCTAACCGCAGTTCAAAGTC	0.637																																					p.L191P		Atlas-SNP	.											.	RTKN	80	.	0			c.T572C						PASS	.						44	50	48					2																	74657138		2177	4287	6464	SO:0001583	missense	6242	exon6			AACCGCAGTTCAA	AF049227	CCDS1941.1, CCDS33226.1, CCDS42699.1	2p13.1	2013-01-10			ENSG00000114993	ENSG00000114993		"Pleckstrin homology (PH) domain containing"	10466	protein-coding gene	gene with protein product		602288				9073523, 10940294	Standard	XM_005264478		Approved	B5	uc002sle.3	Q9BST9	OTTHUMG00000129955	ENST00000233330.6:c.422T>C	chr2.hg19:g.74657138A>G	ENSP00000233330:p.Leu141Pro	131.0	0.0	.		128.0	32.0	.	NM_001015055		Missense_Mutation	SNP	ENST00000233330.6	hg19	CCDS42699.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.446605	0.84101	.	.	ENSG00000114993	ENST00000305557;ENST00000272430;ENST00000233330	T;T;T	0.50548	0.74;0.74;0.74	5.04	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.66557	0.2801	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.70450	-0.4868	10	0.87932	D	0	.	12.7821	0.57483	1.0:0.0:0.0:0.0	.	191;178	Q9BST9;Q9BST9-2	RTKN_HUMAN;.	P	178;191;141	ENSP00000305298:L178P;ENSP00000272430:L191P;ENSP00000233330:L141P	ENSP00000233330:L141P	L	-	2	0	RTKN	74510646	1.000000	0.71417	0.985000	0.45067	0.858000	0.48976	8.586000	0.90806	2.117000	0.64856	0.459000	0.35465	CTG	.	.	.	none		0.637	RTKN-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000328236.3	NM_001015055		G	74657138	A	G	74657138	3	3	273	1	0	0	0	0	1	0	0	0	13735	188	7	3	1147	3	RTKN	2	74657138	Missense_Mutation	SNP	A	TCGA-WN-AB4C-01A-11D-A42J-10	4128069	74657138	168542235	17	17242											
TTN	7273	hgsc.bcm.edu	37	chr2	179482094	179482094	+	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	agtttcatattgcaacgaatCcaattatcttttccttcttc	10	18	3	10	1	3	0	1	0	2	0	6	1	5	0	2	0	2	2	2	0	5	8			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr2:179482094C>G	ENST00000591111.1	-	204	43019	c.42795G>C	c.(42793-42795)tgG>tgC	p.W14265C	RP11-171I2.4_ENST00000605334.1_lincRNA|TTN-AS1_ENST00000604956.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.W13338C|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.W6966C|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.W7033C|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.W15906C|TTN_ENST00000460472.2_Missense_Mutation_p.W6841C			Q8WZ42	TITIN_HUMAN	titin	14265	Fibronectin type-III 3. {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)			TGCAACGAATCCAATTATCTT	0.378																																					p.W15906C		Atlas-SNP	.											.	TTN	18412	.	0			c.G47718C						PASS	.						104	92	96					2																	179482094		1853	4092	5945	SO:0001583	missense	7273	exon254			ACGAATCCAATTA	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.42795G>C	chr2.hg19:g.179482094C>G	ENSP00000465570:p.Trp14265Cys	140.0	0.0	.		115.0	23.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	12.62	1.992752	0.35131	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.51325	0.71;0.71;0.71;0.71	5.93	5.93	0.95920	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.76793	0.4037	M	0.90425	3.115	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.80369	-0.1411	9	0.87932	D	0	.	20.3507	0.98813	0.0:1.0:0.0:0.0	.	6841;6966;7033;14265	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	C	13338;6841;7033;6966;6841	ENSP00000343764:W13338C;ENSP00000434586:W6841C;ENSP00000340554:W7033C;ENSP00000352154:W6966C	ENSP00000340554:W7033C	W	-	3	0	TTN	179190339	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.770000	0.85390	2.808000	0.96608	0.655000	0.94253	TGG	.	.	.	none		0.378	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179482094	C	G	179482094	3	3	273	1	0	0	0	0	1	0	0	0	16747	856	30	4	60411	4	TTN	2	179482094	Missense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	104824956	179482094	63717279	18	17243											
UGT1A1	54578	hgsc.bcm.edu	37	chr2	234675730	234675741	+	In_Frame_Del	DEL	CTCTTTGGGATC	CTCTTTGGGATC	-																															gaacatggaattgtggttttCtctttgggatcaatggtctc																								rs62625011		TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	CTCTTTGGGATC	CTCTTTGGGATC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr2:234675730_234675741delCTCTTTGGGATC	ENST00000305139.6	+	2	1051_1062	c.912_923delCTCTTTGGGATC	c.(910-924)ttctctttgggatca>tta	p.304_308FSLGS>L	UGT1A8_ENST00000305208.5_In_Frame_Del_p.305_309FSLGS>L|UGT1A6_ENST00000373424.1_In_Frame_Del_p.37_41FSLGS>L|UGT1A1_ENST00000608381.1_In_Frame_Del_p.306_310FSLGS>L|UGT1A5_ENST00000373414.3_In_Frame_Del_p.306_310FSLGS>L|UGT1A1_ENST00000360418.3_In_Frame_Del_p.305_309FSLGS>L|UGT1A1_ENST00000609637.1_In_Frame_Del_p.302_306FSLGS>L|UGT1A9_ENST00000354728.4_In_Frame_Del_p.302_306FSLGS>L|UGT1A4_ENST00000373409.3_In_Frame_Del_p.306_310FSLGS>L|UGT1A10_ENST00000344644.5_In_Frame_Del_p.302_306FSLGS>L|UGT1A1_ENST00000609767.1_In_Frame_Del_p.306_310FSLGS>L|UGT1A1_ENST00000373450.4_In_Frame_Del_p.302_306FSLGS>L|UGT1A10_ENST00000373445.1_In_Frame_Del_p.302_306FSLGS>L|UGT1A3_ENST00000482026.1_In_Frame_Del_p.306_310FSLGS>L|UGT1A6_ENST00000406651.1_In_Frame_Del_p.37_41FSLGS>L|UGT1A7_ENST00000373426.3_In_Frame_Del_p.302_306FSLGS>L|UGT1A1_ENST00000608383.1_In_Frame_Del_p.305_309FSLGS>L	NM_001072.3	NP_001063.2	P19224	UD16_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A6	304					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)	TTGTGGTTTTCTCTTTGGGATCAATGGTCTCA	0.368																																					p.306_310del		Atlas-Indel,Pindel	.											.	UGT1A5	66	.	0			c.917_928del	GRCh37	CM941351	UGT1A1	M	rs62625011	PASS	.																																			SO:0001651	inframe_deletion	54579	exon2			.	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.912_923delCTCTTTGGGATC	chr2.hg19:g.234675730_234675741delCTCTTTGGGATC	ENSP00000303174:p.Phe304_Ser308delinsLeu	93.0	0.0	0		109.0	30.0	0.275229	NM_019078	A6NKK6|B8K289|Q96TE7	In_Frame_Del	DEL	ENST00000305139.6	hg19	CCDS2507.1																																																																																			.	.	.	none		0.368	UGT1A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130988.1	NM_205862		-	234675741	CTCTTTGGGATC	-	234675730	7	5	273	1	0	1	0	1	0	0	0	0	16956	912	32	0	921	0	UGT1A1	2	234675730	In_Frame_Del	DEL	CTCTTTGGGATC	TCGA-WN-AB4C-01A-11D-A42J-10	55193636	234675730	8523643	19	17244											
DNAH12	201625	hgsc.bcm.edu	37	chr3	57419487	57419487	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agccatgttcattcattaaaGttagcgtatccgccagcaca	12	11	7	11	2	2	0	2	0	0	0	3	0	3	0	3	0	3	4	3	0	4	5			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr3:57419487G>A	ENST00000351747.2	-	31	4835	c.4655C>T	c.(4654-4656)aCt>aTt	p.T1552I		NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	1552	AAA 2. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						ATTCATTAAAGTTAGCGTATC	0.363																																					p.T1552I		Atlas-SNP	.											.	DNAH12	182	.	0			c.C4655T						PASS	.						177	157	163					3																	57419487		692	1591	2283	SO:0001583	missense	201625	exon31			ATTAAAGTTAGCG	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.4655C>T	chr3.hg19:g.57419487G>A	ENSP00000295937:p.Thr1552Ile	75.0	0.0	.		78.0	16.0	.	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000351747.2	hg19		.	.	.	.	.	.	.	.	.	.	G	6.016	0.371430	0.11409	.	.	ENSG00000174844	ENST00000351747;ENST00000495027	T;T	0.26223	1.91;1.75	5.73	2.83	0.33086	ATPase, dynein-related, AAA domain (1);	.	.	.	.	T	0.42562	0.1208	M	0.85041	2.73	0.46222	D	0.998934	P	0.38335	0.627	P	0.46076	0.503	T	0.41910	-0.9482	9	0.45353	T	0.12	.	13.9721	0.64247	0.0:0.2366:0.6588:0.1046	.	1552	Q6ZR08	DYH12_HUMAN	I	1552;1575	ENSP00000295937:T1552I;ENSP00000418137:T1575I	ENSP00000295937:T1552I	T	-	2	0	DNAH12	57394527	1.000000	0.71417	0.550000	0.28217	0.030000	0.12068	3.845000	0.55880	0.348000	0.23949	-0.795000	0.03280	ACT	.	.	.	none		0.363	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504		A	57419487	G	A	57419487	3	1	273	1	0	0	0	0	1	0	0	0	4602	1029	36	2	4739	2	DNAH12	3	57419487	Missense_Mutation	SNP	G	TCGA-WN-AB4C-01A-11D-A42J-10		57419487	140602943	20	17245											
DNAJC13	23317	hgsc.bcm.edu	37	chr3	132165336	132165336	+	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	taggtataagcgtgtcttttCagttggaactcatgcgatta	10	15	10	6	2	3	0	2	0	1	0	3	2	3	1	0	2	3	2	0	2	5	7			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr3:132165336C>T	ENST00000260818.6	+	3	334	c.86C>T	c.(85-87)tCa>tTa	p.S29L	DNAJC13_ENST00000486798.1_3'UTR	NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	29					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						CGTGTCTTTTCAGTTGGAACT	0.303																																					p.S29L		Atlas-SNP	.											.	DNAJC13	253	.	0			c.C86T						PASS	.						84	81	82					3																	132165336		2203	4300	6503	SO:0001583	missense	23317	exon3			TCTTTTCAGTTGG	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.86C>T	chr3.hg19:g.132165336C>T	ENSP00000260818:p.Ser29Leu	77.0	0.0	.		93.0	26.0	.	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	hg19	CCDS33857.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.970699	0.92919	.	.	ENSG00000138246	ENST00000260818	T	0.19669	2.13	5.53	5.53	0.82687	.	0.075189	0.56097	D	0.000030	T	0.28830	0.0715	M	0.67953	2.075	0.80722	D	1	B;P	0.43750	0.206;0.816	B;B	0.39068	0.063;0.289	T	0.12785	-1.0534	10	0.87932	D	0	.	19.4758	0.94987	0.0:1.0:0.0:0.0	.	29;29	A7E2Y5;O75165	.;DJC13_HUMAN	L	29	ENSP00000260818:S29L	ENSP00000260818:S29L	S	+	2	0	DNAJC13	133648026	1.000000	0.71417	1.000000	0.80357	0.821000	0.46438	7.818000	0.86416	2.607000	0.88179	0.563000	0.77884	TCA	.	.	.	none		0.303	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		T	132165336	C	T	132165336	3	4	273	1	0	0	0	0	1	0	0	0	4634	838	29	2	92	2	DNAJC13	3	132165336	Missense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	74745849	132165336	65857094	21	17246											
PSMD2	5708	hgsc.bcm.edu	37	chr3	184020504	184020504	+	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	tggcattcatgctaggccggCatggggtgttcctggagctg	5	11	16	9	1	1	0	1	0	0	0	2	1	2	1	2	6	2	5	2	6	1	3			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr3:184020504C>A	ENST00000310118.4	+	7	1459	c.901C>A	c.(901-903)Cat>Aat	p.H301N	PSMD2_ENST00000439383.1_Missense_Mutation_p.H171N|PSMD2_ENST00000435761.1_Missense_Mutation_p.H142N|EIF2B5_ENST00000444495.1_Intron	NM_002808.3	NP_002799.3	Q13200	PSMD2_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 2	301					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)	p.H301Y(1)		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)	GCTAGGCCGGCATGGGGTGTT	0.517																																					p.H301N	Colon(24;313 636 6917 9932 15554)	Atlas-SNP	.											PSMD2,NS,carcinoma,0,1	PSMD2	56	.	1	Substitution - Missense(1)	prostate(1)	c.C901A						PASS	.						148	146	147					3																	184020504		2203	4300	6503	SO:0001583	missense	5708	exon7			GGCCGGCATGGGG	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.901C>A	chr3.hg19:g.184020504C>A	ENSP00000310129:p.His301Asn	97.0	0.0	.		69.0	17.0	.	NM_002808	B4DX07|B4DXY1|E7EW34|E9PCS3|Q12932|Q15321|Q53XQ4|Q96I12	Missense_Mutation	SNP	ENST00000310118.4	hg19	CCDS3258.1	.	.	.	.	.	.	.	.	.	.	C	18.22	3.574928	0.65878	.	.	ENSG00000175166	ENST00000310118;ENST00000538096;ENST00000435761;ENST00000439383	T;T;T	0.32272	2.09;1.46;1.46	5.16	5.16	0.70880	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.36110	0.0955	M	0.64170	1.965	0.80722	D	1	P;B	0.36789	0.57;0.118	B;B	0.35114	0.196;0.054	T	0.33548	-0.9864	10	0.72032	D	0.01	-18.9005	19.2107	0.93753	0.0:1.0:0.0:0.0	.	142;301	E9PCS3;Q13200	.;PSMD2_HUMAN	N	301;293;142;171	ENSP00000310129:H301N;ENSP00000402618:H142N;ENSP00000416028:H171N	ENSP00000310129:H301N	H	+	1	0	PSMD2	185503198	1.000000	0.71417	0.994000	0.49952	0.953000	0.61014	7.207000	0.77899	2.845000	0.97973	0.603000	0.83216	CAT	.	.	.	none		0.517	PSMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345843.1	NM_002808		A	184020504	C	A	184020504	3	1	273	1	0	0	0	0	1	0	0	0	12708	710	25	4	927	4	PSMD2	3	184020504	Missense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	51855168	184020504	14001926	22	17247											
KNG1	3827	hgsc.bcm.edu	37	chr3	186459563	186459563	+	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	atgggcaccaaagaggacatGgccttggccatggacacgaa	13	5	13	10	1	0	1	0	0	0	1	0	4	0	3	3	5	0	1	3	5	2	1			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr3:186459563G>T	ENST00000265023.4	+	10	1590	c.1378G>T	c.(1378-1380)Ggc>Tgc	p.G460C	RP11-573D15.8_ENST00000599314.1_RNA|RP11-573D15.8_ENST00000596632.1_RNA|RP11-573D15.8_ENST00000609652.1_RNA|RP11-573D15.8_ENST00000354642.2_RNA|KNG1_ENST00000447445.1_Intron|RP11-573D15.8_ENST00000609726.1_RNA|RP11-573D15.8_ENST00000596329.1_RNA|KNG1_ENST00000287611.2_Intron	NM_001102416.2	NP_001095886.1	P01042	KNG1_HUMAN	kininogen 1	460	His-rich.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|inflammatory response (GO:0006954)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|smooth muscle contraction (GO:0006939)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			endometrium(1)|lung(15)|prostate(1)|skin(2)|stomach(2)	21	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)		AAGAGGACATGGCCTTGGCCA	0.478																																					p.G460C		Atlas-SNP	.											.	KNG1	129	.	0			c.G1378T						PASS	.						77	74	75					3																	186459563		2079	4216	6295	SO:0001583	missense	3827	exon10			GGACATGGCCTTG		CCDS3281.1, CCDS43183.1, CCDS54695.1	3q27.3	2014-05-15	2004-05-21	2004-05-26	ENSG00000113889	ENSG00000113889		"Endogenous ligands"	6383	protein-coding gene	gene with protein product	"alpha-2-thiol proteinase inhibitor", "bradykinin"	612358	"kininogen"	KNG, BDK		1733668	Standard	NM_000893		Approved	BK	uc011bsa.2	P01042	OTTHUMG00000150348	ENST00000265023.4:c.1378G>T	chr3.hg19:g.186459563G>T	ENSP00000265023:p.Gly460Cys	214.0	0.0	.		177.0	45.0	.	NM_001102416	A8K474|B2RCR2|C9JEX1|P01043|Q53EQ0|Q6PAU9|Q7M4P1	Missense_Mutation	SNP	ENST00000265023.4	hg19	CCDS43183.1	.	.	.	.	.	.	.	.	.	.	G	12.62	1.991379	0.35131	.	.	ENSG00000113889	ENST00000265023	T	0.76186	-1.0	5.85	3.96	0.45880	.	0.134445	0.34750	N	0.003704	T	0.68686	0.3028	M	0.76574	2.34	0.80722	D	1	B	0.28783	0.222	B	0.25759	0.063	T	0.66122	-0.6002	9	.	.	.	-2.8329	7.0488	0.25061	0.0857:0.0:0.744:0.1703	.	460	P01042	KNG1_HUMAN	C	460	ENSP00000265023:G460C	.	G	+	1	0	KNG1	187942257	0.999000	0.42202	0.470000	0.27216	0.065000	0.16274	3.350000	0.52224	1.636000	0.50526	-0.136000	0.14681	GGC	.	.	.	none		0.478	KNG1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317738.1	NM_001102416		T	186459563	G	T	186459563	3	4	273	1	0	0	0	0	1	0	0	0	8434	1348	47	4	1416	4	KNG1	3	186459563	Missense_Mutation	SNP	G	TCGA-WN-AB4C-01A-11D-A42J-10	2439059	186459563	11562867	23	17248											
FBXL5	26234	hgsc.bcm.edu	37	chr4	15638133	15638133	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctacctctggcccaatgaacAgggtaaagatgtttccaaag	13	9	9	10	0	1	2	0	1	1	1	2	2	2	2	3	2	2	2	3	2	6	3			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr4:15638133A>G	ENST00000341285.3	-	5	874	c.750T>C	c.(748-750)ccT>ccC	p.P250P	FBXL5_ENST00000382358.4_Silent_p.P124P|FBXL5_ENST00000412094.2_Silent_p.P233P	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	250					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						cccaatgaacagggtaaagat	0.373																																					p.P250P		Atlas-SNP	.											.	FBXL5	52	.	0			c.T750C						PASS	.						76	65	69					4																	15638133		2203	4300	6503	SO:0001819	synonymous_variant	26234	exon5			ATGAACAGGGTAA	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.750T>C	chr4.hg19:g.15638133A>G		91.0	0.0	.		121.0	28.0	.	NM_012161	A8MSK4|B4DIB5|Q4W5A8|Q8NHP3|Q9NXN2|Q9P0I0|Q9P0X5|Q9UJT7|Q9UKC8	Silent	SNP	ENST00000341285.3	hg19	CCDS3415.1	.	.	.	.	.	.	.	.	.	.	A	8.941	0.965827	0.18583	.	.	ENSG00000118564	ENST00000513163	.	.	.	5.28	5.28	0.74379	.	.	.	.	.	T	0.62768	0.2455	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61950	-0.6957	4	.	.	.	-26.0422	10.7035	0.45942	0.8576:0.0:0.0:0.1424	.	.	.	.	R	171	.	.	C	-	1	0	FBXL5	15247231	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.656000	0.37355	2.121000	0.65114	0.482000	0.46254	TGT	.	.	.	none		0.373	FBXL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214235.2			G	15638133	A	G	15638133	2	3	273	1	0	0	0	0	0	0	0	1	5729	175	7	3		3	FBXL5	4	15638133	Silent	SNP	A	TCGA-WN-AB4C-01A-11D-A42J-10		15638133	175516143	24	17249											
SLC34A2	10568	hgsc.bcm.edu	37	chr4	25667838	25667838	+	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	ggggtgctggtgaccgtcttGgtgcagagctccagcacctc	5	9	15	12	1	1	2	0	1	1	1	3	2	2	2	3	4	4	4	3	4	0	1			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr4:25667838G>C	ENST00000382051.3	+	5	518	c.468G>C	c.(466-468)ttG>ttC	p.L156F	SLC34A2_ENST00000504570.1_Missense_Mutation_p.L155F|SLC34A2_ENST00000503434.1_Missense_Mutation_p.L155F|SLC34A2_ENST00000510033.2_3'UTR	NM_001177998.1|NM_006424.2	NP_001171469.1|NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 2	156					aging (GO:0007568)|cellular phosphate ion homeostasis (GO:0030643)|in utero embryonic development (GO:0001701)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|response to fructose (GO:0009750)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	phosphate ion binding (GO:0042301)|sodium ion binding (GO:0031402)|sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)		SLC34A2/ROS1(14)	breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(4)	41		Breast(46;0.0503)				TGACCGTCTTGGTGCAGAGCT	0.542			T	ROS1	NSCLC																																p.L156F		Atlas-SNP	.		Dom	yes		4	4p15.2	10568	"solute carrier family 34 (sodium phosphate), member 2"		E	.	SLC34A2	93	.	0			c.G468C						PASS	.						133	123	126					4																	25667838		2203	4300	6503	SO:0001583	missense	10568	exon5			CGTCTTGGTGCAG	AF111856	CCDS3435.1, CCDS54750.1	4p15.2	2013-07-17	2013-07-17		ENSG00000157765	ENSG00000157765		"Solute carriers"	11020	protein-coding gene	gene with protein product		604217	"solute carrier family 34 (sodium phosphate), member 2"			10329428, 10610722	Standard	NM_006424		Approved	NAPI-3B	uc003grr.3	O95436	OTTHUMG00000097757	ENST00000382051.3:c.468G>C	chr4.hg19:g.25667838G>C	ENSP00000371483:p.Leu156Phe	52.0	0.0	.		71.0	28.0	.	NM_006424	A5PL17|Q8N2K2|Q8WYA9|Q9P0V7	Missense_Mutation	SNP	ENST00000382051.3	hg19	CCDS3435.1	.	.	.	.	.	.	.	.	.	.	G	14.50	2.554825	0.45487	.	.	ENSG00000157765	ENST00000513204;ENST00000504570;ENST00000382051;ENST00000503434;ENST00000507530	D;D;D;D;D	0.88741	-2.42;-2.42;-2.42;-2.42;-2.42	5.22	3.48	0.39840	.	0.417009	0.25890	N	0.027622	D	0.95557	0.8556	H	0.96269	3.795	0.39001	D	0.95935	P;D	0.53619	0.952;0.961	P;P	0.62649	0.807;0.905	D	0.95577	0.8643	10	0.66056	D	0.02	-6.4871	12.5273	0.56093	0.0:0.1133:0.6559:0.2308	.	155;156	O95436-2;O95436	.;NPT2B_HUMAN	F	155;155;156;155;156	ENSP00000423038:L155F;ENSP00000425501:L155F;ENSP00000371483:L156F;ENSP00000423021:L155F;ENSP00000424266:L156F	ENSP00000371483:L156F	L	+	3	2	SLC34A2	25276936	1.000000	0.71417	0.820000	0.32676	0.765000	0.43378	2.164000	0.42387	0.301000	0.22738	-1.268000	0.01426	TTG	.	.	.	none		0.542	SLC34A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214990.1	NM_006424		C	25667838	G	C	25667838	3	2	273	1	0	0	0	0	1	0	0	0	14581	1339	47	4	482	4	SLC34A2	4	25667838	Missense_Mutation	SNP	G	TCGA-WN-AB4C-01A-11D-A42J-10	10029705	25667838	165486438	25	17250											
RNF150	57484	hgsc.bcm.edu	37	chr4	141868823	141868823	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaccggcagggcaggatcCggacaacgtcattgggcttg	8	7	14	12	3	2	0	2	0	0	0	3	2	3	2	2	5	1	3	2	5	1	2			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr4:141868823C>T	ENST00000515673.2	-	4	908	c.875G>A	c.(874-876)cGg>cAg	p.R292Q	RNF150_ENST00000507500.1_Missense_Mutation_p.R292Q|RNF150_ENST00000306799.3_Missense_Mutation_p.R250Q|RNF150_ENST00000379512.2_Missense_Mutation_p.R151Q|RNF150_ENST00000420921.2_Missense_Mutation_p.R151Q|RNF150_ENST00000515057.1_5'UTR			Q9ULK6	RN150_HUMAN	ring finger protein 150	292						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|large_intestine(10)|lung(7)|ovary(1)	19	all_hematologic(180;0.162)					GGGCAGGATCCGGACAACGTC	0.547																																					p.R292Q		Atlas-SNP	.											.	RNF150	94	.	0			c.G875A						PASS	.						149	116	127					4																	141868823		2203	4300	6503	SO:0001583	missense	57484	exon4			AGGATCCGGACAA	AB033040	CCDS34065.1	4q31.1	2013-01-09			ENSG00000170153	ENSG00000170153		"RING-type (C3HC4) zinc fingers"	23138	protein-coding gene	gene with protein product						10574462	Standard	XM_005263150		Approved	KIAA1214	uc003iio.1	Q9ULK6	OTTHUMG00000161380	ENST00000515673.2:c.875G>A	chr4.hg19:g.141868823C>T	ENSP00000425840:p.Arg292Gln	274.0	0.0	.		337.0	62.0	.	NM_020724	Q3T1D0|Q6ZNW6	Missense_Mutation	SNP	ENST00000515673.2	hg19	CCDS34065.1	.	.	.	.	.	.	.	.	.	.	C	35	5.493712	0.96339	.	.	ENSG00000170153	ENST00000379512;ENST00000420921;ENST00000306799;ENST00000515673;ENST00000507500;ENST00000506101	T;T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87;0.87	5.95	5.95	0.96441	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, RING-H2-type (1);	0.000000	0.85682	D	0.000000	T	0.72938	0.3523	M	0.90483	3.12	0.80722	D	1	D;D;D	0.89917	0.997;0.986;1.0	D;P;D	0.97110	0.918;0.902;1.0	T	0.77517	-0.2558	10	0.87932	D	0	.	19.1739	0.93594	0.0:1.0:0.0:0.0	.	250;292;292	Q9ULK6-2;Q9ULK6-3;Q9ULK6	.;.;RN150_HUMAN	Q	151;151;250;292;292;123	ENSP00000368827:R151Q;ENSP00000394581:R151Q;ENSP00000304321:R250Q;ENSP00000425840:R292Q;ENSP00000425568:R292Q;ENSP00000425947:R123Q	ENSP00000304321:R250Q	R	-	2	0	RNF150	142088273	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.133000	0.77259	2.827000	0.97445	0.650000	0.86243	CGG	.	.	.	none		0.547	RNF150-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364739.2	XM_291090		T	141868823	C	T	141868823	3	4	273	1	0	0	0	0	1	0	0	0	13464	652	23	1	457	1	RNF150	4	141868823	Missense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	116200985	141868823	49285453	26	17251											
FAT1	2195	hgsc.bcm.edu	37	chr4	187509944	187509944	+	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	ggcgcctcgaagtgtctttgAtaccctggcgggtaaggggc	6	9	16	10	3	1	1	0	1	1	0	2	2	1	1	2	5	1	1	2	5	3	3			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr4:187509944A>T	ENST00000441802.2	-	27	13778	c.13569T>A	c.(13567-13569)taT>taA	p.Y4523*		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	4523					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						AGTGTCTTTGATACCCTGGCG	0.547										HNSCC(5;0.00058)																											p.Y4523X	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T13569A						PASS	.						63	72	69					4																	187509944		2036	4200	6236	SO:0001587	stop_gained	2195	exon27			TCTTTGATACCCT	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.13569T>A	chr4.hg19:g.187509944A>T	ENSP00000406229:p.Tyr4523*	134.0	0.0	.		154.0	29.0	.	NM_005245		Nonsense_Mutation	SNP	ENST00000441802.2	hg19	CCDS47177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	53|53	20.095451|20.095451	0.99927|0.99927	.|.	.|.	ENSG00000083857|ENSG00000083857	ENST00000512772|ENST00000441802;ENST00000260147	.|.	.|.	.|.	5.37|5.37	-2.79|-2.79	0.05841|0.05841	.|.	.|0.240542	.|0.45606	.|D	.|0.000360	T|.	0.34658|.	0.0905|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.33189|.	-0.9878|.	4|.	.|0.02654	.|T	.|1	.|.	13.069|13.069	0.59050|0.59050	0.4573:0.0:0.5427:0.0|0.4573:0.0:0.5427:0.0	.|.	.|.	.|.	.|.	T|X	303|4523;4525	.|.	.|ENSP00000260147:Y4525X	S|Y	-|-	1|3	0|2	FAT1|FAT1	187746938|187746938	0.161000|0.161000	0.22892|0.22892	0.498000|0.498000	0.27564|0.27564	0.191000|0.191000	0.23601|0.23601	0.242000|0.242000	0.18087|0.18087	-0.311000|-0.311000	0.08754|0.08754	0.374000|0.374000	0.22700|0.22700	TCA|TAT	.	.	.	none		0.547	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		T	187509944	A	T	187509944	4	4	273	1	0	0	0	0	0	1	0	0	5696	340	12	5	201	5	FAT1	4	187509944	Nonsense_Mutation	SNP	A	TCGA-WN-AB4C-01A-11D-A42J-10	45641121	187509944	3644332	27	17252											
CDH12	1010	hgsc.bcm.edu	37	chr5	22078621	22078621	+	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	aaaaattgattccatacccaGccacgtttaacacgttggaa	15	10	6	10	2	0	1	0	1	0	0	1	2	1	2	3	1	3	2	3	1	5	6			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr5:22078621G>A	ENST00000382254.1	-	5	1251	c.165C>T	c.(163-165)ggC>ggT	p.G55G	CDH12_ENST00000522262.1_Silent_p.G55G|CDH12_ENST00000504376.2_Silent_p.G55G	NM_004061.3	NP_004052.2	P55289	CAD12_HUMAN	cadherin 12, type 2 (N-cadherin 2)	55	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(19)|lung(75)|ovary(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	120						TCCATACCCAGCCACGTTTAA	0.463										HNSCC(59;0.17)																											p.G55G		Atlas-SNP	.											.	CDH12	238	.	0			c.C165T						PASS	.						152	151	151					5																	22078621		2203	4300	6503	SO:0001819	synonymous_variant	1010	exon5			TACCCAGCCACGT	L33477	CCDS3890.1	5p14.3	2010-01-26			ENSG00000154162	ENSG00000154162		"Cadherins / Major cadherins"	1751	protein-coding gene	gene with protein product		600562				7731968	Standard	NM_004061		Approved	Br-cadherin, CDHB	uc003jgk.2	P55289	OTTHUMG00000090591	ENST00000382254.1:c.165C>T	chr5.hg19:g.22078621G>A		150.0	0.0	.		141.0	47.0	.	NM_004061	B2RBT1|B7Z2U6|Q86UD2	Silent	SNP	ENST00000382254.1	hg19	CCDS3890.1																																																																																			.	.	.	none		0.463	CDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207139.1	NM_004061		A	22078621	G	A	22078621	2	1	273	1	0	0	0	0	0	0	0	1	3100	958	34	2		2	CDH12	5	22078621	Silent	SNP	G	TCGA-WN-AB4C-01A-11D-A42J-10		22078621	158836639	28	17253											
TNPO1	3842	hgsc.bcm.edu	37	chr5	72192967	72192968	+	Frame_Shift_Ins	INS	-	-	AG																															aacacaccaaagacgttgttINSagagaatacaggtaccatat																										TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr5:72192967_72192968insAG	ENST00000337273.5	+	20	2753_2754	c.2327_2328insAG	c.(2326-2331)ttagagfs	p.LE776fs	TNPO1_ENST00000506351.2_Frame_Shift_Ins_p.LE768fs|TNPO1_ENST00000454282.1_Frame_Shift_Ins_p.LE726fs|TNPO1_ENST00000523768.1_Frame_Shift_Ins_p.LE726fs	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1	776					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)		AAGACGTTGTTAGAGAATACAG	0.371																																					p.L776fs		Atlas-Indel,Pindel	.											.	TNPO1	90	.	0			c.2327_2328insAG						PASS	.																																			SO:0001589	frameshift_variant	3842	exon20			.	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.2330_2331dupAG	chr5.hg19:g.72192970_72192971dupAG	ENSP00000336712:p.Leu776fs	228.0	0.0	0		226.0	51.0	0.225664	NM_002270	B4DVC6|Q92957|Q92975	Frame_Shift_Ins	INS	ENST00000337273.5	hg19	CCDS43329.1																																																																																			.	.	.	none		0.371	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	NM_002270		AG	72192968	-	AG	72192967	7	5	273	1	0	1	1	0	0	0	0	0	16347	1764	61	0	2405	0	TNPO1	5	72192967	Frame_Shift_Ins	INS	-	TCGA-WN-AB4C-01A-11D-A42J-10	50114346	72192967	108722293	29	17254											
AP3B1	8546	hgsc.bcm.edu	37	chr5	77536710	77536710	+	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	atatttttactggccacattCttcacaacagcaggaaacag	14	11	6	10	0	2	0	1	0	1	0	2	1	2	1	1	2	4	1	1	2	4	6			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr5:77536710C>A	ENST00000255194.6	-	3	430	c.255G>T	c.(253-255)aaG>aaT	p.K85N	AP3B1_ENST00000519295.1_Missense_Mutation_p.K36N	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	85					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)		TGGCCACATTCTTCACAACAG	0.303									Hermansky-Pudlak syndrome																												p.K85N		Atlas-SNP	.											.	AP3B1	94	.	0			c.G255T						PASS	.						115	125	122					5																	77536710		2203	4295	6498	SO:0001583	missense	8546	exon3	Familial Cancer Database	HPS, HPS1-8	CACATTCTTCACA	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.255G>T	chr5.hg19:g.77536710C>A	ENSP00000255194:p.Lys85Asn	661.0	0.0	.		612.0	150.0	.	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Missense_Mutation	SNP	ENST00000255194.6	hg19	CCDS4041.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.259112	0.80246	.	.	ENSG00000132842	ENST00000255194;ENST00000519295;ENST00000535760	T;T	0.33654	1.4;1.4	5.33	5.33	0.75918	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.57388	0.2050	M	0.72479	2.2	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.57207	-0.7851	10	0.46703	T	0.11	-18.0561	12.3808	0.55305	0.0:0.9228:0.0:0.0772	.	85	O00203	AP3B1_HUMAN	N	85;36;85	ENSP00000255194:K85N;ENSP00000430597:K36N	ENSP00000255194:K85N	K	-	3	2	AP3B1	77572466	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.623000	0.54224	2.489000	0.83994	0.591000	0.81541	AAG	.	.	.	none		0.303	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2			A	77536710	C	A	77536710	3	1	273	1	0	0	0	0	1	0	0	0	744	912	32	4	3129	4	AP3B1	5	77536710	Missense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	5343743	77536710	103378550	30	17255											
MEGF10	84466	hgsc.bcm.edu	37	chr5	126705644	126705644	+	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	ccatggtcgctgtattgctcCaaacacctgtcagtgtgagc	8	11	10	12	1	1	1	1	1	0	0	3	1	2	1	3	1	3	3	3	1	2	2			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr5:126705644C>G	ENST00000274473.6	+	6	629	c.362C>G	c.(361-363)cCa>cGa	p.P121R	MEGF10_ENST00000508365.1_Missense_Mutation_p.P121R|MEGF10_ENST00000503335.2_Missense_Mutation_p.P121R|MEGF10_ENST00000418761.2_Missense_Mutation_p.P121R	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10	121	EGF-like 1. {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)		TGTATTGCTCCAAACACCTGT	0.473																																					p.P121R		Atlas-SNP	.											.	MEGF10	152	.	0			c.C362G						PASS	.						194	160	172					5																	126705644		2203	4300	6503	SO:0001583	missense	84466	exon6			TTGCTCCAAACAC	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.362C>G	chr5.hg19:g.126705644C>G	ENSP00000274473:p.Pro121Arg	52.0	0.0	.		51.0	16.0	.	NM_032446	Q68DE5|Q8WUL3	Missense_Mutation	SNP	ENST00000274473.6	hg19	CCDS4142.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.445120	0.83993	.	.	ENSG00000145794	ENST00000503335;ENST00000508365;ENST00000418761;ENST00000274473	T;T;T;T	0.58210	0.35;0.35;0.35;0.35	5.16	5.16	0.70880	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.64402	D	0.000001	T	0.80778	0.4688	H	0.94582	3.555	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	D	0.84847	0.0811	10	0.45353	T	0.12	-7.4634	18.7442	0.91787	0.0:1.0:0.0:0.0	.	121;121	Q96KG7-2;Q96KG7	.;MEG10_HUMAN	R	121	ENSP00000423354:P121R;ENSP00000423195:P121R;ENSP00000416284:P121R;ENSP00000274473:P121R	ENSP00000274473:P121R	P	+	2	0	MEGF10	126733543	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.800000	0.85949	2.422000	0.82143	0.558000	0.71614	CCA	.	.	.	none		0.473	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446		G	126705644	C	G	126705644	3	3	273	1	0	0	0	0	1	0	0	0	9467	594	21	4	376	4	MEGF10	5	126705644	Missense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	49168934	126705644	54209616	31	17256											
KDM3B	51780	hgsc.bcm.edu	37	chr5	137760025	137760025	+	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	tccgggagtgttggaagcaaGgtcaggtaagcaagaataag	14	7	15	5	1	1	1	1	0	0	1	2	3	2	3	1	4	2	4	1	4	6	3			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr5:137760025G>C	ENST00000314358.5	+	16	4434	c.4234G>C	c.(4234-4236)Ggt>Cgt	p.G1412R	KDM3B_ENST00000394866.1_Missense_Mutation_p.G1068R|KDM3B_ENST00000542866.1_Missense_Mutation_p.G444R	NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	1412					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						TTGGAAGCAAGGTCAGGTAAG	0.488																																					p.G1412R		Atlas-SNP	.											.	KDM3B	177	.	0			c.G4234C						PASS	.						85	83	84					5																	137760025		2203	4300	6503	SO:0001583	missense	51780	exon16			AAGCAAGGTCAGG	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.4234G>C	chr5.hg19:g.137760025G>C	ENSP00000326563:p.Gly1412Arg	107.0	0.0	.		99.0	25.0	.	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Missense_Mutation	SNP	ENST00000314358.5	hg19	CCDS34242.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.894733	0.91962	.	.	ENSG00000120733	ENST00000314358;ENST00000545151;ENST00000394866;ENST00000542866	T;T;T	0.72835	-0.69;-0.69;-0.69	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	D	0.85965	0.5820	M	0.82323	2.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.87723	0.2574	10	0.72032	D	0.01	-26.8379	19.036	0.92978	0.0:0.0:1.0:0.0	.	1068;1412	Q7LBC6-2;Q7LBC6	.;KDM3B_HUMAN	R	1412;1202;1068;444	ENSP00000326563:G1412R;ENSP00000378335:G1068R;ENSP00000439462:G444R	ENSP00000326563:G1412R	G	+	1	0	KDM3B	137787924	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.869000	0.99810	2.486000	0.83907	0.563000	0.77884	GGT	.	.	.	none		0.488	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604		C	137760025	G	C	137760025	3	2	273	1	0	0	0	0	1	0	0	0	8134	1000	35	4	4296	4	KDM3B	5	137760025	Missense_Mutation	SNP	G	TCGA-WN-AB4C-01A-11D-A42J-10	11054381	137760025	43155235	32	17257											
FAM71B	153745	hgsc.bcm.edu	37	chr5	156590429	156590429	+	Missense_Mutation	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	cattgctgcccctgctattgCcacatctgttctaggtcctg	5	14	8	14	0	2	0	0	0	2	0	3	0	3	0	4	1	4	3	4	1	2	5			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr5:156590429C>T	ENST00000302938.4	-	2	942	c.847G>A	c.(847-849)Gca>Aca	p.A283T		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	283	Ala-rich.					nucleus (GO:0005634)				NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CCTGCTATTGCCACATCTGTT	0.582																																					p.A283T		Atlas-SNP	.											.	FAM71B	145	.	0			c.G847A						PASS	.						126	104	111					5																	156590429		2203	4300	6503	SO:0001583	missense	153745	exon2			CTATTGCCACATC		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.847G>A	chr5.hg19:g.156590429C>T	ENSP00000305596:p.Ala283Thr	55.0	0.0	.		53.0	15.0	.	NM_130899	Q1EDD9|Q8TC64|Q96LY8	Missense_Mutation	SNP	ENST00000302938.4	hg19	CCDS4335.1	.	.	.	.	.	.	.	.	.	.	C	11.10	1.539642	0.27563	.	.	ENSG00000170613	ENST00000302938	T	0.04809	3.55	3.7	1.86	0.25419	.	0.829219	0.10160	N	0.708438	T	0.04770	0.0129	L	0.45137	1.4	0.09310	N	1	B	0.29909	0.261	B	0.22880	0.042	T	0.38373	-0.9664	10	0.48119	T	0.1	-2.3928	6.3492	0.21367	0.0:0.7665:0.0:0.2335	.	283	Q8TC56	FA71B_HUMAN	T	283	ENSP00000305596:A283T	ENSP00000305596:A283T	A	-	1	0	FAM71B	156523007	0.000000	0.05858	0.001000	0.08648	0.066000	0.16364	-0.131000	0.10482	0.506000	0.28125	0.467000	0.42956	GCA	.	.	.	none		0.582	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899		T	156590429	C	T	156590429	3	4	273	1	0	0	0	0	1	0	0	0	5615	739	26	2	974	2	FAM71B	5	156590429	Missense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	18830404	156590429	24324831	33	17258											
PECI	10455	hgsc.bcm.edu	37	chr6	4131018	4131018	+	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	caccttgggcaggctgccaaGggcattccatgcgtcccatt	7	9	11	14	1	0	0	0	0	0	0	2	0	2	0	4	3	2	3	4	3	1	3			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr6:4131018G>A	ENST00000380118.3	-	3	331	c.295C>T	c.(295-297)Ctt>Ttt	p.L99F	C6orf201_ENST00000380175.4_3'UTR|ECI2_ENST00000380125.2_Missense_Mutation_p.L69F|ECI2_ENST00000413766.2_5'UTR|ECI2_ENST00000465828.1_Missense_Mutation_p.L69F|ECI2_ENST00000361538.2_Missense_Mutation_p.L69F			O75521	ECI2_HUMAN	enoyl-CoA delta isomerase 2	99	ACB. {ECO:0000255|PROSITE- ProRule:PRU00573}.				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						AGGCTGCCAAGGGCATTCCAT	0.458																																					p.L99F		Atlas-SNP	.											.	ECI2	59	.	0			c.C295T						PASS	.						158	143	148					6																	4131018		2203	4300	6503	SO:0001583	missense	10455	exon3			TGCCAAGGGCATT	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.295C>T	chr6.hg19:g.4131018G>A	ENSP00000369461:p.Leu99Phe	104.0	0.0	.		91.0	25.0	.	NM_206836	Q5JYK5|Q5JYK7|Q7L124|Q8N0X0|Q9BUE9|Q9H0T9|Q9NQH1|Q9NYH7|Q9UN55	Missense_Mutation	SNP	ENST00000380118.3	hg19	CCDS43420.2	.	.	.	.	.	.	.	.	.	.	G	21.3	4.131222	0.77549	.	.	ENSG00000198721	ENST00000380118;ENST00000380125;ENST00000361538;ENST00000465828;ENST00000495548	T;T;T;T;T	0.26518	1.73;1.73;1.73;1.73;1.73	6.06	5.19	0.71726	FERM/acyl-CoA-binding protein, 3-helical bundle (1);Acyl-CoA-binding protein, ACBP (3);	0.404887	0.25316	N	0.031541	T	0.29126	0.0724	M	0.82433	2.59	0.80722	D	1	B	0.34061	0.436	P	0.45829	0.494	T	0.19192	-1.0313	10	0.54805	T	0.06	.	9.0981	0.36651	0.163:0.0:0.837:0.0	.	99	O75521	ECI2_HUMAN	F	99;69;69;69;146	ENSP00000369461:L99F;ENSP00000369468:L69F;ENSP00000354737:L69F;ENSP00000420309:L69F;ENSP00000417459:L146F	ENSP00000354737:L69F	L	-	1	0	ECI2	4076017	1.000000	0.71417	0.871000	0.34182	0.983000	0.72400	5.373000	0.66162	1.569000	0.49696	0.655000	0.94253	CTT	.	.	.	none		0.458	ECI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039716.4	NM_006117		A	4131018	G	A	4131018	3	1	273	1	0	0	0	0	1	0	0	0	11723	1000	35	2	921	2	PECI	6	4131018	Missense_Mutation	SNP	G	TCGA-WN-AB4C-01A-11D-A42J-10		4131018	166984049	34	17259											
MRS2	57380	hgsc.bcm.edu	37	chr6	24405466	24405466	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgtagccccagtatttacTgtggtgagtatgtacagtac	10	13	11	7	0	0	1	0	1	0	0	0	1	0	1	2	1	4	5	2	1	6	7			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr6:24405466T>C	ENST00000378386.3	+	2	354	c.261T>C	c.(259-261)acT>acC	p.T87T	MRS2_ENST00000443868.2_Silent_p.T87T|MRS2_ENST00000378353.1_Silent_p.T87T|MRS2_ENST00000535061.1_Silent_p.T87T|MRS2_ENST00000483634.1_3'UTR|MRS2_ENST00000274747.7_Silent_p.T87T|MRS2_ENST00000543597.1_Intron	NM_020662.2	NP_065713.1	Q9HD23	MRS2_HUMAN	MRS2 magnesium transporter	87						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						CAGTATTTACTGTGGTGAGTA	0.423																																					p.T87T		Atlas-SNP	.											.	MRS2	31	.	0			c.T261C						PASS	.						118	105	109					6																	24405466		2203	4300	6503	SO:0001819	synonymous_variant	57380	exon2			ATTTACTGTGGTG	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.261T>C	chr6.hg19:g.24405466T>C		64.0	0.0	.		43.0	12.0	.	NM_020662	A8K4U3|B3KNN2|B4DQL2|Q5T3Y1|Q6NTG4|Q96KF8|Q9BVP1	Silent	SNP	ENST00000378386.3	hg19	CCDS4552.1	.	.	.	.	.	.	.	.	.	.	T	10.76	1.442039	0.25900	.	.	ENSG00000124532	ENST00000446191	.	.	.	5.0	2.61	0.31194	.	.	.	.	.	T	0.36166	0.0957	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21381	-1.0247	4	.	.	.	-10.5347	4.7063	0.12851	0.1739:0.1633:0.0:0.6628	.	.	.	.	P	39	.	.	L	+	2	0	MRS2	24513445	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	0.331000	0.19733	0.484000	0.27630	0.533000	0.62120	CTG	.	.	.	none		0.423	MRS2-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040002.1			C	24405466	T	C	24405466	2	2	273	1	0	0	0	0	0	0	0	1	9858	1567	55	3		3	MRS2	6	24405466	Silent	SNP	T	TCGA-WN-AB4C-01A-11D-A42J-10	20274448	24405466	146709601	35	17260											
SLC25A27	9481	hgsc.bcm.edu	37	chr6	46626712	46626712	+	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	tacccagtgtattctggaggTcgaatggtcacatatgaaca	12	11	10	8	1	2	1	1	1	1	0	3	3	2	2	1	3	2	1	1	3	5	4			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr6:46626712T>A	ENST00000371347.5	+	3	564	c.312T>A	c.(310-312)ggT>ggA	p.G104G	SLC25A27_ENST00000604908.1_3'UTR|SLC25A27_ENST00000411689.2_Silent_p.G104G|SLC25A27_ENST00000452689.2_Silent_p.G18G	NM_001204051.1|NM_004277.4	NP_001190980.1|NP_004268.3	O95847	UCP4_HUMAN	solute carrier family 25, member 27	104					cellular triglyceride homeostasis (GO:0035356)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mitochondrial calcium ion concentration (GO:0051562)|negative regulation of mitochondrial membrane potential (GO:0010917)|neuron death (GO:0070997)|positive regulation of cell proliferation (GO:0008284)|regulation of glucose import (GO:0046324)|transport (GO:0006810)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)				central_nervous_system(1)|kidney(1)|lung(4)|prostate(1)|urinary_tract(1)	8			Lung(136;0.192)			ATTCTGGAGGTCGAATGGTCA	0.353																																					p.G104G		Atlas-SNP	.											.	SLC25A27	22	.	0			c.T312A						PASS	.						242	226	231					6																	46626712		1842	4090	5932	SO:0001819	synonymous_variant	9481	exon3			TGGAGGTCGAATG	AK090871	CCDS43470.1, CCDS56431.1	6p12.3	2013-05-22			ENSG00000153291	ENSG00000153291		"Solute carriers"	21065	protein-coding gene	gene with protein product		613725				10025957, 10772343	Standard	NM_004277		Approved	UCP4, FLJ33552	uc003oyh.3	O95847	OTTHUMG00000014786	ENST00000371347.5:c.312T>A	chr6.hg19:g.46626712T>A		140.0	0.0	.		128.0	31.0	.	NM_001204051	F5GWR4|Q5VTS9|Q8N518	Silent	SNP	ENST00000371347.5	hg19	CCDS43470.1																																																																																			.	.	.	none		0.353	SLC25A27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040791.1	NM_004277		A	46626712	T	A	46626712	2	1	273	1	0	0	0	0	0	0	0	1	14503	1654	58	5		5	SLC25A27	6	46626712	Silent	SNP	T	TCGA-WN-AB4C-01A-11D-A42J-10	22221246	46626712	124488355	36	17261											
CASP8AP2	9994	hgsc.bcm.edu	37	chr6	90571848	90571848	+	RNA	SNP	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	tttttatttcataatagattGtctgagtttccacattttcg	9	21	5	6	1	2	2	1	1	1	1	4	2	3	2	1	0	0	1	1	0	3	10			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr6:90571848G>A	ENST00000551025.1	+	0	1857									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)		ATAATAGATTGTCTGAGTTTC	0.269																																					p.L140L	Colon(187;1656 2025 17045 31481 39901)	Atlas-SNP	.											.	CASP8AP2	108	.	0			c.G420A						PASS	.						25	22	23					6																	90571848		1786	4055	5841			9994	exon7			TAGATTGTCTGAG	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"FLICE-associated huge protein"	606880	"CASP8 associated protein 2"			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		chr6.hg19:g.90571848G>A		102.0	0.0	.		86.0	22.0	.	NM_001137667		Silent	SNP	ENST00000551025.1	hg19																																																																																				.	.	.	none		0.269	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667		A	90571848	G	A	90571848	1	1	273	0	1	0	0	0	0	0	0	0	2680	1368	48	2		2	CASP8AP2	6	90571848	RNA	SNP	G	TCGA-WN-AB4C-01A-11D-A42J-10	43945136	90571848	80543219	37	17262											
L3MBTL3	84456	hgsc.bcm.edu	37	chr6	130415502	130415502	+	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	tcaagagagcgagacatctgGgccctcacaggtatgtggta	11	8	13	9	1	3	2	2	0	1	2	3	4	3	2	1	3	1	2	1	3	3	2			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr6:130415502G>A	ENST00000529410.1	+	20	2205	c.1726G>A	c.(1726-1728)Ggc>Agc	p.G576S	L3MBTL3_ENST00000533560.1_Missense_Mutation_p.G551S|L3MBTL3_ENST00000368136.2_Missense_Mutation_p.G576S|L3MBTL3_ENST00000526019.1_Missense_Mutation_p.G551S|L3MBTL3_ENST00000361794.2_Missense_Mutation_p.G576S|L3MBTL3_ENST00000368139.2_Missense_Mutation_p.G551S			Q96JM7	LMBL3_HUMAN	l(3)mbt-like 3 (Drosophila)	576					chromatin modification (GO:0016568)|erythrocyte maturation (GO:0043249)|granulocyte differentiation (GO:0030851)|macrophage differentiation (GO:0030225)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				cervix(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|skin(4)|stomach(1)|urinary_tract(1)	43				GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)		GAGACATCTGGGCCCTCACAG	0.413																																					p.G576S		Atlas-SNP	.											.	L3MBTL3	99	.	0			c.G1726A						PASS	.						73	67	69					6																	130415502		2203	4300	6503	SO:0001583	missense	84456	exon18			CATCTGGGCCCTC	AB058701	CCDS34537.1, CCDS34538.1	6q23	2013-01-10			ENSG00000198945	ENSG00000198945		"Sterile alpha motif (SAM) domain containing"	23035	protein-coding gene	gene with protein product							Standard	NM_032438		Approved	KIAA1798	uc003qbt.3	Q96JM7	OTTHUMG00000015554	ENST00000529410.1:c.1726G>A	chr6.hg19:g.130415502G>A	ENSP00000431962:p.Gly576Ser	91.0	0.0	.		95.0	23.0	.	NM_032438	Q4VXE1|Q5VUM9|Q6P9B5	Missense_Mutation	SNP	ENST00000529410.1	hg19	CCDS34537.1	.	.	.	.	.	.	.	.	.	.	G	16.51	3.143485	0.57044	.	.	ENSG00000198945	ENST00000529410;ENST00000533560;ENST00000361794;ENST00000368139;ENST00000526019;ENST00000368136	T;T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99;0.99	6.05	5.19	0.71726	.	0.268826	0.43110	N	0.000601	T	0.11665	0.0284	N	0.20328	0.56	0.45704	D	0.998618	B;B	0.10296	0.003;0.0	B;B	0.12156	0.007;0.002	T	0.09707	-1.0662	10	0.09338	T	0.73	.	12.3272	0.55018	0.0785:0.0:0.9215:0.0	.	551;576	Q96JM7-2;Q96JM7	.;LMBL3_HUMAN	S	576;551;576;551;551;576	ENSP00000431962:G576S;ENSP00000437185:G551S;ENSP00000354526:G576S;ENSP00000357121:G551S;ENSP00000436706:G551S;ENSP00000357118:G576S	ENSP00000354526:G576S	G	+	1	0	L3MBTL3	130457195	0.998000	0.40836	1.000000	0.80357	0.994000	0.84299	2.838000	0.48199	1.565000	0.49641	0.650000	0.86243	GGC	.	.	.	none		0.413	L3MBTL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042195.2	XM_027074		A	130415502	G	A	130415502	3	1	273	1	0	0	0	0	1	0	0	0	8600	1232	43	2	1788	2	L3MBTL3	6	130415502	Missense_Mutation	SNP	G	TCGA-WN-AB4C-01A-11D-A42J-10	39843654	130415502	40699565	38	17263											
MAP3K4	4216	hgsc.bcm.edu	37	chr6	161470102	161470103	+	Frame_Shift_Del	DEL	AG	AG	-																															tctaacgaactgatctggttAgagctacaagcctggcatgc																										TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr6:161470102_161470103delAG	ENST00000392142.4	+	3	946_947	c.798_799delAG	c.(796-801)ttagagfs	p.E267fs	MAP3K4_ENST00000366920.2_Frame_Shift_Del_p.E267fs|MAP3K4_ENST00000366919.2_Frame_Shift_Del_p.E267fs|MAP3K4_ENST00000348824.7_Frame_Shift_Del_p.E267fs	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	267					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)		TGATCTGGTTAGAGCTACAAGC	0.421																																					p.266_266del		Atlas-Indel,Pindel	.											.	MAP3K4	364	.	0			c.797_798del						PASS	.																																			SO:0001589	frameshift_variant	4216	exon3			.	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.798_799delAG	chr6.hg19:g.161470104_161470105delAG	ENSP00000375986:p.Glu267fs	233.0	0.0	0		187.0	57.0	0.304813	NM_006724	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Frame_Shift_Del	DEL	ENST00000392142.4	hg19	CCDS34565.1																																																																																			.	.	.	none		0.421	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			-	161470103	AG	-	161470102	7	5	273	1	0	1	0	1	0	0	0	0	9259	417	15	0	808	0	MAP3K4	6	161470102	Frame_Shift_Del	DEL	AG	TCGA-WN-AB4C-01A-11D-A42J-10	31054600	161470102	9644965	39	17264											
ZMIZ2	83637	hgsc.bcm.edu	37	chr7	44801088	44801088	+	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	ttgcggctgaccttccctgtGcgcgatggggtggtcctgga	3	11	16	11	3	0	1	0	1	0	0	2	3	2	2	3	5	2	1	3	5	0	2			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr7:44801088G>A	ENST00000309315.4	+	10	1404	c.1281G>A	c.(1279-1281)gtG>gtA	p.V427V	ZMIZ2_ENST00000441627.1_Silent_p.V427V|ZMIZ2_ENST00000265346.7_Silent_p.V401V|ZMIZ2_ENST00000433667.1_Silent_p.V395V|ZMIZ2_ENST00000413916.1_Silent_p.V369V	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2	427					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						CCTTCCCTGTGCGCGATGGGG	0.612																																					p.V427V	NSCLC(20;604 852 1948 16908 50522)	Atlas-SNP	.											.	ZMIZ2	82	.	0			c.G1281A						PASS	.						55	66	62					7																	44801088		2203	4300	6503	SO:0001819	synonymous_variant	83637	exon10			CCCTGTGCGCGAT	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.1281G>A	chr7.hg19:g.44801088G>A		58.0	0.0	.		37.0	10.0	.	NM_031449	A4D2K7|D3DVL1|O94790|Q0VGB4|Q659A8|Q6JKL5|Q8WTX8|Q96Q01|Q9BQH7	Silent	SNP	ENST00000309315.4	hg19	CCDS43576.1																																																																																			.	.	.	none		0.612	ZMIZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341790.1	NM_031449		A	44801088	G	A	44801088	2	1	273	1	0	0	0	0	0	0	0	1	17709	1306	46	2		2	ZMIZ2	7	44801088	Silent	SNP	G	TCGA-WN-AB4C-01A-11D-A42J-10		44801088	114337575	40	17265											
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47832364	47832364	+	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	tcttcatcagaagttcgtctAacagatttgcaaattcatcc	12	14	5	10	1	5	2	3	0	2	2	7	2	6	2	1	0	2	2	1	0	3	5			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr7:47832364A>T	ENST00000289672.2	-	56	8437	c.8387T>A	c.(8386-8388)tTa>tAa	p.L2796*	C7orf69_ENST00000418326.2_5'Flank|C7orf69_ENST00000258776.4_5'Flank	NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2796					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						AAGTTCGTCTAACAGATTTGC	0.398																																					p.L2796X		Atlas-SNP	.											.	PKD1L1	328	.	0			c.T8387A						PASS	.						113	105	108					7																	47832364		2203	4300	6503	SO:0001587	stop_gained	168507	exon56			TCGTCTAACAGAT	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.8387T>A	chr7.hg19:g.47832364A>T	ENSP00000289672:p.Leu2796*	83.0	0.0	.		92.0	26.0	.	NM_138295	Q6UWK1	Nonsense_Mutation	SNP	ENST00000289672.2	hg19	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	A	49	15.550097	0.99837	.	.	ENSG00000158683	ENST00000289672	.	.	.	4.95	4.95	0.65309	.	1.192360	0.06551	N	0.745053	.	.	.	.	.	.	0.58432	A	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.9412	10.9277	0.47199	1.0:0.0:0.0:0.0	.	.	.	.	X	2796	.	ENSP00000289672:L2796X	L	-	2	0	PKD1L1	47798889	0.009000	0.17119	0.021000	0.16686	0.942000	0.58702	2.146000	0.42216	2.086000	0.62901	0.533000	0.62120	TTA	.	.	.	none		0.398	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		T	47832364	A	T	47832364	4	4	273	1	0	0	0	0	0	1	0	0	11971	372	13	5	170	5	PKD1L1	7	47832364	Nonsense_Mutation	SNP	A	TCGA-WN-AB4C-01A-11D-A42J-10	3031276	47832364	111306299	41	17266											
PON2	5445	hgsc.bcm.edu	37	chr7	95064242	95064247	+	In_Frame_Del	DEL	CCACAG	CCACAG	-																															cagcgcgatccccagcaagcCcacagccaccagccgcccca																										TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	CCACAG	CCACAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr7:95064242_95064247delCCACAG	ENST00000222572.3	-	1	263_268	c.17_22delCTGTGG	c.(16-24)gctgtgggc>ggc	p.AV6del	PON2_ENST00000536183.1_In_Frame_Del_p.AV27del|PON2_ENST00000433091.2_In_Frame_Del_p.AV6del			Q15165	PON2_HUMAN	paraoxonase 2	6					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)			CCCAGCAAGCCCACAGCCACCAGCCG	0.757																																					p.6_8del	GBM(42;803 823 13649 23368 31463)	Atlas-Indel,Pindel	.											.	PON2	32	.	0			c.18_23del						PASS	.																																			SO:0001651	inframe_deletion	5445	exon1			.	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.17_22delCTGTGG	chr7.hg19:g.95064242_95064247delCCACAG	ENSP00000222572:p.Ala6_Val7del	101.0	0.0	0		101.0	18.0	0.178218	NM_000305	A4D1H7|B2RCP9|B4DJD5|O15114|O15115|O75856|Q5FBX7|Q86YL0	In_Frame_Del	DEL	ENST00000222572.3	hg19	CCDS5640.1																																																																																			.	.	.	none		0.757	PON2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333142.1	NM_000305		-	95064247	CCACAG	-	95064242	7	5	273	1	0	1	0	1	0	0	0	0	12256	623	22	0	1078	0	PON2	7	95064242	In_Frame_Del	DEL	CCACAG	TCGA-WN-AB4C-01A-11D-A42J-10	47231878	95064242	64074421	42	17267											
CADPS2	93664	hgsc.bcm.edu	37	chr7	121960313	121960313	+	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	tggcctcctctactgttaaaCgtctgtgcacagtatcataa	10	13	7	11	1	3	0	1	0	2	0	4	0	4	0	2	1	3	3	2	1	5	4			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr7:121960313C>T	ENST00000449022.2	-	30	3816	c.3797G>A	c.(3796-3798)cGt>cAt	p.R1266H	CADPS2_ENST00000313070.7_Missense_Mutation_p.R1225H|CADPS2_ENST00000412584.2_Missense_Mutation_p.R1225H|CADPS2_ENST00000334010.7_Missense_Mutation_p.R1264H	NM_017954.10	NP_060424.9	Q86UW7	CAPS2_HUMAN	Ca++-dependent secretion activator 2	1266					cellular response to starvation (GO:0009267)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasmic membrane-bounded vesicle (GO:0016023)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(2)	43						TACTGTTAAACGTCTGTGCAC	0.433																																					p.R1270H		Atlas-SNP	.											.	CADPS2	116	.	0			c.G3809A						PASS	.						188	178	181					7																	121960313		1913	4121	6034	SO:0001583	missense	93664	exon30			GTTAAACGTCTGT		CCDS47691.1, CCDS55158.1	7q31.32	2013-01-10	2008-08-28		ENSG00000081803	ENSG00000081803		"Pleckstrin homology (PH) domain containing"	16018	protein-coding gene	gene with protein product		609978	"Ca++-dependent activator protein for secretion 2"				Standard	NM_017954		Approved		uc010lkq.3	Q86UW7	OTTHUMG00000157093	ENST00000449022.2:c.3797G>A	chr7.hg19:g.121960313C>T	ENSP00000398481:p.Arg1266His	76.0	0.0	.		93.0	20.0	.	NM_001167940	A4D0X3|B7ZM56|Q658Q2|Q7Z5T7|Q8IZW9|Q8N7M4|Q9H6P4|Q9HCI1|Q9NWK8	Missense_Mutation	SNP	ENST00000449022.2	hg19	CCDS55158.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	34|34	5.308018|5.308018	0.95629|0.95629	.|.	.|.	ENSG00000081803|ENSG00000081803	ENST00000360097;ENST00000313070;ENST00000334010;ENST00000420900;ENST00000545465;ENST00000412584;ENST00000449022|ENST00000462699	T;T;T;T|.	0.35236|.	1.32;1.32;1.32;1.32|.	5.63|5.63	5.63|5.63	0.86233|0.86233	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.83193|0.83193	0.5201|0.5201	M|M	0.84585|0.84585	2.705|2.705	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|.	0.97110|.	0.992;1.0;0.991;0.994|.	D|D	0.84139|0.84139	0.0416|0.0416	10|5	0.87932|.	D|.	0|.	-10.5465|-10.5465	19.6777|19.6777	0.95943|0.95943	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1270;1225;1266;1220|.	B7ZM57;Q86UW7-2;Q86UW7;Q86UW7-3|.	.;.;CAPS2_HUMAN;.|.	H|I	439;1225;1264;1271;1192;1225;1266|460	ENSP00000325581:R1225H;ENSP00000333940:R1264H;ENSP00000400401:R1225H;ENSP00000398481:R1266H|.	ENSP00000325581:R1225H|.	R|V	-|-	2|1	0|0	CADPS2|CADPS2	121747549|121747549	1.000000|1.000000	0.71417|0.71417	0.907000|0.907000	0.35723|0.35723	0.986000|0.986000	0.74619|0.74619	7.487000|7.487000	0.81328|0.81328	2.669000|2.669000	0.90835|0.90835	0.650000|0.650000	0.86243|0.86243	CGT|GTT	.	.	.	none		0.433	CADPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347414.2	NM_017954		T	121960313	C	T	121960313	3	4	273	1	0	0	0	0	1	0	0	0	2573	536	19	1	97	1	CADPS2	7	121960313	Missense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	26896071	121960313	37178350	43	17268											
TRPV5	56302	hgsc.bcm.edu	37	chr7	142609899	142609899	+	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	actggttgggtcctctgtctGgaaaatgatatagaacgctg	10	12	12	7	1	2	2	0	1	2	1	3	3	3	3	1	3	1	2	1	3	5	3			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr7:142609899G>T	ENST00000265310.1	-	13	1885	c.1537C>A	c.(1537-1539)Cag>Aag	p.Q513K		NM_019841.4	NP_062815.2	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel, subfamily V, member 5	513					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|ion transmembrane transport (GO:0034220)|protein tetramerization (GO:0051262)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(14)|lung(32)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	67	Melanoma(164;0.059)					TCCTCTGTCTGGAAAATGATA	0.463																																					p.Q513K		Atlas-SNP	.											.	TRPV5	164	.	0			c.C1537A						PASS	.						114	107	109					7																	142609899		2203	4300	6503	SO:0001583	missense	56302	exon13			CTGTCTGGAAAAT	AJ271207	CCDS5875.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000127412	ENSG00000127412		"Voltage-gated ion channels / Transient receptor potential cation channels", "Ankyrin repeat domain containing"	3145	protein-coding gene	gene with protein product		606679	"epithelial calcium channel 1"	ECAC1		10944439, 10945469, 16382100	Standard	NM_019841		Approved	CaT2	uc003wby.1	Q9NQA5	OTTHUMG00000157157	ENST00000265310.1:c.1537C>A	chr7.hg19:g.142609899G>T	ENSP00000265310:p.Gln513Lys	113.0	0.0	.		96.0	25.0	.	NM_019841	A4D2H7|E9PBZ6|Q8N4C1|Q8NDW5|Q8NDX7|Q8NDX8|Q96PM6	Missense_Mutation	SNP	ENST00000265310.1	hg19	CCDS5875.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.165969	0.78339	.	.	ENSG00000127412	ENST00000265310;ENST00000439304	D;D	0.85411	-1.98;-1.98	5.52	5.52	0.82312	Ion transport (1);	0.108012	0.64402	D	0.000006	D	0.92319	0.7563	M	0.85197	2.74	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	D	0.89121	0.3503	10	0.09843	T	0.71	-3.8699	18.8051	0.92034	0.0:0.0:1.0:0.0	.	513	Q9NQA5	TRPV5_HUMAN	K	513;458	ENSP00000265310:Q513K;ENSP00000406361:Q458K	ENSP00000265310:Q513K	Q	-	1	0	TRPV5	142320021	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.486000	0.73629	2.751000	0.94390	0.655000	0.94253	CAG	.	.	.	none		0.463	TRPV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347660.1	NM_019841		T	142609899	G	T	142609899	3	4	273	1	0	0	0	0	1	0	0	0	16611	1357	47	4	664	4	TRPV5	7	142609899	Missense_Mutation	SNP	G	TCGA-WN-AB4C-01A-11D-A42J-10	20649586	142609899	16528764	44	17269											
SLC7A2	6542	hgsc.bcm.edu	37	chr8	17419548	17419548	+	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	tcgctctcctcgcgctgtttCttgttctcttcgttgccatc	1	18	7	15	4	3	0	0	0	3	0	9	0	3	0	2	0	1	5	2	0	0	5			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr8:17419548C>A	ENST00000494857.1	+	11	1818	c.1600C>A	c.(1600-1602)Ctt>Att	p.L534I	SLC7A2_ENST00000398090.3_Missense_Mutation_p.L573I|SLC7A2_ENST00000522656.1_Missense_Mutation_p.L534I|SLC7A2_ENST00000004531.10_Missense_Mutation_p.L574I|SLC7A2_ENST00000470360.1_Missense_Mutation_p.L573I	NM_001008539.3	NP_001008539.3	P52569	CTR2_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	534					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)	CGCGCTGTTTCTTGTTCTCTT	0.527																																					p.L574I		Atlas-SNP	.											.	SLC7A2	157	.	0			c.C1720A						PASS	.						130	112	118					8																	17419548		2203	4300	6503	SO:0001583	missense	6542	exon10			CTGTTTCTTGTTC	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.1600C>A	chr8.hg19:g.17419548C>A	ENSP00000419140:p.Leu534Ile	39.0	0.0	.		40.0	15.0	.	NM_001164771	B7ZL54|O15291|O15292|Q14CQ6|Q6NSZ7|Q86TC6	Missense_Mutation	SNP	ENST00000494857.1	hg19	CCDS34852.1	.	.	.	.	.	.	.	.	.	.	C	11.08	1.532320	0.27387	.	.	ENSG00000003989	ENST00000494857;ENST00000522656;ENST00000470360;ENST00000004531;ENST00000398090	D;D;D;D;D	0.89617	-2.37;-2.37;-2.54;-2.4;-2.54	4.83	2.88	0.33553	.	0.195656	0.45606	D	0.000357	T	0.80747	0.4682	L	0.33485	1.01	0.09310	N	0.999998	B;B;B	0.19331	0.035;0.0;0.004	B;B;B	0.29663	0.105;0.012;0.003	T	0.68907	-0.5285	10	0.49607	T	0.09	.	3.2225	0.06720	0.3854:0.3832:0.1468:0.0846	.	574;573;534	P52569-3;P52569-2;P52569	.;.;CTR2_HUMAN	I	534;534;573;574;573	ENSP00000419140:L534I;ENSP00000430464:L534I;ENSP00000419873:L573I;ENSP00000004531:L574I;ENSP00000381164:L573I	ENSP00000004531:L574I	L	+	1	0	SLC7A2	17463840	0.301000	0.24444	0.021000	0.16686	0.010000	0.07245	0.849000	0.27723	1.381000	0.46364	0.563000	0.77884	CTT	.	.	.	none		0.527	SLC7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253367.3	NM_003046		A	17419548	C	A	17419548	3	1	273	1	0	0	0	0	1	0	0	0	14710	913	32	4	1899	4	SLC7A2	8	17419548	Missense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10		17419548	128944474	45	17270											
ANXA13	312	hgsc.bcm.edu	37	chr8	124705533	124705533	+	Silent	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	tcagtgccccagcggccttcCcctgcctcaagggtcaaata	8	8	9	16	1	3	0	3	0	0	0	4	0	4	0	6	2	3	0	6	2	3	2			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr8:124705533C>T	ENST00000419625.1	-	8	618	c.546G>A	c.(544-546)ggG>ggA	p.G182G	ANXA13_ENST00000262219.6_Silent_p.G223G	NM_004306.2	NP_004297.2	P27216	ANX13_HUMAN	annexin A13	182					cell differentiation (GO:0030154)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|exocytic vesicle (GO:0070382)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylglycerol binding (GO:1901611)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	25	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)			AGCGGCCTTCCCCTGCCTCAA	0.458																																					p.G223G		Atlas-SNP	.											.	ANXA13	38	.	0			c.G669A						PASS	.						118	120	120					8																	124705533		2203	4300	6503	SO:0001819	synonymous_variant	312	exon9			GCCTTCCCCTGCC	Z11502	CCDS34939.1, CCDS47917.1	8q24.13	2005-11-09			ENSG00000104537	ENSG00000104537		"Annexins"	536	protein-coding gene	gene with protein product		602573		ANX13		9503022	Standard	NM_004306		Approved		uc003yqt.3	P27216	OTTHUMG00000164987	ENST00000419625.1:c.546G>A	chr8.hg19:g.124705533C>T		109.0	0.0	.		123.0	36.0	.	NM_001003954	Q9BQR5	Silent	SNP	ENST00000419625.1	hg19	CCDS47917.1																																																																																			.	.	.	none		0.458	ANXA13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381308.1	NM_004306		T	124705533	C	T	124705533	2	4	273	1	0	0	0	0	0	0	0	1	717	610	22	2		2	ANXA13	8	124705533	Silent	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	107285985	124705533	21658489	46	17271											
SMC5	23137	hgsc.bcm.edu	37	chr9	72961521	72961521	+	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	gacccattctaccaattcagCaagtacccaccattccaaat	14	9	3	15	0	2	0	1	0	1	0	3	1	3	0	5	0	3	2	5	0	5	5			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr9:72961521C>A	ENST00000361138.5	+	19	2582	c.2524C>A	c.(2524-2526)Caa>Aaa	p.Q842K	SMC5_ENST00000471372.1_3'UTR	NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	842					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						ACCAATTCAGCAAGTACCCAC	0.433																																					p.Q842K		Atlas-SNP	.											.	SMC5	96	.	0			c.C2524A						PASS	.						265	238	247					9																	72961521		2203	4300	6503	SO:0001630	splice_region_variant	23137	exon19			ATTCAGCAAGTAC	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.2524-1C>A	chr9.hg19:g.72961521C>A		144.0	0.0	.		138.0	38.0	.	NM_015110	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Missense_Mutation	SNP	ENST00000361138.5	hg19	CCDS6632.1	.	.	.	.	.	.	.	.	.	.	C	3.903	-0.021568	0.07634	.	.	ENSG00000198887	ENST00000361138	T	0.16324	2.35	4.67	4.67	0.58626	RecF/RecN/SMC (1);	0.831596	0.11061	N	0.603970	T	0.18800	0.0451	N	0.08118	0	0.28736	N	0.902223	P	0.44776	0.843	D	0.64506	0.926	T	0.01715	-1.1289	10	0.02654	T	1	-23.2503	13.3897	0.60816	0.0:1.0:0.0:0.0	.	842	Q8IY18	SMC5_HUMAN	K	842	ENSP00000354957:Q842K	ENSP00000354957:Q842K	Q	+	1	0	SMC5	72151341	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.018000	0.49625	2.882000	0.98803	0.655000	0.94253	CAA	.	.	.	none		0.433	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110	Missense_Mutation	A	72961521	C	A	72961521	5	1	273	1	0	0	0	0	0	0	1	0	14799	724	25	4	2598	4	SMC5	9	72961521	Splice_Site	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10		72961521	68251910	47	17272											
C9orf84	158401	hgsc.bcm.edu	37	chr9	114500784	114500784	+	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	taactgaatattggctgtggGgctcttgaattcttggcact	8	15	11	7	0	2	2	0	2	2	0	2	2	2	2	0	4	1	3	0	4	4	6			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr9:114500784G>A	ENST00000318737.4	-	10	1129	c.1001C>T	c.(1000-1002)cCc>cTc	p.P334L	C9orf84_ENST00000394779.3_Missense_Mutation_p.P295L|C9orf84_ENST00000394777.4_Missense_Mutation_p.P295L|C9orf84_ENST00000374283.5_Missense_Mutation_p.P398L|C9orf84_ENST00000374287.3_Missense_Mutation_p.P334L	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	334										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						TTGGCTGTGGGGCTCTTGAAT	0.333																																					p.P334L		Atlas-SNP	.											.	C9orf84	207	.	0			c.C1001T						PASS	.						50	52	51					9																	114500784		2200	4298	6498	SO:0001583	missense	158401	exon10			CTGTGGGGCTCTT	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.1001C>T	chr9.hg19:g.114500784G>A	ENSP00000322108:p.Pro334Leu	52.0	0.0	.		56.0	12.0	.	NM_173521	A2A2V3|Q2M1H8|Q96M73	Missense_Mutation	SNP	ENST00000318737.4	hg19	CCDS6781.3	.	.	.	.	.	.	.	.	.	.	G	5.618	0.298823	0.10622	.	.	ENSG00000165181	ENST00000394779;ENST00000394777;ENST00000374287;ENST00000318737;ENST00000374283	T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74	4.88	1.98	0.26296	.	0.650771	0.14383	N	0.322984	T	0.32852	0.0843	L	0.32530	0.975	0.26719	N	0.970828	B;B;B;B	0.19073	0.033;0.033;0.021;0.01	B;B;B;B	0.19946	0.027;0.027;0.021;0.009	T	0.23297	-1.0192	10	0.48119	T	0.1	1.5768	5.0158	0.14335	0.1887:0.1728:0.6386:0.0	.	295;398;334;295	A6PVK7;Q5VXU9-2;Q5VXU9;A2A2V3	.;.;CI084_HUMAN;.	L	295;295;334;334;398	ENSP00000378259:P295L;ENSP00000378257:P295L;ENSP00000363405:P334L;ENSP00000322108:P334L;ENSP00000363401:P398L	ENSP00000322108:P334L	P	-	2	0	C9orf84	113540605	0.177000	0.23109	0.334000	0.25495	0.236000	0.25371	1.009000	0.29886	0.335000	0.23614	0.460000	0.39030	CCC	.	.	.	none		0.333	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521		A	114500784	G	A	114500784	3	1	273	1	0	0	0	0	1	0	0	0	2502	1232	43	2	3401	2	C9orf84	9	114500784	Missense_Mutation	SNP	G	TCGA-WN-AB4C-01A-11D-A42J-10	41539263	114500784	26712647	48	17273											
HSDL2	84263	hgsc.bcm.edu	37	chr9	115179215	115179215	+	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	taaatccagtttggttcaaaCagcactgtggtaggtggtag	11	12	12	6	0	1	0	1	0	0	0	2	0	2	0	1	4	2	5	1	4	5	5			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr9:115179215C>T	ENST00000398805.3	+	5	717	c.490C>T	c.(490-492)Cag>Tag	p.Q164*	HSDL2_ENST00000488101.1_3'UTR|HSDL2_ENST00000262542.7_Nonsense_Mutation_p.Q44*|HSDL2_ENST00000398803.1_Intron|HSDL2_ENST00000539114.1_Intron	NM_032303.4	NP_115679.2	Q6YN16	HSDL2_HUMAN	hydroxysteroid dehydrogenase like 2	164						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						TTGGTTCAAACAGCACTGTGG	0.388																																					p.Q164X		Atlas-SNP	.											.	HSDL2	24	.	0			c.C490T						PASS	.						85	80	82					9																	115179215		1872	4106	5978	SO:0001587	stop_gained	84263	exon5			TTCAAACAGCACT	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.490C>T	chr9.hg19:g.115179215C>T	ENSP00000381785:p.Gln164*	70.0	0.0	.		57.0	19.0	.	NM_032303	A8K1L4|A8K8X1|A8MSV3|Q658M8|Q9BT58	Nonsense_Mutation	SNP	ENST00000398805.3	hg19	CCDS43864.1	.	.	.	.	.	.	.	.	.	.	C	38	6.743467	0.97805	.	.	ENSG00000119471	ENST00000398805;ENST00000262542	.	.	.	6.06	4.23	0.50019	.	0.149056	0.56097	D	0.000026	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	.	7.0545	0.25091	0.1958:0.6377:0.0983:0.0682	.	.	.	.	X	164;44	.	ENSP00000262542:Q44X	Q	+	1	0	HSDL2	114219036	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	3.972000	0.56838	0.459000	0.27016	-0.795000	0.03280	CAG	.	.	.	none		0.388	HSDL2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053681.1	NM_032303		T	115179215	C	T	115179215	4	4	273	1	0	0	0	0	0	1	0	0	7401	479	17	2	508	2	HSDL2	9	115179215	Nonsense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	678431	115179215	26034216	49	17274											
DENND1A	57706	hgsc.bcm.edu	37	chr9	126144822	126144822	+	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	ccatgtcgtcctggcccaggCtccagagcttgttgtacggg	5	10	13	13	2	0	1	0	0	0	1	3	1	2	1	4	3	2	4	4	3	1	3			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr9:126144822C>G	ENST00000373624.2	-	22	2120	c.1919G>C	c.(1918-1920)aGc>aCc	p.S640T	DENND1A_ENST00000473039.1_5'UTR|DENND1A_ENST00000394219.3_Missense_Mutation_p.S651T|DENND1A_ENST00000542603.1_Missense_Mutation_p.S425T	NM_020946.1	NP_065997.1	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A	640					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						CTGGCCCAGGCTCCAGAGCTT	0.657																																					p.S640T		Atlas-SNP	.											.	DENND1A	112	.	0			c.G1919C						PASS	.						58	62	60					9																	126144822		2203	4300	6503	SO:0001583	missense	57706	exon22			CCCAGGCTCCAGA	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.1919G>C	chr9.hg19:g.126144822C>G	ENSP00000362727:p.Ser640Thr	85.0	0.0	.		53.0	13.0	.	NM_020946	A8MZA3|B1AM80|B7Z3C8|B7Z669|D3PFD3|Q05C88|Q5VWF0|Q6PJZ5|Q8IVD6|Q9H796	Missense_Mutation	SNP	ENST00000373624.2	hg19	CCDS35133.1	.	.	.	.	.	.	.	.	.	.	C	18.43	3.621236	0.66787	.	.	ENSG00000119522	ENST00000373624;ENST00000542603;ENST00000394219	T;T;T	0.34472	2.81;1.36;2.66	5.06	4.1	0.47936	.	0.130939	0.64402	D	0.000002	T	0.43986	0.1272	M	0.61703	1.905	0.80722	D	1	D;D;P;P	0.58268	0.962;0.982;0.835;0.651	P;P;B;B	0.52598	0.677;0.703;0.322;0.165	T	0.28681	-1.0036	10	0.37606	T	0.19	-18.4894	10.3178	0.43747	0.0:0.7878:0.1361:0.076	.	651;641;640;503	Q8TEH3-6;Q8TEH3-7;Q8TEH3;Q9HCG4	.;.;DEN1A_HUMAN;.	T	640;425;651	ENSP00000362727:S640T;ENSP00000437457:S425T;ENSP00000377766:S651T	ENSP00000362727:S640T	S	-	2	0	DENND1A	125184643	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	3.426000	0.52778	2.352000	0.79861	0.563000	0.77884	AGC	.	.	.	none		0.657	DENND1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053997.1	NM_024820		G	126144822	C	G	126144822	3	3	273	1	0	0	0	0	1	0	0	0	4428	797	28	4	1114	4	DENND1A	9	126144822	Missense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	10965607	126144822	15068609	50	17275											
GAPVD1	26130	hgsc.bcm.edu	37	chr9	128104522	128104522	+	Frame_Shift_Del	DEL	A	A	-																															tataccatttagaaagaaagAaaaacaagaaaaagacaaag																										TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr9:128104522delA	ENST00000495955.1	+	19	3280	c.2990delA	c.(2989-2991)gaafs	p.E997fs	GAPVD1_ENST00000265956.4_Frame_Shift_Del_p.E971fs|GAPVD1_ENST00000470056.1_Intron|GAPVD1_ENST00000297933.6_Frame_Shift_Del_p.E997fs|GAPVD1_ENST00000312123.9_Frame_Shift_Del_p.E976fs|GAPVD1_ENST00000394104.2_Frame_Shift_Del_p.E997fs|GAPVD1_ENST00000394083.2_Intron|GAPVD1_ENST00000394105.2_Frame_Shift_Del_p.E1024fs			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	997					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						AGAAAGAAAGAAAAACAAGAA	0.408																																					p.E1024fs		Atlas-Indel,Pindel	.											.	GAPVD1	124	.	0			c.3070delG						PASS	.						115	117	116					9																	128104522		2203	4300	6503	SO:0001589	frameshift_variant	26130	exon18			.		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.2990delA	chr9.hg19:g.128104522delA	ENSP00000419063:p.Glu997fs	43.0	0.0	0		66.0	26.0	0.393939	NM_015635	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Frame_Shift_Del	DEL	ENST00000495955.1	hg19																																																																																				.	.	.	none		0.408	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1			-	128104522	A	-	128104522	7	5	273	1	0	1	0	1	0	0	0	0	6246	246	9	0	3137	0	GAPVD1	9	128104522	Frame_Shift_Del	DEL	A	TCGA-WN-AB4C-01A-11D-A42J-10	1959700	128104522	13108909	51	17276											
NOTCH1	4851	hgsc.bcm.edu	37	chr9	139409835	139409835	+	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	gctggcacagtcatccaggtTgatctcgcagttgggtcctg	6	11	13	11	1	2	1	1	1	1	0	5	1	4	1	2	3	0	5	2	3	0	2			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr9:139409835T>A	ENST00000277541.6	-	12	1996	c.1921A>T	c.(1921-1923)Aac>Tac	p.N641Y		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	641	EGF-like 17; 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)		TCATCCAGGTTGATCTCGCAG	0.687			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)																											p.N641Y		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	.	NOTCH1	1980	.	0			c.A1921T						PASS	.						73	81	78					9																	139409835		2131	4246	6377	SO:0001583	missense	4851	exon12			CCAGGTTGATCTC	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.1921A>T	chr9.hg19:g.139409835T>A	ENSP00000277541:p.Asn641Tyr	81.0	0.0	.		82.0	18.0	.	NM_017617	Q59ED8|Q5SXM3	Missense_Mutation	SNP	ENST00000277541.6	hg19	CCDS43905.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.204226	0.79127	.	.	ENSG00000148400	ENST00000277541	D	0.87029	-2.2	4.92	4.92	0.64577	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	U	0.000000	D	0.92437	0.7599	M	0.79614	2.46	0.80722	D	1	D	0.63880	0.993	D	0.64595	0.927	D	0.93392	0.6752	10	0.87932	D	0	.	13.7467	0.62879	0.0:0.0:0.0:1.0	.	641	P46531	NOTC1_HUMAN	Y	641	ENSP00000277541:N641Y	ENSP00000277541:N641Y	N	-	1	0	NOTCH1	138529656	1.000000	0.71417	1.000000	0.80357	0.762000	0.43233	7.846000	0.86887	1.831000	0.53308	0.460000	0.39030	AAC	.	.	.	none		0.687	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		A	139409835	T	A	139409835	3	1	273	1	0	0	0	0	1	0	0	0	10554	1812	63	5	5838	5	NOTCH1	9	139409835	Missense_Mutation	SNP	T	TCGA-WN-AB4C-01A-11D-A42J-10	11305313	139409835	1803596	52	17277											
ITGA8	8516	hgsc.bcm.edu	37	chr10	15688924	15688924	+	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	aacgtctcggtgccagtgagGatctgggggtctctgaagag	8	9	16	8	2	3	3	0	2	3	1	5	4	3	4	1	4	2	0	1	4	2	0			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr10:15688924G>A	ENST00000378076.3	-	12	1481	c.1128C>T	c.(1126-1128)atC>atT	p.I376I		NM_003638.1	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8	376					brain development (GO:0007420)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|metanephros development (GO:0001656)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|substrate adhesion-dependent cell spreading (GO:0034446)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|dendritic spine membrane (GO:0032591)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integrin alpha8-beta1 complex (GO:0034678)|integrin complex (GO:0008305)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	metal ion binding (GO:0046872)			NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	96						TGCCAGTGAGGATCTGGGGGT	0.478																																					p.I376I		Atlas-SNP	.											ITGA8,colon,carcinoma,0,1	ITGA8	230	.	0			c.C1128T						PASS	.						121	108	112					10																	15688924		2203	4300	6503	SO:0001819	synonymous_variant	8516	exon12			AGTGAGGATCTGG	L36531	CCDS31155.1	10p13	2010-03-23			ENSG00000077943	ENSG00000077943		"Integrins"	6144	protein-coding gene	gene with protein product		604063				7768999	Standard	XM_005252633		Approved		uc001ioc.1	P53708	OTTHUMG00000017733	ENST00000378076.3:c.1128C>T	chr10.hg19:g.15688924G>A		123.0	0.0	.		126.0	29.0	.	NM_003638	B0YJ31|Q5VX94	Silent	SNP	ENST00000378076.3	hg19	CCDS31155.1																																																																																			.	.	.	none		0.478	ITGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046987.1	NM_003638		A	15688924	G	A	15688924	2	1	273	1	0	0	0	0	0	0	0	1	7889	1164	41	2		2	ITGA8	10	15688924	Silent	SNP	G	TCGA-WN-AB4C-01A-11D-A42J-10		15688924	119845823	53	17278											
FZD8	8325	hgsc.bcm.edu	37	chr10	35929628	35929628	+	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	gttgtagagcgggtggcgctCgctggacacgctcaccatag	7	8	15	11	4	1	1	1	0	0	1	2	2	1	2	1	3	1	5	1	3	2	3			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr10:35929628C>A	ENST00000374694.1	-	1	734	c.730G>T	c.(730-732)Gag>Tag	p.E244*	MIR4683_ENST00000579659.1_RNA	NM_031866.2	NP_114072.1	Q9H461	FZD8_HUMAN	frizzled class receptor 8	244					axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|gonad development (GO:0008406)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|T cell differentiation in thymus (GO:0033077)|vasculature development (GO:0001944)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	11						GGGTGGCGCTCGCTGGACACG	0.731																																					p.E244X		Atlas-SNP	.											.	FZD8	41	.	0			c.G730T						PASS	.						29	31	30					10																	35929628		2201	4299	6500	SO:0001587	stop_gained	8325	exon1			GGCGCTCGCTGGA	AB043703	CCDS7192.1	10p11.2	2014-01-29	2014-01-29		ENSG00000177283	ENSG00000177283		"GPCR / Class F : Frizzled receptors"	4046	protein-coding gene	gene with protein product		606146	"frizzled (Drosophila) homolog 8", "frizzled homolog 8 (Drosophila)", "frizzled 8, seven transmembrane spanning receptor", "frizzled family receptor 8"			11295046	Standard	NM_031866		Approved		uc001iyz.1	Q9H461	OTTHUMG00000017956	ENST00000374694.1:c.730G>T	chr10.hg19:g.35929628C>A	ENSP00000363826:p.Glu244*	45.0	0.0	.		39.0	12.0	.	NM_031866		Nonsense_Mutation	SNP	ENST00000374694.1	hg19	CCDS7192.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.952465	0.92660	.	.	ENSG00000177283	ENST00000374694	.	.	.	2.46	2.46	0.29980	.	0.344379	0.25338	U	0.031393	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.14656	T	0.56	.	11.9654	0.53031	0.0:1.0:0.0:0.0	.	.	.	.	X	244	.	ENSP00000363826:E244X	E	-	1	0	FZD8	35969634	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	6.333000	0.72939	1.356000	0.45884	0.289000	0.19496	GAG	.	.	.	none		0.731	FZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047575.2	NM_031866		A	35929628	C	A	35929628	4	1	273	1	0	0	0	0	0	1	0	0	6143	893	31	4	1358	4	FZD8	10	35929628	Nonsense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	20240704	35929628	99605119	54	17279											
MYST4	23522	hgsc.bcm.edu	37	chr10	76789888	76789888	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagccagcagctggctcagtGcagcatggctgctaacttca	9	8	11	13	0	2	0	2	0	0	0	2	0	2	0	1	2	7	7	1	2	1	2			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr10:76789888G>A	ENST00000287239.4	+	18	5795	c.5306G>A	c.(5305-5307)tGc>tAc	p.C1769Y	KAT6B_ENST00000372711.1_Missense_Mutation_p.C1586Y|KAT6B_ENST00000372725.1_Missense_Mutation_p.C1477Y|KAT6B_ENST00000372714.1_Missense_Mutation_p.C1477Y|KAT6B_ENST00000372724.1_Missense_Mutation_p.C1477Y	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1769	Interaction with RUNX1 and RUNX2.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										CTGGCTCAGTGCAGCATGGCT	0.592																																					p.C1769Y		Atlas-SNP	.											.	.	.	.	0			c.G5306A						PASS	.						43	40	41					10																	76789888		2203	4300	6503	SO:0001583	missense	23522	exon18			CTCAGTGCAGCAT	AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"Chromatin-modifying enzymes / K-acetyltransferases", "Zinc fingers, C2HC-type containing", "Zinc fingers, PHD-type"	17582	protein-coding gene	gene with protein product	"MOZ-related factor"	605880	"MYST histone acetyltransferase (monocytic leukemia) 4"	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.5306G>A	chr10.hg19:g.76789888G>A	ENSP00000287239:p.Cys1769Tyr	86.0	0.0	.		69.0	13.0	.	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Missense_Mutation	SNP	ENST00000287239.4	hg19	CCDS7345.1	.	.	.	.	.	.	.	.	.	.	G	14.62	2.590079	0.46214	.	.	ENSG00000156650	ENST00000372725;ENST00000372724;ENST00000287239;ENST00000372714;ENST00000372711	T;T;T;T;T	0.80033	-1.29;-1.29;-1.33;-1.29;-1.29	5.54	5.54	0.83059	.	0.000000	0.53938	D	0.000041	D	0.85296	0.5664	L	0.29908	0.895	0.80722	D	1	D;D;D	0.76494	0.995;0.999;0.997	D;D;D	0.79108	0.992;0.971;0.96	D	0.86746	0.1957	10	0.72032	D	0.01	-7.6819	19.4767	0.94992	0.0:0.0:1.0:0.0	.	1586;1477;1769	Q8WYB5-2;Q8WYB5-3;Q8WYB5	.;.;KAT6B_HUMAN	Y	1477;1477;1769;1477;1586	ENSP00000361810:C1477Y;ENSP00000361809:C1477Y;ENSP00000287239:C1769Y;ENSP00000361799:C1477Y;ENSP00000361796:C1586Y	ENSP00000287239:C1769Y	C	+	2	0	KAT6B	76459894	1.000000	0.71417	0.991000	0.47740	0.981000	0.71138	9.476000	0.97823	2.592000	0.87571	0.563000	0.77884	TGC	.	.	.	none		0.592	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330		A	76789888	G	A	76789888	3	1	273	1	0	0	0	0	1	0	0	0	10112	1319	46	2	5368	2	MYST4	10	76789888	Missense_Mutation	SNP	G	TCGA-WN-AB4C-01A-11D-A42J-10	40860260	76789888	58744859	55	17280											
CRTAC1	55118	hgsc.bcm.edu	37	chr10	99656744	99656744	+	Missense_Mutation	SNP	T	T	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	gtctccgtgctctctacggaTgacgctgcaggagaggagac	8	8	14	11	3	2	3	0	1	2	2	4	6	2	4	1	3	3	3	1	3	1	1			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr10:99656744T>G	ENST00000370597.3	-	9	1493	c.1138A>C	c.(1138-1140)Atc>Ctc	p.I380L	CRTAC1_ENST00000370591.2_Missense_Mutation_p.I380L|CRTAC1_ENST00000298819.4_Missense_Mutation_p.I380L	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1	380						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)		TCTCTACGGATGACGCTGCAG	0.667																																					p.I380L		Atlas-SNP	.											.	CRTAC1	86	.	0			c.A1138C						PASS	.						32	25	28					10																	99656744		2188	4268	6456	SO:0001583	missense	55118	exon9			TACGGATGACGCT	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.1138A>C	chr10.hg19:g.99656744T>G	ENSP00000359629:p.Ile380Leu	54.0	0.0	.		33.0	10.0	.	NM_001206528	B1ALN4|Q5T4F8|Q8N4H6|Q8TE52|Q9NQ78|Q9NQ80|Q9NW46	Missense_Mutation	SNP	ENST00000370597.3	hg19	CCDS31266.1	.	.	.	.	.	.	.	.	.	.	T	7.593	0.671122	0.14776	.	.	ENSG00000095713	ENST00000413387;ENST00000370597;ENST00000298819;ENST00000309155;ENST00000370591	T;T;T;T;T	0.21031	2.03;2.03;2.03;2.03;2.03	5.04	5.04	0.67666	.	0.176405	0.50627	D	0.000113	T	0.11239	0.0274	N	0.22421	0.69	0.29887	N	0.825497	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.06405	0.002;0.0;0.001	T	0.25187	-1.0139	10	0.02654	T	1	-26.2583	9.3467	0.38113	0.0:0.08:0.0:0.92	.	380;380;276	Q9NQ79-2;Q9NQ79;Q5T4F6	.;CRAC1_HUMAN;.	L	276;380;380;372;380	ENSP00000408445:I276L;ENSP00000359629:I380L;ENSP00000298819:I380L;ENSP00000310810:I372L;ENSP00000359623:I380L	ENSP00000298819:I380L	I	-	1	0	CRTAC1	99646734	0.998000	0.40836	1.000000	0.80357	0.807000	0.45602	0.559000	0.23485	1.887000	0.54652	0.459000	0.35465	ATC	.	.	.	none		0.667	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049754.1	NM_018058		G	99656744	T	G	99656744	3	3	273	1	0	0	0	0	1	0	0	0	3898	1464	51	5	875	5	CRTAC1	10	99656744	Missense_Mutation	SNP	T	TCGA-WN-AB4C-01A-11D-A42J-10	22866856	99656744	35878003	56	17281											
OR51I2	390064	hgsc.bcm.edu	37	chr11	5475536	5475536	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatgtcccatgctacatacAtgtcctcatgtcaaatgtgt	10	13	7	11	0	2	0	2	0	0	0	4	0	4	0	2	0	3	2	2	0	3	2			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr11:5475536A>G	ENST00000341449.2	+	1	899	c.818A>G	c.(817-819)cAt>cGt	p.H273R	AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron	NM_001004754.2	NP_001004754.1	Q9H344	O51I2_HUMAN	olfactory receptor, family 51, subfamily I, member 2	273					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)		TGCTACATACATGTCCTCATG	0.478																																					p.H273R		Atlas-SNP	.											.	OR51I2	76	.	0			c.A818G						PASS	.						214	184	194					11																	5475536		2201	4297	6498	SO:0001583	missense	390064	exon1			ACATACATGTCCT	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.818A>G	chr11.hg19:g.5475536A>G	ENSP00000341987:p.His273Arg	77.0	0.0	.		47.0	14.0	.	NM_001004754	Q6IF81	Missense_Mutation	SNP	ENST00000341449.2	hg19	CCDS31383.1	.	.	.	.	.	.	.	.	.	.	A	9.364	1.068810	0.20147	.	.	ENSG00000187918	ENST00000341449	T	0.00058	8.79	5.45	4.32	0.51571	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000006	T	0.00440	0.0014	M	0.80847	2.515	0.20703	N	0.999865	D	0.69078	0.997	D	0.80764	0.994	T	0.37888	-0.9686	10	0.59425	D	0.04	.	10.9472	0.47308	0.8598:0.0:0.0:0.1401	.	273	Q9H344	O51I2_HUMAN	R	273	ENSP00000341987:H273R	ENSP00000341987:H273R	H	+	2	0	OR51I2	5432112	0.076000	0.21285	0.967000	0.41034	0.011000	0.07611	3.394000	0.52551	1.065000	0.40693	0.460000	0.39030	CAT	.	.	.	none		0.478	OR51I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143385.1	NM_001004754		G	5475536	A	G	5475536	3	3	273	1	0	0	0	0	1	0	0	0	11108	217	8	3	820	3	OR51I2	11	5475536	Missense_Mutation	SNP	A	TCGA-WN-AB4C-01A-11D-A42J-10		5475536	129530980	57	17282											
DNHD1	144132	hgsc.bcm.edu	37	chr11	6588531	6588531	+	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	tgcactgggccttacccaagTacccttggtgggtgcattgg	6	11	13	11	0	0	0	0	0	0	0	0	0	0	0	3	4	4	3	3	4	3	4			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr11:6588531T>A	ENST00000527990.2	+	34	11792	c.11792T>A	c.(11791-11793)gTa>gAa	p.V3931E	DNHD1_ENST00000254579.6_Missense_Mutation_p.V3931E			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	3931					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)		CTTACCCAAGTACCCTTGGTG	0.597																																					p.V3931E		Atlas-SNP	.											.	DNHD1	198	.	0			c.T11792A						PASS	.						64	71	69					11																	6588531		2117	4226	6343	SO:0001583	missense	144132	exon36			CCCAAGTACCCTT	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.11792T>A	chr11.hg19:g.6588531T>A	ENSP00000436180:p.Val3931Glu	78.0	0.0	.		76.0	21.0	.	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	hg19	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	T	0.015	-1.561834	0.00903	.	.	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000525883;ENST00000530197	T;T	0.24538	1.85;1.85	4.54	2.19	0.27852	.	1.287750	0.05610	N	0.578019	T	0.16041	0.0386	N	0.19112	0.55	0.09310	N	1	B;B;B	0.30482	0.281;0.244;0.281	B;B;B	0.29440	0.102;0.073;0.102	T	0.28713	-1.0035	10	0.46703	T	0.11	-0.0209	3.0352	0.06119	0.0:0.2537:0.23:0.5163	.	3019;199;3931	B0I1S4;D3DQT9;Q96M86	.;.;DNHD1_HUMAN	E	3931;3931;199;199	ENSP00000254579:V3931E;ENSP00000436180:V3931E	ENSP00000254579:V3931E	V	+	2	0	DNHD1	6545107	0.001000	0.12720	0.040000	0.18447	0.153000	0.21895	0.341000	0.19909	0.795000	0.33922	0.459000	0.35465	GTA	.	.	.	none		0.597	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		A	6588531	T	A	6588531	3	1	273	1	0	0	0	0	1	0	0	0	4670	1638	57	5	11935	5	DNHD1	11	6588531	Missense_Mutation	SNP	T	TCGA-WN-AB4C-01A-11D-A42J-10	1112995	6588531	128417985	58	17283											
CKAP5	9793	hgsc.bcm.edu	37	chr11	46832664	46832664	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgaacagccttctctcgagActcaaagagttttggcaaca	12	10	8	11	2	2	2	1	0	1	2	5	4	2	2	1	1	3	2	1	1	3	3			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr11:46832664A>G	ENST00000529230.1	-	5	569	c.523T>C	c.(523-525)Tct>Cct	p.S175P	CKAP5_ENST00000415402.1_Missense_Mutation_p.S175P|CKAP5_ENST00000354558.3_Missense_Mutation_p.S175P|CKAP5_ENST00000312055.5_Missense_Mutation_p.S175P			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	175					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						TTCTCTCGAGACTCAAAGAGT	0.388																																					p.S175P	Ovarian(4;85 273 2202 4844 13323)	Atlas-SNP	.											.	CKAP5	134	.	0			c.T523C						PASS	.						91	85	87					11																	46832664		2201	4299	6500	SO:0001583	missense	9793	exon5			CTCGAGACTCAAA		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.523T>C	chr11.hg19:g.46832664A>G	ENSP00000432768:p.Ser175Pro	128.0	0.0	.		120.0	39.0	.	NM_001008938	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	Missense_Mutation	SNP	ENST00000529230.1	hg19	CCDS31477.1	.	.	.	.	.	.	.	.	.	.	A	28.2	4.896892	0.91962	.	.	ENSG00000175216	ENST00000529230;ENST00000415402;ENST00000312055;ENST00000378629;ENST00000354558	T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39	5.61	5.61	0.85477	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.72653	0.3487	L	0.28115	0.83	0.80722	D	1	D;D;D	0.71674	0.997;0.997;0.998	D;D;P	0.78314	0.991;0.991;0.899	T	0.75522	-0.3288	10	0.56958	D	0.05	-2.057	15.7997	0.78443	1.0:0.0:0.0:0.0	.	175;175;175	Q14008-3;Q14008-2;Q14008	.;.;CKAP5_HUMAN	P	175	ENSP00000432768:S175P;ENSP00000395302:S175P;ENSP00000310227:S175P;ENSP00000346566:S175P	ENSP00000310227:S175P	S	-	1	0	CKAP5	46789240	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.213000	0.95133	2.140000	0.66376	0.460000	0.39030	TCT	.	.	.	none		0.388	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	NM_014756		G	46832664	A	G	46832664	3	3	273	1	0	0	0	0	1	0	0	0	3447	275	10	3	5735	3	CKAP5	11	46832664	Missense_Mutation	SNP	A	TCGA-WN-AB4C-01A-11D-A42J-10	40244133	46832664	88173852	59	17284											
PPP1CA	5499	hgsc.bcm.edu	37	chr11	67168588	67168588	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaagaatgggctggctcagAaaaatctcccgggatttcag	13	8	12	8	1	3	3	2	0	1	3	4	4	3	4	1	3	0	2	1	3	4	1			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr11:67168588A>G	ENST00000376745.4	-	2	286	c.138T>C	c.(136-138)ttT>ttC	p.F46F	PPP1CA_ENST00000532446.1_5'UTR|PPP1CA_ENST00000358239.4_Intron|PPP1CA_ENST00000312989.7_Silent_p.F57F|TBC1D10C_ENST00000526387.1_5'Flank|TBC1D10C_ENST00000312390.5_5'Flank	NM_001008709.1|NM_002708.3	NP_001008709.1|NP_002699.1	P62136	PP1A_HUMAN	protein phosphatase 1, catalytic subunit, alpha isozyme	46					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)			GCTGGCTCAGAAAAATCTCCC	0.617																																					p.F57F		Atlas-SNP	.											.	PPP1CA	83	.	0			c.T171C						PASS	.						55	63	60					11																	67168588		2200	4295	6495	SO:0001819	synonymous_variant	5499	exon2			GCTCAGAAAAATC		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.138T>C	chr11.hg19:g.67168588A>G		102.0	0.0	.		100.0	26.0	.	NM_001008709	A6NNR3|B2R908|P08129|P20653|P22802|Q07161	Silent	SNP	ENST00000376745.4	hg19	CCDS8160.1																																																																																			.	.	.	none		0.617	PPP1CA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395487.1	NM_002708		G	67168588	A	G	67168588	2	3	273	1	0	0	0	0	0	0	0	1	12359	243	9	3		3	PPP1CA	11	67168588	Silent	SNP	A	TCGA-WN-AB4C-01A-11D-A42J-10	20335924	67168588	67837928	60	17285											
ARHGEF17	9828	hgsc.bcm.edu	37	chr11	73022203	73022203	+	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	cgtggggagctggctgggccTggattcgagggccctggagg	4	7	21	9	2	0	0	0	0	0	0	1	4	0	3	2	8	1	2	2	8	0	1			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr11:73022203T>A	ENST00000263674.3	+	1	2870	c.2520T>A	c.(2518-2520)ccT>ccA	p.P840P	RP11-800A3.7_ENST00000546324.1_RNA	NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	840					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						TGGCTGGGCCTGGATTCGAGG	0.657																																					p.P840P		Atlas-SNP	.											.	ARHGEF17	117	.	0			c.T2520A						PASS	.						41	49	46					11																	73022203		2200	4293	6493	SO:0001819	synonymous_variant	9828	exon1			TGGGCCTGGATTC	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.2520T>A	chr11.hg19:g.73022203T>A		146.0	0.0	.		121.0	47.0	.	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Silent	SNP	ENST00000263674.3	hg19	CCDS8221.1																																																																																			.	.	.	none		0.657	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		A	73022203	T	A	73022203	2	1	273	1	0	0	0	0	0	0	0	1	900	1567	55	5		5	ARHGEF17	11	73022203	Silent	SNP	T	TCGA-WN-AB4C-01A-11D-A42J-10	5853615	73022203	61984313	61	17286											
TXNRD1	7296	hgsc.bcm.edu	37	chr12	104681125	104681125	+	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	aagcttcagcatgtcatgtgGtaggtgaggccggcgcctgt	7	10	15	9	2	2	1	2	1	0	0	2	1	2	1	2	4	2	3	2	4	2	2			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr12:104681125G>T	ENST00000526691.1	+	1	466		c.e1+1		TXNRD1_ENST00000540716.1_Intron|TXNRD1_ENST00000526390.1_Intron|TXNRD1_ENST00000503506.2_Intron|TXNRD1_ENST00000529546.1_Intron|TXNRD1_ENST00000354940.6_Splice_Site|TXNRD1_ENST00000525566.1_Intron|TXNRD1_ENST00000524698.1_5'Flank|TXNRD1_ENST00000378070.4_5'Flank|TXNRD1_ENST00000388854.3_Splice_Site|TXNRD1_ENST00000542918.1_5'Flank|TXNRD1_ENST00000429002.2_Intron	NM_001261445.1|NM_003330.3	NP_001248374.1|NP_003321.3	Q16881	TRXR1_HUMAN	thioredoxin reductase 1						cell proliferation (GO:0008283)|cell redox homeostasis (GO:0045454)|cellular lipid metabolic process (GO:0044255)|mesoderm formation (GO:0001707)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|NADP binding (GO:0050661)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(5)|skin(1)|stomach(1)|urinary_tract(1)	16					Arsenic trioxide(DB01169)|Flavin adenine dinucleotide(DB03147)	ATGTCATGTGGTAGGTGAGGC	0.547																																					.	Ovarian(139;555 1836 9186 9946 10884)	Atlas-SNP	.											.	TXNRD1	77	.	0			c.10+1G>T						PASS	.						222	228	226					12																	104681125		1962	4143	6105	SO:0001630	splice_region_variant	7296	exon1			CATGTGGTAGGTG		CCDS53820.1, CCDS53821.1, CCDS53823.1, CCDS58274.1	12q23-q24.1	2012-03-01							12437	protein-coding gene	gene with protein product		601112				7589432	Standard	NM_001093771		Approved	TXNR, GRIM-12, Trxr1	uc021rcx.2	Q16881		ENST00000526691.1:c.10+1G>T	chr12.hg19:g.104681125G>T		65.0	0.0	.		53.0	14.0	.	NM_003330	B7Z1F4|B7Z3Y8|B7Z904|E9PMY9|F5H780|Q6FI31|Q6VB40|Q6VB41|Q6VB42|Q6VBP2|Q6VBP3|Q6VBP4|Q6VBP5|Q6VBP9|Q6VBQ0|Q6YNQ1|Q76P53|Q7LA96|Q8WVC8|Q99475|Q9UES8|Q9UH79	Splice_Site	SNP	ENST00000526691.1	hg19	CCDS53821.1	.	.	.	.	.	.	.	.	.	.	G	5.535	0.283666	0.10458	.	.	ENSG00000198431	ENST00000526691;ENST00000388854	.	.	.	3.21	-3.02	0.05446	.	.	.	.	.	.	.	.	.	.	.	0.18873	N	0.999988	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1.979	0.03422	0.1043:0.3057:0.2794:0.3105	.	.	.	.	.	-1	.	.	.	+	.	.	TXNRD1	103205255	0.000000	0.05858	0.000000	0.03702	0.134000	0.20937	-0.113000	0.10774	-0.676000	0.05238	0.555000	0.69702	.	.	.	.	none		0.547	TXNRD1-002	KNOWN	basic|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000389970.2	NM_003330	Intron	T	104681125	G	T	104681125	5	4	273	1	0	0	0	0	0	0	1	0	16819	1275	44	4	329	4	TXNRD1	12	104681125	Splice_Site	SNP	G	TCGA-WN-AB4C-01A-11D-A42J-10		104681125	29170770	62	17287											
WDR66	144406	hgsc.bcm.edu	37	chr12	122389412	122389412	+	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	gagagggatacactggctcaCagtgccccacttttaactga	11	9	10	11	0	1	2	1	1	0	1	1	4	1	3	2	2	3	1	2	2	2	3			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr12:122389412C>T	ENST00000288912.4	+	9	2150	c.1296C>T	c.(1294-1296)caC>caT	p.H432H	WDR66_ENST00000397454.2_Silent_p.H432H	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	432							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)		CACTGGCTCACAGTGCCCCAC	0.368																																					p.H432H	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											.	WDR66	143	.	0			c.C1296T						PASS	.						103	88	93					12																	122389412		1836	4098	5934	SO:0001819	synonymous_variant	144406	exon9			GGCTCACAGTGCC	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.1296C>T	chr12.hg19:g.122389412C>T		102.0	0.0	.		97.0	24.0	.	NM_001178003	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Silent	SNP	ENST00000288912.4	hg19	CCDS41853.1																																																																																			.	.	.	none		0.368	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668		T	122389412	C	T	122389412	2	4	273	1	0	0	0	0	0	0	0	1	17329	477	17	2		2	WDR66	12	122389412	Silent	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	17708287	122389412	11462483	63	17288											
DIAPH3	81624	hgsc.bcm.edu	37	chr13	60384950	60384950	+	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	atttctaataaacgctttttCttttgttggcgttcgagtct	7	20	7	7	3	3	0	0	0	3	0	4	1	3	0	0	1	1	3	0	1	3	9			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr13:60384950C>T	ENST00000400324.4	-	25	3355	c.3135G>A	c.(3133-3135)aaG>aaA	p.K1045K	DIAPH3_ENST00000465066.1_5'UTR|DIAPH3_ENST00000400320.1_Silent_p.K999K|DIAPH3_ENST00000400319.1_Silent_p.K975K|DIAPH3_ENST00000267215.4_Silent_p.K1045K|DIAPH3_ENST00000400330.1_Silent_p.K1045K|DIAPH3_ENST00000377908.2_Silent_p.K1034K	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	1045					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)		AACGCTTTTTCTTTTGTTGGC	0.308																																					p.K1045K		Atlas-SNP	.											DIAPH3,right_lower_lobe,carcinoma,0,1	DIAPH3	139	.	0			c.G3135A						PASS	.						156	144	148					13																	60384950		1799	4059	5858	SO:0001819	synonymous_variant	81624	exon25			CTTTTTCTTTTGT	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.3135G>A	chr13.hg19:g.60384950C>T		73.0	0.0	.		69.0	16.0	.	NM_001042517	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Silent	SNP	ENST00000400324.4	hg19	CCDS41898.1																																																																																			.	.	.	none		0.308	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517		T	60384950	C	T	60384950	2	4	273	1	0	0	0	0	0	0	0	1	4522	912	32	2		2	DIAPH3	13	60384950	Silent	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10		60384950	54784928	64	17289											
PABPN1	8106	hgsc.bcm.edu	37	chr14	23792661	23792661	+	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	cagtcaaccgtgttaccataCtgtgtgacaaatttagtggc	11	12	9	9	1	1	1	1	1	0	0	1	1	1	1	2	1	3	1	2	1	5	4	rs145369012		TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr14:23792661C>A	ENST00000216727.4	+	4	791	c.610C>A	c.(610-612)Ctg>Atg	p.L204M	PABPN1_ENST00000397276.2_Missense_Mutation_p.L204M|BCL2L2-PABPN1_ENST00000553781.1_Missense_Mutation_p.L231M|BCL2L2-PABPN1_ENST00000557008.1_Missense_Mutation_p.L231M|PABPN1_ENST00000556821.1_Missense_Mutation_p.L76M|PABPN1_ENST00000557702.1_Missense_Mutation_p.L76M|AL049829.1_ENST00000594872.1_5'Flank	NM_004643.3	NP_004634.1	Q86U42	PABP2_HUMAN	poly(A) binding protein, nuclear 1	204	Necessary for homooligomerization.|RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|modification by virus of host mRNA processing (GO:0046778)|modulation by virus of host morphology or physiology (GO:0019048)|modulation by virus of host process (GO:0019054)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|muscle contraction (GO:0006936)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)|viral life cycle (GO:0019058)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			large_intestine(1)|lung(1)|ovary(2)	4	all_cancers(95;6.69e-06)			GBM - Glioblastoma multiforme(265;0.00643)		TGTTACCATACTGTGTGACAA	0.383																																					p.L231M		Atlas-SNP	.											.	.	.	.	0			c.C691A						PASS	.						95	94	94					14																	23792661		2203	4300	6503	SO:0001583	missense	100529063	exon6			ACCATACTGTGTG	AF026029	CCDS9592.1	14q11.2	2013-02-12	2001-11-28		ENSG00000100836	ENSG00000100836		"RNA binding motif (RRM) containing"	8565	protein-coding gene	gene with protein product		602279	"poly(A)-binding protein, nuclear 1"	OPMD, PABP2		7795598	Standard	NM_004643		Approved	PAB2		Q86U42	OTTHUMG00000028739	ENST00000216727.4:c.610C>A	chr14.hg19:g.23792661C>A	ENSP00000216727:p.Leu204Met	47.0	0.0	.		58.0	12.0	.	NM_001199864	D3DS49|O43484	Missense_Mutation	SNP	ENST00000216727.4	hg19	CCDS9592.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.62|19.62	3.862406|3.862406	0.71949|0.71949	.|.	.|.	ENSG00000258643;ENSG00000258643;ENSG00000100836;ENSG00000100836;ENSG00000100836;ENSG00000100836|ENSG00000100836	ENST00000553781;ENST00000557008;ENST00000216727;ENST00000397276;ENST00000556821;ENST00000557702|ENST00000555295	T;T;T;T;T;T|.	0.15834|.	2.39;2.39;2.39;2.39;2.39;2.39|.	4.88|4.88	4.88|4.88	0.63580|0.63580	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.58032|0.58032	0.2094|0.2094	L|L	0.33137|0.33137	0.985|0.985	0.53688|0.53688	D|D	0.999979|0.999979	D;D;P|.	0.62365|.	0.983;0.991;0.592|.	D;P;P|.	0.69142|.	0.962;0.907;0.823|.	T|T	0.54050|0.54050	-0.8351|-0.8351	10|5	0.51188|.	T|.	0.08|.	-13.407|-13.407	17.1586|17.1586	0.86798|0.86798	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	204;204;231|.	Q86U42;Q86U42-2;G3V5R7|.	PABP2_HUMAN;.;.|.	M|N	231;231;204;204;76;76|3	ENSP00000451320:L231M;ENSP00000452479:L231M;ENSP00000216727:L204M;ENSP00000380446:L204M;ENSP00000451970:L76M;ENSP00000450724:L76M|.	ENSP00000216727:L204M|.	L|T	+|+	1|2	2|0	PABPN1;RP11-124D2.2|PABPN1	22862501|22862501	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	4.154000|4.154000	0.58125|0.58125	2.401000|2.401000	0.81631|0.81631	0.555000|0.555000	0.69702|0.69702	CTG|ACT	.	C|1.000;T|0.000	.	alt		0.383	PABPN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071767.4	NM_004643		A	23792661	C	A	23792661	3	1	273	1	0	0	0	0	1	0	0	0	11375	564	20	4	624	4	PABPN1	14	23792661	Missense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10		23792661	83556879	65	17290											
SCNN1B	6338	hgsc.bcm.edu	37	chr16	23391419	23391421	+	In_Frame_Del	DEL	GGA	GGA	-																															tcgctgcctcctgcaggaagGgaattgtcaagctcaacatc																										TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr16:23391419_23391421delGGA	ENST00000343070.2	+	12	1647_1649	c.1471_1473delGGA	c.(1471-1473)ggadel	p.G491del	SCNN1B_ENST00000568923.1_In_Frame_Del_p.G464del|SCNN1B_ENST00000307331.5_In_Frame_Del_p.G536del|SCNN1B_ENST00000568085.1_In_Frame_Del_p.G455del	NM_000336.2	NP_000327.2	P51168	SCNNB_HUMAN	sodium channel, non-voltage-gated 1, beta subunit	491					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)	CTGCAGGAAGGGAATTGTCAAGC	0.493																																					p.490_491del		Atlas-Indel,Pindel	.											.	SCNN1B	81	.	0			c.1470_1472del						PASS	.																																			SO:0001651	inframe_deletion	6338	exon12			.	X87159	CCDS10609.1	16p12.2-p12.1	2012-02-28	2012-02-28		ENSG00000168447	ENSG00000168447		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10600	protein-coding gene	gene with protein product	"Liddle syndrome"	600760	"sodium channel, nonvoltage-gated 1, beta", "sodium channel, non-voltage-gated 1, beta"				Standard	NM_000336		Approved	ENaCbeta	uc002dln.3	P51168	OTTHUMG00000131608	ENST00000343070.2:c.1471_1473delGGA	chr16.hg19:g.23391419_23391421delGGA	ENSP00000345751:p.Gly491del	144.0	0.0	0		128.0	38.0	0.296875	NM_000336	C5HTZ2|O60891|Q96KG2|Q9UJ32|Q9UMU5	In_Frame_Del	DEL	ENST00000343070.2	hg19	CCDS10609.1																																																																																			.	.	.	none		0.493	SCNN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254495.2			-	23391421	GGA	-	23391419	7	5	273	1	0	1	0	1	0	0	0	0	13941	1233	43	0	1513	0	SCNN1B	16	23391419	In_Frame_Del	DEL	GGA	TCGA-WN-AB4C-01A-11D-A42J-10		23391419	66963334	66	17291											
DOC2A	8448	hgsc.bcm.edu	37	chr16	30021517	30021517	+	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	tgctcctggatgttgatggtCatgcgatcgcccctgcggcc	4	11	13	13	3	1	1	1	1	0	0	3	3	2	2	4	3	3	2	4	3	0	1			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr16:30021517C>T	ENST00000350119.4	-	2	217	c.27G>A	c.(25-27)atG>atA	p.M9I	DOC2A_ENST00000564979.1_Missense_Mutation_p.M9I|DOC2A_ENST00000567824.1_5'Flank|DOC2A_ENST00000564944.1_Missense_Mutation_p.M9I	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	9	Interaction with UNC13D and DYNLT1.				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						TGTTGATGGTCATGCGATCGC	0.652																																					p.M9I		Atlas-SNP	.											.	DOC2A	40	.	0			c.G27A						PASS	.						67	68	68					16																	30021517		2197	4300	6497	SO:0001583	missense	8448	exon2			GATGGTCATGCGA	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.27G>A	chr16.hg19:g.30021517C>T	ENSP00000340017:p.Met9Ile	113.0	0.0	.		70.0	8.0	.	NM_003586	B4DEJ2|H3BNH6|Q6P4G4|Q7Z5G0|Q8IVX0	Missense_Mutation	SNP	ENST00000350119.4	hg19	CCDS10666.1	.	.	.	.	.	.	.	.	.	.	c	11.50	1.657555	0.29425	.	.	ENSG00000149927	ENST00000350119	D	0.91011	-2.77	4.14	4.14	0.48551	.	0.000000	0.45126	U	0.000382	T	0.79452	0.4448	N	0.08118	0	0.30052	N	0.811696	B	0.13145	0.007	B	0.09377	0.004	T	0.69049	-0.5248	10	0.17832	T	0.49	.	13.9735	0.64257	0.0:1.0:0.0:0.0	.	9	Q14183	DOC2A_HUMAN	I	9	ENSP00000340017:M9I	ENSP00000340017:M9I	M	-	3	0	DOC2A	29929018	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.871000	0.48459	2.149000	0.67028	0.457000	0.33378	ATG	.	.	.	none		0.652	DOC2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255148.2	NM_003586		T	30021517	C	T	30021517	3	4	273	1	0	0	0	0	1	0	0	0	4685	826	29	2	1215	2	DOC2A	16	30021517	Missense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	6630098	30021517	60333236	67	17292											
SLC5A2	6524	hgsc.bcm.edu	37	chr16	31500225	31500225	+	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	tgggtggtgttcatcgtggtAgtgtcggtggcctggcttcc	2	14	17	8	2	1	0	1	0	0	0	4	0	2	0	2	6	0	3	2	6	1	3			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr16:31500225A>T	ENST00000330498.3	+	11	1324	c.1305A>T	c.(1303-1305)gtA>gtT	p.V435V	AC026471.6_ENST00000565137.1_RNA	NM_003041.3	NP_003032.1	P31639	SC5A2_HUMAN	solute carrier family 5 (sodium/glucose cotransporter), member 2	435					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)	TCATCGTGGTAGTGTCGGTGG	0.692																																					p.V435V		Atlas-SNP	.											.	SLC5A2	58	.	0			c.A1305T						PASS	.						56	53	54					16																	31500225		2197	4299	6496	SO:0001819	synonymous_variant	6524	exon11			CGTGGTAGTGTCG		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.1305A>T	chr16.hg19:g.31500225A>T		46.0	0.0	.		40.0	11.0	.	NM_003041	A2RRD2	Silent	SNP	ENST00000330498.3	hg19	CCDS10714.1																																																																																			.	.	.	none		0.692	SLC5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255627.2			T	31500225	A	T	31500225	2	4	273	1	0	0	0	0	0	0	0	1	14678	407	15	5		5	SLC5A2	16	31500225	Silent	SNP	A	TCGA-WN-AB4C-01A-11D-A42J-10	1478708	31500225	58854528	68	17293											
BRD7	29117	hgsc.bcm.edu	37	chr16	50373920	50373920	+	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	ttcattcctgagtgcaacagCttctttgcagctttataata	10	16	6	9	0	2	1	1	1	1	0	3	1	3	1	1	0	5	4	1	0	4	8	rs150219867		TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr16:50373920C>T	ENST00000394688.3	-	6	828	c.669G>A	c.(667-669)aaG>aaA	p.K223K	BRD7_ENST00000394689.2_Silent_p.K223K			Q9NPI1	BRD7_HUMAN	bromodomain containing 7	223					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)				AGTGCAACAGCTTCTTTGCAG	0.343																																					p.K223K		Atlas-SNP	.											.	BRD7	61	.	0			c.G669A						PASS	.	C	,	0,4396		0,0,2198	120	121	120		669,669	5.3	1	16	dbSNP_134	120	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous,coding-synonymous	BRD7	NM_001173984.2,NM_013263.4	,	0,1,6494	TT,TC,CC		0.0116,0.0,0.0077	,	223/653,223/652	50373920	1,12989	2198	4297	6495	SO:0001819	synonymous_variant	29117	exon6			CAACAGCTTCTTT	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.669G>A	chr16.hg19:g.50373920C>T		156.0	0.0	.		165.0	45.0	.	NM_013263	Q4VC09|Q8N2L9|Q96KA4|Q9BV48|Q9UH59	Silent	SNP	ENST00000394688.3	hg19	CCDS10742.1																																																																																			.	C|1.000;T|0.000	0.000	weak		0.343	BRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256874.3	NM_013263		T	50373920	C	T	50373920	2	4	273	1	0	0	0	0	0	0	0	1	1507	796	28	2		2	BRD7	16	50373920	Silent	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	18873695	50373920	39980833	69	17294											
KIAA0174	9798	hgsc.bcm.edu	37	chr16	71950997	71950997	+	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	tgtgtctacattgatctgggCtgctcctcgactccagtcag	6	13	10	12	1	3	1	1	1	2	0	6	2	5	1	2	1	2	2	2	1	1	2			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr16:71950997C>A	ENST00000378799.6	+	4	673	c.317C>A	c.(316-318)gCt>gAt	p.A106D	IST1_ENST00000378798.5_Missense_Mutation_p.A106D|RP11-498D10.5_ENST00000567146.1_RNA|IST1_ENST00000541571.2_Missense_Mutation_p.A106D|IST1_ENST00000329908.8_Missense_Mutation_p.A106D|IST1_ENST00000538850.1_Intron|IST1_ENST00000606369.1_Intron|IST1_ENST00000535424.1_Missense_Mutation_p.A119D|IST1_ENST00000544564.1_Missense_Mutation_p.A106D|IST1_ENST00000538565.1_Intron			P53990	IST1_HUMAN	increased sodium tolerance 1 homolog (yeast)	106	Interaction with CHMP1A and CHMP1B.|Interaction with VPS37B.				abscission (GO:0009838)|cell division (GO:0051301)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of proteolysis (GO:0045862)|protein localization (GO:0008104)|viral capsid secondary envelopment (GO:0046745)|viral release from host cell (GO:0019076)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Flemming body (GO:0090543)|midbody (GO:0030496)	MIT domain binding (GO:0090541)|protein complex binding (GO:0032403)|protein domain specific binding (GO:0019904)										TTGATCTGGGCTGCTCCTCGA	0.368																																					p.A119D		Atlas-SNP	.											.	.	.	.	0			c.C356A						PASS	.						87	85	86					16																	71950997		2198	4298	6496	SO:0001583	missense	9798	exon5			TCTGGGCTGCTCC	BC004359	CCDS10905.1, CCDS59271.1, CCDS59272.1, CCDS59273.1, CCDS59274.1	16q22.2	2011-08-18	2011-08-18	2011-08-18	ENSG00000182149	ENSG00000182149			28977	protein-coding gene	gene with protein product			"KIAA0174"	KIAA0174		8724849, 19129480	Standard	NM_001270975		Approved		uc002fbm.2	P53990	OTTHUMG00000137597	ENST00000378799.6:c.317C>A	chr16.hg19:g.71950997C>A	ENSP00000368076:p.Ala106Asp	56.0	0.0	.		50.0	11.0	.	NM_001270976	A8KAH5|J3QLU7|Q3SYM4|Q9BQ81|Q9BWN2	Missense_Mutation	SNP	ENST00000378799.6	hg19	CCDS59272.1	.	.	.	.	.	.	.	.	.	.	C	35	5.586842	0.96578	.	.	ENSG00000182149	ENST00000535424;ENST00000378799;ENST00000424485;ENST00000329908;ENST00000378798;ENST00000456820	.	.	.	5.81	5.81	0.92471	Domain of unknown function DUF292, eukaryotic (1);	0.000000	0.85682	D	0.000000	D	0.86611	0.5974	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	0.85130	0.995;0.984;0.987;0.997	D	0.88631	0.3169	9	0.87932	D	0	-6.0333	20.0758	0.97742	0.0:1.0:0.0:0.0	.	106;106;106;119	P53990;P53990-2;P53990-3;A8KAH5	IST1_HUMAN;.;.;.	D	119;106;106;106;106;44	.	ENSP00000330408:A106D	A	+	2	0	KIAA0174	70508498	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.783000	0.85696	2.763000	0.94921	0.650000	0.86243	GCT	.	.	.	none		0.368	IST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269005.2	NM_014761		A	71950997	C	A	71950997	3	1	273	1	0	0	0	0	1	0	0	0	8165	797	28	4	327	4	KIAA0174	16	71950997	Missense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	21577077	71950997	18403756	70	17295											
C16orf46	123775	hgsc.bcm.edu	37	chr16	81094893	81094893	+	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	cctgcttggcctttgggagaAcatgctttcgggtgatcaca	7	12	12	10	1	1	2	1	1	0	1	2	3	1	2	2	3	3	2	2	3	1	3			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr16:81094893A>T	ENST00000299578.5	-	4	1296	c.1061T>A	c.(1060-1062)gTt>gAt	p.V354D	C16orf46_ENST00000444657.3_5'Flank|C16orf46_ENST00000378611.4_Missense_Mutation_p.V354D|RP11-303E16.8_ENST00000564536.1_RNA	NM_152337.2	NP_689550.2	Q6P387	CP046_HUMAN	chromosome 16 open reading frame 46	354						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|large_intestine(3)|lung(9)|prostate(1)|stomach(1)|urinary_tract(1)	18						CTTTGGGAGAACATGCTTTCG	0.498																																					p.V354D		Atlas-SNP	.											.	C16orf46	57	.	0			c.T1061A						PASS	.						160	153	155					16																	81094893		2202	4300	6502	SO:0001583	missense	123775	exon3			GGGAGAACATGCT	BC064143	CCDS10932.1, CCDS42201.1	16q23.2	2012-10-09			ENSG00000166455	ENSG00000166455			26525	protein-coding gene	gene with protein product							Standard	NM_152337		Approved	FLJ32702	uc002fgc.4	Q6P387	OTTHUMG00000137629	ENST00000299578.5:c.1061T>A	chr16.hg19:g.81094893A>T	ENSP00000299578:p.Val354Asp	87.0	0.0	.		94.0	26.0	.	NM_001100873	Q96MA7	Missense_Mutation	SNP	ENST00000299578.5	hg19	CCDS10932.1	.	.	.	.	.	.	.	.	.	.	A	11.97	1.797893	0.31777	.	.	ENSG00000166455	ENST00000378611;ENST00000444657;ENST00000299578	T;T	0.19105	2.17;2.17	4.95	0.684	0.18003	.	1.443920	0.04336	N	0.353206	T	0.12008	0.0292	N	0.19112	0.55	0.09310	N	1	P;P	0.43701	0.815;0.815	B;B	0.37304	0.246;0.246	T	0.16335	-1.0406	10	0.59425	D	0.04	.	1.2725	0.02024	0.4007:0.2939:0.0958:0.2095	.	354;354	Q6P387-2;Q6P387	.;CP046_HUMAN	D	354;81;354	ENSP00000367874:V354D;ENSP00000299578:V354D	ENSP00000299578:V354D	V	-	2	0	C16orf46	79652394	0.000000	0.05858	0.000000	0.03702	0.307000	0.27823	0.226000	0.17776	0.317000	0.23160	0.450000	0.29827	GTT	.	.	.	none		0.498	C16orf46-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269054.2	NM_152337		T	81094893	A	T	81094893	3	4	273	1	0	0	0	0	1	0	0	0	1817	43	2	5	158	5	C16orf46	16	81094893	Missense_Mutation	SNP	A	TCGA-WN-AB4C-01A-11D-A42J-10	9143896	81094893	9259860	71	17296											
MED11	400569	hgsc.bcm.edu	37	chr17	4636405	4636405	+	Missense_Mutation	SNP	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	cgaggaaggactgtcagatgGctctgaagcgagtggactat	11	8	15	7	2	2	2	1	1	1	1	2	7	2	5	0	4	1	1	0	4	3	1	rs376931968		TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr17:4636405G>A	ENST00000293777.5	+	3	333	c.277G>A	c.(277-279)Gct>Act	p.A93T	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	93						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			lung(2)|ovary(2)	4						CTGTCAGATGGCTCTGAAGCG	0.567																																					p.A93T		Atlas-SNP	.											.	MED11	5	.	0			c.G277A						PASS	.	G	THR/ALA	0,4406		0,0,2203	109	85	93		277	5.7	1	17		93	1,8599	1.2+/-3.3	0,1,4299	no	missense	MED11	NM_001001683.2	58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	93/118	4636405	1,13005	2203	4300	6503	SO:0001583	missense	400569	exon3			CAGATGGCTCTGA	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.277G>A	chr17.hg19:g.4636405G>A	ENSP00000293777:p.Ala93Thr	92.0	0.0	.		69.0	31.0	.	NM_001001683	Q6NS89	Missense_Mutation	SNP	ENST00000293777.5	hg19	CCDS32533.1	.	.	.	.	.	.	.	.	.	.	G	34	5.390757	0.95988	0.0	1.16E-4	ENSG00000161920	ENST00000293777	.	.	.	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.77805	0.4185	M	0.62266	1.93	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.79017	-0.1975	9	0.87932	D	0	-5.2699	17.3997	0.87456	0.0:0.0:1.0:0.0	.	93	Q9P086	MED11_HUMAN	T	93	.	ENSP00000293777:A93T	A	+	1	0	MED11	4583154	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.027000	0.70881	2.703000	0.92315	0.655000	0.94253	GCT	.	.	.	weak		0.567	MED11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439574.1	NM_001001683		A	4636405	G	A	4636405	3	1	273	1	0	0	0	0	1	0	0	0	9434	1203	42	2	287	2	MED11	17	4636405	Missense_Mutation	SNP	G	TCGA-WN-AB4C-01A-11D-A42J-10		4636405	76558805	72	17297											
NLRP1	22861	hgsc.bcm.edu	37	chr17	5461748	5461748	+	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	tggcggctgaatttaatgcaGaaagtgcacactaagagctc	13	9	11	8	1	0	3	0	1	0	2	1	3	0	3	0	2	3	4	0	2	4	3			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr17:5461748G>A	ENST00000572272.1	-	4	2267	c.2268C>T	c.(2266-2268)ttC>ttT	p.F756F	NLRP1_ENST00000269280.4_Silent_p.F756F|NLRP1_ENST00000345221.3_Silent_p.F756F|NLRP1_ENST00000577119.1_Silent_p.F756F|NLRP1_ENST00000354411.3_Silent_p.F756F|NLRP1_ENST00000571307.1_5'UTR|NLRP1_ENST00000262467.5_Silent_p.F756F			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	756					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)				ATTTAATGCAGAAAGTGCACA	0.498																																					p.F756F		Atlas-SNP	.											.	NLRP1	358	.	0			c.C2268T						PASS	.						101	101	101					17																	5461748		2203	4300	6503	SO:0001819	synonymous_variant	22861	exon4			AATGCAGAAAGTG	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.2268C>T	chr17.hg19:g.5461748G>A		134.0	0.0	.		65.0	24.0	.	NM_033007	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Silent	SNP	ENST00000572272.1	hg19	CCDS42246.1																																																																																			.	.	.	none		0.498	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004		A	5461748	G	A	5461748	2	1	273	1	0	0	0	0	0	0	0	1	10478	933	33	2		2	NLRP1	17	5461748	Silent	SNP	G	TCGA-WN-AB4C-01A-11D-A42J-10	825343	5461748	75733462	73	17298											
FLCN	201163	hgsc.bcm.edu	37	chr17	17117172	17117172	+	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	aaaaagcaccttcactttgcTgaagaaaaccaaaacaaaac	21	6	4	10	0	1	2	1	1	0	1	1	2	1	2	2	0	5	2	2	0	9	2			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr17:17117172T>G	ENST00000285071.4	-	14	1993		c.e14-2		RP11-45M22.4_ENST00000427497.3_Intron	NM_144997.5	NP_659434.2	Q8NFG4	FLCN_HUMAN	folliculin						cell-cell junction assembly (GO:0007043)|hemopoiesis (GO:0030097)|in utero embryonic development (GO:0001701)|negative regulation of ATP biosynthetic process (GO:2001170)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation involved in kidney development (GO:1901723)|negative regulation of energy homeostasis (GO:2000506)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of gene expression (GO:0010629)|negative regulation of mitochondrion organization (GO:0010823)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of gene expression (GO:0010628)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cytokinesis (GO:0032465)|regulation of histone acetylation (GO:0035065)|regulation of pro-B cell differentiation (GO:2000973)|regulation of protein phosphorylation (GO:0001932)|regulation of TOR signaling (GO:0032006)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(11)|stomach(1)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						TTCACTTTGCTGAAGAAAACC	0.547									Familial Non-VHL Clear Cell Renal Cancer;Birt-Hogg-Dub syndrome																												.		Atlas-SNP	.											.	FLCN	87	.	0			c.1539-2A>C						PASS	.						136	125	129					17																	17117172		2203	4300	6503	SO:0001630	splice_region_variant	201163	exon15	Familial Cancer Database	Familial Clear Cell Renal Cell Cancer, FcRCC, Familial Non-VHL Non-Papillary Clear Cell Renal Cancer;BHD, Fibrofolliculomas with Trichodiscomas and Acrochordons, incl.: Hornstein-Knickenberg syndrome, Perifollicular Fibromatosis	CTTTGCTGAAGAA	AF517523	CCDS32579.1, CCDS32580.1	17p11.2	2014-09-17			ENSG00000154803	ENSG00000154803			27310	protein-coding gene	gene with protein product		607273					Standard	NM_144997		Approved	BHD, MGC17998, MGC23445	uc002gra.4	Q8NFG4	OTTHUMG00000059275	ENST00000285071.4:c.1539-2A>C	chr17.hg19:g.17117172T>G		37.0	0.0	.		33.0	10.0	.	NM_144997	A6NJJ8|Q6ZRX1|Q96BD2|Q96BE4	Splice_Site	SNP	ENST00000285071.4	hg19	CCDS32579.1	.	.	.	.	.	.	.	.	.	.	T	14.84	2.654937	0.47467	.	.	ENSG00000154803	ENST00000285071	.	.	.	5.21	5.21	0.72293	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0781	0.72093	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	FLCN	17057897	1.000000	0.71417	0.982000	0.44146	0.327000	0.28475	7.762000	0.85270	1.960000	0.56953	0.459000	0.35465	.	.	.	.	none		0.547	FLCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131577.1	NM_144606	Intron	G	17117172	T	G	17117172	5	3	273	1	0	0	0	0	0	0	1	0	5928	1594	55	5	206	5	FLCN	17	17117172	Splice_Site	SNP	T	TCGA-WN-AB4C-01A-11D-A42J-10	11655424	17117172	64078038	74	17299											
MED1	5469	hgsc.bcm.edu	37	chr17	37566430	37566430	+	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	cttggtcttgttgctccccgAgcatatttccatgcggggtg	4	14	12	11	2	1	0	0	0	1	0	3	1	3	0	3	3	3	3	3	3	1	5			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr17:37566430A>T	ENST00000300651.6	-	17	2267	c.2044T>A	c.(2044-2046)Tcg>Acg	p.S682T	MED1_ENST00000394287.3_Intron	NM_004774.3	NP_004765.2	O95243	MBD4_HUMAN	mediator complex subunit 1	0					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)			NS(1)|breast(2)|cervix(3)|kidney(3)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(7)|urinary_tract(1)	59		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)		TTGCTCCCCGAGCATATTTCC	0.453										HNSCC(31;0.082)																											p.S682T	Pancreas(21;279 768 2492 4877 24026)	Atlas-SNP	.											.	MED1	123	.	0			c.T2044A						PASS	.						98	103	101					17																	37566430		2203	4300	6503	SO:0001583	missense	5469	exon17			TCCCCGAGCATAT	L40366	CCDS11336.1	17q12	2007-07-30	2007-07-30	2007-07-30	ENSG00000125686	ENSG00000125686			9234	protein-coding gene	gene with protein product		604311	"PPAR binding protein"	TRIP2, PPARGBP, PPARBP		9325263, 10485914	Standard	NM_004774		Approved	PBP, TRAP220, RB18A, DRIP230, CRSP200, CRSP1	uc002hrv.4	Q15648	OTTHUMG00000133216	ENST00000300651.6:c.2044T>A	chr17.hg19:g.37566430A>T	ENSP00000300651:p.Ser682Thr	122.0	0.0	.		122.0	69.0	.	NM_004774	B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Missense_Mutation	SNP	ENST00000300651.6	hg19	CCDS11336.1	.	.	.	.	.	.	.	.	.	.	A	7.772	0.707664	0.15239	.	.	ENSG00000125686	ENST00000300651	T	0.49139	0.79	5.59	0.884	0.19182	.	.	.	.	.	T	0.25269	0.0614	N	0.14661	0.345	0.36509	D	0.869482	B	0.23058	0.079	B	0.23574	0.047	T	0.18023	-1.0350	9	0.09843	T	0.71	2.8342	9.0782	0.36536	0.5401:0.0:0.4599:0.0	.	682	Q15648	MED1_HUMAN	T	682	ENSP00000300651:S682T	ENSP00000300651:S682T	S	-	1	0	MED1	34819956	0.989000	0.36119	0.921000	0.36526	0.904000	0.53231	1.350000	0.34010	0.081000	0.16988	-0.379000	0.06801	TCG	.	.	.	none		0.453	MED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256943.3	NM_004774		T	37566430	A	T	37566430	3	4	273	1	0	0	0	0	1	0	0	0	9432	304	11	5	2705	5	MED1	17	37566430	Missense_Mutation	SNP	A	TCGA-WN-AB4C-01A-11D-A42J-10	20449258	37566430	43628780	75	17300											
KRT24	192666	hgsc.bcm.edu	37	chr17	38858105	38858105	+	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	agtctttatgtttcttacttCagtctgaagtcatcagcagc	9	16	7	9	0	6	1	3	1	3	0	6	1	6	1	0	0	3	2	0	0	3	5			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr17:38858105C>A	ENST00000264651.2	-	2	752	c.696G>T	c.(694-696)ctG>ctT	p.L232L		NM_019016.2	NP_061889.2	Q2M2I5	K1C24_HUMAN	keratin 24	232	Coil 1B.|Rod.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00526)				TTTCTTACTTCAGTCTGAAGT	0.279																																					p.L232L	GBM(61;380 1051 14702 23642 31441)	Atlas-SNP	.											.	KRT24	60	.	0			c.G696T						PASS	.						77	70	73					17																	38858105		2203	4300	6503	SO:0001819	synonymous_variant	192666	exon2			TTACTTCAGTCTG		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.696G>T	chr17.hg19:g.38858105C>A		381.0	0.0	.		524.0	88.0	.	NM_019016	Q9NXG7	Silent	SNP	ENST00000264651.2	hg19	CCDS11372.1																																																																																			.	.	.	none		0.279	KRT24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257217.1	NM_019016		A	38858105	C	A	38858105	2	1	273	1	0	0	0	0	0	0	0	1	8468	813	29	4		4	KRT24	17	38858105	Silent	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	1291675	38858105	42337105	76	17301											
CCR10	2826	hgsc.bcm.edu	37	chr17	40831918	40831918	+	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	cgccaccagagccaccacgaCgcgcagcgcacgccggcgct	8	1	12	20	8	0	1	0	0	0	1	0	2	0	1	5	1	2	3	5	1	0	0			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr17:40831918C>G	ENST00000332438.4	-	2	761	c.742G>C	c.(742-744)Gtc>Ctc	p.V248L	PLEKHH3_ENST00000412503.1_5'Flank|CNTNAP1_ENST00000264638.4_5'Flank|CTD-3193K9.4_ENST00000593139.1_RNA|PLEKHH3_ENST00000293349.6_5'Flank|CCR10_ENST00000591765.1_Missense_Mutation_p.V26L|PLEKHH3_ENST00000591022.1_5'Flank	NM_016602.2	NP_057686.2	P46092	CCR10_HUMAN	chemokine (C-C motif) receptor 10	248					chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|G-protein coupled receptor activity (GO:0004930)			lung(1)|ovary(1)|skin(1)	3		Breast(137;0.000153)		BRCA - Breast invasive adenocarcinoma(366;0.14)		GCCACCACGACGCGCAGCGCA	0.731																																					p.V248L		Atlas-SNP	.											.	CCR10	7	.	0			c.G742C						PASS	.						4	5	5					17																	40831918		1909	3828	5737	SO:0001583	missense	2826	exon2			CCACGACGCGCAG	AF215981	CCDS11435.1	17q21.1-q21.3	2012-08-08	2004-11-12	2004-11-12	ENSG00000184451	ENSG00000184451		"GPCR / Class A : Chemokine receptors : C-C motif"	4474	protein-coding gene	gene with protein product		600240	"G protein-coupled receptor 2"	GPR2		7851889	Standard	NM_016602		Approved		uc002iax.4	P46092	OTTHUMG00000132301	ENST00000332438.4:c.742G>C	chr17.hg19:g.40831918C>G	ENSP00000332504:p.Val248Leu	42.0	0.0	.		67.0	32.0	.	NM_016602	Q4V749|Q6T7X2|Q9NZG2	Missense_Mutation	SNP	ENST00000332438.4	hg19	CCDS11435.1	.	.	.	.	.	.	.	.	.	.	C	18.81	3.704066	0.68615	.	.	ENSG00000184451	ENST00000332438	T	0.35048	1.33	4.24	4.24	0.50183	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36740	N	0.002421	T	0.24470	0.0593	N	0.21508	0.67	0.30823	N	0.737579	B	0.33103	0.397	B	0.36608	0.229	T	0.15780	-1.0425	10	0.26408	T	0.33	.	9.4162	0.38523	0.2122:0.7878:0.0:0.0	.	248	P46092	CCR10_HUMAN	L	248	ENSP00000332504:V248L	ENSP00000332504:V248L	V	-	1	0	CCR10	38085444	0.699000	0.27786	0.998000	0.56505	0.949000	0.60115	1.382000	0.34374	2.192000	0.70111	0.462000	0.41574	GTC	.	.	.	none		0.731	CCR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255406.1	NM_016602		G	40831918	C	G	40831918	3	3	273	1	0	0	0	0	1	0	0	0	2942	536	19	4	350	4	CCR10	17	40831918	Missense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	1973813	40831918	40363292	77	17302											
LGALS3BP	3959	hgsc.bcm.edu	37	chr17	76972059	76972059	+	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	ggccctaccttgcccgaaggCagctctgcccagagcctggg	6	6	13	16	1	1	1	0	0	1	1	1	2	1	1	5	3	5	2	5	3	2	2			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr17:76972059C>A	ENST00000262776.3	-	3	540	c.232G>T	c.(232-234)Gcc>Tcc	p.A78S	LGALS3BP_ENST00000585407.1_Missense_Mutation_p.A78S|LGALS3BP_ENST00000591778.1_Missense_Mutation_p.A78S	NM_005567.3	NP_005558.1	Q08380	LG3BP_HUMAN	lectin, galactoside-binding, soluble, 3 binding protein	78	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)			TGCCCGAAGGCAGCTCTGCCC	0.642																																					p.A78S	GBM(89;1105 1755 18102 21513)	Atlas-SNP	.											.	LGALS3BP	47	.	0			c.G232T						PASS	.						32	27	29					17																	76972059		2203	4300	6503	SO:0001583	missense	3959	exon3			CGAAGGCAGCTCT	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.232G>T	chr17.hg19:g.76972059C>A	ENSP00000262776:p.Ala78Ser	109.0	0.0	.		115.0	25.0	.	NM_005567	Q7M4S0|Q9UCH8|Q9UCH9|Q9UCI0	Missense_Mutation	SNP	ENST00000262776.3	hg19	CCDS11759.1	.	.	.	.	.	.	.	.	.	.	C	2.801	-0.249233	0.05867	.	.	ENSG00000108679	ENST00000262776;ENST00000536190	T	0.44482	0.92	3.54	0.364	0.16124	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.000000	0.37955	N	0.001871	T	0.28532	0.0706	L	0.43598	1.365	0.09310	N	1	B	0.13594	0.008	B	0.23716	0.048	T	0.15925	-1.0420	10	0.22706	T	0.39	-21.8161	5.4055	0.16318	0.0:0.6289:0.1678:0.2033	.	78	Q08380	LG3BP_HUMAN	S	78	ENSP00000262776:A78S	ENSP00000262776:A78S	A	-	1	0	LGALS3BP	74483654	0.000000	0.05858	0.132000	0.22025	0.005000	0.04900	0.048000	0.14078	0.137000	0.18759	-0.175000	0.13238	GCC	.	.	.	none		0.642	LGALS3BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437785.3	NM_005567		A	76972059	C	A	76972059	3	1	273	1	0	0	0	0	1	0	0	0	8751	710	25	4	1541	4	LGALS3BP	17	76972059	Missense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	36140141	76972059	4223151	78	17303											
ILVBL	10994	hgsc.bcm.edu	37	chr19	15230035	15230035	+	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	ctgcggttctcccggatgtgGagggggtggttgcggcctaa	4	10	18	9	3	1	0	0	0	1	0	2	2	1	2	2	7	2	2	2	7	1	3	rs372631950		TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr19:15230035G>C	ENST00000263383.3	-	9	1132	c.993C>G	c.(991-993)ctC>ctG	p.L331L	ILVBL_ENST00000531635.1_5'Flank|ILVBL_ENST00000534378.1_Silent_p.L224L	NM_006844.3	NP_006835.2	A1L0T0	ILVBL_HUMAN	ilvB (bacterial acetolactate synthase)-like	331						integral component of membrane (GO:0016021)|membrane (GO:0016020)	magnesium ion binding (GO:0000287)|thiamine pyrophosphate binding (GO:0030976)|transferase activity (GO:0016740)			NS(3)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)	26						CCCGGATGTGGAGGGGGTGGT	0.642																																					p.L331L		Atlas-SNP	.											.	ILVBL	54	.	0			c.C993G						PASS	.						63	60	61					19																	15230035		2203	4300	6503	SO:0001819	synonymous_variant	10994	exon9			GATGTGGAGGGGG	U61263	CCDS12325.1	19p13.1	2008-07-16			ENSG00000105135	ENSG00000105135			6041	protein-coding gene	gene with protein product	"acetolactate synthase homolog"	605770				8954801	Standard	NM_006844		Approved	209L8, AHAS, ILV2H, MGC1269, FLJ39061, MGC19535	uc002nam.3	A1L0T0	OTTHUMG00000165630	ENST00000263383.3:c.993C>G	chr19.hg19:g.15230035G>C		114.0	0.0	.		95.0	24.0	.	NM_006844	O43341|Q96F08|Q99651|Q9BWN5|Q9UEB2	Silent	SNP	ENST00000263383.3	hg19	CCDS12325.1																																																																																			.	.	.	alt		0.642	ILVBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385439.1	NM_006844		C	15230035	G	C	15230035	2	2	273	1	0	0	0	0	0	0	0	1	7722	1161	41	4		4	ILVBL	19	15230035	Silent	SNP	G	TCGA-WN-AB4C-01A-11D-A42J-10		15230035	43898948	79	17304											
OCEL1	79629	hgsc.bcm.edu	37	chr19	17338767	17338767	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgtgcacaggcaaagctcAggcagctggaggccctgctg	8	6	16	11	0	1	0	1	0	0	0	1	1	1	1	1	5	4	6	1	5	1	0			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr19:17338767A>G	ENST00000215061.4	+	4	615	c.571A>G	c.(571-573)Agg>Ggg	p.R191G	OCEL1_ENST00000601529.1_Intron|OCEL1_ENST00000597836.1_Missense_Mutation_p.R135G	NM_024578.1	NP_078854.1	Q9H607	OCEL1_HUMAN	occludin/ELL domain containing 1	191										central_nervous_system(2)|endometrium(2)|kidney(1)|lung(2)	7						GGCAAAGCTCAGGCAGCTGGA	0.647																																					p.R191G		Atlas-SNP	.											.	OCEL1	20	.	0			c.A571G						PASS	.						77	71	73					19																	17338767		2203	4300	6503	SO:0001583	missense	79629	exon4			AAGCTCAGGCAGC	BC029361	CCDS12351.1	19p13.11	2008-02-05				ENSG00000099330			26221	protein-coding gene	gene with protein product						12477932	Standard	NM_024578		Approved	FLJ22709	uc002nfp.3	Q9H607		ENST00000215061.4:c.571A>G	chr19.hg19:g.17338767A>G	ENSP00000215061:p.Arg191Gly	90.0	0.0	.		66.0	16.0	.	NM_024578		Missense_Mutation	SNP	ENST00000215061.4	hg19	CCDS12351.1	.	.	.	.	.	.	.	.	.	.	A	6.428	0.447122	0.12223	.	.	ENSG00000099330	ENST00000215061	T	0.22134	1.97	4.38	0.922	0.19408	Occludin/RNA polymerase II elongation factor, ELL domain (1);	0.416025	0.24722	N	0.036134	T	0.15132	0.0365	L	0.29908	0.895	0.09310	N	1	B	0.33777	0.425	B	0.39971	0.315	T	0.14448	-1.0472	10	0.46703	T	0.11	-49.3573	4.741	0.13012	0.4036:0.4895:0.0:0.107	.	191	Q9H607	OCEL1_HUMAN	G	191	ENSP00000215061:R191G	ENSP00000215061:R191G	R	+	1	2	OCEL1	17199767	0.033000	0.19621	0.011000	0.14972	0.023000	0.10783	0.392000	0.20801	0.090000	0.17273	-0.396000	0.06452	AGG	.	.	.	none		0.647	OCEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463307.1	NM_024578		G	17338767	A	G	17338767	3	3	273	1	0	0	0	0	1	0	0	0	10823	179	7	3	585	3	OCEL1	19	17338767	Missense_Mutation	SNP	A	TCGA-WN-AB4C-01A-11D-A42J-10	2108732	17338767	41790216	80	17305											
ZNF302	55900	hgsc.bcm.edu	37	chr19	35175271	35175271	+	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	aaaacaaagttatgaattttCaaattctaataagaatttgg	19	14	5	3	0	2	2	1	1	1	1	2	2	2	2	0	1	1	1	0	1	9	7			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr19:35175271C>T	ENST00000446502.2	+	6	669	c.461C>T	c.(460-462)tCa>tTa	p.S154L	ZNF302_ENST00000423823.2_Missense_Mutation_p.S110L|ZNF302_ENST00000505242.1_Missense_Mutation_p.S110L|ZNF302_ENST00000505365.2_3'UTR|ZNF302_ENST00000509528.1_3'UTR|ZNF302_ENST00000457781.2_Missense_Mutation_p.S110L|ZNF302_ENST00000507959.1_3'UTR			Q9NR11	ZN302_HUMAN	zinc finger protein 302	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|lung(2)|skin(1)	6	all_lung(56;6.16e-07)|Lung NSC(56;9.71e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			TATGAATTTTCAAATTCTAAT	0.313																																					p.S110L		Atlas-SNP	.											.	ZNF302	27	.	0			c.C329T						PASS	.						34	36	36					19																	35175271		2068	4215	6283	SO:0001583	missense	55900	exon5			AATTTTCAAATTC	AF155656	CCDS46042.1, CCDS74330.1, CCDS74331.1, CCDS74332.1, CCDS74333.1	19q13.2	2013-01-08			ENSG00000089335	ENSG00000089335		"Zinc fingers, C2H2-type", "-"	13848	protein-coding gene	gene with protein product							Standard	NM_018675		Approved	ZNF327, ZNF135L, ZNF140L	uc002nvq.1	Q9NR11	OTTHUMG00000163329	ENST00000446502.2:c.461C>T	chr19.hg19:g.35175271C>T	ENSP00000396379:p.Ser154Leu	638.0	1.0	.		579.0	137.0	.	NM_018443	Q658J3|Q9BZD8|Q9P0J4	Missense_Mutation	SNP	ENST00000446502.2	hg19		.	.	.	.	.	.	.	.	.	.	C	7.884	0.730866	0.15507	.	.	ENSG00000089335	ENST00000457781;ENST00000505242;ENST00000505163;ENST00000423823;ENST00000446502	T;T;T;T;T	0.05447	3.48;3.48;5.94;3.48;3.44	0.967	0.967	0.19674	.	.	.	.	.	T	0.06096	0.0158	L	0.49699	1.58	0.09310	N	1	B;B	0.27656	0.18;0.184	B;B	0.30029	0.11;0.1	T	0.42344	-0.9457	9	0.16896	T	0.51	.	5.2771	0.15655	0.0:1.0:0.0:0.0	.	154;110	E7EVR1;Q9NR11-2	.;.	L	110;110;110;110;154	ENSP00000391067:S110L;ENSP00000421028:S110L;ENSP00000421696:S110L;ENSP00000405219:S110L;ENSP00000396379:S154L	ENSP00000405219:S110L	S	+	2	0	ZNF302	39867111	0.970000	0.33590	0.035000	0.18076	0.038000	0.13279	1.590000	0.36654	0.822000	0.34565	0.467000	0.42956	TCA	.	.	.	none		0.313	ZNF302-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000372731.1			T	35175271	C	T	35175271	3	4	273	1	0	0	0	0	1	0	0	0	17844	838	29	2	343	2	ZNF302	19	35175271	Missense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	17836504	35175271	23953712	81	17306											
DBP	1628	hgsc.bcm.edu	37	chr19	49136816	49136816	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggtctcgtggccaggaatgCttgatagggcaagatcagct	10	9	14	8	1	2	2	1	1	1	1	3	3	2	3	1	4	2	3	1	4	3	2			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr19:49136816C>T	ENST00000222122.5	-	3	1090	c.647G>A	c.(646-648)aGc>aAc	p.S216N	DBP_ENST00000601104.1_Missense_Mutation_p.S216N|DBP_ENST00000593500.1_Missense_Mutation_p.S14N|DBP_ENST00000599385.1_Missense_Mutation_p.S14N	NM_001352.3	NP_001343.2	Q10586	DBP_HUMAN	D site of albumin promoter (albumin D-box) binding protein	216	Pro-rich (proline/acidic region (PAR)).				liver development (GO:0001889)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|rhythmic process (GO:0048511)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;9.98e-05)|all cancers(93;0.000112)|GBM - Glioblastoma multiforme(486;0.00615)|Epithelial(262;0.0155)		GCCAGGAATGCTTGATAGGGC	0.547																																					p.S216N		Atlas-SNP	.											.	DBP	16	.	0			c.G647A						PASS	.						206	187	194					19																	49136816		2203	4300	6503	SO:0001583	missense	1628	exon3			GGAATGCTTGATA	U06936	CCDS12728.1	19q13.33	2013-09-20			ENSG00000105516	ENSG00000105516			2697	protein-coding gene	gene with protein product		124097				1535333, 7835883	Standard	XR_243907		Approved	DABP	uc002pjx.4	Q10586	OTTHUMG00000183319	ENST00000222122.5:c.647G>A	chr19.hg19:g.49136816C>T	ENSP00000222122:p.Ser216Asn	69.0	0.0	.		71.0	20.0	.	NM_001352	A2I2P4	Missense_Mutation	SNP	ENST00000222122.5	hg19	CCDS12728.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.491562	0.84962	.	.	ENSG00000105516	ENST00000222122	.	.	.	4.9	4.9	0.64082	.	0.125072	0.56097	U	0.000037	T	0.76062	0.3935	M	0.80183	2.485	0.48452	D	0.99965	B	0.33826	0.427	B	0.43916	0.436	T	0.79470	-0.1790	9	0.72032	D	0.01	-16.9925	15.9611	0.79930	0.0:1.0:0.0:0.0	.	216	Q10586	DBP_HUMAN	N	216	.	ENSP00000222122:S216N	S	-	2	0	DBP	53828628	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.956000	0.70315	2.443000	0.82685	0.655000	0.94253	AGC	.	.	.	none		0.547	DBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466167.1	NM_001352		T	49136816	C	T	49136816	3	4	273	1	0	0	0	0	1	0	0	0	4258	797	28	2	338	2	DBP	19	49136816	Missense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	13961545	49136816	9992167	82	17307											
ZNF615	284370	hgsc.bcm.edu	37	chr19	52496921	52496921	+	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	tcgctgatgtacaatgaggtCactcttcatggtgaaacctt	10	13	9	9	1	3	3	2	3	1	0	4	3	3	3	1	2	2	2	1	2	3	3			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr19:52496921C>G	ENST00000602063.1	-	6	1757	c.1408G>C	c.(1408-1410)Gac>Cac	p.D470H	ZNF615_ENST00000391795.3_Missense_Mutation_p.D475H|ZNF615_ENST00000594083.1_Missense_Mutation_p.D481H|ZNF615_ENST00000376716.5_Missense_Mutation_p.D470H|ZNF615_ENST00000598071.1_Missense_Mutation_p.D481H			Q8N8J6	ZN615_HUMAN	zinc finger protein 615	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)			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)		ACAATGAGGTCACTCTTCATG	0.448																																					p.D481H		Atlas-SNP	.											.	ZNF615	111	.	0			c.G1441C						PASS	.						117	94	102					19																	52496921		2203	4300	6503	SO:0001583	missense	284370	exon7			TGAGGTCACTCTT	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.1408G>C	chr19.hg19:g.52496921C>G	ENSP00000473089:p.Asp470His	104.0	0.0	.		117.0	35.0	.	NM_001199324	B7ZKW9|Q2M2Y6|Q5CZB0|Q6ZMT7|Q6ZRB3	Missense_Mutation	SNP	ENST00000602063.1	hg19	CCDS12846.1	.	.	.	.	.	.	.	.	.	.	C	8.278	0.814789	0.16607	.	.	ENSG00000197619	ENST00000376716;ENST00000354939;ENST00000391795;ENST00000391793	T;T	0.07800	3.16;3.16	2.85	0.197	0.15164	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01905	0.0060	N	0.01631	-0.79	0.09310	N	1	B;B;B;B	0.29612	0.251;0.212;0.212;0.251	B;B;B;B	0.19666	0.026;0.015;0.015;0.026	T	0.42224	-0.9464	9	0.14656	T	0.56	.	0.347	0.00343	0.2249:0.3157:0.2214:0.238	.	475;477;481;470	B4DH87;Q8N8J6-3;Q8N8J6-2;Q8N8J6	.;.;.;ZN615_HUMAN	H	470;480;475;480	ENSP00000365906:D470H;ENSP00000375672:D475H	ENSP00000347019:D480H	D	-	1	0	ZNF615	57188733	0.000000	0.05858	0.070000	0.20053	0.934000	0.57294	-3.862000	0.00348	0.463000	0.27118	0.484000	0.47621	GAC	.	.	.	none		0.448	ZNF615-009	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462391.1	NM_198480		G	52496921	C	G	52496921	3	3	273	1	0	0	0	0	1	0	0	0	18052	826	29	4	791	4	ZNF615	19	52496921	Missense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	3360105	52496921	6632062	83	17308											
GPCPD1	56261	hgsc.bcm.edu	37	chr20	5528358	5528358	+	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	gcatccacatggatatcagaCtccccacacaaagatgaggg	14	6	9	12	0	1	3	1	1	0	2	3	4	3	4	3	2	0	1	3	2	2	1			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr20:5528358C>A	ENST00000379019.4	-	20	2180	c.1968G>T	c.(1966-1968)gaG>gaT	p.E656D	GPCPD1_ENST00000481038.1_5'UTR	NM_019593.3	NP_062539.1	Q9NPB8	GPCP1_HUMAN	glycerophosphocholine phosphodiesterase GDE1 homolog (S. cerevisiae)	656					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						GGATATCAGACTCCCCACACA	0.493																																					p.E656D		Atlas-SNP	.											.	GPCPD1	52	.	0			c.G1968T						PASS	.						172	153	160					20																	5528358		2203	4300	6503	SO:0001583	missense	56261	exon20			ATCAGACTCCCCA		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.1968G>T	chr20.hg19:g.5528358C>A	ENSP00000368305:p.Glu656Asp	173.0	0.0	.		200.0	88.0	.	NM_019593	D3DW06|Q9BQL8|Q9NUX0	Missense_Mutation	SNP	ENST00000379019.4	hg19	CCDS13090.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	0.001|0.001	-2.880142|-2.880142	0.00061|0.00061	.|.	.|.	ENSG00000125772|ENSG00000125772	ENST00000378992;ENST00000379019|ENST00000418646	T|.	0.45276|.	0.9|.	5.1|5.1	-4.36|-4.36	0.03645|0.03645	.|.	0.767687|.	0.12385|.	N|.	0.473542|.	T|T	0.17066|0.17066	0.0410|0.0410	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.27054|0.27054	-1.0085|-1.0085	10|5	0.17832|.	T|.	0.49|.	-3.4601|-3.4601	2.3414|2.3414	0.04261|0.04261	0.3675:0.2675:0.239:0.126|0.3675:0.2675:0.239:0.126	.|.	656|.	Q9NPB8|.	GPCP1_HUMAN|.	D|F	273;656|248	ENSP00000368305:E656D|.	ENSP00000368277:E273D|.	E|V	-|-	3|1	2|0	GPCPD1|GPCPD1	5476358|5476358	0.000000|0.000000	0.05858|0.05858	0.011000|0.011000	0.14972|0.14972	0.022000|0.022000	0.10575|0.10575	-0.385000|-0.385000	0.07379|0.07379	-0.580000|-0.580000	0.05944|0.05944	-2.769000|-2.769000	0.00120|0.00120	GAG|GTC	.	.	.	none		0.493	GPCPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077869.1	NM_019593		A	5528358	C	A	5528358	3	1	273	1	0	0	0	0	1	0	0	0	6610	564	20	4	54	4	GPCPD1	20	5528358	Missense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10		5528358	57497162	84	17309											
MYT1	4661	hgsc.bcm.edu	37	chr20	62839660	62839660	+	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	ctgacgagtcggagatgcagGacatgatgacccggggaaac	12	5	15	9	3	0	4	0	3	0	1	1	8	0	6	1	4	2	1	1	4	1	0			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr20:62839660G>A	ENST00000328439.1	+	7	1475	c.1111G>A	c.(1111-1113)Gac>Aac	p.D371N	MYT1_ENST00000536311.1_Missense_Mutation_p.D371N|MYT1_ENST00000360149.4_Intron	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(12)|liver(1)|lung(17)|ovary(5)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					GGAGATGCAGGACATGATGAC	0.622																																					p.D371N	GBM(59;481 1041 20555 21139 33705)	Atlas-SNP	.											.	MYT1	152	.	0			c.G1111A						PASS	.						81	74	77					20																	62839660		2203	4300	6503	SO:0001583	missense	4661	exon7			ATGCAGGACATGA	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.1111G>A	chr20.hg19:g.62839660G>A	ENSP00000327465:p.Asp371Asn	197.0	0.0	.		219.0	92.0	.	NM_004535	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000328439.1	hg19	CCDS13558.1	.	.	.	.	.	.	.	.	.	.	g	17.27	3.348108	0.61183	.	.	ENSG00000196132	ENST00000328439;ENST00000536311	T;T	0.29142	2.62;1.58	4.46	4.46	0.54185	.	0.055231	0.64402	D	0.000001	T	0.51686	0.1689	M	0.67700	2.07	0.80722	D	1	D;D	0.71674	0.998;0.983	D;P	0.81914	0.995;0.824	T	0.47420	-0.9119	10	0.17369	T	0.5	-22.5659	17.157	0.86794	0.0:0.0:1.0:0.0	.	371;371	F5H7M8;Q01538	.;MYT1_HUMAN	N	371	ENSP00000327465:D371N;ENSP00000442412:D371N	ENSP00000327465:D371N	D	+	1	0	MYT1	62310104	1.000000	0.71417	0.902000	0.35471	0.467000	0.32768	9.529000	0.98049	2.051000	0.60960	0.450000	0.29827	GAC	.	.	.	none		0.622	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535		A	62839660	G	A	62839660	3	1	273	1	0	0	0	0	1	0	0	0	10113	1174	41	2	1129	2	MYT1	20	62839660	Missense_Mutation	SNP	G	TCGA-WN-AB4C-01A-11D-A42J-10	57311302	62839660	185860	85	17310											
MRPL39	54148	hgsc.bcm.edu	37	chr21	26979768	26979768	+	Missense_Mutation	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	agagccgcagcgcccgggaaCccatggccagcgcctccata	9	3	12	17	4	0	1	0	0	0	1	1	2	1	2	6	2	4	1	6	2	2	1	rs115649519	byFrequency	TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr21:26979768C>T	ENST00000352957.4	-	1	61	c.20G>A	c.(19-21)gGt>gAt	p.G7D	MRPL39_ENST00000307301.7_Missense_Mutation_p.G7D	NM_017446.3	NP_059142	Q9NYK5	RM39_HUMAN	mitochondrial ribosomal protein L39	7						mitochondrial ribosome (GO:0005761)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(4)|ovary(1)	10						CGCCCGGGAACCCATGGCCAG	0.667											OREG0026146	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G7D		Atlas-SNP	.											.	MRPL39	61	.	0			c.G20A						PASS	.						42	45	44					21																	26979768		2203	4300	6503	SO:0001583	missense	54148	exon1			CGGGAACCCATGG	AB051346	CCDS13573.1, CCDS33522.1	21q11.2-q21	2012-09-13			ENSG00000154719	ENSG00000154719		"Mitochondrial ribosomal proteins / large subunits"	14027	protein-coding gene	gene with protein product		611845				11543634	Standard	NM_080794		Approved	RPML5, MRP-L5, MGC104174, PRED66, PRED22, C21orf92, L39mt, MSTP003, MGC3400, FLJ20451	uc002yln.3	Q9NYK5	OTTHUMG00000078371	ENST00000352957.4:c.20G>A	chr21.hg19:g.26979768C>T	ENSP00000284967:p.Gly7Asp	33.0	0.0	.	790	27.0	5.0	.	NM_017446	C9JYA5|Q32Q74|Q5QTR3|Q96Q65|Q9BSQ7|Q9BZV6|Q9NX44	Missense_Mutation	SNP	ENST00000352957.4	hg19	CCDS13573.1	.	.	.	.	.	.	.	.	.	.	C	13.36	2.214123	0.39102	.	.	ENSG00000154719	ENST00000352957;ENST00000307301;ENST00000419219	T;T;T	0.42131	0.98;0.98;0.98	4.08	-1.2	0.09554	.	1.221540	0.06023	N	0.651593	T	0.23492	0.0568	N	0.08118	0	0.09310	N	1	P;P	0.36837	0.571;0.571	B;B	0.35688	0.161;0.208	T	0.28235	-1.0050	10	0.72032	D	0.01	-9.7196	8.1526	0.31150	0.2611:0.2352:0.5037:0.0	.	7;7	Q9NYK5;Q9NYK5-2	RM39_HUMAN;.	D	7	ENSP00000284967:G7D;ENSP00000305682:G7D;ENSP00000404426:G7D	ENSP00000305682:G7D	G	-	2	0	MRPL39	25901639	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.262000	0.18460	-0.234000	0.09782	0.655000	0.94253	GGT	.	C|0.999;A|0.001	.	alt		0.667	MRPL39-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000171194.1	NM_017446		T	26979768	C	T	26979768	3	4	273	1	0	0	0	0	1	0	0	0	9809	507	18	2	1129	2	MRPL39	21	26979768	Missense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10		26979768	21150127	86	17311											
TUBA8	51807	hgsc.bcm.edu	37	chr22	18609451	18609451	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctcatcagtcagattgtgTcctcaatcactgcttctctc	7	14	6	14	0	6	1	5	0	1	1	9	1	7	1	2	0	1	1	2	0	1	2			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr22:18609451T>C	ENST00000330423.3	+	4	779	c.706T>C	c.(706-708)Tcc>Ccc	p.S236P	TUBA8_ENST00000316027.6_Missense_Mutation_p.S170P	NM_018943.2	NP_061816.1	Q9NY65	TBA8_HUMAN	tubulin, alpha 8	236					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						TCAGATTGTGTCCTCAATCAC	0.557																																					p.S236P		Atlas-SNP	.											.	TUBA8	36	.	0			c.T706C						PASS	.						149	128	135					22																	18609451		2203	4300	6503	SO:0001583	missense	51807	exon4			ATTGTGTCCTCAA	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.706T>C	chr22.hg19:g.18609451T>C	ENSP00000333326:p.Ser236Pro	87.0	0.0	.		99.0	35.0	.	NM_018943	B2RCX2|B3KPW9|B4DWG3|Q2M3N4	Missense_Mutation	SNP	ENST00000330423.3	hg19	CCDS13751.1	.	.	.	.	.	.	.	.	.	.	.	17.58	3.426055	0.62733	.	.	ENSG00000183785	ENST00000316027;ENST00000330423;ENST00000416740	T;T;T	0.71103	-0.54;-0.54;-0.54	5.67	5.67	0.87782	Tubulin/FtsZ, GTPase domain (3);	0.000000	0.85682	D	0.000000	D	0.87277	0.6137	M	0.91459	3.21	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.986;0.978;0.999	D	0.90047	0.4146	10	0.87932	D	0	.	15.3851	0.74691	0.0:0.0:0.0:1.0	.	170;260;236	B3KPW9;C9J2C0;Q9NY65	.;.;TBA8_HUMAN	P	170;236;260	ENSP00000318575:S170P;ENSP00000333326:S236P;ENSP00000412646:S260P	ENSP00000318575:S170P	S	+	1	0	TUBA8	16989451	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.040000	0.89188	2.288000	0.76882	0.533000	0.62120	TCC	.	.	.	none		0.557	TUBA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316232.3	NM_018943		C	18609451	T	C	18609451	3	2	273	1	0	0	0	0	1	0	0	0	16762	1667	58	3	720	3	TUBA8	22	18609451	Missense_Mutation	SNP	T	TCGA-WN-AB4C-01A-11D-A42J-10		18609451	32695115	87	17312											
LZTR1	8216	hgsc.bcm.edu	37	chr22	21340180	21340180	+	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	cgatgtgaaagactgctcctGgtgcaggtgggtggccccgt	6	9	16	10	2	0	2	0	1	0	1	1	3	1	2	3	4	2	2	3	4	1	0			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr22:21340180G>T	ENST00000215739.8	+	3	673	c.314G>T	c.(313-315)tGg>tTg	p.W105L	LZTR1_ENST00000479606.1_3'UTR|LZTR1_ENST00000389355.3_Intron	NM_006767.3	NP_006758.2	Q8N653	LZTR1_HUMAN	leucine-zipper-like transcription regulator 1	105					anatomical structure morphogenesis (GO:0009653)|regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)	p.W105L(1)		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)			GACTGCTCCTGGTGCAGGTGG	0.582																																					p.W105L		Atlas-SNP	.											LZTR1,NS,carcinoma,0,1	LZTR1	99	.	1	Substitution - Missense(1)	ovary(1)	c.G314T						PASS	.						86	67	74					22																	21340180		2203	4300	6503	SO:0001583	missense	8216	exon3			GCTCCTGGTGCAG	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.314G>T	chr22.hg19:g.21340180G>T	ENSP00000215739:p.Trp105Leu	50.0	0.0	.		54.0	19.0	.	NM_006767	Q14776|Q20WK0	Missense_Mutation	SNP	ENST00000215739.8	hg19	CCDS33606.1	.	.	.	.	.	.	.	.	.	.	G	31	5.075613	0.94000	.	.	ENSG00000099949	ENST00000539817;ENST00000215739	T	0.61627	0.09	4.52	4.52	0.55395	.	0.145322	0.53938	D	0.000057	D	0.83940	0.5363	H	0.97491	4.015	0.80722	D	1	D;D	0.89917	1.0;0.996	D;D	0.87578	0.998;0.991	D	0.89514	0.3773	10	0.87932	D	0	-23.9298	15.1436	0.72630	0.0:0.0:1.0:0.0	.	105;64	Q8N653;F5GXU8	LZTR1_HUMAN;.	L	64;105	ENSP00000215739:W105L	ENSP00000215739:W105L	W	+	2	0	LZTR1	19670180	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.398000	0.97281	2.516000	0.84829	0.643000	0.83706	TGG	.	.	.	none		0.582	LZTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320387.1	NM_006767		T	21340180	G	T	21340180	3	4	273	1	0	0	0	0	1	0	0	0	9144	1357	47	4	324	4	LZTR1	22	21340180	Missense_Mutation	SNP	G	TCGA-WN-AB4C-01A-11D-A42J-10	2730729	21340180	29964386	88	17313											
CACNG2	10369	hgsc.bcm.edu	37	chr22	37098524	37098524	+	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	aaacccctctggagtagagcCaatagtcggttcccacagct	11	8	9	13	1	1	1	0	0	1	1	3	2	2	2	4	2	3	3	4	2	4	3			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr22:37098524C>G	ENST00000300105.6	-	1	1079	c.98G>C	c.(97-99)tGg>tCg	p.W33S	RP1-293L6.1_ENST00000430281.1_RNA	NM_006078.3	NP_006069.1	Q9Y698	CCG2_HUMAN	calcium channel, voltage-dependent, gamma subunit 2	33					membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|neuromuscular junction development (GO:0007528)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	18						GGAGTAGAGCCAATAGTCGGT	0.473																																					p.W33S		Atlas-SNP	.											.	CACNG2	43	.	0			c.G98C						PASS	.						228	202	211					22																	37098524		2203	4300	6503	SO:0001583	missense	10369	exon1			TAGAGCCAATAGT	AF096322	CCDS13931.1	22q13.1	2006-08-01			ENSG00000166862	ENSG00000166862		"Calcium channel subunits"	1406	protein-coding gene	gene with protein product		602911					Standard	NM_006078		Approved	stargazin, MGC138502, MGC138504	uc003aps.2	Q9Y698	OTTHUMG00000030612	ENST00000300105.6:c.98G>C	chr22.hg19:g.37098524C>G	ENSP00000300105:p.Trp33Ser	135.0	0.0	.		115.0	37.0	.	NM_006078	Q2M1M1|Q5TGT3|Q9UGZ7	Missense_Mutation	SNP	ENST00000300105.6	hg19	CCDS13931.1	.	.	.	.	.	.	.	.	.	.	c	16.00	2.997271	0.54147	.	.	ENSG00000166862	ENST00000300105	D	0.98493	-4.96	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	D	0.98280	0.9430	M	0.90650	3.135	0.80722	D	1	P	0.41748	0.761	B	0.42361	0.385	D	0.99919	1.1242	10	0.87932	D	0	-4.7655	17.8661	0.88795	0.0:1.0:0.0:0.0	.	33	Q9Y698	CCG2_HUMAN	S	33	ENSP00000300105:W33S	ENSP00000300105:W33S	W	-	2	0	CACNG2	35428470	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.565000	0.67365	2.192000	0.70111	0.546000	0.68486	TGG	.	.	.	none		0.473	CACNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075500.2			G	37098524	C	G	37098524	3	3	273	1	0	0	0	0	1	0	0	0	2559	595	21	4	889	4	CACNG2	22	37098524	Missense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	15758344	37098524	14206042	89	17314											
UPK3A	7380	hgsc.bcm.edu	37	chr22	45689097	45689097	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgatcgacacgtggccaggcCggcggagcggaggcatgatc	8	4	17	12	6	0	1	0	1	0	0	2	5	0	3	2	6	1	1	2	6	0	0	rs200899354		TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chr22:45689097C>T	ENST00000216211.4	+	5	639	c.607C>T	c.(607-609)Cgg>Tgg	p.R203W	UPK3A_ENST00000396082.2_Missense_Mutation_p.R82W	NM_006953.3	NP_008884.1	O75631	UPK3A_HUMAN	uroplakin 3A	203					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)		GTGGCCAGGCCGGCGGAGCGG	0.617																																					p.R203W		Atlas-SNP	.											.	UPK3A	14	.	0			c.C607T						PASS	.						136	94	108					22																	45689097		2203	4300	6503	SO:0001583	missense	7380	exon5			CCAGGCCGGCGGA	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.607C>T	chr22.hg19:g.45689097C>T	ENSP00000216211:p.Arg203Trp	51.0	0.0	.		63.0	14.0	.	NM_006953	B0QY25|O60261|Q32N05|Q5TII6	Missense_Mutation	SNP	ENST00000216211.4	hg19	CCDS14064.1	.	.	.	.	.	.	.	.	.	.	C	17.81	3.480696	0.63849	.	.	ENSG00000100373	ENST00000216211;ENST00000396082	T;D	0.86164	-0.29;-2.08	5.2	1.63	0.23807	.	0.236572	0.34484	N	0.003922	D	0.90359	0.6983	L	0.56280	1.765	0.39790	D	0.972412	D;P	0.89917	1.0;0.534	D;B	0.91635	0.999;0.097	D	0.90197	0.4254	10	0.87932	D	0	-19.1562	11.5381	0.50651	0.6617:0.3383:0.0:0.0	.	82;203	O75631-2;O75631	.;UPK3A_HUMAN	W	203;82	ENSP00000216211:R203W;ENSP00000379391:R82W	ENSP00000216211:R203W	R	+	1	2	UPK3A	44067761	0.991000	0.36638	0.998000	0.56505	0.998000	0.95712	0.578000	0.23773	0.544000	0.28883	0.650000	0.86243	CGG	.	C|1.000;A|0.000	.	alt		0.617	UPK3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000322276.1	NM_006953		T	45689097	C	T	45689097	3	4	273	1	0	0	0	0	1	0	0	0	17022	643	23	1	625	1	UPK3A	22	45689097	Missense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	8590573	45689097	5615469	90	17315											
MXRA5	25878	hgsc.bcm.edu	37	chrX	3242168	3242168	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atccatgggcgctttcaggaTggagccatctggaagcaccc	9	8	12	12	1	2	0	1	0	1	0	3	3	3	3	3	4	2	2	3	4	1	1			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chrX:3242168T>C	ENST00000217939.6	-	5	1712	c.1558A>G	c.(1558-1560)Atc>Gtc	p.I520V		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	520	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)				GCTTTCAGGATGGAGCCATCT	0.532																																					p.I520V		Atlas-SNP	.											.	MXRA5	815	.	0			c.A1558G						PASS	.						57	52	54					X																	3242168		2203	4300	6503	SO:0001583	missense	25878	exon5			TCAGGATGGAGCC	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.1558A>G	chrX.hg19:g.3242168T>C	ENSP00000217939:p.Ile520Val	114.0	0.0	.		167.0	29.0	.	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	hg19	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	T	0	-2.732748	0.00089	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.65916	-0.18	3.63	0.014	0.14098	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.103140	0.07167	N	0.851802	T	0.31638	0.0803	N	0.03194	-0.395	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.23261	-1.0193	10	0.02654	T	1	.	7.5318	0.27687	0.0:0.341:0.0:0.659	.	520	Q9NR99	MXRA5_HUMAN	V	520	ENSP00000217939:I520V	ENSP00000217939:I520V	I	-	1	0	MXRA5	3252168	0.000000	0.05858	0.000000	0.03702	0.278000	0.26855	0.427000	0.21379	0.001000	0.14605	-0.517000	0.04412	ATC	.	.	.	none		0.532	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		C	3242168	T	C	3242168	3	2	273	1	0	0	0	0	1	0	0	0	10010	1464	51	3	6940	3	MXRA5	23	3242168	Missense_Mutation	SNP	T	TCGA-WN-AB4C-01A-11D-A42J-10		3242168	152028392	91	17316											
P2RY10	27334	hgsc.bcm.edu	37	chrX	78216602	78216602	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caaatgaatgcagttgcgttGgtcgggatgattacagttgc	10	12	13	6	2	0	2	0	2	0	0	1	3	0	3	0	2	4	4	0	2	3	4			TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chrX:78216602G>A	ENST00000171757.2	+	4	865	c.585G>A	c.(583-585)ttG>ttA	p.L195L	P2RY10_ENST00000544091.1_Silent_p.L195L	NM_014499.2	NP_055314.1	O00398	P2Y10_HUMAN	purinergic receptor P2Y, G-protein coupled, 10	195						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)	p.L195F(1)		breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(22)|ovary(3)|skin(2)	42						CAGTTGCGTTGGTCGGGATGA	0.458																																					p.L195L		Atlas-SNP	.											.	P2RY10	99	.	1	Substitution - Missense(1)	large_intestine(1)	c.G585A						PASS	.						162	120	134					X																	78216602		2203	4300	6503	SO:0001819	synonymous_variant	27334	exon2			TGCGTTGGTCGGG	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.585G>A	chrX.hg19:g.78216602G>A		94.0	0.0	.		150.0	48.0	.	NM_198333	D3DTE5|Q4VBN7|Q86V16	Silent	SNP	ENST00000171757.2	hg19	CCDS14442.1																																																																																			.	.	.	none		0.458	P2RY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057323.1			A	78216602	G	A	78216602	2	1	273	1	0	0	0	0	0	0	0	1	11354	1339	47	2		2	P2RY10	23	78216602	Silent	SNP	G	TCGA-WN-AB4C-01A-11D-A42J-10	74974434	78216602	77053958	92	17317											
FRMD7	90167	hgsc.bcm.edu	37	chrX	131212370	131212370	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tacattgatgttgctcctacCgctagtcctggctatagctt	7	15	8	11	1	0	1	0	1	0	0	2	1	2	1	3	1	4	5	3	1	5	8	rs140383991		TCGA-WN-AB4C-01A-11D-A42J-10	TCGA-WN-AB4C-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4f3eeaa4-6cb3-4b92-bdcb-4a9da48af742	b00bdf7f-b2b2-4333-add6-643ac5104d48	g.chrX:131212370C>T	ENST00000298542.4	-	12	1850	c.1675G>A	c.(1675-1677)Ggt>Agt	p.G559S	FRMD7_ENST00000370879.1_Missense_Mutation_p.G439S|FRMD7_ENST00000464296.1_Missense_Mutation_p.G544S	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	559					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)					TTGCTCCTACCGCTAGTCCTG	0.448													C|||	2	0.000529801	0.0015	0	3775	,	,		15652	0		0	False		,,,				2504	0				p.G559S		Atlas-SNP	.											.	FRMD7	69	.	0			c.G1675A						PASS	.	C	SER/GLY	0,3835		0,0,0,1632,571	150	139	143		1675	3.3	0.5	X	dbSNP_134	143	1,6727		0,0,1,2428,1871	no	missense	FRMD7	NM_194277.2	56	0,0,1,4060,2442	TT,TC,T,CC,C		0.0149,0.0,0.0095	benign	559/715	131212370	1,10562	2203	4300	6503	SO:0001583	missense	90167	exon12			TCCTACCGCTAGT	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.1675G>A	chrX.hg19:g.131212370C>T	ENSP00000298542:p.Gly559Ser	126.0	0.0	.		150.0	25.0	.	NM_194277	C0LLJ3|Q5JX99	Missense_Mutation	SNP	ENST00000298542.4	hg19	CCDS35397.1	.	.	.	.	.	.	.	.	.	.	C	2.408	-0.335970	0.05278	0.0	1.49E-4	ENSG00000165694	ENST00000370879;ENST00000298542;ENST00000464296	D;D;D	0.86097	-2.07;-1.73;-1.83	5.26	3.33	0.38152	.	0.116186	0.39210	N	0.001440	T	0.77785	0.4182	L	0.61218	1.895	0.09310	N	1	B;B	0.22746	0.074;0.029	B;B	0.15870	0.01;0.014	T	0.63607	-0.6599	10	0.37606	T	0.19	.	2.8408	0.05528	0.2811:0.4776:0.1451:0.0962	.	544;559	Q6ZUT3-2;Q6ZUT3	.;FRMD7_HUMAN	S	439;559;544	ENSP00000359916:G439S;ENSP00000298542:G559S;ENSP00000417996:G544S	ENSP00000298542:G559S	G	-	1	0	FRMD7	131040051	0.001000	0.12720	0.535000	0.28026	0.006000	0.05464	0.170000	0.16663	2.190000	0.69967	0.594000	0.82650	GGT	.	C|1.000;T|0.000	0.000	weak		0.448	FRMD7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355031.1	NM_194277		T	131212370	C	T	131212370	3	4	273	1	0	0	0	0	1	0	0	0	6062	652	23	1	473	1	FRMD7	23	131212370	Missense_Mutation	SNP	C	TCGA-WN-AB4C-01A-11D-A42J-10	52995768	131212370	24058190	93	17318											
MMEL1	79258	hgsc.bcm.edu	37	chr1	2560821	2560821	+	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	caccagggcagcggtcaccaGcagcagcagcagcagcagcc	11	1	13	16	1	1	0	1	0	0	0	1	0	1	0	3	2	8	7	3	2	0	0			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr1:2560821G>C	ENST00000378412.3	-	2	264	c.103C>G	c.(103-105)Ctg>Gtg	p.L35V	MMEL1_ENST00000511099.1_5'Flank|MMEL1_ENST00000502556.1_Missense_Mutation_p.L35V|MMEL1_ENST00000288709.6_Missense_Mutation_p.L26V			Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	35						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)		GCGGTCACcagcagcagcagc	0.741																																					p.L35V		Atlas-SNP	.											.	MMEL1	64	.	0			c.C103G						PASS	.						11	12	12					1																	2560821		1935	3820	5755	SO:0001583	missense	79258	exon2			TCACCAGCAGCAG	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.103C>G	chr1.hg19:g.2560821G>C	ENSP00000367668:p.Leu35Val	137.0	0.0	.		211.0	10.0	.	NM_033467	B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9	Missense_Mutation	SNP	ENST00000378412.3	hg19	CCDS30569.2	.	.	.	.	.	.	.	.	.	.	g	11.62	1.692616	0.30052	.	.	ENSG00000142606	ENST00000378411;ENST00000288709;ENST00000378412;ENST00000502556	D;D;D	0.91295	-1.94;-2.1;-2.82	3.02	2.09	0.27110	.	0.745425	0.11907	N	0.518068	D	0.91199	0.7227	L	0.47016	1.485	0.36062	D	0.84151	D	0.69078	0.997	D	0.78314	0.991	D	0.86623	0.1880	10	0.19590	T	0.45	-17.4114	6.0244	0.19646	0.1499:0.0:0.8501:0.0	.	35	Q495T6	MMEL1_HUMAN	V	35;26;35;35	ENSP00000288709:L26V;ENSP00000367668:L35V;ENSP00000422492:L35V	ENSP00000288709:L26V	L	-	1	2	MMEL1	2550681	0.981000	0.34729	0.993000	0.49108	0.754000	0.42855	4.457000	0.60088	0.604000	0.29930	0.455000	0.32223	CTG	.	.	.	none		0.741	MMEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002395.2	NM_033467		C	2560821	G	C	2560821	3	2	274	1	0	0	0	0	1	0	0	0	9653	962	34	4	2328	4	MMEL1	1	2560821	Missense_Mutation	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10		2560821	246689800	1	17319											
PRAMEF1	65121	hgsc.bcm.edu	37	chr1	12855755	12855756	+	Frame_Shift_Ins	INS	-	-	AA																															ccctcggagctctgctggagINSaaaattgctgcctctctcaa																										TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr1:12855755_12855756insAA	ENST00000332296.7	+	4	1138_1139	c.1035_1036insAA	c.(1036-1038)aaafs	p.K346fs	PRAMEF1_ENST00000400814.3_Frame_Shift_Ins_p.K101fs	NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	346					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)					cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35	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;0.00812)|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)		CTCTGCTGGAGAAAATTGCTGC	0.559																																					p.E345fs		Atlas-Indel,Pindel	.											.	PRAMEF1	78	.	0			c.1035_1036insAA						PASS	.																																			SO:0001589	frameshift_variant	65121	exon4			.	AL049686	CCDS148.1	1p36.21	2013-01-17			ENSG00000116721	ENSG00000116721		"-"	28840	protein-coding gene	gene with protein product							Standard	NM_023013		Approved		uc001auj.2	O95521	OTTHUMG00000001928	ENST00000332296.7:c.1038_1039dupAA	chr1.hg19:g.12855758_12855759dupAA	ENSP00000332134:p.Lys346fs	179.0	0.0	0		261.0	99.0	0.37931	NM_023013	Q9UQP2	Frame_Shift_Ins	INS	ENST00000332296.7	hg19	CCDS148.1																																																																																			.	.	.	none		0.559	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005458.1	NM_023013		AA	12855756	-	AA	12855755	7	5	274	1	0	1	1	0	0	0	0	0	12435	933	33	0	1045	0	PRAMEF1	1	12855755	Frame_Shift_Ins	INS	-	TCGA-Y8-A894-01A-11D-A35Z-10	10294934	12855755	236394866	2	17320											
C1orf89	79363	hgsc.bcm.edu	37	chr1	16563166	16563167	+	Frame_Shift_Ins	INS	-	-	T																															tgcgcagaatgcaagccaggINStactccttgccctcggcact																										TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr1:16563166_16563167insT	ENST00000375599.3	-	1	490_491	c.71_72insA	c.(70-72)tacfs	p.Y24fs		NM_030907.3	NP_112169.2	Q9BU20	RSG1_HUMAN	REM2 and RAB-like small GTPase 1	24					cellular protein localization (GO:0034613)|cilium assembly (GO:0042384)|exocytosis (GO:0006887)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|regulation of vesicle fusion (GO:0031338)|small GTPase mediated signal transduction (GO:0007264)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)	GTP binding (GO:0005525)			large_intestine(2)|lung(2)|pancreas(1)|prostate(1)	6						TGCAAGCCAGGTACTCCTTGCC	0.639																																					p.Y24_L25delinsX		Atlas-Indel,Pindel	.											.	RSG1	18	.	0			c.72_73insA						PASS	.																																			SO:0001589	frameshift_variant	79363	exon1			.	BC008702	CCDS171.1	1p36.13	2014-02-21	2011-02-22	2011-02-22	ENSG00000132881	ENSG00000132881			28127	protein-coding gene	gene with protein product	"Rem/Rab-Similar GTPase 1"		"chromosome 1 open reading frame 89"	C1orf89		19767740	Standard	NM_030907		Approved	MGC10731	uc001ayd.3	Q9BU20	OTTHUMG00000002214	ENST00000375599.3:c.72dupA	chr1.hg19:g.16563167_16563167dupT	ENSP00000364749:p.Tyr24fs	133.0	0.0	0		205.0	85.0	0.414634	NM_030907	Q5TEV7	Frame_Shift_Ins	INS	ENST00000375599.3	hg19	CCDS171.1																																																																																			.	.	.	none		0.639	RSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006279.2	NM_030907		T	16563167	-	T	16563166	7	5	274	1	0	1	1	0	0	0	0	0	2068	1256	44	0	724	0	C1orf89	1	16563166	Frame_Shift_Ins	INS	-	TCGA-Y8-A894-01A-11D-A35Z-10	3707411	16563166	232687455	3	17321											
CAMK2N1	55450	hgsc.bcm.edu	37	chr1	20811794	20811796	+	In_Frame_Del	DEL	AGG	AGG	-																															gttggtgtcctgcaggcggcAggagaagatctggcccacgt																										TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr1:20811794_20811796delAGG	ENST00000375078.3	-	1	917_919	c.77_79delCCT	c.(76-81)tcctgc>tgc	p.S26del	CAMK2N1_ENST00000489020.1_5'Flank	NM_018584.5	NP_061054.2	Q7Z7J9	CK2N1_HUMAN	calcium/calmodulin-dependent protein kinase II inhibitor 1	26						cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	calcium-dependent protein kinase inhibitor activity (GO:0008427)			lung(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000247)|Lung NSC(340;0.000285)|Breast(348;0.0013)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|COAD - Colon adenocarcinoma(152;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000132)|Kidney(64;0.00016)|GBM - Glioblastoma multiforme(114;0.00116)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.195)		TGCAGGCGGCAGGAGAAGATCTG	0.709																																					p.26_27del		Atlas-Indel,Pindel	.											.	CAMK2N1	7	.	0			c.78_80del						PASS	.																																			SO:0001651	inframe_deletion	55450	exon1			.	AY204901	CCDS207.1	1p36.12	2008-02-05			ENSG00000162545	ENSG00000162545			24190	protein-coding gene	gene with protein product		614986				12477932	Standard	NM_018584		Approved	CaMKIINalpha	uc001bdh.3	Q7Z7J9	OTTHUMG00000002837	ENST00000375078.3:c.77_79delCCT	chr1.hg19:g.20811794_20811796delAGG	ENSP00000364219:p.Ser26del	59.0	0.0	0		78.0	48.0	0.615385	NM_018584		In_Frame_Del	DEL	ENST00000375078.3	hg19	CCDS207.1																																																																																			.	.	.	none		0.709	CAMK2N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007949.1	NM_018584		-	20811796	AGG	-	20811794	7	5	274	1	0	1	0	1	0	0	0	0	2605	188	7	0	165	0	CAMK2N1	1	20811794	In_Frame_Del	DEL	AGG	TCGA-Y8-A894-01A-11D-A35Z-10	4248628	20811794	228438827	4	17322											
RNF19B	127544	hgsc.bcm.edu	37	chr1	33429684	33429684	+	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	gccgggcaccagcggcagtcGgggtccgaggctaggtagcg	6	4	19	12	5	0	0	0	0	0	0	2	1	1	0	3	6	2	4	3	6	2	2	rs369366328	byFrequency	TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr1:33429684G>T	ENST00000373456.7	-	1	602	c.603C>A	c.(601-603)ccC>ccA	p.P201P	RNF19B_ENST00000235150.4_Silent_p.P201P|RNF19B_ENST00000356990.5_Silent_p.P201P	NM_153341.2	NP_699172.2	Q6ZMZ0	RN19B_HUMAN	ring finger protein 19B	201					interferon-gamma secretion (GO:0072643)|natural killer cell mediated cytotoxicity (GO:0042267)|protein ubiquitination (GO:0016567)	cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(2)|large_intestine(3)|lung(4)	13		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				AGCGGCAGTCGGGGTCCGAGG	0.736																																					p.P201P		Atlas-SNP	.											.	RNF19B	43	.	0			c.C603A						PASS	.						15	12	13					1																	33429684		1776	3352	5128	SO:0001819	synonymous_variant	127544	exon1			GCAGTCGGGGTCC	AK074486	CCDS372.2, CCDS44107.1, CCDS72754.1	1p35.1	2010-05-11	2007-08-20	2007-08-20	ENSG00000116514	ENSG00000116514		"RING-type (C3HC4) zinc fingers"	26886	protein-coding gene	gene with protein product		610872	"IBR domain containing 3"	IBRDC3		12477932	Standard	XM_006710356		Approved	FLJ90005	uc010oho.2	Q6ZMZ0	OTTHUMG00000004013	ENST00000373456.7:c.603C>A	chr1.hg19:g.33429684G>T		85.0	0.0	.		94.0	44.0	.	NM_001127361	B7ZLB2|E9PAW6|G3XA82|Q0VG77|Q5TH44|Q5TH45|Q6P6A4|Q8N2S8|Q8WUF3	Silent	SNP	ENST00000373456.7	hg19	CCDS372.2																																																																																			.	.	.	none		0.736	RNF19B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011465.3	NM_153341		T	33429684	G	T	33429684	2	4	274	1	0	0	0	0	0	0	0	1	13484	1103	39	4		4	RNF19B	1	33429684	Silent	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10	12617890	33429684	215820937	5	17323											
ANGPTL3	27329	hgsc.bcm.edu	37	chr1	63070461	63070462	+	Frame_Shift_Ins	INS	-	-	C																															caaccaaaatgttgatccatINSccaacagattcagaaagctt																										TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr1:63070461_63070462insC	ENST00000371129.3	+	7	1436_1437	c.1356_1357insC	c.(1357-1359)ccafs	p.P453fs	DOCK7_ENST00000404627.2_Intron|DOCK7_ENST00000251157.5_Intron|DOCK7_ENST00000340370.5_Intron|AL138847.1_ENST00000593719.1_5'Flank	NM_014495.2	NP_055310.1	Q9Y5C1	ANGL3_HUMAN	angiopoietin-like 3	453	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				acylglycerol homeostasis (GO:0055090)|artery morphogenesis (GO:0048844)|cell-matrix adhesion (GO:0007160)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|fatty acid metabolic process (GO:0006631)|glycerol metabolic process (GO:0006071)|integrin-mediated signaling pathway (GO:0007229)|lipid homeostasis (GO:0055088)|lipid storage (GO:0019915)|negative regulation of lipoprotein lipase activity (GO:0051005)|negative regulation of phospholipase activity (GO:0010519)|phospholipid catabolic process (GO:0009395)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of lipid catabolic process (GO:0050996)|response to hormone (GO:0009725)|signal transduction (GO:0007165)|triglyceride homeostasis (GO:0070328)	cell surface (GO:0009986)|extracellular space (GO:0005615)	enzyme inhibitor activity (GO:0004857)|growth factor activity (GO:0008083)|integrin binding (GO:0005178)|phospholipase inhibitor activity (GO:0004859)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(3)|urinary_tract(1)	13						TGTTGATCCATCCAACAGATTC	0.337																																					p.N452fs		Pindel	.											.	ANGPTL3	42	.	0			c.1356_1357insC						PASS	.																																			SO:0001589	frameshift_variant	27329	exon7			.	AF152562	CCDS622.1	1p31.3	2013-02-06			ENSG00000132855	ENSG00000132855		"Fibrinogen C domain containing"	491	protein-coding gene	gene with protein product	"angiopoietin 5"	604774		ANGPT5		10644446	Standard	NM_014495		Approved		uc001das.2	Q9Y5C1	OTTHUMG00000009146	ENST00000371129.3:c.1358dupC	chr1.hg19:g.63070463_63070463dupC	ENSP00000360170:p.Pro453fs	234.0	0.0	.		363.0	90.0	0.248	NM_014495	A0JLS0|B1ALJ0|B2RCW1	Frame_Shift_Ins	INS	ENST00000371129.3	hg19	CCDS622.1																																																																																			.	.	.	none		0.337	ANGPTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025344.1	NM_014495		C	63070462	-	C	63070461	7	5	274	1	0	1	1	0	0	0	0	0	615	1432	50	0	1382	0	ANGPTL3	1	63070461	Frame_Shift_Ins	INS	-	TCGA-Y8-A894-01A-11D-A35Z-10	29640777	63070461	186180160	6	17324											
MOV10	4343	hgsc.bcm.edu	37	chr1	113237494	113237494	+	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	ccaggcaccggcaagactgtCacgttagtggaggcaattaa	12	7	12	10	2	1	1	1	0	0	1	1	2	1	2	2	4	0	4	2	4	4	2			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr1:113237494C>A	ENST00000413052.2	+	10	1986	c.1596C>A	c.(1594-1596)gtC>gtA	p.V532V	MOV10_ENST00000468624.1_3'UTR|MOV10_ENST00000369644.1_Silent_p.V476V|RP11-426L16.3_ENST00000421943.1_RNA|MOV10_ENST00000369645.1_Silent_p.V532V|MOV10_ENST00000357443.2_Silent_p.V532V	NM_001130079.1|NM_020963.3	NP_001123551.1|NP_066014.1	Q9HCE1	MOV10_HUMAN	Mov10 RISC complex RNA helicase	532					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(3)	38	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)		GCAAGACTGTCACGTTAGTGG	0.582																																					p.V532V		Atlas-SNP	.											.	MOV10	74	.	0			c.C1596A						PASS	.						58	53	55					1																	113237494		2203	4300	6503	SO:0001819	synonymous_variant	4343	exon10			GACTGTCACGTTA	AL833353	CCDS853.1, CCDS65615.1	1p13.2	2014-07-02	2014-07-02		ENSG00000155363	ENSG00000155363			7200	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 113"	610742	"Mov10 (Moloney leukemia virus 10, mouse) homolog", "Mov10, Moloney leukemia virus 10, homolog (mouse)"			12226669	Standard	NM_001286072		Approved	gb110, MGC2948, fSAP113	uc001eck.3	Q9HCE1	OTTHUMG00000011906	ENST00000413052.2:c.1596C>A	chr1.hg19:g.113237494C>A		139.0	0.0	.		202.0	86.0	.	NM_020963	Q5JR03|Q8TEF0|Q9BSY3|Q9BUJ9	Silent	SNP	ENST00000413052.2	hg19	CCDS853.1																																																																																			.	.	.	none		0.582	MOV10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032906.1	NM_020963		A	113237494	C	A	113237494	2	1	274	1	0	0	0	0	0	0	0	1	9725	813	29	4		4	MOV10	1	113237494	Silent	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10	50167033	113237494	136013127	7	17325											
LCE4A	199834	hgsc.bcm.edu	37	chr1	152681689	152681689	+	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	tgctgtggctccagctctggGggctgtggttgctgcagctc	2	12	16	11	0	1	0	0	0	1	0	3	0	2	0	1	4	5	8	1	4	0	1	rs200223098	byFrequency	TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr1:152681689G>C	ENST00000368777.1	+	2	394	c.138G>C	c.(136-138)ggG>ggC	p.G46G	LCE4A_ENST00000335535.3_Silent_p.G46G			Q5TA78	LCE4A_HUMAN	late cornified envelope 4A	46	Cys-rich.				keratinization (GO:0031424)					endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.116)			CCAGCTCTGGGGGCTGTGGTT	0.577													G|||	245	0.0489217	0.003	0.0821	5008	,	,		16464	0.129		0.0109	False		,,,				2504	0.044				p.G46G		Atlas-SNP	.											.,2	LCE4A	37	.	0			c.G138C						PASS	.						81	94	90					1																	152681689		2203	4300	6503	SO:0001819	synonymous_variant	199834	exon1			CTCTGGGGGCTGT	BI670517	CCDS1022.1	1q22	2008-02-05	2004-10-11	2004-10-15	ENSG00000187170	ENSG00000187170		"Late cornified envelopes"	16613	protein-coding gene	gene with protein product		612618	"small proline rich-like (epidermal differentiation complex) 4A"	SPRL4A		11698679	Standard	NM_178356		Approved	LEP8	uc001fak.2	Q5TA78	OTTHUMG00000014394	ENST00000368777.1:c.138G>C	chr1.hg19:g.152681689G>C		132.0	0.0	.		241.0	66.0	.	NM_178356	Q14D97	Silent	SNP	ENST00000368777.1	hg19	CCDS1022.1																																																																																			.	G|0.999;C|0.001	0.001	weak		0.577	LCE4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040048.1	NM_178356		C	152681689	G	C	152681689	2	2	274	1	0	0	0	0	0	0	0	1	8681	1219	43	4		4	LCE4A	1	152681689	Silent	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10	39444195	152681689	96568932	8	17326											
PIGM	93183	hgsc.bcm.edu	37	chr1	160001302	160001303	+	Frame_Shift_Ins	INS	-	-	T																															gccaacccagcagcggggtgINStaacggtacgtggctctcag																										TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr1:160001302_160001303insT	ENST00000368090.2	-	1	480_481	c.227_228insA	c.(226-228)tacfs	p.Y76fs		NM_145167.2	NP_660150.1	Q9H3S5	PIGM_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class M	76					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)			kidney(1)|large_intestine(4)|lung(9)|ovary(2)|skin(1)	17	all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GCAGCGGGGTGTAACGGTACGT	0.594																																					p.Y76_T77delinsX		Atlas-Indel,Pindel	.											.	PIGM	27	.	0			c.228_229insA						PASS	.																																			SO:0001589	frameshift_variant	93183	exon1			.	AB028127	CCDS1192.1	1q23.2	2013-02-26	2006-06-28		ENSG00000143315	ENSG00000143315		"Dolichyl D-mannosyl phosphate dependent mannosyltransferases", "Phosphatidylinositol glycan anchor biosynthesis"	18858	protein-coding gene	gene with protein product	"GPI mannosyltransferase 1", "DPM:GlcN-(acyl-)PI mannosyltransferase", "dol-P-Man dependent GPI mannosyltransferase"	610273	"phosphatidylinositol glycan, class M"			11226175	Standard	NM_145167		Approved	GPI-MT-I	uc001fuv.1	Q9H3S5	OTTHUMG00000024081	ENST00000368090.2:c.228dupA	chr1.hg19:g.160001303_160001303dupT	ENSP00000357069:p.Tyr76fs	233.0	0.0	0		380.0	171.0	0.45	NM_145167		Frame_Shift_Ins	INS	ENST00000368090.2	hg19	CCDS1192.1																																																																																			.	.	.	none		0.594	PIGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060643.2	NM_145167		T	160001303	-	T	160001302	7	5	274	1	0	1	1	0	0	0	0	0	11899	1372	48	0	1047	0	PIGM	1	160001302	Frame_Shift_Ins	INS	-	TCGA-Y8-A894-01A-11D-A35Z-10	7319613	160001302	89249319	9	17327											
RGS4	5999	hgsc.bcm.edu	37	chr1	163039075	163039075	+	5'UTR	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	agagggagacagaggagctgGtactgcagagcggtcgtctg	10	6	18	7	2	1	4	0	0	1	4	2	6	1	5	0	4	4	3	0	4	1	1			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr1:163039075G>C	ENST00000367909.6	+	0	141				RGS4_ENST00000531057.1_5'Flank|RGS4_ENST00000367908.4_5'Flank|RGS4_ENST00000421743.2_Missense_Mutation_p.G31A|RGS4_ENST00000367906.3_5'Flank|RGS4_ENST00000527809.1_5'Flank	NM_001113380.1|NM_005613.5	NP_001106851.1|NP_005604.1	P49798	RGS4_HUMAN	regulator of G-protein signaling 4						inactivation of MAPK activity (GO:0000188)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|upper_aerodigestive_tract(2)	21						AGAGGAGCTGGTACTGCAGAG	0.517											OREG0013952	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G31A	Ovarian(76;1257 1738 3039 6086)	Atlas-SNP	.											.	RGS4	97	.	0			c.G92C						PASS	.						13	17	15					1																	163039075		1269	2285	3554	SO:0001623	5_prime_UTR_variant	5999	exon2			GAGCTGGTACTGC	BC051869	CCDS1243.1, CCDS44270.1, CCDS44271.1, CCDS44272.1	1q23.3	2008-05-14	2007-08-14		ENSG00000117152	ENSG00000117152		"Regulators of G-protein signaling"	10000	protein-coding gene	gene with protein product		602516	"regulator of G-protein signalling 4", "schizophrenia disorder 9"	SCZD9		8602223, 8756726	Standard	NM_001102445		Approved		uc001gcl.4	P49798	OTTHUMG00000034417	ENST00000367909.6:c.-200G>C	chr1.hg19:g.163039075G>C		141.0	0.0	.	1828	231.0	105.0	.	NM_001102445	A7XA56|A7XA58|A7XA59|A7YVV7|B1APZ3	Missense_Mutation	SNP	ENST00000367909.6	hg19	CCDS1243.1	.	.	.	.	.	.	.	.	.	.	G	17.42	3.384567	0.61845	.	.	ENSG00000117152	ENST00000421743	T	0.60548	0.18	4.35	2.27	0.28462	.	.	.	.	.	T	0.15522	0.0374	N	0.08118	0	0.20403	N	0.999902	B	0.22800	0.075	B	0.17433	0.018	T	0.05194	-1.0900	8	0.87932	D	0	.	5.0814	0.14659	0.3474:0.0:0.6526:0.0	.	31	A7XA59	.	A	31	ENSP00000397181:G31A	ENSP00000397181:G31A	G	+	2	0	RGS4	161305699	0.000000	0.05858	0.000000	0.03702	0.655000	0.38815	0.346000	0.19997	0.424000	0.26061	0.563000	0.77884	GGT	.	.	.	none		0.517	RGS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083197.2	NM_005613		C	163039075	G	C	163039075	1	2	274	0	1	0	0	0	0	0	0	0	13320	1261	44	4		4	RGS4	1	163039075	5'UTR	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10	3037773	163039075	86211546	10	17328											
GREB1	9687	hgsc.bcm.edu	37	chr2	11725936	11725936	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggttggcttggtgggaccagCttcagtcacctttccagtgg	5	12	14	10	0	2	0	2	0	0	0	3	1	3	1	3	5	1	3	3	5	0	4			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr2:11725936C>T	ENST00000381486.2	+	9	1364	c.1064C>T	c.(1063-1065)gCt>gTt	p.A355V	GREB1_ENST00000381483.2_Missense_Mutation_p.A355V|GREB1_ENST00000234142.5_Missense_Mutation_p.A355V|RN7SL674P_ENST00000463397.2_RNA|GREB1_ENST00000263834.5_Missense_Mutation_p.A355V	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	355						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)		GTGGGACCAGCTTCAGTCACC	0.507																																					p.A355V	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.C1064T						PASS	.						95	83	87					2																	11725936		2203	4300	6503	SO:0001583	missense	9687	exon9			GACCAGCTTCAGT		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.1064C>T	chr2.hg19:g.11725936C>T	ENSP00000370896:p.Ala355Val	133.0	0.0	.		178.0	79.0	.	NM_148903	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	hg19	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	C	19.08	3.757093	0.69648	.	.	ENSG00000196208	ENST00000381486;ENST00000263834;ENST00000381483;ENST00000234142	T;T;T;T	0.17528	3.28;2.27;2.28;3.28	4.93	4.93	0.64822	.	0.493025	0.20158	N	0.098007	T	0.18299	0.0439	L	0.50333	1.59	0.33208	D	0.552986	B;B;B	0.28419	0.015;0.006;0.211	B;B;B	0.21360	0.014;0.011;0.034	T	0.11060	-1.0603	10	0.25106	T	0.35	-11.9668	18.3234	0.90246	0.0:1.0:0.0:0.0	.	355;355;355	Q4ZG55-2;Q4ZG55-3;Q4ZG55	.;.;GREB1_HUMAN	V	355	ENSP00000370896:A355V;ENSP00000263834:A355V;ENSP00000370892:A355V;ENSP00000234142:A355V	ENSP00000234142:A355V	A	+	2	0	GREB1	11643387	0.090000	0.21635	0.506000	0.27664	0.870000	0.49936	2.467000	0.45093	2.568000	0.86640	0.650000	0.86243	GCT	.	.	.	none		0.507	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		T	11725936	C	T	11725936	3	4	274	1	0	0	0	0	1	0	0	0	6767	797	28	2	1094	2	GREB1	2	11725936	Missense_Mutation	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10		11725936	231473437	11	17329											
RGPD4	285190	hgsc.bcm.edu	37	chr2	108488143	108488143	+	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	taagggttcaggtacaggtgCggccggtgcctcagacacaa	10	7	14	10	2	2	1	2	0	0	1	2	1	2	1	2	5	3	2	2	5	3	3			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr2:108488143C>T	ENST00000408999.3	+	20	3760	c.3683C>T	c.(3682-3684)gCg>gTg	p.A1228V	RGPD4_ENST00000354986.4_Missense_Mutation_p.A1228V	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	1228					protein targeting to Golgi (GO:0000042)					breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						GGTACAGGTGCGGCCGGTGCC	0.408																																					p.A1228V		Atlas-SNP	.											.	RGPD4	112	.	0			c.C3683T						PASS	.						10	8	9					2																	108488143		683	1575	2258	SO:0001583	missense	285190	exon20			CAGGTGCGGCCGG	BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"Tetratricopeptide (TTC) repeat domain containing"	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.3683C>T	chr2.hg19:g.108488143C>T	ENSP00000386810:p.Ala1228Val	141.0	0.0	.		227.0	92.0	.	NM_182588	B9A029	Missense_Mutation	SNP	ENST00000408999.3	hg19	CCDS46381.1	.	.	.	.	.	.	.	.	.	.	-	5.045	0.194017	0.09599	.	.	ENSG00000196862	ENST00000354986;ENST00000408999	T;T	0.44482	0.92;0.92	2.33	2.33	0.28932	.	.	.	.	.	T	0.22322	0.0538	N	0.17082	0.46	0.09310	N	1	B	0.28512	0.214	B	0.16289	0.015	T	0.11421	-1.0588	9	0.15066	T	0.55	-3.8053	9.6885	0.40114	0.0:1.0:0.0:0.0	.	1228	Q7Z3J3	RGPD4_HUMAN	V	1228	ENSP00000347081:A1228V;ENSP00000386810:A1228V	ENSP00000347081:A1228V	A	+	2	0	RGPD4	107854575	0.105000	0.21958	0.001000	0.08648	0.006000	0.05464	3.069000	0.50026	1.303000	0.44873	0.162000	0.16502	GCG	.	.	.	none		0.408	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581		T	108488143	C	T	108488143	3	4	274	1	0	0	0	0	1	0	0	0	13301	768	27	1	3761	1	RGPD4	2	108488143	Missense_Mutation	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10	96762207	108488143	134711230	12	17330											
PSD4	23550	hgsc.bcm.edu	37	chr2	113956437	113956437	+	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	ttcgtgcggcccatcctgccCgtgggccccgcccagagctc	3	7	12	19	4	0	1	0	0	0	1	3	1	1	1	6	2	3	1	6	2	0	1	rs369985754	byFrequency	TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr2:113956437C>A	ENST00000245796.6	+	15	2940	c.2745C>A	c.(2743-2745)ccC>ccA	p.P915P	PSD4_ENST00000441564.3_Silent_p.P886P	NM_012455.2	NP_036587.2	Q8NDX1	PSD4_HUMAN	pleckstrin and Sec7 domain containing 4	915					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						CCATCCTGCCCGTGGGCCCCG	0.721																																					p.P915P		Atlas-SNP	.											.	PSD4	74	.	0			c.C2745A						PASS	.						8	9	9					2																	113956437		2162	4208	6370	SO:0001819	synonymous_variant	23550	exon15			CCTGCCCGTGGGC	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.2745C>A	chr2.hg19:g.113956437C>A		44.0	0.0	.		52.0	31.0	.	NM_012455	A6NEG7|A8K1Y0|O95621|Q4ZG34|Q6GPH8|Q8IYP4	Silent	SNP	ENST00000245796.6	hg19	CCDS33276.1																																																																																			.	.	.	alt		0.721	PSD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330789.1	NM_012455		A	113956437	C	A	113956437	2	1	274	1	0	0	0	0	0	0	0	1	12659	639	23	4		4	PSD4	2	113956437	Silent	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10	5468294	113956437	129242936	13	17331											
FAM119A	151194	hgsc.bcm.edu	37	chr2	208486600	208486600	+	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	acggcagagcggcccctgagCtccacagctcccatctccag	8	5	10	18	2	1	2	0	1	1	1	4	2	3	2	5	2	3	3	5	2	0	0			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr2:208486600C>T	ENST00000411432.1	-	3	405	c.189G>A	c.(187-189)gaG>gaA	p.E63E	METTL21A_ENST00000432416.1_Silent_p.E63E|METTL21A_ENST00000272839.3_Silent_p.E63E|METTL21A_ENST00000458426.1_Silent_p.E63E|METTL21A_ENST00000448007.2_Silent_p.E63E|METTL21A_ENST00000425132.1_Silent_p.E63E|METTL21A_ENST00000448823.2_Intron|METTL21A_ENST00000442521.1_Silent_p.E63E|METTL21A_ENST00000426075.1_Silent_p.E63E|METTL21A_ENST00000406927.2_Silent_p.E63E	NM_001127395.1	NP_001120867.1	Q8WXB1	MT21A_HUMAN	methyltransferase like 21A	63					peptidyl-lysine methylation (GO:0018022)|protein methylation (GO:0006479)	cytoplasm (GO:0005737)	ATPase binding (GO:0051117)|Hsp70 protein binding (GO:0030544)|protein-lysine N-methyltransferase activity (GO:0016279)			endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|stomach(1)	10						GGCCCCTGAGCTCCACAGCTC	0.567																																					p.E63E		Atlas-SNP	.											.	METTL21A	24	.	0			c.G189A						PASS	.						78	73	75					2																	208486600		2203	4300	6503	SO:0001819	synonymous_variant	151194	exon3			CCTGAGCTCCACA	AK093812, AF455817	CCDS2376.1	2q33.3	2013-09-30	2011-03-03	2011-03-03	ENSG00000144401	ENSG00000144401			30476	protein-coding gene	gene with protein product	"Hepatocellular carcinoma-associated antigen 557b", "heat shock protein 70kDa lysine (K) methyltransferase"	615257	"family with sequence similarity 119, member A"	FAM119A		23921388	Standard	NM_145280		Approved	LOC151194, HCA557b, HSPA-KMT	uc010fuk.1	Q8WXB1	OTTHUMG00000132934	ENST00000411432.1:c.189G>A	chr2.hg19:g.208486600C>T		128.0	0.0	.		161.0	11.0	.	NM_145280	Q53RV0|Q8N1Z9|Q96GH6	Silent	SNP	ENST00000411432.1	hg19	CCDS2376.1																																																																																			.	.	.	none		0.567	METTL21A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337044.1	NM_145280		T	208486600	C	T	208486600	2	4	274	1	0	0	0	0	0	0	0	1	5417	796	28	2		2	FAM119A	2	208486600	Silent	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10	94530163	208486600	34712773	14	17332											
ESPNL	339768	hgsc.bcm.edu	37	chr2	239039152	239039153	+	Missense_Mutation	DNP	GG	GG	AT																															tgcagccacatctcccgcctGgtacgcagcctgtccctgct																								rs199652360		TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr2:239039152_239039153GG>AT	ENST00000343063.3	+	9	2060_2061	c.1797_1798GG>AT	c.(1795-1800)ctGGta>ctATta	p.V600L	ESPNL_ENST00000409169.1_Missense_Mutation_p.V556L|ESPNL_ENST00000477241.1_3'UTR|ESPNL_ENST00000409506.1_Missense_Mutation_p.V232L	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	600										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)		TCTCCCGCCTGGTACGCAGCCT	0.693																																					p.L599L|p.V600L		Atlas-SNP	.											.	ESPNL	63	.	0			c.G1797A|c.G1798T						PASS	.																																			SO:0001583	missense	339768	exon9			CCGCCTGGTACGC|CGCCTGGTACGCA	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	Exception_encountered	chr2.hg19:g.239039152_239039153delinsAT	ENSP00000339115:p.Val600Leu	105.0|106.0	0.0	.		119.0|122.0	62.0|64.0	.	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Silent|Missense_Mutation	SNP	ENST00000343063.3	hg19	CCDS2525.1																																																																																			.	.|G|1.000;C|0.000	.	none|alt		0.693	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312		AT	239039153	GG	AT	239039152	3	1	274	1	0	0	0	0	1	0	0	0	5257	1335	47	2	1831	2	ESPNL	2	239039152	Missense_Mutation	DNP	GG	TCGA-Y8-A894-01A-11D-A35Z-10	30552552	239039152	4160221	15	17333											
MON1A	84315	hgsc.bcm.edu	37	chr3	49949382	49949382	+	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	cccagaagctgccccatcctCtgactcagtcaggtcctcgt	7	9	8	17	1	3	2	2	1	1	1	6	2	5	2	5	1	2	1	5	1	1	0			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr3:49949382C>A	ENST00000417270.1	-	4	907	c.214G>T	c.(214-216)Gag>Tag	p.E72*	MON1A_ENST00000455683.2_Intron|MON1A_ENST00000483022.1_5'UTR|CTD-2330K9.3_ENST00000419183.1_Intron|MON1A_ENST00000296473.3_Nonsense_Mutation_p.E161*			Q86VX9	MON1A_HUMAN	MON1 secretory trafficking family member A	64										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)	13				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		GCCCCATCCTCTGACTCAGTC	0.622																																					p.E161X		Atlas-SNP	.											.	MON1A	41	.	0			c.G481T						PASS	.						40	41	41					3																	49949382		2203	4300	6503	SO:0001587	stop_gained	84315	exon3			CATCCTCTGACTC	AK074404	CCDS2808.2, CCDS46830.1	3p21.31	2013-08-21	2013-08-21		ENSG00000164077	ENSG00000164077			28207	protein-coding gene	gene with protein product		611464	"MON1 homolog A (yeast)"			12477932	Standard	NM_032355		Approved	MGC13272, SAND1	uc003cxz.3	Q86VX9	OTTHUMG00000156737	ENST00000417270.1:c.214G>T	chr3.hg19:g.49949382C>A	ENSP00000399613:p.Glu72*	70.0	0.0	.		106.0	47.0	.	NM_032355	B2RDQ1|G5E9N1|Q8NAV7|Q9BRF3	Nonsense_Mutation	SNP	ENST00000417270.1	hg19		.	.	.	.	.	.	.	.	.	.	C	36	5.611852	0.96637	.	.	ENSG00000164077	ENST00000296473;ENST00000417270	.	.	.	5.0	5.0	0.66597	.	0.269864	0.42682	D	0.000679	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-21.7631	18.2971	0.90150	0.0:1.0:0.0:0.0	.	.	.	.	X	161;72	.	.	E	-	1	0	MON1A	49924386	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.799000	0.62517	2.319000	0.78375	0.561000	0.74099	GAG	.	.	.	none		0.622	MON1A-005	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000345538.2	NM_032355		A	49949382	C	A	49949382	4	1	274	1	0	0	0	0	0	1	0	0	9705	922	32	4	1493	4	MON1A	3	49949382	Nonsense_Mutation	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10		49949382	148073048	16	17334											
PPM1M	132160	hgsc.bcm.edu	37	chr3	52282984	52282984	+	Frame_Shift_Del	DEL	G	G	-																															tccctcaggctcggttactaGgaacactggctgtctcccgg																										TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr3:52282984delG	ENST00000296487.4	+	8	912	c.508delG	c.(508-510)ggafs	p.G170fs	PPM1M_ENST00000323588.4_Frame_Shift_Del_p.G170fs|PPM1M_ENST00000457351.2_Frame_Shift_Del_p.G331fs|PPM1M_ENST00000409502.3_Frame_Shift_Del_p.G119fs			Q96MI6	PPM1M_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1M	170	PP2C-like.				protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|manganese ion binding (GO:0030145)			prostate(1)|urinary_tract(1)	2				BRCA - Breast invasive adenocarcinoma(193;2.4e-05)|Kidney(197;0.00171)|KIRC - Kidney renal clear cell carcinoma(197;0.00194)		TCGGTTACTAGGAACACTGGC	0.572																																					p.L330fs	NSCLC(151;810 2688 34365 49863)	Atlas-Indel,Pindel	.											.	PPM1M	9	.	0			c.990delA						PASS	.						48	46	47					3																	52282984		2203	4299	6502	SO:0001589	frameshift_variant	132160	exon8			.	AK096681	CCDS46840.1	3p21.31	2012-04-17	2010-03-05		ENSG00000164088	ENSG00000164088		"Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"	26506	protein-coding gene	gene with protein product	"protein phosphatase 2C eta"	608979	"protein phosphatase 1M (PP2C domain containing)"			12477932	Standard	NM_001122870		Approved	PP2Ceta, FLJ32332	uc011bed.2	Q96MI6	OTTHUMG00000153046	ENST00000296487.4:c.508delG	chr3.hg19:g.52282984delG	ENSP00000296487:p.Gly170fs	58.0	0.0	0		94.0	53.0	0.56383	NM_144641	Q8N8J9|Q96DB8	Frame_Shift_Del	DEL	ENST00000296487.4	hg19																																																																																				.	.	.	none		0.572	PPM1M-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000329230.2	NM_144641		-	52282984	G	-	52282984	7	5	274	1	0	1	0	1	0	0	0	0	12355	1001	35	0	530	0	PPM1M	3	52282984	Frame_Shift_Del	DEL	G	TCGA-Y8-A894-01A-11D-A35Z-10	2333602	52282984	145739446	17	17335											
C3orf38	285237	hgsc.bcm.edu	37	chr3	88205465	88205465	+	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	tagattcacatggactgaaaTgtgcatcttctcctcatggg	10	13	9	9	0	4	2	2	1	2	1	5	3	4	3	1	2	1	1	1	2	2	3			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr3:88205465T>A	ENST00000318887.3	+	3	980	c.670T>A	c.(670-672)Tgt>Agt	p.C224S	C3orf38_ENST00000486971.1_3'UTR	NM_173824.3	NP_776185.2	Q5JPI3	CC038_HUMAN	chromosome 3 open reading frame 38	224					apoptotic process (GO:0006915)					breast(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	12		Lung NSC(201;0.17)		UCEC - Uterine corpus endometrioid carcinoma (27;0.194)|LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00661)		TGGACTGAAATGTGCATCTTC	0.438																																					p.C224S		Atlas-SNP	.											.	C3orf38	29	.	0			c.T670A						PASS	.						134	129	131					3																	88205465		2203	4300	6503	SO:0001583	missense	285237	exon3			CTGAAATGTGCAT	AL832398	CCDS2921.1, CCDS2921.2	3p11.1	2011-01-25			ENSG00000179021	ENSG00000179021			28384	protein-coding gene	gene with protein product						12477932	Standard	NM_173824		Approved	MGC26717	uc003dqw.3	Q5JPI3	OTTHUMG00000155752	ENST00000318887.3:c.670T>A	chr3.hg19:g.88205465T>A	ENSP00000322469:p.Cys224Ser	75.0	0.0	.		164.0	80.0	.	NM_173824	B2R8X6|Q8TC85	Missense_Mutation	SNP	ENST00000318887.3	hg19	CCDS2921.2	.	.	.	.	.	.	.	.	.	.	T	14.70	2.614253	0.46631	.	.	ENSG00000179021	ENST00000318887	.	.	.	5.73	5.73	0.89815	.	0.250711	0.49305	D	0.000154	T	0.50429	0.1615	L	0.52759	1.655	0.80722	D	1	P	0.39282	0.666	B	0.35312	0.2	T	0.48906	-0.8993	9	0.24483	T	0.36	-3.1452	15.1867	0.73009	0.0:0.0:0.0:1.0	.	224	Q5JPI3	CC038_HUMAN	S	224	.	ENSP00000322469:C224S	C	+	1	0	C3orf38	88288155	1.000000	0.71417	0.992000	0.48379	0.963000	0.63663	5.952000	0.70282	2.175000	0.68902	0.455000	0.32223	TGT	.	.	.	none		0.438	C3orf38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341513.1	NM_173824		A	88205465	T	A	88205465	3	1	274	1	0	0	0	0	1	0	0	0	2230	1464	51	5	680	5	C3orf38	3	88205465	Missense_Mutation	SNP	T	TCGA-Y8-A894-01A-11D-A35Z-10	35922481	88205465	109816965	18	17336											
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113377181	113377181	+	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	ctgtcacatgtattagttgtTgcattgctggtcacatcttc	7	17	8	9	0	3	0	2	0	1	0	4	0	3	0	0	1	2	5	0	1	2	6			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr3:113377181T>A	ENST00000478658.1	-	5	3365	c.3348A>T	c.(3346-3348)gcA>gcT	p.A1116A	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Silent_p.A1116A			Q68DE3	K2018_HUMAN	KIAA2018	1116						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						TATTAGTTGTTGCATTGCTGG	0.458																																					p.A1116A		Atlas-SNP	.											.	KIAA2018	180	.	0			c.A3348T						PASS	.						143	134	137					3																	113377181		1982	4170	6152	SO:0001819	synonymous_variant	205717	exon7			AGTTGTTGCATTG	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.3348A>T	chr3.hg19:g.113377181T>A		55.0	0.0	.		92.0	48.0	.	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	hg19	CCDS43133.1																																																																																			.	.	.	none		0.458	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		A	113377181	T	A	113377181	2	1	274	1	0	0	0	0	0	0	0	1	8275	1799	63	5		5	KIAA2018	3	113377181	Silent	SNP	T	TCGA-Y8-A894-01A-11D-A35Z-10	25171716	113377181	84645249	19	17337											
LRRC58	116064	hgsc.bcm.edu	37	chr3	120054774	120054774	+	Frame_Shift_Del	DEL	T	T	-																															gtgggatttctttaatgaaaTttcctccaagatataaacac																										TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr3:120054774delT	ENST00000295628.3	-	2	622	c.527delA	c.(526-528)aatfs	p.N176fs		NM_001099678.1	NP_001093148.1	Q96CX6	LRC58_HUMAN	leucine rich repeat containing 58	176										large_intestine(2)|lung(5)	7				GBM - Glioblastoma multiforme(114;0.147)		TTTAATGAAATTTCCTCCAAG	0.308																																					p.N176fs		Atlas-Indel,Pindel	.											.	LRRC58	18	.	0			c.528delT						PASS	.						72	67	68					3																	120054774		1796	4060	5856	SO:0001589	frameshift_variant	116064	exon2			.	BC013757	CCDS46892.1	3q13.33	2006-01-06			ENSG00000163428	ENSG00000163428			26968	protein-coding gene	gene with protein product							Standard	NM_001099678		Approved		uc003edr.2	Q96CX6	OTTHUMG00000159407	ENST00000295628.3:c.527delA	chr3.hg19:g.120054774delT	ENSP00000295628:p.Asn176fs	55.0	0.0	0		58.0	20.0	0.344828	NM_001099678		Frame_Shift_Del	DEL	ENST00000295628.3	hg19	CCDS46892.1																																																																																			.	.	.	none		0.308	LRRC58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355142.1	XM_057296		-	120054774	T	-	120054774	7	5	274	1	0	1	0	1	0	0	0	0	9021	1493	52	0	600	0	LRRC58	3	120054774	Frame_Shift_Del	DEL	T	TCGA-Y8-A894-01A-11D-A35Z-10	6677593	120054774	77967656	20	17338											
ZNF148	7707	hgsc.bcm.edu	37	chr3	125032253	125032253	+	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	ctcatggaccatgagttcatCatgtgatatcatatcctgtt	10	15	7	9	0	4	2	4	2	0	0	5	3	5	3	2	1	0	2	2	1	2	4			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr3:125032253C>T	ENST00000360647.4	-	4	717	c.232G>A	c.(232-234)Gat>Aat	p.D78N	ZNF148_ENST00000485866.1_Missense_Mutation_p.D78N|ZNF148_ENST00000492394.1_Missense_Mutation_p.D78N|ZNF148_ENST00000544464.1_Intron|ZNF148_ENST00000484491.1_Missense_Mutation_p.D78N|ZNF148_ENST00000468369.1_Intron	NM_021964.2	NP_068799.2	Q9UQR1	ZN148_HUMAN	zinc finger protein 148	78					cellular defense response (GO:0006968)|gamete generation (GO:0007276)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein complex assembly (GO:0006461)|substantia nigra development (GO:0021762)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|liver(1)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)	28						ATGAGTTCATCATGTGATATC	0.413																																					p.D78N		Atlas-SNP	.											.	ZNF148	84	.	0			c.G232A						PASS	.						332	271	292					3																	125032253		2203	4300	6503	SO:0001583	missense	7707	exon4			GTTCATCATGTGA	U09851	CCDS3031.1	3q21.2	2013-01-08	2006-06-13		ENSG00000163848	ENSG00000163848		"Zinc fingers, C2H2-type"	12933	protein-coding gene	gene with protein product		601897	"zinc finger protein 148 (pHZ-52)"			7557990, 9925940	Standard	NM_021964		Approved	BERF-1, ZBP-89, BFCOL1, HT-BETA, ZFP148, pHZ-52	uc003ehx.4	Q9UQR1	OTTHUMG00000159448	ENST00000360647.4:c.232G>A	chr3.hg19:g.125032253C>T	ENSP00000353863:p.Asp78Asn	83.0	0.0	.		152.0	72.0	.	NM_021964	D3DN27|O00389|O43591|Q58EY5|Q6PJ98	Missense_Mutation	SNP	ENST00000360647.4	hg19	CCDS3031.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.030061	0.93575	.	.	ENSG00000163848	ENST00000360647;ENST00000484491;ENST00000492394;ENST00000485866;ENST00000543574;ENST00000465763	T;T;T;T	0.08282	3.11;3.11;3.11;3.11	5.15	5.15	0.70609	.	0.050494	0.85682	D	0.000000	T	0.18383	0.0441	N	0.24115	0.695	0.80722	D	1	D	0.63880	0.993	D	0.72338	0.977	T	0.02560	-1.1141	10	0.49607	T	0.09	-16.8398	18.8154	0.92075	0.0:1.0:0.0:0.0	.	78	Q9UQR1	ZN148_HUMAN	N	78	ENSP00000353863:D78N;ENSP00000420335:D78N;ENSP00000419322:D78N;ENSP00000420448:D78N	ENSP00000353863:D78N	D	-	1	0	ZNF148	126514943	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.845000	0.69437	2.669000	0.90835	0.650000	0.86243	GAT	.	.	.	none		0.413	ZNF148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355452.4	NM_021964		T	125032253	C	T	125032253	3	4	274	1	0	0	0	0	1	0	0	0	17746	826	29	2	2176	2	ZNF148	3	125032253	Missense_Mutation	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10	4977479	125032253	72990177	21	17339											
PSMD2	5708	hgsc.bcm.edu	37	chr3	184025149	184025149	+	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	tttcttggatcatcagctgaGatatggggagcctacactcc	9	12	10	10	0	3	1	2	1	1	1	4	4	4	3	2	3	3	1	2	3	2	4			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr3:184025149G>C	ENST00000310118.4	+	17	2597	c.2039G>C	c.(2038-2040)aGa>aCa	p.R680T	PSMD2_ENST00000435761.1_Missense_Mutation_p.R521T|EIF2B5_ENST00000444495.1_Intron|PSMD2_ENST00000439383.1_Missense_Mutation_p.R550T	NM_002808.3	NP_002799.3	Q13200	PSMD2_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 2	680					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)	CATCAGCTGAGATATGGGGAG	0.463																																					p.R680T	Colon(24;313 636 6917 9932 15554)	Atlas-SNP	.											.	PSMD2	56	.	0			c.G2039C						PASS	.						101	92	95					3																	184025149		2203	4300	6503	SO:0001583	missense	5708	exon17			AGCTGAGATATGG	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.2039G>C	chr3.hg19:g.184025149G>C	ENSP00000310129:p.Arg680Thr	56.0	0.0	.		75.0	42.0	.	NM_002808	B4DX07|B4DXY1|E7EW34|E9PCS3|Q12932|Q15321|Q53XQ4|Q96I12	Missense_Mutation	SNP	ENST00000310118.4	hg19	CCDS3258.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.0|23.0	4.362690|4.362690	0.82353|0.82353	.|.	.|.	ENSG00000175166|ENSG00000175166	ENST00000432855|ENST00000310118;ENST00000358216;ENST00000538096;ENST00000435761;ENST00000439383	.|T;T;T	.|0.40476	.|1.03;1.03;1.03	5.66|5.66	5.66|5.66	0.87406|0.87406	.|Armadillo-like helical (1);Armadillo-type fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.66509|0.66509	0.2796|0.2796	M|M	0.79123|0.79123	2.44|2.44	0.80722|0.80722	D|D	1|1	.|P;D	.|0.54601	.|0.668;0.967	.|B;D	.|0.63597	.|0.441;0.916	T|T	0.68577|0.68577	-0.5372|-0.5372	5|10	.|0.66056	.|D	.|0.02	-12.9315|-12.9315	19.7566|19.7566	0.96296|0.96296	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|521;680	.|E9PCS3;Q13200	.|.;PSMD2_HUMAN	H|T	113|680;352;672;521;550	.|ENSP00000310129:R680T;ENSP00000402618:R521T;ENSP00000416028:R550T	.|ENSP00000310129:R680T	D|R	+|+	1|2	0|0	PSMD2|PSMD2	185507843|185507843	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.940000|0.940000	0.58332|0.58332	9.321000|9.321000	0.96353|0.96353	2.671000|2.671000	0.90904|0.90904	0.563000|0.563000	0.77884|0.77884	GAT|AGA	.	.	.	none		0.463	PSMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345843.1	NM_002808		C	184025149	G	C	184025149	3	2	274	1	0	0	0	0	1	0	0	0	12708	942	33	4	2105	4	PSMD2	3	184025149	Missense_Mutation	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10	58992896	184025149	13997281	22	17340											
GALNTL6	442117	hgsc.bcm.edu	37	chr4	173961238	173961238	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttagaaaaatttaaccaccAtgccaactcctagaaagaag	18	9	5	9	0	0	3	0	0	0	3	1	3	1	3	4	0	3	0	4	0	8	5			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr4:173961238A>G	ENST00000506823.1	+	13	2450	c.1793A>G	c.(1792-1794)cAt>cGt	p.H598R	GALNTL6_ENST00000508122.1_Missense_Mutation_p.H581R	NM_001034845.2	NP_001030017.2	Q49A17	GLTL6_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 6	598					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						TTTAACCACCATGCCAACTCC	0.378																																					p.H598R		Atlas-SNP	.											.	GALNTL6	102	.	0			c.A1793G						PASS	.						57	57	57					4																	173961238		2203	4300	6503	SO:0001583	missense	442117	exon13			ACCACCATGCCAA		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.1793A>G	chr4.hg19:g.173961238A>G	ENSP00000423313:p.His598Arg	90.0	0.0	.		98.0	48.0	.	NM_001034845	Q2L4S6	Missense_Mutation	SNP	ENST00000506823.1	hg19	CCDS34104.1	.	.	.	.	.	.	.	.	.	.	A	2.776	-0.254643	0.05829	.	.	ENSG00000174473	ENST00000506823;ENST00000508122	T;T	0.54675	0.57;0.56	5.7	5.7	0.88788	.	0.322502	0.26407	N	0.024559	T	0.32852	0.0843	N	0.08118	0	0.24470	N	0.994397	B	0.09022	0.002	B	0.08055	0.003	T	0.08513	-1.0718	10	0.15066	T	0.55	.	15.9765	0.80071	1.0:0.0:0.0:0.0	.	598	Q49A17	GLTL6_HUMAN	R	598;581	ENSP00000423313:H598R;ENSP00000423827:H581R	ENSP00000423313:H598R	H	+	2	0	GALNTL6	174197813	0.981000	0.34729	1.000000	0.80357	0.385000	0.30292	2.146000	0.42216	2.172000	0.68678	0.533000	0.62120	CAT	.	.	.	none		0.378	GALNTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362395.1	NM_001034845		G	173961238	A	G	173961238	3	3	274	1	0	0	0	0	1	0	0	0	6232	217	8	3	1839	3	GALNTL6	4	173961238	Missense_Mutation	SNP	A	TCGA-Y8-A894-01A-11D-A35Z-10		173961238	17193038	23	17341											
GALNT7	51809	hgsc.bcm.edu	37	chr4	174239640	174239640	+	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	tgaccagtgtttgacaaaggGagctgatggatcaaaagtta	14	10	12	5	0	1	3	1	3	0	0	1	5	1	5	1	2	1	3	1	2	4	2			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr4:174239640G>C	ENST00000265000.4	+	11	1849	c.1766G>C	c.(1765-1767)gGa>gCa	p.G589A		NM_017423.2	NP_059119.2	Q86SF2	GALT7_HUMAN	polypeptide N-acetylgalactosaminyltransferase 7	589	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)|protein O-linked glycosylation (GO:0006493)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			central_nervous_system(1)|kidney(3)|large_intestine(5)|liver(1)|lung(9)	19		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;1.87e-18)|Epithelial(43;3.44e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-09)|STAD - Stomach adenocarcinoma(60;0.0019)|GBM - Glioblastoma multiforme(59;0.0119)|LUSC - Lung squamous cell carcinoma(193;0.0199)		TTGACAAAGGGAGCTGATGGA	0.343																																					p.G589A		Atlas-SNP	.											.	GALNT7	61	.	0			c.G1766C						PASS	.						115	118	117					4																	174239640		2203	4300	6503	SO:0001583	missense	51809	exon11			CAAAGGGAGCTGA	AJ002744	CCDS3815.1	4q31.1	2014-03-13	2014-03-13		ENSG00000109586	ENSG00000109586		"Glycosyltransferase family 2 domain containing"	4129	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 7"	605005	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7)"			10544240	Standard	NM_017423		Approved	GALNAC-T7	uc003isz.4	Q86SF2	OTTHUMG00000160817	ENST00000265000.4:c.1766G>C	chr4.hg19:g.174239640G>C	ENSP00000265000:p.Gly589Ala	156.0	0.0	.		205.0	99.0	.	NM_017423	B3KQU3|Q7Z5W7|Q9UJ28	Missense_Mutation	SNP	ENST00000265000.4	hg19	CCDS3815.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.595|9.595	1.127164|1.127164	0.20959|0.20959	.|.	.|.	ENSG00000109586|ENSG00000109586	ENST00000505308|ENST00000265000	.|T	.|0.77229	.|-1.08	4.92|4.92	4.92|4.92	0.64577|0.64577	.|Ricin B-related lectin (1);Ricin B lectin (3);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.63462|0.63462	0.2513|0.2513	N|N	0.16266|0.16266	0.395|0.395	0.80722|0.80722	D|D	1|1	.|B	.|0.22983	.|0.078	.|B	.|0.18871	.|0.023	T|T	0.59616|0.59616	-0.7421|-0.7421	5|10	.|0.10111	.|T	.|0.7	.|.	18.9993|18.9993	0.92826|0.92826	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|589	.|Q86SF2	.|GALT7_HUMAN	Q|A	386|589	.|ENSP00000265000:G589A	.|ENSP00000265000:G589A	E|G	+|+	1|2	0|0	GALNT7|GALNT7	174476215|174476215	1.000000|1.000000	0.71417|0.71417	0.957000|0.957000	0.39632|0.39632	0.831000|0.831000	0.47069|0.47069	5.713000|5.713000	0.68415|0.68415	2.645000|2.645000	0.89757|0.89757	0.555000|0.555000	0.69702|0.69702	GAG|GGA	.	.	.	none		0.343	GALNT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362456.2	NM_017423		C	174239640	G	C	174239640	3	2	274	1	0	0	0	0	1	0	0	0	6225	1174	41	4	1808	4	GALNT7	4	174239640	Missense_Mutation	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10	278402	174239640	16914636	24	17342											
ODZ3	55714	hgsc.bcm.edu	37	chr4	183245238	183245238	+	Missense_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	cagacgagagaaggaacggcGctacacaaattcctccgcag	14	4	11	12	4	0	2	0	0	0	2	2	5	2	3	2	2	2	2	2	2	4	2			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr4:183245238G>A	ENST00000511685.1	+	2	188	c.65G>A	c.(64-66)cGc>cAc	p.R22H	TENM3_ENST00000406950.2_Missense_Mutation_p.R22H			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	22	Teneurin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00694}.				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)										AAGGAACGGCGCTACACAAAT	0.512																																					p.R22H		Atlas-SNP	.											.	.	.	.	0			c.G65A						PASS	.						101	103	102					4																	183245238		1988	4168	6156	SO:0001583	missense	55714	exon1			AACGGCGCTACAC	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.65G>A	chr4.hg19:g.183245238G>A	ENSP00000424226:p.Arg22His	97.0	0.0	.		129.0	65.0	.	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	hg19	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	G	18.76	3.691681	0.68271	.	.	ENSG00000218336	ENST00000512480;ENST00000511685;ENST00000406950	T;T;T	0.45668	0.89;0.89;0.89	5.65	5.65	0.86999	Teneurin intracellular, N-terminal (2);	.	.	.	.	T	0.55065	0.1897	L	0.27053	0.805	0.51482	D	0.999923	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.991	T	0.55560	-0.8122	9	0.62326	D	0.03	.	19.9142	0.97043	0.0:0.0:1.0:0.0	.	22;22	D6RGC5;Q9P273	.;TEN3_HUMAN	H	22	ENSP00000421320:R22H;ENSP00000424226:R22H;ENSP00000385276:R22H	ENSP00000385276:R22H	R	+	2	0	ODZ3	183482232	1.000000	0.71417	0.974000	0.42286	0.613000	0.37349	7.379000	0.79691	2.941000	0.99782	0.655000	0.94253	CGC	.	.	.	none		0.512	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			A	183245238	G	A	183245238	3	1	274	1	0	0	0	0	1	0	0	0	10843	1087	38	1	67	1	ODZ3	4	183245238	Missense_Mutation	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10	9005598	183245238	7909038	25	17343											
TLR3	7098	hgsc.bcm.edu	37	chr4	187004353	187004353	+	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	ctccttcaccattccagcctCttcgtaacttgaccattctg	7	14	4	16	1	3	1	1	1	2	0	6	1	5	1	5	0	2	1	5	0	1	6			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr4:187004353C>A	ENST00000296795.3	+	4	1617	c.1513C>A	c.(1513-1515)Ctt>Att	p.L505I	TLR3_ENST00000504367.1_Missense_Mutation_p.L228I	NM_003265.2	NP_003256.1	O15455	TLR3_HUMAN	toll-like receptor 3	505					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)		ATTCCAGCCTCTTCGTAACTT	0.453																																					p.L505I		Atlas-SNP	.											.	TLR3	83	.	0			c.C1513A						PASS	.						100	104	103					4																	187004353		2203	4300	6503	SO:0001583	missense	7098	exon4			CAGCCTCTTCGTA	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.1513C>A	chr4.hg19:g.187004353C>A	ENSP00000296795:p.Leu505Ile	111.0	0.0	.		152.0	63.0	.	NM_003265	B2RAI7|B7Z7K0|E6Y0F0|E6Y0F1|E9PGH4|Q4VAL2|Q504W0	Missense_Mutation	SNP	ENST00000296795.3	hg19	CCDS3846.1	.	.	.	.	.	.	.	.	.	.	C	13.46	2.244447	0.39697	.	.	ENSG00000164342	ENST00000296795;ENST00000542020;ENST00000504367	T;T	0.70749	-0.51;-0.51	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	D	0.85809	0.5783	M	0.89904	3.07	0.58432	D	0.999996	D	0.56035	0.974	D	0.66602	0.945	D	0.88167	0.2861	10	0.87932	D	0	.	13.9953	0.64392	0.0:0.9278:0.0:0.0722	.	505	O15455	TLR3_HUMAN	I	505;505;228	ENSP00000296795:L505I;ENSP00000423684:L228I	ENSP00000296795:L505I	L	+	1	0	TLR3	187241347	0.985000	0.35326	0.813000	0.32504	0.060000	0.15804	2.694000	0.47035	2.683000	0.91414	0.557000	0.71058	CTT	.	.	.	none		0.453	TLR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360313.4			A	187004353	C	A	187004353	3	1	274	1	0	0	0	0	1	0	0	0	15964	913	32	4	1523	4	TLR3	4	187004353	Missense_Mutation	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10	3759115	187004353	4149923	26	17344											
PCDHB2	56133	hgsc.bcm.edu	37	chr5	140476411	140476411	+	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	ctgctgctcccggaggcggcAccggcccaggcccaggccga	5	3	15	18	4	0	0	0	0	0	0	1	2	1	1	5	6	2	3	5	6	0	0			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr5:140476411A>C	ENST00000194155.4	+	1	2185	c.2037A>C	c.(2035-2037)gcA>gcC	p.A679A		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	679					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A679A(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(22)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGGAGGCGGCACCGGCCCAGG	0.687																																					p.A679A		Atlas-SNP	.											PCDHB2,NS,carcinoma,0,1	PCDHB2	163	.	1	Substitution - coding silent(1)	lung(1)	c.A2037C						PASS	.						65	67	66					5																	140476411		2178	4247	6425	SO:0001819	synonymous_variant	56133	exon1			GGCGGCACCGGCC	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.2037A>C	chr5.hg19:g.140476411A>C		66.0	1.0	.		127.0	7.0	.	NM_018936	Q4KMU1	Silent	SNP	ENST00000194155.4	hg19	CCDS4244.1																																																																																			.	.	.	none		0.687	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936		C	140476411	A	C	140476411	2	2	274	1	0	0	0	0	0	0	0	1	11549	146	6	5		5	PCDHB2	5	140476411	Silent	SNP	A	TCGA-Y8-A894-01A-11D-A35Z-10		140476411	40438849	27	17345											
DCTN4	51164	hgsc.bcm.edu	37	chr5	150133041	150133041	+	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	ttgaagtccatctcactcacCtacagatttgtctgccatgc	9	13	6	13	0	3	2	2	1	2	1	5	2	4	2	3	0	3	0	3	0	2	3			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr5:150133041C>A	ENST00000447998.2	-	3	500	c.385G>T	c.(385-387)Gct>Tct	p.A129S	DCTN4_ENST00000446090.2_Splice_Site_p.A129S|DCTN4_ENST00000424236.1_Splice_Site_p.A72S|DCTN4_ENST00000521093.1_5'UTR	NM_016221.3	NP_057305.1	Q9UJW0	DCTN4_HUMAN	dynactin 4 (p62)	129					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|nucleus (GO:0005634)	protein N-terminus binding (GO:0047485)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	10		Medulloblastoma(196;0.167)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCTCACTCACCTACAGATTTG	0.438																																					p.A129S		Atlas-SNP	.											.	DCTN4	35	.	0			c.G385T						PASS	.						95	83	87					5																	150133041		2203	4300	6503	SO:0001630	splice_region_variant	51164	exon3			ACTCACCTACAGA	AF195120	CCDS4310.1, CCDS47310.1, CCDS47311.1	5q31-q32	2008-05-23			ENSG00000132912	ENSG00000132912			15518	protein-coding gene	gene with protein product		614758				10843801, 16554302	Standard	NM_016221		Approved		uc010jhi.3	Q9UJW0	OTTHUMG00000130079	ENST00000447998.2:c.385+1G>T	chr5.hg19:g.150133041C>A		48.0	0.0	.		66.0	30.0	.	NM_016221	B3KWW0|D3DQH0|E5RGT5|Q8TAN8	Missense_Mutation	SNP	ENST00000447998.2	hg19	CCDS4310.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.383083	0.82792	.	.	ENSG00000132912	ENST00000447998;ENST00000424236;ENST00000446090;ENST00000518015;ENST00000521533	T;T;T;T;T	0.48201	2.08;2.09;2.11;0.82;0.86	5.99	5.99	0.97316	.	0.050995	0.85682	D	0.000000	T	0.69278	0.3093	M	0.70275	2.135	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.996;0.998	T	0.66416	-0.5929	9	.	.	.	-21.9701	18.6582	0.91462	0.0:1.0:0.0:0.0	.	129;129	Q9UJW0-3;Q9UJW0	.;DCTN4_HUMAN	S	129;72;129;72;72	ENSP00000416968:A129S;ENSP00000411251:A72S;ENSP00000414906:A129S;ENSP00000430993:A72S;ENSP00000430183:A72S	.	A	-	1	0	DCTN4	150113234	1.000000	0.71417	1.000000	0.80357	0.356000	0.29392	7.734000	0.84928	2.840000	0.97914	0.655000	0.94253	GCT	.	.	.	none		0.438	DCTN4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252372.1		Missense_Mutation	A	150133041	C	A	150133041	5	1	274	1	0	0	0	0	0	0	1	0	4311	695	24	4	1066	4	DCTN4	5	150133041	Splice_Site	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10	9656630	150133041	30782219	28	17346											
ITK	3702	hgsc.bcm.edu	37	chr5	156671455	156671455	+	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	gtgtgtgagggcatggcctaCctggaagaggcatgtgtcat	8	10	16	7	0	1	2	1	1	0	1	1	3	1	3	2	4	1	2	2	4	2	1			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr5:156671455C>A	ENST00000422843.3	+	13	1568	c.1416C>A	c.(1414-1416)taC>taA	p.Y472*	ITK_ENST00000519749.1_3'UTR	NM_005546.3	NP_005537.3	Q08881	ITK_HUMAN	IL2-inducible T-cell kinase	472	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cellular defense response (GO:0006968)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|intracellular signal transduction (GO:0035556)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|signal transduction (GO:0007165)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(25)|ovary(8)|prostate(2)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	70	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.1)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		Pazopanib(DB06589)	GCATGGCCTACCTGGAAGAGG	0.552			T	SYK	peripheral T-cell lymphoma																																p.Y472X	Esophageal Squamous(70;1378 1469 8785 19883)	Atlas-SNP	.		Dom	yes		5	5q31-q32	3702	IL2-inducible T-cell kinase		L	.	ITK	136	.	0			c.C1416A						PASS	.						87	83	84					5																	156671455		2203	4300	6503	SO:0001587	stop_gained	3702	exon13			GGCCTACCTGGAA	D13720	CCDS4336.1	5q31-q32	2014-09-17			ENSG00000113263	ENSG00000113263		"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	6171	protein-coding gene	gene with protein product		186973				8364206	Standard	NM_005546		Approved	EMT, PSCTK2, LYK	uc003lwo.1	Q08881	OTTHUMG00000130245	ENST00000422843.3:c.1416C>A	chr5.hg19:g.156671455C>A	ENSP00000398655:p.Tyr472*	46.0	0.0	.		80.0	41.0	.	NM_005546	B2R752|Q32ML7	Nonsense_Mutation	SNP	ENST00000422843.3	hg19	CCDS4336.1	.	.	.	.	.	.	.	.	.	.	C	39	7.388191	0.98252	.	.	ENSG00000113263	ENST00000422843	.	.	.	6.08	4.31	0.51392	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.2076	0.31465	0.0:0.7457:0.0:0.2543	.	.	.	.	X	472	.	ENSP00000398655:Y472X	Y	+	3	2	ITK	156604033	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.970000	0.40520	1.590000	0.49995	0.591000	0.81541	TAC	.	.	.	none		0.552	ITK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252569.2			A	156671455	C	A	156671455	4	1	274	1	0	0	0	0	0	1	0	0	7916	518	18	4	1466	4	ITK	5	156671455	Nonsense_Mutation	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10	6538414	156671455	24243805	29	17347											
FLT4	2324	hgsc.bcm.edu	37	chr5	180045796	180045796	+	Missense_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	ggtctggagaagcccgcctcGctccgccctcggtcttcgag	4	8	13	16	5	2	1	0	0	2	1	6	3	3	1	4	3	1	1	4	3	1	1			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr5:180045796G>A	ENST00000261937.6	-	21	3053	c.2975C>T	c.(2974-2976)gCg>gTg	p.A992V	FLT4_ENST00000393347.3_Missense_Mutation_p.A992V|FLT4_ENST00000502649.1_Missense_Mutation_p.A992V|FLT4_ENST00000424276.2_5'Flank	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	992	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AGCCCGCCTCGCTCCGCCCTC	0.672																																					p.A992V	Colon(97;1075 1466 27033 27547 35871)	Atlas-SNP	.											.	FLT4	356	.	0			c.C2975T						PASS	.						17	23	21					5																	180045796		2181	4288	6469	SO:0001583	missense	2324	exon21			CGCCTCGCTCCGC	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.2975C>T	chr5.hg19:g.180045796G>A	ENSP00000261937:p.Ala992Val	71.0	0.0	.		88.0	47.0	.	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Missense_Mutation	SNP	ENST00000261937.6	hg19	CCDS4457.1	.	.	.	.	.	.	.	.	.	.	G	0.021	-1.422924	0.01126	.	.	ENSG00000037280	ENST00000261937;ENST00000393347;ENST00000502649;ENST00000512795	T;T;T;T	0.79940	-1.08;-1.08;-1.08;-1.32	4.91	3.13	0.36017	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.63271	0.2497	N	0.12746	0.255	0.09310	N	1	B;B	0.16396	0.001;0.017	B;B	0.19148	0.005;0.024	T	0.49072	-0.8977	9	0.24483	T	0.36	.	8.8003	0.34905	0.1751:0.0:0.8249:0.0	.	992;992	E9PD35;P35916	.;VGFR3_HUMAN	V	992;992;992;30	ENSP00000261937:A992V;ENSP00000377016:A992V;ENSP00000426057:A992V;ENSP00000421535:A30V	ENSP00000261937:A992V	A	-	2	0	FLT4	179978402	0.019000	0.18553	0.011000	0.14972	0.002000	0.02628	1.930000	0.40124	0.605000	0.29947	0.542000	0.68232	GCG	.	.	.	none		0.672	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4			A	180045796	G	A	180045796	3	1	274	1	0	0	0	0	1	0	0	0	5951	1087	38	1	1164	1	FLT4	5	180045796	Missense_Mutation	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10	23374341	180045796	869464	30	17348											
TJAP1	93643	hgsc.bcm.edu	37	chr6	43466745	43466745	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccgtcacctcccagaatgacTagtgccgcccctgctaagaa	10	7	8	16	2	1	3	1	1	0	2	2	3	2	3	6	0	2	1	6	0	4	2			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr6:43466745T>C	ENST00000372445.5	+	4	382	c.6T>C	c.(4-6)acT>acC	p.T2T	TJAP1_ENST00000259751.1_Silent_p.T2T|TJAP1_ENST00000372452.1_Silent_p.T2T|TJAP1_ENST00000372449.1_Silent_p.T2T|TJAP1_ENST00000438588.2_Silent_p.T2T|TJAP1_ENST00000372444.2_Silent_p.T2T|TJAP1_ENST00000483640.1_3'UTR|TJAP1_ENST00000436109.2_Silent_p.T2T	NM_001146016.1	NP_001139488.1	Q5JTD0	TJAP1_HUMAN	tight junction associated protein 1 (peripheral)	2					Golgi organization (GO:0007030)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)|trans-Golgi network (GO:0005802)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|urinary_tract(2)	21	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			CCAGAATGACTAGTGCCGCCC	0.567																																					p.T2T		Atlas-SNP	.											.	TJAP1	35	.	0			c.T6C						PASS	.						72	60	64					6																	43466745		2203	4300	6503	SO:0001819	synonymous_variant	93643	exon4			AATGACTAGTGCC	AK024269	CCDS4898.1, CCDS55004.1	6p21.1	2008-02-05	2005-07-05	2005-07-05	ENSG00000137221	ENSG00000137221			17949	protein-coding gene	gene with protein product		612658	"tight junction protein 4 (peripheral)"	TJP4		11602598	Standard	NM_001146016		Approved	PILT	uc011dvh.1	Q5JTD0	OTTHUMG00000014736	ENST00000372445.5:c.6T>C	chr6.hg19:g.43466745T>C		30.0	0.0	.		69.0	40.0	.	NM_080604	Q05BH9|Q5JTD1|Q5JWW1|Q68DB2|Q6P2P3|Q9H7V7	Silent	SNP	ENST00000372445.5	hg19	CCDS55004.1																																																																																			.	.	.	none		0.567	TJAP1-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040629.1	NM_080604		C	43466745	T	C	43466745	2	2	274	1	0	0	0	0	0	0	0	1	15940	1509	53	3		3	TJAP1	6	43466745	Silent	SNP	T	TCGA-Y8-A894-01A-11D-A35Z-10		43466745	127648322	31	17349											
STX11	8676	hgsc.bcm.edu	37	chr6	144508308	144508308	+	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	accagatcgaggacatgttcGagcagggtaagtgggacgtg	11	7	16	7	3	0	1	0	0	0	1	2	5	0	3	1	3	1	3	1	3	1	2			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr6:144508308G>T	ENST00000367568.4	+	2	727	c.544G>T	c.(544-546)Gag>Tag	p.E182*		NM_003764.3	NP_003755.2	O75558	STX11_HUMAN	syntaxin 11	182					cytotoxic T cell degranulation (GO:0043316)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|natural killer cell degranulation (GO:0043320)|neutrophil degranulation (GO:0043312)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	SNAP receptor activity (GO:0005484)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	12				OV - Ovarian serous cystadenocarcinoma(155;2.17e-06)|GBM - Glioblastoma multiforme(68;0.0492)		GGACATGTTCGAGCAGGGTAA	0.627									Familial Hemophagocytic Lymphohistiocytosis																												p.E182X		Atlas-SNP	.											.	STX11	34	.	0			c.G544T						PASS	.						51	57	55					6																	144508308		2203	4300	6503	SO:0001587	stop_gained	8676	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	ATGTTCGAGCAGG	AF044309	CCDS5205.1	6q24.1	2014-09-17			ENSG00000135604	ENSG00000135604			11429	protein-coding gene	gene with protein product		605014				9553086	Standard	NM_003764		Approved		uc003qks.4	O75558	OTTHUMG00000015739	ENST00000367568.4:c.544G>T	chr6.hg19:g.144508308G>T	ENSP00000356540:p.Glu182*	109.0	0.0	.		118.0	61.0	.	NM_003764	E1P598|O75378|O95148|Q5TCL6	Nonsense_Mutation	SNP	ENST00000367568.4	hg19	CCDS5205.1	.	.	.	.	.	.	.	.	.	.	G	37	6.277586	0.97435	.	.	ENSG00000135604	ENST00000367568	.	.	.	5.45	4.56	0.56223	.	0.050373	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-31.1219	15.5981	0.76602	0.0:0.1384:0.8616:0.0	.	.	.	.	X	182	.	ENSP00000356540:E182X	E	+	1	0	STX11	144550001	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.844000	0.86867	1.246000	0.43901	0.655000	0.94253	GAG	.	.	.	none		0.627	STX11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042544.1			T	144508308	G	T	144508308	4	4	274	1	0	0	0	0	0	1	0	0	15349	1059	37	4	546	4	STX11	6	144508308	Nonsense_Mutation	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10	101041563	144508308	26606759	32	17350											
PLEKHG1	57480	hgsc.bcm.edu	37	chr6	151054930	151054930	+	Missense_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	aatgaccttagtttcaaataGccacatgggcttgtttaacc	12	13	7	9	0	1	1	1	1	0	0	1	1	1	1	3	1	2	3	3	1	5	6			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr6:151054930G>A	ENST00000358517.2	+	2	324	c.113G>A	c.(112-114)aGc>aAc	p.S38N	PLEKHG1_ENST00000367328.1_Missense_Mutation_p.S38N			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	38							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)		GTTTCAAATAGCCACATGGGC	0.547																																					p.S38N		Atlas-SNP	.											.	PLEKHG1	97	.	0			c.G113A						PASS	.						77	78	78					6																	151054930		2203	4300	6503	SO:0001583	missense	57480	exon3			CAAATAGCCACAT	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.113G>A	chr6.hg19:g.151054930G>A	ENSP00000351318:p.Ser38Asn	82.0	0.0	.		118.0	59.0	.	NM_001029884	Q5T1F2	Missense_Mutation	SNP	ENST00000358517.2	hg19	CCDS34552.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.604559	0.87157	.	.	ENSG00000120278	ENST00000367328;ENST00000367326;ENST00000535018;ENST00000358517	T;T	0.62639	0.01;0.01	5.81	5.81	0.92471	.	0.125351	0.64402	D	0.000001	T	0.63546	0.2520	M	0.63428	1.95	0.34174	D	0.670101	D;D	0.53619	0.961;0.961	P;P	0.49637	0.617;0.617	T	0.68685	-0.5343	10	0.62326	D	0.03	.	20.0762	0.97745	0.0:0.0:1.0:0.0	.	38;38	Q5JYA6;Q9ULL1	.;PKHG1_HUMAN	N	38	ENSP00000356297:S38N;ENSP00000351318:S38N	ENSP00000351318:S38N	S	+	2	0	PLEKHG1	151096623	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	5.440000	0.66563	2.756000	0.94617	0.655000	0.94253	AGC	.	.	.	none		0.547	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1			A	151054930	G	A	151054930	3	1	274	1	0	0	0	0	1	0	0	0	12075	971	34	2	115	2	PLEKHG1	6	151054930	Missense_Mutation	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10	6546622	151054930	20060137	33	17351											
RSPH3	83861	hgsc.bcm.edu	37	chr6	159420999	159420999	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggcggccttggctggctTgaccgtcatccttgaggcct	4	10	15	12	2	1	2	1	2	0	0	2	3	2	3	4	6	0	2	4	6	0	3			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr6:159420999T>C	ENST00000252655.1	-	1	199	c.10A>G	c.(10-12)Aag>Gag	p.K4E	RSPH3_ENST00000367069.2_5'UTR|RP1-111C20.4_ENST00000606470.1_RNA|RSPH3_ENST00000297262.3_Missense_Mutation_p.K4E|RP1-111C20.4_ENST00000607391.1_RNA|RP1-111C20.4_ENST00000607796.1_RNA|RSPH3_ENST00000449822.1_5'Flank	NM_031924.4	NP_114130.3	Q86UC2	RSPH3_HUMAN	radial spoke 3 homolog (Chlamydomonas)	4										endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|skin(1)|stomach(7)	23		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.36e-16)|BRCA - Breast invasive adenocarcinoma(81;5.92e-06)		TTGGCTGGCTTGACCGTCATC	0.667																																					p.K4E		Atlas-SNP	.											.	RSPH3	48	.	0			c.A10G						PASS	.						15	14	14					6																	159420999		2149	4219	6368	SO:0001583	missense	83861	exon1			CTGGCTTGACCGT	AF353618	CCDS5260.1	6q25.3	2014-05-16	2008-07-04	2007-06-26	ENSG00000130363	ENSG00000130363			21054	protein-coding gene	gene with protein product		615876	"radial spokehead-like 2"	RSHL2		12477932	Standard	NM_031924		Approved	dJ111C20.1, RSP3	uc003qrx.3	Q86UC2	OTTHUMG00000015924	ENST00000252655.1:c.10A>G	chr6.hg19:g.159420999T>C	ENSP00000252655:p.Lys4Glu	104.0	0.0	.		175.0	82.0	.	NM_031924	Q96LQ5|Q96LX2|Q9BX75	Missense_Mutation	SNP	ENST00000252655.1	hg19	CCDS5260.1	.	.	.	.	.	.	.	.	.	.	T	11.10	1.538607	0.27475	.	.	ENSG00000130363	ENST00000252655;ENST00000297262	T;T	0.17370	2.42;2.28	1.12	-0.411	0.12370	.	8.538430	0.00166	U	0.000002	T	0.02727	0.0082	N	0.24115	0.695	0.09310	N	1	B;B	0.27625	0.183;0.115	B;B	0.17722	0.019;0.009	T	0.31194	-0.9952	10	0.23891	T	0.37	.	2.954	0.05870	0.4349:0.0:0.0:0.5651	.	4;4	Q86UC2-2;Q86UC2	.;RSPH3_HUMAN	E	4	ENSP00000252655:K4E;ENSP00000297262:K4E	ENSP00000252655:K4E	K	-	1	0	RSPH3	159340987	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-1.681000	0.01937	-0.117000	0.11872	0.379000	0.24179	AAG	.	.	.	none		0.667	RSPH3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031924		C	159420999	T	C	159420999	3	2	274	1	0	0	0	0	1	0	0	0	13718	1821	63	3	1704	3	RSPH3	6	159420999	Missense_Mutation	SNP	T	TCGA-Y8-A894-01A-11D-A35Z-10	8366069	159420999	11694068	34	17352											
CAMK2B	816	hgsc.bcm.edu	37	chr7	44268995	44268995	+	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	caggctacttacatggggctGgcagggggctaaagggagcc	9	6	17	9	0	0	0	0	0	0	0	0	1	0	1	1	7	3	4	1	7	4	3			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr7:44268995G>T	ENST00000395749.2	-	18	1407	c.1331C>A	c.(1330-1332)cCa>cAa	p.P444Q	CAMK2B_ENST00000489429.1_5'UTR|CAMK2B_ENST00000457475.1_Intron|CAMK2B_ENST00000358707.3_Intron|CAMK2B_ENST00000502837.2_Intron|CAMK2B_ENST00000440254.2_Intron|CAMK2B_ENST00000346990.4_Intron|CAMK2B_ENST00000350811.3_Intron|CAMK2B_ENST00000353625.4_Intron|CAMK2B_ENST00000347193.4_Intron|CAMK2B_ENST00000258682.6_Intron|CAMK2B_ENST00000395747.2_Intron	NM_001220.4	NP_001211.3	Q13554	KCC2B_HUMAN	calcium/calmodulin-dependent protein kinase II beta	444					activation of meiosis involved in egg activation (GO:0060466)|calcium ion transport (GO:0006816)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|inhibitory G-protein coupled receptor phosphorylation (GO:0002030)|interferon-gamma-mediated signaling pathway (GO:0060333)|neuromuscular process controlling balance (GO:0050885)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of neuron projection development (GO:0010976)|positive regulation of synapse maturation (GO:0090129)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of calcium ion transport (GO:0051924)|regulation of dendritic spine development (GO:0060998)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of skeletal muscle adaptation (GO:0014733)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, cholinergic (GO:0032222)|response to cadmium ion (GO:0046686)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)	18						ACATGGGGCTGGCAGGGGGCT	0.687																																					p.P444Q		Atlas-SNP	.											.	CAMK2B	56	.	0			c.C1331A						PASS	.						5	5	5					7																	44268995		1932	3820	5752	SO:0001583	missense	816	exon18			GGGGCTGGCAGGG	U50358	CCDS5483.1, CCDS5484.1, CCDS5485.1, CCDS5486.1, CCDS5487.1, CCDS5488.1, CCDS5489.1, CCDS43573.1	7p14.3-p14.1	2008-10-30	2008-10-30		ENSG00000058404	ENSG00000058404			1461	protein-coding gene	gene with protein product	"CaM-kinase II beta chain", "calcium/calmodulin-dependent protein kinase type II beta chain", "CaM kinase II beta subunit", "proline rich calmodulin-dependent protein kinase"	607707	"calcium/calmodulin-dependent protein kinase (CaM kinase) II beta"	CAMKB			Standard	NM_172079		Approved	CAM2, CAMK2	uc003tkq.2	Q13554	OTTHUMG00000023491	ENST00000395749.2:c.1331C>A	chr7.hg19:g.44268995G>T	ENSP00000379098:p.Pro444Gln	314.0	0.0	.		456.0	231.0	.	NM_001220	A4D2K0|A4D2K1|A4D2K2|A4D2K3|A4D2K4|A4D2K5|A4D2K6|O95437|O95438|O95599|Q9UGH7|Q9UGH8|Q9UGH9|Q9UNX0|Q9UNX7|Q9UP00|Q9Y5N4|Q9Y6F4	Missense_Mutation	SNP	ENST00000395749.2	hg19	CCDS5483.1	.	.	.	.	.	.	.	.	.	.	g	11.40	1.628866	0.28978	.	.	ENSG00000058404	ENST00000395749	T	0.66995	-0.24	3.66	-0.42	0.12336	Protein kinase-like domain (1);	.	.	.	.	T	0.46639	0.1403	L	0.38175	1.15	0.24473	N	0.994385	B	0.34015	0.435	B	0.29524	0.103	T	0.27365	-1.0076	9	0.12430	T	0.62	.	6.8313	0.23911	0.4498:0.0:0.5502:0.0	.	444	Q13554	KCC2B_HUMAN	Q	444	ENSP00000379098:P444Q	ENSP00000379098:P444Q	P	-	2	0	CAMK2B	44235520	0.000000	0.05858	0.458000	0.27068	0.879000	0.50718	0.020000	0.13466	-0.092000	0.12417	0.558000	0.71614	CCA	.	.	.	none		0.687	CAMK2B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251138.2	NM_172084		T	44268995	G	T	44268995	3	4	274	1	0	0	0	0	1	0	0	0	2602	1348	47	4	693	4	CAMK2B	7	44268995	Missense_Mutation	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10		44268995	114869668	35	17353											
STEAP4	79689	hgsc.bcm.edu	37	chr7	87912402	87912402	+	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	ggctgccatgagtgatccttGatccattggagtaagtccaa	10	11	11	9	0	0	3	0	3	0	0	3	4	3	4	4	2	1	2	4	2	2	3			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr7:87912402G>T	ENST00000380079.4	-	3	639	c.538C>A	c.(538-540)Caa>Aaa	p.Q180K	AC003991.3_ENST00000595121.1_RNA|STEAP4_ENST00000301959.5_Intron|AC003991.3_ENST00000447758.1_RNA|AC003991.3_ENST00000600908.1_RNA|STEAP4_ENST00000414498.1_Missense_Mutation_p.Q180K|AC003991.3_ENST00000434733.1_RNA	NM_001205315.1|NM_024636.3	NP_001192244.1|NP_078912.2	Q687X5	STEA4_HUMAN	STEAP family member 4	180					copper ion import (GO:0015677)|fat cell differentiation (GO:0045444)|ferric iron import into cell (GO:0097461)|iron ion homeostasis (GO:0055072)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cupric reductase activity (GO:0008823)|ferric-chelate reductase (NADPH) activity (GO:0052851)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(3)	15	Esophageal squamous(14;0.00802)					AGTGATCCTTGATCCATTGGA	0.418																																					p.Q180K		Atlas-SNP	.											.	STEAP4	54	.	0			c.C538A						PASS	.						82	77	79					7																	87912402		1901	4131	6032	SO:0001583	missense	79689	exon4			ATCCTTGATCCAT	AK026806	CCDS43611.1, CCDS56494.1	7q21.13	2014-01-28	2005-06-15	2005-06-15	ENSG00000127954	ENSG00000127954			21923	protein-coding gene	gene with protein product		611098	"tumor necrosis factor, alpha-induced protein 9"	TNFAIP9		11443137, 15897894	Standard	NM_024636		Approved	FLJ23153, TIARP, STAMP2	uc003ujs.3	Q687X5	OTTHUMG00000153853	ENST00000380079.4:c.538C>A	chr7.hg19:g.87912402G>T	ENSP00000369419:p.Gln180Lys	78.0	0.0	.		101.0	57.0	.	NM_001205315	Q658Q9|Q687X4|Q8WWB0|Q9H5R1	Missense_Mutation	SNP	ENST00000380079.4	hg19	CCDS43611.1	.	.	.	.	.	.	.	.	.	.	G	0.091	-1.167648	0.01660	.	.	ENSG00000127954	ENST00000380079;ENST00000414498	T;T	0.16597	2.33;2.33	5.98	3.12	0.35913	NAD(P)-binding domain (1);	0.395807	0.33691	N	0.004657	T	0.10078	0.0247	N	0.16862	0.45	0.29002	N	0.887404	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.19095	-1.0316	10	0.27785	T	0.31	-1.2064	10.4832	0.44706	0.0633:0.0:0.358:0.5787	.	180;180	C9JS50;Q687X5	.;STEA4_HUMAN	K	180	ENSP00000369419:Q180K;ENSP00000394399:Q180K	ENSP00000369419:Q180K	Q	-	1	0	STEAP4	87750338	1.000000	0.71417	0.998000	0.56505	0.557000	0.35523	1.336000	0.33850	0.375000	0.24679	0.591000	0.81541	CAA	.	.	.	none		0.418	STEAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332712.4	NM_024636		T	87912402	G	T	87912402	3	4	274	1	0	0	0	0	1	0	0	0	15292	1299	45	4	853	4	STEAP4	7	87912402	Missense_Mutation	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10	43643407	87912402	71226261	36	17354											
LAMB1	3912	hgsc.bcm.edu	37	chr7	107577548	107577548	+	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	aaatgctcaccccgaatatcTgagtttttgataaattccag	13	13	6	9	1	2	2	1	2	1	0	3	3	3	2	3	0	1	2	3	0	5	5			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr7:107577548T>A	ENST00000222399.6	-	26	4166	c.3936A>T	c.(3934-3936)tcA>tcT	p.S1312S	LAMB1_ENST00000474380.1_5'UTR|LAMB1_ENST00000393561.1_Silent_p.S1336S	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	1312	Domain II.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						CCCGAATATCTGAGTTTTTGA	0.383																																					p.S1312S		Atlas-SNP	.											.	LAMB1	185	.	0			c.A3936T						PASS	.						163	143	150					7																	107577548		2203	4300	6503	SO:0001819	synonymous_variant	3912	exon26			AATATCTGAGTTT	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.3936A>T	chr7.hg19:g.107577548T>A		78.0	0.0	.		101.0	50.0	.	NM_002291	Q14D91	Silent	SNP	ENST00000222399.6	hg19	CCDS5750.1																																																																																			.	.	.	none		0.383	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291		A	107577548	T	A	107577548	2	1	274	1	0	0	0	0	0	0	0	1	8617	1567	55	5		5	LAMB1	7	107577548	Silent	SNP	T	TCGA-Y8-A894-01A-11D-A35Z-10	19665146	107577548	51561115	37	17355											
ZNF395	55893	hgsc.bcm.edu	37	chr8	28209284	28209284	+	Missense_Mutation	SNP	A	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	ctgcacctctgtgtagtagaAatcctcctcccgcttgaact	8	12	7	14	1	1	2	0	1	1	1	4	2	4	2	4	0	2	4	4	0	4	3			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr8:28209284A>C	ENST00000344423.5	-	7	1092	c.961T>G	c.(961-963)Ttc>Gtc	p.F321V	ZNF395_ENST00000523095.1_Missense_Mutation_p.F321V|ZNF395_ENST00000523202.1_Missense_Mutation_p.F321V	NM_018660.2	NP_061130.1	Q9H8N7	ZN395_HUMAN	zinc finger protein 395	321					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(5)|large_intestine(6)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.102)|Kidney(114;0.123)|Colorectal(74;0.142)		GTGTAGTAGAAATCCTCCTCC	0.617																																					p.F321V		Atlas-SNP	.											.	ZNF395	54	.	0			c.T961G						PASS	.						102	108	106					8																	28209284		2203	4300	6503	SO:0001583	missense	55893	exon7			AGTAGAAATCCTC	AB044750	CCDS6067.1	8p21	2008-05-02			ENSG00000186918	ENSG00000186918		"Zinc fingers, C2H2-type"	18737	protein-coding gene	gene with protein product		609494				14625278	Standard	NM_018660		Approved	PRF-1, HDBP2, PBF, DKFZp434K1210	uc003xgr.3	Q9H8N7	OTTHUMG00000102137	ENST00000344423.5:c.961T>G	chr8.hg19:g.28209284A>C	ENSP00000340494:p.Phe321Val	7.0	0.0	.		14.0	7.0	.	NM_018660	B3KUY7|D3DST4|Q6F6H2|Q9BY72|Q9NPB2|Q9NS57|Q9NS58|Q9NS59	Missense_Mutation	SNP	ENST00000344423.5	hg19	CCDS6067.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.695035	0.88830	.	.	ENSG00000186918	ENST00000344423;ENST00000523202;ENST00000523095	T;T;T	0.60040	0.22;0.22;0.22	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.76622	0.4013	M	0.83384	2.64	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.80560	-0.1328	10	0.87932	D	0	-20.2258	12.6693	0.56858	1.0:0.0:0.0:0.0	.	321	Q9H8N7	ZN395_HUMAN	V	321	ENSP00000340494:F321V;ENSP00000429640:F321V;ENSP00000428452:F321V	ENSP00000340494:F321V	F	-	1	0	ZNF395	28265203	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.081000	0.94049	1.895000	0.54865	0.459000	0.35465	TTC	.	.	.	none		0.617	ZNF395-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219976.1			C	28209284	A	C	28209284	3	2	274	1	0	0	0	0	1	0	0	0	17893	14	1	5	596	5	ZNF395	8	28209284	Missense_Mutation	SNP	A	TCGA-Y8-A894-01A-11D-A35Z-10		28209284	118154738	38	17356											
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110477416	110477416	+	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	tattctcacacaccgaacaaGgctggctttcgctgggaaca	11	9	9	12	2	1	0	1	0	1	0	3	2	1	1	1	3	2	3	1	3	4	3			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr8:110477416G>T	ENST00000378402.5	+	49	8459	c.8355G>T	c.(8353-8355)aaG>aaT	p.K2785N		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	2785					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)			CACCGAACAAGGCTGGCTTTC	0.403										HNSCC(38;0.096)																											p.K2785N		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.G8355T						PASS	.						85	88	87					8																	110477416		1953	4133	6086	SO:0001583	missense	93035	exon49			GAACAAGGCTGGC	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.8355G>T	chr8.hg19:g.110477416G>T	ENSP00000367655:p.Lys2785Asn	125.0	0.0	.		185.0	83.0	.	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	hg19	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.693236	0.30052	.	.	ENSG00000205038	ENST00000378402	D	0.87650	-2.28	5.82	3.62	0.41486	.	0.000000	0.85682	D	0.000000	D	0.87485	0.6189	M	0.80422	2.495	0.32991	D	0.524954	B	0.25667	0.131	B	0.33690	0.168	D	0.88712	0.3223	10	0.48119	T	0.1	.	10.1947	0.43047	0.2039:0.0:0.7961:0.0	.	2785	Q86WI1	PKHL1_HUMAN	N	2785	ENSP00000367655:K2785N	ENSP00000367655:K2785N	K	+	3	2	PKHD1L1	110546592	1.000000	0.71417	1.000000	0.80357	0.140000	0.21249	2.278000	0.43426	1.382000	0.46385	0.557000	0.71058	AAG	.	.	.	none		0.403	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		T	110477416	G	T	110477416	3	4	274	1	0	0	0	0	1	0	0	0	11979	991	35	4	8549	4	PKHD1L1	8	110477416	Missense_Mutation	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10	82268132	110477416	35886606	39	17357											
FAM91A1	157769	hgsc.bcm.edu	37	chr8	124786386	124786386	+	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	acagtatccgcaatcagttaCgatatagaaataacttaggt	16	11	7	7	2	1	1	1	0	0	1	2	2	2	1	1	1	2	3	1	1	8	6			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr8:124786386C>T	ENST00000334705.7	+	2	385	c.139C>T	c.(139-141)Cga>Tga	p.R47*	FAM91A1_ENST00000521166.1_Nonsense_Mutation_p.R47*	NM_144963.2	NP_659400	Q658Y4	F91A1_HUMAN	family with sequence similarity 91, member A1	47										breast(4)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28	Lung NSC(37;8.76e-13)|Ovarian(258;0.00744)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00192)			CAATCAGTTACGATATAGAAA	0.333																																					p.R47X		Atlas-SNP	.											.	FAM91A1	77	.	0			c.C139T						PASS	.						146	151	149					8																	124786386		1842	4096	5938	SO:0001587	stop_gained	157769	exon2			CAGTTACGATATA	AK074370	CCDS6346.2	8q24.13	2005-10-04			ENSG00000176853	ENSG00000176853			26306	protein-coding gene	gene with protein product						12477932	Standard	XM_005250806		Approved	FLJ23790	uc003yqv.3	Q658Y4	OTTHUMG00000133021	ENST00000334705.7:c.139C>T	chr8.hg19:g.124786386C>T	ENSP00000335082:p.Arg47*	91.0	0.0	.		134.0	46.0	.	NM_144963	B6YY23|Q658T5|Q8TE89	Nonsense_Mutation	SNP	ENST00000334705.7	hg19	CCDS6346.2	.	.	.	.	.	.	.	.	.	.	C	28.1	4.890996	0.91889	.	.	ENSG00000176853	ENST00000521166;ENST00000334705;ENST00000395537	.	.	.	5.73	5.73	0.89815	.	0.000000	0.64402	U	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.7109	0.69232	0.1448:0.8551:0.0:0.0	.	.	.	.	X	47	.	ENSP00000335082:R47X	R	+	1	2	FAM91A1	124855567	1.000000	0.71417	1.000000	0.80357	0.385000	0.30292	4.279000	0.58953	2.706000	0.92434	0.655000	0.94253	CGA	.	.	.	none		0.333	FAM91A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256607.1	NM_144963		T	124786386	C	T	124786386	4	4	274	1	0	0	0	0	0	1	0	0	5658	528	19	1	145	1	FAM91A1	8	124786386	Nonsense_Mutation	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10	14308970	124786386	21577636	40	17358											
FAM122A	116224	hgsc.bcm.edu	37	chr9	71395705	71395705	+	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	tgaaaagaaaatgtgaaatgGaaactgaatatcagccaaag	21	7	9	4	0	1	4	1	3	0	1	1	5	1	5	1	1	2	0	1	1	9	1			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr9:71395705G>A	ENST00000394264.3	+	1	742	c.625G>A	c.(625-627)Gaa>Aaa	p.E209K	PIP5K1B_ENST00000265382.3_Intron|PIP5K1B_ENST00000541509.1_Intron	NM_138333.3	NP_612206.3	Q96E09	F122A_HUMAN	family with sequence similarity 122A	209										endometrium(1)|lung(2)	3						ATGTGAAATGGAAACTGAATA	0.468																																					p.E209K		Atlas-SNP	.											.	FAM122A	14	.	0			c.G625A						PASS	.						98	97	97					9																	71395705		2203	4300	6503	SO:0001583	missense	116224	exon1			GAAATGGAAACTG	AK126379	CCDS6623.1	9q21.13	2011-02-10	2006-07-11	2006-07-11	ENSG00000187866	ENSG00000187866			23490	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 42"	C9orf42		12477932	Standard	NM_138333		Approved	MGC17347	uc004agw.1	Q96E09	OTTHUMG00000019971	ENST00000394264.3:c.625G>A	chr9.hg19:g.71395705G>A	ENSP00000377807:p.Glu209Lys	85.0	0.0	.		127.0	59.0	.	NM_138333		Missense_Mutation	SNP	ENST00000394264.3	hg19	CCDS6623.1	.	.	.	.	.	.	.	.	.	.	G	19.45	3.829420	0.71258	.	.	ENSG00000187866	ENST00000394264;ENST00000377279	T	0.55234	0.53	4.42	4.42	0.53409	.	0.000000	0.85682	D	0.000000	T	0.67316	0.2880	M	0.64404	1.975	0.40534	D	0.980958	D	0.67145	0.996	D	0.73708	0.981	T	0.69247	-0.5195	10	0.59425	D	0.04	-51.6435	12.8382	0.57786	0.0:0.0:1.0:0.0	.	209	Q96E09	F122A_HUMAN	K	209;193	ENSP00000377807:E209K	ENSP00000366492:E193K	E	+	1	0	FAM122A	70585525	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	7.304000	0.78882	2.758000	0.94735	0.563000	0.77884	GAA	.	.	.	none		0.468	FAM122A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052556.1	NM_138333		A	71395705	G	A	71395705	3	1	274	1	0	0	0	0	1	0	0	0	5423	1175	41	2	627	2	FAM122A	9	71395705	Missense_Mutation	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10		71395705	69817726	41	17359											
KIF27	55582	hgsc.bcm.edu	37	chr9	86495384	86495384	+	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	acagtgatgccagtttcttaCtatcttgttgcttcttctgc	6	18	7	10	0	4	1	0	1	4	0	4	1	4	1	1	0	4	3	1	0	2	7			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr9:86495384C>A	ENST00000297814.2	-	11	2614	c.2471G>T	c.(2470-2472)aGt>aTt	p.S824I	KIF27_ENST00000376347.1_Missense_Mutation_p.S215I|KIF27_ENST00000413982.1_Intron|KIF27_ENST00000334204.2_Missense_Mutation_p.S824I	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	824					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						CAGTTTCTTACTATCTTGTTG	0.343																																					p.S824I		Atlas-SNP	.											.	KIF27	103	.	0			c.G2471T						PASS	.						179	161	167					9																	86495384		2203	4300	6503	SO:0001583	missense	55582	exon11			TTCTTACTATCTT	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.2471G>T	chr9.hg19:g.86495384C>A	ENSP00000297814:p.Ser824Ile	27.0	0.0	.		26.0	13.0	.	NM_017576	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Missense_Mutation	SNP	ENST00000297814.2	hg19	CCDS6665.1	.	.	.	.	.	.	.	.	.	.	C	15.49	2.849807	0.51270	.	.	ENSG00000165115	ENST00000297814;ENST00000334204;ENST00000376347	T;T;T	0.31247	1.5;1.5;1.5	4.92	1.56	0.23342	.	0.214282	0.30320	N	0.009884	T	0.24547	0.0595	L	0.54323	1.7	0.32967	D	0.5218	P;P	0.42620	0.785;0.679	B;B	0.39258	0.295;0.231	T	0.34204	-0.9838	10	0.23891	T	0.37	.	9.2369	0.37473	0.0:0.3622:0.5428:0.095	.	824;824	Q86VH2-3;Q86VH2	.;KIF27_HUMAN	I	824;824;215	ENSP00000297814:S824I;ENSP00000333928:S824I;ENSP00000365525:S215I	ENSP00000297814:S824I	S	-	2	0	KIF27	85685204	1.000000	0.71417	0.996000	0.52242	0.992000	0.81027	4.424000	0.59868	0.561000	0.29186	0.484000	0.47621	AGT	.	.	.	none		0.343	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576		A	86495384	C	A	86495384	3	1	274	1	0	0	0	0	1	0	0	0	8303	565	20	4	1766	4	KIF27	9	86495384	Missense_Mutation	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10	15099679	86495384	54718047	42	17360											
LHX6	26468	hgsc.bcm.edu	37	chr9	124979514	124979514	+	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	tgccgcgagctctccgcaccCagtcgctggcgtagatctgt	5	9	12	15	5	2	1	0	0	2	1	4	2	2	1	3	1	2	4	3	1	1	1			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr9:124979514C>A	ENST00000373755.2	-	4	536	c.428G>T	c.(427-429)tGg>tTg	p.W143L	LHX6_ENST00000340587.3_Missense_Mutation_p.W172L|LHX6_ENST00000559895.1_5'UTR|LHX6_ENST00000373754.2_Missense_Mutation_p.W143L|LHX6_ENST00000394319.4_Missense_Mutation_p.W172L|LHX6_ENST00000541397.2_Missense_Mutation_p.W161L	NM_001242334.1	NP_001229263.1	Q9UPM6	LHX6_HUMAN	LIM homeobox 6	143	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.|Required for interaction with LDB1. {ECO:0000250}.				cell maturation (GO:0048469)|cerebral cortex GABAergic interneuron migration (GO:0021853)|cerebral cortex radially oriented cell migration (GO:0021799)|cerebral cortex tangential migration (GO:0021800)|forebrain neuron fate commitment (GO:0021877)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(5)	8						TCTCCGCACCCAGTCGCTGGC	0.667																																					p.W172L		Atlas-SNP	.											.	LHX6	73	.	0			c.G515T						PASS	.						48	48	48					9																	124979514		2203	4300	6503	SO:0001583	missense	26468	exon5			CGCACCCAGTCGC	AB031041	CCDS6837.2, CCDS6838.2, CCDS56583.1, CCDS56584.1, CCDS59144.1	9q33.2	2011-06-20			ENSG00000106852	ENSG00000106852		"Homeoboxes / LIM class"	21735	protein-coding gene	gene with protein product		608215				10393337	Standard	NM_014368		Approved	LHX6.1	uc004blx.4	Q9UPM6	OTTHUMG00000020601	ENST00000373755.2:c.428G>T	chr9.hg19:g.124979514C>A	ENSP00000362860:p.Trp143Leu	64.0	0.0	.		143.0	91.0	.	NM_014368	A6PVQ1|A6PVQ2|A8K1B2|B7Z4D0|H0YN76|Q5T7S7|Q5T7S8|Q9NTK3|Q9UPM5	Missense_Mutation	SNP	ENST00000373755.2	hg19	CCDS56583.1	.	.	.	.	.	.	.	.	.	.	C	35	5.590064	0.96590	.	.	ENSG00000106852	ENST00000373755;ENST00000373754;ENST00000394319;ENST00000340587;ENST00000541397	D;D;D;D;D	0.85629	-2.01;-2.01;-2.01;-2.01;-2.01	5.87	5.87	0.94306	Zinc finger, LIM-type (5);	0.000000	0.85682	D	0.000000	D	0.85427	0.5694	N	0.11789	0.175	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	0.82366	-0.0493	10	0.17369	T	0.5	.	19.1961	0.93690	0.0:1.0:0.0:0.0	.	143;172;172	Q9UPM6;Q9UPM6-4;Q9UPM6-3	LHX6_HUMAN;.;.	L	143;143;172;172;161	ENSP00000362860:W143L;ENSP00000362859:W143L;ENSP00000377854:W172L;ENSP00000340137:W172L;ENSP00000441464:W161L	ENSP00000340137:W172L	W	-	2	0	LHX6	124019335	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.920000	0.70017	2.781000	0.95711	0.655000	0.94253	TGG	.	.	.	none		0.667	LHX6-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053924.2	NM_014368		A	124979514	C	A	124979514	3	1	274	1	0	0	0	0	1	0	0	0	8782	595	21	4	746	4	LHX6	9	124979514	Missense_Mutation	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10	38484130	124979514	16233917	43	17361											
MAPKAP1	79109	hgsc.bcm.edu	37	chr9	128230280	128230280	+	Missense_Mutation	SNP	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	tctcttcagcaaggtcacagGcacagagcaggtcggaatcg	11	7	12	11	2	3	1	2	0	1	1	6	2	3	2	0	4	2	3	0	4	2	1			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr9:128230280G>A	ENST00000373498.1	-	9	1384	c.1316C>T	c.(1315-1317)gCc>gTc	p.A439V	MAPKAP1_ENST00000265960.3_Missense_Mutation_p.A439V|MAPKAP1_ENST00000350766.3_Missense_Mutation_p.A403V|MAPKAP1_ENST00000373511.2_Missense_Mutation_p.A392V|MAPKAP1_ENST00000483937.1_5'UTR|MAPKAP1_ENST00000373503.3_Missense_Mutation_p.A247V|MAPKAP1_ENST00000394063.1_Missense_Mutation_p.A247V|MAPKAP1_ENST00000373497.5_Missense_Mutation_p.A152V			Q9BPZ7	SIN1_HUMAN	mitogen-activated protein kinase associated protein 1	439					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						AAGGTCACAGGCACAGAGCAG	0.468																																					p.A439V		Atlas-SNP	.											.	MAPKAP1	68	.	0			c.C1316T						PASS	.						175	170	172					9																	128230280		2203	4300	6503	SO:0001583	missense	79109	exon10			TCACAGGCACAGA	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.1316C>T	chr9.hg19:g.128230280G>A	ENSP00000362597:p.Ala439Val	82.0	0.0	.		227.0	66.0	.	NM_001006617	A8K1Z5|B1AMA4|B7Z309|Q00426|Q5JSV5|Q5JSV6|Q5JSV9|Q658R0|Q699U1|Q699U2|Q699U3|Q699U4|Q6GVJ0|Q6GVJ1|Q6GVJ2	Missense_Mutation	SNP	ENST00000373498.1	hg19	CCDS35140.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.959084	0.74016	.	.	ENSG00000119487	ENST00000373511;ENST00000350766;ENST00000373503;ENST00000373498;ENST00000265960;ENST00000394063;ENST00000373497;ENST00000420643	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.67239	0.2872	M	0.69823	2.125	0.80722	D	1	P;P;P;P	0.40534	0.72;0.702;0.649;0.629	B;B;B;B	0.42959	0.335;0.342;0.254;0.403	T	0.61802	-0.6988	9	0.17369	T	0.5	-9.146	20.6593	0.99626	0.0:0.0:1.0:0.0	.	152;392;403;439	B7Z5E5;Q9BPZ7-3;Q9BPZ7-2;Q9BPZ7	.;.;.;SIN1_HUMAN	V	392;403;247;439;439;247;152;211	.	ENSP00000265960:A439V	A	-	2	0	MAPKAP1	127270101	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.885000	0.99019	0.655000	0.94253	GCC	.	.	.	none		0.468	MAPKAP1-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054092.1			A	128230280	G	A	128230280	3	1	274	1	0	0	0	0	1	0	0	0	9295	1203	42	2	264	2	MAPKAP1	9	128230280	Missense_Mutation	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10	3250766	128230280	12983151	44	17362											
URM1	81605	hgsc.bcm.edu	37	chr9	131151666	131151667	+	Frame_Shift_Del	DEL	GG	GG	-																															aagcgttgggcctctcctcaGgcacatatagagtggctggg																										TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr9:131151666_131151667delGG	ENST00000452446.1	+	4	377_378	c.315_316delGG	c.(313-318)caggcafs	p.QA105fs	RP11-339B21.11_ENST00000609303.1_lincRNA|URM1_ENST00000483206.1_3'UTR|URM1_ENST00000372853.4_Intron|URM1_ENST00000372850.1_3'UTR	NM_001135947.2	NP_001129419.1			ubiquitin related modifier 1											cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)	5						CCTCTCCTCAGGCACATATAGA	0.629																																					p.105_105del		Atlas-Indel,Pindel	.											.	URM1	19	.	0			c.314_315del						PASS	.																																			SO:0001589	frameshift_variant	81605	exon4			.	AK097029	CCDS6900.1, CCDS48035.1, CCDS59148.1	9q34.13	2010-06-24	2010-06-24	2006-11-28	ENSG00000167118	ENSG00000167118			28378	protein-coding gene	gene with protein product		612693	"chromosome 9 open reading frame 74", "ubiquitin related modifier 1 homolog (S. cerevisiae)"	C9orf74		16046629, 16864801	Standard	NM_030914		Approved	MGC2668	uc011may.2	Q9BTM9	OTTHUMG00000020742	ENST00000452446.1:c.315_316delGG	chr9.hg19:g.131151666_131151667delGG	ENSP00000412922:p.Gln105fs	62.0	0.0	0		169.0	41.0	0.242604	NM_001135947		Frame_Shift_Del	DEL	ENST00000452446.1	hg19	CCDS48035.1																																																																																			.	.	.	none		0.629	URM1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_030914		-	131151667	GG	-	131151666	7	5	274	1	0	1	0	1	0	0	0	0	17039	991	35	0	329	0	URM1	9	131151666	Frame_Shift_Del	DEL	GG	TCGA-Y8-A894-01A-11D-A35Z-10	2921386	131151666	10061765	45	17363											
PITRM1	10531	hgsc.bcm.edu	37	chr10	3208566	3208567	+	Missense_Mutation	DNP	CT	CT	TG																															tccatgggagtagtacggaaCtgcacgctagggaaggagaa																								rs28416720|rs33996077|rs4266975|rs148472807|rs114690446	byFrequency	TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr10:3208566_3208567CT>TG	ENST00000224949.4	-	4	306_307	c.272_273AG>CA	c.(271-273)cAG>cCA	p.Q91P	PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000451104.2_Missense_Mutation_p.Q59P|PITRM1-AS1_ENST00000601046.1_RNA|PITRM1_ENST00000380989.2_Missense_Mutation_p.Q91P			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	91					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						TAGTACGGAACTGCACGCTAGG	0.49																																					p.Q91Q|p.Q91P		Atlas-SNP	.											PITRM1,colon,carcinoma,-1,3|PITRM1,colon,carcinoma,0,3	PITRM1	109	.	0			c.G273A|c.A272C						PASS	.																																			SO:0001583	missense	10531	exon4			ACGGAACTGCACG|CGGAACTGCACGC	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"PreP peptidasome"		"pitrilysin metalloproteinase 1"			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.272_273delinsTG	chr10.hg19:g.3208566_3208567delinsTG	ENSP00000224949:p.Gln91Pro	48.0|47.0	0.0	.		58.0|57.0	6.0	.	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Silent|Missense_Mutation	SNP	ENST00000224949.4	hg19	CCDS59208.1																																																																																			.	.	.	weak		0.49	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2			TG	3208567	CT	TG	3208566	3	4	274	1	0	0	0	0	1	0	0	0	11960	564	20	2	2936	2	PITRM1	10	3208566	Missense_Mutation	DNP	CT	TCGA-Y8-A894-01A-11D-A35Z-10		3208566	132326181	46	17364											
HSPA14	51182	hgsc.bcm.edu	37	chr10	14909284	14909284	+	Frame_Shift_Del	DEL	T	T	-																															agagtgttcagccagagataTtttagttaaggtatgtttag																										TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr10:14909284delT	ENST00000378372.3	+	11	1435	c.1196delT	c.(1195-1197)attfs	p.I399fs		NM_016299.2	NP_057383.2	Q0VDF9	HSP7E_HUMAN	heat shock 70kDa protein 14	399					'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						GCCAGAGATATTTTAGTTAAG	0.318																																					p.I399fs		Atlas-Indel,Pindel	.											.	HSPA14	42	.	0			c.1195delA						PASS	.						80	82	81					10																	14909284		2203	4300	6503	SO:0001589	frameshift_variant	51182	exon11			.	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.1196delT	chr10.hg19:g.14909284delT	ENSP00000367623:p.Ile399fs	74.0	0.0	0		127.0	66.0	0.519685	NM_016299	A8K8F8|B0YIY9|Q9P0X2|Q9UI07	Frame_Shift_Del	DEL	ENST00000378372.3	hg19	CCDS7103.1																																																																																			.	.	.	none		0.318	HSPA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046910.1	NM_016299		-	14909284	T	-	14909284	7	5	274	1	0	1	0	1	0	0	0	0	7414	1493	52	0	1238	0	HSPA14	10	14909284	Frame_Shift_Del	DEL	T	TCGA-Y8-A894-01A-11D-A35Z-10	11700718	14909284	120625463	47	17365											
ANK3	288	hgsc.bcm.edu	37	chr10	61868591	61868591	+	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	ttgacaaaacaacttaccctAaaaattgtgcccctgcagga	15	9	6	11	0	0	1	0	1	0	0	0	2	0	2	3	1	5	1	3	1	7	4			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr10:61868591A>T	ENST00000280772.2	-	27	3361	c.3170T>A	c.(3169-3171)tTa>tAa	p.L1057*	ANK3_ENST00000355288.2_Nonsense_Mutation_p.L191*|ANK3_ENST00000503366.1_Nonsense_Mutation_p.L1058*|ANK3_ENST00000373827.2_Nonsense_Mutation_p.L1051*	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	1057	ZU5 1. {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						AACTTACCCTAAAAATTGTGC	0.433																																					p.L1058X		Atlas-SNP	.											.	ANK3	703	.	0			c.T3173A						PASS	.						55	59	58					10																	61868591		2203	4300	6503	SO:0001587	stop_gained	288	exon28			TACCCTAAAAATT	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.3170T>A	chr10.hg19:g.61868591A>T	ENSP00000280772:p.Leu1057*	101.0	0.0	.		145.0	66.0	.	NM_001204404	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Nonsense_Mutation	SNP	ENST00000280772.2	hg19	CCDS7258.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	42|42	9.181035|9.181035	0.99092|0.99092	.|.	.|.	ENSG00000151150|ENSG00000151150	ENST00000280772;ENST00000373827;ENST00000355288;ENST00000423532;ENST00000503366;ENST00000395299;ENST00000373817;ENST00000395293;ENST00000395304;ENST00000544789;ENST00000536348;ENST00000373815|ENST00000467420	.|.	.|.	.|.	6.04|6.04	6.04|6.04	0.98038|0.98038	.|.	0.000000|.	0.33401|.	N|.	0.004958|.	.|.	.|.	.|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.02654|.	T|.	1|.	.|.	16.5885|16.5885	0.84745|0.84745	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|.	.|.	.|.	X|K	1057;1051;191;191;1058;1037;292;692;692;190;590;182|82	.|.	ENSP00000280772:L1057X|.	L|X	-|-	2|1	0|0	ANK3|ANK3	61538597|61538597	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	9.339000|9.339000	0.96797|0.96797	2.317000|2.317000	0.78254|0.78254	0.460000|0.460000	0.39030|0.39030	TTA|TAG	.	.	.	none		0.433	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		T	61868591	A	T	61868591	4	4	274	1	0	0	0	0	0	1	0	0	622	372	13	5	10344	5	ANK3	10	61868591	Nonsense_Mutation	SNP	A	TCGA-Y8-A894-01A-11D-A35Z-10	46959307	61868591	73666156	48	17366											
VCL	7414	hgsc.bcm.edu	37	chr10	75877813	75877813	+	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	ctggttcacaatgcccagaaCctcatgcagtctgtgaagga	11	9	10	11	0	3	2	2	1	1	1	3	3	3	3	2	2	3	2	2	2	3	1			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr10:75877813C>G	ENST00000211998.4	+	22	3385	c.3291C>G	c.(3289-3291)aaC>aaG	p.N1097K	RP11-178G16.4_ENST00000598318.1_lincRNA|VCL_ENST00000417648.2_Missense_Mutation_p.N290K|VCL_ENST00000372755.3_Missense_Mutation_p.N1029K|RP11-178G16.5_ENST00000599110.1_lincRNA	NM_014000.2	NP_054706.1	P18206	VINC_HUMAN	vinculin	1097	C-terminal tail.				adherens junction assembly (GO:0034333)|apical junction assembly (GO:0043297)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|epithelial cell-cell adhesion (GO:0090136)|lamellipodium assembly (GO:0030032)|morphogenesis of an epithelium (GO:0002009)|muscle contraction (GO:0006936)|negative regulation of cell migration (GO:0030336)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|protein localization to cell surface (GO:0034394)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cell-substrate junction (GO:0030055)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	actin binding (GO:0003779)|alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)		VCL/ALK(4)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	20	Prostate(51;0.0112)					ATGCCCAGAACCTCATGCAGT	0.493																																					p.N1097K		Atlas-SNP	.											.	VCL	77	.	0			c.C3291G						PASS	.						160	144	149					10																	75877813		2203	4300	6503	SO:0001583	missense	7414	exon22			CCAGAACCTCATG	M33308	CCDS7340.1, CCDS7341.1	10q22.1-q23	2014-09-17			ENSG00000035403	ENSG00000035403			12665	protein-coding gene	gene with protein product	"metavinculin"	193065				1339348	Standard	NM_014000		Approved		uc001jwd.3	P18206	OTTHUMG00000018498	ENST00000211998.4:c.3291C>G	chr10.hg19:g.75877813C>G	ENSP00000211998:p.Asn1097Lys	68.0	0.0	.		104.0	51.0	.	NM_014000	Q16450|Q5SWX2|Q7Z3B8|Q8IXU7	Missense_Mutation	SNP	ENST00000211998.4	hg19	CCDS7341.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.228247	0.79576	.	.	ENSG00000035403	ENST00000372755;ENST00000211998;ENST00000417648;ENST00000537043;ENST00000436396	T;T;T;T	0.61980	0.06;0.06;0.06;0.06	5.5	4.6	0.57074	.	0.043322	0.85682	D	0.000000	T	0.77458	0.4133	M	0.75777	2.31	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;0.999;0.999	D;D;D;D	0.85130	0.997;0.978;0.977;0.945	T	0.79971	-0.1578	10	0.87932	D	0	.	12.3333	0.55051	0.0:0.8596:0.0:0.1404	.	290;956;1029;1097	B4DTM7;F5H7T3;P18206-2;P18206	.;.;.;VINC_HUMAN	K	1029;1097;290;956;769	ENSP00000361841:N1029K;ENSP00000211998:N1097K;ENSP00000411887:N290K;ENSP00000415489:N769K	ENSP00000211998:N1097K	N	+	3	2	VCL	75547819	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.553000	0.36255	1.325000	0.45301	0.655000	0.94253	AAC	.	.	.	none		0.493	VCL-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003373, NM_014000		G	75877813	C	G	75877813	3	3	274	1	0	0	0	0	1	0	0	0	17151	506	18	4	3377	4	VCL	10	75877813	Missense_Mutation	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10	14009222	75877813	59656934	49	17367											
RRP12	23223	hgsc.bcm.edu	37	chr10	99120318	99120318	+	Missense_Mutation	SNP	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	ctcaccttggtactgaggggGtatctccagctcctcctcct	5	12	9	15	0	2	1	1	1	1	0	6	1	5	1	5	3	2	3	5	3	2	3	rs370146748		TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr10:99120318G>A	ENST00000370992.4	-	31	3736	c.3625C>T	c.(3625-3627)Ccc>Tcc	p.P1209S	RRP12_ENST00000479481.1_5'UTR|RRP12_ENST00000536831.1_Missense_Mutation_p.P927S|RRP12_ENST00000414986.1_Missense_Mutation_p.P1148S|RRP12_ENST00000315563.6_Missense_Mutation_p.P1109S	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	1209						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)		TACTGAGGGGGTATCTCCAGC	0.557																																					p.P1209S		Atlas-SNP	.											.	RRP12	97	.	0			c.C3625T						PASS	.	G	SER/PRO,SER/PRO	1,4405	2.1+/-5.4	0,1,2202	178	150	160		3442,3625	4.5	0.4	10		160	0,8600		0,0,4300	no	missense,missense	RRP12	NM_001145114.1,NM_015179.3	74,74	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign	1148/1237,1209/1298	99120318	1,13005	2203	4300	6503	SO:0001583	missense	23223	exon31			GAGGGGGTATCTC		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.3625C>T	chr10.hg19:g.99120318G>A	ENSP00000360031:p.Pro1209Ser	36.0	0.0	.		69.0	37.0	.	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Missense_Mutation	SNP	ENST00000370992.4	hg19	CCDS7457.1	.	.	.	.	.	.	.	.	.	.	G	10.48	1.361285	0.24684	2.27E-4	0.0	ENSG00000052749	ENST00000370992;ENST00000315563;ENST00000414986;ENST00000536831	T;T;T;T	0.26957	1.7;1.7;1.7;1.7	5.44	4.52	0.55395	.	0.325404	0.32459	N	0.006067	T	0.13329	0.0323	N	0.25060	0.705	0.09310	N	1	B;B;B;B	0.31769	0.339;0.154;0.332;0.121	B;B;B;B	0.30572	0.055;0.02;0.117;0.021	T	0.23940	-1.0174	10	0.08599	T	0.76	-13.4716	7.0747	0.25197	0.087:0.0:0.7401:0.1729	.	1148;1109;927;1209	E9PCK7;Q5JTH9-2;F5H456;Q5JTH9	.;.;.;RRP12_HUMAN	S	1209;1109;1148;927	ENSP00000360031:P1209S;ENSP00000324315:P1109S;ENSP00000414863:P1148S;ENSP00000446184:P927S	ENSP00000324315:P1109S	P	-	1	0	RRP12	99110308	0.708000	0.27876	0.416000	0.26546	0.833000	0.47200	3.456000	0.53000	1.253000	0.44018	0.462000	0.41574	CCC	.	.	.	none		0.557	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179		A	99120318	G	A	99120318	3	1	274	1	0	0	0	0	1	0	0	0	13699	1261	44	2	284	2	RRP12	10	99120318	Missense_Mutation	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10	23242505	99120318	36414429	50	17368											
RRP12	23223	hgsc.bcm.edu	37	chr10	99126540	99126540	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctcctcctcctcctcctcCtcttcttcctcctccacggc	1	13	4	23	1	2	0	0	0	2	0	11	0	11	0	9	2	0	1	9	2	0	2			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr10:99126540C>T	ENST00000370992.4	-	27	3285	c.3174G>A	c.(3172-3174)gaG>gaA	p.E1058E	RRP12_ENST00000479481.1_5'UTR|RRP12_ENST00000536831.1_Silent_p.E776E|RRP12_ENST00000414986.1_Silent_p.E997E|RRP12_ENST00000315563.6_Silent_p.E958E	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	1058	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)		cctcctcctcctcttcttcct	0.662																																					p.E1058E		Atlas-SNP	.											.	RRP12	97	.	0			c.G3174A						PASS	.						94	108	103					10																	99126540		2203	4300	6503	SO:0001819	synonymous_variant	23223	exon27			CTCCTCCTCTTCT		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.3174G>A	chr10.hg19:g.99126540C>T		32.0	0.0	.		69.0	6.0	.	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	hg19	CCDS7457.1																																																																																			.	.	.	none		0.662	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179		T	99126540	C	T	99126540	2	4	274	1	0	0	0	0	0	0	0	1	13699	680	24	2		2	RRP12	10	99126540	Silent	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10	6222	99126540	36408207	51	17369											
GBF1	8729	hgsc.bcm.edu	37	chr10	104136491	104136491	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgtgatgctgcccacatcAcacctgacaactttgagctc	9	10	8	14	1	1	3	1	3	0	0	2	3	1	3	2	0	5	2	2	0	1	1			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr10:104136491A>G	ENST00000369983.3	+	32	4479	c.4219A>G	c.(4219-4221)Aca>Gca	p.T1407A		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	1407					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		TGCCCACATCACACCTGACAA	0.552																																					p.T1408A		Atlas-SNP	.											.	GBF1	142	.	0			c.A4222G						PASS	.						91	86	88					10																	104136491		2203	4300	6503	SO:0001583	missense	8729	exon32			CACATCACACCTG	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"golgi-specific brefeldin A resistance factor 1"			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.4219A>G	chr10.hg19:g.104136491A>G	ENSP00000359000:p.Thr1407Ala	29.0	0.0	.		48.0	26.0	.	NM_001199378	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	hg19	CCDS7533.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.437435	0.83885	.	.	ENSG00000107862	ENST00000369983	T	0.24350	1.86	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.54447	0.1859	M	0.82193	2.58	0.80722	D	1	D;D;P	0.89917	1.0;0.997;0.901	D;P;P	0.85130	0.997;0.872;0.458	T	0.61686	-0.7012	10	0.72032	D	0.01	-11.5608	14.8604	0.70376	1.0:0.0:0.0:0.0	.	1407;1407;1407	Q149P1;Q149P0;Q92538	.;.;GBF1_HUMAN	A	1407	ENSP00000359000:T1407A	ENSP00000359000:T1407A	T	+	1	0	GBF1	104126481	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.139000	0.94554	2.100000	0.63781	0.379000	0.24179	ACA	.	.	.	none		0.552	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1			G	104136491	A	G	104136491	3	3	274	1	0	0	0	0	1	0	0	0	6278	159	6	3	4341	3	GBF1	10	104136491	Missense_Mutation	SNP	A	TCGA-Y8-A894-01A-11D-A35Z-10	5009951	104136491	31398256	52	17370											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1256589	1256589	+	Frame_Shift_Del	DEL	C	C	-																															cgcatcgtcaccgagaacatCccctgtgggaccaccggcac																										TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr11:1256589delC	ENST00000529681.1	+	23	2884	c.2826delC	c.(2824-2826)atcfs	p.I942fs	MUC5B_ENST00000447027.1_Frame_Shift_Del_p.I945fs	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	942	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)		CCGAGAACATCCCCTGTGGGA	0.647																																					p.I942fs		Atlas-Indel,Pindel	.											.	MUC5B	473	.	0			c.2825delT						PASS	.						53	60	58					11																	1256589		2118	4223	6341	SO:0001589	frameshift_variant	727897	exon23			.	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.2826delC	chr11.hg19:g.1256589delC	ENSP00000436812:p.Ile942fs	105.0	0.0	0		124.0	57.0	0.459677	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Frame_Shift_Del	DEL	ENST00000529681.1	hg19	CCDS44515.2																																																																																			.	.	.	weak		0.647	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		-	1256589	C	-	1256589	7	5	274	1	0	1	0	1	0	0	0	0	9986	845	30	0	2925	0	MUC5B	11	1256589	Frame_Shift_Del	DEL	C	TCGA-Y8-A894-01A-11D-A35Z-10		1256589	133749927	53	17371											
SFRS2IP	9169	hgsc.bcm.edu	37	chr12	46327006	46327006	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgatttcactggcttctatAaattctgtactaaaagataa	14	15	5	7	0	3	2	1	1	2	1	3	2	3	2	0	1	1	2	0	1	7	8			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr12:46327006A>G	ENST00000369367.3	-	9	875	c.642T>C	c.(640-642)ttT>ttC	p.F214F	SCAF11_ENST00000419565.2_Silent_p.F214F|SCAF11_ENST00000549162.1_Silent_p.F22F	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	214					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						TGGCTTCTATAAATTCTGTAC	0.328																																					p.F214F		Atlas-SNP	.											.	SCAF11	145	.	0			c.T642C						PASS	.						78	73	75					12																	46327006		1813	4064	5877	SO:0001819	synonymous_variant	9169	exon9			TTCTATAAATTCT	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.642T>C	chr12.hg19:g.46327006A>G		33.0	0.0	.		67.0	23.0	.	NM_004719	A6NEU9|A6NLW5|Q8IW59	Silent	SNP	ENST00000369367.3	hg19	CCDS8748.2																																																																																			.	.	.	none		0.328	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719		G	46327006	A	G	46327006	2	3	274	1	0	0	0	0	0	0	0	1	14190	359	13	3		3	SFRS2IP	12	46327006	Silent	SNP	A	TCGA-Y8-A894-01A-11D-A35Z-10		46327006	87524889	54	17372											
GRASP	160622	hgsc.bcm.edu	37	chr12	52401044	52401044	+	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	ccgggggcaccctgccccgcCgaaaggtgcgtcccccgccc	4	3	13	21	5	0	0	0	0	0	0	1	1	1	0	8	3	2	1	8	3	1	0			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr12:52401044C>T	ENST00000293662.4	+	1	321	c.241C>T	c.(241-243)Cga>Tga	p.R81*		NM_181711.2	NP_859062.1	Q7Z6J2	GRASP_HUMAN	GRP1 (general receptor for phosphoinositides 1)-associated scaffold protein	81					protein localization (GO:0008104)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				central_nervous_system(1)|large_intestine(1)|lung(1)|skin(2)	5				BRCA - Breast invasive adenocarcinoma(357;0.0967)		CCTGCCCCGCCGAAAGGTGCG	0.731																																					p.R81X		Atlas-SNP	.											.	GRASP	23	.	0			c.C241T						PASS	.						9	10	10					12																	52401044		1849	3898	5747	SO:0001587	stop_gained	160622	exon1			CCCCGCCGAAAGG	AC019244	CCDS8817.1, CCDS61124.1	12q13.13	2011-09-02			ENSG00000161835	ENSG00000161835			18707	protein-coding gene	gene with protein product		612027				10828067	Standard	NM_001271856		Approved		uc001rzo.2	Q7Z6J2	OTTHUMG00000169595	ENST00000293662.4:c.241C>T	chr12.hg19:g.52401044C>T	ENSP00000293662:p.Arg81*	38.0	0.0	.		71.0	35.0	.	NM_181711	Q6PIF8|Q7Z741	Nonsense_Mutation	SNP	ENST00000293662.4	hg19	CCDS8817.1	.	.	.	.	.	.	.	.	.	.	C	33	5.198082	0.94997	.	.	ENSG00000161835	ENST00000293662	.	.	.	4.74	3.78	0.43462	.	0.563109	0.17616	N	0.167905	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	-0.1895	10.1004	0.42502	0.0:0.7959:0.2041:0.0	.	.	.	.	X	81	.	ENSP00000293662:R81X	R	+	1	2	GRASP	50687311	1.000000	0.71417	1.000000	0.80357	0.333000	0.28666	1.223000	0.32527	2.194000	0.70268	0.549000	0.68633	CGA	.	.	.	none		0.731	GRASP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404972.1			T	52401044	C	T	52401044	4	4	274	1	0	0	0	0	0	1	0	0	6762	644	23	1	243	1	GRASP	12	52401044	Nonsense_Mutation	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10	6074038	52401044	81450851	55	17373											
ANKS1B	56899	hgsc.bcm.edu	37	chr12	99478796	99478796	+	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	tcctgatcttccataacattGcttccctgaaacaaaacaga	14	11	4	12	0	1	3	0	2	1	1	4	3	4	3	3	0	4	1	3	0	4	4			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr12:99478796G>A	ENST00000547776.2	-	16	2531	c.2532C>T	c.(2530-2532)agC>agT	p.S844S	ANKS1B_ENST00000546960.1_Silent_p.S70S|ANKS1B_ENST00000550693.2_Silent_p.S70S|ANKS1B_ENST00000547446.1_Silent_p.S39S|ANKS1B_ENST00000549025.2_Silent_p.S13S|ANKS1B_ENST00000329257.7_Silent_p.S844S|ANKS1B_ENST00000549493.2_Silent_p.S70S|ANKS1B_ENST00000547010.1_Silent_p.S420S|RNA5SP366_ENST00000365454.1_RNA|ANKS1B_ENST00000549558.2_Silent_p.S70S|ANKS1B_ENST00000332712.7_Silent_p.S70S|ANKS1B_ENST00000546568.1_Silent_p.S70S	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	844	SAM 1. {ECO:0000255|PROSITE- ProRule:PRU00184}.					cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		CCATAACATTGCTTCCCTGAA	0.358																																					p.S844S		Atlas-SNP	.											.	ANKS1B	180	.	0			c.C2532T						PASS	.						70	66	67					12																	99478796		1839	4088	5927	SO:0001819	synonymous_variant	56899	exon16			AACATTGCTTCCC	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.2532C>T	chr12.hg19:g.99478796G>A		70.0	0.0	.		131.0	55.0	.	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Silent	SNP	ENST00000547776.2	hg19	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	G	9.174	1.021948	0.19433	.	.	ENSG00000185046	ENST00000550778	.	.	.	5.29	5.29	0.74685	.	.	.	.	.	T	0.71745	0.3376	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.70554	-0.4840	4	.	.	.	-9.1482	15.8445	0.78876	0.0:0.0:1.0:0.0	.	.	.	.	V	116	.	.	A	-	2	0	ANKS1B	98002927	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.521000	0.45563	2.491000	0.84063	0.561000	0.74099	GCA	.	.	.	none		0.358	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140		A	99478796	G	A	99478796	2	1	274	1	0	0	0	0	0	0	0	1	689	1310	46	2		2	ANKS1B	12	99478796	Silent	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10	47077752	99478796	34373099	56	17374											
CCDC63	160762	hgsc.bcm.edu	37	chr12	111345141	111345141	+	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	tgatcttggtgcagtggaacAgcccctggaccacagcagcc	9	7	12	13	0	1	1	0	1	1	0	1	3	1	3	4	3	5	2	4	3	1	1			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr12:111345141A>T	ENST00000308208.5	+	12	1795	c.1553A>T	c.(1552-1554)cAg>cTg	p.Q518L	CCDC63_ENST00000545036.1_Missense_Mutation_p.Q478L|CCDC63_ENST00000552694.1_Missense_Mutation_p.Q439L	NM_152591.1	NP_689804.1	Q8NA47	CCD63_HUMAN	coiled-coil domain containing 63	518										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						GCAGTGGAACAGCCCCTGGAC	0.567																																					p.Q518L		Atlas-SNP	.											.	CCDC63	89	.	0			c.A1553T						PASS	.						47	42	44					12																	111345141		2203	4300	6503	SO:0001583	missense	160762	exon12			TGGAACAGCCCCT	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.1553A>T	chr12.hg19:g.111345141A>T	ENSP00000312399:p.Gln518Leu	40.0	0.0	.		48.0	25.0	.	NM_152591	B4DY03|Q0P603|Q6P2E1	Missense_Mutation	SNP	ENST00000308208.5	hg19	CCDS9151.1	.	.	.	.	.	.	.	.	.	.	A	0.037	-1.304034	0.01353	.	.	ENSG00000173093	ENST00000545036;ENST00000308208;ENST00000552694	T;T;T	0.31247	1.51;1.5;1.5	4.01	2.83	0.33086	.	0.831369	0.10661	N	0.648749	T	0.27967	0.0689	L	0.60455	1.87	0.09310	N	1	B	0.25904	0.137	B	0.18561	0.022	T	0.18461	-1.0336	10	0.35671	T	0.21	.	7.749	0.28886	0.7879:0.2121:0.0:0.0	.	518	Q8NA47	CCD63_HUMAN	L	478;518;439	ENSP00000445881:Q478L;ENSP00000312399:Q518L;ENSP00000450217:Q439L	ENSP00000312399:Q518L	Q	+	2	0	CCDC63	109829524	0.002000	0.14202	0.164000	0.22755	0.032000	0.12392	1.254000	0.32897	0.679000	0.31345	0.444000	0.29173	CAG	.	.	.	none		0.567	CCDC63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404673.2	NM_152591		T	111345141	A	T	111345141	3	4	274	1	0	0	0	0	1	0	0	0	2836	188	7	5	1595	5	CCDC63	12	111345141	Missense_Mutation	SNP	A	TCGA-Y8-A894-01A-11D-A35Z-10	11866345	111345141	22506754	57	17375											
WDR66	144406	hgsc.bcm.edu	37	chr12	122406042	122406042	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcactgcgggagggcacgAtcgctcggtggtgcagtgga	6	8	17	10	4	1	0	1	0	0	0	3	3	1	2	0	5	2	3	0	5	0	1			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr12:122406042A>G	ENST00000288912.4	+	17	3592	c.2738A>G	c.(2737-2739)gAt>gGt	p.D913G	WDR66_ENST00000397454.2_Missense_Mutation_p.D913G|WDR66_ENST00000545752.1_3'UTR	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	913							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)		GGAGGGCACGATCGCTCGGTG	0.527																																					p.D913G	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											.	WDR66	143	.	0			c.A2738G						PASS	.						57	58	58					12																	122406042		1997	4168	6165	SO:0001583	missense	144406	exon17			GGCACGATCGCTC	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.2738A>G	chr12.hg19:g.122406042A>G	ENSP00000288912:p.Asp913Gly	69.0	0.0	.		120.0	72.0	.	NM_001178003	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	hg19	CCDS41853.1	.	.	.	.	.	.	.	.	.	.	A	16.56	3.157682	0.57368	.	.	ENSG00000158023	ENST00000288912;ENST00000397454	T;T	0.64803	-0.12;0.59	5.19	5.19	0.71726	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.80171	0.4574	M	0.88979	2.995	0.58432	D	0.999997	D	0.71674	0.998	P	0.61003	0.882	D	0.84817	0.0794	10	0.87932	D	0	.	15.0447	0.71819	1.0:0.0:0.0:0.0	.	913	Q8TBY9	WDR66_HUMAN	G	913	ENSP00000288912:D913G;ENSP00000380595:D913G	ENSP00000288912:D913G	D	+	2	0	WDR66	120890425	1.000000	0.71417	0.039000	0.18376	0.027000	0.11550	7.687000	0.84139	1.960000	0.56953	0.459000	0.35465	GAT	.	.	.	none		0.527	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668		G	122406042	A	G	122406042	3	3	274	1	0	0	0	0	1	0	0	0	17329	333	12	3	2800	3	WDR66	12	122406042	Missense_Mutation	SNP	A	TCGA-Y8-A894-01A-11D-A35Z-10	11060901	122406042	11445853	58	17376											
SHISA2	387914	hgsc.bcm.edu	37	chr13	26621071	26621071	+	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	gtctccatcaagcggttaccCcctggggctcggctctgctg	4	10	12	15	2	3	0	1	0	2	0	5	0	3	0	3	4	3	4	3	4	2	1			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr13:26621071C>A	ENST00000319420.3	-	2	523	c.468G>T	c.(466-468)ggG>ggT	p.G156G		NM_001007538.1	NP_001007539.1	Q6UWI4	SHSA2_HUMAN	shisa family member 2	156					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(2)|skin(1)	17						AGCGGTTACCCCCTGGGGCTC	0.632																																					p.G156G		Atlas-SNP	.											.	SHISA2	43	.	0			c.G468T						PASS	.						39	40	40					13																	26621071		2203	4300	6503	SO:0001819	synonymous_variant	387914	exon2			GTTACCCCCTGGG		CCDS31951.1	13q12.13	2013-07-31	2013-07-31	2008-04-01	ENSG00000180730	ENSG00000180730		"Shisa homologs"	20366	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 13", "transmembrane protein 46", "shisa homolog 2 (Xenopus laevis)"	C13orf13, TMEM46			Standard	NM_001007538		Approved	bA398O19.2, PRO28631, WGAR9166, hShisa	uc001uqm.1	Q6UWI4	OTTHUMG00000016612	ENST00000319420.3:c.468G>T	chr13.hg19:g.26621071C>A		68.0	0.0	.		110.0	54.0	.	NM_001007538	B9EH70|Q5W0G8	Silent	SNP	ENST00000319420.3	hg19	CCDS31951.1																																																																																			.	.	.	none		0.632	SHISA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044239.2	NM_001007538		A	26621071	C	A	26621071	2	1	274	1	0	0	0	0	0	0	0	1	14293	610	22	4		4	SHISA2	13	26621071	Silent	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10		26621071	88548807	59	17377											
TSC22D1	8848	hgsc.bcm.edu	37	chr13	45149121	45149121	+	Missense_Mutation	SNP	A	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	accattgcccatgccactcaAgatattcacattaacaccac	14	9	3	15	0	2	1	2	0	0	1	2	1	2	1	4	0	3	0	4	0	3	4			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr13:45149121A>C	ENST00000458659.2	-	1	1580	c.1090T>G	c.(1090-1092)Ttg>Gtg	p.L364V	TSC22D1_ENST00000501704.2_Missense_Mutation_p.L364V|TSC22D1_ENST00000460842.1_5'Flank	NM_183422.3	NP_904358.2	Q15714	T22D1_HUMAN	TSC22 domain family, member 1	364					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)		ATGCCACTCAAGATATTCACA	0.463																																					p.L364V		Atlas-SNP	.											.	TSC22D1	88	.	0			c.T1090G						PASS	.						112	96	102					13																	45149121		2203	4300	6503	SO:0001583	missense	8848	exon1			CACTCAAGATATT	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.1090T>G	chr13.hg19:g.45149121A>C	ENSP00000397435:p.Leu364Val	53.0	0.0	.		77.0	44.0	.	NM_183422	B3KRL7|B9EGI0|O00666|Q6AHX5|Q6IBU1|Q8NCN1|Q96JS5	Missense_Mutation	SNP	ENST00000458659.2	hg19	CCDS31966.1	.	.	.	.	.	.	.	.	.	.	A	13.02	2.111211	0.37242	.	.	ENSG00000102804	ENST00000458659;ENST00000501704	T;T	0.26067	1.76;1.76	4.49	3.31	0.37934	.	0.000000	0.43260	D	0.000582	T	0.21962	0.0529	L	0.29908	0.895	0.26148	N	0.980186	P;P	0.50528	0.936;0.895	P;P	0.50934	0.654;0.452	T	0.04467	-1.0949	10	0.27785	T	0.31	.	6.2454	0.20813	0.7965:0.0:0.2035:0.0	.	364;364	B3KRL7;Q15714	.;T22D1_HUMAN	V	364	ENSP00000397435:L364V;ENSP00000437414:L364V	ENSP00000397435:L364V	L	-	1	2	TSC22D1	44047121	0.151000	0.22747	1.000000	0.80357	0.998000	0.95712	0.029000	0.13666	1.874000	0.54306	0.459000	0.35465	TTG	.	.	.	none		0.463	TSC22D1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044743.2	NM_006022		C	45149121	A	C	45149121	3	2	274	1	0	0	0	0	1	0	0	0	16619	69	3	5	2272	5	TSC22D1	13	45149121	Missense_Mutation	SNP	A	TCGA-Y8-A894-01A-11D-A35Z-10	18528050	45149121	70020757	60	17378											
EDDM3A	10876	hgsc.bcm.edu	37	chr14	21215971	21215972	+	Frame_Shift_Ins	INS	-	-	CT																															cttatggttcaaaattcagcINSgtgcatgcatcaatgagaag																								rs149270684	byFrequency	TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr14:21215971_21215972insCT	ENST00000326842.2	+	2	359_360	c.232_233insCT	c.(232-234)cgtfs	p.R78fs		NM_006683.4	NP_006674.2	Q14507	EP3A_HUMAN	epididymal protein 3A	78					sperm displacement (GO:0007321)	extracellular space (GO:0005615)				breast(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	6						CAAAATTCAGCGTGCATGCATC	0.436																																					p.R78fs		Atlas-INDEL	.											.	EDDM3A	15	.	0			c.232_233insCT						PASS	.																																			SO:0001589	frameshift_variant	10876	exon2			.	X76383	CCDS9556.1	14q11.1	2010-03-19	2010-01-27	2010-01-27	ENSG00000181562	ENSG00000181562			16978	protein-coding gene	gene with protein product		611580	"family with sequence similarity 12, member A"	FAM12A		7514008	Standard	NM_006683		Approved	HE3-ALPHA	uc001vyc.3	Q14507	OTTHUMG00000029581	Exception_encountered	chr14.hg19:g.21215971_21215972insCT	ENSP00000315098:p.Arg78fs	68.0	0.0	0		93.0	29.0	0.311828	NM_006683	Q4KN33	Frame_Shift_Ins	INS	ENST00000326842.2	hg19	CCDS9556.1																																																																																			.	.	.	none		0.436	EDDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073742.3			CT	21215972	-	CT	21215971	7	5	274	1	0	1	1	0	0	0	0	0	4911	768	27	0	234	0	EDDM3A	14	21215971	Frame_Shift_Ins	INS	-	TCGA-Y8-A894-01A-11D-A35Z-10		21215971	86133569	61	17379	179	2									
EDDM3A	10876	hgsc.bcm.edu	37	chr14	21215972	21215972	+	Missense_Mutation	SNP	G	G	C																															cttatggttcaaaattcagcGtgcatgcatcaatgagaagg																								rs149270684	byFrequency	TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr14:21215972G>C	ENST00000326842.2	+	2	360	c.233G>C	c.(232-234)cGt>cCt	p.R78P		NM_006683.4	NP_006674.2	Q14507	EP3A_HUMAN	epididymal protein 3A	78					sperm displacement (GO:0007321)	extracellular space (GO:0005615)				breast(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	6						AAAATTCAGCGTGCATGCATC	0.438																																					p.R78P		Atlas-SNP	.											.	EDDM3A	15	.	0			c.G233C						PASS	.						103	100	101					14																	21215972		2203	4300	6503	SO:0001583	missense	10876	exon2			TTCAGCGTGCATG	X76383	CCDS9556.1	14q11.1	2010-03-19	2010-01-27	2010-01-27	ENSG00000181562	ENSG00000181562			16978	protein-coding gene	gene with protein product		611580	"family with sequence similarity 12, member A"	FAM12A		7514008	Standard	NM_006683		Approved	HE3-ALPHA	uc001vyc.3	Q14507	OTTHUMG00000029581	ENST00000326842.2:c.233G>C	chr14.hg19:g.21215972G>C	ENSP00000315098:p.Arg78Pro	67.0	0.0	.		92.0	35.0	.	NM_006683	Q4KN33	Missense_Mutation	SNP	ENST00000326842.2	hg19	CCDS9556.1	.	.	.	.	.	.	.	.	.	.	G	12.09	1.833295	0.32421	.	.	ENSG00000181562	ENST00000326842	T	0.73469	-0.75	2.46	-0.0476	0.13842	Ribonuclease A, domain (2);	1.533360	0.04073	N	0.308328	T	0.73636	0.3612	L	0.40543	1.245	0.09310	N	1	P	0.52842	0.956	P	0.53224	0.721	T	0.59188	-0.7501	10	0.66056	D	0.02	.	4.437	0.11555	0.6155:0.0:0.3845:0.0	.	78	Q14507	EP3A_HUMAN	P	78	ENSP00000315098:R78P	ENSP00000315098:R78P	R	+	2	0	EDDM3A	20285812	0.000000	0.05858	0.002000	0.10522	0.167000	0.22549	0.137000	0.15995	-0.150000	0.11195	0.313000	0.20887	CGT	.	G|0.999;A|0.001	.	alt		0.438	EDDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073742.3			C	21215972	G	C	21215972	3	2	274	1	0	0	0	0	1	0	0	0	4911	1145	40	4	235	4	EDDM3A	14	21215972	Missense_Mutation	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10	1	21215972	86133568	62	17380	179	2									
PPP2R5E	5529	hgsc.bcm.edu	37	chr14	63860645	63860645	+	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	taaagcaaagccattgataaTactagggagaaaaaagagac	21	6	9	5	0	0	3	0	1	0	2	0	5	0	3	1	1	3	1	1	1	9	5			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr14:63860645T>A	ENST00000337537.3	-	8	1344	c.742A>T	c.(742-744)Att>Ttt	p.I248F	PPP2R5E_ENST00000553266.1_5'UTR|PPP2R5E_ENST00000422769.2_Splice_Site_p.I172F|PPP2R5E_ENST00000555899.1_Splice_Site_p.I248F	NM_001282179.1|NM_001282180.1|NM_001282181.1|NM_001282182.1|NM_006246.2	NP_001269108.1|NP_001269109.1|NP_001269110.1|NP_001269111.1|NP_006237.1	Q16537	2A5E_HUMAN	protein phosphatase 2, regulatory subunit B', epsilon isoform	248					regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)	15				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)		CCATTGATAATACTAGGGAGA	0.353																																					p.I248F		Atlas-SNP	.											.	PPP2R5E	43	.	0			c.A742T						PASS	.						69	68	68					14																	63860645		2203	4300	6503	SO:0001630	splice_region_variant	5529	exon8			TGATAATACTAGG	L76703	CCDS9758.1, CCDS61467.1, CCDS61468.1	14q23.2	2010-06-18	2007-01-22		ENSG00000154001	ENSG00000154001		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9313	protein-coding gene	gene with protein product		601647	"protein phosphatase 2, regulatory subunit B (B56), epsilon isoform"			7592815	Standard	NM_006246		Approved		uc001xgd.1	Q16537	OTTHUMG00000140341	ENST00000337537.3:c.741-1A>T	chr14.hg19:g.63860645T>A		47.0	0.0	.		83.0	40.0	.	NM_006246	A4FU37|B7ZAW5|B7ZKK8|B7ZKK9|J3KQN6|Q52LW4	Missense_Mutation	SNP	ENST00000337537.3	hg19	CCDS9758.1	.	.	.	.	.	.	.	.	.	.	T	29.3	4.990233	0.93106	.	.	ENSG00000154001	ENST00000337537;ENST00000555899;ENST00000422769	.	.	.	5.66	5.66	0.87406	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.88070	0.6338	H	0.97186	3.955	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92017	0.5623	9	0.87932	D	0	-10.0146	16.1852	0.81946	0.0:0.0:0.0:1.0	.	248;248	B7ZKK9;Q16537	.;2A5E_HUMAN	F	248;248;172	.	ENSP00000337641:I248F	I	-	1	0	PPP2R5E	62930398	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	7.936000	0.87665	2.277000	0.76020	0.528000	0.53228	ATT	.	.	.	none		0.353	PPP2R5E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276973.1	NM_006246	Missense_Mutation	A	63860645	T	A	63860645	5	1	274	1	0	0	0	0	0	0	1	0	12406	1420	49	5	689	5	PPP2R5E	14	63860645	Splice_Site	SNP	T	TCGA-Y8-A894-01A-11D-A35Z-10	42644673	63860645	43488895	63	17381											
DDX24	57062	hgsc.bcm.edu	37	chr14	94545834	94545834	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gactttccctcctcctcctcCtcttcttctgaaacagcttg	5	15	4	17	0	3	1	0	1	3	0	8	2	8	1	5	0	2	1	5	0	1	4			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr14:94545834C>T	ENST00000330836.5	-	2	386	c.255G>A	c.(253-255)gaG>gaA	p.E85E	IFI27L1_ENST00000554544.1_5'Flank|IFI27L1_ENST00000555523.1_5'Flank|DDX24_ENST00000544005.1_Intron|IFI27L1_ENST00000393115.3_5'Flank|IFI27L1_ENST00000553664.1_5'Flank|DDX24_ENST00000555054.1_Silent_p.E42E|IFI27L1_ENST00000556381.1_5'Flank|IFI27L1_ENST00000557066.1_5'Flank|IFI27L1_ENST00000557218.1_5'Flank	NM_020414.3	NP_065147.1	Q9GZR7	DDX24_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 24	85	Poly-Glu.				RNA metabolic process (GO:0016070)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			cervix(3)|endometrium(4)|kidney(4)|large_intestine(5)|lung(3)|ovary(2)|skin(1)|urinary_tract(1)	23		all_cancers(154;0.12)		Epithelial(152;0.114)|all cancers(159;0.19)|COAD - Colon adenocarcinoma(157;0.207)		CCTCCTCCTCCTCTTCTTCTG	0.438																																					p.E85E		Atlas-SNP	.											.	DDX24	82	.	0			c.G255A						PASS	.						165	161	163					14																	94545834		2203	4300	6503	SO:0001819	synonymous_variant	57062	exon2			CTCCTCCTCTTCT	AF214731	CCDS9918.1	14q32	2013-07-16	2013-07-16			ENSG00000089737		"DEAD-boxes"	13266	protein-coding gene	gene with protein product		606181	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 24", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 24"			10936056, 18289627	Standard	NM_020414		Approved		uc001ycj.3	Q9GZR7		ENST00000330836.5:c.255G>A	chr14.hg19:g.94545834C>T		61.0	0.0	.		91.0	4.0	.	NM_020414	E7EMJ4|Q4V9L5	Silent	SNP	ENST00000330836.5	hg19	CCDS9918.1																																																																																			.	.	.	none		0.438	DDX24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412861.1	NM_020414		T	94545834	C	T	94545834	2	4	274	1	0	0	0	0	0	0	0	1	4353	680	24	2		2	DDX24	14	94545834	Silent	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10	30685189	94545834	12803706	64	17382											
DICER1	23405	hgsc.bcm.edu	37	chr14	95590600	95590600	+	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	gcacaaaatgttggtaaaagGagaaggaaaatttgtctctg	16	10	11	4	0	1	1	0	0	1	1	2	3	1	2	0	3	0	3	0	3	7	3			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr14:95590600G>C	ENST00000526495.1	-	10	1600	c.1309C>G	c.(1309-1311)Cct>Gct	p.P437A	DICER1_ENST00000343455.3_Missense_Mutation_p.P437A|DICER1_ENST00000393063.1_Missense_Mutation_p.P437A|DICER1_ENST00000541352.1_Missense_Mutation_p.P437A|DICER1_ENST00000527414.1_Missense_Mutation_p.P437A			Q9UPY3	DICER_HUMAN	dicer 1, ribonuclease type III	437	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.|Required for interaction with PRKRA and TARBP2.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac muscle cell development (GO:0055013)|cerebral cortex development (GO:0021987)|defense response to virus (GO:0051607)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|hair follicle cell proliferation (GO:0071335)|hair follicle morphogenesis (GO:0031069)|inner ear receptor cell development (GO:0060119)|intestinal epithelial cell development (GO:0060576)|lung development (GO:0030324)|mRNA stabilization (GO:0048255)|multicellular organism growth (GO:0035264)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|olfactory bulb interneuron differentiation (GO:0021889)|peripheral nervous system myelin formation (GO:0032290)|positive regulation of gene expression (GO:0010628)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of myelination (GO:0031643)|positive regulation of Schwann cell differentiation (GO:0014040)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|production of siRNA involved in RNA interference (GO:0030422)|regulation of cell cycle (GO:0051726)|regulation of enamel mineralization (GO:0070173)|regulation of neuron differentiation (GO:0045664)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of viral genome replication (GO:0045069)|reproductive structure development (GO:0048608)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|spinal cord motor neuron differentiation (GO:0021522)|spindle assembly (GO:0051225)|spleen development (GO:0048536)|stem cell maintenance (GO:0019827)|targeting of mRNA for destruction involved in RNA interference (GO:0030423)|zygote asymmetric cell division (GO:0010070)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|growth cone (GO:0030426)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|ribonuclease III activity (GO:0004525)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(13)|kidney(3)|large_intestine(10)|lung(33)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	75		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		TTGGTAAAAGGAGAAGGAAAA	0.353			"Mis F, N"		"sex cord-stromal tumour, TGCT, embryonal rhadomyosarcoma"	pleuropulmonary blastoma			Familial Multinodular Goiter ;DICER 1 syndrome																												p.P437A		Atlas-SNP	.	yes	Rec	yes	Familial Pleuropulmonary Blastoma	14	14q32.13	23405	"dicer 1, ribonuclease type III "		"E, M, O"	.	DICER1	181	.	0			c.C1309G						PASS	.						80	85	83					14																	95590600		2203	4300	6503	SO:0001583	missense	23405	exon9	Familial Cancer Database	Adolescent Multinodular Goiter, incl. Multinodular Euthyroid Goiter & Non-Medullary Thyroid Cancer;incl. Pleuropulmonary Blastoma, Familial ; Cystic Nephroma, Familial	TAAAAGGAGAAGG	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.1309C>G	chr14.hg19:g.95590600G>C	ENSP00000437256:p.Pro437Ala	47.0	0.0	.		74.0	42.0	.	NM_030621	A7E2D3|B3KRG4|E0AD28|O95943|Q9UQ02	Missense_Mutation	SNP	ENST00000526495.1	hg19	CCDS9931.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.568453	0.86439	.	.	ENSG00000100697	ENST00000343455;ENST00000526495;ENST00000393063;ENST00000527414;ENST00000541352	T;T;T;T;T	0.71341	-0.56;-0.56;-0.56;-0.56;-0.56	5.41	5.41	0.78517	Helicase, C-terminal (1);	0.219441	0.48286	D	0.000182	T	0.63534	0.2519	N	0.19112	0.55	0.80722	D	1	P	0.39717	0.684	P	0.45037	0.467	T	0.58595	-0.7609	10	0.13853	T	0.58	-14.9718	19.1956	0.93686	0.0:0.0:1.0:0.0	.	437	Q9UPY3	DICER_HUMAN	A	437	ENSP00000343745:P437A;ENSP00000437256:P437A;ENSP00000376783:P437A;ENSP00000435681:P437A;ENSP00000444719:P437A	ENSP00000343745:P437A	P	-	1	0	DICER1	94660353	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.187000	0.94912	2.524000	0.85096	0.591000	0.81541	CCT	.	.	.	none		0.353	DICER1-004	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387997.1			C	95590600	G	C	95590600	3	2	274	1	0	0	0	0	1	0	0	0	4523	1174	41	4	4539	4	DICER1	14	95590600	Missense_Mutation	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10	1044766	95590600	11758940	65	17383											
MYO5A	4644	hgsc.bcm.edu	37	chr15	52615613	52615613	+	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	atgtgttagagagccagaagGagacggtttcaaaatcatca	15	9	11	6	1	3	3	3	0	0	3	3	5	3	3	1	2	1	2	1	2	4	2			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr15:52615613G>C	ENST00000399231.3	-	36	4907	c.4664C>G	c.(4663-4665)tCc>tGc	p.S1555C	MYO5A_ENST00000358212.6_Missense_Mutation_p.S1580C|MYO5A_ENST00000356338.6_Missense_Mutation_p.S1528C|MYO5A_ENST00000553916.1_Missense_Mutation_p.S1553C|MYO5A_ENST00000399233.2_Missense_Mutation_p.S1552C	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1555	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.				actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		GAGCCAGAAGGAGACGGTTTC	0.373																																					p.S1555C		Atlas-SNP	.											.	MYO5A	145	.	0			c.C4664G						PASS	.						130	120	123					15																	52615613		1837	4087	5924	SO:0001583	missense	4644	exon36			CAGAAGGAGACGG		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.4664C>G	chr15.hg19:g.52615613G>C	ENSP00000382177:p.Ser1555Cys	96.0	0.0	.		138.0	59.0	.	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	hg19	CCDS42037.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.538273	0.85917	.	.	ENSG00000197535	ENST00000399231;ENST00000399229;ENST00000399233;ENST00000356338;ENST00000358212;ENST00000546028;ENST00000553916	T;T;T;T;T	0.25414	1.8;1.8;1.8;1.8;1.8	6.17	6.17	0.99709	Dilute (1);	0.000000	0.85682	D	0.000000	T	0.54334	0.1852	M	0.78637	2.42	0.80722	D	1	D;D;D	0.63880	0.993;0.967;0.992	D;P;P	0.64687	0.928;0.806;0.863	T	0.48502	-0.9030	10	0.51188	T	0.08	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	285;1555;1528	B5LY56;Q9Y4I1;Q9Y4I1-2	.;MYO5A_HUMAN;.	C	1555;1062;1552;1528;1580;1158;1553	ENSP00000382177:S1555C;ENSP00000382179:S1552C;ENSP00000348693:S1528C;ENSP00000350945:S1580C;ENSP00000451109:S1553C	ENSP00000348693:S1528C	S	-	2	0	MYO5A	50402905	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.876000	0.87215	2.941000	0.99782	0.655000	0.94253	TCC	.	.	.	none		0.373	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259		C	52615613	G	C	52615613	3	2	274	1	0	0	0	0	1	0	0	0	10085	1174	41	4	927	4	MYO5A	15	52615613	Missense_Mutation	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10		52615613	49915779	66	17384											
CGNL1	84952	hgsc.bcm.edu	37	chr15	57730578	57730578	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctccatgagggcaagaaTggagttctagatcgcaaaga	13	8	12	8	1	1	4	0	1	1	3	3	5	2	5	1	2	1	4	1	2	4	2			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr15:57730578T>C	ENST00000281282.5	+	2	459	c.381T>C	c.(379-381)aaT>aaC	p.N127N		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	127	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)		AGGGCAAGAATGGAGTTCTAG	0.493																																					p.N127N		Atlas-SNP	.											.	CGNL1	125	.	0			c.T381C						PASS	.						50	50	50					15																	57730578		2192	4292	6484	SO:0001819	synonymous_variant	84952	exon3			CAAGAATGGAGTT	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.381T>C	chr15.hg19:g.57730578T>C		108.0	0.0	.		146.0	69.0	.	NM_001252335	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Silent	SNP	ENST00000281282.5	hg19	CCDS10161.1																																																																																			.	.	.	none		0.493	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866		C	57730578	T	C	57730578	2	2	274	1	0	0	0	0	0	0	0	1	3306	1461	51	3		3	CGNL1	15	57730578	Silent	SNP	T	TCGA-Y8-A894-01A-11D-A35Z-10	5114965	57730578	44800814	67	17385											
LRRC49	54839	hgsc.bcm.edu	37	chr15	71193333	71193333	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acgttcttctgaagagaaaaTtctttactcagacaggttga	13	13	8	7	1	4	4	1	2	3	2	4	5	4	4	0	1	1	2	0	1	4	6			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr15:71193333T>C	ENST00000260382.5	+	4	526	c.266T>C	c.(265-267)aTt>aCt	p.I89T	LRRC49_ENST00000560691.1_5'UTR|LRRC49_ENST00000544974.2_Missense_Mutation_p.I79T|LRRC49_ENST00000560369.1_Missense_Mutation_p.I94T|LRRC49_ENST00000443425.2_Missense_Mutation_p.I45T|LRRC49_ENST00000436542.2_3'UTR	NM_001199017.1|NM_017691.3	NP_001185946.1|NP_060161.2	Q8IUZ0	LRC49_HUMAN	leucine rich repeat containing 49	89						cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(3)|skin(3)	34						GAAGAGAAAATTCTTTACTCA	0.318																																					p.I94T		Atlas-SNP	.											.	LRRC49	73	.	0			c.T281C						PASS	.						79	82	81					15																	71193333		2199	4295	6494	SO:0001583	missense	54839	exon4			AGAAAATTCTTTA		CCDS32282.1, CCDS55971.1, CCDS58376.1, CCDS61694.1	15q23	2005-08-09				ENSG00000137821			25965	protein-coding gene	gene with protein product						12477932	Standard	NM_001199017		Approved	FLJ20156	uc010ukf.2	Q8IUZ0		ENST00000260382.5:c.266T>C	chr15.hg19:g.71193333T>C	ENSP00000260382:p.Ile89Thr	160.0	0.0	.		297.0	144.0	.	NM_001199017	B3KVX1|B7Z366|F5H1J4|G5E9T5|H0YLN4|Q9NXM6	Missense_Mutation	SNP	ENST00000260382.5	hg19	CCDS32282.1	.	.	.	.	.	.	.	.	.	.	T	7.971	0.749171	0.15710	.	.	ENSG00000137821	ENST00000544974;ENST00000260382;ENST00000443425;ENST00000436542	T;T;T	0.33865	1.4;1.93;1.39	5.86	2.15	0.27550	.	0.459688	0.21102	N	0.080154	T	0.17704	0.0425	N	0.14661	0.345	0.25035	N	0.99125	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;0.001;0.001	T	0.18618	-1.0331	10	0.24483	T	0.36	-4.7976	5.7854	0.18331	0.0:0.0863:0.3278:0.5859	.	94;61;45;89;79	B7Z366;G5E9Q1;G5E9T5;Q8IUZ0;F5H1J4	.;.;.;LRC49_HUMAN;.	T	79;89;45;61	ENSP00000439600:I79T;ENSP00000260382:I89T;ENSP00000414065:I45T	ENSP00000260382:I89T	I	+	2	0	LRRC49	68980387	0.991000	0.36638	0.985000	0.45067	0.999000	0.98932	0.715000	0.25822	0.170000	0.19704	0.528000	0.53228	ATT	.	.	.	none		0.318	LRRC49-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417209.3	NM_017691		C	71193333	T	C	71193333	3	2	274	1	0	0	0	0	1	0	0	0	9013	1493	52	3	280	3	LRRC49	15	71193333	Missense_Mutation	SNP	T	TCGA-Y8-A894-01A-11D-A35Z-10	13462755	71193333	31338059	68	17386											
ARIH1	25820	hgsc.bcm.edu	37	chr15	72874471	72874471	+	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	gctctcgggctaccttgaacGagatatttcccaagattctc	9	12	8	12	2	2	3	0	1	2	2	5	4	3	3	2	1	2	2	2	1	4	5			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr15:72874471G>C	ENST00000379887.4	+	13	1846	c.1532G>C	c.(1531-1533)cGa>cCa	p.R511P	ARIH1_ENST00000562891.1_3'UTR	NM_005744.3	NP_005735.2	Q9Y4X5	ARI1_HUMAN	ariadne RBR E3 ubiquitin protein ligase 1	511					cytokine-mediated signaling pathway (GO:0019221)|protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|ubiquitin ligase complex (GO:0000151)	small conjugating protein ligase activity (GO:0019787)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R511Q(1)		endometrium(1)|kidney(4)|large_intestine(3)|lung(4)|prostate(1)|skin(1)	14						TACCTTGAACGAGATATTTCC	0.363																																					p.R511P		Atlas-SNP	.											ARIH1,face,carcinoma,0,1	ARIH1	42	.	1	Substitution - Missense(1)	skin(1)	c.G1532C						PASS	.						102	105	104					15																	72874471		2198	4297	6495	SO:0001583	missense	25820	exon13			TTGAACGAGATAT	AF072832	CCDS10244.1	15q24	2013-10-03	2013-10-03		ENSG00000166233	ENSG00000166233			689	protein-coding gene	gene with protein product	"ariadne, Drosophila, homolog of"	605624	"ariadne (Drosophila) homolog, ubiquitin-conjugating enzyme E2-binding protein, 1", "ariadne homolog, ubiquitin-conjugating enzyme E2 binding protein, 1 (Drosophila)"			10521492, 24058416	Standard	NM_005744		Approved	HARI, HHARI, UBCH7BP, ARI	uc002aut.4	Q9Y4X5	OTTHUMG00000133474	ENST00000379887.4:c.1532G>C	chr15.hg19:g.72874471G>C	ENSP00000369217:p.Arg511Pro	225.0	0.0	.		318.0	149.0	.	NM_005744	B2R6U3|O76026|Q9H3T6|Q9UEN0|Q9UP39	Missense_Mutation	SNP	ENST00000379887.4	hg19	CCDS10244.1	.	.	.	.	.	.	.	.	.	.	G	32	5.162819	0.94727	.	.	ENSG00000166233	ENST00000379887;ENST00000299305	D	0.87491	-2.26	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	D	0.95494	0.8536	M	0.93763	3.455	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.96236	0.9172	10	0.87932	D	0	.	19.5444	0.95285	0.0:0.0:1.0:0.0	.	511	Q9Y4X5	ARI1_HUMAN	P	511;481	ENSP00000369217:R511P	ENSP00000299305:R481P	R	+	2	0	ARIH1	70661525	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.356000	0.97091	2.621000	0.88768	0.644000	0.83932	CGA	.	.	.	none		0.363	ARIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257350.1	NM_005744		C	72874471	G	C	72874471	3	2	274	1	0	0	0	0	1	0	0	0	923	1058	37	4	1582	4	ARIH1	15	72874471	Missense_Mutation	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10	1681138	72874471	29656921	69	17387											
BLM	641	hgsc.bcm.edu	37	chr15	91298123	91298123	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttttgtcaaaacctgagaaaAtgagtatgcaggagctgaat	15	11	10	5	0	1	3	1	3	0	1	1	5	1	4	1	1	3	3	1	1	6	3			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr15:91298123A>G	ENST00000355112.3	+	5	1160	c.1042A>G	c.(1042-1044)Atg>Gtg	p.M348V	BLM_ENST00000560509.1_Missense_Mutation_p.M348V|SNORD18_ENST00000363807.1_RNA	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	348	Necessary for interaction with SPIDR.				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)			ACCTGAGAAAATGAGTATGCA	0.363			"Mis, N, F"			"leukemia, lymphoma, skin squamous cell , other cancers"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome																												p.M348V		Atlas-SNP	.	yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"L, E"	.	BLM	122	.	0			c.A1042G						PASS	.						93	89	91					15																	91298123		2198	4298	6496	SO:0001583	missense	641	exon5	Familial Cancer Database		GAGAAAATGAGTA	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.1042A>G	chr15.hg19:g.91298123A>G	ENSP00000347232:p.Met348Val	63.0	0.0	.		103.0	49.0	.	NM_000057	Q52M96	Missense_Mutation	SNP	ENST00000355112.3	hg19	CCDS10363.1	.	.	.	.	.	.	.	.	.	.	A	13.23	2.175834	0.38413	.	.	ENSG00000197299	ENST00000355112;ENST00000536925	T	0.42513	0.97	5.33	0.151	0.14888	.	0.794395	0.11183	N	0.590713	T	0.31327	0.0793	M	0.63428	1.95	0.09310	N	1	B;B	0.22480	0.07;0.07	B;B	0.19148	0.024;0.024	T	0.30387	-0.9980	10	0.22706	T	0.39	-15.1694	1.0454	0.01568	0.5054:0.1741:0.1756:0.145	.	348;348	B2RAN0;P54132	.;BLM_HUMAN	V	348;1	ENSP00000347232:M348V	ENSP00000347232:M348V	M	+	1	0	BLM	89099127	0.808000	0.29022	0.000000	0.03702	0.430000	0.31655	1.450000	0.35134	-0.233000	0.09797	0.374000	0.22700	ATG	.	.	.	none		0.363	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1			G	91298123	A	G	91298123	3	3	274	1	0	0	0	0	1	0	0	0	1445	101	4	3	1056	3	BLM	15	91298123	Missense_Mutation	SNP	A	TCGA-Y8-A894-01A-11D-A35Z-10	18423652	91298123	11233269	70	17388											
LRRK1	79705	hgsc.bcm.edu	37	chr15	101589985	101589985	+	Frame_Shift_Del	DEL	C	C	-																															ccttgattgatcagtggtttCccggtaagaggagatgctag																										TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr15:101589985delC	ENST00000388948.3	+	23	3795	c.3436delC	c.(3436-3438)cccfs	p.P1146fs	RP11-505E24.2_ENST00000559857.1_RNA|LRRK1_ENST00000284395.5_Frame_Shift_Del_p.P1143fs|RP11-505E24.3_ENST00000558979.1_RNA	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TCAGTGGTTTCCCGGTAAGAG	0.473																																					p.F1145fs		Atlas-Indel,Pindel	.											.	LRRK1	310	.	0			c.3435delT						PASS	.						67	67	67					15																	101589985		1922	4123	6045	SO:0001589	frameshift_variant	79705	exon23			.	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.3436delC	chr15.hg19:g.101589985delC	ENSP00000373600:p.Pro1146fs	41.0	0.0	0		62.0	28.0	0.451613	NM_024652		Frame_Shift_Del	DEL	ENST00000388948.3	hg19	CCDS42086.1																																																																																			.	.	.	none		0.473	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		-	101589985	C	-	101589985	7	5	274	1	0	1	0	1	0	0	0	0	9039	855	30	0	3522	0	LRRK1	15	101589985	Frame_Shift_Del	DEL	C	TCGA-Y8-A894-01A-11D-A35Z-10	10291862	101589985	941407	71	17389											
SNRPA1	6627	hgsc.bcm.edu	37	chr15	101833253	101833253	+	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	attctgttgttgttcactaaCaatgttttcagtcttctcaa	9	19	5	8	0	5	0	3	0	3	0	6	0	5	0	0	0	1	4	0	0	3	8			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr15:101833253C>T	ENST00000254193.6	-	2	279	c.207G>A	c.(205-207)ttG>ttA	p.L69L	RP11-299G20.2_ENST00000558838.1_RNA|SNRPA1_ENST00000560856.1_5'UTR	NM_003090.2	NP_003081.2	P09661	RU2A_HUMAN	small nuclear ribonucleoprotein polypeptide A'	69					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)			TGTTCACTAACAATGTTTTCA	0.383																																					p.L69L		Atlas-SNP	.											.	SNRPA1	11	.	0			c.G207A						PASS	.						86	79	81					15																	101833253		2203	4300	6503	SO:0001819	synonymous_variant	6627	exon2			CACTAACAATGTT	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.207G>A	chr15.hg19:g.101833253C>T		258.0	0.0	.		387.0	101.0	.	NM_003090	B2R5I6|Q8TBD2	Silent	SNP	ENST00000254193.6	hg19	CCDS10391.1																																																																																			.	.	.	none		0.383	SNRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313621.2	NM_003090		T	101833253	C	T	101833253	2	4	274	1	0	0	0	0	0	0	0	1	14873	477	17	2		2	SNRPA1	15	101833253	Silent	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10	243268	101833253	698139	72	17390											
AXIN1	8312	hgsc.bcm.edu	37	chr16	343699	343699	+	Missense_Mutation	SNP	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	ggagttctcatggggctgtgGcttcctcgtccccgaagacc	5	10	13	13	2	1	1	1	0	1	1	5	3	3	2	4	4	0	3	4	4	1	2			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr16:343699G>A	ENST00000262320.3	-	8	2346	c.1975C>T	c.(1975-1977)Cca>Tca	p.P659S	AXIN1_ENST00000354866.3_Missense_Mutation_p.P659S	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	659	Interaction with PPP2CA.|Interaction with RNF111.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				TGGGGCTGTGGCTTCCTCGTC	0.622																																					p.P659S		Atlas-SNP	.											.	AXIN1	290	.	0			c.C1975T						PASS	.						96	107	103					16																	343699		2203	4300	6503	SO:0001583	missense	8312	exon8			GCTGTGGCTTCCT	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	903	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 49"	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.1975C>T	chr16.hg19:g.343699G>A	ENSP00000262320:p.Pro659Ser	29.0	0.0	.		39.0	13.0	.	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Missense_Mutation	SNP	ENST00000262320.3	hg19	CCDS10405.1	.	.	.	.	.	.	.	.	.	.	G	3.721	-0.057561	0.07317	.	.	ENSG00000103126	ENST00000262320;ENST00000354866	T;T	0.58060	0.36;0.38	4.17	4.17	0.49024	.	0.581013	0.19003	N	0.125294	T	0.40423	0.1116	L	0.38175	1.15	0.23210	N	0.998116	B;B	0.10296	0.003;0.001	B;B	0.15052	0.012;0.005	T	0.16600	-1.0397	10	0.06757	T	0.87	-2.6259	15.6374	0.76966	0.0:0.0:1.0:0.0	.	659;659	O15169-2;O15169	.;AXIN1_HUMAN	S	659	ENSP00000262320:P659S;ENSP00000346935:P659S	ENSP00000262320:P659S	P	-	1	0	AXIN1	283700	1.000000	0.71417	1.000000	0.80357	0.402000	0.30811	3.455000	0.52993	2.185000	0.69588	0.478000	0.44815	CCA	.	.	.	none		0.622	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			A	343699	G	A	343699	3	1	274	1	0	0	0	0	1	0	0	0	1236	1203	42	2	629	2	AXIN1	16	343699	Missense_Mutation	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10		343699	90011054	73	17391											
TUSC5	286753	hgsc.bcm.edu	37	chr17	1183315	1183315	+	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	catggcccacccggtgcagtCcgagtttccttcagcacagg	7	8	11	15	2	1	0	1	0	0	0	3	1	3	0	4	3	2	3	4	3	0	2			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr17:1183315C>A	ENST00000333813.3	+	1	359	c.20C>A	c.(19-21)tCc>tAc	p.S7Y		NM_172367.2	NP_758955.2	Q8IXB3	TUSC5_HUMAN	tumor suppressor candidate 5	7					response to biotic stimulus (GO:0009607)	integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|prostate(4)|skin(2)	15				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CCGGTGCAGTCCGAGTTTCCT	0.657																																					p.S7Y		Atlas-SNP	.											.	TUSC5	25	.	0			c.C20A						PASS	.						33	38	36					17																	1183315		1975	4144	6119	SO:0001583	missense	286753	exon1			TGCAGTCCGAGTT	AB090231	CCDS42225.1	17p13.3	2009-10-16			ENSG00000184811	ENSG00000184811			29592	protein-coding gene	gene with protein product	"located at seventeen p thirteen point three 1", "interferon induced transmembrane protein domain containing 3"	612211				12660825	Standard	NM_172367		Approved	LOST1, IFITMD3	uc002fsi.1	Q8IXB3	OTTHUMG00000132196	ENST00000333813.3:c.20C>A	chr17.hg19:g.1183315C>A	ENSP00000329548:p.Ser7Tyr	88.0	0.0	.		161.0	88.0	.	NM_172367	A6NMK4	Missense_Mutation	SNP	ENST00000333813.3	hg19	CCDS42225.1	.	.	.	.	.	.	.	.	.	.	C	15.86	2.956707	0.53293	.	.	ENSG00000184811	ENST00000333813	T	0.72394	-0.65	5.22	4.24	0.50183	.	0.684498	0.13729	U	0.366858	T	0.50394	0.1613	N	0.14661	0.345	0.23401	N	0.997759	B	0.31519	0.327	B	0.24541	0.054	T	0.47661	-0.9100	10	0.87932	D	0	-2.8288	8.7819	0.34795	0.0:0.8988:0.0:0.1012	.	7	Q8IXB3	TUSC5_HUMAN	Y	7	ENSP00000329548:S7Y	ENSP00000329548:S7Y	S	+	2	0	TUSC5	1130065	0.041000	0.20044	1.000000	0.80357	0.013000	0.08279	0.831000	0.27476	2.475000	0.83589	0.537000	0.68136	TCC	.	.	.	none		0.657	TUSC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255249.1	NM_172367		A	1183315	C	A	1183315	3	1	274	1	0	0	0	0	1	0	0	0	16791	855	30	4	22	4	TUSC5	17	1183315	Missense_Mutation	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10		1183315	80011895	74	17392											
KIAA0664	23277	hgsc.bcm.edu	37	chr17	2599551	2599552	+	Splice_Site	DEL	CC	CC	-																															gcaggactcagggaaacgaaCccctggaggagggagagcag																										TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr17:2599551_2599552delCC	ENST00000570628.2	-	13	2280_2281	c.2175_2176delGG	c.(2173-2178)ggggtt>ggtt	p.V726fs	CLUH_ENST00000435359.1_Splice_Site_p.V726fs|CLUH_ENST00000538975.1_Splice_Site_p.V726fs			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	726					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)											GGGAAACGAACCCCTGGAGGAG	0.634																																					p.726_726del		Atlas-Indel,Pindel	.											.	.	.	.	0			c.2176_2177del						PASS	.																																			SO:0001630	splice_region_variant	23277	exon13			.	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.2174-1GG>-	chr17.hg19:g.2599553_2599554delCC		122.0	0.0	0		169.0	91.0	0.538462	NM_015229	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Frame_Shift_Del	DEL	ENST00000570628.2	hg19	CCDS45572.1																																																																																			.	.	.	none		0.634	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229	Frame_Shift_Del	-	2599552	CC	-	2599551	8	5	274	1	0	1	0	1	0	0	1	0	8196	507	18	0	1809	0	KIAA0664	17	2599551	Splice_Site	DEL	CC	TCGA-Y8-A894-01A-11D-A35Z-10	1416236	2599551	78595659	75	17393											
MYH8	4626	hgsc.bcm.edu	37	chr17	10315977	10315977	+	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	ctcattgccaaccttgacccTagggtagcagagggctttga	9	10	11	11	0	1	3	1	2	0	1	1	3	1	3	3	2	3	3	3	2	3	5			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr17:10315977T>A	ENST00000403437.2	-	13	1310	c.1216A>T	c.(1216-1218)Agg>Tgg	p.R406W	RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	406	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						ACCTTGACCCTAGGGTAGCAG	0.507									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																												p.R406W		Atlas-SNP	.											.	MYH8	346	.	0			c.A1216T						PASS	.						317	277	290					17																	10315977		2203	4300	6503	SO:0001583	missense	4626	exon13	Familial Cancer Database	Carney Complex Variant	TGACCCTAGGGTA		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.1216A>T	chr17.hg19:g.10315977T>A	ENSP00000384330:p.Arg406Trp	120.0	0.0	.		213.0	104.0	.	NM_002472	Q14910	Missense_Mutation	SNP	ENST00000403437.2	hg19	CCDS11153.1	.	.	.	.	.	.	.	.	.	.	T	17.44	3.389055	0.61956	.	.	ENSG00000133020	ENST00000252173;ENST00000403437	D	0.88509	-2.39	4.6	3.51	0.40186	Myosin head, motor domain (2);	0.000000	0.43919	U	0.000513	D	0.96371	0.8816	H	0.98629	4.285	0.50171	D	0.999856	D	0.89917	1.0	D	0.97110	1.0	D	0.96185	0.9133	10	0.87932	D	0	.	11.3654	0.49668	0.0:0.0:0.3067:0.6933	.	406	P13535	MYH8_HUMAN	W	406	ENSP00000384330:R406W	ENSP00000252173:R406W	R	-	1	2	MYH8	10256702	0.997000	0.39634	1.000000	0.80357	0.749000	0.42624	1.754000	0.38369	0.789000	0.33779	-0.299000	0.09455	AGG	.	.	.	none		0.507	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		A	10315977	T	A	10315977	3	1	274	1	0	0	0	0	1	0	0	0	10048	1521	53	5	4709	5	MYH8	17	10315977	Missense_Mutation	SNP	T	TCGA-Y8-A894-01A-11D-A35Z-10	7716426	10315977	70879233	76	17394											
ERBB2	2064	hgsc.bcm.edu	37	chr17	37880219	37880220	+	Missense_Mutation	DNP	TT	TT	CC																															ttccagtggccatcaaagtgTtgagggaaaacacatccccc																								rs121913470|rs121913469		TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr17:37880219_37880220TT>CC	ENST00000269571.5	+	19	2422_2423	c.2263_2264TT>CC	c.(2263-2265)TTg>CCg	p.L755P	ERBB2_ENST00000584450.1_Missense_Mutation_p.L755P|ERBB2_ENST00000540147.1_Missense_Mutation_p.L725P|MIR4728_ENST00000580969.1_RNA|ERBB2_ENST00000584601.1_Missense_Mutation_p.L725P|ERBB2_ENST00000406381.2_Missense_Mutation_p.L725P|ERBB2_ENST00000541774.1_Missense_Mutation_p.L740P|ERBB2_ENST00000445658.2_Missense_Mutation_p.L479P			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	755	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		L -> P (in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:15457249}.		axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)	p.L755S(10)|p.L755P(2)|p.L755_S760>A(1)		NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	CATCAAAGTGTTGAGGGAAAAC	0.53	L755S(LN229_CENTRAL_NERVOUS_SYSTEM)	1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)																											p.L755L|p.L755S		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,NS,carcinoma,-1,1|ERBB2,NS,carcinoma,0,20	ERBB2	429	.	13	Substitution - Missense(12)|Complex - insertion inframe(1)	breast(7)|lung(3)|stomach(2)|large_intestine(1)	c.T2263C|c.T2264C						PASS	.																																			SO:0001583	missense	2064	exon19			AAAGTGTTGAGGG|AAGTGTTGAGGGA	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		Exception_encountered	chr17.hg19:g.37880219_37880220delinsCC	ENSP00000269571:p.Leu755Pro	57.0|56.0	0.0	.		60.0	27.0	.	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Silent|Missense_Mutation	SNP	ENST00000269571.5	hg19	CCDS32642.1																																																																																			.	.	.	alt|weak		0.53	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			CC	37880220	TT	CC	37880219	3	2	274	1	0	0	0	0	1	0	0	0	5208	1722	60	3	2337	3	ERBB2	17	37880219	Missense_Mutation	DNP	TT	TCGA-Y8-A894-01A-11D-A35Z-10	27564242	37880219	43314991	77	17395											
RHBDF2	79651	hgsc.bcm.edu	37	chr17	74473013	74473013	+	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	accacgccgaggccgtagtgCcgcttcttccgatcaaaggc	8	7	11	15	5	2	0	1	0	1	0	3	2	3	0	5	2	1	2	5	2	2	3			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr17:74473013C>T	ENST00000313080.4	-	9	1374	c.1101G>A	c.(1099-1101)cgG>cgA	p.R367R	RHBDF2_ENST00000592378.1_5'Flank|RHBDF2_ENST00000591885.1_Silent_p.R338R|RHBDF2_ENST00000389760.4_Silent_p.R338R	NM_024599.5	NP_078875.4	Q6PJF5	RHDF2_HUMAN	rhomboid 5 homolog 2 (Drosophila)	367					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						GGCCGTAGTGCCGCTTCTTCC	0.667																																					p.R367R		Atlas-SNP	.											.	RHBDF2	57	.	0			c.G1101A						PASS	.						37	48	44					17																	74473013		2202	4300	6502	SO:0001819	synonymous_variant	79651	exon9			GTAGTGCCGCTTC	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.1101G>A	chr17.hg19:g.74473013C>T		81.0	0.0	.		135.0	62.0	.	NM_024599	A6NEM3|A8K801|Q5U607|Q5YGQ8|Q9H6E9	Silent	SNP	ENST00000313080.4	hg19	CCDS32743.1																																																																																			.	.	.	none		0.667	RHBDF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450134.1	NM_024599		T	74473013	C	T	74473013	2	4	274	1	0	0	0	0	0	0	0	1	13333	726	26	2		2	RHBDF2	17	74473013	Silent	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10	36592794	74473013	6722197	78	17396											
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385790	58385790	+	Missense_Mutation	SNP	G	G	T																															cacattctccacattcataaGgtcttttcccagtgtgaact																								rs111727691		TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr19:58385790G>T	ENST00000435989.2	-	3	1202	c.968C>A	c.(967-969)cCt>cAt	p.P323H	ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597342.1_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	chr19.hg19:g.58385790G>T	ENSP00000410545:p.Pro323His	48.0	0.0	.		101.0	10.0	.	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	hg19	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	274	1	0	0	0	0	1	0	0	0	18188	1000	35	4	1603	4	ZNF814	19	58385790	Missense_Mutation	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10		58385790	743193	79	17397	180	2									
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385793	58385793	+	Missense_Mutation	SNP	C	C	T																															attctccacattcataaggtCttttcccagtgtgaactctc																								rs113623532		TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr19:58385793C>T	ENST00000435989.2	-	3	1199	c.965G>A	c.(964-966)aGa>aAa	p.R322K	ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597342.1_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	chr19.hg19:g.58385793C>T	ENSP00000410545:p.Arg322Lys	45.0	0.0	.		96.0	11.0	.	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	hg19	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	274	1	0	0	0	0	1	0	0	0	18188	913	32	2	1606	2	ZNF814	19	58385793	Missense_Mutation	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10	3	58385793	743190	80	17398	180	2									
ZNF512B	57473	hgsc.bcm.edu	37	chr20	62595674	62595674	+	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	caccgggctggggtcttaccTttgagcccaaaggtccctga	7	9	12	13	1	1	2	0	2	1	0	2	2	2	2	4	4	2	1	4	4	2	2			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr20:62595674T>C	ENST00000450537.1	-	7	1392	c.1332A>G	c.(1330-1332)aaA>aaG	p.K444K	ZNF512B_ENST00000369888.1_Splice_Site_p.K444K|ZNF512B_ENST00000217130.3_Splice_Site_p.K444K			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	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)			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)					GGGTCTTACCTTTGAGCCCAA	0.587																																					p.K444K		Atlas-SNP	.											.	ZNF512B	72	.	0			c.A1332G						PASS	.						161	176	171					20																	62595674		2203	4300	6503	SO:0001630	splice_region_variant	57473	exon7			CTTACCTTTGAGC	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.1333+1A>G	chr20.hg19:g.62595674T>C		64.0	0.0	.		102.0	45.0	.	NM_020713	Q08AK9|Q9ULM4	Silent	SNP	ENST00000450537.1	hg19	CCDS13548.1																																																																																			.	.	.	none		0.587	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713	Silent	C	62595674	T	C	62595674	5	2	274	1	0	0	0	0	0	0	1	0	17969	1623	56	3	1390	3	ZNF512B	20	62595674	Splice_Site	SNP	T	TCGA-Y8-A894-01A-11D-A35Z-10		62595674	429846	81	17399											
DYRK1A	1859	hgsc.bcm.edu	37	chr21	38878548	38878548	+	Intron	SNP	T	T	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	tgagctcgcacgtggttcatTtgcttgtgtcacctgccatt	5	15	10	11	2	2	1	2	1	0	0	3	1	2	1	2	1	3	4	2	1	0	4			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr21:38878548T>A	ENST00000398960.2	+	10	1746				DYRK1A_ENST00000451934.1_Missense_Mutation_p.L565M|DYRK1A_ENST00000455387.2_Intron|DYRK1A_ENST00000339659.4_Intron|DYRK1A_ENST00000398956.2_Intron|DYRK1A_ENST00000321219.8_Intron|DYRK1A_ENST00000338785.3_Missense_Mutation_p.L565M	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A						circadian rhythm (GO:0007623)|mitotic cell cycle (GO:0000278)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|nervous system development (GO:0007399)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of protein deacetylation (GO:0090312)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|tau protein binding (GO:0048156)			breast(4)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CGTGGTTCATTTGCTTGTGTC	0.567																																					p.L565M	Melanoma(114;464 1602 31203 43785 45765)	Atlas-SNP	.											.	DYRK1A	85	.	0			c.T1693A						PASS	.						89	81	83					21																	38878548		2203	4300	6503	SO:0001627	intron_variant	1859	exon12			GTTCATTTGCTTG	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.1671+22T>A	chr21.hg19:g.38878548T>A		91.0	0.0	.		126.0	67.0	.	NM_101395	O60769|Q92582|Q92810|Q9UNM5	Missense_Mutation	SNP	ENST00000398960.2	hg19	CCDS42925.1	.	.	.	.	.	.	.	.	.	.	T	8.552	0.875746	0.17395	.	.	ENSG00000157540	ENST00000338785;ENST00000451934	T;T	0.59502	0.26;0.26	1.61	-1.09	0.09904	.	.	.	.	.	T	0.57799	0.2078	.	.	.	0.09310	N	1	P	0.47106	0.89	P	0.57425	0.82	T	0.48198	-0.9056	8	0.34782	T	0.22	.	2.9833	0.05960	0.0:0.1875:0.2532:0.5593	.	565	Q13627-5	.	M	565	ENSP00000342690:L565M;ENSP00000416089:L565M	ENSP00000342690:L565M	L	+	1	2	DYRK1A	37800418	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.375000	0.07475	-0.286000	0.09076	0.477000	0.44152	TTG	.	.	.	none		0.567	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1	NM_001396		A	38878548	T	A	38878548	1	1	274	0	1	0	0	0	0	0	0	0	4856	1838	64	5		5	DYRK1A	21	38878548	Intron	SNP	T	TCGA-Y8-A894-01A-11D-A35Z-10		38878548	9251347	82	17400											
GGT5	2687	hgsc.bcm.edu	37	chr22	24622177	24622177	+	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	ctggtggtccccccggccatCgatctgttggcggatgagct	4	10	14	13	3	1	1	0	1	1	0	3	3	2	2	4	5	1	2	4	5	0	1	rs372349468		TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr22:24622177C>T	ENST00000327365.4	-	8	1512	c.1096G>A	c.(1096-1098)Gat>Aat	p.D366N	GGT5_ENST00000418439.2_Missense_Mutation_p.D289N|GGT5_ENST00000263112.7_Missense_Mutation_p.D334N|GGT5_ENST00000398292.3_Missense_Mutation_p.D366N	NM_001099781.1|NM_004121.2	NP_001093251.1|NP_004112.2	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5	366					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						CCCCGGCCATCGATCTGTTGG	0.697																																					p.D366N		Atlas-SNP	.											.	GGT5	61	.	0			c.G1096A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP	0,4406		0,0,2203	31	34	33		1096,1000,1096	1.2	0.1	22		33	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense,missense	GGT5	NM_001099781.1,NM_001099782.1,NM_004121.2	23,23,23	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	366/588,334/555,366/587	24622177	1,13003	2203	4299	6502	SO:0001583	missense	2687	exon8			GGCCATCGATCTG	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.1096G>A	chr22.hg19:g.24622177C>T	ENSP00000330080:p.Asp366Asn	42.0	0.0	.		61.0	32.0	.	NM_001099781	Q53XM9|Q6GMP0|Q96FC1|Q9UFM5	Missense_Mutation	SNP	ENST00000327365.4	hg19	CCDS13825.1	.	.	.	.	.	.	.	.	.	.	C	1.035	-0.680699	0.03353	0.0	1.16E-4	ENSG00000099998	ENST00000327365;ENST00000263112;ENST00000438024;ENST00000398292;ENST00000418439	T;T;T;T	0.23552	1.9;1.9;1.9;1.9	4.51	1.16	0.20824	.	0.478235	0.23454	N	0.048014	T	0.16938	0.0407	L	0.37466	1.105	0.09310	N	1	B;B;B;B;B	0.29766	0.256;0.0;0.005;0.001;0.005	B;B;B;B;B	0.29524	0.103;0.002;0.013;0.005;0.013	T	0.14615	-1.0466	10	0.35671	T	0.21	-24.4893	7.3329	0.26592	0.0:0.6111:0.0:0.3889	.	289;334;366;366;366	E7EUG3;P36269-2;Q53XM9;Q6GMP0;P36269	.;.;.;.;GGT5_HUMAN	N	366;334;281;366;289	ENSP00000330080:D366N;ENSP00000263112:D334N;ENSP00000381340:D366N;ENSP00000392146:D289N	ENSP00000263112:D334N	D	-	1	0	GGT5	22952177	0.044000	0.20184	0.083000	0.20561	0.267000	0.26476	0.520000	0.22878	0.480000	0.27534	-0.440000	0.05779	GAT	.	.	.	weak		0.697	GGT5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320119.1	NM_004121		T	24622177	C	T	24622177	3	4	274	1	0	0	0	0	1	0	0	0	6369	884	31	1	687	1	GGT5	22	24622177	Missense_Mutation	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10		24622177	26682389	83	17401											
INPP5J	27124	hgsc.bcm.edu	37	chr22	31529898	31529898	+	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	agtgaccagcatttcccccaGatctcgctgccttcctcgga	7	10	8	16	2	1	2	0	1	1	1	5	3	3	3	5	1	2	2	5	1	0	2			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chr22:31529898G>T	ENST00000331075.5	+	13	2563		c.e13-1		INPP5J_ENST00000404390.3_Splice_Site|INPP5J_ENST00000412277.2_Splice_Site|INPP5J_ENST00000405300.1_Splice_Site|INPP5J_ENST00000401755.1_Splice_Site|INPP5J_ENST00000400294.2_Splice_Site|INPP5J_ENST00000402238.1_Splice_Site|INPP5J_ENST00000404453.1_Splice_Site	NM_001284285.1	NP_001271214.1	Q15735	PI5PA_HUMAN	inositol polyphosphate-5-phosphatase J						inositol phosphate metabolic process (GO:0043647)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of neuron projection development (GO:0010977)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|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)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:0034485)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(1)	12						ATTTCCCCCAGATCTCGCTGC	0.632																																					.		Atlas-SNP	.											.	INPP5J	94	.	0			c.1411-1G>T						PASS	.						29	33	32					22																	31529898		2138	4236	6374	SO:0001630	splice_region_variant	27124	exon13			CCCCCAGATCTCG	U45975	CCDS46687.1, CCDS63453.1, CCDS63454.1, CCDS63455.1, CCDS74847.1	22q12.2	2008-09-09	2008-09-09	2008-09-09	ENSG00000185133	ENSG00000185133			8956	protein-coding gene	gene with protein product		606481	"phosphatidylinositol (4,5) bisphosphate 5-phosphatase, A"	PIB5PA		10591208	Standard	NM_001284287		Approved	INPP5	uc003aju.4	Q15735	OTTHUMG00000151206	ENST00000331075.5:c.2515-1G>T	chr22.hg19:g.31529898G>T		86.0	0.0	.		105.0	59.0	.	NM_001002837	B3KS54|Q32M61|Q6ZTH6|Q8N902|Q9UDT9	Splice_Site	SNP	ENST00000331075.5	hg19		.	.	.	.	.	.	.	.	.	.	G	11.73	1.726006	0.30593	.	.	ENSG00000185133	ENST00000331075;ENST00000412277;ENST00000400294;ENST00000405300;ENST00000404390;ENST00000402238;ENST00000404453;ENST00000401755	.	.	.	5.54	4.52	0.55395	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.2368	0.59974	0.0781:0.0:0.9219:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	INPP5J	29859898	1.000000	0.71417	0.996000	0.52242	0.284000	0.27059	8.400000	0.90200	1.338000	0.45544	0.655000	0.94253	.	.	.	.	none		0.632	INPP5J-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000321784.1	NM_001002837	Intron	T	31529898	G	T	31529898	5	4	274	1	0	0	0	0	0	0	1	0	7766	956	33	4	1460	4	INPP5J	22	31529898	Splice_Site	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10	6907721	31529898	19774668	84	17402											
CDKL5	6792	hgsc.bcm.edu	37	chrX	18598004	18598004	+	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	tggaagaaatgccaaatggaGttccacctgagaaagtaaaa	18	7	10	6	0	0	2	0	1	0	2	1	5	1	4	3	2	1	2	3	2	6	2			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chrX:18598004G>T	ENST00000379989.3	+	7	604	c.319G>T	c.(319-321)Gtt>Ttt	p.V107F	CDKL5_ENST00000379996.3_Missense_Mutation_p.V107F	NM_001037343.1	NP_001032420.1	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	107	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of Rac GTPase activity (GO:0032855)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite development (GO:0050773)	cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic growth cone (GO:0044294)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|skin(5)|stomach(1)	44	Hepatocellular(33;0.183)					GCCAAATGGAGTTCCACCTGA	0.348																																					p.V107F		Atlas-SNP	.											.	CDKL5	124	.	0			c.G319T						PASS	.						104	96	99					X																	18598004		2203	4300	6503	SO:0001583	missense	6792	exon6			AATGGAGTTCCAC	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.319G>T	chrX.hg19:g.18598004G>T	ENSP00000369325:p.Val107Phe	222.0	0.0	.		310.0	151.0	.	NM_003159	G9B9X4|Q14198|Q5H985|Q8IYC7|Q9UJL6	Missense_Mutation	SNP	ENST00000379989.3	hg19	CCDS14186.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.812212	0.90707	.	.	ENSG00000008086	ENST00000379996;ENST00000379989	T;T	0.64991	-0.13;-0.13	5.98	5.98	0.97165	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.053035	0.85682	D	0.000000	T	0.54255	0.1847	N	0.00738	-1.235	0.58432	D	0.99999	D	0.76494	0.999	D	0.71184	0.972	T	0.77297	-0.2640	10	0.87932	D	0	-18.1427	19.3864	0.94557	0.0:0.0:1.0:0.0	.	107	O76039	CDKL5_HUMAN	F	107	ENSP00000369332:V107F;ENSP00000369325:V107F	ENSP00000369325:V107F	V	+	1	0	CDKL5	18507925	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.869000	0.99810	2.532000	0.85374	0.594000	0.82650	GTT	.	.	.	none		0.348	CDKL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055945.2	NM_003159		T	18598004	G	T	18598004	3	4	274	1	0	0	0	0	1	0	0	0	3159	1029	36	4	337	4	CDKL5	23	18598004	Missense_Mutation	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10		18598004	136672556	85	17403											
YIPF6	286451	hgsc.bcm.edu	37	chrX	67731818	67731818	+	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	tgaatctgttcgcaataccaTcgtaagttagactagttgag	12	13	9	7	2	1	3	0	2	1	1	3	3	1	3	1	0	1	5	1	0	6	6			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chrX:67731818T>A	ENST00000462683.1	+	2	929	c.185T>A	c.(184-186)aTc>aAc	p.I62N	YIPF6_ENST00000374622.2_Intron|YIPF6_ENST00000470730.1_3'UTR	NM_173834.3	NP_776195.2	Q96EC8	YIPF6_HUMAN	Yip1 domain family, member 6	62					intestinal epithelial cell development (GO:0060576)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|urinary_tract(1)	7						CGCAATACCATCGTAAGTTAG	0.383																																					p.I62N		Atlas-SNP	.											.	YIPF6	27	.	0			c.T185A						PASS	.						127	110	116					X																	67731818		2203	4300	6503	SO:0001630	splice_region_variant	286451	exon2			ATACCATCGTAAG	BC012469	CCDS14389.1, CCDS56604.1	Xq13.1	2008-02-05			ENSG00000181704	ENSG00000181704		"Yip1 domain family"	28304	protein-coding gene	gene with protein product						12477932	Standard	NM_173834		Approved	MGC21416, FinGER6	uc004dwz.3	Q96EC8	OTTHUMG00000021745	ENST00000462683.1:c.186+1T>A	chrX.hg19:g.67731818T>A		47.0	0.0	.		49.0	29.0	.	NM_173834	B4E1U7|G5E997|Q5JP08	Missense_Mutation	SNP	ENST00000462683.1	hg19	CCDS14389.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.566668	0.86439	.	.	ENSG00000181704	ENST00000462683	T	0.48836	0.8	5.66	5.66	0.87406	Yip1 domain (1);	0.175871	0.51477	D	0.000083	T	0.70228	0.3200	M	0.86651	2.83	0.80722	D	1	P	0.50528	0.936	P	0.62813	0.907	T	0.75944	-0.3139	10	0.87932	D	0	0.0812	12.7643	0.57383	0.0:0.0:0.0:1.0	.	62	Q96EC8	YIPF6_HUMAN	N	62	ENSP00000417573:I62N	ENSP00000417573:I62N	I	+	2	0	YIPF6	67648543	1.000000	0.71417	0.905000	0.35620	0.893000	0.52053	6.142000	0.71750	1.921000	0.55644	0.427000	0.28365	ATC	.	.	.	none		0.383	YIPF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057016.1	NM_173834	Missense_Mutation	A	67731818	T	A	67731818	5	1	274	1	0	0	0	0	0	0	1	0	17494	1449	50	5	191	5	YIPF6	23	67731818	Splice_Site	SNP	T	TCGA-Y8-A894-01A-11D-A35Z-10	49133814	67731818	87538742	86	17404											
TEX11	56159	hgsc.bcm.edu	37	chrX	69844743	69844743	+	Missense_Mutation	SNP	A	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	aatgttgagctaaatattccAaagctttttctgccacaatt	13	15	5	8	0	1	1	0	1	1	0	2	1	2	1	2	0	3	3	2	0	6	7			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chrX:69844743A>C	ENST00000395889.2	-	20	1840	c.1685T>G	c.(1684-1686)tTg>tGg	p.L562W	TEX11_ENST00000344304.3_Missense_Mutation_p.L562W|TEX11_ENST00000374333.2_Missense_Mutation_p.L547W|TEX11_ENST00000374320.2_Missense_Mutation_p.L237W	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	562					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					TAAATATTCCAAAGCTTTTTC	0.323																																					p.L562W		Atlas-SNP	.											.	TEX11	132	.	0			c.T1685G						PASS	.						128	110	116					X																	69844743		2202	4300	6502	SO:0001583	missense	56159	exon20			TATTCCAAAGCTT	AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"testis expressed sequence 11"			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.1685T>G	chrX.hg19:g.69844743A>C	ENSP00000379226:p.Leu562Trp	92.0	0.0	.		162.0	67.0	.	NM_001003811	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Missense_Mutation	SNP	ENST00000395889.2	hg19	CCDS35323.1	.	.	.	.	.	.	.	.	.	.	A	16.42	3.117493	0.56505	.	.	ENSG00000120498	ENST00000374333;ENST00000395889;ENST00000374320;ENST00000344304	T;T;T;T	0.55588	0.51;0.51;0.51;0.51	3.73	3.73	0.42828	.	0.000000	0.56097	D	0.000027	T	0.67692	0.2920	M	0.76328	2.33	0.29556	N	0.850963	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.64093	-0.6488	9	.	.	.	-4.4846	8.0729	0.30699	1.0:0.0:0.0:0.0	.	547;562	Q8IYF3-3;Q8IYF3	.;TEX11_HUMAN	W	547;562;237;562	ENSP00000363453:L547W;ENSP00000379226:L562W;ENSP00000363440:L237W;ENSP00000340995:L562W	.	L	-	2	0	TEX11	69761468	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	4.154000	0.58125	1.494000	0.48533	0.477000	0.44152	TTG	.	.	.	none		0.323	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1			C	69844743	A	C	69844743	3	2	274	1	0	0	0	0	1	0	0	0	15786	131	5	5	1185	5	TEX11	23	69844743	Missense_Mutation	SNP	A	TCGA-Y8-A894-01A-11D-A35Z-10	2112925	69844743	85425817	87	17405											
MED12	9968	hgsc.bcm.edu	37	chrX	70350038	70350038	+	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	aggatggggaaaacccccagCggcagcgcataaagcgcatt	13	4	13	11	3	0	0	0	0	0	0	0	2	0	2	2	4	4	3	2	4	4	2			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chrX:70350038C>T	ENST00000374080.3	+	28	4053	c.4021C>T	c.(4021-4023)Cgg>Tgg	p.R1341W	MED12_ENST00000333646.6_Missense_Mutation_p.R1341W|MED12_ENST00000374102.1_Missense_Mutation_p.R1341W			Q93074	MED12_HUMAN	mediator complex subunit 12	1341					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)					AAACCCCCAGCGGCAGCGCAT	0.577			"M, S"		uterine leiomyoma		Opitz-Kaveggia Syndrome																														p.R1341W		Atlas-SNP	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	0			c.C4021T						PASS	.						32	30	31					X																	70350038		1982	4146	6128	SO:0001583	missense	9968	exon28			CCCCAGCGGCAGC	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.4021C>T	chrX.hg19:g.70350038C>T	ENSP00000363193:p.Arg1341Trp	317.0	0.0	.		521.0	255.0	.	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Missense_Mutation	SNP	ENST00000374080.3	hg19	CCDS43970.1	.	.	.	.	.	.	.	.	.	.	C	17.18	3.324558	0.60634	.	.	ENSG00000184634	ENST00000333646;ENST00000536756;ENST00000374102;ENST00000374080;ENST00000430072;ENST00000439750	D;D;D;D;T	0.84298	-1.83;-1.83;-1.83;-1.83;1.22	4.93	3.09	0.35607	.	0.060839	0.64402	D	0.000005	D	0.89989	0.6875	M	0.64404	1.975	0.58432	D	0.999992	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.79108	0.992;0.989;0.992;0.982	D	0.89606	0.3838	10	0.87932	D	0	-21.2152	12.2156	0.54404	0.4466:0.5534:0.0:0.0	.	1341;1188;1341;1341	F5H3Y1;Q7Z3Z5;Q93074-3;Q93074	.;.;.;MED12_HUMAN	W	1341;1341;1341;1341;1309;86	ENSP00000333125:R1341W;ENSP00000363215:R1341W;ENSP00000363193:R1341W;ENSP00000414203:R1309W;ENSP00000408388:R86W	ENSP00000333125:R1341W	R	+	1	2	MED12	70266763	1.000000	0.71417	0.993000	0.49108	0.987000	0.75469	0.934000	0.28910	0.539000	0.28788	0.544000	0.68410	CGG	.	.	.	none		0.577	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120		T	70350038	C	T	70350038	3	4	274	1	0	0	0	0	1	0	0	0	9435	759	27	1	4131	1	MED12	23	70350038	Missense_Mutation	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10	505295	70350038	84920522	88	17406											
VGLL1	51442	hgsc.bcm.edu	37	chrX	135630875	135630875	+	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	ggtcccatggctgtgaatcaGttctcaccgtccctggctag	6	11	11	13	1	2	1	2	1	1	0	5	1	4	1	3	3	0	3	3	3	2	2			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chrX:135630875G>C	ENST00000370634.3	+	3	512	c.342G>C	c.(340-342)caG>caC	p.Q114H	MIR934_ENST00000401241.1_RNA	NM_016267.3	NP_057351.1	Q99990	VGLL1_HUMAN	vestigial-like family member 1	114					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Acute lymphoblastic leukemia(192;0.000127)					CTGTGAATCAGTTCTCACCGT	0.587																																					p.Q114H		Atlas-SNP	.											.	VGLL1	41	.	0			c.G342C						PASS	.						267	214	232					X																	135630875		2203	4300	6503	SO:0001583	missense	51442	exon3			GAATCAGTTCTCA	AF137387	CCDS14658.1	Xq26.3	2014-03-03	2014-03-03		ENSG00000102243	ENSG00000102243			20985	protein-coding gene	gene with protein product		300583	"vestigial like 1 (Drosophila)"			10518497	Standard	NM_016267		Approved	TONDU, TDU	uc004ezy.3	Q99990	OTTHUMG00000022509	ENST00000370634.3:c.342G>C	chrX.hg19:g.135630875G>C	ENSP00000359668:p.Gln114His	78.0	0.0	.		112.0	53.0	.	NM_016267	Q5H915	Missense_Mutation	SNP	ENST00000370634.3	hg19	CCDS14658.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	2.891|2.891	-0.229591|-0.229591	0.06022|0.06022	.|.	.|.	ENSG00000102243|ENSG00000102243	ENST00000370634|ENST00000440515	T|.	0.48836|.	0.8|.	5.48|5.48	0.23|0.23	0.15372|0.15372	.|.	1.039970|.	0.07456|.	N|.	0.899768|.	T|T	0.18467|0.18467	0.0443|0.0443	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	B|.	0.09022|.	0.002|.	B|.	0.06405|.	0.002|.	T|T	0.21999|0.21999	-1.0229|-1.0229	10|5	0.13853|.	T|.	0.58|.	1.3295|1.3295	1.6736|1.6736	0.02817|0.02817	0.1814:0.2982:0.3651:0.1553|0.1814:0.2982:0.3651:0.1553	.|.	114|.	Q99990|.	VGLL1_HUMAN|.	H|L	114|79	ENSP00000359668:Q114H|.	ENSP00000359668:Q114H|.	Q|V	+|+	3|1	2|0	VGLL1|VGLL1	135458541|135458541	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.006000|0.006000	0.05464|0.05464	-0.138000|-0.138000	0.10374|0.10374	-0.018000|-0.018000	0.14079|0.14079	0.600000|0.600000	0.82982|0.82982	CAG|GTT	.	.	.	none		0.587	VGLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058493.1	NM_016267		C	135630875	G	C	135630875	3	2	274	1	0	0	0	0	1	0	0	0	17170	1020	36	4	348	4	VGLL1	23	135630875	Missense_Mutation	SNP	G	TCGA-Y8-A894-01A-11D-A35Z-10	65280837	135630875	19639685	89	17407											
BCAP31	10134	hgsc.bcm.edu	37	chrX	152988658	152988658	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaacacaacaaagacctcCgcatagaggaaggtggcaac	17	3	10	11	1	0	2	0	0	0	2	1	3	1	3	2	3	4	3	2	3	6	1			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chrX:152988658C>T	ENST00000345046.6	-	2	449	c.42G>A	c.(40-42)gcG>gcA	p.A14A	BCAP31_ENST00000458587.2_Silent_p.A81A|BCAP31_ENST00000441714.1_Silent_p.A14A|ABCD1_ENST00000218104.3_5'Flank|BCAP31_ENST00000468947.1_5'Flank|ABCD1_ENST00000370129.4_5'Flank	NM_001256447.1	NP_001243376.1	P51572	BAP31_HUMAN	B-cell receptor-associated protein 31	14					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|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 intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|protein localization to endoplasmic reticulum exit site (GO:0070973)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lipid particle (GO:0005811)|membrane (GO:0016020)				endometrium(2)|large_intestine(2)|lung(2)|prostate(1)	7	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CAAAGACCTCCGCATAGAGGA	0.522																																					p.A81A		Atlas-SNP	.											.	BCAP31	33	.	0			c.G243A						PASS	.						103	81	89					X																	152988658		2203	4299	6502	SO:0001819	synonymous_variant	10134	exon2			GACCTCCGCATAG	X81109	CCDS14727.1, CCDS48191.1	Xq28	2005-10-11			ENSG00000185825	ENSG00000185825			16695	protein-coding gene	gene with protein product		300398					Standard	NM_001139441		Approved	DXS1357E, BAP31, 6C6-Ag, CDM	uc011mza.1	P51572	OTTHUMG00000024218	ENST00000345046.6:c.42G>A	chrX.hg19:g.152988658C>T		314.0	1.0	.		473.0	206.0	.	NM_001139457	B3KQ79|D3DWV5|Q13836|Q96CF0	Silent	SNP	ENST00000345046.6	hg19	CCDS14727.1																																																																																			.	.	.	none		0.522	BCAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061071.1	NM_005745		T	152988658	C	T	152988658	2	4	274	1	0	0	0	0	0	0	0	1	1347	639	23	1		1	BCAP31	23	152988658	Silent	SNP	C	TCGA-Y8-A894-01A-11D-A35Z-10	17357783	152988658	2281902	90	17408											
HCFC1	3054	hgsc.bcm.edu	37	chrX	153216353	153216353	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgaagggcccccggccacAggcattgattccggcaacac	9	5	12	15	2	0	2	0	2	0	0	1	2	1	2	4	4	1	3	4	4	2	2			TCGA-Y8-A894-01A-11D-A35Z-10	TCGA-Y8-A894-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5b9ebe3e-3992-4806-934e-c135aa155ff9	a1ac890b-98dd-4011-aee1-b4409f2a659a	g.chrX:153216353A>G	ENST00000310441.7	-	23	6580	c.5614T>C	c.(5614-5616)Tgt>Cgt	p.C1872R	HCFC1_ENST00000354233.3_Missense_Mutation_p.C1803R|HCFC1_ENST00000369984.4_Missense_Mutation_p.C1917R	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	1872	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)					CCCCGGCCACAGGCATTGATT	0.547																																					p.C1872R		Atlas-SNP	.											.	HCFC1	284	.	0			c.T5614C						PASS	.						136	147	143					X																	153216353		1983	4139	6122	SO:0001583	missense	3054	exon23			GGCCACAGGCATT		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.5614T>C	chrX.hg19:g.153216353A>G	ENSP00000309555:p.Cys1872Arg	275.0	0.0	.		360.0	177.0	.	NM_005334	Q6P4G5	Missense_Mutation	SNP	ENST00000310441.7	hg19	CCDS44020.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.0|22.0	4.232555|4.232555	0.79688|0.79688	.|.	.|.	ENSG00000172534|ENSG00000172534	ENST00000310441;ENST00000369984;ENST00000354233|ENST00000444191	T;T;T|.	0.52526|.	0.66;0.66;0.66|.	5.64|5.64	5.64|5.64	0.86602|0.86602	Fibronectin, type III (2);Immunoglobulin-like fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.78253|0.78253	0.4254|0.4254	M|M	0.85630|0.85630	2.765|2.765	0.58432|0.58432	D|D	0.999999|0.999999	D|.	0.71674|.	0.998|.	P|.	0.61940|.	0.896|.	T|T	0.80933|0.80933	-0.1161|-0.1161	10|5	0.87932|.	D|.	0|.	.|.	13.8588|13.8588	0.63548|0.63548	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1872|.	P51610|.	HCFC1_HUMAN|.	R|P	1872;1917;1803|447	ENSP00000309555:C1872R;ENSP00000359001:C1917R;ENSP00000346174:C1803R|.	ENSP00000309555:C1872R|.	C|L	-|-	1|2	0|0	HCFC1|HCFC1	152869547|152869547	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	7.161000|7.161000	0.77505|0.77505	1.917000|1.917000	0.55516|0.55516	0.424000|0.424000	0.28305|0.28305	TGT|CTG	.	.	.	none		0.547	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061099.4	NM_005334		G	153216353	A	G	153216353	3	3	274	1	0	0	0	0	1	0	0	0	6998	188	7	3	509	3	HCFC1	23	153216353	Missense_Mutation	SNP	A	TCGA-Y8-A894-01A-11D-A35Z-10	227695	153216353	2054207	91	17409											
NOL9	79707	hgsc.bcm.edu	37	chr1	6586011	6586011	+	Missense_Mutation	SNP	A	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	ttttctctgatgctccaggaAgtttaaaattgtaatccgtt	10	17	7	7	1	1	1	0	1	1	0	4	2	3	2	2	1	1	4	2	1	4	7			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr1:6586011A>C	ENST00000377705.5	-	12	2044	c.2012T>G	c.(2011-2013)cTt>cGt	p.L671R		NM_024654.4	NP_078930	Q5SY16	NOL9_HUMAN	nucleolar protein 9	671					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)		TGCTCCAGGAAGTTTAAAATT	0.453																																					p.L671R		Atlas-SNP	.											.	NOL9	49	.	0			c.T2012G						PASS	.						147	143	144					1																	6586011		2203	4300	6503	SO:0001583	missense	79707	exon12			CCAGGAAGTTTAA	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.2012T>G	chr1.hg19:g.6586011A>C	ENSP00000366934:p.Leu671Arg	106.0	0.0	.		105.0	47.0	.	NM_024654	Q2NL84|Q4VBY3|Q6P472|Q7L4D6|Q96EE0|Q9H5L4	Missense_Mutation	SNP	ENST00000377705.5	hg19	CCDS80.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.159128	0.78226	.	.	ENSG00000162408	ENST00000377705	T	0.25414	1.8	5.29	5.29	0.74685	.	0.313337	0.30483	N	0.009529	T	0.24736	0.0600	N	0.24115	0.695	0.26608	N	0.972888	P	0.38223	0.623	P	0.46718	0.525	T	0.13818	-1.0495	10	0.31617	T	0.26	-17.1771	11.6254	0.51142	1.0:0.0:0.0:0.0	.	671	Q5SY16	NOL9_HUMAN	R	671	ENSP00000366934:L671R	ENSP00000366934:L671R	L	-	2	0	NOL9	6508598	1.000000	0.71417	0.913000	0.36048	0.959000	0.62525	4.940000	0.63533	2.010000	0.58986	0.533000	0.62120	CTT	.	.	.	none		0.453	NOL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002625.1	NM_024654		C	6586011	A	C	6586011	3	2	275	1	0	0	0	0	1	0	0	0	10535	72	3	5	100	5	NOL9	1	6586011	Missense_Mutation	SNP	A	TCGA-Y8-A895-01A-11D-A35Z-10		6586011	242664610	1	17410											
EVI5	7813	hgsc.bcm.edu	37	chr1	93029241	93029241	+	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	tgatctttcagttccccaatAtactggttagaatcagactt	11	15	6	9	0	3	3	2	1	1	2	4	3	4	3	2	1	1	2	2	1	5	6			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr1:93029241A>C	ENST00000370331.1	-	17	2085	c.2076T>G	c.(2074-2076)taT>taG	p.Y692*	EVI5_ENST00000540033.1_Nonsense_Mutation_p.Y692*|EVI5_ENST00000543509.1_Nonsense_Mutation_p.Y703*|EVI5_ENST00000491940.1_5'UTR	NM_005665.4	NP_005656.4	O60447	EVI5_HUMAN	ecotropic viral integration site 5	692	Dimerization.|Interaction with AURKB and INCENP.|Targeting to the centrosomes.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|retrograde transport, endosome to Golgi (GO:0042147)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|skin(1)	38		all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203)		Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211)		GTTCCCCAATATACTGGTTAG	0.353																																					p.Y692X		Atlas-SNP	.											.	EVI5	94	.	0			c.T2076G						PASS	.						238	220	226					1																	93029241		2203	4300	6503	SO:0001587	stop_gained	7813	exon17			CCCAATATACTGG	AF008915	CCDS30774.1	1p22	2013-07-09			ENSG00000067208	ENSG00000067208			3501	protein-coding gene	gene with protein product	"neuroblastoma stage 4S gene"	602942				9618176	Standard	XM_005271180		Approved	NB4S	uc001dox.3	O60447	OTTHUMG00000010895	ENST00000370331.1:c.2076T>G	chr1.hg19:g.93029241A>C	ENSP00000359356:p.Tyr692*	88.0	0.0	.		60.0	14.0	.	NM_005665	A6NKX8|B9A6J0|Q9H1Y9	Nonsense_Mutation	SNP	ENST00000370331.1	hg19	CCDS30774.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.957523	0.73902	.	.	ENSG00000067208	ENST00000370331;ENST00000540033;ENST00000543509	.	.	.	5.13	-1.66	0.08265	.	0.072010	0.64402	D	0.000020	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	-0.5212	12.6233	0.56616	0.5336:0.0:0.4664:0.0	.	.	.	.	X	692;692;703	.	ENSP00000359356:Y692X	Y	-	3	2	EVI5	92801829	1.000000	0.71417	0.994000	0.49952	0.969000	0.65631	1.810000	0.38932	-0.197000	0.10350	0.260000	0.18958	TAT	.	.	.	none		0.353	EVI5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030047.1	NM_005665		C	93029241	A	C	93029241	4	2	275	1	0	0	0	0	0	1	0	0	5291	456	16	5	364	5	EVI5	1	93029241	Nonsense_Mutation	SNP	A	TCGA-Y8-A895-01A-11D-A35Z-10	86443230	93029241	156221380	2	17411											
SV2A	9900	hgsc.bcm.edu	37	chr1	149882136	149882136	+	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	catcacctctaggaagaaacGggggctctcaggctgcgtgg	9	7	14	11	2	3	1	2	0	2	1	4	2	3	2	1	5	2	2	1	5	3	1			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr1:149882136G>C	ENST00000369146.3	-	5	1565	c.1075C>G	c.(1075-1077)Cgt>Ggt	p.R359G	SV2A_ENST00000369145.1_Missense_Mutation_p.R359G	NM_001278719.1|NM_014849.3	NP_001265648.1|NP_055664.3	Q7L0J3	SV2A_HUMAN	synaptic vesicle glycoprotein 2A	359					cellular calcium ion homeostasis (GO:0006874)|neurotransmitter transport (GO:0006836)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	protein kinase binding (GO:0019901)|receptor activity (GO:0004872)|transmembrane transporter activity (GO:0022857)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(16)|ovary(6)|pancreas(1)|prostate(8)|skin(2)|urinary_tract(2)	55	Breast(34;0.00769)|all_hematologic(923;0.127)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)		Levetiracetam(DB01202)	AGGAAGAAACGGGGGCTCTCA	0.607																																					p.R359G		Atlas-SNP	.											.	SV2A	123	.	0			c.C1075G						PASS	.						39	36	37					1																	149882136		2203	4299	6502	SO:0001583	missense	9900	exon5			AGAAACGGGGGCT	AB018279	CCDS940.1	1q21.2	2008-02-05			ENSG00000159164	ENSG00000159164			20566	protein-coding gene	gene with protein product		185860				7681585, 10611374	Standard	NM_014849		Approved	SV2, KIAA0736	uc001etg.3	Q7L0J3	OTTHUMG00000012209	ENST00000369146.3:c.1075C>G	chr1.hg19:g.149882136G>C	ENSP00000358142:p.Arg359Gly	76.0	0.0	.		68.0	33.0	.	NM_014849	D3DUZ7|O94841|Q5QNX8|Q7Z3L6|Q8NBJ6|Q9BVZ9	Missense_Mutation	SNP	ENST00000369146.3	hg19	CCDS940.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.532504	0.85812	.	.	ENSG00000159164	ENST00000369146;ENST00000369145	T;T	0.79845	-1.31;-1.31	5.09	5.09	0.68999	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.91185	0.7223	H	0.96048	3.76	0.80722	D	1	P	0.51240	0.943	P	0.60117	0.869	D	0.93350	0.6717	10	0.87932	D	0	-13.1584	16.0247	0.80536	0.0:0.0:1.0:0.0	.	359	Q7L0J3	SV2A_HUMAN	G	359	ENSP00000358142:R359G;ENSP00000358141:R359G	ENSP00000358141:R359G	R	-	1	0	SV2A	148148760	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.691000	0.84191	2.638000	0.89438	0.650000	0.86243	CGT	.	.	.	none		0.607	SV2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033754.1			C	149882136	G	C	149882136	3	2	275	1	0	0	0	0	1	0	0	0	15429	1116	39	4	1189	4	SV2A	1	149882136	Missense_Mutation	SNP	G	TCGA-Y8-A895-01A-11D-A35Z-10	56852895	149882136	99368485	3	17412											
SETDB1	9869	hgsc.bcm.edu	37	chr1	150936091	150936091	+	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	attgcaattaaatcaaccaaCatggcctctgtggacaaggg	14	9	9	9	0	2	0	1	0	1	0	2	1	2	1	2	3	3	1	2	3	6	2	rs148647469	byFrequency	TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr1:150936091C>A	ENST00000271640.5	+	20	3733	c.3543C>A	c.(3541-3543)aaC>aaA	p.N1181K	RP11-316M1.12_ENST00000560481.1_RNA|CERS2_ENST00000345896.4_5'Flank|RP11-316M1.12_ENST00000561111.1_RNA|SETDB1_ENST00000368969.4_Missense_Mutation_p.N1181K	NM_001145415.1|NM_012432.3	NP_001138887.1|NP_036564.3	Q15047	SETB1_HUMAN	SET domain, bifurcated 1	1181	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				bone development (GO:0060348)|histone H3-K9 trimethylation (GO:0036124)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)			AATCAACCAACATGGCCTCTG	0.493																																					p.N1181K		Atlas-SNP	.											.	SETDB1	204	.	0			c.C3543A						PASS	.						194	192	192					1																	150936091		2203	4300	6503	SO:0001583	missense	9869	exon20			AACCAACATGGCC	D31891	CCDS972.1, CCDS44217.1, CCDS58026.1	1q21	2013-01-23			ENSG00000143379	ENSG00000143379		"Chromatin-modifying enzymes / K-methyltransferases", "Tudor domain containing"	10761	protein-coding gene	gene with protein product	"tudor domain containing 21"	604396				10343109	Standard	NM_001145415		Approved	KG1T, KIAA0067, ESET, KMT1E, TDRD21	uc001evu.2	Q15047	OTTHUMG00000035003	ENST00000271640.5:c.3543C>A	chr1.hg19:g.150936091C>A	ENSP00000271640:p.Asn1181Lys	223.0	0.0	.		230.0	19.0	.	NM_012432	A6NEW2|Q5SZD8|Q5SZD9|Q5SZE0|Q5SZE7|Q96GM9	Missense_Mutation	SNP	ENST00000271640.5	hg19	CCDS44217.1	.	.	.	.	.	.	.	.	.	.	C	12.41	1.929543	0.34096	.	.	ENSG00000143379	ENST00000271640;ENST00000368969;ENST00000498193	D;D;D	0.81659	-1.52;-1.52;-1.52	5.79	4.88	0.63580	SET domain (3);	0.148570	0.64402	D	0.000009	T	0.47801	0.1465	N	0.19112	0.55	0.80722	D	1	B;P;B	0.43287	0.096;0.802;0.017	B;B;B	0.40477	0.089;0.33;0.025	T	0.59279	-0.7484	10	0.06099	T	0.92	.	11.6707	0.51399	0.0:0.7451:0.1871:0.0678	.	1181;1181;1181	E9PRF4;Q15047-3;Q15047	.;.;SETB1_HUMAN	K	1181	ENSP00000271640:N1181K;ENSP00000357965:N1181K;ENSP00000432348:N1181K	ENSP00000271640:N1181K	N	+	3	2	SETDB1	149202715	1.000000	0.71417	0.998000	0.56505	0.326000	0.28443	1.921000	0.40035	1.454000	0.47793	0.561000	0.74099	AAC	.	C|1.000;T|0.000	.	alt		0.493	SETDB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084717.2			A	150936091	C	A	150936091	3	1	275	1	0	0	0	0	1	0	0	0	14151	477	17	4	3617	4	SETDB1	1	150936091	Missense_Mutation	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10	1053955	150936091	98314530	4	17413											
ZNF687	57592	hgsc.bcm.edu	37	chr1	151259239	151259239	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaaaggcatggaaggcaaaActcccttggacctgtttgct	13	9	10	9	0	0	0	0	0	0	0	1	2	1	2	2	4	2	4	2	4	5	2			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr1:151259239A>G	ENST00000368879.2	+	2	570	c.472A>G	c.(472-474)Act>Gct	p.T158A		NM_020832.1	NP_065883.1	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	158	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	32	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			GGAAGGCAAAACTCCCTTGGA	0.602																																					p.T158A		Atlas-SNP	.											.	ZNF687	94	.	0			c.A472G						PASS	.						58	61	60					1																	151259239		2203	4300	6503	SO:0001583	missense	57592	exon2			GGCAAAACTCCCT		CCDS992.1	1q21.2	2008-05-02			ENSG00000143373	ENSG00000143373			29277	protein-coding gene	gene with protein product		610568				10718198	Standard	NM_020832		Approved	KIAA1441	uc001exq.3	Q8N1G0	OTTHUMG00000012347	ENST00000368879.2:c.472A>G	chr1.hg19:g.151259239A>G	ENSP00000357874:p.Thr158Ala	91.0	0.0	.		74.0	33.0	.	NM_020832	D3DV17|Q68DQ8|Q9H937|Q9P2A7	Missense_Mutation	SNP	ENST00000368879.2	hg19		.	.	.	.	.	.	.	.	.	.	A	0.013	-1.628884	0.00813	.	.	ENSG00000143373	ENST00000336715;ENST00000324048;ENST00000368879	T;T;T	0.00768	5.72;5.72;6.05	4.52	-0.232	0.13082	.	0.511841	0.14589	N	0.310353	T	0.00144	0.0004	N	0.04508	-0.205	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.13388	-1.0511	9	.	.	.	.	5.0653	0.14578	0.5089:0.1725:0.3187:0.0	.	158;158;158	Q8N1G0-2;Q8N1G0;F8WCX2	.;ZN687_HUMAN;.	A	158	ENSP00000336620:T158A;ENSP00000319829:T158A;ENSP00000357874:T158A	.	T	+	1	0	ZNF687	149525863	0.204000	0.23447	0.537000	0.28052	0.887000	0.51463	0.182000	0.16900	0.144000	0.18951	-0.736000	0.03550	ACT	.	.	.	none		0.602	ZNF687-201	KNOWN	basic	protein_coding	protein_coding		NM_020832		G	151259239	A	G	151259239	3	3	275	1	0	0	0	0	1	0	0	0	18104	43	2	3	474	3	ZNF687	1	151259239	Missense_Mutation	SNP	A	TCGA-Y8-A895-01A-11D-A35Z-10	323148	151259239	97991382	5	17414											
CRTC2	200186	hgsc.bcm.edu	37	chr1	153921707	153921707	+	Missense_Mutation	SNP	A	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	gcctgggggctgcccacctgAggactgcactgaacaagact	9	6	13	13	0	0	3	0	2	0	1	0	4	0	4	3	3	3	2	3	3	2	0			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr1:153921707A>C	ENST00000368633.1	-	12	1685	c.1558T>G	c.(1558-1560)Tca>Gca	p.S520A	CRTC2_ENST00000368630.3_Missense_Mutation_p.S200A|DENND4B_ENST00000361217.4_5'Flank	NM_181715.2	NP_859066.1	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2	520					gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|histone H3-K9 acetylation (GO:0043970)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cAMP response element binding protein binding (GO:0008140)			NS(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	27	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			TGCCCACCTGAGGACTGCACT	0.612																																					p.S520A		Atlas-SNP	.											.	CRTC2	58	.	0			c.T1558G						PASS	.						63	61	62					1																	153921707		2203	4300	6503	SO:0001583	missense	200186	exon12			CACCTGAGGACTG	AY360172	CCDS30875.1	1q21.3	2008-02-05			ENSG00000160741	ENSG00000160741			27301	protein-coding gene	gene with protein product		608972				14506290, 14536081	Standard	NM_181715		Approved	TORC2	uc021pab.1	Q53ET0	OTTHUMG00000037156	ENST00000368633.1:c.1558T>G	chr1.hg19:g.153921707A>C	ENSP00000357622:p.Ser520Ala	139.0	0.0	.		100.0	39.0	.	NM_181715	Q6UUV8|Q7Z3X7|Q8N332	Missense_Mutation	SNP	ENST00000368633.1	hg19	CCDS30875.1	.	.	.	.	.	.	.	.	.	.	a	6.444	0.450124	0.12223	.	.	ENSG00000160741	ENST00000368630;ENST00000368633	T;T	0.44083	0.93;2.76	4.71	0.983	0.19767	.	0.524627	0.17767	N	0.162703	T	0.07369	0.0186	L	0.36672	1.1	0.09310	N	1	B;B	0.09022	0.0;0.002	B;B	0.04013	0.0;0.001	T	0.34279	-0.9835	10	0.06365	T	0.9	-0.5344	2.5058	0.04645	0.5691:0.0:0.2289:0.202	.	520;200	Q53ET0;Q5T4K5	CRTC2_HUMAN;.	A	200;520	ENSP00000357619:S200A;ENSP00000357622:S520A	ENSP00000357619:S200A	S	-	1	0	CRTC2	152188331	0.041000	0.20044	0.971000	0.41717	0.514000	0.34195	0.883000	0.28200	0.298000	0.22638	0.370000	0.22315	TCA	.	.	.	none		0.612	CRTC2-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090272.3	NM_181715		C	153921707	A	C	153921707	3	2	275	1	0	0	0	0	1	0	0	0	3902	304	11	5	535	5	CRTC2	1	153921707	Missense_Mutation	SNP	A	TCGA-Y8-A895-01A-11D-A35Z-10	2662468	153921707	95328914	6	17415											
DCAF8	50717	hgsc.bcm.edu	37	chr1	160206968	160206968	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtcaatggtgaaaacaactgCatcttcacctgcagataaga	15	9	8	9	0	3	3	2	1	1	2	3	3	3	3	1	1	4	2	1	1	5	2			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr1:160206968C>T	ENST00000368073.3	-	6	1350	c.916G>A	c.(916-918)Gca>Aca	p.A306T	DCAF8_ENST00000608310.1_Missense_Mutation_p.A460T|DCAF8_ENST00000556710.1_Missense_Mutation_p.A460T|DCAF8_ENST00000368074.1_Missense_Mutation_p.A306T|DCAF8_ENST00000326837.2_Missense_Mutation_p.A306T			Q5TAQ9	DCAF8_HUMAN	DDB1 and CUL4 associated factor 8	306					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						AAAACAACTGCATCTTCACCT	0.408																																					p.A306T		Atlas-SNP	.											.	DCAF8	64	.	0			c.G916A						PASS	.						68	58	62					1																	160206968		2203	4297	6500	SO:0001583	missense	50717	exon6			CAACTGCATCTTC	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.916G>A	chr1.hg19:g.160206968C>T	ENSP00000357052:p.Ala306Thr	321.0	0.0	.		249.0	96.0	.	NM_015726	D3DVE6|Q12839|Q4QQI6|Q53F14|Q66K50|Q68CS7|Q96E00	Missense_Mutation	SNP	ENST00000368073.3	hg19	CCDS1200.1	.	.	.	.	.	.	.	.	.	.	C	36	5.645604	0.96704	.	.	ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000258465	ENST00000368073;ENST00000326837;ENST00000368074;ENST00000555195;ENST00000540855;ENST00000556710	T;T;T;T;T	0.80909	-1.43;-1.43;-1.43;-1.43;-1.43	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	0.64402	U	0.000001	D	0.85801	0.5781	L	0.52364	1.645	0.80722	D	1	D;D	0.71674	0.996;0.998	D;D	0.79784	0.993;0.948	D	0.86237	0.1641	10	0.72032	D	0.01	-8.7602	18.8801	0.92352	0.0:1.0:0.0:0.0	.	460;306	G3V3G9;Q5TAQ9	.;DCAF8_HUMAN	T	306;306;306;460;287;460	ENSP00000357052:A306T;ENSP00000318227:A306T;ENSP00000357053:A306T;ENSP00000451989:A460T;ENSP00000451235:A460T	ENSP00000318227:A306T	A	-	1	0	RP11-574F21.3;DCAF8	158473592	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.768000	0.74980	2.756000	0.94617	0.563000	0.77884	GCA	.	.	.	none		0.408	DCAF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077402.2	NM_015726		T	160206968	C	T	160206968	3	4	275	1	0	0	0	0	1	0	0	0	4278	710	25	2	913	2	DCAF8	1	160206968	Missense_Mutation	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10	6285261	160206968	89043653	7	17416											
CDC42BPA	8476	hgsc.bcm.edu	37	chr1	227182647	227182647	+	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	tagcttcctccagagaattcCctctttaatgcgctgccatt	8	14	6	13	1	1	1	0	0	1	1	4	2	4	1	4	0	3	2	4	0	3	6			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr1:227182647C>A	ENST00000366769.3	-	35	6196	c.4905G>T	c.(4903-4905)agG>agT	p.R1635S	CDC42BPA_ENST00000366764.2_Missense_Mutation_p.R1607S|CDC42BPA_ENST00000535525.1_Missense_Mutation_p.R1615S|CDC42BPA_ENST00000366766.2_Missense_Mutation_p.R1670S|RP5-1087E8.3_ENST00000433837.1_RNA|CDC42BPA_ENST00000334218.5_Missense_Mutation_p.R1697S|CDC42BPA_ENST00000366765.3_Missense_Mutation_p.R1648S|CDC42BPA_ENST00000366767.3_Missense_Mutation_p.R1554S	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)				CAGAGAATTCCCTCTTTAATG	0.527																																					p.R1635S		Atlas-SNP	.											.	CDC42BPA	528	.	0			c.G4905T						PASS	.						127	120	122					1																	227182647		2203	4300	6503	SO:0001583	missense	8476	exon35			GAATTCCCTCTTT	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.4905G>T	chr1.hg19:g.227182647C>A	ENSP00000355731:p.Arg1635Ser	52.0	0.0	.		32.0	14.0	.	NM_003607		Missense_Mutation	SNP	ENST00000366769.3	hg19	CCDS1558.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.01|15.01	2.705914|2.705914	0.48412|0.48412	.|.	.|.	ENSG00000143776|ENSG00000143776	ENST00000448940;ENST00000442054|ENST00000366769;ENST00000366767;ENST00000334218;ENST00000366766;ENST00000366764;ENST00000535525;ENST00000366765	.|T;T;T;T;T;T;T	.|0.70164	.|-0.24;-0.23;-0.46;-0.24;-0.3;-0.3;-0.23	5.09|5.09	3.14|3.14	0.36123|0.36123	.|.	.|0.161634	.|0.52532	.|D	.|0.000075	.|T	.|0.66257	.|0.2771	L|L	0.28014|0.28014	0.82|0.82	0.51482|0.51482	D|D	0.999926|0.999926	.|D;D;D;D;D;D	.|0.69078	.|0.997;0.996;0.997;0.996;0.996;0.991	.|D;D;D;D;D;D	.|0.81914	.|0.993;0.99;0.995;0.99;0.99;0.992	.|T	.|0.62728	.|-0.6793	.|10	.|0.34782	.|T	.|0.22	.|.	7.1194|7.1194	0.25435|0.25435	0.0:0.7042:0.0:0.2958|0.0:0.7042:0.0:0.2958	.|.	.|1615;1607;1554;1635;1670;899	.|F5H5N0;Q5VT25-4;Q5VT25-3;Q5VT25-5;Q5VT25-2;Q5T799	.|.;.;.;.;.;.	X|S	900;964|1635;1554;1697;1670;1607;1615;1648	.|ENSP00000355731:R1635S;ENSP00000355729:R1554S;ENSP00000335341:R1697S;ENSP00000355728:R1670S;ENSP00000355726:R1607S;ENSP00000443275:R1615S;ENSP00000355727:R1648S	.|ENSP00000335341:R1697S	G|R	-|-	1|3	0|2	CDC42BPA|CDC42BPA	225249270|225249270	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	1.345000|1.345000	0.33953|0.33953	1.064000|1.064000	0.40671|0.40671	0.655000|0.655000	0.94253|0.94253	GGA|AGG	.	.	.	none		0.527	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826		A	227182647	C	A	227182647	3	1	275	1	0	0	0	0	1	0	0	0	3074	622	22	4	262	4	CDC42BPA	1	227182647	Missense_Mutation	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10	66975679	227182647	22067974	8	17417											
SMYD3	64754	hgsc.bcm.edu	37	chr1	246021812	246021812	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acttgcctgtatggctccatGgtccgagtaccatagaacaa	11	10	9	11	1	0	1	0	0	0	1	2	2	2	1	4	2	3	3	4	2	5	4			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr1:246021812G>A	ENST00000388985.4	-	10	1061	c.1062C>T	c.(1060-1062)acC>acT	p.T354T	SMYD3_ENST00000541742.1_Silent_p.T295T|SMYD3_ENST00000366517.1_5'UTR|SMYD3_ENST00000490107.1_Silent_p.T295T			Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3	354					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)		ATGGCTCCATGGTCCGAGTAC	0.532																																					p.T354T		Atlas-SNP	.											.	SMYD3	77	.	0			c.C1062T						PASS	.						90	75	80					1																	246021812		2203	4300	6503	SO:0001819	synonymous_variant	64754	exon10			CTCCATGGTCCGA	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.1062C>T	chr1.hg19:g.246021812G>A		125.0	0.0	.		86.0	35.0	.	NM_001167740	A8K0P0|B1AN38|Q86TL8|Q8N5Z6|Q96AI5	Silent	SNP	ENST00000388985.4	hg19	CCDS53486.1																																																																																			.	.	.	none		0.532	SMYD3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022743		A	246021812	G	A	246021812	2	1	275	1	0	0	0	0	0	0	0	1	14836	1335	47	2		2	SMYD3	1	246021812	Silent	SNP	G	TCGA-Y8-A895-01A-11D-A35Z-10	18839165	246021812	3228809	9	17418											
HS1BP3	64342	hgsc.bcm.edu	37	chr2	20840800	20840800	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagacacagcgcaggatctcAttgaacacggctctcctctc	10	8	9	14	2	3	2	1	1	3	1	6	4	3	3	1	2	2	2	1	2	1	1			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr2:20840800A>G	ENST00000304031.3	-	3	364	c.339T>C	c.(337-339)aaT>aaC	p.N113N	HS1BP3_ENST00000406618.3_Silent_p.N113N|HS1BP3_ENST00000402541.1_Silent_p.N113N	NM_022460.3	NP_071905.3	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3	113	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)					GCAGGATCTCATTGAACACGG	0.587																																					p.N113N		Atlas-SNP	.											.	HS1BP3	33	.	0			c.T339C						PASS	.						164	162	163					2																	20840800		2203	4300	6503	SO:0001819	synonymous_variant	64342	exon3			GATCTCATTGAAC		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.339T>C	chr2.hg19:g.20840800A>G		62.0	0.0	.		57.0	21.0	.	NM_022460	B2RAW2|D6W529|Q86VC2|Q8N367	Silent	SNP	ENST00000304031.3	hg19	CCDS1700.1																																																																																			.	.	.	none		0.587	HS1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242863.1	NM_022460		G	20840800	A	G	20840800	2	3	275	1	0	0	0	0	0	0	0	1	7368	214	8	3		3	HS1BP3	2	20840800	Silent	SNP	A	TCGA-Y8-A895-01A-11D-A35Z-10		20840800	222358573	10	17419											
C2orf78	388960	hgsc.bcm.edu	37	chr2	74044108	74044108	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaattgctgaatactatggcTacacaatctaagagctgaga	16	10	8	7	0	1	3	0	2	1	2	1	4	1	3	0	1	4	3	0	1	7	5			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr2:74044108T>C	ENST00000409561.1	+	3	2879	c.2758T>C	c.(2758-2760)Tac>Cac	p.Y920H		NM_001080474.1	NP_001073943.1	A6NCI8	CB078_HUMAN	chromosome 2 open reading frame 78	920										cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|soft_tissue(1)|urinary_tract(1)	34						ATACTATGGCTACACAATCTA	0.343																																					p.Y920H		Atlas-SNP	.											.	C2orf78	150	.	0			c.T2758C						PASS	.						25	27	26					2																	74044108		1850	4087	5937	SO:0001583	missense	388960	exon3			TATGGCTACACAA	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.2758T>C	chr2.hg19:g.74044108T>C	ENSP00000387124:p.Tyr920His	100.0	0.0	.		81.0	26.0	.	NM_001080474		Missense_Mutation	SNP	ENST00000409561.1	hg19	CCDS46338.1	.	.	.	.	.	.	.	.	.	.	T	16.94	3.259717	0.59321	.	.	ENSG00000187833	ENST00000409561;ENST00000342345	T	0.59224	0.28	5.34	5.34	0.76211	.	0.000000	0.44483	D	0.000445	T	0.74696	0.3750	M	0.79475	2.455	0.23916	N	0.996475	D	0.89917	1.0	D	0.81914	0.995	T	0.68957	-0.5272	10	0.87932	D	0	-20.0405	12.0119	0.53293	0.0:0.0:0.0:1.0	.	920	A6NCI8	CB078_HUMAN	H	920;890	ENSP00000387124:Y920H	ENSP00000340692:Y890H	Y	+	1	0	C2orf78	73897616	0.987000	0.35691	0.039000	0.18376	0.004000	0.04260	3.487000	0.53222	2.159000	0.67721	0.455000	0.32223	TAC	.	.	.	none		0.343	C2orf78-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000328083.1	NM_001080474		C	74044108	T	C	74044108	3	2	275	1	0	0	0	0	1	0	0	0	2197	1522	53	3	2768	3	C2orf78	2	74044108	Missense_Mutation	SNP	T	TCGA-Y8-A895-01A-11D-A35Z-10	53203308	74044108	169155265	11	17420											
SEPT10	151011	hgsc.bcm.edu	37	chr2	110323346	110323346	+	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	tttgtctcatttaccttgtaCaacaccccaagggtactggc	9	13	7	12	0	1	0	1	0	1	0	2	0	1	0	3	2	4	2	3	2	5	6			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr2:110323346C>G	ENST00000397712.2	-	7	1231	c.853G>C	c.(853-855)Gta>Cta	p.V285L	SEPT10_ENST00000545389.1_Missense_Mutation_p.V118L|SEPT10_ENST00000334001.6_Missense_Mutation_p.V152L|SEPT10_ENST00000415095.1_Missense_Mutation_p.V285L|SEPT10_ENST00000437928.1_Missense_Mutation_p.V270L|SEPT10_ENST00000468616.1_5'UTR|SEPT10_ENST00000397714.2_Missense_Mutation_p.V262L|SEPT10_ENST00000356688.4_Missense_Mutation_p.V285L	NM_144710.3	NP_653311.1	Q9P0V9	SEP10_HUMAN	septin 10	285	Septin-type G.				cell cycle (GO:0007049)|cell division (GO:0051301)	septin complex (GO:0031105)	GTP binding (GO:0005525)			breast(2)|endometrium(3)|large_intestine(4)|lung(8)|prostate(1)	18						TTACCTTGTACAACACCCCAA	0.428																																					p.V285L		Atlas-SNP	.											.	SEPT10	58	.	0			c.G853C						PASS	.						210	196	201					2																	110323346		1960	4139	6099	SO:0001583	missense	151011	exon7			CTTGTACAACACC	AF146760	CCDS42726.1, CCDS46383.1	2q13	2013-01-21			ENSG00000186522	ENSG00000186522		"Septins"	14349	protein-coding gene	gene with protein product	"sept1-like"	611737				12711328	Standard	NM_144710		Approved	FLJ11619	uc002tew.4	Q9P0V9	OTTHUMG00000154957	ENST00000397712.2:c.853G>C	chr2.hg19:g.110323346C>G	ENSP00000380824:p.Val285Leu	101.0	0.0	.		70.0	26.0	.	NM_144710	B3KRQ9|Q86VP5|Q9HAH6	Missense_Mutation	SNP	ENST00000397712.2	hg19	CCDS46383.1	.	.	.	.	.	.	.	.	.	.	C	18.95	3.731374	0.69189	.	.	ENSG00000186522	ENST00000352314;ENST00000356688;ENST00000397712;ENST00000397714;ENST00000334001;ENST00000437928;ENST00000545389;ENST00000415095;ENST00000493445	T;T;T;T;T;T;T;T	0.57273	0.41;0.41;0.41;0.41;0.41;0.41;0.41;0.41	5.25	5.25	0.73442	.	0.000000	0.64402	D	0.000007	T	0.71846	0.3388	M	0.67953	2.075	0.80722	D	1	B;D;P;B;B;P	0.76494	0.017;0.999;0.869;0.047;0.014;0.869	B;D;B;B;B;B	0.85130	0.051;0.997;0.433;0.086;0.03;0.433	T	0.71487	-0.4578	10	0.46703	T	0.11	.	18.7996	0.92010	0.0:1.0:0.0:0.0	.	152;118;285;285;262;285	B7Z371;B7Z277;A8K7M3;B5ME97;Q9P0V9-3;Q9P0V9	.;.;.;.;.;SEP10_HUMAN	L	243;285;285;262;152;270;118;285;92	ENSP00000349116:V285L;ENSP00000380824:V285L;ENSP00000380826:V262L;ENSP00000334234:V152L;ENSP00000407790:V270L;ENSP00000439364:V118L;ENSP00000396728:V285L;ENSP00000445707:V92L	ENSP00000334234:V152L	V	-	1	0	SEPT10	109680635	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	7.338000	0.79269	2.600000	0.87896	0.650000	0.86243	GTA	.	.	.	none		0.428	SEPT10-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337804.1	NM_144710		G	110323346	C	G	110323346	3	3	275	1	0	0	0	0	1	0	0	0	14073	478	17	4	531	4	SEPT10	2	110323346	Missense_Mutation	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10	36279238	110323346	132876027	12	17421											
MYO1B	4430	hgsc.bcm.edu	37	chr2	192194689	192194689	+	Missense_Mutation	SNP	T	T	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	tttcggatgaagcatacagaTccctacgagatcaagataag	15	9	9	8	2	1	4	1	1	0	3	3	6	2	5	1	1	3	1	1	1	5	4			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr2:192194689T>G	ENST00000392318.3	+	4	527	c.280T>G	c.(280-282)Tcc>Gcc	p.S94A	MYO1B_ENST00000304164.4_Missense_Mutation_p.S94A|MYO1B_ENST00000339514.4_Missense_Mutation_p.S94A|MYO1B_ENST00000392316.1_Missense_Mutation_p.S94A	NM_001130158.1	NP_001123630.1	O43795	MYO1B_HUMAN	myosin IB	94	Myosin motor.				actin filament bundle assembly (GO:0051017)|actin filament organization (GO:0007015)|actin filament-based movement (GO:0030048)|metabolic process (GO:0008152)|post-Golgi vesicle-mediated transport (GO:0006892)	actin filament (GO:0005884)|brush border (GO:0005903)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			NS(1)|central_nervous_system(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(19)|ovary(1)	55			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			AGCATACAGATCCCTACGAGA	0.413																																					p.S94A		Atlas-SNP	.											.	MYO1B	160	.	0			c.T280G						PASS	.						216	213	214					2																	192194689		2203	4300	6503	SO:0001583	missense	4430	exon4			TACAGATCCCTAC	L29138	CCDS2311.1, CCDS46477.1	2q12-q34	2011-09-27			ENSG00000128641	ENSG00000128641		"Myosins / Myosin superfamily : Class I"	7596	protein-coding gene	gene with protein product		606537				8022818, 8449985	Standard	NM_012223		Approved	myr1	uc010fsg.2	O43795	OTTHUMG00000132718	ENST00000392318.3:c.280T>G	chr2.hg19:g.192194689T>G	ENSP00000376132:p.Ser94Ala	121.0	0.0	.		116.0	8.0	.	NM_012223	O43794|Q7Z6L5	Missense_Mutation	SNP	ENST00000392318.3	hg19	CCDS46477.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.163706	0.78226	.	.	ENSG00000128641	ENST00000418908;ENST00000339514;ENST00000439452;ENST00000392318;ENST00000304164;ENST00000438652;ENST00000451437;ENST00000392316	D;D;D;D;D;D;D	0.87256	-2.23;-2.23;-2.23;-2.23;-2.23;-2.23;-2.23	5.76	5.76	0.90799	Myosin head, motor domain (2);	0.124736	0.56097	D	0.000027	D	0.84651	0.5519	N	0.26162	0.8	0.80722	D	1	B;P	0.44627	0.333;0.839	B;P	0.51266	0.326;0.664	T	0.82331	-0.0510	10	0.22706	T	0.39	.	13.5956	0.61987	0.0:0.0:0.0:1.0	.	94;94	O43795;O43795-2	MYO1B_HUMAN;.	A	94	ENSP00000401324:S94A;ENSP00000341903:S94A;ENSP00000376132:S94A;ENSP00000306382:S94A;ENSP00000399459:S94A;ENSP00000388140:S94A;ENSP00000376130:S94A	ENSP00000306382:S94A	S	+	1	0	MYO1B	191902934	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.872000	0.75536	2.189000	0.69895	0.528000	0.53228	TCC	.	.	.	none		0.413	MYO1B-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334774.1	NM_012223		G	192194689	T	G	192194689	3	3	275	1	0	0	0	0	1	0	0	0	10076	1435	50	5	290	5	MYO1B	2	192194689	Missense_Mutation	SNP	T	TCGA-Y8-A895-01A-11D-A35Z-10	81871343	192194689	51004684	13	17422											
C3orf31	132001	hgsc.bcm.edu	37	chr3	11851067	11851067	+	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	tccacatctctgttttttccAggagggtccataatatgatt	9	16	7	9	0	1	1	0	1	1	0	5	2	4	2	3	2	0	1	3	2	2	6			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr3:11851067A>T	ENST00000444133.2	-	6	940	c.798T>A	c.(796-798)ccT>ccA	p.P266P	TAMM41_ENST00000273037.5_Silent_p.P266P|TAMM41_ENST00000455809.1_Silent_p.P266P			Q96BW9	TAM41_HUMAN	TAM41, mitochondrial translocator assembly and maintenance protein, homolog (S. cerevisiae)	266					cardiolipin biosynthetic process (GO:0032049)|CDP-diacylglycerol biosynthetic process (GO:0016024)	extrinsic component of mitochondrial inner membrane (GO:0031314)	phosphatidate cytidylyltransferase activity (GO:0004605)										TGTTTTTTCCAGGAGGGTCCA	0.428																																					p.P266P		Atlas-SNP	.											.	.	.	.	0			c.T798A						PASS	.						134	127	129					3																	11851067		2203	4300	6503	SO:0001819	synonymous_variant	132001	exon6			TTTTCCAGGAGGG		CCDS2607.1, CCDS68345.1	3p25.2	2013-10-18	2011-08-09	2011-08-09	ENSG00000144559	ENSG00000144559			25187	protein-coding gene	gene with protein product		614948	"chromosome 3 open reading frame 31"	C3orf31		19237595	Standard	XM_005264873		Approved	MGC16471, DKFZp434E0519	uc003bwh.3	Q96BW9	OTTHUMG00000129741	ENST00000444133.2:c.798T>A	chr3.hg19:g.11851067A>T		115.0	0.0	.		156.0	38.0	.	NM_138807	B4DIY7|C9J2U4	Silent	SNP	ENST00000444133.2	hg19																																																																																				.	.	.	none		0.428	TAMM41-008	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000339258.2	NM_138807		T	11851067	A	T	11851067	2	4	275	1	0	0	0	0	0	0	0	1	2223	175	7	5		5	C3orf31	3	11851067	Silent	SNP	A	TCGA-Y8-A895-01A-11D-A35Z-10		11851067	186171363	14	17423											
LTF	4057	hgsc.bcm.edu	37	chr3	46477717	46477717	+	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	ggaattcacaggcttccaggAgggctgtgggacacaacaga	12	6	14	9	0	1	1	1	0	0	1	2	4	2	4	1	5	1	2	1	5	2	2			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr3:46477717A>T	ENST00000231751.4	-	17	2397	c.2102T>A	c.(2101-2103)cTc>cAc	p.L701H	LTF_ENST00000417439.1_Missense_Mutation_p.L699H|LTF_ENST00000493056.1_5'Flank|LTF_ENST00000426532.2_Missense_Mutation_p.L657H	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	701					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)		GGCTTCCAGGAGGGCTGTGGG	0.453																																					p.L701H		Atlas-SNP	.											.	LTF	98	.	0			c.T2102A						PASS	.						108	112	110					3																	46477717		2203	4296	6499	SO:0001583	missense	4057	exon17			TCCAGGAGGGCTG		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.2102T>A	chr3.hg19:g.46477717A>T	ENSP00000231751:p.Leu701His	85.0	0.0	.		100.0	50.0	.	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Missense_Mutation	SNP	ENST00000231751.4	hg19	CCDS33747.1	.	.	.	.	.	.	.	.	.	.	A	16.44	3.124032	0.56613	.	.	ENSG00000012223	ENST00000231751;ENST00000426532;ENST00000417439;ENST00000443496	T;T;T;T	0.08193	3.12;3.12;3.12;3.12	5.42	4.22	0.49857	.	0.241563	0.35013	N	0.003507	T	0.33147	0.0853	M	0.93016	3.37	0.44110	D	0.996887	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.70227	0.968;0.911;0.968	T	0.16158	-1.0412	10	0.87932	D	0	-3.841	8.6047	0.33767	0.9111:0.0:0.0889:0.0	.	699;688;701	E7ER44;E7EQB2;P02788	.;.;TRFL_HUMAN	H	701;657;699;688	ENSP00000231751:L701H;ENSP00000405719:L657H;ENSP00000405546:L699H;ENSP00000397427:L688H	ENSP00000231751:L701H	L	-	2	0	LTF	46452721	0.951000	0.32395	0.576000	0.28549	0.698000	0.40448	2.102000	0.41796	0.959000	0.37980	0.533000	0.62120	CTC	.	.	.	none		0.453	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343		T	46477717	A	T	46477717	3	4	275	1	0	0	0	0	1	0	0	0	9086	304	11	5	34	5	LTF	3	46477717	Missense_Mutation	SNP	A	TCGA-Y8-A895-01A-11D-A35Z-10	34626650	46477717	151544713	15	17424											
C3orf63	23272	hgsc.bcm.edu	37	chr3	56680758	56680758	+	Frame_Shift_Del	DEL	T	T	-																															taatccaaagaatgagatgaTctttgctttccagatataat																										TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr3:56680758delT	ENST00000493960.2	-	14	2017	c.2007delA	c.(2005-2007)agafs	p.R669fs	FAM208A_ENST00000355628.5_Frame_Shift_Del_p.R669fs|FAM208A_ENST00000431842.2_Frame_Shift_Del_p.R273fs	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	669							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						AATGAGATGATCTTTGCTTTC	0.343																																					p.S670fs		Atlas-Indel,Pindel	.											.	FAM208A	113	.	0			c.2008delT						PASS	.						138	128	132					3																	56680758		2203	4300	6503	SO:0001589	frameshift_variant	23272	exon14			.	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.2007delA	chr3.hg19:g.56680758delT	ENSP00000417509:p.Arg669fs	110.0	0.0	0		130.0	73.0	0.561538	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Frame_Shift_Del	DEL	ENST00000493960.2	hg19	CCDS46853.1																																																																																			.	.	.	none		0.343	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224		-	56680758	T	-	56680758	7	5	275	1	0	1	0	1	0	0	0	0	2241	1432	50	0	3109	0	C3orf63	3	56680758	Frame_Shift_Del	DEL	T	TCGA-Y8-A895-01A-11D-A35Z-10	10203041	56680758	141341672	16	17425											
MCM2	4171	hgsc.bcm.edu	37	chr3	127335805	127335805	+	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	ctcaagtatattgagaaagtGtccagccgagccatcttcac	12	10	8	11	1	3	1	2	1	1	1	4	3	4	1	3	0	2	1	3	0	4	4			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr3:127335805G>A	ENST00000265056.7	+	10	1861	c.1617G>A	c.(1615-1617)gtG>gtA	p.V539V		NM_004526.2	NP_004517.2	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	539	MCM.				cell cycle (GO:0007049)|cellular response to interleukin-4 (GO:0071353)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|MCM complex (GO:0042555)|microtubule cytoskeleton (GO:0015630)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA replication origin binding (GO:0003688)|metal ion binding (GO:0046872)			ovary(3)|skin(2)|stomach(1)	6						TTGAGAAAGTGTCCAGCCGAG	0.597																																					p.V539V		Atlas-SNP	.											.	MCM2	79	.	0			c.G1617A						PASS	.						68	72	71					3																	127335805		2203	4300	6503	SO:0001819	synonymous_variant	4171	exon10			GAAAGTGTCCAGC	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.1617G>A	chr3.hg19:g.127335805G>A		145.0	0.0	.		166.0	47.0	.	NM_004526	Q14577|Q15023|Q8N2V1|Q969W7|Q96AE1|Q9BRM7	Silent	SNP	ENST00000265056.7	hg19	CCDS3043.1	.	.	.	.	.	.	.	.	.	.	G	10.86	1.469285	0.26423	.	.	ENSG00000073111	ENST00000491422	.	.	.	5.7	3.88	0.44766	.	.	.	.	.	T	0.59348	0.2187	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56763	-0.7925	4	.	.	.	-38.8032	9.3198	0.37957	0.2753:0.0:0.7247:0.0	.	.	.	.	Y	471	.	.	C	+	2	0	MCM2	128818495	0.996000	0.38824	0.979000	0.43373	0.983000	0.72400	0.345000	0.19979	1.379000	0.46325	0.585000	0.79938	TGT	.	.	.	none		0.597	MCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356612.1			A	127335805	G	A	127335805	2	1	275	1	0	0	0	0	0	0	0	1	9393	1364	48	2		2	MCM2	3	127335805	Silent	SNP	G	TCGA-Y8-A895-01A-11D-A35Z-10	70655047	127335805	70686625	17	17426											
TLR1	7096	hgsc.bcm.edu	37	chr4	38799493	38799493	+	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	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-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr4:38799493A>T	ENST00000502213.2	-	3	1189	c.960T>A	c.(958-960)taT>taA	p.Y320*	TLR1_ENST00000308979.2_Nonsense_Mutation_p.Y320*			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.Y320X	GBM(5;216 373 40795 46382)	Atlas-SNP	.											.	TLR1	70	.	0			c.T960A						PASS	.						58	61	60					4																	38799493		2203	4300	6503	SO:0001587	stop_gained	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>A	chr4.hg19:g.38799493A>T	ENSP00000421259:p.Tyr320*	100.0	0.0	.		68.0	22.0	.	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Nonsense_Mutation	SNP	ENST00000502213.2	hg19	CCDS33973.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.155114	0.78114	.	.	ENSG00000174125	ENST00000308979;ENST00000502213	.	.	.	4.79	-4.83	0.03161	.	0.000000	0.56097	D	0.000027	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.9609	0.71156	0.6105:0.0:0.3895:0.0	.	.	.	.	X	320	.	ENSP00000354932:Y320X	Y	-	3	2	TLR1	38475888	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.219000	0.09228	-0.993000	0.03467	-1.832000	0.00591	TAT	.	A|0.999;G|0.001	.	alt		0.413	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3			T	38799493	A	T	38799493	4	4	275	1	0	0	0	0	0	1	0	0	15961	224	8	5	1404	5	TLR1	4	38799493	Nonsense_Mutation	SNP	A	TCGA-Y8-A895-01A-11D-A35Z-10		38799493	152354783	18	17427											
SHISA3	152573	hgsc.bcm.edu	37	chr4	42400345	42400345	+	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	actggagcacccaggcatcaCtgcgcgtaagtgcggggccc	8	5	14	14	3	1	0	1	0	0	0	1	1	1	1	2	4	3	3	2	4	1	1			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr4:42400345C>A	ENST00000319234.4	+	1	490	c.272C>A	c.(271-273)aCt>aAt	p.T91N		NM_001080505.1	NP_001073974.1	A0PJX4	SHSA3_HUMAN	shisa family member 3	91					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	12						CCAGGCATCACTGCGCGTAAG	0.711																																					p.T91N		Atlas-SNP	.											.	SHISA3	27	.	0			c.C272A						PASS	.						6	8	7					4																	42400345		2133	4188	6321	SO:0001583	missense	152573	exon1			GCATCACTGCGCG	BC012029	CCDS33979.1	4p13	2013-07-31	2013-07-31		ENSG00000178343	ENSG00000178343		"Shisa homologs"	25159	protein-coding gene	gene with protein product			"shisa homolog 3 (Xenopus laevis)"				Standard	NM_001080505		Approved	hShisa3	uc003gwp.3	A0PJX4	OTTHUMG00000161043	ENST00000319234.4:c.272C>A	chr4.hg19:g.42400345C>A	ENSP00000326445:p.Thr91Asn	73.0	0.0	.		64.0	29.0	.	NM_001080505	A0PJX3|Q96EQ5	Missense_Mutation	SNP	ENST00000319234.4	hg19	CCDS33979.1	.	.	.	.	.	.	.	.	.	.	C	13.02	2.113082	0.37339	.	.	ENSG00000178343	ENST00000319234	T	0.46451	0.87	4.08	4.08	0.47627	.	0.156884	0.41605	D	0.000850	T	0.30947	0.0781	L	0.34521	1.04	0.33420	D	0.579773	B	0.27498	0.18	B	0.28305	0.088	T	0.37407	-0.9707	10	0.16896	T	0.51	-5.7558	13.2055	0.59793	0.0:0.6802:0.3198:0.0	.	91	A0PJX4	SHSA3_HUMAN	N	91	ENSP00000326445:T91N	ENSP00000326445:T91N	T	+	2	0	SHISA3	42095102	0.988000	0.35896	0.904000	0.35570	0.554000	0.35429	2.805000	0.47939	2.073000	0.62155	0.467000	0.42956	ACT	.	.	.	none		0.711	SHISA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363539.1	NM_001080505		A	42400345	C	A	42400345	3	1	275	1	0	0	0	0	1	0	0	0	14294	565	20	4	274	4	SHISA3	4	42400345	Missense_Mutation	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10	3600852	42400345	148753931	19	17428											
CEP135	9662	hgsc.bcm.edu	37	chr4	56858116	56858116	+	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	atagcttgaaagcgaaaaatAtgaattaaagtctaaagtgt	19	11	8	3	1	1	2	0	2	1	0	1	3	1	2	0	0	2	1	0	0	10	5			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr4:56858116A>T	ENST00000257287.4	+	15	1998	c.1874A>T	c.(1873-1875)tAt>tTt	p.Y625F		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	625					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)					AGCGAAAAATATGAATTAAAG	0.274																																					p.Y625F		Atlas-SNP	.											.	CEP135	115	.	0			c.A1874T						PASS	.						20	22	22					4																	56858116		2158	4284	6442	SO:0001583	missense	9662	exon15			AAAAATATGAATT	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.1874A>T	chr4.hg19:g.56858116A>T	ENSP00000257287:p.Tyr625Phe	515.0	1.0	.		458.0	176.0	.	NM_025009	B2RMY0|O75130|Q58F25|Q9H8H7	Missense_Mutation	SNP	ENST00000257287.4	hg19	CCDS33986.1	.	.	.	.	.	.	.	.	.	.	A	6.409	0.443572	0.12164	.	.	ENSG00000174799	ENST00000257287	T	0.41065	1.01	5.18	1.9	0.25705	.	0.556091	0.21438	N	0.074528	T	0.22936	0.0554	N	0.22421	0.69	0.27898	N	0.939079	B	0.02656	0.0	B	0.06405	0.002	T	0.09400	-1.0676	10	0.34782	T	0.22	.	3.6031	0.08032	0.3009:0.0:0.5027:0.1965	.	625	Q66GS9	CP135_HUMAN	F	625	ENSP00000257287:Y625F	ENSP00000257287:Y625F	Y	+	2	0	CEP135	56552873	0.998000	0.40836	0.999000	0.59377	0.990000	0.78478	0.320000	0.19540	0.530000	0.28619	-0.256000	0.11100	TAT	.	.	.	none		0.274	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009		T	56858116	A	T	56858116	3	4	275	1	0	0	0	0	1	0	0	0	3249	449	16	5	1928	5	CEP135	4	56858116	Missense_Mutation	SNP	A	TCGA-Y8-A895-01A-11D-A35Z-10	14457771	56858116	134296160	20	17429											
NAIP	4671	hgsc.bcm.edu	37	chr5	70316605	70316606	+	5'UTR	INS	-	-	A																															gaagcagtgagaaaatatttINSaaggaactaaaatgcaaaaa																										TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr5:70316605_70316606insA	ENST00000517649.1	-	0	167_168				NAIP_ENST00000508426.2_5'Flank|NAIP_ENST00000523981.1_Frame_Shift_Ins_p.L21fs|NAIP_ENST00000194097.4_5'UTR|NAIP_ENST00000503719.2_Frame_Shift_Ins_p.L21fs	NM_004536.2	NP_004527.2	Q13075	BIRC1_HUMAN	NLR family, apoptosis inhibitory protein						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)		AGAAAATATTTAAGGAACTAAA	0.406																																					p.L21fs		Atlas-Indel,Pindel	.											.	NAIP	38	.	0			c.63_64insT						PASS	.																																			SO:0001623	5_prime_UTR_variant	4671	exon3			.	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.-124->T	chr5.hg19:g.70316607_70316607dupA		214.0	0.0	0		199.0	17.0	0.0854271	NM_022892	B9EG72|E9PHD1|O75857|Q13730|Q59GI6|Q8TDZ4|Q99796	Frame_Shift_Ins	INS	ENST00000517649.1	hg19	CCDS4009.1																																																																																			.	.	.	none		0.406	NAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372649.6	NM_004536		A	70316606	-	A	70316605	6	5	275	0	1	1	1	0	0	0	0	0	10154	1751	61	0		0	NAIP	5	70316605	5'UTR	INS	-	TCGA-Y8-A895-01A-11D-A35Z-10		70316605	110598655	21	17430											
KIF20A	10112	hgsc.bcm.edu	37	chr5	137519054	137519055	+	Splice_Site	INS	-	-	A																															gcaatccctatgtgaaaggtINSaaaggaacatggggaaagct																										TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr5:137519054_137519055insA	ENST00000394894.3	+	8	1253		c.e8+2		KIF20A_ENST00000508792.1_Splice_Site	NM_005733.2	NP_005724.1	O95235	KI20A_HUMAN	kinesin family member 20A						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)			ATGTGAAAGGTAAAGGAACATG	0.515																																					.		Atlas-Indel,Pindel	.											.	KIF20A	53	.	0			c.1027+2->A						PASS	.																																			SO:0001630	splice_region_variant	10112	exon8			.	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.1027+2->A	chr5.hg19:g.137519057_137519057dupA		102.0	0.0	0		99.0	21.0	0.212121	NM_005733	B4DL79|D3DQB6	Splice_Site	INS	ENST00000394894.3	hg19	CCDS4199.1																																																																																			.	.	.	none		0.515	KIF20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251272.1	NM_005733	Intron	A	137519055	-	A	137519054	8	5	275	1	0	1	1	0	0	0	1	0	8293	1652	57	0	1055	0	KIF20A	5	137519054	Splice_Site	INS	-	TCGA-Y8-A895-01A-11D-A35Z-10	67202449	137519054	43396206	22	17431											
GPR151	134391	hgsc.bcm.edu	37	chr5	145894580	145894580	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctttgccagaggagggagagCtgggtttctctttttctggt	5	15	14	7	0	2	2	0	0	2	2	3	4	2	3	1	4	2	2	1	4	0	4			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr5:145894580C>T	ENST00000311104.2	-	1	1173	c.1097G>A	c.(1096-1098)aGc>aAc	p.S366N		NM_194251.2	NP_919227.2	Q8TDV0	GP151_HUMAN	G protein-coupled receptor 151	366						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)			GGAGGGAGAGCTGGGTTTCTC	0.512																																					p.S366N	Pancreas(78;420 1386 18535 37114 49710)	Atlas-SNP	.											.	GPR151	35	.	0			c.G1097A						PASS	.						150	142	145					5																	145894580		2203	4300	6503	SO:0001583	missense	134391	exon1			GGAGAGCTGGGTT	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.1097G>A	chr5.hg19:g.145894580C>T	ENSP00000308733:p.Ser366Asn	102.0	0.0	.		94.0	29.0	.	NM_194251	Q86SN8|Q8NGV2	Missense_Mutation	SNP	ENST00000311104.2	hg19	CCDS34266.1	.	.	.	.	.	.	.	.	.	.	C	2.219	-0.378822	0.05000	.	.	ENSG00000173250	ENST00000311104	T	0.75154	-0.91	6.17	1.22	0.21188	.	0.449653	0.23110	N	0.051804	T	0.50188	0.1601	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.25984	-1.0116	10	0.15952	T	0.53	.	6.8972	0.24262	0.0:0.4445:0.3541:0.2014	.	366	Q8TDV0	GP151_HUMAN	N	366	ENSP00000308733:S366N	ENSP00000308733:S366N	S	-	2	0	GPR151	145874773	0.000000	0.05858	0.003000	0.11579	0.084000	0.17831	0.106000	0.15354	0.138000	0.18790	0.655000	0.94253	AGC	.	.	.	none		0.512	GPR151-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373457.1	NM_194251		T	145894580	C	T	145894580	3	4	275	1	0	0	0	0	1	0	0	0	6664	797	28	2	166	2	GPR151	5	145894580	Missense_Mutation	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10	8375526	145894580	35020680	23	17432											
SLC34A1	6569	hgsc.bcm.edu	37	chr5	176815315	176815316	+	Frame_Shift_Ins	INS	-	-	TGAGTCCC																															accagcattgccactggtgaINStgagtccctgaggaaccaca																										TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr5:176815315_176815316insTGAGTCCC	ENST00000324417.5	+	8	969_970	c.878_879insTGAGTCCC	c.(877-882)gatgagfs	p.-296fs	SLC34A1_ENST00000512593.1_Frame_Shift_Ins_p.-296fs	NM_003052.4	NP_003043.3	Q06495	NPT2A_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 1						arsenate ion transmembrane transport (GO:1901684)|bone remodeling (GO:0046849)|cellular response to metal ion (GO:0071248)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to staurosporine (GO:0072734)|dentinogenesis (GO:0097187)|gentamycin metabolic process (GO:1901128)|glycoprotein metabolic process (GO:0009100)|indole metabolic process (GO:0042431)|ion transport (GO:0006811)|kidney development (GO:0001822)|ossification (GO:0001503)|phosphate ion homeostasis (GO:0055062)|phosphate ion transport (GO:0006817)|positive regulation of membrane potential (GO:0045838)|positive regulation of phosphate transmembrane transport (GO:2000187)|positive regulation of sodium-dependent phosphate transport (GO:2000120)|protein homooligomerization (GO:0051260)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to growth hormone (GO:0060416)|response to lead ion (GO:0010288)|response to magnesium ion (GO:0032026)|response to mercury ion (GO:0046689)|response to potassium ion (GO:0035864)|response to thyroid hormone (GO:0097066)|response to vitamin A (GO:0033189)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|tricarboxylic acid metabolic process (GO:0072350)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|membrane-bounded vesicle (GO:0031988)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|symporter activity (GO:0015293)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCCACTGGTGATGAGTCCCTGA	0.579																																					p.D293fs		Atlas-Indel,Pindel	.											.	SLC34A1	73	.	0			c.878_879insTGAGTCCC						PASS	.																																			SO:0001589	frameshift_variant	6569	exon8			.	L13258	CCDS4418.1, CCDS54953.1	5q35.3	2013-07-17	2013-07-17		ENSG00000131183	ENSG00000131183		"Solute carriers"	11019	protein-coding gene	gene with protein product	"sodium/phosphate co-transporter", "solute carrier family 17 (sodium phosphate), member 2", "Na+-phosphate cotransporter type II"	182309	"solute carrier family 34 (sodium phosphate), member 1"	NPT2, SLC17A2		8327470, 8693007	Standard	NM_003052		Approved	NAPI-3, NPTIIa, SLC11	uc003mgk.4	Q06495	OTTHUMG00000130857	ENST00000324417.5:c.879_886dupTGAGTCCC	chr5.hg19:g.176815316_176815323dupTGAGTCCC	ENSP00000321424:p.Leu296fs	117.0	0.0	0		72.0	13.0	0.180556	NM_003052	B4DPE3	Frame_Shift_Ins	INS	ENST00000324417.5	hg19	CCDS4418.1																																																																																			.	.	.	none		0.579	SLC34A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253431.1	NM_003052		TGAGTCCC	176815316	-	TGAGTCCC	176815315	7	5	275	1	0	1	1	0	0	0	0	0	14580	333	12	0	904	0	SLC34A1	5	176815315	Frame_Shift_Ins	INS	-	TCGA-Y8-A895-01A-11D-A35Z-10	30920735	176815315	4099945	24	17433											
DSP	1832	hgsc.bcm.edu	37	chr6	7578083	7578083	+	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	aacatacctatcaagaggacCatgattcagtccccttctgg	12	10	7	12	0	3	2	2	1	1	1	4	3	4	3	4	2	2	0	4	2	4	4			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr6:7578083C>G	ENST00000379802.3	+	21	3290	c.2949C>G	c.(2947-2949)acC>acG	p.T983T	DSP_ENST00000418664.2_Silent_p.T983T	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	983	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)		TCAAGAGGACCATGATTCAGT	0.453																																					p.T983T		Atlas-SNP	.											.	DSP	306	.	0			c.C2949G						PASS	.						128	122	124					6																	7578083		2203	4300	6503	SO:0001819	synonymous_variant	1832	exon21			GAGGACCATGATT	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.2949C>G	chr6.hg19:g.7578083C>G		57.0	0.0	.		58.0	23.0	.	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	hg19	CCDS4501.1																																																																																			.	.	.	none		0.453	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		G	7578083	C	G	7578083	2	3	275	1	0	0	0	0	0	0	0	1	4783	581	21	4		4	DSP	6	7578083	Silent	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10		7578083	163536984	25	17434											
ZNF76	7629	hgsc.bcm.edu	37	chr6	35262232	35262232	+	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	agacctccttttgtctttcaGgtcacaatcattacctctgg	8	15	6	12	0	5	1	3	0	2	1	6	1	6	1	3	2	1	0	3	2	2	4			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr6:35262232G>A	ENST00000373953.3	+	13	1760		c.e13-1		ZNF76_ENST00000339411.5_Splice_Site|ZNF76_ENST00000440666.2_Splice_Site	NM_003427.3	NP_003418.2	P36508	ZNF76_HUMAN	zinc finger protein 76						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						TTGTCTTTCAGGTCACAATCA	0.512											OREG0017373	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.	Esophageal Squamous(52;92 1039 20612 23956 34676)	Atlas-SNP	.											.	ZNF76	37	.	0			c.1495-1G>A						PASS	.						203	155	171					6																	35262232		2203	4300	6503	SO:0001630	splice_region_variant	7629	exon13			CTTTCAGGTCACA	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.1495-1G>A	chr6.hg19:g.35262232G>A		123.0	0.0	.	854	88.0	23.0	.	NM_003427	Q9BQB2	Splice_Site	SNP	ENST00000373953.3	hg19	CCDS4801.1	.	.	.	.	.	.	.	.	.	.	G	15.58	2.875635	0.51695	.	.	ENSG00000065029	ENST00000373953;ENST00000440666;ENST00000339411;ENST00000498555	.	.	.	5.62	5.62	0.85841	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.846	0.85981	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ZNF76	35370210	1.000000	0.71417	1.000000	0.80357	0.496000	0.33645	8.445000	0.90326	2.648000	0.89879	0.650000	0.86243	.	.	.	.	none		0.512	ZNF76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040279.2	NM_003427	Intron	A	35262232	G	A	35262232	5	1	275	1	0	0	0	0	0	0	1	0	18147	1014	35	2	1540	2	ZNF76	6	35262232	Splice_Site	SNP	G	TCGA-Y8-A895-01A-11D-A35Z-10	27684149	35262232	135852835	26	17435											
DNAH8	1769	hgsc.bcm.edu	37	chr6	38850785	38850785	+	Missense_Mutation	SNP	T	T	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	ggttccaaatgttgacaataTtagaacaaattttttgatag	15	15	7	4	0	0	3	0	2	0	1	1	3	1	3	1	1	1	2	1	1	7	8			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr6:38850785T>G	ENST00000359357.3	+	52	7561	c.7307T>G	c.(7306-7308)aTt>aGt	p.I2436S	DNAH8_ENST00000441566.1_Missense_Mutation_p.I2400S|DNAH8_ENST00000449981.2_Missense_Mutation_p.I2653S			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2436	AAA 3. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						GTTGACAATATTAGAACAAAT	0.338																																					p.I2653S		Atlas-SNP	.											.	DNAH8	1239	.	0			c.T7958G						PASS	.						89	101	97					6																	38850785		2203	4290	6493	SO:0001583	missense	1769	exon54			ACAATATTAGAAC	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.7307T>G	chr6.hg19:g.38850785T>G	ENSP00000352312:p.Ile2436Ser	452.0	1.0	.		408.0	144.0	.	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	T	13.60	2.285225	0.40394	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.18960	2.18;2.18;2.18	5.87	5.87	0.94306	.	0.571036	0.18592	N	0.136716	T	0.14399	0.0348	M	0.62154	1.92	0.29889	N	0.825339	B	0.26318	0.146	B	0.32928	0.155	T	0.10428	-1.0630	10	0.87932	D	0	.	12.0815	0.53673	0.0:0.0685:0.0:0.9315	.	2436	Q96JB1	DYH8_HUMAN	S	2641;2641;2436;2400	ENSP00000333363:I2641S;ENSP00000352312:I2436S;ENSP00000402294:I2400S	ENSP00000333363:I2641S	I	+	2	0	DNAH8	38958763	0.056000	0.20664	0.802000	0.32245	0.693000	0.40251	2.250000	0.43178	2.239000	0.73571	0.528000	0.53228	ATT	.	.	.	none		0.338	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		G	38850785	T	G	38850785	3	3	275	1	0	0	0	0	1	0	0	0	4609	1493	52	5	7505	5	DNAH8	6	38850785	Missense_Mutation	SNP	T	TCGA-Y8-A895-01A-11D-A35Z-10	3588553	38850785	132264282	27	17436											
TFAP2B	7021	hgsc.bcm.edu	37	chr6	50791382	50791382	+	Missense_Mutation	SNP	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	acggcagcggcaagaagtggGttcggaagccggctctctcc	8	6	15	12	4	1	1	0	0	1	1	4	2	2	2	2	5	2	4	2	5	3	1			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr6:50791382G>A	ENST00000393655.3	+	2	513	c.344G>A	c.(343-345)gGt>gAt	p.G115D	TFAP2B_ENST00000489228.1_3'UTR|TFAP2B_ENST00000263046.4_Missense_Mutation_p.G124D	NM_003221.3	NP_003212.2	Q92481	AP2B_HUMAN	transcription factor AP-2 beta (activating enhancer binding protein 2 beta)	115	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)					CAAGAAGTGGGTTCGGAAGCC	0.697																																					p.G115D	Pancreas(116;1373 2332 5475 10752)	Atlas-SNP	.											.	TFAP2B	91	.	0			c.G344A						PASS	.						33	36	35					6																	50791382		2202	4300	6502	SO:0001583	missense	7021	exon2			AAGTGGGTTCGGA	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.344G>A	chr6.hg19:g.50791382G>A	ENSP00000377265:p.Gly115Asp	203.0	0.0	.		268.0	110.0	.	NM_003221	Q5JYX6|Q9NQ63|Q9NU99|Q9UJI7|Q9Y214|Q9Y3K3	Missense_Mutation	SNP	ENST00000393655.3	hg19	CCDS4934.2	.	.	.	.	.	.	.	.	.	.	G	24.7	4.562855	0.86335	.	.	ENSG00000008196	ENST00000393655;ENST00000344788;ENST00000263046	D;D;D	0.82619	-1.63;-1.63;-1.63	5.36	4.49	0.54785	.	0.245560	0.40064	N	0.001183	T	0.67401	0.2889	L	0.41961	1.31	0.58432	D	0.999999	B	0.24186	0.099	B	0.17098	0.017	T	0.69131	-0.5226	10	0.56958	D	0.05	-1.1452	14.0148	0.64517	0.073:0.0:0.927:0.0	.	115	Q92481	AP2B_HUMAN	D	115;113;124	ENSP00000377265:G115D;ENSP00000342252:G113D;ENSP00000263046:G124D	ENSP00000263046:G124D	G	+	2	0	TFAP2B	50899341	1.000000	0.71417	0.885000	0.34714	0.992000	0.81027	6.504000	0.73704	1.278000	0.44430	0.563000	0.77884	GGT	.	.	.	none		0.697	TFAP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040886.3	NM_003221		A	50791382	G	A	50791382	3	1	275	1	0	0	0	0	1	0	0	0	15800	1261	44	2	350	2	TFAP2B	6	50791382	Missense_Mutation	SNP	G	TCGA-Y8-A895-01A-11D-A35Z-10	11940597	50791382	120323685	28	17437											
PHIP	55023	hgsc.bcm.edu	37	chr6	79672856	79672856	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctgccacaattctttcacAttcttcatccctgggattgg	7	15	6	13	0	4	0	2	0	2	0	6	1	6	1	3	2	1	0	3	2	1	5			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr6:79672856A>G	ENST00000275034.4	-	30	3660	c.3493T>C	c.(3493-3495)Tgt>Cgt	p.C1165R	PHIP_ENST00000479165.1_5'UTR|AL356776.1_ENST00000516160.2_RNA	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1165					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)		ATTCTTTCACATTCTTCATCC	0.403																																					p.C1165R		Atlas-SNP	.											.	PHIP	177	.	0			c.T3493C						PASS	.						285	268	274					6																	79672856		2203	4300	6503	SO:0001583	missense	55023	exon30			TTTCACATTCTTC	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.3493T>C	chr6.hg19:g.79672856A>G	ENSP00000275034:p.Cys1165Arg	91.0	0.0	.		96.0	42.0	.	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	hg19	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.626396	0.87560	.	.	ENSG00000146247	ENST00000275034	T	0.17054	2.3	5.89	5.89	0.94794	Bromodomain (3);	0.000000	0.85682	D	0.000000	T	0.42539	0.1207	M	0.89601	3.045	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.998	T	0.53158	-0.8478	9	.	.	.	-15.5431	15.4894	0.75593	1.0:0.0:0.0:0.0	.	1165;1165	A7J992;Q8WWQ0	.;PHIP_HUMAN	R	1165	ENSP00000275034:C1165R	.	C	-	1	0	PHIP	79729575	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.962000	0.93254	2.250000	0.74265	0.455000	0.32223	TGT	.	.	.	none		0.403	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			G	79672856	A	G	79672856	3	3	275	1	0	0	0	0	1	0	0	0	11849	217	8	3	2016	3	PHIP	6	79672856	Missense_Mutation	SNP	A	TCGA-Y8-A895-01A-11D-A35Z-10	28881474	79672856	91442211	29	17438											
BCLAF1	9774	hgsc.bcm.edu	37	chr6	136597062	136597062	+	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	cactcgctatcattttgatcCtaagtgggctttcctctctg	6	16	7	12	1	2	1	1	1	1	0	6	1	4	1	2	1	0	2	2	1	2	5			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr6:136597062C>T	ENST00000531224.1	-	5	1853	c.1601G>A	c.(1600-1602)aGg>aAg	p.R534K	BCLAF1_ENST00000527759.1_Missense_Mutation_p.R532K|BCLAF1_ENST00000353331.4_Missense_Mutation_p.R532K|BCLAF1_ENST00000392348.2_Missense_Mutation_p.R532K|BCLAF1_ENST00000530767.1_Missense_Mutation_p.R361K|BCLAF1_ENST00000527536.1_Missense_Mutation_p.R534K	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	534					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)		CATTTTGATCCTAAGTGGGCT	0.428																																					p.R534K	Colon(142;1534 1789 5427 7063 28491)	Atlas-SNP	.											.	BCLAF1	203	.	0			c.G1601A						PASS	.						210	212	211					6																	136597062		2203	4300	6503	SO:0001583	missense	9774	exon5			TTGATCCTAAGTG	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.1601G>A	chr6.hg19:g.136597062C>T	ENSP00000435210:p.Arg534Lys	96.0	0.0	.		138.0	41.0	.	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	hg19	CCDS5177.1	.	.	.	.	.	.	.	.	.	.	C	13.26	2.184251	0.38609	.	.	ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000530767;ENST00000527759;ENST00000392348;ENST00000529826	T;T;T;T;T;T;T	0.13089	2.62;2.62;2.62;2.62;2.62;2.62;2.62	5.5	5.5	0.81552	.	0.000000	0.64402	D	0.000001	T	0.04998	0.0134	N	0.08118	0	0.80722	D	1	P;B;P;B	0.47350	0.894;0.092;0.894;0.192	P;B;P;B	0.53988	0.739;0.043;0.739;0.123	T	0.19192	-1.0313	10	0.05833	T	0.94	-8.9698	13.0391	0.58889	0.0:0.9261:0.0:0.0739	.	532;532;534;361	Q9NYF8-2;Q9NYF8-3;Q9NYF8;Q9NYF8-4	.;.;BCLF1_HUMAN;.	K	534;532;534;361;532;532;534	ENSP00000435210:R534K;ENSP00000229446:R532K;ENSP00000435441:R534K;ENSP00000436501:R361K;ENSP00000434826:R532K;ENSP00000376159:R532K;ENSP00000431734:R534K	ENSP00000229446:R532K	R	-	2	0	BCLAF1	136638755	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.269000	0.43346	2.747000	0.94245	0.460000	0.39030	AGG	.	.	.	none		0.428	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		T	136597062	C	T	136597062	3	4	275	1	0	0	0	0	1	0	0	0	1383	681	24	2	1197	2	BCLAF1	6	136597062	Missense_Mutation	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10	56924206	136597062	34518005	30	17439											
GRM1	2911	hgsc.bcm.edu	37	chr6	146720170	146720170	+	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	ctccagcgcctcttggttggCctctcctctgcgatgtgcta	3	13	10	15	2	3	0	0	0	3	0	5	1	4	0	4	2	3	2	4	2	1	3			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr6:146720170C>T	ENST00000282753.1	+	7	2230	c.1995C>T	c.(1993-1995)ggC>ggT	p.G665G	GRM1_ENST00000492807.2_Silent_p.G665G|GRM1_ENST00000355289.4_Silent_p.G665G|GRM1_ENST00000392299.2_Silent_p.G665G|GRM1_ENST00000507907.1_Silent_p.G665G|GRM1_ENST00000361719.2_Silent_p.G665G			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	665					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)		TCTTGGTTGGCCTCTCCTCTG	0.522																																					p.G665G		Atlas-SNP	.											.	GRM1	419	.	0			c.C1995T						PASS	.						325	300	308					6																	146720170		2203	4300	6503	SO:0001819	synonymous_variant	2911	exon8			GGTTGGCCTCTCC	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.1995C>T	chr6.hg19:g.146720170C>T		142.0	0.0	.		127.0	58.0	.	NM_000838	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Silent	SNP	ENST00000282753.1	hg19	CCDS5209.1																																																																																			.	.	.	none		0.522	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838		T	146720170	C	T	146720170	2	4	275	1	0	0	0	0	0	0	0	1	6803	726	26	2		2	GRM1	6	146720170	Silent	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10	10123108	146720170	24394897	31	17440											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152675910	152675910	+	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	tacttgctgaaacttttgctCcattagcctcaatttgttca	9	17	5	10	0	2	1	2	1	0	0	3	1	3	1	2	0	5	3	2	0	4	7			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr6:152675910C>G	ENST00000367255.5	-	67	11411	c.10810G>C	c.(10810-10812)Gag>Cag	p.E3604Q	SYNE1_ENST00000341594.5_Missense_Mutation_p.E3575Q|SYNE1_ENST00000265368.4_Missense_Mutation_p.E3604Q|SYNE1_ENST00000423061.1_Missense_Mutation_p.E3611Q|SYNE1_ENST00000448038.1_Missense_Mutation_p.E3611Q	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3604					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)		AACTTTTGCTCCATTAGCCTC	0.488										HNSCC(10;0.0054)																											p.E3611Q		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G10831C						PASS	.						206	181	190					6																	152675910		2203	4300	6503	SO:0001583	missense	23345	exon67			TTTGCTCCATTAG	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.10810G>C	chr6.hg19:g.152675910C>G	ENSP00000356224:p.Glu3604Gln	110.0	0.0	.		91.0	35.0	.	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	hg19	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	15.34	2.803502	0.50315	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.34859	1.34;1.34;1.34;1.34;1.34	5.26	5.26	0.73747	.	0.000000	0.64402	D	0.000017	T	0.47507	0.1449	M	0.66939	2.045	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.71656	0.959;0.959;0.959;0.974	T	0.25257	-1.0137	10	0.25751	T	0.34	.	16.2563	0.82519	0.0:0.8675:0.1325:0.0	.	3604;3604;3604;3611	B7ZBC3;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	Q	3604;3611;3604;3611;3575	ENSP00000356224:E3604Q;ENSP00000396024:E3611Q;ENSP00000265368:E3604Q;ENSP00000390975:E3611Q;ENSP00000341887:E3575Q	ENSP00000265368:E3604Q	E	-	1	0	SYNE1	152717603	1.000000	0.71417	1.000000	0.80357	0.535000	0.34838	5.740000	0.68629	2.607000	0.88179	0.555000	0.69702	GAG	.	.	.	none		0.488	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		G	152675910	C	G	152675910	3	3	275	1	0	0	0	0	1	0	0	0	15457	864	30	4	15976	4	SYNE1	6	152675910	Missense_Mutation	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10	5955740	152675910	18439157	32	17441											
FAM20C	56975	hgsc.bcm.edu	37	chr7	208912	208912	+	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	ctgcagccatgaagtcggggGgcacgcagctgaagctcatc	9	6	14	12	2	1	2	1	2	0	0	3	2	1	2	1	3	4	5	1	3	2	0			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr7:208912G>A	ENST00000313766.5	+	3	1030	c.799G>A	c.(799-801)Ggc>Agc	p.G267S		NM_020223.3	NP_064608.2	Q8IXL6	DMP4_HUMAN	family with sequence similarity 20, member C	267					dentinogenesis (GO:0097187)|enamel mineralization (GO:0070166)|odontoblast differentiation (GO:0071895)|osteoclast maturation (GO:0036179)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|protein phosphorylation (GO:0006468)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of phosphorus metabolic process (GO:0051174)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|lung(2)|urinary_tract(1)	4		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.57e-17)|Epithelial(4;1.26e-16)|all cancers(6;4.79e-14)		GAAGTCGGGGGGCACGCAGCT	0.597																																					p.G267S		Atlas-SNP	.											.	FAM20C	18	.	0			c.G799A						PASS	.						44	52	49					7																	208912		2079	4193	6272	SO:0001583	missense	56975	exon3			TCGGGGGGCACGC	BC040074	CCDS47522.1	7p22.3	2012-11-29			ENSG00000177706	ENSG00000177706			22140	protein-coding gene	gene with protein product	"dentin matrix protein 4"	611061				17369251, 17924334	Standard	NM_020223		Approved	IMAGE:4942737, DKFZp547D065, DMP4	uc003sip.3	Q8IXL6	OTTHUMG00000151401	ENST00000313766.5:c.799G>A	chr7.hg19:g.208912G>A	ENSP00000322323:p.Gly267Ser	117.0	0.0	.		107.0	37.0	.	NM_020223	A4D2Q5|L8B5W8|Q5I0W9|Q7Z4I0|Q9NPT2	Missense_Mutation	SNP	ENST00000313766.5	hg19	CCDS47522.1	.	.	.	.	.	.	.	.	.	.	G	33	5.198539	0.94997	.	.	ENSG00000177706	ENST00000313766	T	0.75704	-0.96	5.1	5.1	0.69264	.	0.802912	0.11006	N	0.610002	D	0.89938	0.6860	M	0.91561	3.22	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89700	0.3904	10	0.87932	D	0	.	17.2657	0.87086	0.0:0.0:1.0:0.0	.	267	Q8IXL6	DMP4_HUMAN	S	267	ENSP00000322323:G267S	ENSP00000322323:G267S	G	+	1	0	FAM20C	303995	1.000000	0.71417	0.850000	0.33497	0.941000	0.58515	8.209000	0.89751	2.369000	0.80426	0.561000	0.74099	GGC	.	.	.	none		0.597	FAM20C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322476.2	NM_020223		A	208912	G	A	208912	3	1	275	1	0	0	0	0	1	0	0	0	5543	1232	43	2	809	2	FAM20C	7	208912	Missense_Mutation	SNP	G	TCGA-Y8-A895-01A-11D-A35Z-10		208912	158929751	33	17442											
RAPGEF5	9771	hgsc.bcm.edu	37	chr7	22200164	22200164	+	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	gtgcattccaagtatcttttGaaattctttcaattcttttt	9	21	4	7	0	4	1	1	1	3	0	5	1	5	1	1	0	1	2	1	0	4	9			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr7:22200164G>A	ENST00000401957.2	-	4	836	c.589C>T	c.(589-591)Caa>Taa	p.Q197*	RAPGEF5_ENST00000344041.6_Nonsense_Mutation_p.Q347*			Q92565	RPGF5_HUMAN	Rap guanine nucleotide exchange factor (GEF) 5	197	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				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						AGTATCTTTTGAAATTCTTTC	0.318																																					p.Q347X		Atlas-SNP	.											.	RAPGEF5	96	.	0			c.C1039T						PASS	.						51	46	48					7																	22200164		1774	3985	5759	SO:0001587	stop_gained	9771	exon14			TCTTTTGAAATTC	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	ENST00000401957.2:c.589C>T	chr7.hg19:g.22200164G>A	ENSP00000384044:p.Gln197*	43.0	0.0	.		71.0	31.0	.	NM_012294	A4D140|Q8IXU5	Nonsense_Mutation	SNP	ENST00000401957.2	hg19		.	.	.	.	.	.	.	.	.	.	G	40	8.118746	0.98662	.	.	ENSG00000136237	ENST00000344041;ENST00000425852;ENST00000258735;ENST00000401957;ENST00000458533	.	.	.	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	.	20.5605	0.99326	0.0:0.0:1.0:0.0	.	.	.	.	X	347;197;197;197;85	.	ENSP00000258735:Q197X	Q	-	1	0	RAPGEF5	22166689	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.518000	0.90559	2.868000	0.98415	0.637000	0.83480	CAA	.	.	.	none		0.318	RAPGEF5-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000326590.2	NM_012294		A	22200164	G	A	22200164	4	1	275	1	0	0	0	0	0	1	0	0	13060	1299	45	2	1205	2	RAPGEF5	7	22200164	Nonsense_Mutation	SNP	G	TCGA-Y8-A895-01A-11D-A35Z-10	21991252	22200164	136938499	34	17443											
TARP	6966	hgsc.bcm.edu	37	chr7	38305038	38305038	+	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	catctgtgttctttgtccagTgacttttctggcaccgttaa	6	17	8	10	1	3	1	0	1	3	0	4	1	4	1	2	1	0	3	2	1	1	5			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr7:38305038T>C	ENST00000443402.2	-	0	241					NM_001003799.1|NM_001003806.1	NP_001003799.1|NP_001003806.1	P0CF51	TRGC1_HUMAN	T cell receptor gamma constant 1							integral component of membrane (GO:0016021)											CTTTGTCCAGTGACTTTTCTG	0.398																																					p.S19S		Atlas-SNP	.											.	.	.	.	0			c.A57G						PASS	.						196	183	187					7																	38305038		1843	4101	5944			0	exon2			GTCCAGTGACTTT	M14996		7p14	2012-02-07			ENSG00000211689	ENSG00000211689		"T cell receptors / TRG locus"	12275	other	T cell receptor gene	"T-cell receptor, gamma, constant region C1"	186970		TCRGC1		2879283	Standard	NG_001336		Approved	C1		P0CF51	OTTHUMG00000155219		chr7.hg19:g.38305038T>C		99.0	0.0	.		160.0	31.0	.	NM_001003806		Silent	SNP	ENST00000443402.2	hg19																																																																																				.	.	.	none		0.398	TRGC1-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	TR_C_gene	TR_C_gene	OTTHUMT00000338825.3	NG_001336		C	38305038	T	C	38305038	1	2	275	0	1	0	0	0	0	0	0	0	15570	1683	59	3		3	TARP	7	38305038	RNA	SNP	T	TCGA-Y8-A895-01A-11D-A35Z-10	16104874	38305038	120833625	35	17444											
C7orf63	79846	hgsc.bcm.edu	37	chr7	89936365	89936368	+	Frame_Shift_Del	DEL	AGCC	AGCC	-																															tgcaaagtgatataattgaaAgccaagcatgccaagacatg																										TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	AGCC	AGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr7:89936365_89936368delAGCC	ENST00000389297.4	+	20	2667_2670	c.2416_2419delAGCC	c.(2416-2421)agccaafs	p.SQ806fs	C7orf63_ENST00000497910.1_Frame_Shift_Del_p.SQ788fs|C7orf63_ENST00000316089.8_Frame_Shift_Del_p.SQ760fs	NM_001039706.2|NM_001160138.1	NP_001034795.2|NP_001153610.1	A5D8W1	CG063_HUMAN		806										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|prostate(3)	37						TATAATTGAAAGCCAAGCATGCCA	0.373																																					p.805_806del		Pindel	.											.	C7orf63	158	.	0			c.2415_2418del						PASS	.																																			SO:0001589	frameshift_variant	79846	exon20			.																												ENST00000389297.4:c.2416_2419delAGCC	chr7.hg19:g.89936365_89936368delAGCC	ENSP00000373948:p.Ser806fs	306.0	0.0	.		329.0	101.0	0.307	NM_001039706	A3KMP9|B4DYW6|B4DZP7|B9EIM7|Q6V705|Q8IY89|Q9H7C2	Frame_Shift_Del	DEL	ENST00000389297.4	hg19	CCDS43613.2																																																																																			.	.	.	none		0.373	C7orf63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139891.4			-	89936368	AGCC	-	89936365	7	5	275	1	0	1	0	1	0	0	0	0	2411	72	3	0	2494	0	C7orf63	7	89936365	Frame_Shift_Del	DEL	AGCC	TCGA-Y8-A895-01A-11D-A35Z-10	51631327	89936365	69202298	36	17445											
TRRAP	8295	hgsc.bcm.edu	37	chr7	98562256	98562256	+	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	aatttctacattttagggacCcttatgatcctcaagtctgc	10	15	6	10	0	3	1	1	1	2	0	4	2	4	2	2	1	2	0	2	1	5	5			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr7:98562256C>A	ENST00000359863.4	+	47	7022	c.6813C>A	c.(6811-6813)acC>acA	p.T2271T	TRRAP_ENST00000446306.3_Silent_p.T2252T|TRRAP_ENST00000355540.3_Silent_p.T2253T	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	2271	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)			TTTTAGGGACCCTTATGATCC	0.438																																					p.T2271T		Atlas-SNP	.											.	TRRAP	863	.	0			c.C6813A						PASS	.						102	97	99					7																	98562256		2203	4300	6503	SO:0001819	synonymous_variant	8295	exon47			AGGGACCCTTATG	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.6813C>A	chr7.hg19:g.98562256C>A		114.0	0.0	.		140.0	84.0	.	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Silent	SNP	ENST00000359863.4	hg19	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	C	5.374	0.254196	0.10185	.	.	ENSG00000196367	ENST00000456197	.	.	.	5.17	-7.53	0.01336	.	.	.	.	.	T	0.35008	0.0917	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39820	-0.9595	4	.	.	.	.	1.8561	0.03179	0.3258:0.1995:0.3247:0.15	.	.	.	.	H	1993	.	.	P	+	2	0	TRRAP	98400192	0.004000	0.15560	0.082000	0.20525	0.804000	0.45430	-1.218000	0.02976	-1.446000	0.01945	-0.717000	0.03617	CCC	.	.	.	none		0.438	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		A	98562256	C	A	98562256	2	1	275	1	0	0	0	0	0	0	0	1	16613	610	22	4		4	TRRAP	7	98562256	Silent	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10	8625891	98562256	60576407	37	17446											
PLAG1	5324	hgsc.bcm.edu	37	chr8	57079249	57079250	+	Frame_Shift_Ins	INS	-	-	A																															aactctcaatttccccctttINSaatggctgttctttttcagg																										TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr8:57079249_57079250insA	ENST00000316981.3	-	5	1534_1535	c.1055_1056insT	c.(1054-1056)ttafs	p.L352fs	PLAG1_ENST00000429357.2_Frame_Shift_Ins_p.L352fs|PLAG1_ENST00000423799.2_Frame_Shift_Ins_p.L270fs	NM_001114634.1|NM_002655.2	NP_001108106.1|NP_002646.2	Q6DJT9	PLAG1_HUMAN	pleiomorphic adenoma gene 1	352	Activates transcription; Inhibition of nuclear import due to lack of NLS and KPNA2 interaction.|Repression domain; contains 3 sumoylation motifs and massively decrease transcription activity.				gland morphogenesis (GO:0022612)|multicellular organism growth (GO:0035264)|negative regulation of gene expression (GO:0010629)|organ growth (GO:0035265)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		CTNNB1/PLAG1(60)|LIFR_ENST00000263409/PLAG1(10)|HAS2/PLAG1(10)|FGFR1_ENST00000447712/PLAG1(28)|COL1A2/PLAG1(3)|CHCHD7/PLAG1(12)|TCEA1_ENST00000521604/PLAG1(3)	breast(3)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(7)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28		all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.125)	Epithelial(17;0.00179)|all cancers(17;0.0125)			TTTCCCCCTTTAATGGCTGTTC	0.426			T	"TCEA1, LIFR, CTNNB1, CHCHD7"	salivary adenoma																																p.L352fs		Atlas-Indel,Pindel	.		Dom	yes		8	8q12	5324	pleiomorphic adenoma gene 1		E	.	PLAG1	123	.	0			c.1056_1057insT						PASS	.																																			SO:0001589	frameshift_variant	5324	exon5			.	U65002	CCDS6165.1, CCDS47860.1	8q12	2010-07-30				ENSG00000181690		"Zinc fingers, C2H2-type"	9045	protein-coding gene	gene with protein product		603026				9268638	Standard	NM_002655		Approved	ZNF912	uc010lyi.3	Q6DJT9		ENST00000316981.3:c.1056dupT	chr8.hg19:g.57079251_57079251dupA	ENSP00000325546:p.Leu352fs	102.0	0.0	0		93.0	40.0	0.430108	NM_002655	B4DLC2|Q59GH8|Q9Y4L2	Frame_Shift_Ins	INS	ENST00000316981.3	hg19	CCDS6165.1																																																																																			.	.	.	none		0.426	PLAG1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378212.1	NM_002655		A	57079250	-	A	57079249	7	5	275	1	0	1	1	0	0	0	0	0	12025	1751	61	0	450	0	PLAG1	8	57079249	Frame_Shift_Ins	INS	-	TCGA-Y8-A895-01A-11D-A35Z-10		57079249	89284773	38	17447											
E2F5	1875	hgsc.bcm.edu	37	chr8	86119659	86119659	+	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	tttatatttatttttgaccaGgtgatacacttttggccatt	9	20	6	6	0	0	2	0	2	0	0	0	2	0	2	2	2	1	0	2	2	4	11			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr8:86119659G>C	ENST00000416274.2	+	5	584		c.e5-1		E2F5_ENST00000521429.1_Splice_Site|E2F5_ENST00000519128.1_Splice_Site|E2F5_ENST00000418930.2_Splice_Site|E2F5_ENST00000256117.5_Splice_Site|E2F5_ENST00000517476.1_Splice_Site	NM_001083588.1|NM_001951.3	NP_001077057.1|NP_001942.2	Q15329	E2F5_HUMAN	E2F transcription factor 5, p130-binding						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 cycle (GO:0051726)|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)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			NS(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)	8						TTTTTGACCAGGTGATACACT	0.383																																					.		Atlas-SNP	.											.	E2F5	31	.	0			c.551-1G>C						PASS	.						39	39	39					8																	86119659		1808	4065	5873	SO:0001630	splice_region_variant	1875	exon5			TGACCAGGTGATA	X86097	CCDS47885.1, CCDS47886.1, CCDS55254.1	8q21.2	2004-01-29			ENSG00000133740	ENSG00000133740			3119	protein-coding gene	gene with protein product		600967				7892279	Standard	NM_001083588		Approved		uc003ycz.4	Q15329	OTTHUMG00000164785	ENST00000416274.2:c.551-1G>C	chr8.hg19:g.86119659G>C		77.0	0.0	.		52.0	15.0	.	NM_001951	E9PBN9|Q16601|Q92756	Splice_Site	SNP	ENST00000416274.2	hg19	CCDS47885.1	.	.	.	.	.	.	.	.	.	.	G	18.95	3.730840	0.69074	.	.	ENSG00000133740	ENST00000418930;ENST00000256117;ENST00000416274;ENST00000517476;ENST00000521429;ENST00000518234	.	.	.	5.98	5.98	0.97165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.4366	0.99092	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	E2F5	86306911	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	7.029000	0.76477	2.843000	0.97960	0.585000	0.79938	.	.	.	.	none		0.383	E2F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380274.1	NM_001951	Intron	C	86119659	G	C	86119659	5	2	275	1	0	0	0	0	0	0	1	0	4872	1014	35	4	568	4	E2F5	8	86119659	Splice_Site	SNP	G	TCGA-Y8-A895-01A-11D-A35Z-10	29040410	86119659	60244363	39	17448											
ANGPT1	284	hgsc.bcm.edu	37	chr8	108509678	108509679	+	IGR	DNP	GA	GA	TC																															gtaggcacattgcccatgttGaatccggttatatcttctcc																										TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr8:108509678_108509679GA>TC								ANGPT1 (160928 upstream) : RNA5SP275 (387042 downstream)														p.Q37K(1)									TGCCCATGTTGAATCCGGTTAT	0.48																																					p.Q37K|p.I36M		Atlas-SNP	.											ANGPT1,rectum,carcinoma,0,1|.	ANGPT1	111	.	1	Substitution - Missense(1)	large_intestine(1)	c.C109A|c.T108G						PASS	.																																			SO:0001628	intergenic_variant	284	exon1			CATGTTGAATCCG|ATGTTGAATCCGG																													chr8.hg19:g.108509678_108509679delinsTC		74.0|75.0	0.0	.		98.0|99.0	38.0|40.0	.	NM_001199859		Missense_Mutation	SNP		hg19																																																																																				.	.	.	none	0	0.48									TC	108509679	GA	TC	108509678	1	4	275	0	1	0	0	0	0	0	0	0	610	1299	45	4		4	ANGPT1	8	108509678	IGR	DNP	GA	TCGA-Y8-A895-01A-11D-A35Z-10	22390019	108509678	37854344	40	17449											
CSMD3	114788	hgsc.bcm.edu	37	chr8	113662424	113662425	+	Frame_Shift_Ins	INS	-	-	T																															gtggatgactccaccagtggINStttttttcgcatagaagggg																										TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr8:113662424_113662425insT	ENST00000297405.5	-	19	3402_3403	c.3158_3159insA	c.(3157-3159)aacfs	p.N1053fs	CSMD3_ENST00000455883.2_Frame_Shift_Ins_p.N949fs|CSMD3_ENST00000343508.3_Frame_Shift_Ins_p.N1013fs|CSMD3_ENST00000352409.3_Frame_Shift_Ins_p.N1053fs	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1053	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						TCCACCAGTGGTTTTTTTCGCA	0.376										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.N1053fs		Atlas-Indel,Pindel	.											.	CSMD3	2325	.	0			c.3159_3160insA						PASS	.																																			SO:0001589	frameshift_variant	114788	exon19			.	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.3159dupA	chr8.hg19:g.113662431_113662431dupT	ENSP00000297405:p.Asn1053fs	228.0	0.0	0		228.0	26.0	0.114035	NM_198123	Q96PZ3	Frame_Shift_Ins	INS	ENST00000297405.5	hg19	CCDS6315.1																																																																																			.	.	.	none		0.376	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113662425	-	T	113662424	7	5	275	1	0	1	1	0	0	0	0	0	3948	1252	44	0	8176	0	CSMD3	8	113662424	Frame_Shift_Ins	INS	-	TCGA-Y8-A895-01A-11D-A35Z-10	5152746	113662424	32701598	41	17450											
SMU1	55234	hgsc.bcm.edu	37	chr9	33048246	33048246	+	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	ctcttttaccagaactgaagCttctgacaatctagatcaca	13	12	5	11	0	4	4	1	2	3	2	4	4	4	4	1	0	3	1	1	0	5	4			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr9:33048246C>A	ENST00000397149.3	-	11	1351	c.1301G>T	c.(1300-1302)aGc>aTc	p.S434I	SMU1_ENST00000536631.1_Missense_Mutation_p.S273I	NM_018225.2	NP_060695.2	Q2TAY7	SMU1_HUMAN	smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans)	434						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)		AGAACTGAAGCTTCTGACAAT	0.448																																					p.S434I		Atlas-SNP	.											.	SMU1	29	.	0			c.G1301T						PASS	.						118	107	111					9																	33048246		2203	4300	6503	SO:0001583	missense	55234	exon11			CTGAAGCTTCTGA	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.1301G>T	chr9.hg19:g.33048246C>A	ENSP00000380336:p.Ser434Ile	90.0	0.0	.		63.0	20.0	.	NM_018225	B4E3L0|Q9BU59|Q9HA96|Q9NVD1	Missense_Mutation	SNP	ENST00000397149.3	hg19	CCDS6534.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.362286	0.82353	.	.	ENSG00000122692	ENST00000397149;ENST00000536631	T;T	0.81415	-1.49;-1.49	5.25	5.25	0.73442	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.036452	0.85682	D	0.000000	D	0.89047	0.6604	M	0.90595	3.13	0.80722	D	1	P;D;P	0.56287	0.737;0.975;0.737	B;P;B	0.53549	0.374;0.729;0.374	D	0.91156	0.4957	10	0.66056	D	0.02	-19.5603	16.6926	0.85326	0.0:1.0:0.0:0.0	.	434;273;434	A0MNN4;B4E3L0;Q2TAY7	.;.;SMU1_HUMAN	I	434;273	ENSP00000380336:S434I;ENSP00000443639:S273I	ENSP00000380336:S434I	S	-	2	0	SMU1	33038246	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.832000	0.62759	2.596000	0.87737	0.591000	0.81541	AGC	.	.	.	none		0.448	SMU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052022.1	NM_018225		A	33048246	C	A	33048246	3	1	275	1	0	0	0	0	1	0	0	0	14830	797	28	4	248	4	SMU1	9	33048246	Missense_Mutation	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10		33048246	108165185	42	17451											
GNA14	9630	hgsc.bcm.edu	37	chr9	80043875	80043875	+	Frame_Shift_Del	DEL	A	A	-																															attcactcagagcaaccaagAaaataatggaggtgacactc																										TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr9:80043875delA	ENST00000341700.6	-	5	1184	c.671delT	c.(670-672)ttcfs	p.F224fs	GNA14_ENST00000464095.1_5'UTR	NM_004297.3	NP_004288.1	O95837	GNA14_HUMAN	guanine nucleotide binding protein (G protein), alpha 14	224					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						AGCAACCAAGAAAATAATGGA	0.502																																					p.F224fs		Atlas-Indel,Pindel	.											.	GNA14	50	.	0			c.672delC						PASS	.						199	188	192					9																	80043875		2203	4300	6503	SO:0001589	frameshift_variant	9630	exon5			.	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.671delT	chr9.hg19:g.80043875delA	ENSP00000365807:p.Phe224fs	122.0	0.0	0		117.0	46.0	0.393162	NM_004297	B1ALW3	Frame_Shift_Del	DEL	ENST00000341700.6	hg19	CCDS6657.1																																																																																			.	.	.	none		0.502	GNA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052759.1			-	80043875	A	-	80043875	7	5	275	1	0	1	0	1	0	0	0	0	6509	246	9	0	408	0	GNA14	9	80043875	Frame_Shift_Del	DEL	A	TCGA-Y8-A895-01A-11D-A35Z-10	46995629	80043875	61169556	43	17452											
FAM13C	220965	hgsc.bcm.edu	37	chr10	61023877	61023877	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tacgacctttagccaaatcaTtcatccatttcaggacttca	12	13	4	12	1	4	0	4	0	0	0	5	2	5	1	3	1	2	0	3	1	3	6			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr10:61023877T>C	ENST00000373868.2	-	9	1079	c.992A>G	c.(991-993)aAt>aGt	p.N331S	FAM13C_ENST00000422313.2_Missense_Mutation_p.N331S|FAM13C_ENST00000419214.2_Intron|FAM13C_ENST00000277705.6_Missense_Mutation_p.N352S|FAM13C_ENST00000442566.3_Missense_Mutation_p.N352S|FAM13C_ENST00000468840.2_Missense_Mutation_p.N248S|FAM13C_ENST00000373867.3_Missense_Mutation_p.N248S|FAM13C_ENST00000435852.2_Missense_Mutation_p.N331S	NM_198215.3	NP_937858.2	Q8NE31	FA13C_HUMAN	family with sequence similarity 13, member C	331										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						AGCCAAATCATTCATCCATTT	0.448																																					p.N331S		Atlas-SNP	.											.	FAM13C	124	.	0			c.A992G						PASS	.						142	128	133					10																	61023877		2203	4300	6503	SO:0001583	missense	220965	exon9			AAATCATTCATCC	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.992A>G	chr10.hg19:g.61023877T>C	ENSP00000362975:p.Asn331Ser	79.0	0.0	.		65.0	23.0	.	NM_198215	B7ZB77|Q5T631|Q6P2M3|Q99787	Missense_Mutation	SNP	ENST00000373868.2	hg19	CCDS7255.1	.	.	.	.	.	.	.	.	.	.	T	12.24	1.878710	0.33162	.	.	ENSG00000148541	ENST00000373867;ENST00000373868;ENST00000442566;ENST00000277705;ENST00000468840;ENST00000435852;ENST00000422313;ENST00000468696	T;T;T;T;T;T;T;T	0.76448	-1.02;-1.02;-1.02;-1.02;-1.02;-1.02;-1.02;-1.02	5.93	4.8	0.61643	.	0.064498	0.64402	N	0.000007	D	0.84786	0.5549	M	0.64997	1.995	0.35420	D	0.793198	D;P;P;D	0.89917	1.0;0.663;0.89;1.0	D;B;P;D	0.85130	0.997;0.286;0.6;0.997	D	0.86877	0.2039	10	0.34782	T	0.22	-23.903	11.962	0.53013	0.0:0.0675:0.0:0.9325	.	331;248;331;331	B7Z2K3;B7ZB77;Q8NE31-2;Q8NE31	.;.;.;FA13C_HUMAN	S	248;331;352;352;248;331;331;109	ENSP00000362974:N248S;ENSP00000362975:N331S;ENSP00000395661:N352S;ENSP00000277705:N352S;ENSP00000423896:N248S;ENSP00000392302:N331S;ENSP00000400241:N331S;ENSP00000445068:N109S	ENSP00000277705:N352S	N	-	2	0	FAM13C	60693883	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.771000	0.55318	1.067000	0.40740	-0.256000	0.11100	AAT	.	.	.	none		0.448	FAM13C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048162.2			C	61023877	T	C	61023877	3	2	275	1	0	0	0	0	1	0	0	0	5458	1493	52	3	789	3	FAM13C	10	61023877	Missense_Mutation	SNP	T	TCGA-Y8-A895-01A-11D-A35Z-10		61023877	74510870	44	17453											
GLUD1	2746	hgsc.bcm.edu	37	chr10	88819991	88819991	+	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	ttggcccattggcaccttcaGcaatgatctgcaagagagtc	10	10	10	11	0	2	2	1	1	1	1	3	3	2	2	2	2	2	3	2	2	2	3			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr10:88819991G>T	ENST00000277865.4	-	9	1301	c.1205C>A	c.(1204-1206)gCt>gAt	p.A402D	GLUD1_ENST00000544149.1_Missense_Mutation_p.A269D|GLUD1_ENST00000537649.1_Missense_Mutation_p.A235D|GLUD1_ENST00000465164.1_5'Flank	NM_005271.3	NP_005262.1	P00367	DHE3_HUMAN	glutamate dehydrogenase 1	402					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamine metabolic process (GO:0006541)|positive regulation of insulin secretion (GO:0032024)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|tricarboxylic acid metabolic process (GO:0072350)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|identical protein binding (GO:0042802)|leucine binding (GO:0070728)|NAD+ binding (GO:0070403)			endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(11)|prostate(1)	22					Hexachlorophene(DB00756)	GGCACCTTCAGCAATGATCTG	0.443																																					p.A402D		Atlas-SNP	.											.	GLUD1	30	.	0			c.C1205A						PASS	.						137	135	136					10																	88819991		2203	4296	6499	SO:0001583	missense	2746	exon9			CCTTCAGCAATGA	M20867	CCDS7382.1	10q23.2	2010-03-17			ENSG00000148672	ENSG00000148672	1.4.1.3		4335	protein-coding gene	gene with protein product		138130		GLUD		2757358	Standard	NM_005271		Approved	GDH	uc001keh.3	P00367	OTTHUMG00000018666	ENST00000277865.4:c.1205C>A	chr10.hg19:g.88819991G>T	ENSP00000277865:p.Ala402Asp	140.0	0.0	.		100.0	37.0	.	NM_005271	B3KV55|B4DGN5|Q5TBU3	Missense_Mutation	SNP	ENST00000277865.4	hg19	CCDS7382.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.996133	0.93167	.	.	ENSG00000148672	ENST00000277865;ENST00000394415;ENST00000537649;ENST00000535802;ENST00000513510;ENST00000544149	D;D;D	0.97186	-4.28;-4.28;-4.28	5.11	5.11	0.69529	Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal (2);NAD(P)-binding domain (1);	0.051018	0.85682	N	0.000000	D	0.99121	0.9697	H	0.98256	4.185	0.80722	D	1	D;D	0.71674	0.994;0.998	D;D	0.70016	0.967;0.967	D	0.99032	1.0821	10	0.72032	D	0.01	.	18.9599	0.92674	0.0:0.0:1.0:0.0	.	269;402	B4DGN5;P00367	.;DHE3_HUMAN	D	402;359;235;101;334;269	ENSP00000277865:A402D;ENSP00000439291:A235D;ENSP00000444732:A269D	ENSP00000277865:A402D	A	-	2	0	GLUD1	88809971	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.414000	0.97362	2.541000	0.85698	0.558000	0.71614	GCT	.	.	.	none		0.443	GLUD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049188.1	NM_005271		T	88819991	G	T	88819991	3	4	275	1	0	0	0	0	1	0	0	0	6483	971	34	4	491	4	GLUD1	10	88819991	Missense_Mutation	SNP	G	TCGA-Y8-A895-01A-11D-A35Z-10	27796114	88819991	46714756	45	17454											
HMX3	340784	hgsc.bcm.edu	37	chr10	124896686	124896686	+	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	aaggagctggactccaagagCccggacgagatcattctgga	12	6	13	10	2	2	2	1	0	1	2	3	7	3	6	2	4	2	1	2	4	2	1			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr10:124896686C>G	ENST00000357878.5	+	2	602	c.513C>G	c.(511-513)agC>agG	p.S171R		NM_001105574.1	NP_001099044.1	A6NHT5	HMX3_HUMAN	H6 family homeobox 3	171					brain development (GO:0007420)|cell differentiation (GO:0030154)|embryo implantation (GO:0007566)|inner ear morphogenesis (GO:0042472)|maternal process involved in female pregnancy (GO:0060135)|neuromuscular process controlling balance (GO:0050885)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			lung(4)	4		all_neural(114;0.0765)|Colorectal(57;0.102)|all_lung(145;0.11)|Lung NSC(174;0.163)		Colorectal(40;0.122)|COAD - Colon adenocarcinoma(40;0.141)		ACTCCAAGAGCCCGGACGAGA	0.682																																					p.S171R		Atlas-SNP	.											.	HMX3	24	.	0			c.C513G						PASS	.						14	17	16					10																	124896686		1934	4150	6084	SO:0001583	missense	340784	exon2			CAAGAGCCCGGAC		CCDS41575.1	10q26.13	2011-06-20	2007-07-09		ENSG00000188620	ENSG00000188620		"Homeoboxes / ANTP class : NKL subclass"	5019	protein-coding gene	gene with protein product		613380	"homeo box (H6 family) 3"				Standard	NM_001105574		Approved	NKX5-1	uc010quc.2	A6NHT5	OTTHUMG00000019199	ENST00000357878.5:c.513C>G	chr10.hg19:g.124896686C>G	ENSP00000350549:p.Ser171Arg	278.0	0.0	.		200.0	72.0	.	NM_001105574	A8MU06	Missense_Mutation	SNP	ENST00000357878.5	hg19	CCDS41575.1	.	.	.	.	.	.	.	.	.	.	C	17.93	3.508747	0.64410	.	.	ENSG00000188620	ENST00000357878	D	0.91894	-2.93	4.52	3.62	0.41486	.	0.000000	0.85682	D	0.000000	D	0.88983	0.6586	L	0.27053	0.805	0.45118	D	0.998134	D	0.65815	0.995	P	0.53185	0.72	D	0.85166	0.0995	10	0.17369	T	0.5	.	12.1028	0.53794	0.0:0.9151:0.0:0.0849	.	171	A6NHT5	HMX3_HUMAN	R	171	ENSP00000350549:S171R	ENSP00000350549:S171R	S	+	3	2	HMX3	124886676	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.512000	0.53407	1.122000	0.41944	0.455000	0.32223	AGC	.	.	.	none		0.682	HMX3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050842.4	XM_291716		G	124896686	C	G	124896686	3	3	275	1	0	0	0	0	1	0	0	0	7255	738	26	4	519	4	HMX3	10	124896686	Missense_Mutation	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10	36076695	124896686	10638061	46	17455											
EPS8L2	64787	hgsc.bcm.edu	37	chr11	720135	720135	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccatccggaagctggtgcAgctgagctccaaggagaaga	11	5	14	11	2	0	3	0	1	0	2	2	5	2	4	3	3	4	4	3	3	3	0			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr11:720135A>G	ENST00000533256.1	+	6	614	c.239A>G	c.(238-240)cAg>cGg	p.Q80R	AP006621.9_ENST00000527021.2_RNA|EPS8L2_ENST00000526198.1_Missense_Mutation_p.Q80R|EPS8L2_ENST00000530636.1_Missense_Mutation_p.Q80R|EPS8L2_ENST00000318562.8_Missense_Mutation_p.Q80R			Q9H6S3	ES8L2_HUMAN	EPS8-like 2	80	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	actin binding (GO:0003779)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|pancreas(1)|prostate(2)|soft_tissue(1)|urinary_tract(1)	13		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.37e-27)|Epithelial(43;2.81e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-20)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AAGCTGGTGCAGCTGAGCTCC	0.622																																					p.Q80R		Atlas-SNP	.											.	EPS8L2	42	.	0			c.A239G						PASS	.						78	59	65					11																	720135		2203	4300	6503	SO:0001583	missense	64787	exon5			TGGTGCAGCTGAG	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.239A>G	chr11.hg19:g.720135A>G	ENSP00000435585:p.Gln80Arg	343.0	0.0	.		238.0	87.0	.	NM_022772	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Missense_Mutation	SNP	ENST00000533256.1	hg19	CCDS31328.1	.	.	.	.	.	.	.	.	.	.	A	16.94	3.261711	0.59431	.	.	ENSG00000177106	ENST00000524763;ENST00000318562;ENST00000533256;ENST00000533500;ENST00000531348;ENST00000530636;ENST00000526198	T;T;T;T;T;T;T	0.30981	1.51;2.0;2.0;1.51;1.51;2.0;1.51	3.81	3.81	0.43845	Phosphotyrosine interaction domain (1);Pleckstrin homology-type (1);Tensin phosphotyrosine-binding domain (1);	0.079131	0.51477	D	0.000096	T	0.36608	0.0973	L	0.49350	1.555	0.37273	D	0.907506	P;P;B	0.45827	0.608;0.867;0.379	B;P;B	0.50082	0.171;0.63;0.171	T	0.36915	-0.9728	10	0.39692	T	0.17	-27.9678	11.9851	0.53142	1.0:0.0:0.0:0.0	.	80;108;80	B7ZKL3;B4DFD2;Q9H6S3	.;.;ES8L2_HUMAN	R	80	ENSP00000435128:Q80R;ENSP00000320828:Q80R;ENSP00000435585:Q80R;ENSP00000433223:Q80R;ENSP00000432765:Q80R;ENSP00000436035:Q80R;ENSP00000436230:Q80R	ENSP00000320828:Q80R	Q	+	2	0	EPS8L2	710135	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.101000	0.50283	1.726000	0.51525	0.418000	0.28097	CAG	.	.	.	none		0.622	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772		G	720135	A	G	720135	3	3	275	1	0	0	0	0	1	0	0	0	5198	188	7	3	253	3	EPS8L2	11	720135	Missense_Mutation	SNP	A	TCGA-Y8-A895-01A-11D-A35Z-10		720135	134286381	47	17456											
HIPK3	10114	hgsc.bcm.edu	37	chr11	33373178	33373178	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcagatgaagagcaagaaagTagttgtgatacggtggatgg	14	9	15	3	1	1	5	1	2	0	3	1	6	1	6	0	3	2	3	0	3	5	3			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr11:33373178T>C	ENST00000303296.4	+	15	3137	c.2832T>C	c.(2830-2832)agT>agC	p.S944S	HIPK3_ENST00000525975.1_Silent_p.S923S|AL122015.1_ENST00000411202.1_RNA|HIPK3_ENST00000456517.1_Silent_p.S923S|HIPK3_ENST00000379016.3_Silent_p.S923S	NM_005734.3	NP_005725.3	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3	944	Interaction with AR. {ECO:0000250}.|Required for localization to nuclear speckles. {ECO:0000250}.|Ser-rich.				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						AGCAAGAAAGTAGTTGTGATA	0.388																																					p.S944S		Atlas-SNP	.											.	HIPK3	92	.	0			c.T2832C						PASS	.						89	87	88					11																	33373178		2202	4298	6500	SO:0001819	synonymous_variant	10114	exon15			AGAAAGTAGTTGT	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.2832T>C	chr11.hg19:g.33373178T>C		276.0	0.0	.		279.0	23.0	.	NM_005734	O14632|Q2PBG4|Q2PBG5|Q92632|Q9HAS2	Silent	SNP	ENST00000303296.4	hg19	CCDS7884.1																																																																																			.	.	.	none		0.388	HIPK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255358.1	NM_005734		C	33373178	T	C	33373178	2	2	275	1	0	0	0	0	0	0	0	1	7125	1635	57	3		3	HIPK3	11	33373178	Silent	SNP	T	TCGA-Y8-A895-01A-11D-A35Z-10	32653043	33373178	101633338	48	17457											
MRPL16	54948	hgsc.bcm.edu	37	chr11	59573911	59573911	+	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	ctttccgtatgcccagcatgTtggcagtggctattcgctca	6	13	10	12	2	1	0	1	0	0	0	3	0	2	0	2	2	2	6	2	2	2	5			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr11:59573911T>A	ENST00000300151.4	-	4	878	c.665A>T	c.(664-666)aAc>aTc	p.N222I		NM_017840.3	NP_060310.1	Q9NX20	RM16_HUMAN	mitochondrial ribosomal protein L16	222					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|endometrium(1)|liver(1)|lung(8)	11						GCCCAGCATGTTGGCAGTGGC	0.502																																					p.N222I		Atlas-SNP	.											.	MRPL16	25	.	0			c.A665T						PASS	.						267	247	254					11																	59573911		2201	4295	6496	SO:0001583	missense	54948	exon4			AGCATGTTGGCAG	AF183428	CCDS7976.1	11q12.1	2012-09-13			ENSG00000166902	ENSG00000166902		"Mitochondrial ribosomal proteins / large subunits"	14476	protein-coding gene	gene with protein product		611829					Standard	NM_017840		Approved	FLJ20484, PNAS-111	uc001noh.2	Q9NX20	OTTHUMG00000167410	ENST00000300151.4:c.665A>T	chr11.hg19:g.59573911T>A	ENSP00000300151:p.Asn222Ile	80.0	0.0	.		82.0	34.0	.	NM_017840	Q9BYD0|Q9HB70	Missense_Mutation	SNP	ENST00000300151.4	hg19	CCDS7976.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.420646	0.83559	.	.	ENSG00000166902	ENST00000300151	T	0.38077	1.16	6.07	4.93	0.64822	.	0.038078	0.85682	N	0.000000	T	0.61800	0.2376	M	0.83774	2.66	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.66360	-0.5943	10	0.87932	D	0	-27.3401	11.7445	0.51811	0.1321:0.0:0.0:0.8679	.	222	Q9NX20	RM16_HUMAN	I	222	ENSP00000300151:N222I	ENSP00000300151:N222I	N	-	2	0	MRPL16	59330487	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.019000	0.88732	1.093000	0.41377	0.533000	0.62120	AAC	.	.	.	none		0.502	MRPL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394521.1	NM_017840		A	59573911	T	A	59573911	3	1	275	1	0	0	0	0	1	0	0	0	9788	1725	60	5	94	5	MRPL16	11	59573911	Missense_Mutation	SNP	T	TCGA-Y8-A895-01A-11D-A35Z-10	26200733	59573911	75432605	49	17458			1	41		2	2	27	N	T_C	8.230506e-05
MRPL16	54948	hgsc.bcm.edu	37	chr11	59573937	59573937	+	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	gtggctattcgctcaaatgtCcaggggttctggttgttacg	6	14	13	8	2	2	0	1	0	1	0	4	0	3	0	1	4	1	5	1	4	3	5			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr11:59573937C>G	ENST00000300151.4	-	4	852	c.639G>C	c.(637-639)tgG>tgC	p.W213C		NM_017840.3	NP_060310.1	Q9NX20	RM16_HUMAN	mitochondrial ribosomal protein L16	213					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|endometrium(1)|liver(1)|lung(8)	11						GCTCAAATGTCCAGGGGTTCT	0.512																																					p.W213C		Atlas-SNP	.											.	MRPL16	25	.	0			c.G639C						PASS	.						286	265	272					11																	59573937		2201	4295	6496	SO:0001583	missense	54948	exon4			AAATGTCCAGGGG	AF183428	CCDS7976.1	11q12.1	2012-09-13			ENSG00000166902	ENSG00000166902		"Mitochondrial ribosomal proteins / large subunits"	14476	protein-coding gene	gene with protein product		611829					Standard	NM_017840		Approved	FLJ20484, PNAS-111	uc001noh.2	Q9NX20	OTTHUMG00000167410	ENST00000300151.4:c.639G>C	chr11.hg19:g.59573937C>G	ENSP00000300151:p.Trp213Cys	80.0	0.0	.		77.0	37.0	.	NM_017840	Q9BYD0|Q9HB70	Missense_Mutation	SNP	ENST00000300151.4	hg19	CCDS7976.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.421247	0.83559	.	.	ENSG00000166902	ENST00000300151	T	0.27557	1.66	6.07	6.07	0.98685	.	0.049798	0.85682	D	0.000000	T	0.58466	0.2124	M	0.77820	2.39	0.80722	D	1	D	0.89917	1.0	D	0.65987	0.94	T	0.59451	-0.7452	10	0.87932	D	0	-13.0683	19.222	0.93801	0.0:1.0:0.0:0.0	.	213	Q9NX20	RM16_HUMAN	C	213	ENSP00000300151:W213C	ENSP00000300151:W213C	W	-	3	0	MRPL16	59330513	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.797000	0.85911	2.884000	0.98904	0.655000	0.94253	TGG	.	.	.	none		0.512	MRPL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394521.1	NM_017840		G	59573937	C	G	59573937	3	3	275	1	0	0	0	0	1	0	0	0	9788	856	30	4	120	4	MRPL16	11	59573937	Missense_Mutation	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10	26	59573937	75432579	50	17459			1	41		2	2	27	N	T_C	8.230506e-05
BEST1	7439	hgsc.bcm.edu	37	chr11	61730245	61730245	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaggaaaactgtggagtttaAcctgacggatatgccagaga	14	8	13	6	1	0	2	0	1	0	1	0	7	0	5	2	3	3	1	2	3	4	3			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr11:61730245A>G	ENST00000378043.4	+	10	2262	c.1619A>G	c.(1618-1620)aAc>aGc	p.N540S	FTH1_ENST00000529631.1_Intron|BEST1_ENST00000378042.3_Missense_Mutation_p.N453S|BEST1_ENST00000534553.1_3'UTR|BEST1_ENST00000449131.2_Missense_Mutation_p.N480S|FTH1_ENST00000529191.1_Intron|BEST1_ENST00000301774.9_Missense_Mutation_p.N168S	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1	540					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						GTGGAGTTTAACCTGACGGAT	0.463																																					p.N540S		Atlas-SNP	.											.	BEST1	85	.	0			c.A1619G						PASS	.						117	121	119					11																	61730245		2202	4299	6501	SO:0001583	missense	7439	exon10			AGTTTAACCTGAC	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.1619A>G	chr11.hg19:g.61730245A>G	ENSP00000367282:p.Asn540Ser	181.0	0.0	.		124.0	36.0	.	NM_004183	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Missense_Mutation	SNP	ENST00000378043.4	hg19	CCDS31580.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.735650	0.89482	.	.	ENSG00000167995	ENST00000378043;ENST00000378042;ENST00000301774;ENST00000449131	D;D;T;D	0.97976	-4.57;-4.46;-0.84;-4.64	5.16	3.86	0.44501	.	0.843087	0.10155	N	0.709046	D	0.93943	0.8061	L	0.32530	0.975	0.80722	D	1	B;B;P	0.37101	0.408;0.075;0.582	B;B;B	0.33392	0.065;0.015;0.163	D	0.91941	0.5563	10	0.59425	D	0.04	-29.6263	6.2971	0.21091	0.8282:0.0:0.1718:0.0	.	453;540;480	O76090-4;O76090;O76090-3	.;BEST1_HUMAN;.	S	540;453;168;480	ENSP00000367282:N540S;ENSP00000367281:N453S;ENSP00000301774:N168S;ENSP00000399709:N480S	ENSP00000301774:N168S	N	+	2	0	BEST1	61486821	1.000000	0.71417	0.980000	0.43619	0.854000	0.48673	2.647000	0.46639	2.089000	0.63090	0.533000	0.62120	AAC	.	.	.	none		0.463	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1	NM_004183		G	61730245	A	G	61730245	3	3	275	1	0	0	0	0	1	0	0	0	1404	43	2	3	1653	3	BEST1	11	61730245	Missense_Mutation	SNP	A	TCGA-Y8-A895-01A-11D-A35Z-10	2156308	61730245	73276271	51	17460											
LTBP3	4054	hgsc.bcm.edu	37	chr11	65308749	65308749	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtagcactccttcttgtggTggggctgctccacctctgag	4	12	13	12	0	2	1	0	1	2	0	4	1	4	1	3	4	2	4	3	4	1	3			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr11:65308749T>C	ENST00000301873.5	-	20	3009	c.2741A>G	c.(2740-2742)cAc>cGc	p.H914R	LTBP3_ENST00000322147.4_Missense_Mutation_p.H914R|LTBP3_ENST00000536982.1_Missense_Mutation_p.H540R|LTBP3_ENST00000529189.1_5'UTR|LTBP3_ENST00000530785.1_5'UTR|LTBP3_ENST00000532932.1_Missense_Mutation_p.H344R	NM_001130144.2	NP_001123616.1	Q9NS15	LTBP3_HUMAN	latent transforming growth factor beta binding protein 3	914					bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|extracellular matrix organization (GO:0030198)|lung saccule development (GO:0060430)|negative regulation of bone mineralization (GO:0030502)|negative regulation of chondrocyte differentiation (GO:0032331)|positive regulation of bone resorption (GO:0045780)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of mesenchymal stem cell proliferation (GO:1902462)|transforming growth factor beta activation (GO:0036363)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(3)	23						CTTCTTGTGGTGGGGCTGCTC	0.627											OREG0021080	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H914R		Atlas-SNP	.											.	LTBP3	55	.	0			c.A2741G						PASS	.						111	99	103					11																	65308749		2201	4297	6498	SO:0001583	missense	4054	exon20			TTGTGGTGGGGCT	AF135960	CCDS8103.1, CCDS44647.1	11q12	2011-10-20			ENSG00000168056	ENSG00000168056		"Latent transforming growth factor, beta binding proteins"	6716	protein-coding gene	gene with protein product		602090		LTBP2		7719025	Standard	NM_001164266		Approved		uc001oej.3	Q9NS15	OTTHUMG00000166575	ENST00000301873.5:c.2741A>G	chr11.hg19:g.65308749T>C	ENSP00000301873:p.His914Arg	24.0	0.0	.	1083	22.0	10.0	.	NM_001130144	O15107|Q96HB9|Q9H7K2|Q9UFN4	Missense_Mutation	SNP	ENST00000301873.5	hg19	CCDS44647.1	.	.	.	.	.	.	.	.	.	.	T	13.01	2.108115	0.37242	.	.	ENSG00000168056	ENST00000322147;ENST00000301873;ENST00000532932;ENST00000536982;ENST00000530866	D;D;D;D;D	0.92299	-3.01;-3.01;-3.01;-3.01;-3.01	4.32	4.32	0.51571	Matrix fibril-associated (2);	0.439740	0.23281	U	0.049905	D	0.86802	0.6020	N	0.13327	0.33	0.28670	N	0.90566	D;P;P;D;P;P	0.60575	0.988;0.919;0.867;0.974;0.919;0.645	P;B;B;P;P;B	0.53102	0.718;0.434;0.316;0.621;0.514;0.25	T	0.79482	-0.1785	10	0.24483	T	0.36	.	7.1975	0.25862	0.1989:0.0:0.0:0.8011	.	825;540;797;914;914;344	E9PKW1;F5GWC4;B9EG76;Q9NS15;Q9NS15-2;E9PJR2	.;.;.;LTBP3_HUMAN;.;.	R	914;914;344;540;825	ENSP00000326647:H914R;ENSP00000301873:H914R;ENSP00000435530:H344R;ENSP00000441912:H540R;ENSP00000435276:H825R	ENSP00000301873:H914R	H	-	2	0	LTBP3	65065325	.	.	1.000000	0.80357	0.856000	0.48823	.	.	1.591000	0.50007	0.240000	0.17902	CAC	.	.	.	none		0.627	LTBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390538.1	NM_021070		C	65308749	T	C	65308749	3	2	275	1	0	0	0	0	1	0	0	0	9082	1696	59	3	1206	3	LTBP3	11	65308749	Missense_Mutation	SNP	T	TCGA-Y8-A895-01A-11D-A35Z-10	3578504	65308749	69697767	52	17461											
MTMR2	8898	hgsc.bcm.edu	37	chr11	95580921	95580921	+	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	tagattccaagttagacaacCagtgggtttcctcaatgttg	11	13	9	8	0	1	2	1	0	0	2	3	2	3	2	3	1	1	3	3	1	5	5			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr11:95580921C>A	ENST00000346299.5	-	10	1476	c.1136G>T	c.(1135-1137)tGg>tTg	p.W379L	MTMR2_ENST00000409459.1_Missense_Mutation_p.W307L|MTMR2_ENST00000393223.3_Missense_Mutation_p.W307L|MTMR2_ENST00000352297.7_Missense_Mutation_p.W307L|MTMR2_ENST00000484818.1_5'Flank	NM_016156.5	NP_057240.3	Q13614	MTMR2_HUMAN	myotubularin related protein 2	379	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				cell death (GO:0008219)|dendritic spine maintenance (GO:0097062)|inositol phosphate dephosphorylation (GO:0046855)|myelin assembly (GO:0032288)|negative regulation of endocytosis (GO:0045806)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of myelination (GO:0031642)|negative regulation of receptor catabolic process (GO:2000645)|negative regulation of receptor internalization (GO:0002091)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of early endosome to late endosome transport (GO:2000643)|protein dephosphorylation (GO:0006470)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endosome (GO:0005768)|neuronal postsynaptic density (GO:0097481)|nucleus (GO:0005634)|synaptic membrane (GO:0097060)|synaptic vesicle (GO:0008021)|vacuolar membrane (GO:0005774)	phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	19		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GTTAGACAACCAGTGGGTTTC	0.378																																					p.W379L		Atlas-SNP	.											.	MTMR2	79	.	0			c.G1136T						PASS	.						132	133	133					11																	95580921		2201	4298	6499	SO:0001583	missense	8898	exon10			GACAACCAGTGGG	U58033	CCDS8305.1, CCDS8306.1	11q22	2014-09-17			ENSG00000087053	ENSG00000087053		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	7450	protein-coding gene	gene with protein product		603557		CMT4B		8640223, 9736772	Standard	NM_016156		Approved	KIAA1073	uc001pfu.3	Q13614	OTTHUMG00000153837	ENST00000346299.5:c.1136G>T	chr11.hg19:g.95580921C>A	ENSP00000345752:p.Trp379Leu	185.0	0.0	.		143.0	56.0	.	NM_016156	A6NN98|Q9UPS9	Missense_Mutation	SNP	ENST00000346299.5	hg19	CCDS8305.1	.	.	.	.	.	.	.	.	.	.	C	34	5.354464	0.95830	.	.	ENSG00000087053	ENST00000346299;ENST00000393223;ENST00000409459;ENST00000352297;ENST00000444541	D;D;D;D;D	0.92752	-3.1;-3.1;-3.1;-3.1;-3.1	5.69	5.69	0.88448	Myotubularin phosphatase domain (1);	0.000000	0.85682	D	0.000000	D	0.97093	0.9050	M	0.90870	3.155	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.991	D	0.97490	1.0053	10	0.87932	D	0	.	19.8165	0.96571	0.0:1.0:0.0:0.0	.	379;379	A8K5G2;Q13614	.;MTMR2_HUMAN	L	379;307;307;307;307	ENSP00000345752:W379L;ENSP00000376915:W307L;ENSP00000386882:W307L;ENSP00000343737:W307L;ENSP00000396020:W307L	ENSP00000345752:W379L	W	-	2	0	MTMR2	95220569	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.755000	0.85180	2.683000	0.91414	0.655000	0.94253	TGG	.	.	.	none		0.378	MTMR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332620.1	NM_016156		A	95580921	C	A	95580921	3	1	275	1	0	0	0	0	1	0	0	0	9951	595	21	4	819	4	MTMR2	11	95580921	Missense_Mutation	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10	30272172	95580921	39425595	53	17462											
C11orf1	64776	hgsc.bcm.edu	37	chr11	111753128	111753128	+	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	gtttcctcacaaacccacacTgtggcagccttgttaatgca	10	11	7	13	0	1	0	1	0	0	0	2	0	2	0	3	1	3	4	3	1	2	3			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr11:111753128T>A	ENST00000260276.3	+	2	419	c.82T>A	c.(82-84)Tgt>Agt	p.C28S	C11orf1_ENST00000528125.1_De_novo_Start_OutOfFrame|C11orf1_ENST00000530214.1_Missense_Mutation_p.C28S|C11orf1_ENST00000529270.1_Missense_Mutation_p.C68S|ALG9_ENST00000524880.1_5'Flank	NM_022761.2	NP_073598.1	Q9H5F2	CK001_HUMAN	chromosome 11 open reading frame 1	28						nucleus (GO:0005634)				kidney(2)|lung(3)	5		all_cancers(61;1.26e-15)|all_epithelial(67;9.52e-10)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|Medulloblastoma(222;0.0228)|all_neural(223;0.0281)		all cancers(92;6.28e-09)|Epithelial(105;4.11e-08)|OV - Ovarian serous cystadenocarcinoma(223;1.52e-07)|BRCA - Breast invasive adenocarcinoma(274;1.1e-06)		AAACCCACACTGTGGCAGCCT	0.428																																					p.C28S		Atlas-SNP	.											.	C11orf1	15	.	0			c.T82A						PASS	.						101	82	89					11																	111753128		2201	4297	6498	SO:0001583	missense	64776	exon2			CCACACTGTGGCA	AJ250229	CCDS8350.1	11q23.1	2012-05-30			ENSG00000137720	ENSG00000137720			1163	protein-coding gene	gene with protein product						10873569	Standard	NM_022761		Approved	FLJ23499	uc001pmd.3	Q9H5F2	OTTHUMG00000166884	ENST00000260276.3:c.82T>A	chr11.hg19:g.111753128T>A	ENSP00000260276:p.Cys28Ser	119.0	0.0	.		122.0	45.0	.	NM_022761	Q6I9X7|Q9NQC6	Missense_Mutation	SNP	ENST00000260276.3	hg19	CCDS8350.1	.	.	.	.	.	.	.	.	.	.	T	7.970	0.748848	0.15710	.	.	ENSG00000137720	ENST00000260276;ENST00000530214;ENST00000530799;ENST00000529270	T;T;T;T	0.22336	1.96;1.96;1.96;1.96	5.33	5.33	0.75918	.	0.795295	0.11705	N	0.537529	T	0.10208	0.0250	N	0.08118	0	0.18873	N	0.999987	B;B	0.16166	0.016;0.001	B;B	0.19391	0.025;0.002	T	0.24728	-1.0152	10	0.23891	T	0.37	-4.0562	4.784	0.13217	0.1655:0.0852:0.0:0.7492	.	68;28	E9PMC1;Q9H5F2	.;CK001_HUMAN	S	28;28;44;68	ENSP00000260276:C28S;ENSP00000435864:C28S;ENSP00000432128:C44S;ENSP00000431180:C68S	ENSP00000260276:C28S	C	+	1	0	C11orf1	111258338	0.312000	0.24545	0.960000	0.40013	0.737000	0.42083	1.146000	0.31589	2.237000	0.73441	0.459000	0.35465	TGT	.	.	.	none		0.428	C11orf1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391650.1	NM_022761		A	111753128	T	A	111753128	3	1	275	1	0	0	0	0	1	0	0	0	1631	1580	55	5	88	5	C11orf1	11	111753128	Missense_Mutation	SNP	T	TCGA-Y8-A895-01A-11D-A35Z-10	16172207	111753128	23253388	54	17463											
THY1	7070	hgsc.bcm.edu	37	chr11	119290952	119290959	+	Frame_Shift_Del	DEL	TGCTTCTT	TGCTTCTT	-																															ccacagtgccaaagagcacgTgcttctttgtctcacgggtc																										TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	TGCTTCTT	TGCTTCTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr11:119290952_119290959delTGCTTCTT	ENST00000284240.5	-	3	1214_1221	c.175_182delAAGAAGCA	c.(175-183)aagaagcacfs	p.KKH59fs	THY1_ENST00000527590.1_5'UTR|RP11-334E6.12_ENST00000578216.1_RNA|THY1_ENST00000580275.1_Frame_Shift_Del_p.KKH42fs|USP2-AS1_ENST00000498979.2_RNA|USP2-AS1_ENST00000578923.1_RNA|USP2-AS1_ENST00000500970.1_RNA|USP2-AS1_ENST00000530002.1_RNA|THY1_ENST00000528522.1_Frame_Shift_Del_p.KKH59fs	NM_006288.3	NP_006279.2	P04216	THY1_HUMAN	Thy-1 cell surface antigen	59	Ig-like V-type.				angiogenesis (GO:0001525)|cytoskeleton organization (GO:0007010)|focal adhesion assembly (GO:0048041)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of GTPase activity (GO:0043547)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of T cell activation (GO:0050870)|retinal cone cell development (GO:0046549)|single organismal cell-cell adhesion (GO:0016337)|T cell receptor signaling pathway (GO:0050852)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	GPI anchor binding (GO:0034235)|integrin binding (GO:0005178)|Rho GTPase activator activity (GO:0005100)	p.K59N(1)		breast(1)|kidney(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12		Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.83e-05)		AAAGAGCACGTGCTTCTTTGTCTCACGG	0.553																																					p.59_61del		Atlas-Indel,Pindel	.											.	THY1	21	.	1	Substitution - Missense(1)	breast(1)	c.176_183del						PASS	.																																			SO:0001589	frameshift_variant	7070	exon3			.	M11749	CCDS8424.1	11q23.3	2013-01-14				ENSG00000154096		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	11801	protein-coding gene	gene with protein product		188230				2864690	Standard	NM_006288		Approved	CD90	uc001pwr.3	P04216		ENST00000284240.5:c.175_182delAAGAAGCA	chr11.hg19:g.119290952_119290959delTGCTTCTT	ENSP00000284240:p.Lys59fs	98.0	0.0	0		80.0	23.0	0.2875	NM_006288	Q16008|Q9NSP1	Frame_Shift_Del	DEL	ENST00000284240.5	hg19	CCDS8424.1																																																																																			.	.	.	none		0.553	THY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388370.2	NM_006288		-	119290959	TGCTTCTT	-	119290952	7	5	275	1	0	1	0	1	0	0	0	0	15897	1696	59	0	311	0	THY1	11	119290952	Frame_Shift_Del	DEL	TGCTTCTT	TCGA-Y8-A895-01A-11D-A35Z-10	7537824	119290952	15715564	55	17464											
SORL1	6653	hgsc.bcm.edu	37	chr11	121430332	121430332	+	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	aaccagctcacggggctcatGgacatgaagattttctacaa	13	9	9	10	1	3	2	2	1	1	1	3	3	3	3	1	3	3	2	1	3	4	3			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr11:121430332G>T	ENST00000260197.7	+	21	3144	c.3015G>T	c.(3013-3015)atG>atT	p.M1005I		NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	1005					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)		CGGGGCTCATGGACATGAAGA	0.488																																					p.M1005I		Atlas-SNP	.											.	SORL1	218	.	0			c.G3015T						PASS	.						91	90	90					11																	121430332		2203	4299	6502	SO:0001583	missense	6653	exon21			GCTCATGGACATG	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.3015G>T	chr11.hg19:g.121430332G>T	ENSP00000260197:p.Met1005Ile	119.0	0.0	.		103.0	42.0	.	NM_003105	B2RNX7|Q92856	Missense_Mutation	SNP	ENST00000260197.7	hg19	CCDS8436.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.830325	0.91036	.	.	ENSG00000137642	ENST00000260197	D	0.91124	-2.79	5.24	5.24	0.73138	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.92355	0.7574	M	0.84511	2.7	0.80722	D	1	P	0.45078	0.85	B	0.41917	0.37	D	0.93769	0.7073	10	0.72032	D	0.01	.	18.8284	0.92127	0.0:0.0:1.0:0.0	.	1005	Q92673	SORL_HUMAN	I	1005	ENSP00000260197:M1005I	ENSP00000260197:M1005I	M	+	3	0	SORL1	120935542	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	9.614000	0.98353	2.441000	0.82636	0.655000	0.94253	ATG	.	.	.	none		0.488	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105		T	121430332	G	T	121430332	3	4	275	1	0	0	0	0	1	0	0	0	14947	1348	47	4	3097	4	SORL1	11	121430332	Missense_Mutation	SNP	G	TCGA-Y8-A895-01A-11D-A35Z-10	2139380	121430332	13576184	56	17465											
SCN3B	55800	hgsc.bcm.edu	37	chr11	123516378	123516378	+	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	ctctctcttcatgcaggagaTgcagcgcagcttcatggggt	7	11	12	11	1	4	1	2	0	2	1	5	2	4	1	0	3	4	4	0	3	0	2			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr11:123516378T>A	ENST00000392770.2	-	2	938	c.136A>T	c.(136-138)Atc>Ttc	p.I46F	SCN3B_ENST00000530277.1_Missense_Mutation_p.I46F|SCN3B_ENST00000299333.3_Missense_Mutation_p.I46F	NM_018400.3	NP_060870.1	Q9NY72	SCN3B_HUMAN	sodium channel, voltage-gated, type III, beta subunit	46	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)	ATGCAGGAGATGCAGCGCAGC	0.577																																					p.I46F		Atlas-SNP	.											.	SCN3B	53	.	0			c.A136T						PASS	.						125	121	122					11																	123516378		2202	4299	6501	SO:0001583	missense	55800	exon2			AGGAGATGCAGCG	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.136A>T	chr11.hg19:g.123516378T>A	ENSP00000376523:p.Ile46Phe	128.0	0.0	.		93.0	35.0	.	NM_018400	A5H1I5|Q17RL3|Q9ULR2	Missense_Mutation	SNP	ENST00000392770.2	hg19	CCDS8442.1	.	.	.	.	.	.	.	.	.	.	T	34	5.372748	0.95923	.	.	ENSG00000166257	ENST00000392770;ENST00000299333;ENST00000530277;ENST00000527836;ENST00000528267	T;T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01;-0.01	5.96	5.96	0.96718	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.79499	0.4456	M	0.75777	2.31	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.81404	-0.0948	10	0.66056	D	0.02	-3.7292	16.443	0.83907	0.0:0.0:0.0:1.0	.	46	Q9NY72	SCN3B_HUMAN	F	46	ENSP00000376523:I46F;ENSP00000299333:I46F;ENSP00000432785:I46F;ENSP00000435554:I46F;ENSP00000434363:I46F	ENSP00000299333:I46F	I	-	1	0	SCN3B	123021588	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.691000	0.84191	2.275000	0.75901	0.496000	0.49642	ATC	.	.	.	none		0.577	SCN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387412.1	NM_018400		A	123516378	T	A	123516378	3	1	275	1	0	0	0	0	1	0	0	0	13932	1464	51	5	527	5	SCN3B	11	123516378	Missense_Mutation	SNP	T	TCGA-Y8-A895-01A-11D-A35Z-10	2086046	123516378	11490138	57	17466											
PLCZ1	89869	hgsc.bcm.edu	37	chr12	18854673	18854673	+	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	gggtttcctttaaggttcctAttttcttatttttaactaat	8	22	5	6	0	1	0	0	0	1	0	3	0	3	0	2	2	1	2	2	2	5	12			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr12:18854673A>T	ENST00000538330.1	-	5	506	c.125T>A	c.(124-126)aTa>aAa	p.I42K	PLCZ1_ENST00000266505.7_Missense_Mutation_p.I301K|PLCZ1_ENST00000435379.1_Missense_Mutation_p.I106K|PLCZ1_ENST00000447925.2_Missense_Mutation_p.I299K|PLCZ1_ENST00000542762.1_5'UTR|PLCZ1_ENST00000541695.1_Missense_Mutation_p.I164K|PLCZ1_ENST00000539875.1_Missense_Mutation_p.I108K					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)					TAAGGTTCCTATTTTCTTATT	0.358																																					p.I301K		Atlas-SNP	.											.	PLCZ1	107	.	0			c.T902A						PASS	.						64	63	63					12																	18854673		2203	4297	6500	SO:0001583	missense	89869	exon8			GTTCCTATTTTCT	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.125T>A	chr12.hg19:g.18854673A>T	ENSP00000445880:p.Ile42Lys	87.0	0.0	.		74.0	31.0	.	NM_033123		Missense_Mutation	SNP	ENST00000538330.1	hg19		.	.	.	.	.	.	.	.	.	.	A	16.14	3.038007	0.54896	.	.	ENSG00000139151	ENST00000538330;ENST00000266505;ENST00000447925;ENST00000435379;ENST00000541695;ENST00000539875;ENST00000540421;ENST00000543242;ENST00000539072	T;T;T;T;T;T;T;T;T	0.63580	-0.05;0.65;0.65;-0.05;0.65;-0.05;-0.05;0.65;-0.05	5.35	5.35	0.76521	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	0.571765	0.18358	N	0.143647	T	0.57051	0.2027	L	0.50333	1.59	0.41644	D	0.989096	P;P	0.38335	0.514;0.627	B;B	0.37650	0.106;0.255	T	0.60286	-0.7293	10	0.48119	T	0.1	.	12.02	0.53337	1.0:0.0:0.0:0.0	.	301;42	Q86YW0;Q8N7S5	PLCZ1_HUMAN;.	K	42;301;299;106;164;108;36;42;128	ENSP00000445880:I42K;ENSP00000266505:I301K;ENSP00000402358:I299K;ENSP00000400504:I106K;ENSP00000443349:I164K;ENSP00000445026:I108K;ENSP00000445889:I36K;ENSP00000443762:I42K;ENSP00000438629:I128K	ENSP00000266505:I301K	I	-	2	0	PLCZ1	18745940	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.675000	0.46875	2.156000	0.67533	0.533000	0.62120	ATA	.	.	.	none		0.358	PLCZ1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000401666.3	NM_033123		T	18854673	A	T	18854673	3	4	275	1	0	0	0	0	1	0	0	0	12051	449	16	5	956	5	PLCZ1	12	18854673	Missense_Mutation	SNP	A	TCGA-Y8-A895-01A-11D-A35Z-10		18854673	114997222	58	17467											
SLCO1A2	6579	hgsc.bcm.edu	37	chr12	21459852	21459852	+	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	tggtcttaaaatctgggttcCattttccatacacaagaaac	13	13	6	9	0	2	1	0	0	2	1	4	1	4	1	2	2	2	1	2	2	5	5			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr12:21459852C>A	ENST00000307378.6	-	6	1126	c.406G>T	c.(406-408)Gga>Tga	p.G136*	SLCO1A2_ENST00000458504.1_Nonsense_Mutation_p.G4*|SLCO1A2_ENST00000537524.1_Nonsense_Mutation_p.G4*|SLCO1A2_ENST00000452078.1_Nonsense_Mutation_p.G136*|SLCO1A2_ENST00000390670.3_Nonsense_Mutation_p.G134*	NM_134431.3	NP_602307.1	P46721	SO1A2_HUMAN	solute carrier organic anion transporter family, member 1A2	136					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(6)|upper_aerodigestive_tract(1)	48					Aminohippurate(DB00345)|Atorvastatin(DB01076)|Bumetanide(DB00887)|Chlorambucil(DB00291)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dexamethasone(DB01234)|Digitoxin(DB01396)|Digoxin(DB00390)|Dinoprostone(DB00917)|Enalapril(DB00584)|Erythromycin(DB00199)|Estradiol(DB00783)|Estriol(DB04573)|Estrone(DB00655)|Fexofenadine(DB00950)|Glyburide(DB01016)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Indinavir(DB00224)|Indomethacin(DB00328)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Methyltestosterone(DB06710)|Mirabegron(DB08893)|Naloxone(DB01183)|Naproxen(DB00788)|Nelfinavir(DB00220)|Ouabain(DB01092)|Pravastatin(DB00175)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rocuronium(DB00728)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Simvastatin(DB00641)|Spironolactone(DB00421)|Sumatriptan(DB00669)|Tauroursodeoxycholic acid(DB08834)|Testosterone(DB00624)|Tolbutamide(DB01124)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)	ATCTGGGTTCCATTTTCCATA	0.358																																					p.G136X		Atlas-SNP	.											.	SLCO1A2	107	.	0			c.G406T						PASS	.						119	109	112					12																	21459852		2203	4300	6503	SO:0001587	stop_gained	6579	exon6			GGGTTCCATTTTC		CCDS8686.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000084453	ENSG00000084453		"Solute carriers"	10956	protein-coding gene	gene with protein product		602883	"solute carrier family 21 (organic anion transporter), member 3"	SLC21A3		9007731	Standard	NM_134431		Approved	OATP, OATP1A2, OATP-A	uc001rer.3	P46721	OTTHUMG00000156259	ENST00000307378.6:c.406G>T	chr12.hg19:g.21459852C>A	ENSP00000305974:p.Gly136*	127.0	0.0	.		127.0	41.0	.	NM_134431	Q9UGP7|Q9UL38	Nonsense_Mutation	SNP	ENST00000307378.6	hg19	CCDS8686.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.530205	0.85706	.	.	ENSG00000084453	ENST00000307378;ENST00000452078;ENST00000458504;ENST00000537524;ENST00000390670;ENST00000413682;ENST00000422327;ENST00000453443	.	.	.	4.2	3.3	0.37823	.	1.613170	0.03170	N	0.170528	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	.	5.1289	0.14899	0.0:0.6678:0.2145:0.1177	.	.	.	.	X	136;136;4;4;134;4;136;136	.	ENSP00000305974:G136X	G	-	1	0	SLCO1A2	21351119	0.980000	0.34600	0.995000	0.50966	0.982000	0.71751	0.404000	0.20999	0.959000	0.37980	0.557000	0.71058	GGA	.	.	.	none		0.358	SLCO1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343648.3	NM_021094		A	21459852	C	A	21459852	4	1	275	1	0	0	0	0	0	1	0	0	14735	603	21	4	1650	4	SLCO1A2	12	21459852	Nonsense_Mutation	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10	2605179	21459852	112392043	59	17468											
TROAP	10024	hgsc.bcm.edu	37	chr12	49717698	49717698	+	Frame_Shift_Del	DEL	C	C	-																															agcaggccccaggccgaaagCcaggcaccaggcagagacat																										TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr12:49717698delC	ENST00000257909.3	+	3	291	c.215delC	c.(214-216)gccfs	p.A72fs	TROAP_ENST00000380327.5_Frame_Shift_Del_p.A72fs|TROAP_ENST00000551245.1_Frame_Shift_Del_p.A72fs|TROAP_ENST00000547923.1_5'Flank|RP11-161H23.9_ENST00000553259.1_RNA|TROAP_ENST00000549275.1_Intron|TROAP_ENST00000550709.1_Frame_Shift_Del_p.A72fs|TROAP_ENST00000549534.1_3'UTR|TROAP_ENST00000548311.1_Frame_Shift_Del_p.A72fs	NM_005480.3	NP_005471.3	Q12815	TROAP_HUMAN	trophinin associated protein	72					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	32						AGGCCGAAAGCCAGGCACCAG	0.582																																					p.A72fs		Pindel	.											.	TROAP	80	.	0			c.214delG						PASS	.						83	83	83					12																	49717698		2203	4300	6503	SO:0001589	frameshift_variant	10024	exon3			.	U04810	CCDS8784.1, CCDS41779.1, CCDS61117.1	12q13.12	2012-10-17	2012-10-17		ENSG00000135451	ENSG00000135451			12327	protein-coding gene	gene with protein product	"tastin"	603872				7758945	Standard	NM_005480		Approved	TASTIN	uc001rtx.4	Q12815	OTTHUMG00000169486	ENST00000257909.3:c.215delC	chr12.hg19:g.49717698delC	ENSP00000257909:p.Ala72fs	130.0	0.0	.		101.0	25.0	0.248	NM_001100620	F8VSF9|Q6PJU7|Q8N5B2	Frame_Shift_Del	DEL	ENST00000257909.3	hg19	CCDS8784.1																																																																																			.	.	.	none		0.582	TROAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404300.1	NM_005480		-	49717698	C	-	49717698	7	5	275	1	0	1	0	1	0	0	0	0	16587	739	26	0	221	0	TROAP	12	49717698	Frame_Shift_Del	DEL	C	TCGA-Y8-A895-01A-11D-A35Z-10	28257846	49717698	84134197	60	17469											
BAZ2A	11176	hgsc.bcm.edu	37	chr12	56994768	56994768	+	Missense_Mutation	SNP	T	T	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	cttcctgcaagaagtccctgTgcttgttaaggtgtttgtga	7	15	11	8	0	0	2	0	1	0	1	2	2	2	2	2	1	2	4	2	1	3	4			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr12:56994768T>G	ENST00000551812.1	-	22	4608	c.4415A>C	c.(4414-4416)cAc>cCc	p.H1472P	BAZ2A_ENST00000179765.5_Missense_Mutation_p.H1440P|BAZ2A_ENST00000549884.1_Missense_Mutation_p.H1470P|BAZ2A_ENST00000553222.1_5'UTR|BAZ2A_ENST00000379441.3_Missense_Mutation_p.H1442P	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	1472					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						GAAGTCCCTGTGCTTGTTAAG	0.537																																					p.H1472P		Atlas-SNP	.											.	BAZ2A	263	.	0			c.A4415C						PASS	.						47	51	49					12																	56994768		1991	4172	6163	SO:0001583	missense	11176	exon22			TCCCTGTGCTTGT	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.4415A>C	chr12.hg19:g.56994768T>G	ENSP00000446880:p.His1472Pro	124.0	0.0	.		101.0	39.0	.	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Missense_Mutation	SNP	ENST00000551812.1	hg19	CCDS44924.1	.	.	.	.	.	.	.	.	.	.	T	19.99	3.928810	0.73327	.	.	ENSG00000076108	ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549787;ENST00000549884	T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.52273	0.1724	L	0.60455	1.87	0.80722	D	1	D;D;B;D	0.89917	0.999;0.988;0.23;1.0	D;D;B;D	0.91635	0.996;0.979;0.305;0.999	T	0.54009	-0.8357	10	0.72032	D	0.01	-16.147	14.9092	0.70743	0.0:0.0:0.0:1.0	.	1470;1468;1472;1445	F8VU39;Q9UIF9-3;Q9UIF9;Q9UIF9-2	.;.;BAZ2A_HUMAN;.	P	1442;1440;1472;404;1470	ENSP00000368754:H1442P;ENSP00000179765:H1440P;ENSP00000446880:H1472P;ENSP00000448760:H404P;ENSP00000447941:H1470P	ENSP00000179765:H1440P	H	-	2	0	BAZ2A	55281035	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.657000	0.83745	2.231000	0.72958	0.459000	0.35465	CAC	.	.	.	none		0.537	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449		G	56994768	T	G	56994768	3	3	275	1	0	0	0	0	1	0	0	0	1331	1696	59	5	1334	5	BAZ2A	12	56994768	Missense_Mutation	SNP	T	TCGA-Y8-A895-01A-11D-A35Z-10	7277070	56994768	76857127	61	17470											
LRP1	4035	hgsc.bcm.edu	37	chr12	57600368	57600368	+	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	cagggtgacgagagtgtccgCattgatgctatggatgtcca	9	10	14	8	2	0	3	0	2	0	1	2	5	2	4	2	2	1	2	2	2	1	2			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr12:57600368C>T	ENST00000243077.3	+	76	12169	c.11703C>T	c.(11701-11703)cgC>cgT	p.R3901R		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3901					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)	AGAGTGTCCGCATTGATGCTA	0.597																																					p.R3901R		Atlas-SNP	.											.	LRP1	428	.	0			c.C11703T						PASS	.						218	136	164					12																	57600368		2203	4300	6503	SO:0001819	synonymous_variant	4035	exon76			TGTCCGCATTGAT	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.11703C>T	chr12.hg19:g.57600368C>T		123.0	0.0	.		119.0	56.0	.	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	hg19	CCDS8932.1																																																																																			.	.	.	none		0.597	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		T	57600368	C	T	57600368	2	4	275	1	0	0	0	0	0	0	0	1	8958	697	25	2		2	LRP1	12	57600368	Silent	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10	605600	57600368	76251527	62	17471											
KIF5A	3798	hgsc.bcm.edu	37	chr12	57969029	57969029	+	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	aagtgaccgggcgggagctcTcatcctgccagctcctcatc	7	8	11	15	2	2	1	2	1	1	0	6	2	4	2	4	2	3	2	4	2	1	0			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr12:57969029T>A	ENST00000455537.2	+	16	2153	c.1879T>A	c.(1879-1881)Tca>Aca	p.S627T	KIF5A_ENST00000286452.5_Missense_Mutation_p.S538T	NM_004984.2	NP_004975.2	Q12840	KIF5A_HUMAN	kinesin family member 5A	627					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein localization (GO:0008104)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(32)|ovary(2)|prostate(2)|skin(2)	62						GCGGGAGCTCTCATCCTGCCA	0.537																																					p.S627T		Atlas-SNP	.											.	KIF5A	143	.	0			c.T1879A						PASS	.						42	41	41					12																	57969029		2203	4300	6503	SO:0001583	missense	3798	exon16			GAGCTCTCATCCT	U06698	CCDS8945.1	12q13.13	2011-07-15	2004-02-13			ENSG00000155980		"Kinesins"	6323	protein-coding gene	gene with protein product		602821	"spastic paraplegia 10 (autosomal dominant)"	SPG10		9858832, 10441583, 16489470	Standard	NM_004984		Approved	D12S1889, NKHC, MY050	uc001sor.1	Q12840	OTTHUMG00000170143	ENST00000455537.2:c.1879T>A	chr12.hg19:g.57969029T>A	ENSP00000408979:p.Ser627Thr	98.0	0.0	.		117.0	9.0	.	NM_004984	A6H8M5|Q4LE26	Missense_Mutation	SNP	ENST00000455537.2	hg19	CCDS8945.1	.	.	.	.	.	.	.	.	.	.	T	16.06	3.014980	0.54468	.	.	ENSG00000155980	ENST00000455537;ENST00000286452	D;D	0.85702	-2.02;-2.02	4.52	4.52	0.55395	.	0.000000	0.85682	D	0.000000	T	0.80607	0.4655	L	0.52759	1.655	0.54753	D	0.99998	B;B	0.17852	0.024;0.008	B;B	0.20184	0.028;0.022	T	0.75402	-0.3330	10	0.22706	T	0.39	.	13.2727	0.60170	0.0:0.0:0.0:1.0	.	538;627	B7Z2M7;Q12840	.;KIF5A_HUMAN	T	627;538	ENSP00000408979:S627T;ENSP00000286452:S538T	ENSP00000286452:S538T	S	+	1	0	KIF5A	56255296	0.990000	0.36364	0.947000	0.38551	0.992000	0.81027	2.229000	0.42990	2.027000	0.59764	0.533000	0.62120	TCA	.	.	.	none		0.537	KIF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407634.1	NM_004984		A	57969029	T	A	57969029	3	1	275	1	0	0	0	0	1	0	0	0	8312	1551	54	5	1941	5	KIF5A	12	57969029	Missense_Mutation	SNP	T	TCGA-Y8-A895-01A-11D-A35Z-10	368661	57969029	75882866	63	17472											
MED13L	23389	hgsc.bcm.edu	37	chr12	116460358	116460358	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctccacacttgtgcatacAttactttctccatgcagaaa	12	13	4	12	0	2	1	0	0	2	1	4	1	2	1	2	0	4	2	2	0	3	4			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr12:116460358A>G	ENST00000281928.3	-	5	734	c.528T>C	c.(526-528)aaT>aaC	p.N176N		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	176						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)		TTGTGCATACATTACTTTCTC	0.408																																					p.N176N		Atlas-SNP	.											.	MED13L	193	.	0			c.T528C						PASS	.						98	82	88					12																	116460358		2203	4300	6503	SO:0001819	synonymous_variant	23389	exon5			GCATACATTACTT	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.528T>C	chr12.hg19:g.116460358A>G		92.0	0.0	.		88.0	32.0	.	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Silent	SNP	ENST00000281928.3	hg19	CCDS9177.1																																																																																			.	.	.	none		0.408	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3			G	116460358	A	G	116460358	2	3	275	1	0	0	0	0	0	0	0	1	9438	214	8	3		3	MED13L	12	116460358	Silent	SNP	A	TCGA-Y8-A895-01A-11D-A35Z-10	58491329	116460358	17391537	64	17473											
SLC15A4	121260	hgsc.bcm.edu	37	chr12	129293996	129293996	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatcctcaaatgaagactcTgtaaaacatatgttgtctgc	14	12	7	8	0	3	2	1	1	2	1	4	3	4	2	1	0	2	2	1	0	6	3			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr12:129293996T>C	ENST00000266771.5	-	4	1073	c.1034A>G	c.(1033-1035)cAg>cGg	p.Q345R	SLC15A4_ENST00000539703.1_5'UTR|SLC15A4_ENST00000544112.1_Missense_Mutation_p.Q8R	NM_145648.3	NP_663623.1	Q8N697	S15A4_HUMAN	solute carrier family 15 (oligopeptide transporter), member 4	345					ion transport (GO:0006811)|oligopeptide transport (GO:0006857)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	L-histidine transmembrane transporter activity (GO:0005290)|symporter activity (GO:0015293)			endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|skin(1)	22	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.69e-06)|Epithelial(86;1.17e-05)|all cancers(50;5.07e-05)		ATGAAGACTCTGTAAAACATA	0.363																																					p.Q345R		Atlas-SNP	.											.	SLC15A4	41	.	0			c.A1034G						PASS	.						169	176	174					12																	129293996		2203	4300	6503	SO:0001583	missense	121260	exon4			AGACTCTGTAAAA	AY038999	CCDS9264.1	12q24.32	2013-07-18	2013-07-18		ENSG00000139370	ENSG00000139370		"Solute carriers"	23090	protein-coding gene	gene with protein product		615806	"solute carrier family 15, member 4"			11741232	Standard	NM_145648		Approved	PHT1, PTR4	uc001uhu.2	Q8N697	OTTHUMG00000168415	ENST00000266771.5:c.1034A>G	chr12.hg19:g.129293996T>C	ENSP00000266771:p.Gln345Arg	101.0	0.0	.		82.0	11.0	.	NM_145648	A6H8Y9|B3KTK1|Q71M34|Q7Z5F8|Q8TAH0	Missense_Mutation	SNP	ENST00000266771.5	hg19	CCDS9264.1	.	.	.	.	.	.	.	.	.	.	T	27.9	4.869237	0.91587	.	.	ENSG00000139370	ENST00000266771;ENST00000544112;ENST00000376740	T;T;T	0.58797	0.31;3.61;3.61	5.92	5.92	0.95590	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	T	0.81969	0.4935	M	0.92691	3.335	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.86441	0.1767	10	0.87932	D	0	.	16.3544	0.83230	0.0:0.0:0.0:1.0	.	345	Q8N697	S15A4_HUMAN	R	345;8;45	ENSP00000266771:Q345R;ENSP00000439946:Q8R;ENSP00000365930:Q45R	ENSP00000266771:Q345R	Q	-	2	0	SLC15A4	127859949	1.000000	0.71417	0.998000	0.56505	0.969000	0.65631	7.246000	0.78247	2.265000	0.75225	0.459000	0.35465	CAG	.	.	.	none		0.363	SLC15A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399663.1	NM_145648		C	129293996	T	C	129293996	3	2	275	1	0	0	0	0	1	0	0	0	14414	1580	55	3	719	3	SLC15A4	12	129293996	Missense_Mutation	SNP	T	TCGA-Y8-A895-01A-11D-A35Z-10	12833638	129293996	4557899	65	17474											
COG3	83548	hgsc.bcm.edu	37	chr13	46054274	46054274	+	Frame_Shift_Del	DEL	A	A	-																															ttctagacagatgagggattActtgtctgggtttcaggagc																										TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr13:46054274delA	ENST00000349995.5	+	4	510	c.398delA	c.(397-399)tacfs	p.Y133fs		NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	133					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)		ATGAGGGATTACTTGTCTGGG	0.398																																					p.Y133fs	Ovarian(150;1048 1859 18083 21577 42700)	Atlas-Indel,Pindel	.											.	COG3	52	.	0			c.397delT						PASS	.						125	126	126					13																	46054274		2203	4300	6503	SO:0001589	frameshift_variant	83548	exon4			.	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.398delA	chr13.hg19:g.46054274delA	ENSP00000258654:p.Tyr133fs	137.0	0.0	0		93.0	30.0	0.322581	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Frame_Shift_Del	DEL	ENST00000349995.5	hg19	CCDS9398.1																																																																																			.	.	.	none		0.398	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2			-	46054274	A	-	46054274	7	5	275	1	0	1	0	1	0	0	0	0	3661	391	14	0	412	0	COG3	13	46054274	Frame_Shift_Del	DEL	A	TCGA-Y8-A895-01A-11D-A35Z-10		46054274	69115604	66	17475											
FLVCR2	55640	hgsc.bcm.edu	37	chr14	76045630	76045630	+	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	tcctttcagtggatccagtaCggctccatcaataacatctt	10	13	6	12	1	3	0	2	0	1	0	6	1	6	1	3	2	2	2	3	2	3	4			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr14:76045630C>G	ENST00000238667.4	+	1	671	c.315C>G	c.(313-315)taC>taG	p.Y105*	AC007182.6_ENST00000455232.1_RNA	NM_017791.2	NP_060261.2	Q9UPI3	FLVC2_HUMAN	feline leukemia virus subgroup C cellular receptor family, member 2	105					heme transport (GO:0015886)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	heme binding (GO:0020037)|heme transporter activity (GO:0015232)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	15				BRCA - Breast invasive adenocarcinoma(234;0.029)		GGATCCAGTACGGCTCCATCA	0.537																																					p.Y105X		Atlas-SNP	.											.	FLVCR2	39	.	0			c.C315G						PASS	.						160	129	139					14																	76045630		2203	4300	6503	SO:0001587	stop_gained	55640	exon1			CCAGTACGGCTCC	AK000378	CCDS9844.1, CCDS55933.1	14q24.3	2013-05-22	2007-05-01	2007-05-01	ENSG00000119686	ENSG00000119686		"Solute carriers"	20105	protein-coding gene	gene with protein product		610865	"chromosome 14 open reading frame 58", "feline leukemia virus subgroup C cellular receptor 2"	C14orf58		16439531, 20206334	Standard	NM_017791		Approved	FLJ20371, MFSD7C	uc001xrs.2	Q9UPI3	OTTHUMG00000171487	ENST00000238667.4:c.315C>G	chr14.hg19:g.76045630C>G	ENSP00000238667:p.Tyr105*	111.0	0.0	.		96.0	11.0	.	NM_017791	B7Z485|Q53ZT9|Q96JY3|Q9NX90	Nonsense_Mutation	SNP	ENST00000238667.4	hg19	CCDS9844.1	.	.	.	.	.	.	.	.	.	.	C	40	8.087835	0.98648	.	.	ENSG00000119686	ENST00000238667	.	.	.	5.9	-0.175	0.13315	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	-11.5956	10.1313	0.42680	0.0:0.5239:0.0:0.4761	.	.	.	.	X	105	.	ENSP00000238667:Y105X	Y	+	3	2	AC007182.1	75115383	0.547000	0.26465	0.752000	0.31206	0.929000	0.56500	-0.123000	0.10611	0.116000	0.18110	0.650000	0.86243	TAC	.	.	.	none		0.537	FLVCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413672.1	NM_017791		G	76045630	C	G	76045630	4	3	275	1	0	0	0	0	0	1	0	0	5953	547	19	4	317	4	FLVCR2	14	76045630	Nonsense_Mutation	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10		76045630	31303910	67	17476											
KCNK10	54207	hgsc.bcm.edu	37	chr14	88707144	88707144	+	Missense_Mutation	SNP	A	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	cctattggactgactcccgcAttgtcagcatcaagagcatg	10	10	9	12	1	2	2	2	1	0	1	3	3	3	3	2	1	2	3	2	1	2	3			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr14:88707144A>C	ENST00000340700.5	-	3	859	c.408T>G	c.(406-408)aaT>aaG	p.N136K	KCNK10_ENST00000319231.5_Missense_Mutation_p.N141K|KCNK10_ENST00000312350.5_Missense_Mutation_p.N141K	NM_021161.4	NP_066984.1	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	136					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						TGACTCCCGCATTGTCAGCAT	0.403																																					p.N141K		Atlas-SNP	.											.	KCNK10	273	.	0			c.T423G						PASS	.						91	82	85					14																	88707144		2203	4300	6503	SO:0001583	missense	54207	exon3			TCCCGCATTGTCA	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.408T>G	chr14.hg19:g.88707144A>C	ENSP00000343104:p.Asn136Lys	50.0	0.0	.		56.0	24.0	.	NM_138318	B2R8T4|B2RCT3|B5TJL4|Q6B014|Q8TDK7|Q8TDK8|Q9HB59	Missense_Mutation	SNP	ENST00000340700.5	hg19	CCDS9880.1	.	.	.	.	.	.	.	.	.	.	A	15.61	2.883721	0.51908	.	.	ENSG00000100433	ENST00000340700;ENST00000312350;ENST00000319231;ENST00000556282	D;D;D;T	0.90676	-2.7;-2.71;-2.7;0.98	5.91	-7.33	0.01431	.	0.042994	0.85682	D	0.000000	T	0.81427	0.4820	N	0.11789	0.175	0.50632	D	0.999881	B;B;B	0.32467	0.372;0.372;0.027	B;B;B	0.42959	0.314;0.403;0.063	T	0.68792	-0.5315	10	0.18710	T	0.47	.	15.1307	0.72520	0.5942:0.0:0.4058:0.0	.	136;141;141	P57789;B2R8T4;Q6B014	KCNKA_HUMAN;.;.	K	136;141;141;124	ENSP00000343104:N136K;ENSP00000310568:N141K;ENSP00000312811:N141K;ENSP00000452587:N124K	ENSP00000310568:N141K	N	-	3	2	KCNK10	87776897	0.346000	0.24844	0.451000	0.26982	0.989000	0.77384	-0.115000	0.10741	-1.842000	0.01181	-0.250000	0.11733	AAT	.	.	.	none		0.403	KCNK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410167.1	NM_021161		C	88707144	A	C	88707144	3	2	275	1	0	0	0	0	1	0	0	0	8066	214	8	5	1228	5	KCNK10	14	88707144	Missense_Mutation	SNP	A	TCGA-Y8-A895-01A-11D-A35Z-10	12661514	88707144	18642396	68	17477											
ZC3H14	79882	hgsc.bcm.edu	37	chr14	89061310	89061310	+	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	gtgtccaagaatgaagcaaaAatttcatctttggaggttaa	15	12	9	5	0	2	2	1	1	1	1	3	3	3	3	1	2	1	2	1	2	6	3			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr14:89061310A>C	ENST00000251038.5	+	10	1504				ZC3H14_ENST00000555755.1_Intron|ZC3H14_ENST00000359301.3_Intron|ZC3H14_ENST00000393514.5_Intron|ZC3H14_ENST00000406216.3_Missense_Mutation_p.K80N|ZC3H14_ENST00000302216.8_Intron|ZC3H14_ENST00000555900.1_Missense_Mutation_p.K80N|ZC3H14_ENST00000556945.1_Intron|ZC3H14_ENST00000318308.6_Missense_Mutation_p.K80N|ZC3H14_ENST00000557607.1_Intron|ZC3H14_ENST00000336693.4_Intron	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							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						ATGAAGCAAAAATTTCATCTT	0.318																																					p.K80N		Atlas-SNP	.											.	ZC3H14	71	.	0			c.A240C						PASS	.						48	47	48					14																	89061310		2202	4300	6502	SO:0001627	intron_variant	79882	exon1			AGCAAAAATTTCA	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.1280-1768A>C	chr14.hg19:g.89061310A>C		214.0	0.0	.		148.0	54.0	.	NM_207662	A8MY46|B4DXU8|B4DZW7|B4E2H4|G3V5R4|Q6MZU4|Q6PJ32|Q6PUI6|Q6PUI8|Q86TQ5|Q86TW0|Q86TW1|Q8NCT6|Q8NCZ3|Q8TDE2|Q9HAC9|Q9Y5A0	Missense_Mutation	SNP	ENST00000251038.5	hg19	CCDS32133.1	.	.	.	.	.	.	.	.	.	.	A	15.01	2.707408	0.48412	.	.	ENSG00000100722	ENST00000318308;ENST00000555900;ENST00000406216;ENST00000557737	T;T;T;T	0.80909	-1.43;-1.43;-1.43;-1.43	5.61	4.47	0.54385	.	.	.	.	.	D	0.84234	0.5427	L	0.47716	1.5	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.994	D	0.83799	0.0235	9	0.72032	D	0.01	.	8.1105	0.30911	0.9088:0.0:0.0912:0.0	.	80;80	Q6PJT7-8;Q6PJT7-6	.;.	N	80	ENSP00000327176:K80N;ENSP00000451530:K80N;ENSP00000384682:K80N;ENSP00000451941:K80N	ENSP00000327176:K80N	K	+	3	2	ZC3H14	88131063	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.955000	0.29188	0.964000	0.38108	0.533000	0.62120	AAA	.	.	.	none		0.318	ZC3H14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410387.1	NM_024824		C	89061310	A	C	89061310	1	2	275	0	1	0	0	0	0	0	0	0	17578	11	1	5		5	ZC3H14	14	89061310	Intron	SNP	A	TCGA-Y8-A895-01A-11D-A35Z-10	354166	89061310	18288230	69	17478											
EML5	161436	hgsc.bcm.edu	37	chr14	89128042	89128042	+	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	cacaaatcccaaatcgtcccCggtagctagaaccattttgt	12	10	6	13	2	0	1	0	0	0	1	3	1	2	1	4	1	2	2	4	1	5	4			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr14:89128042C>A	ENST00000380664.5	-	25	3630	c.3631G>T	c.(3631-3633)Ggg>Tgg	p.G1211W	EML5_ENST00000554922.1_Missense_Mutation_p.G1211W|EML5_ENST00000352093.5_Missense_Mutation_p.G1173W			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	1211						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						AAATCGTCCCCGGTAGCTAGA	0.363																																					p.G1211W		Atlas-SNP	.											.	EML5	141	.	0			c.G3631T						PASS	.						60	57	58					14																	89128042		1842	4093	5935	SO:0001583	missense	161436	exon25			CGTCCCCGGTAGC	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.3631G>T	chr14.hg19:g.89128042C>A	ENSP00000370039:p.Gly1211Trp	145.0	0.0	.		144.0	57.0	.	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	hg19	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.075896	0.76415	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.59083	0.29;0.94;0.29	4.42	4.42	0.53409	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.81163	0.4765	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	0.86422	0.1755	10	0.87932	D	0	-11.0346	17.2287	0.86978	0.0:1.0:0.0:0.0	.	1211;1211	Q05BV3-5;Q05BV3	.;EMAL5_HUMAN	W	1211;1173;1211	ENSP00000451998:G1211W;ENSP00000298315:G1173W;ENSP00000370039:G1211W	ENSP00000298315:G1173W	G	-	1	0	EML5	88197795	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	7.320000	0.79064	2.284000	0.76573	0.460000	0.39030	GGG	.	.	.	none		0.363	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			A	89128042	C	A	89128042	3	1	275	1	0	0	0	0	1	0	0	0	5102	652	23	4	2378	4	EML5	14	89128042	Missense_Mutation	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10	66732	89128042	18221498	70	17479											
ADSSL1	122622	hgsc.bcm.edu	37	chr14	105207480	105207480	+	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	gctgagcggatcagacccatGgtccgagatggtgtttactt	8	11	13	9	2	1	3	1	1	0	2	2	5	2	4	2	3	2	2	2	3	1	3			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr14:105207480G>T	ENST00000330877.2	+	8	778	c.693G>T	c.(691-693)atG>atT	p.M231I	ADSSL1_ENST00000332972.5_Missense_Mutation_p.M274I	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)		TCAGACCCATGGTCCGAGATG	0.612																																					p.M274I		Atlas-SNP	.											.	ADSSL1	37	.	0			c.G822T						PASS	.						88	84	85					14																	105207480		2203	4299	6502	SO:0001583	missense	122622	exon8			ACCCATGGTCCGA	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.693G>T	chr14.hg19:g.105207480G>T	ENSP00000331260:p.Met231Ile	64.0	0.0	.		53.0	23.0	.	NM_199165		Missense_Mutation	SNP	ENST00000330877.2	hg19	CCDS9990.1	.	.	.	.	.	.	.	.	.	.	G	18.37	3.609432	0.66558	.	.	ENSG00000185100	ENST00000330877;ENST00000332972	T;T	0.41065	1.01;1.01	5.14	5.14	0.70334	.	0.040897	0.85682	D	0.000000	T	0.47581	0.1453	M	0.64170	1.965	0.80722	D	1	B;B	0.30634	0.288;0.123	B;B	0.34489	0.113;0.184	T	0.52124	-0.8617	10	0.72032	D	0.01	-9.8453	18.57	0.91132	0.0:0.0:1.0:0.0	.	274;231	Q8N142-2;Q8N142	.;PURA1_HUMAN	I	231;274	ENSP00000331260:M231I;ENSP00000333019:M274I	ENSP00000331260:M231I	M	+	3	0	ADSSL1	104278525	1.000000	0.71417	0.998000	0.56505	0.737000	0.42083	9.711000	0.98735	2.394000	0.81467	0.655000	0.94253	ATG	.	.	.	none		0.612	ADSSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410529.1			T	105207480	G	T	105207480	3	4	275	1	0	0	0	0	1	0	0	0	348	1348	47	4	1048	4	ADSSL1	14	105207480	Missense_Mutation	SNP	G	TCGA-Y8-A895-01A-11D-A35Z-10	16079438	105207480	2142060	71	17480											
HERC2	8924	hgsc.bcm.edu	37	chr15	28499655	28499655	+	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	cttctgtgcttcttttttggCttcaatatcctgtaattcat	6	21	5	9	0	4	0	2	0	2	0	5	0	5	0	1	1	1	3	1	1	3	9			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr15:28499655C>T	ENST00000261609.7	-	20	2989	c.2881G>A	c.(2881-2883)Gcc>Acc	p.A961T		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)		TCTTTTTTGGCTTCAATATCC	0.403																																					p.A961T		Atlas-SNP	.											.	HERC2	501	.	0			c.G2881A						PASS	.						81	63	69					15																	28499655		2203	4300	6503	SO:0001583	missense	8924	exon20			TTTTGGCTTCAAT	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.2881G>A	chr15.hg19:g.28499655C>T	ENSP00000261609:p.Ala961Thr	24.0	0.0	.		20.0	6.0	.	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	C	15.86	2.957966	0.53400	.	.	ENSG00000128731	ENST00000261609	T	0.37915	1.17	5.67	4.76	0.60689	.	0.055869	0.64402	N	0.000001	T	0.30885	0.0779	L	0.44542	1.39	0.80722	D	1	B	0.21452	0.056	B	0.19666	0.026	T	0.06267	-1.0836	10	0.20046	T	0.44	.	14.1746	0.65532	0.0:0.9285:0.0:0.0715	.	961	O95714	HERC2_HUMAN	T	961	ENSP00000261609:A961T	ENSP00000261609:A961T	A	-	1	0	HERC2	26173250	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.086000	0.71352	1.402000	0.46780	0.585000	0.79938	GCC	.	.	.	none		0.403	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		T	28499655	C	T	28499655	3	4	275	1	0	0	0	0	1	0	0	0	7065	797	28	2	11919	2	HERC2	15	28499655	Missense_Mutation	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10		28499655	74031737	72	17481											
HERC1	8925	hgsc.bcm.edu	37	chr15	64025169	64025169	+	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	gggtcttcatcaaaatttcaGccaggtgggtatctggatgg	9	12	13	7	0	5	0	3	0	2	0	5	1	5	1	1	5	1	1	1	5	3	3			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr15:64025169G>T	ENST00000443617.2	-	14	2909	c.2822C>A	c.(2821-2823)gCt>gAt	p.A941D		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	941					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						CAAAATTTCAGCCAGGTGGGT	0.413																																					p.A941D		Atlas-SNP	.											.	HERC1	624	.	0			c.C2822A						PASS	.						60	57	58					15																	64025169		1838	4084	5922	SO:0001583	missense	8925	exon14			ATTTCAGCCAGGT	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.2822C>A	chr15.hg19:g.64025169G>T	ENSP00000390158:p.Ala941Asp	167.0	0.0	.		131.0	50.0	.	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	G	35	5.519645	0.96416	.	.	ENSG00000103657	ENST00000443617	T	0.32988	1.43	5.67	5.67	0.87782	.	0.000000	0.64402	U	0.000001	T	0.47097	0.1427	L	0.29908	0.895	0.80722	D	1	D	0.71674	0.998	D	0.80764	0.994	T	0.45086	-0.9285	10	0.72032	D	0.01	.	19.7607	0.96316	0.0:0.0:1.0:0.0	.	941	Q15751	HERC1_HUMAN	D	941	ENSP00000390158:A941D	ENSP00000390158:A941D	A	-	2	0	HERC1	61812222	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.727000	0.98787	2.658000	0.90341	0.655000	0.94253	GCT	.	.	.	none		0.413	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		T	64025169	G	T	64025169	3	4	275	1	0	0	0	0	1	0	0	0	7064	971	34	4	12023	4	HERC1	15	64025169	Missense_Mutation	SNP	G	TCGA-Y8-A895-01A-11D-A35Z-10	35525514	64025169	38506223	73	17482											
PKD1	5310	hgsc.bcm.edu	37	chr16	2168325	2168325	+	Missense_Mutation	SNP	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	accagccctgctccgagaggGctgcgaggccctggccggtg	5	5	16	15	3	0	1	0	0	0	1	1	3	1	1	5	4	3	2	5	4	0	0			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr16:2168325G>A	ENST00000262304.4	-	5	876	c.668C>T	c.(667-669)gCc>gTc	p.A223V	RP11-304L19.2_ENST00000562027.1_RNA|PKD1_ENST00000423118.1_Missense_Mutation_p.A223V	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	223	WSC. {ECO:0000255|PROSITE- ProRule:PRU00558}.				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						CTCCGAGAGGGCTGCGAGGCC	0.706																																					p.A223V		Atlas-SNP	.											.	PKD1	184	.	0			c.C668T						PASS	.						1	1	1					16																	2168325		1019	1899	2918	SO:0001583	missense	5310	exon5			GAGAGGGCTGCGA	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.668C>T	chr16.hg19:g.2168325G>A	ENSP00000262304:p.Ala223Val	136.0	0.0	.		150.0	31.0	.	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	hg19	CCDS32369.1	.	.	.	.	.	.	.	.	.	.	g	9.660	1.143801	0.21205	.	.	ENSG00000008710	ENST00000262304;ENST00000423118	T;T	0.59638	0.25;0.25	5.0	1.54	0.23209	Carbohydrate-binding WSC (2);Carbohydrate-binding WSC, subgroup (1);Polycystin cation channel (1);	0.130110	0.50627	D	0.000102	T	0.65386	0.2686	M	0.63428	1.95	0.09310	N	1	D;D	0.61080	0.989;0.957	P;P	0.58266	0.836;0.799	T	0.58584	-0.7611	10	0.72032	D	0.01	.	10.6659	0.45731	0.0806:0.3285:0.591:0.0	.	223;223	P98161-3;P98161	.;PKD1_HUMAN	V	223	ENSP00000262304:A223V;ENSP00000399501:A223V	ENSP00000262304:A223V	A	-	2	0	PKD1	2108326	0.746000	0.28272	0.021000	0.16686	0.027000	0.11550	0.703000	0.25646	0.516000	0.28340	0.450000	0.29827	GCC	.	.	.	none		0.706	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			A	2168325	G	A	2168325	3	1	275	1	0	0	0	0	1	0	0	0	11970	1203	42	2	12411	2	PKD1	16	2168325	Missense_Mutation	SNP	G	TCGA-Y8-A895-01A-11D-A35Z-10		2168325	88186428	74	17483											
MYH11	4629	hgsc.bcm.edu	37	chr16	15820719	15820720	+	Frame_Shift_Ins	INS	-	-	TT																															ctcacctgcagcttgtggacINStttgtcattgagctccgccc																										TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr16:15820719_15820720insTT	ENST00000300036.5	-	28	3952_3953	c.3843_3844insAA	c.(3841-3846)aaagtcfs	p.V1282fs	MYH11_ENST00000452625.2_Frame_Shift_Ins_p.V1289fs|AF001548.5_ENST00000574212.1_RNA|MYH11_ENST00000396324.3_Frame_Shift_Ins_p.V1289fs|MYH11_ENST00000576790.2_Frame_Shift_Ins_p.V1282fs	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1282					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						AGCTTGTGGACTTTGTCATTGA	0.639			T	CBFB	AML																																p.V1289fs		Atlas-INDEL	.		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	.	MYH11	520	.	0			c.3865_3866insAA						PASS	.																																			SO:0001589	frameshift_variant	4629	exon29			.	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.3842_3843dupAA	chr16.hg19:g.15820720_15820721dupTT	ENSP00000300036:p.Val1282fs	60.0	0.0	0		47.0	10.0	0.212766	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Frame_Shift_Ins	INS	ENST00000300036.5	hg19	CCDS10565.1																																																																																			.	.	.	none		0.639	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		TT	15820720	-	TT	15820719	7	5	275	1	0	1	1	0	0	0	0	0	10038	565	20	0	2165	0	MYH11	16	15820719	Frame_Shift_Ins	INS	-	TCGA-Y8-A895-01A-11D-A35Z-10	13652394	15820719	74534034	75	17484											
ANKS4B	257629	hgsc.bcm.edu	37	chr16	21261239	21261239	+	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	atgaatgtgttgctctcctgGacaaggctgccactgcacag	9	10	11	11	0	1	1	0	1	1	0	2	2	1	2	2	2	3	4	2	2	2	1			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr16:21261239G>C	ENST00000311620.5	+	2	425	c.352G>C	c.(352-354)Gac>Cac	p.D118H		NM_145865.2	NP_665872.2	Q8N8V4	ANS4B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 4B	118					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)		TGCTCTCCTGGACAAGGCTGC	0.522																																					p.D118H		Atlas-SNP	.											.	ANKS4B	43	.	0			c.G352C						PASS	.						65	64	65					16																	21261239		2106	4244	6350	SO:0001583	missense	257629	exon2			CTCCTGGACAAGG	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.352G>C	chr16.hg19:g.21261239G>C	ENSP00000308772:p.Asp118His	106.0	0.0	.		150.0	49.0	.	NM_145865		Missense_Mutation	SNP	ENST00000311620.5	hg19	CCDS42130.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.430655	0.83776	.	.	ENSG00000175311	ENST00000311620	T	0.63913	-0.07	5.81	5.81	0.92471	Ankyrin repeat-containing domain (4);	0.106321	0.64402	D	0.000011	T	0.65344	0.2682	N	0.08118	0	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73193	-0.4060	10	0.72032	D	0.01	-25.3375	19.0439	0.93012	0.0:0.0:1.0:0.0	.	118	Q8N8V4	ANS4B_HUMAN	H	118	ENSP00000308772:D118H	ENSP00000308772:D118H	D	+	1	0	ANKS4B	21168740	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	9.813000	0.99286	2.741000	0.93983	0.591000	0.81541	GAC	.	.	.	none		0.522	ANKS4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436535.1	NM_145865		C	21261239	G	C	21261239	3	2	275	1	0	0	0	0	1	0	0	0	691	1174	41	4	358	4	ANKS4B	16	21261239	Missense_Mutation	SNP	G	TCGA-Y8-A895-01A-11D-A35Z-10	5440520	21261239	69093514	76	17485											
IL4R	3566	hgsc.bcm.edu	37	chr16	27374814	27374814	+	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	gggcagtggcattgtctactCagcccttacctgccacctgt	6	11	10	14	0	2	0	1	0	1	0	2	0	2	0	4	2	4	2	4	2	2	3	rs370734074		TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr16:27374814C>A	ENST00000395762.2	+	11	2400	c.2141C>A	c.(2140-2142)tCa>tAa	p.S714*	IL4R_ENST00000380922.3_Nonsense_Mutation_p.S699*|IL4R_ENST00000170630.2_Nonsense_Mutation_p.S714*|IL4R_ENST00000543915.2_Nonsense_Mutation_p.S714*	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	714					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						ATTGTCTACTCAGCCCTTACC	0.627																																					p.S714X		Atlas-SNP	.											.	IL4R	70	.	0			c.C2141A						PASS	.						65	62	63					16																	27374814		2197	4300	6497	SO:0001587	stop_gained	3566	exon11			TCTACTCAGCCCT	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.2141C>A	chr16.hg19:g.27374814C>A	ENSP00000379111:p.Ser714*	73.0	0.0	.		99.0	35.0	.	NM_000418	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Nonsense_Mutation	SNP	ENST00000395762.2	hg19	CCDS10629.1	.	.	.	.	.	.	.	.	.	.	C	42	9.662478	0.99233	.	.	ENSG00000077238	ENST00000395762;ENST00000543915;ENST00000380922;ENST00000170630	.	.	.	5.18	5.18	0.71444	.	0.679297	0.12852	N	0.433821	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-28.6605	14.1998	0.65696	0.0:1.0:0.0:0.0	.	.	.	.	X	714;714;699;714	.	ENSP00000170630:S714X	S	+	2	0	IL4R	27282315	0.962000	0.33011	0.972000	0.41901	0.945000	0.59286	2.233000	0.43027	2.415000	0.81967	0.655000	0.94253	TCA	.	.	.	alt		0.627	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4			A	27374814	C	A	27374814	4	1	275	1	0	0	0	0	0	1	0	0	7705	838	29	4	2193	4	IL4R	16	27374814	Nonsense_Mutation	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10	6113575	27374814	62979939	77	17486											
ZNF629	23361	hgsc.bcm.edu	37	chr16	30794005	30794005	+	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	ccgagccccagcaggctgtcGccctgggccctacgcgctgg	4	5	14	18	4	0	0	0	0	0	0	1	1	0	0	5	3	3	3	5	3	1	1	rs372927017		TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr16:30794005G>A	ENST00000262525.4	-	3	1851	c.1644C>T	c.(1642-1644)ggC>ggT	p.G548G	RP11-2C24.6_ENST00000575562.1_RNA	NM_001080417.1	NP_001073886.1	Q9UEG4	ZN629_HUMAN	zinc finger protein 629	548					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(3)|urinary_tract(1)	22			Colorectal(24;0.198)			GCAGGCTGTCGCCCTGGGCCC	0.692																																					p.G548G		Atlas-SNP	.											.	ZNF629	44	.	0			c.C1644T						PASS	.	G		0,4036		0,0,2018	18	19	18		1644	-11.6	0	16		18	1,8315		0,1,4157	no	coding-synonymous	ZNF629	NM_001080417.1		0,1,6175	AA,AG,GG		0.012,0.0,0.0081		548/870	30794005	1,12351	2018	4158	6176	SO:0001819	synonymous_variant	23361	exon3			GCTGTCGCCCTGG	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.1644C>T	chr16.hg19:g.30794005G>A		64.0	0.0	.		72.0	30.0	.	NM_001080417	Q15938	Silent	SNP	ENST00000262525.4	hg19	CCDS45463.1																																																																																			.	.	.	weak		0.692	ZNF629-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434291.1	NM_015309		A	30794005	G	A	30794005	2	1	275	1	0	0	0	0	0	0	0	1	18065	1074	38	1		1	ZNF629	16	30794005	Silent	SNP	G	TCGA-Y8-A895-01A-11D-A35Z-10	3419191	30794005	59560748	78	17487											
CHD9	80205	hgsc.bcm.edu	37	chr16	53301225	53301225	+	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	gaacagcttggttattgacaCtccaagaattaggaagcaaa	16	9	9	7	0	0	2	0	1	0	1	1	4	1	3	1	2	3	3	1	2	7	4			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr16:53301225C>G	ENST00000398510.3	+	20	4427	c.4340C>G	c.(4339-4341)aCt>aGt	p.T1447S	CHD9_ENST00000447540.1_Missense_Mutation_p.T1447S|CHD9_ENST00000564845.1_Missense_Mutation_p.T1447S|CHD9_ENST00000566029.1_Missense_Mutation_p.T1447S			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	1447					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)				GTTATTGACACTCCAAGAATT	0.358																																					p.T1447S		Atlas-SNP	.											.	CHD9	203	.	0			c.C4340G						PASS	.						78	75	76					16																	53301225		1862	4111	5973	SO:0001583	missense	80205	exon21			TTGACACTCCAAG	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.4340C>G	chr16.hg19:g.53301225C>G	ENSP00000381522:p.Thr1447Ser	94.0	0.0	.		126.0	7.0	.	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Missense_Mutation	SNP	ENST00000398510.3	hg19		.	.	.	.	.	.	.	.	.	.	C	23.3	4.396994	0.83120	.	.	ENSG00000177200	ENST00000447540;ENST00000398510;ENST00000219084	D;D	0.85702	-2.02;-2.02	5.24	5.24	0.73138	.	0.206501	0.33631	N	0.004702	D	0.90225	0.6944	L	0.57536	1.79	0.80722	D	1	B;B;D;D	0.67145	0.024;0.198;0.993;0.996	B;B;D;D	0.73380	0.041;0.343;0.956;0.98	D	0.86487	0.1795	10	0.16420	T	0.52	-6.1431	19.1729	0.93588	0.0:1.0:0.0:0.0	.	973;1447;1447;1447	B4DR07;Q3L8U1-3;Q3L8U1;Q3L8U1-2	.;.;CHD9_HUMAN;.	S	1447;1447;973	ENSP00000396345:T1447S;ENSP00000381522:T1447S	ENSP00000219084:T973S	T	+	2	0	CHD9	51858726	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.973000	0.70456	2.588000	0.87417	0.650000	0.86243	ACT	.	.	.	none		0.358	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		G	53301225	C	G	53301225	3	3	275	1	0	0	0	0	1	0	0	0	3334	565	20	4	4418	4	CHD9	16	53301225	Missense_Mutation	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10	22507220	53301225	37053528	79	17488											
RPA1	6117	hgsc.bcm.edu	37	chr17	1787152	1787152	+	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	atggtgtttccatctctgatCtaaagagcggcggagtcgga	9	11	13	8	3	2	2	0	1	2	1	5	4	3	4	1	4	1	1	1	4	2	2			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr17:1787152C>T	ENST00000254719.5	+	13	1398	c.1288C>T	c.(1288-1290)Cta>Tta	p.L430L		NM_002945.3	NP_002936.1	P27694	RFA1_HUMAN	replication protein A1, 70kDa	430					base-excision repair (GO:0006284)|DNA recombinase assembly (GO:0000730)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|hemopoiesis (GO:0030097)|homeostasis of number of cells within a tissue (GO:0048873)|in utero embryonic development (GO:0001701)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of cell proliferation (GO:0008284)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|DNA replication factor A complex (GO:0005662)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|metal ion binding (GO:0046872)|single-stranded DNA binding (GO:0003697)			breast(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(2)	10						CATCTCTGATCTAAAGAGCGG	0.502								Nucleotide excision repair (NER)																													p.L430L		Atlas-SNP	.											.	RPA1	48	.	0			c.C1288T						PASS	.						169	145	153					17																	1787152		2203	4300	6503	SO:0001819	synonymous_variant	6117	exon13			TCTGATCTAAAGA	M63488	CCDS11014.1	17p13.3	2008-02-05	2002-08-29		ENSG00000132383	ENSG00000132383			10289	protein-coding gene	gene with protein product		179835	"replication protein A1 (70kD)"			8454588	Standard	NM_002945		Approved	REPA1, RPA70, HSSB, RF-A, RP-A	uc002fto.2	P27694	OTTHUMG00000090579	ENST00000254719.5:c.1288C>T	chr17.hg19:g.1787152C>T		188.0	0.0	.		240.0	50.0	.	NM_002945	A8K0Y9|Q59ES9	Silent	SNP	ENST00000254719.5	hg19	CCDS11014.1																																																																																			.	.	.	none		0.502	RPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207118.2	NM_002945		T	1787152	C	T	1787152	2	4	275	1	0	0	0	0	0	0	0	1	13549	912	32	2		2	RPA1	17	1787152	Silent	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10		1787152	79408058	80	17489											
DNAH9	1770	hgsc.bcm.edu	37	chr17	11584061	11584062	+	Frame_Shift_Ins	INS	-	-	AC																															gctgcctgagaaatggaacaINSacataaaaaaggtggccatt																										TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr17:11584061_11584062insAC	ENST00000262442.4	+	19	3666_3667	c.3598_3599insAC	c.(3598-3600)aacfs	p.N1200fs	DNAH9_ENST00000454412.2_Frame_Shift_Ins_p.N1200fs	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	1200	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)		GAAATGGAACAACATAAAAAAG	0.535																																					p.N1200fs		Atlas-Indel,Pindel	.											.	DNAH9	695	.	0			c.3598_3599insAC						PASS	.																																			SO:0001589	frameshift_variant	1770	exon19			.	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.3599_3600dupAC	chr17.hg19:g.11584062_11584063dupAC	ENSP00000262442:p.Asn1200fs	175.0	0.0	0		235.0	66.0	0.280851	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Frame_Shift_Ins	INS	ENST00000262442.4	hg19	CCDS11160.1																																																																																			.	.	.	none		0.535	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		AC	11584062	-	AC	11584061	7	5	275	1	0	1	1	0	0	0	0	0	4610	130	5	0	3672	0	DNAH9	17	11584061	Frame_Shift_Ins	INS	-	TCGA-Y8-A895-01A-11D-A35Z-10	9796909	11584061	69611149	81	17490											
KRT15	3866	hgsc.bcm.edu	37	chr17	39674603	39674617	+	In_Frame_Del	DEL	GGTCTTGAAGTATTG	GGTCTTGAAGTATTG	-																															ttgtcccggagctcttcaatGgtcttgaagtattggctgta																								rs373600329|rs139517360	byFrequency	TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	GGTCTTGAAGTATTG	GGTCTTGAAGTATTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr17:39674603_39674617delGGTCTTGAAGTATTG	ENST00000254043.3	-	1	4048_4062	c.463_477delCAATACTTCAAGACC	c.(463-477)caatacttcaagaccdel	p.QYFKT155del	KRT15_ENST00000393981.3_In_Frame_Del_p.NTSRP18del|KRT15_ENST00000393976.2_In_Frame_Del_p.QYFKT155del|KRT15_ENST00000393974.3_In_Frame_Del_p.NTSRP18del	NM_002275.3	NP_002266	P19012	K1C15_HUMAN	keratin 15	155	Linker 1.|Rod.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)	p.Q155R(1)		NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16		Breast(137;0.000286)				GCTCTTCAATGGTCTTGAAGTATTGGCTGTAGTCG	0.544																																					p.155_160del		Atlas-Indel,Pindel	.											.	KRT15	60	.	1	Substitution - Missense(1)	endometrium(1)	c.464_478del						PASS	.																																			SO:0001651	inframe_deletion	3866	exon1			.		CCDS11398.1	17q21.2	2013-06-20			ENSG00000171346	ENSG00000171346		"-", "Intermediate filaments type I, keratins (acidic)"	6421	protein-coding gene	gene with protein product	"keratin-15, basic", "keratin-15, beta", "type I cytoskeletal 15", "cytokeratin 15"	148030				16831889	Standard	NM_002275		Approved	K15, CK15, K1CO	uc002hwy.3	P19012	OTTHUMG00000133435	ENST00000254043.3:c.463_477delCAATACTTCAAGACC	chr17.hg19:g.39674603_39674617delGGTCTTGAAGTATTG	ENSP00000254043:p.Gln155_Thr159del	87.0	0.0	0		68.0	27.0	0.397059	NM_002275	B3KQY1|B3KRA2|E0CX14|Q53XV8|Q9BUG4	In_Frame_Del	DEL	ENST00000254043.3	hg19	CCDS11398.1																																																																																			.	.	.	none		0.544	KRT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257301.1	NM_002275		-	39674617	GGTCTTGAAGTATTG	-	39674603	7	5	275	1	0	1	0	1	0	0	0	0	8459	1335	47	0	925	0	KRT15	17	39674603	In_Frame_Del	DEL	GGTCTTGAAGTATTG	TCGA-Y8-A895-01A-11D-A35Z-10	28090542	39674603	41520607	82	17491											
FAM134C	162427	hgsc.bcm.edu	37	chr17	40744166	40744171	+	In_Frame_Del	DEL	GTCAGG	GTCAGG	-																															aaaacacaagacgaagagatGtcagggcaaaaaacctacag																										TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	GTCAGG	GTCAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr17:40744166_40744171delGTCAGG	ENST00000309428.5	-	2	308_313	c.249_254delCCTGAC	c.(247-255)gccctgaca>gca	p.LT84del	FAM134C_ENST00000543197.1_5'UTR|FAM134C_ENST00000585894.1_5'UTR	NM_178126.3	NP_835227.1	Q86VR2	F134C_HUMAN	family with sequence similarity 134, member C	84						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|liver(1)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	11		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.134)		ACGAAGAGATGTCAGGGCAAAAAACC	0.379																																					p.84_85del		Atlas-Indel,Pindel	.											.	FAM134C	26	.	0			c.250_255del						PASS	.																																			SO:0001651	inframe_deletion	162427	exon2			.	BC049370	CCDS11432.1	17q21.2	2007-05-01							27258	protein-coding gene	gene with protein product						12477932	Standard	NM_178126		Approved	DKFZp686B1036, FLJ33806	uc002ial.2	Q86VR2		ENST00000309428.5:c.249_254delCCTGAC	chr17.hg19:g.40744166_40744171delGTCAGG	ENSP00000309432:p.Leu84_Thr85del	75.0	0.0	0		59.0	31.0	0.525424	NM_178126	B3KR75	In_Frame_Del	DEL	ENST00000309428.5	hg19	CCDS11432.1																																																																																			.	.	.	none		0.379	FAM134C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450536.1	NM_178126		-	40744171	GTCAGG	-	40744166	7	5	275	1	0	1	0	1	0	0	0	0	5451	1377	48	0	1178	0	FAM134C	17	40744166	In_Frame_Del	DEL	GTCAGG	TCGA-Y8-A895-01A-11D-A35Z-10	1069563	40744166	40451044	83	17492											
TBC1D16	125058	hgsc.bcm.edu	37	chr17	77987194	77987194	+	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	tgctcccccagcccctgcagCccctccggcgggtgcacgca	4	5	11	21	3	0	0	0	0	0	0	2	0	2	0	7	2	5	4	7	2	0	0			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr17:77987194C>T	ENST00000310924.2	-	2	268	c.153G>A	c.(151-153)ggG>ggA	p.G51G		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	51							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)			GCCCCTGCAGCCCCTCCGGCG	0.667																																					p.G51G	Ovarian(14;397 562 4850 31922 49378)	Atlas-SNP	.											.	TBC1D16	48	.	0			c.G153A						PASS	.						11	13	12					17																	77987194		2197	4290	6487	SO:0001819	synonymous_variant	125058	exon2			CTGCAGCCCCTCC	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.153G>A	chr17.hg19:g.77987194C>T		117.0	0.0	.		115.0	61.0	.	NM_019020	B9A6L7|I3L1E0|I3L4U2|Q8N3Z4|Q96DH7	Silent	SNP	ENST00000310924.2	hg19	CCDS11766.1																																																																																			.	.	.	none		0.667	TBC1D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437145.1	NM_019020		T	77987194	C	T	77987194	2	4	275	1	0	0	0	0	0	0	0	1	15617	726	26	2		2	TBC1D16	17	77987194	Silent	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10	37243028	77987194	3208016	84	17493											
MIDN	90007	hgsc.bcm.edu	37	chr19	1251579	1251580	+	Frame_Shift_Ins	INS	-	-	C																															gccggctcagttcggggaagINSctgcaggagttcggcgtggg																								rs375683589		TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr19:1251579_1251580insC	ENST00000591446.2	+	2	661_662	c.252_253insC	c.(253-255)ctgfs	p.L85fs	MIDN_ENST00000300952.2_Frame_Shift_Ins_p.L85fs			Q504T8	MIDN_HUMAN	midnolin	85	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.					cytosol (GO:0005829)|nucleolus (GO:0005730)				NS(1)|endometrium(3)|kidney(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTTCGGGGAAGCTGCAGGAGTT	0.668																																					p.K84fs		Atlas-Indel,Pindel	.											.	MIDN	34	.	0			c.252_253insC						PASS	.																																			SO:0001589	frameshift_variant	90007	exon3			.	AC004221	CCDS32864.1	19p13.3	2013-09-20			ENSG00000167470	ENSG00000167470			16298	protein-coding gene	gene with protein product		606700				10974535	Standard	XM_005259671		Approved		uc002lrp.3	Q504T8	OTTHUMG00000180144	ENST00000591446.2:c.253dupC	chr19.hg19:g.1251580_1251580dupC	ENSP00000467679:p.Leu85fs	88.0	0.0	0		72.0	22.0	0.305556	NM_177401	Q96BW8	Frame_Shift_Ins	INS	ENST00000591446.2	hg19	CCDS32864.1																																																																																			.	.	.	none		0.668	MIDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449965.2			C	1251580	-	C	1251579	7	5	275	1	0	1	1	0	0	0	0	0	9586	962	34	0	258	0	MIDN	19	1251579	Frame_Shift_Ins	INS	-	TCGA-Y8-A895-01A-11D-A35Z-10		1251579	57877404	85	17494											
CACNA1A	773	hgsc.bcm.edu	37	chr19	13394119	13394119	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggctgcacagggtcctcggCggccagggcgatgctgctca	5	6	17	13	3	1	0	1	0	0	0	3	1	2	0	2	5	3	4	2	5	0	0			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr19:13394119C>T	ENST00000360228.5	-	22	3783	c.3784G>A	c.(3784-3786)Gcc>Acc	p.A1262T	CACNA1A_ENST00000573710.2_Missense_Mutation_p.A1263T	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	1263					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)	GGGTCCTCGGCGGCCAGGGCG	0.602																																					p.A1263T		Atlas-SNP	.											.	CACNA1A	715	.	0			c.G3787A						PASS	.						96	104	101					19																	13394119		2181	4283	6464	SO:0001583	missense	773	exon22			CCTCGGCGGCCAG	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.3784G>A	chr19.hg19:g.13394119C>T	ENSP00000353362:p.Ala1262Thr	118.0	0.0	.		117.0	46.0	.	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	hg19	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.103620	0.76983	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.97505	-4.41	4.92	3.86	0.44501	.	0.000000	0.85682	D	0.000000	D	0.97785	0.9273	M	0.75777	2.31	0.80722	D	1	D;D;D	0.69078	0.987;0.997;0.994	P;P;P	0.62014	0.777;0.897;0.521	D	0.98041	1.0382	10	0.87932	D	0	.	13.5836	0.61917	0.1565:0.8435:0.0:0.0	.	1263;1266;1262	O00555;E9PD31;Q9NS88	CAC1A_HUMAN;.;.	T	1262;1266;1263;1263	ENSP00000353362:A1262T	ENSP00000317661:A1263T	A	-	1	0	CACNA1A	13255119	1.000000	0.71417	0.987000	0.45799	0.998000	0.95712	5.699000	0.68310	1.054000	0.40438	0.561000	0.74099	GCC	.	.	.	none		0.602	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		T	13394119	C	T	13394119	3	4	275	1	0	0	0	0	1	0	0	0	2540	768	27	1	3942	1	CACNA1A	19	13394119	Missense_Mutation	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10	12142540	13394119	45734864	86	17495											
UNC13A	23025	hgsc.bcm.edu	37	chr19	17740112	17740112	+	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	gagatgatgtctgcatactgGaggagcacattactgatggt	11	11	13	6	0	1	3	0	2	1	1	1	6	1	5	0	3	4	2	0	3	2	2			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr19:17740112G>A	ENST00000519716.2	-	31	3689	c.3690C>T	c.(3688-3690)ctC>ctT	p.L1230L	UNC13A_ENST00000552293.1_Silent_p.L1230L|UNC13A_ENST00000428389.2_Silent_p.L1318L|UNC13A_ENST00000551649.1_Silent_p.L1230L|UNC13A_ENST00000550896.1_Silent_p.L1228L|UNC13A_ENST00000252773.7_Silent_p.L1230L	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	1230	MHD1. {ECO:0000255|PROSITE- ProRule:PRU00587}.				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						CTGCATACTGGAGGAGCACAT	0.572																																					p.L1230L		Atlas-SNP	.											.	UNC13A	299	.	0			c.C3690T						PASS	.						86	83	84					19																	17740112		2083	4212	6295	SO:0001819	synonymous_variant	23025	exon30			ATACTGGAGGAGC	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.3690C>T	chr19.hg19:g.17740112G>A		70.0	0.0	.		50.0	15.0	.	NM_001080421	E5RHY9	Silent	SNP	ENST00000519716.2	hg19	CCDS46013.2																																																																																			.	.	.	none		0.572	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		A	17740112	G	A	17740112	2	1	275	1	0	0	0	0	0	0	0	1	16996	1161	41	2		2	UNC13A	19	17740112	Silent	SNP	G	TCGA-Y8-A895-01A-11D-A35Z-10	4345993	17740112	41388871	87	17496											
KLHL26	55295	hgsc.bcm.edu	37	chr19	18778568	18778568	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcggcacatcatcgacttcGcctacagcgccgaggtgaca	9	7	11	14	5	1	1	1	1	0	0	3	3	1	1	2	2	3	1	2	2	1	2			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr19:18778568G>A	ENST00000300976.4	+	3	451	c.361G>A	c.(361-363)Gcc>Acc	p.A121T	KLHL26_ENST00000596843.1_3'UTR|KLHL26_ENST00000599006.1_Missense_Mutation_p.A121T	NM_018316.1	NP_060786.1	Q53HC5	KLH26_HUMAN	kelch-like family member 26	121	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.									breast(1)|central_nervous_system(1)|kidney(1)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						CATCGACTTCGCCTACAGCGC	0.667																																					p.A121T		Atlas-SNP	.											.	KLHL26	43	.	0			c.G361A						PASS	.						71	68	69					19																	18778568		2203	4298	6501	SO:0001583	missense	55295	exon3			GACTTCGCCTACA		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.361G>A	chr19.hg19:g.18778568G>A	ENSP00000300976:p.Ala121Thr	92.0	0.0	.		87.0	27.0	.	NM_018316	Q8TAP0|Q9NUX3	Missense_Mutation	SNP	ENST00000300976.4	hg19	CCDS12384.1	.	.	.	.	.	.	.	.	.	.	G	16.94	3.261341	0.59431	.	.	ENSG00000167487	ENST00000431920;ENST00000300976	T	0.71461	-0.57	5.04	5.04	0.67666	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.82121	0.4968	M	0.68317	2.08	0.80722	D	1	D	0.71674	0.998	D	0.67725	0.953	T	0.83101	-0.0128	10	0.51188	T	0.08	.	17.3648	0.87360	0.0:0.0:1.0:0.0	.	121	Q53HC5	KLH26_HUMAN	T	121	ENSP00000300976:A121T	ENSP00000300976:A121T	A	+	1	0	KLHL26	18639568	1.000000	0.71417	0.988000	0.46212	0.027000	0.11550	6.507000	0.73717	2.341000	0.79615	0.591000	0.81541	GCC	.	.	.	none		0.667	KLHL26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465145.1	NM_018316		A	18778568	G	A	18778568	3	1	275	1	0	0	0	0	1	0	0	0	8388	1087	38	1	371	1	KLHL26	19	18778568	Missense_Mutation	SNP	G	TCGA-Y8-A895-01A-11D-A35Z-10	1038456	18778568	40350415	88	17497											
ZNF790	388536	hgsc.bcm.edu	37	chr19	37309949	37309949	+	Missense_Mutation	SNP	A	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	ttgagcaagatacgaagcccAagtaaaagtcttcccgcatt	14	9	8	10	2	1	2	0	1	1	1	2	3	2	2	2	0	3	3	2	0	6	5			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr19:37309949A>C	ENST00000356725.4	-	5	1417	c.1297T>G	c.(1297-1299)Tgg>Ggg	p.W433G	CTD-2162K18.5_ENST00000588906.1_RNA|CTD-2162K18.5_ENST00000587278.1_RNA	NM_001242802.1|NM_206894.3	NP_001229731.1|NP_996777.2	Q6PG37	ZN790_HUMAN	zinc finger protein 790	433					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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)			TACGAAGCCCAAGTAAAAGTC	0.413																																					p.W433G		Atlas-SNP	.											.	ZNF790	89	.	0			c.T1297G						PASS	.						91	92	92					19																	37309949		2203	4300	6503	SO:0001583	missense	388536	exon5			AAGCCCAAGTAAA	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.1297T>G	chr19.hg19:g.37309949A>C	ENSP00000349161:p.Trp433Gly	107.0	0.0	.		91.0	39.0	.	NM_206894		Missense_Mutation	SNP	ENST00000356725.4	hg19	CCDS12496.1	.	.	.	.	.	.	.	.	.	.	A	3.322	-0.138613	0.06669	.	.	ENSG00000197863	ENST00000356725	T	0.07327	3.2	3.14	0.93	0.19454	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04770	0.0129	N	0.22421	0.69	0.09310	N	1	P	0.42123	0.771	B	0.39217	0.294	T	0.35101	-0.9802	9	0.27785	T	0.31	.	2.8271	0.05488	0.5719:0.0:0.2386:0.1895	.	433	Q6PG37	ZN790_HUMAN	G	433	ENSP00000349161:W433G	ENSP00000349161:W433G	W	-	1	0	ZNF790	42001789	0.000000	0.05858	0.004000	0.12327	0.486000	0.33341	-2.685000	0.00834	0.021000	0.15133	0.402000	0.26972	TGG	.	.	.	none		0.413	ZNF790-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385341.2	NM_206894		C	37309949	A	C	37309949	3	2	275	1	0	0	0	0	1	0	0	0	18174	130	5	5	617	5	ZNF790	19	37309949	Missense_Mutation	SNP	A	TCGA-Y8-A895-01A-11D-A35Z-10	18531381	37309949	21819034	89	17498											
ZNF546	339327	hgsc.bcm.edu	37	chr19	40521132	40521132	+	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	ctttattcgtagcactcatcTcacgcaacatcacagaattc	12	12	4	13	2	3	1	3	0	1	1	6	1	3	1	0	0	2	3	0	0	4	5			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr19:40521132T>A	ENST00000347077.4	+	7	2171	c.1955T>A	c.(1954-1956)cTc>cAc	p.L652H	ZNF546_ENST00000596894.1_Intron|ZNF546_ENST00000600094.1_Missense_Mutation_p.L626H	NM_178544.3	NP_848639.2	Q86UE3	ZN546_HUMAN	zinc finger protein 546	652			L -> F (in dbSNP:rs12373540).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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)					AGCACTCATCTCACGCAACAT	0.413																																					p.L652H		Atlas-SNP	.											.	ZNF546	93	.	0			c.T1955A						PASS	.						68	65	66					19																	40521132		2203	4300	6503	SO:0001583	missense	339327	exon7			CTCATCTCACGCA	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.1955T>A	chr19.hg19:g.40521132T>A	ENSP00000339823:p.Leu652His	101.0	0.0	.		107.0	39.0	.	NM_178544	A8K913	Missense_Mutation	SNP	ENST00000347077.4	hg19	CCDS12548.1	.	.	.	.	.	.	.	.	.	.	t	15.45	2.835827	0.50951	.	.	ENSG00000187187	ENST00000347077;ENST00000392042	T	0.54071	0.59	2.91	2.91	0.33838	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.81024	0.4737	H	0.98612	4.28	0.09310	N	1	D	0.89917	1.0	D	0.81914	0.995	T	0.70662	-0.4810	9	0.72032	D	0.01	.	9.5661	0.39400	0.0:0.0:0.0:1.0	.	652	Q86UE3	ZN546_HUMAN	H	652;261	ENSP00000339823:L652H	ENSP00000339823:L652H	L	+	2	0	ZNF546	45212972	0.327000	0.24678	0.218000	0.23776	0.862000	0.49288	3.930000	0.56522	1.564000	0.49628	0.482000	0.46254	CTC	.	.	.	none		0.413	ZNF546-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462495.2	NM_178544		A	40521132	T	A	40521132	3	1	275	1	0	0	0	0	1	0	0	0	17990	1551	54	5	1973	5	ZNF546	19	40521132	Missense_Mutation	SNP	T	TCGA-Y8-A895-01A-11D-A35Z-10	3211183	40521132	18607851	90	17499											
ZNF600	162966	hgsc.bcm.edu	37	chr19	53268927	53268927	+	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	0	0	0	0	0	0	0	0	0	ttgccacactcattacacttGtaaggtttctctccagtgtg	8	15	7	11	0	2	0	1	0	1	0	4	0	3	0	2	1	2	2	2	1	2	5			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr19:53268927G>C	ENST00000338230.3	-	3	2349	c.2082C>G	c.(2080-2082)taC>taG	p.Y694*		NM_198457.2	NP_940859	Q6ZNG1	ZN600_HUMAN	zinc finger protein 600	694					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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(2)|kidney(4)|large_intestine(9)|liver(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(262;0.0241)|GBM - Glioblastoma multiforme(134;0.0404)		CATTACACTTGTAAGGTTTCT	0.408																																					p.Y694X	Esophageal Squamous(196;1235 2112 2375 33339 34207)	Atlas-SNP	.											.	ZNF600	75	.	0			c.C2082G						PASS	.						107	100	102					19																	53268927		2203	4300	6503	SO:0001587	stop_gained	162966	exon3			ACACTTGTAAGGT	U52096	CCDS12856.1	19q13.42	2013-01-08				ENSG00000189190		"Zinc fingers, C2H2-type"	30951	protein-coding gene	gene with protein product						12576331	Standard	NM_198457		Approved	KR-ZNF1, DKFZp686F06123	uc002qab.4	Q6ZNG1		ENST00000338230.3:c.2082C>G	chr19.hg19:g.53268927G>C	ENSP00000344791:p.Tyr694*	117.0	0.0	.		110.0	43.0	.	NM_198457	Q6MZR0	Nonsense_Mutation	SNP	ENST00000338230.3	hg19	CCDS12856.1	.	.	.	.	.	.	.	.	.	.	.	23.9	4.472178	0.84533	.	.	ENSG00000189190	ENST00000338230	.	.	.	1.62	0.531	0.17108	.	.	.	.	.	.	.	.	.	.	.	0.47862	D	0.999534	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.0679	0.14591	0.3334:0.0:0.6666:0.0	.	.	.	.	X	694	.	ENSP00000344791:Y694X	Y	-	3	2	ZNF600	57960739	0.000000	0.05858	0.014000	0.15608	0.009000	0.06853	-1.193000	0.03049	0.938000	0.37419	0.289000	0.19496	TAC	.	.	.	none		0.408	ZNF600-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463093.1	NM_198457		C	53268927	G	C	53268927	4	2	275	1	0	0	0	0	0	1	0	0	18042	1372	48	4	90	4	ZNF600	19	53268927	Nonsense_Mutation	SNP	G	TCGA-Y8-A895-01A-11D-A35Z-10	12747795	53268927	5860056	91	17500											
TMEM190	147744	hgsc.bcm.edu	37	chr19	55889450	55889456	+	Frame_Shift_Del	DEL	CGCCGTC	CGCCGTC	-																															gcaccgagggaccaagaagaCgccgtccacgggcagcgtgc																								rs200141569|rs558548585|rs77912983	byFrequency	TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	CGCCGTC	CGCCGTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr19:55889450_55889456delCGCCGTC	ENST00000291934.3	+	5	431_437	c.413_419delCGCCGTC	c.(412-420)acgccgtccfs	p.TPS138fs	CTD-2105E13.15_ENST00000595064.1_RNA	NM_139172.1	NP_631911.1	Q8WZ59	TM190_HUMAN	transmembrane protein 190	138					hematopoietic progenitor cell differentiation (GO:0002244)	inner acrosomal membrane (GO:0002079)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	5	Breast(117;0.191)		BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		ACCAAGAAGACGCCGTCCACGGGCAGC	0.657																																					p.138_140del		Atlas-Indel,Pindel	.											.	TMEM190	17	.	0			c.412_418del						PASS	.																																			SO:0001589	frameshift_variant	147744	exon5			.	AF442729	CCDS33113.1	19q13.42	2011-09-28				ENSG00000160472			29632	protein-coding gene	gene with protein product						21273369	Standard	NM_139172		Approved	MDAC1	uc002qkt.1	Q8WZ59		ENST00000291934.3:c.413_419delCGCCGTC	chr19.hg19:g.55889450_55889456delCGCCGTC	ENSP00000291934:p.Thr138fs	107.0	0.0	0		80.0	17.0	0.2125	NM_139172	A6NJL5	Frame_Shift_Del	DEL	ENST00000291934.3	hg19	CCDS33113.1																																																																																			.	.	.	none		0.657	TMEM190-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453042.1	NM_139172		-	55889456	CGCCGTC	-	55889450	7	5	275	1	0	1	0	1	0	0	0	0	16126	536	19	0	431	0	TMEM190	19	55889450	Frame_Shift_Del	DEL	CGCCGTC	TCGA-Y8-A895-01A-11D-A35Z-10	2620523	55889450	3239533	92	17501	181	2									
TMEM190	147744	hgsc.bcm.edu	37	chr19	55889460	55889460	+	Silent	SNP	G	G	C																															accaagaagacgccgtccacGggcagcgtgccagtcgccct																										TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr19:55889460G>C	ENST00000291934.3	+	5	441	c.423G>C	c.(421-423)acG>acC	p.T141T	CTD-2105E13.15_ENST00000595064.1_RNA	NM_139172.1	NP_631911.1	Q8WZ59	TM190_HUMAN	transmembrane protein 190	141					hematopoietic progenitor cell differentiation (GO:0002244)	inner acrosomal membrane (GO:0002079)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	5	Breast(117;0.191)		BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		CGCCGTCCACGGGCAGCGTGC	0.647																																					p.T141T		Atlas-SNP	.											.	TMEM190	17	.	0			c.G423C						PASS	.						36	35	35					19																	55889460		2200	4300	6500	SO:0001819	synonymous_variant	147744	exon5			GTCCACGGGCAGC	AF442729	CCDS33113.1	19q13.42	2011-09-28				ENSG00000160472			29632	protein-coding gene	gene with protein product						21273369	Standard	NM_139172		Approved	MDAC1	uc002qkt.1	Q8WZ59		ENST00000291934.3:c.423G>C	chr19.hg19:g.55889460G>C		115.0	0.0	.		88.0	26.0	.	NM_139172	A6NJL5	Silent	SNP	ENST00000291934.3	hg19	CCDS33113.1																																																																																			.	.	.	none		0.647	TMEM190-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453042.1	NM_139172		C	55889460	G	C	55889460	2	2	275	1	0	0	0	0	0	0	0	1	16126	1103	39	4		4	TMEM190	19	55889460	Silent	SNP	G	TCGA-Y8-A895-01A-11D-A35Z-10	10	55889460	3239523	93	17502	181	2									
ZNF444	55311	hgsc.bcm.edu	37	chr19	56671522	56671522	+	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	agcgcgcagggggcggtagcTccgggcccggatggtggagg	5	4	22	10	5	0	0	0	0	0	0	1	2	1	2	2	8	2	3	2	8	1	1			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr19:56671522T>A	ENST00000337080.3	+	5	1303	c.936T>A	c.(934-936)gcT>gcA	p.A312A	ZNF444_ENST00000592949.1_Silent_p.A311A	NM_001253792.1|NM_018337.3	NP_001240721.1|NP_060807.2	Q8N0Y2	ZN444_HUMAN	zinc finger protein 444	312					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)		GGGCGGTAGCTCCGGGCCCGG	0.766																																					p.A312A		Atlas-SNP	.											.	ZNF444	15	.	0			c.T936A						PASS	.						2	3	3					19																	56671522		1380	3123	4503	SO:0001819	synonymous_variant	55311	exon5			GGTAGCTCCGGGC	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.936T>A	chr19.hg19:g.56671522T>A		36.0	0.0	.		23.0	10.0	.	NM_018337	Q8TEQ9|Q8WU35|Q9NUU1	Silent	SNP	ENST00000337080.3	hg19	CCDS12939.1																																																																																			.	.	.	none		0.766	ZNF444-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457503.1	NM_018337		A	56671522	T	A	56671522	2	1	275	1	0	0	0	0	0	0	0	1	17929	1538	54	5		5	ZNF444	19	56671522	Silent	SNP	T	TCGA-Y8-A895-01A-11D-A35Z-10	782062	56671522	2457461	94	17503											
COMMD7	149951	hgsc.bcm.edu	37	chr20	31292673	31292673	+	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	catcagagtctgacctatggCccatcgagcaagggtgggag	10	7	14	10	1	2	2	1	1	1	1	3	4	2	3	2	3	1	1	2	3	2	1			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr20:31292673C>T	ENST00000278980.6	-	6	975	c.370G>A	c.(370-372)Gcc>Acc	p.A124T	COMMD7_ENST00000446419.2_Missense_Mutation_p.A123T	NM_001099339.1|NM_053041.2	NP_001092809.1|NP_444269.2	Q86VX2	COMD7_HUMAN	COMM domain containing 7	124					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription, DNA-templated (GO:0045892)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	extracellular vesicular exosome (GO:0070062)	NF-kappaB binding (GO:0051059)			breast(1)|endometrium(1)|lung(3)	5						TGACCTATGGCCCATCGAGCA	0.458																																					p.A124T		Atlas-SNP	.											COMMD7,NS,carcinoma,0,1	COMMD7	16	.	0			c.G370A						PASS	.						96	90	92					20																	31292673		1935	4140	6075	SO:0001583	missense	149951	exon6			CTATGGCCCATCG	AY542162	CCDS42864.1, CCDS46587.1	20q11	2004-03-02	2004-02-13	2004-02-18	ENSG00000149600	ENSG00000149600			16223	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 92"	C20orf92		15799966	Standard	NM_001099339		Approved	dJ1085F17.3	uc002wya.4	Q86VX2	OTTHUMG00000032229	ENST00000278980.6:c.370G>A	chr20.hg19:g.31292673C>T	ENSP00000278980:p.Ala124Thr	103.0	0.0	.		103.0	28.0	.	NM_053041	A2BHJ2|B3KTZ2|Q5JYB0|Q96SI7|Q9BW53	Missense_Mutation	SNP	ENST00000278980.6	hg19	CCDS42864.1	.	.	.	.	.	.	.	.	.	.	c	20.1	3.936810	0.73557	.	.	ENSG00000149600	ENST00000278980;ENST00000446419	T;T	0.10288	2.89;2.89	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.24928	0.0605	M	0.72894	2.215	0.80722	D	1	P;D	0.58268	0.873;0.982	P;P	0.53988	0.523;0.739	T	0.00216	-1.1910	10	0.35671	T	0.21	.	15.9723	0.80031	0.0:1.0:0.0:0.0	.	123;124	Q86VX2-2;Q86VX2	.;COMD7_HUMAN	T	124;123	ENSP00000278980:A124T;ENSP00000395339:A123T	ENSP00000278980:A124T	A	-	1	0	COMMD7	30756334	1.000000	0.71417	0.995000	0.50966	0.359000	0.29487	5.844000	0.69430	2.788000	0.95919	0.650000	0.86243	GCC	.	.	.	none		0.458	COMMD7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078648.2	NM_053041		T	31292673	C	T	31292673	3	4	275	1	0	0	0	0	1	0	0	0	3723	739	26	2	248	2	COMMD7	20	31292673	Missense_Mutation	SNP	C	TCGA-Y8-A895-01A-11D-A35Z-10		31292673	31732847	95	17504											
MYH7B	57644	hgsc.bcm.edu	37	chr20	33585257	33585257	+	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	ctgcggcgggagctggaggaGgcggcgctgcggcacgaggc	5	3	22	11	6	0	0	0	0	0	0	0	4	0	3	0	8	3	3	0	8	0	0			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr20:33585257G>T	ENST00000262873.7	+	30	3779	c.3687G>T	c.(3685-3687)gaG>gaT	p.E1229D		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	1187						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)			AGCTGGAGGAGGCGGCGCTGC	0.786																																					p.E1229D		Atlas-SNP	.											.	MYH7B	145	.	0			c.G3687T						PASS	.						3	5	5					20																	33585257		1494	3137	4631	SO:0001583	missense	57644	exon32			GGAGGAGGCGGCG	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.3687G>T	chr20.hg19:g.33585257G>T	ENSP00000262873:p.Glu1229Asp	32.0	0.0	.		64.0	40.0	.	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Missense_Mutation	SNP	ENST00000262873.7	hg19	CCDS42869.1	.	.	.	.	.	.	.	.	.	.	G	18.63	3.664731	0.67700	.	.	ENSG00000078814	ENST00000262873	D	0.86865	-2.18	4.73	1.66	0.24008	Myosin tail (1);	0.000000	0.38326	N	0.001738	D	0.83575	0.5284	M	0.71036	2.16	0.42950	D	0.994374	B	0.25235	0.121	B	0.22601	0.04	T	0.79626	-0.1725	10	0.54805	T	0.06	.	8.5311	0.33335	0.3076:0.0:0.6924:0.0	.	1187	A7E2Y1	MYH7B_HUMAN	D	1229	ENSP00000262873:E1229D	ENSP00000262873:E1229D	E	+	3	2	MYH7B	33048918	1.000000	0.71417	0.980000	0.43619	0.956000	0.61745	2.850000	0.48294	0.612000	0.30071	0.563000	0.77884	GAG	.	.	.	none		0.786	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884		T	33585257	G	T	33585257	3	4	275	1	0	0	0	0	1	0	0	0	10047	991	35	4	3805	4	MYH7B	20	33585257	Missense_Mutation	SNP	G	TCGA-Y8-A895-01A-11D-A35Z-10	2292584	33585257	29440263	96	17505											
BCR	613	hgsc.bcm.edu	37	chr22	23632573	23632573	+	Missense_Mutation	SNP	T	T	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	ttctgaatgtcatcgtccacTcagccactggatttaagcag	10	12	8	11	1	3	1	2	1	1	0	5	2	4	2	2	1	2	1	2	1	2	3			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr22:23632573T>G	ENST00000305877.8	+	14	3506	c.2755T>G	c.(2755-2757)Tca>Gca	p.S919A	BCR_ENST00000359540.3_Missense_Mutation_p.S919A	NM_004327.3	NP_004318.3	P11274	BCR_HUMAN	breakpoint cluster region	919	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				actin cytoskeleton organization (GO:0030036)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of phagocytosis (GO:0050766)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)		BCR/JAK2(6)	central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	35					Bosutinib(DB06616)|Ponatinib(DB08901)	CATCGTCCACTCAGCCACTGG	0.557			T	"ABL1,  FGFR1, JAK2 "	"CML, ALL, AML"						OREG0026390	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S919A		Atlas-SNP	.		Dom	yes		22	22q11.21	613	breakpoint cluster region		L	.	BCR	74	.	0			c.T2755G						PASS	.						216	206	209					22																	23632573		2203	4300	6503	SO:0001583	missense	613	exon14			GTCCACTCAGCCA		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.2755T>G	chr22.hg19:g.23632573T>G	ENSP00000303507:p.Ser919Ala	70.0	0.0	.	765	58.0	29.0	.	NM_021574	P78501|Q12842|Q4LE80|Q6NZI3	Missense_Mutation	SNP	ENST00000305877.8	hg19	CCDS13806.1	.	.	.	.	.	.	.	.	.	.	T	27.2	4.807539	0.90623	.	.	ENSG00000186716	ENST00000305877;ENST00000359540;ENST00000334149	T;T	0.81078	0.94;-1.45	4.47	4.47	0.54385	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.82875	0.5132	L	0.49126	1.545	0.80722	D	1	D;P;P	0.55605	0.972;0.924;0.877	P;P;P	0.55615	0.679;0.747;0.78	T	0.82853	-0.0252	10	0.41790	T	0.15	.	13.6416	0.62255	0.0:0.0:0.0:1.0	.	508;919;919	B4E065;P11274-2;P11274	.;.;BCR_HUMAN	A	919;919;584	ENSP00000303507:S919A;ENSP00000352535:S919A	ENSP00000303507:S919A	S	+	1	0	BCR	21962573	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.790000	0.85794	1.961000	0.56991	0.529000	0.55759	TCA	.	.	.	none		0.557	BCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075819.1	NM_004327		G	23632573	T	G	23632573	3	3	275	1	0	0	0	0	1	0	0	0	1388	1551	54	5	2809	5	BCR	22	23632573	Missense_Mutation	SNP	T	TCGA-Y8-A895-01A-11D-A35Z-10		23632573	27671993	97	17506											
HSCB	150274	hgsc.bcm.edu	37	chr22	29138082	29138085	+	Start_Codon_Del	DEL	AGAT	AGAT	-																															ggctagataggccgccggccAgatgtggcgggggagagccg																										TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	AGAT	AGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chr22:29138082_29138085delAGAT	ENST00000216027.3	+	0	64_67				CHEK2_ENST00000382565.1_5'Flank|CHEK2_ENST00000544772.1_5'UTR|CHEK2_ENST00000348295.3_5'Flank|CHEK2_ENST00000328354.6_5'Flank|CHEK2_ENST00000405598.1_5'Flank|HSCB_ENST00000398941.2_Start_Codon_Del|CHEK2_ENST00000382578.1_5'Flank|CHEK2_ENST00000382580.2_5'Flank|CHEK2_ENST00000382566.1_5'Flank	NM_172002.3	NP_741999.3	Q8IWL3	HSC20_HUMAN	HscB mitochondrial iron-sulfur cluster co-chaperone						iron-sulfur cluster assembly (GO:0016226)|protein folding (GO:0006457)|protein oligomerization (GO:0051259)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			kidney(1)|lung(2)|skin(1)	4						GCCGCCGGCCAGATGTGGCGGGGG	0.642																																					.		Atlas-Indel,Pindel	.											.	HSCB	16	.	0			.						PASS	.																																			SO:0001582	initiator_codon_variant	150274	wholegene			.	AY191719	CCDS13845.1	22q12.1	2013-09-12	2013-09-12		ENSG00000100209	ENSG00000100209		"Heat shock proteins / DNAJ (HSP40)"	28913	protein-coding gene	gene with protein product	"DnaJ (Hsp40) homolog, subfamily C, member 20"	608142	"HscB iron-sulfur cluster co-chaperone homolog (E. coli)"			12938016, 16952052	Standard	NM_172002		Approved	HSC20, DNAJC20, Jac1	uc003aea.3	Q8IWL3	OTTHUMG00000151092		chr22.hg19:g.29138082_29138085delAGAT		93.0	0.0	0		86.0	43.0	0.5	NM_172002	Q9BWS7	Frame_Shift_Del	DEL	ENST00000216027.3	hg19	CCDS13845.1																																																																																			.	.	.	none		0.642	HSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321263.1	NM_172002		-	29138085	AGAT	-	29138082	7	5	275	1	0	1	0	1	0	0	0	0	7381	203	7	0	1	0	HSCB	22	29138082	Start_Codon_Del	DEL	AGAT	TCGA-Y8-A895-01A-11D-A35Z-10	5505509	29138082	22166484	98	17507											
AKAP4	8852	hgsc.bcm.edu	37	chrX	49957181	49957181	+	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	tgggcttatttgccgaggctGcttgttcttccaactcagca	6	14	10	11	1	2	0	1	0	1	0	3	1	3	0	2	2	4	5	2	2	2	5			TCGA-Y8-A895-01A-11D-A35Z-10	TCGA-Y8-A895-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2ddcb521-adce-4fcc-8f3b-0cfd15f4274b	404c87ca-74c1-4140-bb3c-0186ece2d39e	g.chrX:49957181G>T	ENST00000376056.2	-	5	2306	c.2156C>A	c.(2155-2157)gCa>gAa	p.A719E	AKAP4_ENST00000376064.3_Missense_Mutation_p.A719E|AKAP4_ENST00000481402.1_5'UTR|AKAP4_ENST00000376058.2_Missense_Mutation_p.A345E|AKAP4_ENST00000358526.2_Missense_Mutation_p.A728E					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)					TGCCGAGGCTGCTTGTTCTTC	0.448																																					p.A728E		Atlas-SNP	.											.	AKAP4	131	.	0			c.C2183A						PASS	.						100	73	82					X																	49957181		2203	4300	6503	SO:0001583	missense	8852	exon5			GAGGCTGCTTGTT	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.2156C>A	chrX.hg19:g.49957181G>T	ENSP00000365224:p.Ala719Glu	46.0	0.0	.		52.0	11.0	.	NM_003886		Missense_Mutation	SNP	ENST00000376056.2	hg19	CCDS14330.1	.	.	.	.	.	.	.	.	.	.	G	9.242	1.038460	0.19669	.	.	ENSG00000147081	ENST00000376056;ENST00000376058;ENST00000358526;ENST00000376064	T;T;T;T	0.07327	3.2;3.2;3.2;3.2	4.82	3.94	0.45596	A-kinase anchor 110kDa, C-terminal (1);	0.251365	0.27927	N	0.017300	T	0.09598	0.0236	M	0.63428	1.95	0.28373	N	0.9199	B;P	0.34934	0.018;0.476	B;B	0.32393	0.031;0.145	T	0.09952	-1.0651	9	.	.	.	-6.048	9.5338	0.39209	0.0:0.0:0.7893:0.2107	.	728;345	Q5JQC9;A6ND82	AKAP4_HUMAN;.	E	719;345;728;719	ENSP00000365224:A719E;ENSP00000365226:A345E;ENSP00000351327:A728E;ENSP00000365232:A719E	.	A	-	2	0	AKAP4	49843921	0.109000	0.22037	0.627000	0.29227	0.261000	0.26267	0.407000	0.21049	0.805000	0.34159	0.529000	0.55759	GCA	.	.	.	none		0.448	AKAP4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056552.1	NM_003886		T	49957181	G	T	49957181	3	4	275	1	0	0	0	0	1	0	0	0	453	1319	46	4	389	4	AKAP4	23	49957181	Missense_Mutation	SNP	G	TCGA-Y8-A895-01A-11D-A35Z-10		49957181	105313379	99	17508											
ESPN	83715	hgsc.bcm.edu	37	chr1	6517308	6517308	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcgggacctcctgcggaagaAgctggaagaagagaggtgag	12	4	18	7	2	0	4	0	1	0	3	1	8	1	7	2	4	2	1	2	4	4	0			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr1:6517308A>G	ENST00000377828.1	+	11	2558	c.2390A>G	c.(2389-2391)aAg>aGg	p.K797R	ESPN_ENST00000416731.1_Missense_Mutation_p.K231R|ESPN_ENST00000475228.1_3'UTR|ESPN_ENST00000461727.1_Missense_Mutation_p.K231R	NM_031475.2	NP_113663.2	B1AK53	ESPN_HUMAN	espin	797	Glu-rich.				locomotory behavior (GO:0007626)|negative regulation of cytoskeleton organization (GO:0051494)|parallel actin filament bundle assembly (GO:0030046)|positive regulation of filopodium assembly (GO:0051491)|sensory perception of sound (GO:0007605)	brush border (GO:0005903)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|microvillus (GO:0005902)|stereocilium bundle tip (GO:0032426)	actin filament binding (GO:0051015)|SH3 domain binding (GO:0017124)			NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)	17	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;3.6e-37)|all_epithelial(116;2.56e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|all_hematologic(16;6.92e-06)|Colorectal(325;4.47e-05)|Acute lymphoblastic leukemia(12;4.92e-05)|Breast(487;7.61e-05)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)		Epithelial(90;1.82e-35)|GBM - Glioblastoma multiforme(13;3e-28)|Kidney(185;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(229;5.63e-08)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;1.41e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000109)|STAD - Stomach adenocarcinoma(132;0.00167)|Lung(427;0.0108)|LUSC - Lung squamous cell carcinoma(448;0.0253)|READ - Rectum adenocarcinoma(331;0.0419)		CTGCGGAAGAAGCTGGAAGAA	0.637																																					p.K797R		Atlas-SNP	.											.	ESPN	32	.	0			c.A2390G						PASS	.						31	35	34					1																	6517308		2203	4300	6503	SO:0001583	missense	83715	exon11			GGAAGAAGCTGGA	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.2390A>G	chr1.hg19:g.6517308A>G	ENSP00000367059:p.Lys797Arg	213.0	0.0	.		176.0	48.0	.	NM_031475	Q6XYB2|Q9H0A2|Q9Y329	Missense_Mutation	SNP	ENST00000377828.1	hg19	CCDS70.1	.	.	.	.	.	.	.	.	.	.	A	25.7	4.661993	0.88251	.	.	ENSG00000187017	ENST00000377828;ENST00000416731	D;D	0.87650	-2.28;-2.28	5.08	5.08	0.68730	.	0.600841	0.16868	N	0.196249	D	0.91758	0.7393	L	0.56769	1.78	0.39690	D	0.971021	D;D	0.76494	0.999;0.998	D;D	0.80764	0.994;0.993	D	0.92281	0.5833	10	0.66056	D	0.02	-26.7453	13.6632	0.62378	1.0:0.0:0.0:0.0	.	231;797	B1AK53-2;B1AK53	.;ESPN_HUMAN	R	797;231	ENSP00000367059:K797R;ENSP00000399239:K231R	ENSP00000367059:K797R	K	+	2	0	ESPN	6439895	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	8.312000	0.89976	1.903000	0.55091	0.459000	0.35465	AAG	.	.	.	none		0.637	ESPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001887.3	NM_031475		G	6517308	A	G	6517308	3	3	276	1	0	0	0	0	1	0	0	0	5256	72	3	3	2432	3	ESPN	1	6517308	Missense_Mutation	SNP	A	TCGA-Y8-A896-01A-11D-A35Z-10		6517308	242733313	1	17509											
SPEN	23013	hgsc.bcm.edu	37	chr1	16199544	16199544	+	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	tcgtagtagagaggtttctgGgttcagaggaggtggtggag	8	11	19	3	1	2	2	1	0	1	2	3	5	2	4	0	6	0	4	0	6	2	4			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr1:16199544G>T	ENST00000375759.3	+	2	521	c.317G>T	c.(316-318)gGg>gTg	p.G106V		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	106					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)		GAGGTTTCTGGGTTCAGAGGA	0.532																																					p.G106V		Atlas-SNP	.											.	SPEN	374	.	0			c.G317T						PASS	.						113	102	106					1																	16199544		2203	4300	6503	SO:0001583	missense	23013	exon2			TTTCTGGGTTCAG		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.317G>T	chr1.hg19:g.16199544G>T	ENSP00000364912:p.Gly106Val	148.0	0.0	.		119.0	30.0	.	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	hg19	CCDS164.1	.	.	.	.	.	.	.	.	.	.	G	12.51	1.959099	0.34565	.	.	ENSG00000065526	ENST00000375759	T	0.11604	2.76	5.57	5.57	0.84162	.	.	.	.	.	T	0.22781	0.0550	L	0.32530	0.975	0.80722	D	1	D	0.76494	0.999	D	0.72075	0.976	T	0.00327	-1.1814	9	0.62326	D	0.03	0.0158	14.7284	0.69362	0.0713:0.0:0.9287:0.0	.	106	Q96T58	MINT_HUMAN	V	106	ENSP00000364912:G106V	ENSP00000364912:G106V	G	+	2	0	SPEN	16072131	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.659000	0.83766	2.635000	0.89317	0.555000	0.69702	GGG	.	.	.	none		0.532	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		T	16199544	G	T	16199544	3	4	276	1	0	0	0	0	1	0	0	0	15050	1232	43	4	323	4	SPEN	1	16199544	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	9682236	16199544	233051077	2	17510											
AHDC1	27245	hgsc.bcm.edu	37	chr1	27874121	27874121	+	Silent	SNP	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	ggtgggctagccaggtgaggGgcactgaggcacgcggcctc	6	5	19	11	2	0	2	0	2	0	0	1	2	0	2	2	7	1	3	2	7	1	1			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr1:27874121G>A	ENST00000247087.5	-	5	5102	c.4506C>T	c.(4504-4506)gcC>gcT	p.A1502A	AHDC1_ENST00000374011.2_Silent_p.A1502A			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	1502							DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		CCAGGTGAGGGGCACTGAGGC	0.711																																					p.A1502A		Atlas-SNP	.											.	AHDC1	98	.	0			c.C4506T						PASS	.						12	11	12					1																	27874121		2174	4277	6451	SO:0001819	synonymous_variant	27245	exon6			GTGAGGGGCACTG	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.4506C>T	chr1.hg19:g.27874121G>A		111.0	0.0	.		103.0	25.0	.	NM_001029882	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Silent	SNP	ENST00000247087.5	hg19	CCDS30652.1																																																																																			.	.	.	none		0.711	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3			A	27874121	G	A	27874121	2	1	276	1	0	0	0	0	0	0	0	1	412	1219	43	2		2	AHDC1	1	27874121	Silent	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	11674577	27874121	221376500	3	17511											
C1orf123	54987	hgsc.bcm.edu	37	chr1	53684086	53684086	+	Splice_Site	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	gtacgcacagcctgacctacCgatggaattttctcttgcac	9	11	8	13	2	1	1	0	1	1	0	2	3	1	2	3	1	4	3	3	1	3	5			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr1:53684086C>G	ENST00000294360.4	-	4	270	c.229G>C	c.(229-231)Gag>Cag	p.E77Q	RP5-1024G6.7_ENST00000569869.1_RNA|C1orf123_ENST00000470385.1_5'UTR	NM_017887.1	NP_060357.1	Q9NWV4	CA123_HUMAN	chromosome 1 open reading frame 123	77						extracellular vesicular exosome (GO:0070062)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|pancreas(2)|skin(1)	6						CCTGACCTACCGATGGAATTT	0.562																																					p.E77Q		Atlas-SNP	.											.	C1orf123	9	.	0			c.G229C						PASS	.						112	87	96					1																	53684086		2203	4300	6503	SO:0001630	splice_region_variant	54987	exon4			ACCTACCGATGGA	BC010908	CCDS576.1	1p32.3	2011-02-18			ENSG00000162384	ENSG00000162384			26059	protein-coding gene	gene with protein product						12477932	Standard	NM_017887		Approved	FLJ20580	uc001cvd.3	Q9NWV4	OTTHUMG00000008940	ENST00000294360.4:c.229+1G>C	chr1.hg19:g.53684086C>G		93.0	0.0	.		96.0	34.0	.	NM_017887		Missense_Mutation	SNP	ENST00000294360.4	hg19	CCDS576.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.173882	0.78452	.	.	ENSG00000162384	ENST00000294360;ENST00000371480	.	.	.	5.15	5.15	0.70609	.	0.259745	0.42420	D	0.000720	T	0.44519	0.1297	N	0.20685	0.6	0.43959	D	0.996632	P;P	0.42908	0.637;0.793	B;B	0.43838	0.33;0.433	T	0.31586	-0.9938	8	.	.	.	-7.8057	18.6318	0.91363	0.0:1.0:0.0:0.0	.	47;77	D3DQ38;Q9NWV4	.;CA123_HUMAN	Q	77;58	.	.	E	-	1	0	C1orf123	53456674	1.000000	0.71417	0.983000	0.44433	0.886000	0.51366	7.300000	0.78841	2.404000	0.81709	0.655000	0.94253	GAG	.	.	.	none		0.562	C1orf123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024751.1	NM_017887	Missense_Mutation	G	53684086	C	G	53684086	5	3	276	1	0	0	0	0	0	0	1	0	1993	666	23	4	273	4	C1orf123	1	53684086	Splice_Site	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10	25809965	53684086	195566535	4	17512											
ATXN7L2	127002	hgsc.bcm.edu	37	chr1	110031671	110031671	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agcggtggctgctcccagcaGcaccttctctgttcgtgcca	5	10	11	15	2	1	0	0	0	1	0	4	0	2	0	3	2	5	5	3	2	0	2			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr1:110031671G>A	ENST00000369870.3	+	7	1001	c.986G>A	c.(985-987)aGc>aAc	p.S329N		NM_153340.4	NP_699171.3	Q5T6C5	AT7L2_HUMAN	ataxin 7-like 2	329										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)	17		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0426)|Epithelial(280;0.0675)|READ - Rectum adenocarcinoma(129;0.0693)|all cancers(265;0.071)|LUSC - Lung squamous cell carcinoma(189;0.228)		GCTCCCAGCAGCACCTTCTCT	0.612																																					p.S329N		Atlas-SNP	.											.	ATXN7L2	60	.	0			c.G986A						PASS	.						65	60	61					1																	110031671		2203	4300	6503	SO:0001583	missense	127002	exon7			CCAGCAGCACCTT	BC037582	CCDS30794.1	1p13.2	2008-02-05			ENSG00000162650	ENSG00000162650			28713	protein-coding gene	gene with protein product						12477932	Standard	NM_153340		Approved	MGC46534, FLJ00381	uc001dxr.3	Q5T6C5	OTTHUMG00000011027	ENST00000369870.3:c.986G>A	chr1.hg19:g.110031671G>A	ENSP00000358886:p.Ser329Asn	87.0	0.0	.		85.0	24.0	.	NM_153340		Missense_Mutation	SNP	ENST00000369870.3	hg19	CCDS30794.1	.	.	.	.	.	.	.	.	.	.	G	10.37	1.332103	0.24167	.	.	ENSG00000162650	ENST00000369870;ENST00000541125	T	0.32272	1.46	5.97	0.693	0.18056	.	0.533090	0.19790	N	0.106016	T	0.03011	0.0089	N	0.02011	-0.69	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.32587	-0.9901	10	0.19590	T	0.45	-1.696	5.8764	0.18832	0.2166:0.2562:0.5272:0.0	.	329	Q5T6C5	AT7L2_HUMAN	N	329	ENSP00000358886:S329N	ENSP00000358886:S329N	S	+	2	0	ATXN7L2	109833194	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	1.475000	0.35409	0.130000	0.18549	-0.136000	0.14681	AGC	.	.	.	none		0.612	ATXN7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030331.1	NM_153340		A	110031671	G	A	110031671	3	1	276	1	0	0	0	0	1	0	0	0	1217	971	34	2	1012	2	ATXN7L2	1	110031671	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	56347585	110031671	139218950	5	17513											
NUP210L	91181	hgsc.bcm.edu	37	chr1	154099879	154099879	+	Missense_Mutation	SNP	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	tagactccatcggtttccagGttggacagtgaaacctatac	11	11	9	10	1	0	2	0	1	0	1	3	3	2	3	3	3	2	2	3	3	4	5			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr1:154099879G>A	ENST00000368559.3	-	9	1164	c.1093C>T	c.(1093-1095)Cct>Tct	p.P365S	NUP210L_ENST00000271854.3_Missense_Mutation_p.P365S	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	365					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)			CGGTTTCCAGGTTGGACAGTG	0.353																																					p.P365S		Atlas-SNP	.											.	NUP210L	181	.	0			c.C1093T						PASS	.						74	68	70					1																	154099879		1821	4086	5907	SO:0001583	missense	91181	exon9			TTCCAGGTTGGAC	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.1093C>T	chr1.hg19:g.154099879G>A	ENSP00000357547:p.Pro365Ser	106.0	0.0	.		78.0	14.0	.	NM_001159484	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Missense_Mutation	SNP	ENST00000368559.3	hg19	CCDS41399.1	.	.	.	.	.	.	.	.	.	.	G	14.60	2.584027	0.46110	.	.	ENSG00000143552	ENST00000368559;ENST00000271854	T;T	0.04406	3.63;3.63	4.44	4.44	0.53790	.	0.000000	0.52532	D	0.000061	T	0.02571	0.0078	L	0.42581	1.335	0.45366	D	0.998358	B;B	0.29766	0.256;0.162	B;B	0.21917	0.037;0.023	T	0.40175	-0.9577	10	0.56958	D	0.05	-0.9036	15.0178	0.71600	0.0:0.0:1.0:0.0	.	365;365	E7EP56;Q5VU65	.;P210L_HUMAN	S	365	ENSP00000357547:P365S;ENSP00000271854:P365S	ENSP00000271854:P365S	P	-	1	0	NUP210L	152366503	1.000000	0.71417	0.933000	0.37362	0.876000	0.50452	4.820000	0.62671	2.302000	0.77476	0.313000	0.20887	CCT	.	.	.	none		0.353	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308		A	154099879	G	A	154099879	3	1	276	1	0	0	0	0	1	0	0	0	10768	1261	44	2	4701	2	NUP210L	1	154099879	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	44068208	154099879	95150742	6	17514											
KCNN3	3782	hgsc.bcm.edu	37	chr1	154842333	154842333	+	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	ggtggctgctgctgctgttgCtgctgctgctgctgctgctg	0	14	16	11	0	0	0	0	0	0	0	0	0	0	0	0	2	10	12	0	2	0	1			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr1:154842333C>T	ENST00000271915.4	-	1	423	c.108G>A	c.(106-108)caG>caA	p.Q36Q	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	36	Gln-rich.				potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	gctgctgttgctgctgctgct	0.672																																					p.Q36Q		Atlas-SNP	.											.	KCNN3	141	.	0			c.G108A						PASS	.						8	8	8					1																	154842333		1967	3874	5841	SO:0001819	synonymous_variant	3782	exon1			CTGTTGCTGCTGC	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"Potassium channels", "Voltage-gated ion channels / Potassium channels, calcium-activated"	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.108G>A	chr1.hg19:g.154842333C>T		104.0	0.0	.		93.0	6.0	.	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Silent	SNP	ENST00000271915.4	hg19	CCDS30880.1																																																																																			.	.	.	none		0.672	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249		T	154842333	C	T	154842333	2	4	276	1	0	0	0	0	0	0	0	1	8087	796	28	2		2	KCNN3	1	154842333	Silent	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10	742454	154842333	94408288	7	17515											
F5	2153	hgsc.bcm.edu	37	chr1	169528453	169528453	+	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	gggatgatgactggctccagCtcttgctttcatcaaacaca	10	11	9	11	0	3	2	2	2	1	0	4	3	4	3	1	2	3	3	1	2	1	2			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr1:169528453C>A	ENST00000367797.3	-	5	869	c.668G>T	c.(667-669)aGc>aTc	p.S223I	F5_ENST00000546081.1_Missense_Mutation_p.S86I|F5_ENST00000367796.3_Missense_Mutation_p.S223I	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	223	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)	CTGGCTCCAGCTCTTGCTTTC	0.443																																					p.S223I		Atlas-SNP	.											F5,NS,carcinoma,0,1	F5	301	.	0			c.G668T						PASS	.						172	135	147					1																	169528453		2203	4300	6503	SO:0001583	missense	2153	exon5			CTCCAGCTCTTGC	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.668G>T	chr1.hg19:g.169528453C>A	ENSP00000356771:p.Ser223Ile	98.0	0.0	.		77.0	30.0	.	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	hg19	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.651866	0.88056	.	.	ENSG00000198734	ENST00000367797;ENST00000367796;ENST00000546081	D;D;D	0.99105	-5.43;-5.43;-5.43	5.95	5.04	0.67666	Cupredoxin (2);	0.035814	0.85682	D	0.000000	D	0.99293	0.9753	M	0.89601	3.045	0.42717	D	0.993664	D	0.76494	0.999	D	0.69307	0.963	D	0.98776	1.0730	9	0.87932	D	0	-21.326	15.0853	0.72148	0.0:0.9322:0.0:0.0678	.	223	P12259	FA5_HUMAN	I	223;223;86	ENSP00000356771:S223I;ENSP00000356770:S223I;ENSP00000439664:S86I	ENSP00000356770:S223I	S	-	2	0	F5	167795077	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.733000	0.74796	1.518000	0.48934	0.650000	0.86243	AGC	.	.	.	none		0.443	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		A	169528453	C	A	169528453	3	1	276	1	0	0	0	0	1	0	0	0	5350	797	28	4	6090	4	F5	1	169528453	Missense_Mutation	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10	14686120	169528453	79722168	8	17516											
C1orf125	126859	hgsc.bcm.edu	37	chr1	179494536	179494538	+	In_Frame_Del	DEL	AGG	AGG	-																															agaagatgaagaagaaagtaAggaggataggaaacttcagg																										TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr1:179494536_179494538delAGG	ENST00000367618.3	+	22	2951_2953	c.2564_2566delAGG	c.(2563-2568)aaggag>aag	p.E856del		NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	856	Glu-rich.									NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						GAAGAAAGTAAGGAGGATAGGAA	0.335																																					p.855_855del		Atlas-Indel,Pindel	.											.	AXDND1	142	.	0			c.2563_2565del						PASS	.																																			SO:0001651	inframe_deletion	126859	exon22			.	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.2564_2566delAGG	chr1.hg19:g.179494539_179494541delAGG	ENSP00000356590:p.Glu856del	741.0	0.0	0		705.0	192.0	0.27234	NM_144696	Q6AWB2|Q96LJ3|Q96M01	In_Frame_Del	DEL	ENST00000367618.3	hg19	CCDS30948.1																																																																																			.	.	.	none		0.335	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696		-	179494538	AGG	-	179494536	7	5	276	1	0	1	0	1	0	0	0	0	1995	72	3	0	2646	0	C1orf125	1	179494536	In_Frame_Del	DEL	AGG	TCGA-Y8-A896-01A-11D-A35Z-10	9966083	179494536	69756085	9	17517											
LAMC1	3915	hgsc.bcm.edu	37	chr1	183072766	183072766	+	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	tgacaatagccctgtgctgcAggtaaattctcacaggttgg	10	11	11	9	0	1	1	1	1	1	0	2	1	1	1	1	3	3	4	1	3	4	4			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr1:183072766A>G	ENST00000258341.4	+	2	979	c.722A>G	c.(721-723)cAg>cGg	p.Q241R		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	241	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				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						CCTGTGCTGCAGGTAAATTCT	0.517																																					p.Q241R		Atlas-SNP	.											.	LAMC1	176	.	0			c.A722G						PASS	.						42	43	43					1																	183072766		2203	4300	6503	SO:0001630	splice_region_variant	3915	exon2			TGCTGCAGGTAAA	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.723+1A>G	chr1.hg19:g.183072766A>G		99.0	0.0	.		96.0	34.0	.	NM_002293	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	hg19	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.776337	0.90195	.	.	ENSG00000135862	ENST00000258341	T	0.78003	-1.14	5.23	5.23	0.72850	Laminin, N-terminal (3);	0.000000	0.85682	D	0.000000	D	0.86581	0.5967	M	0.65498	2.005	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.87578	0.998;0.964	D	0.87656	0.2531	10	0.59425	D	0.04	.	15.1384	0.72590	1.0:0.0:0.0:0.0	.	241;241	P11047;Q6NVY8	LAMC1_HUMAN;.	R	241	ENSP00000258341:Q241R	ENSP00000258341:Q241R	Q	+	2	0	LAMC1	181339389	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	9.020000	0.93667	1.978000	0.57642	0.533000	0.62120	CAG	.	.	.	none		0.517	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293	Missense_Mutation	G	183072766	A	G	183072766	5	3	276	1	0	0	0	0	0	0	1	0	8621	202	7	3	728	3	LAMC1	1	183072766	Splice_Site	SNP	A	TCGA-Y8-A896-01A-11D-A35Z-10	3578230	183072766	66177855	10	17518											
PGBD5	79605	hgsc.bcm.edu	37	chr1	230486768	230486768	+	Missense_Mutation	SNP	T	T	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	tgaatttccgctttttcctcTttcgcagctcccgctctgtg	3	17	7	14	3	2	1	0	1	2	0	6	1	5	1	3	0	1	4	3	0	1	4			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr1:230486768T>G	ENST00000525115.1	-	3	646	c.623A>C	c.(622-624)aAg>aCg	p.K208T	PGBD5_ENST00000391860.1_Missense_Mutation_p.K162T|PGBD5_ENST00000321327.2_Missense_Mutation_p.K307T			Q8N414	PGBD5_HUMAN	piggyBac transposable element derived 5	208						integral component of membrane (GO:0016021)				biliary_tract(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(2)|skin(1)	33	Breast(184;0.0397)	Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;0.201)		CTTTTTCCTCTTTCGCAGCTC	0.557																																					p.K277T		Atlas-SNP	.											.	PGBD5	73	.	0			c.A830C						PASS	.						124	112	116					1																	230486768		2203	4300	6503	SO:0001583	missense	79605	exon3			TTCCTCTTTCGCA	AK021475		1q42.13	2008-02-05			ENSG00000177614	ENSG00000177614			19405	protein-coding gene	gene with protein product							Standard	NM_001258311		Approved	DKFZp761A0620, FLJ11413	uc031psq.1	Q8N414	OTTHUMG00000037759	ENST00000525115.1:c.623A>C	chr1.hg19:g.230486768T>G	ENSP00000431404:p.Lys208Thr	72.0	0.0	.		55.0	17.0	.	NM_001258311	A0PJF3|B9EK58|Q5SR37|Q6PJN2	Missense_Mutation	SNP	ENST00000525115.1	hg19		.	.	.	.	.	.	.	.	.	.	T	20.6	4.016450	0.75161	.	.	ENSG00000177614	ENST00000391860;ENST00000321327;ENST00000525115	T;T;T	0.18657	2.2;2.2;2.2	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.31040	0.0784	N	0.24115	0.695	0.58432	D	0.999994	D	0.69078	0.997	P	0.62560	0.904	T	0.06991	-1.0796	10	0.62326	D	0.03	-43.6433	15.9745	0.80049	0.0:0.0:0.0:1.0	.	208	Q8N414	PGBD5_HUMAN	T	162;307;208	ENSP00000375733:K162T;ENSP00000322530:K307T;ENSP00000431404:K208T	ENSP00000322530:K307T	K	-	2	0	PGBD5	228553391	1.000000	0.71417	0.998000	0.56505	0.935000	0.57460	6.086000	0.71352	2.168000	0.68352	0.533000	0.62120	AAG	.	.	.	none		0.557	PGBD5-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000382617.1	NM_024554		G	230486768	T	G	230486768	3	3	276	1	0	0	0	0	1	0	0	0	11791	1609	56	5	764	5	PGBD5	1	230486768	Missense_Mutation	SNP	T	TCGA-Y8-A896-01A-11D-A35Z-10	47414002	230486768	18763853	11	17519											
ASAP2	8853	hgsc.bcm.edu	37	chr2	9496455	9496455	+	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	atgacgggcaatgacgtctgCtgtgactgtggggcgccagg	7	8	17	9	3	1	3	0	3	1	0	1	3	1	3	1	4	1	2	1	4	1	0			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr2:9496455C>T	ENST00000281419.3	+	14	1648	c.1308C>T	c.(1306-1308)tgC>tgT	p.C436C	ASAP2_ENST00000315273.4_Silent_p.C436C	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	436	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						ATGACGTCTGCTGTGACTGTG	0.498																																					p.C436C		Atlas-SNP	.											.	ASAP2	91	.	0			c.C1308T						PASS	.						55	53	54					2																	9496455		2203	4300	6503	SO:0001819	synonymous_variant	8853	exon14			CGTCTGCTGTGAC	AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"ADP-ribosylation factor GTPase activating proteins", "Pleckstrin homology (PH) domain containing", "Ankyrin repeat domain containing"	2721	protein-coding gene	gene with protein product	"centaurin, beta 3"	603817	"development and differentiation enhancing factor 2"	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.1308C>T	chr2.hg19:g.9496455C>T		111.0	0.0	.		108.0	31.0	.	NM_001135191	D6W4Y8	Silent	SNP	ENST00000281419.3	hg19	CCDS1661.1																																																																																			.	.	.	none		0.498	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887		T	9496455	C	T	9496455	2	4	276	1	0	0	0	0	0	0	0	1	1011	805	28	2		2	ASAP2	2	9496455	Silent	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10		9496455	233702918	12	17520											
ITGB1BP1	9270	hgsc.bcm.edu	37	chr2	9547719	9547719	+	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	aagtagagagcatgcctgtgCaaaacatcctgcagaagtca	15	7	10	9	0	1	2	1	0	0	2	2	3	2	2	2	0	5	4	2	0	5	1			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr2:9547719C>A	ENST00000360635.3	-	7	1286	c.390G>T	c.(388-390)ttG>ttT	p.L130F	ITGB1BP1_ENST00000490426.1_5'UTR|ITGB1BP1_ENST00000355346.4_Missense_Mutation_p.L130F|ITGB1BP1_ENST00000238091.4_Intron|ITGB1BP1_ENST00000488451.1_Intron|ITGB1BP1_ENST00000359712.3_Missense_Mutation_p.L130F|ITGB1BP1_ENST00000456913.2_Missense_Mutation_p.L130F			O14713	ITBP1_HUMAN	integrin beta 1 binding protein 1	130	PID.				activation of protein kinase B activity (GO:0032148)|biomineral tissue development (GO:0031214)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|myoblast migration (GO:0051451)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of protein binding (GO:0032091)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|Notch signaling pathway (GO:0007219)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein transport (GO:0015031)|receptor clustering (GO:0043113)|regulation of blood vessel size (GO:0050880)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of integrin-mediated signaling pathway (GO:2001044)|transcription, DNA-templated (GO:0006351)|tube formation (GO:0035148)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	GDP-dissociation inhibitor activity (GO:0005092)|integrin binding (GO:0005178)|protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)			kidney(2)|large_intestine(2)|lung(2)|prostate(2)	8	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.23)		CATGCCTGTGCAAAACATCCT	0.498																																					p.L130F		Atlas-SNP	.											.	ITGB1BP1	13	.	0			c.G390T						PASS	.						97	84	88					2																	9547719		2203	4300	6503	SO:0001583	missense	9270	exon6			CCTGTGCAAAACA	AF012023	CCDS1662.1, CCDS1663.1	2p25.2	2008-02-05			ENSG00000119185	ENSG00000119185			23927	protein-coding gene	gene with protein product	"integrin cytoplasmic domain-associated protein 1", "integrin cytoplasmic domain-associated protein 1-beta", "integrin cytoplasmic domain-associated protein 1-alpha", "bodenin"	607153				11854171, 9281591	Standard	NM_004763		Approved	ICAP-1A, ICAP-1B, ICAP1, ICAP1A, ICAP1B, ICAP-1alpha	uc002qzj.3	O14713	OTTHUMG00000090414	ENST00000360635.3:c.390G>T	chr2.hg19:g.9547719C>A	ENSP00000353850:p.Leu130Phe	62.0	0.0	.		64.0	23.0	.	NM_004763	D6W4Y9|O14714|Q53RS0	Missense_Mutation	SNP	ENST00000360635.3	hg19	CCDS1662.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.946386	0.73672	.	.	ENSG00000119185	ENST00000360635;ENST00000355346;ENST00000359712;ENST00000456913;ENST00000492079	.	.	.	5.77	0.913	0.19354	Phosphotyrosine interaction domain (1);Pleckstrin homology-type (1);	0.062448	0.64402	D	0.000005	T	0.62332	0.2419	L	0.32530	0.975	0.58432	D	0.999997	D;P;D	0.76494	0.978;0.713;0.999	P;P;D	0.87578	0.864;0.662;0.998	T	0.60500	-0.7251	9	0.54805	T	0.06	-5.2216	11.4453	0.50120	0.0:0.6025:0.0:0.3975	.	86;130;130	B4DQY5;A8MPU2;O14713	.;.;ITBP1_HUMAN	F	130	.	ENSP00000347504:L130F	L	-	3	2	ITGB1BP1	9465170	0.992000	0.36948	0.414000	0.26521	0.936000	0.57629	0.352000	0.20113	0.167000	0.19631	0.655000	0.94253	TTG	.	.	.	none		0.498	ITGB1BP1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314623.2	NM_004763, NM_022334		A	9547719	C	A	9547719	3	1	276	1	0	0	0	0	1	0	0	0	7898	709	25	4	220	4	ITGB1BP1	2	9547719	Missense_Mutation	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10	51264	9547719	233651654	13	17521											
TTC32	130502	hgsc.bcm.edu	37	chr2	20101507	20101507	+	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	ggaggccgcgcaagcgcaccGgcgaatgtaagcggagtaca	11	3	16	11	6	0	0	0	0	0	0	0	3	0	2	2	4	3	4	2	4	4	2	rs138752655		TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr2:20101507G>T	ENST00000333610.3	-	1	240	c.109C>A	c.(109-111)Cgg>Agg	p.R37R	RP11-79O8.1_ENST00000607190.1_lincRNA|TTC32_ENST00000402414.1_Silent_p.R37R	NM_001008237.1	NP_001008238.1	Q5I0X7	TTC32_HUMAN	tetratricopeptide repeat domain 32	37										kidney(2)|large_intestine(1)|lung(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAAGCGCACCGGCGAATGTAA	0.642																																					p.R37R		Atlas-SNP	.											.	TTC32	13	.	0			c.C109A						PASS	.						83	80	81					2																	20101507		2203	4300	6503	SO:0001819	synonymous_variant	130502	exon1			CGCACCGGCGAAT	BC057850	CCDS33151.1	2p24.1	2013-01-10			ENSG00000183891	ENSG00000183891		"Tetratricopeptide (TTC) repeat domain containing"	32954	protein-coding gene	gene with protein product							Standard	NM_001008237		Approved		uc002rdg.3	Q5I0X7	OTTHUMG00000151776	ENST00000333610.3:c.109C>A	chr2.hg19:g.20101507G>T		57.0	0.0	.		42.0	15.0	.	NM_001008237		Silent	SNP	ENST00000333610.3	hg19	CCDS33151.1																																																																																			.	G|1.000;A|0.000	.	alt		0.642	TTC32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323868.1	NM_001008237		T	20101507	G	T	20101507	2	4	276	1	0	0	0	0	0	0	0	1	16713	1115	39	4		4	TTC32	2	20101507	Silent	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	10553788	20101507	223097866	14	17522											
ALMS1	7840	hgsc.bcm.edu	37	chr2	73613036	73613036	+	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	catggccgggcgagctggagGaggaggaggaggaggaggag	10	2	24	5	2	0	0	0	0	0	0	0	9	0	8	1	10	1	1	1	10	0	0	rs61156725|rs72319667|rs3074417	byFrequency	TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr2:73613036G>C	ENST00000264448.6	+	1	151	c.40G>C	c.(40-42)Gag>Cag	p.E14Q	ALMS1_ENST00000409009.1_Missense_Mutation_p.E14Q|ALMS1_ENST00000377715.1_Missense_Mutation_p.E14Q	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	14	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CGAGCTggaggaggaggagga	0.692																																					p.E14Q		Atlas-SNP	.											.	ALMS1	384	.	1	Deletion - In frame(1)	ovary(1)	c.G40C						PASS	.						3	4	4					2																	73613036		1509	3234	4743	SO:0001583	missense	7840	exon1			CTGGAGGAGGAGG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.40G>C	chr2.hg19:g.73613036G>C	ENSP00000264448:p.Glu14Gln	203.0	0.0	.		243.0	12.0	.	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.731519	0.48939	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.26373	2.4;2.61;1.74	3.19	3.19	0.36642	.	0.259523	0.20097	U	0.099311	T	0.32436	0.0829	N	0.19112	0.55	0.22317	N	0.999202	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.03493	-1.1031	10	0.87932	D	0	.	10.1262	0.42652	0.0:0.0:1.0:0.0	.	14;14	B8ZZJ3;Q8TCU4	.;ALMS1_HUMAN	Q	14	ENSP00000386627:E14Q;ENSP00000264448:E14Q;ENSP00000366944:E14Q	ENSP00000264448:E14Q	E	+	1	0	ALMS1	73466544	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	2.034000	0.41145	2.070000	0.61991	0.484000	0.47621	GAG	.	.	.	none		0.692	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		C	73613036	G	C	73613036	3	2	276	1	0	0	0	0	1	0	0	0	535	1175	41	4	42	4	ALMS1	2	73613036	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	53511529	73613036	169586337	15	17523			1	42		2	2	30	G		9.742159e-05
ALMS1	7840	hgsc.bcm.edu	37	chr2	73613065	73613065	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggaggaggaggaggaggaGgaggaagaggaggaggctgc	13	1	25	2	0	0	1	0	0	0	1	0	12	0	11	0	11	1	1	0	11	1	0			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr2:73613065G>A	ENST00000264448.6	+	1	180	c.69G>A	c.(67-69)gaG>gaA	p.E23E	ALMS1_ENST00000409009.1_Silent_p.E23E|ALMS1_ENST00000377715.1_Silent_p.E23E	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	23	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						aggaggaggaggaggaagagg	0.687																																					p.E23E		Atlas-SNP	.											.	ALMS1	384	.	0			c.G69A						PASS	.						6	9	8					2																	73613065		1849	3831	5680	SO:0001819	synonymous_variant	7840	exon1			GGAGGAGGAGGAA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.69G>A	chr2.hg19:g.73613065G>A		527.0	0.0	.		525.0	43.0	.	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.	.	none		0.687	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		A	73613065	G	A	73613065	2	1	276	1	0	0	0	0	0	0	0	1	535	991	35	2		2	ALMS1	2	73613065	Silent	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	29	73613065	169586308	16	17524			1	42		2	2	30	G		9.742159e-05
LBX2	85474	hgsc.bcm.edu	37	chr2	74725195	74725196	+	Frame_Shift_Ins	INS	-	-	GCGA																															gggacaacgcgcgtagcgagINSgcgacgtcggcgcgcatctc																										TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr2:74725195_74725196insGCGA	ENST00000377566.4	-	2	633_634	c.455_456insTCGC	c.(454-456)gccfs	p.-152fs	LBX2_ENST00000460508.3_Frame_Shift_Ins_p.-148fs|AC005041.17_ENST00000479098.1_RNA|LBX2_ENST00000341396.2_3'UTR|LBX2_ENST00000550249.1_5'UTR	NM_001282430.1	NP_001269359.1	Q6XYB7	LBX2_HUMAN	ladybird homeobox 2						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(1)	4						CGCGTAGCGAGGCGACGTCGGC	0.688																																					p.A148fs		Atlas-Indel,Pindel	.											.	LBX2	13	.	0			c.444_445insTCGC						PASS	.																																			SO:0001589	frameshift_variant	85474	exon2			.	AC005041	CCDS33228.1, CCDS62938.1	2p13.1	2014-05-06	2007-02-15		ENSG00000179528	ENSG00000179528		"Homeoboxes / ANTP class : NKL subclass"	15525	protein-coding gene	gene with protein product		607164	"ladybird homeobox homolog 2 (Drosophila)"			11386758	Standard	NM_001282430		Approved		uc002slw.3	Q6XYB7	OTTHUMG00000170595	ENST00000377566.4:c.452_455dupTCGC	chr2.hg19:g.74725196_74725199dupGCGA	ENSP00000366789:p.Ala152fs	154.0	0.0	0		112.0	29.0	0.258929	NM_001009812	Q7Z5Y8	Frame_Shift_Ins	INS	ENST00000377566.4	hg19																																																																																				.	.	.	none		0.688	LBX2-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000328490.1	NM_001009812		GCGA	74725196	-	GCGA	74725195	7	5	276	1	0	1	1	0	0	0	0	0	8661	987	35	0	144	0	LBX2	2	74725195	Frame_Shift_Ins	INS	-	TCGA-Y8-A896-01A-11D-A35Z-10	1112130	74725195	168474178	17	17525											
SEMA4F	10505	hgsc.bcm.edu	37	chr2	74902678	74902678	+	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	gacacctccaccgagcagtgCggatcggagctcagctcagc	9	5	12	15	3	2	0	2	0	0	0	4	4	3	2	3	2	5	3	3	2	0	0			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr2:74902678C>T	ENST00000357877.2	+	11	1548	c.1399C>T	c.(1399-1401)Cgg>Tgg	p.R467W	SEMA4F_ENST00000473350.1_3'UTR|SEMA4F_ENST00000339773.5_Missense_Mutation_p.R312W	NM_004263.3	NP_004254.2	O95754	SEM4F_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F	467	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						CCGAGCAGTGCGGATCGGAGC	0.483																																					p.R467W		Atlas-SNP	.											.	SEMA4F	89	.	0			c.C1399T						PASS	.						121	114	116					2																	74902678		2203	4300	6503	SO:0001583	missense	10505	exon11			GCAGTGCGGATCG	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.1399C>T	chr2.hg19:g.74902678C>T	ENSP00000350547:p.Arg467Trp	108.0	0.0	.		98.0	24.0	.	NM_004263	Q542Y7|Q9NS35	Missense_Mutation	SNP	ENST00000357877.2	hg19	CCDS1955.1	.	.	.	.	.	.	.	.	.	.	C	13.70	2.315378	0.40996	.	.	ENSG00000135622	ENST00000357877;ENST00000339773	T;T	0.11169	2.8;2.8	4.5	3.62	0.41486	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.422729	0.21018	N	0.081569	T	0.17238	0.0414	L	0.42245	1.32	0.28984	N	0.888469	D;P	0.65815	0.995;0.932	P;P	0.54924	0.764;0.625	T	0.02042	-1.1224	10	0.66056	D	0.02	.	10.0793	0.42379	0.0:0.9018:0.0:0.0982	.	312;467	O95754-2;O95754	.;SEM4F_HUMAN	W	467;312	ENSP00000350547:R467W;ENSP00000342675:R312W	ENSP00000342675:R312W	R	+	1	2	SEMA4F	74756186	0.001000	0.12720	0.818000	0.32626	0.290000	0.27261	0.047000	0.14056	1.116000	0.41820	0.467000	0.42956	CGG	.	.	.	none		0.483	SEMA4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252214.2	NM_004263		T	74902678	C	T	74902678	3	4	276	1	0	0	0	0	1	0	0	0	14048	759	27	1	1441	1	SEMA4F	2	74902678	Missense_Mutation	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10	177483	74902678	168296695	18	17526											
SLC20A1	6574	hgsc.bcm.edu	37	chr2	113405235	113405235	+	Missense_Mutation	SNP	T	T	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	tgtgttctattccagtgatgTcttggttcgtgtccccactg	4	17	10	10	1	2	1	0	1	2	0	5	1	4	1	3	1	0	2	3	1	1	5			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr2:113405235T>G	ENST00000272542.3	+	4	1020	c.481T>G	c.(481-483)Tct>Gct	p.S161A	AC079922.3_ENST00000457336.1_lincRNA	NM_005415.4	NP_005406.3	Q8WUM9	S20A1_HUMAN	solute carrier family 20 (phosphate transporter), member 1	161					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						TCCAGTGATGTCTTGGTTCGT	0.363																																					p.S161A		Atlas-SNP	.											.	SLC20A1	59	.	0			c.T481G						PASS	.						210	211	211					2																	113405235		2203	4300	6503	SO:0001583	missense	6574	exon4			GTGATGTCTTGGT		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.481T>G	chr2.hg19:g.113405235T>G	ENSP00000272542:p.Ser161Ala	125.0	0.0	.		95.0	31.0	.	NM_005415	Q08344|Q6DHX8|Q9UQ82	Missense_Mutation	SNP	ENST00000272542.3	hg19	CCDS2099.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.9|28.9	4.959704|4.959704	0.92791|0.92791	.|.	.|.	ENSG00000144136|ENSG00000144136	ENST00000423633|ENST00000272542	.|D	.|0.91521	.|-2.86	5.45|5.45	5.45|5.45	0.79879|0.79879	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.93458|0.93458	0.7913|0.7913	L|L	0.58925|0.58925	1.835|1.835	0.80722|0.80722	D|D	1|1	.|D	.|0.76494	.|0.999	.|D	.|0.79784	.|0.993	D|D	0.92321|0.92321	0.5866|0.5866	5|10	.|0.32370	.|T	.|0.25	-11.006|-11.006	13.4819|13.4819	0.61340|0.61340	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|161	.|Q8WUM9	.|S20A1_HUMAN	W|A	8|161	.|ENSP00000272542:S161A	.|ENSP00000272542:S161A	C|S	+|+	3|1	2|0	SLC20A1|SLC20A1	113121706|113121706	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	8.036000|8.036000	0.88901|0.88901	2.067000|2.067000	0.61834|0.61834	0.533000|0.533000	0.62120|0.62120	TGT|TCT	.	.	.	none		0.363	SLC20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254086.2	NM_005415		G	113405235	T	G	113405235	3	3	276	1	0	0	0	0	1	0	0	0	14451	1667	58	5	491	5	SLC20A1	2	113405235	Missense_Mutation	SNP	T	TCGA-Y8-A896-01A-11D-A35Z-10	38502557	113405235	129794138	19	17527											
INHBB	3625	hgsc.bcm.edu	37	chr2	121107030	121107030	+	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	ccggtgttcgtggacccaggCgaagagtcgcaccggccctt	6	7	14	14	5	0	1	0	0	0	1	2	3	0	2	4	4	0	2	4	4	1	2	rs201383879		TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr2:121107030C>G	ENST00000295228.3	+	2	850	c.804C>G	c.(802-804)ggC>ggG	p.G268G		NM_002193.2	NP_002184.2	P09529	INHBB_HUMAN	inhibin, beta B	268					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)				TGGACCCAGGCGAAGAGTCGC	0.672																																					p.G268G		Atlas-SNP	.											.	INHBB	29	.	0			c.C804G						PASS	.						59	63	62					2																	121107030		2203	4299	6502	SO:0001819	synonymous_variant	3625	exon2			CCCAGGCGAAGAG		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.804C>G	chr2.hg19:g.121107030C>G		152.0	0.0	.		143.0	38.0	.	NM_002193	Q53T31|Q8N1D3	Silent	SNP	ENST00000295228.3	hg19	CCDS2132.1																																																																																			.	C|1.000;T|0.000	.	alt		0.672	INHBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254234.1			G	121107030	C	G	121107030	2	3	276	1	0	0	0	0	0	0	0	1	7749	755	27	4		4	INHBB	2	121107030	Silent	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10	7701795	121107030	122092343	20	17528											
ANKAR	150709	hgsc.bcm.edu	37	chr2	190557049	190557049	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagattttaaatgccagaatTttcactacaaagagaatcaa	18	11	6	6	0	2	3	2	0	0	3	2	5	2	3	1	0	2	0	1	0	7	5			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr2:190557049T>C	ENST00000520309.1	+	4	1196	c.1108T>C	c.(1108-1110)Ttt>Ctt	p.F370L	ANKAR_ENST00000313581.4_Missense_Mutation_p.F370L|ANKAR_ENST00000438402.2_Missense_Mutation_p.F370L|ANKAR_ENST00000431575.2_Missense_Mutation_p.F299L|ANKAR_ENST00000461516.1_Intron|ANKAR_ENST00000281412.6_Missense_Mutation_p.F134L	NM_144708.3	NP_653309.3	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing	370						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)			ATGCCAGAATTTTCACTACAA	0.318																																					p.F370L		Atlas-SNP	.											.	ANKAR	184	.	0			c.T1108C						PASS	.						66	70	69					2																	190557049		2203	4299	6502	SO:0001583	missense	150709	exon4			CAGAATTTTCACT	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.1108T>C	chr2.hg19:g.190557049T>C	ENSP00000427882:p.Phe370Leu	206.0	0.0	.		206.0	48.0	.	NM_144708	Q3ZCS6|Q4G0M2|Q6ZU02	Missense_Mutation	SNP	ENST00000520309.1	hg19	CCDS33351.2	.	.	.	.	.	.	.	.	.	.	T	30	5.054111	0.93793	.	.	ENSG00000151687	ENST00000520309;ENST00000313581;ENST00000438402;ENST00000431575;ENST00000281412	T;T;T;T;T	0.61040	0.19;0.19;0.14;0.19;0.14	5.65	5.65	0.86999	.	0.266234	0.27016	N	0.021353	T	0.73814	0.3635	M	0.65498	2.005	0.46823	D	0.999216	D	0.69078	0.997	D	0.75020	0.985	T	0.76578	-0.2908	10	0.72032	D	0.01	-2.0555	14.8681	0.70434	0.0:0.0:0.0:1.0	.	370	Q7Z5J8	ANKAR_HUMAN	L	370;370;370;299;134	ENSP00000427882:F370L;ENSP00000313513:F370L;ENSP00000397243:F370L;ENSP00000393043:F299L;ENSP00000281412:F134L	ENSP00000281412:F134L	F	+	1	0	ANKAR	190265294	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	5.531000	0.67148	2.150000	0.67090	0.455000	0.32223	TTT	.	.	.	none		0.318	ANKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335045.3	NM_144708		C	190557049	T	C	190557049	3	2	276	1	0	0	0	0	1	0	0	0	623	1841	64	3	1118	3	ANKAR	2	190557049	Missense_Mutation	SNP	T	TCGA-Y8-A896-01A-11D-A35Z-10	69450019	190557049	52642324	21	17529											
FASTKD2	22868	hgsc.bcm.edu	37	chr2	207631966	207631966	+	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	cccacatttcctagtagcaaCtatttcacagcaatgtggac	12	11	6	12	0	1	0	1	0	0	0	2	1	2	1	2	1	3	3	2	1	5	5			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr2:207631966C>A	ENST00000236980.6	+	2	897	c.549C>A	c.(547-549)aaC>aaA	p.N183K	FASTKD2_ENST00000402774.3_Missense_Mutation_p.N183K|MDH1B_ENST00000392214.2_5'Flank|MDH1B_ENST00000374412.3_5'Flank|FASTKD2_ENST00000403094.3_Missense_Mutation_p.N183K|MDH1B_ENST00000449792.1_5'Flank|MDH1B_ENST00000454776.2_5'Flank	NM_014929.3	NP_055744.2	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	183					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)		CTAGTAGCAACTATTTCACAG	0.418																																					p.N183K		Atlas-SNP	.											.	FASTKD2	49	.	0			c.C549A						PASS	.						121	119	120					2																	207631966		2203	4300	6503	SO:0001583	missense	22868	exon2			TAGCAACTATTTC	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.549C>A	chr2.hg19:g.207631966C>A	ENSP00000236980:p.Asn183Lys	103.0	0.0	.		68.0	23.0	.	NM_001136193	Q9NVX6|Q9Y2H7	Missense_Mutation	SNP	ENST00000236980.6	hg19	CCDS2371.1	.	.	.	.	.	.	.	.	.	.	C	13.90	2.374586	0.42105	.	.	ENSG00000118246	ENST00000236980;ENST00000402774;ENST00000403094	T;T;T	0.15603	2.41;2.41;2.41	5.31	1.09	0.20402	.	0.195508	0.41823	N	0.000814	T	0.16128	0.0388	L	0.52573	1.65	0.44234	D	0.997071	B;B	0.25667	0.084;0.131	B;B	0.28916	0.037;0.096	T	0.06180	-1.0841	10	0.42905	T	0.14	-19.5825	10.2914	0.43599	0.2493:0.5094:0.2413:0.0	.	183;183	Q9NYY8-2;Q9NYY8	.;FAKD2_HUMAN	K	183	ENSP00000236980:N183K;ENSP00000385990:N183K;ENSP00000384929:N183K	ENSP00000236980:N183K	N	+	3	2	FASTKD2	207340211	1.000000	0.71417	0.999000	0.59377	0.957000	0.61999	1.884000	0.39668	0.194000	0.20326	0.561000	0.74099	AAC	.	.	.	none		0.418	FASTKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256428.2	NM_014929		A	207631966	C	A	207631966	3	1	276	1	0	0	0	0	1	0	0	0	5693	564	20	4	551	4	FASTKD2	2	207631966	Missense_Mutation	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10	17074917	207631966	35567407	22	17530											
ATG9A	79065	hgsc.bcm.edu	37	chr2	220090237	220090237	+	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	atcttgttggcaaataggatGtcatagtccacgcagctgac	11	11	10	9	1	2	1	1	1	1	0	3	2	3	2	1	2	1	4	1	2	3	4			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr2:220090237G>A	ENST00000409618.1	-	6	709	c.270C>T	c.(268-270)gaC>gaT	p.D90D	ATG9A_ENST00000361242.4_Silent_p.D90D|ATG9A_ENST00000488833.1_5'Flank|ATG9A_ENST00000409422.1_Silent_p.D29D|ATG9A_ENST00000396761.2_Silent_p.D90D|AC068946.1_ENST00000408417.1_RNA			Q7Z3C6	ATG9A_HUMAN	autophagy related 9A	90					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)		CAAATAGGATGTCATAGTCCA	0.532																																					p.D90D		Atlas-SNP	.											.	ATG9A	50	.	0			c.C270T						PASS	.						109	114	113					2																	220090237		2067	4222	6289	SO:0001819	synonymous_variant	79065	exon6			TAGGATGTCATAG	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.270C>T	chr2.hg19:g.220090237G>A		143.0	0.0	.		133.0	38.0	.	NM_001077198	Q3ZAQ6|Q6P0N7|Q7Z317|Q7Z320|Q8NDK6|Q8WU65|Q9BVL5|Q9H6L1|Q9HAG7	Silent	SNP	ENST00000409618.1	hg19	CCDS42820.1																																																																																			.	.	.	none		0.532	ATG9A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335930.1	NM_024085		A	220090237	G	A	220090237	2	1	276	1	0	0	0	0	0	0	0	1	1102	1368	48	2		2	ATG9A	2	220090237	Silent	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	12458271	220090237	23109136	23	17531											
CHRND	1144	hgsc.bcm.edu	37	chr2	233394851	233394851	+	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	ttctacctaccggctgacagTgagcctccaggccccgtccc	6	8	9	18	2	1	2	0	2	1	0	3	2	3	2	7	2	3	1	7	2	2	3			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr2:233394851T>C	ENST00000258385.3	+	7	852		c.e7+2		CHRND_ENST00000536614.1_Splice_Site|CHRND_ENST00000543200.1_Splice_Site|CHRND_ENST00000457943.2_Intron	NM_000751.2	NP_000742.1	Q07001	ACHD_HUMAN	cholinergic receptor, nicotinic, delta (muscle)						cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|musculoskeletal movement (GO:0050881)|neuromuscular process (GO:0050905)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)	34		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.89e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00078)|Lung(119;0.00579)|LUSC - Lung squamous cell carcinoma(224;0.00754)	Galantamine(DB00674)	CGGCTGACAGTGAGCCTCCAG	0.647																																					.		Atlas-SNP	.											.	CHRND	67	.	0			c.775+2T>C	GRCh37	CD012239	CHRND	D		PASS	.						125	106	112					2																	233394851		2203	4300	6503	SO:0001630	splice_region_variant	1144	exon6			TGACAGTGAGCCT	X55019	CCDS2494.1, CCDS58754.1	2q37.1	2012-02-11	2012-02-07		ENSG00000135902	ENSG00000135902		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1965	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, delta (muscle)"	100720	"cholinergic receptor, nicotinic, delta"	ACHRD			Standard	NM_000751		Approved		uc002vsw.4	Q07001	OTTHUMG00000133261	ENST00000258385.3:c.820+2T>C	chr2.hg19:g.233394851T>C		55.0	0.0	.		38.0	8.0	.	NM_001256657	A8K661|B4DT92|Q52LH4	Splice_Site	SNP	ENST00000258385.3	hg19	CCDS2494.1	.	.	.	.	.	.	.	.	.	.	T	18.45	3.625679	0.66901	.	.	ENSG00000135902	ENST00000543200;ENST00000258385	.	.	.	5.18	5.18	0.71444	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3496	0.74373	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	CHRND	233103095	1.000000	0.71417	1.000000	0.80357	0.700000	0.40528	7.896000	0.87350	2.105000	0.64084	0.533000	0.62120	.	.	.	.	none		0.647	CHRND-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257038.2		Intron	C	233394851	T	C	233394851	5	2	276	1	0	0	0	0	0	0	1	0	3396	1710	59	3	848	3	CHRND	2	233394851	Splice_Site	SNP	T	TCGA-Y8-A896-01A-11D-A35Z-10	13304614	233394851	9804522	24	17532											
TOP2B	7155	hgsc.bcm.edu	37	chr3	25675377	25675377	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagctgatttgctggaatccTttttcactcaatgtgagaca	11	14	8	8	0	2	2	2	2	0	1	3	4	3	3	1	1	2	2	1	1	3	3			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr3:25675377T>C	ENST00000264331.4	-	8	980	c.981A>G	c.(979-981)aaA>aaG	p.K327K	TOP2B_ENST00000435706.2_Silent_p.K322K	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	327					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)	GCTGGAATCCTTTTTCACTCA	0.348																																					p.K322K		Atlas-SNP	.											TOP2B,right_upper_lobe,carcinoma,0,1	TOP2B	98	.	0			c.A966G						PASS	.						162	156	158					3																	25675377		1848	4087	5935	SO:0001819	synonymous_variant	7155	exon8			GAATCCTTTTTCA	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.981A>G	chr3.hg19:g.25675377T>C		77.0	0.0	.		74.0	3.0	.	NM_001068	Q13600|Q9UMG8|Q9UQP8	Silent	SNP	ENST00000264331.4	hg19																																																																																				.	.	.	none		0.348	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				C	25675377	T	C	25675377	2	2	276	1	0	0	0	0	0	0	0	1	16378	1606	56	3		3	TOP2B	3	25675377	Silent	SNP	T	TCGA-Y8-A896-01A-11D-A35Z-10		25675377	172347053	25	17533											
FYCO1	79443	hgsc.bcm.edu	37	chr3	45972569	45972569	+	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	gagcccagccttaccttacaCtgatccagcggtgtgtcctc	7	10	9	15	1	0	1	0	1	0	0	3	2	2	1	5	1	5	0	5	1	2	2			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr3:45972569C>G	ENST00000296137.2	-	16	4450	c.4245G>C	c.(4243-4245)caG>caC	p.Q1415H	FYCO1_ENST00000438446.1_Missense_Mutation_p.Q86H|FYCO1_ENST00000535325.1_Missense_Mutation_p.Q1435H	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	1415	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.				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)		TTACCTTACACTGATCCAGCG	0.592																																					p.Q1415H		Atlas-SNP	.											.	FYCO1	115	.	0			c.G4245C						PASS	.						73	59	64					3																	45972569		2203	4300	6503	SO:0001583	missense	79443	exon16			CTTACACTGATCC	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.4245G>C	chr3.hg19:g.45972569C>G	ENSP00000296137:p.Gln1415His	147.0	0.0	.		127.0	48.0	.	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	hg19	CCDS2734.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.61|13.61	2.289406|2.289406	0.40494|0.40494	.|.	.|.	ENSG00000163820|ENSG00000163820	ENST00000296137;ENST00000438446;ENST00000535325|ENST00000433878	T;T;T|.	0.43688|.	0.94;0.94;0.94|.	5.1|5.1	3.28|3.28	0.37604|0.37604	GOLD (2);|.	0.130764|.	0.52532|.	D|.	0.000067|.	T|T	0.50616|0.50616	0.1626|0.1626	L|L	0.37630|0.37630	1.12|1.12	0.43512|0.43512	D|D	0.995777|0.995777	P;B|.	0.35033|.	0.481;0.005|.	B;B|.	0.41135|.	0.348;0.017|.	T|T	0.40327|0.40327	-0.9569|-0.9569	10|5	0.44086|.	T|.	0.13|.	-24.5306|-24.5306	8.1734|8.1734	0.31268|0.31268	0.0:0.7558:0.0:0.2442|0.0:0.7558:0.0:0.2442	.|.	1435;1415|.	B7ZKT7;Q9BQS8|.	.;FYCO1_HUMAN|.	H|T	1415;86;1435|204	ENSP00000296137:Q1415H;ENSP00000398517:Q86H;ENSP00000441178:Q1435H|.	ENSP00000296137:Q1415H|.	Q|S	-|-	3|2	2|0	FYCO1|FYCO1	45947573|45947573	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.702000|0.702000	0.40608|0.40608	1.765000|1.765000	0.38481|0.38481	1.142000|1.142000	0.42291|0.42291	0.655000|0.655000	0.94253|0.94253	CAG|AGT	.	.	.	none		0.592	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513		G	45972569	C	G	45972569	3	3	276	1	0	0	0	0	1	0	0	0	6132	564	20	4	203	4	FYCO1	3	45972569	Missense_Mutation	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10	20297192	45972569	152049861	26	17534											
SMARCC1	6599	hgsc.bcm.edu	37	chr3	47680268	47680268	+	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	cattttttcctcttcagctcCttctacaagtaaaagaataa	13	15	3	10	0	3	1	1	0	2	1	5	1	5	1	2	0	2	2	2	0	6	8			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr3:47680268C>T	ENST00000254480.5	-	22	2442	c.2323G>A	c.(2323-2325)Gga>Aga	p.G775R	SMARCC1_ENST00000425518.1_5'UTR	NM_003074.3	NP_003065.3	Q92922	SMRC1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	775	Glu-rich.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|insulin receptor signaling pathway (GO:0008286)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(15)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)		TCTTCAGCTCCTTCTACAAGT	0.393																																					p.G775R		Atlas-SNP	.											.	SMARCC1	85	.	0			c.G2323A						PASS	.						123	122	122					3																	47680268		2203	4300	6503	SO:0001583	missense	6599	exon22			CAGCTCCTTCTAC	U66615	CCDS2758.1	3p21.31	2008-05-15			ENSG00000173473	ENSG00000173473			11104	protein-coding gene	gene with protein product		601732				8804307	Standard	NM_003074		Approved	BAF155, SRG3, Rsc8, CRACC1	uc003crq.2	Q92922	OTTHUMG00000133519	ENST00000254480.5:c.2323G>A	chr3.hg19:g.47680268C>T	ENSP00000254480:p.Gly775Arg	128.0	0.0	.		97.0	26.0	.	NM_003074	Q17RS0|Q6P172|Q8IWH2	Missense_Mutation	SNP	ENST00000254480.5	hg19	CCDS2758.1	.	.	.	.	.	.	.	.	.	.	C	18.14	3.556937	0.65425	.	.	ENSG00000173473	ENST00000254480	T	0.37915	1.17	5.16	5.16	0.70880	.	0.346611	0.29987	N	0.010684	T	0.32010	0.0815	L	0.40543	1.245	0.53005	D	0.999965	B	0.30763	0.294	B	0.27262	0.078	T	0.13926	-1.0491	10	0.59425	D	0.04	-10.0611	15.7325	0.77817	0.0:1.0:0.0:0.0	.	775	Q92922	SMRC1_HUMAN	R	775	ENSP00000254480:G775R	ENSP00000254480:G775R	G	-	1	0	SMARCC1	47655272	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	4.646000	0.61411	2.564000	0.86499	0.655000	0.94253	GGA	.	.	.	none		0.393	SMARCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257491.1			T	47680268	C	T	47680268	3	4	276	1	0	0	0	0	1	0	0	0	14788	690	24	2	1022	2	SMARCC1	3	47680268	Missense_Mutation	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10	1707699	47680268	150342162	27	17535											
CDC25A	993	hgsc.bcm.edu	37	chr3	48200920	48200920	+	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	ggggtattcattacccaggcGatctctctctctcacatacc	8	12	7	14	1	4	0	2	0	3	0	7	1	4	0	2	3	2	1	2	3	3	4			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr3:48200920G>A	ENST00000302506.3	-	14	1756	c.1348C>T	c.(1348-1350)Cgc>Tgc	p.R450C	CDC25A_ENST00000351231.3_Missense_Mutation_p.R410C	NM_001789.2	NP_001780.2	P30304	MPIP1_HUMAN	cell division cycle 25A	450	Rhodanese. {ECO:0000255|PROSITE- ProRule:PRU00173}.				cell proliferation (GO:0008283)|cellular response to UV (GO:0034644)|DNA replication (GO:0006260)|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)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to radiation (GO:0009314)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.000685)|KIRC - Kidney renal clear cell carcinoma(197;0.00596)|Kidney(197;0.00684)		TTACCCAGGCGATCTCTCTCT	0.512																																					p.R450C		Atlas-SNP	.											.	CDC25A	40	.	0			c.C1348T						PASS	.						106	90	96					3																	48200920		2203	4300	6503	SO:0001583	missense	993	exon14			CCAGGCGATCTCT	M81933	CCDS2760.1, CCDS2761.1	3p21	2013-01-17	2013-01-17		ENSG00000164045	ENSG00000164045		"Protein tyrosine phosphatases / Class III Cys-based PTPs"	1725	protein-coding gene	gene with protein product		116947	"cell division cycle 25A", "cell division cycle 25 homolog A (S. cerevisiae)", "cell division cycle 25 homolog A (S. pombe)"			1836978	Standard	NM_001789		Approved		uc003csh.1	P30304	OTTHUMG00000133535	ENST00000302506.3:c.1348C>T	chr3.hg19:g.48200920G>A	ENSP00000303706:p.Arg450Cys	92.0	0.0	.		67.0	21.0	.	NM_001789	Q8IZH5|Q96IL3|Q9H2F2	Missense_Mutation	SNP	ENST00000302506.3	hg19	CCDS2760.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.344385	0.82022	.	.	ENSG00000164045	ENST00000302506;ENST00000351231	T;T	0.25749	1.78;1.78	5.76	4.86	0.63082	Rhodanese-like (5);	0.000000	0.85682	D	0.000000	T	0.65502	0.2697	H	0.97291	3.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.78298	-0.2258	10	0.87932	D	0	.	13.531	0.61621	0.0:0.0:0.8379:0.1621	.	410;450	P30304-2;P30304	.;MPIP1_HUMAN	C	450;410	ENSP00000303706:R450C;ENSP00000343166:R410C	ENSP00000303706:R450C	R	-	1	0	CDC25A	48175924	1.000000	0.71417	0.930000	0.37139	0.702000	0.40608	3.997000	0.57016	1.369000	0.46134	0.655000	0.94253	CGC	.	.	.	none		0.512	CDC25A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257512.2	NM_001789		A	48200920	G	A	48200920	3	1	276	1	0	0	0	0	1	0	0	0	3064	1058	37	1	234	1	CDC25A	3	48200920	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	520652	48200920	149821510	28	17536											
PLXNB1	5364	hgsc.bcm.edu	37	chr3	48465669	48465669	+	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	caggcgccgctgttcacagaCcccctggtgcacgctcccgc	5	6	11	19	4	1	1	1	0	0	1	2	1	2	1	4	2	1	4	4	2	0	1	rs368626600		TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr3:48465669C>A	ENST00000358536.4	-	3	621	c.352G>T	c.(352-354)Gtc>Ttc	p.V118F	PLXNB1_ENST00000358459.4_Missense_Mutation_p.V118F|PLXNB1_ENST00000448774.2_Intron|PLXNB1_ENST00000456774.1_Missense_Mutation_p.V118F|PLXNB1_ENST00000296440.6_Missense_Mutation_p.V118F	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	118	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		TGTTCACAGACCCCCTGGTGC	0.667																																					p.V118F		Atlas-SNP	.											.	PLXNB1	150	.	0			c.G352T						PASS	.						17	20	19					3																	48465669		2199	4294	6493	SO:0001583	missense	5364	exon3			CACAGACCCCCTG	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"Plexins"	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.352G>T	chr3.hg19:g.48465669C>A	ENSP00000351338:p.Val118Phe	123.0	0.0	.		106.0	40.0	.	NM_001130082	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Missense_Mutation	SNP	ENST00000358536.4	hg19	CCDS2765.1	.	.	.	.	.	.	.	.	.	.	C	14.58	2.577137	0.45902	.	.	ENSG00000164050	ENST00000296440;ENST00000358459;ENST00000358536;ENST00000456774	T;T;T;T	0.04862	3.54;3.54;3.54;3.54	4.14	2.3	0.28687	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.184288	0.36338	N	0.002654	T	0.08670	0.0215	L	0.29908	0.895	0.80722	D	1	D;P	0.56521	0.976;0.953	P;P	0.56514	0.563;0.8	T	0.32534	-0.9903	10	0.38643	T	0.18	.	6.0703	0.19885	0.0:0.5327:0.0:0.4673	.	118;118	O43157;O43157-2	PLXB1_HUMAN;.	F	118	ENSP00000296440:V118F;ENSP00000351242:V118F;ENSP00000351338:V118F;ENSP00000414199:V118F	ENSP00000296440:V118F	V	-	1	0	PLXNB1	48440673	0.980000	0.34600	0.607000	0.28956	0.655000	0.38815	2.140000	0.42159	0.216000	0.20781	-0.136000	0.14681	GTC	.	.	.	weak		0.667	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673		A	48465669	C	A	48465669	3	1	276	1	0	0	0	0	1	0	0	0	12130	507	18	4	6199	4	PLXNB1	3	48465669	Missense_Mutation	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10	264749	48465669	149556761	29	17537											
COL7A1	1294	hgsc.bcm.edu	37	chr3	48619024	48619024	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acccggtctccagggtctccCttggggccagggtctccagg	4	8	14	15	1	3	0	0	0	3	0	6	0	3	0	5	6	0	0	5	6	0	1			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr3:48619024C>T	ENST00000328333.8	-	49	4871	c.4764G>A	c.(4762-4764)aaG>aaA	p.K1588K	MIR711_ENST00000390201.1_RNA|COL7A1_ENST00000454817.1_Silent_p.K1588K	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	1588	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CAGGGTCTCCCTTGGGGCCAG	0.587																																					p.K1588K		Atlas-SNP	.											.	COL7A1	320	.	0			c.G4764A						PASS	.						103	107	106					3																	48619024		2203	4300	6503	SO:0001819	synonymous_variant	1294	exon49			GTCTCCCTTGGGG	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"Collagens", "Fibronectin type III domain containing"	2214	protein-coding gene	gene with protein product	"collagen VII, alpha-1 polypeptide", "LC collagen"	120120	"epidermolysis bullosa, dystrophic, dominant and recessive"	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.4764G>A	chr3.hg19:g.48619024C>T		96.0	0.0	.		90.0	15.0	.	NM_000094	Q14054|Q16507	Silent	SNP	ENST00000328333.8	hg19	CCDS2773.1																																																																																			.	.	.	none		0.587	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094		T	48619024	C	T	48619024	2	4	276	1	0	0	0	0	0	0	0	1	3706	680	24	2		2	COL7A1	3	48619024	Silent	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10	153355	48619024	149403406	30	17538											
IMPDH2	54870	hgsc.bcm.edu	37	chr3	49064477	49064477	+	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	caagtcttccctctttgtcaTtatctacgtgggaggtgaga	8	14	10	9	1	4	1	1	1	3	1	5	3	5	2	1	2	1	0	1	2	3	4			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr3:49064477T>C	ENST00000395443.2	-	0	3549				RP13-131K19.6_ENST00000607245.1_RNA|IMPDH2_ENST00000326739.4_Missense_Mutation_p.M179V	NM_198880.1	NP_942581.1	Q2TAL8	QRIC1_HUMAN	glutamine-rich 1							nucleus (GO:0005634)				breast(2)|endometrium(5)|large_intestine(8)|lung(8)|ovary(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(193;8.88e-05)|Kidney(197;0.00239)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		CTCTTTGTCATTATCTACGTG	0.507																																					p.M179V		Atlas-SNP	.											.	IMPDH2	47	.	0			c.A535G						PASS	.						159	146	150					3																	49064477		2203	4300	6503	SO:0001628	intergenic_variant	3615	exon6			TTGTCATTATCTA		CCDS2787.1	3p21.31	2011-06-03			ENSG00000198218	ENSG00000198218			24713	protein-coding gene	gene with protein product						12477932	Standard	NM_017730		Approved	FLJ20259	uc003cvv.3	Q2TAL8	OTTHUMG00000156772		chr3.hg19:g.49064477T>C		58.0	0.0	.		65.0	15.0	.	NM_000884	Q4G0F7|Q7L621|Q8TEA5	Missense_Mutation	SNP	ENST00000395443.2	hg19	CCDS2787.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.1|20.1	3.937086|3.937086	0.73557|0.73557	.|.	.|.	ENSG00000178035|ENSG00000178035	ENST00000537036;ENST00000326739;ENST00000442157|ENST00000429182	D;D|.	0.96136|.	-3.92;-3.92|.	6.08|6.08	6.08|6.08	0.98989|0.98989	Aldolase-type TIM barrel (1);Cystathionine beta-synthase, core (2);IMP dehydrogenase/GMP reductase (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.88987|0.88987	0.6587|0.6587	H|H	0.97918|0.97918	4.105|4.105	0.80722|0.80722	D|D	1|1	D|.	0.71674|.	0.998|.	D|.	0.91635|.	0.999|.	D|D	0.92898|0.92898	0.6337|0.6337	10|5	0.87932|.	D|.	0|.	-37.003|-37.003	16.6438|16.6438	0.85155|0.85155	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	179|.	P12268|.	IMDH2_HUMAN|.	V|S	179;179;154|110	ENSP00000321584:M179V;ENSP00000403502:M154V|.	ENSP00000321584:M179V|.	M|N	-|-	1|2	0|0	IMPDH2|IMPDH2	49039481|49039481	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.919000|0.919000	0.55068|0.55068	5.943000|5.943000	0.70211|0.70211	2.333000|2.333000	0.79357|0.79357	0.533000|0.533000	0.62120|0.62120	ATG|AAT	.	.	.	none		0.507	QRICH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345669.1	NM_017730		C	49064477	T	C	49064477	1	2	276	0	1	0	0	0	0	0	0	0	7734	1493	52	3		3	IMPDH2	3	49064477	IGR	SNP	T	TCGA-Y8-A896-01A-11D-A35Z-10	445453	49064477	148957953	31	17539											
RNF123	63891	hgsc.bcm.edu	37	chr3	49734840	49734840	+	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	catccactgtggtcctggacCacacaggcggctttgagggg	7	8	14	12	1	0	1	0	1	0	0	2	2	2	2	3	6	0	1	3	6	0	1			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr3:49734840C>A	ENST00000327697.6	+	5	436	c.292C>A	c.(292-294)Cac>Aac	p.H98N	RNF123_ENST00000432042.1_5'UTR	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	98	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				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)		GGTCCTGGACCACACAGGCGG	0.602																																					p.H98N		Atlas-SNP	.											.	RNF123	100	.	0			c.C292A						PASS	.						53	53	53					3																	49734840		2203	4300	6503	SO:0001583	missense	63891	exon5			CTGGACCACACAG	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.292C>A	chr3.hg19:g.49734840C>A	ENSP00000328287:p.His98Asn	90.0	0.0	.		63.0	18.0	.	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	hg19	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	C	33	5.209517	0.95069	.	.	ENSG00000164068	ENST00000327697;ENST00000389066	T	0.72942	-0.7	6.17	6.17	0.99709	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	0.144593	0.47852	D	0.000201	T	0.80019	0.4547	L	0.40543	1.245	0.80722	D	1	D	0.63880	0.993	D	0.70227	0.968	T	0.78404	-0.2217	10	0.52906	T	0.07	-39.2141	19.8676	0.96824	0.0:1.0:0.0:0.0	.	98	Q5XPI4	RN123_HUMAN	N	98	ENSP00000328287:H98N	ENSP00000328287:H98N	H	+	1	0	RNF123	49709844	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.621000	0.67743	2.941000	0.99782	0.655000	0.94253	CAC	.	.	.	none		0.602	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064		A	49734840	C	A	49734840	3	1	276	1	0	0	0	0	1	0	0	0	13446	594	21	4	306	4	RNF123	3	49734840	Missense_Mutation	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10	670363	49734840	148287590	32	17540											
UBA5	79876	hgsc.bcm.edu	37	chr3	132395353	132395353	+	Frame_Shift_Del	DEL	A	A	-																															gcttggaagacctcatggccAaaatgaagaatatgtagata																										TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr3:132395353delA	ENST00000356232.4	+	12	2270	c.1198delA	c.(1198-1200)aaafs	p.K400fs	UBA5_ENST00000473651.1_3'UTR|UBA5_ENST00000493720.2_Intron|UBA5_ENST00000494238.2_Frame_Shift_Del_p.K344fs|UBA5_ENST00000264991.4_Frame_Shift_Del_p.K344fs	NM_024818.3	NP_079094.1	Q9GZZ9	UBA5_HUMAN	ubiquitin-like modifier activating enzyme 5	400					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						CCTCATGGCCAAAATGAAGAA	0.323																																					p.A399fs		Atlas-Indel,Pindel	.											.	UBA5	33	.	0			c.1197delC						PASS	.						92	92	92					3																	132395353		2202	4300	6502	SO:0001589	frameshift_variant	79876	exon12			.	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.1198delA	chr3.hg19:g.132395353delA	ENSP00000348565:p.Lys400fs	149.0	0.0	0		133.0	31.0	0.233083	NM_024818	A6NJL3|D3DNC8|Q96ST1	Frame_Shift_Del	DEL	ENST00000356232.4	hg19	CCDS3076.1																																																																																			.	.	.	none		0.323	UBA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357187.2	NM_024818		-	132395353	A	-	132395353	7	5	276	1	0	1	0	1	0	0	0	0	16842	131	5	0	1244	0	UBA5	3	132395353	Frame_Shift_Del	DEL	A	TCGA-Y8-A896-01A-11D-A35Z-10	82660513	132395353	65627077	33	17541											
FXR1	8087	hgsc.bcm.edu	37	chr3	180688019	180688019	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatcagactgcagacactgaTgccagcgaatctcatcacag	13	7	9	12	1	3	3	3	1	1	2	4	5	3	3	1	0	3	1	1	0	1	0			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr3:180688019T>C	ENST00000357559.4	+	15	1860	c.1476T>C	c.(1474-1476)gaT>gaC	p.D492D	FXR1_ENST00000305586.7_Silent_p.D407D|FXR1_ENST00000491062.1_Silent_p.D443D|FXR1_ENST00000445140.2_Silent_p.D492D|FXR1_ENST00000480918.1_Silent_p.D479D|FXR1_ENST00000468861.1_Silent_p.D407D	NM_001013438.2|NM_005087.3	NP_001013456.1|NP_005078.2	P51114	FXR1_HUMAN	fragile X mental retardation, autosomal homolog 1	492					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)			CAGACACTGATGCCAGCGAAT	0.433																																					p.D492D		Atlas-SNP	.											.	FXR1	75	.	0			c.T1476C						PASS	.						135	117	123					3																	180688019		2203	4300	6503	SO:0001819	synonymous_variant	8087	exon15			CACTGATGCCAGC	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.1476T>C	chr3.hg19:g.180688019T>C		146.0	0.0	.		138.0	36.0	.	NM_001013438	A8K9B8|Q7Z450|Q8N6R8	Silent	SNP	ENST00000357559.4	hg19	CCDS3238.1	.	.	.	.	.	.	.	.	.	.	T	10.53	1.376178	0.24857	.	.	ENSG00000114416	ENST00000482125	.	.	.	5.91	0.686	0.18015	.	.	.	.	.	T	0.58293	0.2112	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52283	-0.8596	4	.	.	.	-18.2892	10.2884	0.43581	0.0:0.3977:0.0:0.6023	.	.	.	.	T	93	.	.	M	+	2	0	FXR1	182170713	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.600000	0.24104	0.091000	0.17302	0.528000	0.53228	ATG	.	.	.	none		0.433	FXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350265.5			C	180688019	T	C	180688019	2	2	276	1	0	0	0	0	0	0	0	1	6122	1461	51	3		3	FXR1	3	180688019	Silent	SNP	T	TCGA-Y8-A896-01A-11D-A35Z-10	48292666	180688019	17334411	34	17542											
ABCC5	10057	hgsc.bcm.edu	37	chr3	183700580	183700580	+	Frame_Shift_Del	DEL	T	T	-																															acctcacccagggatttctcTttaatgttctttaacttaag																										TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr3:183700580delT	ENST00000334444.6	-	6	1047	c.807delA	c.(805-807)aaafs	p.K269fs	ABCC5_ENST00000492216.1_5'UTR|ABCC5_ENST00000265586.6_Frame_Shift_Del_p.K269fs	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	269	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	GGGATTTCTCTTTAATGTTCT	0.488																																					p.E270fs		Atlas-Indel,Pindel	.											.	ABCC5	142	.	0			c.808delG						PASS	.						68	72	71					3																	183700580		1908	4132	6040	SO:0001589	frameshift_variant	10057	exon6			.	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.807delA	chr3.hg19:g.183700580delT	ENSP00000333926:p.Lys269fs	165.0	0.0	0		149.0	31.0	0.208054	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Frame_Shift_Del	DEL	ENST00000334444.6	hg19	CCDS43176.1																																																																																			.	.	.	none		0.488	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688		-	183700580	T	-	183700580	7	5	276	1	0	1	0	1	0	0	0	0	56	1606	56	0	3606	0	ABCC5	3	183700580	Frame_Shift_Del	DEL	T	TCGA-Y8-A896-01A-11D-A35Z-10	3012561	183700580	14321850	35	17543											
IGF2BP2	10644	hgsc.bcm.edu	37	chr3	185364916	185364916	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcactggttaagttctgcAgttcgttcacctgtgaaggg	7	13	12	9	1	2	1	1	1	1	0	3	1	2	1	1	2	2	6	1	2	2	4			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr3:185364916A>G	ENST00000382199.2	-	15	1699	c.1604T>C	c.(1603-1605)cTg>cCg	p.L535P	IGF2BP2_ENST00000457616.2_Missense_Mutation_p.L541P|IGF2BP2_ENST00000494906.1_5'Flank|IGF2BP2_ENST00000421047.2_Missense_Mutation_p.L478P|IGF2BP2_ENST00000346192.3_Missense_Mutation_p.L492P	NM_006548.4	NP_006539.3	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding protein 2	535	KH 4. {ECO:0000255|PROSITE- ProRule:PRU00117}.				anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)	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)			TAAGTTCTGCAGTTCGTTCAC	0.542																																					p.L535P		Atlas-SNP	.											.	IGF2BP2	69	.	0			c.T1604C						PASS	.						174	149	157					3																	185364916		2203	4300	6503	SO:0001583	missense	10644	exon15			TTCTGCAGTTCGT	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.1604T>C	chr3.hg19:g.185364916A>G	ENSP00000371634:p.Leu535Pro	56.0	0.0	.		49.0	9.0	.	NM_006548	A0A4Z0|B3FTN2|B3FTN3|B3FTN4	Missense_Mutation	SNP	ENST00000382199.2	hg19	CCDS3273.2	.	.	.	.	.	.	.	.	.	.	A	22.9	4.352874	0.82132	.	.	ENSG00000073792	ENST00000382199;ENST00000421047;ENST00000457616;ENST00000346192	T;T;T;T	0.38240	1.15;1.15;1.15;1.15	5.02	5.02	0.67125	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.075107	0.56097	D	0.000032	T	0.66446	0.2790	M	0.90759	3.145	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	0.74705	-0.3575	10	0.87932	D	0	-8.7264	14.0216	0.64558	1.0:0.0:0.0:0.0	.	429;472;478;541;492;535	Q9Y6M1-5;Q9Y6M1-3;Q9Y6M1-4;F8W930;Q9Y6M1-1;Q9Y6M1	.;.;.;.;.;IF2B2_HUMAN	P	535;478;541;492	ENSP00000371634:L535P;ENSP00000413787:L478P;ENSP00000410242:L541P;ENSP00000320204:L492P	ENSP00000320204:L492P	L	-	2	0	IGF2BP2	186847610	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	9.339000	0.96797	2.022000	0.59522	0.454000	0.30748	CTG	.	.	.	none		0.542	IGF2BP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157087.2	NM_006548		G	185364916	A	G	185364916	3	3	276	1	0	0	0	0	1	0	0	0	7581	188	7	3	203	3	IGF2BP2	3	185364916	Missense_Mutation	SNP	A	TCGA-Y8-A896-01A-11D-A35Z-10	1664336	185364916	12657514	36	17544											
CDH18	1016	hgsc.bcm.edu	37	chr5	19473544	19473544	+	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	gctagggtctaggtctgcttCtgccagtctttgcttaataa	7	15	10	9	0	4	0	0	0	4	0	4	0	4	0	1	2	3	3	1	2	4	6	rs376117433		TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr5:19473544C>T	ENST00000507958.1	-	15	3154	c.2164G>A	c.(2164-2166)Gaa>Aaa	p.E722K	CDH18_ENST00000274170.4_Missense_Mutation_p.E722K|CDH18_ENST00000510297.1_5'UTR|CDH18_ENST00000382275.1_Missense_Mutation_p.E722K			Q13634	CAD18_HUMAN	cadherin 18, type 2	722					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)					AGGTCTGCTTCTGCCAGTCTT	0.488																																					p.E722K		Atlas-SNP	.											.	CDH18	561	.	0			c.G2164A						PASS	.	C	LYS/GLU,	0,4406		0,0,2203	187	172	177		2164,	6	1	5		177	1,8599	1.2+/-3.3	0,1,4299	no	missense,utr-3	CDH18	NM_004934.3,NM_001167667.1	56,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,	722/791,	19473544	1,13005	2203	4300	6503	SO:0001583	missense	1016	exon13			CTGCTTCTGCCAG	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.2164G>A	chr5.hg19:g.19473544C>T	ENSP00000425093:p.Glu722Lys	147.0	0.0	.		108.0	33.0	.	NM_004934	A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	hg19	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.025527	0.93518	0.0	1.16E-4	ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170	T;T;T	0.78126	-1.15;-1.15;-1.15	6.01	6.01	0.97437	Cadherin, cytoplasmic domain (1);	0.049556	0.85682	D	0.000000	D	0.86192	0.5874	M	0.71581	2.175	0.58432	D	0.999999	D	0.53619	0.961	P	0.59012	0.85	D	0.84732	0.0746	9	.	.	.	.	19.085	0.93200	0.0:1.0:0.0:0.0	.	722	Q13634	CAD18_HUMAN	K	722	ENSP00000371710:E722K;ENSP00000425093:E722K;ENSP00000274170:E722K	.	E	-	1	0	CDH18	19509301	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	6.085000	0.71343	2.861000	0.98227	0.650000	0.86243	GAA	.	.	.	weak		0.488	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		T	19473544	C	T	19473544	3	4	276	1	0	0	0	0	1	0	0	0	3105	922	32	2	212	2	CDH18	5	19473544	Missense_Mutation	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10		19473544	161441716	37	17545											
CMYA5	202333	hgsc.bcm.edu	37	chr5	79031309	79031309	+	Missense_Mutation	SNP	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	ctgatcattcattatcagagGtaaaacttaaaactgctgat	15	13	6	7	0	3	3	3	2	0	1	3	3	3	3	0	1	3	2	0	1	5	4			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr5:79031309G>A	ENST00000446378.2	+	2	6752	c.6721G>A	c.(6721-6723)Gta>Ata	p.V2241I		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2241					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)		ATTATCAGAGGTAAAACTTAA	0.363																																					p.V2241I		Atlas-SNP	.											.	CMYA5	643	.	0			c.G6721A						PASS	.						100	100	100					5																	79031309		1821	4086	5907	SO:0001583	missense	202333	exon2			TCAGAGGTAAAAC	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.6721G>A	chr5.hg19:g.79031309G>A	ENSP00000394770:p.Val2241Ile	270.0	0.0	.		231.0	60.0	.	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	hg19	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	G	3.106	-0.183619	0.06340	.	.	ENSG00000164309	ENST00000446378	T	0.19938	2.11	5.94	-0.798	0.10905	.	1.045130	0.07537	N	0.913225	T	0.12732	0.0309	L	0.34521	1.04	0.09310	N	1	B	0.14805	0.011	B	0.08055	0.003	T	0.37291	-0.9712	10	0.19147	T	0.46	.	3.6087	0.08052	0.3329:0.0:0.3348:0.3323	.	2241	Q8N3K9	CMYA5_HUMAN	I	2241	ENSP00000394770:V2241I	ENSP00000394770:V2241I	V	+	1	0	CMYA5	79067065	0.001000	0.12720	0.017000	0.16124	0.000000	0.00434	-0.426000	0.07008	-0.068000	0.12953	-0.912000	0.02778	GTA	.	.	.	none		0.363	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		A	79031309	G	A	79031309	3	1	276	1	0	0	0	0	1	0	0	0	3592	1261	44	2	6727	2	CMYA5	5	79031309	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	59557765	79031309	101883951	38	17546											
COX7C	1350	hgsc.bcm.edu	37	chr5	85915264	85915264	+	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	tacacccttccttgtagtaaGacaccaactgcttaaaacat	14	11	4	12	0	0	1	0	0	0	1	1	1	1	1	3	0	4	3	3	0	6	6			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr5:85915264G>A	ENST00000509578.1	+	2	270	c.170G>A	c.(169-171)aGa>aAa	p.R57K	COX7C_ENST00000515763.1_Intron|COX7C_ENST00000247655.3_Missense_Mutation_p.R57K|MIR3607_ENST00000362392.1_RNA|COX7C_ENST00000513124.1_3'UTR			P15954	COX7C_HUMAN	cytochrome c oxidase subunit VIIc	57					cellular metabolic process (GO:0044237)|generation of precursor metabolites and energy (GO:0006091)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)			endometrium(1)|lung(1)	2		all_cancers(142;7e-06)|Lung NSC(167;0.000601)|all_lung(232;0.000693)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;1.56e-40)|Epithelial(54;3.17e-34)|all cancers(79;3.36e-29)		CTTGTAGTAAGACACCAACTG	0.373																																					p.R57K		Atlas-SNP	.											.	COX7C	5	.	0			c.G170A						PASS	.						170	160	163					5																	85915264		2203	4300	6503	SO:0001583	missense	1350	exon2			TAGTAAGACACCA	BC001005	CCDS4063.1	5q14	2011-07-04			ENSG00000127184	ENSG00000127184	1.9.3.1	"Mitochondrial respiratory chain complex / Complex IV"	2292	protein-coding gene	gene with protein product		603774				10072584	Standard	NM_001867		Approved		uc003kir.3	P15954	OTTHUMG00000119049	ENST00000509578.1:c.170G>A	chr5.hg19:g.85915264G>A	ENSP00000425759:p.Arg57Lys	69.0	0.0	.		50.0	11.0	.	NM_001867	Q6NR81	Missense_Mutation	SNP	ENST00000509578.1	hg19	CCDS4063.1	.	.	.	.	.	.	.	.	.	.	G	16.60	3.167360	0.57476	.	.	ENSG00000127184	ENST00000247655;ENST00000509578	.	.	.	5.6	5.6	0.85130	Cytochrome c oxidase, subunit VIIc domain (2);	0.000000	0.85682	D	0.000000	T	0.79076	0.4385	.	.	.	0.80722	D	1	D	0.63046	0.992	D	0.76071	0.987	T	0.80130	-0.1511	8	0.54805	T	0.06	-20.5435	15.1019	0.72284	0.0:0.0:1.0:0.0	.	57	P15954	COX7C_HUMAN	K	57	.	ENSP00000247655:R57K	R	+	2	0	COX7C	85951020	1.000000	0.71417	0.999000	0.59377	0.331000	0.28603	6.772000	0.75001	2.622000	0.88805	0.655000	0.94253	AGA	.	.	.	none		0.373	COX7C-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369746.1	NM_001867		A	85915264	G	A	85915264	3	1	276	1	0	0	0	0	1	0	0	0	3786	942	33	2	176	2	COX7C	5	85915264	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	6883955	85915264	94999996	39	17547											
PCDHB1	29930	hgsc.bcm.edu	37	chr5	140431589	140431589	+	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	ctgagtgccaatgggtatttCcacctgcacacccgcttctg	7	11	9	14	1	1	1	0	1	1	0	2	1	2	1	4	1	2	3	4	1	2	3			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr5:140431589C>T	ENST00000306549.3	+	1	611	c.534C>T	c.(532-534)ttC>ttT	p.F178F		NM_013340.2	NP_037472.2	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1	178	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			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)			ATGGGTATTTCCACCTGCACA	0.567																																					p.F178F		Atlas-SNP	.											.	PCDHB1	148	.	0			c.C534T						PASS	.						47	47	47					5																	140431589		2203	4300	6503	SO:0001819	synonymous_variant	29930	exon1			GTATTTCCACCTG	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.534C>T	chr5.hg19:g.140431589C>T		86.0	0.0	.		89.0	21.0	.	NM_013340	Q2M257	Silent	SNP	ENST00000306549.3	hg19	CCDS4243.1																																																																																			.	.	.	none		0.567	PCDHB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251822.2	NM_013340		T	140431589	C	T	140431589	2	4	276	1	0	0	0	0	0	0	0	1	11541	854	30	2		2	PCDHB1	5	140431589	Silent	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10	54516325	140431589	40483671	40	17548											
GLRA1	2741	hgsc.bcm.edu	37	chr5	151231124	151231124	+	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	aatcaggtagtaacccatctGccgctccaggtggaaccggg	10	7	12	12	2	2	0	1	0	1	0	3	1	3	1	4	4	3	3	4	4	4	2			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr5:151231124G>A	ENST00000455880.2	-	7	1025	c.739C>T	c.(739-741)Cag>Tag	p.Q247*	GLRA1_ENST00000471351.2_5'UTR|GLRA1_ENST00000545569.1_Nonsense_Mutation_p.Q164*|GLRA1_ENST00000274576.4_Nonsense_Mutation_p.Q247*			P23415	GLRA1_HUMAN	glycine receptor, alpha 1	247					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)	TAACCCATCTGCCGCTCCAGG	0.498																																					p.Q247X		Atlas-SNP	.											.	GLRA1	61	.	0			c.C739T						PASS	.						108	102	104					5																	151231124		2203	4300	6503	SO:0001587	stop_gained	2741	exon7			CCATCTGCCGCTC		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.739C>T	chr5.hg19:g.151231124G>A	ENSP00000411593:p.Gln247*	124.0	0.0	.		123.0	38.0	.	NM_000171	B2R6T3|Q14C77|Q6DJV9	Nonsense_Mutation	SNP	ENST00000455880.2	hg19	CCDS54942.1	.	.	.	.	.	.	.	.	.	.	G	38	7.160538	0.98103	.	.	ENSG00000145888	ENST00000274576;ENST00000455880;ENST00000545569	.	.	.	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	.	19.1084	0.93307	0.0:0.0:1.0:0.0	.	.	.	.	X	247;247;164	.	ENSP00000274576:Q247X	Q	-	1	0	GLRA1	151211317	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.640000	0.98453	2.579000	0.87056	0.655000	0.94253	CAG	.	.	.	none		0.498	GLRA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373959.1			A	151231124	G	A	151231124	4	1	276	1	0	0	0	0	0	1	0	0	6461	1328	46	2	646	2	GLRA1	5	151231124	Nonsense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	10799535	151231124	29684136	41	17549											
GRIA1	2890	hgsc.bcm.edu	37	chr5	153078598	153078598	+	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	cccgagaccctgacacgaagGcctggaatggcatggtggga	10	5	15	11	2	0	2	0	1	0	1	0	6	0	4	3	5	0	1	3	5	2	0			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr5:153078598G>T	ENST00000285900.5	+	10	1760	c.1417G>T	c.(1417-1419)Gcc>Tcc	p.A473S	GRIA1_ENST00000448073.4_Missense_Mutation_p.A483S|GRIA1_ENST00000518783.1_Missense_Mutation_p.A483S|GRIA1_ENST00000340592.5_Missense_Mutation_p.A473S|GRIA1_ENST00000521843.2_Missense_Mutation_p.A404S|GRIA1_ENST00000518142.1_Missense_Mutation_p.A393S	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	473					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)	TGACACGAAGGCCTGGAATGG	0.547																																					p.A483S		Atlas-SNP	.											.	GRIA1	321	.	0			c.G1447T						PASS	.						59	58	58					5																	153078598		2203	4300	6503	SO:0001583	missense	2890	exon10			ACGAAGGCCTGGA		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.1417G>T	chr5.hg19:g.153078598G>T	ENSP00000285900:p.Ala473Ser	97.0	0.0	.		79.0	24.0	.	NM_001258021	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Missense_Mutation	SNP	ENST00000285900.5	hg19	CCDS4322.1	.	.	.	.	.	.	.	.	.	.	G	6.497	0.459981	0.12342	.	.	ENSG00000155511	ENST00000285900;ENST00000544403;ENST00000518142;ENST00000537037;ENST00000340592;ENST00000521843;ENST00000544794;ENST00000518783;ENST00000448073	T;T;T;T;T;T;T	0.32515	1.45;1.45;1.45;1.45;1.45;1.45;1.45	5.44	5.44	0.79542	Glutamate receptor, L-glutamate/glycine-binding (2);Ionotropic glutamate receptor (1);	0.146227	0.64402	D	0.000011	T	0.16171	0.0389	N	0.03115	-0.41	0.41460	D	0.988037	B;B;B;B;B;B	0.21225	0.053;0.053;0.0;0.053;0.012;0.0	B;B;B;B;B;B	0.28465	0.09;0.09;0.005;0.09;0.033;0.01	T	0.11372	-1.0590	10	0.38643	T	0.18	.	11.6187	0.51104	0.0906:0.0:0.9094:0.0	.	483;483;393;483;473;473	E7ESV8;B7Z9G9;B7Z3F6;B7Z2W8;P42261-2;P42261	.;.;.;.;.;GRIA1_HUMAN	S	473;473;393;427;473;404;404;483;483	ENSP00000285900:A473S;ENSP00000427920:A393S;ENSP00000339343:A473S;ENSP00000427864:A404S;ENSP00000442108:A404S;ENSP00000428994:A483S;ENSP00000415569:A483S	ENSP00000285900:A473S	A	+	1	0	GRIA1	153058791	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	3.074000	0.50065	2.548000	0.85928	0.655000	0.94253	GCC	.	.	.	none		0.547	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3			T	153078598	G	T	153078598	3	4	276	1	0	0	0	0	1	0	0	0	6774	1203	42	4	1455	4	GRIA1	5	153078598	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	1847474	153078598	27836662	42	17550											
GRM4	2914	hgsc.bcm.edu	37	chr6	34100828	34100828	+	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	caccgatgacacccaccacaCgttcaggcttggtgatgatg	10	8	10	13	2	1	3	1	3	0	0	1	4	1	3	3	2	0	2	3	2	0	2			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr6:34100828C>A	ENST00000538487.2	-	2	889	c.446G>T	c.(445-447)cGt>cTt	p.R149L	GRM4_ENST00000374177.3_Intron|GRM4_ENST00000374181.4_Missense_Mutation_p.R149L	NM_000841.2|NM_001256811.1	NP_000832.1|NP_001243740.1	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4	149					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						ACCCACCACACGTTCAGGCTT	0.607																																					p.R149L		Atlas-SNP	.											.	GRM4	317	.	0			c.G446T						PASS	.						66	54	58					6																	34100828		2203	4300	6503	SO:0001583	missense	2914	exon2			ACCACACGTTCAG	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.446G>T	chr6.hg19:g.34100828C>A	ENSP00000440556:p.Arg149Leu	85.0	0.0	.		63.0	21.0	.	NM_001256811	B3KVL9|B7Z1T9|B7Z1U6|F5GXM5|Q5SZ84|Q6ZMQ2	Missense_Mutation	SNP	ENST00000538487.2	hg19	CCDS4787.1	.	.	.	.	.	.	.	.	.	.	C	13.67	2.305763	0.40795	.	.	ENSG00000124493	ENST00000374181;ENST00000538487	D;D	0.86694	-2.16;-2.16	4.29	4.29	0.51040	Extracellular ligand-binding receptor (1);	0.000000	0.64402	D	0.000002	D	0.86443	0.5934	L	0.52011	1.625	0.80722	D	1	B;P;D	0.53462	0.0;0.8;0.96	B;P;P	0.54965	0.01;0.573;0.765	D	0.85668	0.1293	10	0.37606	T	0.19	.	16.5082	0.84278	0.0:1.0:0.0:0.0	.	149;149;149	B7ZLU9;A1L4F9;Q14833	.;.;GRM4_HUMAN	L	149	ENSP00000363296:R149L;ENSP00000440556:R149L	ENSP00000363296:R149L	R	-	2	0	GRM4	34208806	0.993000	0.37304	0.990000	0.47175	0.980000	0.70556	3.896000	0.56266	2.230000	0.72887	0.467000	0.42956	CGT	.	.	.	none		0.607	GRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040213.2			A	34100828	C	A	34100828	3	1	276	1	0	0	0	0	1	0	0	0	6806	536	19	4	2332	4	GRM4	6	34100828	Missense_Mutation	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10		34100828	137014239	43	17551											
RSPH10B	728194	hgsc.bcm.edu	37	chr7	6797488	6797488	+	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	gaagtgaaacccaaaaaagaCcgccaaaacgttcagcagaa	20	3	8	10	2	1	3	1	1	0	2	1	4	1	3	3	0	3	2	3	0	8	1			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr7:6797488C>A	ENST00000403107.1	+	2	567	c.180C>A	c.(178-180)gaC>gaA	p.D60E	RSPH10B2_ENST00000297186.3_Missense_Mutation_p.D60E|RSPH10B2_ENST00000404077.1_Missense_Mutation_p.D60E|RSPH10B2_ENST00000433859.2_Missense_Mutation_p.D60E|RSPH10B2_ENST00000359718.3_5'UTR			B2RC85	R10B2_HUMAN	radial spoke head 10 homolog B2 (Chlamydomonas)	60										breast(3)|endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|skin(2)	15						CCAAAAAAGACCGCCAAAACG	0.488																																					p.D60E		Atlas-SNP	.											RSPH10B2,NS,carcinoma,0,2	RSPH10B	28	.	0			c.C180A						PASS	.						104	117	113					7																	6797488		2156	4264	6420	SO:0001583	missense	222967	exon3			AAAAGACCGCCAA		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	ENST00000403107.1:c.180C>A	chr7.hg19:g.6797488C>A	ENSP00000384766:p.Asp60Glu	294.0	0.0	.		311.0	61.0	.	NM_173565	A6NMW7|B2RXI4|B2RXJ0|Q86ST9|Q8NE68	Missense_Mutation	SNP	ENST00000403107.1	hg19	CCDS43552.1	.	.	.	.	.	.	.	.	.	.	C	0.024	-1.389722	0.01185	.	.	ENSG00000169402	ENST00000403107;ENST00000404077;ENST00000297186;ENST00000433859	T;T;T;T	0.47869	0.83;0.83;0.83;0.83	2.65	-1.66	0.08265	.	29.558000	0.00166	U	0.000000	T	0.18383	0.0441	N	0.02368	-0.58	0.20926	N	0.99983	B	0.06786	0.001	B	0.06405	0.002	T	0.30679	-0.9970	10	0.02654	T	1	.	4.2993	0.10916	0.0:0.3509:0.2772:0.3719	.	60	B2RC85	R10B2_HUMAN	E	60	ENSP00000384766:D60E;ENSP00000386102:D60E;ENSP00000297186:D60E;ENSP00000416710:D60E	ENSP00000297186:D60E	D	+	3	2	RSPH10B2	6764013	0.004000	0.15560	0.001000	0.08648	0.064000	0.16182	-0.256000	0.08757	-0.632000	0.05553	0.392000	0.25879	GAC	.	.	.	none		0.488	RSPH10B2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324184.4	NM_001099697		A	6797488	C	A	6797488	3	1	276	1	0	0	0	0	1	0	0	0	13716	506	18	4	2871	4	RSPH10B	7	6797488	Missense_Mutation	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10		6797488	152341175	44	17552											
HOXA1	3198	hgsc.bcm.edu	37	chr7	27135159	27135159	+	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	gtaaacagcgggagcgcactGggggtacccaccacttacgt	10	6	13	12	3	0	0	0	0	0	0	0	1	0	1	2	3	5	3	2	3	4	3			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr7:27135159G>A	ENST00000343060.4	-	1	434	c.373C>T	c.(373-375)Cag>Tag	p.Q125*	HOTAIRM1_ENST00000429611.3_RNA|HOTAIRM1_ENST00000434063.3_RNA|HOTAIRM1_ENST00000495032.1_RNA|HOXA1_ENST00000355633.5_Intron|HOTAIRM1_ENST00000425358.2_RNA	NM_005522.4	NP_005513	P49639	HXA1_HUMAN	homeobox A1	125					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						GGAGCGCACTGGGGGTACCCA	0.577																																					p.Q125X		Atlas-SNP	.											.	HOXA1	64	.	0			c.C373T						PASS	.						76	80	79					7																	27135159		2203	4300	6503	SO:0001587	stop_gained	3198	exon1			CGCACTGGGGGTA		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.373C>T	chr7.hg19:g.27135159G>A	ENSP00000343246:p.Gln125*	94.0	0.0	.		122.0	25.0	.	NM_005522	A4D184|B2R8U7|O43363	Nonsense_Mutation	SNP	ENST00000343060.4	hg19	CCDS5401.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.982192	0.74474	.	.	ENSG00000105991	ENST00000343060	.	.	.	4.88	-1.21	0.09524	.	0.879495	0.10099	N	0.716190	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	.	5.9292	0.19130	0.4767:0.1382:0.3852:0.0	.	.	.	.	X	125	.	ENSP00000343246:Q125X	Q	-	1	0	HOXA1	27101684	1.000000	0.71417	0.996000	0.52242	0.957000	0.61999	1.690000	0.37711	-0.079000	0.12707	0.462000	0.41574	CAG	.	.	.	none		0.577	HOXA1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358454.1			A	27135159	G	A	27135159	4	1	276	1	0	0	0	0	0	1	0	0	7295	1357	47	2	642	2	HOXA1	7	27135159	Nonsense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	20337671	27135159	132003504	45	17553											
TAX1BP1	8887	hgsc.bcm.edu	37	chr7	27809433	27809433	+	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	atgagaaagaaagatgtgacCaactgcaagcagaacaaaag	21	4	10	6	0	0	5	0	2	0	4	0	6	0	5	1	0	4	2	1	0	7	0			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr7:27809433C>A	ENST00000396319.2	+	5	680	c.592C>A	c.(592-594)Caa>Aaa	p.Q198K	TAX1BP1_ENST00000543117.1_Missense_Mutation_p.Q198K|TAX1BP1_ENST00000409980.1_Missense_Mutation_p.Q198K|TAX1BP1_ENST00000265393.6_Missense_Mutation_p.Q198K|TAX1BP1_ENST00000494033.1_3'UTR|TAX1BP1_ENST00000433216.2_Missense_Mutation_p.Q41K	NM_006024.6	NP_006015.4	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I) binding protein 1	198					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	kinase binding (GO:0019900)			breast(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(8)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31			GBM - Glioblastoma multiforme(3;0.0823)			AAGATGTGACCAACTGCAAGC	0.368																																					p.Q198K		Atlas-SNP	.											.	TAX1BP1	71	.	0			c.C592A						PASS	.						86	78	81					7																	27809433		2203	4300	6503	SO:0001583	missense	8887	exon5			TGTGACCAACTGC	U33821	CCDS5415.1, CCDS43561.1, CCDS56471.1	7p15	2010-08-05			ENSG00000106052	ENSG00000106052			11575	protein-coding gene	gene with protein product		605326				10435631	Standard	NM_006024		Approved	TXBP151, CALCOCO3	uc003szl.3	Q86VP1	OTTHUMG00000023377	ENST00000396319.2:c.592C>A	chr7.hg19:g.27809433C>A	ENSP00000379612:p.Gln198Lys	264.0	0.0	.		320.0	74.0	.	NM_006024	B4DKU7|E7ENV2|O60398|O95770|Q13311|Q9BQG5|Q9UI88	Missense_Mutation	SNP	ENST00000396319.2	hg19	CCDS5415.1	.	.	.	.	.	.	.	.	.	.	C	16.13	3.037273	0.54896	.	.	ENSG00000106052	ENST00000543117;ENST00000265393;ENST00000409980;ENST00000433216;ENST00000396319	T;T;T;T;T	0.08984	3.03;3.03;3.03;3.03;3.03	5.57	4.68	0.58851	.	0.000000	0.51477	D	0.000093	T	0.14184	0.0343	L	0.42245	1.32	0.53005	D	0.999969	P;P;P	0.49783	0.928;0.605;0.734	P;P;B	0.51266	0.664;0.497;0.302	T	0.04870	-1.0921	10	0.27082	T	0.32	-2.1773	15.6661	0.77230	0.1384:0.8616:0.0:0.0	.	41;198;198	E7ENV2;Q86VP1;Q86VP1-2	.;TAXB1_HUMAN;.	K	198;198;198;41;198	ENSP00000444811:Q198K;ENSP00000265393:Q198K;ENSP00000386515:Q198K;ENSP00000391907:Q41K;ENSP00000379612:Q198K	ENSP00000265393:Q198K	Q	+	1	0	TAX1BP1	27775958	0.991000	0.36638	0.954000	0.39281	0.630000	0.37929	4.066000	0.57520	1.316000	0.45131	0.650000	0.86243	CAA	.	.	.	none		0.368	TAX1BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214142.1	NM_006024		A	27809433	C	A	27809433	3	1	276	1	0	0	0	0	1	0	0	0	15606	595	21	4	606	4	TAX1BP1	7	27809433	Missense_Mutation	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10	674274	27809433	131329230	46	17554											
GNAI1	2770	hgsc.bcm.edu	37	chr7	79840317	79840317	+	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	gggaggtcagagatctgagcGgaagaagtggattcattgct	11	9	16	5	1	3	3	2	1	1	2	3	7	3	6	0	4	2	1	0	4	2	2			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr7:79840317G>C	ENST00000351004.3	+	6	996	c.623G>C	c.(622-624)cGg>cCg	p.R208P	GNAI1_ENST00000457358.2_Missense_Mutation_p.R156P	NM_002069.5	NP_002060.4	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	208					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)	p.R208Q(1)		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						AGATCTGAGCGGAAGAAGTGG	0.423																																					p.R208P		Atlas-SNP	.											GNAI1,colon,carcinoma,0,1	GNAI1	44	.	1	Substitution - Missense(1)	large_intestine(1)	c.G623C						PASS	.						164	139	148					7																	79840317		2203	4300	6503	SO:0001583	missense	2770	exon6			CTGAGCGGAAGAA	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.623G>C	chr7.hg19:g.79840317G>C	ENSP00000343027:p.Arg208Pro	98.0	0.0	.		108.0	28.0	.	NM_002069	A8KA88|B4E2V1|C9J3A4|P04898|P11015|P31871|Q5U074|Q8TAN5|Q9UGA4	Missense_Mutation	SNP	ENST00000351004.3	hg19	CCDS5595.1	.	.	.	.	.	.	.	.	.	.	G	33	5.234999	0.95207	.	.	ENSG00000127955	ENST00000351004;ENST00000457358	D;D	0.92911	-3.13;-3.13	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.97993	0.9339	H	0.98612	4.28	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.99041	1.0824	9	.	.	.	.	19.8478	0.96722	0.0:0.0:1.0:0.0	.	208	P63096	GNAI1_HUMAN	P	208;156	ENSP00000343027:R208P;ENSP00000410572:R156P	.	R	+	2	0	GNAI1	79678253	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.813000	0.99286	2.685000	0.91497	0.650000	0.86243	CGG	.	.	.	none		0.423	GNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253254.1	NM_002069		C	79840317	G	C	79840317	3	2	276	1	0	0	0	0	1	0	0	0	6511	1116	39	4	645	4	GNAI1	7	79840317	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	52030884	79840317	79298346	47	17555											
HGF	3082	hgsc.bcm.edu	37	chr7	81331961	81331961	+	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	attttgcataatatgctactCggacaaaaataccaggacga	16	10	7	8	2	0	0	0	0	0	0	1	3	0	2	1	2	4	2	1	2	6	6			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr7:81331961C>T	ENST00000222390.5	-	18	2349	c.2123G>A	c.(2122-2124)cGa>cAa	p.R708Q	HGF_ENST00000457544.2_Missense_Mutation_p.R703Q	NM_000601.4	NP_000592.3	P14210	HGF_HUMAN	hepatocyte growth factor (hepapoietin A; scatter factor)	708	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				activation of MAPK activity (GO:0000187)|blood coagulation (GO:0007596)|cell chemotaxis (GO:0060326)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epithelial to mesenchymal transition (GO:0001837)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|hyaluronan metabolic process (GO:0030212)|liver development (GO:0001889)|mitotic nuclear division (GO:0007067)|myoblast proliferation (GO:0051450)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of hydrogen peroxide-mediated programmed cell death (GO:1901299)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|organ regeneration (GO:0031100)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	catalytic activity (GO:0003824)|chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|identical protein binding (GO:0042802)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(41)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	75						ATATGCTACTCGGACAAAAAT	0.398																																					p.R708Q		Atlas-SNP	.											.	HGF	171	.	0			c.G2123A						PASS	.						130	124	126					7																	81331961		2203	4299	6502	SO:0001583	missense	3082	exon18			GCTACTCGGACAA		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.2123G>A	chr7.hg19:g.81331961C>T	ENSP00000222390:p.Arg708Gln	346.0	0.0	.		386.0	175.0	.	NM_000601	A1L3U6|Q02935|Q13494|Q14519|Q3KRB2|Q8TCE2|Q9BYL9|Q9BYM0|Q9UDU6	Missense_Mutation	SNP	ENST00000222390.5	hg19	CCDS5597.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.554522	0.86231	.	.	ENSG00000019991	ENST00000222390;ENST00000457544	D;D	0.84589	-1.87;-1.87	5.3	5.3	0.74995	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.233781	0.41823	D	0.000816	D	0.91882	0.7430	M	0.71920	2.185	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.992;0.995	D	0.90969	0.4818	10	0.42905	T	0.14	.	19.3172	0.94220	0.0:1.0:0.0:0.0	.	703;708	P14210-3;P14210	.;HGF_HUMAN	Q	708;703	ENSP00000222390:R708Q;ENSP00000391238:R703Q	ENSP00000222390:R708Q	R	-	2	0	HGF	81169897	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.736000	0.62059	2.643000	0.89663	0.655000	0.94253	CGA	.	.	.	none		0.398	HGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253315.2	NM_000601		T	81331961	C	T	81331961	3	4	276	1	0	0	0	0	1	0	0	0	7092	884	31	1	67	1	HGF	7	81331961	Missense_Mutation	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10	1491644	81331961	77806702	48	17556											
TRRAP	8295	hgsc.bcm.edu	37	chr7	98576479	98576479	+	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	ccctacctcgtcctggagtgCgcctggcgggtgtccaactg	4	9	13	15	3	0	0	0	0	0	0	3	1	2	1	5	3	3	0	5	3	2	1			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr7:98576479C>T	ENST00000359863.4	+	57	8774	c.8565C>T	c.(8563-8565)tgC>tgT	p.C2855C	TRRAP_ENST00000446306.3_Silent_p.C2837C|TRRAP_ENST00000355540.3_Silent_p.C2837C	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	2855	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)	p.C2837C(1)|p.C2855C(1)		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)			TCCTGGAGTGCGCCTGGCGGG	0.617																																					p.C2855C		Atlas-SNP	.											TRRAP_ENST00000359863,NS,carcinoma,0,2	TRRAP	863	.	2	Substitution - coding silent(2)	endometrium(2)	c.C8565T						PASS	.						75	78	77					7																	98576479		2203	4300	6503	SO:0001819	synonymous_variant	8295	exon57			GGAGTGCGCCTGG	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.8565C>T	chr7.hg19:g.98576479C>T		72.0	0.0	.		58.0	10.0	.	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Silent	SNP	ENST00000359863.4	hg19	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	C	10.77	1.443777	0.25987	.	.	ENSG00000196367	ENST00000456197	.	.	.	6.03	-0.483	0.12075	.	.	.	.	.	T	0.57725	0.2073	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51748	-0.8666	4	.	.	.	.	10.7505	0.46207	0.0:0.4332:0.0:0.5668	.	.	.	.	V	2577	.	.	A	+	2	0	TRRAP	98414415	0.995000	0.38212	0.987000	0.45799	0.991000	0.79684	0.304000	0.19228	-0.300000	0.08895	-0.302000	0.09304	GCG	.	.	.	none		0.617	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		T	98576479	C	T	98576479	2	4	276	1	0	0	0	0	0	0	0	1	16613	776	27	1		1	TRRAP	7	98576479	Silent	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10	17244518	98576479	60562184	49	17557											
POP7	10248	hgsc.bcm.edu	37	chr7	100304790	100304790	+	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	agcttgttgatgagctggagCcagagaccgacacacgggag	11	6	15	9	2	0	3	0	2	0	1	0	7	0	5	2	2	3	3	2	2	0	2			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr7:100304790C>A	ENST00000303151.4	+	2	599	c.337C>A	c.(337-339)Cca>Aca	p.P113T		NM_005837.2	NP_005828.2	O75817	POP7_HUMAN	processing of precursor 7, ribonuclease P/MRP subunit (S. cerevisiae)	113					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|nucleolar ribonuclease P complex (GO:0005655)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|ribonuclease P activity (GO:0004526)			endometrium(2)|kidney(1)|ovary(1)	4	Lung NSC(181;0.041)|all_lung(186;0.0581)					TGAGCTGGAGCCAGAGACCGA	0.592																																					p.P113T		Atlas-SNP	.											.	POP7	8	.	0			c.C337A						PASS	.						67	68	68					7																	100304790		2203	4300	6503	SO:0001583	missense	10248	exon2			CTGGAGCCAGAGA	U94316	CCDS5704.1	7q22	2012-05-21	2007-06-26		ENSG00000172336	ENSG00000172336			19949	protein-coding gene	gene with protein product	"ribonuclease P protein subunit p20"	606113	"processing of precursor 7, ribonuclease P subunit (S. cerevisiae)"			9630247	Standard	NM_005837		Approved	RPP20, RPP2	uc003uwh.4	O75817	OTTHUMG00000044311	ENST00000303151.4:c.337C>A	chr7.hg19:g.100304790C>A	ENSP00000304353:p.Pro113Thr	172.0	0.0	.		177.0	42.0	.	NM_005837	A4D2E0|Q9BV74	Missense_Mutation	SNP	ENST00000303151.4	hg19	CCDS5704.1	.	.	.	.	.	.	.	.	.	.	C	19.83	3.900727	0.72754	.	.	ENSG00000172336	ENST00000303151;ENST00000457480	.	.	.	5.67	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.75199	0.3817	M	0.65975	2.015	0.52501	D	0.999954	D	0.76494	0.999	D	0.70935	0.971	T	0.77576	-0.2536	9	0.87932	D	0	-13.8558	11.755	0.51870	0.176:0.824:0.0:0.0	.	113	O75817	POP7_HUMAN	T	113	.	ENSP00000304353:P113T	P	+	1	0	POP7	100142726	1.000000	0.71417	0.891000	0.34965	0.608000	0.37181	3.598000	0.54038	1.325000	0.45301	0.561000	0.74099	CCA	.	.	.	none		0.592	POP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103070.1	NM_005837		A	100304790	C	A	100304790	3	1	276	1	0	0	0	0	1	0	0	0	12261	739	26	4	339	4	POP7	7	100304790	Missense_Mutation	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10	1728311	100304790	58833873	50	17558											
PODXL	5420	hgsc.bcm.edu	37	chr7	131241055	131241055	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcgacggcgacggcgacgAcggcagcagcggcggcgttg	6	2	20	13	11	0	0	0	0	0	0	0	4	0	0	0	6	2	3	0	6	0	1			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr7:131241055A>G	ENST00000378555.3	-	1	311	c.64T>C	c.(64-66)Tcg>Ccg	p.S22P	PODXL_ENST00000537928.1_Missense_Mutation_p.S22P|PODXL_ENST00000322985.9_Missense_Mutation_p.S22P|PODXL_ENST00000541194.1_Missense_Mutation_p.S22P|PODXL_ENST00000465001.1_Intron			O00592	PODXL_HUMAN	podocalyxin-like	22					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					gacggcgacgacggcagcagc	0.741																																					p.S22P		Atlas-SNP	.											.	PODXL	53	.	0			c.T64C						PASS	.						5	8	7					7																	131241055		1914	3836	5750	SO:0001583	missense	5420	exon1			GCGACGACGGCAG		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.64T>C	chr7.hg19:g.131241055A>G	ENSP00000367817:p.Ser22Pro	112.0	0.0	.		139.0	14.0	.	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Missense_Mutation	SNP	ENST00000378555.3	hg19	CCDS34755.1	.	.	.	.	.	.	.	.	.	.	A	10.93	1.488975	0.26686	.	.	ENSG00000128567	ENST00000541194;ENST00000537928;ENST00000378555;ENST00000322985	T;T;T;T	0.12774	2.82;2.65;2.82;2.85	.	.	.	.	7739.210000	0.00166	U	0.000000	T	0.08670	0.0215	N	0.14661	0.345	0.09310	N	0.999994	.	.	.	.	.	.	T	0.24728	-1.0152	6	0.29301	T	0.29	.	.	.	.	.	22;22	O00592-2;O00592	.;PODXL_HUMAN	P	22	ENSP00000440518:S22P;ENSP00000442655:S22P;ENSP00000367817:S22P;ENSP00000319782:S22P	ENSP00000319782:S22P	S	-	1	0	PODXL	130891595	0.001000	0.12720	0.027000	0.17364	0.027000	0.11550	0.743000	0.26231	0.056000	0.16144	0.055000	0.15244	TCG	.	.	.	none		0.741	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111		G	131241055	A	G	131241055	3	3	276	1	0	0	0	0	1	0	0	0	12187	275	10	3	1648	3	PODXL	7	131241055	Missense_Mutation	SNP	A	TCGA-Y8-A896-01A-11D-A35Z-10	30936265	131241055	27897608	51	17559											
MFHAS1	9258	hgsc.bcm.edu	37	chr8	8654999	8654999	+	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	tctgggctgactcagcaactCccctgtaggaggagagagaa	11	7	13	10	0	2	3	1	1	1	2	3	6	3	4	2	3	2	3	2	3	3	1			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr8:8654999C>G	ENST00000276282.6	-	2	3587	c.3001G>C	c.(3001-3003)Gag>Cag	p.E1001Q	MFHAS1_ENST00000520091.1_5'UTR	NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	1001		Breakpoint for translocation to form chimeric MASL1.								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)		CTCAGCAACTCCCCTGTAGGA	0.552																																					p.E1001Q	Melanoma(103;1201 2045 17515 28966)	Atlas-SNP	.											.	MFHAS1	58	.	0			c.G3001C						PASS	.						81	68	72					8																	8654999		2203	4300	6503	SO:0001583	missense	9258	exon2			GCAACTCCCCTGT	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.3001G>C	chr8.hg19:g.8654999C>G	ENSP00000276282:p.Glu1001Gln	93.0	0.0	.		84.0	17.0	.	NM_004225	Q96CI0	Missense_Mutation	SNP	ENST00000276282.6	hg19	CCDS34844.1	.	.	.	.	.	.	.	.	.	.	C	18.02	3.529145	0.64860	.	.	ENSG00000147324	ENST00000276282	T	0.38401	1.14	5.73	5.73	0.89815	.	0.068346	0.56097	D	0.000026	T	0.56292	0.1975	L	0.54323	1.7	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.43956	-0.9359	10	0.29301	T	0.29	.	18.882	0.92358	0.0:1.0:0.0:0.0	.	1001	Q9Y4C4	MFHA1_HUMAN	Q	1001	ENSP00000276282:E1001Q	ENSP00000276282:E1001Q	E	-	1	0	MFHAS1	8692409	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.251000	0.78297	2.703000	0.92315	0.551000	0.68910	GAG	.	.	.	none		0.552	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225		G	8654999	C	G	8654999	3	3	276	1	0	0	0	0	1	0	0	0	9528	864	30	4	165	4	MFHAS1	8	8654999	Missense_Mutation	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10		8654999	137709023	52	17560											
TERF1	7013	hgsc.bcm.edu	37	chr8	73921213	73921213	+	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	tgaggagcagatggcagaaaCagagagaaacgacgaggagc	17	2	16	6	2	0	5	0	1	0	4	0	10	0	7	0	3	4	2	0	3	2	0			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr8:73921213C>G	ENST00000276603.5	+	1	115	c.92C>G	c.(91-93)aCa>aGa	p.T31R	TERF1_ENST00000276602.6_Missense_Mutation_p.T31R	NM_017489.2	NP_059523.2	P54274	TERF1_HUMAN	telomeric repeat binding factor (NIMA-interacting) 1	31	Asp/Glu-rich (acidic).				age-dependent telomere shortening (GO:0001309)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of DNA replication (GO:0008156)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via semi-conservative replication (GO:0032214)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of apoptotic process (GO:0043065)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of mitosis (GO:0045840)|positive regulation of mitotic cell cycle (GO:0045931)|protein homooligomerization (GO:0051260)|response to drug (GO:0042493)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere shortening (GO:0010834)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear telomere cap complex (GO:0000783)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|double-stranded telomeric DNA binding (GO:0003691)|microtubule binding (GO:0008017)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|telomeric DNA binding (GO:0042162)			central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	9	Breast(64;0.218)		Epithelial(68;0.0984)			ATGGCAGAAACAGAGAGAAAC	0.637																																					p.T31R		Atlas-SNP	.											.	TERF1	48	.	0			c.C92G						PASS	.						21	23	22					8																	73921213		2201	4299	6500	SO:0001583	missense	7013	exon1			CAGAAACAGAGAG	U74382	CCDS6210.1, CCDS6211.1	8q21.11	2011-05-24			ENSG00000147601	ENSG00000147601			11728	protein-coding gene	gene with protein product		600951		TRBF1		9391075	Standard	NM_003218		Approved	PIN2, TRF1, TRF	uc003xzd.2	P54274	OTTHUMG00000164522	ENST00000276603.5:c.92C>G	chr8.hg19:g.73921213C>G	ENSP00000276603:p.Thr31Arg	198.0	0.0	.		183.0	38.0	.	NM_017489	A7XP29|Q15553|Q8NHT6|Q93029	Missense_Mutation	SNP	ENST00000276603.5	hg19	CCDS6211.1	.	.	.	.	.	.	.	.	.	.	C	13.34	2.207086	0.39003	.	.	ENSG00000147601	ENST00000276603;ENST00000276602;ENST00000518874	.	.	.	4.04	-2.49	0.06403	.	1.175850	0.05898	N	0.629573	T	0.22627	0.0546	N	0.24115	0.695	0.09310	N	1	B;B	0.31548	0.328;0.22	B;B	0.32928	0.155;0.074	T	0.29640	-1.0005	9	0.72032	D	0.01	.	3.719	0.08449	0.4111:0.334:0.0:0.255	.	31;31	P54274-2;P54274	.;TERF1_HUMAN	R	31	.	ENSP00000276602:T31R	T	+	2	0	TERF1	74083767	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-2.062000	0.01390	-0.546000	0.06216	0.557000	0.71058	ACA	.	.	.	none		0.637	TERF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379093.1	NM_017489		G	73921213	C	G	73921213	3	3	276	1	0	0	0	0	1	0	0	0	15773	478	17	4	94	4	TERF1	8	73921213	Missense_Mutation	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10	65266214	73921213	72442809	53	17561											
FAM91A1	157769	hgsc.bcm.edu	37	chr8	124799974	124799974	+	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	tgagtctctggacagctttcTtatagaactagaaaaggtaa	14	12	9	6	0	2	3	0	1	2	2	3	4	2	4	0	2	2	2	0	2	7	5			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr8:124799974T>A	ENST00000334705.7	+	14	1508	c.1262T>A	c.(1261-1263)cTt>cAt	p.L421H	FAM91A1_ENST00000521166.1_Missense_Mutation_p.L421H	NM_144963.2	NP_659400	Q658Y4	F91A1_HUMAN	family with sequence similarity 91, member A1	421										breast(4)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28	Lung NSC(37;8.76e-13)|Ovarian(258;0.00744)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00192)			GACAGCTTTCTTATAGAACTA	0.363																																					p.L421H		Atlas-SNP	.											.	FAM91A1	77	.	0			c.T1262A						PASS	.						91	88	89					8																	124799974		1846	4099	5945	SO:0001583	missense	157769	exon14			GCTTTCTTATAGA	AK074370	CCDS6346.2	8q24.13	2005-10-04			ENSG00000176853	ENSG00000176853			26306	protein-coding gene	gene with protein product						12477932	Standard	XM_005250806		Approved	FLJ23790	uc003yqv.3	Q658Y4	OTTHUMG00000133021	ENST00000334705.7:c.1262T>A	chr8.hg19:g.124799974T>A	ENSP00000335082:p.Leu421His	75.0	0.0	.		66.0	23.0	.	NM_144963	B6YY23|Q658T5|Q8TE89	Missense_Mutation	SNP	ENST00000334705.7	hg19	CCDS6346.2	.	.	.	.	.	.	.	.	.	.	T	19.98	3.926656	0.73327	.	.	ENSG00000176853	ENST00000521166;ENST00000334705	T;T	0.43294	0.95;0.95	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.68118	0.2966	M	0.84082	2.675	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.73575	-0.3939	10	0.87932	D	0	.	16.0241	0.80528	0.0:0.0:0.0:1.0	.	421;421	E7ER68;Q658Y4	.;F91A1_HUMAN	H	421	ENSP00000429491:L421H;ENSP00000335082:L421H	ENSP00000335082:L421H	L	+	2	0	FAM91A1	124869155	1.000000	0.71417	0.932000	0.37286	0.493000	0.33554	7.938000	0.87678	2.248000	0.74166	0.533000	0.62120	CTT	.	.	.	none		0.363	FAM91A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256607.1	NM_144963		A	124799974	T	A	124799974	3	1	276	1	0	0	0	0	1	0	0	0	5658	1609	56	5	1316	5	FAM91A1	8	124799974	Missense_Mutation	SNP	T	TCGA-Y8-A896-01A-11D-A35Z-10	50878761	124799974	21564048	54	17562											
ADCY8	114	hgsc.bcm.edu	37	chr8	132051979	132051979	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggggccgaggccaggctcaAgtgtaggaccaagagagtga	11	4	18	8	1	1	2	1	1	0	1	1	5	1	3	3	5	0	2	3	5	3	1			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr8:132051979A>G	ENST00000286355.5	-	1	2693	c.601T>C	c.(601-603)Ttg>Ctg	p.L201L	ADCY8_ENST00000377928.3_Silent_p.L201L	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	201					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			GCCAGGCTCAAGTGTAGGACC	0.587										HNSCC(32;0.087)																											p.L201L		Atlas-SNP	.											.	ADCY8	291	.	0			c.T601C						PASS	.						83	86	85					8																	132051979		2203	4300	6503	SO:0001819	synonymous_variant	114	exon1			GGCTCAAGTGTAG	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"Adenylate cyclases"	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.601T>C	chr8.hg19:g.132051979A>G		148.0	0.0	.		111.0	18.0	.	NM_001115		Silent	SNP	ENST00000286355.5	hg19	CCDS6363.1																																																																																			.	.	.	none		0.587	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1			G	132051979	A	G	132051979	2	3	276	1	0	0	0	0	0	0	0	1	300	69	3	3		3	ADCY8	8	132051979	Silent	SNP	A	TCGA-Y8-A896-01A-11D-A35Z-10	7252005	132051979	14312043	55	17563											
ZFAT	57623	hgsc.bcm.edu	37	chr8	135596131	135596131	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcccttttgatttgaatttcTtgccacacatgtcacatagg	9	16	6	10	0	2	2	1	2	1	0	3	2	3	2	2	1	1	0	2	1	2	6			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr8:135596131T>C	ENST00000377838.3	-	10	3005	c.2831A>G	c.(2830-2832)aAg>aGg	p.K944R	ZFAT_ENST00000520214.1_Missense_Mutation_p.K932R|ZFAT_ENST00000517307.1_5'UTR|ZFAT_ENST00000520727.1_Missense_Mutation_p.K932R|ZFAT_ENST00000520356.1_Missense_Mutation_p.K932R|ZFAT_ENST00000523399.1_Missense_Mutation_p.K882R|ZFAT_ENST00000429442.2_Missense_Mutation_p.K932R	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	944					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)			TTTGAATTTCTTGCCACACAT	0.438																																					p.K944R		Atlas-SNP	.											.	ZFAT	265	.	0			c.A2831G						PASS	.						162	144	150					8																	135596131		1953	4163	6116	SO:0001583	missense	57623	exon10			AATTTCTTGCCAC	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.2831A>G	chr8.hg19:g.135596131T>C	ENSP00000367069:p.Lys944Arg	128.0	0.0	.		105.0	27.0	.	NM_020863	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Missense_Mutation	SNP	ENST00000377838.3	hg19	CCDS47924.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.906547	0.92107	.	.	ENSG00000066827	ENST00000520356;ENST00000520727;ENST00000429442;ENST00000377838;ENST00000520214;ENST00000318135;ENST00000523399	T;T;T;T;T;T	0.12879	2.64;2.64;2.64;2.64;2.64;2.64	5.68	5.68	0.88126	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.29652	0.0740	L	0.41710	1.295	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.998;0.999;0.996	T	0.01252	-1.1405	10	0.59425	D	0.04	-35.6191	15.1066	0.72326	0.0:0.0:0.0:1.0	.	882;932;944	E9PER3;E9PBN4;Q9P243	.;.;ZFAT_HUMAN	R	932;932;932;944;932;831;882	ENSP00000427879:K932R;ENSP00000427831:K932R;ENSP00000394501:K932R;ENSP00000367069:K944R;ENSP00000428483:K932R;ENSP00000429091:K882R	ENSP00000326997:K831R	K	-	2	0	ZFAT	135665313	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.929000	0.87595	2.156000	0.67533	0.460000	0.39030	AAG	.	.	.	none		0.438	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939		C	135596131	T	C	135596131	3	2	276	1	0	0	0	0	1	0	0	0	17644	1609	56	3	928	3	ZFAT	8	135596131	Missense_Mutation	SNP	T	TCGA-Y8-A896-01A-11D-A35Z-10	3544152	135596131	10767891	56	17564											
CER1	9350	hgsc.bcm.edu	37	chr9	14722265	14722265	+	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	agtttttctgaacatgaagtGgtgccagaatttcttggctt	9	16	10	6	0	2	3	0	2	2	1	2	3	2	3	1	2	2	2	1	2	3	5			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr9:14722265G>C	ENST00000380911.3	-	1	450	c.406C>G	c.(406-408)Cac>Gac	p.H136D		NM_005454.2	NP_005445.1	O95813	CER1_HUMAN	cerberus 1, DAN family BMP antagonist	136					anterior/posterior axis specification (GO:0009948)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|bone mineralization (GO:0030282)|cell migration involved in gastrulation (GO:0042074)|cellular response to BMP stimulus (GO:0071773)|determination of dorsal identity (GO:0048263)|gastrulation (GO:0007369)|growth plate cartilage chondrocyte proliferation (GO:0003419)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mesoderm development (GO:2000381)|nervous system development (GO:0007399)|sequestering of BMP in extracellular matrix (GO:0035582)|signal transduction involved in regulation of gene expression (GO:0023019)|ureteric bud development (GO:0001657)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	BMP binding (GO:0036122)|morphogen activity (GO:0016015)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(3)|lung(6)	11				GBM - Glioblastoma multiforme(50;3.16e-06)		AACATGAAGTGGTGCCAGAAT	0.517																																					p.H136D		Atlas-SNP	.											.	CER1	41	.	0			c.C406G						PASS	.						92	92	92					9																	14722265		2203	4300	6503	SO:0001583	missense	9350	exon1			TGAAGTGGTGCCA	AF090189	CCDS6476.1	9p23-p22	2013-02-26	2013-02-26		ENSG00000147869	ENSG00000147869			1862	protein-coding gene	gene with protein product		603777	"cerberus 1 (Xenopus laevis) homolog (cysteine knot superfamily)", "cerberus 1, cysteine knot superfamily, homolog (Xenopus laevis)"			10049596	Standard	NM_005454		Approved	DAND4	uc003zlj.3	O95813	OTTHUMG00000021022	ENST00000380911.3:c.406C>G	chr9.hg19:g.14722265G>C	ENSP00000370297:p.His136Asp	155.0	0.0	.		99.0	39.0	.	NM_005454	Q6ISJ1|Q6ISJ6|Q6ISQ2|Q6ISS1	Missense_Mutation	SNP	ENST00000380911.3	hg19	CCDS6476.1	.	.	.	.	.	.	.	.	.	.	G	12.53	1.965365	0.34659	.	.	ENSG00000147869	ENST00000380911	T	0.28454	1.61	5.21	2.9	0.33743	DAN (1);	0.482217	0.21040	N	0.081195	T	0.36468	0.0968	L	0.51422	1.61	0.25991	N	0.982241	P	0.48998	0.918	P	0.52386	0.697	T	0.09997	-1.0649	10	0.37606	T	0.19	-4.9758	9.5839	0.39504	0.1638:0.0:0.8362:0.0	.	136	O95813	CER1_HUMAN	D	136	ENSP00000370297:H136D	ENSP00000370297:H136D	H	-	1	0	CER1	14712265	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.053000	0.30442	0.682000	0.31407	0.655000	0.94253	CAC	.	.	.	none		0.517	CER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055453.1	NM_005454		C	14722265	G	C	14722265	3	2	276	1	0	0	0	0	1	0	0	0	3267	1348	47	4	405	4	CER1	9	14722265	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10		14722265	126491166	57	17565											
DENND4C	55667	hgsc.bcm.edu	37	chr9	19372144	19372144	+	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	gccagtgtcgagtggtgcagGaagtgttttggagcgcctct	6	11	16	8	2	1	0	0	0	1	0	2	3	1	2	2	3	2	2	2	3	1	2			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr9:19372144G>A	ENST00000380432.2	+	28	5028	c.4995G>A	c.(4993-4995)agG>agA	p.R1665R	RP11-513M16.7_ENST00000609609.1_RNA|DENND4C_ENST00000602925.1_Silent_p.R1901R|DENND4C_ENST00000434457.2_Silent_p.R1950R			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	1665					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						AGTGGTGCAGGAAGTGTTTTG	0.393																																					p.R1901R		Atlas-SNP	.											.	DENND4C	120	.	0			c.G5703A						PASS	.						117	123	121					9																	19372144		2203	4300	6503	SO:0001819	synonymous_variant	55667	exon32			GTGCAGGAAGTGT	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.4995G>A	chr9.hg19:g.19372144G>A		156.0	0.0	.		87.0	23.0	.	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Silent	SNP	ENST00000380432.2	hg19																																																																																				.	.	.	none		0.393	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925		A	19372144	G	A	19372144	2	1	276	1	0	0	0	0	0	0	0	1	4437	1165	41	2		2	DENND4C	9	19372144	Silent	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	4649879	19372144	121841287	58	17566											
TTC16	158248	hgsc.bcm.edu	37	chr9	130480052	130480052	+	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	cctttgtgctctacctacagGtgcctggggcctcccgggcc	3	10	12	16	1	1	0	0	0	1	0	2	0	2	0	6	4	4	1	6	4	2	3			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr9:130480052G>A	ENST00000373289.3	+	4	506		c.e4+1		PTRH1_ENST00000423807.1_5'Flank|PTRH1_ENST00000543175.1_5'Flank|TTC16_ENST00000393748.4_Splice_Site|PTRH1_ENST00000419060.1_Intron|PTRH1_ENST00000429848.1_Intron	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16											central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						CTACCTACAGGTGCCTGGGGC	0.622																																					.		Atlas-SNP	.											.	TTC16	55	.	0			c.426+1G>A						PASS	.						44	47	46					9																	130480052		2203	4300	6503	SO:0001630	splice_region_variant	158248	exon4			CTACAGGTGCCTG	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.426+1G>A	chr9.hg19:g.130480052G>A		78.0	0.0	.		49.0	23.0	.	NM_144965	B4DYG4|B5ME24|Q5JU66|Q96M72	Splice_Site	SNP	ENST00000373289.3	hg19	CCDS6875.1	.	.	.	.	.	.	.	.	.	.	G	10.53	1.374900	0.24857	.	.	ENSG00000167094	ENST00000373289	.	.	.	4.6	4.6	0.57074	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8947	0.70636	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TTC16	129519873	1.000000	0.71417	1.000000	0.80357	0.057000	0.15508	6.991000	0.76232	2.132000	0.65825	0.313000	0.20887	.	.	.	.	none		0.622	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054224.1	NM_144965	Intron	A	130480052	G	A	130480052	5	1	276	1	0	0	0	0	0	0	1	0	16695	1275	44	2	441	2	TTC16	9	130480052	Splice_Site	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	111107908	130480052	10733379	59	17567											
C9orf96	169436	hgsc.bcm.edu	37	chr9	136249679	136249679	+	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	attacgccagtcaggccctgGaggaggtaactctcagggta	10	8	13	10	1	2	0	2	0	1	0	3	2	2	2	2	5	2	2	2	5	3	3			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr9:136249679G>A	ENST00000371957.3	+	3	321	c.214G>A	c.(214-216)Gag>Aag	p.E72K	C9orf96_ENST00000426926.2_Missense_Mutation_p.E72K|C9orf96_ENST00000468046.1_3'UTR|C9orf96_ENST00000371955.1_5'UTR	NM_153710.3	NP_714921.4	Q8NE28	STKL1_HUMAN		72	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|stomach(2)	25				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		TCAGGCCCTGGAGGAGGTAAC	0.483																																					p.E72K		Atlas-SNP	.											.	C9orf96	77	.	0			c.G214A						PASS	.						218	189	199					9																	136249679		2203	4300	6503	SO:0001583	missense	169436	exon3			GCCCTGGAGGAGG																												ENST00000371957.3:c.214G>A	chr9.hg19:g.136249679G>A	ENSP00000361025:p.Glu72Lys	85.0	0.0	.		74.0	29.0	.	NM_153710	Q5T8U8|Q6ZMP6|Q6ZMQ5	Missense_Mutation	SNP	ENST00000371957.3	hg19	CCDS35169.1	.	.	.	.	.	.	.	.	.	.	G	3.589	-0.083913	0.07141	.	.	ENSG00000198870	ENST00000426926;ENST00000371957	T;T	0.17370	2.28;2.28	3.83	2.92	0.33932	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.477248	0.18996	N	0.125463	T	0.07234	0.0183	N	0.12471	0.22	0.80722	D	1	B	0.12013	0.005	B	0.13407	0.009	T	0.16158	-1.0412	10	0.02654	T	1	-21.1225	8.7429	0.34569	0.1179:0.0:0.8821:0.0	.	72	Q8NE28	SGK71_HUMAN	K	72	ENSP00000398807:E72K;ENSP00000361025:E72K	ENSP00000361025:E72K	E	+	1	0	C9orf96	135239500	1.000000	0.71417	1.000000	0.80357	0.800000	0.45204	1.805000	0.38883	2.086000	0.62901	0.379000	0.24179	GAG	.	.	.	none		0.483	C9orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054855.1			A	136249679	G	A	136249679	3	1	276	1	0	0	0	0	1	0	0	0	2510	1175	41	2	224	2	C9orf96	9	136249679	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	5769627	136249679	4963752	60	17568											
RNF208	727800	hgsc.bcm.edu	37	chr9	140115231	140115231	+	Missense_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	cattgtaggagtgcccacagGtggggcactccaggggctcg	7	7	16	11	1	0	0	0	0	0	0	2	1	1	1	2	6	1	3	2	6	1	2			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr9:140115231G>A	ENST00000392827.1	-	2	602	c.434C>T	c.(433-435)aCc>aTc	p.T145I	RNF208_ENST00000391553.1_Missense_Mutation_p.T145I			Q9H0X6	RN208_HUMAN	ring finger protein 208	145					protein autoubiquitination (GO:0051865)		ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			lung(1)	1	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		GTGCCCACAGGTGGGGCACTC	0.647																																					p.T145I		Atlas-SNP	.											.	RNF208	11	.	0			c.C434T						PASS	.						14	18	17					9																	140115231		2180	4291	6471	SO:0001583	missense	727800	exon1			CCACAGGTGGGGC	AF416715	CCDS7037.2	9q34.3	2007-01-19				ENSG00000212864		"RING-type (C3HC4) zinc fingers"	25420	protein-coding gene	gene with protein product						11230166	Standard	NM_031297		Approved	DKFZP761H1710	uc004clz.2	Q9H0X6		ENST00000392827.1:c.434C>T	chr9.hg19:g.140115231G>A	ENSP00000376572:p.Thr145Ile	146.0	0.0	.		95.0	35.0	.	NM_031297	A2BFA0	Missense_Mutation	SNP	ENST00000392827.1	hg19	CCDS7037.2	.	.	.	.	.	.	.	.	.	.	G	12.78	2.040448	0.35989	.	.	ENSG00000212864	ENST00000392827;ENST00000391553	T;T	0.46063	0.88;0.88	4.01	4.01	0.46588	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);	0.137415	0.47093	D	0.000241	T	0.13713	0.0332	N	0.00569	-1.365	0.53005	D	0.999961	P	0.50156	0.932	P	0.47470	0.548	T	0.36383	-0.9750	10	0.02654	T	1	-17.7848	8.7913	0.34852	0.1066:0.0:0.8934:0.0	.	145	Q9H0X6	RN208_HUMAN	I	145	ENSP00000376572:T145I;ENSP00000375397:T145I	ENSP00000375397:T145I	T	-	2	0	RNF208	139235052	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	8.150000	0.89634	2.057000	0.61298	0.491000	0.48974	ACC	.	.	.	none		0.647	RNF208-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254714.1	NM_031297		A	140115231	G	A	140115231	3	1	276	1	0	0	0	0	1	0	0	0	13488	1261	44	2	355	2	RNF208	9	140115231	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	3865552	140115231	1098200	61	17569											
CAMK1D	57118	hgsc.bcm.edu	37	chr10	12870792	12870792	+	Frame_Shift_Del	DEL	G	G	-																															ggcaccttccacgctctgtaGtttcatttcttcttcgtcgg																										TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr10:12870792delG	ENST00000378847.3	+	11	1401	c.1064delG	c.(1063-1065)agtfs	p.S355fs		NM_153498.2	NP_705718.1	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID	355	Ser-rich.				inflammatory response (GO:0006954)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis (GO:0050766)|positive regulation of respiratory burst (GO:0060267)|regulation of dendrite development (GO:0050773)|regulation of granulocyte chemotaxis (GO:0071622)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)	16				GBM - Glioblastoma multiforme(1;3.16e-05)		ACGCTCTGTAGTTTCATTTCT	0.577																																					p.S355fs		Atlas-INDEL	.											.	CAMK1D	99	.	0			c.1063delA						PASS	.						81	78	79					10																	12870792		2203	4300	6503	SO:0001589	frameshift_variant	57118	exon11			.	AF286366	CCDS7091.1, CCDS7092.1	10p13	2003-11-05			ENSG00000183049	ENSG00000183049			19341	protein-coding gene	gene with protein product		607957				11050006	Standard	XM_006717481		Approved	CKLiK	uc001ilo.3	Q8IU85	OTTHUMG00000017683	ENST00000378847.3:c.1064delG	chr10.hg19:g.12870792delG	ENSP00000368124:p.Ser355fs	48.0	0.0	0		47.0	12.0	0.255319	NM_153498	B0YIY0|Q9HD31	Frame_Shift_Del	DEL	ENST00000378847.3	hg19	CCDS7091.1																																																																																			.	.	.	none		0.577	CAMK1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046820.1	NM_020397		-	12870792	G	-	12870792	7	5	276	1	0	1	0	1	0	0	0	0	2599	1029	36	0	1141	0	CAMK1D	10	12870792	Frame_Shift_Del	DEL	G	TCGA-Y8-A896-01A-11D-A35Z-10		12870792	122663955	62	17570											
BMS1	9790	hgsc.bcm.edu	37	chr10	43326332	43326332	+	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	agatccttgcactgctggatGctctgagtacggtgcatagt	8	12	12	9	1	1	2	0	1	1	1	2	3	2	3	1	2	5	5	1	2	2	3			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr10:43326332G>C	ENST00000374518.5	+	23	3700	c.3637G>C	c.(3637-3639)Gct>Cct	p.A1213P	RNU6-885P_ENST00000516607.1_RNA	NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	1213					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						ACTGCTGGATGCTCTGAGTAC	0.512																																					p.A1213P		Atlas-SNP	.											.	BMS1	132	.	0			c.G3637C						PASS	.						33	31	32					10																	43326332		2203	4300	6503	SO:0001583	missense	9790	exon23			CTGGATGCTCTGA	BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"BMS1-like, ribosome assembly protein (yeast)", "BMS1 homolog, ribosome assembly protein (yeast)"	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.3637G>C	chr10.hg19:g.43326332G>C	ENSP00000363642:p.Ala1213Pro	123.0	0.0	.		115.0	32.0	.	NM_014753	Q5QPT5|Q86XJ9	Missense_Mutation	SNP	ENST00000374518.5	hg19	CCDS7199.1	.	.	.	.	.	.	.	.	.	.	G	18.46	3.628175	0.66901	.	.	ENSG00000165733	ENST00000374518	T	0.27720	1.65	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.59797	0.2220	M	0.81682	2.555	0.54753	D	0.999981	D	0.76494	0.999	D	0.83275	0.996	T	0.62572	-0.6826	10	0.48119	T	0.1	.	18.6554	0.91452	0.0:0.0:1.0:0.0	.	1213	Q14692	BMS1_HUMAN	P	1213	ENSP00000363642:A1213P	ENSP00000363642:A1213P	A	+	1	0	BMS1	42646338	1.000000	0.71417	1.000000	0.80357	0.670000	0.39368	6.200000	0.72118	2.395000	0.81488	0.462000	0.41574	GCT	.	.	.	none		0.512	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753		C	43326332	G	C	43326332	3	2	276	1	0	0	0	0	1	0	0	0	1472	1319	46	4	3723	4	BMS1	10	43326332	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	30455540	43326332	92208415	63	17571											
TMEM26	219623	hgsc.bcm.edu	37	chr10	63188776	63188776	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaagttgagagagttgatcTcgagtgatcccgcctccaat	11	10	11	9	2	1	5	0	3	1	2	4	7	3	5	3	0	0	2	3	0	2	2			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr10:63188776T>C	ENST00000399298.3	-	4	881	c.513A>G	c.(511-513)cgA>cgG	p.R171R	TMEM26_ENST00000399293.1_Silent_p.R171R	NM_178505.6	NP_848600.2	Q6ZUK4	TMM26_HUMAN	transmembrane protein 26	171						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	18	Prostate(12;0.0112)					AGAGTTGATCTCGAGTGATCC	0.443																																					p.R171R		Atlas-SNP	.											.	TMEM26	47	.	0			c.A513G						PASS	.						112	113	112					10																	63188776		1932	4132	6064	SO:0001819	synonymous_variant	219623	exon4			TTGATCTCGAGTG	BC042872	CCDS41530.1	10q21.3	2008-10-20			ENSG00000196932	ENSG00000196932			28550	protein-coding gene	gene with protein product						12477932	Standard	NM_178505		Approved	MGC35010, Em:AC068892.1	uc001jlo.2	Q6ZUK4	OTTHUMG00000018293	ENST00000399298.3:c.513A>G	chr10.hg19:g.63188776T>C		126.0	0.0	.		97.0	30.0	.	NM_178505	Q6ZVM0|Q8IVN9	Silent	SNP	ENST00000399298.3	hg19	CCDS41530.1																																																																																			.	.	.	none		0.443	TMEM26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359121.1	NM_178505		C	63188776	T	C	63188776	2	2	276	1	0	0	0	0	0	0	0	1	16163	1538	54	3		3	TMEM26	10	63188776	Silent	SNP	T	TCGA-Y8-A896-01A-11D-A35Z-10	19862444	63188776	72345971	64	17572											
JMJD1C	221037	hgsc.bcm.edu	37	chr10	64966402	64966402	+	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	tacttctttctttggcactcCtgctgagaactccattgggt	6	16	8	11	0	2	1	0	1	2	1	4	2	4	1	2	2	3	2	2	2	2	5			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr10:64966402C>A	ENST00000399262.2	-	10	5245	c.5027G>T	c.(5026-5028)aGg>aTg	p.R1676M	JMJD1C_ENST00000542921.1_Missense_Mutation_p.R1494M|JMJD1C_ENST00000399251.1_Missense_Mutation_p.R1457M|JMJD1C_ENST00000402544.1_Missense_Mutation_p.R1457M	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	1676					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)					TTTGGCACTCCTGCTGAGAAC	0.348																																					p.R1676M		Atlas-SNP	.											.	JMJD1C	347	.	0			c.G5027T						PASS	.						141	125	130					10																	64966402		1829	4095	5924	SO:0001583	missense	221037	exon10			GCACTCCTGCTGA	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.5027G>T	chr10.hg19:g.64966402C>A	ENSP00000382204:p.Arg1676Met	81.0	0.0	.		86.0	21.0	.	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	hg19	CCDS41532.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.84|16.84	3.233815|3.233815	0.58886|0.58886	.|.	.|.	ENSG00000171988|ENSG00000171988	ENST00000327520|ENST00000399262;ENST00000402544;ENST00000399251;ENST00000542921	.|T;T;T;T	.|0.61742	.|0.42;0.08;1.82;0.42	5.74|5.74	5.74|5.74	0.90152|0.90152	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.75744	.|0.3891	M|M	0.64997|0.64997	1.995|1.995	0.58432|0.58432	D|D	0.999992|0.999992	.|D;D;D	.|0.89917	.|1.0;1.0;0.999	.|D;D;D	.|0.83275	.|0.991;0.996;0.988	.|T	.|0.76669	.|-0.2874	.|10	.|0.87932	.|D	.|0	-12.9833|-12.9833	19.9283|19.9283	0.97112|0.97112	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1217;1676;1494	.|A6PW35;Q15652;A0T124	.|.;JHD2C_HUMAN;.	X|M	362|1676;1457;1457;1494	.|ENSP00000382204:R1676M;ENSP00000384990:R1457M;ENSP00000382195:R1457M;ENSP00000444682:R1494M	.|ENSP00000382195:R1457M	G|R	-|-	1|2	0|0	JMJD1C|JMJD1C	64636408|64636408	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.818000|7.818000	0.86416|0.86416	2.708000|2.708000	0.92522|0.92522	0.585000|0.585000	0.79938|0.79938	GGA|AGG	.	.	.	none		0.348	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		A	64966402	C	A	64966402	3	1	276	1	0	0	0	0	1	0	0	0	7957	681	24	4	2663	4	JMJD1C	10	64966402	Missense_Mutation	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10	1777626	64966402	70568345	65	17573											
IFIT1	3434	hgsc.bcm.edu	37	chr10	91162887	91162887	+	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	caggaaacacccacttctgtCttactgcatcaccagatagg	12	9	7	13	0	3	1	1	0	2	1	3	2	3	2	2	2	3	1	2	2	3	3	rs373034374		TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr10:91162887C>T	ENST00000371804.3	+	2	1022	c.855C>T	c.(853-855)gtC>gtT	p.V285V	IFIT1_ENST00000546318.1_Silent_p.V254V|LIPA_ENST00000371837.1_Intron	NM_001270927.1|NM_001548.4	NP_001257856.1|NP_001539.3	P09914	IFIT1_HUMAN	interferon-induced protein with tetratricopeptide repeats 1	285					cellular response to exogenous dsRNA (GO:0071360)|cellular response to type I interferon (GO:0071357)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|intracellular transport of viral protein in host cell (GO:0019060)|negative regulation of defense response to virus by host (GO:0050689)|negative regulation of helicase activity (GO:0051097)|negative regulation of protein binding (GO:0032091)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(2)|prostate(2)|upper_aerodigestive_tract(1)	15						CCACTTCTGTCTTACTGCATC	0.443																																					p.V285V		Atlas-SNP	.											.	IFIT1	30	.	0			c.C855T						PASS	.						71	72	72					10																	91162887		2203	4300	6503	SO:0001819	synonymous_variant	3434	exon3			TTCTGTCTTACTG	M24594	CCDS31243.1, CCDS59220.1	10q23.31	2014-05-22			ENSG00000185745	ENSG00000185745		"Tetratricopeptide (TTC) repeat domain containing"	5407	protein-coding gene	gene with protein product		147690		G10P1, IFI56, IFNAI1		1377167, 3360121	Standard	NM_001548		Approved	GARG-16	uc001kgi.4	P09914	OTTHUMG00000018712	ENST00000371804.3:c.855C>T	chr10.hg19:g.91162887C>T		118.0	0.0	.		92.0	25.0	.	NM_001270927	B3KS50|D3DR31|Q5T7J1|Q96QM5	Silent	SNP	ENST00000371804.3	hg19	CCDS31243.1																																																																																			.	.	.	none		0.443	IFIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049302.1	NM_001548		T	91162887	C	T	91162887	2	4	276	1	0	0	0	0	0	0	0	1	7528	900	32	2		2	IFIT1	10	91162887	Silent	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10	26196485	91162887	44371860	66	17574											
TMEM20	159371	hgsc.bcm.edu	37	chr10	95660559	95660559	+	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	aattttcctcattctcagagGagtccttggttctaccgcca	8	14	7	12	1	3	1	2	0	2	1	6	2	5	2	4	2	1	1	4	2	2	6			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr10:95660559G>A	ENST00000427197.1	+	3	471	c.410G>A	c.(409-411)gGa>gAa	p.G137E	SLC35G1_ENST00000371408.3_Missense_Mutation_p.G136E	NM_001134658.1|NM_153226.2	NP_001128130.1|NP_694958.1	Q2M3R5	S35G1_HUMAN	solute carrier family 35, member G1	137	EamA 1.				calcium ion export from cell (GO:1990034)|cytosolic calcium ion homeostasis (GO:0051480)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											ATTCTCAGAGGAGTCCTTGGT	0.383																																					p.G137E		Atlas-SNP	.											.	.	.	.	0			c.G410A						PASS	.						122	114	116					10																	95660559		2203	4299	6502	SO:0001583	missense	159371	exon3			TCAGAGGAGTCCT	AK091309	CCDS7432.1, CCDS44459.1	10q23.33	2013-05-22	2011-08-03	2011-08-03	ENSG00000176273	ENSG00000176273		"Solute carriers"	26607	protein-coding gene	gene with protein product			"transmembrane protein 20"	TMEM20		21569384	Standard	NM_153226		Approved	FLJ33990, C10orf60	uc001kjg.2	Q2M3R5	OTTHUMG00000018779	ENST00000427197.1:c.410G>A	chr10.hg19:g.95660559G>A	ENSP00000400932:p.Gly137Glu	91.0	0.0	.		96.0	24.0	.	NM_001134658	Q86YG5|Q8NBA5	Missense_Mutation	SNP	ENST00000427197.1	hg19	CCDS44459.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.268246	0.80469	.	.	ENSG00000176273	ENST00000371408;ENST00000427197	T;T	0.59502	0.26;0.26	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	D	0.83575	0.5284	M	0.93375	3.41	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.997	D	0.86713	0.1937	10	0.87932	D	0	.	20.3812	0.98933	0.0:0.0:1.0:0.0	.	120;137;136	B7ZKP0;Q2M3R5;Q2M3R5-2	.;S35G1_HUMAN;.	E	136;137	ENSP00000360462:G136E;ENSP00000400932:G137E	ENSP00000360462:G136E	G	+	2	0	SLC35G1	95650549	1.000000	0.71417	0.977000	0.42913	0.924000	0.55760	7.540000	0.82074	2.821000	0.97095	0.650000	0.86243	GGA	.	.	.	none		0.383	SLC35G1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_153226		A	95660559	G	A	95660559	3	1	276	1	0	0	0	0	1	0	0	0	16134	1174	41	2	420	2	TMEM20	10	95660559	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	4497672	95660559	39874188	67	17575											
SORBS1	10580	hgsc.bcm.edu	37	chr10	97143753	97143753	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcacttacctttctgagctTgacttcagtgaggaagagcg	9	11	12	9	1	2	4	1	3	1	1	2	5	2	5	1	2	3	2	1	2	2	4			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr10:97143753T>C	ENST00000361941.3	-	15	1553	c.1527A>G	c.(1525-1527)tcA>tcG	p.S509S	SORBS1_ENST00000371247.2_Silent_p.S509S|SORBS1_ENST00000371241.1_Silent_p.S299S|SORBS1_ENST00000474353.2_5'UTR|SORBS1_ENST00000353505.5_Silent_p.S394S|SORBS1_ENST00000277982.5_Silent_p.S531S|SORBS1_ENST00000393949.1_Silent_p.S479S|SORBS1_ENST00000371249.2_Silent_p.S431S|SORBS1_ENST00000371227.4_Silent_p.S463S|SORBS1_ENST00000371246.2_Silent_p.S531S|SORBS1_ENST00000607232.1_Silent_p.S298S|SORBS1_ENST00000371245.3_Silent_p.S394S|SORBS1_ENST00000347291.4_Silent_p.S377S|SORBS1_ENST00000354106.3_Silent_p.S479S|SORBS1_ENST00000306402.6_Silent_p.S340S|SORBS1_ENST00000371239.1_Silent_p.S308S	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)		TTTCTGAGCTTGACTTCAGTG	0.502																																					p.S531S		Atlas-SNP	.											.	SORBS1	185	.	0			c.A1593G						PASS	.						92	88	89					10																	97143753		2203	4300	6503	SO:0001819	synonymous_variant	10580	exon15			TGAGCTTGACTTC	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.1527A>G	chr10.hg19:g.97143753T>C		136.0	0.0	.		108.0	26.0	.	NM_001034955		Silent	SNP	ENST00000361941.3	hg19	CCDS31255.1																																																																																			.	.	.	none		0.502	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049517.1			C	97143753	T	C	97143753	2	2	276	1	0	0	0	0	0	0	0	1	14940	1799	63	3		3	SORBS1	10	97143753	Silent	SNP	T	TCGA-Y8-A896-01A-11D-A35Z-10	1483194	97143753	38390994	68	17576											
GAL3ST3	89792	hgsc.bcm.edu	37	chr11	65810751	65810751	+	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	ctcgagcgaggcgttgggtaCgcgccggaaggccgggcagt	6	5	19	11	7	0	0	0	0	0	0	1	3	0	1	2	5	2	3	2	5	2	2			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr11:65810751C>T	ENST00000312006.4	-	3	804	c.523G>A	c.(523-525)Gta>Ata	p.V175I	GAL3ST3_ENST00000527878.1_Missense_Mutation_p.V175I	NM_033036.2	NP_149025.1	Q96A11	G3ST3_HUMAN	galactose-3-O-sulfotransferase 3	175					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)	p.V175I(1)		kidney(1)|lung(9)|ovary(2)|skin(2)	14						GCGTTGGGTACGCGCCGGAAG	0.662																																					p.V175I		Atlas-SNP	.											GAL3ST3,NS,carcinoma,0,1	GAL3ST3	40	.	1	Substitution - Missense(1)	ovary(1)	c.G523A						PASS	.						36	40	39					11																	65810751		2201	4292	6493	SO:0001583	missense	89792	exon3			TGGGTACGCGCCG	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.523G>A	chr11.hg19:g.65810751C>T	ENSP00000308591:p.Val175Ile	160.0	0.0	.		98.0	22.0	.	NM_033036	Q14D05	Missense_Mutation	SNP	ENST00000312006.4	hg19	CCDS8128.1	.	.	.	.	.	.	.	.	.	.	C	19.94	3.919606	0.73098	.	.	ENSG00000175229	ENST00000312006;ENST00000527878	T;T	0.15139	2.45;2.45	4.65	4.65	0.58169	.	0.000000	0.64402	D	0.000002	T	0.30916	0.0780	L	0.51422	1.61	0.49130	D	0.99975	D	0.71674	0.998	P	0.59171	0.853	T	0.01273	-1.1399	10	0.37606	T	0.19	-34.5923	15.4161	0.74970	0.0:1.0:0.0:0.0	.	175	Q96A11	G3ST3_HUMAN	I	175	ENSP00000308591:V175I;ENSP00000434829:V175I	ENSP00000308591:V175I	V	-	1	0	GAL3ST3	65567327	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	4.992000	0.63889	2.304000	0.77564	0.561000	0.74099	GTA	.	.	.	none		0.662	GAL3ST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391052.1	NM_033036		T	65810751	C	T	65810751	3	4	276	1	0	0	0	0	1	0	0	0	6206	536	19	1	776	1	GAL3ST3	11	65810751	Missense_Mutation	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10		65810751	69195765	69	17577											
OR2AT4	341152	hgsc.bcm.edu	37	chr11	74800264	74800264	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccatctgggaggtccttacTactgctgggatgggcaggag	7	9	16	9	0	1	0	0	0	1	0	2	3	2	3	2	5	3	2	2	5	2	2			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr11:74800264T>C	ENST00000305159.3	-	1	535	c.495A>G	c.(493-495)gtA>gtG	p.V165V		NM_001005285.1	NP_001005285.1	A6NND4	O2AT4_HUMAN	olfactory receptor, family 2, subfamily AT, member 4	165						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(2)	12						AGGTCCTTACTACTGCTGGGA	0.572																																					p.V165V		Atlas-SNP	.											.	OR2AT4	32	.	0			c.A495G						PASS	.						101	94	96					11																	74800264		2200	4293	6493	SO:0001819	synonymous_variant	341152	exon1			CCTTACTACTGCT	BK004820	CCDS31639.1	11q13.4	2012-08-09			ENSG00000171561	ENSG00000171561		"GPCR / Class A : Olfactory receptors"	19620	protein-coding gene	gene with protein product							Standard	NM_001005285		Approved		uc010rro.2	A6NND4	OTTHUMG00000165370	ENST00000305159.3:c.495A>G	chr11.hg19:g.74800264T>C		74.0	0.0	.		60.0	15.0	.	NM_001005285	B9EGZ8	Silent	SNP	ENST00000305159.3	hg19	CCDS31639.1																																																																																			.	.	.	none		0.572	OR2AT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383734.1	NM_001005285		C	74800264	T	C	74800264	2	2	276	1	0	0	0	0	0	0	0	1	10994	1509	53	3		3	OR2AT4	11	74800264	Silent	SNP	T	TCGA-Y8-A896-01A-11D-A35Z-10	8989513	74800264	60206252	70	17578											
ANKK1	255239	hgsc.bcm.edu	37	chr11	113270138	113270138	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcacggcttctggtctccCgtcaggctgaccccaacctg	5	9	11	16	2	3	1	1	1	2	0	4	1	3	1	4	4	1	3	4	4	1	1	rs533347208		TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr11:113270138C>T	ENST00000303941.3	+	8	1541	c.1447C>T	c.(1447-1449)Cgt>Tgt	p.R483C		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	483							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)		TCTGGTCTCCCGTCAGGCTGA	0.607													C|||	1	0.000199681	0	0	5008	,	,		19582	0		0	False		,,,				2504	0.001				p.R483C		Atlas-SNP	.											.	ANKK1	83	.	0			c.C1447T						PASS	.						15	17	17					11																	113270138		2044	4191	6235	SO:0001583	missense	255239	exon8			GTCTCCCGTCAGG	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.1447C>T	chr11.hg19:g.113270138C>T	ENSP00000306678:p.Arg483Cys	54.0	0.0	.		60.0	14.0	.	NM_178510		Missense_Mutation	SNP	ENST00000303941.3	hg19	CCDS44734.1	.	.	.	.	.	.	.	.	.	.	C	9.382	1.073302	0.20147	.	.	ENSG00000170209	ENST00000303941	T	0.65732	-0.17	4.72	3.8	0.43715	Ankyrin repeat-containing domain (4);	0.098482	0.44285	D	0.000477	T	0.56558	0.1993	L	0.50993	1.605	0.50467	D	0.999877	B	0.26512	0.151	B	0.28385	0.089	T	0.58075	-0.7700	10	0.54805	T	0.06	-5.0248	12.429	0.55563	0.0:0.918:0.0:0.082	.	483	Q8NFD2	ANKK1_HUMAN	C	483	ENSP00000306678:R483C	ENSP00000306678:R483C	R	+	1	0	ANKK1	112775348	0.033000	0.19621	0.646000	0.29493	0.265000	0.26407	0.648000	0.24828	1.210000	0.43336	0.557000	0.71058	CGT	.	.	.	none		0.607	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510		T	113270138	C	T	113270138	3	4	276	1	0	0	0	0	1	0	0	0	631	652	23	1	1477	1	ANKK1	11	113270138	Missense_Mutation	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10	38469874	113270138	21736378	71	17579											
UBE4A	9354	hgsc.bcm.edu	37	chr11	118250311	118250315	+	Frame_Shift_Del	DEL	CATGA	CATGA	-																															tatctttctaccaagactgcCatgacagagccacaaatgct																										TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	CATGA	CATGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr11:118250311_118250315delCATGA	ENST00000431736.2	+	11	1815_1819	c.1743_1747delCATGA	c.(1741-1749)gccatgacafs	p.MT582fs	UBE4A_ENST00000545354.1_Frame_Shift_Del_p.MT47fs|UBE4A_ENST00000252108.3_Frame_Shift_Del_p.MT575fs					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)		CCAAGACTGCCATGACAGAGCCACA	0.493																																					p.581_582del		Atlas-Indel,Pindel	.											.	UBE4A	97	.	0			c.1742_1746del						PASS	.																																			SO:0001589	frameshift_variant	9354	exon11			.	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.1743_1747delCATGA	chr11.hg19:g.118250311_118250315delCATGA	ENSP00000387362:p.Met582fs	152.0	0.0	0		104.0	38.0	0.365385	NM_004788		Frame_Shift_Del	DEL	ENST00000431736.2	hg19	CCDS8396.1																																																																																			.	.	.	none		0.493	UBE4A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398143.1	NM_004788		-	118250315	CATGA	-	118250311	7	5	276	1	0	1	0	1	0	0	0	0	16894	581	21	0	1781	0	UBE4A	11	118250311	Frame_Shift_Del	DEL	CATGA	TCGA-Y8-A896-01A-11D-A35Z-10	4980173	118250311	16756205	72	17580											
CLSTN3	9746	hgsc.bcm.edu	37	chr12	7293886	7293886	+	Missense_Mutation	SNP	A	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	ctctgaacctcgagttccccAcagtcacactctataccgac	10	9	5	17	2	3	1	1	1	2	0	5	3	4	1	4	0	2	1	4	0	3	3			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr12:7293886A>C	ENST00000266546.6	+	9	1822	c.1372A>C	c.(1372-1374)Aca>Cca	p.T458P	CLSTN3_ENST00000537408.1_Missense_Mutation_p.T470P	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	458					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						CGAGTTCCCCACAGTCACACT	0.562											OREG0021650	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T458P		Atlas-SNP	.											.	CLSTN3	84	.	0			c.A1372C						PASS	.						358	263	295					12																	7293886		2203	4300	6503	SO:0001583	missense	9746	exon9			TTCCCCACAGTCA	AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182		"Cadherins / Cadherin-related"	18371	protein-coding gene	gene with protein product	"cadherin-related family member 14"	611324				12498782	Standard	NM_014718		Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167	ENST00000266546.6:c.1372A>C	chr12.hg19:g.7293886A>C	ENSP00000266546:p.Thr458Pro	137.0	0.0	.	640	147.0	36.0	.	NM_014718	D3DUT6|O94831|Q2T9J5|Q5UE57	Missense_Mutation	SNP	ENST00000266546.6	hg19	CCDS8575.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.337391	0.81911	.	.	ENSG00000139182	ENST00000266546;ENST00000537408	T;T	0.76060	-0.99;-0.99	5.38	5.38	0.77491	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.053114	0.85682	D	0.000000	T	0.79764	0.4502	L	0.50333	1.59	0.50632	D	0.99988	D;P	0.59767	0.986;0.888	P;P	0.58928	0.848;0.817	T	0.77814	-0.2448	10	0.30854	T	0.27	-11.2766	15.395	0.74784	1.0:0.0:0.0:0.0	.	470;458	Q5UE57;Q9BQT9	.;CSTN3_HUMAN	P	458;470	ENSP00000266546:T458P;ENSP00000440679:T470P	ENSP00000266546:T458P	T	+	1	0	CLSTN3	7185153	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.596000	0.67570	2.033000	0.60031	0.374000	0.22700	ACA	.	.	.	none		0.562	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398560.2	NM_014718		C	7293886	A	C	7293886	3	2	276	1	0	0	0	0	1	0	0	0	3565	159	6	5	1406	5	CLSTN3	12	7293886	Missense_Mutation	SNP	A	TCGA-Y8-A896-01A-11D-A35Z-10		7293886	126558009	73	17581											
PUS7L	83448	hgsc.bcm.edu	37	chr12	44142290	44142290	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctaacaaccattgcttgatAggtgatggctttcttgtctt	8	17	8	8	0	3	2	0	2	3	0	3	2	3	2	1	2	3	2	1	2	3	7			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr12:44142290A>G	ENST00000416848.2	-	3	1521	c.1033T>C	c.(1033-1035)Tat>Cat	p.Y345H	PUS7L_ENST00000431332.3_Missense_Mutation_p.Y32H|PUS7L_ENST00000344862.5_Missense_Mutation_p.Y345H|PUS7L_ENST00000551923.1_Missense_Mutation_p.Y345H|PUS7L_ENST00000553166.1_Missense_Mutation_p.Y345H	NM_001098615.1|NM_001271826.1	NP_001092085.1|NP_001258755.1	Q9H0K6	PUS7L_HUMAN	pseudouridylate synthase 7 homolog (S. cerevisiae)-like	345					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)	p.Y345H(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(15)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	all_cancers(12;0.00027)	Lung NSC(34;0.114)|all_lung(34;0.24)		GBM - Glioblastoma multiforme(48;0.0402)		ATTGCTTGATAGGTGATGGCT	0.343																																					p.Y345H		Atlas-SNP	.											PUS7L,NS,carcinoma,0,1	PUS7L	73	.	1	Substitution - Missense(1)	kidney(1)	c.T1033C						PASS	.						140	144	143					12																	44142290		2203	4300	6503	SO:0001583	missense	83448	exon3			CTTGATAGGTGAT	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.1033T>C	chr12.hg19:g.44142290A>G	ENSP00000415899:p.Tyr345His	128.0	0.0	.		110.0	24.0	.	NM_001098614	B3KUJ1|Q05CU0|Q6AHZ3|Q6NUP2	Missense_Mutation	SNP	ENST00000416848.2	hg19	CCDS8743.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.483340	0.84854	.	.	ENSG00000129317	ENST00000416848;ENST00000344862;ENST00000551923;ENST00000431332;ENST00000550784;ENST00000547156;ENST00000553166	T;T;T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98;0.98;0.98	4.79	4.79	0.61399	Pseudouridine synthase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.65037	0.2653	M	0.83953	2.67	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.65138	-0.6241	10	0.23891	T	0.37	-21.9291	15.0286	0.71687	1.0:0.0:0.0:0.0	.	345	Q9H0K6	PUS7L_HUMAN	H	345;345;345;32;32;32;345	ENSP00000415899:Y345H;ENSP00000343081:Y345H;ENSP00000447706:Y345H;ENSP00000398497:Y32H;ENSP00000449222:Y32H;ENSP00000450341:Y32H;ENSP00000446865:Y345H	ENSP00000343081:Y345H	Y	-	1	0	PUS7L	42428557	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.003000	0.93577	2.068000	0.61886	0.460000	0.39030	TAT	.	.	.	none		0.343	PUS7L-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403931.1	NM_031292		G	44142290	A	G	44142290	3	3	276	1	0	0	0	0	1	0	0	0	12847	420	15	3	1100	3	PUS7L	12	44142290	Missense_Mutation	SNP	A	TCGA-Y8-A896-01A-11D-A35Z-10	36848404	44142290	89709605	74	17582											
ATP12A	479	hgsc.bcm.edu	37	chr13	25284611	25284611	+	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	ttaacagacaaggtaccagaGggaatacctagaatggacgg	16	6	12	7	1	0	3	0	0	0	3	0	5	0	5	2	4	3	1	2	4	7	4			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr13:25284611G>C	ENST00000381946.3	+	20	2944	c.2777G>C	c.(2776-2778)aGg>aCg	p.R926T	ATP12A_ENST00000218548.6_Missense_Mutation_p.R932T			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	926					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		AGGTACCAGAGGGAATACCTA	0.453																																					p.R932T	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.G2795C						PASS	.						90	89	89					13																	25284611		2203	4300	6503	SO:0001583	missense	479	exon20			ACCAGAGGGAATA	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.2777G>C	chr13.hg19:g.25284611G>C	ENSP00000371372:p.Arg926Thr	141.0	0.0	.		143.0	38.0	.	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	hg19	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	G	16.34	3.095193	0.56075	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	D;D	0.88818	-2.43;-2.43	5.19	5.19	0.71726	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.96068	0.8719	H	0.94771	3.58	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.97076	0.9781	10	0.87932	D	0	.	16.5892	0.84760	0.0:0.0:1.0:0.0	.	932;926	P54707-2;P54707	.;AT12A_HUMAN	T	932;926	ENSP00000218548:R932T;ENSP00000371372:R926T	ENSP00000218548:R932T	R	+	2	0	ATP12A	24182611	1.000000	0.71417	0.966000	0.40874	0.025000	0.11179	9.393000	0.97256	2.565000	0.86533	0.655000	0.94253	AGG	.	.	.	none		0.453	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		C	25284611	G	C	25284611	3	2	276	1	0	0	0	0	1	0	0	0	1122	1000	35	4	2873	4	ATP12A	13	25284611	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10		25284611	89885267	75	17583											
TSC22D1	8848	hgsc.bcm.edu	37	chr13	45148256	45148256	+	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	gttgtacatactctgaagcaGgattttgagtcactgatttg	10	15	10	6	0	2	3	1	3	1	0	2	4	2	4	0	1	3	3	0	1	3	6	rs370025988		TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr13:45148256G>A	ENST00000458659.2	-	1	2445	c.1955C>T	c.(1954-1956)cCt>cTt	p.P652L	TSC22D1_ENST00000501704.2_Intron|TSC22D1_ENST00000460842.1_5'Flank	NM_183422.3	NP_904358.2	Q15714	T22D1_HUMAN	TSC22 domain family, member 1	652	Gln-rich.		P -> S (in dbSNP:rs9525983).		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)		CTCTGAAGCAGGATTTTGAGT	0.502																																					p.P652L		Atlas-SNP	.											.	TSC22D1	88	.	0			c.C1955T						PASS	.	G	LEU/PRO	0,4406		0,0,2203	108	102	104		1955	3	0	13		104	1,8599		0,1,4299	no	missense	TSC22D1	NM_183422.3	98	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	652/1074	45148256	1,13005	2203	4300	6503	SO:0001583	missense	8848	exon1			GAAGCAGGATTTT	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.1955C>T	chr13.hg19:g.45148256G>A	ENSP00000397435:p.Pro652Leu	55.0	0.0	.		53.0	21.0	.	NM_183422	B3KRL7|B9EGI0|O00666|Q6AHX5|Q6IBU1|Q8NCN1|Q96JS5	Missense_Mutation	SNP	ENST00000458659.2	hg19	CCDS31966.1	.	.	.	.	.	.	.	.	.	.	G	6.215	0.407805	0.11754	0.0	1.16E-4	ENSG00000102804	ENST00000458659	T	0.33654	1.4	4.74	3.02	0.34903	.	0.346611	0.25065	N	0.033401	T	0.23926	0.0579	L	0.27053	0.805	0.23260	N	0.998024	B	0.06786	0.001	B	0.04013	0.001	T	0.15350	-1.0440	10	0.33940	T	0.23	.	9.9987	0.41916	0.1633:0.0:0.8367:0.0	.	652	Q15714	T22D1_HUMAN	L	652	ENSP00000397435:P652L	ENSP00000397435:P652L	P	-	2	0	TSC22D1	44046256	0.997000	0.39634	0.037000	0.18230	0.867000	0.49689	5.011000	0.64011	0.626000	0.30322	0.491000	0.48974	CCT	.	.	.	weak		0.502	TSC22D1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044743.2	NM_006022		A	45148256	G	A	45148256	3	1	276	1	0	0	0	0	1	0	0	0	16619	1000	35	2	1407	2	TSC22D1	13	45148256	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	19863645	45148256	70021622	76	17584											
CDC16	8881	hgsc.bcm.edu	37	chr13	115008769	115008769	+	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	tcactaccccttagcaagctGtgtaatgaagaacaggaatt	14	10	8	9	0	1	2	1	1	0	1	1	3	1	3	2	1	4	3	2	1	7	4			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr13:115008769G>T	ENST00000356221.3	+	7	687	c.579G>T	c.(577-579)ctG>ctT	p.L193L	CDC16_ENST00000375308.1_Silent_p.L99L|CDC16_ENST00000252457.5_Silent_p.L192L|MIR548AR_ENST00000582191.1_RNA|CDC16_ENST00000375312.3_Silent_p.L99L|CDC16_ENST00000375310.1_Silent_p.L99L|CDC16_ENST00000252458.6_Silent_p.L99L|CDC16_ENST00000360383.3_Silent_p.L193L			Q13042	CDC16_HUMAN	cell division cycle 16	193					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)			TTAGCAAGCTGTGTAATGAAG	0.308																																					p.L193L		Atlas-SNP	.											.	CDC16	50	.	0			c.G579T						PASS	.						77	82	81					13																	115008769		2203	4298	6501	SO:0001819	synonymous_variant	8881	exon7			CAAGCTGTGTAAT	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.579G>T	chr13.hg19:g.115008769G>T		565.0	0.0	.		467.0	135.0	.	NM_003903	A2A365|Q5T8C8|Q96AE6|Q9Y564	Silent	SNP	ENST00000356221.3	hg19	CCDS9542.2																																																																																			.	.	.	none		0.308	CDC16-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276737.1	NM_003903		T	115008769	G	T	115008769	2	4	276	1	0	0	0	0	0	0	0	1	3060	1364	48	4		4	CDC16	13	115008769	Silent	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	69860513	115008769	161109	77	17585											
CHMP4A	29082	hgsc.bcm.edu	37	chr14	24682658	24682658	+	5'UTR	SNP	T	T	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	ccactcatcgcgagctcgccTctcccgcctccgcccctcag	4	7	7	23	5	3	0	2	0	1	0	7	1	4	0	7	0	1	1	7	0	0	0			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr14:24682658T>A	ENST00000609024.1	-	0	36				MDP1_ENST00000532557.1_5'Flank|CHMP4A_ENST00000530996.1_5'UTR|TM9SF1_ENST00000530611.1_5'UTR|AL136419.6_ENST00000565988.1_RNA|NEDD8-MDP1_ENST00000604306.1_5'Flank|CHMP4A_ENST00000542700.2_5'Flank|TM9SF1_ENST00000556387.1_5'UTR|CHMP4A_ENST00000347519.6_Missense_Mutation_p.R39S			Q9BY43	CHM4A_HUMAN	charged multivesicular body protein 4A						endosomal transport (GO:0016197)|membrane budding (GO:0006900)|membrane organization (GO:0061024)|membrane tubulation (GO:0097320)|negative regulation of autophagic vacuole assembly (GO:1902902)|negative regulation of neuron death (GO:1901215)|posttranslational protein targeting to membrane (GO:0006620)|protein homooligomerization (GO:0051260)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|ESCRT III complex (GO:0000815)|extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|nucleus (GO:0005634)	ATPase binding (GO:0051117)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)			NS(1)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)	9				GBM - Glioblastoma multiforme(265;0.0181)		CGAGCTCGCCTCTCCCGCCTC	0.667																																					p.R39S		Atlas-SNP	.											.	CHMP4A	20	.	0			c.A117T						PASS	.						45	42	43					14																	24682658		2203	4300	6503	SO:0001623	5_prime_UTR_variant	29082	exon1			CTCGCCTCTCCCG	AF212243	CCDS9619.1	14q12	2012-10-04	2011-09-21	2005-04-04	ENSG00000254505	ENSG00000254505		"Charged multivesicular body proteins"	20274	protein-coding gene	gene with protein product		610051	"chromosome 14 open reading frame 123", "chromatin modifying protein 4A"	C14orf123			Standard	NM_014169		Approved	HSPC134, VPS32A		Q9BY43	OTTHUMG00000167036	ENST00000609024.1:c.-13A>T	chr14.hg19:g.24682658T>A		99.0	0.0	.		88.0	23.0	.	NM_014169	Q14D22|Q32Q79|Q86SZ8|Q96QJ9|Q9P026	Missense_Mutation	SNP	ENST00000609024.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.19|13.19	2.163255|2.163255	0.38217|0.38217	.|.	.|.	ENSG00000254505|ENSG00000254505	ENST00000347519|ENST00000548308	T|.	0.60171|.	0.21|.	4.72|4.72	2.17|2.17	0.27698|0.27698	.|.	.|.	.|.	.|.	.|.	T|T	0.18800|0.18800	0.0451|0.0451	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B|.	0.24186|.	0.099|.	B|.	0.17433|.	0.018|.	T|T	0.19745|0.19745	-1.0296|-1.0296	9|6	0.08599|0.66056	T|D	0.76|0.02	-4.2019|-4.2019	4.1034|4.1034	0.10025|0.10025	0.0:0.1223:0.2032:0.6745|0.0:0.1223:0.2032:0.6745	.|.	39|.	Q14D22|.	.|.	S|W	39|16	ENSP00000324205:R39S|.	ENSP00000324205:R39S|ENSP00000448488:R16W	R|R	-|-	3|1	2|2	AL096870.1|AL096870.1	23752498|23752498	0.004000|0.004000	0.15560|0.15560	0.043000|0.043000	0.18650|0.18650	0.292000|0.292000	0.27327|0.27327	-0.000000|-0.000000	0.12993|0.12993	0.257000|0.257000	0.21650|0.21650	0.533000|0.533000	0.62120|0.62120	AGA|AGG	.	.	.	none		0.667	CHMP4A-012	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471846.1	NM_014169		A	24682658	T	A	24682658	1	1	276	0	1	0	0	0	0	0	0	0	3358	1548	54	5		5	CHMP4A	14	24682658	5'UTR	SNP	T	TCGA-Y8-A896-01A-11D-A35Z-10		24682658	82666882	78	17586											
NID2	22795	hgsc.bcm.edu	37	chr14	52534874	52534874	+	Missense_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	gagtggagatgatgccgttgGtgcccacctgggagaggaga	9	7	18	7	1	0	4	0	1	0	3	0	8	0	4	3	4	2	1	3	4	0	1			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr14:52534874G>A	ENST00000216286.5	-	2	235	c.236C>T	c.(235-237)aCc>aTc	p.T79I	NID2_ENST00000541773.1_Missense_Mutation_p.T26I	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	79					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)					GATGCCGTTGGTGCCCACCTG	0.582																																					p.T79I		Atlas-SNP	.											.	NID2	201	.	0			c.C236T						PASS	.						44	56	52					14																	52534874		2203	4300	6503	SO:0001583	missense	22795	exon2			CCGTTGGTGCCCA	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.236C>T	chr14.hg19:g.52534874G>A	ENSP00000216286:p.Thr79Ile	54.0	0.0	.		47.0	9.0	.	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	hg19	CCDS9706.1	.	.	.	.	.	.	.	.	.	.	G	19.93	3.918213	0.73098	.	.	ENSG00000087303	ENST00000216286;ENST00000316204;ENST00000541773;ENST00000395707	T;T	0.26067	1.76;1.76	5.26	4.35	0.52113	.	0.044090	0.85682	D	0.000000	T	0.56470	0.1987	M	0.89840	3.065	0.38188	D	0.939836	D;D;D	0.64830	0.98;0.994;0.993	P;D;D	0.64595	0.837;0.919;0.927	T	0.70880	-0.4752	10	0.72032	D	0.01	.	15.0557	0.71912	0.0:0.0:0.8565:0.1435	.	26;81;79	Q14112-2;Q5CZI2;Q14112	.;.;NID2_HUMAN	I	79;79;26;81	ENSP00000216286:T79I;ENSP00000443730:T26I	ENSP00000216286:T79I	T	-	2	0	NID2	51604624	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	9.186000	0.94906	1.169000	0.42739	0.563000	0.77884	ACC	.	.	.	none		0.582	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			A	52534874	G	A	52534874	3	1	276	1	0	0	0	0	1	0	0	0	10422	1261	44	2	3975	2	NID2	14	52534874	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	27852216	52534874	54814666	79	17587											
NAA30	122830	hgsc.bcm.edu	37	chr14	57863579	57863579	+	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	agccgtggattccaaatacaGgagaaatggcattggtaaga	15	8	12	6	1	0	2	0	0	0	2	1	4	1	3	2	4	2	2	2	4	4	4			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr14:57863579G>A	ENST00000556492.1	+	3	1035	c.881G>A	c.(880-882)aGg>aAg	p.R294K	NAA30_ENST00000554703.1_Missense_Mutation_p.R36K|NAA30_ENST00000555166.1_Missense_Mutation_p.R36K	NM_001011713.2	NP_001011713.2	Q147X3	NAA30_HUMAN	N(alpha)-acetyltransferase 30, NatC catalytic subunit	294	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				metabolic process (GO:0008152)	cytoplasm (GO:0005737)|NatC complex (GO:0031417)	peptide alpha-N-acetyltransferase activity (GO:0004596)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(2)|skin(2)	13						TCCAAATACAGGAGAAATGGC	0.358																																					p.R294K		Atlas-SNP	.											.	NAA30	30	.	0			c.G881A						PASS	.						136	127	130					14																	57863579		2203	4300	6503	SO:0001583	missense	122830	exon3			AATACAGGAGAAA	AK092674	CCDS32088.1	14q22.2	2010-05-07	2010-01-14	2010-01-14		ENSG00000139977	2.3.1.88	"N(alpha)-acetyltransferase subunits"	19844	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 35", "N-acetyltransferase 12", "N-acetyltransferase 12 (GCN5-related, putative)"	C14orf35, NAT12		19660095	Standard	NM_001011713		Approved	FLJ35355, MAK3, Mak3p	uc001xcx.4	Q147X3		ENST00000556492.1:c.881G>A	chr14.hg19:g.57863579G>A	ENSP00000452521:p.Arg294Lys	96.0	0.0	.		95.0	37.0	.	NM_001011713	Q0IIN2	Missense_Mutation	SNP	ENST00000556492.1	hg19	CCDS32088.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	35|35	5.542518|5.542518	0.96474|0.96474	.|.	.|.	ENSG00000139977|ENSG00000139977	ENST00000298406|ENST00000555166;ENST00000556492;ENST00000554703;ENST00000395257	.|T;T;T	.|0.37584	.|1.19;1.19;1.19	5.95|5.95	5.95|5.95	0.96441|0.96441	.|GCN5-related N-acetyltransferase (GNAT) domain (2);Acyl-CoA N-acyltransferase (2);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.67173|0.67173	0.2865|0.2865	M|M	0.85373|0.85373	2.75|2.75	0.80722|0.80722	D|D	1|1	.|D	.|0.60160	.|0.987	.|D	.|0.74348	.|0.983	T|T	0.70219|0.70219	-0.4932|-0.4932	5|10	.|0.87932	.|D	.|0	-9.037|-9.037	20.3931|20.3931	0.98965|0.98965	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|294	.|Q147X3	.|NAA30_HUMAN	R|K	106|36;294;36;257	.|ENSP00000450939:R36K;ENSP00000452521:R294K;ENSP00000451255:R36K	.|ENSP00000298406:R294K	G|R	+|+	1|2	0|0	NAA30|NAA30	56933332|56933332	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	9.600000|9.600000	0.98282|0.98282	2.824000|2.824000	0.97209|0.97209	0.655000|0.655000	0.94253|0.94253	GGA|AGG	.	.	.	none		0.358	NAA30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412925.1	NM_001011713		A	57863579	G	A	57863579	3	1	276	1	0	0	0	0	1	0	0	0	10129	1000	35	2	887	2	NAA30	14	57863579	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	5328705	57863579	49485961	80	17588											
PTPN21	11099	hgsc.bcm.edu	37	chr14	88935278	88935278	+	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	acctcattgtgttccaggcaGgcgatcatgatctccgacaa	10	10	9	12	2	3	1	2	1	1	0	5	3	4	1	3	2	0	2	3	2	1	2			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr14:88935278G>C	ENST00000556564.1	-	18	3662	c.3378C>G	c.(3376-3378)gcC>gcG	p.A1126A	PTPN21_ENST00000328736.3_Silent_p.A1126A	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	1126	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|liver(1)|lung(7)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						GTTCCAGGCAGGCGATCATGA	0.532																																					p.A1126A		Atlas-SNP	.											.	PTPN21	113	.	0			c.C3378G						PASS	.						115	99	105					14																	88935278		2203	4300	6503	SO:0001819	synonymous_variant	11099	exon18			CAGGCAGGCGATC	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.3378C>G	chr14.hg19:g.88935278G>C		99.0	0.0	.		92.0	28.0	.	NM_007039		Silent	SNP	ENST00000556564.1	hg19	CCDS9884.1																																																																																			.	.	.	none		0.532	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1			C	88935278	G	C	88935278	2	2	276	1	0	0	0	0	0	0	0	1	12799	987	35	4		4	PTPN21	14	88935278	Silent	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	31071699	88935278	18414262	81	17589											
ZNF839	55778	hgsc.bcm.edu	37	chr14	102800982	102800982	+	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	gtatgagtttcttctgatgaAggtgagtactcttagtgttt	8	18	11	4	0	3	4	0	4	3	0	3	4	3	4	0	1	1	4	0	1	4	6			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr14:102800982A>C	ENST00000558850.1	+	4	1510	c.1160A>C	c.(1159-1161)aAg>aCg	p.K387T	ZNF839_ENST00000442396.2_Splice_Site_p.K503T|ZNF839_ENST00000262236.5_Splice_Site_p.K387T|ZNF839_ENST00000559185.1_Splice_Site_p.K387T	NM_001267827.1	NP_001254756.1	A8K0R7	ZN839_HUMAN	zinc finger protein 839	387							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						CTTCTGATGAAGGTGAGTACT	0.398																																					p.K503T		Atlas-SNP	.											.	ZNF839	41	.	0			c.A1508C						PASS	.						126	116	119					14																	102800982		1913	4131	6044	SO:0001630	splice_region_variant	55778	exon4			TGATGAAGGTGAG	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.1161+1A>C	chr14.hg19:g.102800982A>C		90.0	0.0	.		97.0	33.0	.	NM_018335	B3KSD2|Q53FH5|Q6GPI5|Q86TU1|Q9BQ86|Q9NUU3	Missense_Mutation	SNP	ENST00000558850.1	hg19	CCDS58336.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.215665	0.79352	.	.	ENSG00000022976	ENST00000442396;ENST00000262236;ENST00000398436	T;T	0.37915	1.17;1.17	4.89	4.89	0.63831	.	0.506554	0.19538	N	0.111863	T	0.58906	0.2155	M	0.67397	2.05	0.40741	D	0.982836	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	0.63875	-0.6538	10	0.87932	D	0	.	14.8202	0.70068	1.0:0.0:0.0:0.0	.	503;387;266;387	A8K0R7-5;A8K0R7-2;Q9NT83;A8K0R7	.;.;.;ZN839_HUMAN	T	503;387;55	ENSP00000399863:K503T;ENSP00000262236:K387T	ENSP00000262236:K387T	K	+	2	0	ZNF839	101870735	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	5.967000	0.70403	1.967000	0.57214	0.459000	0.35465	AAG	.	.	.	none		0.398	ZNF839-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415492.2	NM_018335	Missense_Mutation	C	102800982	A	C	102800982	5	2	276	1	0	0	0	0	0	0	1	0	18200	86	3	5	1522	5	ZNF839	14	102800982	Splice_Site	SNP	A	TCGA-Y8-A896-01A-11D-A35Z-10	13865704	102800982	4548558	82	17590											
RORA	6095	hgsc.bcm.edu	37	chr15	60797807	60797807	+	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	aggtttccagatgcgatttaGatatattctgtgcaaggtgt	10	15	11	5	1	1	2	0	0	1	2	2	3	2	2	1	2	2	2	1	2	4	6			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr15:60797807G>A	ENST00000335670.6	-	6	942	c.842C>T	c.(841-843)tCt>tTt	p.S281F	RP11-219B17.1_ENST00000558235.1_RNA|RP11-219B17.1_ENST00000558140.1_RNA|RP11-219B17.1_ENST00000559824.1_RNA|RORA_ENST00000449337.2_Missense_Mutation_p.S226F|RORA_ENST00000261523.5_Missense_Mutation_p.S314F|RORA_ENST00000309157.4_Missense_Mutation_p.S306F|RP11-219B17.1_ENST00000501579.2_RNA	NM_134261.2	NP_599023.1	P35398	RORA_HUMAN	RAR-related orphan receptor A	281	Ligand-binding.				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						ATGCGATTTAGATATATTCTG	0.373																																					p.S314F		Atlas-SNP	.											.	RORA	114	.	0			c.C941T						PASS	.						123	127	126					15																	60797807		2203	4300	6503	SO:0001583	missense	6095	exon7			GATTTAGATATAT	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.842C>T	chr15.hg19:g.60797807G>A	ENSP00000335087:p.Ser281Phe	102.0	0.0	.		48.0	20.0	.	NM_134260	P35397|P35399|P45445|Q495X4|Q96H83	Missense_Mutation	SNP	ENST00000335670.6	hg19	CCDS10177.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.853080	0.91355	.	.	ENSG00000069667	ENST00000335670;ENST00000449337;ENST00000309157;ENST00000261523	D;D;D;D	0.95001	-3.58;-3.58;-3.58;-3.58	5.78	5.78	0.91487	Nuclear hormone receptor, ligand-binding (2);	0.000000	0.85682	D	0.000000	D	0.94558	0.8247	L	0.29908	0.895	0.80722	D	1	D;D;D;P	0.58620	0.979;0.978;0.983;0.891	P;P;P;P	0.56916	0.809;0.809;0.648;0.707	D	0.93871	0.7162	10	0.44086	T	0.13	.	20.3668	0.98882	0.0:0.0:1.0:0.0	.	281;306;314;226	P35398-2;P35398-3;P35398;P35398-4	.;.;RORA_HUMAN;.	F	281;226;306;314	ENSP00000335087:S281F;ENSP00000402971:S226F;ENSP00000309753:S306F;ENSP00000261523:S314F	ENSP00000261523:S314F	S	-	2	0	RORA	58585099	1.000000	0.71417	0.993000	0.49108	0.985000	0.73830	6.688000	0.74557	2.894000	0.99253	0.655000	0.94253	TCT	.	.	.	none		0.373	RORA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256142.2			A	60797807	G	A	60797807	3	1	276	1	0	0	0	0	1	0	0	0	13541	942	33	2	753	2	RORA	15	60797807	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10		60797807	41733585	83	17591											
SALL1	6299	hgsc.bcm.edu	37	chr16	51173002	51173006	+	Frame_Shift_Del	DEL	AAATT	AAATT	-																															gtgtcaacatgtgctgcttcAaattaccctttgtggaaaag																										TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	AAATT	AAATT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr16:51173002_51173006delAAATT	ENST00000251020.4	-	2	3160_3164	c.3127_3131delAATTT	c.(3127-3132)aatttgfs	p.NL1043fs	SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Frame_Shift_Del_p.NL946fs|SALL1_ENST00000541611.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	1043					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)			GTGCTGCTTCAAATTACCCTTTGTG	0.463																																					p.1043_1044del	GBM(103;1352 1446 1855 4775 8890)	Atlas-Indel,Pindel	.											.	SALL1	301	.	0			c.3128_3132del						PASS	.																																			SO:0001589	frameshift_variant	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.3127_3131delAATTT	chr16.hg19:g.51173002_51173006delAAATT	ENSP00000251020:p.Asn1043fs	83.0	0.0	0		95.0	30.0	0.315789	NM_002968	Q99881|Q9NSC3|Q9P1R0	Frame_Shift_Del	DEL	ENST00000251020.4	hg19	CCDS10747.1																																																																																			.	.	.	none		0.463	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		-	51173006	AAATT	-	51173002	7	5	276	1	0	1	0	1	0	0	0	0	13823	131	5	0	851	0	SALL1	16	51173002	Frame_Shift_Del	DEL	AAATT	TCGA-Y8-A896-01A-11D-A35Z-10		51173002	39181751	84	17592											
PSMD7	5713	hgsc.bcm.edu	37	chr16	74335517	74335517	+	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	cacaagaatgacattgccatCaacgaactcatgaaaagata	19	7	6	9	1	2	4	2	2	0	2	2	5	2	4	1	0	3	0	1	0	7	2			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr16:74335517C>G	ENST00000219313.4	+	4	464	c.324C>G	c.(322-324)atC>atG	p.I108M	PSMD7_ENST00000540379.1_Missense_Mutation_p.I31M|PSMD7_ENST00000567958.1_Missense_Mutation_p.I108M|PSMD7_ENST00000568615.2_Missense_Mutation_p.I108M	NM_002811.4	NP_002802.2	P51665	PSMD7_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 7	108	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						ACATTGCCATCAACGAACTCA	0.388																																					p.I108M		Atlas-SNP	.											.	PSMD7	29	.	0			c.C324G						PASS	.						127	121	123					16																	74335517		2198	4300	6498	SO:0001583	missense	5713	exon4			TGCCATCAACGAA	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.324C>G	chr16.hg19:g.74335517C>G	ENSP00000219313:p.Ile108Met	108.0	0.0	.		74.0	15.0	.	NM_002811	D3DWS9|Q6PKI2|Q96E97	Missense_Mutation	SNP	ENST00000219313.4	hg19	CCDS10910.1	.	.	.	.	.	.	.	.	.	.	C	17.95	3.514066	0.64522	.	.	ENSG00000103035	ENST00000219313;ENST00000540379	T;T	0.58060	0.36;0.36	5.71	4.73	0.59995	.	0.000000	0.85682	D	0.000000	T	0.80319	0.4601	H	0.97587	4.035	0.80722	D	1	D	0.71674	0.998	D	0.77004	0.989	D	0.84892	0.0837	10	0.87932	D	0	-19.7916	10.1812	0.42968	0.0:0.8438:0.0:0.1562	.	108	P51665	PSD7_HUMAN	M	108;31	ENSP00000219313:I108M;ENSP00000443925:I31M	ENSP00000219313:I108M	I	+	3	3	PSMD7	72893018	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.033000	0.41136	1.354000	0.45846	0.467000	0.42956	ATC	.	.	.	none		0.388	PSMD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269010.2	NM_002811		G	74335517	C	G	74335517	3	3	276	1	0	0	0	0	1	0	0	0	12713	816	29	4	338	4	PSMD7	16	74335517	Missense_Mutation	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10	23162515	74335517	16019236	85	17593											
KIAA0664	23277	hgsc.bcm.edu	37	chr17	2595757	2595757	+	Missense_Mutation	SNP	A	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	cgtactccatcaccccgtgcAgcaccagcccgatgttgttc	7	9	8	17	3	1	0	1	0	0	0	3	1	2	0	5	0	4	5	5	0	1	3			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr17:2595757A>C	ENST00000570628.2	-	22	3446	c.3341T>G	c.(3340-3342)cTg>cGg	p.L1114R	CLUH_ENST00000538975.1_Missense_Mutation_p.L1114R|CLUH_ENST00000435359.1_Missense_Mutation_p.L1114R			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	1114					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)											CACCCCGTGCAGCACCAGCCC	0.711																																					p.L1114R		Atlas-SNP	.											.	.	.	.	0			c.T3341G						PASS	.						22	24	23					17																	2595757		1990	4162	6152	SO:0001583	missense	23277	exon22			CCGTGCAGCACCA	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.3341T>G	chr17.hg19:g.2595757A>C	ENSP00000458986:p.Leu1114Arg	55.0	0.0	.		36.0	11.0	.	NM_015229	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Missense_Mutation	SNP	ENST00000570628.2	hg19	CCDS45572.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.535700	0.85812	.	.	ENSG00000132361	ENST00000435359;ENST00000322335;ENST00000538975	D;D	0.95690	-3.78;-3.78	4.79	4.79	0.61399	Tetratricopeptide-like helical (1);	0.000000	0.64402	D	0.000001	D	0.97642	0.9227	M	0.85945	2.785	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98327	1.0531	10	0.72032	D	0.01	.	13.6522	0.62318	1.0:0.0:0.0:0.0	.	1114;1115	O75153;C9J6D7	K0664_HUMAN;.	R	1114;1115;1114	ENSP00000388872:L1114R;ENSP00000439628:L1114R	ENSP00000320468:L1115R	L	-	2	0	KIAA0664	2542507	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.139000	0.94554	2.017000	0.59298	0.459000	0.35465	CTG	.	.	.	none		0.711	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229		C	2595757	A	C	2595757	3	2	276	1	0	0	0	0	1	0	0	0	8196	188	7	5	608	5	KIAA0664	17	2595757	Missense_Mutation	SNP	A	TCGA-Y8-A896-01A-11D-A35Z-10		2595757	78599453	86	17594											
PER1	5187	hgsc.bcm.edu	37	chr17	8049997	8049997	+	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	ctcctcagggaccaaggctaGtggggcctggacgggagcag	8	5	17	11	1	1	0	1	0	0	0	2	3	2	3	3	6	1	2	3	6	2	1			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr17:8049997G>T	ENST00000317276.4	-	15	2059	c.1822C>A	c.(1822-1824)Cta>Ata	p.L608I	PER1_ENST00000354903.5_Missense_Mutation_p.L592I|PER1_ENST00000578089.1_5'Flank|PER1_ENST00000581082.1_Missense_Mutation_p.L588I	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	608	Required for phosphorylation by CSNK1E. {ECO:0000250}.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						ACCAAGGCTAGTGGGGCCTGG	0.627			T	ETV6	"AML, CMML"			Other conserved DNA damage response genes																													p.L608I		Atlas-SNP	.		Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	.	PER1	104	.	0			c.C1822A						PASS	.						41	44	43					17																	8049997		2203	4300	6503	SO:0001583	missense	5187	exon15			AGGCTAGTGGGGC	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.1822C>A	chr17.hg19:g.8049997G>T	ENSP00000314420:p.Leu608Ile	34.0	0.0	.		38.0	9.0	.	NM_002616	B2RPA8|B4DI49|D3DTR3	Missense_Mutation	SNP	ENST00000317276.4	hg19	CCDS11131.1	.	.	.	.	.	.	.	.	.	.	G	7.390	0.630516	0.14322	.	.	ENSG00000179094	ENST00000317276;ENST00000354903	T;T	0.36340	2.64;1.26	5.16	-0.88	0.10610	.	0.701833	0.13793	N	0.362378	T	0.26048	0.0635	L	0.50333	1.59	0.09310	N	1	B;B	0.22480	0.003;0.07	B;B	0.18263	0.003;0.021	T	0.18967	-1.0320	10	0.28530	T	0.3	-0.3823	5.9627	0.19308	0.2405:0.255:0.5045:0.0	.	592;608	B4DI49;O15534	.;PER1_HUMAN	I	608;592	ENSP00000314420:L608I;ENSP00000346979:L592I	ENSP00000314420:L608I	L	-	1	2	PER1	7990722	0.000000	0.05858	0.000000	0.03702	0.392000	0.30506	-0.131000	0.10482	0.014000	0.14944	0.453000	0.30009	CTA	.	.	.	none		0.627	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2			T	8049997	G	T	8049997	3	4	276	1	0	0	0	0	1	0	0	0	11736	1020	36	4	2086	4	PER1	17	8049997	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	5454240	8049997	73145213	87	17595											
KRTAP17-1	83902	hgsc.bcm.edu	37	chr17	39471781	39471781	+	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	agccagagcccccgcagccaGagcccccacagccacagcag	11	0	10	20	1	0	2	0	0	0	2	0	2	0	2	7	0	6	2	7	0	0	0	rs62640394		TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr17:39471781G>C	ENST00000334202.3	-	1	166	c.122C>G	c.(121-123)tCt>tGt	p.S41C		NM_031964.1	NP_114170.1	Q9BYP8	KR171_HUMAN	keratin associated protein 17-1	41						intermediate filament (GO:0005882)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			cccgcagccagagcccccaca	0.687																																					p.S41C		Atlas-SNP	.											KRTAP17-1,caecum,carcinoma,0,1	KRTAP17-1	14	.	0			c.C122G						PASS	.						10	13	12					17																	39471781		2171	4248	6419	SO:0001583	missense	83902	exon1			CAGCCAGAGCCCC	AJ406952	CCDS11387.1	17q21.2	2013-06-20			ENSG00000186860	ENSG00000186860		"Keratin associated proteins"	18917	protein-coding gene	gene with protein product							Standard	NM_031964		Approved	KAP17.1	uc002hwj.3	Q9BYP8	OTTHUMG00000133433	ENST00000334202.3:c.122C>G	chr17.hg19:g.39471781G>C	ENSP00000333993:p.Ser41Cys	63.0	0.0	.		51.0	3.0	.	NM_031964		Missense_Mutation	SNP	ENST00000334202.3	hg19	CCDS11387.1	.	.	.	.	.	.	.	.	.	.	G	1.949	-0.441645	0.04604	.	.	ENSG00000186860	ENST00000334202	.	.	.	4.26	-0.59	0.11679	.	.	.	.	.	T	0.20455	0.0492	N	0.02539	-0.55	0.09310	N	1	B	0.12013	0.005	B	0.10450	0.005	T	0.24548	-1.0157	8	0.87932	D	0	0.3694	13.4773	0.61316	0.0:0.6456:0.3544:0.0	rs62640394	41	Q9BYP8	KR171_HUMAN	C	41	.	ENSP00000333993:S41C	S	-	2	0	KRTAP17-1	36725307	0.000000	0.05858	0.000000	0.03702	0.315000	0.28087	-0.356000	0.07661	-0.221000	0.09973	0.462000	0.41574	TCT	.	G|0.984;C|0.016	0.016	weak		0.687	KRTAP17-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257296.1			C	39471781	G	C	39471781	3	2	276	1	0	0	0	0	1	0	0	0	8534	942	33	4	199	4	KRTAP17-1	17	39471781	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	31421784	39471781	41723429	88	17596											
EPB41L3	23136	hgsc.bcm.edu	37	chr18	5397279	5397279	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatccccgctgtctcccgcCgagtaagaagcatccccact	8	7	8	18	3	1	1	0	0	1	1	4	2	3	1	6	0	1	4	6	0	2	1			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr18:5397279C>T	ENST00000341928.2	-	18	2959	c.2619G>A	c.(2617-2619)tcG>tcA	p.S873S	EPB41L3_ENST00000427684.2_Silent_p.S170S|EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000540638.2_Silent_p.S651S|EPB41L3_ENST00000400111.3_Silent_p.S651S|EPB41L3_ENST00000342933.3_Silent_p.S873S|EPB41L3_ENST00000544123.1_Silent_p.S704S|EPB41L3_ENST00000542146.1_Silent_p.S178S	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	873	C-terminal (CTD).				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						TGTCTCCCGCCGAGTAAGAAG	0.627																																					p.S873S		Atlas-SNP	.											EPB41L3,NS,carcinoma,0,1	EPB41L3	222	.	0			c.G2619A						PASS	.						73	67	69					18																	5397279		2203	4300	6503	SO:0001819	synonymous_variant	23136	exon18			TCCCGCCGAGTAA	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.2619G>A	chr18.hg19:g.5397279C>T		54.0	0.0	.		54.0	16.0	.	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Silent	SNP	ENST00000341928.2	hg19	CCDS11838.1																																																																																			.	.	.	none		0.627	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		T	5397279	C	T	5397279	2	4	276	1	0	0	0	0	0	0	0	1	5156	639	23	1		1	EPB41L3	18	5397279	Silent	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10		5397279	72679969	89	17597											
KCTD1	284252	hgsc.bcm.edu	37	chr18	24056561	24056561	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgtccatctctgtcaatgAaatagtgctgtttgagactg	9	15	9	8	0	3	2	1	2	2	1	5	3	4	2	1	0	1	2	1	0	3	2			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr18:24056561A>G	ENST00000408011.3	-	3	786	c.227T>C	c.(226-228)tTc>tCc	p.F76S	KCTD1_ENST00000579973.1_Missense_Mutation_p.F76S|KCTD1_ENST00000417602.1_Missense_Mutation_p.F684S|KCTD1_ENST00000580059.1_Missense_Mutation_p.F76S|KCTD1_ENST00000317932.7_Missense_Mutation_p.F76S	NM_001136205.2	NP_001129677.1	Q719H9	KCTD1_HUMAN	potassium channel tetramerization domain containing 1	76	BTB.				negative regulation of transcription, DNA-templated (GO:0045892)|protein homooligomerization (GO:0051260)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(3)	12	all_cancers(21;0.00191)|Lung NSC(5;0.000698)|all_lung(6;0.0019)|Ovarian(20;0.0848)		Epithelial(2;7.8e-06)|OV - Ovarian serous cystadenocarcinoma(3;9.02e-06)|all cancers(3;3.37e-05)			TCTGTCAATGAAATAGTGCTG	0.383																																					p.F684S		Atlas-SNP	.											.	KCTD1	76	.	0			c.T2051C						PASS	.						110	93	99					18																	24056561		2203	4300	6503	SO:0001583	missense	284252	exon3			TCAATGAAATAGT	AF542549	CCDS11888.1	18q11.2	2013-09-20	2013-06-20		ENSG00000134504	ENSG00000134504			18249	protein-coding gene	gene with protein product		613420	"potassium channel tetramerisation domain containing 1"	C18orf5			Standard	NM_001142730		Approved		uc010xbj.3	Q719H9	OTTHUMG00000131947	ENST00000408011.3:c.227T>C	chr18.hg19:g.24056561A>G	ENSP00000384367:p.Phe76Ser	100.0	0.0	.		82.0	24.0	.	NM_001142730	A8K1F5	Missense_Mutation	SNP	ENST00000408011.3	hg19	CCDS11888.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.803009	0.90623	.	.	ENSG00000134504	ENST00000317932;ENST00000417602;ENST00000408011	D;D;D	0.84730	-1.89;-1.89;-1.89	5.78	5.78	0.91487	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.85682	D	0.000000	D	0.95500	0.8538	H	0.98199	4.17	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97229	0.9883	10	0.87932	D	0	.	16.1031	0.81201	1.0:0.0:0.0:0.0	.	76	Q719H9	KCTD1_HUMAN	S	76;684;76	ENSP00000314831:F76S;ENSP00000408405:F684S;ENSP00000384367:F76S	ENSP00000314831:F76S	F	-	2	0	KCTD1	22310559	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.860000	0.92272	2.197000	0.70478	0.528000	0.53228	TTC	.	.	.	none		0.383	KCTD1-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000446265.1	XM_209091		G	24056561	A	G	24056561	3	3	276	1	0	0	0	0	1	0	0	0	8103	246	9	3	558	3	KCTD1	18	24056561	Missense_Mutation	SNP	A	TCGA-Y8-A896-01A-11D-A35Z-10	18659282	24056561	54020687	90	17598											
ZNF24	7572	hgsc.bcm.edu	37	chr18	32920341	32920349	+	In_Frame_Del	DEL	AGATTTGTT	AGATTTGTT	-																															ctccagcactaccagctccaAgatttgttcttttgtgtgcg																								rs570943082		TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	AGATTTGTT	AGATTTGTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr18:32920341_32920349delAGATTTGTT	ENST00000261332.6	-	2	445_453	c.266_274delAACAAATCT	c.(265-276)gaacaaatcttg>gtg	p.89_92EQIL>V	ZNF24_ENST00000589881.1_In_Frame_Del_p.89_92EQIL>V|ZNF24_ENST00000399061.3_In_Frame_Del_p.89_92EQIL>V	NM_006965.2	NP_008896.2	P17028	ZNF24_HUMAN	zinc finger protein 24	89	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				myelination (GO:0042552)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	15						ACCAGCTCCAAGATTTGTTCTTTTGTGTG	0.541																																					p.89_92del	Colon(42;769 913 8916 19469 46270)	Atlas-Indel,Pindel	.											.	ZNF24	40	.	0			c.267_275del						PASS	.																																			SO:0001651	inframe_deletion	7572	exon2			.	AF016052	CCDS11912.1	18q12	2013-01-09	2006-05-10		ENSG00000172466	ENSG00000172466		"-", "Zinc fingers, C2H2-type"	13032	protein-coding gene	gene with protein product		194534	"zinc finger protein 24 (KOX 17)"	ZNF191			Standard	NM_006965		Approved	ZSCAN3, Zfp191, KOX17	uc002kys.2	P17028	OTTHUMG00000132565	ENST00000261332.6:c.266_274delAACAAATCT	chr18.hg19:g.32920341_32920349delAGATTTGTT	ENSP00000261332:p.Glu89_Leu92delinsVal	165.0	0.0	0		148.0	41.0	0.277027	NM_006965	O14754|Q53YE4|Q6ICR5|Q8IZN4	In_Frame_Del	DEL	ENST00000261332.6	hg19	CCDS11912.1																																																																																			.	.	.	none		0.541	ZNF24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255769.1	NM_006965		-	32920349	AGATTTGTT	-	32920341	7	5	276	1	0	1	0	1	0	0	0	0	17804	69	3	0	844	0	ZNF24	18	32920341	In_Frame_Del	DEL	AGATTTGTT	TCGA-Y8-A896-01A-11D-A35Z-10	8863780	32920341	45156907	91	17599											
POLI	11201	hgsc.bcm.edu	37	chr18	51820257	51820257	+	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	agaaatcctttctggaaaatCtagggaaaaatttcaaggga	17	10	9	5	0	3	1	1	0	2	1	4	4	4	4	1	3	0	0	1	3	7	3			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr18:51820257C>A	ENST00000579534.1	+	10	1786	c.1643C>A	c.(1642-1644)tCt>tAt	p.S548Y	POLI_ENST00000579434.1_Missense_Mutation_p.S445Y|POLI_ENST00000217800.5_Missense_Mutation_p.S422Y|POLI_ENST00000406285.3_Missense_Mutation_p.S469Y	NM_007195.2	NP_009126.2	Q9UNA4	POLI_HUMAN	polymerase (DNA directed) iota	548					DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)	intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(5)|ovary(3)|urinary_tract(1)	26				Colorectal(16;0.0234)|READ - Rectum adenocarcinoma(59;0.197)		TCTGGAAAATCTAGGGAAAAA	0.368								DNA polymerases (catalytic subunits)																													p.S548Y		Atlas-SNP	.											.	POLI	132	.	0			c.C1643A						PASS	.						30	31	31					18																	51820257		2203	4299	6502	SO:0001583	missense	11201	exon10			GAAAATCTAGGGA		CCDS11954.2	18q21.1	2012-05-18			ENSG00000101751	ENSG00000101751		"DNA polymerases"	9182	protein-coding gene	gene with protein product		605252		RAD3OB, RAD30B		17609217	Standard	NM_007195		Approved		uc002lfj.4	Q9UNA4	OTTHUMG00000132704	ENST00000579534.1:c.1643C>A	chr18.hg19:g.51820257C>A	ENSP00000462664:p.Ser548Tyr	231.0	0.0	.		231.0	67.0	.	NM_007195	Q8N590|Q9H0S1|Q9NYH6	Missense_Mutation	SNP	ENST00000579534.1	hg19	CCDS11954.2	.	.	.	.	.	.	.	.	.	.	C	8.727	0.915756	0.17907	.	.	ENSG00000101751	ENST00000406285;ENST00000217800	T	0.50277	0.75	5.51	3.72	0.42706	.	0.614028	0.17190	N	0.183543	T	0.55768	0.1941	M	0.62723	1.935	0.36421	D	0.864307	D;D	0.67145	0.996;0.976	P;P	0.56700	0.804;0.726	T	0.61277	-0.7095	10	0.46703	T	0.11	-4.9843	8.2416	0.31662	0.0:0.6203:0.2987:0.081	.	468;548	B7Z780;Q9UNA4	.;POLI_HUMAN	Y	469;548	ENSP00000385196:S469Y	ENSP00000217800:S548Y	S	+	2	0	POLI	50074255	0.135000	0.22499	0.993000	0.49108	0.925000	0.55904	0.998000	0.29744	0.789000	0.33779	-0.176000	0.13171	TCT	.	.	.	none		0.368	POLI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256002.3	NM_007195		A	51820257	C	A	51820257	3	1	276	1	0	0	0	0	1	0	0	0	12210	913	32	4	1681	4	POLI	18	51820257	Missense_Mutation	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10	18899916	51820257	26256991	92	17600											
PDE4A	5141	hgsc.bcm.edu	37	chr19	10563954	10563954	+	Intron	DEL	T	T	-																															tccaagatgcccttggtggaTttcttctgcgagacctgctc																										TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr19:10563954delT	ENST00000352831.6	+	7	893				PDE4A_ENST00000592685.1_Intron|PDE4A_ENST00000380702.2_Intron|PDE4A_ENST00000440014.2_Intron|PDE4A_ENST00000344979.3_Frame_Shift_Del_p.D5fs|PDE4A_ENST00000293683.5_Intron	NM_001111307.1	NP_001104777.1	P27815	PDE4A_HUMAN	phosphodiesterase 4A, cAMP-specific						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)	CCTTGGTGGATTTCTTCTGCG	0.647																																					p.D5fs		Atlas-INDEL	.											.	PDE4A	236	.	0			c.14delA						PASS	.						62	47	52					19																	10563954		2203	4300	6503	SO:0001627	intron_variant	5141	exon1			.		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.784-1551T>-	chr19.hg19:g.10563954delT		57.0	0.0	0		36.0	12.0	0.333333	NM_006202	O75522|O76092|Q16255|Q16691|Q5DM53|Q6PMT2|Q8IVA7|Q8WUQ3|Q9H3H2	Frame_Shift_Del	DEL	ENST00000352831.6	hg19	CCDS45961.1																																																																																			.	.	.	none		0.647	PDE4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451244.1			-	10563954	T	-	10563954	6	5	276	0	1	1	0	1	0	0	0	0	11646	1490	52	0		0	PDE4A	19	10563954	Intron	DEL	T	TCGA-Y8-A896-01A-11D-A35Z-10		10563954	48565029	93	17601	182	3									
PDE4A	5141	hgsc.bcm.edu	37	chr19	10563955	10563957	+	Intron	DEL	TTC	TTC	-																															ccaagatgcccttggtggatTtcttctgcgagacctgctct																										TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr19:10563955_10563957delTTC	ENST00000352831.6	+	7	893				PDE4A_ENST00000592685.1_Intron|PDE4A_ENST00000380702.2_Intron|PDE4A_ENST00000440014.2_Intron|PDE4A_ENST00000344979.3_In_Frame_Del_p.F7del|PDE4A_ENST00000293683.5_Intron	NM_001111307.1	NP_001104777.1	P27815	PDE4A_HUMAN	phosphodiesterase 4A, cAMP-specific						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)	CTTGGTGGATTTCTTCTGCGAGA	0.65																																					p.5_6del		Pindel	.											.	PDE4A	236	.	0			c.15_17del						PASS	.																																			SO:0001627	intron_variant	5141	exon1			.		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.784-1548TTC>-	chr19.hg19:g.10563958_10563960delTTC		56.0	0.0	.		37.0	10.0	0.270	NM_006202	O75522|O76092|Q16255|Q16691|Q5DM53|Q6PMT2|Q8IVA7|Q8WUQ3|Q9H3H2	In_Frame_Del	DEL	ENST00000352831.6	hg19	CCDS45961.1																																																																																			.	.	.	none		0.65	PDE4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451244.1			-	10563957	TTC	-	10563955	6	5	276	0	1	1	0	1	0	0	0	0	11646	1841	64	0		0	PDE4A	19	10563955	Intron	DEL	TTC	TCGA-Y8-A896-01A-11D-A35Z-10	1	10563955	48565028	94	17602	182	3									
PDE4A	5141	hgsc.bcm.edu	37	chr19	10563956	10563957	+	Intron	DNP	TC	TC	AA																															caagatgcccttggtggattTcttctgcgagacctgctcta																										TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr19:10563956_10563957TC>AA	ENST00000352831.6	+	7	893				PDE4A_ENST00000592685.1_Intron|PDE4A_ENST00000380702.2_Intron|PDE4A_ENST00000440014.2_Intron|PDE4A_ENST00000344979.3_Nonsense_Mutation_p.F6*|PDE4A_ENST00000293683.5_Intron	NM_001111307.1	NP_001104777.1	P27815	PDE4A_HUMAN	phosphodiesterase 4A, cAMP-specific						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)	TTGGTGGATTTCTTCTGCGAGA	0.653																																					p.F6Y|p.F6L		Atlas-SNP	.											.	PDE4A	236	.	0			c.T17A|c.C18A						PASS	.																																			SO:0001627	intron_variant	5141	exon1			TGGATTTCTTCTG|GGATTTCTTCTGC		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		Exception_encountered	chr19.hg19:g.10563956_10563957delinsAA		54.0	0.0	.		36.0	12.0	.	NM_006202	O75522|O76092|Q16255|Q16691|Q5DM53|Q6PMT2|Q8IVA7|Q8WUQ3|Q9H3H2	Missense_Mutation	SNP	ENST00000352831.6	hg19	CCDS45961.1																																																																																			.	.	.	none		0.653	PDE4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451244.1			AA	10563957	TC	AA	10563956	1	1	276	0	1	0	0	0	0	0	0	0	11646	1783	62	5		5	PDE4A	19	10563956	Intron	DNP	TC	TCGA-Y8-A896-01A-11D-A35Z-10	1	10563956	48565027	95	17603	182	3									
ELL	8178	hgsc.bcm.edu	37	chr19	18555598	18555598	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agctgccgctggtcgtactcGgcgatgagcctcttgatgtg	5	11	14	11	4	1	2	0	2	1	0	3	3	1	2	2	2	4	3	2	2	1	2			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr19:18555598G>A	ENST00000262809.4	-	12	1901	c.1830C>T	c.(1828-1830)gcC>gcT	p.A610A	ELL_ENST00000596124.3_Silent_p.A477A|CTD-3137H5.1_ENST00000594590.2_RNA	NM_006532.3	NP_006523.1	P55199	ELL_HUMAN	elongation factor RNA polymerase II	610					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)		GGTCGTACTCGGCGATGAGCC	0.627			T	MLL	AL																																p.A610A		Atlas-SNP	.		Dom	yes		19	19p13.1	8178	ELL gene (11-19 lysine-rich leukemia gene)		L	.	ELL	52	.	0			c.C1830T						PASS	.						103	85	91					19																	18555598		2203	4300	6503	SO:0001819	synonymous_variant	8178	exon12			GTACTCGGCGATG	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.1830C>T	chr19.hg19:g.18555598G>A		25.0	0.0	.		22.0	5.0	.	NM_006532		Silent	SNP	ENST00000262809.4	hg19	CCDS12380.1																																																																																			.	.	.	none		0.627	ELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466362.1	NM_006532		A	18555598	G	A	18555598	2	1	276	1	0	0	0	0	0	0	0	1	5064	1103	39	1		1	ELL	19	18555598	Silent	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	7991642	18555598	40573385	96	17604											
PSG1	5669	hgsc.bcm.edu	37	chr19	43376066	43376066	+	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	cttcaagctgtgagtcatagGgaggctctgaccattcatcc	9	11	10	11	0	4	2	3	2	1	0	5	3	5	3	2	2	1	2	2	2	2	3	rs368581835		TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr19:43376066G>A	ENST00000436291.2	-	3	678	c.562C>T	c.(562-564)Cct>Tct	p.P188S	PSG1_ENST00000244296.2_Missense_Mutation_p.P188S|PSG1_ENST00000595356.1_Missense_Mutation_p.P188S|PSG1_ENST00000312439.6_Missense_Mutation_p.P188S|PSG1_ENST00000403380.3_Intron|PSG1_ENST00000595124.1_Intron	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	188	Ig-like C2-type 1.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				TGAGTCATAGGGAGGCTCTGA	0.498																																					p.P188S		Atlas-SNP	.											.	PSG1	196	.	0			c.C562T						PASS	.	G	SER/PRO,SER/PRO,SER/PRO	1,4403		0,1,2201	281	273	276		562,562,562	1.5	0	19		276	0,8598		0,0,4299	no	missense,missense,missense	PSG1	NM_001184825.1,NM_001184826.1,NM_006905.2	74,74,74	0,1,6500	AA,AG,GG		0.0,0.0227,0.0077	,,	188/420,188/418,188/427	43376066	1,13001	2202	4299	6501	SO:0001583	missense	5669	exon3			TCATAGGGAGGCT		CCDS12612.1, CCDS54275.1, CCDS59392.1, CCDS74380.1	19q13.2	2013-01-29			ENSG00000231924	ENSG00000231924		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9514	protein-coding gene	gene with protein product		176390		PSBG1			Standard	NM_006905		Approved	PSGGA, CD66f, PBG1		P11464	OTTHUMG00000151123	ENST00000436291.2:c.562C>T	chr19.hg19:g.43376066G>A	ENSP00000413041:p.Pro188Ser	104.0	0.0	.		103.0	26.0	.	NM_001184826	O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Missense_Mutation	SNP	ENST00000436291.2	hg19	CCDS54275.1	.	.	.	.	.	.	.	.	.	.	N	9.391	1.075520	0.20227	2.27E-4	0.0	ENSG00000231924	ENST00000436291;ENST00000312439;ENST00000244296	T;T;T	0.11169	2.8;2.8;2.8	1.46	1.46	0.22682	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.23330	0.0564	L	0.58354	1.805	0.09310	N	1	D;D;D;P;P;D;D;D	0.89917	1.0;1.0;0.999;0.533;0.738;0.992;0.994;1.0	D;D;D;B;P;D;D;D	0.87578	0.998;0.991;0.988;0.439;0.522;0.955;0.981;0.994	T	0.06373	-1.0830	9	0.39692	T	0.17	.	6.2767	0.20985	0.0:0.0:1.0:0.0	.	188;188;188;188;188;60;188;188	O75238;P11464-4;P11464;P11464-3;Q9UPK8;B4DTG5;O75237;P11464-2	.;.;PSG1_HUMAN;.;.;.;.;.	S	188	ENSP00000413041:P188S;ENSP00000308970:P188S;ENSP00000244296:P188S	ENSP00000244296:P188S	P	-	1	0	PSG1	48067906	0.003000	0.15002	0.003000	0.11579	0.013000	0.08279	0.913000	0.28611	0.782000	0.33613	0.184000	0.17185	CCT	.	.	.	weak		0.498	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1			A	43376066	G	A	43376066	3	1	276	1	0	0	0	0	1	0	0	0	12663	1232	43	2	766	2	PSG1	19	43376066	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	24820468	43376066	15752917	97	17605											
MBOAT7	79143	hgsc.bcm.edu	37	chr19	54684568	54684568	+	Missense_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	cggggtaggccccaaagccgGcggcaatgcagccgcactcg	8	3	15	15	5	0	0	0	0	0	0	1	0	0	0	4	5	3	4	4	5	3	1			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr19:54684568G>A	ENST00000245615.1	-	6	1256	c.776C>T	c.(775-777)gCc>gTc	p.A259V	MBOAT7_ENST00000338624.6_Missense_Mutation_p.A186V|MBOAT7_ENST00000431666.2_Missense_Mutation_p.A186V|MBOAT7_ENST00000391754.1_Missense_Mutation_p.A259V|MBOAT7_ENST00000474910.1_5'Flank	NM_024298.3	NP_077274.3	Q96N66	MBOA7_HUMAN	membrane bound O-acyltransferase domain containing 7	259					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)					CCCAAAGCCGGCGGCAATGCA	0.716											OREG0003644	type=REGULATORY REGION|Gene=AK123290|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.A259V	NSCLC(97;826 2151 10470 22540)	Atlas-SNP	.											.	MBOAT7	37	.	0			c.C776T						PASS	.						9	11	10					19																	54684568		2158	4240	6398	SO:0001583	missense	79143	exon6			AAGCCGGCGGCAA	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.776C>T	chr19.hg19:g.54684568G>A	ENSP00000245615:p.Ala259Val	113.0	0.0	.	1002	104.0	27.0	.	NM_001146082	A9C4B6|B0V3I5|B4DQ87|Q05DF0|Q7L5N2|Q99908|Q9BPV2|Q9BRE9	Missense_Mutation	SNP	ENST00000245615.1	hg19	CCDS12883.1	.	.	.	.	.	.	.	.	.	.	g	36	5.810866	0.96975	.	.	ENSG00000125505	ENST00000431666;ENST00000338624;ENST00000245615;ENST00000391754	T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.66	4.59	4.59	0.56863	.	0.173558	0.50627	D	0.000116	T	0.80686	0.4670	M	0.77486	2.375	0.80722	D	1	P;D;P	0.61697	0.955;0.99;0.885	P;P;P	0.55011	0.763;0.766;0.666	D	0.83970	0.0326	10	0.62326	D	0.03	-10.7127	16.6251	0.84968	0.0:0.0:1.0:0.0	.	241;186;259	B4DDH8;Q96N66-2;Q96N66	.;.;MBOA7_HUMAN	V	186;186;259;259	ENSP00000410503:A186V;ENSP00000344377:A186V;ENSP00000245615:A259V;ENSP00000375634:A259V	ENSP00000245615:A259V	A	-	2	0	MBOAT7	59376380	1.000000	0.71417	0.983000	0.44433	0.997000	0.91878	8.293000	0.89932	2.296000	0.77279	0.546000	0.68486	GCC	.	.	.	none		0.716	MBOAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142203.1	NM_024298		A	54684568	G	A	54684568	3	1	276	1	0	0	0	0	1	0	0	0	9365	1203	42	2	658	2	MBOAT7	19	54684568	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	11308502	54684568	4444415	98	17606											
SGK2	10110	hgsc.bcm.edu	37	chr20	42198049	42198049	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccacatcatggcagagcgcAgtgtgcttctgaagaacgtg	10	8	13	10	2	2	3	1	1	1	2	2	3	2	3	1	1	3	3	1	1	2	1			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr20:42198049A>G	ENST00000341458.4	+	5	652	c.433A>G	c.(433-435)Agt>Ggt	p.S145G	SGK2_ENST00000373100.1_Missense_Mutation_p.S85G|SGK2_ENST00000423407.3_Missense_Mutation_p.S85G|SGK2_ENST00000373092.3_Missense_Mutation_p.S85G|SGK2_ENST00000373077.1_Missense_Mutation_p.S84G|SGK2_ENST00000426287.1_Missense_Mutation_p.S111G	NM_016276.3	NP_057360.2	Q9HBY8	SGK2_HUMAN	serum/glucocorticoid regulated kinase 2	145	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)			GGCAGAGCGCAGTGTGCTTCT	0.567																																					p.S145G		Atlas-SNP	.											.	SGK2	50	.	0			c.A433G						PASS	.						86	65	72					20																	42198049		2203	4300	6503	SO:0001583	missense	10110	exon5			GAGCGCAGTGTGC	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.433A>G	chr20.hg19:g.42198049A>G	ENSP00000340608:p.Ser145Gly	54.0	0.0	.		40.0	11.0	.	NM_016276	Q52PK5|Q5H8Y6|Q5H8Z1|Q5TZR3|Q9UKG6	Missense_Mutation	SNP	ENST00000341458.4	hg19	CCDS13320.1	.	.	.	.	.	.	.	.	.	.	A	17.13	3.311220	0.60414	.	.	ENSG00000101049	ENST00000373100;ENST00000373092;ENST00000373077;ENST00000412111;ENST00000423407;ENST00000341458;ENST00000426287	T;T;T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21	4.24	4.24	0.50183	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.191710	0.56097	D	0.000040	T	0.63379	0.2506	L	0.41492	1.28	0.36156	D	0.847752	B;B;B	0.25809	0.135;0.117;0.013	B;B;B	0.37601	0.107;0.254;0.062	T	0.71227	-0.4655	10	0.59425	D	0.04	.	13.0383	0.58885	1.0:0.0:0.0:0.0	.	111;145;85	Q9HBY8-3;Q9HBY8;Q9HBY8-2	.;SGK2_HUMAN;.	G	85;85;84;84;85;145;111	ENSP00000362192:S85G;ENSP00000362184:S85G;ENSP00000362168:S84G;ENSP00000396222:S84G;ENSP00000392795:S85G;ENSP00000340608:S145G;ENSP00000412214:S111G	ENSP00000340608:S145G	S	+	1	0	SGK2	41631463	1.000000	0.71417	0.901000	0.35422	0.822000	0.46500	9.255000	0.95524	1.873000	0.54277	0.454000	0.30748	AGT	.	.	.	none		0.567	SGK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080383.1			G	42198049	A	G	42198049	3	3	276	1	0	0	0	0	1	0	0	0	14222	188	7	3	451	3	SGK2	20	42198049	Missense_Mutation	SNP	A	TCGA-Y8-A896-01A-11D-A35Z-10		42198049	20827471	99	17607											
SGK2	10110	hgsc.bcm.edu	37	chr20	42199282	42199282	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttccacctgcagcgggagcGccggttcctggagccccggg	4	6	15	16	4	0	0	0	0	0	0	2	2	2	2	6	4	4	2	6	4	0	2	rs559824768		TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr20:42199282G>A	ENST00000341458.4	+	6	785	c.566G>A	c.(565-567)cGc>cAc	p.R189H	SGK2_ENST00000373100.1_Missense_Mutation_p.R129H|SGK2_ENST00000485914.1_3'UTR|SGK2_ENST00000423407.3_Missense_Mutation_p.R129H|SGK2_ENST00000373092.3_Missense_Mutation_p.R129H|SGK2_ENST00000373077.1_Missense_Mutation_p.R128H|SGK2_ENST00000426287.1_Missense_Mutation_p.R155H	NM_016276.3	NP_057360.2	Q9HBY8	SGK2_HUMAN	serum/glucocorticoid regulated kinase 2	189	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)	p.R189H(2)		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)			CAGCGGGAGCGCCGGTTCCTG	0.637																																					p.R189H		Atlas-SNP	.											SGK2,NS,carcinoma,0,1	SGK2	50	.	2	Substitution - Missense(2)	lung(2)	c.G566A						PASS	.						61	62	62					20																	42199282		2203	4300	6503	SO:0001583	missense	10110	exon6			GGGAGCGCCGGTT	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.566G>A	chr20.hg19:g.42199282G>A	ENSP00000340608:p.Arg189His	58.0	0.0	.		47.0	8.0	.	NM_016276	Q52PK5|Q5H8Y6|Q5H8Z1|Q5TZR3|Q9UKG6	Missense_Mutation	SNP	ENST00000341458.4	hg19	CCDS13320.1	.	.	.	.	.	.	.	.	.	.	G	18.59	3.656820	0.67586	.	.	ENSG00000101049	ENST00000373100;ENST00000373092;ENST00000373077;ENST00000412111;ENST00000423407;ENST00000341458;ENST00000426287	T;T;T;T;T;T;T	0.25579	1.79;1.79;1.79;1.79;1.79;1.79;1.79	4.77	2.75	0.32379	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.148295	0.64402	N	0.000014	T	0.21267	0.0512	L	0.52905	1.665	0.58432	D	0.999999	B;P;B	0.35872	0.424;0.525;0.167	B;B;B	0.28465	0.032;0.09;0.038	T	0.04373	-1.0956	10	0.51188	T	0.08	.	10.9474	0.47308	0.163:0.0:0.837:0.0	.	155;189;129	Q9HBY8-3;Q9HBY8;Q9HBY8-2	.;SGK2_HUMAN;.	H	129;129;128;128;129;189;155	ENSP00000362192:R129H;ENSP00000362184:R129H;ENSP00000362168:R128H;ENSP00000396222:R128H;ENSP00000392795:R129H;ENSP00000340608:R189H;ENSP00000412214:R155H	ENSP00000340608:R189H	R	+	2	0	SGK2	41632696	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.835000	0.48175	0.660000	0.30964	0.655000	0.94253	CGC	.	.	.	none		0.637	SGK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080383.1			A	42199282	G	A	42199282	3	1	276	1	0	0	0	0	1	0	0	0	14222	1087	38	1	588	1	SGK2	20	42199282	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	1233	42199282	20826238	100	17608											
SLC2A4RG	56731	hgsc.bcm.edu	37	chr20	62373951	62373951	+	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	ctaacccccagtcctgtcacAgtgaccgtgtctaccaggtg	8	9	9	15	1	2	1	1	1	1	0	3	1	3	1	5	1	2	0	5	1	2	2			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr20:62373951A>T	ENST00000266077.2	+	6	995	c.943A>T	c.(943-945)Agt>Tgt	p.S315C	RP4-583P15.10_ENST00000447343.2_RNA|RP4-583P15.10_ENST00000433905.2_RNA|SLC2A4RG_ENST00000493772.1_3'UTR	NM_020062.3	NP_064446.2	Q9NR83	S2A4R_HUMAN	SLC2A4 regulator	315					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|kidney(1)|lung(2)|prostate(2)|skin(1)	7	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					GTCCTGTCACAGTGACCGTGT	0.706																																					p.S315C		Atlas-SNP	.											.	SLC2A4RG	20	.	0			c.A943T						PASS	.						8	10	9					20																	62373951		1947	3998	5945	SO:0001583	missense	56731	exon6			TGTCACAGTGACC	AF249267	CCDS13537.1	20q13.33	2010-03-11			ENSG00000125520	ENSG00000125520			15930	protein-coding gene	gene with protein product	"GLUT4 enhancer factor", "Huntington's disease gene regulatory region-binding protein 1"	609493				10825161	Standard	NM_020062		Approved	GEF, HDBP1, Si-1-2, Si-1-2-19	uc002ygq.3	Q9NR83	OTTHUMG00000032997	ENST00000266077.2:c.943A>T	chr20.hg19:g.62373951A>T	ENSP00000266077:p.Ser315Cys	113.0	0.0	.		99.0	27.0	.	NM_020062	Q2PHL5|Q6F6I6|Q6F6I7|Q6GTK5|Q8TAH5|Q8WVW7|Q96QD3|Q9BV85	Missense_Mutation	SNP	ENST00000266077.2	hg19	CCDS13537.1	.	.	.	.	.	.	.	.	.	.	A	18.77	3.694866	0.68386	.	.	ENSG00000125520	ENST00000266077	T	0.50277	0.75	3.92	-1.6	0.08426	.	1.162140	0.06883	U	0.802854	T	0.50309	0.1608	L	0.55481	1.735	0.25308	N	0.989226	D	0.69078	0.997	P	0.57468	0.821	T	0.38650	-0.9651	10	0.54805	T	0.06	-35.2735	0.6983	0.00903	0.4697:0.1693:0.1973:0.1637	.	315	Q9NR83	S2A4R_HUMAN	C	315	ENSP00000266077:S315C	ENSP00000266077:S315C	S	+	1	0	SLC2A4RG	61844395	0.018000	0.18449	0.010000	0.14722	0.278000	0.26855	1.400000	0.34577	-0.793000	0.04475	0.260000	0.18958	AGT	.	.	.	none		0.706	SLC2A4RG-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080202.1	NM_020062		T	62373951	A	T	62373951	3	4	276	1	0	0	0	0	1	0	0	0	14560	188	7	5	965	5	SLC2A4RG	20	62373951	Missense_Mutation	SNP	A	TCGA-Y8-A896-01A-11D-A35Z-10	20174669	62373951	651569	101	17609											
MYT1	4661	hgsc.bcm.edu	37	chr20	62851316	62851316	+	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	caccaagcctagccgcctgaGagaggaggaacctgaggagg	12	3	15	11	1	0	3	0	2	0	1	0	7	0	6	5	4	3	0	5	4	3	1			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr20:62851316G>A	ENST00000328439.1	+	13	2586	c.2222G>A	c.(2221-2223)aGa>aAa	p.R741K	MYT1_ENST00000360149.4_Missense_Mutation_p.R443K|MYT1_ENST00000536311.1_Missense_Mutation_p.R768K	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(12)|liver(1)|lung(17)|ovary(5)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					AGCCGCCTGAGAGAGGAGGAA	0.662																																					p.R741K	GBM(59;481 1041 20555 21139 33705)	Atlas-SNP	.											.	MYT1	152	.	0			c.G2222A						PASS	.						13	12	12					20																	62851316		2088	4125	6213	SO:0001583	missense	4661	exon13			GCCTGAGAGAGGA	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.2222G>A	chr20.hg19:g.62851316G>A	ENSP00000327465:p.Arg741Lys	110.0	0.0	.		83.0	26.0	.	NM_004535	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000328439.1	hg19	CCDS13558.1	.	.	.	.	.	.	.	.	.	.	G	14.42	2.528721	0.44969	.	.	ENSG00000196132	ENST00000360149;ENST00000328439;ENST00000536311	T;T;T	0.42131	0.98;4.41;4.41	5.49	5.49	0.81192	Myelin transcription factor 1 (1);	0.137517	0.48767	D	0.000168	T	0.37945	0.1022	L	0.34521	1.04	0.44843	D	0.997853	B;B;B	0.32781	0.384;0.085;0.061	B;B;B	0.36534	0.227;0.086;0.047	T	0.09443	-1.0674	10	0.19147	T	0.46	-10.7664	19.3807	0.94532	0.0:0.0:1.0:0.0	.	768;741;443	F5H7M8;Q01538;Q6P6D5	.;MYT1_HUMAN;.	K	443;741;768	ENSP00000353269:R443K;ENSP00000327465:R741K;ENSP00000442412:R768K	ENSP00000327465:R741K	R	+	2	0	MYT1	62321760	1.000000	0.71417	0.112000	0.21494	0.991000	0.79684	4.913000	0.63341	2.575000	0.86900	0.561000	0.74099	AGA	.	.	.	none		0.662	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535		A	62851316	G	A	62851316	3	1	276	1	0	0	0	0	1	0	0	0	10113	942	33	2	2264	2	MYT1	20	62851316	Missense_Mutation	SNP	G	TCGA-Y8-A896-01A-11D-A35Z-10	477365	62851316	174204	102	17610											
UMODL1	89766	hgsc.bcm.edu	37	chr21	43529755	43529755	+	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	tggagggctcctacacctgcCagtgccgtaccaccagggac	8	6	12	15	1	0	0	0	0	0	0	1	2	1	2	6	3	4	2	6	3	2	2			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr21:43529755C>T	ENST00000408910.2	+	10	1603	c.1603C>T	c.(1603-1605)Cag>Tag	p.Q535*	C21orf128_ENST00000329015.2_5'Flank|UMODL1_ENST00000400424.2_Nonsense_Mutation_p.Q463*|UMODL1_ENST00000408989.2_Nonsense_Mutation_p.Q535*|UMODL1_ENST00000400427.1_Nonsense_Mutation_p.Q463*	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	535	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				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						CTACACCTGCCAGTGCCGTAC	0.692																																					p.Q535X	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.C1603T						PASS	.						44	56	52					21																	43529755		2037	4156	6193	SO:0001587	stop_gained	89766	exon10			ACCTGCCAGTGCC		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.1603C>T	chr21.hg19:g.43529755C>T	ENSP00000386147:p.Gln535*	48.0	0.0	.		34.0	8.0	.	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Nonsense_Mutation	SNP	ENST00000408910.2	hg19	CCDS42936.1	.	.	.	.	.	.	.	.	.	.	C	37	6.085419	0.97271	.	.	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910	.	.	.	3.23	2.32	0.28847	.	0.203527	0.22116	N	0.064402	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	-8.5657	8.3767	0.32447	0.0:0.758:0.242:0.0	.	.	.	.	X	463;463;535;535	.	ENSP00000383276:Q463X	Q	+	1	0	UMODL1	42402824	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	1.215000	0.32431	0.919000	0.36945	0.655000	0.94253	CAG	.	.	.	none		0.692	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2			T	43529755	C	T	43529755	4	4	276	1	0	0	0	0	0	1	0	0	16992	595	21	2	1641	2	UMODL1	21	43529755	Nonsense_Mutation	SNP	C	TCGA-Y8-A896-01A-11D-A35Z-10		43529755	4600140	103	17611											
NF2	4771	hgsc.bcm.edu	37	chr22	30060995	30060996	+	Frame_Shift_Ins	INS	-	-	GG																															cagtttactattaaaccactINSggataagaaaattgatgtct																								rs549225513		TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr22:30060995_30060996insGG	ENST00000338641.4	+	9	1268_1269	c.827_828insGG	c.(826-831)ctggatfs	p.D277fs	NF2_ENST00000361166.4_Frame_Shift_Ins_p.D277fs|NF2_ENST00000334961.7_Frame_Shift_Ins_p.D194fs|NF2_ENST00000361452.4_Frame_Shift_Ins_p.D236fs|NF2_ENST00000347330.5_Frame_Shift_Ins_p.D118fs|NF2_ENST00000403435.1_Frame_Shift_Ins_p.D277fs|NF2_ENST00000353887.4_Frame_Shift_Ins_p.D194fs|NF2_ENST00000413209.2_Intron|NF2_ENST00000361676.4_Frame_Shift_Ins_p.D235fs|NF2_ENST00000397789.3_Frame_Shift_Ins_p.D277fs|NF2_ENST00000403999.3_Frame_Shift_Ins_p.D277fs	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	277	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(3)|p.F271_L295del(1)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						ATTAAACCACTGGATAAGAAAA	0.386			"D, Mis, N, F, S, O"		"meningioma, acoustic neuroma, renal "	"meningioma, acoustic neuroma"			Neurofibromatosis, type 2																												p.L276fs		Atlas-Indel,Pindel	.	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	.	NF2	1312	.	4	Unknown(3)|Deletion - In frame(1)	central_nervous_system(2)|large_intestine(1)|stomach(1)	c.827_828insGG						PASS	.																																			SO:0001589	frameshift_variant	4771	exon9	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	.	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"A-kinase anchor proteins"	7773	protein-coding gene	gene with protein product	"moesin-ezrin-radixin like", "schwannomin"	607379	"neurofibromin 2 (bilateral acoustic neuroma)"			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.828_829dupGG	chr22.hg19:g.30060996_30060997dupGG	ENSP00000344666:p.Asp277fs	155.0	0.0	0		84.0	36.0	0.428571	NM_181832	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Frame_Shift_Ins	INS	ENST00000338641.4	hg19	CCDS13861.1																																																																																			.	.	.	none		0.386	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3	NM_000268		GG	30060996	-	GG	30060995	7	5	276	1	0	1	1	0	0	0	0	0	10364	1580	55	0	861	0	NF2	22	30060995	Frame_Shift_Ins	INS	-	TCGA-Y8-A896-01A-11D-A35Z-10		30060995	21243571	104	17612											
NCF4	4689	hgsc.bcm.edu	37	chr22	37266586	37266587	+	Splice_Site	DEL	TA	TA	-																															gcccgcgcacccggaaagtgTaagtgaccagcccctgggct																										TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chr22:37266586_37266587delTA	ENST00000248899.6	+	5	654		c.e5+2		CTA-833B7.2_ENST00000431290.1_RNA|CTA-833B7.2_ENST00000330602.2_RNA|NCF4_ENST00000397147.4_Splice_Site	NM_000631.4	NP_000622.2	Q15080	NCF4_HUMAN	neutrophil cytosolic factor 4, 40kDa						antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|interaction with host (GO:0051701)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|positive regulation of catalytic activity (GO:0043085)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|membrane (GO:0016020)|NADPH oxidase complex (GO:0043020)|phagolysosome (GO:0032010)	phosphatidylinositol-3-phosphate binding (GO:0032266)|protein dimerization activity (GO:0046983)|superoxide-generating NADPH oxidase activator activity (GO:0016176)			cervix(1)|endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16					Dextromethorphan(DB00514)	CCGGAAAGTGTAAGTGACCAGC	0.589																																					.		Atlas-INDEL	.											.	NCF4	66	.	0			.						PASS	.																																			SO:0001630	splice_region_variant	4689	.			.	X77094	CCDS13934.1, CCDS13935.1	22q13.1	2014-09-17	2002-08-29		ENSG00000100365	ENSG00000100365			7662	protein-coding gene	gene with protein product	"neutrophil NADPH oxidase factor 4"	601488	"neutrophil cytosolic factor 4 (40kD)"			8839867	Standard	NM_013416		Approved	p40phox, SH3PXD4	uc003apy.4	Q15080	OTTHUMG00000150548	ENST00000248899.6:c.470+2TA>-	chr22.hg19:g.37266586_37266587delTA		43.0	0.0	0		29.0	11.0	0.37931	.	A8K4F9|O60808|Q86U56|Q9BU98|Q9NP45	Splice_Site	DEL	ENST00000248899.6	hg19	CCDS13934.1																																																																																			.	.	.	none		0.589	NCF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318863.1	NM_000631	Intron	-	37266587	TA	-	37266586	8	5	276	1	0	1	0	1	0	0	1	0	10225	1652	57	0	490	0	NCF4	22	37266586	Splice_Site	DEL	TA	TCGA-Y8-A896-01A-11D-A35Z-10	7205591	37266586	14037980	105	17613											
OGT	8473	hgsc.bcm.edu	37	chrX	70756180	70756180	+	Missense_Mutation	SNP	A	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	tgcttttattactttcatctAtacacttccagtgtcgaagg	9	17	6	9	1	2	0	1	0	1	0	4	1	3	0	1	1	3	1	1	1	5	7			TCGA-Y8-A896-01A-11D-A35Z-10	TCGA-Y8-A896-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1d456468-7272-4470-892b-437ed167c716	35a2ebd1-9aa7-4978-92e8-f2b148b69622	g.chrX:70756180A>C	ENST00000373719.3	+	2	407	c.190A>C	c.(190-192)Ata>Cta	p.I64L	OGT_ENST00000373701.3_Missense_Mutation_p.I54L|OGT_ENST00000498566.1_3'UTR	NM_181672.2|NM_181673.2	NP_858058.1|NP_858059.1	O15294	OGT1_HUMAN	O-linked N-acetylglucosamine (GlcNAc) transferase	64					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)					ACTTTCATCTATACACTTCCA	0.463																																					p.I64L		Atlas-SNP	.											.	OGT	207	.	0			c.A190C						PASS	.						98	70	79					X																	70756180		2203	4300	6503	SO:0001583	missense	8473	exon2			TCATCTATACACT	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.190A>C	chrX.hg19:g.70756180A>C	ENSP00000362824:p.Ile64Leu	102.0	0.0	.		79.0	46.0	.	NM_181672	Q7Z3K0|Q8WWM8|Q96CC1|Q9UG57	Missense_Mutation	SNP	ENST00000373719.3	hg19	CCDS14414.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.502221	0.85176	.	.	ENSG00000147162	ENST00000373719;ENST00000373701;ENST00000444774	T;T;T	0.72167	0.47;-0.63;1.22	5.22	5.22	0.72569	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	D	0.82623	0.5077	M	0.71206	2.165	0.80722	D	1	B;P;B	0.41748	0.0;0.761;0.001	B;D;B	0.68483	0.0;0.958;0.025	T	0.80195	-0.1483	10	0.27785	T	0.31	-7.2745	14.2165	0.65797	1.0:0.0:0.0:0.0	.	64;54;64	B4DTL6;O15294-3;O15294	.;.;OGT1_HUMAN	L	64;54;47	ENSP00000362824:I64L;ENSP00000362805:I54L;ENSP00000399729:I47L	ENSP00000362805:I54L	I	+	1	0	OGT	70672905	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.929000	0.92859	1.932000	0.55993	0.430000	0.28490	ATA	.	.	.	none		0.463	OGT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000081829.3	NM_003605, NM_181672		C	70756180	A	C	70756180	3	2	276	1	0	0	0	0	1	0	0	0	10854	449	16	5	196	5	OGT	23	70756180	Missense_Mutation	SNP	A	TCGA-Y8-A896-01A-11D-A35Z-10		70756180	84514380	106	17614											
EXTL1	2134	hgsc.bcm.edu	37	chr1	26358007	26358007	+	Frame_Shift_Del	DEL	C	C	-																															gggtggggcccccaggccagCcccctctgaagctcatccag																										TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr1:26358007delC	ENST00000374280.3	+	6	2158	c.1291delC	c.(1291-1293)cccfs	p.P432fs	EXTL1_ENST00000484339.1_3'UTR	NM_004455.2	NP_004446.2	Q92935	EXTL1_HUMAN	exostosin-like glycosyltransferase 1	432					protein glycosylation (GO:0006486)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|stomach(1)|urinary_tract(1)	23		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00594)|READ - Rectum adenocarcinoma(331;0.0649)		CCCAGGCCAGCCCCCTCTGAA	0.662																																					p.Q430fs		Atlas-Indel,Pindel	.											.	EXTL1	61	.	0			c.1290delG						PASS	.						12	15	14					1																	26358007		2197	4291	6488	SO:0001589	frameshift_variant	2134	exon6			.	U67191	CCDS271.1	1p36.1	2013-03-01	2013-03-01		ENSG00000158008	ENSG00000158008	2.4.1.224	"Exostosin glycosyltransferase family"	3515	protein-coding gene	gene with protein product	"glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase", "alpha-N-acetylglucosaminyltransferase II", "glucuronyl-N-acetylglucosaminylproteoglycan alpha-1,4-N- acetylglucosaminyltransferase", "exostosin-L"	601738	"exostoses (multiple)-like 1"			9037597	Standard	NM_004455		Approved	EXTL, MGC70794	uc001blf.3	Q92935	OTTHUMG00000007509	ENST00000374280.3:c.1291delC	chr1.hg19:g.26358007delC	ENSP00000363398:p.Pro432fs	168.0	0.0	0		118.0	43.0	0.364407	NM_004455	Q6GSC1	Frame_Shift_Del	DEL	ENST00000374280.3	hg19	CCDS271.1																																																																																			.	.	.	none		0.662	EXTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019749.1	NM_004455		-	26358007	C	-	26358007	7	5	277	1	0	1	0	1	0	0	0	0	5327	739	26	0	1313	0	EXTL1	1	26358007	Frame_Shift_Del	DEL	C	TCGA-Y8-A897-01A-11D-A35Z-10		26358007	222892614	1	17615											
AKR1A1	10327	hgsc.bcm.edu	37	chr1	46034873	46034873	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctaaatgccctgaacaaaaAttggagatatattgtgccta	15	11	8	7	0	0	2	0	1	0	1	0	3	0	2	2	1	3	1	2	1	8	6			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr1:46034873A>G	ENST00000372070.3	+	9	1631	c.884A>G	c.(883-885)aAt>aGt	p.N295S	AKR1A1_ENST00000473038.1_3'UTR|AKR1A1_ENST00000351829.4_Missense_Mutation_p.N295S	NM_001202413.1|NM_001202414.1|NM_006066.3	NP_001189342.1|NP_001189343.1|NP_006057.1	P14550	AK1A1_HUMAN	aldo-keto reductase family 1, member A1 (aldehyde reductase)	295					aldehyde catabolic process (GO:0046185)|cellular aldehyde metabolic process (GO:0006081)|D-glucuronate catabolic process (GO:0042840)|glucose metabolic process (GO:0006006)|L-ascorbic acid biosynthetic process (GO:0019853)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|electron carrier activity (GO:0009055)|L-glucuronate reductase activity (GO:0047939)			lung(3)|prostate(1)|urinary_tract(1)	5	Acute lymphoblastic leukemia(166;0.155)				Doxorubicin(DB00997)	CTGAACAAAAATTGGAGATAT	0.483																																					p.N295S		Atlas-SNP	.											.	AKR1A1	25	.	0			c.A884G						PASS	.						122	118	119					1																	46034873		2203	4300	6503	SO:0001583	missense	10327	exon9			ACAAAAATTGGAG	J04794	CCDS523.1	1p33-p32	2010-04-08			ENSG00000117448	ENSG00000117448	1.1.1.2	"Aldo-keto reductases"	380	protein-coding gene	gene with protein product	"dihydrodiol dehydrogenase 3"	103830				2498333, 10393438	Standard	NM_001202414		Approved	ALR, DD3	uc001coe.3	P14550	OTTHUMG00000007740	ENST00000372070.3:c.884A>G	chr1.hg19:g.46034873A>G	ENSP00000361140:p.Asn295Ser	113.0	0.0	.		112.0	37.0	.	NM_001202413	A8KAL8|D3DQ04|Q6IAZ4	Missense_Mutation	SNP	ENST00000372070.3	hg19	CCDS523.1	.	.	.	.	.	.	.	.	.	.	A	17.53	3.412079	0.62511	.	.	ENSG00000117448	ENST00000372070;ENST00000351829	T;T	0.31247	1.5;1.5	6.04	6.04	0.98038	NADP-dependent oxidoreductase domain (2);	0.088191	0.85682	D	0.000000	T	0.22589	0.0545	N	0.14661	0.345	0.47737	D	0.999502	B	0.13145	0.007	B	0.08055	0.003	T	0.03202	-1.1061	10	0.72032	D	0.01	.	16.6349	0.85050	1.0:0.0:0.0:0.0	.	295	P14550	AK1A1_HUMAN	S	295	ENSP00000361140:N295S;ENSP00000312606:N295S	ENSP00000312606:N295S	N	+	2	0	AKR1A1	45807460	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.649000	0.74364	2.330000	0.79161	0.477000	0.44152	AAT	.	.	.	none		0.483	AKR1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020851.1	NM_006066		G	46034873	A	G	46034873	3	3	277	1	0	0	0	0	1	0	0	0	465	101	4	3	910	3	AKR1A1	1	46034873	Missense_Mutation	SNP	A	TCGA-Y8-A897-01A-11D-A35Z-10	19676866	46034873	203215748	2	17616											
GDAP2	54834	hgsc.bcm.edu	37	chr1	118420604	118420614	+	Intron	DEL	TGAGGGAGAAC	TGAGGGAGAAC	-																															agttaatataccataccaggTgagggagaacttctggtact																								rs549457373		TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	TGAGGGAGAAC	TGAGGGAGAAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr1:118420604_118420614delTGAGGGAGAAC	ENST00000369443.5	-	13	1696				GDAP2_ENST00000369442.3_Frame_Shift_Del_p.SSPS488fs	NM_017686.3	NP_060156.1	Q9NXN4	GDAP2_HUMAN	ganglioside induced differentiation associated protein 2						response to retinoic acid (GO:0032526)	lysosomal membrane (GO:0005765)				kidney(2)|large_intestine(3)|lung(9)|ovary(2)	16		all_cancers(81;0.0156)|all_lung(203;5.81e-05)|Lung NSC(69;0.000446)|all_epithelial(167;0.00295)		Lung(183;0.0583)|LUSC - Lung squamous cell carcinoma(189;0.194)		CCATACCAGGTGAGGGAGAACTTCTGGTACT	0.408																																					p.488_492del		Atlas-Indel,Pindel	.											.	GDAP2	37	.	0			c.1464_1474del						PASS	.																																			SO:0001627	intron_variant	54834	exon13			.	AK000149	CCDS897.1, CCDS44201.1	1q11	2011-10-20			ENSG00000196505	ENSG00000196505			18010	protein-coding gene	gene with protein product						1021725	Standard	NM_017686		Approved	FLJ20142, dJ776P7.1, MACROD3	uc001ehf.3	Q9NXN4	OTTHUMG00000012199	ENST00000369443.5:c.1446+16GTTCTCCCTCA>-	chr1.hg19:g.118420604_118420614delTGAGGGAGAAC		63.0	0.0	0		92.0	31.0	0.336957	NM_001135589	Q96DZ0	Frame_Shift_Del	DEL	ENST00000369443.5	hg19	CCDS897.1																																																																																			.	.	.	none		0.408	GDAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033732.2	NM_017686		-	118420614	TGAGGGAGAAC	-	118420604	6	5	277	0	1	1	0	1	0	0	0	0	6316	1683	59	0		0	GDAP2	1	118420604	Intron	DEL	TGAGGGAGAAC	TCGA-Y8-A897-01A-11D-A35Z-10	72385731	118420604	130830017	3	17617											
SETDB1	9869	hgsc.bcm.edu	37	chr1	150915165	150915168	+	Splice_Site	DEL	GTAT	GTAT	-																															tattgccatccagacagttgGtatgtgcaaacttggaggaa																										TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	GTAT	GTAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr1:150915165_150915168delGTAT	ENST00000271640.5	+	6	863		c.e6+1		SETDB1_ENST00000368963.1_Splice_Site|SETDB1_ENST00000368962.2_Splice_Site|SETDB1_ENST00000459773.1_Intron|SETDB1_ENST00000368969.4_Splice_Site	NM_001145415.1|NM_012432.3	NP_001138887.1|NP_036564.3	Q15047	SETB1_HUMAN	SET domain, bifurcated 1						bone development (GO:0060348)|histone H3-K9 trimethylation (GO:0036124)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)			CAGACAGTTGGTATGTGCAAACTT	0.475																																					p.225_225del		Atlas-INDEL	.											.	SETDB1	204	.	0			c.673_673del						PASS	.																																			SO:0001630	splice_region_variant	9869	exon6			.	D31891	CCDS972.1, CCDS44217.1, CCDS58026.1	1q21	2013-01-23			ENSG00000143379	ENSG00000143379		"Chromatin-modifying enzymes / K-methyltransferases", "Tudor domain containing"	10761	protein-coding gene	gene with protein product	"tudor domain containing 21"	604396				10343109	Standard	NM_001145415		Approved	KG1T, KIAA0067, ESET, KMT1E, TDRD21	uc001evu.2	Q15047	OTTHUMG00000035003	ENST00000271640.5:c.673+1GTAT>-	chr1.hg19:g.150915165_150915168delGTAT		78.0	0.0	0		110.0	34.0	0.309091	NM_012432	A6NEW2|Q5SZD8|Q5SZD9|Q5SZE0|Q5SZE7|Q96GM9	Frame_Shift_Del	DEL	ENST00000271640.5	hg19	CCDS44217.1																																																																																			.	.	.	none		0.475	SETDB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084717.2		Intron	-	150915168	GTAT	-	150915165	8	5	277	1	0	1	0	1	0	0	1	0	14151	1275	44	0	692	0	SETDB1	1	150915165	Splice_Site	DEL	GTAT	TCGA-Y8-A897-01A-11D-A35Z-10	32494561	150915165	98335456	4	17618	183	2									
SETDB1	9869	hgsc.bcm.edu	37	chr1	150915166	150915170	+	Splice_Site	DEL	TATGT	TATGT	-																															attgccatccagacagttggTatgtgcaaacttggaggaac																										TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	TATGT	TATGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr1:150915166_150915170delTATGT	ENST00000271640.5	+	6	863		c.e6+2		SETDB1_ENST00000368963.1_Splice_Site|SETDB1_ENST00000368962.2_Splice_Site|SETDB1_ENST00000459773.1_Intron|SETDB1_ENST00000368969.4_Splice_Site	NM_001145415.1|NM_012432.3	NP_001138887.1|NP_036564.3	Q15047	SETB1_HUMAN	SET domain, bifurcated 1						bone development (GO:0060348)|histone H3-K9 trimethylation (GO:0036124)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)			AGACAGTTGGTATGTGCAAACTTGG	0.478																																					.		Pindel	.											.	SETDB1	204	.	0			.						PASS	.																																			SO:0001630	splice_region_variant	9869	.			.	D31891	CCDS972.1, CCDS44217.1, CCDS58026.1	1q21	2013-01-23			ENSG00000143379	ENSG00000143379		"Chromatin-modifying enzymes / K-methyltransferases", "Tudor domain containing"	10761	protein-coding gene	gene with protein product	"tudor domain containing 21"	604396				10343109	Standard	NM_001145415		Approved	KG1T, KIAA0067, ESET, KMT1E, TDRD21	uc001evu.2	Q15047	OTTHUMG00000035003	ENST00000271640.5:c.673+2TATGT>-	chr1.hg19:g.150915166_150915170delTATGT		79.0	0.0	.		109.0	27.0	0.248	.	A6NEW2|Q5SZD8|Q5SZD9|Q5SZE0|Q5SZE7|Q96GM9	Splice_Site	DEL	ENST00000271640.5	hg19	CCDS44217.1																																																																																			.	.	.	none		0.478	SETDB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084717.2		Intron	-	150915170	TATGT	-	150915166	8	5	277	1	0	1	0	1	0	0	1	0	14151	1652	57	0	693	0	SETDB1	1	150915166	Splice_Site	DEL	TATGT	TCGA-Y8-A897-01A-11D-A35Z-10	1	150915166	98335455	5	17619	183	2									
PEAR1	375033	hgsc.bcm.edu	37	chr1	156878561	156878561	+	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	tgccaggagcactgtctctgCctgcacggtggcgtctgcca	5	9	13	14	2	2	0	0	0	2	0	3	1	2	1	3	3	5	2	3	3	0	0			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr1:156878561C>T	ENST00000338302.3	+	11	1455	c.1230C>T	c.(1228-1230)tgC>tgT	p.C410C	PEAR1_ENST00000292357.7_Silent_p.C410C			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	410	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076}.				recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					ACTGTCTCTGCCTGCACGGTG	0.711																																					p.C410C		Atlas-SNP	.											.	PEAR1	118	.	0			c.C1230T						PASS	.						20	18	18					1																	156878561		2191	4287	6478	SO:0001819	synonymous_variant	375033	exon10			TCTCTGCCTGCAC	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.1230C>T	chr1.hg19:g.156878561C>T		94.0	0.0	.		51.0	12.0	.	NM_001080471	Q8TEK2	Silent	SNP	ENST00000338302.3	hg19	CCDS30892.1																																																																																			.	.	.	none		0.711	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471		T	156878561	C	T	156878561	2	4	277	1	0	0	0	0	0	0	0	1	11719	747	26	2		2	PEAR1	1	156878561	Silent	SNP	C	TCGA-Y8-A897-01A-11D-A35Z-10	5963395	156878561	92372060	6	17620											
C1orf9	51430	hgsc.bcm.edu	37	chr1	172543034	172543034	+	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	ttttgttctttttgaaggttTgttattgaactttgtgaacc	7	22	8	4	0	1	3	0	3	1	0	1	3	1	3	1	1	2	3	1	1	4	9			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr1:172543034T>A	ENST00000263688.3	+	10	1272	c.1053T>A	c.(1051-1053)ttT>ttA	p.F351L	SUCO_ENST00000367723.4_Missense_Mutation_p.F509L|SUCO_ENST00000610051.1_Missense_Mutation_p.F314L|SUCO_ENST00000608151.1_Missense_Mutation_p.F510L	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	351	SUN. {ECO:0000255|PROSITE- ProRule:PRU00802}.				multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											TTTGAAGGTTTGTTATTGAAC	0.264																																					p.F351L		Atlas-SNP	.											.	.	.	.	0			c.T1053A						PASS	.						49	53	52					1																	172543034		2199	4287	6486	SO:0001583	missense	51430	exon10			AAGGTTTGTTATT	AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"SUN-like protein 1", "osteopotentia"		"chromosome 1 open reading frame 9"	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.1053T>A	chr1.hg19:g.172543034T>A	ENSP00000263688:p.Phe351Leu	25.0	0.0	.		61.0	15.0	.	NM_014283	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Missense_Mutation	SNP	ENST00000263688.3	hg19	CCDS1303.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.038021	0.75617	.	.	ENSG00000094975	ENST00000367723;ENST00000263688	T;T	0.39592	1.07;1.07	5.44	4.32	0.51571	Galactose-binding domain-like (1);Sad1/UNC-like, C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.44138	0.1279	L	0.47078	1.49	0.80722	D	1	D;P;D;D	0.76494	0.992;0.861;0.999;0.999	D;P;D;D	0.87578	0.987;0.89;0.998;0.998	T	0.49021	-0.8982	10	0.87932	D	0	-19.703	10.1906	0.43024	0.0:0.0795:0.0:0.9205	.	314;351;510;351	B4DYM4;B4DZJ3;Q5H945;Q9UBS9	.;.;.;OSPT_HUMAN	L	510;351	ENSP00000356696:F510L;ENSP00000263688:F351L	ENSP00000263688:F351L	F	+	3	2	C1orf9	170809657	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.414000	0.52693	0.897000	0.36392	0.383000	0.25322	TTT	.	.	.	none		0.264	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227		A	172543034	T	A	172543034	3	1	277	1	0	0	0	0	1	0	0	0	2069	1809	63	5	1091	5	C1orf9	1	172543034	Missense_Mutation	SNP	T	TCGA-Y8-A897-01A-11D-A35Z-10	15664473	172543034	76707587	7	17621											
USH2A	7399	hgsc.bcm.edu	37	chr1	216495239	216495239	+	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	actcacatgaagtccttcagTgaagctctcctgggagcaga	11	9	10	11	0	3	3	2	2	1	1	5	4	4	4	2	1	2	2	2	1	2	1			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr1:216495239T>A	ENST00000307340.3	-	9	2016	c.1630A>T	c.(1630-1632)Act>Tct	p.T544S	USH2A_ENST00000366942.3_Missense_Mutation_p.T544S|USH2A_ENST00000366943.2_Missense_Mutation_p.T544S	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	544	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)		AGTCCTTCAGTGAAGCTCTCC	0.413										HNSCC(13;0.011)																											p.T544S		Atlas-SNP	.											.	USH2A	1168	.	0			c.A1630T						PASS	.						153	141	145					1																	216495239		2203	4300	6503	SO:0001583	missense	7399	exon9			CTTCAGTGAAGCT	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.1630A>T	chr1.hg19:g.216495239T>A	ENSP00000305941:p.Thr544Ser	72.0	0.0	.		113.0	42.0	.	NM_007123	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.029846	0.75504	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.64438	-0.1;-0.1;-0.1	5.65	4.49	0.54785	EGF-like, laminin (3);	0.000000	0.43579	U	0.000554	D	0.86451	0.5936	H	0.98466	4.24	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.87578	0.992;0.998	D	0.90034	0.4137	10	0.87932	D	0	.	12.6812	0.56922	0.0:0.0:0.1379:0.8621	.	544;544	O75445-2;O75445	.;USH2A_HUMAN	S	544	ENSP00000305941:T544S;ENSP00000355910:T544S;ENSP00000355909:T544S	ENSP00000305941:T544S	T	-	1	0	USH2A	214561862	1.000000	0.71417	0.960000	0.40013	0.643000	0.38383	4.814000	0.62627	0.911000	0.36747	0.455000	0.32223	ACT	.	.	.	none		0.413	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		A	216495239	T	A	216495239	3	1	277	1	0	0	0	0	1	0	0	0	17048	1696	59	5	14248	5	USH2A	1	216495239	Missense_Mutation	SNP	T	TCGA-Y8-A897-01A-11D-A35Z-10	43952205	216495239	32755382	8	17622											
NUP133	55746	hgsc.bcm.edu	37	chr1	229631660	229631660	+	Missense_Mutation	SNP	T	T	A																															caaatagcatcggtaatgttTtccttcagggctctatttat																										TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr1:229631660T>A	ENST00000261396.3	-	7	1045	c.954A>T	c.(952-954)gaA>gaT	p.E318D	NUP133_ENST00000537506.1_Missense_Mutation_p.E302D	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	318					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)				CGGTAATGTTTTCCTTCAGGG	0.333																																					p.E318D		Atlas-SNP	.											.	NUP133	111	.	0			c.A954T						PASS	.						121	122	122					1																	229631660		2203	4300	6503	SO:0001583	missense	55746	exon7			AATGTTTTCCTTC		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.954A>T	chr1.hg19:g.229631660T>A	ENSP00000261396:p.Glu318Asp	21.0	0.0	.		33.0	13.0	.	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Missense_Mutation	SNP	ENST00000261396.3	hg19	CCDS1579.1	.	.	.	.	.	.	.	.	.	.	T	14.25	2.480586	0.44044	.	.	ENSG00000069248	ENST00000366681;ENST00000261396;ENST00000366679;ENST00000537506	T;T;T	0.26518	1.73;1.73;1.73	5.57	-5.85	0.02311	WD40/YVTN repeat-like-containing domain (1);Nucleoporin, Nup133/Nup155-like, N-terminal (1);	0.045027	0.85682	D	0.000000	T	0.25419	0.0618	L	0.44542	1.39	0.47819	D	0.999526	P	0.46784	0.884	P	0.50490	0.642	T	0.10613	-1.0622	10	0.30854	T	0.27	-4.8162	14.423	0.67196	0.0:0.5307:0.0:0.4693	.	318	Q8WUM0	NU133_HUMAN	D	318;318;318;302	ENSP00000261396:E318D;ENSP00000355640:E318D;ENSP00000443496:E302D	ENSP00000261396:E318D	E	-	3	2	NUP133	227698283	0.689000	0.27690	0.051000	0.19133	0.954000	0.61252	-0.292000	0.08332	-1.201000	0.02659	-0.263000	0.10527	GAA	.	.	.	none		0.333	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230		A	229631660	T	A	229631660	3	1	277	1	0	0	0	0	1	0	0	0	10761	1838	64	5	2596	5	NUP133	1	229631660	Missense_Mutation	SNP	T	TCGA-Y8-A897-01A-11D-A35Z-10	13136421	229631660	19618961	9	17623	184	2									
NUP133	55746	hgsc.bcm.edu	37	chr1	229631662	229631662	+	Frame_Shift_Del	DEL	C	C	-																															aatagcatcggtaatgttttCcttcagggctctatttatat																										TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr1:229631662delC	ENST00000261396.3	-	7	1043	c.952delG	c.(952-954)gaafs	p.E318fs	NUP133_ENST00000537506.1_Frame_Shift_Del_p.E302fs	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	318					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)				GTAATGTTTTCCTTCAGGGCT	0.333																																					p.E318fs		Atlas-INDEL	.											.	NUP133	111	.	0			c.953delA						PASS	.						120	121	121					1																	229631662		2203	4300	6503	SO:0001589	frameshift_variant	55746	exon7			.		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.952delG	chr1.hg19:g.229631662delC	ENSP00000261396:p.Glu318fs	20.0	0.0	0		34.0	14.0	0.411765	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Frame_Shift_Del	DEL	ENST00000261396.3	hg19	CCDS1579.1																																																																																			.	.	.	none		0.333	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230		-	229631662	C	-	229631662	7	5	277	1	0	1	0	1	0	0	0	0	10761	864	30	0	2598	0	NUP133	1	229631662	Frame_Shift_Del	DEL	C	TCGA-Y8-A897-01A-11D-A35Z-10	2	229631662	19618959	10	17624	184	2									
PREPL	9581	hgsc.bcm.edu	37	chr2	44549877	44549877	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggggtctcctaccttcaccTgtgtccttagcatgctccgc	4	12	10	15	1	2	0	1	0	1	0	5	0	4	0	5	2	3	2	5	2	2	3			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr2:44549877T>C	ENST00000409936.1	-	13	2450	c.2013A>G	c.(2011-2013)acA>acG	p.T671T	PREPL_ENST00000409272.1_Silent_p.T671T|PREPL_ENST00000378520.3_Silent_p.T605T|PREPL_ENST00000409411.1_Silent_p.T582T|PREPL_ENST00000378511.3_Silent_p.T609T|PREPL_ENST00000541738.1_Silent_p.T582T|PREPL_ENST00000409957.1_Silent_p.T582T|PREPL_ENST00000260648.6_Silent_p.T671T|PREPL_ENST00000410081.1_Silent_p.T671T	NM_001171606.1	NP_001165077.1	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like	671						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)				TACCTTCACCTGTGTCCTTAG	0.468																																					p.T671T		Atlas-SNP	.											.	PREPL	69	.	0			c.A2013G						PASS	.						218	209	212					2																	44549877		2203	4300	6503	SO:0001819	synonymous_variant	9581	exon13			TTCACCTGTGTCC	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.2013A>G	chr2.hg19:g.44549877T>C		54.0	0.0	.		95.0	35.0	.	NM_001171603	A7E2X6|D6W5A3|O43163|Q4J6C3|Q4J6C4|Q4ZG39|Q6ZMW7|Q96DW7	Silent	SNP	ENST00000409936.1	hg19	CCDS33190.1	.	.	.	.	.	.	.	.	.	.	T	8.440	0.850530	0.17034	.	.	ENSG00000138078	ENST00000420756	.	.	.	5.42	-10.8	0.00216	.	.	.	.	.	T	0.14098	0.0341	.	.	.	0.09310	N	0.99999	.	.	.	.	.	.	T	0.07829	-1.0752	4	.	.	.	1.8666	1.7996	0.03068	0.1889:0.2778:0.3326:0.2007	.	.	.	.	R	53	.	.	Q	-	2	0	PREPL	44403381	0.000000	0.05858	0.000000	0.03702	0.264000	0.26372	-2.011000	0.01452	-3.526000	0.00147	-0.256000	0.11100	CAG	.	.	.	none		0.468	PREPL-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327900.1	NM_006036		C	44549877	T	C	44549877	2	2	277	1	0	0	0	0	0	0	0	1	12485	1567	55	3		3	PREPL	2	44549877	Silent	SNP	T	TCGA-Y8-A897-01A-11D-A35Z-10		44549877	198649496	11	17625											
GPD2	2820	hgsc.bcm.edu	37	chr2	157407170	157407170	+	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	atgccacgggacctttcacgGactctgtgcgcaaaatggat	10	9	11	11	3	2	0	1	0	1	0	2	3	2	3	2	3	2	1	2	3	2	1			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr2:157407170G>A	ENST00000310454.6	+	8	1255	c.883G>A	c.(883-885)Gac>Aac	p.D295N	GPD2_ENST00000409125.4_Missense_Mutation_p.D68N|GPD2_ENST00000409674.1_Missense_Mutation_p.D295N|GPD2_ENST00000438166.2_Missense_Mutation_p.D295N|GPD2_ENST00000540309.1_Missense_Mutation_p.D295N	NM_001083112.2	NP_001076581.2	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2 (mitochondrial)	295					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						ACCTTTCACGGACTCTGTGCG	0.463																																					p.D295N		Atlas-SNP	.											.	GPD2	59	.	0			c.G883A						PASS	.						130	113	119					2																	157407170		2203	4300	6503	SO:0001583	missense	2820	exon8			TTCACGGACTCTG		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.883G>A	chr2.hg19:g.157407170G>A	ENSP00000308610:p.Asp295Asn	54.0	0.0	.		65.0	20.0	.	NM_001083112	A8K4V0|B3KSA9|Q59FR1|Q9HAP9	Missense_Mutation	SNP	ENST00000310454.6	hg19	CCDS2202.1	.	.	.	.	.	.	.	.	.	.	G	36	5.650365	0.96714	.	.	ENSG00000115159	ENST00000310454;ENST00000409125;ENST00000438166;ENST00000540309;ENST00000409674	D;D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54;-1.54	5.68	5.68	0.88126	FAD dependent oxidoreductase (1);	0.041854	0.85682	N	0.000000	D	0.92642	0.7662	M	0.86651	2.83	0.80722	D	1	B	0.24920	0.114	P	0.56278	0.795	D	0.91028	0.4862	10	0.87932	D	0	.	19.7855	0.96434	0.0:0.0:1.0:0.0	.	295	P43304	GPDM_HUMAN	N	295;68;295;295;295	ENSP00000308610:D295N;ENSP00000386484:D68N;ENSP00000409708:D295N;ENSP00000440892:D295N;ENSP00000386425:D295N	ENSP00000308610:D295N	D	+	1	0	GPD2	157115416	1.000000	0.71417	0.994000	0.49952	0.958000	0.62258	9.824000	0.99380	2.675000	0.91044	0.563000	0.77884	GAC	.	.	.	none		0.463	GPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254910.3			A	157407170	G	A	157407170	3	1	277	1	0	0	0	0	1	0	0	0	6613	1174	41	2	909	2	GPD2	2	157407170	Missense_Mutation	SNP	G	TCGA-Y8-A897-01A-11D-A35Z-10	112857293	157407170	85792203	12	17626											
ABCB6	10058	hgsc.bcm.edu	37	chr2	220081117	220081117	+	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	gtgccacccccctggaggaaCttgaggaagacgtaactggt	10	7	13	11	1	0	2	0	1	0	1	0	5	0	5	4	4	3	1	4	4	3	2			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr2:220081117C>G	ENST00000265316.3	-	4	1255	c.939G>C	c.(937-939)aaG>aaC	p.K313N	ABCB6_ENST00000439002.2_Missense_Mutation_p.K267N	NM_005689.2	NP_005680.1	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 6 (Langereis blood group)	313	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				brain development (GO:0007420)|cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|porphyrin-containing compound biosynthetic process (GO:0006779)|skin development (GO:0043588)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial envelope (GO:0005740)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|efflux transmembrane transporter activity (GO:0015562)|heme binding (GO:0020037)|heme transporter activity (GO:0015232)|heme-transporting ATPase activity (GO:0015439)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	34		Renal(207;0.0474)		Epithelial(149;1.22e-06)|all cancers(144;0.000201)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCTGGAGGAACTTGAGGAAGA	0.562																																					p.K313N		Atlas-SNP	.											.	ABCB6	76	.	0			c.G939C						PASS	.						96	104	101					2																	220081117		2203	4300	6503	SO:0001583	missense	10058	exon4			GAGGAACTTGAGG	AF070598	CCDS2436.1	2q36	2014-08-27	2014-08-27		ENSG00000115657	ENSG00000115657		"ATP binding cassette transporters / subfamily B"	47	protein-coding gene	gene with protein product	"ATP-binding cassette half-transporter"	605452	"ATP-binding cassette, sub-family B (MDR/TAP), member 6"			8894702, 9110174	Standard	NM_005689		Approved	EST45597, umat, MTABC3	uc002vkc.2	Q9NP58	OTTHUMG00000133131	ENST00000265316.3:c.939G>C	chr2.hg19:g.220081117C>G	ENSP00000265316:p.Lys313Asn	144.0	0.0	.		151.0	46.0	.	NM_005689	O75542|Q49A66|Q59GQ5|Q6ZME6|Q96ME8|Q9HAQ6|Q9HAQ7	Missense_Mutation	SNP	ENST00000265316.3	hg19	CCDS2436.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.1|25.1	4.601897|4.601897	0.87055|0.87055	.|.	.|.	ENSG00000115657|ENSG00000115657	ENST00000265316;ENST00000439002|ENST00000295750	D;D|.	0.94497|.	-3.39;-3.44|.	5.17|5.17	4.28|4.28	0.50868|0.50868	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|.	T|T	0.78604|0.78604	0.4309|0.4309	M|M	0.86343|0.86343	2.81|2.81	0.80722|0.80722	D|D	1|1	D;D|.	0.71674|.	0.992;0.998|.	D;D|.	0.77004|.	0.948;0.989|.	T|T	0.81326|0.81326	-0.0983|-0.0983	10|5	0.56958|.	D|.	0.05|.	-25.1829|-25.1829	14.1461|14.1461	0.65351|0.65351	0.0:0.927:0.0:0.073|0.0:0.927:0.0:0.073	.|.	267;313|.	Q9NP58-4;Q9NP58|.	.;ABCB6_HUMAN|.	N|T	313;267|161	ENSP00000265316:K313N;ENSP00000394333:K267N|.	ENSP00000265316:K313N|.	K|S	-|-	3|2	2|0	ABCB6|ABCB6	219789361|219789361	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.831000|3.831000	0.55776|0.55776	2.683000|2.683000	0.91414|0.91414	0.650000|0.650000	0.86243|0.86243	AAG|AGT	.	.	.	none		0.562	ABCB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256820.2	NM_005689		G	220081117	C	G	220081117	3	3	277	1	0	0	0	0	1	0	0	0	45	564	20	4	1653	4	ABCB6	2	220081117	Missense_Mutation	SNP	C	TCGA-Y8-A897-01A-11D-A35Z-10	62673947	220081117	23118256	13	17627											
KIF1A	547	hgsc.bcm.edu	37	chr2	241689964	241689964	+	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	ttgctcaggtacacgaaggcCctggggagaagcagaggcgg	10	5	17	9	2	1	2	1	0	0	2	1	4	1	2	1	6	3	3	1	6	3	2			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr2:241689964C>T	ENST00000320389.7	-	26	2714	c.2556G>A	c.(2554-2556)agG>agA	p.R852R	KIF1A_ENST00000498729.2_Splice_Site_p.R953R	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	852					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)		ACACGAAGGCCCTGGGGAGAA	0.642																																					p.R953R		Atlas-SNP	.											.	KIF1A	152	.	0			c.G2859A						PASS	.						46	53	51					2																	241689964		2134	4240	6374	SO:0001630	splice_region_variant	547	exon28			GAAGGCCCTGGGG	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.2556-1G>A	chr2.hg19:g.241689964C>T		135.0	0.0	.		88.0	29.0	.	NM_001244008	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Silent	SNP	ENST00000320389.7	hg19	CCDS46561.1																																																																																			.	.	.	none		0.642	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483	Silent	T	241689964	C	T	241689964	5	4	277	1	0	0	0	0	0	0	1	0	8290	637	22	2	2604	2	KIF1A	2	241689964	Splice_Site	SNP	C	TCGA-Y8-A897-01A-11D-A35Z-10	21608847	241689964	1509409	14	17628											
RBM6	10180	hgsc.bcm.edu	37	chr3	50103677	50103677	+	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	ctggccttctccttccagccTaaagtggtaaacccactgat	9	11	7	14	0	1	1	0	1	1	0	3	1	2	1	5	2	2	1	5	2	4	4			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr3:50103677T>G	ENST00000266022.4	+	17	2944	c.2685T>G	c.(2683-2685)ccT>ccG	p.P895P	RBM6_ENST00000539992.1_Silent_p.P237P|RBM6_ENST00000442092.1_Silent_p.P373P|RBM6_ENST00000443081.1_Silent_p.P763P|RBM6_ENST00000421682.1_5'Flank|RBM6_ENST00000441115.1_3'UTR|RBM6_ENST00000422955.1_Silent_p.P373P	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	895	Poly-Pro.				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)		CCTTCCAGCCTAAAGTGGTAA	0.463																																					p.P895P		Atlas-SNP	.											.	RBM6	85	.	0			c.T2685G						PASS	.						35	38	37					3																	50103677		2203	4300	6503	SO:0001819	synonymous_variant	10180	exon17			CCAGCCTAAAGTG	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.2685T>G	chr3.hg19:g.50103677T>G		77.0	0.0	.		72.0	25.0	.	NM_005777	O60549|O75524|Q86SS3	Silent	SNP	ENST00000266022.4	hg19	CCDS2809.1																																																																																			.	.	.	none		0.463	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777		G	50103677	T	G	50103677	2	3	277	1	0	0	0	0	0	0	0	1	13157	1509	53	5		5	RBM6	3	50103677	Silent	SNP	T	TCGA-Y8-A897-01A-11D-A35Z-10		50103677	147918753	15	17629											
MYNN	55892	hgsc.bcm.edu	37	chr3	169496760	169496761	+	Frame_Shift_Ins	INS	-	-	G																															ataatcgagagaaatcagaaINSgtatctacagatttgattca																										TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr3:169496760_169496761insG	ENST00000349841.5	+	3	1134_1135	c.471_472insG	c.(472-474)gtafs	p.V158fs	MYNN_ENST00000392733.1_Frame_Shift_Ins_p.V158fs|RP11-362K14.5_ENST00000602342.1_RNA|MYNN_ENST00000356716.4_Frame_Shift_Ins_p.V158fs|MYNN_ENST00000544106.1_Frame_Shift_Ins_p.V158fs	NM_018657.4	NP_061127.1	Q9NPC7	MYNN_HUMAN	myoneurin	158					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_cancers(22;9.55e-22)|all_epithelial(15;2.04e-26)|all_lung(20;5.05e-16)|Lung NSC(18;2.19e-15)|Ovarian(172;0.000223)|Breast(254;0.197)		Epithelial(2;4.03e-64)|all cancers(2;2.19e-58)|Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00676)			AGAAATCAGAAGTATCTACAGA	0.366																																					p.E157fs		Atlas-Indel,Pindel	.											.	MYNN	36	.	0			c.471_472insG						PASS	.																																			SO:0001589	frameshift_variant	55892	exon3			.	AF148848	CCDS3207.1, CCDS54671.1	3q26.31	2013-01-09			ENSG00000085274	ENSG00000085274		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	14955	protein-coding gene	gene with protein product		606042				10873615	Standard	NM_001185118		Approved	SBBIZ1, ZBTB31, ZNF902	uc010hwo.3	Q9NPC7		ENST00000349841.5:c.472dupG	chr3.hg19:g.169496761_169496761dupG	ENSP00000326240:p.Val158fs	57.0	0.0	0		71.0	23.0	0.323944	NM_018657	B2R6C9|Q6QHA6|Q6QHA7|Q6R3G1|Q6R3G2|Q6R4A0|Q7Z716|Q7Z717|Q86Z11|Q86Z12|Q9NS01|Q9UIW8	Frame_Shift_Ins	INS	ENST00000349841.5	hg19	CCDS3207.1																																																																																			.	.	.	none		0.366	MYNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467801.1	NM_018657		G	169496761	-	G	169496760	7	5	277	1	0	1	1	0	0	0	0	0	10068	69	3	0	477	0	MYNN	3	169496760	Frame_Shift_Ins	INS	-	TCGA-Y8-A897-01A-11D-A35Z-10	119393083	169496760	28525670	16	17630											
HERC6	55008	hgsc.bcm.edu	37	chr4	89361324	89361324	+	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	caaagtatgagcaaggatacCaaaaatcacatcctactata	19	8	5	9	0	1	1	1	1	0	0	2	2	2	2	2	1	3	2	2	1	9	5			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr4:89361324C>A	ENST00000264346.7	+	22	2823	c.2764C>A	c.(2764-2766)Caa>Aaa	p.Q922K	HERC6_ENST00000380265.5_Missense_Mutation_p.Q886K	NM_017912.3	NP_060382.3	Q8IVU3	HERC6_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6	922	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				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)		GCAAGGATACCAAAAATCACA	0.368																																					p.Q922K		Atlas-SNP	.											.	HERC6	104	.	0			c.C2764A						PASS	.						58	52	54					4																	89361324		1835	4092	5927	SO:0001583	missense	55008	exon22			GGATACCAAAAAT	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.2764C>A	chr4.hg19:g.89361324C>A	ENSP00000264346:p.Gln922Lys	109.0	0.0	.		152.0	52.0	.	NM_017912	B4DIY5|Q5GC90|Q5GRH3|Q5HYM6|Q5JPB6|Q6PIF4|Q8NAN3|Q9NWS4	Missense_Mutation	SNP	ENST00000264346.7	hg19	CCDS47098.1	.	.	.	.	.	.	.	.	.	.	C	1.116	-0.656611	0.03480	.	.	ENSG00000138642	ENST00000380265;ENST00000264346	T;T	0.56444	0.46;0.46	5.0	-2.57	0.06248	HECT (4);	0.912860	0.09345	N	0.814981	T	0.24624	0.0597	N	0.16903	0.455	0.25165	N	0.990324	B;B	0.16802	0.015;0.019	B;B	0.22152	0.023;0.038	T	0.26467	-1.0102	10	0.05959	T	0.93	.	0.9787	0.01431	0.4096:0.2078:0.1032:0.2795	.	886;922	Q8IVU3-2;Q8IVU3	.;HERC6_HUMAN	K	886;922	ENSP00000369617:Q886K;ENSP00000264346:Q922K	ENSP00000264346:Q922K	Q	+	1	0	HERC6	89580347	0.000000	0.05858	0.001000	0.08648	0.059000	0.15707	-4.663000	0.00201	-0.733000	0.04850	-0.237000	0.12165	CAA	.	.	.	none		0.368	HERC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363259.2			A	89361324	C	A	89361324	3	1	277	1	0	0	0	0	1	0	0	0	7069	595	21	4	2647	4	HERC6	4	89361324	Missense_Mutation	SNP	C	TCGA-Y8-A897-01A-11D-A35Z-10		89361324	101792952	17	17631											
CMYA5	202333	hgsc.bcm.edu	37	chr5	79025276	79025276	+	Missense_Mutation	SNP	A	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	gaacagtacaatataaaattAagatgtttaattcggttaaa	19	13	6	3	1	0	1	0	0	0	1	1	2	0	1	0	1	2	3	0	1	10	8	rs114327893		TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr5:79025276A>C	ENST00000446378.2	+	2	719	c.688A>C	c.(688-690)Aag>Cag	p.K230Q		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	230					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)		ATATAAAATTAAGATGTTTAA	0.323																																					p.K230Q		Atlas-SNP	.											.	CMYA5	643	.	0			c.A688C						PASS	.						46	45	45					5																	79025276		1808	4080	5888	SO:0001583	missense	202333	exon2			AAAATTAAGATGT	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.688A>C	chr5.hg19:g.79025276A>C	ENSP00000394770:p.Lys230Gln	134.0	0.0	.		264.0	85.0	.	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	hg19	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	A	15.86	2.956820	0.53293	.	.	ENSG00000164309	ENST00000446378	T	0.61392	0.11	6.06	6.06	0.98353	.	0.000000	0.56097	D	0.000038	T	0.54481	0.1861	L	0.34521	1.04	0.24052	N	0.996045	P	0.52463	0.953	P	0.49387	0.609	T	0.56159	-0.8025	10	0.87932	D	0	.	11.3193	0.49412	0.8036:0.1964:0.0:0.0	.	230	Q8N3K9	CMYA5_HUMAN	Q	230	ENSP00000394770:K230Q	ENSP00000394770:K230Q	K	+	1	0	CMYA5	79061032	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.987000	0.56944	2.315000	0.78130	0.533000	0.62120	AAG	.	A|0.999;G|0.001	.	alt		0.323	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		C	79025276	A	C	79025276	3	2	277	1	0	0	0	0	1	0	0	0	3592	363	13	5	694	5	CMYA5	5	79025276	Missense_Mutation	SNP	A	TCGA-Y8-A897-01A-11D-A35Z-10		79025276	101889984	18	17632											
GPR98	84059	hgsc.bcm.edu	37	chr5	90073763	90073763	+	Missense_Mutation	SNP	T	T	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	tttgggggaggtcacagtgtTctggaggatattccctcctt	6	14	13	8	0	2	0	1	0	1	0	4	3	4	3	2	5	0	1	2	5	1	5			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr5:90073763T>G	ENST00000405460.2	+	62	12665	c.12569T>G	c.(12568-12570)tTc>tGc	p.F4190C		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4190	Calx-beta 28. {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)		GTCACAGTGTTCTGGAGGATA	0.428																																					p.F4190C		Atlas-SNP	.											.	GPR98	605	.	0			c.T12569G						PASS	.						72	73	73					5																	90073763		1891	4109	6000	SO:0001583	missense	84059	exon62			CAGTGTTCTGGAG	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.12569T>G	chr5.hg19:g.90073763T>G	ENSP00000384582:p.Phe4190Cys	96.0	0.0	.		127.0	57.0	.	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	T	10.71	1.427948	0.25726	.	.	ENSG00000164199	ENST00000405460;ENST00000296619	T	0.27557	1.66	5.24	-5.55	0.02536	.	0.648335	0.17229	N	0.182009	T	0.12008	0.0292	N	0.14661	0.345	0.09310	N	0.999991	P	0.52463	0.953	B	0.43155	0.41	T	0.18429	-1.0337	10	0.38643	T	0.18	.	2.0846	0.03643	0.4047:0.1855:0.0698:0.34	.	4190	Q8WXG9	GPR98_HUMAN	C	4190	ENSP00000384582:F4190C	ENSP00000296619:F4190C	F	+	2	0	GPR98	90109519	0.003000	0.15002	0.106000	0.21319	0.384000	0.30261	-0.029000	0.12329	-1.402000	0.02056	0.368000	0.22195	TTC	.	.	.	none		0.428	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		G	90073763	T	G	90073763	3	3	277	1	0	0	0	0	1	0	0	0	6728	1783	62	5	12815	5	GPR98	5	90073763	Missense_Mutation	SNP	T	TCGA-Y8-A897-01A-11D-A35Z-10	11048487	90073763	90841497	19	17633											
ZNF318	24149	hgsc.bcm.edu	37	chr6	43305308	43305308	+	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	actcttgtttgtctaattggGaagattcttttacttcctca	8	19	6	8	0	4	1	1	0	3	1	5	2	5	2	1	1	1	1	1	1	3	8			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr6:43305308G>A	ENST00000361428.2	-	10	6505	c.6428C>T	c.(6427-6429)tCc>tTc	p.S2143F	ZNF318_ENST00000318149.3_Intron	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	2143					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)			GTCTAATTGGGAAGATTCTTT	0.473																																					p.S2143F		Atlas-SNP	.											.	ZNF318	175	.	0			c.C6428T						PASS	.						60	57	58					6																	43305308		2203	4300	6503	SO:0001583	missense	24149	exon10			AATTGGGAAGATT	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.6428C>T	chr6.hg19:g.43305308G>A	ENSP00000354964:p.Ser2143Phe	77.0	0.0	.		89.0	32.0	.	NM_014345	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Missense_Mutation	SNP	ENST00000361428.2	hg19	CCDS4895.2	.	.	.	.	.	.	.	.	.	.	G	11.91	1.778572	0.31502	.	.	ENSG00000171467	ENST00000361428	T	0.12774	2.65	5.86	2.62	0.31277	.	0.382752	0.22732	N	0.056305	T	0.03783	0.0107	N	0.20986	0.625	0.45621	D	0.998558	B	0.14438	0.01	B	0.16722	0.016	T	0.21348	-1.0248	10	0.46703	T	0.11	-2.181	10.7458	0.46179	0.0744:0.2474:0.6782:0.0	.	2143	Q5VUA4	ZN318_HUMAN	F	2143	ENSP00000354964:S2143F	ENSP00000354964:S2143F	S	-	2	0	ZNF318	43413286	0.978000	0.34361	0.993000	0.49108	0.933000	0.57130	1.404000	0.34623	0.786000	0.33708	-0.176000	0.13171	TCC	.	.	.	none		0.473	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345		A	43305308	G	A	43305308	3	1	277	1	0	0	0	0	1	0	0	0	17848	1174	41	2	415	2	ZNF318	6	43305308	Missense_Mutation	SNP	G	TCGA-Y8-A897-01A-11D-A35Z-10		43305308	127809759	20	17634											
CDC5L	988	hgsc.bcm.edu	37	chr6	44392211	44392211	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttgggccttcctgcccctaAgaatgattttgaaattgttc	8	15	9	9	0	0	3	0	2	0	1	2	3	1	3	4	1	1	2	4	1	3	7			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr6:44392211A>G	ENST00000371477.3	+	11	1759	c.1460A>G	c.(1459-1461)aAg>aGg	p.K487R		NM_001253.3	NP_001244.1	Q99459	CDC5L_HUMAN	cell division cycle 5-like	487	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)			CCTGCCCCTAAGAATGATTTT	0.413																																					p.K487R		Atlas-SNP	.											.	CDC5L	86	.	0			c.A1460G						PASS	.						107	101	103					6																	44392211		2203	4300	6503	SO:0001583	missense	988	exon11			CCCCTAAGAATGA	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.1460A>G	chr6.hg19:g.44392211A>G	ENSP00000360532:p.Lys487Arg	78.0	0.0	.		117.0	39.0	.	NM_001253	Q76N46|Q99974	Missense_Mutation	SNP	ENST00000371477.3	hg19	CCDS4912.1	.	.	.	.	.	.	.	.	.	.	A	15.44	2.835675	0.50951	.	.	ENSG00000096401	ENST00000371477	T	0.49139	0.79	6.05	6.05	0.98169	.	0.000000	0.85682	D	0.000000	T	0.36358	0.0964	M	0.69248	2.105	0.58432	D	0.999999	B	0.24618	0.107	B	0.27262	0.078	T	0.23084	-1.0198	10	0.33141	T	0.24	-20.4495	16.5932	0.84781	1.0:0.0:0.0:0.0	.	487	Q99459	CDC5L_HUMAN	R	487	ENSP00000360532:K487R	ENSP00000360532:K487R	K	+	2	0	CDC5L	44500189	1.000000	0.71417	0.999000	0.59377	0.960000	0.62799	7.569000	0.82380	2.320000	0.78422	0.528000	0.53228	AAG	.	.	.	none		0.413	CDC5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040743.1			G	44392211	A	G	44392211	3	3	277	1	0	0	0	0	1	0	0	0	3084	72	3	3	1502	3	CDC5L	6	44392211	Missense_Mutation	SNP	A	TCGA-Y8-A897-01A-11D-A35Z-10	1086903	44392211	126722856	21	17635											
SYNJ2	8871	hgsc.bcm.edu	37	chr6	158504535	158504535	+	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	ttgcgagaggagatcattcgGaaacgagacagcatggcccc	12	6	13	10	3	1	3	1	0	0	3	2	7	1	4	2	3	3	1	2	3	1	2			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr6:158504535G>A	ENST00000355585.4	+	21	3015	c.2940G>A	c.(2938-2940)cgG>cgA	p.R980R	SYNJ2_ENST00000367122.2_Silent_p.R980R|SYNJ2_ENST00000367112.1_Silent_p.R65R|SYNJ2_ENST00000367121.3_Silent_p.R980R	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	980					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)		AGATCATTCGGAAACGAGACA	0.532																																					p.R980R		Atlas-SNP	.											.	SYNJ2	111	.	0			c.G2940A						PASS	.						105	97	100					6																	158504535		2203	4300	6503	SO:0001819	synonymous_variant	8871	exon21			CATTCGGAAACGA	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.2940G>A	chr6.hg19:g.158504535G>A		99.0	0.0	.		76.0	26.0	.	NM_003898	Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	Silent	SNP	ENST00000355585.4	hg19	CCDS5254.1																																																																																			.	.	.	none		0.532	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2			A	158504535	G	A	158504535	2	1	277	1	0	0	0	0	0	0	0	1	15465	1161	41	2		2	SYNJ2	6	158504535	Silent	SNP	G	TCGA-Y8-A897-01A-11D-A35Z-10	114112324	158504535	12610532	22	17636											
FAM20C	56975	hgsc.bcm.edu	37	chr7	208977	208977	+	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	gcgctgttcaaacccatgaaGtaagtgccgaggcctgtggg	9	8	14	10	2	1	1	1	1	0	0	1	2	1	1	3	2	2	3	3	2	3	2			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr7:208977G>A	ENST00000313766.5	+	3	1094		c.e3+1			NM_020223.3	NP_064608.2	Q8IXL6	DMP4_HUMAN	family with sequence similarity 20, member C						dentinogenesis (GO:0097187)|enamel mineralization (GO:0070166)|odontoblast differentiation (GO:0071895)|osteoclast maturation (GO:0036179)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|protein phosphorylation (GO:0006468)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of phosphorus metabolic process (GO:0051174)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|lung(2)|urinary_tract(1)	4		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.57e-17)|Epithelial(4;1.26e-16)|all cancers(6;4.79e-14)		AACCCATGAAGTAAGTGCCGA	0.627																																					.		Atlas-SNP	.											.	FAM20C	18	.	0			c.863+1G>A						PASS	.						46	48	48					7																	208977		2038	4186	6224	SO:0001630	splice_region_variant	56975	exon3			CATGAAGTAAGTG	BC040074	CCDS47522.1	7p22.3	2012-11-29			ENSG00000177706	ENSG00000177706			22140	protein-coding gene	gene with protein product	"dentin matrix protein 4"	611061				17369251, 17924334	Standard	NM_020223		Approved	IMAGE:4942737, DKFZp547D065, DMP4	uc003sip.3	Q8IXL6	OTTHUMG00000151401	ENST00000313766.5:c.863+1G>A	chr7.hg19:g.208977G>A		95.0	0.0	.		49.0	12.0	.	NM_020223	A4D2Q5|L8B5W8|Q5I0W9|Q7Z4I0|Q9NPT2	Splice_Site	SNP	ENST00000313766.5	hg19	CCDS47522.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.660989	0.88154	.	.	ENSG00000177706	ENST00000313766	.	.	.	5.23	5.23	0.72850	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.5659	0.87919	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FAM20C	304060	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	8.213000	0.89758	2.439000	0.82584	0.655000	0.94253	.	.	.	.	none		0.627	FAM20C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322476.2	NM_020223	Intron	A	208977	G	A	208977	5	1	277	1	0	0	0	0	0	0	1	0	5543	1043	36	2	874	2	FAM20C	7	208977	Splice_Site	SNP	G	TCGA-Y8-A897-01A-11D-A35Z-10		208977	158929686	23	17637											
SLC4A2	6522	hgsc.bcm.edu	37	chr7	150771852	150771852	+	Missense_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	gagagaagagccccttccctGtgtggatgatggttgccagc	8	9	14	10	0	0	3	0	1	0	2	1	6	1	4	4	2	3	1	4	2	1	2			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr7:150771852G>A	ENST00000485713.1	+	19	4011	c.2971G>A	c.(2971-2973)Gtg>Atg	p.V991M	RP11-148K1.12_ENST00000485974.1_RNA|FASTK_ENST00000489884.1_5'Flank|SLC4A2_ENST00000392826.2_Missense_Mutation_p.V982M|SLC4A2_ENST00000413384.2_Missense_Mutation_p.V991M|SLC4A2_ENST00000461735.1_Missense_Mutation_p.V977M|SLC4A2_ENST00000310317.5_Missense_Mutation_p.V909M	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	991	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)		CCCCTTCCCTGTGTGGATGAT	0.582																																					p.V991M		Atlas-SNP	.											.	SLC4A2	98	.	0			c.G2971A						PASS	.						76	80	79					7																	150771852		2203	4300	6503	SO:0001583	missense	6522	exon19			TTCCCTGTGTGGA		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.2971G>A	chr7.hg19:g.150771852G>A	ENSP00000419412:p.Val991Met	92.0	0.0	.		73.0	24.0	.	NM_003040	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Missense_Mutation	SNP	ENST00000485713.1	hg19	CCDS5917.1	.	.	.	.	.	.	.	.	.	.	G	15.94	2.982076	0.53827	.	.	ENSG00000164889	ENST00000485713;ENST00000413384;ENST00000310317;ENST00000392826;ENST00000461735	T;T;T;T;T	0.79454	-1.27;-1.27;-1.27;-1.27;-1.27	5.29	5.29	0.74685	Bicarbonate transporter, C-terminal (1);	0.211754	0.41294	D	0.000916	T	0.78923	0.4360	M	0.73372	2.23	0.40710	D	0.982567	B;B;B	0.34290	0.393;0.393;0.447	B;B;B	0.40329	0.312;0.219;0.326	T	0.77413	-0.2597	10	0.34782	T	0.22	.	13.4146	0.60961	0.0:0.1576:0.8424:0.0	.	982;977;991	F8W682;P04920-2;P04920	.;.;B3A2_HUMAN	M	991;991;909;982;977	ENSP00000419412:V991M;ENSP00000405600:V991M;ENSP00000311402:V909M;ENSP00000376571:V982M;ENSP00000419164:V977M	ENSP00000311402:V909M	V	+	1	0	SLC4A2	150402785	0.013000	0.17824	1.000000	0.80357	0.997000	0.91878	0.192000	0.17096	2.756000	0.94617	0.561000	0.74099	GTG	.	.	.	none		0.582	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040		A	150771852	G	A	150771852	3	1	277	1	0	0	0	0	1	0	0	0	14667	1377	48	2	3041	2	SLC4A2	7	150771852	Missense_Mutation	SNP	G	TCGA-Y8-A897-01A-11D-A35Z-10	150562875	150771852	8366811	24	17638											
PTK2	5747	hgsc.bcm.edu	37	chr8	141669756	141669756	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcacccaggtcagagttcaAtagcttctgtgccatctcaa	10	11	7	13	0	5	1	4	0	2	1	6	1	5	1	2	1	2	2	2	1	3	3			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr8:141669756A>G	ENST00000522684.1	-	32	3197	c.2968T>C	c.(2968-2970)Ttg>Ctg	p.L990L	PTK2_ENST00000521059.1_Silent_p.L990L|PTK2_ENST00000522950.1_3'UTR|PTK2_ENST00000340930.3_Silent_p.L1003L|PTK2_ENST00000517712.1_Silent_p.L53L|PTK2_ENST00000430260.2_Silent_p.L300L|PTK2_ENST00000517887.1_Silent_p.L1034L|PTK2_ENST00000538769.1_Silent_p.L658L|PTK2_ENST00000535192.1_Silent_p.L944L|PTK2_ENST00000519419.1_Silent_p.L1034L|PTK2_ENST00000519465.1_Silent_p.L618L|PTK2_ENST00000395218.2_Silent_p.L1003L	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	990	Interaction with ARHGEF28. {ECO:0000250}.|Interaction with TGFB1I1.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell motility (GO:0048870)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|central nervous system neuron axonogenesis (GO:0021955)|embryo development (GO:0009790)|endothelial cell migration (GO:0043542)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|establishment of nucleus localization (GO:0040023)|extracellular matrix organization (GO:0030198)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|growth hormone receptor signaling pathway (GO:0060396)|heart morphogenesis (GO:0003007)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of organ growth (GO:0046621)|negative regulation of synapse assembly (GO:0051964)|netrin-activated signaling pathway (GO:0038007)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|placenta development (GO:0001890)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|regulation of endothelial cell migration (GO:0010594)|regulation of focal adhesion assembly (GO:0051893)|regulation of osteoblast differentiation (GO:0045667)|regulation of Rho GTPase activity (GO:0032319)|signal complex assembly (GO:0007172)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	apical plasma membrane (GO:0016324)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|stress fiber (GO:0001725)	actin binding (GO:0003779)|ATP binding (GO:0005524)|JUN kinase binding (GO:0008432)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(6)|lung(23)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	48	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			TCAGAGTTCAATAGCTTCTGT	0.418																																					p.L1012L		Atlas-SNP	.											.	PTK2	311	.	0			c.T3034C						PASS	.						111	95	101					8																	141669756		2203	4300	6503	SO:0001819	synonymous_variant	5747	exon32			AGTTCAATAGCTT	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.2968T>C	chr8.hg19:g.141669756A>G		90.0	0.0	.		121.0	42.0	.	NM_005607	B4E2N6|F5H4S4|Q14291|Q9UD85	Silent	SNP	ENST00000522684.1	hg19	CCDS6381.1	.	.	.	.	.	.	.	.	.	.	A	7.471	0.646717	0.14516	.	.	ENSG00000169398	ENST00000519654	.	.	.	5.75	-0.279	0.12890	.	.	.	.	.	T	0.58192	0.2105	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53251	-0.8465	4	.	.	.	.	11.0584	0.47933	0.3482:0.0:0.6518:0.0	.	.	.	.	T	954	.	.	I	-	2	0	PTK2	141738938	1.000000	0.71417	0.967000	0.41034	0.939000	0.58152	1.934000	0.40163	-0.104000	0.12154	-0.256000	0.11100	ATT	.	.	.	none		0.418	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607		G	141669756	A	G	141669756	2	3	277	1	0	0	0	0	0	0	0	1	12773	98	4	3		3	PTK2	8	141669756	Silent	SNP	A	TCGA-Y8-A897-01A-11D-A35Z-10		141669756	4694266	25	17639											
GAPVD1	26130	hgsc.bcm.edu	37	chr9	128116938	128116939	+	Frame_Shift_Ins	INS	-	-	A																															atttttccttttagaaaaagINSagccccatatattgcttatc																										TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr9:128116938_128116939insA	ENST00000495955.1	+	24	3919_3920	c.3629_3630insA	c.(3628-3633)agagccfs	p.A1211fs	GAPVD1_ENST00000394083.2_Frame_Shift_Ins_p.A1145fs|GAPVD1_ENST00000470056.1_Frame_Shift_Ins_p.A1166fs|GAPVD1_ENST00000297933.6_Frame_Shift_Ins_p.A1193fs|GAPVD1_ENST00000312123.9_Frame_Shift_Ins_p.A1172fs|GAPVD1_ENST00000394104.2_Frame_Shift_Ins_p.A1211fs|GAPVD1_ENST00000394105.2_Frame_Shift_Ins_p.A1220fs|GAPVD1_ENST00000265956.4_Frame_Shift_Ins_p.A1185fs			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	1211					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						TTTAGAAAAAGAGCCCCATATA	0.386																																					p.R1219fs		Atlas-INDEL	.											.	GAPVD1	124	.	0			c.3656_3657insA						PASS	.																																			SO:0001589	frameshift_variant	26130	exon23			.		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.3630dupA	chr9.hg19:g.128116939_128116939dupA	ENSP00000419063:p.Ala1211fs	60.0	0.0	0		79.0	23.0	0.291139	NM_015635	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Frame_Shift_Ins	INS	ENST00000495955.1	hg19																																																																																				.	.	.	none		0.386	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1			A	128116939	-	A	128116938	7	5	277	1	0	1	1	0	0	0	0	0	6246	942	33	0	3742	0	GAPVD1	9	128116938	Frame_Shift_Ins	INS	-	TCGA-Y8-A897-01A-11D-A35Z-10		128116938	13096493	26	17640	185	2									
GAPVD1	26130	hgsc.bcm.edu	37	chr9	128116940	128116940	+	Missense_Mutation	SNP	G	G	A																															tttttccttttagaaaaagaGccccatatattgcttatctc																										TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr9:128116940G>A	ENST00000495955.1	+	24	3921	c.3631G>A	c.(3631-3633)Gcc>Acc	p.A1211T	GAPVD1_ENST00000394083.2_Missense_Mutation_p.A1145T|GAPVD1_ENST00000470056.1_Missense_Mutation_p.A1166T|GAPVD1_ENST00000297933.6_Missense_Mutation_p.A1193T|GAPVD1_ENST00000312123.9_Missense_Mutation_p.A1172T|GAPVD1_ENST00000394104.2_Missense_Mutation_p.A1211T|GAPVD1_ENST00000394105.2_Missense_Mutation_p.A1220T|GAPVD1_ENST00000265956.4_Missense_Mutation_p.A1185T			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	1211					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						TAGAAAAAGAGCCCCATATAT	0.383																																					p.A1220T		Atlas-SNP	.											.	GAPVD1	124	.	0			c.G3658A						PASS	.						86	88	87					9																	128116940		2203	4300	6503	SO:0001583	missense	26130	exon23			AAAAGAGCCCCAT		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.3631G>A	chr9.hg19:g.128116940G>A	ENSP00000419063:p.Ala1211Thr	61.0	0.0	.		82.0	25.0	.	NM_015635	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Missense_Mutation	SNP	ENST00000495955.1	hg19		.	.	.	.	.	.	.	.	.	.	G	27.5	4.841442	0.91197	.	.	ENSG00000165219	ENST00000470056;ENST00000394105;ENST00000394104;ENST00000265956;ENST00000394083;ENST00000495955;ENST00000297933;ENST00000312123	.	.	.	6.08	5.19	0.71726	.	0.044268	0.85682	N	0.000000	T	0.58337	0.2115	L	0.39020	1.185	0.80722	D	1	B;P;B;B;B;P	0.40834	0.333;0.73;0.43;0.298;0.298;0.672	B;B;P;P;P;P	0.48334	0.28;0.147;0.471;0.471;0.471;0.574	T	0.62364	-0.6870	9	0.72032	D	0.01	.	14.2482	0.66001	0.0706:0.0:0.9294:0.0	.	1211;226;1166;1172;1193;1220	Q14C86;B3KTX2;Q14C86-3;Q14C86-4;Q14C86-2;Q14C86-6	GAPD1_HUMAN;.;.;.;.;.	T	1166;1220;1211;1185;1145;1211;1193;1172	.	ENSP00000265956:A1185T	A	+	1	0	GAPVD1	127156761	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.562000	0.73960	1.589000	0.49982	0.591000	0.81541	GCC	.	.	.	none		0.383	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1			A	128116940	G	A	128116940	3	1	277	1	0	0	0	0	1	0	0	0	6246	971	34	2	3744	2	GAPVD1	9	128116940	Missense_Mutation	SNP	G	TCGA-Y8-A897-01A-11D-A35Z-10	2	128116940	13096491	27	17641	185	2									
LAMC3	10319	hgsc.bcm.edu	37	chr9	133884789	133884789	+	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	cccgcccgaggacttctgtcCccacgtgggcgccgcgggcg	3	5	15	18	7	1	0	0	0	1	0	2	2	2	1	5	3	0	0	5	3	0	1			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr9:133884789C>A	ENST00000361069.4	+	1	321	c.188C>A	c.(187-189)cCc>cAc	p.P63H	LAMC3_ENST00000480883.1_3'UTR	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	63	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		GACTTCTGTCCCCACGTgggc	0.751																																					p.P63H		Atlas-SNP	.											.	LAMC3	167	.	0			c.C188A						PASS	.						2	3	3					9																	133884789		1613	3200	4813	SO:0001583	missense	10319	exon1			TCTGTCCCCACGT	AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"Laminins"	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.188C>A	chr9.hg19:g.133884789C>A	ENSP00000354360:p.Pro63His	76.0	0.0	.		46.0	21.0	.	NM_006059	B1APX9|B1APY0|Q59H72	Missense_Mutation	SNP	ENST00000361069.4	hg19	CCDS6938.1	.	.	.	.	.	.	.	.	.	.	C	16.74	3.205952	0.58234	.	.	ENSG00000050555	ENST00000361069;ENST00000355048;ENST00000320021	T	0.74947	-0.89	3.94	2.85	0.33270	Laminin, N-terminal (3);	0.116020	0.64402	D	0.000020	T	0.73590	0.3606	L	0.50333	1.59	0.34047	D	0.655667	D	0.55800	0.973	P	0.59115	0.852	T	0.76305	-0.3008	10	0.36615	T	0.2	.	3.1416	0.06457	0.0:0.5194:0.0:0.4806	.	63	Q9Y6N6	LAMC3_HUMAN	H	63	ENSP00000354360:P63H	ENSP00000325873:P63H	P	+	2	0	LAMC3	132874610	1.000000	0.71417	0.987000	0.45799	0.144000	0.21451	3.770000	0.55310	1.709000	0.51313	0.313000	0.20887	CCC	.	.	.	none		0.751	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059		A	133884789	C	A	133884789	3	1	277	1	0	0	0	0	1	0	0	0	8623	623	22	4	190	4	LAMC3	9	133884789	Missense_Mutation	SNP	C	TCGA-Y8-A897-01A-11D-A35Z-10	5767849	133884789	7328642	28	17642											
PTEN	5728	hgsc.bcm.edu	37	chr10	89624274	89624274	+	Frame_Shift_Del	DEL	T	T	-																															agcagaaacaaaaggagataTcaagaggatggattcgactt																								rs587782187		TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr10:89624274delT	ENST00000371953.3	+	1	1405	c.48delT	c.(46-48)tatfs	p.Y16fs	KLLN_ENST00000445946.3_5'Flank	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	16	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.		Y -> C (loss of phosphatase activity towards Ins(1,3,4,5)P4; retains the ability to bind phospholipid membranes).		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.?(13)|p.Y16*(2)|p.Y16fs*1(2)|p.R15fs*23(1)|p.R14fs*26(1)|p.Y16fs*21(1)|p.N12fs*6(1)|p.R14_D22del(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)		AAAGGAGATATCAAGAGGATG	0.473		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.Y16fs		Atlas-Indel,Pindel	.	yes	Rec	yes	"Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"	10	10q23.3	5728	phosphatase and tensin homolog gene		"L, E, M, O"	PTEN,NS,adenocarcinoma,-1,1	PTEN	3652	.	59	Whole gene deletion(37)|Unknown(13)|Deletion - Frameshift(5)|Substitution - Nonsense(2)|Deletion - In frame(1)|Insertion - Frameshift(1)	prostate(14)|central_nervous_system(12)|skin(7)|endometrium(6)|lung(6)|ovary(3)|haematopoietic_and_lymphoid_tissue(2)|bone(2)|breast(2)|biliary_tract(1)|stomach(1)|soft_tissue(1)|urinary_tract(1)|kidney(1)	c.47delA						PASS	.						184	176	179					10																	89624274		2203	4300	6503	SO:0001589	frameshift_variant	5728	exon1	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"	9588	protein-coding gene	gene with protein product	"mutated in multiple advanced cancers 1"	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.48delT	chr10.hg19:g.89624274delT	ENSP00000361021:p.Tyr16fs	58.0	0.0	0		64.0	39.0	0.609375	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Frame_Shift_Del	DEL	ENST00000371953.3	hg19	CCDS31238.1																																																																																			.	.	.	none		0.473	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		-	89624274	T	-	89624274	7	5	277	1	0	1	0	1	0	0	0	0	12748	1442	50	0	50	0	PTEN	10	89624274	Frame_Shift_Del	DEL	T	TCGA-Y8-A897-01A-11D-A35Z-10		89624274	45910473	29	17643											
OR51D1	390038	hgsc.bcm.edu	37	chr11	4661150	4661150	+	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	acttttggctggctttcccaCtgtgttttatgtatgccttg	4	19	9	9	0	0	0	0	0	0	0	1	0	1	0	2	2	1	4	2	2	2	7			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr11:4661150C>A	ENST00000357605.2	+	1	206	c.130C>A	c.(130-132)Ctg>Atg	p.L44M		NM_001004751.2	NP_001004751.1	Q8NGF3	O51D1_HUMAN	olfactory receptor, family 51, subfamily D, member 1	44						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|liver(2)|lung(14)|prostate(1)|skin(2)|urinary_tract(1)	27		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;2.74e-13)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|GBM - Glioblastoma multiforme(2;0.0841)|LUSC - Lung squamous cell carcinoma(625;0.19)		GGCTTTCCCACTGTGTTTTAT	0.527																																					p.L44M		Atlas-SNP	.											.	OR51D1	49	.	0			c.C130A						PASS	.						180	145	157					11																	4661150		2201	4298	6499	SO:0001583	missense	390038	exon1			TTCCCACTGTGTT	AB065855	CCDS31357.1	11p15.4	2012-08-09			ENSG00000197428	ENSG00000197428		"GPCR / Class A : Olfactory receptors"	15193	protein-coding gene	gene with protein product							Standard	NM_001004751		Approved	OR51D1Q	uc010qyk.2	Q8NGF3	OTTHUMG00000165724	ENST00000357605.2:c.130C>A	chr11.hg19:g.4661150C>A	ENSP00000350222:p.Leu44Met	82.0	0.0	.		72.0	21.0	.	NM_001004751	B9EIK4	Missense_Mutation	SNP	ENST00000357605.2	hg19	CCDS31357.1	.	.	.	.	.	.	.	.	.	.	C	9.503	1.103608	0.20632	.	.	ENSG00000197428	ENST00000357605	T	0.17054	2.3	4.84	1.95	0.26073	.	0.000000	0.35320	N	0.003294	T	0.30634	0.0771	L	0.49256	1.55	0.31172	N	0.703044	D	0.89917	1.0	D	0.83275	0.996	T	0.17899	-1.0354	10	0.87932	D	0	.	8.0546	0.30598	0.0:0.6497:0.0:0.3503	.	44	Q8NGF3	O51D1_HUMAN	M	44	ENSP00000350222:L44M	ENSP00000350222:L44M	L	+	1	2	OR51D1	4617726	0.006000	0.16342	0.240000	0.24138	0.011000	0.07611	-0.039000	0.12124	0.335000	0.23614	-0.214000	0.12660	CTG	.	.	.	none		0.527	OR51D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385956.1	NM_001004751		A	4661150	C	A	4661150	3	1	277	1	0	0	0	0	1	0	0	0	11100	564	20	4	132	4	OR51D1	11	4661150	Missense_Mutation	SNP	C	TCGA-Y8-A897-01A-11D-A35Z-10		4661150	130345366	30	17644											
OR52E2	119678	hgsc.bcm.edu	37	chr11	5080608	5080609	+	Missense_Mutation	DNP	GC	GC	AT																															gttgatccagaagattccaaGcatcttagggatggtagctg																								rs369925067		TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr11:5080608_5080609GC>AT	ENST00000321522.2	-	1	248_249	c.249_250GC>AT	c.(247-252)atGCtt>atATtt	p.83_84ML>IF		NM_001005164.2	NP_001005164.2	Q8NGJ4	O52E2_HUMAN	olfactory receptor, family 52, subfamily E, member 2	83						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(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)		AAGATTCCAAGCATCTTAGGGA	0.49																																					p.L84F|p.M83I		Atlas-SNP	.											.	OR52E2	63	.	0			c.C250T|c.G249A						PASS	.																																			SO:0001583	missense	119678	exon1			TTCCAAGCATCTT|TCCAAGCATCTTA	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.249_250delinsAT	chr11.hg19:g.5080608_5080609delinsAT	ENSP00000322088:p.M83_L84delinsIF	91.0|93.0	0.0	.		126.0	40.0	.	NM_001005164		Missense_Mutation	SNP	ENST00000321522.2	hg19	CCDS31371.1																																																																																			.	.	.	none|alt		0.49	OR52E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142815.1	NM_001005164		AT	5080609	GC	AT	5080608	3	1	277	1	0	0	0	0	1	0	0	0	11122	971	34	2	730	2	OR52E2	11	5080608	Missense_Mutation	DNP	GC	TCGA-Y8-A897-01A-11D-A35Z-10	419458	5080608	129925908	31	17645											
MYBPC3	4607	hgsc.bcm.edu	37	chr11	47373013	47373013	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgaacacggcagggctgccTgcggccacttccactgaccg	7	6	12	16	4	0	1	0	1	0	0	2	2	1	1	4	3	3	2	4	3	1	1			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr11:47373013T>C	ENST00000545968.1	-	2	123	c.69A>G	c.(67-69)gcA>gcG	p.A23A	MYBPC3_ENST00000399249.2_Silent_p.A23A|MYBPC3_ENST00000256993.4_Silent_p.A23A	NM_000256.3	NP_000247.2	Q14896	MYPC3_HUMAN	myosin binding protein C, cardiac	23					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)		CAGGGCTGCCTGCGGCCACTT	0.662																																					p.A23A		Atlas-SNP	.											.	MYBPC3	102	.	0			c.A69G						PASS	.						16	19	18					11																	47373013		2102	4223	6325	SO:0001819	synonymous_variant	4607	exon2			GCTGCCTGCGGCC	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.69A>G	chr11.hg19:g.47373013T>C		49.0	0.0	.		22.0	4.0	.	NM_000256	A5PL00|Q16410|Q6R2F7|Q9UE27|Q9UM53	Silent	SNP	ENST00000545968.1	hg19	CCDS53621.1																																																																																			.	.	.	none		0.662	MYBPC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392271.3			C	47373013	T	C	47373013	2	2	277	1	0	0	0	0	0	0	0	1	10020	1567	55	3		3	MYBPC3	11	47373013	Silent	SNP	T	TCGA-Y8-A897-01A-11D-A35Z-10	42292405	47373013	87633503	32	17646											
GRM5	2915	hgsc.bcm.edu	37	chr11	88300498	88300498	+	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	gattggcacaaaagctagccAtataatgcaggtcgtgtaca	14	9	10	8	1	0	0	0	0	0	0	1	1	0	0	1	2	4	4	1	2	6	5			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr11:88300498A>T	ENST00000305447.4	-	7	2502	c.2353T>A	c.(2353-2355)Tgg>Agg	p.W785R	GRM5_ENST00000455756.2_Missense_Mutation_p.W785R|GRM5_ENST00000305432.5_Missense_Mutation_p.W785R|GRM5_ENST00000393297.1_Missense_Mutation_p.W785R|GRM5_ENST00000418177.2_Missense_Mutation_p.W785R	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	785					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)	AAAGCTAGCCATATAATGCAG	0.468																																					p.W785R		Atlas-SNP	.											.	GRM5	414	.	0			c.T2353A						PASS	.						168	152	158					11																	88300498		2201	4299	6500	SO:0001583	missense	2915	exon8			CTAGCCATATAAT	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.2353T>A	chr11.hg19:g.88300498A>T	ENSP00000306138:p.Trp785Arg	59.0	0.0	.		56.0	18.0	.	NM_000842	Q6J164	Missense_Mutation	SNP	ENST00000305447.4	hg19	CCDS44694.1	.	.	.	.	.	.	.	.	.	.	A	19.49	3.838346	0.71373	.	.	ENSG00000168959	ENST00000418177;ENST00000455756;ENST00000305432;ENST00000305447;ENST00000393297	D;D;D;D;D	0.92299	-3.01;-3.01;-3.01;-3.01;-3.01	5.58	5.58	0.84498	GPCR, family 3, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.97402	0.9150	H	0.96239	3.79	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.98698	1.0699	9	.	.	.	.	15.7446	0.77929	1.0:0.0:0.0:0.0	.	785;785	P41594-2;P41594	.;GRM5_HUMAN	R	785	ENSP00000402912:W785R;ENSP00000405690:W785R;ENSP00000305905:W785R;ENSP00000306138:W785R;ENSP00000376975:W785R	.	W	-	1	0	GRM5	87940146	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	9.315000	0.96313	2.133000	0.65898	0.459000	0.35465	TGG	.	.	.	none		0.468	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259226.1	NM_000842		T	88300498	A	T	88300498	3	4	277	1	0	0	0	0	1	0	0	0	6807	217	8	5	1297	5	GRM5	11	88300498	Missense_Mutation	SNP	A	TCGA-Y8-A897-01A-11D-A35Z-10	40927485	88300498	46706018	33	17647											
MAML2	84441	hgsc.bcm.edu	37	chr11	95826314	95826315	+	Missense_Mutation	DNP	CC	CC	GA																															gttgttctccagggtcgtctCcgtacctattaggaaaaata																								rs369905258		TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr11:95826314_95826315CC>GA	ENST00000524717.1	-	2	2164_2165	c.880_881GG>TC	c.(880-882)GGa>TCa	p.G294S		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	294					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)				AGGGTCGTCTCCGTACCTATTA	0.48			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.G294A|p.G294X		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2	94	.	0			c.G881C|c.G880T						PASS	.																																			SO:0001583	missense	84441	exon2			TCGTCTCCGTACC|CGTCTCCGTACCT	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.880_881delinsGA	chr11.hg19:g.95826314_95826315delinsGA	ENSP00000434552:p.Gly294Ser	55.0	0.0	.		82.0|80.0	31.0|28.0	.	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Missense_Mutation|Nonsense_Mutation	SNP	ENST00000524717.1	hg19	CCDS44714.1																																																																																			.	.	.	none|alt		0.48	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			GA	95826315	CC	GA	95826314	3	3	277	1	0	0	0	0	1	0	0	0	9213	855	30	4	2605	4	MAML2	11	95826314	Missense_Mutation	DNP	CC	TCGA-Y8-A897-01A-11D-A35Z-10	7525816	95826314	39180202	34	17648											
ITGA5	3678	hgsc.bcm.edu	37	chr12	54801981	54801981	+	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	caggtactcggggtaataagAttctgcaatctgctcctgag	10	11	11	9	1	2	2	0	1	2	1	4	2	3	2	1	3	3	4	1	3	4	4			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr12:54801981A>T	ENST00000293379.4	-	7	991	c.730T>A	c.(730-732)Tct>Act	p.S244T	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)	244					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						GGGTAATAAGATTCTGCAATC	0.547																																					p.S244T		Atlas-SNP	.											.	ITGA5	99	.	0			c.T730A						PASS	.						81	78	79					12																	54801981		2203	4300	6503	SO:0001583	missense	3678	exon7			AATAAGATTCTGC		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.730T>A	chr12.hg19:g.54801981A>T	ENSP00000293379:p.Ser244Thr	69.0	0.0	.		53.0	24.0	.	NM_002205	Q96HA5	Missense_Mutation	SNP	ENST00000293379.4	hg19	CCDS8880.1	.	.	.	.	.	.	.	.	.	.	A	8.780	0.928036	0.18131	.	.	ENSG00000161638	ENST00000293379	T	0.22134	1.97	5.13	5.13	0.70059	.	0.062472	0.64402	D	0.000004	T	0.11024	0.0269	N	0.11255	0.115	0.39220	D	0.963471	B	0.23377	0.084	B	0.18871	0.023	T	0.15093	-1.0449	10	0.35671	T	0.21	.	9.438	0.38650	0.8211:0.1789:0.0:0.0	.	244	P08648	ITA5_HUMAN	T	244	ENSP00000293379:S244T	ENSP00000293379:S244T	S	-	1	0	ITGA5	53088248	0.985000	0.35326	0.904000	0.35570	0.413000	0.31143	2.610000	0.46325	2.075000	0.62263	0.391000	0.25812	TCT	.	.	.	none		0.547	ITGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406174.1			T	54801981	A	T	54801981	3	4	277	1	0	0	0	0	1	0	0	0	7886	333	12	5	2515	5	ITGA5	12	54801981	Missense_Mutation	SNP	A	TCGA-Y8-A897-01A-11D-A35Z-10		54801981	79049914	35	17649											
BAZ2A	11176	hgsc.bcm.edu	37	chr12	56992544	56992544	+	Missense_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	ataccaggagggcatcagccGcaaactcctctgagctggtg	10	7	12	12	1	2	1	1	1	1	0	3	2	3	2	3	3	4	3	3	3	2	1			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr12:56992544G>A	ENST00000551812.1	-	29	5769	c.5576C>T	c.(5575-5577)gCg>gTg	p.A1859V	BAZ2A_ENST00000179765.5_Missense_Mutation_p.A1827V|BAZ2A_ENST00000549884.1_Missense_Mutation_p.A1857V|BAZ2A_ENST00000379441.3_Missense_Mutation_p.A1829V|BAZ2A_ENST00000553222.1_5'Flank	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	1859	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						GGCATCAGCCGCAAACTCCTC	0.567																																					p.A1859V		Atlas-SNP	.											.	BAZ2A	263	.	0			c.C5576T						PASS	.						37	39	38					12																	56992544		1979	4155	6134	SO:0001583	missense	11176	exon29			TCAGCCGCAAACT	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.5576C>T	chr12.hg19:g.56992544G>A	ENSP00000446880:p.Ala1859Val	60.0	0.0	.		50.0	15.0	.	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Missense_Mutation	SNP	ENST00000551812.1	hg19	CCDS44924.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.553834	0.86231	.	.	ENSG00000076108	ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549787;ENST00000549884	T;T;T;T;T	0.28454	1.61;1.61;1.61;1.61;1.61	5.85	5.85	0.93711	Bromodomain (6);Bromodomain, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.38081	0.1027	N	0.20445	0.575	0.80722	D	1	D;P;P;D	0.89917	1.0;0.851;0.877;1.0	D;P;P;D	0.91635	0.995;0.682;0.848;0.999	T	0.02781	-1.1111	10	0.02654	T	1	-13.7142	19.3175	0.94220	0.0:0.0:1.0:0.0	.	1857;1855;1859;1832	F8VU39;Q9UIF9-3;Q9UIF9;Q9UIF9-2	.;.;BAZ2A_HUMAN;.	V	1829;1827;1859;791;1857	ENSP00000368754:A1829V;ENSP00000179765:A1827V;ENSP00000446880:A1859V;ENSP00000448760:A791V;ENSP00000447941:A1857V	ENSP00000179765:A1827V	A	-	2	0	BAZ2A	55278811	1.000000	0.71417	0.995000	0.50966	0.891000	0.51852	7.370000	0.79589	2.941000	0.99782	0.655000	0.94253	GCG	.	.	.	none		0.567	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449		A	56992544	G	A	56992544	3	1	277	1	0	0	0	0	1	0	0	0	1331	1087	38	1	145	1	BAZ2A	12	56992544	Missense_Mutation	SNP	G	TCGA-Y8-A897-01A-11D-A35Z-10	2190563	56992544	76859351	36	17650											
ATP6V0A2	23545	hgsc.bcm.edu	37	chr12	124236887	124236887	+	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	aagtttcattgctgggaagcCaagatatagaagagggaaat	16	9	12	4	0	1	3	1	0	0	3	1	5	1	5	1	2	2	2	1	2	7	4			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr12:124236887C>T	ENST00000330342.3	+	17	2361	c.2113C>T	c.(2113-2115)Caa>Taa	p.Q705*	ATP6V0A2_ENST00000544833.1_5'Flank	NM_012463.3	NP_036595.2	Q9Y487	VPP2_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a2	705					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|immune response (GO:0006955)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|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)	hydrogen ion transmembrane transporter activity (GO:0015078)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.000625)|all cancers(50;0.00775)		GCTGGGAAGCCAAGATATAGA	0.403																																					p.Q705X		Atlas-SNP	.											.	ATP6V0A2	68	.	0			c.C2113T						PASS	.						128	126	127					12																	124236887		2203	4300	6503	SO:0001587	stop_gained	23545	exon17			GGAAGCCAAGATA	AF112972	CCDS9254.1	12q24.31	2010-04-21	2006-01-20		ENSG00000185344	ENSG00000185344		"ATPases / V-type"	18481	protein-coding gene	gene with protein product	"infantile malignant osteopetrosis"	611716	"infantile malignant osteopetrosis", "ATPase, H+ transporting, lysosomal V0 subunit a isoform 2", "ATPase, H+ transporting, lysosomal V0 subunit A2"			2247090, 18157129	Standard	NM_012463		Approved	TJ6, a2, TJ6s, TJ6M, ATP6a2, J6B7, ATP6N1D, Vph1, Stv1	uc001ufr.3	Q9Y487	OTTHUMG00000168723	ENST00000330342.3:c.2113C>T	chr12.hg19:g.124236887C>T	ENSP00000332247:p.Gln705*	83.0	0.0	.		116.0	38.0	.	NM_012463	A8K026|Q6NUM0	Nonsense_Mutation	SNP	ENST00000330342.3	hg19	CCDS9254.1	.	.	.	.	.	.	.	.	.	.	C	40	8.390644	0.98791	.	.	ENSG00000185344	ENST00000330342	.	.	.	5.76	4.86	0.63082	.	0.048315	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.17832	T	0.49	-9.4353	16.4274	0.83818	0.0:0.8683:0.1317:0.0	.	.	.	.	X	705	.	ENSP00000332247:Q705X	Q	+	1	0	ATP6V0A2	122802840	0.994000	0.37717	0.333000	0.25482	0.718000	0.41266	3.320000	0.51991	1.409000	0.46915	0.655000	0.94253	CAA	.	.	.	none		0.403	ATP6V0A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400765.2	NM_012463		T	124236887	C	T	124236887	4	4	277	1	0	0	0	0	0	1	0	0	1169	595	21	2	2179	2	ATP6V0A2	12	124236887	Nonsense_Mutation	SNP	C	TCGA-Y8-A897-01A-11D-A35Z-10	67244343	124236887	9615008	37	17651											
HECTD1	25831	hgsc.bcm.edu	37	chr14	31637663	31637663	+	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	tatcatctcctttattaactGgacacatccaatcacctaca	13	13	2	13	0	3	0	2	0	1	0	5	1	4	1	3	1	2	0	3	1	5	5			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr14:31637663G>A	ENST00000399332.1	-	10	1951	c.1463C>T	c.(1462-1464)cCa>cTa	p.P488L	HECTD1_ENST00000553700.1_Missense_Mutation_p.P488L	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	488					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)		TTTATTAACTGGACACATCCA	0.318																																					p.P488L		Atlas-SNP	.											.	HECTD1	159	.	0			c.C1463T						PASS	.						173	166	168					14																	31637663		1802	4072	5874	SO:0001583	missense	25831	exon10			TTAACTGGACACA	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.1463C>T	chr14.hg19:g.31637663G>A	ENSP00000382269:p.Pro488Leu	50.0	0.0	.		65.0	25.0	.	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	hg19	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.688626	0.88639	.	.	ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332;ENST00000556224	T;T;T	0.71579	1.04;1.04;-0.58	5.23	5.23	0.72850	Ankyrin repeat-containing domain (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.80281	0.4594	L	0.43152	1.355	0.80722	D	1	P;D	0.71674	0.702;0.998	B;D	0.73708	0.177;0.981	T	0.81534	-0.0889	10	0.66056	D	0.02	-12.7472	19.1631	0.93543	0.0:0.0:1.0:0.0	.	488;488	D3DS86;Q9ULT8	.;HECD1_HUMAN	L	488	ENSP00000450697:P488L;ENSP00000382269:P488L;ENSP00000452015:P488L	ENSP00000261312:P488L	P	-	2	0	HECTD1	30707414	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.568000	0.98166	2.585000	0.87301	0.467000	0.42956	CCA	.	.	.	none		0.318	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			A	31637663	G	A	31637663	3	1	277	1	0	0	0	0	1	0	0	0	7046	1348	47	2	6505	2	HECTD1	14	31637663	Missense_Mutation	SNP	G	TCGA-Y8-A897-01A-11D-A35Z-10		31637663	75711877	38	17652											
NAA30	122830	hgsc.bcm.edu	37	chr14	57857993	57857993	+	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	tccctcaagagcaaggtcctGagcgtagcagaggtggccgc	9	6	14	12	2	1	3	1	1	0	2	3	3	3	3	3	3	3	3	3	3	3	1			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr14:57857993G>C	ENST00000556492.1	+	2	472	c.318G>C	c.(316-318)ctG>ctC	p.L106L	NAA30_ENST00000554703.1_Intron|NAA30_ENST00000555166.1_Intron	NM_001011713.2	NP_001011713.2	Q147X3	NAA30_HUMAN	N(alpha)-acetyltransferase 30, NatC catalytic subunit	106					metabolic process (GO:0008152)	cytoplasm (GO:0005737)|NatC complex (GO:0031417)	peptide alpha-N-acetyltransferase activity (GO:0004596)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(2)|skin(2)	13						GCAAGGTCCTGAGCGTAGCAG	0.687																																					p.L106L		Atlas-SNP	.											.	NAA30	30	.	0			c.G318C						PASS	.						17	20	19					14																	57857993		2144	4189	6333	SO:0001819	synonymous_variant	122830	exon2			GGTCCTGAGCGTA	AK092674	CCDS32088.1	14q22.2	2010-05-07	2010-01-14	2010-01-14		ENSG00000139977	2.3.1.88	"N(alpha)-acetyltransferase subunits"	19844	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 35", "N-acetyltransferase 12", "N-acetyltransferase 12 (GCN5-related, putative)"	C14orf35, NAT12		19660095	Standard	NM_001011713		Approved	FLJ35355, MAK3, Mak3p	uc001xcx.4	Q147X3		ENST00000556492.1:c.318G>C	chr14.hg19:g.57857993G>C		146.0	0.0	.		107.0	33.0	.	NM_001011713	Q0IIN2	Silent	SNP	ENST00000556492.1	hg19	CCDS32088.1																																																																																			.	.	.	none		0.687	NAA30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412925.1	NM_001011713		C	57857993	G	C	57857993	2	2	277	1	0	0	0	0	0	0	0	1	10129	1277	45	4		4	NAA30	14	57857993	Silent	SNP	G	TCGA-Y8-A897-01A-11D-A35Z-10	26220330	57857993	49491547	39	17653											
ZFYVE1	53349	hgsc.bcm.edu	37	chr14	73442299	73442299	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagtaggcaggggcgatcTggtctgtcagccaggaagtc	8	8	15	10	1	3	0	1	0	2	0	5	2	4	1	2	5	1	2	2	5	2	1			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr14:73442299T>C	ENST00000556143.1	-	9	2486	c.1766A>G	c.(1765-1767)cAg>cGg	p.Q589R	ZFYVE1_ENST00000553891.1_Missense_Mutation_p.Q589R|ZFYVE1_ENST00000318876.5_Missense_Mutation_p.Q575R|ZFYVE1_ENST00000394207.2_Missense_Mutation_p.Q174R|ZFYVE1_ENST00000554145.1_5'UTR|ZFYVE1_ENST00000555072.1_Missense_Mutation_p.Q174R	NM_001281735.1|NM_021260.2	NP_001268664.1|NP_067083.1	Q9HBF4	ZFYV1_HUMAN	zinc finger, FYVE domain containing 1	589					negative regulation of phosphatase activity (GO:0010923)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|ER-mitochondrion membrane contact site (GO:0044233)|Golgi stack (GO:0005795)|perinuclear region of cytoplasm (GO:0048471)|pre-autophagosomal structure (GO:0000407)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(17)|ovary(1)|prostate(2)|skin(1)	35		all_lung(585;1.33e-09)		OV - Ovarian serous cystadenocarcinoma(108;1.6e-46)|BRCA - Breast invasive adenocarcinoma(234;0.00349)		AGGGGCGATCTGGTCTGTCAG	0.602																																					p.Q589R		Atlas-SNP	.											.	ZFYVE1	67	.	0			c.A1766G						PASS	.						117	101	106					14																	73442299		2203	4300	6503	SO:0001583	missense	53349	exon9			GCGATCTGGTCTG	AF251025	CCDS9811.1, CCDS41969.1, CCDS61498.1	14q24.2	2014-06-13	2003-02-28	2003-03-07		ENSG00000165861		"Zinc fingers, FYVE domain containing"	13180	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 172"	605471	"zinc finger protein, subfamily 2A (FYVE domain containing), 1"	ZNFN2A1		11024279, 11256955	Standard	NM_021260		Approved	DFCP1, KIAA1589, TAFF1, PPP1R172	uc001xnm.3	Q9HBF4		ENST00000556143.1:c.1766A>G	chr14.hg19:g.73442299T>C	ENSP00000450742:p.Gln589Arg	90.0	0.0	.		78.0	26.0	.	NM_021260	J3KNL9|Q8WYX7|Q96K57|Q9BXP9|Q9HCI3	Missense_Mutation	SNP	ENST00000556143.1	hg19	CCDS9811.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.232219	0.79688	.	.	ENSG00000165861	ENST00000553891;ENST00000318876;ENST00000556143;ENST00000394207;ENST00000555072	T;T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0;-1.0	6.17	6.17	0.99709	Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	T	0.75309	0.3832	M	0.66506	2.035	0.80722	D	1	P;B	0.39071	0.658;0.417	B;B	0.38954	0.286;0.075	T	0.77120	-0.2705	10	0.54805	T	0.06	-28.7588	16.8222	0.85835	0.0:0.0:0.0:1.0	.	589;589	G3V5N8;Q9HBF4	.;ZFYV1_HUMAN	R	589;575;589;174;174	ENSP00000452442:Q589R;ENSP00000326921:Q575R;ENSP00000450742:Q589R;ENSP00000377757:Q174R;ENSP00000452232:Q174R	ENSP00000326921:Q589R	Q	-	2	0	ZFYVE1	72512052	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.040000	0.89188	2.371000	0.80710	0.533000	0.62120	CAG	.	.	.	none		0.602	ZFYVE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413172.1	NM_021260		C	73442299	T	C	73442299	3	2	277	1	0	0	0	0	1	0	0	0	17675	1580	55	3	583	3	ZFYVE1	14	73442299	Missense_Mutation	SNP	T	TCGA-Y8-A897-01A-11D-A35Z-10	15584306	73442299	33907241	40	17654											
KIF26A	26153	hgsc.bcm.edu	37	chr14	104641420	104641420	+	Frame_Shift_Del	DEL	C	C	-																															ccacgcactgtggccctggaCcccgaccgcacgcctccctg																										TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr14:104641420delC	ENST00000423312.2	+	12	2295	c.2295delC	c.(2293-2295)gacfs	p.D765fs	KIF26A_ENST00000315264.7_Frame_Shift_Del_p.D626fs	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	765					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)		TGGCCCTGGACCCCGACCGCA	0.726																																					p.D765fs		Atlas-Indel,Pindel	.											.	KIF26A	84	.	0			c.2294delA						PASS	.						20	24	23					14																	104641420		2039	4175	6214	SO:0001589	frameshift_variant	26153	exon12			.	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.2295delC	chr14.hg19:g.104641420delC	ENSP00000388241:p.Asp765fs	113.0	0.0	0		66.0	22.0	0.333333	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Frame_Shift_Del	DEL	ENST00000423312.2	hg19	CCDS45171.1																																																																																			.	.	.	none		0.726	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1			-	104641420	C	-	104641420	7	5	277	1	0	1	0	1	0	0	0	0	8301	506	18	0	2341	0	KIF26A	14	104641420	Frame_Shift_Del	DEL	C	TCGA-Y8-A897-01A-11D-A35Z-10	31199121	104641420	2708120	41	17655											
SSTR5	6755	hgsc.bcm.edu	37	chr16	1129708	1129708	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggcgctgccccaggagccCgcctccgccggcctctactt	3	7	12	19	4	1	0	0	0	1	0	2	1	2	1	7	3	3	1	7	3	1	2			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr16:1129708C>T	ENST00000293897.4	+	1	928	c.840C>T	c.(838-840)ccC>ccT	p.P280P	SSTR5_ENST00000397547.2_Silent_p.P280P|SSTR5-AS1_ENST00000569832.1_RNA|SSTR5_ENST00000562758.1_Intron	NM_001053.3	NP_001044.1	P35346	SSR5_HUMAN	somatostatin receptor 5	280					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)	CCCAGGAGCCCGCCTCCGCCG	0.627																																					p.P280P		Atlas-SNP	.											.	SSTR5	36	.	0			c.C840T						PASS	.						97	100	99					16																	1129708		2194	4297	6491	SO:0001819	synonymous_variant	6755	exon2			GGAGCCCGCCTCC	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.840C>T	chr16.hg19:g.1129708C>T		64.0	0.0	.		98.0	46.0	.	NM_001172560	P34988|Q541E0|Q9UJI5	Silent	SNP	ENST00000293897.4	hg19	CCDS10429.1																																																																																			.	.	.	none		0.627	SSTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420836.1			T	1129708	C	T	1129708	2	4	277	1	0	0	0	0	0	0	0	1	15213	639	23	1		1	SSTR5	16	1129708	Silent	SNP	C	TCGA-Y8-A897-01A-11D-A35Z-10		1129708	89225045	42	17656											
GRIN2A	2903	hgsc.bcm.edu	37	chr16	10031887	10031887	+	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	ctggccttggcctcggggatGtaggagaacttctccagcat	7	10	13	11	1	1	1	0	0	1	1	3	3	1	2	3	5	2	2	3	5	2	3			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr16:10031887G>A	ENST00000396573.2	-	4	1245	c.936C>T	c.(934-936)taC>taT	p.Y312Y	GRIN2A_ENST00000330684.3_Silent_p.Y312Y|GRIN2A_ENST00000566670.1_5'Flank|GRIN2A_ENST00000404927.2_Silent_p.Y312Y|GRIN2A_ENST00000562109.1_Silent_p.Y312Y|GRIN2A_ENST00000396575.2_Silent_p.Y312Y|GRIN2A_ENST00000535259.1_Silent_p.Y155Y	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	312					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)	CCTCGGGGATGTAGGAGAACT	0.577																																					p.Y312Y		Atlas-SNP	.											.	GRIN2A	366	.	0			c.C936T						PASS	.						73	61	65					16																	10031887		2197	4300	6497	SO:0001819	synonymous_variant	2903	exon4			GGGGATGTAGGAG		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.936C>T	chr16.hg19:g.10031887G>A		94.0	0.0	.		143.0	78.0	.	NM_000833	O00669|Q17RZ6	Silent	SNP	ENST00000396573.2	hg19	CCDS10539.1																																																																																			.	.	.	none		0.577	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			A	10031887	G	A	10031887	2	1	277	1	0	0	0	0	0	0	0	1	6786	1372	48	2		2	GRIN2A	16	10031887	Silent	SNP	G	TCGA-Y8-A897-01A-11D-A35Z-10	8902179	10031887	80322866	43	17657											
KARS	3735	hgsc.bcm.edu	37	chr16	75662551	75662551	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggggggcagcccatattcCagggcagtacagaagttttc	9	9	14	9	0	0	1	0	0	0	1	2	1	1	1	2	4	2	4	2	4	3	5			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr16:75662551C>T	ENST00000302445.3	-	13	1650	c.1611G>A	c.(1609-1611)ctG>ctA	p.L537L	KARS_ENST00000319410.5_Silent_p.L565L|KARS_ENST00000568378.1_Intron	NM_005548.2	NP_005539.1	Q15046	SYK_HUMAN	lysyl-tRNA synthetase	537					cell death (GO:0008219)|diadenosine tetraphosphate biosynthetic process (GO:0015966)|gene expression (GO:0010467)|lysyl-tRNA aminoacylation (GO:0006430)|tRNA aminoacylation for protein translation (GO:0006418)|tRNA processing (GO:0008033)|viral process (GO:0016032)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|microtubule cytoskeleton (GO:0015630)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	amino acid binding (GO:0016597)|ATP binding (GO:0005524)|lysine-tRNA ligase activity (GO:0004824)|metal ion binding (GO:0046872)|tRNA binding (GO:0000049)			kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	18					L-Lysine(DB00123)	GCCCATATTCCAGGGCAGTAC	0.517																																					p.L565L		Atlas-SNP	.											.	KARS	77	.	0			c.G1695A						PASS	.						86	81	82					16																	75662551		2198	4300	6498	SO:0001819	synonymous_variant	3735	exon14			ATATTCCAGGGCA	AF285758	CCDS10923.1, CCDS45532.1	16q23.1	2014-09-17			ENSG00000065427	ENSG00000065427	6.1.1.6	"Aminoacyl tRNA synthetases / Class II"	6215	protein-coding gene	gene with protein product	"lysine tRNA ligase"	601421	"deafness, autosomal recessive 89"	DFNB89		8812440, 9278442, 23768514	Standard	NM_005548		Approved	KARS2, KARS1	uc002fer.3	Q15046	OTTHUMG00000137609	ENST00000302445.3:c.1611G>A	chr16.hg19:g.75662551C>T		89.0	0.0	.		129.0	72.0	.	NM_001130089	A8MSK1|D3DUK4|O14946|Q96J25|Q9HB23	Silent	SNP	ENST00000302445.3	hg19	CCDS10923.1																																																																																			.	.	.	none		0.517	KARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269023.1	NM_005548		T	75662551	C	T	75662551	2	4	277	1	0	0	0	0	0	0	0	1	7987	581	21	2		2	KARS	16	75662551	Silent	SNP	C	TCGA-Y8-A897-01A-11D-A35Z-10	65630664	75662551	14692202	44	17658											
RAP1GAP2	23108	hgsc.bcm.edu	37	chr17	2888281	2888281	+	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	ttgccacattttccaggcctCccaaatgattgtgtcctatg	8	14	7	12	0	0	1	0	1	0	0	3	1	3	1	5	1	1	0	5	1	2	5			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr17:2888281C>A	ENST00000254695.8	+	11	824	c.734C>A	c.(733-735)tCc>tAc	p.S245Y	RAP1GAP2_ENST00000540393.2_Missense_Mutation_p.S226Y|RAP1GAP2_ENST00000366401.4_Missense_Mutation_p.S230Y|RAP1GAP2_ENST00000542807.1_Missense_Mutation_p.S245Y	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	245					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						TTCCAGGCCTCCCAAATGATT	0.423																																					p.S245Y		Atlas-SNP	.											.	RAP1GAP2	90	.	0			c.C734A						PASS	.						154	149	151					17																	2888281		1902	4130	6032	SO:0001583	missense	23108	exon11			AGGCCTCCCAAAT	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.734C>A	chr17.hg19:g.2888281C>A	ENSP00000254695:p.Ser245Tyr	49.0	0.0	.		62.0	20.0	.	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Missense_Mutation	SNP	ENST00000254695.8	hg19	CCDS45573.1	.	.	.	.	.	.	.	.	.	.	C	18.97	3.735492	0.69189	.	.	ENSG00000132359	ENST00000254695;ENST00000366401;ENST00000540393;ENST00000542807	D;D;D;D	0.93811	-3.29;-3.29;-3.29;-3.29	4.02	4.02	0.46733	.	0.189194	0.49305	D	0.000149	D	0.96367	0.8815	M	0.81942	2.565	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74023	0.982;0.956	D	0.96644	0.9476	10	0.56958	D	0.05	-15.0803	15.585	0.76475	0.0:1.0:0.0:0.0	.	230;245	Q684P5-2;Q684P5	.;RPGP2_HUMAN	Y	245;230;226;245	ENSP00000254695:S245Y;ENSP00000389824:S230Y;ENSP00000439688:S226Y;ENSP00000444890:S245Y	ENSP00000254695:S245Y	S	+	2	0	RAP1GAP2	2835031	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	6.743000	0.74848	2.166000	0.68216	0.462000	0.41574	TCC	.	.	.	none		0.423	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2			A	2888281	C	A	2888281	3	1	277	1	0	0	0	0	1	0	0	0	13051	855	30	4	776	4	RAP1GAP2	17	2888281	Missense_Mutation	SNP	C	TCGA-Y8-A897-01A-11D-A35Z-10		2888281	78306929	45	17659											
FBF1	85302	hgsc.bcm.edu	37	chr17	73916469	73916469	+	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	agctgcttctggtattctgtGctcggcagcaggctccgggc	4	11	14	12	2	2	0	0	0	2	0	4	0	3	0	1	4	4	7	1	4	1	3			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr17:73916469G>C	ENST00000586717.1	-	17	1947	c.1674C>G	c.(1672-1674)agC>agG	p.S558R	FBF1_ENST00000319129.5_Missense_Mutation_p.S557R|FBF1_ENST00000389570.4_Missense_Mutation_p.S558R			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	558					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						GGTATTCTGTGCTCGGCAGCA	0.647																																					p.S557R		Atlas-SNP	.											.	FBF1	48	.	0			c.C1671G						PASS	.						17	21	19					17																	73916469		1972	4147	6119	SO:0001583	missense	85302	exon17			TTCTGTGCTCGGC	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.1674C>G	chr17.hg19:g.73916469G>C	ENSP00000465132:p.Ser558Arg	170.0	0.0	.		107.0	32.0	.	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000586717.1	hg19		.	.	.	.	.	.	.	.	.	.	G	8.952	0.968338	0.18659	.	.	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	T;T	0.18960	2.18;2.21	5.22	-3.18	0.05186	.	.	.	.	.	T	0.10121	0.0248	N	0.14661	0.345	0.09310	N	1	B;B;B	0.31040	0.256;0.305;0.256	B;B;B	0.34138	0.132;0.175;0.176	T	0.41610	-0.9499	9	0.16896	T	0.51	-12.3052	6.6412	0.22911	0.3899:0.0:0.4887:0.1214	.	572;558;557	Q8TES7-6;Q8TES7;A6NLR5	.;FBF1_HUMAN;.	R	558;558;557;571	ENSP00000374221:S558R;ENSP00000324292:S557R	ENSP00000324292:S557R	S	-	3	2	FBF1	71428064	0.000000	0.05858	0.001000	0.08648	0.171000	0.22731	0.222000	0.17699	-0.141000	0.11374	-0.122000	0.15005	AGC	.	.	.	none		0.647	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542		C	73916469	G	C	73916469	3	2	277	1	0	0	0	0	1	0	0	0	5702	1310	46	4	1782	4	FBF1	17	73916469	Missense_Mutation	SNP	G	TCGA-Y8-A897-01A-11D-A35Z-10	71028188	73916469	7278741	46	17660											
TNRC6C	57690	hgsc.bcm.edu	37	chr17	76087521	76087521	+	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	aaccgcatctctctctttagCtggactgaacccaaacatga	12	10	6	13	1	2	2	0	2	2	0	4	3	2	3	2	1	4	2	2	1	4	2			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr17:76087521C>G	ENST00000588061.1	+	16	4530	c.3803C>G	c.(3802-3804)gCt>gGt	p.A1268G	TNRC6C_ENST00000335749.4_Splice_Site_p.A1265G|TNRC6C_ENST00000544502.1_Splice_Site_p.A1265G|TNRC6C_ENST00000301624.4_Splice_Site_p.A1268G|TNRC6C_ENST00000588847.1_Splice_Site_p.A1265G|TNRC6C_ENST00000541771.1_Splice_Site_p.A1268G			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	1268	Silencing domain; interaction with CNOT1 and PAN3.				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)			CTCTCTTTAGCTGGACTGAAC	0.498																																					p.A1268G		Atlas-SNP	.											.	TNRC6C	173	.	0			c.C3803G						PASS	.						94	90	91					17																	76087521		1990	4164	6154	SO:0001630	splice_region_variant	57690	exon15			CTTTAGCTGGACT	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.3803-1C>G	chr17.hg19:g.76087521C>G		83.0	0.0	.		91.0	35.0	.	NM_018996	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Missense_Mutation	SNP	ENST00000588061.1	hg19	CCDS45798.1	.	.	.	.	.	.	.	.	.	.	C	15.57	2.872451	0.51695	.	.	ENSG00000078687	ENST00000455761;ENST00000395801;ENST00000335749;ENST00000301624;ENST00000541771;ENST00000544502	T;T;T;T	0.15139	2.45;2.45;2.45;2.45	5.97	5.97	0.96955	.	0.218024	0.48286	D	0.000187	T	0.17492	0.0420	L	0.36672	1.1	0.80722	D	1	B;B	0.12630	0.003;0.006	B;B	0.15870	0.011;0.014	T	0.07481	-1.0770	9	.	.	.	.	20.4251	0.99070	0.0:1.0:0.0:0.0	.	1265;1268	G3XAB8;Q9HCJ0	.;TNR6C_HUMAN	G	1268;1265;1265;1268;1268;1265	ENSP00000336783:A1265G;ENSP00000301624:A1268G;ENSP00000440310:A1268G;ENSP00000442421:A1265G	.	A	+	2	0	TNRC6C	73599116	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	6.086000	0.71352	2.829000	0.97493	0.650000	0.86243	GCT	.	.	.	none		0.498	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996	Missense_Mutation	G	76087521	C	G	76087521	5	3	277	1	0	0	0	0	0	0	1	0	16354	811	28	4	3849	4	TNRC6C	17	76087521	Splice_Site	SNP	C	TCGA-Y8-A897-01A-11D-A35Z-10	2171052	76087521	5107689	47	17661											
USP36	57602	hgsc.bcm.edu	37	chr17	76802272	76802272	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggccaagtggaggcaacgaCggggtgagaggttttcatgg	9	7	19	6	2	1	1	1	1	0	1	1	4	1	2	1	7	1	2	1	7	2	2			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr17:76802272C>T	ENST00000542802.3	-	15	2625	c.2182G>A	c.(2182-2184)Gtc>Atc	p.V728I	USP36_ENST00000449938.2_Missense_Mutation_p.V428I|USP36_ENST00000312010.6_Missense_Mutation_p.V728I|USP36_ENST00000588467.1_5'Flank			Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	728					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)			GAGGCAACGACGGGGTGAGAG	0.637																																					p.V728I		Atlas-SNP	.											.	USP36	243	.	0			c.G2182A						PASS	.						90	83	86					17																	76802272		2203	4300	6503	SO:0001583	missense	57602	exon15			CAACGACGGGGTG	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.2182G>A	chr17.hg19:g.76802272C>T	ENSP00000441214:p.Val728Ile	98.0	0.0	.		68.0	17.0	.	NM_025090	Q05C98|Q05DD0|Q6IQ38|Q8NDM8|Q9NVC8	Missense_Mutation	SNP	ENST00000542802.3	hg19	CCDS32755.1	.	.	.	.	.	.	.	.	.	.	C	7.088	0.571496	0.13623	.	.	ENSG00000055483	ENST00000312010;ENST00000449938;ENST00000542802	T;T;T	0.19394	3.17;2.15;3.17	5.36	1.2	0.21068	.	0.950666	0.08909	N	0.876186	T	0.17365	0.0417	L	0.39397	1.21	0.09310	N	1	B;B	0.21309	0.032;0.054	B;B	0.22386	0.017;0.039	T	0.34800	-0.9814	10	0.28530	T	0.3	-11.5013	8.2243	0.31560	0.0:0.678:0.0:0.322	.	728;728	Q9P275;Q9P275-2	UBP36_HUMAN;.	I	728;428;728	ENSP00000310590:V728I;ENSP00000401119:V428I;ENSP00000441214:V728I	ENSP00000310590:V728I	V	-	1	0	USP36	74313867	0.006000	0.16342	0.366000	0.25914	0.382000	0.30200	0.376000	0.20535	0.023000	0.15187	-0.766000	0.03442	GTC	.	.	.	none		0.637	USP36-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437472.3	NM_025090		T	76802272	C	T	76802272	3	4	277	1	0	0	0	0	1	0	0	0	17079	536	19	1	1213	1	USP36	17	76802272	Missense_Mutation	SNP	C	TCGA-Y8-A897-01A-11D-A35Z-10	714751	76802272	4392938	48	17662											
PTPRM	5797	hgsc.bcm.edu	37	chr18	7774145	7774145	+	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	tttttattcttttacattttAggtggctgcctctttgatga	6	22	7	6	0	2	2	0	2	2	0	2	2	2	2	1	2	2	1	1	2	3	9			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr18:7774145A>C	ENST00000332175.8	+	2	1110		c.e2-1		PTPRM_ENST00000580170.1_Splice_Site|PTPRM_ENST00000400053.4_Splice_Site|PTPRM_ENST00000400060.4_Splice_Site	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				TTTACATTTTAGGTGGCTGCC	0.398																																					.		Atlas-SNP	.											.	PTPRM	185	.	0			c.74-2A>C						PASS	.						122	115	117					18																	7774145		2203	4300	6503	SO:0001630	splice_region_variant	5797	exon2			CATTTTAGGTGGC	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.74-1A>C	chr18.hg19:g.7774145A>C		64.0	0.0	.		82.0	26.0	.	NM_002845	A7MBN1|D3DUH8|J3QL11	Splice_Site	SNP	ENST00000332175.8	hg19	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	A	18.59	3.657315	0.67586	.	.	ENSG00000173482	ENST00000332175;ENST00000400060	.	.	.	5.76	5.76	0.90799	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3444	0.74324	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PTPRM	7764145	1.000000	0.71417	0.994000	0.49952	0.850000	0.48378	6.965000	0.76067	2.324000	0.78689	0.533000	0.62120	.	.	.	.	none		0.398	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1		Intron	C	7774145	A	C	7774145	5	2	277	1	0	0	0	0	0	0	1	0	12819	434	15	5	78	5	PTPRM	18	7774145	Splice_Site	SNP	A	TCGA-Y8-A897-01A-11D-A35Z-10		7774145	70303103	49	17663											
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43503240	43503240	+	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	agagaaggaaatacctgcttCatactttcagagagaatccc	15	9	8	9	0	2	3	2	0	0	3	3	6	3	4	2	1	3	1	2	1	5	4			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr18:43503240C>T	ENST00000282041.5	-	15	2866	c.2832G>A	c.(2830-2832)atG>atA	p.M944I		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	944					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						ATACCTGCTTCATACTTTCAG	0.378																																					p.M944I		Atlas-SNP	.											.	EPG5	199	.	0			c.G2832A						PASS	.						84	76	79					18																	43503240		1843	4098	5941	SO:0001583	missense	57724	exon15			CTGCTTCATACTT	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.2832G>A	chr18.hg19:g.43503240C>T	ENSP00000282041:p.Met944Ile	32.0	0.0	.		34.0	11.0	.	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	hg19	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	C	3.452	-0.111780	0.06881	.	.	ENSG00000152223	ENST00000282041	T	0.06933	3.24	5.49	3.43	0.39272	.	0.084546	0.49916	D	0.000132	T	0.02304	0.0071	N	0.04203	-0.255	0.31848	N	0.622549	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.44314	-0.9336	10	0.02654	T	1	-23.3105	0.8864	0.01245	0.2312:0.3676:0.2247:0.1765	.	944;944	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	I	944	ENSP00000282041:M944I	ENSP00000282041:M944I	M	-	3	0	EPG5	41757238	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.851000	0.39338	2.575000	0.86900	0.650000	0.86243	ATG	.	.	.	none		0.378	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		T	43503240	C	T	43503240	3	4	277	1	0	0	0	0	1	0	0	0	8256	826	29	2	5027	2	KIAA1632	18	43503240	Missense_Mutation	SNP	C	TCGA-Y8-A897-01A-11D-A35Z-10	35729095	43503240	34574008	50	17664											
DSEL	92126	hgsc.bcm.edu	37	chr18	65179563	65179563	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggggaaaataatcctatcAtgtcttacaggctttactat	14	13	7	7	0	2	0	1	0	1	0	3	1	3	1	1	3	2	1	1	3	8	6			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr18:65179563A>G	ENST00000310045.7	-	2	3786	c.2313T>C	c.(2311-2313)caT>caC	p.H771H	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	761					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)				TAATCCTATCATGTCTTACAG	0.383																																					p.H771H		Atlas-SNP	.											.	DSEL	196	.	0			c.T2313C						PASS	.						50	53	52					18																	65179563		2203	4300	6503	SO:0001819	synonymous_variant	92126	exon2			CCTATCATGTCTT	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.2313T>C	chr18.hg19:g.65179563A>G		70.0	0.0	.		87.0	33.0	.	NM_032160	Q17RH1|Q6P5Z3	Silent	SNP	ENST00000310045.7	hg19	CCDS11995.1																																																																																			.	.	.	none		0.383	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160		G	65179563	A	G	65179563	2	3	277	1	0	0	0	0	0	0	0	1	4777	214	8	3		3	DSEL	18	65179563	Silent	SNP	A	TCGA-Y8-A897-01A-11D-A35Z-10	21676323	65179563	12897685	51	17665											
CNDP2	55748	hgsc.bcm.edu	37	chr18	72186228	72186228	+	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	ccagggaaggcggcagtattCccgtgaccttgacctttcag	8	9	12	12	2	1	2	1	2	0	0	2	3	2	3	4	3	0	2	4	3	2	4			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr18:72186228C>T	ENST00000324262.4	+	11	1571	c.1255C>T	c.(1255-1257)Ccc>Tcc	p.P419S	CNDP2_ENST00000324301.8_Missense_Mutation_p.P335S|CNDP2_ENST00000579847.1_Missense_Mutation_p.P419S	NM_018235.2	NP_060705.2	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2 (metallopeptidase M20 family)	419					cellular nitrogen compound metabolic process (GO:0034641)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)			breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(5)|ovary(2)|skin(2)|stomach(3)	24		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)		CGGCAGTATTCCCGTGACCTT	0.547																																					p.P419S		Atlas-SNP	.											.	CNDP2	55	.	0			c.C1255T						PASS	.						99	102	101					18																	72186228		2203	4300	6503	SO:0001583	missense	55748	exon11			AGTATTCCCGTGA	AK001692	CCDS12006.1, CCDS54190.1	18q22.3	2014-07-14	2004-07-12		ENSG00000133313	ENSG00000133313	3.4.13.18		24437	protein-coding gene	gene with protein product	"cytosolic nonspecific dipeptidase"	169800	"peptidase A"	PEPA		12473676	Standard	NM_018235		Approved	FLJ10830, CN2, HsT2298, CPGL	uc002llm.2	Q96KP4	OTTHUMG00000132853	ENST00000324262.4:c.1255C>T	chr18.hg19:g.72186228C>T	ENSP00000325548:p.Pro419Ser	131.0	0.0	.		108.0	31.0	.	NM_018235	B3KUG4|Q8WY59|Q9BQ94|Q9NVB4	Missense_Mutation	SNP	ENST00000324262.4	hg19	CCDS12006.1	.	.	.	.	.	.	.	.	.	.	C	33	5.255471	0.95336	.	.	ENSG00000133313	ENST00000324262;ENST00000324301	T;T	0.09163	3.01;3.01	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.53465	0.1798	H	0.98295	4.195	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.73855	-0.3851	10	0.87932	D	0	-2.6596	19.1765	0.93604	0.0:1.0:0.0:0.0	.	335;419	Q96KP4-2;Q96KP4	.;CNDP2_HUMAN	S	419;335	ENSP00000325548:P419S;ENSP00000325756:P335S	ENSP00000325548:P419S	P	+	1	0	CNDP2	70337208	1.000000	0.71417	0.841000	0.33234	0.961000	0.63080	7.731000	0.84895	2.538000	0.85594	0.650000	0.86243	CCC	.	.	.	none		0.547	CNDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256327.1	NM_018235		T	72186228	C	T	72186228	3	4	277	1	0	0	0	0	1	0	0	0	3596	855	30	2	1293	2	CNDP2	18	72186228	Missense_Mutation	SNP	C	TCGA-Y8-A897-01A-11D-A35Z-10	7006665	72186228	5891020	52	17666											
ZNF285	26974	hgsc.bcm.edu	37	chr19	44892064	44892064	+	Frame_Shift_Del	DEL	A	A	-																															attttcagaaatctgaagagAaatgcctgcccactcttcac																										TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr19:44892064delA	ENST00000330997.4	-	4	407	c.343delT	c.(343-345)tctfs	p.S115fs	ZNF285_ENST00000544719.2_Frame_Shift_Del_p.S115fs|ZNF285_ENST00000591679.1_Frame_Shift_Del_p.S122fs|CTC-512J12.6_ENST00000588212.1_Intron	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	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)			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						ATCTGAAGAGAAATGCCTGCC	0.408																																					p.S115fs		Atlas-Indel,Pindel	.											.	ZNF285	86	.	0			c.344delC						PASS	.						87	86	86					19																	44892064		2203	4300	6503	SO:0001589	frameshift_variant	26974	exon4			.	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.343delT	chr19.hg19:g.44892064delA	ENSP00000333595:p.Ser115fs	79.0	0.0	0		127.0	48.0	0.377953	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Frame_Shift_Del	DEL	ENST00000330997.4	hg19	CCDS12638.1																																																																																			.	.	.	none		0.408	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354		-	44892064	A	-	44892064	7	5	277	1	0	1	0	1	0	0	0	0	17834	246	9	0	1433	0	ZNF285	19	44892064	Frame_Shift_Del	DEL	A	TCGA-Y8-A897-01A-11D-A35Z-10		44892064	14236919	53	17667											
OXT	5020	hgsc.bcm.edu	37	chr20	3052889	3052889	+	Missense_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	gaaggcgtgcgggagcggggGccgctgcgcggtcttgggcc	3	5	22	11	6	1	0	0	0	1	0	1	2	1	1	2	6	3	1	2	6	1	1			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr20:3052889G>A	ENST00000217386.2	+	2	323	c.287G>A	c.(286-288)gGc>gAc	p.G96D		NM_000915.2	NP_000906.1	P01178	NEU1_HUMAN	oxytocin/neurophysin I prepropeptide	96					drinking behavior (GO:0042756)|eating behavior (GO:0042755)|female pregnancy (GO:0007565)|grooming behavior (GO:0007625)|heart development (GO:0007507)|hyperosmotic salinity response (GO:0042538)|male mating behavior (GO:0060179)|maternal aggressive behavior (GO:0002125)|maternal behavior (GO:0042711)|memory (GO:0007613)|negative regulation of blood pressure (GO:0045776)|negative regulation of gastric acid secretion (GO:0060455)|negative regulation of urine volume (GO:0035811)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of female receptivity (GO:0045925)|positive regulation of hindgut contraction (GO:0060450)|positive regulation of norepinephrine secretion (GO:0010701)|positive regulation of ossification (GO:0045778)|positive regulation of penile erection (GO:0060406)|positive regulation of prostaglandin secretion (GO:0032308)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission (GO:0050806)|positive regulation of uterine smooth muscle contraction (GO:0070474)|regulation of heart rate (GO:0002027)|regulation of sensory perception of pain (GO:0051930)|response to activity (GO:0014823)|response to amphetamine (GO:0001975)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to ether (GO:0045472)|response to food (GO:0032094)|response to glucocorticoid (GO:0051384)|response to peptide hormone (GO:0043434)|response to progesterone (GO:0032570)|response to prostaglandin E (GO:0034695)|response to retinoic acid (GO:0032526)|response to sucrose (GO:0009744)|signal transduction (GO:0007165)|sleep (GO:0030431)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)				lung(2)	2					Oxytocin(DB00107)	GGGAGCGGGGGCCGCTGCGCG	0.766																																					p.G96D		Atlas-SNP	.											OXT,NS,carcinoma,0,1	OXT	9	.	0			c.G287A						PASS	.						7	9	9					20																	3052889		2026	4087	6113	SO:0001583	missense	5020	exon2			GCGGGGGCCGCTG		CCDS13044.1	20p13	2013-02-28	2012-10-23		ENSG00000101405	ENSG00000101405		"Endogenous ligands"	8528	protein-coding gene	gene with protein product	"oxytocin", "neurophysin I"	167050	"oxytocin, prepro- (neurophysin I)", "oxytocin, prepropeptide"	OT			Standard	NM_000915		Approved	OXT-NPI, OT-NPI	uc002wht.1	P01178	OTTHUMG00000031724	ENST00000217386.2:c.287G>A	chr20.hg19:g.3052889G>A	ENSP00000217386:p.Gly96Asp	434.0	0.0	.		235.0	75.0	.	NM_000915	Q3MIG0	Missense_Mutation	SNP	ENST00000217386.2	hg19	CCDS13044.1	.	.	.	.	.	.	.	.	.	.	G	18.11	3.551282	0.65311	.	.	ENSG00000101405	ENST00000217386	D	0.97404	-4.37	4.35	3.37	0.38596	.	0.106321	0.64402	D	0.000004	D	0.98635	0.9543	M	0.92122	3.275	0.58432	D	0.999997	D	0.76494	0.999	D	0.80764	0.994	D	0.99334	1.0910	10	0.87932	D	0	-22.9506	13.9613	0.64182	0.0:0.1534:0.8466:0.0	.	96	P01178	NEU1_HUMAN	D	96	ENSP00000217386:G96D	ENSP00000217386:G96D	G	+	2	0	OXT	3000889	1.000000	0.71417	0.997000	0.53966	0.212000	0.24457	5.958000	0.70330	0.767000	0.33267	0.491000	0.48974	GGC	.	.	.	none		0.766	OXT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077698.2	NM_000915		A	3052889	G	A	3052889	3	1	277	1	0	0	0	0	1	0	0	0	11344	1203	42	2	293	2	OXT	20	3052889	Missense_Mutation	SNP	G	TCGA-Y8-A897-01A-11D-A35Z-10		3052889	59972631	54	17668											
PRIC285	85441	hgsc.bcm.edu	37	chr20	62199985	62199985	+	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	ctgctcctcaggcagtgtgtCcactgcctggtgccagaggc	5	9	13	14	0	1	1	1	0	0	1	3	1	3	1	4	3	3	2	4	3	0	0	rs547559351		TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr20:62199985C>T	ENST00000467148.1	-	5	1525	c.1456G>A	c.(1456-1458)Gac>Aac	p.D486N	HELZ2_ENST00000427522.2_5'Flank|HELZ2_ENST00000479540.1_5'Flank	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	486					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)										GGCAGTGTGTCCACTGCCTGG	0.672													C|||	1	0.000199681	0	0	5008	,	,		16690	0.001		0	False		,,,				2504	0				p.D486N		Atlas-SNP	.											.	.	.	.	0			c.G1456A						PASS	.						11	13	12					20																	62199985		2171	4255	6426	SO:0001583	missense	85441	exon6			GTGTGTCCACTGC	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.1456G>A	chr20.hg19:g.62199985C>T	ENSP00000417401:p.Asp486Asn	47.0	0.0	.		51.0	16.0	.	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	hg19	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.227891	0.79576	.	.	ENSG00000130589	ENST00000467148	D	0.83755	-1.76	4.67	4.67	0.58626	.	0.124802	0.52532	D	0.000078	D	0.90796	0.7110	M	0.74258	2.255	0.48571	D	0.999675	D	0.89917	1.0	D	0.91635	0.999	D	0.92003	0.5612	10	0.66056	D	0.02	-29.1757	17.577	0.87953	0.0:1.0:0.0:0.0	.	486	Q9BYK8	PR285_HUMAN	N	486	ENSP00000417401:D486N	ENSP00000417401:D486N	D	-	1	0	RP4-697K14.7	61670429	1.000000	0.71417	0.898000	0.35279	0.228000	0.25075	7.448000	0.80631	2.157000	0.67596	0.563000	0.77884	GAC	.	.	.	none		0.672	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		T	62199985	C	T	62199985	3	4	277	1	0	0	0	0	1	0	0	0	12495	855	30	2	6576	2	PRIC285	20	62199985	Missense_Mutation	SNP	C	TCGA-Y8-A897-01A-11D-A35Z-10	59147096	62199985	825535	55	17669											
PCNT	5116	hgsc.bcm.edu	37	chr21	47831328	47831328	+	Frame_Shift_Del	DEL	G	G	-																															agctgctctgctcccaggccGggggccctcgtgggcaggcc																								rs200137805	byFrequency	TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr21:47831328delG	ENST00000359568.5	+	28	5448	c.5341delG	c.(5341-5343)gggfs	p.G1782fs	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1782					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)		p.G1781R(1)		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)					CTCCCAGGCCGGGGGCCCTCG	0.692																																					p.A1780fs		Pindel	.											.	PCNT	283	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.5340delC						PASS	.						27	33	31					21																	47831328		2198	4296	6494	SO:0001589	frameshift_variant	5116	exon28			.	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.5341delG	chr21.hg19:g.47831328delG	ENSP00000352572:p.Gly1782fs	145.0	0.0	.		90.0	24.0	0.267	NM_006031	O43152|Q7Z7C9	Frame_Shift_Del	DEL	ENST00000359568.5	hg19	CCDS33592.1																																																																																			.	.	.	none		0.692	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		-	47831328	G	-	47831328	7	5	277	1	0	1	0	1	0	0	0	0	11597	1116	39	0	5451	0	PCNT	21	47831328	Frame_Shift_Del	DEL	G	TCGA-Y8-A897-01A-11D-A35Z-10		47831328	298567	56	17670											
PNPLA5	150379	hgsc.bcm.edu	37	chr22	44287719	44287719	+	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	cccaggtagccggcgccggaGaaggacaggttccatctgcc	8	5	14	14	3	1	1	0	0	1	1	2	3	2	2	5	5	2	2	5	5	2	2			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chr22:44287719G>T	ENST00000597664.1	-	1	171	c.42C>A	c.(40-42)ttC>ttA	p.F14L	PNPLA5_ENST00000593866.1_Missense_Mutation_p.F14L|PNPLA5_ENST00000216177.4_Missense_Mutation_p.F14L|PNPLA5_ENST00000381198.2_Missense_Mutation_p.F14L			Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	14	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)				CGGCGCCGGAGAAGGACAGGT	0.706																																					p.F14L		Atlas-SNP	.											.	PNPLA5	46	.	0			c.C42A						PASS	.						6	7	7					22																	44287719		1700	3173	4873	SO:0001583	missense	150379	exon1			GCCGGAGAAGGAC	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.42C>A	chr22.hg19:g.44287719G>T	ENSP00000471069:p.Phe14Leu	347.0	0.0	.		206.0	11.0	.	NM_138814	B1AHL8|B3KPR1|Q6ZST0	Missense_Mutation	SNP	ENST00000597664.1	hg19		.	.	.	.	.	.	.	.	.	.	G	17.99	3.522118	0.64747	.	.	ENSG00000100341	ENST00000216177;ENST00000381198;ENST00000438734	T;T;T	0.66280	-0.2;-0.2;-0.2	5.03	2.9	0.33743	Acyl transferase/acyl hydrolase/lysophospholipase (1);Patatin/Phospholipase A2-related (1);	0.000000	0.64402	D	0.000001	T	0.73125	0.3547	M	0.63843	1.955	0.24854	N	0.99238	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	T	0.62955	-0.6744	10	0.51188	T	0.08	-37.3994	10.5912	0.45310	0.1639:0.0:0.8361:0.0	.	14;14	Q7Z6Z6-2;Q7Z6Z6	.;PLPL5_HUMAN	L	14	ENSP00000216177:F14L;ENSP00000370595:F14L;ENSP00000405732:F14L	ENSP00000216177:F14L	F	-	3	2	PNPLA5	42619052	0.904000	0.30761	0.803000	0.32268	0.107000	0.19398	1.167000	0.31847	1.115000	0.41800	0.313000	0.20887	TTC	.	.	.	none		0.706	PNPLA5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000075667.4	NM_138814		T	44287719	G	T	44287719	3	4	277	1	0	0	0	0	1	0	0	0	12175	933	33	4	1283	4	PNPLA5	22	44287719	Missense_Mutation	SNP	G	TCGA-Y8-A897-01A-11D-A35Z-10		44287719	7016847	57	17671											
SLC9A7	84679	hgsc.bcm.edu	37	chrX	46541773	46541773	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagtgtccccagctcacctTccgtagcatatcattctgct	7	13	7	14	1	3	1	2	1	1	0	5	1	5	1	4	0	3	4	4	0	2	4			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chrX:46541773T>C	ENST00000328306.4	-	2	548	c.523A>G	c.(523-525)Aag>Gag	p.K175E		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	175					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						CAGCTCACCTTCCGTAGCATA	0.463																																					p.K175E	Pancreas(118;454 1696 1930 13865 39976)	Atlas-SNP	.											.	SLC9A7	73	.	0			c.A523G						PASS	.						143	97	112					X																	46541773		2203	4300	6503	SO:0001583	missense	84679	exon2			TCACCTTCCGTAG	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.523A>G	chrX.hg19:g.46541773T>C	ENSP00000330320:p.Lys175Glu	51.0	0.0	.		60.0	30.0	.	NM_001257291	O75827|Q5JXP9	Missense_Mutation	SNP	ENST00000328306.4	hg19	CCDS14269.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.484663	0.84854	.	.	ENSG00000065923	ENST00000328306	T	0.56776	0.44	5.7	5.7	0.88788	Cation/H+ exchanger (1);	0.000000	0.85682	D	0.000000	T	0.66771	0.2823	M	0.65677	2.01	0.80722	D	1	D	0.56287	0.975	P	0.60541	0.876	T	0.64639	-0.6360	10	0.27785	T	0.31	.	14.9741	0.71257	0.0:0.0:0.0:1.0	.	175	Q96T83	SL9A7_HUMAN	E	175	ENSP00000330320:K175E	ENSP00000330320:K175E	K	-	1	0	SLC9A7	46426717	1.000000	0.71417	1.000000	0.80357	0.792000	0.44763	7.611000	0.82962	1.918000	0.55548	0.486000	0.48141	AAG	.	.	.	none		0.463	SLC9A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056370.1	NM_032591		C	46541773	T	C	46541773	3	2	277	1	0	0	0	0	1	0	0	0	14732	1792	62	3	1718	3	SLC9A7	23	46541773	Missense_Mutation	SNP	T	TCGA-Y8-A897-01A-11D-A35Z-10		46541773	108728787	58	17672											
IQSEC2	23096	hgsc.bcm.edu	37	chrX	53350189	53350189	+	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	cagctggccctccagctcctCgatgcgccgccgctgggttt	3	9	12	17	4	0	0	0	0	0	0	3	1	2	0	5	2	3	4	5	2	0	1			TCGA-Y8-A897-01A-11D-A35Z-10	TCGA-Y8-A897-10A-01D-A35Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	a18fd0a9-7914-410c-8f2f-0b8c86803b88	56e7a4a9-632d-45d1-a1b1-f3ed4e689c9e	g.chrX:53350189C>T	ENST00000375368.5	-	1	333	c.133G>A	c.(133-135)Gag>Aag	p.E45K	IQSEC2_ENST00000396435.3_Missense_Mutation_p.E45K			Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2	45					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						TCCAGCTCCTCGATGCGCCGC	0.677																																					p.E45K		Atlas-SNP	.											.	IQSEC2	195	.	0			c.G133A						PASS	.						3	3	3					X																	53350189		634	1433	2067	SO:0001583	missense	23096	exon1			GCTCCTCGATGCG	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.133G>A	chrX.hg19:g.53350189C>T	ENSP00000364517:p.Glu45Lys	97.0	0.0	.		46.0	19.0	.	NM_001111125	B3KT97|C7SDG1|O60275|Q5JUX1	Missense_Mutation	SNP	ENST00000375368.5	hg19		.	.	.	.	.	.	.	.	.	.	c	15.76	2.928174	0.52759	.	.	ENSG00000124313	ENST00000396435;ENST00000375368	T;T	0.17854	2.25;2.27	2.73	2.73	0.32206	.	0.699468	0.11421	U	0.565815	T	0.20007	0.0481	L	0.27053	0.805	0.33140	D	0.544226	D	0.69078	0.997	P	0.53006	0.715	T	0.29941	-0.9995	10	0.72032	D	0.01	.	10.7028	0.45937	0.0:1.0:0.0:0.0	.	45	Q5JU85-2	.	K	45	ENSP00000379712:E45K;ENSP00000364517:E45K	ENSP00000364517:E45K	E	-	1	0	IQSEC2	53366914	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	5.250000	0.65432	1.641000	0.50575	0.284000	0.19432	GAG	.	.	.	none		0.677	IQSEC2-201	KNOWN	basic	protein_coding	protein_coding		XM_291345		T	53350189	C	T	53350189	3	4	277	1	0	0	0	0	1	0	0	0	7825	893	31	1	4523	1	IQSEC2	23	53350189	Missense_Mutation	SNP	C	TCGA-Y8-A897-01A-11D-A35Z-10	6808416	53350189	101920371	59	17673											
CAMTA1	23261	hgsc.bcm.edu	37	chr1	7724719	7724719	+	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	gcggaagggagcgaggtcctGctcaagtctggggagctgca	8	6	18	9	2	2	0	1	0	1	0	3	4	3	3	1	5	4	3	1	5	2	0			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr1:7724719G>T	ENST00000303635.7	+	9	2319	c.2112G>T	c.(2110-2112)ctG>ctT	p.L704L	CAMTA1_ENST00000439411.2_Silent_p.L704L	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	704					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)		GCGAGGTCCTGCTCAAGTCTG	0.662			T	WWTR1	epitheliod hemangioendothelioma																																p.L704L		Atlas-SNP	.		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	.	CAMTA1	226	.	0			c.G2112T						PASS	.						43	46	45					1																	7724719		2203	4300	6503	SO:0001819	synonymous_variant	23261	exon9			GGTCCTGCTCAAG	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.2112G>T	chr1.hg19:g.7724719G>T		32.0	0.0	.		48.0	13.0	.	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Silent	SNP	ENST00000303635.7	hg19	CCDS30576.1																																																																																			.	.	.	none		0.662	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215		T	7724719	G	T	7724719	2	4	278	1	0	0	0	0	0	0	0	1	2615	1306	46	4		4	CAMTA1	1	7724719	Silent	SNP	G	TCGA-Y8-A898-01A-11D-A34Z-10		7724719	241525902	1	17674											
PDPN	10630	hgsc.bcm.edu	37	chr1	13910573	13910573	+	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	ttcgttttgggaagcgcgtcGctctgggtcctggcagaagg	5	11	16	9	4	1	1	0	0	1	1	4	2	2	2	1	4	1	3	1	4	2	3			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr1:13910573G>T	ENST00000294489.6	+	1	614	c.273G>T	c.(271-273)tcG>tcT	p.S91S	PDPN_ENST00000513143.1_5'Flank|PDPN_ENST00000475043.1_5'Flank|PDPN_ENST00000376061.4_5'Flank|PDPN_ENST00000509009.1_5'Flank|PDPN_ENST00000376057.4_Silent_p.S91S|PDPN_ENST00000487038.1_5'Flank					podoplanin									p.S91S(1)		endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	16	Ovarian(185;0.249)	all_lung(284;2.29e-05)|Lung NSC(185;4.37e-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;0.00969)|Colorectal(212;4.48e-06)|COAD - Colon adenocarcinoma(227;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000347)|Kidney(185;0.00087)|KIRC - Kidney renal clear cell carcinoma(229;0.0027)|STAD - Stomach adenocarcinoma(313;0.00802)|READ - Rectum adenocarcinoma(331;0.0678)		GAAGCGCGTCGCTCTGGGTCC	0.612																																					p.S91S		Atlas-SNP	.											PDPN,colon,carcinoma,0,1	PDPN	44	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G273T						PASS	.						41	31	35					1																	13910573		2194	4272	6466	SO:0001819	synonymous_variant	10630	exon1			CGCGTCGCTCTGG	AB127958, AY194238	CCDS30602.1, CCDS41266.1, CCDS44060.1, CCDS53270.1	1p36.21	2008-02-05			ENSG00000162493	ENSG00000162493			29602	protein-coding gene	gene with protein product	"lung type I cell membrane associated glycoprotein"	608863				10393083, 9651190	Standard	NM_006474		Approved	T1A-2, Gp38, aggrus, GP40, PA2.26	uc001avd.3	Q86YL7	OTTHUMG00000007912	ENST00000294489.6:c.273G>T	chr1.hg19:g.13910573G>T		35.0	0.0	.		58.0	3.0	.	NM_006474		Silent	SNP	ENST00000294489.6	hg19	CCDS30602.1																																																																																			.	.	.	none		0.612	PDPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021783.2	NM_006474		T	13910573	G	T	13910573	2	4	278	1	0	0	0	0	0	0	0	1	11695	1074	38	4		4	PDPN	1	13910573	Silent	SNP	G	TCGA-Y8-A898-01A-11D-A34Z-10	6185854	13910573	235340048	2	17675											
XKR8	55113	hgsc.bcm.edu	37	chr1	28290159	28290159	+	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	cggcaccacagctcacgctgGtgctggccatcatgctgcag	7	7	12	15	2	2	0	2	0	0	0	2	0	2	0	2	3	4	6	2	3	0	0			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr1:28290159G>C	ENST00000373884.5	+	2	1053	c.445G>C	c.(445-447)Gtg>Ctg	p.V149L	XKR8_ENST00000481387.1_3'UTR	NM_018053.2	NP_060523.2	Q9H6D3	XKR8_HUMAN	XK, Kell blood group complex subunit-related family, member 8	149					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)		GCTCACGCTGGTGCTGGCCAT	0.622																																					p.V149L		Atlas-SNP	.											.	XKR8	15	.	0			c.G445C						PASS	.						22	19	20					1																	28290159		2203	4300	6503	SO:0001583	missense	55113	exon2			ACGCTGGTGCTGG	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.445G>C	chr1.hg19:g.28290159G>C	ENSP00000362991:p.Val149Leu	97.0	0.0	.		128.0	32.0	.	NM_018053		Missense_Mutation	SNP	ENST00000373884.5	hg19	CCDS315.1	.	.	.	.	.	.	.	.	.	.	G	4.622	0.115616	0.08831	.	.	ENSG00000158156	ENST00000373884	T	0.61980	0.06	5.58	3.68	0.42216	.	0.247521	0.39834	N	0.001241	T	0.48714	0.1515	L	0.31752	0.955	0.27758	N	0.943911	B	0.09022	0.002	B	0.10450	0.005	T	0.40720	-0.9548	10	0.39692	T	0.17	.	11.5401	0.50661	0.0735:0.5532:0.3733:0.0	.	149	Q9H6D3	XKR8_HUMAN	L	149	ENSP00000362991:V149L	ENSP00000362991:V149L	V	+	1	0	XKR8	28162746	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	1.076000	0.30729	0.680000	0.31366	0.655000	0.94253	GTG	.	.	.	none		0.622	XKR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011175.1	NM_018053		C	28290159	G	C	28290159	3	2	278	1	0	0	0	0	1	0	0	0	17449	1261	44	4	451	4	XKR8	1	28290159	Missense_Mutation	SNP	G	TCGA-Y8-A898-01A-11D-A34Z-10	14379586	28290159	220960462	3	17676											
EBNA1BP2	10969	hgsc.bcm.edu	37	chr1	43632514	43632514	+	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	caccccttcctcatctgctgGcctttggctcctgccttctt	2	15	6	18	0	3	0	1	0	2	0	5	0	5	0	6	2	2	2	6	2	0	4			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr1:43632514G>A	ENST00000236051.2	-	7	831	c.690C>T	c.(688-690)ggC>ggT	p.G230G	EBNA1BP2_ENST00000431635.2_Silent_p.G285G	NM_006824.2	NP_006815.2	Q99848	EBP2_HUMAN	EBNA1 binding protein 2	230					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)				TCATCTGCTGGCCTTTGGCTC	0.507																																					p.G285G		Atlas-SNP	.											.	EBNA1BP2	37	.	0			c.C855T						PASS	.						177	169	172					1																	43632514		2203	4300	6503	SO:0001819	synonymous_variant	10969	exon8			CTGCTGGCCTTTG	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.690C>T	chr1.hg19:g.43632514G>A		70.0	0.0	.		84.0	26.0	.	NM_001159936	Q96A66	Silent	SNP	ENST00000236051.2	hg19	CCDS478.1																																																																																			.	.	.	none		0.507	EBNA1BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019015.1			A	43632514	G	A	43632514	2	1	278	1	0	0	0	0	0	0	0	1	4887	1190	42	2		2	EBNA1BP2	1	43632514	Silent	SNP	G	TCGA-Y8-A898-01A-11D-A34Z-10	15342355	43632514	205618107	4	17677											
MPL	4352	hgsc.bcm.edu	37	chr1	43814558	43814558	+	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	cgaggagggaccctggagctGcgcccgcgatctcgctaccg	6	5	15	15	6	1	0	0	0	1	0	2	5	1	3	3	3	3	2	3	3	1	1			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr1:43814558G>T	ENST00000372470.3	+	9	1395	c.1353G>T	c.(1351-1353)ctG>ctT	p.L451L	MPL_ENST00000413998.2_Silent_p.L451L	NM_005373.2	NP_005364.1	P40238	TPOR_HUMAN	MPL proto-oncogene, thrombopoietin receptor	451	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|platelet activation (GO:0030168)|regulation of chemokine production (GO:0032642)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(551)|large_intestine(3)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	567	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			Eltrombopag(DB06210)|Romiplostim(DB05332)	CCCTGGAGCTGCGCCCGCGAT	0.687			Mis		MPD	MPD	congenital amegakaryocytic thrombocytopenia																														p.L451L	NSCLC(52;534 1204 10016 41452 44427)	Atlas-SNP	.	yes	Dom	yes	Familial essential thrombocythemia	1	p34	4352	"myeloproliferative leukemia virus oncogene, thrombopoietin receptor"	yes	L	.	MPL	651	.	0			c.G1353T						PASS	.						9	12	11					1																	43814558		2132	4173	6305	SO:0001819	synonymous_variant	4352	exon9			GGAGCTGCGCCCG	M90102	CCDS483.1	1p34	2014-09-17	2014-06-26		ENSG00000117400	ENSG00000117400		"CD molecules", "Fibronectin type III domain containing"	7217	protein-coding gene	gene with protein product		159530	"myeloproliferative leukemia virus oncogene"			1608974	Standard	NM_005373		Approved	CD110, TPOR	uc001ciw.3	P40238	OTTHUMG00000007429	ENST00000372470.3:c.1353G>T	chr1.hg19:g.43814558G>T		55.0	0.0	.		64.0	20.0	.	NM_005373	Q5JUZ0	Silent	SNP	ENST00000372470.3	hg19	CCDS483.1																																																																																			.	.	.	none		0.687	MPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019522.1	NM_005373		T	43814558	G	T	43814558	2	4	278	1	0	0	0	0	0	0	0	1	9737	1306	46	4		4	MPL	1	43814558	Silent	SNP	G	TCGA-Y8-A898-01A-11D-A34Z-10	182044	43814558	205436063	5	17678											
CCBL2	56267	hgsc.bcm.edu	37	chr1	89418774	89418774	+	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	gagttgcacaagtataaatcGtgttttgttgaactgtctgt	10	16	10	5	1	1	1	0	1	1	0	2	2	1	1	0	0	2	5	0	0	5	6	rs577169250		TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr1:89418774G>T	ENST00000260508.4	-	10	1263	c.926C>A	c.(925-927)aCg>aAg	p.T309K	CCBL2_ENST00000370485.2_3'UTR|CCBL2_ENST00000370491.3_Missense_Mutation_p.T275K|CCBL2_ENST00000446900.2_5'UTR	NM_001008661.2	NP_001008661.1	Q6YP21	KAT3_HUMAN	cysteine conjugate-beta lyase 2	309					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)		AGTATAAATCGTGTTTTGTTG	0.333																																					p.T309K		Atlas-SNP	.											.	CCBL2	138	.	0			c.C926A						PASS	.						125	126	125					1																	89418774		2203	4300	6503	SO:0001583	missense	56267	exon10			TAAATCGTGTTTT	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.926C>A	chr1.hg19:g.89418774G>T	ENSP00000260508:p.Thr309Lys	108.0	0.0	.		154.0	36.0	.	NM_001008661	B3KQ13|O95335|Q5JS27|Q5T9T7|Q5T9T8|Q6AI27|Q6ICW1|Q9BVY5	Missense_Mutation	SNP	ENST00000260508.4	hg19	CCDS30766.1	.	.	.	.	.	.	.	.	.	.	G	15.04	2.715737	0.48622	.	.	ENSG00000137944	ENST00000370491;ENST00000260508	D;D	0.90676	-2.71;-2.71	5.72	-1.29	0.09288	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.489469	0.24876	N	0.034886	D	0.86932	0.6052	M	0.86502	2.82	0.19300	N	0.99998	B	0.34103	0.437	B	0.41946	0.371	D	0.83437	0.0041	10	0.51188	T	0.08	-2.7189	10.0336	0.42116	0.0618:0.5605:0.2757:0.102	.	309	Q6YP21	KAT3_HUMAN	K	275;309	ENSP00000359522:T275K;ENSP00000260508:T309K	ENSP00000260508:T309K	T	-	2	0	CCBL2	89191362	0.407000	0.25352	0.015000	0.15790	0.808000	0.45660	0.714000	0.25808	-0.200000	0.10300	0.585000	0.79938	ACG	.	.	.	none		0.333	CCBL2-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000029300.3	NM_001008661		T	89418774	G	T	89418774	3	4	278	1	0	0	0	0	1	0	0	0	2735	1145	40	4	458	4	CCBL2	1	89418774	Missense_Mutation	SNP	G	TCGA-Y8-A898-01A-11D-A34Z-10	45604216	89418774	159831847	6	17679											
FRRS1	391059	hgsc.bcm.edu	37	chr1	100214136	100214149	+	Frame_Shift_Del	DEL	CTGATCTCCTGGCC	CTGATCTCCTGGCC	-																															cccagcacggtaccttcaatCtgatctcctggcctgaatgt																										TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	CTGATCTCCTGGCC	CTGATCTCCTGGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr1:100214136_100214149delCTGATCTCCTGGCC	ENST00000414213.1	-	3	777_790	c.176_189delGGCCAGGAGATCAG	c.(175-189)aggccaggagatcagfs	p.RPGDQ59fs	FRRS1_ENST00000287474.5_Frame_Shift_Del_p.RPGDQ59fs			Q6ZNA5	FRRS1_HUMAN	ferric-chelate reductase 1	59	Reelin. {ECO:0000255|PROSITE- ProRule:PRU00363}.					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)		TACCTTCAATCTGATCTCCTGGCCTGAATGTCAT	0.374																																					p.59_64del		Atlas-Indel,Pindel	.											.	FRRS1	50	.	0			c.177_190del						PASS	.																																			SO:0001589	frameshift_variant	391059	exon3			.	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.176_189delGGCCAGGAGATCAG	chr1.hg19:g.100214136_100214149delCTGATCTCCTGGCC	ENSP00000393884:p.Arg59fs	95.0	0.0	0		131.0	19.0	0.145038	NM_001013660	A6NLN7	Frame_Shift_Del	DEL	ENST00000414213.1	hg19																																																																																				.	.	.	none		0.374	FRRS1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001013660		-	100214149	CTGATCTCCTGGCC	-	100214136	7	5	278	1	0	1	0	1	0	0	0	0	6067	912	32	0	1751	0	FRRS1	1	100214136	Frame_Shift_Del	DEL	CTGATCTCCTGGCC	TCGA-Y8-A898-01A-11D-A34Z-10	10795362	100214136	149036485	7	17680											
CNST	163882	hgsc.bcm.edu	37	chr1	246811232	246811232	+	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	acgacgactccgatctccttCaagatctctctcctgaagaa	11	10	6	14	3	4	3	1	1	3	2	8	6	5	3	3	0	0	0	3	0	3	1			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr1:246811232C>G	ENST00000366513.4	+	9	1998	c.1729C>G	c.(1729-1731)Caa>Gaa	p.Q577E	CNST_ENST00000366512.3_Missense_Mutation_p.Q577E|CNST_ENST00000483271.1_3'UTR	NM_152609.2	NP_689822.2	Q6PJW8	CNST_HUMAN	consortin, connexin sorting protein	577					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						CGATCTCCTTCAAGATCTCTC	0.408																																					p.Q577E		Atlas-SNP	.											.	CNST	73	.	0			c.C1729G						PASS	.						118	125	122					1																	246811232		2203	4300	6503	SO:0001583	missense	163882	exon9			CTCCTTCAAGATC	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.1729C>G	chr1.hg19:g.246811232C>G	ENSP00000355470:p.Gln577Glu	161.0	0.0	.		239.0	69.0	.	NM_152609	Q5VSY9|Q5VTM7|Q8IYA9|Q8N3L5|Q8NB09|Q8TEI2|Q96MR5	Missense_Mutation	SNP	ENST00000366513.4	hg19	CCDS1628.1	.	.	.	.	.	.	.	.	.	.	C	2.651	-0.282026	0.05642	.	.	ENSG00000162852	ENST00000366513;ENST00000366512	T;T	0.18960	2.18;2.22	5.5	5.5	0.81552	.	0.394117	0.24537	N	0.037675	T	0.24967	0.0606	M	0.66939	2.045	0.80722	D	1	P;P	0.46142	0.571;0.873	B;P	0.44811	0.359;0.461	T	0.02560	-1.1141	10	0.09338	T	0.73	-12.0106	12.3059	0.54902	0.0:0.9218:0.0:0.0782	.	577;577	Q6PJW8;Q6PJW8-2	CNST_HUMAN;.	E	577	ENSP00000355470:Q577E;ENSP00000355469:Q577E	ENSP00000355469:Q577E	Q	+	1	0	CNST	244877855	1.000000	0.71417	0.936000	0.37596	0.562000	0.35680	3.027000	0.49697	2.750000	0.94351	0.467000	0.42956	CAA	.	.	.	none		0.408	CNST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096780.1	NM_152609		G	246811232	C	G	246811232	3	3	278	1	0	0	0	0	1	0	0	0	3636	827	29	4	1759	4	CNST	1	246811232	Missense_Mutation	SNP	C	TCGA-Y8-A898-01A-11D-A34Z-10	146597096	246811232	2439389	8	17681											
ADAM17	6868	hgsc.bcm.edu	37	chr2	9668056	9668056	+	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	aactaacattcttttgtcttTggtatcattaacaaatctcc	12	17	3	9	0	4	0	1	0	3	0	5	0	4	0	1	1	3	1	1	1	5	7			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr2:9668056T>A	ENST00000310823.3	-	5	660	c.478A>T	c.(478-480)Aaa>Taa	p.K160*	ADAM17_ENST00000497134.1_Nonsense_Mutation_p.K160*	NM_003183.4	NP_003174.3	P78536	ADA17_HUMAN	ADAM metallopeptidase domain 17	160					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell motility (GO:0048870)|collagen catabolic process (GO:0030574)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|germinal center formation (GO:0002467)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil mediated immunity (GO:0002446)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of chemokine production (GO:0032722)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|proteolysis (GO:0006508)|regulation of mast cell apoptotic process (GO:0033025)|response to drug (GO:0042493)|response to high density lipoprotein particle (GO:0055099)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|wound healing, spreading of epidermal cells (GO:0035313)	actin cytoskeleton (GO:0015629)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|interleukin-6 receptor binding (GO:0005138)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|Notch binding (GO:0005112)|PDZ domain binding (GO:0030165)|zinc ion binding (GO:0008270)			breast(1)|cervix(4)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	28	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.225)		CTTTTGTCTTTGGTATCATTA	0.294																																					p.K160X		Atlas-SNP	.											.	ADAM17	61	.	0			c.A478T						PASS	.						69	68	69					2																	9668056		2203	4300	6503	SO:0001587	stop_gained	6868	exon5			TGTCTTTGGTATC	U69611	CCDS1665.1	2p25	2010-08-05	2008-07-31		ENSG00000151694	ENSG00000151694		"ADAM metallopeptidase domain containing", "CD molecules"	195	protein-coding gene	gene with protein product		603639	"tumor necrosis factor, alpha, converting enzyme"	TACE		9034190, 9574564	Standard	NM_003183		Approved	cSVP, CD156B	uc002qzu.3	P78536	OTTHUMG00000090425	ENST00000310823.3:c.478A>T	chr2.hg19:g.9668056T>A	ENSP00000309968:p.Lys160*	95.0	0.0	.		132.0	37.0	.	NM_003183	O60226	Nonsense_Mutation	SNP	ENST00000310823.3	hg19	CCDS1665.1	.	.	.	.	.	.	.	.	.	.	T	17.99	3.524081	0.64747	.	.	ENSG00000151694	ENST00000310823;ENST00000497134;ENST00000538558	.	.	.	5.43	-8.22	0.01037	.	1.461700	0.03587	N	0.231252	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.1158	0.10081	0.1471:0.3652:0.3488:0.139	.	.	.	.	X	160	.	ENSP00000309968:K160X	K	-	1	0	ADAM17	9585507	0.000000	0.05858	0.001000	0.08648	0.916000	0.54674	-0.458000	0.06737	-0.879000	0.04002	-0.644000	0.03951	AAA	.	.	.	none		0.294	ADAM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206857.1			A	9668056	T	A	9668056	4	1	278	1	0	0	0	0	0	1	0	0	238	1821	63	5	2056	5	ADAM17	2	9668056	Nonsense_Mutation	SNP	T	TCGA-Y8-A898-01A-11D-A34Z-10		9668056	233531317	9	17682											
SLC35F5	80255	hgsc.bcm.edu	37	chr2	114513109	114513109	+	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	tcagtctaaaaggaggtgaaGaactcagcacccctaaaaac	17	6	8	10	0	3	2	2	1	1	1	3	3	3	3	2	2	3	1	2	2	7	2			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr2:114513109G>T	ENST00000245680.2	-	2	466	c.53C>A	c.(52-54)tCt>tAt	p.S18Y	SLC35F5_ENST00000409342.1_Missense_Mutation_p.S12Y	NM_025181.2	NP_079457.2	Q8WV83	S35F5_HUMAN	solute carrier family 35, member F5	18					transport (GO:0006810)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(4)|large_intestine(2)|lung(7)|ovary(2)|prostate(3)|skin(1)	20						AGGAGGTGAAGAACTCAGCAC	0.398																																					p.S18Y		Atlas-SNP	.											.	SLC35F5	60	.	0			c.C53A						PASS	.						98	95	96					2																	114513109		2203	4300	6503	SO:0001583	missense	80255	exon2			GGTGAAGAACTCA	AF529364	CCDS2119.1	2q14.1	2013-05-22			ENSG00000115084	ENSG00000115084		"Solute carriers"	23617	protein-coding gene	gene with protein product							Standard	XM_005263799		Approved	FLJ22004	uc002tku.1	Q8WV83	OTTHUMG00000131361	ENST00000245680.2:c.53C>A	chr2.hg19:g.114513109G>T	ENSP00000245680:p.Ser18Tyr	105.0	0.0	.		144.0	48.0	.	NM_025181	Q9H6P8|Q9H7D8	Missense_Mutation	SNP	ENST00000245680.2	hg19	CCDS2119.1	.	.	.	.	.	.	.	.	.	.	G	14.72	2.620816	0.46736	.	.	ENSG00000115084	ENST00000245680;ENST00000409106;ENST00000409342	T;T	0.50548	0.75;0.74	5.36	1.42	0.22433	.	0.141760	0.33895	N	0.004453	T	0.28665	0.0710	N	0.22421	0.69	0.27104	N	0.962557	B;B;B	0.26809	0.099;0.16;0.005	B;B;B	0.26969	0.034;0.075;0.007	T	0.19160	-1.0314	10	0.87932	D	0	-7.2459	4.9691	0.14105	0.2587:0.1537:0.5875:0.0	.	18;12;18	B2RDY0;B8ZZV6;Q8WV83	.;.;S35F5_HUMAN	Y	18;12;12	ENSP00000245680:S18Y;ENSP00000386754:S12Y	ENSP00000245680:S18Y	S	-	2	0	SLC35F5	114229579	0.999000	0.42202	0.989000	0.46669	0.778000	0.44026	0.739000	0.26173	0.377000	0.24735	0.650000	0.86243	TCT	.	.	.	none		0.398	SLC35F5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254150.1	NM_025181		T	114513109	G	T	114513109	3	4	278	1	0	0	0	0	1	0	0	0	14605	942	33	4	1574	4	SLC35F5	2	114513109	Missense_Mutation	SNP	G	TCGA-Y8-A898-01A-11D-A34Z-10	104845053	114513109	128686264	10	17683											
ITGA6	3655	hgsc.bcm.edu	37	chr2	173335733	173335733	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtagagcaaaagaataacacTttttttgacatgaacatctt	16	13	6	6	0	1	4	0	2	1	2	1	4	1	4	0	0	3	2	0	0	6	6			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr2:173335733T>C	ENST00000264106.6	+	5	878	c.675T>C	c.(673-675)acT>acC	p.T225T	ITGA6_ENST00000409080.1_Silent_p.T225T|ITGA6_ENST00000264107.7_Silent_p.T225T|ITGA6_ENST00000375221.2_Silent_p.T225T|ITGA6_ENST00000409532.1_Intron|ITGA6_ENST00000343713.4_Intron			P23229	ITA6_HUMAN	integrin, alpha 6	225					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)			AGAATAACACTTTTTTTGACA	0.348																																					p.T225T		Atlas-SNP	.											.,2	ITGA6	171	.	0			c.T675C						PASS	.						119	105	110					2																	173335733		2203	4300	6503	SO:0001819	synonymous_variant	3655	exon5			TAACACTTTTTTT		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.675T>C	chr2.hg19:g.173335733T>C		81.0	0.0	.		95.0	26.0	.	NM_000210	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Silent	SNP	ENST00000264106.6	hg19																																																																																				.	.	.	none		0.348	ITGA6-201	KNOWN	basic	protein_coding	protein_coding				C	173335733	T	C	173335733	2	2	278	1	0	0	0	0	0	0	0	1	7887	1596	56	3		3	ITGA6	2	173335733	Silent	SNP	T	TCGA-Y8-A898-01A-11D-A34Z-10	58822624	173335733	69863640	11	17684											
FZD7	8324	hgsc.bcm.edu	37	chr2	202900385	202900386	+	Frame_Shift_Del	DEL	CT	CT	-																															agaaggagggctgcaccatcCtcttcatggtgctctacttc																										TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr2:202900385_202900386delCT	ENST00000286201.1	+	1	1076_1077	c.1015_1016delCT	c.(1015-1017)ctcfs	p.L339fs	RP11-107N15.1_ENST00000608741.1_lincRNA	NM_003507.1	NP_003498.1	O75084	FZD7_HUMAN	frizzled class receptor 7	339					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						CTGCACCATCCTCTTCATGGTG	0.629											OREG0015146	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.338_339del		Atlas-Indel,Pindel	.											.	FZD7	70	.	0			c.1014_1015del						PASS	.																																			SO:0001589	frameshift_variant	8324	exon1			.	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.1015_1016delCT	chr2.hg19:g.202900387_202900388delCT	ENSP00000286201:p.Leu339fs	80.0	0.0	0	2133	82.0	12.0	0.146341	NM_003507	O94816|Q53S59|Q96B74	Frame_Shift_Del	DEL	ENST00000286201.1	hg19	CCDS2351.1																																																																																			.	.	.	none		0.629	FZD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256314.1	NM_003507		-	202900386	CT	-	202900385	7	5	278	1	0	1	0	1	0	0	0	0	6142	681	24	0	1017	0	FZD7	2	202900385	Frame_Shift_Del	DEL	CT	TCGA-Y8-A898-01A-11D-A34Z-10	29564652	202900385	40298988	12	17685											
FARP2	9855	hgsc.bcm.edu	37	chr2	242312532	242312532	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catggtgaagaatgggggagAtagaaggaacatacagagtc	16	6	15	4	0	0	5	0	1	0	4	1	7	0	6	0	4	2	0	0	4	6	2			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr2:242312532A>G	ENST00000264042.3	+	2	180	c.10A>G	c.(10-12)Ata>Gta	p.I4V	FARP2_ENST00000373287.4_Missense_Mutation_p.I4V|FARP2_ENST00000545004.1_Missense_Mutation_p.I4V|FARP2_ENST00000479427.1_3'UTR	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	4					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)		AATGGGGGAGATAGAAGGAAC	0.448																																					p.I4V		Atlas-SNP	.											.	FARP2	92	.	0			c.A10G						PASS	.						50	52	51					2																	242312532		2203	4300	6503	SO:0001583	missense	9855	exon2			GGGGAGATAGAAG	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.10A>G	chr2.hg19:g.242312532A>G	ENSP00000264042:p.Ile4Val	101.0	0.0	.		139.0	35.0	.	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Missense_Mutation	SNP	ENST00000264042.3	hg19	CCDS33424.1	.	.	.	.	.	.	.	.	.	.	A	17.59	3.426334	0.62733	.	.	ENSG00000006607	ENST00000264042;ENST00000545004;ENST00000373287;ENST00000418082;ENST00000445489	T;D;D;T;T	0.82167	-0.95;-1.57;-1.58;-0.18;-1.02	5.65	3.27	0.37495	.	0.114499	0.56097	D	0.000032	D	0.85932	0.5812	M	0.75447	2.3	0.30670	N	0.753496	D;B;D	0.61697	0.988;0.42;0.99	P;B;P	0.55713	0.741;0.09;0.782	T	0.83177	-0.0091	10	0.54805	T	0.06	.	7.4465	0.27213	0.7743:0.1525:0.0732:0.0	.	4;4;4	O94887-2;F5GZ84;O94887	.;.;FARP2_HUMAN	V	4	ENSP00000264042:I4V;ENSP00000443876:I4V;ENSP00000362384:I4V;ENSP00000393376:I4V;ENSP00000388167:I4V	ENSP00000264042:I4V	I	+	1	0	FARP2	241961205	1.000000	0.71417	0.987000	0.45799	0.873000	0.50193	3.527000	0.53517	0.407000	0.25591	0.460000	0.39030	ATA	.	.	.	none		0.448	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1			G	242312532	A	G	242312532	3	3	278	1	0	0	0	0	1	0	0	0	5684	333	12	3	12	3	FARP2	2	242312532	Missense_Mutation	SNP	A	TCGA-Y8-A898-01A-11D-A34Z-10	39412147	242312532	886841	13	17686											
PLXNB1	5364	hgsc.bcm.edu	37	chr3	48461649	48461649	+	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	ccacctcttgcaggagggtcTggggagacaagcgggctctg	7	7	16	11	1	3	1	0	0	3	1	3	3	3	2	2	5	2	2	2	5	1	1			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr3:48461649T>A	ENST00000358536.4	-	11	2315	c.2046A>T	c.(2044-2046)ccA>ccT	p.P682P	PLXNB1_ENST00000358459.4_Silent_p.P682P|PLXNB1_ENST00000456774.1_Silent_p.P682P|PLXNB1_ENST00000296440.6_Silent_p.P682P|PLXNB1_ENST00000448774.2_Intron	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	682	Pro-rich.				axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CAGGAGGGTCTGGGGAGACAA	0.677																																					p.P682P		Atlas-SNP	.											.	PLXNB1	150	.	0			c.A2046T						PASS	.						3	3	3					3																	48461649		1845	3666	5511	SO:0001819	synonymous_variant	5364	exon11			AGGGTCTGGGGAG	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"Plexins"	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.2046A>T	chr3.hg19:g.48461649T>A		23.0	0.0	.		28.0	11.0	.	NM_001130082	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Silent	SNP	ENST00000358536.4	hg19	CCDS2765.1																																																																																			.	.	.	none		0.677	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673		A	48461649	T	A	48461649	2	1	278	1	0	0	0	0	0	0	0	1	12130	1567	55	5		5	PLXNB1	3	48461649	Silent	SNP	T	TCGA-Y8-A898-01A-11D-A34Z-10		48461649	149560781	14	17687											
BBX	56987	hgsc.bcm.edu	37	chr3	107508715	107508715	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaggagaagcccaatgttcCggaaaaaggtattggtgccc	14	7	12	8	1	0	1	0	0	0	1	1	3	1	2	3	4	2	2	3	4	6	3	rs374184448		TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr3:107508715C>T	ENST00000325805.8	+	14	2572	c.2285C>T	c.(2284-2286)cCg>cTg	p.P762L	BBX_ENST00000402543.1_Intron|BBX_ENST00000416476.2_Missense_Mutation_p.R426W|BBX_ENST00000406780.1_Intron|BBX_ENST00000415149.2_Intron|BBX_ENST00000473542.1_3'UTR			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	762	Lys-rich.				bone development (GO:0060348)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(18)|ovary(4)|pancreas(1)|skin(2)	49			OV - Ovarian serous cystadenocarcinoma(3;0.112)			CCCAATGTTCCGGAAAAAGGT	0.413																																					p.P762L		Atlas-SNP	.											.	BBX	156	.	0			c.C2285T						PASS	.						94	87	89					3																	107508715		692	1591	2283	SO:0001583	missense	56987	exon14			ATGTTCCGGAAAA	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.2285C>T	chr3.hg19:g.107508715C>T	ENSP00000319974:p.Pro762Leu	297.0	0.0	.		401.0	90.0	.	NM_001142568	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	Missense_Mutation	SNP	ENST00000325805.8	hg19	CCDS46881.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.37|18.37	3.609699|3.609699	0.66558|0.66558	.|.	.|.	ENSG00000114439|ENSG00000114439	ENST00000325805|ENST00000416476	T|D	0.56611|0.99098	0.45|-5.42	5.62|5.62	5.62|5.62	0.85841|0.85841	.|.	0.373129|.	0.27245|.	N|.	0.020258|.	D|D	0.97626|0.97626	0.9222|0.9222	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	D|D	1|1	B|D	0.30709|0.65815	0.291|0.995	B|P	0.16289|0.49387	0.015|0.609	D|D	0.98570|0.98570	1.0645|1.0645	10|9	0.19590|0.87932	T|D	0.45|0	-5.4091|-5.4091	19.0118|19.0118	0.92875|0.92875	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	762|426	Q8WY36|A2RRM7	BBX_HUMAN|.	L|W	762|426	ENSP00000319974:P762L|ENSP00000403860:R426W	ENSP00000319974:P762L|ENSP00000403860:R426W	P|R	+|+	2|1	0|2	BBX|BBX	108991405|108991405	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	3.061000|3.061000	0.49963|0.49963	2.809000|2.809000	0.96659|0.96659	0.655000|0.655000	0.94253|0.94253	CCG|CGG	.	.	.	weak		0.413	BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235		T	107508715	C	T	107508715	3	4	278	1	0	0	0	0	1	0	0	0	1343	652	23	1	2327	1	BBX	3	107508715	Missense_Mutation	SNP	C	TCGA-Y8-A898-01A-11D-A34Z-10	59047066	107508715	90513715	15	17688											
COL6A5	256076	hgsc.bcm.edu	37	chr3	130159453	130159453	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggtctcagctggagaaaatTatgagagaaaagaatttgta	16	11	11	3	0	1	4	1	1	1	3	2	6	1	4	0	2	1	2	0	2	7	3	rs550946747		TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr3:130159453T>C	ENST00000432398.2	+	35	6765	c.6271T>C	c.(6271-6273)Tat>Cat	p.Y2091H	COL6A5_ENST00000265379.6_Missense_Mutation_p.Y2091H	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	2091	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 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						TGGAGAAAATTATGAGAGAAA	0.403																																					p.Y2091H		Atlas-SNP	.											.	COL6A5	205	.	0			c.T6271C						PASS	.						82	79	80					3																	130159453		1841	4089	5930	SO:0001583	missense	256076	exon35			GAAAATTATGAGA	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.6271T>C	chr3.hg19:g.130159453T>C	ENSP00000390895:p.Tyr2091His	96.0	0.0	.		93.0	23.0	.	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	1.170|1.170	-0.641239|-0.641239	0.03557|0.03557	.|.	.|.	ENSG00000172752|ENSG00000172752	ENST00000512836|ENST00000432398;ENST00000265379;ENST00000373157	.|D;D;T	.|0.82803	.|-1.65;-1.65;2.59	5.76|5.76	3.56|3.56	0.40772|0.40772	.|von Willebrand factor, type A (3);	.|1.326970	.|0.05194	.|N	.|0.503656	T|T	0.58552|0.58552	0.2130|0.2130	N|N	0.01352|0.01352	-0.895|-0.895	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	0.54248|0.54248	-0.8322|-0.8322	5|10	.|0.10377	.|T	.|0.69	.|.	6.7824|6.7824	0.23654|0.23654	0.1484:0.6619:0.0:0.1897|0.1484:0.6619:0.0:0.1897	.|.	.|2091;2091	.|A8TX70;A8TX70-2	.|CO6A5_HUMAN;.	S|H	342|2091;2091;34	.|ENSP00000390895:Y2091H;ENSP00000265379:Y2091H;ENSP00000362250:Y34H	.|ENSP00000265379:Y2091H	L|Y	+|+	2|1	0|0	COL6A5|COL6A5	131642143|131642143	0.000000|0.000000	0.05858|0.05858	0.055000|0.055000	0.19348|0.19348	0.233000|0.233000	0.25261|0.25261	-0.242000|-0.242000	0.08928|0.08928	1.242000|1.242000	0.43836|0.43836	-0.408000|-0.408000	0.06270|0.06270	TTA|TAT	.	.	.	none		0.403	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		C	130159453	T	C	130159453	3	2	278	1	0	0	0	0	1	0	0	0	3704	1754	61	3	6405	3	COL6A5	3	130159453	Missense_Mutation	SNP	T	TCGA-Y8-A898-01A-11D-A34Z-10	22650738	130159453	67862977	16	17689											
VPS8	23355	hgsc.bcm.edu	37	chr3	184714225	184714225	+	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	tgaatcccaaacaagattacTgctctatatgtttgcagcag	13	12	7	9	0	1	2	0	1	1	1	2	2	2	2	1	0	5	4	1	0	6	4			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr3:184714225T>A	ENST00000437079.3	+	44	3943	c.3772T>A	c.(3772-3774)Tgc>Agc	p.C1258S	VPS8_ENST00000436792.2_Missense_Mutation_p.C1256S|VPS8_ENST00000446204.2_Missense_Mutation_p.C1166S|VPS8_ENST00000287546.4_Missense_Mutation_p.C1258S	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	1258							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)			ACAAGATTACTGCTCTATATG	0.418																																					p.C1258S		Atlas-SNP	.											.	VPS8	109	.	0			c.T3772A						PASS	.						82	79	80					3																	184714225		1896	4114	6010	SO:0001583	missense	23355	exon43			GATTACTGCTCTA	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.3772T>A	chr3.hg19:g.184714225T>A	ENSP00000397879:p.Cys1258Ser	41.0	0.0	.		89.0	36.0	.	NM_001009921	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Missense_Mutation	SNP	ENST00000437079.3	hg19	CCDS46971.1	.	.	.	.	.	.	.	.	.	.	T	32	5.159102	0.94686	.	.	ENSG00000156931	ENST00000287546;ENST00000437079;ENST00000436792;ENST00000446204	D;D;D;D	0.99809	-6.86;-6.86;-6.86;-6.86	6.03	6.03	0.97812	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);	0.000000	0.85682	D	0.000000	D	0.99729	0.9894	M	0.78916	2.43	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	0.97382	0.9983	10	0.87932	D	0	-15.9436	16.5655	0.84588	0.0:0.0:0.0:1.0	.	1258;1166;1256	Q8N3P4;Q8N3P4-2;Q8N3P4-3	VPS8_HUMAN;.;.	S	1258;1258;1256;1166	ENSP00000287546:C1258S;ENSP00000397879:C1258S;ENSP00000404704:C1256S;ENSP00000405483:C1166S	ENSP00000287546:C1258S	C	+	1	0	VPS8	186196919	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.446000	0.80609	2.302000	0.77476	0.533000	0.62120	TGC	.	.	.	none		0.418	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015303		A	184714225	T	A	184714225	3	1	278	1	0	0	0	0	1	0	0	0	17230	1580	55	5	3938	5	VPS8	3	184714225	Missense_Mutation	SNP	T	TCGA-Y8-A898-01A-11D-A34Z-10	54554772	184714225	13308205	17	17690											
WDR19	57728	hgsc.bcm.edu	37	chr4	39218827	39218827	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcattctgactatgctgcTgcactttttgaaggcaaagt	9	15	8	9	0	2	2	1	2	1	0	2	2	2	2	0	1	3	4	0	1	3	5			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr4:39218827T>C	ENST00000399820.3	+	13	1477	c.1323T>C	c.(1321-1323)gcT>gcC	p.A441A	WDR19_ENST00000288634.7_Silent_p.A281A|WDR19_ENST00000506503.1_Silent_p.A441A	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	441					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						ACTATGCTGCTGCACTTTTTG	0.368																																					p.A441A		Atlas-SNP	.											.	WDR19	96	.	0			c.T1323C						PASS	.						82	77	78					4																	39218827		1844	4096	5940	SO:0001819	synonymous_variant	57728	exon13			TGCTGCTGCACTT	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.1323T>C	chr4.hg19:g.39218827T>C		82.0	0.0	.		95.0	28.0	.	NM_025132	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Silent	SNP	ENST00000399820.3	hg19	CCDS47042.1																																																																																			.	.	.	none		0.368	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1			C	39218827	T	C	39218827	2	2	278	1	0	0	0	0	0	0	0	1	17291	1567	55	3		3	WDR19	4	39218827	Silent	SNP	T	TCGA-Y8-A898-01A-11D-A34Z-10		39218827	151935449	18	17691											
WDFY3	23001	hgsc.bcm.edu	37	chr4	85636511	85636511	+	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	ggaggtaattccgtccatctCcagagaaaacttccacagca	13	8	8	12	1	1	1	0	0	1	1	5	3	4	2	4	2	2	2	4	2	3	3			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr4:85636511C>T	ENST00000295888.4	-	50	8308	c.7901G>A	c.(7900-7902)gGa>gAa	p.G2634E	WDFY3_ENST00000322366.6_Missense_Mutation_p.G2617E	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	2634	Interaction with SQSTM1.|Sufficient for translocalization to p62 bodies/ALIS.				aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)	p.G2634E(1)		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)		CCGTCCATCTCCAGAGAAAAC	0.328																																					p.G2634E		Atlas-SNP	.											WDFY3,colon,carcinoma,+1,1	WDFY3	314	.	1	Substitution - Missense(1)	skin(1)	c.G7901A						PASS	.						86	91	89					4																	85636511		2203	4300	6503	SO:0001583	missense	23001	exon50			CCATCTCCAGAGA	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.7901G>A	chr4.hg19:g.85636511C>T	ENSP00000295888:p.Gly2634Glu	50.0	0.0	.		75.0	21.0	.	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	hg19	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	C	9.744	1.165669	0.21538	.	.	ENSG00000163625	ENST00000322366;ENST00000295888;ENST00000514711	T;T;T	0.62105	0.05;0.06;0.08	5.7	5.7	0.88788	PH-BEACH domain (1);	0.053412	0.85682	D	0.000000	T	0.48259	0.1490	L	0.28192	0.835	0.80722	D	1	B	0.22746	0.074	B	0.18263	0.021	T	0.48790	-0.9004	10	0.02654	T	1	.	19.8448	0.96704	0.0:1.0:0.0:0.0	.	2634	Q8IZQ1	WDFY3_HUMAN	E	2617;2634;237	ENSP00000318466:G2617E;ENSP00000295888:G2634E;ENSP00000424987:G237E	ENSP00000295888:G2634E	G	-	2	0	WDFY3	85855535	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.825000	0.69286	2.686000	0.91538	0.650000	0.86243	GGA	.	.	.	none		0.328	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		T	85636511	C	T	85636511	3	4	278	1	0	0	0	0	1	0	0	0	17282	855	30	2	2755	2	WDFY3	4	85636511	Missense_Mutation	SNP	C	TCGA-Y8-A898-01A-11D-A34Z-10	46417684	85636511	105517765	19	17692											
KIAA0922	23240	hgsc.bcm.edu	37	chr4	154478175	154478175	+	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	ttttcttacctactgaagaaGgaagcattgaaagttcctta	13	14	7	7	0	1	3	0	2	1	1	2	4	2	4	2	1	3	2	2	1	7	7			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr4:154478175G>T	ENST00000409663.3	+	6	542	c.490G>T	c.(490-492)Gga>Tga	p.G164*	KIAA0922_ENST00000409959.3_Nonsense_Mutation_p.G164*|KIAA0922_ENST00000440693.1_Nonsense_Mutation_p.G164*	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	164						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)				TACTGAAGAAGGAAGCATTGA	0.398																																					p.G164X		Atlas-SNP	.											.	KIAA0922	214	.	0			c.G490T						PASS	.						91	94	93					4																	154478175		2203	4300	6503	SO:0001587	stop_gained	23240	exon6			GAAGAAGGAAGCA	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.490G>T	chr4.hg19:g.154478175G>T	ENSP00000386574:p.Gly164*	172.0	0.0	.		223.0	87.0	.	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Nonsense_Mutation	SNP	ENST00000409663.3	hg19	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	G	36	5.615280	0.96649	.	.	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	.	.	.	5.64	4.78	0.61160	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-18.5311	15.6869	0.77418	0.0:0.0:0.862:0.138	.	.	.	.	X	164;164;164;25	.	ENSP00000240487:G25X	G	+	1	0	KIAA0922	154697625	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.124000	0.77185	1.333000	0.45449	0.650000	0.86243	GGA	.	.	.	none		0.398	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196		T	154478175	G	T	154478175	4	4	278	1	0	0	0	0	0	1	0	0	8208	1001	35	4	512	4	KIAA0922	4	154478175	Nonsense_Mutation	SNP	G	TCGA-Y8-A898-01A-11D-A34Z-10	68841664	154478175	36676101	20	17693											
PALLD	23022	hgsc.bcm.edu	37	chr4	169842683	169842683	+	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	atgtatttcttttatgatttAggtcagtgggttaccaaccc	9	17	8	7	0	2	1	1	1	1	0	2	1	2	1	2	2	2	2	2	2	5	7			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr4:169842683A>G	ENST00000505667.1	+	18	3023		c.e18-1		CBR4_ENST00000509108.1_Intron|PALLD_ENST00000507735.1_Splice_Site|PALLD_ENST00000335742.7_Splice_Site|PALLD_ENST00000512127.1_Splice_Site|PALLD_ENST00000261509.6_Splice_Site			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein						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)		TTTATGATTTAGGTCAGTGGG	0.433									Pancreatic Cancer, Familial Clustering of																												.	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.2800-2A>G						PASS	.						30	27	28					4																	169842683		2203	4300	6503	SO:0001630	splice_region_variant	23022	exon17	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	TGATTTAGGTCAG	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.2851-1A>G	chr4.hg19:g.169842683A>G		48.0	0.0	.		60.0	19.0	.	NM_016081	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Splice_Site	SNP	ENST00000505667.1	hg19	CCDS54818.1	.	.	.	.	.	.	.	.	.	.	A	13.19	2.162369	0.38217	.	.	ENSG00000129116	ENST00000261509;ENST00000335742;ENST00000505667;ENST00000512127;ENST00000507735	.	.	.	5.46	5.46	0.80206	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5257	0.75901	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PALLD	170079258	1.000000	0.71417	0.960000	0.40013	0.319000	0.28217	9.339000	0.96797	2.075000	0.62263	0.454000	0.30748	.	.	.	.	none		0.433	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	Intron	G	169842683	A	G	169842683	5	3	278	1	0	0	0	0	0	0	1	0	11414	434	15	3	3422	3	PALLD	4	169842683	Splice_Site	SNP	A	TCGA-Y8-A898-01A-11D-A34Z-10	15364508	169842683	21311593	21	17694											
DMXL1	1657	hgsc.bcm.edu	37	chr5	118484771	118484771	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgtaagtatttttgaatgTgagtcaacaggaggttcatg	12	14	11	4	0	2	2	2	2	0	0	2	3	2	3	0	2	1	3	0	2	4	5			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr5:118484771T>C	ENST00000311085.8	+	18	3329	c.3249T>C	c.(3247-3249)tgT>tgC	p.C1083C	DMXL1_ENST00000539542.1_Silent_p.C1083C	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	1083										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)		TTTTTGAATGTGAGTCAACAG	0.393																																					p.C1083C		Atlas-SNP	.											.	DMXL1	268	.	0			c.T3249C						PASS	.						162	164	163					5																	118484771		2202	4300	6502	SO:0001819	synonymous_variant	1657	exon18			TGAATGTGAGTCA	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.3249T>C	chr5.hg19:g.118484771T>C		97.0	0.0	.		185.0	57.0	.	NM_005509		Silent	SNP	ENST00000311085.8	hg19	CCDS4125.1																																																																																			.	.	.	none		0.393	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		C	118484771	T	C	118484771	2	2	278	1	0	0	0	0	0	0	0	1	4596	1702	59	3		3	DMXL1	5	118484771	Silent	SNP	T	TCGA-Y8-A898-01A-11D-A34Z-10		118484771	62430489	22	17695											
CTNNA1	1495	hgsc.bcm.edu	37	chr5	138145868	138145869	+	Missense_Mutation	DNP	AC	AC	CT																															ggctgacatggcagatgtctAcaaattacttgttcagctga																										TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	A|C	A|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr5:138145868_138145869AC>CT	ENST00000302763.7	+	4	533_534	c.443_444AC>CT	c.(442-444)tAC>tCT	p.Y148S	CTNNA1_ENST00000355078.5_Missense_Mutation_p.Y45S|CTNNA1_ENST00000518825.1_Missense_Mutation_p.Y148S	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	148	Interaction with JUP and CTNNB1.|Involved in homodimerization.				adherens junction organization (GO:0034332)|aging (GO:0007568)|apical junction assembly (GO:0043297)|axon regeneration (GO:0031103)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular protein localization (GO:0034613)|cellular response to indole-3-methanol (GO:0071681)|epithelial cell-cell adhesion (GO:0090136)|establishment or maintenance of cell polarity (GO:0007163)|gap junction assembly (GO:0016264)|male gonad development (GO:0008584)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell motility (GO:2000146)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|negative regulation of neuroblast proliferation (GO:0007406)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of smoothened signaling pathway (GO:0045880)|protein heterooligomerization (GO:0051291)|response to estrogen (GO:0043627)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|catenin complex (GO:0016342)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|gamma-catenin binding (GO:0045295)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|vinculin binding (GO:0017166)			NS(1)|breast(7)|cervix(2)|endometrium(4)|kidney(6)|large_intestine(16)|lung(9)|oesophagus(2)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	52			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GCAGATGTCTACAAATTACTTG	0.46																																					p.Y148S|p.Y148Y		Atlas-SNP	.											.	CTNNA1	114	.	0			c.A443C|c.C444T						PASS	.																																			SO:0001583	missense	1495	exon4			ATGTCTACAAATT|TGTCTACAAATTA	D13866	CCDS34243.1, CCDS75315.1	5q31.2	2008-02-05	2002-08-29			ENSG00000044115			2509	protein-coding gene	gene with protein product		116805	"catenin (cadherin-associated protein), alpha 1 (102kD)"			1924379	Standard	XM_005271898		Approved	CAP102	uc003ldh.3	P35221		Exception_encountered	chr5.hg19:g.138145868_138145869delinsCT	ENSP00000304669:p.Tyr148Ser	82.0	0.0	.		133.0|131.0	35.0|36.0	.	NM_001903	Q12795|Q8N1C0	Missense_Mutation|Silent	SNP	ENST00000302763.7	hg19	CCDS34243.1																																																																																			.	.	.	none		0.46	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903		CT	138145869	AC	CT	138145868	3	2	278	1	0	0	0	0	1	0	0	0	4014	391	14	5	453	5	CTNNA1	5	138145868	Missense_Mutation	DNP	AC	TCGA-Y8-A898-01A-11D-A34Z-10	19661097	138145868	42769392	23	17696											
SKIV2L	6499	hgsc.bcm.edu	37	chr6	31930543	31930543	+	Missense_Mutation	SNP	T	T	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	gggacctggagtgggtcatcTttgatgaggttcactatatc	8	13	13	7	0	3	2	2	2	1	0	4	4	3	4	1	4	0	1	1	4	2	4			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr6:31930543T>G	ENST00000375394.2	+	12	1377	c.1264T>G	c.(1264-1266)Ttt>Gtt	p.F422V	SKIV2L_ENST00000544581.1_Missense_Mutation_p.F229V	NM_006929.4	NP_008860.4	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like (S. cerevisiae)	422	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				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						GTGGGTCATCTTTGATGAGGT	0.557																																					p.F422V		Atlas-SNP	.											.	SKIV2L	97	.	0			c.T1264G						PASS	.						136	128	131					6																	31930543		1511	2709	4220	SO:0001583	missense	6499	exon12			GTCATCTTTGATG		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.1264T>G	chr6.hg19:g.31930543T>G	ENSP00000364543:p.Phe422Val	69.0	0.0	.		67.0	15.0	.	NM_006929	O15005|Q12902|Q15476|Q5ST66	Missense_Mutation	SNP	ENST00000375394.2	hg19	CCDS4731.1	.	.	.	.	.	.	.	.	.	.	T	31	5.081039	0.94050	.	.	ENSG00000204351	ENST00000375394;ENST00000433155;ENST00000544581	T;T	0.13538	2.58;2.58	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	0.25975	0.0633	M	0.63208	1.945	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.01889	-1.1253	10	0.87932	D	0	-13.5265	14.575	0.68240	0.0:0.0:0.0:1.0	.	422	Q15477	SKIV2_HUMAN	V	422;264;229	ENSP00000364543:F422V;ENSP00000442645:F229V	ENSP00000364543:F422V	F	+	1	0	SKIV2L	32038522	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.359000	0.79477	2.094000	0.63399	0.533000	0.62120	TTT	.	.	.	none		0.557	SKIV2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076264.3			G	31930543	T	G	31930543	3	3	278	1	0	0	0	0	1	0	0	0	14372	1609	56	5	1310	5	SKIV2L	6	31930543	Missense_Mutation	SNP	T	TCGA-Y8-A898-01A-11D-A34Z-10		31930543	139184524	24	17697											
HLA-DOB	3112	hgsc.bcm.edu	37	chr6	32783066	32783067	+	Frame_Shift_Ins	INS	-	-	C																															gttggtgaagtaacagtcagINScctttgcctgaatcacaaaa																										TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr6:32783066_32783067insC	ENST00000438763.2	-	2	211_212	c.115_116insG	c.(115-117)gctfs	p.A39fs	TAP2_ENST00000452392.2_Intron	NM_002120.3	NP_002111.1	P13765	DOB_HUMAN	major histocompatibility complex, class II, DO beta	39	Beta-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)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|MHC class II protein complex (GO:0042613)	MHC class II protein complex binding (GO:0023026)|MHC class II receptor activity (GO:0032395)			endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	9						GTAACAGTCAGCCTTTGCCTGA	0.46																																					p.A39fs		Atlas-Indel,Pindel	.											.	HLA-DOB	17	.	0			c.116_117insG						PASS	.																																			SO:0001589	frameshift_variant	3112	exon2			.		CCDS4754.1	6p21.3	2013-01-11			ENSG00000241106	ENSG00000241106		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4937	protein-coding gene	gene with protein product		600629					Standard	NM_002120		Approved			P13765	OTTHUMG00000031213	ENST00000438763.2:c.116dupG	chr6.hg19:g.32783068_32783068dupC	ENSP00000390020:p.Ala39fs	88.0	0.0	0		121.0	35.0	0.289256	NM_002120	B0V0Y0|Q29746|Q29825|Q6FHC2	Frame_Shift_Ins	INS	ENST00000438763.2	hg19	CCDS4754.1																																																																																			.	.	.	none		0.46	HLA-DOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076439.1	NM_002120		C	32783067	-	C	32783066	7	5	278	1	0	1	1	0	0	0	0	0	7208	971	34	0	725	0	HLA-DOB	6	32783066	Frame_Shift_Ins	INS	-	TCGA-Y8-A898-01A-11D-A34Z-10	852523	32783066	138332001	25	17698											
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138615186	138615186	+	Missense_Mutation	SNP	A	A	C																															ggccttgggaggttttctttAccagctgaagaaagcatcgc																										TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr6:138615186A>C	ENST00000251691.4	+	20	3591	c.3425A>C	c.(3424-3426)tAc>tCc	p.Y1142S		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)		GGTTTTCTTTACCAGCTGAAG	0.423																																					p.Y1142S		Atlas-SNP	.											.	KIAA1244	236	.	0			c.A3425C						PASS	.						153	138	143					6																	138615186		2203	4300	6503	SO:0001583	missense	57221	exon20			TTCTTTACCAGCT	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.3425A>C	chr6.hg19:g.138615186A>C	ENSP00000251691:p.Tyr1142Ser	88.0	0.0	.		115.0	25.0	.	NM_020340		Missense_Mutation	SNP	ENST00000251691.4	hg19	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	A	14.05	2.421030	0.42918	.	.	ENSG00000112379	ENST00000251691	T	0.16457	2.34	5.56	5.56	0.83823	.	0.467432	0.26828	N	0.022290	T	0.08846	0.0219	L	0.36672	1.1	0.49130	D	0.999755	B	0.32245	0.361	B	0.32980	0.156	T	0.07065	-1.0792	10	0.46703	T	0.11	-28.8225	15.7152	0.77663	1.0:0.0:0.0:0.0	.	1142	Q5TH69	BIG3_HUMAN	S	1142	ENSP00000251691:Y1142S	ENSP00000251691:Y1142S	Y	+	2	0	KIAA1244	138656879	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	8.516000	0.90552	2.119000	0.64992	0.533000	0.62120	TAC	.	.	.	none		0.423	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		C	138615186	A	C	138615186	3	2	278	1	0	0	0	0	1	0	0	0	8224	391	14	5	3503	5	KIAA1244	6	138615186	Missense_Mutation	SNP	A	TCGA-Y8-A898-01A-11D-A34Z-10	105832120	138615186	32499881	26	17699	186	2									
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138615192	138615194	+	In_Frame_Del	DEL	TGA	TGA	-																															gggaggttttctttaccagcTgaagaaagcatcgcagtctc																										TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr6:138615192_138615194delTGA	ENST00000251691.4	+	20	3597_3599	c.3431_3433delTGA	c.(3430-3435)ctgaag>cag	p.1144_1145LK>Q		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)		CTTTACCAGCTGAAGAAAGCATC	0.424																																					p.1144_1144del		Atlas-Indel,Pindel	.											.	KIAA1244	236	.	0			c.3430_3432del						PASS	.																																			SO:0001651	inframe_deletion	57221	exon20			.	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.3431_3433delTGA	chr6.hg19:g.138615192_138615194delTGA	ENSP00000251691:p.Leu1144_Lys1145delinsGln	89.0	0.0	0		121.0	28.0	0.231405	NM_020340		In_Frame_Del	DEL	ENST00000251691.4	hg19	CCDS5189.2																																																																																			.	.	.	none		0.424	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		-	138615194	TGA	-	138615192	7	5	278	1	0	1	0	1	0	0	0	0	8224	1580	55	0	3509	0	KIAA1244	6	138615192	In_Frame_Del	DEL	TGA	TCGA-Y8-A898-01A-11D-A34Z-10	6	138615192	32499875	27	17700	186	2									
FNDC1	84624	hgsc.bcm.edu	37	chr6	159653341	159653341	+	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	cgaagggaaggcgtagataaGcctggcttttccctggccac	9	8	13	11	2	0	1	0	0	0	1	1	3	1	2	3	4	1	2	3	4	4	4			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr6:159653341G>A	ENST00000297267.9	+	11	1997	c.1797G>A	c.(1795-1797)aaG>aaA	p.K599K	FNDC1_ENST00000340366.6_Silent_p.K536K	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	599					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)		GCGTAGATAAGCCTGGCTTTT	0.701																																					p.K599K		Atlas-SNP	.											.	FNDC1	250	.	0			c.G1797A						PASS	.						20	25	24					6																	159653341		2008	4175	6183	SO:0001819	synonymous_variant	84624	exon11			AGATAAGCCTGGC	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.1797G>A	chr6.hg19:g.159653341G>A		42.0	0.0	.		46.0	22.0	.	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Silent	SNP	ENST00000297267.9	hg19	CCDS47512.1	.	.	.	.	.	.	.	.	.	.	G	4.335	0.061579	0.08339	.	.	ENSG00000164694	ENST00000329629	.	.	.	4.54	1.64	0.23874	.	.	.	.	.	T	0.09291	0.0229	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24657	-1.0154	4	.	.	.	-0.0117	2.6758	0.05081	0.2678:0.0:0.3704:0.3618	.	.	.	.	T	495	.	.	A	+	1	0	FNDC1	159573331	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	0.540000	0.23191	1.126000	0.42016	-0.140000	0.14226	GCC	.	.	.	none		0.701	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		A	159653341	G	A	159653341	2	1	278	1	0	0	0	0	0	0	0	1	5975	962	34	2		2	FNDC1	6	159653341	Silent	SNP	G	TCGA-Y8-A898-01A-11D-A34Z-10	21038149	159653341	11461726	28	17701											
POLM	27434	hgsc.bcm.edu	37	chr7	44116188	44116188	+	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	gtccttcccggtaccaccggTcagcagtcttcacaccgacc	7	8	8	18	3	3	0	2	0	1	0	5	1	5	0	6	2	2	2	6	2	1	3			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr7:44116188T>A	ENST00000242248.5	-	6	856	c.755A>T	c.(754-756)gAc>gTc	p.D252V	POLM_ENST00000492971.1_5'UTR|POLM_ENST00000335195.6_Missense_Mutation_p.D252V|POLM_ENST00000395831.3_Intron	NM_013284.2	NP_037416.1	Q9NP87	DPOLM_HUMAN	polymerase (DNA directed), mu	252					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						GTACCACCGGTCAGCAGTCTT	0.592								DNA polymerases (catalytic subunits)																													p.D252V		Atlas-SNP	.											.	POLM	50	.	0			c.A755T						PASS	.						114	107	109					7																	44116188		2203	4300	6503	SO:0001583	missense	27434	exon6			CACCGGTCAGCAG	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.755A>T	chr7.hg19:g.44116188T>A	ENSP00000242248:p.Asp252Val	72.0	0.0	.		99.0	43.0	.	NM_013284	D3DVK4|Q6P5X8|Q86WQ9	Missense_Mutation	SNP	ENST00000242248.5	hg19	CCDS34625.1	.	.	.	.	.	.	.	.	.	.	T	16.81	3.225055	0.58668	.	.	ENSG00000122678	ENST00000335195;ENST00000242248	T;T	0.44881	0.91;0.91	5.68	4.49	0.54785	DNA-directed DNA polymerase X (1);DNA polymerase lambda, fingers domain (2);	.	.	.	.	T	0.55146	0.1902	L	0.58101	1.795	0.80722	D	1	D;D	0.62365	0.991;0.972	D;P	0.64877	0.93;0.824	T	0.56269	-0.8007	9	0.87932	D	0	.	8.717	0.34416	0.0:0.0875:0.0:0.9125	.	252;252	Q6P5X8;Q9NP87	.;DPOLM_HUMAN	V	252	ENSP00000335141:D252V;ENSP00000242248:D252V	ENSP00000242248:D252V	D	-	2	0	POLM	44082713	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	1.366000	0.34193	0.935000	0.37341	0.528000	0.53228	GAC	.	.	.	none		0.592	POLM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339594.1	NM_013284		A	44116188	T	A	44116188	3	1	278	1	0	0	0	0	1	0	0	0	12213	1667	58	5	753	5	POLM	7	44116188	Missense_Mutation	SNP	T	TCGA-Y8-A898-01A-11D-A34Z-10		44116188	115022475	29	17702											
MAGI2	9863	hgsc.bcm.edu	37	chr7	77764393	77764393	+	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	cctgcatccttgatgagcttCacgatgtcagcgtgaggcat	8	11	11	11	2	2	3	2	3	0	0	3	4	3	3	2	1	3	3	2	1	0	2			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr7:77764393C>A	ENST00000354212.4	-	17	3229	c.2976G>T	c.(2974-2976)gtG>gtT	p.V992V	MAGI2_ENST00000419488.1_Silent_p.V978V|MAGI2_ENST00000522391.1_Silent_p.V992V	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	992	PDZ 5. {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)				TGATGAGCTTCACGATGTCAG	0.537																																					p.V992V		Atlas-SNP	.											.	MAGI2	246	.	0			c.G2976T						PASS	.						264	194	217					7																	77764393		2203	4300	6503	SO:0001819	synonymous_variant	9863	exon17			GAGCTTCACGATG	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.2976G>T	chr7.hg19:g.77764393C>A		110.0	0.0	.		209.0	42.0	.	NM_012301	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Silent	SNP	ENST00000354212.4	hg19	CCDS5594.1																																																																																			.	.	.	none		0.537	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		A	77764393	C	A	77764393	2	1	278	1	0	0	0	0	0	0	0	1	9198	813	29	4		4	MAGI2	7	77764393	Silent	SNP	C	TCGA-Y8-A898-01A-11D-A34Z-10	33648205	77764393	81374270	30	17703											
CPA1	1357	hgsc.bcm.edu	37	chr7	130021580	130021594	+	In_Frame_Del	DEL	ATGAGACCATGATCG	ATGAGACCATGATCG	-																															ggagtcccacggcatcagctAtgagaccatgatcgaggacg																										TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	ATGAGACCATGATCG	ATGAGACCATGATCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr7:130021580_130021594delATGAGACCATGATCG	ENST00000011292.3	+	3	407_421	c.257_271delATGAGACCATGATCG	c.(256-273)tatgagaccatgatcgag>tag	p.86_91YETMIE>*	CPA1_ENST00000484324.1_Start_Codon_Del	NM_001868.2	NP_001859.1	P15085	CBPA1_HUMAN	carboxypeptidase A1 (pancreatic)	86					proteolysis (GO:0006508)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)	21	Melanoma(18;0.0435)					GGCATCAGCTATGAGACCATGATCGAGGACGTGCA	0.637											OREG0018314	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.86_90del		Atlas-INDEL	.											.	CPA1	73	.	0			c.256_270del						PASS	.																																			SO:0001651	inframe_deletion	1357	exon3			.		CCDS5820.1	7q32	2012-02-10			ENSG00000091704	ENSG00000091704	3.4.17.1		2296	protein-coding gene	gene with protein product	"pancreatic carboxypeptidase A"	114850		CPA			Standard	NM_001868		Approved		uc003vpx.3	P15085	OTTHUMG00000157826	ENST00000011292.3:c.257_271delATGAGACCATGATCG	chr7.hg19:g.130021580_130021594delATGAGACCATGATCG	ENSP00000011292:p.Tyr86_Glu91delins*	63.0	0.0	0	1576	76.0	14.0	0.184211	NM_001868	A4D1M1|Q53XU0|Q9BS67|Q9UCF2	In_Frame_Del	DEL	ENST00000011292.3	hg19	CCDS5820.1																																																																																			.	.	.	none		0.637	CPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349736.2	NM_001868		-	130021594	ATGAGACCATGATCG	-	130021580	7	5	278	1	0	1	0	1	0	0	0	0	3791	449	16	0	267	0	CPA1	7	130021580	In_Frame_Del	DEL	ATGAGACCATGATCG	TCGA-Y8-A898-01A-11D-A34Z-10	52257187	130021580	29117083	31	17704											
AMAC1L2	83650	hgsc.bcm.edu	37	chr8	11189416	11189416	+	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	atcctcgccttggtctccttCacatgtgtgggctatgcggt	4	14	11	12	2	2	0	1	0	1	0	5	0	3	0	3	3	1	1	3	3	1	3			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr8:11189416C>T	ENST00000382435.4	+	1	1020	c.801C>T	c.(799-801)ttC>ttT	p.F267F		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	267						integral component of membrane (GO:0016021)											TGGTCTCCTTCACATGTGTGG	0.597																																					p.F267F		Atlas-SNP	.											.	.	.	.	0			c.C801T						PASS	.						113	111	112					8																	11189416		2203	4300	6503	SO:0001819	synonymous_variant	83650	exon1			CTCCTTCACATGT	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"Solute carriers"	15546	protein-coding gene	gene with protein product		615199	"acyl-malonyl condensing enzyme 1-like 2"	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.801C>T	chr8.hg19:g.11189416C>T		90.0	0.0	.		113.0	6.0	.	NM_054028	A2RRL6	Silent	SNP	ENST00000382435.4	hg19	CCDS5980.1																																																																																			.	.	.	none		0.597	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028		T	11189416	C	T	11189416	2	4	278	1	0	0	0	0	0	0	0	1	560	825	29	2		2	AMAC1L2	8	11189416	Silent	SNP	C	TCGA-Y8-A898-01A-11D-A34Z-10		11189416	135174606	32	17705											
NRG1	3084	hgsc.bcm.edu	37	chr8	31497511	31497511	+	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	acctcgcaccatgagatggcGacgcgccccgcgccgctccg	6	4	12	19	8	0	1	0	1	0	1	2	3	1	1	6	1	0	2	6	1	0	0	rs367543150	byFrequency	TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr8:31497511G>C	ENST00000520407.1	+	1	241	c.11G>C	c.(10-12)cGa>cCa	p.R4P	NRG1_ENST00000519301.1_Intron	NM_013962.2	NP_039256.2	Q02297	NRG1_HUMAN	neuregulin 1	0					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)		ATGAGATGGCGAcgcgccccg	0.761																																					p.R4P		Atlas-SNP	.											.	NRG1	260	.	0			c.G11C						PASS	.						2	2	2					8																	31497511		1218	2257	3475	SO:0001583	missense	3084	exon1			GATGGCGACGCGC	L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"Immunoglobulin superfamily / I-set domain containing"	7997	protein-coding gene	gene with protein product		142445	"NRG1 intronic transcript 2 (non-protein coding)"	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000520407.1:c.11G>C	chr8.hg19:g.31497511G>C	ENSP00000434640:p.Arg4Pro	1.0	0.0	.		5.0	4.0	.	NM_013962	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Missense_Mutation	SNP	ENST00000520407.1	hg19	CCDS47836.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.919846	0.33908	.	.	ENSG00000157168	ENST00000520407	T	0.78707	-1.2	2.91	1.98	0.26296	.	.	.	.	.	T	0.61652	0.2364	.	.	.	0.80722	D	1	P	0.47409	0.895	B	0.34346	0.18	T	0.64339	-0.6431	8	0.87932	D	0	.	5.1615	0.15064	0.1749:0.0:0.8251:0.0	.	4	Q02297-9	.	P	4	ENSP00000434640:R4P	ENSP00000434640:R4P	R	+	2	0	NRG1	31617053	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	3.653000	0.54446	1.332000	0.45431	0.297000	0.19635	CGA	.	.	.	weak		0.761	NRG1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376412.2			C	31497511	G	C	31497511	3	2	278	1	0	0	0	0	1	0	0	0	10654	1058	37	4	13	4	NRG1	8	31497511	Missense_Mutation	SNP	G	TCGA-Y8-A898-01A-11D-A34Z-10	20308095	31497511	114866511	33	17706											
ADAM32	203102	hgsc.bcm.edu	37	chr8	39044451	39044451	+	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	cccaaggagataactctggaGgcatttgcagttattgtcac	11	11	10	9	0	2	1	1	0	1	1	2	3	2	2	1	3	2	3	1	3	3	4			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr8:39044451G>C	ENST00000379907.4	+	11	1066	c.939G>C	c.(937-939)gaG>gaC	p.E313D	ADAM32_ENST00000437682.2_Intron|ADAM32_ENST00000519315.1_Intron	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	313	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)			TAACTCTGGAGGCATTTGCAG	0.353																																					p.E313D		Atlas-SNP	.											.	ADAM32	70	.	0			c.G939C						PASS	.						77	73	74					8																	39044451		1813	4075	5888	SO:0001583	missense	203102	exon11			TCTGGAGGCATTT	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.939G>C	chr8.hg19:g.39044451G>C	ENSP00000369238:p.Glu313Asp	72.0	0.0	.		86.0	19.0	.	NM_145004	Q8TC42	Missense_Mutation	SNP	ENST00000379907.4	hg19	CCDS47846.1	.	.	.	.	.	.	.	.	.	.	G	12.56	1.974271	0.34848	.	.	ENSG00000197140	ENST00000379907	T	0.10099	2.91	5.47	2.72	0.32119	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.33591	U	0.004753	T	0.24928	0.0605	M	0.81341	2.54	0.26818	N	0.968841	D	0.55172	0.97	D	0.63283	0.913	T	0.12218	-1.0556	10	0.15952	T	0.53	.	7.6636	0.28417	0.2647:0.0:0.7353:0.0	.	313	Q8TC27	ADA32_HUMAN	D	313	ENSP00000369238:E313D	ENSP00000369238:E313D	E	+	3	2	ADAM32	39163608	0.973000	0.33851	0.979000	0.43373	0.049000	0.14656	0.873000	0.28052	0.378000	0.24764	-0.142000	0.14014	GAG	.	.	.	none		0.353	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004		C	39044451	G	C	39044451	3	2	278	1	0	0	0	0	1	0	0	0	249	991	35	4	981	4	ADAM32	8	39044451	Missense_Mutation	SNP	G	TCGA-Y8-A898-01A-11D-A34Z-10	7546940	39044451	107319571	34	17707											
NKAIN3	286183	hgsc.bcm.edu	37	chr8	63659504	63659504	+	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	cacctaggacaccgatctaaTgacattcaatatctctgtac	13	11	5	12	1	3	1	1	1	2	0	4	3	3	2	2	1	1	1	2	1	5	5			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr8:63659504T>A	ENST00000523211.1	+	4	419	c.287T>A	c.(286-288)aTg>aAg	p.M96K	NKAIN3_ENST00000328472.5_Missense_Mutation_p.M96K|NKAIN3_ENST00000519049.1_3'UTR	NM_173688.2	NP_775959.1	Q8N8D7	NKAI3_HUMAN	Na+/K+ transporting ATPase interacting 3	96						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(3)|large_intestine(2)|lung(8)	13	Breast(64;0.127)	Lung NSC(129;0.187)				ACCGATCTAATGACATTCAAT	0.463																																					p.M96K		Atlas-SNP	.											.	NKAIN3	32	.	0			c.T287A						PASS	.						121	116	117					8																	63659504		2002	4170	6172	SO:0001583	missense	286183	exon4			ATCTAATGACATT	AK096949	CCDS55239.1	8q12.3	2014-08-12	2007-10-04	2007-10-04	ENSG00000185942	ENSG00000185942		"Na+/K+ transporting ATPase interacting"	26829	protein-coding gene	gene with protein product		612872	"family with sequence similarity 77, member D"	FAM77D		17606467	Standard	NM_173688		Approved	FLJ39630	uc010lyq.1	Q8N8D7	OTTHUMG00000164361	ENST00000523211.1:c.287T>A	chr8.hg19:g.63659504T>A	ENSP00000429073:p.Met96Lys	56.0	0.0	.		68.0	21.0	.	NM_173688		Missense_Mutation	SNP	ENST00000523211.1	hg19	CCDS55239.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.632134	0.87660	.	.	ENSG00000185942	ENST00000545532;ENST00000523211;ENST00000524201;ENST00000328472	T;T;T	0.15487	2.42;2.42;2.42	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.22166	0.0534	L	0.41824	1.3	0.54753	D	0.99998	P	0.44877	0.845	P	0.46172	0.506	T	0.00745	-1.1584	10	0.87932	D	0	-2.0704	15.1705	0.72869	0.0:0.0:0.0:1.0	.	96	Q8N8D7	NKAI3_HUMAN	K	96;96;69;96	ENSP00000429073:M96K;ENSP00000429393:M69K;ENSP00000333627:M96K	ENSP00000333627:M96K	M	+	2	0	NKAIN3	63822058	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.608000	0.82898	2.181000	0.69327	0.528000	0.53228	ATG	.	.	.	none		0.463	NKAIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378447.2	NM_173688		A	63659504	T	A	63659504	3	1	278	1	0	0	0	0	1	0	0	0	10444	1464	51	5	301	5	NKAIN3	8	63659504	Missense_Mutation	SNP	T	TCGA-Y8-A898-01A-11D-A34Z-10	24615053	63659504	82704518	35	17708											
COPS5	10987	hgsc.bcm.edu	37	chr8	67955532	67955532	+	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	gagacatcaatccatggataGcttctatggtagttttacag	12	13	9	7	0	2	1	1	0	1	1	3	3	3	2	1	2	2	3	1	2	5	6			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr8:67955532G>T	ENST00000357849.4	-	8	1261	c.941C>A	c.(940-942)gCt>gAt	p.A314D	PPP1R42_ENST00000517834.1_Intron|COPS5_ENST00000517736.1_3'UTR	NM_006837.2	NP_006828.2	Q92905	CSN5_HUMAN	COP9 signalosome subunit 5	314					cullin deneddylation (GO:0010388)|exosomal secretion (GO:1990182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein deneddylation (GO:0000338)|protein deubiquitination (GO:0016579)|regulation of cell cycle (GO:0051726)|regulation of JNK cascade (GO:0046328)|transcription from RNA polymerase II promoter (GO:0006366)|translation (GO:0006412)|translational initiation (GO:0006413)	cell junction (GO:0030054)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|eukaryotic translation initiation factor 3 complex (GO:0005852)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|transcription coactivator activity (GO:0003713)|translation initiation factor activity (GO:0003743)|ubiquitin-specific protease activity (GO:0004843)			endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|skin(3)	14	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00389)|OV - Ovarian serous cystadenocarcinoma(28;0.00691)|all cancers(69;0.0205)|BRCA - Breast invasive adenocarcinoma(89;0.153)			TCCATGGATAGCTTCTATGGT	0.338																																					p.A314D		Atlas-SNP	.											.	COPS5	29	.	0			c.C941A						PASS	.						84	80	82					8																	67955532		2201	4300	6501	SO:0001583	missense	10987	exon8			TGGATAGCTTCTA	U65928	CCDS6198.1	8q13.1	2013-03-14	2013-03-14		ENSG00000121022	ENSG00000121022			2240	protein-coding gene	gene with protein product		604850	"COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 5", "COP9 constitutive photomorphogenic homolog subunit 5 (Arabidopsis)"			8837781, 9341143	Standard	NM_006837		Approved	JAB1, SGN5, MOV-34, CSN5	uc003xxe.3	Q92905	OTTHUMG00000164563	ENST00000357849.4:c.941C>A	chr8.hg19:g.67955532G>T	ENSP00000350512:p.Ala314Asp	98.0	0.0	.		103.0	22.0	.	NM_006837	O15386|Q6AW95|Q86WQ4|Q9BQ17	Missense_Mutation	SNP	ENST00000357849.4	hg19	CCDS6198.1	.	.	.	.	.	.	.	.	.	.	G	13.71	2.319312	0.41096	.	.	ENSG00000121022	ENST00000357849	.	.	.	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.71400	0.3335	M	0.70903	2.155	0.80722	D	1	B	0.27380	0.177	B	0.37780	0.258	T	0.67102	-0.5755	9	0.22109	T	0.4	-10.6585	18.5697	0.91130	0.0:0.0:1.0:0.0	.	314	Q92905	CSN5_HUMAN	D	314	.	ENSP00000350512:A314D	A	-	2	0	COPS5	68118086	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.965000	0.87945	2.559000	0.86315	0.555000	0.69702	GCT	.	.	.	none		0.338	COPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379245.2			T	67955532	G	T	67955532	3	4	278	1	0	0	0	0	1	0	0	0	3738	971	34	4	67	4	COPS5	8	67955532	Missense_Mutation	SNP	G	TCGA-Y8-A898-01A-11D-A34Z-10	4296028	67955532	78408490	36	17709											
POLR2K	5440	hgsc.bcm.edu	37	chr8	101163593	101163593	+	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	aggggctaacaatggacaccCagaaggacgttcaacctcca	14	5	10	12	1	1	1	1	0	0	1	2	3	2	3	3	4	2	2	3	4	4	2			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr8:101163593C>G	ENST00000353107.3	+	2	145	c.10C>G	c.(10-12)Cag>Gag	p.Q4E	POLR2K_ENST00000522439.1_Missense_Mutation_p.Q4E|POLR2K_ENST00000519765.1_3'UTR	NM_005034.3	NP_005025.1	P53803	RPAB4_HUMAN	polymerase (RNA) II (DNA directed) polypeptide K, 7.0kDa	4					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)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|RNA splicing (GO:0008380)|termination of RNA polymerase I transcription (GO:0006363)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	cytosol (GO:0005829)|DNA-directed RNA polymerase I complex (GO:0005736)|DNA-directed RNA polymerase II, core complex (GO:0005665)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|prostate(1)	3	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.59e-09)|all cancers(13;1.74e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)			AATGGACACCCAGAAGGACGT	0.393																																					p.Q4E		Atlas-SNP	.											.	POLR2K	6	.	0			c.C10G						PASS	.						100	99	99					8																	101163593		2203	4300	6503	SO:0001583	missense	5440	exon2			GACACCCAGAAGG		CCDS6285.1	8q22	2013-01-21	2002-08-29		ENSG00000147669	ENSG00000147669		"RNA polymerase subunits"	9198	protein-coding gene	gene with protein product		606033	"polymerase (RNA) II (DNA directed) polypeptide K (7.0kD)"				Standard	NM_005034		Approved	RPB10alpha	uc003yjf.3	P53803	OTTHUMG00000164705	ENST00000353107.3:c.10C>G	chr8.hg19:g.101163593C>G	ENSP00000342889:p.Gln4Glu	73.0	0.0	.		88.0	24.0	.	NM_005034	Q6IBD4	Missense_Mutation	SNP	ENST00000353107.3	hg19	CCDS6285.1	.	.	.	.	.	.	.	.	.	.	C	18.34	3.602006	0.66445	.	.	ENSG00000147669	ENST00000353107;ENST00000522439	.	.	.	5.96	5.96	0.96718	.	0.069273	0.64402	D	0.000017	T	0.54464	0.1860	.	.	.	0.51233	D	0.999916	B	0.13594	0.008	B	0.12156	0.007	T	0.44667	-0.9313	8	0.22706	T	0.39	.	20.017	0.97481	0.0:1.0:0.0:0.0	.	4	P53803	RPAB4_HUMAN	E	4	.	ENSP00000342889:Q4E	Q	+	1	0	POLR2K	101232769	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	4.451000	0.60047	2.832000	0.97577	0.655000	0.94253	CAG	.	.	.	none		0.393	POLR2K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379849.1	NM_005034		G	101163593	C	G	101163593	3	3	278	1	0	0	0	0	1	0	0	0	12233	595	21	4	12	4	POLR2K	8	101163593	Missense_Mutation	SNP	C	TCGA-Y8-A898-01A-11D-A34Z-10	33208061	101163593	45200429	37	17710											
TRMT12	55039	hgsc.bcm.edu	37	chr8	125463695	125463695	+	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	cgtccagcgtttggcaaaacGagggcgggtatcaccggatg	9	7	15	10	5	1	0	1	0	0	0	2	2	2	1	2	4	2	3	2	4	3	2			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr8:125463695G>T	ENST00000328599.3	+	1	648	c.527G>T	c.(526-528)cGa>cTa	p.R176L	TRMT12_ENST00000521443.1_Intron	NM_017956.3	NP_060426.2	Q53H54	TYW2_HUMAN	tRNA methyltransferase 12 homolog (S. cerevisiae)	176					tRNA processing (GO:0008033)		transferase activity (GO:0016740)			breast(2)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			TTGGCAAAACGAGGGCGGGTA	0.542																																					p.R176L		Atlas-SNP	.											.	TRMT12	28	.	0			c.G527T						PASS	.						96	91	93					8																	125463695		2203	4300	6503	SO:0001583	missense	55039	exon1			CAAAACGAGGGCG	AF313041	CCDS6349.1	8q24.13	2011-05-09	2006-11-16		ENSG00000183665	ENSG00000183665			26091	protein-coding gene	gene with protein product	"tRNA-yW synthesizing protein 2"	611244	"tRNA methyltranferase 12 homolog (S. cerevisiae)"			16005430, 17150819	Standard	NM_017956		Approved	FLJ20772, Trm12, TYW2	uc003yra.4	Q53H54	OTTHUMG00000165022	ENST00000328599.3:c.527G>T	chr8.hg19:g.125463695G>T	ENSP00000329858:p.Arg176Leu	60.0	0.0	.		93.0	37.0	.	NM_017956	Q6PKB9|Q96F21|Q9NWK6	Missense_Mutation	SNP	ENST00000328599.3	hg19	CCDS6349.1	.	.	.	.	.	.	.	.	.	.	G	19.18	3.777863	0.70107	.	.	ENSG00000183665	ENST00000328599	T	0.23950	1.88	4.65	3.76	0.43208	.	0.201412	0.45126	D	0.000382	T	0.26448	0.0646	L	0.45581	1.43	0.37375	D	0.911792	P	0.43973	0.823	P	0.47891	0.56	T	0.11567	-1.0582	10	0.35671	T	0.21	-10.3012	6.4557	0.21928	0.0944:0.0:0.7222:0.1834	.	176	Q53H54	TYW2_HUMAN	L	176	ENSP00000329858:R176L	ENSP00000329858:R176L	R	+	2	0	TRMT12	125532876	1.000000	0.71417	0.968000	0.41197	0.984000	0.73092	3.567000	0.53813	1.245000	0.43885	0.561000	0.74099	CGA	.	.	.	none		0.542	TRMT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381465.1	NM_017956		T	125463695	G	T	125463695	3	4	278	1	0	0	0	0	1	0	0	0	16576	1058	37	4	529	4	TRMT12	8	125463695	Missense_Mutation	SNP	G	TCGA-Y8-A898-01A-11D-A34Z-10	24300102	125463695	20900327	38	17711											
QSOX2	169714	hgsc.bcm.edu	37	chr9	139100813	139100813	+	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	atgcaagctctctggaagggCaggcctggggcccagtgcac	8	6	15	12	0	1	0	0	0	1	0	2	1	1	1	2	5	3	4	2	5	2	0			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr9:139100813C>A	ENST00000358701.5	-	12	1895	c.1858G>T	c.(1858-1860)Gcc>Tcc	p.A620S		NM_181701.3	NP_859052.3	Q6ZRP7	QSOX2_HUMAN	quiescin Q6 sulfhydryl oxidase 2	620					cell redox homeostasis (GO:0045454)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	thiol oxidase activity (GO:0016972)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(178;0.0511)		Epithelial(140;7.78e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.55e-07)		TCTGGAAGGGCAGGCCTGGGG	0.657																																					p.A620S		Atlas-SNP	.											.	QSOX2	63	.	0			c.G1858T						PASS	.						69	68	68					9																	139100813		2203	4300	6503	SO:0001583	missense	169714	exon12			GAAGGGCAGGCCT	AJ318051	CCDS35178.1	9q34.3	2008-02-05	2007-04-23	2007-04-23	ENSG00000165661	ENSG00000165661			30249	protein-coding gene	gene with protein product		612860	"quiescin Q6-like 1"	QSCN6L1		12176051	Standard	NM_181701		Approved	SOXN, DKFZp762A2013	uc010nbi.2	Q6ZRP7	OTTHUMG00000020923	ENST00000358701.5:c.1858G>T	chr9.hg19:g.139100813C>A	ENSP00000351536:p.Ala620Ser	51.0	0.0	.		75.0	25.0	.	NM_181701	A2CEE0|A6NLB0|Q5TB37|Q7Z7B6|Q86VV7|Q8N3G2	Missense_Mutation	SNP	ENST00000358701.5	hg19	CCDS35178.1	.	.	.	.	.	.	.	.	.	.	C	3.024	-0.201068	0.06219	.	.	ENSG00000165661	ENST00000358701	T	0.04809	3.55	4.38	-1.36	0.09085	.	5.338950	0.00508	N	0.000160	T	0.03095	0.0091	N	0.08118	0	0.09310	N	1	B	0.25105	0.118	B	0.19946	0.027	T	0.43376	-0.9395	10	0.08179	T	0.78	2.4215	12.0025	0.53240	0.0:0.6163:0.269:0.1147	.	620	Q6ZRP7	QSOX2_HUMAN	S	620	ENSP00000351536:A620S	ENSP00000351536:A620S	A	-	1	0	QSOX2	138240634	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.007000	0.13174	-0.531000	0.06340	-0.448000	0.05591	GCC	.	.	.	none		0.657	QSOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055046.2	NM_181701		A	139100813	C	A	139100813	3	1	278	1	0	0	0	0	1	0	0	0	12897	710	25	4	242	4	QSOX2	9	139100813	Missense_Mutation	SNP	C	TCGA-Y8-A898-01A-11D-A34Z-10		139100813	2112618	39	17712											
MYO3A	53904	hgsc.bcm.edu	37	chr10	26385347	26385347	+	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	atattttttactacatttatGctggtttggctgaaaagaag	12	17	8	4	0	0	2	0	1	0	1	0	2	0	2	0	2	3	3	0	2	7	8			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr10:26385347G>C	ENST00000265944.5	+	16	1766	c.1600G>C	c.(1600-1602)Gct>Cct	p.A534P	MYO3A_ENST00000543632.1_Missense_Mutation_p.A534P	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	534	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						CTACATTTATGCTGGTTTGGC	0.323																																					p.A534P		Atlas-SNP	.											.	MYO3A	371	.	0			c.G1600C						PASS	.						51	55	53					10																	26385347		2200	4298	6498	SO:0001583	missense	53904	exon16			ATTTATGCTGGTT	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.1600G>C	chr10.hg19:g.26385347G>C	ENSP00000265944:p.Ala534Pro	193.0	0.0	.		246.0	65.0	.	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	hg19	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.126447	0.77549	.	.	ENSG00000095777	ENST00000265944;ENST00000543632	D;D	0.89196	-2.48;-2.48	5.13	4.23	0.50019	Myosin head, motor domain (2);	0.049751	0.85682	D	0.000000	D	0.95692	0.8599	H	0.95470	3.675	0.80722	D	1	D;D;D	0.57899	0.971;0.977;0.981	P;P;D	0.69142	0.763;0.847;0.962	D	0.96034	0.9019	10	0.48119	T	0.1	.	13.983	0.64317	0.0734:0.0:0.9266:0.0	.	534;534;534	F5H0U9;Q0VD65;Q8NEV4	.;.;MYO3A_HUMAN	P	534	ENSP00000265944:A534P;ENSP00000445909:A534P	ENSP00000265944:A534P	A	+	1	0	MYO3A	26425353	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.600000	0.82769	1.304000	0.44892	0.655000	0.94253	GCT	.	.	.	none		0.323	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		C	26385347	G	C	26385347	3	2	278	1	0	0	0	0	1	0	0	0	10083	1319	46	4	1654	4	MYO3A	10	26385347	Missense_Mutation	SNP	G	TCGA-Y8-A898-01A-11D-A34Z-10		26385347	109149400	40	17713											
MUC15	143662	hgsc.bcm.edu	37	chr11	26582626	26582626	+	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	ttagttctatacagaagtacGaagtggaggtatgtcatcca	13	12	10	6	1	2	1	1	0	1	1	3	3	3	2	1	2	2	3	1	2	7	6	rs375176901		TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr11:26582626G>T	ENST00000455601.2	-	4	1109	c.991C>A	c.(991-993)Cgt>Agt	p.R331S	MUC15_ENST00000281268.8_Missense_Mutation_p.R308S|MUC15_ENST00000529533.1_Missense_Mutation_p.R358S|ANO3_ENST00000525139.1_Intron|ANO3_ENST00000529242.1_Intron|MUC15_ENST00000436318.2_Missense_Mutation_p.R358S|MUC15_ENST00000527569.1_Missense_Mutation_p.R308S|ANO3_ENST00000537978.1_Intron|ANO3_ENST00000531568.1_Intron|ANO3_ENST00000256737.3_Intron	NM_145650.3	NP_663625.2	Q8N387	MUC15_HUMAN	mucin 15, cell surface associated	331					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						ACAGAAGTACGAAGTGGAGGT	0.383																																					p.R358S		Atlas-SNP	.											.	MUC15	88	.	0			c.C1072A						PASS	.						180	165	170					11																	26582626		2203	4300	6503	SO:0001583	missense	143662	exon5			AAGTACGAAGTGG	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.991C>A	chr11.hg19:g.26582626G>T	ENSP00000397339:p.Arg331Ser	114.0	0.0	.		165.0	51.0	.	NM_001135091	B3KY00|E9PII6|F8W945|Q6UWS3|Q8IXI8|Q8WW41	Missense_Mutation	SNP	ENST00000455601.2	hg19	CCDS7859.1	.	.	.	.	.	.	.	.	.	.	G	18.19	3.569502	0.65765	.	.	ENSG00000169550	ENST00000455601;ENST00000436318;ENST00000281268;ENST00000529533;ENST00000527569	T;T;T;T;T	0.39229	1.14;1.09;1.14;1.09;1.14	5.33	5.33	0.75918	.	0.000000	0.49916	D	0.000136	T	0.55641	0.1933	L	0.32530	0.975	0.19300	N	0.999979	D;D;D	0.89917	1.0;0.998;0.998	D;D;D	0.79108	0.992;0.955;0.955	T	0.52260	-0.8599	10	0.87932	D	0	-10.0199	18.1491	0.89668	0.0:0.0:1.0:0.0	.	308;331;358	F8W945;Q8N387;E9PII6	.;MUC15_HUMAN;.	S	331;358;308;358;308	ENSP00000397339:R331S;ENSP00000416753:R358S;ENSP00000281268:R308S;ENSP00000431983:R358S;ENSP00000431945:R308S	ENSP00000281268:R308S	R	-	1	0	MUC15	26539202	0.953000	0.32496	0.797000	0.32132	0.278000	0.26855	3.311000	0.51919	2.652000	0.90054	0.591000	0.81541	CGT	.	.	.	alt		0.383	MUC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387866.1	NM_145650		T	26582626	G	T	26582626	3	4	278	1	0	0	0	0	1	0	0	0	9979	1058	37	4	17	4	MUC15	11	26582626	Missense_Mutation	SNP	G	TCGA-Y8-A898-01A-11D-A34Z-10		26582626	108423890	41	17714											
KIAA0652	9776	hgsc.bcm.edu	37	chr11	46671731	46671731	+	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	tctttgtgcctggcaggtgtGataaagaaatcaaagtttcc	11	13	10	7	0	2	2	1	1	1	1	3	2	3	2	2	2	1	2	2	2	4	3			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr11:46671731G>A	ENST00000434074.1	+	6	1011	c.322G>A	c.(322-324)Gat>Aat	p.D108N	ATG13_ENST00000451945.1_Missense_Mutation_p.D108N|ATG13_ENST00000312040.4_Missense_Mutation_p.D108N|ATG13_ENST00000526508.1_Missense_Mutation_p.D108N|ATG13_ENST00000524625.1_Missense_Mutation_p.D108N|ATG13_ENST00000528494.1_Missense_Mutation_p.D108N|ATG13_ENST00000359513.4_Missense_Mutation_p.D108N|ATG13_ENST00000529655.1_Missense_Mutation_p.D108N|ATG13_ENST00000530500.1_Missense_Mutation_p.D29N	NM_001205120.1	NP_001192049.1	O75143	ATG13_HUMAN	autophagy related 13	108					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						TGGCAGGTGTGATAAAGAAAT	0.428																																					p.D108N		Atlas-SNP	.											ATG13_ENST00000528494,NS,carcinoma,0,2	ATG13	60	.	0			c.G322A						PASS	.						114	108	110					11																	46671731		2201	4299	6500	SO:0001583	missense	9776	exon7			AGGTGTGATAAAG	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.322G>A	chr11.hg19:g.46671731G>A	ENSP00000400642:p.Asp108Asn	28.0	0.0	.		31.0	9.0	.	NM_001142673	B4DFI4|D3DQQ1|D3DQQ2|E9PQZ8|Q53EN6|Q9BRL3|Q9H8B0	Missense_Mutation	SNP	ENST00000434074.1	hg19	CCDS44582.1	.	.	.	.	.	.	.	.	.	.	G	35	5.431312	0.96150	.	.	ENSG00000175224	ENST00000395549;ENST00000434074;ENST00000312040;ENST00000451945;ENST00000529655;ENST00000533325;ENST00000530500;ENST00000526508;ENST00000524625;ENST00000359513;ENST00000528494;ENST00000526078	.	.	.	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.75339	0.3836	L	0.46157	1.445	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.996;0.997;0.997;0.983	T	0.73126	-0.4081	9	0.42905	T	0.14	-12.925	19.7319	0.96186	0.0:0.0:1.0:0.0	.	29;108;108;108	B4DFI4;O75143;E9PQZ8;O75143-2	.;ATG13_HUMAN;.;.	N	108;108;108;108;108;108;29;108;108;108;108;108	.	ENSP00000310321:D108N	D	+	1	0	ATG13	46628307	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.827000	0.99397	2.668000	0.90789	0.655000	0.94253	GAT	.	.	.	none		0.428	ATG13-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390300.2	NM_014741		A	46671731	G	A	46671731	3	1	278	1	0	0	0	0	1	0	0	0	8195	1290	45	2	340	2	KIAA0652	11	46671731	Missense_Mutation	SNP	G	TCGA-Y8-A898-01A-11D-A34Z-10	20089105	46671731	88334785	42	17715											
MADD	8567	hgsc.bcm.edu	37	chr11	47298344	47298344	+	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	tgtgatggcattcgtggcaaTgatctacccactggagtata	10	12	11	8	1	1	2	0	2	1	0	2	3	1	3	1	3	1	3	1	3	4	4			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr11:47298344T>A	ENST00000311027.5	+	5	1190	c.1025T>A	c.(1024-1026)aTg>aAg	p.M342K	MADD_ENST00000395336.3_Missense_Mutation_p.M342K|MADD_ENST00000406482.1_Missense_Mutation_p.M342K|MADD_ENST00000402799.1_Missense_Mutation_p.M342K|MADD_ENST00000342922.4_Missense_Mutation_p.M342K|MADD_ENST00000407859.3_Missense_Mutation_p.M342K|MADD_ENST00000349238.3_Missense_Mutation_p.M342K|MADD_ENST00000402192.2_Missense_Mutation_p.M342K|MADD_ENST00000395344.3_Missense_Mutation_p.M342K|MADD_ENST00000489415.1_3'UTR	NM_003682.3	NP_003673.3			MAP-kinase activating death domain											breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		TTCGTGGCAATGATCTACCCA	0.512																																					p.M342K		Atlas-SNP	.											.	MADD	172	.	0			c.T1025A						PASS	.						286	217	241					11																	47298344		2201	4298	6499	SO:0001583	missense	8567	exon5			TGGCAATGATCTA	AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"DENN/MADD domain containing"	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.1025T>A	chr11.hg19:g.47298344T>A	ENSP00000310933:p.Met342Lys	70.0	0.0	.		97.0	21.0	.	NM_130474		Missense_Mutation	SNP	ENST00000311027.5	hg19	CCDS7930.1	.	.	.	.	.	.	.	.	.	.	T	30	5.056526	0.93793	.	.	ENSG00000110514	ENST00000342922;ENST00000395342;ENST00000428807;ENST00000402799;ENST00000406482;ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395344;ENST00000395336;ENST00000402192	T;T;T;T;T;T;T;T;T;T	0.11821	2.74;2.74;2.74;2.74;2.74;2.74;2.74;2.74;2.74;2.74	5.93	5.93	0.95920	DENN (3);	0.000000	0.85682	D	0.000000	T	0.40372	0.1114	M	0.79258	2.445	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.65815	0.992;0.98;0.995;0.988;0.988;0.988;0.988;0.994;0.99;0.995	D;P;D;P;P;P;P;D;D;D	0.74348	0.91;0.845;0.961;0.836;0.836;0.836;0.883;0.983;0.952;0.962	T	0.27640	-1.0068	10	0.87932	D	0	-26.4751	16.3943	0.83563	0.0:0.0:0.0:1.0	.	342;342;342;342;342;342;342;342;342;342	B5MEE5;A8K8S7;Q8WXG6-7;F8W9P9;Q8WXG6-6;Q8WXG6-5;Q8WXG6-2;Q8WXG6-4;Q8WXG6;Q8WXG6-3	.;.;.;.;.;.;.;.;MADD_HUMAN;.	K	342;342;120;342;342;342;342;342;342;342;342	ENSP00000343902:M342K;ENSP00000398167:M120K;ENSP00000385585:M342K;ENSP00000384435:M342K;ENSP00000304505:M342K;ENSP00000310933:M342K;ENSP00000384204:M342K;ENSP00000378753:M342K;ENSP00000378745:M342K;ENSP00000384287:M342K	ENSP00000310933:M342K	M	+	2	0	MADD	47254920	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.698000	0.84413	2.281000	0.76405	0.533000	0.62120	ATG	.	.	.	none		0.512	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1			A	47298344	T	A	47298344	3	1	278	1	0	0	0	0	1	0	0	0	9159	1464	51	5	1039	5	MADD	11	47298344	Missense_Mutation	SNP	T	TCGA-Y8-A898-01A-11D-A34Z-10	626613	47298344	87708172	43	17716											
DDB1	1642	hgsc.bcm.edu	37	chr11	61079364	61079364	+	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	gacacttcctggtagcagatCttcctgcagaacaagtacag	12	9	9	11	0	1	2	0	0	1	2	3	3	3	2	2	1	4	4	2	1	4	4			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr11:61079364C>T	ENST00000301764.7	-	18	2566	c.2169G>A	c.(2167-2169)aaG>aaA	p.K723K	DDB1_ENST00000545930.1_5'Flank|DDB1_ENST00000450997.2_Intron	NM_001923.4	NP_001914.3	Q16531	DDB1_HUMAN	damage-specific DNA binding protein 1, 127kDa	723	Interaction with CDT1.|WD repeat beta-propeller C.				DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of mitotic cell cycle phase transition (GO:1901990)|UV-damage excision repair (GO:0070914)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	48						GGTAGCAGATCTTCCTGCAGA	0.567								Nucleotide excision repair (NER)																													p.K723K		Atlas-SNP	.											.	DDB1	100	.	0			c.G2169A						PASS	.						109	101	104					11																	61079364		2203	4299	6502	SO:0001819	synonymous_variant	1642	exon18			GCAGATCTTCCTG	AJ002955	CCDS31576.1	11q12-q13	2014-09-17	2002-08-29		ENSG00000167986	ENSG00000167986			2717	protein-coding gene	gene with protein product		600045	"damage-specific DNA binding protein 1 (127kD)"			8530102, 10574459	Standard	NM_001923		Approved	XPE	uc001nrc.5	Q16531	OTTHUMG00000168209	ENST00000301764.7:c.2169G>A	chr11.hg19:g.61079364C>T		55.0	0.0	.		51.0	10.0	.	NM_001923	A6NG77|B2R648|B4DG00|O15176|Q13289|Q58F96	Silent	SNP	ENST00000301764.7	hg19	CCDS31576.1																																																																																			.	.	.	none		0.567	DDB1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398816.1	NM_001923		T	61079364	C	T	61079364	2	4	278	1	0	0	0	0	0	0	0	1	4325	912	32	2		2	DDB1	11	61079364	Silent	SNP	C	TCGA-Y8-A898-01A-11D-A34Z-10	13781020	61079364	73927152	44	17717											
MAP4K2	5871	hgsc.bcm.edu	37	chr11	64557689	64557689	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgatggggaaatcaaaggtcAgctcaggtgccagtgtggcc	10	7	15	9	1	3	0	3	0	0	0	3	2	3	1	2	5	2	1	2	5	2	0			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr11:64557689A>G	ENST00000294066.2	-	29	2310	c.2219T>C	c.(2218-2220)cTg>cCg	p.L740P	MAP4K2_ENST00000377350.3_Missense_Mutation_p.L732P	NM_004579.3	NP_004570.2	Q12851	M4K2_HUMAN	mitogen-activated protein kinase kinase kinase kinase 2	740	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				activation of JUN kinase activity (GO:0007257)|immune response (GO:0006955)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|positive regulation of JNK cascade (GO:0046330)|protein phosphorylation (GO:0006468)|vesicle targeting (GO:0006903)	Golgi membrane (GO:0000139)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			cervix(1)|lung(3)|ovary(1)|pancreas(1)|urinary_tract(2)	8						ATCAAAGGTCAGCTCAGGTGC	0.632																																					p.L740P		Atlas-SNP	.											.	MAP4K2	83	.	0			c.T2219C						PASS	.						118	107	111					11																	64557689		2201	4297	6498	SO:0001583	missense	5871	exon29			AAGGTCAGCTCAG	BC047865	CCDS8082.1	11q13.1	2011-06-09			ENSG00000168067	ENSG00000168067		"Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"	6864	protein-coding gene	gene with protein product		603166		RAB8IP		7515885	Standard	NM_004579		Approved	GCK, BL44	uc001obh.3	Q12851	OTTHUMG00000045328	ENST00000294066.2:c.2219T>C	chr11.hg19:g.64557689A>G	ENSP00000294066:p.Leu740Pro	34.0	0.0	.		27.0	9.0	.	NM_004579	Q86VU3	Missense_Mutation	SNP	ENST00000294066.2	hg19	CCDS8082.1	.	.	.	.	.	.	.	.	.	.	A	16.08	3.022010	0.54576	.	.	ENSG00000168067	ENST00000294066;ENST00000377350	T;T	0.08370	3.1;3.1	5.28	5.28	0.74379	Citron-like (3);	0.090204	0.46442	D	0.000281	T	0.23766	0.0575	L	0.58510	1.815	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.75484	0.961;0.986	T	0.00415	-1.1753	10	0.87932	D	0	.	11.6762	0.51432	1.0:0.0:0.0:0.0	.	732;740	Q86VU3;Q12851	.;M4K2_HUMAN	P	740;732	ENSP00000294066:L740P;ENSP00000366567:L732P	ENSP00000294066:L740P	L	-	2	0	MAP4K2	64314265	1.000000	0.71417	0.995000	0.50966	0.867000	0.49689	7.737000	0.84957	2.019000	0.59389	0.454000	0.30748	CTG	.	.	.	none		0.632	MAP4K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105239.1	NM_004579		G	64557689	A	G	64557689	3	3	278	1	0	0	0	0	1	0	0	0	9267	188	7	3	259	3	MAP4K2	11	64557689	Missense_Mutation	SNP	A	TCGA-Y8-A898-01A-11D-A34Z-10	3478325	64557689	70448827	45	17718											
MAML2	84441	hgsc.bcm.edu	37	chr11	95825254	95825254	+	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	tgttgttgctgctgctgctgCtgttgttgctgctgctgctg	0	18	14	9	0	0	0	0	0	0	0	0	0	0	0	0	0	9	13	0	0	0	4	rs61749250		TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr11:95825254C>T	ENST00000524717.1	-	2	3225	c.1941G>A	c.(1939-1941)caG>caA	p.Q647Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	647					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.Q647Q(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)				gctgctgctgctgttgttgct	0.512			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.Q647Q		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	MAML2,caecum,carcinoma,0,2	MAML2	94	.	1	Substitution - coding silent(1)	endometrium(1)	c.G1941A						PASS	.	C		0,4198		0,0,2099	35	40	38		1941	1.7	0.1	11	dbSNP_129	38	5,8237		0,5,4116	no	coding-synonymous	MAML2	NM_032427.1		0,5,6215	TT,TC,CC		0.0607,0.0,0.0402		647/1157	95825254	5,12435	2099	4121	6220	SO:0001819	synonymous_variant	84441	exon2			CTGCTGCTGTTGT	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.1941G>A	chr11.hg19:g.95825254C>T		122.0	1.0	.		143.0	6.0	.	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	hg19	CCDS44714.1																																																																																			.	.	.	weak		0.512	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95825254	C	T	95825254	2	4	278	1	0	0	0	0	0	0	0	1	9213	796	28	2		2	MAML2	11	95825254	Silent	SNP	C	TCGA-Y8-A898-01A-11D-A34Z-10	31267565	95825254	39181262	46	17719											
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103128412	103128412	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttctgatttgtccaaaattAataacatgtaccgttttagt	12	18	5	6	1	1	1	0	1	1	0	2	1	2	1	2	0	2	2	2	0	6	7			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr11:103128412A>G	ENST00000375735.2	+	69	10681	c.10537A>G	c.(10537-10539)Aat>Gat	p.N3513D	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.N3520D|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	3513					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)		GTCCAAAATTAATAACATGTA	0.443																																					p.N3520D		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.A10558G						PASS	.						146	133	137					11																	103128412		1861	4099	5960	SO:0001583	missense	79659	exon70			AAAATTAATAACA	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.10537A>G	chr11.hg19:g.103128412A>G	ENSP00000364887:p.Asn3513Asp	73.0	0.0	.		93.0	20.0	.	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	A	31	5.077452	0.94000	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.36520	1.25;1.25	6.06	6.06	0.98353	.	0.152305	0.56097	D	0.000024	T	0.48447	0.1500	L	0.45228	1.405	0.80722	D	1	P;D	0.64830	0.931;0.994	P;P	0.61592	0.688;0.891	T	0.26087	-1.0113	10	0.19590	T	0.45	.	16.6093	0.84858	1.0:0.0:0.0:0.0	.	3513;3520	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	D	3513;3520	ENSP00000364887:N3513D;ENSP00000381167:N3520D	ENSP00000364887:N3513D	N	+	1	0	DYNC2H1	102633622	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.228000	0.95250	2.324000	0.78689	0.533000	0.62120	AAT	.	.	.	none		0.443	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		G	103128412	A	G	103128412	3	3	278	1	0	0	0	0	1	0	0	0	4848	362	13	3	10836	3	DYNC2H1	11	103128412	Missense_Mutation	SNP	A	TCGA-Y8-A898-01A-11D-A34Z-10	7303158	103128412	31878104	47	17720											
SIK3	23387	hgsc.bcm.edu	37	chr11	116717228	116717228	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaatgctggctgccatcacTcaggtctgggtgctcatgac	8	11	11	11	0	4	1	3	1	1	0	4	1	4	1	1	3	3	3	1	3	2	1			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr11:116717228T>C	ENST00000292055.4	-	23	3711	c.3676A>G	c.(3676-3678)Agt>Ggt	p.S1226G	SIK3_ENST00000434315.2_Missense_Mutation_p.S1065G|SIK3_ENST00000488337.1_5'UTR|SIK3_ENST00000446921.2_Missense_Mutation_p.S1224G|AP006216.12_ENST00000444200.1_RNA|SIK3_ENST00000542607.1_Missense_Mutation_p.S1166G|SIK3_ENST00000375300.1_Missense_Mutation_p.S1284G|SIK3_ENST00000375288.1_Missense_Mutation_p.S561G	NM_025164.3	NP_079440.3	Q9Y2K2	SIK3_HUMAN	SIK family kinase 3	1226					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						CTGCCATCACTCAGGTCTGGG	0.517																																					p.S1226G		Atlas-SNP	.											.	SIK3	112	.	0			c.A3676G						PASS	.						145	123	130					11																	116717228		2201	4292	6493	SO:0001583	missense	23387	exon23			CATCACTCAGGTC	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.3676A>G	chr11.hg19:g.116717228T>C	ENSP00000292055:p.Ser1226Gly	63.0	0.0	.		93.0	21.0	.	NM_025164	A1A5A8|Q59FY2|Q5M9N1|Q6P3R6|Q8IYM8|Q9HA50	Missense_Mutation	SNP	ENST00000292055.4	hg19	CCDS8379.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.38|11.38	1.620458|1.620458	0.28801|0.28801	.|.	.|.	ENSG00000160584|ENSG00000160584	ENST00000445177;ENST00000446921|ENST00000375300;ENST00000292055;ENST00000375288;ENST00000542607;ENST00000434315	.|T;T;T;T;T	.|0.70869	.|-0.46;-0.5;1.46;-0.52;-0.12	5.13|5.13	0.277|0.277	0.15668|0.15668	.|.	.|0.839139	.|0.09863	.|N	.|0.745920	T|T	0.42177|0.42177	0.1191|0.1191	N|N	0.04880|0.04880	-0.145|-0.145	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	.|0.01281	.|0.0;0.0;0.0;0.0	T|T	0.26744|0.26744	-1.0094|-1.0094	5|10	.|0.02654	.|T	.|1	.|.	8.8093|8.8093	0.34956|0.34956	0.0:0.5814:0.0:0.4186|0.0:0.5814:0.0:0.4186	.|.	.|1166;1065;1226;561	.|A1A5A8;A1A5A9;Q9Y2K2;Q9Y2K2-2	.|.;.;SIK3_HUMAN;.	G|G	1325;1188|1284;1226;561;1166;1065	.|ENSP00000364449:S1284G;ENSP00000292055:S1226G;ENSP00000364437:S561G;ENSP00000438108:S1166G;ENSP00000415873:S1065G	.|ENSP00000292055:S1226G	E|S	-|-	2|1	0|0	SIK3|SIK3	116222438|116222438	0.561000|0.561000	0.26578|0.26578	0.405000|0.405000	0.26409|0.26409	0.996000|0.996000	0.88848|0.88848	0.821000|0.821000	0.27338|0.27338	0.012000|0.012000	0.14892|0.14892	0.533000|0.533000	0.62120|0.62120	GAG|AGT	.	.	.	none		0.517	SIK3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_025164		C	116717228	T	C	116717228	3	2	278	1	0	0	0	0	1	0	0	0	14332	1551	54	3	119	3	SIK3	11	116717228	Missense_Mutation	SNP	T	TCGA-Y8-A898-01A-11D-A34Z-10	13588816	116717228	18289288	48	17721											
ATN1	1822	hgsc.bcm.edu	37	chr12	7045900	7045900	+	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	cagcaacagcaacagcagcaGcagcagcagcagcagcagca	16	0	11	14	0	0	0	0	0	0	0	0	0	0	0	0	0	13	11	0	0	2	0	rs377147612|rs60216939		TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr12:7045900G>C	ENST00000356654.4	+	5	1707	c.1470G>C	c.(1468-1470)caG>caC	p.Q490H	ATN1_ENST00000396684.2_Missense_Mutation_p.Q490H	NM_001007026.1	NP_001007027.1	P54259	ATN1_HUMAN	atrophin 1	490	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						aacagcagcagcagcagcagc	0.642																																					p.Q490H		Atlas-SNP	.											.	ATN1	95	.	0			c.G1470C						PASS	.						50	62	58					12																	7045900		2202	4291	6493	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.1470G>C	chr12.hg19:g.7045900G>C	ENSP00000349076:p.Gln490His	18.0	0.0	.		43.0	7.0	.	NM_001007026	Q99495|Q99621|Q9UEK7	Missense_Mutation	SNP	ENST00000356654.4	hg19	CCDS31734.1	.	.	.	.	.	.	.	.	.	.	g	0.018	-1.486452	0.01018	.	.	ENSG00000111676	ENST00000356654;ENST00000396684;ENST00000544325;ENST00000229279	T;T;T	0.50277	0.75;0.75;0.75	2.95	-0.471	0.12119	.	.	.	.	.	T	0.19167	0.0460	N	0.08118	0	0.22412	N	0.999122	B	0.02656	0.0	B	0.04013	0.001	T	0.19614	-1.0300	9	0.15499	T	0.54	.	0.8057	0.01084	0.255:0.248:0.3392:0.1578	.	490	P54259	ATN1_HUMAN	H	490;490;490;75	ENSP00000349076:Q490H;ENSP00000379915:Q490H;ENSP00000441744:Q490H	ENSP00000229279:Q75H	Q	+	3	2	ATN1	6916161	0.012000	0.17670	0.065000	0.19835	0.080000	0.17528	0.084000	0.14891	0.105000	0.17753	-0.342000	0.07992	CAG	.	.	.	none		0.642	ATN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401948.2	NM_001940		C	7045900	G	C	7045900	3	2	278	1	0	0	0	0	1	0	0	0	1111	962	34	4	1484	4	ATN1	12	7045900	Missense_Mutation	SNP	G	TCGA-Y8-A898-01A-11D-A34Z-10		7045900	126805995	49	17722											
OR6C75	390323	hgsc.bcm.edu	37	chr12	55759766	55759767	+	Frame_Shift_Ins	INS	-	-	A																															cccttcatatacacactgagINSaaataagcaagtgaagcaag																										TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr12:55759766_55759767insA	ENST00000343399.3	+	1	872_873	c.872_873insA	c.(871-876)agaaatfs	p.N292fs		NM_001005497.1	NP_001005497.1	A6NL08	O6C75_HUMAN	olfactory receptor, family 6, subfamily C, member 75	292						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						TACACACTGAGAAATAAGCAAG	0.391																																					p.R291fs		Atlas-Indel,Pindel	.											.	OR6C75	67	.	0			c.872_873insA						PASS	.																																			SO:0001589	frameshift_variant	390323	exon1			.		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.875dupA	chr12.hg19:g.55759769_55759769dupA	ENSP00000368987:p.Asn292fs	53.0	0.0	0		60.0	18.0	0.3	NM_001005497		Frame_Shift_Ins	INS	ENST00000343399.3	hg19	CCDS31820.1																																																																																			.	.	.	none		0.391	OR6C75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406418.1			A	55759767	-	A	55759766	7	5	278	1	0	1	1	0	0	0	0	0	11206	942	33	0	874	0	OR6C75	12	55759766	Frame_Shift_Ins	INS	-	TCGA-Y8-A898-01A-11D-A34Z-10	48713866	55759766	78092129	50	17723											
PLBD2	196463	hgsc.bcm.edu	37	chr12	113825565	113825565	+	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	ccaggtacaatgacttcctcCatgaccctctgtcactgtgc	8	11	7	15	0	2	2	1	2	1	0	4	2	4	2	4	1	2	1	4	1	2	2			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr12:113825565C>T	ENST00000280800.3	+	11	1487	c.1456C>T	c.(1456-1458)Cat>Tat	p.H486Y	PLBD2_ENST00000545182.2_Missense_Mutation_p.H454Y	NM_173542.3	NP_775813.2	Q8NHP8	PLBL2_HUMAN	phospholipase B domain containing 2	486					lipid catabolic process (GO:0016042)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)			breast(1)|endometrium(1)|large_intestine(3)|lung(7)|prostate(1)	13						TGACTTCCTCCATGACCCTCT	0.592																																					p.H486Y		Atlas-SNP	.											.	PLBD2	33	.	0			c.C1456T						PASS	.						331	324	326					12																	113825565		2203	4300	6503	SO:0001583	missense	196463	exon11			TTCCTCCATGACC	BC030618	CCDS9168.1, CCDS53834.1	12q24.13	2013-10-11				ENSG00000151176			27283	protein-coding gene	gene with protein product	"PLB homolog 2 (Dictyostelium)", "mannose-6-phosphate protein associated protein p76"					17105447, 15193148, 19019078	Standard	NM_001159727		Approved	p76	uc001tve.2	Q8NHP8	OTTHUMG00000169567	ENST00000280800.3:c.1456C>T	chr12.hg19:g.113825565C>T	ENSP00000280800:p.His486Tyr	54.0	0.0	.		62.0	15.0	.	NM_173542	F5H5E2	Missense_Mutation	SNP	ENST00000280800.3	hg19	CCDS9168.1	.	.	.	.	.	.	.	.	.	.	C	14.00	2.405656	0.42715	.	.	ENSG00000151176	ENST00000545182;ENST00000280800	T;T	0.17691	2.26;2.26	5.07	5.07	0.68467	.	0.296342	0.38272	N	0.001754	T	0.20577	0.0495	L	0.53249	1.67	0.28038	N	0.933883	B;B	0.29571	0.166;0.249	B;B	0.31495	0.063;0.131	T	0.12837	-1.0532	10	0.72032	D	0.01	-36.6143	14.5605	0.68133	0.1469:0.8531:0.0:0.0	.	454;486	F5H5E2;Q8NHP8	.;PLBL2_HUMAN	Y	454;486	ENSP00000443463:H454Y;ENSP00000280800:H486Y	ENSP00000280800:H486Y	H	+	1	0	PLBD2	112309948	0.977000	0.34250	0.996000	0.52242	0.981000	0.71138	1.463000	0.35277	2.533000	0.85409	0.555000	0.69702	CAT	.	.	.	none		0.592	PLBD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404835.1	NM_173542		T	113825565	C	T	113825565	3	4	278	1	0	0	0	0	1	0	0	0	12033	594	21	2	1498	2	PLBD2	12	113825565	Missense_Mutation	SNP	C	TCGA-Y8-A898-01A-11D-A34Z-10	58065799	113825565	20026330	51	17724											
SLC7A8	23428	hgsc.bcm.edu	37	chr14	23634614	23634615	+	Missense_Mutation	DNP	TC	TC	AT																															agcctggttggtggggtagaTcaccagcacagcaatccaca																								rs371235147		TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr14:23634614_23634615TC>AT	ENST00000316902.7	-	3	1112_1113	c.387_388GA>AT	c.(385-390)gtGAtc>gtATtc	p.I130F	SLC7A8_ENST00000469263.1_Missense_Mutation_p.I130F	NM_012244.3	NP_036376.2	Q9UHI5	LAT2_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 8	130					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|metal ion homeostasis (GO:0055065)|neutral amino acid transport (GO:0015804)|organic cation transport (GO:0015695)|response to toxic substance (GO:0009636)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|organic cation transmembrane transporter activity (GO:0015101)|peptide antigen binding (GO:0042605)|toxin transporter activity (GO:0019534)			autonomic_ganglia(1)|endometrium(6)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|skin(1)	24	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00809)	L-Alanine(DB00160)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	GTGGGGTAGATCACCAGCACAG	0.629																																					p.I130F|p.V129V		Atlas-SNP	.											.	SLC7A8	54	.	0			c.A388T|c.G387A						PASS	.																																			SO:0001583	missense	23428	exon3			GGTAGATCACCAG|GTAGATCACCAGC	Y18483	CCDS9590.1, CCDS41924.1, CCDS58304.1, CCDS58305.1	14q11.2	2013-05-22	2011-07-12		ENSG00000092068	ENSG00000092068		"Solute carriers"	11066	protein-coding gene	gene with protein product		604235				10080183, 10391915	Standard	NM_001267036		Approved	LPI-PC1, LAT2	uc001wiz.4	Q9UHI5	OTTHUMG00000028720	ENST00000316902.7:c.387_388delinsAT	chr14.hg19:g.23634614_23634615delinsAT	ENSP00000320378:p.Ile130Phe	31.0|30.0	0.0	.		41.0	14.0	.	NM_012244	B2R8Q4|B4DKT4|B4DTV6|D3DS46|F2Z2J4|Q86U05|Q9UKQ6|Q9UKQ7|Q9UKQ8|Q9Y445	Missense_Mutation|Silent	SNP	ENST00000316902.7	hg19	CCDS9590.1																																																																																			.	.	.	alt|none		0.629	SLC7A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071718.3			AT	23634615	TC	AT	23634614	3	1	278	1	0	0	0	0	1	0	0	0	14717	1435	50	5	1255	5	SLC7A8	14	23634614	Missense_Mutation	DNP	TC	TCGA-Y8-A898-01A-11D-A34Z-10		23634614	83714926	52	17725											
KIAA0391	9692	hgsc.bcm.edu	37	chr14	35735939	35735939	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgtgttttttagctcttgAatgtcgtctctcaactagcc	6	19	7	9	1	3	1	1	1	2	0	5	1	3	1	1	0	3	2	1	0	4	6			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr14:35735939A>G	ENST00000557565.1	+	6	1663	c.1282A>G	c.(1282-1284)Aat>Gat	p.N428D	KIAA0391_ENST00000604948.1_Missense_Mutation_p.N333D|KIAA0391_ENST00000534898.4_Missense_Mutation_p.N428D|KIAA0391_ENST00000605870.1_Missense_Mutation_p.N56D|KIAA0391_ENST00000603544.1_Missense_Mutation_p.N412D|KIAA0391_ENST00000321130.10_Missense_Mutation_p.N412D|KIAA0391_ENST00000250377.7_Missense_Mutation_p.N333D	NM_001282234.1	NP_001269163.1	O15091	MRRP3_HUMAN	KIAA0391	428					tRNA processing (GO:0008033)	mitochondrion (GO:0005739)				central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	14	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)		TTAGCTCTTGAATGTCGTCTC	0.488																																					p.N428D		Atlas-SNP	.											.	KIAA0391	35	.	0			c.A1282G						PASS	.						179	173	175					14																	35735939		2203	4300	6503	SO:0001583	missense	9692	exon6			CTCTTGAATGTCG	AB002389	CCDS32063.1, CCDS58312.1, CCDS58313.1, CCDS58314.1	14q13.2	2013-06-18			ENSG00000100890	ENSG00000100890			19958	protein-coding gene	gene with protein product	"mitochondrial RNase P subunit 3", "proteinaceous RNase P"	609947				9205841, 18984158	Standard	NM_001256678		Approved	MRPP3, PRORP	uc001wsy.2	O15091		ENST00000557565.1:c.1282A>G	chr14.hg19:g.35735939A>G	ENSP00000454657:p.Asn428Asp	135.0	0.0	.		172.0	59.0	.	NM_014672	B4DXD9|B4E0S8|B4E211|C4AM93|D3DS99|D3DSA1|Q86SZ4|Q86YB5|Q8N5L5	Missense_Mutation	SNP	ENST00000557565.1	hg19	CCDS32063.1	.	.	.	.	.	.	.	.	.	.	A	2.018	-0.425485	0.04701	.	.	ENSG00000100890	ENST00000554896;ENST00000250377;ENST00000321130;ENST00000534898;ENST00000556121;ENST00000556912;ENST00000557404	T;T;T;T	0.46063	0.88;0.9;0.9;0.99	5.62	-4.39	0.03611	.	1.007910	0.07948	N	0.980404	T	0.20088	0.0483	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.36648	-0.9739	10	0.11485	T	0.65	1.9621	12.9831	0.58575	0.6052:0.0:0.3948:0.0	.	412;428	O15091-2;O15091	.;MRRP3_HUMAN	D	333;333;412;428;412;56;56	ENSP00000250377:N333D;ENSP00000324697:N412D;ENSP00000440915:N428D;ENSP00000450898:N56D	ENSP00000250377:N333D	N	+	1	0	KIAA0391	34805690	0.521000	0.26258	0.002000	0.10522	0.342000	0.28953	0.425000	0.21346	-1.023000	0.03342	-0.248000	0.11899	AAT	.	.	.	none		0.488	KIAA0391-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000411280.1	NM_014672		G	35735939	A	G	35735939	3	3	278	1	0	0	0	0	1	0	0	0	8179	246	9	3	1300	3	KIAA0391	14	35735939	Missense_Mutation	SNP	A	TCGA-Y8-A898-01A-11D-A34Z-10	12101325	35735939	71613601	53	17726											
ARID4A	5926	hgsc.bcm.edu	37	chr14	58832872	58832872	+	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	agaatatccccgcacatcaaAgatggagagaaagataaaca	20	5	8	8	1	1	4	1	0	0	4	2	6	2	5	2	1	1	1	2	1	6	2			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr14:58832872A>T	ENST00000355431.3	+	22	3820	c.3447A>T	c.(3445-3447)aaA>aaT	p.K1149N	ARID4A_ENST00000348476.3_Intron|ARID4A_ENST00000395168.3_Intron|ARID4A_ENST00000431317.2_Intron	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	1149					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						CGCACATCAAAGATGGAGAGA	0.388																																					p.K1149N		Atlas-SNP	.											.	ARID4A	222	.	0			c.A3447T						PASS	.						154	163	160					14																	58832872		2203	4300	6503	SO:0001583	missense	5926	exon22			CATCAAAGATGGA	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.3447A>T	chr14.hg19:g.58832872A>T	ENSP00000347602:p.Lys1149Asn	79.0	0.0	.		105.0	24.0	.	NM_002892	Q15991|Q15992|Q15993	Missense_Mutation	SNP	ENST00000355431.3	hg19	CCDS9732.1	.	.	.	.	.	.	.	.	.	.	A	19.90	3.913602	0.72983	.	.	ENSG00000032219	ENST00000355431	T	0.20200	2.09	5.12	3.97	0.46021	.	0.000000	0.85682	D	0.000000	T	0.41328	0.1154	M	0.66939	2.045	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.23762	-1.0179	10	0.87932	D	0	-27.7345	9.6558	0.39925	0.8524:0.0:0.1476:0.0	.	1149	P29374	ARI4A_HUMAN	N	1149	ENSP00000347602:K1149N	ENSP00000347602:K1149N	K	+	3	2	ARID4A	57902625	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.682000	0.46934	0.890000	0.36211	0.528000	0.53228	AAA	.	.	.	none		0.388	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001		T	58832872	A	T	58832872	3	4	278	1	0	0	0	0	1	0	0	0	919	69	3	5	3529	5	ARID4A	14	58832872	Missense_Mutation	SNP	A	TCGA-Y8-A898-01A-11D-A34Z-10	23096933	58832872	48516668	54	17727											
GTF2A1	2957	hgsc.bcm.edu	37	chr14	81662499	81662499	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accaggctgcatttgtggtaTaacctgttgttgtagaacca	10	13	10	8	0	0	1	0	0	0	1	0	1	0	1	3	2	3	6	3	2	4	6	rs535983219		TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr14:81662499T>C	ENST00000553612.1	-	6	968	c.565A>G	c.(565-567)Ata>Gta	p.I189V	GTF2A1_ENST00000434192.2_Missense_Mutation_p.I150V	NM_001278940.1|NM_015859.3	NP_001265869.1|NP_056943.1	P52655	TF2AA_HUMAN	general transcription factor IIA, 1, 19/37kDa	189					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)		ATTTGTGGTATAACCTGTTGT	0.428																																					p.I189V		Atlas-SNP	.											.	GTF2A1	34	.	0			c.A565G						PASS	.						182	163	169					14																	81662499		2203	4300	6503	SO:0001583	missense	2957	exon6			GTGGTATAACCTG	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.565A>G	chr14.hg19:g.81662499T>C	ENSP00000452454:p.Ile189Val	58.0	0.0	.		87.0	29.0	.	NM_015859	Q3KNQ9	Missense_Mutation	SNP	ENST00000553612.1	hg19	CCDS9873.1	.	.	.	.	.	.	.	.	.	.	T	10.86	1.470284	0.26423	.	.	ENSG00000165417	ENST00000553612;ENST00000344860;ENST00000434192	T;T	0.40756	1.02;1.02	5.38	5.38	0.77491	.	0.181773	0.47455	D	0.000232	T	0.37919	0.1021	L	0.46614	1.455	0.35724	D	0.817382	B	0.26445	0.149	B	0.29663	0.105	T	0.42378	-0.9455	10	0.16420	T	0.52	-13.0773	15.3865	0.74706	0.0:0.0:0.0:1.0	.	189	P52655	TF2AA_HUMAN	V	189;150;150	ENSP00000452454:I189V;ENSP00000409492:I150V	ENSP00000298173:I189V	I	-	1	0	GTF2A1	80732252	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.640000	0.61368	2.025000	0.59659	0.459000	0.35465	ATA	.	.	.	none		0.428	GTF2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413309.1	NM_015859		C	81662499	T	C	81662499	3	2	278	1	0	0	0	0	1	0	0	0	6859	1406	49	3	581	3	GTF2A1	14	81662499	Missense_Mutation	SNP	T	TCGA-Y8-A898-01A-11D-A34Z-10	22829627	81662499	25687041	55	17728											
C14orf49	161176	hgsc.bcm.edu	37	chr14	95903278	95903278	+	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	agttcctcaggagctgggagAaatcttcatggctcccttct	8	12	10	11	0	4	1	2	0	2	1	6	3	6	2	2	3	1	3	2	3	1	3			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr14:95903278A>T	ENST00000334258.5	-	14	2431	c.2417T>A	c.(2416-2418)tTc>tAc	p.F806Y	SYNE3_ENST00000554873.1_Missense_Mutation_p.F563Y|SYNE3_ENST00000557275.1_Missense_Mutation_p.F801Y	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	806					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						GAGCTGGGAGAAATCTTCATG	0.517																																					p.F806Y		Atlas-SNP	.											.	SYNE3	130	.	0			c.T2417A						PASS	.						100	96	97					14																	95903278		2203	4300	6503	SO:0001583	missense	161176	exon14			TGGGAGAAATCTT	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.2417T>A	chr14.hg19:g.95903278A>T	ENSP00000334308:p.Phe806Tyr	71.0	0.0	.		68.0	18.0	.	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	hg19	CCDS9935.1	.	.	.	.	.	.	.	.	.	.	A	8.638	0.895334	0.17613	.	.	ENSG00000176438	ENST00000334258;ENST00000554873;ENST00000557275	T;T;T	0.12672	3.49;2.66;3.5	5.13	-6.79	0.01715	.	1.951040	0.02897	N	0.134895	T	0.07052	0.0179	L	0.40543	1.245	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.06405	0.002;0.001	T	0.40683	-0.9550	10	0.02654	T	1	-0.2886	0.1537	0.00096	0.2263:0.2228:0.217:0.3339	.	801;806	Q6ZMZ3-2;Q6ZMZ3	.;SYNE3_HUMAN	Y	806;563;801	ENSP00000334308:F806Y;ENSP00000452154:F563Y;ENSP00000450562:F801Y	ENSP00000334308:F806Y	F	-	2	0	C14orf49	94973031	0.011000	0.17503	0.000000	0.03702	0.134000	0.20937	0.178000	0.16820	-1.516000	0.01782	0.459000	0.35465	TTC	.	.	.	none		0.517	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592		T	95903278	A	T	95903278	3	4	278	1	0	0	0	0	1	0	0	0	1778	246	9	5	526	5	C14orf49	14	95903278	Missense_Mutation	SNP	A	TCGA-Y8-A898-01A-11D-A34Z-10	14240779	95903278	11446262	56	17729											
HERC2	8924	hgsc.bcm.edu	37	chr15	28437274	28437274	+	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	cttcagctgttttccagaacGgccacaaaataccgcagact	12	9	7	13	2	1	2	1	0	0	2	2	2	2	2	3	1	3	3	3	1	4	4	rs543946257		TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr15:28437274G>C	ENST00000261609.7	-	53	8392	c.8284C>G	c.(8284-8286)Cgt>Ggt	p.R2762G		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2									p.R2762G(3)		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)		TTTCCAGAACGGCCACAAAAT	0.493											OREG0022997	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	8e-04	0	5008	,	,		17962	0		0	False		,,,				2504	0				p.R2762G		Atlas-SNP	.											HERC2,colon,carcinoma,+2,3	HERC2	501	.	3	Substitution - Missense(3)	ovary(1)|NS(1)|central_nervous_system(1)	c.C8284G						PASS	.						97	96	96					15																	28437274		2203	4300	6503	SO:0001583	missense	8924	exon53			CAGAACGGCCACA	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.8284C>G	chr15.hg19:g.28437274G>C	ENSP00000261609:p.Arg2762Gly	38.0	0.0	.	801	60.0	13.0	.	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	G	19.69	3.874685	0.72180	.	.	ENSG00000128731	ENST00000261609	T	0.62788	0.0	5.67	5.67	0.87782	Anaphase-promoting complex, subunit 10/DOC domain (1);Galactose-binding domain-like (1);	0.054132	0.85682	D	0.000000	T	0.77157	0.4089	L	0.53249	1.67	0.80722	D	1	D;D	0.69078	0.997;0.987	D;D	0.76071	0.987;0.953	T	0.77861	-0.2430	10	0.72032	D	0.01	.	19.7646	0.96335	0.0:0.0:1.0:0.0	.	229;2762	A8KAQ8;O95714	.;HERC2_HUMAN	G	2762	ENSP00000261609:R2762G	ENSP00000261609:R2762G	R	-	1	0	HERC2	26110869	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.808000	0.99193	2.675000	0.91044	0.471000	0.43371	CGT	.	.	.	none		0.493	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		C	28437274	G	C	28437274	3	2	278	1	0	0	0	0	1	0	0	0	7065	1116	39	4	6384	4	HERC2	15	28437274	Missense_Mutation	SNP	G	TCGA-Y8-A898-01A-11D-A34Z-10		28437274	74094118	57	17730											
CCPG1	9236	hgsc.bcm.edu	37	chr15	55652607	55652607	+	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	gttttccattttgatcttttGcctcaacatacaatctttcc	8	19	3	11	0	3	1	1	1	2	0	5	1	5	1	3	0	3	1	3	0	3	8			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr15:55652607G>C	ENST00000310958.6	-	8	1662	c.1364C>G	c.(1363-1365)gCa>gGa	p.A455G	CCPG1_ENST00000569205.1_Missense_Mutation_p.A455G|CCPG1_ENST00000442196.3_Missense_Mutation_p.A455G|DYX1C1-CCPG1_ENST00000565113.1_RNA|CCPG1_ENST00000425574.3_Intron	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	455					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)		TTGATCTTTTGCCTCAACATA	0.418																																					p.A455G		Atlas-SNP	.											.	CCPG1	74	.	0			c.C1364G						PASS	.						257	236	243					15																	55652607		1848	4104	5952	SO:0001583	missense	9236	exon8			TCTTTTGCCTCAA	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.1364C>G	chr15.hg19:g.55652607G>C	ENSP00000311656:p.Ala455Gly	83.0	0.0	.		95.0	27.0	.	NM_020739	A0PJH3|A8K9T0|O14712|Q05DG4|Q5U5S7|Q8IYV8|Q9BY53|Q9HA17	Missense_Mutation	SNP	ENST00000310958.6	hg19	CCDS42039.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.382990	0.82792	.	.	ENSG00000256061	ENST00000310958;ENST00000442196	T;T	0.37058	1.22;1.22	5.93	5.93	0.95920	.	0.207171	0.50627	D	0.000102	T	0.59514	0.2199	M	0.63843	1.955	0.58432	D	0.999998	D;D;D;D	0.76494	0.998;0.999;0.998;0.999	D;D;D;D	0.70935	0.947;0.947;0.947;0.971	T	0.56823	-0.7915	10	0.56958	D	0.05	.	19.3421	0.94347	0.0:0.0:1.0:0.0	.	455;455;455;311	A8K9T0;Q9ULG6-4;Q9ULG6;Q9ULG6-2	.;.;CCPG1_HUMAN;.	G	455	ENSP00000311656:A455G;ENSP00000403400:A455G	ENSP00000311656:A455G	A	-	2	0	DYX1C1	53439899	1.000000	0.71417	0.999000	0.59377	0.959000	0.62525	3.604000	0.54081	2.826000	0.97356	0.655000	0.94253	GCA	.	.	.	none		0.418	CCPG1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419850.1	NM_004748		C	55652607	G	C	55652607	3	2	278	1	0	0	0	0	1	0	0	0	2940	1319	46	4	913	4	CCPG1	15	55652607	Missense_Mutation	SNP	G	TCGA-Y8-A898-01A-11D-A34Z-10	27215333	55652607	46878785	58	17731											
SPESP1	246777	hgsc.bcm.edu	37	chr15	69238832	69238832	+	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	tttagatattaaatgtgttcCaccagagatgagagaaaaag	17	11	9	4	0	0	4	0	1	0	3	1	6	1	4	2	0	0	1	2	0	6	5			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr15:69238832C>T	ENST00000310673.3	+	2	1113	c.959C>T	c.(958-960)cCa>cTa	p.P320L	RP11-809H16.2_ENST00000557966.1_RNA|NOX5_ENST00000448182.3_Intron|NOX5_ENST00000455873.3_Intron|NOX5_ENST00000260364.5_Intron	NM_145658.3	NP_663633.1	Q6UW49	SPESP_HUMAN	sperm equatorial segment protein 1	320					acrosome reaction (GO:0007340)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organismal development (GO:0007275)	acrosomal vesicle (GO:0001669)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|prostate(1)|skin(1)|urinary_tract(1)	19						AAATGTGTTCCACCAGAGATG	0.294																																					p.P320L		Atlas-SNP	.											.	SPESP1	39	.	0			c.C959T						PASS	.						51	58	56					15																	69238832		2172	4265	6437	SO:0001583	missense	246777	exon2			GTGTTCCACCAGA	AF275321	CCDS10230.1	15q22.31	2011-04-15				ENSG00000258484			15570	protein-coding gene	gene with protein product		609399				12773409	Standard	NM_145658		Approved	SP-ESP	uc002arn.2	Q6UW49		ENST00000310673.3:c.959C>T	chr15.hg19:g.69238832C>T	ENSP00000312284:p.Pro320Leu	80.0	0.0	.		99.0	30.0	.	NM_145658	Q8NG22|Q8WVH8	Missense_Mutation	SNP	ENST00000310673.3	hg19	CCDS10230.1	.	.	.	.	.	.	.	.	.	.	C	17.27	3.346513	0.61073	.	.	ENSG00000258484	ENST00000310673	T	0.24908	1.83	5.33	5.33	0.75918	.	0.000000	0.47455	D	0.000236	T	0.41719	0.1171	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.22487	-1.0215	10	0.87932	D	0	-14.4125	14.8728	0.70471	0.0:1.0:0.0:0.0	.	320	Q6UW49	SPESP_HUMAN	L	320	ENSP00000312284:P320L	ENSP00000312284:P320L	P	+	2	0	SPESP1	67025886	0.918000	0.31147	0.972000	0.41901	0.486000	0.33341	3.109000	0.50345	2.651000	0.90000	0.655000	0.94253	CCA	.	.	.	none		0.294	SPESP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257125.1	NM_145658		T	69238832	C	T	69238832	3	4	278	1	0	0	0	0	1	0	0	0	15052	594	21	2	965	2	SPESP1	15	69238832	Missense_Mutation	SNP	C	TCGA-Y8-A898-01A-11D-A34Z-10	13586225	69238832	33292560	59	17732											
CHSY1	22856	hgsc.bcm.edu	37	chr15	101718483	101718483	+	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	cttcttcagggagtttgagaGaaaggacaaggatccagatt	13	10	12	6	0	2	3	1	1	1	2	3	7	3	6	1	3	0	1	1	3	2	4			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr15:101718483G>A	ENST00000254190.3	-	3	1994	c.1519C>T	c.(1519-1521)Ctc>Ttc	p.L507F	CHSY1_ENST00000543813.1_5'UTR	NM_014918.4	NP_055733.2	Q86X52	CHSS1_HUMAN	chondroitin sulfate synthase 1	507					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|negative regulation of ossification (GO:0030279)|response to nutrient levels (GO:0031667)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(5)|skin(1)	24	Lung NSC(78;0.00217)|all_lung(78;0.00271)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			GAGTTTGAGAGAAAGGACAAG	0.453																																					p.L507F		Atlas-SNP	.											.	CHSY1	60	.	0			c.C1519T						PASS	.						84	89	87					15																	101718483		2203	4300	6503	SO:0001583	missense	22856	exon3			TTGAGAGAAAGGA	AB023207	CCDS10390.1	15q26.3	2013-02-19	2008-01-24	2008-01-24	ENSG00000131873	ENSG00000131873	2.4.1.175, 2.4.1.226	"Beta 3-glycosyltransferases", "Beta 4-glycosyltransferases"	17198	protein-coding gene	gene with protein product		608183	"carbohydrate (chondroitin) synthase 1"			11514575	Standard	NM_014918		Approved	KIAA0990, CSS1	uc021sxt.1	Q86X52	OTTHUMG00000149873	ENST00000254190.3:c.1519C>T	chr15.hg19:g.101718483G>A	ENSP00000254190:p.Leu507Phe	65.0	0.0	.		69.0	19.0	.	NM_014918	Q6UX38|Q7LFU5|Q9Y2J5	Missense_Mutation	SNP	ENST00000254190.3	hg19	CCDS10390.1	.	.	.	.	.	.	.	.	.	.	G	9.498	1.102392	0.20632	.	.	ENSG00000131873	ENST00000254190;ENST00000543813	T	0.37411	1.2	5.69	5.69	0.88448	.	0.073492	0.53938	N	0.000046	T	0.26846	0.0657	N	0.25890	0.77	0.80722	D	1	B	0.18741	0.03	B	0.24006	0.05	T	0.06516	-1.0822	10	0.21540	T	0.41	-56.0537	13.0568	0.58984	0.0732:0.0:0.9268:0.0	.	507	Q86X52	CHSS1_HUMAN	F	507;235	ENSP00000254190:L507F	ENSP00000254190:L507F	L	-	1	0	CHSY1	99536006	1.000000	0.71417	0.966000	0.40874	0.457000	0.32468	4.748000	0.62148	2.676000	0.91093	0.655000	0.94253	CTC	.	.	.	none		0.453	CHSY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313624.1	NM_014918		A	101718483	G	A	101718483	3	1	278	1	0	0	0	0	1	0	0	0	3414	942	33	2	893	2	CHSY1	15	101718483	Missense_Mutation	SNP	G	TCGA-Y8-A898-01A-11D-A34Z-10	32479651	101718483	812909	60	17733											
C16orf13	84326	hgsc.bcm.edu	37	chr16	684782	684782	+	Frame_Shift_Del	DEL	C	C	-																															aggagggctgtgtcccgaagCccccattctgggttcctgca																										TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr16:684782delC	ENST00000301686.8	-	5	515	c.504delG	c.(502-504)gggfs	p.G168fs	C16orf13_ENST00000397666.2_Frame_Shift_Del_p.A146fs|C16orf13_ENST00000338401.4_Frame_Shift_Del_p.G71fs|C16orf13_ENST00000397664.4_Frame_Shift_Del_p.G91fs|C16orf13_ENST00000397665.2_Frame_Shift_Del_p.A126fs	NM_032366.3	NP_115742.3	Q96S19	CP013_HUMAN	chromosome 16 open reading frame 13	168										large_intestine(1)	1		Hepatocellular(780;0.00335)				TGTCCCGAAGCCCCCATTCTG	0.677																																					p.L169fs		Atlas-Indel,Pindel	.											.	C16orf13	11	.	0			c.505delC						PASS	.						32	35	34					16																	684782		2192	4295	6487	SO:0001589	frameshift_variant	84326	exon5			.		CCDS32352.1, CCDS42090.1, CCDS42091.1, CCDS45367.1, CCDS45368.1, CCDS73798.1	16p13.3	2012-10-09			ENSG00000130731	ENSG00000130731			14141	protein-coding gene	gene with protein product							Standard	NM_001040160		Approved	MGC13114	uc002chw.1	Q96S19	OTTHUMG00000047855	ENST00000301686.8:c.504delG	chr16.hg19:g.684782delC	ENSP00000445926:p.Gly168fs	22.0	0.0	0		57.0	12.0	0.210526	NM_032366	A8MTR1|A8MWJ8|A8MZA1|B4DG95|B4DIJ3|D6REA6|F6TF62|F6VM53|Q96IW1|Q96MD6	Frame_Shift_Del	DEL	ENST00000301686.8	hg19	CCDS45368.1																																																																																			.	.	.	none		0.677	C16orf13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109081.2	NM_001040160		-	684782	C	-	684782	7	5	278	1	0	1	0	1	0	0	0	0	1813	739	26	0	189	0	C16orf13	16	684782	Frame_Shift_Del	DEL	C	TCGA-Y8-A898-01A-11D-A34Z-10		684782	89669971	61	17734											
SRRM2	23524	hgsc.bcm.edu	37	chr16	2819139	2819139	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcctcctcctcctcctcCtcttcttcctcctcctcttc	0	17	0	24	0	3	0	0	0	3	0	14	0	13	0	10	0	0	0	10	0	0	3			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr16:2819139C>T	ENST00000301740.8	+	12	8424	c.7875C>T	c.(7873-7875)tcC>tcT	p.S2625S	AC092117.2_ENST00000581119.1_RNA|SRRM2_ENST00000574593.1_3'UTR	NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	2625	Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						cctcctcctcctcttcttcct	0.592																																					p.S2625S		Atlas-SNP	.											.	SRRM2	263	.	0			c.C7875T						PASS	.						141	121	128					16																	2819139		2198	4300	6498	SO:0001819	synonymous_variant	23524	exon12			CTCCTCCTCTTCT	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.7875C>T	chr16.hg19:g.2819139C>T		22.0	0.0	.		46.0	5.0	.	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Silent	SNP	ENST00000301740.8	hg19	CCDS32373.1																																																																																			.	.	.	none		0.592	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			T	2819139	C	T	2819139	2	4	278	1	0	0	0	0	0	0	0	1	15181	668	24	2		2	SRRM2	16	2819139	Silent	SNP	C	TCGA-Y8-A898-01A-11D-A34Z-10	2134357	2819139	87535614	62	17735											
NLRC3	197358	hgsc.bcm.edu	37	chr16	3599167	3599167	+	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	gttcttcagggtgctgttggCgcagagggcatgagcgatgg	6	10	18	7	2	2	2	1	1	1	1	2	3	2	2	0	4	2	5	0	4	0	3			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr16:3599167C>T	ENST00000301749.7	-	0	2983				NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000603507.1_RNA|NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_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						GTGCTGTTGGCGCAGAGGGCA	0.597																																					p.A860T		Atlas-SNP	.											NLRC3,colon,carcinoma,0,1	NLRC3	103	.	0			c.G2578A						PASS	.						36	39	38					16																	3599167		2092	4208	6300			197358	exon14			TGTTGGCGCAGAG	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		chr16.hg19:g.3599167C>T		55.0	0.0	.		105.0	26.0	.	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	hg19		.	.	.	.	.	.	.	.	.	.	C	0.013	-1.640859	0.00799	.	.	ENSG00000167984	ENST00000301749;ENST00000359128;ENST00000448023	T;T;T	0.52754	0.65;0.65;0.65	4.95	0.257	0.15574	.	0.860278	0.10393	N	0.680227	T	0.22975	0.0555	N	0.11364	0.135	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.04013	0.001;0.0	T	0.26395	-1.0104	10	0.10111	T	0.7	.	7.158	0.25649	0.0:0.3789:0.0:0.6211	.	860;906	Q7RTR2;C9JLH9	NLRC3_HUMAN;.	T	860;859;906	ENSP00000301749:A860T;ENSP00000352039:A859T;ENSP00000414415:A906T	ENSP00000301749:A860T	A	-	1	0	NLRC3	3539168	0.000000	0.05858	0.021000	0.16686	0.019000	0.09904	-0.096000	0.11059	-0.005000	0.14395	-1.287000	0.01368	GCC	.	.	.	none		0.597	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844		T	3599167	C	T	3599167	1	4	278	0	1	0	0	0	0	0	0	0	10475	768	27	1		1	NLRC3	16	3599167	RNA	SNP	C	TCGA-Y8-A898-01A-11D-A34Z-10	780028	3599167	86755586	63	17736											
NUDT16L1	84309	hgsc.bcm.edu	37	chr16	4744082	4744082	+	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	ccgggtgctgggcctgggccTgggctgcctgcgcctcaccg	1	7	17	16	3	1	0	1	0	0	0	1	0	1	0	6	4	3	2	6	4	0	0			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr16:4744082T>A	ENST00000304301.6	+	2	290	c.257T>A	c.(256-258)cTg>cAg	p.L86Q	NUDT16L1_ENST00000586252.1_Missense_Mutation_p.L86Q|NUDT16L1_ENST00000405142.1_Missense_Mutation_p.L86Q|NUDT16L1_ENST00000586536.1_Missense_Mutation_p.L86Q	NM_032349.3	NP_115725.1	Q9BRJ7	SDOS_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 16-like 1	86						cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)|poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)			endometrium(1)|large_intestine(1)|lung(1)|skin(1)	4						GGCCTGGGCCTGGGCTGCCTG	0.721																																					p.L86Q		Atlas-SNP	.											.	NUDT16L1	13	.	0			c.T257A						PASS	.						17	21	19					16																	4744082		2185	4292	6477	SO:0001583	missense	84309	exon2			TGGGCCTGGGCTG	BC006223	CCDS10519.1, CCDS59257.1	16p13.3	2008-02-05			ENSG00000168101	ENSG00000168101		"Nudix motif containing"	28154	protein-coding gene	gene with protein product						11805099	Standard	NM_032349		Approved	SDOS	uc002cxe.3	Q9BRJ7	OTTHUMG00000129471	ENST00000304301.6:c.257T>A	chr16.hg19:g.4744082T>A	ENSP00000306670:p.Leu86Gln	36.0	0.0	.		75.0	34.0	.	NM_032349	Q8NAI2	Missense_Mutation	SNP	ENST00000304301.6	hg19	CCDS10519.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.362056	0.82353	.	.	ENSG00000168101	ENST00000304301;ENST00000405142	.	.	.	4.28	4.28	0.50868	NUDIX hydrolase domain-like (1);	0.305277	0.26499	N	0.024037	T	0.75064	0.3799	M	0.61703	1.905	0.45883	D	0.998732	D;D	0.89917	1.0;0.96	D;P	0.83275	0.996;0.463	T	0.77720	-0.2482	9	0.87932	D	0	.	12.2661	0.54679	0.0:0.0:0.0:1.0	.	86;86	Q9BRJ7-2;Q9BRJ7	.;SDOS_HUMAN	Q	86	.	ENSP00000306670:L86Q	L	+	2	0	NUDT16L1	4684083	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	2.439000	0.44846	1.583000	0.49898	0.528000	0.53228	CTG	.	.	.	none		0.721	NUDT16L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251634.1	NM_032349		A	4744082	T	A	4744082	3	1	278	1	0	0	0	0	1	0	0	0	10740	1580	55	5	263	5	NUDT16L1	16	4744082	Missense_Mutation	SNP	T	TCGA-Y8-A898-01A-11D-A34Z-10	1144915	4744082	85610671	64	17737											
CLEC18A	348174	hgsc.bcm.edu	37	chr16	69988435	69988436	+	Missense_Mutation	DNP	GG	GG	AA																															agcggtacagccacgcggcaGgagagtgtgctcgcaacgcc																										TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr16:69988435_69988436GG>AA	ENST00000288040.6	+	3	602_603	c.415_416GG>AA	c.(415-417)GGa>AAa	p.G139K	CLEC18A_ENST00000393701.2_Missense_Mutation_p.G139K|CLEC18A_ENST00000568461.1_Missense_Mutation_p.G139K|CLEC18A_ENST00000449317.2_Missense_Mutation_p.G139K	NM_001136214.2	NP_001129686.1	A5D8T8	CL18A_HUMAN	C-type lectin domain family 18, member A	139	SCP.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(2)|lung(1)|skin(1)	5						CCACGCGGCAGGAGAGTGTGCT	0.624																																					p.G139R|p.G139E		Atlas-SNP	.											.	CLEC18A	9	.	0			c.G415A|c.G416A						PASS	.																																			SO:0001583	missense	348174	exon4			GCGGCAGGAGAGT|CGGCAGGAGAGTG	AF428259	CCDS10886.1	16q22.1	2010-04-27	2009-03-10	2009-03-10		ENSG00000157322		"C-type lectin domain containing"	30388	protein-coding gene	gene with protein product	"mannose receptor-like"					12975309	Standard	NM_001136214		Approved	MRCL	uc010vlo.3	A5D8T8		Exception_encountered	chr16.hg19:g.69988435_69988436delinsAA	ENSP00000288040:p.Gly139Lys	222.0|220.0	0.0	.		284.0|283.0	51.0|52.0	.	NM_001271197	A8K1G9|Q6DCB3|Q7Z5K9|Q96HH2	Missense_Mutation	SNP	ENST00000288040.6	hg19	CCDS10886.1																																																																																			.	.	.	none		0.624	CLEC18A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268955.2	NM_182619		AA	69988436	GG	AA	69988435	3	1	278	1	0	0	0	0	1	0	0	0	3504	1001	35	2	425	2	CLEC18A	16	69988435	Missense_Mutation	DNP	GG	TCGA-Y8-A898-01A-11D-A34Z-10	65244353	69988435	20366318	65	17738											
HYDIN	54768	hgsc.bcm.edu	37	chr16	70977738	70977738	+	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	tatccgctctgccaggatctGcacgagaagttcatccggga	9	9	11	12	3	3	1	1	0	2	1	5	4	5	3	3	2	2	3	3	2	2	2			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr16:70977738G>T	ENST00000393567.2	-	42	6796	c.6646C>A	c.(6646-6648)Cag>Aag	p.Q2216K		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2216					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)				GCCAGGATCTGCACGAGAAGT	0.632																																					p.Q2216K		Atlas-SNP	.											.	HYDIN	788	.	0			c.C6646A						PASS	.						32	33	32					16																	70977738		2048	4193	6241	SO:0001583	missense	54768	exon42			GGATCTGCACGAG	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.6646C>A	chr16.hg19:g.70977738G>T	ENSP00000377197:p.Gln2216Lys	22.0	0.0	.		28.0	9.0	.	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	hg19	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	G	12.01	1.809392	0.31961	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.20598	2.06	4.95	3.92	0.45320	.	0.789986	0.09983	U	0.730756	T	0.21509	0.0518	L	0.51422	1.61	0.80722	D	1	P	0.37500	0.597	B	0.34722	0.188	T	0.06427	-1.0827	10	0.39692	T	0.17	.	12.555	0.56248	0.0:0.352:0.648:0.0	.	2215	F8WD23	.	K	2216;2215	ENSP00000377197:Q2216K	ENSP00000313052:Q2215K	Q	-	1	0	HYDIN	69535239	0.999000	0.42202	0.944000	0.38274	0.128000	0.20619	3.698000	0.54771	2.442000	0.82660	0.609000	0.83330	CAG	.	.	.	none		0.632	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			T	70977738	G	T	70977738	3	4	278	1	0	0	0	0	1	0	0	0	7474	1328	46	4	8899	4	HYDIN	16	70977738	Missense_Mutation	SNP	G	TCGA-Y8-A898-01A-11D-A34Z-10	989303	70977738	19377015	66	17739											
CHMP1A	5119	hgsc.bcm.edu	37	chr16	89715757	89715757	+	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	agcaccagggcccagcactcAcccccttcatagtcacagct	10	6	7	18	0	3	0	3	0	0	0	3	0	3	0	4	1	3	3	4	1	1	2			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr16:89715757A>G	ENST00000397901.3	-	4	509		c.e4+1		CHMP1A_ENST00000550102.1_Intron|CHMP1A_ENST00000547614.1_Splice_Site|CHMP1A_ENST00000535997.2_Splice_Site|CHMP1A_ENST00000253475.5_Splice_Site	NM_002768.3	NP_002759.2	Q9HD42	CHM1A_HUMAN	charged multivesicular body protein 1A						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)		CCCAGCACTCACCCCCTTCAT	0.617																																					.		Atlas-SNP	.											.	CHMP1A	15	.	0			c.232+2T>C						PASS	.						102	119	113					16																	89715757		2180	4282	6462	SO:0001630	splice_region_variant	5119	exon4			GCACTCACCCCCT	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.252+1T>C	chr16.hg19:g.89715757A>G		46.0	0.0	.		66.0	19.0	.	NM_001083314	A2RU09|Q14468|Q15779|Q96G31	Splice_Site	SNP	ENST00000397901.3	hg19	CCDS45552.1	.	.	.	.	.	.	.	.	.	.	.	18.86	3.712432	0.68730	.	.	ENSG00000131165	ENST00000397901;ENST00000253475;ENST00000535997	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7909	0.78364	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CHMP1A	88243258	1.000000	0.71417	1.000000	0.80357	0.740000	0.42216	8.591000	0.90824	2.128000	0.65567	0.459000	0.35465	.	.	.	.	none		0.617	CHMP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404581.1	NM_002768	Intron	G	89715757	A	G	89715757	5	3	278	1	0	0	0	0	0	0	1	0	3354	173	6	3	504	3	CHMP1A	16	89715757	Splice_Site	SNP	A	TCGA-Y8-A898-01A-11D-A34Z-10	18738019	89715757	638996	67	17740											
WDR81	124997	hgsc.bcm.edu	37	chr17	1629728	1629728	+	Frame_Shift_Del	DEL	T	T	-																															ctggaccccggatgagtgcaTtccggagttctacaccgatc																										TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr17:1629728delT	ENST00000409644.1	+	1	1475	c.1475delT	c.(1474-1476)attfs	p.I492fs	WDR81_ENST00000446363.1_Intron|WDR81_ENST00000309182.5_Intron|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000437219.2_Intron|WDR81_ENST00000419248.1_Intron	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	492	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.				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)		GATGAGTGCATTCCGGAGTTC	0.632																																					p.I492fs		Atlas-Indel,Pindel	.											.	WDR81	180	.	0			c.1474delA						PASS	.						25	27	26					17																	1629728		692	1585	2277	SO:0001589	frameshift_variant	124997	exon1			.	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.1475delT	chr17.hg19:g.1629728delT	ENSP00000386609:p.Ile492fs	73.0	0.0	0		93.0	44.0	0.473118	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Frame_Shift_Del	DEL	ENST00000409644.1	hg19	CCDS54062.1																																																																																			.	.	.	none		0.632	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348		-	1629728	T	-	1629728	7	5	278	1	0	1	0	1	0	0	0	0	17342	1493	52	0	1539	0	WDR81	17	1629728	Frame_Shift_Del	DEL	T	TCGA-Y8-A898-01A-11D-A34Z-10		1629728	79565482	68	17741											
TMEM98	26022	hgsc.bcm.edu	37	chr17	31258638	31258638	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctggtttgcaggcagcgctActgccggccgcgagacctgc	5	7	15	14	4	0	1	0	0	0	1	0	2	0	1	3	3	5	5	3	3	1	2			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr17:31258638A>G	ENST00000579849.1	+	3	523	c.92A>G	c.(91-93)tAc>tGc	p.Y31C	TMEM98_ENST00000578289.1_Missense_Mutation_p.Y31C|TMEM98_ENST00000394642.3_Missense_Mutation_p.Y31C	NM_015544.2	NP_056359.2	Q9Y2Y6	TMM98_HUMAN	transmembrane protein 98	31						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				kidney(2)|large_intestine(1)	3		Ovarian(249;0.182)|Breast(31;0.244)	BRCA - Breast invasive adenocarcinoma(9;0.0769)			AGGCAGCGCTACTGCCGGCCG	0.552																																					p.Y31C		Atlas-SNP	.											TMEM98,NS,malignant_melanoma,0,1	TMEM98	23	.	0			c.A92G						PASS	.						96	74	82					17																	31258638		2203	4300	6503	SO:0001583	missense	26022	exon2			AGCGCTACTGCCG	CR605381	CCDS11274.1	17q11.2	2005-12-16			ENSG00000006042	ENSG00000006042			24529	protein-coding gene	gene with protein product		615949				11230166	Standard	NM_001301746		Approved	DKFZP564K1964	uc002hhr.3	Q9Y2Y6	OTTHUMG00000132882	ENST00000579849.1:c.92A>G	chr17.hg19:g.31258638A>G	ENSP00000463245:p.Tyr31Cys	88.0	0.0	.		151.0	69.0	.	NM_001033504	E1P631|Q9UFK2	Missense_Mutation	SNP	ENST00000579849.1	hg19	CCDS11274.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.199358	0.79015	.	.	ENSG00000006042	ENST00000394642;ENST00000261713;ENST00000395149;ENST00000439138	T;T;T;T	0.52057	0.68;0.8;0.78;0.7	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	T	0.54208	0.1844	L	0.32530	0.975	0.58432	D	0.999998	D	0.71674	0.998	P	0.62813	0.907	T	0.56366	-0.7991	10	0.59425	D	0.04	-5.672	12.5682	0.56322	1.0:0.0:0.0:0.0	.	31	Q9Y2Y6	TMM98_HUMAN	C	31	ENSP00000378138:Y31C;ENSP00000261713:Y31C;ENSP00000398446:Y31C;ENSP00000406394:Y31C	ENSP00000261713:Y31C	Y	+	2	0	TMEM98	28282751	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.376000	0.90138	1.289000	0.44618	0.655000	0.94253	TAC	.	.	.	none		0.552	TMEM98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256372.2	NM_015544		G	31258638	A	G	31258638	3	3	278	1	0	0	0	0	1	0	0	0	16237	391	14	3	94	3	TMEM98	17	31258638	Missense_Mutation	SNP	A	TCGA-Y8-A898-01A-11D-A34Z-10	29628910	31258638	49936572	69	17742											
TMEM49	81671	hgsc.bcm.edu	37	chr17	57917269	57917269	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aactcagaggagaaaactaaAtaagtagagaaagttttaaa	22	8	8	3	0	1	3	1	0	0	3	1	5	1	3	0	1	2	2	0	1	10	5			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr17:57917269A>G	ENST00000262291.4	+	12	1528	c.1218A>G	c.(1216-1218)aaA>aaG	p.K406K	VMP1_ENST00000588617.1_3'UTR|VMP1_ENST00000537567.1_Silent_p.K272K|VMP1_ENST00000536180.1_Silent_p.K309K|VMP1_ENST00000539763.1_Silent_p.K214K|VMP1_ENST00000545362.1_Silent_p.K350K|MIR21_ENST00000362134.1_RNA	NM_030938.3	NP_112200.2	Q96GC9	VMP1_HUMAN	vacuole membrane protein 1	406					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						AGAAAACTAAATAAGTAGAGA	0.418																																					p.K406K		Atlas-SNP	.											.	VMP1	49	.	0			c.A1218G						PASS	.						91	88	89					17																	57917269		2203	4300	6503	SO:0001819	synonymous_variant	81671	exon12			AACTAAATAAGTA		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.1218A>G	chr17.hg19:g.57917269A>G		79.0	0.0	.		173.0	15.0	.	NM_030938	B4DVV9|Q9H0P4|Q9P089	Silent	SNP	ENST00000262291.4	hg19	CCDS11619.1																																																																																			.	.	.	none		0.418	VMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448793.1	NM_030938		G	57917269	A	G	57917269	2	3	278	1	0	0	0	0	0	0	0	1	16185	98	4	3		3	TMEM49	17	57917269	Silent	SNP	A	TCGA-Y8-A898-01A-11D-A34Z-10	26658631	57917269	23277941	70	17743											
COLEC12	81035	hgsc.bcm.edu	37	chr18	321780	321780	+	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	ggcccatggccatgaccccaGttatccggctgtccagcttt	6	10	10	15	1	0	1	0	1	0	0	2	1	2	1	6	3	1	3	6	3	1	2			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr18:321780G>C	ENST00000400256.3	-	9	2298	c.2091C>G	c.(2089-2091)aaC>aaG	p.N697K	RP11-720L2.4_ENST00000580756.1_lincRNA	NM_130386.2	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	697	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)	p.N697K(1)		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)				CATGACCCCAGTTATCCGGCT	0.443																																					p.N697K		Atlas-SNP	.											COLEC12,NS,NS,0,1	COLEC12	121	.	1	Substitution - Missense(1)	pancreas(1)	c.C2091G						PASS	.						126	131	129					18																	321780		2203	4300	6503	SO:0001583	missense	81035	exon9			ACCCCAGTTATCC	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.2091C>G	chr18.hg19:g.321780G>C	ENSP00000383115:p.Asn697Lys	82.0	0.0	.		100.0	29.0	.	NM_130386	Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7	Missense_Mutation	SNP	ENST00000400256.3	hg19	CCDS32782.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.957920	0.73902	.	.	ENSG00000158270	ENST00000400256	T	0.21361	2.01	5.68	4.8	0.61643	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.152725	0.56097	D	0.000026	T	0.46776	0.1410	M	0.90369	3.11	0.80722	D	1	D	0.56746	0.977	P	0.57776	0.827	T	0.55147	-0.8186	10	0.59425	D	0.04	-14.8511	11.0473	0.47865	0.1436:0.0:0.8564:0.0	.	697	Q5KU26	COL12_HUMAN	K	697	ENSP00000383115:N697K	ENSP00000383115:N697K	N	-	3	2	COLEC12	311780	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.866000	0.63005	1.375000	0.46248	0.563000	0.77884	AAC	.	.	.	none		0.443	COLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440746.1			C	321780	G	C	321780	3	2	278	1	0	0	0	0	1	0	0	0	3714	1020	36	4	145	4	COLEC12	18	321780	Missense_Mutation	SNP	G	TCGA-Y8-A898-01A-11D-A34Z-10		321780	77755468	71	17744											
EID2	163126	hgsc.bcm.edu	37	chr19	40030283	40030283	+	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	aattgatgcctaaaacgctaAgtgggtggcggagacggaga	13	7	15	6	3	0	3	0	1	0	2	0	5	0	3	1	4	2	1	1	4	4	3			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr19:40030283A>T	ENST00000390658.2	-	1	587	c.437T>A	c.(436-438)cTt>cAt	p.L146H		NM_153232.3	NP_694964.3			EP300 interacting inhibitor of differentiation 2											large_intestine(2)|lung(1)|urinary_tract(1)	4	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;3.2e-25)|all cancers(26;8.83e-23)|LUSC - Lung squamous cell carcinoma(53;0.00281)			TAAAACGCTAAGTGGGTGGCG	0.592																																					p.L146H		Atlas-SNP	.											.	EID2	14	.	0			c.T437A						PASS	.						89	100	96					19																	40030283		1982	4149	6131	SO:0001583	missense	163126	exon1			ACGCTAAGTGGGT	BC030137	CCDS12540.2	19q13.2	2008-10-24	2006-10-12	2006-10-12	ENSG00000176396	ENSG00000176396			28292	protein-coding gene	gene with protein product		609773	"CREBBP/EP300 inhibitory protein 2", "CREBBP/EP300 inhibitor 2"	CRI2		14585496	Standard	NM_153232		Approved	EID-2, MGC20452	uc002oma.3	Q8N6I1	OTTHUMG00000074073	ENST00000390658.2:c.437T>A	chr19.hg19:g.40030283A>T	ENSP00000375073:p.Leu146His	43.0	0.0	.		68.0	25.0	.	NM_153232		Missense_Mutation	SNP	ENST00000390658.2	hg19	CCDS12540.2	.	.	.	.	.	.	.	.	.	.	.	16.21	3.057749	0.55325	.	.	ENSG00000176396	ENST00000390658;ENST00000539700	T	0.57107	0.42	3.71	2.69	0.31865	.	0.226724	0.22676	N	0.057002	T	0.58538	0.2129	L	0.50333	1.59	0.09310	N	1	D	0.76494	0.999	D	0.64237	0.923	T	0.47328	-0.9126	10	0.87932	D	0	.	5.5698	0.17190	0.8743:0.0:0.1257:0.0	.	146	Q8N6I1	EID2_HUMAN	H	146;97	ENSP00000375073:L146H	ENSP00000375073:L146H	L	-	2	0	EID2	44722123	0.078000	0.21339	0.003000	0.11579	0.103000	0.19146	2.696000	0.47052	0.797000	0.33971	0.445000	0.29226	CTT	.	.	.	none		0.592	EID2-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157251.1	NM_153232		T	40030283	A	T	40030283	3	4	278	1	0	0	0	0	1	0	0	0	4989	72	3	5	277	5	EID2	19	40030283	Missense_Mutation	SNP	A	TCGA-Y8-A898-01A-11D-A34Z-10		40030283	19098700	72	17745											
ETFB	2109	hgsc.bcm.edu	37	chr19	51857559	51857559	+	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	ggtcctgtcaggcttcactcGgatctgcccagcaggagggg	6	8	15	12	1	3	0	2	0	1	0	5	2	4	2	2	6	2	2	2	6	0	1	rs374288379		TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr19:51857559G>A	ENST00000309244.4	-	2	152	c.61C>T	c.(61-63)Cga>Tga	p.R21*	ETFB_ENST00000354232.4_Nonsense_Mutation_p.R112*|CTD-2616J11.11_ENST00000600067.1_Missense_Mutation_p.P40L|CTD-2616J11.9_ENST00000600974.1_RNA	NM_001985.2	NP_001976.1	P38117	ETFB_HUMAN	electron-transfer-flavoprotein, beta polypeptide	21					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)		GGCTTCACTCGGATCTGCCCA	0.627																																					p.R112X		Atlas-SNP	.											.	ETFB	46	.	0			c.C334T						PASS	.	G	stop/ARG,stop/ARG	0,4406		0,0,2203	79	67	71		334,61	4.2	1	19		71	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained,stop-gained	ETFB	NM_001014763.1,NM_001985.2	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	112/347,21/256	51857559	1,13005	2203	4300	6503	SO:0001587	stop_gained	2109	exon1			TCACTCGGATCTG	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.61C>T	chr19.hg19:g.51857559G>A	ENSP00000311930:p.Arg21*	37.0	0.0	.		37.0	8.0	.	NM_001014763	A8K766|B3KNY2|Q6IBH7|Q71RF6|Q9Y3S7	Nonsense_Mutation	SNP	ENST00000309244.4	hg19	CCDS12828.1	.	.	.	.	.	.	.	.	.	.	g	36	5.716959	0.96830	0.0	1.16E-4	ENSG00000105379	ENST00000309244;ENST00000354232	.	.	.	5.22	4.17	0.49024	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.901	0.58125	0.0:0.0:0.8361:0.1639	.	.	.	.	X	21;112	.	ENSP00000311930:R21X	R	-	1	2	ETFB	56549371	1.000000	0.71417	0.991000	0.47740	0.168000	0.22595	5.166000	0.64965	1.194000	0.43101	-0.187000	0.12897	CGA	.	.	.	weak		0.627	ETFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464273.1			A	51857559	G	A	51857559	4	1	278	1	0	0	0	0	0	1	0	0	5272	1124	39	1	726	1	ETFB	19	51857559	Nonsense_Mutation	SNP	G	TCGA-Y8-A898-01A-11D-A34Z-10	11827276	51857559	7271424	73	17746											
ZNF841	284371	hgsc.bcm.edu	37	chr19	52568431	52568431	+	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	gagtttagttgtaaggttctCtccagcatgttttatctgat	8	18	9	6	0	2	1	0	1	2	0	4	2	3	1	1	1	1	6	1	1	3	7			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr19:52568431C>T	ENST00000426391.2	-	5	2907	c.2356G>A	c.(2356-2358)Gag>Aag	p.E786K	ZNF841_ENST00000389534.4_Missense_Mutation_p.E902K|CTC-471J1.2_ENST00000569091.1_RNA|ZNF841_ENST00000594295.1_Missense_Mutation_p.E902K|ZNF432_ENST00000598446.1_Intron|ZNF841_ENST00000359973.2_Missense_Mutation_p.E478K			Q6ZN19	ZN841_HUMAN	zinc finger protein 841	786					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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						GTAAGGTTCTCTCCAGCATGT	0.363																																					p.E902K		Atlas-SNP	.											.	ZNF841	183	.	0			c.G2704A						PASS	.						259	217	230					19																	52568431		692	1591	2283	SO:0001583	missense	284371	exon7			GGTTCTCTCCAGC	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.2356G>A	chr19.hg19:g.52568431C>T	ENSP00000415453:p.Glu786Lys	156.0	0.0	.		194.0	59.0	.	NM_001136499	B9EG58|Q6ZN82|Q6ZP71|Q8N9U7	Missense_Mutation	SNP	ENST00000426391.2	hg19		.	.	.	.	.	.	.	.	.	.	C	19.00	3.742051	0.69418	.	.	ENSG00000197608	ENST00000389534;ENST00000426391;ENST00000359973	T;T;T	0.08370	3.49;3.31;3.1	1.69	-1.02	0.10135	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09024	0.0223	N	0.08118	0	0.21740	N	0.999565	D;P;P	0.63046	0.992;0.525;0.911	D;B;P	0.67548	0.952;0.022;0.78	T	0.29549	-1.0008	9	0.59425	D	0.04	.	4.9331	0.13926	0.0:0.6374:0.2172:0.1454	.	902;478;786	Q6ZN19-3;Q6ZN19-2;Q6ZN19	.;.;ZN841_HUMAN	K	902;786;478	ENSP00000374185:E902K;ENSP00000415453:E786K;ENSP00000353060:E478K	ENSP00000353060:E478K	E	-	1	0	ZNF841	57260243	0.000000	0.05858	0.001000	0.08648	0.480000	0.33159	0.344000	0.19962	-0.398000	0.07679	0.313000	0.20887	GAG	.	.	.	none		0.363	ZNF841-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000462435.1	XM_209155		T	52568431	C	T	52568431	3	4	278	1	0	0	0	0	1	0	0	0	18201	922	32	2	74	2	ZNF841	19	52568431	Missense_Mutation	SNP	C	TCGA-Y8-A898-01A-11D-A34Z-10	710872	52568431	6560552	74	17747											
RALGAPA2	57186	hgsc.bcm.edu	37	chr20	20392748	20392749	+	Frame_Shift_Ins	INS	-	-	GGTTCTGAATTATTGCTTCGAGATACAG																															gaatgtcattacttcgcggtINSggttctgaattattgcttcg																								rs535510713		TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr20:20392748_20392749insGGTTCTGAATTATTGCTTCGAGATACAG	ENST00000202677.7	-	38	5546_5547	c.5539_5540insCTGTATCTCGAAGCAATAATTCAGAACC	c.(5539-5541)cacfs	p.H1847fs		NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	1847					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						TACTTCGCGGTGGTTCTGAATT	0.49																																					p.H1847fs		Pindel	.											.	RALGAPA2	274	.	0			c.5540_5541insCTGTATCTCGAAGCAATAATTCAGAACC						PASS	.																																			SO:0001589	frameshift_variant	57186	exon38			.	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.5512_5539dupCTGTATCTCGAAGCAATAATTCAGAACC	chr20.hg19:g.20392748_20392749insGGTTCTGAATTATTGCTTCGAGATACAG	ENSP00000202677:p.His1847fs	74.0	0.0	.		89.0	11.0	0.124	NM_020343	Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	Frame_Shift_Ins	INS	ENST00000202677.7	hg19	CCDS46584.1																																																																																			.	.	.	none		0.49	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471941.1	NM_020343		GGTTCTGAATTATTGCTTCGAGATACAG	20392749	-	GGTTCTGAATTATTGCTTCGAGATACAG	20392748	7	5	278	1	0	1	1	0	0	0	0	0	13027	1696	59	0	89	0	RALGAPA2	20	20392748	Frame_Shift_Ins	INS	-	TCGA-Y8-A898-01A-11D-A34Z-10		20392748	42632772	75	17748											
TSHZ2	128553	hgsc.bcm.edu	37	chr20	51871518	51871519	+	Frame_Shift_Ins	INS	-	-	GATG																															taagggaggaagacttggaaINSgatggctcaaagggtggagg																										TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr20:51871518_51871519insGATG	ENST00000371497.5	+	2	2408_2409	c.1521_1522insGATG	c.(1522-1524)gatfs	p.-509fs	RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000329613.6_Frame_Shift_Ins_p.-506fs|TSHZ2_ENST00000603338.2_Frame_Shift_Ins_p.-506fs	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2						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)	p.D508H(1)		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)			AAGACTTGGAAGATGGCTCAAA	0.455																																					p.E507fs		Atlas-Indel,Pindel	.											.	TSHZ2	209	.	1	Substitution - Missense(1)	lung(1)	c.1521_1522insGATG						PASS	.																																			SO:0001589	frameshift_variant	128553	exon2			.	AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"Teashirt zinc fingers", "Homeoboxes / ZF class", "Zinc fingers, C2H2-type"	13010	protein-coding gene	gene with protein product		614118	"chromosome 20 open reading frame 17", "zinc finger protein 218", "teashirt family zinc finger 2"	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.1522_1525dupGATG	chr20.hg19:g.51871519_51871522dupGATG	ENSP00000360552:p.Gly509fs	64.0	0.0	0		58.0	11.0	0.189655	NM_173485	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Frame_Shift_Ins	INS	ENST00000371497.5	hg19	CCDS33490.1																																																																																			.	.	.	none		0.455	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485		GATG	51871519	-	GATG	51871518	7	5	278	1	0	1	1	0	0	0	0	0	16636	69	3	0	1527	0	TSHZ2	20	51871518	Frame_Shift_Ins	INS	-	TCGA-Y8-A898-01A-11D-A34Z-10	31478770	51871518	11154002	76	17749											
LAMA5	3911	hgsc.bcm.edu	37	chr20	60904037	60904037	+	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	ctacttcgtggcagccacatGgacgggctccgttgttatag	7	11	12	11	3	0	0	0	0	0	0	2	1	1	1	2	3	2	4	2	3	3	5			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr20:60904037G>A	ENST00000252999.3	-	34	4376	c.4310C>T	c.(4309-4311)cCa>cTa	p.P1437L		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1437	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)			GCAGCCACATGGACGGGCTCC	0.632																																					p.P1437L		Atlas-SNP	.											.	LAMA5	268	.	0			c.C4310T						PASS	.						56	58	57					20																	60904037		2203	4297	6500	SO:0001583	missense	3911	exon34			CCACATGGACGGG	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.4310C>T	chr20.hg19:g.60904037G>A	ENSP00000252999:p.Pro1437Leu	51.0	0.0	.		67.0	15.0	.	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	hg19	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	G	17.60	3.429028	0.62844	.	.	ENSG00000130702	ENST00000252999	T	0.21191	2.02	4.47	4.47	0.54385	.	0.000000	0.85682	D	0.000000	T	0.44540	0.1298	M	0.78049	2.395	0.80722	D	1	D	0.69078	0.997	D	0.64687	0.928	T	0.48681	-0.9014	10	0.72032	D	0.01	.	13.0337	0.58859	0.0:0.0:0.838:0.162	.	1437	O15230	LAMA5_HUMAN	L	1437	ENSP00000252999:P1437L	ENSP00000252999:P1437L	P	-	2	0	LAMA5	60337432	1.000000	0.71417	0.016000	0.15963	0.513000	0.34164	5.138000	0.64795	2.001000	0.58596	0.455000	0.32223	CCA	.	.	.	none		0.632	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		A	60904037	G	A	60904037	3	1	278	1	0	0	0	0	1	0	0	0	8616	1348	47	2	6965	2	LAMA5	20	60904037	Missense_Mutation	SNP	G	TCGA-Y8-A898-01A-11D-A34Z-10	9032519	60904037	2121483	77	17750											
MICAL3	57553	hgsc.bcm.edu	37	chr22	18347671	18347671	+	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	ggaagtgaggctacctggggTtctctcagtggagctggcca	7	9	16	9	0	2	1	1	1	1	0	3	3	2	3	2	6	2	3	2	6	2	2			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr22:18347671T>A	ENST00000441493.2	-	19	2951	c.2599A>T	c.(2599-2601)Acc>Tcc	p.T867S	MICAL3_ENST00000400561.2_Missense_Mutation_p.T867S|MICAL3_ENST00000585038.1_Missense_Mutation_p.T991S|MICAL3_ENST00000444520.1_Missense_Mutation_p.T867S|MICAL3_ENST00000383094.3_Missense_Mutation_p.T867S|MICAL3_ENST00000429452.1_Missense_Mutation_p.T991S|MICAL3_ENST00000414725.2_Missense_Mutation_p.T895S|MICAL3_ENST00000207726.7_Missense_Mutation_p.T895S	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	867					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)		CTACCTGGGGTTCTCTCAGTG	0.602																																					p.T991S		Atlas-SNP	.											.	MICAL3	53	.	0			c.A2971T						PASS	.						92	89	90					22																	18347671		1568	3582	5150	SO:0001583	missense	57553	exon23			CTGGGGTTCTCTC	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.2599A>T	chr22.hg19:g.18347671T>A	ENSP00000416015:p.Thr867Ser	62.0	0.0	.		83.0	26.0	.	NM_001136004	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Missense_Mutation	SNP	ENST00000441493.2	hg19	CCDS46659.1	.	.	.	.	.	.	.	.	.	.	T	10.23	1.293575	0.23564	.	.	ENSG00000093100;ENSG00000093100;ENSG00000243156;ENSG00000243156;ENSG00000243156;ENSG00000243156;ENSG00000243156	ENST00000441493;ENST00000429452;ENST00000400561;ENST00000444520;ENST00000414725;ENST00000383094;ENST00000207726	T;T;T;T;T;T;T	0.66638	-0.02;-0.22;-0.11;-0.11;-0.1;-0.12;-0.1	5.72	4.68	0.58851	.	0.901642	0.09446	N	0.801150	T	0.41558	0.1164	N	0.11927	0.2	0.19945	N	0.999943	P;B;B;B;B	0.34546	0.456;0.0;0.0;0.0;0.0	B;B;B;B;B	0.31614	0.133;0.001;0.001;0.001;0.001	T	0.31558	-0.9939	10	0.02654	T	1	.	7.0794	0.25223	0.133:0.0762:0.0:0.7908	.	991;895;867;867;867	B2RXJ5;Q7RTP6-3;Q7RTP6-2;Q7RTP6-4;Q7RTP6	.;.;.;.;MICA3_HUMAN	S	867;991;867;867;895;867;895	ENSP00000416015:T867S;ENSP00000414846:T991S;ENSP00000383406:T867S;ENSP00000410315:T867S;ENSP00000391827:T895S;ENSP00000372574:T867S;ENSP00000207726:T895S	ENSP00000207726:T895S	T	-	1	0	XXbac-B461K10.4;MICAL3	16727671	0.999000	0.42202	0.926000	0.36857	0.664000	0.39144	1.693000	0.37742	0.970000	0.38263	0.533000	0.62120	ACC	.	.	.	none		0.602	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			A	18347671	T	A	18347671	3	1	278	1	0	0	0	0	1	0	0	0	9578	1725	60	5	3814	5	MICAL3	22	18347671	Missense_Mutation	SNP	T	TCGA-Y8-A898-01A-11D-A34Z-10		18347671	32956895	78	17751											
MYO18B	84700	hgsc.bcm.edu	37	chr22	26351226	26351226	+	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	ccacctccgagtcccagcagCgggagagcagccagtactac	10	4	11	16	2	0	1	0	0	0	1	2	3	2	1	5	1	6	3	5	1	2	2			TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr22:26351226C>T	ENST00000407587.2	+	39	6224	c.6055C>T	c.(6055-6057)Cgg>Tgg	p.R2019W	MYO18B_ENST00000536101.1_Missense_Mutation_p.R2018W|MYO18B_ENST00000335473.7_Missense_Mutation_p.R2018W			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2018	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						GTCCCAGCAGCGGGAGAGCAG	0.662																																					p.R2018W		Atlas-SNP	.											.	MYO18B	322	.	0			c.C6052T						PASS	.						19	25	23					22																	26351226		1941	4143	6084	SO:0001583	missense	84700	exon39			CAGCAGCGGGAGA	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.6055C>T	chr22.hg19:g.26351226C>T	ENSP00000386096:p.Arg2019Trp	46.0	0.0	.		94.0	25.0	.	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	hg19		.	.	.	.	.	.	.	.	.	.	C	16.13	3.036701	0.54896	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.87729	-2.26;-2.26;-2.29	4.86	0.906	0.19314	.	0.256362	0.29355	N	0.012391	D	0.86560	0.5962	L	0.40543	1.245	0.34839	D	0.740504	D;D;D;D;D	0.71674	0.998;0.997;0.997;0.998;0.998	P;P;P;P;P	0.55713	0.782;0.61;0.61;0.721;0.782	D	0.89330	0.3646	10	0.87932	D	0	.	12.3547	0.55167	0.6837:0.3163:0.0:0.0	.	1531;2020;2018;2019;2018	Q8IUG5-2;B0QYF5;Q8IUG5;F5GXR6;F5GYU7	.;.;MY18B_HUMAN;.;.	W	2018;2018;2019	ENSP00000441229:R2018W;ENSP00000334563:R2018W;ENSP00000386096:R2019W	ENSP00000334563:R2018W	R	+	1	2	MYO18B	24681226	1.000000	0.71417	0.998000	0.56505	0.218000	0.24690	1.990000	0.40717	0.548000	0.28955	-0.293000	0.09583	CGG	.	.	.	none		0.662	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		T	26351226	C	T	26351226	3	4	278	1	0	0	0	0	1	0	0	0	10073	759	27	1	6202	1	MYO18B	22	26351226	Missense_Mutation	SNP	C	TCGA-Y8-A898-01A-11D-A34Z-10	8003555	26351226	24953340	79	17752											
EP300	2033	hgsc.bcm.edu	37	chr22	41545134	41545134	+	Frame_Shift_Del	DEL	A	A	-																															tcacagggaatgaatgtaacAaatatccctttggctccgtc																								rs374281264	byFrequency	TCGA-Y8-A898-01A-11D-A34Z-10	TCGA-Y8-A898-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8c71a07f-83ad-4612-a896-217d2fde9904	b87bb919-a7fb-44d5-a76a-872cb44c2dc0	g.chr22:41545134delA	ENST00000263253.7	+	13	3553	c.2334delA	c.(2332-2334)acafs	p.T778fs		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	778					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						TGAATGTAACAAATATCCCTT	0.453			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.T778fs		Atlas-Indel,Pindel	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300	367	.	0			c.2333delC						PASS	.						143	123	129					22																	41545134		2203	4300	6503	SO:0001589	frameshift_variant	2033	exon13	Familial Cancer Database	Broad Thumb-Hallux syndrome	.	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"Chromatin-modifying enzymes / K-acetyltransferases"	3373	protein-coding gene	gene with protein product	"histone acetyltransferase p300"	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.2334delA	chr22.hg19:g.41545134delA	ENSP00000263253:p.Thr778fs	121.0	0.0	0		193.0	58.0	0.300518	NM_001429	B1AKC2	Frame_Shift_Del	DEL	ENST00000263253.7	hg19	CCDS14010.1																																																																																			.	.	.	none		0.453	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		-	41545134	A	-	41545134	7	5	278	1	0	1	0	1	0	0	0	0	5150	117	5	0	2384	0	EP300	22	41545134	Frame_Shift_Del	DEL	A	TCGA-Y8-A898-01A-11D-A34Z-10	15193908	41545134	9759432	80	17753											
TEKT2	27285	hgsc.bcm.edu	37	chr1	36553152	36553152	+	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	ccggctagaggccagaacctAccggcccaacgtggaactct	10	5	11	15	3	1	2	0	0	1	2	1	3	1	3	5	4	4	1	5	4	5	2			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr1:36553152A>T	ENST00000207457.3	+	8	1095	c.968A>T	c.(967-969)tAc>tTc	p.Y323F	ADPRHL2_ENST00000373178.4_5'Flank	NM_014466.2	NP_055281.2	Q9UIF3	TEKT2_HUMAN	tektin 2 (testicular)	323					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)				GCCAGAACCTACCGGCCCAAC	0.617																																					p.Y323F		Atlas-SNP	.											.	TEKT2	32	.	0			c.A968T						PASS	.						41	48	45					1																	36553152		2203	4300	6503	SO:0001583	missense	27285	exon8			GAACCTACCGGCC	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.968A>T	chr1.hg19:g.36553152A>T	ENSP00000207457:p.Tyr323Phe	275.0	0.0	.		213.0	85.0	.	NM_014466	A6NIS6|O60638	Missense_Mutation	SNP	ENST00000207457.3	hg19	CCDS401.1	.	.	.	.	.	.	.	.	.	.	A	14.51	2.557648	0.45590	.	.	ENSG00000092850	ENST00000207457	T	0.02579	4.24	5.4	1.66	0.24008	.	0.609329	0.18043	N	0.153548	T	0.04182	0.0116	L	0.42245	1.32	0.30668	N	0.75363	P	0.52316	0.952	P	0.52386	0.697	T	0.22836	-1.0205	10	0.11485	T	0.65	.	5.9945	0.19487	0.7415:0.0:0.1373:0.1212	.	323	Q9UIF3	TEKT2_HUMAN	F	323	ENSP00000207457:Y323F	ENSP00000207457:Y323F	Y	+	2	0	TEKT2	36325739	0.898000	0.30612	0.999000	0.59377	0.992000	0.81027	1.330000	0.33781	0.329000	0.23460	0.460000	0.39030	TAC	.	.	.	none		0.617	TEKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020200.1	NM_014466		T	36553152	A	T	36553152	3	4	279	1	0	0	0	0	1	0	0	0	15765	391	14	5	994	5	TEKT2	1	36553152	Missense_Mutation	SNP	A	TCGA-Y8-A8RY-01A-11D-A36X-10		36553152	212697469	1	17754											
RIMKLA	284716	hgsc.bcm.edu	37	chr1	42875853	42875853	+	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	acggatgcagagcaactgctCtctcggtaaggtataaaagc	13	8	11	9	2	1	1	0	0	1	1	3	2	1	2	0	3	5	5	0	3	5	3			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr1:42875853C>T	ENST00000431473.3	+	4	809	c.680C>T	c.(679-681)tCt>tTt	p.S227F		NM_173642.3	NP_775913.2	Q8IXN7	RIMKA_HUMAN	ribosomal modification protein rimK-like family member A	227	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.				cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|N-acetyl-L-aspartate-L-glutamate ligase activity (GO:0072590)			NS(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	13						AGCAACTGCTCTCTCGGTAAG	0.512																																					p.S227F		Atlas-SNP	.											.	RIMKLA	32	.	0			c.C680T						PASS	.						86	85	85					1																	42875853		2203	4300	6503	SO:0001583	missense	284716	exon4			ACTGCTCTCTCGG	BC039737	CCDS466.2	1p34.2	2011-09-21	2008-10-13	2008-10-13	ENSG00000177181	ENSG00000177181	6.3.2.N6		28725	protein-coding gene	gene with protein product	"N-acetylaspartylglutamate synthetase II"		"family with sequence similarity 80, member A"	FAM80A		20657015, 21454531	Standard	NM_173642		Approved	MGC47816, RP11-157D18.1, NAAGS-II	uc001chi.2	Q8IXN7	OTTHUMG00000007335	ENST00000431473.3:c.680C>T	chr1.hg19:g.42875853C>T	ENSP00000414330:p.Ser227Phe	83.0	0.0	.		63.0	19.0	.	NM_173642	Q5VUS5	Missense_Mutation	SNP	ENST00000431473.3	hg19	CCDS466.2	.	.	.	.	.	.	.	.	.	.	C	15.40	2.823247	0.50739	.	.	ENSG00000177181	ENST00000431473	.	.	.	5.74	4.82	0.62117	ATP-grasp fold (1);ATP-grasp fold, RimK-type (1);ATP-grasp fold, subdomain 2 (1);	0.171847	0.53938	N	0.000060	T	0.63873	0.2548	M	0.87900	2.915	0.44469	D	0.9974	B	0.13145	0.007	B	0.20577	0.03	T	0.61941	-0.6959	8	.	.	.	-5.9282	7.5817	0.27970	0.0:0.744:0.1669:0.0891	.	227	Q8IXN7	RIMKA_HUMAN	F	227	.	.	S	+	2	0	RIMKLA	42648440	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.316000	0.59178	1.402000	0.46780	0.650000	0.86243	TCT	.	.	.	none		0.512	RIMKLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019174.3	NM_173642		T	42875853	C	T	42875853	3	4	279	1	0	0	0	0	1	0	0	0	13378	913	32	2	694	2	RIMKLA	1	42875853	Missense_Mutation	SNP	C	TCGA-Y8-A8RY-01A-11D-A36X-10	6322701	42875853	206374768	2	17755											
MAST2	23139	hgsc.bcm.edu	37	chr1	46501468	46501468	+	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	gggaagacacagccacctagTgcccccagactggcccatcc	10	4	10	17	0	0	2	0	0	0	2	1	3	1	3	6	2	2	0	6	2	2	1			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr1:46501468T>A	ENST00000361297.2	+	29	5410	c.5127T>A	c.(5125-5127)agT>agA	p.S1709R	MAST2_ENST00000372009.2_Missense_Mutation_p.S1519R	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)					AGCCACCTAGTGCCCCCAGAC	0.582																																					p.S1709R		Atlas-SNP	.											.	MAST2	136	.	0			c.T5127A						PASS	.						58	66	63					1																	46501468		1967	4153	6120	SO:0001583	missense	23139	exon29			ACCTAGTGCCCCC	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.5127T>A	chr1.hg19:g.46501468T>A	ENSP00000354671:p.Ser1709Arg	207.0	0.0	.		156.0	62.0	.	NM_015112		Missense_Mutation	SNP	ENST00000361297.2	hg19	CCDS41326.1	.	.	.	.	.	.	.	.	.	.	t	9.412	1.080872	0.20309	.	.	ENSG00000086015	ENST00000361297;ENST00000372009	T;T	0.66280	-0.11;-0.2	5.67	1.86	0.25419	.	2.019210	0.01799	N	0.032797	T	0.49406	0.1555	N	0.24115	0.695	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.11329	0.006;0.006	T	0.42327	-0.9458	10	0.59425	D	0.04	1.5002	4.9458	0.13989	0.0:0.1837:0.1615:0.6549	.	1519;1709	E7ERL6;Q6P0Q8	.;MAST2_HUMAN	R	1709;1519	ENSP00000354671:S1709R;ENSP00000361079:S1519R	ENSP00000354671:S1709R	S	+	3	2	MAST2	46274055	0.000000	0.05858	0.009000	0.14445	0.492000	0.33523	0.007000	0.13174	0.981000	0.38548	0.454000	0.30748	AGT	.	.	.	none		0.582	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112		A	46501468	T	A	46501468	3	1	279	1	0	0	0	0	1	0	0	0	9332	1693	59	5	5241	5	MAST2	1	46501468	Missense_Mutation	SNP	T	TCGA-Y8-A8RY-01A-11D-A36X-10	3625615	46501468	202749153	3	17756											
ACOT11	26027	hgsc.bcm.edu	37	chr1	55060319	55060319	+	Frame_Shift_Del	DEL	G	G	-																															ggcgcatgcgccttgtctatGcagacaccatcaaggacctc																										TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr1:55060319delG	ENST00000371316.3	+	6	644	c.562delG	c.(562-564)gcafs	p.A188fs	ACOT11_ENST00000343744.2_Frame_Shift_Del_p.A188fs|ACOT11_ENST00000481208.1_3'UTR	NM_015547.3	NP_056362.1	Q8WXI4	ACO11_HUMAN	acyl-CoA thioesterase 11	188					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						CCTTGTCTATGCAGACACCAT	0.637																																					p.Y187X	Ovarian(148;1440 1861 22015 32453 51933)	Atlas-Indel,Pindel	.											.	ACOT11	105	.	0			c.561delT						PASS	.						56	52	53					1																	55060319		2203	4300	6503	SO:0001589	frameshift_variant	26027	exon6			.	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.562delG	chr1.hg19:g.55060319delG	ENSP00000360366:p.Ala188fs	175.0	0.0	0		166.0	59.0	0.355422	NM_147161	B1AQ22|D3DQ50|O75187|Q52LP1|Q53ER9|Q96DI1|Q9H883	Frame_Shift_Del	DEL	ENST00000371316.3	hg19	CCDS592.1																																																																																			.	.	.	none		0.637	ACOT11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027356.1	NM_015547		-	55060319	G	-	55060319	7	5	279	1	0	1	0	1	0	0	0	0	149	1319	46	0	584	0	ACOT11	1	55060319	Frame_Shift_Del	DEL	G	TCGA-Y8-A8RY-01A-11D-A36X-10	8558851	55060319	194190302	4	17757											
L1TD1	54596	hgsc.bcm.edu	37	chr1	62675664	62675664	+	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	acctcagggctggaggaggaGgaggaagagccctcagggct	10	4	18	9	0	2	1	2	0	0	1	2	6	2	6	2	7	1	2	2	7	1	0	rs200931139|rs532563709		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr1:62675664G>T	ENST00000498273.1	+	4	1513	c.1218G>T	c.(1216-1218)gaG>gaT	p.E406D	Y_RNA_ENST00000363304.1_RNA	NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	406	Glu-rich.									breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						Tggaggaggaggaggaagagc	0.547																																					p.E406D		Atlas-SNP	.											.,1	L1TD1	114	.	0			c.G1218T						PASS	.						36	40	39					1																	62675664		2200	4298	6498	SO:0001583	missense	54596	exon5			GGAGGAGGAGGAA	BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.1218G>T	chr1.hg19:g.62675664G>T	ENSP00000419901:p.Glu406Asp	132.0	0.0	.		169.0	38.0	.	NM_001164835	Q8NDA1|Q9NUV8|Q9NV78	Missense_Mutation	SNP	ENST00000498273.1	hg19	CCDS619.1	.	.	.	.	.	.	.	.	.	.	G	7.766	0.706401	0.15239	.	.	ENSG00000240563	ENST00000498273	T	0.18810	2.19	3.4	-2.4	0.06583	.	.	.	.	.	T	0.07683	0.0193	N	0.12182	0.205	0.09310	N	1	B	0.15473	0.013	B	0.11329	0.006	T	0.38001	-0.9681	9	0.15952	T	0.53	.	0.3571	0.00358	0.2201:0.167:0.2729:0.34	.	406	Q5T7N2	LITD1_HUMAN	D	406	ENSP00000419901:E406D	ENSP00000419901:E406D	E	+	3	2	L1TD1	62448252	0.053000	0.20554	0.000000	0.03702	0.031000	0.12232	0.041000	0.13927	-0.479000	0.06813	0.448000	0.29417	GAG	.	.	.	alt		0.547	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079		T	62675664	G	T	62675664	3	4	279	1	0	0	0	0	1	0	0	0	8596	991	35	4	1224	4	L1TD1	1	62675664	Missense_Mutation	SNP	G	TCGA-Y8-A8RY-01A-11D-A36X-10	7615345	62675664	186574957	5	17758											
PGM1	5236	hgsc.bcm.edu	37	chr1	64125282	64125282	+	Frame_Shift_Del	DEL	T	T	-																															gttggccccccttatttccaTtgctctgaaagtgtcccagc																										TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr1:64125282delT	ENST00000371084.3	+	11	1838	c.1625delT	c.(1624-1626)attfs	p.I542fs	PGM1_ENST00000540265.1_Frame_Shift_Del_p.I345fs|PGM1_ENST00000371083.4_Frame_Shift_Del_p.I560fs	NM_002633.2	NP_002624.2	P36871	PGM1_HUMAN	phosphoglucomutase 1	542					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						CTTATTTCCATTGCTCTGAAA	0.532																																					p.I560fs		Atlas-Indel,Pindel	.											.	PGM1	75	.	0			c.1678delA						PASS	.						168	132	144					1																	64125282		2203	4300	6503	SO:0001589	frameshift_variant	5236	exon11			.	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.1625delT	chr1.hg19:g.64125282delT	ENSP00000360125:p.Ile542fs	110.0	0.0	0		77.0	22.0	0.285714	NM_001172818	B2R5N9|B4DPV0|Q16105|Q16106|Q5BKZ9|Q6NW22|Q86U74|Q96J40|Q9NTY4	Frame_Shift_Del	DEL	ENST00000371084.3	hg19	CCDS625.1																																																																																			.	.	.	none		0.532	PGM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024868.1	NM_002633		-	64125282	T	-	64125282	7	5	279	1	0	1	0	1	0	0	0	0	11804	1493	52	0	1971	0	PGM1	1	64125282	Frame_Shift_Del	DEL	T	TCGA-Y8-A8RY-01A-11D-A36X-10	1449618	64125282	185125339	6	17759											
APH1A	51107	hgsc.bcm.edu	37	chr1	150239509	150239509	+	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	gtaggtgactcccaaccaccAggcccaaagcccagtaccgt	11	5	9	16	1	0	1	0	1	0	0	1	1	1	1	6	2	3	2	6	2	4	2			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr1:150239509A>T	ENST00000369109.3	-	5	763	c.575T>A	c.(574-576)cTg>cAg	p.L192Q	C1orf54_ENST00000369102.1_5'Flank|APH1A_ENST00000461320.1_5'UTR|APH1A_ENST00000360244.4_Missense_Mutation_p.L192Q|APH1A_ENST00000414276.2_Missense_Mutation_p.L122Q	NM_001077628.2	NP_001071096.1	Q96BI3	APH1A_HUMAN	APH1A gamma secretase subunit	192					amyloid precursor protein catabolic process (GO:0042987)|apoptotic signaling pathway (GO:0097190)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|metanephros development (GO:0001656)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|protein processing (GO:0016485)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase activity (GO:0004175)			breast(1)|lung(4)|ovary(1)|skin(1)|urinary_tract(2)	9	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)			CCCAACCACCAGGCCCAAAGC	0.537																																					p.L192Q		Atlas-SNP	.											.	APH1A	21	.	0			c.T575A						PASS	.						89	92	91					1																	150239509		1983	4183	6166	SO:0001583	missense	51107	exon5			ACCACCAGGCCCA	AF151835	CCDS41390.1, CCDS41391.1, CCDS58025.1	1q21.2	2013-05-01	2013-05-01		ENSG00000117362	ENSG00000117362			29509	protein-coding gene	gene with protein product		607629	"anterior pharynx defective 1 homolog A (C. elegans)"			10810093, 12110170	Standard	NM_001077628		Approved	APH-1A, CGI-78	uc001ety.2	Q96BI3	OTTHUMG00000012545	ENST00000369109.3:c.575T>A	chr1.hg19:g.150239509A>T	ENSP00000358105:p.Leu192Gln	188.0	0.0	.		189.0	67.0	.	NM_016022	B4DQK0|Q5TB22|Q5TB23|Q969R6|Q9BVG0|Q9Y386	Missense_Mutation	SNP	ENST00000369109.3	hg19	CCDS41390.1	.	.	.	.	.	.	.	.	.	.	A	14.46	2.542455	0.45280	.	.	ENSG00000117362	ENST00000369109;ENST00000360244;ENST00000414276;ENST00000236017	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	5.18	5.18	0.71444	.	0.292176	0.26658	N	0.023175	T	0.47229	0.1434	L	0.60455	1.87	0.33621	D	0.604855	P;D;D;P;P;P	0.71674	0.791;0.973;0.998;0.897;0.916;0.952	P;P;D;P;P;P	0.63488	0.5;0.761;0.915;0.648;0.761;0.761	T	0.52230	-0.8603	10	0.51188	T	0.08	-5.2965	13.2852	0.60239	1.0:0.0:0.0:0.0	.	76;135;122;192;192;192	B4DMX8;B4DUG7;B4DQK0;Q96BI3-2;Q5TB22;Q96BI3	.;.;.;.;.;APH1A_HUMAN	Q	192;192;122;135	ENSP00000358105:L192Q;ENSP00000353380:L192Q;ENSP00000397473:L122Q;ENSP00000236017:L135Q	ENSP00000236017:L135Q	L	-	2	0	APH1A	148506133	0.142000	0.22610	1.000000	0.80357	0.995000	0.86356	1.200000	0.32247	2.297000	0.77311	0.533000	0.62120	CTG	.	.	.	none		0.537	APH1A-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000035048.1	NM_016022		T	150239509	A	T	150239509	3	4	279	1	0	0	0	0	1	0	0	0	771	188	7	5	245	5	APH1A	1	150239509	Missense_Mutation	SNP	A	TCGA-Y8-A8RY-01A-11D-A36X-10	86114227	150239509	99011112	7	17760											
TMEM79	84283	hgsc.bcm.edu	37	chr1	156261269	156261269	+	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	ctgctgtcgatgctgatgtgGaacctctactacatgttcgt	7	14	10	10	2	1	1	0	1	1	0	3	3	1	2	1	1	5	3	1	1	3	3			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr1:156261269G>C	ENST00000405535.2	+	4	1236	c.1065G>C	c.(1063-1065)tgG>tgC	p.W355C	TMEM79_ENST00000295694.5_Missense_Mutation_p.W355C|TMEM79_ENST00000357501.2_Missense_Mutation_p.E117Q|TMEM79_ENST00000495881.1_3'UTR|C1orf85_ENST00000482579.1_5'Flank	NM_032323.2	NP_115699.1	Q9BSE2	TMM79_HUMAN	transmembrane protein 79	355					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)					TGCTGATGTGGAACCTCTACT	0.632																																					p.W355C		Atlas-SNP	.											.	TMEM79	43	.	0			c.G1065C						PASS	.						141	132	135					1																	156261269		2203	4300	6503	SO:0001583	missense	84283	exon4			GATGTGGAACCTC	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.1065G>C	chr1.hg19:g.156261269G>C	ENSP00000384748:p.Trp355Cys	70.0	0.0	.		50.0	19.0	.	NM_032323	B2RE22|D3DVB8	Missense_Mutation	SNP	ENST00000405535.2	hg19	CCDS1138.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.12|12.12	1.844054|1.844054	0.32606|0.32606	.|.	.|.	ENSG00000163472|ENSG00000163472	ENST00000357501;ENST00000456810|ENST00000295694;ENST00000405535	.|T;T	.|0.48201	.|0.82;0.82	5.7|5.7	4.78|4.78	0.61160|0.61160	.|.	.|0.368304	.|0.30374	.|N	.|0.009780	T|T	0.25717|0.25717	0.0626|0.0626	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	.|P	.|0.42941	.|0.794	.|B	.|0.43052	.|0.406	T|T	0.06058|0.06058	-1.0848|-1.0848	6|10	0.87932|0.41790	D|T	0|0.15	-3.2299|-3.2299	12.6166|12.6166	0.56580|0.56580	0.0:0.0:0.6985:0.3015|0.0:0.0:0.6985:0.3015	.|.	.|355	.|Q9BSE2	.|TMM79_HUMAN	Q|C	117|355	.|ENSP00000295694:W355C;ENSP00000384748:W355C	ENSP00000350100:E117Q|ENSP00000295694:W355C	E|W	+|+	1|3	0|0	TMEM79|TMEM79	154527893|154527893	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.325000|0.325000	0.28411|0.28411	4.330000|4.330000	0.59266|0.59266	1.390000|1.390000	0.46547|0.46547	-0.181000|-0.181000	0.13052|0.13052	GAA|TGG	.	.	.	none		0.632	TMEM79-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052101.1	NM_032323		C	156261269	G	C	156261269	3	2	279	1	0	0	0	0	1	0	0	0	16215	1183	41	4	1075	4	TMEM79	1	156261269	Missense_Mutation	SNP	G	TCGA-Y8-A8RY-01A-11D-A36X-10	6021760	156261269	92989352	8	17761											
POU2F1	5451	hgsc.bcm.edu	37	chr1	167343522	167343522	+	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	tccccctgtctcagcccataCagatcgcacaggtgagtgag	9	8	10	14	1	1	3	1	2	1	1	4	3	2	3	3	1	2	1	3	1	1	1			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr1:167343522C>T	ENST00000541643.3	+	7	673	c.511C>T	c.(511-513)Cag>Tag	p.Q171*	POU2F1_ENST00000367866.2_Nonsense_Mutation_p.Q194*|POU2F1_ENST00000367865.1_3'UTR|POU2F1_ENST00000367862.5_Nonsense_Mutation_p.Q183*|POU2F1_ENST00000452019.1_Nonsense_Mutation_p.Q171*|POU2F1_ENST00000429375.2_Intron|POU2F1_ENST00000420254.3_Nonsense_Mutation_p.Q171*			P14859	PO2F1_HUMAN	POU class 2 homeobox 1	171					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						TCAGCCCATACAGATCGCACA	0.532																																					p.Q194X		Atlas-SNP	.											.	POU2F1	120	.	0			c.C580T						PASS	.						26	27	26					1																	167343522		2203	4300	6503	SO:0001587	stop_gained	5451	exon6			CCCATACAGATCG	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.511C>T	chr1.hg19:g.167343522C>T	ENSP00000441285:p.Gln171*	201.0	0.0	.		199.0	82.0	.	NM_002697	B1AL91|B1AL93|B4E029|J3KP77|Q5TBT7|Q6PK46|Q8NEU9|Q9BPV1	Nonsense_Mutation	SNP	ENST00000541643.3	hg19		.	.	.	.	.	.	.	.	.	.	C	38	6.800924	0.97849	.	.	ENSG00000143190	ENST00000367866;ENST00000452019;ENST00000492850;ENST00000367865;ENST00000420254;ENST00000541643;ENST00000367862;ENST00000443275	.	.	.	5.77	5.77	0.91146	.	0.232564	0.28952	N	0.013612	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	20.0589	0.97667	0.0:1.0:0.0:0.0	.	.	.	.	X	194;171;48;169;171;171;183;79	.	ENSP00000356836:Q183X	Q	+	1	0	POU2F1	165610146	1.000000	0.71417	0.993000	0.49108	0.998000	0.95712	7.453000	0.80700	2.732000	0.93576	0.650000	0.86243	CAG	.	.	.	none		0.532	POU2F1-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_002697		T	167343522	C	T	167343522	4	4	279	1	0	0	0	0	0	1	0	0	12278	479	17	2	529	2	POU2F1	1	167343522	Nonsense_Mutation	SNP	C	TCGA-Y8-A8RY-01A-11D-A36X-10	11082253	167343522	81907099	9	17762											
QSOX1	5768	hgsc.bcm.edu	37	chr1	180148011	180148011	+	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	aaaagggaggctcctacctgGgtagagaggtgagctgccct	10	7	15	9	0	0	2	0	1	0	1	1	4	1	3	3	4	3	3	3	4	4	2			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr1:180148011G>C	ENST00000367602.3	+	5	672	c.598G>C	c.(598-600)Ggt>Cgt	p.G200R	QSOX1_ENST00000367600.5_Missense_Mutation_p.G200R			O00391	QSOX1_HUMAN	quiescin Q6 sulfhydryl oxidase 1	200			G -> A (in dbSNP:rs17855475). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16806532, ECO:0000269|Ref.4}.		cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of Golgi membrane (GO:0030173)	flavin-linked sulfhydryl oxidase activity (GO:0016971)|protein disulfide isomerase activity (GO:0003756)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						CTCCTACCTGGGTAGAGAGGT	0.507											OREG0014018	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G200R		Atlas-SNP	.											.	QSOX1	79	.	0			c.G598C						PASS	.						100	104	103					1																	180148011		2203	4300	6503	SO:0001583	missense	5768	exon5			TACCTGGGTAGAG	U97276	CCDS1337.1, CCDS30950.1	1q24	2008-02-05	2007-04-23	2007-04-23	ENSG00000116260	ENSG00000116260			9756	protein-coding gene	gene with protein product		603120	"quiescin Q6"	QSCN6		9878249, 8396966	Standard	NM_002826		Approved		uc001gnz.3	O00391	OTTHUMG00000035256	ENST00000367602.3:c.598G>C	chr1.hg19:g.180148011G>C	ENSP00000356574:p.Gly200Arg	74.0	0.0	.	1959	57.0	19.0	.	NM_002826	Q59G29|Q5T2X0|Q8TDL6|Q8WVP4	Missense_Mutation	SNP	ENST00000367602.3	hg19	CCDS1337.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.026464	0.93518	.	.	ENSG00000116260	ENST00000367602;ENST00000367600	T;T	0.08807	3.08;3.05	5.91	5.91	0.95273	.	0.144731	0.64402	D	0.000007	T	0.36744	0.0978	M	0.89287	3.02	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.15809	-1.0424	10	0.56958	D	0.05	-15.3101	17.2153	0.86941	0.0:0.0:1.0:0.0	.	200;200	O00391;O00391-2	QSOX1_HUMAN;.	R	200	ENSP00000356574:G200R;ENSP00000356572:G200R	ENSP00000356572:G200R	G	+	1	0	QSOX1	178414634	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.654000	0.83653	2.793000	0.96121	0.655000	0.94253	GGT	.	.	.	none		0.507	QSOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085289.1	NM_002826		C	180148011	G	C	180148011	3	2	279	1	0	0	0	0	1	0	0	0	12896	1232	43	4	616	4	QSOX1	1	180148011	Missense_Mutation	SNP	G	TCGA-Y8-A8RY-01A-11D-A36X-10	12804489	180148011	69102610	10	17763											
C2orf65	130951	hgsc.bcm.edu	37	chr2	74802619	74802619	+	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	tgatttgtctccagctcatcCcagtccagctgccaacagct	8	11	7	15	0	2	1	1	1	1	0	5	1	4	1	4	0	5	3	4	0	1	1			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr2:74802619C>T	ENST00000290536.5	-	7	1136	c.1020G>A	c.(1018-1020)tgG>tgA	p.W340*	M1AP_ENST00000358434.2_Nonsense_Mutation_p.W58*|M1AP_ENST00000464686.1_5'UTR|M1AP_ENST00000536235.1_Nonsense_Mutation_p.W340*|M1AP_ENST00000409585.1_Nonsense_Mutation_p.W340*	NM_001281296.1|NM_138804.3	NP_001268225.1|NP_620159.2	Q8TC57	M1AP_HUMAN	meiosis 1 associated protein	340					cell differentiation (GO:0030154)|chromatin assembly (GO:0031497)|female gamete generation (GO:0007292)|male meiosis chromosome separation (GO:0051308)|RNA processing (GO:0006396)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)											CCAGCTCATCCCAGTCCAGCT	0.478																																					p.W340X		Atlas-SNP	.											.	.	.	.	0			c.G1020A						PASS	.						126	117	120					2																	74802619		2203	4300	6503	SO:0001587	stop_gained	130951	exon7			CTCATCCCAGTCC		CCDS33229.1, CCDS62941.1	2p13.1	2013-02-05	2013-02-05	2013-01-16	ENSG00000159374	ENSG00000159374			25183	protein-coding gene	gene with protein product	"meiosis 1 arresting protein", "spermatogenesis associated 37"		"chromosome 2 open reading frame 65"	C2orf65		16881047, 23269666	Standard	NM_138804		Approved	D6Mm5e, SPATA37	uc002smy.3	Q8TC57	OTTHUMG00000152918	ENST00000290536.5:c.1020G>A	chr2.hg19:g.74802619C>T	ENSP00000290536:p.Trp340*	86.0	0.0	.		80.0	30.0	.	NM_138804	B7Z6E7|E9PGG8|Q6ZP30|Q96L07	Nonsense_Mutation	SNP	ENST00000290536.5	hg19	CCDS33229.1	.	.	.	.	.	.	.	.	.	.	C	36	5.900307	0.97081	.	.	ENSG00000159374	ENST00000290536;ENST00000409585;ENST00000536235;ENST00000358434	.	.	.	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.4491	13.5676	0.61828	0.0:1.0:0.0:0.0	.	.	.	.	X	340;340;340;58	.	ENSP00000290536:W340X	W	-	3	0	C2orf65	74656127	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.201000	0.72124	2.550000	0.86006	0.655000	0.94253	TGG	.	.	.	none		0.478	M1AP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328569.1	NM_138804		T	74802619	C	T	74802619	4	4	279	1	0	0	0	0	0	1	0	0	2186	624	22	2	592	2	C2orf65	2	74802619	Nonsense_Mutation	SNP	C	TCGA-Y8-A8RY-01A-11D-A36X-10		74802619	168396754	11	17764											
ACVR2A	92	hgsc.bcm.edu	37	chr2	148677844	148677844	+	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	ttgaaaaacaacctgacagcTtgcattgctgactttgggtt	11	13	9	8	0	0	3	0	3	0	0	0	3	0	3	1	1	5	4	1	1	3	5			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr2:148677844T>A	ENST00000241416.7	+	8	1644	c.1008T>A	c.(1006-1008)gcT>gcA	p.A336A	ACVR2A_ENST00000404590.1_Silent_p.A336A|ACVR2A_ENST00000535787.1_Silent_p.A228A	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	336	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		ACCTGACAGCTTGCATTGCTG	0.348																																					p.A336A		Atlas-SNP	.											.	ACVR2A	125	.	0			c.T1008A						PASS	.						93	97	96					2																	148677844		2203	4300	6503	SO:0001819	synonymous_variant	92	exon8			GACAGCTTGCATT		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"activin A receptor, type II"	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.1008T>A	chr2.hg19:g.148677844T>A		149.0	0.0	.		95.0	30.0	.	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Silent	SNP	ENST00000241416.7	hg19	CCDS33301.1																																																																																			.	.	.	none		0.348	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616		A	148677844	T	A	148677844	2	1	279	1	0	0	0	0	0	0	0	1	223	1596	56	5		5	ACVR2A	2	148677844	Silent	SNP	T	TCGA-Y8-A8RY-01A-11D-A36X-10	73875225	148677844	94521529	12	17765											
CRYGD	1421	hgsc.bcm.edu	37	chr2	208988981	208988981	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagccgctgtccacgcgcGccgagttgcagcggctcaag	7	5	14	15	6	1	0	1	0	0	0	2	1	2	0	3	1	4	5	3	1	1	1	rs200234608		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr2:208988981G>A	ENST00000264376.4	-	2	134	c.107C>T	c.(106-108)gCg>gTg	p.A36V		NM_006891.3	NP_008822.2	P07320	CRGD_HUMAN	crystallin, gamma D	36	Beta/gamma crystallin 'Greek key' 1. {ECO:0000255|PROSITE-ProRule:PRU00028}.				cellular response to reactive oxygen species (GO:0034614)|lens development in camera-type eye (GO:0002088)|lens fiber cell differentiation (GO:0070306)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	structural constituent of eye lens (GO:0005212)			breast(1)|endometrium(1)|lung(3)	5				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.0858)|Lung(261;0.133)		GTCCACGCGCGCCGAGTTGCA	0.652																																					p.A36V		Atlas-SNP	.											CRYGD,NS,neuroblastoma,0,1	CRYGD	18	.	0			c.C107T						PASS	.						11	13	12					2																	208988981		2179	4274	6453	SO:0001583	missense	1421	exon2			ACGCGCGCCGAGT		CCDS2378.1	2q33.3	2013-02-14			ENSG00000118231	ENSG00000118231			2411	protein-coding gene	gene with protein product		123690		CRYG4			Standard	NM_006891		Approved		uc002vcn.4	P07320	OTTHUMG00000132944	ENST00000264376.4:c.107C>T	chr2.hg19:g.208988981G>A	ENSP00000264376:p.Ala36Val	146.0	0.0	.		125.0	5.0	.	NM_006891	Q17RF7|Q53R51|Q99681	Missense_Mutation	SNP	ENST00000264376.4	hg19	CCDS2378.1	.	.	.	.	.	.	.	.	.	.	G	11.40	1.627591	0.28978	.	.	ENSG00000118231	ENST00000264376	T	0.72051	-0.62	4.35	3.19	0.36642	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.184420	0.36703	N	0.002444	T	0.29389	0.0732	N	0.00166	-1.94	0.09310	N	0.999995	B	0.02656	0.0	B	0.01281	0.0	T	0.34875	-0.9811	10	0.32370	T	0.25	.	8.1681	0.31239	0.9021:0.0:0.0979:0.0	.	36	P07320	CRGD_HUMAN	V	36	ENSP00000264376:A36V	ENSP00000264376:A36V	A	-	2	0	CRYGD	208697226	0.280000	0.24249	0.067000	0.19924	0.966000	0.64601	2.073000	0.41519	0.695000	0.31675	-0.573000	0.04149	GCG	.	G|0.998;A|0.002	0.002	weak		0.652	CRYGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256476.2	NM_006891		A	208988981	G	A	208988981	3	1	279	1	0	0	0	0	1	0	0	0	3919	1087	38	1	425	1	CRYGD	2	208988981	Missense_Mutation	SNP	G	TCGA-Y8-A8RY-01A-11D-A36X-10	60311137	208988981	34210392	13	17766											
ABCA12	26154	hgsc.bcm.edu	37	chr2	215820066	215820067	+	Frame_Shift_Del	DEL	TC	TC	-																															gagcccagccagcaagtacaTccaggaaaatgttgcatacc																										TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr2:215820066_215820067delTC	ENST00000272895.7	-	43	6471_6472	c.6252_6253delGA	c.(6250-6255)tggatgfs	p.WM2084fs	AC072062.1_ENST00000607412.1_RNA|ABCA12_ENST00000389661.4_Frame_Shift_Del_p.WM1766fs	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	2084					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)		AGCAAGTACATCCAGGAAAATG	0.436																																					p.2085_2085del	Ovarian(66;664 1488 5121 34295)	Atlas-Indel,Pindel	.											.	ABCA12	368	.	0			c.6253_6254del						PASS	.																																			SO:0001589	frameshift_variant	26154	exon43			.	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.6252_6253delGA	chr2.hg19:g.215820066_215820067delTC	ENSP00000272895:p.Trp2084fs	299.0	0.0	0		253.0	95.0	0.375494	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Frame_Shift_Del	DEL	ENST00000272895.7	hg19	CCDS33372.1																																																																																			.	.	.	none		0.436	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		-	215820067	TC	-	215820066	7	5	279	1	0	1	0	1	0	0	0	0	30	1435	50	0	1578	0	ABCA12	2	215820066	Frame_Shift_Del	DEL	TC	TCGA-Y8-A8RY-01A-11D-A36X-10	6831085	215820066	27379307	14	17767											
CTDSP1	58190	hgsc.bcm.edu	37	chr2	219268024	219268024	+	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	cccggctgtttcgagagtccTgcgtcttccaccgggggaac	5	9	13	14	4	1	1	0	0	1	1	4	3	3	2	4	3	2	2	4	3	1	2			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr2:219268024T>A	ENST00000273062.2	+	6	877	c.541T>A	c.(541-543)Tgc>Agc	p.C181S	CTDSP1_ENST00000443891.1_Missense_Mutation_p.C180S|MIR26B_ENST00000362251.2_RNA|CTDSP1_ENST00000488627.1_3'UTR	NM_021198.2|NM_182642.2	NP_067021.1|NP_872580.1	Q9GZU7	CTDS1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1	181	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.				negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|protein dephosphorylation (GO:0006470)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|metal ion binding (GO:0046872)			NS(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	8		Renal(207;0.0915)		Epithelial(149;9.96e-07)|all cancers(144;0.00017)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCGAGAGTCCTGCGTCTTCCA	0.632																																					p.C181S		Atlas-SNP	.											.	CTDSP1	19	.	0			c.T541A						PASS	.						56	65	62					2																	219268024		2203	4300	6503	SO:0001583	missense	58190	exon6			GAGTCCTGCGTCT	AF229162	CCDS2416.1, CCDS56166.1	2q35	2010-06-21			ENSG00000144579	ENSG00000144579		"Serine/threonine phosphatases / CTD aspartate-based phosphatases"	21614	protein-coding gene	gene with protein product	"nuclear LIM interactor-interacting factor", "small CTD phosphatase 1"	605323				11950066, 12721286	Standard	NM_021198		Approved	NLIIF, SCP1	uc021vwv.1	Q9GZU7	OTTHUMG00000133109	ENST00000273062.2:c.541T>A	chr2.hg19:g.219268024T>A	ENSP00000273062:p.Cys181Ser	94.0	0.0	.		68.0	30.0	.	NM_021198	C9IYG0|Q7Z5Q3|Q7Z5Q4	Missense_Mutation	SNP	ENST00000273062.2	hg19	CCDS2416.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.013625	0.75161	.	.	ENSG00000144579	ENST00000443891;ENST00000273062	T;T	0.20463	2.07;2.07	4.64	3.45	0.39498	NLI interacting factor (3);Dullard phosphatase domain, eukaryotic (1);HAD-like domain (2);	0.000000	0.85682	D	0.000000	T	0.56202	0.1969	H	0.96239	3.79	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.63829	-0.6548	10	0.87932	D	0	-31.262	9.6028	0.39615	0.1571:0.0:0.0:0.8429	.	181;180	Q9GZU7;C9IYG0	CTDS1_HUMAN;.	S	180;181	ENSP00000392248:C180S;ENSP00000273062:C181S	ENSP00000273062:C181S	C	+	1	0	CTDSP1	218976268	1.000000	0.71417	0.227000	0.23927	0.942000	0.58702	7.985000	0.88162	0.607000	0.29982	0.402000	0.26972	TGC	.	.	.	none		0.632	CTDSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256774.1	NM_182642, NM_021198		A	219268024	T	A	219268024	3	1	279	1	0	0	0	0	1	0	0	0	4005	1580	55	5	563	5	CTDSP1	2	219268024	Missense_Mutation	SNP	T	TCGA-Y8-A8RY-01A-11D-A36X-10	3447958	219268024	23931349	15	17768											
NBEAL2	23218	hgsc.bcm.edu	37	chr3	47038846	47038846	+	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	tgaagcaggtccagctgaaaCgcatgacctcgtgggtcctg	9	8	13	11	2	0	3	0	3	0	0	3	3	2	3	3	2	3	3	3	2	2	0			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr3:47038846C>T	ENST00000450053.3	+	19	2926	c.2747C>T	c.(2746-2748)aCg>aTg	p.T916M	NBEAL2_ENST00000292309.5_Missense_Mutation_p.T916M|NBEAL2_ENST00000383740.2_5'UTR	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	916					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)		CCAGCTGAAACGCATGACCTC	0.577																																					p.T916M		Atlas-SNP	.											.	NBEAL2	267	.	0			c.C2747T						PASS	.						44	49	47					3																	47038846		2046	4200	6246	SO:0001583	missense	23218	exon19			CTGAAACGCATGA	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.2747C>T	chr3.hg19:g.47038846C>T	ENSP00000415034:p.Thr916Met	22.0	0.0	.		15.0	7.0	.	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Missense_Mutation	SNP	ENST00000450053.3	hg19	CCDS46817.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.77|12.77	2.036230|2.036230	0.35893|0.35893	.|.	.|.	ENSG00000160796|ENSG00000160796	ENST00000416683|ENST00000292309;ENST00000450053	.|T;T	.|0.58358	.|0.34;0.35	5.41|5.41	4.54|4.54	0.55810|0.55810	.|.	.|0.371656	.|0.27700	.|N	.|0.018211	T|T	0.51787|0.51787	0.1695|0.1695	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	D|D	1|1	.|P	.|0.52577	.|0.954	.|P	.|0.45276	.|0.475	T|T	0.56763|0.56763	-0.7925|-0.7925	5|10	.|0.56958	.|D	.|0.05	.|.	12.9387|12.9387	0.58329|0.58329	0.0:0.9216:0.0:0.0784|0.0:0.9216:0.0:0.0784	.|.	.|916	.|Q6ZNJ1	.|NBEL2_HUMAN	C|M	388|916	.|ENSP00000292309:T916M;ENSP00000415034:T916M	.|ENSP00000292309:T916M	R|T	+|+	1|2	0|0	NBEAL2|NBEAL2	47013850|47013850	0.988000|0.988000	0.35896|0.35896	0.202000|0.202000	0.23494|0.23494	0.028000|0.028000	0.11728|0.11728	2.750000|2.750000	0.47500|0.47500	1.521000|1.521000	0.48983|0.48983	0.561000|0.561000	0.74099|0.74099	CGC|ACG	.	.	.	none		0.577	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		T	47038846	C	T	47038846	3	4	279	1	0	0	0	0	1	0	0	0	10196	536	19	1	2821	1	NBEAL2	3	47038846	Missense_Mutation	SNP	C	TCGA-Y8-A8RY-01A-11D-A36X-10		47038846	150983584	16	17769											
COL6A5	256076	hgsc.bcm.edu	37	chr3	130120011	130120011	+	Frame_Shift_Del	DEL	G	G	-																															ctgggcaaaaaactatcacaGtacctggtgagttgttgaac																										TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr3:130120011delG	ENST00000432398.2	+	11	4622	c.4128delG	c.(4126-4128)cagfs	p.Q1376fs	COL6A5_ENST00000265379.6_Frame_Shift_Del_p.Q1376fs	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1376	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						AACTATCACAGTACCTGGTGA	0.388																																					p.Q1376fs		Atlas-Indel,Pindel	.											.	COL6A5	205	.	0			c.4127delA						PASS	.						113	98	103					3																	130120011		692	1591	2283	SO:0001589	frameshift_variant	256076	exon11			.	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.4128delG	chr3.hg19:g.130120011delG	ENSP00000390895:p.Gln1376fs	206.0	0.0	0		137.0	49.0	0.357664	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Frame_Shift_Del	DEL	ENST00000432398.2	hg19																																																																																				.	.	.	none		0.388	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		-	130120011	G	-	130120011	7	5	279	1	0	1	0	1	0	0	0	0	3704	1020	36	0	4166	0	COL6A5	3	130120011	Frame_Shift_Del	DEL	G	TCGA-Y8-A8RY-01A-11D-A36X-10	83081165	130120011	67902419	17	17770											
BOD1L	259282	hgsc.bcm.edu	37	chr4	13616300	13616300	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggaagtttttttgacgctcTctcactggtcttggcatttg	5	18	10	8	1	3	1	1	1	2	0	4	2	3	2	0	3	0	3	0	3	1	5			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr4:13616300T>C	ENST00000040738.5	-	4	829	c.694A>G	c.(694-696)Aga>Gga	p.R232G		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	232						nucleus (GO:0005634)	DNA binding (GO:0003677)										TTTGACGCTCTCTCACTGGTC	0.418																																					p.R232G		Atlas-SNP	.											.	.	.	.	0			c.A694G						PASS	.						143	117	126					4																	13616300		2203	4300	6503	SO:0001583	missense	259282	exon4			ACGCTCTCTCACT	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.694A>G	chr4.hg19:g.13616300T>C	ENSP00000040738:p.Arg232Gly	89.0	0.0	.		62.0	4.0	.	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	hg19	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	T	15.15	2.748965	0.49257	.	.	ENSG00000038219	ENST00000040738	T	0.12255	2.7	5.74	4.54	0.55810	.	0.000000	0.53938	D	0.000052	T	0.30603	0.0770	M	0.62723	1.935	0.35742	D	0.818752	D	0.76494	0.999	D	0.64144	0.922	T	0.32295	-0.9912	10	0.40728	T	0.16	-13.193	12.9123	0.58187	0.0:0.0:0.1359:0.8641	.	232	Q8NFC6	BOD1L_HUMAN	G	232	ENSP00000040738:R232G	ENSP00000040738:R232G	R	-	1	2	BOD1L	13225398	1.000000	0.71417	0.997000	0.53966	0.164000	0.22412	4.222000	0.58580	0.967000	0.38186	0.477000	0.44152	AGA	.	.	.	none		0.418	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		C	13616300	T	C	13616300	3	2	279	1	0	0	0	0	1	0	0	0	1483	1559	54	3	8553	3	BOD1L	4	13616300	Missense_Mutation	SNP	T	TCGA-Y8-A8RY-01A-11D-A36X-10		13616300	177537976	18	17771											
COL25A1	84570	hgsc.bcm.edu	37	chr4	109861784	109861784	+	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	gccagggggtcctggaggccCtgcctgtccttggtcaccct	3	9	14	15	0	1	0	1	0	0	0	3	1	3	1	6	5	1	0	6	5	0	1			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr4:109861784C>G	ENST00000399132.1	-	10	1113	c.583G>C	c.(583-585)Ggg>Cgg	p.G195R	COL25A1_ENST00000399126.1_Missense_Mutation_p.G195R|COL25A1_ENST00000399127.1_Missense_Mutation_p.G191R	NM_198721.2	NP_942014.1			collagen, type XXV, alpha 1											NS(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	49		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)		CCTGGAGGCCCTGCCTGTCCT	0.562																																					p.G195R		Atlas-SNP	.											.	COL25A1	178	.	0			c.G583C						PASS	.						51	52	52					4																	109861784		1883	4103	5986	SO:0001583	missense	84570	exon9			GAGGCCCTGCCTG	AF293340	CCDS43258.1, CCDS43259.1, CCDS58922.1	4q25	2013-01-16			ENSG00000188517	ENSG00000188517		"Collagens"	18603	protein-coding gene	gene with protein product		610004				11927537	Standard	NM_001256074		Approved		uc003hze.2	Q9BXS0	OTTHUMG00000150039	ENST00000399132.1:c.583G>C	chr4.hg19:g.109861784C>G	ENSP00000382083:p.Gly195Arg	63.0	0.0	.		42.0	17.0	.	NM_198721		Missense_Mutation	SNP	ENST00000399132.1	hg19	CCDS43258.1	.	.	.	.	.	.	.	.	.	.	C	18.34	3.603104	0.66445	.	.	ENSG00000188517	ENST00000399132;ENST00000333642;ENST00000401873;ENST00000399127;ENST00000399126	D;D;D	0.98807	-5.15;-5.15;-5.15	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	D	0.99582	0.9849	H	0.98951	4.38	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.97654	1.0156	9	.	.	.	-3.9504	19.3339	0.94307	0.0:1.0:0.0:0.0	.	195;195	Q9BXS0-2;Q9BXS0	.;COPA1_HUMAN	R	195;197;191;191;195	ENSP00000382083:G195R;ENSP00000382078:G191R;ENSP00000382077:G195R	.	G	-	1	0	COL25A1	110081233	1.000000	0.71417	0.996000	0.52242	0.992000	0.81027	7.172000	0.77604	2.557000	0.86248	0.555000	0.69702	GGG	.	.	.	none		0.562	COL25A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315938.2	NM_032518		G	109861784	C	G	109861784	3	3	279	1	0	0	0	0	1	0	0	0	3686	681	24	4	1581	4	COL25A1	4	109861784	Missense_Mutation	SNP	C	TCGA-Y8-A8RY-01A-11D-A36X-10	96245484	109861784	81292492	19	17772											
ADAD1	132612	hgsc.bcm.edu	37	chr4	123333812	123333812	+	Frame_Shift_Del	DEL	T	T	-																															cgtggctgttgaaggcaaaaTttatctgactgtttactgtc																										TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr4:123333812delT	ENST00000296513.2	+	10	1282	c.1097delT	c.(1096-1098)attfs	p.I366fs	ADAD1_ENST00000388725.2_Frame_Shift_Del_p.I348fs|ADAD1_ENST00000388724.2_Frame_Shift_Del_p.I355fs	NM_139243.3	NP_640336.1	Q96M93	ADAD1_HUMAN	adenosine deaminase domain containing 1 (testis-specific)	366	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				multicellular organismal development (GO:0007275)|RNA processing (GO:0006396)|spermatid development (GO:0007286)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	35						GAAGGCAAAATTTATCTGACT	0.393																																					p.I366fs		Atlas-Indel,Pindel	.											.	ADAD1	94	.	0			c.1096delA						PASS	.						187	176	180					4																	123333812		2203	4300	6503	SO:0001589	frameshift_variant	132612	exon10			.	AK057303	CCDS34058.1, CCDS54800.1, CCDS54801.1	4q27	2007-05-31			ENSG00000164113	ENSG00000164113			30713	protein-coding gene	gene with protein product		614130				7543294, 9541871	Standard	NM_139243		Approved	Tenr	uc003iep.3	Q96M93	OTTHUMG00000150128	ENST00000296513.2:c.1097delT	chr4.hg19:g.123333812delT	ENSP00000296513:p.Ile366fs	108.0	0.0	0		90.0	41.0	0.455556	NM_139243	A6NKN4|B7WPB0|D3DNX2|Q8IWG6|Q8NA06	Frame_Shift_Del	DEL	ENST00000296513.2	hg19	CCDS34058.1																																																																																			.	.	.	none		0.393	ADAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316452.1	NM_139243		-	123333812	T	-	123333812	7	5	279	1	0	1	0	1	0	0	0	0	231	1493	52	0	1127	0	ADAD1	4	123333812	Frame_Shift_Del	DEL	T	TCGA-Y8-A8RY-01A-11D-A36X-10	13472028	123333812	67820464	20	17773											
ODZ3	55714	hgsc.bcm.edu	37	chr4	183674665	183674665	+	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	gaaccatgattaggaaagttGaccaaaatggaatcatatca	18	9	8	6	0	2	2	2	2	0	0	2	5	2	4	2	2	1	1	2	2	7	3			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr4:183674665G>A	ENST00000511685.1	+	21	4048	c.3925G>A	c.(3925-3927)Gac>Aac	p.D1309N	TENM3_ENST00000406950.2_Missense_Mutation_p.D1309N|TENM3_ENST00000502950.1_3'UTR			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1309					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)										TAGGAAAGTTGACCAAAATGG	0.373																																					p.D1309N		Atlas-SNP	.											.	.	.	.	0			c.G3925A						PASS	.						113	112	112					4																	183674665		1915	4137	6052	SO:0001583	missense	55714	exon20			AAAGTTGACCAAA	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.3925G>A	chr4.hg19:g.183674665G>A	ENSP00000424226:p.Asp1309Asn	183.0	0.0	.		120.0	43.0	.	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	hg19	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	G	18.74	3.688166	0.68271	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.91996	-2.95;-2.95	5.65	5.65	0.86999	Six-bladed beta-propeller, TolB-like (1);	.	.	.	.	D	0.96166	0.8750	M	0.78801	2.425	0.80722	D	1	D	0.63880	0.993	D	0.74674	0.984	D	0.95850	0.8874	9	0.72032	D	0.01	.	19.9142	0.97043	0.0:0.0:1.0:0.0	.	1309	Q9P273	TEN3_HUMAN	N	1309	ENSP00000424226:D1309N;ENSP00000385276:D1309N	ENSP00000385276:D1309N	D	+	1	0	ODZ3	183911659	1.000000	0.71417	0.998000	0.56505	0.235000	0.25334	9.657000	0.98554	2.941000	0.99782	0.655000	0.94253	GAC	.	.	.	none		0.373	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			A	183674665	G	A	183674665	3	1	279	1	0	0	0	0	1	0	0	0	10843	1290	45	2	4003	2	ODZ3	4	183674665	Missense_Mutation	SNP	G	TCGA-Y8-A8RY-01A-11D-A36X-10	60340853	183674665	7479611	21	17774											
ADAMTS6	11174	hgsc.bcm.edu	37	chr5	64510676	64510682	+	IGR	DEL	AACTTCA	AACTTCA	-																															tgatgattccatgtaaagccAacttcattatctccactgcc																										TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	AACTTCA	AACTTCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr5:64510676_64510682delAACTTCA								ADAMTS6 (16084 upstream) : ADAMTS6 (82352 downstream)																							ATGTAAAGCCAACTTCATTATCTCCAC	0.464																																					p.839_841del		Atlas-Indel,Pindel	.											.	ADAMTS6	174	.	0			c.2515_2521del						PASS	.																																			SO:0001628	intergenic_variant	11174	exon20			.																													chr5.hg19:g.64510676_64510682delAACTTCA		121.0	0.0	0		77.0	17.0	0.220779	NM_197941		Frame_Shift_Del	DEL		hg19																																																																																				.	.	.	none	0	0.464									-	64510682	AACTTCA	-	64510676	6	5	279	0	1	1	0	1	0	0	0	0	270	117	5	0		0	ADAMTS6	5	64510676	IGR	DEL	AACTTCA	TCGA-Y8-A8RY-01A-11D-A36X-10		64510676	116404584	22	17775											
CHD1	1105	hgsc.bcm.edu	37	chr5	98235232	98235232	+	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	tataattatccaattttttcAttcctctaacattctgctgc	10	19	2	10	0	3	0	1	0	2	0	5	0	5	0	2	0	3	1	2	0	5	9			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr5:98235232A>T	ENST00000284049.3	-	7	1186	c.1037T>A	c.(1036-1038)aTg>aAg	p.M346K		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	346	Chromo 1. {ECO:0000255|PROSITE- ProRule:PRU00053}.				chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	CAATTTTTTCATTCCTCTAAC	0.323																																					p.M346K		Atlas-SNP	.											.	CHD1	137	.	0			c.T1037A						PASS	.						112	124	120					5																	98235232		2203	4300	6503	SO:0001583	missense	1105	exon7			TTTTTCATTCCTC	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.1037T>A	chr5.hg19:g.98235232A>T	ENSP00000284049:p.Met346Lys	59.0	0.0	.		46.0	15.0	.	NM_001270	Q17RZ3	Missense_Mutation	SNP	ENST00000284049.3	hg19	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.814508	0.90790	.	.	ENSG00000153922	ENST00000284049	T	0.70631	-0.5	5.74	5.74	0.90152	Chromo domain (1);Chromo domain-like (1);Chromo domain/shadow (2);	0.000000	0.40469	U	0.001094	T	0.74733	0.3755	L	0.42529	1.33	0.80722	D	1	D	0.54772	0.968	P	0.54060	0.741	T	0.77778	-0.2460	10	0.87932	D	0	.	16.0292	0.80564	1.0:0.0:0.0:0.0	.	346	O14646	CHD1_HUMAN	K	346	ENSP00000284049:M346K	ENSP00000284049:M346K	M	-	2	0	CHD1	98263132	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.962000	0.93254	2.187000	0.69744	0.533000	0.62120	ATG	.	.	.	none		0.323	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270		T	98235232	A	T	98235232	3	4	279	1	0	0	0	0	1	0	0	0	3325	217	8	5	4211	5	CHD1	5	98235232	Missense_Mutation	SNP	A	TCGA-Y8-A8RY-01A-11D-A36X-10	33724556	98235232	82680028	23	17776											
SHROOM1	134549	hgsc.bcm.edu	37	chr5	132160915	132160915	+	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	cccaagacttcgcctgaagcGctccgactccgactggcggg	7	6	12	16	5	0	2	0	1	0	1	3	4	2	2	4	2	1	1	4	2	2	1			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr5:132160915G>T	ENST00000378679.3	-	4	1722	c.918C>A	c.(916-918)agC>agA	p.S306R	SHROOM1_ENST00000378676.1_Missense_Mutation_p.S306R|SHROOM1_ENST00000319854.3_Missense_Mutation_p.S306R|SHROOM1_ENST00000488072.1_5'Flank	NM_001172700.1	NP_001166171.1	Q2M3G4	SHRM1_HUMAN	shroom family member 1	306					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)			CGCCTGAAGCGCTCCGACTCC	0.617																																					p.S306R		Atlas-SNP	.											.	SHROOM1	35	.	0			c.C918A						PASS	.						37	41	40					5																	132160915		2203	4300	6503	SO:0001583	missense	134549	exon1			TGAAGCGCTCCGA	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.918C>A	chr5.hg19:g.132160915G>T	ENSP00000367950:p.Ser306Arg	89.0	0.0	.		71.0	20.0	.	NM_133456	B7WP40|B7ZL01|Q8TDP0|Q8TF41	Missense_Mutation	SNP	ENST00000378679.3	hg19	CCDS54902.1	.	.	.	.	.	.	.	.	.	.	G	16.55	3.154073	0.57259	.	.	ENSG00000164403	ENST00000378679;ENST00000319854;ENST00000378676;ENST00000440118	T;T;T;T	0.23950	1.88;1.88;1.88;1.88	4.7	-1.49	0.08718	.	0.564112	0.19160	N	0.121214	T	0.32224	0.0822	L	0.32530	0.975	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.98	T	0.13818	-1.0495	10	0.59425	D	0.04	-17.2468	8.5248	0.33298	0.6377:0.0:0.3623:0.0	.	306;306	Q2M3G4-2;Q2M3G4	.;SHRM1_HUMAN	R	306	ENSP00000367950:S306R;ENSP00000324245:S306R;ENSP00000367947:S306R;ENSP00000388049:S306R	ENSP00000324245:S306R	S	-	3	2	SHROOM1	132188814	0.000000	0.05858	0.064000	0.19789	0.026000	0.11368	-0.578000	0.05841	-0.211000	0.10124	0.561000	0.74099	AGC	.	.	.	none		0.617	SHROOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133033.1	NM_133456		T	132160915	G	T	132160915	3	4	279	1	0	0	0	0	1	0	0	0	14306	1078	38	4	1668	4	SHROOM1	5	132160915	Missense_Mutation	SNP	G	TCGA-Y8-A8RY-01A-11D-A36X-10	33925683	132160915	48754345	24	17777											
TMEM173	340061	hgsc.bcm.edu	37	chr5	138856029	138856029	+	Missense_Mutation	SNP	A	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	gacagcgagaagctgctgtcAtctgcaggttctggaacagg	10	8	14	9	1	3	1	1	0	2	1	3	4	3	2	0	3	5	4	0	3	2	1			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr5:138856029A>C	ENST00000330794.4	-	8	1290	c.957T>G	c.(955-957)gaT>gaG	p.D319E	TMEM173_ENST00000511850.1_5'Flank	NM_198282.2	NP_938023.1	Q86WV6	STING_HUMAN	transmembrane protein 173	319	c-di-GMP-binding domain (CBD).				activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	cyclic-di-GMP binding (GO:0035438)|cyclic-GMP-AMP binding (GO:0061507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|lung(6)|upper_aerodigestive_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AGCTGCTGTCATCTGCAGGTT	0.542																																					p.D319E		Atlas-SNP	.											.	TMEM173	19	.	0			c.T957G						PASS	.						49	48	48					5																	138856029		2203	4300	6503	SO:0001583	missense	340061	exon8			GCTGTCATCTGCA		CCDS4215.1	5q31.2	2009-11-06			ENSG00000184584	ENSG00000184584			27962	protein-coding gene	gene with protein product		612374				12477932	Standard	XM_005268445		Approved	FLJ38577, NET23	uc003lep.3	Q86WV6	OTTHUMG00000129239	ENST00000330794.4:c.957T>G	chr5.hg19:g.138856029A>C	ENSP00000331288:p.Asp319Glu	58.0	0.0	.		49.0	10.0	.	NM_198282	A8K3P6|B6EB35|D6RBX0|D6RE01|D6RID9	Missense_Mutation	SNP	ENST00000330794.4	hg19	CCDS4215.1	.	.	.	.	.	.	.	.	.	.	A	0.011	-1.696860	0.00725	.	.	ENSG00000184584	ENST00000330794	T	0.19938	2.11	5.19	-4.23	0.03789	.	0.353151	0.28135	N	0.016478	T	0.06872	0.0175	N	0.14661	0.345	0.19300	N	0.999972	B	0.06786	0.001	B	0.08055	0.003	T	0.35773	-0.9775	10	0.08179	T	0.78	-5.2849	4.5484	0.12092	0.4244:0.2109:0.2966:0.0681	.	319	Q86WV6	TM173_HUMAN	E	319	ENSP00000331288:D319E	ENSP00000331288:D319E	D	-	3	2	TMEM173	138836213	0.000000	0.05858	0.474000	0.27266	0.039000	0.13416	-0.774000	0.04684	-0.365000	0.08076	-0.648000	0.03929	GAT	.	.	.	none		0.542	TMEM173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251338.1	NM_198282		C	138856029	A	C	138856029	3	2	279	1	0	0	0	0	1	0	0	0	16101	214	8	5	186	5	TMEM173	5	138856029	Missense_Mutation	SNP	A	TCGA-Y8-A8RY-01A-11D-A36X-10	6695114	138856029	42059231	25	17778											
FGFR4	2264	hgsc.bcm.edu	37	chr5	176523128	176523128	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtgatgaagattgctgactTtgggctggcccgcggcgtcc	5	11	15	10	3	0	4	0	3	0	1	1	4	1	4	2	3	1	2	2	3	1	2			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr5:176523128T>C	ENST00000292408.4	+	14	2137	c.1892T>C	c.(1891-1893)tTt>tCt	p.F631S	FGFR4_ENST00000393637.1_Missense_Mutation_p.F591S|FGFR4_ENST00000292410.3_Missense_Mutation_p.F591S|FGFR4_ENST00000502906.1_Missense_Mutation_p.F631S|FGFR4_ENST00000393648.2_Missense_Mutation_p.F563S	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4	631	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	ATTGCTGACTTTGGGCTGGCC	0.607										TSP Lung(9;0.080)																											p.F631S		Atlas-SNP	.											.	FGFR4	174	.	0			c.T1892C						PASS	.						60	58	59					5																	176523128		2203	4300	6503	SO:0001583	missense	2264	exon14			CTGACTTTGGGCT	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.1892T>C	chr5.hg19:g.176523128T>C	ENSP00000292408:p.Phe631Ser	96.0	0.0	.		77.0	35.0	.	NM_002011	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Missense_Mutation	SNP	ENST00000292408.4	hg19	CCDS4410.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.367713	0.82463	.	.	ENSG00000160867	ENST00000292408;ENST00000393648;ENST00000502906;ENST00000292410;ENST00000393637;ENST00000377207	D;D;D;D;D	0.96830	-4.14;-4.14;-4.14;-4.14;-4.14	4.66	4.66	0.58398	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	0.98915	0.9632	H	0.98701	4.305	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	0.99084	1.0838	10	0.87932	D	0	.	13.7959	0.63171	0.0:0.0:0.0:1.0	.	563;591;631	B4DVP5;P22455-2;P22455	.;.;FGFR4_HUMAN	S	631;563;631;591;591;859	ENSP00000292408:F631S;ENSP00000377259:F563S;ENSP00000424960:F631S;ENSP00000292410:F591S;ENSP00000377254:F591S	ENSP00000292408:F631S	F	+	2	0	FGFR4	176455734	1.000000	0.71417	0.998000	0.56505	0.776000	0.43924	8.040000	0.89188	1.745000	0.51790	0.459000	0.35465	TTT	.	.	.	none		0.607	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1			C	176523128	T	C	176523128	3	2	279	1	0	0	0	0	1	0	0	0	5875	1841	64	3	2012	3	FGFR4	5	176523128	Missense_Mutation	SNP	T	TCGA-Y8-A8RY-01A-11D-A36X-10	37667099	176523128	4392132	26	17779											
GFPT2	9945	hgsc.bcm.edu	37	chr5	179743359	179743359	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acctgactggctgatgaaaaAgcaaacgtcatccctgaaca	15	7	8	11	1	1	4	1	4	0	0	2	4	2	4	2	1	3	2	2	1	4	0			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr5:179743359A>G	ENST00000253778.8	-	13	1424	c.1255T>C	c.(1255-1257)Ttt>Ctt	p.F419L	GFPT2_ENST00000520165.1_5'Flank	NM_005110.2	NP_005101.1	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2	419	SIS 1. {ECO:0000255|PROSITE- ProRule:PRU00797}.				carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|energy reserve metabolic process (GO:0006112)|fructose 6-phosphate metabolic process (GO:0006002)|glutamine metabolic process (GO:0006541)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)	carbohydrate binding (GO:0030246)|glutamine-fructose-6-phosphate transaminase (isomerizing) activity (GO:0004360)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)	CTGATGAAAAAGCAAACGTCA	0.502																																					p.F419L		Atlas-SNP	.											.	GFPT2	74	.	0			c.T1255C						PASS	.						76	79	78					5																	179743359		2106	4233	6339	SO:0001583	missense	9945	exon13			TGAAAAAGCAAAC	AB016789	CCDS43411.1	5q	2008-07-18			ENSG00000131459	ENSG00000131459			4242	protein-coding gene	gene with protein product	"glutamine: fructose-6-phosphate aminotransferase 2"	603865				10198162	Standard	NM_005110		Approved	GFAT2	uc003mlw.1	O94808	OTTHUMG00000163442	ENST00000253778.8:c.1255T>C	chr5.hg19:g.179743359A>G	ENSP00000253778:p.Phe419Leu	151.0	0.0	.		122.0	38.0	.	NM_005110	Q53XM2|Q9BWS4	Missense_Mutation	SNP	ENST00000253778.8	hg19	CCDS43411.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.929944	0.92389	.	.	ENSG00000131459	ENST00000253778	T	0.61274	0.12	5.89	5.89	0.94794	Sugar isomerase (SIS) (2);	0.000000	0.85682	D	0.000000	T	0.48059	0.1479	N	0.11284	0.12	0.80722	D	1	P	0.41159	0.74	P	0.47645	0.553	T	0.47355	-0.9124	9	.	.	.	-22.0601	16.3123	0.82883	1.0:0.0:0.0:0.0	.	419	O94808	GFPT2_HUMAN	L	419	ENSP00000253778:F419L	.	F	-	1	0	GFPT2	179675965	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.157000	0.94714	2.254000	0.74563	0.459000	0.35465	TTT	.	.	.	none		0.502	GFPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373444.4	NM_005110		G	179743359	A	G	179743359	3	3	279	1	0	0	0	0	1	0	0	0	6353	72	3	3	821	3	GFPT2	5	179743359	Missense_Mutation	SNP	A	TCGA-Y8-A8RY-01A-11D-A36X-10	3220231	179743359	1171901	27	17780											
ATXN1	6310	hgsc.bcm.edu	37	chr6	16327864	16327864	+	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	agccccggagccctgctgagGtgctgctgctgctgctgctg	3	9	15	14	1	0	1	0	1	0	0	0	2	0	2	3	2	9	7	3	2	0	0			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr6:16327864G>C	ENST00000244769.4	-	8	1614	c.678C>G	c.(676-678)caC>caG	p.H226Q	ATXN1_ENST00000436367.1_Missense_Mutation_p.H226Q	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	226					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				CCCTGCTGAGGtgctgctgct	0.652																																					p.H226Q		Atlas-SNP	.											.,1	ATXN1	117	.	0			c.C678G						PASS	.						11	15	13					6																	16327864		2150	4194	6344	SO:0001583	missense	6310	exon7			GCTGAGGTGCTGC	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"Ataxins"	10548	protein-coding gene	gene with protein product		601556	"spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.678C>G	chr6.hg19:g.16327864G>C	ENSP00000244769:p.His226Gln	67.0	2.0	.		64.0	3.0	.	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	hg19	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	G	1.926	-0.447046	0.04572	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.27256	1.68;1.68	4.74	0.503	0.16940	.	0.308295	0.34291	N	0.004091	T	0.05686	0.0149	L	0.39397	1.21	0.09310	N	0.999995	B	0.32245	0.361	B	0.28638	0.092	T	0.23976	-1.0173	10	0.48119	T	0.1	-16.8942	3.2876	0.06937	0.3032:0.0:0.385:0.3119	.	226	P54253	ATX1_HUMAN	Q	226	ENSP00000244769:H226Q;ENSP00000416360:H226Q	ENSP00000244769:H226Q	H	-	3	2	ATXN1	16435843	0.437000	0.25593	0.006000	0.13384	0.009000	0.06853	0.925000	0.28791	0.191000	0.20236	0.563000	0.77884	CAC	.	.	.	none		0.652	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332		C	16327864	G	C	16327864	3	2	279	1	0	0	0	0	1	0	0	0	1209	1252	44	4	1777	4	ATXN1	6	16327864	Missense_Mutation	SNP	G	TCGA-Y8-A8RY-01A-11D-A36X-10		16327864	154787203	28	17781											
HIST1H2AH	85235	hgsc.bcm.edu	37	chr6	27115069	27115069	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgccagtgtacctggctgcGgtgctggagtacctgaccgc	5	8	15	13	3	0	1	0	1	0	0	0	2	0	2	4	3	4	4	4	3	2	2	rs7756481	byFrequency	TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr6:27115069G>A	ENST00000377459.1	+	1	209	c.162G>A	c.(160-162)gcG>gcA	p.A54A	MIR3143_ENST00000584253.1_RNA|HIST1H2BK_ENST00000356950.1_5'Flank|HIST1H2BK_ENST00000396891.4_5'Flank	NM_080596.1	NP_542163.1	Q96KK5	H2A1H_HUMAN	histone cluster 1, H2ah	54						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)|prostate(1)|skin(1)	12						ACCTGGCTGCGGTGCTGGAGT	0.657																																					p.A54A		Atlas-SNP	.											.	HIST1H2AH	26	.	0			c.G162A						PASS	.						52	53	53					6																	27115069		2203	4300	6503	SO:0001819	synonymous_variant	85235	exon1			GGCTGCGGTGCTG	AY131988	CCDS4622.1	6p22.1	2011-01-27	2006-10-11			ENSG00000274997		"Histones / Replication-dependent"	13671	protein-coding gene	gene with protein product		615013	"histone 1, H2ah"			12408966	Standard	NM_080596		Approved	H2AFALii, dJ86C11.1, H2A/S	uc003niz.4	Q96KK5		ENST00000377459.1:c.162G>A	chr6.hg19:g.27115069G>A		131.0	0.0	.		142.0	8.0	.	NM_080596		Silent	SNP	ENST00000377459.1	hg19	CCDS4622.1																																																																																			.	G|0.936;C|0.064	.	alt		0.657	HIST1H2AH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040136.1	NM_080596		A	27115069	G	A	27115069	2	1	279	1	0	0	0	0	0	0	0	1	7141	1103	39	1		1	HIST1H2AH	6	27115069	Silent	SNP	G	TCGA-Y8-A8RY-01A-11D-A36X-10	10787205	27115069	143999998	29	17782											
PHF3	23469	hgsc.bcm.edu	37	chr6	64404652	64404653	+	Frame_Shift_Ins	INS	-	-	AGGT																															ggagaaaaagcttcaaaaccINSaggtagtgagatgaacagaa																										TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr6:64404652_64404653insAGGT	ENST00000262043.3	+	6	3018_3019	c.2678_2679insAGGT	c.(2677-2682)ccaggtfs	p.-894fs	PHF3_ENST00000393387.1_Frame_Shift_Ins_p.-894fs			Q92576	PHF3_HUMAN	PHD finger protein 3						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)			GCTTCAAAACCAGGTAGTGAGA	0.292																																					p.P893fs	GBM(135;136 1820 29512 34071 46235)	Pindel	.											.	PHF3	191	.	0			c.2678_2679insAGGT						PASS	.																																			SO:0001589	frameshift_variant	23469	exon5			.	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.2679_2682dupAGGT	chr6.hg19:g.64404653_64404656dupAGGT	ENSP00000262043:p.Gly894fs	266.0	0.0	.		199.0	34.0	0.171	NM_015153	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Frame_Shift_Ins	INS	ENST00000262043.3	hg19	CCDS4966.1																																																																																			.	.	.	none		0.292	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2			AGGT	64404653	-	AGGT	64404652	7	5	279	1	0	1	1	0	0	0	0	0	11843	594	21	0	2696	0	PHF3	6	64404652	Frame_Shift_Ins	INS	-	TCGA-Y8-A8RY-01A-11D-A36X-10	37289583	64404652	106710415	30	17783											
BEND3	57673	hgsc.bcm.edu	37	chr6	107390745	107390745	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgctgagcaggcagtcggcAccgggcacctcgaagtcagg	8	6	15	12	3	1	1	1	1	0	0	3	2	1	1	2	4	2	5	2	4	1	1			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr6:107390745A>G	ENST00000369042.1	-	4	1840	c.1650T>C	c.(1648-1650)ggT>ggC	p.G550G	BEND3_ENST00000429433.2_Silent_p.G550G			Q5T5X7	BEND3_HUMAN	BEN domain containing 3	550	BEN 3. {ECO:0000255|PROSITE- ProRule:PRU00784}.									central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(7)|lung(10)|ovary(4)|prostate(3)	30						GGCAGTCGGCACCGGGCACCT	0.647																																					p.G550G		Atlas-SNP	.											.	BEND3	70	.	0			c.T1650C						PASS	.						33	32	32					6																	107390745		2203	4300	6503	SO:0001819	synonymous_variant	57673	exon5			GTCGGCACCGGGC	AB046773	CCDS34507.1	6q21	2012-11-22	2008-10-03	2008-10-03	ENSG00000178409	ENSG00000178409		"BEN domain containing"	23040	protein-coding gene	gene with protein product			"KIAA1553"	KIAA1553			Standard	NM_001080450		Approved		uc003prs.2	Q5T5X7	OTTHUMG00000015308	ENST00000369042.1:c.1650T>C	chr6.hg19:g.107390745A>G		40.0	0.0	.		34.0	12.0	.	NM_001080450	A2RRH2|Q9HCL9	Silent	SNP	ENST00000369042.1	hg19	CCDS34507.1																																																																																			.	.	.	none		0.647	BEND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041686.1	NM_020913		G	107390745	A	G	107390745	2	3	279	1	0	0	0	0	0	0	0	1	1399	146	6	3		3	BEND3	6	107390745	Silent	SNP	A	TCGA-Y8-A8RY-01A-11D-A36X-10	42986093	107390745	63724322	31	17784											
TTYH3	80727	hgsc.bcm.edu	37	chr7	2686778	2686778	+	Frame_Shift_Del	DEL	C	C	-																															cgggcccgccctctccagcgCcggcatcgcagtgggattct																										TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr7:2686778delC	ENST00000258796.7	+	3	501	c.296delC	c.(295-297)gccfs	p.A99fs	TTYH3_ENST00000403167.1_5'Flank|TTYH3_ENST00000407643.1_Frame_Shift_Del_p.A99fs	NM_025250.2	NP_079526.1	Q9C0H2	TTYH3_HUMAN	tweety family member 3	99					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|intracellular calcium activated chloride channel activity (GO:0005229)			kidney(1)|large_intestine(3)|lung(9)|prostate(2)|upper_aerodigestive_tract(2)	17		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.04e-14)		CTCTCCAGCGCCGGCATCGCA	0.731																																					p.A99fs		Atlas-Indel,Pindel	.											.	TTYH3	36	.	0			c.295delG						PASS	.						13	16	15					7																	2686778		2173	4284	6457	SO:0001589	frameshift_variant	80727	exon3			.		CCDS34588.1	7p22	2013-09-02	2013-09-02		ENSG00000136295	ENSG00000136295			22222	protein-coding gene	gene with protein product		608919	"tweety homolog 3 (Drosophila)"				Standard	NM_025250		Approved	KIAA1691	uc003smp.3	Q9C0H2	OTTHUMG00000152050	ENST00000258796.7:c.296delC	chr7.hg19:g.2686778delC	ENSP00000258796:p.Ala99fs	54.0	0.0	0		74.0	40.0	0.540541	NM_025250	A4D201|B7WP98|Q6L749|Q6ZVG3|Q8TEG6	Frame_Shift_Del	DEL	ENST00000258796.7	hg19	CCDS34588.1																																																																																			.	.	.	none		0.731	TTYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325082.2	XM_166523		-	2686778	C	-	2686778	7	5	279	1	0	1	0	1	0	0	0	0	16753	739	26	0	306	0	TTYH3	7	2686778	Frame_Shift_Del	DEL	C	TCGA-Y8-A8RY-01A-11D-A36X-10		2686778	156451885	32	17785											
ZSCAN21	7589	hgsc.bcm.edu	37	chr7	99661446	99661446	+	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	cccagcacgaggaatcagcaGatgagcagaaaggttctgaa	15	5	12	9	1	2	4	1	2	1	2	2	6	2	5	1	2	3	4	1	2	3	1			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr7:99661446G>T	ENST00000292450.4	+	4	792	c.628G>T	c.(628-630)Gat>Tat	p.D210Y	ZSCAN21_ENST00000456748.2_Missense_Mutation_p.D210Y|ZSCAN21_ENST00000477297.1_Intron|ZSCAN21_ENST00000543588.1_Missense_Mutation_p.D210Y	NM_145914.2	NP_666019.1	Q9Y5A6	ZSC21_HUMAN	zinc finger and SCAN domain containing 21	210					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)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|skin(1)	21	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			GGAATCAGCAGATGAGCAGAA	0.433																																					p.D210Y		Atlas-SNP	.											.	ZSCAN21	29	.	0			c.G628T						PASS	.						89	91	90					7																	99661446		2203	4300	6503	SO:0001583	missense	7589	exon4			TCAGCAGATGAGC	AL136865	CCDS5681.1	7q11.1	2013-01-08	2006-10-06	2006-10-06	ENSG00000166529	ENSG00000166529		"-", "Zinc fingers, C2H2-type"	13104	protein-coding gene	gene with protein product		601261	"zinc finger protein 38 (KOX 25)", "zinc finger protein 38"	ZNF38		2288909, 2014798	Standard	NM_145914		Approved	DKFZp434L134, NY-REN-21, Zipro1	uc003uso.3	Q9Y5A6	OTTHUMG00000154583	ENST00000292450.4:c.628G>T	chr7.hg19:g.99661446G>T	ENSP00000292450:p.Asp210Tyr	103.0	0.0	.		176.0	113.0	.	NM_145914	A4D2A6|D6W5T9|Q9H0B5	Missense_Mutation	SNP	ENST00000292450.4	hg19	CCDS5681.1	.	.	.	.	.	.	.	.	.	.	G	11.29	1.593776	0.28445	.	.	ENSG00000166529	ENST00000543588;ENST00000292450;ENST00000456748;ENST00000379635	T;T;T	0.05925	4.04;3.37;4.04	4.79	2.91	0.33838	.	0.353172	0.20787	N	0.085686	T	0.11196	0.0273	L	0.29908	0.895	0.27965	N	0.936625	P;D	0.76494	0.454;0.999	B;D	0.68943	0.259;0.961	T	0.03630	-1.1018	10	0.66056	D	0.02	.	5.8826	0.18864	0.1063:0.2119:0.6818:0.0	.	210;210	Q9Y5A6;G3V1M0	ZSC21_HUMAN;.	Y	210;210;210;185	ENSP00000441212:D210Y;ENSP00000292450:D210Y;ENSP00000390960:D210Y	ENSP00000292450:D210Y	D	+	1	0	ZSCAN21	99499382	0.175000	0.23083	1.000000	0.80357	0.157000	0.22087	0.687000	0.25407	1.249000	0.43950	-0.140000	0.14226	GAT	.	.	.	none		0.433	ZSCAN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336166.1	NM_145914		T	99661446	G	T	99661446	3	4	279	1	0	0	0	0	1	0	0	0	18245	942	33	4	638	4	ZSCAN21	7	99661446	Missense_Mutation	SNP	G	TCGA-Y8-A8RY-01A-11D-A36X-10	96974668	99661446	59477217	33	17786											
BRAF	673	hgsc.bcm.edu	37	chr7	140507811	140507811	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aacacttccacatgcaattcTtctccagtaagccaggaaat	14	10	5	12	0	2	0	0	0	2	0	4	1	3	1	3	1	3	2	3	1	4	4			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr7:140507811T>C	ENST00000288602.6	-	5	720	c.660A>G	c.(658-660)gaA>gaG	p.E220E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	220	RBD. {ECO:0000255|PROSITE- ProRule:PRU00262}.				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)	CATGCAATTCTTCTCCAGTAA	0.328		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.E220E	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.A660G						PASS	.						153	134	140					7																	140507811		2203	4300	6503	SO:0001819	synonymous_variant	673	exon5	Familial Cancer Database	CFC, CFCS	CAATTCTTCTCCA	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.660A>G	chr7.hg19:g.140507811T>C		80.0	0.0	.		126.0	29.0	.	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Silent	SNP	ENST00000288602.6	hg19	CCDS5863.1																																																																																			.	.	.	none		0.328	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		C	140507811	T	C	140507811	2	2	279	1	0	0	0	0	0	0	0	1	1498	1606	56	3		3	BRAF	7	140507811	Silent	SNP	T	TCGA-Y8-A8RY-01A-11D-A36X-10	40846365	140507811	18630852	34	17787											
DUSP4	1846	hgsc.bcm.edu	37	chr8	29197704	29197704	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgggggtgggatggctgccaGggccttggttttagaacaga	7	9	18	7	1	0	2	0	0	0	2	0	3	0	3	2	6	2	2	2	6	2	3			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr8:29197704G>A	ENST00000240100.2	-	2	879	c.490C>T	c.(490-492)Ctg>Ttg	p.L164L	DUSP4_ENST00000240101.2_Silent_p.L73L	NM_001394.6	NP_001385.1	Q13115	DUS4_HUMAN	dual specificity phosphatase 4	164					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)		ATGGCTGCCAGGGCCTTGGTT	0.582											OREG0018686	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L164L		Atlas-SNP	.											.	DUSP4	58	.	0			c.C490T						PASS	.						22	28	26					8																	29197704		2203	4300	6503	SO:0001819	synonymous_variant	1846	exon2			CTGCCAGGGCCTT	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.490C>T	chr8.hg19:g.29197704G>A		56.0	0.0	.	807	55.0	22.0	.	NM_001394	B2RBU5|D3DSU4|G5E930|Q13524	Silent	SNP	ENST00000240100.2	hg19	CCDS6072.1																																																																																			.	.	.	none		0.582	DUSP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257249.1	NM_001394		A	29197704	G	A	29197704	2	1	279	1	0	0	0	0	0	0	0	1	4829	991	35	2		2	DUSP4	8	29197704	Silent	SNP	G	TCGA-Y8-A8RY-01A-11D-A36X-10		29197704	117166318	35	17788											
NCOA2	10499	hgsc.bcm.edu	37	chr8	71068654	71068654	+	Frame_Shift_Del	DEL	G	G	-																															gcgagggctccatctgatcaGatttggtggtcagcagctgc																										TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr8:71068654delG	ENST00000452400.2	-	11	2127	c.1946delC	c.(1945-1947)tctfs	p.S649fs	NCOA2_ENST00000524223.1_5'UTR	NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	649					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)			CATCTGATCAGATTTGGTGGT	0.567			T	"RUNXBP2, HEY1"	"AML, Chondrosarcoma"																																p.S649fs		Atlas-Indel,Pindel	.		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	.	NCOA2	147	.	0			c.1947delT						PASS	.						93	92	92					8																	71068654		2000	4181	6181	SO:0001589	frameshift_variant	10499	exon11			.	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.1946delC	chr8.hg19:g.71068654delG	ENSP00000399968:p.Ser649fs	75.0	0.0	0		54.0	27.0	0.5	NM_006540	Q14CD2	Frame_Shift_Del	DEL	ENST00000452400.2	hg19	CCDS47872.1																																																																																			.	.	.	none		0.567	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1			-	71068654	G	-	71068654	7	5	279	1	0	1	0	1	0	0	0	0	10236	942	33	0	2500	0	NCOA2	8	71068654	Frame_Shift_Del	DEL	G	TCGA-Y8-A8RY-01A-11D-A36X-10	41870950	71068654	75295368	36	17789											
VPS13B	157680	hgsc.bcm.edu	37	chr8	100836128	100836128	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attcagattgaagacaagacTacaataatcaataatacacc	20	9	4	8	0	2	4	2	1	0	3	2	4	2	4	1	0	2	0	1	0	8	6			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr8:100836128T>C	ENST00000358544.2	+	51	9438	c.9327T>C	c.(9325-9327)acT>acC	p.T3109T	VPS13B_ENST00000395996.1_3'UTR|VPS13B_ENST00000357162.2_Silent_p.T3084T	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	3109					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)			AAGACAAGACTACAATAATCA	0.323																																					p.T3109T	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.T9327C						PASS	.						161	166	165					8																	100836128		2203	4297	6500	SO:0001819	synonymous_variant	157680	exon51			CAAGACTACAATA	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.9327T>C	chr8.hg19:g.100836128T>C		66.0	0.0	.		80.0	35.0	.	NM_017890	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Silent	SNP	ENST00000358544.2	hg19	CCDS6280.1																																																																																			.	.	.	none		0.323	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		C	100836128	T	C	100836128	2	2	279	1	0	0	0	0	0	0	0	1	17202	1509	53	3		3	VPS13B	8	100836128	Silent	SNP	T	TCGA-Y8-A8RY-01A-11D-A36X-10	29767474	100836128	45527894	37	17790											
GPSM1	26086	hgsc.bcm.edu	37	chr9	139231429	139231429	+	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	ggaacgtgtaccacgccaaaGgcaagcaactgtcctggaac	13	5	11	12	2	0	0	0	0	0	0	1	2	1	2	3	3	5	3	3	3	6	1			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr9:139231429G>T	ENST00000440944.1	+	4	698	c.478G>T	c.(478-480)Ggc>Tgc	p.G160C	GPSM1_ENST00000392945.3_Missense_Mutation_p.G160C	NM_001145638.1	NP_001139110	Q86YR5	GPSM1_HUMAN	G-protein signaling modulator 1	160	Mediates association with membranes. {ECO:0000250}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GDP-dissociation inhibitor activity (GO:0005092)			biliary_tract(1)|endometrium(1)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)		CCACGCCAAAGGCAAGCAACT	0.662																																					p.G160C		Atlas-SNP	.											.	GPSM1	50	.	0			c.G478T						PASS	.						61	50	54					9																	139231429		2163	4259	6422	SO:0001583	missense	26086	exon4			GCCAAAGGCAAGC	AI272212	CCDS6996.2, CCDS48055.1, CCDS48056.1	9q34.3	2013-01-10	2010-06-24		ENSG00000160360	ENSG00000160360		"Tetratricopeptide (TTC) repeat domain containing"	17858	protein-coding gene	gene with protein product	"AGS3 homolog (C. elegans)"	609491	"G-protein signalling modulator 1 (AGS3-like, C. elegans)"			11278352, 10969064	Standard	NM_001145639		Approved	AGS3, DKFZP727I051	uc004chd.2	Q86YR5	OTTHUMG00000020930	ENST00000440944.1:c.478G>T	chr9.hg19:g.139231429G>T	ENSP00000392828:p.Gly160Cys	142.0	0.0	.		107.0	49.0	.	NM_015597	A9Z1X4|B1B0W3|Q86SR5|Q969T1|Q9UFS8	Missense_Mutation	SNP	ENST00000440944.1	hg19	CCDS48055.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.802739	0.90623	.	.	ENSG00000160360	ENST00000392945;ENST00000440944;ENST00000354753	D;D;D	0.97016	-4.21;-4.21;-4.21	3.94	3.94	0.45596	Tetratricopeptide-like helical (1);	0.135266	0.48767	U	0.000165	D	0.98845	0.9610	H	0.98027	4.13	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99346	1.0913	10	0.87932	D	0	-36.4254	15.833	0.78773	0.0:0.0:1.0:0.0	.	160;160	Q86YR5;Q86YR5-3	GPSM1_HUMAN;.	C	160;160;137	ENSP00000376674:G160C;ENSP00000392828:G160C;ENSP00000346797:G137C	ENSP00000346797:G137C	G	+	1	0	GPSM1	138351250	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.573000	0.98181	2.122000	0.65172	0.563000	0.77884	GGC	.	.	.	none		0.662	GPSM1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015597		T	139231429	G	T	139231429	3	4	279	1	0	0	0	0	1	0	0	0	6741	1000	35	4	492	4	GPSM1	9	139231429	Missense_Mutation	SNP	G	TCGA-Y8-A8RY-01A-11D-A36X-10		139231429	1982002	38	17791											
ANKRD16	54522	hgsc.bcm.edu	37	chr10	5922267	5922267	+	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	aaattaaacggtacctgatcGatttttttcatctttagaat	13	17	5	6	2	2	2	1	1	1	1	3	3	2	2	1	1	2	1	1	1	6	7			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr10:5922267G>A	ENST00000380094.5	-	6	1465	c.922C>T	c.(922-924)Cga>Tga	p.R308*	ANKRD16_ENST00000191063.8_Intron|ANKRD16_ENST00000380092.4_Nonsense_Mutation_p.R308*	NM_019046.2	NP_061919.1	Q6P6B7	ANR16_HUMAN	ankyrin repeat domain 16	308								p.R308*(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(3)|stomach(2)	12						GTACCTGATCGATTTTTTTCA	0.294																																					p.R308X		Atlas-SNP	.											ANKRD16,NS,carcinoma,0,2	ANKRD16	32	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C922T						PASS	.						77	75	76					10																	5922267		2203	4300	6503	SO:0001587	stop_gained	54522	exon6			CTGATCGATTTTT	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.922C>T	chr10.hg19:g.5922267G>A	ENSP00000369436:p.Arg308*	69.0	0.0	.		38.0	19.0	.	NM_001009941	A6NEF0|F8WEI4|Q9NT01	Nonsense_Mutation	SNP	ENST00000380094.5	hg19	CCDS31136.1	.	.	.	.	.	.	.	.	.	.	G	40	8.179958	0.98693	.	.	ENSG00000134461	ENST00000380094;ENST00000380092	.	.	.	4.41	4.41	0.53225	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.17369	T	0.5	-5.1798	10.9767	0.47469	0.0:0.0:0.813:0.187	.	.	.	.	X	308	.	ENSP00000369434:R308X	R	-	1	2	ANKRD16	5962273	1.000000	0.71417	1.000000	0.80357	0.754000	0.42855	3.339000	0.52135	2.023000	0.59567	0.478000	0.44815	CGA	.	.	.	none		0.294	ANKRD16-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046611.2	XM_166138		A	5922267	G	A	5922267	4	1	279	1	0	0	0	0	0	1	0	0	645	1066	37	1	171	1	ANKRD16	10	5922267	Nonsense_Mutation	SNP	G	TCGA-Y8-A8RY-01A-11D-A36X-10		5922267	129612480	39	17792											
KNDC1	85442	hgsc.bcm.edu	37	chr10	135012281	135012281	+	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	tgcagcgtgactcagcccagGgccgcccctgccctccaccc	5	5	10	21	2	1	1	1	1	0	0	2	1	2	1	7	1	4	1	7	1	0	0			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr10:135012281G>A	ENST00000304613.3	+	14	2290	c.2269G>A	c.(2269-2271)Ggc>Agc	p.G757S	KNDC1_ENST00000368572.2_Missense_Mutation_p.G757S|KNDC1_ENST00000368571.2_Missense_Mutation_p.G692S			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	757	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)		CTCAGCCCAGGGCCGCCCCTG	0.736																																					p.G757S		Atlas-SNP	.											.	KNDC1	155	.	0			c.G2269A						PASS	.						5	8	7					10																	135012281		2096	4169	6265	SO:0001583	missense	85442	exon14			GCCCAGGGCCGCC	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.2269G>A	chr10.hg19:g.135012281G>A	ENSP00000304437:p.Gly757Ser	91.0	0.0	.		74.0	20.0	.	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	hg19	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	G	16.33	3.092782	0.56075	.	.	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.20200	2.61;2.61;2.09	4.0	4.0	0.46444	.	0.312106	0.24429	U	0.038609	T	0.32912	0.0845	L	0.50333	1.59	0.09310	N	1	D;P;B	0.61697	0.99;0.944;0.421	P;P;B	0.58721	0.844;0.548;0.086	T	0.05354	-1.0890	10	0.41790	T	0.15	-6.823	11.9945	0.53194	0.0:0.0:1.0:0.0	.	757;692;757	Q76NI1-4;Q76NI1-2;Q76NI1	.;.;VKIND_HUMAN	S	757;757;692	ENSP00000304437:G757S;ENSP00000357561:G757S;ENSP00000357560:G692S	ENSP00000304437:G757S	G	+	1	0	KNDC1	134862271	0.033000	0.19621	0.010000	0.14722	0.175000	0.22909	0.981000	0.29526	1.954000	0.56735	0.306000	0.20318	GGC	.	.	.	none		0.736	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		A	135012281	G	A	135012281	3	1	279	1	0	0	0	0	1	0	0	0	8433	1232	43	2	2323	2	KNDC1	10	135012281	Missense_Mutation	SNP	G	TCGA-Y8-A8RY-01A-11D-A36X-10	129090014	135012281	522466	40	17793											
GTF2H1	2965	hgsc.bcm.edu	37	chr11	18382179	18382179	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taggtagtgaaaatgaaaagTaatttggaacgattccaagt	17	11	10	3	1	0	2	0	2	0	0	1	4	1	3	1	2	1	2	1	2	9	5			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr11:18382179T>C	ENST00000265963.4	+	14	1645	c.1485T>C	c.(1483-1485)agT>agC	p.S495S	GTF2H1_ENST00000534641.1_Silent_p.S379S|GTF2H1_ENST00000453096.2_Silent_p.S495S|GTF2H1_ENST00000526630.2_Silent_p.S85S|GTF2H1_ENST00000530496.2_Silent_p.S183S	NM_005316.3	NP_005307.1	P32780	TF2H1_HUMAN	general transcription factor IIH, polypeptide 1, 62kDa	495					7-methylguanosine mRNA capping (GO:0006370)|ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|gene expression (GO:0010467)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	core TFIIH complex (GO:0000439)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	20						AAATGAAAAGTAATTTGGAAC	0.343								Nucleotide excision repair (NER)																													p.S495S		Atlas-SNP	.											.	GTF2H1	35	.	0			c.T1485C						PASS	.						77	83	81					11																	18382179		2199	4293	6492	SO:0001819	synonymous_variant	2965	exon15			GAAAAGTAATTTG		CCDS7838.1	11p15.1-p14	2012-11-05	2002-08-29		ENSG00000110768	ENSG00000110768		"General transcription factors", "General transcription factor IIH complex subunits"	4655	protein-coding gene	gene with protein product		189972	"general transcription factor IIH, polypeptide 1 (62kD subunit)"			1529339, 8162052	Standard	NM_005316		Approved	BTF2, P62, TFIIH	uc001moh.2	P32780	OTTHUMG00000167690	ENST00000265963.4:c.1485T>C	chr11.hg19:g.18382179T>C		66.0	0.0	.		44.0	17.0	.	NM_001142307	B3KXE0|D3DQY2|Q6I9Y7|Q9H5K5|Q9NQD9	Silent	SNP	ENST00000265963.4	hg19	CCDS7838.1																																																																																			.	.	.	none		0.343	GTF2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395627.2	NM_005316		C	18382179	T	C	18382179	2	2	279	1	0	0	0	0	0	0	0	1	6867	1635	57	3		3	GTF2H1	11	18382179	Silent	SNP	T	TCGA-Y8-A8RY-01A-11D-A36X-10		18382179	116624337	41	17794											
DAGLA	747	hgsc.bcm.edu	37	chr11	61490356	61490356	+	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	ctggtgatcgagttcatctaCgccatcgtgggcatcgtctg	6	12	12	11	4	3	1	1	1	2	0	6	2	3	1	1	2	1	2	1	2	1	2	rs374808753		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr11:61490356C>T	ENST00000257215.5	+	4	449	c.333C>T	c.(331-333)taC>taT	p.Y111Y		NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	111					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)		AGTTCATCTACGCCATCGTGG	0.607																																					p.Y111Y		Atlas-SNP	.											.	DAGLA	109	.	0			c.C333T						PASS	.	C		1,4403	2.1+/-5.4	0,1,2201	248	163	192		333	-6.6	0.7	11		192	0,8598		0,0,4299	no	coding-synonymous	DAGLA	NM_006133.2		0,1,6500	TT,TC,CC		0.0,0.0227,0.0077		111/1043	61490356	1,13001	2202	4299	6501	SO:0001819	synonymous_variant	747	exon4			CATCTACGCCATC	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.333C>T	chr11.hg19:g.61490356C>T		85.0	0.0	.		67.0	27.0	.	NM_006133	A7E233|Q6WQJ0	Silent	SNP	ENST00000257215.5	hg19	CCDS31578.1																																																																																			.	.	.	weak		0.607	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133		T	61490356	C	T	61490356	2	4	279	1	0	0	0	0	0	0	0	1	4228	547	19	1		1	DAGLA	11	61490356	Silent	SNP	C	TCGA-Y8-A8RY-01A-11D-A36X-10	43108177	61490356	73516160	42	17795											
INPPL1	3636	hgsc.bcm.edu	37	chr11	71941503	71941503	+	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	cgcaaggacttcatctttgtCagtgcccgggtgagcagcag	8	9	13	11	2	3	1	2	1	1	0	3	2	3	2	1	2	3	3	1	2	1	2			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr11:71941503C>A	ENST00000298229.2	+	10	1392	c.1188C>A	c.(1186-1188)gtC>gtA	p.V396V	INPPL1_ENST00000538751.1_Silent_p.V154V|INPPL1_ENST00000541756.1_Silent_p.V154V	NM_001567.3	NP_001558.3	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	396					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						TCATCTTTGTCAGTGCCCGGG	0.582																																					p.V396V		Atlas-SNP	.											.	INPPL1	120	.	0			c.C1188A						PASS	.						78	77	77					11																	71941503		2200	4293	6493	SO:0001819	synonymous_variant	3636	exon10			CTTTGTCAGTGCC	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.1188C>A	chr11.hg19:g.71941503C>A		92.0	0.0	.		87.0	39.0	.	NM_001567	B2RTX5|Q13577|Q13578	Silent	SNP	ENST00000298229.2	hg19	CCDS8213.1																																																																																			.	.	.	none		0.582	INPPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396789.1	NM_001567		A	71941503	C	A	71941503	2	1	279	1	0	0	0	0	0	0	0	1	7768	813	29	4		4	INPPL1	11	71941503	Silent	SNP	C	TCGA-Y8-A8RY-01A-11D-A36X-10	10451147	71941503	63065013	43	17796											
FCHSD2	9873	hgsc.bcm.edu	37	chr11	72700036	72700036	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgatgtcagctttctctcgtActgcatgagccatctgttca	7	14	8	12	2	4	1	2	1	2	0	6	2	4	1	1	0	4	4	1	0	1	3			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr11:72700036A>G	ENST00000409418.4	-	6	877	c.494T>C	c.(493-495)gTa>gCa	p.V165A	FCHSD2_ENST00000409314.1_Missense_Mutation_p.V165A|FCHSD2_ENST00000458644.2_Missense_Mutation_p.V5A|FCHSD2_ENST00000311172.7_Missense_Mutation_p.V109A|FCHSD2_ENST00000409853.1_Missense_Mutation_p.V109A	NM_014824.2	NP_055639.2	O94868	FCSD2_HUMAN	FCH and double SH3 domains 2	165										endometrium(2)|large_intestine(11)|lung(5)|ovary(2)|prostate(1)|skin(1)	22			BRCA - Breast invasive adenocarcinoma(5;3.3e-05)			TTTCTCTCGTACTGCATGAGC	0.338																																					p.V165A		Atlas-SNP	.											.	FCHSD2	106	.	0			c.T494C						PASS	.						214	178	190					11																	72700036		2198	4290	6488	SO:0001583	missense	9873	exon6			TCTCGTACTGCAT	AB018312	CCDS8218.2	11q13.3	2008-02-05	2004-04-14	2004-04-16	ENSG00000137478	ENSG00000137478			29114	protein-coding gene	gene with protein product			"SH3 multiple domains 3"	SH3MD3		9872452, 15067381	Standard	NM_014824		Approved	KIAA0769	uc009ytl.3	O94868	OTTHUMG00000153082	ENST00000409418.4:c.494T>C	chr11.hg19:g.72700036A>G	ENSP00000386722:p.Val165Ala	94.0	0.0	.		78.0	31.0	.	NM_014824	B4DNI3|Q7L8J9|Q8WVM2|Q96FV7|Q9UF77	Missense_Mutation	SNP	ENST00000409418.4	hg19	CCDS8218.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.34|11.34	1.610376|1.610376	0.28712|0.28712	.|.	.|.	ENSG00000137478|ENSG00000137478	ENST00000311172;ENST00000409314;ENST00000409418;ENST00000458644;ENST00000409853|ENST00000543644	T;T;T;T;T|.	0.18502|.	3.13;3.13;3.13;2.21;3.13|.	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	0.124939|.	0.53938|.	D|.	0.000050|.	T|T	0.52041|0.52041	0.1710|0.1710	N|N	0.21324|0.21324	0.655|0.655	0.51233|0.51233	D|D	0.999913|0.999913	P;P;B|.	0.50066|.	0.931;0.792;0.075|.	B;B;B|.	0.41332|.	0.354;0.138;0.046|.	T|T	0.49273|0.49273	-0.8957|-0.8957	10|5	0.02654|.	T|.	1|.	-18.7119|-18.7119	14.7885|14.7885	0.69821|0.69821	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	5;165;109|.	E7ENZ2;O94868;O94868-3|.	.;FCSD2_HUMAN;.|.	A|H	109;165;165;5;109|8	ENSP00000308978:V109A;ENSP00000386987:V165A;ENSP00000386722:V165A;ENSP00000402972:V5A;ENSP00000386314:V109A|.	ENSP00000308978:V109A|.	V|Y	-|-	2|1	0|0	FCHSD2|FCHSD2	72377684|72377684	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.970000|0.970000	0.65996|0.65996	8.932000|8.932000	0.92897|0.92897	2.093000|2.093000	0.63338|0.63338	0.379000|0.379000	0.24179|0.24179	GTA|TAC	.	.	.	none		0.338	FCHSD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329429.2	NM_014824		G	72700036	A	G	72700036	3	3	279	1	0	0	0	0	1	0	0	0	5797	391	14	3	1788	3	FCHSD2	11	72700036	Missense_Mutation	SNP	A	TCGA-Y8-A8RY-01A-11D-A36X-10	758533	72700036	62306480	44	17797											
RSF1	51773	hgsc.bcm.edu	37	chr11	77412208	77412208	+	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	cagaaggctcctctatgccaGaggtctgggcattgtccaga	9	9	12	11	0	2	3	0	0	2	3	4	3	4	3	3	3	1	2	3	3	2	2			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr11:77412208G>T	ENST00000308488.6	-	6	2368	c.2066C>A	c.(2065-2067)tCt>tAt	p.S689Y	RSF1_ENST00000360355.2_Missense_Mutation_p.S658Y|RSF1_ENST00000480887.1_Missense_Mutation_p.S437Y			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	689					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)			CTCTATGCCAGAGGTCTGGGC	0.413																																					p.S689Y		Atlas-SNP	.											.	RSF1	105	.	0			c.C2066A						PASS	.						98	100	99					11																	77412208		2199	4291	6490	SO:0001583	missense	51773	exon6			ATGCCAGAGGTCT	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.2066C>A	chr11.hg19:g.77412208G>T	ENSP00000311513:p.Ser689Tyr	81.0	0.0	.		78.0	31.0	.	NM_016578	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Missense_Mutation	SNP	ENST00000308488.6	hg19	CCDS8253.1	.	.	.	.	.	.	.	.	.	.	G	4.376	0.069294	0.08436	.	.	ENSG00000048649	ENST00000308488;ENST00000480887;ENST00000360355;ENST00000526324;ENST00000528095	D;D;D;D;T	0.86769	-2.14;-2.14;-2.13;-2.17;0.95	5.23	3.22	0.36961	.	0.380726	0.23067	N	0.052308	T	0.80221	0.4583	L	0.27053	0.805	0.09310	N	1	D	0.56521	0.976	P	0.44732	0.459	T	0.73569	-0.3941	10	0.72032	D	0.01	-3.2478	10.3956	0.44198	0.0:0.2723:0.5869:0.1407	.	689	Q96T23	RSF1_HUMAN	Y	689;437;658;490;688	ENSP00000311513:S689Y;ENSP00000434509:S437Y;ENSP00000353511:S658Y;ENSP00000432022:S490Y;ENSP00000436408:S688Y	ENSP00000311513:S689Y	S	-	2	0	RSF1	77089856	0.469000	0.25846	0.312000	0.25196	0.045000	0.14185	2.914000	0.48797	1.399000	0.46721	0.655000	0.94253	TCT	.	.	.	none		0.413	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578		T	77412208	G	T	77412208	3	4	279	1	0	0	0	0	1	0	0	0	13712	942	33	4	2303	4	RSF1	11	77412208	Missense_Mutation	SNP	G	TCGA-Y8-A8RY-01A-11D-A36X-10	4712172	77412208	57594308	45	17798											
ATM	472	hgsc.bcm.edu	37	chr11	108213973	108213973	+	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	ttcccctctctcagcgaagtGgtgttcttgaatggtgcaca	7	13	10	11	1	3	1	1	1	2	0	5	2	4	1	2	2	2	2	2	2	2	3			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr11:108213973G>A	ENST00000452508.2	+	58	8482	c.8293G>A	c.(8293-8295)Ggt>Agt	p.G2765S	C11orf65_ENST00000526725.1_Intron|C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Missense_Mutation_p.G2765S			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2765	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		G -> S (may contribute to breast cancer). {ECO:0000269|PubMed:10534763}.		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)	TCAGCGAAGTGGTGTTCTTGA	0.398			"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.G2765S		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	.	ATM	1657	.	0			c.G8293A	GRCh37	CM994662	ATM	M		PASS	.						168	155	160					11																	108213973		2201	4298	6499	SO:0001583	missense	472	exon57	Familial Cancer Database	AT, Louis-Bar syndrome	CGAAGTGGTGTTC	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.8293G>A	chr11.hg19:g.108213973G>A	ENSP00000388058:p.Gly2765Ser	104.0	0.0	.		136.0	8.0	.	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	hg19	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	G	36	5.764800	0.96906	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	D;D	0.81659	-1.52;-1.52	5.56	5.56	0.83823	Protein kinase-like domain (1);Armadillo-type fold (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	D	0.93963	0.8067	H	0.97315	3.98	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95499	0.8576	10	0.87932	D	0	.	19.8788	0.96888	0.0:0.0:1.0:0.0	.	2765	Q13315	ATM_HUMAN	S	2765	ENSP00000278616:G2765S;ENSP00000388058:G2765S	ENSP00000278616:G2765S	G	+	1	0	ATM	107719183	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.391000	0.97249	2.779000	0.95612	0.561000	0.74099	GGT	.	.	.	none		0.398	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		A	108213973	G	A	108213973	3	1	279	1	0	0	0	0	1	0	0	0	1109	1348	47	2	8515	2	ATM	11	108213973	Missense_Mutation	SNP	G	TCGA-Y8-A8RY-01A-11D-A36X-10	30801765	108213973	26792543	46	17799											
DLAT	1737	hgsc.bcm.edu	37	chr11	111933142	111933142	+	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	ttttctaggtttgatgtggcTagcatgatgtctgttacact	7	18	10	6	0	2	2	0	2	2	0	2	2	2	2	0	2	2	4	0	2	3	6			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr11:111933142T>A	ENST00000280346.6	+	14	2486	c.1827T>A	c.(1825-1827)gcT>gcA	p.A609A	DLAT_ENST00000537636.1_Silent_p.A380A|DLAT_ENST00000393051.1_Silent_p.A504A	NM_001931.4	NP_001922.2	P10515	ODP2_HUMAN	dihydrolipoamide S-acetyltransferase	609	Catalytic. {ECO:0000250}.				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)		TTGATGTGGCTAGCATGATGT	0.423																																					p.A609A		Atlas-SNP	.											.	DLAT	39	.	0			c.T1827A						PASS	.						154	159	157					11																	111933142		2201	4297	6498	SO:0001819	synonymous_variant	1737	exon14			TGTGGCTAGCATG	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.1827T>A	chr11.hg19:g.111933142T>A		56.0	0.0	.		50.0	11.0	.	NM_001931	Q16783|Q53EP3	Silent	SNP	ENST00000280346.6	hg19	CCDS8354.1																																																																																			.	.	.	none		0.423	DLAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258167.1	NM_001931		A	111933142	T	A	111933142	2	1	279	1	0	0	0	0	0	0	0	1	4551	1509	53	5		5	DLAT	11	111933142	Silent	SNP	T	TCGA-Y8-A8RY-01A-11D-A36X-10	3719169	111933142	23073374	47	17800											
TMPRSS13	84000	hgsc.bcm.edu	37	chr11	117789218	117789218	+	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	ggtgttgctctaacaaggtaCactctggttggggaggttgt	7	13	15	6	0	2	0	0	0	2	0	2	1	2	1	0	6	3	5	0	6	3	5			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr11:117789218C>T	ENST00000430170.2	-	2	444	c.357G>A	c.(355-357)gtG>gtA	p.V119V	TMPRSS13_ENST00000528626.1_Silent_p.V119V|TMPRSS13_ENST00000524993.1_Silent_p.V119V|TMPRSS13_ENST00000445164.2_Silent_p.V119V|TMPRSS13_ENST00000526090.1_Silent_p.V119V	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	119						blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		TAACAAGGTACACTCTGGTTG	0.617																																					p.V119V		Atlas-SNP	.											.	TMPRSS13	75	.	0			c.G357A						PASS	.						80	91	87					11																	117789218		2096	4215	6311	SO:0001819	synonymous_variant	84000	exon2			AAGGTACACTCTG	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.357G>A	chr11.hg19:g.117789218C>T		112.0	0.0	.		89.0	40.0	.	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Silent	SNP	ENST00000430170.2	hg19	CCDS58185.1																																																																																			.	.	.	none		0.617	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046		T	117789218	C	T	117789218	2	4	279	1	0	0	0	0	0	0	0	1	16257	465	17	2		2	TMPRSS13	11	117789218	Silent	SNP	C	TCGA-Y8-A8RY-01A-11D-A36X-10	5856076	117789218	17217298	48	17801											
KIF21A	55605	hgsc.bcm.edu	37	chr12	39695383	39695383	+	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	ataaaagtatccatgttccaGactttcaaaatgccccctct	13	12	4	12	0	2	1	1	0	1	1	4	1	4	1	4	0	1	2	4	0	5	4	rs576774677		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr12:39695383G>C	ENST00000361418.5	-	37	4845	c.4830C>G	c.(4828-4830)gtC>gtG	p.V1610V	KIF21A_ENST00000544797.2_Silent_p.V1573V|KIF21A_ENST00000361961.3_Silent_p.V1597V|KIF21A_ENST00000541463.2_Silent_p.V1557V|KIF21A_ENST00000395670.3_Silent_p.V1611V			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	1610					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)				CCATGTTCCAGACTTTCAAAA	0.478													G|||	1	0.000199681	0	0	5008	,	,		16506	0		0	False		,,,				2504	0.001				p.V1610V		Atlas-SNP	.											.	KIF21A	238	.	0			c.C4830G						PASS	.						153	158	156					12																	39695383		2203	4300	6503	SO:0001819	synonymous_variant	55605	exon37			GTTCCAGACTTTC	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.4830C>G	chr12.hg19:g.39695383G>C		226.0	1.0	.		243.0	123.0	.	NM_001173464	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Silent	SNP	ENST00000361418.5	hg19	CCDS53776.1	.	.	.	.	.	.	.	.	.	.	G	8.051	0.766015	0.15983	.	.	ENSG00000139116	ENST00000552961	.	.	.	4.71	0.618	0.17624	.	.	.	.	.	T	0.51058	0.1652	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35025	-0.9805	4	.	.	.	.	5.3056	0.15801	0.2279:0.277:0.4952:0.0	.	.	.	.	C	911	.	.	S	-	2	0	KIF21A	37981650	0.996000	0.38824	0.987000	0.45799	0.989000	0.77384	0.321000	0.19558	-0.055000	0.13244	-0.145000	0.13849	TCT	.	.	.	none		0.478	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641		C	39695383	G	C	39695383	2	2	279	1	0	0	0	0	0	0	0	1	8295	929	33	4		4	KIF21A	12	39695383	Silent	SNP	G	TCGA-Y8-A8RY-01A-11D-A36X-10		39695383	94156512	49	17802											
GXYLT1	283464	hgsc.bcm.edu	37	chr12	42538257	42538295	+	In_Frame_Del	DEL	GCCCGCGACGCCGGCGCCTCTCACGGCGCCGCGTCCGCC	GCCCGCGACGCCGGCGCCTCTCACGGCGCCGCGTCCGCC	-																															acgccgggatgcgctgcgggGcccgcgacgccggcgcctct																								rs549907912|rs560905337	byFrequency	TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	GCCCGCGACGCCGGCGCCTCTCACGGCGCCGCGTCCGCC	GCCCGCGACGCCGGCGCCTCTCACGGCGCCGCGTCCGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr12:42538257_42538295delGCCCGCGACGCCGGCGCCTCTCACGGCGCCGCGTCCGCC	ENST00000398675.3	-	1	386_424	c.154_192delGGCGGACGCGGCGCCGTGAGAGGCGCCGGCGTCGCGGGC	c.(154-192)ggcggacgcggcgccgtgagaggcgccggcgtcgcgggcdel	p.GGRGAVRGAGVAG52del	GXYLT1_ENST00000280876.6_In_Frame_Del_p.GGRGAVRGAGVAG52del	NM_001099650.1|NM_173601.1	NP_001093120.1|NP_775872.1	Q4G148	GXLT1_HUMAN	glucoside xylosyltransferase 1	52					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|O-glycan processing (GO:0016266)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	UDP-xylosyltransferase activity (GO:0035252)			kidney(2)|large_intestine(4)|liver(3)|lung(8)	17						GCGCTGCGGGGCCCGCGACGCCGGCGCCTCTCACGGCGCCGCGTCCGCCGCCCGCGAGC	0.778														45	0.00898562	0.0272	0.0029	5008	,	,		10151	0.001		0.005	False		,,,				2504	0.001				p.52_65del		Pindel	.											.	GXYLT1	47	.	0			c.155_193del						PASS	.																																			SO:0001651	inframe_deletion	283464	exon1			.	BC015597	CCDS41771.1, CCDS41772.1	12q12	2013-10-11	2009-11-17	2009-11-17	ENSG00000151233	ENSG00000151233		"Glycosyltransferase family 8 domain containing"	27482	protein-coding gene	gene with protein product		613321	"glycosyltransferase 8 domain containing 3"	GLT8D3		19940119	Standard	NM_001099650		Approved	FLJ43151	uc001rms.4	Q4G148	OTTHUMG00000169379	ENST00000398675.3:c.154_192delGGCGGACGCGGCGCCGTGAGAGGCGCCGGCGTCGCGGGC	chr12.hg19:g.42538257_42538295delGCCCGCGACGCCGGCGCCTCTCACGGCGCCGCGTCCGCC	ENSP00000381666:p.Gly52_Gly64del	7.0	0.0	.		8.0	11.0	1.375	NM_001099650	B3KWJ2|Q8IXV1|Q96BH4	In_Frame_Del	DEL	ENST00000398675.3	hg19	CCDS41772.1																																																																																			.	.	.	none		0.778	GXYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403778.1	XM_290597		-	42538295	GCCCGCGACGCCGGCGCCTCTCACGGCGCCGCGTCCGCC	-	42538257	7	5	279	1	0	1	0	1	0	0	0	0	6910	1190	42	0	1162	0	GXYLT1	12	42538257	In_Frame_Del	DEL	GCCCGCGACGCCGGCGCCTCTCACGGCGCCGCGTCCGCC	TCGA-Y8-A8RY-01A-11D-A36X-10	2842874	42538257	91313638	50	17803											
HDAC7	51564	hgsc.bcm.edu	37	chr12	48181543	48181543	+	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	ccatgggggggtccagacctCcagcccaggccacattgaca	9	5	12	15	0	0	2	0	1	0	1	2	2	2	2	6	4	1	0	6	4	0	1			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr12:48181543C>G	ENST00000427332.2	-	21	2444	c.2288G>C	c.(2287-2289)gGa>gCa	p.G763A	HDAC7_ENST00000354334.3_Missense_Mutation_p.G765A|HDAC7_ENST00000080059.7_Missense_Mutation_p.G802A|HDAC7_ENST00000552960.1_Missense_Mutation_p.G785A|HDAC7_ENST00000488927.1_5'Flank|HDAC7_ENST00000380610.4_Missense_Mutation_p.G819A			Q8WUI4	HDAC7_HUMAN	histone deacetylase 7	763	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)		GTCCAGACCTCCAGCCCAGGC	0.617																																					p.G802A		Atlas-SNP	.											.	HDAC7	71	.	0			c.G2405C						PASS	.						30	32	31					12																	48181543		2201	4300	6501	SO:0001583	missense	51564	exon21			AGACCTCCAGCCC	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.2288G>C	chr12.hg19:g.48181543C>G	ENSP00000404394:p.Gly763Ala	151.0	0.0	.		134.0	68.0	.	NM_015401	B3KY08|B4DWI0|B4E0Q5|Q6P1W9|Q6W9G7|Q7Z4K2|Q7Z5I1|Q96K01|Q9BR73|Q9H7L0|Q9NW41|Q9NWA9|Q9NYK9|Q9UFU7	Missense_Mutation	SNP	ENST00000427332.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.8|26.8	4.771508|4.771508	0.90108|0.90108	.|.	.|.	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	4.97|4.97	4.97|4.97	0.65823|0.65823	.|Histone deacetylase domain (2);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.73552|0.73552	0.3601|0.3601	L|L	0.35644|0.35644	1.08|1.08	0.80722|0.80722	D|D	1|1	.|D;P;P;D	.|0.63046	.|0.971;0.918;0.955;0.992	.|P;P;P;P	.|0.62649	.|0.786;0.516;0.809;0.905	T|T	0.76575|0.76575	-0.2909|-0.2909	5|10	.|0.72032	.|D	.|0.01	.|.	17.2281|17.2281	0.86977|0.86977	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|763;802;785;765	.|Q8WUI4;Q8WUI4-5;Q8WUI4-6;Q8WUI4-7	.|HDAC7_HUMAN;.;.;.	Q|A	195|802;765;785;819;763	.|ENSP00000080059:G802A;ENSP00000351326:G765A;ENSP00000448532:G785A;ENSP00000369984:G819A;ENSP00000404394:G763A	.|ENSP00000080059:G802A	E|G	-|-	1|2	0|0	HDAC7|HDAC7	46467810|46467810	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.988000|0.988000	0.76386|0.76386	6.037000|6.037000	0.70956|0.70956	2.487000|2.487000	0.83934|0.83934	0.485000|0.485000	0.47835|0.47835	GAG|GGA	.	.	.	none		0.617	HDAC7-013	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000328804.2			G	48181543	C	G	48181543	3	3	279	1	0	0	0	0	1	0	0	0	7019	855	30	4	594	4	HDAC7	12	48181543	Missense_Mutation	SNP	C	TCGA-Y8-A8RY-01A-11D-A36X-10	5643286	48181543	85670352	51	17804											
NAA16	79612	hgsc.bcm.edu	37	chr13	41936177	41936177	+	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	tccatttcaggaaggaacatCtgccatggaaaatctaaatg	15	10	8	8	0	3	0	1	0	2	0	4	3	4	3	2	3	2	0	2	3	6	2			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr13:41936177C>T	ENST00000379406.3	+	13	1745	c.1421C>T	c.(1420-1422)tCt>tTt	p.S474F	NAA16_ENST00000379367.3_Missense_Mutation_p.S474F	NM_024561.4	NP_078837.3	Q6N069	NAA16_HUMAN	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	474					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						GAAGGAACATCTGCCATGGAA	0.388																																					p.S474F		Atlas-SNP	.											.	NAA16	74	.	0			c.C1421T						PASS	.						101	99	100					13																	41936177		2203	4300	6503	SO:0001583	missense	79612	exon13			GAACATCTGCCAT	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.1421C>T	chr13.hg19:g.41936177C>T	ENSP00000368716:p.Ser474Phe	65.0	0.0	.		63.0	22.0	.	NM_024561	B0QZ59|Q5VSP9|Q6P2D5|Q8N5J3|Q8N870	Missense_Mutation	SNP	ENST00000379406.3	hg19	CCDS9379.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.028782	0.75504	.	.	ENSG00000172766	ENST00000379367;ENST00000379406	T;T	0.47869	0.83;0.83	5.26	5.26	0.73747	Tetratricopeptide-like helical (1);	0.076588	0.56097	D	0.000030	T	0.71384	0.3333	M	0.81497	2.545	0.58432	D	0.999999	D	0.69078	0.997	D	0.71414	0.973	T	0.74907	-0.3504	10	0.66056	D	0.02	-13.9844	19.2111	0.93755	0.0:1.0:0.0:0.0	.	474	Q6N069	NAA16_HUMAN	F	474	ENSP00000368674:S474F;ENSP00000368716:S474F	ENSP00000368674:S474F	S	+	2	0	NAA16	40834177	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.307000	0.78920	2.623000	0.88846	0.655000	0.94253	TCT	.	.	.	none		0.388	NAA16-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044672.2	NM_018527		T	41936177	C	T	41936177	3	4	279	1	0	0	0	0	1	0	0	0	10126	913	32	2	1504	2	NAA16	13	41936177	Missense_Mutation	SNP	C	TCGA-Y8-A8RY-01A-11D-A36X-10		41936177	73233701	52	17805											
DCT	1638	hgsc.bcm.edu	37	chr13	95121020	95121020	+	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	ctaataatgtatctctaacaGaataataatggagccacaca	18	10	5	8	0	1	1	0	0	1	1	2	2	1	2	1	1	2	1	1	1	7	6			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr13:95121020G>A	ENST00000377028.5	-	2	988	c.575C>T	c.(574-576)tCt>tTt	p.S192F	DCT_ENST00000446125.1_Missense_Mutation_p.S192F|DCT_ENST00000490854.1_5'Flank	NM_001922.3	NP_001913.2	P40126	TYRP2_HUMAN	dopachrome tautomerase	192					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)		ATCTCTAACAGAATAATAATG	0.438																																					p.S192F		Atlas-SNP	.											.	DCT	186	.	0			c.C575T						PASS	.						102	107	105					13																	95121020		2203	4300	6503	SO:0001583	missense	1638	exon2			CTAACAGAATAAT	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.575C>T	chr13.hg19:g.95121020G>A	ENSP00000366227:p.Ser192Phe	54.0	0.0	.		44.0	17.0	.	NM_001129889	Q09GT4	Missense_Mutation	SNP	ENST00000377028.5	hg19	CCDS9470.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.782531	0.90282	.	.	ENSG00000080166	ENST00000377028;ENST00000446125	D;D	0.98792	-5.14;-5.14	5.69	5.69	0.88448	Tyrosinase (1);Uncharacterised domain, di-copper centre (2);	0.000000	0.85682	D	0.000000	D	0.99045	0.9673	M	0.71206	2.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.99869	1.1094	10	0.62326	D	0.03	-23.5448	19.8199	0.96589	0.0:0.0:1.0:0.0	.	192;192	Q09GT4;P40126	.;TYRP2_HUMAN	F	192	ENSP00000366227:S192F;ENSP00000392762:S192F	ENSP00000366227:S192F	S	-	2	0	DCT	93919021	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.476000	0.97823	2.677000	0.91161	0.655000	0.94253	TCT	.	.	.	none		0.438	DCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045461.3			A	95121020	G	A	95121020	3	1	279	1	0	0	0	0	1	0	0	0	4306	942	33	2	1119	2	DCT	13	95121020	Missense_Mutation	SNP	G	TCGA-Y8-A8RY-01A-11D-A36X-10	53184843	95121020	20048858	53	17806											
COL4A2	1284	hgsc.bcm.edu	37	chr13	111082947	111082947	+	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	gggtccagttggagctccagGgagaccagtaagtacctgga	10	7	15	9	0	0	1	0	0	0	1	2	4	2	3	4	4	2	4	4	4	2	3			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr13:111082947G>A	ENST00000360467.5	+	10	947	c.641G>A	c.(640-642)gGg>gAg	p.G214E	COL4A2_ENST00000462309.1_3'UTR	NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	214	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)			GGAGCTCCAGGGAGACCAGTA	0.567																																					p.G214E		Atlas-SNP	.											.	COL4A2	178	.	0			c.G641A						PASS	.						90	94	93					13																	111082947		1911	4118	6029	SO:0001583	missense	1284	exon10			CTCCAGGGAGACC	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.641G>A	chr13.hg19:g.111082947G>A	ENSP00000353654:p.Gly214Glu	145.0	0.0	.		100.0	45.0	.	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Missense_Mutation	SNP	ENST00000360467.5	hg19	CCDS41907.1	.	.	.	.	.	.	.	.	.	.	G	17.23	3.336498	0.60963	.	.	ENSG00000134871	ENST00000360467;ENST00000257309	D	0.99353	-5.77	5.28	4.44	0.53790	.	0.119241	0.37530	N	0.002060	D	0.99190	0.9719	H	0.97265	3.97	0.80722	D	1	P	0.36974	0.576	B	0.39706	0.307	D	0.98740	1.0716	10	0.87932	D	0	.	11.9483	0.52940	0.0805:0.0:0.9195:0.0	.	214	P08572	CO4A2_HUMAN	E	214	ENSP00000353654:G214E	ENSP00000257309:G214E	G	+	2	0	COL4A2	109880948	1.000000	0.71417	0.780000	0.31762	0.927000	0.56198	6.287000	0.72671	1.215000	0.43411	0.650000	0.86243	GGG	.	.	.	none		0.567	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846		A	111082947	G	A	111082947	3	1	279	1	0	0	0	0	1	0	0	0	3692	1232	43	2	675	2	COL4A2	13	111082947	Missense_Mutation	SNP	G	TCGA-Y8-A8RY-01A-11D-A36X-10	15961927	111082947	4086931	54	17807											
PELI2	57161	hgsc.bcm.edu	37	chr14	56746403	56746403	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttattattaggctatcagcTgcaaaggtcaacacagtata	14	13	7	7	0	2	0	2	0	0	0	2	0	2	0	0	2	3	4	0	2	8	7			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr14:56746403T>C	ENST00000267460.4	+	3	503	c.217T>C	c.(217-219)Tgc>Cgc	p.C73R		NM_021255.2	NP_067078.1	Q9HAT8	PELI2_HUMAN	pellino E3 ubiquitin protein ligase family member 2	73	FHA; atypical.				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						GGCTATCAGCTGCAAAGGTCA	0.363																																					p.C73R		Atlas-SNP	.											.	PELI2	55	.	0			c.T217C						PASS	.						116	113	114					14																	56746403		2203	4300	6503	SO:0001583	missense	57161	exon3			ATCAGCTGCAAAG	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.217T>C	chr14.hg19:g.56746403T>C	ENSP00000267460:p.Cys73Arg	47.0	0.0	.		44.0	17.0	.	NM_021255	B2RDY5	Missense_Mutation	SNP	ENST00000267460.4	hg19	CCDS9726.1	.	.	.	.	.	.	.	.	.	.	T	10.43	1.348530	0.24426	.	.	ENSG00000139946	ENST00000267460	T	0.40225	1.04	4.84	3.66	0.41972	.	0.233454	0.51477	D	0.000086	T	0.24547	0.0595	N	0.11427	0.14	0.80722	D	1	B	0.22909	0.077	B	0.28139	0.086	T	0.05582	-1.0876	10	0.42905	T	0.14	-17.5883	9.3117	0.37910	0.2868:0.0:0.0:0.7132	.	73	Q9HAT8	PELI2_HUMAN	R	73	ENSP00000267460:C73R	ENSP00000267460:C73R	C	+	1	0	PELI2	55816156	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	0.741000	0.26202	0.937000	0.37394	0.455000	0.32223	TGC	.	.	.	none		0.363	PELI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276925.1			C	56746403	T	C	56746403	3	2	279	1	0	0	0	0	1	0	0	0	11729	1580	55	3	227	3	PELI2	14	56746403	Missense_Mutation	SNP	T	TCGA-Y8-A8RY-01A-11D-A36X-10		56746403	50603137	55	17808											
C14orf148	122945	hgsc.bcm.edu	37	chr14	77872299	77872299	+	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	ataggctttgctgacaaaatCtgttaattgcaactttgggc	11	14	9	7	0	1	1	0	1	1	0	1	1	1	1	0	2	3	4	0	2	5	5			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr14:77872299C>A	ENST00000380835.2	-	5	1028	c.862G>T	c.(862-864)Gat>Tat	p.D288Y		NM_001113475.2	NP_001106946.1	Q6NXP6	NXRD1_HUMAN	NADP-dependent oxidoreductase domain containing 1	288					proline biosynthetic process (GO:0006561)		pyrroline-5-carboxylate reductase activity (GO:0004735)			NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	9						CTGACAAAATCTGTTAATTGC	0.458																																					p.D288Y		Atlas-SNP	.											.	NOXRED1	23	.	0			c.G862T						PASS	.						99	90	92					14																	77872299		1568	3582	5150	SO:0001583	missense	122945	exon5			CAAAATCTGTTAA	AK057371	CCDS45142.1	14q24.3	2011-09-30	2011-09-30	2011-09-30	ENSG00000165555	ENSG00000165555			20487	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 148"	C14orf148			Standard	NM_001113475		Approved	FLJ32809	uc001xtr.3	Q6NXP6	OTTHUMG00000171554	ENST00000380835.2:c.862G>T	chr14.hg19:g.77872299C>A	ENSP00000370215:p.Asp288Tyr	67.0	0.0	.		56.0	19.0	.	NM_001113475	B3KQ47|O95435	Missense_Mutation	SNP	ENST00000380835.2	hg19	CCDS45142.1	.	.	.	.	.	.	.	.	.	.	C	16.19	3.053689	0.55218	.	.	ENSG00000165555	ENST00000380835	T	0.58060	0.36	5.66	1.33	0.21861	.	0.389223	0.26446	N	0.024337	T	0.58779	0.2146	L	0.56769	1.78	0.30911	N	0.729061	D	0.61697	0.99	P	0.57009	0.811	T	0.62728	-0.6793	10	0.72032	D	0.01	-7.4072	9.5769	0.39463	0.1517:0.4074:0.4409:0.0	.	288	Q6NXP6	NXRD1_HUMAN	Y	288	ENSP00000370215:D288Y	ENSP00000370215:D288Y	D	-	1	0	C14orf148	76942052	0.233000	0.23772	0.081000	0.20488	0.896000	0.52359	0.741000	0.26202	0.267000	0.21916	0.460000	0.39030	GAT	.	.	.	none		0.458	NOXRED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414103.1	NM_138791		A	77872299	C	A	77872299	3	1	279	1	0	0	0	0	1	0	0	0	1753	913	32	4	225	4	C14orf148	14	77872299	Missense_Mutation	SNP	C	TCGA-Y8-A8RY-01A-11D-A36X-10	21125896	77872299	29477241	56	17809											
EIF2AK4	440275	hgsc.bcm.edu	37	chr15	40226434	40226434	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcccccgggcgcggccgggAcgagcctccggagagctacc	5	2	17	17	6	0	1	0	0	0	1	1	4	1	2	6	5	3	1	6	5	1	1			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr15:40226434A>G	ENST00000263791.5	+	1	81	c.38A>G	c.(37-39)gAc>gGc	p.D13G	EIF2AK4_ENST00000560648.1_Missense_Mutation_p.D13G|EIF2AK4_ENST00000382727.2_Missense_Mutation_p.D13G|EIF2AK4_ENST00000559624.1_Missense_Mutation_p.D13G	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	13					cellular response to starvation (GO:0009267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of translation (GO:0017148)|protein phosphorylation (GO:0006468)|regulation of translational initiation (GO:0006446)|regulation of translational initiation in response to stress (GO:0043558)	cytosolic ribosome (GO:0022626)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		cgcggccgggACGAGCCTCCG	0.756																																					p.D13G		Atlas-SNP	.											.	EIF2AK4	107	.	0			c.A38G						PASS	.						12	16	14					15																	40226434		1850	4077	5927	SO:0001583	missense	440275	exon1			GCCGGGACGAGCC	AB037759	CCDS42016.1	15q13.3	2008-08-18				ENSG00000128829			19687	protein-coding gene	gene with protein product		609280				10504407	Standard	XM_005254392		Approved	GCN2, KIAA1338	uc001zkm.1	Q9P2K8		ENST00000263791.5:c.38A>G	chr15.hg19:g.40226434A>G	ENSP00000263791:p.Asp13Gly	101.0	0.0	.		79.0	16.0	.	NM_001013703	C9JEC4|Q69YL7|Q6DC97|Q96GN6|Q9H5K1|Q9NSQ3|Q9NSZ5|Q9UJ56	Missense_Mutation	SNP	ENST00000263791.5	hg19	CCDS42016.1	.	.	.	.	.	.	.	.	.	.	A	16.20	3.055510	0.55325	.	.	ENSG00000128829	ENST00000263791;ENST00000382727	T;T	0.69306	-0.39;-0.38	4.33	0.326	0.15908	.	0.311332	0.29551	N	0.011825	T	0.34687	0.0906	N	0.03608	-0.345	0.20975	N	0.999813	B;B	0.16603	0.018;0.013	B;B	0.19391	0.011;0.025	T	0.16305	-1.0407	10	0.23302	T	0.38	-2.8305	4.9778	0.14149	0.4581:0.4284:0.1134:0.0	.	13;13	Q9P2K8;Q9P2K8-3	E2AK4_HUMAN;.	G	13	ENSP00000263791:D13G;ENSP00000372174:D13G	ENSP00000263791:D13G	D	+	2	0	EIF2AK4	38013726	1.000000	0.71417	0.777000	0.31699	0.957000	0.61999	0.557000	0.23454	0.188000	0.20168	0.374000	0.22700	GAC	.	.	.	none		0.756	EIF2AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418395.1			G	40226434	A	G	40226434	3	3	279	1	0	0	0	0	1	0	0	0	5001	275	10	3	40	3	EIF2AK4	15	40226434	Missense_Mutation	SNP	A	TCGA-Y8-A8RY-01A-11D-A36X-10		40226434	62304958	57	17810											
FBN1	2200	hgsc.bcm.edu	37	chr15	48780565	48780565	+	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	cttaaggctcattaactgacCtgtgcagttcctttcttcag	8	15	7	11	0	3	1	2	1	1	0	4	1	4	1	2	1	2	3	2	1	2	5			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr15:48780565C>T	ENST00000316623.5	-	26	3663	c.3208G>A	c.(3208-3210)Gac>Aac	p.D1070N		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1070	EGF-like 16; 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)		ATTAACTGACCTGTGCAGTTC	0.473																																					p.D1070N		Atlas-SNP	.											.	FBN1	310	.	0			c.G3208A						PASS	.						91	87	88					15																	48780565		2198	4296	6494	SO:0001630	splice_region_variant	2200	exon26			ACTGACCTGTGCA	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.3208+1G>A	chr15.hg19:g.48780565C>T		79.0	0.0	.		75.0	21.0	.	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	hg19	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	C	36	5.830889	0.97003	.	.	ENSG00000166147	ENST00000316623	D	0.99051	-5.37	6.17	6.17	0.99709	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.99184	0.9717	M	0.69248	2.105	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.99659	1.0993	9	.	.	.	.	20.4745	0.99168	0.0:1.0:0.0:0.0	.	1070	P35555	FBN1_HUMAN	N	1070	ENSP00000325527:D1070N	.	D	-	1	0	FBN1	46567857	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.818000	0.86416	2.941000	0.99782	0.655000	0.94253	GAC	.	.	.	none		0.473	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1		Missense_Mutation	T	48780565	C	T	48780565	5	4	279	1	0	0	0	0	0	0	1	0	5709	695	24	2	5571	2	FBN1	15	48780565	Splice_Site	SNP	C	TCGA-Y8-A8RY-01A-11D-A36X-10	8554131	48780565	53750827	58	17811											
CEP152	22995	hgsc.bcm.edu	37	chr15	49031304	49031304	+	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	tttatgctctgatgctctgaGttctctaacagcctttgtaa	8	17	7	9	0	3	2	0	2	3	0	4	2	3	2	1	0	4	4	1	0	3	6			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr15:49031304G>A	ENST00000380950.2	-	27	4462	c.4275C>T	c.(4273-4275)aaC>aaT	p.N1425N	CEP152_ENST00000399334.3_Silent_p.N1369N	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	1425					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		GATGCTCTGAGTTCTCTAACA	0.443																																					p.N1425N		Atlas-SNP	.											.	CEP152	145	.	0			c.C4275T						PASS	.						172	159	163					15																	49031304		1905	4128	6033	SO:0001819	synonymous_variant	22995	exon27			CTCTGAGTTCTCT	AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"asterless"	613529	"microcephaly, primary autosomal recessive 4"	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.4275C>T	chr15.hg19:g.49031304G>A		85.0	0.0	.		74.0	30.0	.	NM_001194998	E7ER66|Q17RV1|Q6NTA0	Silent	SNP	ENST00000380950.2	hg19	CCDS58361.1																																																																																			.	.	.	none		0.443	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985		A	49031304	G	A	49031304	2	1	279	1	0	0	0	0	0	0	0	1	3250	1020	36	2		2	CEP152	15	49031304	Silent	SNP	G	TCGA-Y8-A8RY-01A-11D-A36X-10	250739	49031304	53500088	59	17812											
AGBL1	123624	hgsc.bcm.edu	37	chr15	86790909	86790909	+	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	cctttgttttcagagtcgaaCggccgcagagcagtgaaccg	9	9	12	11	4	1	3	1	1	0	2	2	4	1	3	3	1	3	3	3	1	2	3	rs370819428		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr15:86790909C>A	ENST00000441037.2	+	6	491	c.396C>A	c.(394-396)aaC>aaA	p.N132K	AGBL1_ENST00000421325.2_Missense_Mutation_p.N132K	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	132					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						CAGAGTCGAACGGCCGCAGAG	0.557																																					p.N132K		Atlas-SNP	.											.	AGBL1	151	.	0			c.C396A						PASS	.						20	22	21					15																	86790909		2113	4233	6346	SO:0001583	missense	123624	exon6			GTCGAACGGCCGC	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.396C>A	chr15.hg19:g.86790909C>A	ENSP00000413001:p.Asn132Lys	102.0	0.0	.		94.0	5.0	.	NM_152336	A1A4X5|A6NJH6|C9JHL5	Missense_Mutation	SNP	ENST00000441037.2	hg19	CCDS58398.1	.	.	.	.	.	.	.	.	.	.	C	19.78	3.891754	0.72524	.	.	ENSG00000166748	ENST00000441037;ENST00000421325	T	0.41400	1.0	5.16	4.25	0.50352	Armadillo-like helical (1);Armadillo-type fold (1);	.	.	.	.	T	0.63129	0.2485	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.66492	-0.5910	9	0.72032	D	0.01	-11.8366	11.0423	0.47838	0.0:0.9138:0.0:0.0862	.	132	Q96MI9	CBPC4_HUMAN	K	161;132	ENSP00000397173:N132K	ENSP00000397173:N132K	N	+	3	2	AGBL1	84591913	1.000000	0.71417	0.988000	0.46212	0.915000	0.54546	1.427000	0.34881	1.170000	0.42753	0.561000	0.74099	AAC	.	.	.	alt		0.557	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336		A	86790909	C	A	86790909	3	1	279	1	0	0	0	0	1	0	0	0	375	535	19	4	414	4	AGBL1	15	86790909	Missense_Mutation	SNP	C	TCGA-Y8-A8RY-01A-11D-A36X-10	37759605	86790909	15740483	60	17813											
ZNF689	115509	hgsc.bcm.edu	37	chr16	30616527	30616527	+	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	ctgaccagcagggatggataGgaaaagcggcgcccacagtc	12	4	14	11	2	0	1	0	1	0	0	1	4	0	4	2	4	2	1	2	4	3	1			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr16:30616527G>T	ENST00000287461.3	-	3	898	c.561C>A	c.(559-561)tcC>tcA	p.S187S	ZNF689_ENST00000566673.1_5'UTR|RP11-146F11.5_ENST00000563540.1_RNA	NM_138447.1	NP_612456.1	Q96CS4	ZN689_HUMAN	zinc finger protein 689	187					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)			GGGATGGATAGGAAAAGCGGC	0.587																																					p.S187S		Atlas-SNP	.											.	ZNF689	48	.	0			c.C561A						PASS	.						71	75	74					16																	30616527		2197	4300	6497	SO:0001819	synonymous_variant	115509	exon3			TGGATAGGAAAAG	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.561C>A	chr16.hg19:g.30616527G>T		125.0	0.0	.		79.0	26.0	.	NM_138447	Q658J5	Silent	SNP	ENST00000287461.3	hg19	CCDS10686.1																																																																																			.	.	.	none		0.587	ZNF689-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255552.1	NM_138447		T	30616527	G	T	30616527	2	4	279	1	0	0	0	0	0	0	0	1	18106	987	35	4		4	ZNF689	16	30616527	Silent	SNP	G	TCGA-Y8-A8RY-01A-11D-A36X-10		30616527	59738226	61	17814											
MYH1	4619	hgsc.bcm.edu	37	chr17	10404987	10404987	+	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	tcttgctttgcagaccgctcAtttcaaactctttcctatta	8	17	4	12	1	4	1	2	0	2	1	5	1	5	1	2	0	3	3	2	0	3	6			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr17:10404987A>T	ENST00000226207.5	-	26	3366	c.3272T>A	c.(3271-3273)aTg>aAg	p.M1091K	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1091					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						CAGACCGCTCATTTCAAACTC	0.378																																					p.M1091K		Atlas-SNP	.											.	MYH1	403	.	0			c.T3272A						PASS	.						102	96	98					17																	10404987		2203	4299	6502	SO:0001583	missense	4619	exon26			CCGCTCATTTCAA		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.3272T>A	chr17.hg19:g.10404987A>T	ENSP00000226207:p.Met1091Lys	151.0	0.0	.		129.0	80.0	.	NM_005963	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	hg19	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	A	16.68	3.189938	0.58017	.	.	ENSG00000109061	ENST00000226207	D	0.82893	-1.66	5.51	5.51	0.81932	Myosin tail (1);	0.122232	0.36519	U	0.002544	D	0.84306	0.5443	M	0.81239	2.535	0.58432	D	0.999997	B	0.09022	0.002	B	0.09377	0.004	T	0.82299	-0.0526	10	0.72032	D	0.01	.	15.9255	0.79611	1.0:0.0:0.0:0.0	.	1091	P12882	MYH1_HUMAN	K	1091	ENSP00000226207:M1091K	ENSP00000226207:M1091K	M	-	2	0	MYH1	10345712	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.129000	0.71657	2.221000	0.72209	0.528000	0.53228	ATG	.	.	.	none		0.378	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		T	10404987	A	T	10404987	3	4	279	1	0	0	0	0	1	0	0	0	10036	217	8	5	2607	5	MYH1	17	10404987	Missense_Mutation	SNP	A	TCGA-Y8-A8RY-01A-11D-A36X-10		10404987	70790223	62	17815											
PHF12	57649	hgsc.bcm.edu	37	chr17	27251300	27251300	+	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	agtccattgacatgacccagCtcctttttctgctctcgttt	6	16	6	13	1	2	2	0	2	2	0	5	2	4	2	3	0	2	3	3	0	0	4	rs200428291		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr17:27251300C>T	ENST00000332830.4	-	4	1152	c.342G>A	c.(340-342)gaG>gaA	p.E114E	PHF12_ENST00000268756.3_Silent_p.E114E|RP11-20B24.5_ENST00000582631.1_RNA|PHF12_ENST00000577226.1_Silent_p.E114E|RP11-20B24.5_ENST00000580782.1_RNA|PHF12_ENST00000582655.1_5'UTR	NM_001033561.1	NP_001028733.1			PHD finger protein 12											breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_cancers(5;1.95e-14)|all_epithelial(6;5e-18)|Lung NSC(42;0.01)		Epithelial(11;1.64e-05)|all cancers(11;7.47e-05)|BRCA - Breast invasive adenocarcinoma(11;9.79e-05)			CATGACCCAGCTCCTTTTTCT	0.488																																					p.E114E		Atlas-SNP	.											.	PHF12	69	.	0			c.G342A						PASS	.						169	138	149					17																	27251300		2203	4300	6503	SO:0001819	synonymous_variant	57649	exon4			ACCCAGCTCCTTT	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.342G>A	chr17.hg19:g.27251300C>T		53.0	0.0	.		86.0	22.0	.	NM_020889		Silent	SNP	ENST00000332830.4	hg19	CCDS32598.1																																																																																			.	C|0.999;G|0.001	.	alt		0.488	PHF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255941.1	NM_020889		T	27251300	C	T	27251300	2	4	279	1	0	0	0	0	0	0	0	1	11830	796	28	2		2	PHF12	17	27251300	Silent	SNP	C	TCGA-Y8-A8RY-01A-11D-A36X-10	16846313	27251300	53943910	63	17816											
NBR1	4077	hgsc.bcm.edu	37	chr17	41341718	41341718	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccctcagaagtctcaatgccTacttcagaagaaacattgtt	13	11	6	11	0	3	3	3	0	1	3	4	3	3	3	2	0	3	1	2	0	5	4			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr17:41341718T>C	ENST00000422280.1	+	8	1053	c.594T>C	c.(592-594)ccT>ccC	p.P198P	NBR1_ENST00000341165.6_Silent_p.P198P|NBR1_ENST00000589872.1_Silent_p.P198P|NBR1_ENST00000542611.1_Silent_p.P177P|NBR1_ENST00000590996.1_Silent_p.P198P|NBR1_ENST00000389312.4_Silent_p.P198P	NM_031858.2	NP_114064.1	Q14596	NBR1_HUMAN	neighbor of BRCA1 gene 1	198					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)		TCTCAATGCCTACTTCAGAAG	0.438																																					p.P198P		Atlas-SNP	.											.	NBR1	55	.	0			c.T594C						PASS	.						141	135	137					17																	41341718		1864	4098	5962	SO:0001819	synonymous_variant	4077	exon8			AATGCCTACTTCA	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.594T>C	chr17.hg19:g.41341718T>C		114.0	0.0	.		123.0	23.0	.	NM_031862	Q13173|Q15026|Q5J7Q8|Q96GB6|Q9NRF7	Silent	SNP	ENST00000422280.1	hg19	CCDS45694.1																																																																																			.	.	.	none		0.438	NBR1-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453461.1	NM_005899		C	41341718	T	C	41341718	2	2	279	1	0	0	0	0	0	0	0	1	10207	1509	53	3		3	NBR1	17	41341718	Silent	SNP	T	TCGA-Y8-A8RY-01A-11D-A36X-10	14090418	41341718	39853492	64	17817											
SLC4A1	6521	hgsc.bcm.edu	37	chr17	42335164	42335164	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgacactcccatctggttccGggtcttttctcctgtgggta	4	14	10	13	2	3	0	0	0	3	0	6	1	5	0	3	3	0	2	3	3	1	4	rs373768879		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr17:42335164G>A	ENST00000262418.6	-	12	1449	c.1294C>T	c.(1294-1296)Cgg>Tgg	p.R432W	AC003043.1_ENST00000597382.1_5'Flank|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)	432	Membrane (anion exchange).		R -> W (in ELO antigen).		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)		ATCTGGTTCCGGGTCTTTTCT	0.587																																					p.R432W		Atlas-SNP	.											.	SLC4A1	104	.	0			c.C1294T	GRCh37	CM983769	SLC4A1	M		PASS	.	G	TRP/ARG	0,4406		0,0,2203	76	70	72		1294	-11.1	0	17		72	1,8599	1.2+/-3.3	0,1,4299	no	missense	SLC4A1	NM_000342.3	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	432/912	42335164	1,13005	2203	4300	6503	SO:0001583	missense	6521	exon12			GGTTCCGGGTCTT		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.1294C>T	chr17.hg19:g.42335164G>A	ENSP00000262418:p.Arg432Trp	82.0	0.0	.		105.0	66.0	.	NM_000342	G4V2I6|P78487|Q1ZZ45|Q4KKW9|Q4VB84|Q9UCY7|Q9UDJ1	Missense_Mutation	SNP	ENST00000262418.6	hg19	CCDS11481.1	.	.	.	.	.	.	.	.	.	.	g	9.617	1.132909	0.21041	0.0	1.16E-4	ENSG00000004939	ENST00000262418	T	0.79554	-1.28	5.57	-11.1	0.00147	Bicarbonate transporter, C-terminal (1);	1.964930	0.02322	N	0.073075	T	0.78616	0.4311	L	0.48642	1.525	0.09310	N	1	D;P	0.57571	0.98;0.903	P;P	0.56088	0.571;0.791	T	0.80233	-0.1467	10	0.87932	D	0	.	5.1981	0.15249	0.1499:0.4325:0.2322:0.1855	.	432;432	E2RVJ0;P02730	.;B3AT_HUMAN	W	432	ENSP00000262418:R432W	ENSP00000262418:R432W	R	-	1	2	SLC4A1	39690690	0.000000	0.05858	0.000000	0.03702	0.267000	0.26476	-2.027000	0.01433	-3.368000	0.00177	-2.455000	0.00206	CGG	.	.	.	weak		0.587	SLC4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346194.1	NM_000342		A	42335164	G	A	42335164	3	1	279	1	0	0	0	0	1	0	0	0	14663	1115	39	1	1477	1	SLC4A1	17	42335164	Missense_Mutation	SNP	G	TCGA-Y8-A8RY-01A-11D-A36X-10	993446	42335164	38860046	65	17818											
MYL12B	103910	hgsc.bcm.edu	37	chr18	3272961	3272961	+	Frame_Shift_Del	DEL	T	T	-																															tcagcgtgcaacatccaatgTgtttgccatgtttgaccagt																										TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr18:3272961delT	ENST00000581193.1	+	2	448	c.65delT	c.(64-66)gtgfs	p.V22fs	MYL12B_ENST00000584539.1_Frame_Shift_Del_p.V22fs|MYL12B_ENST00000237500.5_Frame_Shift_Del_p.V22fs|MYL12B_ENST00000400175.5_Frame_Shift_Del_p.V22fs	NM_001144945.1	NP_001138417.1	O14950	ML12B_HUMAN	myosin, light chain 12B, regulatory	22					axon guidance (GO:0007411)|muscle contraction (GO:0006936)|regulation of cell shape (GO:0008360)	apical part of cell (GO:0045177)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)			breast(1)|large_intestine(1)|lung(2)	4						ACATCCAATGTGTTTGCCATG	0.428																																					p.V22fs		Atlas-Indel,Pindel	.											.	MYL12B	11	.	0			c.64delG						PASS	.						180	165	170					18																	3272961		2203	4300	6503	SO:0001589	frameshift_variant	103910	exon2			.	AY320408	CCDS11831.1	18p11.31	2013-01-10			ENSG00000118680	ENSG00000118680		"Myosins / Light chain", "EF-hand domain containing"	29827	protein-coding gene	gene with protein product	"myosin regulatory light chain 2"	609211				11942626	Standard	NM_033546		Approved	MRLC2	uc002klt.4	O14950	OTTHUMG00000131510	ENST00000581193.1:c.65delT	chr18.hg19:g.3272961delT	ENSP00000463559:p.Val22fs	201.0	0.0	0		157.0	58.0	0.369427	NM_033546	D3DUH6|Q13182|Q7Z5Z4	Frame_Shift_Del	DEL	ENST00000581193.1	hg19	CCDS11831.1																																																																																			.	.	.	none		0.428	MYL12B-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258908.1	NM_033546		-	3272961	T	-	3272961	7	5	279	1	0	1	0	1	0	0	0	0	10053	1696	59	0	67	0	MYL12B	18	3272961	Frame_Shift_Del	DEL	T	TCGA-Y8-A8RY-01A-11D-A36X-10		3272961	74804287	66	17819											
PSMG2	56984	hgsc.bcm.edu	37	chr18	12720515	12720515	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgattatttctagtactccCttccggtacctacttacacc	9	15	4	13	1	1	1	0	1	1	0	3	1	3	1	4	1	4	2	4	1	6	8			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr18:12720515C>T	ENST00000317615.6	+	5	1096	c.414C>T	c.(412-414)ccC>ccT	p.P138P	PSMG2_ENST00000590217.1_Silent_p.P138P|PSMG2_ENST00000585331.2_Silent_p.P107P	NM_020232.4	NP_064617.2			proteasome (prosome, macropain) assembly chaperone 2											lung(1)|prostate(2)|skin(1)	4						CTAGTACTCCCTTCCGGTACC	0.348																																					p.P138P		Atlas-SNP	.											.	PSMG2	17	.	0			c.C414T						PASS	.						49	48	48					18																	12720515		2203	4299	6502	SO:0001819	synonymous_variant	56984	exon5			TACTCCCTTCCGG	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.414C>T	chr18.hg19:g.12720515C>T		118.0	0.0	.		94.0	4.0	.	NM_020232		Silent	SNP	ENST00000317615.6	hg19	CCDS11862.1																																																																																			.	.	.	none		0.348	PSMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254615.1	NM_020232		T	12720515	C	T	12720515	2	4	279	1	0	0	0	0	0	0	0	1	12722	668	24	2		2	PSMG2	18	12720515	Silent	SNP	C	TCGA-Y8-A8RY-01A-11D-A36X-10	9447554	12720515	65356733	67	17820											
DEFB116	245930	hgsc.bcm.edu	37	chr20	29891079	29891080	+	Missense_Mutation	DNP	TT	TT	CC																															agttagagtcgtaatcctccTtcacatttttagaactggtt																										TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr20:29891079_29891080TT>CC	ENST00000400549.1	-	2	243_244	c.244_245AA>GG	c.(244-246)AAg>GGg	p.K82G		NM_001037731.1	NP_001032820.1	Q30KQ4	DB116_HUMAN	defensin, beta 116	82					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				kidney(2)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)	12	all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			GTAATCCTCCTTCACATTTTTA	0.386																																					p.K82R|p.K82E		Atlas-SNP	.											.	DEFB116	18	.	0			c.A245G|c.A244G						PASS	.																																			SO:0001583	missense	245930	exon2			TCCTCCTTCACAT|CCTCCTTCACATT	DQ012020	CCDS42860.1	20q11.21	2008-07-17			ENSG00000215545	ENSG00000215545		"Defensins, beta"	18097	protein-coding gene	gene with protein product	"defensin, beta 16"					11854508, 16033865	Standard	NM_001037731		Approved	DEFB-16	uc010ztm.2	Q30KQ4	OTTHUMG00000159285	ENST00000400549.1:c.244_245delinsCC	chr20.hg19:g.29891079_29891080delinsCC	ENSP00000383396:p.Lys82Gly	124.0|121.0	0.0	.		76.0|77.0	28.0|29.0	.	NM_001037731		Missense_Mutation	SNP	ENST00000400549.1	hg19	CCDS42860.1																																																																																			.	.	.	none		0.386	DEFB116-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354403.1	NM_001037731		CC	29891080	TT	CC	29891079	3	2	279	1	0	0	0	0	1	0	0	0	4407	1609	56	3	66	3	DEFB116	20	29891079	Missense_Mutation	DNP	TT	TCGA-Y8-A8RY-01A-11D-A36X-10		29891079	33134441	68	17821											
CBFA2T2	9139	hgsc.bcm.edu	37	chr20	32199106	32199106	+	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	atgacatctcccctgagattGgggagaaggtgcggactctt	9	10	13	9	1	2	3	0	2	2	2	3	6	2	4	2	4	1	0	2	4	1	2			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chr20:32199106G>C	ENST00000346541.3	+	4	949	c.412G>C	c.(412-414)Ggg>Cgg	p.G138R	CBFA2T2_ENST00000375279.2_Missense_Mutation_p.G138R|CBFA2T2_ENST00000492345.1_Missense_Mutation_p.G109R|CBFA2T2_ENST00000342704.6_Missense_Mutation_p.G129R|CBFA2T2_ENST00000397800.1_Missense_Mutation_p.G109R|CBFA2T2_ENST00000397798.2_Missense_Mutation_p.G109R|CBFA2T2_ENST00000359606.3_Missense_Mutation_p.G148R|CBFA2T2_ENST00000344201.3_Missense_Mutation_p.G109R	NM_005093.3	NP_005084.1	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 2	138	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						CCCTGAGATTGGGGAGAAGGT	0.507																																					p.G138R	Esophageal Squamous(174;142 1955 14837 21276 28041)	Atlas-SNP	.											.	CBFA2T2	93	.	0			c.G412C						PASS	.						107	103	104					20																	32199106		2203	4300	6503	SO:0001583	missense	9139	exon4			GAGATTGGGGAGA	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.412G>C	chr20.hg19:g.32199106G>C	ENSP00000262653:p.Gly138Arg	83.0	0.0	.		80.0	32.0	.	NM_005093	B2RAE6|F8W6D7|Q5TGE4|Q5TGE5|Q5TGE6|Q5TGE7|Q8IWF3|Q96B06|Q96L00|Q9H436|Q9UJP8|Q9UJP9|Q9UP24	Missense_Mutation	SNP	ENST00000346541.3	hg19	CCDS13221.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.962319	0.92791	.	.	ENSG00000078699	ENST00000375279;ENST00000342704;ENST00000417366;ENST00000344201;ENST00000346541;ENST00000397800;ENST00000397798;ENST00000359606	T;T;T;T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83	5.69	5.69	0.88448	TAFH/NHR1 (3);	0.000000	0.85682	D	0.000000	T	0.71151	0.3306	M	0.74258	2.255	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.73248	-0.4043	10	0.87932	D	0	-8.4321	19.812	0.96551	0.0:0.0:1.0:0.0	.	138;129	O43439;F8W6D7	MTG8R_HUMAN;.	R	138;129;129;109;138;109;109;148	ENSP00000364428:G138R;ENSP00000345810:G129R;ENSP00000408352:G129R;ENSP00000341865:G109R;ENSP00000262653:G138R;ENSP00000380902:G109R;ENSP00000380900:G109R;ENSP00000352622:G148R	ENSP00000345810:G129R	G	+	1	0	CBFA2T2	31662767	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.685000	0.91497	0.655000	0.94253	GGG	.	.	.	none		0.507	CBFA2T2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078708.2	NM_001032999		C	32199106	G	C	32199106	3	2	279	1	0	0	0	0	1	0	0	0	2699	1348	47	4	460	4	CBFA2T2	20	32199106	Missense_Mutation	SNP	G	TCGA-Y8-A8RY-01A-11D-A36X-10	2308027	32199106	30826414	69	17822											
FAM123B	139285	hgsc.bcm.edu	37	chrX	63411064	63411064	+	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	gttccttcataacgcttctcCagaggacggaagtccctcca	9	10	8	14	2	2	1	1	0	1	1	6	3	5	3	4	2	1	2	4	2	2	4			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chrX:63411064C>G	ENST00000330258.3	-	2	2375	c.2103G>C	c.(2101-2103)ctG>ctC	p.L701L	AMER1_ENST00000403336.1_Silent_p.L701L|AMER1_ENST00000374869.3_Silent_p.L701L	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	701					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)									AACGCTTCTCCAGAGGACGGA	0.537																																					p.L701L		Atlas-SNP	.											.	.	.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.G2103C						PASS	.						52	46	48					X																	63411064		2203	4300	6503	SO:0001819	synonymous_variant	139285	exon2			CTTCTCCAGAGGA	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.2103G>C	chrX.hg19:g.63411064C>G		75.0	0.0	.		60.0	49.0	.	NM_152424	A2IB86|Q8N885	Silent	SNP	ENST00000330258.3	hg19	CCDS14377.2																																																																																			.	.	.	none		0.537	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		G	63411064	C	G	63411064	2	3	279	1	0	0	0	0	0	0	0	1	5427	581	21	4		4	FAM123B	23	63411064	Silent	SNP	C	TCGA-Y8-A8RY-01A-11D-A36X-10		63411064	91859496	70	17823											
RPL36A	6173	hgsc.bcm.edu	37	chrX	100650416	100650416	+	Missense_Mutation	SNP	T	T	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	ctattaaaagatgcaagcatTttgaactgggaggagataag	16	10	11	4	0	0	3	0	1	0	2	0	5	0	4	0	2	3	2	0	2	6	5			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chrX:100650416T>G	ENST00000553110.3	+	4	355	c.271T>G	c.(271-273)Ttt>Gtt	p.F91V	RPL36A_ENST00000471855.1_Missense_Mutation_p.F10V|RPL36A_ENST00000427805.2_Missense_Mutation_p.F127V|RPL36A-HNRNPH2_ENST00000409170.3_Missense_Mutation_p.I101M			P83881	RL36A_HUMAN	ribosomal protein L36a	91					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			liver(4)|lung(1)|prostate(1)	6						ATGCAAGCATTTTGAACTGGG	0.368																																					p.F127V		Atlas-SNP	.											.	.	.	.	0			c.T379G						PASS	.						38	43	41					X																	100650416		1376	2562	3938	SO:0001583	missense	0	exon4			AAGCATTTTGAAC	BC001781	CCDS14483.1, CCDS14483.2	Xq22.1	2011-04-06	2002-01-15	2002-01-18	ENSG00000241343	ENSG00000241343		"L ribosomal proteins"	10359	protein-coding gene	gene with protein product		300902	"ribosomal protein L44"	RPL44		3461443	Standard	NM_021029		Approved	L36A		P83881	OTTHUMG00000022027	ENST00000553110.3:c.271T>G	chrX.hg19:g.100650416T>G	ENSP00000446503:p.Phe91Val	118.0	0.0	.		115.0	87.0	.	NM_001199973	P09896|P10661|Q08ES5|Q5J9I6	Missense_Mutation	SNP	ENST00000553110.3	hg19		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	24.2|24.2|24.2	4.502877|4.502877|4.502877	0.85176|0.85176|0.85176	.|.|.	.|.|.	ENSG00000241343|ENSG00000241343|ENSG00000257529	ENST00000392994|ENST00000427805;ENST00000553110|ENST00000409170	.|T;T|.	.|0.51817|.	.|0.69;0.69|.	5.35|5.35|5.35	5.35|5.35|5.35	0.76521|0.76521|0.76521	.|Ribosomal protein, zinc-binding domain (1);|.	0.000000|0.000000|.	0.64402|0.64402|.	U|U|.	0.000006|0.000006|.	T|T|T	0.72930|0.72930|0.72930	0.3522|0.3522|0.3522	M|M|M	0.72894|0.72894|0.72894	2.215|2.215|2.215	0.41580|0.41580|0.41580	D|D|D	0.988736|0.988736|0.988736	.|D|.	.|0.62365|.	.|0.991|.	.|D|.	.|0.65684|.	.|0.937|.	T|T|T	0.73943|0.73943|0.73943	-0.3823|-0.3823|-0.3823	6|10|5	.|0.49607|.	.|T|.	.|0.09|.	.|.|.	14.3765|14.3765|14.3765	0.66881|0.66881|0.66881	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.|.	.|91|.	.|P83881|.	.|RL36A_HUMAN|.	C|V|M	109|127;91|101	.|ENSP00000404375:F127V;ENSP00000446503:F91V|.	.|ENSP00000404375:F127V|.	F|F|I	+|+|+	2|1|3	0|0|3	RPL36A|RPL36A|RP1-164F3.9	100537072|100537072|100537072	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.997000|0.997000|0.997000	0.91878|0.91878|0.91878	7.651000|7.651000|7.651000	0.83577|0.83577|0.83577	1.773000|1.773000|1.773000	0.52216|0.52216|0.52216	0.486000|0.486000|0.486000	0.48141|0.48141|0.48141	TTT|TTT|ATT	.	.	.	none		0.368	RPL36A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_021029		G	100650416	T	G	100650416	3	3	279	1	0	0	0	0	1	0	0	0	13600	1841	64	5	285	5	RPL36A	23	100650416	Missense_Mutation	SNP	T	TCGA-Y8-A8RY-01A-11D-A36X-10	37239352	100650416	54620144	71	17824											
ENOX2	10495	hgsc.bcm.edu	37	chrX	129822852	129822852	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attacttggatttggagggaAgagcgtgcagcttttacagt	10	13	13	5	1	0	1	0	0	0	1	0	4	0	4	0	3	5	2	0	3	3	5			TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	g.chrX:129822852A>G	ENST00000370927.1	-	3	346	c.325T>C	c.(325-327)Ttc>Ctc	p.F109L	ENOX2_ENST00000370935.1_Missense_Mutation_p.F80L|ENOX2_ENST00000492263.1_5'UTR|ENOX2_ENST00000394363.1_Missense_Mutation_p.F80L|ENOX2_ENST00000338144.3_Missense_Mutation_p.F109L			Q16206	ENOX2_HUMAN	ecto-NOX disulfide-thiol exchanger 2	109	Pro-rich.				cell growth (GO:0016049)|oxidation-reduction process (GO:0055114)|regulation of growth (GO:0040008)|ultradian rhythm (GO:0007624)	cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)	nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|protein disulfide oxidoreductase activity (GO:0015035)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(3)	33						TTTGGAGGGAAGAGCGTGCAG	0.388																																					p.F109L	Ovarian(101;828 1506 2951 9500 35258)	Atlas-SNP	.											.	ENOX2	70	.	0			c.T325C						PASS	.						262	216	232					X																	129822852		2203	4300	6503	SO:0001583	missense	10495	exon6			GAGGGAAGAGCGT	AF207881	CCDS14626.1, CCDS14627.1	Xq25	2013-02-12	2007-03-23	2007-03-23	ENSG00000165675	ENSG00000165675		"RNA binding motif (RRM) containing"	2259	protein-coding gene	gene with protein product		300282	"cytosolic ovarian carcinoma antigen 1"	COVA1		8150545, 11888291	Standard	NM_006375		Approved	APK1, tNOX	uc004evw.3	Q16206	OTTHUMG00000022401	ENST00000370927.1:c.325T>C	chrX.hg19:g.129822852A>G	ENSP00000359965:p.Phe109Leu	49.0	0.0	.		53.0	38.0	.	NM_182314	A8K197|A8K1C2|Q5VTJ1|Q5VTJ2|Q8WUX0|Q9NTP6|Q9UH82	Missense_Mutation	SNP	ENST00000370927.1	hg19	CCDS14626.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.491368	0.84962	.	.	ENSG00000165675	ENST00000538435;ENST00000370935;ENST00000338144;ENST00000394363;ENST00000350369;ENST00000370927;ENST00000432489	T;T;T;T;T	0.73152	-0.72;-0.72;-0.72;-0.72;-0.72	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.81536	0.4843	M	0.73217	2.22	0.54753	D	0.999983	D	0.71674	0.998	D	0.79784	0.993	T	0.82112	-0.0618	9	.	.	.	-10.6533	11.7235	0.51696	1.0:0.0:0.0:0.0	.	109	Q16206	ENOX2_HUMAN	L	80;80;109;80;137;109;80	ENSP00000359973:F80L;ENSP00000337146:F109L;ENSP00000377890:F80L;ENSP00000359965:F109L;ENSP00000400304:F80L	.	F	-	1	0	ENOX2	129650533	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	8.761000	0.91691	1.897000	0.54924	0.417000	0.27973	TTC	.	.	.	none		0.388	ENOX2-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058277.1	NM_182314		G	129822852	A	G	129822852	3	3	279	1	0	0	0	0	1	0	0	0	5129	72	3	3	1551	3	ENOX2	23	129822852	Missense_Mutation	SNP	A	TCGA-Y8-A8RY-01A-11D-A36X-10	29172436	129822852	25447708	72	17825											
SPEN	23013	hgsc.bcm.edu	37	chr1	16265370	16265370	+	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	tcccaaccctggctccaatcAggtcggttgtcctgtgtcct	5	12	9	15	1	1	0	1	0	0	0	6	0	5	0	5	3	1	2	5	3	2	1			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr1:16265370A>G	ENST00000375759.3	+	14	11066	c.10862A>G	c.(10861-10863)cAg>cGg	p.Q3621R		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	3621	SPOC. {ECO:0000255|PROSITE- ProRule:PRU00249}.				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)		GGCTCCAATCAGGTCGGTTGT	0.587																																					p.Q3621R		Atlas-SNP	.											.	SPEN	374	.	0			c.A10862G						PASS	.						150	113	126					1																	16265370		2203	4300	6503	SO:0001630	splice_region_variant	23013	exon14			CCAATCAGGTCGG		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.10863+1A>G	chr1.hg19:g.16265370A>G		34.0	0.0	.		13.0	10.0	.	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	hg19	CCDS164.1	.	.	.	.	.	.	.	.	.	.	A	16.43	3.121904	0.56613	.	.	ENSG00000065526	ENST00000375759	T	0.11169	2.8	5.62	5.62	0.85841	Spen Paralogue and Orthologue SPOC, C-terminal-like (2);Spen paralogue/orthologue C-terminal, metazoa (1);Spen paralogue and orthologue SPOC, C-terminal (1);	.	.	.	.	T	0.22742	0.0549	M	0.65498	2.005	0.58432	D	0.999991	P	0.35628	0.513	P	0.45406	0.479	T	0.00717	-1.1596	9	0.48119	T	0.1	-17.7469	15.807	0.78520	1.0:0.0:0.0:0.0	.	3621	Q96T58	MINT_HUMAN	R	3621	ENSP00000364912:Q3621R	ENSP00000364912:Q3621R	Q	+	2	0	SPEN	16137957	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	8.904000	0.92590	2.128000	0.65567	0.533000	0.62120	CAG	.	.	.	none		0.587	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001	Missense_Mutation	G	16265370	A	G	16265370	5	3	280	1	0	0	0	0	0	0	1	0	15050	202	7	3	10916	3	SPEN	1	16265370	Splice_Site	SNP	A	TCGA-Y8-A8RZ-01A-11D-A36X-10		16265370	232985251	1	17826											
CDCA8	55143	hgsc.bcm.edu	37	chr1	38158699	38158699	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcgagatgaactggcttgacTacttcggtaagagctggaga	11	9	14	7	2	0	5	0	2	0	3	1	7	0	5	0	3	3	3	0	3	3	4			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr1:38158699T>C	ENST00000373055.1	+	2	490	c.217T>C	c.(217-219)Tac>Cac	p.Y73H	C1orf109_ENST00000464085.1_5'Flank|CDCA8_ENST00000327331.2_Missense_Mutation_p.Y73H|C1orf109_ENST00000358011.4_5'Flank	NM_001256875.1|NM_018101.3	NP_001243804.1|NP_060571.1	Q53HL2	BOREA_HUMAN	cell division cycle associated 8	73	Required for centromere localization.|Required for interaction with INCENP and BIRC5.|Required for interaction with SENP3.|Required to form a minimal CPC core complex that localizes to the central spindle and midbody and properly executes the role of the CPC during cytokinesis.				chromosome organization (GO:0051276)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)	chromocenter (GO:0010369)|chromosome passenger complex (GO:0032133)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|midbody (GO:0030496)|nucleolus (GO:0005730)|nucleus (GO:0005634)|protein complex (GO:0043234)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(3)|skin(1)|stomach(1)	11		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CTGGCTTGACTACTTCGGTAA	0.567																																					p.Y73H		Atlas-SNP	.											.	CDCA8	25	.	0			c.T217C						PASS	.						48	49	49					1																	38158699		2203	4300	6503	SO:0001583	missense	55143	exon2			CTTGACTACTTCG	BG354581	CCDS424.1	1p34.3	2013-01-17			ENSG00000134690	ENSG00000134690			14629	protein-coding gene	gene with protein product	"borealin"	609977				12188893, 15260989	Standard	NM_001256875		Approved	FLJ12042, MESRGP, BOR, DasraB	uc001cbs.4	Q53HL2	OTTHUMG00000004320	ENST00000373055.1:c.217T>C	chr1.hg19:g.38158699T>C	ENSP00000362146:p.Tyr73His	144.0	0.0	.		129.0	56.0	.	NM_001256875	D3DPT4|Q53HN1|Q96AM3|Q9NVW5	Missense_Mutation	SNP	ENST00000373055.1	hg19	CCDS424.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.168750	0.78339	.	.	ENSG00000134690	ENST00000373055;ENST00000327331	T;T	0.48201	0.82;0.82	5.92	5.92	0.95590	Borealin-like, N-terminal (1);	0.442552	0.26658	N	0.023175	T	0.55016	0.1894	L	0.42245	1.32	0.42852	D	0.994089	P	0.45569	0.861	P	0.56042	0.79	T	0.53121	-0.8483	10	0.39692	T	0.17	-4.406	12.7362	0.57225	0.0:0.0:0.0:1.0	.	73	Q53HL2	BOREA_HUMAN	H	73	ENSP00000362146:Y73H;ENSP00000316121:Y73H	ENSP00000316121:Y73H	Y	+	1	0	CDCA8	37931286	0.997000	0.39634	0.999000	0.59377	0.989000	0.77384	2.888000	0.48594	2.265000	0.75225	0.533000	0.62120	TAC	.	.	.	none		0.567	CDCA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012473.1	NM_018101		C	38158699	T	C	38158699	3	2	280	1	0	0	0	0	1	0	0	0	3094	1522	53	3	223	3	CDCA8	1	38158699	Missense_Mutation	SNP	T	TCGA-Y8-A8RZ-01A-11D-A36X-10	21893329	38158699	211091922	2	17827											
ARHGAP29	9411	hgsc.bcm.edu	37	chr1	94639617	94639617	+	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	gacttcaccacgagaccgtgGggatcgtgatctgtgccagg	8	8	14	11	3	2	2	1	1	1	1	3	5	2	3	3	3	1	0	3	3	0	1			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr1:94639617G>T	ENST00000260526.6	-	23	3776	c.3594C>A	c.(3592-3594)ccC>ccA	p.P1198P	ARHGAP29_ENST00000482481.1_5'Flank	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	1198					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)		CGAGACCGTGGGGATCGTGAT	0.527																																					p.P1198P		Atlas-SNP	.											.	ARHGAP29	132	.	0			c.C3594A						PASS	.						85	76	79					1																	94639617		2203	4300	6503	SO:0001819	synonymous_variant	9411	exon23			ACCGTGGGGATCG		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.3594C>A	chr1.hg19:g.94639617G>T		77.0	0.0	.		105.0	40.0	.	NM_004815	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Silent	SNP	ENST00000260526.6	hg19	CCDS748.1																																																																																			.	.	.	none		0.527	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815		T	94639617	G	T	94639617	2	4	280	1	0	0	0	0	0	0	0	1	878	1219	43	4		4	ARHGAP29	1	94639617	Silent	SNP	G	TCGA-Y8-A8RZ-01A-11D-A36X-10	56480918	94639617	154611004	3	17828											
BNIPL	149428	hgsc.bcm.edu	37	chr1	151011013	151011013	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggctggcacttctgaagaTcctgaagaccctaaaggaga	13	7	12	9	0	1	5	0	2	1	3	2	7	2	5	2	3	0	2	2	3	4	2			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr1:151011013T>C	ENST00000368931.3	+	3	327	c.171T>C	c.(169-171)gaT>gaC	p.D57D	BNIPL_ENST00000295294.7_5'UTR	NM_138278.3	NP_612122.2	Q7Z465	BNIPL_HUMAN	BCL2/adenovirus E1B 19kD interacting protein like	57					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|regulation of growth rate (GO:0040009)	cytosol (GO:0005829)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|endometrium(3)|large_intestine(1)|lung(4)|skin(1)	10	Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CTTCTGAAGATCCTGAAGACC	0.473																																					p.D57D		Atlas-SNP	.											.	BNIPL	45	.	0			c.T171C						PASS	.						106	102	103					1																	151011013		1884	4122	6006	SO:0001819	synonymous_variant	149428	exon3			TGAAGATCCTGAA	AF193056	CCDS978.2, CCDS53362.1	1q21.2	2008-02-05			ENSG00000163141	ENSG00000163141			16976	protein-coding gene	gene with protein product		611275				12681488, 11741952	Standard	NM_138278		Approved	BNIPl-1, BNIPL-2, PP753	uc001ewl.2	Q7Z465	OTTHUMG00000035157	ENST00000368931.3:c.171T>C	chr1.hg19:g.151011013T>C		128.0	0.0	.		149.0	60.0	.	NM_138278	Q6DK43|Q8TCY7|Q8WYG2	Silent	SNP	ENST00000368931.3	hg19	CCDS978.2																																																																																			.	.	.	none		0.473	BNIPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085092.1	NM_138279		C	151011013	T	C	151011013	2	2	280	1	0	0	0	0	0	0	0	1	1480	1432	50	3		3	BNIPL	1	151011013	Silent	SNP	T	TCGA-Y8-A8RZ-01A-11D-A36X-10	56371396	151011013	98239608	4	17829											
CLK2	1196	hgsc.bcm.edu	37	chr1	155238100	155238100	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttacctgcgatggtcaacacAttgtacaactcggccgaagg	11	9	10	11	3	1	0	1	0	0	0	2	2	1	0	2	3	5	1	2	3	5	3			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr1:155238100A>G	ENST00000368361.4	-	5	853	c.538T>C	c.(538-540)Tgt>Cgt	p.C180R	CLK2_ENST00000361168.5_Missense_Mutation_p.C179R|CLK2_ENST00000497188.1_5'UTR|CLK2_ENST00000536801.1_Missense_Mutation_p.C180R|CLK2_ENST00000355560.4_Missense_Mutation_p.C178R			P49760	CLK2_HUMAN	CDC-like kinase 2	180	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of gluconeogenesis (GO:0045721)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)|response to ionizing radiation (GO:0010212)|response to retinoic acid (GO:0032526)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			endometrium(4)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	22	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			TGGTCAACACATTGTACAACT	0.507								Other conserved DNA damage response genes																													p.C179R		Atlas-SNP	.											.	CLK2	55	.	0			c.T535C						PASS	.						72	69	70					1																	155238100		2203	4300	6503	SO:0001583	missense	1196	exon5			CAACACATTGTAC	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.538T>C	chr1.hg19:g.155238100A>G	ENSP00000357345:p.Cys180Arg	206.0	0.0	.		224.0	81.0	.	NM_003993	B1AVS9|B5MBX6|Q96CQ0	Missense_Mutation	SNP	ENST00000368361.4	hg19		.	.	.	.	.	.	.	.	.	.	.	17.70	3.453811	0.63290	.	.	ENSG00000176444	ENST00000361168;ENST00000368361;ENST00000355560;ENST00000536801	T;T;T;T	0.20881	2.04;2.04;2.04;2.04	5.41	5.41	0.78517	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.46521	0.1397	M	0.90309	3.105	0.80722	D	1	D;D	0.89917	1.0;0.993	D;D	0.83275	0.996;0.962	T	0.58086	-0.7698	10	0.87932	D	0	.	14.4034	0.67065	1.0:0.0:0.0:0.0	.	180;179	P49760;P49760-3	CLK2_HUMAN;.	R	179;180;178;180	ENSP00000354856:C179R;ENSP00000357345:C180R;ENSP00000347759:C178R;ENSP00000441023:C180R	ENSP00000347759:C178R	C	-	1	0	CLK2	153504724	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.326000	0.79133	2.271000	0.75665	0.459000	0.35465	TGT	.	.	.	none		0.507	CLK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000087391.1	NM_003993		G	155238100	A	G	155238100	3	3	280	1	0	0	0	0	1	0	0	0	3539	217	8	3	997	3	CLK2	1	155238100	Missense_Mutation	SNP	A	TCGA-Y8-A8RZ-01A-11D-A36X-10	4227087	155238100	94012521	5	17830											
BIRC6	57448	hgsc.bcm.edu	37	chr2	32702603	32702603	+	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	aaacttgttctgtttcttctCtccatggactttacatgtca	8	18	5	10	0	4	0	1	0	3	0	6	1	5	1	1	1	2	2	1	1	2	6			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr2:32702603C>A	ENST00000421745.2	+	35	7154	c.7020C>A	c.(7018-7020)ctC>ctA	p.L2340L		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	2340					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)					TGTTTCTTCTCTCCATGGACT	0.423																																					p.L2340L	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.C7020A						PASS	.						146	121	129					2																	32702603		2203	4300	6503	SO:0001819	synonymous_variant	57448	exon35			TCTTCTCTCCATG	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.7020C>A	chr2.hg19:g.32702603C>A		121.0	0.0	.		149.0	56.0	.	NM_016252	Q9ULD1	Silent	SNP	ENST00000421745.2	hg19	CCDS33175.2																																																																																			.	.	.	none		0.423	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		A	32702603	C	A	32702603	2	1	280	1	0	0	0	0	0	0	0	1	1438	900	32	4		4	BIRC6	2	32702603	Silent	SNP	C	TCGA-Y8-A8RZ-01A-11D-A36X-10		32702603	210496770	6	17831											
TCF7L1	83439	hgsc.bcm.edu	37	chr2	85533645	85533645	+	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	gaaggagcggcagcttcactCgcagctctacccaacctggt	9	7	11	14	2	2	0	1	0	1	0	3	2	2	1	2	3	5	4	2	3	3	2			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr2:85533645C>T	ENST00000282111.3	+	10	1495	c.1220C>T	c.(1219-1221)tCg>tTg	p.S407L		NM_031283.2	NP_112573.1	Q9HCS4	TF7L1_HUMAN	transcription factor 7-like 1 (T-cell specific, HMG-box)	407					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						CAGCTTCACTCGCAGCTCTAC	0.602																																					p.S407L		Atlas-SNP	.											.	TCF7L1	44	.	0			c.C1220T						PASS	.						56	53	54					2																	85533645		2203	4300	6503	SO:0001583	missense	83439	exon10			TTCACTCGCAGCT	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.1220C>T	chr2.hg19:g.85533645C>T	ENSP00000282111:p.Ser407Leu	183.0	0.0	.		157.0	64.0	.	NM_031283	Q53R97|Q6PD70|Q9NP00	Missense_Mutation	SNP	ENST00000282111.3	hg19	CCDS1971.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.327451	0.81690	.	.	ENSG00000152284	ENST00000282111	D	0.97870	-4.58	4.74	3.87	0.44632	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.055635	0.85682	D	0.000000	D	0.95586	0.8565	N	0.03999	-0.3	0.43683	D	0.996123	D	0.76494	0.999	D	0.67382	0.951	D	0.95575	0.8641	10	0.66056	D	0.02	.	10.6733	0.45770	0.0:0.9072:0.0:0.0928	.	407	Q9HCS4	TF7L1_HUMAN	L	407	ENSP00000282111:S407L	ENSP00000282111:S407L	S	+	2	0	TCF7L1	85387156	0.900000	0.30661	0.960000	0.40013	0.866000	0.49608	2.024000	0.41049	1.228000	0.43614	-0.245000	0.11935	TCG	.	.	.	none		0.602	TCF7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252301.2	NM_031283		T	85533645	C	T	85533645	3	4	280	1	0	0	0	0	1	0	0	0	15709	893	31	1	1258	1	TCF7L1	2	85533645	Missense_Mutation	SNP	C	TCGA-Y8-A8RZ-01A-11D-A36X-10	52831042	85533645	157665728	7	17832											
CUL3	8452	hgsc.bcm.edu	37	chr2	225378239	225378239	+	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	tatttacattttcacggattAcctgaaaaaattctgcagac	14	14	5	8	1	2	2	1	1	1	1	2	3	2	3	1	1	3	1	1	1	6	7			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr2:225378239A>G	ENST00000264414.4	-	5	993		c.e5+1		CUL3_ENST00000409096.1_Splice_Site|CUL3_ENST00000409777.1_Splice_Site|CUL3_ENST00000344951.4_Splice_Site|CUL3_ENST00000432260.2_5'Flank	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3						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)		TTCACGGATTACCTGAAAAAA	0.299																																					.		Atlas-SNP	.											.	CUL3	96	.	0			c.654+2T>C						PASS	.						45	48	47					2																	225378239		2202	4299	6501	SO:0001630	splice_region_variant	8452	exon6			CGGATTACCTGAA	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.654+1T>C	chr2.hg19:g.225378239A>G		179.0	0.0	.		120.0	71.0	.	NM_003590	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Splice_Site	SNP	ENST00000264414.4	hg19	CCDS2462.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.302813	0.81136	.	.	ENSG00000036257	ENST00000264414;ENST00000344951;ENST00000409096;ENST00000409777	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.1491	0.81599	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CUL3	225086483	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	8.681000	0.91228	2.227000	0.72691	0.524000	0.50904	.	.	.	.	none		0.299	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2		Intron	G	225378239	A	G	225378239	5	3	280	1	0	0	0	0	0	0	1	0	4058	405	14	3	1698	3	CUL3	2	225378239	Splice_Site	SNP	A	TCGA-Y8-A8RZ-01A-11D-A36X-10	139844594	225378239	17821134	8	17833											
RBM15B	29890	hgsc.bcm.edu	37	chr3	51430385	51430385	+	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	tgctcacagatggatacaccCggcaccgcaacctggacgcc	10	5	10	16	3	1	1	1	0	0	1	1	3	1	3	4	3	3	3	4	3	2	1			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr3:51430385C>G	ENST00000323686.4	+	1	1655	c.1555C>G	c.(1555-1557)Cgg>Ggg	p.R519G		NM_013286.4	NP_037418.3	Q8NDT2	RB15B_HUMAN	RNA binding motif protein 15B	519					mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|large_intestine(5)|lung(3)	12				BRCA - Breast invasive adenocarcinoma(193;0.000224)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		TGGATACACCCGGCACCGCAA	0.612																																					p.R519G		Atlas-SNP	.											.	RBM15B	47	.	0			c.C1555G						PASS	.						48	54	52					3																	51430385		2203	4300	6503	SO:0001583	missense	29890	exon1			TACACCCGGCACC	AL831838	CCDS33764.1	3p21.1	2013-02-12			ENSG00000179837	ENSG00000259956		"RNA binding motif (RRM) containing"	24303	protein-coding gene	gene with protein product		612602				16129689	Standard	NM_013286		Approved	HUMAGCGB, OTT3	uc003dbd.3	Q8NDT2	OTTHUMG00000156896	ENST00000323686.4:c.1555C>G	chr3.hg19:g.51430385C>G	ENSP00000313890:p.Arg519Gly	63.0	0.0	.		34.0	25.0	.	NM_013286	A4QPG7|Q6QE19|Q9BV96	Missense_Mutation	SNP	ENST00000323686.4	hg19	CCDS33764.1	.	.	.	.	.	.	.	.	.	.	C	11.60	1.685730	0.29962	.	.	ENSG00000179837	ENST00000323686;ENST00000541145	T	0.16073	2.37	5.55	3.56	0.40772	.	.	.	.	.	T	0.24967	0.0606	L	0.46157	1.445	0.47862	D	0.999532	D	0.60575	0.988	P	0.54100	0.742	T	0.01762	-1.1279	9	0.28530	T	0.3	-18.1931	13.5402	0.61671	0.4569:0.5431:0.0:0.0	.	519	Q8NDT2	RB15B_HUMAN	G	519;192	ENSP00000313890:R519G	ENSP00000313890:R519G	R	+	1	2	RBM15B	51405425	0.998000	0.40836	0.948000	0.38648	0.889000	0.51656	3.085000	0.50151	1.314000	0.45095	0.655000	0.94253	CGG	.	.	.	none		0.612	RBM15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346489.1	NM_013286		G	51430385	C	G	51430385	3	3	280	1	0	0	0	0	1	0	0	0	13130	643	23	4	1557	4	RBM15B	3	51430385	Missense_Mutation	SNP	C	TCGA-Y8-A8RZ-01A-11D-A36X-10		51430385	146592045	9	17834											
BAP1	8314	hgsc.bcm.edu	37	chr3	52437846	52437846	+	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	gatggtgttgggctgcagcaCtgacagttgcccatcagcag	8	9	14	10	0	1	1	1	1	0	0	1	2	1	1	1	2	4	6	1	2	0	2			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr3:52437846C>A	ENST00000460680.1	-	13	1786	c.1315G>T	c.(1315-1317)Gtg>Ttg	p.V439L	BAP1_ENST00000296288.5_Missense_Mutation_p.V421L	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		GGCTGCAGCACTGACAGTTGC	0.567			"N, Mis, F, S, O"		"uveal melanoma, breast, NSCLC, RCC"	"mesothelioma, uveal melanoma"																															p.V439L	GBM(101;493 1458 7992 21037 25532)	Atlas-SNP	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	0			c.G1315T						PASS	.						101	103	103					3																	52437846		2203	4300	6503	SO:0001583	missense	8314	exon13			GCAGCACTGACAG	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1315G>T	chr3.hg19:g.52437846C>A	ENSP00000417132:p.Val439Leu	40.0	0.0	.		27.0	15.0	.	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Missense_Mutation	SNP	ENST00000460680.1	hg19	CCDS2853.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	3.198|3.198	-0.164260|-0.164260	0.06502|0.06502	.|.	.|.	ENSG00000163930|ENSG00000163930	ENST00000469613|ENST00000460680;ENST00000296288	.|T;T	.|0.56444	.|0.47;0.46	6.05|6.05	6.05|6.05	0.98169|0.98169	.|Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (1);	.|0.126603	.|0.53938	.|D	.|0.000045	T|T	0.37705|0.37705	0.1013|0.1013	N|N	0.19112|0.19112	0.55|0.55	0.35702|0.35702	D|D	0.81573|0.81573	.|B	.|0.12013	.|0.005	.|B	.|0.10450	.|0.005	T|T	0.38564|0.38564	-0.9655|-0.9655	5|10	.|0.27785	.|T	.|0.31	.|.	13.0153|13.0153	0.58753|0.58753	0.0:0.9266:0.0:0.0734|0.0:0.9266:0.0:0.0734	.|.	.|439	.|Q92560	.|BAP1_HUMAN	H|L	30|439;421	.|ENSP00000417132:V439L;ENSP00000296288:V421L	.|ENSP00000296288:V421L	Q|V	-|-	3|1	2|0	BAP1|BAP1	52412886|52412886	0.781000|0.781000	0.28676|0.28676	1.000000|1.000000	0.80357|0.80357	0.886000|0.886000	0.51366|0.51366	1.300000|1.300000	0.33436|0.33436	2.880000|2.880000	0.98712|0.98712	0.655000|0.655000	0.94253|0.94253	CAG|GTG	.	.	.	none		0.567	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			A	52437846	C	A	52437846	3	1	280	1	0	0	0	0	1	0	0	0	1311	565	20	4	894	4	BAP1	3	52437846	Missense_Mutation	SNP	C	TCGA-Y8-A8RZ-01A-11D-A36X-10	1007461	52437846	145584584	10	17835											
ROBO1	6091	hgsc.bcm.edu	37	chr3	78680444	78680444	+	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	tgttcttgcccctttcttgtGcccctgactccctagaaagg	5	14	8	14	0	2	2	0	1	2	1	3	2	3	2	5	1	2	1	5	1	2	5			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr3:78680444G>T	ENST00000464233.1	-	25	3606	c.3493C>A	c.(3493-3495)Cac>Aac	p.H1165N	ROBO1_ENST00000495273.1_Missense_Mutation_p.H1120N|ROBO1_ENST00000436010.2_Missense_Mutation_p.H1126N|ROBO1_ENST00000467549.1_Missense_Mutation_p.H1065N	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	1165					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)		CCTTTCTTGTGCCCCTGACTC	0.443																																					p.H1165N		Atlas-SNP	.											.	ROBO1	833	.	0			c.C3493A						PASS	.						139	138	138					3																	78680444		2034	4173	6207	SO:0001583	missense	6091	exon25			TCTTGTGCCCCTG	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.3493C>A	chr3.hg19:g.78680444G>T	ENSP00000420321:p.His1165Asn	70.0	0.0	.		36.0	24.0	.	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	hg19	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	G	17.34	3.366106	0.61513	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414	D;D;D;D	0.82711	-1.64;-1.64;-1.64;-1.64	5.37	5.37	0.77165	.	0.092179	0.85682	D	0.000000	T	0.79511	0.4458	L	0.36672	1.1	0.58432	D	0.999992	B;B;B;B;B	0.33739	0.187;0.031;0.304;0.422;0.147	B;B;B;B;B	0.37422	0.152;0.032;0.139;0.078;0.249	T	0.75411	-0.3327	9	.	.	.	.	19.484	0.95022	0.0:0.0:1.0:0.0	.	1129;1165;1120;1065;1126	Q9Y6N7-3;Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4	.;ROBO1_HUMAN;.;.;.	N	1126;1120;1165;1120;1065;1169	ENSP00000406043:H1126N;ENSP00000420321:H1165N;ENSP00000420637:H1120N;ENSP00000417992:H1065N	.	H	-	1	0	ROBO1	78763134	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	9.420000	0.97426	2.669000	0.90835	0.650000	0.86243	CAC	.	.	.	none		0.443	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		T	78680444	G	T	78680444	3	4	280	1	0	0	0	0	1	0	0	0	13526	1319	46	4	1490	4	ROBO1	3	78680444	Missense_Mutation	SNP	G	TCGA-Y8-A8RZ-01A-11D-A36X-10	26242598	78680444	119341986	11	17836											
GCET2	257144	hgsc.bcm.edu	37	chr3	111849299	111849306	+	Frame_Shift_Del	DEL	TTCTCTGT	TTCTCTGT	-																															attttgctctcacctggatgTtctctgtttggggctttgca																										TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	TTCTCTGT	TTCTCTGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr3:111849299_111849306delTTCTCTGT	ENST00000308910.4	-	2	268_275	c.84_91delACAGAGAA	c.(82-93)aaacagagaacafs	p.KQRT28fs	GCSAM_ENST00000484193.1_Frame_Shift_Del_p.KQRT30fs|RP11-757F18.5_ENST00000563632.1_RNA|C3orf52_ENST00000467942.2_3'UTR	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	28					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)										CACCTGGATGTTCTCTGTTTGGGGCTTT	0.49																																					p.31_33del		Pindel	.											.	.	.	.	0			c.91_98del						PASS	.																																			SO:0001589	frameshift_variant	257144	exon2			.	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.84_91delACAGAGAA	chr3.hg19:g.111849299_111849306delTTCTCTGT	ENSP00000309487:p.Lys28fs	61.0	0.0	.		47.0	10.0	0.213	NM_001190259	C9JD17|C9JUG6	Frame_Shift_Del	DEL	ENST00000308910.4	hg19	CCDS2964.1																																																																																			.	.	.	none		0.49	GCSAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353967.2	NM_152785		-	111849306	TTCTCTGT	-	111849299	7	5	280	1	0	1	0	1	0	0	0	0	6295	1725	60	0	465	0	GCET2	3	111849299	Frame_Shift_Del	DEL	TTCTCTGT	TCGA-Y8-A8RZ-01A-11D-A36X-10	33168855	111849299	86173131	12	17837											
FOXL2	668	hgsc.bcm.edu	37	chr3	138664642	138664642	+	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	cggccccgtggtgcggtgggGcaggcggcggtgcggcggcc	1	4	23	13	7	0	0	0	0	0	0	0	0	0	0	3	10	2	1	3	10	0	0			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr3:138664642G>C	ENST00000330315.3	-	1	1340	c.923C>G	c.(922-924)gCc>gGc	p.A308G	RP11-548O1.3_ENST00000495287.1_lincRNA|C3orf72_ENST00000383165.3_5'Flank	NM_023067.3	NP_075555.1	P58012	FOXL2_HUMAN	forkhead box L2	308					apoptotic DNA fragmentation (GO:0006309)|cell differentiation (GO:0030154)|embryonic eye morphogenesis (GO:0048048)|extraocular skeletal muscle development (GO:0002074)|female somatic sex determination (GO:0019101)|granulosa cell differentiation (GO:0060014)|menstruation (GO:0042703)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|ovarian follicle development (GO:0001541)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	cysteine-type endopeptidase regulator activity involved in apoptotic process (GO:0043028)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin conjugating enzyme binding (GO:0031624)			large_intestine(1)|lung(1)|ovary(333)|skin(1)	336						gtgcggtggggcaggcggcgg	0.836			Mis		granulosa-cell tumour of the ovary		"Blepharophimosis, ptosis and epicanthus inversus Types I, II; Premature ovarian failure type III"																														p.A308G		Atlas-SNP	.		Dom	yes		3	3q23	668	forkhead box L2	yes	O	.	FOXL2	408	.	0			c.C923G						PASS	.						1	1	1					3																	138664642		130	327	457	SO:0001583	missense	668	exon1			GGTGGGGCAGGCG	AF301906	CCDS3105.1	3q23	2008-04-10			ENSG00000183770	ENSG00000183770		"Forkhead boxes"	1092	protein-coding gene	gene with protein product		605597		BPES		1941972	Standard	NM_023067		Approved	BPES1	uc003esw.3	P58012	OTTHUMG00000159889	ENST00000330315.3:c.923C>G	chr3.hg19:g.138664642G>C	ENSP00000333188:p.Ala308Gly	35.0	0.0	.		19.0	10.0	.	NM_023067	Q4ZGJ3	Missense_Mutation	SNP	ENST00000330315.3	hg19	CCDS3105.1	.	.	.	.	.	.	.	.	.	.	G	11.19	1.565020	0.27915	.	.	ENSG00000183770	ENST00000330315	D	0.94457	-3.43	3.31	-0.235	0.13071	.	0.588514	0.17202	U	0.183069	D	0.86079	0.5847	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.71632	-0.4534	10	0.22706	T	0.39	.	2.9753	0.05935	0.1129:0.1716:0.5406:0.1749	.	308	P58012	FOXL2_HUMAN	G	308	ENSP00000333188:A308G	ENSP00000333188:A308G	A	-	2	0	FOXL2	140147332	0.017000	0.18338	0.340000	0.25575	0.931000	0.56810	0.275000	0.18698	0.040000	0.15660	0.449000	0.29647	GCC	.	.	.	none		0.836	FOXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357999.1			C	138664642	G	C	138664642	3	2	280	1	0	0	0	0	1	0	0	0	6024	1203	42	4	211	4	FOXL2	3	138664642	Missense_Mutation	SNP	G	TCGA-Y8-A8RZ-01A-11D-A36X-10	26815343	138664642	59357788	13	17838											
KIAA1530	57654	hgsc.bcm.edu	37	chr4	1379721	1379721	+	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	gaagaagcacgagaagttttCaaaccagtttaactacgcac	16	8	8	9	2	1	2	1	0	0	2	1	4	1	2	1	0	4	4	1	0	6	5			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr4:1379721C>A	ENST00000389851.4	+	14	2549	c.2102C>A	c.(2101-2103)tCa>tAa	p.S701*	UVSSA_ENST00000511216.1_Nonsense_Mutation_p.S701*|UVSSA_ENST00000507531.1_Nonsense_Mutation_p.S701*|UVSSA_ENST00000511563.1_Nonsense_Mutation_p.S252*|UVSSA_ENST00000512728.1_Nonsense_Mutation_p.S252*	NM_020894.2	NP_065945.2	Q2YD98	UVSSA_HUMAN	UV-stimulated scaffold protein A	701					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)										GAGAAGTTTTCAAACCAGTTT	0.572																																					p.S701X		Atlas-SNP	.											.	.	.	.	0			c.C2102A						PASS	.						150	122	131					4																	1379721		2203	4300	6503	SO:0001587	stop_gained	57654	exon14			AGTTTTCAAACCA	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.2102C>A	chr4.hg19:g.1379721C>A	ENSP00000374501:p.Ser701*	111.0	0.0	.		91.0	32.0	.	NM_020894	A8K9E6|B2RU11|Q8WTX4|Q9P1Z8	Nonsense_Mutation	SNP	ENST00000389851.4	hg19	CCDS33938.1	.	.	.	.	.	.	.	.	.	.	C	40	8.268854	0.98735	.	.	ENSG00000163945	ENST00000511216;ENST00000389851;ENST00000507531;ENST00000511563;ENST00000512728	.	.	.	5.19	5.19	0.71726	.	0.111807	0.64402	D	0.000009	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	.	18.6999	0.91617	0.0:1.0:0.0:0.0	.	.	.	.	X	701;701;701;252;252	.	ENSP00000374501:S701X	S	+	2	0	KIAA1530	1369721	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.554000	0.73923	2.400000	0.81607	0.655000	0.94253	TCA	.	.	.	none		0.572	UVSSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359480.1	NM_020894		A	1379721	C	A	1379721	4	1	280	1	0	0	0	0	0	1	0	0	8248	838	29	4	2152	4	KIAA1530	4	1379721	Nonsense_Mutation	SNP	C	TCGA-Y8-A8RZ-01A-11D-A36X-10		1379721	189774555	14	17839											
RAP1GDS1	5910	hgsc.bcm.edu	37	chr4	99342409	99342409	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccttctttcctatagcagAagctgctgaacaattgggaa	11	12	9	9	0	1	2	0	1	1	1	2	3	2	3	2	1	5	3	2	1	6	5			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr4:99342409A>G	ENST00000408927.3	+	12	1417	c.1304A>G	c.(1303-1305)gAa>gGa	p.E435G	RAP1GDS1_ENST00000339360.5_Missense_Mutation_p.E436G|RAP1GDS1_ENST00000264572.7_Missense_Mutation_p.E344G|RAP1GDS1_ENST00000408900.3_Missense_Mutation_p.E386G|RAP1GDS1_ENST00000380158.4_Missense_Mutation_p.E387G|RAP1GDS1_ENST00000453712.2_Splice_Site_p.E435G	NM_001100426.1|NM_001100427.1|NM_021159.4	NP_001093896.1|NP_001093897.1|NP_066982.3	P52306	GDS1_HUMAN	RAP1, GTP-GDP dissociation stimulator 1	435					myosin filament assembly (GO:0031034)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of Rho GTPase activity (GO:0032321)|vascular smooth muscle contraction (GO:0014829)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)	28				OV - Ovarian serous cystadenocarcinoma(123;2.9e-07)|LUSC - Lung squamous cell carcinoma(1;0.0253)|Lung(1;0.0576)		CCTATAGCAGAAGCTGCTGAA	0.408			T	NUP98	T-ALL																																p.E436G		Atlas-SNP	.		Dom	yes		4	4q21-q25	5910	"RAP1, GTP-GDP dissociation stimulator 1"		L	.	RAP1GDS1	61	.	0			c.A1307G						PASS	.						111	105	107					4																	99342409		1919	4142	6061	SO:0001583	missense	5910	exon12			TAGCAGAAGCTGC		CCDS43253.1, CCDS43254.1, CCDS47105.1, CCDS47106.1, CCDS47107.1, CCDS47108.1	4q23-q25	2013-02-14			ENSG00000138698	ENSG00000138698		"Armadillo repeat containing"	9859	protein-coding gene	gene with protein product		179502				8262526, 17951244	Standard	NM_001100426		Approved	SmgGDS	uc003htw.4	P52306	OTTHUMG00000160987	ENST00000408927.3:c.1304A>G	chr4.hg19:g.99342409A>G	ENSP00000386153:p.Glu435Gly	84.0	0.0	.		74.0	34.0	.	NM_001100426	E9PH06|G5E9P9|Q499L7|Q4KMV2|Q4QQI8|Q9BUW9|Q9BUX6|Q9NYM2|Q9NZA8	Missense_Mutation	SNP	ENST00000408927.3	hg19	CCDS43253.1	.	.	.	.	.	.	.	.	.	.	A	33	5.194788	0.94960	.	.	ENSG00000138698	ENST00000380158;ENST00000264572;ENST00000408927;ENST00000453712;ENST00000408900;ENST00000339360	T;T;T;T;T;T	0.55052	2.85;2.85;2.85;0.54;2.85;2.85	5.79	5.79	0.91817	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.63153	0.2487	L	0.36672	1.1	0.80722	D	1	D;D;D;B;B;D	0.62365	0.991;0.989;0.981;0.073;0.342;0.983	P;D;D;B;B;P	0.72982	0.831;0.979;0.954;0.031;0.093;0.813	T	0.60281	-0.7294	10	0.33141	T	0.24	-18.4441	16.1415	0.81528	1.0:0.0:0.0:0.0	.	344;386;387;435;436;435	E9PH06;P52306-2;Q499L7;P52306;Q4QQI8;G5E9P9	.;.;.;GDS1_HUMAN;.;.	G	387;344;435;435;386;436	ENSP00000369503:E387G;ENSP00000264572:E344G;ENSP00000386153:E435G;ENSP00000407157:E435G;ENSP00000386223:E386G;ENSP00000340454:E436G	ENSP00000264572:E344G	E	+	2	0	RAP1GDS1	99561432	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.810000	0.91950	2.198000	0.70561	0.533000	0.62120	GAA	.	.	.	none		0.408	RAP1GDS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363273.2	NM_001100426		G	99342409	A	G	99342409	3	3	280	1	0	0	0	0	1	0	0	0	13052	260	9	3	1353	3	RAP1GDS1	4	99342409	Missense_Mutation	SNP	A	TCGA-Y8-A8RZ-01A-11D-A36X-10	97962688	99342409	91811867	15	17840											
KIAA1109	84162	hgsc.bcm.edu	37	chr4	123255556	123255556	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctaatgcctccaggggatctTccttgccaagaacactgtcc	9	10	8	14	0	1	1	0	0	1	1	4	2	4	2	5	2	3	0	5	2	3	3			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr4:123255556T>C	ENST00000264501.4	+	69	12077	c.11704T>C	c.(11704-11706)Tcc>Ccc	p.S3902P	KIAA1109_ENST00000388738.3_Missense_Mutation_p.S3902P			Q2LD37	K1109_HUMAN	KIAA1109	3902					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CAGGGGATCTTCCTTGCCAAG	0.388																																					p.S3902P		Atlas-SNP	.											.	KIAA1109	424	.	0			c.T11704C						PASS	.						123	120	121					4																	123255556		1956	4147	6103	SO:0001583	missense	84162	exon67			GGATCTTCCTTGC	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"fragile site-associated"	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.11704T>C	chr4.hg19:g.123255556T>C	ENSP00000264501:p.Ser3902Pro	283.0	0.0	.		271.0	105.0	.	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.408409	0.83340	.	.	ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000438707	T;T;T	0.35605	2.32;2.32;1.3	5.21	5.21	0.72293	.	0.131937	0.52532	D	0.000067	T	0.53578	0.1805	L	0.50333	1.59	0.80722	D	1	D;D	0.69078	0.997;0.995	D;D	0.78314	0.991;0.979	T	0.50550	-0.8815	10	0.39692	T	0.17	.	15.3741	0.74590	0.0:0.0:0.0:1.0	.	3901;3902	Q2LD37-4;Q2LD37	.;K1109_HUMAN	P	3902;3902;606	ENSP00000264501:S3902P;ENSP00000373390:S3902P;ENSP00000410874:S606P	ENSP00000264501:S3902P	S	+	1	0	KIAA1109	123475006	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.997000	0.88414	2.097000	0.63578	0.454000	0.30748	TCC	.	.	.	none		0.388	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797		C	123255556	T	C	123255556	3	2	280	1	0	0	0	0	1	0	0	0	8215	1783	62	3	11970	3	KIAA1109	4	123255556	Missense_Mutation	SNP	T	TCGA-Y8-A8RZ-01A-11D-A36X-10	23913147	123255556	67898720	16	17841											
STOX2	56977	hgsc.bcm.edu	37	chr4	184930877	184930877	+	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	agtttcctcctgaagagtggCccctgcgagacgaggacacg	9	7	13	12	3	0	3	0	1	0	2	2	6	2	4	4	2	1	1	4	2	1	1			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr4:184930877C>G	ENST00000308497.4	+	3	2321	c.886C>G	c.(886-888)Ccc>Gcc	p.P296A	STOX2_ENST00000438269.1_Missense_Mutation_p.P296A	NM_020225.1	NP_064610.1	Q9P2F5	STOX2_HUMAN	storkhead box 2	296					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)		TGAAGAGTGGCCCCTGCGAGA	0.478																																					p.P296A		Atlas-SNP	.											.	STOX2	142	.	0			c.C886G						PASS	.						23	24	24					4																	184930877		1915	4136	6051	SO:0001583	missense	56977	exon3			GAGTGGCCCCTGC	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.886C>G	chr4.hg19:g.184930877C>G	ENSP00000311257:p.Pro296Ala	99.0	0.0	.		96.0	32.0	.	NM_020225	A6H8U4|Q9NPS8	Missense_Mutation	SNP	ENST00000308497.4	hg19	CCDS47167.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.348435	0.82132	.	.	ENSG00000173320	ENST00000308497;ENST00000438269	T;D	0.86694	-1.23;-2.16	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	D	0.93884	0.8043	M	0.78456	2.415	0.80722	D	1	D	0.69078	0.997	D	0.73380	0.98	D	0.93553	0.6888	10	0.87932	D	0	-25.0726	20.6634	0.99662	0.0:1.0:0.0:0.0	.	296	Q9P2F5	STOX2_HUMAN	A	296	ENSP00000311257:P296A;ENSP00000390127:P296A	ENSP00000311257:P296A	P	+	1	0	STOX2	185167871	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	7.818000	0.86416	2.894000	0.99253	0.655000	0.94253	CCC	.	.	.	none		0.478	STOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361433.3	NM_020225		G	184930877	C	G	184930877	3	3	280	1	0	0	0	0	1	0	0	0	15332	739	26	4	896	4	STOX2	4	184930877	Missense_Mutation	SNP	C	TCGA-Y8-A8RZ-01A-11D-A36X-10	61675321	184930877	6223399	17	17842											
ZFR	51663	hgsc.bcm.edu	37	chr5	32364329	32364329	+	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	ttctcagtgcatccccagggCtctgagggctagaagcactg	8	9	12	12	0	2	2	1	1	2	1	4	2	3	2	2	2	2	4	2	2	2	2			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr5:32364329C>A	ENST00000265069.8	-	18	2990	c.2888G>T	c.(2887-2889)aGc>aTc	p.S963I	ZFR_ENST00000510369.1_5'UTR	NM_016107.3	NP_057191.2	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein	963	DZF. {ECO:0000255|PROSITE- ProRule:PRU01040}.				multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|upper_aerodigestive_tract(2)	32				STAD - Stomach adenocarcinoma(35;0.19)		ATCCCCAGGGCTCTGAGGGCT	0.348																																					p.S963I		Atlas-SNP	.											.	ZFR	98	.	0			c.G2888T						PASS	.						83	86	85					5																	32364329		2203	4300	6503	SO:0001583	missense	51663	exon18			CCAGGGCTCTGAG	AF100742	CCDS34139.1	5p15.2	2014-03-03			ENSG00000056097	ENSG00000056097			17277	protein-coding gene	gene with protein product		615635				11574164, 24482476	Standard	NM_016107		Approved	ZFR1, SPG71	uc003jhr.1	Q96KR1	OTTHUMG00000161979	ENST00000265069.8:c.2888G>T	chr5.hg19:g.32364329C>A	ENSP00000265069:p.Ser963Ile	245.0	0.0	.		241.0	96.0	.	NM_016107	B2RNR5|Q05C08|Q3B7X5|Q6P5A3|Q86UA0|Q9H6V4|Q9NTI1|Q9Y687	Missense_Mutation	SNP	ENST00000265069.8	hg19	CCDS34139.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.027756	0.75390	.	.	ENSG00000056097	ENST00000265069;ENST00000382126	T	0.44482	0.92	5.74	5.74	0.90152	DZF (2);	0.000000	0.85682	D	0.000000	T	0.69251	0.3090	M	0.81112	2.525	0.80722	D	1	D;D	0.69078	0.997;0.996	D;D	0.83275	0.996;0.99	T	0.72110	-0.4389	10	0.87932	D	0	.	19.9357	0.97140	0.0:1.0:0.0:0.0	.	942;963	B5MEH6;Q96KR1	.;ZFR_HUMAN	I	963;942	ENSP00000265069:S963I	ENSP00000265069:S963I	S	-	2	0	ZFR	32400086	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.382000	0.79729	2.715000	0.92844	0.655000	0.94253	AGC	.	.	.	none		0.348	ZFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366586.1			A	32364329	C	A	32364329	3	1	280	1	0	0	0	0	1	0	0	0	17671	797	28	4	348	4	ZFR	5	32364329	Missense_Mutation	SNP	C	TCGA-Y8-A8RZ-01A-11D-A36X-10		32364329	148550931	18	17843											
C9	735	hgsc.bcm.edu	37	chr5	39364500	39364500	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actgactcacctggtcgtgtActgtgctgtgaggatgctta	7	13	12	9	1	1	2	1	2	0	0	2	3	1	3	1	2	3	3	1	2	2	2			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr5:39364500A>G	ENST00000263408.4	-	1	162	c.67T>C	c.(67-69)Tac>Cac	p.Y23H	C9_ENST00000509186.1_Intron	NM_001737.3	NP_001728.1	P02748	CO9_HUMAN	complement component 9	23					complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|hemolysis by symbiont of host erythrocytes (GO:0019836)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane attack complex (GO:0005579)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	32	all_lung(31;0.000197)	all_neural(839;7.57e-10)|Lung NSC(810;2.62e-08)|Ovarian(839;0.00384)|Breast(839;0.0184)|Myeloproliferative disorder(839;0.0511)	Epithelial(62;0.158)			CTGGTCGTGTACTGTGCTGTG	0.488																																					p.Y23H		Atlas-SNP	.											.	C9	116	.	0			c.T67C						PASS	.						108	97	100					5																	39364500		2203	4300	6503	SO:0001583	missense	735	exon1			TCGTGTACTGTGC		CCDS3929.1	5p14-p12	2014-09-17			ENSG00000113600	ENSG00000113600		"Complement system"	1358	protein-coding gene	gene with protein product		120940					Standard	NM_001737		Approved		uc003jlv.4	P02748	OTTHUMG00000094767	ENST00000263408.4:c.67T>C	chr5.hg19:g.39364500A>G	ENSP00000263408:p.Tyr23His	54.0	0.0	.		68.0	32.0	.	NM_001737		Missense_Mutation	SNP	ENST00000263408.4	hg19	CCDS3929.1	.	.	.	.	.	.	.	.	.	.	A	3.190	-0.165949	0.06461	.	.	ENSG00000113600	ENST00000263408	T	0.30182	1.54	4.45	-2.14	0.07123	.	1.608480	0.03288	N	0.187176	T	0.14657	0.0354	N	0.08118	0	0.09310	N	1	B	0.26120	0.142	B	0.28139	0.086	T	0.13683	-1.0500	10	0.15499	T	0.54	-0.1471	4.7136	0.12884	0.5465:0.0:0.2939:0.1596	.	23	P02748	CO9_HUMAN	H	23	ENSP00000263408:Y23H	ENSP00000263408:Y23H	Y	-	1	0	C9	39400257	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.222000	0.02965	-0.430000	0.07318	-0.366000	0.07423	TAC	.	.	.	none		0.488	C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211576.3			G	39364500	A	G	39364500	3	3	280	1	0	0	0	0	1	0	0	0	2445	391	14	3	1656	3	C9	5	39364500	Missense_Mutation	SNP	A	TCGA-Y8-A8RZ-01A-11D-A36X-10	7000171	39364500	141550760	19	17844											
FOXF2	2295	hgsc.bcm.edu	37	chr6	1390659	1390659	+	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	tcgctcaacgagtgcttcatCaagctgcctaagggcctcgg	8	9	11	13	3	3	0	3	0	0	0	5	1	3	0	2	2	4	3	2	2	3	2			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr6:1390659C>G	ENST00000259806.1	+	1	591	c.477C>G	c.(475-477)atC>atG	p.I159M		NM_001452.1	NP_001443.1	Q12947	FOXF2_HUMAN	forkhead box F2	159					embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digestive tract development (GO:0048566)|epithelial to mesenchymal transition (GO:0001837)|establishment of planar polarity of embryonic epithelium (GO:0042249)|extracellular matrix organization (GO:0030198)|genitalia development (GO:0048806)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	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)			large_intestine(2)|lung(5)|prostate(1)	8	Ovarian(93;0.0733)	all_lung(73;0.0713)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.095)		AGTGCTTCATCAAGCTGCCTA	0.657																																					p.I159M		Atlas-SNP	.											.	FOXF2	28	.	0			c.C477G						PASS	.						47	55	53					6																	1390659		2203	4300	6503	SO:0001583	missense	2295	exon1			CTTCATCAAGCTG	U13220	CCDS4472.1	6p25.3	2008-04-10			ENSG00000137273	ENSG00000137273		"Forkhead boxes"	3810	protein-coding gene	gene with protein product		603250		FKHL6		9799607, 7957066	Standard	NM_001452		Approved	FREAC2	uc003mtm.3	Q12947	OTTHUMG00000016243	ENST00000259806.1:c.477C>G	chr6.hg19:g.1390659C>G	ENSP00000259806:p.Ile159Met	142.0	0.0	.		158.0	58.0	.	NM_001452	Q5TGJ1|Q9UQ85	Missense_Mutation	SNP	ENST00000259806.1	hg19	CCDS4472.1	.	.	.	.	.	.	.	.	.	.	C	18.76	3.692590	0.68271	.	.	ENSG00000137273	ENST00000259806	D	0.95690	-3.78	4.53	4.53	0.55603	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.000000	0.85682	D	0.000000	D	0.95560	0.8557	L	0.53617	1.68	0.58432	D	0.999998	D	0.71674	0.998	D	0.75020	0.985	D	0.95812	0.8842	10	0.72032	D	0.01	.	9.8127	0.40833	0.0:0.9032:0.0:0.0968	.	159	Q12947	FOXF2_HUMAN	M	159	ENSP00000259806:I159M	ENSP00000259806:I159M	I	+	3	3	FOXF2	1335658	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.881000	0.48538	2.106000	0.64143	0.536000	0.68110	ATC	.	.	.	none		0.657	FOXF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043558.1			G	1390659	C	G	1390659	3	3	280	1	0	0	0	0	1	0	0	0	6013	816	29	4	479	4	FOXF2	6	1390659	Missense_Mutation	SNP	C	TCGA-Y8-A8RZ-01A-11D-A36X-10		1390659	169724408	20	17845											
CFB	629	hgsc.bcm.edu	37	chr6	31916623	31916623	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagaccacaagttgaagtcAgggactaacaccaagaaggc	17	4	10	10	0	1	3	1	1	0	2	1	4	1	4	2	2	1	1	2	2	5	2			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr6:31916623A>G	ENST00000425368.2	+	8	1566	c.1053A>G	c.(1051-1053)tcA>tcG	p.S351S	CFB_ENST00000477310.1_Silent_p.S702S|CFB_ENST00000556679.1_Silent_p.S853S|CFB_ENST00000497841.1_3'UTR|CFB_ENST00000456570.1_Silent_p.S853S	NM_001710.5	NP_001701.2	P00751	CFAB_HUMAN	complement factor B	351	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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						AGTTGAAGTCAGGGACTAACA	0.542																																					p.S351S		Atlas-SNP	.											.	CFB	33	.	0			c.A1053G						PASS	.						123	110	115					6																	31916623		1510	2708	4218	SO:0001819	synonymous_variant	629	exon8			GAAGTCAGGGACT	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.1053A>G	chr6.hg19:g.31916623A>G		56.0	0.0	.		69.0	36.0	.	NM_001710	B0QZQ6|O15006|Q29944|Q53F89|Q5JP67|Q5ST50|Q96HX6|Q9BTF5|Q9BX92	Silent	SNP	ENST00000425368.2	hg19	CCDS4729.1																																																																																			.	.	.	none		0.542	CFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076395.3	NM_001710		G	31916623	A	G	31916623	2	3	280	1	0	0	0	0	0	0	0	1	3280	175	7	3		3	CFB	6	31916623	Silent	SNP	A	TCGA-Y8-A8RZ-01A-11D-A36X-10	30525964	31916623	139198444	21	17846											
TAF8	129685	hgsc.bcm.edu	37	chr6	42044861	42044862	+	Missense_Mutation	DNP	GA	GA	CT																															gattctggagccgagaaggaGaacacctctgtcctgcagca																										TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr6:42044861_42044862GA>CT	ENST00000372977.3	+	8	822_823	c.804_805GA>CT	c.(802-807)gaGAac>gaCTac	p.268_269EN>DY	TAF8_ENST00000456846.2_Missense_Mutation_p.268_269EN>DY|TAF8_ENST00000465926.1_Missense_Mutation_p.192_193EN>DY|TAF8_ENST00000494547.1_Missense_Mutation_p.R309T|TAF8_ENST00000372982.4_Missense_Mutation_p.R309T	NM_138572.2	NP_612639.2	Q7Z7C8	TAF8_HUMAN	TAF8 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 43kDa	268					cell differentiation (GO:0030154)|inner cell mass cell proliferation (GO:0001833)|maintenance of protein location in nucleus (GO:0051457)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fat cell differentiation (GO:0045598)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|transcription factor TFIID complex (GO:0005669)				endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	6	Colorectal(47;0.196)		STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00179)			CCGAGAAGGAGAACACCTCTGT	0.49																																					p.E268D|p.N269Y		Atlas-SNP	.											.	TAF8	25	.	0			c.G804C|c.A805T						PASS	.																																			SO:0001583	missense	129685	exon8			GAAGGAGAACACC|AAGGAGAACACCT	AK057383	CCDS43462.1	6p21.1	2008-10-23	2007-07-30	2007-07-30	ENSG00000137413	ENSG00000137413			17300	protein-coding gene	gene with protein product		609514	"TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 45/50kDa", "taube nuss homolog (mouse)"	TBN			Standard	NM_138572		Approved	FLJ32821, TAF(II)43	uc003ors.3	Q7Z7C8	OTTHUMG00000014692	Exception_encountered	chr6.hg19:g.42044861_42044862delinsCT	ENSP00000362068:p.E268_N269delinsDY	146.0	0.0	.		146.0	51.0	.	NM_138572	Q5T0K1|Q8N4R9|Q96M52	Missense_Mutation	SNP	ENST00000372977.3	hg19	CCDS43462.1																																																																																			.	.	.	none		0.49	TAF8-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000357901.1	NM_138572		CT	42044862	GA	CT	42044861	3	2	280	1	0	0	0	0	1	0	0	0	15546	933	33	4	834	4	TAF8	6	42044861	Missense_Mutation	DNP	GA	TCGA-Y8-A8RZ-01A-11D-A36X-10	10128238	42044861	129070206	22	17847											
UTRN	7402	hgsc.bcm.edu	37	chr6	144806574	144806574	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tatttggatcttgaaactacCtggttaaacactttggaaga	13	14	8	6	0	1	2	0	1	1	1	1	4	1	4	1	3	3	1	1	3	6	6			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr6:144806574C>T	ENST00000367545.3	+	27	3741	c.3741C>T	c.(3739-3741)acC>acT	p.T1247T		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	1247					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)		TTGAAACTACCTGGTTAAACA	0.443																																					p.T1247T		Atlas-SNP	.											.	UTRN	327	.	0			c.C3741T						PASS	.						241	236	237					6																	144806574		2203	4300	6503	SO:0001819	synonymous_variant	7402	exon27			AACTACCTGGTTA	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.3741C>T	chr6.hg19:g.144806574C>T		131.0	0.0	.		160.0	63.0	.	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Silent	SNP	ENST00000367545.3	hg19	CCDS34547.1																																																																																			.	.	.	none		0.443	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			T	144806574	C	T	144806574	2	4	280	1	0	0	0	0	0	0	0	1	17115	668	24	2		2	UTRN	6	144806574	Silent	SNP	C	TCGA-Y8-A8RZ-01A-11D-A36X-10	102761713	144806574	26308493	23	17848											
STXBP5	134957	hgsc.bcm.edu	37	chr6	147636834	147636834	+	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	agctcatgtcattatttataGattcagcaagcaggaagtaa	15	12	8	6	0	3	1	3	0	0	1	3	2	3	2	0	1	3	4	0	1	6	6			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr6:147636834G>A	ENST00000321680.6	+	15	1586	c.1586G>A	c.(1585-1587)aGa>aAa	p.R529K	STXBP5_ENST00000367480.3_Missense_Mutation_p.R529K|STXBP5_ENST00000367481.3_Missense_Mutation_p.R529K|STXBP5_ENST00000179882.6_Missense_Mutation_p.R200K	NM_001127715.2	NP_001121187.1	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn)	529					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)		ATTATTTATAGATTCAGCAAG	0.368																																					p.R529K		Atlas-SNP	.											.	STXBP5	163	.	0			c.G1586A						PASS	.						153	148	150					6																	147636834		2203	4300	6503	SO:0001583	missense	134957	exon15			TTTATAGATTCAG	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.1586G>A	chr6.hg19:g.147636834G>A	ENSP00000321826:p.Arg529Lys	196.0	0.0	.		207.0	74.0	.	NM_139244	Q14DF3|Q5T5C1|Q5T5C2|Q8NBG8|Q96NG9	Missense_Mutation	SNP	ENST00000321680.6	hg19	CCDS47499.1	.	.	.	.	.	.	.	.	.	.	G	9.754	1.168167	0.21621	.	.	ENSG00000164506	ENST00000367481;ENST00000321680;ENST00000367480;ENST00000179882	T;T;T;T	0.65549	2.81;2.81;1.64;-0.16	5.78	4.91	0.64330	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (2);	0.048956	0.85682	N	0.000000	T	0.52108	0.1714	L	0.31804	0.96	0.58432	D	0.999999	D;D;D	0.61697	0.99;0.987;0.986	D;P;D	0.72982	0.979;0.787;0.965	T	0.54490	-0.8286	10	0.07644	T	0.81	.	14.5713	0.68213	0.07:0.0:0.93:0.0	.	529;529;200	Q5T5C0-2;Q5T5C0;B3KXX0	.;STXB5_HUMAN;.	K	529;529;529;200	ENSP00000356451:R529K;ENSP00000321826:R529K;ENSP00000356450:R529K;ENSP00000179882:R200K	ENSP00000179882:R200K	R	+	2	0	STXBP5	147678527	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.424000	0.73366	1.442000	0.47568	0.563000	0.77884	AGA	.	.	.	none		0.368	STXBP5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042606.1			A	147636834	G	A	147636834	3	1	280	1	0	0	0	0	1	0	0	0	15368	942	33	2	1644	2	STXBP5	6	147636834	Missense_Mutation	SNP	G	TCGA-Y8-A8RZ-01A-11D-A36X-10	2830260	147636834	23478233	24	17849											
SDK1	221935	hgsc.bcm.edu	37	chr7	4051838	4051838	+	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	ccacccccagaaacagagcaCaacggggtgttgcgtggata	12	5	12	12	2	0	2	0	0	0	2	0	3	0	3	3	3	4	2	3	3	3	2			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr7:4051838C>A	ENST00000404826.2	+	16	2530	c.2391C>A	c.(2389-2391)caC>caA	p.H797Q	SDK1_ENST00000389531.3_Missense_Mutation_p.H797Q	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	797	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		AAACAGAGCACAACGGGGTGT	0.542																																					p.H797Q		Atlas-SNP	.											.	SDK1	361	.	0			c.C2391A						PASS	.						112	114	113					7																	4051838		2203	4300	6503	SO:0001583	missense	221935	exon16			AGAGCACAACGGG	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.2391C>A	chr7.hg19:g.4051838C>A	ENSP00000385899:p.His797Gln	58.0	0.0	.		57.0	17.0	.	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	hg19	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	C	0.033	-1.323101	0.01320	.	.	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.56103	0.48;0.48	5.15	1.22	0.21188	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.075263	0.53938	D	0.000045	T	0.30792	0.0776	N	0.00765	-1.205	0.33596	D	0.601748	B;D	0.76494	0.034;0.999	B;P	0.60541	0.016;0.876	T	0.40251	-0.9573	10	0.21540	T	0.41	.	7.3399	0.26632	0.12:0.5964:0.0:0.2836	.	797;797	F8W6X9;Q7Z5N4	.;SDK1_HUMAN	Q	797	ENSP00000385899:H797Q;ENSP00000374182:H797Q	ENSP00000374182:H797Q	H	+	3	2	SDK1	4018364	0.403000	0.25319	0.990000	0.47175	0.402000	0.30811	-0.398000	0.07259	0.344000	0.23847	0.563000	0.77884	CAC	.	.	.	none		0.542	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		A	4051838	C	A	4051838	3	1	280	1	0	0	0	0	1	0	0	0	13981	477	17	4	2453	4	SDK1	7	4051838	Missense_Mutation	SNP	C	TCGA-Y8-A8RZ-01A-11D-A36X-10		4051838	155086825	25	17850											
ELMO1	9844	hgsc.bcm.edu	37	chr7	36895202	36895202	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agttgctgggctccttgggaAtcggcggaggtgcgtcaggg	5	9	19	8	3	1	0	1	0	0	0	3	2	2	2	1	6	2	3	1	6	1	2			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr7:36895202A>G	ENST00000310758.4	-	22	2785	c.2138T>C	c.(2137-2139)aTt>aCt	p.I713T	ELMO1_ENST00000442504.1_Missense_Mutation_p.I713T|ELMO1_ENST00000396040.2_Missense_Mutation_p.I233T|ELMO1_ENST00000341056.3_Missense_Mutation_p.I415T|ELMO1_ENST00000448602.1_Missense_Mutation_p.I713T|ELMO1_ENST00000396045.3_Missense_Mutation_p.I233T	NM_001206480.1|NM_014800.10	NP_001193409.1|NP_055615.8	Q92556	ELMO1_HUMAN	engulfment and cell motility 1	713					actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|phagocytosis, engulfment (GO:0006911)|Rac protein signal transduction (GO:0016601)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(28)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	58						CTCCTTGGGAATCGGCGGAGG	0.562																																					p.I713T		Atlas-SNP	.											.	ELMO1	141	.	0			c.T2138C						PASS	.						122	123	123					7																	36895202		2203	4300	6503	SO:0001583	missense	9844	exon22			TTGGGAATCGGCG	AF398885	CCDS5449.1, CCDS5450.1	7p14.1	2012-07-10	2006-01-20		ENSG00000155849	ENSG00000155849		"Engulfment and cell motility proteins"	16286	protein-coding gene	gene with protein product		606420	"engulfment and cell motility 1 (ced-12 homolog, C. elegans)"			11595183	Standard	NM_001039459		Approved	KIAA0281, CED12, ELMO-1, CED-12	uc003tfk.2	Q92556	OTTHUMG00000023701	ENST00000310758.4:c.2138T>C	chr7.hg19:g.36895202A>G	ENSP00000312185:p.Ile713Thr	117.0	0.0	.		115.0	44.0	.	NM_014800	A4D1X6|Q29R79|Q6ZTJ0|Q96PB0|Q9H0I1	Missense_Mutation	SNP	ENST00000310758.4	hg19	CCDS5449.1	.	.	.	.	.	.	.	.	.	.	A	17.40	3.379922	0.61845	.	.	ENSG00000155849	ENST00000341056;ENST00000396045;ENST00000310758;ENST00000361912;ENST00000396040;ENST00000442504;ENST00000448602	T;T;T;T;T;T	0.51325	1.27;0.71;2.25;0.71;2.25;2.25	4.77	4.77	0.60923	.	0.061993	0.64402	D	0.000006	T	0.54647	0.1871	M	0.73962	2.25	0.80722	D	1	B	0.29627	0.252	B	0.36989	0.238	T	0.60969	-0.7157	10	0.72032	D	0.01	.	14.759	0.69590	1.0:0.0:0.0:0.0	.	713	Q92556	ELMO1_HUMAN	T	415;233;713;617;233;713;713	ENSP00000342142:I415T;ENSP00000379360:I233T;ENSP00000312185:I713T;ENSP00000379355:I233T;ENSP00000406952:I713T;ENSP00000394458:I713T	ENSP00000312185:I713T	I	-	2	0	ELMO1	36861727	1.000000	0.71417	0.981000	0.43875	0.875000	0.50365	9.139000	0.94554	2.132000	0.65825	0.528000	0.53228	ATT	.	.	.	none		0.562	ELMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219830.4	NM_130442		G	36895202	A	G	36895202	3	3	280	1	0	0	0	0	1	0	0	0	5067	101	4	3	49	3	ELMO1	7	36895202	Missense_Mutation	SNP	A	TCGA-Y8-A8RZ-01A-11D-A36X-10	32843364	36895202	122243461	26	17851											
IQUB	154865	hgsc.bcm.edu	37	chr7	123143385	123143385	+	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	ctgtggcttaactccatgttGtactagagtctcattatttt	8	18	7	8	0	1	1	1	0	1	1	3	1	2	1	1	1	2	3	1	1	4	7			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr7:123143385G>A	ENST00000466202.1	-	4	1141	c.565C>T	c.(565-567)Caa>Taa	p.Q189*	IQUB_ENST00000324698.6_Nonsense_Mutation_p.Q189*|IQUB_ENST00000434450.1_Nonsense_Mutation_p.Q189*|IQUB_ENST00000488987.1_Intron	NM_001282855.1	NP_001269784.1	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	189	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				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						ACTCCATGTTGTACTAGAGTC	0.284																																					p.Q189X		Atlas-SNP	.											.	IQUB	117	.	0			c.C565T						PASS	.						102	109	107					7																	123143385		2203	4300	6503	SO:0001587	stop_gained	154865	exon4			CATGTTGTACTAG	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.565C>T	chr7.hg19:g.123143385G>A	ENSP00000417769:p.Gln189*	102.0	0.0	.		132.0	49.0	.	NM_178827	A4D0X0|Q49AL6|Q4G189|Q5BJD9|Q6NUH6|Q8N9Y2	Nonsense_Mutation	SNP	ENST00000466202.1	hg19	CCDS5787.1	.	.	.	.	.	.	.	.	.	.	G	12.53	1.965645	0.34659	.	.	ENSG00000164675	ENST00000466202;ENST00000324698;ENST00000434450	.	.	.	5.31	4.37	0.52481	.	0.486665	0.19520	N	0.112302	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	.	3.6964	0.08365	0.0835:0.1402:0.52:0.2564	.	.	.	.	X	189	.	ENSP00000324882:Q189X	Q	-	1	0	IQUB	122930621	0.004000	0.15560	0.899000	0.35326	0.132000	0.20833	0.148000	0.16224	2.637000	0.89404	0.655000	0.94253	CAA	.	.	.	none		0.284	IQUB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348529.1	NM_178827		A	123143385	G	A	123143385	4	1	280	1	0	0	0	0	0	1	0	0	7827	1386	48	2	1850	2	IQUB	7	123143385	Nonsense_Mutation	SNP	G	TCGA-Y8-A8RZ-01A-11D-A36X-10	86248183	123143385	35995278	27	17852											
ZNF212	7988	hgsc.bcm.edu	37	chr7	148947628	148947629	+	Missense_Mutation	DNP	GA	GA	CC																															tgcccccgggcagcaaggggGaggcccccaaggtagtctca																										TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr7:148947628_148947629GA>CC	ENST00000335870.2	+	2	531_532	c.403_404GA>CC	c.(403-405)GAg>CCg	p.E135P		NM_012256.3	NP_036388.2	Q9UDV6	ZN212_HUMAN	zinc finger protein 212	135					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)			CAGCAAGGGGGAGGCCCCCAAG	0.559																																					p.E135Q|p.E135A		Atlas-SNP	.											.	ZNF212	28	.	0			c.G403C|c.A404C						PASS	.																																			SO:0001583	missense	7988	exon2			AAGGGGGAGGCCC|AGGGGGAGGCCCC	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	Exception_encountered	chr7.hg19:g.148947628_148947629delinsCC	ENSP00000338572:p.Glu135Pro	53.0	0.0	.		59.0|58.0	20.0|19.0	.	NM_012256	B2RCF4|Q13396|Q8N664	Missense_Mutation	SNP	ENST00000335870.2	hg19	CCDS5896.1																																																																																			.	.	.	none		0.559	ZNF212-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352710.1	NM_012256		CC	148947629	GA	CC	148947628	3	2	280	1	0	0	0	0	1	0	0	0	17780	1175	41	4	409	4	ZNF212	7	148947628	Missense_Mutation	DNP	GA	TCGA-Y8-A8RZ-01A-11D-A36X-10	25804243	148947628	10191035	28	17853											
NOM1	64434	hgsc.bcm.edu	37	chr7	156759786	156759786	+	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	ctttccctttccatcttaaaGgttcgtgtaacgtgtgaaaa	10	15	7	9	2	1	1	0	1	1	0	4	1	3	1	2	1	1	2	2	1	5	5			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr7:156759786G>C	ENST00000275820.3	+	9	2313	c.2298G>C	c.(2296-2298)aaG>aaC	p.K766N		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	766	MI. {ECO:0000255|PROSITE- ProRule:PRU00698}.					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)		CCATCTTAAAGGTTCGTGTAA	0.403																																					p.K766N		Atlas-SNP	.											.	NOM1	73	.	0			c.G2298C						PASS	.						107	99	101					7																	156759786		2203	4300	6503	SO:0001630	splice_region_variant	64434	exon9			CTTAAAGGTTCGT	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.2298+1G>C	chr7.hg19:g.156759786G>C		65.0	0.0	.		64.0	17.0	.	NM_138400	Q96I08	Missense_Mutation	SNP	ENST00000275820.3	hg19	CCDS34787.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.757513	0.49468	.	.	ENSG00000146909	ENST00000275820	T	0.17213	2.29	4.73	4.73	0.59995	Initiation factor eIF-4 gamma, MA3 (1);	0.000000	0.85682	D	0.000000	T	0.51210	0.1661	M	0.89968	3.075	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.63537	-0.6615	10	0.72032	D	0.01	-36.156	18.0532	0.89356	0.0:0.0:1.0:0.0	.	766	Q5C9Z4	NOM1_HUMAN	N	766	ENSP00000275820:K766N	ENSP00000275820:K766N	K	+	3	2	NOM1	156452547	1.000000	0.71417	0.991000	0.47740	0.037000	0.13140	6.007000	0.70731	2.317000	0.78254	0.655000	0.94253	AAG	.	.	.	none		0.403	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400	Missense_Mutation	C	156759786	G	C	156759786	5	2	280	1	0	0	0	0	0	0	1	0	10537	1014	35	4	2332	4	NOM1	7	156759786	Splice_Site	SNP	G	TCGA-Y8-A8RZ-01A-11D-A36X-10	7812158	156759786	2378877	29	17854											
GBA2	57704	hgsc.bcm.edu	37	chr9	35740323	35740323	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggaaacacacacagctccaGcaatgcctactcctttctgc	11	9	6	15	0	1	0	0	0	1	0	3	1	3	1	3	1	6	2	3	1	3	2			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr9:35740323G>A	ENST00000378103.3	-	7	1689	c.1166C>T	c.(1165-1167)gCt>gTt	p.A389V	GBA2_ENST00000467252.1_5'UTR|GBA2_ENST00000378094.4_Missense_Mutation_p.A389V|GBA2_ENST00000378088.1_5'Flank|GBA2_ENST00000545786.1_Missense_Mutation_p.A395V	NM_020944.2	NP_065995.1	Q9HCG7	GBA2_HUMAN	glucosidase, beta (bile acid) 2	389					bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|central nervous system neuron development (GO:0021954)|glucosylceramide catabolic process (GO:0006680)|glycoside catabolic process (GO:0016139)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)	beta-glucosidase activity (GO:0008422)|glucosylceramidase activity (GO:0004348)			NS(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(4)|skin(3)	21	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CACAGCTCCAGCAATGCCTAC	0.547																																					p.A389V		Atlas-SNP	.											.	GBA2	77	.	0			c.C1166T						PASS	.						54	50	51					9																	35740323		2203	4300	6503	SO:0001583	missense	57704	exon7			GCTCCAGCAATGC	AJ309567	CCDS6589.1	9p13.2	2013-09-11			ENSG00000070610	ENSG00000070610			18986	protein-coding gene	gene with protein product	"bile acid beta-glucosidase", "non-lysosomal glucosylceramidase"	609471	"spastic paraplegia 46 (autosomal recessive)"	SPG46		11489889, 23332916, 23332917	Standard	NM_020944		Approved	KIAA1605, AD035, DKFZp762K054	uc003zxw.3	Q9HCG7	OTTHUMG00000021024	ENST00000378103.3:c.1166C>T	chr9.hg19:g.35740323G>A	ENSP00000367343:p.Ala389Val	54.0	0.0	.		55.0	16.0	.	NM_020944	D3DRP2|Q5TCV6|Q96A51|Q96LY1|Q96SJ2|Q9H2L8	Missense_Mutation	SNP	ENST00000378103.3	hg19	CCDS6589.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.768382	0.90020	.	.	ENSG00000070610	ENST00000378103;ENST00000378094;ENST00000545786	.	.	.	5.6	4.66	0.58398	Beta-glucosidase, GBA2 type, N-terminal (1);	0.051116	0.85682	D	0.000000	T	0.79557	0.4466	M	0.89095	3.005	0.80722	D	1	D;D;P	0.67145	0.971;0.996;0.955	P;P;P	0.59357	0.651;0.856;0.763	T	0.83056	-0.0150	9	0.59425	D	0.04	-8.1199	15.9277	0.79632	0.0:0.135:0.865:0.0	.	395;389;389	F5H7P6;Q9HCG7-2;Q9HCG7	.;.;GBA2_HUMAN	V	389;389;395	.	ENSP00000367334:A389V	A	-	2	0	GBA2	35730323	1.000000	0.71417	0.987000	0.45799	0.979000	0.70002	6.041000	0.70988	2.798000	0.96311	0.650000	0.86243	GCT	.	.	.	none		0.547	GBA2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055456.1	NM_020944		A	35740323	G	A	35740323	3	1	280	1	0	0	0	0	1	0	0	0	6274	971	34	2	1661	2	GBA2	9	35740323	Missense_Mutation	SNP	G	TCGA-Y8-A8RZ-01A-11D-A36X-10		35740323	105473108	30	17855											
NPR2	4882	hgsc.bcm.edu	37	chr9	35808792	35808794	+	In_Frame_Del	DEL	TTA	TTA	-																															gttggcctgaagatgccccgTtattgtctttttggagacac																										TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	TTA	TTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr9:35808792_35808794delTTA	ENST00000342694.2	+	20	3183_3185	c.2928_2930delTTA	c.(2926-2931)cgttat>cgt	p.Y977del	SPAG8_ENST00000479751.1_5'Flank|SPAG8_ENST00000340291.2_Intron|AL133410.1_ENST00000582432.1_RNA	NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2	977	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.				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)	AGATGCCCCGTTATTGTCTTTTT	0.498																																					p.976_977del		Atlas-Indel,Pindel	.											.	NPR2	162	.	0			c.2927_2929del						PASS	.																																			SO:0001651	inframe_deletion	4882	exon20			.	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.2928_2930delTTA	chr9.hg19:g.35808792_35808794delTTA	ENSP00000341083:p.Tyr977del	127.0	0.0	0		100.0	41.0	0.41	NM_003995	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	In_Frame_Del	DEL	ENST00000342694.2	hg19	CCDS6590.1																																																																																			.	.	.	none		0.498	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1			-	35808794	TTA	-	35808792	7	5	280	1	0	1	0	1	0	0	0	0	10602	1712	60	0	3006	0	NPR2	9	35808792	In_Frame_Del	DEL	TTA	TCGA-Y8-A8RZ-01A-11D-A36X-10	68469	35808792	105404639	31	17856											
NUP214	8021	hgsc.bcm.edu	37	chr9	134003841	134003841	+	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	aatatggttccattattgctTtttttgatgttcgcacattc	8	20	6	7	1	0	1	0	1	0	0	3	1	1	1	1	1	1	4	1	1	3	9			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr9:134003841T>A	ENST00000359428.5	+	3	508	c.364T>A	c.(364-366)Ttt>Att	p.F122I	RNU6-881P_ENST00000516813.1_RNA|NUP214_ENST00000411637.2_Missense_Mutation_p.F122I|NUP214_ENST00000451030.1_Missense_Mutation_p.F122I			P35658	NU214_HUMAN	nucleoporin 214kDa	122	Seven-bladed beta propeller.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		CATTATTGCTTTTTTTGATGT	0.398			T	"DEK, SET, ABL1"	"AML, T-ALL"																																p.F122I	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.T364A						PASS	.						245	198	214					9																	134003841		2203	4300	6503	SO:0001583	missense	8021	exon3			ATTGCTTTTTTTG	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.364T>A	chr9.hg19:g.134003841T>A	ENSP00000352400:p.Phe122Ile	50.0	0.0	.		78.0	32.0	.	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	hg19	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	T	34	5.324616	0.95708	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000531584	D;D;D;D	0.94046	-3.34;-3.34;-3.34;-3.34	5.94	5.94	0.96194	WD40/YVTN repeat-like-containing domain (1);	0.000000	0.44097	D	0.000484	D	0.95364	0.8495	M	0.61703	1.905	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.93373	0.6737	10	0.11485	T	0.65	-11.7116	15.5751	0.76373	0.0:0.0:0.0:1.0	.	122;122	P35658-4;P35658	.;NU214_HUMAN	I	122;122;122;122;32	ENSP00000352400:F122I;ENSP00000396576:F122I;ENSP00000405014:F122I;ENSP00000435874:F32I	ENSP00000352400:F122I	F	+	1	0	NUP214	132993662	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.343000	0.72986	2.276000	0.75962	0.455000	0.32223	TTT	.	.	.	none		0.398	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		A	134003841	T	A	134003841	3	1	280	1	0	0	0	0	1	0	0	0	10769	1841	64	5	374	5	NUP214	9	134003841	Missense_Mutation	SNP	T	TCGA-Y8-A8RZ-01A-11D-A36X-10	98195049	134003841	7209590	32	17857											
GDF10	2662	hgsc.bcm.edu	37	chr10	48426591	48426591	+	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	caccggcaggcacaggtgtcCacggacatgttggggtacac	9	6	14	12	2	0	0	0	0	0	0	1	1	1	1	2	6	1	4	2	6	1	2			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr10:48426591C>A	ENST00000224605.2	-	3	1681	c.1416G>T	c.(1414-1416)gtG>gtT	p.V472V		NM_004962.3	NP_004953.1	P55107	BMP3B_HUMAN	growth differentiation factor 10	472					fat cell differentiation (GO:0045444)|growth (GO:0040007)|skeletal system development (GO:0001501)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)	growth factor activity (GO:0008083)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(20)|skin(1)	31						CACAGGTGTCCACGGACATGT	0.577											OREG0020165	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V472V		Atlas-SNP	.											.	GDF10	79	.	0			c.G1416T						PASS	.						96	98	97					10																	48426591		2203	4300	6503	SO:0001819	synonymous_variant	2662	exon3			GGTGTCCACGGAC	L42113	CCDS73117.1	10q11.22	2014-04-10			ENSG00000107623	ENSG00000266524		"Endogenous ligands"	4215	protein-coding gene	gene with protein product		601361				8679252	Standard	NM_004962		Approved	BMP-3b	uc001jfb.3	P55107	OTTHUMG00000188319	ENST00000224605.2:c.1416G>T	chr10.hg19:g.48426591C>A		75.0	0.0	.	954	79.0	30.0	.	NM_004962	Q5VSQ8|Q9UCX6	Silent	SNP	ENST00000224605.2	hg19	CCDS7220.1																																																																																			.	.	.	none		0.577	GDF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047884.1	NM_004962		A	48426591	C	A	48426591	2	1	280	1	0	0	0	0	0	0	0	1	6318	581	21	4		4	GDF10	10	48426591	Silent	SNP	C	TCGA-Y8-A8RZ-01A-11D-A36X-10		48426591	87108156	33	17858											
OR5D16	390144	hgsc.bcm.edu	37	chr11	55606280	55606280	+	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	ggccacattcactctcttggGcttctcagattacctggaac	8	12	8	13	0	3	1	2	0	2	1	5	2	3	2	2	3	2	1	2	3	2	4			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr11:55606280G>C	ENST00000378396.1	+	1	53	c.53G>C	c.(52-54)gGc>gCc	p.G18A		NM_001005496.1	NP_001005496.1	Q8NGK9	OR5DG_HUMAN	olfactory receptor, family 5, subfamily D, member 16	18						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)				ACTCTCTTGGGCTTCTCAGAT	0.418																																					p.G18A		Atlas-SNP	.											.	OR5D16	94	.	0			c.G53C						PASS	.						100	91	94					11																	55606280		2201	4296	6497	SO:0001583	missense	390144	exon1			TCTTGGGCTTCTC	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.53G>C	chr11.hg19:g.55606280G>C	ENSP00000367649:p.Gly18Ala	120.0	0.0	.		159.0	49.0	.	NM_001005496	Q6IF65|Q96RB4	Missense_Mutation	SNP	ENST00000378396.1	hg19	CCDS31512.1	.	.	.	.	.	.	.	.	.	.	.	15.72	2.916894	0.52546	.	.	ENSG00000205029	ENST00000378396	T	0.00651	5.97	4.15	1.15	0.20763	.	.	.	.	.	T	0.02970	0.0088	M	0.86502	2.82	0.26922	N	0.966655	D	0.60160	0.987	D	0.66084	0.941	T	0.25813	-1.0121	9	0.87932	D	0	-12.1839	6.3729	0.21491	0.175:0.1508:0.6741:0.0	.	18	Q8NGK9	OR5DG_HUMAN	A	18	ENSP00000367649:G18A	ENSP00000367649:G18A	G	+	2	0	OR5D16	55362856	1.000000	0.71417	0.079000	0.20413	0.900000	0.52787	3.721000	0.54941	0.048000	0.15891	0.530000	0.56133	GGC	.	.	.	none		0.418	OR5D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334506.1	NM_001005496		C	55606280	G	C	55606280	3	2	280	1	0	0	0	0	1	0	0	0	11163	1203	42	4	55	4	OR5D16	11	55606280	Missense_Mutation	SNP	G	TCGA-Y8-A8RZ-01A-11D-A36X-10		55606280	79400236	34	17859											
TMEM179B	374395	hgsc.bcm.edu	37	chr11	62556681	62556681	+	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	gctgcatcgaggactcccacAggtgactgcctaaccctgag	9	7	11	14	1	0	2	0	2	0	0	2	4	1	3	3	2	3	2	3	2	1	1			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr11:62556681A>T	ENST00000333449.4	+	2	288	c.283A>T	c.(283-285)Aga>Tga	p.R95*	RP11-727F15.12_ENST00000601484.1_RNA|TMEM223_ENST00000525631.1_Intron|TMEM223_ENST00000527073.1_Intron|TMEM179B_ENST00000533861.1_Splice_Site_p.R95*	NM_199337.2	NP_955369.1	Q7Z7N9	T179B_HUMAN	transmembrane protein 179B	95						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)|liver(1)|lung(1)	4						GGACTCCCACAGGTGACTGCC	0.587																																					p.R95X		Atlas-SNP	.											.	TMEM179B	13	.	0			c.A283T						PASS	.						82	69	73					11																	62556681		2201	4299	6500	SO:0001630	splice_region_variant	374395	exon2			TCCCACAGGTGAC	BC051355	CCDS8036.1	11q12.3	2007-11-26			ENSG00000185475	ENSG00000185475			33744	protein-coding gene	gene with protein product							Standard	NM_199337		Approved		uc001nvd.4	Q7Z7N9	OTTHUMG00000167611	ENST00000333449.4:c.284+1A>T	chr11.hg19:g.62556681A>T		64.0	0.0	.		72.0	28.0	.	NM_199337		Nonsense_Mutation	SNP	ENST00000333449.4	hg19	CCDS8036.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	32|32	5.192393|5.192393	0.94960|0.94960	.|.	.|.	ENSG00000185475|ENSG00000185475	ENST00000526546|ENST00000533861;ENST00000333449	.|.	.|.	.|.	5.68|5.68	5.68|5.68	0.88126|0.88126	.|.	.|0.097909	.|0.64402	.|D	.|0.000002	T|.	0.33556|.	0.0867|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.36817|.	-0.9732|.	3|.	.|0.02654	.|T	.|1	.|.	12.3273|12.3273	0.55018|0.55018	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|.	.|.	.|.	L|X	14|95	.|.	.|ENSP00000333697:R95X	Q|R	+|+	2|1	0|2	TMEM179B|TMEM179B	62313257|62313257	0.952000|0.952000	0.32445|0.32445	1.000000|1.000000	0.80357|0.80357	0.869000|0.869000	0.49853|0.49853	2.064000|2.064000	0.41432|0.41432	2.179000|2.179000	0.69175|0.69175	0.459000|0.459000	0.35465|0.35465	CAG|AGA	.	.	.	none		0.587	TMEM179B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395362.2	NM_199337	Nonsense_Mutation	T	62556681	A	T	62556681	5	4	280	1	0	0	0	0	0	0	1	0	16109	202	7	5	289	5	TMEM179B	11	62556681	Splice_Site	SNP	A	TCGA-Y8-A8RZ-01A-11D-A36X-10	6950401	62556681	72449835	35	17860											
LRP5	4041	hgsc.bcm.edu	37	chr11	68154171	68154171	+	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	ccgagccatcgcactgcaccCcgtgatggggtaagacgggc	8	5	14	14	4	0	2	0	1	0	1	1	3	0	2	4	3	2	3	4	3	1	1			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr11:68154171C>T	ENST00000294304.7	+	6	1509	c.1403C>T	c.(1402-1404)cCc>cTc	p.P468L		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	468	Beta-propeller 2.				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						GCACTGCACCCCGTGATGGGG	0.677																																					p.P468L		Atlas-SNP	.											.	LRP5	136	.	0			c.C1403T						PASS	.						24	24	24					11																	68154171		2193	4281	6474	SO:0001583	missense	4041	exon6			TGCACCCCGTGAT	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.1403C>T	chr11.hg19:g.68154171C>T	ENSP00000294304:p.Pro468Leu	81.0	0.0	.		90.0	35.0	.	NM_002335	Q96TD6|Q9UES7|Q9UP66	Missense_Mutation	SNP	ENST00000294304.7	hg19	CCDS8181.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.727213	0.89390	.	.	ENSG00000162337	ENST00000294304	D	0.95518	-3.73	3.94	3.94	0.45596	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.48767	U	0.000167	D	0.98785	0.9591	H	0.99130	4.44	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99157	1.0860	10	0.66056	D	0.02	.	16.5321	0.84364	0.0:1.0:0.0:0.0	.	468	O75197	LRP5_HUMAN	L	468	ENSP00000294304:P468L	ENSP00000294304:P468L	P	+	2	0	LRP5	67910747	1.000000	0.71417	0.991000	0.47740	0.846000	0.48090	7.339000	0.79282	2.228000	0.72767	0.455000	0.32223	CCC	.	.	.	none		0.677	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335		T	68154171	C	T	68154171	3	4	280	1	0	0	0	0	1	0	0	0	8967	623	22	2	1425	2	LRP5	11	68154171	Missense_Mutation	SNP	C	TCGA-Y8-A8RZ-01A-11D-A36X-10	5597490	68154171	66852345	36	17861											
SAPS3	55291	hgsc.bcm.edu	37	chr11	68377430	68377430	+	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	gtaaagacgcagaggagtgtCccgagactgcagaggcgaag	13	4	16	8	3	0	4	0	0	0	4	1	7	1	5	1	2	1	3	1	2	3	1			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr11:68377430C>A	ENST00000393800.2	+	23	2763	c.2509C>A	c.(2509-2511)Ccc>Acc	p.P837T	PPP6R3_ENST00000265637.4_Missense_Mutation_p.P791T|PPP6R3_ENST00000524845.1_Missense_Mutation_p.P808T|PPP6R3_ENST00000527403.2_Missense_Mutation_p.P802T|PPP6R3_ENST00000534534.1_Missense_Mutation_p.P605T|PPP6R3_ENST00000265636.5_Missense_Mutation_p.P757T|PPP6R3_ENST00000393799.2_Missense_Mutation_p.P843T|PPP6R3_ENST00000529710.1_Missense_Mutation_p.P757T|PPP6R3_ENST00000524904.1_Missense_Mutation_p.P831T|PPP6R3_ENST00000393801.3_Missense_Mutation_p.P843T	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	837					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						AGAGGAGTGTCCCGAGACTGC	0.602																																					p.P843T		Atlas-SNP	.											.	PPP6R3	159	.	0			c.C2527A						PASS	.						114	99	104					11																	68377430		2200	4294	6494	SO:0001583	missense	55291	exon24			GAGTGTCCCGAGA	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.2509C>A	chr11.hg19:g.68377430C>A	ENSP00000377389:p.Pro837Thr	69.0	0.0	.		91.0	49.0	.	NM_001164160	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Missense_Mutation	SNP	ENST00000393800.2	hg19	CCDS53672.1	.	.	.	.	.	.	.	.	.	.	C	5.098	0.203685	0.09704	.	.	ENSG00000110075	ENST00000393799;ENST00000393800;ENST00000534534;ENST00000524845;ENST00000265637;ENST00000524904;ENST00000393801;ENST00000265636;ENST00000529710;ENST00000527403;ENST00000534190	T;T;T;T;T;T;T;T;T;T;T	0.69561	-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41	5.38	4.38	0.52667	.	0.726852	0.13772	N	0.363810	T	0.47838	0.1467	N	0.22421	0.69	0.19575	N	0.999961	B;B;B;B;B;B;B;B	0.06786	0.0;0.0;0.001;0.0;0.0;0.0;0.0;0.001	B;B;B;B;B;B;B;B	0.09377	0.001;0.0;0.004;0.001;0.001;0.0;0.001;0.004	T	0.16600	-1.0397	10	0.37606	T	0.19	.	4.8595	0.13575	0.2207:0.5836:0.1117:0.0839	.	520;605;757;808;831;837;843;757	B4DYU6;E9PQP7;Q5H9R7-3;Q5H9R7-6;Q5H9R7-2;Q5H9R7;Q5H9R7-5;Q5H9R7-4	.;.;.;.;.;PP6R3_HUMAN;.;.	T	843;837;605;808;791;831;843;757;757;802;544	ENSP00000377388:P843T;ENSP00000377389:P837T;ENSP00000434429:P605T;ENSP00000431415:P808T;ENSP00000265637:P791T;ENSP00000433058:P831T;ENSP00000377390:P843T;ENSP00000265636:P757T;ENSP00000437329:P757T;ENSP00000433565:P802T;ENSP00000436209:P544T	ENSP00000265636:P757T	P	+	1	0	PPP6R3	68134006	0.133000	0.22466	0.839000	0.33178	0.002000	0.02628	-0.056000	0.11787	2.512000	0.84698	0.561000	0.74099	CCC	.	.	.	none		0.602	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1	NM_018312		A	68377430	C	A	68377430	3	1	280	1	0	0	0	0	1	0	0	0	13851	855	30	4	2613	4	SAPS3	11	68377430	Missense_Mutation	SNP	C	TCGA-Y8-A8RZ-01A-11D-A36X-10	223259	68377430	66629086	37	17862											
PIK3C2G	5288	hgsc.bcm.edu	37	chr12	18699304	18699304	+	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	agtggaattcaagacctgaaAtatgtgtataataatcttcg	15	13	8	5	1	2	2	1	1	1	1	3	3	2	3	1	1	0	1	1	1	7	6	rs552965370		TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr12:18699304A>T	ENST00000266497.5	+	24	3443	c.3405A>T	c.(3403-3405)aaA>aaT	p.K1135N	PIK3C2G_ENST00000433979.1_Missense_Mutation_p.K1135N|PIK3C2G_ENST00000538779.1_Missense_Mutation_p.K1176N			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	1135	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)				AAGACCTGAAATATGTGTATA	0.393																																					p.K1135N		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.A3405T						PASS	.						121	109	113					12																	18699304		1971	4159	6130	SO:0001583	missense	5288	exon25			CCTGAAATATGTG	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.3405A>T	chr12.hg19:g.18699304A>T	ENSP00000266497:p.Lys1135Asn	129.0	0.0	.		125.0	56.0	.	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	hg19	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	A	17.42	3.385183	0.61956	.	.	ENSG00000139144	ENST00000433979;ENST00000266497;ENST00000538779	D;D;D	0.81821	-1.54;-1.54;-1.54	4.07	2.87	0.33458	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.155509	0.42682	D	0.000680	T	0.74084	0.3670	N	0.20304	0.555	0.44302	D	0.997173	P;P;P	0.52463	0.921;0.953;0.921	P;P;P	0.53401	0.535;0.725;0.535	T	0.71073	-0.4698	10	0.36615	T	0.2	-21.2283	9.6631	0.39967	0.9141:0.0:0.0859:0.0	.	1175;1176;1135	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	N	1135;1135;1176	ENSP00000404845:K1135N;ENSP00000266497:K1135N;ENSP00000445381:K1176N	ENSP00000266497:K1135N	K	+	3	2	PIK3C2G	18590571	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	2.472000	0.45136	0.862000	0.35528	0.533000	0.62120	AAA	.	.	.	none		0.393	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570		T	18699304	A	T	18699304	3	4	280	1	0	0	0	0	1	0	0	0	11918	98	4	5	3499	5	PIK3C2G	12	18699304	Missense_Mutation	SNP	A	TCGA-Y8-A8RZ-01A-11D-A36X-10		18699304	115152591	38	17863											
DENND5B	160518	hgsc.bcm.edu	37	chr12	31633023	31633023	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagcgttgtgcatctggtaaAgtgtctgcattgctgtgcag	7	13	13	8	1	2	0	0	0	2	0	2	0	2	0	0	1	5	6	0	1	2	3			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr12:31633023A>G	ENST00000389082.5	-	3	668	c.404T>C	c.(403-405)cTt>cCt	p.L135P	DENND5B_ENST00000306833.6_Missense_Mutation_p.L170P|DENND5B_ENST00000536562.1_Missense_Mutation_p.L170P|DENND5B_ENST00000354285.4_Missense_Mutation_p.L157P|DENND5B_ENST00000545147.1_Intron	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	135					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						CATCTGGTAAAGTGTCTGCAT	0.408																																					p.L135P		Atlas-SNP	.											.	DENND5B	114	.	0			c.T404C						PASS	.						90	87	88					12																	31633023		2068	4221	6289	SO:0001583	missense	160518	exon3			TGGTAAAGTGTCT	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.404T>C	chr12.hg19:g.31633023A>G	ENSP00000373734:p.Leu135Pro	101.0	0.0	.		103.0	44.0	.	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Missense_Mutation	SNP	ENST00000389082.5	hg19	CCDS44857.1	.	.	.	.	.	.	.	.	.	.	A	19.94	3.920322	0.73098	.	.	ENSG00000170456	ENST00000389082;ENST00000306833;ENST00000536562;ENST00000354285;ENST00000546299	T;T;T;T;T	0.11712	3.31;3.43;3.43;2.75;2.77	4.65	4.65	0.58169	.	0.000000	0.64402	D	0.000004	T	0.33000	0.0848	M	0.73962	2.25	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	0.97110	0.999;0.999;1.0;0.999;1.0	T	0.10245	-1.0638	10	0.87932	D	0	-17.2544	14.2554	0.66048	1.0:0.0:0.0:0.0	.	170;57;157;135;170	Q6ZUT9-2;Q6ZUT9-3;Q6ZUT9-4;Q6ZUT9;G3V1S3	.;.;.;DEN5B_HUMAN;.	P	135;170;170;157;87	ENSP00000373734:L135P;ENSP00000306482:L170P;ENSP00000444889:L170P;ENSP00000346238:L157P;ENSP00000442938:L87P	ENSP00000306482:L170P	L	-	2	0	DENND5B	31524290	1.000000	0.71417	0.901000	0.35422	0.908000	0.53690	8.897000	0.92532	1.955000	0.56771	0.533000	0.62120	CTT	.	.	.	none		0.408	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973		G	31633023	A	G	31633023	3	3	280	1	0	0	0	0	1	0	0	0	4439	72	3	3	3496	3	DENND5B	12	31633023	Missense_Mutation	SNP	A	TCGA-Y8-A8RZ-01A-11D-A36X-10	12933719	31633023	102218872	39	17864											
PDE1B	5153	hgsc.bcm.edu	37	chr12	54964116	54964116	+	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	tgtttttgagttgctgactcGgcataacctcatcagccgct	7	14	9	11	2	2	2	2	2	0	0	3	2	2	2	2	1	3	5	2	1	1	4	rs568969611		TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr12:54964116G>C	ENST00000243052.3	+	6	1005	c.569G>C	c.(568-570)cGg>cCg	p.R190P	PDE1B_ENST00000394277.3_3'UTR|PDE1B_ENST00000550620.1_Missense_Mutation_p.R170P|PDE1B_ENST00000538346.1_Missense_Mutation_p.R149P	NM_000924.3	NP_000915.1	Q01064	PDE1B_HUMAN	phosphodiesterase 1B, calmodulin-dependent	190					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)	TTGCTGACTCGGCATAACCTC	0.512																																					p.R190P		Atlas-SNP	.											.	PDE1B	76	.	0			c.G569C						PASS	.						184	153	163					12																	54964116		2203	4300	6503	SO:0001583	missense	5153	exon6			TGACTCGGCATAA	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.569G>C	chr12.hg19:g.54964116G>C	ENSP00000243052:p.Arg190Pro	50.0	0.0	.		72.0	19.0	.	NM_000924	Q92825|Q96KP3	Missense_Mutation	SNP	ENST00000243052.3	hg19	CCDS8882.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.561493	0.86335	.	.	ENSG00000123360	ENST00000243052;ENST00000538346;ENST00000550620	T;T;T	0.71461	-0.57;-0.54;-0.55	3.84	3.84	0.44239	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.065176	0.56097	D	0.000021	T	0.82116	0.4967	M	0.80183	2.485	0.80722	D	1	D;P	0.54397	0.966;0.921	P;P	0.61533	0.89;0.841	D	0.85159	0.0991	10	0.87932	D	0	.	14.0587	0.64786	0.0:0.0:1.0:0.0	.	170;190	Q01064-2;Q01064	.;PDE1B_HUMAN	P	190;149;170	ENSP00000243052:R190P;ENSP00000442559:R149P;ENSP00000448519:R170P	ENSP00000243052:R190P	R	+	2	0	PDE1B	53250383	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.570000	0.82390	2.433000	0.82419	0.561000	0.74099	CGG	.	.	.	none		0.512	PDE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406203.1			C	54964116	G	C	54964116	3	2	280	1	0	0	0	0	1	0	0	0	11641	1116	39	4	644	4	PDE1B	12	54964116	Missense_Mutation	SNP	G	TCGA-Y8-A8RZ-01A-11D-A36X-10	23331093	54964116	78887779	40	17865											
DCTN2	10540	hgsc.bcm.edu	37	chr12	57925883	57925883	+	Missense_Mutation	SNP	T	T	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	gtgtcaggagctgaccaaacTgcatggctacaaaagaaaag	16	6	11	8	0	1	2	1	1	0	1	1	3	1	3	1	2	4	3	1	2	6	1			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr12:57925883T>G	ENST00000548249.1	-	13	1301	c.1034A>C	c.(1033-1035)cAg>cCg	p.Q345P	DCTN2_ENST00000543672.1_Missense_Mutation_p.Q350P|DCTN2_ENST00000537439.1_Missense_Mutation_p.Q322P|DCTN2_ENST00000434715.3_Missense_Mutation_p.Q350P|DCTN2_ENST00000551400.1_5'Flank	NM_001261412.1|NM_001261413.1	NP_001248341.1|NP_001248342.1	Q13561	DCTN2_HUMAN	dynactin 2 (p50)	345					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|vesicle (GO:0031982)	motor activity (GO:0003774)|spectrin binding (GO:0030507)			endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|upper_aerodigestive_tract(2)	11						CTGACCAAACTGCATGGCTAC	0.473																																					p.Q347P		Atlas-SNP	.											.	DCTN2	51	.	0			c.A1040C						PASS	.						88	91	90					12																	57925883		1967	4139	6106	SO:0001583	missense	10540	exon13			CCAAACTGCATGG	U50733	CCDS44930.1, CCDS58245.1, CCDS73489.1	12q13.3	2008-05-14				ENSG00000175203			2712	protein-coding gene	gene with protein product		607376				8647893	Standard	NM_001261412		Approved	RBP50, DCTN-50	uc001som.2	Q13561	OTTHUMG00000170124	ENST00000548249.1:c.1034A>C	chr12.hg19:g.57925883T>G	ENSP00000447824:p.Gln345Pro	169.0	0.0	.		127.0	49.0	.	NM_001261412	B2RBK5|Q86YN2|Q9BW17	Missense_Mutation	SNP	ENST00000548249.1	hg19	CCDS58245.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.973025	0.74246	.	.	ENSG00000175203	ENST00000548249;ENST00000434715;ENST00000543672;ENST00000537439;ENST00000354743;ENST00000543105;ENST00000546758	.	.	.	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	T	0.60547	0.2277	M	0.69823	2.125	0.80722	D	1	P;P;P	0.39311	0.616;0.616;0.667	B;B;B	0.42138	0.377;0.326;0.301	T	0.62086	-0.6928	9	0.36615	T	0.2	-16.689	14.0463	0.64706	0.0:0.0:0.0:1.0	.	321;350;345	F8WAG8;F5H2S7;Q13561	.;.;DCTN2_HUMAN	P	345;350;350;322;321;258;212	.	ENSP00000346785:Q321P	Q	-	2	0	DCTN2	56212150	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.474000	0.66781	2.210000	0.71456	0.533000	0.62120	CAG	.	.	.	none		0.473	DCTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407393.2	NM_006400		G	57925883	T	G	57925883	3	3	280	1	0	0	0	0	1	0	0	0	4309	1580	55	5	179	5	DCTN2	12	57925883	Missense_Mutation	SNP	T	TCGA-Y8-A8RZ-01A-11D-A36X-10	2961767	57925883	75926012	41	17866											
UBC	7316	hgsc.bcm.edu	37	chr12	125398244	125398244	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttggatctttgccttgacaTtctcgatggtgtcactgggc	5	15	11	10	1	3	1	1	1	2	0	4	3	3	2	1	3	1	0	1	3	0	4			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr12:125398244T>C	ENST00000538617.1	-	3	390	c.74A>G	c.(73-75)aAt>aGt	p.N25S	UBC_ENST00000536769.1_Missense_Mutation_p.N25S|UBC_ENST00000339647.5_Missense_Mutation_p.N25S|MIR5188_ENST00000583467.1_RNA|UBC_ENST00000536661.1_5'UTR|UBC_ENST00000546120.1_Missense_Mutation_p.N25S			P0CG48	UBC_HUMAN	ubiquitin C	405	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)	poly(A) RNA binding (GO:0044822)|protease binding (GO:0002020)			breast(3)|endometrium(4)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.17e-05)|Epithelial(86;0.000207)|all cancers(50;0.00308)		TGCCTTGACATTCTCGATGGT	0.507																																					p.N25S		Atlas-SNP	.											.	UBC	79	.	0			c.A74G						PASS	.						208	195	200					12																	125398244		2203	4300	6503	SO:0001583	missense	7316	exon2			TTGACATTCTCGA		CCDS9260.1	12q24.3	2008-09-08			ENSG00000150991	ENSG00000150991			12468	protein-coding gene	gene with protein product	"polyubiquitin-C"	191340				1315303, 11872750	Standard	NM_021009		Approved		uc001ugs.4	P0CG48		ENST00000538617.1:c.74A>G	chr12.hg19:g.125398244T>C	ENSP00000443053:p.Asn25Ser	136.0	0.0	.		105.0	39.0	.	NM_021009	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Missense_Mutation	SNP	ENST00000538617.1	hg19		.	.	.	.	.	.	.	.	.	.	-	15.27	2.784882	0.49997	.	.	ENSG00000150991	ENST00000536769;ENST00000535460;ENST00000538617;ENST00000541046;ENST00000339647;ENST00000546120;ENST00000544656;ENST00000541272;ENST00000540351;ENST00000541645;ENST00000535131;ENST00000546271;ENST00000540700;ENST00000535859;ENST00000542416	T;T;T;T;T;T;T;T;T;T;T;T	0.73363	-0.74;-0.74;-0.74;-0.74;-0.74;-0.74;-0.74;-0.74;-0.74;-0.74;-0.74;-0.74	4.34	4.34	0.51931	Ubiquitin supergroup (1);Ubiquitin (2);	0.256216	0.22998	U	0.053119	T	0.71626	0.3362	N	0.12920	0.275	0.45427	D	0.998403	B;B;B	0.30870	0.164;0.103;0.298	B;P;P	0.49561	0.438;0.48;0.615	T	0.74970	-0.3482	10	0.87932	D	0	.	11.7986	0.52114	0.0:0.0:0.0:1.0	.	114;25;25	Q66K58;F5H7K6;P0CG48	.;.;UBC_HUMAN	S	25	ENSP00000441543:N25S;ENSP00000443053:N25S;ENSP00000344818:N25S;ENSP00000438394:N25S;ENSP00000440205:N25S;ENSP00000442800:N25S;ENSP00000445337:N25S;ENSP00000439492:N25S;ENSP00000438289:N25S;ENSP00000441238:N25S;ENSP00000437452:N25S;ENSP00000441556:N25S	ENSP00000344818:N25S	N	-	2	0	UBC	123964197	1.000000	0.71417	0.997000	0.53966	0.954000	0.61252	7.223000	0.78033	1.730000	0.51580	0.528000	0.53228	AAT	.	.	.	none		0.507	UBC-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000400179.1	NM_021009		C	125398244	T	C	125398244	3	2	280	1	0	0	0	0	1	0	0	0	16854	1493	52	3	1987	3	UBC	12	125398244	Missense_Mutation	SNP	T	TCGA-Y8-A8RZ-01A-11D-A36X-10	67472361	125398244	8453651	42	17867											
POLE	5426	hgsc.bcm.edu	37	chr12	133252404	133252404	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaccacctttggatcagatgAgcctgaacccaagtcacagc	13	7	8	13	0	2	3	2	2	0	1	2	4	2	4	4	1	4	0	4	1	3	1			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr12:133252404A>G	ENST00000320574.5	-	11	1066	c.1023T>C	c.(1021-1023)gcT>gcC	p.A341A	POLE_ENST00000535270.1_Silent_p.A314A	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	341					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)	GGATCAGATGAGCCTGAACCC	0.488								DNA polymerases (catalytic subunits)																													p.A341A		Atlas-SNP	.											.	POLE	416	.	0			c.T1023C						PASS	.						90	88	88					12																	133252404		2203	4300	6503	SO:0001819	synonymous_variant	5426	exon11			CAGATGAGCCTGA		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.1023T>C	chr12.hg19:g.133252404A>G		87.0	0.0	.		80.0	23.0	.	NM_006231	Q13533|Q86VH9	Silent	SNP	ENST00000320574.5	hg19	CCDS9278.1																																																																																			.	.	.	none		0.488	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231		G	133252404	A	G	133252404	2	3	280	1	0	0	0	0	0	0	0	1	12203	291	11	3		3	POLE	12	133252404	Silent	SNP	A	TCGA-Y8-A8RZ-01A-11D-A36X-10	7854160	133252404	599491	43	17868											
INTS6	26512	hgsc.bcm.edu	37	chr13	51952382	51952382	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatgattattaccttattcAgcaaagcaacttggaaccca	14	12	5	10	0	2	1	2	1	0	0	2	2	2	2	2	1	5	2	2	1	6	5			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr13:51952382A>G	ENST00000311234.4	-	12	2067	c.1595T>C	c.(1594-1596)cTg>cCg	p.L532P	INTS6_ENST00000490542.1_Missense_Mutation_p.L216P|INTS6_ENST00000497989.1_Missense_Mutation_p.L354P|INTS6_ENST00000398119.2_Missense_Mutation_p.L519P|INTS6_ENST00000463928.1_Intron|INTS6_ENST00000425000.1_Missense_Mutation_p.L100P	NM_012141.2	NP_036273.1	Q9UL03	INT6_HUMAN	integrator complex subunit 6	532					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)		TACCTTATTCAGCAAAGCAAC	0.363																																					p.L532P		Atlas-SNP	.											.	INTS6	72	.	0			c.T1595C						PASS	.						142	137	139					13																	51952382		2203	4300	6503	SO:0001583	missense	26512	exon12			TTATTCAGCAAAG	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.1595T>C	chr13.hg19:g.51952382A>G	ENSP00000310260:p.Leu532Pro	86.0	0.0	.		110.0	38.0	.	NM_012141	Q0P664|Q6PJP4|Q9UFK0|Q9Y5M9	Missense_Mutation	SNP	ENST00000311234.4	hg19	CCDS9428.1	.	.	.	.	.	.	.	.	.	.	A	11.33	1.605479	0.28623	.	.	ENSG00000102786	ENST00000311234;ENST00000398119;ENST00000497989;ENST00000425000;ENST00000490542	T;T;T;T;T	0.38077	1.16;1.16;1.16;1.16;1.16	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.29288	0.0729	L	0.31294	0.92	0.80722	D	1	B	0.24823	0.112	B	0.27715	0.082	T	0.06215	-1.0839	10	0.33141	T	0.24	-3.8626	14.2307	0.65890	1.0:0.0:0.0:0.0	.	532	Q9UL03	INT6_HUMAN	P	532;519;354;100;216	ENSP00000310260:L532P;ENSP00000381187:L519P;ENSP00000419871:L354P;ENSP00000406915:L100P;ENSP00000419984:L216P	ENSP00000310260:L532P	L	-	2	0	INTS6	50850383	1.000000	0.71417	1.000000	0.80357	0.234000	0.25298	9.264000	0.95635	1.956000	0.56807	0.460000	0.39030	CTG	.	.	.	none		0.363	INTS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045023.1	NM_012141		G	51952382	A	G	51952382	3	3	280	1	0	0	0	0	1	0	0	0	7789	188	7	3	1096	3	INTS6	13	51952382	Missense_Mutation	SNP	A	TCGA-Y8-A8RZ-01A-11D-A36X-10		51952382	63217496	44	17869											
SCFD1	23256	hgsc.bcm.edu	37	chr14	31164021	31164021	+	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	ttgaatatgaagaaaaaataAtgagcaaaactactctggat	20	10	7	4	0	1	4	0	3	1	1	1	5	1	5	0	1	3	1	0	1	10	4			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr14:31164021A>T	ENST00000458591.2	+	15	1512	c.1285A>T	c.(1285-1287)Atg>Ttg	p.M429L	SCFD1_ENST00000421551.3_Missense_Mutation_p.M370L|SCFD1_ENST00000554486.1_3'UTR|SCFD1_ENST00000541123.1_Missense_Mutation_p.M244L|SCFD1_ENST00000544052.2_Missense_Mutation_p.M362L|SCFD1_ENST00000396629.2_Missense_Mutation_p.M337L	NM_016106.3	NP_057190.2	Q8WVM8	SCFD1_HUMAN	sec1 family domain containing 1	429					post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|regulation of ER to Golgi vesicle-mediated transport (GO:0060628)|response to hypoxia (GO:0001666)|response to toxic substance (GO:0009636)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle docking involved in exocytosis (GO:0006904)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|Golgi transport complex (GO:0017119)|Golgi-associated vesicle (GO:0005798)|plasma membrane (GO:0005886)	syntaxin binding (GO:0019905)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)	13	Hepatocellular(127;0.0877)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)	GBM - Glioblastoma multiforme(265;0.0181)		AGAAAAAATAATGAGCAAAAC	0.269																																					p.M429L		Atlas-SNP	.											.	SCFD1	43	.	0			c.A1285T						PASS	.						56	65	62					14																	31164021		2199	4289	6488	SO:0001583	missense	23256	exon15			AAAATAATGAGCA	AF110646	CCDS9639.1, CCDS45092.1, CCDS58308.1	14q12	2006-04-04	2004-01-15	2004-01-16	ENSG00000092108	ENSG00000092108			20726	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 163"	C14orf163			Standard	NM_016106		Approved	RA410, KIAA0917, STXBP1L2, SLY1	uc001wqm.2	Q8WVM8	OTTHUMG00000029420	ENST00000458591.2:c.1285A>T	chr14.hg19:g.31164021A>T	ENSP00000390783:p.Met429Leu	339.0	0.0	.		347.0	129.0	.	NM_016106	A8K2Z5|B7Z4U7|B7Z594|O60754|O94990|Q7Z529|Q9BZI3|Q9UNL3|Q9Y6A8	Missense_Mutation	SNP	ENST00000458591.2	hg19	CCDS9639.1	.	.	.	.	.	.	.	.	.	.	A	13.86	2.363162	0.41902	.	.	ENSG00000092108	ENST00000458591;ENST00000544052;ENST00000421551;ENST00000541123;ENST00000396629	T;T;T;T;T	0.74737	-0.87;-0.87;-0.87;-0.87;-0.87	5.95	4.79	0.61399	.	0.036511	0.85682	D	0.000000	T	0.64193	0.2576	L	0.35793	1.09	0.54753	D	0.999982	B;B;B;B	0.09022	0.0;0.002;0.002;0.002	B;B;B;B	0.13407	0.004;0.007;0.009;0.007	T	0.56595	-0.7953	10	0.22706	T	0.39	-10.3234	12.9787	0.58552	0.8647:0.1353:0.0:0.0	.	370;362;337;429	B7Z738;B7Z4U7;B7Z594;Q8WVM8	.;.;.;SCFD1_HUMAN	L	429;362;370;244;337	ENSP00000390783:M429L;ENSP00000443010:M362L;ENSP00000388078:M370L;ENSP00000443537:M244L;ENSP00000379870:M337L	ENSP00000309417:M437L	M	+	1	0	SCFD1	30233772	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.314000	0.78988	1.047000	0.40274	0.533000	0.62120	ATG	.	.	.	none		0.269	SCFD1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276612.3	NM_182835		T	31164021	A	T	31164021	3	4	280	1	0	0	0	0	1	0	0	0	13902	101	4	5	1343	5	SCFD1	14	31164021	Missense_Mutation	SNP	A	TCGA-Y8-A8RZ-01A-11D-A36X-10		31164021	76185519	45	17870											
AKAP13	11214	hgsc.bcm.edu	37	chr15	86122543	86122543	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtaaagggcacggaaggccTttcgtcctgtggaaacagaa	13	7	13	8	2	0	1	0	0	0	1	2	3	1	3	2	4	1	2	2	4	5	2			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr15:86122543T>C	ENST00000394518.2	+	7	1339	c.1244T>C	c.(1243-1245)cTt>cCt	p.L415P	AKAP13_ENST00000361243.2_Missense_Mutation_p.L415P|RP11-815J21.2_ENST00000561409.1_RNA	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	415					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						ACGGAAGGCCTTTCGTCCTGT	0.507																																					p.L415P	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.T1244C						PASS	.						72	79	77					15																	86122543		2202	4299	6501	SO:0001583	missense	11214	exon7			AAGGCCTTTCGTC	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.1244T>C	chr15.hg19:g.86122543T>C	ENSP00000378026:p.Leu415Pro	152.0	0.0	.		140.0	42.0	.	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	hg19	CCDS32319.1	.	.	.	.	.	.	.	.	.	.	T	11.76	1.734133	0.30684	.	.	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540	T;T	0.15256	2.47;2.44	5.45	1.74	0.24563	.	.	.	.	.	T	0.13200	0.0320	N	0.24115	0.695	0.09310	N	0.999999	P;P	0.39883	0.567;0.693	B;B	0.43018	0.229;0.405	T	0.18053	-1.0349	9	0.66056	D	0.02	.	6.0258	0.19654	0.0:0.0831:0.3161:0.6008	.	415;415	Q12802;Q12802-2	AKP13_HUMAN;.	P	415;415;414;414	ENSP00000354718:L415P;ENSP00000378026:L415P	ENSP00000354718:L415P	L	+	2	0	AKAP13	83923547	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.266000	0.18534	0.093000	0.17368	-0.291000	0.09656	CTT	.	.	.	none		0.507	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		C	86122543	T	C	86122543	3	2	280	1	0	0	0	0	1	0	0	0	449	1609	56	3	1266	3	AKAP13	15	86122543	Missense_Mutation	SNP	T	TCGA-Y8-A8RZ-01A-11D-A36X-10		86122543	16408849	46	17871											
CLCN7	1186	hgsc.bcm.edu	37	chr16	1505758	1505760	+	In_Frame_Del	DEL	AGA	AGA	-																															ccaggtcaggaactggttccAgaaggacgcaccctcctcca																										TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr16:1505758_1505760delAGA	ENST00000382745.4	-	11	1558_1560	c.953_955delTCT	c.(952-957)ttctgg>tgg	p.F318del	CLCN7_ENST00000262318.8_In_Frame_Del_p.F294del|CLCN7_ENST00000448525.1_In_Frame_Del_p.F294del	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	318			F -> L (in OPTA2). {ECO:0000269|PubMed:19953639}.		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)				AACTGGTTCCAGAAGGACGCACC	0.626																																					p.318_319del		Atlas-Indel,Pindel	.											.	CLCN7	53	.	0			c.954_956del						PASS	.																																			SO:0001651	inframe_deletion	1186	exon11			.	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.953_955delTCT	chr16.hg19:g.1505758_1505760delAGA	ENSP00000372193:p.Phe318del	70.0	0.0	0		70.0	25.0	0.357143	NM_001287	A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	In_Frame_Del	DEL	ENST00000382745.4	hg19	CCDS32361.1																																																																																			.	.	.	none		0.626	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287		-	1505760	AGA	-	1505758	7	5	280	1	0	1	0	1	0	0	0	0	3470	188	7	0	1522	0	CLCN7	16	1505758	In_Frame_Del	DEL	AGA	TCGA-Y8-A8RZ-01A-11D-A36X-10		1505758	88848995	47	17872											
CNGB1	1258	hgsc.bcm.edu	37	chr16	57984325	57984325	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttgttctcttcttcataagCtggaaccacctctgtaccct	7	16	5	13	0	4	0	1	0	3	0	5	1	4	1	3	1	3	3	3	1	3	6			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr16:57984325C>T	ENST00000251102.8	-	13	1054	c.994G>A	c.(994-996)Gct>Act	p.A332T	CNGB1_ENST00000564448.1_Missense_Mutation_p.A326T	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	332					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						TCTTCATAAGCTGGAACCACC	0.517																																					p.A332T	Colon(156;1293 1853 16336 28962 38659)	Atlas-SNP	.											.	CNGB1	105	.	0			c.G994A						PASS	.						122	124	123					16																	57984325		2000	4159	6159	SO:0001583	missense	1258	exon13			CATAAGCTGGAAC	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.994G>A	chr16.hg19:g.57984325C>T	ENSP00000251102:p.Ala332Thr	74.0	0.0	.		88.0	37.0	.	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Missense_Mutation	SNP	ENST00000251102.8	hg19	CCDS42169.1	.	.	.	.	.	.	.	.	.	.	C	12.47	1.948067	0.34377	.	.	ENSG00000070729	ENST00000251102	T	0.22134	1.97	4.16	0.746	0.18365	.	.	.	.	.	T	0.14313	0.0346	L	0.38175	1.15	0.09310	N	1	B	0.14438	0.01	B	0.10450	0.005	T	0.26326	-1.0106	9	0.48119	T	0.1	.	3.9774	0.09479	0.0:0.5783:0.1979:0.2237	.	332	Q14028	CNGB1_HUMAN	T	332	ENSP00000251102:A332T	ENSP00000251102:A332T	A	-	1	0	CNGB1	56541826	0.000000	0.05858	0.001000	0.08648	0.117000	0.20001	0.544000	0.23253	0.472000	0.27344	0.563000	0.77884	GCT	.	.	.	none		0.517	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297		T	57984325	C	T	57984325	3	4	280	1	0	0	0	0	1	0	0	0	3602	797	28	2	2845	2	CNGB1	16	57984325	Missense_Mutation	SNP	C	TCGA-Y8-A8RZ-01A-11D-A36X-10	56478567	57984325	32370428	48	17873											
NF1	4763	hgsc.bcm.edu	37	chr17	29527522	29527522	+	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	agaaagtgctgcaattgcctGtgtcaaactgtgtaaagcaa	14	10	10	7	0	1	1	1	0	0	1	1	1	1	1	1	0	5	4	1	0	6	2			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr17:29527522G>C	ENST00000358273.4	+	9	1354	c.971G>C	c.(970-972)tGt>tCt	p.C324S	NF1_ENST00000431387.4_Missense_Mutation_p.C324S|NF1_ENST00000356175.3_Missense_Mutation_p.C324S	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	324			C -> R (in NF1; dbSNP:rs199474735). {ECO:0000269|PubMed:15060124}.		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)		GCAATTGCCTGTGTCAAACTG	0.408			"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.C324S		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.G971C						PASS	.						124	105	112					17																	29527522		2203	4300	6503	SO:0001583	missense	4763	exon9	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	TTGCCTGTGTCAA		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.971G>C	chr17.hg19:g.29527522G>C	ENSP00000351015:p.Cys324Ser	86.0	0.0	.		98.0	35.0	.	NM_001128147	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	hg19	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	G	17.15	3.316574	0.60524	.	.	ENSG00000196712	ENST00000431387;ENST00000358273;ENST00000356175	T;T;T	0.64618	2.82;-0.11;-0.11	5.39	5.39	0.77823	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.60741	0.2292	L	0.51422	1.61	0.80722	D	1	B;B;B;B;B	0.17268	0.021;0.0;0.0;0.004;0.002	B;B;B;B;B	0.17098	0.017;0.003;0.004;0.003;0.003	T	0.57625	-0.7779	10	0.52906	T	0.07	.	19.1503	0.93485	0.0:0.0:1.0:0.0	.	324;324;324;324;324	E1P657;P21359-2;P21359;Q14931;P21359-3	.;.;NF1_HUMAN;.;.	S	324	ENSP00000412921:C324S;ENSP00000351015:C324S;ENSP00000348498:C324S	ENSP00000348498:C324S	C	+	2	0	NF1	26551648	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.082000	0.94059	2.542000	0.85734	0.591000	0.81541	TGT	.	.	.	none		0.408	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		C	29527522	G	C	29527522	3	2	280	1	0	0	0	0	1	0	0	0	10363	1377	48	4	1005	4	NF1	17	29527522	Missense_Mutation	SNP	G	TCGA-Y8-A8RZ-01A-11D-A36X-10		29527522	51667688	49	17874											
ABCC3	8714	hgsc.bcm.edu	37	chr17	48738388	48738388	+	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	ctccttcctgaaggccctgcTggccaccttcggctccagct	4	10	9	18	1	0	1	0	1	0	0	4	1	3	1	6	3	2	3	6	3	1	2			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr17:48738388T>A	ENST00000285238.8	+	8	991	c.911T>A	c.(910-912)cTg>cAg	p.L304Q	ABCC3_ENST00000427699.1_Missense_Mutation_p.L304Q	NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	304					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)	AAGGCCCTGCTGGCCACCTTC	0.617																																					p.L304Q		Atlas-SNP	.											.	ABCC3	138	.	0			c.T911A						PASS	.						52	45	47					17																	48738388		2203	4300	6503	SO:0001583	missense	8714	exon8			CCCTGCTGGCCAC	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.911T>A	chr17.hg19:g.48738388T>A	ENSP00000285238:p.Leu304Gln	43.0	0.0	.		65.0	27.0	.	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Missense_Mutation	SNP	ENST00000285238.8	hg19	CCDS32681.1	.	.	.	.	.	.	.	.	.	.	T	10.73	1.431575	0.25813	.	.	ENSG00000108846	ENST00000427699;ENST00000285238	D;D	0.95756	-2.58;-3.8	5.18	2.91	0.33838	ABC transporter, transmembrane domain, type 1 (1);	1.527580	0.04347	N	0.355032	D	0.95040	0.8394	M	0.74467	2.265	0.09310	N	1	P;P	0.43885	0.694;0.82	B;B	0.43575	0.388;0.424	D	0.83488	0.0068	10	0.36615	T	0.2	-0.3139	6.5554	0.22458	0.1376:0.076:0.0:0.7865	.	304;304	O15438;O15438-5	MRP3_HUMAN;.	Q	304	ENSP00000395160:L304Q;ENSP00000285238:L304Q	ENSP00000285238:L304Q	L	+	2	0	ABCC3	46093387	0.001000	0.12720	0.002000	0.10522	0.170000	0.22686	1.077000	0.30741	0.273000	0.22049	-0.669000	0.03829	CTG	.	.	.	none		0.617	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038		A	48738388	T	A	48738388	3	1	280	1	0	0	0	0	1	0	0	0	54	1580	55	5	941	5	ABCC3	17	48738388	Missense_Mutation	SNP	T	TCGA-Y8-A8RZ-01A-11D-A36X-10	19210866	48738388	32456822	50	17875											
SMURF2	64750	hgsc.bcm.edu	37	chr17	62542409	62542409	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctttcggcaggttgttagTgcaggcatcaatctggtgta	7	13	14	7	1	2	0	1	0	1	0	3	0	2	0	0	5	1	7	0	5	3	4			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr17:62542409T>C	ENST00000262435.9	-	18	2306	c.2119A>G	c.(2119-2121)Act>Gct	p.T707A		NM_022739.3	NP_073576.1	Q9HAU4	SMUF2_HUMAN	SMAD specific E3 ubiquitin protein ligase 2	707	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				BMP signaling pathway (GO:0030509)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|SMAD binding (GO:0046332)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)|skin(4)	22	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)			AGGTTGTTAGTGCAGGCATCA	0.443																																					p.T707A		Atlas-SNP	.											.	SMURF2	63	.	0			c.A2119G						PASS	.						138	117	124					17																	62542409		2203	4300	6503	SO:0001583	missense	64750	exon18			TGTTAGTGCAGGC	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.2119A>G	chr17.hg19:g.62542409T>C	ENSP00000262435:p.Thr707Ala	86.0	0.0	.		91.0	38.0	.	NM_022739	Q52LL1|Q9H260	Missense_Mutation	SNP	ENST00000262435.9	hg19	CCDS32707.1	.	.	.	.	.	.	.	.	.	.	T	2.270	-0.367160	0.05069	.	.	ENSG00000108854	ENST00000262435	T	0.57273	0.41	5.62	4.53	0.55603	HECT (4);	0.102243	0.64402	N	0.000003	T	0.45577	0.1349	L	0.52759	1.655	0.80722	D	1	B	0.02656	0.0	B	0.09377	0.004	T	0.30268	-0.9984	10	0.32370	T	0.25	.	11.3438	0.49548	0.0:0.0711:0.0:0.9289	.	707	Q9HAU4	SMUF2_HUMAN	A	707	ENSP00000262435:T707A	ENSP00000262435:T707A	T	-	1	0	SMURF2	59972871	1.000000	0.71417	0.998000	0.56505	0.217000	0.24651	4.099000	0.57755	0.955000	0.37878	0.402000	0.26972	ACT	.	.	.	none		0.443	SMURF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445227.1	NM_022739		C	62542409	T	C	62542409	3	2	280	1	0	0	0	0	1	0	0	0	14833	1696	59	3	135	3	SMURF2	17	62542409	Missense_Mutation	SNP	T	TCGA-Y8-A8RZ-01A-11D-A36X-10	13804021	62542409	18652801	51	17876											
HGS	9146	hgsc.bcm.edu	37	chr17	79660684	79660684	+	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	ccctccccgcttgtcctcagCtgccccccaagagggacgag	6	6	10	19	2	1	1	1	0	0	1	3	3	3	2	7	1	2	2	7	1	1	1			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr17:79660684C>T	ENST00000329138.4	+	10	877	c.742C>T	c.(742-744)Ctg>Ttg	p.L248L		NM_004712.4	NP_004703.1	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine kinase substrate	248	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)			TTGTCCTCAGCTGCCCCCCAA	0.701																																					p.L248L		Atlas-SNP	.											.	HGS	54	.	0			c.C742T						PASS	.						10	11	11					17																	79660684		2149	4193	6342	SO:0001630	splice_region_variant	9146	exon10			CCTCAGCTGCCCC	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.742-1C>T	chr17.hg19:g.79660684C>T		117.0	0.0	.		115.0	5.0	.	NM_004712	Q9NR36	Silent	SNP	ENST00000329138.4	hg19	CCDS11784.1																																																																																			.	.	.	none		0.701	HGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440541.1	NM_004712	Silent	T	79660684	C	T	79660684	5	4	280	1	0	0	0	0	0	0	1	0	7094	811	28	2	780	2	HGS	17	79660684	Splice_Site	SNP	C	TCGA-Y8-A8RZ-01A-11D-A36X-10	17118275	79660684	1534526	52	17877											
APCDD1	147495	hgsc.bcm.edu	37	chr18	10471923	10471923	+	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	catgaacttcagctcatccgGgtggagaagcagtaccttca	11	9	10	11	1	3	2	3	1	0	1	4	3	4	2	2	2	4	3	2	2	3	3			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr18:10471923G>C	ENST00000355285.5	+	3	993	c.639G>C	c.(637-639)cgG>cgC	p.R213R	APCDD1_ENST00000578882.1_Intron	NM_153000.4	NP_694545.1			adenomatosis polyposis coli down-regulated 1											NS(1)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				READ - Rectum adenocarcinoma(15;0.08)		AGCTCATCCGGGTGGAGAAGC	0.577																																					p.R213R		Atlas-SNP	.											.	APCDD1	57	.	0			c.G639C						PASS	.						136	124	128					18																	10471923		2203	4300	6503	SO:0001819	synonymous_variant	147495	exon3			CATCCGGGTGGAG	AB056722	CCDS11849.1	18p11.21	2006-07-07			ENSG00000154856	ENSG00000154856			15718	protein-coding gene	gene with protein product		607479				12384519	Standard	NM_153000		Approved	B7323	uc002kom.4	Q8J025	OTTHUMG00000131635	ENST00000355285.5:c.639G>C	chr18.hg19:g.10471923G>C		91.0	0.0	.		110.0	39.0	.	NM_153000		Silent	SNP	ENST00000355285.5	hg19	CCDS11849.1																																																																																			.	.	.	none		0.577	APCDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254529.2	NM_153000		C	10471923	G	C	10471923	2	2	280	1	0	0	0	0	0	0	0	1	765	1219	43	4		4	APCDD1	18	10471923	Silent	SNP	G	TCGA-Y8-A8RZ-01A-11D-A36X-10		10471923	67605325	53	17878											
KANK3	256949	hgsc.bcm.edu	37	chr19	8389663	8389663	+	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	acacgccagtagggttgccaCcatgtcctgtcggccatggc	7	8	12	14	2	0	0	0	0	0	0	2	0	1	0	5	3	1	2	5	3	1	2			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr19:8389663C>T	ENST00000593649.1	-	9	2199	c.2134G>A	c.(2134-2136)Gtg>Atg	p.V712M	KANK3_ENST00000330915.3_Missense_Mutation_p.V712M			Q6NY19	KANK3_HUMAN	KN motif and ankyrin repeat domains 3	712										breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	9						AGGGTTGCCACCATGTCCTGT	0.642																																					p.V712M		Atlas-SNP	.											.	KANK3	35	.	0			c.G2134A						PASS	.						51	41	45					19																	8389663		2203	4300	6503	SO:0001583	missense	256949	exon9			TTGCCACCATGTC	AK128815	CCDS12199.1	19p13.2	2013-01-10	2008-01-29	2008-01-29		ENSG00000186994		"KN motif and ankyrin repeat domain containing", "Ankyrin repeat domain containing"	24796	protein-coding gene	gene with protein product		614611	"ankyrin repeat domain 47"	ANKRD47		17996375, 19554261	Standard	NM_198471		Approved	FLJ46061	uc010dwa.3	Q6NY19		ENST00000593649.1:c.2134G>A	chr19.hg19:g.8389663C>T	ENSP00000470728:p.Val712Met	42.0	0.0	.		68.0	25.0	.	NM_198471	Q6NZI1|Q6ZQR3|Q8IUV2	Missense_Mutation	SNP	ENST00000593649.1	hg19		.	.	.	.	.	.	.	.	.	.	C	22.6	4.317784	0.81469	.	.	ENSG00000186994	ENST00000330915	T	0.71222	-0.55	4.67	4.67	0.58626	.	.	.	.	.	D	0.82618	0.5076	M	0.69463	2.115	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.84855	0.0816	9	0.87932	D	0	-25.0819	16.3	0.82806	0.0:1.0:0.0:0.0	.	712	Q6NY19-2	.	M	712	ENSP00000328923:V712M	ENSP00000328923:V712M	V	-	1	0	KANK3	8295663	1.000000	0.71417	1.000000	0.80357	0.767000	0.43475	7.513000	0.81739	2.416000	0.81992	0.561000	0.74099	GTG	.	.	.	none		0.642	KANK3-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000461379.1	NM_198471		T	8389663	C	T	8389663	3	4	280	1	0	0	0	0	1	0	0	0	7985	507	18	2	343	2	KANK3	19	8389663	Missense_Mutation	SNP	C	TCGA-Y8-A8RZ-01A-11D-A36X-10		8389663	50739320	54	17879											
TMED1	11018	hgsc.bcm.edu	37	chr19	10945667	10945667	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctccacagcctctgcccaTccttcgacctcctcgtcatc	5	10	6	20	2	2	0	1	0	1	0	8	1	5	0	6	1	2	1	6	1	0	1			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr19:10945667T>C	ENST00000214869.2	-	3	506	c.408A>G	c.(406-408)ggA>ggG	p.G136G	TMED1_ENST00000588289.1_5'UTR|C19orf38_ENST00000592854.1_5'Flank|TMED1_ENST00000591695.1_Intron	NM_006858.2	NP_006849.1	Q13445	TMED1_HUMAN	transmembrane emp24 protein transport domain containing 1	136					cell-cell signaling (GO:0007267)|protein transport (GO:0015031)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|lung(2)|ovary(3)|prostate(1)|skin(1)	10						CCTCTGCCCATCCTTCGACCT	0.542																																					p.G136G		Atlas-SNP	.											.	TMED1	22	.	0			c.A408G						PASS	.						166	154	158					19																	10945667		2203	4300	6503	SO:0001819	synonymous_variant	11018	exon3			TGCCCATCCTTCG	U41804	CCDS12249.1	19p13.2	2008-02-05	2005-08-26			ENSG00000099203			17291	protein-coding gene	gene with protein product		605395	"transmembrane emp24 domain containing 1"			11466339, 8621446	Standard	NM_006858		Approved	ST2L, MGC1270, IL1RL1LG, Il1rl1l	uc002mpy.3	Q13445		ENST00000214869.2:c.408A>G	chr19.hg19:g.10945667T>C		69.0	0.0	.		88.0	37.0	.	NM_006858		Silent	SNP	ENST00000214869.2	hg19	CCDS12249.1																																																																																			.	.	.	none		0.542	TMED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452614.1	NM_006858		C	10945667	T	C	10945667	2	2	280	1	0	0	0	0	0	0	0	1	16014	1422	50	3		3	TMED1	19	10945667	Silent	SNP	T	TCGA-Y8-A8RZ-01A-11D-A36X-10	2556004	10945667	48183316	55	17880											
USP29	57663	hgsc.bcm.edu	37	chr19	57642200	57642200	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatggcttttatgactgtaaAgaaaacaggattccagaagg	16	10	10	5	0	0	3	0	1	0	2	1	4	1	4	1	3	1	2	1	3	7	4	rs562830906		TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr19:57642200A>G	ENST00000254181.4	+	4	2611	c.2157A>G	c.(2155-2157)aaA>aaG	p.K719K	USP29_ENST00000598197.1_Silent_p.K719K	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	719	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)		ATGACTGTAAAGAAAACAGGA	0.423																																					p.K719K		Atlas-SNP	.											USP29,caecum,carcinoma,0,2	USP29	186	.	0			c.A2157G						PASS	.						73	71	72					19																	57642200		2203	4300	6503	SO:0001819	synonymous_variant	57663	exon4			CTGTAAAGAAAAC		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.2157A>G	chr19.hg19:g.57642200A>G		231.0	0.0	.		236.0	95.0	.	NM_020903		Silent	SNP	ENST00000254181.4	hg19	CCDS33124.1																																																																																			.	.	.	none		0.423	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1			G	57642200	A	G	57642200	2	3	280	1	0	0	0	0	0	0	0	1	17071	69	3	3		3	USP29	19	57642200	Silent	SNP	A	TCGA-Y8-A8RZ-01A-11D-A36X-10	46696533	57642200	1486783	56	17881											
ZNF544	27300	hgsc.bcm.edu	37	chr19	58772847	58772847	+	Missense_Mutation	SNP	A	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	gaatgaacagaagccagtgcAttttgggaaaagtcagtatg	15	9	12	5	0	1	2	1	1	0	1	1	4	1	3	1	1	3	2	1	1	6	3			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr19:58772847A>C	ENST00000596652.1	+	6	1109	c.875A>C	c.(874-876)cAt>cCt	p.H292P	ZNF544_ENST00000599953.1_Missense_Mutation_p.H150P|ZNF544_ENST00000600044.1_Missense_Mutation_p.H264P|ZNF544_ENST00000599227.1_3'UTR|ZNF544_ENST00000596825.1_3'UTR|CTD-3138B18.4_ENST00000600029.1_Intron|ZNF544_ENST00000595981.1_Intron|ZNF544_ENST00000269829.4_Missense_Mutation_p.H292P|ZNF544_ENST00000415203.2_Missense_Mutation_p.H264P|ZNF544_ENST00000596929.1_Intron|CTD-3138B18.5_ENST00000597230.1_RNA|ZNF544_ENST00000600220.1_Missense_Mutation_p.H264P			Q6NX49	ZN544_HUMAN	zinc finger protein 544	292					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|skin(1)|urinary_tract(1)	18		all_cancers(17;4.17e-12)|all_epithelial(17;1.25e-08)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.17)|GBM - Glioblastoma multiforme(193;0.018)		AAGCCAGTGCATTTTGGGAAA	0.443																																					p.H292P		Atlas-SNP	.											.	ZNF544	57	.	0			c.A875C						PASS	.						71	70	71					19																	58772847		2203	4300	6503	SO:0001583	missense	27300	exon7			CAGTGCATTTTGG	AF020591	CCDS12973.1	19q13.43	2013-01-08				ENSG00000198131		"Zinc fingers, C2H2-type", "-"	16759	protein-coding gene	gene with protein product	"zinc finger protein AF020591"						Standard	NM_014480		Approved	AF020591	uc010euo.3	Q6NX49		ENST00000596652.1:c.875A>C	chr19.hg19:g.58772847A>C	ENSP00000469635:p.His292Pro	137.0	0.0	.		122.0	51.0	.	NM_014480	A8K6J1|Q9UEX4	Missense_Mutation	SNP	ENST00000596652.1	hg19	CCDS12973.1	.	.	.	.	.	.	.	.	.	.	A	11.31	1.599650	0.28534	.	.	ENSG00000198131	ENST00000269829;ENST00000415203	T;T	0.29142	1.58;1.58	3.37	-3.78	0.04333	.	.	.	.	.	T	0.49626	0.1568	M	0.84585	2.705	0.09310	N	1	B;D;D	0.89917	0.001;1.0;0.963	B;D;P	0.68192	0.001;0.956;0.468	T	0.43180	-0.9407	9	0.62326	D	0.03	.	5.5574	0.17123	0.3664:0.4309:0.2027:0.0	.	264;264;292	B7ZAY1;B4DL50;Q6NX49	.;.;ZN544_HUMAN	P	292;264	ENSP00000269829:H292P;ENSP00000394341:H264P	ENSP00000269829:H292P	H	+	2	0	ZNF544	63464659	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.063000	0.11655	-0.641000	0.05487	0.533000	0.62120	CAT	.	.	.	none		0.443	ZNF544-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466754.1	NM_014480		C	58772847	A	C	58772847	3	2	280	1	0	0	0	0	1	0	0	0	17989	217	8	5	889	5	ZNF544	19	58772847	Missense_Mutation	SNP	A	TCGA-Y8-A8RZ-01A-11D-A36X-10	1130647	58772847	356136	57	17882											
PCSK2	5126	hgsc.bcm.edu	37	chr20	17462589	17462589	+	Silent	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	ctgcatggcactcagagtgcCccgtacatcgaccaggtggt	8	8	12	13	2	1	1	1	0	0	1	2	2	1	1	3	3	3	3	3	3	1	1			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chr20:17462589C>T	ENST00000262545.2	+	12	2106	c.1791C>T	c.(1789-1791)gcC>gcT	p.A597A	PCSK2_ENST00000459871.1_3'UTR|PCSK2_ENST00000536609.1_Silent_p.A562A|PCSK2_ENST00000377899.1_Silent_p.A578A	NM_002594.3	NP_002585.2	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	597					cellular protein metabolic process (GO:0044267)|embryo development (GO:0009790)|enkephalin processing (GO:0034230)|insulin processing (GO:0030070)|islet amyloid polypeptide processing (GO:0034231)|nervous system development (GO:0007399)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	dendrite (GO:0030425)|extracellular space (GO:0005615)|membrane (GO:0016020)|perikaryon (GO:0043204)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|lung(17)|ovary(3)|pancreas(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	53					"""Insulin(DB00071)|Insulin Regular(DB00030)"	CTCAGAGTGCCCCGTACATCG	0.622																																					p.A597A		Atlas-SNP	.											.	PCSK2	112	.	0			c.C1791T						PASS	.						32	29	30					20																	17462589		2203	4300	6503	SO:0001819	synonymous_variant	5126	exon12			GAGTGCCCCGTAC	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.1791C>T	chr20.hg19:g.17462589C>T		122.0	0.0	.		105.0	46.0	.	NM_002594	B1ANH9|B4DFQ3|Q14927|Q5JYQ1|Q8IWA8|Q9NQG3|Q9NUG1|Q9UJC6	Silent	SNP	ENST00000262545.2	hg19	CCDS13125.1																																																																																			.	.	.	none		0.622	PCSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078120.2	NM_002594		T	17462589	C	T	17462589	2	4	280	1	0	0	0	0	0	0	0	1	11608	610	22	2		2	PCSK2	20	17462589	Silent	SNP	C	TCGA-Y8-A8RZ-01A-11D-A36X-10		17462589	45562931	58	17883											
MAGEA4	4103	hgsc.bcm.edu	37	chrX	151092151	151092151	+	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	gtcatcatgtcttctgagcaGaagagtcagcactgcaagcc	11	9	10	11	0	5	3	3	1	2	2	5	3	5	3	1	0	4	3	1	0	2	1			TCGA-Y8-A8RZ-01A-11D-A36X-10	TCGA-Y8-A8RZ-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	63f0d3c3-071e-44c7-863d-72f0242c5b93	2a0d89df-334c-4d21-ad1d-0040556032a0	g.chrX:151092151G>A	ENST00000360243.2	+	3	282	c.15G>A	c.(13-15)caG>caA	p.Q5Q	MAGEA4_ENST00000370337.4_Silent_p.Q5Q|MAGEA4_ENST00000370340.3_Silent_p.Q5Q|MAGEA4_ENST00000276344.2_Silent_p.Q5Q|MAGEA4_ENST00000393921.1_Silent_p.Q5Q|MAGEA4_ENST00000393920.1_Silent_p.Q5Q|MAGEA4_ENST00000370335.1_Silent_p.Q5Q	NM_001011550.1	NP_001011550.1	P43358	MAGA4_HUMAN	melanoma antigen family A, 4	5										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)					CTTCTGAGCAGAAGAGTCAGC	0.602																																					p.Q5Q		Atlas-SNP	.											.	MAGEA4	68	.	0			c.G15A						PASS	.						44	43	43					X																	151092151		2203	4300	6503	SO:0001819	synonymous_variant	4103	exon3			TGAGCAGAAGAGT		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.15G>A	chrX.hg19:g.151092151G>A		114.0	0.0	.		95.0	54.0	.	NM_001011548	Q14798	Silent	SNP	ENST00000360243.2	hg19	CCDS14702.1																																																																																			.	.	.	none		0.602	MAGEA4-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060898.1	NM_002362		A	151092151	G	A	151092151	2	1	280	1	0	0	0	0	0	0	0	1	9175	933	33	2		2	MAGEA4	23	151092151	Silent	SNP	G	TCGA-Y8-A8RZ-01A-11D-A36X-10		151092151	4178409	59	17884											
LCE2C	353140	hgsc.bcm.edu	37	chr1	152648496	152648496	+	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	ctaaactcctgccagcatgtCttgccagcaaaaccagcagc	12	7	7	15	0	1	0	0	0	1	0	2	0	2	0	4	0	8	3	4	0	4	2			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr1:152648496C>T	ENST00000368783.1	+	2	60	c.5C>T	c.(4-6)tCt>tTt	p.S2F	LCE2B_ENST00000417924.2_Intron	NM_178429.2	NP_848516.1	Q5TA81	LCE2C_HUMAN	late cornified envelope 2C	2					keratinization (GO:0031424)					endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)	13	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCCAGCATGTCTTGCCAGCAA	0.448																																					p.S2F		Atlas-SNP	.											.	LCE2C	24	.	0			c.C5T						PASS	.						106	116	112					1																	152648496		2203	4300	6503	SO:0001583	missense	353140	exon2			GCATGTCTTGCCA		CCDS1019.1	1q21.3	2008-02-05			ENSG00000187180	ENSG00000187180		"Late cornified envelopes"	29460	protein-coding gene	gene with protein product		612611				11698679	Standard	NM_178429		Approved	LEP11	uc001fah.4	Q5TA81	OTTHUMG00000012389	ENST00000368783.1:c.5C>T	chr1.hg19:g.152648496C>T	ENSP00000357772:p.Ser2Phe	116.0	0.0	.		154.0	77.0	.	NM_178429		Missense_Mutation	SNP	ENST00000368783.1	hg19	CCDS1019.1	.	.	.	.	.	.	.	.	.	.	C	6.631	0.484808	0.12641	.	.	ENSG00000187180	ENST00000368783	T	0.06371	3.31	3.27	2.34	0.29019	.	.	.	.	.	T	0.03695	0.0105	M	0.79805	2.47	0.23776	N	0.996871	B	0.09022	0.002	B	0.10450	0.005	T	0.32613	-0.9900	9	0.87932	D	0	.	6.3247	0.21237	0.0:0.8572:0.0:0.1428	.	2	Q5TA81	LCE2C_HUMAN	F	2	ENSP00000357772:S2F	ENSP00000357772:S2F	S	+	2	0	LCE2C	150915120	1.000000	0.71417	0.993000	0.49108	0.731000	0.41821	2.058000	0.41374	0.703000	0.31848	0.563000	0.77884	TCT	.	.	.	none		0.448	LCE2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034509.1	NM_178429		T	152648496	C	T	152648496	3	4	281	1	0	0	0	0	1	0	0	0	8674	913	32	2	7	2	LCE2C	1	152648496	Missense_Mutation	SNP	C	TCGA-Y8-A8S0-01A-11D-A36X-10		152648496	96602125	1	17885											
OLFML2B	25903	hgsc.bcm.edu	37	chr1	161993092	161993092	+	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	tccgcctcgttttgcagagtCtcgtcctccgcaggcgccac	4	10	10	17	5	1	1	0	0	1	1	6	1	4	1	5	1	1	3	5	1	0	2			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr1:161993092C>G	ENST00000294794.3	-	1	552	c.129G>C	c.(127-129)gaG>gaC	p.E43D	OLFML2B_ENST00000367940.2_Missense_Mutation_p.E43D	NM_015441.1	NP_056256.1	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B	43					extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)			TTTGCAGAGTCTCGTCCTCCG	0.597																																					p.E43D		Atlas-SNP	.											.	OLFML2B	114	.	0			c.G129C						PASS	.						149	126	134					1																	161993092		2203	4300	6503	SO:0001583	missense	25903	exon1			CAGAGTCTCGTCC	BX648975	CCDS1236.1, CCDS72966.1	1q23.1	2008-02-05			ENSG00000162745	ENSG00000162745			24558	protein-coding gene	gene with protein product							Standard	XM_005245075		Approved	DKFZP586L151	uc001gbu.3	Q68BL8	OTTHUMG00000024047	ENST00000294794.3:c.129G>C	chr1.hg19:g.161993092C>G	ENSP00000294794:p.Glu43Asp	131.0	0.0	.		118.0	26.0	.	NM_015441	B7ZA39|Q5VU96|Q6NX46|Q86X11|Q9Y3X6	Missense_Mutation	SNP	ENST00000294794.3	hg19	CCDS1236.1	.	.	.	.	.	.	.	.	.	.	C	11.79	1.742353	0.30865	.	.	ENSG00000162745	ENST00000294794;ENST00000367940	T;T	0.50548	0.74;0.74	4.96	1.86	0.25419	.	.	.	.	.	T	0.10852	0.0265	N	0.08118	0	0.24182	N	0.995582	B;B	0.15930	0.015;0.004	B;B	0.12156	0.007;0.003	T	0.16571	-1.0398	8	0.19147	T	0.46	.	12.6021	0.56503	0.0:0.4827:0.5173:0.0	.	43;43	F2Z3N3;Q68BL8	.;OLM2B_HUMAN	D	43	ENSP00000294794:E43D;ENSP00000356917:E43D	ENSP00000294794:E43D	E	-	3	2	OLFML2B	160259716	0.911000	0.30947	0.412000	0.26496	0.824000	0.46624	0.373000	0.20484	0.209000	0.20645	0.561000	0.74099	GAG	.	.	.	none		0.597	OLFML2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060552.2	NM_015441		G	161993092	C	G	161993092	3	3	281	1	0	0	0	0	1	0	0	0	10865	912	32	4	2155	4	OLFML2B	1	161993092	Missense_Mutation	SNP	C	TCGA-Y8-A8S0-01A-11D-A36X-10	9344596	161993092	87257529	2	17886											
PPP1R12B	4660	hgsc.bcm.edu	37	chr1	202418132	202418132	+	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	ttcaggactcctcacaaatcCcaggccgacacaacagcaga	14	5	7	15	1	2	1	2	0	0	1	4	3	4	2	3	2	2	1	3	2	2	1			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr1:202418132C>G	ENST00000608999.1	+	13	1836	c.1683C>G	c.(1681-1683)tcC>tcG	p.S561S	PPP1R12B_ENST00000336894.4_Silent_p.S561S	NM_001197131.1|NM_002481.3	NP_001184060.1|NP_002472.2	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory subunit 12B	561					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)|regulation of muscle contraction (GO:0006937)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	enzyme activator activity (GO:0008047)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(17)|ovary(4)|skin(3)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(75;0.166)			CTCACAAATCCCAGGCCGACA	0.468																																					p.S561S		Atlas-SNP	.											.	PPP1R12B	100	.	0			c.C1683G						PASS	.						99	96	97					1																	202418132		2203	4300	6503	SO:0001819	synonymous_variant	4660	exon13			CAAATCCCAGGCC	AB003062	CCDS1426.1, CCDS44294.1, CCDS44295.1, CCDS53458.1, CCDS53459.1, CCDS73005.1	1q32.1	2013-01-10	2011-10-04	2001-08-10	ENSG00000077157	ENSG00000077157		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "Ankyrin repeat domain containing"	7619	protein-coding gene	gene with protein product	"myosin phosphatase regulatory subunit", "myosin phosphatase, target subunit 2"	603768	"protein phosphatase 1, regulatory (inhibitor) subunit 12B"	MYPT2		9570949	Standard	NM_002481		Approved	MGC87886, MGC131980, PP1bp55	uc001gya.2	O60237	OTTHUMG00000041393	ENST00000608999.1:c.1683C>G	chr1.hg19:g.202418132C>G		145.0	0.0	.		125.0	46.0	.	NM_002481	A8MYF5|B7ZMN6|Q2TAI8|Q5T506|Q5VUK2|Q8N179|Q9HCB7|Q9HCB8	Silent	SNP	ENST00000608999.1	hg19	CCDS1426.1																																																																																			.	.	.	none		0.468	PPP1R12B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099166.3	NM_032105		G	202418132	C	G	202418132	2	3	281	1	0	0	0	0	0	0	0	1	12365	610	22	4		4	PPP1R12B	1	202418132	Silent	SNP	C	TCGA-Y8-A8S0-01A-11D-A36X-10	40425040	202418132	46832489	3	17887											
KCNH1	3756	hgsc.bcm.edu	37	chr1	210857406	210857406	+	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	gggtggtccgggggcaagatCaggggggcctcattctttcg	5	9	18	9	2	3	1	2	0	1	1	5	1	4	1	2	7	0	1	2	7	1	2			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr1:210857406C>A	ENST00000271751.4	-	11	2214	c.2187G>T	c.(2185-2187)ctG>ctT	p.L729L	KCNH1_ENST00000367007.4_Silent_p.L702L			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	729	Calmodulin-binding.				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)		GGGGCAAGATCAGGGGGGCCT	0.577																																					p.L729L		Atlas-SNP	.											.	KCNH1	199	.	0			c.G2187T						PASS	.						59	59	59					1																	210857406		2203	4300	6503	SO:0001819	synonymous_variant	3756	exon11			CAAGATCAGGGGG	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.2187G>T	chr1.hg19:g.210857406C>A		56.0	0.0	.		55.0	21.0	.	NM_172362	B1AQ26|O76035|Q14CL3	Silent	SNP	ENST00000271751.4	hg19	CCDS1496.1																																																																																			.	.	.	none		0.577	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238		A	210857406	C	A	210857406	2	1	281	1	0	0	0	0	0	0	0	1	8038	813	29	4		4	KCNH1	1	210857406	Silent	SNP	C	TCGA-Y8-A8S0-01A-11D-A36X-10	8439274	210857406	38393215	4	17888											
GTF3C2	2976	hgsc.bcm.edu	37	chr2	27556578	27556578	+	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	tggtaggcatccaggccaggCtaaggcactgaccacactca	11	6	11	13	0	1	1	1	1	0	0	2	1	2	1	3	5	0	4	3	5	2	2			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr2:27556578C>T	ENST00000359541.2	-	12	2105	c.1676G>A	c.(1675-1677)aGc>aAc	p.S559N	AC109828.1_ENST00000592265.1_RNA|GTF3C2_ENST00000264720.3_Missense_Mutation_p.S559N|AC109828.1_ENST00000585326.1_RNA|AC109828.1_ENST00000608473.1_RNA|AC109828.1_ENST00000416453.2_RNA			Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide 2, beta 110kDa	559					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)				central_nervous_system(4)|endometrium(6)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	38	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCAGGCCAGGCTAAGGCACTG	0.473																																					p.H559H		Atlas-SNP	.											.	GTF3C2	73	.	0			c.A1676A						PASS	.						120	123	122					2																	27556578		2203	4300	6503	SO:0001583	missense	2976	exon13			GCCAGGCTAAGGC	D13636	CCDS1749.1	2p23.3	2013-01-10	2002-08-29		ENSG00000115207	ENSG00000115207		"General transcription factors", "WD repeat domain containing"	4665	protein-coding gene	gene with protein product		604883	"general transcription factor IIIC, polypeptide 2 (beta subunit, 110kD)"			7729686	Standard	NM_001521		Approved	KIAA0011, TFIIIC110	uc002rjw.2	Q8WUA4	OTTHUMG00000097785	ENST00000359541.2:c.1676G>A	chr2.hg19:g.27556578C>T	ENSP00000352536:p.Ser559Asn	163.0	0.0	.		168.0	10.0	.	NM_001521	D6W557|Q16632|Q9BWI7	Silent	SNP	ENST00000359541.2	hg19	CCDS1749.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.81|15.81	2.943988|2.943988	0.53079|0.53079	.|.	.|.	ENSG00000115207|ENSG00000115207	ENST00000454704|ENST00000359541;ENST00000264720	.|T;T	.|0.68025	.|-0.3;-0.3	5.39|5.39	4.48|4.48	0.54585|0.54585	.|WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	.|0.237726	.|0.43110	.|D	.|0.000610	T|T	0.60209|0.60209	0.2251|0.2251	L|L	0.36672|0.36672	1.1|1.1	0.30311|0.30311	N|N	0.788563|0.788563	.|P;P	.|0.52316	.|0.952;0.651	.|P;B	.|0.46452	.|0.517;0.212	T|T	0.62044|0.62044	-0.6937|-0.6937	5|10	.|0.37606	.|T	.|0.19	-12.0259|-12.0259	12.7939|12.7939	0.57549|0.57549	0.0:0.702:0.298:0.0|0.0:0.702:0.298:0.0	.|.	.|559;559	.|Q8WUA4-2;Q8WUA4	.|.;TF3C2_HUMAN	T|N	68|559	.|ENSP00000352536:S559N;ENSP00000264720:S559N	.|ENSP00000264720:S559N	A|S	-|-	1|2	0|0	GTF3C2|GTF3C2	27410082|27410082	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.290000|2.290000	0.43531|0.43531	2.537000|2.537000	0.85549|0.85549	0.655000|0.655000	0.94253|0.94253	GCC|AGC	.	.	.	none		0.473	GTF3C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215028.2			T	27556578	C	T	27556578	3	4	281	1	0	0	0	0	1	0	0	0	6880	797	28	2	1091	2	GTF3C2	2	27556578	Missense_Mutation	SNP	C	TCGA-Y8-A8S0-01A-11D-A36X-10		27556578	215642795	5	17889											
NEB	4703	hgsc.bcm.edu	37	chr2	152359933	152359933	+	Frame_Shift_Del	DEL	C	C	-																															cagtggttggaatgcctgttCccaagttttctttgtacata																										TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr2:152359933delC	ENST00000172853.10	-	138	18809	c.18662delG	c.(18661-18663)ggafs	p.G6221fs	NEB_ENST00000498015.2_Intron|NEB_ENST00000604864.1_Frame_Shift_Del_p.G7922fs|NEB_ENST00000603639.1_Frame_Shift_Del_p.G7922fs|NEB_ENST00000509223.2_Frame_Shift_Del_p.G52fs|NEB_ENST00000397336.2_5'UTR|NEB_ENST00000427231.2_Frame_Shift_Del_p.G7922fs|NEB_ENST00000409198.1_Frame_Shift_Del_p.G6221fs|NEB_ENST00000397345.3_Frame_Shift_Del_p.G7922fs			P20929	NEBU_HUMAN	nebulin	6221					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)		AATGCCTGTTCCCAAGTTTTC	0.363																																					p.G7957fs		Atlas-INDEL	.											.	NEB	1697	.	0			c.23871delA						PASS	.						89	85	86					2																	152359933		1833	4091	5924	SO:0001589	frameshift_variant	4703	exon167			.	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.18662delG	chr2.hg19:g.152359933delC	ENSP00000172853:p.Gly6221fs	113.0	0.0	0		91.0	43.0	0.472527	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Frame_Shift_Del	DEL	ENST00000172853.10	hg19																																																																																				.	.	.	none		0.363	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		-	152359933	C	-	152359933	7	5	281	1	0	1	0	1	0	0	0	0	10309	855	30	0	1880	0	NEB	2	152359933	Frame_Shift_Del	DEL	C	TCGA-Y8-A8S0-01A-11D-A36X-10	124803355	152359933	90839440	6	17890											
PASK	23178	hgsc.bcm.edu	37	chr2	242077491	242077491	+	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	gcaaagagactgtcacatgaCgtgacggtgccctggaggaa	12	6	14	9	2	1	3	1	2	0	1	1	6	1	5	1	3	1	1	1	3	2	0	rs374396215		TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr2:242077491C>T	ENST00000405260.1	-	6	1451	c.753G>A	c.(751-753)acG>acA	p.T251T	PASK_ENST00000403638.3_Silent_p.T251T|PASK_ENST00000544142.1_Silent_p.T65T|PASK_ENST00000358649.4_Silent_p.T251T|PASK_ENST00000539818.1_Silent_p.T35T|PASK_ENST00000234040.4_Silent_p.T251T	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	251					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)		TGTCACATGACGTGACGGTGC	0.502																																					p.T251T		Atlas-SNP	.											.	PASK	230	.	0			c.G753A						PASS	.						122	96	105					2																	242077491		2203	4300	6503	SO:0001819	synonymous_variant	23178	exon6			ACATGACGTGACG	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.753G>A	chr2.hg19:g.242077491C>T		71.0	0.0	.		74.0	5.0	.	NM_015148	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Silent	SNP	ENST00000405260.1	hg19	CCDS2545.1	.	.	.	.	.	.	.	.	.	.	C	0.164	-1.078021	0.01903	.	.	ENSG00000115687	ENST00000433589	.	.	.	4.63	-8.3	0.01005	.	.	.	.	.	T	0.27169	0.0666	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.30679	-0.9970	4	.	.	.	.	9.3571	0.38173	0.1144:0.1683:0.0:0.7173	.	.	.	.	H	66	.	.	R	-	2	0	PASK	241726164	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.195000	0.01242	-1.859000	0.01156	-0.907000	0.02831	CGT	.	.	.	weak		0.502	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148		T	242077491	C	T	242077491	2	4	281	1	0	0	0	0	0	0	0	1	11479	523	19	1		1	PASK	2	242077491	Silent	SNP	C	TCGA-Y8-A8S0-01A-11D-A36X-10	89717558	242077491	1121882	7	17891											
DLEC1	9940	hgsc.bcm.edu	37	chr3	38103779	38103779	+	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	agaagcttgctgagttcgaaGatgagttagaccacactgtg	12	10	12	7	1	0	5	0	2	0	3	1	6	0	5	1	0	2	4	1	0	3	3			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr3:38103779G>A	ENST00000308059.6	+	4	814	c.793G>A	c.(793-795)Gat>Aat	p.D265N	DLEC1_ENST00000452631.2_Missense_Mutation_p.D265N|DLEC1_ENST00000346219.3_Missense_Mutation_p.D265N					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)		TGAGTTCGAAGATGAGTTAGA	0.458																																					p.D265N		Atlas-SNP	.											.	DLEC1	278	.	0			c.G793A						PASS	.						88	82	84					3																	38103779		1982	4173	6155	SO:0001583	missense	9940	exon4			TTCGAAGATGAGT	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.793G>A	chr3.hg19:g.38103779G>A	ENSP00000308597:p.Asp265Asn	110.0	0.0	.		84.0	40.0	.	NM_007337		Missense_Mutation	SNP	ENST00000308059.6	hg19	CCDS2672.2	.	.	.	.	.	.	.	.	.	.	G	13.20	2.166638	0.38217	.	.	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.05258	3.49;3.47;3.71	3.52	3.52	0.40303	.	0.905722	0.09716	N	0.765070	T	0.07908	0.0198	M	0.62723	1.935	0.09310	N	1	B;P;B	0.40050	0.247;0.7;0.247	B;B;B	0.35278	0.199;0.19;0.199	T	0.19943	-1.0290	10	0.16896	T	0.51	-8.804	10.8549	0.46794	0.0:0.0:1.0:0.0	.	265;265;265	F8W6T4;Q9Y238-3;Q9Y238	.;.;DLEC1_HUMAN	N	265	ENSP00000308597:D265N;ENSP00000315914:D265N;ENSP00000410427:D265N	ENSP00000308597:D265N	D	+	1	0	DLEC1	38078783	0.760000	0.28428	0.021000	0.16686	0.059000	0.15707	3.718000	0.54919	2.278000	0.76064	0.655000	0.94253	GAT	.	.	.	none		0.458	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		A	38103779	G	A	38103779	3	1	281	1	0	0	0	0	1	0	0	0	4554	942	33	2	807	2	DLEC1	3	38103779	Missense_Mutation	SNP	G	TCGA-Y8-A8S0-01A-11D-A36X-10		38103779	159918651	8	17892											
CPNE4	131034	hgsc.bcm.edu	37	chr3	131268825	131268825	+	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	tgttagtttcctctgacgctGacttggcaaccttctggatg	6	15	10	10	1	2	2	0	2	2	0	3	3	3	3	2	2	1	4	2	2	2	4			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr3:131268825G>T	ENST00000512055.1	-	18	3394	c.1268C>A	c.(1267-1269)tCa>tAa	p.S423*	CPNE4_ENST00000502818.1_Nonsense_Mutation_p.S441*|CPNE4_ENST00000511604.1_Nonsense_Mutation_p.S423*|CPNE4_ENST00000512332.1_Nonsense_Mutation_p.S441*|CPNE4_ENST00000429747.1_Nonsense_Mutation_p.S423*			Q96A23	CPNE4_HUMAN	copine IV	423	VWFA.					extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|liver(1)|lung(16)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	39						CTCTGACGCTGACTTGGCAAC	0.522																																					p.S423X		Atlas-SNP	.											.	CPNE4	112	.	0			c.C1268A						PASS	.						156	135	142					3																	131268825		2203	4300	6503	SO:0001587	stop_gained	131034	exon14			GACGCTGACTTGG	H29499	CCDS3072.1, CCDS75010.1	3q22.1	2014-09-04			ENSG00000196353	ENSG00000196353			2317	protein-coding gene	gene with protein product	"copine 8"	604208				9430674, 12670487	Standard	XM_005247107		Approved	COPN4, CPN4	uc003eok.3	Q96A23	OTTHUMG00000159631	ENST00000512055.1:c.1268C>A	chr3.hg19:g.131268825G>T	ENSP00000421705:p.Ser423*	120.0	0.0	.		139.0	57.0	.	NM_130808	D3DNC5|Q8TEX1	Nonsense_Mutation	SNP	ENST00000512055.1	hg19	CCDS3072.1	.	.	.	.	.	.	.	.	.	.	G	39	7.419351	0.98272	.	.	ENSG00000196353	ENST00000512055;ENST00000429747;ENST00000512332;ENST00000511604;ENST00000502818	.	.	.	5.22	5.22	0.72569	.	0.112824	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.46703	T	0.11	-9.0488	18.7675	0.91879	0.0:0.0:1.0:0.0	.	.	.	.	X	423;423;441;423;441	.	ENSP00000411904:S423X	S	-	2	0	CPNE4	132751515	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	5.392000	0.66272	2.436000	0.82500	0.462000	0.41574	TCA	.	.	.	none		0.522	CPNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356583.4	NM_130808		T	131268825	G	T	131268825	4	4	281	1	0	0	0	0	0	1	0	0	3816	1294	45	4	417	4	CPNE4	3	131268825	Nonsense_Mutation	SNP	G	TCGA-Y8-A8S0-01A-11D-A36X-10	93165046	131268825	66753605	9	17893											
RBP1	5947	hgsc.bcm.edu	37	chr3	139236515	139236515	+	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	tgcagaccacaccttccactCtcatctcctgaaacaaaagc	13	8	4	16	0	2	2	1	1	2	1	5	2	3	2	4	0	3	1	4	0	3	1			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr3:139236515C>G	ENST00000232219.2	-	4	658	c.548G>C	c.(547-549)aGa>aCa	p.R183T	RP11-319G6.1_ENST00000515247.1_RNA	NM_002899.3	NP_002890.2	P09455	RET1_HUMAN	retinol binding protein 1, cellular	121					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)	ACCTTCCACTCTCATCTCCTG	0.483																																					p.R183T		Atlas-SNP	.											.	RBP1	39	.	0			c.G548C						PASS	.						204	165	178					3																	139236515		2203	4300	6503	SO:0001583	missense	5947	exon4			TCCACTCTCATCT		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	ENST00000232219.2:c.548G>C	chr3.hg19:g.139236515C>G	ENSP00000232219:p.Arg183Thr	69.0	0.0	.		71.0	11.0	.	NM_002899	A8K2Q0|B7Z7A0|E7EWV0|F2Z2F2|Q6FGX8	Missense_Mutation	SNP	ENST00000232219.2	hg19	CCDS3110.2	.	.	.	.	.	.	.	.	.	.	C	8.862	0.947160	0.18356	.	.	ENSG00000114115	ENST00000232219	T	0.06218	3.33	5.77	5.77	0.91146	Calycin-like (1);Cytosolic fatty-acid binding (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.000000	0.85682	D	0.000000	T	0.02888	0.0086	N	0.01417	-0.88	0.80722	D	1	B	0.06786	0.001	B	0.12837	0.008	T	0.55379	-0.8150	10	0.14656	T	0.56	.	17.4774	0.87662	0.0:1.0:0.0:0.0	.	121	P09455	RET1_HUMAN	T	183	ENSP00000232219:R183T	ENSP00000232219:R183T	R	-	2	0	RBP1	140719205	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.257000	0.72480	2.726000	0.93360	0.655000	0.94253	AGA	.	.	.	none		0.483	RBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341495.1	NM_002899		G	139236515	C	G	139236515	3	3	281	1	0	0	0	0	1	0	0	0	13168	913	32	4	49	4	RBP1	3	139236515	Missense_Mutation	SNP	C	TCGA-Y8-A8S0-01A-11D-A36X-10	7967690	139236515	58785915	10	17894											
BOD1L	259282	hgsc.bcm.edu	37	chr4	13602062	13602062	+	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	gttgttgcactggagataggCaattcgaattcttcccctat	9	14	9	9	1	1	1	0	0	1	1	3	3	2	1	2	2	1	4	2	2	4	7			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr4:13602062C>T	ENST00000040738.5	-	10	6597	c.6462G>A	c.(6460-6462)ttG>ttA	p.L2154L		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	2154						nucleus (GO:0005634)	DNA binding (GO:0003677)										TGGAGATAGGCAATTCGAATT	0.498																																					p.L2154L		Atlas-SNP	.											.	.	.	.	0			c.G6462A						PASS	.						89	77	81					4																	13602062		2203	4300	6503	SO:0001819	synonymous_variant	259282	exon10			GATAGGCAATTCG	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.6462G>A	chr4.hg19:g.13602062C>T		53.0	0.0	.		57.0	30.0	.	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Silent	SNP	ENST00000040738.5	hg19	CCDS3411.2																																																																																			.	.	.	none		0.498	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		T	13602062	C	T	13602062	2	4	281	1	0	0	0	0	0	0	0	1	1483	709	25	2		2	BOD1L	4	13602062	Silent	SNP	C	TCGA-Y8-A8S0-01A-11D-A36X-10		13602062	177552214	11	17895											
WDR19	57728	hgsc.bcm.edu	37	chr4	39233429	39233429	+	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	catcccaggttttctgatgcTtgggaaatgtgcaggattct	8	14	11	8	0	2	1	0	1	2	0	3	3	3	3	1	3	2	3	1	3	1	4			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr4:39233429T>G	ENST00000399820.3	+	18	2149	c.1995T>G	c.(1993-1995)gcT>gcG	p.A665A	WDR19_ENST00000288634.7_Silent_p.A505A|WDR19_ENST00000515631.1_3'UTR	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	665					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						TTTCTGATGCTTGGGAAATGT	0.433																																					p.A665A		Atlas-SNP	.											.	WDR19	96	.	0			c.T1995G						PASS	.						107	101	103					4																	39233429		1949	4150	6099	SO:0001819	synonymous_variant	57728	exon18			TGATGCTTGGGAA	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.1995T>G	chr4.hg19:g.39233429T>G		110.0	0.0	.		76.0	39.0	.	NM_025132	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Silent	SNP	ENST00000399820.3	hg19	CCDS47042.1																																																																																			.	.	.	none		0.433	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1			G	39233429	T	G	39233429	2	3	281	1	0	0	0	0	0	0	0	1	17291	1596	56	5		5	WDR19	4	39233429	Silent	SNP	T	TCGA-Y8-A8S0-01A-11D-A36X-10	25631367	39233429	151920847	12	17896											
METTL14	57721	hgsc.bcm.edu	37	chr4	119613212	119613212	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatagacctcagaatttcaTcagggatgtaggtatgtcag	13	11	10	7	0	4	2	4	0	0	2	4	3	4	3	1	2	0	2	1	2	4	4			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr4:119613212T>C	ENST00000388822.5	+	5	568	c.401T>C	c.(400-402)aTc>aCc	p.I134T	METTL14_ENST00000506780.1_Missense_Mutation_p.I96T			Q9HCE5	MET14_HUMAN	methyltransferase like 14	134					mRNA destabilization (GO:0061157)|mRNA methylation (GO:0080009)|stem cell maintenance (GO:0019827)	MIS complex (GO:0036396)|nucleus (GO:0005634)	mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity (GO:0016422)|RNA binding (GO:0003723)			endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|stomach(1)	16						CAGAATTTCATCAGGGATGTA	0.333																																					p.I134T		Atlas-SNP	.											.	METTL14	41	.	0			c.T401C						PASS	.						169	158	161					4																	119613212		2203	4300	6503	SO:0001583	missense	57721	exon5			ATTTCATCAGGGA	AB046847	CCDS34053.1	4q26	2009-02-24			ENSG00000145388	ENSG00000145388			29330	protein-coding gene	gene with protein product						10997877	Standard	NM_020961		Approved	KIAA1627	uc003icf.3	Q9HCE5	OTTHUMG00000161167	ENST00000388822.5:c.401T>C	chr4.hg19:g.119613212T>C	ENSP00000373474:p.Ile134Thr	69.0	0.0	.		87.0	36.0	.	NM_020961	A6NIG1|Q969V2	Missense_Mutation	SNP	ENST00000388822.5	hg19	CCDS34053.1	.	.	.	.	.	.	.	.	.	.	t	23.9	4.472103	0.84533	.	.	ENSG00000145388	ENST00000388822;ENST00000506780	.	.	.	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.80071	0.4556	M	0.78344	2.41	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.82149	-0.0600	9	0.66056	D	0.02	1.2634	16.4054	0.83662	0.0:0.0:0.0:1.0	.	96;134	D6RBL4;Q9HCE5	.;MTL14_HUMAN	T	134;96	.	ENSP00000373474:I134T	I	+	2	0	METTL14	119832660	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.426000	0.80270	2.282000	0.76494	0.528000	0.53228	ATC	.	.	.	none		0.333	METTL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364034.3	NM_020961		C	119613212	T	C	119613212	3	2	281	1	0	0	0	0	1	0	0	0	9505	1435	50	3	419	3	METTL14	4	119613212	Missense_Mutation	SNP	T	TCGA-Y8-A8S0-01A-11D-A36X-10	80379783	119613212	71541064	13	17897											
ERBB2IP	55914	hgsc.bcm.edu	37	chr5	65350314	65350314	+	Missense_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	ccagcaagacatggggaaatGtgggccatctcaccaaacga	14	5	11	11	1	1	1	1	0	1	1	2	3	1	2	3	3	2	1	3	3	3	0			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr5:65350314G>A	ENST00000284037.5	+	21	3557	c.3168G>A	c.(3166-3168)atG>atA	p.M1056I	ERBB2IP_ENST00000508515.1_Missense_Mutation_p.M1056I|ERBB2IP_ENST00000506030.1_Missense_Mutation_p.M1056I|ERBB2IP_ENST00000416865.2_Intron|ERBB2IP_ENST00000380936.1_Missense_Mutation_p.M1056I|ERBB2IP_ENST00000511297.1_Missense_Mutation_p.M1052I|ERBB2IP_ENST00000380943.2_Missense_Mutation_p.M1056I|ERBB2IP_ENST00000380938.2_Missense_Mutation_p.M1056I|ERBB2IP_ENST00000380935.1_Missense_Mutation_p.M1056I|ERBB2IP_ENST00000380939.2_Missense_Mutation_p.M1056I	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	1056					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)		ATGGGGAAATGTGGGCCATCT	0.438																																					p.M1056I		Atlas-SNP	.											.	ERBB2IP	120	.	0			c.G3168A						PASS	.						132	128	129					5																	65350314		2203	4300	6503	SO:0001583	missense	55914	exon21			GGAAATGTGGGCC		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.3168G>A	chr5.hg19:g.65350314G>A	ENSP00000284037:p.Met1056Ile	84.0	0.0	.		95.0	24.0	.	NM_001253699	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Missense_Mutation	SNP	ENST00000284037.5	hg19	CCDS58953.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.919750	0.33908	.	.	ENSG00000112851	ENST00000284037;ENST00000380943;ENST00000380939;ENST00000380936;ENST00000380935;ENST00000380938;ENST00000511297;ENST00000506030;ENST00000508515	T;T;T;T;T;T;T;T;T	0.38401	1.33;1.33;1.34;1.53;1.14;1.41;1.33;1.37;1.14	5.67	5.67	0.87782	.	0.190134	0.64402	D	0.000016	T	0.30386	0.0763	N	0.17474	0.49	0.58432	D	0.999992	B;P;B;B;B;P;B	0.47762	0.068;0.839;0.023;0.014;0.031;0.9;0.024	B;B;B;B;B;P;B	0.44990	0.045;0.276;0.027;0.006;0.016;0.466;0.013	T	0.02512	-1.1148	10	0.21014	T	0.42	.	19.7424	0.96237	0.0:0.0:1.0:0.0	.	1056;1056;1056;1052;1056;1056;1056	Q96RT1-4;E9PCR8;B7ZLV9;E7EQW9;Q96RT1;Q96RT1-7;Q96RT1-2	.;.;.;.;LAP2_HUMAN;.;.	I	1056;1056;1056;1056;1056;1056;1052;1056;1056	ENSP00000284037:M1056I;ENSP00000370330:M1056I;ENSP00000370326:M1056I;ENSP00000370323:M1056I;ENSP00000370322:M1056I;ENSP00000370325:M1056I;ENSP00000422766:M1052I;ENSP00000426632:M1056I;ENSP00000422015:M1056I	ENSP00000284037:M1056I	M	+	3	0	ERBB2IP	65386070	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.792000	0.91856	2.670000	0.90874	0.655000	0.94253	ATG	.	.	.	none		0.438	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695		A	65350314	G	A	65350314	3	1	281	1	0	0	0	0	1	0	0	0	5209	1377	48	2	3242	2	ERBB2IP	5	65350314	Missense_Mutation	SNP	G	TCGA-Y8-A8S0-01A-11D-A36X-10		65350314	115564946	14	17898											
DDX46	9879	hgsc.bcm.edu	37	chr5	134109546	134109546	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagtggagtttagaggacgAtgatggtatattttttagcc	12	14	12	3	1	0	2	0	1	0	1	0	5	0	4	1	3	1	2	1	3	5	7			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr5:134109546A>G	ENST00000354283.4	+	5	743	c.608A>G	c.(607-609)gAt>gGt	p.D203G	DDX46_ENST00000452510.2_Missense_Mutation_p.D203G			Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	203	Poly-Asp.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TTAGAGGACGATGATGGTATA	0.328																																					p.D203G	Colon(13;391 453 4901 21675 24897)	Atlas-SNP	.											.	DDX46	77	.	0			c.A608G						PASS	.						126	126	126					5																	134109546		2203	4300	6503	SO:0001583	missense	9879	exon5			AGGACGATGATGG		CCDS34240.1, CCDS75306.1	5q31.1	2010-01-25			ENSG00000145833	ENSG00000145833		"DEAD-boxes"	18681	protein-coding gene	gene with protein product							Standard	XM_005272142		Approved	KIAA0801, FLJ25329, PRPF5, Prp5	uc003kzw.3	Q7L014	OTTHUMG00000163072	ENST00000354283.4:c.608A>G	chr5.hg19:g.134109546A>G	ENSP00000346236:p.Asp203Gly	288.0	0.0	.		300.0	15.0	.	NM_014829	O94894|Q96EI0|Q9Y658	Missense_Mutation	SNP	ENST00000354283.4	hg19	CCDS34240.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.514770	0.85389	.	.	ENSG00000145833	ENST00000452510;ENST00000537371;ENST00000354283	T;T	0.27890	1.64;1.64	4.84	4.84	0.62591	.	0.047448	0.85682	D	0.000000	T	0.53883	0.1824	M	0.74647	2.275	0.80722	D	1	D	0.63880	0.993	D	0.68192	0.956	T	0.56547	-0.7961	10	0.48119	T	0.1	-22.7899	14.3642	0.66795	1.0:0.0:0.0:0.0	.	203	Q7L014	DDX46_HUMAN	G	203	ENSP00000416534:D203G;ENSP00000346236:D203G	ENSP00000346236:D203G	D	+	2	0	DDX46	134137445	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.758000	0.91663	1.934000	0.56057	0.528000	0.53228	GAT	.	.	.	none		0.328	DDX46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371584.1	NM_014829		G	134109546	A	G	134109546	3	3	281	1	0	0	0	0	1	0	0	0	4366	333	12	3	626	3	DDX46	5	134109546	Missense_Mutation	SNP	A	TCGA-Y8-A8S0-01A-11D-A36X-10	68759232	134109546	46805714	15	17899											
C6orf27	80737	hgsc.bcm.edu	37	chr6	31740832	31740832	+	Missense_Mutation	SNP	T	T	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	ggattttggcagcgttgatcTcctcacccatgctgcccgtg	5	12	11	13	2	2	1	1	1	1	0	3	2	2	2	3	2	3	3	3	2	0	3			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr6:31740832T>G	ENST00000375688.4	-	7	1186	c.986A>C	c.(985-987)gAg>gCg	p.E329A	VWA7_ENST00000375686.3_Missense_Mutation_p.E329A|VWA7_ENST00000467576.1_5'UTR|VWA7_ENST00000447450.1_Missense_Mutation_p.E329A			Q9Y334	VWA7_HUMAN	von Willebrand factor A domain containing 7	329	VWFA.					extracellular region (GO:0005576)											AGCGTTGATCTCCTCACCCAT	0.612																																					p.E329A		Atlas-SNP	.											.	.	.	.	0			c.A986C						PASS	.						48	36	40					6																	31740832		1511	2709	4220	SO:0001583	missense	80737	exon7			TTGATCTCCTCAC		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.986A>C	chr6.hg19:g.31740832T>G	ENSP00000364840:p.Glu329Ala	61.0	0.0	.		60.0	11.0	.	NM_025258	A2BEX8|A6NHR6|B0V041|Q5SSR5|Q96QC8|Q9UMP9	Missense_Mutation	SNP	ENST00000375688.4	hg19	CCDS4721.2	.	.	.	.	.	.	.	.	.	.	T	23.1	4.379006	0.82682	.	.	ENSG00000204396	ENST00000375688;ENST00000375686;ENST00000447450	D;D;D	0.97731	-4.51;-4.51;-4.51	5.74	5.74	0.90152	von Willebrand factor, type A (1);	0.052325	0.64402	D	0.000001	D	0.97247	0.9100	M	0.78049	2.395	0.47374	D	0.999402	D	0.55385	0.971	P	0.50825	0.651	D	0.97034	0.9752	10	0.51188	T	0.08	-14.2839	13.9835	0.64319	0.0:0.0:0.0:1.0	.	329	Q9Y334	G7C_HUMAN	A	329	ENSP00000364840:E329A;ENSP00000364838:E329A;ENSP00000390554:E329A	ENSP00000364838:E329A	E	-	2	0	C6orf27	31848811	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	6.834000	0.75339	2.186000	0.69663	0.455000	0.32223	GAG	.	.	.	none		0.612	VWA7-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076233.2	NM_025258		G	31740832	T	G	31740832	3	3	281	1	0	0	0	0	1	0	0	0	2364	1551	54	5	1732	5	C6orf27	6	31740832	Missense_Mutation	SNP	T	TCGA-Y8-A8S0-01A-11D-A36X-10		31740832	139374235	16	17900											
HBS1L	10767	hgsc.bcm.edu	37	chr6	135360838	135360838	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcttcagaactgcttcaatTaatatttcatctggcacagc	11	15	5	10	0	5	1	3	0	2	1	5	1	5	1	0	1	3	2	0	1	4	6			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr6:135360838T>C	ENST00000367837.5	-	4	509	c.303A>G	c.(301-303)ttA>ttG	p.L101L	HBS1L_ENST00000367826.2_Silent_p.L59L|HBS1L_ENST00000415177.2_Intron|HBS1L_ENST00000367822.5_Silent_p.L101L|HBS1L_ENST00000314674.3_Silent_p.L101L|HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000525067.1_Silent_p.L37L|HBS1L_ENST00000367820.2_Silent_p.L101L|HBS1L_ENST00000367824.4_Intron	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase	101					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)		CTGCTTCAATTAATATTTCAT	0.413																																					p.L101L		Atlas-SNP	.											.	HBS1L	75	.	0			c.A303G						PASS	.						160	149	153					6																	135360838		2203	4300	6503	SO:0001819	synonymous_variant	10767	exon4			TTCAATTAATATT	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.303A>G	chr6.hg19:g.135360838T>C		64.0	0.0	.		68.0	31.0	.	NM_001145207	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Silent	SNP	ENST00000367837.5	hg19	CCDS5173.1																																																																																			.	.	.	none		0.413	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2			C	135360838	T	C	135360838	2	2	281	1	0	0	0	0	0	0	0	1	6994	1751	61	3		3	HBS1L	6	135360838	Silent	SNP	T	TCGA-Y8-A8S0-01A-11D-A36X-10	103620006	135360838	35754229	17	17901											
KCNU1	157855	hgsc.bcm.edu	37	chr8	36694438	36694438	+	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	cttgtgtaccttcctaacatCtctatttgtggagcaaaaca	11	14	6	10	0	1	0	0	0	1	0	3	1	2	1	2	1	4	2	2	1	5	6			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr8:36694438C>A	ENST00000399881.3	+	14	1530	c.1493C>A	c.(1492-1494)tCt>tAt	p.S498Y		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	498	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)		TTCCTAACATCTCTATTTGTG	0.393																																					p.S498Y		Atlas-SNP	.											.	KCNU1	359	.	0			c.C1493A						PASS	.						193	190	191					8																	36694438		1864	4102	5966	SO:0001583	missense	157855	exon14			TAACATCTCTATT	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.1493C>A	chr8.hg19:g.36694438C>A	ENSP00000382770:p.Ser498Tyr	86.0	0.0	.		96.0	45.0	.	NM_001031836		Missense_Mutation	SNP	ENST00000399881.3	hg19	CCDS55220.1	.	.	.	.	.	.	.	.	.	.	C	19.14	3.769759	0.69992	.	.	ENSG00000215262	ENST00000399881	T	0.44083	0.93	5.34	5.34	0.76211	Potassium channel, calcium-activated, BK, alpha subunit (2);	0.848376	0.09485	U	0.795761	T	0.59797	0.2220	L	0.51422	1.61	0.80722	D	1	D	0.76494	0.999	D	0.69479	0.964	T	0.52646	-0.8548	10	0.87932	D	0	-4.9467	13.1151	0.59295	0.0:0.7923:0.2077:0.0	.	498	A8MYU2	KCNU1_HUMAN	Y	498	ENSP00000382770:S498Y	ENSP00000382770:S498Y	S	+	2	0	KCNU1	36813596	0.975000	0.34042	0.930000	0.37139	0.985000	0.73830	1.363000	0.34159	2.657000	0.90304	0.585000	0.79938	TCT	.	.	.	none		0.393	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836		A	36694438	C	A	36694438	3	1	281	1	0	0	0	0	1	0	0	0	8100	913	32	4	1547	4	KCNU1	8	36694438	Missense_Mutation	SNP	C	TCGA-Y8-A8S0-01A-11D-A36X-10		36694438	109669584	18	17902											
HGSNAT	138050	hgsc.bcm.edu	37	chr8	43048924	43048924	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttaccacaccgaggtggccTatgaccccgagggcatcctg	8	8	11	14	2	0	1	0	1	0	0	1	3	1	1	6	3	1	1	6	3	2	3			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr8:43048924T>C	ENST00000458501.2	+	14	1486	c.1486T>C	c.(1486-1488)Tat>Cat	p.Y496H	HGSNAT_ENST00000521576.1_Missense_Mutation_p.Y185H|HGSNAT_ENST00000297798.7_Missense_Mutation_p.Y200H|HGSNAT_ENST00000379644.4_Missense_Mutation_p.Y468H			Q68CP4	HGNAT_HUMAN	heparan-alpha-glucosaminide N-acetyltransferase	496					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)			CGAGGTGGCCTATGACCCCGA	0.453																																					p.Y468H		Atlas-SNP	.											.	HGSNAT	85	.	0			c.T1402C						PASS	.						144	145	144					8																	43048924		1943	4144	6087	SO:0001583	missense	138050	exon14			GTGGCCTATGACC		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.1486T>C	chr8.hg19:g.43048924T>C	ENSP00000389524:p.Tyr496His	111.0	0.0	.		98.0	40.0	.	NM_152419	B4E2V0	Missense_Mutation	SNP	ENST00000458501.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.24|14.24	2.476133|2.476133	0.44044|0.44044	.|.	.|.	ENSG00000165102|ENSG00000165102	ENST00000524016|ENST00000458501;ENST00000379644;ENST00000521576;ENST00000297798	.|D;D;D;D	.|0.94758	.|-3.51;-3.51;-3.51;-3.51	5.12|5.12	5.12|5.12	0.69794|0.69794	.|.	.|0.069987	.|0.64402	.|D	.|0.000015	D|D	0.91300|0.91300	0.7257|0.7257	L|L	0.46885|0.46885	1.475|1.475	0.43242|0.43242	D|D	0.995157|0.995157	.|B	.|0.34015	.|0.435	.|B	.|0.32149	.|0.141	D|D	0.90493|0.90493	0.4468|0.4468	5|10	.|0.46703	.|T	.|0.11	-14.9366|-14.9366	12.9101|12.9101	0.58175|0.58175	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|496	.|Q68CP4	.|HGNAT_HUMAN	P|H	169|496;468;185;200	.|ENSP00000389524:Y496H;ENSP00000368965:Y468H;ENSP00000429029:Y185H;ENSP00000297798:Y200H	.|ENSP00000297798:Y200H	L|Y	+|+	2|1	0|0	HGSNAT|HGSNAT	43168081|43168081	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.466000|0.466000	0.32739|0.32739	7.539000|7.539000	0.82063|0.82063	1.937000|1.937000	0.56155|0.56155	0.529000|0.529000	0.55759|0.55759	CTA|TAT	.	.	.	none		0.453	HGSNAT-202	KNOWN	basic	protein_coding	protein_coding		XM_372038		C	43048924	T	C	43048924	3	2	281	1	0	0	0	0	1	0	0	0	7095	1522	53	3	1456	3	HGSNAT	8	43048924	Missense_Mutation	SNP	T	TCGA-Y8-A8S0-01A-11D-A36X-10	6354486	43048924	103315098	19	17903											
PI15	51050	hgsc.bcm.edu	37	chr8	75761353	75761354	+	Splice_Site	DNP	GG	GG	TA																															ttttttgttttcccttctagGggcaattggattggagaagc																										TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr8:75761353_75761354GG>TA	ENST00000260113.2	+	6	821_822	c.642_643GG>TA	c.(640-645)aaGGgc>aaTAgc	p.214_215KG>NS	RP11-758M4.4_ENST00000523860.1_RNA|PI15_ENST00000523773.1_Splice_Site_p.214_215KG>NS|RP11-758M4.4_ENST00000522914.1_RNA|RP11-758M4.4_ENST00000518128.1_RNA	NM_015886.3	NP_056970.1	O43692	PI15_HUMAN	peptidase inhibitor 15	214						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)			TCCCTTCTAGGGGCAATTGGAT	0.401																																					p.K214N|p.G215S		Atlas-SNP	.											.	PI15	73	.	0			c.G642T|c.G643A						PASS	.																																			SO:0001630	splice_region_variant	51050	exon6			TTCTAGGGGCAAT|TCTAGGGGCAATT	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	Exception_encountered	chr8.hg19:g.75761353_75761354delinsTA		75.0	0.0	.		74.0|75.0	34.0|35.0	.	NM_015886	Q68CY1	Missense_Mutation	SNP	ENST00000260113.2	hg19	CCDS6218.1																																																																																			.	.	.	none		0.401	PI15-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379115.1	NM_015886	Missense_Mutation	TA	75761354	GG	TA	75761353	5	4	281	1	0	0	0	0	0	0	1	0	11875	1246	43	4	660	4	PI15	8	75761353	Splice_Site	DNP	GG	TCGA-Y8-A8S0-01A-11D-A36X-10	32712429	75761353	70602669	20	17904											
RBM17	84991	hgsc.bcm.edu	37	chr10	6155504	6155504	+	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	gtcagattcaaatccgctgaCtgaaatacttaagtgtccta	13	12	7	9	1	2	3	2	2	0	1	4	3	4	3	2	0	1	1	2	0	5	4			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr10:6155504C>G	ENST00000446108.1	+	9	1534	c.890C>G	c.(889-891)aCt>aGt	p.T297S	RBM17_ENST00000476706.1_3'UTR|RBM17_ENST00000379888.4_Missense_Mutation_p.T297S	NM_001145547.1	NP_001139019.1	Q96I25	SPF45_HUMAN	RNA binding motif protein 17	297					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						AATCCGCTGACTGAAATACTT	0.418																																					p.T297S		Atlas-SNP	.											.	RBM17	45	.	0			c.C890G						PASS	.						132	136	134					10																	6155504		2203	4300	6503	SO:0001583	missense	84991	exon9			CGCTGACTGAAAT	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.890C>G	chr10.hg19:g.6155504C>G	ENSP00000388638:p.Thr297Ser	64.0	0.0	.		52.0	19.0	.	NM_001145547	Q96GY6	Missense_Mutation	SNP	ENST00000446108.1	hg19	CCDS7077.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.827856	0.90955	.	.	ENSG00000134453	ENST00000379888;ENST00000446108	.	.	.	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.75466	0.3853	L	0.60455	1.87	0.80722	D	1	D	0.76494	0.999	D	0.71656	0.974	T	0.69011	-0.5258	9	0.20046	T	0.44	-15.9215	19.5911	0.95511	0.0:1.0:0.0:0.0	.	297	Q96I25	SPF45_HUMAN	S	297	.	ENSP00000369218:T297S	T	+	2	0	RBM17	6195510	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	7.262000	0.78410	2.633000	0.89246	0.561000	0.74099	ACT	.	.	.	none		0.418	RBM17-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046635.1	NM_032905		G	6155504	C	G	6155504	3	3	281	1	0	0	0	0	1	0	0	0	13132	565	20	4	920	4	RBM17	10	6155504	Missense_Mutation	SNP	C	TCGA-Y8-A8S0-01A-11D-A36X-10		6155504	129379243	21	17905											
WAC	51322	hgsc.bcm.edu	37	chr10	28824568	28824568	+	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	atgcgagacgccggagatccTtcaccaccaaataaaatgtt	14	8	8	11	3	1	2	1	0	0	2	2	4	2	2	4	1	1	1	4	1	3	3			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr10:28824568T>A	ENST00000354911.4	+	3	317	c.156T>A	c.(154-156)ccT>ccA	p.P52P	WAC_ENST00000428935.1_Silent_p.P7P|WAC_ENST00000375646.1_Silent_p.P7P|WAC_ENST00000347934.4_Silent_p.P52P|WAC_ENST00000532233.1_3'UTR|WAC_ENST00000375664.4_Silent_p.P7P|WAC-AS1_ENST00000527986.1_RNA	NM_016628.4	NP_057712.2	Q9BTA9	WAC_HUMAN	WW domain containing adaptor with coiled-coil	52					cellular response to DNA damage stimulus (GO:0006974)|G1 DNA damage checkpoint (GO:0044783)|histone H2B conserved C-terminal lysine ubiquitination (GO:0071894)|histone monoubiquitination (GO:0010390)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	chromatin binding (GO:0003682)|RNA polymerase II core binding (GO:0000993)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|urinary_tract(1)	32						CCGGAGATCCTTCACCACCAA	0.458																																					p.P52P		Atlas-SNP	.											.	WAC	77	.	0			c.T156A						PASS	.						106	103	104					10																	28824568		2203	4300	6503	SO:0001819	synonymous_variant	51322	exon3			AGATCCTTCACCA	AK055852	CCDS7159.1, CCDS7160.1, CCDS7161.1	10p12.1	2007-05-17	2003-03-19		ENSG00000095787	ENSG00000095787			17327	protein-coding gene	gene with protein product		615049	"WW domain-containing adaptor with coiled coil"			11827461	Standard	NR_024557		Approved	Wwp4, FLJ31290, PRO1741, BM-016, MGC10753	uc001iuf.3	Q9BTA9	OTTHUMG00000017872	ENST00000354911.4:c.156T>A	chr10.hg19:g.28824568T>A		183.0	0.0	.		192.0	90.0	.	NM_100486	A8K2A9|C9JBT9|D3DRW5|D3DRW6|D3DRW7|Q53EN9|Q5JU75|Q5JU77|Q5VXK0|Q5VXK2|Q8TCK1|Q96DP3|Q96FW6|Q96JI3	Silent	SNP	ENST00000354911.4	hg19	CCDS7159.1																																																																																			.	.	.	none		0.458	WAC-017	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000047371.1	NM_100264		A	28824568	T	A	28824568	2	1	281	1	0	0	0	0	0	0	0	1	17259	1596	56	5		5	WAC	10	28824568	Silent	SNP	T	TCGA-Y8-A8S0-01A-11D-A36X-10	22669064	28824568	106710179	22	17906											
SLC16A12	387700	hgsc.bcm.edu	37	chr10	91196029	91196029	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagatagcagagcccatccAttcccacggcaaagaggtag	14	5	11	11	1	0	3	0	0	0	3	2	4	2	3	3	2	2	3	3	2	3	3			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr10:91196029A>G	ENST00000341233.4	-	7	1376	c.986T>C	c.(985-987)aTg>aCg	p.M329T	SLC16A12_ENST00000371790.4_Missense_Mutation_p.M359T	NM_213606.3	NP_998771.3	Q6ZSM3	MOT12_HUMAN	solute carrier family 16, member 12	329						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						GAGCCCATCCATTCCCACGGC	0.453																																					p.M359T		Atlas-SNP	.											.	SLC16A12	40	.	0			c.T1076C						PASS	.						126	112	117					10																	91196029		2203	4300	6503	SO:0001583	missense	387700	exon7			CCATCCATTCCCA		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.986T>C	chr10.hg19:g.91196029A>G	ENSP00000343022:p.Met329Thr	123.0	0.0	.		124.0	58.0	.	NM_213606	Q5M9M9|Q5T7J2|Q6ZV76	Missense_Mutation	SNP	ENST00000341233.4	hg19		.	.	.	.	.	.	.	.	.	.	A	14.59	2.580520	0.46006	.	.	ENSG00000152779	ENST00000341233;ENST00000371790	T;T	0.80738	-1.41;-1.41	5.81	5.81	0.92471	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.170064	0.49916	D	0.000132	T	0.77798	0.4184	L	0.47716	1.5	0.33209	D	0.553221	B	0.17852	0.024	B	0.29353	0.101	T	0.78954	-0.2000	10	0.35671	T	0.21	.	15.3584	0.74448	1.0:0.0:0.0:0.0	.	329	Q6ZSM3	MOT12_HUMAN	T	329;359	ENSP00000343022:M329T;ENSP00000360855:M359T	ENSP00000343022:M329T	M	-	2	0	SLC16A12	91186009	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	9.339000	0.96797	2.217000	0.71921	0.482000	0.46254	ATG	.	.	.	none		0.453	SLC16A12-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_213606		G	91196029	A	G	91196029	3	3	281	1	0	0	0	0	1	0	0	0	14418	217	8	3	482	3	SLC16A12	10	91196029	Missense_Mutation	SNP	A	TCGA-Y8-A8S0-01A-11D-A36X-10	62371461	91196029	44338718	23	17907											
C10orf119	79892	hgsc.bcm.edu	37	chr10	121602090	121602090	+	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	tctgactggagacaattcggAcatgaaacttgaaacaactg	15	9	9	8	1	1	4	0	3	1	1	2	6	1	5	0	2	3	0	0	2	4	2			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr10:121602090A>T	ENST00000360003.3	-	10	1193	c.1024T>A	c.(1024-1026)Tcc>Acc	p.S342T	MCMBP_ENST00000369077.3_Missense_Mutation_p.S340T|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	342					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						GACAATTCGGACATGAAACTT	0.438																																					p.S342T		Atlas-SNP	.											.	MCMBP	49	.	0			c.T1024A						PASS	.						110	100	103					10																	121602090		2203	4300	6503	SO:0001583	missense	79892	exon10			ATTCGGACATGAA	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.1024T>A	chr10.hg19:g.121602090A>T	ENSP00000353098:p.Ser342Thr	95.0	0.0	.		65.0	32.0	.	NM_024834	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Missense_Mutation	SNP	ENST00000360003.3	hg19	CCDS7617.1	.	.	.	.	.	.	.	.	.	.	A	14.90	2.674108	0.47781	.	.	ENSG00000197771	ENST00000360003;ENST00000369077	T;T	0.30981	1.51;1.51	5.83	4.67	0.58626	.	0.235203	0.45361	D	0.000375	T	0.20495	0.0493	L	0.38175	1.15	0.46774	D	0.999192	P	0.34462	0.454	B	0.24394	0.053	T	0.03051	-1.1078	10	0.15952	T	0.53	-19.2833	12.9785	0.58549	0.8649:0.1351:0.0:0.0	.	342	Q9BTE3	MCMBP_HUMAN	T	342;340	ENSP00000353098:S342T;ENSP00000358073:S340T	ENSP00000353098:S342T	S	-	1	0	MCMBP	121592080	1.000000	0.71417	0.999000	0.59377	0.953000	0.61014	2.129000	0.42055	0.998000	0.38996	0.482000	0.46254	TCC	.	.	.	none		0.438	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834		T	121602090	A	T	121602090	3	4	281	1	0	0	0	0	1	0	0	0	1590	275	10	5	932	5	C10orf119	10	121602090	Missense_Mutation	SNP	A	TCGA-Y8-A8S0-01A-11D-A36X-10	30406061	121602090	13932657	24	17908											
BTBD16	118663	hgsc.bcm.edu	37	chr10	124066782	124066782	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caactgaactacaagattcaGgcaattccgacttatgaaac	16	9	6	10	1	1	3	1	2	0	1	2	4	2	3	1	1	4	1	1	1	7	4			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr10:124066782G>A	ENST00000260723.4	+	10	1121	c.870G>A	c.(868-870)caG>caA	p.Q290Q	BTBD16_ENST00000368994.2_Silent_p.Q291Q	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	290										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)				ACAAGATTCAGGCAATTCCGA	0.333																																					p.Q290Q		Atlas-SNP	.											.	BTBD16	44	.	0			c.G870A						PASS	.						123	124	123					10																	124066782		2202	4300	6502	SO:0001819	synonymous_variant	118663	exon10			GATTCAGGCAATT	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.870G>A	chr10.hg19:g.124066782G>A		134.0	0.0	.		115.0	56.0	.	NM_144587	A6NM63|Q4VXL1|Q96LN0	Silent	SNP	ENST00000260723.4	hg19	CCDS31301.1																																																																																			.	.	.	none		0.333	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587		A	124066782	G	A	124066782	2	1	281	1	0	0	0	0	0	0	0	1	1543	991	35	2		2	BTBD16	10	124066782	Silent	SNP	G	TCGA-Y8-A8S0-01A-11D-A36X-10	2464692	124066782	11467965	25	17909											
CD6	923	hgsc.bcm.edu	37	chr11	60774086	60774086	+	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	cctgaccagctcaacaccagCagtgcagagagtgagctctg	11	6	11	13	0	2	3	1	2	1	1	2	4	2	3	3	0	5	4	3	0	1	0			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr11:60774086C>G	ENST00000313421.7	+	2	276	c.90C>G	c.(88-90)agC>agG	p.S30R	CD6_ENST00000545105.1_3'UTR|CD6_ENST00000346437.4_Missense_Mutation_p.S30R|CD6_ENST00000344028.5_Missense_Mutation_p.S30R|CD6_ENST00000352009.5_Missense_Mutation_p.S30R|CD6_ENST00000452451.2_Missense_Mutation_p.S30R	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	30					cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						TCAACACCAGCAGTGCAGAGA	0.567																																					p.S30R	Pancreas(169;904 2017 4767 38890 42505)	Atlas-SNP	.											.	CD6	122	.	0			c.C90G						PASS	.						83	75	78					11																	60774086		2203	4299	6502	SO:0001583	missense	923	exon2			CACCAGCAGTGCA		CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"CD molecules"	1691	protein-coding gene	gene with protein product		186720	"CD6 antigen"			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.90C>G	chr11.hg19:g.60774086C>G	ENSP00000323280:p.Ser30Arg	60.0	0.0	.		70.0	26.0	.	NM_006725	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Missense_Mutation	SNP	ENST00000313421.7	hg19	CCDS7999.1	.	.	.	.	.	.	.	.	.	.	C	13.67	2.305211	0.40795	.	.	ENSG00000013725	ENST00000344028;ENST00000346437;ENST00000313421;ENST00000542157;ENST00000433107;ENST00000452451;ENST00000352009	T;T;T;T;T;T;T	0.01313	5.02;5.02;5.02;5.03;5.16;5.02;5.02	3.94	3.02	0.34903	.	2.954480	0.01768	N	0.030983	T	0.01976	0.0062	N	0.14661	0.345	0.09310	N	1	P;D;B;P;P	0.53151	0.92;0.958;0.053;0.93;0.93	P;P;B;B;B	0.46796	0.527;0.483;0.032;0.289;0.289	T	0.50980	-0.8763	10	0.37606	T	0.19	.	9.9286	0.41507	0.0:0.8994:0.0:0.1006	.	30;30;30;30;30	E7ER04;P30203-5;P30203-4;P30203;Q8N4Q7	.;.;.;CD6_HUMAN;.	R	30	ENSP00000344108:S30R;ENSP00000345566:S30R;ENSP00000323280:S30R;ENSP00000440055:S30R;ENSP00000410638:S30R;ENSP00000390676:S30R;ENSP00000340628:S30R	ENSP00000323280:S30R	S	+	3	2	CD6	60530662	0.002000	0.14202	0.018000	0.16275	0.026000	0.11368	0.259000	0.18405	1.239000	0.43787	0.561000	0.74099	AGC	.	.	.	none		0.567	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725		G	60774086	C	G	60774086	3	3	281	1	0	0	0	0	1	0	0	0	3030	709	25	4	96	4	CD6	11	60774086	Missense_Mutation	SNP	C	TCGA-Y8-A8S0-01A-11D-A36X-10		60774086	74232430	26	17910											
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103080609	103080609	+	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	tctttttatgttttagatacCtgaaatgttattcagtgaaa	12	19	6	4	0	2	3	1	2	1	1	2	3	2	3	1	0	1	2	1	0	6	8			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr11:103080609C>T	ENST00000375735.2	+	53	8603	c.8459C>T	c.(8458-8460)cCt>cTt	p.P2820L	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.P2820L	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2820	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)		TTTTAGATACCTGAAATGTTA	0.254																																					p.P2820L		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.C8459T						PASS	.						46	43	44					11																	103080609		1405	3082	4487	SO:0001583	missense	79659	exon53			AGATACCTGAAAT	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.8459C>T	chr11.hg19:g.103080609C>T	ENSP00000364887:p.Pro2820Leu	1697.0	1.0	.		1840.0	821.0	.	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	hg19	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.249617	0.80024	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.29142	1.58;1.58	4.7	4.7	0.59300	Dynein heavy chain, P-loop containing D4 domain (1);	0.083808	0.48767	U	0.000170	T	0.46541	0.1398	M	0.84683	2.71	0.80722	D	1	P;P	0.46277	0.875;0.849	P;B	0.46026	0.501;0.368	T	0.58853	-0.7563	10	0.72032	D	0.01	.	15.7886	0.78332	0.0:1.0:0.0:0.0	.	2820;2820	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	L	2820	ENSP00000364887:P2820L;ENSP00000381167:P2820L	ENSP00000364887:P2820L	P	+	2	0	DYNC2H1	102585819	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.771000	0.62318	2.306000	0.77630	0.591000	0.81541	CCT	.	.	.	none		0.254	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		T	103080609	C	T	103080609	3	4	281	1	0	0	0	0	1	0	0	0	4848	681	24	2	8669	2	DYNC2H1	11	103080609	Missense_Mutation	SNP	C	TCGA-Y8-A8S0-01A-11D-A36X-10	42306523	103080609	31925907	27	17911											
COL4A1	1282	hgsc.bcm.edu	37	chr13	110857716	110857716	+	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	ttacctgcgggccctggcggCctatgagtcctgggtacccg	4	9	14	14	3	0	1	0	1	0	0	1	1	1	1	5	4	3	1	5	4	3	3			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr13:110857716C>T	ENST00000375820.4	-	17	1062	c.941G>A	c.(940-942)gGc>gAc	p.G314D	COL4A1_ENST00000543140.1_Missense_Mutation_p.G314D	NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	314	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)			GCCCTGGCGGCCTATGAGTCC	0.507																																					p.G314D		Atlas-SNP	.											.	COL4A1	372	.	0			c.G941A						PASS	.						75	86	83					13																	110857716		2203	4300	6503	SO:0001583	missense	1282	exon17			TGGCGGCCTATGA	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.941G>A	chr13.hg19:g.110857716C>T	ENSP00000364979:p.Gly314Asp	158.0	0.0	.		150.0	6.0	.	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Missense_Mutation	SNP	ENST00000375820.4	hg19	CCDS9511.1	.	.	.	.	.	.	.	.	.	.	C	16.40	3.111503	0.56398	.	.	ENSG00000187498	ENST00000375815;ENST00000375820;ENST00000397198;ENST00000543140	D;D	0.99353	-5.77;-5.77	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	D	0.99677	0.9879	H	0.98370	4.215	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.97315	0.9940	10	0.87932	D	0	.	15.6631	0.77203	0.0:1.0:0.0:0.0	.	314	P02462	CO4A1_HUMAN	D	303;314;314;314	ENSP00000364979:G314D;ENSP00000443348:G314D	ENSP00000364973:G303D	G	-	2	0	COL4A1	109655717	0.987000	0.35691	0.169000	0.22859	0.061000	0.15899	4.641000	0.61375	2.498000	0.84270	0.551000	0.68910	GGC	.	.	.	none		0.507	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3			T	110857716	C	T	110857716	3	4	281	1	0	0	0	0	1	0	0	0	3691	739	26	2	4212	2	COL4A1	13	110857716	Missense_Mutation	SNP	C	TCGA-Y8-A8S0-01A-11D-A36X-10		110857716	4312162	28	17912											
FAM179B	23116	hgsc.bcm.edu	37	chr14	45542589	45542589	+	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	tctcttaggaaatatgacaaAtagtggctctctgcctggag	11	12	10	8	0	2	1	0	1	2	0	4	3	2	3	1	3	1	1	1	3	5	3			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr14:45542589A>T	ENST00000361577.3	+	19	5202	c.4988A>T	c.(4987-4989)aAt>aTt	p.N1663I	FAM179B_ENST00000382233.2_3'UTR|FAM179B_ENST00000361462.2_Missense_Mutation_p.N1716I	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	1663										endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						AATATGACAAATAGTGGCTCT	0.408																																					p.N1663I		Atlas-SNP	.											.	FAM179B	115	.	0			c.A4988T						PASS	.						119	123	122					14																	45542589		2203	4300	6503	SO:0001583	missense	23116	exon19			TGACAAATAGTGG	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.4988A>T	chr14.hg19:g.45542589A>T	ENSP00000355045:p.Asn1663Ile	90.0	0.0	.		96.0	49.0	.	NM_015091	Q68D66|Q6PG27	Missense_Mutation	SNP	ENST00000361577.3	hg19	CCDS9681.1	.	.	.	.	.	.	.	.	.	.	A	12.84	2.058291	0.36277	.	.	ENSG00000198718	ENST00000361577;ENST00000361462;ENST00000556823	T;T;T	0.66460	-0.21;-0.21;2.48	5.42	5.42	0.78866	Armadillo-type fold (1);	0.165528	0.53938	D	0.000052	T	0.52354	0.1729	N	0.22421	0.69	0.80722	D	1	P;P	0.47409	0.895;0.797	B;P	0.44359	0.319;0.447	T	0.49881	-0.8892	10	0.23891	T	0.37	-13.1397	9.3141	0.37924	0.9167:0.0:0.0833:0.0	.	1716;1663	G3XAE9;Q9Y4F4	.;F179B_HUMAN	I	1663;1716;98	ENSP00000355045:N1663I;ENSP00000354917:N1716I;ENSP00000450465:N98I	ENSP00000354917:N1716I	N	+	2	0	FAM179B	44612339	0.996000	0.38824	0.996000	0.52242	0.997000	0.91878	2.779000	0.47734	2.067000	0.61834	0.460000	0.39030	AAT	.	.	.	none		0.408	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781		T	45542589	A	T	45542589	3	4	281	1	0	0	0	0	1	0	0	0	5510	101	4	5	5062	5	FAM179B	14	45542589	Missense_Mutation	SNP	A	TCGA-Y8-A8S0-01A-11D-A36X-10		45542589	61806951	29	17913											
TSNAXIP1	80152	hgsc.bcm.edu	37	chr16	67860650	67860650	+	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	ggagcatcgctttgggcccaGtgatgccatggcctgggctt	5	10	15	11	1	0	1	0	1	0	0	1	2	0	2	3	4	2	3	3	4	0	2			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr16:67860650G>A	ENST00000562787.1	-	0	2345				TSNAXIP1_ENST00000388833.3_Missense_Mutation_p.S432N|TSNAXIP1_ENST00000561639.1_Missense_Mutation_p.S486N|TSNAXIP1_ENST00000415766.3_Missense_Mutation_p.S417N	NM_025082.3	NP_079358.3	Q96BT3	CENPT_HUMAN	centromere protein T						chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|lung(6)|urinary_tract(1)	10		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00429)|Epithelial(162;0.019)|all cancers(182;0.124)		TTTGGGCCCAGTGATGCCATG	0.463																																					p.S432N		Atlas-SNP	.											.	TSNAXIP1	66	.	0			c.G1295A						PASS	.						104	112	109					16																	67860650		2198	4300	6498	SO:0001628	intergenic_variant	55815	exon12			GGCCCAGTGATGC	AK056097	CCDS42182.1	16q22.1	2013-11-05	2006-06-15	2006-06-15		ENSG00000102901			25787	protein-coding gene	gene with protein product		611510	"chromosome 16 open reading frame 56"	C16orf56		16622420, 16622419	Standard	NM_025082		Approved	FLJ13111, CENP-T	uc002eun.4	Q96BT3			chr16.hg19:g.67860650G>A		104.0	0.0	.		141.0	76.0	.	NM_018430	Q96I29|Q96IC6|Q96NK9|Q9H901	Missense_Mutation	SNP	ENST00000562787.1	hg19	CCDS42182.1	.	.	.	.	.	.	.	.	.	.	G	8.363	0.833505	0.16820	.	.	ENSG00000102904	ENST00000415766;ENST00000388833;ENST00000431934	.	.	.	5.8	-3.79	0.04320	.	1.114660	0.06515	N	0.738666	T	0.11067	0.0270	N	0.02011	-0.69	0.09310	N	1	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.04013	0.0;0.001;0.0;0.0;0.0;0.0	T	0.22347	-1.0219	9	0.17369	T	0.5	0.071	3.3508	0.07151	0.3102:0.4161:0.1791:0.0946	.	417;486;222;140;432;417	E7ENJ7;B4DXD0;B4DY78;Q2TAA8-2;Q2TAA8;B4E1H3	.;.;.;.;TXIP1_HUMAN;.	N	417;432;222	.	ENSP00000373485:S432N	S	+	2	0	TSNAXIP1	66418151	0.001000	0.12720	0.228000	0.23943	0.984000	0.73092	-0.275000	0.08525	-0.443000	0.07180	-0.137000	0.14449	AGT	.	.	.	none		0.463	CENPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422020.1	NM_025082		A	67860650	G	A	67860650	1	1	281	0	1	0	0	0	0	0	0	0	16644	1029	36	2		2	TSNAXIP1	16	67860650	IGR	SNP	G	TCGA-Y8-A8S0-01A-11D-A36X-10		67860650	22494103	30	17914											
FXR2	9513	hgsc.bcm.edu	37	chr17	7497273	7497273	+	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	gatactccagcaaagcctggGcattgctgatgttctctcgg	8	11	11	11	1	1	1	0	1	1	0	4	2	2	1	2	2	4	4	2	2	2	3			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr17:7497273G>T	ENST00000250113.7	-	11	1404	c.1070C>A	c.(1069-1071)gCc>gAc	p.A357D	FXR2_ENST00000573057.1_5'Flank	NM_004860.3	NP_004851.2	P51116	FXR2_HUMAN	fragile X mental retardation, autosomal homolog 2	357						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)		CAAAGCCTGGGCATTGCTGAT	0.498																																					p.A357D		Atlas-SNP	.											.	FXR2	44	.	0			c.C1070A						PASS	.						72	70	71					17																	7497273		1893	4116	6009	SO:0001583	missense	9513	exon11			GCCTGGGCATTGC	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.1070C>A	chr17.hg19:g.7497273G>T	ENSP00000250113:p.Ala357Asp	63.0	0.0	.		117.0	5.0	.	NM_004860	B2R9M2|D3DTQ1|Q86V09|Q8WUM2	Missense_Mutation	SNP	ENST00000250113.7	hg19	CCDS45604.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.102122	0.76983	.	.	ENSG00000129245	ENST00000250113	T	0.59502	0.26	5.52	5.52	0.82312	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.108232	0.64402	D	0.000007	T	0.76263	0.3963	M	0.85197	2.74	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.78884	-0.2028	10	0.87932	D	0	1.5053	10.2001	0.43077	0.0872:0.0:0.9128:0.0	.	357	P51116	FXR2_HUMAN	D	357	ENSP00000250113:A357D	ENSP00000250113:A357D	A	-	2	0	FXR2	7437998	1.000000	0.71417	1.000000	0.80357	0.538000	0.34931	3.139000	0.50577	2.873000	0.98535	0.563000	0.77884	GCC	.	.	.	none		0.498	FXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441084.1			T	7497273	G	T	7497273	3	4	281	1	0	0	0	0	1	0	0	0	6123	1203	42	4	879	4	FXR2	17	7497273	Missense_Mutation	SNP	G	TCGA-Y8-A8S0-01A-11D-A36X-10		7497273	73697937	31	17915											
MYH10	4628	hgsc.bcm.edu	37	chr17	8397110	8397110	+	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	cctggcctcctcctcctcctCctgctgctcctgaagactgt	3	12	7	19	0	0	2	0	1	0	1	6	2	6	2	8	1	2	2	8	1	1	0			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr17:8397110C>G	ENST00000269243.4	-	30	4195	c.4057G>C	c.(4057-4059)Gag>Cag	p.E1353Q	MYH10_ENST00000360416.3_Missense_Mutation_p.E1384Q|MYH10_ENST00000396239.1_Missense_Mutation_p.E1374Q|MYH10_ENST00000379980.4_Missense_Mutation_p.E1369Q	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	1353					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						TCCTCCTCCTCCTGCTGCTCC	0.587																																					p.E1384Q		Atlas-SNP	.											MYH10,NS,carcinoma,0,2	MYH10	148	.	0			c.G4150C						PASS	.						85	77	80					17																	8397110		2203	4300	6503	SO:0001583	missense	4628	exon32			CCTCCTCCTGCTG	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.4057G>C	chr17.hg19:g.8397110C>G	ENSP00000269243:p.Glu1353Gln	57.0	2.0	.		74.0	5.0	.	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Missense_Mutation	SNP	ENST00000269243.4	hg19	CCDS11144.1	.	.	.	.	.	.	.	.	.	.	C	17.88	3.496514	0.64186	.	.	ENSG00000133026	ENST00000269243;ENST00000360416;ENST00000396239;ENST00000379980	D;D;D;D	0.84146	-1.81;-1.81;-1.81;-1.81	5.2	4.22	0.49857	Myosin tail (1);	0.051659	0.85682	D	0.000000	D	0.93203	0.7835	M	0.90759	3.145	0.80722	D	1	D;D;D	0.67145	0.996;0.995;0.996	D;D;D	0.70016	0.967;0.959;0.967	D	0.94653	0.7841	10	0.87932	D	0	.	15.2172	0.73277	0.1418:0.8582:0.0:0.0	.	1362;1384;1353	B2RWP9;F8VTL3;P35580	.;.;MYH10_HUMAN	Q	1353;1384;1374;1369	ENSP00000269243:E1353Q;ENSP00000353590:E1384Q;ENSP00000379539:E1374Q;ENSP00000369315:E1369Q	ENSP00000269243:E1353Q	E	-	1	0	MYH10	8337835	1.000000	0.71417	1.000000	0.80357	0.297000	0.27493	7.609000	0.82925	1.401000	0.46761	-0.181000	0.13052	GAG	.	.	.	none		0.587	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			G	8397110	C	G	8397110	3	3	281	1	0	0	0	0	1	0	0	0	10037	864	30	4	1921	4	MYH10	17	8397110	Missense_Mutation	SNP	C	TCGA-Y8-A8S0-01A-11D-A36X-10	899837	8397110	72798100	32	17916											
KRTAP4-7	100132476	hgsc.bcm.edu	37	chr17	39240794	39240794	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcccacctgctgccgcccCagctgctgccgcccctgctg	3	6	10	22	2	0	0	0	0	0	0	0	0	0	0	8	0	7	4	8	0	0	0	rs9894106|rs553572799	byFrequency	TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr17:39240794C>T	ENST00000391417.4	+	1	336	c.336C>T	c.(334-336)ccC>ccT	p.P112P		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	137	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.P112P(1)|p.?(1)		NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						gctgccgccccagctgctgcc	0.667																																					p.P112P		Atlas-SNP	.											KRTAP4-7,NS,carcinoma,0,1	KRTAP4-7	49	.	3	Unknown(1)|Substitution - coding silent(1)|Deletion - In frame(1)	NS(2)|prostate(1)	c.C336T						PASS	.						13	14	14					17																	39240794		691	1589	2280	SO:0001819	synonymous_variant	100132476	exon1			CCGCCCCAGCTGC	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.336C>T	chr17.hg19:g.39240794C>T		15.0	1.0	.		21.0	5.0	.	NM_033061	A0AVM6|A8MQ08|A8MTL4	Silent	SNP	ENST00000391417.4	hg19	CCDS45673.1																																																																																			.	.	.	alt		0.667	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1			T	39240794	C	T	39240794	2	4	281	1	0	0	0	0	0	0	0	1	8562	581	21	2		2	KRTAP4-7	17	39240794	Silent	SNP	C	TCGA-Y8-A8S0-01A-11D-A36X-10	30843684	39240794	41954416	33	17917											
HSPB9	94086	hgsc.bcm.edu	37	chr17	40275296	40275296	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctgaagcccaaacaggacCgtccccgagactcgggagcc	10	3	11	17	3	0	2	0	1	0	1	2	5	1	4	6	2	3	0	6	2	2	0			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr17:40275296C>T	ENST00000355067.3	+	1	541	c.428C>T	c.(427-429)cCg>cTg	p.P143L	CTD-2132N18.3_ENST00000592574.1_Intron|KAT2A_ENST00000225916.5_5'Flank	NM_033194.2	NP_149971.1	Q9BQS6	HSPB9_HUMAN	heat shock protein, alpha-crystallin-related, B9	143					response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	4		all_cancers(22;0.00064)|Breast(137;0.00104)|all_epithelial(22;0.00866)		BRCA - Breast invasive adenocarcinoma(366;0.124)		CAAACAGGACCGTCCCCGAGA	0.632																																					p.P143L		Atlas-SNP	.											.	HSPB9	11	.	0			c.C428T						PASS	.						64	63	63					17																	40275296		2203	4300	6503	SO:0001583	missense	94086	exon1			CAGGACCGTCCCC	AJ302068	CCDS11418.1	17q21	2011-09-02			ENSG00000197723	ENSG00000260325		"Heat shock proteins / HSPB"	30589	protein-coding gene	gene with protein product	"cancer/testis antigen 51"	608344				11470154, 12820654	Standard	NM_033194		Approved	CT51	uc002hyy.2	Q9BQS6	OTTHUMG00000133500	ENST00000355067.3:c.428C>T	chr17.hg19:g.40275296C>T	ENSP00000347178:p.Pro143Leu	35.0	0.0	.		66.0	40.0	.	NM_033194	B3KSG6|Q52LB4	Missense_Mutation	SNP	ENST00000355067.3	hg19	CCDS11418.1	.	.	.	.	.	.	.	.	.	.	C	14.35	2.508520	0.44660	.	.	ENSG00000197723	ENST00000355067	D	0.87966	-2.32	3.68	-0.892	0.10570	.	1.627000	0.03475	N	0.214259	T	0.78704	0.4325	L	0.29908	0.895	0.09310	N	1	B	0.18610	0.029	B	0.10450	0.005	T	0.63296	-0.6669	10	0.72032	D	0.01	-1.2069	2.6526	0.05003	0.4657:0.2817:0.1565:0.0961	.	143	Q9BQS6	HSPB9_HUMAN	L	143	ENSP00000347178:P143L	ENSP00000347178:P143L	P	+	2	0	HSPB9	37528822	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.220000	0.02971	-0.090000	0.12462	-0.311000	0.09066	CCG	.	.	.	none		0.632	HSPB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257438.1	NM_033194		T	40275296	C	T	40275296	3	4	281	1	0	0	0	0	1	0	0	0	7431	652	23	1	430	1	HSPB9	17	40275296	Missense_Mutation	SNP	C	TCGA-Y8-A8S0-01A-11D-A36X-10	1034502	40275296	40919914	34	17918											
ABCA7	10347	hgsc.bcm.edu	37	chr19	1059025	1059025	+	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	gacctgcactctcccaggtaTaccgtgggcagaggatgcca	9	7	12	13	1	1	1	0	0	1	1	2	3	1	2	4	3	3	3	4	3	2	2			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr19:1059025T>A	ENST00000263094.6	+	40	5635	c.5404T>A	c.(5404-5406)Tac>Aac	p.Y1802N	ABCA7_ENST00000435683.2_Missense_Mutation_p.Y1664N|ABCA7_ENST00000433129.1_Missense_Mutation_p.Y1802N	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1802	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)		CTCCCAGGTATACCGTGGGCA	0.617																																					p.Y1802N		Atlas-SNP	.											.	ABCA7	174	.	0			c.T5404A						PASS	.						84	74	78					19																	1059025		2202	4300	6502	SO:0001583	missense	10347	exon40			CAGGTATACCGTG	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.5404T>A	chr19.hg19:g.1059025T>A	ENSP00000263094:p.Tyr1802Asn	101.0	0.0	.		116.0	51.0	.	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	hg19	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	T	15.56	2.869028	0.51588	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.97209	-4.29;-4.29	4.33	4.33	0.51752	ABC transporter-like (1);	.	.	.	.	D	0.99105	0.9692	H	0.99074	4.42	0.45837	D	0.998707	D;D	0.89917	1.0;1.0	D;D	0.91635	0.994;0.999	D	0.98583	1.0651	9	0.87932	D	0	.	12.4481	0.55662	0.0:0.0:0.0:1.0	.	927;1802	D6W5Y0;Q8IZY2	.;ABCA7_HUMAN	N	1802	ENSP00000263094:Y1802N;ENSP00000414062:Y1802N	ENSP00000263094:Y1802N	Y	+	1	0	ABCA7	1010025	0.999000	0.42202	0.805000	0.32314	0.084000	0.17831	3.373000	0.52394	1.814000	0.52955	0.459000	0.35465	TAC	.	.	.	none		0.617	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		A	1059025	T	A	1059025	3	1	281	1	0	0	0	0	1	0	0	0	37	1406	49	5	5558	5	ABCA7	19	1059025	Missense_Mutation	SNP	T	TCGA-Y8-A8S0-01A-11D-A36X-10		1059025	58069958	35	17919											
ZNRF4	148066	hgsc.bcm.edu	37	chr19	5456739	5456739	+	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	actgcagcaccacgtccctgGaggcagagtataccactgtc	10	7	10	14	1	0	1	0	0	0	1	2	2	1	2	3	2	3	4	3	2	2	2	rs551914284		TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr19:5456739G>C	ENST00000222033.4	+	1	1314	c.1237G>C	c.(1237-1239)Gag>Cag	p.E413Q		NM_181710.3	NP_859061.3	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4	413						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)		CACGTCCCTGGAGGCAGAGTA	0.642																																					p.E413Q		Atlas-SNP	.											.	ZNRF4	59	.	0			c.G1237C						PASS	.						20	22	21					19																	5456739		1995	4158	6153	SO:0001583	missense	148066	exon1			TCCCTGGAGGCAG	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.1237G>C	chr19.hg19:g.5456739G>C	ENSP00000222033:p.Glu413Gln	104.0	0.0	.		102.0	45.0	.	NM_181710	A8K886|O75866	Missense_Mutation	SNP	ENST00000222033.4	hg19	CCDS42475.1	.	.	.	.	.	.	.	.	.	.	G	6.853	0.526610	0.13066	.	.	ENSG00000105428	ENST00000222033	T	0.04551	3.6	3.37	0.897	0.19258	.	2.318830	0.03673	U	0.244316	T	0.02929	0.0087	N	0.08118	0	0.09310	N	1	B	0.22604	0.072	B	0.15870	0.014	T	0.38972	-0.9636	10	0.46703	T	0.11	-10.7443	3.2713	0.06883	0.145:0.0:0.5974:0.2576	.	413	Q8WWF5	ZNRF4_HUMAN	Q	413	ENSP00000222033:E413Q	ENSP00000222033:E413Q	E	+	1	0	ZNRF4	5407739	0.853000	0.29707	0.004000	0.12327	0.002000	0.02628	1.479000	0.35453	0.705000	0.31890	0.561000	0.74099	GAG	.	.	.	none		0.642	ZNRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450924.1	NM_181710		C	5456739	G	C	5456739	3	2	281	1	0	0	0	0	1	0	0	0	18226	1175	41	4	1239	4	ZNRF4	19	5456739	Missense_Mutation	SNP	G	TCGA-Y8-A8S0-01A-11D-A36X-10	4397714	5456739	53672244	36	17920											
ZNF536	9745	hgsc.bcm.edu	37	chr19	31039523	31039523	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgtgcaggacagcattgcAtggcacggctgcttgttttg	7	12	13	9	1	0	0	0	0	0	0	0	1	0	1	0	3	4	7	0	3	0	4			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr19:31039523A>G	ENST00000355537.3	+	4	3144	c.2997A>G	c.(2995-2997)gcA>gcG	p.A999A		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	999					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)					ACAGCATTGCATGGCACGGCT	0.567																																					p.A999A		Atlas-SNP	.											.	ZNF536	424	.	0			c.A2997G						PASS	.						74	70	72					19																	31039523		2203	4300	6503	SO:0001819	synonymous_variant	9745	exon4			CATTGCATGGCAC		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.2997A>G	chr19.hg19:g.31039523A>G		56.0	0.0	.		56.0	21.0	.	NM_014717	A2RU18	Silent	SNP	ENST00000355537.3	hg19	CCDS32984.1																																																																																			.	.	.	none		0.567	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		G	31039523	A	G	31039523	2	3	281	1	0	0	0	0	0	0	0	1	17986	204	8	3		3	ZNF536	19	31039523	Silent	SNP	A	TCGA-Y8-A8S0-01A-11D-A36X-10	25582784	31039523	28089460	37	17921											
PLAC4	25825	hgsc.bcm.edu	37	chr21	42551433	42551433	+	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	ggtgaggagtgacggtgtctGgggtgagtgagggtgtccag	6	9	22	4	1	1	4	0	4	1	0	2	5	2	5	1	6	0	0	1	6	0	0			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr21:42551433G>A	ENST00000330333.6	+	1	775				PLAC4_ENST00000414699.1_RNA|PLAC4_ENST00000430327.2_RNA|BACE2-IT1_ENST00000433378.1_RNA|BACE2_ENST00000347667.5_Intron|PLAC4_ENST00000440221.2_RNA|PLAC4_ENST00000536486.1_RNA|BACE2_ENST00000328735.6_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)				GACGGTGTCTGGGGTGAGTGA	0.607																																					p.P41P		Atlas-SNP	.											.	.	.	.	0			c.C123T						PASS	.						124	109	114					21																	42551433		2196	4275	6471	SO:0001627	intron_variant	191585	exon1			GTGTCTGGGGTGA	AF117892	CCDS13668.1, CCDS13669.1, CCDS13670.1	21q22.3	2011-08-11			ENSG00000182240	ENSG00000182240			934	protein-coding gene	gene with protein product		605668		AEPLC		10965118, 10830953	Standard	NM_138991		Approved	CEAP1, DRAP, ALP56	uc002yyw.3	Q9Y5Z0	OTTHUMG00000086742	ENST00000330333.6:c.312+10931G>A	chr21.hg19:g.42551433G>A		100.0	0.0	.		72.0	4.0	.	NM_182832	A8K7P1|Q5DIH8|Q8N2D4|Q9H2V8|Q9NZL1|Q9NZL2|Q9UJT6	Silent	SNP	ENST00000330333.6	hg19	CCDS13668.1																																																																																			.	.	.	none		0.607	BACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195056.1			A	42551433	G	A	42551433	1	1	281	0	1	0	0	0	0	0	0	0	12021	1335	47	2		2	PLAC4	21	42551433	Intron	SNP	G	TCGA-Y8-A8S0-01A-11D-A36X-10		42551433	5578462	38	17922											
COL6A2	1292	hgsc.bcm.edu	37	chr21	47545697	47545703	+	Splice_Site	DEL	TTGCAGG	TTGCAGG	-																															acctcacgcgtgcggcttgcAgggacgcgtgtgggcgtggt																								rs539774519		TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	TTGCAGG	TTGCAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr21:47545697_47545703delTTGCAGG	ENST00000300527.4	+	26	2073_2078	c.1969_1974delTTGCAGG	c.(1969-1974)ttgcagdel	p.LQ657fs	COL6A2_ENST00000409416.1_Splice_Site_p.LQ657fs|COL6A2_ENST00000310645.5_Splice_Site_p.LQ657fs|COL6A2_ENST00000397763.1_Splice_Site_p.LQ657fs|COL6A2_ENST00000357838.4_Splice_Site_p.LQ657fs	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	657	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)		TGCGGCTTGCAGGGACGCGTGTGGGCG	0.652																																					.		Atlas-Indel,Pindel	.											.	COL6A2	351	.	0			.						PASS	.																																			SO:0001630	splice_region_variant	1292	.			.	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.1970-1TTGCAGG>-	chr21.hg19:g.47545697_47545703delTTGCAGG		68.0	0.0	0		51.0	20.0	0.392157	.	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Splice_Site	DEL	ENST00000300527.4	hg19	CCDS13728.1																																																																																			.	.	.	none		0.652	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		Frame_Shift_Del	-	47545703	TTGCAGG	-	47545697	8	5	281	1	0	1	0	1	0	0	1	0	3702	202	7	0	2066	0	COL6A2	21	47545697	Splice_Site	DEL	TTGCAGG	TCGA-Y8-A8S0-01A-11D-A36X-10	4994264	47545697	584198	39	17923											
GAB4	128954	hgsc.bcm.edu	37	chr22	17472825	17472825	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctggacccactcattcatgTcctccctggtctcagccacc	6	11	6	18	0	4	0	3	0	2	0	7	1	6	1	5	2	1	0	5	2	0	1			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chr22:17472825T>C	ENST00000400588.1	-	2	523	c.416A>G	c.(415-417)gAc>gGc	p.D139G	GAB4_ENST00000523144.1_5'UTR	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	139	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)				CTCATTCATGTCCTCCCTGGT	0.522																																					p.D139G		Atlas-SNP	.											.	GAB4	95	.	0			c.A416G						PASS	.						262	266	265					22																	17472825		2203	4300	6503	SO:0001583	missense	128954	exon2			TTCATGTCCTCCC	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.416A>G	chr22.hg19:g.17472825T>C	ENSP00000383431:p.Asp139Gly	77.0	0.0	.		85.0	50.0	.	NM_001037814		Missense_Mutation	SNP	ENST00000400588.1	hg19	CCDS42976.1	.	.	.	.	.	.	.	.	.	.	T	12.32	1.901215	0.33535	.	.	ENSG00000215568	ENST00000400588	T	0.15952	2.38	1.81	1.81	0.25067	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.070922	0.64402	U	0.000018	T	0.35624	0.0938	M	0.84326	2.69	0.47407	D	0.999416	D	0.65815	0.995	P	0.61722	0.893	T	0.19844	-1.0293	10	0.72032	D	0.01	.	7.5812	0.27965	0.0:0.0:0.0:1.0	.	139	Q2WGN9	GAB4_HUMAN	G	139	ENSP00000383431:D139G	ENSP00000383431:D139G	D	-	2	0	GAB4	15852825	1.000000	0.71417	0.995000	0.50966	0.087000	0.18053	7.106000	0.77039	1.071000	0.40834	0.482000	0.46254	GAC	.	.	.	none		0.522	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882		C	17472825	T	C	17472825	3	2	281	1	0	0	0	0	1	0	0	0	6158	1667	58	3	1344	3	GAB4	22	17472825	Missense_Mutation	SNP	T	TCGA-Y8-A8S0-01A-11D-A36X-10		17472825	33831741	40	17924											
MAOA	4128	hgsc.bcm.edu	37	chrX	43603409	43603409	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatatctgggtacaagaaccTgaatcaaaggtaagtttggt	14	11	11	5	0	2	2	1	1	1	1	2	3	2	2	1	3	2	3	1	3	7	4			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chrX:43603409T>C	ENST00000338702.3	+	14	1551	c.1428T>C	c.(1426-1428)ccT>ccC	p.P476P	MAOA_ENST00000542639.1_Silent_p.P343P	NM_000240.3	NP_000231.1	P21397	AOFA_HUMAN	monoamine oxidase A	476					cellular biogenic amine metabolic process (GO:0006576)|dopamine catabolic process (GO:0042420)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	primary amine oxidase activity (GO:0008131)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	18					Almotriptan(DB00918)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Minaprine(DB00805)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Naratriptan(DB00952)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Riboflavin(DB00140)|Rizatriptan(DB00953)|Selegiline(DB01037)|Sertraline(DB01104)|Sumatriptan(DB00669)|Testosterone(DB00624)|Tranylcypromine(DB00752)|Zolmitriptan(DB00315)|Zonisamide(DB00909)	TACAAGAACCTGAATCAAAGG	0.413																																					p.P476P		Atlas-SNP	.											.	MAOA	48	.	0			c.T1428C						PASS	.						144	127	133					X																	43603409		2203	4300	6503	SO:0001819	synonymous_variant	4128	exon14			AGAACCTGAATCA		CCDS14260.1, CCDS59163.1	Xp11.4-p11.3	2008-02-05			ENSG00000189221	ENSG00000189221	1.4.3.4		6833	protein-coding gene	gene with protein product		309850					Standard	NM_000240		Approved		uc004dfy.4	P21397	OTTHUMG00000021387	ENST00000338702.3:c.1428T>C	chrX.hg19:g.43603409T>C		62.0	0.0	.		56.0	52.0	.	NM_000240	B4DF46|Q16426	Silent	SNP	ENST00000338702.3	hg19	CCDS14260.1																																																																																			.	.	.	none		0.413	MAOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056300.1	NM_000240		C	43603409	T	C	43603409	2	2	281	1	0	0	0	0	0	0	0	1	9232	1567	55	3		3	MAOA	23	43603409	Silent	SNP	T	TCGA-Y8-A8S0-01A-11D-A36X-10		43603409	111667151	41	17925											
AR	367	hgsc.bcm.edu	37	chrX	66765228	66765229	+	Missense_Mutation	DNP	AG	AG	GC																															cagcagcagcagcagcagcaAgagactagccccaggcagca																										TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	A|G	A|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chrX:66765228_66765229AG>GC	ENST00000374690.3	+	1	764_765	c.240_241AG>GC	c.(238-243)caAGag>caGCag	p.E81Q	AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.E81Q|AR_ENST00000504326.1_Missense_Mutation_p.E81Q	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	79	Gln-rich.|Modulating.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	agcagcagcaagagactagccc	0.644									Androgen Insensitivity Syndrome																												p.Q80Q|p.E81Q		Atlas-SNP	.											.	AR	249	.	0			c.A240G|c.G241C						PASS	.																																			SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	GCAGCAAGAGACT|CAGCAAGAGACTA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"Nuclear hormone receptors"	644	protein-coding gene	gene with protein product	"testicular feminization", "Kennedy disease"	313700	"dihydrotestosterone receptor", "spinal and bulbar muscular atrophy"	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	Exception_encountered	chrX.hg19:g.66765228_66765229delinsGC	ENSP00000363822:p.Glu81Gln	74.0|75.0	0.0	.		116.0	15.0|10.0	.	NM_000044	A2RUN2|B1AKD7|Q9UD95	Silent|Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1																																																																																			.	.	.	none		0.644	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		GC	66765229	AG	GC	66765228	3	3	281	1	0	0	0	0	1	0	0	0	836	69	3	3	242	3	AR	23	66765228	Missense_Mutation	DNP	AG	TCGA-Y8-A8S0-01A-11D-A36X-10	23161819	66765228	88505332	42	17926											
RENBP	5973	hgsc.bcm.edu	37	chrX	153207005	153207005	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agggtcccatccggagtggaAgggcaacaataggaacttgt	12	7	14	8	1	0	0	0	0	0	0	2	3	2	3	2	5	2	1	2	5	5	2			TCGA-Y8-A8S0-01A-11D-A36X-10	TCGA-Y8-A8S0-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1736e012-2ce0-46e4-ab85-bb0e9449a458	44329552-9eea-40f0-9170-8bc9c77aa51e	g.chrX:153207005A>G	ENST00000393700.3	-	8	951	c.871T>C	c.(871-873)Ttc>Ctc	p.F291L	RENBP_ENST00000462086.1_5'Flank|RENBP_ENST00000369997.3_Missense_Mutation_p.F277L|RENBP_ENST00000412763.1_3'UTR	NM_002910.5	NP_002901.2	P51606	RENBP_HUMAN	renin binding protein	291					N-acetylglucosamine metabolic process (GO:0006044)|N-acetylmannosamine metabolic process (GO:0006051)|N-acetylneuraminate catabolic process (GO:0019262)|regulation of blood pressure (GO:0008217)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|endopeptidase inhibitor activity (GO:0004866)|N-acylglucosamine 2-epimerase activity (GO:0050121)			breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	20	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)				N-Acetyl-D-glucosamine(DB00141)	CCGGAGTGGAAGGGCAACAAT	0.587																																					p.F291L		Atlas-SNP	.											.	RENBP	69	.	0			c.T871C						PASS	.						119	103	109					X																	153207005		2203	4300	6503	SO:0001583	missense	5973	exon8			AGTGGAAGGGCAA		CCDS14738.2	Xq28	2013-09-23	2001-11-28		ENSG00000102032	ENSG00000102032			9959	protein-coding gene	gene with protein product	"N-acylglucosamine 2-epimerase", "GlcNAc 2-epimerase", "N-acetyl-D-glucosamine 2-epimerase"	312420	"renin-binding protein"			1618798	Standard	NM_002910		Approved	RNBP, RBP	uc004fjo.2	P51606	OTTHUMG00000024224	ENST00000393700.3:c.871T>C	chrX.hg19:g.153207005A>G	ENSP00000377303:p.Phe291Leu	149.0	0.0	.		168.0	160.0	.	NM_002910	B4DNZ3|Q96BI6	Missense_Mutation	SNP	ENST00000393700.3	hg19	CCDS14738.2	.	.	.	.	.	.	.	.	.	.	A	12.78	2.040112	0.35989	.	.	ENSG00000102032	ENST00000393700;ENST00000369997	T;T	0.26518	1.73;1.73	5.15	5.15	0.70609	Six-hairpin glycosidase (1);Six-hairpin glycosidase-like (1);	0.054270	0.64402	D	0.000001	T	0.35828	0.0945	L	0.35854	1.095	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.08432	-1.0722	10	0.10377	T	0.69	-19.6509	13.0214	0.58789	1.0:0.0:0.0:0.0	.	291	P51606	RENBP_HUMAN	L	291;277	ENSP00000377303:F291L;ENSP00000359014:F277L	ENSP00000359014:F277L	F	-	1	0	RENBP	152860199	0.998000	0.40836	0.935000	0.37517	0.724000	0.41520	3.764000	0.55264	1.714000	0.51371	0.356000	0.21956	TTC	.	.	.	none		0.587	RENBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061103.3	NM_002910		G	153207005	A	G	153207005	3	3	281	1	0	0	0	0	1	0	0	0	13238	72	3	3	428	3	RENBP	23	153207005	Missense_Mutation	SNP	A	TCGA-Y8-A8S0-01A-11D-A36X-10	86441777	153207005	2063555	43	17927											
TAS1R3	83756	hgsc.bcm.edu	37	chr1	1267161	1267161	+	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	gcctgtggtggccatgaagcCcagcctcatgttcctggcca	6	9	12	14	0	1	1	1	1	0	0	2	1	2	1	6	3	2	1	6	3	1	1			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr1:1267161C>G	ENST00000339381.5	+	2	367	c.335C>G	c.(334-336)cCc>cGc	p.P112R		NM_152228.1	NP_689414	Q7RTX0	TS1R3_HUMAN	taste receptor, type 1, member 3	112					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)		GCCATGAAGCCCAGCCTCATG	0.642																																					p.P112R		Atlas-SNP	.											.	TAS1R3	39	.	0			c.C335G						PASS	.						53	55	55					1																	1267161		2201	4297	6498	SO:0001583	missense	83756	exon2			TGAAGCCCAGCCT	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.335C>G	chr1.hg19:g.1267161C>G	ENSP00000344411:p.Pro112Arg	82.0	0.0	.		65.0	9.0	.	NM_152228	Q5TA49|Q8NGW9	Missense_Mutation	SNP	ENST00000339381.5	hg19	CCDS30556.1	.	.	.	.	.	.	.	.	.	.	C	15.49	2.850317	0.51270	.	.	ENSG00000169962	ENST00000339381	D	0.85556	-2.0	5.0	5.0	0.66597	Extracellular ligand-binding receptor (1);	1.677870	0.04056	N	0.305492	D	0.94324	0.8176	M	0.84511	2.7	0.41984	D	0.990811	D	0.89917	1.0	D	0.78314	0.991	D	0.85678	0.1299	10	0.66056	D	0.02	.	16.4628	0.84069	0.0:1.0:0.0:0.0	.	112	Q7RTX0	TS1R3_HUMAN	R	112	ENSP00000344411:P112R	ENSP00000344411:P112R	P	+	2	0	TAS1R3	1257024	1.000000	0.71417	1.000000	0.80357	0.189000	0.23516	3.974000	0.56852	2.333000	0.79357	0.462000	0.41574	CCC	.	.	.	none		0.642	TAS1R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008493.1			G	1267161	C	G	1267161	3	3	282	1	0	0	0	0	1	0	0	0	15576	623	22	4	341	4	TAS1R3	1	1267161	Missense_Mutation	SNP	C	TCGA-Y8-A8S1-01A-11D-A36X-10		1267161	247983460	1	17928											
KAZ	23254	hgsc.bcm.edu	37	chr1	15382699	15382699	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgggtggtgcaggcggaccTcccgctgaccgcagccatcc	5	6	15	15	3	0	1	0	1	0	0	2	2	2	2	5	4	2	3	5	4	0	0			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr1:15382699T>C	ENST00000376030.2	+	5	1133	c.839T>C	c.(838-840)cTc>cCc	p.L280P	KAZN_ENST00000422387.2_Missense_Mutation_p.L280P|KAZN_ENST00000400797.3_Missense_Mutation_p.L186P|KAZN_ENST00000503743.1_Missense_Mutation_p.L280P|KAZN_ENST00000400798.2_Missense_Mutation_p.L186P|KAZN_ENST00000361144.5_Missense_Mutation_p.L274P	NM_201628.2	NP_963922.2	Q674X7	KAZRN_HUMAN	kazrin, periplakin interacting protein	280	Interaction with PPL.				keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(1)|prostate(2)	25						CAGGCGGACCTCCCGCTGACC	0.657																																					p.L280P		Atlas-SNP	.											.	KAZN	57	.	0			c.T839C						PASS	.						59	54	56					1																	15382699		2203	4300	6503	SO:0001583	missense	23254	exon5			CGGACCTCCCGCT	AY505119	CCDS30604.1, CCDS41267.1, CCDS152.2, CCDS41268.1	1p36.21	2014-02-12	2011-01-31		ENSG00000189337	ENSG00000189337		"Sterile alpha motif (SAM) domain containing"	29173	protein-coding gene	gene with protein product						15337775, 18840647	Standard	NM_015209		Approved	KIAA1026, KAZRIN, FLJ43806	uc001avm.4	Q674X7	OTTHUMG00000002042	ENST00000376030.2:c.839T>C	chr1.hg19:g.15382699T>C	ENSP00000365198:p.Leu280Pro	157.0	0.0	.		170.0	24.0	.	NM_015209	B0QYQ0|B1AK78|Q5TGF1|Q674X4|Q674X6|Q6ZUD1|Q8IYN7|Q8N409|Q9UIL2|Q9UPX4	Missense_Mutation	SNP	ENST00000376030.2	hg19	CCDS152.2	.	.	.	.	.	.	.	.	.	.	T	23.9	4.474863	0.84640	.	.	ENSG00000189337	ENST00000376030;ENST00000503743;ENST00000422387;ENST00000361144;ENST00000400798;ENST00000400797	T;T;T;T;T;T	0.49432	0.78;0.78;0.78;0.78;0.78;0.78	5.8	5.8	0.92144	.	0.121142	0.56097	D	0.000022	T	0.55609	0.1931	L	0.27053	0.805	0.80722	D	1	P;P;D;P	0.89917	0.874;0.874;1.0;0.771	B;P;D;B	0.91635	0.347;0.447;0.999;0.241	T	0.52764	-0.8532	10	0.30078	T	0.28	-17.1885	15.3662	0.74523	0.0:0.0:0.0:1.0	.	280;186;274;280	Q674X7-2;Q674X7-4;Q674X7-3;Q674X7	.;.;.;KAZRN_HUMAN	P	280;280;280;274;186;186	ENSP00000365198:L280P;ENSP00000426015:L280P;ENSP00000391728:L280P;ENSP00000354727:L274P;ENSP00000383602:L186P;ENSP00000383601:L186P	ENSP00000354727:L274P	L	+	2	0	KAZN	15255286	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.404000	0.79996	2.223000	0.72356	0.454000	0.30748	CTC	.	.	.	none		0.657	KAZN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005690.2	NM_001017999		C	15382699	T	C	15382699	3	2	282	1	0	0	0	0	1	0	0	0	7995	1551	54	3	1069	3	KAZ	1	15382699	Missense_Mutation	SNP	T	TCGA-Y8-A8S1-01A-11D-A36X-10	14115538	15382699	233867922	2	17929											
TMEM51	55092	hgsc.bcm.edu	37	chr1	15545932	15545932	+	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	aaggggagaggagcagaaccCgaggttgagcatctctctcc	11	6	14	10	1	2	3	0	1	2	2	4	6	2	4	2	4	3	3	2	4	2	1			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr1:15545932C>G	ENST00000428417.1	+	3	901	c.455C>G	c.(454-456)cCg>cGg	p.P152R	TMEM51_ENST00000376008.2_Missense_Mutation_p.P152R|TMEM51_ENST00000400796.3_Missense_Mutation_p.P152R|TMEM51_ENST00000434578.2_3'UTR|TMEM51_ENST00000376014.3_Missense_Mutation_p.P152R	NM_001136217.1	NP_001129689.1	Q9NW97	TMM51_HUMAN	transmembrane protein 51	152						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(3)|large_intestine(2)|lung(5)|prostate(2)	14		Renal(390;0.00145)|Breast(348;0.00186)|Colorectal(325;0.00215)|all_lung(284;0.00459)|Lung NSC(340;0.0104)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;2.07e-06)|COAD - Colon adenocarcinoma(227;7.14e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000175)|KIRC - Kidney renal clear cell carcinoma(229;0.00141)|STAD - Stomach adenocarcinoma(313;0.00644)|READ - Rectum adenocarcinoma(331;0.0751)		GAGCAGAACCCGAGGTTGAGC	0.582																																					p.P152R		Atlas-SNP	.											.	TMEM51	28	.	0			c.C455G						PASS	.						97	92	94					1																	15545932		2203	4300	6503	SO:0001583	missense	55092	exon3			AGAACCCGAGGTT	AK098467	CCDS154.1	1p36.21	2008-02-05	2005-05-22	2005-05-22	ENSG00000171729	ENSG00000171729			25488	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 72"	C1orf72		12477932	Standard	NM_018022		Approved	FLJ10199	uc001avx.3	Q9NW97	OTTHUMG00000002046	ENST00000428417.1:c.455C>G	chr1.hg19:g.15545932C>G	ENSP00000394899:p.Pro152Arg	286.0	0.0	.		324.0	39.0	.	NM_018022	A8K819	Missense_Mutation	SNP	ENST00000428417.1	hg19	CCDS154.1	.	.	.	.	.	.	.	.	.	.	C	0.013	-1.621990	0.00820	.	.	ENSG00000171729	ENST00000428417;ENST00000376014;ENST00000451326;ENST00000434578;ENST00000400796;ENST00000376008;ENST00000303840	T;T;T;T	0.29142	1.58;1.58;1.58;1.58	5.63	4.72	0.59763	.	0.297924	0.37906	N	0.001882	T	0.19967	0.0480	L	0.31294	0.92	0.09310	N	0.999999	B	0.10296	0.003	B	0.12837	0.008	T	0.21075	-1.0256	10	0.14252	T	0.57	-8.8165	9.3994	0.38424	0.393:0.4774:0.1296:0.0	.	152	Q9NW97	TMM51_HUMAN	R	152	ENSP00000394899:P152R;ENSP00000365182:P152R;ENSP00000383600:P152R;ENSP00000365176:P152R	ENSP00000303666:P152R	P	+	2	0	TMEM51	15418519	0.005000	0.15991	0.860000	0.33809	0.193000	0.23685	0.081000	0.14823	1.378000	0.46305	0.555000	0.69702	CCG	.	.	.	none		0.582	TMEM51-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005699.3	NM_018022		G	15545932	C	G	15545932	3	3	282	1	0	0	0	0	1	0	0	0	16189	652	23	4	461	4	TMEM51	1	15545932	Missense_Mutation	SNP	C	TCGA-Y8-A8S1-01A-11D-A36X-10	163233	15545932	233704689	3	17930											
PADI4	23569	hgsc.bcm.edu	37	chr1	17666248	17666248	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggacttcttcacaaaccatAcactggtgctccacgtggcc	10	9	8	14	1	2	0	1	0	1	0	3	1	3	1	3	3	3	1	3	3	2	3			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr1:17666248A>G	ENST00000375448.4	+	6	618	c.592A>G	c.(592-594)Aca>Gca	p.T198A	AC004824.2_ENST00000602074.1_Intron	NM_012387.2	NP_036519.2	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV	198					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)	CACAAACCATACACTGGTGCT	0.567																																					p.T198A		Atlas-SNP	.											.	PADI4	70	.	0			c.A592G						PASS	.						147	115	125					1																	17666248		2203	4300	6503	SO:0001583	missense	23569	exon6			AACCATACACTGG	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.592A>G	chr1.hg19:g.17666248A>G	ENSP00000364597:p.Thr198Ala	94.0	0.0	.		89.0	4.0	.	NM_012387	A8K392|B2RBW0|Q5VTZ8|Q70SX4	Missense_Mutation	SNP	ENST00000375448.4	hg19	CCDS180.1	.	.	.	.	.	.	.	.	.	.	a	4.235	0.042484	0.08196	.	.	ENSG00000159339	ENST00000375448	T	0.16597	2.33	4.87	0.129	0.14739	Protein-arginine deiminase (PAD), central domain (2);	0.414765	0.24806	N	0.035446	T	0.07007	0.0178	N	0.08118	0	0.09310	N	1	B;B	0.15141	0.012;0.005	B;B	0.19666	0.026;0.018	T	0.38908	-0.9639	10	0.20046	T	0.44	-3.9969	7.645	0.28315	0.4737:0.3836:0.1427:0.0	.	198;198	A8K392;Q9UM07	.;PADI4_HUMAN	A	198	ENSP00000364597:T198A	ENSP00000364597:T198A	T	+	1	0	PADI4	17538835	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.349000	0.07731	0.446000	0.26666	-0.619000	0.04042	ACA	.	.	.	none		0.567	PADI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006799.1	NM_012387		G	17666248	A	G	17666248	3	3	282	1	0	0	0	0	1	0	0	0	11387	391	14	3	614	3	PADI4	1	17666248	Missense_Mutation	SNP	A	TCGA-Y8-A8S1-01A-11D-A36X-10	2120316	17666248	231584373	4	17931											
C1orf172	126695	hgsc.bcm.edu	37	chr1	27278714	27278714	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtaatgctctctggcccaTggtggccagggtccttgggg	5	10	16	10	0	1	0	0	0	1	0	3	0	2	0	3	7	1	2	3	7	1	2			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr1:27278714T>C	ENST00000320567.5	-	2	246	c.158A>G	c.(157-159)cAt>cGt	p.H53R		NM_152365.2	NP_689578.2	Q8NAX2	KDF1_HUMAN		53	Pro-rich.				developmental growth (GO:0048589)|establishment of skin barrier (GO:0061436)|keratinocyte development (GO:0003334)|limb epidermis development (GO:0060887)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of stem cell proliferation (GO:2000647)|positive regulation of epidermal cell differentiation (GO:0045606)|regulation of epidermal cell division (GO:0010482)	cell cortex (GO:0005938)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)				NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.37e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.22e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)		CTCTGGCCCATGGTGGCCAGG	0.632																																					p.H53R		Atlas-SNP	.											.	C1orf172	38	.	0			c.A158G						PASS	.						25	30	28					1																	27278714		2203	4300	6503	SO:0001583	missense	126695	exon2			GGCCCATGGTGGC																												ENST00000320567.5:c.158A>G	chr1.hg19:g.27278714T>C	ENSP00000319179:p.His53Arg	87.0	0.0	.		120.0	15.0	.	NM_152365	Q5QP32|Q8N0S7	Missense_Mutation	SNP	ENST00000320567.5	hg19	CCDS293.1	.	.	.	.	.	.	.	.	.	.	T	3.593	-0.083194	0.07141	.	.	ENSG00000175707	ENST00000320567;ENST00000374109	T	0.19938	2.11	4.78	3.63	0.41609	.	0.140335	0.46442	D	0.000294	T	0.05731	0.0150	N	0.02916	-0.46	0.26831	N	0.968583	B	0.02656	0.0	B	0.01281	0.0	T	0.41520	-0.9504	10	0.02654	T	1	.	3.7038	0.08392	0.0:0.2232:0.0:0.7768	.	53	Q8NAX2	CA172_HUMAN	R	53	ENSP00000319179:H53R	ENSP00000319179:H53R	H	-	2	0	C1orf172	27151301	0.445000	0.25657	1.000000	0.80357	0.998000	0.95712	4.006000	0.57083	2.005000	0.58758	0.528000	0.53228	CAT	.	.	.	none		0.632	C1orf172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012340.1			C	27278714	T	C	27278714	3	2	282	1	0	0	0	0	1	0	0	0	2015	1464	51	3	1050	3	C1orf172	1	27278714	Missense_Mutation	SNP	T	TCGA-Y8-A8S1-01A-11D-A36X-10	9612466	27278714	221971907	5	17932											
NCDN	23154	hgsc.bcm.edu	37	chr1	36026513	36026513	+	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	tttgcccccgacaaccgtgcCccctgaatgctaccgggatc	7	8	9	17	3	0	1	0	1	0	0	1	3	0	2	6	1	5	1	6	1	3	2			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr1:36026513C>G	ENST00000373243.2	+	3	1144	c.761C>G	c.(760-762)cCc>cGc	p.P254R	NCDN_ENST00000356090.4_Missense_Mutation_p.P254R|NCDN_ENST00000373253.3_Missense_Mutation_p.P237R	NM_014284.2	NP_055099.1	Q9UBB6	NCDN_HUMAN	neurochondrin	254					bone resorption (GO:0045453)|neuron projection development (GO:0031175)|regulation of neuronal synaptic plasticity (GO:0048168)	cytosol (GO:0005829)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|pancreas(1)|skin(2)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				ACAACCGTGCCCCCTGAATGC	0.632																																					p.P254R		Atlas-SNP	.											.	NCDN	79	.	0			c.C761G						PASS	.						62	58	60					1																	36026513		2201	4299	6500	SO:0001583	missense	23154	exon3			CCGTGCCCCCTGA	AB011179	CCDS392.1, CCDS30672.1	1p34.3	2008-02-05			ENSG00000020129	ENSG00000020129			17597	protein-coding gene	gene with protein product		608458				15007648	Standard	NM_014284		Approved	NCDN-1, NCDN-2	uc001bza.3	Q9UBB6	OTTHUMG00000059204	ENST00000373243.2:c.761C>G	chr1.hg19:g.36026513C>G	ENSP00000362340:p.Pro254Arg	75.0	0.0	.		71.0	13.0	.	NM_014284	D3DPR9|Q9UBY2|Q9Y4A6|Q9Y4D9	Missense_Mutation	SNP	ENST00000373243.2	hg19	CCDS392.1	.	.	.	.	.	.	.	.	.	.	C	7.506	0.653673	0.14580	.	.	ENSG00000020129	ENST00000373253;ENST00000356090;ENST00000373243;ENST00000437806	T;T;T	0.68331	-0.32;-0.32;-0.32	4.76	4.76	0.60689	.	0.256266	0.37012	N	0.002286	T	0.56529	0.1991	N	0.22421	0.69	0.40225	D	0.977787	P	0.44139	0.827	P	0.45037	0.467	T	0.57676	-0.7770	10	0.33940	T	0.23	.	13.3806	0.60764	0.0:0.8286:0.1714:0.0	.	254	Q9UBB6	NCDN_HUMAN	R	237;254;254;237	ENSP00000362350:P237R;ENSP00000348394:P254R;ENSP00000362340:P254R	ENSP00000348394:P254R	P	+	2	0	NCDN	35799100	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	2.780000	0.47742	2.472000	0.83506	0.561000	0.74099	CCC	.	.	.	none		0.632	NCDN-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131298.1	NM_014284		G	36026513	C	G	36026513	3	3	282	1	0	0	0	0	1	0	0	0	10221	623	22	4	771	4	NCDN	1	36026513	Missense_Mutation	SNP	C	TCGA-Y8-A8S1-01A-11D-A36X-10	8747799	36026513	213224108	6	17933											
KDM4A	9682	hgsc.bcm.edu	37	chr1	44128602	44128602	+	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	tattggccggctgagaacaaTcctggacttggtggaaaagg	11	9	14	7	1	0	1	0	1	0	1	1	4	1	3	2	6	1	1	2	6	5	3			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr1:44128602T>A	ENST00000372396.3	+	5	601	c.467T>A	c.(466-468)aTc>aAc	p.I156N	KDM4A_ENST00000463151.1_3'UTR	NM_014663.2	NP_055478.2	O75164	KDM4A_HUMAN	lysine (K)-specific demethylase 4A	156	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				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						CTGAGAACAATCCTGGACTTG	0.488																																					p.I156N		Atlas-SNP	.											.	KDM4A	74	.	0			c.T467A						PASS	.						191	164	173					1																	44128602		2203	4300	6503	SO:0001583	missense	9682	exon5			GAACAATCCTGGA	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.467T>A	chr1.hg19:g.44128602T>A	ENSP00000361473:p.Ile156Asn	212.0	0.0	.		198.0	21.0	.	NM_014663	Q5VVB1	Missense_Mutation	SNP	ENST00000372396.3	hg19	CCDS491.1	.	.	.	.	.	.	.	.	.	.	T	29.7	5.027980	0.93518	.	.	ENSG00000066135	ENST00000372396	T	0.72051	-0.62	5.88	5.88	0.94601	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.000000	0.85682	D	0.000000	D	0.84982	0.5593	M	0.79693	2.465	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.965;0.997	D	0.86851	0.2023	10	0.72032	D	0.01	-1.527	16.2948	0.82765	0.0:0.0:0.0:1.0	.	156;156	B4DT38;O75164	.;KDM4A_HUMAN	N	156	ENSP00000361473:I156N	ENSP00000361473:I156N	I	+	2	0	KDM4A	43901189	1.000000	0.71417	0.993000	0.49108	0.994000	0.84299	8.027000	0.88791	2.253000	0.74438	0.455000	0.32223	ATC	.	.	.	none		0.488	KDM4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019960.1	NM_014663		A	44128602	T	A	44128602	3	1	282	1	0	0	0	0	1	0	0	0	8135	1435	50	5	481	5	KDM4A	1	44128602	Missense_Mutation	SNP	T	TCGA-Y8-A8S1-01A-11D-A36X-10	8102089	44128602	205122019	7	17934											
LCE4A	199834	hgsc.bcm.edu	37	chr1	152681679	152681680	+	Missense_Mutation	DNP	CC	CC	GT																															aatctcttcctgctgtggctCcagctctgggggctgtggtt																								rs6143428|rs11269814|rs200890315	byFrequency	TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr1:152681679_152681680CC>GT	ENST00000368777.1	+	2	384_385	c.128_129CC>GT	c.(127-129)tCC>tGT	p.S43C	LCE4A_ENST00000335535.3_Missense_Mutation_p.S43C			Q5TA78	LCE4A_HUMAN	late cornified envelope 4A	43	Cys-rich.				keratinization (GO:0031424)					endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.116)			TGCTGTGGCTCCAGCTCTGGGG	0.599																																					p.S43C|p.S43S		Atlas-SNP	.											LCE4A,rectum,carcinoma,0,1|LCE4A,rectum,carcinoma,+1,15	LCE4A	37	.	0			c.C128G|c.C129T						PASS	.																																			SO:0001583	missense	199834	exon1			GTGGCTCCAGCTC|TGGCTCCAGCTCT	BI670517	CCDS1022.1	1q22	2008-02-05	2004-10-11	2004-10-15	ENSG00000187170	ENSG00000187170		"Late cornified envelopes"	16613	protein-coding gene	gene with protein product		612618	"small proline rich-like (epidermal differentiation complex) 4A"	SPRL4A		11698679	Standard	NM_178356		Approved	LEP8	uc001fak.2	Q5TA78	OTTHUMG00000014394	Exception_encountered	chr1.hg19:g.152681679_152681680delinsGT	ENSP00000357766:p.Ser43Cys	219.0|215.0	0.0|1.0	.		195.0|192.0	13.0|9.0	.	NM_178356	Q14D97	Missense_Mutation|Silent	SNP	ENST00000368777.1	hg19	CCDS1022.1																																																																																			.	.	.	none|weak		0.599	LCE4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040048.1	NM_178356		GT	152681680	CC	GT	152681679	3	3	282	1	0	0	0	0	1	0	0	0	8681	855	30	4	130	4	LCE4A	1	152681679	Missense_Mutation	DNP	CC	TCGA-Y8-A8S1-01A-11D-A36X-10	108553077	152681679	96568942	8	17935											
KLF11	8462	hgsc.bcm.edu	37	chr2	10192452	10192453	+	Missense_Mutation	DNP	AA	AA	TT																															gaactcacacaggggagaagAagtttgtgtgcccggtgtgt																										TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr2:10192452_10192453AA>TT	ENST00000305883.1	+	4	1519_1520	c.1357_1358AA>TT	c.(1357-1359)AAg>TTg	p.K453L	RP11-254F7.3_ENST00000607181.1_RNA|KLF11_ENST00000535335.1_Missense_Mutation_p.K436L|KLF11_ENST00000540845.1_Missense_Mutation_p.K436L	NM_003597.4	NP_003588.1	O14901	KLF11_HUMAN	Kruppel-like factor 11	453					apoptotic process (GO:0006915)|cellular response to peptide (GO:1901653)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.133)|OV - Ovarian serous cystadenocarcinoma(76;0.228)		AGGGGAGAAGAAGTTTGTGTGC	0.569																																					p.K453X|p.K453M	Melanoma(56;431 1507 23687 50789)	Atlas-SNP	.											.	KLF11	45	.	0			c.A1357T|c.A1358T						PASS	.																																			SO:0001583	missense	8462	exon4			GAGAAGAAGTTTG|AGAAGAAGTTTGT	AF028008	CCDS1668.1, CCDS54333.1	2p25	2013-01-08	2004-11-29	2004-12-01	ENSG00000172059	ENSG00000172059		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	11811	protein-coding gene	gene with protein product		603301	"TGFB inducible early growth response 2"	TIEG2		9748269, 11087666	Standard	NM_001177716		Approved	Tieg3, MODY7	uc002raf.1	O14901	OTTHUMG00000119004	Exception_encountered	chr2.hg19:g.10192452_10192453delinsTT	ENSP00000307023:p.Lys453Leu	157.0	0.0	.		141.0|137.0	22.0	.	NM_003597	B4DZE7|Q9EPF4	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000305883.1	hg19	CCDS1668.1																																																																																			.	.	.	none		0.569	KLF11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000239202.3	NM_003597		TT	10192453	AA	TT	10192452	3	4	282	1	0	0	0	0	1	0	0	0	8346	247	9	5	1371	5	KLF11	2	10192452	Missense_Mutation	DNP	AA	TCGA-Y8-A8S1-01A-11D-A36X-10		10192452	233006921	9	17936											
SMC6	79677	hgsc.bcm.edu	37	chr2	17888505	17888505	+	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	ccttatttcagaatccacatCtctgcttaggaacttaggtc	10	14	6	11	0	2	1	1	0	1	1	5	2	3	2	2	2	2	1	2	2	5	4			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr2:17888505C>G	ENST00000448223.2	-	18	2256	c.1987G>C	c.(1987-1989)Gat>Cat	p.D663H	SMC6_ENST00000351948.4_Missense_Mutation_p.D663H|SMC6_ENST00000402989.1_Missense_Mutation_p.D663H|SMC6_ENST00000381272.4_Missense_Mutation_p.D689H	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	663					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					GAATCCACATCTCTGCTTAGG	0.363																																					p.D663H		Atlas-SNP	.											.	SMC6	102	.	0			c.G1987C						PASS	.						139	140	139					2																	17888505		2203	4300	6503	SO:0001583	missense	79677	exon18			CCACATCTCTGCT	AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"Structural maintenance of chromosomes proteins"	20466	protein-coding gene	gene with protein product		609387	"SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.1987G>C	chr2.hg19:g.17888505C>G	ENSP00000404092:p.Asp663His	158.0	0.0	.		117.0	19.0	.	NM_001142286	A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Missense_Mutation	SNP	ENST00000448223.2	hg19	CCDS1690.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.660667	0.88154	.	.	ENSG00000163029	ENST00000448223;ENST00000351948;ENST00000381272;ENST00000402989;ENST00000446852	T;T;T;T;T	0.29917	2.54;2.54;2.07;2.54;1.55	6.02	6.02	0.97574	RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	T	0.57814	0.2079	M	0.68593	2.085	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.993;0.998	T	0.54397	-0.8300	10	0.59425	D	0.04	.	20.5373	0.99239	0.0:1.0:0.0:0.0	.	689;689;663	C9JMN1;Q96SB8-2;Q96SB8	.;.;SMC6_HUMAN	H	663;663;689;663;689	ENSP00000404092:D663H;ENSP00000323439:D663H;ENSP00000370672:D689H;ENSP00000384539:D663H;ENSP00000408644:D689H	ENSP00000323439:D663H	D	-	1	0	SMC6	17751986	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	6.427000	0.73378	2.857000	0.98124	0.650000	0.86243	GAT	.	.	.	none		0.363	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207359.1	NM_024624		G	17888505	C	G	17888505	3	3	282	1	0	0	0	0	1	0	0	0	14800	913	32	4	1332	4	SMC6	2	17888505	Missense_Mutation	SNP	C	TCGA-Y8-A8S1-01A-11D-A36X-10	7696053	17888505	225310868	10	17937											
NCL	4691	hgsc.bcm.edu	37	chr2	232325414	232325414	+	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	tcttcctcctcctcatcatcTtcatcatcatcatcttcatc	7	17	0	17	0	10	0	7	0	3	0	14	0	13	0	3	0	0	0	3	0	0	3	rs540030591|rs139777351|rs371359723|rs199689485|rs527711138|rs368566589	byFrequency	TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr2:232325414T>A	ENST00000322723.4	-	4	1017	c.777A>T	c.(775-777)gaA>gaT	p.E259D	SNORD82_ENST00000365530.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	259	Asp/Glu-rich (acidic).				angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		CCtcatcatcttcatcatcat	0.438																																					p.E259D		Atlas-SNP	.											.	NCL	80	.	0			c.A777T						PASS	.						229	194	206					2																	232325414		2203	4300	6503	SO:0001583	missense	4691	exon4			ATCATCTTCATCA		CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"RNA binding motif (RRM) containing"	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.777A>T	chr2.hg19:g.232325414T>A	ENSP00000318195:p.Glu259Asp	65.0	0.0	.		69.0	10.0	.	NM_005381	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	Missense_Mutation	SNP	ENST00000322723.4	hg19	CCDS33397.1	.	.	.	.	.	.	.	.	.	.	T	0.028	-1.357543	0.01245	.	.	ENSG00000115053	ENST00000322723;ENST00000392033	T	0.23552	1.9	4.93	-9.86	0.00473	.	1.633390	0.02710	N	0.112777	T	0.06554	0.0168	N	0.03608	-0.345	0.19945	N	0.999949	B	0.02656	0.0	B	0.08055	0.003	T	0.26677	-1.0096	10	0.02654	T	1	0.5096	0.6058	0.00752	0.2352:0.1751:0.2128:0.3769	.	259	P19338	NUCL_HUMAN	D	259;151	ENSP00000318195:E259D	ENSP00000318195:E259D	E	-	3	2	NCL	232033658	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.197000	0.00276	-4.228000	0.00063	-3.370000	0.00041	GAA	.	.	.	weak		0.438	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381		A	232325414	T	A	232325414	3	1	282	1	0	0	0	0	1	0	0	0	10233	1606	56	5	1399	5	NCL	2	232325414	Missense_Mutation	SNP	T	TCGA-Y8-A8S1-01A-11D-A36X-10	214436909	232325414	10873959	11	17938											
ZNF619	285267	hgsc.bcm.edu	37	chr3	40528724	40528724	+	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	aaagaatgtgggaaaaccttCagatataactcaaaactgtc	18	9	7	7	0	2	2	2	0	0	2	3	3	2	3	1	1	3	0	1	1	8	3			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr3:40528724C>T	ENST00000314686.5	+	6	1080	c.675C>T	c.(673-675)ttC>ttT	p.F225F	ZNF619_ENST00000520737.1_3'UTR|ZNF619_ENST00000521353.1_Silent_p.F281F|ZNF619_ENST00000522736.1_Silent_p.F232F|ZNF619_ENST00000429348.2_Silent_p.F241F|ZNF619_ENST00000432264.2_Silent_p.F241F|ZNF619_ENST00000447116.2_Silent_p.F281F|ZNF619_ENST00000456778.1_Silent_p.F197F			Q8N2I2	ZN619_HUMAN	zinc finger protein 619	225					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		GGAAAACCTTCAGATATAACT	0.438																																					p.F281F		Atlas-SNP	.											.	ZNF619	57	.	0			c.C843T						PASS	.						59	60	60					3																	40528724		2203	4300	6503	SO:0001819	synonymous_variant	285267	exon6			AACCTTCAGATAT	AK075245	CCDS46801.1, CCDS46802.1, CCDS46803.1	3p21.33	2013-01-08			ENSG00000177873	ENSG00000177873		"Zinc fingers, C2H2-type", "-"	26910	protein-coding gene	gene with protein product							Standard	NM_001145083		Approved	FLJ90764	uc011azb.2	Q8N2I2	OTTHUMG00000131391	ENST00000314686.5:c.675C>T	chr3.hg19:g.40528724C>T		129.0	0.0	.		128.0	19.0	.	NM_001145082	B4E271|C9JRN5|D4PHA2|E9PCD9	Silent	SNP	ENST00000314686.5	hg19																																																																																				.	.	.	none		0.438	ZNF619-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000254180.2	NM_173656		T	40528724	C	T	40528724	2	4	282	1	0	0	0	0	0	0	0	1	18055	825	29	2		2	ZNF619	3	40528724	Silent	SNP	C	TCGA-Y8-A8S1-01A-11D-A36X-10		40528724	157493706	12	17939											
TMIE	259236	hgsc.bcm.edu	37	chr3	46751076	46751076	+	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	ccctgccccacagaggataaGaagaagaagaagaagaagaa	20	2	11	8	0	0	8	0	0	0	8	0	9	0	9	3	1	1	0	3	1	8	1	rs552239745|rs397817178|rs10578999|rs544504092|rs538183178|rs71619660|rs75020261	byFrequency	TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr3:46751076G>T	ENST00000326431.3	+	4	524	c.369G>T	c.(367-369)aaG>aaT	p.K123N		NM_147196.2	NP_671729.2	Q8NEW7	TMIE_HUMAN	transmembrane inner ear	123	Lys-rich.				inner ear morphogenesis (GO:0042472)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				endometrium(1)|lung(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000688)|KIRC - Kidney renal clear cell carcinoma(197;0.0177)|Kidney(197;0.0208)		CAGAGGATaagaagaagaaga	0.502																																					p.K123N		Atlas-SNP	.											.	TMIE	16	.	0			c.G369T						PASS	.						56	61	60					3																	46751076		1899	4121	6020	SO:0001583	missense	259236	exon4			GGATAAGAAGAAG	AY081842	CCDS43081.1	3p21	2010-01-06	2004-05-19		ENSG00000181585	ENSG00000181585			30800	protein-coding gene	gene with protein product		607237	"deafness, autosomal recessive 6"	DFNB6		12140191, 12145746	Standard	NM_147196		Approved		uc010hjk.1	Q8NEW7	OTTHUMG00000149909	ENST00000326431.3:c.369G>T	chr3.hg19:g.46751076G>T	ENSP00000324775:p.Lys123Asn	199.0	0.0	.		217.0	17.0	.	NM_147196	A0AV93|A8K0R0	Missense_Mutation	SNP	ENST00000326431.3	hg19	CCDS43081.1	.	.	.	.	.	.	.	.	.	.	G	4.335	0.061563	0.08339	.	.	ENSG00000181585	ENST00000326431	D	0.86230	-2.09	.	.	.	.	0.415784	0.26349	N	0.024899	T	0.76821	0.4041	L	0.40543	1.245	0.09310	N	1	B	0.25441	0.126	B	0.06405	0.002	T	0.64765	-0.6330	8	0.48119	T	0.1	-5.4402	.	.	.	.	123	Q8NEW7	TMIE_HUMAN	N	123	ENSP00000324775:K123N	ENSP00000324775:K123N	K	+	3	2	TMIE	46726080	0.976000	0.34144	0.425000	0.26659	0.475000	0.33008	1.894000	0.39768	0.121000	0.18284	0.123000	0.15791	AAG	.	.	.	weak		0.502	TMIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313853.1	NM_147196		T	46751076	G	T	46751076	3	4	282	1	0	0	0	0	1	0	0	0	16241	933	33	4	383	4	TMIE	3	46751076	Missense_Mutation	SNP	G	TCGA-Y8-A8S1-01A-11D-A36X-10	6222352	46751076	151271354	13	17940											
CELSR3	1951	hgsc.bcm.edu	37	chr3	48690465	48690465	+	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	ctaaagtccagtgagaccatAaggacatggtggccccgccg	11	6	12	12	2	0	1	0	1	0	1	1	3	1	2	5	3	0	0	5	3	3	2			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr3:48690465A>T	ENST00000164024.4	-	10	5884	c.5604T>A	c.(5602-5604)ctT>ctA	p.L1868L	CELSR3_ENST00000544264.1_Silent_p.L1868L	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	1868	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GTGAGACCATAAGGACATGGT	0.597																																					p.L1868L		Atlas-SNP	.											.	CELSR3	237	.	0			c.T5604A						PASS	.						56	66	62					3																	48690465		2203	4300	6503	SO:0001819	synonymous_variant	1951	exon10			GACCATAAGGACA	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.5604T>A	chr3.hg19:g.48690465A>T		109.0	0.0	.		141.0	19.0	.	NM_001407	O75092	Silent	SNP	ENST00000164024.4	hg19	CCDS2775.1																																																																																			.	.	.	none		0.597	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		T	48690465	A	T	48690465	2	4	282	1	0	0	0	0	0	0	0	1	3225	349	13	5		5	CELSR3	3	48690465	Silent	SNP	A	TCGA-Y8-A8S1-01A-11D-A36X-10	1939389	48690465	149331965	14	17941											
TMF1	7110	hgsc.bcm.edu	37	chr3	69097304	69097307	+	Frame_Shift_Del	DEL	TTCT	TTCT	-																															gttggcaccttcatatccgaTtctttattaacagtttcttc																										TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	TTCT	TTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr3:69097304_69097307delTTCT	ENST00000398559.2	-	2	765_768	c.549_552delAGAA	c.(547-552)aaagaafs	p.KE183fs	CTD-2013N24.2_ENST00000596274.1_RNA|CTD-2013N24.2_ENST00000482368.2_RNA|CTD-2013N24.2_ENST00000601735.1_RNA|CTD-2013N24.2_ENST00000596523.1_RNA|CTD-2013N24.2_ENST00000597950.1_RNA|CTD-2013N24.2_ENST00000595925.1_RNA|TMF1_ENST00000543976.1_Frame_Shift_Del_p.KE183fs|CTD-2013N24.2_ENST00000598783.1_RNA|CTD-2013N24.2_ENST00000596732.1_RNA|MIR3136_ENST00000583498.1_RNA			P82094	TMF1_HUMAN	TATA element modulatory factor 1	183					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)		TCATATCCGATTCTTTATTAACAG	0.382																																					p.184_185del		Atlas-Indel,Pindel	.											.	TMF1	77	.	0			c.550_553del						PASS	.																																			SO:0001589	frameshift_variant	7110	exon2			.		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.549_552delAGAA	chr3.hg19:g.69097304_69097307delTTCT	ENSP00000381567:p.Lys183fs	188.0	0.0	0		165.0	19.0	0.115152	NM_007114	B7ZLJ2|Q17R87|Q59GK0	Frame_Shift_Del	DEL	ENST00000398559.2	hg19	CCDS43105.1																																																																																			.	.	.	none		0.382	TMF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352106.1	NM_007114		-	69097307	TTCT	-	69097304	7	5	282	1	0	1	0	1	0	0	0	0	16240	1490	52	0	2793	0	TMF1	3	69097304	Frame_Shift_Del	DEL	TTCT	TCGA-Y8-A8S1-01A-11D-A36X-10	20406839	69097304	128925126	15	17942											
EPHA3	2042	hgsc.bcm.edu	37	chr3	89498468	89498468	+	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	tatggagttatgggattgttCtctgggaggtgatgtcttat	7	17	14	3	0	2	1	0	1	2	0	3	4	2	4	0	4	0	2	0	4	3	5			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr3:89498468C>T	ENST00000336596.2	+	14	2665	c.2440C>T	c.(2440-2442)Ctc>Ttc	p.L814F	EPHA3_ENST00000494014.1_Missense_Mutation_p.L814F	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	814	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)		TGGGATTGTTCTCTGGGAGGT	0.453										TSP Lung(6;0.00050)																											p.L814F		Atlas-SNP	.											.	EPHA3	501	.	0			c.C2440T						PASS	.						260	238	246					3																	89498468		2203	4300	6503	SO:0001583	missense	2042	exon14			ATTGTTCTCTGGG	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.2440C>T	chr3.hg19:g.89498468C>T	ENSP00000337451:p.Leu814Phe	166.0	0.0	.		170.0	26.0	.	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	hg19	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.544374	0.86022	.	.	ENSG00000044524	ENST00000336596;ENST00000494014	T;T	0.69806	-0.43;-0.43	5.34	5.34	0.76211	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.82171	0.4979	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.82186	-0.0582	9	.	.	.	.	19.0702	0.93130	0.0:1.0:0.0:0.0	.	814	P29320	EPHA3_HUMAN	F	814	ENSP00000337451:L814F;ENSP00000419190:L814F	.	L	+	1	0	EPHA3	89581158	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.839000	0.55835	2.507000	0.84556	0.655000	0.94253	CTC	.	.	.	none		0.453	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		T	89498468	C	T	89498468	3	4	282	1	0	0	0	0	1	0	0	0	5170	913	32	2	2520	2	EPHA3	3	89498468	Missense_Mutation	SNP	C	TCGA-Y8-A8S1-01A-11D-A36X-10	20401164	89498468	108523962	16	17943											
OR5H14	403273	hgsc.bcm.edu	37	chr3	97868711	97868711	+	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	tcatgctttaatccatgaagGatttttattcagactaacct	12	16	5	8	0	2	2	2	1	0	1	3	3	3	3	2	1	2	1	2	1	4	7			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr3:97868711G>A	ENST00000437310.1	+	1	542	c.482G>A	c.(481-483)gGa>gAa	p.G161E	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005514.1	NP_001005514.1	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H, member 14	161						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						ATCCATGAAGGATTTTTATTC	0.348																																					p.G161E		Atlas-SNP	.											OR5H14,NS,carcinoma,0,1	OR5H14	56	.	0			c.G482A						PASS	.						102	104	103					3																	97868711		2202	4300	6502	SO:0001583	missense	403273	exon1			ATGAAGGATTTTT		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.482G>A	chr3.hg19:g.97868711G>A	ENSP00000401706:p.Gly161Glu	216.0	0.0	.		248.0	31.0	.	NM_001005514	B9EH15	Missense_Mutation	SNP	ENST00000437310.1	hg19	CCDS33798.1	.	.	.	.	.	.	.	.	.	.	G	7.995	0.754074	0.15778	.	.	ENSG00000236032	ENST00000437310	T	0.37411	1.2	2.49	-1.46	0.08800	GPCR, rhodopsin-like superfamily (1);	0.899723	0.09201	N	0.834639	T	0.43743	0.1261	M	0.83118	2.625	0.09310	N	1	P	0.40731	0.728	P	0.45794	0.493	T	0.37641	-0.9697	10	0.37606	T	0.19	.	5.877	0.18834	0.0:0.4119:0.268:0.3201	.	161	A6NHG9	O5H14_HUMAN	E	161	ENSP00000401706:G161E	ENSP00000401706:G161E	G	+	2	0	OR5H14	99351401	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.034000	0.01424	-0.640000	0.05495	-1.112000	0.02068	GGA	.	.	.	none		0.348	OR5H14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359112.1			A	97868711	G	A	97868711	3	1	282	1	0	0	0	0	1	0	0	0	11167	1174	41	2	484	2	OR5H14	3	97868711	Missense_Mutation	SNP	G	TCGA-Y8-A8S1-01A-11D-A36X-10	8370243	97868711	100153719	17	17944											
PDS5A	23244	hgsc.bcm.edu	37	chr4	39910143	39910143	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcttcttctggatcatgtgAtctaacctttaaatattctg	10	17	6	8	0	5	1	1	1	4	0	5	2	5	2	1	1	2	1	1	1	4	7			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr4:39910143A>G	ENST00000303538.8	-	11	1644	c.1105T>C	c.(1105-1107)Tca>Cca	p.S369P	PDS5A_ENST00000503396.1_Missense_Mutation_p.S369P	NM_001100399.1	NP_001093869.1			PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)											breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						GGATCATGTGATCTAACCTTT	0.343																																					p.S369P		Atlas-SNP	.											.	PDS5A	114	.	0			c.T1105C						PASS	.						99	92	94					4																	39910143		1834	4086	5920	SO:0001583	missense	23244	exon11			CATGTGATCTAAC	AF294791	CCDS47045.1, CCDS54759.1	4p14	2007-06-20			ENSG00000121892	ENSG00000121892			29088	protein-coding gene	gene with protein product		613200				11076961, 15855230	Standard	NM_001100399		Approved	KIAA0648, PIG54, SCC-112	uc003guv.4	Q29RF7	OTTHUMG00000160582	ENST00000303538.8:c.1105T>C	chr4.hg19:g.39910143A>G	ENSP00000303427:p.Ser369Pro	83.0	0.0	.		92.0	15.0	.	NM_001100399		Missense_Mutation	SNP	ENST00000303538.8	hg19	CCDS47045.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.384751	0.82792	.	.	ENSG00000121892	ENST00000303538;ENST00000503396	T;T	0.68765	-0.13;-0.35	4.93	4.93	0.64822	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000001	T	0.76630	0.4014	M	0.62723	1.935	0.80722	D	1	D;P	0.54047	0.964;0.938	P;P	0.60541	0.709;0.876	T	0.76833	-0.2813	9	.	.	.	-4.4602	14.5742	0.68235	1.0:0.0:0.0:0.0	.	369;369	Q29RF7-3;Q29RF7	.;PDS5A_HUMAN	P	369	ENSP00000303427:S369P;ENSP00000426749:S369P	.	S	-	1	0	PDS5A	39586538	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.315000	0.96313	1.853000	0.53794	0.455000	0.32223	TCA	.	.	.	none		0.343	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200		G	39910143	A	G	39910143	3	3	282	1	0	0	0	0	1	0	0	0	11698	333	12	3	3033	3	PDS5A	4	39910143	Missense_Mutation	SNP	A	TCGA-Y8-A8S1-01A-11D-A36X-10		39910143	151244133	18	17945											
SHROOM3	57619	hgsc.bcm.edu	37	chr4	77661777	77661777	+	Frame_Shift_Del	DEL	T	T	-																															ccccacaggaccgtctcaacTtccagtacttctgggaatga																										TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr4:77661777delT	ENST00000296043.6	+	5	3404	c.2451delT	c.(2449-2451)actfs	p.T817fs		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	817					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)			CCGTCTCAACTTCCAGTACTT	0.537																																					p.T817fs		Atlas-Indel,Pindel	.											.	SHROOM3	134	.	0			c.2450delC						PASS	.						67	76	73					4																	77661777		2203	4300	6503	SO:0001589	frameshift_variant	57619	exon5			.	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.2451delT	chr4.hg19:g.77661777delT	ENSP00000296043:p.Thr817fs	130.0	0.0	0		141.0	15.0	0.106383	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Frame_Shift_Del	DEL	ENST00000296043.6	hg19	CCDS3579.2																																																																																			.	.	.	none		0.537	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859		-	77661777	T	-	77661777	7	5	282	1	0	1	0	1	0	0	0	0	14308	1596	56	0	2469	0	SHROOM3	4	77661777	Frame_Shift_Del	DEL	T	TCGA-Y8-A8S1-01A-11D-A36X-10	37751634	77661777	113492499	19	17946											
HNRPDL	9987	hgsc.bcm.edu	37	chr4	83350434	83350434	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gattcttgctcgcgttgatcTtggatccctctgcgaattcc	5	15	9	12	3	3	1	0	1	3	0	6	4	5	2	2	1	2	2	2	1	1	5			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr4:83350434T>C	ENST00000295470.5	-	1	585	c.410A>G	c.(409-411)aAg>aGg	p.K137R	ENOPH1_ENST00000273920.3_5'Flank|HNRNPDL_ENST00000602300.1_Missense_Mutation_p.K18R|HNRNPDL_ENST00000502762.1_Missense_Mutation_p.K137R|ENOPH1_ENST00000509635.1_5'Flank|HNRNPDL_ENST00000514511.1_5'UTR|HNRNPDL_ENST00000349655.4_Missense_Mutation_p.K18R	NM_001207000.1|NM_031372.3	NP_001193929.1|NP_112740.1	O14979	HNRDL_HUMAN	heterogeneous nuclear ribonucleoprotein D-like	137					regulation of gene expression (GO:0010468)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|single-stranded DNA binding (GO:0003697)										CGCGTTGATCTTGGATCCCTC	0.627																																					p.K137R		Atlas-SNP	.											.	HNRPDL	35	.	0			c.A410G						PASS	.						108	119	115					4																	83350434		2203	4300	6503	SO:0001583	missense	9987	exon1			TTGATCTTGGATC	D89092	CCDS3593.1, CCDS75153.1	4q21.22	2013-06-12		2013-06-12	ENSG00000152795	ENSG00000152795		"RNA binding motif (RRM) containing"	5037	protein-coding gene	gene with protein product		607137		HNRPDL		10072754, 9524220	Standard	NM_001207000		Approved	JKTBP, laAUF1	uc003hmr.3	O14979	OTTHUMG00000130299	ENST00000295470.5:c.410A>G	chr4.hg19:g.83350434T>C	ENSP00000295470:p.Lys137Arg	100.0	0.0	.		84.0	9.0	.	NM_031372	Q6SPF2|Q7KZ74|Q7KZ75|Q96IM0|Q96S43	Missense_Mutation	SNP	ENST00000295470.5	hg19	CCDS3593.1	.	.	.	.	.	.	.	.	.	.	t	16.13	3.036489	0.54896	.	.	ENSG00000152795	ENST00000295470;ENST00000502762;ENST00000349655	T;T;T	0.67345	-0.26;-0.26;-0.1	4.84	4.84	0.62591	Nucleotide-binding, alpha-beta plait (1);	0.064498	0.64402	D	0.000016	T	0.62804	0.2458	L	0.58101	1.795	0.43480	D	0.995701	B;B	0.21520	0.038;0.057	B;B	0.24155	0.051;0.034	T	0.59679	-0.7409	10	0.27785	T	0.31	.	14.2367	0.65932	0.0:0.0:0.0:1.0	.	18;137	O14979-3;O14979	.;HNRDL_HUMAN	R	137;137;18	ENSP00000295470:K137R;ENSP00000422040:K137R;ENSP00000338552:K18R	ENSP00000295470:K137R	K	-	2	0	HNRPDL	83569458	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	3.732000	0.55021	2.029000	0.59856	0.397000	0.26171	AAG	.	.	.	none		0.627	HNRNPDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252644.1	NM_005463		C	83350434	T	C	83350434	3	2	282	1	0	0	0	0	1	0	0	0	7283	1609	56	3	880	3	HNRPDL	4	83350434	Missense_Mutation	SNP	T	TCGA-Y8-A8S1-01A-11D-A36X-10	5688657	83350434	107803842	20	17947											
SV2C	22987	hgsc.bcm.edu	37	chr5	75596667	75596667	+	Missense_Mutation	SNP	T	T	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	atagtgcctactggatttatTttgtcaactttctggggaca	9	16	9	7	0	2	0	1	0	1	0	2	2	2	2	1	3	3	0	1	3	4	7			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr5:75596667T>G	ENST00000502798.2	+	11	2192	c.1750T>G	c.(1750-1752)Ttt>Gtt	p.F584V	RP11-466P24.6_ENST00000502589.1_RNA|SV2C_ENST00000322285.7_Missense_Mutation_p.F584V	NM_014979.1	NP_055794.1	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	584					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		CTGGATTTATTTTGTCAACTT	0.403																																					p.F584V		Atlas-SNP	.											.	SV2C	97	.	0			c.T1750G						PASS	.						215	197	203					5																	75596667		1886	4099	5985	SO:0001583	missense	22987	exon11			ATTTATTTTGTCA	AB028977	CCDS43331.1, CCDS75261.1	5q13	2008-02-05			ENSG00000122012	ENSG00000122012			30670	protein-coding gene	gene with protein product		610291				10470851, 9801366	Standard	XM_005248470		Approved		uc003kei.1	Q496J9	OTTHUMG00000162384	ENST00000502798.2:c.1750T>G	chr5.hg19:g.75596667T>G	ENSP00000423541:p.Phe584Val	131.0	0.0	.		125.0	18.0	.	NM_014979	Q496K1|Q9UPU8	Missense_Mutation	SNP	ENST00000502798.2	hg19	CCDS43331.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.539849	0.85917	.	.	ENSG00000122012	ENST00000502798;ENST00000322285	T;T	0.58506	0.48;0.33	5.68	5.68	0.88126	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.54598	0.1868	N	0.17082	0.46	0.80722	D	1	P	0.42871	0.792	P	0.50537	0.643	T	0.59568	-0.7430	10	0.54805	T	0.06	-18.9286	15.9159	0.79517	0.0:0.0:0.0:1.0	.	584	Q496J9	SV2C_HUMAN	V	584	ENSP00000423541:F584V;ENSP00000316983:F584V	ENSP00000316983:F584V	F	+	1	0	SV2C	75632423	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.163000	0.67991	0.482000	0.46254	TTT	.	.	.	none		0.403	SV2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368700.4			G	75596667	T	G	75596667	3	3	282	1	0	0	0	0	1	0	0	0	15431	1841	64	5	1788	5	SV2C	5	75596667	Missense_Mutation	SNP	T	TCGA-Y8-A8S1-01A-11D-A36X-10		75596667	105318593	21	17948											
AFAP1L1	134265	hgsc.bcm.edu	37	chr5	148679111	148679111	+	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	agagctcaccgggctgctcaGcctcctggaccacgagtacc	8	6	11	16	2	2	1	2	0	0	1	3	3	3	2	5	2	4	4	5	2	1	1			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr5:148679111G>T	ENST00000296721.4	+	2	154	c.56G>T	c.(55-57)aGc>aTc	p.S19I	AFAP1L1_ENST00000515000.1_Missense_Mutation_p.S19I|AFAP1L1_ENST00000522492.1_3'UTR	NM_001146337.1|NM_152406.2	NP_001139809.1|NP_689619.1	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1	19						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)			GGGCTGCTCAGCCTCCTGGAC	0.642																																					p.S19I		Atlas-SNP	.											.	AFAP1L1	86	.	0			c.G56T						PASS	.						67	64	65					5																	148679111		2203	4300	6503	SO:0001583	missense	134265	exon2			TGCTCAGCCTCCT	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.56G>T	chr5.hg19:g.148679111G>T	ENSP00000296721:p.Ser19Ile	73.0	0.0	.		88.0	5.0	.	NM_001146337	Q08AN4|Q08AN5|Q8IW82|Q8N8Z5|Q8N9Q4	Missense_Mutation	SNP	ENST00000296721.4	hg19	CCDS34274.1	.	.	.	.	.	.	.	.	.	.	G	15.16	2.749690	0.49257	.	.	ENSG00000157510	ENST00000296721;ENST00000515000	T;T	0.44482	0.92;0.92	4.65	4.65	0.58169	.	0.103899	0.64402	D	0.000002	T	0.44767	0.1309	L	0.47716	1.5	0.30230	N	0.796004	D;P;D	0.59357	0.958;0.93;0.985	P;B;P	0.52217	0.563;0.36;0.693	T	0.50110	-0.8866	10	0.66056	D	0.02	-24.6898	9.2249	0.37400	0.1331:0.0:0.8669:0.0	.	19;19;19	Q8TED9-2;Q8TED9;Q8TED9-3	.;AF1L1_HUMAN;.	I	19	ENSP00000296721:S19I;ENSP00000424427:S19I	ENSP00000296721:S19I	S	+	2	0	AFAP1L1	148659304	1.000000	0.71417	1.000000	0.80357	0.579000	0.36224	4.592000	0.61027	2.563000	0.86464	0.563000	0.77884	AGC	.	.	.	none		0.642	AFAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373443.1	NM_152406		T	148679111	G	T	148679111	3	4	282	1	0	0	0	0	1	0	0	0	354	971	34	4	62	4	AFAP1L1	5	148679111	Missense_Mutation	SNP	G	TCGA-Y8-A8S1-01A-11D-A36X-10	73082444	148679111	32236149	22	17949											
HIST1H1B	3009	hgsc.bcm.edu	37	chr6	27834657	27834701	+	In_Frame_Del	DEL	CTTTGCAGCTTTAGGTTTTGCTGCTTTGGGCTTAGCGGCTTTGGG	CTTTGCAGCTTTAGGTTTTGCTGCTTTGGGCTTAGCGGCTTTGGG	-																															ttggcagccgccttcttggcCtttgcagctttaggttttgc																								rs370043286|rs34144478|rs201436001|rs557184683|rs535793643|rs200074459|rs373472194	byFrequency	TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	CTTTGCAGCTTTAGGTTTTGCTGCTTTGGGCTTAGCGGCTTTGGG	CTTTGCAGCTTTAGGTTTTGCTGCTTTGGGCTTAGCGGCTTTGGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr6:27834657_27834701delCTTTGCAGCTTTAGGTTTTGCTGCTTTGGGCTTAGCGGCTTTGGG	ENST00000331442.3	-	1	658_702	c.607_651delCCCAAAGCCGCTAAGCCCAAAGCAGCAAAACCTAAAGCTGCAAAG	c.(607-651)cccaaagccgctaagcccaaagcagcaaaacctaaagctgcaaagdel	p.PKAAKPKAAKPKAAK203del		NM_005322.2	NP_005313.1	P16401	H15_HUMAN	histone cluster 1, H1b	203					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)	p.K212K(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(12)|prostate(2)|upper_aerodigestive_tract(2)	24						CCTTCTTGGCCTTTGCAGCTTTAGGTTTTGCTGCTTTGGGCTTAGCGGCTTTGGGCTTTGCCGCC	0.547																																					p.203_218del		Pindel	.											.	HIST1H1B	54	.	1	Substitution - coding silent(1)	large_intestine(1)	c.608_652del						PASS	.																																			SO:0001651	inframe_deletion	3009	exon1			.	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.607_651delCCCAAAGCCGCTAAGCCCAAAGCAGCAAAACCTAAAGCTGCAAAG	chr6.hg19:g.27834657_27834701delCTTTGCAGCTTTAGGTTTTGCTGCTTTGGGCTTAGCGGCTTTGGG	ENSP00000330074:p.Pro203_Lys217del	128.0	0.0	.		130.0	11.0	0.085	NM_005322	Q14529|Q3MJ42	In_Frame_Del	DEL	ENST00000331442.3	hg19	CCDS4635.1																																																																																			.	.	.	none		0.547	HIST1H1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043371.1	NM_005322		-	27834701	CTTTGCAGCTTTAGGTTTTGCTGCTTTGGGCTTAGCGGCTTTGGG	-	27834657	7	5	282	1	0	1	0	1	0	0	0	0	7130	680	24	0	33	0	HIST1H1B	6	27834657	In_Frame_Del	DEL	CTTTGCAGCTTTAGGTTTTGCTGCTTTGGGCTTAGCGGCTTTGGG	TCGA-Y8-A8S1-01A-11D-A36X-10		27834657	143280410	23	17950			1	43		2	2	45	N	G_CTTTGCAGCTTTAGGTTTTGCTGCTTTGGGCTTAGCGGCTTTGGG	7.67493e-05
HIST1H1B	3009	hgsc.bcm.edu	37	chr6	27834701	27834701	+	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	tttgggcttagcggctttggGctttgccgccttcggcttaa	3	15	13	10	3	0	0	0	0	0	0	1	0	0	0	2	4	2	4	2	4	2	6			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr6:27834701G>C	ENST00000331442.3	-	1	658	c.607C>G	c.(607-609)Ccc>Gcc	p.P203A		NM_005322.2	NP_005313.1	P16401	H15_HUMAN	histone cluster 1, H1b	203					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						GCGGCTTTGGGCTTTGCCGCC	0.557																																					p.P203A		Atlas-SNP	.											.	HIST1H1B	54	.	0			c.C607G						PASS	.						71	66	68					6																	27834701		2203	4300	6503	SO:0001583	missense	3009	exon1			CTTTGGGCTTTGC	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.607C>G	chr6.hg19:g.27834701G>C	ENSP00000330074:p.Pro203Ala	139.0	0.0	.		138.0	8.0	.	NM_005322	Q14529|Q3MJ42	Missense_Mutation	SNP	ENST00000331442.3	hg19	CCDS4635.1	.	.	.	.	.	.	.	.	.	.	G	6.842	0.524661	0.13066	.	.	ENSG00000184357	ENST00000331442	T	0.16324	2.35	4.79	4.79	0.61399	.	0.398694	0.22302	N	0.061856	T	0.03305	0.0096	N	0.08118	0	0.53688	D	0.999977	B	0.20261	0.043	B	0.15870	0.014	T	0.34650	-0.9820	10	0.12103	T	0.63	-21.4378	14.0627	0.64810	0.0:0.0:1.0:0.0	.	203	P16401	H15_HUMAN	A	203	ENSP00000330074:P203A	ENSP00000330074:P203A	P	-	1	0	HIST1H1B	27942680	0.996000	0.38824	0.330000	0.25442	0.061000	0.15899	2.443000	0.44881	2.600000	0.87896	0.655000	0.94253	CCC	.	.	.	none		0.557	HIST1H1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043371.1	NM_005322		C	27834701	G	C	27834701	3	2	282	1	0	0	0	0	1	0	0	0	7130	1203	42	4	77	4	HIST1H1B	6	27834701	Missense_Mutation	SNP	G	TCGA-Y8-A8S1-01A-11D-A36X-10	44	27834701	143280366	24	17951			1	43		2	2	45	N	G_CTTTGCAGCTTTAGGTTTTGCTGCTTTGGGCTTAGCGGCTTTGGG	7.67493e-05
GABBR1	2550	hgsc.bcm.edu	37	chr6	29581105	29581105	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtagttgaagtcctccaggCgcacaccagaacggccgcct	9	7	11	14	3	0	2	0	1	0	1	2	2	2	2	5	2	1	3	5	2	3	2	rs548511243		TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr6:29581105C>T	ENST00000377034.4	-	12	1816	c.1481G>A	c.(1480-1482)cGc>cAc	p.R494H	GABBR1_ENST00000355973.3_Missense_Mutation_p.R377H|GABBR1_ENST00000377012.4_Missense_Mutation_p.R377H|GABBR1_ENST00000376977.3_Missense_Mutation_p.R494H|GABBR1_ENST00000377016.4_Missense_Mutation_p.R432H	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	494					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)	GTCCTCCAGGCGCACACCAGA	0.552													C|||	1	0.000199681	8e-04	0	5008	,	,		17554	0		0	False		,,,				2504	0				p.R494H		Atlas-SNP	.											.	GABBR1	95	.	0			c.G1481A						PASS	.						106	117	113					6																	29581105		1511	2708	4219	SO:0001583	missense	2550	exon12			TCCAGGCGCACAC	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.1481G>A	chr6.hg19:g.29581105C>T	ENSP00000366233:p.Arg494His	200.0	0.0	.		160.0	22.0	.	NM_001470	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Missense_Mutation	SNP	ENST00000377034.4	hg19	CCDS4663.1	.	.	.	.	.	.	.	.	.	.	C	17.19	3.325374	0.60743	.	.	ENSG00000204681	ENST00000355973;ENST00000376977;ENST00000377016;ENST00000377012;ENST00000377034	D;D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66;-1.66	5.84	5.84	0.93424	Extracellular ligand-binding receptor (1);	0.180709	0.49305	D	0.000155	T	0.67487	0.2898	N	0.25890	0.77	0.58432	D	0.999998	B;B;B;B	0.21147	0.052;0.008;0.005;0.009	B;B;B;B	0.13407	0.009;0.006;0.007;0.008	T	0.66304	-0.5957	10	0.62326	D	0.03	-27.9829	17.64	0.88133	0.0:1.0:0.0:0.0	.	494;432;494;377	Q9UBS5-5;Q9UBS5-3;Q9UBS5;Q5SUJ9	.;.;GABR1_HUMAN;.	H	377;494;432;377;494	ENSP00000348248:R377H;ENSP00000366176:R494H;ENSP00000366215:R432H;ENSP00000366211:R377H;ENSP00000366233:R494H	ENSP00000348248:R377H	R	-	2	0	GABBR1	29689084	1.000000	0.71417	1.000000	0.80357	0.721000	0.41392	7.421000	0.80204	2.769000	0.95229	0.655000	0.94253	CGC	.	.	.	none		0.552	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3			T	29581105	C	T	29581105	3	4	282	1	0	0	0	0	1	0	0	0	6162	768	27	1	1452	1	GABBR1	6	29581105	Missense_Mutation	SNP	C	TCGA-Y8-A8S1-01A-11D-A36X-10	1746404	29581105	141533962	25	17952											
B3GALT4	8705	hgsc.bcm.edu	37	chr6	33246172	33246172	+	Missense_Mutation	SNP	A	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	tagaccggtgctgctatgggAaattcctgctgacgtcccac	8	10	11	12	2	0	2	0	1	0	1	2	3	2	3	3	2	3	3	3	2	3	3			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr6:33246172A>C	ENST00000451237.1	+	1	1256	c.976A>C	c.(976-978)Aaa>Caa	p.K326Q		NM_003782.3	NP_003773.1	O96024	B3GT4_HUMAN	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 4	326					protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	ganglioside galactosyltransferase activity (GO:0047915)|UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|urinary_tract(2)	13						CTGCTATGGGAAATTCCTGCT	0.622																																					p.K326Q		Atlas-SNP	.											.	B3GALT4	30	.	0			c.A976C						PASS	.						89	99	96					6																	33246172		2203	4300	6503	SO:0001583	missense	8705	exon1			TATGGGAAATTCC	Y15061	CCDS34425.1	6p21.3	2013-02-19			ENSG00000235863	ENSG00000235863		"Beta 3-glycosyltransferases"	919	protein-coding gene	gene with protein product		603095				9582303	Standard	NM_003782		Approved	beta3Gal-T4, GalT4	uc003odr.3	O96024	OTTHUMG00000031100	ENST00000451237.1:c.976A>C	chr6.hg19:g.33246172A>C	ENSP00000390784:p.Lys326Gln	79.0	0.0	.		62.0	7.0	.	NM_003782		Missense_Mutation	SNP	ENST00000451237.1	hg19	CCDS34425.1	.	.	.	.	.	.	.	.	.	.	A	12.41	1.929873	0.34096	.	.	ENSG00000235863	ENST00000451237	T	0.50277	0.75	4.29	4.29	0.51040	.	0.350727	0.27424	N	0.019440	T	0.17577	0.0422	N	0.19112	0.55	0.37795	D	0.927492	B	0.27498	0.18	B	0.21360	0.034	T	0.10042	-1.0647	10	0.54805	T	0.06	.	11.4597	0.50202	1.0:0.0:0.0:0.0	.	326	O96024	B3GT4_HUMAN	Q	326	ENSP00000390784:K326Q	ENSP00000390784:K326Q	K	+	1	0	B3GALT4	33354150	0.862000	0.29867	1.000000	0.80357	0.987000	0.75469	3.092000	0.50207	1.815000	0.52974	0.523000	0.50628	AAA	.	.	.	none		0.622	B3GALT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076162.2			C	33246172	A	C	33246172	3	2	282	1	0	0	0	0	1	0	0	0	1249	247	9	5	978	5	B3GALT4	6	33246172	Missense_Mutation	SNP	A	TCGA-Y8-A8S1-01A-11D-A36X-10	3665067	33246172	137868895	26	17953											
DNAH8	1769	hgsc.bcm.edu	37	chr6	38843576	38843576	+	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	cctaaaggctcaaatcaaacCatgtatgagttttatgttac	14	13	6	8	0	2	1	2	1	0	0	2	1	2	1	2	1	2	4	2	1	7	5			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr6:38843576C>A	ENST00000359357.3	+	51	7433	c.7179C>A	c.(7177-7179)acC>acA	p.T2393T	DNAH8_ENST00000441566.1_Silent_p.T2357T|DNAH8_ENST00000449981.2_Silent_p.T2610T			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2393					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						CAAATCAAACCATGTATGAGT	0.353																																					p.T2610T		Atlas-SNP	.											.	DNAH8	1239	.	0			c.C7830A						PASS	.						89	89	89					6																	38843576		2203	4300	6503	SO:0001819	synonymous_variant	1769	exon53			TCAAACCATGTAT	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.7179C>A	chr6.hg19:g.38843576C>A		150.0	0.0	.		111.0	13.0	.	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	hg19																																																																																				.	.	.	none		0.353	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		A	38843576	C	A	38843576	2	1	282	1	0	0	0	0	0	0	0	1	4609	581	21	4		4	DNAH8	6	38843576	Silent	SNP	C	TCGA-Y8-A8S1-01A-11D-A36X-10	5597404	38843576	132271491	27	17954											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51924822	51924822	+	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	tttgtctctggagccacaaaGaacccactgagccgtgctct	9	10	9	13	1	2	2	0	1	2	1	3	3	2	3	3	1	4	1	3	1	2	1			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr6:51924822G>A	ENST00000371117.3	-	15	1412	c.1137C>T	c.(1135-1137)ttC>ttT	p.F379F	PKHD1_ENST00000340994.4_Silent_p.F379F|AL590391.1_ENST00000408630.2_RNA	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	379					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)					GAGCCACAAAGAACCCACTGA	0.443																																					p.F379F		Atlas-SNP	.											.	PKHD1	927	.	0			c.C1137T						PASS	.						84	76	79					6																	51924822		2203	4300	6503	SO:0001819	synonymous_variant	5314	exon15			CACAAAGAACCCA	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.1137C>T	chr6.hg19:g.51924822G>A		88.0	0.0	.		75.0	12.0	.	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	hg19	CCDS4935.1																																																																																			.	.	.	none		0.443	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51924822	G	A	51924822	2	1	282	1	0	0	0	0	0	0	0	1	11978	933	33	2		2	PKHD1	6	51924822	Silent	SNP	G	TCGA-Y8-A8S1-01A-11D-A36X-10	13081246	51924822	119190245	28	17955											
UTRN	7402	hgsc.bcm.edu	37	chr6	144724303	144724303	+	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	aaacctttaccaaatggataAatgctcgattttcaaaggta	16	12	6	7	1	1	0	1	0	0	0	2	2	1	1	2	2	3	2	2	2	7	6			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr6:144724303A>T	ENST00000367545.3	+	2	124	c.124A>T	c.(124-126)Aat>Tat	p.N42Y		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	42	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				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)		CAAATGGATAAATGCTCGATT	0.373																																					p.N42Y		Atlas-SNP	.											.	UTRN	327	.	0			c.A124T						PASS	.						79	76	77					6																	144724303		2202	4300	6502	SO:0001583	missense	7402	exon2			TGGATAAATGCTC	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.124A>T	chr6.hg19:g.144724303A>T	ENSP00000356515:p.Asn42Tyr	102.0	0.0	.		116.0	19.0	.	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	hg19	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	A	15.69	2.907745	0.52333	.	.	ENSG00000152818	ENST00000433557;ENST00000367529;ENST00000367545;ENST00000421035	D;D;D	0.98221	-4.8;-4.8;-4.8	5.48	5.48	0.80851	Actinin-type, actin-binding, conserved site (1);Calponin homology domain (5);	0.000000	0.53938	D	0.000052	D	0.99281	0.9749	H	0.96111	3.77	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.98886	1.0771	10	0.87932	D	0	.	14.8543	0.70323	1.0:0.0:0.0:0.0	.	42	P46939	UTRO_HUMAN	Y	42;42;42;47	ENSP00000390879:N42Y;ENSP00000356515:N42Y;ENSP00000396276:N47Y	ENSP00000356499:N42Y	N	+	1	0	UTRN	144765996	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.728000	0.74769	2.204000	0.70986	0.528000	0.53228	AAT	.	.	.	none		0.373	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			T	144724303	A	T	144724303	3	4	282	1	0	0	0	0	1	0	0	0	17115	14	1	5	130	5	UTRN	6	144724303	Missense_Mutation	SNP	A	TCGA-Y8-A8S1-01A-11D-A36X-10	92799481	144724303	26390764	29	17956											
GRM1	2911	hgsc.bcm.edu	37	chr6	146678763	146678763	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaacattgatgattacaaaaTccagatgaacaagagtggag	18	8	10	5	0	0	5	0	3	0	2	1	7	1	6	1	1	3	0	1	1	6	2			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr6:146678763T>C	ENST00000282753.1	+	5	1770	c.1535T>C	c.(1534-1536)aTc>aCc	p.I512T	GRM1_ENST00000507907.1_Missense_Mutation_p.I512T|GRM1_ENST00000361719.2_Missense_Mutation_p.I512T|GRM1_ENST00000355289.4_Missense_Mutation_p.I512T|GRM1_ENST00000492807.2_Missense_Mutation_p.I512T|GRM1_ENST00000392299.2_Missense_Mutation_p.I512T			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	512					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)		GATTACAAAATCCAGATGAAC	0.443																																					p.I512T		Atlas-SNP	.											.	GRM1	419	.	0			c.T1535C						PASS	.						175	139	152					6																	146678763		2203	4300	6503	SO:0001583	missense	2911	exon6			ACAAAATCCAGAT	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.1535T>C	chr6.hg19:g.146678763T>C	ENSP00000282753:p.Ile512Thr	132.0	0.0	.		120.0	18.0	.	NM_000838	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Missense_Mutation	SNP	ENST00000282753.1	hg19	CCDS5209.1	.	.	.	.	.	.	.	.	.	.	T	17.85	3.490489	0.64074	.	.	ENSG00000152822	ENST00000361719;ENST00000392299;ENST00000492807;ENST00000282753;ENST00000355289;ENST00000507907	D;D;D;D;D;D	0.90788	-2.69;-2.72;-2.72;-2.69;-2.73;-2.72	5.48	5.48	0.80851	.	0.044050	0.85682	D	0.000000	D	0.87601	0.6218	M	0.62723	1.935	0.80722	D	1	P;P;P	0.40144	0.552;0.704;0.696	B;B;B	0.41666	0.133;0.272;0.363	D	0.89914	0.4054	10	0.87932	D	0	.	15.57	0.76326	0.0:0.0:0.0:1.0	.	512;512;512	F8W805;Q13255;Q13255-2	.;GRM1_HUMAN;.	T	512	ENSP00000354896:I512T;ENSP00000376119:I512T;ENSP00000424095:I512T;ENSP00000282753:I512T;ENSP00000347437:I512T;ENSP00000425599:I512T	ENSP00000282753:I512T	I	+	2	0	GRM1	146720456	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.671000	0.83941	2.081000	0.62600	0.533000	0.62120	ATC	.	.	.	none		0.443	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838		C	146678763	T	C	146678763	3	2	282	1	0	0	0	0	1	0	0	0	6803	1435	50	3	1553	3	GRM1	6	146678763	Missense_Mutation	SNP	T	TCGA-Y8-A8S1-01A-11D-A36X-10	1954460	146678763	24436304	30	17957											
ZKSCAN1	7586	hgsc.bcm.edu	37	chr7	99631136	99631136	+	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	tcagggccagctataggaaaGgacaaaaaaaccatcacagg	18	4	10	9	0	2	0	2	0	0	0	2	2	2	2	2	4	2	1	2	4	6	2			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr7:99631136G>T	ENST00000324306.6	+	6	1242	c.1008G>T	c.(1006-1008)aaG>aaT	p.K336N	ZKSCAN1_ENST00000535170.1_Missense_Mutation_p.K123N|ZKSCAN1_ENST00000426572.1_Missense_Mutation_p.K300N	NM_003439.1	NP_003430.1	P17029	ZKSC1_HUMAN	zinc finger with KRAB and SCAN domains 1	336					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			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)			CTATAGGAAAGGACAAAAAAA	0.483																																					p.K336N		Atlas-SNP	.											.	ZKSCAN1	59	.	0			c.G1008T						PASS	.						76	83	81					7																	99631136		2203	4300	6503	SO:0001583	missense	7586	exon6			AGGAAAGGACAAA	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.1008G>T	chr7.hg19:g.99631136G>T	ENSP00000323148:p.Lys336Asn	184.0	0.0	.		172.0	37.0	.	NM_003439	A4D294|P52745|Q2M1U1|Q8TBW5|Q8TEK7	Missense_Mutation	SNP	ENST00000324306.6	hg19	CCDS34698.1	.	.	.	.	.	.	.	.	.	.	G	9.281	1.048151	0.19827	.	.	ENSG00000106261	ENST00000324306;ENST00000426572;ENST00000535170	T;T;T	0.07444	3.27;3.24;3.19	5.18	2.25	0.28309	.	0.208078	0.34133	N	0.004225	T	0.04724	0.0128	N	0.24115	0.695	0.09310	N	0.999992	B	0.02656	0.0	B	0.01281	0.0	T	0.38779	-0.9645	10	0.23891	T	0.37	.	5.162	0.15066	0.1671:0.1743:0.6585:0.0	.	336	P17029	ZKSC1_HUMAN	N	336;300;123	ENSP00000323148:K336N;ENSP00000409172:K300N;ENSP00000443508:K123N	ENSP00000323148:K336N	K	+	3	2	ZKSCAN1	99469072	0.025000	0.19082	0.922000	0.36590	0.034000	0.12701	0.823000	0.27366	0.898000	0.36418	0.557000	0.71058	AAG	.	.	.	none		0.483	ZKSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344550.2	NM_003439		T	99631136	G	T	99631136	3	4	282	1	0	0	0	0	1	0	0	0	17698	991	35	4	1026	4	ZKSCAN1	7	99631136	Missense_Mutation	SNP	G	TCGA-Y8-A8S1-01A-11D-A36X-10		99631136	59507527	31	17958											
ARMC10	83787	hgsc.bcm.edu	37	chr7	102738803	102738803	+	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	tagcaaaggagattcttcttCgagtacttacgctatttcag	11	14	8	8	2	3	1	1	0	2	1	4	3	3	1	0	1	3	3	0	1	5	8			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr7:102738803C>T	ENST00000323716.3	+	7	1227	c.835C>T	c.(835-837)Cga>Tga	p.R279*	ARMC10_ENST00000541300.1_Nonsense_Mutation_p.R161*|ARMC10_ENST00000441711.2_Nonsense_Mutation_p.R244*|ARMC10_ENST00000425331.1_Nonsense_Mutation_p.R220*|ARMC10_ENST00000454559.1_Nonsense_Mutation_p.R185*|ARMC10_ENST00000428183.2_Nonsense_Mutation_p.R220*	NM_031905.4	NP_114111.2	Q8N2F6	ARM10_HUMAN	armadillo repeat containing 10	279					regulation of growth (GO:0040008)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.R279*(2)		NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	11						GATTCTTCTTCGAGTACTTAC	0.343																																					p.R279X		Atlas-SNP	.											ARMC10,NS,carcinoma,0,2	ARMC10	25	.	2	Substitution - Nonsense(2)	NS(1)|breast(1)	c.C835T						PASS	.						73	65	67					7																	102738803		2203	4300	6503	SO:0001587	stop_gained	83787	exon7			CTTCTTCGAGTAC	AY150853	CCDS5728.1, CCDS55145.1, CCDS55146.1, CCDS55147.1, CCDS55148.1, CCDS55149.1	7q22.1	2013-02-14			ENSG00000170632	ENSG00000170632		"Armadillo repeat containing"	21706	protein-coding gene	gene with protein product	"specific Splicing Variant involved in Hepatocarcinogenesis"	611864				12839973	Standard	NM_031905		Approved	MGC3195, SVH	uc003vaw.2	Q8N2F6	OTTHUMG00000157201	ENST00000323716.3:c.835C>T	chr7.hg19:g.102738803C>T	ENSP00000319412:p.Arg279*	521.0	0.0	.		475.0	23.0	.	NM_031905	A8K703|B4DWJ8|F5GX65|Q75K91|Q75MG6|Q75ML8|Q8IZC1|Q8IZC2|Q8IZC3|Q9BTM6	Nonsense_Mutation	SNP	ENST00000323716.3	hg19	CCDS5728.1	.	.	.	.	.	.	.	.	.	.	C	38	7.008041	0.97998	.	.	ENSG00000170632	ENST00000323716;ENST00000428183;ENST00000441711;ENST00000454559;ENST00000425331;ENST00000541300;ENST00000434153;ENST00000431642	.	.	.	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.7948	11.9574	0.52988	0.2764:0.7236:0.0:0.0	.	.	.	.	X	279;220;244;185;220;161;207;121	.	ENSP00000319412:R279X	R	+	1	2	ARMC10	102526039	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	0.632000	0.24583	2.709000	0.92574	0.591000	0.81541	CGA	.	.	.	none		0.343	ARMC10-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347882.1	NM_031905		T	102738803	C	T	102738803	4	4	282	1	0	0	0	0	0	1	0	0	950	876	31	1	861	1	ARMC10	7	102738803	Nonsense_Mutation	SNP	C	TCGA-Y8-A8S1-01A-11D-A36X-10	3107667	102738803	56399860	32	17959											
RBM33	155435	hgsc.bcm.edu	37	chr7	155473562	155473562	+	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	gcagctttacactgatgaagTgttagacatcgagatcaatg	13	11	10	7	1	1	4	1	2	0	2	2	5	1	4	0	0	2	3	0	0	4	3			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr7:155473562T>A	ENST00000401878.3	+	5	725	c.527T>A	c.(526-528)gTg>gAg	p.V176E	RBM33_ENST00000392759.3_Missense_Mutation_p.V176E|RBM33_ENST00000287912.3_Missense_Mutation_p.V176E	NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33	176	Glu-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)		ACTGATGAAGTGTTAGACATC	0.433																																					p.V176E		Atlas-SNP	.											.	RBM33	157	.	0			c.T527A						PASS	.						97	95	96					7																	155473562		1960	4156	6116	SO:0001583	missense	155435	exon5			ATGAAGTGTTAGA	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.527T>A	chr7.hg19:g.155473562T>A	ENSP00000384160:p.Val176Glu	160.0	0.0	.		154.0	17.0	.	NM_053043	A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	Missense_Mutation	SNP	ENST00000401878.3	hg19	CCDS5941.2	.	.	.	.	.	.	.	.	.	.	T	21.8	4.197992	0.79015	.	.	ENSG00000184863	ENST00000287912;ENST00000401878;ENST00000392759;ENST00000440108	T;T;T;T	0.33216	1.42;1.42;1.42;1.42	5.35	5.35	0.76521	.	.	.	.	.	T	0.50582	0.1624	L	0.52573	1.65	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.996	T	0.52697	-0.8541	9	0.87932	D	0	.	15.3587	0.74453	0.0:0.0:0.0:1.0	.	176;176	Q96EV2;Q96EV2-2	RBM33_HUMAN;.	E	176;176;176;67	ENSP00000287912:V176E;ENSP00000384160:V176E;ENSP00000376513:V176E;ENSP00000394987:V67E	ENSP00000287912:V176E	V	+	2	0	RBM33	155166323	1.000000	0.71417	0.998000	0.56505	0.951000	0.60555	5.466000	0.66731	2.029000	0.59856	0.460000	0.39030	GTG	.	.	.	none		0.433	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317225.3	NM_001008408		A	155473562	T	A	155473562	3	1	282	1	0	0	0	0	1	0	0	0	13143	1696	59	5	545	5	RBM33	7	155473562	Missense_Mutation	SNP	T	TCGA-Y8-A8S1-01A-11D-A36X-10	52734759	155473562	3665101	33	17960											
TEX15	56154	hgsc.bcm.edu	37	chr8	30700777	30700777	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaaaggcacatttattcacTctgagtagcctttcttcgtc	10	14	7	10	1	3	1	1	1	2	0	5	2	3	1	1	1	1	2	1	1	4	6			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr8:30700777T>C	ENST00000256246.2	-	1	5831	c.5757A>G	c.(5755-5757)agA>agG	p.R1919R		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1919					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)		ATTTATTCACTCTGAGTAGCC	0.343																																					p.R1919R		Atlas-SNP	.											.	TEX15	350	.	0			c.A5757G						PASS	.						110	105	107					8																	30700777		2202	4299	6501	SO:0001819	synonymous_variant	56154	exon1			ATTCACTCTGAGT	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.5757A>G	chr8.hg19:g.30700777T>C		110.0	0.0	.		114.0	11.0	.	NM_031271		Silent	SNP	ENST00000256246.2	hg19	CCDS6080.1																																																																																			.	.	.	none		0.343	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			C	30700777	T	C	30700777	2	2	282	1	0	0	0	0	0	0	0	1	15791	1548	54	3		3	TEX15	8	30700777	Silent	SNP	T	TCGA-Y8-A8S1-01A-11D-A36X-10		30700777	115663245	34	17961											
STMN2	11075	hgsc.bcm.edu	37	chr8	80567258	80567258	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caaattaaggaaaaccgtgaGgctaatctagctgctattat	15	11	8	7	1	1	1	0	1	1	0	1	2	1	2	1	2	3	3	1	2	8	5			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr8:80567258G>A	ENST00000220876.7	+	4	823	c.441G>A	c.(439-441)gaG>gaA	p.E147E	STMN2_ENST00000518491.1_Silent_p.E136E|STMN2_ENST00000518111.1_Silent_p.E147E	NM_001199214.1|NM_007029.3	NP_001186143.1|NP_008960.2	Q93045	STMN2_HUMAN	stathmin 2	147	SLD. {ECO:0000255|PROSITE- ProRule:PRU00998}.				cellular response to nerve growth factor stimulus (GO:1990090)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of neuron projection development (GO:0010977)|positive regulation of microtubule depolymerization (GO:0031117)|positive regulation of neuron projection development (GO:0010976)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	11	all_lung(9;8.34e-05)		Epithelial(68;0.0229)|all cancers(69;0.0874)			AAAACCGTGAGGCTAATCTAG	0.443																																					p.E147E		Atlas-SNP	.											.	STMN2	23	.	0			c.G441A						PASS	.						89	82	84					8																	80567258		1917	4125	6042	SO:0001819	synonymous_variant	11075	exon4			CCGTGAGGCTAAT		CCDS43748.1, CCDS56542.1	8q21.13	2014-04-01	2014-04-01	2001-07-13	ENSG00000104435	ENSG00000104435			10577	protein-coding gene	gene with protein product		600621	"stathmin-like 2"	SCGN10		8622778, 12140291	Standard	NM_007029		Approved	SCG10	uc022awk.1	Q93045	OTTHUMG00000164610	ENST00000220876.7:c.441G>A	chr8.hg19:g.80567258G>A		131.0	0.0	.		130.0	17.0	.	NM_007029	A8K9M2|G3V110|O14952|Q6PK68	Silent	SNP	ENST00000220876.7	hg19	CCDS43748.1																																																																																			.	.	.	none		0.443	STMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379261.2	NM_007029		A	80567258	G	A	80567258	2	1	282	1	0	0	0	0	0	0	0	1	15321	991	35	2		2	STMN2	8	80567258	Silent	SNP	G	TCGA-Y8-A8S1-01A-11D-A36X-10	49866481	80567258	65796764	35	17962											
DOCK8	81704	hgsc.bcm.edu	37	chr9	441400	441400	+	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	gcaagctgcagagagccttcGacagcatcgttaacaaggta	13	7	11	10	2	0	1	0	0	0	1	2	3	0	1	1	1	5	6	1	1	4	3			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr9:441400G>T	ENST00000453981.1	+	41	5450	c.5338G>T	c.(5338-5340)Gac>Tac	p.D1780Y	DOCK8_ENST00000382329.1_Missense_Mutation_p.D1247Y|DOCK8_ENST00000469391.1_Missense_Mutation_p.D1680Y|DOCK8_ENST00000432829.2_Missense_Mutation_p.D1712Y			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1780	DHR-2.				blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		GAGAGCCTTCGACAGCATCGT	0.552																																					p.D1780Y		Atlas-SNP	.											.	DOCK8	401	.	0			c.G5338T						PASS	.						75	70	72					9																	441400		2203	4300	6503	SO:0001583	missense	81704	exon41			GCCTTCGACAGCA	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.5338G>T	chr9.hg19:g.441400G>T	ENSP00000408464:p.Asp1780Tyr	88.0	0.0	.		70.0	6.0	.	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	hg19	CCDS6440.2	.	.	.	.	.	.	.	.	.	.	G	13.41	2.228460	0.39399	.	.	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391;ENST00000382329	T;T;T;T	0.17213	2.51;2.51;2.51;2.29	5.36	5.36	0.76844	.	0.046369	0.85682	D	0.000000	T	0.27629	0.0679	M	0.64997	1.995	0.80722	D	1	P;P;P	0.38642	0.641;0.641;0.641	B;B;B	0.42062	0.374;0.374;0.374	T	0.02320	-1.1177	10	0.72032	D	0.01	.	19.2822	0.94055	0.0:0.0:1.0:0.0	.	1680;1247;1780	E9PH09;A2A369;Q8NF50	.;.;DOCK8_HUMAN	Y	1780;1748;1712;1680;1247	ENSP00000408464:D1780Y;ENSP00000394888:D1712Y;ENSP00000419438:D1680Y;ENSP00000371766:D1247Y	ENSP00000287364:D1748Y	D	+	1	0	DOCK8	431400	1.000000	0.71417	0.974000	0.42286	0.031000	0.12232	5.138000	0.64795	2.763000	0.94921	0.655000	0.94253	GAC	.	.	.	none		0.552	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307		T	441400	G	T	441400	3	4	282	1	0	0	0	0	1	0	0	0	4695	1058	37	4	5500	4	DOCK8	9	441400	Missense_Mutation	SNP	G	TCGA-Y8-A8S1-01A-11D-A36X-10		441400	140772031	36	17963											
TPD52L3	89882	hgsc.bcm.edu	37	chr9	6328657	6328657	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcccactcgacttctgaacTggaggatctgacagagcccg	10	8	10	13	2	2	3	0	2	2	1	4	6	3	5	2	2	2	0	2	2	1	1			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr9:6328657T>C	ENST00000344545.5	+	1	309	c.62T>C	c.(61-63)cTg>cCg	p.L21P	TPD52L3_ENST00000381428.1_Missense_Mutation_p.L21P|TPD52L3_ENST00000314556.3_Missense_Mutation_p.L21P	NM_033516.5	NP_277051	Q96J77	TPD55_HUMAN	tumor protein D52-like 3	21										large_intestine(1)|lung(9)|skin(1)	11		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0198)|Lung(218;0.1)		ACTTCTGAACTGGAGGATCTG	0.498																																					p.L21P		Atlas-SNP	.											.	TPD52L3	40	.	0			c.T62C						PASS	.						88	89	88					9																	6328657		2203	4300	6503	SO:0001583	missense	89882	exon1			CTGAACTGGAGGA	AY032877	CCDS34984.1, CCDS34985.1, CCDS34986.1	9p24.1	2008-02-05			ENSG00000170777	ENSG00000170777			23382	protein-coding gene	gene with protein product							Standard	NM_033516		Approved	NYD-SP25	uc003zjw.3	Q96J77	OTTHUMG00000019518	ENST00000344545.5:c.62T>C	chr9.hg19:g.6328657T>C	ENSP00000341677:p.Leu21Pro	118.0	0.0	.		115.0	18.0	.	NM_033516	Q5TCR3|Q5TCR4|Q5TCR5|Q8N4P5|Q8WWF7|Q96M09	Missense_Mutation	SNP	ENST00000344545.5	hg19	CCDS34986.1	.	.	.	.	.	.	.	.	.	.	T	5.474	0.272581	0.10349	.	.	ENSG00000170777	ENST00000344545;ENST00000381428;ENST00000314556	T;T;T	0.32515	1.47;1.46;1.45	4.74	0.688	0.18027	.	0.637913	0.15109	N	0.280044	T	0.09024	0.0223	N	0.01473	-0.845	0.09310	N	0.999999	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.26503	-1.0101	10	0.28530	T	0.3	-0.4477	3.543	0.07818	0.175:0.5355:0.0:0.2896	.	21;21;21	Q96J77-2;Q96J77;Q96J77-3	.;TPD55_HUMAN;.	P	21	ENSP00000341677:L21P;ENSP00000370836:L21P;ENSP00000318665:L21P	ENSP00000318665:L21P	L	+	2	0	TPD52L3	6318657	0.000000	0.05858	0.000000	0.03702	0.071000	0.16799	-0.248000	0.08854	0.033000	0.15463	-0.385000	0.06624	CTG	.	.	.	none		0.498	TPD52L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051658.1	NM_033516		C	6328657	T	C	6328657	3	2	282	1	0	0	0	0	1	0	0	0	16412	1580	55	3	64	3	TPD52L3	9	6328657	Missense_Mutation	SNP	T	TCGA-Y8-A8S1-01A-11D-A36X-10	5887257	6328657	134884774	37	17964											
ZNF503	84858	hgsc.bcm.edu	37	chr10	77161118	77161118	+	Silent	SNP	G	G	T																															ccgccgcctccgcctccgccGccgccgccgccgctgtgctt																								rs540164655	byFrequency	TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr10:77161118G>T	ENST00000372524.4	-	1	546	c.60C>A	c.(58-60)ggC>ggA	p.G20G	ZNF503-AS2_ENST00000425916.3_RNA|RP11-399K21.11_ENST00000418818.2_lincRNA|ZNF503_ENST00000535216.1_Silent_p.G20G|ZNF503-AS2_ENST00000466942.2_RNA|ZNF503-AS2_ENST00000486015.1_RNA	NM_032772.4	NP_116161.2	Q96F45	ZN503_HUMAN	zinc finger protein 503	20	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)					cgcctccgccgccgccgccgc	0.736													G|||	57	0.0113818	0.003	0.0202	5008	,	,		9151	0		0.0338	False		,,,				2504	0.0051				p.G20G		Atlas-SNP	.											.	ZNF503	25	.	0			c.C60A						PASS	.						1	2	2					10																	77161118		1017	2414	3431	SO:0001819	synonymous_variant	84858	exon1			TCCGCCGCCGCCG	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.60C>A	chr10.hg19:g.77161118G>T		36.0	0.0	.		27.0	6.0	.	NM_032772	Q8NAC5|Q96E25|Q96IJ0	Silent	SNP	ENST00000372524.4	hg19	CCDS7350.1																																																																																			.	.	.	none		0.736	ZNF503-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048826.1	NM_032772		T	77161118	G	T	77161118	2	4	282	1	0	0	0	0	0	0	0	1	17963	1074	38	4		4	ZNF503	10	77161118	Silent	SNP	G	TCGA-Y8-A8S1-01A-11D-A36X-10		77161118	58373629	38	17965	187	2									
ZNF503	84858	hgsc.bcm.edu	37	chr10	77161124	77161124	+	Silent	SNP	G	G	T																															cctccgcctccgccgccgccGccgccgctgtgcttactgct																								rs576950953	byFrequency	TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr10:77161124G>T	ENST00000372524.4	-	1	540	c.54C>A	c.(52-54)ggC>ggA	p.G18G	ZNF503-AS2_ENST00000425916.3_RNA|RP11-399K21.11_ENST00000418818.2_lincRNA|ZNF503_ENST00000535216.1_Silent_p.G18G|ZNF503-AS2_ENST00000466942.2_RNA|ZNF503-AS2_ENST00000486015.1_RNA	NM_032772.4	NP_116161.2	Q96F45	ZN503_HUMAN	zinc finger protein 503	18	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)					cgccgccgccgccgccgcTGT	0.741													G|||	56	0.0111821	0.003	0.0202	5008	,	,		9831	0		0.0328	False		,,,				2504	0.0051				p.G18G		Atlas-SNP	.											.	ZNF503	25	.	0			c.C54A						PASS	.						1	2	2					10																	77161124		963	2340	3303	SO:0001819	synonymous_variant	84858	exon1			GCCGCCGCCGCCG	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.54C>A	chr10.hg19:g.77161124G>T		34.0	0.0	.		24.0	6.0	.	NM_032772	Q8NAC5|Q96E25|Q96IJ0	Silent	SNP	ENST00000372524.4	hg19	CCDS7350.1																																																																																			.	.	.	none		0.741	ZNF503-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048826.1	NM_032772		T	77161124	G	T	77161124	2	4	282	1	0	0	0	0	0	0	0	1	17963	1074	38	4		4	ZNF503	10	77161124	Silent	SNP	G	TCGA-Y8-A8S1-01A-11D-A36X-10	6	77161124	58373623	39	17966	187	2									
MUC5B	727897	hgsc.bcm.edu	37	chr11	1248326	1248326	+	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	cggggactacatcaaggtcaGcatccggctggtgctgacat	9	8	13	11	2	2	1	2	1	0	0	3	2	3	2	1	5	3	3	1	5	2	1			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr11:1248326G>C	ENST00000529681.1	+	5	585	c.527G>C	c.(526-528)aGc>aCc	p.S176T	MUC5B_ENST00000447027.1_Missense_Mutation_p.S176T	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	176	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		ATCAAGGTCAGCATCCGGCTG	0.667																																					p.S176T		Atlas-SNP	.											.	MUC5B	473	.	0			c.G527C						PASS	.						32	38	36					11																	1248326		2027	4156	6183	SO:0001583	missense	727897	exon5			AGGTCAGCATCCG	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.527G>C	chr11.hg19:g.1248326G>C	ENSP00000436812:p.Ser176Thr	164.0	0.0	.		125.0	15.0	.	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	hg19	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	G	2.178	-0.388258	0.04932	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.58940	0.3;0.3	3.73	-4.11	0.03928	von Willebrand factor, type D domain (3);	.	.	.	.	T	0.33059	0.0850	N	0.16743	0.435	0.09310	N	1	B;B;B	0.21905	0.001;0.062;0.062	B;B;B	0.23716	0.003;0.048;0.048	T	0.30621	-0.9972	9	0.87932	D	0	.	1.502	0.02478	0.2543:0.2611:0.3281:0.1565	.	176;832;176	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	T	176;176;176;209	ENSP00000436812:S176T;ENSP00000415793:S176T	ENSP00000343037:S176T	S	+	2	0	MUC5B	1204902	0.000000	0.05858	0.001000	0.08648	0.059000	0.15707	-0.700000	0.05081	-0.380000	0.07894	0.455000	0.32223	AGC	.	.	.	none		0.667	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		C	1248326	G	C	1248326	3	2	282	1	0	0	0	0	1	0	0	0	9986	971	34	4	545	4	MUC5B	11	1248326	Missense_Mutation	SNP	G	TCGA-Y8-A8S1-01A-11D-A36X-10		1248326	133758190	40	17967											
UBQLN3	50613	hgsc.bcm.edu	37	chr11	5530266	5530266	+	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	cagcagacccgggatgaaggGgtcatcaatgagctgagtca	12	6	14	9	1	3	4	3	3	0	1	3	5	3	5	1	3	2	2	1	3	2	0			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr11:5530266G>T	ENST00000311659.4	-	2	670	c.523C>A	c.(523-525)Ccc>Acc	p.P175T	HBG2_ENST00000380259.2_Intron	NM_017481.2	NP_059509.1	Q9H347	UBQL3_HUMAN	ubiquilin 3	175										NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|prostate(1)|skin(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGGATGAAGGGGTCATCAATG	0.572																																					p.P175T	Ovarian(72;684 1260 12332 41642 52180)	Atlas-SNP	.											.	UBQLN3	107	.	0			c.C523A						PASS	.						70	68	68					11																	5530266		2201	4297	6498	SO:0001583	missense	50613	exon2			TGAAGGGGTCATC	AF230481	CCDS7758.1	11p15	2013-02-12			ENSG00000175520	ENSG00000175520		"Ubiquilin family"	12510	protein-coding gene	gene with protein product		605473				10831842	Standard	NM_017481		Approved	TUP-1	uc001may.1	Q9H347	OTTHUMG00000066886	ENST00000311659.4:c.523C>A	chr11.hg19:g.5530266G>T	ENSP00000347997:p.Pro175Thr	120.0	0.0	.		120.0	16.0	.	NM_017481	Q9NRE0	Missense_Mutation	SNP	ENST00000311659.4	hg19	CCDS7758.1	.	.	.	.	.	.	.	.	.	.	G	17.80	3.477515	0.63849	.	.	ENSG00000175520	ENST00000311659;ENST00000445998	T;T	0.64618	0.34;-0.11	5.55	4.64	0.57946	.	0.298944	0.24215	N	0.040491	D	0.82935	0.5145	M	0.93638	3.44	0.58432	D	0.99999	D	0.58268	0.982	D	0.65010	0.931	D	0.87659	0.2533	10	0.87932	D	0	-9.5212	14.6678	0.68921	0.0:0.1462:0.8538:0.0	.	175	Q9H347	UBQL3_HUMAN	T	175	ENSP00000347997:P175T;ENSP00000412561:P175T	ENSP00000347997:P175T	P	-	1	0	UBQLN3	5486842	1.000000	0.71417	0.994000	0.49952	0.990000	0.78478	1.901000	0.39838	1.479000	0.48272	0.585000	0.79938	CCC	.	.	.	none		0.572	UBQLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143348.1	NM_017481		T	5530266	G	T	5530266	3	4	282	1	0	0	0	0	1	0	0	0	16910	1232	43	4	1448	4	UBQLN3	11	5530266	Missense_Mutation	SNP	G	TCGA-Y8-A8S1-01A-11D-A36X-10	4281940	5530266	129476250	41	17968											
ATXN2	6311	hgsc.bcm.edu	37	chr12	111991980	111991980	+	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	acaacaactgatgtaagtatAtgaaccatcctcatatttgc	15	12	5	9	0	1	2	1	2	0	0	2	2	2	2	2	0	4	2	2	0	7	5			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr12:111991980A>T	ENST00000377617.3	-	3	971	c.810T>A	c.(808-810)caT>caA	p.H270Q	ATXN2_ENST00000535949.1_Missense_Mutation_p.H5Q|ATXN2_ENST00000549455.1_Intron|ATXN2_ENST00000608853.1_Missense_Mutation_p.H110Q|ATXN2_ENST00000389153.4_Missense_Mutation_p.H5Q|ATXN2_ENST00000542287.2_Missense_Mutation_p.H5Q|ATXN2_ENST00000550104.1_Missense_Mutation_p.H270Q	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	270					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						ATGTAAGTATATGAACCATCC	0.284																																					p.H270Q		Atlas-SNP	.											.	ATXN2	99	.	0			c.T810A						PASS	.						48	44	45					12																	111991980		2190	4281	6471	SO:0001583	missense	6311	exon3			AAGTATATGAACC	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.810T>A	chr12.hg19:g.111991980A>T	ENSP00000366843:p.His270Gln	56.0	0.0	.		40.0	7.0	.	NM_002973	A6NLD4|Q6ZQZ7|Q99493	Missense_Mutation	SNP	ENST00000377617.3	hg19	CCDS31902.1	.	.	.	.	.	.	.	.	.	.	A	15.02	2.708827	0.48517	.	.	ENSG00000204842	ENST00000389153;ENST00000377617;ENST00000550104;ENST00000542287;ENST00000535949	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	5.34	4.19	0.49359	Like-Sm ribonucleoprotein (LSM)-related domain (1);	0.000000	0.85682	D	0.000000	T	0.61800	0.2376	M	0.81802	2.56	0.58432	D	0.999998	D;D;D;D	0.76494	0.997;0.999;0.997;0.999	D;D;D;D	0.83275	0.995;0.996;0.995;0.994	T	0.62353	-0.6872	10	0.59425	D	0.04	-12.6924	7.364	0.26762	0.7784:0.0:0.2216:0.0	.	5;270;5;5	B3KT59;Q99700;Q24JQ7;F8VQP2	.;ATX2_HUMAN;.;.	Q	5;270;270;5;5	ENSP00000373805:H5Q;ENSP00000366843:H270Q;ENSP00000446576:H270Q;ENSP00000445583:H5Q	ENSP00000366843:H270Q	H	-	3	2	ATXN2	110476363	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	2.844000	0.48246	0.877000	0.35895	0.260000	0.18958	CAT	.	.	.	none		0.284	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973		T	111991980	A	T	111991980	3	4	282	1	0	0	0	0	1	0	0	0	1211	446	16	5	3223	5	ATXN2	12	111991980	Missense_Mutation	SNP	A	TCGA-Y8-A8S1-01A-11D-A36X-10		111991980	21859915	42	17969											
SBNO1	55206	hgsc.bcm.edu	37	chr12	123829975	123829975	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgacgggcgtgtgcttgcaGtagtctggataaacttagtt	8	13	13	7	2	1	1	0	1	1	0	1	2	1	2	0	2	3	4	0	2	4	5			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr12:123829975G>A	ENST00000602398.1	-	4	507	c.380C>T	c.(379-381)aCt>aTt	p.T127I	SBNO1_ENST00000602750.1_Missense_Mutation_p.T126I|SBNO1_ENST00000420886.2_Missense_Mutation_p.T127I|SBNO1_ENST00000267176.4_Missense_Mutation_p.T126I			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	127					regulation of transcription, DNA-templated (GO:0006355)					NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		TGTGCTTGCAGTAGTCTGGAT	0.423																																					p.T127I		Atlas-SNP	.											.	SBNO1	138	.	0			c.C380T						PASS	.						287	243	258					12																	123829975		2203	4300	6503	SO:0001583	missense	55206	exon3			CTTGCAGTAGTCT	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"sno, strawberry notch homolog 1 (Drosophila)"				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.380C>T	chr12.hg19:g.123829975G>A	ENSP00000473665:p.Thr127Ile	202.0	0.0	.		236.0	29.0	.	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Missense_Mutation	SNP	ENST00000602398.1	hg19	CCDS53844.1	.	.	.	.	.	.	.	.	.	.	G	14.65	2.599804	0.46318	.	.	ENSG00000139697	ENST00000420886;ENST00000267176;ENST00000442601	T;T	0.30981	1.52;1.51	5.74	4.83	0.62350	.	0.337294	0.31721	N	0.007176	T	0.16599	0.0399	N	0.08118	0	0.26828	N	0.968658	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.10222	-1.0639	10	0.38643	T	0.18	-21.286	12.2817	0.54767	0.0:0.3068:0.6932:0.0	.	127;126;125	A3KN83;A3KN83-2;A3KN83-3	SBNO1_HUMAN;.;.	I	127;126;126	ENSP00000387361:T127I;ENSP00000267176:T126I	ENSP00000267176:T126I	T	-	2	0	SBNO1	122395928	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	1.471000	0.35365	2.715000	0.92844	0.655000	0.94253	ACT	.	.	.	none		0.423	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183		A	123829975	G	A	123829975	3	1	282	1	0	0	0	0	1	0	0	0	13875	1029	36	2	3917	2	SBNO1	12	123829975	Missense_Mutation	SNP	G	TCGA-Y8-A8S1-01A-11D-A36X-10	11837995	123829975	10021920	43	17970											
NBEA	26960	hgsc.bcm.edu	37	chr13	35738623	35738623	+	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	gtggaggaattttacctttgCtctctgctgctacatcacca	8	14	8	11	0	2	0	1	0	1	0	3	2	2	2	2	2	5	3	2	2	3	4			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr13:35738623C>A	ENST00000400445.3	+	24	4744	c.4210C>A	c.(4210-4212)Ctc>Atc	p.L1404I	NBEA_ENST00000379939.2_Missense_Mutation_p.L1404I|NBEA_ENST00000540320.1_Missense_Mutation_p.L1404I|NBEA_ENST00000310336.4_Missense_Mutation_p.L1404I	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1404					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)		TTTACCTTTGCTCTCTGCTGC	0.353																																					p.L1404I		Atlas-SNP	.											.	NBEA	340	.	0			c.C4210A						PASS	.						154	143	147					13																	35738623		1929	4159	6088	SO:0001583	missense	26960	exon24			CCTTTGCTCTCTG	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.4210C>A	chr13.hg19:g.35738623C>A	ENSP00000383295:p.Leu1404Ile	113.0	0.0	.		113.0	10.0	.	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	C	18.44	3.624892	0.66901	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518	T;T;T;T	0.71461	-0.56;-0.57;-0.57;-0.56	5.51	4.65	0.58169	.	0.000000	0.64402	D	0.000001	T	0.81418	0.4818	M	0.77616	2.38	0.80722	D	1	D;D	0.71674	0.997;0.998	D;D	0.79108	0.991;0.992	T	0.81686	-0.0820	10	0.56958	D	0.05	.	8.7366	0.34532	0.0:0.7864:0.0:0.2136	.	1404;1404	Q8NFP9;Q5T321	NBEA_HUMAN;.	I	1404;1404;1404;1404;66	ENSP00000440951:L1404I;ENSP00000383295:L1404I;ENSP00000369271:L1404I;ENSP00000308534:L1404I	ENSP00000308534:L1404I	L	+	1	0	NBEA	34636623	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.389000	0.44407	2.734000	0.93682	0.650000	0.86243	CTC	.	.	.	none		0.353	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		A	35738623	C	A	35738623	3	1	282	1	0	0	0	0	1	0	0	0	10194	797	28	4	4304	4	NBEA	13	35738623	Missense_Mutation	SNP	C	TCGA-Y8-A8S1-01A-11D-A36X-10		35738623	79431255	44	17971											
MYH6	4624	hgsc.bcm.edu	37	chr14	23866283	23866283	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatgaccagggggttgtccAtcacccctgtgtcaggaggg	7	8	15	11	0	2	1	2	1	0	0	3	2	3	2	4	4	0	2	4	4	0	1			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr14:23866283A>G	ENST00000356287.3	-	17	2086	c.2057T>C	c.(2056-2058)aTg>aCg	p.M686T	MYH6_ENST00000405093.3_Missense_Mutation_p.M686T			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	686	Myosin motor.				adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		GGGGTTGTCCATCACCCCTGT	0.612																																					p.M686T		Atlas-SNP	.											.	MYH6	274	.	0			c.T2057C						PASS	.						61	61	61					14																	23866283		2203	4300	6503	SO:0001583	missense	4624	exon18			TTGTCCATCACCC	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.2057T>C	chr14.hg19:g.23866283A>G	ENSP00000348634:p.Met686Thr	79.0	0.0	.		69.0	9.0	.	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	hg19	CCDS9600.1	.	.	.	.	.	.	.	.	.	.	.	18.14	3.557260	0.65425	.	.	ENSG00000197616	ENST00000405093;ENST00000356287	T;T	0.71817	-0.6;-0.6	4.14	4.14	0.48551	Myosin head, motor domain (2);	.	.	.	.	D	0.86653	0.5984	M	0.93462	3.42	0.58432	D	0.999993	B	0.25007	0.116	P	0.49683	0.619	D	0.88270	0.2929	9	0.87932	D	0	.	13.6054	0.62044	1.0:0.0:0.0:0.0	.	686	P13533	MYH6_HUMAN	T	686	ENSP00000386041:M686T;ENSP00000348634:M686T	ENSP00000348634:M686T	M	-	2	0	MYH6	22936123	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	8.603000	0.90871	1.872000	0.54250	0.528000	0.53228	ATG	.	.	.	none		0.612	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			G	23866283	A	G	23866283	3	3	282	1	0	0	0	0	1	0	0	0	10045	217	8	3	3850	3	MYH6	14	23866283	Missense_Mutation	SNP	A	TCGA-Y8-A8S1-01A-11D-A36X-10		23866283	83483257	45	17972											
ATG2B	55102	hgsc.bcm.edu	37	chr14	96788562	96788562	+	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	gctttatcctgaaattctgtCatttctacagggtctcctgg	7	16	8	10	0	4	1	1	1	3	0	6	1	5	1	2	2	1	1	2	2	3	5			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr14:96788562C>G	ENST00000359933.4	-	18	3659	c.2766G>C	c.(2764-2766)atG>atC	p.M922I	snoU13_ENST00000458931.1_RNA	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	922					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)		p.M922I(1)		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)		GAAATTCTGTCATTTCTACAG	0.348																																					p.M922I		Atlas-SNP	.											ATG2B,NS,carcinoma,0,1	ATG2B	169	.	1	Substitution - Missense(1)	cervix(1)	c.G2766C						PASS	.						118	113	114					14																	96788562		1840	4087	5927	SO:0001583	missense	55102	exon18			TTCTGTCATTTCT	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.2766G>C	chr14.hg19:g.96788562C>G	ENSP00000353010:p.Met922Ile	117.0	0.0	.		138.0	21.0	.	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	hg19	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	C	31	5.076068	0.94000	.	.	ENSG00000066739	ENST00000359933	T	0.48522	0.81	5.98	5.98	0.97165	.	0.000000	0.85682	U	0.000000	T	0.68284	0.2984	M	0.69823	2.125	0.80722	D	1	D	0.54964	0.969	D	0.63381	0.914	T	0.64993	-0.6276	10	0.45353	T	0.12	.	20.4434	0.99119	0.0:1.0:0.0:0.0	.	922	Q96BY7	ATG2B_HUMAN	I	922	ENSP00000353010:M922I	ENSP00000353010:M922I	M	-	3	0	ATG2B	95858315	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.601000	0.82783	2.838000	0.97847	0.655000	0.94253	ATG	.	.	.	none		0.348	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		G	96788562	C	G	96788562	3	3	282	1	0	0	0	0	1	0	0	0	1094	826	29	4	3570	4	ATG2B	14	96788562	Missense_Mutation	SNP	C	TCGA-Y8-A8S1-01A-11D-A36X-10	72922279	96788562	10560978	46	17973											
MED1	5469	hgsc.bcm.edu	37	chr17	37565772	37565772	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccccaaagtatttagtgccTgagatgcaaatcctttgaaa	13	11	7	10	0	0	2	0	2	0	1	1	3	1	2	4	0	2	2	4	0	5	4			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr17:37565772T>C	ENST00000300651.6	-	17	2925	c.2702A>G	c.(2701-2703)cAg>cGg	p.Q901R	MED1_ENST00000394287.3_Intron	NM_004774.3	NP_004765.2	O95243	MBD4_HUMAN	mediator complex subunit 1	0					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)			NS(1)|breast(2)|cervix(3)|kidney(3)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(7)|urinary_tract(1)	59		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)		ATTTAGTGCCTGAGATGCAAA	0.408										HNSCC(31;0.082)																											p.Q901R	Pancreas(21;279 768 2492 4877 24026)	Atlas-SNP	.											.	MED1	123	.	0			c.A2702G						PASS	.						134	134	134					17																	37565772		2203	4300	6503	SO:0001583	missense	5469	exon17			AGTGCCTGAGATG	L40366	CCDS11336.1	17q12	2007-07-30	2007-07-30	2007-07-30	ENSG00000125686	ENSG00000125686			9234	protein-coding gene	gene with protein product		604311	"PPAR binding protein"	TRIP2, PPARGBP, PPARBP		9325263, 10485914	Standard	NM_004774		Approved	PBP, TRAP220, RB18A, DRIP230, CRSP200, CRSP1	uc002hrv.4	Q15648	OTTHUMG00000133216	ENST00000300651.6:c.2702A>G	chr17.hg19:g.37565772T>C	ENSP00000300651:p.Gln901Arg	143.0	0.0	.		136.0	14.0	.	NM_004774	B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Missense_Mutation	SNP	ENST00000300651.6	hg19	CCDS11336.1	.	.	.	.	.	.	.	.	.	.	T	11.69	1.713193	0.30413	.	.	ENSG00000125686	ENST00000300651	T	0.36157	1.27	5.65	5.65	0.86999	.	.	.	.	.	T	0.23054	0.0557	N	0.14661	0.345	0.45806	D	0.99868	B	0.22346	0.068	B	0.15870	0.014	T	0.05053	-1.0909	9	0.49607	T	0.09	-6.8306	11.9583	0.52995	0.0:0.0:0.1446:0.8554	.	901	Q15648	MED1_HUMAN	R	901	ENSP00000300651:Q901R	ENSP00000300651:Q901R	Q	-	2	0	MED1	34819298	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.342000	0.52159	2.371000	0.80710	0.533000	0.62120	CAG	.	.	.	none		0.408	MED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256943.3	NM_004774		C	37565772	T	C	37565772	3	2	282	1	0	0	0	0	1	0	0	0	9432	1580	55	3	2047	3	MED1	17	37565772	Missense_Mutation	SNP	T	TCGA-Y8-A8S1-01A-11D-A36X-10		37565772	43629438	47	17974											
KIAA1267	284058	hgsc.bcm.edu	37	chr17	44248467	44248467	+	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	tcaaggcagcttcagcctttCgagtcagcatcaactggctc	9	10	9	13	1	4	0	4	0	0	0	6	1	4	0	1	2	4	4	1	2	2	2			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr17:44248467C>A	ENST00000262419.6	-	2	1513	c.1043G>T	c.(1042-1044)cGa>cTa	p.R348L	KANSL1_ENST00000432791.1_Missense_Mutation_p.R348L|KANSL1_ENST00000393476.3_5'UTR|KANSL1_ENST00000572904.1_Missense_Mutation_p.R348L|KANSL1_ENST00000574590.1_Missense_Mutation_p.R348L|KANSL1_ENST00000575318.1_Missense_Mutation_p.R348L|KANSL1_ENST00000576248.1_5'UTR	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	348					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)											TTCAGCCTTTCGAGTCAGCAT	0.458																																					p.R348L		Atlas-SNP	.											.	.	.	.	0			c.G1043T						PASS	.						68	87	80					17																	44248467		2203	4300	6503	SO:0001583	missense	284058	exon2			GCCTTTCGAGTCA	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.1043G>T	chr17.hg19:g.44248467C>A	ENSP00000262419:p.Arg348Leu	42.0	0.0	.		60.0	9.0	.	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	hg19	CCDS11503.1	.	.	.	.	.	.	.	.	.	.	C	17.62	3.434922	0.62955	.	.	ENSG00000120071	ENST00000262419;ENST00000432791	T;T	0.11495	2.77;2.77	5.94	5.94	0.96194	.	0.279693	0.33753	N	0.004596	T	0.22044	0.0531	L	0.27053	0.805	0.80722	D	1	P;D	0.57571	0.761;0.98	B;D	0.63877	0.151;0.919	T	0.00327	-1.1814	10	0.56958	D	0.05	-4.6431	18.9413	0.92607	0.0:1.0:0.0:0.0	.	348;348	C9JHY2;Q7Z3B3	.;K1267_HUMAN	L	348	ENSP00000262419:R348L;ENSP00000387393:R348L	ENSP00000262419:R348L	R	-	2	0	KIAA1267	41604244	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.359000	0.66074	2.826000	0.97356	0.561000	0.74099	CGA	.	.	.	none		0.458	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443		A	44248467	C	A	44248467	3	1	282	1	0	0	0	0	1	0	0	0	8226	884	31	4	2330	4	KIAA1267	17	44248467	Missense_Mutation	SNP	C	TCGA-Y8-A8S1-01A-11D-A36X-10	6682695	44248467	36946743	48	17975											
IMPACT	55364	hgsc.bcm.edu	37	chr18	22020542	22020542	+	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	gcatgtcagccggaaagttcGcttaaagcattggattttga	11	12	11	7	2	1	1	1	1	0	0	2	3	1	3	1	2	2	4	1	2	3	5			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr18:22020542G>C	ENST00000284202.4	+	6	591	c.450G>C	c.(448-450)tcG>tcC	p.S150S	RP11-178F10.1_ENST00000579049.1_RNA	NM_018439.3	NP_060909	Q9P2X3	IMPCT_HUMAN	impact RWD domain protein	150					negative regulation of protein phosphorylation (GO:0001933)|regulation of translational initiation (GO:0006446)	cytoplasm (GO:0005737)				endometrium(1)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(2)	16	all_cancers(21;0.00018)|all_epithelial(16;1.5e-06)|Lung NSC(20;0.0027)|all_lung(20;0.0085)|Colorectal(14;0.0361)|Ovarian(20;0.0991)					CGGAAAGTTCGCTTAAAGCAT	0.363																																					p.S150S		Atlas-SNP	.											.	IMPACT	37	.	0			c.G450C						PASS	.						160	151	154					18																	22020542		2203	4300	6503	SO:0001819	synonymous_variant	55364	exon6			AAGTTCGCTTAAA	AB026264	CCDS11886.1	18q11.2-q12.1	2012-12-07	2012-12-07		ENSG00000154059	ENSG00000154059			20387	protein-coding gene	gene with protein product	"RWD domain containing 5"	615319	"Impact homolog (mouse)"			11116084	Standard	NM_018439		Approved	RWDD5	uc002kvh.4	Q9P2X3	OTTHUMG00000131943	ENST00000284202.4:c.450G>C	chr18.hg19:g.22020542G>C		133.0	0.0	.		130.0	16.0	.	NM_018439	A8MXG0|Q49AM0|Q9H2X4	Silent	SNP	ENST00000284202.4	hg19	CCDS11886.1																																																																																			.	.	.	none		0.363	IMPACT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254901.1	NM_018439		C	22020542	G	C	22020542	2	2	282	1	0	0	0	0	0	0	0	1	7731	1074	38	4		4	IMPACT	18	22020542	Silent	SNP	G	TCGA-Y8-A8S1-01A-11D-A36X-10		22020542	56056706	49	17976											
DYM	54808	hgsc.bcm.edu	37	chr18	46889546	46889546	+	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	cttacaagagtggaatatcaGtgatcaactgcatcaaacag	16	9	8	8	0	3	2	3	1	0	1	3	3	3	3	0	1	4	1	0	1	6	2			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr18:46889546G>C	ENST00000269445.6	-	6	936	c.479C>G	c.(478-480)aCt>aGt	p.T160S	DYM_ENST00000442713.2_Intron|DYM_ENST00000578396.1_Missense_Mutation_p.T5S	NM_017653.3	NP_060123.3	Q7RTS9	DYM_HUMAN	dymeclin	160					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						TGGAATATCAGTGATCAACTG	0.363																																					p.T160S		Atlas-SNP	.											.	DYM	52	.	0			c.C479G						PASS	.						110	107	108					18																	46889546		2203	4300	6503	SO:0001583	missense	54808	exon6			ATATCAGTGATCA	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.479C>G	chr18.hg19:g.46889546G>C	ENSP00000269445:p.Thr160Ser	287.0	0.0	.		219.0	37.0	.	NM_017653	A8K5I8|B2RCF9|B4DKI7|Q3ZTS8|Q6P2P5|Q8N2M0|Q9BVE9|Q9NPU7	Missense_Mutation	SNP	ENST00000269445.6	hg19	CCDS11937.1	.	.	.	.	.	.	.	.	.	.	G	12.00	1.806018	0.31961	.	.	ENSG00000141627	ENST00000269445	D	0.82711	-1.64	5.52	4.53	0.55603	.	0.114501	0.64402	D	0.000019	T	0.67335	0.2882	N	0.17082	0.46	0.26816	N	0.968889	B	0.10296	0.003	B	0.08055	0.003	T	0.55042	-0.8202	10	0.45353	T	0.12	-16.7362	6.2807	0.21005	0.1559:0.0:0.8441:0.0	.	160	Q7RTS9	DYM_HUMAN	S	160	ENSP00000269445:T160S	ENSP00000269445:T160S	T	-	2	0	DYM	45143544	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.136000	0.50554	2.590000	0.87494	0.650000	0.86243	ACT	.	.	.	none		0.363	DYM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255912.3	NM_017653		C	46889546	G	C	46889546	3	2	282	1	0	0	0	0	1	0	0	0	4842	1029	36	4	1578	4	DYM	18	46889546	Missense_Mutation	SNP	G	TCGA-Y8-A8S1-01A-11D-A36X-10	24869004	46889546	31187702	50	17977											
STAP2	55620	hgsc.bcm.edu	37	chr19	4332020	4332020	+	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	agagagccactactcttaccTccaccaccgttaagatgaag	13	8	7	13	1	1	3	0	1	1	2	2	4	2	3	5	0	3	1	5	0	4	3	rs74464159		TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr19:4332020T>G	ENST00000594605.1	-	4	476	c.353A>C	c.(352-354)gAg>gCg	p.E118A	STAP2_ENST00000600324.1_Splice_Site_p.E118A	NM_001013841.1	NP_001013863.1	Q9UGK3	STAP2_HUMAN	signal transducing adaptor family member 2	118	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)		TACTCTTACCTCCACCACCGT	0.463																																					p.E118A		Atlas-SNP	.											.	STAP2	38	.	0			c.A353C						PASS	.						118	99	106					19																	4332020		2203	4300	6503	SO:0001630	splice_region_variant	55620	exon4			CTTACCTCCACCA	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.354+1A>C	chr19.hg19:g.4332020T>G		144.0	0.0	.		131.0	12.0	.	NM_001013841	A6NKK3|Q9NXI2	Missense_Mutation	SNP	ENST00000594605.1	hg19	CCDS45926.1	.	.	.	.	.	.	.	.	.	.	T	17.35	3.366418	0.61513	.	.	ENSG00000178078	ENST00000314714;ENST00000424810	.	.	.	4.06	4.06	0.47325	Pleckstrin homology domain (1);	0.235984	0.42053	D	0.000775	T	0.72961	0.3526	M	0.79475	2.455	0.35553	D	0.804074	D;D	0.76494	0.999;0.99	D;P	0.78314	0.991;0.768	T	0.81136	-0.1070	9	0.87932	D	0	-5.6986	9.6315	0.39782	0.0:0.0:0.0:1.0	.	118;118	Q9UGK3-2;Q9UGK3	.;STAP2_HUMAN	A	118	.	ENSP00000317912:E118A	E	-	2	0	STAP2	4283020	1.000000	0.71417	1.000000	0.80357	0.544000	0.35116	4.878000	0.63093	1.868000	0.54150	0.249000	0.18162	GAG	.	.	.	alt		0.463	STAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458114.2	NM_001013841	Missense_Mutation	G	4332020	T	G	4332020	5	3	282	1	0	0	0	0	0	0	1	0	15265	1565	54	5	1036	5	STAP2	19	4332020	Splice_Site	SNP	T	TCGA-Y8-A8S1-01A-11D-A36X-10		4332020	54796963	51	17978											
TRIP10	9322	hgsc.bcm.edu	37	chr19	6744841	6744841	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttatagagctgcacaagTcaggttttgcccgcccgggc	7	10	11	13	2	1	1	1	0	0	1	2	1	2	1	3	2	3	3	3	2	3	4			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr19:6744841T>C	ENST00000313244.9	+	9	855	c.820T>C	c.(820-822)Tca>Cca	p.S274P	TRIP10_ENST00000596758.1_Missense_Mutation_p.S274P|TRIP10_ENST00000313285.8_Missense_Mutation_p.S274P|TRIP10_ENST00000600428.1_Missense_Mutation_p.S166P			Q15642	CIP4_HUMAN	thyroid hormone receptor interactor 10	274	F-BAR domain.				actin cytoskeleton organization (GO:0030036)|cell communication (GO:0007154)|endocytosis (GO:0006897)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|breast(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	16						GCTGCACAAGTCAGGTTTTGC	0.632																																					p.S274P		Atlas-SNP	.											.	TRIP10	104	.	0			c.T820C						PASS	.						87	84	85					19																	6744841		2203	4300	6503	SO:0001583	missense	9322	exon9			CACAAGTCAGGTT	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.820T>C	chr19.hg19:g.6744841T>C	ENSP00000320117:p.Ser274Pro	85.0	0.0	.		95.0	13.0	.	NM_004240	B2R8A6|B7WP22|D6W645|O15184|Q53G22|Q5TZN1|Q6FI24|Q8NFL1|Q8TCY1|Q8TDX3|Q96RJ1	Missense_Mutation	SNP	ENST00000313244.9	hg19		.	.	.	.	.	.	.	.	.	.	T	31	5.071840	0.93950	.	.	ENSG00000125733	ENST00000313285;ENST00000313244;ENST00000420690	T;T	0.45276	0.9;2.48	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.68183	0.2973	M	0.86502	2.82	0.80722	D	1	D;P;D	0.89917	1.0;0.939;0.998	D;P;D	0.85130	0.997;0.764;0.988	T	0.74636	-0.3599	10	0.87932	D	0	-11.9975	13.123	0.59338	0.0:0.0:0.0:1.0	.	274;274;274	G5E9U1;Q15642;Q15642-2	.;CIP4_HUMAN;.	P	274	ENSP00000320493:S274P;ENSP00000320117:S274P	ENSP00000320117:S274P	S	+	1	0	TRIP10	6695841	1.000000	0.71417	0.995000	0.50966	0.975000	0.68041	7.265000	0.78442	1.993000	0.58246	0.379000	0.24179	TCA	.	.	.	none		0.632	TRIP10-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000317129.2			C	6744841	T	C	6744841	3	2	282	1	0	0	0	0	1	0	0	0	16566	1667	58	3	854	3	TRIP10	19	6744841	Missense_Mutation	SNP	T	TCGA-Y8-A8S1-01A-11D-A36X-10	2412821	6744841	52384142	52	17979											
PRR12	57479	hgsc.bcm.edu	37	chr19	50119450	50119450	+	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	cagctcctcggactcggagtCctcccctggagcccccagcg	5	6	11	19	3	0	0	0	0	0	0	5	3	3	3	6	3	3	1	6	3	0	0			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr19:50119450C>T	ENST00000418929.2	+	9	5483	c.5471C>T	c.(5470-5472)tCc>tTc	p.S1824F		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	1003							DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		GACTCGGAGTCCTCCCCTGGA	0.682																																					p.S1824F		Atlas-SNP	.											.	PRR12	157	.	0			c.C5471T						PASS	.						7	9	8					19																	50119450		1956	4080	6036	SO:0001583	missense	57479	exon9			CGGAGTCCTCCCC	AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"KIAA1205"	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.5471C>T	chr19.hg19:g.50119450C>T	ENSP00000394510:p.Ser1824Phe	172.0	0.0	.		146.0	10.0	.	NM_020719	E9PB06|Q8N4J6	Missense_Mutation	SNP	ENST00000418929.2	hg19	CCDS46143.1	.	.	.	.	.	.	.	.	.	.	C	15.22	2.767465	0.49574	.	.	ENSG00000126464	ENST00000418929;ENST00000246798;ENST00000314734	T	0.47528	0.84	4.75	4.75	0.60458	.	0.000000	0.51477	D	0.000084	T	0.62527	0.2435	L	0.57536	1.79	0.58432	D	0.999999	D	0.76494	0.999	D	0.85130	0.997	T	0.55964	-0.8057	10	0.13470	T	0.59	-24.7453	16.648	0.85181	0.0:1.0:0.0:0.0	.	1824	Q9ULL5-3	.	F	1824;1004;1004	ENSP00000394510:S1824F	ENSP00000246798:S1004F	S	+	2	0	PRR12	54811262	1.000000	0.71417	0.972000	0.41901	0.580000	0.36256	5.691000	0.68249	2.471000	0.83476	0.491000	0.48974	TCC	.	.	.	none		0.682	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719		T	50119450	C	T	50119450	3	4	282	1	0	0	0	0	1	0	0	0	12594	855	30	2	5505	2	PRR12	19	50119450	Missense_Mutation	SNP	C	TCGA-Y8-A8S1-01A-11D-A36X-10	43374609	50119450	9009533	53	17980											
NLRP11	204801	hgsc.bcm.edu	37	chr19	56297223	56297223	+	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	gctgggtttgtgtgttcaggCcagttaatggaagcctgaag	8	12	15	6	0	1	1	1	1	0	0	1	2	1	2	2	3	1	4	2	3	3	3			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr19:56297223C>T	ENST00000589093.1	-	10	2963	c.2870G>A	c.(2869-2871)gGc>gAc	p.G957D	NLRP11_ENST00000592953.1_Missense_Mutation_p.G858D|NLRP11_ENST00000443188.1_Missense_Mutation_p.G957D|NLRP11_ENST00000360133.3_Missense_Mutation_p.G903D|NLRP11_ENST00000589824.2_Missense_Mutation_p.G903D			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	957							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)		TGTGTTCAGGCCAGTTAATGG	0.433																																					p.G957D		Atlas-SNP	.											.	NLRP11	139	.	0			c.G2870A						PASS	.						64	64	64					19																	56297223		2203	4300	6503	SO:0001583	missense	204801	exon12			TTCAGGCCAGTTA	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.2870G>A	chr19.hg19:g.56297223C>T	ENSP00000466285:p.Gly957Asp	135.0	0.0	.		126.0	16.0	.	NM_145007	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Missense_Mutation	SNP	ENST00000589093.1	hg19	CCDS12935.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.796267	0.00076	.	.	ENSG00000179873	ENST00000443188;ENST00000360133	T;T	0.51574	0.7;0.7	1.4	-2.74	0.05932	.	.	.	.	.	T	0.18923	0.0454	N	0.10874	0.06	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.23368	-1.0190	9	0.07990	T	0.79	.	3.0249	0.06087	0.0:0.3766:0.2572:0.3663	.	957;903	P59045;P59045-2	NAL11_HUMAN;.	D	957;903	ENSP00000409898:G957D;ENSP00000353251:G903D	ENSP00000353251:G903D	G	-	2	0	NLRP11	60989035	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.588000	0.02106	-0.970000	0.03569	-2.317000	0.00253	GGC	.	.	.	none		0.433	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007		T	56297223	C	T	56297223	3	4	282	1	0	0	0	0	1	0	0	0	10480	739	26	2	235	2	NLRP11	19	56297223	Missense_Mutation	SNP	C	TCGA-Y8-A8S1-01A-11D-A36X-10	6177773	56297223	2831760	54	17981											
MYBL2	4605	hgsc.bcm.edu	37	chr20	42338684	42338684	+	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	aagaacgccctggagaagtaCggacccctgaagcccctggt	11	5	12	13	2	0	3	0	1	0	2	0	5	0	4	5	3	3	1	5	3	5	1			TCGA-Y8-A8S1-01A-11D-A36X-10	TCGA-Y8-A8S1-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5c980b27-02f4-4e7d-bc5f-59809f2cbfd0	99aa2435-d52d-45ef-a896-64a90cac0ad3	g.chr20:42338684C>T	ENST00000217026.4	+	10	1714	c.1587C>T	c.(1585-1587)taC>taT	p.Y529Y	MYBL2_ENST00000396863.4_Silent_p.Y505Y	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	529					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)			TGGAGAAGTACGGACCCCTGA	0.592																																					p.Y529Y		Atlas-SNP	.											.	MYBL2	82	.	0			c.C1587T						PASS	.						153	151	152					20																	42338684		2203	4300	6503	SO:0001819	synonymous_variant	4605	exon10			GAAGTACGGACCC		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.1587C>T	chr20.hg19:g.42338684C>T		164.0	0.0	.		130.0	6.0	.	NM_002466	B2RBS5|B7Z8D9|F8W6N6|Q53F07	Silent	SNP	ENST00000217026.4	hg19	CCDS13322.1																																																																																			.	.	.	none		0.592	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080408.1	NM_002466		T	42338684	C	T	42338684	2	4	282	1	0	0	0	0	0	0	0	1	10017	547	19	1		1	MYBL2	20	42338684	Silent	SNP	C	TCGA-Y8-A8S1-01A-11D-A36X-10		42338684	20686836	55	17982											
